# hmmscan :: search sequence(s) against a profile database
# HMMER 3.2.1 (June 2018); http://hmmer.org/
# Copyright (C) 2018 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query sequence file:             /oak/stanford/groups/akundaje/marinovg/genomes/Microsporidia/Trachipleistophora_hominis-ASM31613v1/GCA_000316135.1_ASM31613v1_genomic.ORF.faa
# target HMM database:             /oak/stanford/groups/akundaje/marinovg/genomes/PFam/PFam32.0/Pfam-A.hmm
# output directed to file:         /oak/stanford/groups/akundaje/marinovg/genomes/Microsporidia/Trachipleistophora_hominis-ASM31613v1/GCA_000316135.1_ASM31613v1_genomic.ORF.PFam32-A
# per-seq hits tabular output:     /oak/stanford/groups/akundaje/marinovg/genomes/Microsporidia/Trachipleistophora_hominis-ASM31613v1/GCA_000316135.1_ASM31613v1_genomic.ORF.PFam32-A.tblout
# number of worker threads:        20
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       gene0|gene0|rna0|rna0  [L=109]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
       0.17   11.8   0.0         11    6.0   0.0    2.2  2  DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda


Domain annotation for each model (and alignments):
>> DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0    0.0006        11      41      49 ..      74      82 ..      64      82 .. 0.86
   2 ?    3.7   0.0     0.003        53       9      30 ..      83     104 ..      83     109 .] 0.88

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0006
        DNA_pol_lambd_f 41 iGlkyyeDl 49
                           +Glkyy+++
  gene0|gene0|rna0|rna0 74 LGLKYYDEM 82
                           8******98 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.003
        DNA_pol_lambd_f   9 VGpktAkkwyakGirtledlra 30 
                            VG ++A+ +++k +  l+ + +
  gene0|gene0|rna0|rna0  83 VGYEKARTLVEKEMERLKNVIK 104
                            899***********99999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       690  (0.0384851); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.46
# Mc/sec: 704.85
//
Query:       gene100|gene100|rna100|rna100  [L=242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (242 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       862  (0.0480785); expected 358.6 (0.02)
Passed bias filter:                      525  (0.0292822); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.65u 0.34s 00:00:00.99 Elapsed: 00:00:00.57
# Mc/sec: 1281.62
//
Query:       gene1000|gene1000|rna1000|rna1000  [L=240]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
       0.11   12.8   9.2        3.5    8.0   0.2    2.8  2  Tup_N           Tup N-terminal
        0.3    9.9  12.2      0.096   11.5   9.5    1.5  2  Spc7            Spc7 kinetochore protein
       0.53    9.5   4.8          1    8.6   4.8    1.3  1  CorA            CorA-like Mg2+ transporter protein
        1.2    9.3   6.6        1.9    8.7   3.5    2.5  3  DUF4047         Domain of unknown function (DUF4047)
        3.5    8.2  10.0         13    6.3  10.0    2.1  1  APG6_N          Apg6 coiled-coil region
        5.3    7.7   9.9        1.2    9.8   5.1    2.3  2  HIP1_clath_bdg  Clathrin-binding domain of Huntingtin-interac


Domain annotation for each model (and alignments):
>> Tup_N  Tup N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   3.7    0.0025       7.3      35      76 ..     149     189 ..     128     190 .. 0.75
   2 ?    8.0   0.2    0.0012       3.5       1      24 [.     203     226 ..     203     238 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0025
                              Tup_N  35 qsqiqElqqirqtlyeLeeahrkikqqYEeeiarLkaeLesr 76 
                                        q    El+++r+t   + +   ki q+ E+e+a+ k+eL+++
  gene1000|gene1000|rna1000|rna1000 149 QI-QMELDRLRETHRRMFAVKGKIYQAVEKEMAKFKNELKEK 189
                                        22.2488888888888888888999**************986 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0012
                              Tup_N   1 RlnelLdavkqEfdalsqeasslk 24 
                                        R+n  L+a+k+E++a++ e  +++
  gene1000|gene1000|rna1000|rna1000 203 RINGELEALKKEYNAVKDERDKFR 226
                                        78889***********99988776 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0      0.68     2e+03      69     104 ..      38      72 ..      36      78 .. 0.69
   2 ?   11.5   9.5   3.2e-05     0.096     166     249 ..     145     228 ..     132     240 .] 0.75

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.68
                               Spc7  69 eLkkyisegrkiireieeetleenPpLfreYmeadp 104
                                        +Lkk  ++ r++i e  +e +e+ P+L r + ++d 
  gene1000|gene1000|rna1000|rna1000  38 DLKKGAAQDRQVILEGLDE-YENDPELARAFKKIDV 72 
                                        7777777888777776655.6777888888777665 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 3.2e-05
                               Spc7 166 dellpeleeekaeleeeleklqeaaeelesidkeeLeelreelae.lkaeieekkkelaelqeqleeleekieelk 240
                                        +++  +++ e ++l+e+++++ + + ++ +  ++e++++++el+e  + ei++k +e+++ + +le+l+++ +++k
  gene1000|gene1000|rna1000|rna1000 145 QNY-MQIQMELDRLRETHRRMFAVKGKIYQAVEKEMAKFKNELKEkTDLEIRRKDEEINRINGELEALKKEYNAVK 219
                                        332.345555666666666666677777778899*********862689*************************** PP

                               Spc7 241 eqkseleee 249
                                        ++++++++ 
  gene1000|gene1000|rna1000|rna1000 220 DERDKFRTV 228
                                        **9998765 PP

>> CorA  CorA-like Mg2+ transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   4.8   0.00034         1     136     228 ..     130     221 ..     126     224 .. 0.68

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00034
                               CorA 136 eledeledstkkeilrelaqlrrrlvkl....rralapnrevlkrlla...kaddkllddedkeylrdlldelerl 204
                                        +l ++l+ ++k++ ++  +q++ +l +l    rr++a + +++ + ++    +++++l+       +    e++r 
  gene1000|gene1000|rna1000|rna1000 130 DLKERLDVDRKADNVQNYMQIQMELDRLrethRRMFAVKGKIY-QAVEkemAKFKNELK-------EKTDLEIRRK 197
                                        78999***********************777777888888888.444424444444444.......5555555555 PP

                               CorA 205 lemlealrerleslqdtyssllse 228
                                        +e+++ +   le l+ +y+++ +e
  gene1000|gene1000|rna1000|rna1000 198 DEEINRINGELEALKKEYNAVKDE 221
                                        555555555555555555555444 PP

>> DUF4047  Domain of unknown function (DUF4047)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.0       0.3   9.1e+02      31      52 ..      38      59 ..      33      79 .. 0.80
   2 ?    1.5   0.4      0.11   3.2e+02      82     106 ..     167     191 ..     126     197 .. 0.59
   3 ?    8.7   3.5   0.00063       1.9      38      96 ..     181     238 ..     165     240 .] 0.82

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.3
                            DUF4047 31 tlveqakqhkelilheyeemks 52
                                        l++ a q +++il++ +e + 
  gene1000|gene1000|rna1000|rna1000 38 DLKKGAAQDRQVILEGLDEYEN 59
                                       689999*******999888765 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.11
                            DUF4047  82 alqkvyteieepynqvqeelkvnks 106
                                           k+y+ +e+   + ++elk +++
  gene1000|gene1000|rna1000|rna1000 167 VKGKIYQAVEKEMAKFKNELKEKTD 191
                                        3358899999999999999987765 PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.00063
                            DUF4047  38 qhkelilheyeemksklkvdsveeieqalsvwkqgrekikaerealqkvyteieepynq 96 
                                        + k+  l+e  +++ + k + ++ i+ +l+  k++++ +k er+ ++ vy ++ e y+ 
  gene1000|gene1000|rna1000|rna1000 181 KFKNE-LKEKTDLEIRRKDEEINRINGELEALKKEYNAVKDERDKFRTVYFKLKEKYKN 238
                                        44443.466778889999999************************************86 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3  10.0    0.0045        13      26     105 ..     145     229 ..     131     240 .] 0.50

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0045
                             APG6_N  26 daYeeflkklkkekkeeek....qdeeleeleeeleklekeeeelle.eLkelekereeleaelaaleeelealee 96 
                                        ++Y++   +l++ +++ ++    + +  ++ e+e++k ++e +e+   e+++ ++e  +++ el+al++e +a+++
  gene1000|gene1000|rna1000|rna1000 145 QNYMQIQMELDRLRETHRRmfavKGKIYQAVEKEMAKFKNELKEKTDlEIRRKDEEINRINGELEALKKEYNAVKD 220
                                        5555555555555444333444433344445555555555544444325555555555555555555555555555 PP

                             APG6_N  97 eeerfwrey 105
                                        e ++f + y
  gene1000|gene1000|rna1000|rna1000 221 ERDKFRTVY 229
                                        555544443 PP

>> HIP1_clath_bdg  Clathrin-binding domain of Huntingtin-interacting protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.1      0.95   2.8e+03      48      83 ..      12      47 ..       3      81 .. 0.65
   2 ?    9.8   5.1   0.00041       1.2      28      96 ..     146     215 ..     134     218 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.95
                     HIP1_clath_bdg 48 eeqkeelekLkreleakraelarlkssLesseqsge 83
                                       ++   e + Lk+   + ++++a  +s L++ + ++ 
  gene1000|gene1000|rna1000|rna1000 12 DKLLVESDVLKTGKLRDKTNVAGRQSDLKKGAAQDR 47
                                       555555555666555666666666665555544444 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00041
                     HIP1_clath_bdg  28 ekkeleeelerlkeeaerkleeqkeelekLkreleakraelar.lkssLesseqsgeqlssqlaaLqaEk 96 
                                        +  +++ el+rl+e ++r+ + + +  +++++e+++ ++el++     ++++ ++ ++++ +l+aL++E 
  gene1000|gene1000|rna1000|rna1000 146 NYMQIQMELDRLRETHRRMFAVKGKIYQAVEKEMAKFKNELKEkTDLEIRRKDEEINRINGELEALKKEY 215
                                        4578999**********************************75156788899999999*********995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (240 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1742  (0.097161); expected 358.6 (0.02)
Passed bias filter:                      488  (0.0272185); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.67u 0.36s 00:00:01.03 Elapsed: 00:00:00.56
# Mc/sec: 1291.21
//
Query:       gene1001|gene1001|rna1001|rna1001  [L=85]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
       0.08   12.0   0.0        0.1   11.7   0.0    1.0  1  Amidinotransf  Amidinotransferase


Domain annotation for each model (and alignments):
>> Amidinotransf  Amidinotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   5.7e-06       0.1     233     288 ..      28      84 ..      23      84 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 5.7e-06
                                        TEEEEETTEEEE-HHHH.TT-ESS-HHHHHHHHTT-SS..-EEEE-CS-SS-B---S- CS
                      Amidinotransf 233 vftvvdddavvclpsildaegvkakereavaqaLkekg..leiIeigeeeqwnfggNv 288
                                        vf +++++a+++ +++ d+  ++ k+r+++++ L +kg  + ++  ge+e+w++  N+
  gene1001|gene1001|rna1001|rna1001  28 VFRHLQNYAFLYPDEVNDK-VKNMKRRRELEDFLVKKGkkKYFVNGGEKELWKCIRNT 84 
                                        7889999*********977.5999**********887743679***********9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (85 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       551  (0.0307323); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.36s 00:00:00.90 Elapsed: 00:00:00.57
# Mc/sec: 445.35
//
Query:       gene1002|gene1002|rna1002|rna1002  [L=278]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.7e-28   98.7  17.5    2.7e-28   98.7  17.5    2.2  2  DHHC            DHHC palmitoyltransferase
  ------ inclusion threshold ------
      0.021   15.0   1.9      0.036   14.2   1.9    1.4  1  FYVE            FYVE zinc finger
      0.021   14.7   3.8      0.042   13.7   3.8    1.5  1  Ribosomal_L40e  Ribosomal L40e family


Domain annotation for each model (and alignments):
>> DHHC  DHHC palmitoyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   1.6      0.02   1.2e+02      65     100 ..       6      41 ..       1      74 [. 0.51
   2 !   98.7  17.5   4.6e-32   2.7e-28       5     131 ..      87     203 ..      83     206 .. 0.96

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.02
                               DHHC  65 alvlllialvklveeekkseflavtllkkllsilll 100
                                        + v+++++++k+++++++    +v ++ +l+ ++ll
  gene1002|gene1002|rna1002|rna1002   6 YYVVMFVHIQKIYKYRQNIYLFYVVNYVSLYIMILL 41 
                                        555555555555555555444433333221111111 PP

  == domain 2  score: 98.7 bits;  conditional E-value: 4.6e-32
                               DHHC   5 lkfCstcniykpprskHcrvCnrcvlrfDHhCpwlnnciGerNykyFllfllylllllilalvlllialvklveee 80 
                                        +k C +c  y ppr++Hcr+C+ c  ++DHhC +ln ciG  Nyky++lfll+ ++++++ ++lll++ +   ++ 
  gene1002|gene1002|rna1002|rna1002  87 SKTCGKCYAYMPPRTHHCRICDACFTKMDHHCFFLNVCIGLPNYKYYYLFLLINWIYSTFLFILLLYFAIAVKQTP 162
                                        689***********************************************************************99 PP

                               DHHC  81 kkseflavtllkkllsilllvlsllfllllgllllfhlylilrnlTtieam 131
                                        +  +f+          ++ ++  +++l++++++llfh+ l+l n Ttie++
  gene1002|gene1002|rna1002|rna1002 163 NRMTFY----------VIGIISNCIILVITFIFLLFHTRLLLYNETTIERL 203
                                        998888..........99999****************************86 PP

>> FYVE  FYVE zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   1.9     6e-06     0.036      10      36 ..      88     112 ..      81     163 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 6e-06
                                        SB-TTT--B-.-SSS--EE-TTT--EE- CS
                               FYVE  10 kkCeiCakkF.sllrrrhhCrlCGkvvC 36 
                                        k+   C k +  +  r hhCr+C  ++ 
  gene1002|gene1002|rna1002|rna1002  88 KT---CGKCYaYMPPRTHHCRICDACFT 112
                                        44...5555523458********99887 PP

>> Ribosomal_L40e  Ribosomal L40e family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   3.8     7e-06     0.042      16      39 ..      88     108 ..      78     115 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 7e-06
                     Ribosomal_L40e  16 KmiCrkCYArlpprAtnCrkkkCg 39 
                                        K  C kCYA +ppr+ +Cr   C+
  gene1002|gene1002|rna1002|rna1002  88 K-TCGKCYAYMPPRTHHCR--ICD 108
                                        4.5***************9..676 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (278 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1176  (0.0655921); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 1697.80
//
Query:       gene1003|gene1003|rna1003|rna1003  [L=117]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.52   10.4   2.4       0.66   10.1   2.4    1.2  1  DHHC      DHHC palmitoyltransferase


Domain annotation for each model (and alignments):
>> DHHC  DHHC palmitoyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   2.4   3.7e-05      0.66      97     131 ..       5      39 ..       1      42 [. 0.82

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 3.7e-05
                               DHHC  97 illlvlsllfllllgllllfhlylilrnlTtieam 131
                                        +l  +  +++l++ ++ll+ +++lil n Ttie++
  gene1003|gene1003|rna1003|rna1003   5 VLASISNAIILIISFSLLVSNTILILYNETTIERL 39 
                                        445566689999999999***************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       490  (0.02733); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.30s 00:00:00.75 Elapsed: 00:00:00.48
# Mc/sec: 729.91
//
Query:       gene1004|gene1004|rna1004|rna1004  [L=332]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.6e-23   81.8  13.9    4.6e-23   81.8  13.9    2.8  2  DHHC      DHHC palmitoyltransferase
  ------ inclusion threshold ------
      0.061   13.6   0.2       0.12   12.7   0.2    1.4  1  DUF1772   Domain of unknown function (DUF1772)


Domain annotation for each model (and alignments):
>> DHHC  DHHC palmitoyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2  12.9      0.96   8.6e+03      56      92 ..      45      81 ..       5     124 .. 0.56
   2 !   81.8  13.9   5.2e-27   4.6e-23       3     130 ..     134     251 ..     132     255 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 0.96
                               DHHC 56 lylllllilalvlllialvklveeekkseflavtllk 92
                                       +++ll+++ + vl++++ +k+++++k+  f+++ ++ 
  gene1004|gene1004|rna1004|rna1004 45 FVILLFIFNYYVLMFVHTRKIYKYNKNIIFYCIGNFL 81
                                       3334444444444444444444444444444443333 PP

  == domain 2  score: 81.8 bits;  conditional E-value: 5.2e-27
                               DHHC   3 kelkfCstcniykpprskHcrvCnrcvlrfDHhCpwlnnciGerNykyFllfllylllllilalvlllialvklve 78 
                                        +  k C++c +y+ppr++Hc +C+ c +++ Hh  ++n+ciG+ Nyky++l+l++ ++++++ l+lll++ ++  +
  gene1004|gene1004|rna1004|rna1004 134 ETMKTCEKCGMYRPPRAYHCYICDTCFMKMYHHSYIFNTCIGHTNYKYYYLLLMSNFIYSLFQLILLLYFAINARQ 209
                                        56799*********************************************************************** PP

                               DHHC  79 eekkseflavtllkkllsilllvlsllfllllgllllfhlylilrnlTtiea 130
                                        + +  +f+           l +v   +f++  ++ l++++ l+l n Tt e+
  gene1004|gene1004|rna1004|rna1004 210 TPQRMTFY----------ALAIVSNSIFVVTSLIYLIINTKLLLYNETTTER 251
                                        *9998888..........6677777788888888888889999988888886 PP

>> DUF1772  Domain of unknown function (DUF1772)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.2   1.4e-05      0.12      47      95 ..     197     244 ..     176     265 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.4e-05
                            DUF1772  47 alafaylaaraasrgarllylaaaallllsivpyTllvmvPtNnkLaal 95 
                                        +++++y+a +a+++ +r  ++a+a++ + si+++T l+   +N+kL+  
  gene1004|gene1004|rna1004|rna1004 197 LILLLYFAINARQTPQRMTFYALAIV-SNSIFVVTSLIYLIINTKLLLY 244
                                        44555778888888888888776666.557*************997655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (332 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1526  (0.0851135); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 2317.11
//
Query:       gene1005|gene1005|rna1005|rna1005  [L=308]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-26   92.9  19.3    1.7e-26   92.9  19.3    2.3  2  DHHC      DHHC palmitoyltransferase
  ------ inclusion threshold ------
        5.4    6.8   8.9       0.14   12.0   1.9    1.8  2  DUF588    Domain of unknown function (DUF588)


Domain annotation for each model (and alignments):
>> DHHC  DHHC palmitoyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   6.2     0.024   2.1e+02      60     125 ..      19      78 ..       2      88 .. 0.42
   2 !   92.9  19.3   1.9e-30   1.7e-26       5     130 ..     115     231 ..     111     235 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.024
                               DHHC  60 lllilalvlllialvklveeekkseflavtllkkllsilllvlsllfllllgllllfhly.lilrnl 125
                                        +l++l+ +l+++++++lv +            k + ++++l++ l++ +ll++ l+f++  l++ ++
  gene1005|gene1005|rna1005|rna1005  19 ILSTLYPILTIYSYYVLVGKYCI-------DAKRFDTVVVLIMFLIYHVLLIYTLIFYMRiLAIDDT 78 
                                        22222222333332222222222.......1222333555555555555556655555551444333 PP

  == domain 2  score: 92.9 bits;  conditional E-value: 1.9e-30
                               DHHC   5 lkfCstcniykpprskHcrvCnrcvlrfDHhCpwlnnciGerNykyFllfllylllllilalvlllialvklveee 80 
                                        lk C+ c +ykppr++Hc++C++c l+fDHhC  l+ ci ++Nyk+F+lf+ + ++++++ +vll++ ++++ +  
  gene1005|gene1005|rna1005|rna1005 115 LKTCPICVTYKPPRTHHCSICQKCFLKFDHHCGLLGVCIAFHNYKFFYLFVAMNIIYCFFLIVLLMFEVIRNHNLP 190
                                        689********************************************************99999988887777777 PP

                               DHHC  81 kkseflavtllkkllsilllvlsllfllllgllllfhlylilrnlTtiea 130
                                        ++s +           i+l+ l ++ + + +++++ h+  il+n Ttie+
  gene1005|gene1005|rna1005|rna1005 191 TASLVH---------FIVLISLLFIEISVSLHMFIHHTLIILKNETTIEN 231
                                        775444.........255555555666666677777777777******97 PP

>> DUF588  Domain of unknown function (DUF588)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.7      0.36   3.2e+03      54      73 ..      49      68 ..      11      77 .. 0.70
   2 ?   12.0   1.9   1.5e-05      0.14      42      91 ..     153     200 ..     140     211 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.36
                             DUF588 54 vvanaiaavYsllqlvlsvv 73
                                       vv+ ++  +Y++l+++  ++
  gene1005|gene1005|rna1005|rna1005 49 VVVLIMFLIYHVLLIYTLIF 68
                                       55555666666666666555 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 1.5e-05
                             DUF588  42 akfsdlpafvylvvanaiaavYsllqlvlsvvslvrkkersaalalllfl 91 
                                          f +++ f  +v++n+i +++ +++l+++v++       +a+l+ +++l
  gene1005|gene1005|rna1005|rna1005 153 IAFHNYKFFYLFVAMNIIYCFFLIVLLMFEVIRNHN--LPTASLVHFIVL 200
                                        5799*************************9965533..666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (308 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1295  (0.0722293); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.31s 00:00:00.89 Elapsed: 00:00:00.51
# Mc/sec: 1811.62
//
Query:       gene1006|gene1006|rna1006|rna1006  [L=308]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.3e-05   23.1   0.2    0.00072   19.1   0.2    2.0  1  UCH       Ubiquitin carboxyl-terminal hydrolase
  ------ inclusion threshold ------
      0.086   12.9   0.0       0.15   12.1   0.0    1.4  1  Xpo1      Exportin 1-like protein


Domain annotation for each model (and alignments):
>> UCH  Ubiquitin carboxyl-terminal hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.2     8e-08   0.00072      61     245 ..      82     289 ..      17     301 .. 0.63

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 8e-08
                                        HHHHHHHHH..SH-CCEE--..HHHHHHHHHHSGG.GTSSSTCEHHHHHHHHHHHHHHHHCC............HC CS
                                        xxxxxxxxx..xxxxxxxxx..xxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxx............xx RF
                                UCH  61 lkdlfkell..kskskavsP..kklkktlsklaks.fsgykqqDaqEflaflLdqlhedlnr............ev 119
                                        + +++++l    +++  ++P  ++l++ l+ ++k+ f+     D   + +++ +++h+dl +             +
  gene1006|gene1006|rna1006|rna1006  82 FYNFIEDLDekINRKIVYTPfiNSLINYLKDYYKNnFR-DFNDDFMNVYRMICKRIHDDLVDthffeeenwtskIK 156
                                        33333333332112333333445566666666665454.44578999999999999999999******99987433 PP

                                        CCHHHHHHCCCTTSHHHHHH-EEEEE....................................EEEEEEB-SEEEEE CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxx....................................xxxxxxxxxxxxxx RF
                                UCH 120 aeekwkkhlkrndslitdlfegqlks....................................klklkrlPeiLiih 159
                                        ++ k +k++ ++ s+i+++f+g+++                                     ++k+++ P iL+++
  gene1006|gene1006|rna1006|rna1006 157 KSYKSEKKIFEKYSPIVEIFHGKYEGqdgrtfykiyrdhlditvkegtndisgsvrdyfqstNIKVNKYPLILVLK 232
                                        4444499999***************999977777777777777777777777777777777777777777777555 PP

                                        EESEEETEEEEE--SEEB--SEEE-GGGBSS-BTTS-TCS-BEEEEEEEEEESCTTSEEEEEEEECTTTTEEEEEE CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                                UCH 160 lkRfsynssksKlntkvefpeeldlssylaeekkkkteekkkYeLiavvvHsGslssGHYvayiknekngkWykyd 235
                                        ++          +++k+ +++ l++++             +kY+L++++ +  ++ +  Y       ++gkW++++
  gene1006|gene1006|rna1006|rna1006 233 FE----------NKKKLGVQDILTIER-------------TKYNLSGFITYA-EPTHKAYLN-----NHGKWLMCS 279
                                        44..........122333333444432.............337887777554.466666644.....245788888 PP

                                        TTEEEEE-HH CS
                                        xxxxxxxxxx RF
                                UCH 236 Detvkevkee 245
                                        D ++++v+ +
  gene1006|gene1006|rna1006|rna1006 280 DGSITSVDID 289
                                        8777777754 PP

>> Xpo1  Exportin 1-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   1.7e-05      0.15      27      92 ..     102     174 ..      68     188 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.7e-05
                                        HHHHHHHHHCT..........HHHHHHHHHHHHHHHHHHHTSHTTTSCHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                               Xpo1  27 ffddllsllsss.........psglelllriLkvlpeEiadfsrskleqerrndlkdllrsnvqkilelllqile 92 
                                        f+++l++ l+           ++ ++++ +i+k+++++++d  +  +e++ ++++k+ ++s+ +ki+e ++ i+e
  gene1006|gene1006|rna1006|rna1006 102 FINSLINYLKDYyknnfrdfnDDFMNVYRMICKRIHDDLVD-THFFEEENWTSKIKKSYKSE-KKIFEKYSPIVE 174
                                        44444444444367778888899999***************.578999***********999.777777666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (308 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       930  (0.0518713); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 1977.65
//
Query:       gene1007|gene1007|rna1007|rna1007  [L=123]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      4e-11   42.9   8.1    8.2e-11   41.9   8.1    1.6  1  zf-AN1         AN1-like Zinc finger
     0.0055   15.9   1.1     0.0064   15.7   1.1    1.0  1  Fumble         Fumble
     0.0074   16.0   4.3      0.025   14.3   4.3    2.0  1  zinc_ribbon_2  zinc-ribbon domain
  ------ inclusion threshold ------
      0.075   13.1   5.2       0.14   12.2   5.2    1.6  1  DZR            Double zinc ribbon


Domain annotation for each model (and alignments):
>> zf-AN1  AN1-like Zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.9   8.1   1.8e-14   8.2e-11       1      39 [.      63     100 ..      61     101 .. 0.94

  Alignments for each domain:
  == domain 1  score: 41.9 bits;  conditional E-value: 1.8e-14
                             zf-AN1   1 CsfksCkkkdflp..fkCryCgkvFClkHrlpedHdCkkla 39 
                                        C+  +C+kk+ l+  f+Cr Cg+vFC+ Hr++++H+C++++
  gene1007|gene1007|rna1007|rna1007  63 CK--KCGKKLRLMgeFTCR-CGGVFCAMHRFYDQHGCSFDY 100
                                        55..8*****9999*****.*******************98 PP

>> Fumble  Fumble
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   1.1   1.4e-06    0.0064      40     137 ..      11     107 ..       2     118 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.4e-06
                             Fumble  40 eelggrLhfikfetekieevleflkelllkskekekkkktikaTGGGaykyaelikeelgvevekedemeclikGl 115
                                        +++++++   +++ + iee  + l++   +s    + kk++k+ GG   k ++++ +++g +++ + e++c   G+
  gene1007|gene1007|rna1007|rna1007  11 DHSEEEIFSSQIKRKIIEETTKCLTKRRRNS---VSVKKEVKVCGGKNAKNNSKFCKKCGKKLRLMGEFTCRCGGV 83 
                                        3445678888888888888888888884444...345669*********************************999 PP

                             Fumble 116 kfllteipke...vftyseekpkka 137
                                           ++++ ++    f y++ + + +
  gene1007|gene1007|rna1007|rna1007  84 FCAMHRFYDQhgcSFDYRK-EAMAK 107
                                        8777666333222566664.33443 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   4.3   5.6e-06     0.025       5      23 .]      51      70 ..      49      70 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 5.6e-06
                      zinc_ribbon_2  5 CGael.qdnakFCpyCGtpl 23
                                       CG ++ ++n+kFC +CG +l
  gene1007|gene1007|rna1007|rna1007 51 CGGKNaKNNSKFCKKCGKKL 70
                                       77788579*********987 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   5.2   3.2e-05      0.14       4      27 ..      51      75 ..      45      97 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 3.2e-05
                                DZR  4 Cgee.lppdarfCseCgtklkavaa 27
                                       Cg +  +++++fC++Cg+kl+ + +
  gene1007|gene1007|rna1007|rna1007 51 CGGKnAKNNSKFCKKCGKKLRLMGE 75
                                       6555156778899999999985544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (123 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1414  (0.0788666); expected 358.6 (0.02)
Passed bias filter:                      533  (0.0297284); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.31s 00:00:00.79 Elapsed: 00:00:00.50
# Mc/sec: 740.68
//
Query:       gene1008|gene1008|rna1008|rna1008  [L=185]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.6e-15   55.1   2.7    6.6e-15   55.1   2.7    1.7  2  Ribosomal_L10  Ribosomal protein L10


Domain annotation for each model (and alignments):
>> Ribosomal_L10  Ribosomal protein L10
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.1   2.7   3.7e-19   6.6e-15       2      98 ..       6      99 ..       5     101 .. 0.95
   2 ?   -1.6   0.0      0.17   3.1e+03      77      84 ..     137     144 ..     118     169 .. 0.56

  Alignments for each domain:
  == domain 1  score: 55.1 bits;  conditional E-value: 3.7e-19
                                       SCCCHCCCCCCCCCCCTTSSEEEEEE-TTS-HHHHHHCCCHHHHHGCEEEEESCCCCCCCCHCCTSS.SSCGCCSSSE CS
                      Ribosomal_L10  2 tkekKeelvkelkellkkyksvvvvdyegltvaqlqelRkklrengaelkvvKntlmrrAleetgeeeklkellkgpv 79
                                       +kek +  + ++ke+l ky+++++++++ ++++ l+++R+  r++  ++ ++K+ ++r+Al++ +++  + ++++ ++
  gene1008|gene1008|rna1008|rna1008  6 KKEKNAVHYTKIKECLGKYNQIILFEMNPVRTNVLHKMREVTRDT-TKIIFGKKLIIRKALKDVDDD--FLKCMTANT 80
                                       688889999***********************************9.*****************9997..9******** PP

                                       EEEEESS-TCHHHHCCCCC CS
                      Ribosomal_L10 80 alvftnedpvalakvleef 98
                                        lvftned+ ++++v+ ++
  gene1008|gene1008|rna1008|rna1008 81 FLVFTNEDTSKIVDVILKY 99
                                       **************99887 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.17
                                        SSEEEEEE CS
                      Ribosomal_L10  77 gpvalvft 84 
                                         +++++++
  gene1008|gene1008|rna1008|rna1008 137 EKNGVLMV 144
                                        33333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       753  (0.041999); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1387.57
//
Query:       gene1009|gene1009|rna1009|rna1009  [L=85]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (85 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       729  (0.0406604); expected 358.6 (0.02)
Passed bias filter:                      477  (0.0266049); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.29s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 566.68
//
Query:       gene101|gene101|rna101|rna101  [L=137]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.015   16.2   0.0      0.021   15.8   0.0    1.2  1  DUF4834    Domain of unknown function (DUF4834)
      0.019   14.2   0.1      0.023   13.9   0.1    1.2  1  Ion_trans  Ion transport protein
       0.02   14.6   0.0      0.024   14.3   0.0    1.1  1  SARAF      SOCE-associated regulatory factor of calcium homoe
        0.1   12.9   2.4       0.36   11.1   0.2    2.0  2  DUF2304    Uncharacterized conserved protein (DUF2304)


Domain annotation for each model (and alignments):
>> DUF4834  Domain of unknown function (DUF4834)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.8   0.0   4.7e-06     0.021       4      88 ..      15      95 ..      12      98 .. 0.60

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 4.7e-06
                        DUF4834  4 LlfilifiiailviglsilsvilrtvfglgsrkkssksaqkqfgnstnsnqqksqsrsetkeegeiieeersekeakrkkiF 85
                                   L++il+ +++++v +++i+  +  +   +g+r++++    +++g++ + +++ ++++s  +++g + +++ +++  k+ k+ 
  gene101|gene101|rna101|rna101 15 LGVILFTLFICIVGVCIIIYCLNGRS--TGNRNENT-ADGAHKGSAWKASKDGQNDTSGMSNTGFAAKRNANRN-DKQSKVN 92
                                   78999998888888889999888888..66777766.3334445555555555555555555554444444444.3333655 PP

                        DUF4834 86 ekd 88
                                   +k 
  gene101|gene101|rna101|rna101 93 NKL 95
                                   554 PP

>> Ion_trans  Ion transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   5.1e-06     0.023     122     178 ..       7      93 ..       4     136 .. 0.62

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.1e-06
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSCCCC.....................CC.........SCCSTSSSTT CS
                      Ion_trans 122 alirsvkdllnvlllllvvlfifaligvqlfkgklrek.....................ne.........caktwenpnn 171
                                    +l +++k+l+ +l+ l+++++   +i + l +++  ++                     n+          ak+ +n n+
  gene101|gene101|rna101|rna101   7 MLSKAAKKLGVILFTLFICIVGVCIIIYCLNGRSTGNRnentadgahkgsawkaskdgqNDtsgmsntgfAAKRNANRND 86 
                                    6889***************************9999988555555555544444444443003333334443344444444 PP

                                    TSSSSSS CS
                      Ion_trans 172 gntnFdn 178
                                    ++++++n
  gene101|gene101|rna101|rna101  87 KQSKVNN 93 
                                    4444444 PP

>> SARAF  SOCE-associated regulatory factor of calcium homoeostasis
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   5.3e-06     0.024     156     250 ..      11     105 ..       6     126 .. 0.55

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 5.3e-06
                          SARAF 156 ssssasllfvvlvllviayivykaflaaeeereaeaeggrrgeggggggggggpgseeeqddpPppy..sltksqkpsss 233
                                    + +++++++++l++ ++++ +   +l+ ++++++ +e++ +g ++g+ ++  ++g ++++++    +  ++++ ++++++
  gene101|gene101|rna101|rna101  11 AAKKLGVILFTLFICIVGVCIIIYCLNGRSTGNR-NENTADGAHKGSAWKASKDG-QNDTSGMSNTGfaAKRNANRNDKQ 88 
                                    5567888889999999999999999988877444.33333333333333333322.233344444444322222332333 PP

                          SARAF 234 sessqqgeqeeswrpGF 250
                                    s+ +++ e  + ++ GF
  gene101|gene101|rna101|rna101  89 SKVNNKLEGGRPQNAGF 105
                                    33344555555566677 PP

>> DUF2304  Uncharacterized conserved protein (DUF2304)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.2     8e-05      0.36      46      78 ..       3      35 ..       1      43 [. 0.93
   2 ?    1.6   0.1     0.069   3.1e+02      55      77 ..     103     125 ..     101     131 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 8e-05
                        DUF2304 46 lfpqiltvlanllGvgrgtnllfllgivfllvi 78
                                   ++p++l++ a+ lGv   t ++ ++g++++++ 
  gene101|gene101|rna101|rna101  3 CWPSMLSKAAKKLGVILFTLFICIVGVCIIIYC 35
                                   89***************************9986 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.069
                        DUF2304  55 anllGvgrgtnllfllgivfllv 77 
                                    a +lG   +t++ f+  i + + 
  gene101|gene101|rna101|rna101 103 AGFLGYVAKTSMAFYHTISAAIS 125
                                    6899**********999887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (137 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       818  (0.0456244); expected 358.6 (0.02)
Passed bias filter:                      474  (0.0264376); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 985.12
//
Query:       gene1010|gene1010|rna1010|rna1010  [L=621]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.4e-23   82.9   3.6      2e-18   66.7   0.1    3.1  2  Peptidase_C50  Peptidase family C50
      0.005   15.9   0.3      0.027   13.5   0.1    2.1  2  SDH_sah        Serine dehydrogenase proteinase
  ------ inclusion threshold ------
      0.056   13.5   0.7       0.28   11.3   0.1    2.5  3  HTH_22         HTH domain


Domain annotation for each model (and alignments):
>> Peptidase_C50  Peptidase family C50
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.7   2.1e-06     0.013      34      87 ..     364     415 ..     351     421 .. 0.83
   2 !   66.7   0.1   3.4e-22     2e-18     217     395 .]     426     574 ..     418     574 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.1e-06
                                        H....HHHHHHHHHHHHHHHHHHHHCHCCHHCCTHHHHHHHHHHHHHHHHHHHH CS
                      Peptidase_C50  34 eevlsfeevkeelkeiieesnestksakdvktkeakkeWWkeReeLDkrLkeLl 87 
                                         +++++++   +l++++++s+e++ +  +v++ e+ ++WW +R+++D+ L++L+
  gene1010|gene1010|rna1010|rna1010 364 RTSVEISDKILQLRTLLNRSKETVAR--KVTSPESIRKWWIDRYNIDNDLEKLV 415
                                        45677778888999999999998887..999*********************98 PP

  == domain 2  score: 66.7 bits;  conditional E-value: 3.4e-22
                                        EEEEEE-TTCTTS-GGGSTTTTTS-EEEES-HHHHHHHHHHHCTTGCSEEEESTSTEEEEE-TTS-SHHHHHHHHH CS
                      Peptidase_C50 217 htiLvldkelqalPWEslpiLrgqsvsRvpSleslrellekskekeegekvsksskgtyiLnPsgDLksTqetfee 292
                                         + + ld++l+ +P+E+   Lr+ +v R+ + e++++  ++         v k+  ++  +  + +L++T++++++
  gene1010|gene1010|rna1010|rna1010 426 EITICLDEDLTEFPFERTCELRKCNVFRLSCSEYVFRDQKH--------LVLKK-LTISCIAGGINLRKTEQRISK 492
                                        57789*************************99999876533........33444.57888999************9 PP

                                        HHHHHCCT-EEEESS---HHHHHHHHHHSSEEEEESSTTSTTTS-HHHHTT.S--SEEEEESTTTT--ECTTTCEC CS
                      Peptidase_C50 293 wleklekgwkgivgraPteeeleeaLkssdlflYfGHGsGaqYirsreirklercaatlLmGCSSgalkeaGefep 368
                                          ek+  g ++iv +            ++++f +fGHGsG + i+  +    +  ++ lL+GCSS++l e+ +f++
  gene1010|gene1010|rna1010|rna1010 493 FTEKH--GIDSIVSE------------NTEIFAFFGHGSGIKHIQMYT----P--SVMLLFGCSSVRLIERQNFQK 548
                                        99875..57777764............6789**********9999877....4..699****************** PP

                                        CSHHHHHHHTT-SEEEEESS--BHHHH CS
                      Peptidase_C50 369 sGtvlnYllagcpavvanLWDVTDkDI 395
                                         G++++Yl   + +++++LWDVTD DI
  gene1010|gene1010|rna1010|rna1010 549 VGVPVKYLNT-SQIILGCLWDVTDYDI 574
                                        *******975.899************9 PP

>> SDH_sah  Serine dehydrogenase proteinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0     0.068   4.1e+02     199     236 ..       9      48 ..       4      57 .. 0.72
   2 !   13.5   0.1   4.5e-06     0.027     178     260 ..      55     135 ..      50     147 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.068
                            SDH_sah 199 efvyell.kdkydeekakei.akklteGrwthdypltvee 236
                                        e++ el   d+++ee a++i  k+l   + + dy + ++ 
  gene1010|gene1010|rna1010|rna1010   9 EVLNELAhPDGINEEAAQKIiNKILKMDKNAEDYDFHIQL 48 
                                        4455555569999**9988627889999999999987765 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 4.5e-06
                            SDH_sah 178 diddktliladiakkaikqveefvyellkdkydeekakeiakklteGrwthdypltveelkelGlevntnvpeevy 253
                                        +++ +t il+ + ++   q++++++e+l+d+  +  +ke+   +   ++   y +  e+lk l  ++n+++ +++ 
  gene1010|gene1010|rna1010|rna1010  55 KMKKRTKILIALWERGSFQIRKAIFEILRDEKYD--SKELMASFEVIKFRLGYCIDKERLKALLTQINAKLRNKIV 128
                                        5678999*********************885444..67999999999***************************** PP

                            SDH_sah 254 ellelye 260
                                        ++le+y 
  gene1010|gene1010|rna1010|rna1010 129 KILEFYG 135
                                        ****995 PP

>> HTH_22  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   4.6e-05      0.28      19      44 ..      53      78 ..      44      81 .. 0.90
   2 ?   -2.6   0.0         1     6e+03      18      34 ..     173     189 ..     164     189 .. 0.73
   3 ?   -3.8   0.0       2.4   1.4e+04      10      23 ..     546     559 ..     541     560 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 4.6e-05
                             HTH_22 19 rltkeekieivraLdekGiFllkgav 44
                                       +l+ +++ +i  aL e+G F++++a+
  gene1010|gene1010|rna1010|rna1010 53 ALKMKKRTKILIALWERGSFQIRKAI 78
                                       48999********************8 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1
                             HTH_22  18 erltkeekieivraLde 34 
                                        e  ++ +k++iv+  +e
  gene1010|gene1010|rna1010|rna1010 173 EPSNSTKKVKIVSDINE 189
                                        445889999*9998765 PP

  == domain 3  score: -3.8 bits;  conditional E-value: 2.4
                             HTH_22  10 ladlgkpverltke 23 
                                         +++g+pv++l+++
  gene1010|gene1010|rna1010|rna1010 546 FQKVGVPVKYLNTS 559
                                        57899999999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (621 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       888  (0.0495287); expected 358.6 (0.02)
Passed bias filter:                      514  (0.0286686); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.63u 0.28s 00:00:00.91 Elapsed: 00:00:00.47
# Mc/sec: 4004.19
//
Query:       gene1011|gene1011|rna1011|rna1011  [L=334]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.3e-20   72.7   0.0    5.1e-20   72.1   0.0    1.3  1  Ssl1            Ssl1-like
  ------ inclusion threshold ------
       0.41   10.7  10.5        2.2    8.4   1.2    2.9  2  DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domai
          7    7.0  26.0      0.048   13.9   8.9    3.7  3  C1_4            TFIIH C1-like domain


Domain annotation for each model (and alignments):
>> Ssl1  Ssl1-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.1   0.0   8.6e-24   5.1e-20       1     193 []      50     228 ..      50     228 .. 0.88

  Alignments for each domain:
  == domain 1  score: 72.1 bits;  conditional E-value: 8.6e-24
                                        EEE-SGGGGSSSSSS-.HHHHHHHHHHHHHHHHHHHSTT-EEEEEEEETTEEEEEEEEES-HHHHHHHHHHHTTS- CS
                               Ssl1   1 vlDlsrameekdlkps.rlavviklleefveeffdqnPisqlgliavkdkkaekltelsGnprkhikaLkslreve 75 
                                        ++D s ++e +d+ ps r++v+   l++f+++f+d nPis l+l++ +++k e    l       +++ +    v 
  gene1011|gene1011|rna1011|rna1011  50 IIDSSASIELNDFLPSfRYHVT-TKLNHFIKKFYDENPISVLSLLIYRNNKCESYIVLD-----RLSETEGFFGVA 119
                                        69***********998455555.56899*************************988875.....455567777888 PP

                                        --S---HHHHHHHHHHHHSSS-TTSEEEEEEEE-SS----SS-HHHHHHHHHH.TT-EEEEEEESS--HHHHHHHH CS
                               Ssl1  76 akgepsLqnaLelalasLkkvpshasrevliifsslstcDPgdiyetidelkk.ekirvsvigLsaevavckelak 150
                                         +ge+sL n+L+++l+ L++      +e+l+i +sl t+D        +el++ ++i+++ i+  aev   k +a+
  gene1011|gene1011|rna1011|rna1011 120 GTGEFSLINSLNVSLEFLNR--DDYIKEILVITGSLYTIDI-------EELRSfKDIKIHFIAFRAEVYFFKDVAE 186
                                        9*****************97..45679************94.......44444257999***************** PP

                                        HTTTTEEEE-SHHHHHHHHHHHHS------------EEEEE-- CS
                               Ssl1 151 etkgtysvvldethlkelllehvsPppaakskkeaslikmGfP 193
                                        +t+g+y v ++ + +   l +  +P + ++ +   +l+k+GfP
  gene1011|gene1011|rna1011|rna1011 187 KTHGKYYVPVEMSDISLFLESFCMPNSINSGS-AHNLLKLGFP 228
                                        ***************99999999999999988.89*******9 PP

>> DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   2.5    0.0018        11       1       9 [.     249     257 ..     249     260 .. 0.90
   2 ?    8.4   1.2   0.00037       2.2       1      12 [.     263     274 ..     263     302 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0018
                     DNA_ligase_ZBD   1 hCPvCGsav 9  
                                        +CPvC+++v
  gene1011|gene1011|rna1011|rna1011 249 ECPVCHTKV 257
                                        5******98 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00037
                     DNA_ligase_ZBD   1 hCPvCGsavvRe 12 
                                        +CPvC + +v  
  gene1011|gene1011|rna1011|rna1011 263 KCPVCKTQLVTS 274
                                        6********954 PP

>> C1_4  TFIIH C1-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.16   9.4e+02      20      38 ..      85     107 ..      68     108 .. 0.68
   2 ?   -2.3   7.1      0.89   5.3e+03      23      36 ..     245     258 ..     236     272 .. 0.79
   3 ?   13.9   8.9     8e-06     0.048      27      54 ..     307     334 .]     301     334 .] 0.94

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.16
                               C1_4  20 e....ltssryrCekCkndFCiD 38 
                                        +    l+ ++yr +kC+++  +D
  gene1011|gene1011|rna1011|rna1011  85 NpisvLSLLIYRNNKCESYIVLD 107
                                        3444477789******9987776 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.89
                               C1_4  23 ssryrCekCkndFC 36 
                                        +  y+C+ C+++ C
  gene1011|gene1011|rna1011|rna1011 245 KKGYECPVCHTKVC 258
                                        56799999999998 PP

  == domain 3  score: 13.9 bits;  conditional E-value: 8e-06
                               C1_4  27 rCekCkndFCiDCDvFiHesLHnCpGCe 54 
                                        rC+kC +++C  C  FiH+ L  C+ C+
  gene1011|gene1011|rna1011|rna1011 307 RCKKCGSIYCERCSYFIHNDLYFCIYCD 334
                                        8************************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (334 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1217  (0.0678789); expected 358.6 (0.02)
Passed bias filter:                      597  (0.033298); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 2403.79
//
Query:       gene1012|gene1012|rna1012|rna1012  [L=293]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.6e-23   83.2   0.0    2.1e-23   82.8   0.0    1.1  1  Proteasome   Proteasome subunit
  ------ inclusion threshold ------
      0.047   14.0   0.6       0.15   12.4   0.0    1.9  2  Uteroglobin  Uteroglobin family


Domain annotation for each model (and alignments):
>> Proteasome  Proteasome subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.8   0.0   2.4e-27   2.1e-23       8     188 ..     105     276 ..     103     278 .. 0.85

  Alignments for each domain:
  == domain 1  score: 82.8 bits;  conditional E-value: 2.4e-27
                                        EEEEETTEEEEEEEEEEEETTEEEESSSSTSEEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHSSGTCHHH CS
                         Proteasome   8 vGikgkdgvvlaadkratagskllskstveKifkiddhigvafaGlaaDartlvrraraeaqlyrlrygrpipver 83 
                                        +Gik+k++v++a+d+ ++++   ++++  +K   i+d++++a +G++  +  l++++ + ++l+ l+++ p+ ++ 
  gene1012|gene1012|rna1012|rna1012 105 IGIKTKNFVLIASDMVVPSSILCIKSD-ESKFTSIYDTVVLAHCGSFQQCCDLRNFFTETIKLKTLDEQVPLCPQ- 178
                                        8*****************555555555.6************************************9999999999. PP

                                        HHHHHHHHHHHHHHHCTT..TTTSEEEEEEEEETTTEEEEEEEETTSEEEEESSEEEESTTHHHHHHHHHHHHSTT CS
                         Proteasome  84 lvarvaaklqaytqrsgr..rpfgvslliagvdeeggpeLyqidpsGsyieekdavaiGsgseaaktalekeyked 157
                                            +aa   +   +++   +p   +++++g d  g  +Ly +d  G++    +++++G+ + + +++l+key+ed
  gene1012|gene1012|rna1012|rna1012 179 ----TAAFFIQKVIHGQLraQPMESAFMVMGKD--G--SLYAVDQYGALSTS-NYMCMGYSRFFLYGLLDKEYRED 245
                                        ....44444444444444005677777777766..5..9*************.7*****99*************** PP

                                        BSHHHHHHHHHHHHHHHHHHBTTSCSSEEEE CS
                         Proteasome 158 ltleeavelavkalkealerdklsgknieva 188
                                        ++++eav + +k++  +  r  ++ + + v 
  gene1012|gene1012|rna1012|rna1012 246 MSVDEAVNVLQKCIDLMKSRFLFNYQRYMVK 276
                                        ***************9999998888777665 PP

>> Uteroglobin  Uteroglobin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1      0.29   2.6e+03      19      38 ..     148     168 ..     136     172 .. 0.67
   2 ?   12.4   0.0   1.7e-05      0.15      47      87 ..     240     280 ..     235     282 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.29
                                        XXX---HHHHHHHHHHH.HS- CS
                        Uteroglobin  19 gsaegCpaleevvekfl.egs 38 
                                        gs + C +l++++++++  ++
  gene1012|gene1012|rna1012|rna1012 148 GSFQQCCDLRNFFTETIkLKT 168
                                        444578889999988885444 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 1.7e-05
                                        HTT---HHHHHHHHHHHHHHTTS-HHHHHHHHHHHHHHHTS CS
                        Uteroglobin  47 qkynpdpeaeealaelKqcvdklsnetkenvakllekilss 87 
                                        ++y +d ++ ea+  l++c+d ++   + n +  ++ki+++
  gene1012|gene1012|rna1012|rna1012 240 KEYREDMSVDEAVNVLQKCIDLMKSRFLFNYQRYMVKIFEN 280
                                        58999*********************************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (293 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       416  (0.0232026); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 2078.22
//
Query:       gene1013|gene1013|rna1013|rna1013  [L=502]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00059   20.1   3.8      0.064   13.7   0.1    3.7  3  PC_rep    Proteasome/cyclosome repeat
     0.0094   16.0   0.0      0.017   15.1   0.0    1.3  1  FAM60A    Protein Family FAM60A


Domain annotation for each model (and alignments):
>> PC_rep  Proteasome/cyclosome repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.2   0.0    0.0035        32       6      21 ..     153     168 ..     153     172 .. 0.87
   2 !   13.7   0.1   7.1e-06     0.064       3      23 ..     334     354 ..     334     357 .. 0.93
   3 ?   -0.7   0.1      0.26   2.4e+03       4      12 ..     364     372 ..     364     383 .. 0.71

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0035
                                        HHHHCTTSTCHHHHHH CS
                             PC_rep   6 LGlihaGsgneeaisl 21 
                                        LG+++ G+g+ ++i+ 
  gene1013|gene1013|rna1013|rna1013 153 LGMMYQGTGDTSIIEE 168
                                        8**********99875 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 7.1e-06
                                        HHHHHHHCTTSTCHHHHHHHH CS
                             PC_rep   3 llALGlihaGsgneeaislLk 23 
                                        ll++Gl++ Gs+n ++i+ Lk
  gene1013|gene1013|rna1013|rna1013 334 LLGIGLVCSGSNNTTVINALK 354
                                        69***************9997 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.26
                                        HHHHHHCTT CS
                             PC_rep   4 lALGlihaG 12 
                                        lA+G+ ++G
  gene1013|gene1013|rna1013|rna1013 364 LAMGMTNLG 372
                                        799998888 PP

>> FAM60A  Protein Family FAM60A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   1.9e-06     0.017     110     204 ..     202     318 ..     172     322 .. 0.58

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.9e-06
                             FAM60A 110 klkkkkklkktkakasda......sssereaspassdsasedsdesedeeek........................ 155
                                        + k+   +++++ ++++        ++++e+ p+++                                        
  gene1013|gene1013|rna1013|rna1013 202 ISKSDDDETAKTENTNNDeaqegtLTTTKENVPKNDG--------------Isdmdssnntegfaqnghleqlgll 263
                                        1111111111111111111111112222222222222..............0222222234455567889999*** PP

                             FAM60A 156 .....krkkllekkkkrsaeklvsfldlsylkrek.vCCGiifkglsgevlidpk 204
                                             ++ ++l+  + ++  +++s+ld+ +lkr+  +C G +f+g ++++++d+ 
  gene1013|gene1013|rna1013|rna1013 264 aialiSMGDQLSAVMGSRIINASSMLDNVFLKRTIpLCLGLLFNGSNCNFVVDDL 318
                                        ****999999**********************9854999************9974 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (502 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       856  (0.0477439); expected 358.6 (0.02)
Passed bias filter:                      597  (0.033298); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.28s 00:00:00.89 Elapsed: 00:00:00.45
# Mc/sec: 3388.97
//
Query:       gene1014|gene1014|rna1014|rna1014  [L=132]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.1e-12   45.5  25.1      0.015   16.1   0.3    4.3  4  zf-C2H2_4       C2H2-type zinc finger
    1.7e-10   40.8  25.2     0.0023   18.3   1.6    4.3  4  zf-C2H2         Zinc finger, C2H2 type
    1.7e-05   25.0  20.8      0.011   16.0   1.8    4.1  4  zf-C2H2_jaz     Zinc-finger double-stranded RNA-binding
    0.00081   19.7   2.7    0.00081   19.7   2.7    4.7  5  zf-H2C2_2       Zinc-finger double domain
     0.0019   18.5  11.9       0.71   10.3   0.2    3.9  3  zf-met          Zinc-finger of C2H2 type
      0.002   18.4   4.5      0.002   18.4   4.5    2.0  2  zf-C2H2_8       C2H2-type zinc ribbon
     0.0072   16.5   5.7      0.096   12.9   2.1    2.5  2  C1_4            TFIIH C1-like domain
     0.0084   15.7   8.0        1.5    8.5   0.2    3.2  3  zf_C2H2_ZHX     Zinc-fingers and homeoboxes C2H2 finger domai
      0.009   15.7   3.7      0.009   15.7   3.7    2.0  2  zf-SNAP50_C     snRNA-activating protein of 50kDa MW C termin
  ------ inclusion threshold ------
      0.046   13.7   0.1      0.046   13.7   0.1    4.0  4  zf-C2H2_6       C2H2-type zinc finger
      0.046   13.5   0.2      0.046   13.5   0.2    4.7  5  zf-C2H2_11      zinc-finger C2H2-type
       0.14   12.1  16.3       0.41   10.6   3.1    3.1  2  Zn_ribbon_SprT  SprT-like zinc ribbon domain
        4.5    7.5  16.8        7.3    6.8   0.1    4.5  4  zf-AN1          AN1-like Zinc finger


Domain annotation for each model (and alignments):
>> zf-C2H2_4  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.3   1.1e-05     0.015       1      23 [.       8      30 ..       8      31 .. 0.94
   2 !   15.9   2.1   1.2e-05     0.017       1      22 [.      35      56 ..      35      58 .. 0.94
   3 !   13.7   1.0   6.4e-05     0.088       4      23 ..      63      82 ..      57      83 .. 0.92
   4 !   13.6   3.2   6.8e-05     0.093       1      24 []     105     128 ..     105     128 .. 0.98

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.1e-05
                          zf-C2H2_4  1 fkCpiCgksFsskkaLlrHlkth 23
                                       f C iC+++++s k+L+ H   h
  gene1014|gene1014|rna1014|rna1014  8 FACLICQRNYPSEKSLNYHKIIH 30
                                       89*****************9887 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 1.2e-05
                          zf-C2H2_4  1 fkCpiCgksFsskkaLlrHlkt 22
                                       ++C+ C ksF  +++L++Hl t
  gene1014|gene1014|rna1014|rna1014 35 YYCEKCEKSFFYSDKLKKHLIT 56
                                       89*****************986 PP

  == domain 3  score: 13.7 bits;  conditional E-value: 6.4e-05
                          zf-C2H2_4  4 piCgksFsskkaLlrHlkth 23
                                       + Cg++F +kk + rH++ h
  gene1014|gene1014|rna1014|rna1014 63 CSCGRVFVRKKWYDRHMEEH 82
                                       48****************99 PP

  == domain 4  score: 13.6 bits;  conditional E-value: 6.8e-05
                          zf-C2H2_4   1 fkCpiCgksFsskkaLlrHlkthH 24 
                                        fkC++C+k  + +k+L  H +t+H
  gene1014|gene1014|rna1014|rna1014 105 FKCRHCKKGMKKRKTLEVHEQTVH 128
                                        8*********************99 PP

>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.3   0.00023      0.32       1      23 []       8      30 ..       8      30 .. 0.95
   2 !   18.3   1.6   1.7e-06    0.0023       1      21 [.      35      55 ..      35      56 .. 0.94
   3 !   14.3   0.5   3.2e-05     0.044       5      23 .]      64      82 ..      55      82 .. 0.83
   4 !   11.7   3.4   0.00021      0.29       1      23 []     105     128 ..     105     128 .. 0.97

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00023
                                       EEETTTTEEESSHHHHHHHHHCC CS
                            zf-C2H2  1 ykCpdCgksFkrksnLkrHirtH 23
                                       + C +C + +++  +L+ H  +H
  gene1014|gene1014|rna1014|rna1014  8 FACLICQRNYPSEKSLNYHKIIH 30
                                       78*****************9988 PP

  == domain 2  score: 18.3 bits;  conditional E-value: 1.7e-06
                                       EEETTTTEEESSHHHHHHHHH CS
                            zf-C2H2  1 ykCpdCgksFkrksnLkrHir 21
                                       y+C++C ksF  ++ Lk+H+ 
  gene1014|gene1014|rna1014|rna1014 35 YYCEKCEKSFFYSDKLKKHLI 55
                                       99*****************86 PP

  == domain 3  score: 14.3 bits;  conditional E-value: 3.2e-05
                                       TTTEEESSHHHHHHHHHCC CS
                            zf-C2H2  5 dCgksFkrksnLkrHirtH 23
                                        Cg++F rk  + rH+  H
  gene1014|gene1014|rna1014|rna1014 64 SCGRVFVRKKWYDRHMEEH 82
                                       69**************998 PP

  == domain 4  score: 11.7 bits;  conditional E-value: 0.00021
                                        EEETTTTEEESSHHHHHHHHHC.C CS
                            zf-C2H2   1 ykCpdCgksFkrksnLkrHirt.H 23 
                                        +kC +C+k  k +  L++H +t H
  gene1014|gene1014|rna1014|rna1014 105 FKCRHCKKGMKKRKTLEVHEQTvH 128
                                        8*******************9999 PP

>> zf-C2H2_jaz  Zinc-finger double-stranded RNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.1   3.2e-05     0.044       2      21 ..       8      27 ..       7      28 .. 0.92
   2 ?    5.4   3.0     0.017        24       2      21 ..      35      54 ..      34      56 .. 0.86
   3 ?   -0.6   0.1       1.3   1.7e+03       7      21 ..      65      79 ..      64      82 .. 0.77
   4 !   16.0   1.8     8e-06     0.011       2      23 ..     105     126 ..     104     129 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.2e-05
                                       CBBTTTTBBBSSHHHHHCCT CS
                        zf-C2H2_jaz  2 fYCvlCdKyFksenaldnHl 21
                                       f C +C++ + se++l  H+
  gene1014|gene1014|rna1014|rna1014  8 FACLICQRNYPSEKSLNYHK 27
                                       88**************9995 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.017
                                       CBBTTTTBBBSSHHHHHCCT CS
                        zf-C2H2_jaz  2 fYCvlCdKyFksenaldnHl 21
                                       +YC+ C+K F  +  l++Hl
  gene1014|gene1014|rna1014|rna1014 35 YYCEKCEKSFFYSDKLKKHL 54
                                       9*********8888888886 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 1.3
                                       TTBBBSSHHHHHCCT CS
                        zf-C2H2_jaz  7 CdKyFksenaldnHl 21
                                       C + F   + +d H+
  gene1014|gene1014|rna1014|rna1014 65 CGRVFVRKKWYDRHM 79
                                       888888888888887 PP

  == domain 4  score: 16.0 bits;  conditional E-value: 8e-06
                                        CBBTTTTBBBSSHHHHHCCTTS CS
                        zf-C2H2_jaz   2 fYCvlCdKyFksenaldnHlkS 23 
                                        f C +C+K +k+ ++l+ H+ +
  gene1014|gene1014|rna1014|rna1014 105 FKCRHCKKGMKKRKTLEVHEQT 126
                                        99*****************987 PP

>> zf-H2C2_2  Zinc-finger double domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.1      0.13   1.7e+02       9      22 ..       2      15 ..       1      18 [. 0.81
   2 !   19.7   2.7   5.9e-07   0.00081       1      24 [.      22      44 ..      22      46 .. 0.94
   3 ?   -0.9   0.4         2   2.7e+03      19      24 ..      64      69 ..      49      71 .. 0.52
   4 ?    2.6   6.4      0.16   2.2e+02       3      23 ..      76     113 ..      75     116 .. 0.74
   5 ?   -2.8   0.1       7.6     1e+04       3      10 ..     121     129 ..     120     130 .. 0.56

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.13
                          zf-H2C2_2  9 HtgekpyeCplCdk 22
                                       H + +p+ C  C  
  gene1014|gene1014|rna1014|rna1014  2 HAQSFPFACLICQR 15
                                       77889****99976 PP

  == domain 2  score: 19.7 bits;  conditional E-value: 5.9e-07
                          zf-H2C2_2  1 nLrrHirkHtgekpyeCplCdkaF 24
                                       +L++H   Ht ++ y C++C k+F
  gene1014|gene1014|rna1014|rna1014 22 SLNYHKIIHTRPN-YYCEKCEKSF 44
                                       69********999.*********9 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 2
                          zf-H2C2_2 19 lCdkaF 24
                                       +C+ +F
  gene1014|gene1014|rna1014|rna1014 64 SCGRVF 69
                                       355555 PP

  == domain 4  score: 2.6 bits;  conditional E-value: 0.16
                          zf-H2C2_2   3 rrHirkHtgek.................pyeCplCdka 23 
                                         rH+ +H + k                 +++C  C+k 
  gene1014|gene1014|rna1014|rna1014  76 DRHMEEHDVSKylsekkiieikptalkyIFKCRHCKKG 113
                                        699999997775555577777766666567*****995 PP

  == domain 5  score: -2.8 bits;  conditional E-value: 7.6
                          zf-H2C2_2   3 rrHirk.Ht 10 
                                        + H  + H+
  gene1014|gene1014|rna1014|rna1014 121 EVHEQTvHK 129
                                        668775365 PP

>> zf-met  Zinc-finger of C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.2   0.00052      0.71       1      19 [.       8      26 ..       8      28 .. 0.92
   2 ?    3.5   1.2     0.071        99       1      12 [.      35      46 ..      35      54 .. 0.75
   3 !   10.1   0.3   0.00061      0.85       1      21 [.     105     125 ..     105     126 .. 0.95

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00052
                             zf-met  1 fyCelCnvtfnsesqlksH 19
                                       f C +C++ + se++l+ H
  gene1014|gene1014|rna1014|rna1014  8 FACLICQRNYPSEKSLNYH 26
                                       5699************999 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.071
                             zf-met  1 fyCelCnvtfns 12
                                       +yCe C ++f  
  gene1014|gene1014|rna1014|rna1014 35 YYCEKCEKSFFY 46
                                       8*****999965 PP

  == domain 3  score: 10.1 bits;  conditional E-value: 0.00061
                             zf-met   1 fyCelCnvtfnsesqlksHlq 21 
                                        f C  C++ ++ +++l+ H q
  gene1014|gene1014|rna1014|rna1014 105 FKCRHCKKGMKKRKTLEVHEQ 125
                                        78*****************87 PP

>> zf-C2H2_8  C2H2-type zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   4.5   1.4e-06     0.002      35      92 ..       5      60 ..       1      66 [. 0.89
   2 ?    1.2   0.2      0.32   4.5e+02      65      85 ..     103     123 ..      79     129 .. 0.73

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.4e-06
                          zf-C2H2_8 35 lfrcstascaetfpsmqelvahtklhykpnryfkcencllrfrthrslfkhlhvcsdq 92
                                        f  +++ c   +ps + l  h  +h +pn y  ce+c   f     l khl  c  q
  gene1014|gene1014|rna1014|rna1014  5 SFPFACLICQRNYPSEKSLNYHKIIHTRPNYY--CEKCEKSFFYSDKLKKHLITCGRQ 60
                                       56777889**********************87..9********************876 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.32
                          zf-C2H2_8  65 ryfkcencllrfrthrslfkh 85 
                                          fkc  c   ++  ++l  h
  gene1014|gene1014|rna1014|rna1014 103 YIFKCRHCKKGMKKRKTLEVH 123
                                        349999998888877777555 PP

>> C1_4  TFIIH C1-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   2.1   6.9e-05     0.096       2      35 ..      10      44 ..       9      48 .. 0.83
   2 ?    4.5   0.1      0.03        42      21      33 ..     100     112 ..      81     116 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6.9e-05
                               C1_4  2 CygCqkkfpklakkkkdee.ltssryrCekCkndF 35
                                       C+ Cq+++p+ ++ + ++   t   y CekC++ F
  gene1014|gene1014|rna1014|rna1014 10 CLICQRNYPSEKSLNYHKIiHTRPNYYCEKCEKSF 44
                                       99*******98876554443899********9988 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.03
                               C1_4  21 ltssryrCekCkn 33 
                                        + + +++C++Ck+
  gene1014|gene1014|rna1014|rna1014 100 ALKYIFKCRHCKK 112
                                        56889******97 PP

>> zf_C2H2_ZHX  Zinc-fingers and homeoboxes C2H2 finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.1     0.079   1.1e+02       5      23 ..       8      26 ..       6      29 .. 0.90
   2 !    7.7   0.9     0.002       2.8       3      23 ..      33      53 ..      31      57 .. 0.93
   3 !    8.5   0.2    0.0011       1.5       5      28 ..     105     128 ..     102     130 .. 0.94

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.079
                        zf_C2H2_ZHX  5 FvCveCsfsakkfegLalH 23
                                       F C+ C+ +  + ++L+ H
  gene1014|gene1014|rna1014|rna1014  8 FACLICQRNYPSEKSLNYH 26
                                       99*****999999999988 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.002
                        zf_C2H2_ZHX  3 PsFvCveCsfsakkfegLalH 23
                                       P+++C +C+ s    ++L++H
  gene1014|gene1014|rna1014|rna1014 33 PNYYCEKCEKSFFYSDKLKKH 53
                                       9*****************999 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.0011
                        zf_C2H2_ZHX   5 FvCveCsfsakkfegLalHNarsH 28 
                                        F C  C+   kk ++L+ H   +H
  gene1014|gene1014|rna1014|rna1014 105 FKCRHCKKGMKKRKTLEVHEQTVH 128
                                        99******************9999 PP

>> zf-SNAP50_C  snRNA-activating protein of 50kDa MW C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   3.7   6.5e-06     0.009     148     190 ..       9      52 ..       1      58 [. 0.81
   2 ?   -0.3   0.3      0.52   7.2e+02     148     165 ..     106     124 ..      96     131 .. 0.60

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 6.5e-06
                        zf-SNAP50_C 148 kCkvCekfs.akwvvlndkllpedpsyfCdkCfrslhydkngek 190
                                        +C +C+++   ++ ++ +k++   p y+C+kC +s+ y+++ +k
  gene1014|gene1014|rna1014|rna1014   9 ACLICQRNYpSEKSLNYHKIIHTRPNYYCEKCEKSFFYSDKLKK 52 
                                        7****987625566666*********************877654 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.52
                        zf-SNAP50_C 148 kCkvCekfsakwvvln.dk 165
                                        kC+ C+k   k  +l+ ++
  gene1014|gene1014|rna1014|rna1014 106 KCRHCKKGMKKRKTLEvHE 124
                                        6777777666555554344 PP

>> zf-C2H2_6  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   3.3e-05     0.046       2      24 ..       8      30 ..       8      33 .. 0.90
   2 ?    3.2   3.5     0.066        90       3      22 ..      36      55 ..      35      57 .. 0.85
   3 ?   -0.6   0.1         1   1.4e+03       7      12 ..      65      70 ..      64      71 .. 0.84
   4 ?    0.9   0.6      0.35   4.9e+02       2       9 ..     105     112 ..     104     129 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.3e-05
                          zf-C2H2_6  2 heCsvCsksFpslqaLggHkksH 24
                                       + C +C + +ps ++L+ Hk+ H
  gene1014|gene1014|rna1014|rna1014  8 FACLICQRNYPSEKSLNYHKIIH 30
                                       6799****************866 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.066
                          zf-C2H2_6  3 eCsvCsksFpslqaLggHkk 22
                                        C  C ksF + + L +H++
  gene1014|gene1014|rna1014|rna1014 36 YCEKCEKSFFYSDKLKKHLI 55
                                       599******99999999985 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 1
                          zf-C2H2_6  7 CsksFp 12
                                       C+++F 
  gene1014|gene1014|rna1014|rna1014 65 CGRVFV 70
                                       *****5 PP

  == domain 4  score: 0.9 bits;  conditional E-value: 0.35
                          zf-C2H2_6   2 heCsvCsk 9  
                                        ++C  C+k
  gene1014|gene1014|rna1014|rna1014 105 FKCRHCKK 112
                                        99**9*98 PP

>> zf-C2H2_11  zinc-finger C2H2-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.2   3.4e-05     0.046       7      26 ..      10      29 ..       8      30 .. 0.92
   2 ?    0.3   0.9      0.43     6e+02       7      25 ..      37      55 ..      35      57 .. 0.78
   3 ?   -1.0   0.5       1.1   1.5e+03       9      16 ..      56      63 ..      55      66 .. 0.75
   4 ?   -0.8   0.8      0.96   1.3e+03       9      15 ..      64      70 ..      62      80 .. 0.62
   5 ?    0.1   5.1      0.52   7.2e+02       6      12 ..     106     112 ..     105     129 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.4e-05
                         zf-C2H2_11  7 CleCGlcftSqlsLsRHlfI 26
                                       Cl C +++ S+ sL+ H +I
  gene1014|gene1014|rna1014|rna1014 10 CLICQRNYPSEKSLNYHKII 29
                                       *****************876 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.43
                         zf-C2H2_11  7 CleCGlcftSqlsLsRHlf 25
                                       C +C   f  +  L++Hl+
  gene1014|gene1014|rna1014|rna1014 37 CEKCEKSFFYSDKLKKHLI 55
                                       7788777777778999985 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 1.1
                         zf-C2H2_11  9 eCGlcftS 16
                                        CG+ +t 
  gene1014|gene1014|rna1014|rna1014 56 TCGRQWTC 63
                                       59998885 PP

  == domain 4  score: -0.8 bits;  conditional E-value: 0.96
                         zf-C2H2_11  9 eCGlcft 15
                                        CG+ f 
  gene1014|gene1014|rna1014|rna1014 64 SCGRVFV 70
                                       6888875 PP

  == domain 5  score: 0.1 bits;  conditional E-value: 0.52
                         zf-C2H2_11   6 qCleCGl 12 
                                        +C++C+ 
  gene1014|gene1014|rna1014|rna1014 106 KCRHCKK 112
                                        8****96 PP

>> Zn_ribbon_SprT  SprT-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   3.1   0.00029      0.41       3      31 ..       6      41 ..       4      47 .. 0.88
   2 ?    5.5   5.3     0.012        16       5      32 ..      61     113 ..      60     116 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00029
                     Zn_ribbon_SprT  3 yvYrCtgCgreythhlsirrhn.......YrCrrCk 31
                                       +   C  C+r+y+ + s + h+       Y+C +C 
  gene1014|gene1014|rna1014|rna1014  6 FPFACLICQRNYPSEKSLNYHKiihtrpnYYCEKCE 41
                                       6667999****************************6 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.012
                     Zn_ribbon_SprT   5 YrCtgCgreythhlsirrhn.........................YrCrrCk.g 32 
                                        ++C +Cgr + +    +rh                            Cr+Ck g
  gene1014|gene1014|rna1014|rna1014  61 WTC-SCGRVFVRKKWYDRHMeehdvskylsekkiieikptalkyiFKCRHCKkG 113
                                        99*.***8777777779999999999999999999999999**9999****955 PP

>> zf-AN1  AN1-like Zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.1     0.049        67      11      23 ..       5      17 ..       2      20 .. 0.86
   2 ?    4.4   0.3      0.03        42      13      23 ..      33      44 ..      26      44 .. 0.78
   3 ?    0.0   3.0       0.7   9.7e+02      14      23 ..      61      69 ..      50      85 .. 0.77
   4 ?    6.8   0.1    0.0053       7.3      12      21 ..     103     112 ..      93     114 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.049
                             zf-AN1 11 flpfkCryCgkvF 23
                                       + pf C  C++++
  gene1014|gene1014|rna1014|rna1014  5 SFPFACLICQRNY 17
                                       469********99 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.03
                             zf-AN1 13 p.fkCryCgkvF 23
                                       p + C++C+k+F
  gene1014|gene1014|rna1014|rna1014 33 PnYYCEKCEKSF 44
                                       5689******98 PP

  == domain 3  score: 0.0 bits;  conditional E-value: 0.7
                             zf-AN1 14 fkCryCgkvF 23
                                        +C+ Cg+vF
  gene1014|gene1014|rna1014|rna1014 61 WTCS-CGRVF 69
                                       5799.99999 PP

  == domain 4  score: 6.8 bits;  conditional E-value: 0.0053
                             zf-AN1  12 lpfkCryCgk 21 
                                         +fkCr+C+k
  gene1014|gene1014|rna1014|rna1014 103 YIFKCRHCKK 112
                                        359*****97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1159  (0.0646439); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.44u 0.30s 00:00:00.74 Elapsed: 00:00:00.48
# Mc/sec: 820.97
//
Query:       gene1015|gene1015|rna1015|rna1015  [L=285]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-19   70.7   0.1    1.7e-19   70.2   0.1    1.2  1  ATP_bind_3     PP-loop family
    7.6e-05   22.8   0.0    9.4e-05   22.5   0.0    1.2  1  PAPS_reduct    Phosphoadenosine phosphosulfate reductase fami
     0.0002   20.8   4.3     0.0002   20.8   4.3    2.3  2  zn-ribbon_14   Zinc-ribbon
     0.0026   17.4   0.1     0.0043   16.7   0.1    1.2  1  ThiI           Thiamine biosynthesis protein (ThiI)
     0.0039   16.0   0.2     0.0057   15.5   0.2    1.2  1  tRNA_Me_trans  tRNA methyl transferase
  ------ inclusion threshold ------
       0.02   14.9   1.1      0.099   12.7   0.2    2.3  2  DZR            Double zinc ribbon
       0.12   12.2   7.4       0.12   12.3   3.4    2.5  2  HalOD2         Halobacterial output domain 2
       0.13   11.7   4.9       0.27   10.7   0.8    2.9  2  QueC           Queuosine biosynthesis protein QueC
        1.8    8.1   6.9        5.3    6.6   2.1    2.4  2  zf-ribbon_3    zinc-ribbon domain
        7.2    6.4   7.6        3.4    7.5   0.3    2.4  3  Rubredoxin_2   Rubredoxin metal binding domain


Domain annotation for each model (and alignments):
>> ATP_bind_3  PP-loop family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.2   0.1   9.7e-23   1.7e-19       1     168 [.      11     212 ..      11     229 .. 0.85

  Alignments for each domain:
  == domain 1  score: 70.2 bits;  conditional E-value: 9.7e-23
                                        EEEEE--SCHHHHHHHHHHHHHCT..TTTTEEEEEEEE-SSSTCHHHHHHHHHHHHHHTT-EEEEEE--H...... CS
                         ATP_bind_3   1 kvlvAvSgGlDSmaLllllaklkk..klgiklvaihvdhglreeskeeaelvkelckklnikleiekvdv...... 68 
                                        kvlvAvSgG DS++L +++  l+k  + gi+l ++ vd g++   ++  e+vk+  k++n++lei +++       
  gene1015|gene1015|rna1015|rna1015  11 KVLVAVSGGKDSTVLAHIMDLLNKrhDYGINLHLVCVDEGIKGYRDHSLEMVKQNKKEYNLELEIVSFKEmfeltm 86 
                                        689**************9876655005566**************************************99999999 PP

                                        ...HHCTTSTCCCHHHHHHHHHHHHCHHCCT.CEEE---BHHHHHHHHHHHHCCT--CCHHH-S-SEEEE...... CS
                         ATP_bind_3  69 ...akkkgknleeaARelRYevlkealkkegievlllAhhadDqaEtfllrlargsglaglagikeasei...... 135
                                            +kk  +  +    +R ++l+e +++ g++ ++++h+adD aEt++l+l rg   +   +++++++       
  gene1015|gene1015|rna1015|rna1015  87 devMQKKRVGSCTYCGVFRRQALEEGARRIGATKIITGHNADDMAETVVLNLLRGDFNRLKRCTAARTKKnlsdep 162
                                        88866667777888999****************************************9998888888877789*** PP

                                        .................TTCCEE-CCCT--HHHHHHHHHHTT---B--CG CS
                         ATP_bind_3 136 .................asirlvRPlLkvskeeleeylkekkikwveDes 168
                                                         as   v P+  ++ +e+  y+  k++k++  e 
  gene1015|gene1015|rna1015|rna1015 163 niedmkkgcgcdesvysASLVRVKPFKYIYEKEIVFYAYLKNLKYFSTEC 212
                                        *************99544455556********************998765 PP

>> PAPS_reduct  Phosphoadenosine phosphosulfate reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.0   5.2e-08   9.4e-05       2     156 ..      12     208 ..      11     265 .. 0.86

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 5.2e-08
                                        EEEE--SSCTCHHHHHHHHHHCTTH......EEEEEE-STB..-HHHHHHHHHHHHHTT-EEEEEE-SCHH..HHH CS
                        PAPS_reduct   2 lvvsvsgGkdslVllhLalkafkpv......pvvfvdtghe..fpetiefvdeleeryglrlkvyepeeev..aek 67 
                                        + v+vsgGkds+Vl h++   +k        ++v vd g +   +  +e+v++ +++y+l+l++++ +e +  +  
  gene1015|gene1015|rna1015|rna1015  12 VLVAVSGGKDSTVLAHIMDLLNKRHdyginlHLVCVDEGIKgyRDHSLEMVKQNKKEYNLELEIVSFKEMFelTMD 87 
                                        6799**********998766666645678989*******984457899**********888776665555400555 PP

                                        HHHHH-S-THHHC.HHHHHHTHHHHHHHHHCTTECEEE----CCCTTTTTTSSSEEECTTT-S............. CS
                        PAPS_reduct  68 inaekhgsslyee.aaeriaKveplkkaLekldedalltGaRrdesksraklpiveidedfek............. 129
                                        ++++k   + + +  ++ + + ++l++  ++++++ ++tG  +d+ ++   l++++ d +  k             
  gene1015|gene1015|rna1015|rna1015  88 EVMQK---KRVGScTYCGVFRRQALEEGARRIGATKIITGHNADDMAETVVLNLLRGDFNRLKrctaartkknlsd 160
                                        55555...44454689******************************999999999888776668999999999999 PP

                                        .....................CEEE-CCCT--HHHHHHHHHHCT--B- CS
                        PAPS_reduct 130 .....................slrvfPllnWteedvwqyilrenipyn 156
                                                              +rv P     e+++  y++ +n++y 
  gene1015|gene1015|rna1015|rna1015 161 epniedmkkgcgcdesvysasLVRVKPFKYIYEKEIVFYAYLKNLKYF 208
                                        999999999999999999999999999999999999999999999985 PP

>> zn-ribbon_14  Zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.2      0.26   4.7e+02       1       8 [.      96     103 ..      96     109 .. 0.80
   2 !   20.8   4.3   1.1e-07    0.0002       2      25 ..     256     281 ..     255     282 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.26
                       zn-ribbon_14   1 gkCerCGy 8  
                                        g C+ CG 
  gene1015|gene1015|rna1015|rna1015  96 GSCTYCGV 103
                                        57*****7 PP

  == domain 2  score: 20.8 bits;  conditional E-value: 1.1e-07
                       zn-ribbon_14   2 kCerCGylSSq..kiCkACvLLegLn 25 
                                        +C  CG ++S   k CkACvLL +L 
  gene1015|gene1015|rna1015|rna1015 256 RCVSCGKMTSSaaKRCKACVLLSSLQ 281
                                        7*******9963378********996 PP

>> ThiI  Thiamine biosynthesis protein (ThiI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.1   2.4e-06    0.0043       4     129 ..      10     138 ..       7     141 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 2.4e-06
                               ThiI   4 gkvlaLlSgGiDSpVaayll..l.kR...Gcrvvlvhlknepgtseeaiekveklaellaeyqtslevklvvvdfk 73 
                                        +kvl+ +SgG DS V a+++  l kR   G++ +lv +       e  ++ + +  e++ +++   +++l +v+fk
  gene1015|gene1015|rna1015|rna1015  10 EKVLVAVSGGKDSTVLAHIMdlLnKRhdyGINLHLVCV------DEGIKGYRDHSLEMVKQNKKEYNLELEIVSFK 79 
                                        79*************99987432244444666666665......4555666666667777777777799******* PP

                               ThiI  74 evlkeilekvkekltivllkrk..ml.riAekvaeeegakalvtGesLgqVaSqtleNl 129
                                        e+ +  +++v +k ++  +  +  +  ++ e+ a++ ga+ ++tG +    a   + Nl
  gene1015|gene1015|rna1015|rna1015  80 EMFELTMDEVMQKKRVGSCTYCgvFRrQALEEGARRIGATKIITGHNADDMAETVVLNL 138
                                        *99999999877777655555422331455889************99888776666665 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.2   3.2e-06    0.0057       2     131 ..      11     132 ..      10     155 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 3.2e-06
                      tRNA_Me_trans   2 kvvvalSgGVDSsvaaallkeqg.yevigvflklweeedeegkeccaeedlkdaervaeklgiplevvdfekeyke 76 
                                        kv+va+SgG DS+v a+++     ++  g+ l+l+   de   +   ++ l+ +++  ++ +++le+v+f++ +  
  gene1015|gene1015|rna1015|rna1015  11 KVLVAVSGGKDSTVLAHIMDLLNkRHDYGINLHLVCV-DEGI-KGYRDHSLEMVKQNKKEYNLELEIVSFKEMFEL 84 
                                        8**************9976532213335666665555.2222.4678899999******************99964 PP

                      tRNA_Me_trans  77 kvfeefleeyeeGrTPnPdvlCNkeiKfgallekakeelgadalatGHYarvsle 131
                                          ++e++++ + G+    +  C    + +al e a +  ga ++ tGH a  + e
  gene1015|gene1015|rna1015|rna1015  85 -TMDEVMQKKRVGS----CTYCGVF-RRQALEEGARR-IGATKIITGHNADDMAE 132
                                        .5688888888886....8888654.55667777776.99999999998877766 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.0       0.5   8.9e+02      15      19 ..      98     102 ..      88     111 .. 0.70
   2 ?   12.7   0.2   5.5e-05     0.099      29      48 ..     255     274 ..     230     275 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.5
                                DZR  15 CseCg 19 
                                        C +Cg
  gene1015|gene1015|rna1015|rna1015  98 CTYCG 102
                                        44444 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 5.5e-05
                                DZR  29 drCpsCgekvdpearfCpeC 48 
                                         rC+sCg+++++ a+ C++C
  gene1015|gene1015|rna1015|rna1015 255 WRCVSCGKMTSSAAKRCKAC 274
                                        58****************99 PP

>> HalOD2  Halobacterial output domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.1      0.29   5.3e+02      33      42 ..      97     106 ..      94     119 .. 0.63
   2 ?   12.3   3.4   6.6e-05      0.12      28      45 ..     251     268 ..     246     275 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.29
                             HalOD2  33 kCtrCGevqa 42 
                                         Ct CG    
  gene1015|gene1015|rna1015|rna1015  97 SCTYCGVFRR 106
                                        4777775544 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 6.6e-05
                             HalOD2  28 GayvWkCtrCGevqaaAd 45 
                                        Ga vW+C  CG++  +A 
  gene1015|gene1015|rna1015|rna1015 251 GARVWRCVSCGKMTSSAA 268
                                        9***********999885 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.8   0.00015      0.27       1      76 [.      11      93 ..      11     132 .. 0.81
   2 ?    0.8   0.2      0.16   2.9e+02     163     201 ..     240     276 ..     232     279 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00015
                                       EEEEE--SSHHHHHHHHHH......HHH-SEEEEEEEESS-T..TSHHHHHHHHHHHHT--.-EEEEE-GGGGGGSCG CS
                               QueC  1 kavvllSGGlDSttvlala......kkegkevealtfdYgqr..hkkeleaakkiakelgveehkildldllkelggs 70
                                       k++v +SGG DSt+++ ++      ++ g +++++ +d g +  +++ le++k+  ke+++ e +i++ + + el+  
  gene1015|gene1015|rna1015|rna1015 11 KVLVAVSGGKDSTVLAHIMdllnkrHDYGINLHLVCVDEGIKgyRDHSLEMVKQNKKEYNL-ELEIVSFKEMFELTMD 87
                                       57999*********98765332221344567899999999998778889999999999999.9999999888888777 PP

                                       GG---- CS
                               QueC 71 aLtdee 76
                                        +++++
  gene1015|gene1015|rna1015|rna1015 88 EVMQKK 93
                                       666654 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.16
                                        HHHHHHHHHHTTHHHHH-B-STTS.-BTTTTSSSHHHHH CS
                               QueC 163 KaeivklgkelgvpleetlsCYegeeegkaCgeCdaCal 201
                                        K+  +    + g+ +   +sC +   +++a ++C+aC+l
  gene1015|gene1015|rna1015|rna1015 240 KSGEFLERSDAGARVWRCVSCGKM--TSSAAKRCKACVL 276
                                        555555556677888888999887..4568999999986 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.2     0.027        49      18      24 ..      97     103 ..      92     104 .. 0.79
   2 ?    6.6   2.1     0.003       5.3       4      22 ..     256     274 ..     255     274 .. 0.93

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.027
                        zf-ribbon_3  18 vCpyCGt 24 
                                         C+yCG 
  gene1015|gene1015|rna1015|rna1015  97 SCTYCGV 103
                                        6*****5 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.003
                        zf-ribbon_3   4 rCPnCGaplssddnvCpyC 22 
                                        rC +CG+  ss ++ C+ C
  gene1015|gene1015|rna1015|rna1015 256 RCVSCGKMTSSAAKRCKAC 274
                                        8******87*****9*999 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.1      0.28   5.1e+02      11      21 ..      92     102 ..      89     104 .. 0.77
   2 ?    7.5   0.3    0.0019       3.4      13      23 ..     253     263 ..     249     268 .. 0.76
   3 ?    5.8   4.3    0.0063        11       1      20 [.     255     274 ..     255     275 .. 0.94

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.28
                       Rubredoxin_2  11 akwfGrCpsCg 21 
                                         k +G C  Cg
  gene1015|gene1015|rna1015|rna1015  92 KKRVGSCTYCG 102
                                        57789999998 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0019
                       Rubredoxin_2  13 wfGrCpsCgsW 23 
                                         ++rC sCg +
  gene1015|gene1015|rna1015|rna1015 253 RVWRCVSCGKM 263
                                        67999999865 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.0063
                       Rubredoxin_2   1 YvCsqCGfesakwfGrCpsC 20 
                                        ++C +CG  +++   rC++C
  gene1015|gene1015|rna1015|rna1015 255 WRCVSCGKMTSSAAKRCKAC 274
                                        89**********99999999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (285 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       673  (0.037537); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2029.64
//
Query:       gene1016|gene1016|rna1016|rna1016  [L=282]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (282 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       537  (0.0299515); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 2058.77
//
Query:       gene1017|gene1017|rna1017|rna1017  [L=234]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       965  (0.0538234); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1636.09
//
Query:       gene1018|gene1018|rna1018|rna1018  [L=78]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-22   79.8   0.1    1.3e-22   79.7   0.1    1.0  1  Cyt-b5    Cytochrome b5-like Heme/Steroid binding domain


Domain annotation for each model (and alignments):
>> Cyt-b5  Cytochrome b5-like Heme/Steroid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.7   0.1   7.4e-27   1.3e-22       2      73 ..       7      77 ..       6      78 .] 0.96

  Alignments for each domain:
  == domain 1  score: 79.7 bits;  conditional E-value: 7.4e-27
                                       HHHHTTTECTTEEEEEETTEEEECTTTCCCSTTCSHHHHTTTTSBBHHHHHHTTGGCHHHHHHHHGGEEEEE CS
                             Cyt-b5  2 leelskhngkndlwvairgkVYDvskflskhpGgesailkyaGkDateafksvvhsekdaekllkkylvGkl 73
                                       ++ +s+hn+++++wv+++  VYDv+ +l+ hpGg++++l+y GkD+te+f +v h   +++k+l+ +l+G++
  gene1018|gene1018|rna1018|rna1018  7 RDIVSEHNNEKSCWVIYNSCVYDVTGYLKIHPGGSKILLRYGGKDITEIFDVV-HGYVNIHKMLEGCLIGYI 77
                                       6679*************************************************.999*************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       456  (0.0254337); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 518.82
//
Query:       gene1019|gene1019|rna1019|rna1019  [L=153]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0046   17.1   0.9     0.0059   16.7   0.9    1.2  1  CD20      CD20-like family
      0.006   16.5   0.4      0.011   15.6   0.4    1.5  1  DUF3377   Domain of unknown function (DUF3377)
  ------ inclusion threshold ------
      0.019   14.3   1.2      0.025   14.0   1.2    1.1  1  DUF1523   Protein of unknown function (DUF1523)
      0.023   14.3   0.3      0.028   14.0   0.3    1.2  1  SUR7      SUR7/PalI family
      0.032   14.3   1.6       0.06   13.4   1.6    1.4  1  SPC12     Microsomal signal peptidase 12 kDa subunit (SPC12)
      0.038   13.9   3.3      0.053   13.4   3.3    1.2  1  DUF1980   Domain of unknown function (DUF1980)
        0.1   11.4   1.8       0.24   10.1   1.0    1.5  2  DUF2207   Predicted membrane protein (DUF2207)
        0.1   11.9   0.5       0.11   11.8   0.5    1.2  1  CMV_US    CMV US
        0.2   12.0   4.6       0.13   12.5   2.4    1.7  2  Orf78     Orf78 (ac78)
       0.26   11.2   2.3       0.36   10.7   2.3    1.4  1  TMEM154   TMEM154 protein family


Domain annotation for each model (and alignments):
>> CD20  CD20-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.9   3.3e-06    0.0059     101     150 ..      90     141 ..      64     146 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 3.3e-06
                               CD20 101 l.....tsstsrcsskesseeeesraycsslrslltgilavlliltilellvsll 150
                                              ++ +++ + + +++ ++ ++y++++   ++ i+++l+++++l ++v ++
  gene1019|gene1019|rna1019|rna1019  90 NknileEYKKMKIERELDENHNKTMKYVKTI---FLFIIVMLIAFCVLTVIVVIC 141
                                        1344556778888999999999999999999...*****************9775 PP

>> DUF3377  Domain of unknown function (DUF3377)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.4   6.3e-06     0.011       9      57 ..      96     149 ..      90     152 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 6.3e-06
                            DUF3377   9 eeeevdvvvkiddeesgtvnai....aVvvPlvLllciLvliyailq.frrkgt 57 
                                        e + +++  ++d+++++t++ +      ++ ++ + c+L +i++i + f rk  
  gene1019|gene1019|rna1019|rna1019  96 EYKKMKIERELDENHNKTMKYVktifLFIIVMLIAFCVLTVIVVICKwFMRKKR 149
                                        567788999999999999765421114566677778*********999777655 PP

>> DUF1523  Protein of unknown function (DUF1523)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   1.2   1.4e-05     0.025      97     171 ..      61     135 ..      58     144 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.4e-05
                            DUF1523  97 dsadlqaeaqdlastkeePklveikyYGWriellsifpNavsikevaeedtksipwfniillvvlllllllliql 171
                                        +s+d+ ++  ++ +++ +     i+ +  + ++l++++ +   +e++e+++k++ ++++i+l+++++l+ + + +
  gene1019|gene1019|rna1019|rna1019  61 QSTDITTKNVNMYKNELNYYKMFIMCFLFNKNILEEYKKMKIERELDENHNKTMKYVKTIFLFIIVMLIAFCVLT 135
                                        7999*****9**999999999*****************9988899**************9998888776554433 PP

>> SUR7  SUR7/PalI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.3   1.6e-05     0.028      84     138 ..      94     144 ..      56     151 .. 0.63

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.6e-05
                               SUR7  84 leelnsesngkvdlPsnlrktlsklnnltkalfilhiialvlsfi.slvvgllaic 138
                                        lee+++   +++ l +n +kt+++    +k +f ++i+ l++ ++ +++v ++ ++
  gene1019|gene1019|rna1019|rna1019  94 LEEYKKMKIERE-LDENHNKTMKY----VKTIFLFIIVMLIAFCVlTVIVVICKWF 144
                                        244444333333.66666666665....6667777776666555524455555666 PP

>> SPC12  Microsomal signal peptidase 12 kDa subunit (SPC12)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   1.6   3.3e-05      0.06      32      65 ..     119     152 ..     114     152 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.3e-05
                              SPC12  32 qdlkltlyillagvvltllvvvPpWpfYnrnplk 65 
                                          +   +++l+a++vlt++vv+ +W + ++ pl+
  gene1019|gene1019|rna1019|rna1019 119 TIFLFIIVMLIAFCVLTVIVVICKWFMRKKRPLQ 152
                                        5566778889999*****************9986 PP

>> DUF1980  Domain of unknown function (DUF1980)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   3.3   2.9e-05     0.053      16      90 ..      59     135 ..      54     140 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.9e-05
                            DUF1980  16 kLhasgeiskYInpkyapllyfamvvllilalvqliraqkkk....ecghdHeeksfikkllsylilviPlllgll 87 
                                        +L++++  +k +n+  + l y  m+++ +l+  ++++  kk     e + +H  ++ +k +  +++++i +l+++ 
  gene1019|gene1019|rna1019|rna1019  59 YLQSTDITTKNVNMYKNELNYYKMFIMCFLFNKNILEEYKKMkierELDENH--NKTMKYVKTIFLFIIVMLIAFC 132
                                        89999999**************************999999985543244444..7889999999999999999987 PP

                            DUF1980  88 lpt 90 
                                        + t
  gene1019|gene1019|rna1019|rna1019 133 VLT 135
                                        765 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.22   3.9e+02     445     460 ..      50      67 ..      24      81 .. 0.75
   2 ?   10.1   1.0   0.00013      0.24     187     235 ..      95     145 ..      61     152 .. 0.52

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.22
                            DUF2207 445 lakwkgFkkyLe..Dfse 460
                                        l ++++++kyL+  D+  
  gene1019|gene1019|rna1019|rna1019  50 LTEVRALRKYLQstDITT 67 
                                        678999999999777654 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00013
                            DUF2207 187 deilkeeqk..ntreraarlslallillilllilllllllllliklllwkk 235
                                        +e +k+  +   ++  +++ +++ +i+l ++++l+++++l +++ +  w+ 
  gene1019|gene1019|rna1019|rna1019  95 EEYKKMKIEreLDENHNKTMKYVKTIFLFIIVMLIAFCVLTVIVVICKWFM 145
                                        222222222223334445555555555555555555555544444444544 PP

>> CMV_US  CMV US
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.5     6e-05      0.11     188     241 ..      95     149 ..      37     153 .] 0.79

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 6e-05
                             CMV_US 188 dsysvddleRLfyekRyLtlllvvlvq.vklvaLlsyvvvrtvrvalayyLrwha 241
                                        + y   ++eR   e+   t+ +v  +    +v+L+ ++v  ++ v + +++r+++
  gene1019|gene1019|rna1019|rna1019  95 EEYKKMKIERELDENHNKTMKYVKTIFlFIIVMLIAFCVLTVIVVICKWFMRKKR 149
                                        56777889999999999999999999978899*******9999********9986 PP

>> Orf78  Orf78 (ac78)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       1.4   2.4e+03      44      62 ..      60      78 ..      42      94 .. 0.55
   2 ?   12.5   2.4   7.5e-05      0.13      39      90 ..      96     147 ..      89     152 .. 0.73

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1.4
                              Orf78 44 aeknditekesnaaekaqa 62
                                        +++dit+k+ n  +++ +
  gene1019|gene1019|rna1019|rna1019 60 LQSTDITTKNVNMYKNELN 78
                                       4445555555553222222 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 7.5e-05
                              Orf78  39 ekksaaeknditekesnaaekaqalnillisllavvcvlvllyviyYfvilr 90 
                                        e k+++ +++++e+++++++  ++  +++i++l  +cvl ++ vi  +++ +
  gene1019|gene1019|rna1019|rna1019  96 EYKKMKIERELDENHNKTMKYVKTIFLFIIVMLIAFCVLTVIVVICKWFMRK 147
                                        445666677777777777788888888999999999*999999998666655 PP

>> TMEM154  TMEM154 protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   2.3    0.0002      0.36      44      90 ..     101     152 ..      61     153 .] 0.76

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0002
                            TMEM154  44 lssaelsnesdqlel.....vlmiiiPlvllillllvviiliqkkkrkrsKd 90 
                                        + + el+++ ++         l ii+ l+++ +l ++v+i    +++kr  +
  gene1019|gene1019|rna1019|rna1019 101 KIERELDENHNKTMKyvktiFLFIIVMLIAFCVLTVIVVICKWFMRKKRPLQ 152
                                        4455566555554334444489999**********99999988888888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2170  (0.121033); expected 358.6 (0.02)
Passed bias filter:                      903  (0.0503653); expected 358.6 (0.02)
Passed Vit filter:                       137  (0.00764125); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 1020.25
//
Query:       gene102|gene102|rna102|rna102  [L=153]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-27   96.2   0.0    1.8e-27   95.9   0.0    1.1  1  PTH2      Peptidyl-tRNA hydrolase PTH2
  ------ inclusion threshold ------
      0.076   12.9   0.1        0.1   12.4   0.1    1.2  1  Ntox5     Bacterial toxin 5


Domain annotation for each model (and alignments):
>> PTH2  Peptidyl-tRNA hydrolase PTH2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.9   0.0     2e-31   1.8e-27       2     117 .]      46     153 .]      45     153 .] 0.95

  Alignments for each domain:
  == domain 1  score: 95.9 bits;  conditional E-value: 2e-31
                                    EEEEEEESSSSS-HHHHHHHHHHHHHHHHHHHHHH.CHHHHHHHHHHTTTSEEEEEESSHHHHHHHHHHHHHTT-SEEEE CS
                           PTH2   2 kmvlvvrkDLkmskGkiaaqcahAavalvkkllkesnekellkeWeeegqkkivlkveseeeLlelaakakalglpaali 81 
                                    ++v++v+kDLkmskGk++aq++h   ++++k+ +        +eW ++g++kivl++   ee++++ + ak++g+ ++ i
  gene102|gene102|rna102|rna102  46 VLVIIVNKDLKMSKGKVIAQVGHLISKVFRKAVNV-------DEWVDNGEAKIVLRAG-YEEMKNIGRMAKERGILVNGI 117
                                    689********************999999988875.......68************97.899****************** PP

                                    EETSSSSSSTTCEEEEEEEEEEHHHHHHHHTTSEB- CS
                           PTH2  82 rDagrtqiepgtkTvlaigPapksivdkvtgkLkll 117
                                     Dagrtq+++g++T +++gP++k +v  +t++Lk++
  gene102|gene102|rna102|rna102 118 YDAGRTQVPAGSNTLIGLGPWNKAEVSVFTKDLKMY 153
                                    **********************************97 PP

>> Ntox5  Bacterial toxin 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   1.1e-05       0.1      51     105 ..      61     117 ..      49     124 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.1e-05
                          Ntox5  51 rqivqaGhilsdwyvkklsrdeflmledadlnwesqftevs..GavldksavlieGv 105
                                    + i q+Gh+ s+ + k++  de++   +a +   ++++e+   G + ++  +l++G+
  gene102|gene102|rna102|rna102  61 KVIAQVGHLISKVFRKAVNVDEWVDNGEAKIVLRAGYEEMKniGRMAKERGILVNGI 117
                                    5899***************************99999999887788888888888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       480  (0.0267723); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 1222.77
//
Query:       gene1020|gene1020|rna1020|rna1020  [L=384]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
   2.8e-103  345.7   3.3   3.2e-103  345.6   3.3    1.0  1  Ribosomal_L3  Ribosomal protein L3


Domain annotation for each model (and alignments):
>> Ribosomal_L3  Ribosomal protein L3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  345.6   3.3  1.8e-107  3.2e-103       1     369 []       1     368 [.       1     368 [. 0.93

  Alignments for each domain:
  == domain 1  score: 345.6 bits;  conditional E-value: 1.8e-107
                                        XX.S.SXXXXSSXCCCTTXSBXSXSSXXXSX.XXSBTTTTTXBSEEEEEEEEEEEEEEECHHTTSCCC....CCEE CS
                       Ribosomal_L3   1 mshrkfeaprhgslGflprkRaerergkvksfPkddtskpvkltaflGyKaGmthiVrevdkpgskld....kkev 72 
                                        ms rk+eaprhgsl + p+kRa++ r  + + P d+   + +lt+fl yKaGmthi r   + + + +    +kev
  gene1020|gene1020|rna1020|rna1020   1 MSCRKYEAPRHGSLAYCPKKRAKQIRQPAAAAPPDNPADKPHLTSFLAYKAGMTHILRITTRKSNDKKareiRKEV 76 
                                        999*********************999998889999999******************9988876655412226789 PP

                                        EEEEEEEEC--EEEEEEEEEEEETTEEEEEEEEESSS.SHHHHCCCSTSTTTSS.SSSSHCCCCHCSSCCCCCCHH CS
                       Ribosomal_L3  73 veavtvvetppmvivgvvgyvetprGlrslktvwaehlseevkrrlyknwyksk.kkaftkyskkyeskdvkklie 147
                                        v+av+v+e p+m++ g++ y    rGl    +  +++ se +  r+ + +++s  kk   +  ++ + +dv++  e
  gene1020|gene1020|rna1020|rna1020  77 VDAVSVLEAPAMRVYGIRVYTRGVRGLVLADEYVTKNKSECLLARMVRRYHRSAlKKNAGRENVQEDLNDVRARFE 152
                                        **********************************************999999975555555555555555555554 PP

                                        HHHHHHHHSCSCEEEEEEEECCCSS-SCCSSHHEEEEECHCSCHHHHHHHHHHCCTCEEECCCCS-TTSEEEEEEE CS
                       Ribosomal_L3 148 adleeikkeasvvrviahtvirktkslaqKkahllEiqvngGtiaekldfarealektvavaavFrqgeliDvigv 223
                                           ++ +  +  v+v+ ht+i+ +k l  Kkah+lE+qvngG++a+k+++a + l+  + + +vF+++eli + gv
  gene1020|gene1020|rna1020|rna1020 153 ---KYCATSNVLVKVLMHTKIETLK-LDSKKAHVLEVQVNGGSVADKVQYALSVLNTDISIGEVFNEQELISICGV 224
                                        ...577888999*************.************************************************** PP

                                        E---EEE-HHHHCT----STTTSSSSSS-S-SS-SSSSS--TTS--SEEESCCEEEEEEEEEEEEETTTSSTTTSS CS
                       Ribosomal_L3 224 tkGkGfeGvvkRWgvkklprkthrglRkvaaigawdparVsstvaraGqkGyhhRtelnkkiyrigkgedaknast 299
                                        tkGkGf GvvkR+gv+ lprk ++g Rkva+igaw+pa V  tvaraGq+G  +Rt +nkk+ +ig+   +++ +t
  gene1020|gene1020|rna1020|rna1020 225 TKGKGFTGVVKRFGVRILPRKSNKGIRKVACIGAWHPAGVLRTVARAGQMGCFKRTLINKKVLKIGN--ATQSVQT 298
                                        ******************************************************************9..77899** PP

                                        TTT.SS..SS.TTTCTTCB..TSCEEEEES--SSSTTEEEEEEE-SSGGGSCCCSS-EEEEEE-TTCTSS CS
                       Ribosomal_L3 300 efdltekeitPmGGfvhyGevkndfilvkGsvpGpkkrlvklrkslltqtsrkaeeevslkfidtaskfg 369
                                        efdlt+k+i+P+GGfv+yG+vknd+++vkG ++Gp kr+v+l ks +   + ++ e+++ kfidt+sk+g
  gene1020|gene1020|rna1020|rna1020 299 EFDLTDKTINPLGGFVNYGMVKNDYLMVKGPCVGPVKRVVTLCKSYTGSRKLRNTEDIDIKFIDTSSKMG 368
                                        *******************************************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (384 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       629  (0.0350828); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 2616.49
//
Query:       gene1021|gene1021|rna1021|rna1021  [L=364]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.018   15.5   2.1       0.25   11.8   0.2    3.0  3  Phage_TAC_13     Phage tail assembly chaperone, TAC
      0.058   12.8   4.9       0.38   10.1   0.9    2.4  2  AAA-ATPase_like  Predicted AAA-ATPase
       0.41   10.5   4.8        2.8    7.8   0.1    3.2  3  LacI             Bacterial regulatory proteins, lacI family
       0.66    9.8   5.2       0.35   10.7   1.9    2.2  2  FAS_meander      Fatty acid synthase meander beta sheet domai


Domain annotation for each model (and alignments):
>> Phage_TAC_13  Phage tail assembly chaperone, TAC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.1     0.077   3.4e+02      51      79 ..     181     209 ..     151     225 .. 0.69
   2 ?   11.8   0.2   5.6e-05      0.25      29      84 ..     233     288 ..     225     332 .. 0.87
   3 ?   -0.9   0.0      0.53   2.4e+03      15      38 ..     299     321 ..     287     360 .. 0.73

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.077
                       Phage_TAC_13  51 kkedkvAariaaSicdekGkpvftvddit 79 
                                        k+ +k+ +  +  i+d+ G+++f v++ +
  gene1021|gene1021|rna1021|rna1021 181 KNCSKQHSEQVKIIVDDAGTQIFVVAQNY 209
                                        33445555556668899999999877655 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 5.6e-05
                       Phage_TAC_13  29 tatvyvrklsfktaeadlkalkkkedkvAariaaSicdekGkpvf.tvdditgeldp 84 
                                        t +++   +++++ +++ + + +++dk+ +  + Si+d++G  +f  ++di+ ++++
  gene1021|gene1021|rna1021|rna1021 233 TNKIFENAVTYREHKEIHRTFYEQKDKINDA-MHSIVDDNGPRLFlAIADIISDAKK 288
                                        5677778889999999999999999998765.78******************88776 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 0.53
                       Phage_TAC_13  15 ekeikwkqgegeeltatvyvrkls 38 
                                         keik  + ++ +++ +v++  l+
  gene1021|gene1021|rna1021|rna1021 299 TKEIKEIE-NTVTAHNDVFINDLT 321
                                        45555444.667888888887665 PP

>> AAA-ATPase_like  Predicted AAA-ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.9   8.4e-05      0.38      95     159 ..     143     209 ..     108     220 .. 0.82
   2 ?    4.0   0.2    0.0062        28     148     183 ..     229     264 ..     227     270 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 8.4e-05
                    AAA-ATPase_like  95 eeeleeslkeklkelekefgkkke..ekslakrlkelieraaektgkkvvvLiDEYDkpilealeee 159
                                        +  l++s+++ l+e+++++ k  +  +++ +++++ ++++++++++++v +++D+  + i  + +++
  gene1021|gene1021|rna1021|rna1021 143 NIGLQNSIERVLEETAEQMIKIAAevAQQENEQITLILKNCSKQHSEQVKIIVDDAGTQIFVVAQNY 209
                                        4568888999999888888887775677888899999*****************9777776666665 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.0062
                    AAA-ATPase_like 148 YDkpilealeeeelaeelreflrefykvlkkadeyl 183
                                        YD  +++++e+  +++e +e+ r+fy++  k ++++
  gene1021|gene1021|rna1021|rna1021 229 YDLITNKIFENAVTYREHKEIHRTFYEQKDKINDAM 264
                                        999***********************9987766555 PP

>> LacI  Bacterial regulatory proteins, lacI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.1       1.1   4.8e+03      34      46 .]      52      64 ..      50      64 .. 0.82
   2 ?    7.8   0.1   0.00063       2.8      20      41 ..     121     142 ..     118     143 .. 0.88
   3 ?    3.4   0.2     0.015        67      20      42 ..     146     169 ..     145     173 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.1
                                       HHHHHHHTTB-TT CS
                               LacI 34 VeaameelnYiPn 46
                                       V++ ++ lnY +n
  gene1021|gene1021|rna1021|rna1021 52 VNKQIKALNYETN 64
                                       6677899***988 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.00063
                                        CTTSSSSTHHHHHHHHHHHHHT CS
                               LacI  20 LnnkerVseetrerVeaameel 41 
                                        +n+++ + + tr+rV+ a+e  
  gene1021|gene1021|rna1021|rna1021 121 MNDRGDITTHTRKRVNHAVENA 142
                                        7888***************975 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.015
                                        CTTS.SSSTHHHHHHHHHHHHHTT CS
                               LacI  20 Lnnk.erVseetrerVeaameeln 42 
                                        L+n+ erV eet+e   ++++e+ 
  gene1021|gene1021|rna1021|rna1021 146 LQNSiERVLEETAEQMIKIAAEVA 169
                                        567779**************9975 PP

>> FAS_meander  Fatty acid synthase meander beta sheet domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   1.9   7.7e-05      0.35      38     100 ..     146     210 ..     135     218 .. 0.78
   2 ?   -3.5   0.0       1.8     8e+03      84     101 ..     241     258 ..     235     264 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 7.7e-05
                        FAS_meander  38 veNPlrrllaprkgqlveieea.dspektvvtvkeakesgelkkaveiklsed.keIsvtlieer 100
                                         +N + r+l+ +++q+++i+ +  ++e++++t+  ++ s+++++ v+i +++  ++I v   +++
  gene1021|gene1021|rna1021|rna1021 146 LQNSIERVLEETAEQMIKIAAEvAQQENEQITLILKNCSKQHSEQVKIIVDDAgTQIFVVAQNYS 210
                                        68*****************9986677778888887778999999999987765267877666555 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 1.8
                        FAS_meander  84 iklsedkeIsvtlieert 101
                                        ++++e+keI  t++e+++
  gene1021|gene1021|rna1021|rna1021 241 VTYREHKEIHRTFYEQKD 258
                                        566777788888888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (364 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1590  (0.0886831); expected 358.6 (0.02)
Passed bias filter:                      501  (0.0279436); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.44
# Mc/sec: 2475.93
//
Query:       gene1022|gene1022|rna1022|rna1022  [L=474]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.1e-32  113.4   0.3    2.4e-32  112.3   0.3    1.5  1  tRNA-synt_2b  tRNA synthetase class II core domain (G, H, P, 
    3.4e-08   33.7  22.1    1.2e-05   25.5  10.4    2.7  3  Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain
     0.0061   16.2   0.0      0.012   15.2   0.0    1.5  1  NOD           NOTCH protein
  ------ inclusion threshold ------
       0.35   11.3   2.6        1.6    9.1   0.3    2.5  2  Ret2_MD       RNA editing 3' terminal uridylyl transferase 2 


Domain annotation for each model (and alignments):
>> tRNA-synt_2b  tRNA synthetase class II core domain (G, H, P, S and T)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.3   0.3   5.3e-36   2.4e-32       9     179 .]     273     450 ..     265     450 .. 0.95

  Alignments for each domain:
  == domain 1  score: 112.3 bits;  conditional E-value: 5.3e-36
                                        EEEEE-SSSHHHHHHHHHHHEEEBGGSSEEEEEEEEEEBTTTS....TBCTTTB-SEEEEEEEEEEESGGGHHHHH CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2b   9 reyiLkPtneetfvelirdevlrskrLPlklyqiqtkyRdEks....dsrGLlRvreFhqkdgyvfhaeaslddsl 80 
                                        +e +L++t+e+++++l+ +e + +++LP k+   + ++R+E+     d +G++Rv++F++ +++v++a+++++++ 
  gene1022|gene1022|rna1022|rna1022 273 DEQYLIATSEQPLTALYMNERILPEQLPKKFCGQSLCFRREAGaagkDNKGIFRVHQFEKIEQFVICAPEKSEEMH 348
                                        7899**************************************77899999************************** PP

                                        HHHHHHHHHHHHHTT.SCEEEEEEGTTSCBTTSEEEEEEEEETTTSEEEEEEEEEEEETHHHHHTTE..EEECTTS CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxx RF
                       tRNA-synt_2b  81 rdlikaisriferlglefraiielmsaksadykdkkefeavsesltkgieigtiqklgtrlserlga..tvldenn 154
                                        + ++ + ++++++l l +r++  + ++++ ++  k+++ea+++ +++++e+++++++ +++++ l++   + +en+
  gene1022|gene1022|rna1022|rna1022 349 KAMLAVSEQFYQSLRLDYRVVSIVSGEMNDSACLKYDLEAYFPHSKRYRELVSCSNCTDYQARDLEVryGITKEND 424
                                        *******************999998888899***********************************9444589999 PP

                                        SEEEEEEEEEE.EEHHHHHHHHHHHH CS
                                        xxxxxxxxxxx.xxxxxxxxxxxxxx RF
                       tRNA-synt_2b 155 reksvimicaa.igveRllsaileqn 179
                                        r+   +m++ + ++v+R+l++++e++
  gene1022|gene1022|rna1022|rna1022 425 RKVYCHMLNGTlCAVQRTLCCLVENY 450
                                        9**********999**********96 PP

>> Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5  10.4   2.7e-09   1.2e-05       1      94 [.       1      95 [.       1     103 [. 0.86
   2 !   13.8   4.5   1.1e-05      0.05      35     107 ..      86     160 ..      83     161 .. 0.75
   3 ?   -4.0   0.1       3.8   1.7e+04      85      97 ..     257     269 ..     252     275 .. 0.53

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 2.7e-09
                                       ---HHHHHH..-HHHHHHHHCCCTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCC CS
                       Seryl_tRNA_N  1 MLDiklire..npeavkeklkkRgedkadvdelleldekrrelqveleelqaerNelskeIgkakkkkedaeeliaev 76
                                       M+Dikl+r+     +v e+ k+R++d+++v + +eld+ + +++ e e++ +e N++  e++k++k++ d   +  ++
  gene1022|gene1022|rna1022|rna1022  1 MIDIKLLRDekTRREVYESEKNRFKDPEEVMKAYELDQLKIKMMYEKEKIAKEMNRACDEMKKMMKEG-DDGNVEGKG 77
                                       9********88899*****************************************************9.555666666 PP

                                       HHHHHHHHHHHHHHHHHH CS
                       Seryl_tRNA_N 77 kelkeelkaleaelkele 94
                                         +++e ++ e++ + +e
  gene1022|gene1022|rna1022|rna1022 78 GCNGDECADEEDRNARIE 95
                                       666666666666666665 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 1.1e-05
                                        HHHHHHHHHHHHHHHH...HHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCTS--- CS
                       Seryl_tRNA_N  35 dekrrelqveleelqa...erNelskeIgkakkkkedaeeliaevkelkeelkaleaelkeleaeleklllaiPNi 107
                                        de+ r++++e+e++++     +   ++ g +k k++   +l+++++ lk++ ++le ++k+ ++el+ +l +i+N+
  gene1022|gene1022|rna1022|rna1022  86 DEEDRNARIEVEKIKNmsiTEKDDEQNTGGKK-KGNCGVALREKIAGLKARRAELEIKVKQTDEELKRVLKNIGNV 160
                                        77777788888877762221223333333333.3457899***********************************7 PP

  == domain 3  score: -4.0 bits;  conditional E-value: 3.8
                                        HHHHHHHHHHHHH CS
                       Seryl_tRNA_N  85 aleaelkeleael 97 
                                        a++a+l+e +++l
  gene1022|gene1022|rna1022|rna1022 257 AKTAQLSEFDEQL 269
                                        4455555555554 PP

>> NOD  NOTCH protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   2.8e-06     0.012      15      55 ..     141     181 ..     139     182 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.8e-06
                                NOD  15 idpeellnnskeFLrelsalLrtnvrikkdekGepmvypwk 55 
                                        i++++  ++ k+ L++++++L+  v + kde+ +p + +++
  gene1022|gene1022|rna1022|rna1022 141 IKVKQTDEELKRVLKNIGNVLHKDVFVSKDEEHNPVITRYE 181
                                        667777889999**************************997 PP

>> Ret2_MD  RNA editing 3' terminal uridylyl transferase 2 middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.3   0.00037       1.6       2      27 ..      85     110 ..      84     117 .. 0.91
   2 ?    1.3   0.1       0.1   4.5e+02       8      43 ..     133     167 ..     128     174 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00037
                            Ret2_MD   2 seeedrkartalldvrnkkitekele 27 
                                        ++eedr ar  + +++n  itek+ e
  gene1022|gene1022|rna1022|rna1022  85 ADEEDRNARIEVEKIKNMSITEKDDE 110
                                        58********************9955 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.1
                            Ret2_MD   8 kartalldvrnkkitekeleyiaeklgrenvegiyv 43 
                                        kar a l+++ k+  ++el+ +++ +g+   ++++v
  gene1022|gene1022|rna1022|rna1022 133 KARRAELEIKVKQT-DEELKRVLKNIGNVLHKDVFV 167
                                        799999****9985.669999999999766666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (474 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1329  (0.0741257); expected 358.6 (0.02)
Passed bias filter:                      574  (0.0320152); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.44
# Mc/sec: 3248.40
//
Query:       gene1023|gene1023|rna1023|rna1023  [L=96]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       458  (0.0255452); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.27s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 733.47
//
Query:       gene1024|gene1024|rna1024|rna1024  [L=457]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      0.002   18.0   0.1     0.0037   17.1   0.1    1.4  1  Trp_oprn_chp   Tryptophan-associated transmembrane protein (T
  ------ inclusion threshold ------
       0.01   16.2   4.0        0.3   11.5   0.0    3.7  5  FRB_dom        FKBP12-rapamycin binding domain
      0.031   14.7   0.3      0.076   13.5   0.3    1.7  1  MGC-24         Multi-glycosylated core protein 24 (MGC-24), s
      0.063   13.9   0.1       0.77   10.4   0.0    2.6  4  Hemerythrin    Hemerythrin HHE cation binding domain
        0.1   12.8   0.6          2    8.7   0.1    2.9  2  Pox_EPC_I2-L1  Poxvirus entry protein complex L1 and I2
       0.83    9.7  11.5      0.073   13.1   2.4    2.8  3  DUF1664        Protein of unknown function (DUF1664)
        3.7    6.8   9.8        2.1    7.6   2.1    2.7  2  CorA           CorA-like Mg2+ transporter protein


Domain annotation for each model (and alignments):
>> Trp_oprn_chp  Tryptophan-associated transmembrane protein (Trp_oprn_chp)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.1   1.5e-06    0.0037      92     138 ..     401     452 ..     388     454 .. 0.61

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.5e-06
                       Trp_oprn_chp  92 padaaraaaaaatgvasaaaavelta......wpvlalaggvllllagvllll 138
                                        +++a + ++++++++++++ + +  +      w+++ ++g+v+l++ gvl+++
  gene1024|gene1024|rna1024|rna1024 401 AKKASTDKDTTTDTATTGTDEKTS-TpwyknkWVWIFVIGAVVLAAVGVLAAI 452
                                        222233333222222222222222.2467778******************985 PP

>> FRB_dom  FKBP12-rapamycin binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       1.7   4.3e+03      22      46 ..      51      75 ..      42      93 .. 0.67
   2 ?    0.7   0.1      0.27   6.9e+02      28      72 ..     101     144 ..      94     158 .. 0.62
   3 ?   11.5   0.0   0.00012       0.3      30      96 ..     189     266 ..     165     271 .. 0.74
   4 ?    0.3   0.1      0.36   9.2e+02      14      47 ..     237     270 ..     234     308 .. 0.67
   5 ?    2.0   0.2      0.11   2.8e+02       4      53 ..     296     345 ..     295     351 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.7
                            FRB_dom 22 rlyfgeknveamlklleplhellek 46
                                       + ++g++nv  ml+ l p    ++ 
  gene1024|gene1024|rna1024|rna1024 51 EVTQGNNNVLYMLASLLPVTTSTDL 75
                                       4567888999999999888766554 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.27
                            FRB_dom  28 knveamlklleplhellekgpetlreasFaqafgreLkeaeewlk 72 
                                           ++m  lle+  ++++ g +  + ++F+++ ++ ++e ++++k
  gene1024|gene1024|rna1024|rna1024 101 STETKMKTLLEKAVDQFKDG-KPSDKSEFTEMTKQVMSEFHNMVK 144
                                        55577888888888888873.344555555555555555444444 PP

  == domain 3  score: 11.5 bits;  conditional E-value: 0.00012
                            FRB_dom  30 veamlklleplhellekgpetlreasFaqafgreLkeaeewlkky...........kkteneedlnqawdiyyevf 94 
                                        +++ +++l +l e+l k p+  + ++F+ +f++ +  ++++++ +            ++ + +++++    +  +f
  gene1024|gene1024|rna1024|rna1024 189 FDDACETLIDLLEELAKDPNNKNSTKFVVTFKELIDAVKRHIRLFygfhdilsttsDENTHVDNVQKKITKLEAMF 264
                                        5678999************************************998888888655433333333444444555555 PP

                            FRB_dom  95 rr 96 
                                        + 
  gene1024|gene1024|rna1024|rna1024 265 NA 266
                                        54 PP

  == domain 4  score: 0.3 bits;  conditional E-value: 0.36
                            FRB_dom  14 hegLeeAsrlyfgeknveamlklleplhellekg 47 
                                        h+ L   s +  +  nv++ +  le +++ ++k+
  gene1024|gene1024|rna1024|rna1024 237 HDILSTTSDENTHVDNVQKKITKLEAMFNAISKK 270
                                        5667777777777778888888888777777774 PP

  == domain 5  score: 2.0 bits;  conditional E-value: 0.11
                            FRB_dom   4 RvAilwhElwhegLeeAsrlyfgeknveamlklleplhellekgpetlre 53 
                                        R++i++ E+   +  +   l   e   ++ml+ ++  +++++k+++t++e
  gene1024|gene1024|rna1024|rna1024 296 RMSIMIIEQNRAMFVNRYVLRSVEFAESGMLEDIKTHQDEMKKKNTTIEE 345
                                        66777777777777777777777777789**************9999988 PP

>> MGC-24  Multi-glycosylated core protein 24 (MGC-24), sialomucin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.3     3e-05     0.076      53     128 ..     382     457 .]     348     457 .] 0.74

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3e-05
                             MGC-24  53 saaskstpkptnstaktttkpsstttstsvatsgttnttvtptsqparkstFDaAsFiGGivLv.LgvqAviFFly 127
                                        s+++++ + ++++t k++t   +++t + ++t ++t+ t   ts p  k+ +     iG +vL  +gv A i Fl 
  gene1024|gene1024|rna1024|rna1024 382 SSSPSK-SGQQQNTGKKSTDAKKASTDKDTTTDTATTGTDEKTSTPWYKNKWVWIFVIGAVVLAaVGVLAAILFLK 456
                                        222222.23344666666767777777777777778888888899999999999999*****95489*****9996 PP

                             MGC-24 128 k 128
                                        k
  gene1024|gene1024|rna1024|rna1024 457 K 457
                                        5 PP

>> Hemerythrin  Hemerythrin HHE cation binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.0         7   1.8e+04      80      97 ..      35      52 ..      19      64 .. 0.55
   2 ?   -0.1   0.0      0.53   1.4e+03      85     122 ..     108     145 ..      76     157 .. 0.74
   3 ?   10.4   0.0    0.0003      0.77      77     121 ..     187     231 ..     165     232 .. 0.82
   4 ?   -3.9   0.0         7   1.8e+04      31      51 ..     254     274 ..     241     275 .. 0.66

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 7
                                       HHHHHHHHHHHHHHCHTC CS
                        Hemerythrin 80 Hdeirelleelrellkgl 97
                                        d++r  le+l e ++++
  gene1024|gene1024|rna1024|rna1024 35 EDVLRGGLEGLYERVDEV 52
                                       344444444444333333 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.53
                                        HHHHHHHHHCHTCGGSTCHHHHHHHHHHHHHHHHHHHH CS
                        Hemerythrin  85 elleelrellkgleepsaaafaelleeladllreHiak 122
                                         lle++    k+ +++++++f+e+ + +++++++++++
  gene1024|gene1024|rna1024|rna1024 108 TLLEKAVDQFKDGKPSDKSEFTEMTKQVMSEFHNMVKE 145
                                        34444443444444677888888888888888877765 PP

  == domain 3  score: 10.4 bits;  conditional E-value: 0.0003
                                        HHHHHHHHHHHHHHHHHCHTCGGSTCHHHHHHHHHHHHHHHHHHH CS
                        Hemerythrin  77 ereHdeirelleelrellkgleepsaaafaelleeladllreHia 121
                                        e+  d+ + l++ l+el+k++++ ++  f   ++el+d++++Hi+
  gene1024|gene1024|rna1024|rna1024 187 EGFDDACETLIDLLEELAKDPNNKNSTKFVVTFKELIDAVKRHIR 231
                                        4556778888888999999999999999999************97 PP

  == domain 4  score: -3.9 bits;  conditional E-value: 7
                                        CCCHCCHHHHHHHHHHHHHHH CS
                        Hemerythrin  31 hgalrklaelldelvdeleaH 51 
                                        +  ++kl+++++++ + ++ H
  gene1024|gene1024|rna1024|rna1024 254 QKKITKLEAMFNAISKKILNH 274
                                        222788888888888877777 PP

>> Pox_EPC_I2-L1  Poxvirus entry protein complex L1 and I2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.23   5.8e+02      18      38 ..     123     143 ..     116     153 .. 0.76
   2 ?    8.7   0.1    0.0008         2      32      70 ..     419     456 ..     412     457 .] 0.83

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.23
                      Pox_EPC_I2-L1  18 dDfnnFievVksVLtdekask 38 
                                         D  +F e+ k V+++ +++ 
  gene1024|gene1024|rna1024|rna1024 123 SDKSEFTEMTKQVMSEFHNMV 143
                                        57789*********9976544 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0008
                      Pox_EPC_I2-L1  32 tdekaskktassgtklwltlliiliavlilvlllflylK 70 
                                        tdek+s+   ++ +++w+ ++  ++ +++ vl   l+lK
  gene1024|gene1024|rna1024|rna1024 419 TDEKTSTPWYKN-KWVWIFVIGAVVLAAVGVLAAILFLK 456
                                        677777666655.99999899999999*****9999999 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.2      0.06   1.5e+02      59     120 ..     105     167 ..      69     170 .. 0.72
   2 ?   13.1   2.4   2.8e-05     0.073      32     123 ..     215     305 ..     210     306 .. 0.85
   3 ?   -3.4   0.1       3.7   9.4e+03      95     110 ..     328     343 ..     322     356 .. 0.50

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.06
                            DUF1664  59 atkrhLssridrv.dkkldeqkeiskeikeevtevredlseigedvesvkeavegleskleri 120
                                        + k  L++ +d+  d k  + +e ++ +k+ ++e ++ ++ei ++ +s + a   l+ + eri
  gene1024|gene1024|rna1024|rna1024 105 KMKTLLEKAVDQFkDGKPSDKSEFTEMTKQVMSEFHNMVKEIVNKYRSPQGAAAPLQVSTERI 167
                                        556777888888735677888888888888889999999999888888777777666666665 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 2.8e-05
                            DUF1664  32 mfvTkrslsdavesvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvk 107
                                        + vT + l dav++  +    + + l++t ++ + ++d+v+kk+ + +++ ++i++++ + + + +++    +++ 
  gene1024|gene1024|rna1024|rna1024 215 FVVTFKELIDAVKRHIRLFYGFHDILSTTSDE-NTHVDNVQKKITKLEAMFNAISKKILNHQLEKKNFIATAKAIV 289
                                        56777778777777666666666666666665.779**************************************** PP

                            DUF1664 108 eaveglesklerieek 123
                                        + v++l +++  ie++
  gene1024|gene1024|rna1024|rna1024 290 QFVNDLRMSIMIIEQN 305
                                        *************987 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 3.7
                            DUF1664  95 dlseigedvesvkeav 110
                                        d+++ ++++++ ++++
  gene1024|gene1024|rna1024|rna1024 328 DIKTHQDEMKKKNTTI 343
                                        3333333333333333 PP

>> CorA  CorA-like Mg2+ transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   2.1   0.00084       2.1     116     235 ..     182     309 ..     164     310 .. 0.77
   2 ?    2.8   1.0     0.023        59     261     289 ..     425     451 ..     423     457 .] 0.62

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.00084
                               CorA 116 ldeivdrlfellekleeeldeledeledstkkeilrelaqlrrrlvklrralapnrevlkrlla.kaddklldded 190
                                         d iv+ ++++ e+l + l+el +  +++++ +++ +  +l   + +  r +    ++l++  + +  +    +++
  gene1024|gene1024|rna1024|rna1024 182 ADGIVEGFDDACETLIDLLEELAKDPNNKNSTKFVVTFKELIDAVKRHIRLFYGFHDILSTTSDeN-THVDNVQKK 256
                                        68899*********************9999999999999999999999999999999995555532.333333333 PP

                               CorA 191 keylrdlldeler........llemlealrerleslqdtyssllserlNrvmk 235
                                           l+ + + +++          + + + +  ++ ++d+ +s++  ++Nr m 
  gene1024|gene1024|rna1024|rna1024 257 ITKLEAMFNAISKkilnhqleKKNFIATAKAIVQFVNDLRMSIMIIEQNRAMF 309
                                        34477777777777766776677778888899999999999999999999985 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.023
                               CorA 261 lPelewsygypfvlllglmallailllfw 289
                                         P+ ++++++ fv  +g+++l+a+++l+ 
  gene1024|gene1024|rna1024|rna1024 425 TPWYKNKWVWIFV--IGAVVLAAVGVLAA 451
                                        599999**66777..55555555555433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (457 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2463  (0.137375); expected 358.6 (0.02)
Passed bias filter:                      762  (0.042501); expected 358.6 (0.02)
Passed Vit filter:                       104  (0.00580066); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.72u 0.32s 00:00:01.04 Elapsed: 00:00:00.47
# Mc/sec: 2936.77
//
Query:       gene1025|gene1025|rna1025|rna1025  [L=53]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (53 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       354  (0.0197445); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 392.32
//
Query:       gene1026|gene1026|rna1026|rna1026  [L=55]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.9e-12   47.1   0.0      2e-12   47.0   0.0    1.0  1  RT_RNaseH_2  RNase H-like domain found in reverse transcripta
    5.5e-07   29.8   0.0    6.3e-07   29.6   0.0    1.1  1  RT_RNaseH    RNase H-like domain found in reverse transcripta


Domain annotation for each model (and alignments):
>> RT_RNaseH_2  RNase H-like domain found in reverse transcriptase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.0   0.0   2.2e-16     2e-12       6      58 ..       2      54 ..       1      55 [] 0.93

  Alignments for each domain:
  == domain 1  score: 47.0 bits;  conditional E-value: 2.2e-16
                        RT_RNaseH_2  6 ekafeklkealtsapvLahpdpdkpfiletDaSdtgigavLsqedddgkerpi 58
                                       ++af + +  l++a+ L++p+++k+f+l+tDaS+tg+gavL qe+++gk+ p+
  gene1026|gene1026|rna1026|rna1026  2 NEAFAEPNLGLINAQNLKLPEFEKKFTLKTDASNTGLGAVLVQENKNGKLIPV 54
                                       5789999999************************************9997776 PP

>> RT_RNaseH  RNase H-like domain found in reverse transcriptase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6   0.0   7.1e-11   6.3e-07       2      33 ..      23      54 ..      22      55 .] 0.92

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 7.1e-11
                                       TTS-EEEEEEECTEEEEEEEEEETTE..EEEE CS
                          RT_RNaseH  2 pskpfiletDAsddgigavLsqreedgeerpi 33
                                       ++k+f+l+tDAs++g+gavL+q++++g+  p+
  gene1026|gene1026|rna1026|rna1026 23 FEKKFTLKTDASNTGLGAVLVQENKNGKLIPV 54
                                       89********************9999998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (55 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       240  (0.0133861); expected 358.6 (0.02)
Passed bias filter:                      207  (0.0115455); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.34u 0.28s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 402.62
//
Query:       gene1027|gene1027|rna1027|rna1027  [L=97]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.9e-13   50.6   0.1    2.7e-13   50.1   0.1    1.2  1  RT_RNaseH    RNase H-like domain found in reverse transcripta
     0.0099   15.9   0.0      0.017   15.2   0.0    1.4  1  RT_RNaseH_2  RNase H-like domain found in reverse transcripta


Domain annotation for each model (and alignments):
>> RT_RNaseH  RNase H-like domain found in reverse transcriptase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.1   0.1     3e-17   2.7e-13      47     105 .]       3      62 ..       2      62 .. 0.94

  Alignments for each domain:
  == domain 1  score: 50.1 bits;  conditional E-value: 3e-17
                                        S-HHHHHHHHHHHHHHHHHHHHTS--EEEE-SS--TTTTT----..---HHHHHHHC-XX CS
                          RT_RNaseH  47 ystiekellAivaalkkfrhylqgrkftvitDhknlkyllskks.lngrlarWaleLsey 105
                                        y + eke+lA+ + ++kf + l+ r f +itDhk+l+ + +k +  n+rl+rW++ +++y
  gene1027|gene1027|rna1027|rna1027   3 YGISEKEMLAVKWGIDKFSQELKARMFYLITDHKALEVIRNKPEfDNNRLNRWCEAIQQY 62 
                                        8899************************************7777478***********99 PP

>> RT_RNaseH_2  RNase H-like domain found in reverse transcriptase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   1.9e-06     0.017      72      98 ..       3      29 ..       1      31 [. 0.89

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.9e-06
                        RT_RNaseH_2 72 ysttekellAivwalkkfrhyllgrkf 98
                                       y + eke+lA+ w+++kf++ l  r f
  gene1027|gene1027|rna1027|rna1027  3 YGISEKEMLAVKWGIDKFSQELKARMF 29
                                       7889****************9998877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (97 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       542  (0.0302304); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.31s 00:00:00.71 Elapsed: 00:00:00.46
# Mc/sec: 638.43
//
Query:       gene1028|gene1028|rna1028|rna1028  [L=934]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-10   40.6   0.0     0.0016   18.8   0.0    3.0  3  HEAT_2    HEAT repeats
    6.9e-08   32.1   1.9      0.019   15.2   0.1    4.6  4  HEAT      HEAT repeat
    9.5e-06   26.0   0.8     0.0097   16.4   0.1    2.8  2  HEAT_EZ   HEAT-like repeat
     0.0017   18.4   1.9        1.6    8.8   0.1    2.9  2  Cnd1      non-SMC mitotic condensation complex subunit 1
  ------ inclusion threshold ------
       0.83   10.2   0.0       0.83   10.2   0.0    6.9  8  PC_rep    Proteasome/cyclosome repeat


Domain annotation for each model (and alignments):
>> HEAT_2  HEAT repeats
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.3   0.0         5   1.8e+04      19      29 ..     443     453 ..     440     465 .. 0.65
   2 !   18.2   0.0     7e-07    0.0025       8      59 ..     613     668 ..     606     679 .. 0.80
   3 !   18.8   0.0   4.4e-07    0.0016      12      56 ..     684     732 ..     675     740 .. 0.87

  Alignments for each domain:
  == domain 1  score: -4.3 bits;  conditional E-value: 5
                             HEAT_2  19 aairaLgrign 29 
                                        aa++aLg  g 
  gene1028|gene1028|rna1028|rna1028 443 AALHALGLAGK 453
                                        56666665544 PP

  == domain 2  score: 18.2 bits;  conditional E-value: 7e-07
                             HEAT_2   8 lendpdpevrraairaLg....rignpealpaLvellededpavRraaaeaLgaig 59 
                                        l++  + ++r a   +Lg    + gn  +++ L+++++d +++vRraa+ +Lg + 
  gene1028|gene1028|rna1028|rna1028 613 LTKNQNAYLRLAGTLCLGtffvKTGNVAVIDSLLNMVKDNSEDVRRAAILSLGLVV 668
                                        55677888899999999987777788899999999999999999999999999763 PP

  == domain 3  score: 18.8 bits;  conditional E-value: 4.4e-07
                             HEAT_2  12 pdpevrraairaLg....rignpealpaLvellededpavRraaaeaLg 56 
                                         +p vr+a++ ++g      g+ ea++ L  ll d++p v ++a+  Lg
  gene1028|gene1028|rna1028|rna1028 684 HCPFVRAAVALTIGlflcASGDSEAVDVLETLLYDSNPLVVQNACIGLG 732
                                        5788**********887777899**********************9998 PP

>> HEAT  HEAT repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.53   1.9e+03       7      27 ..     612     632 ..     606     633 .. 0.80
   2 !   15.2   0.1   5.2e-06     0.019       2      27 ..     642     667 ..     641     670 .. 0.90
   3 ?    4.6   0.0     0.014        49      12      26 ..     684     698 ..     676     700 .. 0.87
   4 !    7.7   0.1    0.0013       4.8       3      28 ..     710     735 ..     708     738 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.53
                                        HHHT-SSHHHHHHHHHHHHHH CS
                               HEAT   7 kllsDpspeVReaAakaLgal 27 
                                         l + +++  R a  ++Lg++
  gene1028|gene1028|rna1028|rna1028 612 CLTKNQNAYLRLAGTLCLGTF 632
                                        5557889999*********87 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 5.2e-06
                                        HHHHHHHHT-SSHHHHHHHHHHHHHH CS
                               HEAT   2 lPlllkllsDpspeVReaAakaLgal 27 
                                        ++ ll++ +D+s +VR+aA+++Lg +
  gene1028|gene1028|rna1028|rna1028 642 IDSLLNMVKDNSEDVRRAAILSLGLV 667
                                        7889*******************965 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.014
                                        SSHHHHHHHHHHHHH CS
                               HEAT  12 pspeVReaAakaLga 26 
                                         +p+VR+a+a+++g 
  gene1028|gene1028|rna1028|rna1028 684 HCPFVRAAVALTIGL 698
                                        689**********96 PP

  == domain 4  score: 7.7 bits;  conditional E-value: 0.0013
                                        HHHHHHHT-SSHHHHHHHHHHHHHHH CS
                               HEAT   3 PlllkllsDpspeVReaAakaLgala 28 
                                        ++l +ll D++p V ++A+  Lg l+
  gene1028|gene1028|rna1028|rna1028 710 DVLETLLYDSNPLVVQNACIGLGLLL 735
                                        678999****************9875 PP

>> HEAT_EZ  HEAT-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   0.1    0.0018       6.4      28      53 ..     640     665 ..     621     667 .. 0.92
   2 !   16.4   0.1   2.7e-06    0.0097       1      54 [.     686     733 ..     686     734 .. 0.95

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0018
                            HEAT_EZ  28 eilpaLlalLnddsdeVRaaAagaLg 53 
                                        ++++ Ll++ +d s +VR aA+  Lg
  gene1028|gene1028|rna1028|rna1028 640 AVIDSLLNMVKDNSEDVRRAAILSLG 665
                                        58999****************99998 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 2.7e-06
                            HEAT_EZ   1 wrvRraAawaLGrlaggepellqplvpeilpaLlalLnddsdeVRaaAagaLgn 54 
                                        ++vR+a+a+++G  ++ ++  ++    e+++ L  lL d++++V ++A++ Lg 
  gene1028|gene1028|rna1028|rna1028 686 PFVRAAVALTIG--LFLCASGDS----EAVDVLETLLYDSNPLVVQNACIGLGL 733
                                        689*********..999******....***********************9996 PP

>> Cnd1  non-SMC mitotic condensation complex subunit 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.3   0.00078       2.8       8     101 ..     591     682 ..     584     687 .. 0.71
   2 !    8.8   0.1   0.00043       1.6      58     104 ..     707     752 ..     685     766 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00078
                               Cnd1   8 rtlg.cirvpnlveylvepLrkrLkDedpyVRktaaivvakL.ilndmvkekgflselaklleDenprVvanalaa 81 
                                        r l    r ++ +e+lv  +    k +++y R    +++    ++ + v    +++ l+++++D+++ V+  a+++
  gene1028|gene1028|rna1028|rna1028 591 RMLRtEYRENTALENLVGYVLCLTKNQNAYLRLAGTLCLGTFfVKTGNVA---VIDSLLNMVKDNSEDVRRAAILS 663
                                        55555566777777777777778888888888888888887744444443...7899999**********999999 PP

                               Cnd1  82 lteiseksenaiynllpdii 101
                                        l  + + + n++  l+ +++
  gene1028|gene1028|rna1028|rna1028 664 LGLVVRDE-NIVSILNFKVL 682
                                        98777665.66655555555 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00043
                               Cnd1  58 gflselaklleDenprVvanalaalteiseksenaiynllpdiiskl 104
                                        + ++ l++ll D+np Vv+na + l  ++ +  n  +++++ i++k+
  gene1028|gene1028|rna1028|rna1028 707 EAVDVLETLLYDSNPLVVQNACIGLGLLLMQC-NSCVSNFKRIVNKV 752
                                        568889999************99999888887.78888888888876 PP

>> PC_rep  Proteasome/cyclosome repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       2.7   9.6e+03      10      26 ..      58      73 ..      57      74 .. 0.76
   2 ?   -1.7   0.0       1.4     5e+03      14      28 ..     409     425 ..     406     428 .. 0.78
   3 ?   -2.4   0.0       2.3   8.3e+03       3      28 ..     505     530 ..     505     534 .. 0.80
   4 ?    4.9   0.0     0.011        40      13      34 ..     636     657 ..     633     658 .. 0.92
   5 ?   -0.1   0.8      0.44   1.6e+03       1       9 [.     659     667 ..     659     667 .. 0.91
   6 ?   10.2   0.0   0.00023      0.83       6      34 ..     696     724 ..     693     725 .. 0.87
   7 ?    1.2   0.5      0.17     6e+02       1      11 [.     726     736 ..     726     742 .. 0.81
   8 ?   -1.3   0.2         1   3.6e+03       7      19 ..     773     784 ..     773     786 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 2.7
                                       CTTSTCHHHHHHHHHHH CS
                             PC_rep 10 haGsgneeaislLkpyl 26
                                        a+s++  +is+L++ +
  gene1028|gene1028|rna1028|rna1028 58 AANSDTT-GISILLSKI 73
                                       6887777.9**999765 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.4
                                        TCH..HHHHHHHHHHHH CS
                             PC_rep  14 gne..eaislLkpylsd 28 
                                        g++   +i++L+++l++
  gene1028|gene1028|rna1028|rna1028 409 GRDrlKLIEILQDLLPS 425
                                        55556899*****9997 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 2.3
                                        HHHHHHHCTTSTCHHHHHHHHHHHHH CS
                             PC_rep   3 llALGlihaGsgneeaislLkpylsd 28 
                                        ++A+G i+a s +  ++  L++++  
  gene1028|gene1028|rna1028|rna1028 505 AYAIGQINAKSMDLKLLTELESIIRF 530
                                        68999999999999999999888765 PP

  == domain 4  score: 4.9 bits;  conditional E-value: 0.011
                                        STCHHHHHHHHHHHHHHSSHHH CS
                             PC_rep  13 sgneeaislLkpylsdtsaevr 34 
                                        +gn ++i+ L+++++d+s +vr
  gene1028|gene1028|rna1028|rna1028 636 TGNVAVIDSLLNMVKDNSEDVR 657
                                        8999**************9997 PP

  == domain 5  score: -0.1 bits;  conditional E-value: 0.44
                                        HHHHHHHHH CS
                             PC_rep   1 GAllALGli 9  
                                        +A+l+LGl+
  gene1028|gene1028|rna1028|rna1028 659 AAILSLGLV 667
                                        7******97 PP

  == domain 6  score: 10.2 bits;  conditional E-value: 0.00023
                                        HHHHCTTSTCHHHHHHHHHHHHHHSSHHH CS
                             PC_rep   6 LGlihaGsgneeaislLkpylsdtsaevr 34 
                                        +Gl  + sg++ea ++L+++l+d++  v+
  gene1028|gene1028|rna1028|rna1028 696 IGLFLCASGDSEAVDVLETLLYDSNPLVV 724
                                        57777889****************98876 PP

  == domain 7  score: 1.2 bits;  conditional E-value: 0.17
                                        HHHHHHHHHCT CS
                             PC_rep   1 GAllALGliha 11 
                                        +A+++LGl+ +
  gene1028|gene1028|rna1028|rna1028 726 NACIGLGLLLM 736
                                        59******876 PP

  == domain 8  score: -1.3 bits;  conditional E-value: 1
                                        HHHCTTSTCHHHH CS
                             PC_rep   7 GlihaGsgneeai 19 
                                        Gli++G g++ ++
  gene1028|gene1028|rna1028|rna1028 773 GLINLG-GTNLIL 784
                                        9*****.988555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (934 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       704  (0.039266); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.75u 0.35s 00:00:01.10 Elapsed: 00:00:00.54
# Mc/sec: 5172.63
//
Query:       gene1029|gene1029|rna1029|rna1029  [L=252]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      2e-11   44.0   8.1      2e-11   44.0   8.1    2.3  2  zf-RING_2       Ring finger domain
    1.5e-07   31.2  15.8    1.5e-06   27.9   8.5    2.3  2  zf-C3HC4_3      Zinc finger, C3HC4 type (RING finger)
    3.1e-07   30.6   7.4    3.1e-07   30.6   7.4    2.0  2  zf-rbx1         RING-H2 zinc finger domain
    2.9e-06   26.9   6.8    2.9e-06   26.9   6.8    2.4  2  zf-RING_11      RING-like zinc finger
    3.1e-06   26.9   9.6    3.1e-06   26.9   9.6    2.3  2  zf-C3HC4_2      Zinc finger, C3HC4 type (RING finger)
    0.00014   21.8  10.2    0.00014   21.8  10.2    2.2  2  zf-RING_5       zinc-RING finger domain
    0.00023   21.0   9.6    0.00023   21.0   9.6    2.4  2  zf-C3HC4        Zinc finger, C3HC4 type (RING finger)
    0.00065   19.3   0.0     0.0012   18.4   0.0    1.5  1  DOT1            Histone methylation protein DOT1
     0.0029   17.6   5.0     0.0029   17.6   5.0    2.2  2  zf-ANAPC11      Anaphase-promoting complex subunit 11 RING-H2
     0.0038   17.2   2.1     0.0038   17.2   2.1    2.1  2  zf-RING_UBOX    RING-type zinc-finger
      0.004   17.0   8.0      0.004   17.0   8.0    2.5  2  Prok-RING_4     Prokaryotic RING finger family 4
     0.0087   15.7   7.8     0.0087   15.7   7.8    2.3  2  Zn_ribbon_17    Zinc-ribbon, C4HC2 type
     0.0095   16.1   5.7     0.0095   16.1   5.7    1.9  2  zf-HC5HC2H_2    PHD-zinc-finger like domain
  ------ inclusion threshold ------
      0.018   15.3   3.7      0.018   15.3   3.7    2.8  2  zinc_ribbon_9   zinc-ribbon
       0.12   12.0   8.0       0.13   11.9   0.3    2.2  2  TackOD1         Thaumarchaeal output domain 1
          1    9.0   9.7        6.3    6.5   1.7    3.5  3  RecR            RecR protein
        5.8    7.0  11.9         11    6.1   0.4    2.5  2  zinc-ribbons_6  zinc-ribbons
        6.4    6.9  12.4        0.9    9.6   0.5    2.8  3  DZR             Double zinc ribbon
        8.2    6.7  13.0        1.2    9.4   6.9    2.2  2  zf-RING_10      zinc RING finger of MSL2


Domain annotation for each model (and alignments):
>> zf-RING_2  Ring finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   3.0       0.2   1.9e+02      25      43 ..       8      26 ..       3      27 .. 0.76
   2 !   44.0   8.1   2.1e-14     2e-11       2      44 .]     205     247 ..     204     247 .. 0.97

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.2
                          zf-RING_2 25 fhreClerwlrssstCPlC 43
                                       +++ C +r + +++ C +C
  gene1029|gene1029|rna1029|rna1029  8 YCHACGSRTVPHNELCAFC 26
                                       7*******7766666**** PP

  == domain 2  score: 44.0 bits;  conditional E-value: 2.1e-14
                          zf-RING_2   2 eCpICleelssadsvlllpCgHvfhreClerwlrssstCPlCr 44 
                                        +C+ICl+ + ++++ + l C H+fh++C  +w++ ++tCP+Cr
  gene1029|gene1029|rna1029|rna1029 205 KCMICLSTYRKGECGIELSCAHFFHKSCGVKWMKMQNTCPICR 247
                                        7*************99999***********************9 PP

>> zf-C3HC4_3  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.7    0.0031       2.9      24      47 ..       7      30 ..       2      33 .. 0.87
   2 !   27.9   8.5   1.6e-09   1.5e-06       2      49 ..     203     252 .]     202     252 .] 0.85

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0031
                                       EE-HHHHHHHHHTT-B-TTT--B- CS
                         zf-C3HC4_3 24 vlCeeCaekllkrkkkCpiCrrpi 47
                                       ++C++C ++   +++ C +C ++ 
  gene1029|gene1029|rna1029|rna1029  7 YYCHACGSRTVPHNELCAFCDSEF 30
                                       68********99********9875 PP

  == domain 2  score: 27.9 bits;  conditional E-value: 1.6e-09
                                        GSB-TTTSSSBS-...EEETTEEEEEE-HHHHHHHHHTT-B-TTT--B--E CS
                         zf-C3HC4_3   2 deeCviClerprn...vvllpCgHlvlCeeCaekllkrkkkCpiCrrpiek 49 
                                        + +C+iCl++ r+    + l C H+ + ++C  k++k++++CpiCr +iek
  gene1029|gene1029|rna1029|rna1029 203 KGKCMICLSTYRKgecGIELSCAHF-FHKSCGVKWMKMQNTCPICRHEIEK 252
                                        679******866622256679****.***********************86 PP

>> zf-rbx1  RING-H2 zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.3       3.2   3.1e+03       2      10 ..      22      30 ..       9      38 .. 0.75
   2 !   30.6   7.4   3.3e-10   3.1e-07      11      55 .]     203     247 ..     196     247 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 3.2
                            zf-rbx1  2 tCaiCrnel 10
                                        Ca C +e+
  gene1029|gene1029|rna1029|rna1029 22 LCAFCDSEF 30
                                       577777666 PP

  == domain 2  score: 30.6 bits;  conditional E-value: 3.3e-10
                            zf-rbx1  11 eeacieckapgdee.cpvvlGeCgHaFHlhCiskWlktrkvCPlcr 55 
                                        +++c+ c ++ ++  c + l +C H FH+ C  kW+k +++CP+cr
  gene1029|gene1029|rna1029|rna1029 203 KGKCMICLSTYRKGeCGIEL-SCAHFFHKSCGVKWMKMQNTCPICR 247
                                        678999988877777*****.9***********************8 PP

>> zf-RING_11  RING-like zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.9   6.8     3e-09   2.9e-06       2      28 ..     206     232 ..     205     232 .. 0.99
   2 ?    0.3   0.2      0.63   5.9e+02       2      10 ..     243     251 ..     242     252 .] 0.83

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 3e-09
                         zf-RING_11   2 CsICLeefkpgqalfilpCsHtFHfkC 28 
                                        C+ICL+++ +g++ + l+C H FH  C
  gene1029|gene1029|rna1029|rna1029 206 CMICLSTYRKGECGIELSCAHFFHKSC 232
                                        **************************9 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.63
                         zf-RING_11   2 CsICLeefk 10 
                                        C IC  e++
  gene1029|gene1029|rna1029|rna1029 243 CPICRHEIE 251
                                        99**88886 PP

>> zf-C3HC4_2  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   2.0      0.13   1.2e+02      22      40 .]       8      26 ..       4      26 .. 0.92
   2 !   26.9   9.6   3.3e-09   3.1e-06       1      40 []     205     246 ..     205     246 .. 0.94

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.13
                         zf-C3HC4_2 22 fCqkCilrsLeekneCPlC 40
                                       +C  C  r+  +++ C  C
  gene1029|gene1029|rna1029|rna1029  8 YCHACGSRTVPHNELCAFC 26
                                       7********9*999**888 PP

  == domain 2  score: 26.9 bits;  conditional E-value: 3.3e-09
                         zf-C3HC4_2   1 kCpiCldmlkdpsvvt..pCgHvfCqkCilrsLeekneCPlC 40 
                                        kC iCl  + ++   +   C H f+++C  ++++ +n CP+C
  gene1029|gene1029|rna1029|rna1029 205 KCMICLSTYRKGECGIelSCAHFFHKSCGVKWMKMQNTCPIC 246
                                        7**********97766789*********************** PP

>> zf-RING_5  zinc-RING finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   1.6     0.038        36      23      43 ..       7      27 ..       3      28 .. 0.89
   2 !   21.8  10.2   1.5e-07   0.00014       1      44 []     205     248 ..     205     248 .. 0.96

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.038
                          zf-RING_5 23 ifCekClkkllekeavCpiCr 43
                                       ++C++C ++    +  C +C+
  gene1029|gene1029|rna1029|rna1029  7 YYCHACGSRTVPHNELCAFCD 27
                                       48*********9999*****7 PP

  == domain 2  score: 21.8 bits;  conditional E-value: 1.5e-07
                          zf-RING_5   1 hCnkCfeklskeekfyltsCgHifCekClkkllekeavCpiCrk 44 
                                        +C +C + ++k e  + +sC H+f+++C  k ++ +++CpiCr+
  gene1029|gene1029|rna1029|rna1029 205 KCMICLSTYRKGECGIELSCAHFFHKSCGVKWMKMQNTCPICRH 248
                                        6********************************9********95 PP

>> zf-C3HC4  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   3.1       2.2   2.1e+03      21      41 .]       8      26 ..       3      26 .. 0.69
   2 !   21.0   9.6   2.4e-07   0.00023       1      41 []     206     246 ..     206     246 .. 0.97

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 2.2
                                       B-CHHHHHHHHCTSSB--TTT CS
                           zf-C3HC4 21 fCskCirkilksrkkvkCPlC 41
                                       +C++C ++ +    ++ C  C
  gene1029|gene1029|rna1029|rna1029  8 YCHACGSRTVP--HNELCAFC 26
                                       78888888888..44447777 PP

  == domain 2  score: 21.0 bits;  conditional E-value: 2.4e-07
                                        -TTT-S--SS-E...E-TTS--B-CHHHHHHHHCTSSB--TTT CS
                           zf-C3HC4   1 CpiCleeakepn..elleCkHsfCskCirkilksrkkvkCPlC 41 
                                        C iCl+++ +      l C H f+++C +k++k  ++++CP+C
  gene1029|gene1029|rna1029|rna1029 206 CMICLSTYRKGEcgIELSCAHFFHKSCGVKWMK--MQNTCPIC 246
                                        9********999999******************..999***** PP

>> DOT1  Histone methylation protein DOT1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   1.3e-06    0.0012     128     166 ..     160     198 ..     145     214 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.3e-06
                                        E--TT--HHHHHHHHHHHTT--TT-EEEESS-SS-TT-- CS
                               DOT1 128 vNNfaFdaelnkqlkellqdlkegtkiislkslvpskyk 166
                                        +NN+aFd+el++ + e+++ +k  t  +s k + + + +
  gene1029|gene1029|rna1029|rna1029 160 INNYAFDHELEHIIDEIFMSTKVSTSPVSNKYIKALQVS 198
                                        8******************************99887765 PP

>> zf-ANAPC11  Anaphase-promoting complex subunit 11 RING-H2 finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.2       1.1   1.1e+03      16      30 ..      15      29 ..       5      36 .. 0.68
   2 !   17.6   5.0   3.1e-06    0.0029      31      81 ..     202     250 ..     192     252 .] 0.78

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 1.1
                                       B.-SSSSB-TTT-SB CS
                         zf-ANAPC11 16 wdvasddvcGicrvs 30
                                         v+++++c  c  +
  gene1029|gene1029|rna1029|rna1029 15 RTVPHNELCAFCDSE 29
                                       346777777777655 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 3.1e-06
                                        TTS--TTC..STTTTTS-EEEBTTS-EEEHHHHHHHHHHHSTSSB-TTTSSB- CS
                         zf-ANAPC11  31 fdGtcpsc..kfpGddcplvlGkckhnfhlhcilkwletetskglcpmcrqtf 81 
                                         +G c  c  ++   +c + l +c h fh+ c +kw++    ++ cp+cr ++
  gene1029|gene1029|rna1029|rna1029 202 QKGKCMIClsTYRKGECGIEL-SCAHFFHKSCGVKWMKM---QNTCPICRHEI 250
                                        567777773345667888877.6*************986...678*****875 PP

>> zf-RING_UBOX  RING-type zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   2.1     4e-06    0.0038       1      39 []     206     244 ..     206     244 .. 0.86
   2 ?    2.2   0.3       0.2   1.8e+02       1       7 [.     243     249 ..     243     251 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 4e-06
                       zf-RING_UBOX   1 CpIClelft.....dPlvlpCGHtFCreClwelskslegafkCP 39 
                                        C ICl+++          l+C H F+++C     k+ +++ +CP
  gene1029|gene1029|rna1029|rna1029 206 CMICLSTYRkgecgIE--LSCAHFFHKSCG---VKWMKMQNTCP 244
                                        99******97765433..48*********9...999*******9 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.2
                       zf-RING_UBOX   1 CpIClel 7  
                                        CpIC+ +
  gene1029|gene1029|rna1029|rna1029 243 CPICRHE 249
                                        ****865 PP

>> Prok-RING_4  Prokaryotic RING finger family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   1.1      0.39   3.7e+02      21      40 ..       9      30 ..       4      33 .. 0.75
   2 !   17.0   8.0   4.2e-06     0.004       1      41 [.     206     251 ..     206     252 .] 0.75

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.39
                        Prok-RING_4 21 CkeCfdsk.dls.sCPlCqrri 40
                                       C++C + +  ++  C +C +++
  gene1029|gene1029|rna1029|rna1029  9 CHACGSRTvPHNeLCAFCDSEF 30
                                       9999888853445999999875 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 4.2e-06
                        Prok-RING_4   1 CvlCgeq...ekkailepCgHlvCkeCfdsk.dls.sCPlCqrris 41 
                                        C++C +    ++  i  +C+H + k+C  ++ +++ +CP+C+++i+
  gene1029|gene1029|rna1029|rna1029 206 CMICLSTyrkGECGIELSCAHFFHKSCGVKWmKMQnTCPICRHEIE 251
                                        66666654425555667************9974445********96 PP

>> Zn_ribbon_17  Zinc-ribbon, C4HC2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   2.5       2.6   2.5e+03       5      24 ..       7      26 ..       4      28 .. 0.58
   2 !   15.7   7.8   9.2e-06    0.0087       5      46 ..     204     244 ..     200     248 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 2.6
                       Zn_ribbon_17  5 ksCayCelavkgrvvlcgvC 24
                                       ++C+ C  +      lc  C
  gene1029|gene1029|rna1029|rna1029  7 YYCHACGSRTVPHNELCAFC 26
                                       56666666555555555555 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 9.2e-06
                       Zn_ribbon_17   5 ksCayCelav.kgrvvlcgvCeHvlHasCarewfenddlaeCp 46 
                                         +C++C  +  kg + +  +C H  H+sC  +w ++++   Cp
  gene1029|gene1029|rna1029|rna1029 204 GKCMICLSTYrKGECGIELSCAHFFHKSCGVKWMKMQN--TCP 244
                                        58****65551789**********************99..887 PP

>> zf-HC5HC2H_2  PHD-zinc-finger like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.4       7.9   7.4e+03      55      62 ..      20      27 ..       8      34 .. 0.66
   2 !   16.1   5.7     1e-05    0.0095      18      87 ..     166     235 ..     155     248 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 7.9
                       zf-HC5HC2H_2 55 kekCllCk 62
                                       +e C++C+
  gene1029|gene1029|rna1029|rna1029 20 NELCAFCD 27
                                       35566665 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 1e-05
                       zf-HC5HC2H_2  18 derwvHvlCallvpevsfsnvaerepvdvekikkerlkekCllCkkr..kGaciqCskkeCktafHvtCala 87 
                                        d++  H++  +++++   ++  +++ ++  ++ ++r k kC++C ++  kG c    + +C++ fH  C ++
  gene1029|gene1029|rna1029|rna1029 166 DHELEHIIDEIFMSTKVSTSPVSNKYIKALQVSHARQKGKCMICLSTyrKGECG--IELSCAHFFHKSCGVK 235
                                        677789999999998888889999999*****************9986677664..45569********987 PP

>> zinc_ribbon_9  zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   3.7   1.9e-05     0.018       2      35 .]       6      34 ..       5      34 .. 0.77
   2 ?    2.1   0.2      0.25   2.3e+02      23      29 ..     242     248 ..     231     250 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.9e-05
                      zinc_ribbon_9  2 syWChqCdrfVsvspdedsdvlCPhCgggFVEei 35
                                        y+Ch C  +  +    +++  C +C++ F+E++
  gene1029|gene1029|rna1029|rna1029  6 IYYCHACGSRTVP----HNEL-CAFCDSEFIEIY 34
                                       5******943332....4566.**********85 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.25
                      zinc_ribbon_9  23 lCPhCgg 29 
                                        +CP C+ 
  gene1029|gene1029|rna1029|rna1029 242 TCPICRH 248
                                        5****85 PP

>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.3   0.00014      0.13      72     108 ..       5      41 ..       2      50 .. 0.88
   2 ?    3.3   2.3     0.063        59      42      94 ..     195     247 ..     155     251 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00014
                            TackOD1  72 rirlCpsCksghlnvrevCpkCkSidieeqelihhft 108
                                        +i  C+ C s  +   e C  C S  ie   +++ ++
  gene1029|gene1029|rna1029|rna1029   5 TIYYCHACGSRTVPHNELCAFCDSEFIEIYDSVEYYR 41 
                                        6789***********************9999998876 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.063
                            TackOD1  42 lealskekeeseelleelvkrglleeelvdrirlCpsCksghlnvrevCpkCk 94 
                                        l++ +  ++   ++  + +++g +  el   + + +sC  + ++++++Cp C+
  gene1029|gene1029|rna1029|rna1029 195 LQVSHARQKGKCMICLSTYRKGECGIELSCAHFFHKSCGVKWMKMQNTCPICR 247
                                        33333344456666667777788888888888888999999999999999997 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   1.7    0.0067       6.3      15      36 ..       5      28 ..       3      29 .. 0.77
   2 ?    2.0   0.1      0.16   1.5e+02      30      39 ..     205     214 ..     199     214 .. 0.83
   3 ?    3.8   0.2     0.046        43      28      36 ..     240     248 ..     232     249 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0067
                                       H-EE-TTT--E..ESSSS-CCCCS CS
                               RecR 15 kvrhCsrCgnl..teedlCaICsd 36
                                       ++ +C  Cg      ++lCa+C +
  gene1029|gene1029|rna1029|rna1029  5 TIYYCHACGSRtvPHNELCAFCDS 28
                                       5889****976225679*****87 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.16
                                        S-CCCCSTTS CS
                               RecR  30 lCaICsdprR 39 
                                         C IC ++ R
  gene1029|gene1029|rna1029|rna1029 205 KCMICLSTYR 214
                                        6****99988 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.046
                                        SSS-CCCCS CS
                               RecR  28 edlCaICsd 36 
                                        ++ C+IC+ 
  gene1029|gene1029|rna1029|rna1029 240 QNTCPICRH 248
                                        678999985 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.4     0.012        11      17      38 ..       7      29 ..       2      36 .. 0.69
   2 ?    4.3   5.5     0.041        38       3      40 ..     206     251 ..     195     252 .] 0.77

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.012
                                       EE-TTT--.EEEEEEE-SSS-S- CS
                     zinc-ribbons_6 17 yhCeaCqe.dlkkealCpeCeqe 38
                                       y C+aC +  +  + lC  C++e
  gene1029|gene1029|rna1029|rna1029  7 YYCHACGSrTVPHNELCAFCDSE 29
                                       77888876456667777777765 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.041
                                        -SSS-S--EE-S.......SEEE-TTT--.EEEEEEE-SSS-S--- CS
                     zinc-ribbons_6   3 CpeCqqelekrg.......eqyhCeaCqe.dlkkealCpeCeqele 40 
                                        C  C +  +k +       ++++ ++C    +k++++Cp C++e+e
  gene1029|gene1029|rna1029|rna1029 206 CMICLSTYRKGEcgielscAHFFHKSCGVkWMKMQNTCPICRHEIE 251
                                        6666666665556666666778888998736899********9998 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.5   0.00095       0.9      14      37 ..       8      29 ..       3      35 .. 0.72
   2 ?   -2.0   0.1         4   3.7e+03      26      35 ..     201     210 ..     193     217 .. 0.65
   3 ?    4.7   0.5     0.032        30       3      22 ..     231     250 ..     229     252 .] 0.75

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00095
                                DZR 14 fCseCgtklkavaaedrCpsCgek 37
                                       +C++Cg++    ++++ C  C+++
  gene1029|gene1029|rna1029|rna1029  8 YCHACGSRTV--PHNELCAFCDSE 29
                                       7888888763..677777777765 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 4
                                DZR  26 aaedrCpsCg 35 
                                         ++ +C+ C 
  gene1029|gene1029|rna1029|rna1029 201 RQKGKCMICL 210
                                        4467788885 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.032
                                DZR   3 qCgeelppdarfCseCgtkl 22 
                                        +Cg +  + +++C+ C++++
  gene1029|gene1029|rna1029|rna1029 231 SCGVKWMKMQNTCPICRHEI 250
                                        68888888888888888776 PP

>> zf-RING_10  zinc RING finger of MSL2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.3      0.77   7.3e+02      24      44 ..       7      27 ..       4      41 .. 0.77
   2 ?    9.4   6.9    0.0012       1.2       3      44 ..     206     247 ..     205     252 .] 0.92

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.77
                         zf-RING_10 24 yvCrlCvgkkkklkpsCsqCk 44
                                       y C+ C  +    +  C+ C+
  gene1029|gene1029|rna1029|rna1029  7 YYCHACGSRTVPHNELCAFCD 27
                                       669999999888889999997 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0012
                         zf-RING_10   3 CvvCckLLvdPlepkekeCqHyvCrlCvgkkkklkpsCsqCk 44 
                                        C++C +   +     e +C H+  ++C  k +k++ +C+ C+
  gene1029|gene1029|rna1029|rna1029 206 CMICLSTYRKGECGIELSCAHFFHKSCGVKWMKMQNTCPICR 247
                                        999999999999999**************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       930  (0.0518713); expected 358.6 (0.02)
Passed bias filter:                      539  (0.030063); expected 358.6 (0.02)
Passed Vit filter:                        73  (0.00407162); expected 17.9 (0.001)
Passed Fwd filter:                        22  (0.00122706); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1667.48
//
Query:       gene103|gene103|rna103|rna103  [L=56]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (56 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       382  (0.0213063); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.33u 0.28s 00:00:00.61 Elapsed: 00:00:00.41
# Mc/sec: 405.94
//
Query:       gene1030|gene1030|rna1030|rna1030  [L=1381]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   8.8e-127  423.4   0.0   1.2e-126  423.0   0.0    1.2  1  RNA_pol_Rpb2_6   RNA polymerase Rpb2, domain 6
    1.9e-63  213.7   0.1    2.7e-63  213.2   0.1    1.2  1  RNA_pol_Rpb2_1   RNA polymerase beta subunit
    1.7e-42  145.2   0.1    4.2e-42  143.9   0.1    1.7  2  RNA_pol_Rpb2_2   RNA polymerase Rpb2, domain 2
    4.2e-29  100.8   0.2      9e-29   99.7   0.2    1.6  1  RNA_pol_Rpb2_7   RNA polymerase Rpb2, domain 7
    4.7e-27   93.9   0.0    9.5e-27   93.0   0.0    1.5  1  RNA_pol_Rpb2_3   RNA polymerase Rpb2, domain 3
    2.9e-21   75.8   1.0    8.4e-21   74.3   1.0    1.9  1  RNA_pol_Rpb2_5   RNA polymerase Rpb2, domain 5
    6.4e-19   68.0   0.6    1.4e-18   66.9   0.3    1.8  2  RNA_pol_Rpb2_4   RNA polymerase Rpb2, domain 4
  ------ inclusion threshold ------
      0.041   14.1   0.2       0.32   11.3   0.1    2.3  2  RNA_pol_Rpb2_45  RNA polymerase beta subunit external 1 domai
        0.2   11.7   0.8        2.5    8.2   0.2    2.4  2  Nop10p           Nucleolar RNA-binding protein, Nop10p family


Domain annotation for each model (and alignments):
>> RNA_pol_Rpb2_6  RNA polymerase Rpb2, domain 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  423.0   0.0  5.9e-130  1.2e-126       1     390 []     905    1290 ..     905    1290 .. 0.92

  Alignments for each domain:
  == domain 1  score: 423.0 bits;  conditional E-value: 5.9e-130
                                         HHHT-SS-TTB-HHHHHHHHHHGGGB-S---TTTTT---SSEEEESS----SSB-S.TTTTTS........GGG CS
                     RNA_pol_Rpb2_6    1 vaklapvvehvqspriiiqaamekqalgiyslnkfkrsnqktyllcinqkPlvktgdkveagqvldgpatekge 74  
                                         +a+ +p+++h+qspr+++q+am+kqa+g+y++n   r+++ +++l ++qkPlv+t+ ++e+++        + e
  gene1030|gene1030|rna1030|rna1030  905 CASMIPFPDHNQSPRNTYQSAMSKQAMGVYATNFLLRMDSLSNILFYPQKPLVTTR-AMEYLR--------FRE 969 
                                         6999****************************************************.******........*** PP

                                         S-SEEEEEBBBS--TTTTTTT-EEEBCHHHHTTTT-EEEEEE..EEE--SSSS-..--.-S--..-.....-SS CS
                     RNA_pol_Rpb2_6   75 lalGqnavVAvmsyeGYniEDaiilnerlvdrdvftsihikeyeveardtklge..eeitrdipnv.....see 141 
                                         l++Gqna+VA+++y+GYn+ED++i+n++++dr++f+s+ +++  ++ ++t +g+   e+++++ +      ++ 
  gene1030|gene1030|rna1030|rna1030  970 LPAGQNAIVAIACYTGYNQEDSVIMNQSAIDRGLFRSFLYRT--YTDQETMNGPgcVEVFAKPRRGevlrmKNL 1041
                                         ******************************************..666666666655888888877689999999 PP

                                         -GGGS-TTSB--SS-EEETT-EEE---...B-----..........-----------..-B---EE--TT-EEE CS
                     RNA_pol_Rpb2_6  142 alkkLdedGivrvgaevkegdilvgkvt.kgeteltpe.......ekllraifgekarevkdtslrvksgeegv 207 
                                         +++kLdedGiv++g +v+ +d+l+gk+    e    +        +++++++ ++ + + kd+s+ ++++eegv
  gene1030|gene1030|rna1030|rna1030 1042 NYDKLDEDGIVNPGVRVTGEDVLIGKILpVIERMDVNGnslidnrDEKINTESNTMNVSWKDASTAMRPTEEGV 1115
                                         **************************97644433332211221114444444444555589************* PP

                                         EEEEEE.......EE-TT--EEEEEEEEEEE---TT-BEEETTS---BBEEEB-TTTSEEETTS---SEEE-GG CS
                     RNA_pol_Rpb2_6  208 VdkvkvfsrekgdelkagvnklvkvyvaqkRklqvGDKfasrhGqKGvvslilpqeDmPfledGivvDivlNPl 281 
                                         Vd+v+v        ++ +++k+ kv++++ R +++GDKfasrhGqKG+++++l+ eDmPf+++Gi++Di++NP+
  gene1030|gene1030|rna1030|rna1030 1116 VDSVIV--------TNREGYKFTKVKIRSCRVPEMGDKFASRHGQKGTIGITLRAEDMPFTSEGIIPDIIINPH 1181
                                         ******........78899******************************************************* PP

                                         GCHHH-BTTHHHHHHHHHCCCSSSS--B--TT-...-HHHHHHHHHTTS-TT-EE-EEETTTS-B-SS-EEB-E CS
                     RNA_pol_Rpb2_6  282 gvPSRmtigqllEtllgkaaalegkkvdatvFdgakeeeikelLeeagleasGkevlydGrtGekleaeifvGv 355 
                                         ++PSRmtig+l+E+llgk++al g++ d+t+F+  +  +i+e+L+  g+e++G e++y+G+tG+kl+a+if+G+
  gene1030|gene1030|rna1030|rna1030 1182 CIPSRMTIGHLIECLLGKVSALAGEEGDGTPFSDVTVGAISEQLKDFGYEHRGLETMYNGMTGRKLDAQIFIGP 1255
                                         *********************************9999************************************* PP

                                         EEEEEBS--CCCS----SS--B-TTT--B-SCGGG CS
                     RNA_pol_Rpb2_6  356 iYylkLkhlvedKihaRstGpyslltqQPlgGkaq 390 
                                         +Yy++Lkh+v+dK+haR+ Gp ++lt+QP +G+++
  gene1030|gene1030|rna1030|rna1030 1256 TYYQRLKHMVQDKVHARAHGPLQVLTRQPAEGRSR 1290
                                         *********************************86 PP

>> RNA_pol_Rpb2_1  RNA polymerase beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  213.2   0.1   1.3e-66   2.7e-63       1     203 []     211     605 ..     211     605 .. 0.97

  Alignments for each domain:
  == domain 1  score: 213.2 bits;  conditional E-value: 1.3e-66
                                        CTTHHHHHHHHHHHHTHHHHHCTTSSECCHCSSSHCSSSC...EEEEEEEEEEESC.SSECTTSCEEES.HHHHHH CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxx RF
                     RNA_pol_Rpb2_1   1 gLvsqqldSFnkfveqdlekiikeeaaieseeeiqssgee...lelkfvsirlgkP.vvdesdasereiyPkearl 72 
                                        gLv+qqldSFn+f+e+++++ii+e++++ +++ ++  +e+   + lkf++i+++kP v++e+d+++ +++P earl
  gene1030|gene1030|rna1030|rna1030 211 GLVRQQLDSFNEFIETTMQEIIDENNTLIVQSIPSAGKESvqkIILKFGQIYISKPpVITEQDGKTSTLFPCEARL 286
                                        69*************************99888776544447779**********9735688*************** PP

                                        CTSBXEEEEEEEEEEEECCCCTCCEEEEEEEEEEEEEXBTTSTTSSSTTS.HHHHHHTTS.TTS..SSEEETTCEE CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     RNA_pol_Rpb2_1  73 rnltYsaplyvklklvvyekdnkeeikeeevyiGelPlMlrskacvlseaseeelvelkEcpldqGGyFiinGtek 148
                                        r+ltY  plyv+++++v+e+++ ++  +++v iG +P+Mlrs+ c+l+++s+++l+el+Ecp+dqGGyF+inG+ek
  gene1030|gene1030|rna1030|rna1030 287 RDLTYACPLYVDVTKSVVENEESDDHFYRQVPIGLVPVMLRSSCCILHGLSDKNLTELGECPYDQGGYFVINGSEK 362
                                        **************************************************************************** PP

                                        EEXEEEE..................................................................... CS
                                        xxxxxxx..................................................................... RF
                     RNA_pol_Rpb2_1 149 vivaqek..................................................................... 155
                                        v++aqe+                                                                     
  gene1030|gene1030|rna1030|rna1030 363 VLIAQERmatnvvhvfekslatythyaeirsapqkgsktpsalivklvkktetefllratlpgvrqdipviviyra 438
                                        **************************************************************************** PP

                                        ............................................................................ CS
                                        ............................................................................ RF
                     RNA_pol_Rpb2_1 156 ............................................................................ 155
                                                                                                                    
  gene1030|gene1030|rna1030|rna1030 439 lgfvsdkeimehliydpndkemlqvirpsieeafviqdqnvaldyigkrsapagsprekriqfakdilireflphi 514
                                        **************************************************************************** PP

                                        ...........................................XHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTSS CS
                                        ...........................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     RNA_pol_Rpb2_1 156 ...........................................laGeLlaslfrvllkklerdvkerlqkslekld 188
                                                                                   laG+Lla+lf+vl++kl ++ ++++qk++e+++
  gene1030|gene1030|rna1030|rna1030 515 gdkqfcetrkafffgymiqrllncamkrvspddrdhygkkrmdLAGPLLAQLFKVLFRKLCQETIKHMQKCIENKR 590
                                        **************************************************************************** PP

                                        SSSHHHHSCSHHHHH CS
                                        xxxxxxxxxxxxxxx RF
                     RNA_pol_Rpb2_1 189 dlmlqllvnakpita 203
                                        d++ +l ++++ it+
  gene1030|gene1030|rna1030|rna1030 591 DFNIALGLKTSIITQ 605
                                        ********9999986 PP

>> RNA_pol_Rpb2_2  RNA polymerase Rpb2, domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  143.9   0.1   2.1e-45   4.2e-42      37     190 .]     415     557 ..     372     557 .. 0.91
   2 ?   -3.2   0.0       2.7   5.4e+03     113     130 ..     732     752 ..     717     762 .. 0.52

  Alignments for each domain:
  == domain 1  score: 143.9 bits;  conditional E-value: 2.1e-45
                                        TSCEEEEECTTSSSEEEHHHHHHHTT--STTHHHHHHTSSSTTHHHHHHHHHHHHHHCTSSSCHHHHHHHHH.CSS CS
                     RNA_pol_Rpb2_2  37 dgktliwtriskkrkipivivlkAlglvsdreIlericydsedsqlleelleeleekeeiqtqeealdyigk.vva 111
                                         +  l++t++ ++++ip++++ +Alg+vsd+eI+e+++yd++d+++l+ ++++ ee+++iq+q++aldyigk +  
  gene1030|gene1030|rna1030|rna1030 415 TEFLLRATLPGVRQDIPVIVIYRALGFVSDKEIMEHLIYDPNDKEMLQVIRPSIEEAFVIQDQNVALDYIGKrSAP 490
                                        44457889999*************************************************************9999 PP

                                        TTSSSCCCCCHHHHHHHCHHHHHHHTTTTSSTTTTTSSSTCHH..HHHHHHHHHHHHHHHHTTSSSS--TTSGGGE CS
                     RNA_pol_Rpb2_2 112 lrrgeearlqsareilqkrydlgeigreklnkhlglseslenkrlkaqdilymidrLlslklgrrevDDiDhlgnk 187
                                        +++++e+r+q a++il          re l+ h+g ++ +e++  ka++++ymi+rLl+++++r ++DD+Dh+g+k
  gene1030|gene1030|rna1030|rna1030 491 AGSPREKRIQFAKDIL---------IREFLP-HIGDKQFCETR--KAFFFGYMIQRLLNCAMKRVSPDDRDHYGKK 554
                                        *************999.........599999.***********..******************************* PP

                                        EEE CS
                     RNA_pol_Rpb2_2 188 Rvr 190
                                        R +
  gene1030|gene1030|rna1030|rna1030 555 RMD 557
                                        *75 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 2.7
                                        TSSSCCCCCHHHHHHH...CH CS
                     RNA_pol_Rpb2_2 113 rrgeearlqsareilq...kr 130
                                         +g    ++++re+l+   kr
  gene1030|gene1030|rna1030|rna1030 732 VNGTWLGITTEREFLYtvlKR 752
                                        555555555555555533332 PP

>> RNA_pol_Rpb2_7  RNA polymerase Rpb2, domain 7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.7   0.2   4.5e-32     9e-29       1      85 [.    1292    1376 ..    1292    1378 .. 0.98

  Alignments for each domain:
  == domain 1  score: 99.7 bits;  conditional E-value: 4.5e-32
                                         BBEEEEHHHHHHHHHHTBHHHHHHHHTTTTTEEEEEEESSSSSCCCEEEBTTTTCSSSEEEEEEEHHHHHHHHH CS
                     RNA_pol_Rpb2_7    1 GGlrfGEMErdaliayGaaalLkerltikSDavevdvcgrckllaaaneCkivkseekiekveipeafklLlqe 74  
                                         GGlrfGEMErd++i++G++ +L+erl++ SD +++ vc++c+l+  ++ Ck + +++k++ ve+p+afklLlqe
  gene1030|gene1030|rna1030|rna1030 1292 GGLRFGEMERDCIISHGTSLFLRERLFEVSDFFSLVVCEQCGLFCLEDGCKGCGNKTKLAIVEMPYAFKLLLQE 1365
                                         9************************************************************************* PP

                                         HHHTTBEEEEE CS
                     RNA_pol_Rpb2_7   75 Lqslgialkll 85  
                                         L++++ia++l 
  gene1030|gene1030|rna1030|rna1030 1366 LMGMNIAPRLR 1376
                                         *******9985 PP

>> RNA_pol_Rpb2_3  RNA polymerase Rpb2, domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.0   0.0   4.8e-30   9.5e-27       1      68 []     631     695 ..     631     695 .. 0.98

  Alignments for each domain:
  == domain 1  score: 93.0 bits;  conditional E-value: 4.8e-30
                     RNA_pol_Rpb2_3   1 qvldrlnplselshlrrvsslrgglskerkttevRdlhpshwGriCpveTPEGencGlvksLallarv 68 
                                        qvl+r+n++s+lshlrrv+s+   + +e k +++R+lh++hwG++Cp+eTPEG+ cGlvk+L+lla++
  gene1030|gene1030|rna1030|rna1030 631 QVLNRYNFISTLSHLRRVNSP---MGREGKLAKPRQLHNTHWGMVCPAETPEGQACGLVKNLSLLAYI 695
                                        89*******************...*****************************************987 PP

>> RNA_pol_Rpb2_5  RNA polymerase Rpb2, domain 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.3   1.0   4.2e-24   8.4e-21       1      58 []     812     898 ..     812     898 .. 0.93

  Alignments for each domain:
  == domain 1  score: 74.3 bits;  conditional E-value: 4.2e-24
                                        HHHHHHTTSEEEEEHHHHTT--EESSTTTCSST.-SSTTTSS-............................-TTSS CS
                     RNA_pol_Rpb2_5   1 wddLlregvvEylDaeEEetamIamtpedleks.reekealee............................kensk 47 
                                        w+dL+++g+vEylD+eEE++amI+m+pe+l+++ + +++ ++e                             + + 
  gene1030|gene1030|rna1030|rna1030 812 WEDLVNNGIVEYLDVEEEDQAMICMSPEELYEQqMVTDRINAElrgesverprervlkhtskhvgsvypgnDPHDL 887
                                        *********************************8888888888************************998866666 PP

                                        SST-SEEES-G CS
                     RNA_pol_Rpb2_5  48 shtyTHcEIhP 58 
                                         ++yTHcEIhP
  gene1030|gene1030|rna1030|rna1030 888 ITNYTHCEIHP 898
                                        66********9 PP

>> RNA_pol_Rpb2_4  RNA polymerase Rpb2, domain 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.0       8.8   1.8e+04      14      28 ..     635     649 ..     632     653 .. 0.81
   2 !   66.9   0.3   6.9e-22   1.4e-18       1      62 []     730     791 ..     730     791 .. 0.99

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 8.8
                                        HCCHHHHHHHHCCTT CS
                     RNA_pol_Rpb2_4  14 pkklvetlRelRRkg 28 
                                          ++++tl +lRR +
  gene1030|gene1030|rna1030|rna1030 635 RYNFISTLSHLRRVN 649
                                        568999******965 PP

  == domain 2  score: 66.9 bits;  conditional E-value: 6.9e-22
                                        EECTT-BEEE-S-HCCHHHHHHHHCCTTSS-TT-EEEE-TTT--EEEE-SSEEB-EEEEE-S CS
                     RNA_pol_Rpb2_4   1 VfvNGrllGvtrdpkklvetlRelRRkgkiseevsivlnekqkevkiatDgGRvcRPliiVe 62 
                                        VfvNG++lG+t++ + l + l++++R+ +i+++vsiv + ++ke++i +D GR cRP ++Ve
  gene1030|gene1030|rna1030|rna1030 730 VFVNGTWLGITTEREFLYTVLKRMKRQARIHKDVSIVQSLRDKEIRILCDVGRPCRPCFVVE 791
                                        9************************************************************7 PP

>> RNA_pol_Rpb2_45  RNA polymerase beta subunit external 1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   0.00016      0.32      11      59 ..     820     867 ..     810     868 .. 0.90
   2 ?   -0.9   0.0         1     2e+03      36      54 ..    1262    1280 ..    1256    1284 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00016
                                        EEEEEEHHHHTTSEEE-SSS-BETTSCBSSSEEEEECSSCEEEEEGGG- CS
                    RNA_pol_Rpb2_45  11 evvYLtAdeEekyviAqAnapldeegrfveerVlaRrkgevelvepeeV 59 
                                         v+YL  +eE++ +i  + ++l e +++v++r++a  +ge ++ ++e+V
  gene1030|gene1030|rna1030|rna1030 820 IVEYLDVEEEDQAMICMSPEELYE-QQMVTDRINAELRGESVERPRERV 867
                                        589*******************76.68999******99**999999988 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1
                                         SCBSSSEEEEECSSCEEEE CS
                    RNA_pol_Rpb2_45   36 grfveerVlaRrkgevelv 54  
                                         +++v+++V+aR +g  ++ 
  gene1030|gene1030|rna1030|rna1030 1262 KHMVQDKVHARAHGPLQVL 1280
                                         6899*******98766555 PP

>> Nop10p  Nucleolar RNA-binding protein, Nop10p family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0       0.2   4.1e+02      34      48 ..     542     558 ..     534     559 .. 0.79
   2 ?    8.2   0.2    0.0013       2.5       5      30 ..    1326    1351 ..    1324    1352 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.2
                                        S--TT-T..TCHHHHHC CS
                             Nop10p  34 RFSPdDk..yskyRral 48 
                                        R SPdD+  y+k R++l
  gene1030|gene1030|rna1030|rna1030 542 RVSPDDRdhYGKKRMDL 558
                                        8899974449**99876 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0013
                                         -EE-TTT--EESSSB-TTT-SB-B-S CS
                             Nop10p    5 lrkcgkcrvYTLkkvcpecggptksa 30  
                                         l +c++c+   L++ c  cg++tk a
  gene1030|gene1030|rna1030|rna1030 1326 LVVCEQCGLFCLEDGCKGCGNKTKLA 1351
                                         568********************876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1381 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       386  (0.0215294); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.83u 0.31s 00:00:01.13 Elapsed: 00:00:00.48
# Mc/sec: 8663.72
//
Query:       gene1031|gene1031|rna1031|rna1031  [L=101]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       465  (0.0259356); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.42
# Mc/sec: 718.35
//
Query:       gene1032|gene1032|rna1032|rna1032  [L=713]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   1.6e-100  337.5   0.1    6.1e-61  206.8   0.0    3.0  2  RdRP      RNA dependent RNA polymerase


Domain annotation for each model (and alignments):
>> RdRP  RNA dependent RNA polymerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.6   0.1   6.7e-41   1.2e-36     173     377 ..       1     171 [.       1     184 [. 0.87
   2 !  206.8   0.0   3.4e-65   6.1e-61     380     586 .]     250     439 ..     235     439 .. 0.88

  Alignments for each domain:
  == domain 1  score: 126.6 bits;  conditional E-value: 6.7e-41
                               RdRP 173 larkiakklglkkaeelPsafQiRigGaKGvlavdkrlkpekielrpSqiKfkseeddsekrtleivkvsskpkpa 248
                                        +a++iakkl+l   +++P+afQiR++G+KGv++ + +  p+++ lr+S++Kf+s +       le+v++s++  ++
  gene1032|gene1032|rna1032|rna1032   1 VAHMIAKKLRL---SFTPTAFQIRFAGYKGVVVRA-HI-PHDLILRKSMRKFNSTY-----TILEVVNYSQPI-EC 65 
                                        589********...69***************8777.55.45699********6654.....56*********9.** PP

                               RdRP 249 yLnrqlikiLedlgvpeevflellkealeelrealkdagaaaellkkagdpskleellaelldsgfdpseldpflr 324
                                        yLnrq+i+iLe lg+p++ f++l++e+l ++++a+++                   l++++ + g        ++ 
  gene1032|gene1032|rna1032|rna1032  66 YLNRQIIMILEGLGIPKHNFISLQNEYLMQMYRAINHS------------------LISKYCRIGG----V-ALVD 118
                                        **********************************9865..................7778777766....3.6799 PP

                               RdRP 325 sllkalvkeslrklkekarIpvpksatllgvaDetgvLkegevfvqlsealdq 377
                                        ++  a++ + +r++  k rI v ++++l+gv+De gvL e+evfv++ ++ d+
  gene1032|gene1032|rna1032|rna1032 119 RMSGAVIGRLFREMCAKGRIFVSNGVVLMGVIDEEGVLGENEVFVRVCDDYDE 171
                                        9*******************************************999654333 PP

  == domain 2  score: 206.8 bits;  conditional E-value: 3.4e-65
                               RdRP 380 eksktkllkgdvlVtRnPalhpgDiqvvkavdv.pelrhlkdviVFstkGdrslaselsGGDlDGDkywViwdpel 454
                                        +++ + ++ g+ +V++nP+lhpgDi++v++v + +el h+k+v+VFs kG+r+  +++sG+DlDGD+y+++wd++l
  gene1032|gene1032|rna1032|rna1032 250 NRTADGVVVGNAIVAKNPCLHPGDIRKVHCV-YkKELLHYKNVLVFSRKGTRPTFNMCSGSDLDGDLYFISWDKRL 324
                                        333566777999*******************.669***************************************** PP

                               RdRP 455 efapakpsneepadyeeakpkeldre.vtvediadffveymksdvlGlisnahlaiadqeegiddpkclkLaelhs 529
                                        +  p +++   p++y+ + ++ l++e + ++d+ +ff+++ k+d lG+isnahl+++d  +gi+dp++lkLa+l+s
  gene1032|gene1032|rna1032|rna1032 325 I--PRNEH--FPQSYQ-S-SSYLSKEhIVTQDMVNFFTRFAKEDELGKISNAHLVYSDI-HGITDPQALKLAYLFS 393
                                        7..66445..489999.4.577886636677***************************7.**************** PP

                               RdRP 530 kaVDypKtGipvdkkeiprelkkpkekPdfkekekkekakkpyykskkilgkLyrev 586
                                        + VD+pKtG+ +    +p++l +p+ +Pdf+e+        ++yks +++g Lyr+v
  gene1032|gene1032|rna1032|rna1032 394 MGVDFPKTGYIAR---LPQNL-EPEVYPDFMERG-------RSYKSGRVMGVLYRRV 439
                                        *************...99999.6999*****654.......58************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (713 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       604  (0.0336884); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.66u 0.26s 00:00:00.92 Elapsed: 00:00:00.45
# Mc/sec: 4732.79
//
Query:       gene1033|gene1033|rna1033|rna1033  [L=1082]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.3e-18   66.2   0.0    3.4e-18   65.6   0.0    1.2  1  RdRP       RNA dependent RNA polymerase


Domain annotation for each model (and alignments):
>> RdRP  RNA dependent RNA polymerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.6   0.0   1.9e-22   3.4e-18       1     152 [.     836     966 ..     836     973 .. 0.85

  Alignments for each domain:
  == domain 1  score: 65.6 bits;  conditional E-value: 1.9e-22
                               RdRP   1 vtptriilegpeleksnrvlRrfkegsdrFlrvkfpdedgerldsedgeellkervkkvlkegiviagrkfeflaf 76 
                                        v+p++i ++ p+ + snr+lR+f    ++ +r++f++           +e + e +++++++gi+i +r + f a 
  gene1033|gene1033|rna1033|rna1033 836 VYPLSIACMYPKNNLSNRILRNF----SNMIRITFKNTC---------DENVMEYIREIMSNGITI-DRPYYFVAT 897
                                        68999******************....89*******975.........45688999*********8.89******* PP

                               RdRP  77 sdsqlrehsvwffapfeeegerisaeeirkwlgdfenisqsvaKyaaRlglalSttrptvvkvereqiiieeidDv 152
                                        s+sqlr++s+wf++p+++ +  +  + +r+w+g +e    ++ Ky+ R+gl+lS+t +  ++   ++++  e dD+
  gene1033|gene1033|rna1033|rna1033 898 SSSQLRSNSAWFISPYRKGNVLVGSDYVRNWMGVIE-C-DNIGKYMIRVGLGLSSTFSM-FE--VDDYV--EEDDI 966
                                        *************997655555*************4.4.79****************94.44..34544..44553 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1082 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1333  (0.0743488); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.70u 0.33s 00:00:01.03 Elapsed: 00:00:00.50
# Mc/sec: 6500.92
//
Query:       gene1034|gene1034|rna1034|rna1034  [L=69]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (69 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       426  (0.0237604); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.43
# Mc/sec: 482.58
//
Query:       gene1035|gene1035|rna1035|rna1035  [L=90]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       500  (0.0278878); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.28s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 671.64
//
Query:       gene1036|gene1036|rna1036|rna1036  [L=77]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.026   14.7   0.0      0.027   14.6   0.0    1.1  1  RTT107_BRCT_6  Regulator of Ty1 transposition protein 107 BRC


Domain annotation for each model (and alignments):
>> RTT107_BRCT_6  Regulator of Ty1 transposition protein 107 BRCT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   1.5e-06     0.027      63     104 ..      28      71 ..       7      76 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.5e-06
                      RTT107_BRCT_6  63 peyvliatka..sqvkkfkkllkeekenkkvlvveWdWcvksif 104
                                        p+y++i ++   ++++ ++kl +++ +nk+ l+v+ d c+ s +
  gene1036|gene1036|rna1036|rna1036  28 PRYLIIHSRFlmNNHEYLNKLYSNDLKNKNKLIVDVDFCIASKY 71 
                                        67888888751145669***********************9866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       532  (0.0296726); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.28s 00:00:00.66 Elapsed: 00:00:00.44
# Mc/sec: 529.23
//
Query:       gene1037|gene1037|rna1037|rna1037  [L=473]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.096   12.6   0.0       0.22   11.4   0.0    1.6  1  EF-hand_8  EF-hand domain pair


Domain annotation for each model (and alignments):
>> EF-hand_8  EF-hand domain pair
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   1.2e-05      0.22      26      45 ..     128     147 ..     115     148 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 1.2e-05
                          EF-hand_8  26 eevdilfrefDtdgdGkisf 45 
                                        e++ ++++++D++++Gki++
  gene1037|gene1037|rna1037|rna1037 128 EQIVHMLNLIDIKCSGKIKL 147
                                        6899**************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (473 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       431  (0.0240393); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 3465.98
//
Query:       gene1038|gene1038|rna1038|rna1038  [L=192]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.043   12.7   0.0       0.06   12.3   0.0    1.1  1  DUF2397         Protein of unknown function (DUF2397)
      0.091   13.4   0.1       0.21   12.3   0.1    1.6  1  DNA_repr_REX1B  DNA repair REX1-B


Domain annotation for each model (and alignments):
>> DUF2397  Protein of unknown function (DUF2397)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   6.7e-06      0.06     133     189 ..      31      86 ..      26      94 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 6.7e-06
                            DUF2397 133 aeedeaddevaellrelferfekLaenaadFlasLqrvlaeedmdteaflayKeaLi 189
                                         +e++++de ++ +r ++++f ++++++++F+   + +++ edm+  +f ++K+++i
  gene1038|gene1038|rna1038|rna1038  31 IHENNNEDEYYNYVRLINTEFNEISKTVRAFMDPVRILRTVEDMQV-DFDTFKNTMI 86 
                                        45566666**************************************.9*****9987 PP

>> DNA_repr_REX1B  DNA repair REX1-B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   2.3e-05      0.21      29      58 ..      33      62 ..      22      76 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.3e-05
                     DNA_repr_REX1B 29 ksgaeeeykqlvkevTeefseiSkevleie 58
                                       ++++e ey ++v+ + +ef+eiSk+v++  
  gene1038|gene1038|rna1038|rna1038 33 ENNNEDEYYNYVRLINTEFNEISKTVRAFM 62
                                       4667777******************98865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (192 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       817  (0.0455686); expected 358.6 (0.02)
Passed bias filter:                      472  (0.0263261); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1517.04
//
Query:       gene1039|gene1039|rna1039|rna1039  [L=179]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      3e-16   59.7   1.1    3.4e-16   59.5   1.1    1.2  1  UCH       Ubiquitin carboxyl-terminal hydrolase
  ------ inclusion threshold ------
      0.017   14.8   0.1      0.029   13.9   0.1    1.5  1  UCH_1     Ubiquitin carboxyl-terminal hydrolase


Domain annotation for each model (and alignments):
>> UCH  Ubiquitin carboxyl-terminal hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.5   1.1   3.8e-20   3.4e-16     145     257 .]      57     175 ..       3     175 .. 0.78

  Alignments for each domain:
  == domain 1  score: 59.5 bits;  conditional E-value: 3.8e-20
                                        E......................EEEEEEB-SEEEEEEESEEETEE.EEE--SEEB--SEEE-GGGBSS-BTTS-T CS
                                        x......................xxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                                UCH 145 s......................klklkrlPeiLiihlkRfsynss.ksKlntkvefpeeldlssylaeekkkkte 197
                                        +                      k ++  lP++Lii+lkRf++n + ++K++t v++  +l ++ +          
  gene1039|gene1039|rna1039|rna1039  57 KeylgldnrlvctycervtvhskKYEIVFLPKYLIIQLKRFNFNGDyQRKIKTFVDYHSTLIINAV---------- 122
                                        15555555566666666666666889999*******************************999952.......... PP

                                        CS-BEEEEEEEEEES.CTTSEEEEEEEECTTTTEEEEEETTEEEEE-HHCCCTTCEEEEEE CS
                                        xxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                                UCH 198 ekkkYeLiavvvHsG.slssGHYvayiknekngkWykydDetvkevkeeeevlssayiLfY 257
                                           +Y L +  +H+  +++sGHY+ay       + ++ +D+ v+evk+    +s+ay+LfY
  gene1039|gene1039|rna1039|rna1039 123 ---RYTLRSTCNHIEiGVGSGHYTAYFY---GDRIVCANDSVVSEVKD--VNKSNAYMLFY 175
                                        ...3**********************99...6789***********93..3456******* PP

>> UCH_1  Ubiquitin carboxyl-terminal hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   3.3e-06     0.029     177     295 ..      45     145 ..       6     174 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.3e-06
                                        xxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              UCH_1 177 vtfasilkssler...ekttrawCekCkryqpteqrktvknlPpvLalnakleeeeelelwktknwlpleiklsld 249
                                         ++++++  +l++     ++r +C  C+r + ++++  +  lP+ L++++k+++ +        +  +++ik+ +d
  gene1039|gene1039|rna1039|rna1039  45 IKLEDCIDLFLSKeylGLDNRLVCTYCERVTVHSKKYEIVFLPKYLIIQLKRFNFN--------GDYQRKIKTFVD 112
                                        555666666666622224789******************************99777........677888888777 PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              UCH_1 250 edknleeklkeerekakaekeikvYeLqsvvvhigdskesghLvsl 295
                                          +             +   + + Y L+s+  hi+ +  sgh+ ++
  gene1039|gene1039|rna1039|rna1039 113 YHS-------------TLIINAVRYTLRSTCNHIEIGVGSGHYTAY 145
                                        643.............345667899999999999988889999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (179 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       536  (0.0298957); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1348.23
//
Query:       gene104|gene104|rna104|rna104  [L=276]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.059   13.6   0.0       0.16   12.2   0.0    1.7  1  Plasmid_RAQPRD  Plasmid protein of unknown function (Plasmid_


Domain annotation for each model (and alignments):
>> Plasmid_RAQPRD  Plasmid protein of unknown function (Plasmid_RAQPRD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   9.2e-06      0.16      29      61 ..      41      73 ..      32      77 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 9.2e-06
                 Plasmid_RAQPRD 29 qakqeekaRvhfdYdrlrrDleriraGIqsYLe 61
                                   +a++ +k+R +++Y+r+++ ++ + +G+++Y++
  gene104|gene104|rna104|rna104 41 SADEIPKKRKRLEYARAEESVRNMVEGVENYVN 73
                                   56666899***********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (276 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       803  (0.0447878); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 2079.95
//
Query:       gene1040|gene1040|rna1040|rna1040  [L=626]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.6e-18   64.9   0.1      1e-17   64.5   0.1    1.2  1  UCH       Ubiquitin carboxyl-terminal hydrolase
    0.00019   21.2   1.4       0.23   11.0   0.0    2.1  2  UCH_1     Ubiquitin carboxyl-terminal hydrolase


Domain annotation for each model (and alignments):
>> UCH  Ubiquitin carboxyl-terminal hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.5   0.1   1.1e-21     1e-17       2     143 ..      37     176 ..      36     312 .. 0.82

  Alignments for each domain:
  == domain 1  score: 64.5 bits;  conditional E-value: 1.1e-21
                                        EES-SSSTHHHHHHHHHHHTSHHHHHHHHTCHHCCSSTCCCCC-.TT.TTS.TTHHHHHHHHHHHHHHSH-CCEE- CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                                UCH   2 GlsNlGntCymnsvlQcLfsipelrdyllsleevkkesrnkkelnesnplgkkgelakalkdlfkellkskskavs 77 
                                        GlsNlGntCymns+lQc++ +p l+++++s       +            + kg+l +a+k+l++e   s s+ v 
  gene1040|gene1040|rna1040|rna1040  37 GLSNLGNTCYMNSALQCMIDLPLLTTFIRS-------N------------TFKGRLTNAYKELLAEYS-SDSALVV 92 
                                        9*********************99999999.......2............234679********9999.689**** PP

                                        -HHHHHHHHHHSGGGTSSSTCEHHHHHHHHHHHHHHHHCC..................HCCCHHHHHHCCCTTSHH CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..................xxxxxxxxxxxxxxxxxx RF
                                UCH  78 PkklkktlsklaksfsgykqqDaqEflaflLdqlhedlnr..................evaeekwkkhlkrndsli 135
                                        P ++++++ +  k+f g+k qDa Efl  +++++ e++++                  ++++++++   ++nd++ 
  gene1040|gene1040|rna1040|rna1040  93 PAEFRRSVVECTKRFYGNKEQDASEFLICVIERMCEEMKEdehgarvssdvqsgtdgmRQHANEFNLFRRNNDNIF 168
                                        ****************************************999999999888888876445555577777777777 PP

                                        HHHH-EEE CS
                                        xxxxxxxx RF
                                UCH 136 tdlfegql 143
                                        t lf   l
  gene1040|gene1040|rna1040|rna1040 169 TALFFSWL 176
                                        77775555 PP

>> UCH_1  Ubiquitin carboxyl-terminal hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.3     9e-05      0.81       2      33 ..      37      68 ..      36      85 .. 0.87
   2 !   11.0   0.0   2.5e-05      0.23     103     196 ..     113     270 ..      79     283 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 9e-05
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              UCH_1  2 GLEnhivnsYlNslLQvlyfipplrnlalshl 33
                                       GL n  +++Y+Ns LQ++  +p+l+ ++ s +
  gene1040|gene1040|rna1040|rna1040 37 GLSNLGNTCYMNSALQCMIDLPLLTTFIRSNT 68
                                       899999******************99988876 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 2.5e-05
                                        xxxxxxxxxxxxxxxxxxxxxx...........................xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              UCH_1 103 qsfnrflldqlekelketkkns...........................seeesaieqllgtkaettirclkCgse 151
                                        q   +fl+  +e+  +e+k+++                           ++++++++ l+   +++ ++c++C+  
  gene1040|gene1040|rna1040|rna1040 113 QDASEFLICVIERMCEEMKEDEhgarvssdvqsgtdgmrqhanefnlfrRNNDNIFTALFFSWLSSCLTCQTCRGV 188
                                        44444444444444444444446678888888888888888899999999999*******9999************ PP

                                        xxxxxxxxxxxxxxx.x...............................xxxx.......xxxxxxxxxxxxxxxxx RF
                              UCH_1 152 ksrksstlvldlkyP.k...............................psne.......kkeakvtfasilkssle 188
                                        k++ + +l+l+l  P +                               +  e       +++++ tf + +k ++e
  gene1040|gene1040|rna1040|rna1040 189 KEKGEAFLSLELPIPnEanyhpsviltfrerrelvggklcvrrrreraE--ErtlarntRTHESRTFVKSIKIFVE 262
                                        **********996664255555556655555555555555554444440..0444444466666777777777777 PP

                                        xxxxxxxx RF
                              UCH_1 189 rekttraw 196
                                        +++t +  
  gene1040|gene1040|rna1040|rna1040 263 STHTVKEL 270
                                        76666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (626 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       451  (0.0251548); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.64u 0.27s 00:00:00.91 Elapsed: 00:00:00.48
# Mc/sec: 3896.96
//
Query:       gene1042|gene1042|rna1042|rna1042  [L=59]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.024   14.5   0.0      0.033   14.1   0.0    1.2  1  DUF3746   Protein of unknown function (DUF3746)


Domain annotation for each model (and alignments):
>> DUF3746  Protein of unknown function (DUF3746)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   1.8e-06     0.033       8      25 ..      37      54 ..      36      56 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.8e-06
                            DUF3746  8 LkvttsskKktCkKhifd 25
                                       Lk++ s++ ++C+K+++ 
  gene1042|gene1042|rna1042|rna1042 37 LKDVLSCGSSYCRKAAYE 54
                                       9***************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       276  (0.0153941); expected 358.6 (0.02)
Passed bias filter:                      237  (0.0132188); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.47
# Mc/sec: 379.09
//
Query:       gene1043|gene1043|rna1043|rna1043  [L=643]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.084   11.7   0.1       0.14   11.0   0.1    1.3  1  YqfD      Putative stage IV sporulation protein YqfD


Domain annotation for each model (and alignments):
>> YqfD  Putative stage IV sporulation protein YqfD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   7.6e-06      0.14     309     369 ..     226     286 ..     184     296 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 7.6e-06
                               YqfD 309 veivketyreyeekeeelteeeakeeaeekaeeelkkklpkdakildekvevekeegkvrv 369
                                         ++v+  y e  + ++elt eea e++ + +e+ l++ +     il +++ev + ++ v +
  gene1043|gene1043|rna1043|rna1043 226 PKLVRSDYLEQASCQQELTPEEAAEAGLKSMEDILQRAMHMRNFILGKQYEVYQMKKLVDI 286
                                        578999*********************************************9988888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (643 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       748  (0.0417201); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.26s 00:00:00.84 Elapsed: 00:00:00.42
# Mc/sec: 4648.87
//
Query:       gene1044|gene1044|rna1044|rna1044  [L=585]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-06   27.7   0.1      0.026   14.4   0.0    5.5  6  TPR_1     Tetratricopeptide repeat
    3.3e-06   26.9   0.3      0.023   14.9   0.0    4.7  4  TPR_8     Tetratricopeptide repeat
    1.4e-05   24.8   0.0       0.12   12.5   0.0    4.5  5  TPR_2     Tetratricopeptide repeat
    5.4e-05   23.7   0.0       0.24   12.3   0.0    3.7  3  TPR_14    Tetratricopeptide repeat
     0.0002   21.8   0.4        3.8    8.1   0.0    4.0  4  TPR_19    Tetratricopeptide repeat
     0.0003   20.4   0.0    0.00079   19.1   0.0    1.7  1  TPR_11    TPR repeat
  ------ inclusion threshold ------
      0.034   14.4   9.5        3.7    7.8   0.4    4.1  4  ANAPC3    Anaphase-promoting complex, cyclosome, subunit 3
      0.087   13.5   0.0        1.1   10.0   0.0    2.5  3  TPR_16    Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.29   6.4e+02       4      18 ..       2      16 ..       1      29 [. 0.82
   2 ?    2.1   0.0     0.083   1.9e+02       4      20 ..     348     364 ..     346     366 .. 0.91
   3 ?    0.9   0.0       0.2   4.5e+02       3      33 ..     387     417 ..     386     418 .. 0.84
   4 ?    0.5   0.0      0.28   6.3e+02      10      24 ..     458     472 ..     457     474 .. 0.82
   5 !   14.4   0.0   1.2e-05     0.026       7      34 .]     502     529 ..     500     529 .. 0.94
   6 ?   -2.2   0.0         2   4.4e+03       2      11 ..     531     540 ..     531     543 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.29
                                       HHHHHHHHHHTT-HH CS
                              TPR_1  4 lynlGnayfklgkyd 18
                                       ++ ++ +y   g+++
  gene1044|gene1044|rna1044|rna1044  2 WCEIAIVYDMIGNFK 16
                                       899999999999987 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.083
                                        HHHHHHHHHHTT-HHHH CS
                              TPR_1   4 lynlGnayfklgkydeA 20 
                                        l++l++++ +  +y+ A
  gene1044|gene1044|rna1044|rna1044 348 LFRLALILKQRRDYKSA 364
                                        79************987 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.2
                                        HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                              TPR_1   3 alynlGnayfklgkydeAleyyekALelnPn 33 
                                        ++ +l++++f +g   e+ +  +  L ++++
  gene1044|gene1044|rna1044|rna1044 387 VHAQLAHLHFVQGATTECRKLLNAILHVDHH 417
                                        7889*********999999888888877765 PP

  == domain 4  score: 0.5 bits;  conditional E-value: 0.28
                                        HHHHTT-HHHHHHHH CS
                              TPR_1  10 ayfklgkydeAleyy 24 
                                        +yf+lg+ +++ + y
  gene1044|gene1044|rna1044|rna1044 458 CYFSLGMIEQCFDVY 472
                                        9******99976655 PP

  == domain 5  score: 14.4 bits;  conditional E-value: 1.2e-05
                                        HHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                              TPR_1   7 lGnayfklgkydeAleyyekALelnPnn 34 
                                        +G +yf+l++     +++++AL+++ ++
  gene1044|gene1044|rna1044|rna1044 502 IGIVYFNLKDVSSSMAAFKRALSIDSDF 529
                                        8************************986 PP

  == domain 6  score: -2.2 bits;  conditional E-value: 2
                                        HHHHHHHHHH CS
                              TPR_1   2 kalynlGnay 11 
                                        +a ynl+++ 
  gene1044|gene1044|rna1044|rna1044 531 EARYNLALVQ 540
                                        5889**9976 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.1      0.22     5e+02       3      31 ..       1      29 [.       1      31 [. 0.90
   2 ?    3.0   0.0     0.068   1.5e+02       4      20 ..     348     364 ..     346     369 .. 0.88
   3 ?    1.0   0.0      0.29   6.6e+02       5      24 ..     453     472 ..     453     473 .. 0.79
   4 !   14.9   0.0     1e-05     0.023       6      33 ..     501     528 ..     498     529 .. 0.92

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.22
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHH CS
                              TPR_8  3 ayynlgsiylklgdyeeAkeyyekaleld 31
                                       +++ ++ +y+  g++++ k ++e al+++
  gene1044|gene1044|rna1044|rna1044  1 MWCEIAIVYDMIGNFKMYKHAIENALKIR 29
                                       599999999999****99******99996 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.068
                                        HHHHHHHHHHTT-HHHH CS
                              TPR_8   4 yynlgsiylklgdyeeA 20 
                                        +++l++i+++  dy++A
  gene1044|gene1044|rna1044|rna1044 348 LFRLALILKQRRDYKSA 364
                                        89*************99 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.29
                                        HHHHHHHHHTT-HHHHHHHH CS
                              TPR_8   5 ynlgsiylklgdyeeAkeyy 24 
                                        y l ++y++lg +e+   +y
  gene1044|gene1044|rna1044|rna1044 453 YFLLRCYFSLGMIEQCFDVY 472
                                        56889999999999876655 PP

  == domain 4  score: 14.9 bits;  conditional E-value: 1e-05
                                        HHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                              TPR_8   6 nlgsiylklgdyeeAkeyyekaleldpd 33 
                                         +g +y++l+d  ++++++++al++d d
  gene1044|gene1044|rna1044|rna1044 501 TIGIVYFNLKDVSSSMAAFKRALSIDSD 528
                                        68999********************987 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       2.4   5.3e+03       4      18 ..       2      16 ..       2      29 .. 0.64
   2 ?    4.1   0.0     0.028        62       4      22 ..     348     366 ..     346     370 .. 0.89
   3 ?    1.9   0.0      0.13     3e+02       3      28 ..     387     412 ..     386     418 .. 0.86
   4 ?   -2.8   0.0       4.4   9.9e+03      10      23 ..     458     471 ..     457     473 .. 0.71
   5 !   12.5   0.0   5.4e-05      0.12       5      33 ..     500     528 ..     497     529 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 2.4
                              TPR_2  4 lynlGlayyklgdye 18
                                       +++++ +y   g+++
  gene1044|gene1044|rna1044|rna1044  2 WCEIAIVYDMIGNFK 16
                                       667777777777775 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.028
                              TPR_2   4 lynlGlayyklgdyeeAle 22 
                                        l++l+l++ ++ dy+ A +
  gene1044|gene1044|rna1044|rna1044 348 LFRLALILKQRRDYKSATR 366
                                        79*************9966 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.13
                              TPR_2   3 alynlGlayyklgdyeeAleafekAl 28 
                                        ++ +l+ +++ +g   e+++++++ l
  gene1044|gene1044|rna1044|rna1044 387 VHAQLAHLHFVQGATTECRKLLNAIL 412
                                        6889****************999877 PP

  == domain 4  score: -2.8 bits;  conditional E-value: 4.4
                              TPR_2  10 ayyklgdyeeAlea 23 
                                        +y+ lg  e++ + 
  gene1044|gene1044|rna1044|rna1044 458 CYFSLGMIEQCFDV 471
                                        78888888877655 PP

  == domain 5  score: 12.5 bits;  conditional E-value: 5.4e-05
                              TPR_2   5 ynlGlayyklgdyeeAleafekAleldPn 33 
                                        + +G +y++l+d     +af++Al++d +
  gene1044|gene1044|rna1044|rna1044 500 NTIGIVYFNLKDVSSSMAAFKRALSIDSD 528
                                        679**********************9975 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0      0.31   7.1e+02       4      24 ..     348     368 ..     346     370 .. 0.89
   2 ?    4.8   0.0     0.027        60       3      28 ..     387     412 ..     385     417 .. 0.91
   3 !   12.3   0.0   0.00011      0.24       8      42 ..     503     537 ..     500     539 .. 0.94

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.31
                             TPR_14   4 llalaeallalGdpdeAiall 24 
                                        l +la +l +++d++ A ++l
  gene1044|gene1044|rna1044|rna1044 348 LFRLALILKQRRDYKSATRVL 368
                                        5689*************9998 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.027
                             TPR_14   3 allalaeallalGdpdeAiallrral 28 
                                        ++++la++++ +G + e ++ll+++l
  gene1044|gene1044|rna1044|rna1044 387 VHAQLAHLHFVQGATTECRKLLNAIL 412
                                        6899*******************987 PP

  == domain 3  score: 12.3 bits;  conditional E-value: 0.00011
                             TPR_14   8 aeallalGdpdeAiallrralalaPddaeawllla 42 
                                        + ++++l d   ++a+++ral+ + d+ ea++ la
  gene1044|gene1044|rna1044|rna1044 503 GIVYFNLKDVSSSMAAFKRALSIDSDFKEARYNLA 537
                                        789****************************9998 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0       0.2   4.5e+02       9      51 ..     330     371 ..     327     377 .. 0.72
   2 !    6.7   0.0    0.0045        10      26      55 ..     386     415 ..     384     422 .. 0.90
   3 ?   -1.2   0.0       1.4     3e+03      30      43 ..     454     467 ..     451     468 .. 0.85
   4 !    8.1   0.0    0.0017       3.8      11      34 ..     516     539 ..     510     544 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.2
                             TPR_19   9 eAlalleqalqedpknaearllLAeallalgqldeAealLdal 51 
                                        + l++l+  + +    +  + +LA +l +  +++ A ++L+ l
  gene1044|gene1044|rna1044|rna1044 330 DILQYLSHSYRQTE-RSLMLFRLALILKQRRDYKSATRVLNVL 371
                                        55666666655433.44445569*****************987 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0045
                             TPR_19  26 earllLAeallalgqldeAealLdalpeed 55 
                                        ++ ++LA +++ +g ++e ++lL+a++  d
  gene1044|gene1044|rna1044|rna1044 386 DVHAQLAHLHFVQGATTECRKLLNAILHVD 415
                                        68899*********************8765 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 1.4
                             TPR_19  30 lLAeallalgqlde 43 
                                         L +++++lg +++
  gene1044|gene1044|rna1044|rna1044 454 FLLRCYFSLGMIEQ 467
                                        5789******9987 PP

  == domain 4  score: 8.1 bits;  conditional E-value: 0.0017
                             TPR_19  11 lalleqalqedpknaearllLAea 34 
                                        +a++++al+ d +  ear++LA +
  gene1044|gene1044|rna1044|rna1044 516 MAAFKRALSIDSDFKEARYNLALV 539
                                        689******************965 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   3.5e-07   0.00079       3      39 ..     505     541 ..     503     541 .. 0.93

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 3.5e-07
                             TPR_11   3 ayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayy 39 
                                        +y+ + +   +++a+k+Al +d+d+ ea ynL+l+++
  gene1044|gene1044|rna1044|rna1044 505 VYFNLKDVSSSMAAFKRALSIDSDFKEARYNLALVQH 541
                                        68899999999***********************987 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.4    0.0017       3.7       4      61 ..     327     379 ..     324     389 .. 0.75
   2 ?    6.1   0.5    0.0058        13      11      67 ..     374     430 ..     371     435 .. 0.81
   3 ?    4.2   0.1     0.022        50      27      58 ..     453     485 ..     436     489 .. 0.82
   4 ?   -0.5   0.0      0.65   1.5e+03      32      65 ..     505     539 ..     488     544 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0017
                                        -HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCTSHHHC-HHHHHH CS
                             ANAPC3   4 nyknAiflaerllaaetespedayllAlclylngqykrAyellrkaklnskslgcryl 61 
                                         y++++ +++  + ++te++  ++ lAl l ++ +yk+A ++l+ +    + l+ r  
  gene1044|gene1044|rna1044|rna1044 327 SYNDILQYLSHSY-RQTERSLMLFRLALILKQRRDYKSATRVLNVL----SILAERTH 379
                                        5777778888888.777777777779*****************999....44444444 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0058
                                        HHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHH CS
                             ANAPC3  11 laerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcll 67 
                                        laer + a +  + +a  lA  ++ +g  +++ +ll+     ++++l + +l+ +cl+
  gene1044|gene1044|rna1044|rna1044 374 LAERTHCAVSVLDVHAQ-LAHLHFVQGATTECRKLLNAIlHVDHHHLFSTVLKMECLY 430
                                        56666655544444444.5*************************************98 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.022
                                        HHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHH CS
                             ANAPC3  27 yllAlclylngqykrAyellrka.klnskslgc 58 
                                        y+l  c++++g  +++++++ +  ++++ s +c
  gene1044|gene1044|rna1044|rna1044 453 YFLLRCYFSLGMIEQCFDVYTNReRSREYSAEC 485
                                        78889*************999986666665555 PP

  == domain 4  score: -0.5 bits;  conditional E-value: 0.65
                                        HHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHH CS
                             ANAPC3  32 clylngqykrAyellrka.klnskslgcrylfAqc 65 
                                        +++++++  + +  +++a  ++s  +++ry +A +
  gene1044|gene1044|rna1044|rna1044 505 VYFNLKDVSSSMAAFKRAlSIDSDFKEARYNLALV 539
                                        79999999999999999988888778888888865 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.83   1.9e+03      36      53 ..     347     364 ..     334     369 .. 0.79
   2 ?   -2.6   0.0       4.1   9.3e+03       2      24 ..     390     412 ..     389     415 .. 0.79
   3 ?   10.0   0.0   0.00048       1.1       4      47 ..     503     543 ..     501     547 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.83
                             TPR_16  36 AllllgdaalrqgrlaeA 53 
                                        +l+ l++++ ++ +++ A
  gene1044|gene1044|rna1044|rna1044 347 MLFRLALILKQRRDYKSA 364
                                        678888888888888876 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 4.1
                             TPR_16   2 alaraalragdyddAaaaleaal 24 
                                        +la++++ +g  ++ +++l+a l
  gene1044|gene1044|rna1044|rna1044 390 QLAHLHFVQGATTECRKLLNAIL 412
                                        58999999998888888888877 PP

  == domain 3  score: 10.0 bits;  conditional E-value: 0.00048
                             TPR_16   4 araalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrq 47 
                                        +  +++++d     aa+++al  d   +d  eA+++l+++   +
  gene1044|gene1044|rna1044|rna1044 503 GIVYFNLKDVSSSMAAFKRALSID---SDFKEARYNLALVQHIA 543
                                        67899*******************...***********997655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (585 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       776  (0.0432818); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.63u 0.30s 00:00:00.93 Elapsed: 00:00:00.50
# Mc/sec: 3485.42
//
Query:       gene1045|gene1045|rna1045|rna1045  [L=376]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
          8    6.5  13.5         11    6.1  12.5    1.9  1  Eapp_C      E2F-associated phosphoprotein


Domain annotation for each model (and alignments):
>> Eapp_C  E2F-associated phosphoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1  12.5   0.00061        11      63     136 ..     156     225 ..     106     230 .. 0.66

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.00061
                             Eapp_C  63 vlnvkvdkeevlkykeaesekkkkkkkkskkkeekeeeaeaeeaeeeeeeeeeeeesyhpvkCseCstevavld 136
                                        ++n +v kee+++++  ++e++++ ++++k++++k+ee+e+ee++++e   +ee+e+    + + C+ e++v++
  gene1045|gene1045|rna1045|rna1045 156 IVNGEVMKEEIINEE-VMKEENENMNNTRKEEKNKNEEKENEETTNKE---DEETEKKDVGMSNGCKDEISVFN 225
                                        567777777777777.33333333333344434444434433333333...33334444445566777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (376 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2468  (0.137654); expected 358.6 (0.02)
Passed bias filter:                      652  (0.0363657); expected 358.6 (0.02)
Passed Vit filter:                       127  (0.0070835); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.68u 0.32s 00:00:01.00 Elapsed: 00:00:00.47
# Mc/sec: 2386.45
//
Query:       gene1046|gene1046|rna1046|rna1046  [L=34]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (34 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       268  (0.0149478); expected 358.6 (0.02)
Passed bias filter:                      184  (0.0102627); expected 358.6 (0.02)
Passed Vit filter:                         4  (0.000223102); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.30s 00:00:00.65 Elapsed: 00:00:00.46
# Mc/sec: 222.61
//
Query:       gene1047|gene1047|rna1047|rna1047  [L=40]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (40 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       222  (0.0123822); expected 358.6 (0.02)
Passed bias filter:                      163  (0.00909142); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.28s 00:00:00.63 Elapsed: 00:00:00.42
# Mc/sec: 284.34
//
Query:       gene1048|gene1048|rna1048|rna1048  [L=1152]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.063   12.9   0.2       0.35   10.4   0.0    2.3  3  CobU      Cobinamide kinase / cobinamide phosphate guanyltran
       0.14   11.9   2.7         30    4.5   0.0    3.8  4  RICTOR_M  Rapamycin-insensitive companion of mTOR, middle dom
        0.2   11.4   4.7       0.31   10.8   4.7    1.2  1  Collagen  Collagen triple helix repeat (20 copies)
        3.1    7.3   9.7       0.74    9.4   0.1    3.2  4  MMS19_N   Dos2-interacting transcription regulator of RNA-Pol


Domain annotation for each model (and alignments):
>> CobU  Cobinamide kinase / cobinamide phosphate guanyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.0   0.0       2.1   9.5e+03      48      71 ..      83     106 ..      73     114 .. 0.75
   2 ?   -2.9   0.0      0.97   4.4e+03     134     156 ..     785     807 ..     737     812 .. 0.82
   3 ?   10.4   0.0   7.7e-05      0.35      43     153 ..     993    1104 ..     974    1115 .. 0.78

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 2.1
                               CobU  48 erRpaeWetveepldlaealkeee 71 
                                        +r +++++ +ee ++l+  +++++
  gene1048|gene1048|rna1048|rna1048  83 QRKEERYRRIEEDSNLKLEINHDT 106
                                        566889999999999998886655 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 0.97
                               CobU 134 nalgrlfrdllGrlnqrlaaead 156
                                        n + ++fr+++G l + +a+  d
  gene1048|gene1048|rna1048|rna1048 785 NTVNKRFRERIGVLYRCMARWMD 807
                                        56778999999999888887655 PP

  == domain 3  score: 10.4 bits;  conditional E-value: 7.7e-05
                               CobU   43 iarHrerRpaeWetveepldlaealkeeek...kevvLvDcltlwltnllleeeaekveekleeeveellealk 113 
                                         ia H++  +++++t  +++  ++a k++++    ++ L+ c+  +l+n+l +++++   +k + ++ + + +l+
  gene1048|gene1048|rna1048|rna1048  993 IAPHKRINKKKYKTATTNKTNHSAHKKTKRykrISTNLMKCILPVLNNALTQNDKT--LRKHALQLLKYVLHLH 1064
                                         7888888899999988876555555554444347899**************97733..5555556666666778 PP

                               CobU  114 elkatvvlVsnEvglgvvpenalgrlfrdllGrlnqrlaa 153 
                                         +++++++   n   + +  ++++   f +  G   +rl +
  gene1048|gene1048|rna1048|rna1048 1065 AAAEHLIHLFNLFFVNLLCDDEIKEVFDECFGVFVRRLGS 1104
                                         8899999999999999999999999999999998888876 PP

>> RICTOR_M  Rapamycin-insensitive companion of mTOR, middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       0.6   2.7e+03      12      37 ..     231     256 ..     222     263 .. 0.80
   2 ?    4.5   0.0    0.0066        30      18      60 ..     496     538 ..     490     547 .. 0.84
   3 ?   -0.7   0.1      0.28   1.2e+03      61      92 ..     717     750 ..     687     761 .. 0.61
   4 ?    4.3   0.1    0.0076        34      80     102 ..    1037    1059 ..    1026    1061 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.6
                           RICTOR_M  12 kerleetlsrgYfkfiGvlsssknGl 37 
                                        +  l+e  + +Y+k+  +l++ ++ +
  gene1048|gene1048|rna1048|rna1048 231 RVILDEHTTINYLKIARTLCQRAKTI 256
                                        55578889999****99999998866 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.0066
                           RICTOR_M  18 tlsrgYfkfiGvlsssknGlklLekwkiftllyklvelksrdd 60 
                                        +    Y +++Gvl ++++ + ++ +w +  ++  +v+ ++r++
  gene1048|gene1048|rna1048|rna1048 496 KERVMYEELLGVLIEDERCMDVMVDWMMDRVFAAVVQRSKRRC 538
                                        55567889**************************999998655 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.28
                           RICTOR_M  61 llklilssl..dysvdghiRiilskaLtnsseki 92 
                                        l+++++++    +s d  +R++l+++L+n +++ 
  gene1048|gene1048|rna1048|rna1048 717 LCYAVIRKHpqMMSSDALTRTLLKNVLVNIRRDE 750
                                        5555555555556677788888888888766655 PP

  == domain 4  score: 4.3 bits;  conditional E-value: 0.0076
                           RICTOR_M   80 ilskaLtnssekiRlyatkhLrk 102 
                                         +l++aLt++++++R +a+++L+ 
  gene1048|gene1048|rna1048|rna1048 1037 VLNNALTQNDKTLRKHALQLLKY 1059
                                         799****************9985 PP

>> Collagen  Collagen triple helix repeat (20 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   4.7   6.9e-05      0.31      15      52 ..     897     934 ..     884     939 .. 0.43

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 6.9e-05
                                        XXXX-----XXXXEEEE-TTSS---------------- CS
                           Collagen  15 pGkrGepGeaGekGekGpaGekGppGaaGkpGapGekG 52 
                                        +G  G +G+ G+k   G +G++G++G +  +G++G +G
  gene1048|gene1048|rna1048|rna1048 897 NGCVGCDGRVGSKRGVGSEGSEGSKGGEYCNGPNGCNG 934
                                        34444444444444444444444444443344444333 PP

>> MMS19_N  Dos2-interacting transcription regulator of RNA-Pol-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.7     0.021        94      37     117 ..     219     313 ..     185     336 .. 0.67
   2 ?   -1.4   0.1      0.32   1.4e+03      41      71 ..     459     512 ..     434     543 .. 0.56
   3 ?   -3.4   0.0       1.3   5.6e+03      35      83 ..     730     778 ..     712     799 .. 0.51
   4 ?    9.4   0.1   0.00016      0.74       4      56 ..    1038    1087 ..    1036    1104 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.021
                            MMS19_N  37 eeevevLvqFflsrledfavlkealkgllaLlrl...............kkfsaeeavevlralfeevhvqslaqa 97 
                                         ++v+++++F++  + d+ ++ + lk  ++L+++               +++ +++  + l++++  ++   +  +
  gene1048|gene1048|rna1048|rna1048 219 IKHVSTIFDFLTRVILDEHTTINYLKIARTLCQRaktiddlfrtrdesvTTT-ETNGATNLHSIVLYLNHVLHEFK 293
                                        5789999999999999999999999999999955444444444444321222.22233344455556777778888 PP

                            MMS19_N  98 dRklvyelldallekhreal 117
                                        +R ++  l+++l++ h++++
  gene1048|gene1048|rna1048|rna1048 294 HRAEIIALVNTLYDLHSDYF 313
                                        88888888888888777665 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.32
                            MMS19_N  41 evLvqFflsrle.dfavlkealkgllaLlrl......................k 71 
                                        +vLv+ f+ r    f+ ++  ++++++L r+                      +
  gene1048|gene1048|rna1048|rna1048 459 KVLVHLFCARAVhKFDDIALFVHAMHELERVsanfnekervmyeellgvliedE 512
                                        677777777766566667777777777776632333333333333333333333 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 1.3
                            MMS19_N  35 lseeevevLvqFflsrledfavlkealkgllaLlrlkkfsaeeavevlr 83 
                                         s++ +++L++ +l  ++  + + ++++ l ++lr ++++  ++ +v+ 
  gene1048|gene1048|rna1048|rna1048 730 SSDALTRTLLKNVLVNIRRDEPFYACVHLLIKILRSTRVDRRDVLRVAY 778
                                        3334444444444444443333345555555555555555555555444 PP

  == domain 4  score: 9.4 bits;  conditional E-value: 0.00016
                            MMS19_N    4 LgeyLtseddkvRakavslLaevlsrlpkkklseeevevLvqFflsrledfav 56  
                                         L+++Lt++d++ R++a++lL+ vl+ l+  +  e+ ++++  Ff++ l d ++
  gene1048|gene1048|rna1048|rna1048 1038 LNNALTQNDKTLRKHALQLLKYVLH-LH--AAAEHLIHLFNLFFVNLLCDDEI 1087
                                         7889*******************99.44..468999999999*9999998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1136  (0.063361); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.76u 0.29s 00:00:01.05 Elapsed: 00:00:00.43
# Mc/sec: 7998.00
//
Query:       gene1049|gene1049|rna1049|rna1049  [L=585]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-95  311.3  45.4    2.4e-09   37.6   0.1   14.7 15  Sel1      Sel1 repeat
     0.0016   19.0  11.1    1.1e+02    3.7   0.0    8.2  7  TPR_6     Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> Sel1  Sel1 repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.44     4e+03      13      32 ..      16      35 ..      12      40 .. 0.65
   2 !    4.6   0.0    0.0063        57       7      28 ..      47      66 ..      42      66 .. 0.84
   3 !    7.5   0.1   0.00077       6.9      27      38 .]     116     127 ..     113     127 .. 0.88
   4 !   12.6   0.0     2e-05      0.18       1      36 [.     128     161 ..     128     163 .. 0.89
   5 !   21.6   0.1   2.9e-08   0.00026       7      38 .]     170     199 ..     169     199 .. 0.95
   6 !   37.6   0.1   2.6e-13   2.4e-09       2      38 .]     201     235 ..     200     235 .. 0.95
   7 !   31.7   0.6   1.9e-11   1.7e-07       2      38 .]     237     271 ..     236     271 .. 0.95
   8 !   33.4   0.2   5.3e-12   4.7e-08       3      37 ..     274     306 ..     274     307 .. 0.96
   9 !   35.8   0.0   9.7e-13   8.7e-09       1      37 [.     308     342 ..     308     343 .. 0.95
  10 !   25.5   0.0   1.7e-09   1.5e-05       7      36 ..     350     377 ..     348     379 .. 0.92
  11 !   16.3   0.0   1.3e-06     0.012       7      36 ..     386     413 ..     381     415 .. 0.90
  12 !   26.1   0.2   1.1e-09   9.6e-06       1      38 []     416     451 ..     416     451 .. 0.90
  13 !   30.5   0.0   4.6e-11   4.1e-07       3      38 .]     454     487 ..     454     487 .. 0.96
  14 !   32.3   0.2   1.2e-11   1.1e-07       1      38 []     488     523 ..     488     523 .. 0.95
  15 !   18.1   0.5   3.6e-07    0.0032       3      32 ..     526     553 ..     524     555 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.44
                               Sel1 13 ylnGlgvpk..DpekAiewyek 32
                                       +++G  +++  D++ A++ +ek
  gene1049|gene1049|rna1049|rna1049 16 LFFG--IDRdvDESAAVQILEK 35
                                       4555..5663267778887776 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.0063
                               Sel1  7 LGmfylylnGlgvpkDpekAie 28
                                       L    +y++G gv ++++kA++
  gene1049|gene1049|rna1049|rna1049 47 LS--FCYEFGIGVHRNIKKAEY 66
                                       66..899*************87 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.00077
                               Sel1  27 iewyekAAeqGd 38 
                                        + w+ekAA++G+
  gene1049|gene1049|rna1049|rna1049 116 VAWLEKAAKLGN 127
                                        78********97 PP

  == domain 4  score: 12.6 bits;  conditional E-value: 2e-05
                               Sel1   1 aeAmyrLGmfylylnGlgvpkDpekAiewyekAAeq 36 
                                        ++A+y LG   +y++ lgv +  ++ iewy ++A+q
  gene1049|gene1049|rna1049|rna1049 128 SYAQYCLG--TCYHDALGVRRCTKRSIEWYTRSAAQ 161
                                        68******..555********9999*********99 PP

  == domain 5  score: 21.6 bits;  conditional E-value: 2.9e-08
                               Sel1   7 LGmfylylnGlgvpkDpekAiewyekAAeqGd 38 
                                        LG   +yl+G gv+kD+ +A+ +y +AA+++d
  gene1049|gene1049|rna1049|rna1049 170 LG--FCYLEGFGVEKDEYRAFVLYLQAARMND 199
                                        89..999**********************986 PP

  == domain 6  score: 37.6 bits;  conditional E-value: 2.6e-13
                               Sel1   2 eAmyrLGmfylylnGlgvpkDpekAiewyekAAeqGd 38 
                                         A y++G   +y++G+g++k+++ A+ wy++AAe+G+
  gene1049|gene1049|rna1049|rna1049 201 VATYNMG--FCYEEGKGTDKNIKYAFLWYKRAAEMGN 235
                                        699****..999************************7 PP

  == domain 7  score: 31.7 bits;  conditional E-value: 1.9e-11
                               Sel1   2 eAmyrLGmfylylnGlgvpkDpekAiewyekAAeqGd 38 
                                         A++ LG  y+y++Glg++kD++kA+ +y+ +A qG+
  gene1049|gene1049|rna1049|rna1049 237 FAQNSLG--YCYEEGLGTEKDEDKAFALYRASALQGY 271
                                        79*****..**************************96 PP

  == domain 8  score: 33.4 bits;  conditional E-value: 5.3e-12
                               Sel1   3 AmyrLGmfylylnGlgvpkDpekAiewyekAAeqG 37 
                                        A+ +L+  y+++ G gv kD +k +ewye+AA qG
  gene1049|gene1049|rna1049|rna1049 274 AQSNLA--YCFQQGIGVQKDLKKSFEWYERAAIQG 306
                                        899***..************************998 PP

  == domain 9  score: 35.8 bits;  conditional E-value: 9.7e-13
                               Sel1   1 aeAmyrLGmfylylnGlgvpkDpekAiewyekAAeqG 37 
                                        + A+++LG   +y+ G g++k++ +A+ wy++AA+q 
  gene1049|gene1049|rna1049|rna1049 308 SRAQHNLG--HCYHQGMGTDKNVTEAVMWYRRAAKQK 342
                                        57******..*************************97 PP

  == domain 10  score: 25.5 bits;  conditional E-value: 1.7e-09
                               Sel1   7 LGmfylylnGlgvpkDpekAiewyekAAeq 36 
                                        LG   +y+nG gvpkD+++A+++y++AA +
  gene1049|gene1049|rna1049|rna1049 350 LG--NCYQNGEGVPKDEREAVRFYKLAALK 377
                                        89..899*********************76 PP

  == domain 11  score: 16.3 bits;  conditional E-value: 1.3e-06
                               Sel1   7 LGmfylylnGlgvpkDpekAiewyekAAeq 36 
                                        L    +y  Glgv+++  + +++++kAAe+
  gene1049|gene1049|rna1049|rna1049 386 LS--FCYRLGLGVDTNALSSFYYMKKAAEL 413
                                        55..7899********************97 PP

  == domain 12  score: 26.1 bits;  conditional E-value: 1.1e-09
                               Sel1   1 aeAmyrLGmfylylnGlgvpkDpekAiewyekAAeqGd 38 
                                        a+A++ L+ fy  ++G g+++++++Ai wy k+A++++
  gene1049|gene1049|rna1049|rna1049 416 AYAQNCLAFFY--EEGYGTKRNINLAIMWYTKSASANN 451
                                        5788889*777..*********************9875 PP

  == domain 13  score: 30.5 bits;  conditional E-value: 4.6e-11
                               Sel1   3 AmyrLGmfylylnGlgvpkDpekAiewyekAAeqGd 38 
                                        A+ +LG++y  ++G  vp D+ekA++++++AA+qG+
  gene1049|gene1049|rna1049|rna1049 454 AQTNLGTIY--FEGIHVPMDREKAVYYFKLAANQGH 487
                                        899***888..****9999****************9 PP

  == domain 14  score: 32.3 bits;  conditional E-value: 1.2e-11
                               Sel1   1 aeAmyrLGmfylylnGlgvpkDpekAiewyekAAeqGd 38 
                                        + A+ +LG  y+y++G  v k+p+ A+ +y kAAeqG+
  gene1049|gene1049|rna1049|rna1049 488 SRAYSKLG--YCYEEGIVVHKNPSIAFSYYSKAAEQGY 523
                                        57999***..*******9999***************96 PP

  == domain 15  score: 18.1 bits;  conditional E-value: 3.6e-07
                               Sel1   3 AmyrLGmfylylnGlgvpkDpekAiewyek 32 
                                        A+y+LG   +y+ G g+  + ++A+ ++ k
  gene1049|gene1049|rna1049|rna1049 526 AYYALG--KCYERGFGISVNMNQALSYFYK 553
                                        9*****..********************98 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0     0.012   1.1e+02       2      18 ..     202     218 ..     201     223 .. 0.85
   2 ?    3.7   0.1     0.013   1.1e+02       6      24 ..     242     264 ..     241     266 .. 0.89
   3 ?    0.5   0.0      0.13   1.2e+03       2      21 ..     310     333 ..     309     341 .. 0.71
   4 ?    3.2   0.0     0.018   1.6e+02       1      24 [.     345     372 ..     345     376 .. 0.88
   5 ?   -2.2   0.0         1     9e+03       5      24 ..     457     480 ..     454     484 .. 0.67
   6 ?    2.3   0.0     0.035   3.1e+02       2      27 ..     490     519 ..     489     523 .. 0.82
   7 ?    3.3   0.5     0.018   1.6e+02       2      14 ..     526     541 ..     525     574 .. 0.68

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.012
                                        HHHHHHHHHHHHHHHHH CS
                              TPR_6   2 Alyklalsyrklgdtdk 18 
                                        A y+++ +y++++ tdk
  gene1049|gene1049|rna1049|rna1049 202 ATYNMGFCYEEGKGTDK 218
                                        669********988876 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.013
                                        HHHHHHHH....HHHHHHHHHHH CS
                              TPR_6   6 lalsyrkl....gdtdkAleale 24 
                                        l+++y+++    +d dkA ++++
  gene1049|gene1049|rna1049|rna1049 242 LGYCYEEGlgteKDEDKAFALYR 264
                                        79*****669999999**99997 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.13
                                        HHHHHHHHHHH.H...HHHHHHHH CS
                              TPR_6   2 Alyklalsyrk.l...gdtdkAle 21 
                                        A+ +l+ +y + +   ++ ++A+ 
  gene1049|gene1049|rna1049|rna1049 310 AQHNLGHCYHQgMgtdKNVTEAVM 333
                                        7889******95566656667765 PP

  == domain 4  score: 3.2 bits;  conditional E-value: 0.018
                                        HHHHHHHHHHHHH....HHHHHHHHHHH CS
                              TPR_6   1 dAlyklalsyrkl....gdtdkAleale 24 
                                        +A+  l+ +y+++    +d ++A++ ++
  gene1049|gene1049|rna1049|rna1049 345 YAFHSLGNCYQNGegvpKDEREAVRFYK 372
                                        677889******889999999***9986 PP

  == domain 5  score: -2.2 bits;  conditional E-value: 1
                                        HHHHHHHHH...H.HHHHHHHHHH CS
                              TPR_6   5 klalsyrkl...g.dtdkAleale 24 
                                        +l+  y+++     d +kA+ +++
  gene1049|gene1049|rna1049|rna1049 457 NLGTIYFEGihvPmDREKAVYYFK 480
                                        577777776566447777777765 PP

  == domain 6  score: 2.3 bits;  conditional E-value: 0.035
                                        HHHHHHHHHHHH....HHHHHHHHHHHHHH CS
                              TPR_6   2 Alyklalsyrkl....gdtdkAlealerli 27 
                                        A+ kl+++y+++    ++++ A  ++ +  
  gene1049|gene1049|rna1049|rna1049 490 AYSKLGYCYEEGivvhKNPSIAFSYYSKAA 519
                                        5669*******8899999998888888765 PP

  == domain 7  score: 3.3 bits;  conditional E-value: 0.018
                                        HHHHHHHHHHHH...H CS
                              TPR_6   2 Alyklalsyrkl...g 14 
                                        A+y l+++y+++    
  gene1049|gene1049|rna1049|rna1049 526 AYYALGKCYERGfgiS 541
                                        89999***99976662 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (585 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       412  (0.0229795); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.43
# Mc/sec: 4105.21
//
Query:       gene105|gene105|rna105|rna105  [L=218]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.2e-22   77.7   0.6    8.4e-22   77.3   0.6    1.2  1  Cyclin_N  Cyclin, N-terminal domain
  ------ inclusion threshold ------
       0.19   11.5   0.2       0.33   10.7   0.2    1.3  1  DUF1654   Protein of unknown function (DUF1654)


Domain annotation for each model (and alignments):
>> Cyclin_N  Cyclin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.3   0.6   9.4e-26   8.4e-22      27     126 ..      56     157 ..      30     158 .. 0.94

  Alignments for each domain:
  == domain 1  score: 77.3 bits;  conditional E-value: 9.4e-26
                                    -H.HHHHHHHHHHHHHHHHTT--TTHHHHHHHHHHHHHH.HS---CCCHHHHHHHHHHHHHHHHSSS---HHHHHHHTTT CS
                       Cyclin_N  27 np.emRailidwlvevaekfkltpetlflavnyldRfls.kksvpkdklqlvgatcLllAaKveeisppkledlvyitde 104
                                    +  + Ra l+ wl+ev++ fkl+ +t +la++++d +++  + v  d++q  g+ +L+lA+K+ e+++ ++ +++++t++
  gene105|gene105|rna105|rna105  56 HRsTNRAKLLRWLFEVTVDFKLMLDTHILAIRIFDFYVEnMRGVCTDEMQKTGICALFLASKLFEVNVRRACEYACVTGG 135
                                    44489**********************************7789************************************* PP

                                    SS-HHHHHHHHHHHHHHTTT-- CS
                       Cyclin_N 105 afteeeilemErliLetLnfdl 126
                                    a+teee++ mEr iLe Lnf++
  gene105|gene105|rna105|rna105 136 ACTEEEMVSMERMILERLNFEM 157
                                    ********************97 PP

>> DUF1654  Protein of unknown function (DUF1654)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.2   3.6e-05      0.33      21      48 ..     166     193 ..     162     198 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 3.6e-05
                        DUF1654  21 karaavvlrledeseddWerlleeiaet 48 
                                    k + avv+ le+ +  +Wer++ee ++t
  gene105|gene105|rna105|rna105 166 KMKIAVVSVLESTKATEWERVIEEAKKT 193
                                    7899*******************98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       506  (0.0282224); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.35s 00:00:00.96 Elapsed: 00:00:00.58
# Mc/sec: 1140.98
//
Query:       gene1050|gene1050|rna1050|rna1050  [L=39]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (39 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       243  (0.0135535); expected 358.6 (0.02)
Passed bias filter:                      230  (0.0128284); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.33s 00:00:00.80 Elapsed: 00:00:00.53
# Mc/sec: 222.60
//
Query:       gene1051|gene1051|rna1051|rna1051  [L=35]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (35 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       204  (0.0113782); expected 358.6 (0.02)
Passed bias filter:                      137  (0.00764125); expected 358.6 (0.02)
Passed Vit filter:                         2  (0.000111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.30s 00:00:00.65 Elapsed: 00:00:00.45
# Mc/sec: 232.93
//
Query:       gene1052|gene1052|rna1052|rna1052  [L=159]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    0.00054   20.6   0.2    0.00076   20.1   0.2    1.2  1  FliD_N     Flagellar hook-associated protein 2 N-terminus
      0.001   19.3   0.9     0.0016   18.6   0.9    1.2  1  DUF948     Bacterial protein of unknown function (DUF948)
      0.001   18.9   2.2     0.0017   18.2   2.2    1.3  1  DASH_Ask1  DASH complex subunit Ask1
  ------ inclusion threshold ------
       0.03   14.6   0.1      0.049   13.9   0.1    1.3  1  V-SNARE_C  Snare region anchored in the vesicle membrane C-te
      0.043   13.6   0.6      0.069   12.9   0.6    1.3  1  DASH_Duo1  DASH complex subunit Duo1
      0.056   11.7   0.5      0.069   11.4   0.5    1.1  1  COG6       Conserved oligomeric complex COG6
      0.074   12.2   0.2       0.09   12.0   0.2    1.1  1  GLE1       GLE1-like protein


Domain annotation for each model (and alignments):
>> FliD_N  Flagellar hook-associated protein 2 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.2     3e-07   0.00076      14      91 ..       5      82 ..       2      95 .. 0.63

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 3e-07
                                       XXXXXXXXXXXXXXXXXXXXHHHHHHHHHHHHHHHHHHHHHXX.GGGGGXEEEEECST.TTEEEEEETTS-SEEEEEE CS
                             FliD_N 14 kaerakldkleqkktklewkqsayrelnsklsnlksalsalsk.sstfsakkatssde.svvtatassgaaagsysie 89
                                       + e++ +dkleq  +++++  + ++++n+k+++l+++++a+++ ss + +    s+d+ s++    +s+ a+ +y+++
  gene1052|gene1052|rna1052|rna1052  5 ELEEQIIDKLEQIDQTFSSINKVLKDINTKIQQLSQTTTAITTnSSPWLN--FFSTDTpSIAPEDHTSSDATHKYDVS 80
                                       679999******************************88766554666633..22333323332222333333334444 PP

                                       EE CS
                             FliD_N 90 Vk 91
                                       V 
  gene1052|gene1052|rna1052|rna1052 81 VD 82
                                       32 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.9   6.4e-07    0.0016      37      79 ..       5      47 ..       2      51 .. 0.92

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 6.4e-07
                             DUF948 37 elekqvdpilkevedllakvnelledvneklekvdplteavad 79
                                       ele+q+   l++++++ + +n++l+d+n k++++ + t+a+ +
  gene1052|gene1052|rna1052|rna1052  5 ELEEQIIDKLEQIDQTFSSINKVLKDINTKIQQLSQTTTAITT 47
                                       588999999******************************9976 PP

>> DASH_Ask1  DASH complex subunit Ask1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   2.2   6.6e-07    0.0017       4      56 ..       6      57 ..       4      60 .. 0.92

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 6.6e-07
                          DASH_Ask1  4 ldqeitltLqeIDanlsrcfriitkkilPavkrYgeasekiwesakfwksffe 56
                                       l+ +i  +L +ID+ +s +++ + k+i  ++++ ++ +  i+ +++ w +ff 
  gene1052|gene1052|rna1052|rna1052  6 LEEQIIDKLEQIDQTFSSINK-VLKDINTKIQQLSQTTTAITTNSSPWLNFFS 57
                                       899999***********9986.5689**************************6 PP

>> V-SNARE_C  Snare region anchored in the vesicle membrane C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   1.9e-05     0.049      42      65 ..      11      34 ..       8      35 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.9e-05
                          V-SNARE_C 42 rsklhnvanrlgksnsiLrsikrR 65
                                        +kl ++++++  +n++L+ i+++
  gene1052|gene1052|rna1052|rna1052 11 IDKLEQIDQTFSSINKVLKDINTK 34
                                       589*******************98 PP

>> DASH_Duo1  DASH complex subunit Duo1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.6   2.7e-05     0.069       6      40 ..      11      45 ..       6      57 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.7e-05
                          DASH_Duo1  6 leqLrkinevienviesLkkaksniervketvest 40
                                       +++L++i ++++++++ Lk+++++i+++++t++  
  gene1052|gene1052|rna1052|rna1052 11 IDKLEQIDQTFSSINKVLKDINTKIQQLSQTTTAI 45
                                       5799**************************99865 PP

>> COG6  Conserved oligomeric complex COG6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.5   2.7e-05     0.069      25      72 ..       7      47 ..       2      57 .. 0.43

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 2.7e-05
                               COG6 25 ekellkineefleefqpvaeqLkriesdveklnelcdemkkklssake 72
                                       e+++++  e++ + f+ +++ Lk i++++++l+++   ++       +
  gene1052|gene1052|rna1052|rna1052  7 EEQIIDKLEQIDQTFSSINKVLKDINTKIQQLSQTTTAIT-------T 47
                                       3333333333333333333333333333333333333333.......3 PP

>> GLE1  GLE1-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.2   3.5e-05      0.09       6      58 ..       6      58 ..       2      84 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3.5e-05
                               GLE1  6 ikknlleqvkedkelkkllgdlkrkInpkvgQltnsseqlkkitkelkelles 58
                                       +++++++++++  ++ ++++++ + In+k+ Ql+++++ +++ ++   +++++
  gene1052|gene1052|rna1052|rna1052  6 LEEQIIDKLEQIDQTFSSINKVLKDINTKIQQLSQTTTAITTNSSPWLNFFST 58
                                       567888999998899999*******************9999988877777744 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1648  (0.0919181); expected 358.6 (0.02)
Passed bias filter:                     1240  (0.0691617); expected 358.6 (0.02)
Passed Vit filter:                       201  (0.0112109); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.45
# Mc/sec: 1064.08
//
Query:       gene1053|gene1053|rna1053|rna1053  [L=470]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.4e-12   45.8  21.0    8.3e-07   29.1   0.3    4.4  5  ANAPC3        Anaphase-promoting complex, cyclosome, subunit 
    3.4e-11   42.4  17.0       0.13   12.1   0.0    8.2  9  TPR_1         Tetratricopeptide repeat
      7e-09   35.2   5.7      0.084   13.1   0.0    6.8  6  TPR_8         Tetratricopeptide repeat
    1.2e-08   34.4  11.6       0.46   10.7   0.1    8.5  9  TPR_2         Tetratricopeptide repeat
    4.9e-08   33.1   0.2       0.12   13.1   0.0    5.9  6  TPR_6         Tetratricopeptide repeat
    1.4e-06   28.7   2.0       0.14   12.7   0.0    5.3  5  TPR_19        Tetratricopeptide repeat
    2.3e-06   27.8   2.7        4.7    7.6   0.2    6.2  6  TPR_12        Tetratricopeptide repeat
     0.0031   17.5   3.6       0.14   12.2   0.3    2.7  2  SRP_TPR_like  Putative TPR-like repeat
     0.0037   17.2  10.2        5.7    7.2   0.0    6.5  7  TPR_7         Tetratricopeptide repeat
     0.0075   16.1   2.7         20    5.3   0.2    5.2  7  TPR_10        Tetratricopeptide repeat
  ------ inclusion threshold ------
      0.034   13.6   0.5         11    5.6   0.0    3.1  3  SHNi-TPR      SHNi-TPR
      0.056   13.5   0.7         27    4.9   0.0    3.4  4  MIT           MIT (microtubule interacting and transport) dom
      0.066   12.4   0.1          4    6.6   0.0    3.3  3  TPR_15        Tetratricopeptide repeat
       0.88   10.1   6.7         35    5.1   0.0    5.3  5  TPR_17        Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   2.0   2.4e-09   3.1e-06       2      81 ..      12      84 ..      11      85 .. 0.89
   2 ?   -1.7   0.1       2.7   3.4e+03      24      49 ..     109     135 ..      98     147 .. 0.65
   3 ?   -2.4   0.0       4.5   5.7e+03      30      55 ..     201     226 ..     200     253 .. 0.59
   4 ?    0.1   1.7      0.76   9.8e+02      28      62 ..     267     300 ..     235     302 .. 0.85
   5 !   29.1   0.3   6.5e-10   8.3e-07       3      80 ..     309     387 ..     308     389 .. 0.96

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 2.4e-09
                                       TT-HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCTSHHHC-HHHHHHHHHHHHHTT-HHHHHHHH CS
                             ANAPC3  2 qnnyknAiflaerllaaetespedayllAlclylngqykrAyellrkaklnskslgcrylfAqcllkLkkyeeAiaaL 79
                                        +ny  Aif++  +    ++ +   + l+ +ly+n +y+rA+ +l+++    +++   + +A c  ++k+y +Ai+aL
  gene1053|gene1053|rna1053|rna1053 12 YKNYTQAIFVLTHAA---HKEETLKLILGIVLYENREYYRALSILSSF----NTITGMFYAALCHREMKNYADAIDAL 82
                                       5799******99999...6666667778********************....99988899999999***********9 PP

                                       -S CS
                             ANAPC3 80 ek 81
                                        +
  gene1053|gene1053|rna1053|rna1053 83 LH 84
                                       76 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2.7
                                        HHHHH.HHHHHHHTT-HHHHHHHHHCT CS
                             ANAPC3  24 edayl.lAlclylngqykrAyellrka 49 
                                        e++ + l++ + ln+q + A+ ++r++
  gene1053|gene1053|rna1053|rna1053 109 EHVCAlLGELYTLNEQGDDALVYYRRS 135
                                        444441477777777777777777766 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 4.5
                                        HHHHHHTT-HHHHHHHHHCTSHHHC- CS
                             ANAPC3  30 AlclylngqykrAyellrkaklnsks 55 
                                        A +l++ g+  r  + +++  +n+ +
  gene1053|gene1053|rna1053|rna1053 201 ARVLFEHGDVRRSVRCFESVHKNDGT 226
                                        56666677666666666655444333 PP

  == domain 4  score: 0.1 bits;  conditional E-value: 0.76
                                        HHHHHHHHTT-HHHHHHHHHCTSHHHC-HHHHHHH CS
                             ANAPC3  28 llAlclylngqykrAyellrkaklnskslgcrylf 62 
                                        +lA  + l+++++r    l+k+ ln +  +++yl+
  gene1053|gene1053|rna1053|rna1053 267 ALANYFSLRNDHNRSVLCLKKS-LNVRKTAYAYLL 300
                                        37888889999***********.999999999986 PP

  == domain 5  score: 29.1 bits;  conditional E-value: 6.5e-10
                                        T-HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHH CS
                             ANAPC3   3 nnyknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAia 77 
                                        n y+ A +++ r+l+++++++++++  Al++ ++ q + A  ++rka + n++++ +ryl+ + l++ kkye+A++
  gene1053|gene1053|rna1053|rna1053 309 NEYEQAQLFFFRALKMHRNNYNALFGIALVFSKTDQIENADVFFRKAvEVNGHNKVIRYLYVKYLVDNKKYEKAVD 384
                                        78999999999***9************************************************************9 PP

                                        HH- CS
                             ANAPC3  78 aLe 80 
                                        + +
  gene1053|gene1053|rna1053|rna1053 385 VVK 387
                                        976 PP

>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       1.6   2.1e+03      12      21 ..      10      19 ..       7      23 .. 0.83
   2 ?   -0.8   0.0       1.2   1.5e+03       7      21 ..      36      50 ..      35      51 .. 0.89
   3 !    7.8   0.1    0.0023       2.9       8      24 ..      66      82 ..      63      86 .. 0.90
   4 !    9.0   0.1     0.001       1.3       6      28 ..     114     136 ..     111     139 .. 0.89
   5 ?   -3.2   0.0       7.2   9.3e+03      23      28 ..     146     151 ..     146     152 .. 0.76
   6 ?    4.9   0.0      0.02        26       3      29 ..     264     290 ..     262     294 .. 0.91
   7 !   11.7   0.6   0.00014      0.18       1      34 []     295     328 ..     295     328 .. 0.96
   8 !   12.1   0.0    0.0001      0.13       2      34 .]     330     362 ..     329     362 .. 0.93
   9 ?   -0.1   0.0      0.73   9.4e+02      14      22 ..     376     384 ..     373     385 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1.6
                                       HHTT-HHHHH CS
                              TPR_1 12 fklgkydeAl 21
                                       +k ++y +A+
  gene1053|gene1053|rna1053|rna1053 10 LKYKNYTQAI 19
                                       6889999998 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.2
                                       HHHHHHHTT-HHHHH CS
                              TPR_1  7 lGnayfklgkydeAl 21
                                       lG +++++ +y  Al
  gene1053|gene1053|rna1053|rna1053 36 LGIVLYENREYYRAL 50
                                       89999***9999997 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.0023
                                       HHHHHHTT-HHHHHHHH CS
                              TPR_1  8 GnayfklgkydeAleyy 24
                                       +++++++++y +A+++ 
  gene1053|gene1053|rna1053|rna1053 66 ALCHREMKNYADAIDAL 82
                                       79************985 PP

  == domain 4  score: 9.0 bits;  conditional E-value: 0.001
                                        HHHHHHHHTT-HHHHHHHHHHHH CS
                              TPR_1   6 nlGnayfklgkydeAleyyekAL 28 
                                         lG +y  +++ d+Al yy++ +
  gene1053|gene1053|rna1053|rna1053 114 LLGELYTLNEQGDDALVYYRRSV 136
                                        69******************975 PP

  == domain 5  score: -3.2 bits;  conditional E-value: 7.2
                                        HHHHHH CS
                              TPR_1  23 yyekAL 28 
                                        +ye+AL
  gene1053|gene1053|rna1053|rna1053 146 FYERAL 151
                                        599998 PP

  == domain 6  score: 4.9 bits;  conditional E-value: 0.02
                                        HHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                              TPR_1   3 alynlGnayfklgkydeAleyyekALe 29 
                                        +++ l+n +   ++++  + + +k L 
  gene1053|gene1053|rna1053|rna1053 264 TWCALANYFSLRNDHNRSVLCLKKSLN 290
                                        7***********************985 PP

  == domain 7  score: 11.7 bits;  conditional E-value: 0.00014
                                        HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                              TPR_1   1 akalynlGnayfklgkydeAleyyekALelnPnn 34 
                                        a+a+  lG+     ++y++A  ++ +AL+   nn
  gene1053|gene1053|rna1053|rna1053 295 AYAYLLLGHESIIRNEYEQAQLFFFRALKMHRNN 328
                                        78***************************99987 PP

  == domain 8  score: 12.1 bits;  conditional E-value: 0.0001
                                        HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                              TPR_1   2 kalynlGnayfklgkydeAleyyekALelnPnn 34 
                                        +al+++++++ k  + + A  +++kA+e+n +n
  gene1053|gene1053|rna1053|rna1053 330 NALFGIALVFSKTDQIENADVFFRKAVEVNGHN 362
                                        79***************************9765 PP

  == domain 9  score: -0.1 bits;  conditional E-value: 0.73
                                        TT-HHHHHH CS
                              TPR_1  14 lgkydeAle 22 
                                        ++ky++A++
  gene1053|gene1053|rna1053|rna1053 376 NKKYEKAVD 384
                                        799***986 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.1       0.1   1.3e+02       8      28 ..      66      86 ..      63      87 .. 0.89
   2 ?    4.0   0.0     0.057        73       2      30 ..     110     138 ..     109     141 .. 0.91
   3 ?    3.6   0.0     0.077        99       4      31 ..     265     292 ..     263     294 .. 0.91
   4 !    6.5   0.2    0.0086        11       2      31 ..     296     325 ..     295     328 .. 0.89
   5 !   13.1   0.0   6.5e-05     0.084       2      31 ..     330     359 ..     329     362 .. 0.91
   6 ?   -0.1   0.1       1.1   1.5e+03       9      22 ..     371     384 ..     365     388 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.1
                                       HHHHHHTT-HHHHHHHHHHHH CS
                              TPR_8  8 gsiylklgdyeeAkeyyekal 28
                                       +++++++++y  A+ ++ +++
  gene1053|gene1053|rna1053|rna1053 66 ALCHREMKNYADAIDALLHVI 86
                                       68899***********99876 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.057
                                        CHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                              TPR_8   2 eayynlgsiylklgdyeeAkeyyekalel 30 
                                        +++ +lg +y   ++ + A  yy++ + l
  gene1053|gene1053|rna1053|rna1053 110 HVCALLGELYTLNEQGDDALVYYRRSVGL 138
                                        5899********************99987 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.077
                                        HHHHHHHHHHTT-HHHHHHHHHHHHHHH CS
                              TPR_8   4 yynlgsiylklgdyeeAkeyyekaleld 31 
                                        ++ l++  +  +d++ ++ +++k l  +
  gene1053|gene1053|rna1053|rna1053 265 WCALANYFSLRNDHNRSVLCLKKSLNVR 292
                                        999********************99865 PP

  == domain 4  score: 6.5 bits;  conditional E-value: 0.0086
                                        CHHHHHHHHHHHTT-HHHHHHHHHHHHHHH CS
                              TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleld 31 
                                         ay++lg+  +  ++ye+A+ ++ +al++ 
  gene1053|gene1053|rna1053|rna1053 296 YAYLLLGHESIIRNEYEQAQLFFFRALKMH 325
                                        69*********************9999985 PP

  == domain 5  score: 13.1 bits;  conditional E-value: 6.5e-05
                                        CHHHHHHHHHHHTT-HHHHHHHHHHHHHHH CS
                              TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleld 31 
                                         a++ ++++ +k+ ++e+A  +++ka+e +
  gene1053|gene1053|rna1053|rna1053 330 NALFGIALVFSKTDQIENADVFFRKAVEVN 359
                                        68999***********************87 PP

  == domain 6  score: -0.1 bits;  conditional E-value: 1.1
                                        HHHHHTT-HHHHHH CS
                              TPR_8   9 siylklgdyeeAke 22 
                                        + + + ++ye+A+ 
  gene1053|gene1053|rna1053|rna1053 371 KYLVDNKKYEKAVD 384
                                        56788999999986 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.1         2   2.5e+03      12      27 ..      10      25 ..       7      31 .. 0.79
   2 ?    0.4   0.0      0.71     9e+02       7      21 ..      36      50 ..      34      53 .. 0.89
   3 !   10.7   0.1   0.00036      0.46       4      26 ..      62      84 ..      60      87 .. 0.88
   4 ?    3.6   0.1      0.07        89       4      28 ..     112     136 ..     110     139 .. 0.88
   5 ?    4.2   0.0     0.044        56       6      30 ..     199     223 ..     196     227 .. 0.86
   6 ?    1.3   0.0      0.37   4.7e+02       4      29 ..     265     290 ..     263     294 .. 0.91
   7 ?    3.9   0.8     0.057        73       1      34 []     295     328 ..     295     328 .. 0.90
   8 !    6.9   0.0     0.006       7.7       3      33 ..     331     361 ..     329     362 .. 0.92
   9 ?   -1.2   0.0       2.3   2.9e+03      14      22 ..     376     384 ..     372     387 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 2
                              TPR_2 12 yklgdyeeAleafekA 27
                                       +k ++y +A+  +  A
  gene1053|gene1053|rna1053|rna1053 10 LKYKNYTQAIFVLTHA 25
                                       67799****9988877 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.71
                              TPR_2  7 lGlayyklgdyeeAl 21
                                       lG ++y++ +y +Al
  gene1053|gene1053|rna1053|rna1053 36 LGIVLYENREYYRAL 50
                                       899********9997 PP

  == domain 3  score: 10.7 bits;  conditional E-value: 0.00036
                              TPR_2  4 lynlGlayyklgdyeeAleafek 26
                                        ++ +l+++++++y++A++a+  
  gene1053|gene1053|rna1053|rna1053 62 MFYAALCHREMKNYADAIDALLH 84
                                       6999***************9876 PP

  == domain 4  score: 3.6 bits;  conditional E-value: 0.07
                              TPR_2   4 lynlGlayyklgdyeeAleafekAl 28 
                                        +  lG++y  + + ++Al ++++++
  gene1053|gene1053|rna1053|rna1053 112 CALLGELYTLNEQGDDALVYYRRSV 136
                                        6789******************975 PP

  == domain 5  score: 4.2 bits;  conditional E-value: 0.044
                              TPR_2   6 nlGlayyklgdyeeAleafekAlel 30 
                                        n ++++++ gd  + +++fe + + 
  gene1053|gene1053|rna1053|rna1053 199 NAARVLFEHGDVRRSVRCFESVHKN 223
                                        7899***************987765 PP

  == domain 6  score: 1.3 bits;  conditional E-value: 0.37
                              TPR_2   4 lynlGlayyklgdyeeAleafekAle 29 
                                        +++l++    ++d+++ + +++k+l 
  gene1053|gene1053|rna1053|rna1053 265 WCALANYFSLRNDHNRSVLCLKKSLN 290
                                        999********************986 PP

  == domain 7  score: 3.9 bits;  conditional E-value: 0.057
                              TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPnn 34 
                                        a+a+  lG   + +++ye+A  +f +Al+   nn
  gene1053|gene1053|rna1053|rna1053 295 AYAYLLLGHESIIRNEYEQAQLFFFRALKMHRNN 328
                                        689999******************9999987776 PP

  == domain 8  score: 6.9 bits;  conditional E-value: 0.006
                              TPR_2   3 alynlGlayyklgdyeeAleafekAleldPn 33 
                                        al+ ++l+  k ++ e A  +f+kA+e + +
  gene1053|gene1053|rna1053|rna1053 331 ALFGIALVFSKTDQIENADVFFRKAVEVNGH 361
                                        89*************************9866 PP

  == domain 9  score: -1.2 bits;  conditional E-value: 2.3
                              TPR_2  14 lgdyeeAle 22 
                                        +++ye+A++
  gene1053|gene1053|rna1053|rna1053 376 NKKYEKAVD 384
                                        688999875 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       6.1   7.8e+03       6      25 ..      36      55 ..      34      56 .. 0.71
   2 !   13.1   0.0     9e-05      0.12       3      23 ..      62      82 ..      60      87 .. 0.89
   3 ?    0.2   0.0       1.2   1.5e+03       6      25 ..     115     134 ..     114     139 .. 0.83
   4 ?    4.6   0.0     0.046        59       6      29 ..     200     223 ..     199     225 .. 0.90
   5 ?   -0.6   0.1       2.1   2.7e+03       7      23 ..     295     318 ..     293     325 .. 0.58
   6 ?    5.7   0.0      0.02        26       2      28 ..     331     357 ..     330     358 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 6.1
                                       HHHHHHHHHHHHHHHHHHHH CS
                              TPR_6  6 lalsyrklgdtdkAlealer 25
                                       l+  +++  ++ +Al +l +
  gene1053|gene1053|rna1053|rna1053 36 LGIVLYENREYYRALSILSS 55
                                       77777775588899888865 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 9e-05
                                       HHHHHHHHHHHHHHHHHHHHH CS
                              TPR_6  3 lyklalsyrklgdtdkAleal 23
                                       ++++al++r+++++++A++al
  gene1053|gene1053|rna1053|rna1053 62 MFYAALCHREMKNYADAIDAL 82
                                       9******************98 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 1.2
                                        HHHHHHHHHHHHHHHHHHHH CS
                              TPR_6   6 lalsyrklgdtdkAlealer 25 
                                        l+++y    + d+Al +++r
  gene1053|gene1053|rna1053|rna1053 115 LGELYTLNEQGDDALVYYRR 134
                                        799999855999*****998 PP

  == domain 4  score: 4.6 bits;  conditional E-value: 0.046
                                        HHHHHHHHHHHHHHHHHHHHHHHH CS
                              TPR_6   6 lalsyrklgdtdkAlealerlike 29 
                                        +a+ +++ gd +++++ +e++ k+
  gene1053|gene1053|rna1053|rna1053 200 AARVLFEHGDVRRSVRCFESVHKN 223
                                        79999**88***********9987 PP

  == domain 5  score: -0.6 bits;  conditional E-value: 2.1
                                        HHHHHHH.......HHHHHHHHHH CS
                              TPR_6   7 alsyrkl.......gdtdkAleal 23 
                                        a++y+ l       +++++A   +
  gene1053|gene1053|rna1053|rna1053 295 AYAYLLLghesiirNEYEQAQLFF 318
                                        555655434444445888887655 PP

  == domain 6  score: 5.7 bits;  conditional E-value: 0.02
                                        HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              TPR_6   2 AlyklalsyrklgdtdkAlealerlik 28 
                                        Al+ +al + k+++ ++A   +++ ++
  gene1053|gene1053|rna1053|rna1053 331 ALFGIALVFSKTDQIENADVFFRKAVE 357
                                        9**********99*********99875 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0     0.031        39       2      49 ..      10      54 ..       9      56 .. 0.88
   2 ?    1.3   0.1       0.4   5.1e+02      32      49 ..      66      83 ..      60      93 .. 0.77
   3 ?    0.8   0.2      0.55   7.1e+02      20      44 ..     101     128 ..      69     134 .. 0.52
   4 ?    5.1   0.0     0.025        32       4      44 ..     308     348 ..     305     351 .. 0.91
   5 !   12.7   0.0   0.00011      0.14       7      50 ..     345     388 ..     342     389 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.031
                             TPR_19  2 laegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLd 49
                                       l+ ++y++A+  l+ a   + k + ++l L ++l+++ ++  A  +L+
  gene1053|gene1053|rna1053|rna1053 10 LKYKNYTQAIFVLTHA---AHKEETLKLILGIVLYENREYYRALSILS 54
                                       77899**********9...77899999999******999999999886 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.4
                             TPR_19 32 AeallalgqldeAealLd 49
                                       A ++ +++++++A+++L 
  gene1053|gene1053|rna1053|rna1053 66 ALCHREMKNYADAIDALL 83
                                       678888899999988875 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.55
                             TPR_19  20 e...dpknaearllLAeallalgqldeA 44 
                                        +   d +++ + +lL e++  + q d+A
  gene1053|gene1053|rna1053|rna1053 101 DyvlDGNSEHVCALLGELYTLNEQGDDA 128
                                        1344556666666667777777666666 PP

  == domain 4  score: 5.1 bits;  conditional E-value: 0.025
                             TPR_19   4 egdyaeAlalleqalqedpknaearllLAeallalgqldeA 44 
                                        ++ y++A+ ++ +al+   +n +a+ + A +  ++ q++ A
  gene1053|gene1053|rna1053|rna1053 308 RNEYEQAQLFFFRALKMHRNNYNALFGIALVFSKTDQIENA 348
                                        6789***999999******************9999999987 PP

  == domain 5  score: 12.7 bits;  conditional E-value: 0.00011
                             TPR_19   7 yaeAlalleqalqedpknaearllLAeallalgqldeAealLda 50 
                                         ++A  ++++a + + +n  +r+l+++ l+ ++ +++A ++++a
  gene1053|gene1053|rna1053|rna1053 345 IENADVFFRKAVEVNGHNKVIRYLYVKYLVDNKKYEKAVDVVKA 388
                                        6677789*******************************999876 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.2    0.0037       4.7      43      71 ..      57      85 ..      30      89 .. 0.77
   2 ?    4.9   0.0     0.025        32       9      31 ..     115     137 ..     110     141 .. 0.64
   3 ?   -1.9   0.0       3.3   4.2e+03      50      71 ..     199     220 ..     198     224 .. 0.75
   4 ?    4.7   0.0      0.03        38      47      76 ..     264     293 ..     258     294 .. 0.91
   5 ?    2.1   0.2      0.18   2.3e+02      44      76 ..     294     326 ..     292     327 .. 0.85
   6 ?    1.4   0.0      0.31     4e+02      46      73 ..     330     357 ..     329     359 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0037
                             TPR_12 43 ltattlrnLgrlyralgryeeAlelleea 71
                                       +t+t ++  + ++r++++y++A+++l ++
  gene1053|gene1053|rna1053|rna1053 57 NTITGMFYAALCHREMKNYADAIDALLHV 85
                                       57777778888888888888888887665 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.025
                             TPR_12   9 laavlrrlgrydeAlellekale 31 
                                        l+++++  ++ d+Al ++++++ 
  gene1053|gene1053|rna1053|rna1053 115 LGELYTLNEQGDDALVYYRRSVG 137
                                        66667667777777777766654 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 3.3
                             TPR_12  50 nLgrlyralgryeeAlelleea 71 
                                        n +r++++ g+ +  ++ +e +
  gene1053|gene1053|rna1053|rna1053 199 NAARVLFEHGDVRRSVRCFESV 220
                                        6788888888888888877765 PP

  == domain 4  score: 4.7 bits;  conditional E-value: 0.03
                             TPR_12  47 tlrnLgrlyralgryeeAlelleealaiae 76 
                                        t ++L+ ++++++++   +  l+++l++++
  gene1053|gene1053|rna1053|rna1053 264 TWCALANYFSLRNDHNRSVLCLKKSLNVRK 293
                                        67899*********************9987 PP

  == domain 5  score: 2.1 bits;  conditional E-value: 0.18
                             TPR_12  44 tattlrnLgrlyralgryeeAlelleealaiae 76 
                                        ta ++  Lg     +++ye+A+ ++ +al++ +
  gene1053|gene1053|rna1053|rna1053 294 TAYAYLLLGHESIIRNEYEQAQLFFFRALKMHR 326
                                        7778888888888899*************9987 PP

  == domain 6  score: 1.4 bits;  conditional E-value: 0.31
                             TPR_12  46 ttlrnLgrlyralgryeeAlelleeala 73 
                                        ++l++++ +++++++ e A  ++++a++
  gene1053|gene1053|rna1053|rna1053 330 NALFGIALVFSKTDQIENADVFFRKAVE 357
                                        5899999999999999999999999987 PP

>> SRP_TPR_like  Putative TPR-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.3   0.00011      0.14      57     101 ..      11      56 ..       3      92 .. 0.74
   2 ?    5.4   0.2     0.013        17      20      77 ..     333     395 ..     302     407 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00011
                       SRP_TPR_like  57 klkkykkalkilkkveaee.kvkvlksqvlYrlgsyekAYklLske 101
                                        k k+y++a  +l ++  +e  +k ++  vlY  ++y +A ++Ls  
  gene1053|gene1053|rna1053|rna1053  11 KYKNYTQAIFVLTHAAHKEeTLKLILGIVLYENREYYRALSILSSF 56 
                                        6677888888887777666577777888888888888887777654 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.013
                       SRP_TPR_like  20 kvvali..klekyeeaLkllkkgsalsedvrfEk.aYvlYkl..kkykkalkilkkveaeekv 77 
                                          +al+  k ++ e+a  + +k+ +++++ ++ +  Yv Y +  kky+ka+ ++k + ++e++
  gene1053|gene1053|rna1053|rna1053 333 FGIALVfsKTDQIENADVFFRKAVEVNGHNKVIRyLYVKYLVdnKKYEKAVDVVKAMYGVEGC 395
                                        4444443367888888888888888888877654269999754489*********99988754 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0      0.18   2.3e+02       5      22 ..      65      82 ..      62      93 .. 0.83
   2 ?    2.3   0.1      0.16   2.1e+02       2      25 ..     112     135 ..     111     141 .. 0.88
   3 ?   -3.0   0.0       7.9     1e+04      21      29 ..     146     152 ..     144     154 .. 0.70
   4 ?    1.4   0.0      0.31     4e+02       4      24 ..     199     219 ..     198     244 .. 0.85
   5 !    7.2   0.0    0.0045       5.7       1      30 [.     264     293 ..     264     296 .. 0.91
   6 ?    3.9   0.0     0.049        63      12      34 ..     308     330 ..     302     332 .. 0.87
   7 ?   -2.7   0.0       6.5   8.4e+03      14      22 ..     378     386 ..     377     393 .. 0.74

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.18
                              TPR_7  5 LarlysrlGdyeeAiely 22
                                        a +++++ +y++Ai+ +
  gene1053|gene1053|rna1053|rna1053 65 AALCHREMKNYADAIDAL 82
                                       57899**********876 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.16
                              TPR_7   2 LlnLarlysrlGdyeeAielyeqs 25 
                                        +  L++ly    + ++A+ +y++s
  gene1053|gene1053|rna1053|rna1053 112 CALLGELYTLNEQGDDALVYYRRS 135
                                        7889******999********996 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 7.9
                              TPR_7  21 lyeqsLalt 29 
                                        +ye+  al+
  gene1053|gene1053|rna1053|rna1053 146 FYER--ALD 152
                                        7999..554 PP

  == domain 4  score: 1.4 bits;  conditional E-value: 0.31
                              TPR_7   4 nLarlysrlGdyeeAielyeq 24 
                                        n ar+ ++ Gd ++ ++++e 
  gene1053|gene1053|rna1053|rna1053 199 NAARVLFEHGDVRRSVRCFES 219
                                        779999999**********97 PP

  == domain 5  score: 7.2 bits;  conditional E-value: 0.0045
                              TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLaltk 30 
                                        ++++La+ +s ++d+ + + ++++sL ++k
  gene1053|gene1053|rna1053|rna1053 264 TWCALANYFSLRNDHNRSVLCLKKSLNVRK 293
                                        699*********************998776 PP

  == domain 6  score: 3.9 bits;  conditional E-value: 0.049
                              TPR_7  12 lGdyeeAielyeqsLaltkdped 34 
                                        +++ye+A  ++ ++L +++  ++
  gene1053|gene1053|rna1053|rna1053 308 RNEYEQAQLFFFRALKMHRNNYN 330
                                        589************99998776 PP

  == domain 7  score: -2.7 bits;  conditional E-value: 6.5
                              TPR_7  14 dyeeAiely 22 
                                        +ye+A+++ 
  gene1053|gene1053|rna1053|rna1053 378 KYEKAVDVV 386
                                        589998765 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.1       0.7   8.9e+02       8      24 ..      36      52 ..      36      53 .. 0.89
   2 ?   -1.7   0.0       2.3     3e+03      12      29 ..      69      86 ..      68      87 .. 0.82
   3 ?    5.3   0.2     0.015        20       8      32 ..     115     139 ..     112     140 .. 0.92
   4 ?   -1.6   0.0       2.2   2.8e+03       7      26 ..     199     218 ..     198     220 .. 0.85
   5 ?    4.8   0.0     0.022        28       8      35 ..     268     295 ..     267     298 .. 0.94
   6 ?   -1.1   0.0       1.5   1.9e+03       1      33 [.     294     326 ..     294     327 .. 0.76
   7 ?   -3.2   0.0       6.9   8.8e+03      11      30 ..     338     357 ..     335     358 .. 0.75

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.7
                             TPR_10  8 LanalrqrgrydeAeal 24
                                       L+++l++ ++y +A+ +
  gene1053|gene1053|rna1053|rna1053 36 LGIVLYENREYYRALSI 52
                                       8**********999876 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2.3
                             TPR_10 12 lrqrgrydeAealleeal 29
                                       +r++++y++A + l +++
  gene1053|gene1053|rna1053|rna1053 69 HREMKNYADAIDALLHVI 86
                                       68999*****98877766 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.015
                             TPR_10   8 LanalrqrgrydeAealleealair 32 
                                        L+ +++   ++d+A+ ++++++ ++
  gene1053|gene1053|rna1053|rna1053 115 LGELYTLNEQGDDALVYYRRSVGLY 139
                                        8999****************99776 PP

  == domain 4  score: -1.6 bits;  conditional E-value: 2.2
                             TPR_10   7 NLanalrqrgrydeAealle 26 
                                        N a++l++ g+  ++++ +e
  gene1053|gene1053|rna1053|rna1053 199 NAARVLFEHGDVRRSVRCFE 218
                                        88999999999999998887 PP

  == domain 5  score: 4.8 bits;  conditional E-value: 0.022
                             TPR_10   8 LanalrqrgrydeAealleealairrrl 35 
                                        Lan+ + r+++++++  l+++l++r+ +
  gene1053|gene1053|rna1053|rna1053 268 LANYFSLRNDHNRSVLCLKKSLNVRKTA 295
                                        9999*********************987 PP

  == domain 6  score: -1.1 bits;  conditional E-value: 1.5
                             TPR_10   1 tAsslnNLanalrqrgrydeAealleealairr 33 
                                        tA ++  L++    r++y++A  ++ +al ++r
  gene1053|gene1053|rna1053|rna1053 294 TAYAYLLLGHESIIRNEYEQAQLFFFRALKMHR 326
                                        667777777777779999999888888888876 PP

  == domain 7  score: -3.2 bits;  conditional E-value: 6.9
                             TPR_10  11 alrqrgrydeAealleeala 30 
                                        + +++ + + A  ++++a++
  gene1053|gene1053|rna1053|rna1053 338 VFSKTDQIENADVFFRKAVE 357
                                        55667788899999999997 PP

>> SHNi-TPR  SHNi-TPR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       5.7   7.3e+03      16      21 ..      14      19 ..      13      19 .. 0.88
   2 ?    5.6   0.0    0.0083        11       3      31 ..     111     139 ..     110     143 .. 0.92
   3 ?    5.0   0.1     0.013        17       1      36 [.     295     330 ..     295     332 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 5.7
                           SHNi-TPR 16 nFpqAv 21
                                       n++qA+
  gene1053|gene1053|rna1053|rna1053 14 NYTQAI 19
                                       9***97 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0083
                           SHNi-TPR   3 vydlLGEislEnenFpqAveDlrkaLeLr 31 
                                        v+ lLGE+   ne+ ++A+  +r+++ L+
  gene1053|gene1053|rna1053|rna1053 111 VCALLGELYTLNEQGDDALVYYRRSVGLY 139
                                        789**********************9876 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.013
                           SHNi-TPR   1 AdvydlLGEislEnenFpqAveDlrkaLeLreqllp 36 
                                        A+ y+lLG  s+ ++ ++qA+  + +aL+  +++++
  gene1053|gene1053|rna1053|rna1053 295 AYAYLLLGHESIIRNEYEQAQLFFFRALKMHRNNYN 330
                                        899*****************9888888888777777 PP

>> MIT  MIT (microtubule interacting and transport) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.1     0.023        29      24      48 ..      12      34 ..       4      40 .. 0.78
   2 ?    4.9   0.0     0.021        27      25      50 ..      73      96 ..      72     103 .. 0.73
   3 ?   -2.1   0.0       3.4   4.3e+03      21      33 ..     126     138 ..     122     144 .. 0.80
   4 ?   -3.3   0.0       7.8     1e+04      18      25 ..     377     384 ..     376     386 .. 0.58

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.023
                                MIT 24 lelYkealelLlqalkekneerrel 48
                                       +++Y++a+ +L++a +  +ee+ +l
  gene1053|gene1053|rna1053|rna1053 12 YKNYTQAIFVLTHAAH--KEETLKL 34
                                       678************9..5555555 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.021
                                MIT 25 elYkealelLlqalkekneerrellr 50
                                       ++Y +a++ Ll++++   +  +++l 
  gene1053|gene1053|rna1053|rna1053 73 KNYADAIDALLHVIN--GDAPKDTLD 96
                                       78************9..444555555 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 3.4
                                MIT  21 eeAlelYkealel 33 
                                        ++Al +Y+ +++l
  gene1053|gene1053|rna1053|rna1053 126 DDALVYYRRSVGL 138
                                        789*****99987 PP

  == domain 4  score: -3.3 bits;  conditional E-value: 7.8
                                MIT  18 gnyeeAle 25 
                                        ++ye+A++
  gene1053|gene1053|rna1053|rna1053 377 KKYEKAVD 384
                                        56666654 PP

>> TPR_15  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0      0.11   1.4e+02      10      38 ..      30      59 ..      22      97 .. 0.75
   2 ?   -0.6   0.0      0.47   6.1e+02     144     174 ..     107     137 ..      60     140 .. 0.67
   3 ?    6.6   0.0    0.0031         4     148     205 ..     331     388 ..     197     393 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.11
                             TPR_15 10 ealkl..atllykqgdvkkAlevLkeaaqka 38
                                       e lkl    +ly+++++ +Al++L +  +++
  gene1053|gene1053|rna1053|rna1053 30 ETLKLilGIVLYENREYYRALSIL-SSFNTI 59
                                       4454445889**************.667776 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.47
                             TPR_15 144 qsaafllaraelyrqegqtdaAlrdyreAla 174
                                        +s+ + ++++ely+ + q d+Al  yr+ + 
  gene1053|gene1053|rna1053|rna1053 107 NSEHVCALLGELYTLNEQGDDALVYYRRSVG 137
                                        5777778888888888888888888888775 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.0031
                             TPR_15 148 fllaraelyrqegqtdaAlrdyreAlalapdsselraallWlliDlgrraeLrellka 205
                                         l+  a + ++++q ++A   +r+A+++++ ++ +r  ++ +l+D ++++++  ++ka
  gene1053|gene1053|rna1053|rna1053 331 ALFGIALVFSKTDQIENADVFFRKAVEVNGHNKVIRYLYVKYLVDNKKYEKAVDVVKA 388
                                        56677888999**************************************998777765 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.1       5.2   6.7e+03      19      32 ..     115     128 ..     113     134 .. 0.65
   2 ?    1.7   0.0      0.32   4.1e+02      14      31 ..     263     280 ..     251     282 .. 0.84
   3 ?   -1.0   0.1       2.3     3e+03      19      33 ..     296     315 ..     294     315 .. 0.68
   4 ?    5.1   0.0     0.027        35       4      30 ..     320     346 ..     317     349 .. 0.87
   5 ?    1.9   0.0      0.28   3.6e+02       2      33 ..     352     383 ..     351     384 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 5.2
                             TPR_17  19 LAelllknGdlmtA 32 
                                        L+el+  n + ++A
  gene1053|gene1053|rna1053|rna1053 115 LGELYTLNEQGDDA 128
                                        77777766654444 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.32
                             TPR_17  14 daynnLAelllknGdlmt 31 
                                        + ++ LA++++ ++d+ +
  gene1053|gene1053|rna1053|rna1053 263 VTWCALANYFSLRNDHNR 280
                                        57*********9999865 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 2.3
                             TPR_17  19 LAelll.....knGdlmtAr 33 
                                        +A+lll      ++++++A+
  gene1053|gene1053|rna1053|rna1053 296 YAYLLLghesiIRNEYEQAQ 315
                                        56666666666888888886 PP

  == domain 4  score: 5.1 bits;  conditional E-value: 0.027
                             TPR_17   4 kaleldPnnadaynnLAelllknGdlm 30 
                                        +al+ + nn +a++  A +++k  + +
  gene1053|gene1053|rna1053|rna1053 320 RALKMHRNNYNALFGIALVFSKTDQIE 346
                                        89*****************99988766 PP

  == domain 5  score: 1.9 bits;  conditional E-value: 0.28
                             TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtAr 33 
                                        ++ka+e +  n +  +++ ++l  n+++++A+
  gene1053|gene1053|rna1053|rna1053 352 FRKAVEVNGHNKVIRYLYVKYLVDNKKYEKAV 383
                                        899*************************9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (470 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       564  (0.0314574); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.56u 0.26s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 3105.86
//
Query:       gene1054|gene1054|rna1054|rna1054  [L=299]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.3e-10   39.5   1.5    6.2e-10   38.9   1.5    1.2  1  UTP15_C   UTP15 C terminal


Domain annotation for each model (and alignments):
>> UTP15_C  UTP15 C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.9   1.5   3.5e-14   6.2e-10       5     145 ..     160     290 ..     156     292 .. 0.88

  Alignments for each domain:
  == domain 1  score: 38.9 bits;  conditional E-value: 3.5e-14
                            UTP15_C   5 eeadivieekkkkklkkydklLrkfryskALdavlekkvekspevvvtlleeLrhRgalraALagrdeeslepiLk 80 
                                        +e  ++i +k  k  ++y+++L++ +y+++L +vl +    ++  v  +l+ L   g l++A+ +r+ ++l     
  gene1054|gene1054|rna1054|rna1054 160 NEHPVLILRKPFKTYSQYEQMLNSHEYRRCLTTVLTT----NNGLVHRILHHLHVHGVLKQAIFKRNVRQLC---V 228
                                        444555666778999**********************....88***********************988876...5 PP

                            UTP15_C  81 fllkhitdpryvsllvdvanvlldlyseklgqseeldelvkrLkrkvreevelakellelkGmle 145
                                        +l+khi+d++  s+ ++++ ++  ++++ l      +++++r++r+vr+e  ++ke ++   ++e
  gene1054|gene1054|rna1054|rna1054 229 YLCKHIGDVSLKSIALKALVIISTVFERMLVVD---RRMLRRIRRAVRHEEYVQKECIRAYASIE 290
                                        78********************99999999555...799*****************999877776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1100  (0.0613531); expected 358.6 (0.02)
Passed bias filter:                      245  (0.013665); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1957.34
//
Query:       gene1055|gene1055|rna1055|rna1055  [L=358]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    0.00082   18.8   0.0      0.012   15.0   0.0    2.1  2  WD40_like  WD40-like domain
     0.0035   18.2   4.0       0.69   10.9   0.1    3.2  3  WD40       WD domain, G-beta repeat


Domain annotation for each model (and alignments):
>> WD40_like  WD40-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0      0.01        94      21      71 ..      62     112 ..      58     123 .. 0.79
   2 !   15.0   0.0   1.3e-06     0.012      35     173 ..     114     248 ..     108     280 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.01
                          WD40_like  21 ddkctvlkleslesvsivesfedSvifvklldddlilvvtlDGtillslle 71 
                                        d++ t+  +   ++   ++  +  v  v+l+++  +l ++ DGt++   le
  gene1055|gene1055|rna1055|rna1055  62 DHTGTIKLFTDTHILKQFTYHRARVNAVRLIEGRCVLSCSDDGTVVWNELE 112
                                        56667777777777777777888899999999***********99777665 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 1.3e-06
                          WD40_like  35 vsivesfedSvifvklldddlilvvtlDGtillslleneeevenekieedistvkviddklliGtnkGsiyvfskd 110
                                        v ++++ +d v  v  ld+  ++ ++lDG il ++l+++  v    ++  +   +  d+ +++ t +G i  fs  
  gene1055|gene1055|rna1055|rna1055 114 VRVLTGHNDYVRAV-CLDECAVVSGALDGCILVHDLRESAPVARYAMDAPVLHLESSDGVVYVSTPTG-ITRFSVA 187
                                        55555555555433.57777888999*****************************************9.8889998 PP

                          WD40_like 111 lqleevllgqsseIkeikiennkiysLsesafivfdlfsqnieykisvkdiktfeiienkdil 173
                                         q   + +  +  ++++ + n+ +y+ +  a+ v+d   ++    +   +   + ++ n ++l
  gene1055|gene1055|rna1055|rna1055 188 -QRAALRSTVNYGVNDLRVCNGLVYACAARALTVYDRNLEEVFFCRFKDESAGLACV-NGEVL 248
                                        .89999999999***********************9876554443333334445555.55555 PP

>> WD40  WD domain, G-beta repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.1      0.76   6.9e+03      11      16 ..      47      52 ..      26      70 .. 0.47
   2 !    7.4   0.1   0.00099       8.9       7      34 ..      79     106 ..      73     109 .. 0.66
   3 !   10.9   0.1   7.7e-05      0.69       3      37 ..     113     146 ..     111     147 .. 0.72

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.76
                                       SSEEEE CS
                               WD40 11 ssvtsl 16
                                       s++t++
  gene1055|gene1055|rna1055|rna1055 47 SPITAM 52
                                       225555 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.00099
                                        EESS.SSEEEEEEETTSSE.....EEEEETTSEE CS
                               WD40   7 ltGH.ssvtslafspdgaw.....lasGsdDgtv 34 
                                        +t H   v+++      ++     ++s+sdDgtv
  gene1055|gene1055|rna1055|rna1055  79 FTYHrARVNAV------RLiegrcVLSCSDDGTV 106
                                        55565557766......5544444679**9***9 PP

  == domain 3  score: 10.9 bits;  conditional E-value: 7.7e-05
                                        EEEEEESSSS.EEEEEEETTSSE....EEEEETTSEEEEE CS
                               WD40   3 clrtltGHss.vtslafspdgaw....lasGsdDgtvriW 37 
                                         +r+ltGH++ v+++       +    ++sG  Dg + + 
  gene1055|gene1055|rna1055|rna1055 113 SVRVLTGHNDyVRAV------CLdecaVVSGALDGCILVH 146
                                        689*****7778766......333344889999**99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (358 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       345  (0.0192426); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 2400.36
//
Query:       gene1056|gene1056|rna1056|rna1056  [L=146]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.7e-16   59.4   0.6    4.6e-16   59.1   0.6    1.3  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    1.1e-09   38.6   0.7    1.8e-09   37.9   0.7    1.3  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
    1.4e-09   38.0   0.1      2e-09   37.5   0.1    1.2  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    7.6e-07   29.0   0.1    1.4e-06   28.1   0.1    1.4  1  FR47             FR47-like protein
      8e-06   26.0   0.0    1.2e-05   25.4   0.0    1.3  1  Acetyltransf_9   Acetyltransferase (GNAT) domain
    1.6e-05   24.9   0.2    3.4e-05   23.9   0.1    1.6  2  Acetyltransf_CG  GCN5-related N-acetyl-transferase
  ------ inclusion threshold ------
      0.018   14.6   0.0      0.021   14.4   0.0    1.3  1  GNAT_acetyltran  GNAT acetyltransferase
      0.056   13.8   0.0        2.6    8.5   0.0    2.1  2  Phage_BR0599     Phage conserved hypothetical protein BR0599


Domain annotation for each model (and alignments):
>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.1   0.6   2.1e-19   4.6e-16      34     117 .]      49     134 ..       5     134 .. 0.85

  Alignments for each domain:
  == domain 1  score: 59.1 bits;  conditional E-value: 2.1e-19
                                        EEEEEEET..TEEEEEEEEEEEET...TSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHTTESEEEEEEETT CS
                     Acetyltransf_1  34 gllvaeed..geliGfisllkipd...ekggvayieslaVspeyrgkGlGsaLlealeerareegikkivlaveed 104
                                         +lv++++  ++++G+++++  +        v++ie+++V +e+rg+GlG +L++ l+e+a+e+g++k  la++e 
  gene1056|gene1056|rna1056|rna1056  49 VILVVLKNgcDRVLGCATVFFEYKfihGLSVVGHIEDVVVEEEHRGQGLGGMLVNRLVEIAKERGCYKTILACSER 124
                                        445577775777***************44789**********************************8878999999 PP

                                        EHHHHHHHHH.TTE CS
                     Acetyltransf_1 105 ndaairlYek.lGF 117
                                        n   +r+Y k  GF
  gene1056|gene1056|rna1056|rna1056 125 N---VRFY-KgIGF 134
                                        9...****.88999 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.9   0.7     8e-13   1.8e-09       5      76 .]      50     136 ..      45     136 .. 0.75

  Alignments for each domain:
  == domain 1  score: 37.9 bits;  conditional E-value: 8e-13
                                        EEEEEET..TEEEEEEEEEEES.........TCTEEEEE-GGGTTSSHHHHHHH.H.TT...SEEEEEEEEE..TH CS
                     Acetyltransf_7   5 vfVaedd..gkivGfialslld.........aeitrlaVdpeyrgkGiGraLle.a.ae...kgiileqlel..na 62 
                                        ++V+ ++  ++++G++ +  +          ++i+ ++V +e+rg+G+G  L++ + ++   +g+  +   l  ++
  gene1056|gene1056|rna1056|rna1056  50 ILVVLKNgcDRVLGCATVFFEYkfihglsvvGHIEDVVVEEEHRGQGLGGMLVNrLvEIakeRGCYKT--ILacSE 123
                                        566666668889999888888788888888778888*****************963522456887533..333333 PP

                                        HHHHHHHHHTTEEE CS
                     Acetyltransf_7  63 ekaikfYeklGFee 76 
                                         ++++fY+  GFee
  gene1056|gene1056|rna1056|rna1056 124 -RNVRFYKGIGFEE 136
                                        .78*********96 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.5   0.1   8.8e-13     2e-09      23     112 ..      40     140 ..      24     143 .. 0.84

  Alignments for each domain:
  == domain 1  score: 37.5 bits;  conditional E-value: 8.8e-13
                    Acetyltransf_10  23 rerieegealllvaeeg..gkivGviel.rdgs.........hisllfVdpeyrgqGigkaLleaveeeaekdgik 86 
                                        +  ++++++++lv+ ++  ++++G++++  + +         hi+ ++V++e+rgqG+g +L++++ e a+++g  
  gene1056|gene1056|rna1056|rna1056  40 TTLMDKKDYVILVVLKNgcDRVLGCATVfFEYKfihglsvvgHIEDVVVEEEHRGQGLGGMLVNRLVEIAKERGCY 115
                                        455677888777777776778999998887777788888999****************************888776 PP

                    Acetyltransf_10  87 leltvnaspyavpfYeklGFkavgee 112
                                         ++ +  s   v+fY+ +GF++ ++e
  gene1056|gene1056|rna1056|rna1056 116 -KTILACSERNVRFYKGIGFEEKEKE 140
                                        .99999999************98765 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.1   6.4e-10   1.4e-06      21      83 ..      80     140 ..      74     143 .. 0.85

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 6.4e-10
                                        TSSEEEEEE-GGG-SSSHHHHHHHHHHHHHHHS-S-EEEEEETT-HHHHHHHHHHT-EEEEEE CS
                               FR47  21 ggelgalqvlpehrrrGlgsrlvkalakeiaergktvllvvvasNtpsirlyeklGfekieet 83 
                                        +g +  + v++ehr++Glg+ lv+ l +   erg   ++++    ++  r+y+ +Gfe+ e++
  gene1056|gene1056|rna1056|rna1056  80 VGHIEDVVVEEEHRGQGLGGMLVNRLVEIAKERGCYKTILACS--ERNVRFYKGIGFEEKEKE 140
                                        599999********************98777799877776554..46689********99776 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.0   5.4e-09   1.2e-05       4     126 ..       7     135 ..       4     136 .. 0.72

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 5.4e-09
                                        EE-GGG....HHHHHHHHHHHTT----H..HHHHHHHHHHTTSEEEEEEE....TTEEEEEEEEEEEEEEE.TTEE CS
                     Acetyltransf_9   4 elteed....ldevlellkyaFqdeespleeireyfrklleesrvlgaed....ngelvgqlallplelnv.pGkt 70 
                                        el+e+d    +++vl+ l ++ q++++ +    + +  l+++++++++       +++ g+++++ +e ++ +G  
  gene1056|gene1056|rna1056|rna1056   7 ELREQDfdnnFPQVLSGLTTVGQVDKHSA---LQLYTTLMDKKDYVILVVlkngCDRVLGCATVF-FEYKFiHG-L 77 
                                        55555533336677777777777666663...477777777776555444445556777777776.45555155.4 PP

                                        EEEEEEEEEEE-CCGTTS-HHHHHHHHHHHHHHHTT--EEEE--SS..HHHHHTTT-E CS
                     Acetyltransf_9  71 lkaagvtgVavapehrgrgvlskLlaraleemreegqplsllfPss..ipiYrrfGye 126
                                          ++ + +V v  ehrg+g+   L++r++e ++e+g   ++l  s+  +++Y+  G+e
  gene1056|gene1056|rna1056|rna1056  78 SVVGHIEDVVVEEEHRGQGLGGMLVNRLVEIAKERGCYKTILACSErnVRFYKGIGFE 135
                                        4489**************************************9965337*******98 PP

>> Acetyltransf_CG  GCN5-related N-acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.1   1.5e-08   3.4e-05      24      65 ..      80     122 ..      63     125 .. 0.84
   2 ?   -3.0   0.0       3.8   8.5e+03      17      29 ..     134     145 ..     131     145 .. 0.76

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 1.5e-08
                    Acetyltransf_CG  24 vldfthTeVpeelrGkGiAkkLvkaalddareegl.kvvptCs 65 
                                        v +++ ++V+ee+rG+G+++ Lv++ ++ a+e+g  k ++ Cs
  gene1056|gene1056|rna1056|rna1056  80 VGHIEDVVVEEEHRGQGLGGMLVNRLVEIAKERGCyKTILACS 122
                                        4578899**************************9658888886 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 3.8
                    Acetyltransf_CG  17 Yevrkegvldfth 29 
                                        +e +ke++++++h
  gene1056|gene1056|rna1056|rna1056 134 FE-EKEKEMAMYH 145
                                        66.7788999998 PP

>> GNAT_acetyltran  GNAT acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   9.5e-06     0.021     182     238 ..      82     138 ..      28     143 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 9.5e-06
                    GNAT_acetyltran 182 ieieidTkedyrrkgLAtivaaalileclkrglyPsWDaaneaSvaLaekLGYefek 238
                                        +  ++  +e++r++gL  ++ ++l++ + +rg y    a +e  v+ ++ +G+e ++
  gene1056|gene1056|rna1056|rna1056  82 HIEDVVVEEEHRGQGLGGMLVNRLVEIAKERGCYKTILACSERNVRFYKGIGFEEKE 138
                                        4458999******************************9***************9876 PP

>> Phage_BR0599  Phage conserved hypothetical protein BR0599
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.0    0.0011       2.6      22      57 ..      27      62 ..      19      74 .. 0.80
   2 ?    3.2   0.0      0.05   1.1e+02      51      72 ..     112     131 ..     101     136 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0011
                       Phage_BR0599 22 ikshraarqltLweplpaalaagdavrltaGCdkrl 57
                                       + + ++++ l+L ++l+ +      v l  GCd+ l
  gene1056|gene1056|rna1056|rna1056 27 VGQVDKHSALQLYTTLMDKKDYVILVVLKNGCDRVL 62
                                       44444477*************************865 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.05
                       Phage_BR0599  51 aGCdkrletCrakFnNavnFrG 72 
                                         GC k++ +C+++  N   ++G
  gene1056|gene1056|rna1056|rna1056 112 RGCYKTILACSER--NVRFYKG 131
                                        7**********98..6666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       393  (0.0219198); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1016.98
//
Query:       gene1057|gene1057|rna1057|rna1057  [L=360]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    5.4e-18   65.0   0.8    1.2e-17   63.9   0.8    1.6  1  Forkhead   Forkhead domain
  ------ inclusion threshold ------
      0.038   14.5   5.0      0.064   13.7   5.0    1.4  1  AbiJ_NTD4  AbiJ N-terminal domain 4


Domain annotation for each model (and alignments):
>> Forkhead  Forkhead domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.9   0.8   1.4e-21   1.2e-17       6      86 ..     119     198 ..     117     199 .. 0.93

  Alignments for each domain:
  == domain 1  score: 63.9 bits;  conditional E-value: 1.4e-21
                                        -HHHHHHHHHHT-TTT-B-HHHHHHHHHCC-HHHHCC.-CCHHHHHHHHHHHHC--EEETT.-TTSS--EEE--TT CS
                           Forkhead   6 sYaaLIaqAiksspekkltLseIyefieenfpyyrtaakkgWqnSirhnLslnkcFekvpreeeegkgslwtidpe 81 
                                         Y +L ++ i+ss ek+l+LseIy+ + + +++  + ++++W+nSir  Ls +k+F k+p++ ++g+g +w+i+ +
  gene1057|gene1057|rna1057|rna1057 119 EYKKLLVEIILSSAEKRLSLSEIYQKLLSDYNFSTE-KNASWKNSIRCVLSESKIFYKIPKKIKRGRGGYWCINGK 193
                                        599******************************999.59*********************988889*******988 PP

                                        HHHHH CS
                           Forkhead  82 seekf 86 
                                        + +k+
  gene1057|gene1057|rna1057|rna1057 194 ELAKM 198
                                        77765 PP

>> AbiJ_NTD4  AbiJ N-terminal domain 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   5.0   7.1e-06     0.064       3     120 ..     114     247 ..     113     299 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 7.1e-06
                          AbiJ_NTD4   3 FSeRygykpi.eelqvesidkrlrnqlwnileellwkyydegkkpeeqgkkewte.lhkllaee............ 64 
                                        F  R++yk+   e++  s++krl   l  i+++ll +y ++     ++++++w++ ++  l+e             
  gene1057|gene1057|rna1057|rna1057 114 FTVRKEYKKLlVEIILSSAEKRLS--LSEIYQKLLSDYNFS-----TEKNASWKNsIRCVLSESkifykipkkikr 182
                                        889*******988********998..777777777777765.....444555555533333333111112333365 PP

                          AbiJ_NTD4  65 .......lgldelpedtteawkeienyffkcewyevyDfiEfvfrnredqeaeaneslere..ee 120
                                               ++ +el +  +e+ k++e+ ff++ +y+++ ++  +++++  q+++ +e+ e+   ++
  gene1057|gene1057|rna1057|rna1057 183 grggywcINGKELAKMDEESIKKCEKRFFDSFIYDRINVVYTAIDLIRGQQDKHKENIEAYkkSQ 247
                                        57777777777777788899999*******99999766666666666655555555443334433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (360 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       755  (0.0421105); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2561.57
//
Query:       gene1058|gene1058|rna1058|rna1058  [L=212]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
       0.15   12.8   0.2       0.35   11.6   0.2    1.6  1  Acetyltransf_5  Acetyltransferase (GNAT) domain


Domain annotation for each model (and alignments):
>> Acetyltransf_5  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.2     2e-05      0.35      19      66 ..       4      50 ..       1      64 [. 0.76

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2e-05
                     Acetyltransf_5 19 peldiDefDavcdhllvideaeevVGtyRllrpdeaerlegfysesef 66
                                       +eldiD++D   d l ++d++e +V  +  +++++++++e++  +s  
  gene1058|gene1058|rna1058|rna1058  4 QELDIDDYDIDRDELHIMDNRE-IVDICKNFLQTNSQEIEEVHVQSSH 50
                                       46********************.******8888888866544444333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (212 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       827  (0.0461264); expected 358.6 (0.02)
Passed bias filter:                      542  (0.0302304); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1542.57
//
Query:       gene1059|gene1059|rna1059|rna1059  [L=746]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.029   14.1   0.6        2.4    7.9   0.1    2.7  2  HydF_tetramer  Hydrogen maturase F tetramerization domain
        5.2    7.3   7.6        2.5    8.3   0.8    3.1  3  CxC1           CxC1 like cysteine cluster associated with KDZ


Domain annotation for each model (and alignments):
>> HydF_tetramer  Hydrogen maturase F tetramerization domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.1    0.0065        58      16      49 ..     168     201 ..     161     225 .. 0.84
   2 ?    7.9   0.1   0.00027       2.4       9      76 ..     603     669 ..     596     682 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.0065
                                        T-EEEEE-----------TTTTHHHHHHHHHH-- CS
                      HydF_tetramer  16 gdkvliaEaCtHhrqkdDigrvkiPkllkkktgk 49 
                                        ++ ++i E+C+  + k+  g+  iPk+l++  + 
  gene1059|gene1059|rna1059|rna1059 168 NNALVINENCALVKVKNCTGNIIIPKILREDHNL 201
                                        567899**********************998765 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.00027
                                        TSTT--TT-EEEEE-----------TTTTHHHHHHHHHH----EEEEE--SS--HHHTT-SEEEE-TT CS
                      HydF_tetramer   9 aleelkdgdkvliaEaCtHhrqkdDigrvkiPkllkkktgkelefevaagrefpeeleeyklvihCgg 76 
                                        +l ++ +g+ +++  + + + +kdD+     P+ lk+ + k++e ++++g  + ee ee+++ i C g
  gene1059|gene1059|rna1059|rna1059 603 KLPRIVNGQWIYLDSNMSNEYSKDDVPDCIFPNSLKTIVCKKIEHNYSSGLIIGEECEELSI-ISCTG 669
                                        5667778888888888899999***********************************99985.67876 PP

>> CxC1  CxC1 like cysteine cluster associated with KDZ transposases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.8   0.00028       2.5      13      57 ..      13      59 ..       3      62 .. 0.84
   2 ?    1.6   0.1     0.035   3.1e+02      38      60 ..     145     167 ..     117     172 .. 0.75
   3 ?   -2.2   0.1      0.53   4.7e+03      16      54 ..     269     306 ..     259     312 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00028
                               CxC1 13 s.kckceeekktkrtvdlvdllgqkr.ekvefCkCtpdavrllalGy 57
                                          ckc+ + + +  ++ ++l++ k+ e ++ C+ +p+++rl++ Gy
  gene1059|gene1059|rna1059|rna1059 13 AsYCKCRISLIISTFIEKLELVNCKKiEAIDKCQRMPRVLRLINIGY 59
                                       338*************9999887666599*****************9 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.035
                               CxC1  38 ekvefCkCtpdavrllalGylas 60 
                                         + +fC+C  +   l+++  +a+
  gene1059|gene1059|rna1059|rna1059 145 IEQNFCNCSLKYKLLIQNIIIAG 167
                                        6789*****99999998888777 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 0.53
                               CxC1  16 kceeekktkrtvdlvdllgqkrekvefCkCtpdavrlla 54 
                                        +c+  ++ ++++++ d + + r++  +Ck  ++ + +++
  gene1059|gene1059|rna1059|rna1059 269 NCDI-NIYRQVIEVNDNIIKLRTSNVVCKPSTEKIFVVK 306
                                        4444.4578899999999999999999998888877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (746 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       606  (0.0338); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.63u 0.26s 00:00:00.89 Elapsed: 00:00:00.44
# Mc/sec: 5102.41
//
Query:       gene106|gene106|rna106|rna106  [L=67]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.019   15.1   0.6      0.026   14.7   0.6    1.2  1  XhlA             Haemolysin XhlA
       0.04   14.5   0.1      0.044   14.3   0.1    1.1  1  Anti-adapt_IraP  Sigma-S stabilisation anti-adaptor protein
       0.15   11.7   0.0       0.15   11.7   0.0    2.2  3  Nup54_57_C       NUP57/Nup54 C-terminal domain


Domain annotation for each model (and alignments):
>> XhlA  Haemolysin XhlA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.6   4.3e-06     0.026       1      45 [.      23      67 .]      23      67 .] 0.95

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 4.3e-06
                           XhlA  1 eikerlerietkldnleervdkleekaaeaeekiknleedlkkle 45
                                   ei e ++ri +k d+l+++  +le  ++e+e+  k  + +++ ++
  gene106|gene106|rna106|rna106 23 EINEIITRIAGKMDKLMMEEGDLESLKREFESIRKDFNGTINHIK 67
                                   799***************7799********************996 PP

>> Anti-adapt_IraP  Sigma-S stabilisation anti-adaptor protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1   7.4e-06     0.044      28      82 ..       7      63 ..       3      67 .] 0.78

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 7.4e-06
                Anti-adapt_IraP 28 alelllsallltlskekvqeliesvekainsales..sdevlksdaeLLlkqinrll 82
                                      +++ a+ ++  k++++e+i  + +++++   +    e lk+++e ++k +n  +
  gene106|gene106|rna106|rna106  7 IKKIFIMAMESSYRKKEINEIITRIAGKMDKLMMEegDLESLKREFESIRKDFNGTI 63
                                   5689**************************987762234566777777777777655 PP

>> Nup54_57_C  NUP57/Nup54 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.1      0.85   5.1e+03       4       7 ..       7      10 ..       5      11 .. 0.69
   2 ?   -1.7   0.2      0.37   2.2e+03      19      25 ..      21      27 ..      21      28 .. 0.82
   3 ?   11.7   0.0   2.5e-05      0.15      15      29 .]      45      59 ..      42      59 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 0.85
                     Nup54_57_C  4 aKKI 7 
                                    KKI
  gene106|gene106|rna106|rna106  7 IKKI 10
                                   4787 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.37
                     Nup54_57_C 19 kKElEsi 25
                                   kKE+ +i
  gene106|gene106|rna106|rna106 21 KKEINEI 27
                                   8999876 PP

  == domain 3  score: 11.7 bits;  conditional E-value: 2.5e-05
                     Nup54_57_C 15 LqHLkKElEsikkDy 29
                                   L  Lk+E Esi+kD+
  gene106|gene106|rna106|rna106 45 LESLKREFESIRKDF 59
                                   678***********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (67 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       936  (0.0522059); expected 358.6 (0.02)
Passed bias filter:                      538  (0.0300073); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 531.15
//
Query:       gene1060|gene1060|rna1060|rna1060  [L=2764]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (2764 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       629  (0.0350828); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 1.18u 0.31s 00:00:01.49 Elapsed: 00:00:00.51
# Mc/sec: 16338.50
//
Query:       gene1061|gene1061|rna1061|rna1061  [L=61]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       401  (0.022366); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.47
# Mc/sec: 394.10
//
Query:       gene1062|gene1062|rna1062|rna1062  [L=250]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    8.5e-63  212.3  10.1    2.5e-62  210.8  10.1    1.6  1  Kinesin      Kinesin motor domain
      1e-09   38.5   1.0    1.6e-09   37.8   0.1    1.8  2  Microtub_bd  Microtubule binding


Domain annotation for each model (and alignments):
>> Kinesin  Kinesin motor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  210.8  10.1   2.8e-66   2.5e-62      85     332 ..      18     235 ..      16     236 .. 0.92

  Alignments for each domain:
  == domain 1  score: 210.8 bits;  conditional E-value: 2.8e-66
                                        TSSHHHHHTBCTTTSBSHHHHHHHHHHHHHHHCTTTHEEEEEEEEEEEEEETTEEEETTSTTTTSTSSEBEEEECT CS
                            Kinesin  85 gsGKTyTmegkeeeeeGiipraleelFesikkekeekekefsvkvsylEiYneeiyDLLeskkskkkkklkireds 160
                                        g+GKTyTm g+ +++ G+ipra++++++++++      ++f++++ + EiYne++ DL+++++        ++ ++
  gene1062|gene1062|rna1062|rna1062  18 GAGKTYTMLGD-NKSLGLIPRAVNSIYDELDE------TNFTLELRITEIYNEKMKDLISNDN--------VKGNE 78 
                                        9*********8.999***************76......4699******************982........22333 PP

                                        TSCCEEETTS--EEESSHHHHHHHHHHHHHHHTSTTSSCTSHHCCSEEEEEEEEEEEETTTTTCEEEEEEEEEEEE CS
                            Kinesin 161 kkgevyvkgltevevksaeevlellekgeknrkvaetklneeSSRSHavftitleqknlkeeteekvkisklnLvD 236
                                                + t+v ++s +e++++++k+ k r++++t++n+ SSRSH++++++l+ +++ e+       s ln++D
  gene1062|gene1062|rna1062|rna1062  79 L-------ETTSVVIRSKDEIMSYINKSIKYRATESTDCNAFSSRSHSIYSLKLKVRTKGET-----IESMLNFID 142
                                        3.......357899*****************************************9986644.....469****** PP

                                        EEECCCHHHHSSTCHHHHHHHHHHHHHHHHHHHHHHHHHHTCCTSTSCGGGSHHHHHTGGGHSSSSEEEEEEEE-T CS
                            Kinesin 237 LAGsErasktgaaegerlkEaaniNkSLlaLgrvisaLaekkkskhipYRdSkLTrlLqdsLgGnsktlmivtvsp 312
                                        LAGsEr+++++  eg+rlkE++niNkSLl L+ v +++ +k  +kh+pYRdSkLT lL++sL+ +sk+lm+++vs 
  gene1062|gene1062|rna1062|rna1062 143 LAGSERIKESHV-EGKRLKETQNINKSLLSLKIVFNSIINK--EKHVPYRDSKLTYLLKSSLENKSKVLMLLNVSL 215
                                        ***********6.8999************************..********************************* PP

                                        BGGGHHHHHHHHHHHHHHCT CS
                            Kinesin 313 ssenleetlstlkfaerake 332
                                        ++++++etl++l+f++ ++ 
  gene1062|gene1062|rna1062|rna1062 216 DDKDYNETLCSLRFGQVVNA 235
                                        ***************98875 PP

>> Microtub_bd  Microtubule binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.8   0.1   1.8e-13   1.6e-09      84     149 .]       8      69 ..       1      69 [. 0.87
   2 ?   -2.1   0.1      0.37   3.3e+03      54      62 ..     176     184 ..     127     217 .. 0.62

  Alignments for each domain:
  == domain 1  score: 37.8 bits;  conditional E-value: 1.8e-13
                                        EEEEE.EES................ST-HCHHHHHHHHHHCCTSCCCCEEEEEEEEEEESS-EEETT CS
                        Microtub_bd  84 vcifa.ygqTGsGKtyTmegeeeeagmipraveeifetiselkekgwkyeielqfveiynekvqDlL 149
                                        +++f+ + + G+GKtyTm g++++ g iprav++i++++ e+     ++++el++ eiynek++Dl+
  gene1062|gene1062|rna1062|rna1062   8 MSVFSpMVKRGAGKTYTMLGDNKSLGLIPRAVNSIYDELDET-----NFTLELRITEIYNEKMKDLI 69 
                                        5666534566****************************9999.....9*****************96 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.37
                                        -SEEEECTT CS
                        Microtub_bd  54 Fdrvfeses 62 
                                        F+ ++++e+
  gene1062|gene1062|rna1062|rna1062 176 FNSIINKEK 184
                                        333444333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       882  (0.049194); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.49
# Mc/sec: 1549.37
//
Query:       gene1063|gene1063|rna1063|rna1063  [L=90]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       355  (0.0198003); expected 358.6 (0.02)
Passed bias filter:                      244  (0.0136092); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 614.06
//
Query:       gene1064|gene1064|rna1064|rna1064  [L=724]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0021   17.2   1.5        1.3    8.0   0.0    2.3  2  Coatomer_WDAD  Coatomer WD associated region


Domain annotation for each model (and alignments):
>> Coatomer_WDAD  Coatomer WD associated region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.0     7e-05       1.3      88     159 ..     195     268 ..     179     292 .. 0.77
   2 !    7.8   0.3     8e-05       1.4     118     171 ..     580     634 ..     563     679 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 7e-05
                                        XXXXXX.XXXXXXXXXXXXXXXXXXXXXX....XXXXXXXXXX.XXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXX CS
                      Coatomer_WDAD  88 sksvkifknfkekktksikleyqvdkifg....GalLgvksegsvsfYDweqgklvrr.idvkkvknVvwsddgel 158
                                        ++ v+++   +++ +k  + ++qv+++ +    G++ + + +g+++fYD+++g +v r +dv    +V w d+  +
  gene1064|gene1064|rna1064|rna1064 195 TGLVTLLCLKTGEFVKMAQFDVQVRDVCAdlesGMVAVCDVKGVLHFYDVKTGVVVDRmVDVC---RVEWVDEFWV 267
                                        555666555555566778888888888888888***********************8724555...4777766655 PP

                                        X CS
                      Coatomer_WDAD 159 v 159
                                        v
  gene1064|gene1064|rna1064|rna1064 268 V 268
                                        5 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 8e-05
                                        XXXXXXXXX.XXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXX CS
                      Coatomer_WDAD 118 alLgvksegsvsfYDweqgklvrridvkk.vknVvwsddgelvalvskdtvyils 171
                                        ++L+++  + v++ D+e+++lv +i  ++ +++   s d + v lv ++   +++
  gene1064|gene1064|rna1064|rna1064 580 NVLVMRYAKKVVLIDIENQSLVDEILFNDeIRDMCISSDFKRVGLVFERYAAVYE 634
                                        7899999999****************9988****************876655554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (724 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       443  (0.0247086); expected 358.6 (0.02)
Passed bias filter:                      263  (0.014669); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.64u 0.24s 00:00:00.88 Elapsed: 00:00:00.45
# Mc/sec: 4832.74
//
Query:       gene1065|gene1065|rna1065|rna1065  [L=226]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.3e-09   36.6   0.0    5.8e-09   35.8   0.0    1.4  1  tRNA_anti-codon  OB-fold nucleic acid binding domain
    0.00087   19.9   0.2     0.0021   18.7   0.2    1.7  1  RPA_C            Replication protein A C terminal


Domain annotation for each model (and alignments):
>> tRNA_anti-codon  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.8   0.0   6.5e-13   5.8e-09       2      74 ..      52     123 ..      51     125 .. 0.91

  Alignments for each domain:
  == domain 1  score: 35.8 bits;  conditional E-value: 6.5e-13
                                        EEEEEEEEEEEEEETTEEEEEEEETTEEEEEEEET..HHHHHHHTTS-TTSEEEEEEEEEECTTSSEEEEEEEEE CS
                    tRNA_anti-codon   2 tvaGrvtsisdrsggkvifidlrDgtgriqvvlfr..eeatklaenlkeGdvvrvtGrvkrrpggelelkveeie 74 
                                        +vaG+v+s+  r+ ++   + l+Dgt++i++++++     +++a  +++  ++rv G v+ ++g  ++++v+ ++
  gene1065|gene1065|rna1065|rna1065  52 CVAGWVRST--RQAQSGTIFLLDDGTAMINASFWPngLFEEEQAGLIEPSNFLRVIGNVRVYDGD-ISVSVSFLT 123
                                        69*******..7777778889**************98888999999****************999.***998776 PP

>> RPA_C  Replication protein A C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.2   2.3e-07    0.0021      47      99 ..     163     216 ..     145     226 .] 0.77

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 2.3e-07
                                        SXHHHHHHHHHHHH.SXSTTTEEHHHHHHHS..TSXHHHHHHHHHHHHHTTSEEE CS
                              RPA_C  47 ltalaqqvlnlikqspeseeGvhvdeiaqkl..rlsvndvkqavdeLsneGiiYs 99 
                                           l++ vl   ++  ++e+G+hvd + + l  +  ++dv++ v++L+++ +++s
  gene1065|gene1065|rna1065|rna1065 163 TGTLQEDVLMCYRN-NQDEKGLHVDLVVKMLqgKYKEQDVREMVNSLLDDCYLFS 216
                                        34567778877777.79**************999*************99866665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       510  (0.0284455); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1571.05
//
Query:       gene1066|gene1066|rna1066|rna1066  [L=471]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.4e-07   30.1   5.2    1.8e-06   28.4   2.3    2.9  3  AAA              ATPase family associated with various cellul
    1.2e-05   25.6   0.6    5.2e-05   23.5   0.6    1.9  1  AAA_22           AAA domain
    4.1e-05   24.0   0.0     0.0007   20.0   0.0    2.1  1  AAA_16           AAA ATPase domain
    0.00033   20.5   0.2       0.14   11.9   0.0    2.5  2  Viral_helicase1  Viral (Superfamily 1) RNA helicase
     0.0016   18.5   0.7     0.0064   16.5   0.7    2.1  1  ResIII           Type III restriction enzyme, res subunit
     0.0085   16.4   0.8       0.57   10.5   0.0    2.6  3  AAA_19           AAA domain
  ------ inclusion threshold ------
      0.021   14.8   4.6       0.85    9.5   4.6    2.6  1  ATPase_2         ATPase domain predominantly from Archaea
      0.025   14.5   0.2        5.6    6.9   0.0    2.5  2  NACHT            NACHT domain
       0.22   11.2   2.2        7.3    6.2   0.3    2.3  2  CaKB             Calcium-activated potassium channel, beta su


Domain annotation for each model (and alignments):
>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0         2     4e+03      85     105 ..      28      47 ..      22      50 .. 0.71
   2 !   28.4   2.3   9.1e-10   1.8e-06       1     131 [.      48     234 ..      48     235 .. 0.88
   3 ?   -2.2   0.0       2.6   5.2e+03      70      70 ..     402     402 ..     359     429 .. 0.58

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 2
                                        HHHHHHHHHHHTTTSSSTEEE CS
                                AAA  85 vvnqLlteldgvkkkeskviv 105
                                         +n Llt +++++++ +k  v
  gene1066|gene1066|rna1066|rna1066  28 EQNMLLTYIKDFQTN-GKGHV 47 
                                        5899********996.33333 PP

  == domain 2  score: 28.4 bits;  conditional E-value: 9.1e-10
                                        EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSS....................................... CS
                                AAA   1 vllyGppGtGKTllakavakelgvefleisgsellsk....................................... 37 
                                        ++++G pG GKT+++     +++   + +++ +l +k                                       
  gene1066|gene1066|rna1066|rna1066  48 IYISGVPGSGKTYTVINTLLHCNK-AFYFNCGSLKNKstffkrlyglvnsgtgmtgckyvvnggnsvknrlydien 122
                                        5799*********99998888865.5567888888888899999999999999999999999999999******** PP

                                        .............................STTHHHHHHHHHHHHHHHTS..TSEEEEEETGGGHHHHHTTCCCHHH CS
                                AAA  38 .............................yvgesekkirelfkeakeka..kpsilfiDEidalaksrsgseseee 82 
                                                                        +s k++++ f+     +  +  il+iDEid l +++        
  gene1066|gene1066|rna1066|rna1066 123 vknkldnvenegnkclvsnkkttstnvtyRNTNSRKRTKQPFTMSNLTSklTNRILIIDEIDYLLTRN-------- 190
                                        ***********************999996556778888888887544446677***************........ PP

                                        HHHHHHHHHHHHHTTTSSSTEEEEEEESS...GGGSTHHHHSTTSSEEEETT CS
                                AAA  83 ervvnqLlteldgvkkkeskvivigatnr...pdkldpallrgRfdrkieie 131
                                           + +L+t ++  ++    +++i+++n+    +kld ++  +R+d  i++e
  gene1066|gene1066|rna1066|rna1066 191 ---QHVLYTLFEMKTH----TLLICISNTmafTNKLDGKIT-SRIDFFINFE 234
                                        ...*********9999....79*******88889*******.9****99986 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 2.6
                                        H CS
                                AAA  70 l 70 
                                        l
  gene1066|gene1066|rna1066|rna1066 402 L 402
                                        2 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.6   2.6e-08   5.2e-05       5     112 ..      45     197 ..      41     216 .. 0.80

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 2.6e-08
                             AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelka.......... 70 
                                          ++++ G +G+GKT+++ + l            + + +++++ s+++ ++++++l   +++++            
  gene1066|gene1066|rna1066|rna1066  45 GHVIYISGVPGSGKTYTVINTLLH----------CNKAFYFNCGSLKNKSTFFKRLYGLVNSGTGMtgckyvvngg 110
                                        5689***********999888886..........99*************************98888********** PP

                             AAA_22  71 .............................................erlsseellealeqalraravielliiDEaq 101
                                                                                     +r+++++ +++ +  ++ +   ++liiDE++
  gene1066|gene1066|rna1066|rna1066 111 nsvknrlydienvknkldnvenegnkclvsnkkttstnvtyrntnSRKRTKQPFTMSNLTSKLT--NRILIIDEID 184
                                        ******************************9999999988875444444444444333333333..67******** PP

                             AAA_22 102 hlr..seealeeL 112
                                        +l   ++ +l +L
  gene1066|gene1066|rna1066|rna1066 185 YLLtrNQHVLYTL 197
                                        *654434444444 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   3.5e-07    0.0007       5     163 ..      25     202 ..      22     209 .. 0.58

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 3.5e-07
                             AAA_16   5 ReeeleqLlsalervrsgrp.elvllsGesGvGKsslv.rellralekdggiflrgkcdqlesaipysalaqalar 78 
                                        R +e+++Ll+++++  +++  +++++sG +G+GK+  v ++ll + +k+    ++ +c +l+ +   s++ + l  
  gene1066|gene1066|rna1066|rna1066  25 RVHEQNMLLTYIKDFQTNGKgHVIYISGVPGSGKTYTViNTLL-HCNKA----FYFNCGSLKNK---STFFKRL-Y 91 
                                        567899999***966666666**************98878888.89998....66666666322...3344444.2 PP

                             AAA_16  79 eellrqllde.....................aesaeleawrekleeala................avpelagaea. 116
                                         +l++    +                              + kl                           +    
  gene1066|gene1066|rna1066|rna1066  92 -GLVNSGTGMtgckyvvnggnsvknrlydieN-------VKNKL----DnvenegnkclvsnkktT-----STNVt 150
                                        .4444444446666666655444422222221.......22222....133334444444333331.....22225 PP

                             AAA_16 117 ....srllellkrll.allsrderplvlvlDdlqwadeaslqllaaLlrlle 163
                                            ++  ++ + +  + l+++    +l++D+++ + +  +++l++L++  +
  gene1066|gene1066|rna1066|rna1066 151 yrntNSRKRTKQPFTmSNLTSKLTNRILIIDEIDYLLTRNQHVLYTLFEMKT 202
                                        5555444455455554333333334899999999999999999999988755 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.0   6.9e-05      0.14       1      22 [.      48      69 ..      48      96 .. 0.76
   2 !    6.0   0.1    0.0042       8.5      40      71 ..     151     183 ..     123     206 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 6.9e-05
                    Viral_helicase1  1 ivvhGvpGcGKStlirkllrts 22
                                       i+++GvpG+GK+  + + l ++
  gene1066|gene1066|rna1066|rna1066 48 IYISGVPGSGKTYTVINTLLHC 69
                                       679*********8887777663 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0042
                    Viral_helicase1  40 pklpnlsvrtvdsflmalvks.tkgkililDEy 71 
                                         +++n++ rt + f+m+++ s  +++ili+DE+
  gene1066|gene1066|rna1066|rna1066 151 YRNTNSRKRTKQPFTMSNLTSkLTNRILIIDEI 183
                                        567899999999999999999988********8 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.7   3.2e-06    0.0064       5     140 ..      25     182 ..      21     212 .. 0.66

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 3.2e-06
                                        -HHHHHHHHHHT......TTSEEE.EEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHH...HHGGG CS
                             ResIII   5 reyQeeaienlleklkskrdkrgl.ikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtl...eefkk 76 
                                        r ++++++   ++ ++ +++ +++ i    G+GKT++ +++  ++ k+++  ++  l ++ +  ++++   +  + 
  gene1066|gene1066|rna1066|rna1066  25 RVHEQNMLLTYIKDFQTNGKGHVIyISGVPGSGKTYTVINTLLHCNKAFYF-NCGSLKNKSTFFKRLYglvNSGTG 99 
                                        6688899999999999899988887**********************9875.777777777777777744444444 PP

                                        GTGG...............GEEEESSS-B--..............-SEEEEEHHHHHHTH................ CS
                             ResIII  77 flseayke...........igkkvsgdkkka.......kekdstnkkilvttiqsldadseee...........ee 123
                                        ++ ++y                        +        + +++ +k lv++ ++ + + + +             
  gene1066|gene1066|rna1066|rna1066 100 MTGCKYVVnggnsvknrlyD----------IenvknklDNVENEGNKCLVSNKKTTSTNVTYRntnsrkrtkqpFT 165
                                        55544444422222222222..........2333333334467777777777777777774443333333333344 PP

                                        ...HHHTTT-SEEEEET CS
                             ResIII 124 eseellrdrfdviiiDE 140
                                        +s+  ++ ++ ++iiDE
  gene1066|gene1066|rna1066|rna1066 166 MSNLTSKLTNRILIIDE 182
                                        44444444444999998 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.0   0.00029      0.57       9      35 ..      44      70 ..      39      81 .. 0.83
   2 ?    3.7   0.0     0.036        72      87     132 ..     163     205 ..     112     209 .. 0.72
   3 ?   -2.8   0.0       3.5     7e+03     100     130 ..     390     422 ..     362     428 .. 0.58

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00029
                             AAA_19  9 kekvllvtaGpGtGKTrvlkhivallv 35
                                       k +v+ + + pG+GKT+++   + +++
  gene1066|gene1066|rna1066|rna1066 44 KGHVIYISGVPGSGKTYTVINTLLHCN 70
                                       567899***********9987776665 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.036
                             AAA_19  87 alelleeaeeekklqeeellivDEfqdvdelqyrLlkallgek.kkl 132
                                        ++++   ++ ++kl  + +li+DE+  +    +++l +l++ k ++l
  gene1066|gene1066|rna1066|rna1066 163 PFTM---SNLTSKL-TNRILIIDEIDYLLTRNQHVLYTLFEMKtHTL 205
                                        3333...5667788.7779*******999999999999987774434 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 3.5
                             AAA_19 100 lqeee.llivDEfqdvd.elqyrLlkallgekk 130
                                         ++++ + ++D     d ++   +l+++ ++kk
  gene1066|gene1066|rna1066|rna1066 390 YKKQNdMKVIDQLMKSDkPVFSCFLNEIDEQKK 422
                                        333333666777777776677777777765554 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   4.6   0.00043      0.85       8     151 ..      33     203 ..      28     270 .. 0.61

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00043
                           ATPase_2   8 lkeleeilerepneiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefie............. 70 
                                        l +++    +++ ++++i G  gsGKt     +i+ l++ +k  +y++  + ++ s++ + +              
  gene1066|gene1066|rna1066|rna1066  33 LTYIKDFQTNGKGHVIYISGVPGSGKTY---TVINTLLHCNK-AFYFNCGSLKNKSTFFKRLYglvnsgtgmtgck 104
                                        5667777778888888888888888885...56777766554.444444444444444444446776666666666 PP

                           ATPase_2  71 ...........eeeekkklekal.........................giavpkaeleeilkeksklvfkaielll 110
                                                              l                         +++  +++  +  ++k+++    +++l 
  gene1066|gene1066|rna1066|rna1066 105 yvvnggnsvknR----------LydienvknkldnvenegnkclvsnkKTTSTNVTYRNTNSRKRTKQPFTMSNLT 170
                                        655554443331..........133344445445555666665555334444444444433455555556666667 PP

                           ATPase_2 111 ekikkkgkkiiiiiDelqklidlglngaellvkeLlnlies 151
                                         k++++    i+iiDe+ +l   +  +++ +++ L+++  +
  gene1066|gene1066|rna1066|rna1066 171 SKLTNR----ILIIDEIDYLL--T--RNQHVLYTLFEMKTH 203
                                        777666....**********9..5..459999999998665 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.1    0.0086        17       2      17 ..      47      62 ..      46      94 .. 0.78
   2 ?    6.9   0.0    0.0028       5.6      72     115 ..     165     200 ..     136     256 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0086
                                       CEEEEC-TTTCHHHHH CS
                              NACHT  2 lvilqGeaGsGKTtLl 17
                                       ++ + G +GsGKT+ +
  gene1066|gene1066|rna1066|rna1066 47 VIYISGVPGSGKTYTV 62
                                       789**********854 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0028
                                        CHHHHCCSCCCEEEEEE-STT-SS-TCH.........HHHHHCT CS
                              NACHT  72 vwavllelperlLlilDglDelvtdlgqkekqpvrtlLselirk 115
                                         +++l++  +   li+D +D+l t +++        +L +l++ 
  gene1066|gene1066|rna1066|rna1066 165 TMSNLTSKLTNRILIIDEIDYLLTRNQH--------VLYTLFEM 200
                                        57777888888889**********9998........55555555 PP

>> CaKB  Calcium-activated potassium channel, beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.3    0.0036       7.3     104     156 ..     101     153 ..      63     162 .. 0.83
   2 ?    4.4   0.1     0.013        26     118     154 ..     391     426 ..     384     434 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0036
                               CaKB 104 skCfYiPkcqkdkkeleeevenikeklkkqkeqtfsCyydpsekpedvllkrk 156
                                        + C Y+ +  +  k+   ++en+k+kl++ +++  +C ++++++++  +  r 
  gene1066|gene1066|rna1066|rna1066 101 TGCKYVVNGGNSVKNRLYDIENVKNKLDNVENEGNKCLVSNKKTTSTNVTYRN 153
                                        6799999999999*****************9999****998877655554444 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.013
                               CaKB 118 eleeevenikeklkkqkeqtfsCyydpsekpedvllk 154
                                        + +++++ i + +k+  +  fsC++++ +++++++l+
  gene1066|gene1066|rna1066|rna1066 391 KKQNDMKVIDQLMKSD-KPVFSCFLNEIDEQKKMILR 426
                                        4566677777666666.888************99996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (471 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1148  (0.0640303); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.64u 0.30s 00:00:00.94 Elapsed: 00:00:00.48
# Mc/sec: 2962.10
//
Query:       gene1067|gene1067|rna1067|rna1067  [L=421]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0014   18.3   0.1        2.5    7.8   0.0    3.5  3  TFA2_Winged_2   TFA2 Winged helix domain 2
  ------ inclusion threshold ------
       0.14   12.9   0.0       0.29   11.8   0.0    1.5  1  Acetyltransf_5  Acetyltransferase (GNAT) domain


Domain annotation for each model (and alignments):
>> TFA2_Winged_2  TFA2 Winged helix domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.7   0.0    0.0027        24      30      53 ..     169     191 ..     165     200 .. 0.84
   2 !    7.8   0.0   0.00028       2.5      26      53 ..     202     229 ..     201     245 .. 0.84
   3 ?    1.1   0.0     0.037   3.3e+02      31      51 ..     318     338 ..     315     346 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.0027
                      TFA2_Winged_2  30 dveealeeLeaegeilvlrtkkdg 53 
                                        d+ +++++L+  ge +v+++  dg
  gene1067|gene1067|rna1067|rna1067 169 DCNNDVNDLKSNGENIVVKN-SDG 191
                                        8*************999988.555 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.00028
                      TFA2_Winged_2  26 dswpdveealeeLeaegeilvlrtkkdg 53 
                                        ++  d+ +++++L+ +ge +v++++  +
  gene1067|gene1067|rna1067|rna1067 202 EAVGDCNNDVNDLKSDGENIVVKNNDGN 229
                                        56779*************9999885333 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.037
                      TFA2_Winged_2  31 veealeeLeaegeilvlrtkk 51 
                                         ++++++L a++++l + t +
  gene1067|gene1067|rna1067|rna1067 318 TSPTVNALSASHHVLKAQTRC 338
                                        5799**********9887755 PP

>> Acetyltransf_5  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   3.3e-05      0.29      18      84 ..      69     137 ..      57     145 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.3e-05
                     Acetyltransf_5  18 ape.ldiDefDavcdhllvideae.evVGtyRllrpdeaerlegfysesefdlsklaalrrrllElgRs 84 
                                         p+ l  D  D++ +h++ +++++ ++ GtyR +++  +e ++ +  ++++++ k+ + ++++l +gR 
  gene1067|gene1067|rna1067|rna1067  69 IPSpLSNDPIDHIQKHVITRRKKKrRILGTYRPFKSMYDEDIRFLTPRQQLRVMKYLSAKEKFLKTGRI 137
                                        45557789***********9777756******9999999988777778888877888888899999996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (421 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1037  (0.0578393); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 2870.33
//
Query:       gene1068|gene1068|rna1068|rna1068  [L=70]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.9e-08   32.3   0.0      1e-07   32.2   0.0    1.1  1  rve       Integrase core domain
    0.00042   20.0   0.2    0.00071   19.3   0.2    1.5  2  rve_3     Integrase core domain
  ------ inclusion threshold ------
      0.039   14.2   0.2      0.045   14.0   0.2    1.1  1  DUF1977   Domain of unknown function (DUF1977)


Domain annotation for each model (and alignments):
>> rve  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.2   0.0   1.7e-11     1e-07      75     118 ..       6      49 ..       1      50 [. 0.94

  Alignments for each domain:
  == domain 1  score: 32.2 bits;  conditional E-value: 1.7e-11
                                rve  75 gseytskafrefladlgirvsftrpgrpqdnGkvErfhrtlkde 118
                                        g+e++sk ++ f++++gi+  +t   +++ nG+vEr +rt+++ 
  gene1068|gene1068|rna1068|rna1068   6 GKEFKSKLVTSFCEENGIEYHVTSTEHSEANGRVERLNRTIREY 49 
                                        99***************************************975 PP

>> rve_3  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       0.9   5.4e+03       8      22 ..       3      17 ..       2      19 .. 0.69
   2 !   19.3   0.2   1.2e-07   0.00071       1      35 [.      21      55 ..      21      69 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.9
                              rve_3  8 iapgkPqqNglvEsf 22
                                       ++pgk  +  lv sf
  gene1068|gene1068|rna1068|rna1068  3 TNPGKEFKSKLVTSF 17
                                       678887777777776 PP

  == domain 2  score: 19.3 bits;  conditional E-value: 1.2e-07
                              rve_3  1 lgielsyiapgkPqqNglvEsfngtlrdellneel 35
                                       +gie +++   +   Ng vE++n+t+r+ + +++ 
  gene1068|gene1068|rna1068|rna1068 21 NGIEYHVTSTEHSEANGRVERLNRTIREYIRKRSN 55
                                       59*************************98877655 PP

>> DUF1977  Domain of unknown function (DUF1977)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.2   7.6e-06     0.045      23      74 ..      18      67 ..       2      69 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 7.6e-06
                            DUF1977 23 tsnlkvpYyVnpaevskysskklrklekeveeeyvqnlraeCerekeqkerl 74
                                        ++++++Y+V+++e+s+  + ++++l++++  ey+++ ++   r+k++k++l
  gene1068|gene1068|rna1068|rna1068 18 CEENGIEYHVTSTEHSEA-NGRVERLNRTIR-EYIRKRSNPKIRQKNDKRSL 67
                                       56789*************.559********8.67777666666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (70 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       775  (0.0432261); expected 358.6 (0.02)
Passed bias filter:                      496  (0.0276647); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.38u 0.28s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 499.02
//
Query:       gene1069|gene1069|rna1069|rna1069  [L=27]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (27 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       329  (0.0183502); expected 358.6 (0.02)
Passed bias filter:                      111  (0.00619109); expected 358.6 (0.02)
Passed Vit filter:                         2  (0.000111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.31u 0.25s 00:00:00.56 Elapsed: 00:00:00.39
# Mc/sec: 209.12
//
Query:       gene107|gene107|rna107|rna107  [L=374]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.082   13.1   0.0       0.29   11.3   0.0    2.0  1  Cadherin_pro  Cadherin prodomain like


Domain annotation for each model (and alignments):
>> Cadherin_pro  Cadherin prodomain like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   1.6e-05      0.29      52      76 ..     217     241 ..     204     253 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 1.6e-05
                                    TTTEEEEES--S-SSS-EEEEEEEE CS
                   Cadherin_pro  52 eDGtvyakrevklssektsflvhar 76 
                                    +DG+vy+ r+++++++++++lv   
  gene107|gene107|rna107|rna107 217 TDGSVYVIRNISMTDNQKQLLVRHN 241
                                    7********************9765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (374 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       605  (0.0337442); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 2525.77
//
Query:       gene1070|gene1070|rna1070|rna1070  [L=55]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.02   14.3   0.0       0.02   14.3   0.0    1.1  1  DUF4926   Domain of unknown function (DUF4926)


Domain annotation for each model (and alignments):
>> DUF4926  Domain of unknown function (DUF4926)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   1.1e-06      0.02      12      42 ..       6      35 ..       1      50 [. 0.75

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.1e-06
                            DUF4926 12 pekgLrrGqvGTvVevyeegeaYeVEFsddd 42
                                       ++k+Lr G+ G +Ve+  ++  Y+V  + ++
  gene1070|gene1070|rna1070|rna1070  6 SKKNLRYGKTGRIVEEVGKE-NYLVKIFKRN 35
                                       4678*************555.5*99877666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (55 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       340  (0.0189637); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.38s 00:00:00.91 Elapsed: 00:00:00.57
# Mc/sec: 292.53
//
Query:       gene1071|gene1071|rna1071|rna1071  [L=161]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       290  (0.0161749); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 1069.78
//
Query:       gene1072|gene1072|rna1072|rna1072  [L=111]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.019   15.5   0.1       0.03   14.9   0.1    1.3  1  DNApol3-delta_C  DNA polymerase III, delta subunit, C termina


Domain annotation for each model (and alignments):
>> DNApol3-delta_C  DNA polymerase III, delta subunit, C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.1   1.7e-06      0.03      59     109 ..      11      61 ..       4      69 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.7e-06
                                        .--S-TT-HHHHHHHHHHS-HHHHHHHHHHHHHHHHHHHHSTTSSHHHHHH CS
                    DNApol3-delta_C  59 eqlvnqdqlplikqlakrlsiekLlkilqkllelreqLlsisgvNkeLllt 109
                                        +++v     p+i+ +a+ ++++ + +++q+l++ + +L++++ + + Ll +
  gene1072|gene1072|rna1072|rna1072  11 DSVVTYNNEPSIQVFAQCFNLDIVRHAYQALNIINTELQNFTDIHRSLLEI 61 
                                        4677888899************************************99855 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (111 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       558  (0.0311228); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.29s 00:00:00.70 Elapsed: 00:00:00.46
# Mc/sec: 729.81
//
Query:       gene1073|gene1073|rna1073|rna1073  [L=1471]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.076   12.6   2.4       0.14   11.8   1.1    2.1  2  DNA_ligase_A_M  ATP dependent DNA ligase domain


Domain annotation for each model (and alignments):
>> DNA_ligase_A_M  ATP dependent DNA ligase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0      0.24   4.3e+03      78     117 ..     421     460 ..     411     491 .. 0.85
   2 ?   11.8   1.1   7.6e-06      0.14     112     193 ..    1385    1468 ..    1335    1470 .. 0.74

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 0.24
                                        EEEEEEETTTTCBEHHHHHCHHH.HCHCCTHHHHHHSEEEE CS
                     DNA_ligase_A_M  78 GElvavdketgeilpfqklasrk.kkkkkveeklkeaelcl 117
                                        +E +++ k+++e++++  +++ +  k+ +++e +ke elc 
  gene1073|gene1073|rna1073|rna1073 421 CEFILW-KNNDEFIEHLYISNMElHKNWDINENIKELELCN 460
                                        789998.6669999999999999899999999999999885 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 7.6e-06
                                         HSEEEEEEEEEEEETTEEHTTSCHHHHHHHHHHHB--BTTTEEE--EEEESSHHHHHHH..HHHHHHTTECEEE CS
                     DNA_ligase_A_M  112 eaelclfvFDiLyldgesltdeplkeRrklLeeilkesedrvelaeslevkdveeleel..leeaiseglEGlv 183 
                                          +  +++++ i ++d++  +++   +R + ++++++++e  +++   +  + ++++ e+  l+e + e+ EG++
  gene1073|gene1073|rna1073|rna1073 1385 ITCFVFYAYNISAVDKKLNVKKLTIHRYRSMSQVIEQNEIMLKIYLLKIYDFLSQFIEIenLDELVVENTEGVI 1458
                                         4566789999999999888999999999999999944444444443333333444433222789999******* PP

                                         EEETT-CC-T CS
                     DNA_ligase_A_M  184 vKnpdskYep 193 
                                         +K + skY++
  gene1073|gene1073|rna1073|rna1073 1459 IKHTPSKYRE 1468
                                         ********75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1471 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       641  (0.0357521); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.82u 0.29s 00:00:01.10 Elapsed: 00:00:00.47
# Mc/sec: 9480.08
//
Query:       gene1074|gene1074|rna1074|rna1074  [L=256]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.034   14.2   1.6       0.14   12.3   1.6    2.0  1  BCL_N     BCL7, N-terminal conserver region


Domain annotation for each model (and alignments):
>> BCL_N  BCL7, N-terminal conserver region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   1.6   7.7e-06      0.14       8      38 ..     108     138 ..     105     140 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 7.7e-06
                              BCL_N   8 TRsrakddlkrvikslekVrkWEKkWVtvkd 38 
                                        TR+r+ d+ ++v++ + k rk+ Kk +++++
  gene1074|gene1074|rna1074|rna1074 108 TRNRKIDENEKVKTRVAKSRKRSKKNIALSN 138
                                        9************************999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1195  (0.0666518); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1634.37
//
Query:       gene1075|gene1075|rna1075|rna1075  [L=1278]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        2.2    8.8  13.6         21    5.7   0.3    5.7  5  LRR_4     Leucine Rich repeats (2 copies)


Domain annotation for each model (and alignments):
>> LRR_4  Leucine Rich repeats (2 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0      0.77   1.4e+04       5      11 ..     129     135 ..     128     139 .. 0.77
   2 ?    3.1   1.5    0.0078   1.4e+02       6      38 ..     148     179 ..     142     184 .. 0.76
   3 ?   -1.0   0.0      0.15   2.8e+03       2      29 ..     526     550 ..     525     556 .. 0.58
   4 ?    3.7   0.0    0.0052        92      16      36 ..     708     727 ..     704     737 .. 0.77
   5 ?    5.7   0.3    0.0012        21      16      41 ..    1249    1274 ..    1241    1277 .. 0.76

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 0.77
                                        EEE--SS CS
                              LRR_4   5 vLdLsnN 11 
                                        +L++sn+
  gene1075|gene1075|rna1075|rna1075 129 HLHCSNC 135
                                        8999974 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.0078
                                        EE--.SS---E-S-HHH-TT.--EEE-.-S----- CS
                              LRR_4   6 LdLs.nNqltdiplleklpn.LkeLdLsgNnlitd 38 
                                        L L+ +N l d+ +le +p+ Lk+L L  N++i++
  gene1075|gene1075|rna1075|rna1075 148 LVLHdQNSLIDV-NLE-MPHgLKTLKL-ANTQIGQ 179
                                        567766777763.366.8999******.8889865 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.15
                                        S--EEE--SS.---E-S-HHH-TT--EEE CS
                              LRR_4   2 nLevLdLsnN.qltdiplleklpnLkeLd 29 
                                        + e+L+L  + ++   ++++ l++L    
  gene1075|gene1075|rna1075|rna1075 526 KCEKLYLKRCqNIGIMSSCS-LKKL---R 550
                                        67888888753454444544.4444...4 PP

  == domain 4  score: 3.7 bits;  conditional E-value: 0.0052
                                        -S-HHH-TT--EEE-.-S--- CS
                              LRR_4  16 iplleklpnLkeLdLsgNnli 36 
                                        i++ + + +Lk+L+L +N +i
  gene1075|gene1075|rna1075|rna1075 708 IDFSR-CIHLKSLYLYDNQFI 727
                                        66777.999999999888554 PP

  == domain 5  score: 5.7 bits;  conditional E-value: 0.0012
                                         -S-HHH-TT--EEE-.-S-----GGG CS
                              LRR_4   16 iplleklpnLkeLdLsgNnlitdlde 41  
                                         +  +  + +L+eL++ +Nn+ t+l++
  gene1075|gene1075|rna1075|rna1075 1249 LTYFVDFEQLEELSIYSNNQETKLNP 1274
                                         44566799*******99999999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1278 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       791  (0.0441185); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.76u 0.37s 00:00:01.12 Elapsed: 00:00:00.53
# Mc/sec: 7305.76
//
Query:       gene1076|gene1076|rna1076|rna1076  [L=71]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.059   13.2   0.5      0.069   13.0   0.5    1.0  1  3HCDH_N   3-hydroxyacyl-CoA dehydrogenase, NAD binding domain


Domain annotation for each model (and alignments):
>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.5   3.8e-06     0.069      94     139 ..      21      69 ..      16      70 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.8e-06
                                        HHHHHHHHCCS-TTSEEEE--SSS...-HHHHCCCSSSGGGEEEEEE-S CS
                            3HCDH_N  94 rkvfaelekiakpdailasnTSsl...siselaealkrperviglHFfn 139
                                        +  ++  e+++++++il sn+S++   + +++ ++l++ +r+ ++H +n
  gene1076|gene1076|rna1076|rna1076  21 QTSYNLDENHLNSTTILNSNSSTIindKYHDIIKKLTNSSRLQTMHLIN 69 
                                        555666678999************5555678999************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (71 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       768  (0.0428356); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.26s 00:00:00.61 Elapsed: 00:00:00.42
# Mc/sec: 508.79
//
Query:       gene1077|gene1077|rna1077|rna1077  [L=66]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (66 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       682  (0.0380389); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.31s 00:00:00.74 Elapsed: 00:00:00.49
# Mc/sec: 405.78
//
Query:       gene1079|gene1079|rna1079|rna1079  [L=176]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.062   13.1   4.8      0.073   12.9   4.8    1.3  1  Band_3_cyto      Band 3 cytoplasmic domain
       0.45    9.0  22.1       0.51    8.8  22.1    1.2  1  Borrelia_P83     Borrelia P83/100 protein
        1.3    7.7  13.7        1.5    7.5  13.7    1.0  1  SAPS             SIT4 phosphatase-associated protein
        1.4    8.7  27.1        1.9    8.3  27.1    1.2  1  RR_TM4-6         Ryanodine Receptor TM 4-6
        1.5    7.2   2.7        1.3    7.4   2.7    1.1  1  SID-1_RNA_chan   dsRNA-gated channel SID-1
        1.8    8.1  19.0        2.2    7.8  19.0    1.2  1  Spt20            Spt20 family
          2    7.7  37.1        2.5    7.4  37.1    1.0  1  CDC27            DNA polymerase subunit Cdc27
        3.7    5.7  29.4        4.2    5.6  29.4    1.1  1  CDC45            CDC45-like protein
        5.7    5.8  18.4          7    5.6  18.4    1.1  1  SLC12            Solute carrier family 12
        7.4    6.2  13.5        9.3    5.9  13.5    1.3  1  DUF4569          Domain of unknown function (DUF4569)


Domain annotation for each model (and alignments):
>> Band_3_cyto  Band 3 cytoplasmic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   4.8   4.1e-05     0.073      93     157 ..      95     160 ..       3     169 .. 0.47

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 4.1e-05
                                        E-TTS---------..-EE--SSS-SS-HHHHHHTTTTTSS--..........--SSTTGGGCCGGG CS
                        Band_3_cyto  93 rslssigsllsekk..kaskellskqssleteeakaseslskssseeslsssleeekkkkkekilkk 157
                                         ++s+ ++++++ k  +++++++ +q++++++++k++e+++ +++ ++ +++++++kk++k++  +k
  gene1079|gene1079|rna1079|rna1079  95 SKQSGQAEKQEKSKekDTQRQDKAEQQQKKQTDKKEAEEKK-KEKGAEAEKKKSNRKKRQKQRRKRK 160
                                        22222222222222111122222222222222122222211.2222223333333333333333444 PP

>> Borrelia_P83  Borrelia P83/100 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8  22.1   0.00029      0.51     203     275 ..      77     161 ..      13     176 .] 0.51

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00029
                       Borrelia_P83 203 l.......keresqedakraqvlkeeldkkqkdadkakkkadtaednadkqrkevreklqe.....aknlpepadv 266
                                        l       k  e+q +a  +q  + e ++k k+ d ++++   ++++ +  +ke++ek++e     +k+  ++ + 
  gene1079|gene1079|rna1079|rna1079  77 LtaigagaKGGEAQSGAESKQSGQAEKQEKSKEKDTQRQDKAEQQQKKQTDKKEAEEKKKEkgaeaEKKKSNRKKR 152
                                        0444444466677777777776666666666666666665555555555566666666666333322222222222 PP

                       Borrelia_P83 267 sskkedkkv 275
                                        ++++ ++k+
  gene1079|gene1079|rna1079|rna1079 153 QKQRRKRKM 161
                                        222222222 PP

>> SAPS  SIT4 phosphatase-associated protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5  13.7   0.00084       1.5     272     340 ..      68     155 ..      26     172 .. 0.55

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.00084
                               SAPS 272 s...................deaskeesaesedltdkdedvsleesksakdenkesdesesdtaeesseededdas 328
                                                            +++s  es++s + ++++++ ++++++++k+e++++++ ++++aee+++e+  +a+
  gene1079|gene1079|rna1079|rna1079  68 AkkdgdksgltaigagakggEAQSGAESKQSGQAEKQEKSKEKDTQRQDKAEQQQKKQTDKKEAEEKKKEKGAEAE 143
                                        0222234455555566666545555555555555555555555555555555555555555555555555555555 PP

                               SAPS 329 seesalaeetee 340
                                        +++s  ++ +++
  gene1079|gene1079|rna1079|rna1079 144 KKKSNRKKRQKQ 155
                                        554443333332 PP

>> RR_TM4-6  Ryanodine Receptor TM 4-6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3  27.1     0.001       1.9      61     149 ..      68     160 ..      40     175 .. 0.38

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.001
                                        ...XXXXXXXXXXXXXXXXXXXX..XXXXXXXX.XXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXX...... CS
                           RR_TM4-6  61 vvakkseagLgDlseteaeespt..pelkkkla.eeeeaeeekeeeeepeaeaeekadaengekeekeke.keeee 132
                                          +++ ++gL+ ++  +   +++  +e k+  + e++e+++ek+++++ +ae+++k++++++e+eek+ke ++e+e
  gene1079|gene1079|rna1079|rna1079  68 AKKDGDKSGLTAIGAGAKGGEAQsgAESKQSGQaEKQEKSKEKDTQRQDKAEQQQKKQTDKKEAEEKKKEkGAEAE 143
                                        2234445555555554444443322222222112223333333333333333333333333333333333112222 PP

                                        .....XXXXXXXXXXXX CS
                           RR_TM4-6 133 keseeeeeekkkkkkak 149
                                        k+++++++++k+++k+k
  gene1079|gene1079|rna1079|rna1079 144 KKKSNRKKRQKQRRKRK 160
                                        22222222222222222 PP

>> SID-1_RNA_chan  dsRNA-gated channel SID-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   2.7    0.0007       1.3     153     201 ..     100     148 ..       2     174 .. 0.59

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0007
                     SID-1_RNA_chan 153 krvkessssesaseslesvssavrsesessveeesdydtleeiesdknv 201
                                        +  k+++s+e+ ++++++++++ +++++++ +ee++ +  +e+e++k+ 
  gene1079|gene1079|rna1079|rna1079 100 QAEKQEKSKEKDTQRQDKAEQQQKKQTDKKEAEEKKKEKGAEAEKKKSN 148
                                        1112222222222233333333333333333344444444444333222 PP

>> Spt20  Spt20 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8  19.0    0.0012       2.2     106     168 ..      94     159 ..      54     165 .. 0.54

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0012
                              Spt20 106 dqkqsqqnqqqqqqqqqqqqqqqqqqeqqqqqnekdsttteekekks...ksknnssksktttkkp 168
                                        ++kqs q ++q +++++++q+q ++++qq++q++k+++++++kek +   k+k+n +k +++  k 
  gene1079|gene1079|rna1079|rna1079  94 ESKQSGQAEKQEKSKEKDTQRQDKAEQQQKKQTDKKEAEEKKKEKGAeaeKKKSNRKKRQKQRRKR 159
                                        233333555555555555555555444444444444444444444430003333333344444444 PP

>> CDC27  DNA polymerase subunit Cdc27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4  37.1    0.0014       2.5     194     299 ..      55     159 ..      49     169 .. 0.65

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0014
                              CDC27 194 kaekaasskaaslkkkasaksnimksffkakpaekkkkteakeqkveeeseeekekedkeleddsaaeeeeeeeks 269
                                        +++k+ + ++++  kk+ +ks++ + +++ak  e++  +e+k++  ++e++e+++++d +  d+ +  ++++++ +
  gene1079|gene1079|rna1079|rna1079  55 NETKKSELSTEEAAKKDGDKSGLTAIGAGAKGGEAQSGAESKQS-GQAEKQEKSKEKDTQRQDKAE--QQQKKQTD 127
                                        445555656666666799**************999999866666.666667777777777666665..33333333 PP

                              CDC27 270 tkk..ekrrqkklessdeeeeerekekekrkr 299
                                        +k+  ek++ k  e  ++++++++ +k++rkr
  gene1079|gene1079|rna1079|rna1079 128 KKEaeEKKKEKGAEAEKKKSNRKKRQKQRRKR 159
                                        33332334666666666666666666666665 PP

>> CDC45  CDC45-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6  29.4    0.0023       4.2     139     213 ..      97     171 ..      50     176 .] 0.33

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0023
                              CDC45 139 eeeeddddeeeeeeeeedeedeeedeeeskkkrksksdeeee.......sddddersrkrrrsepsakklrrqlkk 207
                                        ++ + +++e+++e++++++++ e+++++++ k++++++++e+       ++++++r+++rr+++  + +lrr+   
  gene1079|gene1079|rna1079|rna1079  97 QSGQAEKQEKSKEKDTQRQDKAEQQQKKQTDKKEAEEKKKEKgaeaekkKSNRKKRQKQRRKRK--MPRLRRR--- 167
                                        1111111111111111111111111111111111111111112111101112222222222222..2222222... PP

                              CDC45 208 errkye 213
                                          r+++
  gene1079|gene1079|rna1079|rna1079 168 --RSNR 171
                                        ..2222 PP

>> SLC12  Solute carrier family 12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6  18.4    0.0039         7     165     232 ..      87     159 ..      45     175 .. 0.28

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0039
                              SLC12 165 e........ekskekeekekleekdsnlslseekkeeekekkkekkkkkekkeklkkkekslllkeaskeekevle 232
                                                 ++s + e++ek +ekd++ ++++ ++ ++k+++++k+++++kkek  ++ek++++++++ ++++  +
  gene1079|gene1079|rna1079|rna1079  87 GeaqsgaesKQSGQAEKQEKSKEKDTQ-RQDKAEQ-QQKKQTDKKEAEEKKKEKGAEAEKKKSNRKKR-QKQRRKR 159
                                        022222211111111111111111111.1111111.11111111111111111111111111111111.1111111 PP

>> DUF4569  Domain of unknown function (DUF4569)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9  13.5    0.0052       9.3      23      98 ..      95     169 ..      41     174 .. 0.56

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0052
                            DUF4569  23 keekeeekeklldseeakslsseaeaqskslskl.sgklissvksseeenskkqqqeleeekkvaksqslllerqv 97 
                                        +++  + ++++ ++e++++ +++ae+q+k+  ++ +++  +++k++  e +kk++++++++k++ k++ + l+r+ 
  gene1079|gene1079|rna1079|rna1079  95 SKQSGQAEKQEKSKEKDTQRQDKAEQQQKK--QTdKKEAEEKKKEKGAEAEKKKSNRKKRQKQRRKRKMPRLRRRR 168
                                        233333333333444444444444444444..22122222233333333344444444444444555555555555 PP

                            DUF4569  98 s 98 
                                        s
  gene1079|gene1079|rna1079|rna1079 169 S 169
                                        4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3478  (0.193987); expected 358.6 (0.02)
Passed bias filter:                      951  (0.0530426); expected 358.6 (0.02)
Passed Vit filter:                       423  (0.0235931); expected 17.9 (0.001)
Passed Fwd filter:                       103  (0.00574488); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.99u 0.38s 00:00:01.37 Elapsed: 00:00:00.53
# Mc/sec: 1000.47
//
Query:       gene108|gene108|rna108|rna108  [L=591]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (591 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1193  (0.0665402); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.62u 0.26s 00:00:00.88 Elapsed: 00:00:00.45
# Mc/sec: 3958.38
//
Query:       gene1080|gene1080|rna1080|rna1080  [L=105]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0059   16.4   1.8     0.0059   16.4   1.8    1.8  2  TRAF_BIRC3_bd  TNF receptor-associated factor BIRC3 binding d


Domain annotation for each model (and alignments):
>> TRAF_BIRC3_bd  TNF receptor-associated factor BIRC3 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1     0.099   1.8e+03      19      28 ..      17      26 ..      11      34 .. 0.79
   2 !   16.4   1.8   3.3e-07    0.0059      19      60 ..      40      81 ..      31      84 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.099
                      TRAF_BIRC3_bd 19 IVsVLnrEve 28
                                       +V V  rEve
  gene1080|gene1080|rna1080|rna1080 17 VVQVALREVE 26
                                       6778889998 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 3.3e-07
                      TRAF_BIRC3_bd 19 IVsVLnrEverssttieaverqrrldqekieaLekKvrqLer 60
                                       + +VL++Ev +   ++ + e q+++ q+  + L+ Kv+ +er
  gene1080|gene1080|rna1080|rna1080 40 VLAVLKKEVLSLFPQVHQAELQNQKHQKRCQLLSLKVQVQER 81
                                       689************************************999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1264  (0.0705003); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.20s 00:00:00.56 Elapsed: 00:00:00.35
# Mc/sec: 887.22
//
Query:       gene1081|gene1081|rna1081|rna1081  [L=274]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.033   14.2   0.1      0.074   13.0   0.1    1.6  1  Fae       Formaldehyde-activating enzyme (Fae)


Domain annotation for each model (and alignments):
>> Fae  Formaldehyde-activating enzyme (Fae)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   4.1e-06     0.074      38      83 ..     165     210 ..     159     244 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4.1e-06
                                Fae  38 skghtpllavlrpnllvkPatlmvnkvtiknekqaellfGpaQaav 83 
                                        +k  t+ll++ ++ ++ kP+t+ +++v +++ +++++ f ++Q   
  gene1081|gene1081|rna1081|rna1081 165 EKTETKLLTLYQSRIIEKPVTITISRVVLSTFTKESQHFSTVQEIR 210
                                        56789*************************************9755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (274 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1043  (0.0581739); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 2158.29
//
Query:       gene1082|gene1082|rna1082|rna1082  [L=309]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.8e-72  243.1   7.5      5e-72  242.7   7.5    1.1  1  PK         Pyruvate kinase, barrel domain
    2.9e-06   26.6   0.2    6.4e-06   25.5   0.2    1.5  1  HpcH_HpaI  HpcH/HpaI aldolase/citrate lyase family


Domain annotation for each model (and alignments):
>> PK  Pyruvate kinase, barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  242.7   7.5   5.6e-76     5e-72     126     339 ..       2     214 ..       1     220 [. 0.95

  Alignments for each domain:
  == domain 1  score: 242.7 bits;  conditional E-value: 5.6e-76
                                        EEETTTTEEEEEEEEETTEEEEEEESS-EEE-SS-BEE-TTS---S-SS-HHHHHHHHHHHHCT-SEEEETTE-SH CS
                                 PK 126 ilvdDGllslkvlevdeekeleveventgvlgskkgvnlpgtkvdlpalsekDkadlrfgvkqgvdliaasfvrka 201
                                        +l+dDG+l + v   d ++ +++ + n+ +++ +k vn+p+ k+d    +ekDk+d+ +g+k+++d +++sfv +a
  gene1082|gene1082|rna1082|rna1082   2 VLIDDGKLRMVVD-LDGDE-IVCVAMNDHMVKPNKAVNIPDMKMDKSVPTEKDKNDIFLGLKNKIDYVFLSFVSNA 75 
                                        89*******9775.55555.89****************************************************** PP

                                        HHHHHHHHHHTCCC.TTSEEEEEE-SCHHHHTHHHHHHHSSEEEEEHHHHHHHSTCCCHHHHHHHHHHHHHHHT-- CS
                                 PK 202 sDvkevrevleeeg.keikiiakienqegvenldeileasDgimvarGDlGieipaekvllvqkklikkcnlagkp 276
                                        +++++vr+ + + + +   +iakien+e+++n++ei+e++Dgim+arGDl +ei+ ++ + +qk++ kkc  + kp
  gene1082|gene1082|rna1082|rna1082  76 AEIRKVRDFIRDMNgHMPVLIAKIENKEAIRNINEIIEEADGIMIARGDLAVEIGIKHCFSAQKMITKKCLVMKKP 151
                                        ********9998873666789******************************************************* PP

                                        EEEESSTTGGGGTSSS--HHHHHHHHHHHHHT-SEEEESHHHHTSS-HHHHHHHHHHHHHHHH CS
                                 PK 277 vitatqmlesmiknPrptraevsDvanavlDGtDavmLsgetakGkyPveavkamaevaleae 339
                                         i atqmlesm+++  ptraevsDv+navlD  D+vmLsgeta G++P++ v++m+++   ae
  gene1082|gene1082|rna1082|rna1082 152 FIMATQMLESMTEESTPTRAEVSDVGNAVLDNCDCVMLSGETASGRHPAHVVRTMKTIISDAE 214
                                        **********************************************************99998 PP

>> HpcH_HpaI  HpcH/HpaI aldolase/citrate lyase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.2   7.1e-10   6.4e-06      75     170 ..      53     141 ..      45     156 .. 0.83

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 7.1e-10
                                        HHHGG.HHHTTSSEEEESS--SHHHHHHHHHHTSHTTTS---HCCC-EEEEEE-SHHHHHTHHHHHTSTTEEEEEE CS
                          HpcH_HpaI  75 kqdle.vldlgaqvvlvPkvetaeealevvsalrepekgirganketrllaqiEsaegvknaeeIaavegldgvfl 149
                                        k+d+   l+ +++ v + +v +a+e+++v   +r  +       +  +l+a iE +e++ n++eI+  e+ dg+++
  gene1082|gene1082|rna1082|rna1082  53 KNDIFlGLKNKIDYVFLSFVSNAAEIRKVRDFIRDMN------GHMPVLIAKIENKEAIRNINEII--EEADGIMI 120
                                        455667789999999999**************99999......455667889*************8..57799999 PP

                                        -HHHHHHHTT-TTSTTSHHHH CS
                          HpcH_HpaI 150 GaeDlsadlgtkrspegtevl 170
                                        +  Dl++++g k   + +++ 
  gene1082|gene1082|rna1082|rna1082 121 ARGDLAVEIGIKHCFSAQKMI 141
                                        **********98866666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (309 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       758  (0.0422779); expected 358.6 (0.02)
Passed bias filter:                      517  (0.028836); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2280.19
//
Query:       gene1083|gene1083|rna1083|rna1083  [L=207]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1056  (0.058899); expected 358.6 (0.02)
Passed bias filter:                      659  (0.0367561); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 1392.25
//
Query:       gene1084|gene1084|rna1084|rna1084  [L=491]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (491 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       662  (0.0369234); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 3353.55
//
Query:       gene1086|gene1086|rna1086|rna1086  [L=456]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0047   16.6   0.3        1.8    8.4   0.2    3.1  2  IDEAL     IDEAL domain


Domain annotation for each model (and alignments):
>> IDEAL  IDEAL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.9   0.0    0.0013        22      17      27 ..     174     184 ..     173     185 .. 0.92
   2 !    8.4   0.2   9.9e-05       1.8      15      29 ..     396     410 ..     391     410 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.0013
                              IDEAL  17 eIDeALdnrDk 27 
                                         ID++L++r++
  gene1086|gene1086|rna1086|rna1086 174 AIDKSLERRNR 184
                                        5********97 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 9.9e-05
                              IDEAL  15 lreIDeALdnrDkea 29 
                                        + +ID  L++r+ke+
  gene1086|gene1086|rna1086|rna1086 396 MMQIDTVLEKRNKEL 410
                                        78***********95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (456 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1811  (0.10101); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.26s 00:00:00.84 Elapsed: 00:00:00.43
# Mc/sec: 3194.19
//
Query:       gene1087|gene1087|rna1087|rna1087  [L=93]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-16   60.4  11.3    1.3e-16   60.4  11.3    1.7  2  Ribosomal_L37e  Ribosomal protein L37e
  ------ inclusion threshold ------
      0.016   15.2   4.9      0.017   15.1   3.4    1.7  2  zf-RING_5       zinc-RING finger domain
      0.036   13.5   0.9       0.04   13.4   0.9    1.2  1  DUF1258         Protein of unknown function (DUF1258)
      0.047   13.4   0.9      0.047   13.4   0.9    2.4  3  zinc_ribbon_2   zinc-ribbon domain
      0.049   13.7   4.1      0.049   13.7   4.1    1.6  2  DZR             Double zinc ribbon
       0.14   12.0   6.4      0.079   12.9   3.7    1.8  2  C1_1            Phorbol esters/diacylglycerol binding domain 
       0.18   11.9   2.5       0.16   12.1   1.4    1.5  2  ASFV_p27        IAP-like protein p27 C-terminus
       0.47   10.4   8.5       0.17   11.7   5.9    1.6  2  zf-C3HC4        Zinc finger, C3HC4 type (RING finger)
       0.87    9.5   7.9       0.28   11.0   4.8    1.8  2  zf-C3HC4_2      Zinc finger, C3HC4 type (RING finger)


Domain annotation for each model (and alignments):
>> Ribosomal_L37e  Ribosomal protein L37e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.4  11.3   6.7e-20   1.3e-16       1      47 [.       2      47 ..       2      57 .. 0.87
   2 ?   -1.1   0.3       1.1   2.1e+03      15      21 ..      58      64 ..      48      77 .. 0.63

  Alignments for each domain:
  == domain 1  score: 60.4 bits;  conditional E-value: 6.7e-20
                     Ribosomal_L37e  1 tkGtssfGkrqkkktHilCrrCgkrsyhvqkktCascGypsaklrky 47
                                       tkGtssfGk+ +k+ H++C rCgk+s++ qk+tC++c+yp+ k+++ 
  gene1087|gene1087|rna1087|rna1087  2 TKGTSSFGKK-NKHNHTFCIRCGKTSFNKQKRTCSACAYPAPKWKRP 47
                                       8*********.666*****************************9854 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.1
                     Ribosomal_L37e 15 tHilCrr 21
                                       +  +Cr+
  gene1087|gene1087|rna1087|rna1087 58 VDKRCRH 64
                                       4445554 PP

>> zf-RING_5  zinc-RING finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   3.4   8.6e-06     0.017      22      42 ..      16      37 ..      15      39 .. 0.95
   2 ?   -1.3   0.0       1.1   2.2e+03      13      22 ..      55      64 ..      48      66 .. 0.66

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 8.6e-06
                          zf-RING_5 22 HifCekClkkll.ekeavCpiC 42
                                       H+fC +C k+++ +++++C++C
  gene1087|gene1087|rna1087|rna1087 16 HTFCIRCGKTSFnKQKRTCSAC 37
                                       ********************** PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.1
                          zf-RING_5 13 ekfyltsCgH 22
                                       +k +  +C H
  gene1087|gene1087|rna1087|rna1087 55 RKNVDKRCRH 64
                                       5555667888 PP

>> DUF1258  Protein of unknown function (DUF1258)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.9     2e-05      0.04       8      48 ..       8      50 ..       4      85 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2e-05
                            DUF1258  8 ykkknfsthkfcnkcGkvvaksek..celcggkvakfvrvgaf 48
                                       + kkn   h+fc +cGk+  +++k  c+ c+ +  k+ r  ++
  gene1087|gene1087|rna1087|rna1087  8 FGKKNKHNHTFCIRCGKTSFNKQKrtCSACAYPAPKWKRPASY 50
                                       56777889*********97665543499999888777776655 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.9   2.4e-05     0.047       6      21 ..       9      24 ..       9      25 .. 0.95
   2 ?    0.8   0.3      0.22   4.3e+02      15      22 ..      33      40 ..      29      40 .. 0.76
   3 ?   -3.1   0.0       3.7   7.3e+03      15      16 ..      61      62 ..      56      64 .. 0.55

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.4e-05
                      zinc_ribbon_2  6 GaelqdnakFCpyCGt 21
                                       G++++ n +FC +CG 
  gene1087|gene1087|rna1087|rna1087  9 GKKNKHNHTFCIRCGK 24
                                       9**************5 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.22
                      zinc_ribbon_2 15 FCpyCGtp 22
                                        C+ C +p
  gene1087|gene1087|rna1087|rna1087 33 TCSACAYP 40
                                       69999765 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 3.7
                      zinc_ribbon_2 15 FC 16
                                        C
  gene1087|gene1087|rna1087|rna1087 61 RC 62
                                       33 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   4.1   2.5e-05     0.049       6      40 ..      10      43 ..       7      50 .. 0.82
   2 ?    6.6   5.6    0.0038       7.6       1      24 [.      19      43 ..      19      72 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.5e-05
                                DZR  6 eelppdarfCseCgtklkavaaedrCpsCgekvdp 40
                                       ++++++  fC +Cg++    +++++C++C +++++
  gene1087|gene1087|rna1087|rna1087 10 KKNKHNHTFCIRCGKTSF-NKQKRTCSACAYPAPK 43
                                       67899999******9964.46799*****999876 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0038
                                DZR  1 CpqCgee.lppdarfCseCgtklka 24
                                       C +Cg+   ++++r+Cs+C  + ++
  gene1087|gene1087|rna1087|rna1087 19 CIRCGKTsFNKQKRTCSACAYPAPK 43
                                       7788776466777788888776544 PP

>> C1_1  Phorbol esters/diacylglycerol binding domain (C1 domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   3.7     4e-05     0.079       3      36 ..       8      39 ..       7      41 .. 0.88
   2 ?   -0.7   0.0      0.68   1.3e+03      37      44 ..      57      64 ..      53      77 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 4e-05
                                       EEEE--SS--B-TTT-SB--SSSS-EEEETTT-- CS
                               C1_1  3 wvhrnfkqptfCkhCgeflwgkekqglkCswCkl 36
                                       + ++n  + tfC  Cg+    ++kq  +Cs+C +
  gene1087|gene1087|rna1087|rna1087  8 FGKKNKHNHTFCIRCGKTS--FNKQKRTCSACAY 39
                                       566777899*********9..9**********86 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.68
                                       EE-CCCCT CS
                               C1_1 37 lvHkkChe 44
                                       +v+k+C +
  gene1087|gene1087|rna1087|rna1087 57 NVDKRCRH 64
                                       45566643 PP

>> ASFV_p27  IAP-like protein p27 C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   1.4   7.9e-05      0.16      83     116 ..       7      39 ..       2      54 .. 0.84
   2 ?   -1.7   0.0       1.5   2.9e+03      30      41 ..      55      66 ..      45      88 .. 0.55

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 7.9e-05
                           ASFV_p27  83 sfhkvnldnqttycmtcgiepikkdenfcnackt 116
                                        sf k n  n+ t+c+ cg    +k++  c ac  
  gene1087|gene1087|rna1087|rna1087   7 SFGKKNKHNH-TFCIRCGKTSFNKQKRTCSACAY 39 
                                        7889898876.79*******************75 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.5
                           ASFV_p27 30 rvythkrledmg 41
                                       r    kr   m 
  gene1087|gene1087|rna1087|rna1087 55 RKNVDKRCRHMK 66
                                       444444444443 PP

>> zf-C3HC4  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   5.9   8.8e-05      0.17      18      41 .]      15      37 ..      11      37 .. 0.96
   2 ?   -2.4   0.0       2.3   4.7e+03      16      19 ..      61      64 ..      52      65 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 8.8e-05
                                       S--B-CHHHHHHHHCTSSB--TTT CS
                           zf-C3HC4 18 kHsfCskCirkilksrkkvkCPlC 41
                                       +H+fC  C ++  + ++k++C  C
  gene1087|gene1087|rna1087|rna1087 15 NHTFCIRCGKTSFN-KQKRTCSAC 37
                                       6*************.9*******9 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 2.3
                                       TTS- CS
                           zf-C3HC4 16 eCkH 19
                                        C+H
  gene1087|gene1087|rna1087|rna1087 61 RCRH 64
                                       5877 PP

>> zf-C3HC4_2  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   4.8   0.00014      0.28      19      40 .]      15      37 ..      10      37 .. 0.92
   2 ?   -2.1   0.0       1.9   3.7e+03      16      20 ..      60      64 ..      56      66 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00014
                         zf-C3HC4_2 19 gHvfCqkCilrsLeekn.eCPlC 40
                                       +H+fC  C ++s ++++  C  C
  gene1087|gene1087|rna1087|rna1087 15 NHTFCIRCGKTSFNKQKrTCSAC 37
                                       7*************99999*888 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.9
                         zf-C3HC4_2 16 tpCgH 20
                                       + C H
  gene1087|gene1087|rna1087|rna1087 60 KRCRH 64
                                       57988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1072  (0.0597914); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 675.81
//
Query:       gene1088|gene1088|rna1088|rna1088  [L=233]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00054   19.7   0.0    0.00076   19.2   0.0    1.3  1  PRKCSH_1  Glucosidase II beta subunit-like protein


Domain annotation for each model (and alignments):
>> PRKCSH_1  Glucosidase II beta subunit-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   4.3e-08   0.00076      70     140 ..     121     194 ..      80     215 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 4.3e-08
                                        EEEEEETTEEEEEE-SB-.TTSSC-.EEEEEEEE-.SS-EEEEEEEEETTEEEEEEEEGGG--XXXXXXXXXXX CS
                           PRKCSH_1  70 efkkqegnklkyekGakC.WnGPvR.saiveveCG.denelvsvseaekCeYllkvkspaaCsnvllkkslaee 140
                                        +f + e++   +ekG kC +n  vR sa v++    d+ ++v   e + C+Y++kv +++   +   k+ ++ +
  gene1088|gene1088|rna1088|rna1088 121 SFIDNESYWQVFEKGDKCgFNKNVRwSARVQFTGSiDNLRVVRLIEGNLCNYEIKVVGDILTRKITNKDTIIYK 194
                                        456789999*********87998886899999865356799******************999776666666544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (233 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1057  (0.0589548); expected 358.6 (0.02)
Passed bias filter:                      557  (0.031067); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 1571.65
//
Query:       gene1089|gene1089|rna1089|rna1089  [L=125]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.2e-05   22.9   7.5      0.004   16.8   4.7    2.0  2  DUF4477   Domain of unknown function (DUF4477)
     0.0035   17.5   1.1     0.0035   17.5   1.1    1.4  2  SPT16     FACT complex subunit (SPT16/CDC68)


Domain annotation for each model (and alignments):
>> DUF4477  Domain of unknown function (DUF4477)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   4.7   4.5e-07     0.004      46      92 ..       7      53 ..       1      56 [. 0.90
   2 !   11.0   0.1   2.6e-05      0.23     134     175 ..      48      89 ..      45      94 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 4.5e-07
                            DUF4477 46 eleteaallsrllyrlknkfrnhkgfralkkveqaLkrlknmdLeke 92
                                       ele+e +ll++lly+ kn++r+   ++++k + + +k+ ++m+  k+
  gene1089|gene1089|rna1089|rna1089  7 ELENEYKLLKQLLYKSKNQHRRTLIYKKMKELFKKIKKRESMCVIKN 53
                                       79****************************************97665 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 2.6e-05
                            DUF4477 134 llrildlckkafllsvkhlrlgefiklntvllallsrlwvls 175
                                        ++ i ++++    ls + + +g+f+ ++ v++++ +++  ++
  gene1089|gene1089|rna1089|rna1089  48 MCVIKNVARGLYVLSSSNIVMGHFVGFTYVIMGISAKVYCIA 89 
                                        999**********************************99876 PP

>> SPT16  FACT complex subunit (SPT16/CDC68)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   1.1   3.9e-07    0.0035      63      99 ..      11      47 ..       3      57 .. 0.89
   2 ?   -3.6   0.0       1.2   1.1e+04      88      98 ..      95     105 ..      92     113 .. 0.48

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 3.9e-07
                              SPT16 63 eaifikeltfrskdekklqevfreikelkkkvkkrea 99
                                       e   +k+l ++sk++++ + +++++kel kk+kkre+
  gene1089|gene1089|rna1089|rna1089 11 EYKLLKQLLYKSKNQHRRTLIYKKMKELFKKIKKRES 47
                                       45679******************************97 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 1.2
                              SPT16  88 kelkkkvkkre 98 
                                         e+k+k +++ 
  gene1089|gene1089|rna1089|rna1089  95 DEIKEKRTNKS 105
                                        44444433333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1667  (0.0929779); expected 358.6 (0.02)
Passed bias filter:                      768  (0.0428356); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 940.84
//
Query:       gene109|gene109|rna109|rna109  [L=628]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.6e-26   90.9   0.3    1.7e-25   89.4   0.3    1.9  1  Evr1_Alr  Erv1 / Alr family
  ------ inclusion threshold ------
      0.046   13.3   0.2       0.08   12.6   0.2    1.3  1  RNF220    E3 ubiquitin-protein ligase RNF220


Domain annotation for each model (and alignments):
>> Evr1_Alr  Erv1 / Alr family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.4   0.3   1.9e-29   1.7e-25       1      94 [.     531     617 ..     531     623 .. 0.93

  Alignments for each domain:
  == domain 1  score: 89.4 bits;  conditional E-value: 1.9e-29
                                    HHHHHHHHHHHHCSHSS..HHHHHHH-CHHHHHHHHHHHSSCHHHHHHHHHHHHHCH.CCCGSSHHHHHHHHHHHHHHHH CS
                       Evr1_Alr   1 cslWtllHtlaaevpekpteeqqkelavlkaflkliakfypCeeCaehfekvlaenppekevesrdelvlWlweaHNeVn 80 
                                    +++W+llHt+a ++p +p+e+++k++    +fl l+ak++pCeeC++hf+k+l+++ p   v+sr+e+ lWl++aHN Vn
  gene109|gene109|rna109|rna109 531 RGTWRLLHTMASKYPINPEERDKKNI---IQFLFLLAKLFPCEECSMHFQKLLNDHAPV--VNSRKEFELWLCNAHNIVN 605
                                    79*************88999999999...99********************99999977..******************* PP

                                    HHTT...T-HHCHH CS
                       Evr1_Alr  81 krlakeefdcsedk 94 
                                    krl+k++fdc+  +
  gene109|gene109|rna109|rna109 606 KRLGKSNFDCE--N 617
                                    **********9..4 PP

>> RNF220  E3 ubiquitin-protein ligase RNF220
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.2   8.9e-06      0.08     117     185 ..     403     471 ..     381     474 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 8.9e-06
                         RNF220 117 kvleeltlhveaclrksesedededdedesidvEge.gesfeeYeWaGqkrvRattlleggfagsglrvt 185
                                    ++ eel++ +++ l+k+  e++++ +++e ++ +g+    +++  W G++   +t++ ++ +++ +l+ t
  gene109|gene109|rna109|rna109 403 TIDEELKQKMDSILKKNF-EGNADVNNEEVVEEDGKkVLDYGVNHWIGKRTSESTSFTSTVYNTCTLIAT 471
                                    567***********9987.7888888888888887766789999**************999998888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (628 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       902  (0.0503096); expected 358.6 (0.02)
Passed bias filter:                      470  (0.0262145); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.26s 00:00:00.86 Elapsed: 00:00:00.42
# Mc/sec: 4503.27
//
Query:       gene1090|gene1090|rna1090|rna1090  [L=185]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-13   51.0   0.3    2.1e-13   50.3   0.2    1.3  1  Peptidase_C65  Peptidase C65 Otubain


Domain annotation for each model (and alignments):
>> Peptidase_C65  Peptidase C65 Otubain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.3   0.2   1.2e-17   2.1e-13     136     204 ..      92     158 ..      73     172 .. 0.90

  Alignments for each domain:
  == domain 1  score: 50.3 bits;  conditional E-value: 1.2e-17
                                        HHHHHHHHHHHHHHHHHTHHHHGGGS-TT--HHHHHHHHTSSTT--B-HHHHHHHHHHTT--EEEEESS CS
                      Peptidase_C65 136 dyivvflRlltsaelkthadeyepFldelstveeFceqevepvnkEaDnvqitaLaealgvkvrVeyld 204
                                        +++ +fl+ll+s e+k ++++y pFl++  +v+++ +++vep+ k+ D v i a++++lg+kv V+ ++
  gene1090|gene1090|rna1090|rna1090  92 NSLTMFLKLLVSTEMKLNEEFYAPFLSK--SVSAYVSESVEPFYKDTDYVDILAFSRMLGIKVLVYTIE 158
                                        7789***********************9..***********************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       495  (0.0276089); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1344.71
//
Query:       gene1091|gene1091|rna1091|rna1091  [L=308]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (308 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1226  (0.0683808); expected 358.6 (0.02)
Passed bias filter:                      479  (0.0267165); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 2297.28
//
Query:       gene1092|gene1092|rna1092|rna1092  [L=185]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.023   14.9   0.2      0.051   13.8   0.0    1.7  2  DUF2666   Protein of unknown function (DUF2666)
       0.13   12.0   0.2       0.42   10.3   0.0    1.8  2  PGAP1     PGAP1-like protein


Domain annotation for each model (and alignments):
>> DUF2666  Protein of unknown function (DUF2666)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.1      0.55   4.9e+03      40      61 ..       2      23 ..       2      31 .. 0.62
   2 ?   13.8   0.0   5.7e-06     0.051      49      74 ..      91     116 ..      84     162 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.55
                                       HHHHHHHHHTT--HHHHHHHTT CS
                            DUF2666 40 tvskkikdylpfDlekleeiad 61
                                       t+++ i++++   +ek ++ + 
  gene1092|gene1092|rna1092|rna1092  2 TIKNTIYEFIRKSVEKAYNKFR 23
                                       5667777777766666665554 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 5.7e-06
                                        TT--HHHHHHHTTT--S--S....HH CS
                            DUF2666  49 lpfDlekleeiadeikkkkkgrvkee 74 
                                        ++fDl++l++++d+++ kkkg v+  
  gene1092|gene1092|rna1092|rna1092  91 IEFDLNDLYKEFDDFYAKKKGMVTAF 116
                                        79*******************99854 PP

>> PGAP1  PGAP1-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.1     0.096   8.6e+02      27      56 ..      15      44 ..       8      55 .. 0.85
   2 ?   10.3   0.0   4.7e-05      0.42     112     181 ..      68     136 ..      63     176 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.096
                              PGAP1 27 aaeayqelrkllknqnkkeldfftvdfnee 56
                                       +++ay + r +++n+ + e+ ++  d++++
  gene1092|gene1092|rna1092|rna1092 15 VEKAYNKFRTEERNKEPVEVGYYPFDYDRK 44
                                       5678999999999**********9999986 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 4.7e-05
                              PGAP1 112 knyikqsvntiltlasPhalpplsfdkdilklyervnefwkkeleekeklenvllvsitggirdsmvpae 181
                                        +++++++++   t +sP+   pl ++ d+ +ly++ ++f+ k+    +++e  l++si   i+d  v + 
  gene1092|gene1092|rna1092|rna1092  68 ASHMESEIHIYDTNGSPVCVIPL-IEFDLNDLYKEFDDFYAKKKGMVTAFEGYLVNSILEFINDKNVTSS 136
                                        5688899999999****988777.6677*************99999999***************998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       681  (0.0379832); expected 358.6 (0.02)
Passed bias filter:                      465  (0.0259356); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1326.31
//
Query:       gene1093|gene1093|rna1093|rna1093  [L=236]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       942  (0.0525406); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 1751.18
//
Query:       gene1094|gene1094|rna1094|rna1094  [L=440]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (440 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       484  (0.0269954); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 3152.47
//
Query:       gene1095|gene1095|rna1095|rna1095  [L=247]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       606  (0.0338); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1670.24
//
Query:       gene1096|gene1096|rna1096|rna1096  [L=503]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        1.2    7.2  19.4       0.66    8.1   5.2    2.1  2  Nop14     Nop14-like family


Domain annotation for each model (and alignments):
>> Nop14  Nop14-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   6.3   0.00032       5.7     347     417 ..      42     112 ..      16     143 .. 0.47
   2 ?    8.1   5.2   3.7e-05      0.66     352     469 ..     255     372 ..     232     388 .. 0.41

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.00032
                              Nop14 347 eeeededdfeedddlveseseeeeeeeeedeeeeedeeeeeeeeededdlsdleseeeeeedeleeellee 417
                                         ++ + +dfe+ d++  s+++e  ++ +e e+++e + e ++++e e+++++ ++e+   +de + +++++
  gene1096|gene1096|rna1096|rna1096  42 RKNTEREDFEIIDNKGRSTKNERGNKTGEVENDKEGDTERKDKNERENTAQTISNEQTVTNDENSIKSNAS 112
                                        33444444554443444444433344444444444444444444444444444444333333321111111 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 3.7e-05
                              Nop14 352 eddfeedddlveseseeeeeeeeedeeeeedeeeeeeeeededdlsdleseeeeeedeleeel...........le 416
                                        e++    dd+ e ++++++ ++++d++++++        ++ d++sd+ + +  ++d++++++           l+
  gene1096|gene1096|rna1096|rna1096 255 EREG--GDDEGEGGNDNDK-NNDNDKNNDKS--------NSRDKSSDKGKGNGRDKDNVNDNNvnttlndinpaLN 319
                                        1111..1111111111111.11111111111........1111111111112222222211111111122233333 PP

                              Nop14 417 eekkaaeekkekkkkkkkseekakeelpytfpcPesheellellekreisaed 469
                                        ++ ++++ k+ +++++ +++ k+ +++   ++   s+++l + l++ + s++d
  gene1096|gene1096|rna1096|rna1096 320 NNINSPALKNVNNHQNFNNTVKTPNTVKLLYKHKLSVNHLTATLSHITSSSAD 372
                                        33333333444445555555556666666666666666666666655445555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (503 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1762  (0.0982765); expected 358.6 (0.02)
Passed bias filter:                      465  (0.0259356); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.74u 0.29s 00:00:01.03 Elapsed: 00:00:00.49
# Mc/sec: 3057.07
//
Query:       gene1097|gene1097|rna1097|rna1097  [L=45]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (45 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       257  (0.0143343); expected 358.6 (0.02)
Passed bias filter:                      189  (0.0105416); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.27s 00:00:00.63 Elapsed: 00:00:00.43
# Mc/sec: 314.75
//
Query:       gene1098|gene1098|rna1098|rna1098  [L=324]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.1e-14   53.2   0.2    4.5e-14   52.1   0.2    1.6  1  TBPIP        TBPIP/Hop2 winged helix domain
  ------ inclusion threshold ------
      0.019   14.9   0.6      0.019   14.9   0.6    3.2  2  Prefoldin_2  Prefoldin subunit
        6.8    5.3  12.0        9.4    4.9  12.0    1.4  1  Presenilin   Presenilin
        7.9    6.8  10.9         13    6.1  10.9    1.4  1  Dsh_C        Segment polarity protein dishevelled (Dsh) C ter


Domain annotation for each model (and alignments):
>> TBPIP  TBPIP/Hop2 winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.1   0.2     1e-17   4.5e-14       3      62 .]     138     197 ..     136     197 .. 0.96

  Alignments for each domain:
  == domain 1  score: 52.1 bits;  conditional E-value: 1e-17
                              TBPIP   3 eelvleylqeqnrPfsvqdvvanlqkklgKtavqkaLdeLvdegkiieKeyGKqkiYlan 62 
                                        e  vl+ ++ ++rP svqd   +++++++K a + aLd Lv++g++i+K y K+++Yl n
  gene1098|gene1098|rna1098|rna1098 138 ERNVLNHMELSYRPHSVQDLLIAFKNEIKKSALVNALDALVEKGRVISKAYNKSAVYLYN 197
                                        67899****************************************************976 PP

>> Prefoldin_2  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -7.1  10.8         4   1.8e+04      17      45 ..      14      42 ..       9      99 .. 0.74
   2 ?   14.9   0.6   4.3e-06     0.019      12      61 ..     206     253 ..     197     270 .. 0.83

  Alignments for each domain:
  == domain 1  score: -7.1 bits;  conditional E-value: 4
                                       HHHHHHHHHHHHHHHHHHHHHHHHS-TT- CS
                        Prefoldin_2 17 laqqikqletqlkelelvleelelldedt 45
                                        + ++ +l +++ke+e +++e+++ d+++
  gene1098|gene1098|rna1098|rna1098 14 AKRKKCTLVMKKKENECIENEINEDDKEK 42
                                       56677788899999999999999877764 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 4.3e-06
                                        HHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-TT--EEEEETTEEEEE-HH CS
                        Prefoldin_2  12 qqlqqlaqqikqletqlkelelvleelelldedtkvyklvGdvlvkqdke 61 
                                         ++++++q ik++e++++ l++ +  l + ++d+   +++G++   ++ke
  gene1098|gene1098|rna1098|rna1098 206 GDMHEVEQCIKNVEQEINALKDSIARLREYPPDEHLIRMIGEL--REKKE 253
                                        67899************************************95..44444 PP

>> Presenilin  Presenilin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9  12.0    0.0021       9.4     235     302 ..      36     103 ..       6     210 .. 0.53

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.0021
                         Presenilin 235 seeeeeaekkkeeasesskeeeseeesseksaqsseseeeseeesseaessaeesseekeseessess 302
                                        +e+++e+e+++ee s + ++++++e+s++++++++ ++++++++++++  +++++++ k++++  +s+
  gene1098|gene1098|rna1098|rna1098  36 NEDDKEKENNTEEGSGTCSDASADEKSTDDESSEECKSSRAKKKEEKKGGRESKNTQGKNNKKGINSK 103
                                        11111111111222211111111111111111111111111111111111111111111111111111 PP

>> Dsh_C  Segment polarity protein dishevelled (Dsh) C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1  10.9     0.003        13      66     164 ..      50     152 ..      26     170 .. 0.50

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.003
                              Dsh_C  66 gsagsqhsegsrssgsnrsegkakreaskeekerkaggsgsesesstrssvsrrerekaqserssaaaserskrss 141
                                        + + s+ s   +s+  + se+ ++++a+k+e++   gg  s+  + ++++   +++++ ++++++++ s++s + +
  gene1098|gene1098|rna1098|rna1098  50 SGTCSDASADEKSTDDESSEECKSSRAKKKEEK--KGGRESKNTQGKNNKKGINSKKSINRNKNANKGSDESDTYV 123
                                        335566666666666555555444444443333..23333333333333322233333444444555555555553 PP

                              Dsh_C 142 klrsksslssha......erssalsygpp 164
                                         +++++s++s a       + ++lsy p 
  gene1098|gene1098|rna1098|rna1098 124 GTTRRNSTQSSAeiernvLNHMELSYRPH 152
                                        32222222222212222245556666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (324 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2676  (0.149255); expected 358.6 (0.02)
Passed bias filter:                      666  (0.0371465); expected 358.6 (0.02)
Passed Vit filter:                       117  (0.00652574); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.77u 0.36s 00:00:01.12 Elapsed: 00:00:00.52
# Mc/sec: 1862.96
//
Query:       gene1099|gene1099|rna1099|rna1099  [L=93]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.1e-07   29.6   0.0    9.9e-07   28.7   0.0    1.4  1  HTH_3     Helix-turn-helix
     0.0034   17.7   0.0     0.0053   17.1   0.0    1.2  1  HTH_31    Helix-turn-helix domain
  ------ inclusion threshold ------
      0.015   15.1   0.0      0.034   14.0   0.0    1.6  1  HTH_25    Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7   0.0   1.7e-10   9.9e-07       4      51 ..      42      88 ..      41      90 .. 0.92

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 1.7e-10
                                       HHHHTTHHHHHHHHHHTSSHHHHHHHHTTSSCSBHHHHHHHHHHHTSE CS
                              HTH_3  4 lRkqlglsqeeLAeklGvsrstisriEnGernPsletlkklakaLgvs 51
                                       +R+  +++q++LA k++ ++s +++iE+Ge     ++++ ++k+Lgv+
  gene1099|gene1099|rna1099|rna1099 42 ARENMKMTQKDLAGKINKPVSVVRDIEKGEE-VERSVVEMVEKTLGVK 88
                                       79***************************55.9999999999999986 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   8.9e-07    0.0053       8      56 ..      41      87 ..      40      90 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 8.9e-07
                             HTH_31  8 alReraGLsqeevAerlgvsestlsrlEqGrrgrpspavlealaralgl 56
                                       ++Re   ++q+++A+ ++  +s ++++E G++  + ++v+e +   lg+
  gene1099|gene1099|rna1099|rna1099 41 HARENMKMTQKDLAGKINKPVSVVRDIEKGEE--VERSVVEMVEKTLGV 87
                                       68******************************..788999888888887 PP

>> HTH_25  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   5.7e-06     0.034       4      34 ..      41      71 ..      38      74 .. 0.94

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.7e-06
                                       HHHHTTT--HHHHHHHSS--HHHHHHHHCT- CS
                             HTH_25  4 aaRearglsleevaketkIrkdylealEedd 34
                                        aRe ++++ +++a +++ ++++++ +E+++
  gene1099|gene1099|rna1099|rna1099 41 HARENMKMTQKDLAGKINKPVSVVRDIEKGE 71
                                       59**************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1096  (0.06113); expected 358.6 (0.02)
Passed bias filter:                      495  (0.0276089); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 667.77
//
Query:       gene11|gene11|rna11|rna11  [L=1015]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   9.9e-192  638.4   0.1   2.9e-190  633.5   0.1    2.1  1  tRNA-synt_1    tRNA synthetases class I (I, L, M and V)
    1.4e-19   70.6   0.3    3.5e-19   69.3   0.3    1.6  1  Anticodon_1    Anticodon-binding domain of tRNA
    3.2e-17   62.3   7.1    4.9e-10   38.7   0.1    5.3  5  tRNA-synt_1g   tRNA synthetases class I (M)
    3.1e-11   43.1   7.8    3.9e-11   42.8   0.1    3.2  3  tRNA-synt_1_2  Leucyl-tRNA synthetase, Domain 2
    0.00026   20.4   0.1        0.9    8.8   0.0    2.9  3  tRNA-synt_1e   tRNA synthetases class I (C) catalytic domain
      0.005   16.2   0.0        1.6    8.0   0.0    2.7  2  tRNA-synt_1b   tRNA synthetases class I (W and Y)


Domain annotation for each model (and alignments):
>> tRNA-synt_1  tRNA synthetases class I (I, L, M and V)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  633.5   0.1  9.7e-194  2.9e-190       2     601 ..      72     690 ..      71     691 .. 0.96

  Alignments for each domain:
  == domain 1  score: 633.5 bits;  conditional E-value: 9.7e-194
                tRNA-synt_1   2 lyekWeeedvfkkel..ekeke.kkefilvdgPPyvtGslHiGhalaktlkdivirykrmkGkevlyvpGwDhaGlaieakvek 82 
                                +y++W+++++fk+e   +++++ +++++++ +PP+vtG+lHiGha+  +++d + rykrm+G+evl+vpG+DhaG+a++++vek
  gene11|gene11|rna11|rna11  72 WYSWWDKKGFFKPEIlkKHRDDvREPYVMALPPPNVTGKLHIGHAMMVAIEDAIARYKRMQGFEVLFVPGCDHAGIATQTVVEK 155
                                8***********98521344557899********************************************************** PP

                tRNA-synt_1  83 klgakekkerkklgreefrekvrewkaeyaeeirkqvkrlGvsvDfdreylTldkeleeavkevfvrladkgliyrgkklvnws 166
                                kl ++++ +r++lgre+f++ v++wk++y ++i +q+krlG+svD  r  +Tldk+++e v+e+fv+l+++ liyr +kl+nw+
  gene11|gene11|rna11|rna11 156 KLYKEKRLTRYDLGREKFIDMVWKWKEKYGDTIIEQIKRLGTSVDMGRYVFTLDKKVNEGVIEAFVQLYERKLIYRESKLINWC 239
                                ************************************************************************************ PP

                tRNA-synt_1 167 tklktalselEveykdkk..............dalihvafpladkee....vklviaTTtPeTllgdtavavnpeldyvitkek 232
                                 kl+tals+lEv++k +k              ++l+ +++pladk +     +++iaTT+PeT++gdta++vnp          
  gene11|gene11|rna11|rna11 240 SKLSTALSDLEVDHKPVKpftklqvdgkkyvfGVLYAIKYPLADKGSaeinDYVEIATTRPETIIGDTALCVNPM--------- 314
                                ******************************************877665666699*********************......... PP

                tRNA-synt_1 233 lilaeallkslvkkesekkiledergkeLegkevelplvnrkipiiaddyvdkeaGtGvVkiaPahdedDyevgkkynlevini 316
                                                      d+r+++L  k +++p++++ ipii d+y+++e+GtGvVki+Pahd++Dy ++kk++l v n+
  gene11|gene11|rna11|rna11 315 ----------------------DKRAQYLRTKVAINPITKEVIPIIFDEYAEMEFGTGVVKITPAHDFNDYDLAKKHGLAVKNV 376
                                ......................99************************************************************ PP

                tRNA-synt_1 317 ldedgtlteeaaefeglkvfdarkkvveelkekglllkaekiehsvpfcerskkpiiyrateqWfvrvkeladaalkave..kv 398
                                l+e+ ++  e + f ++k+f ar kv+e+l+ +gl+++++  e ++p+c+rs++++++++++qW+   k +a +a++ave  + 
  gene11|gene11|rna11|rna11 377 LNENNEVCVE-GSFYKMKRFYARIKVLEYLRSTGLFVSETGYEQTLPICSRSGDVLEPHLKKQWWLDCKGMARKAIEAVEskEL 459
                                ****998776.67999***************************************************************9999* PP

                tRNA-synt_1 399 qfvpkskekryaswleniqdWciSRqrwWGhriplfvsketeevvvreelkelvagreeeeaekkalekeakdklkkekgelek 482
                                ++vp+ + k+++ wl ni+dWc+SRq+wWGh+ip++   + +e         +v +r+++ea++ka   e++ kl++++  l++
  gene11|gene11|rna11|rna11 460 KIVPDIAIKNWNYWLSNIRDWCLSRQLWWGHQIPAYEVLKDGESA------GWVVARTKDEAKHKA---ETTFKLQTGDYVLRQ 534
                                ************************************777766555......599999999888887...445678999****** PP

                tRNA-synt_1 483 dedvlDvWFsSgswpfstlgypeedteelkkffpadmlleGlDiirgWvarlillslaltgsePfkevlvhglvrdeeGrKmSK 566
                                dedvlD+WFsSg+wpf +lg+p   t++++++fp ++l++G+Di+++Wvar+++lsl+ltg++Pf+++l+hg+vrd++GrKmSK
  gene11|gene11|rna11|rna11 535 DEDVLDTWFSSGLWPFVILGWPAA-TDDFARYFPNSILETGSDILFFWVARMVMLSLELTGKVPFNTILLHGIVRDANGRKMSK 617
                                ************************.*********************************************************** PP

                tRNA-synt_1 567 slgNvidpldvik.....................................kygadalRltli.lsdvgrdinl 601
                                slgNvidpl+vi+                                     ++g dalR+tl+ +++ ++d+nl
  gene11|gene11|rna11|rna11 618 SLGNVIDPLYVIEgvqldelaksitatnldpkeikaalegqrkdfpmgipRCGSDALRFTLCsYTSGMKDVNL 690
                                **********************************************************************997 PP

>> Anticodon_1  Anticodon-binding domain of tRNA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.3   0.3   1.2e-22   3.5e-19       3     147 ..     816     948 ..     815     953 .. 0.82

  Alignments for each domain:
  == domain 1  score: 69.3 bits;  conditional E-value: 1.2e-22
                Anticodon_1   3 wilselnklvkevteayeeyrfnkaasalyeffwndlcdwylelvkprlysesaedkraaqevllevletllrllaPfmPfitE 86 
                                w+  + +  ++e+  +++ ++f  a + +++f + ++cd+++e+vk+  ++e         ++l  v++ ++ ll+PfmPfitE
  gene11|gene11|rna11|rna11 816 WLYGKREAMIEEFISSMDTFNFMSATQCIHQFALYTYCDVFIEVVKQCTQTEYV-------AALVLVFRDIILLLHPFMPFITE 892
                                99999*****************************************99987665.......99********************* PP

                Anticodon_1  87 elwqr..eeeelgkkesimlaewpekaeelekeleeeevellkeivkairklrselkikpsse 147
                                el+qr    + l+  esi ++  p    ++e        + + +i ++ r++rs+++ ++ + 
  gene11|gene11|rna11|rna11 893 ELFQRlrALRILNLLESITVERLPR-RFDHE------FTDSFSQITSICRSVRSIMDSNNLKS 948
                                *****963333466699*******4.43332......34445557777777777776665544 PP

>> tRNA-synt_1g  tRNA synthetases class I (M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.4      0.67     2e+03     191     220 ..      12      41 ..       9      49 .. 0.70
   2 !   38.7   0.1   1.6e-13   4.9e-10       8     136 ..     105     252 ..      98     260 .. 0.76
   3 !   13.3   0.1   8.4e-06     0.025     167     240 ..     422     495 ..     414     501 .. 0.90
   4 !    7.8   0.0   0.00039       1.2     313     350 ..     599     637 ..     558     653 .. 0.75
   5 ?   -0.3   0.0      0.12   3.5e+02     344     368 ..     668     692 ..     665     709 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 0.67
                                GHHHHHHHH.HH-TTSHHHHHHHH.HHHHT CS
               tRNA-synt_1g 191 fekklkewieeeekeleenvkkivkewlke 220
                                 +kkl+++i++++k ++++ kk +k  +++
  gene11|gene11|rna11|rna11  12 KQKKLEKFIKKQSKAQQTECKKNIKLQISQ 41 
                                578999999888888777777776655544 PP

  == domain 2  score: 38.7 bits;  conditional E-value: 1.6e-13
                                B--SS---HHHHHHHHHHHHHHHHHHHTT-EEEEEEEE---SHHHHHHHHHTTS-HHHHH.................HHHHHHH CS
               tRNA-synt_1g   8 pYangklHlGhllevisaDifaRykrlrgeevlfvcgtDehGtpielkAekegvtpeelv.................ekvheei 74 
                                p ++gklH+Gh++ v + D++aRykr++g evlfv g D+ G+++++  ek+  + + l+                 ek+ ++i
  gene11|gene11|rna11|rna11 105 PNVTGKLHIGHAMMVAIEDAIARYKRMQGFEVLFVPGCDHAGIATQTVVEKKLYKEKRLTrydlgrekfidmvwkwkEKYGDTI 188
                                6689****************************************9998887655544332111111111122222224566677 PP

                                HHHHHHTT---S..EEEETTSHHHHHHHHHHHHHHHHTT-EEEEEEEEEEETTTTEEE-GGG-E CS
               tRNA-synt_1g  75 kelfkklnisfd..kygrttseehkelvqeifkklkekgliyekeieqlycpkderflpdryve 136
                                 e+ k+l+ s d   y  t +++ +e v e f +l+e++liy+++    +c k ++ l+d +v+
  gene11|gene11|rna11|rna11 189 IEQIKRLGTSVDmgRYVFTLDKKVNEGVIEAFVQLYERKLIYRESKLINWCSKLSTALSDLEVD 252
                                7788888777764469999999999999999999999999999999999999999999998875 PP

  == domain 3  score: 13.3 bits;  conditional E-value: 8.4e-06
                                ..........EEE.EEEEEE-GGGGHHHHHHHH.HH-TT.SHHHHHHHH.HHHHT----EE-ESS-SSS-EETTE CS
               tRNA-synt_1g 167 pksaisgskpevketehlffklskfekklkewieeeeke.leenvkkivkewlkegLkdlaisrdldwGipvPga 240
                                p ++ sg+  e + +++++++ + +++k  e +e++e +  ++ + k  + wl++ ++d+++sr+l wG ++P  
  gene11|gene11|rna11|rna11 422 PICSRSGDVLEPHLKKQWWLDCKGMARKAIEAVESKELKiVPDIAIKNWNYWLSN-IRDWCLSRQLWWGHQIPAY 495
                                788889998888889***********99999998888888999999*******99.*****************65 PP

  == domain 4  score: 7.8 bits;  conditional E-value: 0.00039
                                S-EEEE--E.EE--------------HHHHHHHH-HHHH CS
               tRNA-synt_1g 313 kkvvaheyl.tvegkKlSkSrgvvvkakealerldadll 350
                                +++  h+ +   +g+K+SkS g+v+++  ++e ++ d l
  gene11|gene11|rna11|rna11 599 NTILLHGIVrDANGRKMSKSLGNVIDPLYVIEGVQLDEL 637
                                5566666662479**************999999988876 PP

  == domain 5  score: -0.3 bits;  conditional E-value: 0.12
                                HH-HHHHHHHHHHHS-TTS-EEE-H CS
               tRNA-synt_1g 344 rldadllRYylaaeapekkDldfsw 368
                                r+ +d+lR+ l++ ++ +kD++++ 
  gene11|gene11|rna11|rna11 668 RCGSDALRFTLCSYTSGMKDVNLNI 692
                                5789****************99874 PP

>> tRNA-synt_1_2  Leucyl-tRNA synthetase, Domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   2.3      0.54   1.6e+03      51      74 ..       9      32 ..       5      45 .. 0.80
   2 ?    3.2   0.0     0.019        57      21      46 ..     291     316 ..     275     324 .. 0.76
   3 !   42.8   0.1   1.3e-14   3.9e-11      87     145 ..     324     382 ..     313     402 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.54
              tRNA-synt_1_2 51 laekkkelaafieevkkksesere 74
                                 +k+k+l++fi++ +k +++e +
  gene11|gene11|rna11|rna11  9 ELKKQKKLEKFIKKQSKAQQTECK 32
                               468999*******99998888754 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.019
              tRNA-synt_1_2  21 eklevfttrpdtlfGvtfvalapehp 46 
                                + +e+ ttrp+t++G t + + p  +
  gene11|gene11|rna11|rna11 291 DYVEIATTRPETIIGDTALCVNPMDK 316
                                478999*********99999887665 PP

  == domain 3  score: 42.8 bits;  conditional E-value: 1.3e-14
              tRNA-synt_1_2  87 lkaihPitgekipiwvanyvlmeygtgavmavPahdqrDfeFakkynlpikqvikpede 145
                                  ai+Pit+e ipi   +y  me+gtg+v   Pahd +D++ akk++l +k+v+++++e
  gene11|gene11|rna11|rna11 324 KVAINPITKEVIPIIFDEYAEMEFGTGVVKITPAHDFNDYDLAKKHGLAVKNVLNENNE 382
                                579***************************************************97765 PP

>> tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.0    0.0003       0.9      17      52 ..     105     140 ..      96     230 .. 0.91
   2 !    8.4   0.0   0.00041       1.2     214     264 ..     574     625 ..     501     647 .. 0.78
   3 ?   -3.1   0.0       1.3   3.9e+03      55     115 ..     775     863 ..     773     870 .. 0.57

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0003
                                EBTTS--BHHHHHHHHHHHHHHHHHHHTT-EEEEEE CS
               tRNA-synt_1e  17 ptvydashlGhaRslvafDilrrilqalgYdvqfvq 52 
                                p v  + h+Gha  + + D ++r+ +++g++v fv 
  gene11|gene11|rna11|rna11 105 PNVTGKLHIGHAMMVAIEDAIARYKRMQGFEVLFVP 140
                                678899****************************95 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00041
                                EGGGTTTHHHHHHHHHHHHSS.S--EEEEEEE--EEETTBE--TTTT---BH CS
               tRNA-synt_1e 214 GiDLafPhhenelaqseaafd.kqlvkyflhnghlkiegekmsksLknfiti 264
                                G+D++f      +  s  +++  ++  + lh  +   +g+kmsksL+n+i  
  gene11|gene11|rna11|rna11 574 GSDILFFWVARMVMLSLELTGkVPFNTILLHGIVRDANGRKMSKSLGNVIDP 625
                                66666666666666666667734555566666666799**********9965 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 1.3
                                B--SHHHHHHHHHTTS-.........................HHHHHHHHHHHHHHHHHHTT----SB...--BGGGGHHHHHH CS
               tRNA-synt_1e  55 tDidDkiikrareeeks.........................vkelaekfieefkkdleaLnvlkptl...eprvsekvdeiie 110
                                tD+ Dk+  +  ++ +                          +    e +ieef + +++ n   +t    +     + d  ie
  gene11|gene11|rna11|rna11 775 TDVSDKLFVKTFNKVEPelehsvktlsisenglssvrcviewLYGKREAMIEEFISSMDTFNFMSATQcihQFALYTYCDVFIE 858
                                677777766666655555556666666666666666665554344456777888888888777766541112233455555566 PP

                                HHHHH CS
               tRNA-synt_1e 111 lvekl 115
                                +v++ 
  gene11|gene11|rna11|rna11 859 VVKQC 863
                                66555 PP

>> tRNA-synt_1b  tRNA synthetases class I (W and Y)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.9   0.0    0.0045        13      15      68 ..     108     164 ..     106     184 .. 0.78
   2 !    8.0   0.0   0.00052       1.6     184     210 ..     600     624 ..     582     630 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.0045
                                SSS-BGG..GHHHHHHHHHHHH..TTSEEEEEEEHHHHHTTTTT-SSHHHHHHHHHHH CS
               tRNA-synt_1b  15 TgklHlG..ylvplkklvelqk..aghevffliaDlhAiigdpskaeerklrkreevl 68 
                                TgklH+G   +v+++  ++ +k  +g ev+f+ +  hA i  ++   e+kl k+++ +
  gene11|gene11|rna11|rna11 108 TGKLHIGhaMMVAIEDAIARYKrmQGFEVLFVPGCDHAGIATQT-VVEKKLYKEKRLT 164
                                9******655788988888887889*******999999999999.5566655555444 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.00052
                                EEEEET-BBSTTSSSBTTCETTCGC-B CS
               tRNA-synt_1b 184 egltvplltgldGekKmSKSagnsaIf 210
                                 +l++ ++ +++G  KmSKS gn +I+
  gene11|gene11|rna11|rna11 600 TILLHGIVRDANGR-KMSKSLGN-VID 624
                                567888********.********.775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1015 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1326  (0.0739584); expected 358.6 (0.02)
Passed bias filter:                      737  (0.0411066); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.90u 0.32s 00:00:01.22 Elapsed: 00:00:00.53
# Mc/sec: 5762.93
//
Query:       gene110|gene110|rna110|rna110  [L=441]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        0.3   10.2   5.3       0.78    8.9   0.8    2.2  2  MSP       Manganese-stabilising protein / photosystem II poly
        2.1    8.3   5.0       0.96    9.4   0.4    2.6  2  DUF2719   Protein of unknown function (DUF2719)


Domain annotation for each model (and alignments):
>> MSP  Manganese-stabilising protein / photosystem II polypeptide
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.8   8.7e-05      0.78      10      47 ..     139     176 ..     134     191 .. 0.87
   2 ?    3.2   0.3    0.0046        41      13     105 ..     310     403 ..     304     420 .. 0.69

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 8.7e-05
                                    TTSGGGS-----TT-B--EESHTTSSEEEEEEEEEEEE CS
                            MSP  10 gtGlAnkCpelsesargsisieagksyklkdlClePte 47 
                                    + G  n C +lse+ +++++++++k+++  + Cl+ ++
  gene110|gene110|rna110|rna110 139 NQGNVNPCEQLSEHCKNTVQVSESKTINTAKTCLNDES 176
                                    7899******************************8766 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.0046
                                    GGGS-----TT-B--EESHTTSSEEEEEEEEEEEEEEEE---SSSSSS.T-EEEEEESS-S-SSEEEEEEEEEE-TTS-E CS
                            MSP  13 lAnkCpelsesargsisieagksyklkdlClePteflvkeepankrqe.aefvkgklltrktssldqvegelkvkedgsl 91 
                                    lA++   ++e  +g+i+ + + +++++d C+e  ++  ++++++++++ ++  +   +  ++ss ++ + +++ +++++ 
  gene110|gene110|rna110|rna110 310 LADRNIPINEPLNGTITKNISPDLQFNDKCIETPSLSCECNQQSENRNwKNIKNLSQINNSASSTETDNFSVSSEHSSTN 389
                                    67777788899999999999999*********999999887776533303333444455555566655566666667777 PP

                                    EEEEEEEE-EEEEE CS
                            MSP  92 tlkekdGidfqait 105
                                     +++++G d +  t
  gene110|gene110|rna110|rna110 390 YINNNKGTDNALNT 403
                                    78888888876554 PP

>> DUF2719  Protein of unknown function (DUF2719)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.4   0.00011      0.96      49      74 ..     146     171 ..     129     173 .. 0.89
   2 ?   -0.7   0.4      0.16   1.4e+03      50      74 ..     333     364 ..     326     368 .. 0.54

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00011
                        DUF2719  49 neqfadkcsnnlvvtqpktwsnyknc 74 
                                     eq+ ++c+n+++v ++kt + +k+c
  gene110|gene110|rna110|rna110 146 CEQLSEHCKNTVQVSESKTINTAKTC 171
                                    5899******************9999 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.16
                        DUF2719  50 eqfadkcsnnlvv.......tqpktwsnyknc 74 
                                     qf dkc ++  +        + + w+n+kn 
  gene110|gene110|rna110|rna110 333 LQFNDKCIETPSLscecnqqSENRNWKNIKNL 364
                                    57778886653321111111345667776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (441 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1081  (0.0602934); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 2978.35
//
Query:       gene1100|gene1100|rna1100|rna1100  [L=33]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (33 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       392  (0.021864); expected 358.6 (0.02)
Passed bias filter:                      159  (0.00886831); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.21s 00:00:00.55 Elapsed: 00:00:00.38
# Mc/sec: 259.27
//
Query:       gene1101|gene1101|rna1101|rna1101  [L=218]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.2e-24   83.9   4.3    1.1e-23   83.2   4.3    1.3  1  PSP1      PSP1 C-terminal conserved region


Domain annotation for each model (and alignments):
>> PSP1  PSP1 C-terminal conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.2   4.3   6.4e-28   1.1e-23       1      86 []     120     205 ..     120     205 .. 0.99

  Alignments for each domain:
  == domain 1  score: 83.2 bits;  conditional E-value: 6.4e-28
                               PSP1   1 kqvlrlatpedvstnlenkqdeekalhiaqeklkelnlnmklldaefqfdrkkltfyYvaeervDFreLvkeLfkf 76 
                                        k++ r a ++d++ ++ + ++e+ al  +++++k+  lnm + ++e+q+d +kltf++++e ++DFreLvk+L k 
  gene1101|gene1101|rna1101|rna1101 120 KKIFRRAGENDLKIIDLKTRKERIALADCRTRVKAEMLNMVIDKCEYQWDMNKLTFFFSSEYKIDFRELVKNLYKE 195
                                        79************************************************************************** PP

                               PSP1  77 yktRIwLcai 86 
                                        yk+RIw+cai
  gene1101|gene1101|rna1101|rna1101 196 YKIRIWMCAI 205
                                        ********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       542  (0.0302304); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1576.20
//
Query:       gene1102|gene1102|rna1102|rna1102  [L=323]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
     0.0076   16.5   0.8      0.017   15.4   0.8    1.6  1  Colicin_E5  Colicin E5 ribonuclease domain
  ------ inclusion threshold ------
      0.018   14.9   1.0       0.14   12.1   0.0    2.4  2  TMEM154     TMEM154 protein family
      0.054   13.3   0.4      0.097   12.5   0.4    1.4  1  TMIE        TMIE protein
       0.14   12.0   0.2         16    5.4   0.0    2.9  2  ECSCR       Endothelial cell-specific chemotaxis regulator


Domain annotation for each model (and alignments):
>> Colicin_E5  Colicin E5 ribonuclease domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.8   3.8e-06     0.017      24      85 ..      29      87 ..      14      92 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 3.8e-06
                         Colicin_E5 24 rdvvskgaktkssddkranktsDglrrndsAtvYgekdgkYvvvndrtgevvqvsdkndpeW 85
                                       +++v+ g +++++d    +  sD  +rnd+A+   ++  kYv   ++t e vq  ++  +++
  gene1102|gene1102|rna1102|rna1102 29 EKTVNSGLHGQTNDTVMLE--SDSGSRNDTASEHRKE-TKYVATTNNTAESVQYEEETTSSF 87
                                       6789999999999999999..9**********99887.***************998877766 PP

>> TMEM154  TMEM154 protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   1.6      0.19   8.7e+02      17      36 ..      60      78 ..      13     106 .. 0.61
   2 ?   12.1   0.0   3.1e-05      0.14      48      94 ..     271     316 ..     240     322 .. 0.75

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.19
                            TMEM154 17 leeesadatsaasteseslk 36
                                         +e+   +++ +t  es++
  gene1102|gene1102|rna1102|rna1102 60 HRKETKYVATTNNT-AESVQ 78
                                       22333333333333.44444 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 3.1e-05
                            TMEM154  48 elsnesdqlelvlmiiiPlvllillllvviiliqkkkrkrsKddeks 94 
                                        ++    +++++ lmi    v+l+ll+++ +i+  ++ rk+ + ++++
  gene1102|gene1102|rna1102|rna1102 271 NVPSYTSSMNNGLMIT-AFVALALLIFSCCIVAYRCLRKKWRSEKQK 316
                                        5555566777777764.68**************99988886555433 PP

>> TMIE  TMIE protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.4   2.2e-05     0.097      16      47 ..     284     315 ..     281     323 .] 0.82

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.2e-05
                               TMIE  16 aivllvvlaivillCCvirfRiPRTkqeIead 47 
                                        +i++ v+la++i+ CC++ +R  R k   e +
  gene1102|gene1102|rna1102|rna1102 284 MITAFVALALLIFSCCIVAYRCLRKKWRSEKQ 315
                                        788999***************99998766655 PP

>> ECSCR  Endothelial cell-specific chemotaxis regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0    0.0035        16      46      84 ..     182     221 ..     177     227 .. 0.84
   2 ?    3.2   0.0     0.017        77      31      64 ..     285     318 ..     266     321 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0035
                              ECSCR  46 slrfkcrknkesedpqkpeisglsesc.staigekdsitl 84 
                                        s  fkc k+   +dp+  ++  +   c  t +ge +  tl
  gene1102|gene1102|rna1102|rna1102 182 SNAFKCVKDPHIQDPKPENTLNMKINCvGTDNGELENCTL 221
                                        567************8888889987763699999998887 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.017
                              ECSCR  31 ivilvvvviilvsvvslrfkcrknkesedpqkpe 64 
                                        i  +v + +++ s   + ++c ++k   + qkp+
  gene1102|gene1102|rna1102|rna1102 285 ITAFVALALLIFSCCIVAYRCLRKKWRSEKQKPK 318
                                        4455666677778888889998888888888886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (323 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1208  (0.0673769); expected 358.6 (0.02)
Passed bias filter:                      554  (0.0308997); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.56u 0.25s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 2182.11
//
Query:       gene1103|gene1103|rna1103|rna1103  [L=95]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.086   11.9   0.1       0.11   11.6   0.1    1.1  1  DUF1749   Protein of unknown function (DUF1749)


Domain annotation for each model (and alignments):
>> DUF1749  Protein of unknown function (DUF1749)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   5.9e-06      0.11       9      65 ..      29      86 ..      21      90 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 5.9e-06
                            DUF1749  9 llheyaerlvafeyetsgelkskallFigGLgdGlltvpyvkelanal.deagwsvve 65
                                       +  +y+ ++v ++y+  ++ ++++l+  g   dG+l   yv el + + d+  + vv+
  gene1103|gene1103|rna1103|rna1103 29 IYLQYNGNTVKIKYNNLHKYTKNTLIVTGTYNDGVLEEKYVDELDDDFdDKLFYRVVS 86
                                       56689999**************************************996677777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       729  (0.0406604); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 737.09
//
Query:       gene1104|gene1104|rna1104|rna1104  [L=539]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-23   82.8  54.8    5.8e-08   32.9   3.2    7.0  7  LRR_4     Leucine Rich repeats (2 copies)
    2.6e-21   75.1  49.3    1.5e-11   43.9   8.2    6.7  7  LRR_8     Leucine rich repeat
    1.8e-05   24.3  24.1      0.025   14.1   5.1    3.5  3  LRR_9     Leucine-rich repeat
    0.00054   19.9   4.8      0.016   15.1   2.2    2.6  2  LRR_5     BspA type Leucine rich repeat region (6 copies)
  ------ inclusion threshold ------
        4.3    8.3  37.2        1.9    9.3   0.3    9.0  8  LRR_1     Leucine Rich Repeat


Domain annotation for each model (and alignments):
>> LRR_4  Leucine Rich repeats (2 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   5.0     0.001       3.7       5      37 ..       7      37 ..       6      43 .. 0.86
   2 ?    0.3   3.3      0.29     1e+03       6      39 ..      28      60 ..      23      66 .. 0.73
   3 !   13.7   6.5   1.7e-05     0.062       2      39 ..      69     101 ..      68     106 .. 0.88
   4 !   26.7   2.7   1.5e-09   5.4e-06       2      40 ..     113     151 ..     112     156 .. 0.86
   5 !   32.9   3.2   1.6e-11   5.8e-08       1      40 [.     158     196 ..     158     201 .. 0.94
   6 !    5.5   0.3    0.0066        24      11      39 ..     190     215 ..     190     218 .. 0.85
   7 !   26.0   0.4   2.5e-09   8.8e-06       1      39 [.     220     258 ..     220     262 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.001
                                       EEE--SS---E-S-HHH-TT--EEE-.-S---- CS
                              LRR_4  5 vLdLsnNqltdiplleklpnLkeLdLsgNnlit 37
                                       +LdLs N+lt+ip  +  +  + L Ls+Nnli+
  gene1104|gene1104|rna1104|rna1104  7 TLDLSKNNLTEIPITY--KRVHWLILSNNNLIN 37
                                       7**********99955..99****999999983 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.29
                                       EE--SS---E-S-HHH-TT--EEE-.-S-----G CS
                              LRR_4  6 LdLsnNqltdiplleklpnLkeLdLsgNnlitdl 39
                                       L LsnN+l    +++   + + L L++N ++ +l
  gene1104|gene1104|rna1104|rna1104 28 LILSNNNLINTKNIQYYRDVTRLALNDN-YLIKL 60
                                       8999999887777777888888888666.66666 PP

  == domain 3  score: 13.7 bits;  conditional E-value: 1.7e-05
                                        S--EEE--SS---E-S-HHH-TT--EEE-.-S-----G CS
                              LRR_4   2 nLevLdLsnNqltdiplleklpnLkeLdLsgNnlitdl 39 
                                        nL  LdL  N+l+++p+++ l+nL  L Ls+Nn    +
  gene1104|gene1104|rna1104|rna1104  69 NLNWLDLTRNRLSELPFIN-LKNLNGLGLSENN----F 101
                                        8999***************.***********94....3 PP

  == domain 4  score: 26.7 bits;  conditional E-value: 1.5e-09
                                        S--EEE--SS---E-S-HHH.-TT--EEE-.-S-----GG CS
                              LRR_4   2 nLevLdLsnNqltdipllek.lpnLkeLdLsgNnlitdld 40 
                                        nL++  +++N+l+ i++l + l nL++LdL +Nn+i++l+
  gene1104|gene1104|rna1104|rna1104 113 NLRKFGFFSNRLKVISPLIGnLINLTKLDL-SNNYIKTLP 151
                                        999999***********7744*********.666999884 PP

  == domain 5  score: 32.9 bits;  conditional E-value: 1.6e-11
                                        SS--EEE--SS---E-S-HHH-TT--EEE-.-S-----GG CS
                              LRR_4   1 pnLevLdLsnNqltdiplleklpnLkeLdLsgNnlitdld 40 
                                        ++L+ L+LsnNq+ +++++++l +L+eL L gNn+i+ +d
  gene1104|gene1104|rna1104|rna1104 158 KKLTWLNLSNNQIESVEGINNLVHLEELGL-GNNQIEEID 196
                                        69****************************.999**9996 PP

  == domain 6  score: 5.5 bits;  conditional E-value: 0.0066
                                        S---E-S-HHH-TT--EEE-.-S-----G CS
                              LRR_4  11 NqltdiplleklpnLkeLdLsgNnlitdl 39 
                                        Nq+ +i+    l++Lk L L +Nn+i+++
  gene1104|gene1104|rna1104|rna1104 190 NQIEEIDI--ALTSLKILPL-FNNKIRKV 215
                                        78888877..699****999.99999886 PP

  == domain 7  score: 26.0 bits;  conditional E-value: 2.5e-09
                                        SS--EEE--SS---E-S-..HHH-TT--EEE-.-S-----G CS
                              LRR_4   1 pnLevLdLsnNqltdipl..leklpnLkeLdLsgNnlitdl 39 
                                        ++ e+Ld+s+N l  +++  le +++Lk+L+L  Nn+i+ +
  gene1104|gene1104|rna1104|rna1104 220 TRIEKLDFSDNLLEYFDWrvLE-CKKLKYLNL-KNNRIKEI 258
                                        5789**************9888.*********.999**988 PP

>> LRR_8  Leucine rich repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.6   2.7    0.0077        27      29      61 .]       7      35 ..       6      35 .. 0.68
   2 !   13.9   7.6   9.4e-06     0.034       2      61 .]      24      80 ..      23      80 .. 0.91
   3 !   13.6   3.3   1.2e-05     0.043      20      61 .]      84     124 ..      79     124 .. 0.92
   4 !   43.9   8.2   4.2e-15   1.5e-11       2      61 .]     136     192 ..     135     192 .. 0.98
   5 !   10.8   1.6   8.8e-05      0.32      22      61 .]     177     212 ..     172     212 .. 0.90
   6 ?    4.2   0.6      0.01        36      24      61 .]     199     232 ..     197     232 .. 0.85
   7 !   17.5   0.4     7e-07    0.0025       3      41 ..     222     259 ..     220     265 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.0077
                                       EEE--SS---GGGGGGGTT--S-.EEE--SS-- CS
                              LRR_8 29 vLdLsnNllttlspgafsgLpsLrsLdLsgNrL 61
                                       +LdLs N+lt +        +++ +L Ls+N+L
  gene1104|gene1104|rna1104|rna1104  7 TLDLSKNNLTEIP----ITYKRVHWLILSNNNL 35
                                       5888888888885....4455557777777776 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 9.4e-06
                                       T-SEEE-TTS--SEE-TTSSTT-TT--EEE--SS---GGGGGGGTT--S-.EEE--SS-- CS
                              LRR_8  2 nLtsLdLsnNrltslddeaFkglsnLkvLdLsnNllttlspgafsgLpsLrsLdLsgNrL 61
                                       +++ L+LsnN+l + +  + +  + ++ L L++N l  l + a+  L +L +LdL++NrL
  gene1104|gene1104|rna1104|rna1104 24 RVHWLILSNNNLINTKNIQYY--RDVTRLALNDNYLIKL-ESAINALVNLNWLDLTRNRL 80
                                       6789********877777777..8***************.5*****************98 PP

  == domain 3  score: 13.6 bits;  conditional E-value: 1.2e-05
                                        SSTT-TT--EEE--SS---GGGGGGGTT--S-.EEE--SS-- CS
                              LRR_8  20 aFkglsnLkvLdLsnNllttlspgafsgLpsLrsLdLsgNrL 61 
                                         F +l+nL+ L Ls+N+ + + p +  +L +Lr+    +NrL
  gene1104|gene1104|rna1104|rna1104  84 PFINLKNLNGLGLSENNFDKI-PSCVFNLVNLRKFGFFSNRL 124
                                        599******************.9**********999999887 PP

  == domain 4  score: 43.9 bits;  conditional E-value: 4.2e-15
                                        T-SEEE-TTS--SEE-TTSSTT-TT--EEE--SS---GGGGGGGTT--S-.EEE--SS-- CS
                              LRR_8   2 nLtsLdLsnNrltslddeaFkglsnLkvLdLsnNllttlspgafsgLpsLrsLdLsgNrL 61 
                                        nLt+LdLsnN+++ l++e F+ l++L++L+LsnN++++++   + +L +L++L L +N++
  gene1104|gene1104|rna1104|rna1104 136 NLTKLDLSNNYIKTLPKELFS-LKKLTWLNLSNNQIESVE--GINNLVHLEELGLGNNQI 192
                                        8********************.*****************6..****************98 PP

  == domain 5  score: 10.8 bits;  conditional E-value: 8.8e-05
                                        TT-TT--EEE--SS---GGGGGGGTT--S-.EEE--SS-- CS
                              LRR_8  22 kglsnLkvLdLsnNllttlspgafsgLpsLrsLdLsgNrL 61 
                                        ++l +L++L L+nN+++ ++      L+sL+ L L +N++
  gene1104|gene1104|rna1104|rna1104 177 NNLVHLEELGLGNNQIEEID----IALTSLKILPLFNNKI 212
                                        7899***************9....8999999999999987 PP

  == domain 6  score: 4.2 bits;  conditional E-value: 0.01
                                        -TT--EEE--SS---GGGGGGGTT--S-.EEE--SS-- CS
                              LRR_8  24 lsnLkvLdLsnNllttlspgafsgLpsLrsLdLsgNrL 61 
                                        l++Lk+L L nN+++ ++      ++++++Ld s+N L
  gene1104|gene1104|rna1104|rna1104 199 LTSLKILPLFNNKIRKVR----IRMTRIEKLDFSDNLL 232
                                        789999999999999998....8888888888888876 PP

  == domain 7  score: 17.5 bits;  conditional E-value: 7e-07
                                        -SEEE-TTS--SEE-TTSSTT-TT--EEE--SS---GGG CS
                              LRR_8   3 LtsLdLsnNrltslddeaFkglsnLkvLdLsnNllttls 41 
                                         ++Ld s+N l+  d+ + + +++Lk+L+L+nN+++ ++
  gene1104|gene1104|rna1104|rna1104 222 IEKLDFSDNLLEYFDWRVLE-CKKLKYLNLKNNRIKEIR 259
                                        67888888888888888888.899999999999998886 PP

>> LRR_9  Leucine-rich repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   5.5   2.3e-05     0.084      48     127 ..      29     103 ..      13     119 .. 0.87
   2 !   14.1   5.1   7.1e-06     0.025      17     125 ..     110     212 ..     103     219 .. 0.82
   3 !    7.0   0.5     0.001       3.7      44      80 ..     222     259 ..     212     267 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.3e-05
                              LRR_9  48 dlsdndirkldgfPllkrlktlllnnnrivriaegleevlPnleelvltnnelqeladldPlaslkklellsllkn 123
                                         ls+n++ +  ++ + + +  l ln+n +++++  ++ +l nl+ l lt n+l el    P+++lk+l+ l l +n
  gene1104|gene1104|rna1104|rna1104  29 ILSNNNLINTKNIQYYRDVTRLALNDNYLIKLESAIN-ALVNLNWLDLTRNRLSEL----PFINLKNLNGLGLSEN 99 
                                        499*****************************99886.678**********99998....999********99998 PP

                              LRR_9 124 pvtn 127
                                           +
  gene1104|gene1104|rna1104|rna1104 100 NFDK 103
                                        7655 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 7.1e-06
                              LRR_9  17 nairereldlrgykipvienlGatldqfdtidlsdndirkl.dgfPllkrlktlllnnnrivriaegleevlPnle 91 
                                        n +  r  +  ++++ vi  l   l  +  +dls+n i+ l  ++  lk+l  l l+nn+i  + eg+++ l +le
  gene1104|gene1104|rna1104|rna1104 110 NLVNLRKFGFFSNRLKVISPLIGNLINLTKLDLSNNYIKTLpKELFSLKKLTWLNLSNNQIESV-EGINN-LVHLE 183
                                        66677778888899999999999999999***********9446888**************987.68876.568** PP

                              LRR_9  92 elvltnnelqeladldPlaslkklellsllknpv 125
                                        el l nn+++e+      + l +l++l l++n +
  gene1104|gene1104|rna1104|rna1104 184 ELGLGNNQIEEID-----IALTSLKILPLFNNKI 212
                                        *********9974.....4677777777777766 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.001
                              LRR_9  44 fdtidlsdndirkldg.fPllkrlktlllnnnrivria 80 
                                         + +d+sdn +  +d  +   k+lk l l+nnri  i 
  gene1104|gene1104|rna1104|rna1104 222 IEKLDFSDNLLEYFDWrVLECKKLKYLNLKNNRIKEIR 259
                                        56789****9999985144579************9985 PP

>> LRR_5  BspA type Leucine rich repeat region (6 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   2.2   4.5e-06     0.016       8      94 ..      85     173 ..      78     199 .. 0.76
   2 !    4.7   0.0    0.0078        28      56      94 ..     220     258 ..     196     267 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 4.5e-06
                              LRR_5   8 Fync.nltsitip.ssvtsIgeyaFsnctslksitlpsslteigsyaFsncssltsitips.sltsigeyaFsncs 80 
                                        F n  nl+ + ++ ++  +I +++F+   +l+++ + s+  ++ s    n  +lt++++++  +++++++ Fs  +
  gene1104|gene1104|rna1104|rna1104  85 FINLkNLNGLGLSeNNFDKIPSCVFNLV-NLRKFGFFSNRLKVISPLIGNLINLTKLDLSNnYIKTLPKELFS-LK 158
                                        6666678888887357999******999.*****987776666666677777*******9846999*******.** PP

                              LRR_5  81 slkeitlpsn.ltti 94 
                                        +l+ ++l++n ++++
  gene1104|gene1104|rna1104|rna1104 159 KLTWLNLSNNqIESV 173
                                        ****99988634433 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.0078
                              LRR_5  56 cssltsitipssltsigeyaFsncsslkeitlpsn.ltti 94 
                                        +  +++++++++l +  ++   +c++lk ++l++n +++i
  gene1104|gene1104|rna1104|rna1104 220 T-RIEKLDFSDNLLEYFDWRVLECKKLKYLNLKNNrIKEI 258
                                        4.78888888887666666666699999999987656666 PP

>> LRR_1  Leucine Rich Repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0      0.12   4.2e+02       4      16 ..       7      19 ..       7      22 .. 0.84
   2 ?   -0.9   0.2       1.3   4.6e+03       5      13 ..      28      36 ..      24      42 .. 0.80
   3 ?   -3.2   0.0         5   1.8e+04       5      17 ..      50      62 ..      48      63 .. 0.73
   4 ?   -0.1   5.3      0.67   2.4e+03       1      23 []      69      91 ..      69     111 .. 0.71
   5 ?    9.3   0.3   0.00053       1.9       1      20 [.     136     155 ..     136     157 .. 0.87
   6 ?    4.8   2.2     0.017        60       1      13 [.     159     172 ..     159     203 .. 0.75
   7 ?   -0.7   0.0       1.1   3.9e+03       2      12 ..     222     232 ..     221     240 .. 0.82
   8 ?    5.5   0.1    0.0095        34       1      12 [.     244     255 ..     244     265 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.12
                              LRR_1  4 hLdLsnnpllglp 16
                                       +LdLs n+l+ +p
  gene1104|gene1104|rna1104|rna1104  7 TLDLSKNNLTEIP 19
                                       69*******8776 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.3
                              LRR_1  5 LdLsnnpll 13
                                       L Lsnn+l+
  gene1104|gene1104|rna1104|rna1104 28 LILSNNNLI 36
                                       779***996 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 5
                              LRR_1  5 LdLsnnpllglpp 17
                                       L L++n l+ l++
  gene1104|gene1104|rna1104|rna1104 50 LALNDNYLIKLES 62
                                       5689999987765 PP

  == domain 4  score: -0.1 bits;  conditional E-value: 0.67
                              LRR_1  1 nLrhLdLsnnpllglppnsfqnL 23
                                       nL  LdL++n+l+ lp   ++nL
  gene1104|gene1104|rna1104|rna1104 69 NLNWLDLTRNRLSELPFINLKNL 91
                                       67789999999966665555544 PP

  == domain 5  score: 9.3 bits;  conditional E-value: 0.00053
                              LRR_1   1 nLrhLdLsnnpllglppnsf 20 
                                        nL++LdLsnn +  lp++ f
  gene1104|gene1104|rna1104|rna1104 136 NLTKLDLSNNYIKTLPKELF 155
                                        8**********988887766 PP

  == domain 6  score: 4.8 bits;  conditional E-value: 0.017
                              LRR_1   1 nLrhLdLsnnpl.l 13 
                                        +L+ L+Lsnn++ +
  gene1104|gene1104|rna1104|rna1104 159 KLTWLNLSNNQIeS 172
                                        7999******9962 PP

  == domain 7  score: -0.7 bits;  conditional E-value: 1.1
                              LRR_1   2 LrhLdLsnnpl 12 
                                         ++Ld s+n l
  gene1104|gene1104|rna1104|rna1104 222 IEKLDFSDNLL 232
                                        689*****987 PP

  == domain 8  score: 5.5 bits;  conditional E-value: 0.0095
                              LRR_1   1 nLrhLdLsnnpl 12 
                                        +L++L+L nn++
  gene1104|gene1104|rna1104|rna1104 244 KLKYLNLKNNRI 255
                                        7*********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (539 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       687  (0.0383178); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.60u 0.31s 00:00:00.90 Elapsed: 00:00:00.47
# Mc/sec: 3450.49
//
Query:       gene1105|gene1105|rna1105|rna1105  [L=169]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (169 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       361  (0.020135); expected 358.6 (0.02)
Passed bias filter:                      256  (0.0142785); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1201.13
//
Query:       gene1106|gene1106|rna1106|rna1106  [L=71]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (71 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       260  (0.0145016); expected 358.6 (0.02)
Passed bias filter:                      188  (0.0104858); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.29s 00:00:00.63 Elapsed: 00:00:00.43
# Mc/sec: 495.62
//
Query:       gene1107|gene1107|rna1107|rna1107  [L=220]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00023   20.8   0.2       0.25   11.2   0.0    2.8  2  TPR_1     Tetratricopeptide repeat
    0.00053   19.9   0.3       0.14   12.3   0.1    3.0  2  TPR_2     Tetratricopeptide repeat
     0.0014   18.7   0.0        3.7    8.0   0.0    2.9  2  TPR_8     Tetratricopeptide repeat
     0.0093   15.4   0.5      0.049   13.1   0.2    2.2  2  SHNi-TPR  SHNi-TPR
  ------ inclusion threshold ------
      0.023   15.0   0.0       0.17   12.2   0.0    2.3  3  TPR_12    Tetratricopeptide repeat
      0.087   13.5   0.1         21    6.0   0.0    3.7  3  TPR_6     Tetratricopeptide repeat
       0.14   12.3   1.1        2.5    8.2   0.0    3.0  3  NRN1      Neuritin protein family


Domain annotation for each model (and alignments):
>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.6   0.0    0.0028       7.2       2      28 ..      87     113 ..      87     117 .. 0.90
   2 !   11.2   0.0   9.8e-05      0.25       3      27 ..     126     150 ..     125     155 .. 0.93

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0028
                                        HHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                              TPR_1   2 kalynlGnayfklgkydeAleyyekAL 28 
                                        k+++  G +y+ + ++ +A+  ++++L
  gene1107|gene1107|rna1107|rna1107  87 KVYFLQGEIYLLNDQHADAVREFSECL 113
                                        68999**************99998887 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 9.8e-05
                                        HHHHHHHHHHHTT-HHHHHHHHHHH CS
                              TPR_1   3 alynlGnayfklgkydeAleyyekA 27 
                                        +++++G +yf lg+   A  +yek 
  gene1107|gene1107|rna1107|rna1107 126 VYKRIGDCYFFLGDRMMATTFYEKG 150
                                        69********************995 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.1   5.5e-05      0.14       2      28 ..      87     113 ..      86     118 .. 0.92
   2 ?    4.5   0.0     0.017        44       3      27 ..     126     150 ..     124     156 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5.5e-05
                              TPR_2   2 ealynlGlayyklgdyeeAleafekAl 28 
                                        ++++ +G++y+ ++++++A++ f ++l
  gene1107|gene1107|rna1107|rna1107  87 KVYFLQGEIYLLNDQHADAVREFSECL 113
                                        589*********************998 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.017
                              TPR_2   3 alynlGlayyklgdyeeAleafekA 27 
                                        ++ ++G++y+ lgd   A  ++ek 
  gene1107|gene1107|rna1107|rna1107 126 VYKRIGDCYFFLGDRMMATTFYEKG 150
                                        68899*****999987777777775 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.5   0.0     0.002       5.2       2      28 ..      87     113 ..      86     118 .. 0.92
   2 !    8.0   0.0    0.0014       3.7       6      27 ..     129     150 ..     125     151 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.002
                                        CHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                              TPR_8   2 eayynlgsiylklgdyeeAkeyyekal 28 
                                        ++y++ g iyl   ++  A+  + ++l
  gene1107|gene1107|rna1107|rna1107  87 KVYFLQGEIYLLNDQHADAVREFSECL 113
                                        68*********************9998 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0014
                                        HHHHHHHHTT-HHHHHHHHHHH CS
                              TPR_8   6 nlgsiylklgdyeeAkeyyeka 27 
                                        ++g++y+ lgd  +A  +yek 
  gene1107|gene1107|rna1107|rna1107 129 RIGDCYFFLGDRMMATTFYEKG 150
                                        79******************95 PP

>> SHNi-TPR  SHNi-TPR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.2   1.9e-05     0.049       3      28 ..      88     113 ..      87     114 .. 0.96
   2 ?   -0.8   0.0      0.41   1.1e+03       2       9 ..     132     139 ..     132     148 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.9e-05
                           SHNi-TPR   3 vydlLGEislEnenFpqAveDlrkaL 28 
                                        vy l+GEi l n++  +Av ++ ++L
  gene1107|gene1107|rna1107|rna1107  88 VYFLQGEIYLLNDQHADAVREFSECL 113
                                        99***********************9 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.41
                           SHNi-TPR   2 dvydlLGE 9  
                                        d+y +LG+
  gene1107|gene1107|rna1107|rna1107 132 DCYFFLGD 139
                                        9******8 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.1    0.0037       9.4      26      72 ..      69     113 ..      56     115 .. 0.74
   2 ?   12.2   0.0   6.8e-05      0.17       8      70 ..      91     149 ..      84     151 .. 0.89
   3 ?    4.4   0.0     0.018        45       5      28 ..     126     149 ..     123     160 .. 0.68

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0037
                             TPR_12  26 lekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleeal 72 
                                        le+a+  ++     d++++  +++  g++y++ +++++A++ + e+l
  gene1107|gene1107|rna1107|rna1107  69 LEQARLFFKMK--NDKHQLKKVYFLQGEIYLLNDQHADAVREFSECL 113
                                        56666666555..4455888899999999999999999998777765 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 6.8e-05
                             TPR_12   8 nlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlellee 70 
                                          +++++   ++++A + + ++l +  + + +d     t++  +g++y+ lg+   A  ++e+
  gene1107|gene1107|rna1107|rna1107  91 LQGEIYLLNDQHADAVREFSECLLVEDEQFVCDG----TVYKRIGDCYFFLGDRMMATTFYEK 149
                                        5799**********************99998886....8**************9888888886 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.018
                             TPR_12   5 alnnlaavlrrlgrydeAlellek 28 
                                        ++ +++++++ lg+   A +++ek
  gene1107|gene1107|rna1107|rna1107 126 VYKRIGDCYFFLGDRMMATTFYEK 149
                                        455566666666666666666655 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0       1.2     3e+03       4      15 ..      69      80 ..      68      84 .. 0.73
   2 ?    6.0   0.0    0.0081        21       2      25 ..      88     111 ..      87     113 .. 0.88
   3 ?    2.2   0.0      0.13   3.4e+02       6      23 ..     130     147 ..     129     171 .. 0.59

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 1.2
                                       HHHHHHHHHHHH CS
                              TPR_6  4 yklalsyrklgd 15
                                       + +a++++k+++
  gene1107|gene1107|rna1107|rna1107 69 LEQARLFFKMKN 80
                                       578999*99842 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0081
                                        HHHHHHHHHHHHHHHHHHHHHHHH CS
                              TPR_6   2 AlyklalsyrklgdtdkAlealer 25 
                                        +++++++ y+  +++++A++ + +
  gene1107|gene1107|rna1107|rna1107  88 VYFLQGEIYLLNDQHADAVREFSE 111
                                        689********99******98876 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.13
                                        HHHHHHHHHHHHHHHHHH CS
                              TPR_6   6 lalsyrklgdtdkAleal 23 
                                        ++ +y+ lgd   A + +
  gene1107|gene1107|rna1107|rna1107 130 IGDCYFFLGDRMMATTFY 147
                                        666666655544333333 PP

>> NRN1  Neuritin protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.1      0.28   7.3e+02       4      15 ..      21      32 ..      19      96 .. 0.80
   2 ?    0.1   0.0      0.34   8.7e+02       5      13 ..     106     114 ..     103     120 .. 0.82
   3 ?    8.2   0.0   0.00099       2.5       3      22 ..     125     144 ..     122     153 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.28
                               NRN1  4 iykgfsdCllkl 15
                                       iy ++++Cl++ 
  gene1107|gene1107|rna1107|rna1107 21 IYIEYAHCLIRN 32
                                       788888898874 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.34
                               NRN1   5 ykgfsdCll 13 
                                         ++fs+Cll
  gene1107|gene1107|rna1107|rna1107 106 VREFSECLL 114
                                        589*****9 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.00099
                               NRN1   3 aiykgfsdCllklGdslaey 22 
                                        ++yk + dC + lGd ++ +
  gene1107|gene1107|rna1107|rna1107 125 TVYKRIGDCYFFLGDRMMAT 144
                                        79*************99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       559  (0.0311785); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1611.39
//
Query:       gene1108|gene1108|rna1108|rna1108  [L=111]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.8e-19   69.4   2.6      3e-19   68.6   2.6    1.4  1  Homeodomain  Homeodomain
    3.6e-05   23.6   0.4    0.00014   21.7   0.3    1.9  2  Homeobox_KN  Homeobox KN domain
  ------ inclusion threshold ------
      0.034   14.2   0.0      0.066   13.3   0.0    1.6  1  MerR_1       MerR HTH family regulatory protein
      0.043   14.0   1.5      0.051   13.8   1.5    1.1  1  DUF4770      Domain of unknown function (DUF4770)


Domain annotation for each model (and alignments):
>> Homeodomain  Homeodomain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.6   2.6   6.6e-23     3e-19       1      56 [.      14      69 ..      14      70 .. 0.98

  Alignments for each domain:
  == domain 1  score: 68.6 bits;  conditional E-value: 6.6e-23
                                       ST-SSSS-HHHHHHHHHHHHHSSS-SHHHHHHHHHHHTS-HHHHHHHHHHHHHHHH CS
                        Homeodomain  1 rrkRttftkeqleeLeklFeenrypsaeereeLAkklgLeerqVkvWFqNrRakek 56
                                       +r+Rt +t  q ++L+++F++n  ps+e+reeLAk lg+  r +++WFqN+R+k k
  gene1108|gene1108|rna1108|rna1108 14 KRNRTVMTGAQAKILKNYFQKNMFPSTEAREELAKILGMRPRTIQIWFQNQRQKTK 69
                                       79****************************************************98 PP

>> Homeobox_KN  Homeobox KN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.25   1.1e+03      22      34 ..      20      32 ..      11      35 .. 0.80
   2 !   21.7   0.3   3.1e-08   0.00014       8      39 ..      35      66 ..      32      67 .. 0.93

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.25
                        Homeobox_KN 22 eTglsvkqitnWF 34
                                        Tg+++k ++n+F
  gene1108|gene1108|rna1108|rna1108 20 MTGAQAKILKNYF 32
                                       5888888899999 PP

  == domain 2  score: 21.7 bits;  conditional E-value: 3.1e-08
                        Homeobox_KN  8 nPYPseedKeeLlkeTglsvkqitnWFINaRr 39
                                       n +Ps e +eeL+k  g++ + i+ WF N+R+
  gene1108|gene1108|rna1108|rna1108 35 NMFPSTEAREELAKILGMRPRTIQIWFQNQRQ 66
                                       669****************************6 PP

>> MerR_1  MerR HTH family regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   1.5e-05     0.066       5      21 ..      45      61 ..      43      78 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.5e-05
                                       HHHHHHTS-HHHHHHHH CS
                             MerR_1  5 evakilgvtthtlrywe 21
                                       e+akilg+ ++t++ w 
  gene1108|gene1108|rna1108|rna1108 45 ELAKILGMRPRTIQIWF 61
                                       9***************6 PP

>> DUF4770  Domain of unknown function (DUF4770)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   1.5   1.1e-05     0.051      96     164 ..       5      77 ..       1      83 [. 0.83

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.1e-05
                            DUF4770  96 klkkkkekkrkekekkkkknkkklspYfekqvrpkttrskkfss....kppelkvsfpeypkekkplyeipne 164
                                        +l+k+ e+k++++  ++ ++ k l+ Yf+k++ p t  ++++++    +p+++++ f++ ++++k  y+++++
  gene1108|gene1108|rna1108|rna1108   5 NLQKSFETKKRNRTVMTGAQAKILKNYFQKNMFPSTEAREELAKilgmRPRTIQIWFQNQRQKTKSRYGFDRQ 77 
                                        4455556667777778888888999**********999999999898899**************999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (111 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       746  (0.0416086); expected 358.6 (0.02)
Passed bias filter:                      456  (0.0254337); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 796.36
//
Query:       gene1109|gene1109|rna1109|rna1109  [L=66]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
      0.036   13.8   0.6      0.079   12.7   0.1    1.7  2  GBP_repeat  Glycophorin-binding protein


Domain annotation for each model (and alignments):
>> GBP_repeat  Glycophorin-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   4.4e-06     0.079      19      31 ..      14      26 ..      10      29 .. 0.89
   2 ?   -1.9   0.0      0.17     3e+03      30      37 ..      44      51 ..      39      51 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.4e-06
                         GBP_repeat 19 YRKHlevlYkiLT 31
                                       YR H++vlY  +T
  gene1109|gene1109|rna1109|rna1109 14 YRTHINVLYESIT 26
                                       9********9887 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.17
                         GBP_repeat 30 LTnTDPND 37
                                       L    PND
  gene1109|gene1109|rna1109|rna1109 44 LIRINPND 51
                                       55678998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (66 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       290  (0.0161749); expected 358.6 (0.02)
Passed bias filter:                      209  (0.0116571); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.31u 0.23s 00:00:00.54 Elapsed: 00:00:00.36
# Mc/sec: 556.51
//
Query:       gene111|gene111|rna111|rna111  [L=443]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.074   13.5   0.3       0.17   12.3   0.0    1.6  2  Peptidase_S8_N  N-terminal of Subtilase family
       0.12   12.3   0.4       0.21   11.5   0.4    1.3  1  DeoRC           DeoR C terminal sensor domain
       0.19   11.4   5.6       0.66    9.7   5.6    1.7  1  Geminin         Geminin


Domain annotation for each model (and alignments):
>> Peptidase_S8_N  N-terminal of Subtilase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.2       1.3   7.6e+03     111     111 ..     129     129 ..      99     158 .. 0.52
   2 ?   12.3   0.0   2.9e-05      0.17      13      73 ..     191     248 ..     183     253 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1.3
                 Peptidase_S8_N 111 a 111
                                     
  gene111|gene111|rna111|rna111 129 I 129
                                    1 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 2.9e-05
                 Peptidase_S8_N  13 ealeaaaatrgesvrsgiksldevlaelgavelervfpvdgkfeertrkaGLhlWYdvkfd 73 
                                    ++++ +++ + e ++  i++ld++ ++ + ++   vf++++++++ +++aGL+  +  +f 
  gene111|gene111|rna111|rna111 191 KSMQDTENANVE-AQRKIARLDDITDKFKPYN--AVFSDAQRYRAFQKAAGLDGYFPMHFP 248
                                    455555555555.999************9996..7******************99998885 PP

>> DeoRC  DeoR C terminal sensor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.4   3.5e-05      0.21      53     129 ..      65     139 ..      60     142 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 3.5e-05
                          DeoRC  53 vaeeLsekedikvillGGevrkkseslvgplaeealrqfnvdkaflgangidaegglttsdeeeaevkralieaarr 129
                                    +a++L++  d ++++ G    +++e lvg   ++  +++  d+a++  + i+++++ +++ + ea+++++++ea ++
  gene111|gene111|rna111|rna111  65 TADALHHGGDGEIFVSGPA--ADQENLVGMGLDQLHQKMASDIAVMHNANIESKKKQMEAAMLEAQIAQEMAEAKEE 139
                                    6889999999999999985..5566788888999999***********************************99876 PP

>> Geminin  Geminin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   5.6   0.00011      0.66     119     187 ..     142     208 ..      95     217 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00011
                        Geminin 119 eRrKaLyevLqEnEkLhkeiEqkdeeiarLkeENeeLaelAeHVqymadmieRLtgkspdnleelkela 187
                                     R K L +v + nE  hk+ E   +++  + +  ee + l +HV+y+ +mi+ +++++  n+e+ +++a
  gene111|gene111|rna111|rna111 142 SRLKYLDDVAEINE--HKDPEVLGKQVIPVATFTEETMPLRHHVRYLLNMIKSMQDTENANVEAQRKIA 208
                                    57788888888898..999999999**************************************999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (443 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1085  (0.0605165); expected 358.6 (0.02)
Passed bias filter:                      585  (0.0326287); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.63u 0.32s 00:00:00.95 Elapsed: 00:00:00.48
# Mc/sec: 2759.31
//
Query:       gene1111|gene1111|rna1111|rna1111  [L=341]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (341 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       352  (0.019633); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 2267.52
//
Query:       gene1112|gene1112|rna1112|rna1112  [L=129]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.5e-11   43.1   0.3    5.9e-11   42.4   0.3    1.3  1  Ribosomal_L24e  Ribosomal protein L24e


Domain annotation for each model (and alignments):
>> Ribosomal_L24e  Ribosomal protein L24e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.4   0.3   3.3e-15   5.9e-11       5      63 ..      10      68 ..       6      71 .. 0.96

  Alignments for each domain:
  == domain 1  score: 42.4 bits;  conditional E-value: 3.3e-15
                                       B-TTT-SB--SS--EEEE-TTS-EEEESSHHHHHHHHTT--GGGSTTSTTT-XXXXXXX CS
                     Ribosomal_L24e  5 kCsFsgykiyPGhGkrfvrnDgkvfrFlssKceklfkqkrnPrklkWTkayRrahkkel 63
                                       kC Fsg+ + +++G+  v++Dg+     + K+ ++ k+ ++P+k+ WT  +R  hkk+ 
  gene1112|gene1112|rna1112|rna1112 10 KCVFSGQDVPKAKGTYRVQHDGRAQLTRTTKASSYLKRSIKPQKVLWTLGARFFHKKGG 68
                                       8********************************************************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       454  (0.0253221); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 911.30
//
Query:       gene1113|gene1113|rna1113|rna1113  [L=122]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.1e-10   40.4   0.3    2.1e-10   40.4   0.3    1.9  2  Ribosomal_L29  Ribosomal L29 protein
     0.0013   19.1   0.3     0.0018   18.6   0.3    1.3  1  SPK            Domain of unknown function (DUF545)
  ------ inclusion threshold ------
      0.031   13.1   0.6      0.031   13.1   0.6    1.3  2  Spc7           Spc7 kinetochore protein


Domain annotation for each model (and alignments):
>> Ribosomal_L29  Ribosomal L29 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.4   0.3   3.4e-14   2.1e-10       1      57 []       6      61 ..       6      61 .. 0.98
   2 ?   -0.6   0.1      0.22   1.3e+03       5      12 ..      92      99 ..      85     107 .. 0.65

  Alignments for each domain:
  == domain 1  score: 40.4 bits;  conditional E-value: 3.4e-14
                                       HHHHHS-HHHHHHHHHHHHHHHHHHHHHHHHTSSS-CHHHHHHHHHHHHHHHHHHHH CS
                      Ribosomal_L29  1 kelrelsdeeLkeklkelkkeLfnLrfqkatgqlenpsrirkvRkdIARikTvlrer 57
                                       kelr l   +L+e+ k+ k+eL+  r ++ t ++ +p++i ++ +++A ++ vl+e+
  gene1113|gene1113|rna1113|rna1113  6 KELRTLPLPDLEERYKQIKTELLHVRQKQHTHTV-KPHEIYNAHRNVAVVMSVLTEK 61
                                       79******************************99.*********************8 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.22
                                       HS-HHHHH CS
                      Ribosomal_L29  5 elsdeeLk 12
                                       els+e+L+
  gene1113|gene1113|rna1113|rna1113 92 ELSKEQLR 99
                                       45555554 PP

>> SPK  Domain of unknown function (DUF545)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.3   3.1e-07    0.0018      26      90 ..      33      96 ..      12      98 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 3.1e-07
                                SPK 26 keksgskesestlarrfrqlla.kihkleeydletkvrllFalsapvdedflkelrkdakveldek 90
                                       k+++ + +  +++++  r  +a  +  l+e + e+ v  +Fa s++v  +fl +l+k+  +el ++
  gene1113|gene1113|rna1113|rna1113 33 KQHTHTVK-PHEIYNAHR-NVAvVMSVLTEKKKEEAVAAAFAASGKVPRQFLPRLTKKKRMELSKE 96
                                       55555554.455666455.55559************************************999876 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.6   5.3e-06     0.031     169     222 ..      13      65 ..       3      74 .. 0.90
   2 ?   -3.4   0.0      0.59   3.5e+03      30      32 ..      92      94 ..      79     106 .. 0.45

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 5.3e-06
                               Spc7 169 lpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkel 222
                                        lp+lee++++++ el + +++++   ++++ e+ ++++++a +++ + ekkke 
  gene1113|gene1113|rna1113|rna1113  13 LPDLEERYKQIKTELLHVRQKQH-THTVKPHEIYNAHRNVAVVMSVLTEKKKEE 65 
                                        799*****************766.699*********************999985 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 0.59
                               Spc7 30 tia 32
                                        + 
  gene1113|gene1113|rna1113|rna1113 92 ELS 94
                                       111 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1260  (0.0702772); expected 358.6 (0.02)
Passed bias filter:                      693  (0.0386525); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 888.34
//
Query:       gene1114|gene1114|rna1114|rna1114  [L=702]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.3e-35  120.4   0.0    1.8e-34  119.3   0.0    1.6  1  tRNA-synt_2b    tRNA synthetase class II core domain (G, H, P
      5e-12   45.8   1.1    1.1e-11   44.7   1.1    1.7  1  HGTP_anticodon  Anticodon binding domain
    6.1e-10   39.0   0.0    1.3e-09   38.0   0.0    1.6  1  tRNA_SAD        Threonyl and Alanyl tRNA synthetase second ad


Domain annotation for each model (and alignments):
>> tRNA-synt_2b  tRNA synthetase class II core domain (G, H, P, S and T)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.3   0.0     3e-38   1.8e-34       8     179 .]     388     591 ..     382     591 .. 0.91

  Alignments for each domain:
  == domain 1  score: 119.3 bits;  conditional E-value: 3e-38
                                        SEEEEE-SSSHHHHHHHHHHHEEEB.GGSSEEEEEEEEEEBTTTS.TBCTTTB-SEEEEEEEEEEESGGGHHHHHH CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2b   8 dreyiLkPtneetfvelirdevlrs.krLPlklyqiqtkyRdEks.dsrGLlRvreFhqkdgyvfhaeaslddslr 81 
                                        d e +LkP+n+++++ l+    +rs ++LP+++++++ ++R+E s  ++GL+Rvr F+q+d++vf++  +++ ++ 
  gene1114|gene1114|rna1114|rna1114 388 DAEWALKPMNCPGHCLLYARS-VRSfRELPIRMADFGVLHRNELSgTLSGLTRVRRFQQDDAHVFCLLVQVEHEIL 462
                                        5799***************99.***777****************98999******************999****** PP

                                        HHHHHHHHHHHHTT.SCEEEEEEGTTSC.................................BTTSEEEEEEEEETT CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxx.................................xxxxxxxxxxxxxxx RF
                       tRNA-synt_2b  82 dlikaisriferlglefraiielmsaks.................................adykdkkefeavses 124
                                          ++ + +++  lg+ef  + ++++ k+                                 a+y++k ++ +++  
  gene1114|gene1114|rna1114|rna1114 463 HNLEFMRHVYAVLGFEFE-LALSTRPKKylgdkkdwdtaeeylrralrtfgreytvnegdgAFYGPKIDVVLLDA- 536
                                        **************9975.556655555677777999999**********************************9. PP

                                        TSEEEEEEEEEEEETHHHHHTTEEEECTTSSEEEEEEEEEE.EE.HHHHHHHHHHHH CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xx.xxxxxxxxxxxx RF
                       tRNA-synt_2b 125 ltkgieigtiqklgtrlserlgatvldennreksvimicaa.ig.veRllsaileqn 179
                                        l++ ++++tiq + ++l+ r++++ + +++ +++++mi++a +g veR++++++e++
  gene1114|gene1114|rna1114|rna1114 537 LKRRHQCATIQLD-FQLPARFNLQCKTSEG-VERPVMIHRAlLGsVERFIGILIEHY 591
                                        *************.***********66665.55666******************986 PP

>> HGTP_anticodon  Anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.7   1.1   1.9e-15   1.1e-11       1      93 [.     603     690 ..     603     691 .. 0.95

  Alignments for each domain:
  == domain 1  score: 44.7 bits;  conditional E-value: 1.9e-15
                                        SEEEEESSSSHHHHHHHHHHHHHHHHTTTSEEEEESSSSTHHHHHHHHHHTT-SEEEEE-HHHHHHTEEEEEETTT CS
                     HGTP_anticodon   1 qvvviplnekaeeleeyakklaeeLraagirvelddsnesigkkireadllgipfavvvGekelekgtvtvrdrdt 76 
                                        qv+v+p+++   +l  ya+++++ L + +  v ++d + ++ k++r+a+  g+ +++vvGeke + gtv vr+   
  gene1114|gene1114|rna1114|rna1114 603 QVAVVPVSN---ALSAYAQHVRDVLIDYE--VRVYDGELTLSKRVRNAEVDGYAVVLVVGEKERNAGTVMVRKCGR 673
                                        8********...9*************776..999******************************99********99 PP

                                        CEEEEEETTHHHHHHHH CS
                     HGTP_anticodon  77 reqervsldelveklke 93 
                                         + +++ ++ l+ +++e
  gene1114|gene1114|rna1114|rna1114 674 AMSVEMLRERLERAVRE 690
                                        99999999999988876 PP

>> tRNA_SAD  Threonyl and Alanyl tRNA synthetase second additional domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.0   0.0   2.2e-13   1.3e-09       3      44 .]     237     284 ..     235     284 .. 0.95

  Alignments for each domain:
  == domain 1  score: 38.0 bits;  conditional E-value: 2.2e-13
                                        EEEETT.EEEEESS---SBGGGC-SEEEE.......CCECCCTCEEEEE CS
                           tRNA_SAD   3 vvsiGdisvelCgGtHvpnTgeIgafkil.......seesiakglrRIy 44 
                                         ++ G+ + ++C G+Hv+nT+ I+ f i+        ++++++ l+R+y
  gene1114|gene1114|rna1114|rna1114 237 CYELGT-FLDFCNGPHVHNTRIIKTFEIVktgasyfLGDKDRPSLQRLY 284
                                        689996.****************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (702 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       468  (0.026103); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.24s 00:00:00.81 Elapsed: 00:00:00.39
# Mc/sec: 5397.32
//
Query:       gene1115|gene1115|rna1115|rna1115  [L=79]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.5e-12   45.2   0.1    6.1e-12   45.1   0.1    1.0  1  LSM       LSM domain


Domain annotation for each model (and alignments):
>> LSM  LSM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.1   0.1   3.4e-16   6.1e-12       2      65 ..       9      71 ..       8      73 .. 0.95

  Alignments for each domain:
  == domain 1  score: 45.1 bits;  conditional E-value: 3.4e-16
                                       HHHHTTTSEEEEEETTSEEEEEEEEEEETTSEEEEEEEEEEETTETEEEEEEEEEEEGGGEEEE CS
                                LSM  2 flkklinkkvtvelkngrelrGtLkgfDqfmNlvLedveetlkdkkekrklglvliRGnnivli 65
                                        l++ +n  vt+ ++  +++ G+L+g D+++N+ L+++ e  +d+     +g+ li+G +i+ i
  gene1115|gene1115|rna1115|rna1115  9 YLEQTMNTDVTLYMRKKKKYLGKLIGMDEHCNVLLDNAYEECDDN-VRVEIGRALINGGSIAAI 71
                                       68999***************************************9.9**************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       542  (0.0302304); expected 358.6 (0.02)
Passed bias filter:                      456  (0.0254337); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 562.85
//
Query:       gene1116|gene1116|rna1116|rna1116  [L=190]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-11   44.8   1.0    1.6e-11   44.8   1.0    2.3  2  CDP-OH_P_transf  CDP-alcohol phosphatidyltransferase
  ------ inclusion threshold ------
       0.44    9.5   2.8        0.6    9.0   2.8    1.1  1  CytochromB561_N  Cytochrome B561, N terminal
        1.9    8.1   9.6       0.19   11.4   1.3    2.5  3  Peptidase_M50B   Peptidase M50B-like


Domain annotation for each model (and alignments):
>> CDP-OH_P_transf  CDP-alcohol phosphatidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.8   1.0   2.7e-15   1.6e-11       2      66 .]       9      68 ..       8      68 .. 0.82
   2 ?   -0.7   1.6      0.42   2.5e+03      26      27 ..     118     135 ..      87     180 .. 0.51

  Alignments for each domain:
  == domain 1  score: 44.8 bits;  conditional E-value: 2.7e-15
                                       -HHHHHHHHHHHHHHHHHGGGS-H..HHHHHHHH..HHHHHTTHHHHHHHHTT---HHHHHHHHHHH CS
                    CDP-OH_P_transf  2 lPnaiTllrlllsvlailllltyyplvlaillll..iasltDalDGklARrlnqvstlGkllDslaD 66
                                       +Pn++ +lrlll++++i+l        l +l  +  i+s  D++DG +AR lnq+s+lG+ lD + D
  gene1116|gene1116|rna1116|rna1116  9 IPNLVNYLRLLLIISSIYLH-----GNLFLL--VytISSSIDLIDGTIARSLNQTSKLGACLDMFTD 68
                                       8***********88777533.....233333..25599999*************999******9988 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.42
                                        .................. CS
                    CDP-OH_P_transf  26 p................l 27 
                                                         +
  gene1116|gene1116|rna1116|rna1116 118 LsmlkvyyqkvvlvllcV 135
                                        044443333333322220 PP

>> CytochromB561_N  Cytochrome B561, N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   2.8    0.0001       0.6      19      88 ..      81     151 ..      66     158 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0001
                    CytochromB561_N  19 lrpskseilalvllsiasasvllfvisre.disqkaa.ylfvkllqivvalvailslsalikfislfkalva 88 
                                        +r+++++++ l+++  +++ +llf++s+  ++s+k +  ++ k+++  v+lv++   + ++++++++ +   
  gene1116|gene1116|rna1116|rna1116  81 ERKRSKSMILLLFID-LLSHMLLFTSSMAvNVSHKEPiLSMLKVYYQKVVLVLLCVGTEVYYVMKYLDTYKK 151
                                        334444444444444.45567777777777999877615789**********99999999999999877654 PP

>> Peptidase_M50B  Peptidase M50B-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.1     0.054   3.3e+02     138     162 ..      21      45 ..       2      68 .. 0.60
   2 ?   -0.4   0.2      0.13   7.7e+02      88     114 ..      81     107 ..      69     120 .. 0.62
   3 ?   11.4   1.3   3.1e-05      0.19     104     171 ..     118     185 ..     116     187 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.054
                     Peptidase_M50B 138 lleflllflgvflllgsvrdiddli 162
                                        + + ++l+  +fll++++ +  dli
  gene1116|gene1116|rna1116|rna1116  21 IISSIYLHGNLFLLVYTISSSIDLI 45 
                                        3334445555555555555555555 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.13
                     Peptidase_M50B  88 sasgkarlllvllvllllvllllvrnl 114
                                         ++++++++l l++ ll  +ll++ ++
  gene1116|gene1116|rna1116|rna1116  81 ERKRSKSMILLLFIDLLSHMLLFTSSM 107
                                        233444555666666666777766554 PP

  == domain 3  score: 11.4 bits;  conditional E-value: 3.1e-05
                     Peptidase_M50B 104 llvllllvrnlfglvlllllgallllvlllaedelleflllflgvflllgsvrdiddlirrkapesDa 171
                                        l +l ++++++++++l++++ +  ++  l + +++++ ++l++ +fl++ s+ + ++li+++ + sD 
  gene1116|gene1116|rna1116|rna1116 118 LSMLKVYYQKVVLVLLCVGTEVYYVMKYLDTYKKVNKNVILLFYTFLIVKSFFHFLQLIEGMCRLSDL 185
                                        66777899******************9999*******************************9999995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (190 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       830  (0.0462937); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1316.94
//
Query:       gene1117|gene1117|rna1117|rna1117  [L=180]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.8e-35  120.2   0.0    5.4e-35  120.1   0.0    1.0  1  UQ_con    Ubiquitin-conjugating enzyme


Domain annotation for each model (and alignments):
>> UQ_con  Ubiquitin-conjugating enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.1   0.0     3e-39   5.4e-35       5     138 ..      18     167 ..      13     169 .. 0.91

  Alignments for each domain:
  == domain 1  score: 120.1 bits;  conditional E-value: 3e-39
                                        HHHHHHHSTTTTEEEEEEET....TEECEEEEEEEB.TTSTTTTEEEEEEEE--TTTTTS--EEEESST-SCTTBE CS
                             UQ_con   5 elkelakkkpsgisaklvdd....enlfewkvlikgpedtpYeggvFklelefpedYPlkpPkvkfvtkifHPnvd 76 
                                        e + +++ ++ g+ a+++ +    ++  +w++ i+g e+++Yeg v ++ +ef  dYP++pPk++f++k+fHPn++
  gene1117|gene1117|rna1117|rna1117  18 EKNLVSDAPECGFLAEPQLQpdglRDYGTWDIYINGSEGSLYEGTVLHAVIEFTFDYPITPPKMRFISKMFHPNIY 93 
                                        3336667777788888887555778999************************************************ PP

                                        TTSBB-CGGGS............TTT--TTSHHHHHHHHHHHHHHS--TTS-SSHHHHHHHHHTHHHHHHHHHH CS
                             UQ_con  77 ksGevcldiLk............eekWspaltlesvllsiqsLlaepnpesplnkeaakllkkdreeykkkvke 138
                                        ++G+vc++ L+            +ekW+p++ +++++l ++s+l+epn  sp+n++a k++k+d e+y ++v++
  gene1117|gene1117|rna1117|rna1117  94 SDGKVCISTLHvadddpsayespDEKWTPVHGIRTIVLGVISILNEPNIVSPANVDASKMFKDDYEKYCRTVEA 167
                                        **********************9999*******************************************99975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       299  (0.0166769); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.20s 00:00:00.58 Elapsed: 00:00:00.36
# Mc/sec: 1490.31
//
Query:       gene1118|gene1118|rna1118|rna1118  [L=51]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-05   24.4   0.0    2.1e-05   24.3   0.0    1.1  1  RRM_1     RNA recognition motif. (a.k.a. RRM, RBD, or RNP dom


Domain annotation for each model (and alignments):
>> RRM_1  RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.0   1.2e-09   2.1e-05      35      70 .]       4      39 ..       1      39 [. 0.94

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 1.2e-09
                                       TTSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE CS
                              RRM_1 35 tgkskgfafVeFeskedAekAlealngkklggrelk 70
                                       +g+s++++f+e  s ++  +++e++ngk ++g++l+
  gene1118|gene1118|rna1118|rna1118  4 KGRSRCYGFIELVSGDEFVEIIEKFNGKRVNGKPLR 39
                                       79*******************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (51 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       234  (0.0130515); expected 358.6 (0.02)
Passed bias filter:                      216  (0.0120475); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 372.92
//
Query:       gene1119|gene1119|rna1119|rna1119  [L=335]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   1.6e-106  355.3   0.2   1.9e-106  355.0   0.2    1.1  1  Rad51     Rad51
    1.2e-11   44.7   0.1    1.6e-11   44.2   0.1    1.1  1  RecA      recA bacterial DNA recombination protein
    6.9e-10   38.7   0.1    1.9e-09   37.2   0.1    1.8  1  ATPase    KaiC
    4.5e-06   26.4   0.0    7.2e-06   25.7   0.0    1.2  1  AAA_25    AAA domain
    0.00012   21.5   0.2     0.0051   16.2   0.2    2.2  1  DnaB_C    DnaB-like helicase C terminal domain
  ------ inclusion threshold ------
      0.021   14.6   0.0      0.041   13.6   0.0    1.5  1  AAA_24    AAA domain


Domain annotation for each model (and alignments):
>> Rad51  Rad51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  355.0   0.2  6.3e-110  1.9e-106       1     254 [.      84     332 ..      84     333 .. 0.98

  Alignments for each domain:
  == domain 1  score: 355.0 bits;  conditional E-value: 6.3e-110
                                        -S-EBHHHHHHHHHSS-EE--S-HHHHHHHTSSEESSSEEEEEESTTSSHHHHHHHHHHHTTS-TTTS--SSEEEE CS
                              Rad51   1 lgfvsavellekrsellqlttGskklDelLgGGietgsiteifGefrsGktqlchtlcvtvqlplelgGgegkavy 76 
                                        ++f++a e+++kr++++++ttGs++lD+lL+GG++t+s+teifGefr+Gktq+c tlc+t+ql       ++k++y
  gene1119|gene1119|rna1119|rna1119  84 MDFTTAIEYAAKREQVVRITTGSSDLDALLNGGVQTMSVTEIFGEFRTGKTQICLTLCITAQLQ-----ENSKVAY 154
                                        689************************************************************9.....799**** PP

                                        EESSS---GGGGHHHHHHTT--HHHHGGGEEEEE--STTHHHHHHHHTHHHHHHS.-EEEEEEETTTGGGCH---- CS
                              Rad51  77 idtegtfrperlveiaerykldkeevlenvayaRaytiehqeellqqaaallaed.kfallivDsvtalyRtdfsg 151
                                        idtegtfrperl eia r+++d+e++l+nv +aRay+++hq +ll++++a +++d  ++lli+Dsv+al+Rtdf g
  gene1119|gene1119|rna1119|rna1119 155 IDTEGTFRPERLREIAARFDIDQEQALQNVICARAYNSDHQVDLLNTLSARFSDDpTYRLLIIDSVIALFRTDFIG 230
                                        *****************************************************98469****************** PP

                                        ---THHHHHHHHHHHHHHHHHHHHH--EEEEEEE-------.------------HHHHHHHH-SEEEEEEE-STTE CS
                              Rad51 152 rgelakRqqklgkllrtLrkladefevavvitnqvvaqvdgqaalfsadpkkPigGlvlahasttRlalrkgkgee 227
                                        rgel +Rqqkl+ +l++L+++a+e+++av+itnq+++++ + + +f adpkkPigG+vlahasttR++lrkgkge+
  gene1119|gene1119|rna1119|rna1119 231 RGELGERQQKLNIFLSRLQRMAEEYNIAVLITNQMMSDPSA-TLTFVADPKKPIGGHVLAHASTTRIYLRKGKGET 305
                                        ****************************************9.9********************************* PP

                                        EEEEEES-SSS-S-EEEEEEETTEEE- CS
                              Rad51 228 RivkvvdsPnlpeleavfaigeeGied 254
                                        Ri+k++dsP+lpe+ea++ai++ Gi +
  gene1119|gene1119|rna1119|rna1119 306 RIAKIYDSPELPENEAMYAITSGGIDN 332
                                        ************************976 PP

>> RecA  recA bacterial DNA recombination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.2   0.1   5.3e-15   1.6e-11      26     222 ..      94     301 ..      75     312 .. 0.78

  Alignments for each domain:
  == domain 1  score: 44.2 bits;  conditional E-value: 5.3e-15
                                        -.-----EE--S-HHHHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHHHH.HTT--EEEEESS----HHH... CS
                               RecA  26 keklkvetissGslaldialGiGGlpkGriieiyGpessGkttlalhaiaeaq.kkggvaafidaehaldpky... 97 
                                        +++++v  i++Gs  ld  l  GG+    ++ei+G   +Gkt ++l +   aq +++  +a+id+e ++ p+    
  gene1119|gene1119|rna1119|rna1119  94 AKREQVVRITTGSSDLDALLN-GGVQTMSVTEIFGEFRTGKTQICLTLCITAQlQENSKVAYIDTEGTFRPERlre 168
                                        44678999*********7776.********************9888766555524567789*********976111 PP

                                        .HHHTT--....GGG-EEE--SSHHHHHHHHHHHHTTT--S....EEEEE-TTT---STT-.----------HHHH CS
                               RecA  98 .akklGvd....idellvsqpdtGeqaleiadalvrsgaid....livvdsvaalvpkaei.eGemgdskvglqar 163
                                         a+++ +d    +++++ ++  + ++ ++++++l    + d    l+++dsv al   + i  Ge+g+ +  l+  
  gene1119|gene1119|rna1119|rna1119 169 iAARFDIDqeqaLQNVICARAYNSDHQVDLLNTLSARFSDDptyrLLIIDSVIALFRTDFIgRGELGERQQKLNI- 243
                                        156667773232357888999999*******99976544333333***********9998855999998876654. PP

                                        HHHHHHHHHHHHHTTT--EEEEEEE----..------.-------HHHHHHH-SEEEEEEEE CS
                               RecA 164 lmsqalrkltgaisksntvvifinqirek..iGvmfg.npetttGGralkfyasvrldvrri 222
                                             l +l+ + ++ n++v+  nq+       + f  +p+   GG+ l   ++ r+ +r+ 
  gene1119|gene1119|rna1119|rna1119 244 ----FLSRLQRMAEEYNIAVLITNQMMSDpsATLTFVaDPKKPIGGHVLAHASTTRIYLRKG 301
                                        ....4566777889999********987622445554399*****************99985 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.2   0.1   6.4e-13   1.9e-09       2     194 ..     103     305 ..     102     331 .. 0.76

  Alignments for each domain:
  == domain 1  score: 37.2 bits;  conditional E-value: 6.4e-13
                             ATPase   2 ktgIeglDeilkgGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepa..edlrenakslGwdle 75 
                                         tg   lD +l+gG+   +v+ i Ge  tGKt ++l+  i+   + + ++ ++ +e +   e lre a+++++d e
  gene1119|gene1119|rna1119|rna1119 103 TTGSSDLDALLNGGVQTMSVTEIFGEFRTGKTQICLTLCITAQLQENSKVAYIDTEGTFrpERLREIAARFDIDQE 178
                                        79999*********************************99999999**********97555*************** PP

                             ATPase  76 kleeegklaiidasesaeesaeekdkedleelieelaeai.keikakrvviDsitgl.aye........ekeavaR 141
                                        +  ++  ++   a++s+++            l+++l     ++   + ++iDs+ +l  ++        e+++++ 
  gene1119|gene1119|rna1119|rna1119 179 QALQN--VICARAYNSDHQ------V----DLLNTLSARFsDDPTYRLLIIDSVIALfRTDfigrgelgERQQKLN 242
                                        *9999..555555555433......3....3444444444045555888999998884322222222224566666 PP

                             ATPase 142 eilrqlvrvlkklgvTailvsekss...........seeaaggygveefivdgvivLdlkeiee 194
                                          l +l r+ +++++  ++++++ s            ++ +gg+ +++ +++  i L++ + e+
  gene1119|gene1119|rna1119|rna1119 243 IFLSRLQRMAEEYNIAVLITNQMMSdpsatltfvadPKKPIGGHVLAH-ASTTRIYLRKGKGET 305
                                        677778777799999999999988878888888877667777777777.777777777665555 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   0.0   2.4e-09   7.2e-06      19     186 ..     106     262 ..      90     266 .. 0.73

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 2.4e-09
                             AAA_25  19 ppprrwlvkgllpagelallaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEdsedelrrRlravg 94 
                                           ++ l+ g +   +++ ++G   tGKt ++l l+++  +          e+ kV y+++E++    ++Rlr++ 
  gene1119|gene1119|rna1119|rna1119 106 SSDLDALLNGGVQTMSVTEIFGEFRTGKTQICLTLCITAQLQ---------ENSKVAYIDTEGTF--RPERLREIA 170
                                        5567778888889999**************999988876652.........678**********9..678888877 PP

                             AAA_25  95 ealrddarllvldlagveslpLfakdrggtlltadvdaleaaieevegvrlvviDplsralggdensnsd...... 164
                                        + ++  +++++l+  +v  +  +a  +++++    ++ l a+  + + +rl++iD++ ++++ d     +      
  gene1119|gene1119|rna1119|rna1119 171 ARFD-IDQEQALQ--NV--ICARAYNSDHQV--DLLNTLSARFSDDPTYRLLIIDSVIALFRTDFIGRGElgerqq 239
                                        7763.34444443..23..332333333433..335668888888899********99988885444444443435 PP

                             AAA_25 165 .vgalvealeriarrtgaavllv 186
                                          + ++++l+r+a+++++avl++
  gene1119|gene1119|rna1119|rna1119 240 kLNIFLSRLQRMAEEYNIAVLIT 262
                                        46*******************97 PP

>> DnaB_C  DnaB-like helicase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.2   1.7e-06    0.0051       2     178 ..     102     265 ..     101     273 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.7e-06
                                        BXSSTHHHHHHCT.SBXTTXEEEEEEXTTSSHHHHHHHHHHHHHHCSTSEEEEEESSSXHHHHHHHHHHHHHTXXH CS
                                        xxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             DnaB_C   2 lstgfkdLDklts.GlqkgdliiiAarpsmGktalalniaenaavkeklpvavfslemsaeqlvqRllsseaeids 76 
                                        ++tg +dLD+l++ G+q   ++ i +   +Gkt ++l+++ +a  +e+ +va++  e + +    R ++++ +id+
  gene1119|gene1119|rna1119|rna1119 102 ITTGSSDLDALLNgGVQTMSVTEIFGEFRTGKTQICLTLCITAQLQENSKVAYIDTEGTFRPERLREIAARFDIDQ 177
                                        68999****987527999***********************99999***************99************9 PP

                                        HHHHHTTSXHHHHHHHHHHHHHHHHSEEEEEEXSSXCHHHHHHHHHHHHHHTTEEEEEEEEGGGTBTSCSSSCCCH CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             DnaB_C  77 kklrtgklkeedweklteaieelseaklfiddtpaltvseirskarrlkkekglgliviDyLqlmegseekenreq 152
                                        +++ +  +      +  ++++ l++++  + d p+  +  i s          + l   D++   e      +r+q
  gene1119|gene1119|rna1119|rna1119 178 EQALQNVICA-RAYNSDHQVDLLNTLSARFSDDPTYRLLIIDSV---------IALFRTDFIGRGE----LGERQQ 239
                                        9998877665.455667777888888888888887766666553.........3344446665544....346777 PP

                                        HHHHHHHHHHHHHHHCTSXEEEEEEX CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             DnaB_C 153 evseisrsLkalakelnvpvialsqL 178
                                        ++     +L+ +a e n+ v++  q+
  gene1119|gene1119|rna1119|rna1119 240 KLNIFLSRLQRMAEEYNIAVLITNQM 265
                                        77777777777777777777777776 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   1.4e-05     0.041       7      78 ..     125     224 ..     122     250 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.4e-05
                             AAA_24   7 iyGpsgiGKTtlakel........gpkplfidtekGlksldadkfpdie...................swedflde 55 
                                        i+G+  +GKT ++++l          k+++idte+      + ++ +i                            
  gene1119|gene1119|rna1119|rna1119 125 IFGEFRTGKTQICLTLcitaqlqeNSKVAYIDTEGT---FRPERLREIAarfdidqeqalqnvicaraY------- 190
                                        89********************************94...466666666666777767755444444440....... PP

                             AAA_24  56 vvel..............aaeladyktlviDtidele 78 
                                           +                ++++y+ l+iD++  l 
  gene1119|gene1119|rna1119|rna1119 191 ---NsdhqvdllntlsarFSDDPTYRLLIIDSVIALF 224
                                        ...255555555555666888999*******997665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (335 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       698  (0.0389313); expected 358.6 (0.02)
Passed bias filter:                      609  (0.0339673); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.38
# Mc/sec: 2626.74
//
Query:       gene112|gene112|rna112|rna112  [L=45]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (45 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       366  (0.0204139); expected 358.6 (0.02)
Passed bias filter:                      219  (0.0122148); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.31u 0.25s 00:00:00.56 Elapsed: 00:00:00.37
# Mc/sec: 365.38
//
Query:       gene1120|gene1120|rna1120|rna1120  [L=159]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       786  (0.0438396); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1165.85
//
Query:       gene1121|gene1121|rna1121|rna1121  [L=709]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.8e-87  292.7   0.0    3.5e-87  292.4   0.0    1.0  1  Enolase_C  Enolase, C-terminal TIM barrel domain
    2.8e-32  111.6   0.0    5.9e-32  110.6   0.0    1.5  2  Enolase_N  Enolase, N-terminal domain
    2.5e-07   30.5   0.0    3.5e-07   30.0   0.0    1.1  1  MR_MLE_C   Enolase C-terminal domain-like
     0.0019   17.4   0.0      0.003   16.8   0.0    1.2  1  MAAL_C     Methylaspartate ammonia-lyase C-terminus


Domain annotation for each model (and alignments):
>> Enolase_C  Enolase, C-terminal TIM barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  292.4   0.0   7.7e-91   3.5e-87       4     282 ..     434     704 ..     431     708 .. 0.96

  Alignments for each domain:
  == domain 1  score: 292.4 bits;  conditional E-value: 7.7e-91
                                        E-EE-EEEEE-GGGSSSS--SSEEEEE-TT-SSHHHHHHHHHHHHHHHHHHHHHCC.GGGG-B-TTS-B----SSH CS
                          Enolase_C   4 lPvPalnvinGGshagnklalqefmilPvgassfkealrlGaevyhklksvlkkkygksatnvGdeGGfaPnlqsn 79 
                                        +P+P +n++nGGshagn+l +qe mi   + ++f+  l   a  y +lk v+k+k+g   t  GdeGGf P +++ 
  gene1121|gene1121|rna1121|rna1121 434 MPLPNFNILNGGSHAGNELLFQEIMIS-FQNDTFEKNLESAAGFYATLKCVIKDKFGGIYTGFGDEGGFMPPVRTL 508
                                        8*************************7.5789******************************************** PP

                                        HHHHHHHHHHHHHCT-TCTBEEEEE--GGGCEETCTTEEECTTTTTT..GGCEEEHHHHHHHHHHHHHHS-.EEEE CS
                          Enolase_C  80 kealdliveaiekaGykgkvkialdvassefykekdkkydldfkeeesdkskkltseqladlykelvkkyP.ivsi 154
                                        +e+ldl+ e +++   ++ + ia+d+a+  f+  +++ky ++ k+     +k l+ +++ d+y+ l k+y  i+ i
  gene1121|gene1121|rna1121|rna1121 509 EEGLDLLRE-VQQRTNEKGLRIAVDAAANSFF--SNGKYTVHLKD----GEKELSGDEMIDYYRALLKEYTeIYLI 577
                                        ******998.566677889*************..778*****998....899******************6599** PP

                                        ES-S-TT-HHHHHHHHHHHTTTSEEEESTTTTT-HHHHHHHHHCT--SEEEE-HHHH-SHHHHHHHHHHHHHTT-E CS
                          Enolase_C 155 edpldeddweawkklteelgdkvqivGddltvtnpkrlkeaiekkaanalllkvnqiGsltesleavklakeagyg 230
                                        edp++e d e+wkk+t+e gd++ i+Gddl+vtn+k++kea ekk +na+l+k nqiG+++ +leav+ ake+ + 
  gene1121|gene1121|rna1121|rna1121 578 EDPFAETDLETWKKFTAEFGDRLIILGDDLLVTNSKMIKEAAEKKLCNAVLIKPNQIGTVSGTLEAVQAAKENNFK 653
                                        **************************************************************************** PP

                                        EEEE--SC--S--HHHHHHHHCT-SEEE---S-SHHHHHHHHHHHHHHHHHG CS
                          Enolase_C 231 vvvshrsGetedttiadlavglsaGqiktGaparserlakynqllrieeelg 282
                                        v+vshrsGeted +iadl+vg++a   k+Gap r er+ kynqllriee+l 
  gene1121|gene1121|rna1121|rna1121 654 VMVSHRSGETEDPFIADLSVGVAADFFKSGAP-RGERMVKYNQLLRIEEDLM 704
                                        *******************************8.9***************996 PP

>> Enolase_N  Enolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.6   0.0   1.3e-35   5.9e-32       1     131 []     295     424 ..     295     424 .. 0.98
   2 ?   -3.3   0.0       2.1   9.3e+03      31      51 ..     532     551 ..     512     560 .. 0.57

  Alignments for each domain:
  == domain 1  score: 110.6 bits;  conditional E-value: 1.3e-35
                                        EEEEEEEEEE-TTS-EEEEEEEEETTC-EEEEE--B-BSSSSSS-B----SSTTSGGGT--HHHHHHHHHTHHHHH CS
                          Enolase_N   1 IkkvkareildSrGnpTvevevttedgalgraavpsGaStgekealelrDgdkkrylgkgvekavenvnekiapal 76 
                                        Ik +  r+il SrG pTve++++ ++  ++r+++psG Stg+ke+  l+D+  k y+g++v+ ++++++e+i p +
  gene1121|gene1121|rna1121|rna1121 295 IKAICPRQILSSRGYPTVEIDIVSDQDEVFRSSAPSGDSTGAKEVAVLTDK-GKSYNGRSVTGVLKKFEEEIVPLI 369
                                        88999*******************9999**********************8.899********************* PP

                                        TTSBTT-HHHHHHHHHHHH-STT-TTT-HHHHHHHHHHHHHHHHHHHTS-HHHHH CS
                          Enolase_N  77 igldvtdqeeiDkllielDgtenksklGaNailavSlAvakaaAkakelplyryl 131
                                         + ++++q e+D++l  +D t++ s++GaN++l +Sl+++k +Ak+++l+ly+++
  gene1121|gene1121|rna1121|rna1121 370 FKSRISTQIEFDSVLYIADRTPTLSTYGANTLLPLSLSFCKFQAKTEGLKLYEHI 424
                                        *****************************************************97 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 2.1
                                        EEE--B-BSSSSSS-B----S CS
                          Enolase_N  31 raavpsGaStgekealelrDg 51 
                                         aa+ s  S g++ +  l+Dg
  gene1121|gene1121|rna1121|rna1121 532 DAAANSFFSNGKYTVH-LKDG 551
                                        4455555555555544.5565 PP

>> MR_MLE_C  Enolase C-terminal domain-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.0   0.0   7.9e-11   3.5e-07      25     156 ..     498     658 ..     468     691 .. 0.80

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 7.9e-11
                                        S........HHHHHHHHHHHHHHHHTTTSTSEEEEE-TTTS..................BHHHHHHHHHHH.GGGT CS
                           MR_MLE_C  25 d........dvaedvervravreavgpgddvdlmvDanqaw..................dlatAirvarel.eeld 73 
                                        +        +++e ++ +r+v++++++ + ++++vDa +                    + ++ i + r+l +e+ 
  gene1121|gene1121|rna1121|rna1121 498 EggfmppvrTLEEGLDLLREVQQRTNE-KGLRIAVDAAANSffsngkytvhlkdgekelSGDEMIDYYRALlKEYT 572
                                        155666677899*************65.689*****88874468999999999999999999*********87766 PP

                                        .ESEEESSSSTTTHHHHHHHHHH...HHSSEEEESTTSSS.HHHHHHHHHHTSESEEEEBHHHHTSHHHHHHHHHH CS
                           MR_MLE_C  74 .llwlEEPvppeddleglaelra...rasipiaagEslys.radfrelleagavdivqpdvsrvgGitearkvaal 144
                                         ++++E+P+    dle  ++ +a   + ++ i ++  l +  + ++e++e++ + +v ++++++g ++++++ ++ 
  gene1121|gene1121|rna1121|rna1121 573 eIYLIEDPFAE-TDLETWKKFTAefgD-RLIILGDDLLVTnSKMIKEAAEKKLCNAVLIKPNQIGTVSGTLEAVQA 646
                                        6*********9.67********86542.566777776655599********************************* PP

                                        HHHTT-EEEEBS CS
                           MR_MLE_C 145 aeafgvpvapHs 156
                                        a++++ +v++ +
  gene1121|gene1121|rna1121|rna1121 647 AKENNFKVMVSH 658
                                        ***999987765 PP

>> MAAL_C  Methylaspartate ammonia-lyase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   6.6e-07     0.003     131     216 ..     591     677 ..     552     685 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 6.6e-07
                             MAAL_C 131 eklkekgikvelvaDeWcnt.ledirefvdaeaadlvqiktPDlGginntieavlyckekgvgaylGGscnetdvs 205
                                        +  +e g ++ ++ D+   t  + i+e ++++ +++v ik   +G+++ t+eav+ +ke++ ++++   + et+  
  gene1121|gene1121|rna1121|rna1121 591 KFTAEFGDRLIILGDDLLVTnSKMIKEAAEKKLCNAVLIKPNQIGTVSGTLEAVQAAKENNFKVMVSHRSGETEDP 666
                                        3344445555666666654415679******************************************999999977 PP

                             MAAL_C 206 arvsvhvalat 216
                                          +   v++a+
  gene1121|gene1121|rna1121|rna1121 667 FIADLSVGVAA 677
                                        66666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (709 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       263  (0.014669); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.44
# Mc/sec: 4891.73
//
Query:       gene1122|gene1122|rna1122|rna1122  [L=92]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.062   13.2   0.0      0.078   12.9   0.0    1.1  1  DUF577    Family of unknown function (DUF577)


Domain annotation for each model (and alignments):
>> DUF577  Family of unknown function (DUF577)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   4.3e-06     0.078      56      98 ..      37      77 ..      30      85 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 4.3e-06
                             DUF577 56 ktefvkavyvFidLpmpldeefikkvlenlleeiekvLlppee 98
                                       k+ + ++ +vF  L   l++efi ++l  ll +i+  L +pe+
  gene1122|gene1122|rna1122|rna1122 37 KAPPSRTCSVFSPLR--LNNEFIVRALRPLLIRISALLHEPES 77
                                       56799*******998..**********************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       221  (0.0123264); expected 358.6 (0.02)
Passed bias filter:                      188  (0.0104858); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 659.94
//
Query:       gene1123|gene1123|rna1123|rna1123  [L=35]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (35 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       174  (0.00970495); expected 358.6 (0.02)
Passed bias filter:                      114  (0.00635841); expected 358.6 (0.02)
Passed Vit filter:                         2  (0.000111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.27s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 253.32
//
Query:       gene1124|gene1124|rna1124|rna1124  [L=538]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.3e-32  111.3   5.6    8.5e-32  110.6   5.6    1.3  1  CorA      CorA-like Mg2+ transporter protein
  ------ inclusion threshold ------
        1.4    9.0   4.6        1.1    9.2   0.9    2.7  2  Turandot  Stress-inducible humoral factor Turandot
        2.7    8.5   6.2       0.84   10.1   0.2    2.7  3  DUF2115   Uncharacterized protein conserved in archaea (DUF21


Domain annotation for each model (and alignments):
>> CorA  CorA-like Mg2+ transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.6   5.6   1.4e-35   8.5e-32       2     288 ..     221     522 ..     220     526 .. 0.92

  Alignments for each domain:
  == domain 1  score: 110.6 bits;  conditional E-value: 1.4e-35
                               CorA   2 agfvWldlsspteeeleeLaeelgldelaledlldseerprvedyddylllvlpsveldkseeeeeev.......p 70 
                                        +g++Wl + +p e +l  + + + +++++l+d+ ++++  +ve +++y++++ + +  ++  ++ e+         
  gene1124|gene1124|rna1124|rna1124 221 KGYYWLSIFDPAEKDLIDIGRYFKVHDITLNDIREKNTKEKVELFHNYTFISTRLFSERETRNANENEkiksvdiD 296
                                        689*****************************************************9999888888888899999* PP

                               CorA  71 lsillgdnflitvrreplealdevikrlk.deggkpkspgellyrlldeivdrlfellekleeeldeledel..ed 143
                                        ++il+ +nf++t+++ + +++ ++ + l    +  +  p+++l+ ++ e++++++ lle +  e+   +++     
  gene1124|gene1124|rna1124|rna1124 297 FNILMFRNFIVTLHDTRWNSISDILNFLNlISEYTTVYPEWVLFSIVVEFLQDVRFLLELIVPEVTAMQNNSyvVM 372
                                        ************************99999855589999*********************************99988 PP

                               CorA 144 stkkeilrelaqlrrrlvklrralapnrevlkrllakaddkllddedkeylrdlldelerllemlealrerleslq 219
                                        ++  + l+e + l  +l  lr++ +p+  +l+++++ + + +l +   +++   ++++ +l+++++  ++ le+ q
  gene1124|gene1124|rna1124|rna1124 373 DEIGGVLKENFLLTNSLFSLRTSTKPKIHILNNIIN-KYGRKLRRSVLKHIYFTYQDFLSLDKEMKENSKSLERCQ 447
                                        8999********************************.88888888887999999999999**************** PP

                               CorA 220 dtyssllser.......lNrvmkvLTvltaiflPlTlitGiyGmNfkglPelewsygypfvlllglmallailllf 288
                                        d++ +l++ +       +N+vmk++T++t iflP+  ++G++GmN++  P++++   +pf ll+++  l++++ +f
  gene1124|gene1124|rna1124|rna1124 448 DLFLALVNMEqsregneMNKVMKRFTIITFIFLPMQTVAGLWGMNVP-VPFQDETKLWPFFLLCIVGPLISMVYFF 522
                                        ********99999**********************************.**99999967776555555555544444 PP

>> Turandot  Stress-inducible humoral factor Turandot
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.9   0.00019       1.1       6      49 ..      43      91 ..      41      98 .. 0.62
   2 ?   -0.8   0.1      0.26   1.6e+03       6      23 ..     253     270 ..     251     294 .. 0.61

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00019
                           Turandot  6 tkikniqeliaiYekyss........slqlspderekldrlireykeeevlv 49
                                       + ++ni e+i+iY+++++        +  l++ +++++++ ++ey+   ++v
  gene1124|gene1124|rna1124|rna1124 43 SNSRNIAEIITIYRRMKKgrenqrvyRQMLNVMNEDENNERVDEYE---MVV 91
                                       6789***********9861111111133455555555555555555...555 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.26
                           Turandot   6 tkikniqeliaiYekyss 23 
                                         ++kn++e ++++++y+ 
  gene1124|gene1124|rna1124|rna1124 253 IREKNTKEKVELFHNYTF 270
                                        578999999999888752 PP

>> DUF2115  Uncharacterized protein conserved in archaea (DUF2115)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.1      0.51   3.1e+03      51      83 ..      51      84 ..      36     103 .. 0.48
   2 ?    0.1   0.2      0.17     1e+03      40     113 ..     258     304 ..     234     333 .. 0.48
   3 ?   10.1   0.2   0.00014      0.84      33     112 ..     404     480 ..     374     486 .. 0.71

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.51
                            DUF2115 51 lfeaykelkn.krsgdkseykeevideeelkefl 83
                                       +++ y+++k+  ++++  ++  +v++e+e +e +
  gene1124|gene1124|rna1124|rna1124 51 IITIYRRMKKgRENQRVYRQMLNVMNEDENNERV 84
                                       3334444444322222222222333333333333 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.17
                            DUF2115  40 rkelseslteylfeaykelknkrsgdkseykeevideeelkeflemleeqceeekeekeerlrklyylvslYli 113
                                         ke                             e +++ ++ ++    e++ ++ +e+++ ++  + + + ++  
  gene1124|gene1124|rna1124|rna1124 258 TKEKV---------------------------ELFHNYTFISTRLFSERETRNANENEKIKSVDIDFNILMFRN 304
                                        22222...........................233333333333333333333333333333333333444433 PP

  == domain 3  score: 10.1 bits;  conditional E-value: 0.00014
                            DUF2115  33 kklpekyrkelseslteylfeaykelknkrsgdkseykeevideeelkeflemleeqceeekeek.eerlrklyyl 107
                                        +++ +ky ++l++s+ ++++ +y+++ +     ++e+ke+    e++++++ +l ++ ++++ ++ ++ ++++  +
  gene1124|gene1124|rna1124|rna1124 404 NNIINKYGRKLRRSVLKHIYFTYQDFLS----LDKEMKENSKSLERCQDLFLALVNMEQSREGNEmNKVMKRFTII 475
                                        566789**********************....44444445555666666555544444444443337778888888 PP

                            DUF2115 108 vslYl 112
                                        + ++l
  gene1124|gene1124|rna1124|rna1124 476 TFIFL 480
                                        77775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (538 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1131  (0.0630822); expected 358.6 (0.02)
Passed bias filter:                      575  (0.0320709); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.63u 0.32s 00:00:00.95 Elapsed: 00:00:00.48
# Mc/sec: 3390.96
//
Query:       gene1125|gene1125|rna1125|rna1125  [L=67]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (67 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       600  (0.0334653); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.51u 0.34s 00:00:00.85 Elapsed: 00:00:00.55
# Mc/sec: 364.52
//
Query:       gene1126|gene1126|rna1126|rna1126  [L=169]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (169 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       586  (0.0326845); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.61u 0.36s 00:00:00.97 Elapsed: 00:00:00.59
# Mc/sec: 870.03
//
Query:       gene1127|gene1127|rna1127|rna1127  [L=277]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (277 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       365  (0.0203581); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.63u 0.32s 00:00:00.95 Elapsed: 00:00:00.55
# Mc/sec: 1510.26
//
Query:       gene1128|gene1128|rna1128|rna1128  [L=36]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (36 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       208  (0.0116013); expected 358.6 (0.02)
Passed bias filter:                      153  (0.00853366); expected 358.6 (0.02)
Passed Vit filter:                         5  (0.000278878); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.33u 0.29s 00:00:00.62 Elapsed: 00:00:00.43
# Mc/sec: 251.98
//
Query:       gene1129|gene1129|rna1129|rna1129  [L=80]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       701  (0.0390987); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 608.05
//
Query:       gene113|gene113|rna113|rna113  [L=147]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       812  (0.0452898); expected 358.6 (0.02)
Passed bias filter:                      476  (0.0265492); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 1005.27
//
Query:       gene1130|gene1130|rna1130|rna1130  [L=69]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.046   14.0   0.1       0.06   13.7   0.1    1.2  1  HBS1_N    HBS1 N-terminus


Domain annotation for each model (and alignments):
>> HBS1_N  HBS1 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   3.3e-06      0.06      53      71 ..       3      21 ..       1      26 [. 0.88

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.3e-06
                             HBS1_N 53 AlwkyyyDvekaldyllnk 71
                                       +++ y+yD +kald l ++
  gene1130|gene1130|rna1130|rna1130  3 SIITYNYDLQKALDILSKS 21
                                       6899**********99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (69 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       331  (0.0184617); expected 358.6 (0.02)
Passed bias filter:                      230  (0.0128284); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.29s 00:00:00.69 Elapsed: 00:00:00.45
# Mc/sec: 459.12
//
Query:       gene1131|gene1131|rna1131|rna1131  [L=85]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (85 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       259  (0.0144459); expected 358.6 (0.02)
Passed bias filter:                      187  (0.01043); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 606.57
//
Query:       gene1132|gene1132|rna1132|rna1132  [L=551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.6e-34  117.4   3.3    1.2e-27   96.8   0.3    3.4  3  Dopey_N   Dopey, N-terminal


Domain annotation for each model (and alignments):
>> Dopey_N  Dopey, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.8   0.3   6.9e-32   1.2e-27       7     198 ..      23     194 ..      18     202 .. 0.88
   2 !    8.8   0.0   4.3e-05      0.76     232     263 ..     201     232 ..     194     253 .. 0.85
   3 !   10.9   0.0   9.6e-06      0.17     273     304 ..     292     323 ..     279     326 .. 0.86

  Alignments for each domain:
  == domain 1  score: 96.8 bits;  conditional E-value: 6.9e-32
                            Dopey_N   7 ykkevekaLksfekveeWaDlisfLgkLlkaLqssnskfevipekl..lvakrLaqCLnpalPsgVHqkaLevYel 80 
                                         ++ ++k L+ f++ +eW+D+is+L+ +  aL     +++ +p+ l  l+ +rL q+LnpalP+gVH+kaLe+Y+l
  gene1132|gene1132|rna1132|rna1132  23 NNQRIRKRLEAFKNAKEWSDFISLLAAVDNALL----DVKSLPHDLeaLLFRRLNQSLNPALPAGVHNKALETYKL 94 
                                        5899*****************************....4888888652279************************** PP

                            Dopey_N  81 ifenigseslskdlslylpGLlpllsyaslsvkpqlleliekyllpLgekLrpalkglilslLpGLeeensevfer 156
                                        i++ni+   ls+     l+GL++   y++lsv+ +++e++ k      ++ r   k+ +l+lLp +eeen e+fer
  gene1132|gene1132|rna1132|rna1132  95 IITNIK---LSER---LLLGLFSYGVYSKLSVRNTFFEVMAKL-----KDCRINQKSYVLGLLPFVEEENAEHFER 159
                                        *99997...5555...478******************998775.....6889999********************* PP

                            Dopey_N 157 tlklleklkekvgekyfyqclwlaiirspsrRlgalkylskk 198
                                        + +++ ++ +         +lw  ++ +p+ R+++++y + +
  gene1132|gene1132|rna1132|rna1132 160 ACNMIADIDS-------ADALWANFLCCPELRIAVVNYFKGR 194
                                        ********98.......4788888899999999999998755 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 4.3e-05
                            Dopey_N 232 llvrallatledenllvqRgiLDlLlshlpld 263
                                          +ra++++l d + ++ Rg+LD+L  ++ l 
  gene1132|gene1132|rna1132|rna1132 201 FAIRAICRALYDGDSFTVRGTLDMLNANVTLT 232
                                        679***********************999987 PP

  == domain 3  score: 10.9 bits;  conditional E-value: 9.6e-06
                            Dopey_N 273 kedkellveaalklllrkDmSlnRRlwaWLlg 304
                                        k++  +l   ++kl+l+k+++ln++++aWL +
  gene1132|gene1132|rna1132|rna1132 292 KDEIVQLGVHVIKLFLKKEVTLNKKVNAWLQN 323
                                        6788889999********************76 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (551 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       494  (0.0275531); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.44
# Mc/sec: 3778.89
//
Query:       gene1133|gene1133|rna1133|rna1133  [L=1313]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1313 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       748  (0.0417201); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.82u 0.28s 00:00:01.10 Elapsed: 00:00:00.47
# Mc/sec: 8411.29
//
Query:       gene1134|gene1134|rna1134|rna1134  [L=310]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (310 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       441  (0.024597); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 2119.90
//
Query:       gene1135|gene1135|rna1135|rna1135  [L=246]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.5e-06   27.2   1.5    6.6e-06   25.8   0.5    2.1  2  Synaptobrevin  Synaptobrevin
      0.006   16.5   0.1      0.023   14.6   0.0    2.1  2  FAST_1         FAST kinase-like protein, subdomain 1


Domain annotation for each model (and alignments):
>> Synaptobrevin  Synaptobrevin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.15   1.3e+03      33      49 ..     113     129 ..      91     144 .. 0.61
   2 !   25.8   0.5   7.4e-10   6.6e-06       3      59 ..     185     241 ..     184     244 .. 0.94

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.15
                                        HHHHCCCCHHHHHHHHH CS
                      Synaptobrevin  33 ldeLvdktenLqssaqq 49 
                                         ++L++ t++L+ +  +
  gene1135|gene1135|rna1135|rna1135 113 THDLQEITQELNGKMYK 129
                                        34455555555544444 PP

  == domain 2  score: 25.8 bits;  conditional E-value: 7.4e-10
                                        XHHHHHHHHHHCCCCHHCCHHHHCHCCCCCHHHHCCCCHHHHHHHHHHHHHHHHHHH CS
                      Synaptobrevin   3 dklakikaevdevkdimkeNidkvlergekldeLvdktenLqssaqqFkkqarklkr 59 
                                        d+++ki +e++++k i+++ +++v+ rgekl eL d +++L+ ++++  ++a+++++
  gene1135|gene1135|rna1135|rna1135 185 DTTEKIAKELEDTKVILTRTLESVVLRGEKLGELTDSAKKLEIKSKKLFEKAKEQNK 241
                                        6789*******************************************9999999875 PP

>> FAST_1  FAST kinase-like protein, subdomain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0      0.45     4e+03      20      39 ..      16      35 ..       7      40 .. 0.67
   2 !   14.6   0.0   2.6e-06     0.023      24      65 ..     119     160 ..     114     164 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.45
                             FAST_1 20 Ffeklesrlepylsslspee 39
                                       + ++++++++++l+ ++p++
  gene1135|gene1135|rna1135|rna1135 16 LSPTITHIISQQLFVIPPNH 35
                                       45677788888888887776 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 2.6e-06
                             FAST_1  24 lesrlepylsslspeelldavwsLcileqfpeallnkvlspd 65 
                                        +++ l+ ++ ++  +   d+v+  ci +++p++l+++vl++ 
  gene1135|gene1135|rna1135|rna1135 119 ITQELNGKMYKFYVKVHADIVYIACIQDYYPLDLIDTVLDKC 160
                                        678899999999999999*********************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1255  (0.0699983); expected 358.6 (0.02)
Passed bias filter:                      520  (0.0290033); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1811.95
//
Query:       gene1136|gene1136|rna1136|rna1136  [L=1107]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.2e-59  200.0   4.3    7.5e-59  199.2   4.3    1.5  1  SNF2_N         SNF2 family N-terminal domain
    1.9e-19   70.1   0.0    5.9e-19   68.5   0.0    1.9  1  Helicase_C     Helicase conserved C-terminal domain
    2.5e-16   60.3  15.2    2.5e-16   60.3  15.2    3.2  2  DBINO          DNA-binding domain
    4.7e-08   33.2   0.1    4.7e-08   33.2   0.1    3.3  4  ResIII         Type III restriction enzyme, res subunit
    0.00021   21.1   0.0    0.00063   19.6   0.0    1.8  1  DEAD           DEAD/DEAH box helicase
  ------ inclusion threshold ------
       0.16   11.2   0.0       0.16   11.2   0.0    3.0  4  ERCC3_RAD25_C  ERCC3/RAD25/XPB C-terminal helicase


Domain annotation for each model (and alignments):
>> SNF2_N  SNF2 family N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  199.2   4.3   2.5e-62   7.5e-59      40     318 ..     242     493 ..     178     546 .. 0.87

  Alignments for each domain:
  == domain 1  score: 199.2 bits;  conditional E-value: 2.5e-62
                                        .........HHHHHTT--EEE---TTS--HHHHHHHHH...HHTTTS---.......S-EEEE--HHHHHHHHHHH CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SNF2_N  40 atgevveesaeakqsvrGGiLaDemGLGKTvqvlalilaqrakeekdkekkrkdtlagptLivvPaslldqWenei 115
                                        ++++ v   + ++++  +GiLaD+mGLGKTvq+la+++   +  e+++++         +Liv Pas+l++We+ei
  gene1136|gene1136|rna1136|rna1136 242 YQAKGVCWLINLYNQGINGILADDMGLGKTVQTLAFLT---YLAEHHNKR--------LFLIVTPASTLHNWETEI 306
                                        55555555678899************************...333333322........39**************** PP

                                        HHH-TTS-EEE--SSHHHH-----------------EEEE-HHHHHHHT......TTS-S-S-SEEEES-GGGT-- CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SNF2_N 116 erhvsssalrvlvyggqkkmkkkntkvapklladydvvittYdvlsreaelqkkrsvlkqvewkrvvlDEghtlkn 191
                                        +r+ s+ +++ +++++++        v+ +   +  +v+t+Y+ ++ +        +lk+++ +++v+DE++ +k+
  gene1136|gene1136|rna1136|rna1136 307 KRFNSNFKINLYIGTDRN--------VSIRRIPQPLIVLTSYQLIADR--------KLKRIKYDYLVCDEAQAIKS 366
                                        ***************964........6677889999**********44........5******************* PP

                                        TTSHHHHHHHH---S-EEEE-S--SSS-HHHHHHHHHHH-TTTT--HHHHHHHTHHHHHHHHHHHHHHHHTT-STT CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SNF2_N 192 stskaaeavskLstsnrwiltGTPiqnsledlygLlkfLreepfgekqtfdkllqrpieaqaekgrsrLlqllqrl 267
                                        ++s+  + +++L+ +nr++ltGTPiqns+++l++Ll+f++++ f++++ f ++++++    +++g +rL+++l+++
  gene1136|gene1136|rna1136|rna1136 367 NKSRRWKNINELRCNNRLLLTGTPIQNSMQELWSLLHFIMPGLFDSHTLFLSWFSNEKS-VKKEGLERLHSILKPF 441
                                        **********************************************************9.9*************** PP

                                        EE---GGGT--S---EEEEEEEEE--HHHHHHHH.................. CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxx RF
                             SNF2_N 268 mlrrakkdveknlPpkteeiiflklskverksYnrllevl.rkkalakllkr 318
                                        mlrr kkdv+ +l  kte+ + + +++ ++ +Y+r+ + +  ++++++l+k+
  gene1136|gene1136|rna1136|rna1136 442 MLRREKKDVKNELGTKTEKDVICIMTPLQHALYERVNKEKeSENMMMQLRKI 493
                                        *********999**********************876554045555555554 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.5   0.0     2e-22   5.9e-19       6     111 .]     960    1065 ..     955    1065 .. 0.90

  Alignments for each domain:
  == domain 1  score: 68.5 bits;  conditional E-value: 2e-22
                                         HHHHHHHTTTTSEEEEEESSHHHHHH.HHHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSS.EEEESGGGT CS
                         Helicase_C    6 llellkleeeggkilifvntidrlek.vklllekkgikvavlhgelpqnereeileqfnkgesd.vLiatdvae 77  
                                         l  +l ++ +g+++li+ + +++++   +++ + +++++++l+g  + +er++i+++f+ +++  +L++t++++
  gene1136|gene1136|rna1136|rna1136  960 LDSML-KQMIGRRVLIYFQMTKMIDLfEEYV-KMNNYSYVRLDGGVKVSERKRIVNKFQTEDIFlFLLSTRAGG 1031
                                         44556.6889**************8766666.5568***********************999999********* PP

                                         SSSTSTTESEEEESSSSSSHHHHHHHHTTSSSTT CS
                         Helicase_C   78 rGidipkvnlVinfdlprnvtsyiqriGRtgRag 111 
                                          Gi+++k+n+Vi++d ++n+t   q+++R++R g
  gene1136|gene1136|rna1136|rna1136 1032 LGINLTKANTVIFYDSDWNPTVDLQAMDRAYRLG 1065
                                         ********************************76 PP

>> DBINO  DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.3  15.2   8.4e-20   2.5e-16      11     129 ..      64     173 ..      55     178 .. 0.80
   2 ?   -2.5   0.4       2.1   6.1e+03      51      75 ..     477     501 ..     444     505 .. 0.64

  Alignments for each domain:
  == domain 1  score: 60.3 bits;  conditional E-value: 8.4e-20
                              DBINO  11 nivkkdip...kvyrakaqaekkrlanakkvaklcarevrrkasksskatkdlqlrakrlvremllfwkknekeer 83 
                                        ++vk+++    k+  a+++++++++a++kk+a++care+rr+ +++ k+  ++ l+ +r  +   +  +      +
  gene1136|gene1136|rna1136|rna1136  64 KMVKRKVRpniKAVSAYRAYRNAKMASLKKMASVCARELRRALMRTGKT--NPCLKGRRSGKGFNALTRG-----K 132
                                        5666666511145556677889999************************..***********99987653.....3 PP

                              DBINO  84 eerkkaekealekakkeeeereakRqqrkLnFLitQTELYshFisk 129
                                        ++++k      ek+kk+e+ +e++R qrkLn+Li+QTELY+hF+ +
  gene1136|gene1136|rna1136|rna1136 133 KMKRK-----GEKEKKREDRKEEEREQRKLNYLINQTELYAHFVLR 173
                                        34444.....45567888899999*******************975 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2.1
                              DBINO  51 sksskatkdlqlrakrlvremllfw 75 
                                         +++k + +++++ +++v    lf+
  gene1136|gene1136|rna1136|rna1136 477 VNKEKESENMMMQLRKIVNHPELFM 501
                                        3344555666666666666555555 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.6       1.9   5.7e+03      85     118 ..     139     170 ..     123     211 .. 0.56
   2 !   33.2   0.1   1.6e-11   4.7e-08       3     170 ..     238     391 ..     222     392 .. 0.79
   3 ?   -0.2   0.4      0.29   8.6e+02      85     131 ..     619     665 ..     599     674 .. 0.66
   4 ?   -3.1   0.2       2.2   6.6e+03      75      96 ..     755     776 ..     734     806 .. 0.56

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.9
                                        GEEEESSS-B--.......-SEEEEEHHHHHHTH CS
                             ResIII  85 igkkvsgdkkkakekdstnkkilvttiqsldads 118
                                        +++k+++d+k++  ++++ k  ++++  +l+a+ 
  gene1136|gene1136|rna1136|rna1136 139 EKEKKREDRKEE--EREQRKLNYLINQTELYAHF 170
                                        333333333333..33333344555555555555 PP

  == domain 2  score: 33.2 bits;  conditional E-value: 1.6e-11
                                        EE-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGT CS
                             ResIII   3 elreyQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkfl 78 
                                        +l+eyQ++ +  l++ +  ++  +g+++   G GKT+  +++  +l++++++ + +++v   s l  +++e+k+f 
  gene1136|gene1136|rna1136|rna1136 238 NLKEYQAKGVCWLINLY--NQGINGILADDMGLGKTVQTLAFLTYLAEHHNK-RLFLIVTPASTLHNWETEIKRFN 310
                                        66777777777777666..7999************************97665.55555555666688********* PP

                                        GG....GEEEESSS-B--.......-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.T..TTHH CS
                             ResIII  79 seaykeigkkvsgdkkkakekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakk..swre 152
                                        s+ +  i+  +  d++ +  +++ +  i++t++q +  ++         l+r ++d++++DEa  ++++k   w++
  gene1136|gene1136|rna1136|rna1136 311 SNFK--INLYIGTDRNVS-IRRIPQPLIVLTSYQLIADRK---------LKRIKYDYLVCDEAQAIKSNKsrRWKN 374
                                        9965..666666665555.466667777777777666666.........999************999985679*** PP

                                        HHHT---SEEEEEESS-S CS
                             ResIII 153 ilekfkeavllglTATpe 170
                                        i+e  + + +l lT+Tp 
  gene1136|gene1136|rna1136|rna1136 375 INEL-RCNNRLLLTGTPI 391
                                        8666.8899999****96 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.29
                                        GEEEESSS-B--.......-SEEEEEHHHHHHTH........HHHTT CS
                             ResIII  85 igkkvsgdkkkakekdstnkkilvttiqsldadseeeeeeseellrd 131
                                        ++ ++++++++++++d++n++ + +++  +++d+  +++ +++++rd
  gene1136|gene1136|rna1136|rna1136 619 NEIDYNNNNNDNNNNDNNNISTISANTPHINSDLVLKRKVEQKNDRD 665
                                        44556666666677788888888888888888887776666665555 PP

  == domain 4  score: -3.1 bits;  conditional E-value: 2.2
                                        GGGTGG....GEEEESSS-B-- CS
                             ResIII  75 kkflseaykeigkkvsgdkkka 96 
                                        +k+++++y+++++ ++ dk+k+
  gene1136|gene1136|rna1136|rna1136 755 SKYYEKEYNKENTRINVDKNKE 776
                                        4555555555666666666665 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   2.1e-07   0.00063      10     170 ..     253     391 ..     242     398 .. 0.73

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 2.1e-07
                                        HHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEEETTS CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               DEAD  10 lilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvlliiggv 85 
                                        l  +g + ++a + G GKT   l  +   ++e  + ++   liv+P   L  +  +++k+f ++   +++l ig +
  gene1136|gene1136|rna1136|rna1136 253 LYNQGINGILADDMGLGKTVQTLAFLT-YLAE--HHNKRLFLIVTPASTLH-NWETEIKRFNSNF--KINLYIG-T 321
                                        45566677889999*****98655555.5555..889999*******9995.6889999999975..5655566.6 PP

                                        SHHHHHHHHHTTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCTTSTTTSE CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               DEAD  86 aardqlskldngvdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsdfinrilnqlpqitcdgklqrq 161
                                        +++  ++++  ++ iv++  + ++d    +kl+  +  +lV DEa+ + ++  s+ +++ +n+l    c+     +
  gene1136|gene1136|rna1136|rna1136 322 DRNVSIRRI-PQPLIVLTSYQLIAD----RKLKRIKYDYLVCDEAQAIKSN-KSRRWKN-INEL---RCN-----N 382
                                        677888888.677777777766666....7877777888***********9.5666666.5666...233.....2 PP

                                        EEEEESSBS CS
                                        xxxxxxxxx RF
                               DEAD 162 vivlSATlp 170
                                         ++l+ T+ 
  gene1136|gene1136|rna1136|rna1136 383 RLLLTGTPI 391
                                        566666665 PP

>> ERCC3_RAD25_C  ERCC3/RAD25/XPB C-terminal helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   2.6      0.72   2.1e+03     171     233 ..     146     210 ..     143     227 .. 0.64
   2 ?   -4.1   0.1       2.4   7.2e+03      14      45 ..     461     492 ..     459     497 .. 0.77
   3 ?   -2.2   0.2      0.63   1.9e+03     176     206 ..     733     763 ..     729     794 .. 0.76
   4 ?   11.2   0.0   5.3e-05      0.16      74     133 ..     986    1047 ..     950    1066 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.72
                      ERCC3_RAD25_C 171 DtkemaystkrqqflvdqG..Yafkviteleeleeeeelaystkeeqkellqkvlaakdeeaeee 233
                                        D ke +  +++ ++l++q   Ya+ v+   +e  ++++l++++ +  ++ +++ la+ ++e+++ 
  gene1136|gene1136|rna1136|rna1136 146 DRKEEEREQRKLNYLINQTelYAHFVLRGEHERLKKTKLEWNDDDGAMKEMDEQLAQFKQEEKKM 210
                                        7778888888999****976688888877776666678888777766555555444433333222 PP

  == domain 2  score: -4.1 bits;  conditional E-value: 2.4
                      ERCC3_RAD25_C  14 evWcpmtaefykeylkakskkkkllyvmnpnk 45 
                                        +v c mt+  ++ y + +++k +  ++m  +k
  gene1136|gene1136|rna1136|rna1136 461 DVICIMTPLQHALYERVNKEKESENMMMQLRK 492
                                        57888999888888888888887777777666 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 0.63
                      ERCC3_RAD25_C 176 aystkrqqflvdqGYafkviteleeleeeee 206
                                        +y +  ++f    G +++v+te + +e+e +
  gene1136|gene1136|rna1136|rna1136 733 KYNQVNKEFYYTMGGTYEVVTESKYYEKEYN 763
                                        6777788899999999999999998776433 PP

  == domain 4  score: 11.2 bits;  conditional E-value: 5.3e-05
                      ERCC3_RAD25_C   74 keyakklkkpyi..yGetseaerlkilqkfkknpkvntiflskvgDtsiDlPeanvliqiss 133 
                                         +ey k+ ++ y+   G ++ +er++i++kf++++ +  ++  + g   i+l +an +i  +s
  gene1136|gene1136|rna1136|rna1136  986 EEYVKMNNYSYVrlDGGVKVSERKRIVNKFQTEDIFLFLLSTRAGGLGINLTKANTVIFYDS 1047
                                         566666666665227*********************999999**************997665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1312  (0.0731775); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.79u 0.33s 00:00:01.12 Elapsed: 00:00:00.51
# Mc/sec: 6588.88
//
Query:       gene1137|gene1137|rna1137|rna1137  [L=62]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (62 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       290  (0.0161749); expected 358.6 (0.02)
Passed bias filter:                      263  (0.014669); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.43
# Mc/sec: 433.39
//
Query:       gene1138|gene1138|rna1138|rna1138  [L=230]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.9e-22   77.5   0.0    1.9e-21   76.5   0.0    1.5  2  rve             Integrase core domain
    6.1e-08   32.7   0.6    1.5e-07   31.4   0.3    1.8  2  Integrase_H2C2  Integrase zinc binding domain
    3.6e-07   29.9   0.0    6.8e-07   29.0   0.0    1.4  1  rve_3           Integrase core domain
  ------ inclusion threshold ------
      0.036   14.3   0.0      0.096   12.9   0.0    1.8  1  zf-H2C2         H2C2 zinc finger


Domain annotation for each model (and alignments):
>> rve  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.5   0.0   4.2e-25   1.9e-21       3     118 ..      47     160 ..      45     161 .. 0.94
   2 ?   -2.9   0.0       1.7   7.6e+03      24      35 ..     174     185 ..     167     189 .. 0.69

  Alignments for each domain:
  == domain 1  score: 76.5 bits;  conditional E-value: 4.2e-25
                                rve   3 rpgelwqvDvt.vvripdgggkayllvvvddfsrlilaealsdemdastvlalleravarfggvepervlsDngse 77 
                                         pgel+++D++  +++   +g++++++++d f++ ++a a++++ +a+ vl++l + v   ++   + +lsDng e
  gene1138|gene1138|rna1138|rna1138  47 TPGELIEIDTVgPLPCT-PRGNKFIITAIDHFTKIAWARAVTHK-SADCVLRFLTEDVLTIFPD-AKNILSDNGLE 119
                                        69*********999955.6669**********************.9999999999999999998.8********** PP

                                rve  78 ytskafrefladlgirvsftrpgrpqdnGkvErfhrtlkde 118
                                        ++s ++ ++ ++ gi+++f  p++p+++G++Erf+ t++++
  gene1138|gene1138|rna1138|rna1138 120 FKSATTLKVMNEKGIHWKFGSPYHPETQGVIERFNDTIMRK 160
                                        **************************************986 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.7
                                rve  24 ayllvvvddfsr 35 
                                          ++ ++d++++
  gene1138|gene1138|rna1138|rna1138 174 TAVHLAIDAYNK 185
                                        567788888765 PP

>> Integrase_H2C2  Integrase zinc binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.4   0.3   3.3e-11   1.5e-07      27      55 ..       3      31 ..       1      34 [. 0.90
   2 ?   -2.5   0.0       1.3   5.9e+03       7      23 ..     162     181 ..     160     183 .. 0.77

  Alignments for each domain:
  == domain 1  score: 31.4 bits;  conditional E-value: 3.3e-11
                     Integrase_H2C2 27 erlrrryyWpgmrkdvkkyvksCetCqrr 55
                                         l+++y Wpgm+++++++v++C+tC ++
  gene1138|gene1138|rna1138|rna1138  3 YNLSKKYEWPGMYTQIRNFVSRCQTCLQA 31
                                       5799**********************986 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.3
                     Integrase_H2C2   7 keilkeaHds...agHlGie 23 
                                        k++++  Hd+   a Hl i+
  gene1138|gene1138|rna1138|rna1138 162 KKVCNFSHDTwdtAVHLAID 181
                                        57778889988888888776 PP

>> rve_3  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.0   0.0   1.5e-10   6.8e-07       1      55 [.     132     185 ..     132     192 .. 0.95

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 1.5e-10
                              rve_3   1 lgielsyiapgkPqqNglvEsfngtlrdellneelfrslaearekleawredYNt 55 
                                        +gi ++++ p++P ++g +E+fn t+ ++l +   f s ++ + +++ +++ YN+
  gene1138|gene1138|rna1138|rna1138 132 KGIHWKFGSPYHPETQGVIERFNDTIMRKLKKVCNF-SHDTWDTAVHLAIDAYNK 185
                                        599********************************9.*****************7 PP

>> zf-H2C2  H2C2 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   2.1e-05     0.096      15      38 ..       5      28 ..       1      29 [. 0.93

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.1e-05
                            zf-H2C2 15 larkYhwlgiketvseVissCkaC 38
                                       l +kY w+g ++ +++ +s+C++C
  gene1138|gene1138|rna1138|rna1138  5 LSKKYEWPGMYTQIRNFVSRCQTC 28
                                       6789******************** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       450  (0.025099); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1551.66
//
Query:       gene1139|gene1139|rna1139|rna1139  [L=211]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.069   13.4   0.1        5.5    7.3   0.0    2.2  2  DUF5071   Domain of unknown function (DUF5071)


Domain annotation for each model (and alignments):
>> DUF5071  Domain of unknown function (DUF5071)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.0    0.0003       5.5      63     102 ..      64     103 ..      53     105 .. 0.91
   2 ?    3.9   0.1    0.0034        60      31      66 ..     140     176 ..     129     180 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0003
                                        HHHSS-HHHHHHHHHHHGGGS-HHHHHHHHHHHHHHHTS- CS
                            DUF5071  63 iLeknDeewkyfvleflveklpveskkklkeelerlveep 102
                                        +L+++D+  +  vle+l+ +   e++  l  e+++l+++p
  gene1139|gene1139|rna1139|rna1139  64 LLSNGDNLHIEEVLELLKRRFEGEVRARLLTEMKALSKRP 103
                                        6899********************************9998 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.0034
                                        HGGGS-TTSTTHHHHHHHHHHT.GGGTHHHHHHHHHS CS
                            DUF5071  31 LeWlqDlNwPiaspiaelLarf.peelvkeiaeiLek 66 
                                        L+W+ D   P  + i+   +   +e +v++i eiL++
  gene1139|gene1139|rna1139|rna1139 140 LDWITDNVPPEVNTILATFKITsVELTVPKILEILRS 176
                                        79****888888888888875448999999***9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       455  (0.0253779); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1533.27
//
Query:       gene114|gene114|rna114|rna114  [L=62]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
       0.11   12.4   0.0       0.13   12.2   0.0    1.0  1  Xol-1_GHMP-like  Switch protein XOL-1, GHMP-like


Domain annotation for each model (and alignments):
>> Xol-1_GHMP-like  Switch protein XOL-1, GHMP-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0     7e-06      0.13      70     116 ..      10      56 ..       4      58 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 7e-06
                                    HHHHHHHHHHHHCC-TT----HHHHHHHHHHHHHHHH-TTEEEEEE- CS
                Xol-1_GHMP-like  70 vpayieaysknrvrredytdlekefdsqvaleklvnegeqveGfevv 116
                                        i +y kn + ++    le e  s +  + ++ e+ + eGf+v 
  gene114|gene114|rna114|rna114  10 FTMAIAFYRKNDRAELIRLALEHEKMSMMDEDDMMAEHLRQEGFDVI 56 
                                    4567899*************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (62 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       791  (0.0441185); expected 358.6 (0.02)
Passed bias filter:                      583  (0.0325172); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.31s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 407.17
//
Query:       gene1140|gene1140|rna1140|rna1140  [L=89]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.042   13.7   0.7      0.051   13.5   0.7    1.1  1  Atthog    Attenuator of Hedgehog


Domain annotation for each model (and alignments):
>> Atthog  Attenuator of Hedgehog
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.7   2.8e-06     0.051      57      93 ..      28      64 ..      19      72 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.8e-06
                             Atthog 57 tvillvlshwerevvkyarwlgfsamvlfclaavifp 93
                                       ++i l ls+w+  vv+ a + g++a++ +c+ av++ 
  gene1140|gene1140|rna1140|rna1140 28 NLINLPLSFWKFVVVNPAIYSGWAALIKMCIVAVMYA 64
                                       6778899***************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       491  (0.0273858); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.43
# Mc/sec: 620.37
//
Query:       gene1141|gene1141|rna1141|rna1141  [L=82]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.016   14.7   0.0       0.02   14.4   0.0    1.1  1  RVT_1     Reverse transcriptase (RNA-dependent DNA polymerase


Domain annotation for each model (and alignments):
>> RVT_1  Reverse transcriptase (RNA-dependent DNA polymerase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   1.1e-06      0.02     184     221 ..       1      52 [.       1      53 [. 0.90

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.1e-06
                                        HHHHHHHHHHTT--BEGGG-EEE...................ESSEEETTEE CS
                              RVT_1 184 leaveewlkesglkinpeKtklvlft.............v.kseevkyLGvt 221
                                        ++++++w+k++++++n  K+  ++f                + +++ky G++
  gene1141|gene1141|rna1141|rna1141   1 MQKISDWCKRWRMSLNIGKCGTMVFSsgevckicykeqpIaTVDSYKYFGLP 52 
                                        5899*********************9*******99986537999****9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       571  (0.0318478); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 588.20
//
Query:       gene1142|gene1142|rna1142|rna1142  [L=259]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1184  (0.0660383); expected 358.6 (0.02)
Passed bias filter:                      736  (0.0410508); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.23s 00:00:00.72 Elapsed: 00:00:00.38
# Mc/sec: 2041.79
//
Query:       gene1143|gene1143|rna1143|rna1143  [L=220]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.3e-16   58.2   2.2    7.3e-16   58.2   2.2    2.0  2  TFIIE_beta     TFIIE beta subunit core domain
    1.7e-08   34.0   1.1    3.6e-08   33.0   0.2    2.0  2  TFA2_Winged_2  TFA2 Winged helix domain 2


Domain annotation for each model (and alignments):
>> TFIIE_beta  TFIIE beta subunit core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.2   2.2   8.2e-20   7.3e-16       1      68 []      21      83 ..      21      83 .. 0.93
   2 ?   -2.1   0.1      0.56     5e+03      22      30 ..     166     174 ..     151     199 .. 0.58

  Alignments for each domain:
  == domain 1  score: 58.2 bits;  conditional E-value: 8.2e-20
                         TFIIE_beta  1 iftqLakiveylKkkdgplsleeIlsylslqldlsdknwllleaLknnpkieyDpkkgkfsfkPlyni 68
                                       i++++++i++++K+ d+pl+++eI++ ++l  +l+d n+ ll+ L++npki +   ++++ fkPlyni
  gene1143|gene1143|rna1143|rna1143 21 INSYIHTIIQFIKNYDRPLTFDEIEKSTNL--KLTD-NKRLLKTLTKNPKIVIG--NNTLLFKPLYNI 83
                                       5799**************************..8866.8899************4..47*********9 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.56
                         TFIIE_beta  22 eeIlsylsl 30 
                                        +++l++ls 
  gene1143|gene1143|rna1143|rna1143 166 QDVLKELSS 174
                                        455555553 PP

>> TFA2_Winged_2  TFA2 Winged helix domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.0   0.2     4e-12   3.6e-08       2      61 .]      54     142 ..      53     142 .. 0.87
   2 ?   -1.2   0.0      0.19   1.7e+03      29      40 ..     163     174 ..     155     205 .. 0.60

  Alignments for each domain:
  == domain 1  score: 33.0 bits;  conditional E-value: 4e-12
                      TFA2_Winged_2   2 nkeeLlalLkkrp...............................kaeGikvkdLkdswpdveealeeLeaegeilv 46 
                                        +++ Ll+ L k+p                                + Gi++++L ds+ d ++++  L+++  i+v
  gene1143|gene1143|rna1143|rna1143  54 DNKRLLKTLTKNPkivignntllfkplynirsekdledimiatnAEYGIELEKLLDSPIDIKPFVSNLKRKEVIFV 129
                                        56778888888888888888888888888888888887777775699***********************9999** PP

                      TFA2_Winged_2  47 lrtkkdg.qpkiVfwN 61 
                                        l   kd  +++iVf+N
  gene1143|gene1143|rna1143|rna1143 130 L---KDIdNSEIVFYN 142
                                        *...9999*******9 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.19
                      TFA2_Winged_2  29 pdveealeeLea 40 
                                        p+ ++ l+eL  
  gene1143|gene1143|rna1143|rna1143 163 PNYQDVLKELSS 174
                                        445555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1006  (0.0561102); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1486.80
//
Query:       gene1144|gene1144|rna1144|rna1144  [L=251]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    9.4e-29  100.7  15.5    3.1e-15   56.3   4.2    2.2  2  WD40_like  WD40-like domain
     0.0061   16.6   1.0       0.06   13.4   0.1    2.5  3  BBS2_Mid   Ciliary BBSome complex subunit 2, middle region
  ------ inclusion threshold ------
        2.5    8.7   4.6        8.2    7.1   0.6    3.4  4  PQQ_3      PQQ-like domain


Domain annotation for each model (and alignments):
>> WD40_like  WD40-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.3   4.2   5.1e-19   3.1e-15      79     188 ..       5     110 ..       1     121 [. 0.87
   2 !   50.0   3.5   4.4e-17   2.6e-13     194     299 ..     144     239 ..     138     241 .. 0.81

  Alignments for each domain:
  == domain 1  score: 56.3 bits;  conditional E-value: 5.1e-19
                          WD40_like  79 ekieedistvkviddklliGtnkGsiyvfskdlqleevllgqsseIkeikiennkiysLsesafivfdlfsqniey 154
                                        + ++ dis+v+  ++ lliG + G+i++f k+lq ++ l g++seI  ++i nn+++s s ++fiv+  ++++   
  gene1144|gene1144|rna1144|rna1144   5 RCLHKDISFVTHHKNILLIGCTDGEIHLFYKNLQHHINLAGHKSEITALSILNNYVFSCSAQNFIVY--KNNSVVH 78 
                                        55789**************************************************************..5555777 PP

                          WD40_like 155 kisvkdiktfeiienkdilligtegeililkknv 188
                                        + + ++ k +++i   d + +  + +i +lk++ 
  gene1144|gene1144|rna1144|rna1144  79 NHKTNELKGMRVI--DDRIYLMYNHCIRVLKHDA 110
                                        7777888888888..5667888899999999876 PP

  == domain 2  score: 50.0 bits;  conditional E-value: 4.4e-17
                          WD40_like 194 dvegkPecillvddylivGgsfkyllliNiklnvntfklrlevegiskikkisefvvafsTlcgkvgigDiRdket 269
                                        ++++  eci+ ++d l++Gg+   l+++ +k   ++   r  v+ ++ ++  s+ +v+f+Tl+g++gigD R++  
  gene1144|gene1144|rna1144|rna1144 144 SSNA-TECIAKINDDLVIGGEY--LMVM-VK--GRE--HRTAVQHVNLLVV-SNTIVVFATLDGQIGIGDYREE-Q 209
                                        4555.5*************975..4443.22..233..4556777777765.899*****************76.6 PP

                          WD40_like 270 fkllesgvGviydmkfenntiyvgGeaGlk 299
                                        f + ++gvG +ydm +  n++yv Ge+G +
  gene1144|gene1144|rna1144|rna1144 210 FSMCDGGVGLVYDMVLCGNVVYVAGENGTN 239
                                        ****************************86 PP

>> BBS2_Mid  Ciliary BBSome complex subunit 2, middle region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.1     1e-05      0.06       7      76 ..      13      82 ..      10      95 .. 0.76
   2 ?   -2.5   0.0      0.88   5.3e+03      22      34 ..     101     113 ..      99     120 .. 0.75
   3 ?    0.8   0.0     0.083     5e+02      35      68 ..     173     206 ..     149     214 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1e-05
                           BBS2_Mid  7 vdgdgeneLvvgsddfeirvfkee..elvaeitetekvvslarlekerfayaleNGtvgvyekkerlWrvks 76
                                       + ++ +n L++g +d ei +f ++  + ++ +  ++++++l+ l++  f  + +N    vy+++  + ++k+
  gene1144|gene1144|rna1144|rna1144 13 FVTHHKNILLIGCTDGEIHLFYKNlqHHINLAGHKSEITALSILNNYVFSCSAQNFI--VYKNNSVVHNHKT 82
                                       55667999************98764345566678899*************9999954..5766665555554 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.88
                           BBS2_Mid  22 feirvfkeeelva 34 
                                         +irv+k++   +
  gene1144|gene1144|rna1144|rna1144 101 HCIRVLKHDACFS 113
                                        699**99998765 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.083
                           BBS2_Mid  35 eitetekvvslarlekerfayaleNGtvgvyekk 68 
                                        e +++ + v+l  ++++  ++a   G +g+ + +
  gene1144|gene1144|rna1144|rna1144 173 EHRTAVQHVNLLVVSNTIVVFATLDGQIGIGDYR 206
                                        4555666788888999999999999999885544 PP

>> PQQ_3  PQQ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0      0.86   5.2e+03      23      34 ..      20      31 ..      14      33 .. 0.83
   2 ?   -0.7   0.1      0.38   2.3e+03      19      29 ..     125     135 ..     114     141 .. 0.78
   3 ?    0.1   0.0      0.22   1.3e+03      18      33 ..     185     200 ..     171     200 .. 0.83
   4 ?    7.1   0.6    0.0014       8.2      14      32 ..     220     238 ..     212     238 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.86
                              PQQ_3 23 lvyvgtgdGtly 34
                                       ++ +g++dG ++
  gene1144|gene1144|rna1144|rna1144 20 ILLIGCTDGEIH 31
                                       6899999*9986 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.38
                              PQQ_3  19 vdgglvyvgtg 29 
                                        +++++ y g++
  gene1144|gene1144|rna1144|rna1144 125 FGDNTAYYGSE 135
                                        57999999997 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.22
                              PQQ_3  18 avdgglvyvgtgdGtl 33 
                                        +v++ +v+++t dG +
  gene1144|gene1144|rna1144|rna1144 185 VVSNTIVVFATLDGQI 200
                                        8999999999999975 PP

  == domain 4  score: 7.1 bits;  conditional E-value: 0.0014
                              PQQ_3  14 nsspavdgglvyvgtgdGt 32 
                                        ++ +++ g++vyv++++Gt
  gene1144|gene1144|rna1144|rna1144 220 VYDMVLCGNVVYVAGENGT 238
                                        4567888**********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       623  (0.0347482); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.62u 0.33s 00:00:00.95 Elapsed: 00:00:00.56
# Mc/sec: 1353.69
//
Query:       gene1145|gene1145|rna1145|rna1145  [L=801]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.1e-29  101.1   0.0    1.1e-28   99.7   0.0    1.8  1  Beta-Casp        Beta-Casp domain
    1.8e-23   83.0   0.3      2e-22   79.6   0.1    2.5  2  Lactamase_B_6    Metallo-beta-lactamase superfamily domain
    8.5e-15   55.3   0.4    1.5e-14   54.4   0.4    1.4  1  Lactamase_B      Metallo-beta-lactamase superfamily
    1.2e-14   54.0   0.1    2.3e-14   53.0   0.1    1.6  1  RMMBL            Zn-dependent metallo-hydrolase RNA specifici
    3.8e-09   36.4   0.1    9.1e-09   35.1   0.1    1.6  1  Lactamase_B_2    Beta-lactamase superfamily domain
    8.6e-05   21.9   0.1    0.00025   20.3   0.1    1.7  1  Beta_lactamase3  Putative beta-lactamase-like family
  ------ inclusion threshold ------
      0.065   13.1   0.1       0.23   11.3   0.1    1.9  1  Lactamase_B_3    Beta-lactamase superfamily domain


Domain annotation for each model (and alignments):
>> Beta-Casp  Beta-Casp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.7   0.0   4.4e-32   1.1e-28       1     110 []     313     429 ..     313     429 .. 0.81

  Alignments for each domain:
  == domain 1  score: 99.7 bits;  conditional E-value: 4.4e-32
                                        HHHHHHHH..HCTT..TTS-S-EEEEE-HHHHHHHHHGGGGGG..........E-SHH....HHHH..HH...... CS
                          Beta-Casp   1 aqellylLeelwkekkledlklpiyldsplaskatevYkeyae..........veakslewmeskkeeln...... 60 
                                        aqell++Le++w+++++  +++piy++s la++++++Y++y++                          +      
  gene1145|gene1145|rna1145|rna1145 313 AQELLLILEDYWERNPQ-LHNVPIYYASALANRCLSIYQAYTHmmnlkikkdaF---------------Tfkhirn 372
                                        7***********99883.4558*******************6666655443330...............1333334 PP

                                        .......HS-SSEEEEES-TTSSSSHHHHHHHHHTTSTTSEEEESS---TTSHHHHH CS
                          Beta-Casp  61 .......sskgpkvilassgmlegGrsrellkklledprntvilvgyqaegTlgrkl 110
                                                 k+ +v++as+gml++G srel+++++ed++n  +++gy+++gTl++++
  gene1145|gene1145|rna1145|rna1145 373 lksvdnhLIKNACVVMASPGMLQSGLSRELFESWCEDANNGTVIPGYCVQGTLAKEI 429
                                        444444456789******************************************986 PP

>> Lactamase_B_6  Metallo-beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0     0.057   1.5e+02     129     152 ..       5      28 ..       2      31 .. 0.87
   2 !   79.6   0.1   7.8e-26     2e-22       5     180 ..      28     195 ..      24     206 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.057
                      Lactamase_B_6 129 dgltitaynaGhtlGGtiWkiske 152
                                        d+lti+++ aG+ +G +  +i+ +
  gene1145|gene1145|rna1145|rna1145   5 DNLTIMPLGAGNEVGRSCIHITYK 28 
                                        78**************99999765 PP

  == domain 2  score: 79.6 bits;  conditional E-value: 7.8e-26
                      Lactamase_B_6   5 dnvkiLlDvGwdeskvslesalkelekv.iptvdliLLshatlehlGayallyakfksklllnipvyatlpvvkLG 79 
                                         ++ iLlD+G++   +  + +l +l+ + ++tvd++ ++h  l+h Ga+++l  k       + +v+ t+p++++ 
  gene1145|gene1145|rna1145|rna1145  28 KSLSILLDCGVHPA-YTGTASLPFLDLInLSTVDAVFITHFHLDHAGALPYLTEKT----AFTGKVFMTHPTKAIL 98 
                                        5789********97.5566788888876689******************9999764....4689************ PP

                      Lactamase_B_6  80 rvslldlyaskgllgpedseeleledideafdkiktlkYsQklelkskldgltitaynaGhtlGGtiWkiskesek 155
                                        r +l d+++  ++ +++d+   + +d ++++dki+++ Y+Q++ +k    +  +ta+naGh+lG++++ +++e  +
  gene1145|gene1145|rna1145|rna1145  99 RWLLNDYIRIINTNTEIDF--YTEKDLSNCYDKIIAIDYNQTVIVK----DFRVTALNAGHVLGAAMFMVENERFR 168
                                        *******998877766665..588******************9877....589*********************** PP

                      Lactamase_B_6 156 ivYavdwnhakeshLng..aalldssg 180
                                        ++Y  d++ + ++hL+g  +a++++ g
  gene1145|gene1145|rna1145|rna1145 169 MLYTGDYSTEEDRHLKGadTAWIGKYG 195
                                        *****************3334555555 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.4   0.4     6e-18   1.5e-14       6     162 ..      20     186 ..      15     243 .. 0.89

  Alignments for each domain:
  == domain 1  score: 54.4 bits;  conditional E-value: 6e-18
                                        SEEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHC CS
                        Lactamase_B   6 vnsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapa 81 
                                         +++ i+ +   iL D+G++++++  a+++++  +++  vdav++TH+HlDH+G+l++l+e+t +   +   +  +
  gene1145|gene1145|rna1145|rna1145  20 RSCIHITYKSLSILLDCGVHPAYTGTASLPFLDLINLSTVDAVFITHFHLDHAGALPYLTEKTAFTGKVFMTHPTK 95 
                                        567777778889**************************************************************** PP

                                        CHCHHHHHHHHHCCHH..........TTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEE CS
                        Lactamase_B  82 lfmeeaddaasrkgll..........lagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkvlf 147
                                         + +++  ++ r  +           +     dk ++ +  +++++ + r +    g++ g+  + ve++  ++l+
  gene1145|gene1145|rna1145|rna1145  96 AILRWLLNDYIRIINTnteidfytekDLSNCYDKIIAIDYNQTVIVKDFRVTALNAGHVLGAAMFMVENERFRMLY 171
                                        ******9999999999********996666677889999************************************* PP

                                        ECTTTSSHHCCCCCC CS
                        Lactamase_B 148 tGDallagetgridl 162
                                        tGD + ++++ + + 
  gene1145|gene1145|rna1145|rna1145 172 TGDYSTEEDRHLKGA 186
                                        ****99888777665 PP

>> RMMBL  Zn-dependent metallo-hydrolase RNA specificity domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.0   0.1   9.2e-18   2.3e-14       2      55 ..     444     496 ..     443     542 .. 0.88

  Alignments for each domain:
  == domain 1  score: 53.0 bits;  conditional E-value: 9.2e-18
                              RMMBL   2 ipvkarieeidfSgHadknellelirklkprnvilvHGeeeatsalarllkeee 55 
                                        +++++r+e+i+fS+H d+ +   +i+k  p  v+lvHGe +++ +l+++l e++
  gene1145|gene1145|rna1145|rna1145 444 LRLNMRVEYISFSAHVDYVQNTSFIEKCTPMIVMLVHGEVNEMMRLKAAL-EKR 496
                                        5789**********************************************.443 PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.1   0.1   3.6e-12   9.1e-09       3     162 ..      32     191 ..      31     206 .. 0.73

  Alignments for each domain:
  == domain 1  score: 35.1 bits;  conditional E-value: 3.6e-12
                                        EEES--TT..HHHHHTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCC...C--EEEEEEEEHHHHH..... CS
                      Lactamase_B_2   3 iLiDagpd..lrqqalralqPvelrdelppidaVllthaHyDHlaglltlre...lrpkklplyapkgvla..... 68 
                                        iL+D+g         +  l P   + +l+ +daV++th H DH   l+ l e   ++    +++ +  + a     
  gene1145|gene1145|rna1145|rna1145  32 ILLDCGVHpaY--TGTASL-PFLDLINLSTVDAVFITHFHLDHAGALPYLTEktaFT---GKVFMTHPTKAilrwl 101
                                        89999999542..322233.444788899***********************64432...3566666666633343 PP

                                        ......HCCTTCGHHHCHTT...........TTEEEEEE-TTSEEEECSTTEEEEEEEE-EE--CTCCE-TTTSEE CS
                      Lactamase_B_2  69 ......vleanfvylaleee...........pavnvheldwgesfelgdggleitatparhksgrrldrnagdtlG 127
                                              ++++n+       e           +  ++  +d ++++ ++  ++++ta  a h  g          + 
  gene1145|gene1145|rna1145|rna1145 102 lndyirIINTNT-------EidfytekdlsnCYDKIIAIDYNQTVIVK--DFRVTALNAGHVLGA---------AM 159
                                        333333444554.......15555555999*****************9..577888888888887.........99 PP

                                        EEEECTTEEEEEESS-S---HHHHHHHCT-SEEEE CS
                      Lactamase_B_2 128 lriegggkrvyyigDtgyipeeigerlggadllll 162
                                        +++e+++ r++y+gD  + +   +++l+gad + +
  gene1145|gene1145|rna1145|rna1145 160 FMVENERFRMLYTGDYSTEE---DRHLKGADTAWI 191
                                        ***************99433...459999999874 PP

>> Beta_lactamase3  Putative beta-lactamase-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.1   9.8e-08   0.00025     121     183 ..     120     181 ..     101     189 .. 0.87

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 9.8e-08
                    Beta_lactamase3 121 eidierlkrnvkfiryneliyfddltieakaagtflGWvnyllevekkkilayisslslkkkl 183
                                        e d+ +   +++ i yn+ + ++d+ ++a  ag  lG  ++++e e+ + + y+  +s+++  
  gene1145|gene1145|rna1145|rna1145 120 EKDLSNCYDKIIAIDYNQTVIVKDFRVTALNAGHVLGAAMFMVENERFR-MLYTGDYSTEEDR 181
                                        778999999*************************************999.9999999988765 PP

>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   9.2e-05      0.23       6     116 ..      19     177 ..      17     189 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 9.2e-05
                      Lactamase_B_3   6 ghnsflletagarilvDPfka..nlgyeppa.......eeaDlvlisqaledHahletlkql.............. 58 
                                        g +++ ++ +  +il+D +    ++g++  +        ++D+v i++ + dHa + +   l              
  gene1145|gene1145|rna1145|rna1145  19 GRSCIHITYKSLSILLDCGVHpaYTGTASLPfldlinlSTVDAVFITHFHLDHAGALPY--Ltektaftgkvfmth 92 
                                        889**************985333444444448888899***************865432..222456667777766 PP

                      Lactamase_B_3  59 ..................................aenvkvleegeslevggleiravatshdavggsergenngfl 100
                                                                          ++++  ++  +++ v++++++a ++ h      + g   +f+
  gene1145|gene1145|rna1145|rna1145  93 ptkailrwllndyiriintnteidfytekdlsncYDKIIAIDYNQTVIVKDFRVTALNAGH------VLG-AAMFM 161
                                        6666666666544444444444444444444444333334444444555555555554444......344.46777 PP

                      Lactamase_B_3 101 leqdgltiyhlGhlah 116
                                        +e +  ++++ G+ ++
  gene1145|gene1145|rna1145|rna1145 162 VENERFRMLYTGDYST 177
                                        7777777777777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (801 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1158  (0.0645881); expected 358.6 (0.02)
Passed bias filter:                      498  (0.0277762); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.81u 0.35s 00:00:01.16 Elapsed: 00:00:00.54
# Mc/sec: 4438.05
//
Query:       gene1146|gene1146|rna1146|rna1146  [L=553]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.9e-50  170.2  30.4    9.7e-50  169.7  30.4    1.2  1  TLC              TLC ATP/ADP transporter


Domain annotation for each model (and alignments):
>> TLC  TLC ATP/ADP transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  169.7  30.4   5.4e-54   9.7e-50      15     491 .]      33     534 ..      21     534 .. 0.79

  Alignments for each domain:
  == domain 1  score: 169.7 bits;  conditional E-value: 5.4e-54
                                TLC  15 lwpverlelkkllplllllflilfnysilrdlKDslvvtasesgAEvipFlKvwgvlPsAilftliyaklsnklsk 90 
                                        ++ v   e +kl+ ++ ++fli+++ys+ +dlKD+ v+  +   A  i+ lKv+ v P A +f+l+  k+s ++++
  gene1146|gene1146|rna1146|rna1146  33 IYKVAPAEDRKLMCISGMFFLIVYIYSVSKDLKDAFVIGRQ--VAASISVLKVFWVPPIATCFSLLVQKMSVRMKN 106
                                        6788888999*****************************99..8999***************************** PP

                                TLC  91 ekvFyiivsfflvffllFafvlyPlrellhleaead....klesilppglkgl...ialvrnWsyalfYvlaELWg 159
                                        e++  +++  + ++f+++a  + Plre++ +++ ++    ++ +++++ +  +   i+ +   + +l +v +E+Wg
  gene1146|gene1146|rna1146|rna1146 107 ETILKTFLYAYATYFVVYAAFMLPLREYIEPSKFITidllSDDKMKYKDFLAFaasIMTFTSCTGTLHFVASEVWG 182
                                        *******************************99754111134455555555441113444555668********** PP

                                TLC 160 svvlsllfWgfaneitkveeakrFYsllglvanlalivaGevlillsnirkklasavdsweeslkvlvlivvilgl 235
                                        ++vlsllf +  ne+   ++ krF +++  ++n++l+++  ++ ++  ++++++     +++ + + v +++ +g+
  gene1146|gene1146|rna1146|rna1146 183 TIVLSLLFMQLFNEVCPEKQFKRFVPIVYALSNVGLLMSAATSYIVHYLTSRMEY---DQRVYFYMAVFLLLGAGT 255
                                        **************************************99888777664433332...234456666667777777 PP

                                TLC 236 iil.llyrllnkkvltderlylaekkkkkkkkkklslkesfklllrskyllliavlviayglsinlvEvvWKa... 307
                                        ++l l+ r+l + v+  + +  +++k+k ++k+++++ e +kl+++++ ++ + ++v++y++ i + E  +K+   
  gene1146|gene1146|rna1146|rna1146 256 VALiLIQRYLINCVIPVQICRDTATKHKVRSKEHVGFVEGLKLVFSTNVIVALCTMVLGYNVIIIMNESAYKScqs 331
                                        765157789999***9999988999999999****************************************97333 PP

                                TLC 308 qikelyptpneynafmgklt.sltGvvtilim..llssnilrkfgWtvaAlitPlillvtgvlFFslilfekela. 379
                                        ++ +  ++ +e + + +k    ++ +v +++   l +   ++ +gWt  Al+tP+  +v  v+  +l ++   la 
  gene1146|gene1146|rna1146|rna1146 332 EVAKREKKSTESSVLANKCFeEMVTAVLVMMFfvLPTRDAIKWIGWTKYALVTPIGAFVACVAVLGLAMVATGLAg 407
                                        6777778888999999986514555554444422447889***************988888888887776554431 PP

                                TLC 380 ...eliasl...lgtspllla..v.....vvGaiqnilsksaKyslfDatkemayipldeeskvkgkaaidvvgar 442
                                           + ++++   l  sp  l+  v     ++G +     k  Ky  fD +ke     +d   + + +a+ d+++ar
  gene1146|gene1146|rna1146|rna1146 408 enlSPVNTFmsrLSASPEELTgkVmrweqFFGILSTAGMKVLKYVAFDISKEYFAKRIDIAYRARFRAVYDGICAR 483
                                        111233333111467776665222222225677777777889***********999******************** PP

                                TLC 443 lGKSggsliqqllliifatl...asispllavvlllvilvwiiavkklekqf 491
                                        +GK+ gs++q ++  if tl    s+ p+l    l+++++wi++v  l+k++
  gene1146|gene1146|rna1146|rna1146 484 MGKAVGSILQLIFNQIFNTLdirRSSFPYLV-LALVILCIWILSVVYLGKKY 534
                                        **********999899966522146667765.55677889**********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (553 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       933  (0.0520386); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.45
# Mc/sec: 3663.35
//
Query:       gene1147|gene1147|rna1147|rna1147  [L=24]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (24 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                        96  (0.00535445); expected 358.6 (0.02)
Passed bias filter:                       59  (0.00329076); expected 358.6 (0.02)
Passed Vit filter:                         1  (5.57756e-05); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.31u 0.24s 00:00:00.55 Elapsed: 00:00:00.38
# Mc/sec: 190.41
//
Query:       gene1148|gene1148|rna1148|rna1148  [L=63]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.054   13.8   1.1      0.073   13.4   1.1    1.2  1  HalX      HalX domain


Domain annotation for each model (and alignments):
>> HalX  HalX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   1.1   4.1e-06     0.073      11      56 ..      10      55 ..       8      61 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.1e-06
                               HalX 11 elfaLasKravLeaekseaeLadseeYqeLearleelraqldetld 56
                                       el   + ++  Le e   +  ++ ee+++L+ +l e  a++d++++
  gene1148|gene1148|rna1148|rna1148 10 ELLNTEKRKKCLENETKNEIIENFEEFSQLKHELTERFAEIDAEIQ 55
                                       78889999***********************888888888887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (63 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2030  (0.113224); expected 358.6 (0.02)
Passed bias filter:                      719  (0.0401026); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 452.41
//
Query:       gene1149|gene1149|rna1149|rna1149  [L=383]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.5e-05   24.5   0.5    2.5e-05   24.5   0.5    2.3  2  CPSF100_C  Cleavage and polyadenylation factor 2 C-terminal


Domain annotation for each model (and alignments):
>> CPSF100_C  Cleavage and polyadenylation factor 2 C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.2     0.038   6.8e+02      60      77 ..     105     122 ..      72     192 .. 0.68
   2 !   24.5   0.5   1.4e-09   2.5e-05      99     170 .]     308     379 ..     265     379 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.038
                          CPSF100_C  60 kkqklaeksekeaseees 77 
                                        k+q +++k+++++ e+++
  gene1149|gene1149|rna1149|rna1149 105 KSQGAQHKKNEPDPENTE 122
                                        111111111111111111 PP

  == domain 2  score: 24.5 bits;  conditional E-value: 1.4e-09
                          CPSF100_C  99 s.aaqplfvGdlrLadLkkallssgikAEFrgeGtLvidgaVaVrKsakGrieiegvvletfyeVrkaiYegl 170
                                        +  +++l  G +++++L+k ll++++++  + e tLvi+++V V+  + G +++ g +   ++ Vr++iY++l
  gene1149|gene1149|rna1149|rna1149 308 EsLKESLCLGTVKMTELRKQLLDNNLRVKKADEYTLVIEDQVKVQF-NDGAVKMVGEMNGVYLYVRRIIYKNL 379
                                        3378999*************************************85.67*********************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (383 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       970  (0.0541023); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.40
# Mc/sec: 2873.21
//
Query:       gene115|gene115|rna115|rna115  [L=219]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-32  112.5   0.1    1.8e-32  112.2   0.1    1.1  1  Arf              ADP-ribosylation factor family
    7.4e-13   48.4   0.6      1e-12   47.9   0.6    1.2  1  Gtr1_RagA        Gtr1/RagA G protein conserved region
      1e-09   38.1   0.0    1.4e-09   37.7   0.0    1.2  1  SRPRB            Signal recognition particle receptor beta su
    1.1e-09   38.0   0.9    1.1e-06   28.1   0.2    2.7  2  G-alpha          G-protein alpha subunit
    6.7e-09   35.5   0.1    9.6e-09   35.0   0.1    1.3  1  Ras              Ras family
    1.1e-08   35.3   0.0    2.3e-08   34.2   0.0    1.5  1  Roc              Ras of Complex, Roc, domain of DAPkinase
    1.3e-08   34.9   0.0    2.2e-08   34.2   0.0    1.3  1  MMR_HSR1         50S ribosome-binding GTPase
      1e-05   25.2   3.0     0.0001   22.0   0.3    2.1  2  GTP_EFTU         Elongation factor Tu GTP binding domain
     0.0017   17.9   0.3     0.0042   16.6   0.3    1.7  1  FeoB_N           Ferrous iron transport protein B
     0.0067   16.2   0.4      0.039   13.7   0.2    1.9  2  FANCI_S3         FANCI solenoid 3
  ------ inclusion threshold ------
       0.01   15.4   1.5       0.28   10.8   0.5    2.3  2  cobW             CobW/HypB/UreG, nucleotide-binding domain
      0.034   12.6   0.1      0.048   12.1   0.1    1.1  1  Hanta_nucleocap  Hantavirus nucleocapsid protein
      0.094   12.5   0.1       0.31   10.9   0.1    1.9  1  NOG1             Nucleolar GTP-binding protein 1 (NOG1)


Domain annotation for each model (and alignments):
>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.2   0.1   1.3e-35   1.8e-32      10     148 ..      32     169 ..      23     209 .. 0.90

  Alignments for each domain:
  == domain 1  score: 112.2 bits;  conditional E-value: 1.3e-35
                                    T.TTEEEEEEEESTTSSHHHHHHHHHHSSCEECSSSSSEEEEEEEETTEEEEEEEE-SSGGGGGGGGGGCTTESEEEEEE CS
                            Arf  10 lkkkelrilllGLDnaGKtTilkklkleelvttvPTigfnveeleiknlkftvwDvGGqeklRplWknYfektdavifvv 89 
                                    +  k   il+lG+DnaGKtT+l+klk++ ++t  PT ++   e+ei n+k ++ D+GG++++R  W+++f + d+++f+v
  gene115|gene115|rna115|rna115  32 S--KPSSILFLGIDNAGKTTLLHKLKEDVTNTYEPTHHPMNSEIEIGNMKANIMDLGGHQSARLAWQEFFYNCDGIVFIV 109
                                    3..7788************************************************************************* PP

                                    ETT-CTTHHHHHHHHHHHCTSGCCT.TSEEEEEEE-TTSTTSS-HHHHHHHTTGGGSSSS CS
                            Arf  90 DsadreRleeakeeLkalleeeelk.evallvlaNKqDlpealseeelrellgleelkgk 148
                                    D++d++R +  +e  +++ e +  k + ++ vl NK+Dl +   ++ l+++  +++++++
  gene115|gene115|rna115|rna115 110 DVNDTKRYHLVREVYQSVREIQVGKkKPPIAVLMNKIDLIKHDANSILQDQDVMDQIQKE 169
                                    ***********99999998887655378999********999999999988888888743 PP

>> Gtr1_RagA  Gtr1/RagA G protein conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.9   0.6   7.4e-16     1e-12       2     173 ..      37     203 ..      36     213 .. 0.81

  Alignments for each domain:
  == domain 1  score: 47.9 bits;  conditional E-value: 7.4e-16
                      Gtr1_RagA   2 vLLmGksgsGKtsmrsiiFdnylardtlrlgatidveksevrflgnltlnlwDcgGqeafveeylssqkeeifrnvgvli 81 
                                    +L++G  ++GKt++     +++    t + + t +  +se+   gn++ n++D+gG ++          +e f n++ ++
  gene115|gene115|rna115|rna115  37 ILFLGIDNAGKTTL----LHKLKEDVTNTYEPTHHPMNSEI-EIGNMKANIMDLGGHQSAR-----LAWQEFFYNCDGIV 106
                                    89**********97....578888889999***********.59************98754.....44589********* PP

                      Gtr1_RagA  82 yVfDvesreleedletlkeilealrqyspeakvfvlihKmDliqedereeifeer.keeireeiekleke.....eiqff 155
                                    +++Dv++++  + +++  +++++++  +++  + vl++K+Dli++d+++ +++++ +++i++e+  +e++      + + 
  gene115|gene115|rna115|rna115 107 FIVDVNDTKRYHLVREVYQSVREIQVGKKKPPIAVLMNKIDLIKHDANSILQDQDvMDQIQKETG-IENDdsleqPVLVT 185
                                    ********99999999999*************************999888876651444554444.33223444456666 PP

                      Gtr1_RagA 156 aTSiwdeslykAfssivq 173
                                      S  +es+ +  s i q
  gene115|gene115|rna115|rna115 186 YVSLLNESITDMSSPILQ 203
                                    667777777666666655 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.7   0.0     1e-12   1.4e-09       4     136 ..      35     160 ..      32     179 .. 0.81

  Alignments for each domain:
  == domain 1  score: 37.7 bits;  conditional E-value: 1e-12
                                    -EEEEE-STTSSHHHHHHHHHHSS---B---SS-EEETTG...GGTT-SEEEETT-GCCSHHHHHHHHHHGGEEEEEEEE CS
                          SRPRB   4 pavllvGlsdsGKTslftrLttdsvkktvtSqessaalkvksekgskltliDfPGheklrqklleklkaksslkglvfvv 83 
                                     ++l++G+ ++GKT+l+++L +d v++t+   +  +  ++ +  + k +++D+ Gh++ r    e      +  g+vf+v
  gene115|gene115|rna115|rna115  35 SSILFLGIDNAGKTTLLHKLKED-VTNTYEPTHHPMNSEI-EIGNMKANIMDLGGHQSARLAWQEF---FYNCDGIVFIV 109
                                    689*****************988.4455555544444445.4578999************998877...66799****** PP

                                    ETTS-HHHHHHHHHHHHHHHHHHHHHTT---EEEEEE-TTSTT---HHHHHHH CS
                          SRPRB  84 DStidpkevkevAEllyeilliteklkdavdiliACnKqelflakspklikda 136
                                    D   d k+ + v E + ++  i++  k++++i +  nK +l     +++++d+
  gene115|gene115|rna115|rna115 110 DVN-DTKRYHLVREVYQSVREIQV-GKKKPPIAVLMNKIDLIKHDANSILQDQ 160
                                    *75.99999*****9999998888.67789999999**999887777777765 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.0   0.00042      0.59      23      45 ..      34      56 ..      13      66 .. 0.82
   2 !   28.1   0.2     8e-10   1.1e-06     179     299 ..      56     167 ..      54     200 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00042
                                   EEEEEEEESTTSSHHHHHHHHHH CS
                        G-alpha 23 evkllllGqseSGKsTilkqlkl 45
                                   + ++l+lG +  GK+T+l +lk 
  gene115|gene115|rna115|rna115 34 PSSILFLGIDNAGKTTLLHKLKE 56
                                   568****************9995 PP

  == domain 2  score: 28.1 bits;  conditional E-value: 8e-10
                                    HHHHCS-----SEEEEEEECT-TEEEEEEEE-SSHHHHHGTCCCTTTECEEEEEEEGGGTT-B-SS-TTSBHHHHHHHHH CS
                        G-alpha 179 dDilkarlktvGisetkfevdsklefrivdvgGqrserkkWvpffddvdaiiFlvslsefdqvlyedekvnrleeslklF 258
                                    +D+ ++  +t      ++e++ +++ +i+d+gG++s r +W +ff + d i+F+v +            + r +   +++
  gene115|gene115|rna115|rna115  56 EDVTNTYEPTHHPMNSEIEIG-NMKANIMDLGGHQSARLAWQEFFYNCDGIVFIVDVN----------DTKRYHLVREVY 124
                                    788888889999999999999.********************************9843..........467788888888 PP

                                    HCCCC-GGG.TTSEEEEEEE-HHHHHHHCCCS.-GGGCCTT-- CS
                        G-alpha 259 keicnnkll.kntpiiLflnKlDileeKlkkg.klskyfpsye 299
                                    +++ + +   k+ pi +++nK+D+ ++  ++  + ++++ +++
  gene115|gene115|rna115|rna115 125 QSVREIQVGkKKPPIAVLMNKIDLIKHDANSIlQDQDVMDQIQ 167
                                    8888888873445588888999988887766555555555555 PP

>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.0   0.1   6.9e-12   9.6e-09       2     121 ..      37     165 ..      36     192 .. 0.82

  Alignments for each domain:
  == domain 1  score: 35.0 bits;  conditional E-value: 6.9e-12
                                    EEEEESTTSSHHHHHHHHHHSSCSSSCTTTSSEEEEEEEEEETTEEEEEEEEEETTSGGGHHHHHHHHTTESEEEEEEET CS
                            Ras   2 lvlvGdsavGKtslllrfvkdkFkeeyesTigvdfytkeievdgkevkleiwDTAGqeefkslrelyyrdaegillvydi 81 
                                    ++++G  + GKt+ll++   ++ +++ye+T     +  + e++  ++k +i+D  G +  +   + ++ +++gi+ + d+
  gene115|gene115|rna115|rna115  37 ILFLGIDNAGKTTLLHKLK-EDVTNTYEPTH----HPMNSEIEIGNMKANIMDLGGHQSARLAWQEFFYNCDGIVFIVDV 111
                                    678999**********975.567999****9....55556666678999******************************* PP

                                    TBHHHHHTHHHHHHHHHHHST..TTSEEEEEEETTTGGG............G-S CS
                            Ras  82 tsresfenvkkwveeikrvae..envpivLvGnKvDlee............kra 121
                                    ++++ ++ v++ ++ ++++    ++ pi+++ nK+Dl +              +
  gene115|gene115|rna115|rna115 112 NDTKRYHLVREVYQSVREIQVgkKKPPIAVLMNKIDLIKhdansilqdqdvMDQ 165
                                    ************99999887677889***********99555444444444333 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.2   0.0   1.7e-11   2.3e-08       2     120 .]      37     148 ..      36     148 .. 0.70

  Alignments for each domain:
  == domain 1  score: 34.2 bits;  conditional E-value: 1.7e-11
                                    EEEESSTTSSHHHHHHCHCT-CCC-EEETTTTEEEEEEECGGSGGCTTBTTTTCEEEEEEEE-SGGCTTTT-HHHHCTSC CS
                            Roc   2 vvlvGdsgvGKtsllkrfvedkfsekekstigvdfltkevtkikgvendkkvkkvklniWDtaGqerfrslhplylreaa 81 
                                    ++++G  ++GKt+ll+++ ed   +++++t+      +e+ +         + ++k ni D++G++  r   + ++ + +
  gene115|gene115|rna115|rna115  37 ILFLGIDNAGKTTLLHKLKEDVT-NTYEPTHHPMN--SEI-E---------IGNMKANIMDLGGHQSARLAWQEFFYNCD 103
                                    789***************97666.56666654332..233.2.........2346789***********98888888888 PP

                                    EEEEEEE...GHHHHCHHHHHHHHHHH...CSSS-EEEEEE-TTT CS
                            Roc  82 lailvyd...srssenlkeWlkelkkv...agkspvilvgnkiDl 120
                                     +++++d   +++++ ++e ++++++     +k p+ +++nkiDl
  gene115|gene115|rna115|rna115 104 GIVFIVDvndTKRYHLVREVYQSVREIqvgKKKPPIAVLMNKIDL 148
                                    888888754344444455555555543221566789999****95 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.2   0.0   1.6e-11   2.2e-08       2     114 .]      37     145 ..      36     145 .. 0.73

  Alignments for each domain:
  == domain 1  score: 34.2 bits;  conditional E-value: 1.6e-11
                                    EEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSSHHHHHHHHHHHHHH.HHCTSEEE CS
                       MMR_HSR1   2 vaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgkeielvDtpGliegaseekglgkafla.leeadlil 80 
                                    ++++G  N+GK+tL+ +l +    v+++   T ++   ++++++ + +++D+ G  +      + + a+++   ++d i+
  gene115|gene115|rna115|rna115  37 ILFLGIDNAGKTTLLHKLKE---DVTNTYEPTHHPMNSEIEIGNMKANIMDLGG-HQ------SARLAWQEfFYNCDGIV 106
                                    7899**************76...69*****************************.44......3333333322479**** PP

                                    EEEETT.TTCSHHHHHHHHHHHHH.....TTSEEEEEEES CS
                       MMR_HSR1  81 lvvdas.eeklkpldeeleellee.....akkplilvlnk 114
                                    ++vd++ ++ ++ + +e+ +  +e     +k p+ +++nk
  gene115|gene115|rna115|rna115 107 FIVDVNdTKRYHLV-REVYQSVREiqvgkKKPPIAVLMNK 145
                                    ****9963334333.4444444455666344446667776 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.2     0.021        30       7      31 ..      38      62 ..      35      76 .. 0.77
   2 !   22.0   0.3   7.2e-08    0.0001      67     150 ..      75     166 ..      59     209 .. 0.66

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.021
                                   EEEESTTSSHHHHHHHHHHHTTSSC CS
                       GTP_EFTU  7 giighvDhGKtTLtdrLlyktgais 31
                                    ++g  ++GKtTL+ +L ++  ++ 
  gene115|gene115|rna115|rna115 38 LFLGIDNAGKTTLLHKLKEDVTNTY 62
                                   56666689********988776655 PP

  == domain 2  score: 22.0 bits;  conditional E-value: 7.2e-08
                                    CSSEEEEEEEESSSGGGHHHHHHHHHT-SEEEEEEETTTB.....STHHHHHHHHHHHHTTTE.EEEEEESCGSTHHHHH CS
                       GTP_EFTU  67 tkkylinliDtPGHvdFskevirglrvlDgavlvvdaveG.....vepqteevlrlalkegvp.iivfiNKmDrlkaelk 140
                                      + + n++D  GH++      +    +Dg v++vd+++      v +  + v ++   ++ p i v++NK+D +k++ +
  gene115|gene115|rna115|rna115  75 IGNMKANIMDLGGHQSARLAWQEFFYNCDGIVFIVDVNDTkryhlVREVYQSVREIQVGKKKPpIAVLMNKIDLIKHDAN 154
                                    567899**********99999999**************996555433333333333333333468999*******77777 PP

                                    HHHHH..HHHHH CS
                       GTP_EFTU 141 eivee..vkqkl 150
                                     i ++  v +++
  gene115|gene115|rna115|rna115 155 SILQDqdVMDQI 166
                                    776650033333 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.3     3e-06    0.0042       3     125 ..      37     156 ..      35     173 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 3e-06
                                    EEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEEEETTEEEEEEE----SSSSSSSHHHHHHHHHHHCTSSSEE CS
                         FeoB_N   3 valvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegklklkgkeveivDlPGiYslsayseeekvardflleeepdvv 82 
                                    + ++G  n+Gkttl+ +l   k++v N    t    + ++++ + +++i+Dl G  s     +e    +d ++      +
  gene115|gene115|rna115|rna115  37 ILFLGIDNAGKTTLLHKL---KEDVTNTYEPTHHPMNSEIEIGNMKANIMDLGGHQSARLAWQEFFYNCDGIV-----FI 108
                                    7889**********9877...789******************************9887766666555555554.....67 PP

                                    EEEEEGG..GHHHHHHHHHHHHHTTS...SEEEEEETHHHHHHTTEEE CS
                         FeoB_N  83 vnvvdat..nlernLyLtlqllelgv...pvvlalnmideaekkgiei 125
                                    v+v d++  +l r++y  ++ +++g+   p+ + +n+id ++++  +i
  gene115|gene115|rna115|rna115 109 VDVNDTKryHLVREVYQSVREIQVGKkkpPIAVLMNKIDLIKHDANSI 156
                                    7777775336889999887777666422268899999*9999887776 PP

>> FANCI_S3  FANCI solenoid 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.27   3.7e+02     104     127 ..       8      37 ..       1      69 [. 0.69
   2 !   13.7   0.2   2.8e-05     0.039     128     197 ..     144     213 ..     107     216 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.27
                       FANCI_S3 104 fleilntvqelyesklseFLkai......g 127
                                    f+++ n ++e+ye+ ++ F+++i       
  gene115|gene115|rna115|rna115   8 FSNLKNRILEVYENTIAGFIRSIfskpssI 37 
                                    667778999***********9995555440 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 2.8e-05
                       FANCI_S3 128 eeedlteklkelikqlqrvlvnflsedeedesisKlallLveilelLskklepssrqlvqvltwlvklck 197
                                    +++dl ++ ++ i q q+v++++ +e+  ++ +s +  +Lv+ ++lL ++++  s+ + q+++wl k++ 
  gene115|gene115|rna115|rna115 144 NKIDLIKHDANSILQDQDVMDQIQKETGIENDDSLEQPVLVTYVSLLNESITDMSSPILQSFQWLDKMIH 213
                                    5678889999999********99988766666679999*****************************986 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0     0.042        57      11      21 ..      45      55 ..      37      64 .. 0.78
   2 ?   10.8   0.5    0.0002      0.28     110     171 ..     100     168 ..      82     173 .. 0.66

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.042
                                   CCHHHHHHHHH CS
                           cobW 11 sGKTtLlnhll 21
                                   +GKTtLl +l 
  gene115|gene115|rna115|rna115 45 AGKTTLLHKLK 55
                                   9******9985 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.0002
                                    CCECEEEEEEETTTH.......CCHCCHHHHHHHHHHTSSEEEEE-HHHHCHC...HHHHHHHHHHHHT CS
                           cobW 110 ltldavvavvDaknl......eaeeekieekaedqlaaadllvlnKtDlldee.allekleerlrqlnp 171
                                    ++ d++v++vD++ +       +  ++ +e    + +    +++nK+Dl++++ +++ + +++++q+++
  gene115|gene115|rna115|rna115 100 YNCDGIVFIVDVNDTkryhlvREVYQSVREIQVGKKKPPIAVLMNKIDLIKHDaNSILQDQDVMDQIQK 168
                                    67899999**9988877766422222222222222233346999********95555555566666655 PP

>> Hanta_nucleocap  Hantavirus nucleocapsid protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   3.5e-05     0.048      54     124 ..     142     212 ..     128     215 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.5e-05
                                    HHHHHHHHHHHHHHHHH-XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXSXXXXXHHHHHH CS
                Hanta_nucleocap  54 iqakidelkrqladriatgknlgkeqdptgvepgdhlkersmlsygnvldlnhldideptgqtadwlsiiv 124
                                    +  kid +k++    +     + + q  tg+e  d l +  +++y  +l+    d+  p  q+ +wl  ++
  gene115|gene115|rna115|rna115 142 LMNKIDLIKHDANSILQDQDVMDQIQKETGIENDDSLEQPVLVTYVSLLNESITDMSSPILQSFQWLDKMI 212
                                    4579999998877777777788999*****************************************98665 PP

>> NOG1  Nucleolar GTP-binding protein 1 (NOG1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   0.00022      0.31      17      58 .]     105     147 ..     102     147 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00022
                           NOG1  17 vlFllDpseecgyslee.QlsLleeikelfankpvivvlnKiD 58 
                                    ++F++D+  ++ y l    ++ ++ei+   ++ p+ v +nKiD
  gene115|gene115|rna115|rna115 105 IVFIVDVNDTKRYHLVReVYQSVREIQVGKKKPPIAVLMNKID 147
                                    9***********99875034444555544454569999****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       571  (0.0318478); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 1561.73
//
Query:       gene1150|gene1150|rna1150|rna1150  [L=523]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0075   16.4   3.2      0.018   15.2   0.2    3.1  3  FNIP      FNIP Repeat


Domain annotation for each model (and alignments):
>> FNIP  FNIP Repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0     0.069   1.2e+03      29      41 ..       5      17 ..       4      20 .. 0.71
   2 ?   -2.9   0.1      0.44     8e+03      14      21 ..     221     227 ..     218     237 .. 0.53
   3 !   15.2   0.2     1e-06     0.018       9      43 ..     379     426 ..     352     427 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.069
                               FNIP 29 igsLPnSlkeLyF 41
                                       i ++P+++++L++
  gene1150|gene1150|rna1150|rna1150  5 IVVIPSTCQKLTL 17
                                       5678888888876 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 0.44
                               FNIP  14 leiLilgr 21 
                                        l +Lil +
  gene1150|gene1150|rna1150|rna1150 221 LNYLIL-S 227
                                        455555.2 PP

  == domain 3  score: 15.2 bits;  conditional E-value: 1e-06
                               FNIP   9 eLP............snleiLil.grdFnqkiligsLPnSlkeLyFgy 43 
                                        eLP             nl+ Li+ g+++ ++    +LP+Sl+ L ++y
  gene1150|gene1150|rna1150|rna1150 379 ELPadapiydalmnlVNLKVLIIeGKYYENPAYLFCLPQSLEVLMISY 426
                                        5666666777777778******************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (523 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       651  (0.0363099); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 3359.07
//
Query:       gene1151|gene1151|rna1151|rna1151  [L=46]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (46 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       506  (0.0282224); expected 358.6 (0.02)
Passed bias filter:                      245  (0.013665); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 327.03
//
Query:       gene1152|gene1152|rna1152|rna1152  [L=296]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-23   82.4   2.5    2.8e-23   81.8   2.5    1.3  1  DnaJ      DnaJ domain
      3e-20   72.8   0.4    4.2e-20   72.3   0.4    1.2  1  DnaJ_C    DnaJ C terminal domain
    0.00035   20.6   0.1    0.00096   19.2   0.1    1.7  2  DUF4460   Domain of unknown function (DUF4460)


Domain annotation for each model (and alignments):
>> DnaJ  DnaJ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.8   2.5   4.7e-27   2.8e-23       1      63 []       3      69 ..       3      69 .. 0.90

  Alignments for each domain:
  == domain 1  score: 81.8 bits;  conditional E-value: 4.7e-27
                                       HHHHHHTSSTTG-HHHHHHHHHHHHHHHSTTTS...CCHH.HHHHHHHHHHHHHHHHTSHHHHHHHH CS
                               DnaJ  1 dyYeiLgvskdasedeIkkaYrklalkyHPDkn...pkdp.eaeekFkeineAyevLsdpekRkqYD 63
                                       d+Y+ L++s++a+++eIkkaY+k +l++HPD+    p+ + +aee+Fk+i+ Aye+Lsd++kRk+YD
  gene1152|gene1152|rna1152|rna1152  3 DPYKTLNISRTATQSEIKKAYQKHILRCHPDRVkggPEAKkKAEEQFKKIQSAYEILSDEQKRKEYD 69
                                       78*****************************88445333369999*********************9 PP

>> DnaJ_C  DnaJ C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.3   0.4     7e-24   4.2e-20       2     146 ..     135     280 ..     134     282 .. 0.86

  Alignments for each domain:
  == domain 1  score: 72.3 bits;  conditional E-value: 7e-24
                                        EEEEEE-HHHHHH-.EEE.EEEE.......TEEEEEE-TT--TT-EEEETT-SSSS..S---EEEEEEE---SS-E CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             DnaJ_C   2 eveleisleelykGktkkikikrnvikkekktlevkipaGikdgqkirlegeGdeeggepGDlivtikvkphpvFk 77 
                                        ev++++sl+ely+G tkk+ ++ ++ + +  +++v++++ +k+g+k+++eg Gd+      D+++t+++  +p+F+
  gene1152|gene1152|rna1152|rna1152 135 EVKVRLSLDELYNGITKKVCVNVRRDNARVAEFNVDVKPWYKSGTKFTYEGAGDATRTGYKDVVITVEEIRNPFFT 210
                                        789****************9998877666669**********************888999********98****** PP

                                        EETTEEEEEEEEEHHHHHHTEEE.EEE-SS-EEEE....EE--TT-EEEETT-S-EET...TEE--EEEEEEEE CS
                                        xxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             DnaJ_C  78 rkgndlyveveislaeallGgkl.evptldgkvkl....kitqpgevlrikgkGmpklkkpgkrGdlyvevkve 146
                                        r g+dl + ++  l+e ++ +k   +  ++g+v      ++   g+ +++kg+Gm ++  +g++Gdl v+v v+
  gene1152|gene1152|rna1152|rna1152 211 RSGDDLEYVFRTGLKELVTMNKNvYL--PGGRVYNlrwaDVKVIGDFFVVKGMGMRRK--KGGHGDLKVKVIVD 280
                                        *******9999******999554233..4444332355666667***********999..5**********997 PP

>> DUF4460  Domain of unknown function (DUF4460)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.1   1.6e-07   0.00096       3      56 ..      12      65 ..      10      71 .. 0.92
   2 ?   -3.0   0.0       1.2   7.2e+03      79      95 ..     190     205 ..     181     210 .. 0.73

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.6e-07
                            DUF4460  3 ralskkelrnaLrpFYlavhPDlfgqyPkekkvNeeSLklLnsyleelkkeekk 56
                                       r+++++e+++a ++ +l+ hPD ++  P+ kk  ee  k ++s  e l+ e+k+
  gene1152|gene1152|rna1152|rna1152 12 RTATQSEIKKAYQKHILRCHPDRVKGGPEAKKKAEEQFKKIQSAYEILSDEQKR 65
                                       788999*******************************************99865 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.2
                            DUF4460  79 kkgefkevsiqldentr 95 
                                         ++++k v i+++ ++r
  gene1152|gene1152|rna1152|rna1152 190 TRTGYKDVVITVE-EIR 205
                                        6788999999994.444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (296 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       691  (0.0385409); expected 358.6 (0.02)
Passed bias filter:                      546  (0.0304535); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2161.32
//
Query:       gene1153|gene1153|rna1153|rna1153  [L=585]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        1.1    9.3   4.2         11    6.1   1.5    2.3  2  DUF465    Protein of unknown function (DUF465)


Domain annotation for each model (and alignments):
>> DUF465  Protein of unknown function (DUF465)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.1    0.0041        74       7      19 ..     512     524 ..     510     536 .. 0.81
   2 ?    6.1   1.5   0.00062        11      24      47 .]     557     580 ..     545     580 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.0041
                                        HHHHHHHHHHHHH CS
                             DUF465   7 eHeeLdkeIhale 19 
                                        +++ LdkeI ++ 
  gene1153|gene1153|rna1153|rna1153 512 KYHLLDKEINNEV 524
                                        8********9885 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.00062
                                        S-HHHHHHHHHHHHHHHHHHHHHH CS
                             DUF465  24 tddleierLKkeKLeLKDeIyrll 47 
                                        t  +ei+ LK+e  +LK eI+r++
  gene1153|gene1153|rna1153|rna1153 557 TFLEEIKGLKRENARLKREIERMK 580
                                        6669******************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (585 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       974  (0.0543254); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.46
# Mc/sec: 3827.23
//
Query:       gene1154|gene1154|rna1154|rna1154  [L=106]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       502  (0.0279993); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 745.20
//
Query:       gene1155|gene1155|rna1155|rna1155  [L=460]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.2e-26   93.5   9.1      9e-15   55.6   2.6    2.3  2  Tyrosinase  Common central domain of tyrosinase


Domain annotation for each model (and alignments):
>> Tyrosinase  Common central domain of tyrosinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.6   2.6     5e-19     9e-15       5     100 ..      98     188 ..      94     201 .. 0.70
   2 !   41.6   0.7     9e-15   1.6e-10     173     218 ..     211     256 ..     179     260 .. 0.78

  Alignments for each domain:
  == domain 1  score: 55.6 bits;  conditional E-value: 5e-19
                                        HHHHHCCSSS--SSTSSSSS-TSSTTHHHHHHHHHHHHHHHHHHHHHHTHCSEEEB--TSS-....-SS--HHHH- CS
                         Tyrosinase   5 dqlagiHgipftewkeeeecaHgnalFltWHRaYlllfEqalreicgyapdvtlPYWDwaadksspldespeslgg 80 
                                        d+la +H ++ +++      aH++  Fl+WHRa+ll+fE++++++++  +++++PYWDw+ d    ++++++s+  
  gene1155|gene1155|rna1155|rna1155  98 DDLAILH-TACETY------AHNSTRFLPWHRAFLLYFERIIKTVTN--KKISVPYWDWSID----AHAPTQSFAL 160
                                        7889999.444444......8**********************9955..6************....3333444433 PP

                                        SE.EE-TTCCGE.......-EEEEE-TT CS
                         Tyrosinase  81 dg.atipeenls.......ggcvisnpl 100
                                        +   +i+++n         + cv  +p+
  gene1155|gene1155|rna1155|rna1155 161 QHaWPINDTNHCflvnfpsTHCVKRSPF 188
                                        3313333333334555555566666665 PP

  == domain 2  score: 41.6 bits;  conditional E-value: 9e-15
                                        ---HHHHHHHHHHHHH.ESSSTTSTTCGGGSTHHHHHHHHHHHHHHH CS
                         Tyrosinase 173 esalespHnavHvwvG.angdmgdvataafDPiFflHHaniDrlwai 218
                                        +s++  pH  vH+ vG + gdm+   ++ +DPiFf HH+ iD+lw++
  gene1155|gene1155|rna1155|rna1155 211 TSFEIVPHAIVHLNVGgTDGDMA-MLYSCNDPIFFQHHSYIDYLWSV 256
                                        223445**********8889999.888******************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (460 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       396  (0.0220871); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 3293.94
//
Query:       gene1156|gene1156|rna1156|rna1156  [L=163]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2119  (0.118188); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1071.72
//
Query:       gene1157|gene1157|rna1157|rna1157  [L=134]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       393  (0.0219198); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 940.48
//
Query:       gene1158|gene1158|rna1158|rna1158  [L=233]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.084   12.9   1.0       0.15   12.0   1.0    1.5  1  DUF4446        Protein of unknown function (DUF4446)
       0.14   11.1   1.1       0.15   11.1   0.3    1.4  2  Itfg2          Integrin-alpha FG-GAP repeat-containing protei


Domain annotation for each model (and alignments):
>> DUF4446  Protein of unknown function (DUF4446)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   1.0   1.7e-05      0.15       2      49 ..       7      57 ..       6     100 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.7e-05
                            DUF4446  2 iilvlavlvvilli.llivllvklkklkkkykklmkgk..dgksleellke 49
                                       i++ +++ +++++i ll v +  l+ +++kyk+++ +k  + ++l +++ +
  gene1158|gene1158|rna1158|rna1158  7 IVITAIATIIVMFIlLLYVSHSMLRAVDNKYKTIVDKKlnESAELRNMFLD 57
                                       56666666666666155566777899*********9884444555555544 PP

>> Itfg2  Integrin-alpha FG-GAP repeat-containing protein 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.3   1.6e-05      0.15      29     116 ..       2     104 ..       1     112 [. 0.71
   2 ?   -3.1   0.0      0.35   3.1e+03      30     285 ..     175     196 ..     168     214 .. 0.48

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 1.6e-05
                              Itfg2  29 gknvvvalsaeGwchlfdl...........akkadaseevskelekkeelkpvfsq.hlpantkvvli.aDidgDg 91 
                                        +kn++++++a   + ++ +           a +++ ++ v+k+l+++ el+ +f +     nt   ++ a i+++ 
  gene1158|gene1158|rna1158|rna1158   2 KKNTIIVITAIATIIVMFIlllyvshsmlrAVDNKYKTIVDKKLNESAELRNMFLDgNRRKNTFLGVVsATINNET 77 
                                        58888888887655544444888888887655555556667899999999999877245667766555278***** PP

                              Itfg2  92 kvElvvgytDrvvrayrW..eeseeee 116
                                        k+El +  tD+  + ++W  e+ +++e
  gene1158|gene1158|rna1158|rna1158  78 KIELRAQMTDKNYSKFKWkfENLDNDE 104
                                        ******************543444444 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 0.35
                              Itfg2  30 knvvvalsaeGwchlfdlakkadaseevskelekkeelkpvfsqhlpantkvvliaDidgDgkvElvvgytDrvvr 105
                                        +n+ + l  e  + ++ +                                                          
  gene1158|gene1158|rna1158|rna1158 175 RNIYIILVDEKRYMIYRF--YV------------------------------------------------------ 194
                                        555555555555555555..11...................................................... PP

                              Itfg2 106 ayrWeeseeeeeslskklvllkkWelegqvgslsvnkssdgspellvsqPgctyavlllkwkeeeeakkeeeeeee 181
                                                                                                                    
  gene1158|gene1158|rna1158|rna1158   - ----------------------------------------------------------------------------   -
                                        ............................................................................ PP

                              Itfg2 182 eselkskedvvlhkltssrarnknvsteiigsiskgsseeeedagllAlctLDGtLklvekdkilWslqvdhqlfa 257
                                                                                                                    
  gene1158|gene1158|rna1158|rna1158   - ----------------------------------------------------------------------------   -
                                        ............................................................................ PP

                              Itfg2 258 LekLDvtgdgreEvvaCaWDGqtYiidh 285
                                                                  d+
  gene1158|gene1158|rna1158|rna1158 195 --------------------------DD 196
                                        ..........................11 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (233 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1303  (0.0726756); expected 358.6 (0.02)
Passed bias filter:                      762  (0.042501); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 1573.19
//
Query:       gene1159|gene1159|rna1159|rna1159  [L=399]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.091   12.3   0.1       0.15   11.5   0.1    1.3  1  PDDEXK_2  PD-(D/E)XK nuclease family transposase


Domain annotation for each model (and alignments):
>> PDDEXK_2  PD-(D/E)XK nuclease family transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   8.6e-06      0.15     142     223 ..     149     237 ..     143     239 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 8.6e-06
                           PDDEXK_2 142 tdkleihflELpkfkkkeeelete.......kldkWlkfLknkdkekkeeelleeevikkaieaaeraskdeeere 210
                                        +d  +  f EL +fk ++    ++        +  Wl+ L+++ k+  +    +ee ++ + e++++a++ e+++e
  gene1159|gene1159|rna1159|rna1159 149 SDSPTSLFDELRRFKTISIAWVSSstlrqpkDFLLWLTRLNELRKLFVRYLTAKEERLRGLVEMCRIAKEVEKDIE 224
                                        55555666677777777666555556667777******************************************** PP

                           PDDEXK_2 211 ayeerekalldqk 223
                                        + e++ +++ld++
  gene1159|gene1159|rna1159|rna1159 225 KLESEYNKYLDNQ 237
                                        ****999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (399 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       695  (0.038764); expected 358.6 (0.02)
Passed bias filter:                      617  (0.0344135); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.45
# Mc/sec: 2671.35
//
Query:       gene116|gene116|rna116|rna116  [L=170]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.4e-62  209.6   1.6    2.8e-62  209.4   1.6    1.0  1  DUF5091     Domain of unknown function (DUF5091)
  ------ inclusion threshold ------
      0.022   14.1   0.2      0.034   13.5   0.2    1.3  1  TMEM164     TMEM164 family
       0.15   11.7   2.1       0.54    9.9   0.4    2.4  2  Nup54_57_C  NUP57/Nup54 C-terminal domain


Domain annotation for each model (and alignments):
>> DUF5091  Domain of unknown function (DUF5091)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  209.4   1.6   4.6e-66   2.8e-62       1     146 [.      15     159 ..      15     160 .. 0.99

  Alignments for each domain:
  == domain 1  score: 209.4 bits;  conditional E-value: 4.6e-66
                        DUF5091   1 llkklnnllkkptleeilkiFeadgyiRlnmvyisPislkhlkaklenlglvsweltenglkFifknfilkFkGsltitv 80 
                                    +lk+ln+++++pt+++il++Fe+d++iR+nm+yisPi+l hlkaklenlg++swe+t +g++F+f +f+l+F+G+lt+++
  gene116|gene116|rna116|rna116  15 YLKQLNHVFSSPTFPNILAVFEKDSFIRFNMIYISPITLPHLKAKLENLGMLSWEITSSGINFFFVDFQLQFRGHLTVHR 94 
                                    69****************************************************************************** PP

                        DUF5091  81 kedkifsieidfdpeidsevgieilkeiekylkgcDalfFmtyfvdidkeiLknpLaesveflekr 146
                                    ++ ++f++e+df+p+i++++++ il+e+e+ylkgcD++fFm+yf+++d+eiL+n+La+s+++l +r
  gene116|gene116|rna116|rna116  95 MQ-RVFALELDFEPVISRTERSGILNELESYLKGCDSVFFMSYFINSDYEILSNSLANSISYLGRR 159
                                    **.************************************************************998 PP

>> TMEM164  TMEM164 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.2   5.7e-06     0.034     156     211 ..      38      91 ..      15     100 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5.7e-06
                        TMEM164 156 vyyiqHvlllvvPvyllklggvysveplsdfswsvlslgllllyhfvvlqilallt 211
                                      +i+  ++++ P+ l +l+   ++e+l  +sw + s g+++++  + lq+ + lt
  gene116|gene116|rna116|rna116  38 DSFIRFNMIYISPITLPHLK--AKLENLGMLSWEITSSGINFFFVDFQLQFRGHLT 91 
                                    479***************99..789*************************998877 PP

>> Nup54_57_C  NUP57/Nup54 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.4     9e-05      0.54       8      17 ..      12      21 ..      12      22 .. 0.92
   2 ?    0.2   0.1     0.097   5.8e+02      15      25 ..      53      63 ..      53      64 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 9e-05
                     Nup54_57_C  8 LeDYekQLqH 17
                                   ++DY kQL+H
  gene116|gene116|rna116|rna116 12 MQDYLKQLNH 21
                                   69******** PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.097
                     Nup54_57_C 15 LqHLkKElEsi 25
                                   L HLk  lE +
  gene116|gene116|rna116|rna116 53 LPHLKAKLENL 63
                                   67***999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       304  (0.0169558); expected 358.6 (0.02)
Passed bias filter:                      247  (0.0137766); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 1279.71
//
Query:       gene1160|gene1160|rna1160|rna1160  [L=255]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.7e-19   67.6   0.2    4.7e-19   67.6   0.2    1.7  2  SRF-TF           SRF-type transcription factor (DNA-binding a
  ------ inclusion threshold ------
      0.078   13.2   1.1       0.18   12.0   1.1    1.6  1  DUF3931          Protein of unknown function (DUF3931)
       0.13   11.9   0.1       0.19   11.4   0.1    1.2  1  Acyltransferase  Acyltransferase


Domain annotation for each model (and alignments):
>> SRF-TF  SRF-type transcription factor (DNA-binding and dimerisation domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.2      0.62   3.7e+03       2      17 ..     115     130 ..     114     130 .. 0.82
   2 !   67.6   0.2   7.8e-23   4.7e-19       2      48 .]     136     182 ..     135     182 .. 0.98

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.62
                             SRF-TF   2 IeneraRqvtFsKRrn 17 
                                        Ie+  ++++t s R++
  gene1160|gene1160|rna1160|rna1160 115 IEHVAKKKATKSGRKK 130
                                        8899999999998875 PP

  == domain 2  score: 67.6 bits;  conditional E-value: 7.8e-23
                             SRF-TF   2 IeneraRqvtFsKRrnGLfKKAsELsvLcgvevavvvfspngklytf 48 
                                        Ie +++R+vtFsKR++G++KKA+EL +L+ +++ ++v s++g++ytf
  gene1160|gene1160|rna1160|rna1160 136 IEGKNKRSVTFSKRKKGIMKKAYELNMLTKSQILLLVASESGHVYTF 182
                                        99********************************************9 PP

>> DUF3931  Protein of unknown function (DUF3931)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   1.1     3e-05      0.18       5      38 ..     128     161 ..     124     166 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3e-05
                            DUF3931   5 ekkcnvisidGkkkksdtysypklvvenktyefs 38 
                                         kk  +  i+Gk k+s t+s  k  + +k+ye+ 
  gene1160|gene1160|rna1160|rna1160 128 RKKIKMAYIEGKNKRSVTFSKRKKGIMKKAYELN 161
                                        6899999*************************85 PP

>> Acyltransferase  Acyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   3.1e-05      0.19      76     124 ..     113     161 ..      86     180 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3.1e-05
                    Acyltransferase  76 araagsleniselleegklvviFPEGtrsregellpfkkGlvrlaakak 124
                                         + + + ++++ +  ++k+ + + EG+++r+  + + kkG+++ a ++ 
  gene1160|gene1160|rna1160|rna1160 113 MEIEHVAKKKATKSGRKKIKMAYIEGKNKRSVTFSKRKKGIMKKAYELN 161
                                        3333333444445555566899********************9999884 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1078  (0.0601261); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.37
# Mc/sec: 2052.36
//
Query:       gene1161|gene1161|rna1161|rna1161  [L=112]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       404  (0.0225333); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 848.67
//
Query:       gene1162|gene1162|rna1162|rna1162  [L=1724]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0031   17.5   0.0       0.01   15.8   0.0    2.0  1  KIX_2     KIX domain


Domain annotation for each model (and alignments):
>> KIX_2  KIX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   5.7e-07      0.01       8      70 ..       2      63 ..       1      74 [. 0.92

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 5.7e-07
                              KIX_2  8 lspeeRqkivnkiletLkkhlpvsgpeglnelkkiAvrFEekiFskAtskedYlrkislKmlq 70
                                       +s e+R+++  k+ ++L+++ p+ ++ g +e+ +     Ee  Fs ++s e Ylr+i++K++ 
  gene1162|gene1162|rna1162|rna1162  2 ISIEDRKSVKVKLYNVLSRS-PCFSECGKSEVLRLCGVMEEECFSISNSVEGYLRSINEKINI 63
                                       577999*************9.9999***********************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1724 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1485  (0.0828267); expected 358.6 (0.02)
Passed bias filter:                      255  (0.0142228); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.97u 0.33s 00:00:01.30 Elapsed: 00:00:00.51
# Mc/sec: 10226.88
//
Query:       gene1163|gene1163|rna1163|rna1163  [L=154]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.026   14.8   0.1      0.035   14.3   0.1    1.3  1  DUF1768   Domain of unknown function (DUF1768)


Domain annotation for each model (and alignments):
>> DUF1768  Domain of unknown function (DUF1768)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1     2e-06     0.035      10      61 ..      21      69 ..      17     115 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2e-06
                            DUF1768 10 gflsnwypspftvdgeehkvelealtyntaehymmaqKall...fedtevaeeil 61
                                       +++s +yp++++ ++++     +++ty+ta+h +  +K l+   + ++++++ il
  gene1163|gene1163|rna1163|rna1163 21 QYFSTFYPCTVSQSTNK-----TTITYKTAQHALYTRKVLTntaL-NNHTITFIL 69
                                       79*****9999777777.....899*************6553322.233344444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       714  (0.0398237); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.34s 00:00:00.95 Elapsed: 00:00:00.57
# Mc/sec: 813.65
//
Query:       gene1164|gene1164|rna1164|rna1164  [L=571]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-14   53.4   0.1      1e-13   51.4   0.1    2.1  1  VPS9      Vacuolar sorting protein 9 (VPS9) domain


Domain annotation for each model (and alignments):
>> VPS9  Vacuolar sorting protein 9 (VPS9) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.4   0.1   5.8e-18     1e-13       3     103 ..     423     548 ..     421     549 .. 0.97

  Alignments for each domain:
  == domain 1  score: 51.4 bits;  conditional E-value: 5.8e-18
                               VPS9   3 qaseeLkklseaksPreKlkcllrtieeiteavskseegeslgaDdlLPiliyviikssppnlysnvqfikrF... 75 
                                        +++  ++ +++++s +eKl+++++ti+ ++ +v     g + g + lL +liyv+iks++++l+     +k++   
  gene1164|gene1164|rna1164|rna1164 423 EIITYFRTITHKHSVTEKLNVIIKTIKDVYVTV-----GCEKGIERLLTVLIYVLIKSRVKDLCVIAAVVKEYrrc 493
                                        68899****************************.....9999********************************** PP

                               VPS9  76 ...........................rsktllegeegYylttleaavefiesle 103
                                                                     + l ++e++Yylt +e+a+ fi+++e
  gene1164|gene1164|rna1164|rna1164 494 tyqqcsgaplcthlkgihvyvqpcecyVRPILSDSEIEYYLTVFESALLFIKEIE 548
                                        *************************97799999*******************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (571 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3106  (0.173239); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.88u 0.37s 00:00:01.25 Elapsed: 00:00:00.57
# Mc/sec: 3011.27
//
Query:       gene1165|gene1165|rna1165|rna1165  [L=91]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       476  (0.0265492); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 645.50
//
Query:       gene1166|gene1166|rna1166|rna1166  [L=110]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.057   13.2   0.1      0.072   12.9   0.1    1.3  1  Med6      MED6 mediator sub complex component


Domain annotation for each model (and alignments):
>> Med6  MED6 mediator sub complex component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1     4e-06     0.072      86     123 ..      28      66 ..      13      82 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 4e-06
                               Med6  86 tvlaaYyiiggniYqapsly.svvqsrllsalsslskal 123
                                        + +++Yyii + i q p ++ +v+++r+l++l++   ++
  gene1166|gene1166|rna1166|rna1166  28 NRISTYYIIVEMICQQPRIFeRVLRKRVLRILNQKGFIF 66 
                                        6689*************9873699****99988755555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       416  (0.0232026); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.29s 00:00:00.67 Elapsed: 00:00:00.44
# Mc/sec: 752.49
//
Query:       gene1167|gene1167|rna1167|rna1167  [L=174]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       928  (0.0517597); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 1223.01
//
Query:       gene1168|gene1168|rna1168|rna1168  [L=301]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-10   40.6  13.1    1.4e-10   40.6  13.1    1.5  1  MFS_1_like     MFS_1 like family
    2.7e-06   26.7  13.8    3.5e-06   26.3  13.8    1.1  1  Nuc_H_symport  Nucleoside H+ symporter
  ------ inclusion threshold ------
      0.049   13.9   0.1      0.049   13.9   0.1    4.5  3  DUF4064        Protein of unknown function (DUF4064)
        1.9    8.7   6.3         12    6.1   0.1    3.8  5  MHYT           Bacterial signalling protein N terminal repeat


Domain annotation for each model (and alignments):
>> MFS_1_like  MFS_1 like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.6  13.1   3.1e-14   1.4e-10     178     374 ..      48     246 ..      18     256 .. 0.85

  Alignments for each domain:
  == domain 1  score: 40.6 bits;  conditional E-value: 3.1e-14
                         MFS_1_like 178 p....ysallyvlaallvisllvvlilnetekesklkvtkslqvllnilknpeviifllvalilgmswgiienFlf 249
                                        +    +s  ++++a+ l i ll+ l+ ++++k  k ++t  +  +++++ +p+v++  + ++ +g+   ii nF++
  gene1168|gene1168|rna1168|rna1168  48 KndrlLSLTVCIVAGTLAIILLL-LKTPKFKKDVKENLTR-EGRIMHVILKPSVLLYYASVVAIGVYKCIISNFVT 121
                                        13344555667777777776666.8999999999999996.677******************************** PP

                         MFS_1_like 250 lYLkelgasntllGslvalgvvaeiplfffaeklleklGhvklliiallayilrfllyaii.enawlvlpievLhg 324
                                         +L+  g    ++ +l+  +++ae+ ++++  + + ++    l +i++++ +l    y +   n+ ++++ evL+g
  gene1168|gene1168|rna1168|rna1168 122 TFLQINGLQMNTIRMLWGTRCIAELFTYIIIPY-FAFVPNNILFVISIFVSALSIAFYIFPeLNTTMLVISEVLKG 196
                                        *****************************9987.6799999999**************9998899*********** PP

                         MFS_1_like 325 isfgllwaaaveyvskiapksleatgqgllsglyfglGralGsliGGllw 374
                                        + ++ +  + +   +  a++ +++++qg+ +++y g+   l  +++ +l+
  gene1168|gene1168|rna1168|rna1168 197 AGTASFVYTSILIFKSYATNDIQTQVQGIRNSAYNGFSCILFGILAAVLI 246
                                        ***********************************998777666666666 PP

>> Nuc_H_symport  Nucleoside H+ symporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3  13.8   7.9e-10   3.5e-06     132     366 ..      25     250 ..       9     300 .. 0.75

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 7.9e-10
                      Nuc_H_symport 132 vlGtvGfilaslaflllvvsladlelsrlqlliaagvslllavyaltLPkiPakkkakqslkkllgl..dafvLlk 205
                                        ++  +G   +   f++ v+s +++ + +  l ++  + +   +  l L k+P   k k+++k+ l +  + + ++ 
  gene1168|gene1168|rna1168|rna1168  25 IFSILGNACV--MFIMPVISCTGIIKNDRLLSLTVCIVAGTLAIILLLLKTP---KFKKDVKENLTRegRIMHVIL 95 
                                        5555555444..799999999998777766666555444444456778899*...444444444444113455566 PP

                      Nuc_H_symport 206 nkrllvfflvslllavvlqiyyvfanafLtevakivvklasillslsqvaeilfiLtlpfflkrfGikkvlllslv 281
                                        ++ +l+++   + ++v   i   f  +fL+  + + ++   +l     +ae+++ +++p+f         +++s+ 
  gene1168|gene1168|rna1168|rna1168  96 KPSVLLYYASVVAIGVYKCIISNFVTTFLQING-LQMNTIRMLWGTRCIAELFTYIIIPYFAF-VPNNILFVISIF 169
                                        79999999999999***************8665.99999999999999************963.344556689*** PP

                      Nuc_H_symport 282 aaalrfalfaygaddepvgvvlllLslivyGvaydffyitayvfvdkevpkdirasaqGlflllvnGvGallgsil 357
                                          al  a++++      + + +l++s ++ G   + f  t+ +     + +di++  qG+ +   nG+ ++l +il
  gene1168|gene1168|rna1168|rna1168 170 VSALSIAFYIFP----ELNTTMLVISEVLKGAGTASFVYTSILIFKSYATNDIQTQVQGIRNSAYNGFSCILFGIL 241
                                        **********99....56667778888899*9988777776666688899************************** PP

                      Nuc_H_symport 358 sgalvemft 366
                                        ++ l+++  
  gene1168|gene1168|rna1168|rna1168 242 AAVLIDRDL 250
                                        *99998744 PP

>> DUF4064  Protein of unknown function (DUF4064)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   5.2       0.7   3.1e+03      59      78 ..      49      68 ..      13      82 .. 0.52
   2 ?    0.2   4.1       0.2   8.9e+02      63      86 ..     162     185 ..     108     194 .. 0.79
   3 ?   13.9   0.1   1.1e-05     0.049      17      86 ..     233     301 .]     186     301 .] 0.85

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.7
                            DUF4064 59 tllivlgvialiaivlgivg 78
                                       +  ++ ++++++a+ l i+ 
  gene1168|gene1168|rna1168|rna1168 49 NDRLLSLTVCIVAGTLAIIL 68
                                       33333333344444443333 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.2
                            DUF4064  63 vlgvialiaivlgivgalllkknk 86 
                                        +l+vi+++ ++l+i++ ++ + n+
  gene1168|gene1168|rna1168|rna1168 162 ILFVISIFVSALSIAFYIFPELNT 185
                                        788999999999999888877665 PP

  == domain 3  score: 13.9 bits;  conditional E-value: 1.1e-05
                            DUF4064  17 illglllllflfllssgefsqelteeqalsgedasavleflstllivlgvialiaivlgivgalllkknk 86 
                                        + ++l+++l+++l+ ++ ++    + +  s+e  + +l +++++ +++++ +liaiv  i++ +l k+nk
  gene1168|gene1168|rna1168|rna1168 233 FSCILFGILAAVLIDRDLKDPRTVN-EDESDEMRNRMLNVFESSYFIIFFSLLIAIVPAILARFLKKRNK 301
                                        4455666666666666665555544.8889999999********99999*************99999886 PP

>> MHYT  Bacterial signalling protein N terminal repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.1    0.0027        12      29      46 ..      52      69 ..      51      77 .. 0.88
   2 ?   -2.1   0.0         1   4.6e+03      24      45 ..     103     124 ..      95     132 .. 0.65
   3 ?   -0.5   0.1      0.33   1.5e+03      32      47 ..     164     179 ..     152     191 .. 0.68
   4 ?   -3.5   0.0       2.7   1.2e+04      35      46 ..     235     246 ..     232     253 .. 0.65
   5 ?    2.9   0.0     0.029   1.3e+02      27      45 ..     278     296 ..     273     300 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0027
                               MHYT 29 alSlliaivasvlAlala 46
                                       +lSl+++iva +lA+ l+
  gene1168|gene1168|rna1168|rna1168 52 LLSLTVCIVAGTLAIILL 69
                                       69*************996 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1
                               MHYT  24 dpaltalSlliaivasvlAlal 45 
                                         +  +a+ +  +i+++++  +l
  gene1168|gene1168|rna1168|rna1168 103 YASVVAIGVYKCIISNFVTTFL 124
                                        4555666666677777666665 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.33
                               MHYT  32 lliaivasvlAlalav 47 
                                        ++i+i +s+l +a+ +
  gene1168|gene1168|rna1168|rna1168 164 FVISIFVSALSIAFYI 179
                                        4677777777776644 PP

  == domain 4  score: -3.5 bits;  conditional E-value: 2.7
                               MHYT  35 aivasvlAlala 46 
                                        +i++ +lA +l+
  gene1168|gene1168|rna1168|rna1168 235 CILFGILAAVLI 246
                                        566666666665 PP

  == domain 5  score: 2.9 bits;  conditional E-value: 0.029
                               MHYT  27 ltalSlliaivasvlAlal 45 
                                        +++ Slliaiv ++lA +l
  gene1168|gene1168|rna1168|rna1168 278 IIFFSLLIAIVPAILARFL 296
                                        6789*********999665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (301 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       959  (0.0534888); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 2017.02
//
Query:       gene1169|gene1169|rna1169|rna1169  [L=270]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       609  (0.0339673); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 2025.46
//
Query:       gene117|gene117|rna117|rna117  [L=208]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1058  (0.0590105); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 1521.28
//
Query:       gene1170|gene1170|rna1170|rna1170  [L=155]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-07   31.6   0.1    2.5e-07   30.7   0.1    1.4  1  Integrase_H2C2  Integrase zinc binding domain
  ------ inclusion threshold ------
      0.047   13.9   0.1      0.082   13.1   0.1    1.5  1  zf-H2C2         H2C2 zinc finger


Domain annotation for each model (and alignments):
>> Integrase_H2C2  Integrase zinc binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.7   0.1   2.8e-11   2.5e-07       4      47 ..      98     141 ..      95     143 .. 0.94

  Alignments for each domain:
  == domain 1  score: 30.7 bits;  conditional E-value: 2.8e-11
                     Integrase_H2C2   4 slrkeilkeaHdsagHlGiektlerlrrryyWpgmrkdvkkyvk 47 
                                        + +++++ eaH ++ H G    +  l++ryyW gm++++ +++k
  gene1170|gene1170|rna1170|rna1170  98 ENTEKLIIEAHLKTNHRGLVPIYYELKERYYWLGMKRHITEIIK 141
                                        67899************************************998 PP

>> zf-H2C2  H2C2 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   9.2e-06     0.082      15      33 ..     123     141 ..     110     142 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 9.2e-06
                            zf-H2C2  15 larkYhwlgiketvseVis 33 
                                        l+++Y+wlg k+++ e+i+
  gene1170|gene1170|rna1170|rna1170 123 LKERYYWLGMKRHITEIIK 141
                                        7899*************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       693  (0.0386525); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 1017.18
//
Query:       gene1171|gene1171|rna1171|rna1171  [L=98]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       401  (0.022366); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.28s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 700.38
//
Query:       gene1172|gene1172|rna1172|rna1172  [L=44]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (44 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       332  (0.0185175); expected 358.6 (0.02)
Passed bias filter:                      165  (0.00920297); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.31u 0.26s 00:00:00.57 Elapsed: 00:00:00.40
# Mc/sec: 326.37
//
Query:       gene1173|gene1173|rna1173|rna1173  [L=50]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (50 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       295  (0.0164538); expected 358.6 (0.02)
Passed bias filter:                      216  (0.0120475); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.32u 0.26s 00:00:00.58 Elapsed: 00:00:00.40
# Mc/sec: 379.71
//
Query:       gene1174|gene1174|rna1174|rna1174  [L=31]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (31 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       121  (0.00674884); expected 358.6 (0.02)
Passed bias filter:                       97  (0.00541023); expected 358.6 (0.02)
Passed Vit filter:                         3  (0.000167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.25s 00:00:00.59 Elapsed: 00:00:00.41
# Mc/sec: 226.55
//
Query:       gene1175|gene1175|rna1175|rna1175  [L=60]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.035   13.8   0.0      0.036   13.7   0.0    1.1  1  Syntaxin  Syntaxin


Domain annotation for each model (and alignments):
>> Syntaxin  Syntaxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0     2e-06     0.036     161     196 ..      21      56 ..       7      60 .] 0.82

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2e-06
                           Syntaxin 161 arealseieeRhkevlelekslkeLhqlFldmavLV 196
                                         r+ l + eeRh +++e e+ l+ +++ Fl +   +
  gene1175|gene1175|rna1175|rna1175  21 MRDGLLQLEERHFKIKEPERYLQSIKKCFLAVCACI 56 
                                        389999************************987665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (60 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       638  (0.0355848); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 406.73
//
Query:       gene1176|gene1176|rna1176|rna1176  [L=46]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (46 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       237  (0.0132188); expected 358.6 (0.02)
Passed bias filter:                      199  (0.0110993); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.26s 00:00:00.60 Elapsed: 00:00:00.41
# Mc/sec: 340.82
//
Query:       gene1177|gene1177|rna1177|rna1177  [L=441]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.2e-81  274.2   0.3    1.6e-81  273.9   0.3    1.1  1  tRNA-synt_2  tRNA synthetases class II (D, K and N)


Domain annotation for each model (and alignments):
>> tRNA-synt_2  tRNA synthetases class II (D, K and N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  273.9   0.3   8.7e-86   1.6e-81       5     312 ..     120     434 ..     116     436 .. 0.96

  Alignments for each domain:
  == domain 1  score: 273.9 bits;  conditional E-value: 8.7e-86
                                        HHHTHHHHCCSHHHHHHHHHHHHHHHHHHHHHHHTT-EE----SEESS--SSSS--EEEEETTT.TEEE....-E- CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxx RF
                        tRNA-synt_2   5 rlknryldlrtekvskvlrlrstvtkavrkyleengfieietPiLsksdteegarlFkvksrekekeff....aLt 76 
                                        +l++ +l lr ++    l++rs++++++r+++ e++f+ei++P+L+++++e+g++lFk+       ++f    +Lt
  gene1177|gene1177|rna1177|rna1177 120 LLEKGHLALRMPERMFFLKARSHMLRCFREFFYEKEFTEITPPTLVQTQVEGGSTLFKL-------NYFgkeaYLT 188
                                        68899******************************************************.......66666667** PP

                                        S-SHHHHHHHHHCTHSEEEEEEEEE--S--BTTB-S-CEEEEEEEEET-SCHHHHHHHHHHHHHHHHHHHHCSCCC CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        tRNA-synt_2  77 qspqlylellivagidrvfqiaraFRaEdsrtdrhlaEFtqieaemsfieeedimqvleelikslvkevlessakd 152
                                        qs+qlyle++++    + ++ia ++RaE+s+t+rhl+E+t++eae++ i +ed+++v+e+++ ++v+++ e+++++
  gene1177|gene1177|rna1177|rna1177 189 QSSQLYLETVVPV-AMKAYCIASSYRAEKSNTTRHLTEYTHVEAELADICFEDLLNVIEDMVYTVVTDFYEKMKGE 263
                                        *************.99**********************************************************99 PP

                                        CCHTTTTTS.EE-SSS-EEEEHHHHHHHHHTS............-SS--HHHHHHHHHH.S--SEEEEEEEBGGGS CS
                                        xxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxx............xxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx RF
                        tRNA-synt_2 153 iefvirrns.kdlkkpfkrltykeaieklnei............gkdldkaderalvkk.eknepvfvtdfPaelk 214
                                        i +     +  ++k+pfkr++y++ai+ +n+             g+d+  a e +lvk+  +n p+f+t+f  + k
  gene1177|gene1177|rna1177|rna1177 264 ILELYPYYEfFEFKRPFKRISYEDAIKYFNDVgykkdngldfvsGDDIPDAAEVFLVKSyADNTPLFLTNFETAAK 339
                                        99888765449*******************99*************************9725789************ PP

                                        TTCBBBSTTSTTBBSEEEEEETTE.EEEEEEEB--SHHHHHHHHHHCCHHSSSGGGGHHHHHHHHCT--SEEEEEE CS
                                        xxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        tRNA-synt_2 215 pFyarkeeddkkltesyDllingv.ElvgGslRiedpeeleeklkskgldeeaeekfswylealeyGapphgGlgl 289
                                        pFy+r + d +k tes Dll++++ E++gGs+R ed++el + l+s+g+d   +++++wy+++ +yG ++hgG+gl
  gene1177|gene1177|rna1177|rna1177 340 PFYMRTTAD-PKYTESTDLLFPNIgEILGGSMRKEDYQELVDGLRSEGID---PKPYYWYTDMAQYGPCSHGGFGL 411
                                        *********.9***************************************...*********************** PP

                                        EHHHHHHHHCT-SSGGGCSSS-X CS
                                        xxxxxxxxxxxxxxxxxxxxxxx RF
                        tRNA-synt_2 290 GldRlvmlllgsesIrdviaFPk 312
                                        G++Rl++ l+  +++ +  ++P+
  gene1177|gene1177|rna1177|rna1177 412 GFERLLVGLMRWKNVVKGCLYPR 434
                                        ***************99999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (441 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       355  (0.0198003); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 2977.90
//
Query:       gene1178|gene1178|rna1178|rna1178  [L=256]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    0.00025   20.8  26.0     0.0011   18.6  26.0    2.1  1  DUF4203       Domain of unknown function (DUF4203)
  ------ inclusion threshold ------
      0.092   12.3   0.3      0.092   12.3   0.3    2.0  2  SPW           SPW repeat
       0.81   10.0  12.2       0.17   12.2   6.8    2.1  2  YwiC          YwiC-like protein
        3.2    8.2  13.1        1.1    9.7   0.6    3.5  3  DUF4491       Domain of unknown function (DUF4491)
        8.5    6.3  12.5       0.86    9.5   4.2    2.8  3  Chordopox_L2  Chordopoxvirus L2 protein


Domain annotation for each model (and alignments):
>> DUF4203  Domain of unknown function (DUF4203)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6  26.0   3.1e-07    0.0011       2     199 ..      32     245 ..      31     250 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 3.1e-07
                            DUF4203   2 lgailillGlvlcffGyrlfkltlflsgfllgsllvlvlilkvvvlp....................sslvqgasl 57 
                                        l+++ i++Gl++ ++G+ + +++l +   ++++ +++ + +++   +                     ++++   l
  gene1178|gene1178|rna1178|rna1178  32 LAVLTIIVGLFILVLGISFKRISLTVLSSIFLTQVFWYISENFGEGYifafklprsysgkakevlefLEANKLRLL 107
                                        68999**************************************9999***********999999988777888888 PP

                            DUF4203  58 vaalvvGllgGllallfwelglfllga...lgGlllallilsllegglitslpskaiflvivvlgllgavlslklq 130
                                        + +l++ +++  +++ f +   fl+ +   ++ ++ ++ i +l + g+ ++l      l+++++ +++++l++k++
  gene1178|gene1178|rna1178|rna1178 108 IFILIMSFIVSTVIISFIKSVTFLVLFiatAVAYTEGFHIKLLQKAGIDEPLVR-Y--LLYAAILIVIVLLYIKIP 180
                                        888999999999988888777777766211333444566666665555555544.2..558*************** PP

                            DUF4203 131 klllivatsvvGaaavvlgiDyfvgaglkefll..nlfpratvalltypltrgdwvllalwivlalvGvlv 199
                                          ll   ++++G+ +v++giD  ++  ++ + +  + ++++++   +  ++++  v ++   v +++G+  
  gene1178|gene1178|rna1178|rna1178 181 EFLLAGLFCFIGSLMVTYGIDTAFKLEWNSLEVfsTSLRDFNT---SINMDNKASVTMM---VCFIFGMGA 245
                                        ***********************99986664445544444444...3334444333333...333444443 PP

>> SPW  SPW repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.3   2.6e-05     0.092      18      44 ..      24      50 ..      24      53 .. 0.92
   2 ?   -2.7   0.2       1.2   4.4e+03       5      13 ..     183     191 ..     182     196 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.6e-05
                                SPW 18 lGfsattgaawnnvivGavvavLalaf 44
                                       +G +++ g+a+  +ivG+ ++vL++ f
  gene1178|gene1178|rna1178|rna1178 24 VGENTSSGLAVLTIIVGLFILVLGISF 50
                                       6889999*****************976 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.2
                                SPW   5 lllGlwliv 13 
                                        ll+Gl++++
  gene1178|gene1178|rna1178|rna1178 183 LLAGLFCFI 191
                                        688888876 PP

>> YwiC  YwiC-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.2      0.19     7e+02      49      78 ..      18      46 ..       1      73 [. 0.39
   2 ?   12.2   6.8   4.6e-05      0.17      10      96 ..     110     197 ..     108     205 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.19
                               YwiC 49 lka.rrrarylkplliYgavallllllalll 78
                                       + + +r ++ +++ l+    +++++l++l+l
  gene1178|gene1178|rna1178|rna1178 18 METkKRVGENTSSGLAVL--TIIVGLFILVL 46
                                       222223333333333333..33333333322 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 4.6e-05
                               YwiC  10 mllvPlllGlllag..pvwahllllvawlvgYlaffplllllkarrrarylkplliYgavallllllalllqpall 83 
                                        +l++++++  ++    +++++l+l++a  v+Y   f ++ll ka   + +++  l+Y+a+ ++++ll++ +   ll
  gene1178|gene1178|rna1178|rna1178 110 ILIMSFIVSTVIISfiKSVTFLVLFIATAVAYTEGFHIKLLQKAGIDEPLVRY-LLYAAILIVIVLLYIKIPEFLL 184
                                        789999999988887899*************************9766666654.5677777777777666666688 PP

                               YwiC  84 wwallflplvava 96 
                                        + +++f+  ++v 
  gene1178|gene1178|rna1178|rna1178 185 AGLFCFIGSLMVT 197
                                        8888888777775 PP

>> DUF4491  Domain of unknown function (DUF4491)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.6   0.00031       1.1      33      73 ..      32      72 ..      15      76 .. 0.90
   2 ?    1.3   1.4      0.14   4.9e+02      42      65 ..     108     131 ..      99     140 .. 0.79
   3 ?    3.9   0.2     0.021        74      34      52 ..     179     197 ..     157     219 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00031
                            DUF4491 33 iwwvflvagillivaslfvenvllsavlgvlgfsllWsikE 73
                                       + ++ +++g++++v+ +  + + l+++ +++ + ++W i E
  gene1178|gene1178|rna1178|rna1178 32 LAVLTIIVGLFILVLGISFKRISLTVLSSIFLTQVFWYISE 72
                                       567889*********************************99 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.14
                            DUF4491  42 illivaslfvenvllsavlgvlgf 65 
                                        i+++++s++v+ v++s + +v+ +
  gene1178|gene1178|rna1178|rna1178 108 IFILIMSFIVSTVIISFIKSVTFL 131
                                        677889999999999999888755 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.021
                            DUF4491  34 wwvflvagillivaslfve 52 
                                        ++ fl+ag+++ + sl+v+
  gene1178|gene1178|rna1178|rna1178 179 IPEFLLAGLFCFIGSLMVT 197
                                        6789***********9986 PP

>> Chordopox_L2  Chordopoxvirus L2 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   4.2   0.00024      0.86      40      76 ..     104     140 ..      97     143 .. 0.89
   2 ?    1.1   0.5     0.099   3.6e+02      37      56 ..     157     177 ..     149     185 .. 0.71
   3 ?   -2.9   0.0       1.7   6.2e+03      10      27 ..     225     242 ..     223     252 .. 0.58

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00024
                       Chordopox_L2  40 lrLlfDlLilvivviillfrlvvRNykvllilllvya 76 
                                        lrLl+ +Li++++v+ +++++++    ++l++++++a
  gene1178|gene1178|rna1178|rna1178 104 LRLLIFILIMSFIVSTVIISFIKSVTFLVLFIATAVA 140
                                        7**********************99888888888776 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.099
                       Chordopox_L2  37 rpllr.LlfDlLilvivviil 56 
                                         pl+r Ll+ ++++viv+ ++
  gene1178|gene1178|rna1178|rna1178 157 EPLVRyLLYAAILIVIVLLYI 177
                                        577774667777777777665 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 1.7
                       Chordopox_L2  10 ieeenkanekfldaiite 27 
                                        i+++nka   ++ + i  
  gene1178|gene1178|rna1178|rna1178 225 INMDNKASVTMMVCFIFG 242
                                        666666666666665554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1307  (0.0728987); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 1780.50
//
Query:       gene1179|gene1179|rna1179|rna1179  [L=157]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.3e-11   41.7   0.3    1.1e-10   41.3   0.3    1.2  1  PIF1             PIF1-like helicase
    1.7e-05   23.0   0.0    1.8e-05   22.9   0.0    1.1  1  Herpes_Helicase  Helicase
    0.00048   19.9   0.3     0.0013   18.5   0.1    1.9  2  UvrD_C_2         UvrD-like helicase C-terminal domain
  ------ inclusion threshold ------
      0.068   12.9   0.0       0.11   12.3   0.0    1.4  1  Viral_helicase1  Viral (Superfamily 1) RNA helicase
      0.073   13.1   0.0      0.075   13.0   0.0    1.2  1  DUF3074          Protein of unknown function (DUF3074)


Domain annotation for each model (and alignments):
>> PIF1  PIF1-like helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.3   0.3     3e-14   1.1e-10     328     364 .]       1      37 [.       1      37 [. 0.96

  Alignments for each domain:
  == domain 1  score: 41.3 bits;  conditional E-value: 3e-14
                                        SS-SCEEE-TT-EEEE-S--CTT-SC-TCEEEEEEEE CS
                               PIF1 328 lpnhvLkLkvGvpvmllrNldqsaGLcNGtrlivtql 364
                                        +p+h+L Lk G+ +mllrNld+++GL NGtrliv +l
  gene1179|gene1179|rna1179|rna1179   1 MPPHKLVLKRGALIMLLRNLDPANGLLNGTRLIVDEL 37 
                                        69********************************886 PP

>> Herpes_Helicase  Helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.0     5e-09   1.8e-05     731     777 ..      84     129 ..      60     152 .. 0.86

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 5e-09
                    Herpes_Helicase 731 klamtiaksqGlslekvAicFgnhknlklssvYvalsRatdseflvm 777
                                          amti ksqG s++kv +   +       ++Yval R++d+  l++
  gene1179|gene1179|rna1179|rna1179  84 SFAMTIHKSQGQSFDKVGVYLHSP-VFVHGQLYVALFRVRDASGLKV 129
                                        57*****************99998.677899**********998875 PP

>> UvrD_C_2  UvrD-like helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.1   3.6e-07    0.0013       2      20 ..      84     102 ..      83     122 .. 0.76
   2 ?   -3.0   0.0       1.9   6.8e+03      26      40 ..     138     147 ..     130     152 .. 0.51

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 3.6e-07
                           UvrD_C_2   2 ayaltihkaQGsefpaViv 20 
                                         +a+tihk+QG+ f+ V v
  gene1179|gene1179|rna1179|rna1179  84 SFAMTIHKSQGQSFDKVGV 102
                                        58*************8755 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.9
                           UvrD_C_2  26 aaarmgelrrrlLYt 40 
                                          a++++     +Yt
  gene1179|gene1179|rna1179|rna1179 138 GKADNNM-----VYT 147
                                        4444444.....444 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   2.9e-05      0.11     184     226 ..      85     121 ..      40     127 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.9e-05
                    Viral_helicase1 184 evttvhevqGltfdkVtlvllketdlelisesrenllvAlTRh 226
                                         ++t h  qG++fdkV ++l+++    ++   + +l+vAl R 
  gene1179|gene1179|rna1179|rna1179  85 FAMTIHKSQGQSFDKVGVYLHSP----VFV--HGQLYVALFRV 121
                                        589******************55....444..46789998775 PP

>> DUF3074  Protein of unknown function (DUF3074)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   2.1e-05     0.075      54      92 ..      59      97 ..      31     144 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.1e-05
                            DUF3074 54 gklevvelsakfpgpltpRdFvvllltasseaeeeesea 92
                                        ++++ + +a+fp  l++R+F+vll  a + +++++++ 
  gene1179|gene1179|rna1179|rna1179 59 SRINMAQSEAQFPFILKRRQFPVLLSFAMTIHKSQGQSF 97
                                       4678999****************9988888777666543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       409  (0.0228122); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1136.40
//
Query:       gene118|gene118|rna118|rna118  [L=238]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.24   11.7   2.4       0.45   10.8   2.4    1.4  1  COX6B     Cytochrome oxidase c subunit VIb


Domain annotation for each model (and alignments):
>> COX6B  Cytochrome oxidase c subunit VIb
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   2.4   2.5e-05      0.45      11      51 ..     174     216 ..     167     233 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 2.5e-05
                          COX6B  11 aCwearddyfkCldkkgeekae..kkeeqdekkCkaekkeyes 51 
                                     C+++  dy++C ++ +  +++  +k+++d   C++  +  e+
  gene118|gene118|rna118|rna118 174 SCYDQSSDYYSCFTDYSTVDKHieTKDDEDALGCGKRLDLSEK 216
                                    6**************7665555578888888889987666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (238 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       659  (0.0367561); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1720.73
//
Query:       gene1180|gene1180|rna1180|rna1180  [L=118]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.21   10.9   2.9       0.25   10.7   2.9    1.1  1  AAR2      AAR2 protein


Domain annotation for each model (and alignments):
>> AAR2  AAR2 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   2.9   1.4e-05      0.25     143     201 ..      24      85 ..       9      91 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 1.4e-05
                               AAR2 143 elasseseaes...ekkkawskssseeskgssakrdeeelpslkskegtelrFteiplkrtw 201
                                        +++++++++++    ++++ skss ++ k +++ +d +e++s++s +++e+++++ip+ + +
  gene1180|gene1180|rna1180|rna1180  24 SNQDTQDRRKNgsdVASQESSKSSIDNAKSTETMEDVDEKDSMQSIKSSENQYLKIPKDQGH 85 
                                        222222222224445566666666667777778889999999***************97655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1562  (0.0871214); expected 358.6 (0.02)
Passed bias filter:                      498  (0.0277762); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 865.11
//
Query:       gene1181|gene1181|rna1181|rna1181  [L=54]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (54 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       316  (0.0176251); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.24s 00:00:00.58 Elapsed: 00:00:00.38
# Mc/sec: 421.54
//
Query:       gene1182|gene1182|rna1182|rna1182  [L=180]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.47   10.9   1.9       0.68   10.3   1.9    1.2  1  CCDC53    Subunit CCDC53 of WASH complex


Domain annotation for each model (and alignments):
>> CCDC53  Subunit CCDC53 of WASH complex
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   1.9   3.8e-05      0.68       2      47 ..     127     172 ..     126     178 .. 0.94

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 3.8e-05
                             CCDC53   2 NqfvistvqfLNrFatecEekLvevekrlqrleitlalLEakLsSi 47 
                                        Nqf+++  +fLN ++  ++  +  v ++ ++l+ ++++L++ L+ +
  gene1182|gene1182|rna1182|rna1182 127 NQFLVNLFDFLNCLCVRNDLTVEIVDDKFEQLDEQISILNNNLKKM 172
                                        9***************************************999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1030  (0.0574488); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1249.82
//
Query:       gene1183|gene1183|rna1183|rna1183  [L=605]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.4e-42  144.3  22.2    9.4e-42  143.5  22.2    1.4  1  EXS       EXS family


Domain annotation for each model (and alignments):
>> EXS  EXS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  143.5  22.2   5.2e-46   9.4e-42       7     331 .]     270     561 ..     265     561 .. 0.86

  Alignments for each domain:
  == domain 1  score: 143.5 bits;  conditional E-value: 5.2e-46
                                EXS   7 vlllvvlglllwalnlhvlsklginyalifeldprsslsyrqlyelaalllllllllllllllsaevdalellpll 82 
                                        ++ l+++g++l+++ l +++  +in+++if ++  s+++ ++++ ++a    +l l  l++ ++a  + +++  +l
  gene1183|gene1183|rna1183|rna1183 270 FFSLLFVGFYLFGVSLLIFTWKKINHPFIFSFNLDSHMEVSRYFVCTA----ALHL--LYNAINALPIDAKASFAL 339
                                        56789999************************9988888888883333....2222..233334445556666679 PP

                                EXS  83 lllllllllllplnilyrssrrrflrtllrillaplapvefadfllaDiltSlakvlgDlaltvclyasswseedr 158
                                        +++++ ++++lpl++lyr+sr+++++++l+i++ p ++v+f++f++ D l S+a v + +  + c++  ++ +   
  gene1183|gene1183|rna1183|rna1183 340 AMCAVGACIVLPLDVLYRKSRYYVVYCVLKIVCTPAFKVRFRHFFFTDYLQSFAIVYRKV--LGCFF--TLGP--- 408
                                        99999****************************************************975..67777..3344... PP

                                EXS 159 kcgsssvvvplllslPyliRfrQclreyrdtkkrphllNalKYatafpvivlsalqrlsksd.......esestlr 227
                                              v v+++  +  l+R++Qc r+y+d+ +r h++Na+KY+++++  +l++ + ++++             l+
  gene1183|gene1183|rna1183|rna1183 409 ------VSVFFIGNYGNLVRVMQCGRRYYDKPERVHIYNAGKYVCQIMFSILTITYVHVQDGrtahknaRILFVLK 478
                                        ......56889999******************9************************9999988865433334456 PP

                                EXS 228 vlwllaalvnslysfiWDvtmDWgLlkllksknwflRdellypkkwvYylaivldlvlRftWslklsshlhsiqes 303
                                        +l l++ +++s +sf+WDv  DWgL           R++ll+ k +   + iv++lv R+ W+l+++         
  gene1183|gene1183|rna1183|rna1183 479 YLRLVVGILASSFSFVWDVRVDWGLG----------RKNLLFAK-STLAVLIVFNLVGRYLWLLSAYL-------- 535
                                        777888999*****************..........78899998.799*****************993........ PP

                                EXS 304 elgvfllellEvlRRwvWvffRvEnEhv 331
                                            f++ + E++RR+ W ++RvE Eh+
  gene1183|gene1183|rna1183|rna1183 536 --SDFFVCVYEIVRRTNWGIVRVEYEHL 561
                                        ..347999******************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (605 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1672  (0.0932567); expected 358.6 (0.02)
Passed bias filter:                      615  (0.034302); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.70u 0.35s 00:00:01.04 Elapsed: 00:00:00.51
# Mc/sec: 3603.89
//
Query:       gene1184|gene1184|rna1184|rna1184  [L=212]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.5e-11   42.4   0.0    1.3e-10   41.7   0.0    1.4  1  PseudoU_synth_1  tRNA pseudouridine synthase
  ------ inclusion threshold ------
      0.066   13.5   0.2       0.12   12.6   0.2    1.5  1  UPF0203          Uncharacterised protein family (UPF0203)


Domain annotation for each model (and alignments):
>> PseudoU_synth_1  tRNA pseudouridine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.7   0.0   1.5e-14   1.3e-10       3     102 ..      43     145 ..      41     150 .. 0.78

  Alignments for each domain:
  == domain 1  score: 41.7 bits;  conditional E-value: 1.5e-14
                    PseudoU_synth_1   3 kelvGthdfgsfckqkqekkntvrtileaaieevsgeekellvvtvkgsgFldhqVRamvgvlfav.....gqgkl 73 
                                          + Gt+++ +f  q+++++   r+i+++++e++++   ++++++++g++F+ hq+R m+g +++v     + g  
  gene1184|gene1184|rna1184|rna1184  43 ALYTGTRNYHNF-TQQSNTRGKSRHITNIRVERAHN---GWYEIKITGQSFMMHQIRKMIGFVLLVinwggEDGAV 114
                                        579*********.6888889999*********5555...5***********************9998997544555 PP

                    PseudoU_synth_1  74 sped.vkellnakkrkk.iavetapavglvl 102
                                        +  + ++ l      ++ ++v++apa+ l+l
  gene1184|gene1184|rna1184|rna1184 115 PAMErIRALFGCAFSERvLNVPKAPAHALFL 145
                                        5444044444433344459999999999987 PP

>> UPF0203  Uncharacterised protein family (UPF0203)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.2   1.4e-05      0.12      32      54 ..     183     205 ..     156     212 .] 0.84

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.4e-05
                            UPF0203  32 keeeCeklwkkYreClkkalkek 54 
                                         +e+C +++++++eC+++++ e 
  gene1184|gene1184|rna1184|rna1184 183 MTERCIRMFREWQECVEAHMYEY 205
                                        4789***************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (212 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       683  (0.0380947); expected 358.6 (0.02)
Passed bias filter:                      549  (0.0306208); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1418.42
//
Query:       gene1185|gene1185|rna1185|rna1185  [L=127]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0096   16.0   0.8       0.24   11.5   0.1    2.6  2  zf-Sec23_Sec24  Sec23/Sec24 zinc finger
  ------ inclusion threshold ------
      0.035   14.2   0.0      0.079   13.1   0.0    1.6  1  FYVE            FYVE zinc finger
      0.035   13.8   0.0      0.086   12.5   0.0    1.7  1  DUF5053         Domain of unknown function (DUF5053)
       0.18   12.0   2.2        2.6    8.3   0.3    2.1  2  CTU2            Cytoplasmic tRNA 2-thiolation protein 2


Domain annotation for each model (and alignments):
>> zf-Sec23_Sec24  Sec23/Sec24 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.1     0.033   1.5e+02      22      32 ..      10      20 ..       5      26 .. 0.82
   2 !   11.5   0.1   5.4e-05      0.24      21      35 ..      83      97 ..      78     106 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.033
                     zf-Sec23_Sec24 22 krwiCnfCnhk 32
                                       +r +C +C  +
  gene1185|gene1185|rna1185|rna1185 10 HRIQCRICALR 20
                                       7899***9866 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 5.4e-05
                     zf-Sec23_Sec24 21 gkrwiCnfCnhknev 35
                                       +k+ +Cn+Cn k +v
  gene1185|gene1185|rna1185|rna1185 83 KKLVVCNLCNEKMDV 97
                                       7899********998 PP

>> FYVE  FYVE zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   1.8e-05     0.079      18      66 ..       4      95 ..       2      97 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.8e-05
                                       B--SSS--EE-TTT--EE-.......................STTS-EEE.EE......................... CS
                               FYVE 18 kFsllrrrhhCrlCGkvvC.......................ekCssklvall......................... 47
                                       +Fs+l  r  Cr+C   +                        +                                   
  gene1185|gene1185|rna1185|rna1185  4 RFSILYHRIQCRICALRFTdtdqgktqygmhieehnrrkraeQ---------Hkdtisrtyfpnednwlskkielpva 72
                                       79999**************777666666666655444444430.........03333444444555555555555566 PP

                                       ....GGGTEEEEEEE-HHHHHHH CS
                               FYVE 48 ....ekeaeeksvrvCkeClael 66
                                           +k   +k++ vC+ C +++
  gene1185|gene1185|rna1185|rna1185 73 rqeeHKLFVSKKLVVCNLCNEKM 95
                                       655555555666799****9876 PP

>> DUF5053  Domain of unknown function (DUF5053)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   1.9e-05     0.086      10      29 ..      49      68 ..      47      79 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.9e-05
                            DUF5053 10 syiAkkYFgKsksWlyqrln 29
                                       + i+++YF     Wl+++++
  gene1185|gene1185|rna1185|rna1185 49 DTISRTYFPNEDNWLSKKIE 68
                                       57****************96 PP

>> CTU2  Cytoplasmic tRNA 2-thiolation protein 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.3   0.00059       2.6      47      82 ..      13      49 ..       7      68 .. 0.71
   2 ?    4.0   0.1     0.013        58      30      61 ..      66     101 ..      61     116 .. 0.64

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00059
                               CTU2 47 kCalCglpl.ddkakewkrtitiselseteseeekee 82
                                       +C +C l++ d+++ + +  ++i+e++++++ e+++ 
  gene1185|gene1185|rna1185|rna1185 13 QCRICALRFtDTDQGKTQYGMHIEEHNRRKRAEQHKD 49
                                       8********6666677777888888887777666433 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.013
                               CTU2  30 KLvknksseeae....letsekCalCglplddkake 61 
                                        K++++ +++e++     ++   C+lC+ ++d +  +
  gene1185|gene1185|rna1185|rna1185  66 KIELPVARQEEHklfvSKKLVVCNLCNEKMDVEWDD 101
                                        5555555444445565777889****9999433333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       935  (0.0521501); expected 358.6 (0.02)
Passed bias filter:                      529  (0.0295053); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 824.93
//
Query:       gene1186|gene1186|rna1186|rna1186  [L=614]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.4e-22   77.0   1.1      4e-21   75.0   0.1    2.5  2  PhetRS_B1        Phe-tRNA synthetase beta subunit B1 domain
    8.3e-12   45.1   0.3      6e-11   42.3   0.3    2.0  1  B3_4             B3/4 domain
    1.4e-10   41.3   0.1    3.8e-09   36.7   0.2    2.4  2  B5               tRNA synthetase B5 domain
  ------ inclusion threshold ------
      0.066   12.6   0.0       0.15   11.5   0.0    1.6  1  tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM 


Domain annotation for each model (and alignments):
>> PhetRS_B1  Phe-tRNA synthetase beta subunit B1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.0   0.1     9e-25     4e-21       1      81 [.       1      72 [.       1      74 [. 0.98
   2 ?   -0.9   0.1      0.45     2e+03       8      37 ..     274     306 ..     269     326 .. 0.59

  Alignments for each domain:
  == domain 1  score: 75.0 bits;  conditional E-value: 9e-25
                          PhetRS_B1  1 MPtisvkkeaLfkalgkelteeeledllfefGlElDeiveeeekkkadkkseeviykidipAnryDLLcleglaralk 78
                                       MP i+++k+ +++ l +++t + l++llf +G+El + ++e+          +++yk+dipAnryDLLcleg+ +a++
  gene1186|gene1186|rna1186|rna1186  1 MPAITINKQLFLSSLKNTYTLSSLTELLFTYGIELEDTITENG---------TQYYKLDIPANRYDLLCLEGMITAMQ 69
                                       9******************************************.........89************************ PP

                          PhetRS_B1 79 vFl 81
                                       +++
  gene1186|gene1186|rna1186|rna1186 70 CYE 72
                                       *97 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.45
                          PhetRS_B1   8 keaLfkalg..kelteeeledllfefGlE.lDe 37 
                                        k+ +++ +g  +   ++ +  l+ +fG E + e
  gene1186|gene1186|rna1186|rna1186 274 KNVFIEMTGddRAKVDDTMRYLIHNFGGErVEE 306
                                        455666666334467899999999999762333 PP

>> B3_4  B3/4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.3   0.3   1.3e-14     6e-11       2     138 ..      97     294 ..      96     299 .. 0.90

  Alignments for each domain:
  == domain 1  score: 42.3 bits;  conditional E-value: 1.3e-14
                                        SSEEEEEEEES--.-----HHHHHHHHHTT-----HHHHHHHHHHHHHT-.....-EEEEEGGGTBTEEEEEE--T CS
                               B3_4   2 cpryaarvlrgvkktapspewlqrrLrragirpinnvVDitNyvmlelgq.....PlhafDldkiqgdivvrlake 72 
                                        +p +a++v+r+v+++++                + ++V+ ++ +  ++g+     +++++D+dki  ++  rl ++
  gene1186|gene1186|rna1186|rna1186  97 RPVVACAVVRNVQFDEDV---------------LRSFVNYQDSLNRNVGRnrrcvAIGTHDYDKIRFPVYYRLGEK 157
                                        678899999999999999...............99******************************98999999888 PP

                                        TE.EEEBTTS-EEEE-T........................................................... CS
                               B3_4  73 ge.klvtldgkerelde........................................................... 88 
                                        +   +++l+gk +   +                                                           
  gene1186|gene1186|rna1186|rna1186 158 DRlWITPLNGKGVCSGGsgvmtneknynenykeeneeenkedltrdeninggasqgtatfpkitiaaleerlkndr 233
                                        8547778887755553367888888888888999999999999********************************* PP

                                        ..........TSEEEETEEEEE.EETTTEEBTTTB--TT--EEEEEEEE--HHHHHHHHHH CS
                               B3_4  89 ..........edlviadsekpv.slagvmggeeskvsedTknvfleaaafdpvsirktarr 138
                                                  ++  ++ds++++ s ++v +++e+k++ +Tknvf+e+++ d +++  t r 
  gene1186|gene1186|rna1186|rna1186 234 vfskyitsctSTAYFVDSNGVIiSYPPVLNSDETKITVNTKNVFIEMTGDDRAKVDDTMRY 294
                                        *********9999999*****99**************************999999888875 PP

>> B5  tRNA synthetase B5 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0     0.069   3.1e+02      31      52 ..      34      59 ..      12      65 .. 0.75
   2 !   36.7   0.2   8.4e-13   3.8e-09       2      65 ..     340     402 ..     339     403 .. 0.92

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.069
                                       E.....EESSTTCEEEE--TT-TT-- CS
                                       x....xxxxxxxxxxxxxxxxxxxxx RF
                                 B5 31 e....riekdkdlllVtvPswRsDle 52
                                       e    ++e++++ ++  +P+ R+Dl+
  gene1186|gene1186|rna1186|rna1186 34 EledtITENGTQYYKLDIPANRYDLL 59
                                       2555556788889999********97 PP

  == domain 2  score: 36.7 bits;  conditional E-value: 8.4e-13
                                        EEEHHHHHHHHTS---HHHHHHHHHHTT-E.EESSTTCEEEE--TT-TT--SHHHHHHHHHHHH CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                                 B5   2 slrvekinkllGidlseeeiikiLkrlgceriekdkdlllVtvPswRsDlereeDliEEvaRly 65 
                                        +l+ e++nk l ++l++e i+ +L+r+ +++ + ++  ++Vtv + R D+++ +DliE++a  y
  gene1186|gene1186|rna1186|rna1186 340 TLTREHVNKELRLNLTREMIKYHLERMMHHV-SLEESDMRVTVHPARCDVLHTIDLIEDIAVSY 402
                                        68899*************************9.566666***********************988 PP

>> tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   3.3e-05      0.15      18      53 ..     423     458 ..     411     465 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 3.3e-05
                    tRNA_synthFbeta  18 eqklrrklrdllagaGlnEvitysfvsekeldklle 53 
                                        ++ l++k+r ++a aG+nEv++  + s++e+d l++
  gene1186|gene1186|rna1186|rna1186 423 ANVLSDKIRMECAFAGFNEVVSVCLLSREENDVLRR 458
                                        57799*************************999953 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (614 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       644  (0.0359195); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.62u 0.30s 00:00:00.92 Elapsed: 00:00:00.47
# Mc/sec: 3925.38
//
Query:       gene1187|gene1187|rna1187|rna1187  [L=209]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.3e-31  108.4   0.0    3.9e-31  108.1   0.0    1.0  1  tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM 
    1.3e-05   24.8   0.0    1.8e-05   24.4   0.0    1.2  1  tRNA-synt_2d     tRNA synthetases class II core domain (F)


Domain annotation for each model (and alignments):
>> tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.1   0.0   4.4e-35   3.9e-31      55     214 .]      50     198 ..      35     198 .. 0.95

  Alignments for each domain:
  == domain 1  score: 108.1 bits;  conditional E-value: 4.4e-35
                    tRNA_synthFbeta  55 dderkavelanPlsedqsvlRtsLlpglLevlarNlargnedvrlFEigkvflkd.seeelpeeerhlaivltgkr 129
                                         ++   vel+nP s++++v+R+sLlpglL+ +++N  ++ + +r+FE+g+vf  + ++++++ + r++a++++g++
  gene1187|gene1187|rna1187|rna1187  50 RENGGCVELLNPKSKEYQVMRSSLLPGLLKFIKKNAYHRPP-IRIFEVGDVFNINgDSDTGAINCRRIAGAIAGTT 124
                                        466779***********************************.********************************** PP

                    tRNA_synthFbeta 130 eeeswsekaravdfydlkgivealleslgiekvefepaehpalhpgrsAeikv.dgkevGvlGelhpevleafdlk 204
                                                    +  dl ++++++l ++++ + +f+++e++ +  +r  +i + d++ +G +G +hp++l+ +++ 
  gene1187|gene1187|rna1187|rna1187 125 -----------DGLSDLIAFINQVLTKCKV-NTRFVRKEKSVFLEKRGGRILCdDDVIIGNFGVVHPRILKFYGIG 188
                                        ...........9******************.**********************55579****************** PP

                    tRNA_synthFbeta 205 qrvyvfEldl 214
                                          +++fE+dl
  gene1187|gene1187|rna1187|rna1187 189 MACSIFEIDL 198
                                        ********98 PP

>> tRNA-synt_2d  tRNA synthetases class II core domain (F)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.0     2e-09   1.8e-05      78     206 ..      64     188 ..      28     206 .. 0.84

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 2e-09
                                        CESEEE-SSTHHHHHHHH...TTS-SSEEEEEEEEEEBSST-SSSB-SEEEEEEEEEEETT--HHHHHHHHHHHHH CS
                       tRNA-synt_2d  78 eekllLRthttavqirtl...ekkkppikiisigrvfRrdavDathlaeFhqveglvvdenvsladlkgvleellk 150
                                        +e +++R+   +  ++ +   + ++ppi+i+ +g vf  + +  t  ++   + g ++++   l+dl+++++++l+
  gene1187|gene1187|rna1187|rna1187  64 KEYQVMRSSLLPGLLKFIkknAYHRPPIRIFEVGDVFNINGDSDTGAINCRRIAGAIAGTTDGLSDLIAFINQVLT 139
                                        5678899999999999996555578****************99********************************* PP

                                        HHCTSTEEEEE.EECEETTEEEEEEEEEEECCSSSSEEEEEEEEEE-HHHHHHTT-. CS
                       tRNA-synt_2d 151 klfgaevkvrf.rpsyfpftePsaevdvylvekkkkwlEllgaGmvrpevleavgid 206
                                        k    +v++rf r++++ f e      + +    ++ + ++++G+v+p++l+ +gi 
  gene1187|gene1187|rna1187|rna1187 140 KC---KVNTRFvRKEKSVFLEK-RGGRILC----DDDVIIGNFGVVHPRILKFYGIG 188
                                        **...67899835667777775.5678889....67788****************93 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       414  (0.0230911); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1505.54
//
Query:       gene1188|gene1188|rna1188|rna1188  [L=199]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       638  (0.0355848); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 1429.67
//
Query:       gene1189|gene1189|rna1189|rna1189  [L=400]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.1e-19   68.7  24.2    5.1e-19   68.7  24.2    3.0  3  Choline_transpo  Plasma-membrane choline transporter


Domain annotation for each model (and alignments):
>> Choline_transpo  Plasma-membrane choline transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.1   7.8      0.38   6.8e+03     258     301 ..      20      65 ..      15     112 .. 0.63
   2 !   68.7  24.2   2.8e-23   5.1e-19       4     225 ..     111     300 ..     103     304 .. 0.82
   3 ?   -5.8   1.8         1   1.8e+04     198     204 ..     335     341 ..     318     344 .. 0.49

  Alignments for each domain:
  == domain 1  score: -4.1 bits;  conditional E-value: 0.38
                    Choline_transpo 258 lgkllialltgliaylllkatltnpe..elnsplvpllvvfiiayl 301
                                          +l +++++g+++y  +  ++++      ++ + +l+++f++++l
  gene1189|gene1189|rna1189|rna1189  20 ALALYVVFMAGVLTYTAFMSKTKSYLdlASHFDMKVLIFTFVCGFL 65 
                                        4455566666666553333222222236344444466666666665 PP

  == domain 2  score: 68.7 bits;  conditional E-value: 2.8e-23
                    Choline_transpo   4 livavllllllivlrkrirlaiallkvaskai.ksnpslllvplltllllllvsafwivvavalylassgestdkv 78 
                                        ++ a++l+ +l++lrk i++a+++ k a++ + +s++s+l+v +l+l+   +++ f+++v+ +l    s+      
  gene1189|gene1189|rna1189|rna1189 111 IFSALMLVTYLFYLRKHIKYAAQIAKSAAQLVcTSIFSTLCVLILFLAGWSGMIYFFVTVSTGL----SK------ 176
                                        344566888999***************9998725667888888888888888888888888555....22...... PP

                    Choline_transpo  79 nsgsesglaavefessskvkalllyllfgllWtleflralqqvtvagavasWYfskkkdlpskfpvlkslkralty 154
                                                        +  ++ l++  ++++Wtl +l +  +v +a++++ +Y    ++ ++++ + +++k+ l y
  gene1189|gene1189|rna1189|rna1189 177 ----------------QDRIIGLAIEALAFVWTLFVLCYSLRVFIASIFVVHYLM--RSISPTQRAVEAFKNWL-Y 233
                                        ................2235678999*****************************..34445456889999866.* PP

                    Choline_transpo 155 hlGSialgSlilaivqllrlileylekklkkkenavakcllcclkcclwclekflkflnrnayimvaiyGk 225
                                         lGSi++g+li+a++ +lr+++++     ++++ +v  ++ ++l ++l +l+ +++f n +ay++va++ k
  gene1189|gene1189|rna1189|rna1189 234 ALGSICFGALIIALITVLRMLVDR----ERDRSGSVGSFFYSILLVLLDILQDLVNFSNEWAYCYVALTEK 300
                                        ***********************7....333355677899999999**********************976 PP

  == domain 3  score: -5.8 bits;  conditional E-value: 1
                    Choline_transpo 198 lkcclwc 204
                                         +c++wc
  gene1189|gene1189|rna1189|rna1189 335 PSCFFWC 341
                                        1234444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (400 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1434  (0.0799822); expected 358.6 (0.02)
Passed bias filter:                      493  (0.0274974); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.72u 0.36s 00:00:01.08 Elapsed: 00:00:00.51
# Mc/sec: 2340.18
//
Query:       gene119|gene119|rna119|rna119  [L=121]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       291  (0.0162307); expected 358.6 (0.02)
Passed bias filter:                      233  (0.0129957); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.30s 00:00:00.76 Elapsed: 00:00:00.49
# Mc/sec: 741.61
//
Query:       gene1190|gene1190|rna1190|rna1190  [L=161]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.9e-20   71.9   2.3    5.7e-20   71.7   2.3    1.0  1  NIF       NLI interacting factor-like phosphatase


Domain annotation for each model (and alignments):
>> NIF  NLI interacting factor-like phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.7   2.3   3.2e-24   5.7e-20       3     150 ..       2     154 ..       1     160 [. 0.88

  Alignments for each domain:
  == domain 1  score: 71.7 bits;  conditional E-value: 3.2e-24
                                NIF   3 LVLDLDetLvhsklekskkl.kvegekvevsvlkRpgldefLkel.sklyevvifTasseeyaeavidildpekkl 76 
                                        LV+DL++tLv + +++++ + +++ e  +++vl+Rp+l+e+ ++l  +  + + +T++   +a+++ +il +e+  
  gene1190|gene1190|rna1190|rna1190   2 LVFDLNGTLVKRFYKPNGIItNYDYEYGKFYVLLRPYLRELTNYLhINDLKYMFWTNALAYNADNITQILIKEGMR 77 
                                        9*********9997566655266677899***************83566*************************99 PP

                                NIF  77 lshrlyrescvkkkgeyvKdLsllgr....dlsrvvivDdspdsfelqpengipiksffsdkkDneLlkllpllke 148
                                          + l r++c++ k+ + KdLs++ +    +ls++ +v+d ++      +n+i +++f +d +D++Ll+l+  lk+
  gene1190|gene1190|rna1190|rna1190  78 PVAHLDRQHCTFIKNVCKKDLSVVSKmhniNLSDIFLVEDMETRSV-RGQNVILVDKFDGDATDDALLTLIDDLKK 152
                                        9999******888***********777777********99998766.489********99**********999998 PP

                                NIF 149 la 150
                                        + 
  gene1190|gene1190|rna1190|rna1190 153 IY 154
                                        76 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       714  (0.0398237); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 1067.30
//
Query:       gene1191|gene1191|rna1191|rna1191  [L=357]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (357 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1084  (0.0604607); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 2498.11
//
Query:       gene1192|gene1192|rna1192|rna1192  [L=285]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        2.8    8.3  13.8         17    5.8  12.6    2.8  2  DUF4124   Domain of unknown function (DUF4124)


Domain annotation for each model (and alignments):
>> DUF4124  Domain of unknown function (DUF4124)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8  12.6   0.00097        17      16      53 ..      26      67 ..      23      79 .. 0.70
   2 ?   -0.6   0.0     0.099   1.8e+03      16      24 ..     141     149 ..     140     150 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.00097
                            DUF4124 16 kWvDanGvvhysdqP......ppdgkqaeqvetapppsaaapaa 53
                                       ++vD nG+v ys +       +    ++++v++ap+p++ ++++
  gene1192|gene1192|rna1192|rna1192 26 TCVDQNGTVRYSPATiasyppC--HPGQQSVQQAPQPQQQPQPQ 67
                                       7***********999****553..55555555444444443333 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.099
                            DUF4124  16 kWvDanGvv 24 
                                        ++vD+ G v
  gene1192|gene1192|rna1192|rna1192 141 QCVDSTGSV 149
                                        8******87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (285 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       752  (0.0419432); expected 358.6 (0.02)
Passed bias filter:                      255  (0.0142228); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2039.47
//
Query:       gene1193|gene1193|rna1193|rna1193  [L=84]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (84 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       495  (0.0276089); expected 358.6 (0.02)
Passed bias filter:                      219  (0.0122148); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.47
# Mc/sec: 542.68
//
Query:       gene1194|gene1194|rna1194|rna1194  [L=43]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (43 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       300  (0.0167327); expected 358.6 (0.02)
Passed bias filter:                      192  (0.0107089); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.28s 00:00:00.66 Elapsed: 00:00:00.44
# Mc/sec: 296.73
//
Query:       gene1195|gene1195|rna1195|rna1195  [L=69]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.2e-10   39.5   0.0    3.5e-10   39.4   0.0    1.0  1  LSM       LSM domain


Domain annotation for each model (and alignments):
>> LSM  LSM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.4   0.0   1.9e-14   3.5e-10       3      65 ..       5      67 ..       3      69 .] 0.93

  Alignments for each domain:
  == domain 1  score: 39.4 bits;  conditional E-value: 1.9e-14
                                       HHHTTTSEEEEEETTSEEEEEEEEEEETTSEEEEEEEEEEETTETEEEEEEEEEEEGGGEEEE CS
                                LSM  3 lkklinkkvtvelkngrelrGtLkgfDqfmNlvLedveetlkdkkekrklglvliRGnnivli 65
                                        k++i+k++ ++l+++  ++G L+++D ++Nl L+ v  + ++  e  +   +l++G+n+  i
  gene1195|gene1195|rna1195|rna1195  5 YKSFIRKRIKIKLNDNSSIEGDLISIDGYLNLALQHVLLYEEGIGEPFVFRSCLVKGSNVECI 67
                                       5899*************************************998899999*********9877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (69 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       259  (0.0144459); expected 358.6 (0.02)
Passed bias filter:                      238  (0.0132746); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 488.10
//
Query:       gene1196|gene1196|rna1196|rna1196  [L=881]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-42  145.8   1.6    1.2e-42  145.8   1.6    2.1  2  AAA_12         AAA domain
    2.2e-32  112.9   0.0    2.2e-32  112.9   0.0    3.5  4  AAA_11         AAA domain
    5.3e-14   52.4   0.0      7e-07   29.1   0.0    2.9  3  AAA_30         AAA domain
    1.8e-09   38.1   1.2    1.8e-08   34.8   0.0    3.0  2  AAA_19         AAA domain
    5.6e-09   36.2   0.0    1.6e-07   31.5   0.0    2.9  2  ResIII         Type III restriction enzyme, res subunit
    6.8e-05   22.2   0.2      0.023   13.9   0.0    2.7  2  PIF1           PIF1-like helicase
    0.00016   21.6   0.4      0.065   13.1   0.0    3.3  3  Helicase_RecD  Helicase
    0.00096   18.9   0.3     0.0044   16.8   0.0    2.3  2  UvrD_C_2       UvrD-like helicase C-terminal domain
     0.0018   17.8  15.1     0.0045   16.5   0.0    3.7  4  UvrD-helicase  UvrD/REP helicase N-terminal domain
  ------ inclusion threshold ------
      0.054   13.6   0.1      0.054   13.6   0.1    3.7  5  DUF87          Helicase HerA, central domain
      0.067   12.9   0.0       0.15   11.8   0.0    1.5  1  IstB_IS21      IstB-like ATP binding protein
       0.13   12.6   0.6       0.37   11.1   0.0    2.1  1  AAA_22         AAA domain
        0.2   12.0   0.0       0.36   11.2   0.0    1.3  1  AAA_16         AAA ATPase domain
       0.27   11.2  22.0        6.8    6.7   0.1    2.6  2  Mucin          Mucin-like glycoprotein
        7.6    4.7  35.6        8.4    4.5  16.1    3.2  3  CDC45          CDC45-like protein


Domain annotation for each model (and alignments):
>> AAA_12  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.6       4.7   5.6e+03      46      87 ..     447     481 ..     438     511 .. 0.50
   2 !  145.8   1.6     1e-45   1.2e-42      15     198 ..     681     849 ..     668     850 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 4.7
                             AAA_12  46 aesvkkreleaqealeepleplvfidvekseeekekkeksyi 87 
                                        +++ k++++    + ++  ++ +f+++ k+   ++   +s++
  gene1196|gene1196|rna1196|rna1196 447 KNKYKDSNK----DKNKNRNKHTFHKTTKKGIANK---TSIN 481
                                        333333332....3444445556666543333222...2222 PP

  == domain 2  score: 145.8 bits;  conditional E-value: 1e-45
                             AAA_12  15 ekvvlLdtqYRmhpeIsrfpsklfYkgkLkdaesvkkreleaqealeepleplvfidvekseeekekkeksyiNee 90 
                                         ++vlL++qYRm  ++  f+++ fY++ L++ + ++ +  +         ++l++i++ + +  ++k+  s+iN e
  gene1196|gene1196|rna1196|rna1196 681 LPTVLLNVQYRMPANLIAFSNRFFYRNMLRSVQPLSLQFFD--------HSNLMLINTAHRNFLEHKD-VSIINVE 747
                                        5679*************************998887776666........77899****9888777765.******* PP

                             AAA_12  91 EaelvvklvekllkkgseeerkkigvitpYraqvellkkklkekeeeksekeievntvdgfQGrekdviilslVRs 166
                                        E +lv+ +++ + ++++ +   +igvitpY+aq++ + + ++ +  ++   +++++tvd+fQG+e+dv+++s+VRs
  gene1196|gene1196|rna1196|rna1196 748 EGKLVIAILSFIDRTYNVR---SIGVITPYAAQAQHIMRSIDMSTFRA---HVQISTVDSFQGQERDVVVISMVRS 817
                                        *********9988888877...9*******************766654...49*********************** PP

                             AAA_12 167 nekkeigflkderrlNValTRAkskliivGnk 198
                                        n +keigf++d rr+NVa+TR ++ +++vG+k
  gene1196|gene1196|rna1196|rna1196 818 NWEKEIGFMDDVRRMNVAMTRCRMGMVMVGDK 849
                                        ******************************98 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.2       2.3   2.7e+03      53      82 ..       8      44 ..       3     132 .. 0.65
   2 ?   -1.1   1.0       1.1   1.3e+03     132     173 ..     256     297 ..     227     302 .. 0.47
   3 !  112.9   0.0   1.9e-35   2.2e-32       1     257 [.     304     553 ..     304     554 .. 0.74
   4 ?    0.1   8.2      0.46   5.5e+02     131     186 ..     611     666 ..     566     681 .. 0.47

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 2.3
                             AAA_11 53 akpriLvCapSNaAvDellerllr.......glldse 82
                                       + ++   C+  Na v+ +++ + +       + +ds+
  gene1196|gene1196|rna1196|rna1196  8 RRNKTKECKDKNAPVNTITAGVTNltlndgnNSKDSK 44
                                       5566667777777777777776665333333333333 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.1
                             AAA_11 132 eleklakelrafeeeeekeklkkskekskskleqerrklkke 173
                                        +++ ++++++++ ++  +++ + + + +k+k+++ +++++++
  gene1196|gene1196|rna1196|rna1196 256 SNNGINNSINNSINNGINNSININNNINKNKNKTHEKEINDA 297
                                        333333333333333333333333333333333333333333 PP

  == domain 3  score: 112.9 bits;  conditional E-value: 1.9e-35
                             AAA_11   1 klndsqreaiksalseseitliqGPPGtgKTktivellsqllsrrkseeeksakpriLvCapSNaAvDellerllr 76 
                                        kln+sq++a++ + s+ +   i GPPGtgKT t+++++++l          + ++r+LvCapSN A D+l    ++
  gene1196|gene1196|rna1196|rna1196 304 KLNASQNKALSMCTSSLK---ILGPPGTGKTYTLIHIIKKL---------LNDGKRVLVCAPSNLALDNLRRWFSE 367
                                        69*************999...9*******************.........799****************9877666 PP

                             AAA_11  77 glldsegekykpkivRvgnee..eriseavksvsleekvekrlekee......................kaqlake 128
                                                    ++vR+g ++  ++ ++ +++ + +++ +  ++++                       +      
  gene1196|gene1196|rna1196|rna1196 368 -----------DECVRIGGKSkfRNYEDIARKEKGRYSKDGDRSSRGsdrgsrgsdrgsrsgdrgryskD------ 426
                                        ...........89********8866677777777777777666554488899999999999996654331...... PP

                             AAA_11 129 iskeleklakelrafeeeeek.....eklkkskekskskleqerrklkkerkelskeleeaeesleeevldeaeiv 199
                                         ++ ++  +k  r +++++ k      +++k+k+ +k + +++ +k  + +++++++  +++++    +l++ ++v
  gene1196|gene1196|rna1196|rna1196 427 GDRGSKGSDKGSRYSNKDKDKnkykdSNKDKNKNRNKHTFHKTTKKGIANKTSINNNKGNIQRTD-YALLRNYDLV 501
                                        33333333333322222222221222445555555555555555555555555555555555554.889******* PP

                             AAA_11 200 ltTlsgagsklleklakkfdvviIDEAaqavEpstliPlrlgakkvvLvGDpkQLpat 257
                                        ++Tl +    +++++   +d+vi+DE++qa E + ++ +++g ++v+L+GDp QL ++
  gene1196|gene1196|rna1196|rna1196 502 FSTLYSL--YKIRDV---YDMVIVDECCQADEDELVMVFFKG-RNVILAGDPYQLGPV 553
                                        ****988..666666...8***********************.************986 PP

  == domain 4  score: 0.1 bits;  conditional E-value: 0.46
                             AAA_11 131 keleklakelrafeeeeekeklkkskekskskleqerrklkkerkelskeleeaee 186
                                        +++ ++ + +++++ + + ++ k++ + s++k++q+++k+k+erk+ ++++++  +
  gene1196|gene1196|rna1196|rna1196 611 DNNSNKGNNNKDNKGKTTTTNGKTTITASSDKNKQKKKKHKEERKTRNRRYKTMAQ 666
                                        22222222222222222224455555555555555555555555554444443332 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1   0.0   5.9e-10     7e-07       2      64 ..     305     363 ..     304     380 .. 0.87
   2 !   19.5   0.0   5.4e-07   0.00064      84     135 ..     509     557 ..     468     569 .. 0.79
   3 ?   -1.2   0.0       1.1   1.4e+03      48      94 ..     767     812 ..     752     851 .. 0.53

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 5.9e-10
                             AAA_30   2 lnaeQaaavealltsgdrvavltGpAGtGKttalkalreaweaaggrviglAptgkaAkvLae 64 
                                        lna+Q +a+  ++ts+     + Gp+GtGKt++l ++ + + ++g+rv+++Ap++ a ++L++
  gene1196|gene1196|rna1196|rna1196 305 LNASQNKALS-MCTSS---LKILGPPGTGKTYTLIHIIKKLLNDGKRVLVCAPSNLALDNLRR 363
                                        89*******6.55555...3488**************999999************99999985 PP

  == domain 2  score: 19.5 bits;  conditional E-value: 5.4e-07
                             AAA_30  84 arlepg.tllivDEagmvdtkqlaallkaaekagakvilvGDerQlasVeaGg 135
                                         ++++  +++ivDE   +d ++l  ++ + ++    vil+GD+ Ql++V++G+
  gene1196|gene1196|rna1196|rna1196 509 YKIRDVyDMVIVDECCQADEDELVMVFFKGRN----VILAGDPYQLGPVDEGH 557
                                        45666669************999888876555....***************97 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 1.1
                             AAA_30  48 rviglAptgkaAkvLaeelgieastiakllkrlkgrarlepgtlliv 94 
                                        ++ +++p +++A+ + +++++ + + +  +++ ++  + ++++++++
  gene1196|gene1196|rna1196|rna1196 767 SIGVITPYAAQAQHIMRSIDMSTFRAHVQISTVDS-FQGQERDVVVI 812
                                        55577888888888888877655555544444442.33344455554 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       5.8     7e+03      46      78 ..      84     133 ..      68     186 .. 0.63
   2 !   34.8   0.0   1.5e-11   1.8e-08       1     142 [.     309     551 ..     309     554 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 5.8
                             AAA_19  46 llvaftgrAakelrerlaalgaeatTiHrlal.................l 78 
                                         ++++ +     l+ +l  l+ + tT H l+                  +
  gene1196|gene1196|rna1196|rna1196  84 NIATYLKNRLPSLKASLPHLKSSSTTAHPLSQsplklllksnhynrsdrI 133
                                        55555555556667777777777999998877555555555555444441 PP

  == domain 2  score: 34.8 bits;  conditional E-value: 1.5e-11
                             AAA_19   1 qreavealkekvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerlaalgae........ 68 
                                        q++a+  +  + l ++++pGtGKT++l hi++ l++ g    +++l++a+ + A ++lr       ++        
  gene1196|gene1196|rna1196|rna1196 309 QNKAL-SMCTSSLKILGPPGTGKTYTLIHIIKKLLNDG----KRVLVCAPSNLALDNLRRWF---SEDecvriggk 376
                                        66777.67778899***********************9....89***************876...22235567777 PP

                             AAA_19  69 ............................................................................ 68 
                                                                                                                    
  gene1196|gene1196|rna1196|rna1196 377 skfrnyediarkekgryskdgdrssrgsdrgsrgsdrgsrsgdrgryskdgdrgskgsdkgsrysnkdkdknkykd 452
                                        8888888888888888888888888888888888888888888888888888888888888888888888888888 PP

                             AAA_19  69 ..........atTiHrlal.......................ldfddlltealelle.......eaeeekklqeee 104
                                                   +T+H+ +                        l             +          +  k+++ +
  gene1196|gene1196|rna1196|rna1196 453 snkdknknrnKHTFHKTTKkgianktsinnnkgniqrtdyalL-------------RnydlvfsTLYSLYKIRDVY 515
                                        8888888888777777765998888888766666555444443.............24444444222445677888 PP

                             AAA_19 105 .llivDEfqdvdelqyrLlkallgekkklllvGDpdQli 142
                                         ++ivDE  + de   +L+   + ++ +++l GDp Ql 
  gene1196|gene1196|rna1196|rna1196 516 dMVIVDECCQADED--ELVMVFF-KGRNVILAGDPYQLG 551
                                        8*******999965..5777777.6666********985 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.5   0.0   1.3e-10   1.6e-07      27     145 ..     320     527 ..     291     544 .. 0.77
   2 ?   -1.8   2.0       2.3   2.7e+03      22     120 ..     618     648 ..     591     667 .. 0.51

  Alignments for each domain:
  == domain 1  score: 31.5 bits;  conditional E-value: 1.3e-10
                                        EEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHG............................ CS
                             ResIII  27 glikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleef............................ 74 
                                        + i  + GtGKT++++++i++ll+ gk  ++l+ +p++  l+ +++ f                            
  gene1196|gene1196|rna1196|rna1196 320 LKILGPPGTGKTYTLIHIIKKLLNDGK--RVLVCAPSNLALDNLRRWFsedecvriggkskfrnyediarkekgry 393
                                        4577789*****************987..9***************99999999*********************** PP

                                        .................................................GGGTGG....GEEEESSS-B--..... CS
                             ResIII  75 .................................................kkflseaykeigkkvsgdkkka..kek 99 
                                                                                         k+  +++yk+ +k++++    +  k+ 
  gene1196|gene1196|rna1196|rna1196 394 skdgdrssrgsdrgsrgsdrgsrsgdrgryskdgdrgskgsdkgsrysnKDKDKNKYKDSNKDKNK----NrnKHT 465
                                        *********************************999999999864333322222222223332222....233345 PP

                                        ....-SEEEEEHHHHHHTH........................HHHTTT-SEEEEETGGGTT CS
                             ResIII 100 dstnkkilvttiqsldadseee................eeeseellrdrfdviiiDEaHrlg 145
                                        + +++k  +++  s+++++ +                 + +s  + rd +d++i+DE+  + 
  gene1196|gene1196|rna1196|rna1196 466 FHKTTKKGIANKTSINNNKGNIqrtdyallrnydlvfsTLYSLYKIRDVYDMVIVDECCQAD 527
                                        666777777777777777744466666666666666666666777777777******96655 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 2.3
                                        .TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG....GEEEESSS-B--. CS
                             ResIII  22 krdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkflseaykeigkkvsgdkkkak 97 
                                        +++k +  k +T  GKT + a+                                                      
  gene1196|gene1196|rna1196|rna1196 618 NNNKDNKGKTTTTNGKTTITASS----------------------------------------------------- 640
                                        23333333333333444333333..................................................... PP

                                        ......-SEEEEEHHHHHHTH.. CS
                             ResIII  98 ekdstnkkilvttiqsldadsee 120
                                                         ++++++
  gene1196|gene1196|rna1196|rna1196 641 ---------------DKNKQKKK 648
                                        ...............22222222 PP

>> PIF1  PIF1-like helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.0     2e-05     0.023      26      66 ..     321     361 ..     304     390 .. 0.85
   2 !    5.3   0.0    0.0077       9.2     135     158 ..     532     555 ..     511     564 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2e-05
                                        EEEESTTSSCHHHHHHHHHHCHCTCCCEEEEESSHHHHHCC CS
                               PIF1  26 FvtGsgGtgKtflwkallkklrsegkivlavAssGvAalll 66 
                                         + G  GtgKt+ + +++kkl + gk vl+ A s +A  +l
  gene1196|gene1196|rna1196|rna1196 321 KILGPPGTGKTYTLIHIIKKLLNDGKRVLVCAPSNLALDNL 361
                                        567999***************************99997666 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0077
                                        .-SCCCC-EEEEE--TTS-----S CS
                               PIF1 135 idkpFGGktvvlgGDfrQilPvie 158
                                        +   F G  v+l+GD  Q+ Pv e
  gene1196|gene1196|rna1196|rna1196 532 VMVFFKGRNVILAGDPYQLGPVDE 555
                                        667799***************975 PP

>> Helicase_RecD  Helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.0   5.4e-05     0.065       2      46 ..     322     365 ..     321     396 .. 0.82
   2 ?    4.3   0.0     0.026        32      37     105 ..     461     529 ..     454     545 .. 0.74
   3 ?   -1.1   0.3       1.3   1.5e+03      28      82 ..     633     694 ..     624     702 .. 0.55

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 5.4e-05
                      Helicase_RecD   2 ltAdRGRGKSaalGlalaaliaegksnilvtapskenvktlfefl 46 
                                        + + +G+GK+ +l  ++++l+++gk ++lv+aps+ ++++l + +
  gene1196|gene1196|rna1196|rna1196 322 ILGPPGTGKTYTLIHIIKKLLNDGK-RVLVCAPSNLALDNLRRWF 365
                                        67899******************98.9********9999998765 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.026
                      Helicase_RecD  37 envktlfeflakglealglkeeekkkkaekaelrvrkqrieyiapdellklkeqadllvvDEAAaiplp 105
                                        +n +t+ +  +kg+ + +  +++k + +++     r+  + + +  +l k ++  d+++vDE+ + + +
  gene1196|gene1196|rna1196|rna1196 461 RNKHTFHKTTKKGIANKTSINNNKGNIQRTDYALLRNYDLVFSTLYSLYKIRDVYDMVIVDECCQADED 529
                                        56677777777777766666667777777777777799**************999*******9876655 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 1.3
                      Helicase_RecD  28 nilvtapskenvktlfeflak.glealglkeeekkkkaekaelrvr......kqrieyiapd 82 
                                        +  +ta s +n ++  ++ ++ + ++ ++k+  + +k++++++  r        +++y +p 
  gene1196|gene1196|rna1196|rna1196 633 KTTITASSDKNKQKKKKHKEErKTRNRRYKTMAQVRKEINNCMFNRirlptvLLNVQYRMPA 694
                                        45677777777666666654313445555555555555545544444455555555555555 PP

>> UvrD_C_2  UvrD-like helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.1       2.7   3.3e+03      15      31 ..     515     529 ..     515     534 .. 0.65
   2 !   16.8   0.0   3.7e-06    0.0044       1      52 []     793     846 ..     793     846 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 2.7
                           UvrD_C_2  15 fpaVivfdpdlaaarmg 31 
                                        +++Viv++   ++a+++
  gene1196|gene1196|rna1196|rna1196 515 YDMVIVDE--CCQADED 529
                                        79****54..4544433 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 3.7e-06
                           UvrD_C_2   1 hayaltihkaQGsefpaVivfdpd..laaarmgelrrrlLYtavTRAreklilv 52 
                                        h+ ++t+  +QG+e ++V++  +   +  + ++++  r   +a+TR+r+  ++v
  gene1196|gene1196|rna1196|rna1196 793 HVQISTVDSFQGQERDVVVISMVRsnWEKEIGFMDDVRRMNVAMTRCRMGMVMV 846
                                        67789**************95554436666677889************988876 PP

>> UvrD-helicase  UvrD/REP helicase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.0   0.3       6.8   8.1e+03     192     200 ..     274     282 ..     223     301 .. 0.46
   2 !   16.5   0.0   3.8e-06    0.0045       1      50 [.     305     350 ..     305     368 .. 0.86
   3 !    5.3   1.5    0.0099        12     188     294 ..     445     549 ..     425     550 .. 0.69
   4 ?    4.1   0.6     0.022        27     150     223 ..     602     674 ..     577     804 .. 0.72

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 6.8
                                        TTCCTTHHC CS
                      UvrD-helicase 192 kqlspkelk 200
                                        + ++ +++ 
  gene1196|gene1196|rna1196|rna1196 274 NSININNNI 282
                                        111111111 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 3.8e-06
                                        SSHHHHHHHHS-SSEEEEEE-TTSSHHHHHHHHHHHHHHTSSSTGGGEEE CS
                      UvrD-helicase   1 lnpeqreaiaslggpilveAsAGsGKTfvlaerilrlikeeeiepdrilv 50 
                                        ln++q++a+   ++++ ++  +G+GKT++l++ i +l++ +    +r+lv
  gene1196|gene1196|rna1196|rna1196 305 LNASQNKALSMCTSSLKILGPPGTGKTYTLIHIIKKLLNDG----KRVLV 350
                                        6899*****************************99999988....55555 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.0099
                                        HHHHTTCCTTHHCHSSTSCSHHHHHHHHHHHHHHHHHHHHTC......EEHHHHHHHHHHHHHHCHHHHHHHHHHS CS
                      UvrD-helicase 188 kakekqlspkelkkafekasdlqkkiaeflkeyqeqkkeena......lDfsdllhallelleeneelaealrery 257
                                        k k+   + k+ +k  +k+++++ + +++ k + ++ +++n+       D++ l ++ l  ++     + ++r  y
  gene1196|gene1196|rna1196|rna1196 445 KDKN---KYKDSNKDKNKNRNKHTFHKTTKKGIANKTSINNNkgniqrTDYALLRNYDLVFSTL--YSLYKIRDVY 515
                                        2222...223333333688999999999999999999999997777666766665555554444..56789***** PP

                                        SEEEESSGGG-BHHHHHHHHHHHTTTTTEEEEE-GGG CS
                      UvrD-helicase 258 keiliDEyQDTnkiQyrilkllasgheelfmvGDpkQ 294
                                        +++ +DE  + ++   +++   ++g +++++ GDp Q
  gene1196|gene1196|rna1196|rna1196 516 DMVIVDECCQADED--ELVMVFFKG-RNVILAGDPYQ 549
                                        *******8777654..344444555.58999999988 PP

  == domain 4  score: 4.1 bits;  conditional E-value: 0.022
                                        HHHHHHHHHHHHHCCCCCHHHHCCCHHHHHCHHHHHHHHHHHTTCCTTHHCHSSTSCSHHHHHHHHHHHHHHHH CS
                      UvrD-helicase 150 dkkkleklikelsksrnikkeelslskskaeelrelvskakekqlspkelkkafekasdlqkkiaeflkeyqeq 223
                                        d++ +++ + + s + n++k ++   +   +++  + s  k+kq ++k++++  +  + ++k +a++ ke+ + 
  gene1196|gene1196|rna1196|rna1196 602 DEERVNEGSDNNSNKGNNNKDNKGKTTTTNGKTTITASSDKNKQKKKKHKEE-RKTRNRRYKTMAQVRKEINNC 674
                                        5555555666666677777777777777777777777777776666666555.236666777777777776554 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       7.3   8.7e+03     116     160 ..      84     131 ..      73     153 .. 0.55
   2 ?   -0.5   2.6      0.89   1.1e+03     152     205 ..     244     294 ..     216     313 .. 0.69
   3 ?   13.6   0.1   4.5e-05     0.054      20      57 ..     314     350 ..     311     351 .. 0.93
   4 ?   -2.9   0.6       4.8   5.8e+03     153     168 ..     472     487 ..     430     510 .. 0.46
   5 ?   -1.8   1.0       2.3   2.8e+03     134     178 ..     631     677 ..     605     692 .. 0.59

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 7.3
                              DUF87 116 vqrsvleealdqaka..keekeklssdepveklleelkkeke.elrkl 160
                                        +   +l++ l ++ka  +++k + ++++p+ ++  +l  +++ ++r++
  gene1196|gene1196|rna1196|rna1196  84 NIATYLKNRLPSLKAslPHLKSSSTTAHPLSQSPLKLLLKSNhYNRSD 131
                                        455566666666666666666666666666666666662222133332 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.89
                              DUF87 152 kekeelrklknqaiarlldkledllrkggsfsnsstdliallleklekegkiti 205
                                        +++ ++++++n++ +++++++++ +++g++    s ++++++ + ++k+++  i
  gene1196|gene1196|rna1196|rna1196 244 NMDGYNNNDNNSSNNGINNSINNSINNGINN---SININNNINKNKNKTHEKEI 294
                                        3446888888888999999999999999888...55555555444444444433 PP

  == domain 3  score: 13.6 bits;  conditional E-value: 4.5e-05
                              DUF87  20 klvtrHlAilgsTGsGKSntvavLleellekkgatili 57 
                                        +++t +l ilg  G+GK++t   ++++ll  +g ++l+
  gene1196|gene1196|rna1196|rna1196 314 SMCTSSLKILGPPGTGKTYTLIHIIKKLL-NDGKRVLV 350
                                        699**************************.88889987 PP

  == domain 4  score: -2.9 bits;  conditional E-value: 4.8
                              DUF87 153 ekeelrklknqaiarl 168
                                        +   ++ + n+ + ++
  gene1196|gene1196|rna1196|rna1196 472 KGIANKTSINNNKGNI 487
                                        1112333333444444 PP

  == domain 5  score: -1.8 bits;  conditional E-value: 2.3
                              DUF87 134 keklssdepveklleelk..kekeelrklknqaiarlldkledllrk 178
                                        ++k+++ ++  k +++ k  ke+++ r+ + +++a++ + +++ +++
  gene1196|gene1196|rna1196|rna1196 631 NGKTTITASSDKNKQKKKkhKEERKTRNRRYKTMAQVRKEINNCMFN 677
                                        33333333333333333333455566666666666666666665555 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00012      0.15      47      86 ..     317     356 ..     277     373 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00012
                          IstB_IS21  47 kenivllGpsGvGKshlaialgveavraglsvlfvrvedL 86 
                                          ++ +lGp+G+GK++  i + ++  ++g++vl +  ++L
  gene1196|gene1196|rna1196|rna1196 317 TSSLKILGPPGTGKTYTLIHIIKKLLNDGKRVLVCAPSNL 356
                                        457889*************************997766555 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00031      0.37       6      59 ..     318     364 ..     316     373 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00031
                             AAA_22   6 gilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllre 59 
                                        ++l + G++GtGKT++l  + ++l +       + + v+v++ps   +++l+r+
  gene1196|gene1196|rna1196|rna1196 318 SSLKILGPPGTGKTYTLIHIIKKLLN-------DGKRVLVCAPSNLALDNLRRW 364
                                        57899************999999986.......444455555554446666555 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0    0.0003      0.36      19     106 ..     312     394 ..     300     428 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0003
                             AAA_16  19 vrsgrpelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqlldeaesael 94 
                                        + s  ++++ + G++G+GK+  + ++ + l  dg  +l +        ++++ l + +  e+ +  ++ +++ ++ 
  gene1196|gene1196|rna1196|rna1196 312 ALSMCTSSLKILGPPGTGKTYTLIHIIKKLLNDGKRVLVCAPSN----LALDNLRRWF-SEDECVRIGGKSKFRNY 382
                                        5555668899*************999999999943333333333....4666677888.44777777777777777 PP

                             AAA_16  95 eawrekleeala 106
                                        e+ ++k +++++
  gene1196|gene1196|rna1196|rna1196 383 EDIARKEKGRYS 394
                                        777777777776 PP

>> Mucin  Mucin-like glycoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5  18.2     0.013        16      62      89 ..      41      79 ..       5     110 .. 0.53
   2 ?    6.7   0.1    0.0057       6.8      28      68 ..     608     646 ..     523     673 .. 0.66

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.013
                              Mucin 62 t...........tasttittkttkattttttttttttat 89
                                       +           t++ t tt+ t++  ttt++t ttt++
  gene1196|gene1196|rna1196|rna1196 41 KdskgkdsnndtTTTDTNTTTDTTTNPTTTNPTITTTTP 79
                                       022233322211111111111111222222222222222 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0057
                              Mucin  28 eGqsdaavveaaegqskltttttttkppttttttttastti 68 
                                        eG  ++++   ++ ++k +ttt  t+  tt t+++   + +
  gene1196|gene1196|rna1196|rna1196 608 EGSDNNSNKGNNNKDNKGKTTT--TNGKTTITASSDKNKQK 646
                                        3443333333333333333333..33333333333222222 PP

>> CDC45  CDC45-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0      0.01        12     136     246 ..     228     343 ..     196     345 .. 0.48
   2 ?    2.2   9.3     0.037        45     119     211 ..     389     482 ..     358     512 .. 0.40
   3 ?    4.5  16.1    0.0071       8.4     134     214 ..     580     669 ..     550     679 .. 0.30

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.01
                              CDC45 136 de....eeeeeddddeeeeeeeeedeedee..edeeeskkkrk...sksdeeee.......sddddersrkrrrse 195
                                        de            ++++e eee+ +  ++  +++++++ +++   s +    +        +++ ++++++++++
  gene1196|gene1196|rna1196|rna1196 228 DEgnvvG-------RSGDEGEEENMDGYNNndNNSSNNGINNSinnSIN----NginnsinINNNINKNKNKTHEK 292
                                        1112221.......11111111111111110011111111111111111....12333443333334444555555 PP

                              CDC45 196 psakklrrqlkkerrkyeavlekyysqgtsygesvsslmYsLaselgredn 246
                                        + +++++++  k++ ++++ l+   s+ ++ g + +   Y L++ +++  n
  gene1196|gene1196|rna1196|rna1196 293 EINDASQHNIPKLNASQNKALSMCTSSLKILGPPGTGKTYTLIHIIKKLLN 343
                                        455566666788888888899999999999999999999999998887655 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.037
                              CDC45 119 ereayealeeeeesdeedeeeeeeddddeeeeeeeeedeedeeedeeeskkkrksksdeeee..sddddersrkrr 192
                                        e+  y +  + +   +++ ++ ++  +++++  + ++d+++ ++   ++k +r s++d++++  +d++++++++r+
  gene1196|gene1196|rna1196|rna1196 389 EKGRYSKDGDRSSRGSDRGSRGSDRGSRSGDRGRYSKDGDRGSKG--SDKGSRYSNKDKDKNkyKDSNKDKNKNRN 462
                                        222333333333322222222212222222222222222222222..22222223333333322333344444444 PP

                              CDC45 193 rsepsakklrrq...lkkerrk 211
                                        +++   +k++++   +k+  ++
  gene1196|gene1196|rna1196|rna1196 463 KHT--FHKTTKKgiaNKTSINN 482
                                        444..22222222333333333 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.0071
                              CDC45 134 eedeeeeeeddddeeeeeeeeedeedeeedeeeskkkrksksdeeee.............sddddersrkrrrsep 196
                                        ++++ +e++++ dee+ +e + dee+ +e ++++++k ++++d+  +               ++d++++k+++++ 
  gene1196|gene1196|rna1196|rna1196 580 SDESGDEKDSSFDEERVNEGNGDEERVNEGSDNNSNKGNNNKDN--KgkttttngkttitA-SSDKNKQKKKKHK- 651
                                        11111111111111111111111111111111111111111111..111222233333421.2222222222222. PP

                              CDC45 197 sakklrrqlkkerrkyea 214
                                        +++k+r+++ k   + ++
  gene1196|gene1196|rna1196|rna1196 652 EERKTRNRRYKTMAQVRK 669
                                        233333333333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (881 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2316  (0.129176); expected 358.6 (0.02)
Passed bias filter:                      456  (0.0254337); expected 358.6 (0.02)
Passed Vit filter:                       108  (0.00602376); expected 17.9 (0.001)
Passed Fwd filter:                        49  (0.002733); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 1.08u 0.30s 00:00:01.38 Elapsed: 00:00:00.50
# Mc/sec: 5331.91
//
Query:       gene1197|gene1197|rna1197|rna1197  [L=505]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (505 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       771  (0.043003); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 3300.36
//
Query:       gene1198|gene1198|rna1198|rna1198  [L=221]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.7e-29  102.4   8.1      7e-26   91.1   4.2    2.0  2  HCO3_cotransp  HCO3- transporter family
  ------ inclusion threshold ------
       0.42   10.5   1.4        5.2    7.0   0.0    2.6  2  Bacillus_PapR  Bacillus PapR protein


Domain annotation for each model (and alignments):
>> HCO3_cotransp  HCO3- transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.1   4.2   7.8e-30     7e-26      58     186 ..       3     131 ..       1     144 [. 0.94
   2 !   13.8   0.3   2.2e-06     0.019     269     309 ..     151     191 ..     127     216 .. 0.70

  Alignments for each domain:
  == domain 1  score: 91.1 bits;  conditional E-value: 7.8e-30
                      HCO3_cotransp  58 eategaigvseslvsaaisgilfalfagqpllilgstgPllvfekilykfckelgldylslrvwiglwlalillil 133
                                        ++t++a gv e+l+s ai+g++f lf+gqpl+i+g tgP+ +f   +y++ + +g  y+ + +w+ lw +++ +++
  gene1198|gene1198|rna1198|rna1198   3 DKTDNAYGVNEVLMSSAIAGVVFGLFSGQPLCIVGVTGPISIFSYTVYELMTPRGTPYFPFMCWVYLWSMVFHILI 78 
                                        89************************************************************************** PP

                      HCO3_cotransp 134 vatdasalvkyitrfteeifallIslifiyealkkllkifkkyplnlklkell 186
                                        ++ +  +++++i+ +  +if ++I +++i + ++ l + f++  l + + +++
  gene1198|gene1198|rna1198|rna1198  79 AVGNYISFMRIISLYSCDIFGFFINMVYIQKGIQILSNQFDEVDLASGYASVM 131
                                        ************************************99999999888777544 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 2.2e-06
                      HCO3_cotransp 269 rflptkvRelisDfavliailvmvlvdvllgvetpklevpe 309
                                        ++++ ++R++++D++v+ ++++++ + +ll v+    ++ +
  gene1198|gene1198|rna1198|rna1198 151 HYFKPWMRKVFADYGVVASVIFFTGFYTLLVVSWTAQRLHD 191
                                        79**********************99998886544433333 PP

>> Bacillus_PapR  Bacillus PapR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.1     0.029   2.6e+02      15      26 ..      20      31 ..      14      34 .. 0.75
   2 ?    7.0   0.0   0.00058       5.2      26      39 ..     112     125 ..     110     129 .. 0.92

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.029
                      Bacillus_PapR 15 LaGvaFGvGqDq 26
                                       +aGv FG    q
  gene1198|gene1198|rna1198|rna1198 20 IAGVVFGLFSGQ 31
                                       7******85555 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.00058
                      Bacillus_PapR  26 qaLtnqqeevqLas 39 
                                        q L nq +ev Las
  gene1198|gene1198|rna1198|rna1198 112 QILSNQFDEVDLAS 125
                                        88***********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       609  (0.0339673); expected 358.6 (0.02)
Passed bias filter:                      244  (0.0136092); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1445.87
//
Query:       gene1199|gene1199|rna1199|rna1199  [L=258]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.6e-21   75.2   0.1    6.1e-21   74.8   0.1    1.1  1  HCO3_cotransp  HCO3- transporter family


Domain annotation for each model (and alignments):
>> HCO3_cotransp  HCO3- transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.8   0.1   3.4e-25   6.1e-21     354     487 ..       2     131 ..       1     136 [. 0.89

  Alignments for each domain:
  == domain 1  score: 74.8 bits;  conditional E-value: 3.4e-25
                      HCO3_cotransp 354 tavivnrkenkLkKgsgyhlDLlvvavlilvlsllGlPwlvaatvlsitHvnslkvesetsapGekpkilgvrEqR 429
                                        ++++ ++ke  L K +g+h+D+l+++++++v +l+G+P   + ++++++H +sl v+ +      + k l+v EqR
  gene1199|gene1199|rna1199|rna1199   2 SSLMCQSKEYPLTKPAGFHWDFLLLGITTGVAGLIGIPPPNGLIPQAPLHTDSLVVYDK------YGKKLSVVEQR 71 
                                        678999*************************************************9997......44558999*** PP

                      HCO3_cotransp 430 vtgllvfili..glsvlltpvlklIPmpVLyGvFLYmgvtsLkgiqlfdRilLllmpakh 487
                                        +t+ l   ++   +s  +  +l l+P +VL G+F+ m+vt L+g+ +++Ri+ ++ ++++
  gene1199|gene1199|rna1199|rna1199  72 LTNTLQGAMTfvMMSRPFLVLLGLVPQAVLSGLFFIMAVTGLHGNIVTNRIRYFFLDKEY 131
                                        ***997666500455558889********************************9998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       679  (0.0378716); expected 358.6 (0.02)
Passed bias filter:                      465  (0.0259356); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.31s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1639.27
//
Query:       gene12|gene12|rna12|rna12  [L=228]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.6e-34  118.5   0.0    3.1e-34  118.2   0.0    1.1  1  Thymidylate_kin  Thymidylate kinase
     0.0004   20.4   0.3    0.00081   19.4   0.1    1.7  2  AAA_14           AAA domain
    0.00064   20.3   0.0     0.0012   19.4   0.0    1.5  1  AAA_18           AAA domain
     0.0013   19.0   0.0     0.0073   16.6   0.0    2.1  1  AAA_22           AAA domain
     0.0073   15.8   0.0      0.014   14.9   0.0    1.4  1  KTI12            Chromatin associated protein KTI12
  ------ inclusion threshold ------
      0.026   14.4   0.0       0.05   13.5   0.0    1.6  1  dNK              Deoxynucleoside kinase
      0.035   14.3   0.0      0.056   13.7   0.0    1.4  1  AAA_28           AAA domain
       0.15   12.2   0.0       0.32   11.2   0.0    1.6  2  AAA_33           AAA domain


Domain annotation for each model (and alignments):
>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.2   0.0   1.4e-37   3.1e-34       1     184 [.      41     219 ..      41     220 .. 0.92

  Alignments for each domain:
  == domain 1  score: 118.2 bits;  conditional E-value: 1.4e-37
                                EEESTTSSHHHHHHHHHHHHHHTTE....EEEESSSTTSHHHHHHHHHHHTCS---HHHHHHHHHHHHHHTTHHHHHHHHHTT- CS
            Thymidylate_kin   1 iEGlDGaGKttqaellkerlkeegik...vvltrepggteiGekirelllkeeeleeqteallfaadriehleekikpalkqgk 81 
                                iEG+D++GK+t ++ l+++lk+++ +   v+++ ++++t iG++++ +l+ke +++++t +llf+a+r ++  e++k+ l++  
  gene12|gene12|rna12|rna12  41 IEGIDRSGKSTLCQGLVQKLKNSAVNsnpVLINYPDRTTAIGKLVNLYLKKELTFNKETSHLLFSANR-WEKNEEVKRLLQD-H 122
                                8********************99887779***************************************.*********6666.* PP

                                EEEEES-HHHHHHHHHTTTTTTCHHHHHHGGGTTSE-SEEEEEESSHHHHHTSCCTTSSTTTSHHHHHHHHHHHHHHHHHHHHT CS
            Thymidylate_kin  82 tvivdRylfSslaYqgakegvdldlvlslnedvllkPdltflldvdpevalkRlakrdeldeeeeeqldflrkvrerylelake 165
                                +vi+dRy +S++aY+ a +  d ++  +  + ++ +Pd+ ++ldv+p    +R  ++de    ++ +ld+++k+  ++++   e
  gene12|gene12|rna12|rna12 123 IVICDRYFYSGIAYSIALG-TDEKWAHEPDKGLV-EPDILVFLDVPPYRTSTRKDFGDE----IYDNLDIQEKIYLQLKKCCTE 200
                                ****************866.46666666666655.************************....99***********9*999999 PP

                                TSTEEEEETTS-HHHHHHH CS
            Thymidylate_kin 166 deriliidasksieevhee 184
                                 ++ ++++ +k i+e+ +e
  gene12|gene12|rna12|rna12 201 SKNCVVVNGQKGIDEIIDE 219
                                9999999999999998665 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.1   3.6e-07   0.00081       2      59 ..      36      91 ..      35     123 .. 0.73
   2 ?   -2.4   0.0       2.1   4.7e+03      83      90 ..     194     201 ..     173     220 .. 0.49

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 3.6e-07
                     AAA_14  2 rkilvitGaRrvGKTtllkqlikell..vkkesilyinldderdkkladpekllelilek 59
                               rk +vi+G+ r+GK+tl++ l+++l   + +++ + in  d +++      kl +l+l+k
  gene12|gene12|rna12|rna12 36 RKFIVIEGIDRSGKSTLCQGLVQKLKnsAVNSNPVLINYPDRTTAI-G---KLVNLYLKK 91
                               799*******************999988666777777777655432.2...234555554 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 2.1
                     AAA_14  83 lkslvdeg 90 
                                lk+++ e+
  gene12|gene12|rna12|rna12 194 LKKCCTES 201
                                22222222 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   5.2e-07    0.0012       1      35 [.      39      74 ..      39     146 .. 0.69

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 5.2e-07
                     AAA_18  1 IlltGtpGvGKttlakeLskrl.gfgvnlrdvaken 35
                               I++ G+ ++GK+tl++ L ++l ++ vn++ v+ + 
  gene12|gene12|rna12|rna12 39 IVIEGIDRSGKSTLCQGLVQKLkNSAVNSNPVLINY 74
                               89****************999955577777776654 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   3.3e-06    0.0073       3      87 ..      34     124 ..      31     207 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 3.3e-06
                     AAA_22   3 ktagilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst....sskdllrellralglelka..........er 72 
                                ++++++v+ G   +GK+tl++ l+++l++ a     ++  v+++ p  t    ++ +l+ +    ++    +          ++
  gene12|gene12|rna12|rna12  34 EKRKFIVIEGIDRSGKSTLCQGLVQKLKNSAV----NSNPVLINYPDRTtaigKLVNLYLKKELTFN----KetshllfsanRW 109
                                4899***********************64433....3333356666555222222222222222222....1223355555555 PP

                     AAA_22  73 lsseellealeqalr 87 
                                 ++ee+ ++l++++ 
  gene12|gene12|rna12|rna12 110 EKNEEVKRLLQDHIV 124
                                666666666666655 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   6.3e-06     0.014       4      81 ..      39     131 ..      37     138 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 6.3e-06
                                EEEE--TTSSHHHHHHHHHHHHHH..................TT--EEEE-THHHH.TTSS.S--GGGH...HHHHHHHHHHHH CS
                      KTI12   4 vvltGlPssGKstrakeLakalee..................ekrsvvviddeslgiekds.ykdsake...kalRsslrsavk 65 
                                +v+ G+  sGKst+ + L ++l++                          +   l ++k+  ++++ +     a R + +++vk
  gene12|gene12|rna12|rna12  39 IVIEGIDRSGKSTLCQGLVQKLKNsavnsnpvlinypdrttaI------GKLVNLYLKKELtFNKETSHllfSANRWEKNEEVK 116
                                89**********************9987777777764433331......33222223333223333322112567888899999 PP

                                HHHTT.SEEEE-S--- CS
                      KTI12  66 rdLskekvVIvDslny 81 
                                r L+  ++VI+D   y
  gene12|gene12|rna12|rna12 117 RLLQD-HIVICDRYFY 131
                                98865.9*****8765 PP

>> dNK  Deoxynucleoside kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   2.2e-05      0.05       1     133 [.      39     167 ..      39     196 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.2e-05
                                EEEEESTTSSHHHHHHHHHCCST.CEEEE-HHHHCCSSSS...HHHHHHHHSHHHHHHHHHHHHHHHHHHHHHCHHSSS-EEEE CS
                        dNK   1 ivveGnIgaGKstlvklLskklg.vkvfeEpvdkwtnvqk...nlLekfYkdpsrwsfalqtyvllsrlkqqlealatkqvvvl 80 
                                iv+eG   +GKstl + L +kl+   v ++pv  + ++++     L ++Y + ++++f+ +t  ll   ++ ++  ++ +  ++
  gene12|gene12|rna12|rna12  39 IVIEGIDRSGKSTLCQGLVQKLKnSAVNSNPVLINYPDRTtaiGKLVNLYLK-KELTFNKETSHLLFSANRWEKN-EEVKRLLQ 120
                                89**************999999867788889999989998455333333432.4466666666666655555444.45555555 PP

                                ES-HHHHHHTHHHHHHHTTSS-HHHHHHHHHHHHHHHHHCCH-SEEEEEE--H CS
                        dNK  81 eRsiysdryiFakalaekgtlseeelkiykelldnlleelakpdlliYLkasl 133
                                +  +  dry +      +g++   +l + +++ +   + l +pd+l++L++++
  gene12|gene12|rna12|rna12 121 DHIVICDRYFY------SGIAYSIALGTDEKWAHEPDKGLVEPDILVFLDVPP 167
                                55555555333......344444455555555555555555677777777666 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   2.5e-05     0.056       2     100 ..      39     147 ..      38     208 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.5e-05
                     AAA_28   2 ivitGgestGKTtlleaLaar.................gypvvpEaareileeklakgedalpwvedllafaervleeqleeea 68 
                                ivi G   +GK+tl++ L ++                  ++ +   +  +l+++l ++++        l f + + e+   e +
  gene12|gene12|rna12|rna12  39 IVIEGIDRSGKSTLCQGLVQKlknsavnsnpvlinypdRTTAIGKLVNLYLKKELTFNKE-----TSHLLFSANRWEKNE-EVK 116
                                889999999******999955555566666677733433335577777777777766665.....355788888776554.444 PP

                     AAA_28  69 aaaankvlfcDrglldtlaYarayggeaeael 100
                                +  ++ +++cDr +   +aY+ a+g + e+  
  gene12|gene12|rna12|rna12 117 RLLQDHIVICDRYFYSGIAYSIALGTD-EKWA 147
                                4479*****************999988.5543 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00014      0.32       2      32 ..      39      69 ..      38     130 .. 0.64
   2 ?   -2.2   0.0       1.9   4.2e+03      28      77 ..     163     208 ..     152     210 .. 0.54

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00014
                     AAA_33  2 vllvGlpGsGKstlaerllkklgavllssdt 32
                               +++ G   sGKstl ++l++kl+   ++s+ 
  gene12|gene12|rna12|rna12 39 IVIEGIDRSGKSTLCQGLVQKLKNSAVNSNP 69
                               57788999***************55555543 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.9
                     AAA_33  28 lssdtlrrrlfgtdqqsktdytrvldrlyqilnelarkalsagrnvilda 77 
                                l+ + +r+  +++  + + d  ++ +++y +l    +k++++ +n+++ +
  gene12|gene12|rna12|rna12 163 LDVPPYRTSTRKDFGDEIYDNLDIQEKIYLQL----KKCCTESKNCVVVN 208
                                55555555555444445555555555555444....55556667776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (228 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       673  (0.037537); expected 358.6 (0.02)
Passed bias filter:                      452  (0.0252106); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 1473.79
//
Query:       gene120|gene120|rna120|rna120  [L=1189]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1189 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       932  (0.0519828); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.81u 0.27s 00:00:01.08 Elapsed: 00:00:00.44
# Mc/sec: 8058.09
//
Query:       gene1200|gene1200|rna1200|rna1200  [L=143]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-19   70.4   0.1    1.6e-19   70.2   0.1    1.0  1  adh_short      short chain dehydrogenase
    4.6e-14   52.6   0.0      6e-14   52.2   0.0    1.0  1  adh_short_C2   Enoyl-(Acyl carrier protein) reductase
    0.00029   20.8   0.0    0.00038   20.4   0.0    1.3  1  KR             KR domain
  ------ inclusion threshold ------
      0.025   15.0   0.0      0.031   14.7   0.0    1.2  1  NAD_binding_7  Putative NAD(P)-binding


Domain annotation for each model (and alignments):
>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.2   0.1   3.5e-23   1.6e-19       1     124 [.       8     141 ..       8     142 .. 0.91

  Alignments for each domain:
  == domain 1  score: 70.2 bits;  conditional E-value: 3.5e-23
                                        SEEEEESTTSHHHHHHHHHHHHTT-EEEE.EESCHHHHHHHHHHHHHT......TSEEEEEE-TTTSHHHHHHHHH CS
                          adh_short   1 kvvlvtGassGIGraiakelakeGakvvv.vdrseekleevakelkee......gakalaiqvDvtdreevealve 69 
                                        kvv+vtG+ sGIG+ +  +l+++Gakvvv    +e+++  v+++++e         ++ ++++++ ++++  +lv+
  gene1200|gene1200|rna1200|rna1200   8 KVVVVTGGLSGIGLSTTIKLLRQGAKVVVgDLAHEQEIDFVVSKINESapdsnvHHNLRFLRTNIHSWQDNVNLVD 83 
                                        89***************************54567788999*****998775545556899**************** PP

                                        HHHHHHSSESEEEE---S...S--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHH CS
                          adh_short  70 kavkklgkldvLvnNAGi...tgsgpfselseeewervievNltgvflltravlpaml 124
                                         a ++++++d +v+NA++   +g g+  e + +e+++v++vNl g+f   ++++++++
  gene1200|gene1200|rna1200|rna1200  84 FALDEYKGIDYVVANAAMirrNGEGASDEPTLDEFNEVVNVNLGGTFAFNKLCINYWK 141
                                        ******************99988999999999****************9999998875 PP

>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.2   0.0   1.3e-17     6e-14       3     117 ..      16     140 ..      13     142 .. 0.88

  Alignments for each domain:
  == domain 1  score: 52.2 bits;  conditional E-value: 1.3e-17
                                        TTSHHHHHHHHHHHTT-EEEEEESSGGH..HHHHHHHHHHTTSE.E......EE--TTSHHHHHHHHHHHHHHHSS CS
                       adh_short_C2   3 asgIGraiAkalaeeGaevvltdlneea..kkrveelaeelgae.v......lecDVtdeeqvealveevvekfgk 69 
                                         sgIG  +  +l ++Ga+vv+ dl  e+  +  v ++ e+ + + v      l++++ + ++  +lv+ + +++++
  gene1200|gene1200|rna1200|rna1200  16 LSGIGLSTTIKLLRQGAKVVVGDLAHEQeiDFVVSKINESAPDSnVhhnlrfLRTNIHSWQDNVNLVDFALDEYKG 91 
                                        59**********************9999776778888888774434455677************************ PP

                                        EEEEEE-----EG.CSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHHHC CS
                       adh_short_C2  70 lDilvnnagiapk.lkgpfletsreefdraldvnlyslfllakaalplm 117
                                        +D++v na++ ++  +g   e + +ef+++++vnl ++f++ k ++++ 
  gene1200|gene1200|rna1200|rna1200  92 IDYVVANAAMIRRnGEGASDEPTLDEFNEVVNVNLGGTFAFNKLCINYW 140
                                        *************888888889*******************99988765 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   8.5e-08   0.00038       3     123 ..      10     136 ..       8     143 .] 0.74

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 8.5e-08
                                        EEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHT.T-..EEEE----TT-HHHHHHHHHHH CS
                                 KR   3 ylitGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaeleal.ga..evevvaaDvsdkdavealleei 75 
                                        +++tGGl g+Gl+++  l+++ga+ +v    ++++ +   ++i+e +   ++  + ++++  + + ++  +l++ +
  gene1200|gene1200|rna1200|rna1200  10 VVVTGGLSGIGLSTTIKLLRQGAKVVVGDLAHEQEIDFVVSKINESAPDsNVhhNLRFLRTNIHSWQDNVNLVDFA 85 
                                        79*********************97764333323333333444444332132558889999999999999999999 PP

                                        HHHSS---EEEE------...---TTT--HHHHHHHHTTTTHHHHHHHHHT CS
                                 KR  76 kaeeppikGvihaAgvlr...dklleemtaedleqvlapKvkGawnLhell 123
                                         +e + i  v+  A ++r   +++ +e t +++++v++  + G+   ++l+
  gene1200|gene1200|rna1200|rna1200  86 LDEYKGIDYVVANAAMIRrngEGASDEPTLDEFNEVVNVNLGGTFAFNKLC 136
                                        999999999987666665344567889999999999999999988877776 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0     7e-06     0.031       7      73 ..       7      90 ..       1     112 [. 0.71

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 7e-06
                      NAD_binding_7  7 gkkvlvvGg.GevAarkvrklleagakvtvvapevkeele................elvklaeeelekdlegadlvia 67
                                       +k v+v Gg   ++++   kll++gakv+v + + ++e++                 ++++ +++++++ +++ lv  
  gene1200|gene1200|rna1200|rna1200  7 NKVVVVTGGlSGIGLSTTIKLLRQGAKVVVGDLAHEQEIDfvvskinesapdsnvhHNLRFLRTNIHSWQDNVNLVDF 84
                                       5555555554579*****************555543444455555555666655555566678889999999999988 PP

                      NAD_binding_7 68 atddre 73
                                       a d+ +
  gene1200|gene1200|rna1200|rna1200 85 ALDEYK 90
                                       888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       420  (0.0234257); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 969.58
//
Query:       gene1201|gene1201|rna1201|rna1201  [L=111]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.5e-28   99.9   0.0    1.6e-28   99.9   0.0    1.0  1  adh_short_C2  Enoyl-(Acyl carrier protein) reductase
    2.2e-08   33.8   0.0    2.7e-08   33.5   0.0    1.1  1  adh_short     short chain dehydrogenase


Domain annotation for each model (and alignments):
>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.9   0.0   1.8e-32   1.6e-28     129     234 .]       5     109 ..       1     109 [. 0.92

  Alignments for each domain:
  == domain 1  score: 99.9 bits;  conditional E-value: 1.8e-32
                                        GGGTSBSTTTTHHHHHHHHHHHHHHHHHHHHGGGTEEEEEEEE--BHCTGGGGSTTHHHHHHHHHHHSTTSS-B-H CS
                       adh_short_C2 129 vgaervvpnynaygaaKaalealtrylAvelgpkgiRvNavspgpikTlaasgikgfdelleelearaplgrlgtp 204
                                        +g +++ pn    + +K +++ lt+++A  +++ giRvN v+pg+ikT++ + + g+ + ++++ + +p++++g+ 
  gene1201|gene1201|rna1201|rna1201   5 FGHKVTDPNLVDLNYSKSGIHTLTKSMALGCASLGIRVNEVCPGFIKTPMLETVLGS-DQYDHIVNGIPMQKIGDG 79 
                                        455566788889999***************************************965.5689999*********** PP

                                        HHHHHHHHHHCSGGGTT--SEEEEESTTGG CS
                       adh_short_C2 205 eevaeaalfLasdeasyitGqtlvvDgGlt 234
                                        ++va+a++fL+sd+a+yitG+ +vvDgG++
  gene1201|gene1201|rna1201|rna1201  80 DDVANAICFLLSDDARYITGASVVVDGGYS 109
                                        ****************************96 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.5   0.0     3e-12   2.7e-08     151     189 ..      19      57 ..       1      62 [. 0.84

  Alignments for each domain:
  == domain 1  score: 33.5 bits;  conditional E-value: 3e-12
                                        HHHHHHHHHHHHHHHHHGGGTEEEEEEEESSBSSHHHHH CS
                          adh_short 151 AsKaavagltrslakelaptgirvnavaPGlvdTdmake 189
                                         sK +++ lt+s+a   a+ girvn v+PG+++T+m ++
  gene1201|gene1201|rna1201|rna1201  19 YSKSGIHTLTKSMALGCASLGIRVNEVCPGFIKTPMLET 57 
                                        59**********************************876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (111 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       206  (0.0114898); expected 358.6 (0.02)
Passed bias filter:                      191  (0.0106531); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.46
# Mc/sec: 732.59
//
Query:       gene1202|gene1202|rna1202|rna1202  [L=131]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.6e-12   46.6   0.0    4.3e-12   46.4   0.0    1.1  1  ResIII     Type III restriction enzyme, res subunit
    0.00012   21.9   0.1    0.00018   21.3   0.1    1.2  1  DEAD       DEAD/DEAH box helicase
    0.00029   20.3   0.0    0.00038   19.9   0.0    1.3  1  TniB       Bacterial TniB protein
     0.0051   16.5   0.0     0.0056   16.4   0.0    1.1  1  SWI2_SNF2  SWI2/SNF2 ATPase


Domain annotation for each model (and alignments):
>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.4   0.0   9.6e-16   4.3e-12      59     169 ..       2     104 ..       1     106 [. 0.90

  Alignments for each domain:
  == domain 1  score: 46.4 bits;  conditional E-value: 9.6e-16
                                        EEESSHHHHHHHHHHGGGGTGG....GEEEESSS-B--.......-SEEEEEHHHHHHTH........HHHTTT-S CS
                             ResIII  59 flvprkslleqtleefkkflseaykeigkkvsgdkkkakekdstnkkilvttiqsldadseeeeeeseellrdrfd 134
                                        +l+++++l++q+ ++++ + +  +  +  +v+ +k ka    s +++++v+++ sl +++       e++++ +f+
  gene1202|gene1202|rna1202|rna1202   2 VLAHTEELIDQAVKKIRLMNPGLK--V--EVEMRKLKA----SPDADVVVASVPSLVRRR-----RFEKFDPMEFK 64 
                                        89*******************974..4..555555555....55****************.....899******** PP

                                        EEEEETGGGTTS.TTTHHHHHT---......SEEEEEESS- CS
                             ResIII 135 viiiDEaHrlgakkswreilekfke......avllglTATp 169
                                         iiiDE+H++ a  ++r++l++fk+        ++g+TAT+
  gene1202|gene1202|rna1202|rna1202  65 SIIIDECHHAPA-ITYRKVLNHFKAldsnltISVIGFTATL 104
                                        ************.**********9999999999*******7 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.1     4e-08   0.00018      55     170 ..       5     105 ..       1     111 [. 0.73

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 4e-08
                                        SSHHHHHHHHHHHHHHTTTSTSEEEEEETTSSHHHHHHHHHTT..CSEEEEEHHHHHHHHHCTSSHCTTEEEEEEE CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               DEAD  55 PtreLaeqtlnnlkkfkkyidlrvlliiggvaardqlskldng..vdivvgtpgrlddllstgklnlsqvrflVlD 128
                                         t+eL+ q +++++ +             g + + +++kl+++  +d+vv+    l++  + +k++  +++ +++D
  gene1202|gene1202|rna1202|rna1202   5 HTEELIDQAVKKIRLMNP-----------GLKVEVEMRKLKASpdADVVVASVPSLVRRRRFEKFDPMEFKSIIID 69 
                                        455555555555544444...........44445556666544559*****999999977778888999999**** PP

                                        THHHHHHTTTHHHHHHHHHHSHHHCTTSTTTSEEEEEESSBS CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               DEAD 129 EadrlldqgfsdfinrilnqlpqitcdgklqrqvivlSATlp 170
                                        E++      +++ +n+ +++l     d +l+  vi ++ATl 
  gene1202|gene1202|rna1202|rna1202  70 ECHHAPAITYRKVLNH-FKAL-----DSNLTISVIGFTATLV 105
                                        ********99988888.7777.....5567778*******95 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   8.5e-08   0.00038     109     160 ..      52     100 ..      32     111 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 8.5e-08
                               TniB 109 qqvlrllrelkvrvLiiDEihnllagsarkqreflnalksLgnelkipivlv 160
                                        ++  + ++ ++ + +iiDE h++ a +    r++ln  k L  +l i+++++
  gene1202|gene1202|rna1202|rna1202  52 RRRFEKFDPMEFKSIIIDECHHAPAIT---YRKVLNHFKALDSNLTISVIGF 100
                                        556677888999**********99655...578*****************97 PP

>> SWI2_SNF2  SWI2/SNF2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   1.2e-06    0.0056      86     175 ..      30     122 ..       1     130 [. 0.65

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.2e-06
                          SWI2_SNF2  86 LkellekesekiifttiqKfeeeekeklevlsereniivlvDEaHRsqygelakklr...kalpn..aafigFTGT 156
                                        +++l ++ +++++++ +  + +++  ++e+++  e   +++DE+H     +++k l+   +   n   ++igFT T
  gene1202|gene1202|rna1202|rna1202  30 MRKLKASPDADVVVASVPSLVRRR--RFEKFDPMEFKSIIIDECHHAPAITYRKVLNhfkALDSNltISVIGFTAT 103
                                        333333447788888888876543..4677777776779*******977766555542204444422578****** PP

                          SWI2_SNF2 157 PilkkdkktkevFgeyidk 175
                                         +  ++++  ++F+e++ +
  gene1202|gene1202|rna1202|rna1202 104 LVRLDKQSLGHIFDEVVYE 122
                                        9999999999999998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       554  (0.0308997); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 984.43
//
Query:       gene1203|gene1203|rna1203|rna1203  [L=61]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       381  (0.0212505); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.27s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 442.67
//
Query:       gene1204|gene1204|rna1204|rna1204  [L=152]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.014   14.8   0.0       0.02   14.2   0.0    1.2  1  DNA_pol_E_B  DNA polymerase alpha/epsilon subunit B


Domain annotation for each model (and alignments):
>> DNA_pol_E_B  DNA polymerase alpha/epsilon subunit B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   1.1e-06      0.02     166     211 .]      14      88 ..      10      88 .. 0.97

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.1e-06
                                        HHHHHTBS---SS..............................--B-GGGGGGGB-GGG---SEEE---SS--EEE CS
                        DNA_pol_E_B 166 tildqrhlaPlap..............................tlrpvswdkddalvleplPdvlvlpdelpeFak 211
                                        ++++qr+++P+ p                              + +  +++ +++l  ++lPdvl+lp+el+ Fak
  gene1204|gene1204|rna1204|rna1204  14 HLFEQRRYYPIMPgsiaktheqdiselsngaagekltgvsvggSSLETPYLGLTELG-NSLPDVLILPSELKVFAK 88 
                                        7899***************************************************99.*************99985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       230  (0.0128284); expected 358.6 (0.02)
Passed bias filter:                      216  (0.0120475); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 1171.45
//
Query:       gene1205|gene1205|rna1205|rna1205  [L=47]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.031   13.6   0.0      0.031   13.6   0.0    1.0  1  DNA_pol_E_B  DNA polymerase alpha/epsilon subunit B


Domain annotation for each model (and alignments):
>> DNA_pol_E_B  DNA polymerase alpha/epsilon subunit B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   1.7e-06     0.031      33      65 ..       3      37 ..       1      47 [] 0.75

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.7e-06
                                       -SEEEEES-SSBTTSHHHHHT---..S--SSHHHH CS
                        DNA_pol_E_B 33 pdvlilaGnfvdaahkaiasskvs..tdekkenfd 65
                                       p ++il G+f+d ++k+ ++++++  +d++ +n d
  gene1205|gene1205|rna1205|rna1205  3 PNLVILNGPFIDLSNKEVEEGNFNfpKDQQPKNLD 37
                                       899*******************9888444433333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (47 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       222  (0.0123822); expected 358.6 (0.02)
Passed bias filter:                      198  (0.0110436); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.27s 00:00:00.62 Elapsed: 00:00:00.43
# Mc/sec: 330.93
//
Query:       gene1206|gene1206|rna1206|rna1206  [L=74]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (74 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       777  (0.0433376); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 524.41
//
Query:       gene1207|gene1207|rna1207|rna1207  [L=1435]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.4e-51  175.3   0.7    1.4e-51  175.3   0.7    2.1  3  SNF2_N      SNF2 family N-terminal domain
    4.8e-18   65.5   0.1    5.4e-17   62.1   0.0    2.7  2  Helicase_C  Helicase conserved C-terminal domain
    1.7e-10   40.7   2.5    0.00073   19.4   0.2    3.6  3  Chromo      Chromo (CHRromatin Organisation MOdifier) domain
    6.3e-08   32.6   0.0    3.2e-07   30.3   0.0    2.2  2  DEAD        DEAD/DEAH box helicase
    8.8e-07   29.1   0.2    4.7e-06   26.7   0.0    2.4  2  ResIII      Type III restriction enzyme, res subunit
    6.4e-06   25.5   0.1    3.2e-05   23.2   0.1    2.2  1  HDA2-3      Class II histone deacetylase complex subunits 2 a


Domain annotation for each model (and alignments):
>> SNF2_N  SNF2 family N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.19   5.8e+02       1      13 [.     392     404 ..     392     408 .. 0.88
   2 !  175.3   0.7   4.6e-55   1.4e-51      55     350 .]     407     662 ..     401     662 .. 0.84
   3 ?   -3.0   0.0      0.77   2.3e+03     231     265 ..    1098    1132 ..    1090    1156 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.19
                                        HHHHHHHHH.... CS
                                        xxxxxxxxxxxxx RF
                             SNF2_N   1 yQkeavkwmlkRe 13 
                                        yQ e+++w+l+R 
  gene1207|gene1207|rna1207|rna1207 392 YQMEGLNWLLNRW 404
                                        9********9995 PP

  == domain 2  score: 175.3 bits;  conditional E-value: 4.6e-55
                                        T--EEE---TTS--HHHHHHHHH...HHTTTS---.......S-EEEE--HHHHHHHHHHHHHH-TTS-EEE--SS CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SNF2_N  55 vrGGiLaDemGLGKTvqvlalilaqrakeekdkekkrkdtlagptLivvPaslldqWeneierhvsssalrvlvyg 130
                                         +G+i+aDemGLGKTvq+++++   +  e+           + p+Liv+P s+l +We+e+++++      +l y+
  gene1207|gene1207|rna1207|rna1207 407 KQGCIMADEMGLGKTVQTVCFVN--KVFET---------GYQHPVLIVAPLSTLIHWEREFRTWTDLR---ILLYH 468
                                        57*********************..22223.........34579********************9755...56666 PP

                                        HHHH.-----------------EEEE-HHHHHHHT......TTS-S-S-SEEEES-GGGT--TTSHHHHHHHH--- CS
                                        xxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SNF2_N 131 gqkk.mkkkntkvapklladydvvittYdvlsreaelqkkrsvlkqvewkrvvlDEghtlknstskaaeavskLst 205
                                        g++  ++   +  + +    +dv+ittY+++ +        ++l + +    v DE+h+lkns+ska + + +Ls 
  gene1207|gene1207|rna1207|rna1207 469 GNNVaRDLIYDYEFYNDGLLFDVLITTYEMVMSGM------KHL-SFNFGIGVFDEAHRLKNSHSKAFQSLISLSF 537
                                        665214444445555555668***********555......444.456667799********************** PP

                                        S-EEEE-S--SSS-HHHHHHHHHHH-TTTT--HHHHHHHTHHHHHHHHHHHHHHHHTT-STTEE---GGGT--S-- CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SNF2_N 206 snrwiltGTPiqnsledlygLlkfLreepfgekqtfdkllqrpieaqaekgrsrLlqllqrlmlrrakkdveknlP 281
                                        +++++l+GTP+qn+l++l++Ll+fL + + ++   f + ++ +      + + rL +ll+++mlrr+k+dv +++P
  gene1207|gene1207|rna1207|rna1207 538 NHKILLSGTPLQNNLTELWSLLHFLDPIKNESLSYFLESYKLEKS----EDVDRLKTLLKPVMLRRMKDDV-EKIP 608
                                        ************************************999888887....99********************.99** PP

                                        -EEEEEEEEE--HHHHHHHH....................HHHHHH-HHH-HHHHHHHHHHHHH---XX CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SNF2_N 282 pkteeiiflklskverksYnrllevlrkkalakllkrseaalkssskskekilelllelrqacnhpqlv 350
                                         k+e i+ ++l+  ++++Y              + +++   ++++s    ++l+ ++elr++c hp+lv
  gene1207|gene1207|rna1207|rna1207 609 IKEETIVEVELTMIQKQFYR------------AIIEKNLSIFEKES---PNLLNVMMELRKCCIHPYLV 662
                                        ********************............33333333444444...569**************986 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 0.77
                                         -TTTT--HHHHHHHTHHHHHHHHHHHHHHHHTT-S CS
                                         xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SNF2_N  231 reepfgekqtfdkllqrpieaqaekgrsrLlqllq 265 
                                          ee f++ +++++ll++   a++e +++rL+  l 
  gene1207|gene1207|rna1207|rna1207 1098 VEEEFDDPDFWQNLLSKRKDAENEMKIKRLIRRLG 1132
                                         578899999*********99999999999988776 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.1   0.0   1.8e-20   5.4e-17       4     111 .]     885     995 ..     882     995 .. 0.88
   2 ?   -0.8   0.0      0.62   1.8e+03      38      77 ..    1022    1061 ..     999    1062 .. 0.77

  Alignments for each domain:
  == domain 1  score: 62.1 bits;  conditional E-value: 1.8e-20
                                        HHHHHHHHHTTTTSEEEEEESSHHHHHH.HHHHHHHTTSTEEEESTTSTHHHHHHHHHHHH...TTSSSEEEESGG CS
                         Helicase_C   4 eallellkleeeggkilifvntidrlek.vklllekkgikvavlhgelpqnereeileqfn...kgesdvLiatdv 75 
                                          l +ll + + ++k+lif++ ++ l+   ++l + k +k+ +++g    + r++++++f    ++++ +L++t++
  gene1207|gene1207|rna1207|rna1207 885 VLLDKLLAKLKGEHKVLIFSQMTRCLDLlSDYL-QYKRYKYERIDGGVRGECRQAAIDRFSsaeSDSFVFLLCTRA 959
                                        5666777777999***********997756666.6668**********************96644556699***** PP

                                        GTSSSTSTTESEEEESSSSSSHHHHHHHHTTSSSTT CS
                         Helicase_C  76 aerGidipkvnlVinfdlprnvtsyiqriGRtgRag 111
                                        +++Gi+++++++V++fd ++n+++  q+  R++R+g
  gene1207|gene1207|rna1207|rna1207 960 GGMGINLTSADTVVIFDSDWNPQNDLQAQARCHRIG 995
                                        **********************************97 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.62
                                         HTTSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGT CS
                         Helicase_C   38 kkgikvavlhgelpqnereeileqfnkgesdvLiatdvae 77  
                                         k g+  a+l+ + + +++e+i +  +kg + vL+  d a+
  gene1207|gene1207|rna1207|rna1207 1022 KLGLDQAILQKNKSVRKKEHIENLLKKGAYGVLMENDEAA 1061
                                         3378889999999999***************999888776 PP

>> Chromo  Chromo (CHRromatin Organisation MOdifier) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   3.8e-07    0.0011      13      48 ..     233     267 ..     220     274 .. 0.77
   2 !   19.4   0.2   2.4e-07   0.00073      21      53 ..     323     357 ..     311     358 .. 0.89
   3 ?   -0.9   0.1      0.54   1.6e+03       2      20 ..    1345    1363 ..    1344    1364 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 3.8e-07
                                        TTEECEEEEEEETTSTGGGTEEEEGGGCSSHSHHHH CS
                             Chromo  13 kdgleleYlVKWkglpysentWEpeenlekcfqeli 48 
                                        ++++ ++++VK ++++y ++ W p+e++ k    +i
  gene1207|gene1207|rna1207|rna1207 233 DSRG-EMFFVKFRNMSYIHCEWVPREEIMKTRAGAI 267
                                        3333.8**********************99855555 PP

  == domain 2  score: 19.4 bits;  conditional E-value: 2.4e-07
                                        EEEETTSTGGGTEEEEGGGCSSH..SHHHHHHHHH CS
                             Chromo  21 lVKWkglpysentWEpeenlekc..fqelideFkk 53 
                                        lVKWk l y+ +t+E +e++ +   f+e ++e+k 
  gene1207|gene1207|rna1207|rna1207 323 LVKWKKLAYELSTFEKIEDIRELegFEEELREYKV 357
                                        9*******************999999999999985 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 0.54
                                         EEEEEEEEEEETTEECEEE CS
                             Chromo    2 eVerIidhrtdkdgleleY 20  
                                          Ve +++ + +k++le  Y
  gene1207|gene1207|rna1207|rna1207 1345 RVEMVMNQKRRKSNLESLY 1363
                                         59***********997655 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.3   0.0   1.1e-10   3.2e-07       2     168 ..     391     546 ..     390     555 .. 0.75
   2 ?   -2.6   0.1       1.4   4.1e+03     118     161 ..    1043    1088 ..    1024    1097 .. 0.75

  Alignments for each domain:
  == domain 1  score: 30.3 bits;  conditional E-value: 1.1e-10
                                        HHHHHHHHHHH....TTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTT CS
                                        xxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               DEAD   2 diQaeaiplil....gggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkky 73 
                                        d+Q e ++++l     ++ +++a e G GKT   +  v + + e  +  +  +liv+P+  L++   ++++++++ 
  gene1207|gene1207|rna1207|rna1207 391 DYQMEGLNWLLnrwyYKQGCIMADEMGLGKTVQTVCFVNKVF-E--TGYQHPVLIVAPLSTLIH-WEREFRTWTD- 461
                                        6777778888855556689*************9888888555.5..566668**********97.5777777777. PP

                                        STSEEEEEETTSSHHHHHHHHH..TT...CSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHH CS
                                        xxxxxxxxxxxxxxxxxxxxxx..xx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               DEAD  74 idlrvlliiggvaardqlskld..ng...vdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsdfinr 144
                                          lr+ll  g++ ard + + +  n+    d++++t +++++ ++  +l   ++ + V+DEa+rl ++  + f + 
  gene1207|gene1207|rna1207|rna1207 462 --LRILLYHGNNVARDLIYDYEfyNDgllFDVLITTYEMVMSGMK--HL-SFNFGIGVFDEAHRLKNSHSKAFQSL 532
                                        ..9**************999966533599************9664..32.3577899*********9954444444 PP

                                        HHHHSHHHCTTSTTTSEEEEEESS CS
                                        xxxxxxxxxxxxxxxxxxxxxxxx RF
                               DEAD 145 ilnqlpqitcdgklqrqvivlSAT 168
                                        i  ++          ++ i+lS T
  gene1207|gene1207|rna1207|rna1207 533 ISLSF----------NHKILLSGT 546
                                        33333..........124555555 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.4
                                         H..CTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCTTSTTTSE CS
                                         x..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               DEAD  118 n..lsqvrflVlDEadrlldqgfsdfinrilnqlpqitcdgklqrq 161 
                                         +  l++  + Vl E d+  ++  +++i+ il++  +i  + ++ +q
  gene1207|gene1207|rna1207|rna1207 1043 EnlLKKGAYGVLMENDEAAQKFCEEDIEMILERRTHIVRHNQEANQ 1088
                                         3447777888999999999999999999999999888877664433 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.7   0.0   1.6e-09   4.7e-06       4     169 ..     389     547 ..     387     549 .. 0.76
   2 ?   -3.9   0.4       4.1   1.2e+04      60     112 ..     682     734 ..     672     775 .. 0.42

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 1.6e-09
                                        E-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTG CS
                             ResIII   4 lreyQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkfls 79 
                                        lr+yQ+e ++ ll+ +  + ++  +++ + G GKT+  + ++ ++++ g++  +l+++p  +l+  +++ef+ +++
  gene1207|gene1207|rna1207|rna1207 389 LRDYQMEGLNWLLNRW--YYKQGCIMADEMGLGKTVQTVCFVNKVFETGYQHPVLIVAPLSTLI-HWEREFRTWTD 461
                                        89**********9999..57777779999**********************9999999999987.47888866665 PP

                                        G.....GEEEESSS-B--.........-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS...TTT CS
                             ResIII  80 eayke.igkkvsgdkkka..kekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgak..ksw 150
                                              +g++v  d      + +d    ++l+tt++++ + +        + l+ +f + ++DEaHrl+ +  k++
  gene1207|gene1207|rna1207|rna1207 462 LRILLyHGNNVARDLIYDyeFYNDGLLFDVLITTYEMVMSGM--------KHLSFNFGIGVFDEAHRLKNShsKAF 529
                                        54322333333333333344444566679*************........88999999***********9755588 PP

                                        HH.HHHT---SEEEEEESS- CS
                             ResIII 151 re.ilekfkeavllglTATp 169
                                        ++ i  +f+   ++ l++Tp
  gene1207|gene1207|rna1207|rna1207 530 QSlISLSFN--HKILLSGTP 547
                                        883444445..555556777 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 4.1
                                        EESSHHHHHHHHHHG..GGGTGG...........GEEEESSS-B--.......-SEEEEEHH CS
                             ResIII  60 lvprkslleqtleef..kkflseayke.......igkkvsgdkkkakekdstnkkilvttiq 112
                                        + +r+ l e +++ f  k+ +  ++ke                +k+  ++++n++  + t +
  gene1207|gene1207|rna1207|rna1207 682 IKQRRMLGEEAEDGFarKDEAGGEVKEsrmesgeS--------NKE-GSKEENRESRLDTPK 734
                                        55555566666665533122222222122211111........111.222222222222222 PP

>> HDA2-3  Class II histone deacetylase complex subunits 2 and 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.1   1.1e-08   3.2e-05      76     247 ..     867    1019 ..     864    1053 .. 0.77

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 1.1e-08
                                         -S-STTHHHHHHHT-HHHHHHHHHHHHHTTSS....EEEEEEE-STHHHHHHHHHHTTSSSEEEESSS--S--S CS
                             HDA2-3   76 klllkelpeklaetSgKFkvlndlvnliierkrksslnvlvvakskkeldLiEalllGkklkikrysgeklyde 149 
                                         +l++ e  ++l+++SgK+ +l +l+  +  ++     +vl+ ++  + ldL+  +l+ k+ k++r +g  + +e
  gene1207|gene1207|rna1207|rna1207  867 ELTVDEYYKILIQSSGKLVLLDKLLAKLKGEH-----KVLIFSQMTRCLDLLSDYLQYKRYKYERIDGG-VRGE 934 
                                         678889999********************999.....*****************************996.5666 PP

                                         ---S-..................-SEEEEEEESS---TTTS--TT-S-EEEEEE-SST--TTSHHHHHHH---- CS
                             HDA2-3  150 kkkkskdtkknsrktkeklkkkihsltihllsttrqltkdksllenikfdliiafDssvdtsspsveslrtqnr 223 
                                          ++ +            +  + + s+ + +l  tr         + + +d ++ fDs+ +++++   + r ++ 
  gene1207|gene1207|rna1207|rna1207  935 CRQAA-----------IDRFSSAESDSFVFLLCTRAGG---MGINLTSADTVVIFDSDWNPQNDLQAQARCHRI 994 
                                         66666...........1223445666777777777663...446677889**************9999998875 PP

                                         ----.--EEEEEETTSHHHHHHHHT CS
                             HDA2-3  224 kknk.lpiirlvpinSieHvkLcfk 247 
                                          + k + i+rl++ n+ e  +    
  gene1207|gene1207|rna1207|rna1207  995 GQTKsVKIYRLITRNTYEREMFDKA 1019
                                         444349**********998776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1435 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1271  (0.0708907); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.93u 0.26s 00:00:01.19 Elapsed: 00:00:00.46
# Mc/sec: 9447.20
//
Query:       gene1208|gene1208|rna1208|rna1208  [L=330]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.9e-20   73.2   0.0    1.1e-19   71.7   0.0    1.6  1  4HBT_3         Thioesterase-like superfamily
    4.6e-05   23.3   0.0      0.018   14.9   0.0    3.1  3  Acyl_CoA_thio  Acyl-CoA thioesterase
     0.0015   18.5   0.0     0.0023   17.8   0.0    1.3  1  Prefoldin      Prefoldin subunit


Domain annotation for each model (and alignments):
>> 4HBT_3  Thioesterase-like superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.7   0.0   1.8e-23   1.1e-19       2     248 .]      17     324 ..      16     324 .. 0.67

  Alignments for each domain:
  == domain 1  score: 71.7 bits;  conditional E-value: 1.8e-23
                                        -GGGECTTC...-HHHHHHHHHHHHHHT..-S.SSEEEEEEE-S---SE.EEEEEEEEEE--SS-EEEEEEEEETT CS
                             4HBT_3   2 rppwtpgga.g.yGGyvlAlalraaqrtv.pdprlhslhvyFlrpgdag.pviyhvervrdGrsfstrtvelsqgg 73 
                                        +++w+p    + +GG +++l l aa+    ++p   s+h yFl+pg+ g p+ ++v+ +r+Gr++  + ++ +q  
  gene1208|gene1208|rna1208|rna1208  17 SELWSPFPLyPaFGGHLVSLSLLAAEMYAdARP--SSIHTYFLLPGKIGtPMSFEVKFLREGRTTKAVNIRGYQSN 90 
                                        688999999988**************9973344..8**************************************99 PP

                                        EEEEEEEEEEE---T.......................................---EE-------.GGGE---.. CS
                             4HBT_3  74 rpiftatasfgraes...................................tgwelepaaapppvpppdeaalaad. 113
                                        + i+t  + + ++ +                                        ++                 + 
  gene1208|gene1208|rna1208|rna1208  91 ELIVTSDCLMNNELAstvfykipieiyddvyvhisthfmnllspcttnalL----KS-----------------Ev 145
                                        999998888888775689999999888887777765554444444322111....11.................11 PP

                                        ..................--SSGGGSGG..TEEEE-HHT-.--S.......S-EEEEEEEET.TTS-SSHHHHHHH CS
                             4HBT_3 114 ..................eaplplfrrvpgflepfeprpa.eggkpdspagpkrvrqWvrlr.eggepahlaaLay 169
                                                          +   + +r+v+++ + +e  +    g   +p+g+kr+   ++   ++   + +  +a+
  gene1208|gene1208|rna1208|rna1208 146 hknssalesgkaerqrlhHGVNEMIRMVDENYKKLEKYFSvYIG---KPNGTKRQ---FKIIfHDKYHDFNVLMAF 215
                                        11111111222111112133333333444444444444442222...44555555...333222343344668*** PP

                                        HTT-.-GGGGTSS-.......................................SB--EEEEEEEE-S--S-...EE CS
                             4HBT_3 170 lsDsfpvprvhglrld................aea.................sgwmpsldltiyfhrepaedeWll 212
                                        +sD f   +++  + +                + +                 s +  sld+ i+fh +    + l 
  gene1208|gene1208|rna1208|rna1208 216 ISDLFL-CNTSLAWIKqryerrmngndsdhsnV-KdcmldgkcnsdtcidlnSVVKKSLDHKIHFHSNK-FYDELI 288
                                        ****86.67777775545556666666655550.05566666666677777744555*********953.456899 PP

                                        EEEE-SEEETTEEEEEEEEE-TTS-EEEEEEEEEET CS
                             4HBT_3 213 leaetpwagdgrglvearlwdedGrlvAtstQeglv 248
                                        + +e++  g+  +l e++l+  +G lvA++tQeg++
  gene1208|gene1208|rna1208|rna1208 289 FVTECQLLGEKKALFEGKLLGPEGALVASVTQEGII 324
                                        99*******************************986 PP

>> Acyl_CoA_thio  Acyl-CoA thioesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.3   0.0    0.0055        33      81     126 ..      53      95 ..      28     125 .. 0.89
   2 ?   -0.3   0.0      0.14   8.6e+02      50      82 ..     211     245 ..     203     250 .. 0.79
   3 !   14.9   0.0     3e-06     0.018      75     131 ..     268     322 ..     252     323 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.0055
                                        EEEEE-S--BTTS-EEEEEEEEEEETTEEEEEECCEE......ECTTEEEEE CS
                      Acyl_CoA_thio  81 HsvyFlrpgdlnewilydvespsasggrgLrqGriFs......tqdgklias 126
                                        H+ yFl pg++ +++ ++v+         Lr+Gr  +      +q+++li +
  gene1208|gene1208|rna1208|rna1208  53 HT-YFLLPGKIGTPMSFEVKF--------LREGRTTKavnirgYQSNELIVT 95 
                                        99.999999999999999999........99999888888888999999987 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.14
                                        CHHHHHTTSSSGGGGGGGGT.TTSTTEEE.EEEEE CS
                      Acyl_CoA_thio  50 vllaYlSDltllltalttHe.lledslqv.sldHs 82 
                                        vl+a++SDl l +t l   +  +e +++    dHs
  gene1208|gene1208|rna1208|rna1208 211 VLMAFISDLFLCNTSLAWIKqRYERRMNGnDSDHS 245
                                        67899***999998887666688888877777777 PP

  == domain 3  score: 14.9 bits;  conditional E-value: 3e-06
                                        EEEEEEEEEEE-S--BTTS-EEEEEEEEEEETTEEEEEECCEEECTTEEEEEEEEEE CS
                      Acyl_CoA_thio  75 lqvsldHsvyFlrpgdlnewilydvespsasggrgLrqGriFstqdgkliasvqqeG 131
                                        ++ sldH ++F+   ++ +++++ +e +   ++++L +G+     +g l+asv qeG
  gene1208|gene1208|rna1208|rna1208 268 VKKSLDHKIHFHSN-KFYDELIFVTECQLLGEKKALFEGKLL-GPEGALVASVTQEG 322
                                        4559********86.67788999999999999**********.*************9 PP

>> Prefoldin  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   3.9e-07    0.0023      44     120 .]     103     179 ..      92     179 .. 0.95

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 3.9e-07
                                        EEETTEEEEEE--STTEEEEEEETTEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Prefoldin  44 plgaglyvkaevkdtdkvlvdlGagyyveksleeAiellkkkleelekqlekleeeleklkdqittleanlaqlyq 119
                                        +l ++++ k+ +++ d+v+v++ + ++  +s     +llk ++ + +++le+ ++e + l   ++++ ++++++y+
  gene1208|gene1208|rna1208|rna1208 103 ELASTVFYKIPIEIYDDVYVHISTHFMNLLSPCTTNALLKSEVHKNSSALESGKAERQRLHHGVNEMIRMVDENYK 178
                                        7899********************************************************************9998 PP

                                        H CS
                          Prefoldin 120 k 120
                                        k
  gene1208|gene1208|rna1208|rna1208 179 K 179
                                        5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (330 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       818  (0.0456244); expected 358.6 (0.02)
Passed bias filter:                      581  (0.0324056); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 2210.81
//
Query:       gene1209|gene1209|rna1209|rna1209  [L=56]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (56 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       221  (0.0123264); expected 358.6 (0.02)
Passed bias filter:                      194  (0.0108205); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 418.50
//
Query:       gene121|gene121|rna121|rna121  [L=324]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.7e-51  175.2   5.1      2e-51  174.9   5.1    1.1  1  Pkinase         Protein kinase domain
    3.2e-23   82.4   0.3    5.5e-23   81.6   0.3    1.5  1  Pkinase_Tyr     Protein tyrosine kinase
    0.00036   19.4   0.0       0.48    9.2   0.0    2.4  2  Pkinase_fungal  Fungal protein kinase
    0.00037   19.9   0.6      0.046   13.0   0.0    3.1  4  Kinase-like     Kinase-like
  ------ inclusion threshold ------
      0.023   14.3   4.3       0.22   11.1   0.5    2.5  3  FTA2            Kinetochore Sim4 complex subunit FTA2
       0.11   11.9   1.9       0.32   10.3   0.0    2.5  3  Kdo             Lipopolysaccharide kinase (Kdo/WaaP) family


Domain annotation for each model (and alignments):
>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  174.9   5.1   6.6e-55     2e-51       2     264 .]      36     319 ..      35     319 .. 0.86

  Alignments for each domain:
  == domain 1  score: 174.9 bits;  conditional E-value: 6.6e-55
                                    EEEEEEEEESSEEEEEEEETTTTEEEEEEEEECHCHCHHHHHHHHHHHHHHHHHSCTTB--EEEEEEE.....SSEEEEE CS
                        Pkinase   2 ekleklGeGsfGkVykaveketgkivAvKkikkekakkkkekkvlrEikilkklkhpnivrlyevfee.....kdelylv 76 
                                    + +ek+G+G+fG V+k+ e++tg+ +A+K++ +++      k++ rE +il++lk+++ vrlye+ +       +++ lv
  gene121|gene121|rna121|rna121  36 KYVEKIGKGTFGFVVKIEENNTGNVFALKTVYEDN------KHYYREKEILENLKSKHFVRLYEYAYFeesteGRYVQLV 109
                                    6789***************************9874......35799*****************986654466667788** PP

                                    EE--TTEB...........HHHHHHHHSS--HHHHHHHHHHHHHHHHHHHHTTEE-SS-SGGGEEEETTTEEEE-SGTTS CS
                        Pkinase  77 leyvegge...........ladllerkgslseeeakkiakqilegleylHskgiiHrDlKpeNiLidekgelKitDFGla 145
                                    ley++              l++++e k ++ +e +k+++kq +egl ylHs +i HrD+Kp+NiLid +g+lK +D+G a
  gene121|gene121|rna121|rna121 110 LEYIPFSLrnliisdrfdfLKKFYEGKENFVDEMVKDFMKQGFEGLCYLHSFNIAHRDIKPANILIDYDGKLKFCDLGSA 189
                                    *****8866677777666666666688889999*********************************************** PP

                                    EESSSSCSBCTTTSCGGGS-HHHH.TTSCBSHHHHHHHHHHHHHHHHHSS-STTTSSHHHHHHHHHHTHHHHHHHCTSHH CS
                        Pkinase 146 kelessskltsfvgtseYlAPEvl.keneyskkvDvWslGvilyelltgkppfsgekgkekvekeldqlekilkilgetk 224
                                    k+le+++  t+++++++Y++PE + + ++y++k+D+Ws  + ++e++t+k +f+g+++ ++ ek+l+ l+ ++k l ++k
  gene121|gene121|rna121|rna121 190 KKLENKN-NTTYICSRYYRSPENIiGLKNYTTKIDIWSFSLSIAEIITRKVIFKGQSNVNQLEKILNLLKISQKDLLTMK 268
                                    *****98.9*************99899***************************66666655555555444444444656 PP

                                    ...HHHTTS...........-HHHHHHHHHHT-SSGCCSTTHHHHHTSGGG CS
                        Pkinase 225 eklpeasei...........seeakdllkkllkkdpkkRltaeellqhpyl 264
                                    +   +++++           ++++ ++ +k +k + kkR +a+++l+ + +
  gene121|gene121|rna121|rna121 269 LRRSKRETMgikkymkkytsNKKLVEVFDKTIKFNFKKRRSAKQVLEMELF 319
                                    666666666889999999999*************************98765 PP

>> Pkinase_Tyr  Protein tyrosine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.6   0.3   1.8e-26   5.5e-23       2     227 ..      36     262 ..      35     316 .. 0.82

  Alignments for each domain:
  == domain 1  score: 81.6 bits;  conditional E-value: 1.8e-26
                                    EEEEEEEEESSEEEEEEEEETTTTSSEEEEEEEEESTTSSHHHHHHHHHHHHHHHTS-BTTB--EEEEEE.....SSSSE CS
                    Pkinase_Tyr   2 elgkklGeGafGkVvegtlkgekekkevkVavKtlkeeateeekeelleeakimkklkhpnivkllgvct.....keepl 76 
                                    ++ +k+G+G+fG Vv+ + +    ++    a+Kt+ e++     ++ ++e +i+++lk ++ v+l+   +     +++ +
  gene121|gene121|rna121|rna121  36 KYVEKIGKGTFGFVVKIEEN----NTGNVFALKTVYEDN-----KHYYREKEILENLKSKHFVRLYEYAYfeestEGRYV 106
                                    56799**********99888....888889*****5544.....5569******************99887654445559 PP

                                    EEEEE--TTEBHHHHHHHT..........CTTTSBHHHHHHHHHHHHHHHHHHHHTTEEEST-SGGGEEEEETTEEEE-S CS
                    Pkinase_Tyr  77 livteyvkgGdLlkfLrkk..........ekekltlkdllsfalqvAkGmeyLeskklvHrdlaarNvLlsenkvvkisD 146
                                     +v+ey++  +L++ + ++           ke++  + + +f+ q  +G+ yL+s ++ Hrd+   N+L++ + + k +D
  gene121|gene121|rna121|rna121 107 QLVLEYIPF-SLRNLIISDrfdflkkfyeGKENFVDEMVKDFMKQGFEGLCYLHSFNIAHRDIKPANILIDYDGKLKFCD 185
                                    ********9.6777777777999999998788888888999*************************************** PP

                                    TTTHEETTTSSEEEETTSSTSGGGGS-HHHHHHSE.EEHHHHHHHHHHHHHHHHTTSSGTTTTSHHHHHHHHHHTTEES- CS
                    Pkinase_Tyr 147 fGLardiekddeyvkkeeaklpvkWmapEslkekk.ftsksDvWsfGvllwEiftlgespypglkneevleklkegkrle 225
                                     G a+++e     +++++  ++  + +pE +   k +t+k D+Wsf+  + Ei+t  +  ++g +n + lek+ +  +++
  gene121|gene121|rna121|rna121 186 LGSAKKLE----NKNNTTYICSRYYRSPENIIGLKnYTTKIDIWSFSLSIAEIIT-RKVIFKGQSNVNQLEKILNLLKIS 260
                                    *******3....33344455566677***9877655******************9.566666666666666665555554 PP

                                    BB CS
                    Pkinase_Tyr 226 kp 227
                                    + 
  gene121|gene121|rna121|rna121 261 QK 262
                                    44 PP

>> Pkinase_fungal  Fungal protein kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.0    0.0004       1.2     139     203 ..      26      92 ..       8     107 .. 0.80
   2 !    9.2   0.0   0.00016      0.48     317     367 ..     153     197 ..     137     216 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0004
                 Pkinase_fungal 139 ekleleeplarqraivgRgTtcwrarkeger.gkeyvvKdsWrdaerk.sEaelLkkaeergvegva 203
                                     +  l +++++  + +g+gT  + ++ e+++ g+ + +K + +d++   +E+e+L++ +++    + 
  gene121|gene121|rna121|rna121  26 IETNLRTLFFKYVEKIGKGTFGFVVKIEENNtGNVFALKTVYEDNKHYyREKEILENLKSKHFVRLY 92 
                                    5566777777777889*****99999887777889************99*********776655444 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00016
                 Pkinase_fungal 317 kghrsLflkagiLHrDiSenNilitdskkegerkglLiDLDlakelsddss 367
                                    +g+  L+   +i HrDi   Nili       + k    DL  ak+l+++++
  gene121|gene121|rna121|rna121 153 EGLCYLH-SFNIAHRDIKPANILID-----YDGKLKFCDLGSAKKLENKNN 197
                                    5666788.99**************9.....677777888888888886554 PP

>> Kinase-like  Kinase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.1       0.1   3.1e+02      98     128 ..       4      34 ..       3      41 .. 0.86
   2 ?    3.2   0.1     0.016        47      14      64 ..      35      88 ..      20      93 .. 0.75
   3 !   13.0   0.0   1.5e-05     0.046     159     255 ..     157     246 ..     155     276 .. 0.80
   4 ?   -0.1   0.1      0.16   4.8e+02     101     152 ..     244     317 ..     231     320 .. 0.62

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.1
                    Kinase-like  98 fiqlkskesiywvvnallllpaasvdleiln 128
                                    ++q k ++ i  + +++l+ + ++++l +l+
  gene121|gene121|rna121|rna121   4 LFQDKLNNAITKINDLMLVDQSIETNLRTLF 34 
                                    6899999****9*99************8764 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.016
                    Kinase-like 14 lvrgellkkgdrsvvfevkdqetgeplavkvfllpsea...skkdlerlkeqel 64
                                   ++ +e ++kg ++ v+++++++tg+ +a+k  +  ++     k+ le+lk +++
  gene121|gene121|rna121|rna121 35 FKYVEKIGKGTFGFVVKIEENNTGNVFALKTVYEDNKHyyrEKEILENLKSKHF 88
                                   4667889***********************999988651213445778777766 PP

  == domain 3  score: 13.0 bits;  conditional E-value: 1.5e-05
                    Kinase-like 159 nLqakglvhgkftvdnllldekgglmlggftaLvragtkvvlseve.kgfaPpEllgsrggytrknktkmthkldaWqlG 237
                                    +L++  + h ++++ n+l d +g+l+  ++++  +  +k     ++ + +  pE +            ++t k+d W   
  gene121|gene121|rna121|rna121 157 YLHSFNIAHRDIKPANILIDYDGKLKFCDLGSAKKLENKNNTTYICsRYYRSPENIIG--------LKNYTTKIDIWSFS 228
                                    79999***************************99999999987777577777775544........247899******** PP

                    Kinase-like 238 lviyriwclklPltlate 255
                                    l+i  i  +k+ +  + +
  gene121|gene121|rna121|rna121 229 LSIAEIITRKVIFKGQSN 246
                                    ***999988876666555 PP

  == domain 4  score: -0.1 bits;  conditional E-value: 0.16
                    Kinase-like 101 lkskesiywvvnallllpaasvdl......................eilnkvlqkrsethkkletiarlllTlq 152
                                    +++ ++   ++n+l + ++  + +                      + l++v +k  ++++k    a+++l ++
  gene121|gene121|rna121|rna121 244 QSNVNQLEKILNLLKISQKDLLTMklrrskretmgikkymkkytsnKKLVEVFDKTIKFNFKKRRSAKQVLEME 317
                                    44445555666666666665555566777777766666667766667777777777777777777777777665 PP

>> FTA2  Kinetochore Sim4 complex subunit FTA2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.5   7.5e-05      0.22      24      84 ..      35      99 ..      22     105 .. 0.76
   2 ?    4.3   0.0    0.0092        28     176     214 ..     146     189 ..     126     190 .. 0.73
   3 ?   -2.9   0.1       1.4   4.2e+03     176     191 ..     248     263 ..     234     303 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 7.5e-05
                           FTA2 24 iefleyLgkglhsiVlkvkirgk..eYALKlFrfleaeele..eaeedlkiprealkelasysdp 84
                                   ++++e +gkg+ ++V+k++ ++   ++ALK  ++ ++++ +  e  e+lk +++++   ++y++ 
  gene121|gene121|rna121|rna121 35 FKYVEKIGKGTFGFVVKIEENNTgnVFALKTVYEDNKHYYRekEILENLKSKHFVRLYEYAYFEE 99
                                   6889999***********9886656*****77777666666666667777777777666666665 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.0092
                           FTA2 176 sqlpkllrdlkklhklgIvvrDlkeenyi...dgkL..vDlsaa 214
                                    + +++  + l  lh+  I +rD+k+ n++   dgkL  +Dl++a
  gene121|gene121|rna121|rna121 146 DFMKQGFEGLCYLHSFNIAHRDIKPANILidyDGKLkfCDLGSA 189
                                    445556677999***************96555776444888876 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 1.4
                           FTA2 176 sqlpkllrdlkklhkl 191
                                    +ql+k+l+ lk+ +k 
  gene121|gene121|rna121|rna121 248 NQLEKILNLLKISQKD 263
                                    4444444444443332 PP

>> Kdo  Lipopolysaccharide kinase (Kdo/WaaP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.1      0.17   5.2e+02      25      61 ..      63      99 ..      48     102 .. 0.69
   2 ?   10.3   0.0   0.00011      0.32     133     167 ..     157     187 ..     124     227 .. 0.82
   3 ?   -1.7   0.1       0.5   1.5e+03     181     202 ..     245     266 ..     236     309 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.17
                            Kdo 25 aekvnaalrkyyrggllgklskdlyrfklgrtravrE 61
                                    + v  + ++yyr + + +  k++ +++l +   ++E
  gene121|gene121|rna121|rna121 63 LKTVYEDNKHYYREKEILENLKSKHFVRLYEYAYFEE 99
                                   4444678899999999888888888888666655555 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00011
                            Kdo 133 klhragvnHadlyaknillqqeeeeeaeiwliDld 167
                                     lh+ ++ H+d+ + nil++ ++    ++ + Dl 
  gene121|gene121|rna121|rna121 157 YLHSFNIAHRDIKPANILIDYDG----KLKFCDLG 187
                                    69*******************99....77777775 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 0.5
                            Kdo 181 kdLarLkrsflkielteadwea 202
                                     + ++L++ ++  +++++d   
  gene121|gene121|rna121|rna121 245 SNVNQLEKILNLLKISQKDLLT 266
                                    5677777777777777776543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (324 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1319  (0.073568); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 2233.81
//
Query:       gene1210|gene1210|rna1210|rna1210  [L=451]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.6e-13   49.9   0.7    6.3e-12   45.4   0.0    3.0  3  Thioredoxin    Thioredoxin
    1.9e-09   37.7   9.9    6.8e-08   32.6   0.2    3.9  3  Thioredoxin_6  Thioredoxin-like domain
    0.00042   20.5   0.1    0.00042   20.5   0.1    2.3  2  Thioredoxin_4  Thioredoxin
  ------ inclusion threshold ------
      0.027   14.2   0.2        7.2    6.3   0.0    2.5  2  Redoxin        Redoxin
       0.25   11.5   0.1       0.44   10.8   0.1    1.3  1  DUF5351        Family of unknown function (DUF5351)
          8    7.1  12.9        8.5    7.0   4.3    3.4  3  YtxH           YtxH-like protein


Domain annotation for each model (and alignments):
>> Thioredoxin  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0      0.11   3.4e+02      34     101 ..     206     273 ..     182     275 .. 0.70
   2 !   45.4   0.0   2.1e-15   6.3e-12       3     102 ..     298     399 ..     296     400 .. 0.90
   3 ?   -1.9   0.1       1.1   3.4e+03      34      49 ..     427     442 ..     408     448 .. 0.56

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.11
                                        HCHHHHHHHHHHHCTTTSEEEEEETTTSHHHHHHTT-..SSSSEEEEEETTEEEEEEESS-HHHHHHHHH CS
                        Thioredoxin  34 kalaPeleklaeelkdkvklakvdvdenedlakkyev..egiPtlklfkngkevkkyegarekeklaafl 101
                                        k+l  e++++a++l+dk k+  +     ++  ++++v  e++P+l+ + +gk+ + ++ +r+  +l++f+
  gene1210|gene1210|rna1210|rna1210 206 KQLRDEIKSVATDLRDKYKFGMLRYIPGRTDLNHFKVteEQMPALVHLIEGKKYRLVNVTRD--ALVQFI 273
                                        77888888888888888888888888877777778874446888888888886666555444..666665 PP

  == domain 2  score: 45.4 bits;  conditional E-value: 2.1e-15
                                        EESSHHHHHHHHTTTSSEEEEEEE-TTSHHHHCHHHHHHHHHHHCTT..TSEEEEEETTTSHHHHHHTT-SSSSEE CS
                        Thioredoxin   3 lvltkenFeeevakekklvlveFyApwCghCkalaPeleklaeelkd..kvklakvdvdenedlakkyevegiPtl 76 
                                        ++++ +++++ v++++++ ++ + ++ C+hC +l P++ekla ++kd  kvk+  ++  en   + +++++++Pt+
  gene1210|gene1210|rna1210|rna1210 298 VKVVGTTHNDFVSDDRRDTFIVYGSETCPHCVSLLPTIEKLAARTKDntKVKVGYINLYEN--DVPDVNIKAFPTI 371
                                        56778899***************************************99999999999998..45678******** PP

                                        EEEETTE.EEEEEESS.-HHHHHHHHHH CS
                        Thioredoxin  77 klfkngk.evkkyega.rekeklaaflk 102
                                        +l+ +gk e+ +y+   r++e++++f+k
  gene1210|gene1210|rna1210|rna1210 372 MLYAAGKkEPIEYKDFnRTEENFISFIK 399
                                        *******988888886588999999997 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 1.1
                                        HCHHHHHHHHHHHCTT CS
                        Thioredoxin  34 kalaPeleklaeelkd 49 
                                        k l+ ++e++++e+k+
  gene1210|gene1210|rna1210|rna1210 427 KDLEKKIEEVKSEIKE 442
                                        3444455555555555 PP

>> Thioredoxin_6  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.1     0.044   1.3e+02      92     122 ..      99     126 ..      89     128 .. 0.83
   2 !   32.6   0.2   2.3e-11   6.8e-08      21     166 ..     127     260 ..     120     275 .. 0.83
   3 !    5.6   2.6    0.0044        13      32      74 ..     358     401 ..     334     447 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.044
                                        TSS--EEEEEEE-TTSTTHHHHHHHHHHHHH CS
                      Thioredoxin_6  92 eeglppllllflkkddeeteklkkaiekvak 122
                                        + g+++++++f +   + t++ k++i+kv +
  gene1210|gene1210|rna1210|rna1210  99 RAGKRTFFIFFAD---QITNEQKQQIMKVKE 126
                                        5688999999994...699999999999976 PP

  == domain 2  score: 32.6 bits;  conditional E-value: 2.3e-11
                                        .TSEEEEE--HHHHHHTT--SSEEEEEETTTTEEEEEETHT--HHHHHHHHHHH---SEEE-SHHHHHHHHTSS-- CS
                      Thioredoxin_6  21 gdvrfgvtkskevadklgvkepavllfrkfdeekvkydgekitvddlkkfieknslplvreltpenaeelfeeglp 96 
                                         d+ + ++++k++a+ lg+++p v+ f+++++  v+y        ++ + + + + p+  +lt++    + e++lp
  gene1210|gene1210|rna1210|rna1210 127 DDIPYFISSDKKLAKSLGASFPGVYAFNTTEN--VSYRI------NIDHAFGTVMAPVLSVLTSDAIRHIDESKLP 194
                                        458999***********************766..46665......5889999**********************99 PP

                                        EEEEEEE-TTSTTHHHHHHHHHHHHHHTTTT-EEEEEETTGGHHHHHHTT--GGG-SEEEEEESSSS-EE CS
                      Thioredoxin_6  97 pllllflkkddeeteklkkaiekvakefkdkinfaladaksfkrpleylglsssdlPvivivdsashkyk 166
                                         ++++f++   + +++l+++i++va++++dk++f  +        l+++++++++ P++v +  + +ky 
  gene1210|gene1210|rna1210|rna1210 195 -AFYIFYT--GTQDKQLRDEIKSVATDLRDKYKFGMLRYIPGRTDLNHFKVTEEQMPALVHLI-EGKKYR 260
                                        .6677774..5679**********************************************443.445544 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.0044
                                        HHHHHTT--S.SEEEEEETTTTEEEEEETHT--HHHHHHHHHHH CS
                      Thioredoxin_6  32 evadklgvke.pavllfrkfdeekvkydgekitvddlkkfiekn 74 
                                        + + ++++k  p++ l+ +  +e+++y++ + t ++  +fi++n
  gene1210|gene1210|rna1210|rna1210 358 NDVPDVNIKAfPTIMLYAAGKKEPIEYKDFNRTEENFISFIKEN 401
                                        35677999999*******************99*********998 PP

>> Thioredoxin_4  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   1.3      0.39   1.2e+03     101     133 ..      56      89 ..       9     147 .. 0.68
   2 !   20.5   0.1   1.4e-07   0.00042      15     133 ..     315     440 ..     310     447 .. 0.63

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.39
                                        HHH.....HHHH.HTS-------HHHHHHHHHHH CS
                      Thioredoxin_4 101 elaaealdkdek.feacleeekldalveaeskea 133
                                        ++++e+++++++ ++++l+ ++ ++ ++ae+++ 
  gene1210|gene1210|rna1210|rna1210  56 QVDKEDVQDMAEcVQSALQMPSDMKSIAAELEKK 89 
                                        3556677775441444777777777777776665 PP

  == domain 2  score: 20.5 bits;  conditional E-value: 1.4e-07
                                        EEEEEEE-TT-HHHHHHHHHHHHHHHHHHHTTSEEEEEEE-..---S.TTTHHHHHHHTT--TTHHHHHHHHHHHH CS
                      Thioredoxin_4  15 vtvieyedlrCphCakfeeeveklleeyidtGkvkfiirdfpldkek.eslkaamaarcageespeaflaikally 89 
                                         t i+y + +CphC  +  ++ekl ++  d+ kvk+ +++++ ++     +ka    + ++   ++   ++k+ ++
  gene1210|gene1210|rna1210|rna1210 315 DTFIVYGSETCPHCVSLLPTIEKLAARTKDNTKVKVGYINLYENDVPdVNIKAFPTIMLYAAG-KKEPIEYKD-FN 388
                                        6899***********************98899*********8886664445554443333322.234456666.56 PP

                                        THHHHTTS-HHHHH.............HHHHHTS-------HHHHHHHHHHH CS
                      Thioredoxin_4  90 sqqeewaeslkelaae........aldkdekfeacleeekldalveaeskea 133
                                        +++e++    ke  ++        +   +e++++  ++++l++++e+ + e 
  gene1210|gene1210|rna1210|rna1210 389 RTEENFISFIKENGSLgvdlaktgQNVSEEDVKDEAAKKDLEKKIEEVKSEI 440
                                        6666665553332222221221123333566666666666666666665555 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0    0.0046        14      67     118 ..     107     150 ..      83     167 .. 0.68
   2 ?    6.3   0.0    0.0024       7.2      34      65 ..     318     350 ..     298     381 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0046
                                        EEEESSSHH.HHHHHHH.TT-TSEEEE-TTSHHHHHTT-TTEEE.GGGEEE-EE CS
                            Redoxin  67 avvadndaf.vkefwgk.eglkfpvlsDgsaaftkalGlrleedaseglrtpry 118
                                        +  ad+ +  +k+ + k ++ ++p++++ +++++k+lG+            p +
  gene1210|gene1210|rna1210|rna1210 107 IFFADQITNeQKQQIMKvKEDDIPYFISSDKKLAKSLGAS----------FPGV 150
                                        4444444445444444457889****************55..........4444 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0024
                                        EEESTTT-HHHHHTHHHHHTHHHHHHCS.TTTE CS
                            Redoxin  34 nfvpgafcPtCsaehpyleklaellkek.gvdv 65 
                                        +++ + +cP C   +p +ekla++ k++  v+v
  gene1210|gene1210|rna1210|rna1210 318 IVYGSETCPHCVSLLPTIEKLAARTKDNtKVKV 350
                                        5677889**************888555413444 PP

>> DUF5351  Family of unknown function (DUF5351)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   0.00015      0.44      14      23 ..     319     328 ..     316     329 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00015
                            DUF5351  14 LGGSETCesC 23 
                                        + GSETC++C
  gene1210|gene1210|rna1210|rna1210 319 VYGSETCPHC 328
                                        66******** PP

>> YtxH  YtxH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.6       0.6   1.8e+03      41      54 ..      62      81 ..      29     127 .. 0.61
   2 ?    3.8   0.0     0.029        86      16      41 ..     198     223 ..     195     226 .. 0.84
   3 ?    7.0   4.3    0.0028       8.5      44      73 ..     420     450 ..     398     451 .] 0.72

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.6
                               YtxH 41 akelleeakeka......ke 54
                                       +++++e +++        k+
  gene1210|gene1210|rna1210|rna1210 62 VQDMAECVQSALqmpsdmKS 81
                                       33333322222233222233 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.029
                               YtxH  16 lLlAPksGketRkdlkekaddlkeka 41 
                                        ++++    k++R+++k  a dl++k 
  gene1210|gene1210|rna1210|rna1210 198 IFYTGTQDKQLRDEIKSVATDLRDKY 223
                                        6777777899*************996 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.0028
                               YtxH  44 lleeakeka.kekaedlkekvkekadelkek 73 
                                        +++ea++k  ++k+e++k+++kek++ +ke+
  gene1210|gene1210|rna1210|rna1210 420 VKDEAAKKDlEKKIEEVKSEIKEKVEAVKEE 450
                                        2333333334999***********9999996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (451 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1634  (0.0911373); expected 358.6 (0.02)
Passed bias filter:                      696  (0.0388198); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.44
# Mc/sec: 3074.79
//
Query:       gene1211|gene1211|rna1211|rna1211  [L=90]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0006   19.4  15.3          2    8.1   0.2    5.6  8  AbrB_C    AbrB C-terminal domain
  ------ inclusion threshold ------
      0.012   15.9   5.2       0.54   10.6   0.6    2.3  2  TEX12     Testis-expressed 12
      0.074   12.7   0.5        2.8    7.6   0.1    2.0  2  Secretin  Bacterial type II and III secretion system protein
       0.14   11.9   4.8         18    5.2   4.8    2.6  1  LpxD      UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltran
       0.46   10.8   4.0         14    6.1   0.3    2.6  3  UPF0058   Uncharacterised protein family UPF0058
        1.1    9.2   3.1         49    3.8   0.2    3.3  3  YycC      YycC-like protein


Domain annotation for each model (and alignments):
>> AbrB_C  AbrB C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.3   0.1    0.0052        15      21      33 ..       5      17 ..       5      18 .. 0.90
   2 !    8.1   0.2   0.00068         2      20      33 ..      12      25 ..      11      25 .. 0.92
   3 !    7.5   0.4     0.001       3.1      20      33 ..      20      33 ..      18      34 .. 0.90
   4 !    6.0   0.3     0.003       9.1      20      33 ..      28      41 ..      27      42 .. 0.90
   5 !    6.4   0.5    0.0023       6.8      20      33 ..      36      49 ..      32      49 .. 0.91
   6 !    7.0   0.8    0.0015       4.6      20      33 ..      44      57 ..      43      62 .. 0.90
   7 ?    2.4   0.0     0.041   1.2e+02      20      30 ..      60      70 ..      58      72 .. 0.89
   8 ?   -1.8   0.0      0.82   2.5e+03      17      22 ..      73      78 ..      71      79 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0052
                             AbrB_C 21 vLSkeGAeiLikE 33
                                       vLSke++ iL kE
  gene1211|gene1211|rna1211|rna1211  5 VLSKEAVVILSKE 17
                                       89*****999887 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.00068
                             AbrB_C 20 ivLSkeGAeiLikE 33
                                       ++LSke+A iL kE
  gene1211|gene1211|rna1211|rna1211 12 VILSKEAAVILSKE 25
                                       79*********887 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.001
                             AbrB_C 20 ivLSkeGAeiLikE 33
                                       ++LSke+A iL +E
  gene1211|gene1211|rna1211|rna1211 20 VILSKEAAVILSEE 33
                                       89********9776 PP

  == domain 4  score: 6.0 bits;  conditional E-value: 0.003
                             AbrB_C 20 ivLSkeGAeiLikE 33
                                       ++LS e+A iL kE
  gene1211|gene1211|rna1211|rna1211 28 VILSEEAAVILSKE 41
                                       89********9887 PP

  == domain 5  score: 6.4 bits;  conditional E-value: 0.0023
                             AbrB_C 20 ivLSkeGAeiLikE 33
                                       ++LSke++ iL kE
  gene1211|gene1211|rna1211|rna1211 36 VILSKEAVVILSKE 49
                                       89********9887 PP

  == domain 6  score: 7.0 bits;  conditional E-value: 0.0015
                             AbrB_C 20 ivLSkeGAeiLikE 33
                                       ++LSke+A iL +E
  gene1211|gene1211|rna1211|rna1211 44 VILSKEAAVILSEE 57
                                       79******999776 PP

  == domain 7  score: 2.4 bits;  conditional E-value: 0.041
                             AbrB_C 20 ivLSkeGAeiL 30
                                       ++LS ++A +L
  gene1211|gene1211|rna1211|rna1211 60 VILSEDAAVYL 70
                                       79******887 PP

  == domain 8  score: -1.8 bits;  conditional E-value: 0.82
                             AbrB_C 17 nGkivL 22
                                       nG i+L
  gene1211|gene1211|rna1211|rna1211 73 NGTIIL 78
                                       899998 PP

>> TEX12  Testis-expressed 12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.6   0.00018      0.54      25      56 ..       4      37 ..       1      41 [. 0.71
   2 ?    7.9   0.5    0.0012       3.7      34      55 ..      46      68 ..      37      79 .. 0.51

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00018
                              TEX12 25 evlekv.lndmskeinlllskya.kilseraavd 56
                                        vl k+ +  +ske  ++lsk a  ilse aav 
  gene1211|gene1211|rna1211|rna1211  4 RVLSKEaVVILSKEAAVILSKEAaVILSEEAAVI 37
                                       5666542456899999999987516899999995 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0012
                              TEX12 34 mskeinlllskya.kilseraav 55
                                       +ske  ++ls+ a  ilse aav
  gene1211|gene1211|rna1211|rna1211 46 LSKEAAVILSEEAvVILSEDAAV 68
                                       45555555555442345555554 PP

>> Secretin  Bacterial type II and III secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.1    0.0064        19       7      35 ..       2      30 ..       1      36 [. 0.84
   2 ?    7.6   0.1   0.00093       2.8       4      37 ..      31      64 ..      28      79 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.0064
                           Secretin  7 kakvlstPklltldneeAeievgqevpvq 35
                                       k +vls+  +++l++e+A+i +++  ++ 
  gene1211|gene1211|rna1211|rna1211  2 KSRVLSKEAVVILSKEAAVILSKEAAVIL 30
                                       5799****************999887776 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.00093
                           Secretin  4 qegkakvlstPklltldneeAeievgqevpvqvt 37
                                       +e+ a +ls+  +++l++e+A+i + + v++  +
  gene1211|gene1211|rna1211|rna1211 31 SEEAAVILSKEAVVILSKEAAVILSEEAVVILSE 64
                                       5678899********************9999833 PP

>> LpxD  UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   4.8    0.0061        18      44      52 ..      34      42 ..       6      86 .. 0.61

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0061
                                       HHCCHTTSC CS
                               LpxD 44 laealpana 52
                                       +a  l+++a
  gene1211|gene1211|rna1211|rna1211 34 AAVILSKEA 42
                                       222222222 PP

>> UPF0058  Uncharacterised protein family UPF0058
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.3    0.0045        14      46      71 ..       3      28 ..       1      39 [. 0.78
   2 ?    5.5   0.3    0.0068        20      51      71 ..      40      60 ..      35      77 .. 0.75
   3 ?    2.3   0.0     0.069   2.1e+02      51      71 ..      56      76 ..      53      86 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0045
                                       -HHHHHHHHHHHHHHHHHHHHHHHHC CS
                            UPF0058 46 sKaehkaAifvLgnaiakalsekees 71
                                       s+   k+A+ +L+++ a +ls++   
  gene1211|gene1211|rna1211|rna1211  3 SRVLSKEAVVILSKEAAVILSKEAAV 28
                                       55567999999999999999998765 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0068
                                       HHHHHHHHHHHHHHHHHHHHC CS
                            UPF0058 51 kaAifvLgnaiakalsekees 71
                                       k+A+ +L+++ a +lse+   
  gene1211|gene1211|rna1211|rna1211 40 KEAVVILSKEAAVILSEEAVV 60
                                       789999999999999998765 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.069
                                       HHHHHHHHHHHHHHHHHHHHC CS
                            UPF0058 51 kaAifvLgnaiakalsekees 71
                                       ++A+ +L++  a +l+e+ + 
  gene1211|gene1211|rna1211|rna1211 56 EEAVVILSEDAAVYLNENGTI 76
                                       579*********999999876 PP

>> YycC  YycC-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.2     0.016        49       6      19 ..      14      27 ..       1      32 [. 0.77
   2 ?    2.6   0.1      0.04   1.2e+02       6      17 ..      30      41 ..      27      47 .. 0.86
   3 ?    2.5   0.1     0.043   1.3e+02       6      17 ..      46      57 ..      44      72 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.016
                               YycC  6 iSpeTAvkLskkLn 19
                                       +S e Av Lsk+  
  gene1211|gene1211|rna1211|rna1211 14 LSKEAAVILSKEAA 27
                                       67788888888654 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.04
                               YycC  6 iSpeTAvkLskk 17
                                       +S e Av Lsk+
  gene1211|gene1211|rna1211|rna1211 30 LSEEAAVILSKE 41
                                       799*******97 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.043
                               YycC  6 iSpeTAvkLskk 17
                                       +S e Av Ls++
  gene1211|gene1211|rna1211|rna1211 46 LSKEAAVILSEE 57
                                       689999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       401  (0.022366); expected 358.6 (0.02)
Passed bias filter:                      223  (0.0124379); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 672.62
//
Query:       gene1212|gene1212|rna1212|rna1212  [L=934]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    6.9e-34  117.1   0.0    2.3e-33  115.4   0.0    1.8  2  DEAD        DEAD/DEAH box helicase
    5.2e-29  100.8   0.2    1.3e-27   96.4   0.1    2.6  2  Helicase_C  Helicase conserved C-terminal domain
     0.0006   19.8   0.1     0.0011   18.9   0.1    1.4  1  Flavi_DEAD  Flavivirus DEAD domain
     0.0013   18.8   0.0     0.0013   18.8   0.0    2.9  3  ResIII      Type III restriction enzyme, res subunit


Domain annotation for each model (and alignments):
>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.47   2.1e+03      58      97 ..     517     555 ..     513     561 .. 0.87
   2 !  115.4   0.0   5.2e-37   2.3e-33       2     173 ..     581     748 ..     580     751 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.47
                                        HHHHHHHHHHHHHTTTSTSEEEEEETTSSHHHHHHHHHTT CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               DEAD  58 eLaeqtlnnlkkfkkyidlrvlliiggvaardqlskldng 97 
                                         L++  ++nlk   +++++ vl  +++v+++d++s++ +g
  gene1212|gene1212|rna1212|rna1212 517 RLMKSLFKNLKLAEEKYGIDVLNEYKNVRRSDDVSEF-KG 555
                                        68999999999999999999***********999998.65 PP

  == domain 2  score: 115.4 bits;  conditional E-value: 5.2e-37
                                        HHHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSE CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               DEAD   2 diQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlr 77 
                                        ++Q++++ +    ++++v+a+ G+GKTla+l+p+l+++++ +++++ k++i++PtreLa q+++ +k++  + d +
  gene1212|gene1212|rna1212|rna1212 581 PVQKQVLSTSR--NNLVVRAKNGTGKTLAYLLPILNNILKAEESKRVKTIILVPTRELAMQVAKVAKRLATHFDKS 654
                                        78888877755..89*************************9*******************************9977 PP

                                        EEEE..ETTSSHHHHHHHHHTTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHH CS
                                        xxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               DEAD  78 vlli..iggvaardqlskldngvdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsdfinrilnqlpq 151
                                        v+l+  +gg++  +++ ++++g+d +++tpgr++dl++++ l l +v+ ++lDEad+ll+ +++d++++il+++++
  gene1212|gene1212|rna1212|rna1212 655 VVLMpsYGGSNLYEDVIRIKAGIDGIISTPGRILDLIERQVLLLGSVNDVILDEADKLLSLEYKDTLRKILRNINS 730
                                        77666799***********9******************************************************65 PP

                                        HCTTSTTTSEEEEEESSBSHHH CS
                                        xxxxxxxxxxxxxxxxxxxxxx RF
                               DEAD 152 itcdgklqrqvivlSATlpkdv 173
                                          +  +    + ++SAT+p  v
  gene1212|gene1212|rna1212|rna1212 731 RRNVYN----LRLFSATFPLPV 748
                                        554444....88*****99555 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0     0.085   3.8e+02       6      33 ..     613     645 ..     606     662 .. 0.67
   2 !   96.4   0.1   2.8e-31   1.3e-27       2     111 .]     785     893 ..     784     893 .. 0.92

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.085
                                        HHHHH.HHTTTTSEEEEEESSHH...HHHH.HH CS
                         Helicase_C   6 llell.kleeeggkilifvntid...rlek.vk 33 
                                        l ++l  +e+++ k++i v+t++   ++ k +k
  gene1212|gene1212|rna1212|rna1212 613 LNNILkAEESKRVKTIILVPTRElamQVAKvAK 645
                                        4455677889999**********6442222333 PP

  == domain 2  score: 96.4 bits;  conditional E-value: 2.8e-31
                                        HHHHHHHHHHHTTTTSEEEEEESSHHHHHHHHHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGT CS
                         Helicase_C   2 kleallellkleeeggkilifvntidrlekvklllekkgikvavlhgelpqnereeileqfnkgesdvLiatdvae 77 
                                        kl++l+ ll ++++  +++if+n+++++e + +  ++ g+++  l g+++q+er+ i+ +f + ++++L++td   
  gene1212|gene1212|rna1212|rna1212 785 KLHCLITLL-RKVKYTQTIIFCNRTKTAELLAYRITELGYSCYFLSGKMTQDERNTIFYSFTNLKINILVSTDLTT 859
                                        788999999.99**************995533333455************************************** PP

                                        SSSTSTTESEEEESSSSSSHHHHHHHHTTSSSTT CS
                         Helicase_C  78 rGidipkvnlVinfdlprnvtsyiqriGRtgRag 111
                                        rGid+p++nlVinfd pr+++sy +riGR+gR+g
  gene1212|gene1212|rna1212|rna1212 860 RGIDVPGINLVINFDWPRTIESYLHRIGRAGRFG 893
                                        ********************************86 PP

>> Flavi_DEAD  Flavivirus DEAD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.1   2.5e-07    0.0011       6      65 ..     593     656 ..     588     667 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 2.5e-07
                                        EEEEE--TTS-TTTTHH....HHHHHHHHHTT--EEEEESSHHHHHHHHHHTTTS-EEE----- CS
                         Flavi_DEAD   6 ltvldlhPGaGktrkvl....pelvkeaierrlrtlvLaPtrvvlaemeealkglevryktsav 65 
                                          v+ ++ G+Gkt  +l     +++k+  ++r++t++L+Ptr  +  +++  k l  ++++s+v
  gene1212|gene1212|rna1212|rna1212 593 NLVVRAKNGTGKTLAYLlpilNNILKAEESKRVKTIILVPTRELAMQVAKVAKRLATHFDKSVV 656
                                        56889999*****986511115778888899*******************99999999999877 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -5.1   5.3         4   1.8e+04     105     121 ..     225     241 ..     181     291 .. 0.49
   2 !   18.8   0.0   2.8e-07    0.0013      22     157 ..     589     728 ..     542     746 .. 0.66
   3 ?   -2.2   0.2      0.82   3.7e+03      38     110 ..     782     855 ..     781     859 .. 0.71

  Alignments for each domain:
  == domain 1  score: -5.1 bits;  conditional E-value: 4
                                        SEEEEEHHHHHHTH... CS
                             ResIII 105 kilvttiqsldadseee 121
                                        + ++ + ++ ++ds ++
  gene1212|gene1212|rna1212|rna1212 225 EDIINNSNTNNEDSINN 241
                                        22222222222222111 PP

  == domain 2  score: 18.8 bits;  conditional E-value: 2.8e-07
                                        .TTSEEEEEESTTSTHHHHH.HHHHHHH-S........-EEEEESSHHHHHHHHHHGGGGTGG...........GE CS
                             ResIII  22 krdkrglikmaTGtGKTlva.aklierllkkgkee...kflflvprkslleqtleefkkflseayke.......ig 86 
                                        + ++++++ +  GtGKTl + + +  ++lk+++ +   k+++lvp+++l  q  +  k+++   +k+        g
  gene1212|gene1212|rna1212|rna1212 589 TSRNNLVVRAKNGTGKTLAYlLPILNNILKAEE-SkrvKTIILVPTRELAMQVAKVAKRLATHFDKSvvlmpsyGG 663
                                        56678889999*********5555556666555.4599**************997766666554444554444333 PP

                                        EEESSS-B--.......-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS....TTTHHHHHT- CS
                             ResIII  87 kkvsgdkkkakekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgak...kswreilekf 157
                                         ++ +d  ++    +  ++ +++t  ++   +     e++ ll ++ + +i DEa +l +    ++ r+il+++
  gene1212|gene1212|rna1212|rna1212 664 SNLYEDVIRI----KAGIDGIISTPGRILDLI-----ERQVLLLGSVNDVILDEADKLLSLeykDTLRKILRNI 728
                                        3333333333....566666666666666666.....5566666666666666666666543323555555555 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 0.82
                                        HHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG....GEEEESSS-B--.........-SEEEEE CS
                             ResIII  38 Tlvaaklierllkkgkeekflflvprkslleqtleefkkflseaykeigkkvsgdkkka..kekdstnkkilvtt 110
                                        T   ++    ll+k k+ +++++++r++  e +  +++++  ++y   ++k+++d+++   ++  + +++ilv+t
  gene1212|gene1212|rna1212|rna1212 782 TEYKLHCLITLLRKVKYTQTIIFCNRTKTAELLAYRITELGYSCYF-LSGKMTQDERNTifYSFTNLKINILVST 855
                                        5555666666777788889999999999999999999999998875.5666666655554555556666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (934 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1361  (0.0759105); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.87u 0.31s 00:00:01.18 Elapsed: 00:00:00.44
# Mc/sec: 6409.25
//
Query:       gene1213|gene1213|rna1213|rna1213  [L=322]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-15   56.4   0.9    4.8e-15   55.7   0.9    1.3  1  RhoGAP    RhoGAP domain


Domain annotation for each model (and alignments):
>> RhoGAP  RhoGAP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.7   0.9   2.7e-19   4.8e-15       1     148 [.      91     251 ..      91     255 .. 0.91

  Alignments for each domain:
  == domain 1  score: 55.7 bits;  conditional E-value: 2.7e-19
                                        BHHHHHHHHHHHHHTTTSTTTTTS-S-HHHHHHHHHHHHHTGGGCT.......TTTTSCHHHHHHHHHHHHHHSSS CS
                             RhoGAP   1 PiivekcvefiekrgldtegiyRvsgskarvkelreafdkgkavds.......dleeedvhavaslLKrfLrelpe 69 
                                        Pi ++ ++e+i  + l+  g++R+s+s ++++++ + ++ +++ +        +l  +d+ +++ + Kr + ++  
  gene1213|gene1213|rna1213|rna1213  91 PIEFNCIMEAILTKNLNISGLFRKSASISEFERCFSLINDQETRSMcrleiknRLLPFDIITLTVVYKRLFDNYDM 166
                                        7888999*******************************999998779***************************** PP

                                        TTTTGGHHHHHHHHHTSSSHHHHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHHH....THHH..H---HHHHHHHH CS
                             RhoGAP  70 pLltkelyeelieaaksedeeerlealkellekLPkenrdtLryLlehLkrvae....nske..nkMtaknLaivf 139
                                         ++++++++ l+++ k e++ e++  lk +l  +Pk nr+++ ++ +++         ++k    +M+++  a+v+
  gene1213|gene1213|rna1213|rna1213 167 TIIPQSFLKVLLNVSKLESKYEQVIILKYVLYMMPKSNRNMMDSIAQFFALMRYliiyYNKTptPNMDMYGFAVVI 242
                                        ***********************************************998655433333333559*********** PP

                                        HHHHHT-TS CS
                             RhoGAP 140 aPtLlrpks 148
                                        +P ++ +++
  gene1213|gene1213|rna1213|rna1213 243 MPKIFLKPA 251
                                        ****98876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (322 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       650  (0.0362541); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 1996.26
//
Query:       gene1214|gene1214|rna1214|rna1214  [L=423]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (423 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1023  (0.0570584); expected 358.6 (0.02)
Passed bias filter:                      536  (0.0298957); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.62u 0.29s 00:00:00.90 Elapsed: 00:00:00.49
# Mc/sec: 2607.68
//
Query:       gene1215|gene1215|rna1215|rna1215  [L=178]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       345  (0.0192426); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 1204.08
//
Query:       gene1216|gene1216|rna1216|rna1216  [L=71]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.12   12.0   0.0       0.13   11.9   0.0    1.0  1  FSH1      Serine hydrolase (FSH1)


Domain annotation for each model (and alignments):
>> FSH1  Serine hydrolase (FSH1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   7.2e-06      0.13      63     107 ..      16      59 ..       2      60 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 7.2e-06
                               FSH1  63 kseeeeesraWfrkkdekneyegleesldavkdyikengpfdGii 107
                                        ++ ++ + ra+f++k+  +ey +  ++++ v++y+k+n++ +G++
  gene1216|gene1216|rna1216|rna1216  16 TNFKNRNIRAYFKRKA-FDEYLECVNGVRPVEKYLKDNEELKGVM 59 
                                        5567888999999998.**************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (71 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       533  (0.0297284); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.29s 00:00:00.67 Elapsed: 00:00:00.44
# Mc/sec: 485.71
//
Query:       gene1217|gene1217|rna1217|rna1217  [L=107]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       263  (0.014669); expected 358.6 (0.02)
Passed bias filter:                      237  (0.0132188); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.44
# Mc/sec: 737.83
//
Query:       gene1218|gene1218|rna1218|rna1218  [L=196]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.5e-18   67.2  21.4    1.4e-16   60.7  21.4    2.1  1  YIF1         YIF1


Domain annotation for each model (and alignments):
>> YIF1  YIF1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.7  21.4     8e-21   1.4e-16      11     238 ..       4     195 ..       1     196 [] 0.89

  Alignments for each domain:
  == domain 1  score: 60.7 bits;  conditional E-value: 8e-21
                               YIF1  11 lGqsalsqgqeyveknlnryvsvsalkyyFnVsnsYVlkKlllllfPflhksWsrkseqseesseylppredvnap 86 
                                        lGq+al++g+ yv+ +++ + s s l+ yF+V+ + Vl+++ lllfPf  ++W+                  + +p
  gene1218|gene1218|rna1218|rna1218   4 LGQNALNAGKSYVNTRIHTL-SPSILRPYFKVTPNHVLSRIILLLFPFKTSRWT------------------LFSP 60 
                                        8****************966.6679****************************9..................568* PP

                               YIF1  87 DLYiPlmalvtYillaglllGlqgkFspelLgikassalavvllevlilklglYllnissasslldlvaysgYkfv 162
                                        DLY+P++++ +++l+ +l +      +++l+ + ++++l++ +l ++++k   +++ ++    +++lva s  k++
  gene1218|gene1218|rna1218|rna1218  61 DLYVPFVSYQSFLLVKALCIK-----NNKLFAYYFTKTLVIEVLLIVFVKALSFFMDVEI--MVINLVAVSFHKYI 129
                                        ****************99875.....4678899*************************95..89************ PP

                               YIF1 163 gvivtlllklllgeglvyylvllylvlalafFllrsLklvllpeasetvkksqrkkrkqflflvaavlQlllmllL 238
                                         +++ ll++++  +  v  l+++ylv+a+ +F  r +k+v+ +          r+k ++fl++v+ vl ++++llL
  gene1218|gene1218|rna1218|rna1218 130 VMVAGLLCGSF--NLFVGRLAWMYLVVAMFVFFCRGFKYVIGSCGV-------RRKSVYFLMFVV-VLECFYVLLL 195
                                        *********99..666899*********************987654.......466666666555.8888777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       853  (0.0475766); expected 358.6 (0.02)
Passed bias filter:                      227  (0.0126611); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 1351.56
//
Query:       gene1219|gene1219|rna1219|rna1219  [L=56]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (56 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       227  (0.0126611); expected 358.6 (0.02)
Passed bias filter:                      160  (0.00892409); expected 358.6 (0.02)
Passed Vit filter:                         7  (0.000390429); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.33u 0.28s 00:00:00.61 Elapsed: 00:00:00.42
# Mc/sec: 397.98
//
Query:       gene122|gene122|rna122|rna122  [L=757]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.8e-52  175.3   2.5    2.3e-29  101.9   0.1    2.9  3  SIS       SIS domain
    5.3e-17   62.3   0.0    9.6e-17   61.4   0.0    1.3  1  GATase_6  Glutamine amidotransferase domain
    2.6e-13   49.9   0.0    5.6e-13   48.9   0.0    1.5  1  GATase_7  Glutamine amidotransferase domain
    2.6e-05   23.3   0.1    4.3e-05   22.5   0.1    1.3  1  GATase_4  Glutamine amidotransferases class-II
     0.0097   14.7   0.1      0.017   13.9   0.1    1.4  1  GATase_2  Glutamine amidotransferases class-II
  ------ inclusion threshold ------
      0.081   12.9   0.0        1.1    9.3   0.0    2.7  2  SIS_2     SIS domain


Domain annotation for each model (and alignments):
>> SIS  SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.0   0.0       4.2   1.2e+04      51      86 ..      42      78 ..      40      80 .. 0.74
   2 !  101.9   0.1   7.7e-33   2.3e-29       3     129 ..     439     564 ..     437     566 .. 0.96
   3 !   72.7   0.0   8.2e-24   2.4e-20       4     130 ..     611     739 ..     608     740 .. 0.89

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 4.2
                                   -STTCEEEEEESSSHHHHHHHHHHHHHHTTSEE.EEE CS
                            SIS 51 ideddlvilisfsgetkdlvaaaelakergaki.iaI 86
                                   ++++d + +i  +g   +l++a++ ++++ ++  ++I
  gene122|gene122|rna122|rna122 42 VRNNDGFTIIKKTGKVEELARAINILTQDTMESsVSI 78
                                   6677777788899999999999998887765554666 PP

  == domain 2  score: 101.9 bits;  conditional E-value: 7.7e-33
                                    CTSSEEEEEESHHHHHHHHHHHHHHHHHHTSEEEEEEHHHHHHTGGGG-STTCEEEEEESSSHHHHHHHHHHHHHHTTSE CS
                            SIS   3 akakriyvlGaGtsyaiakelalkleeiggivvevedaselkhgvlalideddlvilisfsgetkdlvaaaelakergak 82 
                                      + r++++++Gtsy++a+  +  +ee+  i+v++e as + ++   +i + d+v++is+sget+d+++a+ ++k+++a 
  gene122|gene122|rna122|rna122 439 KRSSRLIFIACGTSYHTAMATQSLFEELIDIPVSIEIASNFLDR-QCPIFRSDCVFFISQSGETADTLNALMYCKSKQAL 517
                                    5678****************************************.667999***************************** PP

                                    EEEEESSTTSHHHHHSSEEEEEEEECHCSSSHCHHHHHHHHHHHHHH CS
                            SIS  83 iiaITdskgsplareadlalyinaepetlvastksltaqlaaldala 129
                                    +++IT+  gs+++re+ + +++n +pe++vastk++++q+++l ++a
  gene122|gene122|rna122|rna122 518 CVGITNTVGSTICRETECGVHVNCGPEIGVASTKAYSSQFIVLVMIA 564
                                    ******************************************99987 PP

  == domain 3  score: 72.7 bits;  conditional E-value: 8.2e-24
                                    TSSEEEEEESHHHHHHHHHHHHHHHHHHTSEEEEEEHHHHHHTGGGG-STTCEEEEEESSSHHHHHHHHHH.HHHHTTSE CS
                            SIS   4 kakriyvlGaGtsyaiakelalkleeiggivvevedaselkhgvlalideddlvilisfsgetkdlvaaae.lakergak 82 
                                    +   +++lG+G++ a+++e+alk++e++++++e+ +++elkhg++ali++++lvi+i ++++  ++ ++a  ++ +r +k
  gene122|gene122|rna122|rna122 611 DRGDMLILGRGYQHALCLEAALKIKEVAYMHAEGILTGELKHGPIALIEPETLVIMIITNDHVLKKSENAVsELMARRGK 690
                                    556789*********************************************************999999999******** PP

                                    EEEEESSTTSHHHHHSSEEEEEEEECHC...SSSHCHHHHHHHHHHHHHHH CS
                            SIS  83 iiaITdskgsplareadlalyinaepet...lvastksltaqlaaldalav 130
                                    +i++T+++     ++ +   +++  p t   l++++ +++ ql++++++++
  gene122|gene122|rna122|rna122 691 PIIVTNNELVD--QFKKMGCMTIGIPTTvdcLQGLLTVIPMQLLSYHLAVI 739
                                    *****887754..444556666666666799*****************997 PP

>> GATase_6  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.4   0.0   3.2e-20   9.6e-17      10     113 ..      72     188 ..      61     204 .. 0.84

  Alignments for each domain:
  == domain 1  score: 61.4 bits;  conditional E-value: 3.2e-20
                       GATase_6  10 vedevalaHvRlaivglaeeegaqPf.psedgrlllvhNGeiynykelreelpalkglafrsrsDtevllall....... 81 
                                    +e++v +aH+R+a++g + e+  +P+ +  + ++++vhNG i nykel+e l++ ++++f +++Dte  ++l+       
  gene122|gene122|rna122|rna122  72 MESSVSIAHTRWATHGFPCEKNSHPIsSDINNEFVVVHNGIITNYKELNEFLKK-RNYSFHTDTDTETAAKLAlyfyern 150
                                    57789*************77777***6677888*********************.**************99665899865 PP

                       GATase_6  82 eelG.......eevlerlrGmfafaiwdk.rentlilard 113
                                    +          + v++ ++G+faf ++++  +n++i +r 
  gene122|gene122|rna122|rna122 151 K--NasfmsiiKNVVRCCDGAFAFIFVSShFPNEMIAVRK 188
                                    3..234778989999*************988999888865 PP

>> GATase_7  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.9   0.0   1.9e-16   5.6e-13       9     108 ..      90     198 ..      80     208 .. 0.84

  Alignments for each domain:
  == domain 1  score: 48.9 bits;  conditional E-value: 1.9e-16
                       GATase_7   9 seagaQPmvssedgrlvivfnGeiyNykelreeLeakghrfrtksDtevllallea...........ewgeealerlnGm 77 
                                     e+++ P++s+ ++++v+v+nG i+Nykel e L++++++f+t++Dte+ ++l  +             ++++++ ++G 
  gene122|gene122|rna122|rna122  90 CEKNSHPISSDINNEFVVVHNGIITNYKELNEFLKKRNYSFHTDTDTETAAKLALYfyernknasfmSIIKNVVRCCDGA 169
                                    577889999988999**********************************88876667799*******9************ PP

                       GATase_7  78 fAfaiwdeeek.rlllaRDrlGikPLyygedk 108
                                    fAf+ + ++   +++++R      PL +g ++
  gene122|gene122|rna122|rna122 170 FAFIFVSSHFPnEMIAVRK---SSPLLIGVKS 198
                                    ****998765437888887...4777777665 PP

>> GATase_4  Glutamine amidotransferases class-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.1   1.4e-08   4.3e-05      63     133 ..      66     139 ..      48     175 .. 0.84

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 1.4e-08
                       GATase_4  63 lvreypiksknvvaHiRkatqGevklenthpFvRelwgrewifAHnGdlkeykpkl....egrfePvGsTDsEla 133
                                    ++ +  ++s++ +aH R at+G   ++n+hp + +  ++e++  HnG +++yk+      + +++   +TD+E+a
  gene122|gene122|rna122|rna122  66 ILTQDTMESSVSIAHTRWATHGFPCEKNSHPISSDI-NNEFVVVHNGIITNYKELNeflkKRNYSFHTDTDTETA 139
                                    4555569************************99886.5789********99887666667677888889999987 PP

>> GATase_2  Glutamine amidotransferases class-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.1   5.6e-06     0.017     188     266 ..      59     144 ..       2     164 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.6e-06
                                    GHHHHBHGGGSTT--BSEEEEEE---SSSS--GGGSSS-S.......SEEEEE--TTHHHHHHHHHHHCTT--BT-HH.H CS
                       GATase_2 188 qlkefykdlkdeelesalalvHsRfstntfPsWelaqPlR.......llaHnGEintlrGnknwmkareaelksellgde 260
                                    +l +  + l+++++es++ + H+R++t  fP  + ++P+        ++ HnG i   +  +++ k r+ ++++++ +++
  gene122|gene122|rna122|rna122  59 ELARAINILTQDTMESSVSIAHTRWATHGFPCEKNSHPISsdinnefVVVHNGIITNYKELNEFLKKRNYSFHTDTDTET 138
                                    555556678999**************************864444444799*********999*********999988887 PP

                                    HHTC-- CS
                       GATase_2 261 lekllP 266
                                     +kl+ 
  gene122|gene122|rna122|rna122 139 AAKLAL 144
                                    777765 PP

>> SIS_2  SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0   0.00037       1.1      97     137 ..     482     522 ..     472     523 .. 0.87
   2 ?   -0.4   0.0      0.37   1.1e+03      19      65 ..     596     642 ..     588     683 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00037
                                    HHTT--TT-EEEEE-SS--SHHHHHHHHHHHHHT-EEEEEE CS
                          SIS_2  97 rlvrlkpgDvLlviSnsGnnavvveaaeaakergmkviAlt 137
                                    r+ ++  +D  + iS+sG+ a  ++a++++k++++  +++t
  gene122|gene122|rna122|rna122 482 RQCPIFRSDCVFFISQSGETADTLNALMYCKSKQALCVGIT 522
                                    56788999***************************999998 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.37
                                    HHHHHHHHHHHHHHHTT--EEEEESGGGHHHHHHTSSSTT-BTTEEE CS
                          SIS_2  19 eaiekaaeliadslenggkvlvfGsGhSaalaeelaaragglaefer 65 
                                     +i++ ++++a+ + + g  l++G G  +al+ e+a ++  +a +++
  gene122|gene122|rna122|rna122 596 LEIDEYIKVLAQKICDRGDMLILGRGYQHALCLEAALKIKEVAYMHA 642
                                    57888889999999999999999999999999999988877666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (757 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       813  (0.0453455); expected 358.6 (0.02)
Passed bias filter:                      523  (0.0291706); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.74u 0.31s 00:00:01.05 Elapsed: 00:00:00.50
# Mc/sec: 4542.54
//
Query:       gene1220|gene1220|rna1220|rna1220  [L=48]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (48 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       462  (0.0257683); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.27s 00:00:00.61 Elapsed: 00:00:00.41
# Mc/sec: 350.74
//
Query:       gene1221|gene1221|rna1221|rna1221  [L=63]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (63 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       250  (0.0139439); expected 358.6 (0.02)
Passed bias filter:                      192  (0.0107089); expected 358.6 (0.02)
Passed Vit filter:                         7  (0.000390429); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.32u 0.27s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 478.71
//
Query:       gene1222|gene1222|rna1222|rna1222  [L=142]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      3e-44  151.7   0.1    3.2e-44  151.6   0.1    1.0  1  Trehalase  Trehalase


Domain annotation for each model (and alignments):
>> Trehalase  Trehalase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  151.6   0.1   1.8e-48   3.2e-44      44     183 ..       4     140 ..       1     142 [] 0.94

  Alignments for each domain:
  == domain 1  score: 151.6 bits;  conditional E-value: 1.8e-48
                                        HHHHHHCE-SGGGS.EEE-TT-HHHHHHHHHHHCTGGHH.EECCHHCCTTCCCCHTTTS-SCE-TTECEEE-TT-E CS
                          Trehalase  44 kfvedtfeetgselerivpkdekeqpeyflkkaedeelrleaeelnklwkalvrkikkkvgllpeassllplpkpf 119
                                        +f+e++f+e+ s+ +  +  + ++ p+ f+  +++++lr+  ++l++ w+ l++  +  ++++   s+l+ lp+pf
  gene1222|gene1222|rna1222|rna1222   4 SFLEKYFSEPASDIKSYNSLELAKPPK-FSIGINNSRLRNLLQALHERWNMLYK--ETIPNANDCMSTLIELPHPF 76 
                                        79999****988888888888887777.99999*********************..8889999999********** PP

                                        E-SBTTB-S-BCCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHSS--SBSBGGGTT---S-- CS
                          Trehalase 120 vVPGgRFrElYyWDsYfvilGLleskkvdlakgmvenfiyliekYGkilNgnRsYYlsRSQPPl 183
                                        +VPGgRFrElYyWD++fv +GL++s+  +   +m++nfiyli++YG+i+Ng+R YYl+RSQPP+
  gene1222|gene1222|rna1222|rna1222  77 IVPGGRFRELYYWDTWFVLEGLIASGLKEASVNMLKNFIYLIDQYGFIPNGTRKYYLNRSQPPF 140
                                        ***************************************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       362  (0.0201908); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1042.77
//
Query:       gene1223|gene1223|rna1223|rna1223  [L=263]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1265  (0.0705561); expected 358.6 (0.02)
Passed bias filter:                      656  (0.0365888); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.21s 00:00:00.68 Elapsed: 00:00:00.38
# Mc/sec: 2069.39
//
Query:       gene1224|gene1224|rna1224|rna1224  [L=281]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       685  (0.0382063); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1867.70
//
Query:       gene1225|gene1225|rna1225|rna1225  [L=161]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0035   17.1   0.0     0.0056   16.4   0.0    1.5  1  TRAPP     Transport protein particle (TRAPP) component


Domain annotation for each model (and alignments):
>> TRAPP  Transport protein particle (TRAPP) component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   3.1e-07    0.0056      28      73 ..      35      81 ..      28     149 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 3.1e-07
                              TRAPP 28 kmGyrvGlrllelllarer.pretdilevlkfickdlWkllfgkqid 73
                                       ++G ++G rl++++++++  +r++ i e ++ +++d++ ++f   ++
  gene1225|gene1225|rna1225|rna1225 35 SLGESIGNRLADDFILHTGiSRKLSIDEFVHTVQNDFFPHYFSYSPK 81
                                       68***************9999*********************98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       460  (0.0256568); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.28s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 1147.96
//
Query:       gene1226|gene1226|rna1226|rna1226  [L=127]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       499  (0.027832); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.29s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 885.96
//
Query:       gene1227|gene1227|rna1227|rna1227  [L=173]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.013   16.2   0.7      0.022   15.4   0.7    1.4  1  Hydrophobin  Fungal hydrophobin


Domain annotation for each model (and alignments):
>> Hydrophobin  Fungal hydrophobin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   0.7   1.2e-06     0.022      24      67 ..      31      74 ..      20      90 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.2e-06
                        Hydrophobin 24 llgllglelkdltgqvgltCspinvvgvgggssCtqqpvCCenn 67
                                       +++ll  +lk++++q++l+ +  +++++ + ++C++  vCC   
  gene1227|gene1227|rna1227|rna1227 31 IVQLLASDLKGIEEQLTLKLKLNKIISILQTNECKNMMVCCRFD 74
                                       668999999****99999988888999999***********855 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (173 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       645  (0.0359752); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.46
# Mc/sec: 1140.43
//
Query:       gene1228|gene1228|rna1228|rna1228  [L=248]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.011   16.3   0.5      0.011   16.3   0.5    1.9  2  YuiB         Putative membrane protein
        1.6    9.1   5.0        1.4    9.3   1.9    2.5  3  Sigma_reg_N  Sigma factor regulator N-terminal


Domain annotation for each model (and alignments):
>> YuiB  Putative membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   16.3   0.5   1.3e-06     0.011      18      71 ..       7      59 ..       4      83 .. 0.85
   2 ?   -0.6   0.1      0.23     2e+03      16      54 ..     161     198 ..     146     233 .. 0.66

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.3e-06
                               YuiB 18 filnmllrttWilaviypivvllivdkvklleyltepkeafaslleklvelalv 71
                                       f+l +l+  ++i++v++pi++l +  kv +++y++++k+++++++++++++a  
  gene1228|gene1228|rna1228|rna1228  7 FLL-LLILFAFIFLVVLPILILQVALKVGTYTYMQHSKSTINKFFADVQAFASN 59
                                       555.55667899************************************999764 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.23
                               YuiB  16 igfilnmllrttWilaviypivvllivdkvklleyltep 54 
                                        +  ++n ll +  + +v+ p v++l  d++ ++ y  e+
  gene1228|gene1228|rna1228|rna1228 161 VDKMINFLLGNKPF-TVLKPNVFILNYDTEYFTIYEVET 198
                                        55566777766554.466777777788877777665444 PP

>> Sigma_reg_N  Sigma factor regulator N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   1.9   0.00015       1.4      10      55 ..       2      56 ..       1      59 [. 0.72
   2 ?   -2.1   0.0      0.56     5e+03      55      62 ..      86      93 ..      70     102 .. 0.78
   3 ?   -1.4   0.0      0.33     3e+03      55      72 ..     176     191 ..     159     203 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00015
                        Sigma_reg_N 10 ksilrivlislivlllifvil.vvtllyl........aekegnklrevlelavei 55
                                       k++l+  l+ ++++++++v+l +++l+          ++++++ +++++ ++ ++
  gene1228|gene1228|rna1228|rna1228  2 KNWLKFLLLLILFAFIFLVVLpILILQVAlkvgtytyMQHSKSTINKFFADVQAF 56
                                       6778888888888888888887777766666677777777788888888777666 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.56
                        Sigma_reg_N 55 itsPNvyv 62
                                       +++PNv+ 
  gene1228|gene1228|rna1228|rna1228 86 LMKPNVQK 93
                                       68999985 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.33
                        Sigma_reg_N  55 itsPNvyvdsgsvsqsgf 72 
                                        + +PNv++   +++++ f
  gene1228|gene1228|rna1228|rna1228 176 VLKPNVFI--LNYDTEYF 191
                                        66899998..44444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (248 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1011  (0.0563891); expected 358.6 (0.02)
Passed bias filter:                      556  (0.0310112); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 1727.24
//
Query:       gene1229|gene1229|rna1229|rna1229  [L=181]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       470  (0.0262145); expected 358.6 (0.02)
Passed bias filter:                      240  (0.0133861); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 1233.21
//
Query:       gene123|gene123|rna123|rna123  [L=496]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    6.6e-20   71.2   1.6      1e-11   44.2   0.0    4.3  3  GDA1_CD39  GDA1/CD39 (nucleoside phosphatase) family
  ------ inclusion threshold ------
        5.2    6.1  14.6        2.3    7.3   1.4    2.1  2  MMU163     Mitochondrial protein up-regulated during meiosis


Domain annotation for each model (and alignments):
>> GDA1_CD39  GDA1/CD39 (nucleoside phosphatase) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.2   0.0   1.1e-15     1e-11       8     147 ..      26     157 ..      24     249 .. 0.89
   2 !   13.0   0.5   3.4e-06      0.03     155     180 ..     324     349 ..     278     406 .. 0.77
   3 !    5.2   0.0   0.00077       6.9     356     409 ..     441     492 ..     425     495 .. 0.79

  Alignments for each domain:
  == domain 1  score: 44.2 bits;  conditional E-value: 1.1e-15
                      GDA1_CD39   8 ekygiviDAGSsgsrlhvykwkdekesllqivklieevkklePGlSsfekkpeeaaeylkpllelaeeviPee..krset 85 
                                    +++++++DAG + ++l vy++       +++  +  +++  +PG+ +     +e+++ ++ +l  a++++ e+    + t
  gene123|gene123|rna123|rna123  26 KQFVVILDAGFTSTKLNVYTF-------SDMIVVSSYTRFYHPGVHE--LRMNEIEHMIECMLSDARKFVEENggDVHRT 96 
                                    68*******************.......22233345688899**965..56799****************997446899* PP

                      GDA1_CD39  86 pvlikATAGlRLlkeekkekilkalrnklkklsefkvedqgiriidGeeEGiYgWiaiNYll 147
                                     +++ AT GlR l    ++ il+ ++  l + s f +  + ++++dG  EG+Y++ a+ Yll
  gene123|gene123|rna123|rna123  97 RIALVATEGLRSLGRTCADVILRCIKG-LIDRSGFVSGRHSVSVMDGVFEGLYAYEALVYLL 157
                                    ***********************9975.5567899999**********************98 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 3.4e-06
                      GDA1_CD39 155 pevskqetvgvlDlGGaStQiafepq 180
                                      ++++   g++++GG+S Qiaf  +
  gene123|gene123|rna123|rna123 324 LTTNSKLSLGIIEMGGGSMQIAFSTN 349
                                    456777889**************876 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.00077
                      GDA1_CD39 356 keksiseeeaCfkgayvlslLhdGfdldktveelqsvekiaekelgWtLGamln 409
                                    k + +   ++C ++ y++ + ++G  l+ +  ++++ + i++k+l+W L  +l+
  gene123|gene123|rna123|rna123 441 KTRCVRRTKNCNDLEYMVLV-LKGIGLKGD-TRVEIGRMIDDKNLNWGLAKALE 492
                                    3344444579******9975.58****999.99****************99987 PP

>> MMU163  Mitochondrial protein up-regulated during meiosis
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   6.8    0.0045        40     113     185 ..     161     234 ..     152     253 .. 0.67
   2 ?    7.3   1.4   0.00026       2.3     136     215 ..     289     368 ..     238     371 .. 0.57

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.0045
                         MMU163 113 eeedlgdeklvvrWktegkeskkkeeg.gka.ekekveksasskssksekskkeesksalssskegvnkglsvll 185
                                    +++d+  e+lv r++ +  + +++e g +++ ++  ++++ ++k+++ ++++++++k+a++++++++  +  +l 
  gene123|gene123|rna123|rna123 161 DNKDILGEQLVDRYRKNK-TRRDDEVGrSDRnAVRVSKNWWNEKKNNGQSTENRDKKTASDNTQDNITDSSNKLT 234
                                    4678899*******9994.55555555433335666667777777777777777777777777777766655554 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.00026
                         MMU163 136 keeggkaekekveksasskssksekskkeesksalssskegvnkglsvllggdapifklekeeeftGlfifefDeeGRia 215
                                    +e ++ +  ++ ++++ss +s++  +++++++s++ ++++++  g+  + gg + i  +++ ++   lfi +f + G i+
  gene123|gene123|rna123|rna123 289 NEFDKVTYLKPRNNTTSSIKSENYLQREHSTTSHSLTTNSKLSLGIIEMGGGSMQIAFSTNVGNKYQLFIHSFHNLGLIK 368
                                    1111111222222222222222223333333333333444455566678899999988888888889*******999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (496 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1387  (0.0773607); expected 358.6 (0.02)
Passed bias filter:                      484  (0.0269954); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.64u 0.32s 00:00:00.96 Elapsed: 00:00:00.48
# Mc/sec: 3082.56
//
Query:       gene1230|gene1230|rna1230|rna1230  [L=188]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       585  (0.0326287); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.29s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 1264.21
//
Query:       gene1231|gene1231|rna1231|rna1231  [L=395]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.9e-43  147.1   6.1    4.2e-41  141.2   6.1    2.3  1  VID27     VID27 C-terminal WD40-like domain


Domain annotation for each model (and alignments):
>> VID27  VID27 C-terminal WD40-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  141.2   6.1   2.3e-45   4.2e-41      11     343 ..     117     395 .]     110     395 .] 0.87

  Alignments for each domain:
  == domain 1  score: 141.2 bits;  conditional E-value: 2.3e-45
                              VID27  11 kndrsfvvrgdkiGvfkhtddnelefstaiskvetlkgkllsPkkvmlheedrklilqdekdknklykmDlerGkv 86 
                                         +d +fv rg+ +Gvf++   ++l f+ +i++ve +k k l+        +d++l++ de+ k  +  +Dle+G+v
  gene1231|gene1231|rna1231|rna1231 117 DKDTAFVARGNTVGVFNTA--DRLTFNCSIKNVEGKKRKFLK--------KDNQLLFLDENRK-DVKFLDLEKGRV 181
                                        5899************875..579*********988777664........6777777777554.55569******* PP

                              VID27  87 vdewkvhddipvvefapekkfaqlteeqtllGlsknalfriDPrlsgnklvdselkqyaskndfsavattekGyia 162
                                        v+   +  d+           + + ++  llG+++n++f +D r +g        ++y++k+ f+  ++t+  + a
  gene1231|gene1231|rna1231|rna1231 182 VERIGLTRDV----------NDVMLRDSELLGMNDNSVFVVDSRTKGI----GRDNTYKTKTYFTK-GSTNGTFSA 242
                                        **99998888..........36789999****************9984....34578999998875.67788899* PP

                              VID27 163 vasekGdirlfdrlginaktalPalgdpiigldvsadGrwvlatcktyllLiDalikegkneGklgfeksfakdsk 238
                                        ++s kGd+r++  + ++a+  +  lgd ++g+d+ +  ++v+ t k+yl+L+    +e kn+              
  gene1231|gene1231|rna1231|rna1231 243 IGSVKGDLRVYKDVFKRARILVSGLGDEVLGIDIGN--EYVILTFKNYLILFKI--EERKNS-------------- 300
                                        **********************************87..5************854..444443.............. PP

                              VID27 239 pkprrLklkpehvaqlqeetkkpvsftkakfntgldseettivtstGpfvitwslkkvlkgkkdpYkikryeeevv 314
                                         k  rL+l+pehva+l+++    vsft akfnt+    +t i+tstG++v+tw + +vl+g+   Yk++ y +evv
  gene1231|gene1231|rna1231|rna1231 301 RKVVRLQLRPEHVAFLKHS----VSFTAAKFNTS----NTDIITSTGQYVVTWRVCDVLNGNLYAYKMREYGSEVV 368
                                        45689***********885....*********98....789*********************************** PP

                              VID27 315 adnfkfgsdknvivalkndvsmvkkkslk 343
                                        +d+f  g+d+ v+v+lk+d++m +kk++k
  gene1231|gene1231|rna1231|rna1231 369 DDSFV-GEDR-VLVTLKDDLKMLNKKNIK 395
                                        **995.7776.999************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (395 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       546  (0.0304535); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.22s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2798.02
//
Query:       gene1232|gene1232|rna1232|rna1232  [L=76]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       417  (0.0232584); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.28s 00:00:00.64 Elapsed: 00:00:00.43
# Mc/sec: 525.39
//
Query:       gene1233|gene1233|rna1233|rna1233  [L=180]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.7e-14   52.3  12.6    6.9e-14   51.8   8.1    3.1  2  PAP2      PAP2 superfamily
      1e-07   31.9   8.9    2.3e-07   30.7   8.9    1.8  1  PAP2_3    PAP2 superfamily
  ------ inclusion threshold ------
       0.19   11.9   3.9       0.33   11.1   0.1    2.5  3  DUF212    Divergent PAP2 family
        2.9    8.5  15.3       0.98   10.0   1.4    2.8  2  PAP2_C    PAP2 superfamily C-terminal


Domain annotation for each model (and alignments):
>> PAP2  PAP2 superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.1      0.24   1.1e+03      10      30 ..      16      38 ..       5      66 .. 0.51
   2 !   51.8   8.1   1.5e-17   6.9e-14       4     130 ..      72     173 ..      68     178 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.24
                               PAP2 10 alaalltsv.lKdlvg.rpRPff 30
                                       +l + ++ + +  + +  +RP++
  gene1233|gene1233|rna1233|rna1233 16 ILYTTIHFLpIRIVTNtTTRPST 38
                                       22222222222333332344444 PP

  == domain 2  score: 51.8 bits;  conditional E-value: 1.5e-17
                               PAP2   4 alllalalaalltsvlKdlvgrpRPfflaeetkldtqvstletseskeakesfPSgHsafafalalllalllrrkr 79 
                                        ++  +l+++  lt+v+K  v++ RP++   +++                  sfPSgHs+ +f++a++++       
  gene1233|gene1233|rna1233|rna1233  72 VYYAGLFITETLTHVIKLCVREKRPYWQ--QERRGME--------------SFPSGHSSDMFYMATMFMNESIV-- 129
                                        4555666677778888999999999754..4444443..............89*********999987643333.. PP

                               PAP2  80 kkiglvllalillllavlvalsRlylgvHflsDvlaGlliGialaalayrl 130
                                               ++  ++++av+v+ +R+++g Hf++Dv++G+l+G+++++ ++r+
  gene1233|gene1233|rna1233|rna1233 130 -------CTSAFYVWAVVVGTTRVIDGKHFVWDVVGGALLGLMVGWGMKRV 173
                                        .......345699*********************************99886 PP

>> PAP2_3  PAP2 superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.7   8.9   5.2e-11   2.3e-07      30     187 ..      11     166 ..       6     169 .. 0.73

  Alignments for each domain:
  == domain 1  score: 30.7 bits;  conditional E-value: 5.2e-11
                             PAP2_3  30 vilala.Yaslhfqvtllvlvllflrrrerlr.eflttlllatllgll...vyalfPaagPrlleeagfvdtvaaa 100
                                        +il+++ Y ++hf+ + +v+    + r++ +  ++l + +++t +g++   +y   ++   +l+  ag+  t++ +
  gene1233|gene1233|rna1233|rna1233  11 FILSIIlYTTIHFLPIRIVTNT--TTRPSTYPsQLLMLSVYITPIGVFawqIYRNKYTSTVFLVYYAGLFITETLT 84 
                                        5677777999999999888888..4455555404444445555554441113333334444444667777777777 PP

                             PAP2_3 101 slagalrdgasravllrgtienglaafPSlHvawallvalalwrlrrkrllrvlalllnvlmivatvatgnHYlvD 176
                                        ++ + l   + r +++++   +g+ +fPS H    + +a +   ++++ + + ++ +++v++ ++ v  g H++ D
  gene1233|gene1233|rna1233|rna1233  85 HVIK-LCVREKRPYWQQER--RGMESFPSGHSSDMFYMATM--FMNESIVCTSAFYVWAVVVGTTRVIDGKHFVWD 155
                                        7777.77777788999998..**********9998888888..5666778999*********************** PP

                             PAP2_3 177 viaGvalalva 187
                                        v++G++l+l++
  gene1233|gene1233|rna1233|rna1233 156 VVGGALLGLMV 166
                                        *******9976 PP

>> DUF212  Divergent PAP2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0      0.77   3.5e+03      30      53 ..      23      46 ..       5      53 .. 0.53
   2 ?   11.1   0.1   7.3e-05      0.33       4      73 ..      68     139 ..      65     150 .. 0.74
   3 ?    1.6   0.2     0.063   2.8e+02     113     128 .]     151     166 ..     146     166 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.77
                             DUF212 30 kldlkllvstGgmPSsHsalvtal 53
                                        l ++++++t   PS++ +    l
  gene1233|gene1233|rna1233|rna1233 23 FLPIRIVTNTTTRPSTYPSQLLML 46
                                       333566666666666666655555 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 7.3e-05
                             DUF212   4 kvllaallawlvaqllKvliellkekkld.l.kllvstGgmPSsHsalvtalatavgleegldsslfalalv 73 
                                        +v+l+  ++++++ +l  +i+l++++k   + +   +   +PS Hs+ +  +at+ + e+ + +s f + +v
  gene1233|gene1233|rna1233|rna1233  68 TVFLVYYAGLFITETLTHVIKLCVREKRPyWqQERRGMESFPSGHSSDMFYMATMFMNESIVCTSAFYVWAV 139
                                        6889999999****999999987665544142344566789*********9999999888777776665444 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.063
                             DUF212 113 HtpleVlvGallGiiv 128
                                        H   +V++GallG++v
  gene1233|gene1233|rna1233|rna1233 151 HFVWDVVGGALLGLMV 166
                                        78899********986 PP

>> PAP2_C  PAP2 superfamily C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   6.5     0.042   1.9e+02      30      72 ..      38      84 ..       6      86 .. 0.74
   2 ?   10.0   1.4   0.00022      0.98       8      68 ..     110     166 ..     108     171 .. 0.74

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.042
                             PAP2_C 30 a...ilkvillllallglfliiasrkHYtvDVllglyittlvf.lly 72
                                       +    l +++++++ +g+f   + r+ Yt  V+l +y   ++  +l 
  gene1233|gene1233|rna1233|rna1233 38 TypsQLLMLSVYITPIGVFAWQIYRNKYTSTVFLVYYAGLFITeTLT 84
                                       244556788999999**********************9998876655 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00022
                             PAP2_C   8 SGHtvvltlavlfileyspkklailkvillllallglfliiasrkHYtvDVllglyittlv 68 
                                        SGH+  +  ++++ + + ++ +        ++a++     ++  kH+  DV+ g+++  +v
  gene1233|gene1233|rna1233|rna1233 110 SGHSSDM--FYMATMFMNESIV--CTSAFYVWAVVVGTTRVIDGKHFVWDVVGGALLGLMV 166
                                        6776554..4444555555555..667777888888999999************9998877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       636  (0.0354733); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.62u 0.38s 00:00:01.00 Elapsed: 00:00:00.58
# Mc/sec: 930.11
//
Query:       gene1234|gene1234|rna1234|rna1234  [L=611]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.4e-17   63.4   0.6    1.7e-07   30.2   0.0    3.0  2  Actin       Actin


Domain annotation for each model (and alignments):
>> Actin  Actin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8   0.3   1.2e-11   2.2e-07       6     243 ..       2     224 ..       1     249 [. 0.77
   2 !   30.2   0.0   9.6e-12   1.7e-07     202     399 ..     360     607 ..     342     610 .. 0.73

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 1.2e-11
                              Actin   6 avVlDnGssttraGyagedaPkavipslvgkprgrkveaklyvgdealtkrpelevrspvedGvvedwdaveelwe 81 
                                        +vV+DnG++t++ G ag   P++   +++ k++++     + +  +     +   ++++  + + +++d+ e +++
  gene1234|gene1234|rna1234|rna1234   2 TVVIDNGTHTIKYGIAGTR-PRTK-ENVLYKSKHN-----YSFTPS-----KDSYIKKMFVNNIPVNYDVLEGMLD 65 
                                        79**************964.6654.5555566664.....555544.....444566666678899********** PP

                              Actin  82 hvlkeelkvdpeehpllltepplnppkqrekalEivfEkfkvpalylaksavlsafasgks...tglvvDsGasvt 154
                                         v+ e l ++ + h ++lt  + +p+  + +++E+++E ++v+ l l+ + v s   ++k+   + +vv s +s+t
  gene1234|gene1234|rna1234|rna1234  66 CVFSE-LGIT-KVHDIVLTLGVCTPKVVKREIAELLIEVYNVHKLQLGIDSVYSYLHNVKQrnaCDIVVSSSHSET 139
                                        99987.6665.5799********************************************988889*********** PP

                              Actin 155 svvpVldGyvLkkairrsdlgGkaLteqlkellssknvevtpryl.ikkkkvveaessaekeelekltesyktlee 229
                                        + v           ++ ++ gG+    ++++ll+ kn++ t  y+ +++   +ea + + + ++++l+ sy   e+
  gene1234|gene1234|rna1234|rna1234 140 HLVRMDR----LDDVMALPYGGERARAYYNALLRPKNIRKTDFYVrVAQDYRREALAIYDRLRNRDLKGSYVLEER 211
                                        *997532....468999******************99999887751444455555555557788888888865444 PP

                              Actin 230 eevleeiKesvcev 243
                                        ++v e++ +  ++v
  gene1234|gene1234|rna1234|rna1234 212 KSV-EKAENMKMNV 224
                                        443.4433333333 PP

  == domain 2  score: 30.2 bits;  conditional E-value: 9.6e-12
                              Actin 202 kkkvveaessae.keelekltesyktleeeevleeiKesvcevsedpegdeekss...................ss 257
                                        +k+++e+   a+ ++ ++  ++++k++e e+ l+ iKe+   v+  +e++e+ ++                   ++
  gene1234|gene1234|rna1234|rna1234 360 NKQKIEKCLLAMrDSLTQLEERHFKMSEPEKYLQSIKERFFVVRARIEAKENLKRklrnkrsresallsratnmNE 435
                                        4444444444442444455567899999999999999999999998888555555555555666666666665433 PP

                              Actin 258 peksYeLPDg....................................................seiklgeeRfkvpE 281
                                        +e+ ++                                                          +  ++e  +v E
  gene1234|gene1234|rna1234|rna1234 436 NEQMFTQ--DeaqiieqineidhedsaseqkcskllneiyaldpsfefldfstveimngdhmGLTLSNTESLRVGE 509
                                        3333333..13477777777777777777777777777777777888888899999999875466778899***** PP

                              Actin 282 iLFdpsligsesaleeekskllgiselivaainacdvdlrpeLlanivvtGGnsllpglteRlekelaqlaskgvk 357
                                        + F+ps+++             g+se+i  a++ +    r++   n+ vtGG s ++g+ eR+ +e +  a+    
  gene1234|gene1234|rna1234|rna1234 510 AVFNPSIMNCALP---------GLSEMIESALQGIG---RAHGSVNVFVTGGFSQIEGFFERVVAECTMNAYG--G 571
                                        ******9998777.........**********9987...677778**********************996666..6 PP

                              Actin 358 vkiiapeeerkysaWiGGSiLAslgtfqqlwvskqEYeEqGs 399
                                        vk+i+++ ++   a+ G+S     + f+  ++s++ Y E+G+
  gene1234|gene1234|rna1234|rna1234 572 VKCIKAN-DPVLDAFYGASFC---EYFP--VISREMYREEGP 607
                                        899***9.***********74...3333..567777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (611 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1799  (0.10034); expected 358.6 (0.02)
Passed bias filter:                      501  (0.0279436); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); expected 17.9 (0.001)
Passed Fwd filter:                        25  (0.00139439); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 1.02u 0.38s 00:00:01.40 Elapsed: 00:00:00.57
# Mc/sec: 3248.63
//
Query:       gene1235|gene1235|rna1235|rna1235  [L=316]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.8e-49  166.3   0.7      8e-48  163.1   0.7    2.0  1  DS        Deoxyhypusine synthase


Domain annotation for each model (and alignments):
>> DS  Deoxyhypusine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  163.1   0.7   4.4e-52     8e-48       2     286 ..      53     302 ..      52     304 .. 0.91

  Alignments for each domain:
  == domain 1  score: 163.1 bits;  conditional E-value: 4.4e-52
                                 DS   2 llesyekigfqatslgeaidilnkmrkdekctiflgltsnlissGlreiiadlvkeklvdvivtTaggieeDlika 77 
                                        ll+s++++g+q+t+l +ai+ l++     k  i+lg+tsn++s+Glr++i++l+   +  ++vtT g ieeD+ik+
  gene1235|gene1235|rna1235|rna1235  53 LLSSFRSTGYQSTNLWRAISTLKRS----KHGIVLGFTSNIVSCGLRDTIRYLIP--YCKAVVTTTGAIEEDIIKT 122
                                        899******************9998....678**********************6..89***************** PP

                                 DS  78 lgkktylgdf.elddeeLrekginRignllvpnenyckfedwvreildkleeeqkvwspselikelGkeindeeSi 152
                                        +++ +y+ d     + eLr +g+nRignl v+n++y  fe+++++ l ++e    ++s++e+++ ++   +d +S+
  gene1235|gene1235|rna1235|rna1235 123 VHD-FYVTDYhAHAGCELRANGYNRIGNLAVHNDSYVWFEQYLQDKLCSIEG---TLSTAEFVDMIAP--DDAQSF 192
                                        *99.77765516789***********************************98...49*******9987..588*** PP

                                 DS 153 lywAykndipvfcpaltDgslGdqlllfhsvkekkklkldivkDirelndialkakktgaiilGGGvpKhhilnan 228
                                        ++ A + ++pvf+ al Dgs+Gd + +f    ++ ++ +d++kD+r++ d+a  +   + +++G G ++h ++ a+
  gene1235|gene1235|rna1235|rna1235 193 VACAKRLKVPVFVCALGDGSIGD-IYTFG---RNMQFAIDAAKDFRQFLDVAKGC---TGLVVGDGAVRHRMAYAQ 261
                                        ***********************.77777...5667************9986544...56899**********999 PP

                                 DS 229 lmrngadyavyittaqefdGslsgatldEavSwgkikaeaksvkvyaDaTivlPLlva 286
                                        l +      v itt + +dGs+    ld            +sv+v+++a++++PLlv 
  gene1235|gene1235|rna1235|rna1235 262 LSS-----TVHITTRTAYDGSDMERMLD------------SSVRVVGEASVLMPLLVY 302
                                        887.....9*************987776............468999999999999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (316 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       592  (0.0330191); expected 358.6 (0.02)
Passed bias filter:                      531  (0.0296168); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 2139.78
//
Query:       gene1236|gene1236|rna1236|rna1236  [L=428]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0065   16.3   0.0        1.4    8.7   0.0    2.2  2  DUF3237   Protein of unknown function (DUF3237)


Domain annotation for each model (and alignments):
>> DUF3237  Protein of unknown function (DUF3237)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.3   0.0   0.00091        16      76      99 ..     161     184 ..     143     214 .. 0.88
   2 !    8.7   0.0   8.1e-05       1.4      55      99 ..     290     334 ..     278     362 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.00091
                                        EEEEEEEEEEE--GGGHHHHHHT- CS
                            DUF3237  76 liyirytGvvtldeevlavlggge 99 
                                         +yi+ytG+ ++d++  ++++++ 
  gene1236|gene1236|rna1236|rna1236 161 ALYISYTGINSMDQAFIENFSQKT 184
                                        69******************9965 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 8.1e-05
                                        E-TTS-EEEEEEEEEEETTS-EEEEEEEEEEE--GGGHHHHHHT- CS
                            DUF3237  55 idpggtarldaryvlktddgaliyirytGvvtldeevlavlggge 99 
                                           +++++  a+++l+t+ + +i+++ +G ++ +e++ ++++g++
  gene1236|gene1236|rna1236|rna1236 290 LYRDNSLEFMAQLNLQTNIQNIIRMSLNGSIENNEQMSRRFDGNS 334
                                        3447889999*******************************9954 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (428 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1050  (0.0585643); expected 358.6 (0.02)
Passed bias filter:                      498  (0.0277762); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.62u 0.29s 00:00:00.90 Elapsed: 00:00:00.51
# Mc/sec: 2533.87
//
Query:       gene1237|gene1237|rna1237|rna1237  [L=267]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    5.1e-42  143.5   1.8    6.5e-42  143.2   1.8    1.1  1  Proteasome  Proteasome subunit


Domain annotation for each model (and alignments):
>> Proteasome  Proteasome subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  143.2   1.8   3.7e-46   6.5e-42       2     190 .]      41     221 ..      40     221 .. 0.97

  Alignments for each domain:
  == domain 1  score: 143.2 bits;  conditional E-value: 3.7e-46
                                        HHS-EEEEEEETTEEEEEEEEEEEETTEEEESSSSTSEEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHSS CS
                         Proteasome   2 kkGttvvGikgkdgvvlaadkratagskllskstveKifkiddhigvafaGlaaDartlvrraraeaqlyrlrygr 77 
                                        k+Gtt+vGik+++gv+l+ad+rat+g  +++k  + K+++i+d i++a aG+aaD++ ++++a++ ++ ++ +y r
  gene1237|gene1237|rna1237|rna1237  41 KTGTTIVGIKSEHGVILCADTRATSGPFVVDKA-CFKLHRISDDIYCAGAGTAADTDRVTSYASSMVRIFETKYSR 115
                                        89***************************8888.9***************************************** PP

                                        GTCHHHHHHHHHHHHHHHHHHCTTTTTSEEEEEEEEETTTEEEEEEEETTSEEEEESSEEEESTTHHHHHHHHHHH CS
                         Proteasome  78 pipverlvarvaaklqaytqrsgrrpfgvslliagvdeeggpeLyqidpsGsyieekdavaiGsgseaaktaleke 153
                                        + pv+    +v + ++++++++ ++   ++l++ag  +   ++Ly+i p+G++     + ++Gsgs aa ++le++
  gene1237|gene1237|rna1237|rna1237 116 KAPVK----YVISVISKHLFQY-QGAVSAALIVAGRYKST-YHLYSIAPDGTVNPG-FYLSMGSGSLAAVSVLEAR 184
                                        *****....*********9999.899***********665.9**************.7****************** PP

                                        HSTTBSHHHHHHHHHHHHHHHHHHBTTSCSSEEEEEE CS
                         Proteasome 154 ykedltleeavelavkalkealerdklsgknievavi 190
                                        y+  +++ e++el   a+k+++ +d +sg+n++++vi
  gene1237|gene1237|rna1237|rna1237 185 YRAGMSMHEIKELGACAVKAGIMNDLYSGSNVDCVVI 221
                                        **********************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       592  (0.0330191); expected 358.6 (0.02)
Passed bias filter:                      483  (0.0269396); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1779.69
//
Query:       gene1238|gene1238|rna1238|rna1238  [L=204]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      9e-26   90.5   0.0    1.2e-25   90.0   0.0    1.2  1  SNase     Staphylococcal nuclease homologue
  ------ inclusion threshold ------
       0.14   12.2   0.2       0.14   12.2   0.2    1.7  2  BTP       Chlorhexidine efflux transporter
       0.21   11.8   0.0       0.32   11.2   0.0    1.2  1  FlaG      FlaG protein


Domain annotation for each model (and alignments):
>> SNase  Staphylococcal nuclease homologue
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.0   0.0   2.1e-29   1.2e-25       2     108 .]      77     182 ..      76     182 .. 0.98

  Alignments for each domain:
  == domain 1  score: 90.0 bits;  conditional E-value: 2.1e-29
                                        EEETTEE-STSSBTTTTTSTTHHHHHHHHHHHHHHCSSEEEEE-SSBSTTSEEEEEEEETTEEHHHHHHHTTSSEE CS
                              SNase   2 vrLvgidaPetakpkktvqpfgkeAkeflkklvlqkkvvvleldkkkDkygrllayvylnkknineeLvkeGlArv 77 
                                        vrL gidaPe a++++++qp+ ke+++ l+k v++kkv v++l++  D+y+r++++v++++ +++  +v++G+A v
  gene1238|gene1238|rna1238|rna1238  77 VRLYGIDAPECAHFGMPAQPYSKESTALLRKYVMGKKVYVTKLGT--DRYDRCIGRVVVDGVDVSVMMVRMGMACV 150
                                        8********************************************..***************************** PP

                                        ---BTT.STTTHHHHHHHHHHHHHTT-GGGCT CS
                              SNase  78 yevyek.neekkkellkaeeeAkkkrkglWse 108
                                        y  y++     +++l + e+ Akk+ +g+W+e
  gene1238|gene1238|rna1238|rna1238 151 YVGYNAiYGRWYDKLVRCEKRAKKRALGMWKE 182
                                        **999988899*******************85 PP

>> BTP  Chlorhexidine efflux transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.4       1.4   8.3e+03      21      24 ..      11      14 ..       3      23 .. 0.45
   2 ?   12.2   0.2   2.4e-05      0.14      36      62 ..     140     166 ..     133     168 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 1.4
                                BTP 21 lvpl 24
                                        +pl
  gene1238|gene1238|rna1238|rna1238 11 ALPL 14
                                       2222 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 2.4e-05
                                BTP  36 agvldiglslfalvwnfvyNllFDrlf 62 
                                        ++++ +g++++++ +n +y   +D+l 
  gene1238|gene1238|rna1238|rna1238 140 VMMVRMGMACVYVGYNAIYGRWYDKLV 166
                                        678999******************986 PP

>> FlaG  FlaG protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   5.4e-05      0.32      37      75 ..      21      59 ..      17      74 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 5.4e-05
                                       HHHHHHHHHTTSS--EEEEEEEETTEEEEEEEETTT-SE CS
                               FlaG 37 aveklnkklsslnteleFsvdedtkrvvVkviDketgev 75
                                       +++ l k++  ++t+ +F+++++ + +v kv D +t +v
  gene1238|gene1238|rna1238|rna1238 21 LAKLLHKRFRPIQTNKQFKLNHTIHAIVTKVCDGDTIRV 59
                                       567789999*************************99776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       679  (0.0378716); expected 358.6 (0.02)
Passed bias filter:                      540  (0.0301188); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 1529.90
//
Query:       gene1239|gene1239|rna1239|rna1239  [L=582]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0013   17.5   0.6     0.0027   16.5   0.6    1.5  1  Glyco_hydro_7  Glycosyl hydrolase family 7
     0.0018   17.9  35.4       0.01   15.5  11.6    3.2  4  HAUS-augmin3   HAUS augmin-like complex subunit 3
  ------ inclusion threshold ------
      0.044   14.4   0.0        2.7    8.6   0.0    3.0  1  DUF3800        Protein of unknown function (DUF3800)
       0.38   11.0  19.4      0.078   13.2   0.7    4.6  4  DUF948         Bacterial protein of unknown function (DUF948)
        1.2    8.4  29.1      0.068   12.5   6.5    3.0  3  DUF4407        Domain of unknown function (DUF4407)
        1.3    8.9  14.6        4.2    7.1   5.4    3.2  2  Bacillus_HBL   Bacillus haemolytic enterotoxin (HBL)
        2.4    6.6   5.9        5.3    5.5   6.0    1.6  1  FUSC           Fusaric acid resistance protein family
          6    6.8  10.6         41    4.1   5.7    3.3  2  Serine_rich    Serine rich protein interaction domain
        7.9    6.5  10.3       0.96    9.5   3.0    2.7  4  Baculo_PEP_C   Baculovirus polyhedron envelope protein, PEP, 


Domain annotation for each model (and alignments):
>> Glyco_hydro_7  Glycosyl hydrolase family 7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.6   1.4e-06    0.0027     291     415 ..     275     398 ..     270     409 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.4e-06
                                        TTSSTTS.EEEEEEEEEETTEEEE---EESTTCE.S.SSBCHHHHHHHHHHHT-.-HHHHTTHHHHHHHHHHSEEE CS
                      Glyco_hydro_7 291 ddetskgelkeirrlyvqdgkvienskskleglk.kvnsitdefCeaqkkvfgdedkfkkkgglkkmgealergmv 365
                                        +d++ +g l+e++rly q+++ i++ +++++ l+ + n +++e+ e+++  ++  +  + +  +k++++++++ m 
  gene1239|gene1239|rna1239|rna1239 275 NDGSFEGYLQELERLYEQNENRIKQLEQEIRRLRdENNRLENEYDENAEVHMKALE--RLLAEIKAIEQEIQQLMS 348
                                        57778999************************9977899*****988655555544..445778999999999998 PP

                                        EEEEEEE-TTTTTHHHHSBSSTTS-TTSTTTB-SSS-TTTT-HHHHHHHT CS
                      Glyco_hydro_7 366 LvlsiwddkaanmlwLdskyptdkdaskpgvargpCsatsgkpkevekek 415
                                         +  ++ d +++m+ ++s+    +++ ++ +++ +   t+++pk+v+  +
  gene1239|gene1239|rna1239|rna1239 349 SMDELMIDVEEQMQEIESEIRIIEEQMEHIMSERKTVITKSAPKKVRVVQ 398
                                        8889999999*********9998888888777777788888888876554 PP

>> HAUS-augmin3  HAUS augmin-like complex subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.4     0.056   1.1e+02      59      98 ..     156     195 ..     148     202 .. 0.80
   2 !   15.5  11.6     5e-06      0.01      48     137 ..     179     271 ..     171     277 .. 0.87
   3 !   12.7   9.7   3.6e-05     0.072      84     164 ..     280     360 ..     275     381 .. 0.91
   4 ?   -2.5   0.3       1.5     3e+03     113     145 ..     490     522 ..     473     540 .. 0.56

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.056
                       HAUS-augmin3  59 sdlkqedvellevileeeeesleaLeqelqeLqkekalkl 98 
                                        +  + e++ +++  ++ ++e ++ L++e+++L + ++ ++
  gene1239|gene1239|rna1239|rna1239 156 RIHNGETELSYSNYTKTMREEIQRLREEIKTLSQKRNTQT 195
                                        455667888888999999999***********99999887 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 5e-06
                       HAUS-augmin3  48 aLeeaLktiepsdlkq....edvellevileeeeesleaLeqelqeLqkekalklkrlnkLqvqaaslqqelrkle 119
                                        +L e  kt+++++++q    ++ve+ e + +++e s+ ++ +el+ L++ k+ ++++++kL    +  ++e+ +le
  gene1239|gene1239|rna1239|rna1239 179 RLREEIKTLSQKRNTQtvilQAVEQPE-ERSAIEYSTVEYDKELEILKQRKETLINEYQKLVQIHTRSTDERAYLE 253
                                        688999999977777767877777754.5567799999************************************** PP

                       HAUS-augmin3 120 eeekeakkklkeaqeelr 137
                                        +e k+ +++l ++ ee +
  gene1239|gene1239|rna1239|rna1239 254 AEVKTRREELAKLREEYE 271
                                        ************999876 PP

  == domain 3  score: 12.7 bits;  conditional E-value: 3.6e-05
                       HAUS-augmin3  84 eqelqeLqkekalklkrlnkLqvqaaslqqelrkleeeekeakkklkeaqeelraenaetnavLqqlteeakqlae 159
                                        e  lqeL++  +  ++r ++L+  +  l +e+++le+e +e +++  +a e l ae++ ++++ qql+++  +l+ 
  gene1239|gene1239|rna1239|rna1239 280 EGYLQELERLYEQNENRIKQLEQEIRRLRDENNRLENEYDENAEVHMKALERLLAEIKAIEQEIQQLMSSMDELMI 355
                                        6679*****************************************************************9999986 PP

                       HAUS-augmin3 160 yfeea 164
                                          ee+
  gene1239|gene1239|rna1239|rna1239 356 DVEEQ 360
                                        66555 PP

  == domain 4  score: -2.5 bits;  conditional E-value: 1.5
                       HAUS-augmin3 113 qelrkleeeekeakkklkeaqeelraenaetna 145
                                        +e+r+++++ k+ k +l + q++  ++   t+a
  gene1239|gene1239|rna1239|rna1239 490 REQRERAAALKSRKVVLVKEQAKEHENVQSTTA 522
                                        444444444444444444444444443333333 PP

>> DUF3800  Protein of unknown function (DUF3800)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.0    0.0014       2.7      24      45 ..     119     326 ..      93     465 .. 0.48

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0014
                            DUF3800  24 g...................................................kkie.eikkleekikelkkky... 44 
                                                                                            k ++ ei+ l+e+ik l +k    
  gene1239|gene1239|rna1239|rna1239 119 EehtrstnetseekevkarglytdaipetiafqvyakrihngetelsysnytKTMReEIQRLREEIKTLSQKRntq 194
                                        2555555555555555555555555555555555555555555554444444223333334444444443333555 PP

                            DUF3800  45 ............................................................................ 44 
                                                                                                                    
  gene1239|gene1239|rna1239|rna1239 195 tvilqaveqpeersaieystveydkeleilkqrketlineyqklvqihtrstderayleaevktrreelaklreey 270
                                        5555555555555555555555555555555555333333333333333333333333333333333333333333 PP

                            DUF3800  45 .......................................................k 45 
                                                                                               +
  gene1239|gene1239|rna1239|rna1239 271 ermgndgsfegylqelerlyeqnenrikqleqeirrlrdennrleneydenaevhM 326
                                        55555555544444443333333222222222222222222333333333333332 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.2      0.46   9.2e+02      35      58 ..     170     193 ..     160     207 .. 0.69
   2 ?   13.2   0.7   3.9e-05     0.078      21      88 ..     283     347 ..     281     348 .. 0.94
   3 ?    7.8   1.2    0.0019       3.9      21      75 ..     354     402 ..     349     415 .. 0.78
   4 ?   -0.9   0.5         1     2e+03      52      52 ..     454     454 ..     422     521 .. 0.64

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.46
                             DUF948  35 ieelekqvdpilkevedllakvne 58 
                                         ++++++++ + +e+++l +k n+
  gene1239|gene1239|rna1239|rna1239 170 TKTMREEIQRLREEIKTLSQKRNT 193
                                        566777777777777777777776 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 3.9e-05
                             DUF948  21 llklkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesvseln 88 
                                        l +l+++ ++++++i++le++++ + +e ++l ++  e   + + +++++++l ++++ + + +++l 
  gene1239|gene1239|rna1239|rna1239 283 LQELERLYEQNENRIKQLEQEIRRLRDENNRLENEYDE---NAEVHMKALERLLAEIKAIEQEIQQLM 347
                                        678999***************************99999...9999********************985 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.0019
                             DUF948  21 llklkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplte 75 
                                        ++ +++ ++e+++ i+ +e+q++ i+ e +++++k+        +k+  v++ ++
  gene1239|gene1239|rna1239|rna1239 354 MIDVEEQMQEIESEIRIIEEQMEHIMSERKTVITKSAP------KKVRVVQQAVQ 402
                                        56678889999999999999999999999999999877......55555555544 PP

  == domain 4  score: -0.9 bits;  conditional E-value: 1
                             DUF948  52 l 52 
                                        +
  gene1239|gene1239|rna1239|rna1239 454 T 454
                                        1 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   9.8    0.0049       9.8     130     238 ..     155     275 ..      90     290 .. 0.58
   2 ?   12.5   6.5   3.4e-05     0.068     130     237 ..     285     386 ..     275     391 .. 0.82
   3 ?   -0.7   0.1      0.35     7e+02     208     239 ..     492     523 ..     450     553 .. 0.60

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0049
                            DUF4407 130 a..........ltaelaeleaqiaalqaeidaaearldalraeaqkeldgtk......gtgttgvaGkgpaakekk 189
                                        +          +++ +++++++i++l++ei+++++++++++  +q+  +++       +t       + ++ k++k
  gene1239|gene1239|rna1239|rna1239 155 KrihngetelsYSNYTKTMREEIQRLREEIKTLSQKRNTQTVILQAVEQPEErsaieyST--VEYDKELEILKQRK 228
                                        033334444445555555556666666666666666666666666554443322222111..11333444444455 PP

                            DUF4407 190 aqldaaqaelaelkakldatarlaalraelaeleaerakeraasqaaaa 238
                                        + l    ++l +++++  +t+++a l+ae ++ ++e+ak r++ +++ +
  gene1239|gene1239|rna1239|rna1239 229 ETLINEYQKLVQIHTR--STDERAYLEAEVKTRREELAKLREEYERMGN 275
                                        5555555555555555..7777777777777777777777777776543 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 3.4e-05
                            DUF4407 130 altaelaeleaqiaalqaeidaaearldalraeaqkeldgtkgtgttgvaGkgpaakekkaqldaaqaelaelkak 205
                                        +l+  ++++e++i++l++ei+ ++++ ++l++e++++++       ++ ++  ++ k+ +++++++   ++el  +
  gene1239|gene1239|rna1239|rna1239 285 ELERLYEQNENRIKQLEQEIRRLRDENNRLENEYDENAEV----HMKALERLLAEIKAIEQEIQQLMSSMDELMID 356
                                        56778999***************************99886....33456778888888888888888888888888 PP

                            DUF4407 206 ldatarlaalraelaeleaerakeraasqaaa 237
                                           ++++++ ++e+  +e++++++ ++ ++ +
  gene1239|gene1239|rna1239|rna1239 357 --VEEQMQEIESEIRIIEEQMEHIMSERKTVI 386
                                        ..999999999999999999988888777665 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.35
                            DUF4407 208 atarlaalraelaeleaerakeraasqaaaaa 239
                                        +++r aal++++  l +e+ake+++ q+++a+
  gene1239|gene1239|rna1239|rna1239 492 QRERAAALKSRKVVLVKEQAKEHENVQSTTAQ 523
                                        34444444444444444444444444443333 PP

>> Bacillus_HBL  Bacillus haemolytic enterotoxin (HBL)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   5.4    0.0021       4.2      97     173 ..     225     310 ..     147     314 .. 0.77
   2 ?    3.6   1.7     0.026        52     102     160 ..     324     386 ..     314     402 .. 0.65

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0021
                       Bacillus_HBL  97 kkdkaellellekLqe.......eiqqnqkevkqlikeLkklklkla..kdsknFktdvdeltsilagdsgvisql 163
                                        k+ k++l + ++kL +       e    ++evk+  +eL kl+++ +   ++ +F+  ++el+  ++ ++  i+ql
  gene1239|gene1239|rna1239|rna1239 225 KQRKETLINEYQKLVQihtrstdERAYLEAEVKTRREELAKLREEYErmGNDGSFEGYLQELERLYEQNENRIKQL 300
                                        5666666666666643111111023345788999999*****99876335899*********************** PP

                       Bacillus_HBL 164 qneiedlqgk 173
                                        ++ei +l+++
  gene1239|gene1239|rna1239|rna1239 301 EQEIRRLRDE 310
                                        *****99876 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.026
                       Bacillus_HBL 102 ellellekLqeeiqqnqkevkqlikeLkklklklakdsknFktdv....deltsilagdsgvi 160
                                          +++le+L +ei  +++e++ql+  + +l  ++++  ++ ++++    ++++ i++  + vi
  gene1239|gene1239|rna1239|rna1239 324 VHMKALERLLAEIKAIEQEIQQLMSSMDELMIDVEEQMQEIESEIriieEQMEHIMSERKTVI 386
                                        446677777777777777777777777777776666666666665445455555555555555 PP

>> FUSC  Fusaric acid resistance protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   6.0    0.0026       5.3     223     330 ..     230     345 ..     170     385 .. 0.68

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0026
                               FUSC 223 rllsrmlallallsslarllarlraeeaaavpelaallaelaal...........eaaaaaealeaalaalrarlr 287
                                         l ++ + l+++     ++ a l ae +++++ela+l +e +++           e +++ e+ e ++++l++++r
  gene1239|gene1239|rna1239|rna1239 230 TLINEYQKLVQIHTRSTDERAYLEAEVKTRREELAKLREEYERMgndgsfegylqELERLYEQNENRIKQLEQEIR 305
                                        3455555555665666666667777777777778888888888899999999999888899999999999999999 PP

                               FUSC 288 alrraleadadtaalllarlaellaelaqllaslraleaaiaa 330
                                        +lr ++      + +  +++  ++++l +lla+++a e++i++
  gene1239|gene1239|rna1239|rna1239 306 RLRDENN---RLENEYDENAEVHMKALERLLAEIKAIEQEIQQ 345
                                        9999999...444444455555555555555555555555544 PP

>> Serine_rich  Serine rich protein interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.1     0.037        73      58     101 ..     149     192 ..     102     202 .. 0.79
   2 ?    4.1   5.7     0.021        41      80     146 ..     284     350 ..     215     371 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.037
                        Serine_rich  58 efleFargalanaaklsdknlqtkLrkqlqkledsdqilqetsq 101
                                         f  +a+++    ++ls +n ++ +r+++q+l+++ ++l++ ++
  gene1239|gene1239|rna1239|rna1239 149 AFQVYAKRIHNGETELSYSNYTKTMREEIQRLREEIKTLSQKRN 192
                                        4778899999999999***********************99765 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.021
                        Serine_rich  80 tkLrkqlqkledsdqilqetsqeLdsceWslealasdkkqekpddlDrlvmvartvpdDvkqlasfi 146
                                        + L++++++ e+  + l++  + L + + +le   +++++ +  +l+rl++  +++ ++++ql+s  
  gene1239|gene1239|rna1239|rna1239 284 QELERLYEQNENRIKQLEQEIRRLRDENNRLENEYDENAEVHMKALERLLAEIKAIEQEIQQLMSSM 350
                                        5677788888888888888888888888888888888888889999999999999999999998865 PP

>> Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.2      0.94   1.9e+03      64      81 ..     172     189 ..     153     226 .. 0.62
   2 ?    9.5   3.0   0.00048      0.96      35     102 ..     285     351 ..     280     366 .. 0.75
   3 ?    7.5   0.6     0.002         4      40      84 ..     329     376 ..     322     390 .. 0.52
   4 ?   -0.7   0.0      0.69   1.4e+03      36      64 ..     357     385 ..     352     402 .. 0.60

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.94
                       Baculo_PEP_C  64 rldtlltnLtdalnalqd 81 
                                         + + +++L + +++l++
  gene1239|gene1239|rna1239|rna1239 172 TMREEIQRLREEIKTLSQ 189
                                        333333344444444332 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00048
                       Baculo_PEP_C  35 qlatlldaietqLnalsedlksllaeldtrldtllt.nLtdalnalqdtlrneLtnlnsiltnLlssvt 102
                                        +l++l ++ e+++++l++++++l  + ++rl++  + n +  ++al + l  e++++++++ +L+ss+ 
  gene1239|gene1239|rna1239|rna1239 285 ELERLYEQNENRIKQLEQEIRRLR-DENNRLENEYDeNAEVHMKAL-ERLLAEIKAIEQEIQQLMSSMD 351
                                        789999999999999999999955.556666655540555555555.5888999999999999999875 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.002
                       Baculo_PEP_C  40 ldaietqLnalsedlksllaeldt...rldtlltnLtdalnalqdtlr 84 
                                        l+ +  +++a+++++++l++++d+   +++++++++++ +  ++++++
  gene1239|gene1239|rna1239|rna1239 329 LERLLAEIKAIEQEIQQLMSSMDElmiDVEEQMQEIESEIRIIEEQME 376
                                        344445555555555555555555444444444444444444444443 PP

  == domain 4  score: -0.7 bits;  conditional E-value: 0.69
                       Baculo_PEP_C  36 latlldaietqLnalsedlksllaeldtr 64 
                                        +++++++ie+++  ++e++++ ++e +t 
  gene1239|gene1239|rna1239|rna1239 357 VEEQMQEIESEIRIIEEQMEHIMSERKTV 385
                                        55555666666666666666555555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (582 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3328  (0.185621); expected 358.6 (0.02)
Passed bias filter:                      487  (0.0271627); expected 358.6 (0.02)
Passed Vit filter:                       117  (0.00652574); expected 17.9 (0.001)
Passed Fwd filter:                        63  (0.00351386); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 1.30u 0.32s 00:00:01.62 Elapsed: 00:00:00.53
# Mc/sec: 3316.87
//
Query:       gene124|gene124|rna124|rna124  [L=278]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.15   12.2   0.0       0.33   11.2   0.0    1.5  1  AHSA1     Activator of Hsp90 ATPase homolog 1-like protein


Domain annotation for each model (and alignments):
>> AHSA1  Activator of Hsp90 ATPase homolog 1-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   1.9e-05      0.33      76     117 ..     226     265 ..     198     271 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 1.9e-05
                                    EEEEEEEEEEETTEEEEEEEEEEEEHCHHHHHHHHHHHHHHH CS
                          AHSA1  76 estvtieleeegggTrltlthtglprkqkeeegveeGweqsl 117
                                     s+v ++l+e+++gT++ ++++g+ ++ +e+   ++ w++++
  gene124|gene124|rna124|rna124 226 CSKVQLTLKETESGTEVFMEQSGVIEGGEER--ISAFWKKYF 265
                                    589********************99999988..888888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (278 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       342  (0.0190752); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1947.36
//
Query:       gene1240|gene1240|rna1240|rna1240  [L=44]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (44 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       445  (0.0248201); expected 358.6 (0.02)
Passed bias filter:                      237  (0.0132188); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.32u 0.22s 00:00:00.54 Elapsed: 00:00:00.37
# Mc/sec: 358.74
//
Query:       gene1241|gene1241|rna1241|rna1241  [L=110]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       354  (0.0197445); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 841.30
//
Query:       gene1242|gene1242|rna1242|rna1242  [L=218]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.01   16.1   0.7      0.021   15.1   0.7    1.5  1  DUF3267   Putative zincin peptidase
        0.2   12.0   0.9       0.41   11.0   0.9    1.6  1  Orf78     Orf78 (ac78)


Domain annotation for each model (and alignments):
>> DUF3267  Putative zincin peptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.7   2.3e-06     0.021      34      73 ..     165     204 ..     147     208 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.3e-06
                            DUF3267  34 liayatsseallskkqfiiillaPfvllgilllllalllp 73 
                                        + a++   + + + +++i+ +++P++++ ++l  +++++ 
  gene1242|gene1242|rna1242|rna1242 165 VLAIFKQMQVPTNTNTMILTCIMPLFVIVVILTSIFWYFK 204
                                        44444455556699***********************987 PP

>> Orf78  Orf78 (ac78)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.9   4.6e-05      0.41      56      94 ..     172     210 ..     117     217 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 4.6e-05
                              Orf78  56 aaekaqalnillisllavvcvlvllyviyYfvilrerqk 94 
                                         +  +++ +++l+ ++ +++++v+l  i++++  r r+ 
  gene1242|gene1242|rna1242|rna1242 172 MQVPTNTNTMILTCIMPLFVIVVILTSIFWYFKKRSRPG 210
                                        455667778888999999************998888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       817  (0.0455686); expected 358.6 (0.02)
Passed bias filter:                      532  (0.0296726); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1457.53
//
Query:       gene1243|gene1243|rna1243|rna1243  [L=233]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
       0.22   10.8   0.8        0.4    9.9   0.8    1.4  1  Peptidase_U4  Sporulation factor SpoIIGA


Domain annotation for each model (and alignments):
>> Peptidase_U4  Sporulation factor SpoIIGA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.8   2.2e-05       0.4     192     283 ..     120     206 ..     112     207 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 2.2e-05
                       Peptidase_U4 192 lpeelkeileeeeeedkkklleelseeewakrlrlIpyksvgkenglLlgikpdeveiekkeeeikikkvligisk 267
                                        + +e++e++++++  ++++  +++ +++  + + +I  ++vg+e+   +g + d  +i+++   +  +k ++g s 
  gene1243|gene1243|rna1243|rna1243 120 INNEVNENISSNKAHKENEKKKNNVNRKNDNAINFIDTSAVGSED-NNIGPTSD--IIHNG--AKNANKYILGASA 190
                                        4567777775555555555555788889999*************5.55566666..67765..6799********* PP

                       Peptidase_U4 268 eklskegeYqaLlhpe 283
                                        + + ++++ +++++++
  gene1243|gene1243|rna1243|rna1243 191 DHMKPKDKWNMIINEQ 206
                                        *************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (233 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2601  (0.145072); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        90  (0.0050198); expected 17.9 (0.001)
Passed Fwd filter:                        36  (0.00200792); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.76u 0.35s 00:00:01.10 Elapsed: 00:00:00.51
# Mc/sec: 1366.27
//
Query:       gene1244|gene1244|rna1244|rna1244  [L=273]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (273 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       350  (0.0195214); expected 358.6 (0.02)
Passed bias filter:                      135  (0.0075297); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                        25  (0.00139439); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.77u 0.35s 00:00:01.12 Elapsed: 00:00:00.47
# Mc/sec: 1739.58
//
Query:       gene1245|gene1245|rna1245|rna1245  [L=56]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.014   14.3   1.2      0.014   14.3   1.2    1.0  1  PigN             Phosphatidylinositolglycan class N (PIG-N)
      0.035   15.1   1.3      0.042   14.9   1.3    1.2  1  Conotoxin        Conotoxin
      0.095   12.5   5.6      0.094   12.6   5.6    1.1  1  Cnd1_N           non-SMC mitotic condensation complex subunit
      0.097   13.0  14.1       0.11   12.8  14.1    1.1  1  BRF1             Brf1-like TBP-binding domain
       0.11   12.2   6.1       0.11   12.2   6.1    1.0  1  Connexin         Connexin
       0.21   11.3   4.8       0.22   11.3   4.8    1.0  1  EIIBC-GUT_N      Sorbitol phosphotransferase enzyme II N-term
       0.23   11.4   1.8        0.3   11.0   1.8    1.2  1  PhnG             Phosphonate metabolism protein PhnG
       0.24   11.5   9.3       0.26   11.4   9.3    1.0  1  Eapp_C           E2F-associated phosphoprotein
       0.32   10.0   0.5       0.36    9.8   0.5    1.0  1  PUCC             PUCC protein
       0.52   10.6   4.6       0.57   10.5   4.6    1.0  1  Peroxin-13_N     Peroxin 13, N-terminal region
       0.57   10.4  10.6       0.58   10.4  10.6    1.0  1  DUF4770          Domain of unknown function (DUF4770)
       0.65   10.9  14.4       0.72   10.8  14.4    1.0  1  DUF1764          Eukaryotic protein of unknown function (DUF1
       0.68    9.4  11.1       0.75    9.3  11.1    1.1  1  Sec62            Translocation protein Sec62
        0.8    9.3  29.4       0.85    9.2  29.4    1.0  1  SR-25            Nuclear RNA-splicing-associated protein
          1    9.3   9.4        1.1    9.2   9.4    1.1  1  Jak1_Phl         Jak1 pleckstrin homology-like domain
        1.1    9.2  18.3        1.3    9.1  18.3    1.1  1  Peptidase_S49_N  Peptidase family S49 N-terminal
        1.2    9.1  14.6        1.6    8.7  14.6    1.2  1  Ferlin_C         Ferlin C-terminus
        1.6    9.0   6.9        1.7    8.9   6.9    1.1  1  HA2              Helicase associated domain (HA2)
          2    8.9   5.8        2.6    8.5   5.8    1.2  1  Cucumo_2B        Cucumovirus protein 2B
        2.4    7.9  10.1        3.3    7.5  10.1    1.2  1  BCIP             p21-C-terminal region-binding protein
        2.9    6.6   4.3        3.1    6.5   4.3    1.0  1  Presenilin       Presenilin
        3.6    5.7   6.3        3.2    5.9   6.3    1.0  1  OATP             Organic Anion Transporter Polypeptide (OATP)
        4.2    7.5  14.8          7    6.8  14.8    1.5  1  RAMP4            Ribosome associated membrane protein RAMP4
        4.4    8.3   5.0        5.8    7.9   5.0    1.3  1  EphA2_TM         Ephrin type-A receptor 2 transmembrane domai
        5.8    6.8   5.4        6.1    6.7   5.4    1.1  1  EOS1             N-glycosylation protein
        6.4    7.0   9.8          7    6.9   9.8    1.1  1  MAP17            Membrane-associated protein 117 kDa, PDZK1-i
        6.9    6.6  11.8          9    6.2  11.8    1.2  1  Protocadherin    Protocadherin
        7.1    6.8   8.0        9.7    6.3   8.0    1.3  1  CrgA             Cell division protein CrgA
        9.7    4.3  11.2         10    4.2  11.2    1.0  1  CDC45            CDC45-like protein
        9.8    6.4  26.6         13    6.0  26.6    1.2  1  AP3D1            AP-3 complex subunit delta-1


Domain annotation for each model (and alignments):
>> PigN  Phosphatidylinositolglycan class N (PIG-N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   1.2   2.3e-05     0.014     308     365 ..       2      55 ..       1      56 [] 0.65

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.3e-05
                               PigN 308 lsltlvlwieleaelkqekeesekesesekkekekkksssrsltlsdlRialfflffl 365
                                        +++ +++  + e+    ++++ +ke++++kk+k+kkk++ ++ ++++ ++ +f+lff+
  gene1245|gene1245|rna1245|rna1245   2 MCVNVLIARKKEK----KDKKRKKEKKRKKKKKRKKKKKRKKKKINKSQVEYFLLFFT 55 
                                        4555555555555....34556666666777777777777888888888888999986 PP

>> Conotoxin  Conotoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   1.3     7e-05     0.042       6      47 ..       1      42 [.       1      55 [. 0.55

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 7e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          Conotoxin  6 vlivavLllttlvtadldgdqpadrkakrledrkseekkklk 47
                                       ++ v vL   +    d++++++++rk+k+++++k+++kkk+ 
  gene1245|gene1245|rna1245|rna1245  1 MMCVNVLIARKKEKKDKKRKKEKKRKKKKKRKKKKKRKKKKI 42
                                       677777777744444555555555555555544444444433 PP

>> Cnd1_N  non-SMC mitotic condensation complex subunit 1, N-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   5.6   0.00016     0.094      50      98 ..       3      51 ..       1      56 [] 0.59

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00016
                             Cnd1_N 50 qwlvealekessskssaasasargrkkk.kkkkkkkeeawdweaqreril 98
                                       ++ v ++ k+++++++ +++++r++kkk kkkkk+k+++  +++q+e +l
  gene1245|gene1245|rna1245|rna1245  3 CVNVLIARKKEKKDKKRKKEKKRKKKKKrKKKKKRKKKKI-NKSQVEYFL 51
                                       5556666666666666666666666666455555555555.677777666 PP

>> BRF1  Brf1-like TBP-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8  14.1   0.00019      0.11      35      70 ..      11      42 ..       5      55 .. 0.45

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00019
                               BRF1 35 eqeekrlkeeaeeaeadkkkkkkkrkrkkkekkkge 70
                                       ++e+k +k+++e+++++kkk+kkk+krkk    k+ 
  gene1245|gene1245|rna1245|rna1245 11 KKEKKDKKRKKEKKRKKKKKRKKKKKRKK----KKI 42
                                       34444444444444422222222222222....222 PP

>> Connexin  Connexin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   6.1   0.00018      0.11      98     148 ..      10      42 ..       1      55 [. 0.32

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00018
                           Connexin  98 iakeekekekeeeekeeeekeeekkkkkekkkkkkkeeekekkkeegkrri 148
                                         +ke+k+k++++e+k++++k+++kkkk++kkk                  i
  gene1245|gene1245|rna1245|rna1245  10 RKKEKKDKKRKKEKKRKKKKKRKKKKKRKKKK------------------I 42 
                                        22222222212222222222111111111111..................1 PP

>> EIIBC-GUT_N  Sorbitol phosphotransferase enzyme II N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   4.8   0.00036      0.22     120     153 ..      11      43 ..       2      55 .. 0.34

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00036
                        EIIBC-GUT_N 120 eeeeeeeeeeeekeeaeekekkketkkkiteqee 153
                                        ++e++++++++ek+++++ +k+k++kk+++++ +
  gene1245|gene1245|rna1245|rna1245  11 KKEKKDKKRKKEKKRKKK-KKRKKKKKRKKKKIN 43 
                                        222222222222222221.122222222222222 PP

>> PhnG  Phosphonate metabolism protein PhnG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   1.8   0.00051       0.3     102     139 ..      15      52 ..       4      53 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00051
                                        HHHHHHHHTHHHHHHHHHHHHHHHHHHHGGGEE--EEE CS
                               PhnG 102 reeeleaelieplearlaeeraaraaelaaTkVdFftl 139
                                        + ++ ++e   + +++++++++++++++++++V++f l
  gene1245|gene1245|rna1245|rna1245  15 KDKKRKKEKKRKKKKKRKKKKKRKKKKINKSQVEYFLL 52 
                                        3344445555677788899999999**********976 PP

>> Eapp_C  E2F-associated phosphoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   9.3   0.00043      0.26      61     104 ..       1      44 [.       1      50 [. 0.59

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00043
                             Eapp_C  61 mfvlnvkvdkeevlkykeaesekkkkkkkkskkkeekeeeaeae 104
                                        m+ +nv + +++  k k+ ++ekk+kkkkk+kkk+++++++ ++
  gene1245|gene1245|rna1245|rna1245   1 MMCVNVLIARKKEKKDKKRKKEKKRKKKKKRKKKKKRKKKKINK 44 
                                        67889999988888877655555555555555554444444333 PP

>> PUCC  PUCC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.5   0.00059      0.36     167     215 ..       1      53 [.       1      55 [. 0.63

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00059
                               PUCC 167 tlvlnvlalWkievkskkkk....eekeeeepslleawlklvaekqalaflaf 215
                                        ++ +nvl + k e+k kk+k    ++k++++++ +++ +k ++++q+  fl+f
  gene1245|gene1245|rna1245|rna1245   1 MMCVNVLIARKKEKKDKKRKkekkRKKKKKRKKKKKRKKKKINKSQVEYFLLF 53 
                                        57899999999999988888443333334444444445555577777777766 PP

>> Peroxin-13_N  Peroxin 13, N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   4.6   0.00095      0.57      81     131 ..       9      54 ..       2      56 .] 0.30

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00095
                       Peroxin-13_N  81 glllekkkkekskaeefwkkfessskkkeekeskeekkkk..kisskplllfl 131
                                         ++      +++k ++  kk ++++kkk++k++k++kkkk  k+++  +llf+
  gene1245|gene1245|rna1245|rna1245   9 ARK------KEKKDKKR-KKEKKRKKKKKRKKKKKRKKKKinKSQVEYFLLFF 54 
                                        332......11111222.11111111111122222222222135555555554 PP

>> DUF4770  Domain of unknown function (DUF4770)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4  10.6   0.00096      0.58      84     123 ..      12      50 ..       5      56 .] 0.37

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00096
                            DUF4770  84 rkkqekkkkkrlklkkkkekkrkekekkkkknkkklspYf 123
                                        ++k++kk+kk++k+kkkk++k+k+k+kkkk nk+++  Yf
  gene1245|gene1245|rna1245|rna1245  12 KEKKDKKRKKEKKRKKKKKRKKKKKRKKKKINKSQV-EYF 50 
                                        222222222222333333333333333333333333.344 PP

>> DUF1764  Eukaryotic protein of unknown function (DUF1764)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8  14.4    0.0012      0.72      16      52 ..       9      45 ..       3      51 .. 0.44

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0012
                            DUF1764 16 seskkkkkekekeeeeeekekkkkskkkkkkkkkkee 52
                                       +++k+kk +k+k+e++++k+kk+k+kkk+kkkk +++
  gene1245|gene1245|rna1245|rna1245  9 ARKKEKKDKKRKKEKKRKKKKKRKKKKKRKKKKINKS 45
                                       4444444444444443334444444444333333333 PP

>> Sec62  Translocation protein Sec62
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3  11.1    0.0012      0.75      14      52 ..       9      47 ..       2      53 .. 0.53

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0012
                              Sec62 14 alksekekkkskkkkeklkevkkkekaekvfkelkksql 52
                                       a k+ek++kk+kk+k+++k++k+k+k+++++k+++ksq+
  gene1245|gene1245|rna1245|rna1245  9 ARKKEKKDKKRKKEKKRKKKKKRKKKKKRKKKKINKSQV 47
                                       445555555555555455555555554555555555544 PP

>> SR-25  Nuclear RNA-splicing-associated protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2  29.4    0.0014      0.85      89     122 ..      12      45 ..       3      51 .. 0.37

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0014
                              SR-25  89 rkkrgkkkdkkkkkkkkkkkkkkekkkakekaka 122
                                        ++k+ kk++k kk+kkkkk+kkk+k+k+k+ +k 
  gene1245|gene1245|rna1245|rna1245  12 KEKKDKKRKKEKKRKKKKKRKKKKKRKKKKINKS 45 
                                        2222222222222222223333333333332332 PP

>> Jak1_Phl  Jak1 pleckstrin homology-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   9.4    0.0018       1.1      52      86 ..      14      46 ..       4      55 .. 0.36

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0018
                           Jak1_Phl 52 egeksrkskekkkskkkkaeskkkkqeekekkeek 86
                                       ++   +k+k++kk kkkk ++kkkk+++k+ ++++
  gene1245|gene1245|rna1245|rna1245 14 KK--DKKRKKEKKRKKKKKRKKKKKRKKKKINKSQ 46
                                       11..2222222222222222223333333333333 PP

>> Peptidase_S49_N  Peptidase family S49 N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1  18.3    0.0021       1.3      63     103 ..      12      54 ..       3      56 .] 0.48

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0021
                    Peptidase_S49_N  63 deeelkaaekkekkeekeekkaekkkake..eeekkrvfvldF 103
                                        +e++ k+++k++k+++k+++k++kk++k+  ++++ + f+l F
  gene1245|gene1245|rna1245|rna1245  12 KEKKDKKRKKEKKRKKKKKRKKKKKRKKKkiNKSQVEYFLLFF 54 
                                        3333334444444444444444433444334666667777766 PP

>> Ferlin_C  Ferlin C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7  14.6    0.0026       1.6      19      62 ..      10      51 ..       5      55 .. 0.55

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0026
                           Ferlin_C 19 klkeqediereereakkkkKkkkkrsekkpedlefkdssgntfl 62
                                       + ke++d +r++ +++kkkKk+kk+++ k+++++  +s  ++fl
  gene1245|gene1245|rna1245|rna1245 10 RKKEKKDKKRKKEKKRKKKKKRKKKKKRKKKKIN--KSQVEYFL 51
                                       4566666555554445555555555555666665..45555555 PP

>> HA2  Helicase associated domain (HA2)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   6.9    0.0029       1.7      62      96 ..       5      39 ..       1      49 [. 0.40

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0029
                                HA2 62 eifleeneeekeeeeeeeekakkkrkeeekarrkl 96
                                       ++++  ++e+k++++++e+k+kkk+k+++k++rk+
  gene1245|gene1245|rna1245|rna1245  5 NVLIARKKEKKDKKRKKEKKRKKKKKRKKKKKRKK 39
                                       44555555444444433333333333333322222 PP

>> Cucumo_2B  Cucumovirus protein 2B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   5.8    0.0044       2.6       3      44 ..       1      42 [.       1      55 [. 0.63

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0044
                          Cucumo_2B  3 mtnvelqlarmveakkqrrrshkqnrrerghkspserarsnl 44
                                       m  v++ +ar  e k ++r+  k+ ++++  k   +r + ++
  gene1245|gene1245|rna1245|rna1245  1 MMCVNVLIARKKEKKDKKRKKEKKRKKKKKRKKKKKRKKKKI 42
                                       567889999999999888877777666666665555554433 PP

>> BCIP  p21-C-terminal region-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5  10.1    0.0055       3.3     161     197 ..       8      48 ..       2      52 .. 0.40

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0055
                               BCIP 161 ilskvykevkskedekkkkkkkkkkkkkkk....seedeli 197
                                        i  k  k++k++++ekk+kkkkk+kkkkk+     +++++ 
  gene1245|gene1245|rna1245|rna1245   8 IARKKEKKDKKRKKEKKRKKKKKRKKKKKRkkkkINKSQVE 48 
                                        44444444444444433333333333333211224444444 PP

>> Presenilin  Presenilin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   4.3    0.0051       3.1     232     254 ..      16      38 ..       3      50 .. 0.26

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0051
                         Presenilin 232 vaeseeeeeaekkkeeasesske 254
                                         +++++e++++kkk+++++++++
  gene1245|gene1245|rna1245|rna1245  16 DKKRKKEKKRKKKKKRKKKKKRK 38 
                                        00001111111111111000000 PP

>> OATP  Organic Anion Transporter Polypeptide (OATP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   6.3    0.0054       3.2     238     281 ..      10      48 ..       1      56 [] 0.37

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0054
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               OATP 238 kelpkkkeerakkkseeesaekkeekkkkeksksseeeelkslk 281
                                        ++++kk ++r+k+k+++++  kk++kkkk+k+k+     +++++
  gene1245|gene1245|rna1245|rna1245  10 RKKEKKDKKRKKEKKRKKK--KKRKKKKKRKKKKI---NKSQVE 48 
                                        3333333333333333222..22222222222222...233444 PP

>> RAMP4  Ribosome associated membrane protein RAMP4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8  14.8     0.012         7       6      43 ..      17      54 ..       7      55 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.012
                              RAMP4  6 mrrknekfaknitkrGkvpkslkkkekkspvgpwlLgl 43
                                        +rk ek  k+ +kr k++k +kkk +ks v+++lL++
  gene1245|gene1245|rna1245|rna1245 17 KKRKKEKKRKKKKKRKKKKKRKKKKINKSQVEYFLLFF 54
                                       45666777777799999999999************987 PP

>> EphA2_TM  Ephrin type-A receptor 2 transmembrane domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   5.0    0.0097       5.8      18      50 ..       4      36 ..       1      50 [. 0.43

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0097
                           EphA2_TM 18 lvlvlvrrrsknrkqksdlkskeekkeeensgk 50
                                       + +++ r+++k++k+++++k++++kk++++++k
  gene1245|gene1245|rna1245|rna1245  4 VNVLIARKKEKKDKKRKKEKKRKKKKKRKKKKK 36
                                       334444444444444444432222222222222 PP

>> EOS1  N-glycosylation protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   5.4      0.01       6.1     120     149 ..      14      43 ..       4      53 .. 0.39

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.01
                               EOS1 120 rqgksrhkrsvskseakkkrertsskrtld 149
                                        ++ k+r+k+++ k+++k k++++++k++++
  gene1245|gene1245|rna1245|rna1245  14 KKDKKRKKEKKRKKKKKRKKKKKRKKKKIN 43 
                                        122222222222222223333333333333 PP

>> MAP17  Membrane-associated protein 117 kDa, PDZK1-interacting protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   9.8     0.012         7      74     104 ..      12      42 ..       1      49 [. 0.34

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.012
                              MAP17  74 nkeedvslskeekkeeekekkekkaakegrs 104
                                        ++++d +++ke+k++++k++k+kk++k+ + 
  gene1245|gene1245|rna1245|rna1245  12 KEKKDKKRKKEKKRKKKKKRKKKKKRKKKKI 42 
                                        2222222222222222222222222222222 PP

>> Protocadherin  Protocadherin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2  11.8     0.015         9      74     111 ..       9      45 ..       3      55 .. 0.53

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.015
                      Protocadherin  74 agkKeeedfvtPkqenkeekgkkkkkkkkkkkakseks 111
                                        a kKe++d    k++++++k+k+kkkkk +kk k +ks
  gene1245|gene1245|rna1245|rna1245   9 ARKKEKKDKKRKKEKKRKKKKKRKKKKK-RKKKKINKS 45 
                                        5677777766555444444443333333.333444444 PP

>> CrgA  Cell division protein CrgA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   8.0     0.016       9.7       4      31 ..      16      44 ..       9      55 .. 0.41

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.016
                               CrgA  4 skvrkkaeytpk.aaertpvkakaakpsp 31
                                        k+rkk+++++k +++++++k k++k ++
  gene1245|gene1245|rna1245|rna1245 16 DKKRKKEKKRKKkKKRKKKKKRKKKKINK 44
                                       45555443333322222222222233222 PP

>> CDC45  CDC45-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2  11.2     0.018        10     187     215 ..      14      41 ..       6      52 .. 0.27

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.018
                              CDC45 187 rsrkrrrsepsakklrrqlkkerrkyeav 215
                                        ++ k+r++e +++k+++++kk++++++++
  gene1245|gene1245|rna1245|rna1245  14 KKDKKRKKE-KKRKKKKKRKKKKKRKKKK 41 
                                        111111111.1111111111111111111 PP

>> AP3D1  AP-3 complex subunit delta-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0  26.6     0.022        13      77     111 ..      11      45 ..       5      49 .. 0.43

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.022
                              AP3D1  77 kakkkakeekkkkkkkkkkkkkkkkkkkkkkeees 111
                                        k++kk k+ kk+kk+kkkkk+kkkkk+kkkk ++s
  gene1245|gene1245|rna1245|rna1245  11 KKEKKDKKRKKEKKRKKKKKRKKKKKRKKKKINKS 45 
                                        33333333344444444444444443444443333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (56 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      4313  (0.24056); expected 358.6 (0.02)
Passed bias filter:                     1367  (0.0762452); expected 358.6 (0.02)
Passed Vit filter:                       371  (0.0206927); expected 17.9 (0.001)
Passed Fwd filter:                        57  (0.00317921); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              30  [number of targets reported over threshold]
# CPU time: 0.51u 0.34s 00:00:00.85 Elapsed: 00:00:00.45
# Mc/sec: 376.96
//
Query:       gene1246|gene1246|rna1246|rna1246  [L=905]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.5e-10   40.1   0.5    2.7e-09   37.3   0.5    2.3  1  PFU          PFU (PLAA family ubiquitin binding)
      6e-05   23.7   7.6       0.28   12.1   0.1    4.1  4  WD40         WD domain, G-beta repeat
     0.0014   19.0   6.2       0.34   11.5   0.1    4.5  6  PQQ_3        PQQ-like domain
  ------ inclusion threshold ------
      0.062   13.4   0.0       0.83    9.8   0.0    2.4  2  S10_plectin  Plectin/S10 domain


Domain annotation for each model (and alignments):
>> PFU  PFU (PLAA family ubiquitin binding)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.3   0.5     6e-13   2.7e-09      28     111 ..     481     548 ..     455     549 .. 0.81

  Alignments for each domain:
  == domain 1  score: 37.3 bits;  conditional E-value: 6e-13
                                PFU  28 eekWekiGevvgseessskkkeyeGkeYDyvfdvdiedgkpplkLpynksdnpyeaAekFleknelsqsyleqivn 103
                                         ++W+++G+vv             G + D +f+v+i   + +l+L +++++n+y++A++Fl++n l ++++++iv+
  gene1246|gene1246|rna1246|rna1246 481 GDTWVHVGQVV-------------G-KRDNCFTVEIG--NRKLELGFDNDENVYDVADRFLRENALGEEHRDEIVE 540
                                        44555555555.............2.3499*****95..77899******************************** PP

                                PFU 104 Fiikntkg 111
                                        F+ +n k+
  gene1246|gene1246|rna1246|rna1246 541 FMRRNFKK 548
                                        ****9875 PP

>> WD40  WD domain, G-beta repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0     0.028   1.2e+02      10      36 ..      12      37 ..       3      39 .. 0.70
   2 !    9.8   0.4   0.00034       1.5       9      33 ..     178     201 ..     170     206 .. 0.84
   3 !   12.1   0.1   6.2e-05      0.28       4      37 ..     213     244 ..     209     245 .. 0.83
   4 ?   -2.9   0.1       3.5   1.6e+04      13      33 ..     406     424 ..     396     425 .. 0.61

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.028
                                       S.SSEEEEEEETTSSEEEEEETTSEEEE CS
                               WD40 10 H.ssvtslafspdgawlasGsdDgtvri 36
                                       H +++ +la  p+   ++s+s+D+t+ +
  gene1246|gene1246|rna1246|rna1246 12 HtTDIKALAHLPNT--IVSCSRDKTLSF 37
                                       76778888555554..459******976 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00034
                                        SS.SSEEEEEEETTSSEEEEEETTSE CS
                               WD40   9 GH.ssvtslafspdgawlasGsdDgt 33 
                                         H +++tsl  ++d++ l+s+s+D+t
  gene1246|gene1246|rna1246|rna1246 178 NHsKNITSL--HSDNTILISSSWDNT 201
                                        79888****..*************98 PP

  == domain 3  score: 12.1 bits;  conditional E-value: 6.2e-05
                                        EEEEESS.SSEEEEEEETTSSEEEEEETTSEEEEE CS
                               WD40   4 lrtltGH.ssvtslafspdgawlasGsdDgtvriW 37 
                                        ++++ +H s+v+++   +d +++ s+++Dg +r++
  gene1246|gene1246|rna1246|rna1246 213 IYSY-THpSGVWCV--RKDERYIYSACMDGCIRMF 244
                                        3445.69999****..99*****99999*****86 PP

  == domain 4  score: -2.9 bits;  conditional E-value: 3.5
                                        EEEEEEETTSSEEEEEETTSE CS
                               WD40  13 vtslafspdgawlasGsdDgt 33 
                                         +++ +++dg +++ G+ +g+
  gene1246|gene1246|rna1246|rna1246 406 CWCV-THKDGLLFF-GGANGN 424
                                        4555.777777777.555666 PP

>> PQQ_3  PQQ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.1   7.6e-05      0.34      15      38 ..      56      79 ..      47      81 .. 0.83
   2 ?   -3.2   0.0       3.1   1.4e+04      21      40 .]     189     209 ..     188     209 .. 0.75
   3 ?   -0.7   0.0       0.5   2.2e+03      20      36 ..     228     244 ..     212     245 .. 0.78
   4 ?   -2.4   0.1       1.7   7.6e+03      15      34 ..     261     280 ..     256     283 .. 0.81
   5 ?    0.8   0.0      0.17   7.6e+02      18      28 ..     381     391 ..     367     396 .. 0.87
   6 !    5.5   0.0    0.0056        25      21      36 ..     413     428 ..     403     431 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 7.6e-05
                              PQQ_3 15 sspavdgglvyvgtgdGtlyAlDa 38
                                       +++avd+++vyvg++ G ++ +  
  gene1246|gene1246|rna1246|rna1246 56 TALAVDERYVYVGSEEGVIVVYRR 79
                                       578***************998865 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 3.1
                              PQQ_3  21 gglvyvgtg.dGtlyAlDaet 40 
                                        ++++ ++++ d+t++  D +t
  gene1246|gene1246|rna1246|rna1246 189 DNTILISSSwDNTMTVTDITT 209
                                        777777777799999877766 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.5
                              PQQ_3  20 dgglvyvgtgdGtlyAl 36 
                                        d++++y +++dG ++++
  gene1246|gene1246|rna1246|rna1246 228 DERYIYSACMDGCIRMF 244
                                        7899********99887 PP

  == domain 4  score: -2.4 bits;  conditional E-value: 1.7
                              PQQ_3  15 sspavdgglvyvgtgdGtly 34 
                                        ++++v g+  + ++ dG++ 
  gene1246|gene1246|rna1246|rna1246 261 RGMVVRGDEMVGVSNDGRVL 280
                                        67888898889999999985 PP

  == domain 5  score: 0.8 bits;  conditional E-value: 0.17
                              PQQ_3  18 avdgglvyvgt 28 
                                        ++d+g+vy+++
  gene1246|gene1246|rna1246|rna1246 381 LADDGVVYITD 391
                                        579*****987 PP

  == domain 6  score: 5.5 bits;  conditional E-value: 0.0056
                              PQQ_3  21 gglvyvgtgdGtlyAl 36 
                                        +gl+++g+ +G+++ l
  gene1246|gene1246|rna1246|rna1246 413 DGLLFFGGANGNVTTL 428
                                        9***********9855 PP

>> S10_plectin  Plectin/S10 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.17   7.6e+02       5      26 ..     209     230 ..     206     239 .. 0.88
   2 ?    9.8   0.0   0.00018      0.83      29      76 ..     346     391 ..     330     398 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.17
                                        HHHHHHHHCCCCSCEEEE--SS CS
                        S10_plectin   5 nrkaiyeylfkegvlvakkdfe 26 
                                        ++++iy+y    gv +++kd +
  gene1246|gene1246|rna1246|rna1246 209 THTKIYSYTHPSGVWCVRKDER 230
                                        5689***************976 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00018
                                        --SSS---HHHHHHHHHHCCCCTSEEEEEETTEEEEEE-HHHHHHHHH CS
                        S10_plectin  29 kheelnvpnlqvikalqSLksrgyvkeqfaWrhyYytLtneGieylre 76 
                                         + +lnv+n +++ka +++    y+    a +h+Y +L ++G+ y+ +
  gene1246|gene1246|rna1246|rna1246 346 ANLSLNVTNANIVKAARAFG--TYCYDVIAINHIYIFLADDGVVYITD 391
                                        33455************997..5999*******************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (905 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1180  (0.0658152); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.70u 0.25s 00:00:00.95 Elapsed: 00:00:00.41
# Mc/sec: 6697.33
//
Query:       gene1247|gene1247|rna1247|rna1247  [L=184]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.2e-35  120.2   0.7    4.3e-35  119.8   0.7    1.1  1  RRM_2     RNA recognition motif 2
  ------ inclusion threshold ------
      0.021   14.6   0.1      0.055   13.3   0.0    1.7  2  RRM_1     RNA recognition motif. (a.k.a. RRM, RBD, or RNP dom


Domain annotation for each model (and alignments):
>> RRM_2  RNA recognition motif 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.8   0.7   4.8e-39   4.3e-35       2      97 .]      57     152 ..      56     152 .. 0.98

  Alignments for each domain:
  == domain 1  score: 119.8 bits;  conditional E-value: 4.8e-39
                              RRM_2   2 ttlliknipnkytkkmllaaideknkgtydflylpidfknkcnvgyafinlvepkkivafqkafngkkwekfnsek 77 
                                         t+++knipnkyt+ ml++ ++e + g+ydf+yl++df n cnvgyafin+v+ + + +f+    g+ w k+ s+k
  gene1247|gene1247|rna1247|rna1247  57 LTVMLKNIPNKYTSSMLINLLNEDHYGSYDFVYLRMDFLNECNVGYAFINFVHANYLCSFYYKVHGRGWTKYSSNK 132
                                        59************************************************************************** PP

                              RRM_2  78 vaslayariqgkaaliaklq 97 
                                        +a+++ya iqg +al  k++
  gene1247|gene1247|rna1247|rna1247 133 IAEVTYASIQGIDALYRKFR 152
                                        ***************99986 PP

>> RRM_1  RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   6.2e-06     0.055       1      48 [.      59     109 ..      59     124 .. 0.93
   2 ?   -1.9   0.0      0.33     3e+03      37      55 ..     129     147 ..     126     157 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 6.2e-06
                                        EEEESETTTSSHHHHHHHHHT..TSCEEEEEEEEE.TTTSEEEEEEEEESS CS
                              RRM_1   1 lfVgnLppdvteeeLkelFsk..fGpiksiklvrd.etgkskgfafVeFes 48 
                                        ++++n+p+ +t ++L  l+++  +G++  + l  d  ++ + g+af++F  
  gene1247|gene1247|rna1247|rna1247  59 VMLKNIPNKYTSSMLINLLNEdhYGSYDFVYLRMDfLNECNVGYAFINFVH 109
                                        6789****************999**************************75 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.33
                                        SEEEEEEEEESSHHHHHHH CS
                              RRM_1  37 kskgfafVeFeskedAekA 55 
                                        +s+++a V+++s    ++ 
  gene1247|gene1247|rna1247|rna1247 129 SSNKIAEVTYASIQGIDAL 147
                                        5778888888887766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       386  (0.0215294); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1395.05
//
Query:       gene1248|gene1248|rna1248|rna1248  [L=76]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       442  (0.0246528); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 565.40
//
Query:       gene1249|gene1249|rna1249|rna1249  [L=806]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (806 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2435  (0.135813); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.75u 0.28s 00:00:01.03 Elapsed: 00:00:00.46
# Mc/sec: 5284.48
//
Query:       gene125|gene125|rna125|rna125  [L=181]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.12   12.4   0.2       0.32   11.0   0.0    1.8  2  DUF1788   Domain of unknown function (DUF1788)
       0.13   12.3   0.0       0.29   11.2   0.0    1.5  1  Thg1      tRNAHis guanylyltransferase


Domain annotation for each model (and alignments):
>> DUF1788  Domain of unknown function (DUF1788)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   3.6e-05      0.32      75     109 ..      59      98 ..      33     106 .. 0.86
   2 ?   -1.5   0.2      0.27   2.4e+03     103     121 ..     151     169 ..     148     171 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 3.6e-05
                        DUF1788  75 llRshtlLnnlqsv.vkkvpvvlfyPGeyd....gqslsl 109
                                    +lR+ ++L ++++   + ++v+ +yPG+y+    g+++++
  gene125|gene125|rna125|rna125  59 ILRIAEILIAVDDGrAQGCKVLTVYPGNYEdgygGNNMRF 98 
                                    789999999998754999***********97776666665 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.27
                        DUF1788 103 dgqslslfnelkddnyYra 121
                                    ++ ++++++e ++ ny+r 
  gene125|gene125|rna125|rna125 151 NKDEIRFMDEQNEYNYNRK 169
                                    5678999999999999996 PP

>> Thg1  tRNAHis guanylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   3.2e-05      0.29      48      88 ..     130     170 ..     121     174 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 3.2e-05
                           Thg1  48 lmneaakelvkefedivlaYgqSDEislvlsketklynrra 88 
                                    ++ + a +l+++   + ++Yg+ DEi ++ ++++  ynr+ 
  gene125|gene125|rna125|rna125 130 AVGDDALDLCDRAFRTAIGYGNKDEIRFMDEQNEYNYNRKL 170
                                    5556688899888899******************9**9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       381  (0.0212505); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 1366.37
//
Query:       gene1250|gene1250|rna1250|rna1250  [L=146]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       563  (0.0314016); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 1004.66
//
Query:       gene1251|gene1251|rna1251|rna1251  [L=683]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      2e-72  243.9   1.2    5.9e-50  170.1   0.0    2.8  3  Kinesin      Kinesin motor domain
    5.2e-22   78.4   0.2    5.2e-22   78.4   0.2    2.1  2  Microtub_bd  Microtubule binding
  ------ inclusion threshold ------
          5    5.7   6.7        9.1    4.9   6.7    1.4  1  Raftlin      Raftlin


Domain annotation for each model (and alignments):
>> Kinesin  Kinesin motor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  170.1   0.0   9.9e-54   5.9e-50      23     248 ..     107     310 ..      53     332 .. 0.86
   2 !   80.7   0.9   1.5e-26   9.2e-23     251     333 .]     380     459 ..     371     459 .. 0.93
   3 ?   -4.7   3.3       1.5   8.7e+03      27      41 ..     635     649 ..     591     681 .. 0.53

  Alignments for each domain:
  == domain 1  score: 170.1 bits;  conditional E-value: 9.9e-54
                                        TCTCEEEEEEEEECTTSCEEEEESEEEETTS-HHHHHHHHHHHHHHHHHTTSEEEEEEEESTTSSHHHHHTBCTTT CS
                            Kinesin  23 ekkeeekkskkenkeeeekkfkFdkvfdeeatqeevyeetakplvesvleGynatifaYGqtgsGKTyTmegkeee 98 
                                         +++ +   ++ + + ++ +++F k+f++ ++q+++++++ k+ v + ++Gyn+tifaYGqtgsGKTyT++g+ ++
  gene1251|gene1251|rna1251|rna1251 107 PSDTAQYAVSNGTLTYNNATYTFTKIFTK-SSQSQLFDQIGKQTVINTIKGYNTTIFAYGQTGSGKTYTIKGD-TH 180
                                        556666677788888999*********95.68999*************************************8.99 PP

                                        SBSHHHHHHHHHHHHHHHCTTTHEEEEEEEEEEEEEETTEEEETTSTTTTSTSSEBEEEECTTSCCEEETTS--EE CS
                            Kinesin  99 eeGiipraleelFesikkekeekekefsvkvsylEiYneeiyDLLeskkskkkkklkiredskkgevyvkglteve 174
                                        ++G++pr+l+++Fe   +  +      +v +s+lEiYne+++DLL ++       l ire  + g +yv +l +v 
  gene1251|gene1251|rna1251|rna1251 181 RPGLVPRILNYIFECNVA--D------EVALSMLEIYNEKLRDLLCDE-----GVLCIREGLD-G-TYVGNLGKVV 241
                                        9************98754..2......599****************98.....4699999998.6.9********* PP

                                        ESSHHHHHHHHHHHHHHHTSTTSSCTSHHCCSEEEEEEEEEEEETTTTTCEEEEEEEEEEEEEEECCCHHHHSS CS
                            Kinesin 175 vksaeevlellekgeknrkvaetklneeSSRSHavftitleqknlkeeteekvkisklnLvDLAGsErasktga 248
                                        v+++e ++++ e+g+ +r+v+   +n+eSSRSH+v+++  +  +        vk s++n+vDLAGsEr+++ + 
  gene1251|gene1251|rna1251|rna1251 242 VRDYEMAMDVYERGSVRRRVGWMGMNRESSRSHCVLMVYFRGGEGV-----LVKESRINIVDLAGSERIRDGEW 310
                                        ****************************************998744.....3678*************986553 PP

  == domain 2  score: 80.7 bits;  conditional E-value: 1.5e-26
                                        HHHHHHHHHHHHHHHHHHHHHHHHHHTCCTSTSCGGGSHHHHHTGGGHSSSSEEEEEEEE-TBGGGHHHHHHHHHH CS
                            Kinesin 251 gerlkEaaniNkSLlaLgrvisaLaekkkskhipYRdSkLTrlLqdsLgGnsktlmivtvspssenleetlstlkf 326
                                          ++kE++niNkSLl L++vi++L ++ +++hi YRdSkLT lL+dsLgGns+ ++i t++ +    +e+++tl+f
  gene1251|gene1251|rna1251|rna1251 380 AATIKETGNINKSLLSLREVIKKLGNN-QNDHINYRDSKLTFLLKDSLGGNSNLTIIGTLNLT--YKTESIHTLRF 452
                                        4679***********************.*********************************97..559******** PP

                                        HHHHCTT CS
                            Kinesin 327 aerakei 333
                                         +rak+i
  gene1251|gene1251|rna1251|rna1251 453 LQRAKHI 459
                                        *****97 PP

  == domain 3  score: -4.7 bits;  conditional E-value: 1.5
                                        EEEEEEEEECTTSCE CS
                            Kinesin  27 eekkskkenkeeeek 41 
                                        +++++ ++n ++ +k
  gene1251|gene1251|rna1251|rna1251 635 NNINNINDNINNINK 649
                                        111222222111111 PP

>> Microtub_bd  Microtubule binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.4   0.2   8.7e-26   5.2e-22      22     149 .]      99     217 ..      97     217 .. 0.87
   2 ?   -3.5   0.5       1.5   9.2e+03     105     126 ..     632     653 ..     626     668 .. 0.45

  Alignments for each domain:
  == domain 1  score: 78.4 bits;  conditional E-value: 8.7e-26
                                        -EEEEEEECCCS-T.EEEETTT...TTTEEEE-SEEEECTTHCCCCCCCCHHHHHHHHTT--EEEEEEES...... CS
                        Microtub_bd  22 iRvfarvrpelesekakikfpeeekkkkkefsFdrvfeseseqeevfeeisqlvqsaldgynvcifaygqTGsGKt 97 
                                        i v+ r++p+ + + ++++   + + ++ +++F+++f+++s+++ + +  +q v   ++gyn++ifaygqTGsGKt
  gene1251|gene1251|rna1251|rna1251  99 INVYLRIKPSDTAQ-YAVSNG-TLTYNNATYTFTKIFTKSSQSQLFDQIGKQTVINTIKGYNTTIFAYGQTGSGKT 172
                                        66888888877765.444444.567999*********998877777777799999999****************** PP

                                        ..........ST-HCHHHHHHHHHHCCTSCCCCEEEEEEEEEEESS-EEETT CS
                        Microtub_bd  98 yTmegeeeeagmipraveeifetiselkekgwkyeielqfveiynekvqDlL 149
                                        yT++g+++++g +pr+++ ife            e+ l+++eiynek++DlL
  gene1251|gene1251|rna1251|rna1251 173 YTIKGDTHRPGLVPRILNYIFECNVAD-------EVALSMLEIYNEKLRDLL 217
                                        *********************987776.......89***************8 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 1.5
                                        ...ST-HCHHHHHHHHHHCCTS CS
                        Microtub_bd 105 eeagmipraveeifetiselke 126
                                        +++++i+++ ++i ++ +++++
  gene1251|gene1251|rna1251|rna1251 632 NNNNNINNINDNINNINKQNEK 653
                                        3334444444444333333322 PP

>> Raftlin  Raftlin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   6.7    0.0015       9.1     142     279 ..     547     681 ..     544     683 .] 0.57

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.0015
                            Raftlin 142 kelikkvqeaasrGlkFvgvipqyasqsksansssltsgaaeseeardekkkrsssedkvslenekpgalsgksse 217
                                        + +i +++e  +rG k  g+i + +  ++     +  +++++ ++ + ++++ ++++d + ++n+  +     +++
  gene1251|gene1251|rna1251|rna1251 547 RGVIRRMDEVLRRGSKLGGIIGDNNNDNNDGFDNNI-DNRNDDTNDNIDNNNDNRNDDYIDNRNDGCDNNTNGNNN 621
                                        57899*****************99977665555554.556666666777777777788888888855433222222 PP

                            Raftlin 218 agaeeeaeseegkkgegpaaeqlqlssaeeegsespskskkgeeelsktedklskklelfal 279
                                         + + + ++++++++  + +++ +  ++++e++++   ++k++ ++++ ++++ k+++  ++
  gene1251|gene1251|rna1251|rna1251 622 RNDDTNGNTTNNNNNINNINDNINNINKQNEKENVI--NNKIRVKNTNCDEASVKNVNSNTT 681
                                        222222223323333334455555444444444444..445554445666655555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (683 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1434  (0.0799822); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.73u 0.32s 00:00:01.05 Elapsed: 00:00:00.51
# Mc/sec: 4054.89
//
Query:       gene1252|gene1252|rna1252|rna1252  [L=353]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (353 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       534  (0.0297841); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.58
# Mc/sec: 1832.88
//
Query:       gene1253|gene1253|rna1253|rna1253  [L=187]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-33  114.9   0.0    3.4e-33  114.6   0.0    1.0  1  DHFR_1    Dihydrofolate reductase


Domain annotation for each model (and alignments):
>> DHFR_1  Dihydrofolate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.6   0.0   1.9e-37   3.4e-33       5     143 ..      16     156 ..      12     174 .. 0.87

  Alignments for each domain:
  == domain 1  score: 114.6 bits;  conditional E-value: 1.9e-37
                                        EEEEETT-EEEBTTB-SS..--HHHHHHHHHHHT..TCEEEEEHHHHHCC-.S--TTCEEEEE-S-TT---TTEEE CS
                             DHFR_1   5 ivAvaengvIGkdnklpw..hlpeDlkrFkklTt..gkpvimGrkTfeslgkrpLpnrkniVltrnedlkvegvev 76 
                                        +  ++++++IG+++++pw  +l++D+k+  klTt  + +++mGrkT+es+g rpLp+r niVl+++ + + +g++v
  gene1253|gene1253|rna1253|rna1253  16 VCYTKTKRIIGYQGTIPWmgRLKSDMKFVSKLTTtgNVALVMGRKTYESIG-RPLPKRVNIVLSTTMEDQ-NGIVV 89 
                                        56677899**********777********99765225578**********9.*************99866.69*** PP

                                        ESSHHHHCCCCTTS.SEEEEEE-HHHHHHCGGG-SEEEEEEES.S----SEE-----CCCEEEEEEEE CS
                             DHFR_1  77 vssleealalakeekeevfviGGaeiYkqalpladklylTeid.aefegdtffpeideeewelveree 143
                                         +s++ea+++++e++   +v GG+e+Y+ al+   ++  T id  +f gdtffpe+d  ++e v+++ 
  gene1253|gene1253|rna1253|rna1253  90 KKSFDEAINFCREKEYVTVVFGGEEVYRVALKRRCRIWATVIDdMDFCGDTFFPEVDC-KYECVNEDV 156
                                        **********9999778889**********************9899**********76.788877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       415  (0.0231469); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1300.20
//
Query:       gene1254|gene1254|rna1254|rna1254  [L=267]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-24   86.0   0.0    3.7e-24   84.4   0.0    1.9  2  Ribosomal_S4e  Ribosomal family S4e
    2.6e-20   72.3   5.7    1.2e-18   66.9   4.0    2.3  2  RS4NT          RS4NT (NUC023) domain
      5e-15   54.9   0.0    9.8e-15   53.9   0.0    1.5  1  40S_S4_C       40S ribosomal protein S4 C-terminus
     0.0087   15.8   0.0       0.02   14.6   0.0    1.6  1  S4             S4 domain


Domain annotation for each model (and alignments):
>> Ribosomal_S4e  Ribosomal family S4e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.4   0.0   8.3e-28   3.7e-24       1      75 []      95     169 ..      95     169 .. 0.99
   2 ?   -2.7   0.0       1.3   5.9e+03      45      61 ..     246     262 ..     240     264 .. 0.72

  Alignments for each domain:
  == domain 1  score: 84.4 bits;  conditional E-value: 8.3e-28
                                        TTEEEEEEE-TTSSEEEEEE-TTCCCEEEEEECEEEEECCCEEEEEETTS-EEEESSTT-STTEEEEEETTTTEE CS
                      Ribosomal_S4e   1 tgenyrllydtkgrfalhkItseeakyKLcKikkkttvkkgipqlvthdGrtirypdpdikvnDtvkidleenkI 75 
                                        tge+yrlly++ grf lh+I++ee+k++L  i+kk + k+++p+l t+dG  + y d+di   Dtvk+dle+++I
  gene1254|gene1254|rna1254|rna1254  95 TGEHYRLLYNVAGRFILHQISEEESKFRLSIIRKKLLRKGKVPYLYTNDGASFSYCDQDIVPSDTVKVDLETGRI 169
                                        89**********************************************************************998 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.3
                                        EEETTS-EEEESSTT-S CS
                      Ribosomal_S4e  45 lvthdGrtirypdpdik 61 
                                        l   d ++iry+ +  k
  gene1254|gene1254|rna1254|rna1254 246 LSVFDESNIRYEGETLK 262
                                        55667789999876555 PP

>> RS4NT  RS4NT (NUC023) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.9   4.0   2.8e-22   1.2e-18       1      36 [.       3      38 ..       3      39 .. 0.97
   2 !    4.8   0.0     0.007        31      14      28 ..     207     221 ..     206     222 .. 0.88

  Alignments for each domain:
  == domain 1  score: 66.9 bits;  conditional E-value: 2.8e-22
                                       -S----EETTTS-TTS---SSSSSEE----SSSS-T CS
                              RS4NT  1 rGpkkHLKrlaAPkhWpldkkegvfavkPspGPHkl 36
                                       rGp+kHLKrlaAPk+W+l+k+ gvfa++Ps+GPH l
  gene1254|gene1254|rna1254|rna1254  3 RGPRKHLKRLAAPKSWLLKKNVGVFAPRPSTGPHRL 38
                                       8*********************************97 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.007
                                        TTS---SSSSSEE-- CS
                              RS4NT  14 khWpldkkegvfavk 28 
                                        k +++dkk++vfa++
  gene1254|gene1254|rna1254|rna1254 207 KVYLVDKKGRVFATR 221
                                        56899********87 PP

>> 40S_S4_C  40S ribosomal protein S4 C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.9   0.0   2.2e-18   9.8e-15       1      45 [.     212     256 ..     212     259 .. 0.96

  Alignments for each domain:
  == domain 1  score: 53.9 bits;  conditional E-value: 2.2e-18
                                        -SSS-EEEEEGGGEEE--STTS-SS---SS-S----HHHHHHHHH CS
                           40S_S4_C   1 DaaGntFATRlsNvFvIGkgnkpwvsLPkgkGiklsiaeerdkrl 45 
                                        D++G+ FATR  Nv+vIG + ++w+sLP++ G+kls+ +e + r 
  gene1254|gene1254|rna1254|rna1254 212 DKKGRVFATRKVNVCVIGPDGNSWISLPENEGVKLSVFDESNIRY 256
                                        99**************************************99886 PP

>> S4  S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   4.5e-06      0.02      10      47 ..      52      89 ..      44      90 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 4.5e-06
                                       TTSSSSHHHHHHHHHTTTEEETTEEE--TT-EE-TTCE CS
                                 S4 10 lglassrreArqlIehGrVlVNGkvvkdpsyrVkpgDv 47
                                       l +a + +e+  + +++ +++NG++++d  ++V+  Dv
  gene1254|gene1254|rna1254|rna1254 52 LQYARTGKEVGNILKERMIKINGRIRTDKRFPVGIFDV 89
                                       56788889999999*******************99887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       521  (0.0290591); expected 358.6 (0.02)
Passed bias filter:                      497  (0.0277205); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 2011.27
//
Query:       gene1255|gene1255|rna1255|rna1255  [L=111]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (111 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       622  (0.0346924); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 879.93
//
Query:       gene1256|gene1256|rna1256|rna1256  [L=61]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.15   12.5   3.0       0.17   12.3   3.0    1.1  1  IATP      Mitochondrial ATPase inhibitor, IATP


Domain annotation for each model (and alignments):
>> IATP  Mitochondrial ATPase inhibitor, IATP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   3.0   9.4e-06      0.17      47      90 ..      17      60 ..       7      61 .] 0.82

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 9.4e-06
                               IATP 47 eagdafgkrEaAsEeeyirqrekekLaeLkeklaeqkeHleele 90
                                       ++ daf  +E+   ++ +r++ ++  ++Lk++ ++ ++H ++++
  gene1256|gene1256|rna1256|rna1256 17 KQLDAFHEKEKCPVDKRLRRQLRKIKKKLKKRYNKFQKHVQSIK 60
                                       6679999999999999998877777788898888889**99997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2682  (0.14959); expected 358.6 (0.02)
Passed bias filter:                      923  (0.0514808); expected 358.6 (0.02)
Passed Vit filter:                        87  (0.00485247); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.31s 00:00:00.79 Elapsed: 00:00:00.50
# Mc/sec: 366.72
//
Query:       gene1257|gene1257|rna1257|rna1257  [L=174]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      6e-06   25.9   4.9     0.0017   17.9   0.1    2.5  3  KTI12            Chromatin associated protein KTI12
  ------ inclusion threshold ------
       0.11   12.2   0.2       0.21   11.2   0.2    1.5  1  Fels1            Fels-1 Prophage Protein-like
       0.22   12.1   2.6        4.3    7.9   0.5    2.4  2  Defensin_beta_2  Beta defensin


Domain annotation for each model (and alignments):
>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0      0.35   2.1e+03       1       8 [.      25      32 ..      25      62 .. 0.80
   2 !   10.1   0.7   6.8e-05       0.4      80     105 ..      81     106 ..      33     113 .. 0.94
   3 !   17.9   0.1   2.8e-07    0.0017     138     181 ..     116     158 ..     111     174 .] 0.77

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.35
                                       E.EEEEE- CS
                              KTI12  1 MpLvvltG 8 
                                       Mp+++++G
  gene1257|gene1257|rna1257|rna1257 25 MPIIIVCG 32
                                       88888888 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 6.8e-05
                                        --SHHHHHHHHHHHHHTT-EEEEEEE CS
                              KTI12  80 nyikgfRYeLyciakaakttlcvvyv 105
                                         y k+ RY  yc ak  kt ++vv++
  gene1257|gene1257|rna1257|rna1257  81 SYSKSERYISYCHAKRFKTGYIVVFL 106
                                        699*********************86 PP

  == domain 3  score: 17.9 bits;  conditional E-value: 2.8e-07
                                        --TTSS-GGGS-SEEEE.TTS---HHHHHHHHHHHHTS--SSST CS
                              KTI12 138 eePdsknrWDsPlftvlsaeeklpldeilkaliekkklkpnqat 181
                                        e P ++nr+D+Pl+tv  + ++  +d+i ++l++ k +k + + 
  gene1257|gene1257|rna1257|rna1257 116 EVPLESNRYDNPLITVN-DYKNDIFDNINNVLCNTKMKKFKIKR 158
                                        8899*************.99999*********766655544333 PP

>> Fels1  Fels-1 Prophage Protein-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.2   3.6e-05      0.21      18      33 ..      40      65 ..      40      68 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 3.6e-05
                              Fels1 18 fCDvkerlCrd..........SggiS 33
                                       fCD + ++C+d          S +iS
  gene1257|gene1257|rna1257|rna1257 40 FCDDYTNICSDknvvvhntafSEAIS 65
                                       9**********999999888888887 PP

>> Defensin_beta_2  Beta defensin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.5   0.00071       4.3      13      29 ..      31      48 ..      30      48 .. 0.85
   2 ?    4.0   0.1     0.012        73      15      25 ..      84      95 ..      83      98 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00071
                    Defensin_beta_2 13 CrknEkaigyC.engklC 29
                                       C ++E+   +C  ++ +C
  gene1257|gene1257|rna1257|rna1257 31 CGDDEYVKQFCdDYTNIC 48
                                       ***********7777777 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.012
                    Defensin_beta_2 15 knEkaigyC.en 25
                                       k+E++i yC  +
  gene1257|gene1257|rna1257|rna1257 84 KSERYISYChAK 95
                                       79*******544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       911  (0.0508115); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 1219.86
//
Query:       gene1258|gene1258|rna1258|rna1258  [L=35]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (35 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       271  (0.0151152); expected 358.6 (0.02)
Passed bias filter:                      225  (0.0125495); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.28s 00:00:00.66 Elapsed: 00:00:00.45
# Mc/sec: 231.37
//
Query:       gene1259|gene1259|rna1259|rna1259  [L=423]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0087   16.2   0.3        2.5    8.6   0.0    4.2  4  HEAT            HEAT repeat
  ------ inclusion threshold ------
      0.076   12.7   0.5        4.8    6.8   0.0    2.6  2  DNA_alkylation  DNA alkylation repair enzyme
       0.23   11.6   4.2        1.4    9.1   0.3    3.3  5  RTP1_C1         Required for nuclear transport of RNA pol II 
       0.39   10.7  14.7       0.27   11.3   6.5    3.7  2  Cnd1            non-SMC mitotic condensation complex subunit 
        0.7   10.3   5.8       0.34   11.3   0.2    3.0  3  YgaB            YgaB-like protein


Domain annotation for each model (and alignments):
>> HEAT  HEAT repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.38   1.4e+03       9      24 ..     198     214 ..     194     219 .. 0.80
   2 !    8.6   0.0    0.0007       2.5       4      30 ..     236     262 ..     233     263 .. 0.89
   3 ?    1.3   0.0      0.15   5.5e+02       7      27 ..     280     299 ..     274     303 .. 0.76
   4 ?   -2.2   0.0         2   7.3e+03      14      29 ..     389     404 ..     388     406 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.38
                                        HT-SSHHH.HHHHHHHH CS
                               HEAT   9 lsDpspeV.ReaAakaL 24 
                                        l+D++++V R+ +++ L
  gene1259|gene1259|rna1259|rna1259 198 LMDSEMFVfRSCCIEIL 214
                                        68******898888765 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0007
                                        HHHHHHT-SSHHHHHHHHHHHHHHHHC CS
                               HEAT   4 lllkllsDpspeVReaAakaLgalaev 30 
                                        ++l  l D + +VR+ A++ L+ l+e+
  gene1259|gene1259|rna1259|rna1259 236 TILDRLLDVNHFVRAKAVQILASLVEQ 262
                                        5788889*****************985 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.15
                                        HHHT-SSHHHHHHHHHHHHHH CS
                               HEAT   7 kllsDpspeVReaAakaLgal 27 
                                        + ++D++  VR+ A++ ++ +
  gene1259|gene1259|rna1259|rna1259 280 R-IEDKAVLVRKRALNFCTMV 299
                                        4.68**********9876655 PP

  == domain 4  score: -2.2 bits;  conditional E-value: 2
                                        HHHHHHHHHHHHHHHH CS
                               HEAT  14 peVReaAakaLgalae 29 
                                        +++R+  ++a+ +l +
  gene1259|gene1259|rna1259|rna1259 389 AKQRMLLLQAFIDLFS 404
                                        6889999999988876 PP

>> DNA_alkylation  DNA alkylation repair enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.1     0.016        58      49     108 ..      36      92 ..      14     111 .. 0.77
   2 ?    6.8   0.0    0.0013       4.8     151     193 ..     151     193 ..     139     207 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.016
                     DNA_alkylation  49 eeelqelaeeLwksperEerllAldlltqakkklaeadlelyeklvetinnWdlvDslas 108
                                        +++  +++++L k++ +   +l l+ l  + +kl+ +d+el+ +++++i+n  + D++++
  gene1259|gene1259|rna1259|rna1259  36 SRQKDRILAALQKNGDNSTEMLSLLHL--YCQKLDVDDWELFMSIIDQIKNI-TDDESCW 92 
                                        356678888999999999999999999..448888889***********998.6666665 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0013
                     DNA_alkylation 151 tdlellleiaeelladkedfiqkAiGwaLrelsktdpdlveeF 193
                                        ++ + l++++ + ++ ++   qk i+ +L e+++ +++l   F
  gene1259|gene1259|rna1259|rna1259 151 DEQASLFKCIMSEINTENSVLQKNIASFLVEIANNNAKLFLGF 193
                                        566789*****************************99987654 PP

>> RTP1_C1  Required for nuclear transport of RNA pol II C-terminus 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.88   3.1e+03      34      73 ..      52      91 ..      41     116 .. 0.70
   2 ?   -0.8   0.0      0.48   1.7e+03      48      73 ..     197     223 ..     169     232 .. 0.81
   3 ?    8.8   0.2   0.00051       1.8      34      71 ..     226     263 ..     193     278 .. 0.58
   4 ?    9.1   0.3   0.00039       1.4       3      51 ..     236     283 ..     234     302 .. 0.83
   5 ?    2.5   0.1     0.043   1.6e+02       4      64 ..     277     336 ..     274     369 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.88
                            RTP1_C1 34 avldiekilkllleaLkdedsYvYLnaikgLvaLadvfpe 73
                                       + ++  ++l+l  + L  +d  ++++ i  + +++d  + 
  gene1259|gene1259|rna1259|rna1259 52 NSTEMLSLLHLYCQKLDVDDWELFMSIIDQIKNITDDESC 91
                                       5566667788888888888877777777777777766554 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.48
                            RTP1_C1  48 aLkdedsYvYLn.aikgLvaLadvfpe 73 
                                         L d++ +v+ + +i++L +L+ ++++
  gene1259|gene1259|rna1259|rna1259 197 DLMDSEMFVFRScCIEILFSLIFIYKD 223
                                        477999999976369999999877766 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.00051
                            RTP1_C1  34 avldiekilkllleaLkdedsYvYLnaikgLvaLadvf 71 
                                        +++ i++ ++++l+ L d + +v  +a+++L++L++  
  gene1259|gene1259|rna1259|rna1259 226 NIEGINEFTETILDRLLDVNHFVRAKAVQILASLVEQQ 263
                                        55566666666666666666666666666666666542 PP

  == domain 4  score: 9.1 bits;  conditional E-value: 0.00039
                            RTP1_C1   3 ealkdlqdpllpvrahglvlLrkliekkskeavldiekilkllleaLkd 51 
                                        ++l+ l d    vra++++ L++l+e++   +++ ++k+++ ++  ++d
  gene1259|gene1259|rna1259|rna1259 236 TILDRLLDVNHFVRAKAVQILASLVEQQA-VTLKLKNKVVENVVLRIED 283
                                        678899999999***************97.7777777777766666665 PP

  == domain 5  score: 2.5 bits;  conditional E-value: 0.043
                            RTP1_C1   4 alkdlqdpllpvrahglvlLrkliekkskeavldiekilkllleaLkdedsYvYLnaikgL 64 
                                        ++  ++d+ + vr ++l+  + +i+++s  a+    ++ +++ e L  ed+  Y    k++
  gene1259|gene1259|rna1259|rna1259 277 VVLRIEDKAVLVRKRALNFCTMVIKNHS-FAANRYLRVERVVDEELMSEDEKAYTRDLKMF 336
                                        667899************9999999997.77777778888888888888877666655555 PP

>> Cnd1  non-SMC mitotic condensation complex subunit 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.2       0.1   3.7e+02      59      93 ..     156     190 ..     143     200 .. 0.78
   2 ?   11.3   6.5   7.4e-05      0.27      19      89 ..     230     303 ..     228     418 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.1
                               Cnd1  59 flselaklleDenprVvanalaalteiseksenai 93 
                                        +++ + + ++ en+  ++n  ++l ei++++ +++
  gene1259|gene1259|rna1259|rna1259 156 LFKCIMSEINTENSVLQKNIASFLVEIANNNAKLF 190
                                        55556666788999999999999999999986655 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 7.4e-05
                               Cnd1  19 veylvepLrkrLkDedpyVRktaaivvakLilnd..mvkekg.flselaklleDenprVvanalaalteiseks 89 
                                        + +++e +  rL D +  VR  a+ ++a L++++  + k k+ +++++   +eD+   V++ al++ t + ++ 
  gene1259|gene1259|rna1259|rna1259 230 INEFTETILDRLLDVNHFVRAKAVQILASLVEQQavTLKLKNkVVENVVLRIEDKAVLVRKRALNFCTMVIKNH 303
                                        5678999999********************9888333455556***********************99988875 PP

>> YgaB  YgaB-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.37   1.3e+03      22      58 ..     138     173 ..     131     181 .. 0.74
   2 ?   11.3   0.2   9.5e-05      0.34      29      65 ..     317     353 ..     311     364 .. 0.89
   3 ?   -1.9   0.2       1.3   4.5e+03       8      30 ..     385     407 ..     381     415 .. 0.70

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.37
                               YgaB  22 elerCqeiekeLlklekeaklesiqeeikrkkkeLke 58 
                                        ++e C e+ + +  +e+ + ++ i +ei+  +  L++
  gene1259|gene1259|rna1259|rna1259 138 NVETCLEVFQAMG-DEQASLFKCIMSEINTENSVLQK 173
                                        6788888877664.45666778899999998888875 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 9.5e-05
                               YgaB  29 iekeLlklekeaklesiqeeikrkkkeLkeiqkvFek 65 
                                        +++eL++ +++a  ++++  i+++k  +  iq++F  
  gene1259|gene1259|rna1259|rna1259 317 VDEELMSEDEKAYTRDLKMFIAQMKMVISSIQDIFSC 353
                                        789********************************75 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 1.3
                               YgaB   8 eQmktmdkLLflQselerCqeie 30 
                                        e ++  +++L lQ+ +++   ++
  gene1259|gene1259|rna1259|rna1259 385 ENIDAKQRMLLLQAFIDLFSSLK 407
                                        56667788999999888765544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (423 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1135  (0.0633053); expected 358.6 (0.02)
Passed bias filter:                      604  (0.0336884); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.56u 0.31s 00:00:00.87 Elapsed: 00:00:00.45
# Mc/sec: 2797.13
//
Query:       gene126|gene126|rna126|rna126  [L=36]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (36 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       351  (0.0195772); expected 358.6 (0.02)
Passed bias filter:                      183  (0.0102069); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.42
# Mc/sec: 255.14
//
Query:       gene1260|gene1260|rna1260|rna1260  [L=466]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-05   24.9   2.1    1.7e-05   24.9   2.1    2.4  2  Cnd1      non-SMC mitotic condensation complex subunit 1
     0.0053   16.8   0.3       0.23   11.5   0.0    2.9  2  CARD      Caspase recruitment domain


Domain annotation for each model (and alignments):
>> Cnd1  non-SMC mitotic condensation complex subunit 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.2      0.24   2.2e+03      30      30 ..      57      57 ..       7     129 .. 0.58
   2 !   24.9   2.1   1.9e-09   1.7e-05       1     148 [.     292     427 ..     292     443 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.24
                               Cnd1 30 L 30
                                       +
  gene1260|gene1260|rna1260|rna1260 57 I 57
                                       2 PP

  == domain 2  score: 24.9 bits;  conditional E-value: 1.9e-09
                               Cnd1   1 liRalairtlg..cirvpnlveylvepLrkrLkDedpyVRktaaivvakLilndmvkekgflselaklleDenprV 74 
                                        l+R + +++++   + +++ ve+++  L  +L De++ V k a++++ +L++ ++ k kg  + l kl e +++  
  gene1260|gene1260|rna1260|rna1260 292 LVRYNSLVAMAdfILLYNSYVEKYSYLLFDKLFDENENVVKLALFIIYHLVSSKILKIKGYGAVLCKLHETQHS-- 365
                                        69**********999*********************************************88888888755554.. PP

                               Cnd1  75 vanalaalteiseksenaiynllpdiisklsdalnecsewgqitilefLlsyipkdkqeaeslveklcprlqha 148
                                         +  +++l+ +++ + n+i +++ +++           +   +++++f+   ++++++  e+l+ k+ ++++++
  gene1260|gene1260|rna1260|rna1260 366 -DTIKSLLSSLASDE-NTIASIFYEVMLDE--------KSRNMEVIQFIKCLVKDKTK--ENLFLKILQKFKKE 427
                                        .55566677777766.56665555544332........34456666666666666666..67777777776665 PP

>> CARD  Caspase recruitment domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0     0.026   2.3e+02      63      81 ..     115     133 ..     112     135 .. 0.90
   2 !   11.5   0.0   2.5e-05      0.23      21      74 ..     337     393 ..     328     405 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.026
                                        HHHHHHHHHHHHSHHHHHH CS
                               CARD  63 acqaflealkegqpdlasl 81 
                                         cq++le l+ +++ la+ 
  gene1260|gene1260|rna1260|rna1260 115 LCQLLLEKLCTENKNLAKI 133
                                        59**************986 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 2.5e-05
                                        HHHHHHHTTSS-HHHHHHHHT...SSSHHHHHHHHHHHHHTSCHHHHHHHHHHHHHH CS
                               CARD  21 lldyLlekkVLteeeeekika...kttrlskareLldlvqkkgekacqaflealkeg 74 
                                        +  +L++ k+L+ + + ++++   +t+  +    Ll+++ +  ++ +++f+e+  ++
  gene1260|gene1260|rna1260|rna1260 337 IIYHLVSSKILKIKGYGAVLCklhETQHSDTIKSLLSSLASDENTIASIFYEVMLDE 393
                                        5679*****************9988888899999******************98775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (466 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       713  (0.039768); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.25s 00:00:00.84 Elapsed: 00:00:00.45
# Mc/sec: 3123.86
//
Query:       gene1261|gene1261|rna1261|rna1261  [L=174]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       586  (0.0326845); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1212.45
//
Query:       gene1262|gene1262|rna1262|rna1262  [L=244]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.3e-37  129.5   0.7    1.2e-22   80.5   0.0    2.1  2  Prenyltransf  Putative undecaprenyl diphosphate synthase


Domain annotation for each model (and alignments):
>> Prenyltransf  Putative undecaprenyl diphosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.5   0.0   6.8e-27   1.2e-22       1     131 [.      60     181 ..      60     184 .. 0.91
   2 !   48.2   0.1   5.3e-17   9.5e-13     166     220 ..     185     240 ..     178     243 .. 0.89

  Alignments for each domain:
  == domain 1  score: 80.5 bits;  conditional E-value: 6.8e-27
                                        EE--HHHHHHHTT.S-HHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEEEGGGG.GS-HHHHHHHHHHHHHHHHHHH CS
                       Prenyltransf   1 imDGNrRwAkkrgleereeGhkaGaealkeilelclelgvkvvtvYafSteNf.kRskeevdalmellkeellkee 75 
                                        i+DGNrR+A++r+ ++ ++G k G+ +lk+il+++ ++++k v+vYa+S +Nf +R++ e++ +++ll++e     
  gene1262|gene1262|rna1262|rna1262  60 ILDGNRRYARARN-LSIKDGKKDGLLNLKRILTYIEHTNIKEVSVYAYSLQNFqQRDRIELESVFDLLRTE----- 129
                                        89***********.67777**********************************679999********9653..... PP

                                        HHHHHHTTEEEEEESSGGGS-HHHHHHHHHHHHHHT.TTTSEEEEEEEEE-HHHHH CS
                       Prenyltransf  76 lkellkegvrvrviGdlellpedvlealekaeeatkknnkklvlniavnYgsrdei 131
                                          ++ + + ++r+ G+le l+++ ++ l+ +e++tk +     lni++ Y++  ei
  gene1262|gene1262|rna1262|rna1262 130 --RMEDFNYQLRFYGSLEFLKPKERSILKALESNTKFKG--KRLNICILYSGLLEI 181
                                        ..445569****************************444..69*********9988 PP

  == domain 2  score: 48.2 bits;  conditional E-value: 5.3e-17
                                        SSS-SEEEEESS--S-TTSSTTTTTT-E.EEEESSSGGG--HHHHHHHHHHHHHCH CS
                       Prenyltransf 166 lpdpDlliRtsGeeRlSnFllwqlayse.lyfldvlWPdfskedllealleyqkre 220
                                        + +pD+l+Rt+ ++RlS+Fll ++a+   l fl+ +WP+f+ ++++  l++y+ ++
  gene1262|gene1262|rna1262|rna1262 185 FDKPDILVRTGNQRRLSDFLLLHCANGCnLNFLERMWPEFEVWQFYLLLVKYSIEN 240
                                        578********************877657***********************8765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (244 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       541  (0.0301746); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1696.20
//
Query:       gene1263|gene1263|rna1263|rna1263  [L=311]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       628  (0.0350271); expected 358.6 (0.02)
Passed bias filter:                      511  (0.0285013); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 2097.95
//
Query:       gene1264|gene1264|rna1264|rna1264  [L=177]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-35  121.4   0.0    2.5e-35  121.2   0.0    1.1  1  UQ_con    Ubiquitin-conjugating enzyme


Domain annotation for each model (and alignments):
>> UQ_con  Ubiquitin-conjugating enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  121.2   0.0   1.4e-39   2.5e-35       9     139 ..      17     146 ..       5     147 .. 0.89

  Alignments for each domain:
  == domain 1  score: 121.2 bits;  conditional E-value: 1.4e-39
                                        HHHSTTTTEEEEEEETTEECEEEEEEEB.TTSTTTTEEEEEEEE--TTTTTS--EEEESST-SCTTBE.TTSBB-C CS
                             UQ_con   9 lakkkpsgisaklvddenlfewkvlikgpedtpYeggvFklelefpedYPlkpPkvkfvtkifHPnvd.ksGevcl 83 
                                        + k + +g+ +k+++  + +e+ v + gp+dtp+++g+ ++++ +p dYP+k+P++ fv kifHPn+d +sG+vcl
  gene1264|gene1264|rna1264|rna1264  17 IYKLRAKGYLKKISE--SNDELIVELRGPKDTPFHNGLLTVSIVLPLDYPFKSPSIGFVGKIFHPNIDeSSGSVCL 90 
                                        334555566666555..789******************************************************** PP

                                        GGGSTTT--TTSHHHHHHH.HHHHHHHS--TTS-SSHHHHHHHHHTHHHHHHHHHHH CS
                             UQ_con  84 diLkeekWspaltlesvll.siqsLlaepnpesplnkeaakllkkdreeykkkvkey 139
                                        d+L+ + W+p ++l++++   i +Lla pn  +pln++aa+++ +dr+ y+k ++ey
  gene1264|gene1264|rna1264|rna1264  91 DVLN-QVWTPLYDLQTIVEvFIPQLLAYPNAMDPLNTKAAQMYLNDRDMYNKVAREY 146
                                        ****.66***********989********************************9988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       561  (0.0312901); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1321.83
//
Query:       gene1265|gene1265|rna1265|rna1265  [L=269]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.9e-17   62.8   4.0    7.8e-09   35.1   0.2    2.5  2  CAF1      CAF1 family ribonuclease
  ------ inclusion threshold ------
      0.025   15.1   0.0      0.044   14.3   0.0    1.5  1  RNase_T   Exonuclease


Domain annotation for each model (and alignments):
>> CAF1  CAF1 family ribonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.1   0.2   8.7e-13   7.8e-09       1     126 [.       8     124 ..       8     127 .. 0.78
   2 !   28.3   0.4   1.1e-10   9.6e-07     207     316 ..     144     227 ..     132     230 .. 0.75

  Alignments for each domain:
  == domain 1  score: 35.1 bits;  conditional E-value: 8.7e-13
                                        E-GGGHHHHHHHHHHHHHH-SEEEEEEEES-SS-----------HHHHHHHHHHHTTTB-EEEEEEEEEEEETTTT CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               CAF1   1 VtrsNfkellpeilkaikeasFvAiDlEftGlsegerkesladsleerYeklkqaaesfsilqlGlscfsedkekk 76 
                                        V ++N+++ ++ei+k +++ ++v +D+Ef G+  ++   +        Y++l+ ++   +++q+G+++     +  
  gene1265|gene1265|rna1265|rna1265   8 VWSDNLESSFSEIRKLVQTYNYVTMDTEFPGV-VAKPLGNFTSHSTYAYQQLRCNVDLLKVIQVGITFSDCYGNCP 82 
                                        6789***************************9.334444455555689*******************884444433 PP

                                        E..EEEEEEEEEB----SS---EEEEEHHHHHHHHHTT--HHHHHTT-B- CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               CAF1  77 ekeykvqpynfylfpkeedldrefsvspsslqFLakngfdfnkliseGip 126
                                        +   +++ +nf+       +d+e ++  +sl+ L++ +++f+k   +Gi+
  gene1265|gene1265|rna1265|rna1265  83 A--RNTYQFNFHFD-----IDKE-MYAKDSLKLLVEAQLNFDKHRLQGIE 124
                                        2..34444555433.....4455.677899*************9999985 PP

  == domain 2  score: 28.3 bits;  conditional E-value: 1.1e-10
                                        -EEEESSTHHHHHHHHHHH.T----SSHHHHHHHHHHH-SSEEEHHHHHTSTTTTTT-S--SHHHHHHHTTSTTS- CS
                                        xxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               CAF1 207 kpiVgHNgllDllflyqtf.yaeLPesleeFkaklselFPgiiDtKylakneelearleassLeelfeklkkensk 281
                                         ++ +H   +D+++l++   +++LP++ +eF   ++ lFP+ +D+Kyl          ++++L+   ++++++ + 
  gene1265|gene1265|rna1265|rna1265 144 TWLSFHS-SYDFAYLMKIVtCNPLPATENEFFMFMNILFPNFYDVKYLL---R-----GSKYLKRGLQEIAEDLGL 210
                                        4555554.56*******996778**************************...3.....666777666666444443 PP

                                        -.......--EEE-TTS---------HHHHHHHHH CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               CAF1 282 skdassseekkesekkkaaseesaHeAGyDafmTG 316
                                        +                    + +H+AG Da++T 
  gene1265|gene1265|rna1265|rna1265 211 K------------------RVGVQHQAGSDALLTR 227
                                        3..................2356899999999985 PP

>> RNase_T  Exonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0     5e-06     0.044      35     164 ..      87     229 ..      60     230 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 5e-06
                                        EEEEEEEEHSSHCSSSHHHHHHHHHCHHHHHTCEBHHHHHHHHHHHHHHHTCCCETTTCEEEESSHHHHHHHHHHH CS
                            RNase_T  35 etfhfyvkptelakltdecteftgitqemldeapsfkevleefkellrklallvahnaafdvgflraadkrilkke 110
                                        ++f+f+ + ++     + ++++    q+++d+ +     +eef  ll +  l+  +n+  +  ++ +++  ++k+ 
  gene1265|gene1265|rna1265|rna1265  87 YQFNFHFDIDKE-MYAKDSLKLLVEAQLNFDKHRLQGIEVEEFGNLLITSGLILSKNVTWLSFHSSYDFAYLMKIV 161
                                        566666666665.567777777778888888888888888888888888888888888888888888888777764 PP

                                        HH.....HHHHCSEHCECHHHHHHHHHC.........HHHHHHHHHTTCHSSSSTSSHHHHHHHHHHH CS
                            RNase_T 111 vp.....krnqfldtlildkatlkelar.........tsldklaeklgleedgraHrAldDaeatakl 164
                                        +       +n+f+ +++++   +   ++         ++l+++ae lgl+  g +H+A +Da+ t  +
  gene1265|gene1265|rna1265|rna1265 162 TCnplpaTENEFFMFMNILFPNFYDVKYllrgskylkRGLQEIAEDLGLKRVGVQHQAGSDALLTRDV 229
                                        3368888666666666665555555555666777799*************************987665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (269 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       393  (0.0219198); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 2069.15
//
Query:       gene1266|gene1266|rna1266|rna1266  [L=357]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (357 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       703  (0.0392102); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 2421.39
//
Query:       gene1267|gene1267|rna1267|rna1267  [L=62]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (62 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       501  (0.0279436); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.33u 0.25s 00:00:00.58 Elapsed: 00:00:00.39
# Mc/sec: 479.23
//
Query:       gene1268|gene1268|rna1268|rna1268  [L=65]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (65 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       995  (0.0554967); expected 358.6 (0.02)
Passed bias filter:                      244  (0.0136092); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.32u 0.24s 00:00:00.56 Elapsed: 00:00:00.39
# Mc/sec: 506.07
//
Query:       gene1269|gene1269|rna1269|rna1269  [L=325]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.6e-06   25.7   1.0      0.016   14.8   0.0    2.5  2  GIT_SHD   Spa2 homology domain (SHD) of GIT


Domain annotation for each model (and alignments):
>> GIT_SHD  Spa2 homology domain (SHD) of GIT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   9.2e-07     0.016       4      29 .]      39      64 ..      38      64 .. 0.92
   2 !    8.7   0.7   7.3e-05       1.3       4      21 ..      75      92 ..      75      93 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 9.2e-07
                            GIT_SHD  4 KLarLsnkqFeeLvtDVydEldRRet 29
                                       K++ L++ qFe L+ DV  E++RR+t
  gene1269|gene1269|rna1269|rna1269 39 KMSFLTPLQFECLIKDVKTEINRRIT 64
                                       77779*******************87 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 7.3e-05
                            GIT_SHD  4 KLarLsnkqFeeLvtDVy 21
                                       +L++Ls   F +Lv+D +
  gene1269|gene1269|rna1269|rna1269 75 RLSNLSELKFRDLVIDLF 92
                                       79**************76 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (325 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1326  (0.0739584); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2347.03
//
Query:       gene127|gene127|rna127|rna127  [L=36]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (36 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       310  (0.0172904); expected 358.6 (0.02)
Passed bias filter:                      253  (0.0141112); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.31u 0.25s 00:00:00.56 Elapsed: 00:00:00.39
# Mc/sec: 278.33
//
Query:       gene1270|gene1270|rna1270|rna1270  [L=209]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.6e-15   54.9   0.9    2.7e-14   52.9   0.0    1.9  2  tRNA-synt_1d  tRNA synthetases class I (R)
     0.0079   16.5   0.2      0.014   15.7   0.2    1.4  1  APP_N         Amyloid A4 N-terminal heparin-binding


Domain annotation for each model (and alignments):
>> tRNA-synt_1d  tRNA synthetases class I (R)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.3      0.03   2.7e+02     102     175 ..      54     128 ..      28     135 .. 0.53
   2 !   52.9   0.0     3e-18   2.7e-14      13      59 ..     142     188 ..     130     192 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.03
                                        HHHHHHCCCSHCCCHHHHHHHHHHHCT-HHHHHHHHHH...HHHHHHHHHHHHH..HCT---EC--CCCCCCCHHH CS
                       tRNA-synt_1d 102 keakkdydeeeifaerarnyvvkLqsgdedirklwkll...vditrtelqklyd..rldvtlierGeslykeslne 172
                                         e+ k +d+ +       +  + L+s+++++ ++   +   +d   te +k     ++ +   +  e +y+  + +
  gene1270|gene1270|rna1270|rna1270  54 TEVSKSFDKSDFT----IQLAKVLHSKNNNMVNIDAEIdlqTDDFLTEVSKSKLcyNVKINKAKYCERIYNAIMSS 125
                                        5555555555443....23344555555554444333211134444444444440044444455788888888876 PP

                                        HHH CS
                       tRNA-synt_1d 173 ivk 175
                                         v 
  gene1270|gene1270|rna1270|rna1270 126 DVY 128
                                        665 PP

  == domain 2  score: 52.9 bits;  conditional E-value: 3e-18
                                        .---SST-EEEEE----BTTS--BHHHHHHHHHHHHHHHHHHHCT-E CS
                       tRNA-synt_1d  13 qkksrekkkvvvdfssPniakemhvGhLrstiiGdavsrlleflGyd 59 
                                        +k  ++ +++ +dfssPniak++h+GhLr+ti+G+++s+l+ +l ++
  gene1270|gene1270|rna1270|rna1270 142 SKDVGKGNTIAIDFSSPNIAKKFHAGHLRTTILGNFLSNLYKYLNFQ 188
                                        456778899********************************999875 PP

>> APP_N  Amyloid A4 N-terminal heparin-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.2   1.6e-06     0.014      14      60 ..      86     132 ..      69     150 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.6e-06
                              APP_N  14 ymdletgkwesdpegkasclkdkeeilkyCrkvypklditnvveask 60 
                                         +dl+t+++ ++ ++++ c + k +  kyC ++y+++  ++v +a++
  gene1270|gene1270|rna1270|rna1270  86 EIDLQTDDFLTEVSKSKLCYNVKINKAKYCERIYNAIMSSDVYDAEN 132
                                        5799*******************************999888877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       955  (0.0532657); expected 358.6 (0.02)
Passed bias filter:                      503  (0.0280551); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.72
# Mc/sec: 877.97
//
Query:       gene1271|gene1271|rna1271|rna1271  [L=403]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.6e-42  143.7   4.9    8.8e-42  143.3   4.9    1.2  1  tRNA-synt_1d  tRNA synthetases class I (R)
    1.7e-22   79.9   0.3      4e-22   78.6   0.3    1.7  1  DALR_1        DALR anticodon binding domain


Domain annotation for each model (and alignments):
>> tRNA-synt_1d  tRNA synthetases class I (R)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  143.3   4.9   9.8e-46   8.8e-42     110     348 ..      41     275 ..       4     276 .. 0.86

  Alignments for each domain:
  == domain 1  score: 143.3 bits;  conditional E-value: 9.8e-46
                                        CSHC.....CCHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHCT---EC.--CCCCCCCHHHHHHHHHC CS
                       tRNA-synt_1d 110 eeei.....faerarnyvvkLqsgdedirklwkllvditrtelqklydrldvtlie.rGeslykeslneivkelkk 179
                                         +e      + ++a++y+  L+ gde+  k w++   ++ ++++ ly  l++      Gesly +   e++ + + 
  gene1271|gene1271|rna1271|rna1271  41 GDEKrkiskIDQEAKDYFTALERGDEEKMKQWRRFRSLSIEKYKTLYSTLNIKFDVyGGESLYAKAGLEVITDAE- 115
                                        333346677999***************9999999999999999999999998764347*****999999998865. PP

                                        TT-EEECTTCEEEEECCCTSSCCE.ECC-TTS-B-HHHHHHHHHHHHHHTT--SEEEEEEECCCHHHHHHHHHHHH CS
                       tRNA-synt_1d 180 kglvkesdGalvvfldefgkrlgv.vvqksDGgylytttDiaaakerkeelkadkvlyvidsrqslhlqqiflilk 254
                                            ++ dG +  +l e g      vv k+DG++ly t+D+aaa +r ++ +  k++yv+ s+q+l+++q+f +lk
  gene1271|gene1271|rna1271|rna1271 116 ----VDVDGSMFYDLGELG----KfVVLKNDGSTLYSTRDLAAAEDRIKTYNPVKLVYVVASQQDLYFKQLFSVLK 183
                                        ....678****99999655....4499***********************************************99 PP

                                        C.TT...SSTTTSEEEEEEE--EE-TTSSBSBCSSSTC-BHHHHHHHHHHHHHHHHCCCCCCTS-CCCCHCHHHHH CS
                       tRNA-synt_1d 255 k.ig...yvpeskdlehanfGmvlgkdkkkfktrkGetvkLadlLdealeralqlikeknkdkvlqadelekvaea 326
                                           g    +p+ ++leh++fGmv     ++++trkG+ v+L+d++d a   a++  + kn+ k  + ++ e   ++
  gene1271|gene1271|rna1271|rna1271 184 GeCGnkkRIPDNVELEHIGFGMV-----NGLSTRKGNLVFLEDIIDAAK-EAMHSTMIKNQAKYEEIENVEDTCTT 253
                                        523333367**************.....99***************9775.5788899******************* PP

                                        HHHHHHHCCCCTS-TTS-EE-- CS
                       tRNA-synt_1d 327 vgvgaikyaDlsknrindyifd 348
                                        ++v+a++++D+s +r  +y fd
  gene1271|gene1271|rna1271|rna1271 254 LAVSAMIIQDFSAKRKINYTFD 275
                                        *********************8 PP

>> DALR_1  DALR anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.6   0.3   4.5e-26     4e-22       1     119 []     290     403 .]     290     403 .] 0.92

  Alignments for each domain:
  == domain 1  score: 78.6 bits;  conditional E-value: 4.5e-26
                                        HHHHHHHHHHHHHHTTCTTCCCCHCCHCCS-SHHHHHHHHHHHTHHHHHHHHHHHT-THHHHHHHHHHHHHHHHHH CS
                             DALR_1   1 vqyahaRiksilrkaeeegekleeealalleeeeekeLlkalaqfpevleeaaeelephklaeylyeLaatfhkfY 76 
                                        +qy+h+R+ si +k+    +k    +++l  +ee + L+ +l +f  ++ ++  + ep kl++yl +L++++++ +
  gene1271|gene1271|rna1271|rna1271 290 LQYTHCRLMSIRKKNSSLCAKM---DASL-LSEEALSLIFYLSKFGTAVIDSYTTAEPCKLVTYLMKLSKQVNALF 361
                                        6***********9888766433...3333.699******************************************* PP

                                        HHCTSTTSCTHHH.HHHHHHHHHHHHHHHHHHHHTT----S-- CS
                             DALR_1  77 nkervlkeeeeelaaaRLaLvkavrqvLangLdlLGieapekm 119
                                           rv +eee+   +aRLa ++a+r+vL+ng++++G++++e+m
  gene1271|gene1271|rna1271|rna1271 362 STLRVFGEEEKLA-QARLAVFEAARKVLNNGMKIFGMKPLERM 403
                                        *********9976.****************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (403 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1016  (0.056668); expected 358.6 (0.02)
Passed bias filter:                      539  (0.030063); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 2618.12
//
Query:       gene1272|gene1272|rna1272|rna1272  [L=234]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.3e-24   84.3   0.1    1.2e-23   83.8   0.1    1.2  1  Glycos_transf_2  Glycosyl transferase family 2
    5.1e-06   26.5   0.0    5.9e-06   26.3   0.0    1.1  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
  ------ inclusion threshold ------
      0.016   15.7   0.0      0.036   14.6   0.0    1.5  1  Glyco_tranf_2_4  Glycosyl transferase family 2
       0.21   11.9   0.4        2.2    8.6   0.1    2.5  3  DUF1257          Protein of unknown function (DUF1257)


Domain annotation for each model (and alignments):
>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.8   0.1   2.7e-27   1.2e-23       1     168 [.       3     169 ..       3     171 .. 0.92

  Alignments for each domain:
  == domain 1  score: 83.8 bits;  conditional E-value: 2.7e-27
                                        EEEEEESS-TTTHHHHHHHHHHH..GGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHH CS
                    Glycos_transf_2   1 svviptyNeektlletlesllaq..dpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnag 74 
                                        +v++ptyNe  +++ + + l++   +  + + ii++DD+S+D+t e++ +l++ + ++  irr+++ G+++a+ ++
  gene1272|gene1272|rna1272|rna1272   3 TVIVPTYNECGNVEILCNFLKETftKINLPYNIIFIDDASSDGTYELICQLRN-EFPILAIRRTQKLGLGSAYKHA 77 
                                        69*******666666666666666679************************97.88999999999*********** PP

                                        HHH--SS.EEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SSEEEECCHCCCCHCCCCC CS
                    Glycos_transf_2  75 lraatgd.yilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiernkrvgenerlyfkerkrslkg 149
                                        l++++   +++++DaD+  +p +++ l++  +k ++d+v+g+r+ ++   ++   +k     +r+ +   +  l+ 
  gene1272|gene1272|rna1272|rna1272  78 LKYCDNSeFVIIMDADLSQNPFDIQNLIRVQQKYNYDLVYGTRYNNGNVVNWPFLRK---VISRGANNLAQILLGV 150
                                        ****9888**************************************99999999998...58************** PP

                                        CSTTCSTCCCEEEEHHHHH CS
                    Glycos_transf_2 150 nlsfeigsaallrrealee 168
                                        ++++++ s++l++ ++l+ 
  gene1272|gene1272|rna1272|rna1272 151 DITDYTNSFRLYKTSLLKT 169
                                        ************9999875 PP

>> Glyco_tranf_2_3  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.0   1.3e-09   5.9e-06       4     139 ..       2     135 ..       1     216 [. 0.70

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 1.3e-09
                    Glyco_tranf_2_3   4 lavlVptfneed...vlgevlesllaqeyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgks 76 
                                        ++v+Vpt+ne      l + l ++ +  + ++ +++++d s+++t e + +l  ++p      ++++++lg +++ 
  gene1272|gene1272|rna1272|rna1272   2 YTVIVPTYNECGnveILCNFLKETFTKINLPYNIIFIDDASSDGTYELICQLRNEFPIL---AIRRTQKLGLGSA- 73 
                                        68********774444444555555444577*************************875...4667787998776. PP

                    Glyco_tranf_2_3  77 ralnealravk.sdlvllvDdDtvvePdtlkrllqffltpkvgavgtpvfllnrstlvsalgal 139
                                          +++al+ ++ s++v+++D+D    P  ++ l ++ +  +++ v++ ++++     +++l ++
  gene1272|gene1272|rna1272|rna1272  74 --YKHALKYCDnSEFVIIMDADLSQNPFDIQNLIRVQQKYNYDLVYGTRYNNGNVVNWPFLRKV 135
                                        ..57******999******************999998777999999988877666666666553 PP

>> Glyco_tranf_2_4  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   7.9e-06     0.036      21      81 ..      34      93 ..      15      94 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 7.9e-06
                    Glyco_tranf_2_4 21 rilvydndstDgtrailkelpe.vkllhvdksyederrq.vellkallaryaeadwvlvvDaD 81
                                       +i+++d+ s+Dgt++++ +l +   +l ++   +    +  +++k++l+   ++++v+ +DaD
  gene1272|gene1272|rna1272|rna1272 34 NIIFIDDASSDGTYELICQLRNeFPILAIRRTQK---LGlGSAYKHALKYCDNSEFVIIMDAD 93
                                       599****************977355888888654...55346777777666678*******99 PP

>> DUF1257  Protein of unknown function (DUF1257)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0     0.098   4.4e+02      37      88 ..      34      86 ..      27      88 .. 0.65
   2 ?    8.6   0.1    0.0005       2.2      45      87 ..      83     124 ..      60     128 .. 0.82
   3 ?   -1.1   0.0      0.51   2.3e+03      78      92 ..     184     198 ..     174     201 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.098
                            DUF1257 37 digFrwng..egeYelvaDlqfwkqslsveeflnkltqrYAyktvlaeaekeGf 88
                                       +i F  ++  +g+Yel+  l+    ++   +  +kl    Ayk +l+ + +++f
  gene1272|gene1272|rna1272|rna1272 34 NIIFIDDAssDGTYELICQLRNE-FPILAIRRTQKLGLGSAYKHALKYCDNSEF 86
                                       5556554444999***9985543.366666666676666666666666666666 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0005
                            DUF1257  45 egeYelvaDlqfwkqslsveeflnkltqrYAyktvlaeaekeG 87 
                                        + e+ +++D++  +++ + ++++ +++q+Y y+ v  +  ++G
  gene1272|gene1272|rna1272|rna1272  83 NSEFVIIMDADLSQNPFDIQNLI-RVQQKYNYDLVYGTRYNNG 124
                                        34799*********999999987.6********9988766665 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 0.51
                            DUF1257  78 tvlaeaekeGftvee 92 
                                         v+  a+++Gf++ e
  gene1272|gene1272|rna1272|rna1272 184 EVIYRAARQGFKIGE 198
                                        488899999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       374  (0.0208601); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1815.66
//
Query:       gene1273|gene1273|rna1273|rna1273  [L=174]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.6e-48  161.8   0.0    7.1e-48  161.5   0.0    1.1  1  Ribo_biogen_C  Ribosome biogenesis protein, C-terminal
  ------ inclusion threshold ------
      0.036   13.9   1.7      0.039   13.8   0.3    1.8  2  RLI            Possible Fer4-like domain in RNase L inhibitor


Domain annotation for each model (and alignments):
>> Ribo_biogen_C  Ribosome biogenesis protein, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  161.5   0.0   7.9e-52   7.1e-48       1     127 []      40     166 ..      40     166 .. 0.99

  Alignments for each domain:
  == domain 1  score: 161.5 bits;  conditional E-value: 7.9e-52
                                        EEE-TT-SSB--GGGHHHHHHT-EEEE---TTT--GGGTTT-E....EB--S-B--STTTTT-BS---HHHHHHHH CS
                      Ribo_biogen_C   1 ivlspkakkvlspaDreiveksgiavvdcsWarleevkfkklkakeerlLPyLvAaNpvnYgkplkLscvEAlaaa 76 
                                        i+lspk+++++sp D+ ++ek+gi  +dcsW+++++++fk ++  ++rlLP+LvAaNpvnYgk+++L+cvEAlaa+
  gene1273|gene1273|rna1273|rna1273  40 ILLSPKGTQTISPIDKLLIEKQGIGLIDCSWKKVDSTDFKLFNRCKNRLLPFLVAANPVNYGKACQLNCVEALAAG 115
                                        79****************************************999******************************* PP

                                        HHHTT-HHHHHHHHTSSTTHHHHHHHCHHHHHHH.TT--HHHHHHHHHHHH CS
                      Ribo_biogen_C  77 lyilglkeeaeellskfkwgeeFlelnkelleeYakckdseevvevqkeyl 127
                                        lyi+g+ +ea +++++f++g+eFl++n ell+ Y++ +ds++v+e q++yl
  gene1273|gene1273|rna1273|rna1273 116 LYICGFVDEAYNIIEEFSYGNEFLKINYELLSLYKDSRDSADVIEKQNKYL 166
                                        ************************************************996 PP

>> RLI  Possible Fer4-like domain in RNase L inhibitor, RLI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.3   4.4e-06     0.039       2      30 ..       3      29 ..       2      34 .. 0.90
   2 ?   -2.4   0.1      0.49   4.4e+03       8      13 ..      81      86 ..      81      87 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.4e-06
                                       -EEEES---------TTHHHHHTTSEEEE CS
                                RLI  2 rlAivdadqCdPKKCtgkkcarfcpvrlv 30
                                       r  i+d +qC+ K C+g k++r + v  v
  gene1273|gene1273|rna1273|rna1273  3 RKIIYDIGQCNRKICSGQKLIRANKV--V 29
                                       6679*******************999..5 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.49
                                       ------ CS
                                RLI  8 adqCdP 13
                                       +++C+ 
  gene1273|gene1273|rna1273|rna1273 81 FNRCKN 86
                                       689985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       423  (0.0235931); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.35u 0.26s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 1371.27
//
Query:       gene1274|gene1274|rna1274|rna1274  [L=121]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.022   14.4   0.1      0.035   13.8   0.0    1.3  1  Neurensin  Neurensin
      0.051   12.4   0.0      0.052   12.4   0.0    1.1  1  Anoctamin  Calcium-activated chloride channel
      0.072   13.1   0.6       0.15   12.1   0.6    1.6  1  SNARE      SNARE domain
      0.074   13.4   0.1       0.11   12.8   0.1    1.5  1  Orf78      Orf78 (ac78)


Domain annotation for each model (and alignments):
>> Neurensin  Neurensin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   7.7e-06     0.035      26      63 ..      67     111 ..      44     118 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 7.7e-06
                          Neurensin  26 k.......lllqrakqksesllwkvslvvgtlvlllGvtallvGy 63 
                                        +         + +++++ +  +++vs+ + +l++++G++     y
  gene1274|gene1274|rna1274|rna1274  67 CnqithrrESVMSPRSNPKCNCCHVSILLVFLIVIVGLVLRFFAY 111
                                        255555533444455558999*****************9766655 PP

>> Anoctamin  Calcium-activated chloride channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   1.2e-05     0.052      84     146 ..      51     110 ..       9     119 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.2e-05
                          Anoctamin  84 eeeeeprpefrgelkrespvtgeeefyyppwkrrlfrllvslplvllliclavvgvlilrcla 146
                                         + e  r +  ++  r++++t++ e +++p + + ++ ++ ++++  l++l+v++ l+lr++a
  gene1274|gene1274|rna1274|rna1274  51 TQTEDTRENIDTREDRCNQITHRRESVMSPRS-NPKCNCCHVSIL--LVFLIVIVGLVLRFFA 110
                                        3555778888888888999*********7766.566666666555..5566777777777665 PP

>> SNARE  SNARE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.6   3.4e-05      0.15      32      53 .]      81     102 ..      77     102 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.4e-05
                                        CTXXXXXXXXXXXXXXXXXXXX CS
                              SNARE  32 ksnRklkciillilviillvvl 53 
                                        +sn k+ c+ + il+++l+v++
  gene1274|gene1274|rna1274|rna1274  81 RSNPKCNCCHVSILLVFLIVIV 102
                                        89******************97 PP

>> Orf78  Orf78 (ac78)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   2.4e-05      0.11      32      91 ..      53     114 ..       6     120 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.4e-05
                              Orf78  32 dkaenkkekksaaeknditekesn..........aaekaqalnillisllavvcvlvllyviyYfvilre 91 
                                        +++++++ +++            n          + +++ + n+  +s+l v+ ++++  v+ +f  +r+
  gene1274|gene1274|rna1274|rna1274  53 TEDTRENIDTREDRC--------NqithrresvmSPRSNPKCNCCHVSILLVFLIVIVGLVLRFFAYSRR 114
                                        111111112222222........133334445655566778899999*******9999999999988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1442  (0.0804284); expected 358.6 (0.02)
Passed bias filter:                      690  (0.0384851); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.34s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 761.83
//
Query:       gene1275|gene1275|rna1275|rna1275  [L=327]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.8e-12   46.3   6.8    1.3e-11   44.6   6.8    2.0  1  zf-RING_2     Ring finger domain
    1.1e-09   38.4   9.9    4.6e-09   36.4   9.9    2.1  1  zf-rbx1       RING-H2 zinc finger domain
    5.6e-08   32.5   7.7    5.6e-08   32.5   7.7    2.1  1  zf-C3HC4      Zinc finger, C3HC4 type (RING finger)
    8.5e-08   31.9   7.1    2.5e-07   30.4   7.1    1.9  1  zf-C3HC4_2    Zinc finger, C3HC4 type (RING finger)
    1.3e-07   31.5   6.2    3.1e-07   30.2   6.2    1.7  1  zf-RING_5     zinc-RING finger domain
    1.3e-07   31.6   1.9    2.4e-07   30.7   1.9    1.5  1  zf-ANAPC11    Anaphase-promoting complex subunit 11 RING-H2 f
    9.4e-06   25.3   3.8    9.4e-06   25.3   3.8    2.9  3  zf-RING_11    RING-like zinc finger
      1e-05   25.3   5.5    2.1e-05   24.3   5.5    1.6  1  zf-C3HC4_3    Zinc finger, C3HC4 type (RING finger)
    3.5e-05   23.7   2.7    0.00012   22.0   0.2    2.8  2  zf-RING_UBOX  RING-type zinc-finger
    0.00017   21.4   4.8    0.00042   20.1   4.8    1.7  1  Prok-RING_4   Prokaryotic RING finger family 4
     0.0047   16.7   5.9     0.0047   16.7   5.9    1.9  1  zf-RING_4     RING/Ubox like zinc-binding domain
  ------ inclusion threshold ------
      0.014   15.0   6.0      0.032   13.9   6.0    1.6  1  Zn_ribbon_17  Zinc-ribbon, C4HC2 type
       0.14   12.3   9.5       0.35   11.0   9.5    1.7  1  RINGv         RING-variant domain
       0.19   11.7   3.3       0.36   10.8   1.9    2.2  2  Baculo_RING   Baculovirus U-box/Ring-like domain
       0.24   11.3   6.1       0.55   10.2   6.1    1.7  1  PHD           PHD-finger
       0.27   11.4   6.4       0.25   11.5   3.4    2.6  3  zf-C3HC4_4    zinc finger of C3HC4-type, RING
       0.49   10.6   9.1        5.3    7.3   7.4    3.0  2  FANCL_C       FANCL C-terminal domain
        1.1    9.3   7.1       0.22   11.6   2.5    2.3  1  zf-C3H2C3     Zinc-finger
        3.9    7.1   6.1        7.1    6.3   0.3    2.4  2  RecR          RecR protein


Domain annotation for each model (and alignments):
>> zf-RING_2  Ring finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.6   6.8   1.4e-14   1.3e-11       2      44 .]     260     301 ..     259     301 .. 0.92

  Alignments for each domain:
  == domain 1  score: 44.6 bits;  conditional E-value: 1.4e-14
                          zf-RING_2   2 eCpICleelssadsvlllpCgHvfhreClerwlrssstCPlCr 44 
                                        +C+IC+e++++++  +++ C+H+fh  Cl+rw+++++ CP+Cr
  gene1275|gene1275|rna1275|rna1275 260 TCAICTEDMEEEKGRIIK-CKHSFHLVCLKRWVEQQQVCPICR 301
                                        7********987777777.***********************9 PP

>> zf-rbx1  RING-H2 zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.4   9.9   4.9e-12   4.6e-09       6      55 .]     253     301 ..     251     301 .. 0.84

  Alignments for each domain:
  == domain 1  score: 36.4 bits;  conditional E-value: 4.9e-12
                            zf-rbx1   6 CrneleeacieckapgdeecpvvlGeCgHaFHlhCiskWlktrkvCPlcr 55 
                                        C +  +++c  c+++ +ee +  + +C+H+FHl C+++W+++++vCP+cr
  gene1275|gene1275|rna1275|rna1275 253 CPTVSTGTCAICTEDMEEE-KGRIIKCKHSFHLVCLKRWVEQQQVCPICR 301
                                        5556678999999999985.444448***********************8 PP

>> zf-C3HC4  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.5   7.7   5.9e-11   5.6e-08       1      41 []     261     300 ..     261     300 .. 0.96

  Alignments for each domain:
  == domain 1  score: 32.5 bits;  conditional E-value: 5.9e-11
                                        -TTT-S--SS-E..E-TTS--B-CHHHHHHHHCTSSB--TTT CS
                           zf-C3HC4   1 CpiCleeakepn.elleCkHsfCskCirkilksrkkvkCPlC 41 
                                        C+iC+e ++e++ ++++CkHsf+  C++++++  +++ CP+C
  gene1275|gene1275|rna1275|rna1275 261 CAICTEDMEEEKgRIIKCKHSFHLVCLKRWVE--QQQVCPIC 300
                                        **********999*******************..6677**** PP

>> zf-C3HC4_2  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.4   7.1   2.6e-10   2.5e-07       2      40 .]     261     300 ..     260     300 .. 0.88

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 2.6e-10
                         zf-C3HC4_2   2 CpiCldmlkd.psvvtpCgHvfCqkCilrsLeekneCPlC 40 
                                        C+iC + +++   ++++C+H+f+  C++r+ e+++ CP+C
  gene1275|gene1275|rna1275|rna1275 261 CAICTEDMEEeKGRIIKCKHSFHLVCLKRWVEQQQVCPIC 300
                                        ****977654155999************************ PP

>> zf-RING_5  zinc-RING finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.2   6.2   3.3e-10   3.1e-07       2      43 ..     261     301 ..     260     302 .. 0.97

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 3.3e-10
                          zf-RING_5   2 CnkCfeklskeekfyltsCgHifCekClkkllekeavCpiCr 43 
                                        C +C e + +eek  + +C+H+f+  Clk+  e+++vCpiCr
  gene1275|gene1275|rna1275|rna1275 261 CAICTEDM-EEEKGRIIKCKHSFHLVCLKRWVEQQQVCPICR 301
                                        ********.********************************8 PP

>> zf-ANAPC11  Anaphase-promoting complex subunit 11 RING-H2 finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.7   1.9   2.6e-10   2.4e-07      27      83 ..     253     306 ..     232     308 .. 0.86

  Alignments for each domain:
  == domain 1  score: 30.7 bits;  conditional E-value: 2.6e-10
                                        T-SBTTS--TTCSTTTTTS-EEEBTTS-EEEHHHHHHHHHHHSTSSB-TTTSSB--B CS
                         zf-ANAPC11  27 crvsfdGtcpsckfpGddcplvlGkckhnfhlhcilkwletetskglcpmcrqtfkl 83 
                                        c     Gtc  c+   ++    + kckh+fhl c+ +w+e++   + cp+cr+ ++ 
  gene1275|gene1275|rna1275|rna1275 253 CPTVSTGTCAICTEDMEEEKGRIIKCKHSFHLVCLKRWVEQQ---QVCPICRDVIMS 306
                                        777778*******99999999999***************986...67*****98765 PP

>> zf-RING_11  RING-like zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.3       2.6   2.4e+03      22      26 ..      43      47 ..      42      48 .. 0.87
   2 !   25.3   3.8     1e-08   9.4e-06       2      29 .]     261     287 ..     260     287 .. 0.90
   3 ?   -0.2   0.1      0.94   8.8e+02       2      11 ..     297     306 ..     297     311 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 2.6
                         zf-RING_11 22 HtFHf 26
                                       H+FH 
  gene1275|gene1275|rna1275|rna1275 43 HLFHA 47
                                       ****6 PP

  == domain 2  score: 25.3 bits;  conditional E-value: 1e-08
                         zf-RING_11   2 CsICLeefkpgqalfilpCsHtFHfkCI 29 
                                        C+IC e++++++ ++i +C+H FH+ C+
  gene1275|gene1275|rna1275|rna1275 261 CAICTEDMEEEKGRII-KCKHSFHLVCL 287
                                        ********99888766.*********95 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.94
                         zf-RING_11   2 CsICLeefkp 11 
                                        C IC + +  
  gene1275|gene1275|rna1275|rna1275 297 CPICRDVIMS 306
                                        9***988765 PP

>> zf-C3HC4_3  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   5.5   2.2e-08   2.1e-05       3      47 ..     259     304 ..     257     307 .. 0.90

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 2.2e-08
                                        SB-TTTSS..SBS-EEETTEEEEEE-HHHHHHHHHTT-B-TTT--B- CS
                         zf-C3HC4_3   3 eeCviCle..rprnvvllpCgHlvlCeeCaekllkrkkkCpiCrrpi 47 
                                         +C iC e  ++++  +++C+H  +   C++++ ++++ CpiCr  i
  gene1275|gene1275|rna1275|rna1275 259 GTCAICTEdmEEEKGRIIKCKHS-FHLVCLKRWVEQQQVCPICRDVI 304
                                        68******5559999********.99******************988 PP

>> zf-RING_UBOX  RING-type zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.2   1.3e-07   0.00012       1      39 []     261     298 ..     261     298 .. 0.84
   2 ?    3.1   0.2      0.11     1e+02       1       7 [.     297     303 ..     297     307 .. 0.88

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 1.3e-07
                       zf-RING_UBOX   1 CpIClelftdP...lvlpCGHtFCreClwelskslegafkCP 39 
                                        C IC e++++    ++ +C H+F+  Cl   +++ e++  CP
  gene1275|gene1275|rna1275|rna1275 261 CAICTEDMEEEkgrII-KCKHSFHLVCL---KRWVEQQQVCP 298
                                        *********7766434.7**********...88888888888 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.11
                       zf-RING_UBOX   1 CpIClel 7  
                                        CpIC+++
  gene1275|gene1275|rna1275|rna1275 297 CPICRDV 303
                                        ****996 PP

>> Prok-RING_4  Prokaryotic RING finger family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   4.8   4.5e-07   0.00042       1      40 [.     261     304 ..     261     309 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 4.5e-07
                        Prok-RING_4   1 CvlCgeq..ekkailepCgHlvCkeCfdsk..dlssCPlCqrri 40 
                                        C +C+e   e+k +++ C+H +   C++ +  + + CP+C+  i
  gene1275|gene1275|rna1275|rna1275 261 CAICTEDmeEEKGRIIKCKHSFHLVCLKRWveQQQVCPICRDVI 304
                                        99***987789999*****99888888888656669****9876 PP

>> zf-RING_4  RING/Ubox like zinc-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   5.9     5e-06    0.0047       1      45 [.     261     302 ..     261     303 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 5e-06
                          zf-RING_4   1 cplCdeeldetdkdlkpCeCgyqiClfCyhrileeeegrCPaCre 45 
                                        c +C+e+++e+  ++   +C++ + l C++r +e ++++CP Cr 
  gene1275|gene1275|rna1275|rna1275 261 CAICTEDMEEEKGRII--KCKHSFHLVCLKRWVE-QQQVCPICRD 302
                                        99******77766666..56788889*******7.6*******96 PP

>> Zn_ribbon_17  Zinc-ribbon, C4HC2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   6.0   3.4e-05     0.032       4      46 ..     258     298 ..     255     301 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.4e-05
                       Zn_ribbon_17   4 lksCayCelavkgrvvlcgvCeHvlHasCarewfenddlaeCp 46 
                                        + +Ca+C   ++       +C+H  H  C++ w e+++  +Cp
  gene1275|gene1275|rna1275|rna1275 258 TGTCAICTEDMEEEKGRIIKCKHSFHLVCLKRWVEQQQ--VCP 298
                                        679********************************999..888 PP

>> RINGv  RING-variant domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   9.5   0.00037      0.35       1      48 []     261     300 ..     261     300 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00037
                                        ETTTTEE-SSSS--B-SS--STCCCSB-HHHHHHHHHHTCT-SB-TTT CS
                              RINGv   1 CriCleeeeeseplispCkCrGslklvHesClekWldekeantqCeiC 48 
                                        C iC e++ee++  i +  C+   +++H  Cl++W+++   ++ C iC
  gene1275|gene1275|rna1275|rna1275 261 CAICTEDMEEEKGRIIK--CK---HSFHLVCLKRWVEQ---QQVCPIC 300
                                        99******999955555..55...58999*******99...899***9 PP

>> Baculo_RING  Baculovirus U-box/Ring-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       2.2   2.1e+03      41      59 ..     169     185 ..     157     215 .. 0.60
   2 ?   10.8   1.9   0.00038      0.36       3      74 ..     231     299 ..     227     308 .. 0.73

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 2.2
                        Baculo_RING  41 GvvaitdtGlldlekvlhk 59 
                                        G+v++t+  +  l  ++ +
  gene1275|gene1275|rna1275|rna1275 169 GIVTLTC--IKSLISMFLE 185
                                        3444333..3334444444 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00038
                        Baculo_RING   3 ttftlkdrkaaaeklikeyfhtc....atecaiclediddnrGvvaitdtGlldlekvlhkecikrfrreekrdpy 74 
                                         t  +k  ++ a++ i +y +tc    +  caic ed+++++G +       ++ ++ +h  c kr+  +++  p 
  gene1275|gene1275|rna1275|rna1275 231 KTLFKKINNFRAFLKISKYLETCptvsTGTCAICTEDMEEEKGRI-------IKCKHSFHLVCLKRWVEQQQVCPI 299
                                        566678889999999999999994443448**********98854.......334566777888888655555555 PP

>> PHD  PHD-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   6.1   0.00058      0.55       2      50 ..     261     301 ..     260     307 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00058
                                        BTTTTS.TTSTTSCEEEETTTSCEEETTTSSSTHSHHSHHSSTBSSTTTH CS
                                PHD   2 CavCkk.ksdeeeelvqCdgCkrwfHqkClkppleseekpegewlCekCk 50 
                                        Ca+C +  ++e+++++   +Ck++fH  Clk  +e+++      +C+ C+
  gene1275|gene1275|rna1275|rna1275 261 CAICTEdMEEEKGRII---KCKHSFHLVCLKRWVEQQQ------VCPICR 301
                                        ******7777889998...5789*******99988444......466665 PP

>> zf-C3HC4_4  zinc finger of C3HC4-type, RING
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.1       9.8   9.2e+03      22      28 ..     173     179 ..     171     182 .. 0.75
   2 ?   11.5   3.4   0.00027      0.25       1      42 []     261     300 ..     261     300 .. 0.80
   3 ?    1.4   0.5      0.39   3.7e+02       1       6 [.     297     302 ..     297     304 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 9.8
                         zf-C3HC4_4  22 lsCissl 28 
                                        l+Ci+sl
  gene1275|gene1275|rna1275|rna1275 173 LTCIKSL 179
                                        6799886 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00027
                         zf-C3HC4_4   1 CPiCldYLe..kPvsleCGhsfClsCisslqkepdgeqllCplC 42 
                                        C iC++ +e  k   ++C hsf l C++++ +++      Cp C
  gene1275|gene1275|rna1275|rna1275 261 CAICTEDMEeeKGRIIKCKHSFHLVCLKRWVEQQ----QVCPIC 300
                                        778888876224678**************99988....359999 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.39
                         zf-C3HC4_4   1 CPiCld 6  
                                        CPiC+d
  gene1275|gene1275|rna1275|rna1275 297 CPICRD 302
                                        ****98 PP

>> FANCL_C  FANCL C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.2      0.22   2.1e+02      48      65 ..     251     268 ..     234     273 .. 0.77
   2 ?    7.3   7.4    0.0056       5.3      26      45 ..     276     295 ..     257     308 .. 0.74

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.22
                                        S-TTT--EEE-TTT-SEE CS
                            FANCL_C  48 rqsfdvlfGeCPyCkkki 65 
                                        ++  +v+ G+C  C++ +
  gene1275|gene1275|rna1275|rna1275 251 ETCPTVSTGTCAICTEDM 268
                                        556689999**9999876 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0056
                                        TT----B-SGGGHHHHHHHH CS
                            FANCL_C  26 ekCnkkfHsaCLkeWlrslk 45 
                                        +kC+++fH +CLk W+++++
  gene1275|gene1275|rna1275|rna1275 276 IKCKHSFHLVCLKRWVEQQQ 295
                                        69*************98875 PP

>> zf-C3H2C3  Zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   2.5   0.00023      0.22      16      34 ..     277     300 ..     275     301 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00023
                          zf-C3H2C3  16 sCkHlvHakC.a....deevCPkC 34 
                                        +CkH++H  C      +++vCP C
  gene1275|gene1275|rna1275|rna1275 277 KCKHSFHLVClKrwveQQQVCPIC 300
                                        8*********5245557899**** PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   1.2     0.094        89      21      36 ..     252     266 ..     251     268 .. 0.77
   2 ?    6.3   0.3    0.0075       7.1      27      36 ..     293     302 ..     285     303 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.094
                                        TT--EESSSS-CCCCS CS
                               RecR  21 rCgnlteedlCaICsd 36 
                                         C ++++   CaIC+ 
  gene1275|gene1275|rna1275|rna1275 252 TCPTVSTG-TCAICTE 266
                                        67788887.6****85 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0075
                                        SSSS-CCCCS CS
                               RecR  27 eedlCaICsd 36 
                                         + +C+IC+d
  gene1275|gene1275|rna1275|rna1275 293 QQQVCPICRD 302
                                        5789****99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (327 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1042  (0.0581181); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 2105.87
//
Query:       gene1276|gene1276|rna1276|rna1276  [L=272]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.5e-32  112.0   0.1    1.3e-31  110.1   0.1    1.8  1  MutS_V    MutS domain V
    0.00094   19.2   0.0     0.0019   18.3   0.0    1.5  1  AAA_14    AAA domain
  ------ inclusion threshold ------
      0.019   15.2   0.0      0.062   13.5   0.0    1.9  2  AAA_28    AAA domain


Domain annotation for each model (and alignments):
>> MutS_V  MutS domain V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.1   0.1   2.1e-35   1.3e-31       2     139 ..      61     188 ..      60     226 .. 0.84

  Alignments for each domain:
  == domain 1  score: 110.1 bits;  conditional E-value: 2.1e-35
                                        EEE-STTSSHHHHHHHHHHHHHHHHHT--BSSSEEEEE--SEEEEEE--------SS-HHHHHHHHHHHHHTT--T CS
                             MutS_V   2 litGpnmaGkstylrqvalivllaqiGsfvpaekaeisivdkiftRvgasDdlakgkstFmvEmlEtasilknate 77 
                                        +itGpnm+Gk tyl+ +a+i++l+qiGs + ae+aei+i d++ft+++ +D+       F  E l  +silk++t+
  gene1276|gene1276|rna1276|rna1276  61 VITGPNMGGKTTYLKTIAVISILSQIGSPICAESAEIRIYDQMFTKLAQNDN-------FEKEWLLATSILKKSTD 129
                                        8**********************************************88775.......77899999********* PP

                                        TSEEEEESTS-SS-HHHHHHHHHHHHHHHHHTT--EEEEEES-GGGGGHHHHSTTEEEEEEE CS
                             MutS_V  78 kslvilDElGRGtstydGlaialavaeyllekikaktlfatHyheltklaekleevknlhla 139
                                        ++l++lDE+GR t    Gl+ + a +  l++    + +f+tH+ ++ k  +  ++v+ + ++
  gene1276|gene1276|rna1276|rna1276 130 HTLILLDEMGRSTEYSSGLSFSVAFVLALCR---GTLFFSTHFLDMMKYLKDAKNVNFVGVN 188
                                        **********************999988876...899***********99999998877654 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   3.1e-07    0.0019       6      90 ..      61     180 ..      58     217 .. 0.66

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 3.1e-07
                             AAA_14   6 vitGaRrvGKTtllkqlikell.........vkkesilyinldderdkkladpe......kllelileklkeekkt 66 
                                        vitG+   GKTt+lk+++  ++         +   +  +i + d+ ++kla+++       l + il+k    ++t
  gene1276|gene1276|rna1276|rna1276  61 VITGPNMGGKTTYLKTIAVISIlsqigspicA---ESAEIRIYDQMFTKLAQNDnfekewLLATSILKKS--TDHT 131
                                        8****************877778787877442...33444444444444443331113333445566652..479* PP

                             AAA_14  67 ylflDEiqev.........................pewekalkslvdeg 90 
                                        +++lDE+ ++                         +++ +++k+l d +
  gene1276|gene1276|rna1276|rna1276 132 LILLDEMGRSteyssglsfsvafvlalcrgtlffsTHFLDMMKYLKDAK 180
                                        ********99666666666666666666666666666666666666655 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0     1e-05     0.062       1      48 [.      59     112 ..      59     138 .. 0.79
   2 ?   -2.2   0.0      0.72   4.3e+03      73      91 ..     160     178 ..     154     194 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1e-05
                             AAA_28   1 kivitGgestGKTtlleaLa.....ar.gypvvpEaareileeklakgedalpw 48 
                                        k vitG+  +GKTt l+ +a     ++ g p+ +E+a   + ++++++  + + 
  gene1276|gene1276|rna1276|rna1276  59 KHVITGPNMGGKTTYLKTIAvisilSQiGSPICAESAEIRIYDQMFTKLAQNDN 112
                                        579*************999988777335**********9999999887654443 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.72
                             AAA_28  73 nkvlfcDrglldtlaYara 91 
                                        +++lf+ + +ld + Y++ 
  gene1276|gene1276|rna1276|rna1276 160 RGTLFFSTHFLDMMKYLKD 178
                                        6789999999999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (272 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       526  (0.0293379); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1741.90
//
Query:       gene1277|gene1277|rna1277|rna1277  [L=120]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.024   14.7   0.2      0.041   14.0   0.2    1.3  1  LPD1      Large polyvalent protein-associated domain 1


Domain annotation for each model (and alignments):
>> LPD1  Large polyvalent protein-associated domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.2   2.3e-06     0.041       6      32 ..      50      76 ..      47      82 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.3e-06
                               LPD1  6 gkkYWstpeElfARaFEayvedkleek 32
                                       +k Y ++++E+  Ra E yv+ k++ k
  gene1277|gene1277|rna1277|rna1277 50 DKIYIAEEQEMLCRAIEKYVIVKIARK 76
                                       67899****************999665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       473  (0.0263818); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 870.32
//
Query:       gene1278|gene1278|rna1278|rna1278  [L=328]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.3e-29  101.0   4.3    1.6e-05   25.5   0.2    7.1  7  WD40           WD domain, G-beta repeat
    1.8e-11   44.2   0.2      0.013   15.8   0.0    4.9  5  ANAPC4_WD40    Anaphase-promoting complex subunit 4 WD40 doma
    2.6e-07   29.7   1.3      0.017   13.8   0.0    3.2  3  Nup160         Nucleoporin Nup120/160
      2e-06   27.3   5.1     0.0073   15.7   0.1    2.9  3  WD40_like      WD40-like domain
    3.3e-05   22.4   0.0      0.023   13.0   0.0    2.2  2  Frtz           WD repeat-containing and planar cell polarity 
  ------ inclusion threshold ------
      0.014   15.5   0.6         16    5.6   0.0    4.3  4  BBS2_Mid       Ciliary BBSome complex subunit 2, middle regio
      0.025   13.2   0.1       0.31    9.6   0.0    2.3  3  ELYS-bb        beta-propeller of ELYS nucleoporin
      0.055   12.2   2.3         10    4.8   0.0    3.0  3  Nucleoporin_N  Nup133 N terminal like


Domain annotation for each model (and alignments):
>> WD40  WD domain, G-beta repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.0   0.00017      0.39       9      38 .]      14      46 ..       9      46 .. 0.87
   2 !   21.7   0.0   1.2e-07   0.00027       2      38 .]      57      94 ..      56      94 .. 0.91
   3 !   20.0   0.1   4.1e-07   0.00091       5      38 .]     101     135 ..      97     135 .. 0.90
   4 !   25.5   0.2   7.2e-09   1.6e-05      13      38 .]     156     181 ..     140     181 .. 0.85
   5 !    6.5   0.0    0.0073        16      13      36 ..     213     236 ..     197     237 .. 0.87
   6 ?    3.2   0.0     0.083   1.9e+02       3      34 ..     244     275 ..     242     278 .. 0.81
   7 !    6.8   0.0    0.0061        14      14      38 .]     298     320 ..     288     320 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00017
                                       SSSS.EEEEE..EETTSSEEEEEETTSEEEEEE CS
                               WD40  9 GHss.vtsla..fspdgawlasGsdDgtvriWd 38
                                        H+  vtsl+  +  +++ l s+s+D++v+ W+
  gene1278|gene1278|rna1278|rna1278 14 VHKQlVTSLDvpYTGNSDILYSASRDKKVYQWK 46
                                       585669***9999999999*************6 PP

  == domain 2  score: 21.7 bits;  conditional E-value: 1.2e-07
                                       EEEEEEESSSS.EEEEEEETTSSEEEEEETTSEEEEEE CS
                               WD40  2 qclrtltGHss.vtslafspdgawlasGsdDgtvriWd 38
                                       ++++++tGH++ +t+++ ++ + ++++ s+D+t ri+d
  gene1278|gene1278|rna1278|rna1278 57 TLTKEYTGHNHfITDVKANKTNEMIITTSYDHTARIYD 94
                                       57899****777**************9999*******8 PP

  == domain 3  score: 20.0 bits;  conditional E-value: 4.1e-07
                                        EEEESS.SSEEEEEEETTSSEEEEEETTSEEEEEE CS
                               WD40   5 rtltGH.ssvtslafspdgawlasGsdDgtvriWd 38 
                                        ++l+GH ++ t++  + + + +++Gs Dg++ +W+
  gene1278|gene1278|rna1278|rna1278 101 TILKGHkKDLTGVTINTEDNKIITGSCDGSIALWN 135
                                        6799**999*****999999999**99*******8 PP

  == domain 4  score: 25.5 bits;  conditional E-value: 7.2e-09
                                        EEEEEEETTSSEEEEEETTSEEEEEE CS
                               WD40  13 vtslafspdgawlasGsdDgtvriWd 38 
                                        v++++f p+ ++ ++Gs Dg++riWd
  gene1278|gene1278|rna1278|rna1278 156 VNCVSFVPNTNLCVTGSSDGKLRIWD 181
                                        9***************99*******9 PP

  == domain 5  score: 6.5 bits;  conditional E-value: 0.0073
                                        EEEEEEETTSSEEEEEETTSEEEE CS
                               WD40  13 vtslafspdgawlasGsdDgtvri 36 
                                        +t+l+ s dg++ a G++D+ v+i
  gene1278|gene1278|rna1278|rna1278 213 ITALSISADGSFCAYGGRDCMVYI 236
                                        9***********877999**9987 PP

  == domain 6  score: 3.2 bits;  conditional E-value: 0.083
                                        EEEEEESSSSEEEEEEETTSSEEEEEETTSEE CS
                               WD40   3 clrtltGHssvtslafspdgawlasGsdDgtv 34 
                                        cl  +++ +++tslaf    + +a G+++g +
  gene1278|gene1278|rna1278|rna1278 244 CLLQFETETPITSLAFAITEPIIAVGTRNGII 275
                                        6666666678****999999999999988877 PP

  == domain 7  score: 6.8 bits;  conditional E-value: 0.0061
                                        EEEEEETTSSE....EEEEETTSEEEEEE CS
                               WD40  14 tslafspdgaw....lasGsdDgtvriWd 38 
                                        t+l      +w    l++G  Dgt+ ++d
  gene1278|gene1278|rna1278|rna1278 298 TAL------TWaktrLVTGYNDGTIVLYD 320
                                        566......66777799**99******98 PP

>> ANAPC4_WD40  Anaphase-promoting complex subunit 4 WD40 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1   0.0    0.0029       6.5       3      72 ..      26     100 ..      24     120 .. 0.85
   2 !   15.8   0.0   5.9e-06     0.013      40      78 ..     155     193 ..     106     203 .. 0.82
   3 !    9.1   0.0   0.00069       1.5      38      90 ..     210     260 ..     200     262 .. 0.92
   4 !    8.1   0.0    0.0014       3.2      36      90 ..     249     303 ..     243     305 .. 0.71
   5 !    6.6   0.0    0.0044       9.8       9      67 ..     265     321 ..     257     325 .. 0.68

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0029
                        ANAPC4_WD40   3 wcptmDLiAlatedgellvfRlng...qrvwtl..eedkedsevrsLaWkpdgklLavaysdgevrlldaesgkv 72 
                                        +  + D++  a+ d++++   ln    +rv tl  e +++++ +++++ ++ ++++     d + r++d++++k 
  gene1278|gene1278|rna1278|rna1278  26 YTGNSDILYSASRDKKVYQWKLNTsamERVGTLtkEYTGHNHFITDVKANKTNEMIITTSYDHTARIYDVNTQKY 100
                                        6667899999999999999999985557777777666788899****************************9986 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 5.9e-06
                        ANAPC4_WD40  40 evrsLaWkpdgklLavaysdgevrlldaesgkvvhslsv 78 
                                         v+++++ p+ +l + + sdg++r+ d+ sgk+v+++  
  gene1278|gene1278|rna1278|rna1278 155 WVNCVSFVPNTNLCVTGSSDGKLRIWDIDSGKIVRTFVN 193
                                        48999*****************************99865 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.00069
                        ANAPC4_WD40  38 dsevrsLaWkpdgklLavaysdgevrlldaesgkvvhslsvksekavtclgWg 90 
                                         + +++L+ + dg++ a +  d  v ++  +++ ++ ++++++   +t+l ++
  gene1278|gene1278|rna1278|rna1278 210 ANMITALSISADGSFCAYGGRDCMVYIITLSDAACLLQFETETP--ITSLAFA 260
                                        56799************************************999..9999875 PP

  == domain 4  score: 8.1 bits;  conditional E-value: 0.0014
                        ANAPC4_WD40  36 kedsevrsLaWkpdgklLavaysdgev..rlldaesgkvvhslsvksekavtclgWg 90 
                                        +++  ++sLa+   + ++av++ +g +   ++  e + ++++ s +     t l+W+
  gene1278|gene1278|rna1278|rna1278 249 ETETPITSLAFAITEPIIAVGTRNGIIcwDVIGNERAAIIENESKTVY--CTALTWA 303
                                        56789********************88334555555555555433333..6667776 PP

  == domain 5  score: 6.6 bits;  conditional E-value: 0.0044
                        ANAPC4_WD40   9 LiAlatedgellvfRlngqrvwtleedkedsevrsLaWkpdgklLavaysdgevrllda 67 
                                        +iA++t +g +    +  +r   +e++++    ++L W +  + L+ +y+dg++ l+d 
  gene1278|gene1278|rna1278|rna1278 265 IIAVGTRNGIICWDVIGNERAAIIENESKTVYCTALTWAK--TRLVTGYNDGTIVLYDF 321
                                        4555555555555555555555557788888888899976..689**********9986 PP

>> Nup160  Nucleoporin Nup120/160
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.5   0.1   0.00063       1.4     208     263 ..       9      62 ..       3      70 .. 0.82
   2 !    6.0   0.1    0.0017       3.8     224     252 ..      71     100 ..      62     119 .. 0.84
   3 !   13.8   0.0   7.5e-06     0.017     226     259 ..     159     195 ..     147     242 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.00063
                                        SS---TT-ECEEEEET.....TTTEEEEEETT-EEEEEETTTTEEEEEEE--.-SS CS
                             Nup160 208 rrksgasvalsldvavavveigqtylfalsrdgkLrvWnlltgkclatidllrdee 263
                                        r ks ++ +l++++ v  +  ++++l+++srd+k+  W l+t    ++++l+ +e+
  gene1278|gene1278|rna1278|rna1278   9 RAKSRVHKQLVTSLDVPYTG-NSDILYSASRDKKVYQWKLNTSAMERVGTLT-KEY 62 
                                        56777778888888888888.*********************9998888888.454 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0017
                                        ......TTTEEEEEETT-EEEEEETTTTEE CS
                             Nup160 224 avvei.gqtylfalsrdgkLrvWnlltgkc 252
                                        +v    ++ ++ + s d++ r+ +++t+k 
  gene1278|gene1278|rna1278|rna1278  71 DVKANkTNEMIITTSYDHTARIYDVNTQKY 100
                                        444346899******************986 PP

  == domain 3  score: 13.8 bits;  conditional E-value: 7.5e-06
                                        .....TTTEEEEEETT-EEEEEETTTTEEEEE.EE-- CS
                             Nup160 226 vei..gqtylfalsrdgkLrvWnlltgkclat.idll 259
                                        v+   + ++ ++ s+dgkLr+W++++gk+++t  + +
  gene1278|gene1278|rna1278|rna1278 159 VSFvpNTNLCVTGSSDGKLRIWDIDSGKIVRTfVNGN 195
                                        4445588899999******************955544 PP

>> WD40_like  WD40-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.7   6.3e-05      0.14       6      69 ..      72     133 ..      68     158 .. 0.78
   2 ?    0.6   0.0      0.13   2.9e+02       6      37 ..     159     190 ..     155     195 .. 0.82
   3 !   15.7   0.1   3.2e-06    0.0073       4     108 ..     214     320 ..     211     325 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 6.3e-05
                          WD40_like   6 idiskkgslilyGgkddkctvlkleslesvsivesfedSvifvkl.ldddlilvvtlDGtillsl 69 
                                        +  +k +++i+  + d++++++++++++  +i+++ +  +  v +  +d++i+ ++ DG i   l
  gene1278|gene1278|rna1278|rna1278  72 VKANKTNEMIITTSYDHTARIYDVNTQKY-TILKGHKKDLTGVTInTEDNKIITGSCDGSIA--L 133
                                        778999******************99875.66666666666665526778**********93..3 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.13
                          WD40_like   6 idiskkgslilyGgkddkctvlkleslesvsi 37 
                                        + + ++ +l + G+ d k+++ +++s+++v  
  gene1278|gene1278|rna1278|rna1278 159 VSFVPNTNLCVTGSSDGKLRIWDIDSGKIVRT 190
                                        55667889999999999999999999998864 PP

  == domain 3  score: 15.7 bits;  conditional E-value: 3.2e-06
                          WD40_like   4 YsidiskkgslilyGgkddkctvlkleslesvsivesfedSvifvklldddlilvvtlDGtillsllenee..eve 77 
                                         ++ is +gs+ +yGg+d  + +++l        +e  +     +  + +  i v+t  G i   ++ ne   ++e
  gene1278|gene1278|rna1278|rna1278 214 TALSISADGSFCAYGGRDCMVYIITLSDAACLLQFETETPITSLAFAITEPIIAVGTRNGIICWDVIGNERaaIIE 289
                                        57899*************999999999888777777666544455569999*******************999999 PP

                          WD40_like  78 nekieedistvkviddklliGtnkGsiyvfs 108
                                        ne+     +  +  + +l+ G n G+i +++
  gene1278|gene1278|rna1278|rna1278 290 NESKTVYCTALTWAKTRLVTGYNDGTIVLYD 320
                                        9999999********************9885 PP

>> Frtz  WD repeat-containing and planar cell polarity effector protein Fritz
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.0     1e-05     0.023     263     334 ..     111     188 ..      63     199 .. 0.78
   2 !    7.2   0.0   0.00061       1.4     261     292 ..     294     325 ..     285     327 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1e-05
                               Frtz 263 islafnpdedkLllGceDssviLydeerkitklv......kaevvPsliswhpdsaillvasergelqifDlaLsp 332
                                          +++n++++k++ G+ D+s+ L+++e  + k+        + +  + +s+ p+  + + +s+ g+l+i+D+    
  gene1278|gene1278|rna1278|rna1278 111 TGVTINTEDNKIITGSCDGSIALWNTEGVLSKVLtpenpsSIPIWVNCVSFVPNTNLCVTGSSDGKLRIWDIDSGK 186
                                        5678899******************99887776523311123344566778899999999***********97666 PP

                               Frtz 333 ir 334
                                        i 
  gene1278|gene1278|rna1278|rna1278 187 IV 188
                                        65 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.00061
                               Frtz 261 qvislafnpdedkLllGceDssviLydeerki 292
                                         v ++a   ++ +L+ G +D++++Lyd +r++
  gene1278|gene1278|rna1278|rna1278 294 TVYCTALTWAKTRLVTGYNDGTIVLYDFVRNV 325
                                        5789999********************99987 PP

>> BBS2_Mid  Ciliary BBSome complex subunit 2, middle region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0       0.2   4.5e+02       5      32 ..      70      98 ..      67     108 .. 0.68
   2 ?    5.6   0.0    0.0071        16       9      42 ..     116     149 ..     109     188 .. 0.80
   3 ?    0.4   0.0       0.3   6.8e+02      13      30 ..     166     183 ..     156     202 .. 0.72
   4 ?    2.2   0.0     0.082   1.8e+02      47      66 ..     301     320 ..     266     324 .. 0.71

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.2
                           BBS2_Mid  5 advdgdgeneLvvg.sddfeirvfkeeel 32
                                       +dv+ + +ne+++  s d + r+++ ++ 
  gene1278|gene1278|rna1278|rna1278 70 TDVKANKTNEMIITtSYDHTARIYDVNTQ 98
                                       67777777777765156888898876655 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0071
                           BBS2_Mid   9 gdgeneLvvgsddfeirvfkeeelvaeitetekv 42 
                                        + ++n+++ gs d +i +++ e +++++ + e++
  gene1278|gene1278|rna1278|rna1278 116 NTEDNKIITGSCDGSIALWNTEGVLSKVLTPENP 149
                                        44589***************99999887766655 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.3
                           BBS2_Mid  13 neLvvgsddfeirvfkee 30 
                                        n  v gs d ++r+++ +
  gene1278|gene1278|rna1278|rna1278 166 NLCVTGSSDGKLRIWDID 183
                                        566889999999988755 PP

  == domain 4  score: 2.2 bits;  conditional E-value: 0.082
                           BBS2_Mid  47 rlekerfayaleNGtvgvye 66 
                                        +  k+r++++ + Gt+ +y+
  gene1278|gene1278|rna1278|rna1278 301 TWAKTRLVTGYNDGTIVLYD 320
                                        34677899999999999997 PP

>> ELYS-bb  beta-propeller of ELYS nucleoporin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0     0.059   1.3e+02     230     252 ..     117     139 ..     107     155 .. 0.79
   2 ?    9.6   0.0   0.00014      0.31     217     251 ..     148     184 ..     142     205 .. 0.81
   3 ?   -3.8   0.0       1.6   3.5e+03     231     248 ..     303     320 ..     288     321 .. 0.69

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.059
                            ELYS-bb 230 srtnqlavgfsdgylslwnlktl 252
                                        +  n+++ g  dg ++lwn   +
  gene1278|gene1278|rna1278|rna1278 117 TEDNKIITGSCDGSIALWNTEGV 139
                                        457999*************8765 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00014
                            ELYS-bb 217 sps..gvavsalsyisrtnqlavgfsdgylslwnlkt 251
                                        +ps   + v ++s++  tn  + g sdg l++w++ +
  gene1278|gene1278|rna1278|rna1278 148 NPSsiPIWVNCVSFVPNTNLCVTGSSDGKLRIWDIDS 184
                                        5662235689***********************9976 PP

  == domain 3  score: -3.8 bits;  conditional E-value: 1.6
                            ELYS-bb 231 rtnqlavgfsdgylslwn 248
                                           +l+ g+ dg + l++
  gene1278|gene1278|rna1278|rna1278 303 AKTRLVTGYNDGTIVLYD 320
                                        456899999999998875 PP

>> Nucleoporin_N  Nup133 N terminal like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.1      0.03        68     213     235 ..      30      52 ..      11      63 .. 0.78
   2 ?    3.3   0.2     0.012        28     204     241 ..      69     105 ..      63     134 .. 0.81
   3 ?    4.8   0.0    0.0045        10     197     233 ..     149     184 ..     113     196 .. 0.73

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.03
                                        TCEEEEEETTSEEEEEEEETTCE CS
                      Nucleoporin_N 213 rrilytlsskgvirvydlsasng 235
                                        + ily++s+++++  ++l++s+ 
  gene1278|gene1278|rna1278|rna1278  30 SDILYSASRDKKVYQWKLNTSAM 52 
                                        389***************97743 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.012
                                        EEEEEEECCTCEEEEEETTSEEEEEEEETTCEE-EEEE CS
                      Nucleoporin_N 204 ivqlridssrrilytlsskgvirvydlsasngesslks 241
                                        i+ +++ ++ + ++t s +++ r+yd++  ++   lk+
  gene1278|gene1278|rna1278|rna1278  69 ITDVKANKTNEMIITTSYDHTARIYDVN-TQKYTILKG 105
                                        8899999999*****************9.555555554 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.0045
                                        ----GG-EEEEEEECCTCEEEEEETTSEEEEEEEETT CS
                      Nucleoporin_N 197 gasereeivqlridssrrilytlsskgvirvydlsas 233
                                        ++s +  + ++   + +++ +t ss+g++r++d+  s
  gene1278|gene1278|rna1278|rna1278 149 PSSIPIWVNCVSFVPNTNLCVTGSSDGKLRIWDID-S 184
                                        445555566777778889***************98.3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (328 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       679  (0.0378716); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 2118.94
//
Query:       gene1279|gene1279|rna1279|rna1279  [L=333]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.098   13.6   1.4        2.1    9.4   0.3    2.6  2  WD40           WD domain, G-beta repeat
       0.12   12.4   0.3       0.44   10.6   0.0    2.1  2  BBS2_Mid       Ciliary BBSome complex subunit 2, middle regio
       0.29   11.2   4.9       0.21   11.7   0.9    2.5  3  Spectrin_like  Spectrin like domain


Domain annotation for each model (and alignments):
>> WD40  WD domain, G-beta repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.3   0.00035       2.1       2      38 .]     138     173 ..     137     173 .. 0.75
   2 ?    2.5   0.0     0.051     3e+02      10      36 ..     262     287 ..     253     289 .. 0.64

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00035
                                        EEEEEEESS.SSEEEEEEETTSSEEEEEETTSEEEEEE CS
                               WD40   2 qclrtltGH.ssvtslafspdgawlasGsdDgtvriWd 38 
                                        q++ +l  H s v+++ ++++g+ ++ +++D+ v  Wd
  gene1279|gene1279|rna1279|rna1279 138 QPVFSLNKHtSTVSGI-TCSNGNIFS-CGYDQYVNKWD 173
                                        6888999997667777.555888876.555****9998 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.051
                                        S.SSEEEEEEETTSSEEEEEETTSEEEE CS
                               WD40  10 H.ssvtslafspdgawlasGsdDgtvri 36 
                                        H  ++++++    ++ ++++sdD t+ +
  gene1279|gene1279|rna1279|rna1279 262 HsLGINDFDI--QNDRILTASDDETICV 287
                                        5223666643..4444668999*99976 PP

>> BBS2_Mid  Ciliary BBSome complex subunit 2, middle region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.32   1.9e+03      55      75 ..     153     175 ..     107     190 .. 0.59
   2 ?   10.6   0.0   7.4e-05      0.44       2      52 ..     264     314 ..     263     332 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.32
                           BBS2_Mid  55 yaleNGtv..gvyekkerlWrvk 75 
                                        ++ +NG +    y++   +W + 
  gene1279|gene1279|rna1279|rna1279 153 ITCSNGNIfsCGYDQYVNKWDIE 175
                                        34455555222366666666665 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 7.4e-05
                           BBS2_Mid   2 laladvdgdgeneLvvgsddfeirvfkee.elvaeitetekvvslarleker 52 
                                        l + d+d + ++ ++ +sdd +i v++++ ++++ i++++kv +l    ++r
  gene1279|gene1279|rna1279|rna1279 264 LGINDFDIQ-NDRILTASDDETICVLNNNfDVLKSIKTKNKVFTLNIYPNNR 314
                                        677888886.789*************99989***********9997665555 PP

>> Spectrin_like  Spectrin like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.9   3.4e-05      0.21      35      73 ..      74     112 ..      73     113 .. 0.92
   2 ?    0.1   0.1      0.15   8.8e+02      11      44 ..     167     200 ..     166     222 .. 0.75
   3 ?   -3.6   0.0       2.1   1.2e+04      56      69 ..     247     260 ..     245     264 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.4e-05
                      Spectrin_like  35 nLelhyqdFlrdSqeSelFteedrkqlerevekaqehye 73 
                                        ++e+ y +F   S++SelF + d     + +++++  y+
  gene1279|gene1279|rna1279|rna1279  74 QMESSYLEFHVYSKDSELFLHHDVCVFADIYDACNFRYN 112
                                        699*********************999999999988876 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.15
                      Spectrin_like  11 ekirsltlamlktmkpeeyrqvlknLelhyqdFl 44 
                                        ++++++ +++ k    +  ++ l+++e h +d  
  gene1279|gene1279|rna1279|rna1279 167 QYVNKWDIETRKVKAEKYFNERLDSIENHTSDLS 200
                                        5789999998777777777888999999988865 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 2.1
                      Spectrin_like  56 edrkqlerevekaq 69 
                                         dr+++ ++v+  +
  gene1279|gene1279|rna1279|rna1279 247 RDRRNIRKSVNVKK 260
                                        57777777776544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (333 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       707  (0.0394333); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.32s 00:00:00.84 Elapsed: 00:00:00.50
# Mc/sec: 1996.57
//
Query:       gene128|gene128|rna128|rna128  [L=87]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.021   14.0   0.0      0.023   13.9   0.0    1.0  1  RE_NgoPII  NgoPII restriction endonuclease
      0.046   13.4   0.2      0.053   13.2   0.2    1.1  1  RasGAP     GTPase-activator protein for Ras-like GTPase


Domain annotation for each model (and alignments):
>> RE_NgoPII  NgoPII restriction endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   2.6e-06     0.023     189     261 ..       1      75 [.       1      76 [. 0.84

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.6e-06
                      RE_NgoPII 189 vDpLgitnlrirGmWlienPlkvfkylyeekeskefel.ivlikeekynsfe.eedrnkleklskenltiediki 261
                                    v +L +t+++i     i++Pl+vf+   e++++++ e+  +  ++++y s   +e++n+l++  k+  +i+d  i
  gene128|gene128|rna128|rna128   1 VQNLMLTEFKINNYDVIKDPLNVFEPEREQQSNANSEIgNASTNRDRYCSSAfSENKNELSSNCKNLCEIADAII 75 
                                    67899*********************99999999988845678899**764425667999998899999999765 PP

>> RasGAP  GTPase-activator protein for Ras-like GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.2   5.9e-06     0.053      64     121 ..      18      75 ..       5      77 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 5.9e-06
                         RasGAP  64 lDPrkiyeelkkkkesktgkksessgkksekeaselekvsqmleknldkLkelvneil 121
                                     DP  ++e  ++++   ++++ + s +  +++ s  ++ +++l +n+++L e++++i+
  gene128|gene128|rna128|rna128  18 KDPLNVFEPEREQQSNANSEIGNASTNRDRYCSSAFSENKNELSSNCKNLCEIADAII 75 
                                    59****************************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       587  (0.0327403); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 634.19
//
Query:       gene1280|gene1280|rna1280|rna1280  [L=390]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    6.6e-38  130.6   9.7    4.2e-35  121.4   3.4    3.1  2  ArsA_ATPase  Anion-transporting ATPase
    1.4e-06   28.4   0.9    1.4e-06   28.4   0.9    2.4  2  AAA_31       AAA domain
  ------ inclusion threshold ------
       0.26   11.3   1.1         13    5.8   0.1    2.4  2  CbiA         CobQ/CobB/MinD/ParA nucleotide binding domain


Domain annotation for each model (and alignments):
>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.4   2.4e-05      0.14       2      28 ..      13      39 ..      12      42 .. 0.93
   2 !  121.4   3.4     7e-39   4.2e-35      25     302 ..     142     387 ..     139     390 .] 0.88

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 2.4e-05
                                       EEEEEEESTTSSHHHHHHHHHHHHHHT CS
                        ArsA_ATPase  2 kvilvgGKGGVGKttvsaatavklsek 28
                                       k+ +v G+G  GKt+vsa ++++l+++
  gene1280|gene1280|rna1280|rna1280 13 KWYIVCGRGKSGKTSVSAGIGLRLADT 39
                                       8999********************985 PP

  == domain 2  score: 121.4 bits;  conditional E-value: 7e-39
                                        HHHTTS-EEEEE-STTTHHHHHHTS--BSS-EEETSSEEEEE--HHHHHHHHHCCHHGGGSCCHHHHHHHHHHHHH CS
                        ArsA_ATPase  25 lsekgkkvllistDPAhslsDsfdqklgkeptkvkeNLsavEidpeveleeakqevqkeeeallgleeledvlaee 100
                                        +s+  +k+ll+s+D   +ls  f+++++ +pt++k+N +++E++    +++ k++  ++ +           + + 
  gene1280|gene1280|rna1280|rna1280 142 CSKCLRKILLVSLDQQDNLSETFQTEIETKPTRIKNNFYVMELNRGA-IAQIKENDENNVT-----------ILKS 205
                                        788899*************************************9754.6655554433333...........4456 PP

                                        HTSSTTHHHHHHHHHHHHHHHCSSSSEEEEESBSCCHTCGGGGHHHHHHHHHHHHHHHHHHHHHHHHHHCCCSHCH CS
                        ArsA_ATPase 101 laslPGideilsfeellkyvkeeeydvvvlDtaPTGhtlrllslpevleklleklvklkeklsplakqlvkllglg 176
                                          slPG+ e+l f e++k    +eyd++++Dt P  +tl +ls+p+ l++ll+k++ + + l++l k+        
  gene1280|gene1280|rna1280|rna1280 206 IRSLPGVLEALYFSEIIKIA--REYDTIIIDTWPSFNTLNFLSFPKELNSLLNKIIGMDK-LKNLDKA-------- 270
                                        7899*************986..68*****************************9998887.3333332........ PP

                                        HHHHHHHHHHHHHHHHHHHHHHHHHTSTTTEEEEEEEESSHHHHHHHHHHHHHHHHTT-EEEEEEEEEE-TTCSSS CS
                        ArsA_ATPase 177 gvsieealeeleetkeeikkveeiltdpertsfrlVvipEklslkEteRaikeLkkygikvdavivNkllpeeeqe 252
                                                +++ +   +i+k    l+     sf+lV +pE ls+ E +++i++L+ +gi+v+ +++N++l  +++ 
  gene1280|gene1280|rna1280|rna1280 271 -----PFYQKIVDAASTIEKCGMFLKKSAECSFILVFTPEMLSITEANKLITKLAYVGISVNHLLINQVLRPKTE- 340
                                        .....35567778889999999************************************************88777. PP

                                        TSHHHHHHHHHHHHHHHHHHHHTTTSEEEEEE--SS-S-SHHHHHHHHHH CS
                        ArsA_ATPase 253 nCeflearkkiqkkylkeieelfedlevvklplleeEvvGlekleklsel 302
                                         Ce++ a +  q+k l+++++   +++ ++l + ++ v+G+ +le++s+ 
  gene1280|gene1280|rna1280|rna1280 341 -CEICTAIETKQQKALERVKNC--NINQIYLDFEPNGVRGVTNLERFSRK 387
                                        .******************996..78889999***************986 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.0   0.3       2.1   1.2e+04      11      28 ..      21      38 ..      19      40 .. 0.81
   2 !   28.4   0.9   2.3e-10   1.4e-06      31     133 ..     147     243 ..     141     248 .. 0.78

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 2.1
                             AAA_31 11 GGvGKTTtsvnlaaalak 28
                                       G  GKT  s  ++  la 
  gene1280|gene1280|rna1280|rna1280 21 GKSGKTSVSAGIGLRLAD 38
                                       6689**999999988875 PP

  == domain 2  score: 28.4 bits;  conditional E-value: 2.3e-10
                             AAA_31  31 kkvLlvDlDpQanattglgiekne....iektlyevlieeknikeaiiktkvenldlipssidLaeaeielvelek 102
                                         k+Llv lD Q n++ ++++e ++    i++++y + +++  i+++   ++ +n++++ s  +L ++   l     
  gene1280|gene1280|rna1280|rna1280 147 RKILLVSLDQQDNLSETFQTEIETkptrIKNNFYVMELNRGAIAQIKE-NDENNVTILKSIRSLPGVLEAL---Y- 217
                                        79************9988876555345577888888778888877666.667888****999999987777...2. PP

                             AAA_31 103 keeilkellekvkdeYDyiiiDcpPsLgllt 133
                                            + + + k+  eYD iiiD+ Ps ++l+
  gene1280|gene1280|rna1280|rna1280 218 ----F-SEIIKIAREYDTIIIDTWPSFNTLN 243
                                        ....2.3344899*************99875 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.1    0.0022        13       3      25 ..      16      38 ..      14      42 .. 0.86
   2 ?    4.2   0.1    0.0071        43      26      55 ..     145     227 ..     140     357 .. 0.69

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0022
                                       EEESSTTSSHHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxx RF
                               CbiA  3 iastkGGvGKTtlaanLaralar 25
                                       i+ + G +GKT+++a+++  la+
  gene1280|gene1280|rna1280|rna1280 16 IVCGRGKSGKTSVSAGIGLRLAD 38
                                       67789***********9988886 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.0071
                                        TT--EEEEEEEESSCCCCHHTTEB-HHHH............................................... CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxx............................................... RF
                               CbiA  26 rglrVllvDaDpqannlaileglendiep............................................... 54 
                                        + +++llv +D q n+++  +++e++ +p                                               
  gene1280|gene1280|rna1280|rna1280 145 CLRKILLVSLDQQDNLSE-TFQTEIETKPtriknnfyvmelnrgaiaqikendennvtilksirslpgvlealyfs 219
                                        55799********99999.777777777778888999887777777777777777777777555555555555555 PP

                                        .......C CS
                                        .......x RF
                               CbiA  55 .......d 55 
                                                
  gene1280|gene1280|rna1280|rna1280 220 eiikiarE 227
                                        55555550 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (390 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       962  (0.0536561); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.41
# Mc/sec: 2821.65
//
Query:       gene1281|gene1281|rna1281|rna1281  [L=227]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.6e-06   28.3   0.0    4.7e-06   26.8   0.0    1.7  1  HAD_2       Haloacid dehalogenase-like hydrolase
    7.1e-06   26.5   0.0      0.028   14.7   0.0    2.1  2  Hydrolase   haloacid dehalogenase-like hydrolase
     0.0032   17.2   0.0        2.5    7.9   0.0    2.2  2  NIF         NLI interacting factor-like phosphatase
     0.0086   15.9   0.7        1.8    8.4   0.1    2.6  2  Acid_PPase  Acid Phosphatase
  ------ inclusion threshold ------
      0.056   12.9   0.0       0.17   11.3   0.0    1.7  2  DUF2608     Protein of unknown function (DUF2608)


Domain annotation for each model (and alignments):
>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8   0.0   1.3e-09   4.7e-06       2     174 ..      30     201 ..      29     205 .. 0.78

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 1.3e-09
                              HAD_2   2 iFDlDgTlldteelii.qafnelleey.....glselseeelrkliglslrellrklgeseeeeekieellrkyne 71 
                                        iFD+D+Tl+ +++ +  ++++++l +         +  + e+r+ +g+s + l+ +         +++++ + +  
  gene1281|gene1281|rna1281|rna1281  30 IFDIDNTLYHSKPSLTsHITTQALSKLsinhsAARQKILRECREQYGFSIKGLYARNLL------DYDTYCEVIDG 99 
                                        9*********9987651566677766644332222455556666677777666655554......68899888888 PP

                              HAD_2  72 ekkkkevkpydgvkelLeeLkeagyklgivTsksreaveekleqlgiesyFdvivtsedvekk...KPdpevieka 144
                                          +   v    ++k+lL  L + ++   + T+++r   ++ l++lgi + Fd +v+ ++       KP  + +  +
  gene1281|gene1281|rna1281|rna1281 100 VDYGAIVGCDGDLKSLLGRLDAGKI---CFTNGERMHCMRVLDALGISDAFDYVVCVDHKDPDflcKPMEQAFD-L 171
                                        888878888889********77666...78****************************99888888**988776.6 PP

                              HAD_2 145 leklklkkeeviyvGDsptDieaakkagik 174
                                        le+l   k+ ++++ D p+ i  a + g +
  gene1281|gene1281|rna1281|rna1281 172 LERLFSVKNMTVFFDDDPRNIAVAEQRGWN 201
                                        77777778889999*******999988866 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   7.9e-06     0.028       2      37 ..      27      62 ..      26      90 .. 0.77
   2 !   10.0   0.0   0.00022      0.79     138     208 ..     124     197 ..     109     199 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 7.9e-06
                                       SEEEEESBTTTBCHHHHHHHHHHHHCHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          Hydrolase  2 ktvvfDkdGTLttgepsvedvivsaalalaaaletg 37
                                       ++++fD+d+TL++++ps++  i   al+   +++ +
  gene1281|gene1281|rna1281|rna1281 27 NLFIFDIDNTLYHSKPSLTSHITTQALSKLSINHSA 62
                                       799***************998888856555555444 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00022
                                        EEEESSEHHHHHHHHHHTT.GGGESEEEEHHCES...STTTSHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHHH CS
                                        xxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          Hydrolase 138 vlltgdnpetaeraanqlG.ddyfdaviasdiet...vakpspegkvaaireLqgkpeevamVGDgvnDaaalaa 208
                                        +  t++++ + +r+++ lG  d+fd v+++d +      kp  +++  + r + +k   +++++D +  +a +++
  gene1281|gene1281|rna1281|rna1281 124 ICFTNGERMHCMRVLDALGiSDAFDYVVCVDHKDpdfLCKPMEQAFDLLERLFSVKN-MTVFFDDDPRNIAVAEQ 197
                                        47899*************************9999999**********9999997663.6*******999998876 PP

>> NIF  NLI interacting factor-like phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.5   0.0   0.00088       3.2       3      23 ..      29      49 ..      27      89 .. 0.63
   2 !    7.9   0.0   0.00068       2.5      53     123 ..     124     198 ..     108     222 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.00088
                                NIF  3 LVLDLDetLvhsklekskklk 23
                                        ++D+D+tL hsk + +++++
  gene1281|gene1281|rna1281|rna1281 29 FIFDIDNTLYHSKPSLTSHIT 49
                                       599**********53332222 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.00068
                                NIF  53 vifTasseeyaeavidildpekkllshrlyrescv..kkkgeyvKdLsllgr...dlsrvvivDdspdsfelqpen 123
                                        + fT++ +  + +v+d+l    + ++++++ ++    +  +      +ll+r     + +v++Dd+p++++  ++ 
  gene1281|gene1281|rna1281|rna1281 124 ICFTNGERMHCMRVLDALGISDA-FDYVVCVDHKDpdFLCKPMEQAFDLLERlfsVKNMTVFFDDDPRNIAVAEQR 198
                                        469***************99987.99999999995332233444455556666647779*********99876665 PP

>> Acid_PPase  Acid Phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.1    0.0005       1.8       2      19 ..      25      42 ..      24      80 .. 0.75
   2 !    5.6   0.1    0.0035        13     127     144 ..     182     199 ..     133     218 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0005
                                       --SEEEE-STTTSSSS-T CS
                         Acid_PPase  2 lpklivFDLDyTLWpfev 19
                                       +p+l +FD+D TL + + 
  gene1281|gene1281|rna1281|rna1281 25 YPNLFIFDIDNTLYHSKP 42
                                       8************97554 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0035
                                        EEEEES-HHHHHHHHTTT CS
                         Acid_PPase 127 mlfFDdesrnievesrlg 144
                                         +fFDd  rni v ++ g
  gene1281|gene1281|rna1281|rna1281 182 TVFFDDDPRNIAVAEQRG 199
                                        48*********9988755 PP

>> DUF2608  Protein of unknown function (DUF2608)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   4.9e-05      0.17      20      50 ..      28      58 ..      18      76 .. 0.77
   2 ?   -1.6   0.0      0.43   1.5e+03     172     195 ..     171     194 ..     166     198 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 4.9e-05
                            DUF2608 20 LvvfDiDdtLltstealgsdawydwqgklvi 50
                                       L +fDiD+tL  s+  l s +  +   kl+i
  gene1281|gene1281|rna1281|rna1281 28 LFIFDIDNTLYHSKPSLTSHITTQALSKLSI 58
                                       89***************99998664444444 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.43
                            DUF2608 172 lLdkigrepksviFiDDkkknlas 195
                                        lL+++ +  +  +F DD  +n+a 
  gene1281|gene1281|rna1281|rna1281 171 LLERLFSVKNMTVFFDDDPRNIAV 194
                                        666666667778999999999975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (227 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       410  (0.022868); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1541.48
//
Query:       gene1282|gene1282|rna1282|rna1282  [L=61]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       625  (0.0348597); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 425.58
//
Query:       gene1283|gene1283|rna1283|rna1283  [L=293]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.3e-29  102.6   0.0    1.9e-17   63.9   0.0    2.1  2  NAD_binding_2  NAD binding domain of 6-phosphogluconate dehyd
    2.9e-10   40.0   0.7    2.9e-10   40.0   0.7    1.6  2  6PGD           6-phosphogluconate dehydrogenase, C-terminal d
    0.00017   21.6   0.0    0.00031   20.8   0.0    1.3  1  Shikimate_DH   Shikimate / quinate 5-dehydrogenase
     0.0002   21.9   0.0     0.0012   19.3   0.0    2.0  2  F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
    0.00086   19.7   5.3     0.0011   19.3   5.3    1.1  1  Vfa1           AAA-ATPase Vps4-associated protein 1
     0.0022   17.9   0.0     0.0037   17.2   0.0    1.4  1  3HCDH_N        3-hydroxyacyl-CoA dehydrogenase, NAD binding d
     0.0038   16.8   0.0     0.0064   16.1   0.0    1.3  1  IlvN           Acetohydroxy acid isomeroreductase, NADPH-bind
  ------ inclusion threshold ------
      0.011   15.1   0.1       0.16   11.3   0.0    2.4  2  DUF1776        Fungal family of unknown function (DUF1776)
      0.013   14.9   0.0       0.02   14.3   0.0    1.2  1  2-Hacid_dh_C   D-isomer specific 2-hydroxyacid dehydrogenase,
      0.024   14.3   0.0        3.7    7.2   0.0    2.2  2  ApbA           Ketopantoate reductase PanE/ApbA
       0.12   12.1   6.0       0.16   11.8   6.0    1.1  1  SpoIIIAH       SpoIIIAH-like protein
        6.1    5.0   8.3          8    4.6   8.3    1.1  1  CDC45          CDC45-like protein


Domain annotation for each model (and alignments):
>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.7   0.0     3e-12   4.5e-09       1      42 [.       9      50 ..       9      62 .. 0.89
   2 !   63.9   0.0   1.3e-20   1.9e-17      30     154 ..     110     233 ..     100     236 .. 0.89

  Alignments for each domain:
  == domain 1  score: 36.7 bits;  conditional E-value: 3e-12
                                       EEEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTT CS
                      NAD_binding_2  1 kigfiGlGvMGsnmalnllkagykvavynrtkekveelvaeg 42
                                       ++g+iGl+ MG+ +alnl ++gy vavynrt+++++e+ +e 
  gene1283|gene1283|rna1283|rna1283  9 QVGLIGLAPMGRALALNLRDKGYVVAVYNRTESRTREFEKEC 50
                                       69***********************************99875 PP

  == domain 2  score: 63.9 bits;  conditional E-value: 1.3e-20
                                        SSHHHHHHHHHTT.EEE-SSHHHHHHHC...SEEEE-SSSHHHHHHHHHSHCCC--TT-EEEE-S---HHHHHHHH CS
                      NAD_binding_2  30 rtkekveelvaeg.akaaesieelvasl...dvvitmvkagkavdeviegllealkkgdilidgstsspedtrela 101
                                         +++++++  ++g +  +++i++++++l   ++++t++k+ +a+d+++ +l++ l+k+d+++d+s+s p+ t+ ++
  gene1283|gene1283|rna1283|rna1283 110 TSTSNTNSTPTKGtFIYTYTINAFINALqqpRKILTIIKS-DATDDLLAQLIPLLSKNDYILDFSNSTPDITEIRT 184
                                        5667777777776688899999999999999999999987.789***************************99987 PP

                                        HHHHHTT-EEEEEEEESHHHHHHHT-EEEEEEE-HHHHHHHHHHHHHHEEEEE CS
                      NAD_binding_2 102 kelkekglkfldaPVSGGeegAekGtLsimvGGseeafervkpvleaigakvt 154
                                        ++   + +++l++++SGG+egA++    +mvGG+++a+++v+p+l +i+++v 
  gene1283|gene1283|rna1283|rna1283 185 RD---TPCHYLGIGISGGTEGARNNG-GLMVGGPSAAYAAVQPILFSISNSVG 233
                                        65...78*****************99.9*******************999876 PP

>> 6PGD  6-phosphogluconate dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       1.5   2.2e+03     104     128 ..      32      64 ..      18      86 .. 0.63
   2 !   40.0   0.7   1.9e-13   2.9e-10       1      56 [.     241     289 ..     241     292 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.5
                               6PGD 104 aeavfaRllSslkeervkaskllk........e 128
                                          av+ R+ S  +e  ++ +k ++        +
  gene1283|gene1283|rna1283|rna1283  32 VVAVYNRTESRTREFEKECEKEFEevdnkgrdD 64 
                                        568888888888888888888886333333320 PP

  == domain 2  score: 40.0 bits;  conditional E-value: 1.9e-13
                               6PGD   1 GhyVKmvHNGieygdmqliaEaydllkkvlglsneeiaevFeeWnkgelesyLiei 56 
                                        Gh+VKmvHN++ey+ m +iaE +++l ++ +      +e+ ++Wn+ +++ yL+e 
  gene1283|gene1283|rna1283|rna1283 241 GHFVKMVHNAVEYALMGVIAEFWEVLDRLGK------HELMASWNE-DMRMYLVEA 289
                                        9**************************9764......678899998.789999986 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   2.1e-07   0.00031      11      59 ..       6      53 ..       2      61 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 2.1e-07
                                       TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.E CS
                       Shikimate_DH 11 kekkvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeelkge 59
                                       k+++v liG   m++ +a +L +kg+  v+v NRt +r +e+ +e+++e
  gene1283|gene1283|rna1283|rna1283  6 KQAQVGLIGLAPMGRALALNLRDKGYV-VAVYNRTESRTREFEKECEKE 53
                                       789***********************9.******************665 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   8.2e-07    0.0012       2      56 ..      10      60 ..       9      64 .. 0.92
   2 ?   -0.3   0.0       1.1   1.6e+03      57      96 ..     135     174 ..     113     175 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 8.2e-07
                                       EEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHH CS
                      F420_oxidored  2 igiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdne 56
                                       +g+iG   mg+ala++l  +g   + +  + +r++++ +e+++e + + ++vdn+
  gene1283|gene1283|rna1283|rna1283 10 VGLIGLAPMGRALALNLRDKG---YVVA-VYNRTESRTREFEKECEKEFEEVDNK 60
                                       89*******************...8887.66***************999998886 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.1
                                        HHHHH-SEEEE-S-HHHHHHHHHHCGHHHHTTSEEEEESS CS
                      F420_oxidored  57 eaaeeadvvvlavkpedveevlselakdalkgklvisvla 96 
                                         a+++   ++  +k  +++++l++l + ++k+  +++ ++
  gene1283|gene1283|rna1283|rna1283 135 NALQQPRKILTIIKSDATDDLLAQLIPLLSKNDYILDFSN 174
                                        6777777888889999999999999999999988888766 PP

>> Vfa1  AAA-ATPase Vps4-associated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   5.3   7.5e-07    0.0011      44     134 ..      26     114 ..      23     148 .. 0.62

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 7.5e-07
                               Vfa1  44 LkDkqFatpivdeeeeeaakkkkeleeeiekvkkeyeekqkkkkekekkkkekdkkdkdkkkekekdkkkekekee 119
                                        L+Dk+++  +++ +e+++++ +ke e+e e+v ++ ++  k +k k++k+k++d+kdk+ ++++++d++++ +  +
  gene1283|gene1283|rna1283|rna1283  26 LRDKGYVVAVYNRTESRTREFEKECEKEFEEVDNKGRDDVKDNKGKDNKDKDNDTKDKSINDKSTRDNDASGN--D 99 
                                        89***********999988889999999999999999988888877777655554444444444433333333..2 PP

                               Vfa1 120 ekkkelkkaeeelee 134
                                        e +++l + ++++++
  gene1283|gene1283|rna1283|rna1283 100 ESSTRLCDDDTSTSN 114
                                        222222222211111 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   2.5e-06    0.0037       1      56 [.       9      64 ..       9      87 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 2.5e-06
                                       EEEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCCTTTTSS- CS
                            3HCDH_N  1 kvaviGaGtmGagiaavfasagleVvlvdiseealekalekieksleklvekgklk 56
                                       +v+ iG   mG+ +a  +  +g+ V +++++e++ ++ ++++ek++e++ +kg+ +
  gene1283|gene1283|rna1283|rna1283  9 QVGLIGLAPMGRALALNLRDKGYVVAVYNRTESRTREFEKECEKEFEEVDNKGRDD 64
                                       6999*********************************************9999854 PP

>> IlvN  Acetohydroxy acid isomeroreductase, NADPH-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   4.3e-06    0.0064       4      44 ..       7      47 ..       4      65 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 4.3e-06
                                       TS-EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHH CS
                               IlvN  4 gkkiaviGyGsqGhaqalnlrdsgldvvvglregsksvkkA 44
                                       + ++ +iG    G+a alnlrd g  v+v +r++s++ +  
  gene1283|gene1283|rna1283|rna1283  7 QAQVGLIGLAPMGRALALNLRDKGYVVAVYNRTESRTREFE 47
                                       67899*************************99999754433 PP

>> DUF1776  Fungal family of unknown function (DUF1776)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00011      0.16      14      59 ..      16      64 ..       9      88 .. 0.80
   2 ?    0.9   0.0      0.16   2.4e+02     160     186 ..     245     271 ..     242     277 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00011
                            DUF1776 14 ePltRsialDLerrGFiVfvtvesaeeeklvesed...redIrplsvdd 59
                                        P+ R++al+L  +G++V v  + +++++  e+e    +e+++++  dd
  gene1283|gene1283|rna1283|rna1283 16 APMGRALALNLRDKGYVVAVYNRTESRTREFEKECekeFEEVDNKGRDD 64
                                       59*******************9999999988876421466677766666 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.16
                            DUF1776 160 nlpfhapEalvssalsalfevLkrelr 186
                                        ++++ a+E  + + +  + evL+r  +
  gene1283|gene1283|rna1283|rna1283 245 KMVHNAVEYALMGVIAEFWEVLDRLGK 271
                                        7899******************98655 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   1.3e-05      0.02      34      80 ..       5      50 ..       1      60 [. 0.80

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.3e-05
                                       GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHHHTC CS
                       2-Hacid_dh_C 34 lsgktvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeeeelgv 80
                                        ++ +vG+iGl  +G+a+a  l+  g  v +y+r++++++e+e++ +
  gene1283|gene1283|rna1283|rna1283  5 NKQAQVGLIGLAPMGRALALNLRDKGYVVAVYNRTESRTREFEKE-C 50
                                       57889******************************9988855543.2 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.0    0.0025       3.7       3      44 ..      12      55 ..      10      86 .. 0.74
   2 ?    5.2   0.0    0.0098        15      64     104 ..     135     175 ..      91     194 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0025
                                       EES-SHHHHHHHHHHHHHTHCEEEE-SCH.HHHH.HHHHCEEEE CS
                               ApbA  3 ilGaGaiGsllaakLakagadvtlilrsr.rlea.lkknGlrlt 44
                                        +G+  +G+ la +L  +g+ v +++r++ r  +  k+   +++
  gene1283|gene1283|rna1283|rna1283 12 LIGLAPMGRALALNLRDKGYVVAVYNRTEsRTREfEKECEKEFE 55
                                       689999*********99************888883444444444 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0098
                                        CCCS-ESEEEE-SSGGGHHHHHHHHGGGECTCEEEEEESSS CS
                               ApbA  64 selepidlvivtvKayqteealeeikplldpntvvlllqNG 104
                                          l++   ++  +K+  t++ l+++ pll +n  +l + N 
  gene1283|gene1283|rna1283|rna1283 135 NALQQPRKILTIIKSDATDDLLAQLIPLLSKNDYILDFSNS 175
                                        4566777788999**********************988886 PP

>> SpoIIIAH  SpoIIIAH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   6.0   0.00011      0.16      14      97 ..      32     118 ..      22     154 .. 0.54

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00011
                                        XXXXXXXXXXXX.....XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX. CS
                           SpoIIIAH  14 avagYlnftedsgk...kaaetaeteqeesekaeigddkekdessaasaeaesssetesesseksdiassdedead 86 
                                        +va+Y n te+++    k+ e++ +e++++   +++d+k+kd++++++  ++++++ +++s+ ++d++ +de +++
  gene1283|gene1283|rna1283|rna1283  32 VVAVY-NRTESRTRefeKECEKEFEEVDNKGRDDVKDNKGKDNKDKDN--DTKDKSINDKSTRDNDASGNDESSTR 104
                                        66776.555544446886667777777777777777733333322222..22222223333333333333333333 PP

                                        .....XXXXXXXXX CS
                           SpoIIIAH  87 e...ltsetasaaa 97 
                                             ts+++++++
  gene1283|gene1283|rna1283|rna1283 105 LcddDTSTSNTNST 118
                                        25442333333333 PP

>> CDC45  CDC45-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   8.3    0.0053         8     116     172 ..      46     105 ..      24     133 .. 0.39

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.0053
                              CDC45 116 leeere.ayealeeeeesdeede..eeeeeddddeeeeeeeeedeedeeedeeeskkkrk 172
                                        +e+e e ++e+++++  +d +d+  ++++++d+d+++++ ++++++d++++++++++ r 
  gene1283|gene1283|rna1283|rna1283  46 FEKECEkEFEEVDNKGRDDVKDNkgKDNKDKDNDTKDKSINDKSTRDNDASGNDESSTRL 105
                                        222222122222222222211111122222222222222222222222222222222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (293 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1238  (0.0690501); expected 358.6 (0.02)
Passed bias filter:                      612  (0.0341346); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.44
# Mc/sec: 1990.27
//
Query:       gene1284|gene1284|rna1284|rna1284  [L=476]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.4e-25   88.4   0.1    1.3e-24   87.1   0.0    1.7  2  RFC1      Replication factor RFC1 C terminal domain
    3.1e-10   40.6   0.0    8.2e-10   39.2   0.0    1.7  1  AAA       ATPase family associated with various cellular acti
    0.00014   21.9   0.0    0.00026   21.0   0.0    1.4  1  Rad17     Rad17 P-loop domain
     0.0067   15.8   0.1      0.024   14.0   0.0    1.9  3  AAA_8     P-loop containing dynein motor region D4
     0.0081   15.9   0.0       0.62    9.8   0.0    2.3  2  DEAD      DEAD/DEAH box helicase
  ------ inclusion threshold ------
      0.012   16.0   0.0       0.03   14.7   0.0    1.7  1  AAA_16    AAA ATPase domain
      0.021   15.1   0.1       0.51   10.6   0.1    2.5  2  AAA_22    AAA domain
      0.032   14.3   0.0      0.096   12.7   0.0    1.8  1  AAA_14    AAA domain
      0.045   12.9   0.0       0.12   11.6   0.0    1.7  2  DUF815    Protein of unknown function (DUF815)
      0.063   13.8   0.2        5.8    7.4   0.0    2.9  3  ABC_tran  ABC transporter
      0.073   13.5   0.0         16    6.0   0.0    2.6  2  FaeA      FaeA-like protein


Domain annotation for each model (and alignments):
>> RFC1  Replication factor RFC1 C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       3.9   6.4e+03      10      27 ..     253     271 ..     227     302 .. 0.64
   2 !   87.1   0.0   8.1e-28   1.3e-24       1     157 []     326     465 ..     326     465 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 3.9
                                        HHTT.SS-GGGHHHHHHHH CS
                               RFC1  10 kirs.eqnWsLlpthavls 27 
                                        ki++  q+++++p++   +
  gene1284|gene1284|rna1284|rna1284 253 KIETfFQDYEMMPMMVYEN 271
                                        4444456666666554443 PP

  == domain 2  score: 87.1 bits;  conditional E-value: 8.1e-28
                                        HHHHHHHHHHHTTSS-GGGHHHHHHHHTHHHHHTT-EE-SS-----SHHHHHHHHHHHHHHHHHHHTTTTT----- CS
                               RFC1   1 isdgDlvdkkirseqnWsLlpthavlssvlPaslvrgslegrisFpswLGknSktnKnkRllqelqshlrlktsas 76 
                                        is +D   +k+ ++++WsLl+++av+ +++Pa+ ++   ++ri+Fp++LG+ Sk nK+++++q++++h+   ++++
  gene1284|gene1284|rna1284|rna1284 326 ISLADTYLRKM-GSNDWSLLNQYAVFGALIPAQNIKI--NRRIEFPKILGNTSKGNKHNKIIQTFHFHI--LSRCD 396
                                        67777777776.489********************96..66************************9999..67889 PP

                                        -HHHHHTTTHHHHHHHHS---------HHHHHHTTT--SHHHHHHHHHH-X...XXXXXXXXXXXXXXXXXXXXXX CS
                               RFC1  77 kselrldylpllkkklvkpLkeegkdgveevielmdeysLtkedvdslvelslvkgekkkedplkkidtkvKaaft 152
                                         +e+ ++ +pll k+++ +L++    ++++ ++++ e +L k d d  +++  +   +      k+++tk K+a+t
  gene1284|gene1284|rna1284|rna1284 397 PTEFYFYDMPLLIKTYIANLND---GHIDKNVQFLVENKLLKSDCDDGMSVYGW---E------KNVSTKGKSAMT 460
                                        99********************...36********************9***999...3......59********** PP

                                        XXXXX CS
                               RFC1 153 rkynk 157
                                        r+y+k
  gene1284|gene1284|rna1284|rna1284 461 RAYKK 465
                                        ***97 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.2   0.0     5e-13   8.2e-10       1     115 [.      67     165 ..      67     179 .. 0.88

  Alignments for each domain:
  == domain 1  score: 39.2 bits;  conditional E-value: 5e-13
                                        EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTT CS
                                AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksrsg 76 
                                        +l+ GppG+GK+l++k  + ++  e+ e+++s++++k  g  ++++r++++ a  + k   l++DE d ++++r  
  gene1284|gene1284|rna1284|rna1284  67 LLIAGPPGVGKSLCVKLACASTVYEMTEFNASDVRNK--GSLSERVRQFVNCACISGKRRALVMDECDGMTGDR-- 138
                                        5899*******************************88..9***********998887669**************.. PP

                                        CCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGS CS
                                AAA  77 seseeeervvnqLlteldgvkkkeskvivigatnrpdkl 115
                                                 +++L++ +++ +       vi+++n+   +
  gene1284|gene1284|rna1284|rna1284 139 -------GGMPELVQIIKNARM-----PVICICNDKYAV 165
                                        .......779999999998877.....688888876555 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   1.6e-07   0.00026       6      76 ..      29      95 ..      24     118 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 1.6e-07
                              Rad17  6 nelWfekykPekaeelavhkkkieevkewlkadvLesrkkriLLisGPsGCgkstvvkvLskelgiklrew 76
                                       + lW  ky P  ++e+   k   e++  +l+ ++      + LLi+GP+G gks  vk      ++++ e+
  gene1284|gene1284|rna1284|rna1284 29 GTLWTVKYEPRSLDEVLGNKTAKEHILSFLEQHTP----GKALLIAGPPGVGKSLCVKLACASTVYEMTEF 95
                                       678*************9999988888887776554....446*****************999999999886 PP

>> AAA_8  P-loop containing dynein motor region D4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.0   1.4e-05     0.024      25      90 ..      64     130 ..      52     137 .. 0.88
   2 ?   -3.4   0.0         3   4.9e+03     115     145 ..     177     207 ..     175     222 .. 0.63
   3 ?   -2.8   0.0       1.9   3.2e+03      42      69 ..     253     280 ..     246     295 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.4e-05
                              AAA_8  25 ghaLlv.GvgGsGrqsltkLAafiaelelfqievtkkykekefredlkkllkkagikqkevvfllsd 90 
                                        g+aLl+ G  G G+  ++kLA+  + +e+ +++ +   ++ +  e ++++++ a+i +k+  +++++
  gene1284|gene1284|rna1284|rna1284  64 GKALLIaGPPGVGKSLCVKLACASTVYEMTEFNASDVRNKGSLSERVRQFVNCACISGKRRALVMDE 130
                                        555555499*************************************************999988876 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 3
                              AAA_8 115 fskeekeeiieelrkeakkqgvedskeslln 145
                                        f k e+ +i+ ++r+ +k+++ + + +++++
  gene1284|gene1284|rna1284|rna1284 177 FRKLETRQILGRIRDILKSEHRAVTDKEIVE 207
                                        5666777777777777777766666555554 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 1.9
                              AAA_8  42 kLAafiaelelfqievtkkykekefred 69 
                                        k+ +f +++e++ ++v ++y ++e red
  gene1284|gene1284|rna1284|rna1284 253 KIETFFQDYEMMPMMVYENYLRSEVRED 280
                                        6778888999999999999988888876 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.0   0.00038      0.62      12      42 ..      62      92 ..      48     115 .. 0.80
   2 ?    3.8   0.0     0.027        44     122     141 ..     123     143 ..     105     159 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00038
                                       HTTCEEEEEESTTSSHHHHHHHHHHHHHHHS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               DEAD 12 lgggdvlvaaeTGsGKTlaflipvlqivyet 42
                                         g+ +l+a++ G GK+l+  +++ ++vye+
  gene1284|gene1284|rna1284|rna1284 62 TPGKALLIAGPPGVGKSLCVKLACASTVYEM 92
                                       47899************************97 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.027
                                        EEEEEEETHHHHHHT.TTHHH CS
                                        xxxxxxxxxxxxxxx.xxxxx RF
                               DEAD 122 vrflVlDEadrlldq.gfsdf 141
                                         r lV+DE+d++  + g  ++
  gene1284|gene1284|rna1284|rna1284 123 RRALVMDECDGMTGDrGGMPE 143
                                        588*********987544444 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   1.9e-05      0.03      12      45 ..      54      85 ..      46     132 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.9e-05
                             AAA_16 12 Llsalervrsgrp.elvllsGesGvGKsslvrell 45
                                       +ls le   +++p  ++l+ G++GvGKs  v+ + 
  gene1284|gene1284|rna1284|rna1284 54 ILSFLE---QHTPgKALLIAGPPGVGKSLCVKLAC 85
                                       444444...5555599*************998765 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   0.00031      0.51       5      23 ..      64      82 ..      60      89 .. 0.87
   2 ?    1.0   0.0      0.28   4.6e+02      75     112 ..     107     144 ..      87     161 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00031
                             AAA_22  5 agilvvtGesGtGKTtllr 23
                                        + l++ G++G+GK+++++
  gene1284|gene1284|rna1284|rna1284 64 GKALLIAGPPGVGKSLCVK 82
                                       57899***********998 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.28
                             AAA_22  75 seellealeqalraravielliiDEaqhlr.seealeeL 112
                                        se++++ ++ a+ + ++ ++l+ DE + ++     + eL
  gene1284|gene1284|rna1284|rna1284 107 SERVRQFVNCACISGKR-RALVMDECDGMTgDRGGMPEL 144
                                        44444555555666666.9********996523333333 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   5.9e-05     0.096       3      76 ..      65     134 ..      63     157 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5.9e-05
                             AAA_14   3 kilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelilek.lkeekktylflDEiqev 76 
                                        k+l+i G+  vGK+  +k    +      ++ ++n  d r+k +  + ++ +++    +++ k++ l++DE   +
  gene1284|gene1284|rna1284|rna1284  65 KALLIAGPPGVGKSLCVKLACASTV---YEMTEFNASDVRNKGSLSE-RVRQFVNCAcISG-KRRALVMDECDGM 134
                                        899**************99998888...89***********987755.4555555555666.8999*****8765 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   7.1e-05      0.12       5      77 ..      19      88 ..      15     118 .. 0.76
   2 ?   -3.6   0.0       3.1   5.1e+03      95     115 ..     141     161 ..     139     161 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 7.1e-05
                             DUF815  5 afrwee.keegalepveevdevklddLvgidkqkealventeqfleglpannvLLwGarGtGKSslvkallney 77
                                       a+++ + ++ g+l +v ++++ +ld++ g ++ ke++++  eq+    p + +L+ G  G+GKS +vk + +++
  gene1284|gene1284|rna1284|rna1284 19 AYNYADeSNYGTLWTV-KYEPRSLDEVLGNKTAKEHILSFLEQHT---PGKALLIAGPPGVGKSLCVKLACAST 88
                                       7777764455557777.5678899********9999998777665...5567999*************876554 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 3.1
                             DUF815  95 lpklvellrerperfilfvDD 115
                                        +p+lv++++++++ +i  + D
  gene1284|gene1284|rna1284|rna1284 141 MPELVQIIKNARMPVICICND 161
                                        799**********99999988 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.0    0.0036       5.8      10      32 ..      63      85 ..      59      98 .. 0.86
   2 ?   -0.6   0.0       1.1   1.8e+03      95     135 ..      93     131 ..      84     132 .. 0.74
   3 ?    2.5   0.0      0.12     2e+02      58      80 ..     251     294 ..     224     342 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0036
                                       TTSEEEEEESTTSSHHHHHHHHT CS
                                       xxxxxxxxxxxxxxxxxxxxxxx RF
                           ABC_tran 10 egekvaivGenGaGKStLlklla 32
                                       +g+ + i G+ G GKS  +kl +
  gene1284|gene1284|rna1284|rna1284 63 PGKALLIAGPPGVGKSLCVKLAC 85
                                       7999************9999866 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.1
                                        GGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEEST CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ABC_tran  95 kelkdtvvksspssLSgGqkqrvalarallkkpkllllDEp 135
                                        +e++++ v +++ sLS+  +q v  ++++  k++ l++DE+
  gene1284|gene1284|rna1284|rna1284  93 TEFNASDV-RNKGSLSERVRQFVN-CACISGKRRALVMDEC 131
                                        55555666.566788888888887.5688999999999996 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.12
                                        CHCEEEE-SS--S-TTSBHHHH......................H CS
                                        xxxxxxxxxxxxxxxxxxxxxx......................x RF
                           ABC_tran  58 rkeigvlpqepqlfpeltvren......................e 80 
                                         ++i++++q+ ++ p + v+en                      +
  gene1284|gene1284|rna1284|rna1284 251 AEKIETFFQDYEMMPMM-VYENylrsevredghvkkdrvnahkhN 294
                                        67999************.99*988776665554433332222220 PP

>> FaeA  FaeA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0    0.0096        16       2      26 ..      51      74 ..      50      77 .. 0.86
   2 ?    4.6   0.1     0.026        42      11      48 ..     191     232 ..     182     236 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0096
                                       HHHHHHHHHH.S----HHHHHHHHT CS
                               FaeA  2 keeIleylnsikapckTreiAdalg 26
                                       ke+Il++l + ++p+k   iA   g
  gene1284|gene1284|rna1284|rna1284 51 KEHILSFLEQ-HTPGKALLIAGPPG 74
                                       9*********.*****988886655 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.026
                                        H.....S----HHHHHHHHTS-HHHHHHHHHHHHHHSSEEEE CS
                               FaeA  11 si....kapckTreiAdalglsaYQaRyYLeqLekegkikrs 48 
                                        +i    + +++ +ei +  +++    Ry L++L+   +  ++
  gene1284|gene1284|rna1284|rna1284 191 DIlkseHRAVTDKEIVEVCAMANNDMRYILNCLQGRVMYTKV 232
                                        445555889999*********************987777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (476 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       670  (0.0373696); expected 358.6 (0.02)
Passed bias filter:                      476  (0.0265492); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.43
# Mc/sec: 3344.37
//
Query:       gene1285|gene1285|rna1285|rna1285  [L=88]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       370  (0.020637); expected 358.6 (0.02)
Passed bias filter:                      216  (0.0120475); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.30s 00:00:00.71 Elapsed: 00:00:00.46
# Mc/sec: 573.09
//
Query:       gene1286|gene1286|rna1286|rna1286  [L=361]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      2e-11   44.6   0.0    4.1e-11   43.6   0.0    1.5  1  2OG-FeII_Oxy_3  2OG-Fe(II) oxygenase superfamily
    1.3e-10   41.8   0.1    3.2e-10   40.5   0.1    1.7  1  2OG-FeII_Oxy_4  2OG-Fe(II) oxygenase superfamily
  ------ inclusion threshold ------
      0.032   14.5   0.7       0.88    9.9   0.1    3.5  2  WG_beta_rep     WG containing repeat


Domain annotation for each model (and alignments):
>> 2OG-FeII_Oxy_3  2OG-Fe(II) oxygenase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.6   0.0   6.9e-15   4.1e-11       4      95 ..     107     190 ..     104     191 .. 0.89

  Alignments for each domain:
  == domain 1  score: 43.6 bits;  conditional E-value: 6.9e-15
                                        EEE-TT-EEEEE-SS----TT.-.EEEEEEEEE....ET-B--EEE............---TT-EEEEE-..B-TE CS
                     2OG-FeII_Oxy_3   4 lrygegqeykpHvDnfekeegsgqrrltvllyLnekeseeGGelelyekdk..eavkikpkkgrlvlFesdellpH 77 
                                        + y++g+++ +H+D +      ++r++++ +yLn   +++ Gel l++++   e ++i  kk+r+v+Fe++e + H
  gene1286|gene1286|rna1286|rna1286 107 SYYDTGHYLLCHDDLI------EDRKYAFSFYLN---DFTSGELILFNEKAneEVERIDVKKNRIVIFEVSEKSFH 173
                                        567999********86......56*********7...7999*****99998998899999**********98888* PP

                                        EE--B.-SS-EEEEEEEE CS
                     2OG-FeII_Oxy_3  78 evlpvtkggeRlsltgwi 95 
                                        ev+  t++  R ++tgw+
  gene1286|gene1286|rna1286|rna1286 174 EVNLCTQS-GRKAFTGWY 190
                                        ****9875.9*******8 PP

>> 2OG-FeII_Oxy_4  2OG-Fe(II) oxygenase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.5   0.1   5.3e-14   3.2e-10       3      92 ..     106     190 ..     104     191 .. 0.89

  Alignments for each domain:
  == domain 1  score: 40.5 bits;  conditional E-value: 5.3e-14
                     2OG-FeII_Oxy_4   3 vssYekgdvllnHdDvlegeRrvayilyleeeWkeddGGaL.llsddegdvtksivPkwnqlvlFevkeshsvaev 77 
                                        +s Y +g +ll+HdD  +++R+ a+ +yl++     + G+L l+++++++ +++i  k n++v+Fev +++s++ev
  gene1286|gene1286|rna1286|rna1286 106 ASYYDTGHYLLCHDDL-IEDRKYAFSFYLNDF----TSGELiLFNEKANEEVERIDVKKNRIVIFEV-SEKSFHEV 175
                                        5789************.899999******853....4577769999999999***************.56899999 PP

                     2OG-FeII_Oxy_4  78 asvaekeRlsisgWf 92 
                                        +  ++  R + +gW+
  gene1286|gene1286|rna1286|rna1286 176 NLCTQSGRKAFTGWY 190
                                        99999*********8 PP

>> WG_beta_rep  WG containing repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.1      0.17     1e+03      19      31 ..     274     287 ..     263     289 .. 0.72
   2 ?    9.9   0.1   0.00015      0.88       2      18 ..     313     329 ..     312     340 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.17
                        WG_beta_rep  19 agsFs.eGlaaVkk 31 
                                         + F+ +++++Vk+
  gene1286|gene1286|rna1286|rna1286 274 FYEFNaNNYILVKE 287
                                        45586368****96 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00015
                        WG_beta_rep   2 GyiDknGkivippkYdd 18 
                                         yiDknG+ v+  k+++
  gene1286|gene1286|rna1286|rna1286 313 TYIDKNGNAVFSLKFEN 329
                                        7*************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (361 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       723  (0.0403257); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2711.80
//
Query:       gene1287|gene1287|rna1287|rna1287  [L=489]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.5e-08   33.0   0.9    0.00064   19.0   0.3    3.0  3  NAD_kinase  ATP-NAD kinase


Domain annotation for each model (and alignments):
>> NAD_kinase  ATP-NAD kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.0   1.6e-05      0.29      76      97 ..      23      44 ..      14      50 .. 0.85
   2 ?   -0.1   0.0     0.024   4.3e+02     197     209 ..     270     312 ..     185     314 .. 0.64
   3 !   19.0   0.3   3.6e-08   0.00064     189     266 ..     376     449 ..     324     456 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 1.6e-05
                                       TTSSSEEEEEE-HHHHHHHHHH CS
                         NAD_kinase 76 dagvdliivvGGDGTaldvarl 97
                                       ++++  +iv+GGDGT+l++  +
  gene1287|gene1287|rna1287|rna1287 23 KSDAPNVIVLGGDGTFLSACGM 44
                                       678889***********99765 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.024
                                        ESEE..............................EEE-TGGGG CS
                         NAD_kinase 197 ldgl..............................ivstPtGst 209
                                        +++                               + ++PtG+t
  gene1287|gene1287|rna1287|rna1287 270 CSNCcssncnccncdsnccdecircrccdecsnkCSISPTGGT 312
                                        4444444555555555555555555555555555999999988 PP

  == domain 3  score: 19.0 bits;  conditional E-value: 3.6e-08
                                        TEEEEEEEESEEEEE-TGGGGTHHHHTT--EE-TT---EEEEEESESSS----EEE-TT-EEEEEE-SS--EEEEE CS
                         NAD_kinase 189 telleadqldglivstPtGstayslsaGgplisPgvlailivpicPhslssrpiVvssssklrirvasrseallal 264
                                        +++ +++ +d++++st tGs ay  sa gp+   +     i  i+P+  s   +Vv+ ++++r+rv  +++ + ++
  gene1287|gene1287|rna1287|rna1287 376 NTFKFTIKCDSILISTQTGSSAYNRSAKGPIALMQCHI--INFINPA-HSTNALVVDIRRTIRVRVL-THNGMGVI 447
                                        45667899**********************97555444..6667775.67899**********9976.45555555 PP

                                        TT CS
                         NAD_kinase 265 dG 266
                                        dG
  gene1287|gene1287|rna1287|rna1287 448 DG 449
                                        55 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (489 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1460  (0.0814323); expected 358.6 (0.02)
Passed bias filter:                      256  (0.0142785); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.45
# Mc/sec: 3291.07
//
Query:       gene1288|gene1288|rna1288|rna1288  [L=395]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.28   11.1   2.4       0.74    9.7   2.4    1.7  1  DUF1381   Protein of unknown function (DUF1381)
        7.1    5.8   4.7         13    4.9   4.7    1.3  1  TMPIT     TMPIT-like protein


Domain annotation for each model (and alignments):
>> DUF1381  Protein of unknown function (DUF1381)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   2.4   8.3e-05      0.74      25      43 ..     110     128 ..     106     129 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 8.3e-05
                            DUF1381  25 nqtFtvvEAEskEEAkEkY 43 
                                        n    vv+ Es+EEAkE Y
  gene1288|gene1288|rna1288|rna1288 110 NVEEQVVDNESQEEAKEDY 128
                                        555679***********99 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   4.7    0.0015        13       6      64 ..     286     344 ..     281     359 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.0015
                              TMPIT   6 elekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeee 64 
                                        ++++ +++l++  ke+++k ++ +kl ++ +++ ++q+   +e +s+lk+  k+ +e++
  gene1288|gene1288|rna1288|rna1288 286 QVKEAVRKLNKLVKEMEEKNRSKQKLMDDRKRKKESQRSASRERQSNLKSNAKNENEQK 344
                                        67888999999999999999999999999999999999999999999999888865544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (395 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2686  (0.149813); expected 358.6 (0.02)
Passed bias filter:                      808  (0.0450667); expected 358.6 (0.02)
Passed Vit filter:                       168  (0.00937029); expected 17.9 (0.001)
Passed Fwd filter:                        54  (0.00301188); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 1.27u 0.38s 00:00:01.65 Elapsed: 00:00:00.52
# Mc/sec: 2283.96
//
Query:       gene1289|gene1289|rna1289|rna1289  [L=243]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.7e-09   37.9   4.0      3e-09   37.1   4.0    1.4  1  zf-RING_2      Ring finger domain
    2.3e-07   30.6   4.6    3.9e-07   29.8   4.6    1.4  1  zf-C3HC4_2     Zinc finger, C3HC4 type (RING finger)
    2.5e-07   30.5   2.2    4.4e-07   29.6   2.2    1.4  1  zf-C3HC4_3     Zinc finger, C3HC4 type (RING finger)
    1.1e-06   28.5   2.4    1.2e-06   28.5   1.3    1.7  1  zf-RING_UBOX   RING-type zinc-finger
    7.5e-06   26.1   4.5    2.3e-05   24.6   4.5    1.8  1  zf-rbx1        RING-H2 zinc finger domain
    5.8e-05   22.9   3.7     0.0001   22.1   3.7    1.4  1  zf-C3HC4       Zinc finger, C3HC4 type (RING finger)
    6.1e-05   23.0   0.4     0.0001   22.3   0.4    1.3  1  zf-ANAPC11     Anaphase-promoting complex subunit 11 RING-H2 
     0.0004   20.3   2.6    0.00067   19.6   2.6    1.4  1  zf-RING_5      zinc-RING finger domain
     0.0026   17.6   4.6      0.026   14.4   0.2    2.3  2  Prok-RING_4    Prokaryotic RING finger family 4
     0.0074   16.4   0.1      0.013   15.6   0.1    1.6  1  TerY_C         TerY-C metal binding domain
  ------ inclusion threshold ------
       0.01   15.5   0.6      0.014   15.2   0.6    1.1  1  Laminin_I      Laminin Domain I
      0.062   13.2   3.8       0.74    9.8   0.1    2.4  2  Cys_rich_CPXG  Cysteine-rich CPXCG
      0.071   12.9   0.8       0.19   11.5   0.8    1.8  1  zf-RING_11     RING-like zinc finger
       0.31   11.3   3.7        5.3    7.4   0.2    2.6  2  zf-Di19        Drought induced 19 protein (Di19), zinc-bindin
        1.2    9.3   7.9        2.6    8.3   7.9    1.6  1  zf-C3HC4_4     zinc finger of C3HC4-type, RING
        1.7    8.5  10.5        3.2    7.6   9.3    2.0  2  zf-RING_4      RING/Ubox like zinc-binding domain
        7.5    6.8   8.5    1.4e+03   -0.5   8.5    3.3  1  FANCL_C        FANCL C-terminal domain


Domain annotation for each model (and alignments):
>> zf-RING_2  Ring finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.1   4.0   2.8e-12     3e-09       2      44 .]     189     227 ..     188     227 .. 0.91

  Alignments for each domain:
  == domain 1  score: 37.1 bits;  conditional E-value: 2.8e-12
                          zf-RING_2   2 eCpICleelssadsvlllpCgHvfhreClerwlrssstCPlCr 44 
                                        eCpIC+e+++    ++ +pCgH +   Cl +w+ +++tCP+Cr
  gene1289|gene1289|rna1289|rna1289 189 ECPICYEDYD----LVYTPCGHGYQLPCLYKWMLEKRTCPYCR 227
                                        9****97774....77778***********************9 PP

>> zf-C3HC4_2  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8   4.6   3.7e-10   3.9e-07       1      40 []     189     226 ..     189     226 .. 0.96

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 3.7e-10
                         zf-C3HC4_2   1 kCpiCldmlkdpsvvtpCgHvfCqkCilrsLeekneCPlC 40 
                                        +CpiC++ +   +v tpCgH++   C+ +++ ek  CP C
  gene1289|gene1289|rna1289|rna1289 189 ECPICYEDYD--LVYTPCGHGYQLPCLYKWMLEKRTCPYC 226
                                        6********9..59************************** PP

>> zf-C3HC4_3  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6   2.2   4.2e-10   4.4e-07       3      46 ..     188     229 ..     184     231 .. 0.92

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 4.2e-10
                                        SB-TTTSSSBS-EEETTEEEEEE-HHHHHHHHHTT-B-TTT--B CS
                         zf-C3HC4_3   3 eeCviClerprnvvllpCgHlvlCeeCaekllkrkkkCpiCrrp 46 
                                        +eC+iC+e + + v+ pCgH  +   C+ k++ +k++Cp+Cr++
  gene1289|gene1289|rna1289|rna1289 188 SECPICYE-DYDLVYTPCGHG-YQLPCLYKWMLEKRTCPYCREK 229
                                        69*****7.68999*******.99*******99*********97 PP

>> zf-RING_UBOX  RING-type zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.5   1.3   1.1e-09   1.2e-06       1      39 []     190     224 ..     190     224 .. 0.86

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 1.1e-09
                       zf-RING_UBOX   1 CpIClelftdPlvlpCGHtFCreClwelskslegafkCP 39 
                                        CpIC+e+++    +pCGH +  +Cl    k+   +++CP
  gene1289|gene1289|rna1289|rna1289 190 CPICYEDYDLV-YTPCGHGYQLPCL---YKWMLEKRTCP 224
                                        ********744.457**********...78888899998 PP

>> zf-rbx1  RING-H2 zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   4.5   2.1e-08   2.3e-05      11      55 .]     187     227 ..     174     227 .. 0.81

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 2.1e-08
                            zf-rbx1  11 eeacieckapgdeecpvvlGeCgHaFHlhCiskWlktrkvCPlcr 55 
                                        +++c+ c ++      +v   CgH + l C+ kW+ ++++CP cr
  gene1289|gene1289|rna1289|rna1289 187 SSECPICYED----YDLVYTPCGHGYQLPCLYKWMLEKRTCPYCR 227
                                        4556666544....446889************************8 PP

>> zf-C3HC4  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   3.7   9.8e-08    0.0001       1      41 []     190     226 ..     190     226 .. 0.95

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 9.8e-08
                                        -TTT-S--SS-E.E-TTS--B-CHHHHHHHHCTSSB--TTT CS
                           zf-C3HC4   1 CpiCleeakepnelleCkHsfCskCirkilksrkkvkCPlC 41 
                                        CpiC e +      ++C+H +  +C+ k++   +k++CP C
  gene1289|gene1289|rna1289|rna1289 190 CPICYEDYDLV--YTPCGHGYQLPCLYKWML--EKRTCPYC 226
                                        *******9885..5*****************..999****9 PP

>> zf-ANAPC11  Anaphase-promoting complex subunit 11 RING-H2 finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.4   9.5e-08    0.0001      21      80 ..     176     229 ..     155     232 .. 0.82

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 9.5e-08
                                        SSB-TTT-SBTTS--TTCSTTTTTS-EEEBTTS-EEEHHHHHHHHHHHSTSSB-TTTSSB CS
                         zf-ANAPC11  21 ddvcGicrvsfdGtcpsckfpGddcplvlGkckhnfhlhcilkwletetskglcpmcrqt 80 
                                        d++ G     +   cp c    +d  lv+  c h + l c++kw+ +   k  cp cr++
  gene1289|gene1289|rna1289|rna1289 176 DEISGKRSKRYSSECPICY---EDYDLVYTPCGHGYQLPCLYKWMLE---KRTCPYCREK 229
                                        7888888889999999997...6788******************975...678*****86 PP

>> zf-RING_5  zinc-RING finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   2.6   6.3e-07   0.00067       1      43 [.     189     227 ..     189     228 .. 0.96

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 6.3e-07
                          zf-RING_5   1 hCnkCfeklskeekfyltsCgHifCekClkkllekeavCpiCr 43 
                                        +C++C+e +    + + t+CgH +   Cl k + ++++Cp Cr
  gene1289|gene1289|rna1289|rna1289 189 ECPICYEDY----DLVYTPCGHGYQLPCLYKWMLEKRTCPYCR 227
                                        6********....********************9********9 PP

>> Prok-RING_4  Prokaryotic RING finger family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.6     0.021        22      29      38 ..     185     195 ..     173     198 .. 0.72
   2 !   14.4   0.2   2.4e-05     0.026      12      40 ..     200     230 ..     195     236 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.021
                        Prok-RING_4  29 dls.sCPlCqr 38 
                                         +s  CP+C +
  gene1289|gene1289|rna1289|rna1289 185 RYSsECPICYE 195
                                        44449****75 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 2.4e-05
                        Prok-RING_4  12 ilepCgHlvCkeCfdskdls..sCPlCqrri 40 
                                        +  pCgH     C+ ++ l+  +CP C++++
  gene1289|gene1289|rna1289|rna1289 200 VYTPCGHGYQLPCLYKWMLEkrTCPYCREKL 230
                                        668**************66666******997 PP

>> TerY_C  TerY-C metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1   1.2e-05     0.013      74     124 ..     187     242 ..     146     243 .] 0.89

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.2e-05
                             TerY_C  74 apgCPhCgnalafavCeCg...kllCidg..eeeatCpwCgkevkfgeaseegfdv 124
                                         ++CP C + + ++   Cg   +l C+ +   e+ tCp C++++  + +  +g+d+
  gene1289|gene1289|rna1289|rna1289 187 SSECPICYEDYDLVYTPCGhgyQLPCLYKwmLEKRTCPYCREKLLPDVDPADGLDI 242
                                        579************9999555699*99866899********99988888888887 PP

>> Laminin_I  Laminin Domain I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.6   1.3e-05     0.014      17     111 ..      58     154 ..      52     165 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.3e-05
                          Laminin_I  17 inanledltkeLqeklskesakkskieilekelesLaqeteeLqkkatqvlakaqkvnaesertlnnakeLaekik 92 
                                        + + l   +ke++e l  ++ + + ++++     +L+ ++e++ k+ + v +   k++   +    + ++L + +k
  gene1289|gene1289|rna1289|rna1289  58 LRS-LSSGKKEFNELLLDYQIRYQILKNQSDDHPDLKDDFENYLKEIVLVFRMLYKLRTSDNYSYVKMEKLSADVK 132
                                        544.777899****************************************************************** PP

                          Laminin_I  93 kladnikeilekvatlne...n 111
                                        k+ ++++++ +k  ++n    +
  gene1289|gene1289|rna1289|rna1289 133 KMLESAEALFNKGIKTNRtkhE 154
                                        ************9999884322 PP

>> Cys_rich_CPXG  Cysteine-rich CPXCG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.8     0.053        56      17      31 ..     179     194 ..     172     202 .. 0.76
   2 ?    9.8   0.1    0.0007      0.74       2      19 ..     222     239 ..     222     243 .] 0.88

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.053
                      Cys_rich_CPXG  17 sag.dqeYieDCqvCC 31 
                                        s++ +++Y  +C++C 
  gene1289|gene1289|rna1289|rna1289 179 SGKrSKRYSSECPICY 194
                                        5566888999999995 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0007
                      Cys_rich_CPXG   2 qCPyCgeeievlvDlsag 19 
                                        +CPyC e++  +vD  +g
  gene1289|gene1289|rna1289|rna1289 222 TCPYCREKLLPDVDPADG 239
                                        5************99887 PP

>> zf-RING_11  RING-like zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.8   0.00018      0.19       1      28 [.     189     212 ..     189     213 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00018
                         zf-RING_11   1 eCsICLeefkpgqalfilpCsHtFHfkC 28 
                                        eC IC e++     l+ +pC+H + + C
  gene1289|gene1289|rna1289|rna1289 189 ECPICYEDY----DLVYTPCGHGYQLPC 212
                                        8******99....56777******9999 PP

>> zf-Di19  Drought induced 19 protein (Di19), zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.5     0.049        52       4      13 ..     189     198 ..     172     206 .. 0.81
   2 ?    7.4   0.2     0.005       5.3       4      12 ..     222     230 ..     219     234 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.049
                            zf-Di19   4 tCPyCgkelt 13 
                                         CP C+++++
  gene1289|gene1289|rna1289|rna1289 189 ECPICYEDYD 198
                                        5777777765 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.005
                            zf-Di19   4 tCPyCgkel 12 
                                        tCPyC+++l
  gene1289|gene1289|rna1289|rna1289 222 TCPYCREKL 230
                                        9****9964 PP

>> zf-C3HC4_4  zinc finger of C3HC4-type, RING
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   7.9    0.0024       2.6       1      42 []     190     226 ..     190     226 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0024
                         zf-C3HC4_4   1 CPiCldYLekPvsleCGhsfClsCisslqkepdgeqllCplC 42 
                                        CPiC +   + v+ +CGh + l C+++++ e+     +Cp C
  gene1289|gene1289|rna1289|rna1289 190 CPICYEDY-DLVYTPCGHGYQLPCLYKWMLEK----RTCPYC 226
                                        ****8654.67******************999....469999 PP

>> zf-RING_4  RING/Ubox like zinc-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.8     0.059        62      35      48 .]     185     198 ..     173     198 .. 0.74
   2 ?    7.6   9.3     0.003       3.2       1      46 [.     190     229 ..     190     230 .. 0.73

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.059
                          zf-RING_4  35 eeegrCPaCreeYk 48 
                                        + +  CP C e+Y+
  gene1289|gene1289|rna1289|rna1289 185 RYSSECPICYEDYD 198
                                        45788999999996 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.003
                          zf-RING_4   1 cplCdeeldetdkdlkpCeCgyqiClfCyhrileeeegrCPaCree 46 
                                        cp+C e+    d   +pC  gyq  l C+ + +  e+  CP Cre+
  gene1289|gene1289|rna1289|rna1289 190 CPICYEDY---DLVYTPCGHGYQ--LPCLYKWM-LEKRTCPYCREK 229
                                        88898877...456777777787..56665666.3689******85 PP

>> FANCL_C  FANCL C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   8.5       1.3   1.4e+03      27      65 ..     203     230 ..     186     235 .. 0.62

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 1.3
                                        T----B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-SEE CS
                            FANCL_C  27 kCnkkfHsaCLkeWlrslkesrqsfdvlfGeCPyCkkki 65 
                                         C++ +   CL+ W+ + +           +CPyC++k+
  gene1289|gene1289|rna1289|rna1289 203 PCGHGYQLPCLYKWMLEKR-----------TCPYCREKL 230
                                        4777777778888876655...........477777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1125  (0.0627475); expected 358.6 (0.02)
Passed bias filter:                      648  (0.0361426); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.50
# Mc/sec: 1471.57
//
Query:       gene129|gene129|rna129|rna129  [L=101]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.027   14.5   0.9      0.038   14.0   0.9    1.2  1  DUF1803   Domain of unknown function (DUF1803)


Domain annotation for each model (and alignments):
>> DUF1803  Domain of unknown function (DUF1803)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.9   2.1e-06     0.038       5      65 ..      31      92 ..      27      95 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.1e-06
                        DUF1803  5 enkLtnqplF...keLieyLaehddviLRelkkeFadqkkldrlldelidaglikRenkrYkln 65
                                     kL++++l+   + L+++L+++ +  LR l ++F d ++l+  ld +id  lik e+ + + n
  gene129|gene129|rna129|rna129 31 DVKLSDDELYivvNRLLTFLHDK-RPFLRLLAQQFLDDPELNDRLD-IIDRTLIKEEEEKVEKN 92
                                   55888888873335799999876.568******************8.8*******999886655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       704  (0.039266); expected 358.6 (0.02)
Passed bias filter:                      440  (0.0245412); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.28s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 718.11
//
Query:       gene1290|gene1290|rna1290|rna1290  [L=247]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       697  (0.0388756); expected 358.6 (0.02)
Passed bias filter:                      489  (0.0272742); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 1540.04
//
Query:       gene1291|gene1291|rna1291|rna1291  [L=334]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.012   15.9   0.0      0.026   14.8   0.0    1.5  1  Ricin_B_lectin  Ricin-type beta-trefoil lectin domain


Domain annotation for each model (and alignments):
>> Ricin_B_lectin  Ricin-type beta-trefoil lectin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   1.5e-06     0.026      18      94 ..     122     196 ..     109     211 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.5e-06
                                        TCTTSTEBEEEEE-TSCCGGGEEEEE..TTSEEEETT.TTEEEEESSSSTTSBEEEEETTT..TSGGGCEE.EETT CS
                     Ricin_B_lectin  18 geskagapvglydChgskgkQlwtlt..kdgeirskaqselCldvsstaegakvvlakChk..gkgnqrWe.fdkd 88 
                                        +    + +++l++ hg+ + Q++ l+   +  i+++  +++C+++  +++ + ++  +C+   +k+ q+++ + k+
  gene1291|gene1291|rna1291|rna1291 122 R---SNYDLILFKKHGGWN-QQFVLEtvPRDMIKLRV-GDRCMTT--EKNMKYLTEVDCDTfsKKPGQFFKwISKK 190
                                        2...26799********99.99999988888899987.******7..78888888899988756669998844444 PP

                                        TTEEEE CS
                     Ricin_B_lectin  89 gtqirh 94 
                                         +++++
  gene1291|gene1291|rna1291|rna1291 191 DENVVR 196
                                        443554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (334 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       596  (0.0332422); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 2218.02
//
Query:       gene1292|gene1292|rna1292|rna1292  [L=200]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
        1.4    9.0   3.7       0.75    9.9   1.2    1.8  2  Defensin_beta  Beta defensin


Domain annotation for each model (and alignments):
>> Defensin_beta  Beta defensin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   1.2   4.2e-05      0.75      11      28 ..       1      18 [.       1      21 [. 0.93
   2 ?   -2.5   0.1      0.32   5.7e+03      12      21 ..     179     188 ..     178     190 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 4.2e-05
                                       EEEEST--TTSEEEEEEC CS
                      Defensin_beta 11 iCrpgrCpglerqiGtCs 28
                                       +C+ ++C+ ++  +GtC 
  gene1292|gene1292|rna1292|rna1292  1 VCSSNMCRAFMVCVGTCV 18
                                       6****************6 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.32
                                        EEEST--TTS CS
                      Defensin_beta  12 CrpgrCpgle 21 
                                        C++  C + e
  gene1292|gene1292|rna1292|rna1292 179 CSLELCLSEE 188
                                        9999998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1279  (0.0713369); expected 358.6 (0.02)
Passed bias filter:                      567  (0.0316247); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1411.39
//
Query:       gene1293|gene1293|rna1293|rna1293  [L=109]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       321  (0.017904); expected 358.6 (0.02)
Passed bias filter:                      216  (0.0120475); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 767.67
//
Query:       gene1294|gene1294|rna1294|rna1294  [L=465]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.9e-70  237.3   0.5    2.4e-70  236.9   0.5    1.1  1  Pkinase         Protein kinase domain
    1.1e-43  149.4   0.3    1.6e-43  148.9   0.3    1.1  1  Pkinase_Tyr     Protein tyrosine kinase
    1.8e-10   40.6   0.1    2.5e-10   40.1   0.1    1.2  1  Kinase-like     Kinase-like
    2.1e-05   24.0   0.2    3.8e-05   23.1   0.2    1.3  1  Kdo             Lipopolysaccharide kinase (Kdo/WaaP) family
    0.00048   19.8   1.5     0.0015   18.2   0.3    2.2  3  RIO1            RIO1 family
      0.001   19.4   2.6     0.0026   18.1   1.6    2.2  2  Imm41           Immunity protein 41
  ------ inclusion threshold ------
       0.01   14.6   0.1      0.015   14.1   0.1    1.2  1  Pkinase_fungal  Fungal protein kinase


Domain annotation for each model (and alignments):
>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  236.9   0.5   9.5e-74   2.4e-70       1     264 []      24     270 ..      24     270 .. 0.93

  Alignments for each domain:
  == domain 1  score: 236.9 bits;  conditional E-value: 9.5e-74
                                        EEEEEEEEEESSEEEEEEEETTTTEEEEEEEEECHCHCHHHH.HHHHHHHHHHHHHSCTTB--EEEEEEESSEEEE CS
                            Pkinase   1 yekleklGeGsfGkVykaveketgkivAvKkikkekakkkke.kkvlrEikilkklkhpnivrlyevfeekdelyl 75 
                                        y+  + lG+G+f+++y      t++  ++K++k+++ ++++  +k+ +Ei i +++ hpniv+l ++f+++++++l
  gene1294|gene1294|rna1294|rna1294  24 YTLTKFLGKGAFAQCYA-----TDDNLCLKILKRSELTSDRLrEKLSTEICIQRSVTHPNIVKLHNTFSTDEHIVL 94 
                                        667889******99885.....55899999999999888777799******************************* PP

                                        EEE--TTEBHHHHHHHHSS--HHHHHHHHHHHHHHHHHHHHTTEE-SS-SGGGEEEETTTEEEE-SGTTSEESSSS CS
                            Pkinase  76 vleyveggeladllerkgslseeeakkiakqilegleylHskgiiHrDlKpeNiLidekgelKitDFGlakeless 151
                                        v+e+++ + l dll++++ + e++++ +++qi+++++ylHs +++HrDlK +NiL++ +  +K++DFGl++ ++++
  gene1294|gene1294|rna1294|rna1294  95 VMELCDST-LSDLLKQNKRIRESHTRTFLRQIVSAMAYLHSVNVVHRDLKLSNILLK-NFTVKVADFGLCALINNK 168
                                        ******66.************************************************.999*************** PP

                                        CSBCTTTSCGGGS-HHHHTTSCBSHHHHHHHHHHHHHHHHHSS-STTTSSHHHHHHHHHHTHHHHHHHCTSHH... CS
                            Pkinase 152 skltsfvgtseYlAPEvlkeneyskkvDvWslGvilyelltgkppfsgekgkekvekeldqlekilkilgetkekl 227
                                        +k t+++gt++Y+APE++++  ys ++D+WslGv++y++l g+ppf++++ ke ++++           + ++ k+
  gene1294|gene1294|rna1294|rna1294 169 NKRTTVCGTPNYIAPEIINKVAYSFECDLWSLGVMVYTMLVGTPPFQKKTAKEIYNTI-----------KRNEYKI 233
                                        ***********************************************55555533333...........34589** PP

                                        HHHTTS-HHHHHHHHHHT-SSGCCSTTHHHHHTSGGG CS
                            Pkinase 228 peaseiseeakdllkkllkkdpkkRltaeellqhpyl 264
                                        pe++ iseeakdl+++ll  dp+kRl+ +e+ +hp++
  gene1294|gene1294|rna1294|rna1294 234 PENTLISEEAKDLIQRLLITDPHKRLSLKEIEKHPFF 270
                                        ************************************8 PP

>> Pkinase_Tyr  Protein tyrosine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  148.9   0.3   6.1e-47   1.6e-43       3     257 ..      26     266 ..      24     267 .. 0.90

  Alignments for each domain:
  == domain 1  score: 148.9 bits;  conditional E-value: 6.1e-47
                                        EEEEEEEESSEEEEEEEEETTTTSSEEEEEEEEESTTSSHHH..HHHHHHHHHHHHTS-BTTB--EEEEEESSSSE CS
                        Pkinase_Tyr   3 lgkklGeGafGkVvegtlkgekekkevkVavKtlkeeateee..keelleeakimkklkhpnivkllgvctkeepl 76 
                                        l+k lG+Gaf++ +    +           +K+lk++   ++  +e+l +e+ i +++ hpnivkl+   + +e++
  gene1294|gene1294|rna1294|rna1294  26 LTKFLGKGAFAQCYATDDN---------LCLKILKRSELTSDrlREKLSTEICIQRSVTHPNIVKLHNTFSTDEHI 92 
                                        6678899999887755444.........7788886544333324999***************************** PP

                                        EEEEE--TTEBHHHHHHHTCTTTSBHHHHHHHHHHHHHHHHHHHHTTEEEST-SGGGEEEEETTEEEE-STTTHEE CS
                        Pkinase_Tyr  77 livteyvkgGdLlkfLrkkekekltlkdllsfalqvAkGmeyLeskklvHrdlaarNvLlsenkvvkisDfGLard 152
                                        ++v+e++++ +L++ L+++  ++++ +++  f  q+ ++m+yL+s ++vHrdl   N+Ll+ n +vk++DfGL+  
  gene1294|gene1294|rna1294|rna1294  93 VLVMELCDS-TLSDLLKQN--KRIRESHTRTFLRQIVSAMAYLHSVNVVHRDLKLSNILLK-NFTVKVADFGLCAL 164
                                        *******86.8******98..99*************************************9.99************ PP

                                        TTTSSEEEETTSSTSGGGGS-HHHHHHSEEEHHHHHHHHHHHHHHHHTTSSGTTTTSHHHHHHHHH.HTTEES-BB CS
                        Pkinase_Tyr 153 iekddeyvkkeeaklpvkWmapEslkekkftsksDvWsfGvllwEiftlgespypglkneevlekl.kegkrlekp 227
                                        i   ++ +k+++     +++apE++++  ++ + D Ws Gv+++ ++  g  p+++ +++e+++++ +++++++++
  gene1294|gene1294|rna1294|rna1294 165 I---NNKNKRTTVCGTPNYIAPEIINKVAYSFECDLWSLGVMVYTMLV-GTPPFQKKTAKEIYNTIkRNEYKIPEN 236
                                        *...45555666667789***************************998.*****************78899***** PP

                                        TTSBHHHHHHHHHHT-SSGGGS--HHHHHH CS
                        Pkinase_Tyr 228 ekcpeelyelmkkcweedpeeRptfselve 257
                                        + ++ee ++l+++ + +dp++R +++e+ +
  gene1294|gene1294|rna1294|rna1294 237 TLISEEAKDLIQRLLITDPHKRLSLKEIEK 266
                                        **************************9975 PP

>> Kinase-like  Kinase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.1   0.1   9.9e-14   2.5e-10      99     287 ..      71     257 ..      44     258 .. 0.78

  Alignments for each domain:
  == domain 1  score: 40.1 bits;  conditional E-value: 9.9e-14
                        Kinase-like  99 iqlkskesiywvvnallllpaasvdleilnkvlqkrset.hkkletiarlllTlqlirlaanLqakglvhgkftvd 173
                                        ++   + +i  + n +     +++ +e+  ++l    ++ ++  e + r  l  q++   a+L++  +vh +++  
  gene1294|gene1294|rna1294|rna1294  71 QRSVTHPNIVKLHNTFSTDEHIVLVMELCDSTLSDLLKQnKRIRESHTRTFL-RQIVSAMAYLHSVNVVHRDLKLS 145
                                        455667778888899999999999999999999998888466678999***9.99********************* PP

                        Kinase-like 174 nllldekgglmlggft..aLvragtkvvlseve..kgfaPpEllgsrggytrknktkmthkldaWqlGlviyriwc 245
                                        n+ll+ ++ +++ +f+  aL+  ++k    +v+    +  pE++++         + ++++ d W lG+ +y +  
  gene1294|gene1294|rna1294|rna1294 146 NILLK-NFTVKVADFGlcALINNKNKRT--TVCgtPNYIAPEIINK---------VAYSFECDLWSLGVMVYTMLV 209
                                        **997.79*****997447777777766..5653355777888877.........889****************** PP

                        Kinase-like 246 lklPltlateeakeew......kfklckkipekvkaLlkkfLqlsqed 287
                                         + P++++t + + +       k      i+e+ k L++++L  + ++
  gene1294|gene1294|rna1294|rna1294 210 GTPPFQKKTAKEIYNTikrneyKIPENTLISEEAKDLIQRLLITDPHK 257
                                        *****9988765544223331144444456777788888887666555 PP

>> Kdo  Lipopolysaccharide kinase (Kdo/WaaP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.2   1.5e-08   3.8e-05     104     172 ..     102     165 ..      87     173 .. 0.82

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 1.5e-08
                                Kdo 104 dLedllakwaelaeelkrallkavgrliaklhragvnHadlyaknillqqeeeeeaeiwliDldkarlr 172
                                         L dll++ +++ e+ +r+ l+++  ++a lh+++v H+dl   nill++       + + D+  ++l 
  gene1294|gene1294|rna1294|rna1294 102 TLSDLLKQNKRIRESHTRTFLRQIVSAMAYLHSVNVVHRDLKLSNILLKNFT-----VKVADFGLCALI 165
                                        48899999888*************************************9765.....666666666655 PP

>> RIO1  RIO1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.36   9.2e+02       9      58 ..      41      90 ..      35      94 .. 0.78
   2 !   18.2   0.3   5.8e-07    0.0015      81     150 ..      92     160 ..      84     172 .. 0.82
   3 ?   -2.0   0.0       0.9   2.3e+03      65     133 ..     226     303 ..     216     304 .. 0.51

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.36
                                       TTEEEEEEEE-S---SS-HHHHCTTTSTTSTCG--GS-HHHHHHHHHHHH CS
                               RIO1  9 dgkevaiKiyktstteFkkrkkyvsgekrfkdrksktnprklvklwaekE 58
                                       +++++++Ki k s ++ ++ +++ s e   +++ ++ n  kl ++  + E
  gene1294|gene1294|rna1294|rna1294 41 TDDNLCLKILKRSELTSDRLREKLSTEICIQRSVTHPNIVKLHNTFSTDE 90
                                       4567999************9999999998888877777777776666655 PP

  == domain 2  score: 18.2 bits;  conditional E-value: 5.8e-07
                                        TEEEEE--EETTEEGGBHHHCG-..HHHHHHHHHHHHHHHHHHHHTSTEEESS-STTSEEEETTEEEE--GT CS
                               RIO1  81 hvlvmefigedgvaapklkdvee..eeeaeelyeevleemrklykeaglvHaDLSeyNvlvdedkvviIDvs 150
                                         vlvme+++   +    lk+ ++  e+++++ +++++++m+ l   +++vH DL   N+l+++  v + D++
  gene1294|gene1294|rna1294|rna1294  92 IVLVMELCD--STLSDLLKQNKRirESHTRTFLRQIVSAMAYLH-SVNVVHRDLKLSNILLKNFTVKVADFG 160
                                        389******..666777777773458899999999999887776.9***************99888888875 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 0.9
                                        HHHTT--S--EEEEETTE..EEEE--EETTEEGGBHHHCG.-..HHHHHHHHHHHHHHHHH....HHHTSTEEESS CS
                               RIO1  65 leeagvpvPkpielkrhv..lvmefigedgvaapklkdve.e..eeeaeelyeevleemrk....lykeaglvHaD 131
                                        +++ + ++P+   + +++  l+ +++ +d  +   lk++e +   ++ e+l + vl+++r+    l+   +  HaD
  gene1294|gene1294|rna1294|rna1294 226 IKRNEYKIPENTLISEEAkdLIQRLLITDPHKRLSLKEIEkHpfFNKKESLINVVLNNLRAgtvsLVGGEHGSHAD 301
                                        5555556666655555444467777666666666667666334434445555555554332111144444455777 PP

                                        -S CS
                               RIO1 132 LS 133
                                        LS
  gene1294|gene1294|rna1294|rna1294 302 LS 303
                                        76 PP

>> Imm41  Immunity protein 41
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       2.6   6.6e+03      25      40 ..     265     280 ..     256     284 .. 0.80
   2 !   18.1   1.6     1e-06    0.0026      75     113 ..     371     407 ..     352     408 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 2.6
                              Imm41  25 ndeeyWklenalieil 40 
                                        +++ +++ +++li+++
  gene1294|gene1294|rna1294|rna1294 265 EKHPFFNKKESLINVV 280
                                        6778999999999997 PP

  == domain 2  score: 18.1 bits;  conditional E-value: 1e-06
                              Imm41  75 dlfeisdipdrfiafyERlkyilryiftgfdkeldddkf 113
                                        +++ ++ ip+r+  +yERl y +r+++   ++++++ +f
  gene1294|gene1294|rna1294|rna1294 371 EEYAMESIPERYRDYYERLVYFIRNFYP--EEQINEYQF 407
                                        68999***********************..****99998 PP

>> Pkinase_fungal  Fungal protein kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   5.8e-06     0.015     312     399 ..     122     199 ..      65     206 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 5.8e-06
                     Pkinase_fungal 312 lrDaIkghrsLflkagiLHrDiSenNilitdskkegerkglLiDLDlakelsddssesgarertGTleFmaievlk 387
                                        lr+ + +   L+   +++HrD    Nil+       + +  ++D+ l   +++++   ++ +  GT++++a e+++
  gene1294|gene1294|rna1294|rna1294 122 LRQIVSAMAYLH-SVNVVHRDLKLSNILLK------NFTVKVADFGLCALINNKN---KRTTVCGTPNYIAPEIIN 187
                                        7889999999**.*****************......8999*******99999643...34579************* PP

                     Pkinase_fungal 388 geeHsyrhDLES 399
                                        +   s+  DL S
  gene1294|gene1294|rna1294|rna1294 188 KVAYSFECDLWS 199
                                        999999999866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (465 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       674  (0.0375927); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.61u 0.28s 00:00:00.89 Elapsed: 00:00:00.48
# Mc/sec: 2915.05
//
Query:       gene1295|gene1295|rna1295|rna1295  [L=515]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.1e-16   59.3   0.0    1.9e-07   30.8   0.0    2.6  2  PGM_PMM_I    Phosphoglucomutase/phosphomannomutase, alpha/bet
      9e-07   29.0   0.0    2.8e-06   27.4   0.0    1.8  1  PGM_PMM_IV   Phosphoglucomutase/phosphomannomutase, C-termina
    0.00016   21.9   0.4     0.0036   17.5   0.0    2.4  2  PGM_PMM_III  Phosphoglucomutase/phosphomannomutase, alpha/bet
  ------ inclusion threshold ------
      0.013   16.1   0.5       0.12   13.0   0.2    2.8  3  PGM_PMM_II   Phosphoglucomutase/phosphomannomutase, alpha/bet


Domain annotation for each model (and alignments):
>> PGM_PMM_I  Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.0   1.6e-09   7.2e-06      93     131 ..      57      95 ..      35     102 .. 0.78
   2 !   30.8   0.0   4.3e-11   1.9e-07      38      92 ..     122     176 ..     105     180 .. 0.87

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 1.6e-09
                                        EEEEE--TTS-TTCCCEEEEETTTCE--CHHHHHHHHHH CS
                          PGM_PMM_I  93 agimitaSHnppeyngiKvylsnGgpispeveekIeaii 131
                                         gi +taSHn +++ngiK++++nG  +++  e  + +i+
  gene1295|gene1295|rna1295|rna1295  57 IGILLTASHNDARDNGIKLVDHNGEMFDRTWEGVVDKIV 95 
                                        58**********************999887666665555 PP

  == domain 2  score: 30.8 bits;  conditional E-value: 4.3e-11
                                        STS-EEEEEE-S-TTHHHHHHHHHHHHHCCT-CEEEEEEB-HHHHHHHHHHCCEC CS
                          PGM_PMM_I  38 akkkkvvvGrDtRvssrelaealaaglaanGvevillgllptPavsfairklkad 92 
                                        + k+ ++vGrDtR s+ +l e+++a + + +++v+++g+++tP +++++ + +  
  gene1295|gene1295|rna1295|rna1295 122 GPKANIIVGRDTRESGVKLVEEIVALMGHFNCSVVDYGVVSTPQMHYLVAQSNRL 176
                                        67899*******************************************9987655 PP

>> PGM_PMM_IV  Phosphoglucomutase/phosphomannomutase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   0.0   6.2e-10   2.8e-06      31      58 ..     460     486 ..     431     502 .. 0.85

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 6.2e-10
                                        CCGCCEEEE.EEEETTCCEEEEEEEESS CS
                         PGM_PMM_IV  31 illedGrrlavRpSGTepllrvyvEaks 58 
                                         ++++G ++ vRpSGTe+++r+ +Eak+
  gene1295|gene1295|rna1295|rna1295 460 MKNGKGKVF-VRPSGTENVIRIFCEAKE 486
                                        67899****.****************94 PP

>> PGM_PMM_III  Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   8.1e-07    0.0036       1      74 [.     299     370 ..     299     384 .. 0.86
   2 ?    1.9   0.1     0.054   2.4e+02      23      57 ..     445     479 ..     433     492 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 8.1e-07
                                        HHHHHHHHHHHHHHCH.CSTTTCEEEEETTS-THHHHHHHHTT-EEEEESSSCHHHHHHHHHTTECEEEETTCEE CS
                        PGM_PMM_III   1 dgdqllallakyllee.klkpgagvvktvmtslalervakklgiklvetkvGdkyvleemkeegavlGgEeSghi 74 
                                        dgd+ + +l kyl e+  +k g  v ++ + s a++++  ++ +++v++++G k+++++ ke ++ +  E +gh+
  gene1295|gene1295|rna1295|rna1295 299 DGDRQANILVKYLSEKvSCKIGC-VLSDYSNSAAVNEI--SKYCEAVRARTGIKNFIKKSKEYDIGVYNEPNGHG 370
                                        69999********9997777665.**************..77899*******************9999****664 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.054
                                        EEEEETTS-THHHHHHHHTT-EEEEESSSCHHHHH CS
                        PGM_PMM_III  23 gvvktvmtslalervakklgiklvetkvGdkyvle 57 
                                         vv +v   +++ +v+k+ ++k++  + G  +v++
  gene1295|gene1295|rna1295|rna1295 445 DVVEPVALRNVISNVMKNGKGKVFVRPSGTENVIR 479
                                        699**************************999986 PP

>> PGM_PMM_II  Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.2   2.7e-05      0.12       3     103 .]     185     293 ..     183     293 .. 0.62
   2 ?   -2.0   0.0       1.3   5.6e+03      79      93 ..     354     368 ..     327     376 .. 0.68
   3 ?   -3.6   0.0       3.9   1.7e+04      23      33 ..     498     508 ..     485     509 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.7e-05
                                        HHHHGGGTS-HHHHHHHT-EEEEE-TT-TTHHHHHHHHHHTT-.............EEEES-----TT-TT....S CS
                         PGM_PMM_II   3 YiealkekvdseaikksglkvvidplhGaggeilkellkelgv.............dvvelnaepdpdfpt....k 61 
                                        Y++++ + +     +  + kv +d+ +G++g +l+++ ++l +             +v  +  ++d++       +
  gene1295|gene1295|rna1295|rna1295 185 YFDMFIDFIR---FADLREKVNVDTSNGVAGYVLSSINERLSAmgyfdqhgdgedeQVLFVITNKDGEVNDrcgaQ 257
                                        5555555554...333345699***************999999887765555555433335555555444433222 PP

                                        S----TT-TTTTHHHHGGGGG-SEEEEE-TTS-BEEEEETTE CS
                         PGM_PMM_II  62 apnpeekealkllielvkkegadlglafDgDaDRlgvvderG 103
                                        +++ e+       + +  ++   l ++fDgD DR++ ++ +G
  gene1295|gene1295|rna1295|rna1295 258 YIQYEK------QVPYHLENAKGLYASFDGDMDRFIYFTVNG 293
                                        222222......223334556699************998665 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.3
                                        GGGG-SEEEEE-TTS CS
                         PGM_PMM_II  79 kkegadlglafDgDa 93 
                                        k++++d+g+ + +++
  gene1295|gene1295|rna1295|rna1295 354 KSKEYDIGVYNEPNG 368
                                        233447777777765 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 3.9
                                        EEEE-TT-TTH CS
                         PGM_PMM_II  23 vvidplhGagg 33 
                                         v+d ++G+g+
  gene1295|gene1295|rna1295|rna1295 498 AVYDLCGGVGK 508
                                        59999999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (515 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       588  (0.032796); expected 358.6 (0.02)
Passed bias filter:                      492  (0.0274416); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.44
# Mc/sec: 3491.20
//
Query:       gene1296|gene1296|rna1296|rna1296  [L=283]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.2e-05   22.9   0.2    0.00012   22.2   0.2    1.4  1  Myb_DNA-binding  Myb-like DNA-binding domain
     0.0028   17.9   0.3     0.0054   17.0   0.3    1.5  1  Myb_DNA-bind_6   Myb-like DNA-binding domain
  ------ inclusion threshold ------
      0.015   15.4   0.7      0.061   13.5   0.1    2.1  2  SANT_DAMP1_like  SANT/Myb-like domain of DAMP1
          2    8.2  11.0          3    7.6  11.0    1.3  1  Pox_Ag35         Pox virus Ag35 surface protein
        5.5    6.6   6.8          9    5.9   6.8    1.3  1  FAM176           FAM176 family
        6.8    5.8   8.4         10    5.2   8.4    1.2  1  TRAP_alpha       Translocon-associated protein (TRAP), alpha 


Domain annotation for each model (and alignments):
>> Myb_DNA-binding  Myb-like DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.2     4e-08   0.00012       4      44 ..     143     189 ..     140     191 .. 0.92

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 4e-08
                                        SBHHHHHHHHHHHHHHT.TCHHHHHH....HHT.SS-HHHHHHHHHH CS
                    Myb_DNA-binding   4 WteeEdelLleavkkhG.nrWkkIae....rlg.gRtekqcrsrwrn 44 
                                        W++ E e L ++v+++G +rWkkI +    +++ gR + + ++++r 
  gene1296|gene1296|rna1296|rna1296 143 WSATEIEYLRKGVQMFGcGRWKKIHKayeeHFQrGRRPCDLKDKYRL 189
                                        ************************99888888899*********985 PP

>> Myb_DNA-bind_6  Myb-like DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.3   1.8e-06    0.0054       1      52 [.     143     200 ..     143     206 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1.8e-06
                     Myb_DNA-bind_6   1 WteeEdeiLlklvekyg.ndWknIaealn.....rRtpkqcfdrwknkLrpkisrkkw 52 
                                        W++ E e L+k+v+++g   Wk+I +a+       R+p +++d+++   +   +r+k+
  gene1296|gene1296|rna1296|rna1296 143 WSATEIEYLRKGVQMFGcGRWKKIHKAYEehfqrGRRPCDLKDKYRLLTKRTSYRTKY 200
                                        9****************77*****77775577788**********9844555555555 PP

>> SANT_DAMP1_like  SANT/Myb-like domain of DAMP1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1     2e-05     0.061      28      72 ..     139     187 ..     121     194 .. 0.85
   2 ?   -0.5   0.1      0.49   1.5e+03      62      79 ..     247     264 ..     212     265 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2e-05
                    SANT_DAMP1_like  28 d...WtkeetdyLfdlckeydl.rfvviaDryelekkkkrsledlkery 72 
                                        +   W+ +e++yL + ++ + + r+  i+  ye + ++ r   dlk++y
  gene1296|gene1296|rna1296|rna1296 139 ErtfWSATEIEYLRKGVQMFGCgRWKKIHKAYEEHFQRGRRPCDLKDKY 187
                                        1345****************966***********99999********99 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.49
                    SANT_DAMP1_like  62 krsledlkeryYsvarkl 79 
                                         +s  d   ryY+v + l
  gene1296|gene1296|rna1296|rna1296 247 AKSHSDSSGRYYNVHKYL 264
                                        556666678999998876 PP

>> Pox_Ag35  Pox virus Ag35 surface protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6  11.0     0.001         3      55     119 ..       4      67 ..       1      86 [. 0.53

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.001
                           Pox_Ag35  55 krattprkkpakkekkkkeeekeeaaeeeeledseedeen.endedeseesvqaeeeksnestedd 119
                                        k+  t rk++++k+++k+e+e++ ++      d ++++++  +  ++ e++  +e+ +++ +  d+
  gene1296|gene1296|rna1296|rna1296   4 KKNITARKRTSTKTHEKEEKENTDKEPIT--TDTDNENDDeTQTSESAEDTYVSEQTDTRGDGHDN 67 
                                        56678888877777666666555555544..44433333303444444444444444444444444 PP

>> FAM176  FAM176 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   6.8     0.003         9      45      95 ..       7      60 ..       4      85 .. 0.52

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.003
                             FAM176 45 iscrkdlerlkkkkkklkeeseka....sededeeeeeeeedsseseaeeelsef 95
                                       i+ rk++++++++k+++++++ k+    ++d+++++e+++++s+e++  +e +++
  gene1296|gene1296|rna1296|rna1296  7 ITARKRTSTKTHEKEEKENTD-KEpittDTDNENDDETQTSESAEDTYVSEQTDT 60
                                       556666664444444443333.333533444444444444444444444444333 PP

>> TRAP_alpha  Translocon-associated protein (TRAP), alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   8.4    0.0034        10      19      93 ..      11      92 ..       3     102 .. 0.59

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0034
                         TRAP_alpha 19 satkvvaaaaaeedevdde..lvdvea..edeeveeeeeeeeeeeeeeeedee.....elkaspdadttilFtkpvek 87
                                       ++t+++++++ e++++d+e  ++d+++  +de++++e++e++  +e  ++d +     +   s d ++ ++Ft +v++
  gene1296|gene1296|rna1296|rna1296 11 KRTSTKTHEKEEKENTDKEpiTTDTDNenDDETQTSESAEDTYVSE--QTDTRgdghdNDGFSSDREKRVIFTGAVTE 86
                                       4444445555555556666775565552134444444444333333..2222223344677899*********99988 PP

                         TRAP_alpha 88 aeeelp 93
                                       ++ +++
  gene1296|gene1296|rna1296|rna1296 87 EAYDFE 92
                                       888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (283 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1366  (0.0761894); expected 358.6 (0.02)
Passed bias filter:                      594  (0.0331307); expected 358.6 (0.02)
Passed Vit filter:                        78  (0.00435049); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.46
# Mc/sec: 1844.65
//
Query:       gene1297|gene1297|rna1297|rna1297  [L=196]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       518  (0.0288917); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1424.00
//
Query:       gene1298|gene1298|rna1298|rna1298  [L=484]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      0.006   15.6   0.1      0.006   15.6   0.1    2.1  2  DUF913      Domain of Unknown Function (DUF913)
     0.0062   15.4   6.9      0.097   11.4   1.2    2.2  2  Tim54       Inner membrane protein import complex subunit Tim
  ------ inclusion threshold ------
      0.022   15.1   0.9      0.057   13.8   0.9    1.7  1  Histone     Core histone H2A/H2B/H3/H4
      0.071   13.1  19.0       0.14   12.2  10.4    2.4  2  Apis_Csd    Complementary sex determiner protein
       0.23    9.7  25.3       0.78    8.0  12.0    2.1  2  CDC45       CDC45-like protein
       0.43   10.4  22.3      0.049   13.5   1.2    2.2  2  SpoIIIAH    SpoIIIAH-like protein
        0.8   10.4   4.0        1.9    9.1   0.1    2.2  2  Pex14_N     Peroxisomal membrane anchor protein (Pex14p) cons
        3.4    6.3  14.7      0.047   12.4   0.7    2.4  2  Presenilin  Presenilin
        6.1    6.9  20.8       0.21   11.7   3.6    2.3  2  Gti1_Pac2   Gti1/Pac2 family
        7.1    6.4  17.6        1.8    8.3   3.2    2.2  2  RR_TM4-6    Ryanodine Receptor TM 4-6
        7.3    5.4   8.3        0.4    9.6   0.2    2.1  2  Serinc      Serine incorporator (Serinc)


Domain annotation for each model (and alignments):
>> DUF913  Domain of Unknown Function (DUF913)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1   3.7e-06     0.006     264     338 ..      90     176 ..      19     191 .. 0.55
   2 ?   -2.8   5.9       1.5   2.4e+03     274     317 ..     323     367 ..     268     391 .. 0.44

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 3.7e-06
                             DUF913 264 d..............assasskseasssssssetkeeek.....ssededvemeda...eeetesesdeseeseee 317
                                                       +        +++++s+++++e+e+     +  ++d+e++++   ++++e++++++++++++
  gene1298|gene1298|rna1298|rna1298  90 LlrsrgrngdstgnnD--------NNRENSRENSREKENsrendR--NNDKENSKEdntDKDKENNTNATDNNNNT 155
                                        0333344332222111........111111111111111222121..11111111111111222222222233333 PP

                             DUF913 318 keknslldyilnvakFLeall 338
                                        + ++++l+ + +++kF+++++
  gene1298|gene1298|rna1298|rna1298 156 NINTPYLQHLPPFSKFIKTII 176
                                        444447777778899999887 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.5
                             DUF913 274 asssssssetkeeek..............ssededvemeda........eeetesesdeseeseee 317
                                                      +               ++                 +++++ ++d+ +++ ++
  gene1298|gene1298|rna1298|rna1298 323 V-------------EddklkddnqvkddkLKD--------DnqvkddklKDDNQVKDDKLKDALNS 367
                                        1.............011111111222222111........01112222222233333333333333 PP

>> Tim54  Inner membrane protein import complex subunit Tim54
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   1.2   5.9e-05     0.097     201     255 ..     109     163 ..      95     211 .. 0.64
   2 !    7.1   0.5    0.0012         2     209     274 ..     327     402 ..     292     465 .. 0.48

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 5.9e-05
                              Tim54 201 aeeeeeeeeeekeeeeeeeeeeeeekeeekeeekeeeeeeeekekkkkvpkpyis 255
                                        ++++e+++e+e+++e+++++++e++ke++++++ke++++++++++++++ +py++
  gene1298|gene1298|rna1298|rna1298 109 ENSRENSREKENSRENDRNNDKENSKEDNTDKDKENNTNATDNNNNTNINTPYLQ 163
                                        2222222222222222223344455555555555566666666666666777665 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0012
                              Tim54 209 eeekeeeeeeeeeeeeekeeekeeekeeeeeeeekekkkkvpkpyispedYasaelppe..........iPellqp 274
                                        + +++++ ++++ +++++ ++++ +++++ ++++ ++  +  k+ +s+++Y ++ l ++          + ++ q+
  gene1298|gene1298|rna1298|rna1298 327 KLKDDNQVKDDKLKDDNQVKDDKLKDDNQVKDDKLKDALNSNKNNNSTDQYLNHYLNQHhitykqmkikTCTTAQA 402
                                        1111111111112222222222222223333333333444444455555555555554433333333333333333 PP

>> Histone  Core histone H2A/H2B/H3/H4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.9   3.5e-05     0.057       4      75 ..     103     176 ..     100     194 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.5e-05
                                        ESXEEEXXXXEEXXXXXXXXXXHT..TS-SSSSB--TTT-XTTHHHHHHHHHHHHXXSXXSXHHHHHHHHHHHH CS
                            Histone   4 ekekarkesektapekkvsakker..kasskskkkkkrryrpgtvalkeirkyqkstdlliqklpfaRvvreiv 75 
                                        +++++r+ s+++++ek+ s++++r   ++ +++  ++++  ++t+a ++  +   +t  l +  pf++ ++ i 
  gene1298|gene1298|rna1298|rna1298 103 NNDNNRENSRENSREKENSRENDRnnDKENSKEDNTDKDKENNTNATDNNNNTNINTPYLQHLPPFSKFIKTII 176
                                        6777888888899999999999999888888899999**********************************885 PP

>> Apis_Csd  Complementary sex determiner protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2  10.4   8.3e-05      0.14       8      85 ..      92     166 ..      88     187 .. 0.53
   2 ?    5.7   1.3    0.0083        13      38      83 ..     351     389 ..     312     428 .. 0.54

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 8.3e-05
                           Apis_Csd   8 rsrereqksyknensyre.yretsrersrdrkerersrekkiisslsnlsnnynynnnynnynnynklyyninyie 82 
                                        rsr r+  s  n+++ re  re sre+   r e +r+++k   +s+++++ +++ +nn n   n n+   n  y++
  gene1298|gene1298|rna1298|rna1298  92 RSRGRNGDSTGNNDNNREnSRENSREKENSR-ENDRNNDK--ENSKEDNT-DKDKENNTNATDNNNNTNINTPYLQ 163
                                        8888888888776665541466666664433.22222222..11222221.2222333333333344444555555 PP

                           Apis_Csd  83 qip 85 
                                         +p
  gene1298|gene1298|rna1298|rna1298 164 HLP 166
                                        544 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0083
                           Apis_Csd  38 kerersrekkiisslsnlsnnynynnnynnynnynklyyninyieq 83 
                                        k+ ++ ++ k+  +l       n n+n n   +y ++y n ++i  
  gene1298|gene1298|rna1298|rna1298 351 KDDNQVKDDKLKDAL-------NSNKNNNSTDQYLNHYLNQHHITY 389
                                        222333344443333.......333333444455555555555543 PP

>> CDC45  CDC45-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   5.3   0.00051      0.83     146     183 ..     106     143 ..      78     181 .. 0.43
   2 ?    8.0  12.0   0.00048      0.78     103     222 ..     266     384 ..     203     401 .. 0.47

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00051
                              CDC45 146 deeeeeeeeedeedeeedeeeskkkrksksdeeeesdd 183
                                        +++e+++e+++e++++ ++++++ k++sk+d+++++++
  gene1298|gene1298|rna1298|rna1298 106 NNRENSRENSREKENSRENDRNNDKENSKEDNTDKDKE 143
                                        11111111111111111111111111111111111111 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.00048
                              CDC45 103 rivvf..DDgdieeeleeereayealeeeeesdeedeeeeeeddddeeeeeeeeedeedeeedeeeskkkrksksd 176
                                        +ivvf   +g++++ +++e ++  + ++ e+ + +de         +++ ++++ ++++ ++d++ ++ k k++++
  gene1298|gene1298|rna1298|rna1298 266 DIVVFecSNGNMDDVVDDEVDDEVKDDKVEDGRVDDE--------IKDKVDDNQVEDDKLKDDNQVEDDKLKDDNQ 333
                                        4444433233333333333333333333333322222........1111111111111111111111222221111 PP

                              CDC45 177 eeee..sddddersrkrrrse.psakklrrq..lkkerrkyeavlekyysq 222
                                         +++  +dd++ +  k + ++  +++kl+    ++k++++  + l++y +q
  gene1298|gene1298|rna1298|rna1298 334 VKDDklKDDNQVKDDKLKDDNqVKDDKLKDAlnSNKNNNSTDQYLNHYLNQ 384
                                        111122222222222211111112222222233344444444444444444 PP

>> SpoIIIAH  SpoIIIAH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   1.2     3e-05     0.049      51      93 ..     104     150 ..      45     164 .. 0.60
   2 ?    1.9  13.9      0.11   1.7e+02      39     111 ..     306     386 ..     272     405 .. 0.51

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3e-05
                                        XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.......XXXXX CS
                           SpoIIIAH  51 kdessaasaeaesssetesesseksdiassdedeade....ltseta 93 
                                        +d++ ++s e+++++e++ e++ ++d+++s+ed++d+     t++t 
  gene1298|gene1298|rna1298|rna1298 104 NDNNRENSRENSREKENSRENDRNNDKENSKEDNTDKdkenNTNATD 150
                                        23333333333333333333333334443333333321111111111 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.11
                                        XXXXXXXXX..........XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX...XXXXXXXXXXX--HHH CS
                           SpoIIIAH  39 esekaeigd..........dkekdessaasaeaesssetesesseksdiassdedeadeltsetasaaasasdyfa 104
                                        + ++++++d          d++ +++++ ++++ ++ ++ ++++ k+d++++d++ +d+l+s  +++++s+++y+ 
  gene1298|gene1298|rna1298|rna1298 306 KVDDNQVEDdklkddnqveDDKLKDDNQVKDDKLKDDNQVKDDKLKDDNQVKDDKLKDALNS--NKNNNSTDQYLN 379
                                        22222222233332333332333444444444444445555555555555555555553444..445677777777 PP

                                        HHHHHHH CS
                           SpoIIIAH 105 eakleRe 111
                                         +  +  
  gene1298|gene1298|rna1298|rna1298 380 HYLNQHH 386
                                        7655444 PP

>> Pex14_N  Peroxisomal membrane anchor protein (Pex14p) conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.1    0.0012       1.9      40     106 ..      88     160 ..      85     212 .. 0.42
   2 ?    2.2   0.6      0.16   2.6e+02      66     115 ..     333     394 ..     297     406 .. 0.43

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0012
                            Pex14_N  40 eeaLkraereeease.sa...vaassas.eqa..........qeesasssatpqpqaasqtsqsspspsppaqqqq 100
                                        +++L+  +r+ +++  ++   +++ ++s e +           +e++++++t + ++++++++          +++
  gene1298|gene1298|rna1298|rna1298  88 DTLLRSRGRNGDSTGnNDnnrENSRENSrE-KensrendrnnDKENSKEDNTDKDKENNTNAT---------DNNN 153
                                        566666666655554311222222222221.12222222211111111111111111111111.........1111 PP

                            Pex14_N 101 qqy.rpP 106
                                        ++    P
  gene1298|gene1298|rna1298|rna1298 154 NTNiNTP 160
                                        1112122 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.16
                            Pex14_N  66 a............qeesasssatpqpqaasqtsqsspspsppaqqqqqqy.rpPivtypeflt 115
                                        +            ++++ + +++ +  + + + +s+++++ ++ q  ++y  +  +ty+++  
  gene1298|gene1298|rna1298|rna1298 333 QvkddklkddnqvKDDKLKDDNQVKDDKLKDALNSNKNNN-STDQYLNHYlNQHHITYKQMKI 394
                                        1122223222233444444444444444433333333333.3333333335667788876655 PP

>> Presenilin  Presenilin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.7   2.9e-05     0.047     258     305 ..     105     151 ..      58     169 .. 0.46
   2 ?   -2.0   7.4       0.7   1.1e+03     236     291 ..     318     373 ..     273     410 .. 0.40

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.9e-05
                         Presenilin 258 eeesseksaqsseseeeseeesseaessaeesseekeseessesseee 305
                                        +++ ++++++s+ ++e+s+e+ +++++++++++++++++e++++++++
  gene1298|gene1298|rna1298|rna1298 105 DNNRENSRENSR-EKENSRENDRNNDKENSKEDNTDKDKENNTNATDN 151
                                        111111111111.11111111111111111111111111111111111 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.7
                         Presenilin 236 eeeeeaekkkeeasesskeeeseeesseksaqsseseeeseeesseaessaeesse 291
                                        +++++ e++k +++++ k+++ +++++ k ++ +++++ ++++ ++a +s++++++
  gene1298|gene1298|rna1298|rna1298 318 KDDNQVEDDKLKDDNQVKDDKLKDDNQVKDDKLKDDNQVKDDKLKDALNSNKNNNS 373
                                        11111111111111111111111111111111111222222222222222222211 PP

>> Gti1_Pac2  Gti1/Pac2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   3.6   0.00013      0.21      86     179 ..     103     195 ..      87     197 .. 0.48
   2 ?    0.8   9.3      0.28   4.6e+02      84     176 ..     317     408 ..     293     410 .. 0.55

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00013
                                        ------------------------.................--------------------------....----- CS
                          Gti1_Pac2  86 kkkkkkkkkskestkkeesksekasssssesseakessssseskasksskslekdserslvgsltds....ykfkk 157
                                        ++++++++++++s +k   +++++++ ++++  +++++ ++++ ++++++ ++++++++++ +  ++     kf k
  gene1298|gene1298|rna1298|rna1298 103 NNDNNRENSRENSREK---ENSRENDRNNDK--ENSKEDNTDKDKENNTNATDNNNNTNINTPYLQHlppfSKFIK 173
                                        2222222222222222...222212222222..1122222212244444455555555555555554555677888 PP

                                        ---EEEEEEEEEETTTEEEEEE CS
                          Gti1_Pac2 158 dgLvKkTisvtlkgkelhlisY 179
                                        + ++ +++  +++ +++hl  Y
  gene1298|gene1298|rna1298|rna1298 174 TIILCQSLPFKISFTAHHLLLY 195
                                        8888888888888888888877 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.28
                                        --------------------------.................---.----------------------------- CS
                          Gti1_Pac2  84 akkkkkkkkkkskestkkeesksekasssssesseakesssssesk.asksskslekdserslvgsltdsykfkkd 158
                                         k+ ++ +++k k +++ +++k ++ ++ ++++   k++++ +++k +++ +++++++s +++ ++  ++++++++
  gene1298|gene1298|rna1298|rna1298 317 LKDDNQVEDDKLKDDNQVKDDKLKDDNQVKDDK--LKDDNQVKDDKlKDALNSNKNNNSTDQYLNHYLNQHHITYK 390
                                        222222222222222222222222223333333..44444444445455555555566666666666666789999 PP

                                        --EEEEEEEEEETTTEEE CS
                          Gti1_Pac2 159 gLvKkTisvtlkgkelhl 176
                                        ++  kT +    + ++h+
  gene1298|gene1298|rna1298|rna1298 391 QMKIKTCTTAQANIKIHI 408
                                        999999999888888887 PP

>> RR_TM4-6  Ryanodine Receptor TM 4-6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   3.2    0.0011       1.8      95     145 ..     109     147 ..      76     172 .. 0.41
   2 ?    3.7   6.6     0.028        46      70     162 ..     277     379 ..     265     398 .. 0.64

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0011
                                        XXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXX..........XXXXXXXX CS
                           RR_TM4-6  95 eaeeekeeeeepeaeaeekadaengekeekekekeeeekeseeeeeekkkk 145
                                        e+++e+++e+e+        ++en  +++ke++    +++++ +++e++ +
  gene1298|gene1298|rna1298|rna1298 109 ENSRENSREKEN--------SRENDRNNDKENS----KEDNTDKDKENNTN 147
                                        111111111111........1111111111111....11111111111111 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.028
                                        XXXXXXXXXXXXXX..........XXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXX........ CS
                           RR_TM4-6  70 LgDlseteaeespt..........pelkkklaeeeeaeeekeeeeepeaeaeekadaengekeekekekeeeekes 135
                                        + D+ ++e+ ++ +           e k k+ ++++++++ +++++ e ++ ++ ++ + +k + +++ ++++ + 
  gene1298|gene1298|rna1298|rna1298 277 MDDVVDDEVDDEVKddkvedgrvdDEIKDKVDDNQVEDDKLKDDNQVEDDKLKDDNQVKDDKLKDDNQVKDDKLKD 352
                                        4555555555554444444544556677777788888888888888888887776666666666666656666666 PP

                                        ..XXXXXXXXXXXXXXXXXXXXXXXXX CS
                           RR_TM4-6 136 eeeeeekkkkkkakskkkeeaeaeese 162
                                         ++ +  k k + +s+k+++++++  +
  gene1298|gene1298|rna1298|rna1298 353 DNQVKDDKLKDALNSNKNNNSTDQYLN 379
                                        666666666666666666666665444 PP

>> Serinc  Serine incorporator (Serinc)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.2   0.00024       0.4     289     351 ..      14     151 ..       8     165 .. 0.52
   2 ?   -1.9   3.4      0.72   1.2e+03     320     330 ..     324     340 ..     266     389 .. 0.56

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00024
                             Serinc 289 liltflcvlYstlraass.......................................................... 306
                                        +il++ +++Ys +r+ s                                                           
  gene1298|gene1298|rna1298|rna1298  14 IILVVTAMMYSITRTNSDercytytmnsvyikresdellvvgdgwmytvgiwyfdvlyvlcvlgersvdmvecvdt 89 
                                        5556666666666666666666666666666666666666666666666666666666666666668999999999 PP

                             Serinc 307 ................sqveklralkaaeeegalpesal.eeeeeeeeekekeeeek.kvldd 351
                                                        +++e+ r ++  e+e++ +++ + ++e+++e++++k++e++ +++d+
  gene1298|gene1298|rna1298|rna1298  90 llrsrgrngdstgnndNNRENSRENS-REKENSRENDRNnDKENSKEDNTDKDKENNtNATDN 151
                                        99999888877665432222222221.222222222221122222222222222222244443 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.72
                             Serinc 320 eegalpesal......e 330
                                        e+ +l+++++      +
  gene1298|gene1298|rna1298|rna1298 324 EDDKLKDDNQvkddklK 340
                                        11122221111111111 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (484 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2324  (0.129622); expected 358.6 (0.02)
Passed bias filter:                      540  (0.0301188); expected 358.6 (0.02)
Passed Vit filter:                       120  (0.00669307); expected 17.9 (0.001)
Passed Fwd filter:                        47  (0.00262145); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.97u 0.36s 00:00:01.33 Elapsed: 00:00:00.56
# Mc/sec: 2580.14
//
Query:       gene1299|gene1299|rna1299|rna1299  [L=97]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (97 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       466  (0.0259914); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.45
# Mc/sec: 650.41
//
Query:       gene13|gene13|rna13|rna13  [L=359]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-21   77.6   0.0    7.4e-10   39.0   0.0    2.3  2  Asn_synthase    Asparagine synthase
     0.0084   16.1   0.3      0.018   15.0   0.2    1.6  1  PS_pyruv_trans  Polysaccharide pyruvyl transferase


Domain annotation for each model (and alignments):
>> Asn_synthase  Asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.5   0.0   4.8e-13   4.3e-09       3     144 ..     109     259 ..     108     267 .. 0.71
   2 !   39.0   0.0   8.2e-14   7.4e-10     213     273 ..     267     330 ..     260     354 .. 0.92

  Alignments for each domain:
  == domain 1  score: 36.5 bits;  conditional E-value: 4.8e-13
               Asn_synthase   3 relLedaVkrrlradvpvGalLSGGlDSSliaalaarqsk..splktFsigfee....kgsdeakyakevaehlgtehtelvlt 80 
                                + lL ++ krr++    v +++ GG+DS +ia ++++  +  +p+  +   f+     +++  +k  +++++ l+ +  ++v+ 
  gene13|gene13|rna13|rna13 109 ENLLIQSCKRRTHRFDNV-LFFGGGIDSLIIAITLNKVVEknRPIYLVNTSFDGemswDRFYGLKNYHALCNILKER--KYVFV 189
                                678889999999766666.789***************9997778888888885523345555566667777776666..44444 PP

               Asn_synthase  81 eeel.ldalpdviyhlee.......pfadrsaiplyllsrlakrkgvkvvLsGeGaDElfgGYpyfykaals 144
                                ++++ l+++++++ ++ +       ++     ++ y+ +++a +   kvv +G GaDElfgGY+  y+++  
  gene13|gene13|rna13|rna13 190 RNDIsLEEVKRALPIVKKliypkisIMDLNIGLCHYFSAKKA-QNYTKVVYTGMGADELFGGYS-KYSKKTT 259
                                444315567777776666666555566667777889999999.66699****************.6655544 PP

  == domain 2  score: 39.0 bits;  conditional E-value: 8.2e-14
               Asn_synthase 213 ldlktllpgdllrkDrasmahglEaRvPflDhrlvevalrlppelklrg...gieKyiLReale 273
                                +d+  ++++++ r Dr  + + +E+R PflD++++++al+l++++ ++    g +K+iLRe+l+
  gene13|gene13|rna13|rna13 267 RDVAAIYKDNIGRDDRVVADNAVEMRSPFLDKDVIKFALSLDVKYLVNTgdkGCSKAILRELLT 330
                                7889999*****************************************99999********986 PP

>> PS_pyruv_trans  Polysaccharide pyruvyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.2     2e-06     0.018      52     141 ..     125     198 ..      94     304 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2e-06
                                ...............EEE--E....EEEETT-HHH.HHHHHHHHHHS-SSEEEE-SEEE........-S-HHHHHHHHHHHHHT CS
             PS_pyruv_trans  52 llkrlrkkdiddaddviivGgdgtlgndgdlsrlp.dalrllflakkagkpviilgqgi......Gpflnealrkllkkilaka 128
                                +              ++++Gg           + + +a+ l+++++k ++p++++ +++        f    + + l +il+  
  gene13|gene13|rna13|rna13 125 NV-------------LFFGGG----------IDSLiIAITLNKVVEK-NRPIYLVNTSFdgemswDRFYGLKNYHALCNILKER 184
                                22.............666666..........4445566999999998.569********9777644466667777********* PP

                                TEEEESSHHHHH.. CS
             PS_pyruv_trans 129 dlisvRdelSae.l 141
                                ++++vR+++S+e +
  gene13|gene13|rna13|rna13 185 KYVFVRNDISLEeV 198
                                ************32 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (359 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       434  (0.0242066); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 2316.98
//
Query:       gene130|gene130|rna130|rna130  [L=477]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (477 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       608  (0.0339115); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 3315.06
//
Query:       gene1300|gene1300|rna1300|rna1300  [L=168]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-10   41.9   0.4    4.9e-10   40.1   0.5    1.9  2  CTD_bind  RNA polymerase II-binding domain.
  ------ inclusion threshold ------
      0.027   14.8   0.2      0.054   13.8   0.2    1.6  1  UPF0058   Uncharacterised protein family UPF0058
      0.099   12.7   1.5       0.14   12.2   1.5    1.2  1  CTK3      CTD kinase subunit gamma CTK3


Domain annotation for each model (and alignments):
>> CTD_bind  RNA polymerase II-binding domain.
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.1   0.5   8.1e-14   4.9e-10       1      63 []      56     122 ..      56     122 .. 0.87
   2 ?   -1.8   0.0      0.97   5.8e+03      23      38 ..     151     166 ..     139     168 .] 0.64

  Alignments for each domain:
  == domain 1  score: 40.1 bits;  conditional E-value: 8.1e-14
                           CTD_bind   1 kLnllYLaNdvlqnskrkq..kdefapaFapvlpeafadayk..kapekikkklkrllniWeernvf 63 
                                        kLn++YLaN+++q  k        + ++ ++++++ f day+  ++ + +k kl++l  +W+er++f
  gene1300|gene1300|rna1300|rna1300  56 KLNIFYLANELIQTIKNDEkdLALLHEQIKSFVVSNFDDAYAemSKYPVLKGKLMELKGVWVERKLF 122
                                        9************754333325556999**************99889******************98 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.97
                           CTD_bind  23 fapaFapvlpeafada 38 
                                         ++a+a++l  +++++
  gene1300|gene1300|rna1300|rna1300 151 CREALAEYLDGMVKNL 166
                                        3678888888888775 PP

>> UPF0058  Uncharacterised protein family UPF0058
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.2     9e-06     0.054      30      73 ..      35      77 ..      18     101 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 9e-06
                                       THHHHHH---TT-TTS-HHHHHHHHHHHHHHHHHHHHHHHHCCC CS
                            UPF0058 30 fkeYeeLdisPhhihrsKaehkaAifvLgnaiakalsekeessa 73
                                        ++ ++L i  ++  +s a hk  if L+n++ + ++++e+   
  gene1300|gene1300|rna1300|rna1300 35 TESTRMLRILDQEYAKSNAYHKLNIFYLANELIQTIKNDEKD-L 77
                                       456678889999999***********************9998.3 PP

>> CTK3  CTD kinase subunit gamma CTK3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   1.5   2.3e-05      0.14       7      91 ..       6      85 ..       2     100 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.3e-05
                                       HHHHHHHHTT--SSGGGTHHHHHHHHHTGGGHHH.HHHHHHHHHHHS-HHHHHHHHHHHHHHHHHHHHTT--S..THH CS
                               CTK3  7 rsqFsqlLrkLtasvqslqkaaqfAlknkdkeed.lfscileqlesadlNtranilyfidllleeslkegqsekspYv 83
                                       + +F++ +r+L++ ++ ++  a +  k +++e   + + + ++  +++   + ni+y+ + l++   k++++     +
  gene1300|gene1300|rna1300|rna1300  6 QETFIKEIRTLSPTQEKIKTLALYM-KTTSTESTrMLRILDQEYAKSNAYHKLNIFYLANELIQTI-KNDEKD----L 77
                                       568*************999999995.666665550555555567788***************9864.444443....3 PP

                                       HHHHHTHH CS
                               CTK3 84 eslkrdil 91
                                        +l+++i+
  gene1300|gene1300|rna1300|rna1300 78 ALLHEQIK 85
                                       44444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1133  (0.0631937); expected 358.6 (0.02)
Passed bias filter:                      664  (0.037035); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1270.73
//
Query:       gene1301|gene1301|rna1301|rna1301  [L=850]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.9e-35  121.1   0.0      8e-35  120.1   0.0    1.5  1  GTP_EFTU  Elongation factor Tu GTP binding domain
    1.1e-05   25.4   0.0    2.5e-05   24.2   0.0    1.6  1  EFG_C     Elongation factor G C-terminus
  ------ inclusion threshold ------
       0.16   12.2   0.4       0.71   10.1   0.0    2.1  2  GH97_C    Glycosyl-hydrolase 97 C-terminal, oligomerisation


Domain annotation for each model (and alignments):
>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.1   0.0   1.3e-38     8e-35       5     150 ..       3     140 ..       1     222 [. 0.82

  Alignments for each domain:
  == domain 1  score: 120.1 bits;  conditional E-value: 1.3e-38
                                        EEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHSTHCHSHHHHHHTSCSSCEEEEEETTCSSEEEEEEEESSS CS
                           GTP_EFTU   5 nigiighvDhGKtTLtdrLlyktgaiskkgekaeeervlDtlkeErergiTiksaaisleketkkylinliDtPGH 80 
                                         +++++hvDhGKtTL+d+Ll +t+ is+  + a++ r+lDt+++E+ergiT k +  + +      ++ +iDtPGH
  gene1301|gene1301|rna1301|rna1301   3 IVSVVAHVDHGKTTLLDSLLSYTHVISR--RSAGKLRYLDTRNDEQERGITLKLSFFQAQ------RFIFIDTPGH 70 
                                        589*************************..5556779*****************999999......9********* PP

                                        GGGHHHHHHHHHT-SEEEEEEETTTBSTHHHHHHHHHHHHTTTEEEEEEESCGST..HHHHHHHHHHHHHHH CS
                           GTP_EFTU  81 vdFskevirglrvlDgavlvvdaveGvepqteevlrlalkegvpiivfiNKmDrl..kaelkeiveevkqkl 150
                                         dF + ++ ++r +D  +++vd++eG++p+t   + lal++g +  +++NK+D+l    el  +v  + q++
  gene1301|gene1301|rna1301|rna1301  71 TDFHSLTECSARLCDHFIFIVDVNEGITPRTL--ALLALTKGKRCTLVLNKIDKLlgCPELVPVVLGIVQSM 140
                                        *****************************875..5677888999999*******977555555555555555 PP

>> EFG_C  Elongation factor G C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.0   4.1e-09   2.5e-05       6      82 ..     739     816 ..     739     822 .. 0.87

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 4.1e-09
                                        EEEEEEEEECCCCCCHHHHHHHCT-EEEEEEEE..TTEEEEEEEEEGGG-TTHHHCHHHCTTTS-EEEEEEEEEEE CS
                              EFG_C   6 ivkveievpeeyvgkvisdlssrrGeiedmeqd.asgrviieaeiPlaeligfateLrslTkGegsfsmefsgYee 80 
                                        ++++++++ e+yvgk +++l++ r ++++ e+d ++ ++++e++i      +f++eL+s+T+G+ ++    +gY  
  gene1301|gene1301|rna1301|rna1301 739 YYRCKLSITEQYVGKCYKLLNKYRFKMLSNEYDgTNRFFVVEFRIRRCFYNDFSDELKSVTRGTFYVYAWEEGYVR 814
                                        799******************************66778999***9888888************9777766666666 PP

                                        -- CS
                              EFG_C  81 vp 82 
                                        ++
  gene1301|gene1301|rna1301|rna1301 815 YE 816
                                        55 PP

>> GH97_C  Glycosyl-hydrolase 97 C-terminal, oligomerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00012      0.71       4      49 ..      14      60 ..      11      78 .. 0.86
   2 ?   -1.8   0.6      0.63   3.8e+03      55      76 ..     638     662 ..     606     672 .. 0.54

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00012
                             GH97_C  4 etkvlegeigeyvvvARr.kgnkWyvgaltnekareleldlsflekg 49
                                       +t +l++ +    v+ Rr  g+  y+ + ++e++r ++l+lsf++++
  gene1301|gene1301|rna1301|rna1301 14 KTTLLDSLLSYTHVISRRsAGKLRYLDTRNDEQERGITLKLSFFQAQ 60
                                       6889999999999*****666678********************865 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.63
                             GH97_C  55 eiyaDgknad...nptdykietkkv 76 
                                        +i +D+ +++   n ++++i+t++v
  gene1301|gene1301|rna1301|rna1301 638 TINNDTHDNNnngNDNTININTNDV 662
                                        3333322222234555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (850 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1146  (0.0639188); expected 358.6 (0.02)
Passed bias filter:                      472  (0.0263261); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.75u 0.28s 00:00:01.03 Elapsed: 00:00:00.45
# Mc/sec: 5677.84
//
Query:       gene1302|gene1302|rna1302|rna1302  [L=380]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
      0.047   13.7   4.4       0.26   11.3   0.6    2.7  3  Thg1        tRNAHis guanylyltransferase
      0.054   13.7   0.2        4.4    7.5   0.0    2.7  2  OrfB_IS605  Probable transposase
      0.065   13.8   1.0       0.16   12.6   0.2    2.0  2  Globin      Globin
       0.13   12.6   3.5        0.5   10.6   0.2    2.3  2  zf-C4H2     Zinc finger-containing protein
          2    8.9   8.8        1.2    9.6   0.2    3.0  3  DUF2115     Uncharacterized protein conserved in archaea (DUF


Domain annotation for each model (and alignments):
>> Thg1  tRNAHis guanylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       0.8   2.9e+03      28      28 ..     132     132 ..      76     173 .. 0.64
   2 ?    2.9   0.1      0.03   1.1e+02      28      68 ..     200     239 ..     194     244 .. 0.72
   3 ?   11.3   0.6   7.3e-05      0.26      27      88 ..     266     326 ..     264     359 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.8
                               Thg1  28 F 28 
                                        F
  gene1302|gene1302|rna1302|rna1302 132 F 132
                                        1 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.03
                               Thg1  28 FhkfskkhkfekPnDeralklmneaakelvkefedivlaYg 68 
                                        F k+ + h  ++PnD r+++l ++    l ++  +i+l+Y 
  gene1302|gene1302|rna1302|rna1302 200 FVKMFE-HMETQPNDVRLVNLAKAFYMLLNETRAHIILIYQ 239
                                        444444.55689*******9876666555555568999985 PP

  == domain 3  score: 11.3 bits;  conditional E-value: 7.3e-05
                               Thg1  27 gFhkfskkhkfekPnDeralklmneaakelvkefedivlaYgqSDEislvlsketklynrra 88 
                                        +Fh+f +k+k +  nD+   k + ++ak +v++++d+ +   + DE s++l +    y++r+
  gene1302|gene1302|rna1302|rna1302 266 TFHEFLRKLKAQIDNDRLEKKHFITTAKMIVRTLNDFRMTCIFMDENSIMLANFL-IYQQRK 326
                                        6************************************************998766.777765 PP

>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.0    0.0012       4.4      82     113 ..     133     164 ..     127     167 .. 0.91
   2 ?    3.2   0.1     0.028        99      84     103 ..     321     340 ..     318     354 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0012
                         OrfB_IS605  82 rkrsrrrkhllhklathliktlkevgvetLnv 113
                                         k++++ ++ +h+++++++k++    v++++v
  gene1302|gene1302|rna1302|rna1302 133 TKLAKKFLDEFHEVTSKIVKECGSYDVSHIKV 164
                                        68889999*********************998 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.028
                         OrfB_IS605  84 rsrrrkhllhklathliktl 103
                                        ++++rkhl+h l+ +l+++ 
  gene1302|gene1302|rna1302|rna1302 321 IYQQRKHLHHVLSEELLDYW 340
                                        6799***********99875 PP

>> Globin  Globin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.2   4.4e-05      0.16      28     106 ..     104     176 ..     100     180 .. 0.87
   2 ?   -2.1   0.0       1.6   5.7e+03      78      91 ..     265     278 ..     248     295 .. 0.52

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.4e-05
                                        HHHSGGGGGGSTTTTTTT-HHHHCTSHHHHHHHHHHHHHHHHHHHTTTSHHHHHHHHHHHHHHHHCSTT--HHHHH CS
                             Globin  28 FkaypdtkklFkkfgdlssaedlksspkfkahakkvlaalgeavknldndealkaalkklaarHaergkvdpanFk 103
                                        F    d+ ++ kk+ d+ + ++++    f + akk+l+ ++e+ +++       + +  + ++H++  k+dp+nF+
  gene1302|gene1302|rna1302|rna1302 104 FGSENDMNEILKKVIDKVPSKEIAAENNFTKLAKKFLDEFHEVTSKI------VKECGSYDVSHIKVFKIDPNNFD 173
                                        5566677777789999999**************************98......478*******************9 PP

                                        HHH CS
                             Globin 104 lfg 106
                                           
  gene1302|gene1302|rna1302|rna1302 174 DAI 176
                                        765 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.6
                                        HHHHHHHHHHHHHH CS
                             Globin  78 ealkaalkklaarH 91 
                                        ++++++l+kl a+ 
  gene1302|gene1302|rna1302|rna1302 265 GTFHEFLRKLKAQI 278
                                        33333333333333 PP

>> zf-C4H2  Zinc finger-containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.2   0.00014       0.5      16     108 ..     123     219 ..     110     235 .. 0.78
   2 ?    3.3   0.2     0.025        89      37     102 ..     220     284 ..     209     311 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00014
                            zf-C4H2  16 knklakevealekeekcleeykkelelLeqEk.maHveeLrlIhaDinalEsvikeae...eekekslekakklye 87 
                                        ++++a+e ++++  +k+l e+++  +++ +E   + v +++  + D n+ ++ i   e   +e+e++l++ + +y+
  gene1302|gene1302|rna1302|rna1302 123 SKEIAAENNFTKLAKKFLDEFHEVTSKIVKECgSYDVSHIKVFKIDPNNFDDAIAVIEnglNEEERTLDSFETAYT 198
                                        57899**********************9999725679*************99776666111567777777777777 PP

                            zf-C4H2  88 eykklkeevnelrselglekl 108
                                         + k+ e++++  +++ l +l
  gene1302|gene1302|rna1302|rna1302 199 AFVKMFEHMETQPNDVRLVNL 219
                                        777777777766666666555 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.025
                            zf-C4H2  37 kkelelLeqEkmaHveeLrlIhaDinalEsvikea.eeekekslekakklyeeykklkeevnelrse 102
                                         k   +L +E +aH+  + ++      +Es   ++ +++k+ + e++  ++e ++klk ++++ r e
  gene1302|gene1302|rna1302|rna1302 220 AKAFYMLLNETRAHIILIYQLYGI--LIESSSSKSkDSSKKATAERVGTFHEFLRKLKAQIDNDRLE 284
                                        555666666777776655555432..34555444405566667888999999999******998866 PP

>> DUF2115  Uncharacterized protein conserved in archaea (DUF2115)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.2   0.00034       1.2      41     106 ..     133     198 ..     106     234 .. 0.78
   2 ?    3.0   0.6     0.036   1.3e+02      65     108 ..     253     296 ..     228     332 .. 0.62
   3 ?    0.1   0.4       0.3   1.1e+03      38      76 ..     323     359 ..     297     368 .. 0.62

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00034
                            DUF2115  41 kelseslteylfeaykelkn.krsgdkseykeevideeelkeflemleeqceeekeekeerlrklyy 106
                                        ++l +++ + + e   ++ + + s d s++k  +id+++++++++ +e++ +ee+++  +++++ y+
  gene1302|gene1302|rna1302|rna1302 133 TKLAKKFLDEFHEVTSKIVKeCGSYDVSHIKVFKIDPNNFDDAIAVIENGLNEEERT-LDSFETAYT 198
                                        5678888899999999999999999******9********************99886.444444332 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.036
                            DUF2115  65 dkseykeevideeelkeflemleeqceeekeekeerlrklyylv 108
                                        ++s++k+      +++efl++l++q+++++ ek++ +++ +++v
  gene1302|gene1302|rna1302|rna1302 253 KDSSKKATAERVGTFHEFLRKLKAQIDNDRLEKKHFITTAKMIV 296
                                        22222233344456777777777777777776544444444444 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.3
                            DUF2115  38 kyrkelseslteylfeaykelknkrsgdkseykeevide 76 
                                        + rk+l++ l e l++ +k+  nkr++d +++++   d+
  gene1302|gene1302|rna1302|rna1302 323 QQRKHLHHVLSEELLDYWKSSANKRKNDYEKMES--KDK 359
                                        4566666666666666666666655555555543..333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (380 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1224  (0.0682693); expected 358.6 (0.02)
Passed bias filter:                      512  (0.0285571); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 2395.30
//
Query:       gene1303|gene1303|rna1303|rna1303  [L=181]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    4.7e-25   87.9   0.5    5.8e-25   87.6   0.5    1.1  1  AhpC-TSA   AhpC/TSA family
    1.3e-15   57.4   0.2    1.5e-15   57.2   0.2    1.1  1  Redoxin    Redoxin
  ------ inclusion threshold ------
       0.14   12.1   0.5       0.22   11.4   0.5    1.2  1  SCO1-SenC  SCO1/SenC


Domain annotation for each model (and alignments):
>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.6   0.5   9.7e-29   5.8e-25      10     123 ..      23     143 ..      13     144 .. 0.93

  Alignments for each domain:
  == domain 1  score: 87.6 bits;  conditional E-value: 9.7e-29
                                        EE.STTCEEEECHHHTTSEEEEEEESTST-CCHHHHHHHHHHCHHHCCCTTEEEEEEESSSCHHHHHHHHH-H... CS
                           AhpC-TSA  10 lk.nadgetvslsdykgkpvvlffypkdwcpvCttelpalaklyeefkergvevigvsvdspeshkkfiekes... 81 
                                        +  + + +t+slsdy++k+vvl fyp+d++ vC+te+ a++++  +f++++  v+ vs+ds + h+++++  +   
  gene1303|gene1303|rna1303|rna1303  23 AVyKDKVKTISLSDYANKYVVLIFYPFDFTVVCPTEINAISDNKSKFEDANSVVLFVSCDSIFCHQAWMKISRadk 98 
                                        44456679*************************************************************9999999 PP

                                        .....SSEEEE-TTSHHHHHTT-EETTTTECSCEEEEE-TTSBEEE CS
                           AhpC-TSA  82 ....lnfpllsDeegkvakaygvlkeekglalratfvidkegkiry 123
                                             ++p++sD ++ + + +++  + +g + rat+++dk+ +++y
  gene1303|gene1303|rna1303|rna1303  99 gikgCTWPIVSDYDRSLTQYFNIAEP-AGNCARATVILDKKRNVVY 143
                                        ************************65.5***************998 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.2   0.2   2.5e-19   1.5e-15      16     142 ..      27     157 ..      13     162 .. 0.87

  Alignments for each domain:
  == domain 1  score: 57.2 bits;  conditional E-value: 2.5e-19
                                        TCEEEEEHHHHTTSEEEEEEESTTT-HHHHHTHHHHHTHHHHHHCSTTTEEEEEESSSHHHHHHHHH........T CS
                            Redoxin  16 tdgnsvslsefkgkkvvvnfvpgafcPtCsaehpyleklaellkekgvdvvavvadndafvkefwgk........e 83 
                                        ++ +++sls++++k vv++f+p  f+ +C +e++++ + + +  e +++vv  v+ ++ f  ++w k        +
  gene1303|gene1303|rna1303|rna1303  27 DKVKTISLSDYANKYVVLIFYPFDFTVVCPTEINAISDNKSK-FEDANSVVLFVSCDSIFCHQAWMKisradkgiK 101
                                        45689*****************************99999888.4666777788888889999999999******** PP

                                        T-TSEEEE-TTSHHHHHTT-TTEEE.GGGEEE-EEEEEEETTEEEEEEESSSCHT.STTS CS
                            Redoxin  84 glkfpvlsDgsaaftkalGlrleedaseglrtpryavidedgkvvylevepepet.eesn 142
                                        g ++p++sD + ++t+ ++  ++e+a++  ++++++++d++ +vvy  v++ + +  +++
  gene1303|gene1303|rna1303|rna1303 102 GCTWPIVSDYDRSLTQYFN--IAEPAGN--CARATVILDKKRNVVYFSVGDKRMGrSVDE 157
                                        *******************..88**999..9*******************9885544444 PP

>> SCO1-SenC  SCO1/SenC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.5   3.7e-05      0.22       9      66 ..      27      82 ..      20      89 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3.7e-05
                          SCO1-SenC  9 qdgeavteedlegkpslvffgFthCpdvCpttlanmaevldalgeeaekvqplfiTvD 66
                                        + ++++ +d+++k++++ f     + vCpt+++ +++  ++++++  +  +lf+++D
  gene1303|gene1303|rna1303|rna1303 27 DKVKTISLSDYANKYVVLIFYPFDFTVVCPTEINAISDNKSKFEDA--NSVVLFVSCD 82
                                       45689999*******999998888899****************999..6678888888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       465  (0.0259356); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.30s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 1178.97
//
Query:       gene1304|gene1304|rna1304|rna1304  [L=582]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.2e-26   93.7   3.5    4.3e-26   92.7   3.5    1.4  1  Metallophos  Calcineurin-like phosphoesterase
    0.00018   21.4   0.9       0.67   10.2   0.1    2.9  2  TPR_2        Tetratricopeptide repeat
     0.0015   18.8   0.6        1.5    9.1   0.2    2.8  2  TPR_12       Tetratricopeptide repeat
     0.0051   16.6   0.3       0.21   11.5   0.3    2.6  2  TPR_10       Tetratricopeptide repeat
  ------ inclusion threshold ------
       0.14   12.8   0.0         20    5.9   0.0    3.0  3  TPR_16       Tetratricopeptide repeat
       0.47   10.4   3.2        1.4    8.8   0.1    2.7  3  TPR_1        Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.7   3.5   1.4e-29   4.3e-26       3     201 ..     337     533 ..     336     534 .. 0.87

  Alignments for each domain:
  == domain 1  score: 92.7 bits;  conditional E-value: 1.4e-29
                                        EEEEESBTBTTCCTHHHHHHHHHHHH.....HHHTTESEEEEESTSSSSSHHHHHHHHH.HHHHHHHTSEEEEEC- CS
                        Metallophos   3 ilvigDlHlalgggqlddllkllddl.....lreekpdlvllaGDlvdrgdlekellel.laalvkypipvylllG 72 
                                          v+gD+H     g+l ++ + ++++     l  + +d ++++GD+vdrg    el+ + +  +++yp++v++ +G
  gene1304|gene1304|rna1304|rna1304 337 YYVFGDTH-----GNLVSTYNEIRKItgnfsL--SFRDHLIFNGDFVDRGKHGLELVIFfILLKLSYPKNVHMNRG 405
                                        579*****.....**********999555432..445999999*******66666666659999999********* PP

                                        TTS........CHHHHHHHHHHHHHHHHHHHEHHHCEEETSEEEEEETTEEEEEEEESECEEETHHHHHHHHHHHS CS
                        Metallophos  73 NHe........gfeeellnkygylgifsepwrsdaevfnnlplaslgsgslkvlllhGgspellvsldklgslnle 140
                                        NHe         +++ +  +y++ g+f  ++++ + +f+ lpl+ ++++  +v+++hGg p +  +++++ +ln++
  gene1304|gene1304|rna1304|rna1304 406 NHEfagtnrqfDLYDQIAKRYPFHGTF--VYETINLFFQTLPLCTIVND--DVFVVHGGLPADRFTVQDVYKLNRF 477
                                        ****99999776667788888887755..7777799*************..********77776888888888888 PP

                                        CHHHHCC...HHHHHHHHHHTTCSEEEEEESSESSCSSSCSCCHHHHHHHHHHTTESEEEEESS CS
                        Metallophos 141 leapepg...dewlkdlekrekadwvivlgHsplyrgsgylfgdealedllkkygvdlvisGHt 201
                                           + ++    ++++d        +v + gH p  rg+g ++g++++e++l +++++lv+++H+
  gene1304|gene1304|rna1304|rna1304 478 VSKIKNEllaGLMWSD--------PVEIAGHEPSRRGIGVHYGQDVTERFLSDNNLKLVVRSHE 533
                                        88888889999*****........***************************************7 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.1   0.00023      0.67       7      29 ..       7      29 ..       5      30 .. 0.92
   2 !    8.8   0.1   0.00064       1.9       3      33 ..      99     129 ..      97     130 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00023
                              TPR_2  7 lGlayyklgdyeeAleafekAle 29
                                        G++++k++dy+ Al+++e +l+
  gene1304|gene1304|rna1304|rna1304  7 EGNVAFKSKDYKLALAWYEDSLK 29
                                       79*****************9886 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00064
                              TPR_2   3 alynlGlayyklgdyeeAleafekAleldPn 33 
                                        +l n+  +yy++ d++ A+ + + A ++ ++
  gene1304|gene1304|rna1304|rna1304  99 VLLNISTVYYRQYDLQNAITYAQMAYKIRED 129
                                        6889999******************999876 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.7   0.0    0.0029       8.6      52      72 ..       8      28 ..       5      34 .. 0.70
   2 !    9.1   0.2   0.00052       1.5      47      76 ..      99     128 ..      95     131 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0029
                             TPR_12 52 grlyralgryeeAlelleeal 72
                                       g + +++++y+ Al+++e++l
  gene1304|gene1304|rna1304|rna1304  8 GNVAFKSKDYKLALAWYEDSL 28
                                       566667777777777777776 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00052
                             TPR_12  47 tlrnLgrlyralgryeeAlelleealaiae 76 
                                        +l n++++y+++ +++ A+ + + a++i+e
  gene1304|gene1304|rna1304|rna1304  99 VLLNISTVYYRQYDLQNAITYAQMAYKIRE 128
                                        467888888888888888888888888876 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0     0.066     2e+02       9      29 ..       8      28 ..       8      30 .. 0.88
   2 !   11.5   0.3     7e-05      0.21       5      33 ..     100     128 ..      99     129 .. 0.94

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.066
                             TPR_10  9 analrqrgrydeAealleeal 29
                                       +n+ ++ ++y+ A+a++e++l
  gene1304|gene1304|rna1304|rna1304  8 GNVAFKSKDYKLALAWYEDSL 28
                                       67888899***********98 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 7e-05
                             TPR_10   5 lnNLanalrqrgrydeAealleealairr 33 
                                        l N++ +++++++++ A  +++ a+ ir+
  gene1304|gene1304|rna1304|rna1304 100 LLNISTVYYRQYDLQNAITYAQMAYKIRE 128
                                        679***********************998 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0    0.0068        20      41      61 ..       8      28 ..       4      31 .. 0.82
   2 ?    2.6   0.0     0.075   2.2e+02      23      65 ..      91     128 ..      87     130 .. 0.80
   3 ?   -0.5   0.0      0.69   2.1e+03      19      46 ..     418     442 ..     417     443 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0068
                             TPR_16 41 gdaalrqgrlaeAaalyraal 61
                                       g++a++ +++++A+a+y+  l
  gene1304|gene1304|rna1304|rna1304  8 GNVAFKSKDYKLALAWYEDSL 28
                                       889999999999999998765 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.075
                             TPR_16  23 alkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraap 65 
                                        +lk+      +   ll+   +++rq +l+ A+ + + a++   
  gene1304|gene1304|rna1304|rna1304  91 FLKNE-----HFLVLLNISTVYYRQYDLQNAITYAQMAYKIRE 128
                                        55666.....77778888889****************998765 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.69
                             TPR_16  19 aleaalkrdpssPdaaeAllllgdaalr 46 
                                        ++++  kr+   P++  + ++  +++++
  gene1304|gene1304|rna1304|rna1304 418 LYDQIAKRY---PFHGTFVYETINLFFQ 442
                                        799******...***9999998887776 PP

>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.1   0.00048       1.4       8      28 ..       8      28 ..       7      29 .. 0.92
   2 ?    1.0   0.3      0.15   4.3e+02      10      34 .]     106     130 ..     100     130 .. 0.87
   3 ?   -2.7   0.0       2.1   6.2e+03      10      18 ..     400     408 ..     399     410 .. 0.52

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00048
                                       HHHHHHTT-HHHHHHHHHHHH CS
                              TPR_1  8 GnayfklgkydeAleyyekAL 28
                                       Gn+ fk ++y+ Al+ ye  L
  gene1304|gene1304|rna1304|rna1304  8 GNVAFKSKDYKLALAWYEDSL 28
                                       99***************9777 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.15
                                        HHHHTT-HHHHHHHHHHHHHHSTTH CS
                              TPR_1  10 ayfklgkydeAleyyekALelnPnn 34 
                                        +y+++ +++ A+ y + A ++++++
  gene1304|gene1304|rna1304|rna1304 106 VYYRQYDLQNAITYAQMAYKIREDD 130
                                        68888899**********9998875 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 2.1
                                        HHHHTT-HH CS
                              TPR_1  10 ayfklgkyd 18 
                                        ++++ g+++
  gene1304|gene1304|rna1304|rna1304 400 VHMNRGNHE 408
                                        455555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (582 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       618  (0.0344693); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.42
# Mc/sec: 4208.87
//
Query:       gene1305|gene1305|rna1305|rna1305  [L=297]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
          1   10.0  23.0       0.85   10.3   4.7    4.2  4  DUF883     Bacterial protein of unknown function (DUF883)
        2.8    8.5  48.2        6.2    7.4  12.7    4.8  4  YtxH       YtxH-like protein


Domain annotation for each model (and alignments):
>> DUF883  Bacterial protein of unknown function (DUF883)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.3     0.027   2.4e+02      25      53 ..      55      83 ..      32      96 .. 0.53
   2 ?    6.7   1.1    0.0012        11      24      56 ..     126     158 ..     117     173 .. 0.58
   3 ?   10.3   4.7   9.4e-05      0.85       8      67 ..     175     234 ..     168     238 .. 0.86
   4 ?    1.9   0.1     0.038   3.4e+02      13      42 ..     241     270 ..     238     280 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.027
                             DUF883 25 ageeaeelRerleerlerarerlrdaeea 53
                                       +++++ +++++  +++ +a e+ ++++e+
  gene1305|gene1305|rna1305|rna1305 55 TKQTYGSAKDKGAQMAGAAGEKGEHLKEK 83
                                       44444444444444444444444444333 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0012
                             DUF883  24 eageeaeelRerleerlerarerlrdaeeavae 56 
                                        + ++++ ++++++ e +++a+++ +d++++ a+
  gene1305|gene1305|rna1305|rna1305 126 TMKDKYGTAKKKAGELADSAKQKYEDTRKKTAD 158
                                        344555555555555555555555555554443 PP

  == domain 3  score: 10.3 bits;  conditional E-value: 9.4e-05
                             DUF883   8 eslladleellkeaadeageeaeelRerleerlerarerlrdaeeavaerakeaaeaadd 67 
                                        ++++++++e+ ++++ ++++ a++++e++  +  +ar+++++++ea +e  ++a   ad+
  gene1305|gene1305|rna1305|rna1305 175 NQAINKVKEVGEKTKYKTEKAAATAKEKAAGMKGSARQATEKTKEAGRETKNKAKGGADK 234
                                        788999999999999999***********9999999999999999999988888776665 PP

  == domain 4  score: 1.9 bits;  conditional E-value: 0.038
                             DUF883  13 dleellkeaadeageeaeelRerleerler 42 
                                        d+e+ +k+  +  +e++e++++++e++l++
  gene1305|gene1305|rna1305|rna1305 241 DAEDEVKQVVECPKEDYEKIKKKMEQKLTS 270
                                        6777788888889999*******9999865 PP

>> YtxH  YtxH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   7.1    0.0091        82      35      73 ..      45      83 ..      16      96 .. 0.63
   2 ?    2.8  15.9     0.019   1.7e+02      19      69 ..      62     151 ..      61     184 .. 0.78
   3 ?    7.4  12.7    0.0007       6.2      22      65 ..     173     230 ..     169     236 .. 0.76
   4 ?    5.7   5.6    0.0024        22      21      67 ..     219     270 ..     217     276 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.0091
                               YtxH 35 ddlkekakelleeakekakekaedlkekvkekadelkek 73
                                       dd k+++ + +++++  ak+k+++++ ++ ek ++lkek
  gene1305|gene1305|rna1305|rna1305 45 DDKKKQVVDGTKQTYGSAKDKGAQMAGAAGEKGEHLKEK 83
                                       344444444444444444777777777777777777776 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.019
                               YtxH  19 APksGketRkdlkekaddlkekakelleeakeka.......................................kek 55 
                                        A ++G ++   + ek + lkek+  ++e+a+ek+                                       k+k
  gene1305|gene1305|rna1305|rna1305  62 AKDKGAQMAGAAGEKGEHLKEKTGGMKENAQEKTg*******************lkeksgnvvdtmkdkygtaKKK 137
                                        6788999999999999999999999999999999999999999999999999999777777777775555555555 PP

                               YtxH  56 aedlkekvkekade 69 
                                        a +l++++k+k ++
  gene1305|gene1305|rna1305|rna1305 138 AGELADSAKQKYED 151
                                        55555555555555 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.0007
                               YtxH  22 sGketRkdlkekaddlkekakelleeakeka..............kekaedlkekvke 65 
                                        +G++  +++ke  +++k k+++++ +akeka              ke + + k+k+k 
  gene1305|gene1305|rna1305|rna1305 173 KGNQAINKVKEVGEKTKYKTEKAAATAKEKAagmkgsarqatektKEAGRETKNKAKG 230
                                        899999****************************777766644444444444444444 PP

  == domain 4  score: 5.7 bits;  conditional E-value: 0.0024
                               YtxH  21 ksGketRkdlkekaddlkekakelleeakeka...kekaedlkekvkek..a 67 
                                        + G+et++++k  ad++     ++ +e+k+ +   ke  e++k+k+++k  +
  gene1305|gene1305|rna1305|rna1305 219 EAGRETKNKAKGGADKMTGGDADAEDEVKQVVecpKEDYEKIKKKMEQKltS 270
                                        679*************998888888888888888899999999999998544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (297 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2164  (0.120698); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.29s 00:00:00.88 Elapsed: 00:00:00.46
# Mc/sec: 1924.89
//
Query:       gene1306|gene1306|rna1306|rna1306  [L=475]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.3e-25   90.1   0.5    5.3e-25   88.1   0.5    1.9  1  GTP_EFTU     Elongation factor Tu GTP binding domain
    7.9e-24   83.7   1.8    8.1e-24   83.7   0.2    1.9  2  eIF2_C       Initiation factor eIF2 gamma, C terminal
    3.9e-08   33.6   0.1    1.1e-07   32.2   0.1    1.8  1  GTP_EFTU_D2  Elongation factor Tu domain 2
     0.0029   17.5   0.2      0.026   14.4   0.1    2.2  2  RsgA_GTPase  RsgA GTPase
      0.003   17.6   0.0     0.0069   16.5   0.0    1.7  1  MMR_HSR1     50S ribosome-binding GTPase
  ------ inclusion threshold ------
      0.016   15.2   0.0      0.049   13.6   0.0    1.8  1  SAM_4        SAM domain (Sterile alpha motif)


Domain annotation for each model (and alignments):
>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.1   0.5   1.8e-28   5.3e-25       3     193 ..      51     252 ..      49     253 .. 0.77

  Alignments for each domain:
  == domain 1  score: 88.1 bits;  conditional E-value: 1.8e-28
                                        EEEEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHH..HHHST..................HCHSHHHHHHTSCSSC CS
                           GTP_EFTU   3 irnigiighvDhGKtTLtdrLlyktgaiskkgeka..eeerv..................lDtlkeErergiTiks 58 
                                        ++nig+ighv hGK+T++ ++   + +  +++ ++  +   +                      +      +Ti+ 
  gene1306|gene1306|rna1306|rna1306  51 TINIGTIGHVAHGKSTIVRAISGIHTIRFRSELERniT---IklgyanakiykcdtcprpDCYSAMNSSSPFTISC 123
                                        68******************995554444433333220...13445555666655555532222334444566666 PP

                                        EEEEEE.TTCSSEEEEEEEESSSGGGHHHHHHHHHT-SEEEEEEETTTB.STHHHHHHHHHHHHTTTE.EEEEEES CS
                           GTP_EFTU  59 aaisle.ketkkylinliDtPGHvdFskevirglrvlDgavlvvdaveG.vepqteevlrlalkegvp.iivfiNK 131
                                         + s+e ++t  ++++++D+PGH   + ++ +g++++D a+l+v+a+e  ++pqt+e+l  +  ++++ +i++ NK
  gene1306|gene1306|rna1306|rna1306 124 PNNSCEgTSTLIKHVSFVDCPGHDVLMATMLNGTAIMDAAMLLVAANEPcPQPQTQEHLFAVEIMNLKkFIIVQNK 199
                                        666666558889999********************************9879*****************9******* PP

                                        CGST.HHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTTEEEEEEBTTTTBTHHHHHHHHHHHSH CS
                           GTP_EFTU 132 mDrl.kaelkeiveevkqklsrkeeklekygekgekevpvvfgSalkgegvktllealvellp 193
                                        +D + +++  e+++++   +      +++ ++++    p+v++S+  + +v ++l+ +v+++p
  gene1306|gene1306|rna1306|rna1306 200 IDLVsREQALEQKDQIV-AF------IKNTKAEN---SPIVPASGQLNINVCAILDFIVNYFP 252
                                        ****7777788888888.77......66665555...6***********************98 PP

>> eIF2_C  Initiation factor eIF2 gamma, C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.1       3.3     1e+04       5      32 ..     185     216 ..     183     223 .. 0.63
   2 !   83.7   0.2   2.7e-27   8.1e-24       2      86 .]     377     462 ..     376     462 .. 0.93

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 3.3
                                        EEEEE-SBESSSSSCCC....-----TTEEEE CS
                             eIF2_C   5 ieyellerlvgvkeekk....veklkkkEvLm 32 
                                        +e+  l++ + v+++ +     ++l++k++++
  gene1306|gene1306|rna1306|rna1306 185 VEIMNLKKFIIVQNKIDlvsrEQALEQKDQIV 216
                                        56666777777777733333467777777765 PP

  == domain 2  score: 83.7 bits;  conditional E-value: 2.7e-27
                                        EEEEEEEE-SBESSSSSCCC.-----TTEEEEEEETTEEEEEEEEEEESSEEEEEEEEEEE-STTEEEEEEEEETT CS
                             eIF2_C   2 eleieyellerlvgvkeekk.veklkkkEvLmlniGsastggvvtsvkkdeakvkLkkPvcaekgekialsRrvek 76 
                                        e+ + y+l++++ gv+++ +    ++ +E++++niGs++tg++++++++d+++++L kP+c+ekge++ +s+++++
  gene1306|gene1306|rna1306|rna1306 377 EILVFYSLFQKISGVDKRADkRGLMTLNEQILVNIGSTTTGSTIMKLENDKVRLSLVKPACCEKGERVSISKKIHG 452
                                        67788**********999553788899************************************************* PP

                                        SEEEEEEEEE CS
                             eIF2_C  77 rWrLiGwGei 86 
                                        +WrLiG+G +
  gene1306|gene1306|rna1306|rna1306 453 HWRLIGYGVV 462
                                        ********75 PP

>> GTP_EFTU_D2  Elongation factor Tu domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.2   0.1   3.5e-11   1.1e-07       1      65 [.     284     355 ..     284     366 .. 0.86

  Alignments for each domain:
  == domain 1  score: 32.2 bits;  conditional E-value: 3.5e-11
                                        EEEEEEEEEESEEETTEEEEEEC.TCTTSEE.......EEEEEEEEEEETEEESEEETTSEEEEEEEESSCCS CS
                        GTP_EFTU_D2   1 GtvalgrvysGtlkkGdevrilg.ndtskke.......ivtrissletfhededeavaganaGvivaikgled 65 
                                        G+v++g++  G+l+++de++i++     +k+        +tr++sl+++++ + +a +g+ +Gv++++++  +
  gene1306|gene1306|rna1306|rna1306 284 GGVIGGSLLKGELHVNDEIEIRPgIIY-RKGskveckpFITRVTSLQAEKNLLSTAQPGGLIGVGTLLDPFFC 355
                                        89*********************8554.44457*********************************9998766 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.19   5.7e+02     105     123 ..      57      75 ..      41      85 .. 0.76
   2 !   14.4   0.1   8.8e-06     0.026      13      71 ..     157     215 ..     132     239 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.19
                                        ECSTTSSHHHHHHHHCTT- CS
                        RsgA_GTPase 105 vGqSGvGKStLinallpel 123
                                        +G+   GKSt++ a+ + +
  gene1306|gene1306|rna1306|rna1306  57 IGHVAHGKSTIVRAISGIH 75 
                                        567778******9998754 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 8.8e-06
                                        EES--EEEEEEESTTTT--HHHHHHHHHHHHHTT-.EEEEEEE-GGG--HHHHHHHHHHH CS
                        RsgA_GTPase  13 vaNvdqllivvslkepelslnlldrfLvlaeekgi.epvivlnKiDlleeeeeleelkee 71 
                                         a +d ++++v+++ep  ++++ +  L+++e  ++ + +iv nKiDl+++e++le+  + 
  gene1306|gene1306|rna1306|rna1306 157 TAIMDAAMLLVAANEPCPQPQTQE-HLFAVEIMNLkKFIIVQNKIDLVSREQALEQKDQI 215
                                        567899********8888887655.67777777774788999**********66655544 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   2.3e-06    0.0069       2     114 .]      54     199 ..      53     222 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 2.3e-06
                                        EEEEESTTSSHHHHHHHHHTS...TEEESSSTTSSSSEEEEEEEETTEE........................... CS
                           MMR_HSR1   2 vaivGrpNvGKStLinaltge...kaivsdkpgtTrdinegrvklkgke........................... 47 
                                        ++ +G+   GKSt+++a++g    + + + +   T++  +++ k+ + +                           
  gene1306|gene1306|rna1306|rna1306  54 IGTIGHVAHGKSTIVRAISGIhtiRFRSELERNITIKLGYANAKIYKCDtcprpdcysamnssspftiscpnnsce 129
                                        889****************954456777888888888888888744322456667777777788888888888888 PP

                                        ........EEEEECGGCSSHHHHHHHHHHHHHHHHC.TSEEEEEEETT.....TTCSHHHHHHHHHHHHHTTSEEE CS
                           MMR_HSR1  48 ........ielvDtpGliegaseekglgkaflalee.adlillvvdas.....eeklkpldeeleelleeakkpli 109
                                                + +vD+pG  +       l  ++l+    +d+++l+v a+          + +e+l ++   + k++i
  gene1306|gene1306|rna1306|rna1306 130 gtstlikhVSFVDCPG-HD------VLMATMLNGTAiMDAAMLLVAANepcpqP----QTQEHLFAVEIMNLKKFI 194
                                        88888888********.43......56666666555468888888766333220....122333333333566777 PP

                                        EEEES CS
                           MMR_HSR1 110 lvlnk 114
                                        +v nk
  gene1306|gene1306|rna1306|rna1306 195 IVQNK 199
                                        77776 PP

>> SAM_4  SAM domain (Sterile alpha motif)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   1.6e-05     0.049      30      70 ..     388     428 ..     380     438 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.6e-05
                              SAM_4  30 vsfvdnriqknmlldlskeimnelgitvvgdiiailkhakv 70 
                                        +s vd r +k  l+ l+ +i+ ++g t  g  i  l   kv
  gene1306|gene1306|rna1306|rna1306 388 ISGVDKRADKRGLMTLNEQILVNIGSTTTGSTIMKLENDKV 428
                                        6779***************************9998887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (475 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       555  (0.0309554); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.48
# Mc/sec: 2996.20
//
Query:       gene1308|gene1308|rna1308|rna1308  [L=457]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
   1.8e-188  627.3  30.6     2e-188  627.1  30.6    1.0  1  DUF5098     Domain of unknown function (DUF5098)
  ------ inclusion threshold ------
      0.044   13.2   0.1      0.083   12.3   0.1    1.4  1  DUF2034     Protein of unknown function (DUF2034)
       0.81    9.7   9.1       0.81    9.7   2.8    3.0  3  P4Ha_N      Prolyl 4-Hydroxylase alpha-subunit, N-terminal re
        9.7    6.6  10.9        2.5    8.5   1.2    3.7  4  PfUIS3      Plasmodium falciparum UIS3 membrane protein


Domain annotation for each model (and alignments):
>> DUF5098  Domain of unknown function (DUF5098)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  627.1  30.6  4.5e-192    2e-188       1     463 []      11     450 ..      11     450 .. 0.99

  Alignments for each domain:
  == domain 1  score: 627.1 bits;  conditional E-value: 4.5e-192
                            DUF5098   1 ykllkeKvkwikaflehvetvskraaellfratqiPrntawkDpliiellemsdkqravfdeltrlyeitvvkeld 76 
                                        ykl++eKv+wi++fl+hv+t+s+r+ael+fr+tqiPrnt+w+D++ii+++em+dk+r++fdeltr+yeitvv+e++
  gene1308|gene1308|rna1308|rna1308  11 YKLAEEKVGWILSFLDHVTTISRRTAELYFRCTQIPRNTRWQDVSIINMVEMMDKSRNSFDELTRMYEITVVVECK 86 
                                        89************************************************************************** PP

                            DUF5098  77 allkkledkiaelneeekkfekklkellkelkaardshleAwtegkaDpWlteleLkkaikkylkedeesnellka 152
                                        a+lkkledki+eln+ e++f+k+l+++l++l+++r++hleAw++g+aD+Wlte+eLkka+kkyl+e+e++ne+lk+
  gene1308|gene1308|rna1308|rna1308  87 AILKKLEDKINELNGLEDRFNKALQKYLDDLMVCRQNHLEAWSNGTADTWLTEKELKKALKKYLNENETWNENLKK 162
                                        **************************************************************************** PP

                            DUF5098 153 eisksdkelqelkkkYkeillnflkiqkahyknll...eevdid..rflfdevselkkeifydfpeseeeklqeke 223
                                        ei+++dkel+++++kY+ei++++l+iq++hyk+ll   eev+id  rf        kk++f+dfpe+e++++ +ke
  gene1308|gene1308|rna1308|rna1308 163 EILVYDKELHSISNKYREIIATSLNIQRNHYKSLLmcgEEVLIDeqRF--------KKDFFFDFPENEDCSIGNKE 230
                                        ********************************************7778........******************** PP

                            DUF5098 224 ekeelkekeetkfeelveqIvkelkkkrkqfikkklevkkcgifkvkknksdiktlfiivtetnfiHafdldsive 299
                                        e      k+etkfe+++e+I++++ ++r+++i+++++vkk+gif+v++ ++dik++++ivtet+fiHa+dldsi+ 
  gene1308|gene1308|rna1308|rna1308 231 E------KSETKFEDAYEEIMNDM-RSRNSEITRDISVKKFGIFRVRR-NYDIKHALVIVTETQFIHAYDLDSITL 298
                                        *......99***************.***********************.*************************** PP

                            DUF5098 300 elesLsdeekallkkLndgsykklisfFdkskkealntteekelkeisaavlneidvlssvlkgfpiklkdklvkL 375
                                        +le Lsde+kallkkLnd  y+++isfF++ k+e+lntteek+l+++s +++n+++v++++lkgfp+++kdkl+kL
  gene1308|gene1308|rna1308|rna1308 299 YLE-LSDEHKALLKKLND--YNRGISFFFG-KNEFLNTTEEKQLATFSGYIFNNLNVSRGMLKGFPMTIKDKLIKL 370
                                        ***.**************..**********.********************************************* PP

                            DUF5098 376 dkekreiiitekksntlksiFvsntikiksFtlkdiyelffalldknkkeeseekeeesdeeeedndsvekekeee 451
                                        dk+k+e+iit++ks++lk++Fvsnt+kiksF+l+d+yelff+++++++k++s+++++++++e++++ds        
  gene1308|gene1308|rna1308|rna1308 371 DKDKKELIITARKSPMLKNFFVSNTVKIKSFVLRDAYELFFSFCKTVEKKGSSDAKDIETTEVVPSDS-------- 438
                                        ********************************************************************........ PP

                            DUF5098 452 kiissiedeNPW 463
                                        kii+++edeNPW
  gene1308|gene1308|rna1308|rna1308 439 KIINYKEDENPW 450
                                        9*********** PP

>> DUF2034  Protein of unknown function (DUF2034)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   1.9e-05     0.083      71     118 ..      65     111 ..      34     126 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.9e-05
                            DUF2034  71 ekklkykiidkaedlkVlvqCkalkkkikpkeirELsGsfsshkakkk 118
                                        +++ + + + ++ ++ V+v Cka+ kk++ k i EL G  ++++ + +
  gene1308|gene1308|rna1308|rna1308  65 KSRNSFDELTRMYEITVVVECKAILKKLEDK-INELNGLEDRFNKALQ 111
                                        33445555555889**************976.89****9887776555 PP

>> P4Ha_N  Prolyl 4-Hydroxylase alpha-subunit, N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.1     0.056   2.5e+02       4      26 ..      95     117 ..      92     134 .. 0.83
   2 ?    9.7   2.8   0.00018      0.81      11      60 ..     138     187 ..     130     190 .. 0.90
   3 ?   -2.4   0.0         1   4.6e+03      89     123 ..     242     275 ..     226     278 .. 0.54

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.056
                             P4Ha_N   4 dlekLlklErelveeLesyieee 26 
                                        ++++L  lE+++ ++L++y++++
  gene1308|gene1308|rna1308|rna1308  95 KINELNGLEDRFNKALQKYLDDL 117
                                        6788999*************987 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00018
                             P4Ha_N  11 lErelveeLesyieeeekkleklkrfleeleeehesakedkeeylsnPln 60 
                                        +E+el ++L++y++e+e   e+lk+ +  +++e +s +++ +e ++  ln
  gene1308|gene1308|rna1308|rna1308 138 TEKELKKALKKYLNENETWNENLKKEILVYDKELHSISNKYREIIATSLN 187
                                        79********************************9988888888777665 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 1
                             P4Ha_N  89 eql.ealkkrkeslPteeDlegaakallrLqdtYnL 123
                                        e++ +++++r+++   ++D++    ++ r    Y++
  gene1308|gene1308|rna1308|rna1308 242 EEImNDMRSRNSE--ITRDISVKKFGIFRVRRNYDI 275
                                        2232334444433..556666666777777766666 PP

>> PfUIS3  Plasmodium falciparum UIS3 membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.1      0.36   1.6e+03      49      82 ..      55      89 ..      48     100 .. 0.54
   2 ?    8.5   1.2   0.00056       2.5       9      72 ..      95     158 ..      83     184 .. 0.70
   3 ?    2.2   0.5     0.053   2.4e+02       5      78 ..     159     232 ..     156     241 .. 0.77
   4 ?    0.5   0.1      0.17   7.8e+02      17      37 ..     255     277 ..     241     309 .. 0.71

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.36
                                       HHTT-HHHHHHHHHHHHH.HTT----HHHHHHHHH CS
                             PfUIS3 49 slvndyeylrkivqtlde.srdvslskaqedkavl 82
                                       s +n +e + k  +++de +r  +++ + e ka+l
  gene1308|gene1308|rna1308|rna1308 55 SIINMVEMMDKSRNSFDElTRMYEITVVVECKAIL 89
                                       45555555655555555533444444444444444 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00056
                                        --------S---HHHHHHHHHHHHHHHHHHHHHS-HHHHHHHTT-HHHHHHHHHHHHHHTT--- CS
                             PfUIS3   9 klkenkndvdvslkrynifvdivklaiqkhfedlsndqkdslvndyeylrkivqtldesrdvsl 72 
                                        k+ e +   d   k  ++++d   ++ q+h+e  sn   d  + + e  + + + l+e+   + 
  gene1308|gene1308|rna1308|rna1308  95 KINELNGLEDRFNKALQKYLDDLMVCRQNHLEAWSNGTADTWLTEKELKKALKKYLNENETWNE 158
                                        33333333344445555799***************************99999999999976653 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.053
                                        -TSS--------S---HHHHHHHHHHHHHHHH.HHHHHS-HHHHHHHTT-HHHHHHHHHHHHHHTT----HHHHH CS
                             PfUIS3   5 nlkkklkenkndvdvslkrynifvdivklaiq.khfedlsndqkdslvndyeylrkivqtldesrdvslskaqed 78 
                                        nlkk++   + ++     +y  ++  + l iq +h++ l    ++ l+++  + + +   + e+ d s+   +e+
  gene1308|gene1308|rna1308|rna1308 159 NLKKEILVYDKELHSISNKYREIIA-TSLNIQrNHYKSLLMCGEEVLIDEQRFKKDFFFDFPENEDCSIGNKEEK 232
                                        5666666666666544455666554.457777369*********************************9987765 PP

  == domain 4  score: 0.5 bits;  conditional E-value: 0.17
                                        S..---HHHHHHHHHHHHHHHHH CS
                             PfUIS3  17 v..dvslkrynifvdivklaiqk 37 
                                        +  d+s+k++ if    +  i++
  gene1308|gene1308|rna1308|rna1308 255 ItrDISVKKFGIFRVRRNYDIKH 277
                                        43499*****9997666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (457 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1308  (0.0729544); expected 358.6 (0.02)
Passed bias filter:                      474  (0.0264376); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.40
# Mc/sec: 3443.24
//
Query:       gene1309|gene1309|rna1309|rna1309  [L=121]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0021   17.5   2.0       0.31   10.4   0.9    2.1  2  Tmem26    Transmembrane protein 26


Domain annotation for each model (and alignments):
>> Tmem26  Transmembrane protein 26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.7   0.0   0.00022         4     172     203 ..       2      33 ..       1      45 [. 0.88
   2 !   10.4   0.9   1.7e-05      0.31      18      64 ..      54     103 ..      39     106 .. 0.64

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.00022
                             Tmem26 172 effeslkekevaknallvlavlviwswsllqF 203
                                        ++ + +k++++a +++++++++ i+ ++++  
  gene1309|gene1309|rna1309|rna1309   2 NLHDDIKDQDIAIKSSFIMTTINIYGMCFVVH 33 
                                        67799***********************9765 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 1.7e-05
                             Tmem26  18 slvavlqvvl..vk..kdelywllallllllvlEtiltlilkkgkeykwfc 64 
                                        sl+ ++ +vl  v+   +e+ + +++ l   + E+++t+ + k++ey +f+
  gene1309|gene1309|rna1309|rna1309  54 SLLPLCNTVLflVNrnVRESIFSFTMVL-CNLSEMLYTIRVTKAAEYEFFW 103
                                        5555555443113300334444444433.3468*****************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       584  (0.0325729); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 832.82
//
Query:       gene131|gene131|rna131|rna131  [L=171]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
       0.03   14.7   0.3       0.15   12.5   0.2    2.2  1  TbpB_C      C-lobe handle domain of Tf-binding protein B
      0.033   14.3   5.6       0.18   12.0   1.3    2.9  2  FNIP        FNIP Repeat
      0.035   13.9   1.7       0.17   11.7   1.7    2.3  1  AHD         ANC1 homology domain (AHD)
       0.13   12.4   2.8        0.4   10.8   0.2    2.6  3  DMAP1_like  Putative DMAP1-like


Domain annotation for each model (and alignments):
>> TbpB_C  C-lobe handle domain of Tf-binding protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.2   3.3e-05      0.15      10      39 ..      46      78 ..      37     118 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.3e-05
                                   ET...T-SSEEE-B--S-TTEEEETTEEEES-- CS
                         TbpB_C 10 dl...kklekkeldnFgnaakLvidgkeipLlp 39
                                   dl   + +++++l++++n+++L++dg  i   +
  gene131|gene131|rna131|rna131 46 DLcslDFKTVQNLKKYENIKHLILDGSIIGYES 78
                                   4433466899****************9886555 PP

>> FNIP  FNIP Repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.2     0.022     1e+02      13      40 ..       7      33 ..       6      37 .. 0.75
   2 ?   12.0   1.3   3.9e-05      0.18      12      42 ..      62      93 ..      56      95 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.022
                           FNIP 13 nleiLilgrdFnqkiligsLPnSlkeLy 40
                                   nl+ L + + F   +    +Pn+l++L+
  gene131|gene131|rna131|rna131  7 NLQTLVIDSLFESDLA-KNIPNQLETLE 33
                                   6667777666776666.56999999996 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 3.9e-05
                           FNIP 12 snleiLil.grdFnqkiligsLPnSlkeLyFg 42
                                   +n+++Lil g+    +  +++LP +l++L+F 
  gene131|gene131|rna131|rna131 62 ENIKHLILdGSIIGYESIFDCLPINLESLKFT 93
                                   5999999988888899999**********996 PP

>> AHD  ANC1 homology domain (AHD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   1.7   3.7e-05      0.17      45      60 ..      46      61 ..       1      63 [. 0.73

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.7e-05
                            AHD 45 DLcaLDdeTieklqkc 60
                                   DLc+LD +T+++l+k+
  gene131|gene131|rna131|rna131 46 DLCSLDFKTVQNLKKY 61
                                   *************986 PP

>> DMAP1_like  Putative DMAP1-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.2     9e-05       0.4      69     105 ..      32      69 ..      12      70 .. 0.77
   2 ?   -0.7   0.1      0.34   1.5e+03      46      46 ..     115     115 ..      90     156 .. 0.60
   3 ?    0.6   0.0      0.13   5.8e+02      91     105 ..     146     160 ..     135     165 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 9e-05
                     DMAP1_like  69 wnkkvekiLkkfgld.kklkyptlrnmlrfEkLKyLii 105
                                    ++k  +ki++   ld   l + t++n++++E +K+Li+
  gene131|gene131|rna131|rna131  32 LEKIGKKIFEYQALDlCSLDFKTVQNLKKYENIKHLIL 69 
                                    55555666666666623689****************97 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.34
                     DMAP1_like  46 i 46 
                                    +
  gene131|gene131|rna131|rna131 115 L 115
                                    2 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.13
                     DMAP1_like  91 lrnmlrfEkLKyLii 105
                                    l n + f kL yL++
  gene131|gene131|rna131|rna131 146 LTNFIDFNKLDYLVL 160
                                    579999999999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       459  (0.025601); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1227.52
//
Query:       gene1310|gene1310|rna1310|rna1310  [L=483]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-48  166.4   0.0    1.2e-48  166.2   0.0    1.0  1  Aminotran_1_2    Aminotransferase class I and II
  ------ inclusion threshold ------
      0.012   14.9   0.0      0.018   14.3   0.0    1.3  1  Beta_elim_lyase  Beta-eliminating lyase


Domain annotation for each model (and alignments):
>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  166.2   0.0   1.3e-52   1.2e-48       3     363 .]     109     463 ..     107     463 .. 0.94

  Alignments for each domain:
  == domain 1  score: 166.2 bits;  conditional E-value: 1.3e-52
                                        EEESSSSSTTSTTSS.HHHHHHHHHHHH..HHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEES CS
                      Aminotran_1_2   3 vinLgsneylgdsgk.ptlpevakaeke..galaggtlneygpidglpeleealakflgrseklklkreaavvvgs 75 
                                        ++nL+s +ylg + +  ++ +   a+++   ++  gt+ e+g+  +   le+++a+fl+        +e+ +v+ +
  gene1310|gene1310|rna1310|rna1310 109 LLNLSSYNYLGFGTNkMEVIKNDLATADlfPVNYPGTVSEIGTHPINRNLEKQIARFLR--------KEDCIVFPM 176
                                        79**********8887777766777777999****************************........999****** PP

                                        HHHHHHHHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTE.... CS
                      Aminotran_1_2  76 Gagaliealifllklnpgdeilvpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnk.... 147
                                        G+g +   ++ + +    + il++++++ s++ + ++s+g +++++       h+d+++le++l+   ++ +    
  gene1310|gene1310|rna1310|rna1310 177 GFGTNSCNIPIISD--ENTLILSDELNHMSIIFGSKMSQGCIRTFA-------HNDMDNLEKLLRFYISQGQpdtk 243
                                        *************8..9*****************************.......************99999999*** PP

                                        ...TEEEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTT......EE CS
                      Aminotran_1_2 148 ...ktkvilvesphNPtGtvatleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepn......ll 214
                                            + +++ e+ +++ Gtv++l++l  l    +ky+++lf+Dea++++++g++       +v+e+ n      ++
  gene1310|gene1310|rna1310|rna1310 244 ktwDKIIVIAEGLYSMEGTVLSLKKLIVL---RRKYKFYLFIDEAHSIGAMGAT-----GRGVAEYCNvpfdeiDI 311
                                        999999*****************999999...********************54.....4566666666666669* PP

                                        EEEESSSTTSSGGG-EEEEEEEHHHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHHHH..HHHHHHHHHHHHHHHH CS
                      Aminotran_1_2 215 ivgslsKafGlaGeRvGyilgnaavvsqlrklsrpflsssllqaavaaalsdallkqs..eleemrqrlqkrrkel 288
                                         +g++ K+fG+aG   Gyi+++ +v++ lr+ s + l+ ++l+++va+++ ++ ++++  + +  r+rl ++   l
  gene1310|gene1310|rna1310|rna1310 312 FMGTFTKSFGAAG---GYIAADRKVINFLRNYSDFSLYGEQLSPVVAQHILTSFKIMNspYGNVLRRRLRDNIAML 384
                                        *************...*********************************9999999999***************** PP

                                        HHHHHHSTEEEECCS.CSSEEEEEETHHCHHHHHHHHHHTCTEEEEEGGGGTS...TTEEEEEC.TTS-HHHHHHH CS
                      Aminotran_1_2 289 rdeLaelglkvlasq.sgmflltdlsaetakelskkLleevgvyvtpgtsftv...pgrlRitv.Aglteeeleel 359
                                        r++L ++g+ v++++ s +++l  +++ ++ e+s+++ ++ g++v+ + ++ +   ++r R++v + +tee+++++
  gene1310|gene1310|rna1310|rna1310 385 RKGLIAKGFVVFGEEeSPIIPLLIYNPGKMFEFSRMCMQR-GLAVVVVGYPATpviSNRARFCVsSIHTEEDIKYV 459
                                        ****999******999************************.999999999999999******************** PP

                                        HHHH CS
                      Aminotran_1_2 360 veal 363
                                        ++ +
  gene1310|gene1310|rna1310|rna1310 460 LKVI 463
                                        9876 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0     2e-06     0.018      31     222 ..     152     340 ..     144     435 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2e-06
                                        -HHHHHHHHHHHHHTT-SEEEEES-HHHHHHHHHHHH--TTEEEEEETT-HHHHSSTTHHHHCC--EEEEE-EBTT CS
                    Beta_elim_lyase  31 dktvnrLedavaelfgkeaalfvpqGtaAnsillkillqrgeevivtepahihfdetgaiaelagvklrdlknkea 106
                                         +  ++Le+++a+ + ke  + +p G + ns  + i+   ++ ++ +e +h+       +   +g   r++ +++ 
  gene1310|gene1310|rna1310|rna1310 152 HPINRNLEKQIARFLRKEDCIVFPMGFGTNSCNIPIISDENTLILSDELNHMSIIFGSKM--SQGC-IRTFAHND- 223
                                        566688999999999999999999999999999999997777677777777766543332..2333.44444443. PP

                                        TBE-.HHHHHHHS--S-T...TS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEEETTHHHHHHHH CS
                    Beta_elim_lyase 107 Gkmd.lekleaaikevga...heekiklisltvTnntagGqvvsleelrevaaiakkygiplhlDgARfanaaksl 178
                                          md lekl +    +g+    +   k+i+++    ++ G+v+sl++l     + +ky+  l++D A  + a+ + 
  gene1310|gene1310|rna1310|rna1310 224 --MDnLEKLLRFYISQGQpdtKKTWDKIIVIAEGLYSMEGTVLSLKKL---IVLRRKYKFYLFIDEAHSIGAMGAT 294
                                        ..433677777555667764444455899999***9*******98765...66779******************** PP

                                        TS-CHHHH....TTSSEEEEESSSTT--SS-EEEEE-HH....HHHHH CS
                    Beta_elim_lyase 179 geivkemf....syvDsvtmslkKdllanvGgvlafrddeledylaer 222
                                        g  v+e++    + +D+++  ++K  +a  Gg +a +++   ++l++ 
  gene1310|gene1310|rna1310|rna1310 295 GRGVAEYCnvpfDEIDIFMGTFTKSFGA-AGGYIAADRK-VINFLRNY 340
                                        *******97777789*************.9********9.76666543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (483 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       443  (0.0247086); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.32s 00:00:00.89 Elapsed: 00:00:00.50
# Mc/sec: 2930.37
//
Query:       gene1311|gene1311|rna1311|rna1311  [L=227]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.6e-10   41.1   0.1    2.2e-10   40.6   0.1    1.3  1  Sad1_UNC      Sad1 / UNC-like C-terminal
  ------ inclusion threshold ------
      0.031   14.7   0.3      0.054   13.9   0.3    1.4  1  ocr           DNA mimic ocr
      0.034   14.2   0.0      0.044   13.9   0.0    1.2  1  F5_F8_type_C  F5/8 type C domain
      0.081   13.0   0.2       0.13   12.3   0.2    1.3  1  a_DG1_N2      Alpha-Dystroglycan N-terminal domain 2


Domain annotation for each model (and alignments):
>> Sad1_UNC  Sad1 / UNC-like C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.6   0.1     5e-14   2.2e-10      29     131 ..      60     152 ..      34     153 .. 0.92

  Alignments for each domain:
  == domain 1  score: 40.6 bits;  conditional E-value: 5e-14
                                        EEEEEEEEEEEEEEEEEEE---GGGSG-TTSB-EEEEEEESSTT----EEEEEEE--TTS-SEEEEE--TT----E CS
                           Sad1_UNC  29 gfvvieLseeiiveavtlehveksvapisSapKdfevsgskrypekkwvllgefsydedgknaqtFeleeskdilv 104
                                         +++++L++e++++ v+l + e     +sS p+++++s + +++   wv lg f+  + +++ q F ++++   ++
  gene1311|gene1311|rna1311|rna1311  60 TYIIVKLCNEVKINCVELLNKEY----LSSFPRQIKFSTYIDGN---WVSLGSFN-CKFTREKQLFYIKNDV--FT 125
                                        589********************....**********9887777...********.7**************8..** PP

                                        EEEEEEE--BSS-SSEEEESEEEEEEE CS
                           Sad1_UNC 105 kyvkleilsnyGneeytclyrlrVyGt 131
                                        +++++++l+  G+ +  +++ l+VyG+
  gene1311|gene1311|rna1311|rna1311 126 SILRIDVLNFIGKHSLFTITSLKVYGS 152
                                        **************************8 PP

>> ocr  DNA mimic ocr
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.3   1.2e-05     0.054       7      39 ..     162     194 ..     155     209 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.2e-05
                                        HHHHHHHHHHHHHHHHHTT---GGG-HHHHHHH CS
                                ocr   7 sdvydhayellkeyiryddvrdeddlsdkihea 39 
                                        + vy+  ++l ++ iry+d  d dd+  +i  a
  gene1311|gene1311|rna1311|rna1311 162 NMVYNRVFDLNNKLIRYEDKNDIDDIMKSIRVA 194
                                        45889999999999*************999877 PP

>> F5_F8_type_C  F5/8 type C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   9.8e-06     0.044      27     113 ..      52     133 ..      23     147 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 9.8e-06
                                        EESSSSTTEEEEEEEEEEEEEEEEEEEECSSTTSSEEEEEEEEEESSSSSEEEEEEECEEESSSSSSSEEEEEEEE CS
                       F5_F8_type_C  27 sssssddkqwlqvdLgkpkkidgvvtqgrqdggnayvksykiqvsddgetWttvkdekvpgnsdnstpvtntfdpp 102
                                         + ++  + ++ v+L ++ ki++v++ +     + ++++ k+++  dg +W ++ +    + + + +++   +++ 
  gene1311|gene1311|rna1311|rna1311  52 YAIGELMPTYIIVKLCNEVKINCVELLNKEYL-SSFPRQIKFSTYIDG-NWVSLGS---FNCKFTREKQLFYIKND 122
                                        4444444589******************9655.***************.9*99999...33333566777777777 PP

                                        EEEEEEEEEEE CS
                       F5_F8_type_C 103 vkaryvrltpt 113
                                        v +  +r+ ++
  gene1311|gene1311|rna1311|rna1311 123 VFTSILRIDVL 133
                                        77777777765 PP

>> a_DG1_N2  Alpha-Dystroglycan N-terminal domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.2   2.9e-05      0.13       9      58 ..     123     172 ..     119     187 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.9e-05
                           a_DG1_N2   9 vltvildadltklsskerlellakmkkfskvplellkllpvvnnrlldms 58 
                                        v+t il  d+  +  k+ l  ++ +k + +  le+lk+  +v nr++d+ 
  gene1311|gene1311|rna1311|rna1311 123 VFTSILRIDVLNFIGKHSLFTITSLKVYGSTILENLKVNNMVYNRVFDLN 172
                                        7899********************************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (227 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       642  (0.0358079); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 1564.70
//
Query:       gene1312|gene1312|rna1312|rna1312  [L=89]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0026   18.0   0.3     0.0029   17.9   0.3    1.1  1  Cytomega_UL20A  Cytomegalovirus UL20A protein
  ------ inclusion threshold ------
      0.013   15.4   2.2      0.015   15.1   2.2    1.0  1  SpoIIIAH        SpoIIIAH-like protein
      0.029   14.0   0.1      0.029   14.0   0.1    1.0  1  DUF1411         Protein of unknown function (DUF1411)


Domain annotation for each model (and alignments):
>> Cytomega_UL20A  Cytomegalovirus UL20A protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.3   4.8e-07    0.0029      10      68 ..      11      68 ..       1      77 [. 0.75

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 4.8e-07
                     Cytomega_UL20A 10 llavtltvalaapsqkskrsvtveqpststnsdgnttpsknvtlsqggsttdgdedysg 68
                                       lla   +  +aa s+  k + t ++  +s  sdg+tt sk+    +  s++  d+   g
  gene1312|gene1312|rna1312|rna1312 11 LLAF-AAFVFAANSKTEKETTTEDNDGASGGSDGETTDSKKDKTEEKSSSSSKDKSKNG 68
                                       3333.34568999999999999999**************98877777777666665554 PP

>> SpoIIIAH  SpoIIIAH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   2.2   2.6e-06     0.015       9      73 ..       8      65 ..       4      74 .. 0.38

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.6e-06
                                       XXXXXXXXXXXXXXXXX..XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                           SpoIIIAH  9 LalmiavagYlnftedsgkkaaetaeteqeesekaeigddkekdessaasaeaesssetesesse 73
                                       L +++a a+++ f+ +s   ++ ++et++e+++ a+ g+ ++++++s +++++e++s+++s++++
  gene1312|gene1312|rna1312|rna1312  8 LFVLLAFAAFV-FAANS---KT-EKETTTEDNDGASGGS-DGETTDS-KKDKTEEKSSSSSKDKS 65
                                       67788888886.55444...22.2222222222222222.1111222.22222222222222222 PP

>> DUF1411  Protein of unknown function (DUF1411)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   4.9e-06     0.029      20      84 ..       4      68 ..       1      86 [. 0.86

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.9e-06
                            DUF1411 20 mlasvvvlsalsgnvladeaevskkpvekkkegglfskewneadivkedkkklkalsdltktent 84
                                       +l  + vl a++  v+a + ++ k+++ +  +g   + + + +d++k++++  ++ s+ +k++n 
  gene1312|gene1312|rna1312|rna1312  4 LLKNLFVLLAFAAFVFAANSKTEKETTTEDNDGASGGSDGETTDSKKDKTEEKSSSSSKDKSKNG 68
                                       4778999**************************99999999999999988888788888888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1352  (0.0754086); expected 358.6 (0.02)
Passed bias filter:                      700  (0.0390429); expected 358.6 (0.02)
Passed Vit filter:                        96  (0.00535445); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 620.21
//
Query:       gene1313|gene1313|rna1313|rna1313  [L=138]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.2e-06   27.6   0.0    2.9e-06   27.2   0.0    1.2  1  Thioredoxin  Thioredoxin


Domain annotation for each model (and alignments):
>> Thioredoxin  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2   0.0   1.6e-10   2.9e-06      17      90 ..      43     115 ..      30     131 .. 0.90

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 1.6e-10
                                        TSSEEEEEEE-TTSHHHHCHHHHHHHHHHHCTTTSEEEEEETTTSHHHHHHTT-SSSSEEEEEETTEEEEEEES CS
                        Thioredoxin  17 ekklvlveFyApwCghCkalaPeleklaeelkdkvklakvdvdenedlakkyevegiPtlklfkngkevkkyeg 90 
                                        + + +++ F  p  + C+ +  +l+++a+ ++ ++k+++ +++  ed+++ ++++ +P l +f++gk v+ ++g
  gene1313|gene1313|rna1313|rna1313  43 TTQRCIIHFHNPEFARCRIMDERLAEAADIVS-DIKFYRAEAQLFEDVCEYLKINVLPFLGFFRDGKCVDGIVG 115
                                        348899**************************.**********************************9988877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       425  (0.0237046); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 962.43
//
Query:       gene1314|gene1314|rna1314|rna1314  [L=71]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.037   13.8   0.0      0.052   13.4   0.0    1.2  1  HTH_30    PucR C-terminal helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HTH_30  PucR C-terminal helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   2.9e-06     0.052      30      50 ..      50      70 ..      44      71 .] 0.87

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.9e-06
                                       HHHHHHHHHHHS--TTSHHHH CS
                             HTH_30 30 ryRLrrieellgldlddpddr 50
                                         R+rri+e lgld+d++d+r
  gene1314|gene1314|rna1314|rna1314 50 CGRVRRIKEKLGLDVDEGDRR 70
                                       56***************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (71 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       838  (0.0467399); expected 358.6 (0.02)
Passed bias filter:                      496  (0.0276647); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 519.74
//
Query:       gene1315|gene1315|rna1315|rna1315  [L=336]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   2.3e-100  335.2   0.0   2.7e-100  335.0   0.0    1.0  1  Thymidylat_synt  Thymidylate synthase


Domain annotation for each model (and alignments):
>> Thymidylat_synt  Thymidylate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  335.0   0.0  1.5e-104  2.7e-100       1     268 []      52     336 .]      52     336 .] 0.95

  Alignments for each domain:
  == domain 1  score: 335.0 bits;  conditional E-value: 1.5e-104
                                        HHHHHHHHHHHHH-EEEE-TTSSEEEEEEEEEEEEEGGGCB----SSST--HHHHHHHHHHHHTT--BTHHHHTTT CS
                    Thymidylat_synt   1 kqYldlvrkileeGeekedRtgtgtisvfgaqlrfdlsegefPllTtkkvflksvieEllWflsgetnvkeLqekg 76 
                                        k Yl+l+++++++G +k+dRtgtgt +++g+ lrf+l+++++PllTtkk+++  +++Ell+f++ +t+ k L+ ++
  gene1315|gene1315|rna1315|rna1315  52 KAYLNLIERVIAHGIRKDDRTGTGTFTLTGQVLRFSLENNTLPLLTTKKTAFDIILKELLFFVKAQTDNKILTCQN 127
                                        58************************************************************************** PP

                                        --TTH.....HHHHHT..........TB-SSSHHHHHHHBTST........TTSSB-HHHHHHHHHHHSTT-ST-E CS
                    Thymidylat_synt  77 vkiWd.....ewadee..........gdlgpvYGkqwrkfkae........egkkidqlakvidqlkenpdsRrii 129
                                        vkiW+     e               gdlgpvYG+qwr+f+a+        +g+++dql++vid++k++ +sRr+i
  gene1315|gene1315|rna1315|rna1315 128 VKIWNgnstaE----FfeqycinrpaGDLGPVYGFQWRHFGAQyksssdnyDGQGVDQLQNVIDEIKRDKNSRRLI 199
                                        *****666553....13334666666**************99999******************************* PP

                                        EE---GGGGGGSSS--SEEEEEEEE..SEETEEEEEEEEEEEETTTHHHHHHHHHHHHHHHHHHHHT-EEEEEEEE CS
                    Thymidylat_synt 130 vsawnpaeldkmaLppChvlfqfyvkdkkegkLslqlyqRSaDvflGvpFNiasyalLthmlaqvtglkpgeliht 205
                                        +sawnp  +++maLppCh++fq+ + +   +k+ l +yqRS D++lGvpFNiasy++L+ m+  +tg+ pge++h+
  gene1315|gene1315|rna1315|rna1315 200 ISAWNPLCIKEMALPPCHTMFQILILE---EKVTLIMYQRSGDIGLGVPFNIASYSILAAMIGYMTGYAPGEFVHV 272
                                        *********99**************54...46******************************************** PP

                                        EEEEEEEGGGHHHHHHHHTS---S--EEEE--SSTH.SGGG--GGGEEEES----SXXXXXXX. CS
                    Thymidylat_synt 206 igdaHiYsnhveqvkeqlereprelpklelnkekkv.siedfeledfelenYkphpkikakvav 268
                                        igdaH+Y nhv+++k ql rep+++pkl +++++k  +iedfeledfele+Y++h+ki++++av
  gene1315|gene1315|rna1315|rna1315 273 IGDAHVYLNHVDALKVQLGREPYDFPKLYIRPKRKIqRIEDFELEDFELEGYRHHDKITMQMAV 336
                                        **********************************9999*************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (336 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       840  (0.0468515); expected 358.6 (0.02)
Passed bias filter:                      640  (0.0356964); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 2205.62
//
Query:       gene1316|gene1316|rna1316|rna1316  [L=354]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-15   57.5   0.2    3.4e-15   56.2   0.2    1.6  1  eRF1_1    eRF1 domain 1
      1e-11   45.3   0.3      2e-11   44.4   0.3    1.5  1  eRF1_3    eRF1 domain 3


Domain annotation for each model (and alignments):
>> eRF1_1  eRF1 domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.2   0.2   3.8e-19   3.4e-15      11     122 ..       8     114 ..       3     119 .. 0.90

  Alignments for each domain:
  == domain 1  score: 56.2 bits;  conditional E-value: 3.8e-19
                                        TSCCEEEEEE-SCHHHHHHHHHCHTTHEEEEEEEECHHH.......--CEEEEEEEEEEEEEEECTTSSEEEEEEE CS
                             eRF1_1  11 dgsgsvtLipeddedlwhlynliapgdsvrastvrkvqresstgsreservklkLtikvekvdfdkdagvlrisGk 86 
                                        + + ++++ p  + d+  l++ + p + +   t+rk++      + +++rv ++Lti+v +v+ d ++++l ++G+
  gene1316|gene1316|rna1316|rna1316   8 HSTHTLRITPTHPSDIHILFQNLLPSHTITMPTTRKIEI-----NDQKKRVSINLTIRVCNVTIDLENSLLIVRGQ 78 
                                        56789999*****************************66.....56789*************************** PP

                                        EEEGGGG--TTSEEEEEE-TTSEEEEEECEESHHHH CS
                             eRF1_1  87 vieenehvklgafhtldlelkrpftiikeewdsfal 122
                                        ++ e e vk+g++h++++ l++ f+++ +++   ++
  gene1316|gene1316|rna1316|rna1316  79 IAREIENVKMGSYHNMNIGLNDCFSLEVQGDLWRMV 114
                                        **************************9976544444 PP

>> eRF1_3  eRF1 domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.4   0.3   2.2e-15     2e-11       2     112 ..     253     349 ..     252     350 .. 0.90

  Alignments for each domain:
  == domain 1  score: 44.4 bits;  conditional E-value: 2.2e-15
                                        HHHHHHHHHHHHHHHCTCSSEEESHHHHHHHHHTT-EEEEEEEHCHHTSSSH.HHHHS-HHH-HHHHHHHHHHHHH CS
                             eRF1_3   2 iqekklleefleelakdtgkavYGveevlkalemgAvetLLvseelersrdt.lkekvketgeelelvelieelve 76 
                                        +++  + ++fl++ ++ +++++ G+++vl+a+e++A++t++v+  l  + d+ ++++             i+++ve
  gene1316|gene1316|rna1316|rna1316 253 VKDLMVANQFLKMYERADDLIALGIKDVLAAIEFSAIDTMIVTVGLYCTYDVeERHR-------------IRKMVE 315
                                        566677899*******99****************************99977755555.............999999 PP

                                        HHHHTT-EEEEE-TTSHHHHHHHHHTTTEEEEESS- CS
                             eRF1_3  77 nveesgakveiisseseeGeqlvkafgGiaaiLRyk 112
                                        +v +   kv+iis+ ++ G++l +  gGi+aiL+y+
  gene1316|gene1316|rna1316|rna1316 316 MVGKD-KKVVIISDGHACGNKL-NYIGGIGAILKYN 349
                                        99875.69**************.************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (354 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       566  (0.031569); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 2514.34
//
Query:       gene1317|gene1317|rna1317|rna1317  [L=317]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.5e-61  207.4   0.5    3.1e-61  207.0   0.5    1.1  1  Pkinase         Protein kinase domain
    1.7e-32  112.7   1.2    6.2e-32  110.9   1.2    1.7  1  Pkinase_Tyr     Protein tyrosine kinase
    1.6e-06   27.3   0.6    2.8e-06   26.5   0.6    1.3  1  Haspin_kinase   Haspin like kinase domain
    0.00059   19.5   1.0     0.0011   18.7   1.0    1.4  1  RIO1            RIO1 family
     0.0012   18.2   0.1     0.0019   17.6   0.1    1.2  1  Kdo             Lipopolysaccharide kinase (Kdo/WaaP) family
     0.0017   18.0   0.5        1.9    8.1   0.0    2.3  2  FTA2            Kinetochore Sim4 complex subunit FTA2
     0.0019   17.6   0.0     0.0029   17.0   0.0    1.2  1  Kinase-like     Kinase-like
  ------ inclusion threshold ------
      0.021   13.6   0.5      0.029   13.1   0.5    1.2  1  Pkinase_fungal  Fungal protein kinase
      0.036   14.0   0.2       0.32   10.9   0.1    2.0  2  APH             Phosphotransferase enzyme family
       0.22   11.9   4.8       0.36   11.2   3.4    2.0  2  DUF4894         Domain of unknown function (DUF4894)


Domain annotation for each model (and alignments):
>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  207.0   0.5   1.7e-64   3.1e-61       1     264 []      23     297 ..      23     297 .. 0.91

  Alignments for each domain:
  == domain 1  score: 207.0 bits;  conditional E-value: 1.7e-64
                                        EEEEEEEEEESSEEEEEEEETTTTEEEEEEEEECHCHCHHHHHHHHHHHHHHHHHSCTTB--EEEEEEE....... CS
                            Pkinase   1 yekleklGeGsfGkVykaveketgkivAvKkikkekakkkkekkvlrEikilkklkhpnivrlyevfee....... 69 
                                        y+ ++k+GeG++G+Vy +    +++ +A+Kki++ +  +     v+rEikilk ++hpni++l+++          
  gene1317|gene1317|rna1317|rna1317  23 YKLIRKIGEGTYGTVYLCE--FNSQRYALKKIRNISGGDGLPLVVVREIKILKMVDHPNIIKLVDIKVVesecnnl 96 
                                        7889**************9..799***************************************9875444599999 PP

                                        .SSEEEEEEE--TTEBHHHHHHHHSS--HHHHHHHHHHHHHHHHHHHHTTEE-SS-SGGGEEEETTTEEEE-SGTT CS
                            Pkinase  70 .kdelylvleyveggeladllerkgslseeeakkiakqilegleylHskgiiHrDlKpeNiLidekgelKitDFGl 144
                                          + ++lv+ yve++ l+  +  +++++e+e++ki+ qil+g+++lHs++i+HrDlK++NiLid++ ++Ki+DFGl
  gene1317|gene1317|rna1317|rna1317  97 lGKAVFLVFYYVENDLLQLTM--NKQFNENEIRKIIGQILQGVKFLHSNNIMHRDLKTNNILIDRNLDVKIADFGL 170
                                        99999********99665555..579************************************************** PP

                                        SEESSSSCS.................BCTTTSCGGGS-HHHHTTSCBSHHHHHHHHHHHHHHHHHSS-STTTSSHH CS
                            Pkinase 145 akelesssk.................ltsfvgtseYlAPEvlkeneyskkvDvWslGvilyelltgkppfsgekgk 203
                                        +k+++++ +                 lt+ v+t +Y+APE+l +++ys k+D+Ws+G+il+e++ ++++++g++++
  gene1317|gene1317|rna1317|rna1317 171 SKHIKNGDSayfddndivdetytsnnLTTNVVTLWYRAPEILLDENYSYKIDIWSIGCILMEVTLNRNVMKGRNEN 246
                                        *******99**************************************************************77777 PP

                                        HHHHHHHHTHHHHHHHCTSHH...HHHTTS-HHHHHHHHHHT-SSGCCSTTHHHHHTSGGG CS
                            Pkinase 204 ekvekeldqlekilkilgetkeklpeaseiseeakdllkkllkkdpkkRltaeellqhpyl 264
                                        +       ql+ki ++l             s+++ +l + ll++ +++R+ a+e+l+ +++
  gene1317|gene1317|rna1317|rna1317 247 D-------QLKKIKHVLAR---LGGYFAGRSRNLYELGNGLLAYFEEERFCAKEALECRFF 297
                                        6.......33334444432...334466679************************998887 PP

>> Pkinase_Tyr  Protein tyrosine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.9   1.2   3.4e-35   6.2e-32       2     218 ..      24     252 ..      23     259 .. 0.79

  Alignments for each domain:
  == domain 1  score: 110.9 bits;  conditional E-value: 3.4e-35
                                        EEEEEEEEESSEEEEEEEEETTTTSSEEEEEEEEESTTSSHHH.HHHHHHHHHHHHTS-BTTB--EEEEEE..SSS CS
                        Pkinase_Tyr   2 elgkklGeGafGkVvegtlkgekekkevkVavKtlkeeateee.keelleeakimkklkhpnivkllgvct..kee 74 
                                        +l +k+GeG++G+V+ ++ +      +++ a+K++++ +  +     +++e+ki+k ++hpni+kl+ + +  +  
  gene1317|gene1317|rna1317|rna1317  24 KLIRKIGEGTYGTVYLCEFN------SQRYALKKIRNISGGDGlPLVVVREIKILKMVDHPNIIKLVDIKVveS-- 91 
                                        6789****************......78899****988877763677889*****************9877541.. PP

                                        S........EEEEEE--TTEBHHHHHHHTCTTTSBHHHHHHHHHHHHHHHHHHHHTTEEEST-SGGGEEEEETTEE CS
                        Pkinase_Tyr  75 p........llivteyvkgGdLlkfLrkkekekltlkdllsfalqvAkGmeyLeskklvHrdlaarNvLlsenkvv 142
                                        +        +++v+ yv++  L+  ++k+    ++ +++ +++ q+ +G+++L+s++++Hrdl + N+L+++n  v
  gene1317|gene1317|rna1317|rna1317  92 EcnnllgkaVFLVFYYVENDLLQLTMNKQ----FNENEIRKIIGQILQGVKFLHSNNIMHRDLKTNNILIDRNLDV 163
                                        22455666599999999998887777666....99***************************************** PP

                                        EE-STTTHEETTTSSEE.............EETTSSTSGGGGS.-HHHHHHSEEEHHHHHHHHHHHHHHHHTTSSG CS
                        Pkinase_Tyr 143 kisDfGLardiekddey.............vkkeeaklpvkWm.apEslkekkftsksDvWsfGvllwEiftlges 204
                                        ki+DfGL+++i++ d+              +++ ++++   W+ apE+l +++++ k D+Ws G +l+E+    ++
  gene1317|gene1317|rna1317|rna1317 164 KIADFGLSKHIKNGDSAyfddndivdetytSNNLTTNVVTLWYrAPEILLDENYSYKIDIWSIGCILMEVTL-NRN 238
                                        **********9764433244444444332222223344445555*************************975.556 PP

                                        TTTTSHHHHHHHHH CS
                        Pkinase_Tyr 205 pypglkneevlekl 218
                                         ++g ++++ l+k+
  gene1317|gene1317|rna1317|rna1317 239 VMKGRNENDQLKKI 252
                                        66666555555555 PP

>> Haspin_kinase  Haspin like kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   0.6   1.5e-09   2.8e-06     109     265 ..      30     182 ..       8     192 .. 0.73

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 1.5e-09
                      Haspin_kinase 109 seklssevyqtkekdkevvlKviplevledvtiskelslkelkslklvkgtypglllllqdkvlkekpdfyseqql 184
                                        +e+ ++ vy ++ +++  +lK+i    ++      ++ + e k lk+v    p+++ l+  kv++++  + +    
  gene1317|gene1317|rna1317|rna1317  30 GEGTYGTVYLCEFNSQRYALKKIRN--ISGGDGLPLVVVREIKILKMVDH--PNIIKLVDIKVVESE--CNNLLGK 99 
                                        7888888888888888888888864..33333334455678888888764..688888888888888..7777778 PP

                      Haspin_kinase 185 flvlllkdkGtdLeev...klkswkqalsifwqivkiLyvaEtkfeFEHRdLhldniLvdknlnvtlidlklsRle 257
                                         + l++ +  +dL ++   k  + +++ +i  qi++ ++   ++ +  HRdL+ +niL+d+nl v + d+ ls+  
  gene1317|gene1317|rna1317|rna1317 100 AVFLVFYYVENDLLQLtmnKQFNENEIRKIIGQILQGVKFLHSN-NIMHRDLKTNNILIDRNLDVKIADFGLSKHI 174
                                        88888888888988883334456678888888888888887765.788*************************997 PP

                      Haspin_kinase 258 ssegkvly 265
                                        ++ + +++
  gene1317|gene1317|rna1317|rna1317 175 KNGDSAYF 182
                                        44444444 PP

>> RIO1  RIO1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   1.0   5.9e-07    0.0011      83     167 ..     103     186 ..      83     190 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 5.9e-07
                                        EEEE--EETTEEGGBHHHCG-HHHHHHHHHHHHHHHHHHHHTSTEEESS-STTSEEEETT.EEEE--GTTEEETTS CS
                               RIO1  83 lvmefigedgvaapklkdveeeeeaeelyeevleemrklykeaglvHaDLSeyNvlvded.kvviIDvsQaveldh 157
                                        lv  ++++d ++++  k+ + e+e++++  ++l+ ++ +++ +++ H DL   N+l+d++ +v i D++ + ++++
  gene1317|gene1317|rna1317|rna1317 103 LVFYYVENDLLQLTMNKQFN-ENEIRKIIGQILQGVK-FLHSNNIMHRDLKTNNILIDRNlDVKIADFGLSKHIKN 176
                                        78888886666666666666.99***********765.556***************************98888888 PP

                                        TTHHHHHHHH CS
                               RIO1 158 pnalefLerD 167
                                         +++ f + D
  gene1317|gene1317|rna1317|rna1317 177 GDSAYFDDND 186
                                        7777666666 PP

>> Kdo  Lipopolysaccharide kinase (Kdo/WaaP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.1   1.1e-06    0.0019     109     165 ..     116     167 ..      94     183 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.1e-06
                                Kdo 109 lakwaelaeelkrallkavgrliaklhragvnHadlyaknillqqeeeeeaeiwliD 165
                                          + ++++e+  r+++ ++ + ++ lh+ +++H+dl   nil++ +      + + D
  gene1317|gene1317|rna1317|rna1317 116 TMN-KQFNENEIRKIIGQILQGVKFLHSNNIMHRDLKTNNILIDRNL----DVKIAD 167
                                        332.56899999999****************************9886....444555 PP

>> FTA2  Kinetochore Sim4 complex subunit FTA2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.0    0.0011       1.9      22      52 ..      21      51 ..      13      59 .. 0.89
   2 !    7.8   0.3    0.0013       2.3     174     205 ..     126     157 ..     110     171 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0011
                               FTA2 22 kdiefleyLgkglhsiVlkvkirgkeYALKl 52
                                       + ++++  +g+g+ + V+  + + + YALK 
  gene1317|gene1317|rna1317|rna1317 21 HAYKLIRKIGEGTYGTVYLCEFNSQRYALKK 51
                                       67899************************94 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0013
                               FTA2 174 evsqlpkllrdlkklhklgIvvrDlkeenyid 205
                                        + +++ ++l+ +k lh+  I++rDlk++n++ 
  gene1317|gene1317|rna1317|rna1317 126 IRKIIGQILQGVKFLHSNNIMHRDLKTNNILI 157
                                        45678899999***************999863 PP

>> Kinase-like  Kinase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   1.6e-06    0.0029     130     240 ..     112     230 ..      94     237 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1.6e-06
                        Kinase-like 130 vlqkrsethkkletiarlllTlqlirlaanLqakglvhgkftvdnllldekgglmlggf..taLvragtkvvlsev 203
                                        +lq   ++++++++i r+++  q+++ +  L+++ ++h +++ +n+l d++  +++ +f  ++ ++ g+++    +
  gene1317|gene1317|rna1317|rna1317 112 LLQLTMNKQFNENEI-RKII-GQILQGVKFLHSNNIMHRDLKTNNILIDRNLDVKIADFglSKHIKNGDSAYFDDN 185
                                        555555556666555.5556.5899999*****************************9933467788888887444 PP

                        Kinase-like 204 e...kgfaPpEllgsrgg..ytrkn...ktkmthkldaWqlGlvi 240
                                            +++    l+ +  +  y+  +     ++++k+d W +G   
  gene1317|gene1317|rna1317|rna1317 186 DivdETYTSNNLTTNVVTlwYRAPEillDENYSYKIDIWSIGCIL 230
                                        3446*********999999888765222569***********865 PP

>> Pkinase_fungal  Fungal protein kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.5   1.6e-05     0.029     314     368 ..     132     180 ..     116     231 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.6e-05
                     Pkinase_fungal 314 DaIkghrsLflkagiLHrDiSenNilitdskkegerkglLiDLDlakelsddsse 368
                                        + ++g + L+   +i+HrD  +nNili      ++    ++D+ l k++++ +s+
  gene1317|gene1317|rna1317|rna1317 132 QILQGVKFLH-SNNIMHRDLKTNNILID-----RNLDVKIADFGLSKHIKNGDSA 180
                                        5567888899.9***************9.....5667778888888887754443 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0      0.14   2.5e+02       2      29 ..      26      53 ..      26     141 .. 0.86
   2 ?   10.9   0.1   0.00018      0.32     155     195 ..     132     170 ..      90     174 .. 0.72

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.14
                                       EEEE--.SSCEEEEEEETT--EEEEEE- CS
                                APH  2 vrelsggasnrtylvttpagryvlrrnp 29
                                       +r ++ g++  +yl++  ++ry+l+ ++
  gene1317|gene1317|rna1317|rna1317 26 IRKIGEGTYGTVYLCEFNSQRYALKKIR 53
                                       68999************99*****9865 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00018
                                        HHHHH--SSS-EEEE-SS-SGGGEEEC..TTEEEEE---TT CS
                                APH 155 alaallpgelptvllHgDlhpgNllvdpddgrvtGviDfed 195
                                        ++++ +    +  ++H+Dl+++N+l+d   +  + + Df++
  gene1317|gene1317|rna1317|rna1317 132 QILQGVKFLHSNNIMHRDLKTNNILID--RNLDVKIADFGL 170
                                        55555555667779*************..333224677766 PP

>> DUF4894  Domain of unknown function (DUF4894)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   3.4    0.0002      0.36      11      86 ..      65     168 ..      63     176 .. 0.80
   2 ?   -3.5   0.0       7.2   1.3e+04      74      99 ..     234     259 ..     230     271 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0002
                            DUF4894  11 vsedgvlldvadledvlktl...................avfvleedvvdlildav.........dreilkklpvl 58 
                                        v +++++l+++d  +++k +                     + +e+d  +l++++            +il+ ++ l
  gene1317|gene1317|rna1317|rna1317  65 VVREIKILKMVDHPNIIKLVdikvvesecnnllgkavflVFYYVENDLLQLTMNKQfneneirkiIGQILQGVKFL 140
                                        5678899999999999998788888888888888866653344477777777777788877665566788889999 PP

                            DUF4894  59 kssyvseidfeekkvvLkkgirvkfnew 86 
                                        +s+ +++ d++++++++ ++  vk+ ++
  gene1317|gene1317|rna1317|rna1317 141 HSNNIMHRDLKTNNILIDRNLDVKIADF 168
                                        9************************998 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 7.2
                            DUF4894  74 vLkkgirvkfnewedleekkekleel 99 
                                         L++++    ne ++l++ k++l +l
  gene1317|gene1317|rna1317|rna1317 234 TLNRNVMKGRNENDQLKKIKHVLARL 259
                                        56666666666666666666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (317 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       783  (0.0436723); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.56u 0.33s 00:00:00.89 Elapsed: 00:00:00.51
# Mc/sec: 1887.30
//
Query:       gene1318|gene1318|rna1318|rna1318  [L=169]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.013   15.3   3.6      0.029   14.1   3.6    1.6  1  Synaptobrevin  Synaptobrevin
      0.068   13.0   0.6      0.068   13.0   0.6    1.6  2  DUF2970        Protein of unknown function (DUF2970)
      0.072   13.1   0.7      0.072   13.1   0.7    1.7  2  DUF2116        Uncharacterized protein containing a Zn-ribbon


Domain annotation for each model (and alignments):
>> Synaptobrevin  Synaptobrevin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   3.6   4.9e-06     0.029      53      87 ..     129     163 ..     127     165 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4.9e-06
                                        HHHHHHHHHHHHTXXXXXXXXXXXXXXXXXXXXXX CS
                      Synaptobrevin  53 qarklkrkmwwknmkliiililvvlililiiiivi 87 
                                         +r++k+k +w ++++iii +++++++++ +++++
  gene1318|gene1318|rna1318|rna1318 129 LSREIKKKNCWGKFRYIIIGVILFMVIVIALLSIV 163
                                        599***********988877777766666665554 PP

>> DUF2970  Protein of unknown function (DUF2970)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   1.2       2.2   1.3e+04      43      48 ..       3       8 ..       1      11 [. 0.37
   2 ?   13.0   0.6   1.1e-05     0.068      32      52 ..     143     163 ..     129     165 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 2.2
                            DUF2970 43 lfvllL 48
                                       l++l+L
  gene1318|gene1318|rna1318|rna1318  3 LLILIL 8 
                                       333333 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 1.1e-05
                            DUF2970  32 hviivGlilaalfvllLillV 52 
                                         +ii+G+il ++ v++L+ +V
  gene1318|gene1318|rna1318|rna1318 143 RYIIIGVILFMVIVIALLSIV 163
                                        69****************999 PP

>> DUF2116  Uncharacterized protein containing a Zn-ribbon (DUF2116)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.3   1.4         3   1.8e+04      42      48 ..       2       8 ..       1      11 [. 0.49
   2 ?   13.1   0.7   1.2e-05     0.072      22      58 ..     123     162 ..     117     163 .. 0.82

  Alignments for each domain:
  == domain 1  score: -4.3 bits;  conditional E-value: 3
                            DUF2116 42 lfgilil 48
                                       l++ilil
  gene1318|gene1318|rna1318|rna1318  2 LLLILIL 8 
                                       4555554 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 1.2e-05
                            DUF2116  22 ekCqeeyekkrkkva...rsqqilfgililllavvlvlkf 58 
                                        e+C+ +++++ kk     ++++i++g+++ +++v+++l++
  gene1318|gene1318|rna1318|rna1318 123 EDCRYKLSREIKKKNcwgKFRYIIIGVILFMVIVIALLSI 162
                                        79*****999888654559********9998888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (169 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1183  (0.0659825); expected 358.6 (0.02)
Passed bias filter:                      623  (0.0347482); expected 358.6 (0.02)
Passed Vit filter:                        73  (0.00407162); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.30s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1167.68
//
Query:       gene1319|gene1319|rna1319|rna1319  [L=345]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.7e-38  131.0   2.1    7.7e-38  130.0   2.1    1.5  1  NAD_Gly3P_dh_C  NAD-dependent glycerol-3-phosphate dehydrogen
    9.5e-38  129.6   0.1    2.2e-37  128.4   0.1    1.6  2  NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogen
    1.4e-06   28.8   2.3      0.035   14.7   0.0    3.2  4  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent
  ------ inclusion threshold ------
      0.016   14.5   0.0      0.026   13.8   0.0    1.3  1  Malic_M         Malic enzyme, NAD binding domain
      0.031   14.9   0.2      0.082   13.6   0.2    1.7  1  PglD_N          PglD N-terminal domain
      0.044   14.2   0.3        3.8    8.0   0.0    2.6  3  Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domai
      0.049   13.0   0.1        5.3    6.4   0.0    2.3  2  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
      0.058   13.3   0.2        6.9    6.5   0.0    2.3  2  Rossmann-like   Rossmann-like domain
      0.091   12.3   2.1        3.7    7.1   0.0    3.4  4  IlvN            Acetohydroxy acid isomeroreductase, NADPH-bin
       0.13   12.4   2.2         11    6.2   0.2    3.6  3  NAD_binding_2   NAD binding domain of 6-phosphogluconate dehy


Domain annotation for each model (and alignments):
>> NAD_Gly3P_dh_C  NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.0   2.1   4.3e-41   7.7e-38       1     141 [.     196     340 ..     196     341 .. 0.95

  Alignments for each domain:
  == domain 1  score: 130.0 bits;  conditional E-value: 4.3e-41
                                        -HHHHHHHHHHHHHHHHHHHHHHHTTH-HHHHHHHHHHHHHHHHHHHHHHTSS..GGGGGSTTTHHHHHHHHHSCT CS
                     NAD_Gly3P_dh_C   1 DviGvelagalKNviAiaaGivdglglgdntkaalitrglaEmarlakalgak..petflglaglgDlivtctsgk 74 
                                        D ++vel+galKN++Aia+G++ gl+l  nt+  +++rg+ Em++++k++ ++  + t+l+++g++Dl+v+c  g 
  gene1319|gene1319|rna1319|rna1319 196 DKTSVELFGALKNIVAIAFGVARGLQLSINTQVSIMRRGMLEMIEFVKMVDKNadKLTILESCGIADLMVSCITG- 270
                                        6789*********************************************98864456999***************. PP

                                        .HHHHHHHHHHC.T--HHHHHHHHC.C--HHHHHHHHHHHHHHHTT...G.HHHHHHHHHHHS---HHHHH CS
                     NAD_Gly3P_dh_C  75 sRNrrfGeelgk.gesleeiekeln.qvleGvetakevyellkkkgv..emplleavykilyegkspeeli 141
                                         RN+ +G +++  g ++e+ie+ ++ q+l+G+  a ev+ +l+kk+v  ++p++ +vy i+y++++ ++++
  gene1319|gene1319|rna1319|rna1319 271 -RNAGCGTAIASkGLTIEKIEEDMKgQKLQGTLCAYEVMMYLRKKNVvdKFPVFATVYGICYGKMDSNQIL 340
                                        .**********9899*******8888*******************999*****************999886 PP

>> NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  128.4   0.1   1.3e-40   2.2e-37       2     152 ..       6     174 ..       5     178 .. 0.95
   2 ?   -2.9   0.0       3.3   5.9e+03     121     134 ..     292     302 ..     273     319 .. 0.50

  Alignments for each domain:
  == domain 1  score: 128.4 bits;  conditional E-value: 1.3e-40
                                        EEEE--SHHHHHHHHHHHTTT.......--EEEE-S-H.........HHHHHHHHHSSBTTTBTT----TTEEEES CS
                     NAD_Gly3P_dh_N   2 iavlGaGswGtalAkvlaeng.......hevrlwvree.........elieeineehenvkyLpgiklpenlvatt 61 
                                        i+++G+Gs+Gta+A+++a+          +v++w ++e          l e i++e+env+yLp++klpenl + t
  gene1319|gene1319|rna1319|rna1319   6 IGIIGSGSFGTAIANIIARDVqnksvfdDTVKIWIFDEqvridgskeLLSEYIKRERENVNYLPHVKLPENLLFMT 81 
                                        89*****************99999****9999**999999999998778899************************ PP

                                        -HHHHHTT--EEEE---HHHHHHHHHHHCCC--TT-EEEE---SE....ET.TTEEHHHHHHHHH-S--EEEEESS CS
                     NAD_Gly3P_dh_N  62 dlaealkgadiivlvvPsqalrevlkklkgllkkkailvsliKGi....eegtlkllsevieeelkeekvavlsGp 133
                                        +l+e+++++di+v+vvP+q++++++++lk +  kk+i+ sl+KG     e+ +  l+s++ie+el+   ++ ++G+
  gene1319|gene1319|rna1319|rna1319  82 NLKEVVQKSDILVFVVPHQFIEKIVQDLKSMKLKKKIACSLMKGTlfseETAEIVLISNYIEKELGWP-CSAVMGA 156
                                        ********************************************99998888899*************.******* PP

                                        --HHHHHTT--EEEEEEES CS
                     NAD_Gly3P_dh_N 134 slAeEvakgkptavviask 152
                                        ++A+E   + +++++i+s 
  gene1319|gene1319|rna1319|rna1319 157 NIASEMH-KSVCEMTIGSR 174
                                        *****86.579****9986 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 3.3
                                        HH-S--EEEEESS- CS
                     NAD_Gly3P_dh_N 121 elkeekvavlsGps 134
                                         +k +    l G  
  gene1319|gene1319|rna1319|rna1319 292 DMKGQ---KLQGTL 302
                                        33333...233333 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.1   0.00012      0.22       1      24 [.       5      27 ..       5      35 .. 0.78
   2 !   14.7   0.0     2e-05     0.035      54      95 ..      82     123 ..      55     125 .. 0.88
   3 ?   -1.0   0.0       1.5   2.7e+03      10      59 ..     154     200 ..     153     227 .. 0.70
   4 ?   -2.2   0.0       3.6   6.5e+03      10      64 ..     212     263 ..     202     270 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00012
                                       EEEEETTSHHHHHHHHHHHHTTS- CS
                      F420_oxidored  1 kigiiGaGnmgealasgllaagaq 24
                                       +igiiG+G++g a+a+ + a+++q
  gene1319|gene1319|rna1319|rna1319  5 RIGIIGSGSFGTAIANII-ARDVQ 27
                                       79*************955.44444 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 2e-05
                                        CHHHHHHH-SEEEE-S-HHHHHHHHHHCGHHHHTTSEEEEES CS
                      F420_oxidored  54 dneeaaeeadvvvlavkpedveevlselakdalkgklvisvl 95 
                                        + +e+++++d++v+ v+ + +e+++++l++ +lk+k+  s +
  gene1319|gene1319|rna1319|rna1319  82 NLKEVVQKSDILVFVVPHQFIEKIVQDLKSMKLKKKIACSLM 123
                                        679*********************************988876 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 1.5
                                        HHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHH CS
                      F420_oxidored  10 mgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneeaa 59 
                                        mg+ +as + ++     e++++++ + + +++l ++ +vkv  v  ++ +
  gene1319|gene1319|rna1319|rna1319 154 MGANIASEMHKSV---CEMTIGSRTDGDLLKQLFNTPQVKVNVVRDKTSV 200
                                        6777777777776...8888886666666666767766777666666555 PP

  == domain 4  score: -2.2 bits;  conditional E-value: 3.6
                                        HHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHHH-SE CS
                      F420_oxidored  10 mgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneeaaeeadv 64 
                                        +++++a+gl+ +   ++++ +  +r   ++ e+ + +  ++ + +  e +  ad 
  gene1319|gene1319|rna1319|rna1319 212 IAFGVARGLQLSI--NTQVSIM-RRGMLEMIEFVKMVDKNADKLTILESCGIADL 263
                                        5566666665554..5666644.66666666666666666666666665555555 PP

>> Malic_M  Malic enzyme, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   1.4e-05     0.026      27     135 ..       5     113 ..       1     138 [. 0.76

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.4e-05
                                        -EEEEC-SHHHHHHHHHHHHHHHTTTS-HHHHHTTEEEEETTEE-BTT-S--......-TTTGGGSBS--SS--S. CS
                            Malic_M  27 kivvlGaGsagiGiaeqivealvkeGlseeeakkkiylvDrkGLltedrekl......eeekkpfakkkeelkeak 96 
                                        +i ++G+Gs g+ ia+ i++ ++++ + ++    ki+++D++  +  ++e l      e e+ ++  + +  ++  
  gene1319|gene1319|rna1319|rna1319   5 RIGIIGSGSFGTAIANIIARDVQNKSVFDDT--VKIWIFDEQVRIDGSKELLseyikrERENVNYLPHVKLPENLL 78 
                                        67899*****************999988775..58*******8888777777444444444555555555555555 PP

                                        ...SHHHHHHHH--SEEEE-SSSSS-S-HHHHHHHHHHS CS
                            Malic_M  97 dkltLeevvkkvkptvliGlsgvagafteeivremakst 135
                                         +++L+evv+  k ++l+ +  v++ f e+iv+++++++
  gene1319|gene1319|rna1319|rna1319  79 FMTNLKEVVQ--KSDILVFV--VPHQFIEKIVQDLKSMK 113
                                        8999999998..67888755..8999******9998765 PP

>> PglD_N  PglD N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.2   4.6e-05     0.082       2      56 ..       6      59 ..       5      66 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.6e-05
                             PglD_N  2 ivIiGaGGhgkvvadiieangeyeiigflDdnkk..tevegypvlgkaiellkslse 56
                                       i IiG G +g  +a+ii +    + + ++Dd+ k     e++++ g+  ell+++ +
  gene1319|gene1319|rna1319|rna1319  6 IGIIGSGSFGTAIANIIARD--VQNKSVFDDTVKiwIFDEQVRIDGSK-ELLSEYIK 59
                                       78***************985..58999999998743456678888864.55555544 PP

>> Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0     0.053        96       1      23 [.       5      26 ..       5      32 .. 0.85
   2 ?    8.0   0.0    0.0021       3.8      44      89 ..      67     112 ..      51     119 .. 0.84
   3 ?   -3.0   0.0       5.4   9.6e+03      25      57 ..     166     196 ..     157     211 .. 0.56

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.053
                                       EEEEETTTSHHHHHHHHHHHCTS CS
                     Semialdhyde_dh  1 kvaivGatGyvGqellrlLeehp 23
                                       +++i+G +G  G++++++++++ 
  gene1319|gene1319|rna1319|rna1319  5 RIGIIG-SGSFGTAIANIIARDV 26
                                       69****.***********99865 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0021
                                        HSGGGTTTECEBEEEGGGGGCTT-SEEEE-SCHHHHHHHHHHHHHT CS
                     Semialdhyde_dh  44 avkaleegkdlkvedvdeeelkevdivflalpagvskelapklaea 89 
                                        + ++++  ++l + +  +e +++ di+++ +p++  ++++++l + 
  gene1319|gene1319|rna1319|rna1319  67 YLPHVKLPENLLFMTNLKEVVQKSDILVFVVPHQFIEKIVQDLKSM 112
                                        446888899999999888999*******************999654 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 5.4
                                        EEEEEEEESTTTTTSBHHHHSGGGTTTECEBEE CS
                     Semialdhyde_dh  25 velvvllsssrsaGkklaeavkaleegkdlkve 57 
                                        v ++++ s++  +G  l++++++++ + +++ +
  gene1319|gene1319|rna1319|rna1319 166 VCEMTIGSRT--DGDLLKQLFNTPQVKVNVVRD 196
                                        4444444333..477777766655555555444 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0     0.003       5.3      38      56 ..       5      23 ..       2      56 .. 0.79
   2 ?    4.4   0.0     0.012        22      82     102 ..      80     100 ..      62     119 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.003
                                       EEEEES-SHHHHHHHHHHH CS
                       2-Hacid_dh_C 38 tvGiiGlGrIGqavakrlk 56
                                       ++GiiG G+ G+a+a++++
  gene1319|gene1319|rna1319|rna1319  5 RIGIIGSGSFGTAIANIIA 23
                                       69*************9987 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.012
                                        ECSHHHHHHH-SEEEE-S--S CS
                       2-Hacid_dh_C  82 lvsleellaesDivslhlplt 102
                                        +++l+e++++sDi++ ++p +
  gene1319|gene1319|rna1319|rna1319  80 MTNLKEVVQKSDILVFVVPHQ 100
                                        679***************964 PP

>> Rossmann-like  Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0     0.019        34      12      31 ..       5      24 ..       2      32 .. 0.89
   2 ?    6.5   0.0    0.0039       6.9      59      91 ..      80     112 ..      64     121 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.019
                      Rossmann-like 12 svGiisaGrvGtalgaaler 31
                                        +Gii++G  Gta+++ ++r
  gene1319|gene1319|rna1319|rna1319  5 RIGIIGSGSFGTAIANIIAR 24
                                       68*************99987 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0039
                      Rossmann-like  59 vlevedvaaraellllavPdaelpglvkglaat 91 
                                        + ++++v++++++l++ vP   + ++v++l + 
  gene1319|gene1319|rna1319|rna1319  80 MTNLKEVVQKSDILVFVVPHQFIEKIVQDLKSM 112
                                        56899**********************999765 PP

>> IlvN  Acetohydroxy acid isomeroreductase, NADPH-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0     0.066   1.2e+02       6      23 ..       5      22 ..       1      32 [. 0.84
   2 ?    7.1   0.0     0.002       3.7      52      90 ..      81     119 ..      72     134 .. 0.83
   3 ?   -1.8   0.0       1.1   2.1e+03      16      39 ..     155     178 ..     153     197 .. 0.79
   4 ?   -0.4   0.0      0.43   7.7e+02      72     112 ..     298     342 ..     283     343 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.066
                                       -EEEES-SHHHHHHHHHH CS
                               IlvN  6 kiaviGyGsqGhaqalnl 23
                                       +i +iG Gs G a a+ +
  gene1319|gene1319|rna1319|rna1319  5 RIGIIGSGSFGTAIANII 22
                                       799**********99876 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.002
                                        EEHHHHHHT-SEEEE-S-HHHHHHHHHHHTGGG--TT-E CS
                               IlvN  52 ltvaeavkkadvvmiliPDelqkevyeeeiepnlkegka 90 
                                        ++++e+v+k+d++++++P ++ ++++++  + +lk++ a
  gene1319|gene1319|rna1319|rna1319  81 TNLKEVVQKSDILVFVVPHQFIEKIVQDLKSMKLKKKIA 119
                                        6789*********************98766677777655 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 1.1
                                        HHHHHHHHHHTT--EEEEE-TT-H CS
                               IlvN  16 Ghaqalnlrdsgldvvvglregsk 39 
                                        G + a +++ s +++++g r+++ 
  gene1319|gene1319|rna1319|rna1319 155 GANIASEMHKSVCEMTIGSRTDGD 178
                                        677889999999999999998875 PP

  == domain 4  score: -0.4 bits;  conditional E-value: 0.43
                                        HHHHHHHHHTGGG--TT-EE....EESSSHHHHTTSS---TTSEE CS
                               IlvN  72 lqkevyeeeiepnlkegkal....afahGfnihfglikppkdvdv 112
                                        lq ++   e++ +l++++++    +fa  + i +g+++ ++ ++v
  gene1319|gene1319|rna1319|rna1319 298 LQGTLCAYEVMMYLRKKNVVdkfpVFATVYGICYGKMDSNQILKV 342
                                        667777788999999998874444699999999999998887766 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.2     0.006        11       1      65 [.       5      99 ..       5     137 .. 0.61
   2 ?    2.8   0.1     0.068   1.2e+02       8      33 ..     152     177 ..     145     212 .. 0.81
   3 ?   -1.0   0.0      0.99   1.8e+03     107     144 ..     207     244 ..     191     254 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.006
                                       EEEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTT...............................EEE-S CS
                      NAD_binding_2  1 kigfiGlGvMGsnmalnllkagykvavynrtkekveelvaeg...............................akaae 47
                                       +ig+iG G  G+ +a+ +++  ++ +v++ t + +  + ++                                +  ++
  gene1319|gene1319|rna1319|rna1319  5 RIGIIGSGSFGTAIANIIARDVQNKSVFDDTVK-IWIFDEQVridgskellseyikrerenvnylphvklpenLLFMT 81
                                       589999999999999999999888888887742.11111111222333344444444555555555555555555556 PP

                                       SHHHHHHHCSEEEE-SSS CS
                      NAD_binding_2 48 sieelvasldvvitmvka 65
                                       +++e+v++ d+ +++v++
  gene1319|gene1319|rna1319|rna1319 82 NLKEVVQKSDILVFVVPH 99
                                       666666666666555555 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.068
                                        SHHHHHHHHHHHHTT-EEEEE-SSHH CS
                      NAD_binding_2   8 GvMGsnmalnllkagykvavynrtke 33 
                                        +vMG+n+a+++ k+ +++++  rt  
  gene1319|gene1319|rna1319|rna1319 152 AVMGANIASEMHKSVCEMTIGSRTDG 177
                                        79***********9999999888864 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.99
                                        TT-EEEEEEEESHHHHHHHT-EEEEEEE-HHHHHHHHH CS
                      NAD_binding_2 107 kglkfldaPVSGGeegAekGtLsimvGGseeafervkp 144
                                        k++  +  +V  G +   + ++sim  G  e++e vk 
  gene1319|gene1319|rna1319|rna1319 207 KNIVAIAFGVARGLQLSINTQVSIMRRGMLEMIEFVKM 244
                                        67888999999999999999999999998888887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (345 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       586  (0.0326845); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 2546.32
//
Query:       gene132|gene132|rna132|rna132  [L=939]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (939 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       793  (0.04423); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.68u 0.24s 00:00:00.92 Elapsed: 00:00:00.43
# Mc/sec: 6533.94
//
Query:       gene1320|gene1320|rna1320|rna1320  [L=669]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      7e-20   71.7   0.1    1.2e-16   61.3   0.0    2.4  2  GRASP55_65   GRASP55/65 PDZ-like domain
    7.6e-05   23.0   0.2       0.55   10.6   0.0    3.6  3  PDZ_2        PDZ domain
  ------ inclusion threshold ------
       0.01   15.6   0.0       0.07   13.0   0.0    2.4  2  PDZ_6        PDZ domain
      0.055   13.4   0.5         12    5.9   0.0    3.3  4  Tricorn_PDZ  Tricorn protease PDZ domain


Domain annotation for each model (and alignments):
>> GRASP55_65  GRASP55/65 PDZ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.1   0.00028       1.3      44     126 ..      11      90 ..       3      96 .. 0.86
   2 !   61.3   0.0   2.6e-20   1.2e-16      25     135 ..      84     191 ..      76     193 .. 0.92

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00028
                                        -EEEEEEBTTSHHHHHT--TTTEEEEEEE.SSSSSTSCSHHHHTTTSSS-EEEEEEETTTTEEEEEEE---TTSSS CS
                         GRASP55_65  44 vwhvldvlegsPaakagLvpksDYiiGldkgllkgeedlselveaheekelkLlvYnsesdevrevtvkpsrewGg 119
                                        + ++ +++++s a++ +L+p+   i  ++++++ ++ed+ +   +++++++kL v +  ++++++ ++   ++   
  gene1320|gene1320|rna1320|rna1320  11 TLQITKITQNSRAHRLNLLPFIHTITLVNEKTVGSSEDVKKEFIKWKQHNIKLQVLDLCTQKIKDLEL---EKCVE 83 
                                        578999**********************************************************9988...33333 PP

                                        STTTSEE CS
                         GRASP55_65 120 egalGcd 126
                                          +lG++
  gene1320|gene1320|rna1320|rna1320  84 GESLGIN 90 
                                        3455555 PP

  == domain 2  score: 61.3 bits;  conditional E-value: 2.6e-20
                                        SSSSSEEEEEEE-TTTTTS-EEEEEEBTTSHHHHHT--TTTEEEEEEE.SSSSSTSCSHHHHTTTSSS-EEEEEEE CS
                         GRASP55_65  25 qgllGlslrlaslekaaeevwhvldvlegsPaakagLvpksDYiiGldkgllkgeedlselveaheekelkLlvYn 100
                                         + lG+ +++ + e     +  +++++e+sPa +agL  ++DY+iG++   + +e+++++++     +e +L+v+n
  gene1320|gene1320|rna1320|rna1320  84 GESLGINVKVHKGE-PYCPTLCLVEIDEDSPAYRAGLRVFEDYVIGIEGVYIPNEDAFRRRLYGFIGRECVLFVFN 158
                                        57899999999988.666677899**************************************************** PP

                                        TTTTEEEEEEE---TTSSSSTTTSEEEE-SGGGS- CS
                         GRASP55_65 101 sesdevrevtvkpsrewGgegalGcdvgyGlLhri 135
                                         e++++r+vtv+++++   e ++G ++g+GlL +i
  gene1320|gene1320|rna1320|rna1320 159 RETNTIRRVTVVLNDD--PENLMGAELGTGLLYKI 191
                                        ***********99997..799***********998 PP

>> PDZ_2  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.9   0.1    0.0017       7.6       3      69 ..       1      65 [.       1      79 [. 0.79
   2 !   10.6   0.0   0.00012      0.55       3      58 ..      87     146 ..      85     167 .. 0.82
   3 ?    0.7   0.2      0.15   6.9e+02      32      58 ..     287     314 ..     258     336 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0017
                                       ..XX------..-EEEEEE-TTSGGGGT..--TT-EEEEETTB--SSHHHHHHHHHTS-TT-EEEEEE CS
                              PDZ_2  3 lGvsvsdeedtggvlvvsVkeggPaakag.lkagDvilkvdgkkvksledlislllkkkpGdtVkltv 69
                                       +G +++de+    + ++++++++ a++ + l    +i+ v++k+v s+ed++++  k k+  ++kl+v
  gene1320|gene1320|rna1320|rna1320  1 MGQTITDESV--TLQITKITQNSRAHRLNlLPFIHTITLVNEKTVGSSEDVKKEFIKWKQ-HNIKLQV 65
                                       5777888887..899999*****999999555589*****************99876543.4455555 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00012
                                        ..XX------.....-EEEEEE-TTSGGGGT.--T.T-EEEEETTB--SSHHHHHHHHHT CS
                              PDZ_2   3 lGvsvsdeed...tggvlvvsVkeggPaakaglka.gDvilkvdgkkvksledlislllk 58 
                                        lG+ v+ +++      +  v+++e++Pa +agl+  +D ++ ++g+ + +++ ++++l++
  gene1320|gene1320|rna1320|rna1320  87 LGINVKVHKGepyCPTLCLVEIDEDSPAYRAGLRVfEDYVIGIEGVYIPNEDAFRRRLYG 146
                                        666666666655533455589************998************999999999984 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.15
                                        --TT-.EEEEETTB--SSHHHHHHHHHT CS
                              PDZ_2  32 lkagD.vilkvdgkkvksledlislllk 58 
                                        +k++D +i k++g+k+++  d ++++ +
  gene1320|gene1320|rna1320|rna1320 287 IKINDeEIEKANGVKIEEKNDEQKRIEE 314
                                        66666369999*****888887777763 PP

>> PDZ_6  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   1.6e-05      0.07       4      35 ..     107     137 ..     106     156 .. 0.80
   2 ?   -2.5   0.0         1   4.6e+03      21      37 ..     293     307 ..     288     319 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.6e-05
                              PDZ_6   4 aVdpgsPAdrAGlrv.GDiilsvNGqpveglsl 35 
                                        ++d++sPA+rAGlrv  D+++ + G+ +   + 
  gene1320|gene1320|rna1320|rna1320 107 EIDEDSPAYRAGLRVfEDYVIGIEGVYI--PNE 137
                                        589***********98999999999988..444 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1
                              PDZ_6  21 iilsvNGqpveglslad 37 
                                         i + NG+ +  +  +d
  gene1320|gene1320|rna1320|rna1320 293 EIEKANGVKI--EEKND 307
                                        4667788888..54444 PP

>> Tricorn_PDZ  Tricorn protease PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0     0.012        54      45      77 ..      34      66 ..      33      75 .. 0.92
   2 ?    5.9   0.0    0.0028        12      28      88 .]     109     169 ..     104     169 .. 0.85
   3 ?   -3.7   0.1       2.8   1.3e+04      42      59 ..     247     264 ..     245     281 .. 0.54
   4 ?   -3.0   0.1       1.6   7.2e+03      46      69 ..     294     317 ..     287     325 .. 0.62

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.012
                                       EEEEETTEE-BTTB-HHHHHHTTTTSEEEEEEE CS
                        Tricorn_PDZ 45 lilavdgepvskekgiaelLvgkagkeveLtvk 77
                                       +i+ v+ ++v++++++++ ++  ++++++L+v 
  gene1320|gene1320|rna1320|rna1320 34 TITLVNEKTVGSSEDVKKEFIKWKQHNIKLQVL 66
                                       6999**************************985 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0028
                                        S-B-GGGGGS---.TT-EEEEETTEE-BTTB-HHHHHHTTTTSEEEE.EEE-STT-EEEEEE CS
                        Tricorn_PDZ  28 earSPLaepGvnvreGdlilavdgepvskekgiaelLvgkagkeveL.tvkrkdgkarrvvv 88 
                                        ++ SP  + G++v   d+++ ++g+ + +e+ + + L g  g+e  L  ++r+ ++ rrv+v
  gene1320|gene1320|rna1320|rna1320 109 DEDSPAYRAGLRV-FEDYVIGIEGVYIPNEDAFRRRLYGFIGRECVLfVFNRETNTIRRVTV 169
                                        578999999***9.5599**********************9988766155666669999998 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 2.8
                                        TT-EEEEETTEE-BTTB- CS
                        Tricorn_PDZ  42 eGdlilavdgepvskekg 59 
                                        eG+ +  +  ++v++ek 
  gene1320|gene1320|rna1320|rna1320 247 EGESVAVISEKEVNEEKT 264
                                        566666666666665543 PP

  == domain 4  score: -3.0 bits;  conditional E-value: 1.6
                                        EEEETTEE-BTTB-HHHHHHTTTT CS
                        Tricorn_PDZ  46 ilavdgepvskekgiaelLvgkag 69 
                                        i + +g++++++++ ++ ++++++
  gene1320|gene1320|rna1320|rna1320 294 IEKANGVKIEEKNDEQKRIEEENE 317
                                        555666666666666666555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (669 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3983  (0.222154); expected 358.6 (0.02)
Passed bias filter:                      917  (0.0511462); expected 358.6 (0.02)
Passed Vit filter:                       588  (0.032796); expected 17.9 (0.001)
Passed Fwd filter:                       152  (0.00847788); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 2.99u 0.40s 00:00:03.39 Elapsed: 00:00:00.74
# Mc/sec: 2735.80
//
Query:       gene1321|gene1321|rna1321|rna1321  [L=61]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       399  (0.0222544); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.44
# Mc/sec: 412.88
//
Query:       gene1322|gene1322|rna1322|rna1322  [L=296]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00074   19.7   2.6    0.00074   19.7   2.6    3.7  4  DUF1430   Protein of unknown function (DUF1430)
     0.0015   18.7  10.7     0.0015   18.7  10.7    3.1  2  EamA      EamA-like transporter family


Domain annotation for each model (and alignments):
>> DUF1430  Protein of unknown function (DUF1430)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.1      0.23     2e+03      74      84 ..      45      55 ..      33      79 .. 0.56
   2 !   19.7   2.6   8.2e-08   0.00074      31     100 .]      85     154 ..      84     154 .. 0.98
   3 ?   -1.5   0.4      0.35   3.1e+03      60      60 ..     171     171 ..     155     208 .. 0.55
   4 ?   -0.2   1.1      0.13   1.2e+03      53      82 ..     261     290 ..     252     295 .. 0.65

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.23
                            DUF1430 74 lllielllill 84
                                       ++l++ ++i++
  gene1322|gene1322|rna1322|rna1322 45 IFLFSTIIIFA 55
                                       22222222222 PP

  == domain 2  score: 19.7 bits;  conditional E-value: 8.2e-08
                            DUF1430  31 ihGyslfkrhkeyliiqlivllillvlifiltkekiillvvlvlllielllillvqekiekkkfisvlKG 100
                                        i+Gys ++++  ++i+ql+  ++++++ ++ ++++ ++++ +v++++ ++  ++v++++ ++ + ++lKG
  gene1322|gene1322|rna1322|rna1322  85 IYGYSQTASYFVVFIAQLMYPMMIITTKILFNRNPEMSIFKIVAFIVLVVSCFVVNKYNHNEPLENILKG 154
                                        89*******************************************************************9 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 0.35
                            DUF1430  60 i 60 
                                        +
  gene1322|gene1322|rna1322|rna1322 171 L 171
                                        1 PP

  == domain 4  score: -0.2 bits;  conditional E-value: 0.13
                            DUF1430  53 illvlifiltkekiillvvlvllliellli 82 
                                         +++li i++  +i++l + ++ ++ ++  
  gene1322|gene1322|rna1322|rna1322 261 AYFGLINIYETFEIYVLAAYIICITASIYL 290
                                        556677777777777777777776666543 PP

>> EamA  EamA-like transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7  10.7   1.7e-07    0.0015      13     136 ..      12     140 ..       4     141 .. 0.78
   2 ?   -2.4   9.1      0.55   4.9e+03       2      44 ..     153     199 ..     152     292 .. 0.68

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.7e-07
                               EamA  13 fwaiyfvlskil..lrkvspltltfvrfl.iagillliiallkegklaklslkdwlll.lllgllgtvlafllffy 84 
                                        +  + +++sk    ++k+ p++++   +  ia+i+l+ ++ ++++k  + ++  + l+ ++++++  +l++ +++y
  gene1322|gene1322|rna1322|rna1322  12 LAVAIALVSKSSekMQKIGPFWIFLQDSArIAAIFLFSTIIIFANKG-QQKKGTVPLYnFIICAVTDILGNAFLIY 86 
                                        44445555555555688899999986666799999988888888888.77999999999***************** PP

                               EamA  85 alkktsasnasli.tslePvftlilsvlll.gekltlkqllgivlillGvllil 136
                                        + + t + ++++i +++ P++++   +l+  +  +++++++++++ ++++++++
  gene1322|gene1322|rna1322|rna1322  87 GYSQTASYFVVFIaQLMYPMMIITTKILFNrNPEMSIFKIVAFIVLVVSCFVVN 140
                                        ********9999945555666666666665455678999999999999999986 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.55
                               EamA   2 lgillallaalfwaiyfvlskillrkvspl....tltfvrfliagil 44 
                                        +g+++++l+  f+ +++vl+ ++++ + p+     ++ v+f+++ ++
  gene1322|gene1322|rna1322|rna1322 153 KGLIFVFLSNSFFIANIVLQSKIVKVIGPFpylkKVNIVSFVLSPMI 199
                                        799************************99943333333444333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (296 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       956  (0.0533214); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.22s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2200.64
//
Query:       gene1323|gene1323|rna1323|rna1323  [L=62]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (62 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       231  (0.0128842); expected 358.6 (0.02)
Passed bias filter:                      217  (0.0121033); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 449.63
//
Query:       gene1324|gene1324|rna1324|rna1324  [L=42]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (42 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       212  (0.0118244); expected 358.6 (0.02)
Passed bias filter:                      154  (0.00858944); expected 358.6 (0.02)
Passed Vit filter:                         3  (0.000167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.41
# Mc/sec: 308.50
//
Query:       gene1325|gene1325|rna1325|rna1325  [L=573]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.045   13.6   0.4       0.11   12.3   0.4    1.6  1  Microcin     Colicin E1 (microcin) immunity protein
      0.089   13.0   0.1       0.24   11.6   0.1    1.7  1  DUF5433      Family of unknown function (DUF5433)
       0.15   12.2   0.8        8.1    6.7   0.2    2.5  2  HicB-like_2  HicB_like antitoxin of bacterial toxin-antitoxin


Domain annotation for each model (and alignments):
>> Microcin  Colicin E1 (microcin) immunity protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.4   1.8e-05      0.11      27      46 ..     467     486 ..     463     489 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.8e-05
                           Microcin  27 iEhialkfikkeFfekrknl 46 
                                        iE+++ k++kk F++ + n+
  gene1325|gene1325|rna1325|rna1325 467 IEEMFRKYTKKVFWKNGTNF 486
                                        9****************998 PP

>> DUF5433  Family of unknown function (DUF5433)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1     4e-05      0.24       6      35 ..     479     514 ..     476     537 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 4e-05
                            DUF5433   6 fnvnGtnfilalciifvPtiklyi......qiimrc 35 
                                        f  nGtnfil l    +P +k  i      qi++rc
  gene1325|gene1325|rna1325|rna1325 479 FWKNGTNFILPLYNCIMPLVKESIqryqksQILLRC 514
                                        556*********888889988877222233577777 PP

>> HicB-like_2  HicB_like antitoxin of bacterial toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.2    0.0014       8.1      11      42 ..     218     250 ..     210     258 .. 0.80
   2 ?    3.2   0.0     0.016        96       8      38 ..     283     313 ..     278     321 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0014
                        HicB-like_2  11 eseeyei.tyrdfdelnavayseedveleasei 42 
                                        ese y+   +  f +l +v++s e ve+ a+++
  gene1325|gene1325|rna1325|rna1325 218 ESECYKKyVHETFAKLPSVTHSVEKVEVHAEDV 250
                                        677776414567******************996 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.016
                        HicB-like_2   8 vdeeseeyeityrdfdelnavayseedvele 38 
                                        + e  e y+ t rd   +  v     dvel 
  gene1325|gene1325|rna1325|rna1325 283 YTESLESYHTTERDTRLICDVQEKVSDVELS 313
                                        568889***********************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (573 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1083  (0.0604049); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.63u 0.29s 00:00:00.92 Elapsed: 00:00:00.50
# Mc/sec: 3428.77
//
Query:       gene1326|gene1326|rna1326|rna1326  [L=950]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (950 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       640  (0.0356964); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.70u 0.28s 00:00:00.98 Elapsed: 00:00:00.46
# Mc/sec: 6180.90
//
Query:       gene1327|gene1327|rna1327|rna1327  [L=360]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.015   15.4  11.7      0.015   15.4  11.7    5.3  5  Cnn_1N        Centrosomin N-terminal motif 1


Domain annotation for each model (and alignments):
>> Cnn_1N  Centrosomin N-terminal motif 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4  11.7   8.5e-07     0.015       1      66 [.      18      87 ..      18      94 .. 0.88
   2 ?    0.5   3.3     0.039   6.9e+02      35      70 ..     123     161 ..      99     164 .. 0.73
   3 ?   -3.6   6.5      0.74   1.3e+04       2      60 ..     150     207 ..     149     226 .. 0.55
   4 ?    1.0   8.0     0.026   4.7e+02      11      62 ..     222     272 ..     213     282 .. 0.69
   5 ?   10.3   1.8   3.4e-05      0.61       9      71 ..     298     359 ..     291     360 .] 0.90

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 8.5e-07
                             Cnn_1N  1 TlrEqeeqidkLkKENFdLKLriyfLeerleklse....eqkeellkenielkveveslqkelkekkkll 66
                                       T++E+e++ ++Lk ENF L  ++ + ++r ++  +     ++e+l+ en +lk ++  +  e++++ kl 
  gene1327|gene1327|rna1327|rna1327 18 TIKEYEAENEQLKTENFQLMHQLSYYRNRGDADMQlvnkNDVESLELENAQLKKQISAMIEENNKRMKLD 87
                                       89**************************97666666777***********************98888754 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.039
                             Cnn_1N  35 e...eqkeellkenielkveveslqkelkekkkllreae 70 
                                        +   e+ ++  k   +l+   ++l +++ke++++++++ 
  gene1327|gene1327|rna1327|rna1327 123 TefmEKEKKYSKMISDLRAAEKNLNDQMKEYNNMIEQLT 161
                                        245567777777888888888888888888888888875 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 0.74
                             Cnn_1N   2 lrEqeeqidkLkKENFdLKLri...yfLeerleklseeqkeellkenielkveveslqkelk 60 
                                        ++E+++ i++L+  N   K  +   ++Le++le +     e+l + n +  +++ +l  ++k
  gene1327|gene1327|rna1327|rna1327 150 MKEYNNMIEQLTMQN---KVHVeknNYLEKKLEDTMC-VLEALREDNNDNITNLSKLNEQKK 207
                                        688888888888888...4444444666666665555.334444444444444444444444 PP

  == domain 4  score: 1.0 bits;  conditional E-value: 0.026
                             Cnn_1N  11 kLkKENFdLKLriyfLeerleklse......eqkeellkenielkveveslqkelkek 62 
                                        +L+  N       +fL++++++ ++      e+++ ll+en  +k+ +e+ +k ++  
  gene1327|gene1327|rna1327|rna1327 222 NLEVNN-------NFLRNEVKNAGTashlrdEENKRLLNENKHIKDLLEDERKRMNDN 272
                                        444444.......4555555555555555668****************9999986654 PP

  == domain 5  score: 10.3 bits;  conditional E-value: 3.4e-05
                             Cnn_1N   9 idkLkKENFdLKLriyfLeerleklseeqkeellkenielkveveslqkelkekkkllreaek 71 
                                         ++L  EN  L   i +Le++le +++ + e++lk+   lkv +  l  +lk  + +l + +k
  gene1327|gene1327|rna1327|rna1327 298 AQQLAAENTKLSSAISELENKLEGIRN-EYEKILKNIAPLKVSMPLLSTSLKVNRLMLMDINK 359
                                        578999*********************.889999*9***********9999999888888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (360 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3293  (0.183669); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); expected 358.6 (0.02)
Passed Vit filter:                       105  (0.00585643); expected 17.9 (0.001)
Passed Fwd filter:                        42  (0.00234257); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 1.19u 0.35s 00:00:01.54 Elapsed: 00:00:00.60
# Mc/sec: 1795.58
//
Query:       gene1328|gene1328|rna1328|rna1328  [L=150]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
     0.0069   16.6   0.0      0.017   15.3   0.0    1.7  1  DUF2795      Protein of unknown function (DUF2795)
  ------ inclusion threshold ------
      0.012   14.9   2.5      0.015   14.5   2.5    1.3  1  HAP1_N       HAP1 N-terminal conserved region
       0.03   14.7   0.4       0.03   14.7   0.4    2.2  2  CCDC-167     Coiled-coil domain-containing protein 167
      0.041   14.2   2.2      0.041   14.2   2.2    2.6  3  Mto2_bdg     Micro-tubular organiser Mto1 C-term Mto2-binding
      0.049   13.9   4.9      0.073   13.3   2.7    2.0  2  TMF_TATA_bd  TATA element modulatory factor 1 TATA binding
      0.055   13.7   2.3       0.17   12.1   1.4    2.3  2  Ntox28       Bacterial toxin 28
       0.11   12.6   1.6        2.8    8.1   0.1    2.5  2  VRR_NUC      VRR-NUC domain
        0.2   11.3   3.4       0.42   10.3   0.2    2.5  2  DUF2312      Uncharacterized protein conserved in bacteria (D
       0.25   11.8   8.2          2    8.8   0.5    2.2  2  Syntaxin_2   Syntaxin-like protein
       0.48   11.1   7.2       0.27   11.9   0.4    2.6  2  YabA         Initiation control protein YabA


Domain annotation for each model (and alignments):
>> DUF2795  Protein of unknown function (DUF2795)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   9.7e-06     0.017      10      35 ..      84     109 ..      83     113 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 9.7e-06
                            DUF2795  10 KdeLveyArrngApdevleaLeaLPd 35 
                                        +++++++A++ngA +++++++e++ +
  gene1328|gene1328|rna1328|rna1328  84 RSDILSFAKENGANNRIIKLIEEFSK 109
                                        89*******************99865 PP

>> HAP1_N  HAP1 N-terminal conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   2.5   8.2e-06     0.015     168     243 ..      66     143 ..       7     147 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 8.2e-06
                             HAP1_N 168 LqeklreLeeeNekLreeasqLktetdt..lEekEqqLvldcveqlseanqqiaelseelarkleelerqqeeiss 241
                                        L + ++ L +eN +L +e s++ + +++    ++  +L+ ++ +++++a++ ++e    l++k  e++  + ei +
  gene1328|gene1328|rna1328|rna1328  66 LFKVIHGLRQENGALENERSDILSFAKEngANNRIIKLIEEFSKEFEDARNGLNECRAYLEKKGKENKLLKSEIRK 141
                                        4455789*************99776655114555669*************************************99 PP

                             HAP1_N 242 Ll 243
                                        L+
  gene1328|gene1328|rna1328|rna1328 142 LR 143
                                        97 PP

>> CCDC-167  Coiled-coil domain-containing protein 167
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.4   1.7e-05      0.03       8      66 ..      16      78 ..      14      91 .. 0.91
   2 ?    0.7   1.0      0.38   6.8e+02      36      53 ..     114     131 ..      79     147 .. 0.60

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.7e-05
                           CCDC-167  8 kleeklascrerLeaverrlrkeelseeeResle....eEeaslkeqleenekeLksLrkeNr 66
                                       +++e + ++  ++++ve+++ k +ls+++++ le    +    +++ l++  k  + Lr+eN+
  gene1328|gene1328|rna1328|rna1328 16 NINELINRISLKVKNVESKIVKFQLSDKNKKMLEklniKPTIGINNLLRKLFKVIHGLRQENG 78
                                       68999999**************************776666667999999999999******96 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.38
                           CCDC-167  36 eResleeEeaslkeqlee 53 
                                        +R++l+e +a l+++ +e
  gene1328|gene1328|rna1328|rna1328 114 ARNGLNECRAYLEKKGKE 131
                                        344444333333333222 PP

>> Mto2_bdg  Micro-tubular organiser Mto1 C-term Mto2-binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.1       5.1   9.2e+03      34      42 ..      73      81 ..      70      85 .. 0.63
   2 ?   -0.5   0.0      0.85   1.5e+03      25      37 ..      94     106 ..      91     109 .. 0.86
   3 ?   14.2   2.2   2.3e-05     0.041      25      50 ..     119     144 ..     109     146 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 5.1
                           Mto2_bdg 34 lkaeNrlLk 42
                                       l++eN  L+
  gene1328|gene1328|rna1328|rna1328 73 LRQENGALE 81
                                       566776664 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.85
                           Mto2_bdg  25 sgarerLeelkae 37 
                                        +ga  r+ +l++e
  gene1328|gene1328|rna1328|rna1328  94 NGANNRIIKLIEE 106
                                        89999*9999887 PP

  == domain 3  score: 14.2 bits;  conditional E-value: 2.3e-05
                           Mto2_bdg  25 sgarerLeelkaeNrlLkaeLerdrs 50 
                                        + +r+ Le++ +eN+lLk e+ ++r+
  gene1328|gene1328|rna1328|rna1328 119 NECRAYLEKKGKENKLLKSEIRKLRK 144
                                        559********************996 PP

>> TMF_TATA_bd  TATA element modulatory factor 1 TATA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.1      0.28     5e+02      12      32 ..      19      39 ..      13      54 .. 0.57
   2 ?   13.3   2.7   4.1e-05     0.073      22     109 ..      64     147 ..      43     150 .] 0.86

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.28
                        TMF_TATA_bd 12 qlverlsseirrlEgElaslk 32
                                       +l++r+s +++  E+ + +++
  gene1328|gene1328|rna1328|rna1328 19 ELINRISLKVKNVESKIVKFQ 39
                                       455566666665555554443 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 4.1e-05
                        TMF_TATA_bd  22 rrlEgElaslkeelerleaerdeareeivklmkeneelkelkkeleelekeleelqeryetlLellGeksEeveEL 97 
                                        r+l   ++ l++e+  le+er    ++i++  ken ++++  k +ee +ke+e+ ++ ++++   l +k  e++ L
  gene1328|gene1328|rna1328|rna1328  64 RKLFKVIHGLRQENGALENER----SDILSFAKENGANNRIIKLIEEFSKEFEDARNGLNECRAYLEKKGKENKLL 135
                                        555555666677777776665....689************************************************ PP

                        TMF_TATA_bd  98 raDvaDlKemyk 109
                                        + ++  l++  k
  gene1328|gene1328|rna1328|rna1328 136 KSEIRKLRKCSK 147
                                        *******99766 PP

>> Ntox28  Bacterial toxin 28
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.2      0.32   5.7e+02      42      42 ..      55      55 ..      13     102 .. 0.61
   2 ?   12.1   1.4   9.6e-05      0.17      51      88 ..     109     146 ..      39     150 .] 0.94

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.32
                             Ntox28 42 P 42
                                       P
  gene1328|gene1328|rna1328|rna1328 55 P 55
                                       1 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 9.6e-05
                             Ntox28  51 keltdaqkGLenvrralekelenppdsdteRevLerkl 88 
                                        ke++da++GL++ r  lek+ ++ ++ ++e ++L +  
  gene1328|gene1328|rna1328|rna1328 109 KEFEDARNGLNECRAYLEKKGKENKLLKSEIRKLRKCS 146
                                        899*******************9999999988887755 PP

>> VRR_NUC  VRR-NUC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.3      0.07   1.3e+02      71      95 ..      28      52 ..      20      60 .. 0.88
   2 ?    8.1   0.1    0.0016       2.8      38      96 ..      66     147 ..      57     149 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.07
                                       EEEEEEE-TT----HHHHHHHHHHH CS
                            VRR_NUC 71 flliEvKgpgdrlsdnQrkwldela 95
                                       ++ +E K  + +lsd+ +k l++l+
  gene1328|gene1328|rna1328|rna1328 28 VKNVESKIVKFQLSDKNKKMLEKLN 52
                                       5679******************997 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0016
                                        HHHHHHHHHHCHHHHSSTS-SEEEEETTTTE.........................EEEEEEE-TT----HHHHHH CS
                            VRR_NUC  38 laklfralledyrglrsGvPDLilwieeqkry.......................vflliEvKgpgdrlsdnQrkw 90 
                                        l+k++  l ++++ l + ++D++ + +e+  +                         ++ E Kg++++l ++  ++
  gene1328|gene1328|rna1328|rna1328  66 LFKVIHGLRQENGALENERSDILSFAKENGANnriiklieefskefedarnglneCRAYLEKKGKENKLLKSEIRK 141
                                        34444555599**************999998899888888888888888888888888888888888888888888 PP

                                        HHHHHH CS
                            VRR_NUC  91 ldelar 96 
                                        l+++ +
  gene1328|gene1328|rna1328|rna1328 142 LRKCSK 147
                                        888765 PP

>> DUF2312  Uncharacterized protein conserved in bacteria (DUF2312)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.2   0.00023      0.42       5      53 ..      63     111 ..      60     121 .. 0.85
   2 ?    2.7   1.8     0.054        98       8      54 ..     100     147 ..      99     150 .] 0.82

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00023
                            DUF2312   5 LrqfieRiErleeEkkaiaedikdvyaeaKseGfdtkvlrkivklrkkd 53 
                                        Lr++   i  l +E  a++++  d+ + aK +G + ++++ i +  k  
  gene1328|gene1328|rna1328|rna1328  63 LRKLFKVIHGLRQENGALENERSDILSFAKENGANNRIIKLIEEFSKEF 111
                                        7888888999*****************************9887666655 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.054
                            DUF2312   8 fieRiErleeEkkaiaedikdvyaeaKseGfdtkvlr.kivklrkkdk 54 
                                        +i  iE+  +E ++  + + +  a   ++G + k+l+ +i klrk  k
  gene1328|gene1328|rna1328|rna1328 100 IIKLIEEFSKEFEDARNGLNECRAYLEKKGKENKLLKsEIRKLRKCSK 147
                                        677799999999999999999999999999999999945778888766 PP

>> Syntaxin_2  Syntaxin-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   1.8    0.0043       7.6      40      75 ..      15      51 ..       9      55 .. 0.66
   2 ?    8.8   0.5    0.0011         2       8      71 ..      73     136 ..      58     150 .] 0.78

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0043
                         Syntaxin_2 40 eeinelikktnellkklsqldnsssds.qqklqkekL 75
                                       ++ineli++++ ++k++++ + + + s ++k + ekL
  gene1328|gene1328|rna1328|rna1328 15 NNINELINRISLKVKNVESKIVKFQLSdKNKKMLEKL 51
                                       4677777777777777777666655444555566666 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0011
                         Syntaxin_2   8 insnvstleklvkqLgtkkdteelreklhelieeinelikktnellkklsqldnsssdsqqklq 71 
                                        + + +  le+ ++++ +       ++++ +liee ++ +++  + l+++ ++ +++ ++++ l+
  gene1328|gene1328|rna1328|rna1328  73 LRQENGALENERSDILSFAKENGANNRIIKLIEEFSKEFEDARNGLNECRAYLEKKGKENKLLK 136
                                        5566778888888888888888899***************************999865433332 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   1.7       0.2   3.6e+02      44      52 ..      54      67 ..       6      99 .. 0.45
   2 ?   11.9   0.4   0.00015      0.27       4      51 ..      98     145 ..      95     149 .. 0.92

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.2
                                       H.....HHHHHHHH CS
                               YabA 44 e.....neklrerl 52
                                             n+ lr+++
  gene1328|gene1328|rna1328|rna1328 54 KptigiNNLLRKLF 67
                                       13333333333333 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00015
                                        HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                               YabA   4 kelfdkleeleeqleelleeleelkeelaelleenaeLeleneklrer 51 
                                        + +++ +ee+++++e+  + l+e ++ l++  +en+ L+ e +klr+ 
  gene1328|gene1328|rna1328|rna1328  98 NRIIKLIEEFSKEFEDARNGLNECRAYLEKKGKENKLLKSEIRKLRKC 145
                                        5688999***************************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1485  (0.0828267); expected 358.6 (0.02)
Passed bias filter:                      634  (0.0353617); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 940.37
//
Query:       gene1329|gene1329|rna1329|rna1329  [L=79]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       545  (0.0303977); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.29s 00:00:00.67 Elapsed: 00:00:00.44
# Mc/sec: 543.96
//
Query:       gene133|gene133|rna133|rna133  [L=782]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (782 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1158  (0.0645881); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.67u 0.25s 00:00:00.92 Elapsed: 00:00:00.43
# Mc/sec: 5408.30
//
Query:       gene1330|gene1330|rna1330|rna1330  [L=398]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
       0.13   11.8   1.0       0.26   10.8   1.0    1.5  1  Adeno_E1B_19K  Adenovirus E1B 19K protein / small t-antigen


Domain annotation for each model (and alignments):
>> Adeno_E1B_19K  Adenovirus E1B 19K protein / small t-antigen
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   1.0   1.4e-05      0.26       8      64 ..     210     265 ..     205     290 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 1.4e-05
                      Adeno_E1B_19K   8 edlkslrrllegasnrtsvlkRflFggrlaklvyrvkeeyeeefeelleeneglfds 64 
                                        e++ +l  + e  s r     R +F  +l +l  ++k++++++f  +le+  ++  s
  gene1330|gene1330|rna1330|rna1330 210 ESFPVLNCITELKSLRNYKTERLIFLHNLKNLEKQIKKKENSNFLSSLENRTQYQ-S 265
                                        5788888899999999999*****************************9866543.3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (398 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1436  (0.0800937); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 2955.19
//
Query:       gene1331|gene1331|rna1331|rna1331  [L=639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.6e-93  310.8   0.1    5.5e-93  310.2   0.1    1.3  1  MCM           MCM P-loop domain
    9.9e-28   96.5   0.9    1.7e-27   95.7   0.9    1.3  1  MCM_OB        MCM OB domain
    7.1e-27   93.7   1.8    1.6e-26   92.6   1.8    1.6  1  MCM_lid       MCM AAA-lid domain
    1.3e-05   24.7   0.1      0.008   15.6   0.0    2.3  2  Mg_chelatase  Magnesium chelatase, subunit ChlI
      0.002   18.0   0.1      0.011   15.5   0.1    2.3  2  AAA_3         ATPase family associated with various cellular 
     0.0022   18.0   0.0     0.0059   16.6   0.0    1.7  1  AAA_5         AAA domain (dynein-related subfamily)
  ------ inclusion threshold ------
      0.073   13.7   6.5       0.35   11.5   2.7    3.0  2  MCM_N         MCM N-terminal domain


Domain annotation for each model (and alignments):
>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  310.2   0.1   2.1e-96   5.5e-93       4     223 ..     242     458 ..     239     459 .. 0.95

  Alignments for each domain:
  == domain 1  score: 310.2 bits;  conditional E-value: 2.1e-96
                                        HHHHHHTSSTHHHHHHHHSSTTSSS-HHHHHHHHHHHH---EBBBSSSSBBCSS-EEEEEESSTSTHHHHHHHHHH CS
                                MCM   4 eikelakekdiieklvksiapsiyghedvkkaillqlfggvkkkledktklrgdinvllvgdpgtaKsqlLkyvek 79 
                                        ei+++++  +++++l k+iap+i gh+dvkkai+++lfgg+++ +++++ lrgdinvll+gdpg+aKsq+Lk++++
  gene1331|gene1331|rna1331|rna1331 242 EIHRFKSF-RFFDNLQKIIAPNIAGHDDVKKAIACLLFGGTRR-VKNGVALRGDINVLLLGDPGVAKSQMLKFTSQ 315
                                        56666544.689******************************6.6677**************************** PP

                                        HSSSEEEEESSSSSSSHSSSEEEEESSSSSEEEEETHHHHTTTSEEEEESGGGSTCHHHHHHHHHHHHSEEEEESS CS
                                MCM  80 lapravytsgkgssaagLtaavvrdeetgefvleaGalvladkGvcciDefdkmkeedrsalhEamEqqtisiaKa 155
                                        +ap +vytsgkgssaagLta+v r++  +e++le+Galvl+d GvcciDefdkm+e dr+a+hEamEqqt+siaKa
  gene1331|gene1331|rna1331|rna1331 316 IAPISVYTSGKGSSAAGLTASVIRNS-MREYTLEGGALVLSDMGVCCIDEFDKMDEFDRVAIHEAMEQQTVSIAKA 390
                                        ***********************987.578********************************************** PP

                                        SCEEEEE--EEEEEEE--SSSSCCTTS-HHHHSSSSHHHHHHSSEEEEE-SSTTHHHHHHHHHHHHHH CS
                                MCM 156 GivatLnartsvlaAanpkagrydkkksvaeninlsaalLsrFDlifvllDkvdeekDeelaehivsl 223
                                        Gi+++Ln+rt+vlaAanpk+gryd+ k  aeni++ +++LsrFD if+l+D++  ++D +la+hi+++
  gene1331|gene1331|rna1331|rna1331 391 GITTVLNTRTAVLAAANPKFGRYDDLKAPAENIEFGSTILSRFDCIFILKDEKRMDRDIALAKHILDV 458
                                        *****************************************************************985 PP

>> MCM_OB  MCM OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.7   0.9   6.8e-31   1.7e-27       2     124 ..      91     212 ..      90     214 .. 0.93

  Alignments for each domain:
  == domain 1  score: 95.7 bits;  conditional E-value: 6.8e-31
                                        XGG--GGGTTSEEEEEEEEEEE---EEEEEEEEEEETTT-.-EEES----SB-..TTT-HHH-EEE-GGGSEEEEE CS
                             MCM_OB   2 lRdlrsehigklvkveGivtrasevkpklkkavfeckkcgktveveleePrkCeekeCeskdpfkletekskfvdf 77 
                                        +R+l++++ +k+v+v+Givt++s+v+ k  +++++ck+c  ++ev+   Pr+C ++ C   +pf +++eksk+vd+
  gene1331|gene1331|rna1331|rna1331  91 IRNLDASKTNKIVRVRGIVTSVSNVHAKPLTLYLTCKSCFVVKEVTDVIPRSC-QNGCM-FEPFIIVPEKSKVVDT 164
                                        7***************************************988776666****.779**.89************** PP

                                        EEEEEE-------------EEEEEEEGGGT.T---TT-EEEEEEEEEE CS
                             MCM_OB  78 qklklQEspeevpaGelPrslevileddlv.dkvkPGdrvevtGiyra 124
                                        q+lk+QE  ++vp  e+Pr+ + i+++ l+ +++ PG+++ +tGi+ +
  gene1331|gene1331|rna1331|rna1331 165 QSLKVQEDFDDVPSNEIPRHCTAIINNALCsNELVPGSNIVFTGILLV 212
                                        **************************99983679***********875 PP

>> MCM_lid  MCM AAA-lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.6   1.8   6.2e-30   1.6e-26       1      86 [.     472     558 ..     472     559 .. 0.93

  Alignments for each domain:
  == domain 1  score: 92.6 bits;  conditional E-value: 6.2e-30
                                        HHHHHHHHHHHHTT--BETCHHHHHHHHHHHHHHHHH..TSS.TSSSST--HHHHHHHHHHHHHHHHHHTSSSE-H CS
                            MCM_lid   1 ellrkYiayarekikPklseeakeklseaYvelRkee..eds.krksipitvRqLesliRLseAlAklrlsevvte 73 
                                        e++++Y++ya+  i+P ++ +ak+ ++++Y+++R+    + s k+ sipitvRqLe++iR+seA+A+++l++ v +
  gene1331|gene1331|rna1331|rna1331 472 EFIKRYVTYAK-SISPEMDAQAKQRIKNFYIKTRQAVhsH-SkKEFSIPITVRQLEAVIRISEAFARMSLNTRVLP 545
                                        689********.***********************99543.247889***************************** PP

                                        HHHHHHHHHHHHH CS
                            MCM_lid  74 edveeairllkes 86 
                                        e+v+eai+l++ s
  gene1331|gene1331|rna1331|rna1331 546 EHVDEAIHLFRVS 558
                                        **********987 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.8   0.0    0.0015       3.8      17      47 ..     288     318 ..     280     344 .. 0.87
   2 !   15.6   0.0   3.1e-06     0.008      98     159 ..     348     409 ..     334     425 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0015
                       Mg_chelatase  17 iaaaGgHnlllvGppGsGKtmlakrlpsllp 47 
                                        +a  G  n+ll+G pG  K+ + k  +++ p
  gene1331|gene1331|rna1331|rna1331 288 VALRGDINVLLLGDPGVAKSQMLKFTSQIAP 318
                                        8999****************99998888776 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 3.1e-06
                       Mg_chelatase  98 kpGeislahnGvLfLDElpefkrkvlevLRePledgevtisrakakvefparfqlvaamNpc 159
                                        + G++ l+  Gv  +DE+ ++++    ++ e +e+++v+i++a  ++   +r+ ++aa+Np 
  gene1331|gene1331|rna1331|rna1331 348 EGGALVLSDMGVCCIDEFDKMDEFDRVAIHEAMEQQTVSIAKAGITTVLNTRTAVLAAANPK 409
                                        679999***********999999989999*******************************94 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.1   4.5e-06     0.011       2     112 ..     296     408 ..     295     415 .. 0.79
   2 ?   -2.1   0.0       1.3   3.3e+03      75      91 ..     596     612 ..     521     626 .. 0.58

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 4.5e-06
                              AAA_3   2 vllegvPGlaktllvkalakaldlefkriqftpdllPsdilGtevfeekekefefkkGpvf.an..llladeinra 74 
                                        vll g PG+ak ++ k  +++  +++           +  l ++v++++ +e++++ G+++ ++  +   de ++ 
  gene1331|gene1331|rna1331|rna1331 296 VLLLGDPGVAKSQMLKFTSQIAPISVYTS---GKGSSAAGLTASVIRNSMREYTLEGGALVlSDmgVCCIDEFDKM 368
                                        78889999999999998888877765332...223334445678999999********976233337889****** PP

                              AAA_3  75 ppktqsalleameerqvtve..gethklpepflvlatqnP 112
                                            + a+ eame+++v+++  g t+ l++   vla+ nP
  gene1331|gene1331|rna1331|rna1331 369 DEFDRVAIHEAMEQQTVSIAkaGITTVLNTRTAVLAAANP 408
                                        *****************9972256899************9 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.3
                              AAA_3  75 ppktqsalleameerqv 91 
                                        ++++ +al e   er++
  gene1331|gene1331|rna1331|rna1331 596 NARSIAALAEHFGERDI 612
                                        34455555555555555 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   2.3e-06    0.0059       1     123 [.     295     409 ..     295     420 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 2.3e-06
                                        EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--..........--------G-SEEEEESGG CS
                              AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreik.ngttslvdsplvraaregeilvlDEve 75 
                                        +vlL+G+pG++Ks++ +  ++    ++ ++   ++ +++ l+ ++  + ++++ l+ ++lv       ++++DE++
  gene1331|gene1331|rna1331|rna1331 295 NVLLLGDPGVAKSQMLKFTSQIA--PISVYTSGKGSSAAGLTASVIRNsMREYTLEGGALV--LSDMGVCCIDEFD 366
                                        69*************99999985..666777888999999999988777889999999999..999********** PP

                                        G--HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS- CS
                              AAA_5  76 raesevlnsLlslleerrllleeggelvkaknddllerfrviatanpl 123
                                        +++     + +  +e++++++++ g  +  +       + v+a+anp 
  gene1331|gene1331|rna1331|rna1331 367 KMDEFDRVAIHEAMEQQTVSIAKAGITTVLNTR-----TAVLAAANPK 409
                                        **9888888999999999998887777766654.....7888888886 PP

>> MCM_N  MCM N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   2.7   0.00014      0.35       2      69 ..      27      78 ..      26      80 .. 0.79
   2 ?   -1.4   0.1       1.4   3.6e+03      49      97 ..     469     514 ..     459     524 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00014
                              MCM_N  2 ekFedFLeefkddsededgekkYrdqlqemaerekttLevdlddLaafdeeLaeailenpkeylplle 69
                                       ++F+ FL++f     + +++++Yr+           + +v+l +La fd+ L+++ l +p+e+++l +
  gene1331|gene1331|rna1331|rna1331 27 KQFQAFLSSF-----SINNQYIYRN-----------RKTVQLAHLAVFDQVLYNKFLAKPREFVDLVD 78
                                       6777777777.....4555555553...........2379************************9876 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.4
                              MCM_N  49 fdeeLaeailenpkeylplleealkevvkklepsykddakefpaeltrr 97 
                                        +d e+ ++ +++ k + p +++ +k+ +k+++ +  ++    +++ +++
  gene1331|gene1331|rna1331|rna1331 469 YDAEFIKRYVTYAKSISPEMDAQAKQRIKNFYIKTRQA---VHSHSKKE 514
                                        66677777777777777777777777777777654444...44444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (639 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       752  (0.0419432); expected 358.6 (0.02)
Passed bias filter:                      544  (0.0303419); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.71u 0.29s 00:00:01.00 Elapsed: 00:00:00.50
# Mc/sec: 3842.26
//
Query:       gene1332|gene1332|rna1332|rna1332  [L=490]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      6e-09   35.4   2.0    0.00032   19.8   0.0    2.2  2  tRNA_U5-meth_tr  tRNA (Uracil-5-)-methyltransferase
  ------ inclusion threshold ------
       0.01   15.4   0.4      0.027   14.0   0.1    1.8  2  MTS              Methyltransferase small domain


Domain annotation for each model (and alignments):
>> tRNA_U5-meth_tr  tRNA (Uracil-5-)-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.5   1.2e-06     0.011     176     257 ..     227     307 ..     213     339 .. 0.79
   2 !   19.8   0.0   3.5e-08   0.00032     271     329 ..     392     453 ..     360     475 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.2e-06
                    tRNA_U5-meth_tr 176 ensftqPnaavnekmleWalevtqeskgdllelycGnGnfslalarnfekvlateiakssveaaqyniaankidnv 251
                                          +f q n ++ + ++e  ++++++++  ll+l cG   + + l+  ++ v+  e     v+   +n + n+++n 
  gene1332|gene1332|rna1332|rna1332 227 FFTFFQTNIEMLIAIVEQ-IKAVKKNNPYLLDLCCGSLVLGMMLCSDYKEVIGVENNLECVKDFNVNRDVNEVKNC 301
                                        557899999999999986.5677778889**********************************************9 PP

                    tRNA_U5-meth_tr 252 qiirls 257
                                        +i+ + 
  gene1332|gene1332|rna1332|rna1332 302 RIMGVD 307
                                        987543 PP

  == domain 2  score: 19.8 bits;  conditional E-value: 3.5e-08
                    tRNA_U5-meth_tr 271 frrlkgidlksyafetifvdPPraGldketvklvkk...yerilyiscnPetlkenleelse 329
                                          rl++ ++++ +  t+++dPPraG++k  +k +++    ++++yisc+ +    n+++l++
  gene1332|gene1332|rna1332|rna1332 392 TARLENETINREENITVILDPPRAGVNKRLIKKLREctaIDELFYISCDFNQSIGNIKDLTR 453
                                        568888888888999**************99988762226788*******999999999975 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0      0.64   5.7e+03      36      64 ..      91     120 ..      79     123 .. 0.66
   2 ?   14.0   0.1     3e-06     0.027      28      90 ..     246     309 ..     236     322 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 0.64
                                        EEET-TTSHHHHHHHHHTTC.E.EEEEESB CS
                                MTS  36 lDlGcGaGvlgaalakespeae.vtlvdvd 64 
                                         D   G+G+l ++  +  + +e ++lvd+d
  gene1332|gene1332|rna1332|rna1332  91 YDREKGTGYLRMMKVRVVNGNEhLVLVDID 120
                                        555568888887766554444448888886 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 3e-06
                                        HCCTCSE..EEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC.EEEEE-STT CS
                                MTS  28 pkelsgk..vlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle.vevvasdvl 90 
                                        ++ ++++  +lDl+cG  vlg++l + ++e  v  v+++ + ++  + n   n+++ ++++  dv 
  gene1332|gene1332|rna1332|rna1332 246 KAVKKNNpyLLDLCCGSLVLGMMLCSDYKE--VIGVENNLECVKDFNVNRDVNEVKnCRIMGVDVN 309
                                        4433333449***************99988..99*********************99999988875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (490 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       755  (0.0421105); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.47
# Mc/sec: 3105.53
//
Query:       gene1333|gene1333|rna1333|rna1333  [L=179]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (179 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       689  (0.0384294); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.28s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1330.67
//
Query:       gene1334|gene1334|rna1334|rna1334  [L=220]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0022   17.8   0.5     0.0037   17.0   0.5    1.4  1  UBN_AB    Ubinuclein conserved middle domain


Domain annotation for each model (and alignments):
>> UBN_AB  Ubinuclein conserved middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.5     2e-07    0.0037      56     192 ..      13     149 ..       2     157 .. 0.71

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 2e-07
                             UBN_AB  56 savyshLesvlpcskdtLlkrlkklrlkkeeerlkellekLkeaidevmpeqlekYeeecqalkeakaakkaeeae 131
                                        + ++ hL+++l  s + +  +l  l l+ e ++  e  ++ + a+ e  +++l+kY e++ ++++a a+++a+  +
  gene1334|gene1334|rna1334|rna1334  13 NFYFPHLSYHLNRSTEPINCKLVFLDLEIEIDDEYEDCDQCETAVFELGEKILSKYIEDLSQHQDADASNDASVVN 88 
                                        66899***************************************************************98884445 PP

                             UBN_AB 132 kdteeeedeekkekkvkePrkkFkwneelRelLleivklkeesyelekkkkqsaeeflkkf 192
                                        +++++++++ ++++k+k+   +    e ++++   i k +++s+e + ++++s   + ++f
  gene1334|gene1334|rna1334|rna1334  89 TNAKNDNSTGDNGEKTKNSGSNDGNVEAVKKMEDAIKKKNSKSVENSMQSNTSLQSQCADF 149
                                        5555555555555555444443333344444444444444455555555555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1692  (0.0943722); expected 358.6 (0.02)
Passed bias filter:                      521  (0.0290591); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 1648.04
//
Query:       gene1335|gene1335|rna1335|rna1335  [L=403]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.038   13.9   0.8      0.083   12.8   0.8    1.5  1  DUF1980   Domain of unknown function (DUF1980)


Domain annotation for each model (and alignments):
>> DUF1980  Domain of unknown function (DUF1980)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.8   4.6e-06     0.083     109     175 ..      76     147 ..      36     148 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4.6e-06
                            DUF1980 109 k....eskseqkedegtqeqslkpdtssyvtkd.gydkemkkeakklskkkkItvtdenYlevmeeiynnpd 175
                                              +++eq++de+ ++  ++++t++y+  d   +k    ++ kls+++ I +td   +e+me ++ ++d
  gene1335|gene1335|rna1335|rna1335  76 CttstPQTNEQTSDENGNSCVFESKTQKYMRLDvPVTKSLYMKTTKLSENNDIDLTDSEIVEFMEHLMPFLD 147
                                        02222334455555555555555559999998884444444445889******************9987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (403 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       874  (0.0487478); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 2543.40
//
Query:       gene1336|gene1336|rna1336|rna1336  [L=166]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       817  (0.0455686); expected 358.6 (0.02)
Passed bias filter:                      644  (0.0359195); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1160.75
//
Query:       gene1337|gene1337|rna1337|rna1337  [L=183]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.9e-05   21.4   0.1     0.0001   21.2   0.1    1.1  1  DUF2207   Predicted membrane protein (DUF2207)
  ------ inclusion threshold ------
      0.026   12.6   0.2       0.19    9.7   0.0    1.9  2  IgaA      Intracellular growth attenuator protein IgaA


Domain annotation for each model (and alignments):
>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.1   1.1e-08    0.0001     148     235 ..      79     170 ..      36     181 .. 0.79

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 1.1e-08
                            DUF2207 148 kkddgsvtftarnlppgeglevrvlf..pt..n.narktsgnkldeilkeeqkntreraarlslallillilllil 218
                                        k  + ++ f++ ++  +++ + r +f  +      + + + ++ ++i+++e++ +++ +++++ +++i+ i ll++
  gene1337|gene1337|rna1337|rna1337  79 KPTNYYYGFEVVDVDGNSFYTERYYFgnDRvfYsSKAQVQAEEAADIEEIEED-EYKGKRDKWSVWMIIGIGLLLI 153
                                        444556679999**************852233378999999999999999999.7889999999999998888888 PP

                            DUF2207 219 llllllllliklllwkk 235
                                        ++++  +++i +++ + 
  gene1337|gene1337|rna1337|rna1337 154 FAFATAIVAIIFVYKRI 170
                                        88888888886554444 PP

>> IgaA  Intracellular growth attenuator protein IgaA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.1      0.01        92      86     121 ..      41      76 ..      13      89 .. 0.77
   2 ?    9.7   0.0   2.1e-05      0.19     644     685 ..     136     177 ..     128     180 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.01
                                        GGEEEEEEE-EEEE--S-SSSSS-EEEETTEEEB-- CS
                               IgaA  86 sdnvyavtraitRyglstdepnkWrYyldsvevhlP 121
                                         + v ++t+ai Ry l  d ++      +  ev lP
  gene1337|gene1337|rna1337|rna1337  41 YNVVKRMTNAIERYELVDDVQRDPNDPQEIFEVSLP 76 
                                        5789999********999988776666666666666 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 2.1e-05
                                        XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                               IgaA 644 epdavtlwrylgttlLllvlllllilnavlllrrlrknrqRl 685
                                        + d+ ++w ++g  lLl++ ++++i+ ++++++r+  ++ +l
  gene1337|gene1337|rna1337|rna1337 136 KRDKWSVWMIIGIGLLLIFAFATAIVAIIFVYKRIVTSKDKL 177
                                        569999****************************99988775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1107  (0.0617435); expected 358.6 (0.02)
Passed bias filter:                      620  (0.0345808); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1277.65
//
Query:       gene1338|gene1338|rna1338|rna1338  [L=227]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.2e-14   51.5   1.3    9.7e-14   50.8   1.3    1.3  1  zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal
     0.0083   16.2   3.5      0.016   15.3   3.4    1.5  1  FYVE            FYVE zinc finger
  ------ inclusion threshold ------
      0.033   13.0   0.6      0.042   12.6   0.6    1.2  1  DUF2207         Predicted membrane protein (DUF2207)


Domain annotation for each model (and alignments):
>> zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.8   1.3   1.6e-17   9.7e-14       2      54 .]     149     198 ..     148     198 .. 0.97

  Alignments for each domain:
  == domain 1  score: 50.8 bits;  conditional E-value: 1.6e-17
                     zinc_ribbon_10   2 fDrvldvLvGddetsaknryalICskChshnGlapkeeleevkyrCpkCgaln 54 
                                         D+++ +++Gd++   +++ alIC+kC+ hnGl+ + ++ + k++C +Cg+ln
  gene1338|gene1338|rna1338|rna1338 149 ADKLTNIILGDNP---QQMCALICEKCFAHNGLVFPIQFFNRKFKCISCGTLN 198
                                        59***********...***********************************98 PP

>> FYVE  FYVE zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   3.4   2.7e-06     0.016       9      48 ..     162     211 ..     154     221 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.7e-06
                                        -SB-TT.T--B--.........SSS--EE-TTT--EE-STTS-EEE.EEG CS
                               FYVE   9 vkkCei.CakkFs.........llrrrhhCrlCGkvvCekCssklvalle 48 
                                         + C   C+k F          +++r+  C  CG +  +kC ++l+++ e
  gene1338|gene1338|rna1338|rna1338 162 QQMCALiCEKCFAhnglvfpiqFFNRKFKCISCGTLNITKCEDELLEKKE 211
                                        556665588888646677666679******************99997764 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.6   7.1e-06     0.042     354     433 ..      12      96 ..       3     142 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 7.1e-06
                            DUF2207 354 kkalkkwksavkkkergyfdkkgkkklkklsalglgliilglilillallllvlllvfllilllillliaiivlll 429
                                        +++l  + + ++k++++ +  +++k ++++ + ++ l++l l +++l ++ + + l++ l +l ++l++  ++l++
  gene1338|gene1338|rna1338|rna1338  12 REQLFNLDERIEKRSQKIYYLRKQKSYYSFVVGIIYLFLLPLSAVFLHFYEFSF-LFLGLPILSFVLIQTTVYLVF 86 
                                        555556667777744444444445666666666666666666666666555554.555666666666666666666 PP

                            DUF2207 430 fsr......l 433
                                         +       l
  gene1338|gene1338|rna1338|rna1338  87 TKFidynenL 96 
                                        5334444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (227 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1808  (0.100842); expected 358.6 (0.02)
Passed bias filter:                      591  (0.0329634); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 1668.56
//
Query:       gene1339|gene1339|rna1339|rna1339  [L=247]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.026   15.1   1.1      0.026   15.1   1.1    1.9  2  DUF5344    Family of unknown function (DUF5344)
      0.048   13.8   0.1       0.18   11.9   0.0    2.0  2  ASL_C      Adenylosuccinate lyase C-terminal
      0.086   12.4   5.9       0.16   11.5   4.4    2.2  2  4HB_MCP_1  Four helix bundle sensory module for signal transd


Domain annotation for each model (and alignments):
>> DUF5344  Family of unknown function (DUF5344)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.69   4.2e+03      51      71 ..     148     168 ..     143     176 .. 0.58
   2 ?   15.1   1.1   4.4e-06     0.026      25      62 ..     194     232 ..     178     234 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.69
                            DUF5344  51 eleellkaYktlllknvedte 71 
                                        ++ ++++++k+++++ + +++
  gene1339|gene1339|rna1339|rna1339 148 DILKVFESLKEMISDELRKIQ 168
                                        444555666666665555555 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 4.4e-06
                            DUF5344  25 lk.tsipetisgknsldvvekineleeeleellkaYktl 62 
                                        l+ +++++t ++kn+ d+ + +n+++ e ++++ +Y +l
  gene1339|gene1339|rna1339|rna1339 194 LDlVKMKSTKDKKNQNDYANNFNKINAETQQVIASYNQL 232
                                        556899******************************987 PP

>> ASL_C  Adenylosuccinate lyase C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   3.1e-05      0.18      27     108 ..      77     166 ..      69     171 .. 0.71
   2 ?   -0.1   0.2      0.16   9.5e+02      53      53 ..     168     168 ..     140     223 .. 0.53

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.1e-05
                                        HHHHHHHHCCEEE-HHHHHHHHHT-GGGGHHHHHHHHHHTT-TTHHHHHHHHHTTS.......---HHHHHHHHHC CS
                              ASL_C  27 lksllkglsklevneealaedLdenwevlaEaiqtvlrregiekpYeklkeltrgk.......kitkeslkefies 95 
                                        +k+++k  sk+   +e   + L ++   l+E i+ ++  +gi++p++++k++  ++        +  ++++++++ 
  gene1339|gene1339|rna1339|rna1339  77 VKRVVKTTSKVASPKESPLDSLMQTNPELGEQIKKIFAYQGITEPWDRIKDFFDNRqrlmpdpCMLYKTMRDILKV 152
                                        57888999999988888888888888889**********************9876632212112334455555555 PP

                                        S-.S-HHHHHHHHC CS
                              ASL_C  96 le.vseeakeeLka 108
                                         e ++e +++eL++
  gene1339|gene1339|rna1339|rna1339 153 FEsLKEMISDELRK 166
                                        53355555566655 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.16
                                        G CS
                              ASL_C  53 e 53 
                                        +
  gene1339|gene1339|rna1339|rna1339 168 Q 168
                                        2 PP

>> 4HB_MCP_1  Four helix bundle sensory module for signal transduction
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.22   1.3e+03     155     175 ..      91     111 ..      78     112 .. 0.77
   2 ?   11.5   4.4   2.6e-05      0.16      53     101 ..     184     232 ..     145     234 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.22
                          4HB_MCP_1 155 liealeelvdlnlkvAeeayk 175
                                         ++ l+ l+++n +++e+++k
  gene1339|gene1339|rna1339|rna1339  91 KESPLDSLMQTNPELGEQIKK 111
                                        5677999********999976 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 2.6e-05
                          4HB_MCP_1  53 eikanlrelradlleliltkdkaekdellkdieeleaeidkllekyekt 101
                                        ++k+ l ++  dl+++  tkdk+++++ +++ ++++ae+++ +++y+++
  gene1339|gene1339|rna1339|rna1339 184 KLKDLLSRMSLDLVKMKSTKDKKNQNDYANNFNKINAETQQVIASYNQL 232
                                        67888999**************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1568  (0.0874561); expected 358.6 (0.02)
Passed bias filter:                      651  (0.0363099); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 1762.54
//
Query:       gene134|gene134|rna134|rna134  [L=271]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    7.4e-34  117.3   0.0    8.7e-34  117.0   0.0    1.1  1  TatD_DNase  TatD related DNase
  ------ inclusion threshold ------
        0.1   12.6   0.4       0.28   11.2   0.4    1.7  1  Pept_S41_N  Peptidase S41 N-terminal domain


Domain annotation for each model (and alignments):
>> TatD_DNase  TatD related DNase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.0   0.0   9.7e-38   8.7e-34       1     254 [.       3     247 ..       3     249 .. 0.89

  Alignments for each domain:
  == domain 1  score: 117.0 bits;  conditional E-value: 9.7e-38
                                    EEEEE-TTS.CCCTTTHHHHHHHHHHTTEEEEEEE-SSGGGHHHHHHHHTT.TTTEEEEE---GGGGGCC.CCHHHHHHH CS
                     TatD_DNase   1 iDaHcHlds.kefeedreeileraeeagvaavvvvgtsskdskavlelakkypnkvyavlGiHPnevdeasedlleelke 79 
                                    iD + ++++ k  +++ +++++++ +++   +  vgt++ +sk++l+lakky    ++  GiHP+e+ + s +      e
  gene134|gene134|rna134|rna134   3 IDIAFNITHyK--DKEHDDTIQHCIQNNTMPI-FVGTNVDTSKECLRLAKKYHT--MCYSGIHPTESGRCSGTN-----E 72 
                                    89999999933..5789999999998887777.69*****************97..7888****9999754444.....4 PP

                                    HHHCCCTSEEEEEEEEEET-CCCCCGHHHHHHHHHHHHHHHHHTTEEEEEEEES-HHHHHHHHHHCGGCCSEEEETT--S CS
                     TatD_DNase  80 lanvkhskvvaiGeiGLDyysreestkeaqeevFeeqlrlAkelklplviHlrkaeedlleilkeaaeakakvvlHsfsg 159
                                    l  v++  + a+Ge+GLDy + e + k  q+ vF+++l+        ++ H+r+a++d+l+i+k+  ++++ +++Hsf+g
  gene134|gene134|rna134|rna134  73 L-PVDDCSILALGECGLDYDRLEYASKNDQQVVFKNMLAFSYTN---YFFHSRNAHNDFLSIVKQR-KSGVNGIVHSFTG 147
                                    4.56777************999999************8777766...99****************8.56779******** PP

                                    -HHHHHHHHHTTEEEEE-GGGGTTTTHHHHHHHHHS-GGGEEE---TTSSEE........CCCTT.SE--GGGHHHHHHH CS
                     TatD_DNase 160 saeeakkflklgyyislsglltfknakelrelvkavpldrlLiETDaPyltp........kpyrg.krnepanvayvvek 230
                                    +++e+ ++l+ ++yi+++g++ +    + +++ + +pl+rlL+ETDaP++          +   + ++ + + v+ +++ 
  gene134|gene134|rna134|rna134 148 TKDELVQLLDHNLYIGINGCSLK----NKTDIFEVLPLNRLLLETDAPFCCVrksyyywnDSVPKiRKYRAGDVKIIYDL 223
                                    *******************9888....569********************9988888888555566999999******** PP

                                    HHHHHTS-HHHHHHHHHHHHHHHH CS
                     TatD_DNase 231 laelkaltleelaeitaeNakrlf 254
                                    ++ + ++  +e+++i+++N  r++
  gene134|gene134|rna134|rna134 224 VSGIYGIGRDEMEKIVEDNLVRIY 247
                                    **********************98 PP

>> Pept_S41_N  Peptidase S41 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.4   3.1e-05      0.28      11      22 ..     197     208 ..     197     224 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 3.1e-05
                     Pept_S41_N  11 neyYLWndevpd 22 
                                    ++yY+Wnd vp+
  gene134|gene134|rna134|rna134 197 KSYYYWNDSVPK 208
                                    68*********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (271 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       425  (0.0237046); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1946.97
//
Query:       gene1340|gene1340|rna1340|rna1340  [L=831]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (831 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       802  (0.044732); expected 358.6 (0.02)
Passed bias filter:                      471  (0.0262703); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.68u 0.29s 00:00:00.97 Elapsed: 00:00:00.46
# Mc/sec: 5384.51
//
Query:       gene1341|gene1341|rna1341|rna1341  [L=1136]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-36  125.4   0.5    5.5e-36  124.0   0.1    2.0  2  Sec7      Sec7 domain


Domain annotation for each model (and alignments):
>> Sec7  Sec7 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.1      0.19   3.4e+03      68      99 ..      54      85 ..      41     185 .. 0.51
   2 !  124.0   0.1   3.1e-40   5.5e-36      41     182 ..     387     632 ..     344     633 .. 0.75

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.19
                                       HHHCTS--TT--HHHHHHHHCCCS-B-SSHHH CS
                               Sec7 68 efvdlfdfsglrldeAlRlflssfrlpgEaqk 99
                                       efv+  +f++ ++   l ++++ + l  E   
  gene1341|gene1341|rna1341|rna1341 54 EFVRVRKFRNSEMQFVLEELVNVVGLFDELDV 85
                                       56666666666655555555555555444433 PP

  == domain 2  score: 124.0 bits;  conditional E-value: 3.1e-40
                                        HHTCCS-HHHHHHHHCSGGHHHHHHHHHHHCTS--TT--HHHHHHHHCCCS-B-SSHHHHHHHHHHHHHHHHHTT. CS
                               Sec7  41 ketpgldkkklGeylgkekefnkevlkefvdlfdfsglrldeAlRlflssfrlpgEaqkierilekFaekyfeqn. 115
                                         ++  l+k+ +G++l+++     +vlke++++fdf++l+l  AlR fl++f lp E+q+i++il++F+e+y+e n 
  gene1341|gene1341|rna1341|rna1341 387 LRSFPLNKRSIGKFLSNNP----SVLKEYLTTFDFTNLDLLGALRAFLRNFYLPTESQAINKILSAFSERYYECNk 458
                                        455679**********999....9************************************************9885 PP

                                        .........................................................................CTC CS
                               Sec7 116 .........................................................................pev 118
                                                                                                                 p v
  gene1341|gene1341|rna1341|rna1341 459 egfgsdgneldsivcgnggdvkrvngivgnenagaesdeiydgedvvrgddrgdngddmtnvrgkrlpnesdtP-V 533
                                        55666555665555555666655555555555555555555555555555555555555544444444444440.0 PP

                                        ...................................G-SHHHHHHHHHHHHHHHHHHC-TTSCCS--HHHHHHCTTT CS
                               Sec7 119 ...................................fenadavfvLaysiimLntdlhnpqvkkkmtledFiknnrg 159
                                                                            ++ d+v +L++ i++Lntdlhn +++ k+ + +Fi++ r+
  gene1341|gene1341|rna1341|rna1341 534 qgvceivnqnsidnlmknskehaekdavktgtrntAFDFDSVDILTFCILCLNTDLHNAAIRVKTLKLSFIERARK 609
                                        444444444444444444444455555555544447999************************************* PP

                                        TBTTB---HHHHHHHHHHHHHS- CS
                               Sec7 160 indgkdlpeefLeeiYdsIkeee 182
                                        +n ++ +++++L+ +Yds+k+++
  gene1341|gene1341|rna1341|rna1341 610 CNLSYFFSDRYLSYVYDSVKKDP 632
                                        ***9****************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       724  (0.0403815); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.78u 0.32s 00:00:01.10 Elapsed: 00:00:00.49
# Mc/sec: 6954.50
//
Query:       gene1342|gene1342|rna1342|rna1342  [L=327]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.1e-39  135.0   8.2    4.8e-39  134.8   8.2    1.0  1  vATP-synt_AC39  ATP synthase (C/AC39) subunit


Domain annotation for each model (and alignments):
>> vATP-synt_AC39  ATP synthase (C/AC39) subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  134.8   8.2   2.7e-43   4.8e-39       3     323 ..      16     311 ..      14     322 .. 0.90

  Alignments for each domain:
  == domain 1  score: 134.8 bits;  conditional E-value: 2.7e-43
                                        HHHHHHGGGS--HHHHHHHTTS.-HHHHHHHHHTSGGGGG--.....SSSHHHHHHHHHHHHHHHTTTGGGGS-H. CS
                     vATP-synt_AC39   3 ArvramrsglLteedyenLlqcesledvkryLketdYgnfladelseplsrsdiekalreklarefnklreqapgp 78 
                                        A +++++s++Lt ++y+ Llq+++++dv+  L+ t Y+++l+d+ +   s  ++   l++ + +efn+++e ++g 
  gene1342|gene1342|rna1342|rna1342  16 AEIHGRQSRILTSSEYKALLQSDNIDDVIVKLQGTTYSKYLSDSME--KSKVNLILSLERAFKHEFNEIYERSTGC 89 
                                        789*************************************999987..456677799******************* PP

                                        HHHHHHHHHHHHHHHHHHHHHHHHHH.T--GGGS-..--.SSSS-HHHHHHHHHSSSHHHHHHHHH.T-HHHHHHH CS
                     vATP-synt_AC39  79 srefldyllyrydidNvklllrgklsgdldleeleeklhplgelsaldldklieaksveelyeall.gtpyakyle 153
                                        +r +l ++l  y i+  ++ +      ++  eel  ++    el +l++     +++++e+ + +  +t +++y++
  gene1342|gene1342|rna1342|rna1342  90 LRVLLTFFLESYKIESFIYRVSNPEE-PE--EEL-GFF---VELNTLKF-----SNDMREVKKFVIdETFLSRYFD 153
                                        99**************9998877666.55..665.555...38888899.....********************** PP

                                        H.HHCC...--SHHHHHHHHHHHHHHHHHHHHHTSS-HH...HHHHHHHHHHHHHHHHHHHTTTSS......T... CS
                     vATP-synt_AC39 154 e.aldeleetgdleiienaLdkayledllkfckklggetaeilreilgfeiDlrniniilrskkygelskedrkkl 228
                                        +  +++  e+++++ii+ +L+k+ +ed++ +++  +  +   +r  l+    +  i i+l+++  ++ + ++rkkl
  gene1342|gene1342|rna1342|rna1342 154 RiNVENSIEKNNFQIIKRMLMKYHIEDFYGRIN-GDMGF---MRTVLEVMGSIQIIEIVLNTMH-TNITADNRKKL 224
                                        *7688888899********************99.44568...**********************.8899999**** PP

                                        --SS-S--HHHHHHHHTT-G.....GG.GGSSTSSTTGGGTT--S.HHHHHHHHHHHHHHHHHTTTSSSTSTHHHH CS
                     vATP-synt_AC39 229 lipggslypeglealaeaedveellaalkyteygelleealeeagslksledaldealvkllkkafrqqfsvgvfy 304
                                        +++++ l+  ++ +lae++++++l+a+l +t+y+e +          k+l   l+ + + ++ ++f     + +++
  gene1342|gene1342|rna1342|rna1342 225 FPDVNDLDARTIHSLAECNTIDDLKAILGKTSYKETIL--------SKDLLNGLQFHVLMVYYRSFSVFNDLSCVF 292
                                        ***********************************876........567777777777777777899999****** PP

                                        HHHHHHHHHHHHHHHHHHH CS
                     vATP-synt_AC39 305 aYlklkeqEirnlrwIaeg 323
                                         YlklkeqEi+n+ wI+e 
  gene1342|gene1342|rna1342|rna1342 293 CYLKLKEQEIKNICWIVEF 311
                                        ****************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (327 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       807  (0.0450109); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 2269.32
//
Query:       gene1343|gene1343|rna1343|rna1343  [L=289]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
        6.3    7.1   7.6        4.8    7.4   6.3    1.4  1  DUF3093      Protein of unknown function (DUF3093)


Domain annotation for each model (and alignments):
>> DUF3093  Protein of unknown function (DUF3093)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   6.3   0.00027       4.8      10      60 ..      45      99 ..      39     116 .. 0.70

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.00027
                            DUF3093 10 lwwWllaalvala..aalvaae...vglavavlvaavlvalavvallalsrtrieV 60
                                        wwW l+++v+++  +a++++    +g+ v+ l   ++v+l+++a +++ + r+ V
  gene1343|gene1343|rna1343|rna1343 45 AWWWSLGTGVGIVaiIAVIFLLkglIGMIVNTLL-FIVVLLLIFAQYWFRSERVLV 99
                                       69****9999777432333322333555555555.788888888888888888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (289 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2006  (0.111886); expected 358.6 (0.02)
Passed bias filter:                      741  (0.0413297); expected 358.6 (0.02)
Passed Vit filter:                       100  (0.00557756); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.44
# Mc/sec: 1989.34
//
Query:       gene1344|gene1344|rna1344|rna1344  [L=200]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.5e-31  106.4   1.1    1.1e-30  105.7   1.1    1.4  1  Forkhead  Forkhead domain


Domain annotation for each model (and alignments):
>> Forkhead  Forkhead domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.7   1.1   6.2e-35   1.1e-30       2      84 ..      16      98 ..      15     101 .. 0.92

  Alignments for each domain:
  == domain 1  score: 105.7 bits;  conditional E-value: 6.2e-35
                                       -----HHHHHHHHHHT-TTT-B-HHHHHHHHHCC-HHHHCC.-CCHHHHHHHHHHHHC--EEETT.-T.TSS--EEE- CS
                           Forkhead  2 kPpysYaaLIaqAiksspekkltLseIyefieenfpyyrtaakkgWqnSirhnLslnkcFekvpreee.egkgslwti 78
                                       k ++sYaaLIaqA++ss +++ltL+eIy+fi++n+p y  + k+gWqnSirhnLslnk+F k p+ +  +gkgs w+i
  gene1344|gene1344|rna1344|rna1344 16 KKNISYAALIAQALLSSANNRLTLKEIYHFISTNYPEYTLH-KQGWQNSIRHNLSLNKAFYKEPKIKGtPGKGSHWSI 92
                                       789*************************************6.**********************955538******** PP

                                       -TTHHH CS
                           Forkhead 79 dpesee 84
                                       d ++++
  gene1344|gene1344|rna1344|rna1344 93 DLKAAK 98
                                       987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       429  (0.0239277); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1368.04
//
Query:       gene1345|gene1345|rna1345|rna1345  [L=185]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.4e-38  130.9   0.1    5.1e-38  130.7   0.1    1.0  1  EMG1           EMG1/NEP1 methyltransferase
  ------ inclusion threshold ------
      0.055   13.5   0.1      0.067   13.2   0.1    1.2  1  DDR_swiveling  DD-reactivating factor swiveling domain


Domain annotation for each model (and alignments):
>> EMG1  EMG1/NEP1 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.7   0.1   5.7e-42   5.1e-38      35     190 ..      26     175 ..      15     179 .. 0.92

  Alignments for each domain:
  == domain 1  score: 130.7 bits;  conditional E-value: 5.7e-42
                                        TGGGSS-CHHHHHHHHHHHCSCHHCTT.EEEEEEETTSEEEEE-TT----SSHHHHHHHHHHHHCCSEEEETTEE. CS
                               EMG1  35 reakeaRpDIvHqcLlalldspLnkagllqvyihttknvlIevnpqtRiPrtfkrFagLmvqLLkklsirategee 110
                                        r a+  RpDI+H++Ll+++dspL k+++ ++y++t +n lIe+n+ tRiPrt +rF+gLm ++L+kl+i++++++ 
  gene1345|gene1345|rna1345|rna1345  26 RPAAPPRPDITHHILLTIIDSPLYKSNRCKIYVKTVNNILIEINEGTRIPRTTTRFVGLMKDVLRKLKIKDEDKT- 100
                                        445567*****************************************************************9987. PP

                                        SCEEEECS-HHHHCCC.SEEEEE-TTSEE-.............EEEE-SSSS....---HHEEESSSS---HHHHH CS
                               EMG1 111 kLlkviknpitdhlppgskiillsesaekklvdleefvvkpvvfvigamskgsvkidykeeeisisnypLsaavvc 186
                                         L++v+k++i   +ppg+ +i++s+++e   ++ e+f+ ++vv+++ a ++g++ +d ++  +++s+y+Ls a+++
  gene1345|gene1345|rna1345|rna1345 101 -LMRVVKSKID--FPPGAVKIGMSRKGE--RISKEHFIANDVVLYVNAKQRGEDVFDDVDVLMKVSDYELSGAAAV 171
                                        .********98..8**************..55699*****************99999999**************99 PP

                                        HHHH CS
                               EMG1 187 skil 190
                                         k +
  gene1345|gene1345|rna1345|rna1345 172 GKAI 175
                                        8876 PP

>> DDR_swiveling  DD-reactivating factor swiveling domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   7.4e-06     0.067      27     104 ..      89     165 ..      67     185 .] 0.80

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 7.4e-06
                      DDR_swiveling  27 leelekakkeeevivvvpkevdfeeaaklinealekgvkikgailqkddgvlvenrlekkiPivdevslidkvPlg 102
                                        l++l+ ++++++++ vv++++df   a +i    +kg +i+     ++d vl  n  ++   + d+v ++ kv   
  gene1345|gene1345|rna1345|rna1345  89 LRKLKIKDEDKTLMRVVKSKIDFPPGAVKIGMS-RKGERISKEHFIANDVVLYVNAKQRGEDVFDDVDVLMKVSDY 163
                                        5677788889999*****************876.7889999999999************************99754 PP

                      DDR_swiveling 103 ml 104
                                         l
  gene1345|gene1345|rna1345|rna1345 164 EL 165
                                        43 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       462  (0.0257683); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1402.60
//
Query:       gene1347|gene1347|rna1347|rna1347  [L=61]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0056   16.3   0.0      0.008   15.8   0.0    1.2  1  AraC_N    AraC-type transcriptional regulator N-terminus


Domain annotation for each model (and alignments):
>> AraC_N  AraC-type transcriptional regulator N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   4.4e-07     0.008      54      80 ..      32      58 ..      30      60 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 4.4e-07
                             AraC_N 54 vdlpveievveaspekPylglalaldp 80
                                       v lp++++++ea  + Pyl+++++l +
  gene1347|gene1347|rna1347|rna1347 32 VSLPFSFKFIEAYDDTPYLAIVMKLRE 58
                                       89**********************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       217  (0.0121033); expected 358.6 (0.02)
Passed bias filter:                      194  (0.0108205); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.22s 00:00:00.56 Elapsed: 00:00:00.38
# Mc/sec: 478.90
//
Query:       gene1348|gene1348|rna1348|rna1348  [L=167]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-05   24.8   5.4    0.00013   21.9   1.1    2.2  2  IFN-gamma        Interferon gamma
  ------ inclusion threshold ------
      0.015   15.3   2.9      0.064   13.2   1.9    2.3  2  DUF2095          Uncharacterized protein conserved in archaea
      0.043   14.0   0.4      0.043   14.0   0.4    2.3  2  JIP_LZII         JNK-interacting protein  leucine zipper II
       0.08   13.1   1.8        1.5    9.0   0.2    2.3  2  AcylCoA_dehyd_C  Acyl-CoA dehydrogenase C terminal
       0.21   11.8   2.3       0.57   10.3   0.1    2.1  2  KaiA             KaiA C-terminal domain


Domain annotation for each model (and alignments):
>> IFN-gamma  Interferon gamma
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   1.1   3.5e-08   0.00013      36      99 ..      16      83 ..      11     115 .. 0.88
   2 !    5.1   0.3    0.0051        18      72     107 ..     120     155 ..     107     163 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 3.5e-08
                          IFN-gamma 36 sLfldilknwkeesdkkilq..sqivsfYfklFeklkdnqviqksletikedliak..ffnsssskld 99
                                       + f+d lk+ ++ +  +++q  s i+ fYf +F++ +d q+  + l+++k ++iak  f+ +++ k +
  gene1348|gene1348|rna1348|rna1348 16 TNFVDFLKRVTKTTRVRVFQigSTILPFYFLVFDSRNDLQAAVNILDIVKRQFIAKleFYTEQNIKIQ 83
                                       669***************88779*******************************99334555555555 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0051
                          IFN-gamma  72 nqviqksletikedliakffnssssklddFkkliki 107
                                        n+   k ++ i e+l+++ ++++++ +d+F k ++i
  gene1348|gene1348|rna1348|rna1348 120 NKDPVKEMSAIYEKLVVNWMEQEKEIKDEFLKRLRI 155
                                        5555689******************99999876654 PP

>> DUF2095  Uncharacterized protein conserved in archaea (DUF2095)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.21   7.4e+02      61      76 ..      11      26 ..       7      34 .. 0.82
   2 ?   13.2   1.9   1.8e-05     0.064      84     109 ..     135     160 ..      59     164 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.21
                            DUF2095 61 fsgynptiidflrrce 76
                                       f g++   +dfl+r+ 
  gene1348|gene1348|rna1348|rna1348 11 FPGHKTNFVDFLKRVT 26
                                       8899999******975 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 1.8e-05
                            DUF2095  84 iinwmeergeithemakelrvvlvkk 109
                                        ++nwme++ ei +e+ k lr++  k+
  gene1348|gene1348|rna1348|rna1348 135 VVNWMEQEKEIKDEFLKRLRIIESKR 160
                                        79*******************97765 PP

>> JIP_LZII  JNK-interacting protein  leucine zipper II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.4   1.2e-05     0.043      15      57 ..      52      92 ..      48     113 .. 0.72
   2 ?   -1.9   0.2       1.1   3.9e+03      51      67 ..     141     157 ..     124     161 .. 0.59

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.2e-05
                           JIP_LZII 15 teLletknaLnvvkddLIarvdeLtsereiLreEleslqkake 57
                                       ++L++  n L++vk+  Ia+++  t+++   +  ++sl k ++
  gene1348|gene1348|rna1348|rna1348 52 NDLQAAVNILDIVKRQFIAKLEFYTEQNI--KIQNMSLSKGLS 92
                                       679999***************98888764..333444444444 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.1
                           JIP_LZII  51 slqkakerlesrikelE 67 
                                        + +++k++  +r++ +E
  gene1348|gene1348|rna1348|rna1348 141 QEKEIKDEFLKRLRIIE 157
                                        33445555555555555 PP

>> AcylCoA_dehyd_C  Acyl-CoA dehydrogenase C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.2   0.00042       1.5       4      41 ..      67     104 ..      64     116 .. 0.91
   2 ?    3.7   0.1     0.019        67      24      56 ..     120     152 ..     108     159 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00042
                                        HHHHHHHTGGGS---GGGHHHHHHHHHHHHHHHHHHHH CS
                    AcylCoA_dehyd_C   4 tylaqikeyeaeevseeleelkarlkemtekyeeavak 41 
                                        +++a+++ y +++++ +  +l + l++++++yee+ ++
  gene1348|gene1348|rna1348|rna1348  67 QFIAKLEFYTEQNIKIQNMSLSKGLSAVIKEYEECANE 104
                                        799*******************************9875 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.019
                                        HHHHHHHHHHHHHHHHHHHHTT--HHHHHHHHH CS
                    AcylCoA_dehyd_C  24 lkarlkemtekyeeavakVkeakdqelldflAR 56 
                                         k+ +kem + ye++v +  e++++   +fl R
  gene1348|gene1348|rna1348|rna1348 120 NKDPVKEMSAIYEKLVVNWMEQEKEIKDEFLKR 152
                                        57889*********9999877666555556665 PP

>> KaiA  KaiA C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.5     0.096   3.4e+02      46      79 ..      51      84 ..      13     109 .. 0.57
   2 ?   10.3   0.1   0.00016      0.57      15      54 ..     109     148 ..     104     156 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.096
                                       STTSSHHHHHHHHHHHHHHTT--HHHHHHHHHHH CS
                               KaiA 46 kddsevnqkidefvnkaffadlsvskileihmel 79
                                       ++d +   +i ++v++ f+a l      +i+++ 
  gene1348|gene1348|rna1348|rna1348 51 RNDLQAAVNILDIVKRQFIAKLEFYTEQNIKIQN 84
                                       2344445556678888888877765555554444 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00016
                                        GGSCCCSTHHHHHHHHHHHHHHHHHHHHHCTSTTSSHHHH CS
                               KaiA  15 kkflrnlskeekkelleelkseyreivleyfkddsevnqk 54 
                                        +kf+ +l  +e+k+ ++e+++ y ++v++++++++e++++
  gene1348|gene1348|rna1348|rna1348 109 DKFMSELRGDENKDPVKEMSAIYEKLVVNWMEQEKEIKDE 148
                                        58999******************************99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1383  (0.0771376); expected 358.6 (0.02)
Passed bias filter:                      541  (0.0301746); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1164.36
//
Query:       gene1349|gene1349|rna1349|rna1349  [L=277]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-06   27.1   0.4      1e-05   25.3   0.1    2.0  2  CDC73_C   RNA pol II accessory factor, Cdc73 family, C-termin
  ------ inclusion threshold ------
        3.4    7.8   7.4         11    6.1   0.6    3.1  3  DUF1803   Domain of unknown function (DUF1803)


Domain annotation for each model (and alignments):
>> CDC73_C  RNA pol II accessory factor, Cdc73 family, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.1   1.1e-09     1e-05       3      95 ..     108     191 ..     106     204 .. 0.85
   2 ?   -1.7   0.0      0.24   2.1e+03     146     156 ..     260     270 ..     253     271 .. 0.86

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 1.1e-09
                            CDC73_C   3 kkPiIlvpssasslltlsnvksfledgkyvppdekkkeaskaenevsisrklkkiadskkvrflvvdspekltked 78 
                                        k+ +Ilvp+s+ss ++++n  + + +g++ +p    k++    ne +++rk++      +++f+++++ +      
  gene1349|gene1349|rna1349|rna1349 108 KEYVILVPASYSSKINIFNCLNVFSTGSFKNPPLDIKNM--LVNEHKLKRKMEM----CTANFIFMTKWHGT---V 174
                                        6679***************************99988888..4577777775555....57999999998544...4 PP

                            CDC73_C  79 WerVvAVfvtgqewqfk 95 
                                           VvAVf++g ewq  
  gene1349|gene1349|rna1349|rna1349 175 HADVVAVFLDGSEWQIS 191
                                        678************75 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.24
                            CDC73_C 146 vveefwealee 156
                                         v+++w+++e+
  gene1349|gene1349|rna1349|rna1349 260 LVNKIWRDIEN 270
                                        689******98 PP

>> DUF1803  Domain of unknown function (DUF1803)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.6    0.0013        11      48      83 ..      24      66 ..      13      76 .. 0.70
   2 ?    4.1   0.6    0.0053        48      33      72 ..      89     128 ..      69     153 .. 0.80
   3 ?   -1.3   0.0      0.25   2.2e+03      23      51 ..     245     273 ..     237     275 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0013
                            DUF1803 48 elidaglikRenkrYklnlpife.......ieeaaelileeev 83
                                       ++id+++i+ e+k Y+l   +f         e  a+l+le+ +
  gene1349|gene1349|rna1349|rna1349 24 KIIDNKYIEIEEKTYTLLQILFYvqhetmpFEMYAKLALENDI 66
                                       689*************987777645555555555555555555 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.0053
                            DUF1803  33 kkeFadqkkldrlldelidaglikRenkrYklnlpifeie 72 
                                        k++F+ q ++   l++++ +++++     Y+ +++if+  
  gene1349|gene1349|rna1349|rna1349  89 KNKFNLQYDFRFILNHVVRKEYVILVPASYSSKINIFNCL 128
                                        899999******************************9943 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 0.25
                            DUF1803  23 ehddviLRelkkeFadqkkldrlldelid 51 
                                        e +dv+  +   +F  ++k+ r ++++++
  gene1349|gene1349|rna1349|rna1349 245 EFEDVLVENEAGNFGLVNKIWRDIENYLK 273
                                        55677777777789999999999999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (277 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       503  (0.0280551); expected 358.6 (0.02)
Passed bias filter:                      248  (0.0138323); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.22s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 2102.98
//
Query:       gene135|gene135|rna135|rna135  [L=527]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (527 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2224  (0.124045); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.66u 0.30s 00:00:00.96 Elapsed: 00:00:00.46
# Mc/sec: 3468.37
//
Query:       gene1350|gene1350|rna1350|rna1350  [L=50]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0073   16.2   0.3      0.013   15.3   0.3    1.5  1  DUF2073   Uncharacterized protein conserved in archaea (DUF20
  ------ inclusion threshold ------
      0.045   13.8   0.0          5    7.3   0.0    2.1  2  DUF2619   Protein of unknown function (DUF2619)


Domain annotation for each model (and alignments):
>> DUF2073  Uncharacterized protein conserved in archaea (DUF2073)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.3   1.5e-06     0.013      75     101 ..       9      35 ..       1      37 [. 0.85

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.5e-06
                            DUF2073  75 keseerltvigPanqlktlkkdkdlis 101
                                        ++ +e+lt++gP++q+ +++ + ++++
  gene1350|gene1350|rna1350|rna1350   9 SKMNEKLTMVGPVDQMSKMNEKLTMVT 35 
                                        45789**************99998887 PP

>> DUF2619  Protein of unknown function (DUF2619)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.0   0.00055         5      20      37 ..       4      21 ..       1      28 [. 0.86
   2 ?    5.2   0.0    0.0025        23      13      29 ..      31      47 ..      24      48 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.00055
                            DUF2619 20 dvekalkiNalLalvGPl 37
                                        v+++ k+N  L +vGP+
  gene1350|gene1350|rna1350|rna1350  4 PVDQMSKMNEKLTMVGPV 21
                                       5888999**********7 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0025
                            DUF2619 13 llmlklndvekalkiNa 29
                                       l m++ n+ ek +k+N+
  gene1350|gene1350|rna1350|rna1350 31 LTMVTSNRPEKCVKVNS 47
                                       5699************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (50 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       510  (0.0284455); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 362.80
//
Query:       gene1351|gene1351|rna1351|rna1351  [L=154]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      1e-14   54.1   1.9    1.9e-14   53.2   1.9    1.4  1  Homeodomain  Homeodomain
  ------ inclusion threshold ------
       0.03   14.2   0.1      0.093   12.6   0.0    1.8  1  Homeobox_KN  Homeobox KN domain


Domain annotation for each model (and alignments):
>> Homeodomain  Homeodomain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.2   1.9   2.1e-18   1.9e-14       7      57 .]      41      91 ..      37      91 .. 0.95

  Alignments for each domain:
  == domain 1  score: 53.2 bits;  conditional E-value: 2.1e-18
                                       S-HHHHHHHHHHHHHSSS-SHHHHHHHHHHHTS-HHHHHHHHHHHHHHHHH CS
                        Homeodomain  7 ftkeqleeLeklFeenrypsaeereeLAkklgLeerqVkvWFqNrRakekk 57
                                        t+ q ++L+++++ +  ps+++reeLA  lgL+ r ++vWFqN+R+k ++
  gene1351|gene1351|rna1351|rna1351 41 KTSLQKRVLQEVYKLTDFPSTNTREELALLLGLPHRSIQVWFQNKRQKNRQ 91
                                       6899*********************************************97 PP

>> Homeobox_KN  Homeobox KN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0     1e-05     0.093      10      39 ..      58      87 ..      56      88 .. 0.96

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1e-05
                        Homeobox_KN 10 YPseedKeeLlkeTglsvkqitnWFINaRr 39
                                       +Ps + +eeL+   gl  + i+ WF N R+
  gene1351|gene1351|rna1351|rna1351 58 FPSTNTREELALLLGLPHRSIQVWFQNKRQ 87
                                       8***************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1057  (0.0589548); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1063.65
//
Query:       gene1352|gene1352|rna1352|rna1352  [L=146]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.4e-13   48.1   0.5    1.2e-12   47.4   0.5    1.3  1  Homeodomain     Homeodomain
     0.0034   17.3   0.4      0.011   15.6   0.0    2.1  3  Homeobox_KN     Homeobox KN domain
  ------ inclusion threshold ------
       0.01   15.7   0.1       0.02   14.8   0.1    1.4  1  YdaS_antitoxin  Putative antitoxin of bacterial toxin-antitox
      0.019   15.1   0.2       0.28   11.3   0.0    2.2  2  Phage_CI_repr   Bacteriophage CI repressor helix-turn-helix d
       0.08   13.1   0.0       0.15   12.2   0.0    1.4  1  HTH_28          Helix-turn-helix domain
      0.093   12.8   0.1       0.29   11.2   0.0    1.8  2  HTH_3           Helix-turn-helix


Domain annotation for each model (and alignments):
>> Homeodomain  Homeodomain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.4   0.5   4.1e-16   1.2e-12      10      57 .]      36      83 ..      29      83 .. 0.92

  Alignments for each domain:
  == domain 1  score: 47.4 bits;  conditional E-value: 4.1e-16
                                       HHHHHHHHHHHHSSS-SHHHHHHHHHHHTS-HHHHHHHHHHHHHHHHH CS
                        Homeodomain 10 eqleeLeklFeenrypsaeereeLAkklgLeerqVkvWFqNrRakekk 57
                                        q  +L+++++ ++ ps+e+r eLA  lg+++r V+vWFqN+R+  kk
  gene1352|gene1352|rna1352|rna1352 36 LQQSVLKAVYNITNFPSTETRNELALLLGISQRSVQVWFQNKRQICKK 83
                                       58899**************************************97775 PP

>> Homeobox_KN  Homeobox KN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.89   2.7e+03      16      25 ..      32      41 ..      30      50 .. 0.62
   2 !   15.6   0.0   3.8e-06     0.011      10      38 ..      50      78 ..      44      79 .. 0.96
   3 ?   -3.2   0.0       2.8   8.5e+03      18      28 ..     126     136 ..     122     137 .. 0.56

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.89
                        Homeobox_KN 16 KeeLlkeTgl 25
                                       K++Ll+++ l
  gene1352|gene1352|rna1352|rna1352 32 KKTLLQQSVL 41
                                       5666666554 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 3.8e-06
                        Homeobox_KN 10 YPseedKeeLlkeTglsvkqitnWFINaR 38
                                       +Ps e ++eL+   g+s++ ++ WF N R
  gene1352|gene1352|rna1352|rna1352 50 FPSTETRNELALLLGISQRSVQVWFQNKR 78
                                       8***************************9 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 2.8
                        Homeobox_KN  18 eLlkeTglsvk 28 
                                        e++  +gl++k
  gene1352|gene1352|rna1352|rna1352 126 EIINSCGLQIK 136
                                        45555666554 PP

>> YdaS_antitoxin  Putative antitoxin of bacterial toxin-antitoxin system, YdaS/YdaT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.1   6.5e-06      0.02      11      35 ..      56      80 ..      52      84 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 6.5e-06
                     YdaS_antitoxin 11 qkaLAealgvsqqaVsqWlkgkkqv 35
                                       + +LA +lg+sq+ V+ W + k+q+
  gene1352|gene1352|rna1352|rna1352 56 RNELALLLGISQRSVQVWFQNKRQI 80
                                       789*****************99997 PP

>> Phage_CI_repr  Bacteriophage CI repressor helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.1     0.098   2.9e+02       3      18 ..      20      35 ..      18      38 .. 0.88
   2 ?   11.3   0.0   9.3e-05      0.28      13      34 ..      54      75 ..      40      85 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.098
                                       HHHHHHHHT-SSCHHH CS
                      Phage_CI_repr  3 leRlmsaygvkmqkeL 18
                                       l+R +s yg+k +k L
  gene1352|gene1352|rna1352|rna1352 20 LRRRKSYYGMKVKKTL 35
                                       7999********9988 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 9.3e-05
                                       SSCHHHHCCTT--HHHHHHHHH CS
                      Phage_CI_repr 13 kmqkeLAdlLgiakssvstwvr 34
                                       ++++eLA lLgi++ sv  w +
  gene1352|gene1352|rna1352|rna1352 54 ETRNELALLLGISQRSVQVWFQ 75
                                       6799**************9975 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0     5e-05      0.15      13      32 ..      54      73 ..      52      81 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 5e-05
                             HTH_28 13 hsvreaArelgisrrtvyrW 32
                                       ++++e+A +lgis+r+v++W
  gene1352|gene1352|rna1352|rna1352 54 ETRNELALLLGISQRSVQVW 73
                                       699***************** PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       2.4   7.3e+03      10      20 ..       3      13 ..       3      21 .. 0.77
   2 ?   11.2   0.0   9.8e-05      0.29      11      35 ..      55      79 ..      55      80 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 2.4
                                       HHHHHHHHHHT CS
                              HTH_3 10 lsqeeLAeklG 20
                                       +s++e+ ++lG
  gene1352|gene1352|rna1352|rna1352  3 ISKTEVDAALG 13
                                       57788888888 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 9.8e-05
                                       HHHHHHHHHTSSHHHHHHHHTTSSC CS
                              HTH_3 11 sqeeLAeklGvsrstisriEnGern 35
                                       ++ eLA +lG+s+++++ ++ ++r+
  gene1352|gene1352|rna1352|rna1352 55 TRNELALLLGISQRSVQVWFQNKRQ 79
                                       789****************999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1000  (0.0557756); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.37
# Mc/sec: 1169.29
//
Query:       gene1353|gene1353|rna1353|rna1353  [L=377]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   2.7e-137  457.7   0.0   1.1e-136  455.7   0.0    1.7  1  Actin     Actin


Domain annotation for each model (and alignments):
>> Actin  Actin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  455.7   0.0  6.1e-141  1.1e-136       2     407 .]       4     377 .]       3     377 .] 0.98

  Alignments for each domain:
  == domain 1  score: 455.7 bits;  conditional E-value: 6.1e-141
                              Actin   2 devsavVlDnGssttraGyagedaPkavipslvgkprgrkvea.....klyvgdealtkrpelevrspvedGvved 72 
                                        ++ +a+V+DnGs++++aG+ag+d+P++v+p +vg pr++ v+      + yvgdea++kr+ l++++p+e+G+v d
  gene1353|gene1353|rna1353|rna1353   4 ENAPAIVIDNGSGMCKAGFAGDDSPRSVFPCIVGTPRHQGVMVgmgqkDSYVGDEAQSKRGILSLKYPIEHGIVLD 79 
                                        5679***********************************999999**99*************************** PP

                              Actin  73 wdaveelwehvlkeelkvdpeehpllltepplnppkqrekalEivfEkfkvpalylaksavlsafasgkstglvvD 148
                                        w a+e++w+h++++el+v peehp+l+te+p np+ +re++l+i+fE+f+vp++y++ +avls++asg++tglv+D
  gene1353|gene1353|rna1353|rna1353  80 WGAMEKIWHHTFYNELRVAPEEHPVLMTEAPINPKVNRERMLQIAFETFNVPSFYVSIQAVLSLYASGRTTGLVLD 155
                                        **************************************************************************** PP

                              Actin 149 sGasvtsvvpVldGyvLkkairrsdlgGkaLteqlkellssknvevtprylikkkkvveaessaekeelekltesy 224
                                        sG++vt++vp+++Gy+L +a++r+d++G+++t+++ +ll+++                              ++s+
  gene1353|gene1353|rna1353|rna1353 156 SGDGVTHIVPIYEGYSLPHAMMRLDFAGRDVTDYFIKLLKES------------------------------GYSL 201
                                        *****************************************7..............................9*** PP

                              Actin 225 ktleeeevleeiKesvcevsedpeg...deeksssspeksYeLPDgseiklgeeRfkvpEiLFdpsligsesalee 297
                                         t++e+e+ +++Ke++c+v+ d+++   ++e++++++ k+YeLPDg+++klg++ f++pE+LF psl+g e     
  gene1353|gene1353|rna1353|rna1353 202 VTTAEREIARDCKEKTCYVAVDFANeleRYENAEKEIVKTYELPDGNVLKLGNQVFRAPEMLFSPSLSGFELP--- 274
                                        ***********************99888888888************************************988... PP

                              Actin 298 ekskllgiselivaainacdvdlrpeLlanivvtGGnsllpglteRlekelaqlaskgvkvkiiapeeerkysaWi 373
                                              gi+e i+++i++cdvd+r+ L++niv++GG++++pg+++Rl+ke+++la+++++vk+iap+ erkys+Wi
  gene1353|gene1353|rna1353|rna1353 275 ------GIHETIYNSIMRCDVDIRKCLYSNIVLSGGTTMYPGISDRLQKEVSALAPPSIQVKVIAPP-ERKYSVWI 343
                                        ......*************************************************************.******** PP

                              Actin 374 GGSiLAslgtfqqlwvskqEYeEqGssvverkck 407
                                        GGSiLAsl+tfq +w++k EY   G+svv+ kc+
  gene1353|gene1353|rna1353|rna1353 344 GGSILASLSTFQTMWITKDEYAGIGPSVVHSKCF 377
                                        *********************************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (377 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       389  (0.0216967); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 2551.97
//
Query:       gene1354|gene1354|rna1354|rna1354  [L=72]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (72 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       320  (0.0178482); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 535.01
//
Query:       gene1355|gene1355|rna1355|rna1355  [L=453]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.5e-80  269.6   0.0    8.8e-79  265.3   0.0    2.0  1  Peptidase_M18  Aminopeptidase I zinc metalloprotease (M18)
    2.8e-05   23.3   0.0    4.5e-05   22.6   0.0    1.4  1  Peptidase_M42  M42 glutamyl aminopeptidase


Domain annotation for each model (and alignments):
>> Peptidase_M18  Aminopeptidase I zinc metalloprotease (M18)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  265.3   0.0   9.9e-83   8.8e-79       1     432 []      10     451 ..      10     451 .. 0.87

  Alignments for each domain:
  == domain 1  score: 265.3 bits;  conditional E-value: 9.9e-83
                                        HHHH--SHHHHHHHHHHHHHCTT-EESTTTS-STSTTCEEEEEEETTTEEEEEEEETTS-GGG--EEEEEE---SE CS
                      Peptidase_M18   1 finksptpyhvvaevaekllkagfkelsekekwkiepggkyfvtrngssliAFavgkkykaengfsiigaHtDspt 76 
                                        f+n+  tpyhv++e  + l+++g+k++s ++   i+p gky+++   + +i  +v ++    +g++++++H Dsp 
  gene1355|gene1355|rna1355|rna1355  10 FLNRCLTPYHVISESIKILKDHGYKKISINDLNTITP-GKYYIIAFTTVIIPIIVPNN---PAGVRMVATHNDSPV 81 
                                        89****************************9999***.**********8888777766...78************* PP

                                        EEEECCEEEEETTEEEEEEEEESS.SSGGGTT--EEEEEEEEECTT--EEEEEECCSTT---BBB----GGG-GG. CS
                      Peptidase_M18  77 lrvKpkskkkaegylqvgvetYGggiwetWldrdLsvaGrvlvkkkkeekleaklvnierPvlriPnlaiHLdrdi 152
                                        l++Kp+ + ++e++ +v++ tYGgg w+tW+dr Lsv+G+v++++   +++ ++l +     +++P+l +HL+++ 
  gene1355|gene1355|rna1355|rna1355  82 LKLKPNFSDTVENMSVVRLCTYGGGLWHTWFDRSLSVGGLVVLRDG-RQVIVDRLFD-----VVVPSLPPHLNNSK 151
                                        *********************************************8.4566666555.....589*******9874 PP

                                        ...GSS--TTTTTSEEEEEEEE................------TTCCC....................T.CCHHH CS
                      Peptidase_M18 153 ..neefkfneetelepilglae................eeeeekedkek....................knkhkka 190
                                          n+ f +++e+ l+ ++ + +                +   ++    +                    ++ h++ 
  gene1355|gene1355|rna1355|rna1355 152 vyNNGFLYDKERVLNGLVMVGTkledrvfrgrcgtemdD---KR----EfnedardkshdsgvaecvinDKSHNSG 220
                                        34999*******999988887667888887766653320...22....2344466778889898888875788888 PP

                                        HHHHHHHHHTS-CCC.............CCCCEEEEEE-S--EEETTTT-EEEESSHHHHHHHHHHHHHHCCCCHT CS
                      Peptidase_M18 191 lleliaeelgveved.............ivdlelilvdaqkakivGiekeflfaprlDnkvscfaaleallesaed 253
                                        + e +    +++++d             +v+ +l l+d  +a++  +++++++++r+Dn++s+f +l+al +    
  gene1355|gene1355|rna1355|rna1355 221 IAECVISDDETTCQDgteenavyfkledVVSHNLSLYDLARAEL--LNEQLIMSARQDNLLSTFLGLKALNAE--- 291
                                        8888876655444444444555555555***************9..59*********************9655... PP

                                        -TTTS-SEEEEEEESSCCGTS-STTSGGCTHHHHHHHHHHHHHCSTT-HCHHHHHC-EEEEE--EE---TTSGGGS CS
                      Peptidase_M18 254 sleeedkvrivalfDnEEvGStsaqGadsnfleevlerisialkkseafeeavlakSlliSaDvahaihPnysskh 329
                                             ++++++a+fD EE GS   +Ga+ +fl+ v +r++ +             +S++iS Dv+ha++ ny +++
  gene1355|gene1355|rna1355|rna1355 292 ----GQCIKVLAVFDFEETGSMQVNGARCTFLKDVYNRLQNKD-----P-----HNSMIISLDVTHAYNFNYDECY 353
                                        ....469******************************997655.....3.....489******************* PP

                                        -TTTS--TTSEEEEEEETTSSSTT-HHHHHHHHHHHHHHC-EEEEEEE-TTS----HCHHHHHHHHT-EEEEEE-E CS
                      Peptidase_M18 330 eenhapllnkGvvikvnanqryatnsagaallkevaqkanvklQelvvrndspcGstigpilaaktGirtiDlGaa 405
                                        e++h+ ++++Gvv+k  +   yat++ + a +k++a   + k Q++ +rnd ++G+tig +l++ +G+r +DlG++
  gene1355|gene1355|rna1355|rna1355 354 EKKHRVKFGGGVVVKHGP--AYATDVHSSAFVKRLA---EFKCQDYSLRNDIRGGGTIGTMLSTLLGVRCVDLGTP 424
                                        **************9866..6************997...589********************************** PP

                                        EBSTTSSSEEEECCHHHHHHHHHHHCC CS
                      Peptidase_M18 406 qlsmHSireltgskdveeavklfkaFf 432
                                        +++mHSire+t+ kdv+ + kl+  F+
  gene1355|gene1355|rna1355|rna1355 425 VMAMHSIREATTCKDVMDTFKLLYDFY 451
                                        *************************98 PP

>> Peptidase_M42  M42 glutamyl aminopeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0     5e-09   4.5e-05     183     292 .]     334     446 ..     260     446 .. 0.84

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 5e-09
                                        SEEEEEEEEEE-CSTTSTTTTSS....TTS-CEEEEEETTCCSHHHHHHHHHHHHHHTT--EEEEEESSSSSTHHH CS
                      Peptidase_M42 183 diaiavDvtaagdtpgskekeak....lgkGpvirvkDasgiyhpklrkkllelAkknnipyqlevlsgggtDAga 254
                                        +++i +Dvt+a + + ++ +e+k    +g+G+v++     + ++ + + ++++lA+ +  +y l+   +gg   g+
  gene1355|gene1355|rna1355|rna1355 334 SMIISLDVTHAYNFNYDECYEKKhrvkFGGGVVVKHG-PAYATDVHSSAFVKRLAEFKCQDYSLRNDIRGGGTIGT 408
                                        57899****995544333333333367*******999.788899999999*****999999999955555555778 PP

                                        HHTSTTTSEEEEEEEEEBSTTSTTEEEEHHHHHHHHHH CS
                      Peptidase_M42 255 ihltgegvptalisiptryiHspvevahlddleatvkL 292
                                        +  t  gv+++ +++p+ ++Hs  e ++++d+ +t kL
  gene1355|gene1355|rna1355|rna1355 409 MLSTLLGVRCVDLGTPVMAMHSIREATTCKDVMDTFKL 446
                                        88899*****************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (453 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       416  (0.0232026); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 3224.72
//
Query:       gene1356|gene1356|rna1356|rna1356  [L=707]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-84  282.9   0.2    2.1e-84  282.1   0.2    1.4  1  MCM              MCM P-loop domain
    1.1e-22   80.2   0.3    2.3e-22   79.2   0.3    1.5  1  MCM_OB           MCM OB domain
    1.3e-17   63.9   0.4    4.2e-17   62.3   0.4    1.9  1  MCM_lid          MCM AAA-lid domain
    5.6e-11   42.2   0.2      3e-08   33.3   0.1    2.4  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    3.7e-07   30.2   2.8    1.7e-05   24.9   0.1    3.5  3  AAA_5            AAA domain (dynein-related subfamily)
    2.1e-05   24.7   4.2    2.1e-05   24.7   4.2    2.6  2  MCM6_C           MCM6 C-terminal winged-helix domain
     0.0032   17.2   0.1       0.15   11.7   0.0    2.4  2  Sigma54_activat  Sigma-54 interaction domain
     0.0055   16.6   0.1      0.022   14.6   0.1    2.0  1  AAA_3            ATPase family associated with various cellul
  ------ inclusion threshold ------
      0.085   13.8   1.1        6.8    7.7   0.1    2.8  2  FKBP_N           Domain amino terminal to FKBP-type peptidyl-
       0.93    9.8   4.7       0.38   11.1   1.1    2.2  2  DUF365           Domain of unknown function (DUF365)
        1.2    9.6   3.4        1.3    9.5   0.0    2.8  4  AAA              ATPase family associated with various cellul


Domain annotation for each model (and alignments):
>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  282.1   0.2   1.3e-87   2.1e-84       4     224 .]     230     436 ..     227     436 .. 0.96

  Alignments for each domain:
  == domain 1  score: 282.1 bits;  conditional E-value: 1.3e-87
                                        HHHHHHTSSTHHHHHHHHSSTTSSS-HHHHHHHHHHHH---EBBBSSSSBBCSS-EEEEEESSTSTHHHHHHHHHH CS
                                MCM   4 eikelakekdiieklvksiapsiyghedvkkaillqlfggvkkkledktklrgdinvllvgdpgtaKsqlLkyvek 79 
                                         ++++ + ++++e+l+++++psiygh+++k+aill+++gg++    +    r++in+ll+gdpgtaKsq+Lk+v  
  gene1356|gene1356|rna1356|rna1356 230 VLRKIGNVPNVYETLSHALFPSIYGHKNIKNAILLMMVGGCST---K----RTNINILLLGDPGTAKSQFLKQVP- 297
                                        57899999*********************************93...3....899********************9. PP

                                        HSSSEEEEESSSSSSSHSSSEEEEESSSSSEEEEETHHHHTTTSEEEEESGGGSTCHHHHHHHHHHHHSEEEEESS CS
                                MCM  80 lapravytsgkgssaagLtaavvrdeetgefvleaGalvladkGvcciDefdkmkeedrsalhEamEqqtisiaKa 155
                                            a+yt+gk++s++gLtaav+++e+  e v+eaGalvlad+G+cciDefdk + +dr+alhEamEqqt++i+Ka
  gene1356|gene1356|rna1356|rna1356 298 ----AIYTTGKTASGVGLTAAVTKNEN--ENVVEAGALVLADNGICCIDEFDKLSVADRTALHEAMEQQTVTINKA 367
                                        ....99*****************8775..56********************************************* PP

                                        SCEEEEE--EEEEEEE--SSSSCCTTS-HHHHSSSSHHHHHHSSEEEEE-SSTTHHHHHHHHHHHHHHH CS
                                MCM 156 GivatLnartsvlaAanpkagrydkkksvaeninlsaalLsrFDlifvllDkvdeekDeelaehivslh 224
                                        Gi++tLnar+svlaAanp++gryd+kks+  n++ls+a++srFDl++v++D+vde++D+++a+ ++++h
  gene1356|gene1356|rna1356|rna1356 368 GIHVTLNARASVLAAANPRGGRYDRKKSLRYNVSLSDAVMSRFDLFYVIVDEVDESNDRRIARRVINNH 436
                                        ******************************************************************987 PP

>> MCM_OB  MCM OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.2   0.3   1.4e-25   2.3e-22       2     124 ..      63     184 ..      62     186 .. 0.93

  Alignments for each domain:
  == domain 1  score: 79.2 bits;  conditional E-value: 1.4e-25
                                        XGG--GGGTTSEEEEEEEEEEE---EEEEEEEEEEETTT-.-EE.ES----SB-..TTT-HHH-EEE-GGGSEEEE CS
                             MCM_OB   2 lRdlrsehigklvkveGivtrasevkpklkkavfeckkcgktve.veleePrkCeekeCeskdpfkletekskfvd 76 
                                        lR++ +++++ lv+ +  vtr++ + p+l +a+++c++c+++++  +  + ++C ++ C +++++++ +   +f+d
  gene1356|gene1356|rna1356|rna1356  63 LREICTRQMNCLVSFRARVTRTTAIYPELLSAKLRCESCKAVTReSTHYHSFRCVNHLCANRKNYSVLP--VRFRD 136
                                        89**************************************9888555666789*******999988887..68*** PP

                                        EEEEEEE-------------EEEEEEEGGGTT---TT-EEEEEEEEEE CS
                             MCM_OB  77 fqklklQEspeevpaGelPrslevileddlvdkvkPGdrvevtGiyra 124
                                        +q++++QE   ++  G lPrsle+++ ddl++kvkPG+ v + G++r+
  gene1356|gene1356|rna1356|rna1356 137 YQRISVQEVDADIVGGYLPRSLEIVVLDDLTEKVKPGELVVFNGVVRI 184
                                        *********************************************997 PP

>> MCM_lid  MCM AAA-lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.3   0.4   2.6e-20   4.2e-17       3      86 ..     530     610 ..     528     611 .. 0.91

  Alignments for each domain:
  == domain 1  score: 62.3 bits;  conditional E-value: 2.6e-20
                                        HHHHHHHHHHTT--BETCHHHHHHHHHHHHHHHHHTSSTSSSST--HHHHHHHHHHHHHHHHHHTSSSE-HHHHHH CS
                            MCM_lid   3 lrkYiayarekikPklseeakeklseaYvelRkeeedskrksipitvRqLesliRLseAlAklrlsevvteedvee 78 
                                        +  Yi+  + + +P +++ea++ ++e Y++lR +++  ++k++++ vR+Les+iRLseAlAkl+  + v   +vee
  gene1356|gene1356|rna1356|rna1356 530 ILVYIQHVK-NRRPSMTDEAHKLIVEKYKKLRMQNTV-NHKNYTVGVRTLESMIRLSEALAKLHGTD-VLCMYVEE 602
                                        667******.***********************9964.599***********************987.66789*** PP

                                        HHHHHHHH CS
                            MCM_lid  79 airllkes 86 
                                        a+rl++ s
  gene1356|gene1356|rna1356|rna1356 603 AYRLITGS 610
                                        ****9876 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.9   0.0    0.0022       3.5       5      51 ..     252     305 ..     249     325 .. 0.71
   2 !   33.3   0.1   1.8e-11     3e-08      96     199 ..     323     416 ..     303     424 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0022
                       Mg_chelatase   5 vkGqeeakraleiaaaGgH.......nlllvGppGsGKtmlakrlpsllpplse 51 
                                        + G+++ k+a+ +   Gg        n+ll+G pG+ K+   k++p++ +  ++
  gene1356|gene1356|rna1356|rna1356 252 IYGHKNIKNAILLMMVGGCstkrtniNILLLGDPGTAKSQFLKQVPAIYTTGKT 305
                                        6677777777776666653222233389******************99876555 PP

  == domain 2  score: 33.3 bits;  conditional E-value: 1.8e-11
                       Mg_chelatase  96 kpkpGeislahnGvLfLDElpefkrkvlevLRePledgevtisrakakvefparfqlvaamNpcpcgklkdkekec 171
                                         ++ G++ la nG+  +DE+ +++     +L e +e+++vti++a  +v+  ar  ++aa+Np + g+++      
  gene1356|gene1356|rna1356|rna1356 323 VVEAGALVLADNGICCIDEFDKLSVADRTALHEAMEQQTVTINKAGIHVTLNARASVLAAANP-RGGRYD------ 391
                                        5788**********************************************************9.567666...... PP

                       Mg_chelatase 172 tcsekeierYlsklsgplldRidlqvev 199
                                            k+  rY   ls++++ R+dl   +
  gene1356|gene1356|rna1356|rna1356 392 ---RKKSLRYNVSLSDAVMSRFDLFYVI 416
                                        ...3456799999********9997554 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.1      0.04        65      40      81 ..     148     188 ..     143     236 .. 0.75
   2 !   24.9   0.1     1e-08   1.7e-05       1     125 [.     278     390 ..     278     410 .. 0.87
   3 ?   -3.5   0.0       5.7   9.3e+03      69      92 ..     532     555 ..     495     576 .. 0.59

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.04
                                        HHH--B--.........--------G-SEEEEESGGG--HHH CS
                              AAA_5  40 dlkgrreikngttslvdsplvraaregeilvlDEveraesev 81 
                                        d++g++ +  + +  v   l+++++ ge++v+++v r+e+++
  gene1356|gene1356|rna1356|rna1356 148 DIVGGYLP-RSLEIVVLDDLTEKVKPGELVVFNGVVRIERNA 188
                                        56666665.55566777899****************998653 PP

  == domain 2  score: 24.9 bits;  conditional E-value: 1e-08
                                        EEEEE--SSSSHHHHHHHGGGGB..S--EEEEE--TT--HHHHH--B--.........--------G-SEEEEESG CS
                              AAA_5   1 dvlLvGppGtgKselaerlaaal..nreveyvqltrdtteedlkgrreikngttslvdsplvraaregeilvlDEv 74 
                                        ++lL+G+pGt+Ks++ +++ a +  +++   v lt+  t+++    +e          ++lv       i+++DE+
  gene1356|gene1356|rna1356|rna1356 278 NILLLGDPGTAKSQFLKQVPAIYttGKTASGVGLTAAVTKNENENVVEA---------GALV--LADNGICCIDEF 342
                                        689********************99999999**********99988886.........99*9..77889******* PP

                                        GG--HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--... CS
                              AAA_5  75 eraesevlnsLlslleerrllleeggelvkaknddllerfrviatanpld..r 125
                                        ++++ +   +L+  +e++++ +++ g  v  ++       +v+a+anp+   +
  gene1356|gene1356|rna1356|rna1356 343 DKLSVADRTALHEAMEQQTVTINKAGIHVTLNAR-----ASVLAAANPRGgrY 390
                                        ****99999***************9999999886.....9********99652 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 5.7
                                        EEEESGGG--HHHHHHHHHHHHSS CS
                              AAA_5  69 lvlDEveraesevlnsLlslleer 92 
                                        +++  v++ +++++++ ++l+ e+
  gene1356|gene1356|rna1356|rna1356 532 VYIQHVKNRRPSMTDEAHKLIVEK 555
                                        333344444444444444444443 PP

>> MCM6_C  MCM6 C-terminal winged-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   4.2   1.3e-08   2.1e-05      12      79 ..     633     695 ..     612     699 .. 0.86
   2 ?   -0.5   0.1      0.86   1.4e+03      98     107 ..     697     706 ..     694     707 .] 0.77

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 1.3e-08
                             MCM6_C  12 eianllvlklreeeeeeeeegiekeeLvewYleqieeeleseeeleeekklvekvlkrLvk.dkvLlev 79 
                                        +i n +v  l+++e+       ++e+Lv +Y++++e+++ see leee + +e+vl+ L++ ++v++e 
  gene1356|gene1356|rna1356|rna1356 633 SILNTFVYILKTKERL------TREDLVMYYISSVEDKIMSEEMLEEEHRQAENVLEWLINkEGVFYEN 695
                                        5666777777666665......9*************************************999999876 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.86
                             MCM6_C  98 vvlvvhPnya 107
                                         ++ vhPny+
  gene1356|gene1356|rna1356|rna1356 697 GYVYVHPNYD 706
                                        5778*****7 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0     0.045        74      19      42 ..     273     296 ..     259     323 .. 0.83
   2 !   11.7   0.0   9.5e-05      0.15      85     144 ..     325     386 ..     311     401 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.045
                                        CTSSS-EEEECSTTSSHHHHHHHH CS
                    Sigma54_activat  19 aktdlsvlitGesGtGKellarai 42 
                                         +t++++l++G+ Gt K+ + +++
  gene1356|gene1356|rna1356|rna1356 273 KRTNINILLLGDPGTAKSQFLKQV 296
                                        56889************9997765 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 9.5e-05
                                        BEHHHHHTTTSEEEEETGGGS-HHHHHHHHHHHHHSE..EESBTSSSEEE--EEEEEEESS- CS
                    Sigma54_activat  85 kkGlfekadgGtlfLDeigelplelQekLlrvlqege..vervGsskeikvdvriiaatned 144
                                        ++G++  ad+G+  +De  +l+++  + L +++++++  +++ G + + ++   ++aa+n  
  gene1356|gene1356|rna1356|rna1356 325 EAGALVLADNGICCIDEFDKLSVADRTALHEAMEQQTvtINKAGIHVTLNARASVLAAANPR 386
                                        4699*****************************99862257999999999999999999865 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.1   1.4e-05     0.022      48     112 ..     316     385 ..     278     410 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.4e-05
                              AAA_3  48 eekekefefkkGpvf.an..llladeinrappktqsalleameerqvtvege..thklpepflvlatqnP 112
                                        +++e+e  +++G+++ a+  +   de ++ +   ++al eame+++vt++++    +l+    vla+ nP
  gene1356|gene1356|rna1356|rna1356 316 TKNENENVVEAGALVlADngICCIDEFDKLSVADRTALHEAMEQQTVTINKAgiHVTLNARASVLAAANP 385
                                        445555566666654232337889*************************876225678999********9 PP

>> FKBP_N  Domain amino terminal to FKBP-type peptidyl-prolyl isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.2     0.067   1.1e+02      28      62 ..     511     545 ..     478     579 .. 0.67
   2 ?    7.7   0.1    0.0041       6.8      21      95 ..     627     700 ..     607     701 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.067
                             FKBP_N  28 vlaGlkdalkgkskltdeeiqevlqalqeklqekq 62 
                                         l+++++a++++ ++t+eei  ++q +++++ +  
  gene1356|gene1356|rna1356|rna1356 511 DLKAIEQAYNKELNITKEEILVYIQHVKNRRPSMT 545
                                        46777777777777777777777777766443333 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0041
                             FKBP_N  21 keldkdavlaGlkdalkgkskltde.eiqevlqalqeklqekqeeeaeknkaegeaFlaenkkkeGVkttesGLqY 95 
                                        ++ d++ +l+ +   lk k++lt e  +  +++++++k+++++    e++  ++e+ l+   +keGV   ++G  Y
  gene1356|gene1356|rna1356|rna1356 627 NSKDVESILNTFVYILKTKERLTREdLVMYYISSVEDKIMSEE--MLEEEHRQAENVLEWLINKEGVFYENEGYVY 700
                                        4459999**************9988467778899999998888..7889999999999999999999998888877 PP

>> DUF365  Domain of unknown function (DUF365)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   1.1   0.00023      0.38      25      82 ..     508     566 ..     502     576 .. 0.80
   2 ?   -2.1   0.1       2.9   4.7e+03      23      46 ..     625     652 ..     608     673 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00023
                                        EES-THHHHHHTSTTBSS-HHHHHHHHH.HHHHT----SS---EEEEEEEEEEE--S-B CS
                             DUF365  25 lsedpleifekygdrvfltkeelkkyvk.skerwrkgkkrkkawlvleledikkydkvv 82 
                                        ++ed+++i + y++++ +tkee+  y++  k+r+ + +   ++ +v + ++++  ++v 
  gene1356|gene1356|rna1356|rna1356 508 IKEDLKAIEQAYNKELNITKEEILVYIQhVKNRRPSMTDEAHKLIVEKYKKLRMQNTVN 566
                                        789999**********************6677777777677777777777777776665 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.9
                                        EEEES-THHHHHHT....STTBSS-HHH CS
                             DUF365  23 vvlsedpleifeky....gdrvfltkee 46 
                                        +v s+d+++i++++    + +  lt+e+
  gene1356|gene1356|rna1356|rna1356 625 IVNSKDVESILNTFvyilKTKERLTRED 652
                                        4445666666666622223333445554 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       4.2   6.9e+03      37      62 ..     199     225 ..     184     267 .. 0.57
   2 ?    9.5   0.0   0.00078       1.3       1     127 [.     279     393 ..     279     398 .. 0.70
   3 ?   -2.3   0.1       3.3   5.4e+03      62      83 ..     415     430 ..     408     437 .. 0.77
   4 ?   -2.5   0.0       3.8   6.3e+03      26      58 ..     587     622 ..     571     651 .. 0.61

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 4.2
                                        SSTTHHHHHHHHHHHHHHHTS.TSEEE CS
                                AAA  37 kyvgesekkirelfkeakeka.kpsil 62 
                                        +++++ e++++ +f++++ ++ ++++l
  gene1356|gene1356|rna1356|rna1356 199 SVISAEEDHLKIVFEAMSIEKdSKHVL 225
                                        456777777777777754444334444 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00078
                                        EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTT CS
                                AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksrsg 76 
                                        +ll G pGt K+ + k+v     ++  + sg  l+  + ++ ++++ e  + + + +   i  iDE+d+l  ++  
  gene1356|gene1356|rna1356|rna1356 279 ILLLGDPGTAKSQFLKQVPAI-YTTGKTASGVGLTAAVTKNENENVVEAGALVLADN--GICCIDEFDKLSVAD-- 349
                                        699***************988.56678889999996667777777777766655555..9**********9999.. PP

                                        CCCHHHHHHHHHHHHHHHHTTTS.SSTEEEEEEESSGGGSTHHHHS.TTSSEE CS
                                AAA  77 seseeeervvnqLlteldgvkkk.eskvivigatnrpdkldpallr.gRfdrk 127
                                                   +L +++++++   ++  i ++   r + l  a  r gR drk
  gene1356|gene1356|rna1356|rna1356 350 ---------RTALHEAMEQQTVTiNKAGIHVTLNARASVLAAANPRgGRYDRK 393
                                        .........66677777766666322233344444455666666666666665 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 3.3
                                        EEEETGGGHHHHHTTCCCHHHH CS
                                AAA  62 lfiDEidalaksrsgseseeee 83 
                                        +++DE+d+ + +r       ++
  gene1356|gene1356|rna1356|rna1356 415 VIVDEVDESNDRR------IAR 430
                                        789****998888......444 PP

  == domain 4  score: -2.5 bits;  conditional E-value: 3.8
                                        EEEEETTTCSSSSTTHHHHHHHHHHHHHHHTS...T CS
                                AAA  26 fleisgsellskyvgesekkirelfkeakeka...k 58 
                                        + ++ g+++l +yv+e+ + i + + e+k +    k
  gene1356|gene1356|rna1356|rna1356 587 LAKLHGTDVLCMYVEEAYRLITGSMLEIKMEDvqiK 622
                                        445556666666666666666666555554443333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (707 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       993  (0.0553851); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.69u 0.28s 00:00:00.97 Elapsed: 00:00:00.46
# Mc/sec: 4640.78
//
Query:       gene1357|gene1357|rna1357|rna1357  [L=519]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.6e-55  186.6   0.1    5.8e-55  185.9   0.1    1.3  1  PS_Dcarbxylase  Phosphatidylserine decarboxylase


Domain annotation for each model (and alignments):
>> PS_Dcarbxylase  Phosphatidylserine decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  185.9   0.1   3.3e-59   5.8e-55       1     198 [.     236     514 ..     236     516 .. 0.95

  Alignments for each domain:
  == domain 1  score: 185.9 bits;  conditional E-value: 3.3e-59
                     PS_Dcarbxylase   1 lneffvrklkdgaRpidddpgaivsPaDgrilqigeieegsviqvKgityslrdLlgeasess............. 63 
                                        +n+ff+r+lk+gaR + +d  a++sP+D+r+ +++++ee++ +++Kg ++sl+++l++ + ++             
  gene1357|gene1357|rna1357|rna1357 236 FNDFFCRRLKPGARVV-EDVRALCSPSDCRVIAFENVEESTKFWIKGTKFSLEAFLNGGTAYTtnksreptgcvdt 310
                                        8***************.88889************************************999999************ PP

                     PS_Dcarbxylase  64 .............................................................adsfkngyfvviyLs 78 
                                                                                                     +++++ g++++++L+
  gene1357|gene1357|rna1357|rna1357 311 galadrdgnkdg**************saladrdgnkdghgaltdrdgnkdgrsnktcqtydQHKTSLGTLIICRLA 386
                                        ********************************************************9999989999********** PP

                     PS_Dcarbxylase  79 pgdyHryhaPvsgkveerrhipGellsvnpsalkelrglftlneRvvlview..kGkvavvpvGatnvgsivlnvl 152
                                         +dyHr+h+Pv+g+++ ++ i+G++l+vnp +++++ ++ft+n+Rvv++ie+  +G+v+ v+vGat+vgsi+++v 
  gene1357|gene1357|rna1357|rna1357 387 AQDYHRFHSPVKGRIKMIKEINGDYLTVNPISVERS-NVFTQNKRVVVLIESvqFGNVYAVAVGATMVGSIKISVT 461
                                        ************************************.**************6669********************* PP

                     PS_Dcarbxylase 153 kgdelkkGeelGyFqf.GStvvlvfeag......kfieslvekgqkvkmGekl 198
                                         g e++  +e+GyFq+ GSt+vlv e         +i+s+ + +  vk+G++l
  gene1357|gene1357|rna1357|rna1357 462 VGTEVDVMQEIGYFQMgGSTIVLVCERCldirkeVQINSNAQIETYVKVGNAL 514
                                        **************************664444445667777777799999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (519 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       696  (0.0388198); expected 358.6 (0.02)
Passed bias filter:                      440  (0.0245412); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.26s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 3395.79
//
Query:       gene1358|gene1358|rna1358|rna1358  [L=157]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       782  (0.0436165); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1182.01
//
Query:       gene1359|gene1359|rna1359|rna1359  [L=142]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.078   12.8   0.2      0.078   12.8   0.2    2.0  2  Iron_permease  Low affinity iron permease
          2    9.1  14.4        2.5    8.8  14.0    1.5  1  AATF-Che1      Apoptosis antagonizing transcription factor
        9.9    4.8  10.8         13    4.5  10.8    1.1  1  Presenilin     Presenilin


Domain annotation for each model (and alignments):
>> Iron_permease  Low affinity iron permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.2   1.3e-05     0.078      50     127 ..       6      84 ..       2      88 .. 0.86
   2 ?   -1.2   2.6      0.28   1.7e+03      89     101 ..     111     123 ..      83     141 .. 0.41

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.3e-05
                      Iron_permease  50 tiitFlmvfliqnsqnrdskaiqlkLdeLirasksa.knrlidleelteeeleelakeyerlaeaakeeeevkkas 124
                                        t i F+++ l   +q++ +   +  + +L+++ k+    +++ + +l+++ +++ ++eye+l+++ k+++e ++++
  gene1359|gene1359|rna1359|rna1359   6 THIFFFLLALHCATQTQQQCDYRKRFYDLVQTAKDYyTRSMVYMISLKDDAVRRATTEYEKLKAKYKKASEESEVK 81 
                                        567899999999999999999999******988875156789999******************9999998888877 PP

                      Iron_permease 125 sse 127
                                        ++e
  gene1359|gene1359|rna1359|rna1359  82 KEE 84 
                                        765 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.28
                      Iron_permease  89 lidleelteeele 101
                                        +  +   ++ee +
  gene1359|gene1359|rna1359|rna1359 111 EKTIKAKDDEEAT 123
                                        2222222222222 PP

>> AATF-Che1  Apoptosis antagonizing transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8  14.0   0.00043       2.5      27     108 ..      59     139 ..      35     142 .] 0.76

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00043
                          AATF-Che1  27 kaltaanqLpqpetlkeflesseefeealeeaekalkklleslleLreelleqne.ikklaeskeeeekkkskrkr 101
                                        +a+t   +L    ++k+  e+se  +e+ ++  ++l++lle l++++++   + e + k+++++e++e+++++++r
  gene1359|gene1359|rna1359|rna1359  59 RATTEYEKLKA--KYKKASEESEVKKEEQSDPTDELRQLLEALTAMQSKHQLNTEkTIKAKDDEEATENAEEEKER 132
                                        55666666664..677888889999999********************9955555677666666656666666666 PP

                          AATF-Che1 102 kkkkkee 108
                                        k ++ke+
  gene1359|gene1359|rna1359|rna1359 133 KAESKEK 139
                                        5555543 PP

>> Presenilin  Presenilin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5  10.8    0.0021        13     231     300 ..      58     134 ..      30     141 .. 0.24

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.0021
                         Presenilin 231 evaeseeeeeaekkkeeasesskeeeseeesseksaqsse..........seeeseeesseaessaeesseekese 296
                                        ++a++e e+ + k k++++es+ ++e++++ +++ +   +          +++ ++e++ +a++++e++++ +e++
  gene1359|gene1359|rna1359|rna1359  58 RRATTEYEKLKAKYKKASEESEVKKEEQSDPTDELR---QllealtamqsKHQLNTEKTIKAKDDEEATENAEEEK 130
                                        111111111111111111111111111111111111...1222322221111111111111111111111111111 PP

                         Presenilin 297 esse 300
                                        e++ 
  gene1359|gene1359|rna1359|rna1359 131 ERKA 134
                                        1111 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3392  (0.189191); expected 358.6 (0.02)
Passed bias filter:                      763  (0.0425568); expected 358.6 (0.02)
Passed Vit filter:                       105  (0.00585643); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 909.44
//
Query:       gene136|gene136|rna136|rna136  [L=189]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.9e-08   32.8  11.4    5.6e-08   32.6  10.1    1.8  2  SWIRM-assoc_1  SWIRM-associated region 1


Domain annotation for each model (and alignments):
>> SWIRM-assoc_1  SWIRM-associated region 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.0      0.75   1.3e+04      48      56 ..      83      91 ..      75      96 .. 0.53
   2 !   32.6  10.1   3.1e-12   5.6e-08       3      73 ..     116     186 ..     114     189 .] 0.91

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 0.75
                  SWIRM-assoc_1 48 Eklleaerr 56
                                   E+++++e+ 
  gene136|gene136|rna136|rna136 83 ETTVNKEQH 91
                                   444444444 PP

  == domain 2  score: 32.6 bits;  conditional E-value: 3.1e-12
                  SWIRM-assoc_1   3 ALaaaAakAkvlasqeereiqrlvaqlvetqlkKlelKLkqfeelEklleaerrelekqrqqLlleRlalk 73 
                                    AL+aa  kAk l + ee+++ rlv+ + e+q+kK+elK + f++l   +++er el k r+   +e  ++k
  gene136|gene136|rna136|rna136 116 ALKAAQHKAKELLTIEENKMVRLVKVILEAQMKKMELKEEAFNDLKGNFKNERIELMKIREGYKSEIEEIK 186
                                    9*******************************************************999987666655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (189 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1976  (0.110213); expected 358.6 (0.02)
Passed bias filter:                      490  (0.02733); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1199.13
//
Query:       gene1360|gene1360|rna1360|rna1360  [L=59]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.19   11.6   0.0       0.32   10.9   0.0    1.3  1  SLBB      SLBB domain


Domain annotation for each model (and alignments):
>> SLBB  SLBB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   1.8e-05      0.32       7      24 ..      14      31 ..      14      37 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 1.8e-05
                                       SBSS-EEEEEETT-BHHH CS
                               SLBB  7 eVkrPgnyevpigttlsd 24
                                       e+++P nye+ +g+ ls+
  gene1360|gene1360|rna1360|rna1360 14 EINNPMNYELELGIALSE 31
                                       69************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       364  (0.0203023); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.26s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 438.46
//
Query:       gene1361|gene1361|rna1361|rna1361  [L=375]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (375 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1216  (0.0678231); expected 358.6 (0.02)
Passed bias filter:                      612  (0.0341346); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.41
# Mc/sec: 2775.78
//
Query:       gene1362|gene1362|rna1362|rna1362  [L=293]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.035   14.2   0.4      0.035   14.2   0.4    1.9  2  DnaJ      DnaJ domain


Domain annotation for each model (and alignments):
>> DnaJ  DnaJ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.4     2e-06     0.035      20      63 .]      65     103 ..      42     103 .. 0.86
   2 ?   -2.9   0.1      0.42   7.6e+03      27      34 ..     173     180 ..     171     195 .. 0.47

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2e-06
                                        HHHHHHHHHSTTTSCCHHHHHHHHHHHHHHHHHHTSHHHHHHHH CS
                               DnaJ  20 aYrklalkyHPDknpkdpeaeekFkeineAyevLsdpekRkqYD 63 
                                        +Yr+ +++yHP  +      ++ F  i + ye+L+    +k+YD
  gene1362|gene1362|rna1362|rna1362  65 RYRERIVRYHPNYH-----DDRVFIAIRNGYEILKSTFWKKKYD 103
                                        7*************.....6778**************9999999 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 0.42
                                        HHSTTTSC CS
                               DnaJ  27 kyHPDknp 34 
                                         yHP  ++
  gene1362|gene1362|rna1362|rna1362 173 AYHPGYET 180
                                        58887332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (293 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       606  (0.0338); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 2026.79
//
Query:       gene1363|gene1363|rna1363|rna1363  [L=270]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.1e-67  227.2   5.4    2.4e-67  227.0   5.4    1.0  1  Rcd1            Cell differentiation family, Rcd1-like
  ------ inclusion threshold ------
      0.059   13.9   0.0       0.15   12.5   0.0    1.7  1  Caprin-1_dimer  Caprin-1 dimerization domain


Domain annotation for each model (and alignments):
>> Rcd1  Cell differentiation family, Rcd1-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  227.0   5.4   2.6e-71   2.4e-67       4     254 ..      11     261 ..       8     266 .. 0.97

  Alignments for each domain:
  == domain 1  score: 227.0 bits;  conditional E-value: 2.6e-71
                               Rcd1   4 dlakpekreeaLleLskkresvedlallLwesfgtvaaLLqeivsiYpllspptltaaesnrvcnaLallqcvash 79 
                                        +   ++ +   L++L    e+ ++ +  +w   ++ +++Lqe++  +  ls p++++++ + v+++L++lq+++ +
  gene1363|gene1363|rna1363|rna1363  11 KSLAEKDKSIYLKKLFLYLEKNPSSSYEFWTVDEIPFLILQELITPFSQLSLPEIENKSFSDVITVLNILQIIVTD 86 
                                        55556778999***************************************************************** PP

                               Rcd1  80 petrklflkakiplyLypfLnttsksrefEylRltsLgvigaLvktddkevikflldteivplclrimesGselsk 155
                                        +++r+ fl+a+ p y+yp+Lnt+s +++fE+lR++ Lgvig L+k+ddk+   +l +teivpl l+im++Gs +sk
  gene1363|gene1363|rna1363|rna1363  87 RSVREDFLNAQYPFYIYPYLNTNSLNNQFESLRIAGLGVIGQLLKDDDKKTALYLQNTEIVPLTLKIMDIGSIVSK 162
                                        **************************************************************************** PP

                               Rcd1 156 tvAtfIlqkiLlddeGLeYicqtaerfsavaevLnkmvvslteepssrllkhvircYlrLsdnprareaLkkclpe 231
                                        ++At+I+ ki+ +deGLeY+cqt+erf a++ +Ln+mv +l e+ ++ llk v+rcY+rL ++ ++r   ++  pe
  gene1363|gene1363|rna1363|rna1363 163 KIATYIFLKIIGSDEGLEYACQTFERFIAISVILNTMVAQLLENMDKNLLKSVLRCYVRLVNQDNVRISYATKPPE 238
                                        **************************************************************************** PP

                               Rcd1 232 lLkdktfkellkedpetkkwlkq 254
                                        +L ++++++++++d++++++++ 
  gene1363|gene1363|rna1363|rna1363 239 ALCSREMAKIIEDDKDIRELFSL 261
                                        *****************998875 PP

>> Caprin-1_dimer  Caprin-1 dimerization domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   1.7e-05      0.15       9      41 ..      64      97 ..      58     119 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.7e-05
                     Caprin-1_dimer  9 eaEiarlkevlevqdvLssl.geeevredflnGt 41
                                       e E++ +++v+ v+++L+ + ++ +vredfln +
  gene1363|gene1363|rna1363|rna1363 64 EIENKSFSDVITVLNILQIIvTDRSVREDFLNAQ 97
                                       67999*************9967779******987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       495  (0.0276089); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1841.15
//
Query:       gene1364|gene1364|rna1364|rna1364  [L=328]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.5e-23   82.1   0.2    1.1e-22   80.9   0.0    1.7  1  AAA              ATPase family associated with various cellul
    2.2e-06   28.1   0.7    1.5e-05   25.5   0.7    2.1  1  AAA_16           AAA ATPase domain
    1.2e-05   25.2   0.1    3.3e-05   23.8   0.0    1.7  1  Bac_DnaA         Bacterial dnaA  protein
    1.3e-05   25.5   2.8     0.0014   18.9   0.1    2.7  2  AAA_22           AAA domain
      2e-05   24.4   0.1    8.5e-05   22.4   0.1    1.9  2  IstB_IS21        IstB-like ATP binding protein
    3.8e-05   24.0   0.0    0.00011   22.5   0.0    1.9  1  RNA_helicase     RNA helicase
      7e-05   22.6   0.1     0.0002   21.2   0.1    1.7  1  AAA_30           AAA domain
    0.00014   21.8   0.1    0.00045   20.2   0.0    2.0  1  AAA_5            AAA domain (dynein-related subfamily)
     0.0002   21.4   0.0    0.00043   20.3   0.0    1.5  1  AAA_14           AAA domain
    0.00025   20.3   0.0    0.00046   19.4   0.0    1.4  1  DUF815           Protein of unknown function (DUF815)
    0.00028   20.9   0.2    0.00077   19.4   0.2    1.9  1  NACHT            NACHT domain
    0.00031   20.5   1.8     0.0012   18.7   0.4    2.6  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    0.00077   18.8   0.0     0.0012   18.2   0.0    1.3  1  TIP49            TIP49 P-loop domain
     0.0011   18.5   0.1     0.0034   16.9   0.0    1.8  2  PhoH             PhoH-like protein
     0.0014   18.3   0.6     0.0054   16.4   0.1    2.3  2  Sigma54_activat  Sigma-54 interaction domain
     0.0018   17.7   0.1      0.016   14.6   0.0    2.2  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
     0.0023   17.7   0.0     0.0043   16.8   0.0    1.5  1  Cytidylate_kin   Cytidylate kinase
     0.0024   17.8   0.0     0.0049   16.9   0.0    1.5  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
     0.0029   18.2   0.1       0.01   16.4   0.1    1.9  1  AAA_18           AAA domain
     0.0029   17.1   0.0     0.0082   15.7   0.0    1.8  1  AAA_7            P-loop containing dynein motor region
     0.0029   17.3   0.0     0.0068   16.1   0.0    1.6  1  AAA_24           AAA domain
     0.0048   16.8   0.0      0.023   14.6   0.0    2.1  2  RsgA_GTPase      RsgA GTPase
     0.0055   16.0   0.7      0.013   14.8   0.2    1.9  2  DUF2075          Uncharacterized conserved protein (DUF2075)
     0.0062   16.3   0.1      0.015   15.0   0.1    1.7  1  Viral_helicase1  Viral (Superfamily 1) RNA helicase
  ------ inclusion threshold ------
       0.01   15.7   1.3       0.81    9.6   0.0    2.9  3  ATPase_2         ATPase domain predominantly from Archaea
      0.013   14.5   0.0      0.026   13.5   0.0    1.4  1  AAA_6            Hydrolytic ATP binding site of dynein motor 
      0.018   15.3   0.6        1.1    9.6   0.0    3.0  3  Imm41            Immunity protein 41
      0.022   15.3   0.0      0.051   14.1   0.0    1.7  1  ABC_tran         ABC transporter
      0.029   14.5   0.0      0.057   13.5   0.0    1.4  1  AAA_2            AAA domain (Cdc48 subfamily)
      0.035   13.4   0.0      0.055   12.8   0.0    1.2  1  TcdA_TcdB        TcdA/TcdB catalytic glycosyltransferase doma
       0.05   12.7   0.1      0.087   11.9   0.1    1.5  1  Parvo_NS1        Parvovirus non-structural protein NS1
      0.053   13.3   0.0       0.13   12.0   0.0    1.7  1  AAA_29           P-loop containing region of AAA domain
      0.055   12.7   0.0       0.11   11.7   0.0    1.5  1  NB-ARC           NB-ARC domain
      0.089   11.9   0.1        0.2   10.8   0.0    1.7  2  PIF1             PIF1-like helicase
      0.098   12.2   0.4      0.098   12.2   0.4    2.2  3  AAA_25           AAA domain
        0.1   12.4   0.0       0.23   11.2   0.0    1.7  1  PduV-EutP        Ethanolamine utilisation - propanediol utili
       0.11   12.6   0.8       0.71   10.0   0.1    2.3  2  MMR_HSR1         50S ribosome-binding GTPase
       0.12   12.6   1.7       0.61   10.4   1.6    2.0  1  AAA_19           AAA domain
       0.19   11.5   1.9        1.3    8.7   0.1    2.7  3  AAA_11           AAA domain
       0.19   11.1   2.4          5    6.4   0.0    2.7  3  ATPase           KaiC


Domain annotation for each model (and alignments):
>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.9   0.0   2.4e-25   1.1e-22       1     129 [.     108     236 ..     108     239 .. 0.92

  Alignments for each domain:
  == domain 1  score: 80.9 bits;  conditional E-value: 2.4e-25
                                        EEEESSTTSSHHHHHHHHHHHH.....THEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHH CS
                                AAA   1 vllyGppGtGKTllakavakel.....gvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidala 71 
                                        vll+Gp GtGK++l++a+a ++     +++ +e+  ++ +sk+ ges++k++elfk++ ++   ++++iDE+d+l+
  gene1364|gene1364|rna1364|rna1364 108 VLLHGPAGTGKSALCRAIAAKIavrtkHTKTVEVHSAQYVSKFYGESAHKLNELFKSVDKH---TVVIIDEVDSLI 180
                                        79*******************8555544889************************998765...7*********** PP

                                        HHH....TTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHSTTSSEEEE CS
                                AAA  72 ksr....sgseseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallrgRfdrkie 129
                                         sr     ++e  +++r+vn++l  ld        ++++++tn    +d+a++ +R+d++++
  gene1364|gene1364|rna1364|rna1364 181 VSRdqicARNEPLDSMRIVNTFLVNLDVSG-----CFLMCTTNLLGVVDRAFV-DRMDMVVR 236
                                        ******999*****************9653.....69****************.****9986 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.7   3.3e-08   1.5e-05      16      58 ..      95     133 ..      91     196 .. 0.71

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 3.3e-08
                             AAA_16  16 lervrsgrp..elvllsGesGvGKsslvrellralekdggiflrg 58 
                                        ++r++++ +  + vll+G++G+GKs+l r+++  +  +      +
  gene1364|gene1364|rna1364|rna1364  95 YRRIAKSMGisRTVLLHGPAGTGKSALCRAIAAKIAVR------T 133
                                        666666666679********************866644......2 PP

>> Bac_DnaA  Bacterial dnaA  protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.0   7.3e-08   3.3e-05      25     110 ..      97     180 ..      89     188 .. 0.85

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 7.3e-08
                                        HHHHSTTT.S--EEEE-SSSSSHHHHHHHHHHHHHHHSSSS-EEEEEHHHHHHHHHHHHHTT-HHHHHHHHTT-SE CS
                           Bac_DnaA  25 kvaeapgkkynPlfiygevGlGktHLlkaignevlenapelrvvYltaeeFlnelvkalrdkkaeefkeklrkvDv 100
                                        ++a+  g     ++++g+ G Gk  L +ai+ ++  ++++++ v +++ ++++++      +k++e+ +++ k  v
  gene1364|gene1364|rna1364|rna1364  97 RIAKSMGI-SRTVLLHGPAGTGKSALCRAIAAKIAVRTKHTKTVEVHSAQYVSKFYGES-AHKLNELFKSVDKHTV 170
                                        56666666.45699*****************************************9875.567777778899999* PP

                                        EEEE-GGGGT CS
                           Bac_DnaA 101 LliDDiqfla 110
                                        ++iD++  l 
  gene1364|gene1364|rna1364|rna1364 171 VIIDEVDSLI 180
                                        *****98775 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.1   3.1e-06    0.0014       8      54 ..     108     159 ..     105     167 .. 0.73
   2 ?    7.1   0.2     0.014       6.4      83     107 ..     159     184 ..     153     219 .. 0.66

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 3.1e-06
                             AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaee....erpevv.fvtlpsstssk 54 
                                        ++++G++GtGK+ l+r ++ +   + k+++    +++++v +++  s  ++ 
  gene1364|gene1364|rna1364|rna1364 108 VLLHGPAGTGKSALCRAIAAKIAVRTKHTKtvevHSAQYVsKFYGESAHKLN 159
                                        689******************9998887777766666655544444444444 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.014
                             AAA_22  83 eqalraravielliiDEaqhlr.see 107
                                        ++ +++ +++ ++iiDE++ l+ s +
  gene1364|gene1364|rna1364|rna1364 159 NELFKSVDKHTVVIIDEVDSLIvSRD 184
                                        44445555588*********988422 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.1   1.9e-07   8.5e-05      48     125 ..     106     184 ..      97     188 .. 0.79
   2 ?   -1.3   0.0       3.6   1.6e+03      65      90 ..     283     308 ..     271     323 .. 0.72

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 1.9e-07
                          IstB_IS21  48 enivllGpsGvGKshlaialgve.avr.aglsvlfvrvedLveelkrarrdgklaralkrllkvdllilDdlgllp 121
                                          ++l Gp+G+GKs l  a++ + avr + ++++ v  ++ v++    ++  kl++  k++ k +++i+D++  l 
  gene1364|gene1364|rna1364|rna1364 106 RTVLLHGPAGTGKSALCRAIAAKiAVRtKHTKTVEVHSAQYVSKFYG-ESAHKLNELFKSVDKHTVVIIDEVDSLI 180
                                        5789****************988355534445555566667777654.56689******************99888 PP

                          IstB_IS21 122 ldqa 125
                                        ++++
  gene1364|gene1364|rna1364|rna1364 181 VSRD 184
                                        8776 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 3.6
                          IstB_IS21  65 ialgveavraglsvlfvrvedLveel 90 
                                         a+g++ +r+ +++lf+ +++ v+++
  gene1364|gene1364|rna1364|rna1364 283 RAIGTASARRIKKMLFCAMHRDVRTV 308
                                        47888888888888888887755554 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.0   2.6e-07   0.00011       1      60 [.     108     178 ..     108     211 .. 0.67

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 2.6e-07
                       RNA_helicase   1 iwlyGpsgeGKStlakeLakallkkl.........klkkkdsvys..rnpeddfwdgYtgqevvvidDfgq 60 
                                        ++l+Gp+g+GKS l++ +a++++ +            +  +++y     + ++ +++ ++++vv+id++ +
  gene1364|gene1364|rna1364|rna1364 108 VLLHGPAGTGKSALCRAIAAKIAVRTkhtktvevhSAQYVSKFYGesAHKLNELFKSVDKHTVVIIDEVDS 178
                                        689********************444344666666555556666543455667777777777777777655 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.1   4.4e-07    0.0002      19      97 ..     106     176 ..      95     186 .. 0.77

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 4.4e-07
                             AAA_30  19 rvavltGpAGtGKttalkalreaweaaggrviglAptgkaAkvLaeelgieastiakllkrlkgrarlepgtlliv 94 
                                        r+++l+GpAGtGK+ + +a+++ ++ + +  +  + +   A+ +++  g  a+ +++l k+       +++t++i+
  gene1364|gene1364|rna1364|rna1364 106 RTVLLHGPAGTGKSALCRAIAAKIAVRTK--HTKTVEVHSAQYVSKFYGESAHKLNELFKSV------DKHTVVII 173
                                        4799****************887776643..3445566778888888888888999888444......557***** PP

                             AAA_30  95 DEa 97 
                                        DE+
  gene1364|gene1364|rna1364|rna1364 174 DEV 176
                                        **7 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0     1e-06   0.00045       2      76 ..     108     178 ..     107     230 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 1e-06
                                        EEEE--SSSSHHHHHHHGGGGB...S--EEEEE--TT--HHHHH--B--.........--------G-SEEEEESG CS
                              AAA_5   2 vlLvGppGtgKselaerlaaal...nreveyvqltrdtteedlkgrreikngttslvdsplvraaregeilvlDEv 74 
                                        vlL Gp GtgKs l + +aa +   ++ + +v  ++    +++ g+         ++ ++l +++ +  ++++DEv
  gene1364|gene1364|rna1364|rna1364 108 VLLHGPAGTGKSALCRAIAAKIavrTKHTKTVEVHSAQYVSKFYGESA-------HKLNELFKSVDKHTVVIIDEV 176
                                        89********************99999999999999888888888877.......79999999999*********9 PP

                                        GG CS
                              AAA_5  75 er 76 
                                        + 
  gene1364|gene1364|rna1364|rna1364 177 DS 178
                                        85 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   9.5e-07   0.00043       3      76 ..     106     179 ..     105     203 .. 0.77

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 9.5e-07
                             AAA_14   3 kilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkla..dpe.kllelileklkeekktylflDEiqe 75 
                                        + +++ G+  +GK+ l++ ++ +  v+ +++  +++ + ++ ++   +++ kl+el+++    +k+t++++DE+  
  gene1364|gene1364|rna1364|rna1364 106 RTVLLHGPAGTGKSALCRAIAAKIAVRTKHTKTVEVHSAQYVSKFygESAhKLNELFKSV---DKHTVVIIDEVDS 178
                                        57899****************998899999999999998885433212222555555553...489*******987 PP

                             AAA_14  76 v 76 
                                        +
  gene1364|gene1364|rna1364|rna1364 179 L 179
                                        6 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0     1e-06   0.00046      54     114 ..     106     174 ..      92     178 .. 0.73

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 1e-06
                             DUF815  54 nnvLLwGarGtGKSslvkallneyaeeg..Lrlievekedl......kelpklvellrerperfilfvD 114
                                        + vLL G  GtGKS+l++a+ +++a ++   + +ev+  +       ++  kl el ++++++ ++ +D
  gene1364|gene1364|rna1364|rna1364 106 RTVLLHGPAGTGKSALCRAIAAKIAVRTkhTKTVEVHSAQYvskfygESAHKLNELFKSVDKHTVVIID 174
                                        679******************998766655999999987641111112345666666666666666666 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.2   1.7e-06   0.00077       1      33 [.     106     138 ..     106     217 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 1.7e-06
                                        SCEEEEC-TTTCHHHHHHHHHHHHCTS-SCCCC CS
                              NACHT   1 rlvilqGeaGsGKTtLlqklalawaegklpqga 33 
                                        r+v+l+G+aG GK++L + +a ++a ++   ++
  gene1364|gene1364|rna1364|rna1364 106 RTVLLHGPAGTGKSALCRAIAAKIAVRTKHTKT 138
                                        79***********************99976654 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.4   2.6e-06    0.0012      35     101 ..     107     184 ..      94     237 .. 0.73
   2 ?   -0.8   0.0       2.6   1.2e+03      76     102 ..     294     321 ..     282     323 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 2.6e-06
                             RuvB_N  35 hvllyGpPGlGkttlakiiakelgvklkitsgPvl...........ekagdlaalltnleekdvlfideihrlsra 99 
                                         vll+Gp G Gk++l++ ia+++ v+ k+t +  +           e a  l  l+++++++ v+ ide+  l  +
  gene1364|gene1364|rna1364|rna1364 107 TVLLHGPAGTGKSALCRAIAAKIAVRTKHTKTVEVhsaqyvskfygESAHKLNELFKSVDKHTVVIIDEVDSLIVS 182
                                        59**********************9999886554411111122222345678889999999999999999988665 PP

                             RuvB_N 100 ve 101
                                         +
  gene1364|gene1364|rna1364|rna1364 183 RD 184
                                        55 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 2.6
                             RuvB_N  76 aalltnleekdvlfidei.hrlsravee 102
                                          +l    ++dv  +d+i  rl+r +ee
  gene1364|gene1364|rna1364|rna1364 294 KKMLFCAMHRDVRTVDDIlDRLERIIEE 321
                                        5566666778888898874699999988 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   2.6e-06    0.0012      44     113 ..     100     175 ..      95     206 .. 0.71

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 2.6e-06
                                        XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX...XXX....XXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                              TIP49  44 kekklaGravLlaGpsgtGktalaiaiskelgedvpfva...lsg....sevyslevkktevltqalrksigvrik 112
                                        k+  ++ r+vLl Gp+gtGk+al  ai+ +++  ++ ++   + +    s++y    +k + l + + k   v i 
  gene1364|gene1364|rna1364|rna1364 100 KSMGIS-RTVLLHGPAGTGKSALCRAIAAKIAVRTKHTKtveVHSaqyvSKFYGESAHKLNELFKSVDKHTVVIID 174
                                        555566.9**********************9965555430003321222556666666666666666666666665 PP

                                        X CS
                              TIP49 113 e 113
                                        e
  gene1364|gene1364|rna1364|rna1364 175 E 175
                                        5 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   7.5e-06    0.0034       8      59 ..      94     145 ..      90     193 .. 0.74
   2 ?   -2.5   0.0       6.6     3e+03      32      54 ..     276     298 ..     274     304 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 7.5e-06
                                        HHHHHHHHHHH-SEEEEE--TTSSTTHHHHHHHHHHHHTTS-SEEEEEE-S- CS
                               PhoH   8 eQkeylealkkndivfaiGpaGtGKtylavalavealkkkkvkriiltrpav 59 
                                        + +++++++  +  v   GpaGtGK+ l  a+a+++  + k ++ + +  a 
  gene1364|gene1364|rna1364|rna1364  94 RYRRIAKSMGISRTVLLHGPAGTGKSALCRAIAAKIAVRTKHTKTVEVHSAQ 145
                                        55666777777888999******************99999999888776655 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 6.6
                                        TTHHHHHHHHHHHHTTS-SEEEE CS
                               PhoH  32 Ktylavalavealkkkkvkriil 54 
                                        K +lav+ a+   +++++k++++
  gene1364|gene1364|rna1364|rna1364 276 KRMLAVSRAIGTASARRIKKMLF 298
                                        7789999***9999999999875 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.1   1.2e-05    0.0054      12      62 ..      95     147 ..      90     179 .. 0.82
   2 ?   -2.7   0.0       9.2   4.1e+03     124     146 ..     284     306 ..     281     309 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.2e-05
                                        HHHHHHHCTSSS-EEEECSTTSSHHHHHHHHHH..HSTTTTS-EEEEETTTS- CS
                    Sigma54_activat  12 leqikkvaktdlsvlitGesGtGKellaraihe..askrkekpfvavncaaip 62 
                                        +++i+k +  + +vl++G  GtGK+ l rai +  a + k+++ v+v  a++ 
  gene1364|gene1364|rna1364|rna1364  95 YRRIAKSMGISRTVLLHGPAGTGKSALCRAIAAkiAVRTKHTKTVEVHSAQYV 147
                                        566777777889*******************9944445566677777777765 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 9.2
                                        SBTSSSEEE--EEEEEEESS-HH CS
                    Sigma54_activat 124 rvGsskeikvdvriiaatnedle 146
                                         +G+ + ++++ ++ +a ++d++
  gene1364|gene1364|rna1364|rna1364 284 AIGTASARRIKKMLFCAMHRDVR 306
                                        68999999999999999999976 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   3.6e-05     0.016      24      72 ..     107     156 ..      93     176 .. 0.78
   2 ?    0.5   0.0      0.75   3.3e+02     182     200 ..     220     238 ..     207     245 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.6e-05
                       Mg_chelatase  24 nlllvGppGsGKtmlakrlps.llpplseeealevakiasvagkkeeekl 72 
                                         +ll Gp+G+GK+ l +++++ +  + ++++++ev + + v++   e+++
  gene1364|gene1364|rna1364|rna1364 107 TVLLHGPAGTGKSALCRAIAAkIAVRTKHTKTVEVHSAQYVSKFYGESAH 156
                                        699**************997527778889999999999998885544444 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.75
                       Mg_chelatase 182 lsklsgplldRidlqvevk 200
                                        l  + ++++dR+d+ v++ 
  gene1364|gene1364|rna1364|rna1364 220 LGVVDRAFVDRMDMVVRMY 238
                                        5667889********9984 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   9.7e-06    0.0043       3      29 ..     110     136 ..     108     185 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 9.7e-06
                                        EE-STTSSHHHHHHHHHHHHT-EEEEH CS
                     Cytidylate_kin   3 iDGPagsGKssvaralaeklglkyldt 29 
                                        + GPag+GKs+++ra+a k+ ++   t
  gene1364|gene1364|rna1364|rna1364 110 LHGPAGTGKSALCRAIAAKIAVRTKHT 136
                                        68*****************98876555 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   1.1e-05    0.0049      13      46 ..      97     132 ..      91     158 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.1e-05
                                        HHHHCH..TEEEEEEESTTSSHHHHHHHHHHHTT-- CS
                               TsaE  13 klakal..gdvilLeGdLGaGKTtlvrglakalgve 46 
                                        ++ak++  ++++lL+G+ G+GK++l+r++a+++ v+
  gene1364|gene1364|rna1364|rna1364  97 RIAKSMgiSRTVLLHGPAGTGKSALCRAIAAKIAVR 132
                                        44454444789********************99775 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.1   2.3e-05      0.01       1      81 [.     108     175 ..     108     189 .. 0.56

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 2.3e-05
                             AAA_18   1 IlltGtpGvGKttlakeLskrlgf........gvnlrdvakenglllevdpealdeskrldedkldklldaleens 68 
                                        +ll G++G+GK+ l+++++ + ++                          ++ ++++  +  +kl++l++ ++++ 
  gene1364|gene1364|rna1364|rna1364 108 VLLHGPAGTGKSALCRAIAAKIAVrtkhtktvE-------------VHSAQY-VSKFYGESAHKLNELFKSVDKH- 168
                                        7899**************999633333222221.............222222.3334444455544444444443. PP

                             AAA_18  69 saleegknlvidg 81 
                                               +++id 
  gene1364|gene1364|rna1364|rna1364 169 ------TVVIIDE 175
                                        ......4455555 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   1.8e-05    0.0082      29      73 ..     101     145 ..      87     181 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.8e-05
                              AAA_7  29 llknkkpvllvGptGtGKtviikdllkkldkekylsltinfsaqt 73 
                                         +  ++ vll Gp+GtGK+++++ +  k+  ++  ++t+++++  
  gene1364|gene1364|rna1364|rna1364 101 SMGISRTVLLHGPAGTGKSALCRAIAAKIAVRTKHTKTVEVHSAQ 145
                                        4566789*****************999999777777777766554 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   1.5e-05    0.0068       3      89 ..     106     190 ..     104     197 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.5e-05
                             AAA_24   3 lkiliyGpsgiGKTtlakelgpkplfidtekGlksldadkfpdie.swedfldevvelaaeladyktlviDtidel 77 
                                        + +l+ Gp+g+GK+ l++ +    + + t + +k ++++  ++++  + +  ++++el +  ++  +++iD +d l
  gene1364|gene1364|rna1364|rna1364 106 RTVLLHGPAGTGKSALCRAI-AAKIAVRTKH-TKTVEVHSAQYVSkFYGESAHKLNELFKSVDKHTVVIIDEVDSL 179
                                        5799****************.9999999999.9***********966688999999999999999*********99 PP

                             AAA_24  78 eelclaevirqn 89 
                                            +++++ +n
  gene1364|gene1364|rna1364|rna1364 180 I-VSRDQICARN 190
                                        5.4666667666 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   5.2e-05     0.023      91     131 ..      96     137 ..      76     145 .. 0.82
   2 ?   -1.9   0.0       6.2   2.8e+03      28      49 ..     286     307 ..     277     326 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 5.2e-05
                                        HHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT-----S--- CS
                        RsgA_GTPase  91 eelkellkd.ktsvlvGqSGvGKStLinallpelelktgevs 131
                                        +++++ +   +t++l G+ G GKS+L  a++ +  ++t++++
  gene1364|gene1364|rna1364|rna1364  96 RRIAKSMGIsRTVLLHGPAGTGKSALCRAIAAKIAVRTKHTK 137
                                        55666665558999*******************999998876 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 6.2
                                        TT--HHHHHHHHHHHHHTT-EE CS
                        RsgA_GTPase  28 pelslnlldrfLvlaeekgiep 49 
                                         + s ++++++L+ a +++++ 
  gene1364|gene1364|rna1364|rna1364 286 GTASARRIKKMLFCAMHRDVRT 307
                                        4667888899998888888754 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.2   2.9e-05     0.013       2      75 ..     106     177 ..     105     200 .. 0.80
   2 ?   -3.2   0.0       8.5   3.8e+03     336     350 ..     243     257 ..     240     258 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.9e-05
                            DUF2075   2 avvlVtGvaGtGKtvvllnllaeleddeeertavylsvNhplvlvlrealakkeekkkkkeafeklssfinnls 75 
                                        + vl +G aGtGK+ +  +++a++   + ++t+++ + + + v + + + a k  ++ +k++ +    +i +++
  gene1364|gene1364|rna1364|rna1364 106 RTVLLHGPAGTGKSALCRAIAAKI-AVRTKHTKTVEVHSAQYVSKFYGESAHKL-NELFKSVDKHTVVIIDEVD 177
                                        56899*******************.88888888888999999999999999999.7777777777777777766 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 8.5
                            DUF2075 336 ekaqkllkNayrVLL 350
                                        +  ++++ Na++VL+
  gene1364|gene1364|rna1364|rna1364 243 QHVHRMIVNALHVLM 257
                                        667899*******98 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.1   3.4e-05     0.015       2      71 ..     109     176 ..     108     189 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3.4e-05
                    Viral_helicase1   2 vvhGvpGcGKStlirkllrtsliltvnrptaelltegkpklpnlsvrtvdsflmalvkstkgkililDEy 71 
                                        + hG +G GKS l+r ++ +  + t++++t+e++++  +++ +  ++ + ++ + ++   k  ++i+DE 
  gene1364|gene1364|rna1364|rna1364 109 LLHGPAGTGKSALCRAIAAKIAVRTKHTKTVEVHSA--QYVSKFYGESAHKLNELFKSVDKHTVVIIDEV 176
                                        68****************995555666666666665..56666666666666666655566789999996 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0      0.71   3.2e+02     130     168 ..       8      45 ..       2      68 .. 0.78
   2 ?    9.6   0.0    0.0018      0.81      20      67 ..     105     160 ..      93     168 .. 0.68
   3 ?    3.3   0.5      0.15        66     106     131 ..     158     180 ..     133     187 .. 0.68

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.71
                           ATPase_2 130 lidlglngaellvkeLlnliesltkekhlcvviclsSeg 168
                                        l+ +   + ++l   L+n i+sl  +++    ic    g
  gene1364|gene1364|rna1364|rna1364   8 LV-IETTKRANLKTRLFNTIVSLNTQYNGSTMICEGYTG 45 
                                        44.556678899999*********999999999965555 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0018
                           ATPase_2  20 neiyfiYGpegsGKtaLlkeiienledkdk........yviyyialreesisklde 67 
                                        ++ +++ Gp g GK+aL + i+ +     k           y++++ +es +kl+e
  gene1364|gene1364|rna1364|rna1364 105 SRTVLLHGPAGTGKSALCRAIAAKIAVRTKhtktvevhSAQYVSKFYGESAHKLNE 160
                                        5678999************9988764333322345555555666666666666655 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.15
                           ATPase_2 106 ielllekikkkgkkiiiiiDelqkli 131
                                        ++   e  k   k  ++iiDe+  li
  gene1364|gene1364|rna1364|rna1364 158 LN---ELFKSVDKHTVVIIDEVDSLI 180
                                        33...33344445599******9998 PP

>> AAA_6  Hydrolytic ATP binding site of dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   5.8e-05     0.026      21      78 ..      94     151 ..      84     156 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5.8e-05
                              AAA_6  21 cyltltqAlklklggapaGpagtGKtEtvkdLakalakqvvvfncsdqldykslgkif 78 
                                         y+ +++++ ++    ++GpagtGK+  ++ +a ++a+ +  ++  +  +++ ++k++
  gene1364|gene1364|rna1364|rna1364  94 RYRRIAKSMGISRTVLLHGPAGTGKSALCRAIAAKIAVRTKHTKTVEVHSAQYVSKFY 151
                                        48899999*****************************999888888888888887776 PP

>> Imm41  Immunity protein 41
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0      0.75   3.3e+02       2      69 ..      26      91 ..      25     102 .. 0.67
   2 ?    9.6   0.0    0.0025       1.1       7     106 ..     139     243 ..     134     251 .. 0.77
   3 ?    0.3   0.0       1.9   8.3e+02      61      90 ..     290     319 ..     276     323 .. 0.67

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.75
                              Imm41  2 vltsneeldensfigklleessfn.deeyWklenalieilkkykdkdlkrelvkgisytykrilelllv 69
                                       +++ n+++++ ++i + +  s+      +   ++  i++ k   +  l  elv+ i   y ril+ ++ 
  gene1364|gene1364|rna1364|rna1364 26 IVSLNTQYNGSTMICEGYTGSTRHlSGTFRVTKETKIKVYKG--TARLFYELVIDIAVKY-RILDHFFR 91
                                       678888888888888887766544044555555555555544..5588899999999544.67777655 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0025
                              Imm41   7 eeldensfigklleessfndeeyWk.lenalieilkkykdkdlkrelvkgis..ytykrilelllvhfaksdlfei 79 
                                         e+    ++ k++ es ++ +e +k +++  + i+++  + +++r+ +   +      ri++++lv+ + s  f +
  gene1364|gene1364|rna1364|rna1364 139 VEVHSAQYVSKFYGESAHKLNELFKsVDKHTVVIIDEVDSLIVSRDQICARNepLDSMRIVNTFLVNLDVSGCFLM 214
                                        56777788899999999887776652567778888888899999986544331144679************99999 PP

                              Imm41  80 .....sdipdrfiafyERlkyilryiftgfdk 106
                                              ++ dr  af++R+++++r ++   ++
  gene1364|gene1364|rna1364|rna1364 215 cttnlLGVVDR--AFVDRMDMVVRMYYP-CEQ 243
                                        88888889999..*************97.454 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 1.9
                              Imm41  61 krilelllvhfaksdlfeisdipdrfiafy 90 
                                         r ++ +l+   + d+  ++di dr++  +
  gene1364|gene1364|rna1364|rna1364 290 ARRIKKMLFCAMHRDVRTVDDILDRLERII 319
                                        3445555555555599999*****965555 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   0.00011     0.051      11      37 ..     105     131 ..      95     196 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 0.00011
                                        TSEEEEEESTTSSHHHHHHHHTTSS-- CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ABC_tran  11 gekvaivGenGaGKStLlkllagllkp 37 
                                        +++v + G+ G+GKS L++++a +   
  gene1364|gene1364|rna1364|rna1364 105 SRTVLLHGPAGTGKSALCRAIAAKIAV 131
                                        67899****************998765 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   0.00013     0.057       6      80 ..     108     179 ..     105     189 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.00013
                                        EEEE--TTSSHHHHHHHHHHHTT-.....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTSEEEEETGGG- CS
                              AAA_2   6 illlgptgvGktelakalaellfv.kkekkliradaselleeeevehlvsrligappgyvgaeegGivllDEidKi 80 
                                        +ll gp g+Gk+ l +a+a  + v +k+ k + +   ++      + + ++    ++  ++++++ +v +DE+d  
  gene1364|gene1364|rna1364|rna1364 108 VLLHGPAGTGKSALCRAIAAKIAVrTKHTKTVEVHSAQYVS----KFYGESAHKLNELFKSVDKHTVVIIDEVDSL 179
                                        7899******************9832223333333444444....666677777788889999**********965 PP

>> TcdA_TcdB  TcdA/TcdB catalytic glycosyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   0.00012     0.055     248     330 ..     123     207 ..     111     219 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00012
                                        HHHHHHHHHCC-SSTT...---CCCCTS-CCHHHHHHHHHHC--SGG.GTB------EE-TT-E...EEEEETTEE CS
                          TcdA_TcdB 248 raileailkykkgkaevevassedverldeelktklkallkskeeksielFkslddlkvrplely..kelaalksg 321
                                        rai   i    k +++vev s + v+++  e  +kl++l+ks ++  + +  ++d l+v+   ++  +e   + ++
  gene1364|gene1364|rna1364|rna1364 123 RAIAAKIAVRTKHTKTVEVHSAQYVSKFYGESAHKLNELFKSVDKHTVVIIDEVDSLIVSRDQICarNEPLDSMRI 198
                                        66666777778899999******************************************99888621345567789 PP

                                        EEEEEEE-T CS
                          TcdA_TcdB 322 lNqalvskk 330
                                        +N +lv   
  gene1364|gene1364|rna1364|rna1364 199 VNTFLVNLD 207
                                        999999755 PP

>> Parvo_NS1  Parvovirus non-structural protein NS1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   0.00019     0.087     110     138 ..     101     129 ..      94     187 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00019
                          Parvo_NS1 110 qlgkrntvwfyGpantGktnlaeaIakav 138
                                         +g   tv+++Gpa tGk+ l +aIa  +
  gene1364|gene1364|rna1364|rna1364 101 SMGISRTVLLHGPAGTGKSALCRAIAAKI 129
                                        556667*******************9754 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00029      0.13      20      44 ..     105     127 ..      93     137 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00029
                             AAA_29  20 dlkgatlltGpsGsGKSTllDAiqa 44 
                                        +   ++ll Gp G+GKS+l  Ai+a
  gene1364|gene1364|rna1364|rna1364 105 S--RTVLLHGPAGTGKSALCRAIAA 127
                                        3..469*************999876 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00024      0.11      21      57 ..     106     141 ..      95     186 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00024
                                        EEEEEEESTTSSHHHHHHHHCCSHCCCCCCBTEEEEE CS
                             NB-ARC  21 lvvalvGmgGvGKttlakqilnksdevegrFdsvawv 57 
                                          v l+G +G GK+ l + i  k   v+ +    + v
  gene1364|gene1364|rna1364|rna1364 106 RTVLLHGPAGTGKSALCRAIAAK-IAVRTKHTKTVEV 141
                                        4688****************999.7777666665555 PP

>> PIF1  PIF1-like helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       8.8   3.9e+03       8      34 ..      21      47 ..      19      49 .. 0.82
   2 ?   10.8   0.0   0.00045       0.2      22      55 ..     105     138 ..      93     179 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 8.8
                                       HHHHHH......HCTS-EEEEESTTSS CS
                               PIF1  8 kvfdaiieavlnekgklfFvtGsgGtg 34
                                       + f++i+   ++ +g ++  +G+ G+ 
  gene1364|gene1364|rna1364|rna1364 21 RLFNTIVSLNTQYNGSTMICEGYTGST 47
                                       568889888889999999999999975 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00045
                                        TS-EEEEESTTSSCHHHHHHHHHHCHCTCCCEEE CS
                               PIF1  22 gklfFvtGsgGtgKtflwkallkklrsegkivla 55 
                                        ++++ ++G +GtgK+ l +a+ +k+  + k + +
  gene1364|gene1364|rna1364|rna1364 105 SRTVLLHGPAGTGKSALCRAIAAKIAVRTKHTKT 138
                                        678899*****************99776555433 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.4   0.00022     0.098      34      59 ..     106     133 ..      91     148 .. 0.81
   2 ?   -1.0   0.0       2.4   1.1e+03     131     154 ..     156     179 ..     140     185 .. 0.74
   3 ?   -2.4   0.1       6.5   2.9e+03     115     139 ..     296     321 ..     275     324 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00022
                             AAA_25  34 elallaGapgtGKttlaldlalava..t 59 
                                         ++ll G+ gtGK++l+  +a+++a  t
  gene1364|gene1364|rna1364|rna1364 106 RTVLLHGPAGTGKSALCRAIAAKIAvrT 133
                                        5789********************9633 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 2.4
                             AAA_25 131 daleaaieevegvrlvviDplsra 154
                                        ++l +  ++v +  +v+iD ++++
  gene1364|gene1364|rna1364|rna1364 156 HKLNELFKSVDKHTVVIIDEVDSL 179
                                        455555555555699****98875 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 6.5
                             AAA_25 115 pLfakdrggtl.ltadvdaleaaiee 139
                                        +Lf +++++ + ++  +d+le+ iee
  gene1364|gene1364|rna1364|rna1364 296 MLFCAMHRDVRtVDDILDRLERIIEE 321
                                        35555555555477778888888776 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00052      0.23       2      38 ..     106     143 ..     105     177 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00052
                          PduV-EutP   2 kkilliGkvgsGKttLtqalkge.elkYkktqaiefsd 38 
                                        + +ll G+ g+GK +L++a+  + +++ k t+++e+++
  gene1364|gene1364|rna1364|rna1364 106 RTVLLHGPAGTGKSALCRAIAAKiAVRTKHTKTVEVHS 143
                                        5799****************985377888899988876 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.1       1.6     7e+02      12      42 ..      19      57 ..      19      80 .. 0.72
   2 ?   10.0   0.1    0.0016      0.71       2      36 ..     108     141 ..     107     215 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 1.6
                                       HHHHHHHHH.......TSTEEESSSTTSSSSE.EEEEEE CS
                           MMR_HSR1 12 KStLinalt.......gekaivsdkpgtTrdi.negrvk 42
                                       K+ L+n+++       g++ i + + g Tr+   ++rv+
  gene1364|gene1364|rna1364|rna1364 19 KTRLFNTIVslntqynGSTMICEGYTGSTRHLsGTFRVT 57
                                       888999998444444336889999999999984455554 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0016
                                        EEEEESTTSSHHHHHHHHHTS.TEEESSSTTSSSSE CS
                           MMR_HSR1   2 vaivGrpNvGKStLinaltge.kaivsdkpgtTrdi 36 
                                        v++ G   +GKS L +a+  + +++++++  +T ++
  gene1364|gene1364|rna1364|rna1364 108 VLLHGPAGTGKSALCRAIAAKiAVRTKHT--KTVEV 141
                                        788999************98733344444..44444 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   1.6    0.0014      0.61      10      65 ..     105     165 ..      96     194 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0014
                             AAA_19  10 ekvllvtaGpGtGKTrvlkhivall.velggvkp....eeillvaftgrAakelrerlaal 65 
                                        ++++l+ +++GtGK+ + ++i a + v++++ k        ++  f g +a++l+e  +++
  gene1364|gene1364|rna1364|rna1364 105 SRTVLLHGPAGTGKSALCRAIAAKIaVRTKHTKTvevhSAQYVSKFYGESAHKLNELFKSV 165
                                        6899***********9998887654144444444333333444556777777777766555 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.1    0.0029       1.3      13      42 ..     101     130 ..      91     157 .. 0.69
   2 ?   -0.1   0.1       1.4   6.5e+02     209     225 ..     160     175 ..     150     177 .. 0.75
   3 ?    0.1   0.0       1.2   5.6e+02      47      78 ..     286     318 ..     245     327 .. 0.60

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0029
                             AAA_11  13 alseseitliqGPPGtgKTktivellsqll 42 
                                         +  s  +l++GP GtgK+    ++ ++++
  gene1364|gene1364|rna1364|rna1364 101 SMGISRTVLLHGPAGTGKSALCRAIAAKIA 130
                                        44444468***********87777777774 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1.4
                             AAA_11 209 klleklakkfdvviIDE 225
                                        +l+++++ k  vviIDE
  gene1364|gene1364|rna1364|rna1364 160 ELFKSVD-KHTVVIIDE 175
                                        4455554.999*****9 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 1.2
                             AAA_11  47 seeeksakpriLvCapSN..aAvDellerllrgl 78 
                                          +++++ +++L Ca       vD++l+rl r +
  gene1364|gene1364|rna1364|rna1364 286 GTASARRIKKMLFCAMHRdvRTVDDILDRLER-I 318
                                        55678888999999976522579999999877.3 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.1         2   8.8e+02     127     210 ..       4      88 ..       1     105 [. 0.64
   2 ?    6.4   0.0     0.011         5      19      42 ..     105     128 ..      86     139 .. 0.84
   3 ?    3.5   0.2     0.086        39     105     143 ..     152     191 ..     128     213 .. 0.76

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 2
                             ATPase 127 sitgl.ayeekeavaReilrqlvrvlkklgvTailvsekss..seeaaggygveefivdgvivLdlkeieeelvRt 199
                                        s++ l  +++k a +++ l++ +  l+  +  + +++e  +  + +  g+++v +   +  i++ + +++   + +
  gene1364|gene1364|rna1364|rna1364   4 SLSKLvIETTKRANLKTRLFNTIVSLNTQYNGSTMICEGYTgsTRHLSGTFRVTK---ETKIKVYKGTARLFYELV 76 
                                        6777777788888888888888888877777777777755522222334455555...666666666666666667 PP

                             ATPase 200 lei.vkmRgtkh 210
                                        ++i vk+R+ +h
  gene1364|gene1364|rna1364|rna1364  77 IDIaVKYRILDH 88 
                                        766457776666 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.011
                             ATPase  19 grvvlitGepGtGKtifalqFlik 42 
                                         r+vl+ G +GtGK+ ++   + k
  gene1364|gene1364|rna1364|rna1364 105 SRTVLLHGPAGTGKSALCRAIAAK 128
                                        589************999766655 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.086
                             ATPase 105 eelieelaeaikeika.krvviDsitglayeekeavaRei 143
                                         e +++l+e  k++   + v+iD +++l  + ++  aR++
  gene1364|gene1364|rna1364|rna1364 152 GESAHKLNELFKSVDKhTVVIIDEVDSLIVSRDQICARNE 191
                                        555678888888887758899*******888888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (328 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       940  (0.052429); expected 358.6 (0.02)
Passed bias filter:                      684  (0.0381505); expected 358.6 (0.02)
Passed Vit filter:                       115  (0.00641419); expected 17.9 (0.001)
Passed Fwd filter:                        40  (0.00223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              40  [number of targets reported over threshold]
# CPU time: 0.69u 0.36s 00:00:01.04 Elapsed: 00:00:00.53
# Mc/sec: 1859.58
//
Query:       gene1365|gene1365|rna1365|rna1365  [L=378]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.9e-40  138.3   0.0    3.5e-40  137.4   0.0    1.4  1  NMT             Myristoyl-CoA:protein N-myristoyltransferase,
    8.4e-19   67.9   0.0    1.4e-18   67.2   0.0    1.3  1  NMT_C           Myristoyl-CoA:protein N-myristoyltransferase,
    3.9e-06   27.1   0.2    8.9e-05   22.7   0.0    2.8  2  Acetyltransf_1  Acetyltransferase (GNAT) family
     0.0089   16.4   0.0      0.047   14.1   0.0    2.1  2  Acetyltransf_7  Acetyltransferase (GNAT) domain
  ------ inclusion threshold ------
      0.045   13.8   0.0       0.12   12.5   0.0    1.6  2  Acetyltransf_9  Acetyltransferase (GNAT) domain


Domain annotation for each model (and alignments):
>> NMT  Myristoyl-CoA:protein N-myristoyltransferase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  137.4   0.0   9.8e-44   3.5e-40       7     158 ..      50     196 ..      45     198 .. 0.95

  Alignments for each domain:
  == domain 1  score: 137.4 bits;  conditional E-value: 9.8e-44
                                        -GGGS-SS----STTEEEEE--TTSHHHHHHHHHHHHHHSSCTTTSTEEE---HHHHHHHCTSTT--GGGEEEEEE CS
                                NMT   7 kveevrkeplklpkgfewvtvdledeeelkevyelLsenYvedddamfrfkyskeflkWalkppgykkewhvgvrv 82 
                                        +++ vrk+pl+lp g+++   +   ++e++++y +L++nYvedd  +fr++ys efl W++  ++++++++v v+ 
  gene1365|gene1365|rna1365|rna1365  50 PLKGVRKTPLDLPFGLRFECAQ---PSEYRDIYAFLRDNYVEDDVGSFRLTYSYEFLCWEFGGKRTCPDYCVLVKD 122
                                        6788*************99887...99**********************************************996 PP

                                        TTTTEEEEEEEEEEEEEEETTEEEEEEEEEEEEE-GGGTTSSHHHHHHHHHHHHHHTTT--EEEEEESSTSSSESE CS
                                NMT  83 kkskkLvafisaipvklrvrkkvlklveinfLcvhkklRskrlapvlikEitRrvnlkgifqavytagvvlpkpvs 158
                                          ++++++f+ a ++++ ++ ++  l+++n+Lc+hk++R+k+lap++i Ei+Rrvn++gi  a++t++  lp +++
  gene1365|gene1365|rna1365|rna1365 123 --DHTIIGFVFAKEHDVVINGTKHVLASVNYLCIHKTFRNKNLAPLMITEIQRRVNMRGIACAIFTGALKLPFSIC 196
                                        ..889***************99999***********************************************9886 PP

>> NMT_C  Myristoyl-CoA:protein N-myristoyltransferase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.2   0.0   3.9e-22   1.4e-18      58     193 ..     256     371 ..     223     375 .. 0.83

  Alignments for each domain:
  == domain 1  score: 67.2 bits;  conditional E-value: 3.9e-22
                                        E--HHHHHHHHC-SSTTSBTTTEEEEEEEETTS.EEEEEEEEEE--EEETT-SS-SEEEEEEEEEEEECCCTTHHH CS
                              NMT_C  58 vfseeeveHwllskkkkreeqvvwsYVvedeetkkitDfvSFYslpstvlknpkhktlkaAYlfyyastetkklkk 133
                                        +f          +++ + +e++++ YV+e +    +  f SFY l+s ++kn+  k++k AYl + +  ++     
  gene1365|gene1365|rna1365|rna1365 256 EFC---------TEMLACNERIMQFYVIEHDG--VLQAFGSFYFLSSLAVKNE--KEIKGAYLMHLVGPAK----- 313
                                        332.........22224689********9765..7************999886..68**********9999..... PP

                                        HHHHHHHHHHHHHHHCTESEEEEESSTTGGGCTTTTT-EEEEEEEEEEEETEEE.-..-S CS
                              NMT_C 134 rlkeLvkdalilakkakfDvfnaltlmdnklfleelkFgagdgkLnYYLyNyrvapiagg 193
                                          +eL+++++ +a +++ +vfnal + + + ++e+lkF  g g LnYY++Ny + p+++g
  gene1365|gene1365|rna1365|rna1365 314 --QELLAEMIDVACEQGAHVFNALAIANREGMFEDLKFLRGTGWLNYYFFNYSTLPMTSG 371
                                        ..99**************************************************998765 PP

>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.0   2.5e-08   8.9e-05      30      94 ..     110     180 ..      75     192 .. 0.75
   2 ?    1.6   0.1     0.088   3.2e+02      63      63 ..     241     241 ..     186     338 .. 0.63

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 2.5e-08
                                        STTC.EEEE.EEETTEEEEEEEEEEEET....TSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHTTE CS
                     Acetyltransf_1  30 leae.gllv.aeedgeliGfisllkipd....ekggvayieslaVspeyrgkGlGsaLlealeerareegi 94 
                                        + ++  ++v +++d ++iGf+ ++  +     +k   a ++ l +++++r+k+l+ ++++++ +r+  +gi
  gene1365|gene1365|rna1365|rna1365 110 KRTCpDYCVlVKDDHTIIGFVFAKEHDVvingTKHVLASVNYLCIHKTFRNKNLAPLMITEIQRRVNMRGI 180
                                        34455455559999*******7777777***9999****************************99988877 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.088
                                        E CS
                     Acetyltransf_1  63 i 63 
                                        i
  gene1365|gene1365|rna1365|rna1365 241 I 241
                                        2 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.0   1.3e-05     0.047       3      49 ..     116     171 ..     114     200 .. 0.76
   2 ?   -1.3   0.0      0.88   3.2e+03       4      33 ..     270     295 ..     267     303 .. 0.59

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.3e-05
                                        EEEEEEEETTEEEEEEEEEEES..........TCTEEEEE-GGGTTSSHHHHHHHHT CS
                     Acetyltransf_7   3 gevfVaeddgkivGfialslld..........aeitrlaVdpeyrgkGiGraLleaa 49 
                                        ++v+ ++dd  i+Gf+ ++++d          a+ ++l++++ +r+k ++  +++ +
  gene1365|gene1365|rna1365|rna1365 116 YCVL-VKDDHTIIGFVFAKEHDvvingtkhvlASVNYLCIHKTFRNKNLAPLMITEI 171
                                        4455.899**************999887666555555*************9999852 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.88
                                        EEEEEEETTEEEEEEEEEEESTCTEEEEE- CS
                     Acetyltransf_7   4 evfVaeddgkivGfialslldaeitrlaVd 33 
                                        +++V+e+dg    f +++     +  laV+
  gene1365|gene1365|rna1365|rna1365 270 QFYVIEHDGVLQAFGSFYF----LSSLAVK 295
                                        6899999855544333222....2235655 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   3.3e-05      0.12      13     113 ..      78     186 ..      67     195 .. 0.78
   2 ?   -2.3   0.0       1.2   4.4e+03       3      23 ..     231     251 ..     229     305 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.3e-05
                                        HHHHHHHHTT----H..........HHHHHHHHHHTTSEEEEEEETTEEEEEEEEEEEEEEETTEEEEEEEEEEEE CS
                     Acetyltransf_9  13 vlellkyaFqdeespl.......e.eireyfrklleesrvlgaedngelvgqlallplelnvpGktlkaagvtgVa 80 
                                        ++++l+  + +++          e   +e+  k++ ++ ++++ d+ +++g + +  +++ ++G++   a v   +
  gene1365|gene1365|rna1365|rna1365  78 IYAFLRDNYVEDDVGSfrltysyEfLCWEFGGKRTCPDYCVLVKDDHTIIGFVFAKEHDVVINGTKHVLASVNYLC 153
                                        5555555555544444444444434455666666668999************************************ PP

                                        E-CCGTTS-HHHHHHHHHHHHHHHTT--EEEE- CS
                     Acetyltransf_9  81 vapehrgrgvlskLlaraleemreegqplsllf 113
                                         + + r++ ++  ++++  ++++ +g+  ++ +
  gene1365|gene1365|rna1365|rna1365 154 IHKTFRNKNLAPLMITEIQRRVNMRGIACAIFT 186
                                        ****************99999999999888766 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.2
                                        EEE-GGGHHHHHHHHHHHTT- CS
                     Acetyltransf_9   3 relteedldevlellkyaFqd 23 
                                        r+++ +dl e+ +l ++   +
  gene1365|gene1365|rna1365|rna1365 231 RRARASDLAEIRRLNNELHTY 251
                                        777777777777776655444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (378 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       458  (0.0255452); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 2572.37
//
Query:       gene1366|gene1366|rna1366|rna1366  [L=34]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (34 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       192  (0.0107089); expected 358.6 (0.02)
Passed bias filter:                      157  (0.00875676); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.28s 00:00:00.63 Elapsed: 00:00:00.44
# Mc/sec: 232.62
//
Query:       gene1367|gene1367|rna1367|rna1367  [L=64]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0038   17.7  14.0     0.0043   17.5  14.0    1.0  1  Nop25     Nucleolar protein 12 (25kDa)
  ------ inclusion threshold ------
        1.9    8.6   9.6       0.23   11.5   5.6    1.6  2  REV       REV protein (anti-repression trans-activator protei


Domain annotation for each model (and alignments):
>> Nop25  Nucleolar protein 12 (25kDa)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5  14.0   4.8e-07    0.0043       2      56 ..       5      58 ..       4      62 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 4.8e-07
                              Nop25  2 kkakkkkveevtFDkdsRkeYLTGFhKRKlqRqkkAqeeakeqereerieeRkkl 56
                                       +k+k++++eevtFD++sR+ +L  ++  K+++ k  +e  +++ r++r++ Rk+l
  gene1367|gene1367|rna1367|rna1367  5 RKRKRFQKEEVTFDEASRQAFLNSYKGNKKKKGKSTRESRTNK-RRRRMDRRKEL 58
                                       89999************************99999999887665.66788888875 PP

>> REV  REV protein (anti-repression trans-activator protein)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.1      0.21   1.8e+03      42      49 ..       5      12 ..       3      28 .. 0.61
   2 ?   11.5   5.6   2.6e-05      0.23      23      52 ..      29      58 ..      11      62 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.21
                                REV 42 rrrrrerq 49
                                       r+r+r ++
  gene1367|gene1367|rna1367|rna1367  5 RKRKRFQK 12
                                       33333332 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 2.6e-05
                                REV 23 yqsnPyPqgeGtasarrnrrrrrrerqlrl 52
                                       y+ n   +g+ t+++r n+rrrr +r+++l
  gene1367|gene1367|rna1367|rna1367 29 YKGNKKKKGKSTRESRTNKRRRRMDRRKEL 58
                                       7899999***************99888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (64 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1633  (0.0910815); expected 358.6 (0.02)
Passed bias filter:                      565  (0.0315132); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 470.18
//
Query:       gene1368|gene1368|rna1368|rna1368  [L=144]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.033   14.2   1.9      0.055   13.5   1.9    1.3  1  DUF3593   Protein of unknown function (DUF3593)


Domain annotation for each model (and alignments):
>> DUF3593  Protein of unknown function (DUF3593)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   1.9   3.1e-06     0.055      14      76 ..       2      62 ..       1      64 [. 0.75

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.1e-06
                            DUF3593 14 lFLvll.kkskelpkltlvGfallLlFvavtipagivakevygesLanvDlLHGlaeslLtlsn 76
                                       lFL+ll k++k++ k++++   llL+Fv v  ++ ++  + +  ++a +D+  G +e  +++ n
  gene1368|gene1368|rna1368|rna1368  2 LFLLLLfKNNKKFLKIAIA--LLLLVFVYVVCFM-VYILKNVVIEIASIDIVDGYIETRVSVCN 62
                                       6888884555558777765..7899999986555.55555566789*************99988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1125  (0.0627475); expected 358.6 (0.02)
Passed bias filter:                      540  (0.0301188); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1084.91
//
Query:       gene1369|gene1369|rna1369|rna1369  [L=41]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (41 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       191  (0.0106531); expected 358.6 (0.02)
Passed bias filter:                      169  (0.00942607); expected 358.6 (0.02)
Passed Vit filter:                         5  (0.000278878); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.25s 00:00:00.59 Elapsed: 00:00:00.41
# Mc/sec: 303.17
//
Query:       gene137|gene137|rna137|rna137  [L=128]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       431  (0.0240393); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.28s 00:00:00.67 Elapsed: 00:00:00.44
# Mc/sec: 882.03
//
Query:       gene1370|gene1370|rna1370|rna1370  [L=73]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (73 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       273  (0.0152267); expected 358.6 (0.02)
Passed bias filter:                      224  (0.0124937); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 504.95
//
Query:       gene1371|gene1371|rna1371|rna1371  [L=199]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       460  (0.0256568); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1377.82
//
Query:       gene1372|gene1372|rna1372|rna1372  [L=229]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.029   14.9   4.5       0.22   12.1   0.6    2.9  2  Hrs_helical   Hepatocyte growth factor-regulated tyrosine kin
      0.062   13.5   4.7       0.05   13.8   3.3    1.7  1  DUF3347       Protein of unknown function (DUF3347)
      0.094   11.8   2.2       0.13   11.4   2.2    1.4  1  Atg14         Vacuolar sorting 38 and autophagy-related subun
       0.11   12.4   2.3       0.71    9.8   0.1    2.9  3  Qua1          Qua1 domain
       0.12   12.1  10.7       0.61    9.7  10.5    2.2  2  BAR           BAR domain
       0.12   12.4   8.7       0.22   11.5   2.4    2.7  2  TMF_DNA_bd    TATA element modulatory factor 1 DNA binding
       0.14   12.6   5.4       0.49   10.9   5.2    1.9  1  T3SSipB       Type III cell invasion protein SipB
       0.14   11.3   4.9      0.075   12.3   1.7    1.8  2  TMPIT         TMPIT-like protein
       0.16   12.0   4.5       0.16   12.0   2.0    2.3  1  Laminin_II    Laminin Domain II
       0.25   11.2   6.6       0.31   10.9   6.5    1.3  1  FTA4          Kinetochore complex Fta4 of Sim4 subunit, or CE
       0.31   10.9   5.5       0.62    9.9   1.0    2.9  3  Sec34         Sec34-like family
       0.56   10.5   3.0        2.6    8.4   1.3    2.7  2  Glu-tRNAGln   Glu-tRNAGln amidotransferase C subunit
       0.56   10.3   4.7        2.9    7.9   1.4    3.0  3  DUF1664       Protein of unknown function (DUF1664)
       0.64   10.3  13.6       0.61   10.3   1.9    2.9  3  Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain
       0.68    9.2   6.2       0.94    8.8   6.2    1.2  1  FAM76         FAM76 protein
       0.89   10.2   3.3        1.7    9.4   0.8    2.4  2  DUF4404       Domain of unknown function (DUF4404)
        1.3    8.6   9.3        1.2    8.7   6.9    1.9  2  DUF4795       Domain of unknown function (DUF4795)
        2.5    8.3   7.8        1.8    8.7   4.8    2.3  3  CREPT         Cell-cycle alteration and expression-elevated p


Domain annotation for each model (and alignments):
>> Hrs_helical  Hepatocyte growth factor-regulated tyrosine kinase substrate
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.6   0.00023      0.22      16      85 ..      65     134 ..      60     144 .. 0.84
   2 ?    4.7   0.5     0.043        43      59      83 ..     129     153 ..     125     170 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00023
                        Hrs_helical  16 rmksnsarGrsianDsavqslFqkltamhsqllkriqeqeekraeyeslqdklaqikearealdalreeh 85 
                                         m+  +  Gr + +Ds     F k t++  + ++++q+++  ++  e+  d  + +++a+  +++  e+ 
  gene1372|gene1372|rna1372|rna1372  65 AMRAIEVVGRRVKKDSFEVRSFYKETELTGREIAKVQSNDALKSLAEKYSDAFSAVEDAKVKMNEEYEDI 134
                                        69999999*******97666666779**********************************9887655554 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.043
                        Hrs_helical  59 aeyeslqdklaqikearealdalre 83 
                                        +eye + +++++++e+ +a+d+ r 
  gene1372|gene1372|rna1372|rna1372 129 EEYEDIIKHIKELQESSRAIDEKRA 153
                                        5678888888888888888887665 PP

>> DUF3347  Protein of unknown function (DUF3347)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   3.3     5e-05      0.05      70     145 ..     104     174 ..      39     180 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 5e-05
                            DUF3347  70 keakkaakkleeklkavdtsklkekekkelkeiseelkekaekiaesk.dieeqReaFkklsedliklvkafglke 144
                                        ++ k+ a+k +++++av      e++k +++e  e++ +++++++es+  i+e+R++  +l  dl+k+ k+ +  +
  gene1372|gene1372|rna1372|rna1372 104 DALKSLAEKYSDAFSAV------EDAKVKMNEEYEDIIKHIKELQESSrAIDEKRANVLNLRYDLEKMYKKKSPGN 173
                                        33444455555555555......88888999999**********999879*******************9988776 PP

                            DUF3347 145 k 145
                                        +
  gene1372|gene1372|rna1372|rna1372 174 E 174
                                        6 PP

>> Atg14  Vacuolar sorting 38 and autophagy-related subunit 14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   2.2   0.00013      0.13      33     124 ..      75     168 ..      20     193 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00013
                              Atg14  33 klksekeslkkkiekalegke..eaeqledkiknkkakleelksliadlrerlqelkdklsqlkkeieekkkklak 106
                                        ++k++++++++ +++ + + +  ++ q++d++k++++k ++  s ++d + +++e  +++ +  ke++e ++ + +
  gene1372|gene1372|rna1372|rna1372  75 RVKKDSFEVRSFYKETELTGReiAKVQSNDALKSLAEKYSDAFSAVEDAKVKMNEEYEDIIKHIKELQESSRAIDE 150
                                        455555555555554333333577779999**********************999999999999999999999999 PP

                              Atg14 107 lsdklkkRrsdleslqne 124
                                        +++++   r dle+++++
  gene1372|gene1372|rna1372|rna1372 151 KRANVLNLRYDLEKMYKK 168
                                        999999999998888776 PP

>> Qua1  Qua1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.1   0.00071      0.71      16      49 ..      85     118 ..      76     119 .. 0.86
   2 ?   -3.0   0.2       6.8   6.8e+03      40      49 ..     127     136 ..     121     137 .. 0.68
   3 ?    1.1   0.0      0.35   3.5e+02       9      34 ..     175     200 ..     173     205 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00071
                               Qua1  16 sfthamqLlsaEIekiqkgeskkdeeekYlDlfs 49 
                                        sf   ++L   EI k+q +++ k   ekY D fs
  gene1372|gene1372|rna1372|rna1372  85 SFYKETELTGREIAKVQSNDALKSLAEKYSDAFS 118
                                        7888899************************998 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 6.8
                               Qua1  40 eeekYlDlfs 49 
                                         +e+Y D++ 
  gene1372|gene1372|rna1372|rna1372 127 MNEEYEDIIK 136
                                        5788999875 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.35
                               Qua1   9 ekdSLdPsfthamqLlsaEIekiqkg 34 
                                        e d L  +f     L+++E+ ++ +g
  gene1372|gene1372|rna1372|rna1372 175 ELDNLKAEFNQEANLIKEEMKGYVGG 200
                                        78999999*9999*****99877655 PP

>> BAR  BAR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.1      0.54   5.4e+02     173     194 ..      25      49 ..       4      55 .. 0.64
   2 ?    9.7  10.5   0.00062      0.61     132     199 ..     128     195 ..      27     199 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.54
                                BAR 173 e...ekaeeelrkAqqkfeesneel 194
                                            ek ee++r  ++k e++++ +
  gene1372|gene1372|rna1372|rna1372  25 PagyEKTEEDYRIVKNKMENLKNTF 49 
                                        3556677888888888888777765 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00062
                                BAR 132 ekefkeiqkerkklehkrlDyDaakarlkklktkkskkakdeekaeeelrkAqqkfeesneelkaeLp 199
                                        ++e+++i k++k l++   ++D ++a +  l+ + +k  k+++   eel++ +++f++ ++++k+e++
  gene1372|gene1372|rna1372|rna1372 128 NEEYEDIIKHIKELQESSRAIDEKRANVLNLRYDLEKMYKKKSPGNEELDNLKAEFNQEANLIKEEMK 195
                                        578999999999999999999999999999999999999999999**********************7 PP

>> TMF_DNA_bd  TATA element modulatory factor 1 DNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.8     0.051        51      29      70 ..     100     141 ..      90     145 .. 0.80
   2 ?   11.5   2.4   0.00022      0.22       5      51 ..     146     192 ..     142     195 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.051
                         TMF_DNA_bd  29 lklnntikkLrkknkelekeikelkkkleklekeleeleerl 70 
                                        ++ n ++k+L +k +++ + +++ k k +++ +++ ++ ++l
  gene1372|gene1372|rna1372|rna1372 100 VQSNDALKSLAEKYSDAFSAVEDAKVKMNEEYEDIIKHIKEL 141
                                        578999*******************88887777765555544 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00022
                         TMF_DNA_bd   5 kklkeKDeqIaqLmeEGekLskkelklnntikkLrkknkelekeike 51 
                                          ++eK + + +L++ +ek  kk    n+ +++L+++ ++  + ike
  gene1372|gene1372|rna1372|rna1372 146 RAIDEKRANVLNLRYDLEKMYKKKSPGNEELDNLKAEFNQEANLIKE 192
                                        5699*********************************9999988875 PP

>> T3SSipB  Type III cell invasion protein SipB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   5.2   0.00049      0.49      26      94 ..      95     180 ..      88     224 .. 0.55

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00049
                                        HHHHHHHHHHHTTTTT----STHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH............. CS
                            T3SSipB  26 rlaawkamskaqqeaasklSdelqtalseakgatddleaaiekadqaksaadaatkkvdeaqk............. 88 
                                        r  a ++   a +  a+k Sd++  + ++  ++ +++e+ i+++++++    a ++k  ++++             
  gene1372|gene1372|rna1372|rna1372  95 REIAKVQSNDALKSLAEKYSDAFSAVEDAKVKMNEEYEDIIKHIKELQESSRAIDEKRANVLNlrydlekmykkks 170
                                        3334444455555555666666665555555666666666666666666666665555555554442222111111 PP

                                        ....HHTT-- CS
                            T3SSipB  89 ....rlkeLa 94 
                                             l++L+
  gene1372|gene1372|rna1372|rna1372 171 pgneELDNLK 180
                                        1111555552 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.1      0.41   4.1e+02      14      60 ..       3      49 ..       1     101 [. 0.63
   2 ?   12.3   1.7   7.5e-05     0.075       5      88 ..     111     197 ..     106     207 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.41
                              TMPIT 14 leetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksv 60
                                       +++++k++ +k++++   + ++    +k +++++ +k+++++lk++ 
  gene1372|gene1372|rna1372|rna1372  3 MQSRFKNLLRKVDRIDYVNADFPAGYEKTEEDYRIVKNKMENLKNTF 49
                                       56677777777777777777777777777777777777777777663 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 7.5e-05
                              TMPIT   5 eelekefkeleetakeykqkleelsklqskcs...keikkqkkrlkelksslkklkksvkeeeeeeveelkeelke 77 
                                        e+ ++ f ++e+++ +++++ e++ k++++++   ++i++++ ++ +l+ +l+k+ k+ k+  +ee+++lk+e+++
  gene1372|gene1372|rna1372|rna1372 111 EKYSDAFSAVEDAKVKMNEEYEDIIKHIKELQessRAIDEKRANVLNLRYDLEKMYKK-KSPGNEELDNLKAEFNQ 185
                                        5678889999999999999999988888766511156888899999999*****9999.5688999********** PP

                              TMPIT  78 rkkvlk.evesl 88 
                                        + + +k e++ +
  gene1372|gene1372|rna1372|rna1372 186 EANLIKeEMKGY 197
                                        *99999778776 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   2.0   0.00016      0.16      24      86 ..      88     149 ..      69     164 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00016
                                        XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH.. CS
                         Laminin_II  24 qnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqleeass 86 
                                        +++e t  ++ +++++ +  + ++++++ a   ++++ +k++++ +++++ +kel++ + a  
  gene1372|gene1372|rna1372|rna1372  88 KETELTGREIAKVQSN-DALKSLAEKYSDAFSAVEDAKVKMNEEYEDIIKHIKELQESSRAID 149
                                        5666777788899998.899999999999999*******************999998887744 PP

>> FTA4  Kinetochore complex Fta4 of Sim4 subunit, or CENP-50
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   6.5   0.00031      0.31      86     178 ..      92     180 ..      14     195 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00031
                               FTA4  86 dekleievnedltkeelIkeLPesweveekeaeeepleallerYaelrarLielserrqqlqarlarlrklkalle 161
                                         + +ei   ++  +++  k+L e+ + ++ +a e+ + + +e+Y+++ ++++el+e+ ++  ++ a   +l+  le
  gene1372|gene1372|rna1372|rna1372  92 LTGREI---AKVQSNDALKSLAEKYS-DAFSAVEDAKVKMNEEYEDIIKHIKELQESSRAIDEKRANVLNLRYDLE 163
                                        222222...55566999999999998.55666666677779*********************************** PP

                               FTA4 162 pflgsedpqesvqenlv 178
                                        ++ + ++p ++  +nl 
  gene1372|gene1372|rna1372|rna1372 164 KMYKKKSPGNEELDNLK 180
                                        **998888888877775 PP

>> Sec34  Sec34-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.1      0.24   2.4e+02      42      42 ..      23      23 ..       1      68 [. 0.46
   2 ?    9.9   1.0   0.00062      0.62      20      67 ..     104     151 ..      95     168 .. 0.85
   3 ?   -1.1   0.0       1.5   1.5e+03      35      35 ..     185     185 ..     153     228 .. 0.57

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.24
                              Sec34 42 s 42
                                       +
  gene1372|gene1372|rna1372|rna1372 23 D 23
                                       2 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00062
                              Sec34  20 dealeqLeeleekfksvsektsslheaceqlleeqkrleelaeeieek 67 
                                        d+++++ e+ ++ f++v++   +++e+ e+++++ k+l+e +++i+ek
  gene1372|gene1372|rna1372|rna1372 104 DALKSLAEKYSDAFSAVEDAKVKMNEEYEDIIKHIKELQESSRAIDEK 151
                                        3444455678999*******************************9986 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 1.5
                              Sec34  35 s 35 
                                        +
  gene1372|gene1372|rna1372|rna1372 185 Q 185
                                        2 PP

>> Glu-tRNAGln  Glu-tRNAGln amidotransferase C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.69   6.8e+02       8      28 ..       2      22 ..       1      48 [. 0.78
   2 ?    8.4   1.3    0.0026       2.6       4      27 ..     122     145 ..     120     192 .. 0.72

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.69
                                       HHHHHHHHHHHHHTTCGCS-- CS
                        Glu-tRNAGln  8 klakelnsildyveqLqevdt 28
                                       ++++ +++ l  v+ ++ v+ 
  gene1372|gene1372|rna1372|rna1372  2 QMQSRFKNLLRKVDRIDYVNA 22
                                       689999999999999998884 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0026
                                        HHHHHHHHHHHHHHHHHTTCGCS- CS
                        Glu-tRNAGln   4 eEleklakelnsildyveqLqevd 27 
                                        + + k+ +e ++i++++++Lqe  
  gene1372|gene1372|rna1372|rna1372 122 DAKVKMNEEYEDIIKHIKELQESS 145
                                        55789****************966 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0      0.35   3.5e+02      62     101 ..       8      47 ..       2      54 .. 0.64
   2 ?    7.9   1.4    0.0029       2.9      40     101 ..     103     167 ..      97     185 .. 0.79
   3 ?   -0.9   0.0       1.6   1.6e+03      33      52 ..     208     227 ..     196     229 .] 0.46

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.35
                            DUF1664  62 rhLssridrvdkkldeqkeiskeikeevtevredlseige 101
                                        ++L +++dr+d    +  +  ++++e+   v+++++++++
  gene1372|gene1372|rna1372|rna1372   8 KNLLRKVDRIDYVNADFPAGYEKTEEDYRIVKNKMENLKN 47 
                                        5666677777776666777777777777777777776665 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0029
                            DUF1664  40 sdavesvskqleqvseslaatkrhLssridrvdkkldeqkeiskeike...evtevredlseige 101
                                        +da++s++++  +  ++++++k +++++ + + k+++e +e s++i+e   +v ++r dl+++ +
  gene1372|gene1372|rna1372|rna1372 103 NDALKSLAEKYSDAFSAVEDAKVKMNEEYEDIIKHIKELQESSRAIDEkraNVLNLRYDLEKMYK 167
                                        689999999999999**********9999999988888888887776511157777878777755 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 1.6
                            DUF1664  33 fvTkrslsdavesvskqleq 52 
                                            + ++ + +++s+ le+
  gene1372|gene1372|rna1372|rna1372 208 KRACKAMATFSKEISTALET 227
                                        33334444444444444444 PP

>> Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       3.8   3.8e+03      35      49 ..      32      46 ..      26      49 .. 0.54
   2 ?    5.3   3.5     0.022        22      51      98 ..     101     153 ..      63     158 .. 0.54
   3 ?   10.3   1.9   0.00062      0.61      30      86 ..     161     224 ..     150     229 .] 0.69

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 3.8
                                       HHHHHHHHHHHHHHH CS
                       Seryl_tRNA_N 35 dekrrelqveleelq 49
                                       +e  r +++++e+l+
  gene1372|gene1372|rna1372|rna1372 32 EEDYRIVKNKMENLK 46
                                       444555555555555 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.022
                                        HHHHHHHHCCCCCCTT.....S-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHH CS
                       Seryl_tRNA_N  51 erNelskeIgkakkkk.....edaeeliaevkelkeelkaleaelkeleaele 98 
                                        ++N + k+ +++  +      + + ++ +e +++ + +k+l++  ++++++  
  gene1372|gene1372|rna1372|rna1372 101 QSNDALKSLAEKYSDAfsaveDAKVKMNEEYEDIIKHIKELQESSRAIDEKRA 153
                                        33333334444333333333122233444555555555555555555555544 PP

  == domain 3  score: 10.3 bits;  conditional E-value: 0.00062
                                        HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTT.......S-TCCCCCCCHHHHHHHHHH CS
                       Seryl_tRNA_N  30 elleldekrrelqveleelqaerNelskeIgkakkkk.......edaeeliaevkelkeelkal 86 
                                        +l ++++k+   + el++l+ae N+ ++ I++ +k         e +++  + +++ ++e++++
  gene1372|gene1372|rna1372|rna1372 161 DLEKMYKKKSPGNEELDNLKAEFNQEANLIKEEMKGYvggkgvsEVIKRACKAMATFSKEISTA 224
                                        67888999999999********************865777444444444444444444444443 PP

>> FAM76  FAM76 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   6.2   0.00095      0.94     195     287 ..      90     185 ..      27     195 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00095
                              FAM76 195 k....laeekesnetskksldsnssdhlvavtqLkeeiaslkkqleqkdqellekdkkitelkaellekekelrek 266
                                        +    +  +k +++++ ksl  ++sd + av++ k ++++    + ++ +el e  + i e +a+ l+ + +l+ k
  gene1372|gene1372|rna1372|rna1372  90 TeltgREIAKVQSNDALKSLAEKYSDAFSAVEDAKVKMNEEYEDIIKHIKELQESSRAIDEKRANVLNLRYDLE-K 164
                                        123333444556667778999***********************************************999985.7 PP

                              FAM76 267 lkelekeakekieklekkire 287
                                        + + ++  +e++++l+++ ++
  gene1372|gene1372|rna1372|rna1372 165 MYKKKSPGNEELDNLKAEFNQ 185
                                        888899999999999987653 PP

>> DUF4404  Domain of unknown function (DUF4404)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.1         1   9.9e+02      16      56 ..      96     134 ..      89     139 .. 0.53
   2 ?    9.4   0.8    0.0017       1.7      10      56 ..     139     186 ..     136     194 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 1
                            DUF4404  16 esldeetralLeslaedieellaeedaaaeeeelaerlnea 56 
                                        e ++ ++++ L+slae+ + + +  ++a+ +  ++e+ +++
  gene1372|gene1372|rna1372|rna1372  96 EIAKVQSNDALKSLAEKYSDAFSAVEDAKVK--MNEEYEDI 134
                                        5555566666666666666555555555554..44444444 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0017
                            DUF4404  10 eeLeqnesldeetralLeslaedieellaeedaaaeeee.laerlnea 56 
                                        +eL++++++ +e+ra++ +l+ d+e++ +++++ +ee + l+ + n+ 
  gene1372|gene1372|rna1372|rna1372 139 KELQESSRAIDEKRANVLNLRYDLEKMYKKKSPGNEELDnLKAEFNQE 186
                                        699****************************99998866666666665 PP

>> DUF4795  Domain of unknown function (DUF4795)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       1.5   1.5e+03      35      54 ..      26      45 ..       2      56 .. 0.45
   2 ?    8.7   6.9    0.0012       1.2       4     122 ..     101     221 ..      98     228 .. 0.53

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.5
                            DUF4795 35 krledkekklealkkqieel 54
                                          e++e++   +k+++e+l
  gene1372|gene1372|rna1372|rna1372 26 AGYEKTEEDYRIVKNKMENL 45
                                       33333333333333333333 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0012
                            DUF4795   4 nsaellkklqeaieklqeelekleekvkelekrledkekklealkkqieelekvkadkeeveeelaekadkeaLat 79 
                                        +s+ +lk l e++++     + +e+++ +++++ ed  k+++ l+++ ++ +++ a+       l++  d e++ +
  gene1372|gene1372|rna1372|rna1372 101 QSNDALKSLAEKYSDAF---SAVEDAKVKMNEEYEDIIKHIKELQESSRAIDEKRAN------VLNLRYDLEKMYK 167
                                        55555555555554444...4446666667777777777777777777777777766......5555556666666 PP

                            DUF4795  80 kvsrdq..fDeakkeLekmleellekle.........eqeealkkaldtLqeel 122
                                        k s  +  +D+ k+e+++ ++ + e ++         e+ ++  ka+ t ++e+
  gene1372|gene1372|rna1372|rna1372 168 KKSPGNeeLDNLKAEFNQEANLIKEEMKgyvggkgvsEVIKRACKAMATFSKEI 221
                                        655444446666666666666666665555555533333334444444444444 PP

>> CREPT  Cell-cycle alteration and expression-elevated protein in tumour
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       2.8   2.8e+03      93     109 ..      29      45 ..       2      49 .. 0.65
   2 ?    8.7   4.8    0.0018       1.8      36     122 ..      96     178 ..      89     189 .. 0.71
   3 ?   -1.8   0.0       3.1   3.1e+03      48      70 ..     202     224 ..     184     227 .. 0.73

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 2.8
                              CREPT  93 akaeekleelkeklekv 109
                                        +k+ee ++ +k+k+e++
  gene1372|gene1372|rna1372|rna1372  29 EKTEEDYRIVKNKMENL 45 
                                        45566666666666655 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0018
                              CREPT  36 llekikdkeeaekllkqveealellaeYnkrLeaeleeRkklakmledfleaqkellakaeekleelkeklekvks 111
                                         ++k++++++ ++l+++ ++a +++++   ++++e e+  k  k l++  +a    ++++++++ +l+  lek+ +
  gene1372|gene1372|rna1372|rna1372  96 EIAKVQSNDALKSLAEKYSDAFSAVEDAKVKMNEEYEDIIKHIKELQESSRA----IDEKRANVLNLRYDLEKMYK 167
                                        689*********************************9976666666554333....44444444444544555444 PP

                              CREPT 112 vrkelkshiqs 122
                                        +++  ++ +++
  gene1372|gene1372|rna1372|rna1372 168 KKSPGNEELDN 178
                                        44444444444 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 3.1
                              CREPT  48 kllkqveealellaeYnkrLeae 70 
                                          ++ ++ a++++a + k ++  
  gene1372|gene1372|rna1372|rna1372 202 GVSEVIKRACKAMATFSKEISTA 224
                                        56778888999888888877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (229 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1730  (0.0964917); expected 358.6 (0.02)
Passed bias filter:                      599  (0.0334096); expected 358.6 (0.02)
Passed Vit filter:                        78  (0.00435049); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.59u 0.31s 00:00:00.89 Elapsed: 00:00:00.46
# Mc/sec: 1481.60
//
Query:       gene1373|gene1373|rna1373|rna1373  [L=795]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.9e-99  328.2   0.0    4.2e-49  166.4   0.0    2.5  2  AAA              ATPase family associated with various cellul
    4.4e-24   84.0   4.3    1.5e-12   47.1   0.0    3.5  3  AAA_lid_3        AAA+ lid domain
      5e-15   55.6   0.0    4.6e-07   29.7   0.0    3.0  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    1.7e-13   51.0   0.0    2.4e-06   27.8   0.0    2.8  2  AAA_2            AAA domain (Cdc48 subfamily)
    3.5e-11   43.8   0.1     0.0036   17.7   0.0    4.2  3  AAA_16           AAA ATPase domain
    3.3e-10   40.1   0.2    9.4e-05   22.4   0.0    3.6  2  AAA_5            AAA domain (dynein-related subfamily)
    9.4e-10   39.1   0.0     0.0018   18.8   0.0    2.9  2  AAA_18           AAA domain
    1.7e-09   38.0   0.0    0.00077   19.6   0.0    2.6  2  AAA_33           AAA domain
    1.9e-09   37.9   1.5      0.039   14.2   0.0    4.5  4  AAA_22           AAA domain
    9.2e-09   34.9   0.2     0.0051   16.0   0.0    3.2  3  TIP49            TIP49 P-loop domain
    1.3e-08   34.7   1.1      9e-06   25.6   0.1    2.9  2  Vps4_C           Vps4 C terminal oligomerisation domain
      3e-08   34.0   0.0    0.00047   20.5   0.0    2.7  2  RNA_helicase     RNA helicase
    3.7e-08   33.2   2.5       0.48   10.0   0.0    4.3  4  AAA_25           AAA domain
    3.7e-08   33.5   0.0     0.0033   17.5   0.0    2.7  2  AAA_14           AAA domain
    5.4e-08   32.8   0.3      0.018   14.8   0.0    3.5  3  IstB_IS21        IstB-like ATP binding protein
    3.7e-07   29.7   0.1      0.019   14.4   0.0    2.4  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    9.6e-07   28.4   2.2       0.42    9.9   0.0    3.9  3  ATPase           KaiC
    3.9e-06   27.2   0.0      0.072   13.3   0.0    2.5  2  AAA_28           AAA domain
      7e-06   25.3   0.0      0.043   12.9   0.0    2.5  2  Parvo_NS1        Parvovirus non-structural protein NS1
    1.7e-05   25.4   0.1       0.23   12.0   0.0    3.0  2  ABC_tran         ABC transporter
      3e-05   23.6   0.0       0.27   10.7   0.0    2.7  2  AAA_7            P-loop containing dynein motor region
    8.8e-05   22.4   0.0       0.02   14.7   0.0    2.4  2  Viral_helicase1  Viral (Superfamily 1) RNA helicase
      9e-05   22.5   0.0        0.4   10.7   0.0    2.4  2  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
    0.00013   22.4   0.0       0.88   10.0   0.0    2.8  2  AAA_17           AAA domain
    0.00014   21.6   0.0       0.28   10.9   0.0    2.6  2  AAA_24           AAA domain
    0.00018   21.5   0.2       0.68    9.8   0.0    3.5  3  ATPase_2         ATPase domain predominantly from Archaea
    0.00024   21.0   0.0       0.11   12.3   0.0    2.6  2  Bac_DnaA         Bacterial dnaA  protein
    0.00034   20.6   0.0       0.19   11.6   0.0    2.6  2  Rad17            Rad17 P-loop domain
     0.0005   19.8   0.0       0.64    9.7   0.0    3.1  2  Sigma54_activat  Sigma-54 interaction domain
    0.00051   19.3   0.0       0.44    9.7   0.0    3.1  3  NB-ARC           NB-ARC domain
    0.00054   19.5   0.1        1.2    8.6   0.0    2.6  2  PhoH             PhoH-like protein
    0.00057   19.8   0.2       0.63    9.9   0.0    3.3  3  NACHT            NACHT domain
    0.00065   18.9   0.0       0.21   10.7   0.0    2.4  2  DUF815           Protein of unknown function (DUF815)
     0.0007   19.6   0.0      0.051   13.6   0.0    2.5  2  ResIII           Type III restriction enzyme, res subunit
    0.00071   19.5   0.0        1.1    9.1   0.0    2.6  2  AAA_3            ATPase family associated with various cellul
     0.0023   17.2   0.0       0.47    9.6   0.0    2.4  2  DUF2075          Uncharacterized conserved protein (DUF2075)
     0.0057   16.0   0.0        4.3    6.6   0.0    2.7  2  Zeta_toxin       Zeta toxin
     0.0079   16.3   0.0      0.029   14.6   0.0    2.0  1  CDC48_N          Cell division protein 48 (CDC48), N-terminal
     0.0094   15.8   0.8        3.8    7.2   0.0    3.0  2  AAA_11           AAA domain
  ------ inclusion threshold ------
       0.01   16.1   0.5        2.1    8.7   0.1    2.7  2  AAA_19           AAA domain
       0.01   15.9   0.0       0.82    9.8   0.0    2.6  2  Sigma54_activ_2  Sigma-54 interaction domain
      0.015   15.2   0.4        6.5    6.6   0.0    3.5  3  NTPase_1         NTPase
      0.017   14.9   0.7      0.058   13.2   0.0    2.1  2  CDC48_2          Cell division protein 48 (CDC48), domain 2
      0.051   13.3   0.1        4.5    6.9   0.0    2.5  2  AAA_30           AAA domain
      0.071   12.8   0.1         21    4.7   0.0    2.9  2  Cytidylate_kin   Cytidylate kinase
      0.084   12.2   0.0        2.1    7.7   0.0    2.2  2  IPT              Isopentenyl transferase
       0.14   11.9   0.0         14    5.4   0.0    2.6  2  PduV-EutP        Ethanolamine utilisation - propanediol utili


Domain annotation for each model (and alignments):
>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  159.4   0.0   1.5e-49   5.9e-47       1     131 [.     247     376 ..     247     377 .. 0.98
   2 !  166.4   0.0   1.1e-51   4.2e-49       1     132 []     520     652 ..     520     652 .. 0.97

  Alignments for each domain:
  == domain 1  score: 159.4 bits;  conditional E-value: 1.5e-49
                                        EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTT CS
                                AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksrsg 76 
                                        +ll+GppGtGKTl+a+a+a+e+g+ ++ ++g+e++sk+ gese+++r++fkea+++a psi+fiDEid++a++r++
  gene1373|gene1373|rna1373|rna1373 247 ILLFGPPGTGKTLIARAIANETGAFLYVVNGPEIMSKMSGESESNLRNVFKEAEKNA-PSIIFIDEIDSIAPKREK 321
                                        69******************************************************9.****************** PP

                                        CCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
                                AAA  77 seseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieie 131
                                        s+ e+e+r+v+qLlt +dg kk + +viv+gatnrp+++dpal+r gRf r+iei+
  gene1373|gene1373|rna1373|rna1373 322 SHGEVERRIVSQLLTLMDGIKKAT-NVIVLGATNRPNSIDPALRRyGRFGREIEIG 376
                                        **********************75.5***************************986 PP

  == domain 2  score: 166.4 bits;  conditional E-value: 1.1e-51
                                        EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH.. CS
                                AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksr.. 74 
                                        +l+yGppG+GKTllakava+e++++f++++g+ell+++vgese+++r++f++a+++a p+++f+DE+d++aksr  
  gene1373|gene1373|rna1373|rna1373 520 ILFYGPPGCGKTLLAKAVASECSANFISVKGPELLNMWVGESEANVRDIFDKARSSA-PCVIFFDELDSIAKSRsn 594
                                        69******************************************************9.****************98 PP

                                        TTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETTS CS
                                AAA  75 sgseseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieiel 132
                                        s+s+s++++rv+nq+lte+dg + k++ v+vigatnrpd+ld allr gR+d+ i+i+l
  gene1373|gene1373|rna1373|rna1373 595 SSSDSGVTDRVLNQMLTEMDGISAKKN-VFVIGATNRPDQLDTALLRpGRLDQLIFIPL 652
                                        888999******************755.***************************9985 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.1   0.0   3.9e-15   1.5e-12       1      39 [.     399     437 ..     399     444 .. 0.92
   2 !   36.1   0.3   1.1e-11   4.1e-09       1      37 [.     674     710 ..     674     730 .. 0.92
   3 ?   -0.1   0.1       2.2   8.5e+02      31      44 ..     748     761 ..     741     762 .. 0.85

  Alignments for each domain:
  == domain 1  score: 47.1 bits;  conditional E-value: 3.9e-15
                          AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrrgikeit 39 
                                        dvdl+++A +T+G++G D+a+lc eAa+  +rr++++i+
  gene1373|gene1373|rna1373|rna1373 399 DVDLEKVANETHGFVGSDIASLCSEAAMQQIRRKMPKID 437
                                        9***********************************876 PP

  == domain 2  score: 36.1 bits;  conditional E-value: 1.1e-11
                          AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrrgike 37 
                                        dv+lk +Ae T+G+SGAD+a+++++A   Al+++i+ 
  gene1373|gene1373|rna1373|rna1373 674 DVNLKIIAETTKGCSGADIAEIVQRARKFALKESIQR 710
                                        9********************************9874 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 2.2
                          AAA_lid_3  31 lrrgikeitmedfe 44 
                                        l+ ++ ++t++d+e
  gene1373|gene1373|rna1373|rna1373 748 LKNTRRSVTQKDME 761
                                        7788999*****98 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.7   0.0   1.2e-09   4.6e-07      36     101 ..     247     320 ..     241     371 .. 0.84
   2 !   22.4   0.0   2.2e-07   8.5e-05      35      98 ..     519     590 ..     492     640 .. 0.71

  Alignments for each domain:
  == domain 1  score: 29.7 bits;  conditional E-value: 1.2e-09
                             RuvB_N  36 vllyGpPGlGkttlakiiakelgvklkitsgPvl......ekagdlaalltnleek..dvlfideihrlsrave 101
                                        +ll+GpPG Gkt +a+ ia+e g+ l +  gP +      e +++l  ++++ e++   ++fidei  ++++ e
  gene1373|gene1373|rna1373|rna1373 247 ILLFGPPGTGKTLIARAIANETGAFLYVVNGPEImskmsgESESNLRNVFKEAEKNapSIIFIDEIDSIAPKRE 320
                                        89******************************984433333456788888877765337*******99987765 PP

  == domain 2  score: 22.4 bits;  conditional E-value: 2.2e-07
                             RuvB_N  35 hvllyGpPGlGkttlakiiakelgvklkitsgPvl......ekagdlaalltnleekd..vlfideihrlsr 98 
                                         +l+yGpPG Gkt lak +a+e  +++ +  gP l      e ++++  ++ + +++   v+f de+  +++
  gene1373|gene1373|rna1373|rna1373 519 GILFYGPPGCGKTLLAKAVASECSANFISVKGPELlnmwvgESEANVRDIFDKARSSApcVIFFDELDSIAK 590
                                        58*******************************873333333445555555554443233677777666655 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.8   0.0   6.3e-09   2.4e-06       6     105 ..     247     340 ..     242     346 .. 0.88
   2 !   20.2   0.0   1.4e-06   0.00052       6     102 ..     520     612 ..     515     629 .. 0.71

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 6.3e-09
                                        EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG CS
                              AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidK 79 
                                        ill gp g+Gkt++a+a+a+   +     l +++  e++     + + +++   ++  ++ae++   i+++DEid 
  gene1373|gene1373|rna1373|rna1373 247 ILLFGPPGTGKTLIARAIANETGA----FLYVVNGPEIMS----KMSGESESNLRNVFKEAEKNApsIIFIDEIDS 314
                                        8899****************9995....99**********....99999999999999999999999********* PP

                                        ----.---------HHHHHHHHHHHH- CS
                              AAA_2  80 ihpk.essgadvSregVqrdLLqileg 105
                                        i+pk e+s  +v r  ++  LL +++g
  gene1373|gene1373|rna1373|rna1373 315 IAPKrEKSHGEVERR-IVSQLLTLMDG 340
                                        ****77777777776.66668888887 PP

  == domain 2  score: 20.2 bits;  conditional E-value: 1.4e-06
                                        EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG CS
                              AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidK 79 
                                        il+ gp g+Gkt+laka+a+  ++    ++i +   ell       + +++   ++   +a  +   ++++DE+d 
  gene1373|gene1373|rna1373|rna1373 520 ILFYGPPGCGKTLLAKAVASECSA----NFISVKGPELLN----MWVGESEANVRDIFDKARSSApcVIFFDELDS 587
                                        89********************96....99*999999999....44444444444444444444488********* PP

                                        ----.--------.-HHHHHHHHHH CS
                              AAA_2  80 ihpk.essgadvS.regVqrdLLqi 102
                                        i+++ ++s++d    + V++ +L  
  gene1373|gene1373|rna1373|rna1373 588 IAKSrSNSSSDSGvTDRVLNQMLTE 612
                                        ***6433333332123355555554 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0     4e-05     0.015      24      47 ..     244     267 ..     231     350 .. 0.79
   2 !   17.7   0.0   9.5e-06    0.0036      24      61 ..     516     551 ..     509     564 .. 0.81
   3 ?    3.9   0.0      0.17        64     124     146 ..     566     592 ..     560     625 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 4e-05
                             AAA_16  24 pelvllsGesGvGKsslvrellra 47 
                                        p+ +ll G++G+GK+ ++r+++++
  gene1373|gene1373|rna1373|rna1373 244 PRGILLFGPPGTGKTLIARAIANE 267
                                        699*****************9963 PP

  == domain 2  score: 17.7 bits;  conditional E-value: 9.5e-06
                             AAA_16  24 p.elvllsGesGvGKsslvrellralekdggiflrgkcd 61 
                                        p + +l++G++G+GK+ l+++++ + +++   f++ k  
  gene1373|gene1373|rna1373|rna1373 516 PsRGILFYGPPGCGKTLLAKAVASECSAN---FISVKGP 551
                                        2489*******************988887...6665555 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.17
                             AAA_16 124 krllallsrderplvlvlDdlq.....w 146
                                        +++++++++ + p v+++D+l+     +
  gene1373|gene1373|rna1373|rna1373 566 RDIFDKARS-SAPCVIFFDELDsiaksR 592
                                        667788999.888*********555440 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0   2.5e-07   9.4e-05       2     136 ..     247     365 ..     246     366 .. 0.70
   2 !   12.9   0.0   0.00022     0.085       2      78 ..     520     589 ..     519     640 .. 0.59

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 2.5e-07
                                        EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------.G-SEEEEESGGG CS
                              AAA_5   2 vlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar.egeilvlDEver 76 
                                        +lL GppGtgK+ +a+ +a  +++ + +v++++ +++     + ++         +++++a +  ++i+++DE++ 
  gene1373|gene1373|rna1373|rna1373 247 ILLFGPPGTGKTLIARAIANETGAFLYVVNGPEIMSKMSGESESNL--------RNVFKEAEKnAPSIIFIDEIDS 314
                                        89*******************************9987666666665........4555544447899********9 PP

                                        --HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--.-TT-TTHHHHT CS
                              AAA_5  77 aesevlnsLlslleerrllleeggelvkaknddllerfrviatanpldrslnelspalrs 136
                                        + ++  +s     e+r ++  ++ +l++  ++    ++ v++++n+++    +++palr+
  gene1373|gene1373|rna1373|rna1373 315 IAPKREKSH-GEVERRIVS--QLLTLMDGIKKA--TNVIVLGATNRPN----SIDPALRR 365
                                        988765554.444444444..555555554432..1155555555555....88888876 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 0.00022
                                        EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------..G-SEEEEESGG CS
                              AAA_5   2 vlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar..egeilvlDEve 75 
                                        +l  GppG+gK+ la+ +a+   +++  v +++      l+  +    g+ +     + ++ar   ++++++DE++
  gene1373|gene1373|rna1373|rna1373 520 ILFYGPPGCGKTLLAKAVASECSANFISVKGPE------LLNMWV---GESEANVRDIFDKARssAPCVIFFDELD 586
                                        7899**************998888888777766......444444...3333333444445554456666666666 PP

                                        G-- CS
                              AAA_5  76 rae 78 
                                         + 
  gene1373|gene1373|rna1373|rna1373 587 SIA 589
                                        665 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   4.8e-06    0.0018       1      68 [.     247     342 ..     247     364 .. 0.73
   2 !   17.1   0.0   1.6e-05    0.0062       1      44 [.     520     581 ..     520     628 .. 0.73

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 4.8e-06
                             AAA_18   1 IlltGtpGvGKttlakeLskrl.gf....................gvnlrdvakenglllevdpe.......alde 48 
                                        Ill G+pG+GKt +a+++++++ +f                     +n+ + a +n +++ + +e         ++
  gene1373|gene1373|rna1373|rna1373 247 ILLFGPPGTGKTLIARAIANETgAFlyvvngpeimskmsgesesnLRNVFKEAEKNAPSIIFIDEidsiapkREKS 322
                                        99*******************9667999999988988888886666666666666666666666677777755556 PP

                             AAA_18  49 skrldedkldklldaleens 68 
                                        + ++++  + +ll++++++ 
  gene1373|gene1373|rna1373|rna1373 323 HGEVERRIVSQLLTLMDGIK 342
                                        66666666777777777664 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 1.6e-05
                             AAA_18   1 IlltGtpGvGKttlakeLskrl.gf.................gvnlrdvakenglllevdpe 44 
                                        Il  G+pG+GKt lak++++++ ++                   n+rd++ + +++ +   +
  gene1373|gene1373|rna1373|rna1373 520 ILFYGPPGCGKTLLAKAVASECsANfisvkgpellnmwvgesEANVRDIFDKARSSAPCVIF 581
                                        8999*****************96557888888888889988888888888877776665555 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0     2e-06   0.00077       2      47 ..     247     294 ..     247     375 .. 0.76
   2 !   15.8   0.0   3.1e-05     0.012       2      33 ..     520     584 ..     520     658 .. 0.58

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 2e-06
                             AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlfgtdqqsktd 47 
                                        +ll G+pG+GK+  a+ +++++g   ++++ +++++++ g+ + ++++
  gene1373|gene1373|rna1373|rna1373 247 ILLFGPPGTGKTLIARAIANETGafLYVVNGPEIMSKMSGESESNLRN 294
                                        6899*******************98889***********975555542 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 3.1e-05
                             AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdt...............................l 33 
                                        +l+ G+pG+GK+ la+ ++ +    ++ +  ++                               +
  gene1373|gene1373|rna1373|rna1373 520 ILFYGPPGCGKTLLAKAVASECSanFISVKGPEllnmwvgeseanvrdifdkarssapcviffdE 584
                                        6899*****************99666666677744444444444333333333333333333332 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0    0.0001     0.039       8      29 ..     247     268 ..     242     285 .. 0.85
   2 ?    5.4   0.0     0.056        21      83     131 ..     297     353 ..     278     357 .. 0.73
   3 !   13.4   0.1   0.00018     0.068       8      29 ..     520     541 ..     515     625 .. 0.82
   4 ?   -1.6   0.0       7.9     3e+03      40      71 ..     645     680 ..     628     717 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 0.0001
                             AAA_22   8 lvvtGesGtGKTtllrrlleql 29 
                                        ++++G++GtGKT+ +r ++++ 
  gene1373|gene1373|rna1373|rna1373 247 ILLFGPPGTGKTLIARAIANET 268
                                        89***************99986 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.056
                             AAA_22  83 eqalraravielliiDEaqhlr....s......eealeeLrsllnlsrkgvqliLvGtp 131
                                         +a +++  ++++ iDE++ +     +       +++++L +l++  +k + +i+ G +
  gene1373|gene1373|rna1373|rna1373 297 KEAEKNA--PSIIFIDEIDSIApkreKshgeveRRIVSQLLTLMDGIKKATNVIVLGAT 353
                                        3333333..46**********98765157777899999999999989999999999976 PP

  == domain 3  score: 13.4 bits;  conditional E-value: 0.00018
                             AAA_22   8 lvvtGesGtGKTtllrrlleql 29 
                                        ++ +G++G+GKT+l++ ++++ 
  gene1373|gene1373|rna1373|rna1373 520 ILFYGPPGCGKTLLAKAVASEC 541
                                        7889**************9985 PP

  == domain 4  score: -1.6 bits;  conditional E-value: 7.9
                             AAA_22  40 pevvfvtlpsstsskdllrellralglelka....e 71 
                                        ++++f+ lp ++s+ ++l++ +r++ l+ +      
  gene1373|gene1373|rna1373|rna1373 645 DQLIFIPLPDQESRHSILKATCRKTPLNPDVnlkiI 680
                                        567789999999999999998888876655555552 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.1      0.64   2.4e+02      87     119 ..      72     104 ..      66     136 .. 0.78
   2 !   16.0   0.0   1.3e-05    0.0051      51      97 ..     245     289 ..     241     337 .. 0.86
   3 !   13.8   0.0   6.3e-05     0.024      49      98 ..     516     563 ..     505     573 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.64
                                        XXXXXXXXXXXXXXXXXXXXXXXXXXX-S-EEE CS
                              TIP49  87 evyslevkktevltqalrksigvrikeekevle 119
                                         v+ ++v++t  l ++ r  + vri+++ +++ 
  gene1373|gene1373|rna1373|rna1373  72 RVFNSKVERTIYLSKYARNNLRVRIQDIVKLYP 104
                                        69999**********************999885 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 1.3e-05
                                        XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                              TIP49  51 ravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkkte 97 
                                        r++Ll Gp+gtGkt +a ai++e g+     +++g e+ s     +e
  gene1373|gene1373|rna1373|rna1373 245 RGILLFGPPGTGKTLIARAIANETGA--FLYVVNGPEIMSKMSGESE 289
                                        89*********************994..4556789999887766666 PP

  == domain 3  score: 13.8 bits;  conditional E-value: 6.3e-05
                                        XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                              TIP49  49 aGravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkktev 98 
                                          r++L+ Gp+g Gkt la a++ e +    f++++g e+  + v  +e+
  gene1373|gene1373|rna1373|rna1373 516 PSRGILFYGPPGCGKTLLAKAVASECS--ANFISVKGPELLNMWVGESEA 563
                                        579**********************98..689999999999888887776 PP

>> Vps4_C  Vps4 C terminal oligomerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.1     0.017       6.3      15      44 ..     439     468 ..     421     477 .. 0.73
   2 !   25.6   0.1   2.4e-08     9e-06      26      58 ..     735     768 ..     724     770 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.017
                             Vps4_C  15 twmdipsdkllePpvtlkDflkalkkarpt 44 
                                           +i+++ l   +vt +Df  a+ ++ p+
  gene1373|gene1373|rna1373|rna1373 439 ESDQIDPEVLSSLKVTTEDFTYAVDNTDPS 468
                                        3345556667777**************998 PP

  == domain 2  score: 25.6 bits;  conditional E-value: 2.4e-08
                             Vps4_C  26 eP.pvtlkDflkalkkarptVskeDLekheeFTk 58 
                                        eP  v l++f+++lk++r++V+++D+e++e F +
  gene1373|gene1373|rna1373|rna1373 735 EPlTVGLRHFQESLKNTRRSVTQKDMERYESFAR 768
                                        5668999*************************87 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.0    0.0013      0.51       1      26 [.     247     272 ..     247     313 .. 0.83
   2 !   20.5   0.0   1.2e-06   0.00047       1     100 [.     520     623 ..     520     630 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0013
                       RNA_helicase   1 iwlyGpsgeGKStlakeLakallkkl 26 
                                        i+l+Gp+g+GK+++a+ +a++    l
  gene1373|gene1373|rna1373|rna1373 247 ILLFGPPGTGKTLIARAIANETGAFL 272
                                        689**************999876555 PP

  == domain 2  score: 20.5 bits;  conditional E-value: 1.2e-06
                       RNA_helicase   1 iwlyGpsgeGKStlakeLakallkkl...klkkkdsvysrnped...dfwdgYt.gqevvv.idDfgqvkdee.np 67 
                                        i++yGp+g+GK++lak +a++ + ++   k ++  +++++++e    d++d+ + + ++v+ +d++ ++ ++  n 
  gene1373|gene1373|rna1373|rna1373 520 ILFYGPPGCGKTLLAKAVASECSANFisvKGPELLNMWVGESEAnvrDIFDKARsSAPCVIfFDELDSIAKSRsNS 595
                                        789********************88888855555555555555411156666666556665156688888888888 PP

                       RNA_helicase  68 s.dlaelirlvsstpyplnmasleekgtlftSkv 100
                                        s d     r+ +  ++ ++m+ ++ k+     ++
  gene1373|gene1373|rna1373|rna1373 596 SsDSGVTDRVLN--QMLTEMDGISAKKN----VF 623
                                        888888888876..56777777777753....33 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.1     0.013       4.9      36      53 ..     247     264 ..     240     270 .. 0.87
   2 !   10.0   0.0    0.0012      0.48     121     184 ..     285     350 ..     265     353 .. 0.69
   3 !    8.9   0.1    0.0027         1      36      58 ..     520     542 ..     502     566 .. 0.81
   4 ?    4.5   0.0     0.059        23     128     185 ..     563     626 ..     552     628 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.013
                             AAA_25  36 allaGapgtGKttlaldl 53 
                                        +ll+G+pgtGKt +a  +
  gene1373|gene1373|rna1373|rna1373 247 ILLFGPPGTGKTLIARAI 264
                                        69**********998665 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0012
                             AAA_25 121 rggtlltadvdaleaaieevegvrlvviDplsralggdensnsdv.galveal....eriarrtgaavl 184
                                        +g+   ++ ++++ +++e+ + +  + iD ++++ +  e+s+ +v +++v++l    + i+++t+++vl
  gene1373|gene1373|rna1373|rna1373 285 SGE--SESNLRNVFKEAEK-NAPSIIFIDEIDSIAPKREKSHGEVeRRIVSQLltlmDGIKKATNVIVL 350
                                        333..34677888899999.77**********************6666666651111666777777776 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.0027
                             AAA_25  36 allaGapgtGKttlaldlalava 58 
                                        +l++G+pg+GKt la  +a +++
  gene1373|gene1373|rna1373|rna1373 520 ILFYGPPGCGKTLLAKAVASECS 542
                                        789************99887765 PP

  == domain 4  score: 4.5 bits;  conditional E-value: 0.059
                             AAA_25 128 advdaleaaieevegvrlvviDplsralggdensnsd......v.galvealeriarrtgaavll 185
                                        a v+++ +++++   + ++ +D l+++    +ns+sd      v +++++ ++ i++++++ v++
  gene1373|gene1373|rna1373|rna1373 563 ANVRDIFDKARS-SAPCVIFFDELDSIAKSRSNSSSDsgvtdrVlNQMLTEMDGISAKKNVFVIG 626
                                        567778888888.5699*************99999998988885699999999999999988875 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   8.6e-06    0.0033       5     101 ..     247     353 ..     244     370 .. 0.73
   2 !   13.1   0.0   0.00019     0.071       6      77 ..     521     589 ..     517     656 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 8.6e-06
                             AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyi.nldderdkkladpe.kllelileklkeekktylflDEiqev.. 76 
                                        +++ G+  +GKT +++ +++e       +ly+ n  +   k++ ++e +l ++++e  +++  +++f+DEi  +  
  gene1373|gene1373|rna1373|rna1373 247 ILLFGPPGTGKTLIARAIANETG----AFLYVvNGPEIMSKMSGESEsNLRNVFKEA-EKNAPSIIFIDEIDSIap 317
                                        6889************9998877....677763666666666556652455666665.45599*********9988 PP

                             AAA_14  77 ..........pewekalkslvd.egknldvivtGSn 101
                                                  +++ + l  l+d  +k  +viv G  
  gene1373|gene1373|rna1373|rna1373 318 krekshgeveRRIVSQLLTLMDgIKKATNVIVLGAT 353
                                        888888888777777777777752346677777765 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 0.00019
                             AAA_14   6 vitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqevp 77 
                                        +  G+  +GKT l+k +++e      +++ ++  +  +    ++e + + i++k++++   ++f+DE   + 
  gene1373|gene1373|rna1373|rna1373 521 LFYGPPGCGKTLLAKAVASECS---ANFISVKGPELLNMWVGESEANVRDIFDKARSSAPCVIFFDELDSIA 589
                                        678999***********98877...7777777766666555566656666777655568999*****98883 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   4.7e-05     0.018      48      71 ..     245     268 ..     231     323 .. 0.79
   2 ?    0.9   0.0      0.87   3.3e+02      29      56 ..     325     353 ..     312     355 .. 0.83
   3 !   12.4   0.0   0.00025     0.096      48      76 ..     518     546 ..     512     557 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 4.7e-05
                          IstB_IS21  48 enivllGpsGvGKshlaialgvea 71 
                                         +i+l+Gp+G+GK+ +a a++ e+
  gene1373|gene1373|rna1373|rna1373 245 RGILLFGPPGTGKTLIARAIANET 268
                                        689*****************9864 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.87
                          IstB_IS21  29 sldkrkvkeLat.lsfiekkenivllGps 56 
                                        ++++r+v++L t ++ i+k+ n+++lG +
  gene1373|gene1373|rna1373|rna1373 325 EVERRIVSQLLTlMDGIKKATNVIVLGAT 353
                                        6899999988662699***********86 PP

  == domain 3  score: 12.4 bits;  conditional E-value: 0.00025
                          IstB_IS21  48 enivllGpsGvGKshlaialgveavragl 76 
                                         +i++ Gp+G GK+ la a++ e  ++ +
  gene1373|gene1373|rna1373|rna1373 518 RGILFYGPPGCGKTLLAKAVASECSANFI 546
                                        57999***************998766555 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.0   0.00015     0.059      25      43 ..     247     265 ..     241     275 .. 0.92
   2 !   14.4   0.0   4.9e-05     0.019      22      43 ..     517     538 ..     505     543 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00015
                       Mg_chelatase  25 lllvGppGsGKtmlakrlp 43 
                                        +ll+GppG+GKt++a++++
  gene1373|gene1373|rna1373|rna1373 247 ILLFGPPGTGKTLIARAIA 265
                                        89*************9985 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 4.9e-05
                       Mg_chelatase  22 gHnlllvGppGsGKtmlakrlp 43 
                                        +  +l++GppG+GKt+lak+++
  gene1373|gene1373|rna1373|rna1373 517 SRGILFYGPPGCGKTLLAKAVA 538
                                        5679**************9976 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.1    0.0056       2.1      15      37 ..     240     262 ..     234     271 .. 0.86
   2 !    9.9   0.0    0.0011      0.42     119     166 ..     303     354 ..     265     367 .. 0.68
   3 !    7.9   0.0    0.0046       1.8      13      37 ..     511     535 ..     500     545 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0056
                             ATPase  15 GipegrvvlitGepGtGKtifal 37 
                                        Gi   r +l+ G pGtGKt++a 
  gene1373|gene1373|rna1373|rna1373 240 GINPPRGILLFGPPGTGKTLIAR 262
                                        77777889************986 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0011
                             ATPase 119 kakrvviDsitgl...ayeekeavaReilrqlvrvl.kklgvTailvsekss 166
                                          + + iD i+++    ++++ +v R+i+ ql++ +   ++ T+++v  +++
  gene1373|gene1373|rna1373|rna1373 303 APSIIFIDEIDSIapkREKSHGEVERRIVSQLLTLMdGIKKATNVIVLGATN 354
                                        2356667666666431555666789***********667889****988654 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.0046
                             ATPase  13 kgGipegrvvlitGepGtGKtifal 37 
                                        + G+   r +l +G pG+GKt++a+
  gene1373|gene1373|rna1373|rna1373 511 QLGMTPSRGILFYGPPGCGKTLLAK 535
                                        568888899**************97 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.0   0.00019     0.072       2      38 ..     247     288 ..     246     321 .. 0.77
   2 !   11.4   0.0   0.00073      0.28       2      38 ..     520     561 ..     519     604 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00019
                             AAA_28   2 ivitGgestGKTtlleaLaar...gypvv..pEaareileek 38 
                                        i ++G+++tGKT +++a+a++      vv  pE++ ++  e 
  gene1373|gene1373|rna1373|rna1373 247 ILLFGPPGTGKTLIARAIANEtgaFLYVVngPEIMSKMSGES 288
                                        789****************87654233446888888777555 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00073
                             AAA_28   2 ivitGgestGKTtlleaLaar....gypvv.pEaareileek 38 
                                        i + G++++GKT l++a a++     ++v  pE   + + e 
  gene1373|gene1373|rna1373|rna1373 520 ILFYGPPGCGKTLLAKAVASEcsanFISVKgPELLNMWVGES 561
                                        7899***************65555234444777666666555 PP

>> Parvo_NS1  Parvovirus non-structural protein NS1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.0   0.00011     0.043     117     143 ..     247     273 ..     238     279 .. 0.86
   2 !    9.6   0.0    0.0011      0.44     117     136 ..     520     539 ..     509     549 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00011
                          Parvo_NS1 117 vwfyGpantGktnlaeaIakavplygc 143
                                        ++++Gp+ tGkt +a+aIa+ +  +  
  gene1373|gene1373|rna1373|rna1373 247 ILLFGPPGTGKTLIARAIANETGAFLY 273
                                        8899***************99887755 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0011
                          Parvo_NS1 117 vwfyGpantGktnlaeaIak 136
                                        ++fyGp+ +Gkt la+a a 
  gene1373|gene1373|rna1373|rna1373 520 ILFYGPPGCGKTLLAKAVAS 539
                                        89***************986 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.1     0.002      0.77       5      35 ..     238     268 ..     236     450 .. 0.87
   2 !   12.0   0.0   0.00061      0.23       4      51 ..     510     555 ..     508     623 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.002
                                        EEEEETTSEEEEEESTTSSHHHHHHHHTTSS CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ABC_tran   5 slklkegekvaivGenGaGKStLlkllagll 35 
                                        sl +++ + + ++G+ G+GK+ +++++a+++
  gene1373|gene1373|rna1373|rna1373 238 SLGINPPRGILLFGPPGTGKTLIARAIANET 268
                                        78889999999****************9986 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00061
                                        EEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ABC_tran   4 vslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke 51 
                                        v+l + +++ + + G+ G+GK+ L+k++a + +  +  i ++g +l +
  gene1373|gene1373|rna1373|rna1373 510 VQLGMTPSRGILFYGPPGCGKTLLAKAVASECS--ANFISVKGPELLN 555
                                        778899999999****************99875..4555555555555 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.0    0.0013      0.51      34      59 ..     245     270 ..     235     323 .. 0.80
   2 !   10.7   0.0    0.0007      0.27      27      62 ..     511     545 ..     505     571 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0013
                              AAA_7  34 kpvllvGptGtGKtviikdllkkldk 59 
                                        + +ll Gp GtGKt+i++ + ++   
  gene1373|gene1373|rna1373|rna1373 245 RGILLFGPPGTGKTLIARAIANETGA 270
                                        679**************998887764 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.0007
                              AAA_7  27 elllknkkpvllvGptGtGKtviikdllkkldkeky 62 
                                        +l ++ ++ +l++Gp G+GKt+++k + ++++  ++
  gene1373|gene1373|rna1373|rna1373 511 QLGMTPSRGILFYGPPGCGKTLLAKAVASECS-ANF 545
                                        566777889****************9999888.444 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0     0.038        14       3      71 ..     249     312 ..     247     317 .. 0.73
   2 !   14.7   0.0   5.2e-05      0.02       4      70 ..     523     584 ..     520     588 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.038
                    Viral_helicase1   3 vhGvpGcGKStlirkllrts..liltvnrptaelltegkpklpnlsvrtvdsflmalvkstkgkililDEy 71 
                                          G pG GK+ + r ++++     l v++   e+ ++ + +++++  + ++++++++       i+++DE+
  gene1373|gene1373|rna1373|rna1373 249 LFGPPGTGKTLIARAIANETgaF-LYVVNG-PEIMSKMSGESESNLRNVFKEAEKNAP-----SIIFIDEI 312
                                        5688**************99852.333333.567777776666666677888888764.....49999997 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 5.2e-05
                    Viral_helicase1   4 hGvpGcGKStlirkllrts.liltvnrptaelltegkpklpnlsvrtvdsflmalvkstkgkililDE 70 
                                         G pGcGK+ l + +++++  ++ +++   ell++++ +++++    +d++ +++ +     ++++DE
  gene1373|gene1373|rna1373|rna1373 523 YGPPGCGKTLLAKAVASECsANFISVKG-PELLNMWVGESEANVRDIFDKARSSAPC-----VIFFDE 584
                                        588****************977777777.8*******99999999999999998875.....789998 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.0     0.003       1.2      21      45 ..     246     270 ..     217     280 .. 0.78
   2 !   10.7   0.0    0.0011       0.4      19      51 ..     517     551 ..     491     560 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.003
                                        EEEEEESTTSSHHHHHHHHHHHTT- CS
                               TsaE  21 vilLeGdLGaGKTtlvrglakalgv 45 
                                         ilL G+ G+GKT ++r++a++ g 
  gene1373|gene1373|rna1373|rna1373 246 GILLFGPPGTGKTLIARAIANETGA 270
                                        499*****************99886 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.0011
                                        TEEEEEEESTTSSHHHHHHHHHHHTT--..----T CS
                               TsaE  19 gdvilLeGdLGaGKTtlvrglakalgve..evkSP 51 
                                        ++ il++G+ G+GKT l++++a+++  +  +vk P
  gene1373|gene1373|rna1373|rna1373 517 SRGILFYGPPGCGKTLLAKAVASECSANfiSVKGP 551
                                        3459*******************998877777766 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.0    0.0032       1.2       1      54 [.     250     304 ..     250     333 .. 0.71
   2 !   10.0   0.0    0.0023      0.88       1      35 [.     523     558 ..     523     636 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0032
                                        EE-TTSSHHHHHHHHHHHHT.EEEEEHHHHHHHHHHTTTSHSSHHHHCTSHHHHH CS
                             AAA_17   1 lGgPGsGKgtqceklvekyg.fthlsaGdllreeakrgglakardemrklpleek 54 
                                        +G+PG GK+ +++ ++ + g f ++  G  +++ ++ ++ ++ r+ +++++++  
  gene1373|gene1373|rna1373|rna1373 250 FGPPGTGKTLIARAIANETGaFLYVVNGPEIMSKMSGESESNLRNVFKEAEKNAP 304
                                        6***************999647777778888888776665555666665555444 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0023
                                        EE-TTSSHHHHHHHHHHHHTEEEEEH.HHHHHHHHH CS
                             AAA_17   1 lGgPGsGKgtqceklvekygfthlsa.Gdllreeak 35 
                                        +G+PG+GK+ +++ ++ +    ++s  G  l ++  
  gene1373|gene1373|rna1373|rna1373 523 YGPPGCGKTLLAKAVASECSANFISVkGPELLNMWV 558
                                        7***************99977777654555555444 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.0   0.00073      0.28       5      76 ..     247     314 ..     244     320 .. 0.64
   2 !    7.8   0.0    0.0064       2.4       5      22 ..     520     537 ..     517     572 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00073
                             AAA_24   5 iliyGpsgiGKTtlakel.gpkplfidtekGlksldadkfpdieswedfldevvelaaeladyktlviDtide 76 
                                        il++Gp+g+GKT +a+ +  ++ +f+ + +G   +    ++   s  ++++ ++e +++ +  ++++iD id 
  gene1373|gene1373|rna1373|rna1373 247 ILLFGPPGTGKTLIARAIaNETGAFLYVVNGPEIMSKMSGE---SESNLRNVFKEAEKNAP--SIIFIDEIDS 314
                                        89*************99954444555444444444444443...55566666665555555..6677777765 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0064
                             AAA_24   5 iliyGpsgiGKTtlakel 22 
                                        il yGp+g GKT lak  
  gene1373|gene1373|rna1373|rna1373 520 ILFYGPPGCGKTLLAKAV 537
                                        889***********9976 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.1     0.017       6.4      21      68 ..     245     288 ..     235     350 .. 0.55
   2 !    9.8   0.0    0.0018      0.68      19      43 ..     516     540 ..     507     548 .. 0.82
   3 ?   -0.8   0.0         3   1.2e+03     119     136 ..     574     594 ..     558     628 .. 0.65

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.017
                           ATPase_2  21 eiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldef 68 
                                        + ++++Gp g GKt + + i+++        +y+ +  e+ ++   e+
  gene1373|gene1373|rna1373|rna1373 245 RGILLFGPPGTGKTLIARAIANETGA----FLYVVNGPEIMSKMSGES 288
                                        55789********9888888888743....455555555544444444 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0018
                           ATPase_2  19 pneiyfiYGpegsGKtaLlkeiien 43 
                                        p++ ++ YGp g+GKt L k ++++
  gene1373|gene1373|rna1373|rna1373 516 PSRGILFYGPPGCGKTLLAKAVASE 540
                                        5566788************999876 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 3
                           ATPase_2 119 k...iiiiiDelqklidlgln 136
                                             +i++Del  + +  +n
  gene1373|gene1373|rna1373|rna1373 574 SsapCVIFFDELDSIAKSRSN 594
                                        233378999999988855554 PP

>> Bac_DnaA  Bacterial dnaA  protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.0   0.00029      0.11      37     195 ..     247     406 ..     237     432 .. 0.72
   2 ?    5.8   0.0     0.028        11      37      62 ..     520     545 ..     512     551 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00029
                                        EEEE-SSSSSHHHHHHHHHHHHHHHSSSS-EEEEEHHHHHHHHHHHHHTT-HHHHHHHHTT-.SEEEEE-GGGGTT CS
                           Bac_DnaA  37 lfiygevGlGktHLlkaignevlenapelrvvYltaeeFlnelvkalrdkkaeefkeklrkv.DvLliDDiqflag 111
                                        ++++g+ G Gkt + +ai+ne+      + +  +++ e ++++    +++  + fke  +++  ++ iD+i  +a 
  gene1373|gene1373|rna1373|rna1373 247 ILLFGPPGTGKTLIARAIANETG-----AFLYVVNGPEIMSKMSGESESNLRNVFKEAEKNApSIIFIDEIDSIAP 317
                                        799*************9998764.....445567899********************9996627899*******98 PP

                                        -HH.....HHH....HHHHHHHHHHTTT-EEEEEESS-TTT-SS--HHHHHHHHSSEEEE-----HHHHHHHHHHH CS
                           Bac_DnaA 112 kek.....tqe....elfhtfnalleegkqvvlssDrsPkeleeledrlrsrfeaGlvvdieppdletrlailkkk 178
                                        k +     ++     +l+++++ + ++ + +vl +   P+++   +  lr   + G  ++i  pd+  rl+il+ +
  gene1373|gene1373|rna1373|rna1373 318 KREkshgeVERrivsQLLTLMDGIKKATNVIVLGATNRPNSI---DPALRRYGRFGREIEIGIPDKIGRLEILRIH 390
                                        864111222331111455555555556667999999999765...667777777888999999*********9754 PP

                                        HHHTT----TTH.HHHHH CS
                           Bac_DnaA 179 ieaeklevpeev.lefia 195
                                            ++ + e+v le +a
  gene1373|gene1373|rna1373|rna1373 391 T--RNMALAEDVdLEKVA 406
                                        4..444444444333333 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.028
                                        EEEE-SSSSSHHHHHHHHHHHHHHHS CS
                           Bac_DnaA  37 lfiygevGlGktHLlkaignevlena 62 
                                        +++yg+ G Gkt L ka++ e  +n+
  gene1373|gene1373|rna1373|rna1373 520 ILFYGPPGCGKTLLAKAVASECSANF 545
                                        799****************9988876 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0     0.025       9.6      45      99 ..     244     299 ..     233     321 .. 0.68
   2 !   11.6   0.0    0.0005      0.19      43     113 ..     515     586 ..     503     638 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.025
                              Rad17  45 kriLLisGPsGCgkstvvkvLskelgiklrewlnpvsl.kepdnqksdfkglteke 99 
                                         r +L+ GP+G gk+ + + ++ e g  l     p  + k +   +s+++ +++  
  gene1373|gene1373|rna1373|rna1373 244 PRGILLFGPPGTGKTLIARAIANETGAFLYVVNGPEIMsKMSGESESNLRNVFKEA 299
                                        5556889****************999866544333333022333566666666555 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.0005
                              Rad17  43 rkkriLLisGPsGCgkstvvkvLskelgiklrewlnpvslkepdn.qksdfkgltekesrflsqiesfkele 113
                                         + r +L  GP+GCgk+   k ++ e + +++    p +l+      + +++ +++k  +  + +  f el 
  gene1373|gene1373|rna1373|rna1373 515 TPSRGILFYGPPGCGKTLLAKAVASECSANFISVKGPELLNMWVGeSEANVRDIFDKARSSAPCVIFFDELD 586
                                        556678999******************999999999988776443377788888888888888888888874 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.0    0.0017      0.64      24      45 ..     246     267 ..     236     355 .. 0.90
   2 ?    6.1   0.0     0.021       8.1      23      47 ..     518     542 ..     500     555 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0017
                                        -EEEECSTTSSHHHHHHHHHHH CS
                    Sigma54_activat  24 svlitGesGtGKellaraihea 45 
                                         +l+ G  GtGK+l+arai ++
  gene1373|gene1373|rna1373|rna1373 246 GILLFGPPGTGKTLIARAIANE 267
                                        689***************9875 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.021
                                        S-EEEECSTTSSHHHHHHHHHHHST CS
                    Sigma54_activat  23 lsvlitGesGtGKellaraiheask 47 
                                          +l  G  G+GK+lla+a+ ++ +
  gene1373|gene1373|rna1373|rna1373 518 RGILFYGPPGCGKTLLAKAVASECS 542
                                        56899*************9976554 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0     0.021       8.2      23      43 ..     247     267 ..     241     274 .. 0.89
   2 ?   -2.0   0.0       4.3   1.6e+03     120     174 ..     372     427 ..     371     438 .. 0.75
   3 !    9.7   0.0    0.0011      0.44      23      45 ..     520     542 ..     510     640 .. 0.67

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.021
                                        EEEEESTTSSHHHHHHHHCCS CS
                             NB-ARC  23 valvGmgGvGKttlakqilnk 43 
                                        + l G +G GKt +a+ i n+
  gene1373|gene1373|rna1373|rna1373 247 ILLFGPPGTGKTLIARAIANE 267
                                        5689**************998 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 4.3
                                        ....HHHHCHTTSEEE.EEESBCCCCCCS-S-EEEEEESS--HHHHHHHHHHCCTS CS
                             NB-ARC 120 kigvvlparenrlrvl.lTTRdeevanavsatsekievelLekdeawellenkvfe 174
                                        +i + +p++  rl++l + TR++++a+ v  ++   e++ +   +   l+++ +++
  gene1373|gene1373|rna1373|rna1373 372 EIEIGIPDKIGRLEILrIHTRNMALAEDVDLEKVANETHGFVGSDIASLCSEAAMQ 427
                                        68889999999999986789999999999887777777666666666666666665 PP

  == domain 3  score: 9.7 bits;  conditional E-value: 0.0011
                                        EEEEESTTSSHHHHHHHHCCSHC CS
                             NB-ARC  23 valvGmgGvGKttlakqilnksd 45 
                                        + ++G +G+GKt lak + ++ +
  gene1373|gene1373|rna1373|rna1373 520 ILFYGPPGCGKTLLAKAVASECS 542
                                        678*************9998743 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.0    0.0031       1.2      23      40 ..     248     265 ..     241     270 .. 0.87
   2 !    7.9   0.0    0.0049       1.9      23      42 ..     521     540 ..     506     547 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0031
                                        EEE--TTSSTTHHHHHHH CS
                               PhoH  23 faiGpaGtGKtylavala 40 
                                          +Gp GtGKt++a a+a
  gene1373|gene1373|rna1373|rna1373 248 LLFGPPGTGKTLIARAIA 265
                                        579***********9988 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0049
                                        EEE--TTSSTTHHHHHHHHH CS
                               PhoH  23 faiGpaGtGKtylavalave 42 
                                           Gp G+GKt+la a+a e
  gene1373|gene1373|rna1373|rna1373 521 LFYGPPGCGKTLLAKAVASE 540
                                        568************99976 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0      0.03        11       3      23 ..     247     267 ..     245     270 .. 0.88
   2 ?   -1.9   0.0       7.4   2.8e+03      65     100 ..     288     326 ..     280     358 .. 0.61
   3 !    9.9   0.0    0.0016      0.63       3      24 ..     520     541 ..     518     547 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.03
                                        EEEEC-TTTCHHHHHHHHHHH CS
                              NACHT   3 vilqGeaGsGKTtLlqklala 23 
                                        ++l G++G GKT  ++ +a +
  gene1373|gene1373|rna1373|rna1373 247 ILLFGPPGTGKTLIARAIANE 267
                                        7899*************9976 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 7.4
                                        --SSS-CCHHHHCCSCCCEEEEEE-STT-SS-TCH..... CS
                              NACHT  65 paapvsevwavllelperlLlilDglDelvtdlgq....k 100
                                        ++++ ++v+++  +++ ++ + +D +D ++ + ++     
  gene1373|gene1373|rna1373|rna1373 288 SESNLRNVFKEAEKNAPSIIF-IDEIDSIAPKREKshgeV 326
                                        556666666666666666666.477777776555533322 PP

  == domain 3  score: 9.9 bits;  conditional E-value: 0.0016
                                        EEEEC-TTTCHHHHHHHHHHHH CS
                              NACHT   3 vilqGeaGsGKTtLlqklalaw 24 
                                        ++  G++G+GKT L++ +a++ 
  gene1373|gene1373|rna1373|rna1373 520 ILFYGPPGCGKTLLAKAVASEC 541
                                        6889*************99875 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0      0.02       7.5      54      85 ..     245     275 ..     237     362 .. 0.62
   2 !   10.7   0.0   0.00055      0.21      16      82 ..     471     546 ..     456     596 .. 0.71

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.02
                             DUF815  54 nnvLLwGarGtGKSslvkallneyaeegLrli 85 
                                        + +LL+G  GtGK  + +a+ ne+ +  L ++
  gene1373|gene1373|rna1373|rna1373 245 RGILLFGPPGTGKTLIARAIANETGA-FLYVV 275
                                        679****************9998754.34444 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00055
                             DUF815  16 lepveevdevklddLvgidkqkealvente.......qfle..glpannvLLwGarGtGKSslvkallneyaeegL 82 
                                         e+v e+ +vk++d+ g+++ k++l+e ++       ++++   +p++ +L++G  G+GK  l ka+ +e++++ +
  gene1373|gene1373|rna1373|rna1373 471 RETVVETPNVKWEDIGGLQAVKDELKETVSypikfseKYVQlgMTPSRGILFYGPPGCGKTLLAKAVASECSANFI 546
                                        567788889999999999999999988764333111134433246899*********************9988763 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.0   0.00013     0.051      22      88 ..     242     302 ..     215     350 .. 0.72
   2 ?    3.3   0.0      0.19        72      22      51 ..     515     544 ..     486     590 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 0.00013
                                        .TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG....GEEE CS
                             ResIII  22 krdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkflseaykeigkk 88 
                                        +  + +l+  + GtGKTl+a +++ +         fl +v++ ++++++  e ++ l + +ke++k+
  gene1373|gene1373|rna1373|rna1373 242 NPPRGILLFGPPGTGKTLIARAIANETG------AFLYVVNGPEIMSKMSGESESNLRNVFKEAEKN 302
                                        566778889999******9988887766......59**************77766666666553222 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.19
                                        .TTSEEEEEESTTSTHHHHHHHHHHHH-S. CS
                             ResIII  22 krdkrglikmaTGtGKTlvaaklierllkk 51 
                                        +  + +l+  + G+GKTl+a +++ +++ +
  gene1373|gene1373|rna1373|rna1373 515 TPSRGILFYGPPGCGKTLLAKAVASECSAN 544
                                        4456778999*********98888877664 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.0    0.0071       2.7       2      37 ..     247     281 ..     246     356 .. 0.72
   2 !    9.1   0.0     0.003       1.1       2     112 ..     520     631 ..     519     649 .. 0.59

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0071
                              AAA_3   2 vllegvPGlaktllvkalakaldlefkriqftpdll 37 
                                        +ll g PG++ktl+++a+a+  ++ f  +   p+++
  gene1373|gene1373|rna1373|rna1373 247 ILLFGPPGTGKTLIARAIANETGA-FLYVVNGPEIM 281
                                        78999**************99875.44444556655 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.003
                              AAA_3   2 vllegvPGlaktllvkalakaldlefkriqftpdllPsdilGtevfeeke..kefefkkGpvfanllladeinrap 75 
                                        +l+ g PG +ktll+ka+a+  +++f  ++  p+ll   +  +e   ++   k  +  +  +f + l +    r++
  gene1373|gene1373|rna1373|rna1373 520 ILFYGPPGCGKTLLAKAVASECSANFISVK-GPELLNMWVGESEANVRDIfdKARSSAPCVIFFDELDSIAKSRSN 594
                                        678899*******************99887.577776655333222222211333334444444444333334555 PP

                              AAA_3  76 pktqsalleameerqvtvegethklpepflvlatqnP 112
                                        + ++s + + + ++ +t  +   + ++ f++ at+ P
  gene1373|gene1373|rna1373|rna1373 595 SSSDSGVTDRVLNQMLTEMDGISAKKNVFVIGATNRP 631
                                        5666666666666666665555555555555555555 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.0    0.0012      0.47       6      55 ..     249     292 ..     245     330 .. 0.63
   2 ?    5.2   0.0     0.028        11       5      36 ..     521     545 ..     517     591 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0012
                            DUF2075   6 VtGvaGtGKtvvllnllaeleddeeertavylsvNhplvl.vlrealakke 55 
                                          G +GtGKt+++ ++++e         a + +vN+p+++ ++  + +++ 
  gene1373|gene1373|rna1373|rna1373 249 LFGPPGTGKTLIARAIANET-------GAFLYVVNGPEIMsKMSGESESNL 292
                                        5699*************998.......455555555554413333333333 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.028
                            DUF2075   5 lVtGvaGtGKtvvllnllaeleddeeertavy 36 
                                        l  G +G GKt+++ +++ e+       +a++
  gene1373|gene1373|rna1373|rna1373 521 LFYGPPGCGKTLLAKAVASEC-------SANF 545
                                        6689**************999.......3444 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0     0.011       4.3      16      40 ..     244     268 ..     238     276 .. 0.88
   2 ?    6.2   0.0     0.014       5.4      20      50 ..     521     549 ..     514     557 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.011
                         Zeta_toxin  16 PklillgGqpGAGKselaellkdel 40 
                                        P  ill G pG GK+ +a+++++e+
  gene1373|gene1373|rna1373|rna1373 244 PRGILLFGPPGTGKTLIARAIANET 268
                                        77799*****************997 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.014
                         Zeta_toxin  20 llgGqpGAGKselaellkdelerqgnvvrld 50 
                                        l  G pG+GK+ la++++ e     n++ ++
  gene1373|gene1373|rna1373|rna1373 521 LFYGPPGCGKTLLAKAVASEC--SANFISVK 549
                                        56699***************9..78888776 PP

>> CDC48_N  Cell division protein 48 (CDC48), N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   7.5e-05     0.029      30      84 ..      52     106 ..      41     108 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 7.5e-05
                                        -TTSEEEEECCCC.EEEEEEEBSTTSTTTTEEEE-HHHHHHHT--TTEEEEEEEE- CS
                            CDC48_N  30 epgdvveiegkrk.TvaivwpaepedegkgiIrmdgvtRknagvsiGdkVtVrkae 84 
                                        + g+ +  +gk +  + + ++  ++ + + +I +++++R+n++v+i d V+  +++
  gene1373|gene1373|rna1373|rna1373  52 RDGNHIIARGKGRrECIFRVRVFNS-KVERTIYLSKYARNNLRVRIQDIVKLYPCS 106
                                        5666666666333233333333333.34789********************99986 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.0      0.01       3.8      20      41 ..     247     268 ..     233     307 .. 0.76
   2 ?    5.5   0.3     0.033        13      20      41 ..     520     541 ..     506     784 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.01
                             AAA_11  20 tliqGPPGtgKTktivellsql 41 
                                         l+ GPPGtgKT    ++ ++ 
  gene1373|gene1373|rna1373|rna1373 247 ILLFGPPGTGKTLIARAIANET 268
                                        4788********8877777665 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.033
                             AAA_11  20 tliqGPPGtgKTktivellsql 41 
                                         l+ GPPG+gKT    ++ s+ 
  gene1373|gene1373|rna1373|rna1373 520 ILFYGPPGCGKTLLAKAVASEC 541
                                        5899********6665555554 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.1    0.0054       2.1      12      33 ..     246     267 ..     241     303 .. 0.84
   2 ?    4.5   0.0      0.11        40       9      33 ..     516     540 ..     508     549 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0054
                             AAA_19  12 vllvtaGpGtGKTrvlkhival 33 
                                         +l+ ++pGtGKT + ++i ++
  gene1373|gene1373|rna1373|rna1373 246 GILLFGPPGTGKTLIARAIANE 267
                                        5899*********999988765 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.11
                             AAA_19   9 kekvllvtaGpGtGKTrvlkhival 33 
                                        +++ +l  ++pG+GKT + k++ ++
  gene1373|gene1373|rna1373|rna1373 516 PSRGILFYGPPGCGKTLLAKAVASE 540
                                        56678899********988877665 PP

>> Sigma54_activ_2  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0    0.0022      0.82      24      81 ..     247     315 ..     243     323 .. 0.61
   2 ?    3.1   0.0      0.25        95      24      47 ..     520     543 ..     511     594 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0022
                                        EEEEEETT--HHHHHHCC--TTS-EE--SSTTHHHH-H........HHHHHHT...TTSEEEEEE-TT- CS
                    Sigma54_activ_2  24 vfltGekGsgkelvArlLhknsgpwleifvverlaklp........ldlleqa...kggtLylkdiadl 81 
                                        ++l G++G+gk+l+Ar+++++ g  l +++  + ++           +++++a    + ++++ +i+++
  gene1373|gene1373|rna1373|rna1373 247 ILLFGPPGTGKTLIARAIANETGAFLYVVNGPEIMSKMsgesesnlRNVFKEAeknAPSIIFIDEIDSI 315
                                        799*****************9998666554333222111222333322222223226666666666665 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.25
                                        EEEEEETT--HHHHHHCC--TTS- CS
                    Sigma54_activ_2  24 vfltGekGsgkelvArlLhknsgp 47 
                                        ++  G++G+gk+l A++ +++ + 
  gene1373|gene1373|rna1373|rna1373 520 ILFYGPPGCGKTLLAKAVASECSA 543
                                        6778************99876554 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0      0.17        65       2      22 ..     247     267 ..     246     278 .. 0.83
   2 ?    0.8   0.1       1.1   4.1e+02      84     119 ..     291     327 ..     273     345 .. 0.71
   3 ?    6.6   0.0     0.017       6.5       5      32 ..     523     550 ..     519     556 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.17
                                        EEEE--TTSSHHHHHHHHHHH CS
                           NTPase_1   2 vfiTGppGvGKtTlvkkvlel 22 
                                        +++ GppG+GKt + + ++++
  gene1373|gene1373|rna1373|rna1373 247 ILLFGPPGTGKTLIARAIANE 267
                                        6788********999988876 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 1.1
                                        HHHHHHHHHH.HHH-EEEE---STTGGG-HHHHHHHH CS
                           NTPase_1  84 lalealrkal.seadviviDEiGkmElkskkfkeave 119
                                           +++++a  + + +i iDEi ++  k +k + +ve
  gene1373|gene1373|rna1373|rna1373 291 NLRNVFKEAEkNAPSIIFIDEIDSIAPKREKSHGEVE 327
                                        445556666534555*******777666666555555 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.017
                                        E--TTSSHHHHHHHHHHHH...GGGEEE CS
                           NTPase_1   5 TGppGvGKtTlvkkvlellkssgvkvgG 32 
                                         GppG GKt l k v+++++ + ++v+G
  gene1373|gene1373|rna1373|rna1373 523 YGPPGCGKTLLAKAVASECSANFISVKG 550
                                        59*****************998888888 PP

>> CDC48_2  Cell division protein 48 (CDC48), domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   0.00015     0.058      17      55 ..     145     189 ..     131     197 .. 0.79
   2 ?   -1.5   0.1       5.9   2.3e+03      33      52 ..     457     479 ..     441     481 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00015
                                        EEE-TTEEEEECCTCCCEEEEEEEEC.CCC....SC.EEECTSCC CS
                            CDC48_2  17 rpvtkGdlvvfefkgqeiklvVvste.Pkg....pv.gitetTei 55 
                                         p++kGd+++++  +++++++V + + Pk+    ++  it +T+i
  gene1373|gene1373|rna1373|rna1373 145 VPISKGDIIPITCGMMTVDFKVLELSsPKDtndlKHgLITAETKI 189
                                        69********************99853666888855588888887 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 5.9
                                        CEEEEEEEECCCC...SCEEECT CS
                            CDC48_2  33 eiklvVvstePkg...pvgitet 52 
                                         ++++V +t+P+    +v+ t++
  gene1373|gene1373|rna1373|rna1373 457 DFTYAVDNTDPSSlreTVVETPN 479
                                        5788999****999988888875 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.0     0.012       4.5      22      40 ..     248     266 ..     241     274 .. 0.87
   2 ?    3.5   0.0      0.14        52      21      41 ..     520     540 ..     509     550 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.012
                             AAA_30  22 vltGpAGtGKttalkalre 40 
                                        +l Gp+GtGKt + +a+++
  gene1373|gene1373|rna1373|rna1373 248 LLFGPPGTGKTLIARAIAN 266
                                        678**********999975 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.14
                             AAA_30  21 avltGpAGtGKttalkalrea 41 
                                         +  Gp+G GKt + ka++  
  gene1373|gene1373|rna1373|rna1373 520 ILFYGPPGCGKTLLAKAVASE 540
                                        5678**********9999765 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0     0.056        21       3      24 ..     249     270 ..     247     277 .. 0.86
   2 ?    4.7   0.0     0.056        21       5      28 ..     524     547 ..     520     549 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.056
                                        EE-STTSSHHHHHHHHHHHHT- CS
                     Cytidylate_kin   3 iDGPagsGKssvaralaeklgl 24 
                                        + GP g+GK  +ara+a++ g+
  gene1373|gene1373|rna1373|rna1373 249 LFGPPGTGKTLIARAIANETGA 270
                                        56***************99876 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.056
                                        -STTSSHHHHHHHHHHHHT-EEEE CS
                     Cytidylate_kin   5 GPagsGKssvaralaeklglkyld 28 
                                        GP g GK  +a+a+a++ ++++++
  gene1373|gene1373|rna1373|rna1373 524 GPPGCGKTLLAKAVASECSANFIS 547
                                        9******************99986 PP

>> IPT  Isopentenyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.0    0.0055       2.1       5      29 ..     248     272 ..     245     298 .. 0.88
   2 ?    2.0   0.0      0.31   1.2e+02       5      31 ..     521     547 ..     518     549 .. 0.91

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0055
                                IPT   5 lifGatttGKtaeaiklaketgapv 29 
                                        l+fG+ +tGKt  a ++a+etga +
  gene1373|gene1373|rna1373|rna1373 248 LLFGPPGTGKTLIARAIANETGAFL 272
                                        89********************865 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.31
                                IPT   5 lifGatttGKtaeaiklaketgapviv 31 
                                        l +G+ + GKt  a ++a e +a  i+
  gene1373|gene1373|rna1373|rna1373 521 LFYGPPGCGKTLLAKAVASECSANFIS 547
                                        789*****************9999887 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0      0.13        48       4      24 ..     247     267 ..     244     273 .. 0.89
   2 ?    5.4   0.0     0.038        14       3      23 ..     519     539 ..     517     543 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.13
                          PduV-EutP   4 illiGkvgsGKttLtqalkge 24 
                                        ill+G+ g+GKt +++a+ +e
  gene1373|gene1373|rna1373|rna1373 247 ILLFGPPGTGKTLIARAIANE 267
                                        99***************9987 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.038
                          PduV-EutP   3 killiGkvgsGKttLtqalkg 23 
                                         il+ G+ g+GKt L++a+  
  gene1373|gene1373|rna1373|rna1373 519 GILFYGPPGCGKTLLAKAVAS 539
                                        599*************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (795 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       681  (0.0379832); expected 358.6 (0.02)
Passed bias filter:                      625  (0.0348597); expected 358.6 (0.02)
Passed Vit filter:                        86  (0.0047967); expected 17.9 (0.001)
Passed Fwd filter:                        47  (0.00262145); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              47  [number of targets reported over threshold]
# CPU time: 0.90u 0.32s 00:00:01.22 Elapsed: 00:00:00.48
# Mc/sec: 4945.21
//
Query:       gene1374|gene1374|rna1374|rna1374  [L=407]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.2e-41  139.9   0.4    2.4e-40  138.0   0.0    2.2  3  AAA              ATPase family associated with various cellul
    1.6e-20   72.8   0.2      5e-20   71.2   0.3    1.9  1  Prot_ATP_ID_OB   Proteasomal ATPase OB C-terminal domain
    2.3e-14   52.9   0.2    2.7e-13   49.5   0.1    2.3  2  AAA_lid_3        AAA+ lid domain
    6.6e-06   26.3   0.1    6.2e-05   23.2   0.1    2.5  1  AAA_2            AAA domain (Cdc48 subfamily)
    3.8e-05   23.7   0.1    0.00026   21.0   0.1    2.4  1  AAA_5            AAA domain (dynein-related subfamily)
    4.4e-05   23.9   0.1      0.011   16.2   0.0    2.5  2  AAA_16           AAA ATPase domain
    5.4e-05   23.0   0.1    0.00016   21.5   0.0    1.7  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    0.00033   20.9   0.7       0.26   11.6   0.0    2.6  2  AAA_22           AAA domain
     0.0035   17.5   0.0     0.0069   16.6   0.0    1.5  1  AAA_33           AAA domain
     0.0035   17.1   0.1       0.16   11.6   0.0    3.0  3  Sigma54_activat  Sigma-54 interaction domain
  ------ inclusion threshold ------
      0.012   15.6   0.0      0.031   14.3   0.0    1.7  1  AAA_14           AAA domain
      0.013   14.9   0.0      0.071   12.5   0.0    2.1  2  PhoH             PhoH-like protein
      0.019   14.3   0.1      0.052   12.9   0.1    1.7  1  Mg_chelatase     Magnesium chelatase, subunit ChlI
      0.043   13.3   0.0       0.12   11.8   0.0    1.8  1  AAA_7            P-loop containing dynein motor region
      0.059   13.2   0.1       0.15   11.9   0.0    1.7  2  AAA_11           AAA domain
      0.073   12.7   0.3       0.69    9.6   0.1    2.3  2  Prot_ATP_OB_N    Proteasomal ATPase OB N-terminal domain
      0.079   12.7   0.0        0.2   11.4   0.0    1.6  2  IstB_IS21        IstB-like ATP binding protein
       0.14   11.8   0.3       0.65    9.7   0.3    2.0  1  AAA_30           AAA domain
       0.16   12.3   0.0       0.46   10.9   0.0    1.8  1  RNA_helicase     RNA helicase


Domain annotation for each model (and alignments):
>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       3.9   3.7e+03      89     117 ..      77     103 ..      70     108 .. 0.77
   2 !  138.0   0.0   2.6e-43   2.4e-40       1     132 []     191     324 ..     191     324 .. 0.95
   3 ?   -2.9   0.0       8.8   8.3e+03      15      49 ..     364     395 ..     362     402 .. 0.65

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 3.9
                                        HHHHHHHTTTSSSTEEEEEEESSGGGSTH CS
                                AAA  89 Llteldgvkkkeskvivigatnrpdkldp 117
                                         ++ ld++++++    v+ +++r+ ++ p
  gene1374|gene1374|rna1374|rna1374  77 VVEILDDEENDK--SAVVSTSTRVTSFLP 103
                                        567899999974..599999999887766 PP

  == domain 2  score: 138.0 bits;  conditional E-value: 2.6e-43
                                        EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH.. CS
                                AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksr.. 74 
                                        vl++GppGtGKTl+a+a a +++++fl++ g++l+++y+g+++k +r+ fk a ek+ p+i+fiDEida++++r  
  gene1374|gene1374|rna1374|rna1374 191 VLMHGPPGTGKTLMARACAAKSETTFLKLAGPQLVQMYIGDGAKLVRDAFKLALEKK-PTIIFIDEIDAIGTKRtk 265
                                        79***************************************************9998.****************97 PP

                                        .TTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETTS CS
                                AAA  75 .sgseseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieiel 132
                                         ++  ++e +r++ +Ll++ldg+++++ +v +i+atnr+d ldpallr gRfdrkie++l
  gene1374|gene1374|rna1374|rna1374 266 sDRIGDREVQRTMLELLNQLDGFSSSD-DVKIIAATNRVDILDPALLRsGRFDRKIEFPL 324
                                        5555899999***************85.5****************************985 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 8.8
                                        HHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHH CS
                                AAA  15 akavakelgvefleisgsellskyvgesekkirel 49 
                                        +kav+ e+g+  l+ + +e++   + ++ + i+e+
  gene1374|gene1374|rna1374|rna1374 364 CKAVCVEAGMVALRKDHKEIT---QNDMIDGIQEV 395
                                        788888888888888888888...34444444444 PP

>> Prot_ATP_ID_OB  Proteasomal ATPase OB C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.2   0.3   5.3e-23     5e-20       1      57 []      74     133 ..      74     133 .. 0.99

  Alignments for each domain:
  == domain 1  score: 71.2 bits;  conditional E-value: 5.3e-23
                                        EEEEEEE-TT...SSEEEEE-TTS-EEEEEE-GGGSSST--TTEEEEEETTTTEEEEEE- CS
                     Prot_ATP_ID_OB   1 VatVsEvldd...teraiVktssdeevvvslagavpremLrpgDlVavdkdtgfifEkLP 57 
                                        V++V+E+ldd   +++a+V ts+++++++++ g+v +++LrpgD V+++k t++ifEkLP
  gene1374|gene1374|rna1374|rna1374  74 VGNVVEILDDeenDKSAVVSTSTRVTSFLPMIGLVEAQDLRPGDMVSLHKETNVIFEKLP 133
                                        9**********************************************************9 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.53     5e+02      21      34 ..     234     247 ..     233     262 .. 0.76
   2 !   49.5   0.1   2.8e-16   2.7e-13       1      44 [.     346     389 ..     346     390 .. 0.97

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.53
                          AAA_lid_3  21 alcreAallAlrrg 34 
                                         l+r A  lAl+ +
  gene1374|gene1374|rna1374|rna1374 234 KLVRDAFKLALEKK 247
                                        59*********886 PP

  == domain 2  score: 49.5 bits;  conditional E-value: 2.8e-16
                          AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrrgikeitmedfe 44 
                                        +v+++eLA+ TeG+ GA  +a+c eA+++Alr + keit+ d++
  gene1374|gene1374|rna1374|rna1374 346 NVNFDELARSTEGFNGAQCKAVCVEAGMVALRKDHKEITQNDMI 389
                                        7*****************************************97 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.1   6.5e-08   6.2e-05       6     104 ..     191     283 ..     186     296 .. 0.76

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 6.5e-08
                                        EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG CS
                              AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidK 79 
                                        +l+ gp g+Gkt++a+a a   +     ++  +   +l +      + +  +  +++ + a e+   i+++DEid 
  gene1374|gene1374|rna1374|rna1374 191 VLMHGPPGTGKTLMARACAAKSET----TFLKLAGPQLVQ----MYIGDGAKLVRDAFKLALEKKptIIFIDEIDA 258
                                        68899***********99998884....777666666666....34434333333333333333245********* PP

                                        -------------HHHHHHHHHHHH CS
                              AAA_2  80 ihpkessgadvSregVqrdLLqile 104
                                        i  k++++  +   +Vqr +L +l 
  gene1374|gene1374|rna1374|rna1374 259 IGTKRTKSDRIGDREVQRTMLELLN 283
                                        ***9999999************996 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.1   2.7e-07   0.00026       1     135 [.     190     311 ..     190     313 .. 0.76

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 2.7e-07
                                        EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------.G-SEEEEESGG CS
                              AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar.egeilvlDEve 75 
                                        +vl+ GppGtgK+ +a+  aa  +++++  ++++      l++ +   +++++lv  +++ a + ++ i+++DE++
  gene1374|gene1374|rna1374|rna1374 190 GVLMHGPPGTGKTLMARACAAKSETTFLKLAGPQ------LVQMYI--GDGAKLVRDAFKLALEkKPTIIFIDEID 257
                                        599*****************99999999888887......999888..7888999999998998899********* PP

                                        G--.HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--.-TT-TTHHHH CS
                              AAA_5  76 rae.sevlnsLlslleerrllleeggelvkaknddllerfrviatanpldrslnelspalr 135
                                         +  + + +  +   e +r +le +++l ++++ d   ++ +ia++n++d     l+pal+
  gene1374|gene1374|rna1374|rna1374 258 AIGtKRTKSDRIGDREVQRTMLELLNQLDGFSSSD---DVKIIAATNRVD----ILDPALL 311
                                        99945555555444455555555555555555432...499999999998....6666665 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   1.1e-05     0.011      22      50 ..     186     214 ..     158     229 .. 0.79
   2 ?    5.4   0.0     0.023        22     122     146 ..     235     265 ..     219     291 .. 0.69

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.1e-05
                             AAA_16  22 grpelvllsGesGvGKsslvrellralek 50 
                                          p  vl +G++G+GK+ ++r+++   e+
  gene1374|gene1374|rna1374|rna1374 186 RPPKGVLMHGPPGTGKTLMARACAAKSET 214
                                        34599****************99975554 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.023
                             AAA_16 122 llkrllallsrderplvlvlDdlq.......w 146
                                        l++++++l+ + ++p+++++D+++       +
  gene1374|gene1374|rna1374|rna1374 235 LVRDAFKLALE-KKPTIIFIDEIDaigtkrtK 265
                                        56666777777.999*********44444441 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0   1.6e-07   0.00016      35      96 ..     190     259 ..     170     265 .. 0.79
   2 ?   -3.7   0.0       9.6   9.1e+03      21      38 ..     294     311 ..     291     314 .. 0.62

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 1.6e-07
                             RuvB_N  35 hvllyGpPGlGkttlakiiakelgvklkitsgPvleka..gdlaalltn.....leek.dvlfideihrl 96 
                                         vl++GpPG Gkt +a+  a++ ++++   +gP l +   gd a l+ +     le+k  ++fidei  +
  gene1374|gene1374|rna1374|rna1374 190 GVLMHGPPGTGKTLMARACAAKSETTFLKLAGPQLVQMyiGDGAKLVRDafklaLEKKpTIIFIDEIDAI 259
                                        69*******************************99774347777665432221155442799****9866 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 9.6
                             RuvB_N  21 ifieaakkreealdhvll 38 
                                        + i aa +r + ld  ll
  gene1374|gene1374|rna1374|rna1374 294 VKIIAATNRVDILDPALL 311
                                        455566666666665555 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.0   0.00027      0.26       9      29 ..     192     212 ..     186     233 .. 0.80
   2 !    7.1   0.1    0.0065       6.1      80     126 ..     238     297 ..     224     306 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00027
                             AAA_22   9 vvtGesGtGKTtllrrlleql 29 
                                        + +G++GtGKT+ +r  + + 
  gene1374|gene1374|rna1374|rna1374 192 LMHGPPGTGKTLMARACAAKS 212
                                        679************988875 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0065
                             AAA_22  80 ealeqalraravielliiDEaqhlr....s..........eealeeLrsllnl.srkgvqli 126
                                        +a+  al+++ +  ++ iDE++ +     +           ++le L +l  + s+++v++i
  gene1374|gene1374|rna1374|rna1374 238 DAFKLALEKKPT--IIFIDEIDAIGtkrtKsdrigdrevqRTMLELLNQLDGFsSSDDVKII 297
                                        555556666666..**********88765157788888889999999888888889999987 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   7.3e-06    0.0069       2      28 ..     191     217 ..     191     269 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 7.3e-06
                             AAA_33   2 vllvGlpGsGKstlaerllkklgavll 28 
                                        vl++G+pG+GK+  a+  ++k  +++l
  gene1374|gene1374|rna1374|rna1374 191 VLMHGPPGTGKTLMARACAAKSETTFL 217
                                        79***************9988884443 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.46   4.3e+02      25      51 ..      30      56 ..       7      71 .. 0.80
   2 !   11.6   0.0   0.00017      0.16      23      47 ..     189     213 ..     175     225 .. 0.85
   3 ?    0.1   0.1       0.6   5.7e+02     131     143 ..     290     302 ..     244     320 .. 0.71

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.46
                                       EEEECSTTSSHHHHHHHHHHHSTTTTS CS
                    Sigma54_activat 25 vlitGesGtGKellaraiheaskrkek 51
                                        li+Ge+   K+++++  h+ + +ke+
  gene1374|gene1374|rna1374|rna1374 30 KLIRGETDMIKSVISNIEHQIRVKKEG 56
                                       5999*********99999997766654 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00017
                                        S-EEEECSTTSSHHHHHHHHHHHST CS
                    Sigma54_activat  23 lsvlitGesGtGKellaraiheask 47 
                                          vl++G  GtGK+l+ara+ ++s+
  gene1374|gene1374|rna1374|rna1374 189 KGVLMHGPPGTGKTLMARACAAKSE 213
                                        679****************988876 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.6
                                        EE--EEEEEEESS CS
                    Sigma54_activat 131 ikvdvriiaatne 143
                                         + dv+iiaatn+
  gene1374|gene1374|rna1374|rna1374 290 SSDDVKIIAATNR 302
                                        4457888888886 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   3.3e-05     0.031       5      80 ..     191     263 ..     188     297 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.3e-05
                             AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkla..dpekllelileklkeekktylflDEiqevpe 78 
                                        +++ G+  +GKT +++ ++ ++      + +++l  +++ ++   d +kl +  ++++ e+k t++f+DEi  + +
  gene1374|gene1374|rna1374|rna1374 191 VLMHGPPGTGKTLMARACAAKSE-----TTFLKLAGPQLVQMYigDGAKLVRDAFKLALEKKPTIIFIDEIDAIGT 261
                                        7889**************97776.....66666666666443311544777777776444599********98855 PP

                             AAA_14  79 we 80 
                                         +
  gene1374|gene1374|rna1374|rna1374 262 KR 263
                                        44 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   7.6e-05     0.071      22      42 ..     191     211 ..     178     217 .. 0.87
   2 ?   -1.0   0.0       1.1     1e+03      76     116 ..     274     314 ..     250     320 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 7.6e-05
                                        EEEE--TTSSTTHHHHHHHHH CS
                               PhoH  22 vfaiGpaGtGKtylavalave 42 
                                        v + Gp GtGKt++a a+a++
  gene1374|gene1374|rna1374|rna1374 191 VLMHGPPGTGKTLMARACAAK 211
                                        7899**************987 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.1
                                        --TTTHHHHHHHTTTS-TTCHHHHHHTTSEEEEEGGGGTT- CS
                               PhoH  76 vdpylrplydaLkdllgaekvekllekgkievaplaymRGr 116
                                        v+  +  l ++L+ + +++ v+ +  ++++ +++ a +R  
  gene1374|gene1374|rna1374|rna1374 274 VQRTMLELLNQLDGFSSSDDVKIIAATNRVDILDPALLRSG 314
                                        56667788899999999999999999999999999999954 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   5.5e-05     0.052      25      42 ..     191     208 ..     182     212 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5.5e-05
                       Mg_chelatase  25 lllvGppGsGKtmlakrl 42 
                                        +l+ GppG+GKt++a++ 
  gene1374|gene1374|rna1374|rna1374 191 VLMHGPPGTGKTLMARAC 208
                                        89*************975 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00013      0.12      28      58 ..     183     213 ..     175     262 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00013
                              AAA_7  28 lllknkkpvllvGptGtGKtviikdllkkld 58 
                                        l ++  k vl+ Gp GtGKt++++ +  k +
  gene1374|gene1374|rna1374|rna1374 183 LNIRPPKGVLMHGPPGTGKTLMARACAAKSE 213
                                        55666789***************99877766 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       5.2   4.9e+03      91      94 ..      50      53 ..      18      95 .. 0.54
   2 ?   11.9   0.0   0.00015      0.15      20      36 ..     191     207 ..     178     247 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 5.2
                             AAA_11 91 vRvg 94
                                       +Rv 
  gene1374|gene1374|rna1374|rna1374 50 IRVK 53
                                       1221 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00015
                             AAA_11  20 tliqGPPGtgKTktive 36 
                                        +l++GPPGtgKT +  +
  gene1374|gene1374|rna1374|rna1374 191 VLMHGPPGTGKTLMARA 207
                                        79**********76655 PP

>> Prot_ATP_OB_N  Proteasomal ATPase OB N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.1   0.00073      0.69      10      52 ..      82     128 ..      73     135 .. 0.75
   2 ?    0.3   0.0      0.58   5.5e+02      21      37 ..     338     352 ..     327     354 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00073
                      Prot_ATP_OB_N  10 s...qdgtadVlvggrrm.rVavsPlvdaeeLrpGqeVlLnEalvvV 52 
                                        +   +d++a V+++ r    +++  lv+a++LrpG+ V L    +v+
  gene1374|gene1374|rna1374|rna1374  82 DdeeNDKSAVVSTSTRVTsFLPMIGLVEAQDLRPGDMVSLHKETNVI 128
                                        45557888888888886525788889**************8777776 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.58
                      Prot_ATP_OB_N  21 grrmrVavsPlvdaeeL 37 
                                         r+mrV  s +v+ +eL
  gene1374|gene1374|rna1374|rna1374 338 ARKMRV--SNNVNFDEL 352
                                        699999..777777776 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       9.1   8.6e+03     131     154 ..      78     101 ..      76     106 .. 0.74
   2 ?   11.4   0.0   0.00021       0.2      48      70 ..     189     211 ..     181     229 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 9.1
                          IstB_IS21 131 feviekryerrsiiitsnlpfaew 154
                                         e++++  + +s ++++   + ++
  gene1374|gene1374|rna1374|rna1374  78 VEILDDEENDKSAVVSTSTRVTSF 101
                                        678888888888888888877776 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00021
                          IstB_IS21  48 enivllGpsGvGKshlaialgve 70 
                                        +++++ Gp+G+GK+ +a a + +
  gene1374|gene1374|rna1374|rna1374 189 KGVLMHGPPGTGKTLMARACAAK 211
                                        68999************998876 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.3   0.00068      0.65      21      43 ..     191     213 ..     181     266 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00068
                             AAA_30  21 avltGpAGtGKttalkalreawe 43 
                                        ++++Gp+GtGKt + +a ++  e
  gene1374|gene1374|rna1374|rna1374 191 VLMHGPPGTGKTLMARACAAKSE 213
                                        5789**********999877655 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00049      0.46       1      41 [.     191     222 ..     191     265 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00049
                       RNA_helicase   1 iwlyGpsgeGKStlakeLakallkklklkkkdsvysrnped 41 
                                        ++++Gp+g+GK+++a+  a++         +++++ + +  
  gene1374|gene1374|rna1374|rna1374 191 VLMHGPPGTGKTLMARACAAK---------SETTFLKLAGP 222
                                        679*************94433.........34444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (407 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       741  (0.0413297); expected 358.6 (0.02)
Passed bias filter:                      569  (0.0317363); expected 358.6 (0.02)
Passed Vit filter:                        96  (0.00535445); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.57u 0.32s 00:00:00.88 Elapsed: 00:00:00.45
# Mc/sec: 2716.13
//
Query:       gene1375|gene1375|rna1375|rna1375  [L=107]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.5e-16   57.8   0.0    1.1e-15   57.6   0.0    1.0  1  Frataxin_Cyay  Frataxin-like domain
     0.0093   16.2   0.0      0.015   15.5   0.0    1.3  1  ARD            ARD/ARD' family


Domain annotation for each model (and alignments):
>> Frataxin_Cyay  Frataxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.6   0.0   1.3e-19   1.1e-15       2     101 ..       7      98 ..       6     103 .. 0.91

  Alignments for each domain:
  == domain 1  score: 57.6 bits;  conditional E-value: 1.3e-19
                                        HHHHHHHHHHHHHHHHHHHH.HHHHH--CTS.SEEEETTEEEEEETTS-EEEEEEEGGGTEEEEEES.SEEEEEEE CS
                      Frataxin_Cyay   2 sdeeyhkladelldsleekleelaeeaeedeldveyssgvLtiefekkgtyvinkqppnkqIWlsspisgpkrfdy 77 
                                        +++ y ++a ++l +le+kl    ++   d  ++e +++v++ +++  g yv+++qp   ++W+sspi gp +f +
  gene1375|gene1375|rna1375|rna1375   7 DQRSYLTAAHNTLTALEKKL----DN---DYGEIEHNNNVIEYTVDGVGRYVVSRQPSVMELWVSSPITGPSKFGM 75 
                                        5778999*************....55...3458******************************************* PP

                                        ET.TEEEETTTT-BHHHHHHHHHH CS
                      Frataxin_Cyay  78 dekgeWiskrdgseLkelLeeels 101
                                        +e ++++ k++g e+++ +e e++
  gene1375|gene1375|rna1375|rna1375  76 VE-KKFVEKKNGMEIMKYFEMEME 98 
                                        *9.79**********999999886 PP

>> ARD  ARD/ARD' family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   1.7e-06     0.015      67     112 ..      12      57 ..       2      66 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.7e-06
                                ARD  67 vevlkestpnfdeklekFfeEhlhedeeirliveGtgyFdvrskde 112
                                        +++ +++   +++kl++ + E  h+++ i + v+G g ++v  ++ 
  gene1375|gene1375|rna1375|rna1375  12 LTAAHNTLTALEKKLDNDYGEIEHNNNVIEYTVDGVGRYVVSRQPS 57 
                                        5677789999*******************************98865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       567  (0.0316247); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 715.33
//
Query:       gene1376|gene1376|rna1376|rna1376  [L=614]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (614 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       850  (0.0474092); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.58u 0.23s 00:00:00.81 Elapsed: 00:00:00.41
# Mc/sec: 4537.83
//
Query:       gene1377|gene1377|rna1377|rna1377  [L=187]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.054   13.6   0.0        0.1   12.6   0.0    1.4  1  DUF2269   Predicted integral membrane protein (DUF2269)


Domain annotation for each model (and alignments):
>> DUF2269  Predicted integral membrane protein (DUF2269)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   5.7e-06       0.1      76     125 ..       6      55 ..       2      61 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.7e-06
                            DUF2269  76 qsWlllslvLyllagalwlpVvwlqirlrrlaeaaeeegaalpeeyvrlf 125
                                         +W++ls  ++l+a++  l+++ l i+ +r  +a +++ +++p+  ++l+
  gene1377|gene1377|rna1377|rna1377   6 LKWIVLSFFIFLFAVFTPLLLLTLYIKSKRIDRAFTNAIKDIPATEQTLN 55 
                                        58************************999999988888888887776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       876  (0.0488594); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1306.60
//
Query:       gene1378|gene1378|rna1378|rna1378  [L=121]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       563  (0.0314016); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.30s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 846.90
//
Query:       gene1379|gene1379|rna1379|rna1379  [L=146]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1139  (0.0635284); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.50
# Mc/sec: 876.07
//
Query:       gene138|gene138|rna138|rna138  [L=244]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.1e-24   84.2   0.1    5.1e-24   83.5   0.1    1.4  1  Ribosomal_S5_C  Ribosomal protein S5, C-terminal domain
    7.8e-23   80.2   2.1    1.7e-22   79.2   2.1    1.6  1  Ribosomal_S5    Ribosomal protein S5, N-terminal domain


Domain annotation for each model (and alignments):
>> Ribosomal_S5_C  Ribosomal protein S5, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.5   0.1   5.7e-28   5.1e-24       2      64 ..     149     212 ..     148     219 .. 0.93

  Alignments for each domain:
  == domain 1  score: 83.5 bits;  conditional E-value: 5.7e-28
                                    EEETTEEEEEEE--TT--EES-HHHHHHHHHHT--SEE---BS.-SSHHHHHHHHHHHHHHTTT CS
                 Ribosomal_S5_C   2 gkfgavkvllkpaprGtGiiaggavravlelaGikDvlakslg.srnpinvvkAtfeALkklrs 64 
                                    gk g+v+++l+pap+GtG++agg++r++l++aG+kD+++ks g + n+ n++kAt++AL + ++
  gene138|gene138|rna138|rna138 149 GKAGSVRIKLIPAPKGTGLVAGGVPRTILRMAGVKDIYSKSVGqTCNTENFAKATVDALVRASN 212
                                    9**********************************************************87665 PP

>> Ribosomal_S5  Ribosomal protein S5, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.2   2.1   1.9e-26   1.7e-22       1      65 []      65     129 ..      65     129 .. 0.98

  Alignments for each domain:
  == domain 1  score: 79.2 bits;  conditional E-value: 1.9e-26
                                    XEEEEEEEEEEEEEETTEEEEEEEEEEEEEETTTEEEEEEEEESSHHHHHHHHHHHHHHTEEE-- CS
                   Ribosomal_S5   1 lkekvlkikrvqkvtkgGrrtsfsalvvvGdgnGlvGlGvgkakevatAirkAiekAkknlvpvp 65 
                                    lke+vl +++vqk+tk+G+rt+++alv vGdg+  vG+G + +++ atAir+A+++Ak  l++v+
  gene138|gene138|rna138|rna138  65 LKEEVLCVNSVQKQTKAGQRTRIKALVCVGDGKCFVGIGAKTSRDAATAIRGAVQRAKCALMYVK 129
                                    79*************************************************************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (244 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       414  (0.0230911); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1656.21
//
Query:       gene1380|gene1380|rna1380|rna1380  [L=461]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.4e-12   46.6   0.2    5.7e-12   45.4   0.2    1.6  1  DNA_mis_repair  DNA mismatch repair protein, C-terminal domai
    1.4e-05   24.6   0.4    1.4e-05   24.6   0.4    2.7  3  Mlh1_C          DNA mismatch repair protein Mlh1 C-terminus


Domain annotation for each model (and alignments):
>> DNA_mis_repair  DNA mismatch repair protein, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.4   0.2   6.3e-16   5.7e-12      32     116 ..     107     189 ..      94     192 .. 0.88

  Alignments for each domain:
  == domain 1  score: 45.4 bits;  conditional E-value: 6.3e-16
                                        CCG-BTTGGEEEEEETTEEE--HHHHHHHHHHHHCCSSSSSB-EEEEEEEESSGGEE-TSSTT----EETTHHCHH CS
                     DNA_mis_repair  32 pelsrskrdkqflfvNgRlvkskelkkaireaYkellpkgrypvvvLnleidpeevDvNvhPtKreVrfqdeeevi 107
                                        + ++++k    +l +N+Rlvks++lk  + + Y+ +lp++++p+++++  ++ e++DvNv   K++V f  e+ ++
  gene1380|gene1380|rna1380|rna1380 107 SPVHHQKDLILILSINNRLVKSPTLKSKLYNLYRPFLPNRSFPFIYVE--MKVENCDVNVDAMKQRVLFVGEDDLF 180
                                        4467777788899******************************98876..566899******************** PP

                                        HHHHHHHHH CS
                     DNA_mis_repair 108 eaieealke 116
                                        e + e++ +
  gene1380|gene1380|rna1380|rna1380 181 ERVCEMVGK 189
                                        ***999876 PP

>> Mlh1_C  DNA mismatch repair protein Mlh1 C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.3      0.32   2.9e+03      79     121 ..     214     250 ..     201     259 .. 0.47
   2 !   24.6   0.4   1.6e-09   1.4e-05      12      76 ..     302     366 ..     292     373 .. 0.84
   3 ?    1.4   0.0     0.018   1.6e+02     233     269 ..     426     460 ..     420     460 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.32
                                        -BHHHHHTTS-SHH.................HHHHHHHHHHHT CS
                             Mlh1_C  79 lslkeLlelaleeeeeeeeeeseeedkskeelaekivelLiek 121
                                        l++k+L +  ++++      ++++e++++ee++e+ +++L+ +
  gene1380|gene1380|rna1380|rna1380 214 LKVKNLENYEFKSNT-----NTHREAAAVEEIKEN-TSMLNVQ 250
                                        444444444444443.....222333334444433.3444444 PP

  == domain 2  score: 24.6 bits;  conditional E-value: 1.6e-09
                                        HHHHB-HHHHHHHHT-EEEEEEETTEEEEEETTEEEEEEHHHHHHHHHHHHHHHHTT--EEEE-G CS
                             Mlh1_C  12 veesahkeLteilanltfVGlvderlaliQhgtkLylvdygalskelfyqllLtdFgnfgeikLe 76 
                                         ++ +++  +++++++++VG  +++ +++Q +t L+ +dy++l++ +f q l+t+ g+f++  ++
  gene1380|gene1380|rna1380|rna1380 302 RKNYQKNATNRFVKDMKYVGKLNDEKIFVQLNTFLMQCDYKKLLRCYFVQQLITQKGRFKTTVVK 366
                                        34445566677899********************************************9987665 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.018
                                        THHHHHHHH---BGGGGG..GEEEEEEHHHHHHHS-- CS
                             Mlh1_C 233 vlfpaikarllppksllkdgtvvevasledLYkVFER 269
                                        ++f  ik+ +   +++ +  ++  v+ l++LYk F R
  gene1380|gene1380|rna1380|rna1380 426 TFFSIIKRGINEDEDVFS--CFSVVTGLNELYKAFKR 460
                                        567777777777777777..8999***********87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (461 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1033  (0.0576162); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 3203.12
//
Query:       gene1381|gene1381|rna1381|rna1381  [L=162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.7e-09   37.6   0.1    2.2e-09   37.3   0.1    1.2  1  HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like
    0.00015   22.3   0.0     0.0003   21.2   0.0    1.7  1  HATPase_c    Histidine kinase-, DNA gyrase B-, and HSP90-like
  ------ inclusion threshold ------
      0.093   12.9   0.8       0.15   12.3   0.8    1.5  1  DUF4451      Domain of unknown function (DUF4451)
       0.17   12.1   0.1        0.6   10.3   0.0    2.0  2  NdhO         Cyanobacterial and plant NDH-1 subunit O


Domain annotation for each model (and alignments):
>> HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.3   0.1   4.9e-13   2.2e-09       5     105 ..      25     126 ..      20     155 .. 0.78

  Alignments for each domain:
  == domain 1  score: 37.3 bits;  conditional E-value: 4.9e-13
                        HATPase_c_3   5 kAlaelvdNsldAdaenvkievnknrgktgeivieDdGkGmseeelkn.alrlatsskeakrksts.....lGkkG 74 
                                        +++ el++Ns+dA a  + + + +n      iv eD+G+G++e++++    r+ ts+ + + +++      +  +G
  gene1381|gene1381|rna1381|rna1381  25 SVIKELLENSIDAGASVIRVGYAEN------IVMEDNGSGITEDDFELlCARYCTSKLSDECDKKRdildnVCTYG 94 
                                        6899******************994......****************96667777766655332223577788899 PP

                        HATPase_c_3  75 i.GlklAslslgkkltvitkkegesstltldv 105
                                        + G  lAs+s  +++ v tk+ ++ +   l +
  gene1381|gene1381|rna1381|rna1381  95 FrGEALASISDVSTVVVRTKTTNCAYGHVLVY 126
                                        88999****************99988444433 PP

>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0   6.8e-08    0.0003       5      63 ..      22      73 ..      18     148 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 6.8e-08
                                       HHHHHHHHHHHHHHHHHSTTTEEEEEEEEEETEEEEEEEESSSSSTTHHHTGTCSTTCH CS
                          HATPase_c  5 rLrqiisnlvdNavkfatkageieveikaseddlvisveDnGiGipkedlkklfekfsq 63
                                       r   +i++l++N++++   a+ i+v     e    i  eDnG Gi+++d ++l +++ +
  gene1381|gene1381|rna1381|rna1381 22 RPLSVIKELLENSIDA--GASVIRVGYA--E---NIVMEDNGSGITEDDFELLCARYCT 73
                                       56689**********6..6788888877..4...6779*************87777776 PP

>> DUF4451  Domain of unknown function (DUF4451)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.8   3.3e-05      0.15      34      73 ..     107     148 ..      52     160 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3.3e-05
                            DUF4451  34 ekkekflklknssyekhlsfeHGvl..sngslvpePillrsk 73 
                                        ++ ++  k+ n++y + l +eHGvl  +++ ++++++++ +k
  gene1381|gene1381|rna1381|rna1381 107 STVVVRTKTTNCAYGHVLVYEHGVLisKKKEAMKNGTMITVK 148
                                        44555677889*************998888899999988655 PP

>> NdhO  Cyanobacterial and plant NDH-1 subunit O
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00013       0.6       8      36 ..      25      56 ..      17      71 .. 0.81
   2 ?   -2.2   0.0       1.1   4.7e+03       1      10 [.     139     148 ..     129     151 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00013
                               NdhO  8 rvekekyenSlealAsdgrlp...dYifedkG 36
                                        v+ke +enS++a As+ r+    + + ed+G
  gene1381|gene1381|rna1381|rna1381 25 SVIKELLENSIDAGASVIRVGyaeNIVMEDNG 56
                                       599*************9988666566666666 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.1
                               NdhO   1 lkkGqlVrve 10 
                                        +k G+++ v+
  gene1381|gene1381|rna1381|rna1381 139 MKNGTMITVK 148
                                        6778877775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       559  (0.0311785); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 1037.92
//
Query:       gene1382|gene1382|rna1382|rna1382  [L=327]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (327 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1076  (0.0600145); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 2191.79
//
Query:       gene1383|gene1383|rna1383|rna1383  [L=154]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.4e-19   68.7   0.8    4.7e-19   68.2   0.8    1.2  1  Motile_Sperm  MSP (Major sperm protein) domain


Domain annotation for each model (and alignments):
>> Motile_Sperm  MSP (Major sperm protein) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.2   0.8   2.6e-23   4.7e-19       4     102 ..       8      97 ..       5     103 .. 0.86

  Alignments for each domain:
  == domain 1  score: 68.2 bits;  conditional E-value: 2.6e-23
                                        EESSSEEEEESSTSSHEEEEEEEEE-SSSSEEEEEEES-TTTEEEESSEEEETTTCEEEEEEEEESSSSSTTSTCC CS
                       Motile_Sperm   4 idPsdllvfaaelnkqgtsklklkNtskkrvaFkvkttapkkyrvrPnvGiikpgesveitvtlkpldeepsekkk 79 
                                        i Ps++++  +++   ++ +++l+N+  +  a+k++tt+pk y vrPn+Giikp ++++i+v+l++    +  +k+
  gene1383|gene1383|rna1383|rna1383   8 ILPSKYVTIDNTT---RKGTITLQNNVLSGGAYKIRTTSPKDYSVRPNIGIIKPLQTITINVILQS----ECTSKN 76 
                                        5688888888877...99************************************************....66667* PP

                                        EEEEEEEEES-TT-STHHHHHHH CS
                       Motile_Sperm  80 dkfviqylevpgdekdekeafke 102
                                        +kf+++++ +  d k++ + fk+
  gene1383|gene1383|rna1383|rna1383  77 HKFMVEVYDF--DYKKSVDEFKK 97 
                                        **********..55555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       854  (0.0476323); expected 358.6 (0.02)
Passed bias filter:                      505  (0.0281667); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 1084.97
//
Query:       gene1384|gene1384|rna1384|rna1384  [L=54]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (54 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       337  (0.0187964); expected 358.6 (0.02)
Passed bias filter:                      201  (0.0112109); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 392.05
//
Query:       gene1385|gene1385|rna1385|rna1385  [L=211]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.015   15.7   0.4      0.015   15.7   0.4    2.0  2  HEPN_Apea  Apea-like HEPN
       0.52   10.4   7.1       0.93    9.6   5.6    2.4  2  HTH_56     Cch helix turn helix domain


Domain annotation for each model (and alignments):
>> HEPN_Apea  Apea-like HEPN
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.7   0.4   1.6e-06     0.015      17      84 ..      13      98 ..       9     100 .. 0.75
   2 ?   -0.3   0.6      0.16   1.5e+03      24      40 ..     136     152 ..     101     208 .. 0.54

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.6e-06
                          HEPN_Apea 17 fgeaire.eddedaildlvialEaldll................ldkkeeitekislrsn...aylkedkeerkelkk 74
                                       +++++++ +++  +++ +v  +++l+ +                ++k +++ +ki++ ++   ++++e k+ +k ++ 
  gene1385|gene1385|rna1385|rna1385 13 LKKNCTDaSHNGCKYIIYVNFFDFLHEFgllvshlmvydimkgvTEK-KKVIDKITEEILenrKQFGE-KHRGKTYYA 88
                                       555555413334449999999999977799***********996444.44778887777665577777.9******** PP

                          HEPN_Apea 75 kikklYdlRS 84
                                        +k++Y++ +
  gene1385|gene1385|rna1385|rna1385 89 VWKEAYKISN 98
                                       ******9866 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.16
                          HEPN_Apea  24 eddedaildlvialEal 40 
                                        ++ + + ld+  + E++
  gene1385|gene1385|rna1385|rna1385 136 KYLRYRCLDITESYEIA 152
                                        33333355555555554 PP

>> HTH_56  Cch helix turn helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       0.8   7.2e+03      49      62 ..      28      41 ..      12      45 .. 0.49
   2 ?    9.6   5.6    0.0001      0.93       4      59 ..      60     114 ..      57     180 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 0.8
                             HTH_56 49 Ilknvfdkileeag 62
                                       I+   f ++l+e+g
  gene1385|gene1385|rna1385|rna1385 28 IIYVNFFDFLHEFG 41
                                       33333333444443 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0001
                             HTH_56   4 ekayefilqwiaqnqskFkeegkeasnpneiwGkiekkkektevyIlknvfdkile 59 
                                        +k+++ i + i +n+++F e+++ +     +w    k ++kt++ I  +  ++i++
  gene1385|gene1385|rna1385|rna1385  60 KKVIDKITEEILENRKQFGEKHRGK-TYYAVWKEAYKISNKTNLTINLEPIQDIMN 114
                                        7999*******************95.566899999999999996666666666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1522  (0.0848904); expected 358.6 (0.02)
Passed bias filter:                      479  (0.0267165); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1335.67
//
Query:       gene1386|gene1386|rna1386|rna1386  [L=79]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0082   16.0   0.1     0.0087   16.0   0.1    1.1  1  TMEM154   TMEM154 protein family
  ------ inclusion threshold ------
      0.056   13.3   0.1      0.062   13.1   0.1    1.1  1  Mid2      Mid2 like cell wall stress sensor


Domain annotation for each model (and alignments):
>> TMEM154  TMEM154 protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.1   9.7e-07    0.0087      36      97 ..      12      73 ..       2      78 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 9.7e-07
                            TMEM154 36 kqeeakeslssaelsnesdq.lelvlmiiiPlvllillllvviiliqkkkrkrsKddekseae 97
                                       +q+ a++ +   ++s   +    ++l i+ Plv + +l+++ ++++ + +  + K d +++ +
  gene1386|gene1386|rna1386|rna1386 12 PQTYANKMITTEDISSYGSLiRTNILFIANPLVGITILVILALVFV-YNRCIKPKLDGQKQIQ 73
                                       466677777777776655541457**********************.7887888887666654 PP

>> Mid2  Mid2 like cell wall stress sensor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   6.9e-06     0.062      39      76 ..      29      65 ..       5      70 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 6.9e-06
                               Mid2 39 sGLskknrniviGcvvGigvPlllvillllyifCiksk 76
                                         L + n   +    vGi++  +++ l+++y  Cik+k
  gene1386|gene1386|rna1386|rna1386 29 GSLIRTNILFIANPLVGITIL-VILALVFVYNRCIKPK 65
                                       445666666677778999985.45567899******97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       750  (0.0418317); expected 358.6 (0.02)
Passed bias filter:                      493  (0.0274974); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 567.08
//
Query:       gene1387|gene1387|rna1387|rna1387  [L=69]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (69 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1133  (0.0631937); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.43
# Mc/sec: 482.73
//
Query:       gene1388|gene1388|rna1388|rna1388  [L=55]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (55 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       344  (0.0191868); expected 358.6 (0.02)
Passed bias filter:                      193  (0.0107647); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.31u 0.26s 00:00:00.57 Elapsed: 00:00:00.39
# Mc/sec: 418.49
//
Query:       gene1389|gene1389|rna1389|rna1389  [L=44]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (44 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       354  (0.0197445); expected 358.6 (0.02)
Passed bias filter:                      193  (0.0107647); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.23s 00:00:00.57 Elapsed: 00:00:00.39
# Mc/sec: 336.41
//
Query:       gene139|gene139|rna139|rna139  [L=959]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-05   23.6   1.4    0.00013   21.4   0.1    2.7  2  SH2_2     SH2 domain
     0.0089   16.1   0.1      0.024   14.7   0.1    1.8  1  SH2       SH2 domain


Domain annotation for each model (and alignments):
>> SH2_2  SH2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.2     0.084   7.6e+02      13      37 ..     311     335 ..     300     344 .. 0.54
   2 !   21.4   0.1   1.5e-08   0.00013      34     136 ..     820     912 ..     818     921 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.084
                          SH2_2  13 keeekkkkeekkrkkyvkRvikHpn 37 
                                    k++++k+  ++k k yv R+ kHp 
  gene139|gene139|rna139|rna139 311 KNNTNKESLRRKIKGYVLRMSKHPY 335
                                    2222233323333448888888885 PP

  == domain 2  score: 21.4 bits;  conditional E-value: 1.5e-08
                          SH2_2  34 kHpnFknvsaeeaeellaskerGdvviRPSskgedhLtvtwkvadgvyqhidvlEedkenefslgktLiigkeeyeDLDe 113
                                    +Hp++ + +a+ a ++l+++++  +++R Ss  +++  vt++++d+++ h++++ ++           + ++ +ye+ D 
  gene139|gene139|rna139|rna139 820 SHPLYVDCTAAAAHNILRQRRQL-LLLRKSSS-KQYGVVTLRLTDEIFVHYKIEQDNGG--------VLFNNRRYENVDH 889
                                    6****************987765.66666665.58889***************766655........567999******* PP

                          SH2_2 114 liarhvepmakkveellahekfk 136
                                    +i  + ++m+k + e+++ + + 
  gene139|gene139|rna139|rna139 890 VIYCYFREMVKILAEVMNDKDYG 912
                                    *******************9986 PP

>> SH2  SH2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.1   2.7e-06     0.024      10      77 .]     831     894 ..     825     894 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.7e-06
                                    HHHHHHHTTSSTTEEEEEEESSSTTEEEEEEEETTEEEEEEEEEETTSEEEEETTEEESSHHHHHHHH CS
                            SH2  10 eaerlLleekkdGtFLvReSeskpGdytlsvvedgkvkhykiqstengkyyiteeekfsslaeLvehY 77 
                                     a+++L++  ++   L+R+S+sk+ +++   ++d+ + hyki++++ g  +++++++++++++ ++ Y
  gene139|gene139|rna139|rna139 831 AAHNILRQ--RRQLLLLRKSSSKQYGVVTLRLTDEIFVHYKIEQDNGG--VLFNNRRYENVDHVIYCY 894
                                    56777776..77788*******776666666677789**********9..9999********999988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (959 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       648  (0.0361426); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.66u 0.30s 00:00:00.96 Elapsed: 00:00:00.45
# Mc/sec: 6456.56
//
Query:       gene1390|gene1390|rna1390|rna1390  [L=92]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.017   15.1   0.2      0.019   15.0   0.2    1.1  1  MtlR      Mannitol repressor
      0.075   13.1   0.0      0.078   13.1   0.0    1.0  1  DUF72     Protein of unknown function DUF72


Domain annotation for each model (and alignments):
>> MtlR  Mannitol repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.2   2.1e-06     0.019      84     124 ..      19      59 ..       8      86 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.1e-06
                               MtlR  84 elfiqlkeelnedekeyeFsddeildfikelhlvsekslle 124
                                        +l++++ e +++d++++  +d ei +f ++l+l+ ++++  
  gene1390|gene1390|rna1390|rna1390  19 SLYMKISEMMKKDNHNVWLTDSEIAEFTQHLSLFMDEKVPI 59 
                                        589*****************************998866433 PP

>> DUF72  Protein of unknown function DUF72
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   8.7e-06     0.078      62     110 ..      34      83 ..      14      92 .] 0.77

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 8.7e-06
                                        G-.SCHHHHHHHHHH.CHHHCT-EEEEEEE--TT--S.HHHHHHHHHH.TT CS
                              DUF72  62 ne.daeealerflesalepLgeklgpllfQlppsfkfdeenlerLeaf.la 110
                                        n   +++++++f ++ l+ +++   p+l Q+ ++ ++de+ ++r+++f ++
  gene1390|gene1390|rna1390|rna1390  34 NVwLTDSEIAEFTQH-LSLFMDEKVPILYQIDYQTRCDEKLMDRIKKFcFT 83 
                                        33358999******8.999999999*************99********644 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       707  (0.0394333); expected 358.6 (0.02)
Passed bias filter:                      441  (0.024597); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.28s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 635.31
//
Query:       gene1391|gene1391|rna1391|rna1391  [L=66]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    4.2e-08   33.0   0.0    5.3e-08   32.7   0.0    1.2  1  RVT_1       Reverse transcriptase (RNA-dependent DNA polymera
  ------ inclusion threshold ------
      0.049   12.9   0.0      0.051   12.9   0.0    1.0  1  RE_NgoFVII  NgoFVII restriction endonuclease


Domain annotation for each model (and alignments):
>> RVT_1  Reverse transcriptase (RNA-dependent DNA polymerase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.7   0.0   5.9e-12   5.3e-08      62     148 ..       5      66 .]       1      66 [] 0.93

  Alignments for each domain:
  == domain 1  score: 32.7 bits;  conditional E-value: 5.9e-12
                                        HCCHTS--EEEEEEBCCGCCCSBB-GGGGGGG-EEET.........................TEEEEESB--ST-T CS
                              RVT_1  62 lkkkkkaklllklDlkkaFdsvpleellrkltafkvptklinliksflstrsfsvrvngeeskgryekkglpqGsv 137
                                        ++ +++++ l+ lDlk ++  ++ ee ++ +taf +                             ye++g+ +G++
  gene1391|gene1391|rna1391|rna1391   5 VETTTGSNNLTVLDLKEGYYEIEIEEADKHKTAFEFG-------------------------NNVYEWCGIVMGFK 55 
                                        556789999****************************.........................789*********** PP

                                        THHHHHHHHHH CS
                              RVT_1 138 lSPllfnlfmn 148
                                        ++P++f++++n
  gene1391|gene1391|rna1391|rna1391  56 NAPMIFQRVIN 66 
                                        ********997 PP

>> RE_NgoFVII  NgoFVII restriction endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   5.7e-06     0.051      93     131 ..       4      40 ..       1      49 [. 0.77

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5.7e-06
                                        EEEEEEESXXSXXTTSXXXSBXEEEEEE.HHHHHHHHHH CS
                         RE_NgoFVII  93 plsAliGSANlssnglrtrqrEtlvdldtedafkeldey 131
                                        +++  +GS+Nl+++ l++ ++E+ ++  ++d+ k+  e+
  gene1391|gene1391|rna1391|rna1391   4 IVETTTGSNNLTVLDLKEGYYEIEIE--EADKHKTAFEF 40 
                                        678899*****************988..45655555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (66 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       378  (0.0210832); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.29s 00:00:00.69 Elapsed: 00:00:00.46
# Mc/sec: 435.49
//
Query:       gene1392|gene1392|rna1392|rna1392  [L=269]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.8e-25   88.3   0.5    7.5e-25   88.0   0.5    1.1  1  DDE_Tnp_1_7      Transposase IS4
    0.00057   20.6   7.9     0.0013   19.5   7.9    1.6  1  Tnp_zf-ribbon_2  DDE_Tnp_1-like zinc-ribbon
     0.0091   16.3   3.3     0.0096   16.2   0.9    2.2  2  C1_2             C1 domain
     0.0093   16.0   5.8      0.021   14.9   5.8    1.5  1  Ribosomal_L37ae  Ribosomal L37ae protein family
  ------ inclusion threshold ------
      0.034   14.0   0.2       0.32   10.8   0.1    2.2  2  RMI1_C           Recq-mediated genome instability protein 1, 
        7.3    6.0   9.6         13    5.3   1.1    3.3  3  zf-RanBP         Zn-finger in Ran binding protein and others


Domain annotation for each model (and alignments):
>> DDE_Tnp_1_7  Transposase IS4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.0   0.5   2.5e-28   7.5e-25     194     347 ..       1     154 [.       1     157 [. 0.92

  Alignments for each domain:
  == domain 1  score: 88.0 bits;  conditional E-value: 2.5e-28
                        DDE_Tnp_1_7 194 lvlrLleplqgkgrvvvmdnfftslellqeLakkgtyavGtlkknrsglPkel.tqklpkgellaryggplmllkw 268
                                        +v  L +p+++kg+++++dn ++sl+l++ L +++t + Gt++ +r+++Pk++  +k++ ge  +r+++ l  +kw
  gene1392|gene1392|rna1392|rna1392   1 VVKDLSKPVLHKGHILYLDNWYCSLNLFVTLLNSKTNVIGTVRAKRKNMPKDFlRTKFKTGEYEMRSCNGLLAVKW 76 
                                        6899*************************************************8899******************* PP

                        DDE_Tnp_1_7 269 ndrkkvkllstyssqklveskers.gqkikarpklvedYnqalgavdrhdqllqayraslktskkwykrvliflls 343
                                        +d+  v +lst +++  + ++ ++  + +  + k+v +Yn+ + +vd  dq+l+ +   +k  +k y++++++l++
  gene1392|gene1392|rna1392|rna1392  77 KDKRDVFILSTKHTTVAITQQITKqHNPT-WKLKCVIEYNKEVIGVDLQDQMLACFPLMRKC-MKGYRKIFFYLFD 150
                                        **************888665555505556.9*********************9999999995.9************ PP

                        DDE_Tnp_1_7 344 iavv 347
                                        +a++
  gene1392|gene1392|rna1392|rna1392 151 MALF 154
                                        *986 PP

>> Tnp_zf-ribbon_2  DDE_Tnp_1-like zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   7.9   4.4e-07    0.0013       1      27 [.     229     259 ..     229     261 .. 0.91

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 4.4e-07
                    Tnp_zf-ribbon_2   1 kRCkvClkkkikkeTriiCqeCd....vplC 27 
                                        +RC vC k k ++eT+  C++C     vp+C
  gene1392|gene1392|rna1392|rna1392 229 RRCVVCTKHKQRRETTWECKKCKivlhVPTC 259
                                        7*********************77777***9 PP

>> C1_2  C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.1      0.94   2.8e+03       2      10 ..      10      19 ..      10      38 .. 0.80
   2 !   16.2   0.9   3.2e-06    0.0096      11      44 ..     221     256 ..     202     260 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.94
                               C1_2  2 sHp.HpLtls 10
                                       +H+ H L l+
  gene1392|gene1392|rna1392|rna1392 10 LHKgHILYLD 19
                                       5999999998 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 3.2e-06
                               C1_2  11 kgedssesfnCsaCgrkidgff..YsCseCdfslhv 44 
                                        ++ +++ +++C +C +  +  +   +C++C+++lhv
  gene1392|gene1392|rna1392|rna1392 221 TSLNQHPKRRCVVCTKHKQRREttWECKKCKIVLHV 256
                                        567788899********6555578***********5 PP

>> Ribosomal_L37ae  Ribosomal L37ae protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   5.8   6.9e-06     0.021      18      59 ..     213     252 ..     208     256 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 6.9e-06
                                        HHHHHHHHHHHHHHS-BEESSSSSSEEEEEETTEEEETTTTE CS
                    Ribosomal_L37ae  18 slrkrvkkieisqhakytCpfcgktkvkRkavgiwkCkkcgk 59 
                                          rk +  +  +qh k +C  c k+k +R+ +  w+Ckkc+ 
  gene1392|gene1392|rna1392|rna1392 213 HFRKHIDPTSLNQHPKRRCVVCTKHKQRRETT--WECKKCKI 252
                                        579***********************999986..******85 PP

>> RMI1_C  Recq-mediated genome instability protein 1, C-terminal OB-fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0     0.069   2.1e+02      78     122 ..      38      81 ..      24      91 .. 0.77
   2 ?   10.8   0.1   0.00011      0.32      24      67 ..      84     128 ..      73     131 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.069
                             RMI1_C  78 lkeslalkkdqkkrqklkealkeaqekLidleclmeielnpaskk 122
                                        +  +++ k+++  ++ l++ +k  + ++ + ++l+ ++++ ++ +
  gene1392|gene1392|rna1392|rna1392  38 VIGTVRAKRKNMPKDFLRTKFKTGEYEMRSCNGLLAVKWKDKR-D 81 
                                        55677778888888999999999999*************9984.3 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00011
                             RMI1_C  24 vikikafivtllgkleaskgk.wqlkakisDGsaildvdlssevl 67 
                                            k   v ++++++++++  w+lk++i+   +++ vdl++++l
  gene1392|gene1392|rna1392|rna1392  84 ILSTKHTTVAITQQITKQHNPtWKLKCVIEYNKEVIGVDLQDQML 128
                                        566777889999***9999955*********************98 PP

>> zf-RanBP  Zn-finger in Ran binding protein and others
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0    0.0074        22      13      23 ..     102     112 ..     100     112 .. 0.90
   2 ?   -0.4   0.5      0.25   7.5e+02      19      25 ..     229     235 ..     227     239 .. 0.75
   3 ?    5.3   1.1    0.0042        13       2      11 ..     242     251 ..     241     253 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.0074
                                        EEESSSSB-TT CS
                           zf-RanBP  13 qNfawstkCva 23 
                                        +N+ w++kCv+
  gene1392|gene1392|rna1392|rna1392 102 HNPTWKLKCVI 112
                                        6********95 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.25
                                        SB-TTT- CS
                           zf-RanBP  19 tkCvaCq 25 
                                         +Cv C 
  gene1392|gene1392|rna1392|rna1392 229 RRCVVCT 235
                                        5899996 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.0042
                                        SSSEE-SSS- CS
                           zf-RanBP   2 egdWdCskCl 11 
                                        e  W+C+kC+
  gene1392|gene1392|rna1392|rna1392 242 ETTWECKKCK 251
                                        668******6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (269 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       781  (0.0435607); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1875.28
//
Query:       gene1393|gene1393|rna1393|rna1393  [L=155]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.6e-20   72.2   2.0    5.5e-20   72.0   2.0    1.1  1  DDE_Tnp_1_7   Transposase IS4
  ------ inclusion threshold ------
      0.039   14.1   0.1      0.054   13.7   0.1    1.4  1  Phage_TAC_10  Phage tail assembly chaperone


Domain annotation for each model (and alignments):
>> DDE_Tnp_1_7  Transposase IS4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.0   2.0   6.2e-24   5.5e-20       3      94 ..      53     155 .]      51     155 .] 0.98

  Alignments for each domain:
  == domain 1  score: 72.0 bits;  conditional E-value: 6.2e-24
                        DDE_Tnp_1_7   3 velFelflpdkilerivkatNayakqk...........kkwleltaeElkaFlGllllmglvrlpsvedyWstkdf 67 
                                         e+F+ ++ + ++e++v +tN+ya+q            k+w ++++eElk +++l ++++ v+   +++yWs+++f
  gene1393|gene1393|rna1393|rna1393  53 IEVFNIMFNNIFWENLVTETNQYAEQIinnenkrrkidKAWFPIDREELKVYIALCIISAEVKKLAIQMYWSKRAF 128
                                        589************************************************************999********** PP

                        DDE_Tnp_1_7  68 ygnpllseiMsreRFeeilsalhladn 94 
                                        + +p ++++++++RF +i + lh+a+n
  gene1393|gene1393|rna1393|rna1393 129 IATPIFRQMIPYKRFLQISRFLHFANN 155
                                        ************************996 PP

>> Phage_TAC_10  Phage tail assembly chaperone
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1     6e-06     0.054      15      49 ..      52      86 ..      25     119 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6e-06
                       Phage_TAC_10 15 teeaYnkllNelapnnkvaPsknfLvrivaeeske 49
                                       + e +n ++N++  +n v+ ++++  +i+++e+k 
  gene1393|gene1393|rna1393|rna1393 52 EIEVFNIMFNNIFWENLVTETNQYAEQIINNENKR 86
                                       5688****************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       855  (0.0476881); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 1054.59
//
Query:       gene1394|gene1394|rna1394|rna1394  [L=98]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       612  (0.0341346); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 623.33
//
Query:       gene1395|gene1395|rna1395|rna1395  [L=179]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    0.00035   20.0   0.0    0.00049   19.6   0.0    1.3  1  Adap_comp_sub  Adaptor complexes medium subunit family


Domain annotation for each model (and alignments):
>> Adap_comp_sub  Adaptor complexes medium subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   2.7e-08   0.00049      10      49 ..     101     140 ..      92     169 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 2.7e-08
                                        XXX-EEEEEEEEEEEEEE-TTS-EEEEEEEEEEEEEE--- CS
                      Adap_comp_sub  10 ykkneiyldviErvsvlvdkkGkilksevqGtiackskls 49 
                                         kk+++ +dv E++ ++++++G++l   +qG+i+c+ +  
  gene1395|gene1395|rna1395|rna1395 101 FKKERVKFDVEEKIRAILQDNGTVLCLYAQGRITCCPQFI 140
                                        5899*******************************86655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (179 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       495  (0.0276089); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 1194.21
//
Query:       gene1396|gene1396|rna1396|rna1396  [L=131]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.1e-07   30.6   0.6    2.4e-07   30.4   0.6    1.1  1  Adap_comp_sub  Adaptor complexes medium subunit family


Domain annotation for each model (and alignments):
>> Adap_comp_sub  Adaptor complexes medium subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.4   0.6   1.3e-11   2.4e-07     147     263 ..      25     130 ..       8     131 .] 0.85

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 1.3e-11
                                        EEEEEEEE--TT-EEEEEEESSTT-EEEEETTEEEEEE--EETT-EE..EEEEEEE--------------.EEEEE CS
                      Adap_comp_sub 147 envkisiplpkevsnlaiktskGkakynpeenaleWtikklpggnesslsgeleleaesekkeenprdgklvsveF 222
                                        + ++i++p++k++ n +    +G++k   e   +eW ik+ + +      +e+++++ +  +++++  g+ ++++F
  gene1396|gene1396|rna1396|rna1396  25 SSITIKFPISKKAYNTVADSDIGHIKIMDE--HIEWIIKNEQFKE-----AEIKYDFDLLMSDNEK-LGP-IQISF 91 
                                        689********************9988877..9******955554.....3566666665555554.466.***** PP

                                        EEET--SS---EEEEEEE-------EEEEEEEEEEEEEEE- CS
                      Adap_comp_sub 223 kipgftaSgikVeslkveeresykpfkwvryvtvsgeyeir 263
                                        + + f++S++ ++ ++ +  +++k   wv y++++++ye+r
  gene1396|gene1396|rna1396|rna1396  92 TSKFFSLSELIIKDVRDS--DNVKKEAWVSYMVEAQDYEVR 130
                                        ***************999..8******************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       727  (0.0405488); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 955.15
//
Query:       gene1397|gene1397|rna1397|rna1397  [L=97]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (97 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       431  (0.0240393); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 739.17
//
Query:       gene1399|gene1399|rna1399|rna1399  [L=325]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.6e-19   69.5   0.0    1.2e-18   67.8   0.0    1.8  2  AAA              ATPase family associated with various cellul
    5.5e-18   65.3   0.1    3.5e-15   56.1   0.0    2.5  2  DNA_pol3_delta2  DNA polymerase III, delta subunit
    1.9e-08   34.6   0.1    2.1e-06   28.1   0.1    2.4  1  AAA_22           AAA domain
    2.8e-08   33.7   0.0    1.1e-07   31.8   0.0    2.0  2  DNA_pol3_delta   DNA polymerase III, delta subunit
    1.9e-07   31.2   0.0    4.2e-07   30.1   0.0    1.6  1  AAA_14           AAA domain
    2.4e-07   30.7   0.3    1.2e-06   28.3   0.0    2.2  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    5.7e-07   30.1   0.0    4.7e-06   27.1   0.0    2.2  1  AAA_16           AAA ATPase domain
    1.2e-06   28.6   0.1    4.3e-06   26.8   0.1    1.9  1  AAA_5            AAA domain (dynein-related subfamily)
    1.8e-06   28.0   0.0    6.9e-05   22.8   0.0    2.3  2  Rad17            Rad17 P-loop domain
    3.6e-06   26.8   0.0    9.8e-06   25.4   0.0    1.6  1  AAA_30           AAA domain
    6.6e-06   26.0   0.0    1.2e-05   25.1   0.0    1.4  1  AAA_24           AAA domain
      1e-05   25.4   0.0    1.9e-05   24.5   0.0    1.4  1  Viral_helicase1  Viral (Superfamily 1) RNA helicase
    0.00015   22.1   0.8     0.0048   17.2   0.0    2.6  2  AAA_19           AAA domain
     0.0002   20.8   0.2      0.016   14.6   0.0    2.5  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    0.00024   20.9   0.0    0.00048   20.0   0.0    1.4  1  AAA_3            ATPase family associated with various cellul
    0.00031   21.0   0.1     0.0009   19.5   0.0    1.8  1  AAA_assoc_2      AAA C-terminal domain
     0.0004   20.3   0.0      0.001   19.0   0.0    1.6  1  AAA_11           AAA domain
    0.00067   20.2   0.0     0.0014   19.2   0.0    1.6  1  AAA_18           AAA domain
    0.00084   18.6   0.0     0.0014   17.8   0.0    1.4  1  DUF815           Protein of unknown function (DUF815)
     0.0011   19.5   0.1       0.65   10.5   0.0    2.8  3  ABC_tran         ABC transporter
     0.0013   18.3   0.0     0.0022   17.5   0.0    1.3  1  AAA_7            P-loop containing dynein motor region
     0.0013   19.0   0.2     0.0053   17.1   0.2    2.1  1  Rep_fac_C        Replication factor C C-terminal domain
     0.0028   17.4   0.0     0.0084   15.9   0.0    1.8  1  IstB_IS21        IstB-like ATP binding protein
      0.003   17.5   0.2     0.0085   16.0   0.0    1.8  2  ATPase_2         ATPase domain predominantly from Archaea
     0.0049   17.4   0.4      0.011   16.3   0.4    1.7  1  AAA_23           AAA domain
     0.0051   17.1   0.0     0.0091   16.3   0.0    1.5  1  AAA_28           AAA domain
     0.0056   16.8   0.0      0.011   15.8   0.0    1.5  1  AAA_2            AAA domain (Cdc48 subfamily)
     0.0096   16.3   0.0      0.019   15.4   0.0    1.6  1  RNA_helicase     RNA helicase
  ------ inclusion threshold ------
      0.017   15.1   0.2        0.2   11.5   0.0    2.2  2  NTPase_1         NTPase
      0.017   14.2   0.0      0.042   12.9   0.0    1.6  1  MCM              MCM P-loop domain
      0.026   13.6   0.0      0.045   12.8   0.0    1.4  1  T2SSE            Type II/IV secretion system protein
      0.026   13.9   0.0      0.063   12.6   0.0    1.6  2  ATPase           KaiC
      0.027   13.5   0.0      0.056   12.4   0.0    1.5  1  AAA_6            Hydrolytic ATP binding site of dynein motor 
      0.028   14.4   0.0      0.077   13.0   0.0    1.7  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
      0.033   13.6   0.1       0.38   10.1   0.0    2.2  2  TniB             Bacterial TniB protein
      0.034   14.3   0.0      0.087   13.0   0.0    1.6  1  AAA_33           AAA domain
      0.041   13.6   0.0        4.1    7.1   0.0    2.3  2  Sigma54_activat  Sigma-54 interaction domain
      0.043   13.6   0.2        2.7    7.7   0.0    2.4  2  ATP_bind_1       Conserved hypothetical ATP binding protein
       0.05   13.2   0.0       0.11   12.1   0.0    1.6  1  SRP54            SRP54-type protein, GTPase domain
       0.06   13.3   0.0       0.93    9.4   0.0    2.3  1  NACHT            NACHT domain
       0.09   12.5   0.0       0.17   11.7   0.0    1.3  1  AAA_29           P-loop containing region of AAA domain
      0.093   12.2   0.0       0.18   11.2   0.0    1.5  1  KTI12            Chromatin associated protein KTI12
        0.1   11.8   0.0       0.83    8.8   0.0    2.0  2  NB-ARC           NB-ARC domain
        0.1   11.9   0.0       0.21   10.9   0.0    1.4  1  FtsK_SpoIIIE     FtsK/SpoIIIE family
       0.13   12.6   0.0       0.28   11.6   0.0    1.6  1  AAA_17           AAA domain
       0.13   11.8   0.0       0.23   11.1   0.0    1.4  1  AAA_27           AAA domain
       0.17   11.6   0.4        1.9    8.2   0.1    2.3  2  DEAD             DEAD/DEAH box helicase
       0.25   10.9   0.2       0.91    9.1   0.2    1.9  1  AAA_25           AAA domain


Domain annotation for each model (and alignments):
>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.8   0.0   3.3e-21   1.2e-18       1     129 [.      61     177 ..      61     180 .. 0.80
   2 ?   -1.2   0.0         7   2.6e+03      39      98 ..     209     228 ..     187     252 .. 0.67

  Alignments for each domain:
  == domain 1  score: 67.8 bits;  conditional E-value: 3.3e-21
                                        EEEESSTTSSHHHHHHHHHHHHT.....HEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTS.TSEEEEEETGGGH CS
                                AAA   1 vllyGppGtGKTllakavakelg.....vefleisgsellskyvgesekkirelfkeakeka.kpsilfiDEidal 70 
                                        +llyGppGtGKT+ ++a+ak l       ++le+++s+ +   +    ++i+ +   +++ + k++ +++DE+d++
  gene1399|gene1399|rna1399|rna1399  61 ILLYGPPGTGKTTSIRAIAKFLYkhtimCNVLELNASDDR--GINVVREQIKSFAM-CRSFQnKKKLVILDEADSM 133
                                        69*******************9733334556777777766..66666666655543.333333579********** PP

                                        HHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHSTTSSEEEE CS
                                AAA  71 aksrsgseseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallrgRfdrkie 129
                                         ++            +n+L +++++++    +v +++++n+ +k+ pa+  +R+++  +
  gene1399|gene1399|rna1399|rna1399 134 SRDA-----------QNALRRVIEDYSG---NVRFCLIANYAHKIIPAIQ-SRCSKFRF 177
                                        8888...........*************...6******************.99987655 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 7
                                        TTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTT CS
                                AAA  39 vgesekkirelfkeakekakpsilfiDEidalaksrsgseseeeervvnqLlteldgvkk 98 
                                        v+ese +                                        + +L++ ldg+++
  gene1399|gene1399|rna1399|rna1399 209 VQESEGD----------------------------------------MRTLINTLDGLSQ 228
                                        4444444........................................4445555555444 PP

>> DNA_pol3_delta2  DNA polymerase III, delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.0     0.014       5.1       3      44 ..      43      83 ..      41      95 .. 0.86
   2 !   56.1   0.0   9.5e-18   3.5e-15      84     162 ..     101     180 ..      84     181 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.014
                    DNA_pol3_delta2  3 eealkilskalksgrlahayLfeGdegigkkelalnlakall 44
                                       e +++ l++  ++++l h +L++G+ g+gk ++  ++ak l 
  gene1399|gene1399|rna1399|rna1399 43 ELVISALKSLQEHDNLPH-ILLYGPPGTGKTTSIRAIAKFLY 83
                                       567888999999999999.799**************999876 PP

  == domain 2  score: 56.1 bits;  conditional E-value: 9.5e-18
                    DNA_pol3_delta2  84 kldqir.elieelsrkpreskkkiiiiedaekmtksAaNalLktlEEPsenaifiLitsdtnklLktirSRcqelk 158
                                         ++ +r ++++++  +++++kkk++i+++a+ m++ A+Nal +++E+ s n+ f Li++  +k+++ i+SRc +++
  gene1399|gene1399|rna1399|rna1399 101 GINVVReQIKSFAMCRSFQNKKKLVILDEADSMSRDAQNALRRVIEDYSGNVRFCLIANYAHKIIPAIQSRCSKFR 176
                                        5677885677778889************************************************************ PP

                    DNA_pol3_delta2 159 fspl 162
                                        fsp+
  gene1399|gene1399|rna1399|rna1399 177 FSPV 180
                                        **97 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.1   5.6e-09   2.1e-06       7     128 ..      60     157 ..      55     162 .. 0.86

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 5.6e-09
                             AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdl.lrellralglelkaerlsseellea 81 
                                        +++++G++GtGKTt++r +++ l          ++++ +++ +++ s+d   + + +++++              a
  gene1399|gene1399|rna1399|rna1399  60 HILLYGPPGTGKTTSIRAIAKFL---------YKHTIMCNVLELNASDDRgINVVREQIKS-------------FA 113
                                        79*********************.........9********99997777757777777773.............58 PP

                             AAA_22  82 leqalraravielliiDEaqhlrseealeeLrsllnlsrkgvqliLv 128
                                        + + ++++++  l+i+DEa+ + s +a + Lr+  ++ + +v++ L+
  gene1399|gene1399|rna1399|rna1399 114 MCRSFQNKKK--LVILDEADSM-SRDAQNALRRVIEDYSGNVRFCLI 157
                                        9999999999..**********.*99999998887777777777776 PP

>> DNA_pol3_delta  DNA polymerase III, delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0       2.9   1.1e+03      95     128 ..      60      96 ..      26     112 .. 0.73
   2 !   31.8   0.0     3e-10   1.1e-07      44     172 ..     108     226 ..      78     228 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 2.9
                                        EEEEEES....S--HHHHHHHHHTTTEEEEEE----T CS
                     DNA_pol3_delta  95 lLiliap...kklderkklvklLkkkatvveaktlke 128
                                        +++l++p   +k+++ + + k+L k++++ ++ +l+ 
  gene1399|gene1399|rna1399|rna1399  60 HILLYGPpgtGKTTSIRAIAKFLYKHTIMCNVLELNA 96 
                                        4555555323466666669999999999999988864 PP

  == domain 2  score: 31.8 bits;  conditional E-value: 3e-10
                                        .HTTTSTTTTSSSSEEEEEEE--.....TT-S-TTHHHHHHHHTTT--SSEEEEEEES.S--HHHHHHHHHTTTEE CS
                     DNA_pol3_delta  44 dvleecetlpffsdkrivvlknpklltkesklnekllkeLeeylsnlpedtlLiliapkklderkklvklLkkkat 119
                                        ++ + ++  +f  +k++v+l+ +      ++ + + +++L +++++++ ++ ++lia+     + k++  ++++ +
  gene1399|gene1399|rna1399|rna1399 108 QIKSFAMCRSFQNKKKLVILDEA------DSMSRDAQNALRRVIEDYSGNVRFCLIAN----YAHKIIPAIQSRCS 173
                                        455667778999***********......55899999*********************....7899********** PP

                                        EEEE----TTTHHHHHHHHHHHTT-EE-HHHHHHHHHHHTT-HHHHHHHHHHH CS
                     DNA_pol3_delta 120 vveaktlkeeelkkwiqkraqelglkiekealelLlelvennlsaikqelekL 172
                                         ++++++++  +k+ ++++a+ +++ i+++ +++L++ +e++++++ + l+ L
  gene1399|gene1399|rna1399|rna1399 174 KFRFSPVSSGLIKERVKSIAEMENIPIDDKCIDMLVQESEGDMRTLINTLDGL 226
                                        ************************************************99977 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.1   0.0   1.1e-09   4.2e-07       5      97 ..      61     156 ..      57     181 .. 0.72

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 1.1e-09
                             AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpe....kllelilek.lkeekktylflDEiqe 75 
                                        +++ G+  +GKTt ++ ++k l+   ++++  n+ + + ++ +  +    ++ ++ + + ++ +kk++++lDE+  
  gene1399|gene1399|rna1399|rna1399  61 ILLYGPPGTGKTTSIRAIAKFLY---KHTIMCNVLELNASDDRGINvvreQIKSFAMCRsFQ-NKKKLVILDEADS 132
                                        7899***************9999...666666665555544443321111344444444334.69*********76 PP

                             AAA_14  76 v.pewekalkslvdeg.knldviv 97 
                                        + +++++al+++++++  n+++++
  gene1399|gene1399|rna1399|rna1399 133 MsRDAQNALRRVIEDYsGNVRFCL 156
                                        5378**********8866777776 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   0.0   3.3e-09   1.2e-06       2     112 ..      32     149 ..      31     155 .. 0.65

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 3.3e-09
                             RuvB_N   2 rPksleeyigqekvkeklkifieaakkreealdhvllyGpPGlGkttlakiiakelgvk..........lkitsg. 66 
                                        rP++l+e +g e v + lk     + + +++l h+llyGpPG Gktt  + iak l  +               g 
  gene1399|gene1399|rna1399|rna1399  32 RPSTLDEVLGNELVISALK-----SLQEHDNLPHILLYGPPGTGKTTSIRAIAKFLYKHtimcnvlelnASDDRGi 102
                                        7888888888776666654.....5677899***************987777765544300000000003333331 PP

                             RuvB_N  67 Pvlekagdlaalltnle.ekdvlfideihrlsraveevlysamedfr 112
                                         v+ ++    a+  +++ +k+++ +de   +sr +++ l   +ed++
  gene1399|gene1399|rna1399|rna1399 103 NVVREQIKSFAMCRSFQnKKKLVILDEADSMSRDAQNALRRVIEDYS 149
                                        23444444556666666145677889999999999999999999996 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   0.0   1.3e-08   4.7e-06      14      88 ..      47     121 ..      40     230 .. 0.64

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 1.3e-08
                             AAA_16  14 salervrsgrp.elvllsGesGvGKsslvrellralekdggif..lrgkcdqlesaipysalaqalareellrqll 86 
                                        sal+++ +++  + +ll+G++G+GK++ +r++++ l k+ + +  l+ ++ +  ++i    + ++++    +r   
  gene1399|gene1399|rna1399|rna1399  47 SALKSLQEHDNlPHILLYGPPGTGKTTSIRAIAKFLYKHTIMCnvLELNASDD-RGINV--VREQIKSFAMCRSFQ 119
                                        6788888888889********************99999954444344444433.33322..444444444444444 PP

                             AAA_16  87 de 88 
                                        ++
  gene1399|gene1399|rna1399|rna1399 120 NK 121
                                        44 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8   0.1   1.2e-08   4.3e-06       1      91 [.      60     147 ..      60     152 .. 0.77

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 1.2e-08
                                        EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------.G-SEEEEESGG CS
                              AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar.egeilvlDEve 75 
                                        ++lL GppGtgK++ ++ +a++l + + + +  + ++++d +g +++   +++ +  ++ r+++ ++++++lDE +
  gene1399|gene1399|rna1399|rna1399  60 HILLYGPPGTGKTTSIRAIAKFLYKHTIMCNVLE-LNASDDRG-INV--VREQIKSFAMCRSFQnKKKLVILDEAD 131
                                        79*********************44444333333.44444333.333..4566667888888888999******** PP

                                        G--HHHHHHHHHHHHS CS
                              AAA_5  76 raesevlnsLlsllee 91 
                                         ++++++n+L +++e+
  gene1399|gene1399|rna1399|rna1399 132 SMSRDAQNALRRVIED 147
                                        ************9997 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.0   1.8e-07   6.9e-05       7      78 ..      25      90 ..      21     118 .. 0.83
   2 ?    2.5   0.0      0.31   1.2e+02     128     159 ..     117     148 ..     108     159 .. 0.82

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 1.8e-07
                              Rad17  7 elWfekykPekaeelavhkkkieevkewlkadvLesrkkriLLisGPsGCgkstvvkvLskelgiklrewln 78
                                       ++ +eky+P +++e+      i+++k   + d L++      L+ GP+G gk+t ++ ++k l  +     n
  gene1399|gene1399|rna1399|rna1399 25 QPLVEKYRPSTLDEVLGNELVISALKSLQEHDNLPHI-----LLYGPPGTGKTTSIRAIAKFLYKH-TIMCN 90
                                       7889***********************9999999987.....899****************87543.33445 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.31
                              Rad17 128 dlrtdkklilvedlPnkfyrdsdalrevirky 159
                                          + +kkl+++++  +      +alr vi  y
  gene1399|gene1399|rna1399|rna1399 117 SFQNKKKLVILDEADSMSRDAQNALRRVIEDY 148
                                        6799*********9887777779*****9987 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.0   2.6e-08   9.8e-06      22     121 ..      62     154 ..      47     155 .. 0.74

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 2.6e-08
                             AAA_30  22 vltGpAGtGKttalkalreaweaag..grvi.glAptgkaAkvLaeelgieastiakllkrlkgrarlepgtlliv 94 
                                        +l Gp+GtGKtt+++a+++ + ++    +v+ + A+  +  +v++e++   +  + +      +    ++++l+i 
  gene1399|gene1399|rna1399|rna1399  62 LLYGPPGTGKTTSIRAIAKFLYKHTimCNVLeLNASDDRGINVVREQIK--SFAMCRSF----Q----NKKKLVIL 127
                                        678**************99888775344444255666666666776633..33333333....2....3559**** PP

                             AAA_30  95 DEagmvdtkqlaallkaaekagakvil 121
                                        DEa  ++ +  +al + +e+++  v++
  gene1399|gene1399|rna1399|rna1399 128 DEADSMSRDAQNALRRVIEDYSGNVRF 154
                                        *******************99998886 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.0   3.3e-08   1.2e-05       4      88 ..      60     144 ..      58     155 .. 0.78

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 3.3e-08
                             AAA_24   4 kiliyGpsgiGKTtlakel....gpkplfidtekGlksldadkfpdieswedfldevvel...aaeladyktlviD 72 
                                         il+yGp+g+GKTt+++ +     ++++++++ + l++ d++ +      + ++++++++   +  +++ k +++D
  gene1399|gene1399|rna1399|rna1399  60 HILLYGPPGTGKTTSIRAIakflYKHTIMCNVLE-LNASDDRGI------NVVREQIKSFamcRSFQNKKKLVILD 128
                                        599***************9777777777777777.444444444......4567777777777888999999**** PP

                             AAA_24  73 tideleelclaevirq 88 
                                         +d + + + + ++r 
  gene1399|gene1399|rna1399|rna1399 129 EADSMSRDAQNALRRV 144
                                        ***9999998887765 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.0     5e-08   1.9e-05       4      71 ..      64     130 ..      61     141 .. 0.84

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 5e-08
                    Viral_helicase1   4 hGvpGcGKStlirkllrtsliltvnrptaelltegkpklpnlsvrtvdsflmalvkstkgkililDEy 71 
                                         G pG GK+t+ir +++  ++ t+ ++ +  l+++ ++  n   + ++sf m ++ + k+k++ilDE+
  gene1399|gene1399|rna1399|rna1399  64 YGPPGTGKTTSIRAIAKFLYKHTIMCN-VLELNASDDRGINVVREQIKSFAMCRSFQNKKKLVILDEA 130
                                        588***************655555555.66666667999999999************99********7 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   1.3e-05    0.0048      11      38 ..      59      86 ..      50     115 .. 0.74
   2 ?    3.2   0.0      0.28     1e+02      98     126 ..     116     145 ..      91     158 .. 0.68

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.3e-05
                             AAA_19 11 kvllvtaGpGtGKTrvlkhivallvelg 38
                                       +++l+ ++pGtGKT+ +++i + l + +
  gene1399|gene1399|rna1399|rna1399 59 PHILLYGPPGTGKTTSIRAIAKFLYKHT 86
                                       6799****************99988776 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.28
                             AAA_19  98 kklqeee.llivDEfqdvd.elqyrLlkall 126
                                        + +q+++ l+i DE+  ++ + q++ l+++ 
  gene1399|gene1399|rna1399|rna1399 116 RSFQNKKkLVILDEADSMSrDAQNA-LRRVI 145
                                        445555559******9999455555.55554 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   4.4e-05     0.016      24      50 ..      60      86 ..      35     120 .. 0.75
   2 ?    3.8   0.0     0.085        32     109     133 ..     124     148 ..     118     159 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 4.4e-05
                       Mg_chelatase 24 nlllvGppGsGKtmlakrlpsllppls 50
                                       ++ll+GppG+GKt  ++++++ l + +
  gene1399|gene1399|rna1399|rna1399 60 HILLYGPPGTGKTTSIRAIAKFLYKHT 86
                                       89**************99998886654 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.085
                       Mg_chelatase 109 vLfLDElpefkrkvlevLRePledg 133
                                        +++LDE+  ++r++ ++LR+ +ed 
  gene1399|gene1399|rna1399|rna1399 124 LVILDEADSMSRDAQNALRRVIEDY 148
                                        689*****************99985 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   1.3e-06   0.00048       1      88 [.      60     147 ..      60     154 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 1.3e-06
                              AAA_3   1 hvllegvPGlaktllvkalakaldlefkriqftpdllPsdilGtevfeekekefefkkG.pvfanllladeinrap 75 
                                        h+ll g PG++kt+ ++a+ak l  +   +    +l  sd  G++v++e+ k+f + +     ++l++ de +  +
  gene1399|gene1399|rna1399|rna1399  60 HILLYGPPGTGKTTSIRAIAKFLYKHTI-MCNVLELNASDDRGINVVREQIKSFAMCRSfQNKKKLVILDEADSMS 134
                                        9********************9976654.44567999*****************98766145678999*****999 PP

                              AAA_3  76 pktqsalleamee 88 
                                          +q al  ++e+
  gene1399|gene1399|rna1399|rna1399 135 RDAQNALRRVIED 147
                                        9999999887765 PP

>> AAA_assoc_2  AAA C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   2.4e-06    0.0009       3      41 ..     196     243 ..     194     270 .. 0.69

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 2.4e-06
                                        X.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX..........X CS
                        AAA_assoc_2   3 kklkleddalealaeladGDaRkaLnlLElaaeaaeak.........e 41 
                                        +++ ++d+++++l++ ++GD+R+++n+L+ + + + +          +
  gene1399|gene1399|rna1399|rna1399 196 ENIPIDDKCIDMLVQESEGDMRTLINTLDGLSQFKGKItanmilpelD 243
                                        6899************************96655544333444555554 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   2.7e-06     0.001       9      44 ..      48      85 ..      42     122 .. 0.74

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 2.7e-06
                             AAA_11  9 aiksalsese..itliqGPPGtgKTktivellsqllsr 44
                                       a+ks  ++++    l+ GPPGtgKT+ i ++ + l+++
  gene1399|gene1399|rna1399|rna1399 48 ALKSLQEHDNlpHILLYGPPGTGKTTSIRAIAKFLYKH 85
                                       445555555555589*****************999755 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   3.8e-06    0.0014       1      45 [.      61     108 ..      61     177 .. 0.55

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 3.8e-06
                             AAA_18   1 IlltGtpGvGKttlakeLskrlgf.................gvnlrdvakenglllevdpe....a 45 
                                        Ill G+pG+GKtt  ++++k l +                 g+                 +    +
  gene1399|gene1399|rna1399|rna1399  61 ILLYGPPGTGKTTSIRAIAKFL-YkhtimcnvlelnasddrGI-----------------NvvreQ 108
                                        99****************8876.32233333344444433322.................222221 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   3.8e-06    0.0014      43     104 ..      48     111 ..      20     171 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 3.8e-06
                             DUF815  43 nteqfleglpannvLLwGarGtGKSslvkallneyaeeg..Lrlievekedlkelpklvellre 104
                                          + + e+ +  ++LL+G  GtGK + ++a+ + + +++    ++e++ +d + ++ + e++++
  gene1399|gene1399|rna1399|rna1399  48 ALKSLQEHDNLPHILLYGPPGTGKTTSIRAIAKFLYKHTimCNVLELNASDDRGINVVREQIKS 111
                                        4455666777789********************9999986657788877777777777777763 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.0    0.0017      0.65      14      36 ..      61      83 ..      58     109 .. 0.84
   2 ?    5.9   0.0     0.047        18     116     135 ..     111     130 ..      93     132 .. 0.89
   3 ?   -1.1   0.0       6.9   2.6e+03      26      44 ..     218     235 ..     181     317 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0017
                                       EEEEESTTSSHHHHHHHHTTSS- CS
                                       xxxxxxxxxxxxxxxxxxxxxxx RF
                           ABC_tran 14 vaivGenGaGKStLlkllagllk 36
                                       + + G+ G+GK+t ++++a+ l 
  gene1399|gene1399|rna1399|rna1399 61 ILLYGPPGTGKTTSIRAIAKFLY 83
                                       6799**************99765 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.047
                                        HHHHHHHHHHTSSEEEEEST CS
                                        xxxxxxxxxxxxxxxxxxxx RF
                           ABC_tran 116 rvalarallkkpkllllDEp 135
                                          a++r++ +k+kl++lDE+
  gene1399|gene1399|rna1399|rna1399 111 SFAMCRSFQNKKKLVILDEA 130
                                        57899**************8 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 6.9
                                        HHHHHHTTSS--SEEEEEE CS
                                        xxxxxxxxxxxxxxxxxxx RF
                           ABC_tran  26 tLlkllagllkpteGeill 44 
                                        tL+++l gl++  +G+i+ 
  gene1399|gene1399|rna1399|rna1399 218 TLINTLDGLSQ-FKGKITA 235
                                        44555555444.3444433 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   5.9e-06    0.0022      35      72 ..      60      97 ..      46     117 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 5.9e-06
                              AAA_7 35 pvllvGptGtGKtviikdllkkldkekylsltinfsaq 72
                                       ++ll+Gp GtGKt+ i+ + k l k ++++++++++a+
  gene1399|gene1399|rna1399|rna1399 60 HILLYGPPGTGKTTSIRAIAKFLYKHTIMCNVLELNAS 97
                                       89***************************999999886 PP

>> Rep_fac_C  Replication factor C C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.2   1.4e-05    0.0053      39      85 ..     275     318 ..     239     320 .. 0.63

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.4e-05
                                        HHHHHHHHGCCS..S-HHHHHHHHHHHHHHHHHHHCTH-HHHHHHHH CS
                          Rep_fac_C  39 iltqlhrvvkeqeelpeaqkleilellgeiekrlveGasehlqlsal 85 
                                          + l  ++ e+   +  +  +i e+l++ie+r++ G+se++q++ l
  gene1399|gene1399|rna1399|rna1399 275 FFRRLTGYIRES---KKFVNYDIYEELAQIEHRIAVGCSEKIQIACL 318
                                        444444444442...45678899999*****************9877 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   2.2e-05    0.0084      35     138 ..      46     149 ..      35     163 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2.2e-05
                          IstB_IS21  35 vkeLatlsfiekkenivllGpsGvGKshlaialgveavraglsvlfvrvedL.veelkrarrdgklaralkrl.lk 108
                                        +++L +l+  ++   i+l Gp+G+GK+    a+++   ++ +    + +++   + +++ r++ k   + +++  k
  gene1399|gene1399|rna1399|rna1399  46 ISALKSLQEHDNLPHILLYGPPGTGKTTSIRAIAKFLYKHTIMCNVLELNASdDRGINVVREQIKSFAMCRSFqNK 121
                                        4556666666666679*******************99999887665555443134566666666555555555156 PP

                          IstB_IS21 109 vdllilDdlgllpldqaeaellfeviekry 138
                                         +l+ilD+     +++++++ l +vie+  
  gene1399|gene1399|rna1399|rna1399 122 KKLVILDEA--DSMSRDAQNALRRVIEDYS 149
                                        69******7..5788899999999999865 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   2.3e-05    0.0085       8      68 ..      46     105 ..      42     165 .. 0.65
   2 ?   -1.6   0.0       5.4     2e+03      95      97 ..     248     252 ..     182     292 .. 0.62

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2.3e-05
                           ATPase_2   8 lkeleeilerepneiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldef 68 
                                        ++ l+++ e ++ + +++YGp g GKt+ ++ i++ l + +     + +l+ ++   ++  
  gene1399|gene1399|rna1399|rna1399  46 ISALKSLQEHDNLPHILLYGPPGTGKTTSIRAIAKFLYK-HTIMCNVLELNASDDRGINVV 105
                                        788999999999999****************99998844.445556666665555555555 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 5.4
                           ATPase_2  95 lk..e 97 
                                        ++  +
  gene1399|gene1399|rna1399|rna1399 248 FElsR 252
                                        33321 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.4   2.9e-05     0.011      21      87 ..      60     130 ..      48     306 .. 0.53

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 2.9e-05
                             AAA_23  21 ltlItGpNGaGKTTildAiklaLygetprlsrksgrgfeksdveiesegkvkay.veltfenkdgry....t 87 
                                          l++Gp G+GKTT ++Ai   Ly +t  ++  + + + ++ +++  e + k++ + ++f+nk++       
  gene1399|gene1399|rna1399|rna1399  60 HILLYGPPGTGKTTSIRAIAKFLYKHTIMCNVLELNASDDRGINVVRE-QIKSFaMCRSFQNKKKLVildeA 130
                                        679*********************998666665544444444444443.44555555556555553233331 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   2.4e-05    0.0091       2      34 ..      61     112 ..      60     155 .. 0.67

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 2.4e-05
                             AAA_28   2 ivitGgestGKTtlleaLa...................argypvvpEaarei 34 
                                        i + G+++tGKTt ++a+a                   +rg++vv+E    +
  gene1399|gene1399|rna1399|rna1399  61 ILLYGPPGTGKTTSIRAIAkflykhtimcnvlelnasdDRGINVVREQIKSF 112
                                        889****************666655555544444433223666666655555 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0     3e-05     0.011       5     105 ..      60     147 ..      56     153 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 3e-05
                                        -EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGG CS
                              AAA_2   5 silllgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEid 78 
                                         ill gp g+Gkt   +a+a++l     k+ i+ +  el  +++    v r+++++ ++ +  ++    v lDE d
  gene1399|gene1399|rna1399|rna1399  60 HILLYGPPGTGKTTSIRAIAKFLY----KHTIMCNVLELNASDDRGINVVREQIKSFAMCRSFQNKkkLVILDEAD 131
                                        699********************9....6999999***999888877777777777666666555558******** PP

                                        G-------------HHHHHHHHHHHH- CS
                              AAA_2  79 KihpkessgadvSregVqrdLLqileg 105
                                          ++           + q++L +++e+
  gene1399|gene1399|rna1399|rna1399 132 SMSR-----------DAQNALRRVIED 147
                                        ****...........999999999987 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0     5e-05     0.019       1      27 [.      61      97 ..      61     164 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 5e-05
                       RNA_helicase  1 iwlyGpsgeGKStlakeLakallkkl..........k 27
                                       i+lyGp+g+GK+t ++ +ak l k+            
  gene1399|gene1399|rna1399|rna1399 61 ILLYGPPGTGKTTSIRAIAKFLYKHTimcnvlelnaS 97
                                       789**************99999988777777766543 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00055       0.2       1      25 [.      60      84 ..      60      91 .. 0.88
   2 ?    1.0   0.0      0.93   3.5e+02      89     117 ..     115     143 ..     101     176 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00055
                                       EEEEE--TTSSHHHHHHHHHHHH.. CS
                           NTPase_1  1 kvfiTGppGvGKtTlvkkvlellks 25
                                       ++++ GppG+GKtT ++ +++ l +
  gene1399|gene1399|rna1399|rna1399 60 HILLYGPPGTGKTTSIRAIAKFLYK 84
                                       78999**************998865 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.93
                                        HHHHHHHH-EEEE---STTGGG-HHHHHH CS
                           NTPase_1  89 lrkalseadviviDEiGkmElkskkfkea 117
                                         r  ++++ ++++DE  +m   +++  + 
  gene1399|gene1399|rna1399|rna1399 115 CRSFQNKKKLVILDEADSMSRDAQNALRR 143
                                        344457889******99997776654333 PP

>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   0.00011     0.042      58     147 ..      59     147 ..      44     173 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00011
                                        -EEEEEESSTSTHHHHHHHHHHHSSSEEEEESSSSSSSHSSSEEEEESSSSSEEEEETHHH...HTTTSEEEEESG CS
                                MCM  58 invllvgdpgtaKsqlLkyveklapravytsgkgssaagLtaavvrdeetgefvleaGalv...ladkGvcciDef 130
                                         ++ll g pgt+K++ +++++k++ + + ++       +L a+  r  +     +++ a+       k ++++De 
  gene1399|gene1399|rna1399|rna1399  59 PHILLYGPPGTGKTTSIRAIAKFLYKHTIMC----NVLELNASDDRGINVVREQIKSFAMCrsfQNKKKLVILDEA 130
                                        59******************98876555443....34455555555555555555555554111568899****** PP

                                        GGSTCHHHHHHHHHHHH CS
                                MCM 131 dkmkeedrsalhEamEq 147
                                        d m+++ ++al  ++E+
  gene1399|gene1399|rna1399|rna1399 131 DSMSRDAQNALRRVIED 147
                                        ************99997 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   0.00012     0.045     130     157 ..      59      86 ..      26     121 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00012
                              T2SSE 130 glilvsGgTgsGKttllyallkeinksd 157
                                          il+ G+ g+GKtt++ a+ k++ k++
  gene1399|gene1399|rna1399|rna1399  59 PHILLYGPPGTGKTTSIRAIAKFLYKHT 86 
                                        469*********************9993 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00017     0.063      21     105 ..      60     146 ..      44     165 .. 0.78
   2 ?   -2.3   0.1       6.1   2.3e+03     162     162 ..     239     239 ..     185     301 .. 0.57

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00017
                             ATPase  21 vvlitGepGtGKti...falqFlikgaekygepgvfvtveepaedlrenakslGwdlekleeegklaiidasesae 93 
                                         +l++G pGtGKt+     ++Fl+k     +   +  + +   + +re++ks+ +  + ++++ kl+i+d + s++
  gene1399|gene1399|rna1399|rna1399  60 HILLYGPPGTGKTTsirAIAKFLYKHTIMCNVLELNASDDRGINVVREQIKSFAM-CRSFQNKKKLVILDEADSMS 134
                                        589**********83333579***99777555555555555559*********98.79999999********9999 PP

                             ATPase  94 esaeekdkedle 105
                                        ++a++  +  +e
  gene1399|gene1399|rna1399|rna1399 135 RDAQNALRRVIE 146
                                        977665444444 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 6.1
                             ATPase 162 s 162
                                         
  gene1399|gene1399|rna1399|rna1399 239 L 239
                                        2 PP

>> AAA_6  Hydrolytic ATP binding site of dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00015     0.056      37      66 ..      63      92 ..      57     116 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00015
                              AAA_6 37 paGpagtGKtEtvkdLakalakqvvvfncs 66
                                       ++Gp gtGKt +++ +ak l k+++++n+ 
  gene1399|gene1399|rna1399|rna1399 63 LYGPPGTGKTTSIRAIAKFLYKHTIMCNVL 92
                                       57*******************999998865 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   0.00021     0.077      21      43 ..      55      82 ..      36      91 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00021
                                       E.....EEEEESTTSSHHHHHHHHHHHT CS
                               TsaE 21 v.....ilLeGdLGaGKTtlvrglakal 43
                                             ilL+G+ G+GKTt +r++ak l
  gene1399|gene1399|rna1399|rna1399 55 HdnlphILLYGPPGTGKTTSIRAIAKFL 82
                                       133455*******************987 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0     0.001      0.38      26      59 ..      49      85 ..      42     120 .. 0.75
   2 ?    1.0   0.1      0.64   2.4e+02     119     144 ..     121     143 ..     103     179 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.001
                               TniB 26 LleypkrkrmpnlllvGdsnnGKtmive...kFarlh 59
                                       L +  +++  p++ll+G++ +GKt+ ++   kF  +h
  gene1399|gene1399|rna1399|rna1399 49 LKSLQEHDNLPHILLYGPPGTGKTTSIRaiaKFLYKH 85
                                       5566678889**************9765111555555 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.64
                               TniB 119 kvrvLiiDEihnllagsarkqrefln 144
                                        k +++i+DE +++ +  +++ r    
  gene1399|gene1399|rna1399|rna1399 121 KKKLVILDEADSMSRDAQNALR---R 143
                                        56899*****999854444333...3 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   0.00023     0.087       2      94 ..      61     147 ..      61     159 .. 0.57

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00023
                             AAA_33   2 vllvGlpGsGKstlaerllkklgavllssdtlrrrlfgtdqqsktdytr.vldrlyqilnelarkalsagrnvild 76 
                                        +ll G+pG+GK+t ++ ++k     +l + t++ ++ +    +++  ++ v+++++ +  +++r+ + +++ vild
  gene1399|gene1399|rna1399|rna1399  61 ILLYGPPGTGKTTSIRAIAK-----FLYKHTIMCNVLELNASDDR-GINvVREQIKSF--AMCRSFQNKKKLVILD 128
                                        6789************9984.....45555555555443232222.233133334433..4666666666666666 PP

                             AAA_33  77 at.nlsrrerarflklarr 94 
                                             sr+++ +++++ ++
  gene1399|gene1399|rna1399|rna1399 129 EAdSMSRDAQNALRRVIED 147
                                        6633334555555555555 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.0     0.011       4.1      18      44 ..      52      80 ..      41      99 .. 0.72
   2 ?    4.0   0.0     0.094        35      95     119 ..     123     147 ..     117     152 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.011
                                       HCTSS..S-EEEECSTTSSHHHHHHHHHH CS
                    Sigma54_activat 18 vaktd..lsvlitGesGtGKellaraihe 44
                                       + ++d   ++l+ G  GtGK++  rai +
  gene1399|gene1399|rna1399|rna1399 52 LQEHDnlPHILLYGPPGTGKTTSIRAIAK 80
                                       444444468***********998888765 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.094
                                        SEEEEETGGGS-HHHHHHHHHHHHH CS
                    Sigma54_activat  95 GtlfLDeigelplelQekLlrvlqe 119
                                          + LDe  +++ ++Q+ L rv+++
  gene1399|gene1399|rna1399|rna1399 123 KLVILDEADSMSRDAQNALRRVIED 147
                                        5689******************996 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.0    0.0072       2.7       2      32 ..      64      94 ..      63     100 .. 0.83
   2 ?    3.5   0.0      0.14        51     183     223 ..     118     160 ..      90     173 .. 0.70

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0072
                         ATP_bind_1  2 vGpaGsGKttfvgalseilelrgrsvavvNL 32
                                        Gp+G GKtt ++a++++l +    ++v+ L
  gene1399|gene1399|rna1399|rna1399 64 YGPPGTGKTTSIRAIAKFLYKHTIMCNVLEL 94
                                       69***************99888766666655 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.14
                         ATP_bind_1 183 vealslllekee.....ekykklaeaiaelleefalvlrflplsse 223
                                        +++ ++l          +  ++ ++a+++++e+++ + rf+ +++ 
  gene1399|gene1399|rna1399|rna1399 118 FQNKKKLV---IldeadSMSRDAQNALRRVIEDYSGNVRFCLIANY 160
                                        22222222...133355889999*************9999999875 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0    0.0003      0.11       4      29 ..      61      86 ..      59     153 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.0003
                                       EEEEESTTSSHHHHHHHHHHHHHHTT CS
                              SRP54  4 illvGlqGaGKTttlaKLaallkkeg 29
                                       ill G+ G+GKTt++  +a+ l k+ 
  gene1399|gene1399|rna1399|rna1399 61 ILLYGPPGTGKTTSIRAIAKFLYKHT 86
                                       89*****************9998873 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.0    0.0025      0.93       3      29 ..      61      87 ..      60     158 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0025
                                       EEEEC-TTTCHHHHHHHHHHHHCTS-S CS
                              NACHT  3 vilqGeaGsGKTtLlqklalawaegkl 29
                                       ++l G++G GKTt ++ +a  + + + 
  gene1399|gene1399|rna1399|rna1399 61 ILLYGPPGTGKTTSIRAIAKFLYKHTI 87
                                       7899**************998877664 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00044      0.17      24      50 ..      60      86 ..      46      95 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00044
                             AAA_29 24 atlltGpsGsGKSTllDAiqalLvpak 50
                                        +ll Gp G+GK+T + Ai+  L+ ++
  gene1399|gene1399|rna1399|rna1399 60 HILLYGPPGTGKTTSIRAIAKFLYKHT 86
                                       589*****************9999776 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00048      0.18       2      78 ..      59     129 ..      58     134 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00048
                                        .EEEEE--TTSSHHHHHHHHHHHHHHTT--EEEE-THHHH.TTSSS--GGGHHHHHHHHHH.HHHHHH.TT.SEEE CS
                              KTI12   2 pLvvltGlPssGKstrakeLakaleeekrsvvviddeslgiekdsykdsakekalRsslrs.avkrdL.skekvVI 75 
                                        p ++l G P +GK+t  + +ak l ++ + + v++ ++           +    +R++++s a+ r+  +k+k+VI
  gene1399|gene1399|rna1399|rna1399  59 PHILLYGPPGTGKTTSIRAIAKFLYKHTIMCNVLELNASD--------DRGINVVREQIKSfAMCRSFqNKKKLVI 126
                                        779***********************99999999866544........3556666666665223344414556777 PP

                                        E-S CS
                              KTI12  76 vDs 78 
                                        +D+
  gene1399|gene1399|rna1399|rna1399 127 LDE 129
                                        776 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0    0.0022      0.83       8      41 ..      48      79 ..      42      87 .. 0.83
   2 ?    0.6   0.1      0.71   2.7e+02      76     111 ..      92     129 ..      78     134 .. 0.64

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0022
                                       HHHHHHCTTTSCSEEEEEEESTTSSHHHHHHHHC CS
                             NB-ARC  8 viekLlekdelqslvvalvGmgGvGKttlakqil 41
                                         + L e+d+l    + l+G +G GKtt ++ i 
  gene1399|gene1399|rna1399|rna1399 48 ALKSLQEHDNLP--HILLYGPPGTGKTTSIRAIA 79
                                       567889889988..999***********888776 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.71
                                        HHCCCTTSSSS-STTS..HHHHHHHHCCCTTEEEEEEE CS
                             NB-ARC  76 Lslseddleekeeves..lkrklvrlLltkrfllvlDD 111
                                        L+l+ +d+   + v +  +   ++r  ++k+ l++lD 
  gene1399|gene1399|rna1399|rna1399  92 LELNASDDRGINVVREqiKSFAMCRSFQNKKKLVILDE 129
                                        33333333333322222377799*************95 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00055      0.21      39      59 ..      53      78 ..      31      86 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00055
                                       -......SEEEE--TTSSHHHHHHHH CS
                       FtsK_SpoIIIE 39 a.....shllvaGatgsGKStalntL 59
                                             +h+l+ G +g+GK+t ++++
  gene1399|gene1399|rna1399|rna1399 53 QehdnlPHILLYGPPGTGKTTSIRAI 78
                                       2333457****************985 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00075      0.28       1      46 [.      64     109 ..      64     155 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00075
                                        EE-TTSSHHHHHHHHHHHHTEEEEEHHHHHHHHHHTT.TSHSSHHHH CS
                             AAA_17   1 lGgPGsGKgtqceklvekygfthlsaGdllreeakrg.glakardem 46 
                                        +G+PG GK+t + +   k+ ++h  +  +l  +a+++ g +  r+++
  gene1399|gene1399|rna1399|rna1399  64 YGPPGTGKTTSI-RAIAKFLYKHTIMCNVLELNASDDrGINVVREQI 109
                                        7***********.7777888999888888876665553433334444 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0    0.0006      0.23      30      53 ..      62      85 ..      49     149 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0006
                             AAA_27 30 liyGpNEAGKstalrAisdllfGi 53
                                       l+yGp  +GK+t++rAi ++l+  
  gene1399|gene1399|rna1399|rna1399 62 LLYGPPGTGKTTSIRAIAKFLYKH 85
                                       78*******************975 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0       1.1     4e+02      16      31 ..      60      75 ..      45      93 .. 0.75
   2 ?    8.2   0.1    0.0051       1.9     121     148 ..     121     147 ..     102     155 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 1.1
                                       EEEEEESTTSSHHHHH CS
                                       xxxxxxxxxxxxxxxx RF
                               DEAD 16 dvlvaaeTGsGKTlaf 31
                                       ++l+ ++ G+GKT+  
  gene1399|gene1399|rna1399|rna1399 60 HILLYGPPGTGKTTSI 75
                                       56788999*****873 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0051
                                        TEEEEEEETHHHHHHTTTHHHHHHHHHH CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               DEAD 121 qvrflVlDEadrlldqgfsdfinrilnq 148
                                        + ++++lDEad ++ +  ++ ++r+++ 
  gene1399|gene1399|rna1399|rna1399 121 KKKLVILDEADSMSRD-AQNALRRVIED 147
                                        4589*********998.88888888776 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.2    0.0024      0.91      36      50 ..      61      75 ..      58     147 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0024
                             AAA_25 36 allaGapgtGKttla 50
                                       +ll+G+pgtGKtt  
  gene1399|gene1399|rna1399|rna1399 61 ILLYGPPGTGKTTSI 75
                                       69**********986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (325 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       806  (0.0449551); expected 358.6 (0.02)
Passed bias filter:                      619  (0.0345251); expected 358.6 (0.02)
Passed Vit filter:                       111  (0.00619109); expected 17.9 (0.001)
Passed Fwd filter:                        48  (0.00267723); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              48  [number of targets reported over threshold]
# CPU time: 0.63u 0.33s 00:00:00.96 Elapsed: 00:00:00.47
# Mc/sec: 2097.18
//
Query:       gene14|gene14|rna14|rna14  [L=68]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (68 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       378  (0.0210832); expected 358.6 (0.02)
Passed bias filter:                      252  (0.0140554); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 464.65
//
Query:       gene140|gene140|rna140|rna140  [L=359]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (359 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       661  (0.0368676); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 2523.66
//
Query:       gene1400|gene1400|rna1400|rna1400  [L=41]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (41 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       636  (0.0354733); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.29s 00:00:00.67 Elapsed: 00:00:00.46
# Mc/sec: 268.39
//
Query:       gene1401|gene1401|rna1401|rna1401  [L=255]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-27   97.0  23.4    6.8e-22   78.1   9.2    2.0  2  Zip       ZIP Zinc transporter
  ------ inclusion threshold ------
      0.084   12.9   0.2      0.084   12.9   0.2    2.4  2  DUF1453   Protein of unknown function (DUF1453)


Domain annotation for each model (and alignments):
>> Zip  ZIP Zinc transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   5.2   2.2e-10     2e-06       9     107 ..       5      92 ..       1     101 [. 0.83
   2 !   78.1   9.2   7.6e-26   6.8e-22     180     333 .]      98     246 ..      89     246 .. 0.90

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 2.2e-10
                                Zip   9 iaililsllgllgpllvpkiskllskllls.lllafavGvllgtaflhLlPealealeesqleeehthplagllvl 83 
                                         a+l+ls++++++ ll+++ + l ++  ls + ++f++Gvll+t ++h++P+++    e +         a + + 
  gene1401|gene1401|rna1401|rna1401   5 TALLLLSAFVFVFTLLFSFSYALFKNTKLSlYSKCFSGGVLLSTIIFHIFPDVYT--RENC-------FIAPFSAG 71 
                                        6899999999999999999999966666651679********************9..4445.......899***** PP

                                Zip  84 lGflllllveklltmivekksshk 107
                                        ++fl+l+ ++kl  ++ e+   h+
  gene1401|gene1401|rna1401|rna1401  72 ISFLILFSIDKLYLQYRES---HG 92 
                                        *************999988...33 PP

  == domain 2  score: 78.1 bits;  conditional E-value: 7.6e-26
                                Zip 180 aslkvraiilllglilHsfidGLAlGvssssstgislfiAvllHelpeelglgaiLlkaglsrkkavllnllfalt 255
                                        ++ ++ a++++ +l++Hsf++GL ++v  ++s ++   i +l H+ +e++ + + +  +g+s+   +ll ++++++
  gene1401|gene1401|rna1401|rna1401  98 LNNRLQALVFICALSVHSFMEGLGTSVKTGTSLVWY-AIGLLGHKWIEAFVVSVTMHTSGFSQLETILLLVFYSVL 172
                                        4556679*******************8888888775.789************************************ PP

                                Zip 256 aplGiliGilvrsisessgaeivsgillalsaGtflYvalvellphEllnekgssslkqsllqllglllGfalmll 331
                                        +plG+++G+   ++s+++  + ++++l+++++G f Y+++ e+l  E+ ++      k    +++++++Gf +m  
  gene1401|gene1401|rna1401|rna1401 173 TPLGTVLGMI--MMSSARFPSQTAELLNGVACGSFFYIGFIEMLNSEFESHT--LLRKRDQRKIAAVFAGFFTMTS 244
                                        **********..88899***************************98998888..35567889************98 PP

                                Zip 332 la 333
                                        +a
  gene1401|gene1401|rna1401|rna1401 245 IA 246
                                        86 PP

>> DUF1453  Protein of unknown function (DUF1453)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.9      0.11     1e+03      36      75 ..      14      54 ..       3     113 .. 0.63
   2 ?   12.9   0.2   9.3e-06     0.084      32      97 ..     171     236 ..     169     254 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.11
                            DUF1453 36 lfmstGalmfvfpefrltllevleallvGa.lfsiplikts 75
                                       +f++t ++ f +  f+ t l +    + G  l+s+++ + +
  gene1401|gene1401|rna1401|rna1401 14 VFVFTLLFSFSYALFKNTKLSLYSKCFSGGvLLSTIIFHIF 54
                                       34455557777777776666655544443337776665554 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 9.3e-06
                            DUF1453  32 ilPplfmstGalmfvfpefrltllevleallvGalfsipliktskfevrdgkiylkrskafifill 97 
                                        +l pl++  G++m+    f  +++e+l +++ G +f i  i + + e + ++++ kr +  i+ ++
  gene1401|gene1401|rna1401|rna1401 171 VLTPLGTVLGMIMMSSARFPSQTAELLNGVACGSFFYIGFIEMLNSEFESHTLLRKRDQRKIAAVF 236
                                        6789*******************************************9999999999876555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       838  (0.0467399); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1758.17
//
Query:       gene1402|gene1402|rna1402|rna1402  [L=339]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.3e-23   82.3   4.1      9e-23   81.3   4.1    1.5  1  V-ATPase_C      V-ATPase subunit C
  ------ inclusion threshold ------
       0.14   12.2   2.8        2.2    8.3   0.4    2.3  2  CENP-F_leu_zip  Leucine-rich repeats of kinetochore protein C


Domain annotation for each model (and alignments):
>> V-ATPase_C  V-ATPase subunit C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.3   4.1     1e-26     9e-23       1     324 [.       2     294 ..       2     319 .. 0.85

  Alignments for each domain:
  == domain 1  score: 81.3 bits;  conditional E-value: 1e-26
                         V-ATPase_C   1 ywLisvpgektseqtleelnkalskksknselykfeipdlkvgtLDsLvalsddLgKldafvesvvkKvartlaev 76 
                                        y++is+p +++  ++  +l ++l+k  +  +++k+++p     ++ s+++l ++L  l  +v  + +K+  + ++ 
  gene1402|gene1402|rna1402|rna1402   2 YFFISLPVDSR--TSAINLLTHLKK--HRLDVFKLNVPINHWSSFGSMIELTEQLDGLCRQVLDLFNKLLTVDRDF 73 
                                        77899998744..333456666653..3489999999999999999999999999777666666666666665555 PP

                         V-ATPase_C  77 ledqkdkleenllvngkslesYltkFqWdeakypvkqslkelvdiiskevtqidedlktksaaYnelksslqaler 152
                                               +++   v++++l++ +++F W   kyp   +l+++++++  e++ i +++  +sa+Y+  k++++ + r
  gene1402|gene1402|rna1402|rna1402  74 -------VKSPSFVKNVDLNNKIERFVWPGDKYPR-AALNDMFETFVDELALIRKNFELRSANYERSKRKMEDIRR 141
                                        .......566679********************96.68************************************** PP

                         V-ATPase_C 153 kktgnLltrsLadlvkkedfvldseyLttllViVpknsekewlksYekltdmVVPrSakklaeDneyaLftVtlfk 228
                                        +k+g L   +La+lv+++d +   e+L+   V + +n++ e       ++d ++    k++a D+e  L++   ++
  gene1402|gene1402|rna1402|rna1402 142 RKNGTLREVDLANLVTQNDDF---EFLEYFYVLIDRNERLEN----VDVEDLIC---VKEIAGDEEQRLVQCLGLR 207
                                        ******************988...9************98775....46788886...58***************** PP

                         V-ATPase_C 229 kvveefkakarekkfivReFsydeeeleeekeeltkleaekkkqegelvrllkvnFsevfvawiHlkalrvFvEsv 304
                                        ++ e+  ++  +kk+iv+ F+  +e       ++++++ + +  e+ +   + +   e+f  ++ +k  +++v+sv
  gene1402|gene1402|rna1402|rna1402 208 SKREHIEKQLAAKKYIVKRFESTNE-------DVDRIAIDFSVVEKGYFTFIDTYLLETFDLLLCVKLTKLYVDSV 276
                                        ********************98877.......56666667777777888999999********************* PP

                         V-ATPase_C 305 LRYGlpvnFqalllqpekkk 324
                                        L+YGlp ++ +l  ++  k+
  gene1402|gene1402|rna1402|rna1402 277 LQYGLPNSYIFLGSKD--KS 294
                                        *********9887776..33 PP

>> CENP-F_leu_zip  Leucine-rich repeats of kinetochore protein Cenp-F/LEK1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.1    0.0057        51      20      62 ..     102     144 ..      98     163 .. 0.81
   2 ?    8.3   0.4   0.00024       2.2      77     108 ..     205     236 ..     175     239 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.0057
                     CENP-F_leu_zip  20 dsLkdkvenLerelemseenqekvileaEtskaevetlkeeie 62 
                                        + L+d  e    el  + +n e    + E sk ++e ++  ++
  gene1402|gene1402|rna1402|rna1402 102 AALNDMFETFVDELALIRKNFELRSANYERSKRKMEDIRRRKN 144
                                        5788999999999999999999999999999999999887665 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00024
                     CENP-F_leu_zip  77 alrsekeeLekelqkkqervseLeslnsslen 108
                                         lrs +e++ek+l  k+  v+  es+n+++ +
  gene1402|gene1402|rna1402|rna1402 205 GLRSKREHIEKQLAAKKYIVKRFESTNEDVDR 236
                                        589************************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (339 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       885  (0.0493614); expected 358.6 (0.02)
Passed bias filter:                      566  (0.031569); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 2352.00
//
Query:       gene1403|gene1403|rna1403|rna1403  [L=42]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.048   13.1   0.1      0.048   13.1   0.1    1.0  1  RE_CfrBI  CfrBI restriction endonuclease


Domain annotation for each model (and alignments):
>> RE_CfrBI  CfrBI restriction endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   2.7e-06     0.048      64      96 ..       5      35 ..       1      41 [. 0.77

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.7e-06
                           RE_CfrBI 64 keekfkslwlaGlnkktvknidGsaakdvvldl 96
                                       +  ++k++++ G+n+ t kn+ G    + ++ +
  gene1403|gene1403|rna1403|rna1403  5 TGSEMKKYIFKGMNNETNKNVCG--IGNACFRV 35
                                       667899****************9..44444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (42 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       347  (0.0193541); expected 358.6 (0.02)
Passed bias filter:                      237  (0.0132188); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.26s 00:00:00.61 Elapsed: 00:00:00.41
# Mc/sec: 305.69
//
Query:       gene1405|gene1405|rna1405|rna1405  [L=639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-13   50.1   1.8    9.4e-05   22.5   0.1    3.6  3  Myb_DNA-binding  Myb-like DNA-binding domain
    4.7e-06   26.8   5.9        0.1   12.9   0.2    3.7  3  Myb_DNA-bind_6   Myb-like DNA-binding domain
  ------ inclusion threshold ------
        1.6    8.6  13.2        0.2   11.6   1.4    3.6  3  Myb_DNA-bind_7   Myb DNA-binding like


Domain annotation for each model (and alignments):
>> Myb_DNA-binding  Myb-like DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.1   1.6e-08   9.4e-05       2      43 ..     329     369 ..     328     372 .. 0.89
   2 !   10.2   0.4   0.00011      0.65       3      25 ..     397     419 ..     396     419 .. 0.95
   3 !   14.3   0.0   5.7e-06     0.034       3      45 ..     550     592 ..     549     593 .. 0.93

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 1.6e-08
                                        SSSBHHHHHHHHHHHHHHTTCHHHHHHHHTSS-HHHHHHHHH CS
                    Myb_DNA-binding   2 gkWteeEdelLleavkkhGnrWkkIaerlggRtekqcrsrwr 43 
                                         +W++eE+ ++le+++++ +++  Ia+ lg R   +++ +++
  gene1405|gene1405|rna1405|rna1405 329 EQWSAEEHAQFLEYFALFNKKFHVIAKLLG-RNTQDVIQHYY 369
                                        58***************************5.88888887775 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00011
                                        SSBHHHHHHHHHHHHHHTTCHHH CS
                    Myb_DNA-binding   3 kWteeEdelLleavkkhGnrWkk 25 
                                        +Wte E  +++++   +G++Wk+
  gene1405|gene1405|rna1405|rna1405 397 EWTESERSKFERLYDFYGKNWKA 419
                                        6********************96 PP

  == domain 3  score: 14.3 bits;  conditional E-value: 5.7e-06
                                        SSBHHHHHHHHHHHHHHTTCHHHHHHHHTSS-HHHHHHHHHHH CS
                    Myb_DNA-binding   3 kWteeEdelLleavkkhGnrWkkIaerlggRtekqcrsrwrny 45 
                                         Wt +E +l++      G++W+  ++++ ++ + +cr +++ y
  gene1405|gene1405|rna1405|rna1405 550 DWTIDERQLFAIFYPYIGKNWSDLSQYITTKKPGDCRTYFKFY 592
                                        5999999999999999***********************9877 PP

>> Myb_DNA-bind_6  Myb-like DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.2   1.7e-05       0.1       1      45 [.     331     374 ..     331     389 .. 0.85
   2 ?    3.5   0.1     0.014        86       1      21 [.     398     418 ..     398     427 .. 0.96
   3 !   11.3   0.1   5.2e-05      0.31       1      40 [.     551     590 ..     551     606 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.7e-05
                     Myb_DNA-bind_6   1 WteeEdeiLlklvekygndWknIaealnrRtpkqcfdrwknkLrp 45 
                                        W++eE    l++   ++++++ Ia+ l+ R+ +++ +++ ++ + 
  gene1405|gene1405|rna1405|rna1405 331 WSAEEHAQFLEYFALFNKKFHVIAKLLG-RNTQDVIQHYYCTKKR 374
                                        ****************************.9999999999883333 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.014
                     Myb_DNA-bind_6   1 WteeEdeiLlklvekygndWk 21 
                                        Wte E  +  +l+  yg++Wk
  gene1405|gene1405|rna1405|rna1405 398 WTESERSKFERLYDFYGKNWK 418
                                        ********************8 PP

  == domain 3  score: 11.3 bits;  conditional E-value: 5.2e-05
                     Myb_DNA-bind_6   1 WteeEdeiLlklvekygndWknIaealnrRtpkqcfdrwk 40 
                                        Wt +E ++ +  +   g++W+  ++ +  + p +c+ ++k
  gene1405|gene1405|rna1405|rna1405 551 WTIDERQLFAIFYPYIGKNWSDLSQYITTKKPGDCRTYFK 590
                                        9999999999999999***********88*******9998 PP

>> Myb_DNA-bind_7  Myb DNA-binding like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   1.4   3.4e-05       0.2       7      57 ..     327     377 ..     322     403 .. 0.83
   2 ?    0.3   1.1      0.11   6.6e+02      10      53 ..     397     442 ..     391     468 .. 0.71
   3 ?    2.4   0.3     0.024   1.4e+02       4      50 ..     544     590 ..     541     613 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 3.4e-05
                     Myb_DNA-bind_7   7 ktkkWskeetekFYkaLsqfGtDFsliaklfpkrtrrqlKlKFkkEerknp 57 
                                        ++++Ws ee  +F +    f   F++iakl+ + t++ ++  + + +r++ 
  gene1405|gene1405|rna1405|rna1405 327 PEEQWSAEEHAQFLEYFALFNKKFHVIAKLLGRNTQDVIQHYYCTKKRERY 377
                                        679********************************9999999955554443 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.11
                     Myb_DNA-bind_7  10 kWskeetekFYkaLsqfGtDFsliaklfpkrtrrqlKl..KFkkEe 53 
                                        +W+++e  kF +    +G +++  +  f ++  ++ K+  ++ + +
  gene1405|gene1405|rna1405|rna1405 397 EWTESERSKFERLYDFYGKNWKAYEGSFMGKGVSDFKNyhRYLSKN 442
                                        7999999999999999999999999999888777777533333333 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.024
                     Myb_DNA-bind_7   4 krkktkkWskeetekFYkaLsqfGtDFsliaklfpkrtrrqlKlKFk 50 
                                        k++  ++W+ +e ++F      +G ++s ++++ + ++  + +  Fk
  gene1405|gene1405|rna1405|rna1405 544 KQNVLEDWTIDERQLFAIFYPYIGKNWSDLSQYITTKKPGDCRTYFK 590
                                        5667799*************************999988777666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (639 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1195  (0.0666518); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.61u 0.27s 00:00:00.88 Elapsed: 00:00:00.44
# Mc/sec: 4368.40
//
Query:       gene1406|gene1406|rna1406|rna1406  [L=322]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
      0.031   14.8   0.3      0.085   13.4   0.1    1.8  2  Adhesin_P1  Mycoplasma adhesin P1
       0.15   12.0   0.1        0.3   11.0   0.1    1.4  1  SAYSvFN     Uncharacterized conserved domain (SAYSvFN)


Domain annotation for each model (and alignments):
>> Adhesin_P1  Mycoplasma adhesin P1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   9.5e-06     0.085      19      85 ..      18      84 ..       8      90 .. 0.86
   2 ?   -2.5   0.0      0.86   7.7e+03      62      83 ..     250     271 ..     226     277 .. 0.58

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 9.5e-06
                         Adhesin_P1 19 dslkqdkvdksGdsvsvqeatsgdnltnytnlpPnltPtsdwPnalsftnknnaqraqlflrGllgs 85
                                       d  ++d ++++ d+    + ts++++  y++ p   t t ++P+    t++ ++   +l++rG+ +s
  gene1406|gene1406|rna1406|rna1406 18 DDHHTDELEQNDDQNVNINMTSNEDDYGYEDYPEFATYTVKTPKPFCDTCNHDSISGWLIKRGKNTS 84
                                       777899999999977777788888888************************************9665 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.86
                         Adhesin_P1  62 nalsftnknnaqraqlflrGll 83 
                                        n+l  ++ + a+r+ + +r l+
  gene1406|gene1406|rna1406|rna1406 250 NSLDASSPTGAERISVTRRDLM 271
                                        4444455556666666666665 PP

>> SAYSvFN  Uncharacterized conserved domain (SAYSvFN)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   3.3e-05       0.3      17      40 ..     277     300 ..     270     303 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 3.3e-05
                            SAYSvFN  17 fgavfvilsllvliftnlrsgerk 40 
                                         g+vfvi++++++i++ + +++rk
  gene1406|gene1406|rna1406|rna1406 277 AGPVFVIFAIFIFIYWYFWKRPRK 300
                                        699*************99557776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (322 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       829  (0.0462379); expected 358.6 (0.02)
Passed bias filter:                      613  (0.0341904); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.24s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 2224.59
//
Query:       gene1407|gene1407|rna1407|rna1407  [L=95]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       282  (0.0157287); expected 358.6 (0.02)
Passed bias filter:                      249  (0.0138881); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.45
# Mc/sec: 641.18
//
Query:       gene1408|gene1408|rna1408|rna1408  [L=535]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.3e-76  258.2  11.3    1.9e-76  257.7  11.3    1.2  1  Cpn60_TCP1  TCP-1/cpn60 chaperonin family


Domain annotation for each model (and alignments):
>> Cpn60_TCP1  TCP-1/cpn60 chaperonin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  257.7  11.3     1e-80   1.9e-76       1     488 [.      21     532 ..      21     535 .] 0.85

  Alignments for each domain:
  == domain 1  score: 257.7 bits;  conditional E-value: 1e-80
                                        HHHHHHCCSSTTXXEEEEEETTSEEEEEXSHHHHHHCSXXXSHHHHHHHHHHHHCCCCCTTCHHHHHHHHHHHHHH CS
                         Cpn60_TCP1   1 ladivkttlGPkGmdKmlvnkggkvvvTnDGatilkeleiehPaakllveaaesqdeevGDGTttvviLageLlee 76 
                                        l++++++++GP G+dK+l+ + +k+vvTnDG+tilk+l   hP+ k+l +++ +qd+ +GDGTt+vviL++++le+
  gene1408|gene1408|rna1408|rna1408  21 LKSTLSSSIGPFGLDKLLITPSNKIVVTNDGSTILKNLSSFHPITKILNNVSMTQDKVAGDGTTSVVILTAQILEN 96 
                                        67899*********************************************************************** PP

                                        HHHHHHCTXXHHHHHHHHHHHHHHHHHHHHHHXEEBXSCSTT.HHHHHHHHHHCTTSSXXSTHHHHHHHHHHHHHC CS
                         Cpn60_TCP1  77 aekliaagvhpttiiegyekalekaleaLkeiaveisseekdreeLlkvartslsskltskeaeelsklvvdAvkl 152
                                        a++l++++vh ++ii+ + + ++ +le+ ++   +i++e     + ++++rtslssk++s+  +el  l+++A   
  gene1408|gene1408|rna1408|rna1408  97 AKELMDENVHASAIIRELGRIKQIVLEYFERS--KIRVE-----NFASAVRTSLSSKVVSAAMDELVPLALKAT-- 163
                                        ******************************99..88875.....79***************************9.. PP

                                        HCCCSEECSCCCEECCCCEECECTTSEEESEEEE....SS--SST...........TSSCEE.ECEEEEEESS-BS CS
                         Cpn60_TCP1 153 ieenekeldlgrikvvkieggsledselveGlvl....dkgvlsp...........dmpkkl.enakvllldvsLe 212
                                                + ++ kvvk+ g ++e+ ++v+G+++    d    ++           ++++ l ++ +v+ll+  L+
  gene1408|gene1408|rna1408|rna1408 164 --------QYEKLKVVKKLGDEIENCTVVDGYCVkiksD----EKnsevvdeyaieQLSTALqKKYRVALLQYNLS 227
                                        ........789***********************66541....33234566688877777775666********** PP

                                        --HHCCHHHCCCCSCCHHHHHHHHHHHHHHHHHHHHHHTTECEEEESS-B.....-HHHHHHHHHCT-EEE-S--H CS
                         Cpn60_TCP1 213 iektetkttvvlsdaeeleklekaeekqleellekiiksgvnvvvcqkgi.....ddlalhflakngilalrrvkk 283
                                         +k+++++++++  +e++e++ k+e++++ +l++k++   v++ ++qk+i     +dla+ fl+k +i     +++
  gene1408|gene1408|rna1408|rna1408 228 APKPNIDSKIEI--EEKIEEIIKEEREYVFNLVKKLKMNRVEIALVQKSIlkesvSDLAEYFLNKLKIKF-FVLER 300
                                        ****66666555..789**************************999999988888999999999999974.56788 PP

                                        HHHHHHHHHHT--EBSCGGGGGCGC..........-EEEEEEEECCETTCCEEEEE.................... CS
                         Cpn60_TCP1 284 kdlerlakatGatavssledltpee..........lGtakkveeekigsekttiie.................... 329
                                        +++e ++++   +  s+   +t +           l + ++  e++++ e+ t ++                    
  gene1408|gene1408|rna1408|rna1408 301 EEIEEISRVFEMRTSSTNNIITYDMnvsfyddiilLNETETRVEKTCNGENETNVNekvpvaekegrksevsgaeg 376
                                        8888888888777666664444433445566677766666555555555555555557777777777777777766 PP

                                        ...............CESSSSXEEEEEEESTCCCHHHHHHHHHHHHHHHHHHHHHHEEEETTTCHHHHHHHHHHCC CS
                         Cpn60_TCP1 330 ...............evksgkiatillrgatdtvldeieraiedAlnvvknaiedekvvpGGGatelelakklkey 390
                                                         +++++ ++++r++ +  lde+er+++dA++v++++ +++++vpGGG +e+ +++     
  gene1408|gene1408|rna1408|rna1408 377 vtkgdasannhgekrRKAEKRVGSLIVRASDNILLDETERSLNDAICVARCLKDEPYIVPGGGNVEMNISRLH--- 449
                                        66666666555554422999************************************************99755... PP

                                        CCTSXCCHHHHHHHHHHHHTHHHHHHHHHCTSXHHHHHHHHHHHHHTTXTTEEEETTTTCEEECCCCTXEEEHHHH CS
                         Cpn60_TCP1 391 aksvsgeeqlaieafakALevipktLaeNaGldpievlaklraahnkgekelgidvesgeiidlveagvvDplkvk 466
                                               e+ + + + +A+ +ip+ +++NaGl+  ++  ++ +       + gid+ sg++++++e+++v p+kv 
  gene1408|gene1408|rna1408|rna1408 450 -------ENEIQKRIMSAFVIIPYFICRNAGLNFYKI-GQVAD-------NSGIDCVSGSVENMIEKNIVMPVKVA 510
                                        .......3345568899****************9875.45545.......68************************ PP

                                        HHHHHHHHHHHHHHHCEEEEEX CS
                         Cpn60_TCP1 467 rqalksAteaastiLrideiik 488
                                        ++ + +A e+as iL+id+i+ 
  gene1408|gene1408|rna1408|rna1408 511 KSYFGLALETASFILSIDDILP 532
                                        ********************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (535 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1233  (0.0687713); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.28s 00:00:00.89 Elapsed: 00:00:00.44
# Mc/sec: 3628.90
//
Query:       gene1409|gene1409|rna1409|rna1409  [L=342]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.4e-05   23.8   4.6     0.0059   16.0   3.1    2.7  2  WD40_like  WD40-like domain
    0.00082   20.1   0.4      0.012   16.5   0.0    3.1  5  WD40       WD domain, G-beta repeat
  ------ inclusion threshold ------
      0.028   14.9   0.0        8.5    7.0   0.0    3.7  4  PQQ_3      PQQ-like domain


Domain annotation for each model (and alignments):
>> WD40_like  WD40-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.8   0.0    0.0012       7.2      50     119 ..      17      86 ..       7     100 .. 0.69
   2 !   16.0   3.1   9.8e-07    0.0059      69     144 ..     171     248 ..     133     259 .. 0.71

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0012
                          WD40_like  50 lldddlilvvtlDGtillslleneeevenekiee...distvkviddklliGtnkGsiyvfskdlqleevllg 119
                                        ++d++ +lv t D +i  +++     + ++ + e    is+v+  ++++  G  +G +y  s d++ +  + g
  gene1409|gene1409|rna1409|rna1409  17 QVDGKRVLVSTADCKI--YMVDPP-YTGKKLLFEglsPISCVEHQNGEIFFGDWNGCVYRMSIDVNERDSCTG 86 
                                        5666777777777777..322222.22333222211169999******************9999887766655 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 9.8e-07
                          WD40_like  69 lleneeevene.kieedistvkviddklliGtnkGsiyvfskdlqleevllgqsseIkeikienn.kiysLs.esa 141
                                         + ++ +v+++ ++++ i +  vi+d+l++G +  si  f++  ++ee+   ++s I+ i++++n  i + s +++
  gene1409|gene1409|rna1409|rna1409 171 IMDKNLQVKTRiNLNNKILCFAVINDQLYMGMSIPSILRFNNG-KIEEIPTAHQSSILCISTDENgDIVTSSaDKT 245
                                        2333334544337999999999999999999999999999999.99999999999999999876524544441444 PP

                          WD40_like 142 fiv 144
                                        ++v
  gene1409|gene1409|rna1409|rna1409 246 LMV 248
                                        555 PP

>> WD40  WD domain, G-beta repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.85   5.1e+03      21      36 ..      19      34 ..      11      36 .. 0.66
   2 ?   -2.5   0.0         2   1.2e+04      13      34 ..      52      71 ..      47      72 .. 0.60
   3 !   16.5   0.0     2e-06     0.012       6      36 ..     218     248 ..     213     250 .. 0.85
   4 ?   -3.7   0.0         3   1.8e+04       7      18 ..     254     267 ..     252     273 .. 0.54
   5 ?   -2.0   0.0       1.4   8.3e+03      10      27 ..     288     304 ..     279     321 .. 0.65

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.85
                                       TSSEEEEEETTSEEEE CS
                               WD40 21 dgawlasGsdDgtvri 36
                                       dg+ ++ ++ D+++++
  gene1409|gene1409|rna1409|rna1409 19 DGKRVLVSTADCKIYM 34
                                       5555555555999976 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2
                                       EEEEEEETTSSEEEEEETTSEE CS
                               WD40 13 vtslafspdgawlasGsdDgtv 34
                                       ++++  +++g  ++ G+++g v
  gene1409|gene1409|rna1409|rna1409 52 ISCV-EHQNGEIFF-GDWNGCV 71
                                       6666.444555555.7777765 PP

  == domain 3  score: 16.5 bits;  conditional E-value: 2e-06
                                        EEESS.SSEEEEEEETTSSEEEEEETTSEEEE CS
                               WD40   6 tltGH.ssvtslafspdgawlasGsdDgtvri 36 
                                        + t+H ss+ +++++ +g+ ++s s D+t+++
  gene1409|gene1409|rna1409|rna1409 218 IPTAHqSSILCISTDENGDIVTS-SADKTLMV 248
                                        5689*999************865.55***987 PP

  == domain 4  score: -3.7 bits;  conditional E-value: 3
                                        EESSSSE.EEEE.E CS
                               WD40   7 ltGHssv.tsla.f 18 
                                        +tG  ++  +l+ +
  gene1409|gene1409|rna1409|rna1409 254 YTGAEWIrVCLClY 267
                                        56665554466543 PP

  == domain 5  score: -2.0 bits;  conditional E-value: 1.4
                                        S.SSEEEEEEETTSSEEEE CS
                               WD40  10 H.ssvtslafspdgawlas 27 
                                        H + v +l  +++  wl+s
  gene1409|gene1409|rna1409|rna1409 288 HeGYVVGL--QQNEEWLFS 304
                                        64446677..777788764 PP

>> PQQ_3  PQQ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.0    0.0014       8.5      19      38 ..      18      37 ..      11      37 .. 0.94
   2 ?    0.5   0.0      0.16   9.6e+02      24      34 ..      62      72 ..      57      74 .. 0.87
   3 ?   -1.9   0.0      0.88   5.3e+03      21      27 ..     158     164 ..     149     169 .. 0.80
   4 ?    1.6   0.0     0.073   4.3e+02      15      32 ..     240     272 ..     230     275 .. 0.66

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0014
                              PQQ_3 19 vdgglvyvgtgdGtlyAlDa 38
                                       vdg +v v+t d ++y++D+
  gene1409|gene1409|rna1409|rna1409 18 VDGKRVLVSTADCKIYMVDP 37
                                       899****************7 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.16
                              PQQ_3 24 vyvgtgdGtly 34
                                       +++g+++G +y
  gene1409|gene1409|rna1409|rna1409 62 IFFGDWNGCVY 72
                                       89******999 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 0.88
                              PQQ_3  21 gglvyvg 27 
                                        +g vyvg
  gene1409|gene1409|rna1409|rna1409 158 NGNVYVG 164
                                        7899998 PP

  == domain 4  score: 1.6 bits;  conditional E-value: 0.073
                              PQQ_3  15 ssp....avdgglvyvgtg...........dGt 32 
                                        ss+     v +++vy+g++           dG+
  gene1409|gene1409|rna1409|rna1409 240 SSAdktlMVNNRVVYTGAEwirvclclyftDGN 272
                                        44455557889999*999866666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (342 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       966  (0.0538792); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 2392.58
//
Query:       gene141|gene141|rna141|rna141  [L=842]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (842 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       941  (0.0524848); expected 358.6 (0.02)
Passed bias filter:                      472  (0.0263261); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.76u 0.30s 00:00:01.06 Elapsed: 00:00:00.50
# Mc/sec: 5070.40
//
Query:       gene1410|gene1410|rna1410|rna1410  [L=408]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (408 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                        93  (0.00518713); expected 358.6 (0.02)
Passed bias filter:                       39  (0.00217525); expected 358.6 (0.02)
Passed Vit filter:                         1  (5.57756e-05); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 2925.33
//
Query:       gene1411|gene1411|rna1411|rna1411  [L=349]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.1e-47  160.4   0.0    5.2e-47  159.6   0.0    1.3  1  Sua5_yciO_yrdC  Telomere recombination
    2.2e-22   80.0   0.0    3.1e-22   79.6   0.0    1.2  1  SUA5            Putative GTP-binding controlling metal-bindin


Domain annotation for each model (and alignments):
>> Sua5_yciO_yrdC  Telomere recombination
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  159.6   0.0   5.8e-51   5.2e-47       8     179 .]      24     193 ..      21     193 .. 0.97

  Alignments for each domain:
  == domain 1  score: 159.6 bits;  conditional E-value: 5.8e-51
                                        EEEEE-SSSEEEEEETTSHHHHHHHHHHHTSHCCC--EEEESSCCCCCCCC-TC--HHHHHHHHCT-SSSCEEEEE CS
                     Sua5_yciO_yrdC   8 ivaiptetvYgLacdatneeaverlreiKgrpsdkplavlvasledlkklaeseveeealkllerfwPGpitlllk 83 
                                         +aiptetvYgLa +++n ++ +++++iK+rp+d+pl+v+v+s+++l+ l++ ev+    +l+e++wPGp+tll  
  gene1411|gene1411|rna1411|rna1411  24 PIAIPTETVYGLASKISNTSTLRNIYTIKNRPADNPLIVHVSSVSMLESLVK-EVPPIYRALIEQYWPGPLTLLFL 98 
                                        69*************************************************9.*********************** PP

                                        ..E-TS-HHHHTTTTEEEEEE-SSHHHHHHHHHCTS-EEEEES-STTS-S-SSHHHHHHHC-TTSECB-SS---SS CS
                     Sua5_yciO_yrdC  84 rskeklpkevapglktvGvrlPdtplarlLlealgeplvaTSanlsgepsitdaeeveeelgeivdlildggeiav 159
                                        + ke +++ v+ g+k vG+r+P+++ ar++++ +g pl+a+San+sg+ s+ +a++v+++l ++++li+d g++++
  gene1411|gene1411|rna1411|rna1411  99 K-KECVNDIVTCGSKYVGIRMPSSKCARDIIDITG-PLAAPSANISGNISPSHAQHVYKDLMGKIELIVDDGPCKH 172
                                        5.555****************************98.**************************************** PP

                                        S---EEEETT.SSTSSECEXX CS
                     Sua5_yciO_yrdC 160 gvdstVvdlt.egkpkilRrG 179
                                        g +st+  ++ +g+  +lR+G
  gene1411|gene1411|rna1411|rna1411 173 GLESTIFTCYgGGNGAVLRPG 193
                                        **********988999**998 PP

>> SUA5  Putative GTP-binding controlling metal-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.6   0.0   3.5e-26   3.1e-22       1     134 []     195     346 ..     195     346 .. 0.87

  Alignments for each domain:
  == domain 1  score: 79.6 bits;  conditional E-value: 3.5e-26
                                        .-HHHHHHHS---....-------------S-SSEEEEE--GGGHHHH.......................HHHHH CS
                               SUA5   1 itleeleevldavekkeekpraPGmkyrHYaPkapvvlveaeeeeeaake..................ekleekkk 58 
                                        it e++e v++ + ++      PG kyrHYaP++p +l++++e++ +  +                  ++++++++
  gene1411|gene1411|rna1411|rna1411 195 ITHEMIEMVVGGKVRMGGCEMVPGKKYRHYAPTVPFLLFDSDEQMIDWMRkcagsavyddensinradNTTANHNS 270
                                        899******8533335667799*****************999998887779****************999999999 PP

                                        TTS-EEEEEEGGGTGGTSEEEEE...E-TT-HHHHHHHHHHHHHHHHHS--SEEEEE----STTHHHHHHHHHHHT CS
                               SUA5  59 sgkkvgvlatseskeaassvlsl.slgsrsdleeaarnLFaaLrelDeegvdlilvegvpeeglglAvmnRLrkAA 133
                                        + +++gvl ts+  ++   + ++ ++  ++++++++++L+++Lr+lD+ ++  i + +++ +++g+A+m+R+ +AA
  gene1411|gene1411|rna1411|rna1411 271 ARADLGVLVTSDAIRNYVVSRNIrHIDLERTKQQISSRLYHGLRTLDK-ECARICMVRMDTKDEGMAIMDRVCRAA 345
                                        99*******999888844444443356789*****************5.8999999999999************** PP

                                        T CS
                               SUA5 134 g 134
                                        g
  gene1411|gene1411|rna1411|rna1411 346 G 346
                                        7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (349 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       346  (0.0192983); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2550.19
//
Query:       gene1412|gene1412|rna1412|rna1412  [L=361]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (361 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       667  (0.0372023); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2689.71
//
Query:       gene1413|gene1413|rna1413|rna1413  [L=315]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.031   13.4   0.0       0.21   10.6   0.0    2.0  2  Poty_PP   Potyviridae polyprotein


Domain annotation for each model (and alignments):
>> Poty_PP  Potyviridae polyprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0     0.015   2.7e+02      94     128 ..      14      47 ..      12      71 .. 0.77
   2 ?   10.6   0.0   1.2e-05      0.21      30      62 ..     137     169 ..     106     170 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.015
                            Poty_PP  94 riisdkheevkaekipfhvkdlseklaiklaeavk 128
                                        ++i+  + +  ++k+ f+++ l  k  +kla  ++
  gene1413|gene1413|rna1413|rna1413  14 QRIYRANGQMDDQKLSFFIHHLQLK-PEKLASSIE 47 
                                        56788888889*********99655.456666555 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 1.2e-05
                            Poty_PP  30 vktaaqFElslflvanlvakdGslpsviydllk 62 
                                        v+  + FEl+ ++++  v+++G+l+ +++ +++
  gene1413|gene1413|rna1413|rna1413 137 VVCDNLFELKTYTMSTDVNSAGQLNGAVHPVMS 169
                                        556678***********************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (315 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       504  (0.0281109); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 2408.20
//
Query:       gene1414|gene1414|rna1414|rna1414  [L=945]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (945 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       874  (0.0487478); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.69u 0.31s 00:00:01.00 Elapsed: 00:00:00.46
# Mc/sec: 6234.38
//
Query:       gene1415|gene1415|rna1415|rna1415  [L=506]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   6.7e-178  591.5   0.6   8.4e-178  591.2   0.6    1.1  1  UDPGP     UTP--glucose-1-phosphate uridylyltransferase


Domain annotation for each model (and alignments):
>> UDPGP  UTP--glucose-1-phosphate uridylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  591.2   0.6  4.7e-182  8.4e-178       2     413 .]      44     471 ..      43     471 .. 0.98

  Alignments for each domain:
  == domain 1  score: 591.2 bits;  conditional E-value: 4.7e-182
                              UDPGP   2 esFkklferyleekskqekidwdkieplpeeevvdye.dl......................kekeeekkellnkl 54 
                                        ++F+ l+eryl++++  +kidwdki+++p+e++v+y  d+                      ++ ++e+++ll+kl
  gene1415|gene1415|rna1415|rna1415  44 DNFFLLYERYLHTRN--KKIDWDKIKSPPSEKIVKYPgDVksgghklevddrnvkkgidsssSSIKDERRTLLKKL 117
                                        79**********977..9****************9986789999999***********9986668889999***** PP

                              UDPGP  55 avlkLnGglGtsmGckgpKslieVrdgktfLdlivqqieelnkkynvdvPlvlmnSfnTdedtekilkkykkkkvd 130
                                        avlkLnGglGt+mGc+gpKs+ie++d+++fLdl+v+q+++l+++y+++vP++lmnSfnT+e+t+++l++yk+    
  gene1415|gene1415|rna1415|rna1415 118 AVLKLNGGLGTTMGCVGPKSAIEIKDTSNFLDLCVKQVDTLQRTYDTEVPFILMNSFNTEEKTNRMLRRYKG---- 189
                                        ************************************************************************.... PP

                              UDPGP 131 iltfnqsryPriskesllpvekkakkeekeewyPpGhGdlyesLknsglldkllaeGkeyiFvsniDNlgatvDlk 206
                                        i+tf+qs +Pris++sllp++ +     ++++yPpGhGd++ sLk+sg+ldkll+eG+ey+FvsniDNl+atvD++
  gene1415|gene1415|rna1415|rna1415 190 IRTFTQSVFPRISANSLLPIDPSLG---AKSMYPPGHGDVFISLKDSGMLDKLLQEGREYLFVSNIDNLAATVDFN 262
                                        *********************9996...48********************************************** PP

                              UDPGP 207 ilnllvekkaeflmevtektradvkgGtlieyegklrlleiaqvpkehveefksvkkfkifntnniwinlkalkrl 282
                                        iln++ve++++flmevtektrad+kgGtlie ++kl+lleiaqvp+e++ ef+sv+kfkifntn++winlk+lk+l
  gene1415|gene1415|rna1415|rna1415 263 ILNYVVENDVDFLMEVTEKTRADIKGGTLIELDDKLTLLEIAQVPAEKKGEFTSVRKFKIFNTNSVWINLKKLKTL 338
                                        **************************************************************************** PP

                              UDPGP 283 veekelkleiivnkktld.egekviqletavgaaiksFkkavginVpRsrflpvkttsdlLlvksdlysleegslv 357
                                        ++ek+l l+ii+nkk+++  +e+viqleta+gaaik+F+kavg+ VpRsrflpvkt+sdl+l++s+l+  ++g l+
  gene1415|gene1415|rna1415|rna1415 339 LKEKRLILDIIENKKNIEgIDETVIQLETAMGAAIKYFPKAVGMIVPRSRFLPVKTCSDLFLIRSNLFLEHDGFLT 414
                                        ******************99999***************************************************** PP

                              UDPGP 358 lnpkrsfktvplvkLg.sefkkveefqkrfksipslleldhltvsGdvtfgknvtLk 413
                                        l+pkr+f+++plvkL  +++k+ve+f+k+fk +p++leldhltvsG++tfg+nv+Lk
  gene1415|gene1415|rna1415|rna1415 415 LSPKRMFGCLPLVKLLgKMYKSVESFDKMFKGVPDILELDHLTVSGNITFGRNVVLK 471
                                        **************988**************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (506 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       663  (0.0369792); expected 358.6 (0.02)
Passed bias filter:                      454  (0.0253221); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.45
# Mc/sec: 3383.58
//
Query:       gene1416|gene1416|rna1416|rna1416  [L=551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.058   13.4   0.2       0.14   12.2   0.2    1.6  1  DUF2846   Protein of unknown function (DUF2846)


Domain annotation for each model (and alignments):
>> DUF2846  Protein of unknown function (DUF2846)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.2   7.8e-06      0.14      20      57 ..     246     283 ..     237     307 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 7.8e-06
                            DUF2846  20 eaeapdvfvngkkigelankeYfvaevepGeykister 57 
                                         a+++++++ +k + ++a+ +Y  ++++p +y+i  e 
  gene1416|gene1416|rna1416|rna1416 246 DACKAKIYIKNKTYTSVARSTYEIENIQPINYEIVYEM 283
                                        6899*****************************98875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (551 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       778  (0.0433934); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 3590.62
//
Query:       gene1417|gene1417|rna1417|rna1417  [L=80]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       618  (0.0344693); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 597.34
//
Query:       gene1418|gene1418|rna1418|rna1418  [L=126]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1157  (0.0645323); expected 358.6 (0.02)
Passed bias filter:                      598  (0.0333538); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.30s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 883.96
//
Query:       gene1419|gene1419|rna1419|rna1419  [L=39]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (39 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       598  (0.0333538); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.33u 0.25s 00:00:00.58 Elapsed: 00:00:00.40
# Mc/sec: 295.88
//
Query:       gene142|gene142|rna142|rna142  [L=326]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (326 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       671  (0.0374254); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 2372.44
//
Query:       gene1421|gene1421|rna1421|rna1421  [L=263]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.1e-33  116.7   0.0      1e-32  113.6   0.0    1.9  1  Carb_kinase  Carbohydrate kinase
  ------ inclusion threshold ------
      0.075   12.4   0.1       0.11   11.9   0.1    1.2  1  HK           Hydroxyethylthiazole kinase family


Domain annotation for each model (and alignments):
>> Carb_kinase  Carbohydrate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.6   0.0   1.1e-36     1e-32       1     242 [.      33     258 ..      33     260 .. 0.90

  Alignments for each domain:
  == domain 1  score: 113.6 bits;  conditional E-value: 1.1e-36
                                        EEEEE-BTTCHHHHHHHHHHHHCTT-SEEEEEESSTTTCCCCTTTTTCEECCTTHTTTS...--SSS-SEEEE-TT CS
                        Carb_kinase   1 vlvigGsedytGAallaalaalrlgaglvsvateseaiavlksylpevivhplledeqakileklerldavviGpG 76 
                                        +l+igG++ y GA+    +aa + g++l  ++++ +a ++lk+ lpe i   +++ e  k   +ler+   v+G+G
  gene1421|gene1421|rna1421|rna1421  33 LLLIGGCDLYVGAPCYVSKAAYATGIDLCYILCDGCALIPLKTLLPECIILSFDQFELEKHTFILERVTCCVLGSG 108
                                        589***************************************************6555677889************ PP

                                        -SS.SHCHHH.HCHHHCCCCS-EEEEGGGGGSGGGG...TTTTSSEEEE--HHHHHHHCTTTCHHCCSHHHHHHHH CS
                        Carb_kinase  77 Lgr.dekikk.lleevlekdeplviDAdgLnllaqknelserkaeviLTPhkkEfkrLlkaivkkeddrlelarel 150
                                        Lgr +e++++ + e +   ++pl++D+dgL+l ++ n  +     vi+TP+  E ++ lk ++             
  gene1421|gene1421|rna1421|rna1421 109 LGRlNERVEAvISELIGRIRVPLIVDGDGLYLWDKMN--FTYFDTVIFTPNRNESEKYLKNVD------------- 169
                                        **95667777444556667789*************97..888899***************999............. PP

                                        HHHHTTEEEEESTTSEEEECTTEEEEE----GGG-STTHHHHHHHHHHHHHHCTSSHHHHHHHHHHHHHHHHHHHC CS
                        Carb_kinase 151 aqklnavvllkgekdvivspegevlinstgssalakGGsGDvLaGligalLaqneasyeaaiaaawlhgaasdeaa 226
                                            + +vl kg +d+i + + +++ins+ s+++++GG GDvL G++++l  + e+++ a   a+ ++++as ++ 
  gene1421|gene1421|rna1421|rna1421 170 --LKKDIVLKKGPVDIITYVDSKITINSN-SGLRRCGGIGDVLCGVLASLVNVYEDKMLACKYASLIVRKASYAVY 242
                                        ..335689999********9999888875.679******************************************* PP

                                        CCT-TS-HCHHHHHHH CS
                        Carb_kinase 227 ekkgvgmlatelskii 242
                                        +k g+++ +t+++++i
  gene1421|gene1421|rna1421|rna1421 243 KKMGRSTMPTNIISEI 258
                                        *****88888887766 PP

>> HK  Hydroxyethylthiazole kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   1.2e-05      0.11     154     240 ..     174     258 ..     159     262 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.2e-05
                                        EEEEESSSEEEEESSEEEEEE-S-GGGGGSTTHHHHHHHHHHHHHTTBSSHHHHHHHHHHHHHHHH.HHHHHHHTT CS
                                 HK 154 vvvvtGevDvvsdgkkvyklknGtellgkitasGCllgsvvaaflavkkdkllaaveavllykvAgkeaaarsegs 229
                                        +v+  G vD+++   + +++++ ++ l +  + G +l  v+a+ + v +dk+la   a l+ + A+  a+ ++ g 
  gene1421|gene1421|rna1421|rna1421 174 IVLKKGPVDIITYVDSKITINS-NSGLRRCGGIGDVLCGVLASLVNVYEDKMLACKYASLIVRKAS-YAVYKKMGR 247
                                        78899*************9976.66789***************************99999999999.777788888 PP

                                        HHHHHHHHHHH CS
                                 HK 230 gsFqvelldal 240
                                        ++  ++++ ++
  gene1421|gene1421|rna1421|rna1421 248 STMPTNIISEI 258
                                        77777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       529  (0.0295053); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 1851.82
//
Query:       gene1422|gene1422|rna1422|rna1422  [L=449]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0041   17.5  15.7        2.8    8.5   2.0    6.5  6  LRR_4     Leucine Rich repeats (2 copies)
  ------ inclusion threshold ------
      0.031   14.1   0.1       0.53   10.1   0.0    2.4  2  DUF2153   Uncharacterized protein conserved in archaea (DUF21
       0.12   13.0  15.3         33    5.6   0.0    7.9  8  LRR_1     Leucine Rich Repeat
        8.1    6.8  10.3        7.1    7.0   0.1    5.3  7  LRR_6     Leucine Rich repeat


Domain annotation for each model (and alignments):
>> LRR_4  Leucine Rich repeats (2 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0      0.16     7e+02      12      33 ..     156     174 ..     147     187 .. 0.69
   2 ?   -0.4   0.1      0.39   1.7e+03      22      42 ..     189     208 ..     167     213 .. 0.67
   3 ?    2.7   0.2     0.042   1.9e+02      21      38 ..     219     236 ..     190     262 .. 0.64
   4 !    5.1   0.1    0.0071        32       3      32 ..     292     326 ..     290     340 .. 0.67
   5 !    8.3   1.2   0.00073       3.3       3      39 ..     338     372 ..     336     378 .. 0.81
   6 !    8.5   2.0   0.00062       2.8       2      35 ..     357     392 ..     357     421 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.16
                                        ---E-S-HHH-TT--EEE-.-S CS
                              LRR_4  12 qltdiplleklpnLkeLdLsgN 33 
                                        ++ +++    ++n ++L L+ +
  gene1422|gene1422|rna1422|rna1422 156 MIEKFDI---CKNFEHLELHYC 174
                                        5777777...99*****99665 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.39
                                        -TT--EEE-.-S-----GGGG CS
                              LRR_4  22 lpnLkeLdLsgNnlitdldeL 42 
                                           Lk+L L+g  l++++ +L
  gene1422|gene1422|rna1422|rna1422 189 AVGLKVLKLTGAFLLEKI-NL 208
                                        456999999776577777.45 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.042
                                        H-TT--EEE-.-S----- CS
                              LRR_4  21 klpnLkeLdLsgNnlitd 38 
                                        ++ +L e+d+s++++++d
  gene1422|gene1422|rna1422|rna1422 219 NMNKLIEIDVSHCSRLKD 236
                                        466666666666644433 PP

  == domain 4  score: 5.1 bits;  conditional E-value: 0.0071
                                        --EEE--SS---E-S-.....HHH-TT--EEE-.- CS
                              LRR_4   3 LevLdLsnNqltdipl.....leklpnLkeLdLsg 32 
                                        Le+L+++n+ +  + +     l k++ L++L++ g
  gene1422|gene1422|rna1422|rna1422 292 LEELSIANCPVLFFKGknridLCKFTRLRKLNIEG 326
                                        788888888888777754433338********944 PP

  == domain 5  score: 8.3 bits;  conditional E-value: 0.00073
                                        --EEE--SS.---E-S-HHH-TT--EEE-.-S-----G CS
                              LRR_4   3 LevLdLsnN.qltdiplleklpnLkeLdLsgNnlitdl 39 
                                        Le+L  +n+ +l+ +pl   +++L+ Ld+s  n+ +d+
  gene1422|gene1422|rna1422|rna1422 338 LEELRAANCfNLS-LPLH--NDKLRILDISKINYTRDI 372
                                        9999999976777.6664..6*********98899998 PP

  == domain 6  score: 8.5 bits;  conditional E-value: 0.00062
                                        S--EEE--S.S---E-S-.HHH-TT--EEE-.-S-- CS
                              LRR_4   2 nLevLdLsn.Nqltdipl.leklpnLkeLdLsgNnl 35 
                                        +L++Ld+s  N  +di   l+ l  L++L++s+N +
  gene1422|gene1422|rna1422|rna1422 357 KLRILDISKiNYTRDILAkLNRLSRLEYLNISFNEN 392
                                        6999999963455565555666*********99933 PP

>> DUF2153  Uncharacterized protein conserved in archaea (DUF2153)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00012      0.53      77     108 ..     219     251 ..     211     264 .. 0.82
   2 ?    1.1   0.1     0.072   3.2e+02      82     111 ..     359     388 ..     350     396 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00012
                            DUF2153  77 ilekllelDieHtsevre.lleklskegklnpl 108
                                         ++kl+e+D++H s++++ ++ ++++  +++ l
  gene1422|gene1422|rna1422|rna1422 219 NMNKLIEIDVSHCSRLKDnFIAQVNRYTRIEAL 251
                                        5899***********986379999999999877 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.072
                            DUF2153  82 lelDieHtsevrelleklskegklnpllal 111
                                          lDi+    +r++l kl++  +l+ l ++
  gene1422|gene1422|rna1422|rna1422 359 RILDISKINYTRDILAKLNRLSRLEYLNIS 388
                                        5699****************9999887655 PP

>> LRR_1  Leucine Rich Repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       1.5   6.9e+03       3      10 ..     167     174 ..     158     184 .. 0.77
   2 ?   -2.7   0.1       3.9   1.8e+04       2      13 ..     192     203 ..     192     209 .. 0.56
   3 ?    3.4   0.0     0.039   1.7e+02       1      12 [.     222     233 ..     222     242 .. 0.80
   4 ?    1.3   0.0      0.19   8.6e+02       2      13 ..     248     259 ..     247     272 .. 0.78
   5 ?    2.2   0.0     0.096   4.3e+02       2      12 ..     292     302 ..     292     315 .. 0.81
   6 ?    1.9   0.4      0.12   5.3e+02       2      14 ..     338     350 ..     318     355 .. 0.49
   7 ?    0.2   0.0      0.42   1.9e+03       1       8 [.     357     364 ..     357     369 .. 0.89
   8 ?    5.6   0.0    0.0073        33       1      13 [.     381     395 ..     381     420 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.5
                              LRR_1   3 rhLdLsnn 10 
                                        +hL L ++
  gene1422|gene1422|rna1422|rna1422 167 EHLELHYC 174
                                        78888777 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 3.9
                              LRR_1   2 LrhLdLsnnpll 13 
                                        L++L L++ +ll
  gene1422|gene1422|rna1422|rna1422 192 LKVLKLTGAFLL 203
                                        667777665553 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.039
                              LRR_1   1 nLrhLdLsnnpl 12 
                                        +L ++d+s+++ 
  gene1422|gene1422|rna1422|rna1422 222 KLIEIDVSHCSR 233
                                        799*******95 PP

  == domain 4  score: 1.3 bits;  conditional E-value: 0.19
                              LRR_1   2 LrhLdLsnnpll 13 
                                         + L++s + ++
  gene1422|gene1422|rna1422|rna1422 248 IEALNISFCYGI 259
                                        578******974 PP

  == domain 5  score: 2.2 bits;  conditional E-value: 0.096
                              LRR_1   2 LrhLdLsnnpl 12 
                                        L++L + n+p 
  gene1422|gene1422|rna1422|rna1422 292 LEELSIANCPV 302
                                        89*******94 PP

  == domain 6  score: 1.9 bits;  conditional E-value: 0.12
                              LRR_1   2 LrhLdLsnnpllg 14 
                                        L++L   n+++l+
  gene1422|gene1422|rna1422|rna1422 338 LEELRAANCFNLS 350
                                        4444446666655 PP

  == domain 7  score: 0.2 bits;  conditional E-value: 0.42
                              LRR_1   1 nLrhLdLs 8  
                                        +Lr Ld+s
  gene1422|gene1422|rna1422|rna1422 357 KLRILDIS 364
                                        7*****97 PP

  == domain 8  score: 5.6 bits;  conditional E-value: 0.0073
                              LRR_1   1 nLrhLdLsnnpl..l 13 
                                        +L++L++s n +  +
  gene1422|gene1422|rna1422|rna1422 381 RLEYLNISFNENvdD 395
                                        69********98554 PP

>> LRR_6  Leucine Rich repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       1.6   7.1e+03       3      19 ..     164     181 ..     163     185 .. 0.71
   2 ?    0.4   0.2       0.2   9.2e+02       3      17 ..     221     236 ..     219     237 .. 0.78
   3 ?   -0.4   0.0      0.38   1.7e+03       5      13 ..     248     256 ..     246     263 .. 0.86
   4 ?   -0.9   0.0      0.51   2.3e+03       2      14 ..     289     301 ..     288     302 .. 0.84
   5 ?   -3.6   0.0       3.8   1.7e+04       4      10 ..     318     324 ..     317     325 .. 0.81
   6 ?    0.2   0.0      0.23     1e+03       1      11 [.     354     364 ..     354     365 .. 0.86
   7 ?    7.0   0.1    0.0016       7.1       3      18 ..     380     396 ..     378     396 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.6
                              LRR_6   3 thLteLdLsgNd.IgDeG 19 
                                         + ++L+L +++ + ++ 
  gene1422|gene1422|rna1422|rna1422 164 KNFEHLELHYCGqMKNDD 181
                                        678899999987666665 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.2
                              LRR_6   3 thLteLdLsgNd.IgD 17 
                                        ++L e d+s++  + D
  gene1422|gene1422|rna1422|rna1422 221 NKLIEIDVSHCSrLKD 236
                                        688999****976665 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.38
                              LRR_6   5 LteLdLsgN 13 
                                        +++L++s++
  gene1422|gene1422|rna1422|rna1422 248 IEALNISFC 256
                                        789****99 PP

  == domain 4  score: -0.9 bits;  conditional E-value: 0.51
                              LRR_6   2 nthLteLdLsgNd 14 
                                        ++ L+eL+++ + 
  gene1422|gene1422|rna1422|rna1422 289 CSLLEELSIANCP 301
                                        7789*****9985 PP

  == domain 5  score: -3.6 bits;  conditional E-value: 3.8
                              LRR_6   4 hLteLdL 10 
                                         L++L++
  gene1422|gene1422|rna1422|rna1422 318 RLRKLNI 324
                                        6999997 PP

  == domain 6  score: 0.2 bits;  conditional E-value: 0.23
                              LRR_6   1 snthLteLdLs 11 
                                        +n +L+ Ld+s
  gene1422|gene1422|rna1422|rna1422 354 HNDKLRILDIS 364
                                        6779*****98 PP

  == domain 7  score: 7.0 bits;  conditional E-value: 0.0016
                              LRR_6   3 thLteLdLsgNd.IgDe 18 
                                        + L++L++s+N+ ++D+
  gene1422|gene1422|rna1422|rna1422 380 SRLEYLNISFNEnVDDD 396
                                        679********988885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (449 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       587  (0.0327403); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 3123.11
//
Query:       gene1423|gene1423|rna1423|rna1423  [L=313]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.6e-18   66.7   7.2     0.0002   22.1   0.1    6.2  7  WD40       WD domain, G-beta repeat
  ------ inclusion threshold ------
      0.025   14.2   0.2      0.068   12.7   0.1    1.7  2  SGL        SMP-30/Gluconolactonase/LRE-like region
      0.035   12.4   0.1      0.051   11.9   0.1    1.2  1  Frtz       WD repeat-containing and planar cell polarity effe
       0.15   11.6   0.0       0.25   10.9   0.0    1.4  1  PQQ_2      PQQ-like domain
       0.15   11.3  12.3      0.058   12.7   1.4    3.2  4  WD40_like  WD40-like domain


Domain annotation for each model (and alignments):
>> WD40  WD domain, G-beta repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.2   4.4e-07    0.0016       7      38 .]       9      41 ..       4      41 .. 0.88
   2 !   22.1   0.1   5.5e-08    0.0002       2      38 .]      45      80 ..      44      80 .. 0.83
   3 ?    0.4   0.0       0.4   1.4e+03      13      31 ..      96     112 ..      86     115 .. 0.57
   4 ?   -1.2   0.0       1.3   4.5e+03      14      32 ..     128     148 ..     122     152 .. 0.72
   5 !    6.9   0.0    0.0035        13      10      38 .]     176     205 ..     169     205 .. 0.87
   6 ?   -0.6   0.0      0.82     3e+03       4      26 ..     211     233 ..     208     238 .. 0.75
   7 !   14.9   0.0     1e-05     0.037       4      34 ..     265     296 ..     262     298 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 4.4e-07
                                       EESS.SSEEEEEEETTSSEEEEEETTSEEEEEE CS
                               WD40  7 ltGH.ssvtslafspdgawlasGsdDgtvriWd 38
                                       +t H  ++t+++++ dg++++++s D ++ +Wd
  gene1423|gene1423|rna1423|rna1423  9 FTLHsRPITHVQYNYDGDLIFACSLDSKISLWD 41
                                       6669555*************************9 PP

  == domain 2  score: 22.1 bits;  conditional E-value: 5.5e-08
                                       EEEEEEESS.SSEEEEEEETTSSEEEEEETTSEEEEEE CS
                               WD40  2 qclrtltGH.ssvtslafspdgawlasGsdDgtvriWd 38
                                       ++ +t++GH + vt++  ++    l++Gs D++v +Wd
  gene1423|gene1423|rna1423|rna1423 45 NLKGTYDGHqGAVTCM--DQTEENLLTGSGDRSVILWD 80
                                       67899****777****..555555889*88*******9 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.4
                                        EEEEEEETTSSEEEEEETT CS
                               WD40  13 vtslafspdgawlasGsdD 31 
                                        v s+    d+++l++++ D
  gene1423|gene1423|rna1423|rna1423  96 VKSVNI-NDNNLLICCD-D 112
                                        555533.4556666555.6 PP

  == domain 4  score: -1.2 bits;  conditional E-value: 1.3
                                        EEEEEETTSSEEEEEE..TTS CS
                               WD40  14 tslafspdgawlasGs..dDg 32 
                                        +sl fs + ++++++s  +D+
  gene1423|gene1423|rna1423|rna1423 128 NSLIFSLNLDFIITSSilKDK 148
                                        466677788999998855565 PP

  == domain 5  score: 6.9 bits;  conditional E-value: 0.0035
                                        SSS.EEEEEEETTSSEEEEEETTSEEEEEE CS
                               WD40  10 Hss.vtslafspdgawlasGsdDgtvriWd 38 
                                        H+s ++ ++ sp  ++ +s+s D t +i+d
  gene1423|gene1423|rna1423|rna1423 176 HNSkINEIKPSPCAKYYVSSSNDATTKIFD 205
                                        8455************889999******98 PP

  == domain 6  score: -0.6 bits;  conditional E-value: 0.82
                                        EEEEESSSSEEEEEEETTSSEEE CS
                               WD40   4 lrtltGHssvtslafspdgawla 26 
                                        ++t+    +v+s +  p+++ l+
  gene1423|gene1423|rna1423|rna1423 211 IKTFQSTEPVNSASIFPENNILV 233
                                        6677666679*999999999987 PP

  == domain 7  score: 14.9 bits;  conditional E-value: 1e-05
                                        EEEEESS.SSEEEEEEETTSSEEEEEETTSEE CS
                               WD40   4 lrtltGH.ssvtslafspdgawlasGsdDgtv 34 
                                        ++ +++H + ++ +++ +dg+ +asG++Dg v
  gene1423|gene1423|rna1423|rna1423 265 VGFYSTHfGTINTVDVARDGRSFASGGEDGIV 296
                                        66799**777********************98 PP

>> SGL  SMP-30/Gluconolactonase/LRE-like region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   1.9e-05     0.068      11      91 ..      24     104 ..      17     107 .. 0.85
   2 ?   -2.4   0.0      0.77   2.8e+03      81     100 ..     173     192 ..     127     205 .. 0.56

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.9e-05
                                SGL  11 egaLlwvDilgqrihrldpatgketvldtpe.svGaiaprkdgrlvvasksglall.dlasgeletladeeedekp 84 
                                        +g L++   l ++i  +d +++ + ++d  +  v+++ + ++++l+++s ++ ++l d+++g+ +  ++ +++ ++
  gene1423|gene1423|rna1423|rna1423  24 DGDLIFACSLDSKISLWDTDGNLKGTYDGHQgAVTCMDQ-TEENLLTGSGDRSVILwDITTGKQQLSMS-FKSTVK 97 
                                        789***********************9998878888777.99********9999999*99987665555.678889 PP

                                SGL  85 llrfNDg 91 
                                        ++ +ND 
  gene1423|gene1423|rna1423|rna1423  98 SVNINDN 104
                                        9999995 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.77
                                SGL  81 dekpllrfNDgvvdpdGrlw 100
                                        ++  + ++N+++ +p  +++
  gene1423|gene1423|rna1423|rna1423 173 SKIHNSKINEIKPSPCAKYY 192
                                        33344445555555555555 PP

>> Frtz  WD repeat-containing and planar cell polarity effector protein Fritz
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   1.4e-05     0.051     263     381 ..      56     180 ..      52     184 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.4e-05
                               Frtz 263 islafnpdedkLllGceDssviLydeerkitklv.kaevvPsliswhpdsaillva....sergelqifDlaLspi 333
                                        ++++++++e+ Ll G+ D sviL+d +++  +l    + + + ++   ++ +++ +    +++  +  +D+   ++
  gene1423|gene1423|rna1423|rna1423  56 AVTCMDQTEENLLTGSGDRSVILWDITTGKQQLSmSFKSTVKSVNINDNNLLIC-CddsyNNKPAFNYYDVRSNSL 130
                                        67899*********************9998888733344444444444443333.233335677788888877777 PP

                               Frtz 334 riqllsedvePksvld..lskyfaasskLlklawsrkpevseqteksaei 381
                                           l  + +  +s+l+  +  + +++ +L k+ ++++  v++ + ++++i
  gene1423|gene1423|rna1423|rna1423 131 IFSLNLDFIITSSILKdkFCIFADTEGNLRKFDFAKNEAVQNSKIHNSKI 180
                                        77777777777777752233444555677777777777777666666555 PP

>> PQQ_2  PQQ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0     7e-05      0.25      36      83 ..      64     111 ..      24     133 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 7e-05
                              PQQ_2  36 ggtlfvatgggrlvaldaatGkvlWettlegpvvgaplvaegrvvvva 83 
                                        +  l++++g + ++ +d +tGk+  + +++++v++   ++++ +++ +
  gene1423|gene1423|rna1423|rna1423  64 EENLLTGSGDRSVILWDITTGKQQLSMSFKSTVKSVNINDNNLLICCD 111
                                        56899999************************9999888888877765 PP

>> WD40_like  WD40-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   1.4   1.6e-05     0.058      51     175 ..      23     151 ..       8     161 .. 0.73
   2 ?    4.3   0.2    0.0058        21      42      83 ..     136     177 ..     115     186 .. 0.78
   3 ?    3.3   0.6     0.012        43      92     172 ..     146     231 ..     139     237 .. 0.43
   4 ?    1.3   0.5     0.047   1.7e+02     259     299 ..     254     296 ..     251     298 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.6e-05
                          WD40_like  51 ldddlilvvtlDGtillslleneeevenekieedistvkviddklliGtnkGsiyvfskdlqleevllgqsseIke 126
                                         d+dli  ++lD +i+l +   + +      + ++++++ ++++ll G+   s+ +++     +++ ++ +s +k+
  gene1423|gene1423|rna1423|rna1423  23 YDGDLIFACSLDSKISLWDTDGNLKGTYDGHQGAVTCMDQTEENLLTGSGDRSVILWDITTGKQQLSMSFKSTVKS 98 
                                        4789***********666666555677778999*************************9999************** PP

                          WD40_like 127 ikiennkiysLses......afivfdlfsqnieykisvkdiktfeiienkdilli 175
                                        ++i++n +    ++      af  +d+ s+++   +++  i t +i+  kd ++i
  gene1423|gene1423|rna1423|rna1423  99 VNINDNNLLICCDDsynnkpAFNYYDVRSNSLIFSLNLDFIITSSIL--KDKFCI 151
                                        ***97776655544111111344566666666666665555444444..444555 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.0058
                          WD40_like  42 edSvifvklldddlilvvtlDGtillslleneeevenekiee 83 
                                         d +i + +l+d+  + +  +G++ + ++ ++e v+n ki++
  gene1423|gene1423|rna1423|rna1423 136 LDFIITSSILKDKFCIFADTEGNLRKFDFAKNEAVQNSKIHN 177
                                        478999999********************9999999999976 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.012
                          WD40_like  92 ddklliGt.nkGsiyvfskdlqleevllg..qsseIkeikiennkiysLsesa...fivfdlfsqnieykisvkdi 161
                                        +dk+ i + ++G++ +f+   ++e v  +  ++s+I+eik +    y  s+s+     +fd + ++i++ +s + +
  gene1423|gene1423|rna1423|rna1423 146 KDKFCIFAdTEGNLRKFDFA-KNEAVQNSkiHNSKINEIKPSPCAKYYVSSSNdatTKIFDSKLKEIKTFQSTEPV 220
                                        44444432134555554333.2333322212566666666665555544443311133444444444444444444 PP

                          WD40_like 162 ktfeiienkdi 172
                                        ++ +i+++++i
  gene1423|gene1423|rna1423|rna1423 221 NSASIFPENNI 231
                                        44445544444 PP

  == domain 4  score: 1.3 bits;  conditional E-value: 0.047
                          WD40_like 259 vgigDiRdketfkllesgvGviydmkfennt..iyvgGeaGlk 299
                                        v + Di  +e + ++ ++ G+i  + + ++   ++ gGe G+ 
  gene1423|gene1423|rna1423|rna1423 254 VNFYDIVREERVGFYSTHFGTINTVDVARDGrsFASGGEDGIV 296
                                        6778999999999999999999888888776568999998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (313 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       569  (0.0317363); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 2361.64
//
Query:       gene1424|gene1424|rna1424|rna1424  [L=281]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.5e-30  105.1   2.1    2.3e-19   69.3   0.2    2.6  2  Bromodomain  Bromodomain
    5.1e-06   26.6   1.5    1.3e-05   25.3   1.5    1.8  1  BET          Bromodomain extra-terminal - transcription regul


Domain annotation for each model (and alignments):
>> Bromodomain  Bromodomain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.0   0.1   1.2e-12   1.1e-08      37      83 ..       1      45 [.       1      46 [. 0.92
   2 !   69.3   0.2   2.5e-23   2.3e-19       1      83 [.      68     151 ..      68     152 .. 0.90

  Alignments for each domain:
  == domain 1  score: 35.0 bits;  conditional E-value: 1.2e-12
                                       --HHHHHHHHHTT--SSHHHHHHHHHHHHHHHHHHSHTTSHHHHHHH CS
                        Bromodomain 37 ldLstIkkklesnkYksladfeadlkllfsNarkyngegsviyelae 83
                                       +dL t+ +k   ++Y+s ++f +d+kl+fsN++ ynge+s+i ++a+
  gene1424|gene1424|rna1424|rna1424  1 MDLRTVSQKM--KEYSSQTEFVNDVKLIFSNCYFYNGEDSPISKMAH 45
                                       7899999985..79*****************************9996 PP

  == domain 2  score: 69.3 bits;  conditional E-value: 2.5e-23
                                        HHHHHHHBHTTT...CGGGGCSTT-GCCSTTHHHH.SS---HHHHHHHHHTT--SSHHHHHHHHHHHHHHHHHHSH CS
                        Bromodomain   1 lekilsellehk...laepFlepvdpeefpdyyavikkPldLstIkkklesnkYksladfeadlkllfsNarkyng 73 
                                        + +il+el+++k   ++ pFlepvd++ +p+y +vi++P+dLstIk+kl    Y++  df adl l+++N++k+n 
  gene1424|gene1424|rna1424|rna1424  68 CTNILNELVKTKhkkINWPFLEPVDTKLVPNYLSVIENPIDLSTIKRKL--PFYENRIDFFADLLLMVNNCYKFNA 141
                                        5677776666665569********************************9..68999******************** PP

                                        TTSHHHHHHH CS
                        Bromodomain  74 egsviyelae 83 
                                        +g++iy + e
  gene1424|gene1424|rna1424|rna1424 142 KGTEIYTCGE 151
                                        ******9976 PP

>> BET  Bromodomain extra-terminal - transcription regulation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   1.5   1.4e-09   1.3e-05       3      64 .]     208     270 ..     206     270 .. 0.93

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 1.4e-09
                                BET   3 tyeeKkeLseeInkLpgeklgrvveIIqerepelq.sdedEiElDidaldddtLreLekyvkk 64 
                                        + +e+  +++ ++kL++e+  ++  II+++  ++  ++++E+E+D+  l+d  + e+  ++kk
  gene1424|gene1424|rna1424|rna1424 208 SLDERIRIADIVSKLDEERCVKIALIIKKNDQNFSiAGKEEVEVDFKILPDFIVEEIDTFLKK 270
                                        7899999************************99999***************999999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       814  (0.0454013); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1933.15
//
Query:       gene1425|gene1425|rna1425|rna1425  [L=289]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-41  141.8   0.7    2.1e-41  141.1   0.7    1.3  1  Ribosomal_L2_C  Ribosomal Proteins L2, C-terminal domain
    2.7e-08   33.6   0.2    5.2e-07   29.5   0.1    2.7  2  Ribosomal_L2    Ribosomal Proteins L2, RNA binding domain


Domain annotation for each model (and alignments):
>> Ribosomal_L2_C  Ribosomal Proteins L2, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  141.1   0.7   2.3e-45   2.1e-41       1     118 [.     132     262 ..     132     269 .. 0.91

  Alignments for each domain:
  == domain 1  score: 141.1 bits;  conditional E-value: 2.3e-45
                                        SSSS-EBSSSS-TTB-BBSE-SSTTS--SSS-SSSB-EEBB-B...SSEEEEEETTS-EEEEETTSBEBES-BS-T CS
                     Ribosomal_L2_C   1 kvGnvlplknipeGtivhnielkpgkggklarsaGtyaqvvak..egkkvtvklpSgevrkvssecrAtiGvvsng 74 
                                        kvGn++plkn+peG++v  +e+kp +gg++a+s Gtya vv +  + +++t+klpSge+ +vs+++rA iG++++g
  gene1425|gene1425|rna1425|rna1425 132 KVGNCTPLKNVPEGSYVSMVEKKPYDGGRYAKSCGTYAIVVFHnrDAHTTTLKLPSGEKVSVSADARAFIGIIAGG 207
                                        68****************************************9544899*************************** PP

                                        TCTT----STTHHHHT.....TBS----SSSS-TTTSSS--SS....SS..--SS CS
                     Ribosomal_L2_C  75 ehkekklgkAgrkrwl.....grrpkvrGvamnpvdHphGGGe....Gk..tksr 118
                                        ++ +k+l+kAg+++++     +++pk+rGvamnp+dHphGGG+    G+  t+s+
  gene1425|gene1425|rna1425|rna1425 208 GKDDKPLLKAGAAYHKykalnKVWPKTRGVAMNPTDHPHGGGNhqhiGHpsTISK 262
                                        *******************************************666655533334 PP

>> Ribosomal_L2  Ribosomal Proteins L2, RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.5   0.1   5.8e-11   5.2e-07       9      76 ..      49     124 ..      42     125 .. 0.75
   2 ?    1.0   0.0     0.046   4.2e+02      33      49 ..     147     163 ..     139     180 .. 0.84

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 5.8e-11
                                        SSTT--------EE-B--S---SS........--EEEEEEE--TT-SS-EEEEEETT...TEEEEEE--SS--SS- CS
                       Ribosomal_L2   9 tvrhrggGhkkkyrlidfkrnkek........vkgkVveieyDpgRsApiAlvkyed...gekryiiapeglkvGd 73 
                                          + r+  +k+++r i  +  ++           ++V+ei +  gR Ap+A +++       k +i+apeg++vG+
  gene1425|gene1425|rna1425|rna1425  49 IRKVREE-NKRRFRNIYKN--PKVlipdikegCTAVVKEIVHERGRGAPVAKLNVTRgngVLKAFIVAPEGISVGQ 121
                                        4455555.77777777663..33334555666999*****************999884434577************ PP

                                        EE- CS
                       Ribosomal_L2  74 tvv 76 
                                        t+v
  gene1425|gene1425|rna1425|rna1425 122 TLV 124
                                        987 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.046
                                        --EEEEEEE--TT-SS- CS
                       Ribosomal_L2  33 vkgkVveieyDpgRsAp 49 
                                        +   V+++ yD gR A+
  gene1425|gene1425|rna1425|rna1425 147 YVSMVEKKPYDGGRYAK 163
                                        6678999*******997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (289 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       369  (0.0205812); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.31s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1854.70
//
Query:       gene1426|gene1426|rna1426|rna1426  [L=159]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.077   13.2   0.0       0.56   10.4   0.0    2.3  1  Vps36_ESCRT-II  Vacuolar protein sorting protein 36 Vps36


Domain annotation for each model (and alignments):
>> Vps36_ESCRT-II  Vacuolar protein sorting protein 36 Vps36
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   3.1e-05      0.56      36      55 ..      60      78 ..      17      95 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 3.1e-05
                     Vps36_ESCRT-II 36 qnGrlyLTthriiyvdsadp 55
                                         G+l+LT+ ri+y   a++
  gene1426|gene1426|rna1426|rna1426 60 PTGKLFLTSYRIVYR-PAEI 78
                                       57************5.4444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       482  (0.0268838); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.31s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 1010.18
//
Query:       gene1427|gene1427|rna1427|rna1427  [L=612]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (612 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1225  (0.0683251); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.45
# Mc/sec: 4121.84
//
Query:       gene1428|gene1428|rna1428|rna1428  [L=157]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-05   25.2   0.3    2.3e-05   24.6   0.3    1.4  1  HAD_2          Haloacid dehalogenase-like hydrolase
     0.0031   17.8   0.0     0.0038   17.6   0.0    1.1  1  Hydrolase      haloacid dehalogenase-like hydrolase
      0.006   16.5   0.0      0.017   15.0   0.0    1.6  2  Ribosomal_L30  Ribosomal protein L30p/L7e
  ------ inclusion threshold ------
      0.095   12.8   0.1        0.2   11.8   0.1    1.6  1  Hydrolase_6    Haloacid dehalogenase-like hydrolase


Domain annotation for each model (and alignments):
>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.3   5.1e-09   2.3e-05      61     149 ..      26     115 ..       2     129 .. 0.72

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 5.1e-09
                              HAD_2  61 kieellrkyn.eekkkkevkpydgvkelLeeLkeagyklgivTsksreaveekleqlgiesyFdvivt.sedvekk 134
                                        ++ee+++ +  e  ++  +k  +++++lLe++   +  l i++++++e v++ l+ lgie++F+ +   + d ++ 
  gene1428|gene1428|rna1428|rna1428  26 SYEEYRDYVFpEIDYDGILKKDENIIKLLESI---NKPLFIMSNGTKEHVKKTLTTLGIEHLFKAVFYlGYDSNNY 98 
                                        55666444331444457778888999999999...77**************************9886515555554 PP

                              HAD_2 135 ..KPdpeviekaleklk 149
                                          KPd e ++ + + ++
  gene1428|gene1428|rna1428|rna1428  99 vgKPDVEAYQLVEQLTN 115
                                        78****99998755444 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   8.4e-07    0.0038     124     199 ..      48     125 ..       7     129 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 8.4e-07
                                        HHHHHHHHHTTEEEEEEESSEHHHHHHHHHHTT.GGGE.SEEEEHHCES..STTTSHHHHHHHHHHHTSTGGGEEE CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxx.xxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxx RF
                          Hydrolase 124 aeavasLkaagievvlltgdnpetaeraanqlG.ddyf.daviasdiet..vakpspegkvaaireLqgkpeevam 195
                                        +  ++ L + + ++++++++ +e++++++  lG ++ f ++ + ++++   v+kp+ e+++ + +  ++++  + +
  gene1428|gene1428|rna1428|rna1428  48 ENIIKLLESINKPLFIMSNGTKEHVKKTLTTLGiEHLFkAVFYLGYDSNnyVGKPDVEAYQLVEQLTNARK--IYF 121
                                        5566778888889*********************9999888888888889**********99988887777..999 PP

                                        EESS CS
                                        xxxx RF
                          Hydrolase 196 VGDg 199
                                        ++D 
  gene1428|gene1428|rna1428|rna1428 122 FDDK 125
                                        9885 PP

>> Ribosomal_L30  Ribosomal protein L30p/L7e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       1.4   6.2e+03      12      23 ..      43      54 ..      41      58 .. 0.57
   2 !   15.0   0.0   3.7e-06     0.017      10      33 ..      66      90 ..      64      94 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.4
                                       S-HHHHHHHHHT CS
                      Ribosomal_L30 12 vppkvrktLqlL 23
                                       + +k   +++lL
  gene1428|gene1428|rna1428|rna1428 43 ILKKDENIIKLL 54
                                       445555555555 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 3.7e-06
                                       TTS-HHHHHHHHHTT-SSTT.EEEE CS
                      Ribosomal_L30 10 igvppkvrktLqlLgLrkin.gtvv 33
                                       +g++++v+ktL +Lg  +++ ++++
  gene1428|gene1428|rna1428|rna1428 66 NGTKEHVKKTLTTLGIEHLFkAVFY 90
                                       89********************998 PP

>> Hydrolase_6  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   4.4e-05       0.2      15      58 ..      43      83 ..      38     127 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 4.4e-05
                                       E-TTHHHHHHHHHHTT-EEEEEE---SS-HHHHHHHHHHTT--- CS
                        Hydrolase_6 15 aipgaaealnalraagkpvvllTNnsskseeeyakkleklgvdi 58
                                       ++++ +++++ l++ +kp+++++N+++++   ++k l+ lg++ 
  gene1428|gene1428|rna1428|rna1428 43 ILKKDENIIKLLESINKPLFIMSNGTKEH---VKKTLTTLGIEH 83
                                       55666778999*************99776...888888888874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       696  (0.0388198); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1132.37
//
Query:       gene1429|gene1429|rna1429|rna1429  [L=469]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.7e-17   62.4   0.3    1.5e-16   61.0   0.1    1.9  2  ERCC4     ERCC4 domain
  ------ inclusion threshold ------
      0.017   15.1   3.2      0.039   13.9   1.9    2.3  2  HTH_45    Winged helix-turn-helix
       0.29   10.9   3.8       0.66    9.8   1.4    2.5  2  RICTOR_M  Rapamycin-insensitive companion of mTOR, middle dom
       0.73    9.9   5.5        1.3    9.0   0.1    3.4  3  Swm2      Nucleolar protein Swm2


Domain annotation for each model (and alignments):
>> ERCC4  ERCC4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       2.3     1e+04       9      35 ..      18      44 ..      11      52 .. 0.62
   2 !   61.0   0.1   3.3e-20   1.5e-16       1     156 []     240     360 ..     240     360 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 2.3
                                       HHHH..HHTTTS.EEEEE--SSSSE.EE CS
                              ERCC4  9 gieeylleelgv.evvietlpigdyilw 35
                                       + +++ ++++ v + + ++l+  d i+w
  gene1429|gene1429|rna1429|rna1429 18 SKQHN-FKTRHVlNKILSQLEEKDEITW 44
                                       44555.5666655666666666666666 PP

  == domain 2  score: 61.0 bits;  conditional E-value: 3.3e-20
                                        EEGGGCT.SHHHH..HHTTTSEEEEE--SSSSE.EE...CTT...............EEEEEEEHHHHHHHHCCSH CS
                              ERCC4   1 iDsrelk.sgieeylleelgvevvietlpigdyilwrrkvkaeynleldieepceekvlverksaddlvasikdgr 75 
                                        +Dsre k ++ ++y +e++   +++ +l +gd+ lw   +k ey  +           ++erk+ +d+v+s+ dgr
  gene1429|gene1429|rna1429|rna1429 240 VDSREMKsKNDRGY-FERKLPGSRTLNLVVGDF-LW---IKGEYVVN----------TIIERKKGSDFVSSLYDGR 300
                                        8******8888888.788888************.**...99988876..........******************* PP

                                        HHHHHHHHHH.H-SEEEEEEES-GGGTT................THHH.HHHHHHHHHHHHS-EEEEESSHHHHHH CS
                              ERCC4  76 leeqvsrlkrngykkpillvegldqykrknknsrnkqykakvrqinrktiesaLvqlqldfgvsilttesanetae 151
                                        + eq++rlk++g+k +++l+egl                      +++ iesa+  + l  g++++ t++ +et+ 
  gene1429|gene1429|rna1429|rna1429 301 FVEQKNRLKNTGLKSCVYLIEGLR--------------------SRDNFIESAIFKTKLE-GFTVIETRDIEETVL 355
                                        **********************53....................44455*********99.9************99 PP

                                        HHHHH CS
                              ERCC4 152 wlanl 156
                                        ++ nl
  gene1429|gene1429|rna1429|rna1429 356 FVRNL 360
                                        99886 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       1.8     8e+03      35      49 ..      28      42 ..      22      46 .. 0.70
   2 ?   13.9   1.9   8.7e-06     0.039       7      66 ..     153     218 ..     151     228 .. 0.74

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 1.8
                             HTH_45 35 llnkYLdmLvekgli 49
                                       +lnk L++L ek+ i
  gene1429|gene1429|rna1429|rna1429 28 VLNKILSQLEEKDEI 42
                                       467777777777655 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 8.7e-06
                             HTH_45   7 IiadILeais.egeakkTkimykanLsykllnkY.....LdmLvekglikkskekYvlTekGlell 66 
                                        I ++IL+++s +++  k++i +++    + ++       L++L++k+li+k+++ Y lT kG  l 
  gene1429|gene1429|rna1429|rna1429 153 IAYNILKILSsNDGLCKSQIYLSSKFLEDEISGLhiwcaLKTLLQKNLIQKENKRYFLTYKGTSLC 218
                                        6667777776667777777777776655555432223339**********************9875 PP

>> RICTOR_M  Rapamycin-insensitive companion of mTOR, middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.0      0.16   7.2e+02      69      88 ..      15      36 ..       2      46 .. 0.69
   2 ?    9.8   1.4   0.00015      0.66      10      80 ..     388     460 ..     381     467 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.16
                           RICTOR_M 69 ldys..vdghiRiilskaLtns 88
                                       l++s  ++ ++R++l+k+L + 
  gene1429|gene1429|rna1429|rna1429 15 LNFSkqHNFKTRHVLNKILSQL 36
                                       4565114556899999999865 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00015
                           RICTOR_M  10 lskerleet.lsrgYfkfiGvlsssknGlklLek...wkiftllyklvelksrddllklilssldysvdghiRii 80 
                                        +s+++l+++  s++Y++ +  ls   +G++ L+    ++ f+++++lv++ ++ d lk ils++  + +   +++
  gene1429|gene1429|rna1429|rna1429 388 FSNQSLKTKdFSQQYLLYLSFLS--IKGISHLKAkflCNYFQTFDNLVNECKDVDKLKSILSEMRVNGQLLGKNV 460
                                        899999876589*********98..68******98999**************999********987766555555 PP

>> Swm2  Nucleolar protein Swm2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.1       0.4   1.8e+03      56      75 ..       6      25 ..       2      49 .. 0.57
   2 ?    9.0   0.1   0.00029       1.3      15      84 ..     290     360 ..     281     390 .. 0.76
   3 ?    0.6   0.1      0.12   5.4e+02      76     106 ..     424     455 ..     408     468 .. 0.67

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.4
                               Swm2 56 evvkrcldlwlvlkgkeYkl 75
                                        ++++c++l++  k +++k+
  gene1429|gene1429|rna1429|rna1429  6 HLITKCKKLLNFSKQHNFKT 25
                                       44555555555555544444 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00029
                               Swm2  15 splLspyye..aiakdeelkkkalkkCkevfekweekddavdkevvkrcldlwlvlkgkeYklkeeeslsNl 84 
                                        s+++s+ y+   ++++++lk+  lk C +++e + ++d+ +++ + k  l+ ++v++ ++ +  +   + Nl
  gene1429|gene1429|rna1429|rna1429 290 SDFVSSLYDgrFVEQKNRLKNTGLKSCVYLIEGLRSRDNFIESAIFKTKLEGFTVIETRDIEE-TVLFVRNL 360
                                        556666664226999*****************************************9998776.55555555 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.12
                               Swm2  76 keeeslsNliieevdvsevks.selerlefde 106
                                        +  +++ Nl+ e  dv+++ks   + r++ + 
  gene1429|gene1429|rna1429|rna1429 424 NYFQTFDNLVNECKDVDKLKSiLSEMRVNGQL 455
                                        45678899999999999998876666665554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (469 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1134  (0.0632495); expected 358.6 (0.02)
Passed bias filter:                      472  (0.0263261); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.60u 0.27s 00:00:00.87 Elapsed: 00:00:00.45
# Mc/sec: 3122.84
//
Query:       gene143|gene143|rna143|rna143  [L=972]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
       0.16   11.4   0.0       0.33   10.4   0.0    1.4  1  Adeno_52K  Adenoviral protein L1 52/55-kDa


Domain annotation for each model (and alignments):
>> Adeno_52K  Adenoviral protein L1 52/55-kDa
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   1.8e-05      0.33     116     193 ..     140     208 ..     126     211 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 1.8e-05
                      Adeno_52K 116 lRpevllglmyLwdfvqaylehpeskaltvqlllvaqhvedegvlreallsisekesewlrdliqllqvivqerelsv 193
                                    + +e++l  +yL+         p+ +++t +   +  h++ + ++ + l +i+++ +   +d  ++l++i++ +++ v
  gene143|gene143|rna143|rna143 140 TNEEIYLIFFYLY---------PHKENMTKLTRVICFHLQRNPTMVQELFDIAQDCNIKYNDRMTCLAMIINPECHYV 208
                                    5689999999999.........999999999999999**********************************7777666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (972 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       740  (0.0412739); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.70u 0.31s 00:00:01.01 Elapsed: 00:00:00.49
# Mc/sec: 6003.33
//
Query:       gene1430|gene1430|rna1430|rna1430  [L=185]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1057  (0.0589548); expected 358.6 (0.02)
Passed bias filter:                      540  (0.0301188); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 1217.72
//
Query:       gene1431|gene1431|rna1431|rna1431  [L=470]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0019   18.0   0.3     0.0042   16.9   0.3    1.6  1  PAZ            PAZ domain
  ------ inclusion threshold ------
      0.023   15.0   0.4      0.039   14.2   0.4    1.4  1  CBFD_NFYB_HMF  Histone-like transcription factor (CBF/NF-Y) a


Domain annotation for each model (and alignments):
>> PAZ  PAZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.3   4.7e-07    0.0042      41     118 ..     350     449 ..     334     467 .. 0.69

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 4.7e-07
                                        CEEEEEEEESS--TTSEECCTTCT..CECCHHHHCCT---S....T-TT--EEEEEE................... CS
                                PAZ  41 ktyyvadittdlapsstFpdkdkeneitfaeYfkkkYniei....kdqdqplldvdk................... 93 
                                          y++ d+++   +  +F+++d     t  eYfkkk+n++       ++q l  +d+                   
  gene1431|gene1431|rna1431|rna1431 350 ASYRIPDVDEMCVNAKKFKTSD---WSTNIEYFKKKWNLKFeltdAVKNQILDSCDHffaqlckksinlakisank 422
                                        67*******************4...579***********9888875567888888888887777777777666655 PP

                                        ...S-SS....----EEEEE-CCCCEEESSBC CS
                                PAZ  94 ...ktes....ehssqkqiLvpElcdihpisa 118
                                           +  +       + +++L p+   +    +
  gene1431|gene1431|rna1431|rna1431 423 avkR--KhieyAFYELENYLLPDSSVV---LK 449
                                        4321..123231123456666665555...55 PP

>> CBFD_NFYB_HMF  Histone-like transcription factor (CBF/NF-Y) and archaeal histone
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.4   4.4e-06     0.039      21      64 ..     389     432 ..     380     433 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.4e-06
                                        B-HHHHHHHHHHHHHHHHHHHHHHHHHHCCTTSSCE-HHHHHHH CS
                      CBFD_NFYB_HMF  21 iakdAkeliaecveefieelaseAaeickkekrKtikaehiklA 64 
                                        +++++k  i +++ +f  +l++++  ++k +  K++k++hi+ A
  gene1431|gene1431|rna1431|rna1431 389 LTDAVKNQILDSCDHFFAQLCKKSINLAKISANKAVKRKHIEYA 432
                                        578899999********************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (470 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       986  (0.0549947); expected 358.6 (0.02)
Passed bias filter:                      609  (0.0339673); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.63u 0.28s 00:00:00.91 Elapsed: 00:00:00.45
# Mc/sec: 3108.77
//
Query:       gene1432|gene1432|rna1432|rna1432  [L=231]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.013   15.6   0.0        4.3    7.5   0.0    2.4  2  DUF2973   Protein of unknown function (DUF2973)
      0.087   12.9   0.3        0.3   11.2   0.3    1.8  1  PspB      Phage shock protein B


Domain annotation for each model (and alignments):
>> DUF2973  Protein of unknown function (DUF2973)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0    0.0015        14       2      37 ..      49      84 ..      48     107 .. 0.79
   2 ?    7.5   0.0   0.00048       4.3      35      62 ..     179     206 ..     148     207 .. 0.71

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0015
                            DUF2973  2 LhllYilaftvlaflAvanLirslitlsadsqrkkk 37
                                       L l+ ++ f+ l++  ++n+ rs +    +++ +++
  gene1432|gene1432|rna1432|rna1432 49 LILILLMWFIWLVVYFFKNMNRSSLLSPNKTKDNER 84
                                       77899999**************98877766666333 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.00048
                            DUF2973  35 kkkskksrtkkvtpHPELLDeaGklikE 62 
                                        +  s+ + +k +t  PEL De+G+  kE
  gene1432|gene1432|rna1432|rna1432 179 QFLSQGHYRKVYTHYPELNDETGNRWKE 206
                                        444556666777778********97666 PP

>> PspB  Phage shock protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.3   3.3e-05       0.3       5      40 ..      44      79 ..      41      88 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 3.3e-05
                               PspB  5 lavpliifvlfVapiWLiLHYrskkkrskglsaede 40
                                       l+  l i++l++ +iWL+ ++ +  +rs+ ls + +
  gene1432|gene1432|rna1432|rna1432 44 LIKKLLILILLMWFIWLVVYFFKNMNRSSLLSPNKT 79
                                       6677999********************999998754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1410  (0.0786435); expected 358.6 (0.02)
Passed bias filter:                      686  (0.038262); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 1602.47
//
Query:       gene1433|gene1433|rna1433|rna1433  [L=255]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
       0.11   11.8   7.5       0.14   11.5   1.6    2.8  2  WD40_like  WD40-like domain


Domain annotation for each model (and alignments):
>> WD40_like  WD40-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.1    0.0047        85     126     169 ..      16      59 ..      14      72 .. 0.84
   2 ?   11.5   1.6   7.8e-06      0.14     103     149 ..     108     151 ..     101     167 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.0047
                          WD40_like 126 eikiennkiysLsesafivfdlfsqnieykisvkdiktfeiien 169
                                        +++ie  +i s  ++++  +d+ ++ ++++ s+ +i+++ ++ n
  gene1433|gene1433|rna1433|rna1433  16 NVHIEPPYIISFDDDNLHLYDMNTFTLLKRFSISNIEMVGMLSN 59 
                                        5777788999999************************9998844 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 7.8e-06
                          WD40_like 103 siyvfskdlqleevllgqsseIkeikiennkiysLsesafivfdlfs 149
                                        +++++ ++    ++   q  +Ik++ ++n+ iy+Ls+s++ + d + 
  gene1433|gene1433|rna1433|rna1433 108 NLHIYRNN---SIIKKLQLKNIKQMVSTNSHIYTLSKSHLFILDYDL 151
                                        67888877...4555557789*******************9988665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       776  (0.0432818); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1702.06
//
Query:       gene1434|gene1434|rna1434|rna1434  [L=280]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       660  (0.0368119); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 1802.53
//
Query:       gene1435|gene1435|rna1435|rna1435  [L=513]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.6e-55  183.7   9.2      2e-15   56.3   0.1    4.4  4  RRM_1          RNA recognition motif. (a.k.a. RRM, RBD, or RN
      3e-07   30.4   6.4       0.16   12.0   0.2    4.6  4  RRM_3          RNA binding motif
    6.2e-05   22.9   1.4      0.042   13.9   0.0    4.1  4  Nup35_RRM_2    Nup53/35/40-type RNA recognition motif
     0.0022   17.9   2.3        0.2   11.6   0.1    3.6  4  Nup35_RRM      Nup53/35/40-type RNA recognition motif
  ------ inclusion threshold ------
      0.019   15.1   0.1      0.051   13.8   0.1    1.7  1  PABP           Poly-adenylate binding protein, unique domain
      0.097   12.8   0.2       0.47   10.6   0.0    2.3  2  DNA_ligase_IV  DNA ligase IV


Domain annotation for each model (and alignments):
>> RRM_1  RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.3   0.1     7e-14   2.1e-10       1      69 [.      20      92 ..      20      93 .. 0.95
   2 !   56.3   0.1   6.8e-19     2e-15       1      69 [.     110     178 ..     110     179 .. 0.92
   3 !   54.2   0.3   3.2e-18   9.5e-15       1      64 [.     199     262 ..     199     267 .. 0.95
   4 !   36.4   0.0   1.1e-12   3.4e-09       1      65 [.     304     369 ..     304     374 .. 0.93

  Alignments for each domain:
  == domain 1  score: 40.3 bits;  conditional E-value: 7e-14
                                       EEEESETTTSSHHHHHHHHHTTSCEEEEEEEEE....TTTSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEE CS
                              RRM_1  1 lfVgnLppdvteeeLkelFskfGpiksiklvrd....etgkskgfafVeFeskedAekAlealngkklggrel 69
                                       ++Vg+L+  + e++L+++Fs +G+i +iklv+       + ++++a+V F ++e+A +A+++ln  k++++e+
  gene1435|gene1435|rna1435|rna1435 20 VYVGDLSLKTVESDLYKIFSTVGSIITIKLVKPvmdnFPNYTTCYAYVLFSQEEEALEAVNKLNFFKVHDKEM 92
                                       8*****************************99777789999****************************9987 PP

  == domain 2  score: 56.3 bits;  conditional E-value: 6.8e-19
                                        EEEESETTTSSHHHHHHHHHTTSCEEEEEEEEETTTSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEE CS
                              RRM_1   1 lfVgnLppdvteeeLkelFskfGpiksiklvrdetgkskgfafVeFeskedAekAlealngkklggrel 69 
                                        ++++nL+ d++ ++L++ Fs fG+i s+k+  +++gk kgf+fV+F++k  A+kAl+   +++++g+ +
  gene1435|gene1435|rna1435|rna1435 110 IVIKNLSADCDSKTLHDTFSIFGEILSCKVAQNSQGKCKGFGFVQFKNKNGARKALKFGTEMQMDGHAI 178
                                        79******************************************************9555577777776 PP

  == domain 3  score: 54.2 bits;  conditional E-value: 3.2e-18
                                        EEEESETTTSSHHHHHHHHHTTSCEEEEEEEEETTTSEEEEEEEEESSHHHHHHHHHHHTTEEE CS
                              RRM_1   1 lfVgnLppdvteeeLkelFskfGpiksiklvrdetgkskgfafVeFeskedAekAlealngkkl 64 
                                        +f +n+p+++te++Lke+F  +G+++s+   ++ +g  +gf+f ++e+  dA+kA+++l gk +
  gene1435|gene1435|rna1435|rna1435 199 VFFKNFPSTTTEQQLKEIFMSIGKVSSFYFATKPDGGLRGFGFANYENAADAQKAIDELSGKDI 262
                                        6789*********************************************************776 PP

  == domain 4  score: 36.4 bits;  conditional E-value: 1.1e-12
                                        EEEESETTTSSHHHHHHHHHTTSCEEEEEEEEE.TTTSEEEEEEEEESSHHHHHHHHHHHTTEEET CS
                              RRM_1   1 lfVgnLppdvteeeLkelFskfGpiksiklvrd.etgkskgfafVeFeskedAekAlealngkklg 65 
                                        l+V+ Lp+++ +ee++elFs++G+i s+ + +d   +  k++a+V F + ++A  A+e+ n+  ++
  gene1435|gene1435|rna1435|rna1435 304 LYVTRLPSTYGKEEVEELFSQYGKIISVCVGKDnVVNEDKNWAYVCFSTADEASIAVEKGNEVYID 369
                                        8*********************************************************98877666 PP

>> RRM_3  RNA binding motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0     0.011        34      40      69 ..      65      94 ..      27     104 .. 0.84
   2 !    8.7   0.1    0.0006       1.8       9      72 ..     115     181 ..     108     193 .. 0.70
   3 !    5.1   0.0    0.0078        23       6      58 ..     201     258 ..     198     282 .. 0.72
   4 !   12.0   0.2   5.3e-05      0.16      15      85 ..     315     391 ..     305     407 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.011
                                       EEEEESSHHHHHHHHHHHHHC-B-CCTSSE CS
                              RRM_3 40 gevrFkedeeakkalekateaklkikdaev 69
                                       ++v+F ++eea +a++k+  +k++ k+  v
  gene1435|gene1435|rna1435|rna1435 65 AYVLFSQEEEALEAVNKLNFFKVHDKEMRV 94
                                       79****************999665555444 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0006
                                        -SSS--HHHHHHHCHCCS-ECEEEE-T...TSSE..EEEEESSHHHHHHHHHHHHHC-B-CCTSSEEEE CS
                              RRM_3   9 lnkelsredikellsklgevayvdyek...gdke..gevrFkedeeakkalekateaklkikdaevtle 72 
                                        l+ +   +++++++s +ge+    +++   g+ +  g v+Fk+++ a+kal+  te+  +++ + +++e
  gene1435|gene1435|rna1435|rna1435 115 LSADCDSKTLHDTFSIFGEILSCKVAQnsqGKCKgfGFVQFKNKNGARKALKFGTEM--QMDGHAIKVE 181
                                        6677788999********88765554300133333378**************99999..6666655554 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.0078
                                        EEE-SSS--HHHHHHHCHCCS-EC..EEEE-.TTSSE..EEEEESSHHHHHHHHHHHH CS
                              RRM_3   6 lsGlnkelsredikellsklgeva..yvdye.kgdke..gevrFkedeeakkalekat 58 
                                        ++ + + ++ +++ke++ ++g+v   y + + +g     g   ++++ +a+ka++++ 
  gene1435|gene1435|rna1435|rna1435 201 FKNFPSTTTEQQLKEIFMSIGKVSsfYFATKpDGGLRgfGFANYENAADAQKAIDELS 258
                                        55566778899**********8873333333134333225678888888999998875 PP

  == domain 4  score: 12.0 bits;  conditional E-value: 5.3e-05
                                        HHHHHHHCHCCS-ECEE.....E.E-TTSSEEEEEESSHHHHHHHHHHHHHC-B-CCTSSEEEEE--HHHHHHHHH CS
                              RRM_3  15 redikellsklgevayv.....d.yekgdkegevrFkedeeakkalekateaklkikdaevtlelLeGeeEkeywk 84 
                                        +e++ el+s++g++  v     + ++++++ ++v F +++ea  a+ek  e+ +   + +vt+   + e+E++y +
  gene1435|gene1435|rna1435|rna1435 315 KEEVEELFSQYGKIISVcvgkdNvVNEDKNWAYVCFSTADEASIAVEKGNEVYIDSVKINVTYFKSKNEREQDYIN 390
                                        89999*******99888223321234455669********************999999999999999999*99987 PP

                                        H CS
                              RRM_3  85 k 85 
                                         
  gene1435|gene1435|rna1435|rna1435 391 D 391
                                        6 PP

>> Nup35_RRM_2  Nup53/35/40-type RNA recognition motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0       0.5   1.5e+03      36      53 .]      62      79 ..      38      79 .. 0.82
   2 ?    3.0   0.0     0.035     1e+02      23      53 .]     130     165 ..     122     165 .. 0.86
   3 ?    1.4   0.0      0.11   3.2e+02      21      52 ..     217     253 ..     208     254 .. 0.90
   4 !   13.9   0.0   1.4e-05     0.042      14      53 .]     315     360 ..     311     360 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.5
                        Nup35_RRM_2 36 vsvmyvkfesekdaekAL 53
                                       + ++yv f  e +a  A+
  gene1435|gene1435|rna1435|rna1435 62 TCYAYVLFSQEEEALEAV 79
                                       5689*********99997 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.035
                        Nup35_RRM_2  23 sfGeIvkhyvp.....kevsvmyvkfesekdaekAL 53 
                                         fGeI    v      k + + +v+f+++  a kAL
  gene1435|gene1435|rna1435|rna1435 130 IFGEILSCKVAqnsqgKCKGFGFVQFKNKNGARKAL 165
                                        489999988887777877899*************98 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.11
                        Nup35_RRM_2  21 FasfGeIvkhyvp.....kevsvmyvkfesekdaekA 52 
                                        F s+G++  +y+      + + + +  +e+  da+kA
  gene1435|gene1435|rna1435|rna1435 217 FMSIGKVSSFYFAtkpdgGLRGFGFANYENAADAQKA 253
                                        779999999999999999999999999*******999 PP

  == domain 4  score: 13.9 bits;  conditional E-value: 1.4e-05
                        Nup35_RRM_2  14 ielVlehFasfGeIvkhyvp......kevsvmyvkfesekdaekAL 53 
                                        +e+V e F ++G+I    v+        ++++yv+f + ++a +A+
  gene1435|gene1435|rna1435|rna1435 315 KEEVEELFSQYGKIISVCVGkdnvvnEDKNWAYVCFSTADEASIAV 360
                                        578888999*******999999999988***************997 PP

>> Nup35_RRM  Nup53/35/40-type RNA recognition motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.45   1.3e+03      21      73 ..      32      80 ..      12      89 .. 0.68
   2 ?    3.2   0.1     0.028        85      21      74 ..     122     167 ..     108     190 .. 0.68
   3 ?   -2.1   0.0       1.3   3.9e+03      61      74 ..     243     256 ..     237     266 .. 0.83
   4 !   11.6   0.1   6.6e-05       0.2      22      95 ..     317     383 ..     310     389 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.45
                                       HHHHHHHHTTS-BSS--CCC------------EETTEEEEEBS-HHHHHHHHT CS
                          Nup35_RRM 21 nevlehFskfGeiledvqvlklgkglnpkpiptgenwvkltYksessaskAlq 73
                                       + + + Fs  G+i+      kl k +  +       + ++ +++e +a  A++
  gene1435|gene1435|rna1435|rna1435 32 SDLYKIFSTVGSIITI----KLVKPVMDNFPNYTTCYAYVLFSQEEEALEAVN 80
                                       6677889999999975....334444444333445566666666666666666 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.028
                                        HHHHHHHHTTS-BSS--CCC------------EETTEEEEEBS-HHHHHHHHTT CS
                          Nup35_RRM  21 nevlehFskfGeiledvqvlklgkglnpkpiptgenwvkltYksessaskAlqe 74 
                                         ++   Fs fGeil+   v ++++        + +++  +++k++  a+kAl+ 
  gene1435|gene1435|rna1435|rna1435 122 KTLHDTFSIFGEILSCK-VAQNSQ-------GKCKGFGFVQFKNKNGARKALKF 167
                                        5566789*******984.544433.......34444555567777778888764 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 1.3
                                        EBS-HHHHHHHHTT CS
                          Nup35_RRM  61 tYksessaskAlqe 74 
                                        +Y++  +a+kA+ e
  gene1435|gene1435|rna1435|rna1435 243 NYENAADAQKAIDE 256
                                        699999*****986 PP

  == domain 4  score: 11.6 bits;  conditional E-value: 6.6e-05
                                        HHHHHHHTTS-BSS--CCC------------EETTEEEEEBS-HHHHHHHHTTTTEEETTEEEEEEE--HHHHH CS
                          Nup35_RRM  22 evlehFskfGeiledvqvlklgkglnpkpiptgenwvkltYksessaskAlqengtilngslivgvsyskaaak 95 
                                        ev e Fs++G+i++   v k       + + +++nw ++ +++  +as A+++   +  +s+ + v+y k++++
  gene1435|gene1435|rna1435|rna1435 317 EVEELFSQYGKIISVC-VGK------DNVVNEDKNWAYVCFSTADEASIAVEKGNEVYIDSVKINVTYFKSKNE 383
                                        56678*********97.333......35678899***********************99***999999876554 PP

>> PABP  Poly-adenylate binding protein, unique domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   1.7e-05     0.051      12      62 ..     430     495 ..     422     499 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.7e-05
                               PABP  12 qkqiLGerLypkiqkl...............npelAgKITGMLLemdnsellellesdeeLrekve 62 
                                         k+++G  Ly ++ +l               ++e A KIT +LL     e+ +++   + L +++ 
  gene1435|gene1435|rna1435|rna1435 430 DKKQMGGDLYGLVLSLaptfqqkwknlgikdEEEFATKITDLLLKRSSTEVRNMIGLGNVLTQNIS 495
                                        57889999****9999999999999999998889999**************999988888877776 PP

>> DNA_ligase_IV  DNA ligase IV
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.1         2   6.1e+03      18      30 ..     117     129 ..     117     129 .. 0.87
   2 ?   10.6   0.0   0.00016      0.47      19      34 .]     207     222 ..     203     222 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 2
                      DNA_ligase_IV  18 vDtdeeqLKevFn 30 
                                        +D d ++L + F+
  gene1435|gene1435|rna1435|rna1435 117 ADCDSKTLHDTFS 129
                                        58999***99996 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00016
                      DNA_ligase_IV  19 DtdeeqLKevFnrIdk 34 
                                         t+e+qLKe+F  I+k
  gene1435|gene1435|rna1435|rna1435 207 TTTEQQLKEIFMSIGK 222
                                        59*********99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (513 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       938  (0.0523175); expected 358.6 (0.02)
Passed bias filter:                      508  (0.028334); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.59u 0.26s 00:00:00.85 Elapsed: 00:00:00.43
# Mc/sec: 3609.75
//
Query:       gene1436|gene1436|rna1436|rna1436  [L=238]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.3e-17   63.9   0.1    2.7e-17   62.8   0.1    1.6  1  DWNN          DWNN domain
    3.2e-11   42.8   6.5    3.2e-11   42.8   6.5    2.4  3  zf-CCHC_2     Zinc knuckle
    3.3e-07   30.2   4.9    7.4e-07   29.1   4.9    1.6  1  zf-RING_UBOX  RING-type zinc-finger
    3.6e-05   23.6   6.1    3.6e-05   23.6   6.1    1.9  2  zf-C3HC4      Zinc finger, C3HC4 type (RING finger)
    7.6e-05   22.5   4.9    7.6e-05   22.5   4.9    1.8  2  zf-RING_6     zf-RING of BARD1-type protein
     0.0004   20.5   9.6     0.0004   20.5   9.6    2.0  2  zf-C3HC4_4    zinc finger of C3HC4-type, RING
    0.00048   19.9   7.4    0.00048   19.9   7.4    2.1  2  zf-C3HC4_3    Zinc finger, C3HC4 type (RING finger)
     0.0019   18.2   2.4     0.0019   18.2   2.4    2.4  1  zf-CCHC       Zinc knuckle
     0.0045   16.8  10.6     0.0045   16.8  10.6    2.4  2  zf-C3HC4_2    Zinc finger, C3HC4 type (RING finger)
     0.0049   16.7   5.8     0.0049   16.7   5.8    2.3  2  Prok-RING_4   Prokaryotic RING finger family 4
     0.0063   16.5  10.1     0.0063   16.5  10.1    2.2  2  zf-RING_5     zinc-RING finger domain
  ------ inclusion threshold ------
       0.19   11.7   3.8       0.29   11.1   0.1    2.5  2  zf-CCHC_3     Zinc knuckle
        1.5    9.1  13.2       0.44   10.7   8.5    2.3  2  zf-RING_10    zinc RING finger of MSL2
        9.7    6.2  14.0       0.59   10.1   0.2    3.8  4  DUF4428       Domain of unknown function (DUF4428)


Domain annotation for each model (and alignments):
>> DWNN  DWNN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.8   0.1   2.1e-20   2.7e-17       1      74 []       5      75 ..       5      75 .. 0.95

  Alignments for each domain:
  == domain 1  score: 62.8 bits;  conditional E-value: 2.1e-20
                               DWNN  1 vyYkFksqkdyskitfdgtsisvfeLKreIiekkklgkgtdfdLqiynaqtkeeydddselIprntsvivrRvP 74
                                       ++Y+F s+++++k+tf+g+si ++eL+ eIi+ +++ +++dfdL ++ ++  ++ +++s+ ++rnt+viv+R+P
  gene1436|gene1436|rna1436|rna1436  5 IHYRFVSSTNAQKLTFEGASIPLWELRTEIINMERM-TAKDFDLLFFIDD--NQLTNESTPVYRNTTVIVKRIP 75
                                       8***********************************.99*******9544..56899****************9 PP

>> zf-CCHC_2  Zinc knuckle
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.8   6.5   2.5e-14   3.2e-11       1      21 []      96     116 ..      96     116 .. 0.99
   2 ?   -1.9   0.2       2.5   3.2e+03       5       9 ..     181     185 ..     181     187 .. 0.83
   3 ?   -2.8   0.3       4.6   5.9e+03       6      12 ..     211     217 ..     211     217 .. 0.79

  Alignments for each domain:
  == domain 1  score: 42.8 bits;  conditional E-value: 2.5e-14
                          zf-CCHC_2   1 PpgYvChiCgkkGHyIqdCPt 21 
                                        Pp+YvC +Cg+kGH+Iq+CPt
  gene1436|gene1436|rna1436|rna1436  96 PPNYVCFRCGQKGHFIQHCPT 116
                                        9*******************8 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.5
                          zf-CCHC_2   5 vChiC 9  
                                        vC+ C
  gene1436|gene1436|rna1436|rna1436 181 VCKYC 185
                                        8*999 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 4.6
                          zf-CCHC_2   6 ChiCgkk 12 
                                        C +Cg+k
  gene1436|gene1436|rna1436|rna1436 211 CVVCGAK 217
                                        778*987 PP

>> zf-RING_UBOX  RING-type zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1   4.9   5.8e-10   7.4e-07       1      25 [.     182     206 ..     182     230 .. 0.82

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 5.8e-10
                       zf-RING_UBOX   1 CpIClelftdPlv.lpCGHtFCreCl 25 
                                        C  C +l+++P v ++CGHtFC++C+
  gene1436|gene1436|rna1436|rna1436 182 CKYCTSLMNEP-VmTTCGHTFCKNCV 206
                                        999********.5368*********9 PP

>> zf-C3HC4  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.5       5.6   7.2e+03      22      28 ..     101     107 ..     100     116 .. 0.51
   2 !   23.6   6.1   2.8e-08   3.6e-05       1      26 [.     182     206 ..     182     209 .. 0.96

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 5.6
                                        -CHHHHH CS
                           zf-C3HC4  22 CskCirk 28 
                                        C+ C +k
  gene1436|gene1436|rna1436|rna1436 101 CFRCGQK 107
                                        6666544 PP

  == domain 2  score: 23.6 bits;  conditional E-value: 2.8e-08
                                        -TTT-S--SS-E.E-TTS--B-CHHH CS
                           zf-C3HC4   1 CpiCleeakepnelleCkHsfCskCi 26 
                                        C+ C++ + ep+ +++C+H+fC++C+
  gene1436|gene1436|rna1436|rna1436 182 CKYCTSLMNEPV-MTTCGHTFCKNCV 206
                                        9***********.************8 PP

>> zf-RING_6  zf-RING of BARD1-type protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       4.1   5.2e+03      47      58 ..      73      84 ..      68      89 .. 0.74
   2 !   22.5   4.9     6e-08   7.6e-05       8      45 ..     180     218 ..     175     224 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 4.1
                          zf-RING_6 47 ytpawiqdvkin 58
                                         paw+    i+
  gene1436|gene1436|rna1436|rna1436 73 RIPAWMSKTTIE 84
                                       5799*9887775 PP

  == domain 2  score: 22.5 bits;  conditional E-value: 6e-08
                          zf-RING_6   8 lrcsrctdilrepvclggcehifcsnci..sdcfgsgcpv 45 
                                        l c  ct ++ epv +  c h fc nc+  sdc   g  v
  gene1436|gene1436|rna1436|rna1436 180 LVCKYCTSLMNEPV-MTTCGHTFCKNCVifSDCVVCGAKV 218
                                        67***********9.578*********7669999988776 PP

>> zf-C3HC4_4  zinc finger of C3HC4-type, RING
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.2       3.6   4.6e+03      20      24 ..     100     104 ..      98     107 .. 0.75
   2 !   20.5   9.6   3.1e-07    0.0004       1      26 [.     182     207 ..     182     216 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 3.6
                         zf-C3HC4_4  20 fClsC 24 
                                        +C++C
  gene1436|gene1436|rna1436|rna1436 100 VCFRC 104
                                        68888 PP

  == domain 2  score: 20.5 bits;  conditional E-value: 3.1e-07
                         zf-C3HC4_4   1 CPiCldYLekPvsleCGhsfClsCis 26 
                                        C  C++++++Pv   CGh+fC +C+ 
  gene1436|gene1436|rna1436|rna1436 182 CKYCTSLMNEPVMTTCGHTFCKNCVI 207
                                        99**********************85 PP

>> zf-C3HC4_3  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.4      0.47     6e+02      24      41 ..      99     115 ..      95     116 .. 0.65
   2 !   19.9   7.4   3.8e-07   0.00048       2      49 ..     179     220 ..     178     221 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.47
                                        EE-HHHHHHHHHTT-B-T CS
                         zf-C3HC4_3  24 vlCeeCaekllkrkkkCp 41 
                                        ++C +C +k     ++Cp
  gene1436|gene1436|rna1436|rna1436  99 YVCFRCGQKG-HFIQHCP 115
                                        4688887776.4556665 PP

  == domain 2  score: 19.9 bits;  conditional E-value: 3.8e-07
                                        GSB-TTTSSSBS-EEETTEEEEEE-HHHHHHHHHTT-B-TTT--B--E CS
                         zf-C3HC4_3   2 deeCviClerprnvvllpCgHlvlCeeCaekllkrkkkCpiCrrpiek 49 
                                        +  C+ C +   + v+  CgH+ +C++C+         C +C +++ k
  gene1436|gene1436|rna1436|rna1436 179 KLVCKYCTSLMNEPVMTTCGHT-FCKNCVIFS-----DCVVCGAKVGK 220
                                        578*******************.******988.....9****999865 PP

>> zf-CCHC  Zinc knuckle
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   2.4   1.5e-06    0.0019       2      17 ..     100     115 ..     100     116 .. 0.93

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.5e-06
                                        CTSSSSSSSSTTTTST CS
                            zf-CCHC   2 kCynCGepGHiardCp 17 
                                        +C++CG+ GH+   Cp
  gene1436|gene1436|rna1436|rna1436 100 VCFRCGQKGHFIQHCP 115
                                        6**********99999 PP

>> zf-C3HC4_2  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.8      0.63   8.1e+02      23      39 ..     101     116 ..      99     116 .. 0.71
   2 !   16.8  10.6   3.5e-06    0.0045       2      28 ..     182     207 ..     181     214 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.63
                         zf-C3HC4_2  23 CqkCilrsLeekneCPl 39 
                                        C  C ++  +  ++CP+
  gene1436|gene1436|rna1436|rna1436 101 CFRCGQKG-HFIQHCPT 116
                                        99999984.45568885 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 3.5e-06
                         zf-C3HC4_2   2 CpiCldmlkdpsvvtpCgHvfCqkCil 28 
                                        C+ C   +++p v+t CgH+fC++C+ 
  gene1436|gene1436|rna1436|rna1436 182 CKYCTSLMNEP-VMTTCGHTFCKNCVI 207
                                        999********.999**********86 PP

>> Prok-RING_4  Prokaryotic RING finger family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.4       1.4   1.8e+03      20      34 ..     100     115 ..      99     118 .. 0.68
   2 !   16.7   5.8   3.8e-06    0.0049       1      37 [.     182     215 ..     182     223 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1.4
                        Prok-RING_4  20 vCkeCfdskdls.sCP 34 
                                        vC +C ++  +   CP
  gene1436|gene1436|rna1436|rna1436 100 VCFRCGQKGHFIqHCP 115
                                        6777777665544777 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 3.8e-06
                        Prok-RING_4   1 CvlCgeqekkailepCgHlvCkeCfdskdlssCPlCq 37 
                                        C+ C++  +++++  CgH +Ck+C     +s C +C 
  gene1436|gene1436|rna1436|rna1436 182 CKYCTSLMNEPVMTTCGHTFCKNCVI---FSDCVVCG 215
                                        ************************75...44555665 PP

>> zf-RING_5  zinc-RING finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.7       1.1   1.4e+03      24      40 ..     100     115 ..      96     117 .. 0.68
   2 !   16.5  10.1   4.9e-06    0.0063       2      42 ..     182     214 ..     181     216 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 1.1
                          zf-RING_5  24 fCekClkkllekeavCp 40 
                                        +C +C +k     + Cp
  gene1436|gene1436|rna1436|rna1436 100 VCFRCGQKGH-FIQHCP 115
                                        6777777766.666666 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 4.9e-06
                          zf-RING_5   2 CnkCfeklskeekfyltsCgHifCekClkkllekeavCpiC 42 
                                        C+ C + +    ++++t+CgH+fC++C+  +      C +C
  gene1436|gene1436|rna1436|rna1436 182 CKYCTSLM---NEPVMTTCGHTFCKNCVIFSD-----CVVC 214
                                        88888888...889**************9888.....6666 PP

>> zf-CCHC_3  Zinc knuckle
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   0.00023      0.29       5      22 ..      99     116 ..      96     127 .. 0.80
   2 ?    0.7   0.7      0.42   5.3e+02       3      11 ..     198     206 ..     196     208 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00023
                          zf-CCHC_3   5 aaCQkClkkGHwtYECkn 22 
                                         +C +C++kGH+   C+ 
  gene1436|gene1436|rna1436|rna1436  99 YVCFRCGQKGHFIQHCPT 116
                                        6899********999984 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.42
                          zf-CCHC_3   3 asaaCQkCl 11 
                                        ++++C++C 
  gene1436|gene1436|rna1436|rna1436 198 GHTFCKNCV 206
                                        579*****5 PP

>> zf-RING_10  zinc RING finger of MSL2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.1       1.1   1.4e+03      24      42 ..      99     116 ..      92     123 .. 0.71
   2 ?   10.7   8.5   0.00034      0.44       1      44 [.     180     215 ..     180     237 .. 0.75

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 1.1
                         zf-RING_10  24 yvCrlCvgkkkklkpsCsq 42 
                                        yvC +C g+k ++  +C++
  gene1436|gene1436|rna1436|rna1436  99 YVCFRC-GQKGHFIQHCPT 116
                                        899999.556666667765 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00034
                         zf-RING_10   1 lsCvvCckLLvdPlepkekeCqHyvCrlCvgkkkklkpsCsqCk 44 
                                        l C  C++L+++P+     +C+H  C+ Cv     + + C  C 
  gene1436|gene1436|rna1436|rna1436 180 LVCKYCTSLMNEPVMT---TCGHTFCKNCV-----IFSDCVVCG 215
                                        78*********99865...8*********8.....556666665 PP

>> DUF4428  Domain of unknown function (DUF4428)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.1      0.11   1.4e+02      20      31 ..      98     114 ..      90     130 .. 0.67
   2 ?    1.7   0.5      0.19   2.5e+02      17      27 ..     176     186 ..     166     195 .. 0.88
   3 ?   -2.1   0.4         3   3.8e+03      22      27 ..     201     206 ..     192     207 .. 0.80
   4 ?   10.1   0.2   0.00046      0.59       1      13 [.     210     222 ..     210     229 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.11
                            DUF4428  20 gyvCkdClkKl.....s 31 
                                        +yvC  C +K      +
  gene1436|gene1436|rna1436|rna1436  98 NYVCFRCGQKGhfiqhC 114
                                        69*******95443333 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.19
                            DUF4428  17 leDgyvCkdCl 27 
                                        ++D  vCk C 
  gene1436|gene1436|rna1436|rna1436 176 TSDKLVCKYCT 186
                                        68999*****6 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 3
                            DUF4428  22 vCkdCl 27 
                                         Ck+C 
  gene1436|gene1436|rna1436|rna1436 201 FCKNCV 206
                                        69**95 PP

  == domain 4  score: 10.1 bits;  conditional E-value: 0.00046
                            DUF4428   1 iCaiCgkKigllk 13 
                                        +C +Cg K+g+++
  gene1436|gene1436|rna1436|rna1436 210 DCVVCGAKVGKIT 222
                                        6**********99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (238 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       797  (0.0444531); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 1476.52
//
Query:       gene1437|gene1437|rna1437|rna1437  [L=193]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.9e-15   55.2   0.6    1.2e-14   54.2   0.3    1.7  2  DnaJ      DnaJ domain
     0.0039   17.0   0.0     0.0061   16.4   0.0    1.3  1  REC104    Meiotic recombination protein REC104


Domain annotation for each model (and alignments):
>> DnaJ  DnaJ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.2   0.3   1.3e-18   1.2e-14       1      61 [.      39      98 ..      39      99 .. 0.96
   2 ?   -3.4   0.0       1.3   1.1e+04      51      62 ..     139     150 ..     136     150 .. 0.70

  Alignments for each domain:
  == domain 1  score: 54.2 bits;  conditional E-value: 1.3e-18
                                       HHHHHHTSSTTG-HHHHHHHHHHHHHHHSTTTSCCHHHHHHHHHHHHHHHHHHTSHHHHHH CS
                               DnaJ  1 dyYeiLgvskdasedeIkkaYrklalkyHPDknpkdpeaeekFkeineAyevLsdpekRkq 61
                                       d Y+iL +++ as+ eIkka++kl+l +HPD++ k +++e +Fk++ +A + L d + R++
  gene1437|gene1437|rna1437|rna1437 39 DSYAILDIKRGASDGEIKKAFHKLSLLVHPDRC-KLKNSEAAFKKVLNAKDYLLDRDARAH 98
                                       67*******************************.9999*******************9986 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 1.3
                                        HHHTSHHHHHHH CS
                               DnaJ  51 evLsdpekRkqY 62 
                                        +vL++  +R++Y
  gene1437|gene1437|rna1437|rna1437 139 DVLNNRFERRAY 150
                                        677777777777 PP

>> REC104  Meiotic recombination protein REC104
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   6.8e-07    0.0061      30     105 ..       9      89 ..       2     104 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 6.8e-07
                             REC104  30 qfglnnktvrri..neeefdkaanciltet.sypepelkrtastyllkssfkkpttlslp..filddalclskrve 100
                                         fg + +t rr+  n+++++k ++ il et sy+  ++kr as   +k++f+k ++l  p    l ++ +  k+v 
  gene1437|gene1437|rna1437|rna1437   9 GFGAESQTTRRVvpNKDDIQKKIDNILRETdSYAILDIKRGASDGEIKKAFHKLSLLVHPdrCKLKNSEAAFKKVL 84 
                                        59999******9889************998468999*******************999994445778888888888 PP

                             REC104 101 nnndt 105
                                        n  d 
  gene1437|gene1437|rna1437|rna1437  85 NAKDY 89 
                                        88775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (193 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       669  (0.0373138); expected 358.6 (0.02)
Passed bias filter:                      513  (0.0286129); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 1226.07
//
Query:       gene1438|gene1438|rna1438|rna1438  [L=337]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.7e-30  103.3  12.7    9.7e-30  103.3  12.7    2.6  2  NOT2_3_5  NOT2 / NOT3 / NOT5 family


Domain annotation for each model (and alignments):
>> NOT2_3_5  NOT2 / NOT3 / NOT5 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    2.9   0.5    0.0058     1e+02      95     118 ..      25      50 ..       8      55 .. 0.62
   2 !  103.3  12.7   5.4e-34   9.7e-30      14     131 .]     220     332 ..     209     332 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.0058
                           NOT2_3_5  95 epkekteeyekgsYkyFDye..tWlk 118
                                        +   k+ e +k+ Yk FD++  + ++
  gene1438|gene1438|rna1438|rna1438  25 SDARKNMELKKDVYKAFDQKkdSMRQ 50 
                                        224455667999******65444444 PP

  == domain 2  score: 103.3 bits;  conditional E-value: 5.4e-34
                           NOT2_3_5  14 kprqyepklphptsisypqeplyeklesakklekldedtLFyiFYysqgtleqllAakeLkkrsWryhkelktWfl 89 
                                        +p   +pk  ++++ ++p++ + +++e +++++kld dtLF+iFY+s ++ +q+ +a+eLkk sWr+h++++tWf+
  gene1438|gene1438|rna1438|rna1438 220 RP--SQPKERTTVPDFFPKQGI-HIFEGPEVYHKLDIDTLFFIFYFS-KDEKQYFSARELKKYSWRFHTKYNTWFQ 291
                                        33..566666667788999986.88********************97.5789************************ PP

                           NOT2_3_5  90 reekeepkekteeyekgsYkyFDye.tWlkrrkkdfkleyekL 131
                                        r   eepk +te ye+g + +FDye tW++r+kkdf++ey++L
  gene1438|gene1438|rna1438|rna1438 292 RL--EEPKLITEYYEQGVFLFFDYEvTWTNRKKKDFTFEYKYL 332
                                        **..************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (337 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2122  (0.118356); expected 358.6 (0.02)
Passed bias filter:                      498  (0.0277762); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.62u 0.33s 00:00:00.95 Elapsed: 00:00:00.52
# Mc/sec: 1940.84
//
Query:       gene1439|gene1439|rna1439|rna1439  [L=60]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      0.007   16.2   0.2      0.007   16.2   0.2    1.1  1  DUF3841   Domain of unknown function (DUF3841)


Domain annotation for each model (and alignments):
>> DUF3841  Domain of unknown function (DUF3841)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.2   3.9e-07     0.007      33      74 ..       3      43 ..       1      60 [] 0.76

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 3.9e-07
                            DUF3841 33 eiaelfleaYdWlvkeakkrvkkpeeveypiWvwvrekallr 74
                                        i+++f++aY+ ++  ak+rv+  + +  p+W+ v++ ++  
  gene1439|gene1439|rna1439|rna1439  3 AIRDVFTHAYRIMSSVAKERVGD-KYIALPLWIKVSDAEITW 43
                                       5789*******************.8888*****996655433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (60 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       402  (0.0224218); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.46
# Mc/sec: 388.38
//
Query:       gene144|gene144|rna144|rna144  [L=179]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.038   14.0   0.2      0.038   14.0   0.2    1.7  2  RRP36     rRNA biogenesis protein RRP36


Domain annotation for each model (and alignments):
>> RRP36  rRNA biogenesis protein RRP36
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.2   2.1e-06     0.038      43     121 ..      43     117 ..      12     120 .. 0.87
   2 ?   -1.3   0.3      0.11   1.9e+03     117     145 ..     141     170 ..     138     179 .] 0.57

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.1e-06
                          RRP36  43 dedlfeknYaFLdeyrekEleelkkelkkekdkeeekeelkrelqrlesrekerekkererevlkelkkeekekvkegk 121
                                    + + f+k Y F+ ++  +  +++ + ++ ++d     ++l+  ++++++ +++ +k+e+e+ev    ++ee+ +v++ k
  gene144|gene144|rna144|rna144  43 SLSNFDKFYDFISDITSTTYKDIAAYYRLRHD----LKDLEYLVMEYNTLKNKLDKDEKEDEVIYYNEEEERGLVESSK 117
                                    56789********************9996666....9999999999999999999********9999999999998776 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.11
                          RRP36 117 vkegkk.pfflkksekkklllkekfeelk.k 145
                                    + +gk+   f+k+  kk ++ + +++ ++  
  gene144|gene144|rna144|rna144 141 IGNGKNlVRFMKE-AKKSVMMRGNYNGIElC 170
                                    5667775556654.45666666777766544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (179 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       777  (0.0433376); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1199.98
//
Query:       gene1440|gene1440|rna1440|rna1440  [L=288]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.4e-09   37.4   0.1    8.8e-09   35.5   0.0    2.0  2  NTP_transf_2  Nucleotidyltransferase domain
     0.0037   17.3   0.0     0.0095   16.0   0.0    1.7  1  Polbeta       Polymerase beta, Nucleotidyltransferase


Domain annotation for each model (and alignments):
>> NTP_transf_2  Nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0      0.52   4.7e+03      64      66 ..      46      48 ..       7      78 .. 0.58
   2 !   35.5   0.0   9.8e-13   8.8e-09      13      46 ..     124     160 ..     116     234 .. 0.72

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.52
                                       EEC CS
                       NTP_transf_2 64 eel 66
                                       +el
  gene1440|gene1440|rna1440|rna1440 46 NEL 48
                                       333 PP

  == domain 2  score: 35.5 bits;  conditional E-value: 9.8e-13
                                        T...TSEEEEEHHHHCTTSCTTSSEEEEEEESTTCHH CS
                       NTP_transf_2  13 p...vakvvlfGSyarGtalkgSDiDllvvlpeevsr 46 
                                              +v +fGSy++G++l+gSDiDl ++++e    
  gene1440|gene1440|rna1440|rna1440 124 NqicEDRVECFGSYETGLYLPGSDIDLTLFTDEKDAL 160
                                        4456789*************************99443 PP

>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   1.1e-06    0.0095      18      47 ..     133     162 ..     121     184 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.1e-06
                                        EEEEEE-S------EEEEEEEESS---HHH CS
                            Polbeta  18 lFGSrakgkareeSDiDlavllkekldlee 47 
                                         FGS+ +g + + SDiDl ++++ek+ l++
  gene1440|gene1440|rna1440|rna1440 133 CFGSYETGLYLPGSDIDLTLFTDEKDALKK 162
                                        5***********************955544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (288 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       496  (0.0276647); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 2212.29
//
Query:       gene1441|gene1441|rna1441|rna1441  [L=209]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.6e-07   31.9   0.0      0.069   14.1   0.0    3.8  4  WD40         WD domain, G-beta repeat
    3.1e-06   27.4   0.0     0.0064   16.8   0.0    3.2  3  ANAPC4_WD40  Anaphase-promoting complex subunit 4 WD40 domain
    2.3e-05   23.9   4.0    2.5e-05   23.8   1.6    2.0  3  WD40_like    WD40-like domain
     0.0017   18.4   1.4      0.089   12.8   0.0    2.6  3  BBS2_Mid     Ciliary BBSome complex subunit 2, middle region
      0.006   15.9   0.1      0.012   14.9   0.1    1.5  1  RAB3GAP2_N   Rab3 GTPase-activating protein regulatory subuni
  ------ inclusion threshold ------
      0.011   16.0   0.4      0.026   14.8   0.0    1.8  3  DUF5645      Domain of unknown function (DUF5645)
      0.034   13.1   0.2        3.5    6.5   0.0    2.4  2  Ge1_WD40     WD40 region of Ge1, enhancer of mRNA-decapping p


Domain annotation for each model (and alignments):
>> WD40  WD domain, G-beta repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.0   0.00061       1.6      10      37 ..      14      42 ..       7      43 .. 0.82
   2 !   14.1   0.0   2.7e-05     0.069       6      37 ..      94     125 ..      90     126 .. 0.86
   3 ?   -1.1   0.0       1.7   4.3e+03      13      35 ..     142     162 ..     135     163 .. 0.65
   4 ?    3.1   0.0     0.078     2e+02       9      38 .]     177     205 ..     169     205 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00061
                                       S.SSEEEEEEETTSSEEEEEETTSEEEEE CS
                               WD40 10 H.ssvtslafspdgawlasGsdDgtvriW 37
                                       H  ++  +  s+dg+++++ s+D++v ++
  gene1441|gene1441|rna1441|rna1441 14 HdLGIEKIEISDDGKYVVAVSRDKSVSFY 42
                                       6334888899********99******876 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 2.7e-05
                                        EEESSSS.EEEEEEETTSSEEEEEETTSEEEEE CS
                               WD40   6 tltGHss.vtslafspdgawlasGsdDgtvriW 37 
                                        ++  Hs  v++ +f+  g+++a+Gs+D++v i+
  gene1441|gene1441|rna1441|rna1441  94 IF-SHSRrVNAASFDNLGTMFATGSKDRNVLIY 125
                                        55.48447**********************998 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 1.7
                                        EEEEEEETTSSEEEEEETTSEEE CS
                               WD40  13 vtslafspdgawlasGsdDgtvr 35 
                                        vt+l+f++ + ++  G ++g ++
  gene1441|gene1441|rna1441|rna1441 142 VTALRFHDRHLFV--GLKNGMLK 162
                                        7888777666553..66666666 PP

  == domain 4  score: 3.1 bits;  conditional E-value: 0.078
                                        SS.SSEEEEEEETTSSEEEEEETTSEEEEEE CS
                               WD40   9 GH.ssvtslafspdgawlasGsdDgtvriWd 38 
                                         H +s++ ++f+ +   l++ sdD+  r+++
  gene1441|gene1441|rna1441|rna1441 177 IHaKSINEIKFNNN--RLITISDDNMMRVFN 205
                                        59899999966544..344335599999886 PP

>> ANAPC4_WD40  Anaphase-promoting complex subunit 4 WD40 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0      0.13   3.3e+02      37      67 ..      14      44 ..       6      61 .. 0.83
   2 !   16.8   0.0   2.5e-06    0.0064      37      90 ..      97     148 ..      89     150 .. 0.91
   3 !    8.5   0.0   0.00092       2.4      39      91 ..     140     189 ..     139     190 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.13
                        ANAPC4_WD40 37 edsevrsLaWkpdgklLavaysdgevrllda 67
                                       +d  +++++ + dgk  + +  d +v+++ +
  gene1441|gene1441|rna1441|rna1441 14 HDLGIEKIEISDDGKYVVAVSRDKSVSFYRI 44
                                       67889999999****9999999999987765 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 2.5e-06
                        ANAPC4_WD40  37 edsevrsLaWkpdgklLavaysdgevrlldaesgkvvhslsvksekavtclgWg 90 
                                        ++++v++ ++ + g+++a + +d +v ++++ s +v++++++++e  vt l + 
  gene1441|gene1441|rna1441|rna1441  97 HSRRVNAASFDNLGTMFATGSKDRNVLIYSVDSLDVIETIKCEEE--VTALRFH 148
                                        46789999***********************************99..9999886 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.00092
                        ANAPC4_WD40  39 sevrsLaWkpdgklLavaysdgevrlldaesgkvvhslsvksekavtclgWge 91 
                                        +ev++L+++  ++ L v+ ++g +++l+ e  + + + ++++++ ++ +++++
  gene1441|gene1441|rna1441|rna1441 140 EEVTALRFH--DRHLFVGLKNGMLKILKTEGYNQIYEQRIHAKS-INEIKFNN 189
                                        577777765..789******************999999999995.99998876 PP

>> WD40_like  WD40-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       2.3   5.9e+03       6      26 ..      21      41 ..      18      47 .. 0.66
   2 !    5.8   0.1    0.0028       7.3      10      38 ..     108     136 ..     101     137 .. 0.87
   3 !   23.8   1.6   9.7e-09   2.5e-05      59     145 ..     116     204 ..     109     208 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 2.3
                          WD40_like  6 idiskkgslilyGgkddkctv 26
                                       i+is +g++++  ++d+ +  
  gene1441|gene1441|rna1441|rna1441 21 IEISDDGKYVVAVSRDKSVSF 41
                                       777777777777666666555 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0028
                          WD40_like  10 kkgslilyGgkddkctvlkleslesvsiv 38 
                                        + g++++ G+kd ++ +++++sl+++  +
  gene1441|gene1441|rna1441|rna1441 108 NLGTMFATGSKDRNVLIYSVDSLDVIETI 136
                                        5689********************99765 PP

  == domain 3  score: 23.8 bits;  conditional E-value: 9.7e-09
                          WD40_like  59 vtlDGtillslleneeevenekieedistvkviddklliGtnkGsiyvfskdlqleevllg.qsseIkeikiennk 133
                                        ++ D ++l + +   +++e+ k ee+++  +  d +l +G ++G + +++ +  +++     +   I+eik +nn+
  gene1441|gene1441|rna1441|rna1441 116 GSKDRNVLIYSVDSLDVIETIKCEEEVTALRFHDRHLFVGLKNGMLKILKTEGYNQIYEQRiHAKSINEIKFNNNR 191
                                        56777888888888889***********************************66666544337789********** PP

                          WD40_like 134 iysLsesafi.vf 145
                                        + ++s+++++ vf
  gene1441|gene1441|rna1441|rna1441 192 LITISDDNMMrVF 204
                                        *******999445 PP

>> BBS2_Mid  Ciliary BBSome complex subunit 2, middle region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       1.7   4.5e+03       9      28 ..      25      43 ..      20      49 .. 0.73
   2 !   12.8   0.0   3.5e-05     0.089      15      66 ..     113     165 ..     101     178 .. 0.83
   3 ?    4.0   0.1     0.019        49      11      29 ..     188     206 ..     179     209 .] 0.83

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.7
                           BBS2_Mid  9 gdgeneLvvgsddfeirvfk 28
                                         + +++v+ s d ++  ++
  gene1441|gene1441|rna1441|rna1441 25 D-DGKYVVAVSRDKSVSFYR 43
                                       3.357888889998888775 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 3.5e-05
                           BBS2_Mid  15 Lvvgsddfeirvfkee..elvaeitetekvvslarlekerfayaleNGtvgvye 66 
                                           gs+d ++ +++ +  +++ +i+ +e+v++l r +++++ ++l+NG++++ +
  gene1441|gene1441|rna1441|rna1441 113 FATGSKDRNVLIYSVDslDVIETIKCEEEVTAL-RFHDRHLFVGLKNGMLKILK 165
                                        5679*********99965678888889999888.78999999*******99866 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.019
                           BBS2_Mid  11 geneLvvgsddfeirvfke 29 
                                        ++n L+  sdd+ +rvf+ 
  gene1441|gene1441|rna1441|rna1441 188 NNNRLITISDDNMMRVFNI 206
                                        5799*************85 PP

>> RAB3GAP2_N  Rab3 GTPase-activating protein regulatory subunit N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.1   4.8e-06     0.012      73     115 ..     146     188 ..     113     206 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 4.8e-06
                         RAB3GAP2_N  73 spdwtviavGlssGylrfyteng.elLlsqllheepvlkikcvs 115
                                        + + + + vGl++G+l++++ +g + +++q +h +++++ik ++
  gene1441|gene1441|rna1441|rna1441 146 RFHDRHLFVGLKNGMLKILKTEGyNQIYEQRIHAKSINEIK-FN 188
                                        66778899***********9888689***************.42 PP

>> DUF5645  Domain of unknown function (DUF5645)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       3.7   9.4e+03      73      86 ..      31      42 ..      22      48 .. 0.60
   2 ?   14.8   0.0     1e-05     0.026      40     125 ..      76     165 ..      66     166 .. 0.84
   3 ?   -3.4   0.0       4.3   1.1e+04     103     119 ..     183     199 ..     173     204 .. 0.66

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 3.7
                            DUF5645 73 vslhededqsvsff 86
                                       v++++d  +svsf+
  gene1441|gene1441|rna1441|rna1441 31 VAVSRD--KSVSFY 42
                                       345554..566666 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 1e-05
                            DUF5645  40 qLeeiseleeaslslRkkfythrrg....dfrqtgtfvslhededqsvsfftlq.eepeeLlealedtkriewekg 110
                                         +++i ++ + +lslRk+++ h r+     f + gt  +    +d +v  ++    + +e +++ e+   + ++ +
  gene1441|gene1441|rna1441|rna1441  76 VINKILNDSPYYLSLRKRIFSHSRRvnaaSFDNLGTMFAT-GSKDRNVLIYSVDsLDVIETIKCEEEVTALRFHDR 150
                                        56667778899*********99654333368999**9985.57899999***998899****************** PP

                            DUF5645 111 avltnvddeflerlk 125
                                         +++ +++ +l++lk
  gene1441|gene1441|rna1441|rna1441 151 HLFVGLKNGMLKILK 165
                                        ****99999998887 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 4.3
                            DUF5645 103 kriewekgavltnvdde 119
                                        + i+++++ ++t  dd+
  gene1441|gene1441|rna1441|rna1441 183 NEIKFNNNRLITISDDN 199
                                        45777777777655555 PP

>> Ge1_WD40  WD40 region of Ge1, enhancer of mRNA-decapping protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0    0.0075        19     190     221 ..      18      49 ..       5      60 .. 0.83
   2 ?    6.5   0.0    0.0014       3.5     184     226 ..      94     138 ..      79     150 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.0075
                           Ge1_WD40 190 iveaafspdGtalatasedGevkffqvylede 221
                                        i +  +s dG  + + s d  v f+++  + +
  gene1441|gene1441|rna1441|rna1441  18 IEKIEISDDGKYVVAVSRDKSVSFYRILDTST 49 
                                        667789********************976655 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0014
                           Ge1_WD40 184 ieehs.liveaafspdGtalatasedGevkffqvylede.eeprC 226
                                        i +hs  +  a+f   Gt  at s+d  v  + v   d  e+ +C
  gene1441|gene1441|rna1441|rna1441  94 IFSHSrRVNAASFDNLGTMFATGSKDRNVLIYSVDSLDViETIKC 138
                                        5667768999********************999977665344555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       808  (0.0450667); expected 358.6 (0.02)
Passed bias filter:                      459  (0.025601); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1433.02
//
Query:       gene1442|gene1442|rna1442|rna1442  [L=472]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.5e-09   36.8   8.2       0.01   16.7   0.1    5.2  5  WD40      WD domain, G-beta repeat
     0.0056   16.2   1.1       0.01   15.3   0.2    1.8  2  DUF5046   Domain of unknown function (DUF5046)


Domain annotation for each model (and alignments):
>> WD40  WD domain, G-beta repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.1      0.58   5.2e+03      24      34 ..     139     149 ..     130     150 .. 0.78
   2 !   10.9   0.1   7.8e-05       0.7       7      37 ..     205     234 ..     199     235 .. 0.71
   3 !    9.3   0.1   0.00024       2.1       3      37 ..     241     276 ..     239     277 .. 0.66
   4 !   16.7   0.1   1.1e-06      0.01       2      37 ..     341     375 ..     340     375 .. 0.87
   5 ?   -0.2   0.0      0.24   2.2e+03      19      37 ..     397     413 ..     384     414 .. 0.59

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.58
                                        EEEEEETTSEE CS
                               WD40  24 wlasGsdDgtv 34 
                                        +l++G+ Dg++
  gene1442|gene1442|rna1442|rna1442 139 FLVCGTLDGKI 149
                                        57889889987 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 7.8e-05
                                        EESS.SSEEEEEEETTSSEEEEEETTSEEEEE CS
                               WD40   7 ltGH.ssvtslafspdgawlasGsdDgtvriW 37 
                                        +++H + vt+++   + + ++s+s D+t++i 
  gene1442|gene1442|rna1442|rna1442 205 IKAHdDAVTDIK--INTSIILSSSQDKTIKIH 234
                                        579955577772..23444899********95 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.00024
                                        EEEEEESSSS.EEEEE.EETTSSEEEEEETTSEEEEE CS
                               WD40   3 clrtltGHss.vtsla.fspdgawlasGsdDgtvriW 37 
                                        ++ tl GHs+ v+    +++++  ++s++ D+ v iW
  gene1442|gene1442|rna1442|rna1442 241 HVDTLIGHSDyVYESNfVDKHNE-IVSAGADNCVIIW 276
                                        677999**556965551344444.555555******* PP

  == domain 4  score: 16.7 bits;  conditional E-value: 1.1e-06
                                        EEEEEEESS.SSEEEEEEETTSSEEEEEETTSEEEEE CS
                               WD40   2 qclrtltGH.ssvtslafspdgawlasGsdDgtvriW 37 
                                        +++++  GH + +t l     ++++++Gs D+tvr++
  gene1442|gene1442|rna1442|rna1442 341 ELVHSVGGHvDKITTL--AVKNDFILTGSLDRTVRLY 375
                                        5799*****877*999..55889999*********97 PP

  == domain 5  score: -0.2 bits;  conditional E-value: 0.24
                                        ETTSSEEEEEETTSEEEEE CS
                               WD40  19 spdgawlasGsdDgtvriW 37 
                                          + + ++ Gsd   +r++
  gene1442|gene1442|rna1442|rna1442 397 Y-NDN-VVVGSDESILRVY 413
                                        2.333.445**88888886 PP

>> DUF5046  Domain of unknown function (DUF5046)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0      0.27   2.4e+03      43      78 ..     203     238 ..     185     258 .. 0.55
   2 !   15.3   0.2   1.1e-06      0.01      91     135 ..     398     445 ..     387     454 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.27
                            DUF5046  43 ellatfdrsvstyaPGavvlwnsgedsryelidlet 78 
                                        e +   d  v+     + ++  s +d++ ++++l+t
  gene1442|gene1442|rna1442|rna1442 203 ENIKAHDDAVTDIKINTSIILSSSQDKTIKIHNLQT 238
                                        334444444444444444444455555555555555 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 1.1e-06
                            DUF5046  91 dktvavyatdgilrvydkttG..alltdveve.pveeqqsvrvsavge 135
                                        +++v v + ++ilrvy++ttG  ++l dv+ +  ve  +s+ v+av++
  gene1442|gene1442|rna1442|rna1442 398 NDNVVVGSDESILRVYERTTGveKILRDVDLKmNVESGDSALVTAVAD 445
                                        57888999999*********9778******8747***********987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (472 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       697  (0.0388756); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 3028.58
//
Query:       gene1443|gene1443|rna1443|rna1443  [L=158]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
       0.04   14.0   0.0      0.091   12.8   0.0    1.7  1  DASH_Dad3  DASH complex subunit Dad3


Domain annotation for each model (and alignments):
>> DASH_Dad3  DASH complex subunit Dad3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   5.1e-06     0.091      48      65 ..     106     123 ..      94     135 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 5.1e-06
                          DASH_Dad3  48 iglvyTLlKaSVYsivlq 65 
                                        +++v T +K SVY i++ 
  gene1443|gene1443|rna1443|rna1443 106 TNMVATYFKCSVYDIFTY 123
                                        79*************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       784  (0.043728); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 1191.49
//
Query:       gene1444|gene1444|rna1444|rna1444  [L=953]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.2e-07   29.3   4.2    3.7e-05   24.0   0.0    3.2  3  RhoGEF    RhoGEF domain


Domain annotation for each model (and alignments):
>> RhoGEF  RhoGEF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.1      0.57     1e+04      93     106 ..     196     209 ..     148     227 .. 0.55
   2 !    5.3   0.2    0.0012        21       2      56 ..     316     367 ..     309     436 .. 0.80
   3 !   24.0   0.0   2.1e-09   3.7e-05      71     177 ..     495     595 ..     467     600 .. 0.72

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 0.57
                                        HHHCHHHHHHHHHH CS
                             RhoGEF  93 Ycsnypnalkllke 106
                                        ++   ++  k+l++
  gene1444|gene1444|rna1444|rna1444 196 FLDLETEYNKVLEN 209
                                        33333333333333 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0012
                                        HHHHHHHHHHHHHHHHHHHHHTHCCCHHCTCCHHHHHHHHCTTHHHHHHHHHHHH CS
                             RhoGEF   2 ikElleTErsYvrdLkvlvevylkplselevlseeeikiiFsnieeilelhrsfl 56 
                                          E+++T ++Y   L+  ++++++  +    + + ++k++F n++e+l+  r  +
  gene1444|gene1444|rna1444|rna1444 316 FTEFFQTQNNYHLILESFYDNVVRKCE---SIADLKVKKVFENFQEVLKSERVIF 367
                                        568888888888888888888886555...6889999999999999999886555 PP

  == domain 3  score: 24.0 bits;  conditional E-value: 2.1e-09
                                        SS-S-SHHHHHHHHSTHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHTSGGGTT--HHHHTTHHHHHHHHH CS
                             RhoGEF  71 keaqsigdvflkfadkfkkYseYcsnypnalkllkelskknkkfkafleeaeerpecskldLeslLikPvqRlprY 146
                                        +++ +++d ++k+++ f++Y+e + +y+    l++      ++++ +le+ + +    +  Le   i PvqR++rY
  gene1444|gene1444|rna1444|rna1444 495 ETIGKVSDRVEKIFAFFNQYVELMDKYKGFFTLYSM-----HDITPILESKKVSLSEFEGGLEGVFILPVQRMVRY 565
                                        334455555666666666666666666666666666.....56777888877777767889*************** PP

                                        HHHHHHHHHTS-TTSHHHHHHHHHHHHHHHH CS
                             RhoGEF 147 pLLLkellkntpeshpdyealkkaleaikev 177
                                        + +L++++k+ +++    e+  +al++++++
  gene1444|gene1444|rna1444|rna1444 566 KQFLEKFYKYVDARF-ISEQFTDALTKLSNF 595
                                        ***********7763.346788888887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (953 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       874  (0.0487478); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.71u 0.27s 00:00:00.98 Elapsed: 00:00:00.44
# Mc/sec: 6528.92
//
Query:       gene1445|gene1445|rna1445|rna1445  [L=121]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       780  (0.0435049); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.30s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 794.31
//
Query:       gene1446|gene1446|rna1446|rna1446  [L=470]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
       0.35   11.4   6.9       0.41   11.2   0.0    3.3  3  Baculo_LEF-11  Baculovirus LEF-11 protein


Domain annotation for each model (and alignments):
>> Baculo_LEF-11  Baculovirus LEF-11 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   2.3e-05      0.41      29      76 ..      37      87 ..      31     100 .. 0.81
   2 ?    1.8   0.6     0.019   3.3e+02       7      69 ..     248     317 ..     242     333 .. 0.69
   3 ?   -0.8   0.1      0.12   2.2e+03      25      54 ..     356     390 ..     345     401 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 2.3e-05
                      Baculo_LEF-11 29 ahhldtdsFetirefire...hadvivrknskrkavadHlkRlarLlsldk 76
                                        +h+d +s + i+ +  e    + +i+r n++ k+   H  R+arL++l+ 
  gene1446|gene1446|rna1446|rna1446 37 NEHIDLHSTNFIQFYGVEenfYNGRIMRINFREKLLVSHKIRIARLMDLKL 87
                                       5778888888888887665667899**********************8874 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.019
                      Baculo_LEF-11   7 iialvrevint...lkstndtedvtahh....ldtdsFetirefirehadvivrknskrkavadHlkRla 69 
                                        +++l+  vi +   lk + d e + ++     ld     +++   ++ ++ i +kn   ++  +Hl+ l+
  gene1446|gene1446|rna1446|rna1446 248 VVNLISVVIRKravLKINDDCEILLIDNcdgnLDFSGCTCLKSLTIKNYKFIYHKNIYDNLLSLHLEGLN 317
                                        66777777754222566777776666651111455557899***9************9999999999876 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 0.12
                      Baculo_LEF-11  25 edvtahhldtds.Fetirefire.....hadvivrk 54 
                                         +++ + ld+ + F++ ++          +++i +k
  gene1446|gene1446|rna1446|rna1446 356 RNFVGN-LDISNlFDCFKKLFTGktitiAYEMISDK 390
                                        566666.99999999999876652222344455554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (470 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       537  (0.0299515); expected 358.6 (0.02)
Passed bias filter:                      252  (0.0140554); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 3117.63
//
Query:       gene1447|gene1447|rna1447|rna1447  [L=165]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       582  (0.0324614); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1169.76
//
Query:       gene1448|gene1448|rna1448|rna1448  [L=368]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (368 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       955  (0.0532657); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 2609.74
//
Query:       gene1449|gene1449|rna1449|rna1449  [L=44]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (44 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       334  (0.018629); expected 358.6 (0.02)
Passed bias filter:                      132  (0.00736237); expected 358.6 (0.02)
Passed Vit filter:                         6  (0.000334653); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.26s 00:00:00.60 Elapsed: 00:00:00.42
# Mc/sec: 316.43
//
Query:       gene145|gene145|rna145|rna145  [L=109]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.3e-17   63.2   0.4      3e-17   62.8   0.4    1.1  1  RT_RNaseH    RNase H-like domain found in reverse transcripta
    9.6e-09   35.2   0.1    1.6e-08   34.4   0.1    1.4  1  RT_RNaseH_2  RNase H-like domain found in reverse transcripta


Domain annotation for each model (and alignments):
>> RT_RNaseH  RNase H-like domain found in reverse transcriptase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.8   0.4   3.3e-21     3e-17      33     105 .]       1      74 [.       1      74 [. 0.95

  Alignments for each domain:
  == domain 1  score: 62.8 bits;  conditional E-value: 3.3e-21
                                    EEEEEEE--HHHHTS-HHHHHHHHHHHHHHHHHHHHTS--EEEE-SS--TTTTT----..---HHHHHHHC-XX CS
                      RT_RNaseH  33 iafaSrklsgaernystiekellAivaalkkfrhylqgrkftvitDhknlkyllskks.lngrlarWaleLsey 105
                                    ++ aS+kl+++e +  + eke+lA+ + ++kf + l+ rkf++itDhk+l+++ +k +  n+ l+rW++ +++y
  gene145|gene145|rna145|rna145   1 VQWASKKLTPTEMRCRISEKEMLAVKWGIEKFSYELKARKFHLITDHKALEFIRNKPEfYNNILNRWCEAIQQY 74 
                                    5789**************************************************7777468***********99 PP

>> RT_RNaseH_2  RNase H-like domain found in reverse transcriptase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.4   0.1   1.8e-12   1.6e-08      58      99 ..       1      42 [.       1      43 [. 0.95

  Alignments for each domain:
  == domain 1  score: 34.4 bits;  conditional E-value: 1.8e-12
                    RT_RNaseH_2 58 iafaSrklskaernysttekellAivwalkkfrhyllgrkft 99
                                   ++ aS+kl+++e +  + eke+lA+ w+++kf++ l  rkf+
  gene145|gene145|rna145|rna145  1 VQWASKKLTPTEMRCRISEKEMLAVKWGIEKFSYELKARKFH 42
                                   5789************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       495  (0.0276089); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.34u 0.27s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 815.77
//
Query:       gene1450|gene1450|rna1450|rna1450  [L=39]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (39 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       115  (0.00641419); expected 358.6 (0.02)
Passed bias filter:                       90  (0.0050198); expected 358.6 (0.02)
Passed Vit filter:                         2  (0.000111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.31u 0.26s 00:00:00.57 Elapsed: 00:00:00.39
# Mc/sec: 297.29
//
Query:       gene1451|gene1451|rna1451|rna1451  [L=644]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (644 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       716  (0.0399353); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.63u 0.34s 00:00:00.97 Elapsed: 00:00:00.51
# Mc/sec: 3775.50
//
Query:       gene1452|gene1452|rna1452|rna1452  [L=276]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    5.3e-07   29.3   8.3    1.3e-05   24.7   2.7    2.4  2  WD40_like  WD40-like domain
     0.0081   14.8   0.4      0.016   13.9   0.3    1.4  1  MMS1_N     Mono-functional DNA-alkylating methyl methanesulfo
  ------ inclusion threshold ------
      0.017   14.5   0.3      0.088   12.1   0.1    1.9  2  CPSF_A     CPSF A subunit region


Domain annotation for each model (and alignments):
>> WD40_like  WD40-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   2.7   2.1e-09   1.3e-05      48     155 ..      50     156 ..      26     172 .. 0.77
   2 !    7.7   0.4   0.00033         2      91     137 ..     172     216 ..     161     255 .. 0.79

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 2.1e-09
                          WD40_like  48 vklldddlilvvtlDGtillsllenee.evenekieedistvkviddklliGtnkGsiyvfskdlqleevllgqss 122
                                        + l dd+  lv+ +D  i  + l+     + +++i e  st+ + ++ l++Gt++G+i++f +d+ + +++   + 
  gene1452|gene1452|rna1452|rna1452  50 AALKDDN--LVMVVDQHIHVYSLKTHRrRIIEKQIGE-YSTAIYYNEILAVGTENGDIWLFGEDFVFLTMIKAGKE 122
                                        4444444..5566799999999999886788888876.57777899******************999999888899 PP

                          WD40_like 123 eIkeikiennkiysLses.afivfdlfsqnieyk 155
                                        +I  i  +   i ++s+s ++i++d  s+++ +k
  gene1452|gene1452|rna1452|rna1452 123 KIPVIAHNGTGIVAISHSgELIIYDYNSKKLITK 156
                                        99999999999****98648*****999766555 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.00033
                          WD40_like  91 iddklliGtnkGsiyvfskdlqleevllgqsseIkeikiennkiysL 137
                                         d ++l+G ++G +y  ++dl+ + + ++   eI+ + ++++ iy +
  gene1452|gene1452|rna1452|rna1452 172 NDTRILLGDENGFVYFVNHDLSYKRIRISN-GEIEYLYYHES-IYCI 216
                                        35589********************99985.69999988864.5555 PP

>> MMS1_N  Mono-functional DNA-alkylating methyl methanesulfonate N-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.3   2.6e-06     0.016     124     275 ..      62     233 ..      28     267 .. 0.55

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.6e-06
                             MMS1_N 124 kteltlyewdlglnlvrkisktsepkk.nldsganlLiplpkpgg.vlVcget..iitykdildqed.irkk.... 190
                                         +++++y++++  +   +i +  ++ + +    +n + ++   +g +   ge+  ++t+ +   +++ i +     
  gene1452|gene1452|rna1452|rna1452  62 DQHIHVYSLKTHRR---RIIEK-QIGEySTAIYYNEILAVGTENGdIWLFGEDfvFLTMIKA--GKEkIPVIahng 131
                                        56778888876444...33221.111233455666777776655555555555233333333..221122223334 PP

                             MMS1_N 191 ......swarPrrekatn........................fvaweklds.fffllatedGdLylleiekdedsg 235
                                              s                                    + ++k+++ +++ll++e+G +y+++ + + +  
  gene1452|gene1452|rna1452|rna1452 132 tgivaiS----------HsgeliiydynskklitkhfgskltAMTVQKTKNdTRILLGDENGFVYFVNHDLSYK-- 195
                                        4433330..........03333334444444444444444332367888888***************9955333.. PP

                             MMS1_N 236 kvvtsislkyfdtvsvasalvilksgfLfvasefGdgqly 275
                                             is +++  +   ++++++ +gf+    + G g++y
  gene1452|gene1452|rna1452|rna1452 196 --RIRISNGEIEYLYYHESIYCITEGFVRKINDRGAGKIY 233
                                        ..22233333444445567777777777666666666666 PP

>> CPSF_A  CPSF A subunit region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0     0.054   3.2e+02     113     145 ..      49      78 ..      35     120 .. 0.58
   2 ?   12.1   0.1   1.5e-05     0.088     100     159 ..     132     191 ..     109     201 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.054
                                        EEEE-TTS-EEEEEEEE-SS-EEEEEEETTEEE CS
                             CPSF_A 113 vydlgedktLlrkafldtqlyvvslkvlgnrii 145
                                        v  l++d+ L+ +   d ++ v slk+++ rii
  gene1452|gene1452|rna1452|rna1452  49 VAALKDDN-LVMV--VDQHIHVYSLKTHRRRII 78 
                                        44445555.4433..334555555666555555 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 1.5e-05
                                        TTEEEEE-SSEEEEEEE-TTS-EEEEEEEE-SS-EEEEEEETT..EEEEEESSS-EEEEEE- CS
                             CPSF_A 100 qGrllvgvgqkvrvydlgedktLlrkafldtqlyvvslkvlgn..riivgDlmkSvtfveyd 159
                                         G ++++ +  +++yd++ +k L+ k f   +l +++++ ++n  ri++gD    v+fv++d
  gene1452|gene1452|rna1452|rna1452 132 TGIVAISHSGELIIYDYNSKK-LITKHFG-SKLTAMTVQKTKNdtRILLGDENGFVYFVNHD 191
                                        56688888999**********.*******.555555555555558******98888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (276 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       480  (0.0267723); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1813.52
//
Query:       gene1453|gene1453|rna1453|rna1453  [L=429]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-26   92.3   0.0      2e-13   50.2   0.0    2.4  2  TFIIB           Transcription factor TFIIB repeat
    1.1e-14   54.5   3.3    5.1e-14   52.4   3.3    2.0  1  BRF1            Brf1-like TBP-binding domain
     0.0028   17.1   3.5     0.0065   16.0   3.5    1.7  1  TF_Zn_Ribbon    TFIIB zinc-binding
  ------ inclusion threshold ------
      0.012   15.6   0.3      0.034   14.2   0.2    1.8  2  RB_B            Retinoblastoma-associated protein B domain
       0.03   14.1   0.2       0.69    9.7   0.1    2.4  2  Cyclin_N        Cyclin, N-terminal domain
       0.11   12.2   2.7       0.28   10.9   2.7    1.6  1  Ribosomal_S27e  Ribosomal protein S27


Domain annotation for each model (and alignments):
>> TFIIB  Transcription factor TFIIB repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.2   0.0   6.6e-17     2e-13       1      65 [.      99     163 ..      99     169 .. 0.96
   2 !   39.9   0.0   1.1e-13   3.3e-10       2      71 .]     194     264 ..     193     264 .. 0.97

  Alignments for each domain:
  == domain 1  score: 50.2 bits;  conditional E-value: 6.6e-17
                                        HHHHHHHTT--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHHHHSS CS
                              TFIIB   1 ikrfadaleLpekVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkeissvlq 65 
                                        ik ++  l+L+++Va+ A  ++kl+l+ +++ Gr     ++Ac+yi cr+e++ + +++++++l 
  gene1453|gene1453|rna1453|rna1453  99 IKNICGSLGLSDEVAQSAYRWYKLSLQGNLTRGRNILYTLSACIYIVCRQEKTPHLLIDFAQLLD 163
                                        899**********************************************************9986 PP

  == domain 2  score: 39.9 bits;  conditional E-value: 1.1e-13
                                        HHHHHHTT--H.HHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHHHHSS--SHHH CS
                              TFIIB   2 krfadaleLpe.kVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkeissvlqVsekti 71 
                                         rf ++l+L++ k+   A  l+ ++++++++ Gr+p+++ +A+l  A+r   ++r+  e+++ ++Vs  ti
  gene1453|gene1453|rna1453|rna1453 194 HRFFSKLKLKNgKILLFAMRLISRMKRDWIVVGRRPNNLCGAALVTASRVYAEERSVLEVAKAVKVSPHTI 264
                                        6899**************************************************************99887 PP

>> BRF1  Brf1-like TBP-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.4   3.3   1.7e-17   5.1e-14       2     101 .]     345     429 .]     344     429 .] 0.87

  Alignments for each domain:
  == domain 1  score: 52.4 bits;  conditional E-value: 1.7e-17
                               BRF1   2 didddeideyllseeevkiKeriWvelnkeyLeeqeekrlkeeaeeaeadkkkkkkkrkrkkkekkkgepetaaea 77 
                                         id +e+++++l++ee+k Ke++W+ +   +L+e++ +   +++e+++      +k r            et ++a
  gene1453|gene1453|rna1453|rna1453 345 SIDSEELECFILTKEEAKQKEKVWDAMYDGFLRERAVRGSTRRKEHKK------RKPR--VV-------YETVEDA 405
                                        699******************************998888777776555......3333..22.......389**** PP

                               BRF1  78 vkkmlekkklskkINydaLekLfd 101
                                        +k ++++kk+ +kINy+aL++Lfd
  gene1453|gene1453|rna1453|rna1453 406 LKGVIKEKKMTNKINYEALKGLFD 429
                                        **********************96 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   3.5   2.2e-06    0.0065       2      36 ..      22      56 ..      21      63 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2.2e-06
                                       EETTTTCEECHEE.TSTTCEEESSSSBEEEECCCCC CS
                       TF_Zn_Ribbon  2 kCPnCgstnlveD.pergelvCtdCGlVlednside 36
                                       kC+ Cgst+ + D +++ ++ C +CG++ e+  i +
  gene1453|gene1453|rna1453|rna1453 22 KCKTCGSTD-IDDgHSTSNICCRKCGTLNEELFITS 56
                                       9*******8.6667*************999877765 PP

>> RB_B  Retinoblastoma-associated protein B domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.2   1.1e-05     0.034      13      72 ..      95     152 ..      86     178 .. 0.85
   2 ?   -3.7   0.0       3.8   1.1e+04      11      23 ..     262     274 ..     255     285 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.1e-05
                               RB_B  13 aavrlrdLcerLklsselrekiwtlfehvlveetellkdRhlDqillcavYvvakvtkee 72 
                                           +++++c +L ls+e+ ++++   + +l  + +l + R++   l +++Y+v++ +k+ 
  gene1453|gene1453|rna1453|rna1453  95 IQNQIKNICGSLGLSDEVAQSAYRWYKLSL--QGNLTRGRNILYTLSACIYIVCRQEKTP 152
                                        56789*******************988777..6789******************988654 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 3.8
                               RB_B  11 klaavrlrdLcer 23 
                                        ++  +rl+++c+ 
  gene1453|gene1453|rna1453|rna1453 262 HTINIRLKEMCDT 274
                                        5677899999976 PP

>> Cyclin_N  Cyclin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0     0.067     2e+02      38     103 ..      99     163 ..      76     181 .. 0.80
   2 ?    9.7   0.1   0.00023      0.69      37     104 ..     192     262 ..     189     281 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.067
                                        HHHHHHHTT--TTHHHHHHHHHHHHHHHS---CCCHHHHHHHHHHHHHHHHSSS---HHHHHHHTT CS
                           Cyclin_N  38 lvevaekfkltpetlflavnyldRflskksvpkdklqlvgatcLllAaKveeisppkledlvyitd 103
                                        + +++ ++ l+ e++  a++ +   l+ + ++ +++     +c+++ ++ e++ p  l d++ + d
  gene1453|gene1453|rna1453|rna1453  99 IKNICGSLGLSDEVAQSAYRWYKLSLQGNLTRGRNILYTLSACIYIVCRQEKT-PHLLIDFAQLLD 163
                                        66777778888888888888888888877777788889999********9888.888888877665 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00023
                                        HHHHHHHHTT--T.THHHHHHHHHHHHHHHS---CCCHHHHHHHHHHHHHHH..HSSS---HHHHHHHTTT CS
                           Cyclin_N  37 wlvevaekfkltp.etlflavnyldRflskksvpkdklqlvgatcLllAaKv..eeisppkledlvyitde 104
                                        +l + ++k+kl++ ++l+ a++++ R+ +  +v  ++ + ++ ++L+ A++v  ee s+ ++ + v ++ +
  gene1453|gene1453|rna1453|rna1453 192 FLHRFFSKLKLKNgKILLFAMRLISRMKRDWIVVGRRPNNLCGAALVTASRVyaEERSVLEVAKAVKVSPH 262
                                        7888899999988358889********************************98888889998888887755 PP

>> Ribosomal_S27e  Ribosomal protein S27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   2.7   9.4e-05      0.28       6      34 ..      18      47 ..      14      50 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 9.4e-05
                                       EEE.E-TTTS-EEEEESS-SS-EEESSSTC CS
                     Ribosomal_S27e  6 ldv.kCpdCenetvvFshaatvvkCisCgk 34
                                       +dv kC+ C+ + +  +h+ + + C +Cg+
  gene1453|gene1453|rna1453|rna1453 18 MDVqKCKTCGSTDIDDGHSTSNICCRKCGT 47
                                       66658************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (429 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       721  (0.0402142); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.70u 0.34s 00:00:01.04 Elapsed: 00:00:00.58
# Mc/sec: 2240.32
//
Query:       gene1454|gene1454|rna1454|rna1454  [L=166]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.4e-15   54.8   0.1    1.7e-14   53.8   0.1    1.6  1  CBFD_NFYB_HMF  Histone-like transcription factor (CBF/NF-Y) a
    2.6e-06   27.8  11.8    0.00019   21.8  11.8    2.3  1  Histone        Core histone H2A/H2B/H3/H4
     0.0075   16.2   0.2      0.011   15.7   0.2    1.3  1  DUF4743        Domain of unknown function (DUF4743)
  ------ inclusion threshold ------
      0.028   14.7   0.4      0.028   14.7   0.4    1.9  2  CENP-X         CENP-S associating Centromere protein X


Domain annotation for each model (and alignments):
>> CBFD_NFYB_HMF  Histone-like transcription factor (CBF/NF-Y) and archaeal histone
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.8   0.1   3.8e-18   1.7e-14       2      63 ..      88     148 ..      87     150 .. 0.93

  Alignments for each domain:
  == domain 1  score: 53.8 bits;  conditional E-value: 3.8e-18
                                        XXXHHHHHHHHHCCTTXS-B-HHHHHHHHHHHHHHHHHHHHHHHHHHCCTTSSCE-HHHHHH CS
                      CBFD_NFYB_HMF   2 eLPiarvkkImksdpdarkiakdAkeliaecveefieelaseAaeickkekrKtikaehikl 63 
                                        ++P ar+kkIm+sd+d++ki+  A++++ +++e+f+ el ++A+++++ +krK +  e+++ 
  gene1454|gene1454|rna1454|rna1454  88 RFPTARIKKIMQSDEDVGKISTYAPVVLGKATELFLFELVNAAVKLAESDKRK-VEVEDLER 148
                                        69**************************************************9.67777765 PP

>> Histone  Core histone H2A/H2B/H3/H4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8  11.8   4.3e-08   0.00019      28     117 ..      53     140 ..       1     151 [. 0.69

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 4.3e-08
                                        TS-SSSSB--TTT-XTTHHHHHHHHHHHHXXSXXSXHHHHHHHHHHHH.TTSSSXEEXHHHHHHHHHHHHHHHHHH CS
                            Histone  28 kasskskkkkkrryrpgtvalkeirkyqkstdlliqklpfaRvvreivksekedlrisaeavlalqealEallvel 103
                                        ++ + + +k +  ++++t+a     +   + +++ +++p aR +++i++s+++  +is +a+++l +a+E +l el
  gene1454|gene1454|rna1454|rna1454  53 TSTQAEDSKLTNGSNTNTSACSSVSTLALD-KKKRFRFPTAR-IKKIMQSDEDVGKISTYAPVVLGKATELFLFEL 126
                                        333333333333333333333333333333.3455679****.********************************* PP

                                        HHHHHHHHHHTTXS CS
                            Histone 104 feeAnllakhaKRv 117
                                           A +la+  KR+
  gene1454|gene1454|rna1454|rna1454 127 VNAAVKLAESDKRK 140
                                        ************96 PP

>> DUF4743  Domain of unknown function (DUF4743)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.2   2.4e-06     0.011      14      94 ..      89     166 .]      76     166 .] 0.83

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.4e-06
                                        --GCCEEEEEETTEEEEEEEHHHHHHHCT-TTTEEE-SS.EEEE-TT--SHHHHHHHHHHHHHHHHHTT...SS-- CS
                            DUF4743  14 ssrseflpFvvegqqvGlirpdvaeklrkfpdvFevsekeaveLapslktyeeRtaaveevleelreegsfvalkg 89 
                                        +  +++++ +  ++ vG i++     l k  + F ++    v+ a +l++ ++R  +ve++ + ++e+++f++lk 
  gene1454|gene1454|rna1454|rna1454  89 FPTARIKKIMQSDEDVGKISTYAPVVLGKATELFLFE---LVNAAVKLAESDKRKVEVEDLERVVKENEQFIFLKS 161
                                        5566677777788899999999999999999999886...457777888899************************ PP

                                        --S-E CS
                            DUF4743  90 wRdEl 94 
                                         R+E+
  gene1454|gene1454|rna1454|rna1454 162 YRNEE 166
                                        ***95 PP

>> CENP-X  CENP-S associating Centromere protein X
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.4      0.74   3.3e+03      48      48 ..      28      28 ..       2      70 .. 0.64
   2 ?   14.7   0.4   6.3e-06     0.028       4      67 ..      94     149 ..      91     152 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.74
                                       H CS
                             CENP-X 48 e 48
                                       +
  gene1454|gene1454|rna1454|rna1454 28 T 28
                                       0 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 6.3e-06
                                        HHHHHCCC-SSTT-EE-CCCHHHHHHHHHHHHHHHHHHHHHHHHHTT-SE.....EECHHHHHH CS
                             CENP-X   4 larlLqesfkdektkItkdalelvaeylklFvrEavaRaaeeaeeegkeeseksklevedLeki 67 
                                        +++++q+   ++  kI++ a  ++ +  +lF  E v  a++ ae+++ ++     +evedLe++
  gene1454|gene1454|rna1454|rna1454  94 IKKIMQSD--EDVGKISTYAPVVLGKATELFLFELVNAAVKLAESDK-RK-----VEVEDLERV 149
                                        55666664..46689**********************9999776654.45.....9******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2017  (0.112499); expected 358.6 (0.02)
Passed bias filter:                      600  (0.0334653); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.55u 0.31s 00:00:00.86 Elapsed: 00:00:00.50
# Mc/sec: 995.45
//
Query:       gene1455|gene1455|rna1455|rna1455  [L=849]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.3e-61  206.2   0.0    4.5e-61  205.8   0.0    1.2  1  GTP_EFTU     Elongation factor Tu GTP binding domain
    1.8e-21   76.2   0.0    1.3e-20   73.4   0.0    2.2  2  EFG_IV       Elongation factor G, domain IV
    9.3e-21   73.7   0.0    3.2e-20   71.9   0.0    2.0  1  EFG_C        Elongation factor G C-terminus
    1.7e-15   57.1   1.8    3.6e-15   56.1   1.8    1.6  1  GTP_EFTU_D2  Elongation factor Tu domain 2
    9.3e-11   41.7   0.0    2.3e-10   40.4   0.0    1.6  1  EFG_II       Elongation Factor G, domain II
     0.0046   17.0   0.2     0.0095   16.0   0.2    1.5  1  MMR_HSR1     50S ribosome-binding GTPase


Domain annotation for each model (and alignments):
>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  205.8   0.0   1.5e-64   4.5e-61       2     183 ..      19     281 ..      18     353 .. 0.77

  Alignments for each domain:
  == domain 1  score: 205.8 bits;  conditional E-value: 1.5e-64
                                        CEEEEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHSTHCHSHHHHHHTSCSSCEEEEEE............. CS
                           GTP_EFTU   2 rirnigiighvDhGKtTLtdrLlyktgaiskkgekaeeervlDtlkeErergiTiksaaisle............. 64 
                                        +irni++i+hvDhGK+TLtd+L+ k+++ s+   +a+++r++Dt+++E+ergiTiks+ais++             
  gene1455|gene1455|rna1455|rna1455  19 NIRNISVIAHVDHGKSTLTDCLVIKAKIASE---DASGKRYMDTREDEQERGITIKSTAISMNfmmnnkvlsehmk 91 
                                        79*************************9888...555689**********************************98 PP

                                        ..TTCSSEEEEEEEESSSGGGHHHHHHHHHT-SEEEEEEETTTBSTHHHHHHHHHHHHTTTEEEEEEESCGSTHHH CS
                           GTP_EFTU  65 ..ketkkylinliDtPGHvdFskevirglrvlDgavlvvdaveGvepqteevlrlalkegvpiivfiNKmDrlkae 138
                                           +++++linliD+PGHvdFs+ev+++lrv+Dgav+v+d+v+G+++qte+vlr+a++e++ + v++NK+Dr+  e
  gene1455|gene1455|rna1455|rna1455  92 qpFNGNSFLINLIDSPGHVDFSSEVTAALRVTDGAVVVIDCVDGICVQTETVLRQAIAERIMPTVVLNKLDRALLE 167
                                        655**********************************************************************999 PP

                                        HHHHHHHHHHHHHHH..............HHHHHHHHHTTT.........TTEEEEEEBTTTTBTHH......... CS
                           GTP_EFTU 139 lkeiveevkqklsrk..............eeklekygekge.........kevpvvfgSalkgegvk......... 182
                                        lke++ ++  kl+r+                         +         ++ ++ f+S+l+g+g++         
  gene1455|gene1455|rna1455|rna1455 168 LKESKLDLAAKLRRRvedfnaklqmicqgA----------DdfhveslfpQKNEISFCSGLQGWGFTlksfakyyi 233
                                        999999999999777666644433333331..........25666666777899**********999666666666 PP

                                        ...............................................H CS
                           GTP_EFTU 183 ...............................................t 183
                                                                                       +
  gene1455|gene1455|rna1455|rna1455 234 kqmkqenkpnpetfvckvlwsegvyyssddpfdpngkflkegppersA 281
                                        666666666666555555555555555555555555555555555550 PP

>> EFG_IV  Elongation factor G, domain IV
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.26   7.9e+02       1      42 [.     569     605 ..     569     618 .. 0.70
   2 !   73.4   0.0   4.2e-24   1.3e-20      11     120 ..     619     729 ..     615     730 .. 0.95

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.26
                                        TCCESCEE.SS-CCHCCCCCCCHTSSSHCCCCCEEEECCTTT CS
                             EFG_IV   1 pqVayrEtirkpvkereeklkkqsggdgqyakvileiePlee 42 
                                        pqV y E i   v   e k+ k     ++  ++ ++ieP+ee
  gene1455|gene1455|rna1455|rna1455 569 PQVTYMEGISATVG--EPKMSK---SPNKHNRIFMCIEPMEE 605
                                        78889987777766..555555...35667799999999872 PP

  == domain 2  score: 73.4 bits;  conditional E-value: 4.2e-24
                                        S-CCHCCCCCCCHTSSSHCCCCCEEEECCTTTTSSEEEEE--STCCCHCCCCHHHHCCCCCCTTS-TTTS--EESE CS
                             EFG_IV  11 kpvkereeklkkqsggdgqyakvileiePleegsgnefvdetkggqvpkeyieavekGfqealkeGplagepvtdv 86 
                                        k+ ker+ ++ +  g++ ++ k+il  +P++ ++ n+++d tkg+++++e++e+  +Gf+e++++Gpl+ge ++++
  gene1455|gene1455|rna1455|rna1455 619 KDPKERSVRFREIMGIKDEWVKKILFYGPED-KGPNIVIDSTKGIAYLNEIKEYMREGFREVTARGPLIGESLRGC 693
                                        56677999*********************87.******************************************** PP

                                        EEEEEEEE--T..TTC-HHHHHHHHCHHHHHHHHCC CS
                             EFG_IV  87 kvtLldgslhe..vdsseaafkpaarralkeallkA 120
                                        ++ L+d++lh+  +++++ ++   +  ++k  +l+A
  gene1455|gene1455|rna1455|rna1455 694 RFDLMDCTLHSdaIHRTGNQISAPMTSVCKGLILAA 729
                                        **********************99999999888877 PP

>> EFG_C  Elongation factor G C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.9   0.0   1.1e-23   3.2e-20       1      87 [.     732     818 ..     732     820 .. 0.97

  Alignments for each domain:
  == domain 1  score: 71.9 bits;  conditional E-value: 1.1e-23
                                        EEEEEEEEEEEEEECCCCCCHHHHHHHCT-EEEEEEEE.TTEEEEEEEEEGGG-TTHHHCHHHCTTTS-EEEEEEE CS
                              EFG_C   1 vllEPivkveievpeeyvgkvisdlssrrGeiedmeqdasgrviieaeiPlaeligfateLrslTkGegsfsmefs 76 
                                        +l+EPi+ +ei+v ++ +g v s ls+rrG  e+++ d++ r+ii++ +P++e++gf+++L  +T+Ge+s+ ++fs
  gene1455|gene1455|rna1455|rna1455 732 ILYEPIFLAEISVASDQIGGVNSVLSQRRGVAEEYKCDGGMRTIITGYLPVRESFGFNSALLMATRGEASVVLTFS 807
                                        589************************************************************************* PP

                                        EEEE--HHHHH CS
                              EFG_C  77 gYeevpgdkld 87 
                                        +Y+ +pg++ d
  gene1455|gene1455|rna1455|rna1455 808 HYSVLPGSLSD 818
                                        ******98765 PP

>> GTP_EFTU_D2  Elongation factor Tu domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.1   1.8   1.2e-18   3.6e-15       2      74 .]     404     480 ..     403     480 .. 0.96

  Alignments for each domain:
  == domain 1  score: 56.1 bits;  conditional E-value: 1.2e-18
                                        EEEEEEEEESEEETTEEEEEEC.TCTTSEE...EEEEEEEEEEETEEESEEETTSEEEEEEEESSCCSGSSTTCEE CS
                        GTP_EFTU_D2   2 tvalgrvysGtlkkGdevrilg.ndtskke...ivtrissletfhededeavaganaGvivaikgledaiivGdtl 73 
                                        ++a grv+sG++k+G++vri g ++t +++   +v +i+++ ++++++  ++++++aG+iv+++g+++ ++++ t+
  gene1455|gene1455|rna1455|rna1455 404 FIAMGRVFSGVIKPGMKVRIQGpDYTVGSKtdlHVKTIQRTVVMMGRVVKDIDECPAGNIVGLIGIDSELKKTGTI 479
                                        6899**********************9999**************************************99999888 PP

                                        E CS
                        GTP_EFTU_D2  74 t 74 
                                        t
  gene1455|gene1455|rna1455|rna1455 480 T 480
                                        5 PP

>> EFG_II  Elongation Factor G, domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.4   0.0   7.7e-14   2.3e-10       4      69 ..     497     561 ..     495     567 .. 0.94

  Alignments for each domain:
  == domain 1  score: 40.4 bits;  conditional E-value: 7.7e-14
                             EFG_II   4 PvislaiepkskadedklskaLarlleEDptlrverdeeTketilsGmGelHleivverlkreykv 69 
                                        Pv+++a++p++  d  kl++ L +l++ Dp  +v++  + +e+ l+G GelHlei +e l++ey +
  gene1455|gene1455|rna1455|rna1455 497 PVVKYALRPANPVDLPKLKAGLIKLSKSDPLTQVNFS-DNGELTLAGAGELHLEISLEDLRKEYAC 561
                                        9******************************999996.569**********************975 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.2   3.2e-06    0.0095       3     114 .]      24     160 ..      22     160 .. 0.59

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 3.2e-06
                                        EEEESTTSSHHHHHHHHH...........T.S...TEEESSSTTSSSSEEEEEEEETTEE................ CS
                           MMR_HSR1   3 aivGrpNvGKStLinalt...........g.e...kaivsdkpgtTrdinegrvklkgke................ 47 
                                         ++ +   GKStL   l+           g +   + + +++ g T++ +                          
  gene1455|gene1455|rna1455|rna1455  24 SVIAHVDHGKSTLTDCLVikakiasedasGkRymdTREDEQERGITIKST---------Aismnfmmnnkvlsehm 90 
                                        56667788*********944433333222111111223333334444444.........13444444456777778 PP

                                        ..........EEEEECGGCSSHHHHHHHHHHHHHHHHC.TSEEEEEEETTTTCSHHHHHHHHHHHHHTTSEEEEEE CS
                           MMR_HSR1  48 ..........ielvDtpGliegaseekglgkaflalee.adlillvvdaseeklkpldeeleelleeakkplilvl 112
                                                  i+l+D pG ++       ++ ++ a  + +d +++v+d+  +++  + e++ +    +++  ++vl
  gene1455|gene1455|rna1455|rna1455  91 kqpfngnsflINLIDSPGHVD-------FSSEVTAALRvTDGAVVVIDCV-DGICVQTETVLRQAIAERIMPTVVL 158
                                        8888888999********665.......666666666647********99.4454444555444433444557777 PP

                                        ES CS
                           MMR_HSR1 113 nk 114
                                        nk
  gene1455|gene1455|rna1455|rna1455 159 NK 160
                                        76 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (849 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       579  (0.032294); expected 358.6 (0.02)
Passed bias filter:                      545  (0.0303977); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.73u 0.31s 00:00:01.04 Elapsed: 00:00:00.49
# Mc/sec: 5203.77
//
Query:       gene1456|gene1456|rna1456|rna1456  [L=84]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (84 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       874  (0.0487478); expected 358.6 (0.02)
Passed bias filter:                      255  (0.0142228); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 624.92
//
Query:       gene1457|gene1457|rna1457|rna1457  [L=1518]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1518 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1442  (0.0804284); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 1.15u 0.35s 00:00:01.50 Elapsed: 00:00:00.56
# Mc/sec: 8213.79
//
Query:       gene1458|gene1458|rna1458|rna1458  [L=144]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-07   31.6   8.6    2.2e-07   31.2   8.6    1.1  1  Cornichon        Cornichon protein
  ------ inclusion threshold ------
       0.13   12.0   0.1       0.24   11.1   0.1    1.4  1  Cation_ATPase_N  Cation transporter/ATPase, N-terminus


Domain annotation for each model (and alignments):
>> Cornichon  Cornichon protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.2   8.6   2.5e-11   2.2e-07       6     120 ..      19     130 ..      14     132 .. 0.92

  Alignments for each domain:
  == domain 1  score: 31.2 bits;  conditional E-value: 2.5e-11
                          Cornichon   6 laliltaallflsvyfiialsDleadyinpidlcsklNplvlpelilhafltllfllsgewilfllnlpllayniy 81 
                                        l ++l+++l  + ++ + al  +e +y+ + d++ + N+lv  e++  +++++l +l   +il+   l++ +y+i+
  gene1458|gene1458|rna1458|rna1458  19 LLFFLSLILTSIELHKLEALVHFEKNYKISHDIAYQFNRLVTSEAVPFIIFMILNFLRPTIILL---LIVGFYEIH 91 
                                        67999***************************************99888888888887777777...67789**** PP

                          Cornichon  82 rvmskqglydpteifnqlkkhkkesmiklafylllffiy 120
                                        +v+++q++++p+ +  ++   kke  +k ++yl lf++y
  gene1458|gene1458|rna1458|rna1458  92 KVVKEQNFVNPVYLKDEVGFRKKEVCLKAILYLCLFVFY 130
                                        ***********************************9998 PP

>> Cation_ATPase_N  Cation transporter/ATPase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   2.7e-05      0.24      35      66 ..      55      86 ..      49      88 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 2.7e-05
                    Cation_ATPase_N 35 pNelkekkkkslwvkllkqftnplvilLlvaa 66
                                        N+l   + ++++ + + +f  p++ilLl+++
  gene1458|gene1458|rna1458|rna1458 55 FNRLVTSEAVPFIIFMILNFLRPTIILLLIVG 86
                                       59999************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       744  (0.041497); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 967.29
//
Query:       gene1459|gene1459|rna1459|rna1459  [L=38]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (38 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       304  (0.0169558); expected 358.6 (0.02)
Passed bias filter:                      223  (0.0124379); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.30u 0.26s 00:00:00.56 Elapsed: 00:00:00.39
# Mc/sec: 292.94
//
Query:       gene146|gene146|rna146|rna146  [L=96]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.1e-09   35.6   0.5      1e-08   35.1   0.5    1.3  1  Integrase_H2C2  Integrase zinc binding domain
      0.002   18.3   0.1     0.0042   17.3   0.1    1.5  1  zf-H2C2         H2C2 zinc finger
  ------ inclusion threshold ------
       0.11   12.4   2.4       0.37   10.8   0.0    2.3  2  Hemopexin       Hemopexin


Domain annotation for each model (and alignments):
>> Integrase_H2C2  Integrase zinc binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.1   0.5   1.7e-12     1e-08       7      57 ..      39      88 ..      33      89 .. 0.87

  Alignments for each domain:
  == domain 1  score: 35.1 bits;  conditional E-value: 1.7e-12
                 Integrase_H2C2  7 keilkeaHdsagHlGiektlerlrrryyWpgmrkdvkkyvksCetCqrrkp 57
                                   k i++++ ++  H   e  +  l++ryyW gm++++ +++k+ etCq +++
  gene146|gene146|rna146|rna146 39 KPIIEAYLKT-NHRKLEPIYYELKERYYWLGMKRHITEIIKRYETCQWNNR 88
                                   5567777775.9***********************************8875 PP

>> zf-H2C2  H2C2 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.1   7.1e-07    0.0042      15      39 .]      60      84 ..      59      84 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 7.1e-07
                        zf-H2C2 15 larkYhwlgiketvseVissCkaCq 39
                                   l+++Y+wlg k+++ e+i++  +Cq
  gene146|gene146|rna146|rna146 60 LKERYYWLGMKRHITEIIKRYETCQ 84
                                   6899***************988887 PP

>> Hemopexin  Hemopexin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   6.2e-05      0.37      17      26 ..      17      26 ..      15      39 .. 0.79
   2 ?    0.2   0.8      0.13   7.7e+02      16      21 ..      61      66 ..      57      68 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 6.2e-05
                                   TTEEEEEETT CS
                      Hemopexin 17 GdkYWrfdpq 26
                                   G+kYWrfd+ 
  gene146|gene146|rna146|rna146 17 GKKYWRFDSG 26
                                   9*******87 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.13
                                   ETTEEE CS
                      Hemopexin 16 kGdkYW 21
                                   k ++YW
  gene146|gene146|rna146|rna146 61 KERYYW 66
                                   899*** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       652  (0.0363657); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.46
# Mc/sec: 632.94
//
Query:       gene1460|gene1460|rna1460|rna1460  [L=284]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-36  124.2   9.6    2.9e-15   56.2   0.1    3.5  3  Myb_DNA-binding  Myb-like DNA-binding domain
    1.1e-28   99.3  16.8    3.9e-11   43.0   0.3    4.5  5  Myb_DNA-bind_6   Myb-like DNA-binding domain
    8.1e-08   32.4   6.3     0.0093   16.1   0.1    3.8  3  SANT_DAMP1_like  SANT/Myb-like domain of DAMP1
    0.00097   19.0  10.0      0.027   14.3   0.2    4.2  4  Myb_DNA-bind_7   Myb DNA-binding like
     0.0017   18.2   0.0        1.5    8.5   0.0    2.9  3  DUF4872          Domain of unknown function (DUF4872)
     0.0086   16.8   2.1      0.034   14.9   0.1    2.6  3  DUF4326          Domain of unknown function (DUF4326)
  ------ inclusion threshold ------
       0.01   15.9   0.1        1.3    9.1   0.0    2.9  2  HTH_16           Helix-turn-helix domain
       0.14   12.4   0.8        1.7    8.9   0.1    2.3  2  DUF4279          Domain of unknown function (DUF4279)
        0.9    9.0  12.0       0.48    9.9   1.6    2.7  3  TryThrA_C        Tryptophan-Threonine-rich plasmodium antigen


Domain annotation for each model (and alignments):
>> Myb_DNA-binding  Myb-like DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.9   0.0   6.6e-12   1.3e-08       1      45 [.     137     180 ..     137     181 .. 0.93
   2 !   56.2   0.1   1.4e-18   2.9e-15       2      46 .]     186     230 ..     185     230 .. 0.97
   3 !   36.3   2.5   2.4e-12   4.8e-09       1      45 [.     234     277 ..     234     278 .. 0.95

  Alignments for each domain:
  == domain 1  score: 34.9 bits;  conditional E-value: 6.6e-12
                                        CSSSBHHHHHHHHHHHHHHTTCHHHHHHHHTSS-HHHHHHHHHHH CS
                    Myb_DNA-binding   1 rgkWteeEdelLleavkkhGnrWkkIaerlggRtekqcrsrwrny 45 
                                        + k+t  E ++L ++v khGn+W  Ia++l ++t+ qc   +r+y
  gene1460|gene1460|rna1460|rna1460 137 KDKFTSSEIDKLKDLVSKHGNNWVIIAKYL-NKTPQQCLQCYRRY 180
                                        579***************************.8******8888877 PP

  == domain 2  score: 56.2 bits;  conditional E-value: 1.4e-18
                                        SSSBHHHHHHHHHHHHHHTTCHHHHHHHHTSS-HHHHHHHHHHHT CS
                    Myb_DNA-binding   2 gkWteeEdelLleavkkhGnrWkkIaerlggRtekqcrsrwrnyl 46 
                                        g+W++ EdelL +av+k+G++W +++e++g+R++ qcr+r+ n+l
  gene1460|gene1460|rna1460|rna1460 186 GRWSKKEDELLMQAVQKFGKKWITVSEYIGTRSDLQCRERYINVL 230
                                        89***************************************9986 PP

  == domain 3  score: 36.3 bits;  conditional E-value: 2.4e-12
                                        CSSSBHHHHHHHHHHHHHHTTCHHHHHHHHTSS-HHHHHHHHHHH CS
                    Myb_DNA-binding   1 rgkWteeEdelLleavkkhGnrWkkIaerlggRtekqcrsrwrny 45 
                                        r++Wt+ ++e L ++v k+G +Wk+I + l gR  k+cr r+ ++
  gene1460|gene1460|rna1460|rna1460 234 RKEWTKNDEEELKQLVSKLGQKWKEIGNLL-GRNNKECRRRYFKV 277
                                        789***************************.6**********985 PP

>> Myb_DNA-bind_6  Myb-like DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.1     0.049        97       6      32 ..       6      34 ..       4      45 .. 0.84
   2 ?   -3.2   0.0       5.4   1.1e+04      16      28 ..      65      77 ..      54      81 .. 0.60
   3 !   30.1   0.1   2.1e-10   4.1e-07       1      45 [.     140     183 ..     140     187 .. 0.91
   4 !   43.0   0.3     2e-14   3.9e-11       1      48 [.     188     235 ..     188     236 .. 0.96
   5 !   32.4   1.1     4e-11   7.9e-08       1      44 [.     237     278 ..     237     284 .] 0.91

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.049
                     Myb_DNA-bind_6  6 deiLlklvekygn..dWknIaealnrRtp 32
                                       +++Llk+++  ++    + I +al+ R++
  gene1460|gene1460|rna1460|rna1460  6 KQLLLKYYQLKSFykRLSVIKKALHTRQS 34
                                       589*******996668999*999985665 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 5.4
                     Myb_DNA-bind_6 16 ygndWknIaealn 28
                                       ++  W nI+++ +
  gene1460|gene1460|rna1460|rna1460 65 NNTLWINIESICG 77
                                       3445889988775 PP

  == domain 3  score: 30.1 bits;  conditional E-value: 2.1e-10
                     Myb_DNA-bind_6   1 WteeEdeiLlklvekygndWknIaealnrRtpkqcfdrwknkLrp 45 
                                        +t  E ++L +lv+k+gn+W  Ia+ ln +tp+qc + +++ +r 
  gene1460|gene1460|rna1460|rna1460 140 FTSSEIDKLKDLVSKHGNNWVIIAKYLN-KTPQQCLQCYRRYIRK 183
                                        78999***********************.******9999997765 PP

  == domain 4  score: 43.0 bits;  conditional E-value: 2e-14
                     Myb_DNA-bind_6   1 WteeEdeiLlklvekygndWknIaealnrRtpkqcfdrwknkLrpkis 48 
                                        W++ Ede+L + v+k+g++W +++e ++ R+ +qc++r++n+L+++++
  gene1460|gene1460|rna1460|rna1460 188 WSKKEDELLMQAVQKFGKKWITVSEYIGTRSDLQCRERYINVLDVDRK 235
                                        ***************************99*************998876 PP

  == domain 5  score: 32.4 bits;  conditional E-value: 4e-11
                     Myb_DNA-bind_6   1 WteeEdeiLlklvekygndWknIaealnrRtpkqcfdrwknkLr 44 
                                        Wt+ ++e+L +lv+k g++Wk+I + l+ R+ k+c++r+ + + 
  gene1460|gene1460|rna1460|rna1460 237 WTKNDEEELKQLVSKLGQKWKEIGNLLG-RNNKECRRRYFK-VI 278
                                        ****************************.**********88.43 PP

>> SANT_DAMP1_like  SANT/Myb-like domain of DAMP1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.0   0.00074       1.5      25      53 ..     136     164 ..     127     175 .. 0.83
   2 !   16.1   0.1   4.7e-06    0.0093      18      52 ..     175     211 ..     164     218 .. 0.85
   3 !    7.9   1.1    0.0017       3.4      18      79 ..     224     281 ..     218     282 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00074
                    SANT_DAMP1_like  25 keedWtkeetdyLfdlckeydlrfvviaD 53 
                                        ++++ t +e+d+L dl+++    +v+ia 
  gene1460|gene1460|rna1460|rna1460 136 TKDKFTSSEIDKLKDLVSKHGNNWVIIAK 164
                                        44789*********************985 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 4.7e-06
                    SANT_DAMP1_like  18 eeYeellkeed..WtkeetdyLfdlckeydlrfvvia 52 
                                        + Y+++++++   W+k+e + L++ ++++  +++ + 
  gene1460|gene1460|rna1460|rna1460 175 QCYRRYIRKSAgrWSKKEDELLMQAVQKFGKKWITVS 211
                                        6799999996455*********************986 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.0017
                    SANT_DAMP1_like  18 eeYeellke..edWtkeetdyLfdlckeydlrfvviaDryelekkkkrsledlkeryYsvarkl 79 
                                        e Y ++l    ++Wtk++ + L +l+++   ++  i +    +        + ++ry++v +k+
  gene1460|gene1460|rna1460|rna1460 224 ERYINVLDVdrKEWTKNDEEELKQLVSKLGQKWKEIGNLLGRN------NKECRRRYFKVIKKM 281
                                        6788888774467********************9887765443......345666777776665 PP

>> Myb_DNA-bind_7  Myb DNA-binding like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.1      0.18   3.5e+02      16      44 ..      15      43 ..       5      67 .. 0.76
   2 ?    3.9   0.1     0.026        51       4      40 ..     133     169 ..     132     182 .. 0.84
   3 !   14.3   0.2   1.4e-05     0.027       5      49 ..     182     226 ..     176     228 .. 0.90
   4 ?    3.4   0.4     0.035        69       8      49 ..     234     274 ..     231     282 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.18
                     Myb_DNA-bind_7 16 tekFYkaLsqfGtDFsliaklfpkrtrrq 44
                                        + FYk Ls +   +++ ++lf++  r+q
  gene1460|gene1460|rna1460|rna1460 15 LKSFYKRLSVIKKALHTRQSLFKYPVRSQ 43
                                       56788888888888877777777754444 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.026
                     Myb_DNA-bind_7   4 krkktkkWskeetekFYkaLsqfGtDFsliaklfpkr 40 
                                        k+++++k +++e +k  + +s+ G ++ +iak+++k 
  gene1460|gene1460|rna1460|rna1460 133 KKTTKDKFTSSEIDKLKDLVSKHGNNWVIIAKYLNKT 169
                                        67889999************************99764 PP

  == domain 3  score: 14.3 bits;  conditional E-value: 1.4e-05
                     Myb_DNA-bind_7   5 rkktkkWskeetekFYkaLsqfGtDFsliaklfpkrtrrqlKlKF 49 
                                        rk + +Wsk+e e+  +a+++fG  + +++++   r++ q ++++
  gene1460|gene1460|rna1460|rna1460 182 RKSAGRWSKKEDELLMQAVQKFGKKWITVSEYIGTRSDLQCRERY 226
                                        456789********************************9999988 PP

  == domain 4  score: 3.4 bits;  conditional E-value: 0.035
                     Myb_DNA-bind_7   8 tkkWskeetekFYkaLsqfGtDFsliaklfpkrtrrqlKlKF 49 
                                        +k+W+k++ e+  + +s++G+ ++ i +l+  r+ ++ ++++
  gene1460|gene1460|rna1460|rna1460 234 RKEWTKNDEEELKQLVSKLGQKWKEIGNLLG-RNNKECRRRY 274
                                        689********************99999984.5566666655 PP

>> DUF4872  Domain of unknown function (DUF4872)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0     0.012        24     114     170 ..     139     195 ..     132     198 .. 0.83
   2 ?    4.4   0.0     0.014        28     104     145 ..     177     218 ..     175     232 .. 0.88
   3 !    8.5   0.0   0.00076       1.5     115     158 ..     238     280 ..     223     282 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.012
                            DUF4872 114 llgdealaelseamteaadaWtelAalaaeasksreardlaeaadaleelaelEeel 170
                                         + ++++ +l++++++ +++W  +A+ +++  +++ +   + +++ + + +++E el
  gene1460|gene1460|rna1460|rna1460 139 KFTSSEIDKLKDLVSKHGNNWVIIAKYLNKTPQQCLQCYRRYIRKSAGRWSKKEDEL 195
                                        56678999********************99999997446667888888888888887 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.014
                            DUF4872 104 yadFlqeaaellgdealaelseamteaadaWtelAalaaeas 145
                                        y+++++++a ++++++ + l +a+++ +++W ++++ + ++s
  gene1460|gene1460|rna1460|rna1460 177 YRRYIRKSAGRWSKKEDELLMQAVQKFGKKWITVSEYIGTRS 218
                                        999******************************999886655 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.00076
                            DUF4872 115 lgdealaelseamteaadaWtelAalaaeasksreardlaeaad 158
                                        +++++ +el++++++++++W+e+ +l+ ++ k++++r ++ +++
  gene1460|gene1460|rna1460|rna1460 238 TKNDE-EELKQLVSKLGQKWKEIGNLLGRNNKECRRRYFKVIKK 280
                                        44444.89*************************99777766655 PP

>> DUF4326  Domain of unknown function (DUF4326)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       4.3   8.5e+03      36      36 ..      81      81 ..      40     110 .. 0.56
   2 !   14.9   0.1   1.7e-05     0.034      18      65 ..     152     206 ..     132     211 .. 0.82
   3 ?    0.6   0.1       0.5   9.9e+02      34      64 ..     219     254 ..     209     270 .. 0.74

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 4.3
                            DUF4326 36 e 36
                                       +
  gene1460|gene1460|rna1460|rna1460 81 T 81
                                       2 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 1.7e-05
                            DUF4326  18 gsklgNpFvvgqe..lgereevvekyreyleer.....aekdeelkaaleeLrgk 65 
                                         sk gN +v+ ++   ++ +++++ yr+y++++     +++de l++a+++ ++k
  gene1460|gene1460|rna1460|rna1460 152 VSKHGNNWVIIAKylNKTPQQCLQCYRRYIRKSagrwsKKEDELLMQAVQKFGKK 206
                                        5799*****9999888999*************9999988889999***9999887 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.5
                            DUF4326  34 reevvekyreyleer.....aekdeelkaaleeLrg 64 
                                        + ++ e+y + l  +     ++++eelk+ + +L++
  gene1460|gene1460|rna1460|rna1460 219 DLQCRERYINVLDVDrkewtKNDEEELKQLVSKLGQ 254
                                        457888888888777666655666667777777765 PP

>> HTH_16  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0     0.039        77      21      41 ..      82     102 ..      81     111 .. 0.74
   2 ?    9.1   0.0   0.00067       1.3      17      39 ..     172     194 ..     170     203 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.039
                             HTH_16  21 hYegyIrklSlrklydedgnv 41 
                                        +Y  y++k+++  + de  ++
  gene1460|gene1460|rna1460|rna1460  82 MYGKYLNKYCTHRKDDELDTT 102
                                        8**********7666665555 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00067
                             HTH_16  17 eiLkhYegyIrklSlrklydedg 39 
                                        + L++Y+ yIrk + r  ++ed+
  gene1460|gene1460|rna1460|rna1460 172 QCLQCYRRYIRKSAGRWSKKEDE 194
                                        679***********998888875 PP

>> DUF4279  Domain of unknown function (DUF4279)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0      0.16   3.2e+02      54      87 ..     146     182 ..     131     217 .. 0.63
   2 ?    8.9   0.1   0.00084       1.7      48      85 ..     236     274 ..     224     283 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.16
                            DUF4279  54 eqldklldrlepkaekikelak...kygleiylqvvi 87 
                                        ++l++l+++  +++ +i+++ +   +++l++y ++++
  gene1460|gene1460|rna1460|rna1460 146 DKLKDLVSKHGNNWVIIAKYLNktpQQCLQCYRRYIR 182
                                        3455556666666666666666344444444433333 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00084
                            DUF4279  48 e.sldleeqldklldrlepkaekikelakkygleiylqv 85 
                                        e +++ ee l++l+++l +k+++i +l  + + e++ ++
  gene1460|gene1460|rna1460|rna1460 236 EwTKNDEEELKQLVSKLGQKWKEIGNLLGRNNKECRRRY 274
                                        4578899*********************99998887555 PP

>> TryThrA_C  Tryptophan-Threonine-rich plasmodium antigen C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.1       1.6   3.1e+03     160     185 ..      43      69 ..      16      94 .. 0.53
   2 ?    9.8   4.9   0.00026      0.51      14      92 ..     175     256 ..     162     256 .. 0.80
   3 ?    9.9   1.6   0.00024      0.48      15      52 ..     225     261 ..     221     282 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.6
                          TryThrA_C 160 kkekeewkkWvkekekk.yinkkwkkw 185
                                        +++  ++++ v++++ + +++ +++ w
  gene1460|gene1460|rna1460|rna1460  43 QDKDLNINRIVEKRNIMeLMDINNTLW 69 
                                        444444444444443221222233333 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00026
                          TryThrA_C  14 ekFneslenekkkwlekkekeweewlkeienKWlhynekldeeyksdilkks...skwdeeqweewiktegkklie 86 
                                        + +  +++++  +w +k+++ + + ++++ +KW  ++e++ +  + +  +++   +++d ++w++  ++e+k+l+ 
  gene1460|gene1460|rna1460|rna1460 175 QCYRRYIRKSAGRWSKKEDELLMQAVQKFGKKWITVSEYIGTRSDLQCRERYinvLDVDRKEWTKNDEEELKQLVS 250
                                        5688899999******************************999999988876111556777888877888888887 PP

                          TryThrA_C  87 kdwkkw 92 
                                        k  +kw
  gene1460|gene1460|rna1460|rna1460 251 KLGQKW 256
                                        766666 PP

  == domain 3  score: 9.9 bits;  conditional E-value: 0.00024
                          TryThrA_C  15 kFneslenekkkwlekkekeweewlkeienKWlhynek 52 
                                        ++ + l+ ++k+w ++ e+e+++ ++++ +KW+++  +
  gene1460|gene1460|rna1460|rna1460 225 RYINVLDVDRKEWTKNDEEELKQLVSKLGQKWKEIG-N 261
                                        67788999999*********************9987.3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (284 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1097  (0.0611858); expected 358.6 (0.02)
Passed bias filter:                      489  (0.0272742); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 2058.61
//
Query:       gene1461|gene1461|rna1461|rna1461  [L=280]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       513  (0.0286129); expected 358.6 (0.02)
Passed bias filter:                      192  (0.0107089); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1976.16
//
Query:       gene1462|gene1462|rna1462|rna1462  [L=340]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.1e-09   37.8   4.0    2.6e-05   24.9   0.5    3.5  3  WD40           WD domain, G-beta repeat
     0.0011   17.8   0.4       0.22   10.2   0.1    3.4  3  Nucleoporin_N  Nup133 N terminal like
     0.0062   15.9   9.5       0.18   11.1   3.2    3.2  3  WD40_like      WD40-like domain
  ------ inclusion threshold ------
      0.074   11.7   0.3       0.66    8.6   0.1    2.4  3  Nup160         Nucleoporin Nup120/160


Domain annotation for each model (and alignments):
>> WD40  WD domain, G-beta repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.0   8.1e-05      0.36       7      38 .]      93     126 ..      85     126 .. 0.61
   2 !   24.9   0.5   5.9e-09   2.6e-05       7      38 .]     139     171 ..     131     171 .. 0.86
   3 ?   -0.7   0.0      0.69   3.1e+03      10      19 ..     218     228 ..     213     234 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 8.1e-05
                                        EESS.SSEEEEEEETTSSE.......EEEEETTSEEEEEE CS
                               WD40   7 ltGH.ssvtslafspdgaw.......lasGsdDgtvriWd 38 
                                        l+GH +++ ++               ++s+s D t+r+Wd
  gene1462|gene1462|rna1462|rna1462  93 LKGHgGPIIDML------HkevrpniVFSASSDTTIRMWD 126
                                        567755544552......23333333556666*******9 PP

  == domain 2  score: 24.9 bits;  conditional E-value: 5.9e-09
                                        EESSSS.EEEEEEETTSSEEEEEETTSEEEEEE CS
                               WD40   7 ltGHss.vtslafspdgawlasGsdDgtvriWd 38 
                                        l GH + v s++ s dg++l+s++ D+++++W+
  gene1462|gene1462|rna1462|rna1462 139 LAGHEDvVLSIDISVDGNYLVSSGTDNSIKVWS 171
                                        569*7757************98888*******5 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.69
                                        S.SSEEEEEEE CS
                               WD40  10 H.ssvtslafs 19 
                                        H   +++++f 
  gene1462|gene1462|rna1462|rna1462 218 HkAYINCVKFF 228
                                        7344****775 PP

>> Nucleoporin_N  Nup133 N terminal like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.1   4.9e-05      0.22     202     233 ..      98     129 ..      76     224 .. 0.94
   2 ?    2.0   0.1     0.015        67     210     256 ..     235     280 ..     231     299 .. 0.83
   3 ?    1.4   0.0     0.024   1.1e+02     203     231 ..     304     338 ..     301     340 .] 0.83

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 4.9e-05
                                        G-EEEEEEECCT.CEEEEEETTSEEEEEEEETT CS
                      Nucleoporin_N 202 eeivqlridssr.rilytlsskgvirvydlsas 233
                                         +i+ + + + r +i++++ss+ +ir++dl+ +
  gene1462|gene1462|rna1462|rna1462  98 GPIIDMLHKEVRpNIVFSASSDTTIRMWDLQ-R 129
                                        57999999999*******************9.4 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.015
                                        ECCTCEEEEEETTSEEEEEEEETTCEE-EEEEEEEHHHHHHHH.HHS CS
                      Nucleoporin_N 210 dssrrilytlsskgvirvydlsasngesslksdidirqilleaites 256
                                         +++++l ++  kg+ ++y+ s ++ +  + +++ ++++l++++t +
  gene1462|gene1462|rna1462|rna1462 235 KNISKRLSIVKFKGTYEIYKNSVDS-DVIILKEYKFKEKLIHRFTIF 280
                                        46779999************99665.7**************995544 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.024
                                        -EEEEEEECCT......CEEEEEETTSEEEEEEEE CS
                      Nucleoporin_N 203 eivqlridssr......rilytlsskgvirvydls 231
                                        ++ +  id+ +      ++l+++s+  ++++y ++
  gene1462|gene1462|rna1462|rna1462 304 PVLAAQIDNVKdaslinNLLFIVSNNNEVHCYTIN 338
                                        56667777777888899***************997 PP

>> WD40_like  WD40-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0     0.078   3.5e+02      64     143 ..      35     122 ..      14     135 .. 0.58
   2 !    6.4   0.1    0.0011       4.9       3      38 ..     146     181 ..     144     187 .. 0.87
   3 !   11.1   3.2   4.1e-05      0.18      44     141 ..     230     330 ..     208     339 .. 0.76

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.078
                          WD40_like  64 tillsllenee.evenekieedistv..kviddk.lliGtnkGsiyv..fskdlqleevllgqsseIkeikie... 130
                                        +i++++le+ +   ++ + ee +s+   +  d+  l++ +++G + +  +    ++ + l g++ +I ++  +   
  gene1462|gene1462|rna1462|rna1462  35 YIMNHDLEQLQkYLDEDDKEEFLSCTfyDLKDKTlLVLAGERGILKIidLCTG-SFYMALKGHGGPIIDMLHKevr 109
                                        56666666655456666666655554113333331445667776665222223.4556666777777777554222 PP

                          WD40_like 131 nnkiysLsesafi 143
                                         n+++s s+++ i
  gene1462|gene1462|rna1462|rna1462 110 PNIVFSASSDTTI 122
                                        4677777666554 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0011
                          WD40_like   3 iYsidiskkgslilyGgkddkctvlkleslesvsiv 38 
                                        + sidis +g++++  g d+ ++v ++++ +s  ++
  gene1462|gene1462|rna1462|rna1462 146 VLSIDISVDGNYLVSSGTDNSIKVWSIPNITSEVVI 181
                                        679************************998776555 PP

  == domain 3  score: 11.1 bits;  conditional E-value: 4.1e-05
                          WD40_like  44 SvifvklldddlilvvtlDGtillsllenee...evenekieed.istvkviddklliGtnkGsiyvfskdlqlee 115
                                         vi +k +++ l +v    Gt   ++ + +    + ++ k +e  i   ++ +  l++  +kG+ y+ +  l++e 
  gene1462|gene1462|rna1462|rna1462 230 NVIISKNISKRLSIV-KFKGTYEIYKNSVDSdviILKEYKFKEKlIHRFTIFGTTLVVFDEKGNCYTINLSLCNEP 304
                                        456666666665554.455655444444444335557777777646778888999********************* PP

                          WD40_like 116 vllgqsseIkeikiennkiysLsesa 141
                                        vl  q  ++k+ + +nn ++  s+++
  gene1462|gene1462|rna1462|rna1462 305 VLAAQIDNVKDASLINNLLFIVSNNN 330
                                        ********************999986 PP

>> Nup160  Nucleoporin Nup120/160
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.13   5.8e+02     300     344 ..      22      66 ..      10      78 .. 0.75
   2 ?    8.6   0.1   0.00015      0.66     223     252 ..     105     132 ..      98     140 .. 0.78
   3 ?   -0.9   0.0      0.11   4.9e+02     222     248 ..     148     173 ..     139     177 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.13
                                        GG-EEEEEEEEEEE-...SSSEEEEES-S------S-TT....--EEEE CS
                             Nup160 300 sggefkvwkvkkedtsvslglvdlfleqtivpadpdssn....vweLrD 344
                                         ++ f+v++ + ++    + + dl + q+++++d+++++    +++L+D
  gene1462|gene1462|rna1462|rna1462  22 RKKIFCVYG-RRNAY---IMNHDLEQLQKYLDEDDKEEFlsctFYDLKD 66 
                                        556677777.44444...5567889999999999888889999999999 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00015
                                        T.....TTTEEEEEETT-EEEEEETTTTEE CS
                             Nup160 223 vavveigqtylfalsrdgkLrvWnlltgkc 252
                                         ++v    +++f++s+d ++r+W+l+ +++
  gene1462|gene1462|rna1462|rna1462 105 HKEV--RPNIVFSASSDTTIRMWDLQRACT 132
                                        3444..589****************87665 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 0.11
                                        ET.....TTTEEEEEETT-EEEEEETT CS
                             Nup160 222 avavveigqtylfalsrdgkLrvWnll 248
                                        +++++  + +yl++   d+ ++vW++ 
  gene1462|gene1462|rna1462|rna1462 148 SIDISV-DGNYLVSSGTDNSIKVWSIP 173
                                        444454.8999*************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (340 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       472  (0.0263261); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.21s 00:00:00.68 Elapsed: 00:00:00.38
# Mc/sec: 2657.56
//
Query:       gene1463|gene1463|rna1463|rna1463  [L=203]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.088   13.0   0.1        0.2   11.9   0.1    1.7  1  Clavanin       Clavanin
       0.51    9.4  12.7       0.74    8.8  12.7    1.2  1  Atg14          Vacuolar sorting 38 and autophagy-related subu
       0.52   11.2   4.3         11    7.0   0.1    2.8  3  Cytochrom_C_2  Cytochrome C'
        5.6    6.2   6.2        7.6    5.8   6.2    1.2  1  DUF4407        Domain of unknown function (DUF4407)


Domain annotation for each model (and alignments):
>> Clavanin  Clavanin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   4.5e-05       0.2      24      60 ..      39      75 ..      27     100 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 4.5e-05
                           Clavanin 24 kaeeekvlrllgkvihgvgnlvygisvvlgddqqdng 60
                                         ++e +++l  kvi+++ n   ++ +v+gd+q dn 
  gene1463|gene1463|rna1463|rna1463 39 LNQKEDIIQLQNKVIKQLENNNQKMKMVYGDEQYDND 75
                                       567899*****************************95 PP

>> Atg14  Vacuolar sorting 38 and autophagy-related subunit 14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8  12.7   0.00017      0.74      22     141 ..      16     151 ..       4     178 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00017
                              Atg14  22 erlyelrerlaklksekeslkkkiekalegkeeaeqledkiknkkakleelksliadlrerlqelkdklsqlkkei 97 
                                        e  +++  +l+klk e e++k+ +++++   +    l++k+ ++ ++ +++ + +   ++  + l+ +l  l+++i
  gene1463|gene1463|rna1463|rna1463  16 EEAEKKEMELKKLKREYEHMKGSLNQKEDIIQ----LQNKVIKQLENNNQKMKMVYGDEQYDNDLESSLVLLDRKI 87 
                                        56688999999*****9999999999998888....777777777888888888888999999************* PP

                              Atg14  98 eekkkklaklsdklk....................kRrsdleslqneleerrkkqiaklqdaik 141
                                        ++ kkkl++ +dk+                      ++ +   ++++  ++rk+ ++++ +++k
  gene1463|gene1463|rna1463|rna1463  88 NDNKKKLPETKDKTPmyvdvgdvlqrnndknvqqsIKNPKTGGTNEKSTKKRKTNVKSIKNMVK 151
                                        **************99999****97777777777744444466667777777777777777766 PP

>> Cytochrom_C_2  Cytochrome C'
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.1       0.5   2.3e+03      22      49 ..       5      32 ..       3      43 .. 0.66
   2 ?    4.4   0.1     0.015        66       2      39 ..      45      80 ..      44     107 .. 0.71
   3 ?    7.0   0.1    0.0024        11      10      41 ..     136     168 ..     131     173 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.5
                                       HHHTTSST--HHHHHHHHHHHHHHHCSG CS
                      Cytochrom_C_2 22 amlkgeapydaeavaaaaealaalakkl 49
                                       +mlk++   d+e+++++  +l++l ++ 
  gene1463|gene1463|rna1463|rna1463  5 KMLKDQNFLDREEAEKKEMELKKLKREY 32
                                       5667776667777777777666666554 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.015
                                       HHHHHHHHHHHHHHHHHHHHHHHTTSST--HHHHHHHH CS
                      Cytochrom_C_2  2 aikaRqalfksigknmgklgamlkgeapydaeavaaaa 39
                                       +i+  +++ k++++n +k++++  g+ +yd+  +++++
  gene1463|gene1463|rna1463|rna1463 45 IIQLQNKVIKQLENNNQKMKMVY-GDEQYDN-DLESSL 80
                                       678889999**********9877.6666985.455555 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.0024
                                        HHHHHHHHHHHHHHH.TTSST--HHHHHHHHHH CS
                      Cytochrom_C_2  10 fksigknmgklgaml.kgeapydaeavaaaaea 41 
                                         k+ ++n++++++m+ +++ p++  +v+a++++
  gene1463|gene1463|rna1463|rna1463 136 TKKRKTNVKSIKNMVkDKKVPFSPPKVKAQIKQ 168
                                        577899*********55566*******999875 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   6.2    0.0017       7.6     125     208 ..      15     121 ..       2     157 .. 0.65

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0017
                            DUF4407 125 eqlaaaltaelaeleaqiaalqaeidaaearldalraeaqkeldgtkgtgttgvaGkgpaakekkaqldaaqaela 200
                                        ++ a++ + el++l+++ + +++ ++++e+ + +l++++ k+l+++ +++ + v G++++    ++ l  ++++++
  gene1463|gene1463|rna1463|rna1463  15 REEAEKKEMELKKLKREYEHMKGSLNQKEDII-QLQNKVIKQLENN-NQKMKMVYGDEQYDNDLESSLVLLDRKIN 88 
                                        44444566788888888889999998887655.6788888888875.55667899999999998888888888888 PP

                            DUF4407 201 elkakld.........................a 208
                                        + k+kl                          +
  gene1463|gene1463|rna1463|rna1463  89 DNKKKLPetkdktpmyvdvgdvlqrnndknvqQ 121
                                        888887755555555555555555543333330 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3057  (0.170506); expected 358.6 (0.02)
Passed bias filter:                      606  (0.0338); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.45
# Mc/sec: 1359.84
//
Query:       gene1464|gene1464|rna1464|rna1464  [L=188]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-06   28.1  16.7    0.00049   20.7   2.8    3.4  3  SlyX             SlyX
    0.00023   21.6  30.7      0.018   15.4   5.0    3.9  5  ZapB             Cell division protein ZapB
    0.00024   20.9  18.9    0.00056   19.7  18.1    1.8  1  SHE3             SWI5-dependent HO expression protein 3
    0.00035   20.9  25.7     0.0063   16.8  11.3    2.7  3  ATG16            Autophagy protein 16 (ATG16)
    0.00047   20.1  15.1      0.016   15.2   8.1    2.3  2  FlxA             FlxA-like protein
    0.00062   19.5  28.4      0.044   13.6   5.3    3.8  4  DivIC            Septum formation initiator
    0.00072   19.6  15.8      0.056   13.5   2.6    3.2  3  TolA_bind_tri    TolA binding protein trimerisation
    0.00075   19.3  23.3      0.017   14.9  10.6    2.4  2  DUF4201          Domain of unknown function (DUF4201)
    0.00094   18.8  14.1     0.0014   18.2  14.1    1.3  1  MscS_porin       Mechanosensitive ion channel porin domain
    0.00094   19.0  14.5    0.00094   19.0  14.5    1.7  2  Laminin_I        Laminin Domain I
      0.001   18.3  20.0     0.0095   15.2   9.8    2.4  2  HAP1_N           HAP1 N-terminal conserved region
     0.0017   17.8  16.5     0.0032   16.9  16.4    1.4  1  DUF4407          Domain of unknown function (DUF4407)
     0.0023   18.0  21.0     0.0044   17.1  21.0    1.5  1  TPR_MLP1_2       TPR/MLP1/MLP2-like protein
     0.0024   18.5  19.4      0.022   15.4   7.0    2.6  2  YabA             Initiation control protein YabA
     0.0038   16.6  26.5     0.0051   16.2  26.0    1.4  1  GAS              Growth-arrest specific micro-tubule binding
     0.0043   16.9  24.5      0.066   13.0  22.3    2.6  2  KASH_CCD         Coiled-coil region of CCDC155 or KASH
     0.0074   16.3  35.8       0.72    9.9  16.9    3.6  2  TMF_DNA_bd       TATA element modulatory factor 1 DNA binding
  ------ inclusion threshold ------
      0.012   15.7   5.2      0.012   15.7   5.2    5.0  5  bZIP_1           bZIP transcription factor
      0.012   15.8  15.5        0.4   11.0   6.4    3.0  2  BLOC1_2          Biogenesis of lysosome-related organelles co
      0.014   15.6  19.8       0.16   12.2   6.9    2.3  2  Jnk-SapK_ap_N    JNK_SAPK-associated protein-1
      0.015   14.9  19.6      0.052   13.1  10.9    2.2  2  Filament         Intermediate filament protein
      0.018   15.5  25.5      0.069   13.6  10.7    2.8  2  CENP-H           Centromere protein H (CENP-H)
      0.019   15.4   9.0       0.35   11.4   4.1    2.5  2  NPV_P10          Nucleopolyhedrovirus P10 protein
      0.023   15.6  21.7        5.9    7.9  21.5    2.4  2  PRKG1_interact   cGMP-dependent protein kinase interacting do
      0.024   13.9  17.0      0.038   13.3   7.4    2.2  2  DUF3450          Protein of unknown function (DUF3450)
      0.029   12.5  22.6      0.037   12.1  22.6    1.1  1  DUF5401          Family of unknown function (DUF5401)
       0.05   13.5  13.3       0.82    9.6   0.7    4.2  4  GIT_CC           GIT coiled-coil Rho guanine nucleotide excha
      0.051   13.7  27.4        1.5    8.9  11.1    2.7  3  ADIP             Afadin- and alpha -actinin-Binding
      0.051   14.0  17.8        2.8    8.4   1.5    4.3  3  FlaC_arch        Flagella accessory protein C (FlaC)
      0.053   14.1  26.9       0.17   12.4   8.6    2.3  2  APG6_N           Apg6 coiled-coil region
      0.068   13.6  24.2       0.82   10.1   4.8    3.3  2  DUF4200          Domain of unknown function (DUF4200)
      0.072   12.0  24.8      0.078   11.8   5.0    2.1  2  Spc7             Spc7 kinetochore protein
      0.092   12.9  18.7       0.74   10.0   8.2    3.2  3  IFT20            Intraflagellar transport complex B, subunit 
      0.093   12.6  12.9      0.053   13.4   4.5    2.5  2  Sec34            Sec34-like family
       0.11   12.3   9.0        1.1    9.0   1.2    2.2  2  Mt_ATP-synt_D    ATP synthase D chain, mitochondrial (ATP5H)
       0.15   12.0  10.1      0.077   12.9   6.3    2.0  2  CK2S             Casein Kinase 2 substrate
       0.16   11.9   2.6       0.17   11.8   1.9    1.4  1  Hom_end_hint     Hom_end-associated Hint
       0.17   11.0  20.8        0.2   10.7  20.0    1.5  1  Atg14            Vacuolar sorting 38 and autophagy-related su
       0.22   11.1  19.7       0.67    9.5   2.2    3.0  3  DUF4795          Domain of unknown function (DUF4795)
       0.22   11.6  23.2      0.097   12.8   7.7    2.1  2  UPF0242          Uncharacterised protein family (UPF0242) N-t
       0.28   11.1  24.1        1.9    8.5   7.1    3.4  3  Prefoldin_2      Prefoldin subunit
       0.35   10.9  11.0       0.73    9.9   6.6    2.3  3  DUF1664          Protein of unknown function (DUF1664)
        0.4   10.0  21.0       0.27   10.5   5.2    2.3  2  FAM76            FAM76 protein
       0.44   10.8  23.9        1.9    8.8   4.9    3.2  2  Spc24            Spc24 subunit of Ndc80
        0.5   10.4  16.5       0.11   12.5   6.1    2.3  3  Laminin_II       Laminin Domain II
       0.57    8.7   2.9        1.1    7.8   2.9    1.4  1  FUSC             Fusaric acid resistance protein family
       0.61   10.8  17.8        0.9   10.3   2.1    2.4  2  DUF4472          Domain of unknown function (DUF4472)
       0.62    9.9   7.6        1.4    8.7   0.2    2.9  2  CCDC92           Coiled-coil domain of unknown function
       0.62    9.6  21.7       0.37   10.3   6.4    2.1  2  HAUS-augmin3     HAUS augmin-like complex subunit 3
       0.64    9.2  16.6        6.6    5.9  15.3    2.0  2  TMPIT            TMPIT-like protein
       0.69   10.1   6.8        8.9    6.5   0.5    3.4  3  MbeD_MobD        MbeD/MobD like
       0.71   10.6  14.6        1.9    9.3   3.2    3.1  3  Occludin_ELL     Occludin homology domain
       0.74   10.2  24.6       0.11   13.0  20.3    1.8  1  Fez1             Fez1
       0.77    8.3  20.9       0.74    8.4  18.7    1.7  2  AAA_13           AAA domain
       0.99    8.2  23.7        0.2   10.5  11.5    2.0  2  DUF812           Protein of unknown function (DUF812)
        1.1    9.4  20.7        1.4    9.1  10.5    2.3  2  DivIVA           DivIVA protein
        1.2    9.0  23.4        0.6   10.0   6.3    2.5  3  Ax_dynein_light  Axonemal dynein light chain
        1.3    8.7  16.5        3.1    7.4   8.3    2.2  2  DUF2968          Protein of unknown function (DUF2968)
        1.3    8.8  24.2        5.3    6.8  24.2    1.8  1  ERM              Ezrin/radixin/moesin family
        1.6    8.8  10.8         43    4.1  10.8    2.1  1  DUF87            Helicase HerA, central domain
        1.7    8.9  20.9        4.7    7.5   3.6    3.3  3  ABC_tran_CTD     ABC transporter C-terminal domain
        1.9    8.9  25.2       0.12   12.7   4.2    3.9  3  Csm1_N           Csm1 N-terminal domain
          2    8.8  16.5       0.19   12.1   2.8    3.5  3  TSC22            TSC-22/dip/bun family
        2.1    8.3  19.2          1    9.2   3.6    3.0  3  Wtap             WTAP/Mum2p family
        2.2    7.0   7.8          2    7.1   1.1    2.0  2  DUF3573          Protein of unknown function (DUF3573)
        2.3    7.7  25.2        6.3    6.2   7.6    2.4  2  Leu_zip          Leucine zipper
        2.3    6.0  16.7        2.3    6.0   8.2    2.0  2  V_ATPase_I       V-type ATPase 116kDa subunit family
        2.5    8.5  17.2          4    7.8   1.7    2.8  2  DUF641           Plant protein of unknown function (DUF641)
        2.6    8.4  17.7    3.1e+02    1.8  17.7    2.9  1  CCDC-167         Coiled-coil domain-containing protein 167
        2.8    8.7  11.7        4.8    7.9   3.9    2.5  2  FliD_N           Flagellar hook-associated protein 2 N-termin
        2.9    7.7  19.0       0.14   12.0   3.1    2.1  2  DUF724           Protein of unknown function (DUF724)
          3    8.1  11.6       0.29   11.4   2.6    3.0  2  DUF5446          Family of unknown function (DUF5446)
        3.1    8.0   9.0        1.8    8.7   0.3    3.1  2  DASH_Dad3        DASH complex subunit Dad3
        3.3    7.4  22.9        2.4    7.8   6.6    2.6  2  GrpE             GrpE
        3.5    8.3  17.7        4.6    7.9   2.7    3.1  3  DUF4665          Domain of unknown function (DUF4665)
        3.5    8.0  10.8        1.5    9.2   0.3    3.0  3  kleA_kleC        Uncharacterized KorC regulated protein A
        3.8    7.6  10.6        2.4    8.2   0.9    3.8  4  VGPC1_C          C-terminal membrane-localisation domain of i
        3.9    8.2  12.3        3.3    8.5   4.8    2.3  2  DUF2203          Uncharacterized conserved protein (DUF2203)
          4    7.8  10.4    3.2e+02    1.7   8.5    3.2  1  DUF948           Bacterial protein of unknown function (DUF94
        5.1    7.3  18.8         73    3.6   8.0    3.6  2  Swi5             Swi5
        5.2    7.2  16.9        1.1    9.3   3.1    2.2  2  DUF4337          Domain of unknown function (DUF4337)
        5.2    8.2   9.4        2.9    9.0   0.5    2.9  2  DUF5320          Family of unknown function (DUF5320)
        5.3    7.1  26.7        3.6    7.7   5.0    3.1  3  DHR10            Designed helical repeat protein 10 domain
        5.4    7.4  16.8        7.8    6.9   3.2    3.5  3  HalX             HalX domain
        5.6    7.1  19.1        7.1    6.7   4.1    3.6  3  DUF4315          Domain of unknown function (DUF4315)
        7.4    6.0  17.6         13    5.2  17.6    1.4  1  Exonuc_VII_L     Exonuclease VII, large subunit
        9.5    6.7  12.2        1.5    9.3   3.1    2.5  2  UPF0184          Uncharacterised protein family (UPF0184)


Domain annotation for each model (and alignments):
>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   2.8   2.4e-06   0.00049      11      56 ..      23      68 ..      21      75 .. 0.89
   2 ?    6.9   0.4     0.047       9.6       7      45 ..      75     113 ..      71     120 .. 0.83
   3 !    9.6   0.9    0.0066       1.3      30      55 ..     120     145 ..     116     158 .. 0.63

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 2.4e-06
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXXXXX CS
                               SlyX 11 klafqedtieeLndvvaeqqqqidrlqrqlrllaerlkeleessga 56
                                       ++a   ++  +L+d++ae +++id l++q  +l+ +l++lee++++
  gene1464|gene1464|rna1464|rna1464 23 RVAQFHKLYASLSDQIAEKDERIDTLKKQTTELQHKLEDLEEQNAE 68
                                       56777788899********************************975 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.047
                                        HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                               SlyX   7 eLEiklafqedtieeLndvvaeqqqqidrlqrqlrllae 45 
                                        +L+ +l    + +++L+++ +e +++i++l ++++  ++
  gene1464|gene1464|rna1464|rna1464  75 KLQAELDIVNKDVKRLQAISVEKERKIEKLNAEVESCRK 113
                                        57777777888999999999*********9999987665 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.0066
                                        HHHHHHHHHHHHHHHHT-XXXXXXXX CS
                               SlyX  30 qqqidrlqrqlrllaerlkeleessg 55 
                                        + qidrl+r+l++l+++ ++l+++++
  gene1464|gene1464|rna1464|rna1464 120 NAQIDRLERELEKLRKENAKLADRNK 145
                                        45677777777777666665555544 PP

>> ZapB  Cell division protein ZapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   8.0    0.0001     0.022      18      63 ..      43      88 ..      23      92 .. 0.82
   2 ?    2.8   0.7      0.78   1.6e+02      27      57 ..      87     117 ..      83     121 .. 0.74
   3 !   10.7   8.4    0.0027      0.56      19      68 ..     100     150 ..      98     150 .. 0.88
   4 !   15.4   5.0   8.9e-05     0.018      19      54 ..     122     157 ..     121     159 .. 0.93
   5 ?    0.4   0.1       4.4   9.1e+02      31      58 ..     161     188 .]     158     188 .] 0.82

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 0.0001
                               ZapB 18 dtitlLqmeieeLkeeneelkeenreleeeneqlkeereawqerlk 63
                                       ++i++L+++  eL+++ e l+e+n+e    n++l++e   +++ +k
  gene1464|gene1464|rna1464|rna1464 43 ERIDTLKKQTTELQHKLEDLEEQNAEWGTNNNKLQAELDIVNKDVK 88
                                       7899999999999999999999999999999999999877766555 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.78
                               ZapB  27 ieeLkeeneelkeenreleeeneqlkeerea 57 
                                        +++L++ + e ++++++l++e+e  ++e +a
  gene1464|gene1464|rna1464|rna1464  87 VKRLQAISVEKERKIEKLNAEVESCRKEGNA 117
                                        5677777788888888888888888877666 PP

  == domain 3  score: 10.7 bits;  conditional E-value: 0.0027
                               ZapB  19 titlLqmeieeLkee.neelkeenreleeeneqlkeereawqerlkkLLgk 68 
                                        +i++L  e+e  ++e n++ + ++++le+e+e+l++e +++ +r k L++k
  gene1464|gene1464|rna1464|rna1464 100 KIEKLNAEVESCRKEgNAASNAQIDRLERELEKLRKENAKLADRNKELIDK 150
                                        6999*****99865527888899********************99999987 PP

  == domain 4  score: 15.4 bits;  conditional E-value: 8.9e-05
                               ZapB  19 titlLqmeieeLkeeneelkeenreleeeneqlkee 54 
                                        +i++L  e+e+L++en++l+++n+el  +n++l ++
  gene1464|gene1464|rna1464|rna1464 122 QIDRLERELEKLRKENAKLADRNKELIDKNKKLGND 157
                                        7999****************************9765 PP

  == domain 5  score: 0.4 bits;  conditional E-value: 4.4
                               ZapB  31 keeneelkeenreleeeneqlkeereaw 58 
                                         ++n  l+++ r+l     +l+++  +w
  gene1464|gene1464|rna1464|rna1464 161 GKKNIVLEKNTRRLLTNTMKLRKNTMNW 188
                                        5788999999999999999999887776 PP

>> SHE3  SWI5-dependent HO expression protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7  18.1   2.7e-06   0.00056      42     168 ..      33     156 ..       4     169 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 2.7e-06
                                        HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHH CS
                               SHE3  42 kflenlaslkhENdnLsslLkRKerrlkdlekelselkesveelklekkqlkkrlenssaseteleeelerlkvqY 117
                                        ++ +++a+  +  d L+      + +l dle++++e  +++++l++e + ++k++++++a + e e ++e+l+++ 
  gene1464|gene1464|rna1464|rna1464  33 SLSDQIAEKDERIDTLKKQTTELQHKLEDLEEQNAEWGTNNNKLQAELDIVNKDVKRLQAISVEKERKIEKLNAE- 107
                                        5556666666666777777777789**********************************************9655. PP

                                        HHHHHHHHHH.HHHHHHHHHHHHHHHHHHHHHHHSSSXXXXXXXXXXX.XXX CS
                               SHE3 118 dalvdsqkeY.kehYqqeieeLkesleklklenekqleelqerissndkdid 168
                                           v+s+++      + +i++L+++lekl++en k  + ++e i +n+k  +
  gene1464|gene1464|rna1464|rna1464 108 ---VESCRKEgNAASNAQIDRLERELEKLRKENAKLADRNKELIDKNKKLGN 156
                                        ...77776550556678*****************999999999999887654 PP

>> ATG16  Autophagy protein 16 (ATG16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8  11.3   3.1e-05    0.0063     101     174 ..      21      99 ..      12     107 .. 0.81
   2 !   15.5  22.7   7.7e-05     0.016      78     187 ..      33     143 ..      32     152 .. 0.95
   3 ?    4.6  11.9      0.16        33     145     187 ..     100     143 ..      87     187 .. 0.48

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 3.1e-05
                              ATG16 101 aqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelrekeklvqdlqDElsaLq.....lqlnqaE 171
                                        + r+ +  +  + l +++ e++er++ l+++ ++l+ kl+d+ee+ +e+ + +++lq El+  +     lq+ ++E
  gene1464|gene1464|rna1464|rna1464  21 SARVAQFHKLYASLSDQIAEKDERIDTLKKQTTELQHKLEDLEEQNAEWGTNNNKLQAELDIVNkdvkrLQAISVE 96 
                                        6678888888899999********************************************9876333335555555 PP

                              ATG16 172 ekl 174
                                        +++
  gene1464|gene1464|rna1464|rna1464  97 KER 99 
                                        544 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 7.7e-05
                              ATG16  78 sleqklaqlreelaelyksrgelaqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelrekeklv 153
                                        sl++++a+  e   +l k+ +el+ +l +l+e+ ++  ++ ++ +++l+ +++++++l+    ++e +++ +++ v
  gene1464|gene1464|rna1464|rna1464  33 SLSDQIAEKDERIDTLKKQTTELQHKLEDLEEQNAEWGTNNNKLQAELDIVNKDVKRLQAISVEKERKIEKLNAEV 108
                                        78899999999999************************************************************** PP

                              ATG16 154 qdlqDE.lsaLqlqlnqaEeklrklekENkeLveR 187
                                        +  + E  +a + q   +E +l+kl+kEN++L +R
  gene1464|gene1464|rna1464|rna1464 109 ESCRKEgNAASNAQIDRLERELEKLRKENAKLADR 143
                                        ******44678*********************998 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.16
                              ATG16 145 elrekeklvqdlqDE.lsaLqlqlnqaEeklrklekENkeLveR 187
                                        +++ +++ v+  + E  +a + q   +E +l+kl+kEN++L +R
  gene1464|gene1464|rna1464|rna1464 100 KIEKLNAEVESCRKEgNAASNAQIDRLERELEKLRKENAKLADR 143
                                        33333333333333312233444444444444444444444443 PP

>> FlxA  FlxA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   8.1   7.6e-05     0.016      12      79 ..      38     101 ..      28     120 .. 0.76
   2 !    9.6   1.0    0.0041      0.85       8      47 ..     112     152 ..     105     163 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 7.6e-05
                               FlxA  12 ssgsasqiasLqkQiknlqkqLkelsesdeltkeekkkqqqliqaQIqqlqaQIaqlqqqqaekaqek 79 
                                          + +++i +L+kQ ++lq +L++l e++++      +  + +qa+++++++ +++lq+   ek+++ 
  gene1464|gene1464|rna1464|rna1464  38 IAEKDERIDTLKKQTTELQHKLEDLEEQNAE----WGTNNNKLQAELDIVNKDVKRLQAISVEKERKI 101
                                        5678999*********************333....4458899****************8777666544 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0041
                               FlxA   8 ssssssgsasqiasLqkQiknlqkqLkelses.deltkeek 47 
                                         ++ +  s++qi +L++++++l k+  +l++  +el +++k
  gene1464|gene1464|rna1464|rna1464 112 RKEGNAASNAQIDRLERELEKLRKENAKLADRnKELIDKNK 152
                                        56677888899999999999999999999888444444444 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   4.3    0.0015      0.32      19      53 ..      31      64 ..      25      68 .. 0.89
   2 ?    4.7   5.6      0.12        26      21      57 ..      54      90 ..      49      93 .. 0.69
   3 ?    5.9   3.4     0.053        11      21      52 ..      82     113 ..      71     119 .. 0.78
   4 !   13.6   5.3   0.00021     0.044      23      50 ..     120     147 ..     116     160 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0015
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-XXX CS
                              DivIC 19 ykqlkqeiaalqaelaklkaeneeLeaevkdLksd 53
                                       y +l  +ia++ + +++lk++  eL+++++dL+ +
  gene1464|gene1464|rna1464|rna1464 31 YASLSDQIAEKDERIDTLKKQTTELQHKLEDLE-E 64
                                       668999**************************4.4 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.12
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHCC-XXXXXXX CS
                              DivIC 21 qlkqeiaalqaelaklkaeneeLeaevkdLksdedyi 57
                                       +l+ ++++l++++a+    n++L+ae++  ++d  ++
  gene1464|gene1464|rna1464|rna1464 54 ELQHKLEDLEEQNAEWGTNNNKLQAELDIVNKDVKRL 90
                                       6677777778888888888888888777776665554 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.053
                                        HHHHHHHHHHHHHHHHHHHHHHHHHHHCC-XX CS
                              DivIC  21 qlkqeiaalqaelaklkaeneeLeaevkdLks 52 
                                         +++++++lqa  +++  ++e+L+aev+  ++
  gene1464|gene1464|rna1464|rna1464  82 IVNKDVKRLQAISVEKERKIEKLNAEVESCRK 113
                                        57888899999999999999999999887764 PP

  == domain 4  score: 13.6 bits;  conditional E-value: 0.00021
                                        HHHHHHHHHHHHHHHHHHHHHHHHHCC- CS
                              DivIC  23 kqeiaalqaelaklkaeneeLeaevkdL 50 
                                        +++i++l++el+kl++en++L+++ k+L
  gene1464|gene1464|rna1464|rna1464 120 NAQIDRLERELEKLRKENAKLADRNKEL 147
                                        6777777777777777777777777766 PP

>> TolA_bind_tri  TolA binding protein trimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   2.6   0.00027     0.056       4      55 ..      10      66 ..       7      72 .. 0.82
   2 ?    3.1   0.2      0.49     1e+02      21      51 ..      74     104 ..      69     107 .. 0.81
   3 !   10.2   3.3    0.0029       0.6       3      58 ..      98     154 ..      86     158 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.00027
                      TolA_bind_tri  4 drvarLErilears.....qlllelqqqlealqqelreLRGqiEelqyqleqleerQ 55
                                       +r   LE+++ +       +l   l  q+ +  + +++L+ q+ elq++le+lee+ 
  gene1464|gene1464|rna1464|rna1464 10 SRTRVLEQKFFSARvaqfhKLYASLSDQIAEKDERIDTLKKQTTELQHKLEDLEEQN 66
                                       5666677766665556666788899******************************97 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.49
                      TolA_bind_tri  21 lelqqqlealqqelreLRGqiEelqyqleql 51 
                                         +lq +l+  ++++++L+    e + ++e+l
  gene1464|gene1464|rna1464|rna1464  74 NKLQAELDIVNKDVKRLQAISVEKERKIEKL 104
                                        67999************98777777777666 PP

  == domain 3  score: 10.2 bits;  conditional E-value: 0.0029
                      TolA_bind_tri   3 edrvarLErilea.rsqlllelqqqlealqqelreLRGqiEelqyqleqleerQrdl 58 
                                        e ++++L+  +e+ r++++     q+++l++el +LR ++ +l+ ++++l+ + ++l
  gene1464|gene1464|rna1464|rna1464  98 ERKIEKLNAEVEScRKEGNAASNAQIDRLERELEKLRKENAKLADRNKELIDKNKKL 154
                                        567788888777745688889999**********************99999999887 PP

>> DUF4201  Domain of unknown function (DUF4201)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9  10.6   8.1e-05     0.017      52     136 ..      32     116 ..      25     120 .. 0.92
   2 !    8.4   9.9     0.008       1.7      86     144 ..     102     160 ..      95     185 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 8.1e-05
                            DUF4201  52 qalnkkIeernkeLkrlkkkttktvhalthlkeklhmleselselkkelkekeerlaklrkelykvklerdklrkq 127
                                        ++l+++I+e+++ +  lkk+tt   h+l++l e   +  +++++l+ el+  +++ ++l++   + + + +kl ++
  gene1464|gene1464|rna1464|rna1464  32 ASLSDQIAEKDERIDTLKKQTTELQHKLEDLEEQNAEWGTNNNKLQAELDIVNKDVKRLQAISVEKERKIEKLNAE 107
                                        5799********************************************************9999999999999999 PP

                            DUF4201 128 neklkqqgg 136
                                         e ++++g 
  gene1464|gene1464|rna1464|rna1464 108 VESCRKEGN 116
                                        999999886 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.008
                            DUF4201  86 lhmleselselkkelkekeerlaklrkelykvklerdklrkqneklkqqggllrvPaLl 144
                                        ++ +++  s++k+     ++++++l++el+k+++e++kl ++n++l +++  l++ ++l
  gene1464|gene1464|rna1464|rna1464 102 EKLNAEVESCRKEGNAASNAQIDRLERELEKLRKENAKLADRNKELIDKNKKLGNDKVL 160
                                        4455555566677788999********************************99999987 PP

>> MscS_porin  Mechanosensitive ion channel porin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2  14.1     7e-06    0.0014      46     168 ..      24     140 ..      15     154 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 7e-06
                         MscS_porin  46 iddaPkelrelqqelealqkkkeeaskeilaklsleeLeqrllqtssqlqelqeqlaqlnsqlvelqtrperaqqq 121
                                        ++++ k+ ++l+ ++++       + + +  k  ++eL+ +l++ ++q +e+ ++ ++l+++l   +    r+q+ 
  gene1464|gene1464|rna1464|rna1464  24 VAQFHKLYASLSDQIAEK------DERIDTLKKQTTELQHKLEDLEEQNAEWGTNNNKLQAELDIVNKDVKRLQAI 93 
                                        455555555555555555......3333333556799*************************************** PP

                         MscS_porin 122 ltearqrlqeirnrLnstaaagealsqaqrtalqaelaaleaqieel 168
                                          e  +++++++++ +s +++g+a s+aq + l+ el+ l+ +++ l
  gene1464|gene1464|rna1464|rna1464  94 SVEKERKIEKLNAEVESCRKEGNAASNAQIDRLERELEKLRKENAKL 140
                                        ****************************************9999865 PP

>> Laminin_I  Laminin Domain I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0  14.5   4.6e-06   0.00094      27     130 ..      30     133 ..       6     146 .. 0.90
   2 ?    0.2   0.5       2.4     5e+02      14      58 ..     133     180 ..     130     186 .. 0.49

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 4.6e-06
                          Laminin_I  27 eLqeklskesakkskieilekelesLaqeteeLqkkatqvlakaqkvnaesertlnnakeLaekikkladnikeil 102
                                           +   ++++k ++i+ l+k+ ++L+   e L ++  +   + +k++ae +  ++  k L++  ++ +++i+ ++
  gene1464|gene1464|rna1464|rna1464  30 LYASLSDQIAEKDERIDTLKKQTTELQHKLEDLEEQNAEWGTNNNKLQAELDIVNKDVKRLQAISVEKERKIEKLN 105
                                        4455667899999*************************************************************** PP

                          Laminin_I 103 ekvatlneneealpssklseelaeaqrl 130
                                        + v+   ++++a+++ ++++   e ++l
  gene1464|gene1464|rna1464|rna1464 106 AEVESCRKEGNAASNAQIDRLERELEKL 133
                                        ********************99999887 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 2.4
                          Laminin_I  14 pykinanledltkeLqeklskesakkskie...ilekelesLaqetee 58 
                                        ++k na+l+d +keL  k +k  + k++ +   +lek+   L  +t +
  gene1464|gene1464|rna1464|rna1464 133 LRKENAKLADRNKELIDKNKKLGNDKVLGKkniVLEKNTRRLLTNTMK 180
                                        455556666666666666666655555544222344444444444444 PP

>> HAP1_N  HAP1 N-terminal conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   9.8   4.6e-05    0.0095     200     279 ..      16      92 ..       4     114 .. 0.79
   2 ?    6.1   7.4     0.026       5.3     131     193 ..      89     151 ..      83     160 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 4.6e-05
                             HAP1_N 200 EqqLvldcveqlseanqqiaelseelarkleelerqqeeissLlaqivdlqqklkelgveneelkqhLaaskeaqr 275
                                        Eq+  +  v+q+   ++ +a+ls+++a+k e +++ +++ ++L+ ++ dl+++  e g++n++l+++L +     +
  gene1464|gene1464|rna1464|rna1464  16 EQKFFSARVAQF---HKLYASLSDQIAEKDERIDTLKKQTTELQHKLEDLEEQNAEWGTNNNKLQAELDIVNKDVK 88 
                                        555666666665...456899***********************************************98655555 PP

                             HAP1_N 276 qLta 279
                                        +L+a
  gene1464|gene1464|rna1464|rna1464  89 RLQA 92 
                                        6765 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.026
                             HAP1_N 131 qlysdseeeseeeseeseelreeesleslqklvqldlLqeklreLeeeNekLreeasqLktet 193
                                        +l + s e++ + ++ + e+++ +++  + +  q+d L + l++L +eN kL  + ++L ++ 
  gene1464|gene1464|rna1464|rna1464  89 RLQAISVEKERKIEKLNAEVESCRKEGNAASNAQIDRLERELEKLRKENAKLADRNKELIDKN 151
                                        455555566666666666677777777788888888888889888888888888887775554 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9  16.4   1.5e-05    0.0032     130     249 ..      26     153 ..       7     158 .. 0.50

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.5e-05
                            DUF4407 130 altaelaeleaqiaalqaeidaaearldalraeaqkeldgtk..gtgttgvaGkgpaake....kkaqldaaqael 199
                                        ++ + +a l +qia+ ++ id+++++ ++l+ ++++  +++   gt  ++ + + ++  +     +a   ++++++
  gene1464|gene1464|rna1464|rna1464  26 QFHKLYASLSDQIAEKDERIDTLKKQTTELQHKLEDLEEQNAewGTNNNKLQAELDIVNKdvkrLQAISVEKERKI 101
                                        3555556666666666666666666666666666655555444533333333333333334444444444444444 PP

                            DUF4407 200 aelkakld..atarlaalraelaeleaerakeraasqaaaaaddGllarlea 249
                                        ++l+a+++  +++  aa +a++++le+e++k r+++++ a+ ++ l+++++ 
  gene1464|gene1464|rna1464|rna1464 102 EKLNAEVEscRKEGNAASNAQIDRLERELEKLRKENAKLADRNKELIDKNKK 153
                                        4444444455445555555566666666666666666655555555555554 PP

>> TPR_MLP1_2  TPR/MLP1/MLP2-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1  21.0   2.1e-05    0.0044       5     122 ..      33     154 ..      25     156 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 2.1e-05
                         TPR_MLP1_2   5 sleeeikslkeekeeaeaklqklq...edlekqaeiakeaqqkYerelvkhaedvkelqalreeln.elkaeiael 76 
                                        sl ++i++++e+++ ++++ ++lq   edle+q +++ + ++k + el   ++dvk lqa+  e + ++++  ae+
  gene1464|gene1464|rna1464|rna1464  33 SLSDQIAEKDERIDTLKKQTTELQhklEDLEEQNAEWGTNNNKLQAELDIVNKDVKRLQAISVEKErKIEKLNAEV 108
                                        6777778888887777777766663347999******************************987641334444455 PP

                         TPR_MLP1_2  77 kaeaesakaeleeseesweeqkeelekelselekriedlneqNklL 122
                                        ++ +++ +a+ +++   +e++ e+l+ke ++l  r ++l ++Nk L
  gene1464|gene1464|rna1464|rna1464 109 ESCRKEGNAASNAQIDRLERELEKLRKENAKLADRNKELIDKNKKL 154
                                        5555556666666777888999999999999999999999999876 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   7.0   0.00011     0.022       6      76 ..      34     104 ..      29     117 .. 0.63
   2 ?    8.7   4.3     0.013       2.7      15      50 ..     121     156 ..     115     187 .. 0.52

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 0.00011
                                        HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHXXXXXXXXXXXXXXXXXXXXXXXX CS
                               YabA   6 lfdkleeleeqleelleeleelkeelaelleenaeLeleneklrerleeeekkekekkkelsegkenLarl 76 
                                        l d+++e +e++++l+++ +el+++l++l e+nae  ++n+kl+ +l+  +k+ k+ ++ + e ++++++l
  gene1464|gene1464|rna1464|rna1464  34 LSDQIAEKDERIDTLKKQTTELQHKLEDLEEQNAEWGTNNNKLQAELDIVNKDVKRLQAISVEKERKIEKL 104
                                        56777777777888888888888888888888888888888888777444444433333333333333333 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.013
                                        HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                               YabA  15 eqleelleeleelkeelaelleenaeLeleneklre 50 
                                         q+++l +ele+l++e a+l ++n+eL   n+kl +
  gene1464|gene1464|rna1464|rna1464 121 AQIDRLERELEKLRKENAKLADRNKELIDKNKKLGN 156
                                        345555555555555555555555555555555433 PP

>> GAS  Growth-arrest specific micro-tubule binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2  26.0   2.5e-05    0.0051      19     155 ..      36     175 ..      24     183 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2.5e-05
                                GAS  19 ditrnNLelIkslKeeieelkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslkn..... 89 
                                        d++++  e I++lK++ +el+ k e  e + +e  ++n++l+ +L  ++++v++L++   + e++ ++l++     
  gene1464|gene1464|rna1464|rna1464  36 DQIAEKDERIDTLKKQTTELQHKLEDLEEQNAEWGTNNNKLQAELDIVNKDVKRLQAISVEKERKIEKLNAevesc 111
                                        666666688***********************************************97777777666665422222 PP

                                GAS  90 lkarlkelekelkdlkwehevleqrfekvekerdelykkfeaaiqevqqktglknllLekklkalq 155
                                         k+ +  ++ ++ +l+ e e l+++ +k+ +  +el +k ++  +   +  g kn++Lek   +l 
  gene1464|gene1464|rna1464|rna1464 112 RKEGNAASNAQIDRLERELEKLRKENAKLADRNKELIDKNKKLGN--DKVLGKKNIVLEKNTRRLL 175
                                        456667788899999999999999999999999999999888555..5899********9988775 PP

>> KASH_CCD  Coiled-coil region of CCDC155 or KASH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1  10.7    0.0026      0.54     103     168 ..      44     109 ..       6     115 .. 0.50
   2 !   13.0  22.3   0.00032     0.066      20     156 ..      48     170 ..      46     186 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0026
                           KASH_CCD 103 kiesLqeenikllaekdelkkklkeLlkekaeLkkqlheleellaekealleektkqieeLkltie 168
                                        +i++L+ + + l+   + l+++ +e  +++++L+ +l+ +++ +   +a+ +ek+++ie+L++ +e
  gene1464|gene1464|rna1464|rna1464  44 RIDTLKKQTTELQHKLEDLEEQNAEWGTNNNKLQAELDIVNKDVKRLQAISVEKERKIEKLNAEVE 109
                                        233333333333333333333333333333444555544444444445555555555555555544 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 0.00032
                           KASH_CCD  20 LaeenskLkkavetaeetnakLteeieeLkkklkstQqalqkaklleeEleelkalvkeleEkrarlkaqnkqlek 95 
                                        L+++ + L++++e  ee+na    ++++L+  l ++ + +++ ++++ E e           k ++l+a+ +   k
  gene1464|gene1464|rna1464|rna1464  48 LKKQTTELQHKLEDLEEQNAEWGTNNNKLQAELDIVNKDVKRLQAISVEKE----------RKIEKLNAEVESCRK 113
                                        899******************************999888887777766654..........333344444444444 PP

                           KASH_CCD  96 e.nqsLiakiesLqeenikllaekdelkkklkeLlkekaeLkkqlheleellaekealleek 156
                                        e n   +a+i+ L+ e++kl+ e+ +l+ + keL++++ +L +     +++l++k+ +le+ 
  gene1464|gene1464|rna1464|rna1464 114 EgNAASNAQIDRLERELEKLRKENAKLADRNKELIDKNKKLGN-----DKVLGKKNIVLEKN 170
                                        4234456777777777777777777777777777777755543.....33444444444444 PP

>> TMF_DNA_bd  TATA element modulatory factor 1 DNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9  16.9    0.0035      0.72       2      70 ..      33     108 ..      32     119 .. 0.77
   2 !    9.7  10.1    0.0042      0.86      11      48 ..     120     157 ..     114     176 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0035
                         TMF_DNA_bd   2 slekklkeKDeqIa.......qLmeEGekLskkelklnntikkLrkknkelekeikelkkkleklekeleeleerl 70 
                                        sl ++++eKDe+I+       +L+  +e+L+ ++ +  +   kL++++   +k++k+l+    ++e+++e+l+++ 
  gene1464|gene1464|rna1464|rna1464  33 SLSDQIAEKDERIDtlkkqttELQHKLEDLEEQNAEWGTNNNKLQAELDIVNKDVKRLQAISVEKERKIEKLNAEV 108
                                        68899********722222225566777777777888888999****************88888888888777665 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0042
                         TMF_DNA_bd  11 DeqIaqLmeEGekLskkelklnntikkLrkknkeleke 48 
                                        ++qI+ L  E+ekL+k++ kl    k+L  knk+l ++
  gene1464|gene1464|rna1464|rna1464 120 NAQIDRLERELEKLRKENAKLADRNKELIDKNKKLGND 157
                                        79*******************************99776 PP

>> bZIP_1  bZIP transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.2     0.043       8.8      28      63 ..      17      52 ..       9      58 .. 0.85
   2 ?    4.7   4.0      0.16        33      27      56 ..      51      80 ..      49      95 .. 0.56
   3 ?    0.9   0.7       2.4   4.9e+02      32      48 ..      98     114 ..      88     122 .. 0.60
   4 ?   15.7   5.2   5.9e-05     0.012      26      59 ..     121     154 ..     119     159 .. 0.92
   5 ?   -0.5   0.3       6.4   1.3e+03      37      61 ..     159     183 ..     155     186 .. 0.61

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.043
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             bZIP_1 28 ieeLerrvkaLekeNksLkseleelkkevekLkskv 63
                                       ++  + rv+++ k  +sL++++ e  + +++Lk++ 
  gene1464|gene1464|rna1464|rna1464 17 QKFFSARVAQFHKLYASLSDQIAEKDERIDTLKKQT 52
                                       566678999999999999999999999999999875 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.16
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             bZIP_1 27 eieeLerrvkaLekeNksLkseleelkkev 56
                                       ++ eL+ + + Le++N++    +++l+ e 
  gene1464|gene1464|rna1464|rna1464 51 QTTELQHKLEDLEEQNAEWGTNNNKLQAEL 80
                                       556677777777776665555555554443 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 2.4
                                        HHHHHHHHHHHHHHHHH CS
                             bZIP_1  32 errvkaLekeNksLkse 48 
                                        er+ ++L++e +s ++e
  gene1464|gene1464|rna1464|rna1464  98 ERKIEKLNAEVESCRKE 114
                                        45555555555544444 PP

  == domain 4  score: 15.7 bits;  conditional E-value: 5.9e-05
                                        HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             bZIP_1  26 aeieeLerrvkaLekeNksLkseleelkkevekL 59 
                                        a+i++Ler+ ++L keN++L+++++el ++++kL
  gene1464|gene1464|rna1464|rna1464 121 AQIDRLERELEKLRKENAKLADRNKELIDKNKKL 154
                                        7899***************************998 PP

  == domain 5  score: -0.5 bits;  conditional E-value: 6.4
                                        HHHHHHHHHHHHHHHHHHHHHHHHH CS
                             bZIP_1  37 aLekeNksLkseleelkkevekLks 61 
                                        +L k+N  L +   +l  +  kL++
  gene1464|gene1464|rna1464|rna1464 159 VLGKKNIVLEKNTRRLLTNTMKLRK 183
                                        5666666666666666666666655 PP

>> BLOC1_2  Biogenesis of lysosome-related organelles complex-1 subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   1.7     0.014       2.9      52      86 ..      30      64 ..       3      69 .. 0.52
   2 ?   11.0   6.4     0.002       0.4      10      78 ..      75     141 ..      71     152 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.014
                            BLOC1_2 52 klnekyeelqpylqqidqiekqvteLeeavseLDe 86
                                        + +++++++++ ++id ++kq+teL++  + L+e
  gene1464|gene1464|rna1464|rna1464 30 LYASLSDQIAEKDERIDTLKKQTTELQHKLEDLEE 64
                                       33333344444444444444444444444444443 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.002
                            BLOC1_2  10 yleaeleatvedyklLeklNeaasekykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLe 78 
                                         l+ael+++++d+k L+++  + ++k++kl+ +++s +k+ ++ ++  ++++ + ++++++ k+ ++L 
  gene1464|gene1464|rna1464|rna1464  75 KLQAELDIVNKDVKRLQAISVEKERKIEKLNAEVESCRKEGNAASN--AQIDRLERELEKLRKENAKLA 141
                                        589**************************************99988..666666666666666655554 PP

>> Jnk-SapK_ap_N  JNK_SAPK-associated protein-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   6.4     0.014       2.8      86     138 ..      26      78 ..       4      91 .. 0.78
   2 ?   12.2   6.9   0.00078      0.16      78     150 ..      88     154 ..      83     159 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.014
                      Jnk-SapK_ap_N  86 qweeerkelqekveqleeenrelelkaknaadqlsrleekeaelkkeysklhe 138
                                        q+ +    l++++++ +e+++ l++++ +++ +l++lee++ae+ ++++kl+ 
  gene1464|gene1464|rna1464|rna1464  26 QFHKLYASLSDQIAEKDERIDTLKKQTTELQHKLEDLEEQNAEWGTNNNKLQA 78 
                                        55555567888999999999999999999999999999999999999999876 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00078
                      Jnk-SapK_ap_N  78 eeleeiedqweeerkelqekveqleeenrelelkaknaadqlsrleekeaelkkeysklheretellkklkel 150
                                        ++l+ i  + e++ ++l+++ve+ ++e +  +      + q+ rle++ ++l+ke++kl +r +el+ k k+l
  gene1464|gene1464|rna1464|rna1464  88 KRLQAISVEKERKIEKLNAEVESCRKEGNAAS------NAQIDRLERELEKLRKENAKLADRNKELIDKNKKL 154
                                        67777888888888999999999999999888......9*****************************99976 PP

>> Filament  Intermediate filament protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1  10.9   0.00025     0.052      38     138 ..      16     113 ..       3     117 .. 0.66
   2 ?    6.6   1.6     0.024         5     221     252 ..     119     150 ..     113     161 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00025
                                        XXXX.XXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                           Filament  38 eekk.saevsklkelyekeleelrkqldeltkerarlqleldnlreeledlrkkyekelnkreevEaelkalrkdl 112
                                        e+k  sa+     + ++k  ++l +q+ e  +  + l+ +  +l+++ledl +++++  ++ +++ ael  ++kd+
  gene1464|gene1464|rna1464|rna1464  16 EQKFfSAR----VAQFHKLYASLSDQIAEKDERIDTLKKQTTELQHKLEDLEEQNAEWGTNNNKLQAELDIVNKDV 87 
                                        44422222....2344555566777777777777777777777777777777777777777777777777778888 PP

                                        XXXXXXXXXXXXXXXXXXXXXXXXXX CS
                           Filament 113 deatlarvdLekkvesLkeelaflkk 138
                                        + ++   v+ e+k+e+L+ e++  +k
  gene1464|gene1464|rna1464|rna1464  88 KRLQAISVEKERKIEKLNAEVESCRK 113
                                        88888888888888888888776665 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.024
                                        HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           Filament 221 lrrqiqsleieleslkkqkasleaqlaeleer 252
                                        ++ qi++le ele+l+k++a+l ++ +el ++
  gene1464|gene1464|rna1464|rna1464 119 SNAQIDRLERELEKLRKENAKLADRNKELIDK 150
                                        67899999999999999999999988887655 PP

>> CENP-H  Centromere protein H (CENP-H)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6  10.7   0.00033     0.069       6      80 ..      36     113 ..      31     121 .. 0.87
   2 ?    7.4   6.6     0.028       5.8      17      61 ..     118     162 ..     114     188 .] 0.71

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 0.00033
                             CENP-H   6 eqrdelssellklsqelrelqeeltevekenlrlkrknrelaaellelakekesek...eklkeelekleaelkks 78 
                                        +q+ e  +++  l+++++elq +l+++e++n +  + n++l ael   +k+ ++ +    ++++++ekl ae++  
  gene1464|gene1464|rna1464|rna1464  36 DQIAEKDERIDTLKKQTTELQHKLEDLEEQNAEWGTNNNKLQAELDIVNKDVKRLQaisVEKERKIEKLNAEVESC 111
                                        566666778889999******************************99999998888899778999******99987 PP

                             CENP-H  79 rq 80 
                                        r+
  gene1464|gene1464|rna1464|rna1464 112 RK 113
                                        76 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.028
                             CENP-H  17 klsqelrelqeeltevekenlrlkrknrelaaellelakekesek 61 
                                        + ++++  l++el++++ken +l  +n+el+ +  +l ++k   k
  gene1464|gene1464|rna1464|rna1464 118 ASNAQIDRLERELEKLRKENAKLADRNKELIDKNKKLGNDKVLGK 162
                                        56678999**********************998866666665444 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   4.1    0.0017      0.35      11      68 ..      36      86 ..      30      97 .. 0.76
   2 ?    6.6   0.4     0.054        11      17      56 ..      98     135 ..      87     159 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0017
                            NPV_P10 11 adikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenIqdiLnpd 68
                                       + i++ d+++d l++q +++q++l+d       L++q+a+  + ++k+++  di n+d
  gene1464|gene1464|rna1464|rna1464 36 DQIAEKDERIDTLKKQTTELQHKLED-------LEEQNAEWGTNNNKLQAELDIVNKD 86
                                       67999999999999999999999999.......6666666666666666666666644 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.054
                            NPV_P10  17 ddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaelet 56 
                                        + k++ l+++v++ +++ +  +  n+++d++  +L++l +
  gene1464|gene1464|rna1464|rna1464  98 ERKIEKLNAEVESCRKEGNAAS--NAQIDRLERELEKLRK 135
                                        5799999999999999999855..9999999999998876 PP

>> PRKG1_interact  cGMP-dependent protein kinase interacting domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   2.2     0.086        18       2      41 ..      27      66 ..       7      70 .. 0.72
   2 ?    7.9  21.5     0.029       5.9       5      94 ..      30     148 ..      26     154 .. 0.50

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.086
                     PRKG1_interact  2 YkkLYeeekeenerLkreLeelekelselkseleklkqqr 41
                                       + kLY +  ++  +  +++++l+k+++el+ +le l++q+
  gene1464|gene1464|rna1464|rna1464 27 FHKLYASLSDQIAEKDERIDTLKKQTTELQHKLEDLEEQN 66
                                       5566666666666666777777777777777777766553 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.029
                     PRKG1_interact   5 LYeeekeenerLkreLeelekelselkseleklkqqrqe................svskrssllelekrerrsler 64 
                                        LY +  ++  +  +++++l+k+++el+ +le l++q+ e                +  + ++l  ++ +++r++e+
  gene1464|gene1464|rna1464|rna1464  30 LYASLSDQIAEKDERIDTLKKQTTELQHKLEDLEEQNAEwgtnnnklqaeldivnK--DVKRLQAISVEKERKIEK 103
                                        55555555555555555555555555555555555544444444444444444331..222222222222222333 PP

                     PRKG1_interact  65 kisel.....eeel............keleeLraenqrLkdEngALi 94 
                                          +e+     e               +ele+Lr+en++L d n+ Li
  gene1464|gene1464|rna1464|rna1464 104 LNAEVescrkE--GnaasnaqidrleRELEKLRKENAKLADRNKELI 148
                                        22222222321..13344444455559999*************9998 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   7.4   0.00019     0.038      15      86 ..      21      92 ..      12      99 .. 0.90
   2 ?    6.1   4.4     0.029       6.1      37      93 ..      85     142 ..      83     150 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00019
                            DUF3450 15 aatldqalkeaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiaslee 86
                                       +a ++q +k  ++  ++ a+  ++id l+++++el+ ++++l+e++++    n++l++ ++ +++++++l+ 
  gene1464|gene1464|rna1464|rna1464 21 SARVAQFHKLYASLSDQIAEKDERIDTLKKQTTELQHKLEDLEEQNAEWGTNNNKLQAELDIVNKDVKRLQA 92
                                       677888999999999999999****************************************99999999985 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.029
                            DUF3450  37 kkidklddekqellaeyralkeeleslevy.neqlerlvasqeqeiasleeqieeiee 93 
                                        k +++l+  + e ++++++l++e+es +++ n+  +++++ +e+e+++l+++ +++  
  gene1464|gene1464|rna1464|rna1464  85 KDVKRLQAISVEKERKIEKLNAEVESCRKEgNAASNAQIDRLERELEKLRKENAKLAD 142
                                        6677788888888999999999999988764777888999999999999988877765 PP

>> DUF5401  Family of unknown function (DUF5401)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1  22.6   0.00018     0.037     371     507 ..      55     186 ..      33     187 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00018
                            DUF5401 371 veisrlrelerlqlerqqknervrqeleaark....vkileeerqrkikeqkvemekirkeqeearqeelrrleee 442
                                        +  ++l +le  + e    n++++ el+   k     + +  e++rki++ + e+e  rke + a + ++ rle  
  gene1464|gene1464|rna1464|rna1464  55 L-QHKLEDLEEQNAEWGTNNNKLQAELDIVNKdvkrLQAISVEKERKIEKLNAEVESCRKEGNAASNAQIDRLE-- 127
                                        2.258999*******************9876632112345679*****************************97.. PP

                            DUF5401 443 rarelervreeelerqqqverlrqqeeerkrkklelekekrekkeaeeer.rkilekeleerkqal 507
                                          rele++r+e+ +  +     r++e   k+kkl  +k   +k+ + e++ r++l + ++ rk+++
  gene1464|gene1464|rna1464|rna1464 128 --RELEKLRKENAKLAD-----RNKELIDKNKKLGNDKVLGKKNIVLEKNtRRLLTNTMKLRKNTM 186
                                        ..89******9987654.....677888899*******9999998877777***********9987 PP

>> GIT_CC  GIT coiled-coil Rho guanine nucleotide exchange factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.2     0.079        16      30      64 ..      22      56 ..      19      58 .. 0.89
   2 ?    5.2   0.9     0.096        20      42      61 ..      48      67 ..      31      72 .. 0.70
   3 ?    0.3   6.7       3.2   6.7e+02      20      57 ..      54      91 ..      48     114 .. 0.63
   4 ?    9.6   0.7     0.004      0.82      39      65 ..     116     142 ..      96     143 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.079
                             GIT_CC 30 akiqqLlkvNtslsdelrlLQskvqkLqaeNaqlr 64
                                       a++ q  k  +slsd++++  + +++L++  ++l+
  gene1464|gene1464|rna1464|rna1464 22 ARVAQFHKLYASLSDQIAEKDERIDTLKKQTTELQ 56
                                       7999999********************99888875 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.096
                             GIT_CC 42 lsdelrlLQskvqkLqaeNa 61
                                       l+++ ++LQ k++ L++ Na
  gene1464|gene1464|rna1464|rna1464 48 LKKQTTELQHKLEDLEEQNA 67
                                       55666677777777777776 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 3.2
                             GIT_CC 20 elKkalaaseakiqqLlkvNtslsdelrlLQskvqkLq 57
                                       el  +l   e +  +    N++l+ el    + v++Lq
  gene1464|gene1464|rna1464|rna1464 54 ELQHKLEDLEEQNAEWGTNNNKLQAELDIVNKDVKRLQ 91
                                       33334444444444444455555555555555555555 PP

  == domain 4  score: 9.6 bits;  conditional E-value: 0.004
                             GIT_CC  39 NtslsdelrlLQskvqkLqaeNaqlrd 65 
                                        N+  + ++ +L ++++kL +eNa+l d
  gene1464|gene1464|rna1464|rna1464 116 NAASNAQIDRLERELEKLRKENAKLAD 142
                                        7777899****************9965 PP

>> ADIP  Afadin- and alpha -actinin-Binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9  11.1    0.0075       1.5      58     113 ..      34      89 ..      29     113 .. 0.49
   2 ?    7.3   9.9     0.023       4.7      59     114 ..      98     154 ..      81     170 .. 0.58
   3 ?    8.0   8.8     0.013       2.8      54     124 ..     115     185 ..     112     187 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0075
                               ADIP  58 lnetirkleaeierlqskierlktqleqlerelalvqakerqlekklktleqklkn 113
                                        l+++i +++  i+ l++++  l+ +le+le ++a +  + ++l+++l   ++ +k+
  gene1464|gene1464|rna1464|rna1464  34 LSDQIAEKDERIDTLKKQTTELQHKLEDLEEQNAEWGTNNNKLQAELDIVNKDVKR 89 
                                        45555555555555555555555555555555555555555554444333333332 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.023
                               ADIP  59 netirkleaeierlqskierlk.tqleqlerelalvqakerqlekklktleqklkne 114
                                        +++i+kl+ae e+ +++ +  + +q  +lerel+ + ++ ++l  ++k+l++k+k++
  gene1464|gene1464|rna1464|rna1464  98 ERKIEKLNAEVESCRKEGNAASnAQIDRLERELEKLRKENAKLADRNKELIDKNKKL 154
                                        445555555555555555554445555555555555555555555555555555554 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.013
                               ADIP  54 qreslnetirkleaeierlqskierlktqleqlerelalvqakerqlekklktleqklknekeelqrlkna 124
                                         + ++n++i +le e+e+l+++  +l +++++l  +++ + +++   +k++  ++++ + ++  ++  kn+
  gene1464|gene1464|rna1464|rna1464 115 GNAASNAQIDRLERELEKLRKENAKLADRNKELIDKNKKLGNDKVLGKKNIVLEKNTRRLLTNTMKLRKNT 185
                                        567899********************************999999999999999999888888877766665 PP

>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   1.5     0.014       2.8       7      35 ..      36      64 ..      31      68 .. 0.87
   2 ?    7.0   2.9     0.037       7.6       3      40 ..      53      90 ..      51      93 .. 0.91
   3 ?    7.5   3.7     0.025       5.2      15      41 ..     122     148 ..      95     157 .. 0.63

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.014
                          FlaC_arch  7 nklsklsteletvkkeneelsksveelke 35
                                        ++ + + +++t+kk+  el+ ++e+l+e
  gene1464|gene1464|rna1464|rna1464 36 DQIAEKDERIDTLKKQTTELQHKLEDLEE 64
                                       567778889******************98 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.037
                          FlaC_arch  3 delEnklsklsteletvkkeneelsksveelkenVkdl 40
                                        el+ kl++l+ + +   ++n++l+ +++ ++++Vk+l
  gene1464|gene1464|rna1464|rna1464 53 TELQHKLEDLEEQNAEWGTNNNKLQAELDIVNKDVKRL 90
                                       7999*******************************998 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.025
                          FlaC_arch  15 eletvkkeneelsksveelkenVkdll 41 
                                        +++ +++e+e+l+k+  +l ++ k+l+
  gene1464|gene1464|rna1464|rna1464 122 QIDRLERELEKLRKENAKLADRNKELI 148
                                        666666666666666666666666665 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   8.6   0.00081      0.17      30      99 ..       4      88 ..       1      93 [. 0.77
   2 ?    7.9  13.5      0.02       4.1      13      94 ..      75     154 ..      74     177 .. 0.57

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00081
                             APG6_N 30 eflkklkkekkeeek...............qdeeleeleeeleklekeeeelleeLkelekereeleaelaaleeele 92
                                       e+lk   ++++ e+k                 ++++e +e++++l+k+  el+ +L++le++++e     ++l++el+
  gene1464|gene1464|rna1464|rna1464  4 EYLKLSSRTRVLEQKffsarvaqfhklyasLSDQIAEKDERIDTLKKQTTELQHKLEDLEEQNAEWGTNNNKLQAELD 81
                                       55555555555544466666666666666677889999999************************9999999999999 PP

                             APG6_N 93 aleeeee 99
                                        ++++ +
  gene1464|gene1464|rna1464|rna1464 82 IVNKDVK 88
                                       8877655 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.02
                             APG6_N  13 eldkqleqaekerdaYeeflkklkkekkeeekqdeeleeleee.leklekeeeelleeLkelekereeleaelaal 87 
                                        +l+ +l+ ++k+ + +++   + +++ ++ +    e+e+ ++e  ++ +++ ++l++eL++l ke+++l++  ++l
  gene1464|gene1464|rna1464|rna1464  75 KLQAELDIVNKDVKRLQAISVEKERKIEKLN---AEVESCRKEgNAASNAQIDRLERELEKLRKENAKLADRNKEL 147
                                        4566666666666666666555555544433...355555555222333444455555555555555555555555 PP

                             APG6_N  88 eeeleal 94 
                                          + ++l
  gene1464|gene1464|rna1464|rna1464 148 IDKNKKL 154
                                        5555444 PP

>> DUF4200  Domain of unknown function (DUF4200)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   4.8     0.004      0.82      65     104 ..      28      67 ..      16      81 .. 0.78
   2 ?    4.7  12.2      0.19        39      65     108 ..      84     135 ..      71     154 .. 0.51

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.004
                            DUF4200  65 lkkaeeerklkkekeaeikklkaeietlkseiekleekle 104
                                         k +++ ++++ ek++ i  lk+++++l+ ++e lee+ +
  gene1464|gene1464|rna1464|rna1464  28 HKLYASLSDQIAEKDERIDTLKKQTTELQHKLEDLEEQNA 67 
                                        5666777788888888888888888888888888888765 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.19
                            DUF4200  65 lkkaeeerklkkekeaeikklkaeietlk........seiekleekleeykk 108
                                        +k +++ +    eke++i+kl+ae+e ++        ++i++le++le+++k
  gene1464|gene1464|rna1464|rna1464  84 NKDVKRLQAISVEKERKIEKLNAEVESCRkegnaasnAQIDRLERELEKLRK 135
                                        3344444444445555555555555555555555555555555555554433 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   5.0   0.00038     0.078     198     250 ..      21      73 ..       4      78 .. 0.80
   2 ?    5.8  13.5     0.025       5.2     148     229 ..      73     154 ..      67     184 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00038
                               Spc7 198 keeLeelreelaelkaeieekkkelaelqeqleeleekieelkeqkseleeei 250
                                        +++++++++  a+l+ +i+ek +++++l++q +el+ k+e+l+eq +e+ ++ 
  gene1464|gene1464|rna1464|rna1464  21 SARVAQFHKLYASLSDQIAEKDERIDTLKKQTTELQHKLEDLEEQNAEWGTNN 73 
                                        56678888888999999999999999999999999999999999999886665 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.025
                               Spc7 148 legleedkelLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkela 223
                                         ++l+++ + ++k+ + l+++  e e++ ++l++e+e+ +++ +  ++ + ++Le   e+l++ +a+++ ++kel 
  gene1464|gene1464|rna1464|rna1464  73 NNKLQAELDIVNKDVKRLQAISVEKERKIEKLNAEVESCRKEGNAASNAQIDRLERELEKLRKENAKLADRNKELI 148
                                        4455555556666666666666666666666666666666655555555555555555555555555555555555 PP

                               Spc7 224 elqeql 229
                                        +++++l
  gene1464|gene1464|rna1464|rna1464 149 DKNKKL 154
                                        555544 PP

>> IFT20  Intraflagellar transport complex B, subunit 20
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   8.2    0.0036      0.74      27     118 ..      16     103 ..       4     104 .. 0.79
   2 ?    8.1   1.9     0.014       2.9      67     107 ..      73     113 ..      69     117 .. 0.92
   3 ?    4.1   2.1      0.24        50      78     109 ..     113     144 ..     109     151 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0036
                              IFT20  27 eckeFvkkinefqklvkelievleelakkvekeKlkAigarnllkseakqreaeqqqlqaliaekkaeleRlrvel 102
                                        e k F+ ++ +f+kl  +l++++ e  +++++ K +    + +l++ ++q     ++  ++ ++ +ael+ ++   
  gene1464|gene1464|rna1464|rna1464  16 EQKFFSARVAQFHKLYASLSDQIAEKDERIDTLKKQTTELQHKLEDLEEQN----AEWGTNNNKLQAELDIVNKDV 87 
                                        56678899***************************9999999998887765....455555666677777777777 PP

                              IFT20 103 esLqkveqeqkeliek 118
                                        + Lq +  e++  iek
  gene1464|gene1464|rna1464|rna1464  88 KRLQAISVEKERKIEK 103
                                        7777777777777776 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.014
                              IFT20  67 rnllkseakqreaeqqqlqaliaekkaeleRlrvelesLqk 107
                                         n+l++e +  +++ + lqa   ek+ ++e+l++e es +k
  gene1464|gene1464|rna1464|rna1464  73 NNKLQAELDIVNKDVKRLQAISVEKERKIEKLNAEVESCRK 113
                                        689999999999*************************9887 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.24
                              IFT20  78 eaeqqqlqaliaekkaeleRlrvelesLqkve 109
                                        ++ +++ +a+i   + ele+lr e   L   +
  gene1464|gene1464|rna1464|rna1464 113 KEGNAASNAQIDRLERELEKLRKENAKLADRN 144
                                        55566777888888888888888888776654 PP

>> Sec34  Sec34-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   4.5   0.00026     0.053       3      61 ..      36      94 ..      34     103 .. 0.93
   2 ?    3.6   2.0      0.26        54      13      64 ..     102     154 ..      95     186 .. 0.57

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00026
                              Sec34  3 dqLeskeeecdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleela 61
                                       dq+ +k e++d+l +qt+e++ +Le+lee+  +  ++ ++l+++ + + ++ krl+ ++
  gene1464|gene1464|rna1464|rna1464 36 DQIAEKDERIDTLKKQTTELQHKLEDLEEQNAEWGTNNNKLQAELDIVNKDVKRLQAIS 94
                                       8999*************************************************999876 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.26
                              Sec34  13 delleqtdealeqLeele.ekfksvsektsslheaceqlleeqkrleelaeei 64 
                                        ++l ++++++ ++ +  +  + ++ + + ++l+++  +l + +k+l + ++++
  gene1464|gene1464|rna1464|rna1464 102 EKLNAEVESCRKEGNAASnAQIDRLERELEKLRKENAKLADRNKELIDKNKKL 154
                                        44444444444444333213444444444445544444444444444444444 PP

>> Mt_ATP-synt_D  ATP synthase D chain, mitochondrial (ATP5H)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   2.0     0.027       5.6      64     117 ..      23      80 ..      10      97 .. 0.54
   2 ?    9.0   1.2    0.0055       1.1      84     122 ..      97     135 ..      88     142 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.027
                                        HHHHHHHHHHH-------.-TTTTHHHHHHHHHHHHC...HHHHHHHHHHHHHHHHHH CS
                      Mt_ATP-synt_D  64 lVdeFekkYealkipype.dkyteevdaeekevkkei...kefkeeskkrieelekel 117
                                         V +F k Y +l+  + e d+    + ++++e +++    +e ++e   + ++l+ el
  gene1464|gene1464|rna1464|rna1464  23 RVAQFHKLYASLSDQIAEkDERIDTLKKQTTELQHKLedlEEQNAEWGTNNNKLQAEL 80 
                                        4667777777774444442333344444444444333000333444444555555555 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0055
                                        TTTHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHT- CS
                      Mt_ATP-synt_D  84 yteevdaeekevkkeikefkeeskkrieelekeleklks 122
                                        ++ ++++ + ev+   ke +++s+++i+ le elekl++
  gene1464|gene1464|rna1464|rna1464  97 KERKIEKLNAEVESCRKEGNAASNAQIDRLERELEKLRK 135
                                        568999999***************************975 PP

>> CK2S  Casein Kinase 2 substrate
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.5      0.25        51      38      91 ..      13      64 ..       6      65 .. 0.72
   2 ?   12.9   6.3   0.00037     0.077       2      89 ..      55     147 ..      54     183 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.25
                               CK2S 38 qalqnvklygtplrdfpdlqerLrekqlealeevlakLrekleelqkvrdslek 91
                                       ++l ++k+ ++ +++f++l   L  +++e+ +e +++L+++ +elq   ++le+
  gene1464|gene1464|rna1464|rna1464 13 RVL-EQKFFSARVAQFHKLYASLSDQIAEK-DERIDTLKKQTTELQHKLEDLEE 64
                                       444.45555566999999999998877665.77789999999999987777765 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 0.00037
                               CK2S   2 lrkafrkveeqrekWkellseseslleslsnlaeqlqalqnvklygtp.....lrdfpdlqerLrekqlealeevl 72 
                                        l+ + + +eeq + W   ++++++ l+ +   +++lqa++  k  + +     +++  +   +   +q+  le++l
  gene1464|gene1464|rna1464|rna1464  55 LQHKLEDLEEQNAEWGTNNNKLQAELDIVNKDVKRLQAISVEKERKIEklnaeVESCRKEGNAASNAQIDRLEREL 130
                                        7888999*********************************999887767766677777777788888888888888 PP

                               CK2S  73 akLrekleelqkvrdsl 89 
                                        +kLr++ ++l + +++l
  gene1464|gene1464|rna1464|rna1464 131 EKLRKENAKLADRNKEL 147
                                        88888888887777665 PP

>> Hom_end_hint  Hom_end-associated Hint
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   1.9   0.00081      0.17      94     164 ..      25      92 ..       5     105 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00081
                                        EEEEEEEEEEEEEE-TTS-EEEEEEEEEEEEE.GGGTTHHHHHHHHHHHTS-SSSEEEEEEEGGGGGGS-H CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Hom_end_hint  94 kytsVtyfalekektedgrvieivkevtksfehesegkekaaekakeFastidkeeiewtieardlkklee 164
                                         +++  y +l+++++e++++i+  k++t + +h+ e+ e+++   +e+ ++ +k + e +i  +d+k+l++
  gene1464|gene1464|rna1464|rna1464  25 AQFHKLYASLSDQIAEKDERIDTLKKQTTELQHKLEDLEEQN---AEWGTNNNKLQAELDIVNKDVKRLQA 92 
                                        44555699***************************9887755...89********************9986 PP

>> Atg14  Vacuolar sorting 38 and autophagy-related subunit 14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7  20.0   0.00098       0.2      21     134 ..      35     149 ..      23     166 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00098
                              Atg14  21 perlyelrerlaklksekeslkkkiekalegke....eaeqledkiknkkakleelksliadlrerlqelkdklsq 92 
                                        ++++ e+ er+  lk++  +l+ k+e+++e++     ++++l+++++  ++++++l++ + ++++++++l++ +++
  gene1464|gene1464|rna1464|rna1464  35 SDQIAEKDERIDTLKKQTTELQHKLEDLEEQNAewgtNNNKLQAELDIVNKDVKRLQAISVEKERKIEKLNAEVES 110
                                        6799***************************9999*99************************************99 PP

                              Atg14  93 lkkeieekk.kklaklsdklkkRrsdleslqneleerrkkqia 134
                                         +ke ++++ +++ +l ++l k r++    + +l+ r k++i+
  gene1464|gene1464|rna1464|rna1464 111 CRKEGNAASnAQIDRLERELEKLRKE----NAKLADRNKELID 149
                                        888765555279********988888....6666666666665 PP

>> DUF4795  Domain of unknown function (DUF4795)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   2.2    0.0032      0.67      21      62 ..      22      63 ..      18      69 .. 0.74
   2 ?    9.1   2.1    0.0044      0.91      17      59 ..      74     116 ..      67     122 .. 0.91
   3 ?    3.6   1.3      0.21        42       5      39 ..     119     153 ..     115     174 .. 0.64

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0032
                            DUF4795 21 eelekleekvkelekrledkekklealkkqieelekvkadke 62
                                       +++++ ++  ++l++++++k++ +++lkkq+ el+ + +d e
  gene1464|gene1464|rna1464|rna1464 22 ARVAQFHKLYASLSDQIAEKDERIDTLKKQTTELQHKLEDLE 63
                                       566777778888888888888888888888888887766644 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0044
                            DUF4795  17 eklqeelekleekvkelekrledkekklealkkqieelekvka 59 
                                         klq+el+ +++ vk+l+  + +ke+k+e l  ++e ++k++ 
  gene1464|gene1464|rna1464|rna1464  74 NKLQAELDIVNKDVKRLQAISVEKERKIEKLNAEVESCRKEGN 116
                                        689************************************9874 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.21
                            DUF4795   5 saellkklqeaieklqeelekleekvkelekrled 39 
                                        s+  ++ l+ ++ekl +e +kl ++ kel ++ ++
  gene1464|gene1464|rna1464|rna1464 119 SNAQIDRLERELEKLRKENAKLADRNKELIDKNKK 153
                                        55556666677777777777777777766655443 PP

>> UPF0242  Uncharacterised protein family (UPF0242) N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   7.7   0.00047     0.097      67     137 ..      21      91 ..       1      96 [. 0.77
   2 ?    4.6   8.3      0.15        31      87     134 ..      97     152 ..      89     184 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00047
                            UPF0242  67 kskleekeaklteldeglktkeealeelqeeeeeLkeeldakeeelerlkeenqqLqekleaiaedfeelk 137
                                        +  +++ +++  +l++++++k+e +  l++++ eL+++l+  ee+ ++   +n++Lq +l  + +d+++l+
  gene1464|gene1464|rna1464|rna1464  21 SARVAQFHKLYASLSDQIAEKDERIDTLKKQTTELQHKLEDLEEQNAEWGTNNNKLQAELDIVNKDVKRLQ 91 
                                        333334444555666999*****************************************999999988765 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.15
                            UPF0242  87 keealeelqeeeeeLkee........ldakeeelerlkeenqqLqekleaiaedfe 134
                                        ke ++e+l++e e  ++e        +d  e+ele+l++en++L  + ++    ++
  gene1464|gene1464|rna1464|rna1464  97 KERKIEKLNAEVESCRKEgnaasnaqIDRLERELEKLRKENAKLADRNKELIDKNK 152
                                        44466666666666666666666666888888888888888888777666554443 PP

>> Prefoldin_2  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   7.1    0.0091       1.9      65     102 ..      39      76 ..      26      79 .. 0.59
   2 ?    5.5   2.5     0.075        16      65      99 ..      74     108 ..      69     117 .. 0.85
   3 ?    6.9   2.5     0.028       5.8      72     103 ..     117     148 ..     106     153 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0091
                                        HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC CS
                        Prefoldin_2  65 eeLeerketlekeiktlekqleklekeleelkeelqkk 102
                                        +e +er++tl+k+ ++l+ +le+le++ +e+ ++++k+
  gene1464|gene1464|rna1464|rna1464  39 AEKDERIDTLKKQTTELQHKLEDLEEQNAEWGTNNNKL 76 
                                        34455666666666666666666666666666666655 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.075
                                        HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        Prefoldin_2  65 eeLeerketlekeiktlekqleklekeleelkeel 99 
                                        ++L+++++ ++k +k+l+    ++e+++e+l +e+
  gene1464|gene1464|rna1464|rna1464  74 NKLQAELDIVNKDVKRLQAISVEKERKIEKLNAEV 108
                                        78999999999999999999999999999998776 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.028
                                        HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCT CS
                        Prefoldin_2  72 etlekeiktlekqleklekeleelkeelqkkl 103
                                        +  +++i++le++lekl+ke ++l + +++++
  gene1464|gene1464|rna1464|rna1464 117 AASNAQIDRLERELEKLRKENAKLADRNKELI 148
                                        56678899999999999999999888888776 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   6.6    0.0035      0.73      43     117 ..      31     108 ..      17     113 .. 0.56
   2 ?    7.6   5.6     0.018       3.6      50     121 ..      62     134 ..      52     137 .. 0.78
   3 ?    3.5   1.0      0.34        69      66     114 ..      99     148 ..      94     157 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0035
                            DUF1664  43 vesvskqleqvs...eslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegles 115
                                         +s+s q+ +     ++l+++  +L+++++ ++++  e     +++++e++ v++d+++++  + + ++ +e+l++
  gene1464|gene1464|rna1464|rna1464  31 YASLSDQIAEKDeriDTLKKQTTELQHKLEDLEEQNAEWGTNNNKLQAELDIVNKDVKRLQAISVEKERKIEKLNA 106
                                        4555555554441113444444456666666666666666666666666666666666666666666666666665 PP

                            DUF1664 116 kl 117
                                        ++
  gene1464|gene1464|rna1464|rna1464 107 EV 108
                                        55 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.018
                            DUF1664  50 leqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesv.keaveglesklerie 121
                                        le+  ++  +  ++L++++d v+k ++  ++is e ++++++++ ++++ +++ ++  ++ +  le +le++ 
  gene1464|gene1464|rna1464|rna1464  62 LEEQNAEWGTNNNKLQAELDIVNKDVKRLQAISVEKERKIEKLNAEVESCRKEGNAAsNAQIDRLERELEKLR 134
                                        5555566667788999999999999999999999999999999999999999987761456888998888875 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.34
                            DUF1664  66 sridrvdkkldeq.keiskeikeevtevredlseigedvesvkeavegle 114
                                        ++i++++++++++ ke  ++ ++++++++++l++++++  ++ +  ++l 
  gene1464|gene1464|rna1464|rna1464  99 RKIEKLNAEVESCrKEGNAASNAQIDRLERELEKLRKENAKLADRNKELI 148
                                        46777777777772345566667788888888888877777766655554 PP

>> FAM76  FAM76 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   5.2    0.0013      0.27     221     289 ..      24      91 ..      16      94 .. 0.83
   2 ?    5.9  10.3     0.033       6.9     223     299 ..      75     151 ..      71     153 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0013
                              FAM76 221 vtqLkeeiaslkkqleqkdqellekdkkitelkaellekekelreklkelekeakekieklekkirell 289
                                        v+q+++  asl  q+++kd+ + + +k+ tel+ +l++ e+++ e   +++++ +++++ ++k +++l+
  gene1464|gene1464|rna1464|rna1464  24 VAQFHKLYASLSDQIAEKDERIDTLKKQTTELQHKLEDLEEQNAEWG-TNNNKLQAELDIVNKDVKRLQ 91 
                                        788899999**************************999998877654.445556777888888877775 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.033
                              FAM76 223 qLkeeiaslkkqleqkdqellekdkkitelkaellekekelreklkelekeakekieklekkirellkevaelskk 298
                                        +L+ e+   +k +++ +   +ek++ki +l ae ++ +ke +   +++    ++++ekl+k++++l   + el  k
  gene1464|gene1464|rna1464|rna1464  75 KLQAELDIVNKDVKRLQAISVEKERKIEKLNAEVESCRKEGNAASNAQIDRLERELEKLRKENAKLADRNKELIDK 150
                                        7888999999999999999999**********99999999999999999999999999999999998777666655 PP

                              FAM76 299 k 299
                                        +
  gene1464|gene1464|rna1464|rna1464 151 N 151
                                        4 PP

>> Spc24  Spc24 subunit of Ndc80
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2  11.8      0.24        49       8      49 ..      33      82 ..      26     123 .. 0.78
   2 ?    8.8   4.9    0.0092       1.9      11      44 ..     121     162 ..     114     182 .. 0.73

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.24
                              Spc24  8 riakelsdleselesleselaelkeeleeleeesee...keser.....v 49
                                       +++ ++ + ++ ++ l+++ +el+++le+lee++ e   +++++      
  gene1464|gene1464|rna1464|rna1464 33 SLSDQIAEKDERIDTLKKQTTELQHKLEDLEEQNAEwgtNNNKLqaeldI 82
                                       67788899999999999999999999999999999988744433344441 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0092
                              Spc24  11 kelsdleselesleselaelkeeleeleeesee........k 44 
                                         +++ le+ele+l++e a+l ++ +el +++++        k
  gene1464|gene1464|rna1464|rna1464 121 AQIDRLERELEKLRKENAKLADRNKELIDKNKKlgndkvlgK 162
                                        578899999999999999999999999999888653333332 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   2.8     0.014       2.8      41      84 ..      25      68 ..       8      89 .. 0.55
   2 ?   12.5   6.1   0.00053      0.11       5      69 ..      45     109 ..      41     113 .. 0.94
   3 ?    5.2   9.8     0.098        20      14      87 ..      82     156 ..      72     174 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.014
                                       XXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH CS
                         Laminin_II 41 eetnekvkdankairdArrsvkkLeklapqLldklkelkqleea 84
                                       ++ +++  +++ +i++  + + +L+k+  +L  kl+ l++++ +
  gene1464|gene1464|rna1464|rna1464 25 AQFHKLYASLSDQIAEKDERIDTLKKQTTELQHKLEDLEEQNAE 68
                                       45555555555566666666666666666666666666555443 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00053
                                        XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTT CS
                         Laminin_II   5 aaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklap 69 
                                        ++  +++++e +++l++l+++  ++  + ++++++++ +n++vk ++ + ++ +r++ kL+ +++
  gene1464|gene1464|rna1464|rna1464  45 IDTLKKQTTELQHKLEDLEEQNAEWGTNNNKLQAELDIVNKDVKRLQAISVEKERKIEKLNAEVE 109
                                        66778999*****************************************************9987 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.098
                                        XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH... CS
                         Laminin_II  14 evleqlaplsqnlentkeklseinrsveetnekvk.dankairdArrsvkkLeklapqLldklkelkqleeasss 87 
                                         v ++++ l++   + + k++++n++ve   ++ + ++n +i+  +r+  kL k+  +L d+ kel  ++++ ++
  gene1464|gene1464|rna1464|rna1464  82 IVNKDVKRLQAISVEKERKIEKLNAEVESCRKEGNaASNAQIDRLERELEKLRKENAKLADRNKELIDKNKKLGN 156
                                        588899999998888999************99999788999*********************9999777776554 PP

>> FUSC  Fusaric acid resistance protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   2.9    0.0051       1.1     214     304 ..      38     148 ..       7     156 .. 0.59

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0051
                               FUSC 214 irararalrrllsrmlallallsslarllarlraeeaaavpelaallaelaal....................eaa 269
                                        i++  +++  l  ++++l   l  l+++ a++ +++++ ++el+ + +++++l                    +++
  gene1464|gene1464|rna1464|rna1464  38 IAEKDERIDTLKKQTTELQHKLEDLEEQNAEWGTNNNKLQAELDIVNKDVKRLqaisvekerkieklnaevesCRK 113
                                        4445555555555555555555555555555555555555555555555555566666444444444444444555 PP

                               FUSC 270 aaaealeaalaalrarlralrraleadadtaalll 304
                                        +  +a  a++++l+++l++lr+++++ ad++ +l+
  gene1464|gene1464|rna1464|rna1464 114 EGNAASNAQIDRLERELEKLRKENAKLADRNKELI 148
                                        56666777777777777777777776666666655 PP

>> DUF4472  Domain of unknown function (DUF4472)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   8.4      0.13        27      33     106 ..      34     107 ..      22     120 .. 0.80
   2 ?   10.3   2.1    0.0043       0.9      45      93 ..     124     171 ..     113     185 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.13
                            DUF4472  33 lknkvlalenrvlelelerekaaeeiqslrerlaeleeekkeleeeyvvlkknyqalekefekekkkqqelsle 106
                                        l  ++ + ++r+  l+ +  +++++ ++l+e+ ae  +++++l++e+ +++k+++ l++   ++++k ++l++e
  gene1464|gene1464|rna1464|rna1464  34 LSDQIAEKDERIDTLKKQTTELQHKLEDLEEQNAEWGTNNNKLQAELDIVNKDVKRLQAISVEKERKIEKLNAE 107
                                        55667777778888888888888888888888889999999999999999998888888888888888887766 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.0043
                            DUF4472  45 lelelerekaaeeiqslrerlaeleeekkeleeeyvvlkknyqalekef 93 
                                          le e ek+++e+++l++r +el +++k+l +  v  kkn+ +lek+ 
  gene1464|gene1464|rna1464|rna1464 124 DRLERELEKLRKENAKLADRNKELIDKNKKLGNDKVLGKKNI-VLEKNT 171
                                        5689999*************************9998877775.444444 PP

>> CCDC92  Coiled-coil domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.2    0.0068       1.4      29      44 ..      45      60 ..      43      70 .. 0.85
   2 ?    4.5   0.6      0.14        29      25      39 ..     126     140 ..     121     147 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0068
                             CCDC92 29 IekLqkenkdLtfkli 44
                                       I+ L+k+ ++L++kl+
  gene1464|gene1464|rna1464|rna1464 45 IDTLKKQTTELQHKLE 60
                                       899***********96 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.14
                             CCDC92  25 LHkEIekLqkenkdL 39 
                                        L  E+ekL+ken  L
  gene1464|gene1464|rna1464|rna1464 126 LERELEKLRKENAKL 140
                                        557999999999877 PP

>> HAUS-augmin3  HAUS augmin-like complex subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   6.4    0.0018      0.37      81     144 ..      25      88 ..       7      92 .. 0.77
   2 ?    6.4   8.4     0.029       5.9      64     153 ..      85     177 ..      82     185 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0018
                       HAUS-augmin3  81 eaLeqelqeLqkekalklkrlnkLqvqaaslqqelrkleeeekeakkklkeaqeelraenaetn 144
                                         ++ ++   L  + a k +r + L+ q+++lq++l++lee++ e   +++++q+el   n++++
  gene1464|gene1464|rna1464|rna1464  25 AQFHKLYASLSDQIAEKDERIDTLKKQTTELQHKLEDLEEQNAEWGTNNNKLQAELDIVNKDVK 88 
                                        5566677778888888888888888888888888888888888888888888888887777765 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.029
                       HAUS-augmin3  64 edvellevileeeeesleaLeqelqeLqkeka.lklkrlnkLqvqaaslqqelrkleeeekeakkklkea..qeel 136
                                        +dv+ l++i  e+e ++e+L++e++  +ke +   + + ++L+    +l +e+ kl++++ke   k+k++  ++ l
  gene1464|gene1464|rna1464|rna1464  85 KDVKRLQAISVEKERKIEKLNAEVESCRKEGNaASNAQIDRLERELEKLRKENAKLADRNKELIDKNKKLgnDKVL 160
                                        57888899999999**************9965156789***********************998888886224556 PP

                       HAUS-augmin3 137 raenaetnavLqqltee 153
                                        +++n  +++   +l+ +
  gene1464|gene1464|rna1464|rna1464 161 GKKNIVLEKNTRRLLTN 177
                                        77766666665555555 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   2.2     0.038       7.9       7      67 ..       8      66 ..       3      76 .. 0.69
   2 ?    5.9  15.3     0.032       6.6       3     113 ..      58     172 ..      35     178 .. 0.60

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.038
                              TMPIT  7 lekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeee 67
                                       l+++++ le+++  + +++++ +kl  ++s +i+++ +r+  lk++ ++l++++++ ee++
  gene1464|gene1464|rna1464|rna1464  8 LSSRTRVLEQKF--FSARVAQFHKLYASLSDQIAEKDERIDTLKKQTTELQHKLEDLEEQN 66
                                       555555666665..77777888888888888888888888888888888887766444443 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.032
                              TMPIT   3 eweelekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelker 78 
                                        ++e+le++  e  +++++++++l+ ++k  ++++    ++++++++l++++++++k+ ++ ++ ++++l++el++ 
  gene1464|gene1464|rna1464|rna1464  58 KLEDLEEQNAEWGTNNNKLQAELDIVNKDVKRLQAISVEKERKIEKLNAEVESCRKEGNAASNAQIDRLERELEKL 133
                                        3344444444444445555555555555555555555556666666666666666666677778888888776654 PP

                              TMPIT  79 k...kvlkevesllpkk.nglylklvlGnvnvsllnkqd 113
                                        +   + l++ ++ l  k + l    vlG+ n+ l ++  
  gene1464|gene1464|rna1464|rna1464 134 RkenAKLADRNKELIDKnKKLGNDKVLGKKNIVLEKNTR 172
                                        300044557777777774556667788888887766655 PP

>> MbeD_MobD  MbeD/MobD like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.5     0.043       8.9      21      65 ..      22      66 ..      15      71 .. 0.59
   2 ?    4.4   0.5      0.19        40      18      66 ..      61     109 ..      55     112 .. 0.88
   3 ?    3.7   0.2      0.32        67      41      68 ..     113     140 ..     102     142 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.043
                          MbeD_MobD 21 qrlqeWesafaelqrmfeltqrenaaLseqvtgLsqQVesLseqv 65
                                        r  +    +a+l   +  +      L++q t+L +  e+L eq 
  gene1464|gene1464|rna1464|rna1464 22 ARVAQFHKLYASLSDQIAEKDERIDTLKKQTTELQHKLEDLEEQN 66
                                       555555555666654444444444477777777777777777775 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.19
                          MbeD_MobD  18 dYeqrlqeWesafaelqrmfeltqrenaaLseqvtgLsqQVesLseqvr 66 
                                        d e +  eW    ++lq+  ++ +++   L++   +  + +e+L+ +v+
  gene1464|gene1464|rna1464|rna1464  61 DLEEQNAEWGTNNNKLQAELDIVNKDVKRLQAISVEKERKIEKLNAEVE 109
                                        6789999*******************99999999999999999998886 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.32
                          MbeD_MobD  41 qrenaaLseqvtgLsqQVesLseqvrRl 68 
                                        +  naa ++q+++L +  e+L ++ ++l
  gene1464|gene1464|rna1464|rna1464 113 KEGNAASNAQIDRLERELEKLRKENAKL 140
                                        455899999*******999998877666 PP

>> Occludin_ELL  Occludin homology domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   3.2     0.009       1.9      22      76 ..      36      90 ..      20     112 .. 0.70
   2 ?    3.3   4.8      0.68   1.4e+02      27      78 ..      90     142 ..      63     154 .. 0.59
   3 ?    7.1   1.7     0.042       8.6      33      74 ..     118     159 ..     102     180 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.009
                       Occludin_ELL 22 keYkelhaeleevskkfseLerelkelkegskeykkieeeilqeykklkkdpeyq 76
                                       ++  e  +++++++k+ +eL+++l++l+e++ e+ + +++++ e+  ++kd + +
  gene1464|gene1464|rna1464|rna1464 36 DQIAEKDERIDTLKKQTTELQHKLEDLEEQNAEWGTNNNKLQAELDIVNKDVKRL 90
                                       3334566788999999999999999999999999999999999998777765543 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.68
                       Occludin_ELL  27 lhaeleevskkfseLerelkelkegsk.eykkieeeilqeykklkkdpeyqek 78 
                                        l+a   e ++k+++L++e+++ +++ +   +  ++++ +e++kl+k+++ +++
  gene1464|gene1464|rna1464|rna1464  90 LQAISVEKERKIEKLNAEVESCRKEGNaASNAQIDRLERELEKLRKENAKLAD 142
                                        44444455555555556666655555544444555555666665553333333 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.042
                       Occludin_ELL  33 evskkfseLerelkelkegskeykkieeeilqeykklkkdpe 74 
                                        + ++++ +Lerel++l++++ + +++++e++++ kkl +d+ 
  gene1464|gene1464|rna1464|rna1464 118 ASNAQIDRLERELEKLRKENAKLADRNKELIDKNKKLGNDKV 159
                                        45678999*********************9999999877654 PP

>> Fez1  Fez1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0  20.3   0.00053      0.11      26     136 ..      38     146 ..      30     187 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00053
                               Fez1  26 vtqklseivalkaqlrelrakleekeeeikeleesleektlelevcenelqrkkseaellrekvekleeelkelre 101
                                        +++k + i +lk q+ el++kle+ ee++ e  ++ ++ ++el+ ++++++r ++ +  ++ k+ekl++e+++ r+
  gene1464|gene1464|rna1464|rna1464  38 IAEKDERIDTLKKQTTELQHKLEDLEEQNAEWGTNNNKLQAELDIVNKDVKRLQAISVEKERKIEKLNAEVESCRK 113
                                        4566667778999999999999999999999999999999999999999999998888888899999999999999 PP

                               Fez1 102 elselsleeeeaalesdeakaqrqeaeeleelkre 136
                                        e +++s+ + +  le +  k ++++a +l++ ++e
  gene1464|gene1464|rna1464|rna1464 114 EGNAASNAQIDR-LERELEKLRKENA-KLADRNKE 146
                                        888866544443.3333334444442.22222222 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4  18.7    0.0036      0.74     353     478 ..      13     141 ..       6     154 .. 0.84
   2 ?    3.5   9.8      0.11        22      91     154 ..      94     159 ..      85     186 .. 0.58

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0036
                             AAA_13 353 ksvelesvkakiesikklvaeineliakhNekvanleeekeeakkklelhlveeleseld..eykkkykklekaie 426
                                        + +e++ ++a++ ++ kl a++ ++ia+  e+++ l+++++e++ kle  + +++e   +  +++ +++ ++k+++
  gene1464|gene1464|rna1464|rna1464  13 RVLEQKFFSARVAQFHKLYASLSDQIAEKDERIDTLKKQTTELQHKLEDLEEQNAEWGTNnnKLQAELDIVNKDVK 88 
                                        5667778899999***********************************9887666644443388899999****** PP

                             AAA_13 427 klekelkeeeaelkkleeeikeLekqlrdek.paaeeinkeLkafGlgeleLk 478
                                         l++   e+e++++kl++e++  +k+ +      ++ +++eL++  +++++L+
  gene1464|gene1464|rna1464|rna1464  89 RLQAISVEKERKIEKLNAEVESCRKEGNAASnAQIDRLERELEKLRKENAKLA 141
                                        ***99999****************99876651569999999999877777776 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.11
                             AAA_13  91 siekqekieklkkeikkleek.leaaeaqlqkaekekkklek...eledeawkkivkkknsalsealk 154
                                        s+ek++kiekl+ e+++ +++   a++aq++ +e+e++kl k   +l+d++++ i + kn++l ++  
  gene1464|gene1464|rna1464|rna1464  94 SVEKERKIEKLNAEVESCRKEgNAASNAQIDRLERELEKLRKenaKLADRNKELI-D-KNKKLGNDKV 159
                                        799*************998875556667777777754444430003444444433.2.3333333322 PP

>> DUF812  Protein of unknown function (DUF812)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5  11.5   0.00096       0.2     332     424 ..      24     113 ..      16     115 .. 0.79
   2 ?    3.0   4.9      0.18        37     336     394 ..     120     178 ..     113     185 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00096
                             DUF812 332 leelqeqieeleskieeleeeikklessikqveeeleeekeeneelekevklkkktlellpdaeeniekLqalvea 407
                                        +++ ++ + +l+ +i+e +e i++l++++++++ +le ++e+n+e   ++++ +  l+++   ++ +++Lqa+ ++
  gene1464|gene1464|rna1464|rna1464  24 VAQFHKLYASLSDQIAEKDERIDTLKKQTTELQHKLEDLEEQNAEWGTNNNKLQAELDIV---NKDVKRLQAISVE 96 
                                        566778888888899999999999999999999999999999888887777666666666...7888999999999 PP

                             DUF812 408 saqrlvelakqWekhRv 424
                                        +++++ +l ++ e+ R+
  gene1464|gene1464|rna1464|rna1464  97 KERKIEKLNAEVESCRK 113
                                        99999999998888775 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.18
                             DUF812 336 qeqieeleskieeleeeikklessikqveeeleeekeeneelekevklkkktlellpda 394
                                        + qi++le+++e+l++e +kl+++ k++ ++ +++ + +   +k++ l+k t  ll ++
  gene1464|gene1464|rna1464|rna1464 120 NAQIDRLERELEKLRKENAKLADRNKELIDKNKKLGNDKVLGKKNIVLEKNTRRLLTNT 178
                                        57999999999999999999999999999999999999999999999999999999654 PP

>> DivIVA  DivIVA protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1  10.5    0.0066       1.4      35     124 ..      25     116 ..      20     121 .. 0.83
   2 ?    5.7   2.9      0.07        14      27      75 ..     123     171 ..     116     187 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0066
                                        HHHHHHHHHHHHHHHCCCCTXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXX CS
                             DivIVA  35 eallkeneelkekvkeleeklkeykeleetLkktlv.vaqetaeevkanakkeael.iikeAekkaekiveeaeee 108
                                         +++k  ++l ++++e++e+++  k++ ++L++ l  + ++ ae  ++n k +ael i+++  k+ ++i  e e++
  gene1464|gene1464|rna1464|rna1464  25 AQFHKLYASLSDQIAEKDERIDTLKKQTTELQHKLEdLEEQNAEWGTNNNKLQAELdIVNKDVKRLQAISVEKERK 100
                                        577788899**************************735667778888888889999556666666777778***** PP

                                        XXXXXXXXXXXXXXXX CS
                             DivIVA 109 akkiaeeieelkrqar 124
                                        ++k+++e+e+ +++ +
  gene1464|gene1464|rna1464|rna1464 101 IEKLNAEVESCRKEGN 116
                                        **********999865 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.07
                                        HHHHHHHHHHHHHHHHHHHHHHHCCCCTXXXXXXXXXXXXXXXXXXXXX CS
                             DivIVA  27 LdqvakdyeallkeneelkekvkeleeklkeykeleetLkktlvvaqet 75 
                                        +d + +++e+l ken++l ++ kel +k k+  + +   kk +v+ ++t
  gene1464|gene1464|rna1464|rna1464 123 IDRLERELEKLRKENAKLADRNKELIDKNKKLGNDKVLGKKNIVLEKNT 171
                                        6888899*****************9999998887776666666665554 PP

>> Ax_dynein_light  Axonemal dynein light chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   6.3    0.0029       0.6     122     181 ..      32      90 ..      15      93 .. 0.78
   2 ?    6.1   8.7     0.046       9.4     123     183 ..      82     142 ..      76     146 .. 0.90
   3 ?    3.2   8.9      0.35        72     119     166 ..     114     154 ..      97     184 .. 0.47

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0029
                    Ax_dynein_light 122 selekkikeLeeekeelekqvaelkaklealekrekerrqeeekkheeeieflkksnqql 181
                                        + l+++i+e +e+ ++l+kq +el++kle+le++++e  ++++k  + e++ ++k  ++l
  gene1464|gene1464|rna1464|rna1464  32 ASLSDQIAEKDERIDTLKKQTTELQHKLEDLEEQNAEWGTNNNKL-QAELDIVNKDVKRL 90 
                                        567788999999999999999999999999999999887766654.56677777776666 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.046
                    Ax_dynein_light 123 elekkikeLeeekeelekqvaelkaklealekrekerrqeeekkheeeieflkksnqqlke 183
                                         ++k++k+L++   e e+++++l+a++e+ +k+ +   +++  + e e+e+l+k+n +l +
  gene1464|gene1464|rna1464|rna1464  82 IVNKDVKRLQAISVEKERKIEKLNAEVESCRKEGNAASNAQIDRLERELEKLRKENAKLAD 142
                                        46788999999999******************************************99976 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.35
                    Ax_dynein_light 119 qgkselekkikeLeeekeelekqvaelkaklealekrekerrqeeekk 166
                                        +g++  +++i +Le+e e+l+k++a+l         r+ke  ++++k 
  gene1464|gene1464|rna1464|rna1464 114 EGNAASNAQIDRLERELEKLRKENAKL-------ADRNKELIDKNKKL 154
                                        223333333333333333333333333.......33333333333333 PP

>> DUF2968  Protein of unknown function (DUF2968)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   8.3     0.015       3.1     102     179 ..      32     109 ..       5     110 .. 0.82
   2 ?    6.8   3.2     0.023       4.7     101     161 ..     101     162 ..      94     179 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.015
                            DUF2968 102 ikleaqkaqlerqiaasearaerLqadlavarqQeqavaerQkqarkeaaaLeaqreaaqaqlralqrqirqLqaq 177
                                        + l  q a  ++ i + +++ ++Lq  l+  ++Q+++  ++ +++++e +  +++ +++qa   + +r+i++L+a+
  gene1464|gene1464|rna1464|rna1464  32 ASLSDQIAEKDERIDTLKKQTTELQHKLEDLEEQNAEWGTNNNKLQAELDIVNKDVKRLQAISVEKERKIEKLNAE 107
                                        5677788888888888888888899999999999999999999999999999999999999999999999999988 PP

                            DUF2968 178 qe 179
                                         e
  gene1464|gene1464|rna1464|rna1464 108 VE 109
                                        76 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.023
                            DUF2968 101 rikleaqkaqlerq.iaasearaerLqadlavarqQeqavaerQkqarkeaaaLeaqreaaq 161
                                          kl+a+ ++  ++  aas+a++ rL+ +l+  r+ ++++a+r k++ ++ ++L +++   +
  gene1464|gene1464|rna1464|rna1464 101 IEKLNAEVESCRKEgNAASNAQIDRLERELEKLRKENAKLADRNKELIDKNKKLGNDKVLGK 162
                                        4577788777766525678999*************************999999999987555 PP

>> ERM  Ezrin/radixin/moesin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8  24.2     0.026       5.3      39     177 ..      35     173 ..      15     184 .. 0.64

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.026
                                ERM  39 aekarraeeeaelLeqkaaeaeeeiqrlkesaekeeeekeklerklreaeleaarleeeserkeeeaerLkeelee 114
                                          +  +  e  + L+++ +e++++ + l+e++++   + +kl+++l+ ++  ++rl+  s +ke++ e+L +e+e 
  gene1464|gene1464|rna1464|rna1464  35 SDQIAEKDERIDTLKKQTTELQHKLEDLEEQNAEWGTNNNKLQAELDIVNKDVKRLQAISVEKERKIEKLNAEVES 110
                                        4444444455567888888888888888888888888888888888888888888888888888888888888888 PP

                                ERM 115 areaeeeakekllealstpskseseenveeseteeeeenseeesaeletde...veklsleieeeR 177
                                         r++ + a+++  + l+++ ++  +en +  ++   +++  +++++l +d+    ++++le+++ R
  gene1464|gene1464|rna1464|rna1464 111 CRKEGNAASNAQIDRLERELEKLRKENAKLADR---NKELIDKNKKLGNDKvlgKKNIVLEKNTRR 173
                                        888888888777777777753322222222222...223334555555555444334445444444 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1  10.8      0.21        43     101     196 ..      61     153 ..       7     167 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.21
                              DUF87 101 elldllee..ddkpaaavqrsvleealdqakakeekeklssdepveklleelkkekeelrklknqaiarlldkled 174
                                        +l++   e  +++++ +++ ++++   + +k + +  ++  ++ +ekl+ e++++++e + ++n +i rl++ le+
  gene1464|gene1464|rna1464|rna1464  61 DLEEQNAEwgTNNNKLQAELDIVN---KDVK-RLQAISVEKERKIEKLNAEVESCRKEGNAASNAQIDRLERELEK 132
                                        333333332223333333333333...3333.355677777888888888888999******************** PP

                              DUF87 175 llrkggsfsnsstdlialllek 196
                                        l +++++ ++ +++li++  +k
  gene1464|gene1464|rna1464|rna1464 133 LRKENAKLADRNKELIDKN-KK 153
                                        ********88888888776.33 PP

>> ABC_tran_CTD  ABC transporter C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   3.6     0.023       4.7      27      63 ..      30      65 ..       8      70 .. 0.77
   2 ?    1.7  11.6       1.5     3e+02       2      58 ..      51     105 ..      29     110 .. 0.65
   3 ?    4.9   9.2      0.15        31      11      66 ..      91     146 ..      73     149 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.023
                       ABC_tran_CTD 27 leaeladpelysdpeklaelsaeleeleaeLeelyer 63
                                       l a l+d  + +++e++  l ++ +el+++Le l+e+
  gene1464|gene1464|rna1464|rna1464 30 LYASLSDQ-IAEKDERIDTLKKQTTELQHKLEDLEEQ 65
                                       55566655.4566688888888888888888888875 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 1.5
                       ABC_tran_CTD   2 lsykeqreleeleaeIeaLEeeiaeleaeladpelysdpeklaelsaeleeleaeLe 58 
                                         +   q++le le++ ++  +   +l+ael   +  +d ++l+++s e+e+  ++L+
  gene1464|gene1464|rna1464|rna1464  51 QTTELQHKLEDLEEQNAEWGTNNNKLQAELDIVN--KDVKRLQAISVEKERKIEKLN 105
                                        3445566666666666666666666666666555..666777777777666666555 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.15
                       ABC_tran_CTD  11 e....eleaeIeaLEeeiaeleaeladpelysdpeklaelsaeleeleaeLeelyerWee 66 
                                        +    e e++Ie+L +e ++  +e ++++     +++ +l +ele+l++e ++l +r  e
  gene1464|gene1464|rna1464|rna1464  91 QaisvEKERKIEKLNAEVESCRKEGNAAS----NAQIDRLERELEKLRKENAKLADRNKE 146
                                        2444457999*************999886....4689999999***99999988887555 PP

>> Csm1_N  Csm1 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   4.2    0.0006      0.12      32      65 ..      34      67 ..      32      72 .. 0.93
   2 ?    1.0   3.5       2.6   5.4e+02      38      55 ..      96     113 ..      70     122 .. 0.56
   3 ?    4.7   3.7      0.18        37      29      66 ..     116     153 ..     113     156 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.0006
                             Csm1_N 32 LsqkletkdqeiesLkeqlaeleekvkeleerrk 65
                                       Ls ++  kd++i +Lk+q  el++k+++lee+++
  gene1464|gene1464|rna1464|rna1464 34 LSDQIAEKDERIDTLKKQTTELQHKLEDLEEQNA 67
                                       8899**************************9986 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 2.6
                             Csm1_N  38 tkdqeiesLkeqlaelee 55 
                                         k+++ie+L +++++ ++
  gene1464|gene1464|rna1464|rna1464  96 EKERKIEKLNAEVESCRK 113
                                        355556666666665555 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.18
                             Csm1_N  29 NsvLsqkletkdqeiesLkeqlaeleekvkeleerrkk 66 
                                        N   + +++  ++e+e+L+++ a+l  ++kel +++kk
  gene1464|gene1464|rna1464|rna1464 116 NAASNAQIDRLERELEKLRKENAKLADRNKELIDKNKK 153
                                        55667788888999999999999999999998888776 PP

>> TSC22  TSC-22/dip/bun family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   2.8    0.0009      0.19      14      38 ..      43      67 ..      38      88 .. 0.90
   2 ?    2.1   3.3       1.2   2.5e+02      15      33 ..     129     147 ..     104     153 .. 0.66
   3 ?    3.7   2.0      0.39        80      15      40 ..     129     154 ..     127     169 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.0009
                              TSC22 14 EeVevLkekIkeLeernseleeENs 38
                                       E +++Lk++ +eL+++ + lee+N+
  gene1464|gene1464|rna1464|rna1464 43 ERIDTLKKQTTELQHKLEDLEEQNA 67
                                       789*********************7 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 1.2
                              TSC22  15 eVevLkekIkeLeernsel 33 
                                        e e L+++ + L +rn+el
  gene1464|gene1464|rna1464|rna1464 129 ELEKLRKENAKLADRNKEL 147
                                        3445555555555555554 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.39
                              TSC22  15 eVevLkekIkeLeernseleeENslL 40 
                                        e e L+++ + L +rn+el   N+ L
  gene1464|gene1464|rna1464|rna1464 129 ELEKLRKENAKLADRNKELIDKNKKL 154
                                        78999999999999999999998866 PP

>> Wtap  WTAP/Mum2p family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   3.6    0.0051         1      92     150 ..       9      67 ..       6      80 .. 0.72
   2 ?    1.0   0.6       1.7   3.5e+02     116     151 ..      75     110 ..      70     114 .. 0.68
   3 ?    4.0   6.3       0.2        42     106     147 ..     115     156 ..      95     165 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0051
                               Wtap  92 makcrvLeqENeELgkvleegrvakLeselalqkkfveelkkaleeleelleeleeeve 150
                                         ++ rvLeq+      +      a+L+ ++a +++ ++ lkk+ +el+  le+lee++ 
  gene1464|gene1464|rna1464|rna1464   9 SSRTRVLEQKFFSARVAQFHKLYASLSDQIAEKDERIDTLKKQTTELQHKLEDLEEQNA 67 
                                        56667777776666444445556888888888888888888888888888888888764 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 1.7
                               Wtap 116 kLeselalqkkfveelkkaleeleelleeleeevev 151
                                        kL+ el    k v++l+    e e  +e+l++eve 
  gene1464|gene1464|rna1464|rna1464  75 KLQAELDIVNKDVKRLQAISVEKERKIEKLNAEVES 110
                                        666677777777777777777777777777777775 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.2
                               Wtap 106 gkvleegrvakLeselalqkkfveelkkaleeleelleelee 147
                                        g++++++++ +Le el++++k +++l  +++el + +++l +
  gene1464|gene1464|rna1464|rna1464 115 GNAASNAQIDRLERELEKLRKENAKLADRNKELIDKNKKLGN 156
                                        456677778888888888888888888888888877777755 PP

>> DUF3573  Protein of unknown function (DUF3573)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   1.1    0.0098         2      22      69 ..      26      72 ..       8      85 .. 0.76
   2 ?    3.5   1.2      0.12        25      46     104 ..      95     153 ..      77     172 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0098
                            DUF3573 22 edsasyaesneqtsksnlidkelilklqkqikelqaeinhlketkns...n 69
                                       ++ + ya++++q++       e i  l+kq  elq ++++l+e++     n
  gene1464|gene1464|rna1464|rna1464 26 QFHKLYASLSDQIA----EKDERIDTLKKQTTELQHKLEDLEEQNAEwgtN 72
                                       45566777777777....5567899*****************998754443 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.12
                            DUF3573  46 lklqkqikelqaeinhlketknsnesaqfttysskvedsklprslldnkeskdlsqvqk 104
                                        ++ +++i++l+ae++  ++ +n+  +aq      ++e+ ++ +++l +++   + + +k
  gene1464|gene1464|rna1464|rna1464  95 VEKERKIEKLNAEVESCRKEGNAASNAQIDRLERELEKLRKENAKLADRNKELIDKNKK 153
                                        4667899*****************************99999999887744444444444 PP

>> Leu_zip  Leucine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9  10.9     0.039         8     133     203 ..      43     114 ..       7     125 .. 0.70
   2 ?    6.2   7.6     0.031       6.3     128     170 ..     123     165 ..     112     187 .. 0.73

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.039
                            Leu_zip 133 keierLkeenekLkerlkelEkqatsaleeksklekalkelqkelgekkdeke.nskeiskleeklaelkld 203
                                          i+ Lk++ + L+++l++lE+q  +   +++kl+++l+ ++k+++  ++ +  ++++i+kl++++++ + +
  gene1464|gene1464|rna1464|rna1464  43 ERIDTLKKQTTELQHKLEDLEEQNAEWGTNNNKLQAELDIVNKDVKRLQAISVeKERKIEKLNAEVESCRKE 114
                                        467888888888888888888888888888888888888887777766554443566777777776666555 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.031
                            Leu_zip 128 aeLLkkeierLkeenekLkerlkelEkqatsaleeksklekal 170
                                        ++ L+ e+e+L++en kL +r kel ++ +++ ++k   +k++
  gene1464|gene1464|rna1464|rna1464 123 IDRLERELEKLRKENAKLADRNKELIDKNKKLGNDKVLGKKNI 165
                                        5568999999999999999999999999998888887666554 PP

>> V_ATPase_I  V-type ATPase 116kDa subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   7.6     0.045       9.3      59     126 ..      33     100 ..       5     114 .. 0.59
   2 ?    6.0   8.2     0.011       2.3      37     119 ..      78     170 ..      74     187 .. 0.62

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.045
                         V_ATPase_I  59 aeesleapeekeldeleeelekleeelkelnenleklkkelnelvelkavlekakefleeeeeeeeee 126
                                        + +++ a++++++d+l++++++l+++l++l+e++ +  ++ n+l+ +  +++k  + l++ + e+e++
  gene1464|gene1464|rna1464|rna1464  33 SLSDQIAEKDERIDTLKKQTTELQHKLEDLEEQNAEWGTNNNKLQAELDIVNKDVKRLQAISVEKERK 100
                                        24455667777888888888888888888888888888888888877777777766665442222222 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.011
                         V_ATPase_I  37 rklrfleeeieklekavikeeea...........eesleapeekeldeleeelekleeelkelnenleklkkelne 101
                                         +l+++++ +++l+ + +++e++            ++ +a++++++d+le+elekl +e  +l + +++l ++ ++
  gene1464|gene1464|rna1464|rna1464  78 AELDIVNKDVKRLQAISVEKERKieklnaevescRKEGNAASNAQIDRLERELEKLRKENAKLADRNKELIDKNKK 153
                                        5566666666666666666665555555555555667777788888888888888888888888888888877766 PP

                         V_ATPase_I 102 lvelkavlekakefleee 119
                                        l +  +vl k + +le++
  gene1464|gene1464|rna1464|rna1464 154 LGN-DKVLGKKNIVLEKN 170
                                        654.44566666666554 PP

>> DUF641  Plant protein of unknown function (DUF641)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   1.7     0.019         4      89     127 ..      26      64 ..       7      65 .. 0.84
   2 ?    3.7   9.4      0.36        73      70     127 ..      84     142 ..      61     153 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.019
                             DUF641  89 tyeitvkkleaelkakdseieeLkekLeeaeksnkklek 127
                                           +   +l  ++ +kd+ i+ Lk++ +e++++ + le+
  gene1464|gene1464|rna1464|rna1464  26 QFHKLYASLSDQIAEKDERIDTLKKQTTELQHKLEDLEE 64 
                                        556677889999**************9999999999887 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.36
                             DUF641  70 eaeeseleaeiqeqrsllktyeitvkkleaelk.akdseieeLkekLeeaeksnkklek 127
                                        +++ ++l+a   e+ ++++ +++ v+++++e + a +++i++L+++Le+++k+n kl  
  gene1464|gene1464|rna1464|rna1464  84 NKDVKRLQAISVEKERKIEKLNAEVESCRKEGNaASNAQIDRLERELEKLRKENAKLAD 142
                                        36777888888888899999999999998886515678999999999999999998865 PP

>> CCDC-167  Coiled-coil domain-containing protein 167
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8  17.7       1.5   3.1e+02       6      67 ..      45     139 ..      33     141 .. 0.66

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 1.5
                           CCDC-167   6 IdkleeklascrerLeaverrlrkeelseee.............................Resle.......eEea 45 
                                        Id+l +++++++++Le++e +  +    +++                                         e  a
  gene1464|gene1464|rna1464|rna1464  45 IDTLKKQTTELQHKLEDLEEQNAEWGTNNNKlqaeldivnkdvkrlqaisvekerkieklN---AevescrkEGNA 117
                                        6666666666666666666665555544444666666776666666666666665555441...045566634456 PP

                           CCDC-167  46 slkeqleenekeLksLrkeNrk 67 
                                        + + q+++ e+eL++LrkeN k
  gene1464|gene1464|rna1464|rna1464 118 ASNAQIDRLERELEKLRKENAK 139
                                        6789****************98 PP

>> FliD_N  Flagellar hook-associated protein 2 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   3.9     0.023       4.8      15      54 ..      39      80 ..      30     110 .. 0.68
   2 ?    4.3   2.2      0.32        67      11      51 ..     114     154 ..      91     186 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.023
                                       XXXX.XXXXXXXXXXXXXXXHHHHHHHHHHHHHHHHHHH.HH CS
                             FliD_N 15 aera.kldkleqkktklewkqsayrelnsklsnlksals.al 54
                                       ae+  ++d+l+++ t+l+ k ++++e n +  + +++l+ +l
  gene1464|gene1464|rna1464|rna1464 39 AEKDeRIDTLKKQTTELQHKLEDLEEQNAEWGTNNNKLQaEL 80
                                       344448999999999999999999999999888888775444 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.32
                                        XXXXXXXXXXXXXXXXXXXXXXXHHHHHHHHHHHHHHHHHH CS
                             FliD_N  11 qlmkaerakldkleqkktklewkqsayrelnsklsnlksal 51 
                                        +  +a +a++d+le++ +kl ++ +++ + n++l + +++l
  gene1464|gene1464|rna1464|rna1464 114 EGNAASNAQIDRLERELEKLRKENAKLADRNKELIDKNKKL 154
                                        55578888999999999999999999999999988877766 PP

>> DUF724  Protein of unknown function (DUF724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   3.1   0.00068      0.14     126     184 ..      32      90 ..       6      93 .. 0.60
   2 ?    5.6  18.5     0.061        13      99     184 ..      47     133 ..      36     187 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00068
                             DUF724 126 rkleeeidelekkilelerqlallkekkeaadkeiarlkseaekleeeledveqeFeav 184
                                        ++l+++i+e++++i +l++q + l++k e+ +++ a+  ++++kl+ el+ v+++++++
  gene1464|gene1464|rna1464|rna1464  32 ASLSDQIAEKDERIDTLKKQTTELQHKLEDLEEQNAEWGTNNNKLQAELDIVNKDVKRL 90 
                                        55566666666666666666666666666666666666666666666666666555544 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.061
                             DUF724  99 slkdeqtklleerkklekkieeeesekrkleeeidelekkilelerqlallkekkeaadkeiarlkseaekl.eee 173
                                         lk++ t+l++++++le++ +e  ++++kl++e+d ++k +++l+  ++ + +k e+ ++e+ + ++e +++ + +
  gene1464|gene1464|rna1464|rna1464  47 TLKKQTTELQHKLEDLEEQNAEWGTNNNKLQAELDIVNKDVKRLQAISVEKERKIEKLNAEVESCRKEGNAAsNAQ 122
                                        689********************************77777777777776555555555555555555444331445 PP

                             DUF724 174 ledveqeFeav 184
                                        +++ e+e e++
  gene1464|gene1464|rna1464|rna1464 123 IDRLERELEKL 133
                                        56666655554 PP

>> DUF5446  Family of unknown function (DUF5446)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.5       1.8   3.7e+02      39      59 ..      37      57 ..      27      70 .. 0.77
   2 ?   11.4   2.6    0.0014      0.29      26      57 ..     102     133 ..      93     142 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 1.8
                            DUF5446 39 keekeeerldllekElkdLvl 59
                                       ++ +++er+d l k   +L+ 
  gene1464|gene1464|rna1464|rna1464 37 QIAEKDERIDTLKKQTTELQH 57
                                       567889999999999999875 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.0014
                            DUF5446  26 kelseavneteaekeekeeerldllekElkdL 57 
                                        ++l+  v   ++e + + ++ +d+le+El+ L
  gene1464|gene1464|rna1464|rna1464 102 EKLNAEVESCRKEGNAASNAQIDRLERELEKL 133
                                        469**************************987 PP

>> DASH_Dad3  DASH complex subunit Dad3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.3    0.0088       1.8      12      48 ..      31      66 ..      25      71 .. 0.90
   2 ?    1.8   3.2       1.3   2.7e+02      13      36 ..     124     147 ..      74     183 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0088
                          DASH_Dad3 12 YerLaenlktLaselkeLasnsteeildgLReLErki 48
                                       Y++L++++ + ++++++L ++ t+e+ ++L +LE + 
  gene1464|gene1464|rna1464|rna1464 31 YASLSDQIAEKDERIDTLKKQ-TTELQHKLEDLEEQN 66
                                       99****************988.999*********985 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 1.3
                          DASH_Dad3  13 erLaenlktLaselkeLasnstee 36 
                                         rL+++l++L +e ++La++++e 
  gene1464|gene1464|rna1464|rna1464 124 DRLERELEKLRKENAKLADRNKEL 147
                                        578888888888888888874433 PP

>> GrpE  GrpE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   6.6     0.012       2.4       4      51 ..      42      89 ..      28      98 .. 0.79
   2 ?    3.1  11.0      0.33        68       7      57 ..      94     145 ..      88     186 .. 0.64

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.012
                                       ...CTTTHHHHCCCCCCTTCHHHCTTSCCCCCCTTTTTTTTHHHHHHH CS
                               GrpE  4 eeeeeeeedeeeeleeeleelekevkelkekllrllaefenlrkrtek 51
                                       +e+   ++++++el+ +le+le++ +e+  + ++l+ae++ ++k +++
  gene1464|gene1464|rna1464|rna1464 42 DERIDTLKKQTTELQHKLEDLEEQNAEWGTNNNKLQAELDIVNKDVKR 89
                                       456667778888888888888888888888888999999988888876 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.33
                                        CTTTHHHHCCCCCCTTCHHHCTTSC.CCCCCTTTTTTTTHHHHHHHHHHHHH CS
                               GrpE   7 eeeeedeeeeleeeleelekevkel.kekllrllaefenlrkrtekekeeak 57 
                                        ++e+e ++e+l++e+e+ +ke +++ + +++rl+ e+e+lrk  +k ++  k
  gene1464|gene1464|rna1464|rna1464  94 SVEKERKIEKLNAEVESCRKEGNAAsNAQIDRLERELEKLRKENAKLADRNK 145
                                        5677888888888888866644433244555555555555554444333322 PP

>> DUF4665  Domain of unknown function (DUF4665)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   2.9      0.25        52      40      77 ..      38      75 ..      24      88 .. 0.75
   2 ?    6.3   2.2     0.072        15      31      66 ..      82     120 ..      70     123 .. 0.72
   3 ?    7.9   2.7     0.022       4.6      35      89 ..     111     165 ..     107     177 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.25
                            DUF4665 40 navkkekvenldkalvdiqkdlkslskklkletkkkek 77
                                        a k+e++ +l k+ +++q++l+ l ++ +    +++k
  gene1464|gene1464|rna1464|rna1464 38 IAEKDERIDTLKKQTTELQHKLEDLEEQNAEWGTNNNK 75
                                       47799999***********9999998866655555444 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.072
                            DUF4665  31 pVttnLKkinav...kkekvenldkalvdiqkdlkslsk 66 
                                         V+ + K+++a+   k+ k+e+l+ + +  +k+ ++ s+
  gene1464|gene1464|rna1464|rna1464  82 IVNKDVKRLQAIsveKERKIEKLNAEVESCRKEGNAASN 120
                                        566666666655444999********9999999877765 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.022
                            DUF4665  35 nLKkinavkkekvenldkalvdiqkdlkslskklkletkkkekvkkkkekekvnv 89 
                                          K+ na  + ++ +l+++l++++k+ ++l+ + k    k++k+ ++k   k+n+
  gene1464|gene1464|rna1464|rna1464 111 CRKEGNAASNAQIDRLERELEKLRKENAKLADRNKELIDKNKKLGNDKVLGKKNI 165
                                        557779999*********************9977766666666666655554444 PP

>> kleA_kleC  Uncharacterized KorC regulated protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.3    0.0072       1.5      24      47 ..      36      59 ..      28      71 .. 0.88
   2 ?    0.5   0.4       3.8   7.8e+02      30      52 ..      91     111 ..      59     120 .. 0.69
   3 ?    2.6   2.9      0.85   1.8e+02      23      47 ..     113     137 ..     100     153 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0072
                          kleA_kleC 24 dkiAaklaeAeeLvrqaeeLRakv 47
                                       d+iA+k ++ + L++q  eL +k 
  gene1464|gene1464|rna1464|rna1464 36 DQIAEKDERIDTLKKQTTELQHKL 59
                                       89******************9985 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 3.8
                          kleA_kleC  30 laeAeeLvrqaeeLRakvyeesa 52 
                                        +a   e +r++e+L a+v  es+
  gene1464|gene1464|rna1464|rna1464  91 QAISVEKERKIEKLNAEV--ESC 111
                                        444456677777777666..344 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.85
                          kleA_kleC  23 RdkiAaklaeAeeLvrqaeeLRakv 47 
                                        ++  Aa  a+ + L+r+ e+LR++ 
  gene1464|gene1464|rna1464|rna1464 113 KEGNAASNAQIDRLERELEKLRKEN 137
                                        455699999*************864 PP

>> VGPC1_C  C-terminal membrane-localisation domain of ion-channel, VCN1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.2       3.2   6.5e+02      26      40 ..      40      51 ..      33      58 .. 0.65
   2 ?    0.8   0.6       2.4     5e+02       6      34 ..      48      76 ..      43      81 .. 0.72
   3 ?    8.2   0.9     0.012       2.4      17      36 ..      87     106 ..      73     109 .. 0.86
   4 ?    2.2   0.1      0.89   1.8e+02       2      16 ..     129     143 ..     128     148 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 3.2
                            VGPC1_C 26 EKeqeierLnkLlkq 40
                                       EK+  i+ L   +kq
  gene1464|gene1464|rna1464|rna1464 40 EKDERIDTL---KKQ 51
                                       666666655...554 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 2.4
                            VGPC1_C  6 LkqaNlqLaaKvqqLefscsEKeqeierL 34
                                       Lk     L  K + Le   +E ++  ++L
  gene1464|gene1464|rna1464|rna1464 48 LKKQTTELQHKLEDLEEQNAEWGTNNNKL 76
                                       66666778888999988888877666555 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.012
                            VGPC1_C  17 vqqLefscsEKeqeierLnk 36 
                                        v++L+   +EKe  ie+Ln+
  gene1464|gene1464|rna1464|rna1464  87 VKRLQAISVEKERKIEKLNA 106
                                        89999999**********95 PP

  == domain 4  score: 2.2 bits;  conditional E-value: 0.89
                            VGPC1_C   2 qlskLkqaNlqLaaK 16 
                                         l kL+  N +La +
  gene1464|gene1464|rna1464|rna1464 129 ELEKLRKENAKLADR 143
                                        688*********976 PP

>> DUF2203  Uncharacterized conserved protein (DUF2203)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   2.6      0.11        23      15      69 ..      38      90 ..       7      96 .. 0.55
   2 ?    8.5   4.8     0.016       3.3      10      95 ..      78     159 ..      72     161 .. 0.72

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.11
                            DUF2203 15 lkelleelralrkeleeleeeleeakaeaekseaaeleaeleeleaeieelveei 69
                                       + e+ e++ +l+k+ +el+++le+ ++++++ +  +++++l++  + +++ v+++
  gene1464|gene1464|rna1464|rna1464 38 IAEKDERIDTLKKQTTELQHKLEDLEEQNAEWG--TNNNKLQAELDIVNKDVKRL 90
                                       333344455555555555555555555544322..23333333333333333333 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.016
                            DUF2203  10 alLpllkelleelralrkeleeleeeleeakaeaekseaaeleaeleeleaeieelveeieelGvevkdleaglvD 85 
                                        a L  +++ +++l+a   e e++ e+l+++ ++     ++e +a+ ++  +++e+ +e++++  +++ d ++ l+D
  gene1464|gene1464|rna1464|rna1464  78 AELDIVNKDVKRLQAISVEKERKIEKLNAEVESC----RKEGNAASNAQIDRLERELEKLRKENAKLADRNKELID 149
                                        5566677777777766666666666666666555....67778888888888888888999999999999999999 PP

                            DUF2203  86 Fpakldgeev 95 
                                           kl +++v
  gene1464|gene1464|rna1464|rna1464 150 KNKKLGNDKV 159
                                        8888888777 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   8.5       1.5   3.2e+02      26      61 ..      29      64 ..      19     160 .. 0.68

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 1.5
                             DUF948 26 ktldeaaatieelekqvdpilkevedllakvnelle 61
                                       k+  +++++i+e  +++d + k++++l +k ++l e
  gene1464|gene1464|rna1464|rna1464 29 KLYASLSDQIAEKDERIDTLKKQTTELQHKLEDLEE 64
                                       444455555555555555555555555555555222 PP

>> Swi5  Swi5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   8.0      0.35        73       4      44 ..      44      91 ..      20     106 .. 0.64
   2 ?    1.5   7.7       1.6   3.2e+02       3      35 ..     121     146 ..      84     174 .. 0.68

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.35
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHH........HHHHHHHHHHHHH CS
                               Swi5  4 eikeleeqleelekelaelkeelkekk.......dpeetvkrhIklLh 44
                                       +i +l++q++el+++l++l+e+  e         +  ++v++ +k+L+
  gene1464|gene1464|rna1464|rna1464 44 RIDTLKKQTTELQHKLEDLEEQNAEWGtnnnklqAELDIVNKDVKRLQ 91
                                       455555555555555555555544322334444455555555555554 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 1.6
                                        HHHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHH CS
                               Swi5   3 aeikeleeqleelekelaelkeelkekkdpeet 35 
                                        a+i +le++le+l+ke a+l ++ k       +
  gene1464|gene1464|rna1464|rna1464 121 AQIDRLERELEKLRKENAKLADRNK-------E 146
                                        3444444444444444444444433.......3 PP

>> DUF4337  Domain of unknown function (DUF4337)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   3.1    0.0054       1.1      68     116 ..      27      75 ..       7      83 .. 0.76
   2 ?    3.6   6.0      0.31        63      57     109 ..     101     153 ..      84     159 .. 0.62

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0054
                            DUF4337  68 aeelaaavdkkiakykkkiarykkekkeikkkAkeleaerdeaneasdk 116
                                          +l a  +++ia+  ++i+  kk+ +e+++k ++le++ +e+  +++k
  gene1464|gene1464|rna1464|rna1464  27 FHKLYASLSDQIAEKDERIDTLKKQTTELQHKLEDLEEQNAEWGTNNNK 75 
                                        5566777888899999999999999999999999999999988877766 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.31
                            DUF4337  57 leqlelllkak..aeelaaavdkkiakykkkiarykkekkeikkkAkeleaerde 109
                                         e+l+++   +   +e +aa +++i++++++ ++ +ke ++++++ kel ++ ++
  gene1464|gene1464|rna1464|rna1464 101 IEKLNAEV--EscRKEGNAASNAQIDRLERELEKLRKENAKLADRNKELIDKNKK 153
                                        23333333..234555566667788888888888888888888877777655554 PP

>> DUF5320  Family of unknown function (DUF5320)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.5     0.014       2.9      49      97 ..      18      67 ..       7      69 .. 0.74
   2 ?    3.4   1.6      0.78   1.6e+02      72      97 ..     113     138 ..      91     147 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.014
                            DUF5320 49 gfgrrrraggarla.aaetaeaskeeekelLeeqaeaLeeeleaikkrlk 97
                                        f   r+a + +l+     + a+k+e+++ L++q   L+ +le+++++ +
  gene1464|gene1464|rna1464|rna1464 18 KFFSARVAQFHKLYaSLSDQIAEKDERIDTLKKQTTELQHKLEDLEEQNA 67
                                       4555555555555545566777888899******************9966 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.78
                            DUF5320  72 eeekelLeeqaeaLeeeleaikkrlk 97 
                                        +e +++ ++q++ Le+ele+++k+ +
  gene1464|gene1464|rna1464|rna1464 113 KEGNAASNAQIDRLERELEKLRKENA 138
                                        44555666677777777777766544 PP

>> DHR10  Designed helical repeat protein 10 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   5.0     0.017       3.6      58     103 ..      23      68 ..      15      75 .. 0.83
   2 ?    2.5   2.8       0.7   1.4e+02      52      85 ..      80     113 ..      72     123 .. 0.46
   3 ?    3.1  11.0      0.47        97      15      72 ..      98     153 ..      96     184 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.017
                              DHR10  58 klkelrdaleekeielrelerkeerlqrqlenaeeklerlreqaee 103
                                        ++++ ++ +++++ + +e + +++ l++q    + kle l+eq +e
  gene1464|gene1464|rna1464|rna1464  23 RVAQFHKLYASLSDQIAEKDERIDTLKKQTTELQHKLEDLEEQNAE 68 
                                        5666677778888888999999999999999999999999999765 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.7
                              DHR10  52 leeakkklkelrdaleekeielrelerkeerlqr 85 
                                        l+ ++k++k+l++   eke++ ++l+++ e +++
  gene1464|gene1464|rna1464|rna1464  80 LDIVNKDVKRLQAISVEKERKIEKLNAEVESCRK 113
                                        3334444444444444444444444444333333 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.47
                              DHR10  15 Erkarelqakidalqvvekdlrsciklleeieaelakleeakkklkelrdaleekeie 72 
                                        Erk+ +l a +++  +     ++  ++++ +e+el+kl+++++kl++ +++l +k+++
  gene1464|gene1464|rna1464|rna1464  98 ERKIEKLNAEVESCRKEG--NAASNAQIDRLERELEKLRKENAKLADRNKELIDKNKK 153
                                        555555555555554433..24557899999***********9999988888777765 PP

>> HalX  HalX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   3.2     0.038       7.8      11      60 ..       4      54 ..       2      62 .. 0.84
   2 ?    3.2   0.3      0.53   1.1e+02      38      57 ..      53      72 ..      49      84 .. 0.81
   3 ?    4.5   3.5      0.21        43      26      57 ..     112     143 ..      88     150 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.038
                               HalX 11 elfaLasKravLeaekseaeLad.seeYqeLearleelraqldetldeldd 60
                                       e+  L+s+  vLe    +a  a+ +  Y+ L ++++e  +++d++  + ++
  gene1464|gene1464|rna1464|rna1464  4 EYLKLSSRTRVLEQKFFSARVAQfHKLYASLSDQIAEKDERIDTLKKQTTE 54
                                       8999*********99988888876889****************99887555 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.53
                               HalX 38 qeLearleelraqldetlde 57
                                       +eL+  le+l++q  e+ ++
  gene1464|gene1464|rna1464|rna1464 53 TELQHKLEDLEEQNAEWGTN 72
                                       69999*******99998877 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.21
                               HalX  26 kseaeLadseeYqeLearleelraqldetlde 57 
                                          e + a++ + ++Le++le lr +   ++d+
  gene1464|gene1464|rna1464|rna1464 112 RKEGNAASNAQIDRLERELEKLRKENAKLADR 143
                                        35788899999999999999999987777765 PP

>> DUF4315  Domain of unknown function (DUF4315)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   2.4     0.073        15       9      32 ..      45      68 ..      37      74 .. 0.87
   2 ?    2.9   0.1      0.54   1.1e+02       1      18 [.     100     117 ..     100     121 .. 0.85
   3 ?    6.7   4.1     0.035       7.1       2      31 ..     123     152 ..     122     160 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.073
                            DUF4315  9 ieKakeKiselqarlkelekqktE 32
                                       i+ +k++ +elq +l +le+q  E
  gene1464|gene1464|rna1464|rna1464 45 IDTLKKQTTELQHKLEDLEEQNAE 68
                                       67789999************9987 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.54
                            DUF4315   1 klekieaeieKakeKise 18 
                                        k+ek++ae+e +++  ++
  gene1464|gene1464|rna1464|rna1464 100 KIEKLNAEVESCRKEGNA 117
                                        8*********99987655 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.035
                            DUF4315   2 lekieaeieKakeKiselqarlkelekqkt 31 
                                        ++++e+e+eK+++  + l  r kel  + +
  gene1464|gene1464|rna1464|rna1464 123 IDRLERELEKLRKENAKLADRNKELIDKNK 152
                                        899********************9966655 PP

>> Exonuc_VII_L  Exonuclease VII, large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2  17.6     0.065        13     155     289 ..      29     184 ..       7     186 .. 0.49

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.065
                       Exonuc_VII_L 155 rlekaikrlleekkqrleklasrlkspeellerkrqr..............ldeleerleralkkqlkkkrerlee 216
                                        +l  +++ ++ ek +r+++l+++ ++ +++le+ +++              ld ++++++r l+    +k++++e+
  gene1464|gene1464|rna1464|rna1464  29 KLYASLSDQIAEKDERIDTLKKQTTELQHKLEDLEEQnaewgtnnnklqaeLDIVNKDVKR-LQAISVEKERKIEK 103
                                        4445555566666666666666665555544444444111111111111112223333333.22233444445555 PP

                       Exonuc_VII_L 217 lkerlk...........ekleekkerlkklkerlelleekkerle....eleeklealsplkvLkrGyaivrkedg 277
                                        l+++++           +       ++++l+++le+l++++ +l+    el++k ++l+ +kvL +   +++k+++
  gene1464|gene1464|rna1464|rna1464 104 LNAEVEscrkegnaasnA-------QIDRLERELEKLRKENAKLAdrnkELIDKNKKLGNDKVLGKKNIVLEKNTR 172
                                        554442354433333333.......334444444433333333221111588888888999999988888888778 PP

                       Exonuc_VII_L 278 kvvtsakdlkkg 289
                                        +++t++ +l+k+
  gene1464|gene1464|rna1464|rna1464 173 RLLTNTMKLRKN 184
                                        888888877765 PP

>> UPF0184  Uncharacterised protein family (UPF0184)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   1.2      0.87   1.8e+02      41      65 ..      44      68 ..      26      83 .. 0.78
   2 ?    9.3   3.1     0.007       1.5      16      65 ..     104     153 ..      91     158 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.87
                            UPF0184 41 aLDalEernDdlnskLrELlesnRq 65
                                        +D l +++ +l+ kL++L e n +
  gene1464|gene1464|rna1464|rna1464 44 RIDTLKKQTTELQHKLEDLEEQNAE 68
                                       5799999999999999999988866 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.007
                            UPF0184  16 aeteedefgeeEyeainsmLDqinsaLDalEernDdlnskLrELlesnRq 65 
                                        +++e++   +e  +a n  +D ++  L++l + n +l  + +EL++ n++
  gene1464|gene1464|rna1464|rna1464 104 LNAEVESCRKEGNAASNAQIDRLERELEKLRKENAKLADRNKELIDKNKK 153
                                        577888888889999********************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2534  (0.141335); expected 358.6 (0.02)
Passed bias filter:                      654  (0.0364772); expected 358.6 (0.02)
Passed Vit filter:                       161  (0.00897987); expected 17.9 (0.001)
Passed Fwd filter:                       123  (0.00686039); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              87  [number of targets reported over threshold]
# CPU time: 1.27u 0.32s 00:00:01.59 Elapsed: 00:00:00.51
# Mc/sec: 1112.66
//
Query:       gene1465|gene1465|rna1465|rna1465  [L=429]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-11   44.5   0.0     0.0001   22.1   0.0    2.3  2  UPF0020          Putative RNA methylase family UPF0020
    1.4e-08   34.7   0.1     0.0001   22.1   0.1    2.6  2  N6_N4_Mtase      DNA methylase
    0.00096   18.7   0.0      0.017   14.6   0.0    2.3  2  AviRa            RRNA methyltransferase AviRa
     0.0035   17.1   2.2     0.0035   17.1   0.1    1.9  2  MethyltransfD12  D12 class N6 adenine-specific DNA methyltran
  ------ inclusion threshold ------
       0.08   13.7   0.0        0.2   12.4   0.0    1.7  1  Methyltransf_25  Methyltransferase domain
       0.15   12.7   0.0       0.34   11.6   0.0    1.7  1  Methyltransf_11  Methyltransferase domain


Domain annotation for each model (and alignments):
>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   3.4e-08    0.0001       4      90 ..     193     279 ..     191     307 .. 0.81
   2 !   20.1   0.0   1.4e-07   0.00042     119     164 ..     343     389 ..     329     395 .. 0.87

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 3.4e-08
                                        S-SS---SS-HHHHHHHHHHTT--TTS-EEETT-TTSHHHHHHHHHHTT--TTTT----SSHHHHHHHHHHHH--E CS
                            UPF0020   4 RefngpapLketLAaalvrlagwkpgepllDPmCGsGtilIEaallganiapgllrefvlelkaeaeeearaelkl 79 
                                        R f g +++  +++a + +++  + +  +lDP+ GsG+i +  al+g +++   + ++ +  ++++ee+++++lk 
  gene1465|gene1465|rna1465|rna1465 193 RLFIGHTAMDLEVSAFMFNITVSTGNCIILDPFVGSGSIILYCALMGCYVVGCDISKKQMIGQNTIEENNKKNLKS 268
                                        7788899999999**************************************7777777777888888888888887 PP

                                        EEEES-HHHHH CS
                            UPF0020  80 ygsDldrrvvq 90 
                                        +  D+++ ++ 
  gene1465|gene1465|rna1465|rna1465 269 FDHDIKQMITS 279
                                        77777665554 PP

  == domain 2  score: 20.1 bits;  conditional E-value: 1.4e-07
                                        TS---EEEE----------HHHH.HHHHHHHHHHHHHH-TT..-EEE CS
                            UPF0020 119 egevdvivtnpPYGerlgskkal.ekLYseflrelkrvlrgggrlvl 164
                                         ++vd ++t++PYG+r + +k+   +L + + +   +vl+++gr ++
  gene1465|gene1465|rna1465|rna1465 343 FKKVDHVITDLPYGIRASLQKETmISLIKGLRDLCDEVLHKNGRVCF 389
                                        568**************9766655********************997 PP

>> N6_N4_Mtase  DNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.1   3.3e-08    0.0001     192     226 ..     218     252 ..     205     257 .. 0.91
   2 !    9.8   0.0    0.0002      0.59       1      63 [.     346     398 ..     346     425 .. 0.85

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 3.3e-08
                                        T-EEEETT-TTTHHHHHHHHTT-EEEEEESSHHHH CS
                        N6_N4_Mtase 192 gdivlDpFaGSGtTavaakelgrkfiGieieeeyv 226
                                        + i+lDpF GSG+++ +++ +g   +G++i+++ +
  gene1465|gene1465|rna1465|rna1465 218 NCIILDPFVGSGSIILYCALMGCYVVGCDISKKQM 252
                                        669****************************9865 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0002
                                        EEEEEE--SSSSSCS.....GCCGCCHHHHHHHHHHHHHHHHHHHEEEEEEEEEEE-CCCHHT CS
                        N6_N4_Mtase   1 vdlivtdpPYntgkdyendeqyeeedsyeeyleflekvlkevrrvLkddgsifiniddseikk 63 
                                        vd+++td PY++  +           + e++++++++  +++ +vL ++g ++ +i + + ++
  gene1465|gene1465|rna1465|rna1465 346 VDHVITDLPYGIRAS----------LQKETMISLIKGLRDLCDEVLHKNGRVCFSIIRGYGNE 398
                                        79**********999..........77899*************************98888877 PP

>> AviRa  RRNA methyltransferase AviRa
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.2     0.078   2.3e+02      92     148 ..      68     122 ..      62     153 .. 0.60
   2 !   14.6   0.0   5.6e-06     0.017     151     201 ..     333     381 ..     317     405 .. 0.74

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.078
                              AviRa  92 lelakkNLsLLt.keglakreeelrelaeeyekeshaealesaerleellakkgeeke 148
                                        l +a++N +LL  +e+l+++    ++++ee+ k   +  l+ +++ e+++++++++ +
  gene1465|gene1465|rna1465|rna1465  68 LYVAETNHELLVvDETLKEKL---QRKTEEFVKLYLTGELNRIQHNERVTTETAQKVK 122
                                        778999999986267776665...5555555555444444444444444433333333 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 5.6e-06
                              AviRa 151 vfkaditekeeeaekevdivitDlPYGelvswqgese.epvkqlleslaavl 201
                                        +f+a i+   ++++k+vd vitDlPYG  +s q+e+  + +k l +   +vl
  gene1465|gene1465|rna1465|rna1465 333 IFRASIF---STHFKKVDHVITDLPYGIRASLQKETMiSLIKGLRDLCDEVL 381
                                        6778888...778889***************999854033444433334455 PP

>> MethyltransfD12  D12 class N6 adenine-specific DNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.3      0.49   1.5e+03      73     135 ..      82     143 ..      60     164 .. 0.53
   2 !   17.1   0.1   1.2e-06    0.0035      24     104 ..     221     309 ..     211     347 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.49
                                        HH.TCTTGGC.TSHHHHHHHH..HHHH...H.HH-HHHHHHHHHHHHCCBGGG---B-TTS-B--- CS
                    MethyltransfD12  73 lekllekeelenereyfyelr..eefnkkid.aireaeeaidflylnrllfsglervnkkgnfnvp 135
                                         + l+ek   + ++e+f++l    e n +i+ + r + e ++   +  +++   + +++k++f+  
  gene1465|gene1465|rna1465|rna1465  82 ET-LKEKL--QRKTEEFVKLYltGELN-RIQhNERVTTETAQKVKFKLVTETFGCKIKQKNDFSNK 143
                                        33.34443..34677776666545555.22202222222555555555555555555555555555 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 1.2e-06
                                        EEETT-TTSCCHHCS...SSCEEEEES-HHHHHHHHHHCCH.......SHHHHHHHHH.T.CTTGGC.TSHHHHHH CS
                    MethyltransfD12  24 fvepFaGggaVffeakkqgkkvlinDinedlinlykalikn.......nveelikelekl.lekeelenereyfye 91 
                                        + +pF+G+g++ +++   g  v+ +Di ++ +   + +i++       ++++ ik++ +   +k + + +++++y+
  gene1465|gene1465|rna1465|rna1465 221 ILDPFVGSGSIILYCALMGCYVVGCDISKKQMIGQN-TIEEnnkknlkSFDHDIKQMITSySNKITSTVSSDEYYN 295
                                        68*************99**************99999.555559999995555555543333555556679999999 PP

                                        HHHHHH....HHH- CS
                    MethyltransfD12  92 lreefn.kkidair 104
                                        ++++   +k+  +r
  gene1465|gene1465|rna1465|rna1465 296 VQDKLFlTKLPGVR 309
                                        99877666666555 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   6.7e-05       0.2       1      58 [.     221     276 ..     221     304 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 6.7e-05
                                        EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCGB CS
                    Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl.nvefvqgdaedl 58 
                                        +Ld   G+G ++l++a   g + v+g+Dis++++   ++ +ee++  n++   +d++++
  gene1465|gene1465|rna1465|rna1465 221 ILDPFVGSGSIILYCALM-G-CYVVGCDISKKQMIG-QNTIEENNKkNLKSFDHDIKQM 276
                                        89999***********88.5.*********987643.3334333333888888888775 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00011      0.34       5      54 ..     226     275 ..     222     298 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00011
                                        -TTSHHHHHHHHTTSEEEEEES-HHHH...HHHHHHCCHHT-.EEEETTEECCC CS
                    Methyltransf_11   5 cGtGrlaealakrgarvvgvDlskeml...klakekaseegl.kvefvvadaek 54 
                                        +G+G++  ++a  g+ vvg+D+sk+++   +     ++e++  +++    d+++
  gene1465|gene1465|rna1465|rna1465 226 VGSGSIILYCALMGCYVVGCDISKKQMigqN----TIEENNKkNLKSFDHDIKQ 275
                                        7889999999988***********9883321....2222222345555666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (429 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       886  (0.0494171); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 2854.58
//
Query:       gene1466|gene1466|rna1466|rna1466  [L=376]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    0.00027   20.7   8.9     0.0065   16.3   0.0    3.5  3  TFIIE_alpha  TFIIE alpha subunit
    0.00031   20.8   0.6       0.31   11.2   0.2    2.8  2  HTH_9        RNA polymerase III subunit RPC82 helix-turn-heli


Domain annotation for each model (and alignments):
>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.5   0.9    0.0017        15      15      62 ..      46      93 ..      34     130 .. 0.82
   2 ?    1.9   1.1     0.023     2e+02      17      65 ..     125     181 ..     109     207 .. 0.56
   3 !   16.3   0.0   7.3e-07    0.0065       5      61 ..     262     318 ..     258     321 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0017
                                       HHHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEEEE CS
                        TFIIE_alpha 15 avlvldvLlekgevteedlakelkidlnelrklLnrLyearlvkykrr 62
                                         +v+d +l    vt  +l  ++ +d   l k+L  L + r+v+y   
  gene1466|gene1466|rna1466|rna1466 46 LEPVVDFMLNLKTVTYKQLICNIPLDSVTLTKILKYLIQTRVVEYNIY 93
                                       5678999999999999****************************9755 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.023
                                        HHHHHHHCTTSE..BHHHHHHHH...TS-HHHHHHHHHHHHHCTSEEEEEEEE...T CS
                        TFIIE_alpha  17 lvldvLlekgev..teedlakel...kidlnelrklLnrLyearlvkykrrrd...e 65 
                                        +vl  L +kg++  +++d+   l   ++ lne+++lL   +++  vk  + ++    
  gene1466|gene1466|rna1466|rna1466 125 KVLLELFMKGVTvrKNDDVDAMLfvkSVSLNEVKSLLRLNFSESCVKEEKIKNvgiT 181
                                        555445445543234555555552223445666666655556666655555553332 PP

  == domain 3  score: 16.3 bits;  conditional E-value: 7.3e-07
                                        HHHHHCS-HHHHHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEEE CS
                        TFIIE_alpha   5 evvrkfygeeavlvldvLlekgevteedlakelkidlnelrklLnrLyearlvkykr 61 
                                         +v +  + +  +  + ++ek  v ++++ k++ i++++++++L+ L + +l+ +++
  gene1466|gene1466|rna1466|rna1466 262 WIVNRYLDLDSRKLYNFIAEKLFVPDDQIIKQVLIERQKIKPILFGLMQNGLIAIHK 318
                                        56666666666777788999999********************************98 PP

>> HTH_9  RNA polymerase III subunit RPC82 helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   0.2   3.4e-05      0.31      12      59 ..      43      90 ..      33      92 .. 0.93
   2 !    7.0   0.0   0.00067         6      10      58 ..     267     315 ..     259     319 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 3.4e-05
                                       TTHHHHHHHHHHHHSSBEHHHHHHHHSSTHHHHHHHHHHHHHTTSEEE CS
                              HTH_9 12 GevvakVvetLlrkgrltlrelvkktkLsldqVkksLvvLiqhrlVqy 59
                                       G++ + Vv+++l+  + t ++l+ +++L+     k+L  Liq r V y
  gene1466|gene1466|rna1466|rna1466 43 GTLLEPVVDFMLNLKTVTYKQLICNIPLDSVTLTKILKYLIQTRVVEY 90
                                       888899****************************************99 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.00067
                                        CSTTHHHHHHHHHHHHSSBEHHHHHHHHSSTHHHHHHHHHHHHHTTSEE CS
                              HTH_9  10 hFGevvakVvetLlrkgrltlrelvkktkLsldqVkksLvvLiqhrlVq 58 
                                        +++  ++k + ++ +k + + ++++k++ + ++++k +L  L+q++l+ 
  gene1466|gene1466|rna1466|rna1466 267 YLDLDSRKLYNFIAEKLFVPDDQIIKQVLIERQKIKPILFGLMQNGLIA 315
                                        5555566777777777788889***********************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (376 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       827  (0.0461264); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 2334.75
//
Query:       gene1467|gene1467|rna1467|rna1467  [L=50]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (50 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       450  (0.025099); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.27s 00:00:00.63 Elapsed: 00:00:00.42
# Mc/sec: 355.50
//
Query:       gene1468|gene1468|rna1468|rna1468  [L=66]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (66 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       459  (0.025601); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.32u 0.27s 00:00:00.59 Elapsed: 00:00:00.40
# Mc/sec: 500.15
//
Query:       gene1469|gene1469|rna1469|rna1469  [L=185]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.3e-09   35.7  32.6    4.1e-06   27.0  19.6    2.0  2  EamA      EamA-like transporter family
    0.00092   18.6  21.5     0.0011   18.4  21.5    1.0  1  TPT       Triose-phosphate Transporter family
  ------ inclusion threshold ------
       0.12   12.3   2.1       0.29   11.1   0.0    2.3  3  SLATT_1   SMODS and SLOG-associating 2TM effector domain 1


Domain annotation for each model (and alignments):
>> EamA  EamA-like transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   5.0   3.3e-06      0.02      98     136 ..       3      41 ..       1      42 [. 0.93
   2 !   27.0  19.6   6.8e-10   4.1e-06       5     134 ..      53     180 ..      49     183 .. 0.94

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.3e-06
                               EamA  98 tslePvftlilsvlllgekltlkqllgivlillGvllil 136
                                         s +P+f+l+ s++l +e++++++++ i+li lG++li+
  gene1469|gene1469|rna1469|rna1469   3 KSSSPIFILLSSFVLNNEPVSFLTFFIIFLIGLGTFLIT 41 
                                        5789*********************************97 PP

  == domain 2  score: 27.0 bits;  conditional E-value: 6.8e-10
                               EamA   5 llallaalfwaiyfvlskillrkvspltltfvrfliagillliiallkegklaklslkdwllllllgllgtvlafl 80 
                                        l +l a+l+++i + l+++ l+k+s +t+ +   l  +i+lli+a ++eg + +l+  ++ l+++l++++++l+ +
  gene1469|gene1469|rna1469|rna1469  53 LPILFASLVSGIRWSLIQRYLTKTSIFTFIATINLNISIILLIMAIYFEGLP-VLNMHSFVLIVVLSVISFFLV-W 126
                                        55899**********************9999888899999999999999999.9********************.5 PP

                               EamA  81 lffyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvll 134
                                        + ++ lk  s  +  ++  +  + +++lsv++ + +l+   ++g+vl+++G+++
  gene1469|gene1469|rna1469|rna1469 127 CEYTILKCFSCVFLCVLGIVKEMSVVVLSVYVGKVRLEGVNWIGLVLSVCGLMM 180
                                        9999***********************************************987 PP

>> TPT  Triose-phosphate Transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4  21.5   1.8e-07    0.0011      96     289 ..       1     181 [.       1     182 [. 0.84

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.8e-07
                                TPT  96 tvKasePiFtvilsrlllgeklsllvylsLlpivgGvalasvtElsFnligfisAlisnltfslrnifsKkllkkl 171
                                        +vK+s PiF  + s +l +e +s+l +  +  i  G  l ++   + nl   +  l++ l++ +r  +  + l+k 
  gene1469|gene1469|rna1469|rna1469   1 MVKSSSPIFILLSSFVLNNEPVSFLTFFIIFLIGLGTFLITFSHDTLNLPQVLPILFASLVSGIRWSLIQRYLTK- 75 
                                        59*******76655555566667777777777778*********************************9999999. PP

                                TPT 172 kdldalnlfaiitilslllllPvallvegvlktpsllkstkvslkevllllllsgvlfhlynqvaymvLervspvt 247
                                           +  ++ a i +   ++ll +a+++eg    p+l  +      +++l ++ls + f+l   + y++L+  s v 
  gene1469|gene1469|rna1469|rna1469  76 --TSIFTFIATINLNISIILLIMAIYFEG---LPVLNMH------SFVLIVVLSVISFFL-VWCEYTILKCFSCVF 139
                                        ..566777777777777888889999999...4444433......466666666666666.5799*********** PP

                                TPT 248 hsvantvKrvvvIvlsvlvfknpvsllnaiGtavaivGvflY 289
                                          v   vK + v+vlsv v k +++ +n iG +++++G ++Y
  gene1469|gene1469|rna1469|rna1469 140 LCVLGIVKEMSVVVLSVYVGKVRLEGVNWIGLVLSVCGLMMY 181
                                        *****************************************9 PP

>> SLATT_1  SMODS and SLOG-associating 2TM effector domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   4.9e-05      0.29      24      85 ..      22      83 ..      16      89 .. 0.88
   2 ?   -0.0   0.2      0.13     8e+02      32      70 ..      91     128 ..      81     136 .. 0.54
   3 ?   -1.3   0.0      0.33     2e+03      40      61 ..     153     175 ..     126     180 .. 0.56

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 4.9e-05
                            SLATT_1 24 akrwrlllillellalllaalrafgelsv.dlvgvlaavaaallaWlelkqyeelaaaYslaa 85
                                        ++++  +i+l +l+++l++++   +l++ +++ +l a   +++ W  +++y ++++ ++++a
  gene1469|gene1469|rna1469|rna1469 22 VSFLTFFIIFLIGLGTFLITFS-HDTLNLpQVLPILFASLVSGIRWSLIQRYLTKTSIFTFIA 83
                                       56788899999***********.777888899999999999*************999999877 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.13
                            SLATT_1  32 illellalllaalrafgelsvdlvgvlaavaaallaWle 70 
                                        i+l ++a+ +  l +++  s+ ++ v+ +v++ +l W e
  gene1469|gene1469|rna1469|rna1469  91 IILLIMAIYFEGLPVLNMHSF-VLIVVLSVISFFLVWCE 128
                                        344444444444443333333.45555555555666655 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 0.33
                            SLATT_1  40 llaalr.afgelsvdlvgvlaav 61 
                                        +l ++  ++   +v+++g++ +v
  gene1469|gene1469|rna1469|rna1469 153 VLSVYVgKVRLEGVNWIGLVLSV 175
                                        33322223443444666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1117  (0.0623013); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1338.65
//
Query:       gene147|gene147|rna147|rna147  [L=111]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
     0.0028   18.0   0.4     0.0044   17.5   0.4    1.5  1  GlutR_dimer  Glutamyl-tRNAGlu reductase, dimerisation domain
     0.0035   17.5   0.1     0.0056   16.9   0.1    1.3  1  rve          Integrase core domain
  ------ inclusion threshold ------
      0.036   13.9   0.0      0.046   13.6   0.0    1.3  1  DUF2760      Domain of unknown function (DUF2760)
      0.065   13.5   1.6      0.095   12.9   1.6    1.3  1  SMBP         Small metal-binding protein
       0.11   12.3   0.0       0.15   11.8   0.0    1.4  1  rve_3        Integrase core domain
       0.22   11.2   2.2       0.24   11.0   1.0    1.6  2  pEK499_p136  HEPN pEK499 p136


Domain annotation for each model (and alignments):
>> GlutR_dimer  Glutamyl-tRNAGlu reductase, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.4   1.5e-06    0.0044       8      54 ..      16      60 ..       9      99 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.5e-06
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-S..---- CS
                    GlutR_dimer  8 eeveefeawlkslevvptIkalrekaeeireeeleralkklaldged 54
                                   +e  + e+   + +v+ +I+ +re +e+i+ +e+ +a kk++  ++ 
  gene147|gene147|rna147|rna147 16 HEKTSVESHKSNGHVERVIRTIREAIEKIKVNEIGKAVKKID--DKC 60
                                   555666777777899*************************96..443 PP

>> rve  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.1   1.9e-06    0.0056      83     117 ..       5      39 ..       2      41 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.9e-06
                            rve  83 frefladlgirvsftrpgrpqdnGkvErfhrtlkd 117
                                    ++++  + gi ++ t + + ++nG vEr +rt+++
  gene147|gene147|rna147|rna147   5 TKKWMTEAGIIHEKTSVESHKSNGHVERVIRTIRE 39 
                                    68999****************************97 PP

>> DUF2760  Domain of unknown function (DUF2760)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   1.5e-05     0.046      17      57 ..      32      72 ..      26     102 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.5e-05
                        DUF2760 17 RlvDflqedlsaysDaeiGaaaRkvhegcrkvlkelltlep 57
                                   R++  ++e +++ + +eiG a++k+ ++c+k+ +  ++ +p
  gene147|gene147|rna147|rna147 32 RVIRTIREAIEKIKVNEIGKAVKKIDDKCNKTYHAGMKCTP 72
                                   88999**************************9998887766 PP

>> SMBP  Small metal-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   1.6   3.2e-05     0.095      61     103 ..      18      58 ..       4      66 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.2e-05
                                    HHH...-------HHHHHHHHHHHHHHHHHCT-HHHHHHHHHH CS
                           SMBP  61 kaaaekakeeekehldegikhLeeAIkhgkaghadvAtkaaee 103
                                    k   ++++++++ h+++ i+ ++eAI++ k ++  +A k +++
  gene147|gene147|rna147|rna147  18 K--TSVESHKSNGHVERVIRTIREAIEKIKVNEIGKAVKKIDD 58 
                                    2..46899*******************************9987 PP

>> rve_3  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   5.2e-05      0.15       3      32 ..      14      43 ..      12      64 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 5.2e-05
                          rve_3  3 ielsyiapgkPqqNglvEsfngtlrdelln 32
                                   i ++ + + + + Ng+vE++++t+r+ + +
  gene147|gene147|rna147|rna147 14 IIHEKTSVESHKSNGHVERVIRTIREAIEK 43
                                   5666777888899************98765 PP

>> pEK499_p136  HEPN pEK499 p136
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   1.0   7.9e-05      0.24      73     123 ..      13      60 ..       2      74 .. 0.73
   2 ?   -0.6   0.0       0.3     9e+02     103     128 ..      65      92 ..      61     105 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 7.9e-05
                    pEK499_p136  73 lgirksesfkdkepnislkellrriRNgiAHfgieepitedklikgIkied 123
                                     +i+++ s +++++n  ++ ++r iR +i   +++   + +k +k+I+ + 
  gene147|gene147|rna147|rna147  13 GIIHEKTSVESHKSNGHVERVIRTIREAIEKIKVN---EIGKAVKKIDDKC 60 
                                    3567777888899****************887776...5567777777554 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.3
                    pEK499_p136 103 Hfgie.epitedklikgIk.iedveknr 128
                                    H g +  p++  k+i+gI  +e+v k++
  gene147|gene147|rna147|rna147  65 HAGMKcTPEKAWKDITGIAaVEKVRKED 92 
                                    5555544555556666666444444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (111 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1058  (0.0590105); expected 358.6 (0.02)
Passed bias filter:                      527  (0.0293937); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 791.66
//
Query:       gene1470|gene1470|rna1470|rna1470  [L=31]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (31 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       186  (0.0103743); expected 358.6 (0.02)
Passed bias filter:                      150  (0.00836633); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.27s 00:00:00.61 Elapsed: 00:00:00.41
# Mc/sec: 227.10
//
Query:       gene1471|gene1471|rna1471|rna1471  [L=41]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.07   12.4   0.5        1.3    8.3   0.0    2.0  2  DUF3666   Ribose-5-phosphate isomerase
       0.12   12.8   0.0       0.12   12.7   0.0    1.1  1  DUF4542   Domain of unknown function (DUF4542)


Domain annotation for each model (and alignments):
>> DUF3666  Ribose-5-phosphate isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.0   0.00015       1.3      28      45 ..       8      25 ..       5      26 .. 0.90
   2 ?    2.8   0.2    0.0074        66       2      12 ..      28      38 ..      27      39 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00015
                                       HHHHTTT---HHHHHHHH CS
                            DUF3666 28 qeyFFancqdeeIaayvk 45
                                       ++ F+  ++d++ ++yv+
  gene1471|gene1471|rna1471|rna1471  8 KQPFYSTSKDKQTKEYVR 25
                                       567**************9 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.0074
                                       HB--HHHHHHH CS
                            DUF3666  2 tykdlleiLka 12
                                       t++dll +Lk 
  gene1471|gene1471|rna1471|rna1471 28 TIRDLLAMLKV 38
                                       89*******95 PP

>> DUF4542  Domain of unknown function (DUF4542)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   1.4e-05      0.12      30      54 ..      10      34 ..       2      38 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.4e-05
                            DUF4542 30 ppYnaqkdkhakaYfrsktvkkvLk 54
                                       p Y+  kdk++k+Y r +t++++L 
  gene1471|gene1471|rna1471|rna1471 10 PFYSTSKDKQTKEYVRDTTIRDLLA 34
                                       6799*******************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (41 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       390  (0.0217525); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.35u 0.25s 00:00:00.60 Elapsed: 00:00:00.41
# Mc/sec: 300.49
//
Query:       gene1472|gene1472|rna1472|rna1472  [L=303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.3e-09   37.2   0.4    8.4e-09   35.9   0.1    1.9  2  Plus-3    Plus-3 domain
  ------ inclusion threshold ------
        9.9    6.0  11.9         16    5.3   5.7    2.2  2  CSRNP_N   Cysteine/serine-rich nuclear protein N-terminus


Domain annotation for each model (and alignments):
>> Plus-3  Plus-3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0      0.76   6.8e+03      71      90 ..      34      55 ..      15      64 .. 0.55
   2 !   35.9   0.1   9.3e-13   8.4e-09       5     105 ..      81     173 ..      77     176 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.76
                             Plus-3 71 tnkylklrhgkseks..frlek 90
                                        n y+k++  +++k+  +r+++
  gene1472|gene1472|rna1472|rna1472 34 YNRYMKIKKLEEKKEveHRIDE 55
                                       5555566555333222255554 PP

  == domain 2  score: 35.9 bits;  conditional E-value: 9.3e-13
                             Plus-3   5 irlsRskleklleepffedavkgcfvRvkigeeretgqpvyrlaqivgvkeeekgkpykl.kk.gkkttnkylklr 78 
                                        + + R+ l+k ++ p +++  +g fvRv  +       + y++ +++g++   + ++y + ++ ++ +tnk + + 
  gene1472|gene1472|rna1472|rna1472  81 VLVPRTLLAKNVYRPAIDRL-VGNFVRVCFK-------SGYVVKRVEGMQ---RASEYFVeEStKNYRTNKNICIV 145
                                        7899************9876.599******9.......47********94...6889***54456899******** PP

                             Plus-3  79 hgkseks.frlekvSnspfteeEferwk 105
                                         g+ +++ ++++++Sns+ + +E++ +k
  gene1472|gene1472|rna1472|rna1472 146 RGSGAREcIPMSFISNSRPSFAEYDHFK 173
                                        **655555****************9987 PP

>> CSRNP_N  Cysteine/serine-rich nuclear protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.4     0.003        27      96     143 ..       3      50 ..       1      73 [. 0.80
   2 ?    5.3   5.7    0.0018        16      43     127 ..     193     283 ..     180     302 .. 0.53

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.003
                            CSRNP_N  96 disdedldseaelddylflqplstkkrralLraaGvkkidseekkelr 143
                                        d++ +d++  ++++d   l  l+  +r a+L +  +k    eekke++
  gene1472|gene1472|rna1472|rna1472   3 DMQYNDMNLYQDSEDEEKLMKLPEAQREAILYNRYMKIKKLEEKKEVE 50 
                                        667789999999999999*************88766555556676654 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0018
                            CSRNP_N  43 kkftlaehaieqkrlr.......reklrerlkeeklealklklsssdlleeeeeealevddisdedldseaelddy 111
                                        + +t +  a e++r++       r+k ++ +++ +l   +++  +++  e+  + + ++d+i+++d d  ae ++ 
  gene1472|gene1472|rna1472|rna1472 193 NAMTREMSADERARAQeerskfyRDKRKNLMEKIRLIREREDAFKNGDAEKVRAVQKRIDEIDEKDKD-PAEEKEK 267
                                        44443333333333331111222333333333333333333344555555555556688888888888.5555566 PP

                            CSRNP_N 112 lflqplstkkrralLr 127
                                             + +k+rr+   
  gene1472|gene1472|rna1472|rna1472 268 EIWDRINAKNRRINYE 283
                                        6667888999987654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (303 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1613  (0.089966); expected 358.6 (0.02)
Passed bias filter:                      466  (0.0259914); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.77
# Mc/sec: 1184.81
//
Query:       gene1473|gene1473|rna1473|rna1473  [L=701]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0083   15.7   0.2      0.013   15.0   0.2    1.2  1  Utp21     Utp21 specific WD40 associated putative domain


Domain annotation for each model (and alignments):
>> Utp21  Utp21 specific WD40 associated putative domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.2   7.3e-07     0.013      91     167 ..     570     643 ..     559     692 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 7.3e-07
                                        HHHHHHHTT------.------HHHHHHHHHHSS--HHHHHHHHH-S-HHHHHT--------S-SHHHHHHHHHHH CS
                              Utp21  91 eeeeeeeesrilkldklgteseftklLeegsetgdysefleyLkslspsaidleirsLesaesleelvafvkalta 166
                                        +++e+e+e +i +l   +   +f++ Le+++e+ dy+++++ +k+l    i   i  L++++ +  l+a+++ + +
  gene1473|gene1473|rna1473|rna1473 570 SSSESEDELEIENL---KVYDKFSRALERSKEDADYDALFNAIKELDMGDISSIISGLDNNSLYVVLQALMNNIDY 642
                                        33444444445554...699**************************************888888877777777665 PP

                                        H CS
                              Utp21 167 r 167
                                        +
  gene1473|gene1473|rna1473|rna1473 643 N 643
                                        4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (701 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       481  (0.026828); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.63u 0.31s 00:00:00.94 Elapsed: 00:00:00.49
# Mc/sec: 4283.03
//
Query:       gene1474|gene1474|rna1474|rna1474  [L=81]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      3e-08   33.6   0.0    3.4e-08   33.5   0.0    1.0  1  Ribosomal_L1     Ribosomal protein L1p/L10e family
  ------ inclusion threshold ------
      0.019   13.8   0.0      0.019   13.8   0.0    1.0  1  AdoMet_Synthase  S-adenosylmethionine synthetase (AdoMet synt


Domain annotation for each model (and alignments):
>> Ribosomal_L1  Ribosomal protein L1p/L10e family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.5   0.0   3.7e-12   3.4e-08     134     203 ..       7      75 ..       2      76 .. 0.91

  Alignments for each domain:
  == domain 1  score: 33.5 bits;  conditional E-value: 3.7e-12
                                        -HHHHHHHHCTTEEEEE-TTTSEEEEEEEETTSSHHHHHHHHHHHHHHHHHTSTTTSGSEEEEEEEETTS CS
                       Ribosomal_L1 134 dvkkevekalkstvvvrldkgtclsvkvGklsftaeelaeNieavvkalvekvpkkwkniksiylkttms 203
                                        d+++  +++++  v+++l+k++ +s+ vG++++++ee+  N+++ +++l + ++k+ k++  ++lk+ ++
  gene1474|gene1474|rna1474|rna1474   7 DLQNFYNEVVR-MVKFKLRKTNDISFTVGYCEMSDEEIYTNLNTGLNFLATLLKKGYKSLGGVVLKSCQG 75 
                                        66777788888.899***************************************************9766 PP

>> AdoMet_Synthase  S-adenosylmethionine synthetase (AdoMet synthetase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   2.1e-06     0.019     142     180 ..      14      51 ..       3      70 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.1e-06
                                        HHHCH-SS..-BESSSEEEEEEES--HHHHHHHHHHHHH CS
                    AdoMet_Synthase 142 dvferkkkevplaNDtSfgvgyaplseleklvleterll 180
                                        +v++  k +++++ND Sf+vgy  +s+ e   ++++  l
  gene1474|gene1474|rna1474|rna1474  14 EVVRMVKFKLRKTNDISFTVGYCEMSDEEI-YTNLNTGL 51 
                                        45555556899***************9664.44444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (81 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       648  (0.0361426); expected 358.6 (0.02)
Passed bias filter:                      548  (0.030565); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.30s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 560.13
//
Query:       gene1475|gene1475|rna1475|rna1475  [L=59]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.059   13.5   0.0      0.075   13.2   0.0    1.2  1  DUF1939   Domain of unknown function (DUF1939)


Domain annotation for each model (and alignments):
>> DUF1939  Domain of unknown function (DUF1939)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   4.2e-06     0.075      28      49 ..      25      46 ..      13      48 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.2e-06
                            DUF1939 28 ytGnssvdvtvdedGwvkievp 49
                                       ++Gn+s d+ + ++G+v+i++ 
  gene1475|gene1475|rna1475|rna1475 25 WLGNLSSDKPMAQNGMVNIDIT 46
                                       68*****************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       273  (0.0152267); expected 358.6 (0.02)
Passed bias filter:                      212  (0.0118244); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.46
# Mc/sec: 384.24
//
Query:       gene1476|gene1476|rna1476|rna1476  [L=89]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.065   12.9   0.5       0.18   11.4   0.5    1.7  1  CAP_C     Adenylate cyclase associated (CAP) C terminal


Domain annotation for each model (and alignments):
>> CAP_C  Adenylate cyclase associated (CAP) C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.5     1e-05      0.18      36      96 ..       1      69 [.       1      80 [. 0.69

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 1e-05
                              CAP_C 36 ifkCknstiqikgKvnait....ldnckkvsvvvds....vvSsvevincksvkvqvlgkvptisiDkt 96
                                       + +C++sti++k+K+ +i     ++n++   v+  +    v+   ++   ++++v v +++ ti i ++
  gene1476|gene1476|rna1476|rna1476  1 VLHCNDSTIEVKNKLPSILtalyIQNSYIEGVLESNhrlrVIRLYNIAAEHKLAVFVNERCTTIEITNV 69
                                       568***********9887522225666666655432333377777777788888888888888887766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       408  (0.0227564); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.28s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 668.07
//
Query:       gene1477|gene1477|rna1477|rna1477  [L=157]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       656  (0.0365888); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1146.88
//
Query:       gene1478|gene1478|rna1478|rna1478  [L=407]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (407 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       963  (0.0537119); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2980.91
//
Query:       gene1479|gene1479|rna1479|rna1479  [L=514]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.1e-17   63.1  16.9     0.0088   15.8   0.0    7.1  6  TPR_1        Tetratricopeptide repeat
    5.2e-16   57.4  13.5    0.00036   20.5   0.1    6.1  5  TPR_8        Tetratricopeptide repeat
    9.6e-12   44.1  15.7      0.091   12.9   0.1    7.0  6  TPR_2        Tetratricopeptide repeat
    7.9e-08   32.8   0.0        0.2   12.3   0.2    4.1  4  TPR_16       Tetratricopeptide repeat
    7.2e-07   28.8   1.8       0.43   10.7   0.0    5.8  6  TPR_7        Tetratricopeptide repeat
    1.6e-06   28.3   7.5        1.2    9.5   0.0    6.0  6  TPR_12       Tetratricopeptide repeat
      2e-06   27.4  11.2      0.092   12.5   3.3    5.6  5  TPR_11       TPR repeat
    5.3e-05   23.7   0.1         15    6.7   0.0    4.9  5  TPR_14       Tetratricopeptide repeat
    0.00033   20.8   5.0       0.65   10.5   0.0    5.6  5  TPR_17       Tetratricopeptide repeat
      0.003   17.4   7.0        5.9    6.9   0.1    4.9  5  TPR_10       Tetratricopeptide repeat
  ------ inclusion threshold ------
      0.017   15.6   0.0        2.7    8.6   0.0    2.7  2  TPR_19       Tetratricopeptide repeat
      0.056   13.0   2.6       0.15   11.6   0.6    2.2  2  Foie-gras_1  Foie gras liver health family 1
       0.15   12.8   7.3         41    5.1   0.7    5.1  5  TPR_6        Tetratricopeptide repeat
       0.15   11.9   0.0       0.35   10.8   0.0    1.5  1  PetG         Cytochrome B6-F complex subunit 5
       0.22   11.9   1.2        0.8   10.1   0.1    2.7  2  PPR          PPR repeat


Domain annotation for each model (and alignments):
>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.1       1.1   1.3e+03      10      26 ..     273     289 ..     269     294 .. 0.82
   2 !   15.4   0.0     1e-05     0.012       8      33 ..     334     359 ..     333     360 .. 0.93
   3 !   12.5   0.2     8e-05     0.096       7      25 ..     367     385 ..     365     386 .. 0.92
   4 !    8.2   0.6    0.0019       2.2       2      33 ..     392     422 ..     391     423 .. 0.75
   5 !   15.8   0.0   7.3e-06    0.0088       3      27 ..     426     450 ..     424     453 .. 0.90
   6 !   15.2   0.2   1.2e-05     0.014       3      26 ..     458     481 ..     456     483 .. 0.93

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 1.1
                                        HHHHTT-HHHHHHHHHH CS
                              TPR_1  10 ayfklgkydeAleyyek 26 
                                         ++++++yd  l+ ++ 
  gene1479|gene1479|rna1479|rna1479 273 YFYHKKEYDLSLALFNT 289
                                        57999****99999875 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 1e-05
                                        HHHHHHTT-HHHHHHHHHHHHHHSTT CS
                              TPR_1   8 GnayfklgkydeAleyyekALelnPn 33 
                                        Gn y  ++++  A+ ++++A++ n+ 
  gene1479|gene1479|rna1479|rna1479 334 GNFYSLQKDHTAAIHHFKRAVRFNHR 359
                                        899******************99976 PP

  == domain 3  score: 12.5 bits;  conditional E-value: 8e-05
                                        HHHHHHHTT-HHHHHHHHH CS
                              TPR_1   7 lGnayfklgkydeAleyye 25 
                                        +++ y++l++y+ A++yy+
  gene1479|gene1479|rna1479|rna1479 367 IAHEYMELNQYNTAIKYYS 385
                                        799***************5 PP

  == domain 4  score: 8.2 bits;  conditional E-value: 0.0019
                                        HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                              TPR_1   2 kalynlGnayfklgkydeAleyyekALelnPn 33 
                                        +a++++G+ay  +     A+++++kAL ln +
  gene1479|gene1479|rna1479|rna1479 392 RAYFGMGQAYAMQ-SSRLAIAFFKKALLLNST 422
                                        5667777776544.4689***********987 PP

  == domain 5  score: 15.8 bits;  conditional E-value: 7.3e-06
                                        HHHHHHHHHHHTT-HHHHHHHHHHH CS
                              TPR_1   3 alynlGnayfklgkydeAleyyekA 27 
                                        ++  lG+ y k g+   Ale+y++ 
  gene1479|gene1479|rna1479|rna1479 426 IWQSLGHEYKKFGDIANALECYRRM 450
                                        6999******************996 PP

  == domain 6  score: 15.2 bits;  conditional E-value: 1.2e-05
                                        HHHHHHHHHHHTT-HHHHHHHHHH CS
                              TPR_1   3 alynlGnayfklgkydeAleyyek 26 
                                         +  +G +y + ++y+ A+eyyek
  gene1479|gene1479|rna1479|rna1479 458 GWLMIGDMYKNRKEYKHAVEYYEK 481
                                        6999*******************8 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.0    0.0028       3.4       3      30 ..     329     356 ..     327     357 .. 0.87
   2 !   12.3   0.4   0.00013      0.16       5      24 ..     365     384 ..     363     387 .. 0.91
   3 !    7.1   0.2    0.0062       7.4       2      32 ..     392     421 ..     391     423 .. 0.83
   4 !   14.0   0.0   3.8e-05     0.045       3      26 ..     426     449 ..     426     452 .. 0.92
   5 !   20.5   0.1     3e-07   0.00036       3      28 ..     458     483 ..     456     485 .. 0.93

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0028
                                        HHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                              TPR_8   3 ayynlgsiylklgdyeeAkeyyekalel 30 
                                         +   g+ y+ ++d+ +A+  +++a++ 
  gene1479|gene1479|rna1479|rna1479 329 TMATAGNFYSLQKDHTAAIHHFKRAVRF 356
                                        566789*******************975 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00013
                                        HHHHHHHHHTT-HHHHHHHH CS
                              TPR_8   5 ynlgsiylklgdyeeAkeyy 24 
                                         ++++ y++l++y+ A++yy
  gene1479|gene1479|rna1479|rna1479 365 TLIAHEYMELNQYNTAIKYY 384
                                        589****************9 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.0062
                                        CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                              TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldp 32 
                                        +ay+ +g++y  ++    A+++++kal l+ 
  gene1479|gene1479|rna1479|rna1479 392 RAYFGMGQAY-AMQSSRLAIAFFKKALLLNS 421
                                        7888888888.5888899*********9987 PP

  == domain 4  score: 14.0 bits;  conditional E-value: 3.8e-05
                                        HHHHHHHHHHHTT-HHHHHHHHHH CS
                              TPR_8   3 ayynlgsiylklgdyeeAkeyyek 26 
                                        +++ lg+ y+k gd+ +A e+y++
  gene1479|gene1479|rna1479|rna1479 426 IWQSLGHEYKKFGDIANALECYRR 449
                                        6999******************97 PP

  == domain 5  score: 20.5 bits;  conditional E-value: 3e-07
                                        HHHHHHHHHHHTT-HHHHHHHHHHHH CS
                              TPR_8   3 ayynlgsiylklgdyeeAkeyyekal 28 
                                         ++++g+ y++ ++y+ A+eyyek++
  gene1479|gene1479|rna1479|rna1479 458 GWLMIGDMYKNRKEYKHAVEYYEKYV 483
                                        69**********************97 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.2      0.45   5.4e+02       8      27 ..     271     290 ..     264     296 .. 0.67
   2 !   10.1   0.0    0.0006      0.72       6      31 ..     332     357 ..     327     360 .. 0.87
   3 !    8.2   0.2    0.0025         3       5      24 ..     365     384 ..     361     388 .. 0.86
   4 !    6.5   0.4    0.0085        10       3      33 ..     393     422 ..     391     423 .. 0.83
   5 !   10.2   0.0   0.00058      0.69       2      29 ..     425     452 ..     424     453 .. 0.90
   6 !   12.9   0.1   7.6e-05     0.091       3      26 ..     458     481 ..     456     483 .. 0.93

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.45
                              TPR_2   8 GlayyklgdyeeAleafekA 27 
                                        +   y++++y+  l++f+ +
  gene1479|gene1479|rna1479|rna1479 271 AAYFYHKKEYDLSLALFNTS 290
                                        44556777778888888765 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0006
                              TPR_2   6 nlGlayyklgdyeeAleafekAleld 31 
                                          G+ y  ++d+  A+++f++A++ +
  gene1479|gene1479|rna1479|rna1479 332 TAGNFYSLQKDHTAAIHHFKRAVRFN 357
                                        67999*****************9976 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.0025
                              TPR_2   5 ynlGlayyklgdyeeAleaf 24 
                                          ++  y++l++y+ A++++
  gene1479|gene1479|rna1479|rna1479 365 TLIAHEYMELNQYNTAIKYY 384
                                        568999*************9 PP

  == domain 4  score: 6.5 bits;  conditional E-value: 0.0085
                              TPR_2   3 alynlGlayyklgdyeeAleafekAleldPn 33 
                                        a++ +G+ay+ ++    A+++f+kAl l+ +
  gene1479|gene1479|rna1479|rna1479 393 AYFGMGQAYA-MQSSRLAIAFFKKALLLNST 422
                                        7888888888.888889***********977 PP

  == domain 5  score: 10.2 bits;  conditional E-value: 0.00058
                              TPR_2   2 ealynlGlayyklgdyeeAleafekAle 29 
                                         ++  lG  y k gd + Ale++++ +e
  gene1479|gene1479|rna1479|rna1479 425 FIWQSLGHEYKKFGDIANALECYRRMVE 452
                                        67999*******************9765 PP

  == domain 6  score: 12.9 bits;  conditional E-value: 7.6e-05
                              TPR_2   3 alynlGlayyklgdyeeAleafek 26 
                                        ++ ++G+ y ++++y+ A+e++ek
  gene1479|gene1479|rna1479|rna1479 458 GWLMIGDMYKNRKEYKHAVEYYEK 481
                                        6999*******************8 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0      0.23   2.8e+02      36      58 ..     266     288 ..     258     291 .. 0.83
   2 ?    0.5   0.0      0.82   9.8e+02      46      61 ..     339     354 ..     332     358 .. 0.60
   3 !   12.3   0.2   0.00017       0.2       6      61 ..     370     417 ..     366     424 .. 0.71
   4 !   11.3   0.0   0.00036      0.43       3      62 ..     430     484 ..     429     489 .. 0.95

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.23
                             TPR_16  36 AllllgdaalrqgrlaeAaalyr 58 
                                         ++l++  +++++++++ +al++
  gene1479|gene1479|rna1479|rna1479 266 LRNLSAAYFYHKKEYDLSLALFN 288
                                        5778888999*********9997 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.82
                             TPR_16  46 rqgrlaeAaalyraal 61 
                                         q+++++A+  +++a+
  gene1479|gene1479|rna1479|rna1479 339 LQKDHTAAIHHFKRAV 354
                                        5566666665555554 PP

  == domain 3  score: 12.3 bits;  conditional E-value: 0.00017
                             TPR_16   6 aalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraal 61 
                                        +++++++y  A++++       + s  +++A+++ g+a++ q    +A+a++++al
  gene1479|gene1479|rna1479|rna1479 370 EYMELNQYNTAIKYY-------SLSANDYRAYFGMGQAYAMQ-SSRLAIAFFKKAL 417
                                        555555555555555.......55555899**********99.6677777887776 PP

  == domain 4  score: 11.3 bits;  conditional E-value: 0.00036
                             TPR_16   3 laraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalr 62 
                                        l++++ + gd + A++ +++ ++ +      +  +l  gd++  +++++ A+++y+++++
  gene1479|gene1479|rna1479|rna1479 430 LGHEYKKFGDIANALECYRRMVECG-----EVSGWLMIGDMYKNRKEYKHAVEYYEKYVG 484
                                        8999*********************.....99************************9985 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       5.2   6.2e+03       8      18 ..     180     190 ..     179     191 .. 0.79
   2 ?    1.9   0.0      0.24   2.8e+02       6      28 ..     334     354 ..     330     359 .. 0.88
   3 ?    4.2   0.1     0.043        52       9      22 ..     371     384 ..     366     388 .. 0.90
   4 ?   -0.7   0.0       1.6   1.9e+03      18      28 ..     409     419 ..     406     425 .. 0.76
   5 ?    4.5   0.0     0.034        41       6      24 ..     431     449 ..     427     454 .. 0.83
   6 !   10.7   0.0   0.00036      0.43       3      24 ..     460     481 ..     459     492 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 5.2
                              TPR_7   8 lysrlGdyeeA 18 
                                        + +++Gd+++ 
  gene1479|gene1479|rna1479|rna1479 180 VLFKVGDWRKS 190
                                        56899***986 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.24
                              TPR_7   6 arlysrlGdyeeAielyeqsLal 28 
                                        ++ ys + d+  Ai ++++  a+
  gene1479|gene1479|rna1479|rna1479 334 GNFYSLQKDHTAAIHHFKR--AV 354
                                        789999************9..64 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.043
                              TPR_7   9 ysrlGdyeeAiely 22 
                                        y +l++y +Ai++y
  gene1479|gene1479|rna1479|rna1479 371 YMELNQYNTAIKYY 384
                                        899**********9 PP

  == domain 4  score: -0.7 bits;  conditional E-value: 1.6
                              TPR_7  18 AielyeqsLal 28 
                                        Ai +++++L l
  gene1479|gene1479|rna1479|rna1479 409 AIAFFKKALLL 419
                                        99*****7755 PP

  == domain 5  score: 4.5 bits;  conditional E-value: 0.034
                              TPR_7   6 arlysrlGdyeeAielyeq 24 
                                        ++ y + Gd ++A+e+y++
  gene1479|gene1479|rna1479|rna1479 431 GHEYKKFGDIANALECYRR 449
                                        5558899***********9 PP

  == domain 6  score: 10.7 bits;  conditional E-value: 0.00036
                              TPR_7   3 lnLarlysrlGdyeeAielyeq 24 
                                        l ++++y ++ +y+ A+e+ye+
  gene1479|gene1479|rna1479|rna1479 460 LMIGDMYKNRKEYKHAVEYYEK 481
                                        679******************9 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.1     0.066        79       7      29 ..     267     290 ..     261     297 .. 0.70
   2 !    9.5   0.0   0.00096       1.2      42      73 ..     324     355 ..     310     359 .. 0.82
   3 !    8.4   0.5    0.0022       2.6       8      73 ..     332     355 ..     326     391 .. 0.66
   4 ?    5.7   1.3     0.015        18      46      72 ..     392     417 ..     361     418 .. 0.67
   5 ?    2.0   0.0      0.21   2.5e+02      49      70 ..     428     449 ..     426     455 .. 0.84
   6 ?    4.0   0.0     0.049        59      51      71 ..     462     482 ..     459     488 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.066
                             TPR_12   7 nnlaavl.rrlgrydeAlelleka 29 
                                        +nl a++ ++ ++yd +l+l++++
  gene1479|gene1479|rna1479|rna1479 267 RNLSAAYfYHKKEYDLSLALFNTS 290
                                        355555546788888888887765 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00096
                             TPR_12  42 pltattlrnLgrlyralgryeeAlelleeala 73 
                                        p  ++t+ + g  y++++++ +A+ ++++a++
  gene1479|gene1479|rna1479|rna1479 324 PFSVETMATAGNFYSLQKDHTAAIHHFKRAVR 355
                                        55677888888889999999999999999876 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.0022
                             TPR_12   8 nlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleeala 73 
                                          ++++  +++++ A+ ++++a                                          ++
  gene1479|gene1479|rna1479|rna1479 332 TAGNFYSLQKDHTAAIHHFKRA------------------------------------------VR 355
                                        3455555555555555555555..........................................43 PP

  == domain 4  score: 5.7 bits;  conditional E-value: 0.015
                             TPR_12  46 ttlrnLgrlyralgryeeAlelleeal 72 
                                        ++++++g++y ++   + A++++++al
  gene1479|gene1479|rna1479|rna1479 392 RAYFGMGQAYAMQ-SSRLAIAFFKKAL 417
                                        5778888887666.8888888888876 PP

  == domain 5  score: 2.0 bits;  conditional E-value: 0.21
                             TPR_12  49 rnLgrlyralgryeeAlellee 70 
                                        + Lg  y ++g+ + Ale +++
  gene1479|gene1479|rna1479|rna1479 428 QSLGHEYKKFGDIANALECYRR 449
                                        5789999999999999999998 PP

  == domain 6  score: 4.0 bits;  conditional E-value: 0.049
                             TPR_12  51 LgrlyralgryeeAlelleea 71 
                                        +g++y  +++y+ A+e++e+ 
  gene1479|gene1479|rna1479|rna1479 462 IGDMYKNRKEYKHAVEYYEKY 482
                                        789999889999999999986 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.3   0.0    0.0066       7.9       1      28 [.     334     361 ..     334     364 .. 0.88
   2 !   12.5   3.3   7.7e-05     0.092       2      41 ..     369     404 ..     368     405 .. 0.92
   3 ?    4.4   0.0     0.025        30      13      40 ..     409     436 ..     408     438 .. 0.89
   4 ?    5.1   0.0     0.015        18       1      19 [.     431     449 ..     431     452 .. 0.93
   5 ?    1.4   0.7      0.22   2.6e+02       1      19 [.     463     481 ..     463     481 .. 0.94

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0066
                             TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdna 28 
                                        G+ y  q + ++Ai ++k+A++++  +a
  gene1479|gene1479|rna1479|rna1479 334 GNFYSLQKDHTAAIHHFKRAVRFNHRYA 361
                                        6667778999*************99887 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 7.7e-05
                             TPR_11   2 dayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykq 41 
                                        ++y+e+++y+ Ai+ Y+    l+ ++ +ay+++G+ay++q
  gene1479|gene1479|rna1479|rna1479 369 HEYMELNQYNTAIKYYS----LSANDYRAYFGMGQAYAMQ 404
                                        78999**********96....****************987 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.025
                             TPR_11  13 AieaYkkAlkldPdnaeayynLGlayyk 40 
                                        Ai+ +kkAl l+++++ ++  LG+ y k
  gene1479|gene1479|rna1479|rna1479 409 AIAFFKKALLLNSTDPFIWQSLGHEYKK 436
                                        89999*****************987765 PP

  == domain 4  score: 5.1 bits;  conditional E-value: 0.015
                             TPR_11   1 GdayyeqGkyeeAieaYkk 19 
                                        G++y + G++ +A+e+Y++
  gene1479|gene1479|rna1479|rna1479 431 GHEYKKFGDIANALECYRR 449
                                        8999999**********97 PP

  == domain 5  score: 1.4 bits;  conditional E-value: 0.22
                             TPR_11   1 GdayyeqGkyeeAieaYkk 19 
                                        Gd+y  + +y+ A+e Y+k
  gene1479|gene1479|rna1479|rna1479 463 GDMYKNRKEYKHAVEYYEK 481
                                        99*************9986 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0      0.16     2e+02       5      29 ..     331     355 ..     327     365 .. 0.85
   2 ?    1.4   0.0      0.65   7.8e+02       7      27 ..     367     387 ..     361     400 .. 0.75
   3 ?   -0.3   0.0       2.2   2.6e+03      17      40 ..     406     429 ..     392     431 .. 0.73
   4 ?    5.7   0.0     0.027        33       3      29 ..     426     452 ..     424     455 .. 0.91
   5 ?    6.7   0.0     0.013        15       3      28 ..     458     483 ..     456     498 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.16
                             TPR_14   5 lalaeallalGdpdeAiallrrala 29 
                                        + ++ ++  + d+ +Ai +++ra++
  gene1479|gene1479|rna1479|rna1479 331 ATAGNFYSLQKDHTAAIHHFKRAVR 355
                                        567899999**************87 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.65
                             TPR_14   7 laeallalGdpdeAiallrra 27 
                                        +a+ +++l ++ +Ai+++   
  gene1479|gene1479|rna1479|rna1479 367 IAHEYMELNQYNTAIKYYSLS 387
                                        5788999*********99755 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 2.2
                             TPR_14  17 pdeAiallrralalaPddaeawll 40 
                                         + Aia +++al l+ +d+ +w  
  gene1479|gene1479|rna1479|rna1479 406 SRLAIAFFKKALLLNSTDPFIWQS 429
                                        456999999999999998888865 PP

  == domain 4  score: 5.7 bits;  conditional E-value: 0.027
                             TPR_14   3 allalaeallalGdpdeAiallrrala 29 
                                         ++ l++ +   Gd + A++++rr+++
  gene1479|gene1479|rna1479|rna1479 426 IWQSLGHEYKKFGDIANALECYRRMVE 452
                                        58999*******************986 PP

  == domain 5  score: 6.7 bits;  conditional E-value: 0.013
                             TPR_14   3 allalaeallalGdpdeAiallrral 28 
                                         +l++++ + ++ +++ A++++++++
  gene1479|gene1479|rna1479|rna1479 458 GWLMIGDMYKNRKEYKHAVEYYEKYV 483
                                        59*********************975 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.1       2.5     3e+03      14      26 ..      68      80 ..      60      81 .. 0.79
   2 ?    0.1   0.0       1.2   1.4e+03       9      33 ..     323     347 ..     321     348 .. 0.86
   3 ?    4.6   0.1      0.04        48       2      34 .]     350     382 ..     349     382 .. 0.95
   4 ?    1.4   0.1      0.45   5.4e+02      10      26 ..     388     404 ..     384     407 .. 0.87
   5 !   10.5   0.0   0.00055      0.65       2      33 ..     413     444 ..     412     445 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 2.5
                             TPR_17 14 daynnLAelllkn 26
                                       +++ n+A ll+kn
  gene1479|gene1479|rna1479|rna1479 68 NFLRNYALLLHKN 80
                                       7899*****9987 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 1.2
                             TPR_17   9 dPnnadaynnLAelllknGdlmtAr 33 
                                        +P +++ +   +++++ ++d+  A+
  gene1479|gene1479|rna1479|rna1479 323 YPFSVETMATAGNFYSLQKDHTAAI 347
                                        78999999999******99998875 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.04
                             TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                        +++a++ ++ +a + ++ A  + +++++ tA++
  gene1479|gene1479|rna1479|rna1479 350 FKRAVRFNHRYAFLNTLIAHEYMELNQYNTAIK 382
                                        89*****************************85 PP

  == domain 4  score: 1.4 bits;  conditional E-value: 0.45
                             TPR_17  10 PnnadaynnLAelllkn 26 
                                         n+  ay+ ++++++++
  gene1479|gene1479|rna1479|rna1479 388 ANDYRAYFGMGQAYAMQ 404
                                        69999*********965 PP

  == domain 5  score: 10.5 bits;  conditional E-value: 0.00055
                             TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtAr 33 
                                        ++kal l+ +++  ++ L+  ++k Gd + A+
  gene1479|gene1479|rna1479|rna1479 413 FKKALLLNSTDPFIWQSLGHEYKKFGDIANAL 444
                                        89*************************99886 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.1      0.85     1e+03       5      24 ..     266     286 ..     265     289 .. 0.82
   2 !    6.3   0.0    0.0075         9       4      31 ..     329     356 ..     327     359 .. 0.88
   3 ?   -1.1   0.1       1.6   1.9e+03       9      34 ..     368     393 ..     366     396 .. 0.79
   4 ?    3.2   0.0     0.072        86       8      31 ..     430     453 ..     428     456 .. 0.89
   5 !    6.9   0.1     0.005       5.9       8      27 ..     462     481 ..     461     483 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.85
                             TPR_10   5 lnNLanal.rqrgrydeAeal 24 
                                        l NL++a+ ++ ++yd ++al
  gene1479|gene1479|rna1479|rna1479 266 LRNLSAAYfYHKKEYDLSLAL 286
                                        67******8888888877776 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0075
                             TPR_10   4 slnNLanalrqrgrydeAealleealai 31 
                                        ++   +n ++ ++++++A  ++++a++ 
  gene1479|gene1479|rna1479|rna1479 329 TMATAGNFYSLQKDHTAAIHHFKRAVRF 356
                                        677779*******************975 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 1.6
                             TPR_10   9 analrqrgrydeAealleealairrr 34 
                                        a+ + ++++y+ A +++  + + +r+
  gene1479|gene1479|rna1479|rna1479 368 AHEYMELNQYNTAIKYYSLSANDYRA 393
                                        6779999******9999777777776 PP

  == domain 4  score: 3.2 bits;  conditional E-value: 0.072
                             TPR_10   8 LanalrqrgrydeAealleealai 31 
                                        L++ + + g+ + A++ +++ +++
  gene1479|gene1479|rna1479|rna1479 430 LGHEYKKFGDIANALECYRRMVEC 453
                                        899999*************99987 PP

  == domain 5  score: 6.9 bits;  conditional E-value: 0.005
                             TPR_10   8 LanalrqrgrydeAeallee 27 
                                        ++ ++ +r++y+ A++++e+
  gene1479|gene1479|rna1479|rna1479 462 IGDMYKNRKEYKHAVEYYEK 481
                                        5789**************97 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.0    0.0023       2.7       4      46 ..     340     382 ..     339     394 .. 0.89
   2 ?    4.1   0.0     0.055        66       2      48 ..     401     447 ..     400     453 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0023
                             TPR_19   4 egdyaeAlalleqalqedpknaearllLAeallalgqldeAea 46 
                                        ++d+++A+ ++++a   +  +a +  l A  +++l+q++ A++
  gene1479|gene1479|rna1479|rna1479 340 QKDHTAAIHHFKRAVRFNHRYAFLNTLIAHEYMELNQYNTAIK 382
                                        79************99988888888889***********9987 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.055
                             TPR_19   2 laegdyaeAlalleqalqedpknaearllLAeallalgqldeAealL 48 
                                        +a++    A+a++++al  +  ++ ++  L   + + g+++ A ++ 
  gene1479|gene1479|rna1479|rna1479 401 YAMQSSRLAIAFFKKALLLNSTDPFIWQSLGHEYKKFGDIANALECY 447
                                        67888889*************99999999999999999999998876 PP

>> Foie-gras_1  Foie gras liver health family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.6   0.00013      0.15     146     221 ..     316     392 ..     265     394 .. 0.70
   2 ?    0.8   0.1      0.25     3e+02     195     227 ..     429     461 ..     402     483 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00013
                        Foie-gras_1 146 apepheeyplsgseekgvahskliidlLekaleeFskrkqtRlaeelsl...eiAeeylrlgdwkkalellqpltl 218
                                        + + h +yp s ++       + + +   +a++ F+  ++ R++ + ++    iA ey++l++++ a++ +++ ++
  gene1479|gene1479|rna1479|rna1479 316 CHSMHSKYPFSVETMATAGNFYSLQKDHTAAIHHFK--RAVRFNHRYAFlntLIAHEYMELNQYNTAIKYYSLSAN 389
                                        555555555555544444555555555567888888..666776666555559*********************** PP

                        Foie-gras_1 219 syr 221
                                        +yr
  gene1479|gene1479|rna1479|rna1479 390 DYR 392
                                        **9 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.25
                        Foie-gras_1 195 eiAeeylrlgdwkkalellqpltlsyrkegWws 227
                                         ++ ey + gd ++ale ++ +      +gW  
  gene1479|gene1479|rna1479|rna1479 429 SLGHEYKKFGDIANALECYRRMVECGEVSGWLM 461
                                        578999999999999999999966667777765 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0         4   4.8e+03      10      27 ..     337     354 ..     333     355 .. 0.77
   2 ?    1.1   0.1      0.64   7.7e+02      10      24 ..     371     385 ..     366     391 .. 0.82
   3 ?    5.1   0.7     0.034        41       2      26 ..     393     416 ..     392     421 .. 0.91
   4 ?    1.7   0.0      0.42   5.1e+02      10      26 ..     434     450 ..     428     452 .. 0.81
   5 ?    3.5   0.0      0.11   1.3e+02       4      27 ..     460     483 ..     458     484 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 4
                                        HHHHHHHHHHHHHHHHHH CS
                              TPR_6  10 yrklgdtdkAlealerli 27 
                                        y  ++d+++A+  ++r +
  gene1479|gene1479|rna1479|rna1479 337 YSLQKDHTAAIHHFKRAV 354
                                        445899****99999876 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.64
                                        HHHHHHHHHHHHHHH CS
                              TPR_6  10 yrklgdtdkAleale 24 
                                        y +l+++ +A++++ 
  gene1479|gene1479|rna1479|rna1479 371 YMELNQYNTAIKYYS 385
                                        77889*******995 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.034
                                        HHHHHHHHHHHHHHHHHHHHHHHHH CS
                              TPR_6   2 AlyklalsyrklgdtdkAlealerl 26 
                                        A++ ++++y ++  ++ A++ +++ 
  gene1479|gene1479|rna1479|rna1479 393 AYFGMGQAYAMQ-SSRLAIAFFKKA 416
                                        99********99.*******99986 PP

  == domain 4  score: 1.7 bits;  conditional E-value: 0.42
                                        HHHHHHHHHHHHHHHHH CS
                              TPR_6  10 yrklgdtdkAlealerl 26 
                                        y+k gd ++Ale ++r 
  gene1479|gene1479|rna1479|rna1479 434 YKKFGDIANALECYRRM 450
                                        66757*********996 PP

  == domain 5  score: 3.5 bits;  conditional E-value: 0.11
                                        HHHHHHHHHHHHHHHHHHHHHHHH CS
                              TPR_6   4 yklalsyrklgdtdkAlealerli 27 
                                        ++++  y++ +++  A+e++e+ +
  gene1479|gene1479|rna1479|rna1479 460 LMIGDMYKNRKEYKHAVEYYEKYV 483
                                        799999**999**********975 PP

>> PetG  Cytochrome B6-F complex subunit 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00029      0.35      15      27 ..     120     132 ..     117     133 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00029
                               PetG  15 pVTlaGLFvaAYl 27 
                                        +VT+ GLFv+A++
  gene1479|gene1479|rna1479|rna1479 120 AVTVNGLFVDAWQ 132
                                        69**********7 PP

>> PPR  PPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.1   0.00067       0.8       3      30 ..     427     454 ..     425     455 .. 0.88
   2 ?   -2.9   0.1       9.2   1.1e+04      10      25 ..     466     481 ..     464     481 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00067
                                PPR   3 ynslIsgycknGkleeAlelfkeMkekG 30 
                                        + sl + y k G++  Ale++++M+e+G
  gene1479|gene1479|rna1479|rna1479 427 WQSLGHEYKKFGDIANALECYRRMVECG 454
                                        677777899*****************98 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 9.2
                                PPR  10 ycknGkleeAlelfke 25 
                                        y    +++ A+e++++
  gene1479|gene1479|rna1479|rna1479 466 YKNRKEYKHAVEYYEK 481
                                        667788999**99985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (514 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       735  (0.040995); expected 358.6 (0.02)
Passed bias filter:                      472  (0.0263261); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.43
# Mc/sec: 3564.39
//
Query:       gene148|gene148|rna148|rna148  [L=131]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       804  (0.0448435); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 980.19
//
Query:       gene1480|gene1480|rna1480|rna1480  [L=60]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (60 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       669  (0.0373138); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.29s 00:00:00.67 Elapsed: 00:00:00.45
# Mc/sec: 401.16
//
Query:       gene1481|gene1481|rna1481|rna1481  [L=73]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (73 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       323  (0.0180155); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.31s 00:00:00.73 Elapsed: 00:00:00.48
# Mc/sec: 456.17
//
Query:       gene1482|gene1482|rna1482|rna1482  [L=1042]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.4e-33  114.9  36.4    2.9e-32  111.9  36.4    2.4  1  SMC_N      RecF/RecN/SMC N terminal domain
    9.4e-22   78.2  10.4    1.2e-12   48.3   0.0    3.4  2  AAA_15     AAA ATPase domain
    9.1e-14   51.8   0.0    3.4e-13   49.9   0.0    2.1  1  SMC_hinge  SMC proteins Flexible Hinge Domain
    2.8e-09   37.8  12.6    2.8e-09   37.8  12.6    4.5  3  AAA_23     AAA domain
    3.5e-08   33.6   7.0    0.00024   21.0   0.2    3.6  5  AAA_21     AAA domain, putative AbiEii toxin, Type IV TA syst
    1.5e-06   27.8   0.2    3.7e-06   26.6   0.2    1.7  1  AAA_29     P-loop containing region of AAA domain
    0.00088   19.8  12.4       0.17   12.4   2.1    4.3  4  ABC_tran   ABC transporter
      0.007   15.6   3.2      0.007   15.6   3.2    3.7  3  Tho2       Transcription factor/nuclear export subunit protei
  ------ inclusion threshold ------
      0.076   13.2   0.0        7.7    6.8   0.0    3.1  2  DUF2552    Protein of unknown function (DUF2552)


Domain annotation for each model (and alignments):
>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.9  36.4   1.4e-35   2.9e-32       2     216 ..      30    1034 ..      29    1037 .. 0.99

  Alignments for each domain:
  == domain 1  score: 111.9 bits;  conditional E-value: 1.4e-35
                                         EEEEEEESETTEECEEEEEETTSSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTT CS
                                         xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              SMC_N    2 lkrleienFksyagktvilpfsksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvk 75  
                                         lk+l+i+nFks+  ++++l++ + ftai+G NGSGKsn+ldAi+F+L + +++ +r e ++dli +       +
  gene1482|gene1482|rna1482|rna1482   30 LKQLTITNFKSI--SKTTLNICT-FTAITGLNGSGKSNILDAIMFCLDKGNMRMMRVECYKDLIRA-----GEQ 95  
                                         89**********..588888887.*****************************************8.....789 PP

                                         EEEEEEEEEETTEESSSSSSCEEEEEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STT.............. CS
                                         xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.............. RF
                              SMC_N   76 kaeveitfdnedkklkiekeevsisrrvkrkgeseykingkevtkkevsellesagiske.............. 135 
                                         +++ve++f+           +++i+r+v r+g+s++++n++ ++ + v+ + +  +i                 
  gene1482|gene1482|rna1482|rna1482   96 SCTVEMVFT-----------SLVIRREVTREGKSKVYVNNHPASLSTVRTVTAAFNILLIqqgtitkflhtndl 158 
                                         9*****985...........389**********************999999999988877789*********** PP

                                         .......................................................................... CS
                                         .......................................................................... RF
                              SMC_N  136 .......................................................................... 135 
                                                                                                                   
  gene1482|gene1482|rna1482|rna1482  159 qsfinycvgtvnhykqrlstvmdkenklngvkkqlsdriapffsrlraerentisnrkrmgrkkvveerlayar 232 
                                         ************************************************************************** PP

                                         .......................................................................... CS
                                         .......................................................................... RF
                              SMC_N  136 .......................................................................... 135 
                                                                                                                   
  gene1482|gene1482|rna1482|rna1482  233 rierllelvemqcinehkknikqklerinrsaqrrqhckeekvkmmemkdemnalqerekravpvvqpaktrgk 306 
                                         ************************************************************************** PP

                                         .......................................................................... CS
                                         .......................................................................... RF
                              SMC_N  136 .......................................................................... 135 
                                                                                                                   
  gene1482|gene1482|rna1482|rna1482  307 eieemisimeggmdvvgvdeerlalqedvmriereleghvlerrsgksangndgstgicgknedsvlnykntll 380 
                                         ************************************************************************** PP

                                         .......................................................................... CS
                                         .......................................................................... RF
                              SMC_N  136 .......................................................................... 135 
                                                                                                                   
  gene1482|gene1482|rna1482|rna1482  381 emsndvksvgdnvkklkelsekikfvkneawvsrtegrvfelftlidskykravdtilgnkrnyyvvkssdlvk 454 
                                         ************************************************************************** PP

                                         .......................................................................... CS
                                         .......................................................................... RF
                              SMC_N  136 .......................................................................... 135 
                                                                                                                   
  gene1482|gene1482|rna1482|rna1482  455 diikdgngtfipldkikysdnkykgnlliqkikyreehrnafyflfnnyyvfdndkdarsfsfdkkvitvtleg 528 
                                         ************************************************************************** PP

                                         .......................................................................... CS
                                         .......................................................................... RF
                              SMC_N  136 .......................................................................... 135 
                                                                                                                   
  gene1482|gene1482|rna1482|rna1482  529 tvydyrgvisggmvnvkdmvgkgeiekvnrenmdviremarlidenvgrgvendhgskgglddrnrrggmsgta 602 
                                         ************************************************************************** PP

                                         .......................................................................... CS
                                         .......................................................................... RF
                              SMC_N  136 .......................................................................... 135 
                                                                                                                   
  gene1482|gene1482|rna1482|rna1482  603 rekvignfngvhgeciadslikrlntgasinttlsnhynscntfidtsnkkmekirvlvqkgtrlnainkiieg 676 
                                         ************************************************************************** PP

                                         .......................................................................... CS
                                         .......................................................................... RF
                              SMC_N  136 .......................................................................... 135 
                                                                                                                   
  gene1482|gene1482|rna1482|rna1482  677 kdvnriselraelveerrkeeetkikekerdkiieendkieqhnegvrrrkkeieeylkgcrvdeeeevvdsye 750 
                                         ************************************************************************** PP

                                         .......................................................................... CS
                                         .......................................................................... RF
                              SMC_N  136 .......................................................................... 135 
                                                                                                                   
  gene1482|gene1482|rna1482|rna1482  751 irynlkntlvklegrkieenageqieeimkeglegvekclmdkedvlnnapardaqvttmdtifgtflksgshn 824 
                                         ************************************************************************** PP

                                         .......................................................................... CS
                                         .......................................................................... RF
                              SMC_N  136 .......................................................................... 135 
                                                                                                                   
  gene1482|gene1482|rna1482|rna1482  825 fldlisalnsylsvndclsfihgainkyeqeikdlavtkkemdpknfdllekneeqlteiknkiakleidkkki 898 
                                         ************************************************************************** PP

                                         ..........................................................CS-HHHHHHHHHHHHH CS
                                         ..........................................................xxxxxxxxxxxxxxxx RF
                              SMC_N  136 ..........................................................lLSgGektLvalaLlf 151 
                                                                                                   +LSgG+++L+a+a++f
  gene1482|gene1482|rna1482|rna1482  899 mksinefeiqseakrktfidninntindiisvfipecninihndalnitinnnavsinELSGGQRSLIAVAMMF 972 
                                         ************************************************************************** PP

                                         HHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCCC-SCEEEEEEEET CS
                                         xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              SMC_N  152 AiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivislreemlekadklvgvtkven 216 
                                         +   + +++l+l+Deid+aLD  ++++v+ +l+ k   +Q++v+sl+e++++ ad +++v+k++n
  gene1482|gene1482|rna1482|rna1482  973 SCMDA-RNCLCLFDEIDSALDLGQTQRVSMYLRDKG--CQVVVVSLKEGFYSCADVIYQVYKENN 1034
                                         *9776.68*************************999..***********************9654 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.3   0.0   5.9e-16   1.2e-12       1     262 [.      28     451 ..      28     486 .. 0.74
   2 !   23.2   9.9   2.4e-08   4.8e-05      63     333 ..     641     988 ..     492     991 .. 0.66

  Alignments for each domain:
  == domain 1  score: 48.3 bits;  conditional E-value: 5.9e-16
                             AAA_15   1 MkIkkikikNFRslkdveidlseeltvliGkNnsGKSsilealdlFlnnkekkn...................... 54 
                                        M++k+++i NF+s++++++++   +t + G N+sGKS+il+a+ + l++    n                      
  gene1482|gene1482|rna1482|rna1482  28 MELKQLTITNFKSISKTTLNICT-FTAITGLNGSGKSNILDAIMFCLDKG---Nmrmmrvecykdlirageqsctv 99 
                                        9**********************.*******************8888866...56688999999999999999999 PP

                             AAA_15  55 .......................................kkvikiekedleifeniseskdikIdvef........ 83 
                                                                               ++ + i++  + +f +++  +++ I+++         
  gene1482|gene1482|rna1482|rna1482 100 emvftslvirrevtregkskvyvnnhpaslstvrtvtaaFNILLIQQGTITKFLHTNDLQSF-INYCVgtvnhykq 174
                                        99999999999999999999999999999999999999866777777777777666555554.6777788888888 PP

                             AAA_15  84 .........................................aek...ekakeyektlkskekkkadlllkkkesdl 115
                                                                                 +     +k  e+  + +++ ++  +l  +++++++
  gene1482|gene1482|rna1482|rna1482 175 rlstvmdkenklngvkkqlsdriapffsrlraerentisnrK-RmgrKKVVEERLAYARRIERLLELVEMQCINEH 249
                                        888888999999999999999999999999999998877541.155455555556666677777778888999999 PP

                             AAA_15 116 kktikdkklklkknelsdekisvekkkskkelpkekeeklekekeelkid..kedlkklikkleeslkkee..... 184
                                        kk ik+k   ++    +   ++ e+k +++e ++e +  +e ek  + +    ++  k    +ee ++  e     
  gene1482|gene1482|rna1482|rna1482 250 KKNIKQKLERIN-RSAQRRQHCKEEKVKMMEMKDEMNALQEREKRAVPVVqpAKTRGKE---IEEMISIMEggmdv 321
                                        999999999986.5555555555666667777777777777777777766332222222...33333333344577 PP

                             AAA_15 185 ..............................................elknvlksaiiklllisakRnvsdedsekk 214
                                                                                        ++vl+ + ++l+  +++++v d+ ++  
  gene1482|gene1482|rna1482|rna1482 322 vgvdeerlalqedvmriereleghvlerrsgksangndgstgicgkNEDSVLNYKNTLLEMSNDVKSVGDNVKKL- 396
                                        889999999999999999999999999999999999999999888888888888888888888888888887777. PP

                             AAA_15 215 ssllgklkekileealqekleeelteklkeiqeklkeidkklaeelk........k 262
                                        ++l +k+k  ++e    ++ e ++ e +  i++k+k + +++  ++         +
  gene1482|gene1482|rna1482|rna1482 397 KELSEKIKFVKNEA-WVSRTEGRVFELFTLIDSKYKRAVDTILGNKRnyyvvkssD 451
                                        56666666666664.34445777777777777777777666655555454444442 PP

  == domain 2  score: 23.2 bits;  conditional E-value: 2.4e-08
                             AAA_15  63 edleifeniseskdikIdvef.............................aekekakeyektlkskekkkadlllk 109
                                        +++++f ++s++k+ kI+v                               +   ++ ++e+t+ +++++ + ++ +
  gene1482|gene1482|rna1482|rna1482 641 NSCNTFIDTSNKKMEKIRVLVqkgtrlnainkiiegkdvnriselraelvE---ERRKEEETKIKEKERDKIIEEN 713
                                        567777777788888888877777777777777777777766655433321...2222223333333333334444 PP

                             AAA_15 110 kkesdlkktikdkklklkknelsdekisvekkkskkelpkekeeklekekeelkidkedlkklikkleeslkkee. 184
                                        +k++++ + ++ +k +++    + + + v+++++ ++ +   e   +++++ +k++  ++++   + +e + ke  
  gene1482|gene1482|rna1482|rna1482 714 DKIEQHNEGVRRRKKEIE---EYLKGCRVDEEEEVVDSY---EIRYNLKNTLVKLEGRKIEENAGEQIEEIMKEGl 783
                                        555555555555555554...222233333333322222...3344444455555544444444433333333335 PP

                             AAA_15 185 ...............................................................elknvlksaiikl 197
                                                                                                          n+++++i++l
  gene1482|gene1482|rna1482|rna1482 784 egvekclmdkedvlnnapardaqvttmdtifgtflksgshnfldlisalnsylsvndclsfihGAINKYEQEIKDL 859
                                        67777888888******************99999999999999999988888888877777777777777777777 PP

                             AAA_15 198 llisakRnvsd.edsekkssllgklkekileealqekleeelteklkeiqeklkeidkklaeelkkilkkkidkik 272
                                         + +++ + ++ ++ ek+++ l+++k+ki +           + + k+i ++++e++ + +++ k  ++++ ++i+
  gene1482|gene1482|rna1482|rna1482 860 AVTKKEMDPKNfDLLEKNEEQLTEIKNKIAKL----------EIDKKKIMKSINEFEIQSEAKRKTFIDNINNTIN 925
                                        76666666655577777777777777777664..........4445555555555555555555544444444443 PP

                             AAA_15 273 kfnykgkkneeieik........ddeelplnknGsGvqrllllillileaekkdekeeknvilliEEPE 333
                                        ++     ++ +i+i+        +++ +++n+ + G+++l+ ++++   +  +      n + l++E++
  gene1482|gene1482|rna1482|rna1482 926 DIISVFIPECNINIHndalnitiNNNAVSINELSGGQRSLIAVAMMFSCMDAR------NCLCLFDEID 988
                                        33333333333333355555556********************9986666655......7777777766 PP

>> SMC_hinge  SMC proteins Flexible Hinge Domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.9   0.0   1.7e-16   3.4e-13       6     115 ..     417     514 ..     412     516 .. 0.90

  Alignments for each domain:
  == domain 1  score: 49.9 bits;  conditional E-value: 1.7e-16
                          SMC_hinge   6 Grladlievd.egyekAveaalgnrlqalvvedeetakkiieflkkknagratflpldrikqknkadgandknsga 80 
                                        Gr+++l+++  ++y+ Av+++lgn+ ++ vv++ + +k ii      + g+ tf+pld+ik + ++ + n      
  gene1482|gene1482|rna1482|rna1482 417 GRVFELFTLIdSKYKRAVDTILGNKRNYYVVKSSDLVKDII------KDGNGTFIPLDKIKYSDNKYKGN------ 480
                                        99999999766****************************99......34799**********97666664...... PP

                          SMC_hinge  81 vplidlvevddelrkalryllgdtlvvdsldeAee 115
                                          li+ +++ +e+r+a+++l+ +++v d+ ++A+ 
  gene1482|gene1482|rna1482|rna1482 481 -LLIQKIKYREEHRNAFYFLFNNYYVFDNDKDARS 514
                                        .6***************************999975 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.8  12.6   1.4e-12   2.8e-09       1     196 [.      32     261 ..      32     410 .. 0.70
   2 ?   -1.9   0.6         2   3.9e+03     163     163 ..     404     404 ..     348     521 .. 0.65
   3 ?  -11.1  31.9         9   1.8e+04      68     196 ..     650     892 ..     580     929 .. 0.66

  Alignments for each domain:
  == domain 1  score: 37.8 bits;  conditional E-value: 1.4e-12
                             AAA_23   1 kLkienfrsfrdqeidFskgltlItGpNGaGKTTildAiklaLygetprlsrks......grgfeksdveiesegk 70 
                                        +L+i nf+s+++++++    +t+ItG NG+GK+ ildAi ++L     r+ r +      +  + ++++++e   +
  gene1482|gene1482|rna1482|rna1482  32 QLTITNFKSISKTTLNIC-TFTAITGLNGSGKSNILDAIMFCLDKGNMRMMRVEcykdliR--AGEQSCTVEMVFT 104
                                        599**************8.9***********************654444444333432221..1122222222222 PP

                             AAA_23  71 vkayveltfenkdgry..................................trsiererelskkkgkttkkaklell 112
                                           +++++++++++ +                                  +                         
  gene1482|gene1482|rna1482|rna1482 105 S-LVIRREVTREGKSKvyvnnhpaslstvrtvtaafnilliqqgtitkflH------------------------- 154
                                        2.2233333333332233666655555544333333222222222222221......................... PP

                             AAA_23 113 eideleqfise.........................llgskkiilnlilflgqerfeefelkdkkerleelekele 163
                                         +++l+ fi+                          + + +++i ++++ l +er++ +++ ++  r + +e+ l 
  gene1482|gene1482|rna1482|rna1482 155 -TNDLQSFINYcvgtvnhykqrlstvmdkenklngvKKQLSDRIAPFFSRLRAERENTISNRKRMGRKKVVEERLA 229
                                        .233333333322222222222222333333222222334444889999999999888888888888888888888 PP

                             AAA_23 164 eledekkllekleqekekekeleeleeeleeil 196
                                         +  +++lle +e  +  ++  ++++++le i+
  gene1482|gene1482|rna1482|rna1482 230 YARRIERLLELVE-MQCINEHKKNIKQKLERIN 261
                                        8888888888764.4455555555555555544 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2
                             AAA_23 163 e 163
                                        +
  gene1482|gene1482|rna1482|rna1482 404 K 404
                                        2 PP

  == domain 3  score: -11.1 bits;  conditional E-value: 9
                             AAA_23  68 egkvkayveltfenkdgry.........trsiererelskkkgkttkkaklelleideleqfise..llgskki.. 130
                                        ++k+++ +++ +++ +  +          + + r  el+ +  ++++k+++ +++++e++++i+e  ++++ ++  
  gene1482|gene1482|rna1482|rna1482 650 SNKKMEKIRVLVQKGT--RlnainkiieGKDVNRISELRAELVEERRKEEETKIKEKERDKIIEEndKIEQHNEgv 723
                                        3444444555432222..2235544445333333344444444444444444444444444444433111111122 PP

                             AAA_23 131 ......ilnlilflgqer..............feefelkdkke................................. 153
                                              i +++  +  ++              +         +                                 
  gene1482|gene1482|rna1482|rna1482 724 rrrkkeIEEYLKGCRVDEeeevvdsyeirynlK---------Ntlvklegrkieenageqieeimkeglegvekcl 790
                                        222111223333333333333443333333220.........1222333344444445555567777777888888 PP

                             AAA_23 154 .........................................................rleelekeleeledekkll 172
                                                                                                 +++++e+e+++l  +kk++
  gene1482|gene1482|rna1482|rna1482 791 mdkedvlnnapardaqvttmdtifgtflksgshnfldlisalnsylsvndclsfihgAINKYEQEIKDLAVTKKEM 866
                                        888889999999999999999999999999999***********************************99999988 PP

                             AAA_23 173 ekl..eqekekekeleeleeeleeil 196
                                        + +    ++++e++l+e+++++ +++
  gene1482|gene1482|rna1482|rna1482 867 DPKnfDLLEKNEEQLTEIKNKIAKLE 892
                                        88866355567778888888888775 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.2   1.2e-07   0.00024       1      22 [.      51      72 ..      51      79 .. 0.90
   2 ?   -3.4   0.0       3.2   6.4e+03     104     168 ..     329     389 ..     325     408 .. 0.73
   3 ?   -2.6   0.1       1.9   3.7e+03     164     184 ..     487     512 ..     432     517 .. 0.70
   4 ?   -1.9   0.1       1.2   2.3e+03     116     162 ..     678     724 ..     650     762 .. 0.69
   5 !   14.6   0.0   1.1e-05     0.021     140     294 ..     877    1012 ..     842    1014 .. 0.73

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 1.2e-07
                             AAA_21  1 lnvliGpNgsGKSnLLdaldll 22
                                       +++++G NgsGKSn+Lda+ + 
  gene1482|gene1482|rna1482|rna1482 51 FTAITGLNGSGKSNILDAIMFC 72
                                       89*****************665 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 3.2
                             AAA_21 104 sleeedvfnpeargirggvsvfslkelsvsepndlqfgkaltditsrawsllllldglrkerigl 168
                                         + +edv   e + +  ++  +s k+ + ++ ++ ++gk+ +++ + +++ll+++++     +++
  gene1482|gene1482|rna1482|rna1482 329 LALQEDVMRIERELEGHVLERRSGKSANGNDGSTGICGKNEDSVLNYKNTLLEMSND----VKSV 389
                                        556667777777777788888899999999999999999999999999999998887....4444 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 1.9
                             AAA_21 164 e.....rigllnifadyfgfakekrl 184
                                        +     r +++++f++y+ f++ k+ 
  gene1482|gene1482|rna1482|rna1482 487 KyreehRNAFYFLFNNYYVFDNDKDA 512
                                        12234588888888888888877765 PP

  == domain 4  score: -1.9 bits;  conditional E-value: 1.2
                             AAA_21 116 rgirggvsvfslkelsvsepndlqfgkaltditsrawsllllldglr 162
                                        + +r+ +   +l e  ++e+++++++k +++i+++++++++ ++g r
  gene1482|gene1482|rna1482|rna1482 678 DVNRISELRAELVEERRKEEETKIKEKERDKIIEENDKIEQHNEGVR 724
                                        44444444555555556666666777777777777777666666655 PP

  == domain 5  score: 14.6 bits;  conditional E-value: 1.1e-05
                             AAA_21  140 fgkaltditsrawsllllldglrkerigllnifadyfgfakekrllqrlvrslklveielsdlgegeeliasvd 213 
                                         ++++lt+i++ +++l+ ++ +++  ++ + +  +++++ +  ++ +   ++ +  v+i+  ++++ ++  + ++
  gene1482|gene1482|rna1482|rna1482  877 NEEQLTEIKNKIAKLEIDKKKIM--KSINEFEIQSEAKRKTFIDNINNTINDIISVFIPECNINIHNDALNITI 948 
                                         55566666666666666666666..6666777777777777777777777777777777777777777766666 PP

                             AAA_21  214 erlrergvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr 287 
                                         +               + ++++elS G+++l+a++ ++   +  + l l+DE+++ L+   + r+     +l++
  gene1482|gene1482|rna1482|rna1482  949 NN--------------NAVSINELSGGQRSLIAVAMMFSCMDARNCLCLFDEIDSALDLGQTQRVS---MYLRD 1005
                                         54..............789************97777777777777************997777766...33344 PP

                             AAA_21  288 ngaQvil 294 
                                         +g Qv++
  gene1482|gene1482|rna1482|rna1482 1006 KGCQVVV 1012
                                         4566655 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.2   1.9e-09   3.7e-06       1      46 [.      30      73 ..      30      79 .. 0.90

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 1.9e-09
                             AAA_29  1 LkrlqlvNWgtfdghtieidlkgatlltGpsGsGKSTllDAiqalL 46
                                       Lk+l + N  +++++t++i    +t +tG +GsGKS +lDAi++ L
  gene1482|gene1482|rna1482|rna1482 30 LKQLTITNFKSISKTTLNIC--TFTAITGLNGSGKSNILDAIMFCL 73
                                       78899999999999999998..68******************9876 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   2.1   8.5e-05      0.17       9      67 ..      47     105 ..      41     283 .. 0.73
   2 ?   -3.1   0.0       5.3     1e+04      68     113 ..     497     541 ..     468     544 .. 0.66
   3 ?   -1.0   0.6       1.2   2.4e+03      79      95 ..     704     740 ..     641     782 .. 0.54
   4 !   11.6   0.1   0.00015      0.29      53     134 ..     880     986 ..     840     989 .. 0.48

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 8.5e-05
                                        ETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG..B-HHHCCHCEEEE-SS CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxx RF
                           ABC_tran   9 kegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke..qeleslrkeigvlpqe 67 
                                        +  + +ai+G nG+GKS +l +++  l+  +G++++   +  +  ++  + +  +++++  
  gene1482|gene1482|rna1482|rna1482  47 NICTFTAITGLNGSGKSNILDAIMFCLD--KGNMRMMRVECYKdlIRAGEQSCTVEMVFTS 105
                                        555779*****************98776..4666444444333343333333344444444 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 5.3
                                        --S-TTSBHHHHHHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHH CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ABC_tran  68 pqlfpeltvrenesdeeiekalsklglkelkdtvvksspssLSgGq 113
                                         +lf+++ v +n++d++   + +k+  + l+ tv  +    +SgG+
  gene1482|gene1482|rna1482|rna1482 497 YFLFNNYYVFDNDKDARSFSFDKKVITVTLEGTVY-DYRGVISGGM 541
                                        56777777888888888777777777777666665.5557777776 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 1.2
                                        H....................HHHTCHHHHHHHSTTG CS
                                        x....................xxxxxxxxxxxxxxxx RF
                           ABC_tran  79 n....................esdeeiekalsklglk 95 
                                        +                     +++eie++l+  + +
  gene1482|gene1482|rna1482|rna1482 704 KerdkiieendkieqhnegvrRRKKEIEEYLKGCRVD 740
                                        1222222222333333344444444444444444444 PP

  == domain 4  score: 11.6 bits;  conditional E-value: 0.00015
                                        -HHHCCHCEEEE-SS--S-TTSBHHHH............HHHTCHHHHHHHSTTGG.................... CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxx............xxxxxxxxxxxxxxxxx.................... RF
                           ABC_tran  53 eleslrkeigvlpqepqlfpeltvren............esdeeiekalsklglke.................... 96 
                                        +l++ +++i+ l+ +           +            +s+++ ++++++++++                     
  gene1482|gene1482|rna1482|rna1482 880 QLTEIKNKIAKLEID-----------KkkimksinefeiQSEAKRKTFIDNINNTIndiisvfipecninihndal 944
                                        233333333333333...........02222222333343333322222222222244446666666666677765 PP

                                        ...TTCBGESTTSGGS-HHHHHHHHHHHHHHH...TSSEEEEES CS
                                        ...xxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxx RF
                           ABC_tran  97 ...lkdtvvksspssLSgGqkqrvalarallk...kpkllllDE 134
                                           ++++ v  s ++LSgGq++ +a+a+++ +   +  l l+DE
  gene1482|gene1482|rna1482|rna1482 945 nitINNNAV--SINELSGGQRSLIAVAMMFSCmdaRNCLCLFDE 986
                                        554455555..66*************997754111344555566 PP

>> Tho2  Transcription factor/nuclear export subunit protein 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   9.7       1.5   2.9e+03      26      96 ..     229     296 ..     168     315 .. 0.76
   2 ?   -0.8   5.8      0.36   7.1e+02      47      88 ..     695     735 ..     662     779 .. 0.59
   3 !   15.6   3.2   3.5e-06     0.007      24     113 ..     849     935 ..     841     938 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.5
                               Tho2  26 qYekeieklkseieelakdrsderaaakkkkkekkrlkeliekLeeEkkeqiehvekvkkrLkeekkswfk 96 
                                        +Y + ie+l +   e+ +  ++ ++++k+k ++++r  +++++ +eEk + +e + ++ + L+e  k+ ++
  gene1482|gene1482|rna1482|rna1482 229 AYARRIERLLEL-VEM-QCINEHKKNIKQKLERINRSAQRRQHCKEEKVKMMEMKDEM-NALQEREKRAVP 296
                                        577788888774.444.23344478889999999999999999998888888776665.557777777666 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.36
                               Tho2  47 deraaakkkkkekkrlkeliekLeeEkkeqiehvekvkkrLk 88 
                                        + ++++k k+ke++++ e  +k+e+ ++   +++++++++Lk
  gene1482|gene1482|rna1482|rna1482 695 K-EEETKIKEKERDKIIEENDKIEQHNEGVRRRKKEIEEYLK 735
                                        1.2333333444444444444444444444444444444443 PP

  == domain 3  score: 15.6 bits;  conditional E-value: 3.5e-06
                               Tho2  24 keqYekeieklkseieelakdrsderaaakkkkkekkrlkeliekLeeEkkeqiehvekvkkrLkeekkswfknde 99 
                                         ++Ye+ei+ l    +e++ ++    +  +k++++  ++k+ i+kLe +kk+ +++ ++++ + + ++k++++n +
  gene1482|gene1482|rna1482|rna1482 849 INKYEQEIKDLAVTKKEMDPKN---FDLLEKNEEQLTEIKNKIAKLEIDKKKIMKSINEFEIQSEAKRKTFIDNIN 921
                                        5688889988888777773333...357899999****************************************** PP

                               Tho2 100 kkkkeitdallqrc 113
                                        ++ ++i++ ++ +c
  gene1482|gene1482|rna1482|rna1482 922 NTINDIISVFIPEC 935
                                        ***********999 PP

>> DUF2552  Protein of unknown function (DUF2552)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0      0.09   1.8e+02      13      42 ..     145     174 ..     140     183 .. 0.88
   2 ?    6.8   0.0    0.0038       7.7      19      71 ..     834     884 ..     830     891 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.09
                            DUF2552  13 kektWvsflnenhPysllhWsiaGvesekk 42 
                                        ++ t   fl+ n+  s++ + ++ v++ k+
  gene1482|gene1482|rna1482|rna1482 145 QQGTITKFLHTNDLQSFINYCVGTVNHYKQ 174
                                        7789999****************9999876 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0038
                            DUF2552  19 sflnenhPysllhWsiaGvesekkdvWllqdevtfetkefatldeaiaWieeh 71 
                                        s+l  n+  s++h +i   e+e kd+ + ++e+  + k+f+ l++  + ++e 
  gene1482|gene1482|rna1482|rna1482 834 SYLSVNDCLSFIHGAINKYEQEIKDLAVTKKEM--DPKNFDLLEKNEEQLTEI 884
                                        999*****************************9..567888887766555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1042 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2614  (0.145797); expected 358.6 (0.02)
Passed bias filter:                      593  (0.0330749); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 1.03u 0.33s 00:00:01.36 Elapsed: 00:00:00.51
# Mc/sec: 6151.62
//
Query:       gene1483|gene1483|rna1483|rna1483  [L=60]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
     0.0044   16.6   0.0     0.0045   16.5   0.0    1.0  1  RVT_1        Reverse transcriptase (RNA-dependent DNA polymer
  ------ inclusion threshold ------
      0.055   13.2   0.1      0.061   13.1   0.1    1.0  1  CAP_assoc_N  CAP-associated N-terminal


Domain annotation for each model (and alignments):
>> RVT_1  Reverse transcriptase (RNA-dependent DNA polymerase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0     5e-07    0.0045      44      96 ..      17      59 ..       3      60 .] 0.80

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 5e-07
                                       -HHHH.............HCCHTS--EEEEEEBCCGCCCSBB-GGGGGGG-EE CS
                              RVT_1 44 gfrpgrstldavedllkalkkkkkaklllklDlkkaFdsvpleellrkltafk 96
                                        +++++          +++k++++++ l+ lDlk  + +++ ee ++ +taf+
  gene1483|gene1483|rna1483|rna1483 17 KIPDMK----------RIVKATTGSNNLTVLDLKESYYQIEIEEADKHKTAFG 59
                                       444444..........447889*****************************97 PP

>> CAP_assoc_N  CAP-associated N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   6.8e-06     0.061      47     100 ..       1      54 [.       1      58 [. 0.89

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 6.8e-06
                        CAP_assoc_N  47 Vvtlytngeeiaikpfkigesleevekklgipeeveveikkgsyrfelseedln 100
                                        V  l+ +++ +++ p+ki + +  v+ ++g ++   +++k++ y++e++e d +
  gene1483|gene1483|rna1483|rna1483   1 VSNLMFLNDLTEKYPYKIPDMKRIVKATTGSNNLTVLDLKESYYQIEIEEADKH 54 
                                        667888999999****************99999999***************944 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (60 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       546  (0.0304535); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.44
# Mc/sec: 413.14
//
Query:       gene1484|gene1484|rna1484|rna1484  [L=61]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
      0.025   15.1   0.5      0.031   14.8   0.5    1.2  1  Phospho_p8  DNA-binding nuclear phosphoprotein p8


Domain annotation for each model (and alignments):
>> Phospho_p8  DNA-binding nuclear phosphoprotein p8
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.5   1.7e-06     0.031      22      51 ..      19      46 ..       6      48 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.7e-06
                         Phospho_p8 22 sgkgRtKkEaeehtnrpdPsGHtRKivtkl 51
                                       + k+R+   ae  t++ +++G+ RKi +k+
  gene1484|gene1484|rna1484|rna1484 19 GEKNRS--VAESATKKDSINGDARKIGEKI 46
                                       345444..455667777*********9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       339  (0.0189079); expected 358.6 (0.02)
Passed bias filter:                      231  (0.0128842); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.43
# Mc/sec: 425.20
//
Query:       gene1485|gene1485|rna1485|rna1485  [L=511]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (511 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       599  (0.0334096); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.43
# Mc/sec: 3577.89
//
Query:       gene1486|gene1486|rna1486|rna1486  [L=62]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (62 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1489  (0.0830498); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.43
# Mc/sec: 437.91
//
Query:       gene1487|gene1487|rna1487|rna1487  [L=316]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
       0.59   10.2   6.7        0.6   10.2   4.8    2.1  2  zf-RING_UBOX  RING-type zinc-finger


Domain annotation for each model (and alignments):
>> zf-RING_UBOX  RING-type zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0      0.35   6.4e+03       4      11 ..     199     206 ..     198     211 .. 0.84
   2 ?   10.2   4.8   3.3e-05       0.6       3      39 .]     266     300 ..     260     300 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.35
                       zf-RING_UBOX   4 ClelftdP 11 
                                        C +lf+ P
  gene1487|gene1487|rna1487|rna1487 199 CTDLFNIP 206
                                        999**998 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 3.3e-05
                       zf-RING_UBOX   3 IClelftdPlvlpCGHtFCreClwelskslegafkCP 39 
                                        +C e+   P++l+C H++  e + +  +  +g fkCP
  gene1487|gene1487|rna1487|rna1487 266 VCDESN-PPVLLECRHVISMEAV-KRLNCANGCFKCP 300
                                        344433.55557***********.89**********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (316 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1015  (0.0566122); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 2001.54
//
Query:       gene1488|gene1488|rna1488|rna1488  [L=138]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       298  (0.0166211); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 996.30
//
Query:       gene1489|gene1489|rna1489|rna1489  [L=290]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.034   13.4   0.2      0.066   12.4   0.2    1.4  1  DRAT      Dinitrogenase reductase ADP-ribosyltransferase (DRA
       0.13   12.4   0.0       0.32   11.1   0.0    1.6  1  DUF2258   Uncharacterized protein conserved in archaea (DUF22


Domain annotation for each model (and alignments):
>> DRAT  Dinitrogenase reductase ADP-ribosyltransferase (DRAT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.2   7.3e-06     0.066     130     165 ..     219     254 ..     207     271 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 7.3e-06
                               DRAT 130 eYleekmkgraktnaiesQlDLlyeycQyelarrla 165
                                         Y  + m  +  +n+i  Ql  +y+ycQ++++   +
  gene1489|gene1489|rna1489|rna1489 219 CYRWSLMWEKEGENNISRQLSQMYTYCQTMIESNIT 254
                                        5666777788899*****************998764 PP

>> DUF2258  Uncharacterized protein conserved in archaea (DUF2258)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   3.6e-05      0.32      31      70 ..     172     211 ..     147     218 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 3.6e-05
                                        SS.HHHHHHHHHHHHHHHHHHHHCCTT--TTSEEEEEEEE CS
                            DUF2258  31 keekkeiaraiaeLNkklYevlveklkidKldvvrirvey 70 
                                         + +k  +++++eL  ++Ye+  ++  idK+ +v + ++ 
  gene1489|gene1489|rna1489|rna1489 172 PTLRKLLMEQLSELSSNIYELTHDQSFIDKDCIVMVDLQL 211
                                        456788899**************************99964 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (290 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       779  (0.0434492); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 1972.25
//
Query:       gene149|gene149|rna149|rna149  [L=86]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       686  (0.038262); expected 358.6 (0.02)
Passed bias filter:                      216  (0.0120475); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.33u 0.25s 00:00:00.58 Elapsed: 00:00:00.38
# Mc/sec: 679.69
//
Query:       gene1490|gene1490|rna1490|rna1490  [L=436]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (436 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       463  (0.0258241); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.52u 0.23s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 3220.72
//
Query:       gene1491|gene1491|rna1491|rna1491  [L=225]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (225 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       723  (0.0403257); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.29s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 1667.69
//
Query:       gene1492|gene1492|rna1492|rna1492  [L=721]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.026   15.2   0.1       0.05   14.3   0.1    1.4  1  PHR       PHR domain


Domain annotation for each model (and alignments):
>> PHR  PHR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1   2.8e-06      0.05      21     102 ..     117     210 ..     107     216 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.8e-06
                                PHR  21 rFevdrdIllv..GfglYgskgeaayevklel...........istekqesnekvlaenetevvsdgsekifevkf 83 
                                         F vd++ +++  G+ +Y  +++a y+ + e             +t++++ n++   +n+++v+ dg e++ +vk+
  gene1492|gene1492|rna1492|rna1492 117 DFVVDDELFVIsdGMHVYRRRERALYDREDERtgyskdydqndNHTQNEKDNNNLYDNNDQTVL-DGYERVLSVKL 191
                                        5888885555433888998888855444444445555666676777777777777777777766.999******** PP

                                PHR  84 ekpveiepnvkYtaraklk 102
                                         +p +i    +Yt+ +++ 
  gene1492|gene1492|rna1492|rna1492 192 HTPTKILHVFSYTVLMCTY 210
                                        **************99864 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (721 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       472  (0.0263261); expected 358.6 (0.02)
Passed bias filter:                      246  (0.0137208); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.78u 0.31s 00:00:01.09 Elapsed: 00:00:00.57
# Mc/sec: 3812.75
//
Query:       gene1493|gene1493|rna1493|rna1493  [L=179]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0091   15.8   0.0      0.026   14.3   0.0    1.7  1  DUF3954   Protein of unknown function (DUF3954)


Domain annotation for each model (and alignments):
>> DUF3954  Protein of unknown function (DUF3954)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   1.5e-06     0.026       5      21 ..       7      23 ..       5      27 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.5e-06
                            DUF3954  5 DvtDnkiyvvknGevtL 21
                                        v D  iyv+knGe t+
  gene1493|gene1493|rna1493|rna1493  7 HVCDQFIYVIKNGECTV 23
                                       699***********997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (179 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       452  (0.0252106); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.35s 00:00:00.93 Elapsed: 00:00:00.56
# Mc/sec: 958.62
//
Query:       gene1494|gene1494|rna1494|rna1494  [L=120]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.1e-25   87.5   1.4    6.1e-25   87.2   1.4    1.1  1  Ribosomal_L35Ae  Ribosomal protein L35Ae
  ------ inclusion threshold ------
      0.021   15.0   2.0        1.6    9.0   0.0    2.2  2  RimM             RimM N-terminal domain


Domain annotation for each model (and alignments):
>> Ribosomal_L35Ae  Ribosomal protein L35Ae
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.2   1.4   6.8e-29   6.1e-25       3      94 ..      21     111 ..      19     112 .. 0.92

  Alignments for each domain:
  == domain 1  score: 87.2 bits;  conditional E-value: 6.8e-29
                                        EEEEEEEEE--SSSSS-EEEEEEESS--SHHHHHCCTT-EE..EEE-......TTT-EEEEEEEEECTTTTEEEEE CS
                    Ribosomal_L35Ae   3 vkavflgykrgkrnqrentaLlkiegvkskeeaefylGkrvayvykakkkkkgskvrviwGkvtrahGnsgvvrak 78 
                                        + ++f++++r++r+ +++++L++i++v++ +ea++y+G++v   +    k +++ v++++G+v+++hG++gvv ++
  gene1494|gene1494|rna1494|rna1494  21 ALGKFISHRRAQRRLHPSECLVRIDHVHTAQEAQKYVGNEVELFK-MYVKDSNNVVKSVKGRVVKVHGSRGVVVCR 95 
                                        5699*************************************7644.44557789********************** PP

                                        ETT--SSS-TT-EEEE CS
                    Ribosomal_L35Ae  79 FkknLppkaigarvrv 94 
                                        F++nL+p+++++rv+v
  gene1494|gene1494|rna1494|rna1494  96 FDRNLSPTEVNTRVYV 111
                                        **************98 PP

>> RimM  RimM N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.0   0.00018       1.6      46      78 ..      29      61 ..       8      66 .. 0.84
   2 ?    5.2   0.7    0.0027        24       3      15 ..      80      92 ..      78      97 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00018
                                       -EEEEEEETTEEEEEETT--SHHHHHTTTT-EE CS
                               RimM 46 tvesvrvhkkgvivklegvddrdaAealkgael 78
                                       + ++ r+h +  +v+++ v + ++A++++g e+
  gene1494|gene1494|rna1494|rna1494 29 RRAQRRLHPSECLVRIDHVHTAQEAQKYVGNEV 61
                                       55666799**********************988 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0027
                                       EEEEEEETTTTEE CS
                               RimM  3 GkIvgahGlkGev 15
                                       G++v++hG +G v
  gene1494|gene1494|rna1494|rna1494 80 GRVVKVHGSRGVV 92
                                       9**********87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       708  (0.0394891); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.35s 00:00:00.93 Elapsed: 00:00:00.55
# Mc/sec: 657.68
//
Query:       gene1495|gene1495|rna1495|rna1495  [L=264]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.6e-14   53.4   0.1    4.4e-14   52.7   0.1    1.4  1  rve             Integrase core domain
    9.3e-13   48.1   0.9    2.4e-12   46.7   0.9    1.8  1  Integrase_H2C2  Integrase zinc binding domain
    4.7e-06   26.7   1.0    1.5e-05   25.1   0.4    2.3  2  zf-H2C2         H2C2 zinc finger


Domain annotation for each model (and alignments):
>> rve  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.7   0.1   7.3e-18   4.4e-14       2     118 ..     135     242 ..     134     243 .. 0.96

  Alignments for each domain:
  == domain 1  score: 52.7 bits;  conditional E-value: 7.3e-18
                                rve   2 trpgelwqvDvtvvripdgggkayllvvvddfsrlilaealsdemdastvlalleravarfggvepervlsDngse 77 
                                        trp e++++D+ +++    g  + + + vd fsr+i++  + ++  ++t+++ +++ v+  g   pe++++Dn +e
  gene1495|gene1495|rna1495|rna1495 135 TRPIEKVTIDIAKIK----G--KTVMISVDYFSRRIWVRDVGNR-RKETIIEKMNELVEEWGV--PEMIITDNVKE 201
                                        7999********999....4..57********************.***************999..*********** PP

                                rve  78 ytskafrefladlgirvsftrpgrpqdnGkvErfhrtlkde 118
                                        +++ +++++  + +i ++ t++   ++nG+vEr +rt++++
  gene1495|gene1495|rna1495|rna1495 202 FVAIETKNWMTEAQIVHEKTNAELYKSNGRVERVIRTVREG 242
                                        **************************************975 PP

>> Integrase_H2C2  Integrase zinc binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.7   0.9   4.1e-16   2.4e-12       3      57 ..      69     123 ..      67     124 .. 0.94

  Alignments for each domain:
  == domain 1  score: 46.7 bits;  conditional E-value: 4.1e-16
                     Integrase_H2C2   3 kslrkeilkeaHdsagHlGiektlerlrrryyWpgmrkdvkkyvksCetCqrrkp 57 
                                        k+  ++++ eaH ++ H G e      ++ryyW gm++++ +++k+CetCqr+++
  gene1495|gene1495|rna1495|rna1495  69 KENAEKLVIEAHLKTNHRGLEPICYEPKERYYWLGMKRHITEIIKRCETCQRNNR 123
                                        667889999********************************************97 PP

>> zf-H2C2  H2C2 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.4   2.6e-09   1.5e-05      17      39 .]      97     119 ..      95     119 .. 0.94
   2 ?   -2.7   0.0       1.2   7.5e+03       8      17 ..     178     187 ..     178     187 .. 0.86

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 2.6e-09
                            zf-H2C2  17 rkYhwlgiketvseVissCkaCq 39 
                                        ++Y+wlg k+++ e+i++C +Cq
  gene1495|gene1495|rna1495|rna1495  97 ERYYWLGMKRHITEIIKRCETCQ 119
                                        67********************9 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.2
                            zf-H2C2   8 inkltallar 17 
                                        i+k+ +l+++
  gene1495|gene1495|rna1495|rna1495 178 IEKMNELVEE 187
                                        68*****986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (264 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1306  (0.0728429); expected 358.6 (0.02)
Passed bias filter:                      600  (0.0334653); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.67u 0.31s 00:00:00.98 Elapsed: 00:00:00.55
# Mc/sec: 1447.26
//
Query:       gene1496|gene1496|rna1496|rna1496  [L=36]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (36 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       196  (0.010932); expected 358.6 (0.02)
Passed bias filter:                      174  (0.00970495); expected 358.6 (0.02)
Passed Vit filter:                         6  (0.000334653); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.30s 00:00:00.71 Elapsed: 00:00:00.48
# Mc/sec: 227.25
//
Query:       gene1497|gene1497|rna1497|rna1497  [L=109]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.024   14.0   0.0      0.026   13.9   0.0    1.1  1  P35       Apoptosis preventing protein


Domain annotation for each model (and alignments):
>> P35  Apoptosis preventing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   1.4e-06     0.026     185     239 ..      13      66 ..       6      94 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.4e-06
                                P35 185 eindtglyeydvlayvdnvqfdgeqfeefvqslilpssfknsekvlyyneasknr 239
                                        e+n+t + e+ + + +d v+fdg ++ e+++  i    f +se+ l++++   +r
  gene1497|gene1497|rna1497|rna1497  13 ELNET-IGEFSINSCIDHVNFDGAHYFEMIELGISVHVFDDSEQNLHFKKIDAER 66 
                                        56665.679999***********************************99766555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       278  (0.0155056); expected 358.6 (0.02)
Passed bias filter:                      215  (0.0119917); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 819.09
//
Query:       gene1498|gene1498|rna1498|rna1498  [L=108]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       363  (0.0202465); expected 358.6 (0.02)
Passed bias filter:                      237  (0.0132188); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.28s 00:00:00.66 Elapsed: 00:00:00.43
# Mc/sec: 751.89
//
Query:       gene1499|gene1499|rna1499|rna1499  [L=457]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (457 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       558  (0.0311228); expected 358.6 (0.02)
Passed bias filter:                      249  (0.0138881); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 3178.38
//
Query:       gene15|gene15|rna15|rna15  [L=351]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.8e-72  242.2   1.0    4.8e-72  242.2   1.0    1.5  2  Nop       snoRNA binding domain, fibrillarin


Domain annotation for each model (and alignments):
>> Nop  snoRNA binding domain, fibrillarin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.3      0.18   3.2e+03      64      93 ..      40      69 ..      16      90 .. 0.50
   2 !  242.2   1.0   2.6e-76   4.8e-72       2     229 ..      95     319 ..      94     320 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.18
                               HHHHHHCHHHH-SSS-S-HHHHHHHHHHHH CS
                        Nop 64 vimaakvtastsmgaelseedlknikelcd 93
                               + + ++++++  ++ +l+e+++kn  +++ 
  gene15|gene15|rna15|rna15 40 KRLKIEIETRLLKHFNLTEDEFKNKWRYIA 69
                               233333322345555566655555444444 PP

  == domain 2  score: 242.2 bits;  conditional E-value: 2.6e-76
                                HHHHHHHHHHHHHHHHHHHTTTSTCHHHHS-SHHHHHHHHHHCCCCHCCT.HHTT.HHHHHHHHHHHHCHHHH-SSS-S-HHHH CS
                        Nop   2 ldeidkeintlhkrvrewYswhFpELeslvkdnleYakvvkligneredlekkeedeelakevimaakvtastsmgaelseedl 85 
                                 d+++k+in  ++r++ewY+ hFpEL++l+++n +Y+++v +ig ++e+l+k ++de ++ + +++ +  a++s g++l ++d+
  gene15|gene15|rna15|rna15  95 YDDLEKDINMHSMRIKEWYGLHFPELSNLIENNEKYLRAVDRIG-DKENLSKMKDDECMEFDLKKVREL-ARNSVGSDLRDDDI 176
                                699*****************************************.99***9997766566666666555.777*********** PP

                                HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSHHHHHHCHHHHHHHHHHHHSSHHHHHCS-HHHHTTTT-HHHHCCCHH.T--- CS
                        Nop  86 knikelcdrvleleelrkelleYlesrmsaiAPNlsaLvGeevaarLishaGgLtnLakmPastiqilGaekalfralk.kknt 168
                                k+ike +  vl++ ++r+el +Y++++m++iAPN+++L+G  +++rL+ +aG+L +L+kmPastiqilGaekalf+al+ +++t
  gene15|gene15|rna15|rna15 177 KKIKEDIACVLNMITYRTELVTYITEKMNEIAPNVTELLGVMIGSRLLVKAGSLAALSKMPASTIQILGAEKALFNALRqNGKT 260
                                *******************************************************************************555** PP

                                SSSCHHHCSHHHHHTS-CCCHHHHHHHHHHHHHHHHHHH.HTT----SHHHHHHHHHHHHHH CS
                        Nop 169 pkyGliyhselvqkatppklkkkiaRllaaKvalaaRiD.afsekdgslGkklreeiekklk 229
                                pk G+++h++lv+ +    +k+++aR+laaK+a+aaR+D  ++++dgs+Gkk+ e+++kk +
  gene15|gene15|rna15|rna15 261 PKFGILFHAPLVS-N--CVNKGRMARILAAKIAIAARVDyYKKDRDGSIGKKYYEQLDKKRQ 319
                                ************9.4..78********************5445566************9965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (351 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       886  (0.0494171); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 2376.53
//
Query:       gene150|gene150|rna150|rna150  [L=170]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
          1    8.8   4.8        1.2    8.6   4.8    1.2  1  Stevor    Subtelomeric Variable Open Reading frame
        1.5    8.9   6.9       0.37   10.8   3.8    1.5  2  MerT      MerT mercuric transport protein


Domain annotation for each model (and alignments):
>> Stevor  Subtelomeric Variable Open Reading frame
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   4.8   0.00014       1.2     196     263 ..      65     135 ..      19     145 .. 0.64

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00014
                         Stevor 196 ilnlfsessles.alk.aavsaaaasdlagta.asaassafepygiaalvllilavvliiLYiwlyrRRKn 263
                                    i  ++ +++l    +    ++ +++  la  a   +a + ++   ia+l ++i+ ++ ++ ++wl+    +
  gene150|gene150|rna150|rna150  65 ISVVLVTQNLFMaKVYvVVIAYETVVPLAFLArILTADTKLYGLVIAVLAVVIIDIIEMVTFVWLFSQFER 135
                                    22222222222202222444445555555555467788999999999999***************976555 PP

>> MerT  MerT mercuric transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0      0.57   5.1e+03      55      65 ..      19      29 ..       9      40 .. 0.54
   2 ?   10.8   3.8   4.2e-05      0.37      43     107 ..      53     119 ..      41     130 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.57
                           MerT 55 iaaalvalffa 65
                                   i+  +v+l +a
  gene150|gene150|rna150|rna150 19 ILHSIVLLVYA 29
                                   33333333333 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 4.2e-05
                           MerT  43 nltvlepyrpifiaaalvalffawrriyrpveacepgevca.vpqvrktykvifwlv.avlvlvava 107
                                     lt+l+ y+ +fi+++lv   +   ++y  v a+e     a + ++ +    ++ lv avl++v++ 
  gene150|gene150|rna150|rna150  53 LLTALNLYKTYFISVVLVTQNLFMAKVYVVVIAYETVVPLAfLARILTADTKLYGLViAVLAVVIID 119
                                    699*****************9999**********988766625677777766776651445555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       771  (0.043003); expected 358.6 (0.02)
Passed bias filter:                      211  (0.0117686); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 1076.46
//
Query:       gene1500|gene1500|rna1500|rna1500  [L=56]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (56 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       434  (0.0242066); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.27s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 410.86
//
Query:       gene1501|gene1501|rna1501|rna1501  [L=332]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (332 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2860  (0.159518); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.71u 0.32s 00:00:01.03 Elapsed: 00:00:00.49
# Mc/sec: 2052.95
//
Query:       gene1502|gene1502|rna1502|rna1502  [L=114]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-06   28.0   0.1    2.4e-06   27.3   0.1    1.4  1  RRM_1     RNA recognition motif. (a.k.a. RRM, RBD, or RNP dom
  ------ inclusion threshold ------
       0.13   11.7   0.0       0.15   11.6   0.0    1.1  1  ApbE      ApbE family


Domain annotation for each model (and alignments):
>> RRM_1  RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   0.1   2.7e-10   2.4e-06       1      62 [.      33      96 ..      33     104 .. 0.89

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 2.7e-10
                                       EEEESETTTSSHHHHHHHHHTTS.CEEEEEEEEETTTSEEEEEEEEESSHHHHHHHHHHHTT.E CS
                              RRM_1  1 lfVgnLppdvteeeLkelFskfG.piksiklvrdetgkskgfafVeFeskedAekAlealng.k 62
                                       +f+++L +++t+e + +++s+ G +++++ ++   + k++g++fV+F+ ++  ++ ++++ + k
  gene1502|gene1502|rna1502|rna1502 33 IFISGLKKTLTKELVIDYLSDKGyGVTDVLVPVGGDVKNRGYCFVQFDGESGVKRFKDEYRKyK 96
                                       8********************7745779999999************************998844 PP

>> ApbE  ApbE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   1.7e-05      0.15     111     157 ..      26      73 ..       5      89 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 1.7e-05
                                        EESTT..-----TTTHHHHHHHHHHHHHHH...TT-EEEEEETTEEEEEC CS
                               ApbE 111 lakkgpgmkLDlggiaKGyavdrvaellka...giksalvnlGGdiralG 157
                                        + k++   ++  +g+ K  + + v+++l++   g++++lv +GGd+   G
  gene1502|gene1502|rna1502|rna1502  26 FIKHN--YRIFISGLKKTLTKELVIDYLSDkgyGVTDVLVPVGGDVKNRG 73 
                                        44445..89999****************999777***********98776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (114 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       503  (0.0280551); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 759.99
//
Query:       gene1503|gene1503|rna1503|rna1503  [L=127]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.018   15.2   0.5      0.024   14.8   0.5    1.2  1  DUF4275   Domain of unknown function (DUF4275)
       0.24   11.7   0.1       0.24   11.7   0.1    2.1  3  Mnd1      Mnd1 HTH domain


Domain annotation for each model (and alignments):
>> DUF4275  Domain of unknown function (DUF4275)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.5   2.6e-06     0.024      36     103 ..      45     119 ..      39     127 .] 0.80

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.6e-06
                            DUF4275  36 lseeekeeiflknddgvcgylwhvfsyek.rkclegeeaek......afdeeekkscylfyqhtddvliledaek 103
                                        ++e ek +i  k+ ++ +  l h+ +++k + c+e+e+ e+       f+ee++++ y f   +dd++ le+  +
  gene1503|gene1503|rna1503|rna1503  45 FEEFEKLAISCKEMSNQKDLLKHLVAFNKgNVCMEKEQFERllsigeEFSEEQREELYKFVNVKDDMINLEEFVE 119
                                        56779999999**9*************98467*****988533333379******************99998654 PP

>> Mnd1  Mnd1 HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0      0.57   5.1e+03       6      16 ..       4      14 ..       3      23 .. 0.77
   2 ?   11.7   0.1   2.7e-05      0.24      13      49 ..      44      80 ..      42      81 .. 0.92
   3 ?   -2.7   0.0      0.85   7.6e+03      40      48 ..     107     115 ..     101     121 .. 0.65

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.57
                               Mnd1  6 qeskefytlKe 16
                                       +e++ef+t  e
  gene1503|gene1503|rna1503|rna1503  4 KEKYEFFTKDE 14
                                       57888888655 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 2.7e-05
                               Mnd1 13 tlKeleklapkekgivsqsVkdvlqsLvd..DglveveK 49
                                       t  e+ekla ++k +++q  kd+l++Lv+   g v++eK
  gene1503|gene1503|rna1503|rna1503 44 TFEEFEKLAISCKEMSNQ--KDLLKHLVAfnKGNVCMEK 80
                                       5689**********9888..9*******99899999999 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 0.85
                               Mnd1  40 vdDglveve 48 
                                        v+D++++ e
  gene1503|gene1503|rna1503|rna1503 107 VKDDMINLE 115
                                        345555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1079  (0.0601818); expected 358.6 (0.02)
Passed bias filter:                      561  (0.0312901); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 825.77
//
Query:       gene1504|gene1504|rna1504|rna1504  [L=135]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-45  155.1   0.6    1.2e-45  155.0   0.6    1.0  1  DUF5093   Domain of unknown function (DUF5093)
     0.0085   16.2   2.4      0.017   15.3   2.1    1.5  2  RRP7      Ribosomal RNA-processing protein 7 (RRP7) C-termina
  ------ inclusion threshold ------
      0.052   13.7   0.2      0.056   13.6   0.2    1.2  1  SOUL      SOUL heme-binding protein


Domain annotation for each model (and alignments):
>> DUF5093  Domain of unknown function (DUF5093)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  155.0   0.6     2e-49   1.2e-45       1     131 []       9     134 ..       9     134 .. 0.99

  Alignments for each domain:
  == domain 1  score: 155.0 bits;  conditional E-value: 2e-49
                            DUF5093   1 lkleFpFkvkkvenksklkvkierkenivsFsLpfklkltvkseksssvelisveksedefvYvleFesindaieF 76 
                                        ++l FpF+v++++n+++l+++++++++++sF+Lpf l++t+k++++s++++++v+ks+d+fvY+l+Fe i d+++F
  gene1504|gene1504|rna1504|rna1504   9 ITLVFPFNVPGITNRVTLSTTMHTRDATLSFALPFLLAFTTKPPNNSYPYAVKVKKSNDMFVYILKFEPI-DLKRF 83 
                                        79********************************************************************.***** PP

                            DUF5093  77 ienkevkvvseseltdvkelekeldeameeyektekskkkkkKklvededGfiry 131
                                        i n+e++vv+e++ ++++e+++e+de+meeye+te   k++kKk+++d+dG+iry
  gene1504|gene1504|rna1504|rna1504  84 IVNCELHVVKEMA-DEYEEITREMDERMEEYERTE---KMGKKKKIVDDDGWIRY 134
                                        ********99999.9********************...9***************9 PP

>> RRP7  Ribosomal RNA-processing protein 7 (RRP7) C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0      0.97   5.8e+03      79     101 ..      54      76 ..      49      78 .. 0.70
   2 !   15.3   2.1   2.8e-06     0.017       7      45 ..      99     132 ..      93     134 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.97
                               RRP7  79 dFYrFQirekkkeelaeLrkkFe 101
                                        + Y + ++ kk +++     kFe
  gene1504|gene1504|rna1504|rna1504  54 NSYPYAVKVKKSNDMFVYILKFE 76 
                                        56777777788777776666665 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 2.8e-06
                               RRP7   7 eeelqeevdeymeefdkeeeeekkeekkkeeevDeDGfv 45 
                                         ee+++e+de mee++++e+  k     k++ vD+DG++
  gene1504|gene1504|rna1504|rna1504  99 YEEITREMDERMEEYERTEKMGK-----KKKIVDDDGWI 132
                                        68999***********9977743.....33469*****8 PP

>> SOUL  SOUL heme-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.2   9.4e-06     0.056      60     116 ..       9      77 ..       2     126 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 9.4e-06
                               SOUL  60 iamtaPv...........vtkvkekevtmsfvlpskyq.aeepPkPtddsrVkleevpertvavrrFsG 116
                                        i    P             t++++++ t+sf lp     + +pP+ + + +Vk+++ +++ v++++F+ 
  gene1504|gene1504|rna1504|rna1504   9 ITLVFPFnvpgitnrvtlSTTMHTRDATLSFALPFLLAfTTKPPNNSYPYAVKVKKSNDMFVYILKFEP 77 
                                        555555555555555555445666***********9878888***999*******************84 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1192  (0.0664845); expected 358.6 (0.02)
Passed bias filter:                      668  (0.0372581); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.39u 0.29s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 979.38
//
Query:       gene1505|gene1505|rna1505|rna1505  [L=85]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (85 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       272  (0.015171); expected 358.6 (0.02)
Passed bias filter:                      174  (0.00970495); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.25s 00:00:00.60 Elapsed: 00:00:00.41
# Mc/sec: 625.14
//
Query:       gene1506|gene1506|rna1506|rna1506  [L=318]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      4e-15   55.6   0.2    9.8e-15   54.4   0.1    1.7  2  Acyltransferase  Acyltransferase
     0.0072   16.4   0.0      0.016   15.2   0.0    1.6  1  Acyltransf_C     Acyltransferase C-terminus
  ------ inclusion threshold ------
       0.23   10.6   0.0       0.59    9.3   0.0    1.6  2  DUF3150          Protein of unknown function (DUF3150)


Domain annotation for each model (and alignments):
>> Acyltransferase  Acyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.4   0.1   1.6e-18   9.8e-15       9     133 ..     106     254 ..      97     256 .. 0.81
   2 ?   -2.1   0.0      0.46   2.8e+03      52      84 ..     270     300 ..     260     307 .. 0.75

  Alignments for each domain:
  == domain 1  score: 54.4 bits;  conditional E-value: 1.6e-18
                    Acyltransferase   9 nlpekgpailvaNHqsylDvlllwlllyksngprnvviiakkellsipllgflmrllgfifidRksnaraagslen 84 
                                         +++++++++++NH   +D+l+ + ++  +++ + ++ i+k++l ++p+lg+ +r l f f+dR  +++ ++  ++
  gene1506|gene1506|rna1506|rna1506 106 SIKRDENVLVISNHIGAIDFLMYHEVANMKGMIAHCKYILKRSLGYVPILGPSLRCLCFCFVDRCARKDVESIRKY 181
                                        57789********************99777744*******************************666655555555 PP

                    Acyltransferase  85 iselleeg..klvviFPEGtrsre..................gel.lpfkkGlvrlaakak...kgvpivPva 133
                                        +  + ++g   +++++PEGtr+ +                  + +  p  kG++   ++a+   k++++++v 
  gene1506|gene1506|rna1506|rna1506 182 VDYVHRNGikHWLMLYPEGTRFTQrkkreadeycgqkgvppfTHVlCPRTKGFKVFHEHARhvyKNIVDITVD 254
                                        555777778688**********998999999999999998864334777777766666665788888888875 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.46
                    Acyltransferase  52 llsipllgflmrllgfifidRksnaraagslen 84 
                                         +++++ g++++ +++++++     ++++++++
  gene1506|gene1506|rna1506|rna1506 270 FFTVEIDGTFLMDVRVVPMEE--VHDCEQFMDE 300
                                        467788899999999999987..5566666665 PP

>> Acyltransf_C  Acyltransferase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   2.7e-06     0.016      19      47 ..     283     312 ..     280     317 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.7e-06
                       Acyltransf_C  19 leevPede.eelaeWlhelfeeKDklleeF 47 
                                        +  vP +e ++++++++e+f++KD++l e+
  gene1506|gene1506|rna1506|rna1506 283 VRVVPMEEvHDCEQFMDECFRRKDRILSEW 312
                                        5568888659****************9986 PP

>> DUF3150  Protein of unknown function (DUF3150)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0   9.8e-05      0.59      47     100 ..     197     258 ..     192     262 .. 0.89
   2 ?   -2.9   0.0      0.54   3.2e+03     177     194 ..     291     308 ..     288     313 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 9.8e-05
                            DUF3150  47 dpeaLkvfsklKreaerlllkvGv........rflgGyavpedkaeevvkeLekikqeFeke 100
                                         pe  +  ++ Krea+  + + Gv        +  +G+ v +++a +v+k++ +i  ++ ++
  gene1506|gene1506|rna1506|rna1506 197 YPEGTRFTQRKKREADEYCGQKGVppfthvlcPRTKGFKVFHEHARHVYKNIVDITVDYRNA 258
                                        577778899****************9999998669********************9999876 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 0.54
                            DUF3150 177 akearellekslagreev 194
                                        ++++++++++++++++++
  gene1506|gene1506|rna1506|rna1506 291 VHDCEQFMDECFRRKDRI 308
                                        578999999999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (318 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       837  (0.0466841); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 2190.00
//
Query:       gene1507|gene1507|rna1507|rna1507  [L=344]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    9.6e-11   41.4   0.0      2e-10   40.3   0.0    1.6  1  RRM_1        RNA recognition motif. (a.k.a. RRM, RBD, or RNP 
  ------ inclusion threshold ------
      0.026   14.5   0.3      0.073   13.1   0.0    1.9  2  Nup35_RRM_2  Nup53/35/40-type RNA recognition motif


Domain annotation for each model (and alignments):
>> RRM_1  RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.3   0.0   2.2e-14     2e-10       1      69 [.     264     334 ..     264     335 .. 0.94

  Alignments for each domain:
  == domain 1  score: 40.3 bits;  conditional E-value: 2.2e-14
                                        EEEESETTTSSHHHHHHHHHTTSCEEEEEEEEE..TTTSEEEEEEEEESSHHHHHHHHHHHTT.EEETTEEE CS
                              RRM_1   1 lfVgnLppdvteeeLkelFskfGpiksiklvrd..etgkskgfafVeFeskedAekAlealng.kklggrel 69 
                                        ++V+nL +++t++ L +++  +G iks++++    + +++k++afVeF +++  + A++ ln+   ++gr+l
  gene1507|gene1507|rna1507|rna1507 264 VIVRNLDHTITKQVLIKHLHACGTIKSVEIPQArkSGQPTKNYAFVEFMNRSGVNIAMS-LNNkLVINGRRL 334
                                        68*******************************999999********************.777589999987 PP

>> Nup35_RRM_2  Nup53/35/40-type RNA recognition motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.1      0.53   4.8e+03      38      44 ..       3       9 ..       1      13 [. 0.80
   2 ?   13.1   0.0   8.1e-06     0.073      15      51 ..     275     319 ..     263     321 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.53
                        Nup35_RRM_2 38 vmyvkfe 44
                                       +m++++ 
  gene1507|gene1507|rna1507|rna1507  3 LMWMCYY 9 
                                       79***96 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 8.1e-06
                        Nup35_RRM_2  15 elVle.hFasfGeIvkhyvp.......kevsvmyvkfesekdaek 51 
                                        + Vl  h++ +G I   ++p       + +++++v+f+++   ++
  gene1507|gene1507|rna1507|rna1507 275 KQVLIkHLHACGTIKSVEIPqarksgqPTKNYAFVEFMNRSGVNI 319
                                        456666*********************99*********9876555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (344 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1297  (0.0723409); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 2234.06
//
Query:       gene1508|gene1508|rna1508|rna1508  [L=252]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        6.3    6.6  10.2       0.13   12.2   3.3    1.6  2  DUF1461   Protein of unknown function (DUF1461)


Domain annotation for each model (and alignments):
>> DUF1461  Protein of unknown function (DUF1461)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   3.3   7.1e-06      0.13      98     176 ..       7      89 ..       2      92 .. 0.60
   2 ?   -3.7   0.6      0.54   9.7e+03      26      64 ..     205     242 ..     198     248 .. 0.52

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 7.1e-06
                            DUF1461  98 ivrlvtlillvllllllivlkkkkkkirllk....skslllavilllliliilgllalidFdkaFtlFHki.fFnn 168
                                        i++ +t+i++  +l++  ++kk+   i+ +     s+  + ++   +l      l+++++F+k F +FH    F++
  gene1508|gene1508|rna1508|rna1508   7 ILFTLTIIIINTVLYYRHTIKKR-AIIQKMSsttpSSLAFSSINQHILSYESESLALILNFKKEFDIFHYCtSFTD 81 
                                        56666666664444444444444.3333333455444444444455555566678899***********96269** PP

                            DUF1461 169 dlWlfdpa 176
                                        ++ +f   
  gene1508|gene1508|rna1508|rna1508  82 SYFIFTGY 89 
                                        ***99765 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 0.54
                            DUF1461  26 lyekeikklnvkestgmskedllentdelidYlkgkkke 64 
                                        lye + +k +  ++ +++++d+++   e   Y k+k + 
  gene1508|gene1508|rna1508|rna1508 205 LYEASKQKDES-NKKNVEDKDVKRRERENTGYEKKKDEY 242
                                        44444333333.335677777766666666666555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1664  (0.0928105); expected 358.6 (0.02)
Passed bias filter:                      488  (0.0272185); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1678.17
//
Query:       gene1509|gene1509|rna1509|rna1509  [L=225]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (225 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       480  (0.0267723); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1504.21
//
Query:       gene151|gene151|rna151|rna151  [L=206]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-55  188.8   2.6    1.4e-55  188.6   2.6    1.1  1  Methyltransf_8   Hypothetical methyltransferase
     0.0018   18.9   0.1      0.037   14.7   0.1    2.4  1  Methyltransf_11  Methyltransferase domain
     0.0021   18.7   0.1       0.54   11.0   0.0    2.4  2  Methyltransf_25  Methyltransferase domain
  ------ inclusion threshold ------
      0.018   14.9   0.0      0.029   14.2   0.0    1.3  1  Methyltransf_23  Methyltransferase domain
      0.023   14.3   0.1      0.044   13.3   0.0    1.6  2  MTS              Methyltransferase small domain
      0.027   13.7   0.0        3.8    6.8   0.0    2.2  2  Methyltransf_2   O-methyltransferase domain
      0.031   14.3   0.3      0.098   12.6   0.1    1.8  1  Methyltransf_32  Methyltransferase domain
      0.037   13.3   0.1          2    7.7   0.1    2.1  2  Ubie_methyltran  ubiE/COQ5 methyltransferase family


Domain annotation for each model (and alignments):
>> Methyltransf_8  Hypothetical methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  188.6   2.6   6.1e-59   1.4e-55       4     219 .]       5     206 .]       2     206 .] 0.93

  Alignments for each domain:
  == domain 1  score: 188.6 bits;  conditional E-value: 6.1e-59
                                    XXX-HHHHHHHHHHHHHHHHHS-HHHHHHHHHH-HHHHHHHHHHHHHHHCTSSS-HHHHHHHHHCTS-TTS-EEEES-TT CS
                 Methyltransf_8   4 akikkrldgarfrflneklytgesskavdlfkedpeafdlyhkgfrsqvkkWPenPldviirklkkkkdnlvvadlGcGe 83 
                                    +k +krl+ga+fr++ne +y+ e  +        pe +  yh g+rsq +kWP+nP+d+ii++lk k+ +  +ad+GcGe
  gene151|gene151|rna151|rna151   5 RKYEKRLEGAKFRIINELMYKNEKIE--------PEQLLEYHIGYRSQTQKWPVNPIDTIIEHLKTKEYS-KIADVGCGE 75 
                                    6889****************987655........555588*************************99876.69******* PP

                                    -HHHHH--S-..EEEEESS-SSTTEEES-TTS-S--TT-EEEEEEES---SS-HHHHHHHHHHHEEEEEEEEEEEEGGG- CS
                 Methyltransf_8  84 akiaeavrekekvrsfdlvavnervvacdlakvPledesvdvavfclslmgtnladflkeanrvlkvGGllkvaevksrf 163
                                    a +a   ++  +v s+d  ++ne ++  d++++  ed   + av+clslm +n+   +ke nr++kvGG + +aev sr+
  gene151|gene151|rna151|rna151  76 ALLA---QKIAHVDSYDYYPINESIIKSDINEIKCEDAEYECAVYCLSLMKNNVGAAMKECNRIVKVGGCVVIAEVLSRI 152
                                    ****...556679******************************************************************* PP

                                    S-HHHHHHHHHCTTEEEEEEE--STTEEEEEEEE-SSS-TT---GG--------XX CS
                 Methyltransf_8 164 esvklfaraltklGfevkskdlsnkqfvlfefkkvekkgkkrelglklkpclykkr 219
                                    +s + f  ++  +Gf+ +s+  sn+ f+++ef kv+  +k   + + lk c+ykkr
  gene151|gene151|rna151|rna151 153 SSLNEFYTQMLAMGFKKNSVLASNDFFIIVEFIKVKDCDK--VVDMFLKECVYKKR 206
                                    **********************************987665..457899*******9 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.1   1.7e-05     0.037      44      96 .]      94     145 ..      69     145 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.7e-05
                                    EEEETTEECCCTSS-TT-EEEEEEES-CCC-CCHHHHHHHHHHHEEEEEEEEE CS
                Methyltransf_11  44 kvefvvadaeklpfednsfDlvvssevlhhvedpekalkeiaRvLkpgGllvi 96 
                                    + +++++d+ +++ ed+ + + v   +l+   ++ +a+ke+ R++k gG +vi
  gene151|gene151|rna151|rna151  94 NESIIKSDINEIKCEDAEYECAVYCLSLMKN-NVGAAMKECNRIVKVGGCVVI 145
                                    3356999*************99999988887.7****************9886 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.0     0.011        25       1      17 [.      68      84 ..      68      95 .. 0.85
   2 !   11.0   0.0   0.00024      0.54      49      97 .]      96     141 ..      86     141 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.011
                                   EEEET-TTSHHHHHHHC CS
                Methyltransf_25  1 vLdlGcGtGrltlalak 17
                                   + d+GcG+  l++++a+
  gene151|gene151|rna151|rna151 68 IADVGCGEALLAQKIAH 84
                                   78**********99985 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00024
                                    EEEESBCCGBSSSTTTEEEEEEESTGGGSSHHHHHHHHHHHHHHEEEEE CS
                Methyltransf_25  49 efvqgdaedlpfedgsfDlvvssgalhhlsdedlekalkeiarvLkpgG 97 
                                    ++++ d+++++ ed+++ + v +  l++++ +++ +a+ke+ r++k gG
  gene151|gene151|rna151|rna151  96 SIIKSDINEIKCEDAEYECAVYC--LSLMK-NNVGAAMKECNRIVKVGG 141
                                    67899*************99984..66655.6789***********999 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   1.3e-05     0.029       4     130 ..      44     158 ..      41     183 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.3e-05
                Methyltransf_23   4 qreeelsdklerllpklragg..rvLdiGcGtGillevlrengfsvtgvDlspeaveiaekakkaqkdqfdeqeaaepqg 81 
                                    q ++++   ++ + + l+++   ++ d+GcG+  l++    + ++v+ +D +p++ +i+++++         +e++++++
  gene151|gene151|rna151|rna151  44 QTQKWPVNPIDTIIEHLKTKEysKIADVGCGEALLAQ----KIAHVDSYDYYPINESIIKSDI---------NEIKCEDA 110
                                    55555555555555543333333888*******7766....55899************84444.........45555557 PP

                Methyltransf_23  82 kfdlIvlrevlehvp.dppellrqiatllkpgGylllseplaslkedrll 130
                                     +++  + ++l  ++ ++ ++++  ++++k gG +++ e+l++ ++++ +
  gene151|gene151|rna151|rna151 111 EYEC--AVYCLSLMKnNVGAAMKECNRIVKVGGCVVIAEVLSRISSLNEF 158
                                    7776..568888888459*********************99988666554 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0     2e-05     0.044      23      53 ..      56      86 ..      53     138 .. 0.75
   2 ?   -2.7   0.0       1.7   3.7e+03     145     168 ..     159     182 ..     149     183 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2e-05
                                   HHHHCHCCTCSEEEEET-TTSHHHHHHHHHT CS
                            MTS 23 LletlpkelsgkvlDlGcGaGvlgaalakes 53
                                   ++e+l++++  k++D+GcG  +l+ ++a+  
  gene151|gene151|rna151|rna151 56 IIEHLKTKEYSKIADVGCGEALLAQKIAHVD 86
                                   689*****999************99998754 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.7
                                    HHHHHHHHHS--EEEEEESSEEEE CS
                            MTS 145 yeslleelfgnvevvaktkkfkvl 168
                                    y ++l+  f++  v+a+++ f ++
  gene151|gene151|rna151|rna151 159 YTQMLAMGFKKNSVLASNDFFIIV 182
                                    778888889999999888888775 PP

>> Methyltransf_2  O-methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.0    0.0017       3.8      44      82 ..      45      84 ..      15     112 .. 0.78
   2 ?    5.1   0.1    0.0054        12     147     184 ..     128     165 ..     119     176 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0017
                                   HTTHHHH.HHHHHHSS-GGG-SEEEEET-TTSHHHHHHHH CS
                 Methyltransf_2 44 qessslv.akkvleafdleglkslvDvGGGtGalakaivs 82
                                   ++++ ++  ++++e+ + ++ +++ DvG G   la++i++
  gene151|gene151|rna151|rna151 45 TQKWPVNpIDTIIEHLKTKEYSKIADVGCGEALLAQKIAH 84
                                   4555555368899***********************9975 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0054
                                    HHHHHHHHH--TT-EEEEEE----TTS---HHHHHHHH CS
                 Methyltransf_2 147 klLkrvkkalpagGkvivveavlgadpsgeletelvdl 184
                                      +k++++ ++ gG v+++e++   +  +e  t+++++
  gene151|gene151|rna151|rna151 128 AAMKECNRIVKVGGCVVIAEVLSRISSLNEFYTQMLAM 165
                                    56899*****************9999999999988654 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   4.4e-05     0.098      13      48 ..      53      88 ..      49     116 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.4e-05
                Methyltransf_32 13 vakllkelakesgaltvvDvGaGkgYLsfvlal.kek 48
                                   +++++++  k+++  +++DvG+G++ L++ +a+ ++ 
  gene151|gene151|rna151|rna151 53 IDTIIEH-LKTKEYSKIADVGCGEALLAQKIAHvDSY 88
                                   6777777.5778899***************9995333 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0     0.025        55      39      82 ..      56     104 ..      44     116 .. 0.74
   2 ?    7.7   0.1   0.00088         2     134     157 ..     128     152 ..     116     169 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.025
                                    HHHH--S--TTEEEEES-TT-HHHHHHHHHHHHHH.....EEEEEES-H CS
                Ubie_methyltran  39 veklvavkrgakvlDvagGtgDlafklsdsvgekg.....kvvvlDine 82 
                                    +++   +k+ +k+ Dv +G + la k+++     +      ++  Dine
  gene151|gene151|rna151|rna151  56 IIEHLKTKEYSKIADVGCGEALLAQKIAHVDSYDYypineSIIKSDINE 104
                                    55666778889**********9999998654444455665666666666 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.00088
                                    HHHHHHHHHEEEEEEEEEEEE.--- CS
                Ubie_methyltran 134 kaLkeayrvlkpGGrlvvlef.skv 157
                                     a+ke  r++k+GG +v+ e+ s++
  gene151|gene151|rna151|rna151 128 AAMKECNRIVKVGGCVVIAEVlSRI 152
                                    689***************9962443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       816  (0.0455129); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1357.74
//
Query:       gene1510|gene1510|rna1510|rna1510  [L=197]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.066   13.6   0.4      0.066   13.6   0.4    1.6  2  Ly49         Ly49-like protein, N-terminal region
       0.32   10.7   7.3       0.41   10.3   7.3    1.3  1  Tetraspanin  Tetraspanin family
        8.6    5.4   9.7         11    5.1   9.7    1.0  1  Herpes_LMP1  Herpesvirus latent membrane protein 1 (LMP1)


Domain annotation for each model (and alignments):
>> Ly49  Ly49-like protein, N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.4   1.1         3   1.8e+04      17      22 ..      62      67 ..      53      78 .. 0.46
   2 ?   13.6   0.4   1.1e-05     0.066       5      86 ..      89     170 ..      85     187 .. 0.86

  Alignments for each domain:
  == domain 1  score: -4.4 bits;  conditional E-value: 3
                                       XXXXXX CS
                               Ly49 17 llLvtv 22
                                       +l +++
  gene1510|gene1510|rna1510|rna1510 62 MLVIAL 67
                                       222222 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 1.1e-05
                                        XXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX..HHHHHH CS
                               Ly49   5 klivvalgILc.lllLvtvavLvtkifqysqekheleetlnlsqnysimqndinlkeelLrnkslecsilkdlles 79 
                                         ++v+alg+   ++ L+tv +L +  + ++  ++e +++ n++   s+  + +++k  ++ n++++ ++++ l++ 
  gene1510|gene1510|rna1510|rna1510  89 YVFVIALGVASsSVVLLTVQMLLMLSLDFIIYRRERKKAWNITLDTSAQIKMVYMKRAIVSNRMVDLNMGE-LVQF 163
                                        5789****9862689****************************************************9765.7777 PP

                                        HHHHHHH CS
                               Ly49  80 lkreqkr 86 
                                        +++e + 
  gene1510|gene1510|rna1510|rna1510 164 ISKEGEF 170
                                        7777665 PP

>> Tetraspanin  Tetraspanin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   7.3   6.8e-05      0.41      47     106 ..      47     108 ..      13     172 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 6.8e-05
                                        ......XXXXXX..XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--HHH CS
                                        xxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        Tetraspanin  47 ailaillivvGv..llfllgflGcigalkenkcllltfsllllvlfllelaagilgfvfsdk 106
                                        +  +  l+++Gv  +++++++  ci ++  +k ++++f++l  v+++++ +a   ++ ++ +
  gene1510|gene1510|rna1510|rna1510  47 PLSSHYLLALGVtqVMLVIALSMCIVVWTISKRVMMCFVVLQYVFVIALGVASSSVVLLTVQ 108
                                        33445689999999*************************99999888888887766666555 PP

>> Herpes_LMP1  Herpesvirus latent membrane protein 1 (LMP1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   9.7    0.0018        11      75     183 ..       7     120 ..       3     135 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0018
                                        XXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXX...XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                        Herpes_LMP1  75 dllcplg.alcllllmitlllialwnlhgqaly...lgivlfifgcllvlglwiyllellwrlgatiwqllaffla 146
                                        ++++p+   l +l +++++++ia   l  +a+    l +v +    ll lg+   +l +   +   +w +   ++ 
  gene1510|gene1510|rna1510|rna1510   7 QIFAPMRkYLSILKVFVSFIFIASMILNNKAVIkipLKVVPLSSHYLLALGVTQVMLVIALSMCIVVWTISKRVMM 82 
                                        5566664157899999999999999999988754347888888999***********************9876655 PP

                                        XX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                        Herpes_LMP1 147 ff.ldlilliialylqqnwwtllvdllwlllflailiw 183
                                         f +   +++ial +      ll   + l+l l  +i+
  gene1510|gene1510|rna1510|rna1510  83 CFvVLQYVFVIALGVASSSVVLLTVQMLLMLSLDFIIY 120
                                        55055567899****99999998877777777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1389  (0.0774723); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1386.91
//
Query:       gene1511|gene1511|rna1511|rna1511  [L=59]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.012   14.9   0.2      0.012   14.9   0.2    1.0  1  7tm_2     7 transmembrane receptor (Secretin family)


Domain annotation for each model (and alignments):
>> 7tm_2  7 transmembrane receptor (Secretin family)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.2   6.6e-07     0.012      24      68 ..       3      47 ..       1      57 [. 0.87

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 6.6e-07
                                       HHHHTTTGTTSHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTEEE CS
                              7tm_2 24 lilllfrklrctrnyihlnLflslllrailvlvkdavlkseedes 68
                                        il  f+++rc+r y++ +L++s++   +lvl  ++++ s+++++
  gene1511|gene1511|rna1511|rna1511  3 CILKTFQSFRCERFYVYNDLIMSVIDDVFLVLTVIDQTSSRTTAA 47
                                       68999***************************9999999855544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       370  (0.020637); expected 358.6 (0.02)
Passed bias filter:                      250  (0.0139439); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.23s 00:00:00.57 Elapsed: 00:00:00.39
# Mc/sec: 453.15
//
Query:       gene1512|gene1512|rna1512|rna1512  [L=197]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-20   73.7   0.3    2.9e-19   69.1   0.0    2.2  2  Ribosomal_L5    Ribosomal protein L5
    4.2e-20   71.7   0.0    7.9e-20   70.8   0.0    1.5  1  Ribosomal_L5_C  ribosomal L5P family C-terminus
  ------ inclusion threshold ------
      0.035   13.8   0.0      0.071   12.8   0.0    1.4  1  HTH_ABP1_N      Fission yeast centromere protein N-terminal d


Domain annotation for each model (and alignments):
>> Ribosomal_L5  Ribosomal protein L5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.1   0.0   4.9e-23   2.9e-19       1      57 []      28      81 ..      28      81 .. 0.99
   2 ?    2.7   0.1     0.027   1.6e+02       9      33 ..      84     107 ..      82     114 .. 0.76

  Alignments for each domain:
  == domain 1  score: 69.1 bits;  conditional E-value: 4.9e-23
                                       SCTTS-EEEEEEEEEE-SSSSSCHHHHHCCHHHHCCCHSS--EECC--TTCTTTCSC CS
                       Ribosomal_L5  1 NvMqvPrleKivinmgvGeagedkkllekaakeLaeItGQkPvvtkakksianFkiR 57
                                       N+M+++r++K+ in +vGe+g++   l+kaak+L+++tGQkP ++k++ +i++F+iR
  gene1512|gene1512|rna1512|rna1512 28 NPMEEVRIHKLSINLCVGESGDK---LNKAAKVLEQLTGQKPRFSKSRLTIRTFGIR 81
                                       9**********************...******************************9 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.027
                                        EEEEEEEE-SSSSSCHHHHHCCHHH CS
                       Ribosomal_L5   9 eKivinmgvGeagedkkllekaake 33 
                                        eKi +++ v   ++ k +l++a k+
  gene1512|gene1512|rna1512|rna1512  84 EKIAVHVTVRGEKA-KDILNNALKI 107
                                        8********73333.3689999876 PP

>> Ribosomal_L5_C  ribosomal L5P family C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.8   0.0   1.3e-23   7.9e-20       1      82 [.      85     171 ..      85     183 .. 0.85

  Alignments for each domain:
  == domain 1  score: 70.8 bits;  conditional E-value: 1.3e-23
                     Ribosomal_L5_C   1 piGvkvtLrgekmyefldkllevvlprlrdFkGiskssfdgrGnvsfGikeqiifpeieydkdkgifGmditivtt 76 
                                        +i+v+vt+rgek+ ++l+++l++ + +lr      ++sf+++G+++fGike+i++ +++yd+ +gi+Gmd+++v++
  gene1512|gene1512|rna1512|rna1512  85 KIAVHVTVRGEKAKDILNNALKICEFELR------ETSFSETGTFGFGIKEHIDL-GLKYDPAIGIYGMDFIVVLS 153
                                        69***************************......********************.******************** PP

                     Ribosomal_L5_C  77 ak...tde.........e 82 
                                        ++   + +         +
  gene1512|gene1512|rna1512|rna1512 154 KPglrVCKrkrlrskvgN 171
                                        *97763332334444442 PP

>> HTH_ABP1_N  Fission yeast centromere protein N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   1.2e-05     0.071       9      38 ..     161     189 ..     154     194 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.2e-05
                         HTH_ABP1_N   9 qkkaLRawafqqnprpsqkaliaWFeqeyg 38 
                                        ++k LR+    +++r s+++  +WF ++++
  gene1512|gene1512|rna1512|rna1512 161 KRKRLRSKV-GNKQRVSKEEAKKWFVDTFE 189
                                        799****96.899***************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       504  (0.0281109); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 1336.87
//
Query:       gene1513|gene1513|rna1513|rna1513  [L=117]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       532  (0.0296726); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 780.18
//
Query:       gene1514|gene1514|rna1514|rna1514  [L=119]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       553  (0.0308439); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 910.12
//
Query:       gene1515|gene1515|rna1515|rna1515  [L=84]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (84 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       305  (0.0170115); expected 358.6 (0.02)
Passed bias filter:                      218  (0.0121591); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.46
# Mc/sec: 549.01
//
Query:       gene1516|gene1516|rna1516|rna1516  [L=73]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (73 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       365  (0.0203581); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.43
# Mc/sec: 508.50
//
Query:       gene1517|gene1517|rna1517|rna1517  [L=194]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.051   13.5   0.1       0.44   10.5   0.0    2.2  2  LktC      Actinobacillus actinomycetemcomitans leukotoxin act


Domain annotation for each model (and alignments):
>> LktC  Actinobacillus actinomycetemcomitans leukotoxin activator LktC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0     0.027   4.8e+02      48      66 ..      23      41 ..       9      50 .. 0.71
   2 ?   10.5   0.0   2.4e-05      0.44     121     149 ..     153     181 ..     114     182 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.027
                               LktC 48 vgilsekaiwkyqstfndg 66
                                       + +ls   i+ yq t nd 
  gene1517|gene1517|rna1517|rna1517 23 LKVLSTGNIFEYQPTENDA 41
                                       4466777777777777775 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 2.4e-05
                               LktC 121 kskysplylscllrrrltefkitllplpw 149
                                        + k + l++s ll+  lte+k+t l   w
  gene1517|gene1517|rna1517|rna1517 153 NEKSAKLFFSDLLKTHLTEWKLTSLRYEW 181
                                        568889******************99988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       648  (0.0361426); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1394.69
//
Query:       gene1518|gene1518|rna1518|rna1518  [L=660]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (660 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       736  (0.0410508); expected 358.6 (0.02)
Passed bias filter:                      548  (0.030565); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.62u 0.26s 00:00:00.88 Elapsed: 00:00:00.44
# Mc/sec: 4520.89
//
Query:       gene1519|gene1519|rna1519|rna1519  [L=93]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       446  (0.0248759); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 672.81
//
Query:       gene152|gene152|rna152|rna152  [L=260]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      0.001   18.3   0.5     0.0017   17.6   0.5    1.3  1  Hemocyanin_M     Hemocyanin, copper containing domain
  ------ inclusion threshold ------
      0.049   13.2   0.1       0.67    9.5   0.0    2.1  2  NTP_transf_5     Uncharacterised nucleotidyltransferase
       0.14   12.6   0.1        1.9    8.9   0.0    2.5  2  ATP-gua_PtransN  ATP:guanido phosphotransferase, N-terminal d


Domain annotation for each model (and alignments):
>> Hemocyanin_M  Hemocyanin, copper containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.5   2.9e-07    0.0017     188     253 ..      69     136 ..      49     151 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 2.9e-07
                                    ETTCEEETTSCHHHHHHHHHHHT-GGSB--TTS--HHHHHHHHHCT----SBTTB..----GGG-TTT CS
                   Hemocyanin_M 188 adgkkidLrkpegieilgnilegnvdsidkkfygslevlarkllgdaeepddkyk..vvpsvlenfeT 253
                                    +++k+i++ k+e ie l n+l  n  ++dk + +   +++ + +g  + ++ +y+  v++++le+++ 
  gene152|gene152|rna152|rna152  69 QTDKMINMMKNEVIEKLKNVLTKNDLEFDKIYRERTGMMSSESIGGQDIYEFSYNdeVIFNILEEYQH 136
                                    4568******************************************99999666668*******9985 PP

>> NTP_transf_5  Uncharacterised nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0     0.032   1.9e+02      89     107 ..      51      69 ..      45     102 .. 0.73
   2 ?    9.5   0.0   0.00011      0.67     167     209 ..     108     146 ..      78     161 .. 0.78

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.032
                   NTP_transf_5  89 palRemgDiDllvkredld 107
                                    p++ +  DiD lv++++++
  gene152|gene152|rna152|rna152  51 PEMTPLADIDCLVRENEVQ 69 
                                    5666788888888777644 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00011
                   NTP_transf_5 167 rpveiggksilvlspedlllylalHlakhfwnrglgLrwlvDi 209
                                     +  igg++i+ +s++d++++ +l  ++h ++    +++l+D 
  gene152|gene152|rna152|rna152 108 SSESIGGQDIYEFSYNDEVIFNILEEYQHIVE----MNSLYDE 146
                                    45679*************************95....7777775 PP

>> ATP-gua_PtransN  ATP:guanido phosphotransferase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.0   0.00032       1.9       9      35 ..      75     101 ..      70     114 .. 0.87
   2 ?    0.3   0.0      0.16   9.3e+02       4      21 ..     141     158 ..     139     173 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00032
                                    HC--HHHHHHHTT---TTS--HHHHHH CS
                ATP-gua_PtransN   9 kyLtpeiydklkdkkTrsgftLddvIq 35 
                                    +++++e+ +klk+  T+++  +d++ +
  gene152|gene152|rna152|rna152  75 NMMKNEVIEKLKNVLTKNDLEFDKIYR 101
                                    5789*******************9875 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.16
                                    T-HHHHC--HHHHHHHTT CS
                ATP-gua_PtransN   4 ksllkkyLtpeiydklkd 21 
                                    +sl  +yL  ++y+k + 
  gene152|gene152|rna152|rna152 141 NSLYDEYLRISLYKKQRR 158
                                    89999********99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1354  (0.0755201); expected 358.6 (0.02)
Passed bias filter:                      549  (0.0306208); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 1790.22
//
Query:       gene1520|gene1520|rna1520|rna1520  [L=125]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.7e-10   40.0   1.3    6.5e-10   39.2   1.3    1.5  1  Yippee-Mis18  Yippee zinc-binding/DNA-binding /Mis18, centrom


Domain annotation for each model (and alignments):
>> Yippee-Mis18  Yippee zinc-binding/DNA-binding /Mis18, centromere assembly
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.2   1.3   3.7e-14   6.5e-10       2      75 ..      12      79 ..      11     107 .. 0.81

  Alignments for each domain:
  == domain 1  score: 39.2 bits;  conditional E-value: 3.7e-14
                                       EEEETTTS-EEEECCCEEEEECCCEEEES---CCCEEEECEEEETTSTTEEEEEEEETTT--EEEEEEEECSCC CS
                       Yippee-Mis18  2 vfqCkkCktilgdslqlvsegralnivvlkkvtrnvvvgkelvtdeegkctystlsCkgCnsvlGwkYksteee 75
                                       ++qC++Ckti++ds++l++  ++  +++l+kv++ v  +++   +e+    y  + C+ C++v+G+kY++ +  
  gene1520|gene1520|rna1520|rna1520 12 ILQCAHCKTIIADSFSLIDYVQN--TLTLTKVSSFVKFKEKECPNER---PYAFILCE-CDTVVGKKYRDESVY 79
                                       79****************97766..***********99988887755...69******.*********986655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       652  (0.0363657); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 856.25
//
Query:       gene1521|gene1521|rna1521|rna1521  [L=399]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.8e-07   29.5   7.8      0.088   13.7   0.1    4.6  5  WD40            WD domain, G-beta repeat
     0.0024   18.1   3.2     0.0043   17.3   3.2    1.4  1  Tup_N           Tup N-terminal
  ------ inclusion threshold ------
       0.02   14.4   1.5      0.029   13.9   1.5    1.2  1  Leu_zip         Leucine zipper
      0.068   12.8   2.6       0.12   12.0   2.6    1.3  1  PI3K_P85_iSH2   Phosphatidylinositol 3-kinase regulatory subu
      0.071   11.8   0.5      0.098   11.3   0.5    1.1  1  WEMBL           Weak chloroplast movement under blue light
       0.12   11.7   0.7        0.4   10.0   0.2    2.0  2  WD40_like       WD40-like domain
       0.14   12.2   1.2       0.31   11.2   1.2    1.5  1  YojJ            Bacterial membrane-spanning protein N-terminu
       0.17   11.8   0.2       0.33   10.9   0.2    1.5  1  Phage_tail_APC  Phage tail assembly chaperone protein
       0.33   11.0   3.2       0.58   10.2   3.2    1.3  1  DUF1640         Protein of unknown function (DUF1640)


Domain annotation for each model (and alignments):
>> WD40  WD domain, G-beta repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.0         9   1.8e+04       9      16 ..      91      99 ..      87     101 .. 0.62
   2 ?    0.1   0.1      0.88   1.8e+03       8      28 ..     233     253 ..     227     274 .. 0.72
   3 !   12.0   0.2   0.00015       0.3      10      35 ..     286     312 ..     276     313 .. 0.85
   4 ?    4.5   0.0     0.037        73      23      38 .]     342     357 ..     326     357 .. 0.74
   5 !   13.7   0.1   4.4e-05     0.088       7      38 .]     366     396 ..     360     396 .. 0.68

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 9
                                       SSSS.EEEE CS
                               WD40  9 GHss.vtsl 16
                                       GH++ v ++
  gene1521|gene1521|rna1521|rna1521 91 GHDWvVEGV 99
                                       886644666 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.88
                                        ESSSSEEEEEEETTSSE.EEEE CS
                               WD40   8 tGHssvtslafspdgaw.lasG 28 
                                        +GH  v+++++  d ++ +a++
  gene1521|gene1521|rna1521|rna1521 233 DGH-AVHGVSNAEDRQLcMATC 253
                                        699.899998877777732343 PP

  == domain 3  score: 12.0 bits;  conditional E-value: 0.00015
                                        S.SSEEEEEEETTSSEEEEEETTSEEE CS
                               WD40  10 H.ssvtslafspdgawlasGsdDgtvr 35 
                                        H ++v s+a+s  +++l++Gs D t+ 
  gene1521|gene1521|rna1521|rna1521 286 HtKDVLSVAVSACSSYLVTGSADETIF 312
                                        7888*******************9985 PP

  == domain 4  score: 4.5 bits;  conditional E-value: 0.037
                                        SE.EEEEETTSEEEEEE CS
                               WD40  23 aw.lasGsdDgtvriWd 38 
                                        a+ +asG+ D+ vr++d
  gene1521|gene1521|rna1521|rna1521 342 AFvIASGT-DNVVRFFD 357
                                        44145667.*****998 PP

  == domain 5  score: 13.7 bits;  conditional E-value: 4.4e-05
                                        EESS.SSEEEEEEETTSSE....EEEEETTSEEEEEE CS
                               WD40   7 ltGH.ssvtslafspdgaw....lasGsdDgtvriWd 38 
                                        l GH  +v+s+            ++s+s Dg vriW+
  gene1521|gene1521|rna1521|rna1521 366 LVGHgEPVHSV------GVvggmMVSASGDGRVRIWS 396
                                        67997778888......332443556655*******5 PP

>> Tup_N  Tup N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   3.2   2.1e-06    0.0043       3      58 ..       6      61 ..       4      68 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 2.1e-06
                              Tup_N  3 nelLdavkqEfdalsqeasslkaqkdeyelkiqsqiqElqqirqtlyeLeeahrki 58
                                        el d+ k+E++++ +e+++lk++  e+e k ++ + +l++ r+ + ++++   ++
  gene1521|gene1521|rna1521|rna1521  6 FELHDLMKKEYESILTENTQLKKRLREIEDKQEHILMDLDKSRHCIRDMQNYIASL 61
                                       5999********************************************99876655 PP

>> Leu_zip  Leucine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   1.5   1.5e-05     0.029     129     180 ..      10      61 ..       7      77 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.5e-05
                            Leu_zip 129 eLLkkeierLkeenekLkerlkelEkqatsaleeksklekalkelqkelgek 180
                                        +L+kke e +  en++Lk+rl+e+E++ +++l +  k ++ ++++q+ + + 
  gene1521|gene1521|rna1521|rna1521  10 DLMKKEYESILTENTQLKKRLREIEDKQEHILMDLDKSRHCIRDMQNYIASL 61 
                                        799************************************9999999877665 PP

>> PI3K_P85_iSH2  Phosphatidylinositol 3-kinase regulatory subunit P85 inter-SH2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   2.6     6e-05      0.12      80     129 ..      13      62 ..       4      66 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 6e-05
                      PI3K_P85_iSH2  80 ehEieklqenleqlksrlkelhsskekLeedlkqqkeeereleReinalk 129
                                        ++E e++ + + qlk+rl e+++++e++  dl +     r ++  i +l+
  gene1521|gene1521|rna1521|rna1521  13 KKEYESILTENTQLKKRLREIEDKQEHILMDLDKSRHCIRDMQNYIASLR 62 
                                        799*******************************9999999998888876 PP

>> WEMBL  Weak chloroplast movement under blue light
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.5   4.9e-05     0.098      34      84 ..       6      56 ..       2      72 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 4.9e-05
                              WEMBL 34 verrklveeeLdkvqeeipeykkqaeaaeaaksqvleeLestkrlieeLkl 84
                                        e ++l+++e + + +e ++ kk+++++e +++++l++L++ ++ i +++ 
  gene1521|gene1521|rna1521|rna1521  6 FELHDLMKKEYESILTENTQLKKRLREIEDKQEHILMDLDKSRHCIRDMQN 56
                                       577899****************************************99875 PP

>> WD40_like  WD40-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       2.9   5.8e+03     188     215 ..     105     132 ..     100     139 .. 0.80
   2 ?   10.0   0.2    0.0002       0.4       2      56 ..     289     345 ..     288     353 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 2.9
                          WD40_like 188 vilqkidvegkPecillvddylivGgsf 215
                                         +l+ ++++ +P  ++l+d+  ++G  +
  gene1521|gene1521|rna1521|rna1521 105 SLLHSFNLGCVPAMVVLSDNQRFLGFTT 132
                                        6889999999999999999988888665 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0002
                          WD40_like   2 eiYsidiskkgslilyGgkddkctvlkleslesvsiv..esfedSvifvklldddli 56 
                                        ++ s+ +s  +s+++ G+ d+++ +lk++s+++  ++   sf d v+ v +ld  +i
  gene1521|gene1521|rna1521|rna1521 289 DVLSVAVSACSSYLVTGSADETIFLLKVQSDTLSVVFgpVSFGDTVVNVCFLDAFVI 345
                                        67899***********************9998777763369********99986554 PP

>> YojJ  Bacterial membrane-spanning protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   1.2   0.00015      0.31      23      59 ..      24      60 ..       6      61 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00015
                               YojJ 23 keleevlkaldeedeClLcelesirekfaeletlass 59
                                       ++l++ l++++ ++e +L +l++ r+ + ++++ ++s
  gene1521|gene1521|rna1521|rna1521 24 TQLKKRLREIEDKQEHILMDLDKSRHCIRDMQNYIAS 60
                                       4566667777778888888888888888888888776 PP

>> Phage_tail_APC  Phage tail assembly chaperone protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.2   0.00017      0.33      12      50 ..      33      71 ..      24      82 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00017
                                       HHHTHHHHSTTS---HHHHHHHHHHHHHHHHS---SS-- CS
                     Phage_tail_APC 12 LaasDwvqlpDspldeeerqalkaYrqaLRDlPeqegfP 50
                                       +++     l+D + ++ ++ ++++Y+ +LR +Pe+ g  
  gene1521|gene1521|rna1521|rna1521 33 IEDKQEHILMDLDKSRHCIRDMQNYIASLRRMPEKHGAE 71
                                       4444456799*************************9976 PP

>> DUF1640  Protein of unknown function (DUF1640)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   3.2   0.00029      0.58      76     124 ..      11      58 ..       8      68 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00029
                            DUF1640  76 alrseteklqreleklkqkLreeidklkadirldlnleKgrireelakl 124
                                        ++++e+e++ +e  +lk++Lre i++ +++i +dl++ +  ir++++++
  gene1521|gene1521|rna1521|rna1521  11 LMKKEYESILTENTQLKKRLRE-IEDKQEHILMDLDKSRHCIRDMQNYI 58 
                                        6899*****************8.9999*****************99976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (399 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1038  (0.057895); expected 358.6 (0.02)
Passed bias filter:                      863  (0.0481343); expected 358.6 (0.02)
Passed Vit filter:                       115  (0.00641419); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.44
# Mc/sec: 2739.97
//
Query:       gene1522|gene1522|rna1522|rna1522  [L=690]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00082   19.1   1.8          2    8.4   0.2    3.7  4  TPR_1     Tetratricopeptide repeat
     0.0011   18.8   0.9        6.9    7.0   0.0    3.4  3  TPR_2     Tetratricopeptide repeat
     0.0017   18.3   0.6       0.43   10.7   0.1    2.9  2  TPR_7     Tetratricopeptide repeat
     0.0062   16.7   2.2         13    6.3   0.1    3.6  3  TPR_8     Tetratricopeptide repeat
  ------ inclusion threshold ------
      0.029   14.2   1.7          5    7.1   0.1    2.8  2  TPR_10    Tetratricopeptide repeat
      0.042   14.7   0.2        1.9    9.5   0.0    2.5  2  TPR_14    Tetratricopeptide repeat
      0.048   13.9   1.3        6.1    7.1   0.1    3.4  3  ANAPC3    Anaphase-promoting complex, cyclosome, subunit 3
       0.28   11.5   4.0        8.4    6.8   0.1    3.0  3  TPR_12    Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.2    0.0009         2      11      24 ..      15      28 ..      13      29 .. 0.88
   2 ?    2.3   0.0     0.073   1.6e+02       4      21 ..     192     209 ..     189     211 .. 0.88
   3 !    5.3   0.0    0.0083        19       2      22 ..     223     243 ..     222     244 .. 0.89
   4 ?   -3.0   0.0       3.6   8.1e+03      13      21 ..     485     493 ..     483     495 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0009
                                       HHHTT-HHHHHHHH CS
                              TPR_1 11 yfklgkydeAleyy 24
                                       +++lg+ydeAley 
  gene1522|gene1522|rna1522|rna1522 15 LLSLGRYDEALEYL 28
                                       689*********95 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.073
                                        HHHHHHHHHHTT-HHHHH CS
                              TPR_1   4 lynlGnayfklgkydeAl 21 
                                        +  lG++++k+++ + A+
  gene1522|gene1522|rna1522|rna1522 192 HALLGAIHLKKKDNNRAI 209
                                        778**********99998 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.0083
                                        HHHHHHHHHHHHTT-HHHHHH CS
                              TPR_1   2 kalynlGnayfklgkydeAle 22 
                                         al  l+ ay + g+y  Al 
  gene1522|gene1522|rna1522|rna1522 223 LALSTLASAYINVGDYRRALL 243
                                        58999**************95 PP

  == domain 4  score: -3.0 bits;  conditional E-value: 3.6
                                        HTT-HHHHH CS
                              TPR_1  13 klgkydeAl 21 
                                        ++g++ +A+
  gene1522|gene1522|rna1522|rna1522 485 SNGQFMQAI 493
                                        789*****9 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.4   0.1    0.0048        11      11      24 ..      15      28 ..      13      28 .. 0.87
   2 ?    2.0   0.0      0.12   2.8e+02       3      22 ..     191     210 ..     189     211 .. 0.88
   3 !    7.0   0.0    0.0031       6.9       2      22 ..     223     243 ..     222     244 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0048
                              TPR_2 11 yyklgdyeeAleaf 24
                                       ++ lg+y+eAle++
  gene1522|gene1522|rna1522|rna1522 15 LLSLGRYDEALEYL 28
                                       6789********96 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.12
                              TPR_2   3 alynlGlayyklgdyeeAle 22 
                                        ++  lG +++k++d ++A+ 
  gene1522|gene1522|rna1522|rna1522 191 IHALLGAIHLKKKDNNRAII 210
                                        5789************9985 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.0031
                              TPR_2   2 ealynlGlayyklgdyeeAle 22 
                                         al  l+ ay++ gdy +Al 
  gene1522|gene1522|rna1522|rna1522 223 LALSTLASAYINVGDYRRALL 243
                                        6999***************85 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.1     0.018        40      11      22 ..      17      28 ..      11      32 .. 0.91
   2 !   10.7   0.1   0.00019      0.43       1      21 [.     224     244 ..     224     254 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.018
                              TPR_7 11 rlGdyeeAiely 22
                                       +lG+y+eA+e++
  gene1522|gene1522|rna1522|rna1522 17 SLGRYDEALEYL 28
                                       79********96 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00019
                              TPR_7   1 aLlnLarlysrlGdyeeAiel 21 
                                        aL+ La++y ++Gdy++A+ +
  gene1522|gene1522|rna1522|rna1522 224 ALSTLASAYINVGDYRRALLY 244
                                        7999**************865 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.3   0.1    0.0059        13      11      24 ..      15      28 ..       7      33 .. 0.84
   2 ?    3.4   0.0     0.049   1.1e+02       3      22 ..     191     210 ..     189     221 .. 0.84
   3 ?    4.5   0.1     0.022        49       6      23 ..     227     244 ..     224     249 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0059
                                       HHHTT-HHHHHHHH CS
                              TPR_8 11 ylklgdyeeAkeyy 24
                                       +l+lg+y+eA ey+
  gene1522|gene1522|rna1522|rna1522 15 LLSLGRYDEALEYL 28
                                       789**********8 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.049
                                        HHHHHHHHHHHTT-HHHHHH CS
                              TPR_8   3 ayynlgsiylklgdyeeAke 22 
                                        ++ +lg i+lk++d + A+ 
  gene1522|gene1522|rna1522|rna1522 191 IHALLGAIHLKKKDNNRAII 210
                                        6789**************96 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.022
                                        HHHHHHHHTT-HHHHHHH CS
                              TPR_8   6 nlgsiylklgdyeeAkey 23 
                                         l+s+y++ gdy  A  y
  gene1522|gene1522|rna1522|rna1522 227 TLASAYINVGDYRRALLY 244
                                        69**********999766 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.1    0.0022         5      13      33 ..      16      36 ..      14      38 .. 0.87
   2 ?    5.6   0.2    0.0067        15       4      23 ..     224     243 ..     223     247 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0022
                             TPR_10 13 rqrgrydeAealleealairr 33
                                        ++grydeA+++l  +l  ++
  gene1522|gene1522|rna1522|rna1522 16 LSLGRYDEALEYLYGVLKDYE 36
                                       579**********99998887 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0067
                             TPR_10   4 slnNLanalrqrgrydeAea 23 
                                        +l+ La a+ ++g+y +A+ 
  gene1522|gene1522|rna1522|rna1522 224 ALSTLASAYINVGDYRRALL 243
                                        7999*************985 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0   0.00087       1.9       6      35 ..      10      39 ..       5      44 .. 0.86
   2 ?    2.7   0.1      0.13     3e+02       3      21 ..     224     242 ..     222     263 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00087
                             TPR_14  6 alaeallalGdpdeAiallrralalaPdda 35
                                        +++ ll lG++deA+++l  +l+++ d++
  gene1522|gene1522|rna1522|rna1522 10 WYVKELLSLGRYDEALEYLYGVLKDYEDER 39
                                       5788899*****************999876 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.13
                             TPR_14   3 allalaeallalGdpdeAi 21 
                                        al  la+a+ + Gd+++A+
  gene1522|gene1522|rna1522|rna1522 224 ALSTLASAYINVGDYRRAL 242
                                        7789*************97 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0      0.11   2.4e+02      66      79 ..      15      28 ..       3      31 .. 0.76
   2 ?    7.1   0.1    0.0027       6.1      19      63 ..     218     262 ..     189     270 .. 0.77
   3 ?    1.0   0.0      0.23   5.2e+02      34      47 ..     484     497 ..     481     507 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.11
                                       HHHTT-HHHHHHHH CS
                             ANAPC3 66 llkLkkyeeAiaaL 79
                                       ll L++y+eA+  L
  gene1522|gene1522|rna1522|rna1522 15 LLSLGRYDEALEYL 28
                                       67788888888766 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0027
                                        HH--HHHHHHHHHHHHHTT-HHHHHHHHHCTSHHHC-HHHHHHHH CS
                             ANAPC3  19 etespedayllAlclylngqykrAyellrkaklnskslgcrylfA 63 
                                         te p ++  lA ++ + g+y rA+ + +++     + ++r  +A
  gene1522|gene1522|rna1522|rna1522 218 LTEQPLALSTLASAYINVGDYRRALLYSKRYSVMMDDYESRCRYA 262
                                        5788889999******************99933333334444444 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.23
                                        HHTT-HHHHHHHHH CS
                             ANAPC3  34 ylngqykrAyellr 47 
                                        ++ngq+ +A+++l+
  gene1522|gene1522|rna1522|rna1522 484 LSNGQFMQAIHILQ 497
                                        789*********98 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.1    0.0037       8.4      15      31 ..      17      33 ..      15      42 .. 0.75
   2 ?    4.7   0.2     0.016        36       8      57 ..     194     241 ..     187     248 .. 0.65
   3 ?   -3.0   0.0       4.2   9.4e+03      17      35 ..     487     505 ..     484     507 .. 0.67

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0037
                             TPR_12 15 rlgrydeAlellekale 31
                                        lgrydeAle+l  +l 
  gene1522|gene1522|rna1522|rna1522 17 SLGRYDEALEYLYGVLK 33
                                       58888888888877665 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.016
                             TPR_12   8 nlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyra 57 
                                         l+a++++ ++   A+ +  +++++ ++ l      +a++++n g++ ra
  gene1522|gene1522|rna1522|rna1522 194 LLGAIHLKKKDNNRAIIHSIHSINLTEQPLALST--LASAYINVGDYRRA 241
                                        5888888888888888888888888844433333..66666666665544 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 4.2
                             TPR_12  17 grydeAlellekaleiarr 35 
                                        g++ +A+ +l+  +++ +r
  gene1522|gene1522|rna1522|rna1522 487 GQFMQAIHILQMIYAVKER 505
                                        6777777777777776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (690 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2390  (0.133304); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                       196  (0.010932); expected 17.9 (0.001)
Passed Fwd filter:                        58  (0.00323498); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 1.31u 0.37s 00:00:01.68 Elapsed: 00:00:00.56
# Mc/sec: 3698.94
//
Query:       gene1523|gene1523|rna1523|rna1523  [L=354]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (354 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       393  (0.0219198); expected 358.6 (0.02)
Passed bias filter:                      250  (0.0139439); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.31s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 2222.95
//
Query:       gene1524|gene1524|rna1524|rna1524  [L=46]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (46 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       232  (0.0129399); expected 358.6 (0.02)
Passed bias filter:                      217  (0.0121033); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.28s 00:00:00.66 Elapsed: 00:00:00.43
# Mc/sec: 320.26
//
Query:       gene1525|gene1525|rna1525|rna1525  [L=151]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0018   18.1   0.0     0.0044   16.9   0.0    1.6  1  UPF0086   Domain of unknown function UPF0086


Domain annotation for each model (and alignments):
>> UPF0086  Domain of unknown function UPF0086
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   2.4e-07    0.0044      26      74 ..      97     143 ..      81     150 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2.4e-07
                                        EEEEEEEEETTEEEEEECTTEEEEEESTTCEEEEEE.TTEEEEEECCCC CS
                            UPF0086  26 ikGiVvkEtkntlkivtkksrvktvpKegsvFefevkdvlevevdGsql 74 
                                        ++G+V+ E++ +l +++   r ++v K+g +F+fe k  +++ + G+ +
  gene1525|gene1525|rna1525|rna1525  97 LSGTVIGESRTALLMEC-GGRCRIVGKKGRLFHFEWK-GMKYFLVGDLM 143
                                        69***************.99****************5.66666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       297  (0.0165653); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 1164.41
//
Query:       gene1526|gene1526|rna1526|rna1526  [L=124]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.4e-05   23.2   0.0    9.4e-05   22.6   0.0    1.2  1  CBFD_NFYB_HMF  Histone-like transcription factor (CBF/NF-Y) a
    0.00018   21.8   0.0    0.00024   21.5   0.0    1.2  1  Histone        Core histone H2A/H2B/H3/H4


Domain annotation for each model (and alignments):
>> CBFD_NFYB_HMF  Histone-like transcription factor (CBF/NF-Y) and archaeal histone
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0   1.1e-08   9.4e-05      19      63 ..      39      83 ..      29      85 .. 0.89

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 1.1e-08
                                       S-B-HHHHHHHHHHHHHHHHHHHHHHHHHHCCTTSSCE-HHHHHH CS
                      CBFD_NFYB_HMF 19 rkiakdAkeliaecveefieelaseAaeickkekrKtikaehikl 63
                                        +ia+d    ia ++ +fi e+++ A  +c++e++K i++ hi l
  gene1526|gene1526|rna1526|rna1526 39 LRIARDGINAIALACGFFIAEILDLARHECEAEGKKKITPRHINL 83
                                       46*****************************************86 PP

>> Histone  Core histone H2A/H2B/H3/H4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0   2.7e-08   0.00024      73     128 ..      32      85 ..      27      88 .. 0.91

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 2.7e-08
                                        HHH.TTSSSXEEXHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTXSEEXHHHHHHHH CS
                            Histone  73 eivksekedlrisaeavlalqealEallvelfeeAnllakhaKRvTitpkDiqlAr 128
                                         +++   ++lri ++ ++a++ a+  +++e++ +A   ++   ++ itp++i l +
  gene1526|gene1526|rna1526|rna1526  32 SLKQ--TTGLRIARDGINAIALACGFFIAEILDLARHECEAEGKKKITPRHINLGM 85 
                                        5555..89********************************************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       278  (0.0155056); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.45
# Mc/sec: 831.08
//
Query:       gene1527|gene1527|rna1527|rna1527  [L=136]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.3e-14   52.2   2.0    7.3e-14   51.8   2.0    1.2  1  Forkhead        Forkhead domain
  ------ inclusion threshold ------
      0.032   14.6   0.1      0.052   13.9   0.1    1.3  1  Linker_histone  linker histone H1 and H5 family


Domain annotation for each model (and alignments):
>> Forkhead  Forkhead domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.8   2.0   8.2e-18   7.3e-14       4      83 ..      10      89 ..       8      94 .. 0.87

  Alignments for each domain:
  == domain 1  score: 51.8 bits;  conditional E-value: 8.2e-18
                                       ---HHHHHHHHHHT-TTT-B-HHHHHHHHHCC-HHHHC.C.-CCHHHHHHHHHHHHC--EEETT.-TTSS--EEE--T CS
                           Forkhead  4 pysYaaLIaqAiksspekkltLseIyefieenfpyyrt.aakkgWqnSirhnLslnkcFekvpreeeegkgslwtidp 80
                                       +++Y ++I +Ai+ssp+kklt ++I ++i+++ p     +++ +W+  ir+ Ls n  F+k+++e+ + k ++w+  p
  gene1527|gene1527|rna1527|rna1527 10 DFTYYTIIKEAILSSPHKKLTSNQIFQYIQNKHPNLFLvSNSMTWKGNIRQLLSKNPEFVKIRKEK-SAKLHYWMFVP 86
                                       589**************************9998864443779*********************865.58******999 PP

                                       THH CS
                           Forkhead 81 ese 83
                                         e
  gene1527|gene1527|rna1527|rna1527 87 RRE 89
                                       655 PP

>> Linker_histone  linker histone H1 and H5 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   5.8e-06     0.052       3      38 ..      12      49 ..      11      75 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.8e-06
                     Linker_histone  3 sykdMikeAIkalkerkGsSrqaIkkyikakykvv...d 38
                                       +y  +ikeAI +   +k +S  +I +yi++k++     +
  gene1527|gene1527|rna1527|rna1527 12 TYYTIIKEAILSSPHKKLTSN-QIFQYIQNKHPNLflvS 49
                                       6899********998887775.5*********9765332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       543  (0.0302861); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 960.87
//
Query:       gene1528|gene1528|rna1528|rna1528  [L=64]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.5e-05   24.5   1.5    1.5e-05   24.5   1.5    1.3  1  SPT_ssu-like  Small subunit of serine palmitoyltransferase-li


Domain annotation for each model (and alignments):
>> SPT_ssu-like  Small subunit of serine palmitoyltransferase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   1.5   8.2e-10   1.5e-05       1      35 [.       7      41 ..       7      51 .. 0.91

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 8.2e-10
                       SPT_ssu-like  1 knwlsrkiylyevtfglYMLepwEkflfnilifil 35
                                       k++ sr +++y   fgl+++e wE +++n +++il
  gene1528|gene1528|rna1528|rna1528  7 KRYCSRLYLRYCAEFGLSLMEEWEITIVNFCVLIL 41
                                       6899*****************************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (64 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       491  (0.0273858); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.26s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 475.63
//
Query:       gene1529|gene1529|rna1529|rna1529  [L=137]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (137 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       903  (0.0503653); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 994.64
//
Query:       gene153|gene153|rna153|rna153  [L=424]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-42  145.6   0.0    2.1e-42  144.7   0.0    1.5  1  AAA              ATPase family associated with various cellul
    4.9e-11   42.3   0.1    9.4e-11   41.3   0.1    1.5  1  AAA_lid_3        AAA+ lid domain
    1.9e-09   37.3   0.3    4.3e-09   36.2   0.3    1.6  1  Prot_ATP_ID_OB   Proteasomal ATPase OB C-terminal domain
    7.1e-06   26.1   0.1    3.6e-05   23.8   0.1    2.2  1  AAA_5            AAA domain (dynein-related subfamily)
    1.2e-05   24.6   0.0    1.9e-05   24.0   0.0    1.3  1  DUF815           Protein of unknown function (DUF815)
    1.5e-05   25.2   0.0    3.1e-05   24.2   0.0    1.5  1  AAA_2            AAA domain (Cdc48 subfamily)
    4.6e-05   23.7   0.6      0.031   14.5   0.1    2.5  2  AAA_22           AAA domain
     0.0002   21.8   0.2       0.01   16.2   0.1    2.5  2  AAA_16           AAA ATPase domain
    0.00027   20.7   0.0     0.0005   19.8   0.0    1.4  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    0.00043   19.9   0.0     0.0012   18.4   0.0    1.7  1  Prot_ATP_OB_N    Proteasomal ATPase OB N-terminal domain
    0.00081   18.8   0.1       0.15   11.4   0.0    2.4  2  ATPase           KaiC
     0.0029   16.8   0.1       0.38    9.9   0.1    2.6  2  NB-ARC           NB-ARC domain
     0.0052   16.7   0.0      0.015   15.1   0.0    1.8  1  AAA_3            ATPase family associated with various cellul
     0.0057   16.7   0.0      0.016   15.2   0.0    1.7  1  AAA_14           AAA domain
     0.0073   16.8   0.0      0.032   14.8   0.0    2.1  2  AAA_18           AAA domain
     0.0091   16.2   0.0      0.017   15.3   0.0    1.4  1  AAA_33           AAA domain
  ------ inclusion threshold ------
      0.025   14.3   0.0      0.051   13.3   0.0    1.4  1  IstB_IS21        IstB-like ATP binding protein
      0.048   12.9   0.0      0.085   12.0   0.0    1.4  1  TIP49            TIP49 P-loop domain
      0.088   12.5   0.3       0.32   10.7   0.3    2.0  1  AAA_24           AAA domain
      0.099   12.9   0.0       0.19   11.9   0.0    1.5  1  AAA_28           AAA domain
       0.11   12.2   0.0       0.57    9.9   0.0    1.9  2  Viral_helicase1  Viral (Superfamily 1) RNA helicase
       0.11   12.9   0.0       0.29   11.5   0.0    1.8  1  RNA_helicase     RNA helicase
       0.11   11.7   0.1       0.16   11.2   0.1    1.2  1  DUF2075          Uncharacterized conserved protein (DUF2075)
       0.12   11.7   0.1       0.24   10.7   0.1    1.4  1  Mg_chelatase     Magnesium chelatase, subunit ChlI


Domain annotation for each model (and alignments):
>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  144.7   0.0   2.8e-45   2.1e-42       1     131 [.     206     338 ..     206     339 .. 0.96

  Alignments for each domain:
  == domain 1  score: 144.7 bits;  conditional E-value: 2.8e-45
                                    EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH...TTC CS
                            AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksr...sgs 77 
                                    v+lyG pGtGKTllakava++++++fl+i gsel++ky+g+++k +relfk a + + psi+fiDEid+++++r   s++
  gene153|gene153|rna153|rna153 206 VILYGVPGTGKTLLAKAVANQTSATFLRIVGSELIQKYLGDGPKLVRELFKLADQYS-PSIIFIDEIDSIGEKRydsSSG 284
                                    79******************************************************9.****************987777 PP

                                    CCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
                            AAA  78 eseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieie 131
                                    +++e +r++ +Ll++ldg+++k  +v vi+atnr+d+ldpal+r gR+drkie++
  gene153|gene153|rna153|rna153 285 AQREIQRTMLELLNQLDGFDNK-PDVKVIMATNRIDSLDPALIRpGRIDRKIEFP 338
                                    8899999999***********7.66****************************97 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.3   0.1   1.3e-13   9.4e-11       1      45 []     361     405 ..     361     405 .. 0.97

  Alignments for each domain:
  == domain 1  score: 41.3 bits;  conditional E-value: 1.3e-13
                      AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrrgikeitmedfee 45 
                                    +v+l+eL++  e   G D++a+c eA+++Alr+ + ++ medf++
  gene153|gene153|rna153|rna153 361 SVNLDELVSSKEDLNGSDIKAICTEAGMNALRERRRHVCMEDFIK 405
                                    69*****************************************85 PP

>> Prot_ATP_ID_OB  Proteasomal ATPase OB C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.2   0.3   5.8e-12   4.3e-09       1      56 [.      93     147 ..      93     148 .. 0.96

  Alignments for each domain:
  == domain 1  score: 36.2 bits;  conditional E-value: 5.8e-12
                                    EEEEEEE-TTSSEEEEE-TTS-EEEEEE-GGGSSST--TTEEEEEETTTTEEEEEE CS
                 Prot_ATP_ID_OB   1 VatVsEvlddteraiVktssdeevvvslagavpremLrpgDlVavdkdtgfifEkL 56 
                                    V+t+ E++dd ++aiV t  + e++v++ + v+++ L pg +V+++ + + ++ +L
  gene153|gene153|rna153|rna153  93 VGTLEEFVDD-NHAIVSTGVGPEFYVKILSFVDKDVLEPGSTVLLNYKDNSVVGVL 147
                                    9*********.************************************999998877 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.1   4.8e-08   3.6e-05       1     136 [.     205     327 ..     205     327 .. 0.84

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 4.8e-08
                                    EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------.G-SEEEEESGGG--H CS
                          AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar.egeilvlDEveraes 79 
                                    +v+L G pGtgK+ la+ +a  + ++++ + +++      l++++   +++ +lv   ++ a + +++i+++DE++ +  
  gene153|gene153|rna153|rna153 205 GVILYGVPGTGKTLLAKAVANQTSATFLRIVGSE------LIQKYL--GDGPKLVRELFKLADQySPSIIFIDEIDSIGE 276
                                    59**************************999986......999999..67778888888877779**************9 PP

                                    HHHHHHHHHHHSSEEE..-S.SSEEE---......-EEEEEESS--.-TT-TTHHHHT CS
                          AAA_5  80 evlnsLlslleerrllleeg.gelvkaknddllerfrviatanpldrslnelspalrs 136
                                    +  +s      e ++ + e+ ++l +++n    +++ vi+++n+ d    +l+pal++
  gene153|gene153|rna153|rna153 277 KRYDSSSGAQREIQRTMLELlNQLDGFDN---KPDVKVIMATNRID----SLDPALIR 327
                                    99999999998887776665144555555...356***********....99999875 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.0   2.5e-08   1.9e-05      50     116 ..     200     271 ..     149     314 .. 0.81

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 2.5e-08
                         DUF815  50 glpannvLLwGarGtGKSslvkallneyaeegLrli..evekedlkelpklvellrerperf...ilfvDDL 116
                                     +p + v+L+G  GtGK  l ka+ n+++++ Lr++  e+ ++ l + pklv++l + + ++   i+f+D +
  gene153|gene153|rna153|rna153 200 INPPKGVILYGVPGTGKTLLAKAVANQTSATFLRIVgsELIQKYLGDGPKLVRELFKLADQYspsIIFIDEI 271
                                    367789******************************888999**********99876555443349***976 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.0   4.2e-08   3.1e-05       7     104 ..     207     298 ..     202     309 .. 0.85

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 4.2e-08
                                    EEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG----- CS
                          AAA_2   7 lllgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKihpke 84 
                                    +l g  g+Gkt+laka+a+  ++    ++ r+  sel++    + l +  +  ++  + a++    i+++DEid i +k+
  gene153|gene153|rna153|rna153 207 ILYGVPGTGKTLLAKAVANQTSA----TFLRIVGSELIQ----KYLGDGPKLVRELFKLADQYSpsIIFIDEIDSIGEKR 278
                                    4568889*************996....************....77777777777777777777777************97 PP

                                    --------HHHHHHHHHHHH CS
                          AAA_2  85 ssgadvSregVqrdLLqile 104
                                      ++   + ++qr +L +l 
  gene153|gene153|rna153|rna153 279 YDSSSGAQREIQRTMLELLN 298
                                    7777778899*******996 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.1   4.2e-05     0.031       8      29 ..     206     227 ..     201     235 .. 0.88
   2 !    7.1   0.1    0.0082       6.1      73     127 ..     245     313 ..     228     319 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4.2e-05
                         AAA_22   8 lvvtGesGtGKTtllrrlleql 29 
                                    ++++G +GtGKT+l++ +++q 
  gene153|gene153|rna153|rna153 206 VILYGVPGTGKTLLAKAVANQT 227
                                    689****************997 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0082
                         AAA_22  73 lsseellealeqalraravielliiDEaqhlr.....s.........eealeeLrsllnl.srkgvqliL 127
                                    ++   l++ l + +++++  +++ iDE++ +      s          ++le L +l  + ++ +v++i+
  gene153|gene153|rna153|rna153 245 GDGPKLVRELFKLADQYSP-SIIFIDEIDSIGekrydSssgaqreiqRTMLELLNQLDGFdNKPDVKVIM 313
                                    4555666666777777777.***********887666156778888877777776665555688888876 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1   1.3e-05      0.01      24      51 ..     203     230 ..     193     244 .. 0.80
   2 ?    2.8   0.0      0.19   1.4e+02     122     146 ..     250     278 ..     238     302 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.3e-05
                         AAA_16  24 pelvllsGesGvGKsslvrellralekd 51 
                                    p  v+l+G +G+GK+ l+++++++ +++
  gene153|gene153|rna153|rna153 203 PKGVILYGVPGTGKTLLAKAVANQTSAT 230
                                    589******************9866554 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.19
                         AAA_16 122 llkrllallsrderplvlvlDdlq.....w 146
                                    l+++l++l+ +  +p ++++D+++     +
  gene153|gene153|rna153|rna153 250 LVRELFKLADQ-YSPSIIFIDEIDsigekR 278
                                    56777788888.889*********555443 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   6.7e-07    0.0005      35      96 ..     205     274 ..     179     281 .. 0.77

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 6.7e-07
                         RuvB_N  35 hvllyGpPGlGkttlakiiakelgvk.lkitsgPvleka.gd...laalltnleek...dvlfideihrl 96 
                                     v+lyG PG Gkt lak +a++  ++ l+i  +  ++k  gd   l+  l +l ++    ++fidei  +
  gene153|gene153|rna153|rna153 205 GVILYGVPGTGKTLLAKAVANQTSATfLRIVGSELIQKYlGDgpkLVRELFKLADQyspSIIFIDEIDSI 274
                                    69*******************9988725777778888753553336666666665433379*****9876 PP

>> Prot_ATP_OB_N  Proteasomal ATPase OB N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   1.6e-06    0.0012       1      58 [.      92     150 ..      92     152 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.6e-06
                  Prot_ATP_OB_N   1 tyGtflavnsqdgtadVlvg.grrmrVavsPlvdaeeLrpGqeVlLn.EalvvVealgye 58 
                                    ++Gt+ + + +d++a V++g g ++ V++   vd + L+pG +VlLn   + vV++l+ e
  gene153|gene153|rna153|rna153  92 SVGTLEEFV-DDNHAIVSTGvGPEFYVKILSFVDKDVLEPGSTVLLNyKDNSVVGVLEGE 150
                                    589999999.8********999*************************5467889988876 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.0    0.0002      0.15      13      38 ..     179     222 ..     168     233 .. 0.73
   2 ?    5.1   0.0     0.017        12     102     154 ..     245     300 ..     224     302 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0002
                         ATPase  13 k..................gGipegrvvlitGepGtGKtifalq 38 
                                    +                   Gi   + v ++G+pGtGKt++a+ 
  gene153|gene153|rna153|rna153 179 QeikesvelpltnpelyqeMGINPPKGVILYGVPGTGKTLLAKA 222
                                    44555555555555555557888899999************975 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.017
                         ATPase 102 edleelieelaeaikeikakrvviDsitgl...ayeekeavaReilrqlvrvlkkl 154
                                     d  +l++el +  +++  + + iD i+++    y++++   Rei r++++ l++l
  gene153|gene153|rna153|rna153 245 GDGPKLVRELFKLADQYSPSIIFIDEIDSIgekRYDSSSGAQREIQRTMLELLNQL 300
                                    56678999999************999999974346667777899989998888876 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0     0.027        20     175     209 ..      68     101 ..      53     108 .. 0.73
   2 !    9.9   0.1   0.00051      0.38      23      45 ..     206     228 ..     196     321 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.027
                                    -GGCHH..CHHHHHHHHHHCTT-HHHHHHHHHHHC CS
                         NB-ARC 175 kkleekesleevakeivekckGlPlalkvlgglls 209
                                    ++ +e+e+l ++ k++ve+ +G+Pl++ +l +++ 
  gene153|gene153|rna153|rna153  68 MQEDENENLLDQ-KSMVEQMRGSPLSVGTLEEFVD 101
                                    444445445554.79************99988765 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00051
                                    EEEEESTTSSHHHHHHHHCCSHC CS
                         NB-ARC  23 valvGmgGvGKttlakqilnksd 45 
                                    v l+G +G GKt lak + n+ +
  gene153|gene153|rna153|rna153 206 VILYGVPGTGKTLLAKAVANQTS 228
                                    789***************99844 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0     2e-05     0.015       2      30 ..     206     234 ..     205     243 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2e-05
                          AAA_3   2 vllegvPGlaktllvkalakaldlefkri 30 
                                    v+l gvPG++ktll+ka+a++ +++f ri
  gene153|gene153|rna153|rna153 206 VILYGVPGTGKTLLAKAVANQTSATFLRI 234
                                    7899**********************998 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   2.1e-05     0.016       5      76 ..     206     274 ..     203     315 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.1e-05
                         AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqev 76 
                                    +++ G+  +GKT l+k ++++       +l i   +  +k l d  kl +++++++ +   +++f+DEi  +
  gene153|gene153|rna153|rna153 206 VILYGVPGTGKTLLAKAVANQTS---ATFLRIVGSELIQKYLGDGPKLVRELFKLADQYSPSIIFIDEIDSI 274
                                    899***************98877...7777777766555555554468888888744457899******988 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       3.9   2.9e+03      24      55 ..      51      80 ..      23      94 .. 0.71
   2 !   14.8   0.0   4.3e-05     0.032       1      25 [.     206     251 ..     206     334 .. 0.67

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 3.9
                         AAA_18 24 fgvnlrdvakenglllevdpealdeskrlded 55
                                   +++++ d+++ +++ll+ +++  ++++ ld++
  gene153|gene153|rna153|rna153 51 MHQKILDYLQLEESLLSMQED--ENENLLDQK 80
                                   377788888888888777777..444444443 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 4.3e-05
                         AAA_18   1 IlltGtpGvGKttlakeLskrl.gf....................g 25 
                                    ++l G+pG+GKt lak++++ + +                     +
  gene153|gene153|rna153|rna153 206 VILYGVPGTGKTLLAKAVANQTsATflrivgseliqkylgdgpklV 251
                                    79****************9986332666665444444455544444 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   2.2e-05     0.017       2      28 ..     206     234 ..     206     271 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.2e-05
                         AAA_33   2 vllvGlpGsGKstlaerllkklg..avll 28 
                                    v+l G+pG+GK+ la+ +++++   + ++
  gene153|gene153|rna153|rna153 206 VILYGVPGTGKTLLAKAVANQTSatFLRI 234
                                    7899***************9999544444 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   6.8e-05     0.051      44      71 ..     200     227 ..     179     238 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 6.8e-05
                      IstB_IS21  44 iekkenivllGpsGvGKshlaialgvea 71 
                                    i+  ++++l G +G+GK+ la a++ ++
  gene153|gene153|rna153|rna153 200 INPPKGVILYGVPGTGKTLLAKAVANQT 227
                                    5666789****************99886 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00011     0.085      51      90 ..     204     241 ..     193     256 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00011
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          TIP49  51 ravLlaGpsgtGktalaiaiskelgedvpfvalsgsevys 90 
                                    ++v+l G +gtGkt la a++++ +    f  ++gse+ +
  gene153|gene153|rna153|rna153 204 KGVILYGVPGTGKTLLAKAVANQTS--ATFLRIVGSELIQ 241
                                    89*******************9977..78*******9865 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.3   0.00043      0.32       5      22 ..     206     223 ..     203     280 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00043
                         AAA_24   5 iliyGpsgiGKTtlakel 22 
                                    +++yG +g+GKT lak  
  gene153|gene153|rna153|rna153 206 VILYGVPGTGKTLLAKAV 223
                                    789************987 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00026      0.19       2      34 ..     206     243 ..     205     260 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00026
                         AAA_28   2 ivitGgestGKTtlleaLaar....gypvv.pEaarei 34 
                                    +++ G ++tGKT l++a a++      ++v  E   ++
  gene153|gene153|rna153|rna153 206 VILYGVPGTGKTLLAKAVANQtsatFLRIVgSELIQKY 243
                                    7899***************8743334444445555544 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0       1.1   8.4e+02     109     154 ..      21      65 ..      12      93 .. 0.69
   2 ?    9.9   0.0   0.00076      0.57       3      71 ..     208     271 ..     206     274 .. 0.67

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 1.1
                Viral_helicase1 109 fllahlpsslshrvgrrttyllpsdvaeilsakvgteveversgel 154
                                     l+++ +++ s++v++  t +lp+ +  ++  + +  ++++ +++l
  gene153|gene153|rna153|rna153  21 NLRRKKQVRDSKFVPKLPTTRLPRCRLRLKMHQ-KILDYLQLEESL 65 
                                    345555666699999999999999999988888.555555555544 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00076
                Viral_helicase1   3 vhGvpGcGKStlirkllrts.liltvnrptaelltegkpklpnlsvrtvdsflmalvkstkgkililDEy 71 
                                      GvpG GK+ l + ++++    +  ++   el+ + + + p+l vr + ++  + ++     i+++DE+
  gene153|gene153|rna153|rna153 208 LYGVPGTGKTLLAKAVANQTsATFLRIVG-SELIQKYLGDGPKL-VRELFKLADQYSP----SIIFIDEI 271
                                    56***************996644444444.46666666666666.4434444444444....48888886 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00039      0.29       1      26 [.     206     231 ..     206     283 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00039
                   RNA_helicase   1 iwlyGpsgeGKStlakeLakallkkl 26 
                                    ++lyG +g+GK++lak +a++ + ++
  gene153|gene153|rna153|rna153 206 VILYGVPGTGKTLLAKAVANQTSATF 231
                                    689**************777666544 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00022      0.16       4      25 ..     206     227 ..     203     260 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00022
                        DUF2075   4 vlVtGvaGtGKtvvllnllael 25 
                                    v+  Gv+GtGKt+++ +++++ 
  gene153|gene153|rna153|rna153 206 VILYGVPGTGKTLLAKAVANQT 227
                                    6789***********9999887 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   0.00032      0.24      25      43 ..     206     224 ..     198     230 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00032
                   Mg_chelatase  25 lllvGppGsGKtmlakrlp 43 
                                    ++l+G pG+GKt+lak+++
  gene153|gene153|rna153|rna153 206 VILYGVPGTGKTLLAKAVA 224
                                    79*************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (424 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       674  (0.0375927); expected 358.6 (0.02)
Passed bias filter:                      578  (0.0322383); expected 358.6 (0.02)
Passed Vit filter:                        88  (0.00490825); expected 17.9 (0.001)
Passed Fwd filter:                        24  (0.00133861); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              24  [number of targets reported over threshold]
# CPU time: 0.57u 0.33s 00:00:00.89 Elapsed: 00:00:00.45
# Mc/sec: 2817.28
//
Query:       gene1530|gene1530|rna1530|rna1530  [L=69]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (69 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       716  (0.0399353); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 489.40
//
Query:       gene1531|gene1531|rna1531|rna1531  [L=75]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       653  (0.0364214); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.33u 0.24s 00:00:00.57 Elapsed: 00:00:00.36
# Mc/sec: 615.96
//
Query:       gene1532|gene1532|rna1532|rna1532  [L=498]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (498 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       789  (0.0440069); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.60u 0.27s 00:00:00.87 Elapsed: 00:00:00.50
# Mc/sec: 2986.84
//
Query:       gene1533|gene1533|rna1533|rna1533  [L=817]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (817 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       666  (0.0371465); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.66u 0.25s 00:00:00.91 Elapsed: 00:00:00.44
# Mc/sec: 5581.64
//
Query:       gene1534|gene1534|rna1534|rna1534  [L=651]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.9e-16   59.5   0.1    7.2e-16   58.6   0.1    1.4  1  DNA_photolyase  DNA photolyase


Domain annotation for each model (and alignments):
>> DNA_photolyase  DNA photolyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.6   0.1     4e-20   7.2e-16       1     136 [.      19     144 ..      19     159 .. 0.90

  Alignments for each domain:
  == domain 1  score: 58.6 bits;  conditional E-value: 4e-20
                                        EEEEESS---STT-HHHHHHHCTTSEEEEEEEE-HHHHTCGS-CHHHHHHHHHHHHHHHHHHHHTT--EEEEESSH CS
                     DNA_photolyase   1 vlvWfrrDlRlhDNpALaaAaasgepvipvfvldpekahklrvgaarvdfllesLadLdeeLrelgirLvvrrgdp 76 
                                        vl++ rrD R+hDN+AL +  +  +   ++f ++pe+   +  +  +++f++e+La+L+ ++r+++i++v+++   
  gene1534|gene1534|rna1534|rna1534  19 VLYLSRRDKRIHDNAALFYCYTLTD--RVIFGIKPEY---IVGNYMQRRFIAEGLAELKGACRQHNIPFVLIQ--- 86 
                                        68999***************98887..578******4...233578999**********************86... PP

                                        HHHHHHHHHHCTECEEEEE---SHHHHHHHHHHHHHHHHCTSEEEEE--SSSS-HHHHHT CS
                     DNA_photolyase  77 advlpelakelgasavvanreyepdererdeavkealrkagievesfddhtlvepgevkt 136
                                           + el++++ ++ +v+++++ ++ r+ d+++ ++++ + i++ ++d+h++v+   vk 
  gene1534|gene1534|rna1534|rna1534  87 --RIDELVRTHCIDCIVVDHSPLRYSRAVDDQLYRYCKSNCIALVRVDAHNIVPYAVVKD 144
                                        ..79**************************************************988854 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (651 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2122  (0.118356); expected 358.6 (0.02)
Passed bias filter:                      648  (0.0361426); expected 358.6 (0.02)
Passed Vit filter:                       112  (0.00624686); expected 17.9 (0.001)
Passed Fwd filter:                        50  (0.00278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 1.14u 0.37s 00:00:01.50 Elapsed: 00:00:00.53
# Mc/sec: 3709.24
//
Query:       gene1535|gene1535|rna1535|rna1535  [L=41]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (41 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       203  (0.0113224); expected 358.6 (0.02)
Passed bias filter:                      130  (0.00725082); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.29s 00:00:00.64 Elapsed: 00:00:00.45
# Mc/sec: 274.50
//
Query:       gene1536|gene1536|rna1536|rna1536  [L=894]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.9e-28   99.4   0.1    6.2e-28   97.7   0.0    1.8  2  DEAD          DEAD/DEAH box helicase
    7.2e-27   93.9   0.1    2.4e-26   92.3   0.1    1.9  1  Helicase_C    Helicase conserved C-terminal domain
    6.8e-07   29.5   0.0    1.8e-06   28.0   0.0    1.8  1  ResIII        Type III restriction enzyme, res subunit
  ------ inclusion threshold ------
      0.054   12.9   0.0       0.14   11.5   0.0    1.6  2  Mg_chelatase  Magnesium chelatase, subunit ChlI
      0.054   13.8   0.0       0.11   12.9   0.0    1.5  1  AAA_19        AAA domain
      0.075   12.5   0.1       0.14   11.6   0.1    1.3  1  AAA_7         P-loop containing dynein motor region


Domain annotation for each model (and alignments):
>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.7   0.0   2.1e-31   6.2e-28       3     172 ..     463     627 ..     461     631 .. 0.87
   2 ?   -1.8   0.0      0.76   2.3e+03      84     105 ..     766     787 ..     738     802 .. 0.69

  Alignments for each domain:
  == domain 1  score: 97.7 bits;  conditional E-value: 2.1e-31
                                        HHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHS..TTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTS CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               DEAD   3 iQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyet..kgktgpkalivePtreLaeqtlnnlkkfkkyidl 76 
                                         Q+ a++ i +g++++++a+TG+GKTl +l+p+++++  +   +++  k+l+++PtreLa q++++++k+     l
  gene1536|gene1536|rna1536|rna1536 463 LQRYAMHYIEEGKHMILRAPTGTGKTLTYLLPIVSNIE-KvfVSQRVIKMLVIVPTRELAAQIVSEVNKIST---L 534
                                        6999******************************9994.45879999***********************99...8 PP

                                        EEEEEETTSSHHHHHHHHHTTCSEEEEEHHHHHHHH.........HCTSSH.....CTTEEEEEEETHHHHHHTTT CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.........xxxxxx.....xxxxxxxxxxxxxxxxxxxx RF
                               DEAD  77 rvlliiggvaardqlskldngvdivvgtpgrlddll.........stgkln.....lsqvrflVlDEadrlldqgf 138
                                        +v ++igg ++         + ++vv+tpgrl+d l         +    +     l q++ +VlDE d++ d gf
  gene1536|gene1536|rna1536|rna1536 535 SVRMVIGGGEYG-------MDGNVVVATPGRLIDTLnryyrynhgD---AHgvhplLAQLSAIVLDEGDTMFDLGF 600
                                        89999**98883.......456788*********998888884442...3355578******************** PP

                                        HHHHHHHHHHSHHHCTTSTTTSEEEEEESSBSHH CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               DEAD 139 sdfinrilnqlpqitcdgklqrqvivlSATlpkd 172
                                        +++i ++l+q        + + q+++ SAT ++ 
  gene1536|gene1536|rna1536|rna1536 601 KQDIAAVLSQA-------HRDVQLVIASATYNRG 627
                                        ***********.......34567*******9865 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.76
                                        TSSHHHHHHHHHTTCSEEEEEH CS
                                        xxxxxxxxxxxxxxxxxxxxxx RF
                               DEAD  84 gvaardqlskldngvdivvgtp 105
                                        ++++  +l+++++gv+i+v+t 
  gene1536|gene1536|rna1536|rna1536 766 QHQRAANLAQFHAGVNILVATS 787
                                        566667777778999**99996 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.3   0.1     8e-30   2.4e-26      12     110 ..     729     823 ..     723     824 .. 0.91

  Alignments for each domain:
  == domain 1  score: 92.3 bits;  conditional E-value: 8e-30
                                        HTTTTSEEEEEESSHHHHHHHHHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSSTSTTESE CS
                         Helicase_C  12 leeeggkilifvntidrlekvklllekkgikvavlhgelpqnereeileqfnkgesdvLiatdvaerGidipkvnl 87 
                                        ++e+ +kil+fv+++++++    l ++  +  + lhg++pq +r + l+qf +  +++L+at++a+rG+ i++vnl
  gene1536|gene1536|rna1536|rna1536 729 RKEQANKILVFVKRKRTVD---ALANSLPFVLTSLHGNMPQHQRAANLAQFHA-GVNILVATSIAARGLHIQNVNL 800
                                        578899************6...554555899********************77.56******************** PP

                                        EEESSSSSSHHHHHHHHTTSSST CS
                         Helicase_C  88 VinfdlprnvtsyiqriGRtgRa 110
                                        Vin+dlp+n+++y++riGRtgR+
  gene1536|gene1536|rna1536|rna1536 801 VINYDLPDNIDEYVHRIGRTGRG 823
                                        **********************7 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0   0.0   6.1e-10   1.8e-06      22      78 ..     472     532 ..     433     591 .. 0.82

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 6.1e-10
                                        .TTSEEEEEESTTSTHHHHH.HHHHHHH-S........-EEEEESSHHHHHHHHHHGGGGT CS
                             ResIII  22 krdkrglikmaTGtGKTlva.aklierllkkgkee...kflflvprkslleqtleefkkfl 78 
                                        ++ k++++ ++TGtGKTl++ + ++ ++ k +  +   k+l++vp+++l  q  +e++k++
  gene1536|gene1536|rna1536|rna1536 472 EEGKHMILRAPTGTGKTLTYlLPIVSNIEKVFVSQrviKMLVIVPTRELAAQIVSEVNKIS 532
                                        7889****************555655555555444788****************9998876 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   4.8e-05      0.14      11     110 ..     464     559 ..     456     569 .. 0.74
   2 ?   -3.7   0.0       2.2   6.5e+03     139     185 ..     769     817 ..     767     819 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 4.8e-05
                       Mg_chelatase  11 akraleiaaaGgHnlllvGppGsGKtmlakrlpsllpplseeealevak..iasvagkkeeekllkrrpfraphhs 84 
                                        ++ a++    G+H ++l  p G+GKt+     + llp +s+ e + v++  i+ ++   ++e + +    ++   +
  gene1536|gene1536|rna1536|rna1536 464 QRYAMHYIEEGKH-MILRAPTGTGKTL-----TYLLPIVSNIEKVFVSQrvIKMLVIVPTRELAAQIVSEVNKIST 533
                                        5666666667776.77899******95.....68888888888766554215555555555656666666778889 PP

                       Mg_chelatase  85 askaalvGggskpkpGeislahnGvL 110
                                         s   ++Ggg+  + G++  a+ G L
  gene1536|gene1536|rna1536|rna1536 534 LSVRMVIGGGEYGMDGNVVVATPGRL 559
                                        9999*****************99987 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 2.2
                       Mg_chelatase 139 rakakvefparfqlvaamNpcpcgklkdkekectcs..ekeierYlskl 185
                                        ra++ ++f a + +++a+  +  g + ++ + +     +++i++Y++++
  gene1536|gene1536|rna1536|rna1536 769 RAANLAQFHAGVNILVATSIAARGLHIQNVNLVINYdlPDNIDEYVHRI 817
                                        7778888888888888888777776555544444333477777777776 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   3.5e-05      0.11       1      70 [.     464     532 ..     464     623 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.5e-05
                             AAA_19   1 qreave.alkekvllvtaGpGtGKTrv.lkhivallvelggvkp..eeillvaftgrAakelrerlaalgaeat 70 
                                        qr a++   + k++++ a+ GtGKT + l  iv+ ++++  v+    ++l++ +t+  a ++  ++     +++
  gene1536|gene1536|rna1536|rna1536 464 QRYAMHyIEEGKHMILRAPTGTGKTLTyLLPIVSNIEKV-FVSQrvIKMLVIVPTRELAAQIVSEV----NKIS 532
                                        6677775667899************87333333333333.23221279999999998666555544....2333 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   4.8e-05      0.14      26      89 ..     467     531 ..     457     535 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 4.8e-05
                              AAA_7  26 lelllknkkpvllvGptGtGKtviikd.llkkldkekylsltinfsaqtsanqlqdiiesklekr 89 
                                          ++++++k+++l  ptGtGKt++    ++++++k  ++  +i++      ++l   i s+++k 
  gene1536|gene1536|rna1536|rna1536 467 AMHYIEEGKHMILRAPTGTGKTLTYLLpIVSNIEKVFVSQRVIKMLVIVPTRELAAQIVSEVNKI 531
                                        457899*****************999889999998888888999988888888888888888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (894 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       689  (0.0384294); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.85u 0.34s 00:00:01.19 Elapsed: 00:00:00.57
# Mc/sec: 4739.47
//
Query:       gene1537|gene1537|rna1537|rna1537  [L=78]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.7e-33  114.1   0.3    1.9e-33  114.0   0.3    1.0  1  ubiquitin    Ubiquitin family
    9.7e-17   60.6   0.2    1.1e-16   60.4   0.2    1.0  1  Rad60-SLD    Ubiquitin-2 like Rad60 SUMO-like
    2.7e-06   27.7   0.1    1.1e-05   25.8   0.1    1.8  1  Ubiquitin_2  Ubiquitin-like domain
     0.0018   18.4   0.0     0.0039   17.3   0.0    1.6  1  Rad60-SLD_2  Ubiquitin-2 like Rad60 SUMO-like
     0.0019   18.5   0.0     0.0021   18.4   0.0    1.1  1  Ubiquitin_5  Ubiquitin-like domain
     0.0039   17.2   0.1        1.5    8.9   0.0    2.0  2  Ubiquitin_4  Ubiquitin-like domain
      0.005   16.7   0.0     0.0055   16.6   0.0    1.2  1  TBK1_ULD     TANK binding kinase 1 ubiquitin-like domain
  ------ inclusion threshold ------
      0.012   15.5   0.0      0.015   15.2   0.0    1.0  1  Sde2_N_Ubi   Silencing defective 2 N-terminal ubiquitin domai
      0.044   14.3   0.0      0.053   14.1   0.0    1.2  1  DUF2407      DUF2407 ubiquitin-like domain


Domain annotation for each model (and alignments):
>> ubiquitin  Ubiquitin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.0   0.3   9.7e-37   1.9e-33       1      72 []       3      74 ..       3      74 .. 0.99

  Alignments for each domain:
  == domain 1  score: 114.0 bits;  conditional E-value: 9.7e-37
                                       EEEEETTSEEEEEEEETTSBHHHHHHHHHHHHTSSGGGEEEEETTEEE-TTSBHGGHTTSTTEEEEEEESSC CS
                          ubiquitin  1 itvktldgkkitleveesdtveelKekiaekegipaeqqrLiysGkvLedertleeygiqdgstlhlvlrlr 72
                                       i+vktl+gk+itleve+sdt+ ++K ki++kegip++qqrLi++Gk+Led rtl++y++q++stlhlvlrlr
  gene1537|gene1537|rna1537|rna1537  3 IFVKTLTGKTITLEVEPSDTICDVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNVQKESTLHLVLRLR 74
                                       9********************************************************************986 PP

>> Rad60-SLD  Ubiquitin-2 like Rad60 SUMO-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.4   0.2   5.4e-20   1.1e-16       1      72 []       1      71 [.       1      71 [. 0.98

  Alignments for each domain:
  == domain 1  score: 60.4 bits;  conditional E-value: 5.4e-20
                                       EEEEEEESSS--EEEEEETTSBHHHHHHHHHHHHT----TT-EEEETTEE--TTSBGGGSS--TTEEEEEEX CS
                          Rad60-SLD  1 ikiilkgkdgkevkikVkptttvskLieayrkkkgipeeqkvrLiFDGeeLdpnstvedldiedgdtidvvi 72
                                       ++i++k+ +gk+++++V+p+ t+ +++++ ++k+gip+ +++rLiF G++L++  t+ d+ +++++t+++v+
  gene1537|gene1537|rna1537|rna1537  1 MQIFVKTLTGKTITLEVEPSDTICDVKSKIQDKEGIPP-DQQRLIFAGKQLEDGRTLSDYNVQKESTLHLVL 71
                                       89************************************.******************************996 PP

>> Ubiquitin_2  Ubiquitin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.1   5.6e-09   1.1e-05      14      80 ..      11      69 ..       1      70 [. 0.86

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 5.6e-09
                                       SEEEEEEETTSBHHHHHHHHHHHH---TTCEEEEEE.-SSSSEEECSSGCCSBCCCCT--TTEEEEE CS
                        Ubiquitin_2 14 vsserrfsksltieelKekLelitGtspasmrLqlyddkkdnevsklddddalLgsYgvkdgmrihV 80
                                       +  +  +++s+ti ++K+k++   G++p+++rL +          k  +d ++L++Y+v+  +++h 
  gene1537|gene1537|rna1537|rna1537 11 KTITLEVEPSDTICDVKSKIQDKEGIPPDQQRLIFA--------GKQLEDGRTLSDYNVQKESTLHL 69
                                       56667789**************************99........566789**************995 PP

>> Rad60-SLD_2  Ubiquitin-2 like Rad60 SUMO-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0     2e-06    0.0039      12      87 ..      10      71 ..       1      74 [. 0.71

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 2e-06
                                       S-EEEEEEEETT-BHHHHHHHHHHHS-TT-SSS--SCCCEEEEETTEEE-TTSBCCCCS-TTTTTTTS-EEEEEEE CS
                        Rad60-SLD_2 12 GsDigpvkfsdaatvaelkekviaqWPkdkeekpksvndlklilaGkiLennktlkelrlplgevkggvtvmHvvv 87
                                       G+ +  ++ ++++t+ ++k k+     +dke  p  +++ +li aGk Le+ +tl++++++        +++H+v+
  gene1537|gene1537|rna1537|rna1537 10 GK-TITLEVEPSDTICDVKSKI-----QDKEGIP--PDQQRLIFAGKQLEDGRTLSDYNVQKE------STLHLVL 71
                                       66.6667778888888888888.....4566644..34559*****************65433......3567766 PP

>> Ubiquitin_5  Ubiquitin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0     1e-06    0.0021      35      93 ..      14      73 ..       4      77 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1e-06
                        Ubiquitin_5 35 lletkLdvtgkelvskiaeefglkensiKlilngklleldktLeeQgvknnskv.mvLkl 93
                                       +le++ + t  ++ ski ++ g+  ++ +li  gk+le ++tL + +v+++s + +vL+l
  gene1537|gene1537|rna1537|rna1537 14 TLEVEPSDTICDVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNVQKESTLhLVLRL 73
                                       4555555567788999********************************999875467765 PP

>> Ubiquitin_4  Ubiquitin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.0   0.00075       1.5       1      33 [.       1      33 [.       1      37 [. 0.94
   2 !    6.8   0.0    0.0034       6.9      58      86 ..      43      70 ..      38      73 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00075
                        Ubiquitin_4  1 lkvtvkkldgeslevvvkqnatvkdLkkaierk 33
                                       +++ vk l g+++ ++v+ + t+ d+k  i+ k
  gene1537|gene1537|rna1537|rna1537  1 MQIFVKTLTGKTITLEVEPSDTICDVKSKIQDK 33
                                       7899*************************9975 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0034
                        Ubiquitin_4 58 LsfegekLkddkaklkeygirnkselsFv 86
                                       L+f g++L+ d  +l++y ++++s+l+ v
  gene1537|gene1537|rna1537|rna1537 43 LIFAGKQLE-DGRTLSDYNVQKESTLHLV 70
                                       889999986.6779************976 PP

>> TBK1_ULD  TANK binding kinase 1 ubiquitin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   2.8e-06    0.0055      19      53 ..      17      51 ..       3      71 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 2.8e-06
                           TBK1_ULD 19 ihpyntvaifqeevakqTkiaaekQellfeghrll 53
                                       ++p +t+  +  +++++  i++++Q l+f g++l 
  gene1537|gene1537|rna1537|rna1537 17 VEPSDTICDVKSKIQDKEGIPPDQQRLIFAGKQLE 51
                                       78999***************************973 PP

>> Sde2_N_Ubi  Silencing defective 2 N-terminal ubiquitin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.0   7.3e-06     0.015       2      89 ..       2      77 ..       1      77 [. 0.84

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 7.3e-06
                         Sde2_N_Ubi  2 nvlvssfdgltlpstlsltlpstatvsdlvdklserlpeslkesliLttvsnkqlllssdvslssllassadsellsl 79
                                       +++v+++ g+    t++l++  + t+ d+ +k++++      +   L  + + ql  ++  +ls++  ++++    +l
  gene1537|gene1537|rna1537|rna1537  2 QIFVKTLTGK----TITLEVEPSDTICDVKSKIQDKEGIPPDQ-QRLIFAGK-QL--EDGRTLSDYNVQKES----TL 67
                                       899****996....9999999*************998877555.45555554.66..99999****999999....9* PP

                         Sde2_N_Ubi 80 rllvrlrGGK 89
                                       +l++rlrGG+
  gene1537|gene1537|rna1537|rna1537 68 HLVLRLRGGR 77
                                       ********95 PP

>> DUF2407  DUF2407 ubiquitin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   2.6e-05     0.053      15      67 ..      14      62 ..       5      73 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.6e-05
                            DUF2407 15 eLdipdpntttvagLkqliRerlpaelasrrLrLIyaGrlLedttslasslkl 67
                                       +L+++   + t+  +k  i ++    +   + rLI+aG+ Led  +l++   +
  gene1537|gene1537|rna1537|rna1537 14 TLEVE--PSDTICDVKSKIQDKE--GIPPDQQRLIFAGKQLEDGRTLSDYNVQ 62
                                       55555..4568888999998887..66777779*************9976544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       355  (0.0198003); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.59u 0.32s 00:00:00.90 Elapsed: 00:00:00.55
# Mc/sec: 424.05
//
Query:       gene1538|gene1538|rna1538|rna1538  [L=248]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.7e-11   41.9   3.3    1.3e-10   41.0   3.3    1.5  1  Ribosomal_L30  Ribosomal protein L30p/L7e


Domain annotation for each model (and alignments):
>> Ribosomal_L30  Ribosomal protein L30p/L7e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.0   3.3   7.2e-15   1.3e-10       2      51 .]      91     140 ..      90     140 .. 0.88

  Alignments for each domain:
  == domain 1  score: 41.0 bits;  conditional E-value: 7.2e-15
                                        EEEE-S-STTS-HHHHHHHHHTT-SSTTEEEE--SSHHHHHHHHHCCCGE CS
                      Ribosomal_L30   2 fVtrirsiigvppkvrktLqlLgLrkingtvvklntpsirGmLkkVkhlV 51 
                                         V++irs i +p k +k+ +l++L+kin  v + n+ s r+mL+k +  V
  gene1538|gene1538|rna1538|rna1538  91 VVILIRSMIRMPAKLKKICELFRLKKINTLVMVRNNESNRRMLQKLRNFV 140
                                        69**************************7777777788888****88665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (248 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1775  (0.0990016); expected 358.6 (0.02)
Passed bias filter:                      740  (0.0412739); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.67u 0.37s 00:00:01.04 Elapsed: 00:00:00.55
# Mc/sec: 1353.43
//
Query:       gene1539|gene1539|rna1539|rna1539  [L=123]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.041   14.0   0.2       0.11   12.6   0.1    1.7  1  HTH_48    HTH domain in Mos1 transposase


Domain annotation for each model (and alignments):
>> HTH_48  HTH domain in Mos1 transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   6.1e-06      0.11      21      47 ..      79     105 ..      76     106 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 6.1e-06
                             HTH_48  21 ahrkickvygedvlsertvqfWFnRFk 47 
                                        + +++ k yg +v+ +++ ++ Fn Fk
  gene1539|gene1539|rna1539|rna1539  79 TLKDMKKNYGVNVVHYEERRRMFNGFK 105
                                        678899********************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (123 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       783  (0.0436723); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.50
# Mc/sec: 744.42
//
Query:       gene154|gene154|rna154|rna154  [L=193]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00018   21.4   1.9    0.00067   19.5   0.1    2.5  3  Sec20           Sec20
     0.0054   15.6   0.6     0.0068   15.3   0.6    1.2  1  DUF3573         Protein of unknown function (DUF3573)
     0.0089   16.4   0.1      0.017   15.5   0.1    1.5  1  DUF2564         Protein of unknown function (DUF2564)
  ------ inclusion threshold ------
      0.015   15.6   3.9      0.022   15.1   1.0    2.5  3  V-SNARE_C       Snare region anchored in the vesicle membrane
      0.017   15.4   0.4      0.094   13.1   0.0    2.1  2  TBCA            Tubulin binding cofactor A
       0.02   15.5   0.5      0.072   13.8   0.1    2.0  2  Cytochrom_B562  Cytochrome b562
       0.04   14.5   0.2      0.073   13.7   0.2    1.7  1  DUF4296         Domain of unknown function (DUF4296)
       0.13   12.3   0.7          1    9.5   0.1    2.5  3  CBM_X2          Carbohydrate binding domain X2
       0.24   10.8   7.3        0.3   10.5   7.3    1.1  1  NBP1            Fungal Nap binding protein NBP1
       0.25   11.9   4.6       0.45   11.1   4.6    1.4  1  DUF2408         Protein of unknown function (DUF2408)


Domain annotation for each model (and alignments):
>> Sec20  Sec20
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0       0.6   1.1e+03      58      78 ..      22      42 ..       5      48 .. 0.64
   2 ?   -0.4   0.1      0.61   1.1e+03      26      40 ..      69      83 ..      39     110 .. 0.69
   3 !   19.5   0.1   3.8e-07   0.00067      12      86 ..     114     188 ..     101     193 .] 0.88

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.6
                          Sec20 58 lvkklerrdktdkllvflalg 78
                                   +v  ++r d td  + +++lg
  gene154|gene154|rna154|rna154 22 MVFDINRDDITDMAIEISSLG 42
                                   344567777777777777776 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.61
                          Sec20 26 enleeldastkslek 40
                                   ++l+el+ + ++l++
  gene154|gene154|rna154|rna154 69 KTLNELRDQLNELNR 83
                                   344444444444444 PP

  == domain 3  score: 19.5 bits;  conditional E-value: 3.8e-07
                          Sec20  12 aisqllsqevqqSeenleeldastkslekleeeykqvedvlsrskklvkklerrdktdkllvflalglflacvvy 86 
                                    ++++ l + +    +nl++l ++ + ++k+ + ++  +d +  + k +k++  r + d+   +++l+++++ +v 
  gene154|gene154|rna154|rna154 114 RGNEKLDSIISDAVNNLDSLCKQKRIIHKTRNTLQRGKDRIGSGIKTLKSISDRYLNDYYVFMIGLAIIVFFIVV 188
                                    6788899999999****************************************************9987765543 PP

>> DUF3573  Protein of unknown function (DUF3573)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.6   3.8e-06    0.0068      38     114 ..      57     131 ..      31     156 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 3.8e-06
                        DUF3573  38 nlidkelilklqkqikelqaeinhlketknsnesaqfttysskvedsklprslldnkeskdlsqvqktsvdiltnid 114
                                    + +d e +   +k ++el+ ++n+l++ ++sn s++  +  s+v+d++l +s+   k  +   + +   +d ++n+d
  gene154|gene154|rna154|rna154  57 DEKDTERLFAYKKTLNELRDQLNELNRLRVSNASFEEISRCSEVDDEQLSESQRFYKRGN--EKLDSIISDAVNNLD 131
                                    56799999****************************************998876554332..233334444444444 PP

>> DUF2564  Protein of unknown function (DUF2564)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.1   9.7e-06     0.017      15      78 ..      48     109 ..      40     110 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 9.7e-06
                        DUF2564  15 AqkmvGqATmsmdpdqlesAtqAiedAreqlssaeehatgvdeeFleeseqlldkaehQLdEak 78 
                                    A+k +G+ T ++d + l + ++ +++ r+ql++ +++   v+++ +ee ++  +  ++QL E++
  gene154|gene154|rna154|rna154  48 AEKHIGELTDEKDTERLFAYKKTLNELRDQLNELNRLR--VSNASFEEISRCSEVDDEQLSESQ 109
                                    9*********************************9999..899999999999999999999986 PP

>> V-SNARE_C  Snare region anchored in the vesicle membrane C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       3.3   5.9e+03      40      53 ..      40      53 ..      37      55 .. 0.72
   2 ?    0.1   0.0      0.58     1e+03      27      40 ..      70      83 ..      62      95 .. 0.70
   3 ?   15.1   1.0   1.2e-05     0.022       3      65 ..     105     167 ..     103     168 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 3.3
                      V-SNARE_C 40 rarsklhnvanrlg 53
                                   +  ++l+++ +++g
  gene154|gene154|rna154|rna154 40 SLGNMLLDAEKHIG 53
                                   56788888888887 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.58
                      V-SNARE_C 27 iledLhsQretLkr 40
                                   +l++L+ Q + L+r
  gene154|gene154|rna154|rna154 70 TLNELRDQLNELNR 83
                                   55555555555555 PP

  == domain 3  score: 15.1 bits;  conditional E-value: 1.2e-05
                      V-SNARE_C   3 llresdrlknShrivdetisiGaailedLhsQretLkrarsklhnvanrlgksnsiLrsikrR 65 
                                    l  +++  k+++  +d  is ++  l++L +Q+  +  +r++l+   +r+g   ++L+si+ R
  gene154|gene154|rna154|rna154 105 LSESQRFYKRGNEKLDSIISDAVNNLDSLCKQKRIIHKTRNTLQRGKDRIGSGIKTLKSISDR 167
                                    55566677899999**********************************************976 PP

>> TBCA  Tubulin binding cofactor A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.2       0.6   1.1e+03      49      59 ..      70      80 ..      43     109 .. 0.59
   2 ?   13.1   0.0   5.2e-05     0.094      25      77 ..     115     167 ..     102     172 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.6
                           TBCA 49 vleetkamipd 59
                                    l+e +  + +
  gene154|gene154|rna154|rna154 70 TLNELRDQLNE 80
                                   22222222222 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 5.2e-05
                           TBCA  25 qearleklkadgdedeydlkkqeevleetkamipdlkkrlekavekLeellee 77 
                                     +++l+++ +d  ++  +l kq++++++t++ ++  k r+ + ++ L+++ + 
  gene154|gene154|rna154|rna154 115 GNEKLDSIISDAVNNLDSLCKQKRIIHKTRNTLQRGKDRIGSGIKTLKSISDR 167
                                    578999999999778999******************************99776 PP

>> Cytochrom_B562  Cytochrome b562
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1     4e-05     0.072       9      74 ..      17      84 ..       9     102 .. 0.83
   2 ?    0.1   0.0      0.73   1.3e+03      50      75 ..     105     130 ..      85     147 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4e-05
                 Cytochrom_B562  9 mkkalkqva.kaddaeelkkalkelraaaedakeatpsklek..dseeqkdYqeGldklidqldkaeal 74
                                   +kk l  +  + dd+++++ ++++l ++  da++    +l++  d e+  +Y++ l++l dql+++++l
  gene154|gene154|rna154|rna154 17 IKKDLMVFDiNRDDITDMAIEISSLGNMLLDAEKHIG-ELTDekDTERLFAYKKTLNELRDQLNELNRL 84
                                   666666666689********************99998.665559********************99876 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.73
                 Cytochrom_B562  50 dseeqkdYqeGldklidqldkaeala 75 
                                     se q+ Y+ G +kl + + +a + +
  gene154|gene154|rna154|rna154 105 LSESQRFYKRGNEKLDSIISDAVNNL 130
                                    56677777777777666665555444 PP

>> DUF4296  Domain of unknown function (DUF4296)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.2     4e-05     0.073      37      83 ..      85     132 ..      26     136 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4e-05
                        DUF4296  37 k.keayyeavlkkygitsaefdsSlvyYsrnpeelekiyekvedrlkk 83 
                                    + ++a  e++ +  +++++++++S ++Y r  e+l+ i+  + ++l++
  gene154|gene154|rna154|rna154  85 RvSNASFEEISRCSEVDDEQLSESQRFYKRGNEKLDSIISDAVNNLDS 132
                                    246677789999999*************************99999986 PP

>> CBM_X2  Carbohydrate binding domain X2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0         3   5.4e+03      24      34 ..       2      12 ..       1      14 [. 0.85
   2 ?    9.5   0.1   0.00058         1       2      44 ..      18      60 ..      17      62 .. 0.91
   3 ?    0.2   0.0      0.45   8.2e+02      32      61 ..     140     171 ..     106     184 .. 0.74

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 3
                                   -TT--EEEEEE CS
                         CBM_X2 24 lngntltsikn 34
                                   +n++tl +i+n
  gene154|gene154|rna154|rna154  2 FNSKTLDDIEN 12
                                   79999999987 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00058
                                   ES-SEEEEETTS----EEEEEE-TT--EEEEEETTEE--BTTT CS
                         CBM_X2  2 spsaatFdknspkqadvtvtltlngntltsikngsttLvegtD 44
                                   +++ ++Fd n ++++d+ +++   gn l + ++  ++L+  +D
  gene154|gene154|rna154|rna154 18 KKDLMVFDINRDDITDMAIEISSLGNMLLDAEKHIGELTDEKD 60
                                   667789***********************99999999999887 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.45
                                    EEETTEE--BTTTEEEET.TEE.EE-HHHHHH CS
                         CBM_X2  32 ikngsttLvegtDYtvsg.ntv.tikkeyLak 61 
                                    i +  +tL++g+D   sg +t+  i+  yL+ 
  gene154|gene154|rna154|rna154 140 IHKTRNTLQRGKDRIGSGiKTLkSISDRYLND 171
                                    44555668888887777766665677777766 PP

>> NBP1  Fungal Nap binding protein NBP1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   7.3   0.00016       0.3     101     217 ..      22     136 ..       6     154 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00016
                           NBP1 101 svFsneeqdlkrmknasenlnallp.seelksreerkklkdrilrseaFkkkllelkydkqmleqLrrgrssnkserrvs 179
                                     vF+ ++ d+++m  ++++l ++l   e++ ++  ++k  +r+    a+kk l+el+ + + l++Lr ++ s ++  r s
  gene154|gene154|rna154|rna154  22 MVFDINRDDITDMAIEISSLGNMLLdAEKHIGELTDEKDTERLF---AYKKTLNELRDQLNELNRLRVSNASFEEISRCS 98 
                                    59*****************9888876888889999999999997...8*******************9998888877756 PP

                           NBP1 180 lrnnnleeDqvvlLqkkikklesklkdlekeLeitkkk 217
                                      +++  +   +  ++ ++kl+s ++d+ ++L ++ k+
  gene154|gene154|rna154|rna154  99 EVDDEQLSESQRFYKRGNEKLDSIISDAVNNLDSLCKQ 136
                                    66666666667788999999999999999999876554 PP

>> DUF2408  Protein of unknown function (DUF2408)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   4.6   0.00025      0.45       7      98 ..       6     137 ..       4     168 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00025
                        DUF2408   7 elepiyekLvsirrsLlslaakskaeeakesee.............................vkeelkelkeeLkkiesk 57 
                                    +l  i + +v+i++ L+ +  + ++ +  +  e                              k++l+el+++L++++  
  gene154|gene154|rna154|rna154   6 TLDDIENYIVRIKKDLMVFDINRDDITDMAI-EisslgnmlldaekhigeltdekdterlfaYKKTLNELRDQLNELNRL 84 
                                    6777777888888888888777777633222.2478888888888888888888899999999****************9 PP

                        DUF2408  58 rdeegkFkseegke............vvekgqavlngLlddcfdlvedlkaqd 98 
                                    r+++  F + ++ +              ++g++ l++++ d  + ++ l +q+
  gene154|gene154|rna154|rna154  85 RVSNASFEEISRCSevddeqlsesqrFYKRGNEKLDSIISDAVNNLDSLCKQK 137
                                    99966664443322233333333333666668888888888888887777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (193 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1527  (0.0851693); expected 358.6 (0.02)
Passed bias filter:                      750  (0.0418317); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 1317.68
//
Query:       gene1540|gene1540|rna1540|rna1540  [L=224]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.9e-19   68.6   0.2    8.4e-19   67.1   0.1    1.8  2  Ribosomal_L7Ae  Ribosomal protein L7Ae/L30e/S12e/Gadd45 famil


Domain annotation for each model (and alignments):
>> Ribosomal_L7Ae  Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.14   2.5e+03      62      79 ..       6      23 ..       4      30 .. 0.83
   2 !   67.1   0.1   4.7e-23   8.4e-19      16      82 ..     111     178 ..      98     190 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.14
                                       EEESCHHHHHHHTTSSSE CS
                     Ribosomal_L7Ae 62 vkvkskkeLGelvgkkrp 79
                                       +kv++k +L  ++ kkr 
  gene1540|gene1540|rna1540|rna1540  6 LKVPDKHALTPALYKKRL 23
                                       789999999999999975 PP

  == domain 2  score: 67.1 bits;  conditional E-value: 4.7e-23
                                        EEESHHHHHHHHHTTTESEEEEETTSSSGGHHHHHHHHHHHTTEEEEEESCHHHHHHHTTSSSE.CSE CS
                     Ribosomal_L7Ae  16 lvlGlkevtkalergeaklvilAedvepeekkkllealckekevpyvkvkskkeLGelvgkkrp.vsa 82 
                                        ++ G+++vt ++e+g+aklv++A dv+p e++ +l++lc++++v y +vksk +LG++vg+k + + +
  gene1540|gene1540|rna1540|rna1540 111 VKSGIRHVTDLIEQGKAKLVLIACDVDPVEIVLFLPTLCRKMGVSYAFVKSKYDLGRIVGRKSAtTLC 178
                                        789***********************************************************884444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       544  (0.0303419); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1475.76
//
Query:       gene1541|gene1541|rna1541|rna1541  [L=597]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.099   13.0   0.6       0.23   11.8   0.1    1.9  2  DUF1772        Domain of unknown function (DUF1772)
        2.4    8.5   4.9       0.84   10.0   0.3    2.5  3  FN3_7          Fibronectin type III domain


Domain annotation for each model (and alignments):
>> DUF1772  Domain of unknown function (DUF1772)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   2.5e-05      0.23      23      87 ..     139     221 ..     111     258 .. 0.63
   2 ?   -2.5   0.1      0.64   5.7e+03      38      54 ..     492     509 ..     481     548 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.5e-05
                            DUF1772  23 l..........llkqwrrlfkrgkavfpp.lallsalafa.ylaaraasrgarllylaaaal.lllsivp.yTllv 84 
                                        l          ++++w  + ++ k++  + ++l+ +++f+ +l ++  + +a +++ + a+l ++ si+  +  ++
  gene1541|gene1541|rna1541|rna1541 139 LfivsfsclsvIATHWLCVVTKRKKMSVMsIVLTLIAGFGvLLLVKEECGTADRWL-L-ALLlFVGSIFSgFYTVF 212
                                        36666666666889999999888555555488888888885555555555555555.4.44426666776655555 PP

                            DUF1772  85 m......vP 87 
                                        m      +P
  gene1541|gene1541|rna1541|rna1541 213 MkifmeiRP 221
                                        534444444 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.64
                            DUF1772  38 vfpplallsalafa.yla 54 
                                         ++++++l++l ++ ++ 
  gene1541|gene1541|rna1541|rna1541 492 YLGTTGILTLLFYWpMVI 509
                                        366667777776665444 PP

>> FN3_7  Fibronectin type III domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.1      0.24   2.1e+03      47      71 ..      17      41 ..       3      49 .. 0.60
   2 ?   10.0   0.3   9.4e-05      0.84      50      96 ..     128     174 ..     115     175 .. 0.88
   3 ?   -3.5   0.0       1.5   1.3e+04      62      82 ..     554     573 ..     549     580 .. 0.71

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.24
                                       .SS-SEEE-EEETTEEEEEES-B-S CS
                              FN3_7 47 elevkClklekqedvyflktkkfll 71
                                       +++++ ++++k++++ +++ +++ l
  gene1541|gene1541|rna1541|rna1541 17 HNQTNHSNIKKKKKMRLMNITDVFL 41
                                       3445556666666666666666555 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 9.4e-05
                                        -SEEE-EEETTEEEEEES-B-SSS-EEEEEEETTEEEEEEEE-GGGS CS
                              FN3_7  50 vkClklekqedvyflktkkfllisdskicvklekkkktckslkitki 96 
                                         k ++l+k  d + + ++ +++i ++ +cv +++kk+ + s+++t i
  gene1541|gene1541|rna1541|rna1541 128 PKYFSLNKFSDLFIVSFSCLSVIATHWLCVVTKRKKMSVMSIVLTLI 174
                                        567899*******************************9999988866 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 1.5
                                        EEEEES-B-SSS-EEEEEEET CS
                              FN3_7  62 yflktkkfllisdskicvkle 82 
                                        +f++ +  ++++ + icv++ 
  gene1541|gene1541|rna1541|rna1541 554 HFVQLSG-MILQPTIICVEML 573
                                        5677776.6788888888764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (597 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       982  (0.0547716); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.31s 00:00:00.88 Elapsed: 00:00:00.45
# Mc/sec: 3994.83
//
Query:       gene1542|gene1542|rna1542|rna1542  [L=64]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.19   10.6   0.0        0.2   10.5   0.0    1.0  1  Dapper    Dapper


Domain annotation for each model (and alignments):
>> Dapper  Dapper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   1.1e-05       0.2     211     252 ..       7      45 ..       1      46 [. 0.82

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 1.1e-05
                             Dapper 211 lvkrsldakksasldqgadlkssevdpKyqsdLvsknGndvY 252
                                        ++k   +++k+++ld    ++++  dp +q+++v  +G++v+
  gene1542|gene1542|rna1542|rna1542   7 MYKIPRNMNKMSFLD---IINKRVSDPMFQCNFVNDSGREVF 45 
                                        556666788889999...3579999***************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (64 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       469  (0.0261587); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 457.13
//
Query:       gene1543|gene1543|rna1543|rna1543  [L=256]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       540  (0.0301188); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 1679.93
//
Query:       gene1544|gene1544|rna1544|rna1544  [L=233]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.029   14.4   0.1      0.048   13.7   0.1    1.3  1  DUF1398   Protein of unknown function (DUF1398)


Domain annotation for each model (and alignments):
>> DUF1398  Protein of unknown function (DUF1398)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   2.7e-06     0.048       8      57 ..     135     187 ..     132     216 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.7e-06
                                        HHH---HHHHHHHHHH-SSEEEEE...TTTSEEEEE-SSS-EEEEE-STT--- CS
                            DUF1398   8 ksdadfpafiqelkrlgvskYeyf...vadgnvkyvgendevvevkakrellk 57 
                                        + +++f++f  +lk+l+vs+++y+    +++n+++v+++ + +  +++++ +k
  gene1544|gene1544|rna1544|rna1544 135 RRAQNFQSFPPNLKHLKVSYFDYYescYESNNIRFVLNKLTLLMYHNEESRVK 187
                                        7899***************9999844356888888866555555444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (233 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       490  (0.02733); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1690.31
//
Query:       gene1545|gene1545|rna1545|rna1545  [L=234]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
     0.0028   18.1   7.5     0.0038   17.6   1.6    2.5  2  Enkurin     Calmodulin-binding
  ------ inclusion threshold ------
      0.051   14.0   5.9        4.9    7.6   0.1    3.1  3  FRB_dom     FKBP12-rapamycin binding domain
       0.19   10.7   0.5       0.32    9.9   0.5    1.4  1  MeaB        Methylmalonyl Co-A mutase-associated GTPase MeaB
        9.2    6.7  13.4        1.5    9.2   1.7    3.1  3  Syntaxin_2  Syntaxin-like protein


Domain annotation for each model (and alignments):
>> Enkurin  Calmodulin-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   1.6   8.5e-07    0.0038      28      96 ..      15      83 ..      10      85 .. 0.92
   2 ?    3.5   0.4     0.021        96      32      60 ..     182     218 ..     127     222 .. 0.71

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 8.5e-07
                            Enkurin 28 kkeappgmrllseeerqellegLkkkweelnkeyqslpllidtlskrqrKeklEkeLkqlEkdikllek 96
                                        ke ++g+r+ls+ee + l+ + kk+ e+++  +  ++  i+ ++k  rK + E+  ++ E+++  +++
  gene1545|gene1545|rna1545|rna1545 15 TKESKDGVRVLSKEEDKWLIGMCKKRTEHVKVLFDTISKHIEKVEKEGRKDESEASKQEYEQALLNFKS 83
                                       455689*********************************************************998876 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.021
                            Enkurin  32 p........pgmrllseeerqellegLkkkweelnke 60 
                                        +        + ++  +ee+ ++ +++ k+k++el+++
  gene1545|gene1545|rna1545|rna1545 182 KdfenelanEMVKWFPEEKAKDCVDQVKEKLTELTTN 218
                                        044444444778889999999***********99976 PP

>> FRB_dom  FKBP12-rapamycin binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.2    0.0022       9.9      28      77 ..      42      91 ..      25     101 .. 0.86
   2 ?    7.6   0.1    0.0011       4.9      32      67 ..     119     152 ..     109     158 .. 0.84
   3 ?    1.1   0.1      0.12   5.2e+02      16      51 ..     187     222 ..     178     230 .. 0.67

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0022
                            FRB_dom 28 knveamlklleplhellekgpetlreasFaqafgreLkeaeewlkkykkt 77
                                       + v+ +++++ +  e++ek+    + ++ +q++++ L + ++ +k+y+++
  gene1545|gene1545|rna1545|rna1545 42 EHVKVLFDTISKHIEKVEKEGRKDESEASKQEYEQALLNFKSETKRYSEK 91
                                       557788999999*******88888889999*****************765 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0011
                            FRB_dom  32 amlklleplhellekgpetlreasFaqafgreLkea 67 
                                        a ++++e l++ l+k  +t  e++Fa+++ +++k  
  gene1545|gene1545|rna1545|rna1545 119 AYVSTMEMLKKVLDK--KTPLEDKFAEEYDKSVKAL 152
                                        567888889999998..9*************99876 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.12
                            FRB_dom  16 gLeeAsrlyfgeknveamlklleplhellekgpetl 51 
                                         L + + ++f e+++++ ++++++   +l+++ +t 
  gene1545|gene1545|rna1545|rna1545 187 ELANEMVKWFPEEKAKDCVDQVKEKLTELTTNTNTD 222
                                        455555667777777777777777777777655555 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.5   7.2e-05      0.32     195     253 ..      24      79 ..      12      93 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 7.2e-05
                                        HCSTTBTTB--EEEEEBCCCTBSHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHH CS
                               MeaB 195 leeekekeWrpkvlktsavegeGidelvdaieehrevlkktGllekrrrerakeelrel 253
                                        +++++e++W   ++ +  ++ e ++ l+d+i++h e ++k G++++ +  +++ e   l
  gene1545|gene1545|rna1545|rna1545  24 VLSKEEDKW---LIGMCKKRTEHVKVLFDTISKHIEKVEKEGRKDESEASKQEYEQALL 79 
                                        555666667...45667789999**********************99998887775554 PP

>> Syntaxin_2  Syntaxin-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   1.7   0.00034       1.5      36     100 ..      38      95 ..      13      96 .. 0.84
   2 ?   -0.2   0.1       0.3   1.3e+03      47      86 ..     115     152 ..     108     155 .. 0.55
   3 ?    2.6   2.6     0.038   1.7e+02      26      50 ..     202     227 ..     143     231 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00034
                         Syntaxin_2  36 helieeinelikktnellkklsqldnsssdsqqklqkekLkkdfkealqeFqkiqrqyaekekqi 100
                                        ++ +e+++ l+ +++++++k+++  +++       + e  k+++++al +F++  ++y+ek +++
  gene1545|gene1545|rna1545|rna1545  38 KKRTEHVKVLFDTISKHIEKVEKEGRKD-------ESEASKQEYEQALLNFKSETKRYSEKIRNM 95 
                                        5667788888888888888888855555.......79999*********************9987 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.3
                         Syntaxin_2  47 kktnellkklsqldnsssdsqqklqkekLkkdfkealqeF 86 
                                        k t + ++ ++ l++ ++  ++   ++k ++++ ++++ +
  gene1545|gene1545|rna1545|rna1545 115 KSTIAYVSTMEMLKKVLD--KKTPLEDKFAEEYDKSVKAL 152
                                        555555555665555554..33446666666666666655 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.038
                         Syntaxin_2  26 kd.teelreklhelieeinelikktn 50 
                                        kd  ++++ekl el++++n+  ++tn
  gene1545|gene1545|rna1545|rna1545 202 KDcVDQVKEKLTELTTNTNTDDNQTN 227
                                        44456777777777777777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1943  (0.108372); expected 358.6 (0.02)
Passed bias filter:                      544  (0.0303419); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 1596.84
//
Query:       gene1546|gene1546|rna1546|rna1546  [L=297]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (297 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       471  (0.0262703); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1932.21
//
Query:       gene1547|gene1547|rna1547|rna1547  [L=148]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.056   13.5   0.3       0.11   12.6   0.3    1.4  1  BssC_TutF  BssC/TutF protein
       0.14   12.1   0.0        0.3   11.0   0.0    1.6  1  PhnA       PhnA domain


Domain annotation for each model (and alignments):
>> BssC_TutF  BssC/TutF protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.3   1.2e-05      0.11       8      37 ..     106     136 ..      98     142 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.2e-05
                          BssC_TutF   8 kfffavPedadDfepgkGD.CvrekeDekgk 37 
                                        ++ f++ +d+  fe + GD C+++  D+kg 
  gene1547|gene1547|rna1547|rna1547 106 SSLFKISKDQFGFELSNGDmCITKDMDAKGE 136
                                        5789*************************97 PP

>> PhnA  PhnA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   3.3e-05       0.3       2      31 ..     113     141 ..     112     144 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 3.3e-05
                                        B-SS--B--TTEEEEESS-EEETTTTEEE- CS
                               PhnA   2 kDsnGnvLadGDsVtvikdLkVkGssstiK 31 
                                        kD  G +L++GD   ++kd++ kG +  ++
  gene1547|gene1547|rna1547|rna1547 113 KDQFGFELSNGDM-CITKDMDAKGEHEEVR 141
                                        8999********6.799*******988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       399  (0.0222544); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 986.63
//
Query:       gene1548|gene1548|rna1548|rna1548  [L=219]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       461  (0.0257125); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1545.46
//
Query:       gene1549|gene1549|rna1549|rna1549  [L=87]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      3e-32  110.5   5.9    3.3e-32  110.4   5.9    1.0  1  Ribosomal_L37ae  Ribosomal L37ae protein family
    0.00093   19.1   4.1     0.0017   18.3   4.1    1.5  1  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
      0.009   15.4   3.1       0.18   11.3   2.7    2.8  2  zf-ribbon_3      zinc-ribbon domain
  ------ inclusion threshold ------
      0.016   15.7   9.0      0.029   14.8   1.9    3.0  3  zf-H2C2_2        Zinc-finger double domain
      0.019   15.0   5.6        1.3    9.1   0.1    2.3  2  zf-BED           BED zinc finger
      0.062   13.4   6.4       0.11   12.6   0.8    2.3  2  zf-Sec23_Sec24   Sec23/Sec24 zinc finger
      0.096   13.6   1.7        4.4    8.4   0.1    2.7  2  zf-C2H2_4        C2H2-type zinc finger
      0.099   12.8   3.0       0.18   11.9   1.8    1.9  2  Zn-ribbon_8      Zinc ribbon domain
       0.78    9.7   6.8        2.6    8.0   1.7    2.3  2  PyrI_C           Aspartate carbamoyltransferase regulatory ch
       0.85    9.4   5.8        2.7    7.8   5.8    1.8  1  Rubredoxin_2     Rubredoxin metal binding domain
          2    8.7   6.9         12    6.3   6.9    2.0  1  Prim_Zn_Ribbon   Zinc-binding domain of primase-helicase


Domain annotation for each model (and alignments):
>> Ribosomal_L37ae  Ribosomal L37ae protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.4   5.9     2e-35   3.3e-32       1      83 [.       4      86 ..       4      87 .] 0.97

  Alignments for each domain:
  == domain 1  score: 110.4 bits;  conditional E-value: 2e-35
                                       XXXXXX-GGGGTTSS-HHHHHHHHHHHHHHHS-BEESSSSSSEEEEEETTEEEETTTTEEEE-BSSSSS-HHHHHHHH CS
                    Ribosomal_L37ae  1 rtkkvgiaGkygtrYGaslrkrvkkieisqhakytCpfcgktkvkRkavgiwkCkkcgktvaGgAytpettsaktvks 78
                                       r kkvgi+Gk+g+rYG+slrkr+k ++ ++++ky+Cpfcgk++v+++a+g+wkCk+c+k++ Gg yt+et+ + t+k+
  gene1549|gene1549|rna1549|rna1549  4 RIKKVGITGKFGVRYGSSLRKRAKICMDQKKKKYECPFCGKSNVRWQAIGLWKCKSCEKVMSGGGYTFETPLHCTIKQ 81
                                       579*************************************************************************** PP

                                       -XXXX CS
                    Ribosomal_L37ae 79 airrl 83
                                       +++r+
  gene1549|gene1549|rna1549|rna1549 82 TLSRT 86
                                       *9986 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   4.1     1e-06    0.0017      19      45 ..      37      62 ..      28      63 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1e-06
                      Zn_Tnp_IS1595 19 fvCPhCgsrkayriktrglfqCkeCrk 45
                                         CP+Cg++ ++  ++ gl++Ck+C k
  gene1549|gene1549|rna1549|rna1549 37 YECPFCGKSNVR-WQAIGLWKCKSCEK 62
                                       57*****77443.44458*******86 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.29   4.7e+02       9      19 ..      19      29 ..      19      30 .. 0.87
   2 !   11.3   2.7   0.00011      0.18       2      24 ..      36      62 ..      35      64 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.29
                        zf-ribbon_3  9 GaplssddnvC 19
                                       G+ l++++++C
  gene1549|gene1549|rna1549|rna1549 19 GSSLRKRAKIC 29
                                       77779****** PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00011
                        zf-ribbon_3  2 tvrCPnCGa.plssddn...vCpyCGt 24
                                       +++CP CG+ +++ +++   +C++C +
  gene1549|gene1549|rna1549|rna1549 36 KYECPFCGKsNVRWQAIglwKCKSCEK 62
                                       689******999888876667777766 PP

>> zf-H2C2_2  Zinc-finger double domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   1.9   1.8e-05     0.029      11      23 ..      33      45 ..      30      45 .. 0.87
   2 ?    3.8   0.1     0.053        86      15      22 ..      55      62 ..      52      64 .. 0.87
   3 ?   -0.3   0.1       1.1   1.8e+03      11      17 ..      71      77 ..      70      79 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.8e-05
                          zf-H2C2_2 11 gekpyeCplCdka 23
                                       ++k+yeCp+C+k+
  gene1549|gene1549|rna1549|rna1549 33 KKKKYECPFCGKS 45
                                       5788*******96 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.053
                          zf-H2C2_2 15 yeCplCdk 22
                                       ++C++C k
  gene1549|gene1549|rna1549|rna1549 55 WKCKSCEK 62
                                       69****99 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 1.1
                          zf-H2C2_2 11 gekpyeC 17
                                        e+p++C
  gene1549|gene1549|rna1549|rna1549 71 FETPLHC 77
                                       699*999 PP

>> zf-BED  BED zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   1.8    0.0028       4.6       9      25 ..      29      45 ..      27      49 .. 0.87
   2 ?    9.1   0.1    0.0008       1.3      17      30 ..      55      68 ..      51      73 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0028
                                       ---GGSS--EETTTTEE CS
                             zf-BED  9 pvslkeqkavCryCgki 25
                                       +++ k++k +C +Cgk 
  gene1549|gene1549|rna1549|rna1549 29 CMDQKKKKYECPFCGKS 45
                                       57889**********97 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0008
                                       -EETTTTEE----S CS
                             zf-BED 17 avCryCgkilsrgg 30
                                       ++C+ C+k+ s+gg
  gene1549|gene1549|rna1549|rna1549 55 WKCKSCEKVMSGGG 68
                                       89*********993 PP

>> zf-Sec23_Sec24  Sec23/Sec24 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.8   6.5e-05      0.11      18      33 ..      31      46 ..      26      51 .. 0.87
   2 ?    3.7   0.6     0.039        63      23      31 ..      54      62 ..      47      65 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 6.5e-05
                     zf-Sec23_Sec24 18 dfggkrwiCnfCnhkn 33
                                       d+ +k++ C+fC+++n
  gene1549|gene1549|rna1549|rna1549 31 DQKKKKYECPFCGKSN 46
                                       778999*******999 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.039
                     zf-Sec23_Sec24 23 rwiCnfCnh 31
                                       +w+C  C++
  gene1549|gene1549|rna1549|rna1549 54 LWKCKSCEK 62
                                       688888875 PP

>> zf-C2H2_4  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.1    0.0027       4.4       1       9 [.      37      45 ..      37      52 .. 0.84
   2 ?    4.0   0.1     0.072   1.2e+02       1      10 [.      55      64 ..      55      74 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0027
                          zf-C2H2_4  1 fkCpiCgks 9 
                                       ++Cp+Cgks
  gene1549|gene1549|rna1549|rna1549 37 YECPFCGKS 45
                                       89****997 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.072
                          zf-C2H2_4  1 fkCpiCgksF 10
                                       +kC+ C k+ 
  gene1549|gene1549|rna1549|rna1549 55 WKCKSCEKVM 64
                                       59****9986 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.3   0.00054      0.88      21      37 ..      30      48 ..      22      51 .. 0.75
   2 ?   11.9   1.8   0.00011      0.18       6      34 ..      37      62 ..      36      65 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00054
                        Zn-ribbon_8 21 isdaplta.CPeCgs.evr 37
                                       +++++++  CP Cg+ +vr
  gene1549|gene1549|rna1549|rna1549 30 MDQKKKKYeCPFCGKsNVR 48
                                       5555566669999998876 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00011
                        Zn-ribbon_8  6 YrCeeCghefevlqsisdapltaCPeCgs 34
                                       Y+C  Cg+   ++q+i    l +C++C +
  gene1549|gene1549|rna1549|rna1549 37 YECPFCGKSNVRWQAIG---LWKCKSCEK 62
                                       *******9999***999...888****65 PP

>> PyrI_C  Aspartate carbamoyltransferase regulatory chain, metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   1.7    0.0016       2.6      27      42 ..      30      45 ..      10      52 .. 0.87
   2 ?    5.0   0.2     0.014        23      34      44 ..      55      65 ..      46      67 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0016
                                       EETTTTEEEETTT--E CS
                             PyrI_C 27 edkekvklkCkYCeke 42
                                        d++k k++C +C+k 
  gene1549|gene1549|rna1549|rna1549 30 MDQKKKKYECPFCGKS 45
                                       7899**********96 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.014
                                       EEETTT--EEE CS
                             PyrI_C 34 lkCkYCekeis 44
                                        kCk Cek++s
  gene1549|gene1549|rna1549|rna1549 55 WKCKSCEKVMS 65
                                       69******987 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   5.8    0.0016       2.7       1      21 [.      37      61 ..      37      62 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0016
                       Rubredoxin_2  1 YvCsqCGfesakwf....GrCpsCg 21
                                       Y+C  CG +  +w+    ++C+sC 
  gene1549|gene1549|rna1549|rna1549 37 YECPFCGKSNVRWQaiglWKCKSCE 61
                                       99***********55555******6 PP

>> Prim_Zn_Ribbon  Zinc-binding domain of primase-helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   6.9    0.0071        12       2      35 ..      35      66 ..      34      69 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0071
                                       EEE--TTTT-TTTEEETT....S-EEETTTTB..XX CS
                     Prim_Zn_Ribbon  2 khspCPvCGGrDrFrfddkdgrGtwfCrqCgg..gg 35
                                       k+ +CP CG     r++     G w C++C++  +g
  gene1549|gene1549|rna1549|rna1549 35 KKYECPFCGK-SNVRWQA---IGLWKCKSCEKvmSG 66
                                       789*****85.5679998...8********987744 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       693  (0.0386525); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.43
# Mc/sec: 611.71
//
Query:       gene155|gene155|rna155|rna155  [L=284]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-11   44.3   0.2    7.6e-06   25.6   0.6    2.1  2  UCH       Ubiquitin carboxyl-terminal hydrolase
     0.0027   17.3   1.3          1    8.9   1.0    2.2  2  UCH_1     Ubiquitin carboxyl-terminal hydrolase
  ------ inclusion threshold ------
        2.6    7.8   4.8        4.3    7.2   0.1    2.8  3  Scm3      Centromere protein Scm3


Domain annotation for each model (and alignments):
>> UCH  Ubiquitin carboxyl-terminal hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.6   1.3e-09   7.6e-06       1      68 [.      36     104 ..      36     120 .. 0.74
   2 !   16.7   0.0   6.9e-07    0.0041     188     245 ..     138     267 ..     103     281 .. 0.74

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 1.3e-09
                                    -EES-SSSTHHHHHHHHHHHTSHHHHHHHHTCHHCCSS.TCCCCC-.TT.TTS.TTHHHHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            UCH   1 tGlsNlGntCymnsvlQcLfsipelrdyllsleevkke.srnkkelnesnplgkkgelakalkdlfkel 68 
                                    +Gl+N    Cy+ns++Q+Lfs +++ ++l++++++++e  +n  e+ +   +gk  +l+ ++k++f ++
  gene155|gene155|rna155|rna155  36 CGLKNGMGICYLNSTMQALFSSKQFNELLTKYSSSNNEmIKNLIEIRAMMRKGKTLNLLPRYKKMFDKV 104
                                    79************************9999864443320233333355555555557888888888765 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 6.9e-07
                                    BSS-BTTS-TCS-B.................................................................. CS
                                    xxxxxxxxxxxxxx.................................................................. RF
                            UCH 188 laeekkkkteekkk.................................................................. 201
                                    la+e+++kt++ ++                                                                  
  gene155|gene155|rna155|rna155 138 LAQENYEKTKKIQSdeslkqrflrfypllrgnvdemlknglertidkksfefpkllivclwnvhsytdttcdkivcnpev 217
                                    45555555555544566666666666777777777777777777777777888888888888888888888888888888 PP

                                    ......EEEEEEEE.EES.CTTSEEEEEEEECTTTTEEEEEETTEEEEE-HH CS
                                    ......xxxxxxxx.xxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            UCH 202 ......YeLiavvv.HsG.slssGHYvayiknekngkWykydDetvkevkee 245
                                          Y+L+a+v+  +G   ++ H +a+    + ++Wy ++De ++ +k++
  gene155|gene155|rna155|rna155 218 tifgkkYRLVALVIsVKGkRFGKKHAFAIGL--RGNNWYVFNDEYIELIKNK 267
                                    888888*****76616788888888888777..7899**********99976 PP

>> UCH_1  Ubiquitin carboxyl-terminal hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   1.0   0.00017         1       2      66 ..      37      97 ..      36     163 .. 0.75
   2 !    7.4   0.0   0.00048       2.9     238     317 ..     172     258 ..     122     261 .. 0.65

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00017
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          UCH_1  2 GLEnhivnsYlNslLQvlyfipplrnlalshlakeckkehcLlcElgflfdmldkakglncqasn 66
                                   GL n +  +YlNs +Q+l+  + + +l+++      ++++ ++  l  +  m+ k+k+ln +  +
  gene155|gene155|rna155|rna155 37 GLKNGMGICYLNSTMQALFSSKQFNELLTKYS----SSNNEMIKNLIEIRAMMRKGKTLNLLPRY 97
                                   99999**************9999999877776....66777788888888888888888877665 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.00048
                                    xxxxxxxxxxxxxxxxx................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxx RF
                          UCH_1 238 nwlpleiklsldedknl................eeklkeerekakaekeikvYeLqsvvvhigdske..sghLvslvkva 299
                                    ++l++ ++ ++d+++++                ++  ++   + + +   k+Y L+++v+ ++ +    ++h  ++    
  gene155|gene155|rna155|rna155 172 EMLKNGLERTIDKKSFEfpkllivclwnvhsytDTTCDKIVCNPEVTIFGKKYRLVALVISVKGK-RfgKKHAFAIGL-- 248
                                    55566666666666555666666666666666522233333333456778999999999999944.436777776654.. PP

                                    xxxxxxxxxxxxxxxxxx RF
                          UCH_1 300 ekelerdppesqWylFND 317
                                              ++Wy+FND
  gene155|gene155|rna155|rna155 249 --------RGNNWYVFND 258
                                    ........2469*****9 PP

>> Scm3  Centromere protein Scm3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.1     0.041   2.5e+02      12      28 ..      54      72 ..      47      84 .. 0.73
   2 ?    7.2   0.1   0.00072       4.3      18      37 ..      92     110 ..      82     114 .. 0.86
   3 ?   -1.3   0.2      0.31   1.8e+03       4      16 ..     147     159 ..     145     162 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.041
                                   H..HHHHHHHHHHHHSG.. CS
                           Scm3 12 l..kkrwesifeKYeridf 28
                                   l  +k +++++ KY++ + 
  gene155|gene155|rna155|rna155 54 LfsSKQFNELLTKYSSSNN 72
                                   456899********99544 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.00072
                                    HHHHHHHSG..GGSS--B-T CS
                           Scm3  18 sifeKYeridfedqgDEIDl 37 
                                    +++ +Y++  f+++gDE D 
  gene155|gene155|rna155|rna155  92 NLLPRYKK-MFDKVGDEFDF 110
                                    67789***.9*******997 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 0.31
                                    HHHHHHHHHHHHH CS
                           Scm3   4 lreesderlkkrw 16 
                                    ++ +sde lk+r+
  gene155|gene155|rna155|rna155 147 KKIQSDESLKQRF 159
                                    56799****9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (284 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       903  (0.0503653); expected 358.6 (0.02)
Passed bias filter:                      615  (0.034302); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 1779.41
//
Query:       gene1550|gene1550|rna1550|rna1550  [L=55]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.3e-09   35.9   7.8    6.6e-09   35.3   7.8    1.3  1  DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
     0.0013   19.1   1.8     0.0015   19.0   1.8    1.1  1  zf-C4pol        C4-type zinc-finger of DNA polymerase delta
  ------ inclusion threshold ------
      0.013   15.6   4.7      0.021   15.0   4.7    1.4  1  Zn-ribbon_8     Zinc ribbon domain
      0.014   15.3   1.0      0.015   15.2   1.0    1.0  1  MCM_OB          MCM OB domain
      0.027   14.3   2.7        1.8    8.5   0.2    2.2  2  zinc_ribbon_12  Probable zinc-ribbon domain
       0.28   11.2   5.8        2.5    8.1   0.7    2.2  2  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
        1.7    9.2   7.0       0.98   10.0   1.3    2.2  2  zf-H2C2_2       Zinc-finger double domain


Domain annotation for each model (and alignments):
>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.3   7.8   2.6e-12   6.6e-09       1      30 [.      14      43 ..      14      44 .. 0.98

  Alignments for each domain:
  == domain 1  score: 35.3 bits;  conditional E-value: 2.6e-12
                                       -B-SSS--B----SSS----SSS-----B- CS
                     DNA_RNApol_7kD  1 YiCgeCgaevslkkgdpiRCkeCGhRilYK 30
                                       Y C +C++   + ++dpiRC  CG+Ri+YK
  gene1550|gene1550|rna1550|rna1550 14 YQCKDCKKLEIIGPKDPIRCGSCGCRIFYK 43
                                       9*******999******************9 PP

>> zf-C4pol  C4-type zinc-finger of DNA polymerase delta
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   1.8   5.8e-07    0.0015      33      69 ..       4      43 ..       1      44 [. 0.82

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 5.8e-07
                           zf-C4pol 33 elekklneletvCqsCaqgsl...eeevkCdsrdCpvfYe 69
                                       e +++ + ++ +C++C++ ++   ++ ++C s  C +fY+
  gene1550|gene1550|rna1550|rna1550  4 EEHDQKKMYKYQCKDCKKLEIigpKDPIRCGSCGCRIFYK 43
                                       56677788899*****7666666589*************7 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   4.7   8.1e-06     0.021       3      34 ..      11      38 ..      11      43 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 8.1e-06
                        Zn-ribbon_8  3 iYeYrCeeCghefevlqsisdapltaCPeCgs 34
                                       +Y Y+C++C+ + e++ + +   ++ C +Cg 
  gene1550|gene1550|rna1550|rna1550 11 MYKYQCKDCK-KLEIIGPKD---PIRCGSCGC 38
                                       6*********.999998644...667****95 PP

>> MCM_OB  MCM OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   1.0   5.7e-06     0.015      29      74 ..       8      51 ..       2      54 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 5.7e-06
                                       EEEEEEEEETTT-.-EEES----SB-..TTT-HHH-EEE-GGGSEE CS
                             MCM_OB 29 klkkavfeckkcgktveveleePrkCeekeCeskdpfkletekskf 74
                                       + k  +++ck+c+k + +  ++P +C   +C+ +  +kl  ++s+ 
  gene1550|gene1550|rna1550|rna1550  8 QKKMYKYQCKDCKKLEIIGPKDPIRC--GSCGCRIFYKLPKDESTQ 51
                                       557789*******976689999****..789877788888888875 PP

>> zinc_ribbon_12  Probable zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.2    0.0032       8.2      26      39 ..       8      21 ..       4      25 .. 0.87
   2 ?    8.5   0.2   0.00068       1.8      32      44 ..      31      43 ..      27      44 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0032
                     zinc_ribbon_12 26 kkkqqklrCGaCse 39
                                       +kk++k +C  C++
  gene1550|gene1550|rna1550|rna1550  8 QKKMYKYQCKDCKK 21
                                       6899********97 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00068
                     zinc_ribbon_12 32 lrCGaCsevlsfs 44
                                       +rCG+C + + ++
  gene1550|gene1550|rna1550|rna1550 31 IRCGSCGCRIFYK 43
                                       8*****9987765 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.7   0.00098       2.5      37      45 ..      13      21 ..       3      22 .. 0.86
   2 ?    6.1   0.4    0.0043        11      17      32 ..      29      44 ..      26      52 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00098
                      Zn_Tnp_IS1595 37 lfqCkeCrk 45
                                       ++qCk+C+k
  gene1550|gene1550|rna1550|rna1550 13 KYQCKDCKK 21
                                       7******97 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0043
                      Zn_Tnp_IS1595 17 ngfvCPhCgsrkayri 32
                                       +  +C  Cg+r +y++
  gene1550|gene1550|rna1550|rna1550 29 DPIRCGSCGCRIFYKL 44
                                       4568******988876 PP

>> zf-H2C2_2  Zinc-finger double domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   1.3   0.00038      0.98       8      22 ..       5      21 ..       2      22 .. 0.83
   2 ?    2.7   0.4     0.076     2e+02      11      21 ..      27      37 ..      25      41 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00038
                          zf-H2C2_2  8 kHtgekp..yeCplCdk 22
                                       +H ++k   y+C+ C+k
  gene1550|gene1550|rna1550|rna1550  5 EHDQKKMykYQCKDCKK 21
                                       5889996559*****98 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.076
                          zf-H2C2_2 11 gekpyeCplCd 21
                                       ++ p  C +C+
  gene1550|gene1550|rna1550|rna1550 27 PKDPIRCGSCG 37
                                       4569*****96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (55 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       773  (0.0431145); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.35u 0.22s 00:00:00.56 Elapsed: 00:00:00.38
# Mc/sec: 438.87
//
Query:       gene1551|gene1551|rna1551|rna1551  [L=112]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
       0.12   12.5   0.0       0.49   10.5   0.0    1.8  2  F5_F8_type_C  F5/8 type C domain


Domain annotation for each model (and alignments):
>> F5_F8_type_C  F5/8 type C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   2.7e-05      0.49       2      40 ..       8      42 ..       7      62 .. 0.85
   2 ?   -0.1   0.0     0.054   9.6e+02      94     123 ..      78     106 ..      61     109 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 2.7e-05
                                       EEESSCSSTTTGGGGGGSSSTTSSEEESSSSTTEEEEEE CS
                       F5_F8_type_C  2 itasseesgewpaaaaldGnkntaWsssssddkqwlqvd 40
                                       it ss+   e  a ++ldGn+ t Ws+s   + +++ ++
  gene1551|gene1551|rna1551|rna1551  8 ITVSSN---EKDAPKMLDGNDYTCWSPSLRAP-HYIRIN 42
                                       666777...7799*************888877.999886 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.054
                                        SEEEEEEEEEEEEEEEEEEEE.EESSSSSEE CS
                       F5_F8_type_C  94 pvtntfdppvkaryvrltpts.wnggngial 123
                                        ++++++d+ v++  v +++ + w++++++++
  gene1551|gene1551|rna1551|rna1551  78 VQVINLDEHVNG--VEIKIVDtWDPYGRVCI 106
                                        678889989988..44444444677766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       348  (0.0194099); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 818.62
//
Query:       gene1552|gene1552|rna1552|rna1552  [L=135]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       378  (0.0210832); expected 358.6 (0.02)
Passed bias filter:                      233  (0.0129957); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 1088.20
//
Query:       gene1553|gene1553|rna1553|rna1553  [L=270]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       579  (0.032294); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 2075.77
//
Query:       gene1554|gene1554|rna1554|rna1554  [L=160]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.15   11.5   0.0        3.9    6.9   0.0    2.0  2  NeuB      NeuB family
       0.18   12.0   0.0       0.36   11.1   0.0    1.5  1  RimM      RimM N-terminal domain


Domain annotation for each model (and alignments):
>> NeuB  NeuB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.0   0.00043       3.9      42      88 ..      14      60 ..       3      75 .. 0.84
   2 ?    2.7   0.0     0.008        72      48      88 ..     104     144 ..      98     152 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.00043
                                       S-HHHHHHHH---HHHHHHHHHHHHHTT-EEEEEE-SHHHHHHHHHH CS
                               NeuB 42 esqlellkklelseeehkelkeyceekgieflstpfdlesvdllesl 88
                                       e+    l++++++e +  ++ + c++ +i  +    d ++v+ l+s+
  gene1554|gene1554|rna1554|rna1554 14 ETETLTLENIKMQEGQVLKINTNCKSLKIVSFVGVLDITDVKSLRSV 60
                                       5666678999**********************************876 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.008
                                        HHHH---HHHHHHHHHHHHHTT-EEEEEE-SHHHHHHHHHH CS
                               NeuB  48 lkklelseeehkelkeyceekgieflstpfdlesvdllesl 88 
                                        l+++e++++    ++++c +  i  ++  +dl+ ++ l++l
  gene1554|gene1554|rna1554|rna1554 104 LRNVEFKYSSPLIISQKCIDLSIISCTGNYDLSRIKKLRKL 144
                                        67778888888888899999999999999999999888776 PP

>> RimM  RimM N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0     4e-05      0.36      36      78 ..      21      62 ..       5      67 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 4e-05
                                       E.ETTEEEEE-EEEEEEE.TTEEEEEETT--SHHHHHTTTT-EE CS
                               RimM 36 eakkgetreltvesvrvh.kkgvivklegvddrdaAealkgael 78
                                       e  + +++e +v +++++ k+  iv++ gv d++++++l+   l
  gene1554|gene1554|rna1554|rna1554 21 E--NIKMQEGQVLKINTNcKSLKIVSFVGVLDITDVKSLRSVVL 62
                                       3..445677889999988999******************98766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       535  (0.0298399); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 1221.59
//
Query:       gene1555|gene1555|rna1555|rna1555  [L=89]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.079   12.8   0.1      0.087   12.7   0.1    1.0  1  DUF3877   Domain of unknown function, E. rectale Gene descrip


Domain annotation for each model (and alignments):
>> DUF3877  Domain of unknown function, E. rectale Gene description (DUF3877)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   4.9e-06     0.087      73     127 ..      17      72 ..       2      80 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.9e-06
                            DUF3877  73 drfcveipeegaeyvheeikeneFlkeliellkkhectledilelFkkysk.kvvv 127
                                          +cv++  e +ey  + ++e   l el++ + ++ +++  +++ F+++++ +vv+
  gene1555|gene1555|rna1555|rna1555  17 YDLCVKLVVEVTEYLARVVRELAVLYELVTDFLHEPNQMPAVVASFTDQKNvHVVT 72 
                                        568********************************************998844444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       507  (0.0282782); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.46
# Mc/sec: 581.77
//
Query:       gene1556|gene1556|rna1556|rna1556  [L=107]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0075   16.2   0.1        1.3    9.0   0.0    2.0  2  Nucleocapsid-N  Nucleocapsid protein N


Domain annotation for each model (and alignments):
>> Nucleocapsid-N  Nucleocapsid protein N
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.0   7.2e-05       1.3      89     137 ..       6      56 ..       2      61 .. 0.86
   2 !    5.5   0.1    0.0008        14     132     156 ..      75      99 ..      59     103 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 7.2e-05
                     Nucleocapsid-N  89 nqpspnvpfeqqllmmanetayaatyppemqnv..aptklvkiakraamqi 137
                                        n  s ++p+e++++   n++a a    p++ +v  +  k+vki+k++ +++
  gene1556|gene1556|rna1556|rna1556   6 NTLSNKLPLEDDVVERFNKSAAALNERPDLSKVfsSGNKVVKISKKSNVDL 56 
                                        6778999************************9933457*******998876 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0008
                     Nucleocapsid-N 132 raamqivsghatveisngtedsnkr 156
                                        + a ++   +a +eis+gte  +k 
  gene1556|gene1556|rna1556|rna1556  75 KGAERVEQNKAQIEISDGTEANQKT 99 
                                        5677788899**********87775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       571  (0.0318478); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.48
# Mc/sec: 674.04
//
Query:       gene1557|gene1557|rna1557|rna1557  [L=117]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       248  (0.0138323); expected 358.6 (0.02)
Passed bias filter:                      219  (0.0122148); expected 358.6 (0.02)
Passed Vit filter:                         4  (0.000223102); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 874.82
//
Query:       gene1558|gene1558|rna1558|rna1558  [L=70]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (70 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       248  (0.0138323); expected 358.6 (0.02)
Passed bias filter:                      179  (0.00998383); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.28s 00:00:00.65 Elapsed: 00:00:00.44
# Mc/sec: 477.54
//
Query:       gene1559|gene1559|rna1559|rna1559  [L=95]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       929  (0.0518155); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.30s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 690.50
//
Query:       gene156|gene156|rna156|rna156  [L=151]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       615  (0.034302); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 1096.16
//
Query:       gene1560|gene1560|rna1560|rna1560  [L=136]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       499  (0.027832); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 962.11
//
Query:       gene1561|gene1561|rna1561|rna1561  [L=404]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0015   18.7   0.0      0.059   13.6   0.0    3.8  3  FNIP      FNIP Repeat


Domain annotation for each model (and alignments):
>> FNIP  FNIP Repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.1      0.12   2.1e+03      11      19 ..      17      25 ..      15      31 .. 0.82
   2 ?   -3.1   0.0      0.54   9.6e+03      17      23 ..      56      62 ..      55      64 .. 0.57
   3 !   13.6   0.0   3.3e-06     0.059      11      44 .]     253     322 ..      97     322 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.12
                               FNIP 11 PsnleiLil 19
                                       P+ +eiLil
  gene1561|gene1561|rna1561|rna1561 17 PPTIEILIL 25
                                       888999999 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 0.54
                               FNIP 17 LilgrdF 23
                                       L++++++
  gene1561|gene1561|rna1561|rna1561 56 LKFNQEC 62
                                       6666554 PP

  == domain 3  score: 13.6 bits;  conditional E-value: 3.3e-06
                               FNIP  11 P...................................snleiLilgrdF.nqkiligsLPnSlkeLyFgyf 44 
                                        P                                   +++++L l ++  + ++ +++LP +l++L+F +f
  gene1561|gene1561|rna1561|rna1561 253 PcqletleimdrniykdlfinlrkldwktvqllrkhKSIKHLVLDKSImKYEHIFNCLPVKLESLKFKKF 322
                                        35555555555555555555555555555555555589******7776377888*************876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (404 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       545  (0.0303977); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 2610.44
//
Query:       gene1562|gene1562|rna1562|rna1562  [L=1254]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.1e-39  135.2   0.2    5.6e-39  134.3   0.2    1.3  1  CPSF_A    CPSF A subunit region
  ------ inclusion threshold ------
      0.019   14.6   0.0       0.18   11.5   0.0    2.5  2  YcxB      YcxB-like protein


Domain annotation for each model (and alignments):
>> CPSF_A  CPSF A subunit region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  134.3   0.2   6.3e-43   5.6e-39      14     255 ..     931    1172 ..     923    1175 .. 0.91

  Alignments for each domain:
  == domain 1  score: 134.3 bits;  conditional E-value: 6.3e-43
                                         -EEEEE--TTEEEEEEEE--B-SSTTT---B--EEEEEEE---SSS--E.EEEEEEEEEE-......SS--EEE CS
                             CPSF_A   14 eidsleLeenEavlsvksvelessettkekkellvVGtafnlgedpaarsGrilvfeiiev......petnrkL 81  
                                         +++ + L +nE+v+++k ++l +s++  + ++++vV  ++  + ++  r Grilvfe+i+v       +t++ L
  gene1562|gene1562|rna1562|rna1562  931 RLSIFRLPKNELVTDLKIMSLCDSNG--DHNDFVVVVLSQRTSNEI-LR-GRILVFEVIDVisdtadRKTKKAL 1000
                                         566799***************98776..5579****9**9999999.99.*****************999**** PP

                                         EEEEEEEEES----EEEETTEEEEE-SSEEEEEEE-TTS-EEEEEEEE-SS-EEEEEEETTEEEEEESSS-EEE CS
                             CPSF_A   82 klvhkeevkgavtalaefqGrllvgvgqkvrvydlgedktLlrkafldtqlyvvslkvlgnriivgDlmkSvtf 155 
                                         kl+ +e++kg+++++a ++Gr++v++   ++vy++++++ +++ af+d  +y+vsl v++n+i+vgD+m +++f
  gene1562|gene1562|rna1562|rna1562 1001 KLLGSERTKGPISCCAAVRGRIAVSLATRLMVYEFDRNTGIVAIAFYDLYMYAVSLAVIKNYIVVGDIMMGLHF 1074
                                         ************************************************************************** PP

                                         EEE-SSS--EEEEEEESS---EEEEEEE--SSS.EEEEEETTSEEEEEE--TTSGGGTTTT.EEEEEEEEE-SS CS
                             CPSF_A  156 veydeenyklilfardtqkrwvtaaeflvdged.tvlvaDkfgnlfvlrydpeasessdgdprleeraefhlge 228 
                                         v +++e+ kl+l++++    +  +++f   g++ ++ + Dk g + ++ + p +  s++g+ +l +r +f +  
  gene1562|gene1562|rna1562|rna1562 1075 VYFQSEPVKLHLLSKSGRVANLGSLDFFNAGDRlFITGIDKTGEVQIFSFSPGNLYSNEGE-KLVKRQQFETYA 1147
                                         ****************************88878999999**********************.************ PP

                                         ----E...EEEE.SSS--S-EEEEEE- CS
                             CPSF_A  229 ivtslrkgslvpgeaesssspqllyat 255 
                                         +  s+r  +  +    s+ s+q +++t
  gene1562|gene1562|rna1562|rna1562 1148 HFQSIRTNTYRS--YASFFSSQNFFVT 1172
                                         *99994443222..2223456666666 PP

>> YcxB  YcxB-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   2.1e-05      0.18       4      44 ..     299     340 ..     297     344 .. 0.83
   2 ?   -1.0   0.0      0.16   1.5e+03      20      33 ..     820     833 ..     808     833 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 2.1e-05
                               YcxB   4 dgiev.dsgggesiipWdsiekvkEtkdyfyLflsggsafii 44 
                                        ++i+  ++g ++s  +++si +v E  ++++L l++ +a+++
  gene1562|gene1562|rna1562|rna1562 299 QHIQSvSTGVQRSFHQYESIRRVFEANHFLFLVLEDRTALLL 340
                                        5676635666777788********************999876 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.16
                               YcxB  20 dsiekvkEtkdyfy 33 
                                        +s+e+v+E+ d +y
  gene1562|gene1562|rna1562|rna1562 820 NSFECVVEDADAIY 833
                                        699********998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       568  (0.0316805); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.77u 0.30s 00:00:01.07 Elapsed: 00:00:00.46
# Mc/sec: 8278.25
//
Query:       gene1563|gene1563|rna1563|rna1563  [L=571]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.5e-86  287.2   4.8    8.8e-86  286.5   4.8    1.3  1  Beta_lactamase3  Putative beta-lactamase-like family
  ------ inclusion threshold ------
      0.056   13.5   0.2       0.23   11.6   0.0    2.0  2  Ribonuclease_P   Ribonuclease P


Domain annotation for each model (and alignments):
>> Beta_lactamase3  Putative beta-lactamase-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  286.5   4.8   9.8e-90   8.8e-86       1     213 [.      14     217 ..      14     218 .. 0.99

  Alignments for each domain:
  == domain 1  score: 286.5 bits;  conditional E-value: 9.8e-90
                    Beta_lactamase3   1 MalvklsilkeksyylleteeesllfdypseiygknfrlgtfekrkkklkleiikvkaenidkifvtssnslgifF 76 
                                        M ++k++++ke+s+++++ ++++++fdyp+eiygkn+r+g+        k+++ikvk++n++kif++s+n+lgifF
  gene1563|gene1563|rna1563|rna1563  14 MPAIKFTRCKENSFLSMDLHNDRIQFDYPAEIYGKNHRIGD--------KPILIKVKPVNAKKIFISSNNALGIFF 81 
                                        99***************************************........99************************* PP

                    Beta_lactamase3  77 lkkdvpiYiTkpvYeqlllrlkellslqvvyeeeeekqdlkiveeidierlkrnvkfiryneliyfddltieakaa 152
                                        +kk+vpiYiT+pvYeql+lrl+el+++ v+y++e++k+dl++v++++i++++rn++fi+yne++yfd++++ea+++
  gene1563|gene1563|rna1563|rna1563  82 MKKNVPIYITRPVYEQLVLRLRELQGYLVNYDDEHDKTDLRSVNDANITKAERNIIFITYNEITYFDTFMVEAVSS 157
                                        **************************************************************************** PP

                    Beta_lactamase3 153 gtflGWvnyllevekkkilayisslslkkklslemkpiksdvlllnvnqlktkentiddfs 213
                                        +tflGW+n++l+v+++k lay+s++slk+++s++m+p+k++v+++n++q++t+ +++ddf+
  gene1563|gene1563|rna1563|rna1563 158 NTFLGWSNFILHVQNRK-LAYVSTFSLKGRISFKMEPTKLHVIIYNQRQINTHGHNLDDFL 217
                                        *****************.******************************************7 PP

>> Ribonuclease_P  Ribonuclease P
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0      0.42   3.7e+03      15      52 ..      44      85 ..      43      87 .. 0.73
   2 ?   11.6   0.0   2.5e-05      0.23      54      73 ..     527     547 ..     522     554 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.42
                     Ribonuclease_P 15 avfregkrvaskdlvlyalknsleks.....slrlGlsvskkv 52
                                       +++ + +r++ k++++ +++  ++k+     +  lG+   kk+
  gene1563|gene1563|rna1563|rna1563 44 EIYGKNHRIGDKPILIKVKPV-NAKKifissNNALGIFFMKKN 85
                                       578889999999999999994.333346666667888888887 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 2.5e-05
                     Ribonuclease_P  54 k.AvvRNrikRllReafrlnk 73 
                                        + A +RNr+kR++Re+++l  
  gene1563|gene1563|rna1563|rna1563 527 RlACTRNRLKRMFRETYYLYD 547
                                        5599************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (571 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       557  (0.031067); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.26s 00:00:00.82 Elapsed: 00:00:00.43
# Mc/sec: 3960.98
//
Query:       gene1564|gene1564|rna1564|rna1564  [L=352]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      4e-13   49.6   0.1    9.8e-13   48.3   0.0    1.7  2  CLP1_P    mRNA cleavage and polyadenylation factor CLP1 P-loo
    2.1e-10   40.7   0.0    3.8e-10   39.8   0.0    1.4  1  CLP1_N    N-terminal beta-sandwich domain of polyadenylation 
    6.9e-07   29.7   0.0    1.4e-06   28.8   0.0    1.5  1  Clp1      Pre-mRNA cleavage complex II protein Clp1


Domain annotation for each model (and alignments):
>> CLP1_P  mRNA cleavage and polyadenylation factor CLP1 P-loop
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.3   0.0   1.6e-16   9.8e-13       5      92 ..      95     180 ..      92     207 .. 0.90
   2 ?   -1.6   0.0      0.34   2.1e+03     140     188 .]     199     245 ..     183     245 .. 0.61

  Alignments for each domain:
  == domain 1  score: 48.3 bits;  conditional E-value: 1.6e-16
                             CLP1_P   5 sGKSTlarlLlNyalrkgrkpvyvDlDvGqseispPgtislalverpidveegfsldaplvyffGdtspsdnpsly 80 
                                         G+ T+ ++L+N ++r+g+k+++ ++D+ q+ +  Pg+++ +lve+ +  +++++++ +l yf+Gdt + +n ++y
  gene1564|gene1564|rna1564|rna1564  95 HGRCTFLQTLCNLCVRMGKKVLISEIDPAQGFLVFPGVMGTMLVENLVCYDDDVQNE-KLCYFYGDTEI-KNREYY 168
                                        6999********************************************999998766.599*******9.577889 PP

                             CLP1_P  81 lalvkelareve 92 
                                          l ++++++++
  gene1564|gene1564|rna1564|rna1564 169 DMLSSKVLSHTK 180
                                        998888888877 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.34
                             CLP1_P 140 eellnelkrdlplskvkvvklpkspgvvqrsreerrelreerireYFyg 188
                                        e ++n++    + + ++++k++  ++ v+   +++++  ++ i +YF+g
  gene1564|gene1564|rna1564|rna1564 199 ESSDNFVVVGDE-RMFHTIKSRN-KEFVPCHGYTKKAKTNALIYNYFHG 245
                                        444444444444.4444444444.4445777788888888889999986 PP

>> CLP1_N  N-terminal beta-sandwich domain of polyadenylation factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.8   0.0   6.4e-14   3.8e-10       2      75 ..       7      76 ..       6      89 .. 0.84

  Alignments for each domain:
  == domain 1  score: 39.8 bits;  conditional E-value: 6.4e-14
                                       E-TTEEEEEEE-SSS-EEEEEEEE--EETTEE--TT-EEEE-TT-EEEEEESS-EEEEEES-EEEEEEES--SH CS
                             CLP1_N  2 LekeselrfeveskeklkikllsGtaEifGtELaknkeytfskgtkfaiftwegcklevkgeaeseyvseetpm 75
                                       +++ +elr+e  ++ + ++++++G+ +i G+EL+ +++ytf+   ++   t++gc++e++ + + +y+s+ +++
  gene1564|gene1564|rna1564|rna1564  7 VPALHELRLETGKT-PATLRVVTGSLDILGQELLTDHPYTFT--GTLFFTTFHGCTVELNDDIALQYTST-SNI 76
                                       56789*****9987.6**************************..46778999*******99999999985.444 PP

>> Clp1  Pre-mRNA cleavage complex II protein Clp1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.8   0.0   2.3e-10   1.4e-06      11     115 ..     257     349 ..     251     351 .. 0.76

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 2.3e-10
                                        TS-EEEEE-.------------.------TS-EEEE-.--GGGTTEEEEEESSSS....TCCTT--EEEEEEEEEE CS
                               Clp1  11 ddlsiyrvgeeeaapssalPigeeekeseetklekveepsselqnsilavsqasakdseeevldssvlGFvyVtev 86 
                                        + l+iy vge+   p+salP+g +++  ++++   v++p+s+ q si+a+s+a++   eeev   +v+GFv++ +v
  gene1564|gene1564|rna1564|rna1564 257 ERLRIYSVGEKFVPPTSALPLG-AQR--KMNTC--VATPTSAEQDSIVAISYAKD---EEEVGVRPVAGFVLIRSV 324
                                        6799******************.343..33333..44467889*********977...8**************999 PP

                                        ETTTTEEEEEESSSS.-S-SEEEEEEEE- CS
                               Clp1  87 deekkkltvLsPvpgrlpskalilgslkw 115
                                              lt+L+ + +   +   + g++k+
  gene1564|gene1564|rna1564|rna1564 325 Q----PLTFLCAQTTVSKDALYVQGNIKY 349
                                        4....566666666555555556666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (352 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       354  (0.0197445); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 2485.50
//
Query:       gene1565|gene1565|rna1565|rna1565  [L=946]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (946 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       624  (0.0348039); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.66u 0.26s 00:00:00.92 Elapsed: 00:00:00.43
# Mc/sec: 6617.76
//
Query:       gene1566|gene1566|rna1566|rna1566  [L=104]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-41  141.4   8.7    1.4e-41  141.3   8.7    1.0  1  Ribosomal_S26e  Ribosomal protein S26e


Domain annotation for each model (and alignments):
>> Ribosomal_S26e  Ribosomal protein S26e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  141.3   8.7   7.9e-46   1.4e-41       2      96 ..       7     101 ..       6     104 .] 0.97

  Alignments for each domain:
  == domain 1  score: 141.3 bits;  conditional E-value: 7.9e-46
                                        --S-SSTT----S-S---EEE-TTT--EEES----EEEEEEESS-SSSHHHHTTSBSSSS----EEEEEEE--HHH CS
                     Ribosomal_S26e   2 tkKRrnngrnkkgrghvkivrCsncarlvpkdKaikrfvvrniveaaavrdlseasvyeeyalPklYiklaycvsc 77 
                                         kKRrnngr+kk+rgh   +rC+ncar+vpkdK i +++v+n+++aaa+ d++ asvy++y++Pk+Yikl+ycvsc
  gene1566|gene1566|rna1566|rna1566   7 EKKRRNNGRSKKNRGHPGNIRCDNCARMVPKDKCIVKYQVKNLIDAAAADDIRMASVYDTYEVPKTYIKLQYCVSC 82 
                                        58************************************************************************** PP

                                        HHHTTSS----TTTTS--S CS
                     Ribosomal_S26e  78 aihskvvrvRsredrknre 96 
                                        a+hs++vrvRs+ +rk+r 
  gene1566|gene1566|rna1566|rna1566  83 AVHSRLVRVRSHWERKIRG 101
                                        ****************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       765  (0.0426683); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 718.16
//
Query:       gene1567|gene1567|rna1567|rna1567  [L=51]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (51 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       756  (0.0421663); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.45
# Mc/sec: 338.41
//
Query:       gene1568|gene1568|rna1568|rna1568  [L=907]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (907 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       915  (0.0510346); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.68u 0.27s 00:00:00.95 Elapsed: 00:00:00.44
# Mc/sec: 6138.43
//
Query:       gene1569|gene1569|rna1569|rna1569  [L=151]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.076   12.9   0.0       0.13   12.2   0.0    1.4  1  DUF3746   Protein of unknown function (DUF3746)


Domain annotation for each model (and alignments):
>> DUF3746  Protein of unknown function (DUF3746)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   7.3e-06      0.13       8      25 ..      84     101 ..      83     104 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 7.3e-06
                            DUF3746   8 LkvttsskKktCkKhifd 25 
                                        Lk++ s++ ++C+K+++ 
  gene1569|gene1569|rna1569|rna1569  84 LKDILSCGSSYCRKAAYE 101
                                        9***************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       353  (0.0196888); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 1063.74
//
Query:       gene157|gene157|rna157|rna157  [L=241]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.9e-11   42.1   1.4    1.3e-10   41.0   1.4    1.6  1  TBCC      Tubulin binding cofactor C
  ------ inclusion threshold ------
          2    8.5   6.4        3.5    7.7   2.0    2.4  2  YokU      YokU-like protein, putative antitoxin
        3.2    9.0   6.7        1.3   10.3   0.1    2.6  2  DUF2971   Protein of unknown function (DUF2971)


Domain annotation for each model (and alignments):
>> TBCC  Tubulin binding cofactor C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.0   1.4   2.2e-14   1.3e-10       3      93 ..     126     214 ..     124     230 .. 0.87

  Alignments for each domain:
  == domain 1  score: 41.0 bits;  conditional E-value: 2.2e-14
                                    EEEE-S-BS-EEEE-S--S-EEEES-BS-EEE----SS-EEEES-BS-EEE---SEEEEES-BS-EEE---SSEEEEES- CS
                           TBCC   3 svkisnlsdctiylldplssvtiddcknctivlgpvsgsvfiedcenctivvacrqlrihdctnvdvylltksrPiieds 82 
                                    +v i+n+++ +i l  +++++t++ c+n +i+ + vs+s+fied++++t+ +++ q+r+ +c n++++++tks   ie+s
  gene157|gene157|rna157|rna157 126 KVCITNMHKGQI-LAFDCDELTLKSCNNLNIT-ANVSDSIFIEDVRDSTLKINAGQIRLLNCGNMRLVVYTKSGISIEKS 203
                                    677999999997.5589***********9986.68********************************************* PP

                                    BSEEEE----- CS
                           TBCC  83 kgirfapynls 93 
                                    ++i + + +++
  gene157|gene157|rna157|rna157 204 EQIIIEEWKIQ 214
                                    ***99875544 PP

>> YokU  YokU-like protein, putative antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   2.0   0.00059       3.5      39      83 ..       5      49 ..       3      55 .. 0.85
   2 ?    2.5   0.2     0.024   1.4e+02      10      71 ..     156     218 ..     146     228 .. 0.66

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00059
                           YokU 39 seCglvyqeeevvkeiedqllLvdtkklpesityeeLmkkerlLk 83
                                   ++C+ ++++++  +e+  q++++ +k  +e++ y + + +e++ k
  gene157|gene157|rna157|rna157  5 NKCNTKQHKDTSNREVKSQIIILTNKLRKEKVKYRQNVLQEQIKK 49
                                   68*********************999999*****99776666533 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.024
                           YokU  10 akaststvyW.elpdgtkaieiketPsieCseCglv.yqeeevvkeiedqllLvdtkklpesit 71 
                                    +++   +++  ++ d t  i+  ++  ++C +  lv y++  +  e  +q+ ++++ k+++   
  gene157|gene157|rna157|rna157 156 TANVSDSIFIeDVRDSTLKINAGQIRLLNCGNMRLVvYTKSGISIEKSEQI-IIEEWKIQNMRH 218
                                    334445666526889999999999999999999875266677777776665.577778877544 PP

>> DUF2971  Protein of unknown function (DUF2971)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   2.8      0.32   1.9e+03      38      61 ..      23      58 ..       2     127 .. 0.71
   2 ?   10.3   0.1   0.00021       1.3       7      77 ..     131     229 ..     129     230 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.32
                        DUF2971 38 s............viYeeeeenktileevekeieee 61
                                   +            v Y+++  +++i++ +e + ++ 
  gene157|gene157|rna157|rna157 23 QiiiltnklrkekVKYRQNVLQEQIKKLKELYVQND 58
                                   033444445556677777777777777666666555 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00021
                        DUF2971   7 dnhkGvclgfdkeklkedteeglaeekksses............................viYeeeeenktileevekei 58 
                                    ++hkG  l fd ++l  ++ ++l+++ + s+s                            v+Y+++   ++++e++  e 
  gene157|gene157|rna157|rna157 131 NMHKGQILAFDCDELTLKSCNNLNITANVSDSifiedvrdstlkinagqirllncgnmrlVVYTKSGISIEKSEQIIIEE 210
                                    78************************999999999999999999999999999999999999999877666666665555 PP

                        DUF2971  59 eeeeeeeeekklnKhkdws 77 
                                     ++++  +++  +K +d+s
  gene157|gene157|rna157|rna157 211 WKIQNMRHKNLFMKVNDFS 229
                                    5554333333333887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1532  (0.0854482); expected 358.6 (0.02)
Passed bias filter:                      502  (0.0279993); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 1656.51
//
Query:       gene1570|gene1570|rna1570|rna1570  [L=349]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (349 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       878  (0.0489709); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 2397.25
//
Query:       gene1571|gene1571|rna1571|rna1571  [L=474]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      1e-70  238.8   1.1    1.5e-68  231.6   0.5    2.0  2  Cpn60_TCP1  TCP-1/cpn60 chaperonin family
  ------ inclusion threshold ------
       0.16   11.5   0.0       0.31   10.6   0.0    1.4  1  DUF4283     Domain of unknown function (DUF4283)


Domain annotation for each model (and alignments):
>> Cpn60_TCP1  TCP-1/cpn60 chaperonin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  231.6   0.5   1.7e-72   1.5e-68       2     393 ..      28     410 ..      27     424 .. 0.94
   2 !    6.4   0.0   0.00032       2.9     452     490 ..     425     463 ..     402     464 .. 0.87

  Alignments for each domain:
  == domain 1  score: 231.6 bits;  conditional E-value: 1.7e-72
                                        HHHHHCCSSTTXXEEEEEETTSEEEEEXSHHHHHHCSXXXSHHHHHHHHHHHHCCCCCTTCHHHHHHHHHHHHHHH CS
                         Cpn60_TCP1   2 adivkttlGPkGmdKmlvnkggkvvvTnDGatilkeleiehPaakllveaaesqdeevGDGTttvviLageLleea 77 
                                          +++++lGP +++Kml+n++  ++v +DG +il +++++hP+  ++ +aa +  +  GDG +t v++a+   ++a
  gene1571|gene1571|rna1571|rna1571  28 NALFSSSLGPASTTKMLINSA-GIKVLRDGRSILDSVMFTHPVTTIINKAAVQSHDLLGDGVCTFVVFASLVFQNA 102
                                        56789**************99.7***************************************************** PP

                                        HHHHHCTXXHHHHHHHHHHHHHHHHHHHHHHXEEBXSCSTT.HHHHHHHHHHCTTSSXXSTHHHHHHHHHHHHHCH CS
                         Cpn60_TCP1  78 ekliaagvhpttiiegyekalekaleaLkeiaveisseekdreeLlkvartslsskltskeaeelsklvvdAvkli 153
                                        +  ia+g +  ++ e + k l+ + e++ + +v++      +e+L k+   +l++k+ ++ a +++++v++A    
  gene1571|gene1571|rna1571|rna1571 103 FAQIASGQNVLKVNERILKDLNLLTEIMGAQKVALA-----EEDLSKLLFYVLNTKMGRDAAHHFTQIVLNAY--- 170
                                        *********999999999999999999977734443.....58******************************... PP

                                        CCCSEECSCCCEECCCCEECECTTSEEESEEEESS--SSTTSSCEEECEEEEEESS-BS--HHCCHHHCCCCSCCH CS
                         Cpn60_TCP1 154 eenekeldlgrikvvkieggsledselveGlvldkgvlspdmpkklenakvllldvsLeiektetkttvvlsdaee 229
                                             + +l++++++k++g  l ds  ++Glvld+  ++p mp+++ +a +l+++ sLe+ek+e++t++ +++a+e
  gene1571|gene1571|rna1571|rna1571 171 -----RPNLQMVEILKMDGD-LADSAAIDGLVLDHAGRHPMMPREVLKACILICNISLEYEKPEINTSLHFKSAAE 240
                                        .....579*********965.89***************************************************** PP

                                        HHHHHHHHHHHHHHHHHHHHHTTECE........EEESS-B-HHHHHHHHHCT-EEE-S--HHHHHHHHHHHT--E CS
                         Cpn60_TCP1 230 leklekaeekqleellekiiksgvnv........vvcqkgiddlalhflakngilalrrvkkkdlerlakatGata 297
                                        +e+++  e+++l +++++i +++  v        +++++gid  al+ l  +g+l+lrrvk+++lerl +++G+++
  gene1571|gene1571|rna1571|rna1571 241 RESFVAGERAILNRKIDRILELKSAVesagkklvLMTERGIDLPALDRL--QGMLCLRRVKRRNLERLLRLCGGRL 314
                                        ***********************************************88..69*********************** PP

                                        BSCGGGGGCGC-EEEEEEEECCETTCCEEEEECESSSSXEEEEEEESTCCCHHHHHHHHHHHHHHHHHHHHHHEEE CS
                         Cpn60_TCP1 298 vssledltpeelGtakkveeekigsekttiieevksgkiatillrgatdtvldeieraiedAlnvvknaiedekvv 373
                                        vs  +d+  e+lG+a+++ +++++++ +t++++ +  +++ti++ g + ++++ ++ a++ Al++v+ +   + +v
  gene1571|gene1571|rna1571|rna1571 315 VSAADDVRMECLGYAGSILVKEYKDKAYTYVTKAPYTGCSTIVIHGTNSYEMERVQIALKSALKMVELVKSAPFYV 390
                                        **************************************************************************** PP

                                        ETTTCHHHHHHHHHHCCCCT CS
                         Cpn60_TCP1 374 pGGGatelelakklkeyaks 393
                                         GG   + + +++l++  k 
  gene1571|gene1571|rna1571|rna1571 391 KGGPMNYKRWSEQLSAVNKG 410
                                        ***88888888888766555 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.00032
                                        EECCCCTXEEEHHHHHHHHHHHHHHHHHHHCEEEEEXXX CS
                         Cpn60_TCP1 452 idlveagvvDplkvkrqalksAteaastiLrideiikak 490
                                        i + ++ v+D++   ++ l +A  + st+L++deii+a+
  gene1571|gene1571|rna1571|rna1571 425 IRADDEDVMDCFVGLSRTLFNAGMVSSTLLMVDEIIRAG 463
                                        4566789*****************************986 PP

>> DUF4283  Domain of unknown function (DUF4283)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   3.5e-05      0.31      47      86 ..     365     404 ..     354     413 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 3.5e-05
                            DUF4283  47 gdglflfrfsseedlekvleggpwlingkplilkrwspkf 86 
                                        + +++++ ++s  ++ +++++ p++++g p+  krws++ 
  gene1571|gene1571|rna1571|rna1571 365 EMERVQIALKSALKMVELVKSAPFYVKGGPMNYKRWSEQL 404
                                        55689999*****************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (474 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       492  (0.0274416); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.41
# Mc/sec: 3495.12
//
Query:       gene1572|gene1572|rna1572|rna1572  [L=483]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.9e-36  125.4   0.0    3.7e-36  124.5   0.0    1.5  1  GTP_EFTU     Elongation factor Tu GTP binding domain
    2.7e-12   47.0   0.4    8.4e-12   45.4   0.3    1.9  2  GTP_EFTU_D3  Elongation factor Tu C-terminal domain
    4.6e-06   26.7   0.0    4.6e-06   26.7   0.0    2.4  2  MMR_HSR1     50S ribosome-binding GTPase
    3.7e-05   24.0   2.0    0.00026   21.3   0.2    2.7  2  GTP_EFTU_D2  Elongation factor Tu domain 2


Domain annotation for each model (and alignments):
>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  124.5   0.0   8.2e-40   3.7e-36       2     181 ..       8     198 ..       7     298 .. 0.86

  Alignments for each domain:
  == domain 1  score: 124.5 bits;  conditional E-value: 8.2e-40
                                        CEEEEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHST.............HCHSHHHHHHTSCSSCEEEEEE CS
                           GTP_EFTU   2 rirnigiighvDhGKtTLtdrLlyktgaiskkgekaeeerv.............lDtlkeErergiTiksaaisle 64 
                                        +++ +++ighvD+GK+TL++r+l +++ ++ +  ++ +e+              +Dt ++Ere+g T +++ + le
  gene1572|gene1572|rna1572|rna1572   8 PTISVVFIGHVDAGKSTLSGRILLSLNLVDPRLLEKYKEESrslnreswylswlTDTSPAEREKGKTLETCSTILE 83 
                                        56889**************************99999443334699******************************* PP

                                        TTCSSEEEEEEEESSSGGGHHHHHHHHHT-SEEEEEEETTTB.......STHHHHHHHHHHHHTTTE.EEEEEESC CS
                           GTP_EFTU  65 ketkkylinliDtPGHvdFskevirglrvlDgavlvvdaveG.......vepqteevlrlalkegvp.iivfiNKm 132
                                            + ++nl+DtPGH+ +  ++irg++++D+avlv++a++G          qt+e++ la++ gv+  i++iNKm
  gene1572|gene1572|rna1572|rna1572  84 --LPHNRVNLLDTPGHKLYLTDMIRGANQADVAVLVISARKGefeagfeRSGQTREHVILAKAGGVRhCICVINKM 157
                                        ..**********************************************99************************** PP

                                        GST...HHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTTEEEEEEBTTTTBTH CS
                           GTP_EFTU 133 Drl...kaelkeiveevkqklsrkeeklekygekgekevpvvfgSalkgegv 181
                                        D+       +keiv ++   l       + +     kev  v++S+++g +v
  gene1572|gene1572|rna1572|rna1572 158 DERgfsARCFKEIVGKLDVFL-------RRIF----KEVVYVPVSGYEGVNV 198
                                        **9776666777777777333.......2222....2356777777777655 PP

>> GTP_EFTU_D3  Elongation factor Tu C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       1.8   8.1e+03      10      28 ..     111     130 ..     109     132 .. 0.78
   2 !   45.4   0.3   1.9e-15   8.4e-12       5     111 ..     389     482 ..     385     483 .] 0.91

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.8
                                        EEEEESSS...SS-BSTT-E CS
                        GTP_EFTU_D3  10 Aqvyileke.rhtpitagYr 28 
                                        A v++l    r++++ ag++
  gene1572|gene1572|rna1572|rna1572 111 ADVAVLVISaRKGEFEAGFE 130
                                        77777777779999999985 PP

  == domain 2  score: 45.4 bits;  conditional E-value: 1.9e-15
                                        ECCEEEEEEESSS..SS-BSTT-EEEEESSS-EEEEEEEEEEECCSSTTSB-BSS-SSCCSTT-CEEEEEEECCEE CS
                        GTP_EFTU_D3   5 htkfeAqvyilekerhtpitagYrpvlyirtadvtgkvveLlskldkktekvsekkpefvkpGdnvivevelikpi 80 
                                        +++f++q+ +le   ++ +  gYr+vl+++  +v +kv  L  +++ k +kv   k+e+v++G++v  +v++ ++ 
  gene1572|gene1572|rna1572|rna1572 389 TDTFTCQLNVLEC--KGVLSVGYRAVLHLKMNSVVVKVLGL--QVK-KGDKV--YKAEYVRKGEKVLGKVRIDRKA 457
                                        568**********..**************************..333.44455..689******************* PP

                                        EE--TTTHCCCCEEEEECTTCEEEEEEEEEE CS
                        GTP_EFTU_D3  81 alekgseypqlGrFaiReggrTvaaGvvtei 111
                                         + +g        FaiR++  Tva+Gvv ++
  gene1572|gene1572|rna1572|rna1572 458 YVKEGD------CFAIRDEDITVAIGVVRKV 482
                                        ******......****************998 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.7   0.0     1e-09   4.6e-06       2      90 ..      12     125 ..      11     156 .. 0.72
   2 ?   -4.2   1.9         4   1.8e+04      15      38 ..     238     261 ..     236     279 .. 0.51

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 1e-09
                                        EEEEESTTSSHHHHHHHHH.....................T..........STEEESSSTTSSSSEEEEEEEETTE CS
                           MMR_HSR1   2 vaivGrpNvGKStLinalt.....................g..........ekaivsdkpgtTrdinegrvklkgk 46 
                                        v+++G+  +GKStL  +++                     +          +++ +++++g+T+++    ++l ++
  gene1572|gene1572|rna1572|rna1572  12 VVFIGHVDAGKSTLSGRILlslnlvdprllekykeesrslNreswylswltDTSPAEREKGKTLETCSTILELPHN 87 
                                        89****************9677666666666665555544055555555435888888889999998888888789 PP

                                        EEEEEECGGCSSHHHHHHHHHHHHHHHHCTSEEEEEEETTTTCS CS
                           MMR_HSR1  47 eielvDtpGliegaseekglgkaflaleeadlillvvdaseekl 90 
                                        +++l+DtpG  +    +  l++ ++  ++ad+++lv++a+++++
  gene1572|gene1572|rna1572|rna1572  88 RVNLLDTPG--H----KLYLTDMIRGANQADVAVLVISARKGEF 125
                                        9********..5....5689999999999********9884433 PP

  == domain 2  score: -4.2 bits;  conditional E-value: 4
                                        HHHHHHTS...TEEESSSTTSSSSEEE CS
                           MMR_HSR1  15 Linaltge...kaivsdkpgtTrdine 38 
                                        L n lt+    ++ +  ++gt      
  gene1572|gene1572|rna1572|rna1572 238 LTNNLTNGtnnNSNTDTTNGTNN---N 261
                                        78888885222333333333322...2 PP

>> GTP_EFTU_D2  Elongation factor Tu domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.2   5.7e-08   0.00026       6      73 ..     322     381 ..     319     382 .. 0.81
   2 ?    1.2   0.1      0.11   5.1e+02      13      29 ..     429     446 ..     403     462 .. 0.76

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 5.7e-08
                                        EEEEESEEETTEEEEEEC.TCTTSEEEEEEEEEEEEETEEESEEETTSEEEEEEEESSCCSGSSTTCEE CS
                        GTP_EFTU_D2   6 grvysGtlkkGdevrilg.ndtskkeivtrissletfhededeavaganaGvivaikgledaiivGdtl 73 
                                        ++v+sGt++k+de+  l+ +    k   + i+++   h ded +++ a+aG+iv+i    d +++G++l
  gene1572|gene1572|rna1572|rna1572 322 VKVESGTIRKNDELFALPgD---YK---VCIGAV---HDDEDVEIEDAHAGDIVKIRVNTDMLEIGNVL 381
                                        89**************9955...56...777766...5669**************96666667777776 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.11
                                        EETTEEEEEEC.TCTTSE CS
                        GTP_EFTU_D2  13 lkkGdevrilg.ndtskk 29 
                                        +kkGd+v+    +++++k
  gene1572|gene1572|rna1572|rna1572 429 VKKGDKVYKAEyVRKGEK 446
                                        788888887665555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (483 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       730  (0.0407162); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.44
# Mc/sec: 3291.68
//
Query:       gene1573|gene1573|rna1573|rna1573  [L=946]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.2e-73  246.5   2.2      5e-73  245.9   2.2    1.3  1  VTC       VTC domain
    1.9e-13   50.6   1.8    4.2e-13   49.5   1.8    1.6  1  DUF202    Domain of unknown function (DUF202)
  ------ inclusion threshold ------
       0.78    9.8   5.4        1.4    9.0   5.4    1.3  1  MARVEL    Membrane-associating domain


Domain annotation for each model (and alignments):
>> VTC  VTC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  245.9   2.2   8.4e-77     5e-73       1     275 []     202     461 ..     202     461 .. 0.90

  Alignments for each domain:
  == domain 1  score: 245.9 bits;  conditional E-value: 8.4e-77
                                        --EEEEEEE-HHHHHHHHHHHHTTS-B----------------------EEEEEEE-TT-HHHHHHHHT-TT--EE CS
                                VTC   1 nrnetKywvhsdnvvevktlilkhlpvlvygaseeeiaaallrksadqtitsvYfDnndfelyenrilkmegaeki 76 
                                        +r++ Kywvh+dn+  +k+ il+hlpv +++ + e+      +k++d++its+Y+Dn  fe y++r+ k +g+e i
  gene1573|gene1573|rna1573|rna1573 202 VRRTAKYWVHPDNIDDLKACILRHLPVYIFNPNDENY--DSWTKEHDSAITSIYYDNASFEAYNTRLHKLQGSEAI 275
                                        699****************************754443..344599******************************* PP

                                        EEEEES-GGG--EEEEEEEE--------EEEEEEEE-GGGHHHHH---HHHHHHHHHHHHHT-HHHHHHHHHHHHH CS
                                VTC  77 RlRwygkldnedvflErktkheswtgesstkerftlkqkfvksyllgrlpaeerleklkkkeeekevekleqlaee 152
                                        R+Rwy+  + + vf+Erk +++ wtg +s+k rf++  ++v++y++g+    + ++  +  +e  +  + ++l++e
  gene1573|gene1573|rna1573|rna1573 276 RIRWYKLDEPKVVFVERKRHEDGWTGYQSKKLRFKIPVEHVNAYVNGQ----NVWKHVEPLNE--NKLSTLNLYNE 345
                                        *****855566**********************************776....56666665555..4456889**** PP

                                        HHHHHHHTT-EEEEEEEEEEEEE--TT--SEEEEEEEEEEEEE----SSSS-SS-TSS-SSTTSS-TTTT--GGGE CS
                                VTC 153 iqntilrnslqPvvrtsYlRaaFqlstdnavRitiDtnlcmvredsfeerrkledtwerldedvqqpvkllrkgev 228
                                        iq+ i+ ++l+P vrt Y+R+aFq +++n++R+++Dt+l+m++e+  ++  +   +w+r  ++   p++ lr+ e+
  gene1573|gene1573|rna1573|rna1573 346 IQHSIVYKKLRPSVRTFYRRMAFQMPESNNIRLSLDTDLVMIKENVGDSSAPF--NWRREGIN--WPFDNLRPDEI 417
                                        ********************************************555555554..48888888..*********** PP

                                        EE--SEEEEEEE------HHHHHHHTSTT-EE-TT--HHHHHHHHHH CS
                                VTC 229 vrfpyavlEvKlqtskspewiqeLlashlvievpkfSKYqhgvaslh 275
                                        +rfpy +lEvK+q   +  wi+e    hl+++v+kfSK++hg+a+l+
  gene1573|gene1573|rna1573|rna1573 418 CRFPYGILEVKTQD-DQKIWINEYE--HLIEHVHKFSKFMHGTAVLY 461
                                        **************.9999****88..*****************996 PP

>> DUF202  Domain of unknown function (DUF202)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.5   1.8     7e-17   4.2e-13       1      67 [.     847     908 ..     847     909 .. 0.95

  Alignments for each domain:
  == domain 1  score: 49.5 bits;  conditional E-value: 7e-17
                             DUF202   1 rdglAnERTfLaWlRtslalialglallrffltgepsalgkilglilivlgiltllvglvrylrrqr 67 
                                        ++++AnERTfL+Wl++s+ +++lg a++ +   g+ +a   i g+++iv+++++++++l+ y++r++
  gene1573|gene1573|rna1573|rna1573 847 KVFFANERTFLSWLHFSIFIGGLGSAMVGL---GDYKA--LISGAVFIVVSTIFAVYALYLYMWRAH 908
                                        689*************************97...88888..8***********************987 PP

>> MARVEL  Membrane-associating domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   5.4   0.00023       1.4      16      95 ..     862     936 ..     855     939 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00023
                             MARVEL  16 faiiilgliasliakldqllgspssalnfavfvavfsflyalfllvlylfk.nsaftsilwplidlivdalaallw 90 
                                        f+i+i gl ++++     +lg++ + ++ avf+ v s ++a+++l ly+ + ++ + ++  p+ dli  +++++++
  gene1573|gene1573|rna1573|rna1573 862 FSIFIGGLGSAMV-----GLGDYKALISGAVFIVV-STIFAVYALYLYMWRaHKIRARNPGPYDDLIGPGVLVFVF 931
                                        8999999999999.....89997777777776655.556799999999999************************9 PP

                             MARVEL  91 lvafi 95 
                                        ++a +
  gene1573|gene1573|rna1573|rna1573 932 IAAMA 936
                                        99975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (946 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       718  (0.0400469); expected 358.6 (0.02)
Passed bias filter:                      524  (0.0292264); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.74u 0.31s 00:00:01.05 Elapsed: 00:00:00.46
# Mc/sec: 6214.73
//
Query:       gene1574|gene1574|rna1574|rna1574  [L=129]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       475  (0.0264934); expected 358.6 (0.02)
Passed bias filter:                      189  (0.0105416); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 898.94
//
Query:       gene1575|gene1575|rna1575|rna1575  [L=496]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (496 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       475  (0.0264934); expected 358.6 (0.02)
Passed bias filter:                      254  (0.014167); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 3669.00
//
Query:       gene1576|gene1576|rna1576|rna1576  [L=217]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.052   13.7   3.5       0.29   11.3   0.7    2.9  2  FNIP         FNIP Repeat
      0.057   12.9   0.3       0.13   11.8   0.0    1.6  2  Terminase_3  Phage terminase large subunit


Domain annotation for each model (and alignments):
>> FNIP  FNIP Repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.7   3.2e-05      0.29       9      41 ..       5      74 ..       1      77 [. 0.75
   2 ?    1.7   0.1     0.033     3e+02      13      40 ..     103     131 ..     102     134 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 3.2e-05
                               FNIP  9 eLP.....................................snleiLil.grdFnqkiligsLPnSlkeLyF 41
                                       +++                                     +nl  Li   + F+++il   LP++l++L++
  gene1576|gene1576|rna1576|rna1576  5 TITnilwheslnhnlqcglesltlsgwgleeknimmlrkfQNLRTLIVdSNHFKNEIL-ENLPDQLETLEI 74
                                       55555555555555555555555778888888888888889*******88999****9.88********98 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.033
                               FNIP  13 nleiLil.grdFnqkiligsLPnSlkeLy 40 
                                        n+ +L++ gr   + + + +LP +l  L+
  gene1576|gene1576|rna1576|rna1576 103 NIRNLTFsGRFLRNTHIFACLPINLMVLK 131
                                        78888885555555666778887777665 PP

>> Terminase_3  Phage terminase large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0      0.22     2e+03      37      43 ..      41      47 ..      34      92 .. 0.48
   2 ?   11.8   0.0   1.4e-05      0.13     108     170 ..     145     215 ..     139     217 .] 0.85

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.22
                        Terminase_3 37 lRkvknt 43
                                       lRk++n 
  gene1576|gene1576|rna1576|rna1576 41 LRKFQNL 47
                                       4444432 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 1.4e-05
                        Terminase_3 108 sevseedidelvetlrapeqekqiilsfNPvsesnwvykrffkd..dekekde......kddvlihkstyr 170
                                        + +++ +i++l+  l +p++ ++i++  NP++++ +    f+++  d + +de      +  v i k+tyr
  gene1576|gene1576|rna1576|rna1576 145 NILEKVTIKKLIIGLDEPNLSLRIYININPMKRQYYKTFDFLRNfiDFNSLDElvletaDGVVNIDKTTYR 215
                                        55678899*************************99999999999996666666777767777889999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       413  (0.0230353); expected 358.6 (0.02)
Passed bias filter:                      263  (0.014669); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1631.70
//
Query:       gene1577|gene1577|rna1577|rna1577  [L=59]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       623  (0.0347482); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.40
# Mc/sec: 446.00
//
Query:       gene1578|gene1578|rna1578|rna1578  [L=268]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (268 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1248  (0.0696079); expected 358.6 (0.02)
Passed bias filter:                      496  (0.0276647); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 1928.27
//
Query:       gene1579|gene1579|rna1579|rna1579  [L=56]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (56 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1106  (0.0616878); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.29s 00:00:00.64 Elapsed: 00:00:00.43
# Mc/sec: 391.92
//
Query:       gene158|gene158|rna158|rna158  [L=141]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0014   18.5   2.7       0.86    9.5   2.4    2.3  2  GIT_CC    GIT coiled-coil Rho guanine nucleotide exchange fac
  ------ inclusion threshold ------
       0.17   12.2   2.4       0.29   11.5   0.5    2.0  2  GAT       GAT domain


Domain annotation for each model (and alignments):
>> GIT_CC  GIT coiled-coil Rho guanine nucleotide exchange factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   0.0   0.00045         4       7      47 ..      65     106 ..      60     114 .. 0.81
   2 !    9.5   2.4   9.6e-05      0.86      27      51 ..     114     138 ..     107     139 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.00045
                         GIT_CC   7 dLsdgpVtleeylelKkalaas.eakiqqLlkvNtslsdelr 47 
                                    d+ + ++ ++ y+++K++ +   e  i +L k+  +l + l+
  gene158|gene158|rna158|rna158  65 DIREAAIIIKRYIQIKEQGGELnEENIGHLFKSSGKLGTALT 106
                                    778899***********9876527789999999888877776 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 9.6e-05
                         GIT_CC  27 aseakiqqLlkvNtslsdelrlLQs 51 
                                     s   + +L+k+N +l++ l++LQ+
  gene158|gene158|rna158|rna158 114 KSKNDLSKLIKANDNLKNSLAQLQQ 138
                                    67777899****************6 PP

>> GAT  GAT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.1     0.077   6.9e+02      18      51 ..      32      65 ..      23      82 .. 0.70
   2 ?   11.5   0.5   3.2e-05      0.29      26      74 ..      91     139 ..      77     141 .] 0.73

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.077
                            GAT 18 eellenellkeLyetckamqpriqklieetadee 51
                                   e+++ + l++  ++  k++++  +kl e++ d++
  gene158|gene158|rna158|rna158 32 ESPDRESLVTTIVNLTKQISEDGVKLGEKLKDKD 65
                                   5566677777777777777777777777776665 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 3.2e-05
                            GAT  26 lkeLyetckamqpriqklieetadeedllaelLqlNDeLnnvlerYerl 74 
                                    +  L ++  ++ + +++ + +    ++ l +l+++ND+L n l++ ++l
  gene158|gene158|rna158|rna158  91 IGHLFKSSGKLGTALTEAAKKHKKSKNDLSKLIKANDNLKNSLAQLQQL 139
                                    5555555566666677777776555557*************99987776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1788  (0.0997267); expected 358.6 (0.02)
Passed bias filter:                      950  (0.0529868); expected 358.6 (0.02)
Passed Vit filter:                        90  (0.0050198); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 944.67
//
Query:       gene1580|gene1580|rna1580|rna1580  [L=560]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (560 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1403  (0.0782531); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.62u 0.32s 00:00:00.94 Elapsed: 00:00:00.49
# Mc/sec: 3432.96
//
Query:       gene1581|gene1581|rna1581|rna1581  [L=124]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       943  (0.0525964); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 855.41
//
Query:       gene1582|gene1582|rna1582|rna1582  [L=565]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (565 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1178  (0.0657036); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.62u 0.32s 00:00:00.94 Elapsed: 00:00:00.50
# Mc/sec: 3426.36
//
Query:       gene1583|gene1583|rna1583|rna1583  [L=465]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (465 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1962  (0.109432); expected 358.6 (0.02)
Passed bias filter:                      459  (0.025601); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.59u 0.27s 00:00:00.86 Elapsed: 00:00:00.43
# Mc/sec: 3241.19
//
Query:       gene1584|gene1584|rna1584|rna1584  [L=31]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (31 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       117  (0.00652574); expected 358.6 (0.02)
Passed bias filter:                       90  (0.0050198); expected 358.6 (0.02)
Passed Vit filter:                         4  (0.000223102); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.33u 0.24s 00:00:00.57 Elapsed: 00:00:00.40
# Mc/sec: 232.21
//
Query:       gene1585|gene1585|rna1585|rna1585  [L=645]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.4e-37  128.1   0.1    6.5e-37  127.2   0.1    1.5  1  Dynamin_N  Dynamin family
    1.2e-13   50.9   1.3    9.9e-11   41.4   0.1    3.1  3  Dynamin_M  Dynamin central region
    5.3e-05   23.3   0.1    0.00062   19.8   0.1    2.4  1  MMR_HSR1   50S ribosome-binding GTPase
      0.001   19.4   0.1      0.013   15.8   0.0    2.3  2  PIN_4      PIN domain
     0.0056   16.8   0.6       0.02   15.1   0.1    2.2  2  GED        Dynamin GTPase effector domain
  ------ inclusion threshold ------
       0.11   12.8   0.0       0.24   11.8   0.0    1.5  1  AAA_16     AAA ATPase domain


Domain annotation for each model (and alignments):
>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  127.2   0.1   2.2e-40   6.5e-37       1     167 [.      28     250 ..      28     251 .. 0.95

  Alignments for each domain:
  == domain 1  score: 127.2 bits;  conditional E-value: 2.2e-40
                                        EEEEEBTTTTHHHHHHHHHTS--S---SSS---S-EEEEE.................................... CS
                          Dynamin_N   1 iavvGsqSsGKSSvlnaLlgedilprgpnptTrrplelql.................................... 40 
                                        i+v+G qSsGKSSvl+ ++g+d+lp+g+ ++Tr+p+++ l                                    
  gene1585|gene1585|rna1585|rna1585  28 IIVIGPQSSGKSSVLERIIGHDLLPKGEDLVTRCPIVINLrnagvnywecndkenmengrgntselcessvhsgss 103
                                        89********************************************************************999999 PP

                                        .........CCT---CCS...SSEEEE..T-EB--CHHHHHHHHHHHHHHHTSSSS--SS-EEEEEEETTS-SEEE CS
                          Dynamin_N  41 .........geeeeaseravkeelkek..ekkledfsevreeieketekiagankgiskkvillkilsllvkgltl 105
                                                 ++ ++ ++++v++e+  +  + + +d+s v+ee+++++  + g+ k+is++ i+++ +  +  ++tl
  gene1585|gene1585|rna1585|rna1585 104 tgnacgsidSR-KKGRNDRVTKEYAVFadSNDVYDLSLVKEELKRRMVVLCGNRKEISSQQIVVTLYLRKTVNITL 178
                                        99999988533.3334677888888778899********************************************* PP

                                        EE---B-SSSGTTS.........HHHHHHH.STTEEEEEEEETTS-CCC-CHHHHHHHHSTTBTTEEEEEE- CS
                          Dynamin_N 106 vDlPGldsvnkrdq.........elvkeyi.kkadiilavtsanhdlsnsealflarevdpkgkrtivvltk 167
                                        vDlPGl++v+++ q         +l ++y+ ++++iilav +  +dl nse+l++ar++dp  +rt++v+tk
  gene1585|gene1585|rna1585|rna1585 179 VDLPGLTKVPVGAQpneieqiidDLNMSYCkNNNSIILAVINGCVDLVNSESLKIARLCDPGYTRTMGVVTK 250
                                        ***********************************************************************9 PP

>> Dynamin_M  Dynamin central region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.4   0.1   3.3e-14   9.9e-11       3      86 ..     262     342 ..     260     355 .. 0.92
   2 ?   -0.7   0.0      0.22   6.4e+02     184     228 ..     407     453 ..     398     461 .. 0.81
   3 !    6.2   0.0    0.0017       5.1     240     277 ..     513     550 ..     506     555 .. 0.88

  Alignments for each domain:
  == domain 1  score: 41.4 bits;  conditional E-value: 3.3e-14
                          Dynamin_M   3 dilenkvipLklGYvgVvnRsqkdInkkksieealkkEkaFFeshpayrkladkaGtpyLakkLnqiLvehIrksl 78 
                                         ilen +i+L lGYvgV+nR++k    ++s++e  k+Ek FF++   ++ +  + Gt+yL+++  ++  +  + +l
  gene1585|gene1585|rna1585|rna1585 262 AILENTKIKLGLGYVGVINRNTKAL-YSVSVHEHAKREKGFFRTR--FSAFYPRIGTQYLIERVYDTFKDKTKAFL 334
                                        69**********************8.99*****************..********************999999999 PP

                          Dynamin_M  79 Pelkkkin 86 
                                         +l++ ++
  gene1585|gene1585|rna1585|rna1585 335 DGLRDTLE 342
                                        99998776 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.22
                          Dynamin_M 184 plfvpekaFealvkkqikkleepalkcvelVyeelekiveklek..e 228
                                        + f++e+ F + ++++ + l+   +  + +V e+++  ve++++  e
  gene1585|gene1585|rna1585|rna1585 407 NVFLNEAQFMYYMRRKTDHLHVQIVSKIGKVCEAVKTYVESIRNgtE 453
                                        57899999999999999999999999999999999988888766444 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.0017
                          Dynamin_M 240 kevvedllreqeeptkemienliemelayintnhpdfi 277
                                        +e+   +l +q+++  + ie++++++++y+   hpdf 
  gene1585|gene1585|rna1585|rna1585 513 NEAAVAMLGTQRAKFVQNIEQYFKIQQSYMDVDHPDFN 550
                                        567778889999999**********************5 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.1   2.1e-07   0.00062       1      84 [.      27     220 ..      27     250 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 2.1e-07
                                        EEEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEE............................. CS
                           MMR_HSR1   1 evaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgke............................. 47 
                                        +++++G   +GKS+++ +++g     + +  +Tr ++ ++++  g +                             
  gene1585|gene1585|rna1585|rna1585  27 QIIVIGPQSSGKSSVLERIIGHDLLPKGEDLVTRCPIVINLRNAGVNywecndkenmengrgntselcessvhsgs 102
                                        589*******************999999***********99944433566666778889999999999999***** PP

                                        .........................................................................EEE CS
                           MMR_HSR1  48 .........................................................................iel 50 
                                                                                                                 i+l
  gene1585|gene1585|rna1585|rna1585 103 stgnacgsidsrkkgrndrvtkeyavfadsndvydlslvkeelkrrmvvlcgnrkeissqqivvtlylrktvnITL 178
                                        **************************************************************************** PP

                                        EECGGCSS.......HHHHHH..HHHHHHHHHHCTSEEEEEEE CS
                           MMR_HSR1  51 vDtpGlie.......gaseek..glgkaflaleeadlillvvd 84 
                                        vD+pGl +       ++ e+   +l+ +++++++ ++il v++
  gene1585|gene1585|rna1585|rna1585 179 VDLPGLTKvpvgaqpNEIEQIidDLNMSYCKNNN-SIILAVIN 220
                                        *****84233323322222335578888887666.78888886 PP

>> PIN_4  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   4.2e-06     0.013      84     127 ..     360     401 ..     312     403 .. 0.72
   2 ?    0.4   0.0      0.24   7.3e+02      44      93 ..     432     491 ..     416     497 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 4.2e-06
                              PIN_4  84 seknDnrIlavalelkeekpdrkvvLvskDinlrikAkalgiea 127
                                         +  D+ + +v+l+l++e+  +   L+s+Dinlr  A+  ++++
  gene1585|gene1585|rna1585|rna1585 360 YRIVDEYVHHVCLKLRNEH--TAGRLFSNDINLRAYARLADLHV 401
                                        4589**************9..7889************9998875 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.24
                              PIN_4  44 relarlarqanrlldellekesgrlkvqtsaeelpeee...........seseknDnrIla 93 
                                         ++++ ++ ++++++++ + ++ r + + ++++ +              +++++nD++I++
  gene1585|gene1585|rna1585|rna1585 432 SKIGKVCEAVKTYVESIRNGTELREHAEDEQHDTKG-FfgffspvrfltTKEQTNDESIID 491
                                        456677777777777777777777766666555554.145777777776446899999997 PP

>> GED  Dynamin GTPase effector domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.1       2.3     7e+03      10      20 ..     528     538 ..     523     542 .. 0.77
   2 !   15.1   0.1   6.6e-06      0.02       5      50 ..     569     614 ..     567     641 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 2.3
                                        HHHHHHHHHHH CS
                                GED  10 rslvksYfniv 20 
                                         +++++Yf+i 
  gene1585|gene1585|rna1585|rna1585 528 VQNIEQYFKIQ 538
                                        57899999985 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 6.6e-06
                                        XTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHCCCCCHHHC CS
                                GED   5 eveeirslvksYfnivrktiadqiPkaimhllvneakeslqkella 50 
                                        +++ +  +v+ Y+ i++k++++   k i + +v+ ++++++ ++l+
  gene1585|gene1585|rna1585|rna1585 569 SLDLMTAYVNTYYGIIKKEVEHYFVKSIFFYFVDFFRNEFRMAMLR 614
                                        6788999**********************************99985 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0     8e-05      0.24      11      44 ..      12      45 ..       8      64 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 8e-05
                             AAA_16 11 qLlsalervrsgrpelvllsGesGvGKsslvrel 44
                                       +L+++l+++ + + + ++++G++ +GKss+++++
  gene1585|gene1585|rna1585|rna1585 12 KLQQILQPTTRIELPQIIVIGPQSSGKSSVLERI 45
                                       6889999888888899***************876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (645 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       783  (0.0436723); expected 358.6 (0.02)
Passed bias filter:                      552  (0.0307881); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.70u 0.30s 00:00:01.00 Elapsed: 00:00:00.47
# Mc/sec: 4110.68
//
Query:       gene1586|gene1586|rna1586|rna1586  [L=187]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0027   16.5   2.2     0.0042   15.8   2.2    1.4  1  Peptidase_S46   Peptidase S46
     0.0045   17.4   1.4     0.0045   17.4   1.4    3.0  3  DUF4200         Domain of unknown function (DUF4200)
  ------ inclusion threshold ------
      0.032   14.5   0.2      0.062   13.6   0.2    1.6  1  Syntaxin-18_N   SNARE-complex protein Syntaxin-18 N-terminus
      0.047   13.0   2.0      0.058   12.7   2.0    1.1  1  DUF4407         Domain of unknown function (DUF4407)
      0.072   12.8   5.3       0.13   11.9   0.7    2.2  2  DUF4988         Domain of unknown function
      0.098   13.3   2.1       0.47   11.1   0.3    2.3  2  DUF643          Protein of unknown function (DUF643)
       0.16   11.6  14.8       0.19   11.3  12.9    2.0  2  DUF4795         Domain of unknown function (DUF4795)
       0.63   10.1   5.8          1    9.4   0.5    2.6  2  DUF1664         Protein of unknown function (DUF1664)
       0.64   10.5   8.7       0.15   12.5   0.7    2.3  2  DUF16           Protein of unknown function DUF16
        5.9    6.9   8.7       0.87    9.6   0.9    2.5  2  UCMA            Unique cartilage matrix associated protein


Domain annotation for each model (and alignments):
>> Peptidase_S46  Peptidase S46
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   2.2   2.3e-06    0.0042     260     331 ..      32     103 ..      25     183 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2.3e-06
                                        HHHHHHHHTHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTHHHHHHHH CS
                      Peptidase_S46 260 aeleerrdvalparievleeriallkeemkkdpeirikyasklagleNylKnliGmlealkkkkvlekkqae 331
                                         ++ + ++ al++ i+vl+eri +l+e++ + +e+r +ya++   le ++K+l+G+l ++ k ++ +k  ++
  gene1586|gene1586|rna1586|rna1586  32 LDVSQSVNDALEEEINVLNERIVVLEEKKLALEEKRNEYANHASYLEESIKHLNGRLLSIGKLYLEKKEMSD 103
                                        568899999**************************************************9998876555443 PP

>> DUF4200  Domain of unknown function (DUF4200)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.1      0.91   1.6e+03      30      46 ..       6      22 ..       3      28 .. 0.48
   2 !   17.4   1.4   2.5e-06    0.0045      75     117 ..      39      81 ..      33      83 .. 0.91
   3 ?   -0.0   5.1      0.63   1.1e+03       5      67 ..      98     162 ..      94     187 .] 0.73

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.91
                            DUF4200 30 kqreeelekkeqeleed 46
                                       +++e+el + ++e e+ 
  gene1586|gene1586|rna1586|rna1586  6 QREEKELGALREEVEKY 22
                                       44444444444444443 PP

  == domain 2  score: 17.4 bits;  conditional E-value: 2.5e-06
                            DUF4200  75 kkekeaeikklkaeietlkseiekleekleeykkYeefLekvv 117
                                        ++  e+ei+ l++ i+ l++++  leek +ey ++ ++Le+ +
  gene1586|gene1586|rna1586|rna1586  39 NDALEEEINVLNERIVVLEEKKLALEEKRNEYANHASYLEESI 81 
                                        56789**********************************9865 PP

  == domain 3  score: -0.0 bits;  conditional E-value: 0.63
                            DUF4200   5 kremfevqealeakkeeiq..rleealkqreeelekkeqeleedllkfdkflkendakraralkk 67 
                                        k+em++++e  ++k+ +    +l+++  +  + +  +eq l++  ++ d+ + e+ +++ +  k+
  gene1586|gene1586|rna1586|rna1586  98 KKEMSDLEEHRGRKEMDKLdnELMNLTIESNNSILLSEQALQRVKIQMDRVVGEIRNEQDEVSKE 162
                                        66777777766666555322368888888888888888888888888888888888888776665 PP

>> Syntaxin-18_N  SNARE-complex protein Syntaxin-18 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.2   3.4e-05     0.062      32      82 ..      58     106 ..      18     108 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.4e-05
                      Syntaxin-18_N  32 kkrlkkskekdeFikeAkeilkhItkLrkfLleirkaYlnvrshlmtdqer 82 
                                        +k+l  +++++e+ + A  + ++I+ L+  Ll+i k Yl  ++  m+d e 
  gene1586|gene1586|rna1586|rna1586  58 EKKLALEEKRNEYANHASYLEESIKHLNGRLLSIGKLYLEKKE--MSDLEE 106
                                        45566678899******************************99..999886 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   2.0   3.2e-05     0.058     106     246 ..      17     172 ..       5     182 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.2e-05
                            DUF4407 106 keIdaelaeeqqeeakelkeqlaaaltaelaeleaqiaalqaeidaaearldalraeaqkeldgtk.gtgttgvaG 180
                                        +e+++ +++++  +  ++++++++al++e++ l+++i  l+++  a+e+++++  ++a    +  k  +g  +   
  gene1586|gene1586|rna1586|rna1586  17 EEVEKYVHDFRCVSGLDVSQSVNDALEEEINVLNERIVVLEEKKLALEEKRNEYANHASYLEESIKhLNG--RLLS 90 
                                        5666666666666667778888888999999999999999999999999999988888744443224334..4566 PP

                            DUF4407 181 kgpaakekkaqldaaqaelaelkakld................atarlaalraelaeleaerakeraasqaaaaad 240
                                         g+ + ekk++ d  + +  +  +kld                ++++l++ + +++++  e+++e+++  +++  +
  gene1586|gene1586|rna1586|rna1586  91 IGKLYLEKKEMSDLEEHRGRKEMDKLDnelmnltiesnnsillSEQALQRVKIQMDRVVGEIRNEQDEVSKEIVRF 166
                                        77777777776665544444444444444448888888************************************99 PP

                            DUF4407 241 dGllar 246
                                         G++ +
  gene1586|gene1586|rna1586|rna1586 167 YGMMSN 172
                                        999876 PP

>> DUF4988  Domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.5     0.034        61       1      23 [.      42      64 ..      42      71 .. 0.84
   2 ?   11.9   0.7   7.3e-05      0.13       6      69 ..      68     130 ..      63     136 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.034
                            DUF4988  1 leddvndlkdrvaaleeqvkeln 23
                                       le+++n l++r+  lee+  +l+
  gene1586|gene1586|rna1586|rna1586 42 LEEEINVLNERIVVLEEKKLALE 64
                                       7899************9876665 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 7.3e-05
                            DUF4988   6 ndlkdrvaaleeqvkelndniealkklleegkviteveensdgsyvltlsdgktitltqgkdge 69 
                                        n+  +  + lee +k+ln  + +++kl+ e+k ++++ee   g++++   d++ ++lt ++++ 
  gene1586|gene1586|rna1586|rna1586  68 NEYANHASYLEESIKHLNGRLLSIGKLYLEKKEMSDLEE-HRGRKEMDKLDNELMNLTIESNNS 130
                                        666777789******************************.8899*********99999888765 PP

>> DUF643  Protein of unknown function (DUF643)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.1      0.23   4.1e+02      55      79 ..      35      62 ..       7      90 .. 0.55
   2 ?   11.1   0.3   0.00026      0.47      10      70 ..     104     165 ..      95     177 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.23
                             DUF643 55 eeiindiiepekefikd...vlkdknli 79
                                        + +nd +e e +++ +   vl +k+l 
  gene1586|gene1586|rna1586|rna1586 35 SQSVNDALEEEINVLNErivVLEEKKLA 62
                                       4455555555544444322233333332 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00026
                             DUF643  10 nlskdtkkeinkly.eteqltleqkkqlysavkkiqeykiktGksveeiindiiepekefik 70 
                                           ++ +ke++kl  e  +lt+e  + +  + +++q+ ki+  + v ei n+  e +ke+++
  gene1586|gene1586|rna1586|rna1586 104 LEEHRGRKEMDKLDnELMNLTIESNNSILLSEQALQRVKIQMDRVVGEIRNEQDEVSKEIVR 165
                                        44567899****9626899**********************************999999996 PP

>> DUF4795  Domain of unknown function (DUF4795)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.72   1.3e+03     127     144 ..       8      25 ..       4      33 .. 0.71
   2 ?   11.3  12.9   0.00011      0.19       9     134 ..      39     187 .]      29     187 .] 0.82

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.72
                            DUF4795 127 drlelepLkeqleerlke 144
                                        +++el  L+e++e+ ++ 
  gene1586|gene1586|rna1586|rna1586   8 EEKELGALREEVEKYVHD 25 
                                        567888888888876654 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00011
                            DUF4795   9 lkklqeaieklqeelekleekvkelekrledkekklealkkqieelekvk........adkeeveeel......ae 70 
                                         + l+e+i  l e++  leek+  le++ +++  +   l+++i++l+ +         ++ke  ++e+        
  gene1586|gene1586|rna1586|rna1586  39 NDALEEEINVLNERIVVLEEKKLALEEKRNEYANHASYLEESIKHLNGRLlsigklylEKKEMSDLEEhrgrkeMD 114
                                        5778899999999999999999999999999999999999999999999888888886444444433322222267 PP

                            DUF4795  71 kadkeaLatkvsrdq........fDeakkeLekmleellekleeqeealkkaldtLqeelkekld.rlelepL 134
                                        k d e ++ +++ ++        ++ +k ++++ + e+++  +e+++++ +++  +++el++ +  ++e+++L
  gene1586|gene1586|rna1586|rna1586 115 KLDNELMNLTIESNNsillseqaLQRVKIQMDRVVGEIRNEQDEVSKEIVRFYGMMSNELENAVAvAKEIKEL 187
                                        8888888888888889********************************************9988877888776 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.3     0.064   1.2e+02      55     101 ..      40      86 ..      28     107 .. 0.54
   2 ?    9.4   0.5   0.00058         1      41      91 ..     136     186 ..     133     187 .] 0.79

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.064
                            DUF1664  55 eslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseige 101
                                        ++l++  + L++ri  +++k  + +e  +e +++ + ++e +++++ 
  gene1586|gene1586|rna1586|rna1586  40 DALEEEINVLNERIVVLEEKKLALEEKRNEYANHASYLEESIKHLNG 86 
                                        34444444444444444444444444444444444444444444443 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00058
                            DUF1664  41 davesvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevte 91 
                                        +a+++v  q+++v  ++++ +++ s++i r    + +  e + ++++e++e
  gene1586|gene1586|rna1586|rna1586 136 QALQRVKIQMDRVVGEIRNEQDEVSKEIVRFYGMMSNELENAVAVAKEIKE 186
                                        7999************************88666666666666666655554 PP

>> DUF16  Protein of unknown function DUF16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.7   8.5e-05      0.15      45     102 ..      34      91 ..       6      93 .. 0.85
   2 ?    2.2   2.0      0.14   2.5e+02      13      73 ..     101     161 ..      91     185 .. 0.51

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 8.5e-05
                                        ...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.......HHHHHHHHHHHHHHHHHHH CS
                              DUF16  45 klgeqinkleqkvekqgekikelkveqkaqgeelnkvdetleliletLqkinkRlDsi 102
                                        + +   ++le++++ ++e+i  l+++  a +e+ n+  +    + e+++++n Rl si
  gene1586|gene1586|rna1586|rna1586  34 VSQSVNDALEEEINVLNERIVVLEEKKLALEEKRNEYANHASYLEESIKHLNGRLLSI 91 
                                        555666899*********************************************9766 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.14
                                        .X.XTTB-BHHHHHHB-..BHHHHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              DUF16  13 iPvkteYVTrkqlnefkdsnkqrLkkieakvdklgeqinkleqkvekqgekikelkveqka 73 
                                        +   +e+  rk++++  ++  +  +++++ +   ++ +++++ ++++   +i++ + e+ +
  gene1586|gene1586|rna1586|rna1586 101 MSDLEEHRGRKEMDKLDNELMNLTIESNNSILLSEQALQRVKIQMDRVVGEIRNEQDEVSK 161
                                        4444555556666665555333334444444444444444444444444444443333333 PP

>> UCMA  Unique cartilage matrix associated protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.9   0.00048      0.87      69     102 ..      43      75 ..      32      87 .. 0.81
   2 ?    1.0   1.6      0.22     4e+02      94     116 ..     142     164 ..      89     173 .. 0.59

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00048
                               UCMA  69 qdeinaenrqrlaaderrreyyeeqrnefenyve 102
                                        ++ein+ n  r+ + e ++   ee+rne+ n++ 
  gene1586|gene1586|rna1586|rna1586  43 EEEINVLNE-RIVVLEEKKLALEEKRNEYANHAS 75 
                                        579999885.677777788899*********985 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.22
                               UCMA  94 rnefenyveeendeqeersrekv 116
                                        + +++  v e ++eq+e s+e v
  gene1586|gene1586|rna1586|rna1586 142 KIQMDRVVGEIRNEQDEVSKEIV 164
                                        33456678888899999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1421  (0.0792571); expected 358.6 (0.02)
Passed bias filter:                      503  (0.0280551); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.54u 0.24s 00:00:00.78 Elapsed: 00:00:00.41
# Mc/sec: 1363.55
//
Query:       gene1587|gene1587|rna1587|rna1587  [L=331]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.5e-31  107.6   0.2      1e-30  106.4   0.2    1.6  1  Ndc80_HEC     HEC/Ndc80p family
     0.0028   16.6  12.0     0.0044   16.0  12.0    1.2  1  DUF812        Protein of unknown function (DUF812)
  ------ inclusion threshold ------
      0.073   11.7  12.5        0.1   11.2  12.5    1.2  1  FapA          Flagellar Assembly Protein A
      0.075   12.3   9.2      0.019   14.3   5.7    1.7  1  TMPIT         TMPIT-like protein
       0.11   12.5   6.2       0.19   11.8   0.6    2.7  3  DUF1664       Protein of unknown function (DUF1664)
       0.13   11.6  18.6       0.42    9.9  18.4    1.9  1  Tropomyosin   Tropomyosin
       0.26   11.7   5.1        5.3    7.5   2.2    2.8  2  FlaC_arch     Flagella accessory protein C (FlaC)
       0.48    9.4  10.2        0.6    9.1   9.6    1.4  1  Atg14         Vacuolar sorting 38 and autophagy-related subun
       0.62   10.4   7.2        2.2    8.6   0.0    3.8  4  TSC22         TSC-22/dip/bun family
          1    9.6  19.5      0.054   13.7   5.0    2.6  2  TMF_TATA_bd   TATA element modulatory factor 1 TATA binding
        1.1    8.8   6.6        2.1    7.8   6.6    1.5  1  Exonuc_VII_L  Exonuclease VII, large subunit
        1.9    8.6  16.9       0.13   12.3   9.5    2.3  2  BRE1          BRE1 E3 ubiquitin ligase
        3.7    6.8   7.6        5.3    6.3   7.6    1.2  1  DUF4407       Domain of unknown function (DUF4407)


Domain annotation for each model (and alignments):
>> Ndc80_HEC  HEC/Ndc80p family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.4   0.2   7.6e-34     1e-30      21     145 ..      17     138 ..       2     145 .. 0.90

  Alignments for each domain:
  == domain 1  score: 106.4 bits;  conditional E-value: 7.6e-34
                          Ndc80_HEC  21 kaasverDprplrdksfqseliqellefLkennfehsisaktlksPsqkdfssifkfLykrldpsyefqkkieeev 96 
                                        ++a++  ++r++r  s+q+++i+++l+fL e+n+e ++s+k ++sP+ k+f+++fkf ++++  ++e+ k++e++ 
  gene1587|gene1587|rna1587|rna1587  17 HPAQAVPEKRNVRSPSYQEQCITNVLSFLDEHNYE-NTSQKGVRSPTLKEFQNLFKFTISFFYKNWEC-KRFEDDA 90 
                                        445566789************************97.6799****************************.9****** PP

                          Ndc80_HEC  97 vkilkelrYPfaesisKsqlaAvgtphtwptllaaLhWlvelaklleel 145
                                        ++++k+l+YP++++i+Ks+l++  +ph+wp +l+ + Wl+++++++  +
  gene1587|gene1587|rna1587|rna1587  91 MQLIKQLKYPYINEINKSHLVTT-SPHSWPVVLSFISWLIDMIRFVGVC 138
                                        **********************9.9*****************9997655 PP

>> DUF812  Protein of unknown function (DUF812)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0  12.0   3.2e-06    0.0044     246     405 ..     162     322 ..     154     327 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 3.2e-06
                             DUF812 246 keklqkrlaeqlrkaalkseeae.ssasksksdlaellsefseksetdslktkgsrfthaekl...qftkeelakk 317
                                        +++ + +l+eq+rk+    ++ e +s+  +k++l++ l+e+++k e+  lk k +++++ +k     f++   + k
  gene1587|gene1587|rna1587|rna1587 162 DNHFEDTLSEQFRKKHET-KIREyESRMDRKKELENRLNEWEMKGENAALKRKIEELEDDKKSimeGFKQL--EMK 234
                                        566778899999999655.5555599999******************************999966655555..456 PP

                             DUF812 318 aeteeelkkkreeeleelqeqieeleskieeleeeikklessikqveeeleeekeeneelekevklkkktlellpd 393
                                        +++   ++++ +ee+ el + + +l+ + ++l+e+i k + ++   +e   +++e  ++le  +  k+k + +l +
  gene1587|gene1587|rna1587|rna1587 235 KDKYCKMTQRYKEEIGELGSGMGALQDERNRLKENIGKQKINVDSYKEMNARKNELLKQLERIKPEKEKCFVMLSE 310
                                        788889999999**************************************************************** PP

                             DUF812 394 aeeniekLqalv 405
                                           + ++L++ +
  gene1587|gene1587|rna1587|rna1587 311 KRRSWARLERRL 322
                                        ****99999866 PP

>> FapA  Flagellar Assembly Protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2  12.5   7.5e-05       0.1     318     451 ..     186     310 ..     159     313 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 7.5e-05
                               FapA 318 selgtkteievgldepelkeklkeleeeleeleeeleklkkkikklpklkaekqlesekkeqlkklletkeklkee 393
                                        s+++ k e+e  l+e e+k + ++l++++eele+  + + + +k+l+++k +++      ++ ++++e+  +l + 
  gene1587|gene1587|rna1587|rna1587 186 SRMDRKKELENRLNEWEMKGENAALKRKIEELEDDKKSIMEGFKQLEMKKDKYC------KMTQRYKEEIGELGSG 255
                                        556666677777776777777788888888888888888888888888777777......8888888888888888 PP

                               FapA 394 leeleeelkelkeeleskkeeakikvnkeiypgvkikig...kkkliikreysnttfvlee 451
                                        + +l++e+++lke++ ++    ki+v +  y++   + +   k+ ++ik e++++ ++l+e
  gene1587|gene1587|rna1587|rna1587 256 MGALQDERNRLKENIGKQ----KINVDS--YKEMNARKNellKQLERIKPEKEKCFVMLSE 310
                                        888888888888888888....444444..5554444443339999999999999888765 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   5.7   1.4e-05     0.019       2      98 ..     212     307 ..     204     309 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.4e-05
                              TMPIT   2 eeweelekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelke 77 
                                        +++eele++ k++ e +k+++ k +++ k+ ++ ++ei +    + +l+++ ++lk+++  +++ +v++ ke+ ++
  gene1587|gene1587|rna1587|rna1587 212 RKIEELEDDKKSIMEGFKQLEMKKDKYCKMTQRYKEEIGELGSGMGALQDERNRLKENI-GKQKINVDSYKEMNAR 286
                                        56788888888888888888888888888888888888888888888888888888886.6888999999999999 PP

                              TMPIT  78 rkkvlkevesllpkknglylk 98 
                                        +++ lk++e + p+k+ +++ 
  gene1587|gene1587|rna1587|rna1587 287 KNELLKQLERIKPEKEKCFVM 307
                                        99*************999986 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   1.4    0.0099        14      62     116 ..     175     234 ..     163     236 .. 0.70
   2 ?   11.8   0.6   0.00013      0.19      50     112 ..     210     272 ..     203     279 .. 0.91
   3 ?    3.2   0.2     0.064        88      53      93 ..     279     319 ..     268     329 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0099
                            DUF1664  62 rhLssridrvdkkldeqkeisk.....eikeevtevredlseigedvesvkeaveglesk 116
                                        ++ + +i + ++++d  ke+ +     e+k e ++++++++e+++d +s+ e +++le+k
  gene1587|gene1587|rna1587|rna1587 175 KKHETKIREYESRMDRKKELENrlnewEMKGENAALKRKIEELEDDKKSIMEGFKQLEMK 234
                                        444556666666666666665522223677889999***************999999987 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00013
                            DUF1664  50 leqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeaveg 112
                                        l++  e+l++ k+ +++  ++++ k d+  ++++  kee+ e+ +++ +++++ + +ke + +
  gene1587|gene1587|rna1587|rna1587 210 LKRKIEELEDDKKSIMEGFKQLEMKKDKYCKMTQRYKEEIGELGSGMGALQDERNRLKENIGK 272
                                        6777899************************************************99998865 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.064
                            DUF1664  53 vseslaatkrhLssridrvdkkldeqkeiskeikeevtevr 93 
                                         +++++a k++L ++++r+  + +++  + +e ++  ++++
  gene1587|gene1587|rna1587|rna1587 279 SYKEMNARKNELLKQLERIKPEKEKCFVMLSEKRRSWARLE 319
                                        46899***************999999988887777666655 PP

>> Tropomyosin  Tropomyosin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9  18.4   0.00031      0.42      98     183 ..     166     254 ..     159     303 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00031
                        Tropomyosin  98 eaqlkeakeiaeead.rkyeEvarklvvvesdLeraeeraeaa..eskiveLeeeLkvvgnnlksLevseekaser 170
                                        e+ l+e  + ++e++ r ye    + + +e+ L++ e ++e+a    ki+eLe++ k + +  k+Le++++k+++ 
  gene1587|gene1587|rna1587|rna1587 166 EDTLSEQFRKKHETKiREYESRMDRKKELENRLNEWEMKGENAalKRKIEELEDDKKSIMEGFKQLEMKKDKYCKM 241
                                        67777777777777624455556678999**********997633689**************************** PP

                        Tropomyosin 171 edeyeeeirtLee 183
                                         ++y+eei +L +
  gene1587|gene1587|rna1587|rna1587 242 TQRYKEEIGELGS 254
                                        ********99965 PP

>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   2.2    0.0039       5.3       3      39 ..     192     230 ..     190     232 .. 0.83
   2 ?    3.9   0.0     0.051        70       7      37 ..     247     277 ..     243     292 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0039
                          FlaC_arch   3 delEnklsklst..eletvkkeneelsksveelkenVkd 39 
                                        +elEn+l++ ++  e + +k+++eel+++ + + e +k+
  gene1587|gene1587|rna1587|rna1587 192 KELENRLNEWEMkgENAALKRKIEELEDDKKSIMEGFKQ 230
                                        79*********9888889999999999988887776665 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.051
                          FlaC_arch   7 nklsklsteletvkkeneelsksveelkenV 37 
                                        +++++l + ++ +++e + l++++ + k nV
  gene1587|gene1587|rna1587|rna1587 247 EEIGELGSGMGALQDERNRLKENIGKQKINV 277
                                        6899999***************999887777 PP

>> Atg14  Vacuolar sorting 38 and autophagy-related subunit 14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   9.6   0.00043       0.6      33     123 ..     202     295 ..     187     324 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00043
                              Atg14  33 klksekeslkkkiekalegke....eaeqledkiknkkakleelksliadlrerlqelkdklsqlkkeieekkkkl 104
                                         +k e+++lk+kie+++  k+      +qle+k ++  +  ++ k +i +l + +  l+d + +lk+ i ++k ++
  gene1587|gene1587|rna1587|rna1587 202 EMKGENAALKRKIEELEDDKKsimeGFKQLEMKKDKYCKMTQRYKEEIGELGSGMGALQDERNRLKENIGKQKINV 277
                                        6899****************9888888888999998889999999999999999********************** PP

                              Atg14 105 aklsdklkkRrsdleslqn 123
                                         ++++ ++++++ l+   +
  gene1587|gene1587|rna1587|rna1587 278 DSYKEMNARKNELLKQ-LE 295
                                        ******9855544433.33 PP

>> TSC22  TSC-22/dip/bun family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       4.3   5.9e+03      23      50 ..      38      64 ..      36      69 .. 0.65
   2 ?    2.5   1.3      0.13   1.8e+02      35      44 ..     205     214 ..     189     225 .. 0.56
   3 ?    2.9   0.2     0.097   1.3e+02      18      31 ..     209     222 ..     203     233 .. 0.81
   4 ?    8.6   0.0    0.0016       2.2      20      50 ..     246     276 ..     243     287 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 4.3
                              TSC22 23 IkeLeernseleeENslLkalaspeqle 50
                                       I++ ++   e ++EN+  k   sp +l+
  gene1587|gene1587|rna1587|rna1587 38 ITNVLSFLDEHNYENTSQKGVRSP-TLK 64
                                       666677777888999988854444.454 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.13
                              TSC22  35 eENslLkala 44 
                                         EN+ Lk+ +
  gene1587|gene1587|rna1587|rna1587 205 GENAALKRKI 214
                                        4555555443 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.097
                              TSC22  18 vLkekIkeLeerns 31 
                                         Lk kI eLe++ +
  gene1587|gene1587|rna1587|rna1587 209 ALKRKIEELEDDKK 222
                                        69*******99866 PP

  == domain 4  score: 8.6 bits;  conditional E-value: 0.0016
                              TSC22  20 kekIkeLeernseleeENslLkalaspeqle 50 
                                        ke+I eL + + +l+ E + Lk+++ ++ ++
  gene1587|gene1587|rna1587|rna1587 246 KEEIGELGSGMGALQDERNRLKENIGKQKIN 276
                                        9***********************9887765 PP

>> TMF_TATA_bd  TATA element modulatory factor 1 TATA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   8.6      0.43     6e+02      17      89 ..     177     247 ..     166     253 .. 0.70
   2 ?   13.7   5.0   3.9e-05     0.054      23      92 ..     244     313 ..     240     323 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.43
                        TMF_TATA_bd  17 lsseirrlEgElaslkeelerleaerdeareeivklmkeneelkelkkeleelekeleelqeryetlLellGe 89 
                                         +++ir+ E+ +   ke  +rl++   e++ e ++l ++ eel++ kk++ e  k+le  +++y ++ + ++e
  gene1587|gene1587|rna1587|rna1587 177 HETKIREYESRMDRKKELENRLNE--WEMKGENAALKRKIEELEDDKKSIMEGFKQLEMKKDKYCKMTQRYKE 247
                                        556677777777776666666655..46777888888888888888888888888888888887777666555 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 3.9e-05
                        TMF_TATA_bd  23 rlEgElaslkeelerleaerdeareeivklmkeneelkelkkeleelekeleelqeryetlLellGeksE 92 
                                        r   E+ +l + +  l+ er++++e i k   ++++ ke++++ +el k+le ++ + e++  +l ek  
  gene1587|gene1587|rna1587|rna1587 244 RYKEEIGELGSGMGALQDERNRLKENIGKQKINVDSYKEMNARKNELLKQLERIKPEKEKCFVMLSEKRR 313
                                        567788999999999****************************************************975 PP

>> Exonuc_VII_L  Exonuclease VII, large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   6.6    0.0015       2.1     160     262 ..     184     300 ..     152     327 .. 0.38

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0015
                       Exonuc_VII_L 160 ikrlleekkqrleklasrl.....kspeellerkrqrldeleerleralkkqlkkkrerleelkerlk........ 222
                                         ++++++kk    +l++rl     k  ++ l+rk ++l++ ++++ +   kql+ k+ ++ ++++r+k        
  gene1587|gene1587|rna1587|rna1587 184 YESRMDRKK----ELENRLnewemKGENAALKRKIEELEDDKKSIME-GFKQLEMKKDKYCKMTQRYKeeigelgs 254
                                        222222222....2222221111133344444444444444444444.4444444444444444444223333333 PP

                       Exonuc_VII_L 223 ..ekleekkerlkklkerle.......lleekkerleeleeklealspl 262
                                            l+++++rlk+             + +e + r +el ++le ++p+
  gene1587|gene1587|rna1587|rna1587 255 gmGALQDERNRLKENI---GkqkinvdSYKEMNARKNELLKQLERIKPE 300
                                        3322222222221111...011111223333333333333333333333 PP

>> BRE1  BRE1 E3 ubiquitin ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   3.6      0.59   8.1e+02      55      93 ..     175     218 ..     168     220 .. 0.80
   2 ?   12.3   9.5   9.6e-05      0.13       8      94 ..     210     296 ..     204     297 .. 0.95

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.59
                               BRE1  55 dalenelkkLnkllsKsselieqLke.....lekefvrklkele 93 
                                        ++ e++++   + +++++el ++L+e       ++++rk++ele
  gene1587|gene1587|rna1587|rna1587 175 KKHETKIREYESRMDRKKELENRLNEwemkgENAALKRKIEELE 218
                                        66778888888899999999999999888877888888888888 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 9.6e-05
                               BRE1   8 lekafeelseqlskkvkeltileekklrleaekakadqkyfaamrskdalenelkkLnkllsKsselieqLkelek 83 
                                        l++ +eel++  ++  + ++ le kk ++ ++ ++ ++++ ++   + al+ e ++L++++ K++  ++  ke+ +
  gene1587|gene1587|rna1587|rna1587 210 LKRKIEELEDDKKSIMEGFKQLEMKKDKYCKMTQRYKEEIGELGSGMGALQDERNRLKENIGKQKINVDSYKEMNA 285
                                        678899999999999999*********************************************************9 PP

                               BRE1  84 efvrklkelek 94 
                                          +++lk+le+
  gene1587|gene1587|rna1587|rna1587 286 RKNELLKQLER 296
                                        99999999997 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   7.6    0.0038       5.3     104     230 ..     165     298 ..     163     312 .. 0.68

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0038
                            DUF4407 104 FekeIdaelaeeqqeeakelkeqlaaa..ltaela..eleaqiaalqaeidaaearldalraeaqkeldgtkgtgt 175
                                        Fe+ + ++ +++++ +++e++++++ +  l+++l+  e++ ++aal+++i+++e++ +  ++ ++ +l+ +k + +
  gene1587|gene1587|rna1587|rna1587 165 FEDTLSEQFRKKHETKIREYESRMDRKkeLENRLNewEMKGENAALKRKIEELEDDKKSIMEGFK-QLEMKKDKYC 239
                                        9999999*************999998888444444113455566777777777777766666666.4444556667 PP

                            DUF4407 176 tgvaGkgpaakekkaqldaaqaelaelkakld....atarlaalraelaeleaeraker 230
                                        + ++++ ++  e  + + a+q e + lk+++     + +  ++ +a+++el +++++++
  gene1587|gene1587|rna1587|rna1587 240 KMTQRYKEEIGELGSGMGALQDERNRLKENIGkqkiNVDSYKEMNARKNELLKQLERIK 298
                                        77778888888888888888888888888877666655555555555555555544444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (331 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2041  (0.113838); expected 358.6 (0.02)
Passed bias filter:                      662  (0.0369234); expected 358.6 (0.02)
Passed Vit filter:                        80  (0.00446204); expected 17.9 (0.001)
Passed Fwd filter:                        25  (0.00139439); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.69u 0.27s 00:00:00.96 Elapsed: 00:00:00.45
# Mc/sec: 2231.45
//
Query:       gene1588|gene1588|rna1588|rna1588  [L=67]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (67 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       252  (0.0140554); expected 358.6 (0.02)
Passed bias filter:                      208  (0.0116013); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.32u 0.25s 00:00:00.57 Elapsed: 00:00:00.40
# Mc/sec: 506.23
//
Query:       gene1589|gene1589|rna1589|rna1589  [L=512]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.023   14.7   1.0      0.053   13.6   1.0    1.6  1  CrgA      Cell division protein CrgA
       0.17   11.7   8.8      0.028   14.2   5.2    1.4  2  DUF1282   Protein of unknown function (DUF1282)
       0.46    9.8   3.7       0.86    8.9   3.7    1.4  1  DUF3810   Protein of unknown function (DUF3810)
          2    8.4   5.7        7.1    6.7   5.4    2.0  1  DUF485    Protein of unknown function, DUF485
        2.9    7.9  10.4      0.053   13.6   2.5    1.9  2  MARVEL    Membrane-associating domain


Domain annotation for each model (and alignments):
>> CrgA  Cell division protein CrgA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   1.0   1.5e-05     0.053      32      86 ..     201     262 ..     179     264 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.5e-05
                               CrgA  32 rwyvpvmlglmllGllwlvvyYlageeip.......fmaelgawNlliGfgliivGllmttr 86 
                                        +++  + + l+++G++  v+yY+a+  ++       ++a++ + N  i++ +i++ ll+t  
  gene1589|gene1589|rna1589|rna1589 201 PVFFGIAIVLFIMGCIASVIYYVAQILLKylgdqdgWFATFCSLNCHIAMLIILITLLITFM 262
                                        567778899***************994444455566999*******************9975 PP

>> DUF1282  Protein of unknown function (DUF1282)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.3   0.1       3.8   1.3e+04      25      43 ..     165     183 ..     162     185 .. 0.68
   2 ?   14.2   5.2   7.7e-06     0.028      21     115 ..     202     299 ..     198     320 .. 0.82

  Alignments for each domain:
  == domain 1  score: -4.3 bits;  conditional E-value: 3.8
                            DUF1282  25 vlillllliglvvfiystf 43 
                                        v+ill +l+ ++ + y  f
  gene1589|gene1589|rna1589|rna1589 165 VIILLTALCIPADYTYTCF 183
                                        7788888877776666555 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 7.7e-06
                            DUF1282  21 vlyivlillllliglvvfiystfqvlseiltkqankltlassliisvvfylalgvlvlayliklmgrtydsqhs.. 94 
                                        v++ ++i+l+ ++  ++ iy+++q+l + l  q+  +  + sl + +++ ++l +l++++++k m+   +++ +  
  gene1589|gene1589|rna1589|rna1589 202 VFFGIAIVLFIMGCIASVIYYVAQILLKYLGDQDGWFATFCSLNCHIAMLIILITLLITFMYKRMANLQFAKGTnl 277
                                        67889999999999*****************99999*********************************9998865 PP

                            DUF1282  95 .yskifafaayalvplflggla 115
                                          s ++ +  +a + l l  ++
  gene1589|gene1589|rna1589|rna1589 278 dISHVLSTLLFANFLLTLKTFI 299
                                        5555555555555555555555 PP

>> DUF3810  Protein of unknown function (DUF3810)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   3.7   0.00024      0.86      29      92 ..     208     276 ..     201     334 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00024
                            DUF3810  29 ivllillvilylvlai..klkkrkkkkkrllkvllrvllvllvvyflftllwglnYyre...plserlg 92 
                                        ivl+i+ +i+++++++  +l k    +  ++ ++ ++ + ++++++l tll ++ Y+r+   ++++ ++
  gene1589|gene1589|rna1589|rna1589 208 IVLFIMGCIASVIYYVaqILLKYLGDQDGWFATFCSLNCHIAMLIILITLLITFMYKRManlQFAKGTN 276
                                        55556666666555555544667778899****************************985445555555 PP

>> DUF485  Protein of unknown function, DUF485
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   5.4     0.002       7.1      51      81 ..     242     272 ..     206     276 .. 0.67

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.002
                             DUF485  51 itvglllgllqivltflltglYvrrAnrefD 81 
                                         ++   +++l+i++t l+t++Y r+An +f 
  gene1589|gene1589|rna1589|rna1589 242 CSLNCHIAMLIILITLLITFMYKRMANLQFA 272
                                        456778999******************9885 PP

>> MARVEL  Membrane-associating domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   1.1      0.71   2.6e+03      68     100 ..     139     171 ..     135     174 .. 0.82
   2 ?   13.6   2.5   1.5e-05     0.053      14     117 ..     206     313 ..     197     366 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.71
                             MARVEL  68 saftsilwplidlivdalaallwlvafialaag 100
                                        ++f ++ + ++d +++  ++ ++l + i+l  +
  gene1589|gene1589|rna1589|rna1589 139 THFFRRVFVFFDRLLEIDFIYFFLGSVIILLTA 171
                                        567888999999999999999999999998765 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 1.5e-05
                             MARVEL  14 lvfaiiilgliaslia........kldqllgspssalnfavfvavfsflyalfllvlylfk..nsaftsilwplid 79 
                                        ++  ++i+g+ias+i+        +l +++g+  + +++   +a + +l++l++ ++y      +++  ++  + +
  gene1589|gene1589|rna1589|rna1589 206 IAIVLFIMGCIASVIYyvaqillkYLGDQDGWFATFCSLNCHIAMLIILITLLITFMYKRManLQFAKGTNLDISH 281
                                        4556899999999999999****98899999999999999999999999999999998888989999999****** PP

                             MARVEL  80 livdalaallwlvafialaaglrdiscafesnqysasl 117
                                        ++ ++l+a + l+  +++ ++++         +ys +l
  gene1589|gene1589|rna1589|rna1589 282 VLSTLLFANFLLTLKTFILKKVSL------TFNYSTHL 313
                                        ************999999999987......34455444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (512 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1139  (0.0635284); expected 358.6 (0.02)
Passed bias filter:                      569  (0.0317363); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.60u 0.31s 00:00:00.90 Elapsed: 00:00:00.46
# Mc/sec: 3345.99
//
Query:       gene159|gene159|rna159|rna159  [L=212]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.087   12.7  23.7       0.19   11.6   0.9    2.1  2  RPN2_C          26S proteasome regulatory subunit RPN2 C-term
       0.37    9.7  12.4       0.47    9.4  12.4    1.1  1  SLC12           Solute carrier family 12
       0.46    8.6  28.8       0.53    8.4  28.8    1.0  1  Nop14           Nop14-like family
       0.47    8.5  15.7        0.6    8.2  15.7    1.0  1  Hid1            High-temperature-induced dauer-formation prot
       0.65    8.7  11.9       0.89    8.2  11.9    1.2  1  Presenilin      Presenilin
       0.76    9.8  34.1       0.36   10.9  20.1    2.1  2  RNA_polI_A34    DNA-directed RNA polymerase I subunit RPA34.5
        2.6    7.2  11.6        9.6    5.3   0.2    2.1  2  TRAP_alpha      Translocon-associated protein (TRAP), alpha s
        2.6    6.9   7.9        3.3    6.6   7.9    1.3  1  XRN_M           Xrn1 helical domain
        3.2    8.5  32.9          8    7.3   4.1    2.3  2  DTHCT           DTHCT (NUC029) region
        7.5    4.2  16.6        9.2    3.9  16.6    1.0  1  PI3K_1B_p101    Phosphoinositide 3-kinase gamma adapter prote
        7.7    5.6  12.0         11    5.1   0.2    2.1  2  D123            D123


Domain annotation for each model (and alignments):
>> RPN2_C  26S proteasome regulatory subunit RPN2 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.9   0.00012      0.19      21     101 ..       4      82 ..       2     101 .. 0.52
   2 ?    6.2  15.8    0.0057       9.2      60     105 ..     126     168 ..     113     190 .. 0.45

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00012
                                    S-TTTTSSS-S--HHHHH.HHHHHHHHHHHHHHHHHHHHHHHHHHG....------------------------------ CS
                         RPN2_C  21 akpslFaYPpeleekkek.ekekvatAvLSttakakarakkkekek...eeeekeedkmdvdeekeekekkekekkekek 96 
                                    ++ +lF  P+ ++ +++    +k++  +LS  a   a+   + +++   +     ++    ++++++k+kk++ ++e+e+
  gene159|gene159|rna159|rna159   4 TNVKLFVSPKTIKLENRRlFMNKLHLMILSLIAVVSAKRLARLNNSnliT-----AQRLTSEKSNDKKKKKKSGDDEEEE 78 
                                    66778888888886665515799999999998876666544444442331.....2222222222222222222222221 PP

                                    ----S CS
                         RPN2_C  97 eeekk 101
                                      +kk
  gene159|gene159|rna159|rna159  79 G-DKK 82 
                                    1.111 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0057
                                    HHHHHG.----------------------------------SS--- CS
                         RPN2_C  60 kkekekeeeekeedkmdvdeekeekekkekekkekekeeekkkkek 105
                                    k++++  ++ k++dk+++d +++++e+k++ekk+++k+ ekk+k  
  gene159|gene159|rna159|rna159 126 KEQSA--KKGKTGDKKKKDASENDEEEKKDEKKDEKKD-EKKEKGS 168
                                    22222..2344444444444333333333333333322.2222222 PP

>> SLC12  Solute carrier family 12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4  12.4   0.00029      0.47     113     237 ..      35     176 ..      14     191 .. 0.46

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00029
                          SLC12 113 lavaiLrlkegldvsellqeeeeeeeekekkeaeesekeeeekkkakkkklle........................... 165
                                    +av+  +    l+ s+l+++++ ++e++++k++++++ ++ee++ +kk+kl++                           
  gene159|gene159|rna159|rna159  35 IAVVSAKRLARLNNSNLITAQRLTSEKSNDKKKKKKSGDDEEEEGDKKSKLMAnsfmnthsllasqsglapssdksggdd 114
                                    55555555667888888888877777666666555554344433333333333678889999999888888755444332 PP

                          SLC12 166 ...ekskekeekekleekdsnlslseekk....eeekekkkekkkkkekkeklkkkekslllkeaskeekevleeitqf 237
                                                   ++k+ + + ++ kk    +++k++++e+++      ++kk+ek+  +k+++ke+ + l++ ++f
  gene159|gene159|rna159|rna159 115 dqsG-----------SKKSGSGKEQSAKKgktgDKKKKDASENDE------EEKKDEKKDEKKDEKKEKGSSLKAHNTF 176
                                    2220...........111111111111111111111111111111......1111111111222222222333333333 PP

>> Nop14  Nop14-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4  28.8   0.00033      0.53     288     413 ..      40     167 ..      37     211 .. 0.46

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00033
                          Nop14 288 eeRlkRMrge......edeeeeeekkkkkkkeasaDdldddfvleeeeeeeefglgkgl.ka......taeeeeeededd 354
                                    ++Rl+R +          ++e++++kkkkkk  s+Dd +++   +++  ++ f   ++l ++      ++        d+
  gene159|gene159|rna159|rna159  40 AKRLARLNNSnlitaqRLTSEKSNDKKKKKK--SGDDEEEEGDKKSKLMANSFMNTHSLlASqsglapSS--------DK 109
                                    5899999988899874344444445555555..8999887777777777776665555542134444322........22 PP

                          Nop14 355 feedddlveseseeee........eeeeedeeeeedeeeeeeeeededdlsdleseeeeeedeleee 413
                                    +  ddd++ s+++ +         ++ +++++++++++eee+++e++d+++d+++e         ++
  gene159|gene159|rna159|rna159 110 SGGDDDQSGSKKSGSGkeqsakkgKTGDKKKKDASENDEEEKKDEKKDEKKDEKKE---------KG 167
                                    22222222222222210000011122222222222222222222222222222222.........11 PP

>> Hid1  High-temperature-induced dauer-formation protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2  15.7   0.00037       0.6     571     704 ..      46     181 ..      30     185 .. 0.60

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00037
                           Hid1 571 lrnltlesaseeiersne..sarldsideeeeenssessrieesrsesrspslsevpelksslaitddeskaereksate 648
                                    l n++l  a+   +++ +  +++++s d+eeee +++s+ + +s  + +s   s+   + ss + + d++++ ++ks + 
  gene159|gene159|rna159|rna159  46 LNNSNLITAQRLTSEKSNdkKKKKKSGDDEEEEGDKKSKLMANSFMNTHSLLASQSGLAPSSDKSGGDDDQSGSKKSGSG 125
                                    55554444443322222222344445555555544444444444555566655666656666666666666666666666 PP

                           Hid1 649 ssssqavsqlremsekarakesaesteesrqesatskkspsgmsqsaeekftptse 704
                                    +++s+ + ++   ++k+++++++e+++ +++++++++k+++g s +a+++f  ++ 
  gene159|gene159|rna159|rna159 126 KEQSAKKGKTGDKKKKDASENDEEEKKDEKKDEKKDEKKEKGSSLKAHNTFNSEAL 181
                                    66665555666777777788888888888888899999999999999999987765 PP

>> Presenilin  Presenilin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2  11.9   0.00055      0.89     231     317 ..      55     163 ..      27     197 .. 0.44

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00055
                     Presenilin 231 evaeseeeeeaekkkeeasesskeeesee.esseksaqsse....................................see 273
                                    ++ +se++++++kkk++ +++++e ++++  +++      +                                    +  
  gene159|gene159|rna159|rna159  55 QRLTSEKSNDKKKKKKSGDDEEEEGDKKSkLMAN------SfmnthsllasqsglapssdksggdddqsgskksgsgK-- 126
                                    2222222222222222222222222222212222......12233457777888888888888887776543332221.. PP

                     Presenilin 274 eseeesseaessaeesseekeseessesseeeeeeeeeeeeses 317
                                        e+s+++ ++  ++++++se+++e++++e+++   e++ e+
  gene159|gene159|rna159|rna159 127 ----EQSAKKGKTGDKKKKDASENDEEEKKDEKKD---EKKDEK 163
                                    ....1111111111111111111111111111111...111111 PP

>> RNA_polI_A34  DNA-directed RNA polymerase I subunit RPA34.5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   6.0     0.013        21     164     201 ..      60      82 ..      39      89 .. 0.48
   2 ?   10.9  20.1   0.00022      0.36     127     186 ..     109     168 ..      98     207 .. 0.54

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.013
                                    X.XXXXXXXXXXXXXXXXXXXX..XXXXXX...XXXXX CS
                   RNA_polI_A34 164 deeeeapkkkkkkkkkkkekkeeekkeekeeeskkskk 201
                                    +  +++ kkkkkk+ +++e+++             +kk
  gene159|gene159|rna159|rna159  60 E--KSNDKKKKKKSGDDEEEEG-------------DKK 82 
                                    1..2222333333333222222.............222 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00022
                                    XX............XXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXX. CS
                   RNA_polI_A34 127 gtigssseesegekekkkkpkakkkekkkkkkkaaeedeeeeapkkkkkkkkkkkekkee 186
                                    ++ g++++++++++ + k + akk ++  kkkk+a e++eee++ +kk +kk++k++k++
  gene159|gene159|rna159|rna159 109 KSGGDDDQSGSKKSGSGKEQSAKKGKTGDKKKKDASENDEEEKKDEKKDEKKDEKKEKGS 168
                                    333334444333333333322222222222222222222355555555555555555543 PP

>> TRAP_alpha  Translocon-associated protein (TRAP), alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.2    0.0059       9.6       3      56 ..      30      85 ..      25     110 .. 0.50
   2 ?    5.0   6.5    0.0073        12      27      85 ..     128     186 ..     114     202 .. 0.58

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0059
                     TRAP_alpha  3 llllll.vlpavllll.ssatkvvaaaaaeedevddelvdveaedeeveeeeeeee 56
                                   ++l+l+ v+ a  l   ++++  +a+  + e + d++ +  +++dee+e++++++ 
  gene159|gene159|rna159|rna159 30 MILSLIaVVSAKRLARlNNSNLITAQRLTSEKSNDKKKKKKSGDDEEEEGDKKSKL 85
                                   44555423334444442344444444444444444444444445555555554433 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0073
                     TRAP_alpha  27 aaaeedevdde.lvdveaedeeveeeeeeeeeeeeeeeedeeelkaspdadttilFtkpv 85 
                                    ++a++ ++ d+  +d++ e++e+e+++e+++e+++e +e+ ++lka+   +   l  + v
  gene159|gene159|rna159|rna159 128 QSAKKGKTGDKkKKDAS-ENDEEEKKDEKKDEKKDEKKEKGSSLKAHNTFNSEALLKRRV 186
                                    33333334333155544.444444444455556666666666788888877777777666 PP

>> XRN_M  Xrn1 helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   7.9     0.002       3.3      77     166 ..      50     158 ..       8     190 .. 0.61

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.002
                          XRN_M  77 ekifrkrkeredrkekklakeeeaskedaaneeaavaeeklseskvak.....................saeaeaeaeae 135
                                    + i ++r + e++++kk++k++ + +e++ +++++ + ++  +++                        s ++++ + +e
  gene159|gene159|rna159|rna159  50 NLITAQRLTSEKSNDKKKKKKSGDDEEEEGDKKSKLMANSFMNTH--SllasqsglapssdksggdddqSGSKKSGSGKE 127
                                    445556666666666655555555555554444444333333322..034667899999999999999844444444444 PP

                          XRN_M 136 aeaeakaekekrekaekeleeseeeeeeeDk 166
                                    ++a++ ++ +k++k  +e++e+e+++e++D+
  gene159|gene159|rna159|rna159 128 QSAKKGKTGDKKKKDASENDEEEKKDEKKDE 158
                                    4444444444444444455555554444444 PP

>> DTHCT  DTHCT (NUC029) region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   4.1    0.0049         8      54      81 ..      57      84 ..      39      95 .. 0.55
   2 ?    7.0  20.9    0.0058       9.5       3      68 ..     104     169 ..     103     194 .. 0.64

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0049
                          DTHCT 54 ktskatakKkkKkaseddddfsvdldse 81
                                    ts ++  KkkKk+s dd++ + d++s+
  gene159|gene159|rna159|rna159 57 LTSEKSNDKKKKKKSGDDEEEEGDKKSK 84
                                   4444444444444445554444444433 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0058
                          DTHCT   3 apkakkka.eksssDsdsdagakkkaaaaKgrkarKRktssssedddsdpgkktskatakKkkKkas 68 
                                    ap++ k+  + ++s s+ ++g+ k+ +a+Kg+ + K+k+  s++d++ + ++k   +  +Kk+K +s
  gene159|gene159|rna159|rna159 104 APSSDKSGgDDDQSGSK-KSGSGKEQSAKKGKTGDKKKKDASENDEEEKKDEKKDEKKDEKKEKGSS 169
                                    56666665333333333.455778899999*********9998887777766666666666666432 PP

>> PI3K_1B_p101  Phosphoinositide 3-kinase gamma adapter protein p101 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9  16.6    0.0057       9.2     304     438 ..      60     190 ..      40     204 .. 0.52

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.0057
                   PI3K_1B_p101 304 eselaspeeledeeeedeedvdeeedleeeeeeeeedslarsstlstvsss....skdsmlsllslsssslassvsslss 379
                                    e       +++d+++++++  deee+ +++++   ++ +   s l + s       k    + +s s++s +   +s++ 
  gene159|gene159|rna159|rna159  60 E-------KSNDKKKKKKSGDDEEEEGDKKSKLMANSFMNTHSLLASQSGLapssDKSGGDDDQSGSKKSGSGKEQSAKK 132
                                    2.......222222222222333333333333333333322222222222233213444445577777777777888888 PP

                   PI3K_1B_p101 380 gvds.dyvedsdessssspvaekkekkskkksksrlserlsrlfksksprvlrRakslgn 438
                                    g    +   d+ e+ +++++ ekk++k+ +k+++  s + ++ f+  s+  l+R  sl +
  gene159|gene159|rna159|rna159 133 GKTGdKKKKDASENDEEEKKDEKKDEKKDEKKEKGSSLKAHNTFN--SEALLKRRVSLLS 190
                                    776623455666666666667888888777777777777888887..4555666666654 PP

>> D123  D123
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.2    0.0066        11      32      79 ..      53      95 ..      26     100 .. 0.46
   2 ?    3.9   6.5     0.016        26      41     100 ..     135     201 ..     114     203 .. 0.51

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0066
                                   -----...............------------------..--...HHHHH CS
                           D123 32 lpeeseeekesaeesesdsdseesdsedeeeeeeeeee..pseefpelee 79
                                    +++ ++e       +s++++++++s d+eeee ++++   +++f ++++
  gene159|gene159|rna159|rna159 53 TAQRLTSE-------KSNDKKKKKKSGDDEEEEGDKKSklMANSFMNTHS 95
                                   33333322.......22222222222222222222211246777777775 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.016
                                    ..............------------------....--...HHHHHHHHHHHHHTTS-EEEE-SS-- CS
                           D123  41 e...saeesesdsdseesdsedeeeeeeeeee....pseefpeleekikeaieelggavfpKlnwsa 100
                                    +   ++++ ++++++e++d++++e+++e++e+    ++++  + e+ +k+ ++ l +++ p+ n sa
  gene159|gene159|rna159|rna159 135 TgdkKKKDASENDEEEKKDEKKDEKKDEKKEKgsslKAHNTFNSEALLKRRVSLLSDEIEPRDNLSA 201
                                    0332222333333333333333333333333355443333333456678888888888888777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (212 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2529  (0.141056); expected 358.6 (0.02)
Passed bias filter:                      734  (0.0409393); expected 358.6 (0.02)
Passed Vit filter:                       195  (0.0108762); expected 17.9 (0.001)
Passed Fwd filter:                        84  (0.00468515); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 1.06u 0.35s 00:00:01.41 Elapsed: 00:00:00.52
# Mc/sec: 1223.02
//
Query:       gene1590|gene1590|rna1590|rna1590  [L=724]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      3e-52  176.5   0.1    7.1e-41  139.7   0.0    2.5  2  AAA              ATPase family associated with various cellul
    9.1e-13   48.7   1.0    2.9e-05   24.4   0.0    3.9  3  AAA_22           AAA domain
    1.3e-10   40.9   0.2    6.5e-10   38.7   0.1    2.3  2  AAA_lid_3        AAA+ lid domain
    1.5e-09   38.5   0.0     0.0014   19.1   0.0    3.4  3  AAA_16           AAA ATPase domain
    3.3e-08   33.7   0.9     0.0014   18.6   0.1    2.9  2  AAA_14           AAA domain
      4e-08   33.0   0.7      0.012   15.2   0.1    3.1  4  AAA_7            P-loop containing dynein motor region
    6.5e-08   32.7   0.1    0.00052   20.0   0.0    3.1  2  AAA_5            AAA domain (dynein-related subfamily)
    7.4e-08   32.3   0.0      0.006   16.3   0.0    2.7  2  IstB_IS21        IstB-like ATP binding protein
    1.4e-07   31.8   0.0      3e-05   24.2   0.0    2.6  2  AAA_2            AAA domain (Cdc48 subfamily)
    2.6e-07   31.3   0.1      0.014   15.9   0.0    3.3  2  AAA_18           AAA domain
    3.2e-07   30.7   0.0      0.051   14.0   0.0    3.0  2  RNA_helicase     RNA helicase
    2.5e-06   27.4   0.0       0.02   14.6   0.0    2.7  2  AAA_24           AAA domain
    4.6e-06   26.6   0.0      0.093   12.7   0.0    2.4  2  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
    5.5e-06   26.6   0.0      0.084   13.0   0.0    3.1  3  AAA_33           AAA domain
    9.9e-06   25.3   0.3        0.3   10.6   0.0    3.2  3  AAA_25           AAA domain
    1.3e-05   24.7   0.0     0.0057   16.1   0.0    2.4  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    1.7e-05   24.7   0.0      0.034   13.9   0.0    2.8  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
      2e-05   25.1   0.7       0.04   14.4   0.0    2.5  2  ABC_tran         ABC transporter
    2.3e-05   24.4   0.2        2.5    8.0   0.0    3.9  3  NACHT            NACHT domain
    3.1e-05   23.3   0.0       0.19   10.9   0.0    2.3  2  TIP49            TIP49 P-loop domain
    3.5e-05   23.6   0.0        0.2   11.4   0.0    2.5  2  Sigma54_activat  Sigma-54 interaction domain
    6.2e-05   22.2   0.1      0.046   12.8   0.0    3.3  2  T2SSE            Type II/IV secretion system protein
     0.0001   21.8   0.4       0.96    8.8   0.1    3.4  2  TniB             Bacterial TniB protein
    0.00048   19.6   2.7        0.9    8.8   0.0    3.7  4  ATPase           KaiC
    0.00055   19.4   0.2        1.1    8.6   0.0    3.1  3  PhoH             PhoH-like protein
     0.0018   17.5   1.2       0.52    9.5   0.0    2.9  2  NB-ARC           NB-ARC domain
      0.002   18.0   0.0      0.022   14.6   0.0    2.3  2  AAA_3            ATPase family associated with various cellul
     0.0047   16.9   0.1       0.35   10.9   0.0    2.5  2  ResIII           Type III restriction enzyme, res subunit
     0.0059   16.5   0.1        3.5    7.5   0.0    3.0  2  NTPase_1         NTPase
     0.0063   16.9   0.1       0.46   10.8   0.0    2.7  2  AAA_19           AAA domain
     0.0072   16.0   0.1       0.59    9.9   0.1    2.5  2  AAA_29           P-loop containing region of AAA domain
     0.0075   16.5   0.0       0.28   11.4   0.0    2.6  2  AAA_28           AAA domain
     0.0085   15.9   2.5        2.1    8.1   0.1    3.2  3  DEAD             DEAD/DEAH box helicase
  ------ inclusion threshold ------
      0.012   15.5   0.0      0.066   13.1   0.0    2.1  2  RsgA_GTPase      RsgA GTPase
      0.016   14.5   0.0       0.14   11.4   0.0    2.2  1  KAP_NTPase       KAP family P-loop domain
      0.017   15.3   0.1        1.4    9.1   0.0    3.0  2  Roc              Ras of Complex, Roc, domain of DAPkinase
      0.034   13.8   0.0       0.41   10.3   0.0    2.4  2  AAA_30           AAA domain
      0.038   13.1   0.0       0.66    9.1   0.0    2.4  2  DUF815           Protein of unknown function (DUF815)
      0.049   13.5   5.1        2.6    7.9   0.3    3.8  3  ATPase_2         ATPase domain predominantly from Archaea
      0.072   12.8   0.2          3    7.6   0.0    2.6  2  PduV-EutP        Ethanolamine utilisation - propanediol utili
      0.074   12.3   0.6       0.16   11.2   0.1    1.8  2  DUF2075          Uncharacterized conserved protein (DUF2075)
      0.081   13.0   1.6        6.3    6.9   0.1    3.2  2  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
      0.084   13.1   0.1       0.28   11.4   0.0    1.8  1  CDC48_N          Cell division protein 48 (CDC48), N-terminal
        0.1   12.8   1.2         13    6.1   0.1    3.2  2  DUF3213          Protein of unknown function (DUF3213)
       0.12   12.5   0.0        7.2    6.7   0.0    2.6  2  Sigma54_activ_2  Sigma-54 interaction domain


Domain annotation for each model (and alignments):
>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  139.7   0.0   1.8e-43   7.1e-41       1     131 [.     238     375 ..     238     376 .. 0.93
   2 !   34.4   0.0   6.4e-11   2.5e-08       1     127 [.     555     678 ..     555     683 .. 0.77

  Alignments for each domain:
  == domain 1  score: 139.7 bits;  conditional E-value: 1.8e-43
                                        EEEESSTTSSHHHHHHHHHHHHT.HEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTS......TS.EEEEEETGG CS
                                AAA   1 vllyGppGtGKTllakavakelg.vefleisgsellskyvgesekkirelfkeakeka......kp.silfiDEid 68 
                                        ++lyGppGtGKTl+a+++ + l+ +e   ++g+e+l+kyvg+se++irelfk+a+++       ++ +i+++DEid
  gene1590|gene1590|rna1590|rna1590 238 IMLYGPPGTGKTLIARQIGRLLNaREPKIVNGPEVLNKYVGQSEENIRELFKDAEKEWrkkgsaSHlHIIIFDEID 313
                                        68********************956789**************************6665677789555********* PP

                                        GHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
                                AAA  69 alaksrsgseseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieie 131
                                        a++k+r +++s+ +++vvnqLl+++dgv++  ++++vig+tnr+d +dpallr gRf++++ei+
  gene1590|gene1590|rna1590|rna1590 314 AVCKKR-SENSSITDQVVNQLLSKMDGVESL-NNILVIGMTNRMDLIDPALLRpGRFEIHVEIG 375
                                        ******.88999******************7.66***************************997 PP

  == domain 2  score: 34.4 bits;  conditional E-value: 6.4e-11
                                        EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTS...TSEEEEEETGGGHHHH CS
                                AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakeka...kpsilfiDEidalaks 73 
                                        +ll+G  G+GKT+l    a +++++++++  ++ +   +g se +  +++ke+  +    k++ ++iD+i++l+  
  gene1590|gene1590|rna1590|rna1590 555 ILLCGESGVGKTTLSVRAALSMKIPYVKLISPREV---IGYSEVEKIQFIKEIFINGykcKQCLIIIDDIESLIDY 627
                                        69************************999999988...555555555555555555455558***********999 PP

                                        HTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHSTTSSEE CS
                                AAA  74 rsgseseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallrgRfdrk 127
                                              ++++ v++++ t++  +++  +k++vi+++ + + +++  lr+ fd+ 
  gene1590|gene1590|rna1590|rna1590 628 V-PLGPRFSNAVLQTIKTFVRMESN--GKCFVIATCSSLEIMEELSLRESFDSL 678
                                        9.44566666777776666666666..78*********9998888887777765 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.0   7.2e-08   2.9e-05       8      91 ..     238     338 ..     232     350 .. 0.82
   2 !   13.2   0.2    0.0002      0.08       6      25 ..     553     572 ..     548     593 .. 0.85
   3 ?    6.8   0.0      0.02       7.9      89     131 ..     611     661 ..     595     666 .. 0.75

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 7.2e-08
                             AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaee.erpevv.fvtlpsstsskdllrellralglelka........... 70 
                                        ++++G++GtGKT+ +r++ + l++++     ++pev+ ++  +s+++ ++l+++  +++  +++a           
  gene1590|gene1590|rna1590|rna1590 238 IMLYGPPGTGKTLIARQIGRLLNAREPK-IvNGPEVLnKYVGQSEENIRELFKDAEKEWRKKGSAshlhiiifdei 312
                                        799******************9755433.36******999999999**************9999999999999999 PP

                             AAA_22  71 .....erlsseellealeqalrarav 91 
                                             +r +++ + +++ ++l ++++
  gene1590|gene1590|rna1590|rna1590 313 davckKRSENSSITDQVVNQLLSKMD 338
                                        99988788888888888888888777 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 0.0002
                             AAA_22   6 gilvvtGesGtGKTtllrrl 25 
                                        + ++++GesG+GKTtl  r 
  gene1590|gene1590|rna1590|rna1590 553 SNILLCGESGVGKTTLSVRA 572
                                        679************97665 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.02
                             AAA_22  89 ravielliiDEaqhlr.........seealeeLrsllnlsrkgvqliLvGtp 131
                                        ++ + l+iiD+++ l+         s+++l+++++++  ++ g  ++++ + 
  gene1590|gene1590|rna1590|rna1590 611 CK-QCLIIIDDIESLIdyvplgprfSNAVLQTIKTFVRMESNGKCFVIATCS 661
                                        34.59*********988987776555*********99976666666666555 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.7   0.1   1.6e-12   6.5e-10       2      37 ..     402     437 ..     401     444 .. 0.92
   2 ?   -2.2   0.0       9.5   3.8e+03      37      44 ..     493     500 ..     487     501 .. 0.73

  Alignments for each domain:
  == domain 1  score: 38.7 bits;  conditional E-value: 1.6e-12
                          AAA_lid_3   2 vdlkeLAerTeGySGADlaalcreAallAlrrgike 37 
                                        v+l+e+A++T++y+GA+l a+++ A+  Al+rg+k 
  gene1590|gene1590|rna1590|rna1590 402 VSLEEVAKQTNNYTGAELTAVVKSAVSYALERGLKR 437
                                        99******************************9884 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 9.5
                          AAA_lid_3  37 eitmedfe 44 
                                         +tmedf 
  gene1590|gene1590|rna1590|rna1590 493 RVTMEDFL 500
                                        59****96 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   3.4e-06    0.0014      14      69 ..     225     276 ..     214     349 .. 0.72
   2 !   12.3   0.1   0.00041      0.16      15      41 ..     544     569 ..     535     587 .. 0.77
   3 ?    2.9   0.0      0.33   1.3e+02     127     170 .]     605     657 ..     586     657 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 3.4e-06
                             AAA_16  14 salervrsgrpelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipy 69 
                                        ++++r++ +    ++l+G++G+GK+ ++r++ r l++++   ++g  + +     y
  gene1590|gene1590|rna1590|rna1590 225 DLMDRLHIDHVKGIMLYGPPGTGKTLIARQIGRLLNAREPKIVNGPEVLN----KY 276
                                        5677777777899*******************999999777777776666....33 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00041
                             AAA_16  15 alervrsgrpelvllsGesGvGKsslv 41 
                                        +l+++  ++ +++ll GesGvGK++l 
  gene1590|gene1590|rna1590|rna1590 544 LLKTTFYNT-SNILLCGESGVGKTTLS 569
                                        555555554.89*************95 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.33
                             AAA_16 127 l.allsrderplvlvlDdlq..........wadeaslqllaaLlrlleskpllvv 170
                                        + + +++ ++  ++++Dd++          ++  a lq +++++r  +++ ++v+
  gene1590|gene1590|rna1590|rna1590 605 FiNGYKC-KQ-CLIIIDDIEslidyvplgpRFSNAVLQTIKTFVRMESNGKCFVI 657
                                        4466666.44.8********99999999999999*********999888788776 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.0   0.00028      0.11       5      78 ..     238     317 ..     235     355 .. 0.65
   2 !   18.6   0.1   3.6e-06    0.0014       5     107 ..     555     668 ..     551     692 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00028
                             AAA_14   5 lvitGaRrvGKTtllkqlikell......vkkesilyinldderdkkladpekllelileklkeekktylflDEiq 74 
                                        +++ G+  +GKT +++q+ + l       v+  ++l   + + ++  ++ +++ ++++++k ++++ +++++DEi 
  gene1590|gene1590|rna1590|rna1590 238 IMLYGPPGTGKTLIARQIGRLLNarepkiVNGPEVLNKYVGQSEENIRELFKDAEKEWRKKGSASHLHIIIFDEID 313
                                        6899**************966664444443333333333333333333334456666666633368889******9 PP

                             AAA_14  75 evpe 78 
                                         v +
  gene1590|gene1590|rna1590|rna1590 314 AVCK 317
                                        8843 PP

  == domain 2  score: 18.6 bits;  conditional E-value: 3.6e-06
                             AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderd....kkladpekllelileklkeekktylflDEiqev 76 
                                        +++ G   vGKTtl  + +   l  + +i y++l ++r+    ++ ++ + + e++ + +k  k+ ++++D i  +
  gene1590|gene1590|rna1590|rna1590 555 ILLCGESGVGKTTLSVRAA---L--SMKIPYVKLISPREvigySEVEKIQFIKEIFINGYKC-KQCLIIIDDIESL 624
                                        56778889******86666...3..468*********9975442222222234555555544.8999********* PP

                             AAA_14  77 ...........pewekalkslvdeg..knldvivtGSnskllsk 107
                                                   + + +++k +v+ +   ++ vi+t S++ ++ +
  gene1590|gene1590|rna1590|rna1590 625 idyvplgprfsNAVLQTIKTFVRMEsnGKCFVIATCSSLEIMEE 668
                                        *******9999888999999999552246788889888877644 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       6.4   2.5e+03     156     175 ..     102     121 ..      89     125 .. 0.82
   2 !   14.4   0.0     5e-05      0.02      27      59 ..     229     261 ..     220     269 .. 0.83
   3 !   15.2   0.1     3e-05     0.012      21      52 ..     540     571 ..     533     585 .. 0.86
   4 ?   -2.7   0.0       8.7   3.5e+03      99     110 ..     611     622 ..     602     623 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 6.4
                              AAA_7 156 gppgggrneitpRllrhfnv 175
                                        g +  gr+e+t+R+++ +n 
  gene1590|gene1590|rna1590|rna1590 102 GDKTVGRKEMTERFISLYNN 121
                                        5667799********99886 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 5e-05
                              AAA_7  27 elllknkkpvllvGptGtGKtviikdllkkldk 59 
                                        +l++++ k ++l+Gp GtGKt+i++++ + l+ 
  gene1590|gene1590|rna1590|rna1590 229 RLHIDHVKGIMLYGPPGTGKTLIARQIGRLLNA 261
                                        5789999*****************998777764 PP

  == domain 3  score: 15.2 bits;  conditional E-value: 3e-05
                              AAA_7  21 rysyllelllknkkpvllvGptGtGKtviikd 52 
                                        ++ yll++ + n  ++ll+G++G+GKt++  +
  gene1590|gene1590|rna1590|rna1590 540 KIAYLLKTTFYNTSNILLCGESGVGKTTLSVR 571
                                        689************************98655 PP

  == domain 4  score: -2.7 bits;  conditional E-value: 8.7
                              AAA_7  99 gkklvvFvDDln 110
                                         k++++ +DD+ 
  gene1590|gene1590|rna1590|rna1590 611 CKQCLIIIDDIE 622
                                        599*******95 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   1.3e-06   0.00052       2      75 ..     238     313 ..     237     364 .. 0.67
   2 !    9.4   0.0    0.0026         1       1      22 [.     554     575 ..     554     625 .. 0.75

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 1.3e-06
                                        EEEE--SSSSHHHHHHHGGGGB.S--EEEEE--TT--HHHHH--B--.............--------G-SEEEEE CS
                              AAA_5   2 vlLvGppGtgKselaerlaaal.nreveyvqltrdtteedlkgrreik....ngttslvdsplvraaregeilvlD 72 
                                        ++L GppGtgK+ +a+++ ++l  re  +v++++ +++   + + +i+    + +++++++    +a + +i+++D
  gene1590|gene1590|rna1590|rna1590 238 IMLYGPPGTGKTLIARQIGRLLnAREPKIVNGPEVLNKYVGQSEENIRelfkDAEKEWRKKG---SASHLHIIIFD 310
                                        79********************8777888877765554433333333333333333333332...22366666666 PP

                                        SGG CS
                              AAA_5  73 Eve 75 
                                        E++
  gene1590|gene1590|rna1590|rna1590 311 EID 313
                                        666 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0026
                                        EEEEE--SSSSHHHHHHHGGGG CS
                              AAA_5   1 dvlLvGppGtgKselaerlaaa 22 
                                        ++lL G++G+gK++l+ r a  
  gene1590|gene1590|rna1590|rna1590 554 NILLCGESGVGKTTLSVRAALS 575
                                        689************9776644 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   1.5e-05     0.006      36      71 ..     224     259 ..     204     339 .. 0.68
   2 !   12.9   0.0   0.00017     0.068      31      65 ..     537     570 ..     522     582 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.5e-05
                          IstB_IS21  36 keLatlsfiekkenivllGpsGvGKshlaialgvea 71 
                                        k+L+   +i++ ++i+l Gp+G+GK+ +a  +g+  
  gene1590|gene1590|rna1590|rna1590 224 KDLMDRLHIDHVKGIMLYGPPGTGKTLIARQIGRLL 259
                                        478888899*********************999754 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 0.00017
                          IstB_IS21  31 dkrkvkeLatlsfiekkenivllGpsGvGKshlai 65 
                                         k+k++ L ++ f +   ni+l+G sGvGK+ l++
  gene1590|gene1590|rna1590|rna1590 537 IKEKIAYLLKTTFYN-TSNILLCGESGVGKTTLSV 570
                                        456677777777764.68*************9986 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.0   7.6e-08     3e-05       5     103 ..     237     337 ..     233     343 .. 0.74
   2 ?    4.8   0.0     0.069        28       3      29 ..     552     578 ..     550     622 .. 0.81

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 7.6e-08
                                        -EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG---..----THHHHHHHHHTTT-HHHHTTS....EEEE CS
                              AAA_2   5 silllgptgvGktelakalaellfvkkekkliradaselle..eeevehlvsrligappgyvgaeegG....ivll 74 
                                         i+l gp g+Gkt++a+++ +ll++   ++  +++  e+l     ++e+ + +l   ++   +++ +     i+ +
  gene1590|gene1590|rna1590|rna1590 237 GIMLYGPPGTGKTLIARQIGRLLNA---REPKIVNGPEVLNkyVGQSEENIRELFKDAEKEWRKKGSAshlhIIIF 309
                                        5899*******************95...55555555555553545777777777777777776666668999**** PP

                                        ETGGG-------------HHHHHHHHHHH CS
                              AAA_2  75 DEidKihpkessgadvSregVqrdLLqil 103
                                        DEid +++k+s+++ +  + V++ LL  +
  gene1590|gene1590|rna1590|rna1590 310 DEIDAVCKKRSENSSITDQ-VVNQLLSKM 337
                                        ********87777777666.555555444 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.069
                                        ---EEEE--TTSSHHHHHHHHHHHTT- CS
                              AAA_2   3 iisilllgptgvGktelakalaellfv 29 
                                        +++ill+g++gvGkt l+   a  +++
  gene1590|gene1590|rna1590|rna1590 552 TSNILLCGESGVGKTTLSVRAALSMKI 578
                                        689*************88777766655 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   3.5e-05     0.014       1      34 [.     238     290 ..     238     408 .. 0.74
   2 !   11.7   0.0   0.00074      0.29       1      26 [.     555     578 ..     555     674 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 3.5e-05
                             AAA_18   1 IlltGtpGvGKttlakeLskrlgf...................gvnlrdvake 34 
                                        I+l G+pG+GKt +a+ + ++l+                     +n+r+++k+
  gene1590|gene1590|rna1590|rna1590 238 IMLYGPPGTGKTLIARQIGRLLNArepkivngpevlnkyvgqsEENIRELFKD 290
                                        89****************99996568866666544444443333333333333 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00074
                             AAA_18   1 IlltGtpGvGKttlakeLskrlgfgv 26 
                                        Ill+G +GvGKttl+ + + ++   +
  gene1590|gene1590|rna1590|rna1590 555 ILLCGESGVGKTTLSVRAALSM--KI 578
                                        99*************9886665..44 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.0   0.00013     0.051       1      63 [.     238     292 ..     238     333 .. 0.68
   2 !   13.4   0.0   0.00019     0.074       1      60 [.     555     623 ..     555     646 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 0.00013
                       RNA_helicase   1 iwlyGpsgeGKStlakeLakallkklklkkkdsvysrnpeddfwdgYtgqevvvidDfgqvkd 63 
                                        i+lyGp+g+GK+++a+++ + l       ++++++   +  +++++Y gq    i ++ ++ +
  gene1590|gene1590|rna1590|rna1590 238 IMLYGPPGTGKTLIARQIGRLLN-----AREPKIV---NGPEVLNKYVGQSEENIRELFKDAE 292
                                        78***************666555.....3334453...3556666666665555555555554 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 0.00019
                       RNA_helicase   1 iwlyGpsgeGKStlakeLakallkkl............klkkkdsvysrnpeddfwdgYt.gqevvvidDfgq 60 
                                        i+l+G+sg+GK+tl+ +  +al+ k+            ++ + +++  +  ++ f +gY+ +q  ++idD+ +
  gene1590|gene1590|rna1590|rna1590 555 ILLCGESGVGKTTLSVR--AALSMKIpyvklispreviGYSEVEKI--QFIKEIFINGYKcKQCLIIIDDIES 623
                                        689************99..777777788888888865544444444..44678888****8888888999865 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   5.1e-05      0.02       5      33 ..     238     271 ..     235     329 .. 0.59
   2 !    9.9   0.0    0.0014      0.54       4      23 ..     554     579 ..     551     648 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 5.1e-05
                             AAA_24   5 iliyGpsgiGKTtlakel.....gpkplfidtek 33 
                                        i++yGp+g+GKT +a+++       +p +++  +
  gene1590|gene1590|rna1590|rna1590 238 IMLYGPPGTGKTLIARQIgrllnAREPKIVNGPE 271
                                        89***************96555544444444444 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0014
                             AAA_24   4 kiliyGpsgiGKTtlakel......g 23 
                                        +il+ G+sg+GKTtl  ++      +
  gene1590|gene1590|rna1590|rna1590 554 NILLCGESGVGKTTLSVRAalsmkiP 579
                                        79************987775555555 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.0   0.00063      0.25      21      51 ..     235     270 ..     207     285 .. 0.73
   2 !   12.7   0.0   0.00023     0.093       7      51 ..     534     586 ..     528     590 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00063
                                        E..EEEEESTTSSHHHHHHHHHHHTT--...----T CS
                               TsaE  21 v..ilLeGdLGaGKTtlvrglakalgve...evkSP 51 
                                        v  i+L+G+ G+GKT ++r++ + l+ +    v+ P
  gene1590|gene1590|rna1590|rna1590 235 VkgIMLYGPPGTGKTLIARQIGRLLNARepkIVNGP 270
                                        245********************9988655335555 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00023
                                        HHHHHHHHHHCH......TEEEEEEESTTSSHHHHHHHHHHHTT--..----T CS
                               TsaE   7 tealgkklakal......gdvilLeGdLGaGKTtlvrglakalgve..evkSP 51 
                                        ++++ +k+a  l      ++ ilL G+ G+GKTtl+   a ++++   +  SP
  gene1590|gene1590|rna1590|rna1590 534 MQQIKEKIAYLLkttfynTSNILLCGESGVGKTTLSVRAALSMKIPyvKLISP 586
                                        666777777655544444445**************999888888864555565 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       8.2   3.3e+03     104     123 ..      52      72 ..      48      84 .. 0.74
   2 !   13.0   0.0   0.00021     0.084       2      50 ..     238     289 ..     238     338 .. 0.77
   3 !    9.9   0.0    0.0019      0.77       2      20 ..     555     573 ..     555     659 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 8.2
                             AAA_33 104 vetdeetlkeRlakRaang.d 123
                                        + t++++++ + a+R++++  
  gene1590|gene1590|rna1590|rna1590  52 LPTSNRVIEMNSAQRENHNvA 72 
                                        5689999********998642 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 0.00021
                             AAA_33   2 vllvGlpGsGKstlaerl...lkklgavllssdtlrrrlfgtdqqsktdytr 50 
                                        ++l G+pG+GK+  a+++   l+++   +++ ++++++++g+ +++++++ +
  gene1590|gene1590|rna1590|rna1590 238 IMLYGPPGTGKTLIARQIgrlLNAREPKIVNGPEVLNKYVGQSEENIRELFK 289
                                        6999************973335555599999999999999966666654433 PP

  == domain 3  score: 9.9 bits;  conditional E-value: 0.0019
                             AAA_33   2 vllvGlpGsGKstlaerll 20 
                                        +ll+G +G+GK+tl+ r +
  gene1590|gene1590|rna1590|rna1590 555 ILLCGESGVGKTTLSVRAA 573
                                        689***********98865 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.0    0.0037       1.5      36      53 ..     238     255 ..     221     259 .. 0.78
   2 ?    2.1   0.0       0.3   1.2e+02     142     172 ..     303     333 ..     276     351 .. 0.74
   3 !   10.6   0.0   0.00076       0.3      24      57 ..     543     576 ..     529     578 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0037
                             AAA_25  36 allaGapgtGKttlaldl 53 
                                        ++l+G+pgtGKt +a ++
  gene1590|gene1590|rna1590|rna1590 238 IMLYGPPGTGKTLIARQI 255
                                        78***********99765 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.3
                             AAA_25 142 gvrlvviDplsralggdensnsdvgalveal 172
                                         ++ +++D +++++   ++++s ++++v++l
  gene1590|gene1590|rna1590|rna1590 303 HLHIIIFDEIDAVCKKRSENSSITDQVVNQL 333
                                        3899***********9666666667777766 PP

  == domain 3  score: 10.6 bits;  conditional E-value: 0.00076
                             AAA_25  24 wlvkgllpagelallaGapgtGKttlaldlalav 57 
                                        +l+k      + +ll+G +g+GKttl +  al++
  gene1590|gene1590|rna1590|rna1590 543 YLLKTTFYNTSNILLCGESGVGKTTLSVRAALSM 576
                                        5666666667789****************99987 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   1.4e-05    0.0057      25      49 ..     238     262 ..     232     284 .. 0.88
   2 ?    6.0   0.0     0.017       6.7      18      42 ..     548     572 ..     531     602 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.4e-05
                       Mg_chelatase  25 lllvGppGsGKtmlakrlpsllppl 49 
                                        ++l+GppG+GKt++a+++  ll + 
  gene1590|gene1590|rna1590|rna1590 238 IMLYGPPGTGKTLIARQIGRLLNAR 262
                                        89****************9999765 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.017
                       Mg_chelatase  18 aaaGgHnlllvGppGsGKtmlakrl 42 
                                        +   + n+ll+G +G GKt l  r 
  gene1590|gene1590|rna1590|rna1590 548 TFYNTSNILLCGESGVGKTTLSVRA 572
                                        5556779*************98774 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.0   8.4e-05     0.034      33      68 ..     232     271 ..     221     293 .. 0.81
   2 !    7.5   0.0    0.0077       3.1      33      59 ..     552     578 ..     531     599 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 8.4e-05
                             RuvB_N  33 ldhv...llyGpPGlGkttlakiiakelgvk.lkitsgPv 68 
                                        +dhv   +lyGpPG Gkt +a+ i + l+++  ki  gP 
  gene1590|gene1590|rna1590|rna1590 232 IDHVkgiMLYGPPGTGKTLIARQIGRLLNARePKIVNGPE 271
                                        56643339****************9999875257777775 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0077
                             RuvB_N  33 ldhvllyGpPGlGkttlakiiakelgv 59 
                                           +ll+G  G+Gkttl+   a  +++
  gene1590|gene1590|rna1590|rna1590 552 TSNILLCGESGVGKTTLSVRAALSMKI 578
                                        4579*************9888877765 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0    0.0001      0.04       8      96 ..     232     341 ..     228     359 .. 0.71
   2 !    8.5   0.1    0.0069       2.8       6      27 ..     547     568 ..     544     578 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 0.0001
                                        EETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSB.HHHH... CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxx... RF
                           ABC_tran   8 lkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpelt.vren... 79 
                                        + + + + + G+ G+GK+ +++ + +ll+  e +i ++g ++ ++   +++++i+ l+++++   +++  +++   
  gene1590|gene1590|rna1590|rna1590 232 IDHVKGIMLYGPPGTGKTLIARQIGRLLNAREPKI-VNGPEVLNKYVGQSEENIRELFKDAEKEWRKKgSASHlhi 306
                                        556667899**************************.9999999999999999999999995444444313333677 PP

                                        ..................HHHTCHHHHHHHSTTGG CS
                                        ..................xxxxxxxxxxxxxxxxx RF
                           ABC_tran  80 ..................esdeeiekalsklglke 96 
                                                            d+ ++++lsk++ +e
  gene1590|gene1590|rna1590|rna1590 307 iifdeidavckkrsenssITDQVVNQLLSKMDGVE 341
                                        77766666665555444333333555555555555 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0069
                                        EEEETTSEEEEEESTTSSHHHH CS
                                        xxxxxxxxxxxxxxxxxxxxxx RF
                           ABC_tran   6 lklkegekvaivGenGaGKStL 27 
                                         ++++ + + + Ge+G GK+tL
  gene1590|gene1590|rna1590|rna1590 547 TTFYNTSNILLCGESGVGKTTL 568
                                        5778889999***********9 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.0    0.0063       2.5       3      29 ..     238     264 ..     236     349 .. 0.91
   2 ?    6.6   0.0     0.016       6.5       3      18 ..     555     570 ..     553     583 .. 0.82
   3 ?    4.9   0.0     0.057        23      81     158 ..     612     692 ..     595     697 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0063
                                        EEEEC-TTTCHHHHHHHHHHHHCTS-S CS
                              NACHT   3 vilqGeaGsGKTtLlqklalawaegkl 29 
                                        ++l G++G GKT  ++++ +++ ++++
  gene1590|gene1590|rna1590|rna1590 238 IMLYGPPGTGKTLIARQIGRLLNAREP 264
                                        6899**************999988775 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.016
                                        EEEEC-TTTCHHHHHH CS
                              NACHT   3 vilqGeaGsGKTtLlq 18 
                                        ++l Ge+G+GKTtL  
  gene1590|gene1590|rna1590|rna1590 555 ILLCGESGVGKTTLSV 570
                                        7899*********965 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.057
                                        CCEEEEEE-STT-SS-TCH...........HHHHHCTTTTT--EEEEEEECCCHHH...HCTTSSCE..EEEE--T CS
                              NACHT  81 erlLlilDglDelvtdlgq..kekqpvrtlLselirkkllpeasllltvrpralrd...leeqleeaivlevegfs 151
                                        ++ L+i+D+++ l +  +      ++v + +++ +r ++  ++ +++t+++    +   l+e++ +   + v+ +s
  gene1590|gene1590|rna1590|rna1590 612 KQCLIIIDDIESLIDYVPLgpRFSNAVLQTIKTFVRMESNGKCFVIATCSSLEIMEelsLRESFDSL--VVVRKIS 685
                                        6789******9999876666677899999*********************98886666677777777..9999999 PP

                                        CCHHHHH CS
                              NACHT 152 esrrkql 158
                                         +++++l
  gene1590|gene1590|rna1590|rna1590 686 GNDIEEL 692
                                        9998876 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.0   0.00048      0.19      51      97 ..     236     281 ..     226     296 .. 0.84
   2 !    9.9   0.1   0.00096      0.38      44     103 ..     546     605 ..     533     614 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00048
                                        XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                              TIP49  51 ravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkkte 97 
                                        ++++l Gp+gtGkt +a  i + l++  p  +++g ev    v ++e
  gene1590|gene1590|rna1590|rna1590 236 KGIMLYGPPGTGKTLIARQIGRLLNAREP-KIVNGPEVLNKYVGQSE 281
                                        89**********************98887.57899999888887766 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00096
                                        XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXX.XXXXXXXXXXXXX CS
                              TIP49  44 kekklaGravLlaGpsgtGktalaiaiskelgedvpfval.sgsevys.levkktevltqal 103
                                        k+       +Ll G+sg Gkt l++    +l+ ++p+v+l s  ev   +ev+k   + + +
  gene1590|gene1590|rna1590|rna1590 546 KTTFYNTSNILLCGESGVGKTTLSV--RAALSMKIPYVKLiSPREVIGySEVEKIQFIKEIF 605
                                        555556678************9876..5678999***9861556765326888888877765 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.0    0.0019      0.76      23      50 ..     236     263 ..     219     272 .. 0.81
   2 !   11.4   0.0    0.0005       0.2       6      39 ..     532     569 ..     527     578 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0019
                                        S-EEEECSTTSSHHHHHHHHHHHSTTTT CS
                    Sigma54_activat  23 lsvlitGesGtGKellaraiheaskrke 50 
                                          +++ G  GtGK+l+ar+i +  + +e
  gene1590|gene1590|rna1590|rna1590 236 KGIMLYGPPGTGKTLIARQIGRLLNARE 263
                                        5699***************988666554 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.0005
                                        HHHHHHHHHHHHHCTSS....S-EEEECSTTSSHHHHH CS
                    Sigma54_activat   6 ealkelleqikkvaktd....lsvlitGesGtGKella 39 
                                        + ++++ e+i+ + kt+    +++l+ GesG+GK++l+
  gene1590|gene1590|rna1590|rna1590 532 DIMQQIKEKIAYLLKTTfyntSNILLCGESGVGKTTLS 569
                                        5677777777777666656669************9875 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.0     0.027        11     126     161 ..     232     267 ..      43     268 .. 0.68
   2 !   12.8   0.0   0.00012     0.046     109     148 ..     532     572 ..     482     584 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.027
                              T2SSE 126 vrerglilvsGgTgsGKttllyallkeinksderiv 161
                                        + + + i++ G+ g+GKt ++  +   +n+++ +iv
  gene1590|gene1590|rna1590|rna1590 232 IDHVKGIMLYGPPGTGKTLIARQIGRLLNAREPKIV 267
                                        335567889999999999999999999998887776 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 0.00012
                              T2SSE 109 gaeealkekiaevlrkavrerglilvsGgTgsGKttll.ya 148
                                         ++++ kekia +l++   +  +il+ G  g GKttl   a
  gene1590|gene1590|rna1590|rna1590 532 DIMQQIKEKIAYLLKTTFYNTSNILLCGESGVGKTTLSvRA 572
                                        4567788*****************************86334 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.1    0.0024      0.96      24      60 ..     224     260 ..     215     338 .. 0.76
   2 !    7.7   0.0    0.0052       2.1      16      53 ..     534     570 ..     520     582 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0024
                               TniB  24 eeLleypkrkrmpnlllvGdsnnGKtmivekFarlhp 60 
                                        ++L+++ + + ++ ++l+G++ +GKt i+++  rl +
  gene1590|gene1590|rna1590|rna1590 224 KDLMDRLHIDHVKGIMLYGPPGTGKTLIARQIGRLLN 260
                                        57999999999*****************998766554 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0052
                               TniB  16 akeilerLeeLleypkrkrmpnlllvGdsnnGKtmive 53 
                                        +++i e+++ Ll++   + ++n+ll+G+s +GKt++  
  gene1590|gene1590|rna1590|rna1590 534 MQQIKEKIAYLLKTTFYN-TSNILLCGESGVGKTTLSV 570
                                        567777777777766554.59*************9865 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.2   0.0     0.007       2.8      19      38 ..     235     254 ..     225     255 .. 0.84
   2 ?    0.0   0.1       1.1   4.5e+02      99     154 ..     279     340 ..     258     355 .. 0.73
   3 !    8.8   0.0    0.0023       0.9      11      37 ..     544     570 ..     537     576 .. 0.86
   4 ?   -0.9   0.0       2.2   8.7e+02     105     149 ..     636     680 ..     603     691 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.007
                             ATPase  19 grvvlitGepGtGKtifalq 38 
                                         + + ++G pGtGKt++a q
  gene1590|gene1590|rna1590|rna1590 235 VKGIMLYGPPGTGKTLIARQ 254
                                        566899***********987 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 1.1
                             ATPase  99 kdkedleelieelaeaikeika....krvviDsitgl..ayeekeavaReilrqlvrvlkkl 154
                                        +++e+++el ++ ++  ++++     + ++ D i+++  +++e+++ + + + ql++ + + 
  gene1590|gene1590|rna1590|rna1590 279 QSEENIRELFKDAEKEWRKKGSashlHIIIFDEIDAVckKRSENSSITDQVVNQLLSKMDGV 340
                                        67888899999988888888876654567779999997445555666778888999888655 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.0023
                             ATPase  11 ilkgGipegrvvlitGepGtGKtifal 37 
                                        +lk  +++ + +l++Ge+G GKt+++ 
  gene1590|gene1590|rna1590|rna1590 544 LLKTTFYNTSNILLCGESGVGKTTLSV 570
                                        456779999***************986 PP

  == domain 4  score: -0.9 bits;  conditional E-value: 2.2
                             ATPase 105 eelieelaeaik.eikakrvviDsitglayeekeavaReilrqlvr 149
                                        +++++++++ ++ e + k+ vi + ++l ++++e  +Re ++ lv 
  gene1590|gene1590|rna1590|rna1590 636 NAVLQTIKTFVRmESNGKCFVIATCSSL-EIMEELSLRESFDSLVV 680
                                        4566777777762344588888888888.88888888888888864 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.0    0.0028       1.1      18      40 ..     234     256 ..     221     267 .. 0.78
   2 ?    6.4   0.1     0.013       5.4      20      43 ..     553     576 ..     534     593 .. 0.82
   3 ?   -0.2   0.0       1.5   5.8e+02      91     127 ..     584     620 ..     580     625 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0028
                                        H-SEEEEE--TTSSTTHHHHHHH CS
                               PhoH  18 kndivfaiGpaGtGKtylavala 40 
                                        + + ++  Gp GtGKt++a +++
  gene1590|gene1590|rna1590|rna1590 234 HVKGIMLYGPPGTGKTLIARQIG 256
                                        55667899***********8876 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.013
                                        SEEEEE--TTSSTTHHHHHHHHHH CS
                               PhoH  20 divfaiGpaGtGKtylavalavea 43 
                                        + +   G++G GKt l+v +a+++
  gene1590|gene1590|rna1590|rna1590 553 SNILLCGESGVGKTTLSVRAALSM 576
                                        456789***************986 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 1.5
                                        S-TTCHHHHHHTTSEEEEEGGGGTT--B-SEEEEE-S CS
                               PhoH  91 lgaekvekllekgkievaplaymRGrTlndafvilDE 127
                                        ++ ++v  + e +ki++++  ++ G   +++++i+D+
  gene1590|gene1590|rna1590|rna1590 584 ISPREVIGYSEVEKIQFIKEIFINGYKCKQCLIIIDD 620
                                        56667777889999**********************8 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.0    0.0013      0.52       9      42 ..     227     257 ..     220     344 .. 0.88
   2 ?    5.9   0.0     0.015       6.1      12      40 ..     544     572 ..     533     578 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0013
                                        HHHHHCTTTSCSEEEEEEESTTSSHHHHHHHHCC CS
                             NB-ARC   9 iekLlekdelqslvvalvGmgGvGKttlakqiln 42 
                                        +++L   d ++   + l+G +G GKt +a+qi +
  gene1590|gene1590|rna1590|rna1590 227 MDRLH-IDHVK--GIMLYGPPGTGKTLIARQIGR 257
                                        55555.55555..689***************965 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.015
                                        HHCTTTSCSEEEEEEESTTSSHHHHHHHH CS
                             NB-ARC  12 LlekdelqslvvalvGmgGvGKttlakqi 40 
                                        Ll+    ++  + l G  GvGKttl+  +
  gene1590|gene1590|rna1590|rna1590 544 LLKTTFYNTSNILLCGESGVGKTTLSVRA 572
                                        34455555567899***********8655 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   5.6e-05     0.022       2      78 ..     238     319 ..     237     357 .. 0.75
   2 ?    0.4   0.0       1.4   5.4e+02       2      27 ..     555     580 ..     554     622 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 5.6e-05
                              AAA_3   2 vllegvPGlaktllvkalakaldlefkriqftpdllPsdilGt.....evfeekekefefkkGpvfanllladein 72 
                                        ++l g PG++ktl+++++++ l+++  +i   p++l   +  +     e+f+++eke++ k  +   ++++ dei+
  gene1590|gene1590|rna1590|rna1590 238 IMLYGPPGTGKTLIARQIGRLLNAREPKIVNGPEVLNKYVGQSeenirELFKDAEKEWRKKGSASHLHIIIFDEID 313
                                        68999*******************************8876443222236889999999999999999********9 PP

                              AAA_3  73 rappkt 78 
                                            k 
  gene1590|gene1590|rna1590|rna1590 314 AVCKKR 319
                                        766553 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 1.4
                              AAA_3   2 vllegvPGlaktllvkalakaldlef 27 
                                        +ll g  G++kt+l    a ++++ +
  gene1590|gene1590|rna1590|rna1590 555 ILLCGESGVGKTTLSVRAALSMKIPY 580
                                        789999******99877776666554 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.0   0.00087      0.35      19     120 ..     230     321 ..     207     349 .. 0.76
   2 ?    3.4   0.1      0.17        68      16      46 ..     534     574 ..     519     584 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00087
                                        ....TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG....GEEEESSS-B CS
                             ResIII  19 lkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkflseaykeigkkvsgdkk 94 
                                        l++++ k +++  + GtGKTl+a ++ + l   +++     +v++ ++l++   + ++ + e +k+++k++++++ 
  gene1590|gene1590|rna1590|rna1590 230 LHIDHVKGIMLYGPPGTGKTLIARQIGRLLNAREPK-----IVNGPEVLNKYVGQSEENIRELFKDAEKEWRKKGS 300
                                        4446778889999*********99988888876664.....89**********99999999999999999998888 PP

                                        --.......-SEEEEEHHHHHHTH.. CS
                             ResIII  95 kakekdstnkkilvttiqsldadsee 120
                                         +     +   i++ +i+++ ++++e
  gene1590|gene1590|rna1590|rna1590 301 AS-----HLHIIIFDEIDAVCKKRSE 321
                                        88.....4444555556555555543 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.17
                                        T................TTSEEEEEESTTSTHHHHHHHHHH CS
                             ResIII  16 leklks..........krdkrglikmaTGtGKTlvaaklie 46 
                                        ++++k+          ++  ++l+  + G+GKT ++++++ 
  gene1590|gene1590|rna1590|rna1590 534 MQQIKEkiayllkttfYNTSNILLCGESGVGKTTLSVRAAL 574
                                        44444444456666768888999***********9988765 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0     0.035        14       2      27 ..     238     263 ..     237     272 .. 0.86
   2 !    7.5   0.0    0.0087       3.5       1      20 [.     554     573 ..     554     582 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.035
                                        EEEE--TTSSHHHHHHHHHHHH...G CS
                           NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssg 27 
                                        +++ GppG+GKt + +++ +ll+ ++
  gene1590|gene1590|rna1590|rna1590 238 IMLYGPPGTGKTLIARQIGRLLNARE 263
                                        6889*************999998765 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0087
                                        EEEEE--TTSSHHHHHHHHH CS
                           NTPase_1   1 kvfiTGppGvGKtTlvkkvl 20 
                                        ++++ G++GvGKtTl  +++
  gene1590|gene1590|rna1590|rna1590 554 NILLCGESGVGKTTLSVRAA 573
                                        5899**********987765 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.0    0.0011      0.46      13      66 ..     238     292 ..     231     350 .. 0.70
   2 ?    2.8   0.0      0.35   1.4e+02       9      28 ..     551     570 ..     539     585 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0011
                             AAA_19  13 llvtaGpGtGKTrvlkhivallvelggvkp.eeillvaftgrAakelrerlaalg 66 
                                        +++ ++pGtGKT + ++i +ll++++   +  + +l  + g++ +++re  + ++
  gene1590|gene1590|rna1590|rna1590 238 IMLYGPPGTGKTLIARQIGRLLNAREPKIVnGPEVLNKYVGQSEENIRELFKDAE 292
                                        7899***********9999999877644332344445566666666666665555 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.35
                             AAA_19   9 kekvllvtaGpGtGKTrvlk 28 
                                        + +++l+ +  G GKT++ +
  gene1590|gene1590|rna1590|rna1590 551 NTSNILLCGESGVGKTTLSV 570
                                        567899**********8644 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0      0.19        76      21      36 ..     235     249 ..     222     263 .. 0.79
   2 !    9.9   0.1    0.0015      0.59      23      38 ..     553     568 ..     544     573 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.19
                             AAA_29  21 lkgatlltGpsGsGKS 36 
                                        +kg ++l Gp G+GK+
  gene1590|gene1590|rna1590|rna1590 235 VKG-IMLYGPPGTGKT 249
                                        345.9**********7 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0015
                             AAA_29  23 gatlltGpsGsGKSTl 38 
                                        +++ll G+sG+GK+Tl
  gene1590|gene1590|rna1590|rna1590 553 SNILLCGESGVGKTTL 568
                                        479************8 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.0   0.00069      0.28       2      38 ..     238     280 ..     237     309 .. 0.77
   2 ?    2.2   0.0      0.48   1.9e+02       2      17 ..     555     570 ..     554     590 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00069
                             AAA_28   2 ivitGgestGKTtlleaLa....argypvv..pEaareileek 38 
                                        i++ G+++tGKT +++++     ar+ ++v  pE+  +++ + 
  gene1590|gene1590|rna1590|rna1590 238 IMLYGPPGTGKTLIARQIGrllnAREPKIVngPEVLNKYVGQS 280
                                        789************8877555467888888899999888554 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.48
                             AAA_28   2 ivitGgestGKTtlle 17 
                                        i + G ++ GKTtl+ 
  gene1590|gene1590|rna1590|rna1590 555 ILLCGESGVGKTTLSV 570
                                        889999********84 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0       2.7   1.1e+03      17      31 ..     238     252 ..     231     273 .. 0.85
   2 !    8.1   0.1    0.0052       2.1     112     154 ..     288     338 ..     255     353 .. 0.72
   3 ?    5.6   0.1      0.03        12      11      36 ..     549     574 ..     536     618 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 2.7
                                        EEEEESTTSSHHHHH CS
                                        xxxxxxxxxxxxxxx RF
                               DEAD  17 vlvaaeTGsGKTlaf 31 
                                        +++ ++ G+GKTl++
  gene1590|gene1590|rna1590|rna1590 238 IMLYGPPGTGKTLIA 252
                                        6788999*****986 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0052
                                        H......HCTSSHCTTEEEEEEETHHHHHHT..TTHHHHHHHHHHSHHHCT CS
                                        x......xxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxx RF
                               DEAD 112 l......stgklnlsqvrflVlDEadrlldq..gfsdfinrilnqlpqitc 154
                                        +      +++k + s++ ++++DE+d + ++  + s   ++++nql ++ +
  gene1590|gene1590|rna1590|rna1590 288 FkdaekeWRKKGSASHLHIIIFDEIDAVCKKrsENSSITDQVVNQLLSKMD 338
                                        25555554566679**************99977777888889999855544 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.03
                                        HHTTCEEEEEESTTSSHHHHHHHHHH CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               DEAD  11 ilgggdvlvaaeTGsGKTlaflipvl 36 
                                        +++  ++l+++e G GKT+  + ++l
  gene1590|gene1590|rna1590|rna1590 549 FYNTSNILLCGESGVGKTTLSVRAAL 574
                                        447789************99888777 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       5.1     2e+03     100     117 ..     236     253 ..     215     266 .. 0.75
   2 ?   13.1   0.0   0.00017     0.066      65     116 ..     517     569 ..     507     585 .. 0.69

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 5.1
                                        SEEEEECSTTSSHHHHHH CS
                        RsgA_GTPase 100 ktsvlvGqSGvGKStLin 117
                                        k ++l G+ G GK+ +  
  gene1590|gene1590|rna1590|rna1590 236 KGIMLYGPPGTGKTLIAR 253
                                        567899*******76554 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 0.00017
                                        HHHHHHHHHHTTSEEEE--TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHH CS
                        RsgA_GTPase  65 leelkeelealgyevllvsaktkegleelkellkd.ktsvlvGqSGvGKStLi 116
                                        ++ +k+++ +l  +  ++++ +++ +  lk+ + + + ++l+G+SGvGK+tL 
  gene1590|gene1590|rna1590|rna1590 517 FTIFKKNYYSLRHHADIMQQIKEKIAYLLKTTFYNtSNILLCGESGVGKTTLS 569
                                        55566666666555555555544444455666666577899**********95 PP

>> KAP_NTPase  KAP family P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00035      0.14      23      96 ..     238     560 ..     225     659 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00035
                         KAP_NTPase  23 vgLygkWGsGKssllnkledelkefa.................................................. 48 
                                        ++Lyg+ G+GK+ +   + + l+ +                                                   
  gene1590|gene1590|rna1590|rna1590 238 IMLYGPPGTGKTLIARQIGRLLNAREpkivngpevlnkyvgqseenirelfkdaekewrkkgsashlhiiifdeid 313
                                        89************************************************************************** PP

                         KAP_NTPase  49 ............................................................................ 48 
                                                                                                                    
  gene1590|gene1590|rna1590|rna1590 314 avckkrsenssitdqvvnqllskmdgveslnnilvigmtnrmdlidpallrpgrfeihveiglpnledrkeileih 389
                                        **************************************************************************** PP

                         KAP_NTPase  49 ............................................................................ 48 
                                                                                                                    
  gene1590|gene1590|rna1590|rna1590 390 taalkknnvldgvsleevakqtnnytgaeltavvksavsyalerglkrktgsagddadsgidegssdagsenggdn 465
                                        **************************************************************************** PP

                         KAP_NTPase  49 ...............................................kpvrflfaefnawsfkggddavaellaaL 77 
                                                                                       ++++f++++ n+ s  ++ d+++++ + +
  gene1590|gene1590|rna1590|rna1590 466 yctgsaagrqgasgesspntirvsdnirvtmedflkaidevkpafglNEQEFTIFKKNYYSLRHHADIMQQIKEKI 541
                                        **************************************************************************** PP

                         KAP_NTPase  78 adaleeeygqlatkllrak 96 
                                        a  l++ +   +  ll+++
  gene1590|gene1590|rna1590|rna1590 542 AYLLKTTFYNTSNILLCGE 560
                                        ****999998877666664 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0      0.42   1.7e+02       2      20 ..     238     256 ..     237     287 .. 0.77
   2 ?    9.1   0.0    0.0036       1.4       2      18 ..     555     571 ..     554     582 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.42
                                        EEEESSTTSSHHHHHHCHC CS
                                Roc   2 vvlvGdsgvGKtsllkrfv 20 
                                        ++l G  g+GKt +++++ 
  gene1590|gene1590|rna1590|rna1590 238 IMLYGPPGTGKTLIARQIG 256
                                        7999********9988764 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0036
                                        EEEESSTTSSHHHHHHC CS
                                Roc   2 vvlvGdsgvGKtsllkr 18 
                                        ++l+G+sgvGKt+l  r
  gene1590|gene1590|rna1590|rna1590 555 ILLCGESGVGKTTLSVR 571
                                        89***********9876 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0     0.001      0.41      21      50 ..     238     267 ..     224     322 .. 0.77
   2 ?    0.2   0.0       1.3   5.2e+02      22      34 ..     556     568 ..     546     591 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.001
                             AAA_30  21 avltGpAGtGKttalkalreaweaaggrvi 50 
                                         +l Gp+GtGKt + +++ ++++a++ +++
  gene1590|gene1590|rna1590|rna1590 238 IMLYGPPGTGKTLIARQIGRLLNAREPKIV 267
                                        5789**************999999876654 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 1.3
                             AAA_30  22 vltGpAGtGKtta 34 
                                        +l G  G GKtt+
  gene1590|gene1590|rna1590|rna1590 556 LLCGESGVGKTTL 568
                                        6889*******97 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0       0.5     2e+02      54      79 ..     236     261 ..     225     287 .. 0.82
   2 ?    9.1   0.0    0.0017      0.66      51      85 ..     550     584 ..     518     622 .. 0.62

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.5
                             DUF815  54 nnvLLwGarGtGKSslvkallneyae 79 
                                        + ++L+G  GtGK  + + + + +++
  gene1590|gene1590|rna1590|rna1590 236 KGIMLYGPPGTGKTLIARQIGRLLNA 261
                                        679**********9888777665555 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0017
                             DUF815  51 lpannvLLwGarGtGKSsl.vkallneyaeegLrli 85 
                                        ++++n+LL G+ G+GK +l v+a+l+ ++   ++li
  gene1590|gene1590|rna1590|rna1590 550 YNTSNILLCGESGVGKTTLsVRAALS-MKIPYVKLI 584
                                        5789*************985777664.445556665 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.3    0.0066       2.6      23     110 ..     238     334 ..     224     349 .. 0.58
   2 ?    0.0   0.0       1.7   6.6e+02      10      37 ..     543     569 ..     538     598 .. 0.76
   3 ?    4.1   0.1     0.095        38     117     172 ..     611     668 ..     601     698 .. 0.67

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0066
                           ATPase_2  23 yfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefie......eeeekkklekalgiavpkaele 92 
                                        +++YGp g GKt + ++i   l+  + +++   ++ +++  + +e i+      e+e +kk +   +  +  +e++
  gene1590|gene1590|rna1590|rna1590 238 IMLYGPPGTGKTLIARQIGRLLNAREPKIVNGPEVLNKYVGQSEENIRelfkdaEKEWRKKGSASHLHIIIFDEID 313
                                        689*********9999988877555543333322222222222222224444444444444444445555555666 PP

                           ATPase_2  93 eilk...eksklvfkaielll 110
                                        ++ k   e+s   ++ +++ll
  gene1590|gene1590|rna1590|rna1590 314 AVCKkrsENSSITDQVVNQLL 334
                                        666644444444555555555 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 1.7
                           ATPase_2  10 eleeilerepneiyfiYGpegsGKtaLl 37 
                                        +l++    ++++i ++ G  g+GKt+L 
  gene1590|gene1590|rna1590|rna1590 543 YLLKTTFYNTSNI-LLCGESGVGKTTLS 569
                                        5555555555555.567*********95 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.095
                           ATPase_2 117 gkkiiiiiDelqklidlglngael..lvkeLlnliesltkekhlcvviclsSeglfie 172
                                         k+  iiiD++  lid+   g ++   v + ++ +++  ++ + +v+   sS  ++ e
  gene1590|gene1590|rna1590|rna1590 611 CKQCLIIIDDIESLIDYVPLGPRFsnAVLQTIKTFVRMESNGKCFVIATCSSLEIMEE 668
                                        57899**********9876644431123333445555444444444444555444444 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0      0.32   1.3e+02       2      21 ..     236     255 ..     235     261 .. 0.87
   2 ?    7.6   0.0    0.0075         3       2      20 ..     553     571 ..     552     591 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.32
                          PduV-EutP   2 kkilliGkvgsGKttLtqal 21 
                                        k i+l G+ g+GKt +++++
  gene1590|gene1590|rna1590|rna1590 236 KGIMLYGPPGTGKTLIARQI 255
                                        679***********998876 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0075
                          PduV-EutP   2 kkilliGkvgsGKttLtqa 20 
                                        ++ill G++g+GKttL+ +
  gene1590|gene1590|rna1590|rna1590 553 SNILLCGESGVGKTTLSVR 571
                                        579*************754 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00041      0.16       5     118 ..     239     335 ..     236     352 .. 0.65
   2 ?   -3.2   0.1       9.4   3.7e+03       4      22 ..     555     573 ..     553     578 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00041
                            DUF2075   5 lVtGvaGtGKtvvllnllaeleddeeertavylsvNhplvlvlrealakkeekkkkkeafeklssfinnlsefkka 80 
                                        +  G +GtGKt+++ ++   l      + +   +vN+p+vl   + + ++e  ++++e f++ ++           
  gene1590|gene1590|rna1590|rna1590 239 MLYGPPGTGKTLIARQIGRLL------NAREPKIVNGPEVLN--KYVGQSE--ENIRELFKDAEKEW--------- 295
                                        5689************99888......334445789998754..4455555..33555555544443......... PP

                            DUF2075  81 eekkeepkedvvivDEAhrlltksdqaekqse..enqlke 118
                                         +k +  +++++i+DE   + +k++ + + +    nql +
  gene1590|gene1590|rna1590|rna1590 296 RKKGSASHLHIIIFDEIDAVCKKRSENSSITDqvVNQLLS 335
                                        3455889999999999888888666655544322344444 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 9.4
                            DUF2075   4 vlVtGvaGtGKtvvllnll 22 
                                        +l  G++G GKt + ++++
  gene1590|gene1590|rna1590|rna1590 555 ILLCGESGVGKTTLSVRAA 573
                                        66779*******9988766 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.1      0.14        57       9      30 ..     245     266 ..     239     408 .. 0.88
   2 ?    6.9   0.1     0.016       6.3       6      20 ..     559     573 ..     555     578 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.14
                                        TSSHHHHHHHHHHHHHHTT--E CS
                                        xxxxxxxxxxxxxxxxxxxxxx RF
                               CbiA   9 GvGKTtlaanLaralarrglrV 30 
                                        G+GKT +a  ++r+l+ r+ ++
  gene1590|gene1590|rna1590|rna1590 245 GTGKTLIARQIGRLLNAREPKI 266
                                        9**************9987666 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.016
                                        SSTTSSHHHHHHHHH CS
                                        xxxxxxxxxxxxxxx RF
                               CbiA   6 tkGGvGKTtlaanLa 20 
                                        + +GvGKTtl++  a
  gene1590|gene1590|rna1590|rna1590 559 GESGVGKTTLSVRAA 573
                                        78********99765 PP

>> CDC48_N  Cell division protein 48 (CDC48), N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00069      0.28      47      82 ..      46      81 ..      40      83 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00069
                                       EEEBSTTSTTTTEEEE-HHHHHHHT--TTEEEEEEE CS
                            CDC48_N 47 vwpaepedegkgiIrmdgvtRknagvsiGdkVtVrk 82
                                       +++ +   +++ +I m++ +R+n +v i+ +Vt + 
  gene1590|gene1590|rna1590|rna1590 46 IYAHNALPTSNRVIEMNSAQRENHNVAIDGEVTAKE 81
                                       555556666789********************9876 PP

>> DUF3213  Protein of unknown function (DUF3213)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0      0.15        61      39      70 ..     487     519 ..     481     527 .. 0.84
   2 ?    6.1   0.1     0.032        13      16      43 ..     592     620 ..     579     628 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.15
                                        EE--B-S-SHHHHHHHT...TT-S.S------- CS
                            DUF3213  39 vvideekvnieelkkkleelkgev.veekeltl 70 
                                         v d+ +v +e+++k+++e+k+   ++e+e+t+
  gene1590|gene1590|rna1590|rna1590 487 RVSDNIRVTMEDFLKAIDEVKPAFgLNEQEFTI 519
                                        578999***************985478888886 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.032
                                        HHTTTTTTTB------TT.SS--EEE--B CS
                            DUF3213  16 qyelekdervyrvflngy.akvaevvide 43 
                                          e+ek + +  +f+ngy  k++ ++id+
  gene1590|gene1590|rna1590|rna1590 592 YSEVEKIQFIKEIFINGYkCKQCLIIIDD 620
                                        458888888999******55889999998 PP

>> Sigma54_activ_2  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0      0.35   1.4e+02      24      41 ..     238     255 ..     230     280 .. 0.85
   2 ?    6.7   0.0     0.018       7.2       6      38 ..     533     569 ..     530     582 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.35
                                        EEEEEETT--HHHHHHCC CS
                    Sigma54_activ_2  24 vfltGekGsgkelvArlL 41 
                                        + l G++G+gk+l+Ar +
  gene1590|gene1590|rna1590|rna1590 238 IMLYGPPGTGKTLIARQI 255
                                        5689***********976 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.018
                                        HHHHHHHHHHHHH....T-SS-EEEEEETT--HHHHH CS
                    Sigma54_activ_2   6 aiqelkerLeqaa....qsklpvfltGekGsgkelvA 38 
                                        ++q++ke+++ +     +++++++l Ge G gk++ +
  gene1590|gene1590|rna1590|rna1590 533 IMQQIKEKIAYLLkttfYNTSNILLCGESGVGKTTLS 569
                                        677777777665534448999************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (724 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       740  (0.0412739); expected 358.6 (0.02)
Passed bias filter:                      610  (0.0340231); expected 358.6 (0.02)
Passed Vit filter:                       105  (0.00585643); expected 17.9 (0.001)
Passed Fwd filter:                        45  (0.0025099); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              45  [number of targets reported over threshold]
# CPU time: 0.80u 0.32s 00:00:01.12 Elapsed: 00:00:00.43
# Mc/sec: 5008.27
//
Query:       gene1591|gene1591|rna1591|rna1591  [L=980]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (980 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       572  (0.0319036); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.65u 0.31s 00:00:00.96 Elapsed: 00:00:00.46
# Mc/sec: 6385.66
//
Query:       gene1592|gene1592|rna1592|rna1592  [L=678]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (678 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       905  (0.0504769); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.64u 0.27s 00:00:00.91 Elapsed: 00:00:00.46
# Mc/sec: 4403.51
//
Query:       gene1593|gene1593|rna1593|rna1593  [L=532]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.4e-06   26.6   1.6    6.2e-06   25.8   1.6    1.5  1  SWIM      SWIM zinc finger


Domain annotation for each model (and alignments):
>> SWIM  SWIM zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   1.6   3.5e-10   6.2e-06       1      39 [.     433     473 ..     433     474 .. 0.95

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 3.5e-10
                               SWIM   1 yrVtldder..vrlnkatCsCpefqkngipCkHalAvllal 39 
                                        y Vtl++e+  v+ln+ +C+C+ fq +  pC Hal ++ +l
  gene1593|gene1593|rna1593|rna1593 433 YNVTLGKETcnVSLNDMFCTCGIFQEYACPCTHALVLIRHL 473
                                        89*********************************998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (532 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1781  (0.0993363); expected 358.6 (0.02)
Passed bias filter:                      855  (0.0476881); expected 358.6 (0.02)
Passed Vit filter:                       104  (0.00580066); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.77u 0.35s 00:00:01.12 Elapsed: 00:00:00.54
# Mc/sec: 2963.33
//
Query:       gene1594|gene1594|rna1594|rna1594  [L=278]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (278 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       390  (0.0217525); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 1915.40
//
Query:       gene1595|gene1595|rna1595|rna1595  [L=656]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-16   60.4   4.5    1.9e-16   60.4   4.5    2.0  2  SAS-6_N          Centriolar protein SAS N-terminal
    0.00011   22.0  42.2    0.00015   21.7  36.4    2.5  2  KASH_CCD         Coiled-coil region of CCDC155 or KASH
     0.0019   18.3  35.6       0.13   12.4  13.4    3.2  3  ADIP             Afadin- and alpha -actinin-Binding
  ------ inclusion threshold ------
      0.013   15.1   5.0      0.013   15.1   5.0    2.4  2  DUF2968          Protein of unknown function (DUF2968)
      0.014   15.6  36.1      0.028   14.6  11.2    2.3  2  ATG16            Autophagy protein 16 (ATG16)
      0.044   13.7   0.4      0.044   13.7   0.4    2.5  1  DUF4250          Domain of unknown function (DUF4250)
      0.078   11.9  35.6       0.11   11.4  35.6    1.1  1  DUF812           Protein of unknown function (DUF812)
       0.19   10.6  38.9       0.21   10.4  19.2    2.3  2  Spc7             Spc7 kinetochore protein
       0.33   11.6  33.7       0.24   12.0   7.5    4.2  3  YabA             Initiation control protein YabA
       0.57   10.2  32.5        1.4    8.9   3.2    2.3  2  Rootletin        Ciliary rootlet component, centrosome cohesi
       0.66    9.7  42.4        1.4    8.7  25.1    2.1  2  ERM              Ezrin/radixin/moesin family
       0.68   10.1  27.4       0.11   12.6  14.0    2.9  3  Fib_alpha        Fibrinogen alpha/beta chain family
       0.72    9.3  45.7       0.14   11.6  16.0    2.1  2  HMMR_N           Hyaluronan mediated motility receptor N-term
        1.6    8.8  29.8        0.2   11.7   9.7    3.2  3  Mod_r            Modifier of rudimentary (Mod(r)) protein
        1.7    7.9  24.5        4.2    6.6   6.8    3.0  3  DUF3450          Protein of unknown function (DUF3450)
        1.8    8.7  40.4         16    5.5  15.7    3.3  4  UPF0242          Uncharacterised protein family (UPF0242) N-t
        2.6    7.8  11.9      0.031   14.0   1.0    2.6  3  Lectin_N         Hepatic lectin, N-terminal domain
        3.5    7.0  38.7        3.1    7.2  28.1    2.1  2  Golgin_A5        Golgin subfamily A member 5
        4.9    6.4  46.2       0.39   10.0  20.3    2.5  2  GAS              Growth-arrest specific micro-tubule binding
        5.7    6.8   5.7         10    6.0   0.4    3.3  3  DASH_Dam1        DASH complex subunit Dam1
        5.9    7.6  19.7       0.16   12.7   6.5    2.7  2  DUF2203          Uncharacterized conserved protein (DUF2203)
          8    6.5  26.3        1.3    9.0   9.4    2.7  3  Laminin_II       Laminin Domain II


Domain annotation for each model (and alignments):
>> SAS-6_N  Centriolar protein SAS N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.4   4.5   2.3e-19   1.9e-16       4      92 .]     318     399 ..     315     399 .. 0.92
   2 ?   -1.9   0.2       6.2   5.1e+03      13      33 ..     497     517 ..     487     518 .. 0.83

  Alignments for each domain:
  == domain 1  score: 60.4 bits;  conditional E-value: 2.3e-19
                                        EEEETTEEEEEEEEEEEHHHHHHHHHHCTB-S-CCCHHHHHHHHHHHHHHS...SSEEEECCTTTSSEEEEEEEEE CS
                            SAS-6_N   4 eltdenDlfflytleiseedFeelkeeqnLlvdFaeFpsklikllnscqkpekkkylavlslekdegqakLsivet 79 
                                        +l+d+nD+f +y+++i+++++ +lk+eq+L v+F++F++k+++l+ ++++    +++a +     ++++++ +ve+
  gene1595|gene1595|rna1595|rna1595 318 KLIDTNDIFKFYQCTITSTSYVHLKNEQELRVNFENFVRKVVELFYQVKNG---RMKALFD----KDSGRFIFVEQ 386
                                        689*********************************************775...7776664....6789******* PP

                                        -SSBEEEEEEEEE CS
                            SAS-6_N  80 neFkqlehLslef 92 
                                        neF+++  L+l+f
  gene1595|gene1595|rna1595|rna1595 387 NEFRNIVRLELRF 399
                                        ***********97 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 6.2
                                        EEEEEEEEHHHHHHHHHHCTB CS
                            SAS-6_N  13 flytleiseedFeelkeeqnL 33 
                                          y++e+++++ ee k+eq++
  gene1595|gene1595|rna1595|rna1595 497 ATYKFEVEKNKIEEYKREQEM 517
                                        579999999999999999987 PP

>> KASH_CCD  Coiled-coil region of CCDC155 or KASH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.5      0.11        86      28      54 ..     412     438 ..     404     442 .. 0.64
   2 !   21.7  36.4   1.8e-07   0.00015       5     184 ..     442     614 ..     439     623 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.11
                           KASH_CCD  28 kkavetaeetnakLteeieeLkkklks 54 
                                           +  +e tn kL  ++ +L++ l+ 
  gene1595|gene1595|rna1595|rna1595 412 ADMISRMEVTNVKLKKDNVQLRESLRN 438
                                        555666677777777777777766664 PP

  == domain 2  score: 21.7 bits;  conditional E-value: 1.8e-07
                           KASH_CCD   5 dlistvadLqlnNkkLaeenskLkkavetaeetnakLteeieeLkkklks..tQqalqkaklleeEleelkalvke 78 
                                        ++ + vadL   N+ L e + kLk+ +e +e +n+ L++e e+Lk+++     Q a  k+++ ++ +ee k+  + 
  gene1595|gene1595|rna1595|rna1595 442 EMRTRVADLTDRNRLLDERVDKLKNRLEGVEKENEGLVAEREQLKRQIVEieKQNATYKFEVEKNKIEEYKREQEM 517
                                        77789******************************************97522688888999999999999986655 PP

                           KASH_CCD  79 leEkrarlkaqnkqlekenqsLiakiesLqeenikllaekdelkkklkeLlkekaeLkkqlheleellaekealle 154
                                        +  + ++++  ++ leke +  +  i +L e+ +++   k+e+ + +++L +e+ +L k + e+ +++ eke+   
  gene1595|gene1595|rna1595|rna1595 518 V--RLKEVEECKNGLEKEIKVANDIIRKLREDVRRMNEGKEEMDENVQKLKNENGKLAKSNEEASKTVKEKEER-- 589
                                        4..45678888999*******************************************99999998888777764.. PP

                           KASH_CCD 155 ektkqieeLkltieEyssiieeLraeksrL 184
                                             i  Lk +++     i++L ++k++L
  gene1595|gene1595|rna1595|rna1595 590 -----IRGLKDALKRKDEKIKNLEMDKKQL 614
                                        .....4444444444444444555555444 PP

>> ADIP  Afadin- and alpha -actinin-Binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2  11.2   0.00073       0.6      46     123 ..     431     508 ..     428     521 .. 0.92
   2 ?    4.8   1.1     0.032        26      84     123 ..     514     553 ..     509     558 .. 0.85
   3 !   12.4  13.4   0.00016      0.13      46     146 ..     542     639 ..     534     644 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00073
                               ADIP  46 qardrdleqreslnetirkleaeierlqskierlktqleqlerelalvqakerqlekklktleqklknekeelqrl 121
                                        q r++ ++++e++ +++ +l+  +  l  ++++lk++le  e+e++ + a+  ql++++ + e+++ + k e++++
  gene1595|gene1595|rna1595|rna1595 431 QLRESLRNVEEEMRTRVADLTDRNRLLDERVDKLKNRLEGVEKENEGLVAEREQLKRQIVEIEKQNATYKFEVEKN 506
                                        6677778999****************************************************************99 PP

                               ADIP 122 kn 123
                                        k 
  gene1595|gene1595|rna1595|rna1595 507 KI 508
                                        86 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.032
                               ADIP  84 eqlerelalvqakerqlekklktleqklknekeelqrlkn 123
                                        eq   +l+ v++ ++ lek++k +++ +++++e+++r++ 
  gene1595|gene1595|rna1595|rna1595 514 EQEMVRLKEVEECKNGLEKEIKVANDIIRKLREDVRRMNE 553
                                        5555667788999999*********************985 PP

  == domain 3  score: 12.4 bits;  conditional E-value: 0.00016
                               ADIP  46 qardrdleqreslnetirkleaeierlqskierlktqleqlerelalvqakerqlekklktleqklknekeelqrl 121
                                        +++++d +    +ne  ++++   ++l+++  +l +++e+  + ++  +++ r l+ +lk+ ++k+kn+  + + l
  gene1595|gene1595|rna1595|rna1595 542 RKLREDVR---RMNEGKEEMDENVQKLKNENGKLAKSNEEASKTVKEKEERIRGLKDALKRKDEKIKNLEMDKKQL 614
                                        44444443...35666667777788888888888888888888888888888999999999999999999999999 PP

                               ADIP 122 knalqqiktqyahelkkkdreiekL 146
                                         +++++ k  y+h  kkk+ ei+++
  gene1595|gene1595|rna1595|rna1595 615 VKKMEEAKFVYNHFYKKKEGEISSV 639
                                        9999999999999999999999876 PP

>> DUF2968  Protein of unknown function (DUF2968)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   5.0       0.1        84      93     170 ..     414     495 ..     405     507 .. 0.77
   2 ?   15.1   5.0   1.6e-05     0.013     100     177 ..     519     596 ..     510     599 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.1
                            DUF2968  93 elaeveirrikleaqkaqlerqiaasearaerLqadl....avarqQeqavaerQkqarkeaaaLeaqreaaqaql 164
                                         ++ +e+  +kl+ ++ ql + + + e+++++  adl    ++  +   ++++r + + ke + L a+re++++q+
  gene1595|gene1595|rna1595|rna1595 414 MISRMEVTNVKLKKDNVQLRESLRNVEEEMRTRVADLtdrnRLLDERVDKLKNRLEGVEKENEGLVAEREQLKRQI 489
                                        5678899999999999999999988888777777776211144556667778888889999999999999999999 PP

                            DUF2968 165 ralqrq 170
                                         ++++q
  gene1595|gene1595|rna1595|rna1595 490 VEIEKQ 495
                                        888877 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 1.6e-05
                            DUF2968 100 rrikleaqkaqlerqiaasearaerLqadlavarqQeqavaerQkqarkeaaaLeaqreaaqaqlralqrqirqLq 175
                                        r  ++e  k+ le++i+++++ +++L++d++++++ ++++ e+ +++++e  +L++ +e+a + +++ +++ir L+
  gene1595|gene1595|rna1595|rna1595 519 RLKEVEECKNGLEKEIKVANDIIRKLREDVRRMNEGKEEMDENVQKLKNENGKLAKSNEEASKTVKEKEERIRGLK 594
                                        44457778999**************************************************************998 PP

                            DUF2968 176 aq 177
                                         +
  gene1595|gene1595|rna1595|rna1595 595 DA 596
                                        65 PP

>> ATG16  Autophagy protein 16 (ATG16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3  17.1     0.013        10      85     179 ..     431     522 ..     412     526 .. 0.83
   2 ?   14.6  11.2   3.5e-05     0.028      80     150 ..     538     608 ..     524     625 .. 0.62

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.013
                              ATG16  85 qlreelaelyk.srgelaqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelrekeklvqdlqDE 159
                                        q    l e+++   +e+ +r+ +l++  + l+e+  + ++rl+ +e+e++ l  ++++++ ++ e ek + + + E
  gene1595|gene1595|rna1595|rna1595 431 Q----LRESLRnVEEEMRTRVADLTDRNRLLDERVDKLKNRLEGVEKENEGLVAEREQLKRQIVEIEKQNATYKFE 502
                                        3....33433313789999999999999999999999999999999999999999999999999999999999999 PP

                              ATG16 160 lsaLqlqlnqaEeklrklek 179
                                        ++  +++  ++E++  +l++
  gene1595|gene1595|rna1595|rna1595 503 VEKNKIEEYKREQEMVRLKE 522
                                        99999999999999998875 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 3.5e-05
                              ATG16  80 eqklaqlreelaelyksrgelaqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelreke 150
                                        ++ + +lre++  +   ++e+ + +++l++e  kl ++ +e +++++e e++++ l+++lk+++e+++ +e
  gene1595|gene1595|rna1595|rna1595 538 NDIIRKLREDVRRMNEGKEEMDENVQKLKNENGKLAKSNEEASKTVKEKEERIRGLKDALKRKDEKIKNLE 608
                                        45556666666666666666666666666666666666666666666666666666666666666665543 PP

>> DUF4250  Domain of unknown function (DUF4250)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.4   5.4e-05     0.044      16      50 ..     593     627 ..     592     631 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.4e-05
                            DUF4250  16 LRDeyssldelcedldidkeeleekLasigYeYde 50 
                                        L D  +  de +++l++dk++l++k++++ + Y+ 
  gene1595|gene1595|rna1595|rna1595 593 LKDALKRKDEKIKNLEMDKKQLVKKMEEAKFVYNH 627
                                        567778889999*********************96 PP

>> DUF812  Protein of unknown function (DUF812)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4  35.6   0.00013      0.11     273     489 ..     402     621 ..     387     626 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00013
                             DUF812 273 ksksdlaellsefseksetdslktkgsrfthaekl.qftkeelakkaeteeelkkkreeeleelqeqieeleskie 347
                                        ++++d +  l +++++ e  ++k k+ +++ +e+l ++++e +++++ +  +++   +e +++l++++e +e++ e
  gene1595|gene1595|rna1595|rna1595 402 PDENDYKRYLADMISRMEVTNVKLKKDNVQLRESLrNVEEE-MRTRVADLTDRNRLLDERVDKLKNRLEGVEKENE 476
                                        57778888888888888888999999999999999445555.778999999999999******************* PP

                             DUF812 348 eleeeikklessikqveeeleeekeeneele.kevklkkktlellpdaeeniekLqalveasaqrlvel...akqW 419
                                         l +e ++l+ +i ++e++  + k e e+++ +e+k ++ ++  l++ ee  + L+++++ +++ + +l    +++
  gene1595|gene1595|rna1595|rna1595 477 GLVAEREQLKRQIVEIEKQNATYKFEVEKNKiEEYKREQEMVR-LKEVEECKNGLEKEIKVANDIIRKLredVRRM 551
                                        *********************9998877665266777777766.5688888889998888877766665211679* PP

                             DUF812 420 ekhRvplieeyrelkesksekekeaerkleeikklrekmkevaeelrqkeellkqLvaeleklpkdvsRs 489
                                        ++ ++ + e+ ++lk+++ + +k+ e+  + +k+ +e+++ + + l++k+e++k+L+ + ++l k+++  
  gene1595|gene1595|rna1595|rna1595 552 NEGKEEMDENVQKLKNENGKLAKSNEEASKTVKEKEERIRGLKDALKRKDEKIKNLEMDKKQLVKKMEEA 621
                                        *************************************************************999998755 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4  23.4     0.018        15     137     274 ..     436     568 ..     411     574 .. 0.62
   2 ?   10.4  19.2   0.00026      0.21     148     273 ..     520     641 ..     517     646 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.018
                               Spc7 137 legLkegleenlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeelesid.keeLeelreelael 211
                                        l +++e+++ ++++l++ ++lL+++ ++l++ l+ +e+e + l +e e+l+++  e+e+ +   + e  +++++e 
  gene1595|gene1595|rna1595|rna1595 436 LRNVEEEMRTRVADLTDRNRLLDERVDKLKNRLEGVEKENEGLVAEREQLKRQIVEIEKQNaTYKFEVEKNKIEEY 511
                                        4556667777777777777777777777777777777777777777777777777777744344444455555555 PP

                               Spc7 212 kaeieekkkelaelqeqleeleekieelkeqkseleeeiaeaervleeckgwsesevsrlkee 274
                                        k e e  + +l+e++e ++ le++i+ +++ +++l+e+++     ++e k+  +++v++lk+e
  gene1595|gene1595|rna1595|rna1595 512 KREQE--MVRLKEVEECKNGLEKEIKVANDIIRKLREDVR----RMNEGKEEMDENVQKLKNE 568
                                        54444..445555555555555555555555555555554....3344444445555555554 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00026
                               Spc7 148 legleedkelLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkela 223
                                        l+++ee k+ Lek+ + ++++  +l+e   +++e  e++ e +++l++ ++ +L++     +e++++++ek++++ 
  gene1595|gene1595|rna1595|rna1595 520 LKEVEECKNGLEKEIKVANDIIRKLREDVRRMNEGKEEMDENVQKLKN-ENGKLAKS---NEEASKTVKEKEERIR 591
                                        678888899999999999999999999999999999999998888777.44555554...466788899999**** PP

                               Spc7 224 elqeqleeleekieelkeqkseleeeiaeaervleeckgwsesevsrlke 273
                                         l++ l++++eki++l+  k++l ++++ea+ v++   + +e e+s++ e
  gene1595|gene1595|rna1595|rna1595 592 GLKDALKRKDEKIKNLEMDKKQLVKKMEEAKFVYNHFYKKKEGEISSVSE 641
                                        ***********************************999999999998876 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   1.0     0.031        25      27      66 ..     411     450 ..     385     458 .. 0.77
   2 ?   12.0   7.5    0.0003      0.24       4      67 ..     441     504 ..     439     532 .. 0.77
   3 ?    2.8  12.9      0.23   1.9e+02       9      70 ..     540     611 ..     527     647 .. 0.68

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.031
                                        HHHHHHHHHHHHHHHHHHHHHHHHHHXXXXXXXXXXXXXX CS
                               YabA  27 lkeelaelleenaeLeleneklrerleeeekkekekkkel 66 
                                        l + ++++   n +L+ +n +lre l++ e++ +++ ++l
  gene1595|gene1595|rna1595|rna1595 411 LADMISRMEVTNVKLKKDNVQLRESLRNVEEEMRTRVADL 450
                                        67778889999***************77777666665555 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.0003
                                        HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.....XXXXXXXXXXXXXXX CS
                               YabA   4 kelfdkleeleeqleelleeleelkeelaelleenaeLeleneklrerl.....eeeekkekekkkels 67 
                                        +e+ +++++l+++ + l e++++lk++l+ + +en+ L +e e+l++++     +     +++ k e++
  gene1595|gene1595|rna1595|rna1595 441 EEMRTRVADLTDRNRLLDERVDKLKNRLEGVEKENEGLVAEREQLKRQIveiekQ-----NATYKFEVE 504
                                        67889999***************************************99555441.....333332222 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.23
                                        HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH..........XXXXXXXXXXXXXXXXXX CS
                               YabA   9 kleeleeqleelleeleelkeelaelleenaeLeleneklrerl..........eeeekkekekkkelsegk 70 
                                         +++l e++++++e  ee+ e++++l +en +L   ne+  +++          +++ k+++ek k+l+  k
  gene1595|gene1595|rna1595|rna1595 540 IIRKLREDVRRMNEGKEEMDENVQKLKNENGKLAKSNEEASKTVkekeerirglKDALKRKDEKIKNLEMDK 611
                                        467788888888888888888888888888888888888888884444444555444444444444444444 PP

>> Rootletin  Ciliary rootlet component, centrosome cohesion
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   3.2    0.0017       1.4      93     150 ..     411     468 ..     396     471 .. 0.89
   2 ?    7.2  21.0    0.0057       4.6      26     153 ..     483     607 ..     476     642 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0017
                          Rootletin  93 LreqleearqaneaLtedlqkltkdwerlreeleqkekewreeeeafneylssehsrl 150
                                        L + +  ++ +n +L++d+ +l++ +++++ee++++ +++ ++++ + e +++ ++rl
  gene1595|gene1595|rna1595|rna1595 411 LADMISRMEVTNVKLKKDNVQLRESLRNVEEEMRTRVADLTDRNRLLDERVDKLKNRL 468
                                        5666778899***********************************9999999888887 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0057
                          Rootletin  26 lqYkkrcseleqrllektselektkltlllssareleeeesadleealakLeeErqrseklaqvnslLreqleear 101
                                         q k+++ e+e++ ++ + e+ek+k+++    +re e  + +++ee  + Le E + +++       Lre++  ++
  gene1595|gene1595|rna1595|rna1595 483 EQLKRQIVEIEKQNATYKFEVEKNKIEE---YKREQEMVRLKEVEECKNGLEKEIKVAND---IIRKLREDVRRMN 552
                                        589*************999999999865...5689999999*************999999...5667********* PP

                          Rootletin 102 qaneaLtedlqkltkdwerlreeleqkekewreeeea...fneylssehsrllsL 153
                                        +  e++ e++qkl+++  +l+++ e+ +k+ +e+ee+   +++ l++ ++++ +L
  gene1595|gene1595|rna1595|rna1595 553 EGKEEMDENVQKLKNENGKLAKSNEEASKTVKEKEERirgLKDALKRKDEKIKNL 607
                                        *********************************9999455567777777777666 PP

>> ERM  Ezrin/radixin/moesin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5  17.1     0.033        27       4      98 ..     426     524 ..     423     528 .. 0.77
   2 ?    8.7  25.1    0.0017       1.4       4     119 ..     510     625 ..     506     654 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.033
                                ERM   4 erekreleerLkqlqeeaekaqeaLrese....etaelLaekarraeeeaelLeqkaaeaeeeiqrlkesaek..e 73 
                                        ++++ +l+e L++++ee++ + ++L++ +    e++++L+++++ +e+e e L +++++++++i +++++++    
  gene1595|gene1595|rna1595|rna1595 426 KKDNVQLRESLRNVEEEMRTRVADLTDRNrlldERVDKLKNRLEGVEKENEGLVAEREQLKRQIVEIEKQNATykF 501
                                        56777899*****************987533337999******************************999876115 PP

                                ERM  74 eeekeklerklreaeleaarleees 98 
                                        e ek+k+e+  re e+   rl+e +
  gene1595|gene1595|rna1595|rna1595 502 EVEKNKIEEYKREQEM--VRLKEVE 524
                                        5666677666666554..4444433 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0017
                                ERM   4 erekreleerLkqlqeeaekaqeaLreseetaelLaekarraeeeaelLeqkaaeaeeeiqrlkesaekeeeekek 79 
                                        e ++++ + rLk+++e  +  +++ + +++ +++L e  rr+ e +e+++++ +++++e+ +l++s+e+  ++ ++
  gene1595|gene1595|rna1595|rna1595 510 EYKREQEMVRLKEVEECKNGLEKEIKVANDIIRKLREDVRRMNEGKEEMDENVQKLKNENGKLAKSNEEASKTVKE 585
                                        445566678******************************************************9999999999999 PP

                                ERM  80 lerklreaeleaarleeeserkeeeaerLkeeleeareae 119
                                         e+++r  +  ++r  e+ ++ e ++++L +++eea+   
  gene1595|gene1595|rna1595|rna1595 586 KEERIRGLKDALKRKDEKIKNLEMDKKQLVKKMEEAKFVY 625
                                        9999999999999999999999999999999999988554 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.2       1.1   9.3e+02      86     119 ..     414     448 ..     387     455 .. 0.47
   2 ?    3.3   8.1       0.1        85      27     120 ..     451     550 ..     446     552 .. 0.65
   3 ?   12.6  14.0   0.00014      0.11      37     131 ..     520     617 ..     507     621 .. 0.76

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 1.1
                                        HHHCCCHHHHHHHCCH.HHHHHHHHHHHHHHHHHH CS
                          Fib_alpha  86 leeeilrlketidaqe.snirvLqnvlesneqkiq 119
                                        + ++++  + ++++   +  + L+nv e+ + +++
  gene1595|gene1595|rna1595|rna1595 414 MISRMEVTNVKLKKDNvQLRESLRNVEEEMRTRVA 448
                                        33233333333333331222234444444444444 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.1
                                        CCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH.....HHHHHHHHHHHHHCCCHHHHHH CS
                          Fib_alpha  27 lkyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdn.....dnvikksskeleeeilrlketi 97 
                                        ++ ++ ++++++kl+n+le ++++++      +++k ++ e +k+++       +n i+++++e e   l+  e+ 
  gene1595|gene1595|rna1595|rna1595 451 TDRNRLLDERVDKLKNRLEGVEKENEGLVAEREQLKRQIVEIEKQNATYkfeveKNKIEEYKREQEMVRLKEVEEC 526
                                        56678899**************999876666666655555555555542222358888888877663333222334 PP

                                        HCCH.HHHHHHHHHHHHHHHHHHH CS
                          Fib_alpha  98 daqe.snirvLqnvlesneqkiqk 120
                                        ++   ++i+v  ++++++++++ +
  gene1595|gene1595|rna1595|rna1595 527 KNGLeKEIKVANDIIRKLREDVRR 550
                                        444448888888888888777665 PP

  == domain 3  score: 12.6 bits;  conditional E-value: 0.00014
                                        HCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH...HHHHCCCHHHHHHHCCHHHHHHHHH CS
                          Fib_alpha  37 lekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikkssk...eleeeilrlketidaqesnirvLqn 109
                                        l+++e+  + ++++ k a+++++++++ +r+ ++ k++ d+ ++k+++   +l +  ++  +t++++e++ir L++
  gene1595|gene1595|rna1595|rna1595 520 LKEVEECKNGLEKEIKVANDIIRKLREDVRRMNEGKEEMDENVQKLKNengKLAKSNEEASKTVKEKEERIRGLKD 595
                                        4444444455566777778888888887777777777766666666552227999********************* PP

                                        HHHHHHHHHHHHHHHHHHHHHH CS
                          Fib_alpha 110 vlesneqkiqkLeqdidqkerk 131
                                         l+++++ki++Le d +q+ +k
  gene1595|gene1595|rna1595|rna1595 596 ALKRKDEKIKNLEMDKKQLVKK 617
                                        **************99998765 PP

>> HMMR_N  Hyaluronan mediated motility receptor N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6  16.0   0.00017      0.14     228     335 .]     410     515 ..     398     515 .. 0.86
   2 ?    2.5  23.1     0.099        81     178     302 ..     521     638 ..     513     649 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00017
                             HMMR_N 228 klleyieelsnvseqlekykldiaqleellkekndeiesLkssLeekeqelskqvkdlnekckllekekeelvree 303
                                         l + i++++ +  +l   k+d  ql+e l + ++e+ +   +L +++  l+++v++l+++++ +eke+e lv e 
  gene1595|gene1595|rna1595|rna1595 410 YLADMISRMEVTNVKL---KKDNVQLRESLRNVEEEMRTRVADLTDRNRLLDERVDKLKNRLEGVEKENEGLVAER 482
                                        4667777777777777...***************************************************998776 PP

                             HMMR_N 304 ee.keqtlsaEleelkeklklkeqeaqklqqkl 335
                                        e+ k+q ++ E ++ + k++++++ ++++++++
  gene1595|gene1595|rna1595|rna1595 483 EQlKRQIVEIEKQNATYKFEVEKNKIEEYKREQ 515
                                        65155667788999999************9986 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.099
                             HMMR_N 178 kevsvkQedmeaklqvtqknLeeskakvaqLkeklvslekekieekseteklleyieelsnvseqlekykldiaql 253
                                        kev    +++e++++v++  +++ ++ v+ ++e + ++ ++ ++ k e+ kl + +ee s++ ++    +++i+ l
  gene1595|gene1595|rna1595|rna1595 521 KEVEECKNGLEKEIKVANDIIRKLREDVRRMNEGKEEMDENVQKLKNENGKLAKSNEEASKTVKEK---EERIRGL 593
                                        555555666677777777777777777777777666666666666777777777777766666665...7778888 PP

                             HMMR_N 254 eellkekndeiesLkssLeekeqelskqvkdlnekckllekekeelvre 302
                                        ++ lk k+++i++L    e  +++l k++++++  ++   k+ke +++ 
  gene1595|gene1595|rna1595|rna1595 594 KDALKRKDEKIKNL----EMDKKQLVKKMEEAKFVYNHFYKKKEGEISS 638
                                        88888888888744....4444446777777777777766666665544 PP

>> Mod_r  Modifier of rudimentary (Mod(r)) protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.4      0.25     2e+02      35      68 ..     415     448 ..     402     455 .. 0.73
   2 ?    5.3   6.1     0.025        20      10      75 ..     449     516 ..     444     532 .. 0.65
   3 ?   11.7   9.7   0.00025       0.2       8      87 ..     541     621 ..     534     631 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.25
                              Mod_r  35 keellaeneslaeknlslepeleelrselqekle 68 
                                         + ++ +n++l ++n +l+++l+++ +e+  +  
  gene1595|gene1595|rna1595|rna1595 415 ISRMEVTNVKLKKDNVQLRESLRNVEEEMRTRVA 448
                                        4567778888888888888888888887776655 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.025
                              Mod_r  10 elledeeklealvktl.pevkqlkeekeellaeneslaeknlslepeleelrselqekle.elkelek 75 
                                        +l +   +l+++v++l ++++ +++e e l+ae e+l ++  + e++    + e+++    e+k+ ++
  gene1595|gene1595|rna1595|rna1595 449 DLTDRNRLLDERVDKLkNRLEGVEKENEGLVAEREQLKRQIVEIEKQNATYKFEVEKNKIeEYKREQE 516
                                        66667778888888777778888888888888888887777777665555555554433224544444 PP

  == domain 3  score: 11.7 bits;  conditional E-value: 0.00025
                              Mod_r   8 Lqelledeeklealvktl.pevkqlkeekeellaeneslaeknlslepeleelrselqekleelkelekefeekeq 82 
                                        +++l ed   +++  +++ ++v++lk+e  +l ++ne+  +   ++e++++ l++ l+ k e++k+le   +++ +
  gene1595|gene1595|rna1595|rna1595 541 IRKLREDVRRMNEGKEEMdENVQKLKNENGKLAKSNEEASKTVKEKEERIRGLKDALKRKDEKIKNLEMDKKQLVK 616
                                        5666666677777777785568888888888888888888888888888888888888888888888888888888 PP

                              Mod_r  83 eldel 87 
                                        +++e+
  gene1595|gene1595|rna1595|rna1595 617 KMEEA 621
                                        88775 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.72   5.9e+02     187     220 ..     359     392 ..     327     395 .. 0.74
   2 ?    6.6   6.8    0.0052       4.2      20      82 ..     435     497 ..     418     527 .. 0.60
   3 ?    5.2   9.9     0.014        12      21     106 ..     530     619 ..     517     630 .. 0.70

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.72
                            DUF3450 187 valyyqtlDgkeagawdqetkqWqaldssyrsei 220
                                        v l+yq ++g++ + +d++++ +  ++++  ++i
  gene1595|gene1595|rna1595|rna1595 359 VELFYQVKNGRMKALFDKDSGRFIFVEQNEFRNI 392
                                        789***************9999988877766666 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0052
                            DUF3450  20 qalkeaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeia 82 
                                        ++++++e+  +  a+   +   ld+  ++l+++++ +++e+e l +++eql+r++ + e++ a
  gene1595|gene1595|rna1595|rna1595 435 SLRNVEEEMRTRVADLTDRNRLLDERVDKLKNRLEGVEKENEGLVAEREQLKRQIVEIEKQNA 497
                                        344444555555555555555555555666666666666666666666666666655555444 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.014
                            DUF3450  21 alkeaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasle....eqieeie 92 
                                        ++ke + a+++ ++  + + ++++ k+e+ +++++lk+e+ +l++ ne+ ++ v++ e++i  l+    ++ e+i+
  gene1595|gene1595|rna1595|rna1595 530 LEKEIKVANDIIRKLREDVRRMNEGKEEMDENVQKLKNENGKLAKSNEEASKTVKEKEERIRGLKdalkRKDEKIK 605
                                        5566666777777777888888888888888888888888888888888888888888887654411114555666 PP

                            DUF3450  93 eierelvpllekmi 106
                                        ++e++ ++l +km 
  gene1595|gene1595|rna1595|rna1595 606 NLEMDKKQLVKKME 619
                                        66666666666654 PP

>> UPF0242  Uncharacterised protein family (UPF0242) N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.5     0.069        56      90     133 ..     400     443 ..     371     446 .. 0.83
   2 ?    5.5  15.7     0.019        16      68     157 ..     421     514 ..     406     532 .. 0.68
   3 ?    2.3  22.9      0.19   1.5e+02      69     165 ..     512     618 ..     504     622 .. 0.66
   4 ?    5.3   6.9     0.023        19      87     144 ..     579     636 ..     575     646 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.069
                            UPF0242  90 aleelqeeeeeLkeeldakeeelerlkeenqqLqekleaiaedf 133
                                        ++ + ++ ++ L++ ++ +e +  +lk++n qL+e l ++ e++
  gene1595|gene1595|rna1595|rna1595 400 KVPDENDYKRYLADMISRMEVTNVKLKKDNVQLRESLRNVEEEM 443
                                        667778888999999*********************99988776 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.019
                            UPF0242  68 skleekeaklteldeglktkee....aleelqeeeeeLkeeldakeeelerlkeenqqLqekleaiaedfeel.kl 138
                                         +++ k+ +++  +e+l++ ee     + +l+++++ L e++d+ ++ le  ++en+ L  + e+ ++++ e  k+
  gene1595|gene1595|rna1595|rna1595 421 TNVKLKKDNVQL-RESLRNVEEemrtRVADLTDRNRLLDERVDKLKNRLEGVEKENEGLVAEREQLKRQIVEIeKQ 495
                                        444555555543.346666666566688999999999999999999999999999998888877777776554255 PP

                            UPF0242 139 eleeqLaekqellqeyqet 157
                                        ++  + + ++++++ey+++
  gene1595|gene1595|rna1595|rna1595 496 NATYKFEVEKNKIEEYKRE 514
                                        5666777777777777654 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.19
                            UPF0242  69 kleekeaklteld.......eglktkeealeelqeeeeeLkeeldakeeelerlkeenqqLqekleaiae...dfe 134
                                        k e++   l+e +       +++k+ ++ +++l+e+ ++++e  ++++e++++lk+en +L +  e++++   + e
  gene1595|gene1595|rna1595|rna1595 512 KREQEMVRLKEVEeckngleKEIKVANDIIRKLREDVRRMNEGKEEMDENVQKLKNENGKLAKSNEEASKtvkEKE 587
                                        3333333333333444444466778888888888888888888999999999999999988876666655444777 PP

                            UPF0242 135 elkleleeqLaekqellqeyqetieeqrsvl 165
                                        e  + l+++L++k e++++++   +++ + +
  gene1595|gene1595|rna1595|rna1595 588 ERIRGLKDALKRKDEKIKNLEMDKKQLVKKM 618
                                        7777888888888888888776666655555 PP

  == domain 4  score: 5.3 bits;  conditional E-value: 0.023
                            UPF0242  87 keealeelqeeeeeLkeeldakeeelerlkeenqqLqekleaiaedfeelkleleeqL 144
                                          ++++e +e+ + Lk+ l+ k+e++++l+ +++qL +k+e+++  ++++ ++ e ++
  gene1595|gene1595|rna1595|rna1595 579 ASKTVKEKEERIRGLKDALKRKDEKIKNLEMDKKQLVKKMEEAKFVYNHFYKKKEGEI 636
                                        5578899999999999999999999999999999999999999888888777777666 PP

>> Lectin_N  Hepatic lectin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.1         4   3.2e+03      44      72 ..     331     359 ..     330     369 .. 0.65
   2 ?   14.0   1.0   3.8e-05     0.031      49     102 ..     421     474 ..     413     495 .. 0.87
   3 ?   -0.1   1.3       0.9   7.3e+02      53     104 ..     544     598 ..     534     620 .. 0.47

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 4
                           Lectin_N  44 cVigsqn.sqLqreLetLketfsnfssstl 72 
                                        c i+s +  +L++e + L+ +f+nf  ++ 
  gene1595|gene1595|rna1595|rna1595 331 CTITSTSyVHLKNE-QELRVNFENFVRKVV 359
                                        55555553455555.678888998877654 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 3.8e-05
                           Lectin_N  49 qnsqLqreLetLketfsnfssstlaeiqalssqggslsekvtsleaklekkqqd 102
                                         n +L+++ + L+e+++n+ +++ + + +l+ +++ l+e+v  l+ +le  +++
  gene1595|gene1595|rna1595|rna1595 421 TNVKLKKDNVQLRESLRNVEEEMRTRVADLTDRNRLLDERVDKLKNRLEGVEKE 474
                                        689********************************************9877765 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.9
                           Lectin_N  53 LqreLetL...ketfsnfssstlaeiqalssqggslsekvtsleaklekkqqdlk 104
                                        L+++++ +   ke++++  ++ + e  +l+  ++++s++v+  e +++  + +lk
  gene1595|gene1595|rna1595|rna1595 544 LREDVRRMnegKEEMDENVQKLKNENGKLAKSNEEASKTVKEKEERIRGLKDALK 598
                                        5555555511123333444444444444444444444444444444444444333 PP

>> Golgin_A5  Golgin subfamily A member 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2  11.0      0.03        24     106     194 ..     419     506 ..     400     508 .. 0.78
   2 ?    7.2  28.1    0.0038       3.1      52     213 ..     478     631 ..     468     652 .. 0.58

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.03
                          Golgin_A5 106 rkakeeveaelerlkeelryleeelvrskatlqsrikdrekeieklrnqlttkslsss.seselesRlkqLtesLi 180
                                        + ++ +++++  +l+e lr +eee++   a+l  r +  ++ ++kl+n l   ++++    +e e+  +q++e  i
  gene1595|gene1595|rna1595|rna1595 419 EVTNVKLKKDNVQLRESLRNVEEEMRTRVADLTDRNRLLDERVDKLKNRLEGVEKENEgLVAEREQLKRQIVE--I 492
                                        4456677888889999999999999999999999999999999999999987755544267788888888888..8 PP

                          Golgin_A5 181 qKQtvlEalstekn 194
                                        +KQ+   + + ekn
  gene1595|gene1595|rna1595|rna1595 493 EKQNATYKFEVEKN 506
                                        99999888888888 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0038
                          Golgin_A5  52 lkqerdllreelqklnqqieqlrtelqdleaqqqaeaeslreqlqeleeqleeerkakeeveaelerlkeelryle 127
                                        l +er++l+ ++ + ++q  + + e   +e+++ +e +  +e +     +l+e ++ k+ +e+e++  ++ +r l+
  gene1595|gene1595|rna1595|rna1595 478 LVAEREQLKRQIVEIEKQNATYKFE---VEKNKIEEYKREQEMV-----RLKEVEECKNGLEKEIKVANDIIRKLR 545
                                        3344444444444444444444444...3444433333322222.....233334456667788888888888888 PP

                          Golgin_A5 128 eelvrskatlqsrikdrekeieklrnq...lttk.slsssseselesRlkqLtesLiqKQtvlEalsteknslvlQ 199
                                        e+++r  +      ++ +++++kl+n+   l+++ +  s + +e e+R++ L ++L +K   + +l+ +k+ lv  
  gene1595|gene1595|rna1595|rna1595 546 EDVRRMNE----GKEEMDENVQKLKNEngkLAKSnEEASKTVKEKEERIRGLKDALKRKDEKIKNLEMDKKQLVKK 617
                                        88875433....3345567777777652225544133344778******************************998 PP

                          Golgin_A5 200 LeRleqqikevqse 213
                                        +e +   +++  ++
  gene1595|gene1595|rna1595|rna1595 618 MEEAKFVYNHFYKK 631
                                        88766555554444 PP

>> GAS  Growth-arrest specific micro-tubule binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4  20.0      0.44   3.6e+02      22     128 ..     427     533 ..     423     543 .. 0.81
   2 ?   10.0  20.3   0.00048      0.39      34     139 ..     533     642 ..     528     647 .. 0.73

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.44
                                GAS  22 rnNLelIkslKeeieelkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkel 97 
                                        ++N +l +sl++  ee++++ +  + +   + ++  +lk  L+ +e+e+e L ++ ++ +++ +++++++a +k  
  gene1595|gene1595|rna1595|rna1595 427 KDNVQLRESLRNVEEEMRTRVADLTDRNRLLDERVDKLKNRLEGVEKENEGLVAEREQLKRQIVEIEKQNATYKFE 502
                                        6899999999999999999999999999999999999999999999999999999999999988888888888776 PP

                                GAS  98 ekelkdlkwehevleqrfekvekerdelykk 128
                                         ++ k  +++ e+   r+++ve+ ++ l+k+
  gene1595|gene1595|rna1595|rna1595 503 VEKNKIEEYKREQEMVRLKEVEECKNGLEKE 533
                                        6666666666667777888888888888775 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00048
                                GAS  34 eieelkkkeernekelseisqenkrlkepLkkaeeeveeLrk....qlknyekdkqslknlkarlkelekelkdlk 105
                                        ei+  +   ++ + ++  +++ ++++ e+++k+++e+ +L k    + k+ +++ ++++ lk  lk+ ++++k+l+
  gene1595|gene1595|rna1595|rna1595 533 EIKVANDIIRKLREDVRRMNEGKEEMDENVQKLKNENGKLAKsneeASKTVKEKEERIRGLKDALKRKDEKIKNLE 608
                                        555555555556666666666666666666666666666666222222333344567899**************** PP

                                GAS 106 wehevleqrfekvekerdelykkfeaaiqevqqk 139
                                        +++++l +++e+++  ++ +ykk e  i  v+++
  gene1595|gene1595|rna1595|rna1595 609 MDKKQLVKKMEEAKFVYNHFYKKKEGEISSVSEN 642
                                        *************************999999875 PP

>> DASH_Dam1  DASH complex subunit Dam1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0      0.27   2.2e+02       4      35 ..     446     477 ..     443     480 .. 0.85
   2 ?    6.0   0.4     0.013        10       3      34 ..     546     577 ..     544     580 .. 0.89
   3 ?   -1.9   0.2       3.8   3.1e+03       3      30 ..     588     615 ..     587     620 .. 0.76

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.27
                          DASH_Dam1   4 afaeLaDsletLdknledLqqihesLsdfNeS 35 
                                        + a+L+D  + Ld+++++L++  e +++ Ne+
  gene1595|gene1595|rna1595|rna1595 446 RVADLTDRNRLLDERVDKLKNRLEGVEKENEG 477
                                        67999**************9998888888886 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.013
                          DASH_Dam1   3 pafaeLaDsletLdknledLqqihesLsdfNe 34 
                                        +  +++++  e++d+n+++L++ + +L++ Ne
  gene1595|gene1595|rna1595|rna1595 546 EDVRRMNEGKEEMDENVQKLKNENGKLAKSNE 577
                                        5678899999******************9998 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 3.8
                          DASH_Dam1   3 pafaeLaDsletLdknledLqqihesLs 30 
                                        ++++ L+D+l+  d+++++L+  +++L+
  gene1595|gene1595|rna1595|rna1595 588 ERIRGLKDALKRKDEKIKNLEMDKKQLV 615
                                        5678899999999999988887666665 PP

>> DUF2203  Uncharacterized conserved protein (DUF2203)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   5.2       1.7   1.4e+03      25      71 ..     457     494 ..     409     530 .. 0.51
   2 ?   12.7   6.5   0.00019      0.16       6      80 ..     535     608 ..     533     625 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 1.7
                            DUF2203  25 lrkeleeleeeleeakaeaekseaaeleaeleeleaeieelveeiee 71 
                                        l +++ +l+++le           +++++ l + ++++++ + eie+
  gene1595|gene1595|rna1595|rna1595 457 LDERVDKLKNRLEG---------VEKENEGLVAEREQLKRQIVEIEK 494
                                        22222222222222.........222222222233333333333333 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00019
                            DUF2203   6 eeAnalLpllkelleelralrkeleeleeeleeakaeaekseaaeleaeleeleaeieelveeieelGvevkdle 80 
                                        + An+++ +l+e ++++++ ++e+ e +++l++++ + +ks  +e+ ++++e e++i+ l + +++   ++k+le
  gene1595|gene1595|rna1595|rna1595 535 KVANDIIRKLREDVRRMNEGKEEMDENVQKLKNENGKLAKS-NEEASKTVKEKEERIRGLKDALKRKDEKIKNLE 608
                                        679**************************999999998766.555566666666666666666666666666654 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   8.1     0.096        78      19     105 ..     411     495 ..     406     523 .. 0.79
   2 ?    3.5   0.9     0.084        69      13      51 ..     521     559 ..     505     568 .. 0.60
   3 ?    9.0   9.4    0.0016       1.3       3      79 ..     539     622 ..     537     637 .. 0.74

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.096
                                        XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH...HHHHHH CS
                         Laminin_II  19 laplsqnlentkeklseinrsveetnekvk.dankairdArrsvkkLeklapqLldklkelkqleeassslsdnis 93 
                                        la++  ++e t+ kl++ n +++e   +v+ ++ + ++d  +  + L++ +++L ++l+ +++ +e+   l ++ +
  gene1595|gene1595|rna1595|rna1595 411 LADMISRMEVTNVKLKKDNVQLRESLRNVEeEMRTRVADLTDRNRLLDERVDKLKNRLEGVEKENEG---LVAERE 483
                                        6778888888899999999999999888885677789999************************999...666666 PP

                                        HHHHHHHHHHHH CS
                         Laminin_II  94 eikelIaqARka 105
                                        ++k +I    k+
  gene1595|gene1595|rna1595|rna1595 484 QLKRQIVEIEKQ 495
                                        666666554444 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.084
                                        XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                         Laminin_II  13 kevleqlaplsqnlentkeklseinrsveetnekvkdan 51 
                                        kev+e +++l+++++  ++ + +++++v+++ne  +++ 
  gene1595|gene1595|rna1595|rna1595 521 KEVEECKNGLEKEIKVANDIIRKLREDVRRMNEGKEEMD 559
                                        566666666666666666666666666555554433333 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.0016
                                        XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX...XX....XXXXXXX--TTTTT CS
                         Laminin_II   3 elaaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankair...dA....rrsvkkLeklapqL 71 
                                         ++++  e +    e ++++++n++++k++  ++++s ee  + vk++ + ir   dA     +++k+Le+   qL
  gene1595|gene1595|rna1595|rna1595 539 DIIRKLREDVRRMNEGKEEMDENVQKLKNENGKLAKSNEEASKTVKEKEERIRglkDAlkrkDEKIKNLEMDKKQL 614
                                        5677777888888888888998888888888888888888888887665544311144322267899999999999 PP

                                        GGGHHHHH CS
                         Laminin_II  72 ldklkelk 79 
                                        ++k++e k
  gene1595|gene1595|rna1595|rna1595 615 VKKMEEAK 622
                                        99998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (656 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2621  (0.146188); expected 358.6 (0.02)
Passed bias filter:                      579  (0.032294); expected 358.6 (0.02)
Passed Vit filter:                       149  (0.00831056); expected 17.9 (0.001)
Passed Fwd filter:                        68  (0.00379274); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              22  [number of targets reported over threshold]
# CPU time: 1.34u 0.38s 00:00:01.72 Elapsed: 00:00:00.58
# Mc/sec: 3410.09
//
Query:       gene1596|gene1596|rna1596|rna1596  [L=48]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
       0.21   12.1   0.2       0.23   11.9   0.2    1.2  1  GPS2_interact  G-protein pathway suppressor 2-interacting dom


Domain annotation for each model (and alignments):
>> GPS2_interact  G-protein pathway suppressor 2-interacting domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.2   1.3e-05      0.23      31      47 ..      32      48 .]      16      48 .] 0.81

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.3e-05
                      GPS2_interact 31 eLlqnidkvDREiakve 47
                                        Ll+nid +DRE a+ e
  gene1596|gene1596|rna1596|rna1596 32 RLLNNIDEIDREYARYE 48
                                       7***********99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (48 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       373  (0.0208043); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.37s 00:00:00.88 Elapsed: 00:00:00.55
# Mc/sec: 260.92
//
Query:       gene1597|gene1597|rna1597|rna1597  [L=519]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-06   27.0   0.1    5.2e-06   26.2   0.1    1.4  1  HECT      HECT-domain (ubiquitin-transferase)
  ------ inclusion threshold ------
       0.19   11.6   0.6       0.62   10.0   0.1    2.0  2  DUF5486   Family of unknown function (DUF5486)


Domain annotation for each model (and alignments):
>> HECT  HECT-domain (ubiquitin-transferase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.1   5.8e-10   5.2e-06      35      95 ..     400     478 ..     368     502 .. 0.73

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 5.8e-10
                                        S.........................HHHHHHHHHHHHHTT--BSS-B-HHHHHHHTT-.---TCHHHHH-HHHHH CS
                                        x.....................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               HECT  35 e.....................llklfeflGkvlGkaiyeeilldlpfsraflkfllgeekitledleeidpelak 89 
                                        +                       + +  lG++l+++++++ +++++fs af++ l+g +k tl+++++   ++++
  gene1597|gene1597|rna1597|rna1597 400 KfiedtdpafyaepnintnllsNDEFYAYLGTFLALCFLNREMISVKFSLAFWENLMG-RKYTLRHVQD--TQVQR 472
                                        34444444445555666667777789********************************.7999888775..56667 PP

                                        HHHHHH CS
                                        xxxxxx RF
                               HECT  90 slkell 95 
                                        +l ++l
  gene1597|gene1597|rna1597|rna1597 473 NLLYVL 478
                                        766666 PP

>> DUF5486  Family of unknown function (DUF5486)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.31   2.8e+03      12      20 ..     257     265 ..     255     275 .. 0.71
   2 ?   10.0   0.1     7e-05      0.62       3      20 ..     357     374 ..     355     379 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.31
                            DUF5486  12 sreemmrrf 20 
                                        s e+m+rr 
  gene1597|gene1597|rna1597|rna1597 257 SEENMLRRN 265
                                        679999994 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 7e-05
                            DUF5486   3 eidynkirssreemmrrf 20 
                                        e+d n ++s +e+mmrr+
  gene1597|gene1597|rna1597|rna1597 357 EVDVNAMKSLKEQMMRRL 374
                                        99***************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (519 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       685  (0.0382063); expected 358.6 (0.02)
Passed bias filter:                      487  (0.0271627); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.76u 0.34s 00:00:01.10 Elapsed: 00:00:00.57
# Mc/sec: 2725.85
//
Query:       gene1598|gene1598|rna1598|rna1598  [L=173]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-20   74.0   3.3    1.9e-20   73.6   3.3    1.0  1  HECT      HECT-domain (ubiquitin-transferase)


Domain annotation for each model (and alignments):
>> HECT  HECT-domain (ubiquitin-transferase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.6   3.3     1e-24   1.9e-20     140     305 ..      10     171 ..       6     172 .. 0.95

  Alignments for each domain:
  == domain 1  score: 73.6 bits;  conditional E-value: 1e-24
                                        HHHHHHHHHHHHTGGGHHHHHHHHHHHHTTS-HHHHTTS-HHHHHHHHBCSSS.--HHHHHHTEEEETT--TTSHH CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               HECT 140 keYiklyvnyllkksvekqleaflkGfsevipskalklfdaeelellisGedelidvedlrrnteykggynaeset 215
                                        k+++k++v   l  s ++ ++ ++  f++++p++  ++   +++  +++G++e i+++ l++  +y + +++ s+ 
  gene1598|gene1598|rna1598|rna1598  10 KQFVKKTVYESLFFSKKRAYDIIHYFFYSLMPREFQEIYATQDIYYVLNGKEE-ITFNFLKSAFQYIK-CSEGSKE 83 
                                        7899999999999999999*********************************8.************87.******* PP

                                        HHHHHHHHHHS-HHHHHHHHHHHHSSSS--TTCGGG-B--EEEEE-S..-TTS--EEEGGGTEEEE---SSHHHHH CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               HECT 216 iewlweilkefspeekrlfLqFvTgssrlPlgGfaelhpkftierkskedetrLPtahTCfnlLklpdYsskeilk 291
                                        +  l++i+k+ +++  r+fL+FvTgs+++Pl+  ++l   f+i+ ++ + +++L +a+ C+++L +  Y+++e+++
  gene1598|gene1598|rna1598|rna1598  84 VVFLLNIFKRKNEAYYRKFLKFVTGSENIPLQ-SNKL-DLFKIYVEQIDVKNALFRASSCVKMLFIGCYDTEEEME 157
                                        ********************************.5557.89999999999*************************** PP

                                        HHHHHHHHHHH--X CS
                                        xxxxxxxxxxxxxx RF
                               HECT 292 ekLltAieetegFe 305
                                        + +  +i +tegF+
  gene1598|gene1598|rna1598|rna1598 158 RIMDFSIFNTEGFH 171
                                        *************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (173 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       478  (0.0266607); expected 358.6 (0.02)
Passed bias filter:                      222  (0.0123822); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.54
# Mc/sec: 961.88
//
Query:       gene1599|gene1599|rna1599|rna1599  [L=91]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.5e-12   47.0   0.5    2.2e-12   46.5   0.5    1.2  1  LSM             LSM domain
    1.2e-05   25.3   0.1    1.4e-05   25.1   0.1    1.2  1  SM-ATX          Ataxin 2 SM domain
     0.0088   15.8   0.1       0.01   15.5   0.1    1.2  1  Ribosomal_L15e  Ribosomal L15
  ------ inclusion threshold ------
      0.014   15.5   0.0      0.025   14.7   0.0    1.4  1  LSM14           Scd6-like Sm domain


Domain annotation for each model (and alignments):
>> LSM  LSM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.5   0.5     5e-16   2.2e-12       7      66 ..      11      68 ..       6      69 .. 0.91

  Alignments for each domain:
  == domain 1  score: 46.5 bits;  conditional E-value: 5e-16
                                       TTSEEEEEETTSEEEEEEEEEEETTSEEEEEEEEEEETTETEEEEEEEEEEEGGGEEEEE CS
                                LSM  7 inkkvtvelkngrelrGtLkgfDqfmNlvLedveetlkdkkekrklglvliRGnnivlis 66
                                       +++ + velkn+ ++rGtL+++D  mNl L++v  ++ d+  +++ +++++RG+ +  i 
  gene1599|gene1599|rna1599|rna1599 11 KGSVIDVELKNNDTYRGTLVACDLLMNLRLKNVRLVSSDG--EKDFNECILRGSAVKHIK 68
                                       677899*******************************996..9999********998775 PP

>> SM-ATX  Ataxin 2 SM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.1   3.2e-09   1.4e-05       8      54 ..       7      53 ..       4      80 .. 0.82

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 3.2e-09
                                       HHTTTTSEEEEEETTS-EEEEEEEEE-T..T--EEEEEEEETTS..... CS
                             SM-ATX  8 ltslvGkevevtvknGevyeGifstvslekdfsvvLkmarkvkk..ans 54
                                       +  + G++++v++kn ++y+G + +++l   +++ Lk++r+v++  +++
  gene1599|gene1599|rna1599|rna1599  7 VRISKGSVIDVELKNNDTYRGTLVACDL--LMNLRLKNVRLVSSdgEKD 53
                                       56677***********************..**************44333 PP

>> Ribosomal_L15e  Ribosomal L15
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.1   2.3e-06      0.01     107     160 ..      33      86 ..       8      89 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.3e-06
                                        HHSTTSEEEEEEEEEEESSEEEEEEEEE-TTSHHHHT-TTTGGGGSGGGTTGGG CS
                     Ribosomal_L15e 107 rklpnlrvLnSYwvgeDgtykyyEvilvDpshkairndkkinwickkvhkhRel 160
                                        + l nlr+ n   v  Dg+  + E+il   + k i+ ++k+ ++ + v+++R +
  gene1599|gene1599|rna1599|rna1599  33 DLLMNLRLKNVRLVSSDGEKDFNECILRGSAVKHIKLNNKVLYVQEMVERKRLM 86 
                                        56789*********************************************9976 PP

>> LSM14  Scd6-like Sm domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   5.5e-06     0.025       4      72 ..      12      69 ..      11      72 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 5.5e-06
                              LSM14  4 GskislisksdirYeGilceinledstiaLqnvrsfGtegrkdneqippskevyeyivFrgsDikdLev 72
                                       Gs+i ++ k++  Y G+l++ +    ++ L+nvr    +g kd ++           ++rgs +k +++
  gene1599|gene1599|rna1599|rna1599 12 GSVIDVELKNNDTYRGTLVACD-LLMNLRLKNVRLVSSDGEKDFNE----------CILRGSAVKHIKL 69
                                       899*******************.6789***********99777666..........6677777776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       414  (0.0230911); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 636.68
//
Query:       gene16|gene16|rna16|rna16  [L=89]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       399  (0.0222544); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 602.65
//
Query:       gene160|gene160|rna160|rna160  [L=419]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.8e-43  147.9  13.6    2.8e-43  147.9  13.6    2.0  2  Peptidase_M48_N  CAAX prenyl protease N-terminal, five membra
    3.1e-39  134.8   0.0    4.9e-39  134.1   0.0    1.3  1  Peptidase_M48    Peptidase family M48
     0.0022   17.8   0.0     0.0036   17.1   0.0    1.3  1  SprT-like        SprT-like family


Domain annotation for each model (and alignments):
>> Peptidase_M48_N  CAAX prenyl protease N-terminal, five membrane helices
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  147.9  13.6   4.7e-47   2.8e-43      11     182 .]      33     201 ..      24     201 .. 0.95
   2 ?   -1.8   2.6      0.42   2.5e+03      55     103 ..     296     350 ..     281     352 .. 0.60

  Alignments for each domain:
  == domain 1  score: 147.9 bits;  conditional E-value: 4.7e-47
                Peptidase_M48_N  11 vPeeladaitkekfdksraYgldksrfglvsslyslilllallllgllpflwklsgkllgldaeseilqslvfllllsli 90 
                                      e l+d+i++++f+ +++Y+ +k+ f+l+s+++s+i l++++++  +p+ ++ ++++ g+  +s+++ +++f+l+++ +
  gene160|gene160|rna160|rna160  33 RNELLTDKIEDSDFETMKKYNTEKLIFSLFSGTISFIRLICFIHFHTIPKSYDYLKNISGI--KSDMVLNVLFMLVFLHF 110
                                    5677999**************************************************5554..89*************** PP

                Peptidase_M48_N  91 stlislPfslYstFviEekhGfnkqtlklfikdklkslllalviglpllaallwiiewggeyfylylwlfllvfslllmt 170
                                    + ++++P+sl+stF iEe++Gfnk+t+++f+kd+lk++++ ++i+ pl a++ +i++++ + f+ ++++f++vf+++l++
  gene160|gene160|rna160|rna160 111 ERVMDIPLSLFSTFFIEERYGFNKMTFGIFLKDFLKETIVLTLIISPLYAGIYKIMNYF-DTFFAIIFVFVCVFQIFLVM 189
                                    ***********************************************************.899999************** PP

                Peptidase_M48_N 171 iyPtlIaPLFnK 182
                                    iyP++I+PLFnK
  gene160|gene160|rna160|rna160 190 IYPVVIQPLFNK 201
                                    ***********9 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.42
                Peptidase_M48_N  55 lgllpflwklsgkl......lgldaeseilqslvfllllslistlislPfslYst 103
                                    + +++fl  ++++       ++ ++   i++ ++f +++ ++s ++ l  ++Ys 
  gene160|gene160|rna160|rna160 296 FVFFYFLEVALKNKsfvvslFQTENVPLIVKLVYFSFFMGILSPFLTLLTNMYSR 350
                                    3333333333333333334344455556777777888888889899888888886 PP

>> Peptidase_M48  Peptidase family M48
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  134.1   0.0   8.2e-43   4.9e-39       2     195 ..     205     410 ..     204     411 .. 0.89

  Alignments for each domain:
  == domain 1  score: 134.1 bits;  conditional E-value: 8.2e-43
                                    --SSHHHHHHHHHHHHTT-..-EEEEEEE-GGGT....-EEEEESSS-EEEEEEHHHH-SSB-HHHHHHHHHHHHHHHHT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Peptidase_M48   2 lreaelkevveelakeaglpkpltkvyvvnspkr....NAFalgggknkrivltdgLlkqllseeelaaVlGHElGHikh 77 
                                    l++++lk+ +++lak++g+  +  k++v++++ r    NA+++g + ++rivl+d+L+ +  +e+e+  +lGHE+GH+ h
  gene160|gene160|rna160|rna160 205 LEDGSLKTAIKNLAKNVGF--KCSKIFVMDGSMRsnhsNAYFIGLFGERRIVLFDTLI-KQATEDEIISILGHEIGHWYH 281
                                    78999**************..*********99889999********999*********.999****************** PP

                                    THHHHHHHHHHHHHHHHHHHHHHHTT-SHHHHHTT--S---HHHHHHHHHHTT.............HHHHHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.............xxxxxxxxxxxxxx RF
                  Peptidase_M48  78 rhsvvslivsllasillllglallisraeedaagafldalavliglliillfl.............alSRkrEyqADeag 144
                                     h  ++l+ +   ++++++ l ++   ++++  + f +++  li+ l  ++f               +SR++E+qAD ++
  gene160|gene160|rna160|rna160 282 YHIPKMLVLQFSTQFVFFYFLEVA-LKNKSFVVSLFQTENVPLIVKLVYFSFFmgilspfltlltnMYSRYNERQADLFS 360
                                    ***887666666666666555555.5556666677777777777777788887899************************ PP

                                    HHTTT.HHHHHHHHHHHHHHTT--S---HHHHHHS-SS--HHHHHHHHHH- CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Peptidase_M48 145 vellkrakdlvraliklakdlerqdvsaslrsellstHPplleRiqalkel 195
                                    ++l+   ++l + li+++k+++++   ++l+s+++++HP l+eR++ ++++
  gene160|gene160|rna160|rna160 361 IKLGL-GENLGKGLISIHKENKSNVCPDWLYSTYYHSHPTLVERLEFISDE 410
                                    *****.****************************************99875 PP

>> SprT-like  SprT-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   6.1e-07    0.0036      45      80 ..     249     284 ..     202     290 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 6.1e-07
                      SprT-like  45 hhasIeLseklldsrsedrllntLaHElcHlalfvi 80 
                                    ++ +I L  +l+++ +ed+++++L HE+ H + ++i
  gene160|gene160|rna160|rna160 249 GERRIVLFDTLIKQATEDEIISILGHEIGHWYHYHI 284
                                    6789****************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (419 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1126  (0.0628033); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.31s 00:00:00.86 Elapsed: 00:00:00.46
# Mc/sec: 2728.97
//
Query:       gene1600|gene1600|rna1600|rna1600  [L=65]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (65 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       495  (0.0276089); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.53u 0.37s 00:00:00.90 Elapsed: 00:00:00.56
# Mc/sec: 347.64
//
Query:       gene1601|gene1601|rna1601|rna1601  [L=103]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.058   13.1   0.1      0.086   12.5   0.1    1.3  1  IL1       Interleukin-1 / 18


Domain annotation for each model (and alignments):
>> IL1  Interleukin-1 / 18
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   4.8e-06     0.086      38      69 ..      42      73 ..      32      84 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4.8e-06
                                       EEEEEEE.TEEEEEEEES-GCCCESTSSCCGGG CS
                                IL1 38 ylScvkk.depvLqleevnipkliknkesdkrF 69
                                        lSc +  d+ ++++++++ ++ i+  +++++F
  gene1601|gene1601|rna1601|rna1601 42 LLSCTNIkDNRKIEFKMIE-TDEITAIDNNIVF 73
                                       69****88***********.**********999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       768  (0.0428356); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.34s 00:00:00.90 Elapsed: 00:00:00.54
# Mc/sec: 573.84
//
Query:       gene1602|gene1602|rna1602|rna1602  [L=95]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.6e-06   25.7   4.5    4.2e-05   23.3   4.5    2.0  1  NuA4      Histone acetyltransferase subunit NuA4
     0.0088   15.2   2.5      0.013   14.6   2.5    1.3  1  CCDC144C  CCDC144C protein coiled-coil region
  ------ inclusion threshold ------
      0.014   16.2   0.6      0.019   15.7   0.6    1.3  1  MRP-L46   39S mitochondrial ribosomal protein L46
      0.042   13.7   0.2      0.051   13.4   0.2    1.2  1  DUF1465   Protein of unknown function (DUF1465)


Domain annotation for each model (and alignments):
>> NuA4  Histone acetyltransferase subunit NuA4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   4.5   9.5e-09   4.2e-05       1      72 [.      22      87 ..      22      88 .. 0.81

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 9.5e-09
                               NuA4  1 eLkellkkkrelekelakleeqIydkEteYleetssvGNiikGFdnylkssssssaaerrkrkvtdedriFS 72
                                       +L  ll+++++l ++ ++l+++Iy+ EteYle+  ++  +    d y+      +++e++k  v+ +dr+FS
  gene1602|gene1602|rna1602|rna1602 22 QLSALLERQKQLIRRKNELDNEIYKYETEYLESG-QGYPLTNSLDFYMG-----QRHEKKKYVVQAKDRVFS 87
                                       68899****************************9.33333334455555.....677777899********9 PP

>> CCDC144C  CCDC144C protein coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   2.5   2.9e-06     0.013     262     302 ..      12      52 ..       1      54 [. 0.80

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.9e-06
                           CCDC144C 262 vkkLqaesekqvllleernkeLinecnhlkerlyqyekeka 302
                                         k      +kq   l er+k+Li   n+l +++y+ye+e  
  gene1602|gene1602|rna1602|rna1602  12 SKAALLTLQKQLSALLERQKQLIRRKNELDNEIYKYETEYL 52 
                                        55555567899999************************965 PP

>> MRP-L46  39S mitochondrial ribosomal protein L46
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.7   0.6   4.3e-06     0.019       6      55 ..      24      74 ..      20      88 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 4.3e-06
                                       E-B--B--SB-----HHHHHH....HHHHHHHH.HHT----HHHHTTHHHH CS
                            MRP-L46  6 gliLsRpPvvtrelspfEkefYkYqkellerle.lefskyfyfkkgtlael 55
                                       + +L+R+ ++ r ++++++e+YkY+ e le  + ++++   +f  g+  e+
  gene1602|gene1602|rna1602|rna1602 24 SALLERQKQLIRRKNELDNEIYKYETEYLESGQgYPLTNSLDFYMGQRHEK 74
                                       789*********************998777543344444444444444444 PP

>> DUF1465  Protein of unknown function (DUF1465)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.2   1.1e-05     0.051      87     135 ..       3      50 ..       1      66 [. 0.80

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.1e-05
                                        ------..-----------HHHHHHHHHHHHHHHHHHHHHHHHHT-SSX CS
                            DUF1465  87 rvklaaaeasdaeavaeLpeelqeLierserLyervrrLdrelreeaea 135
                                        r+++++ ++ ++ a+ +L ++l +L+er ++L +r  +Ld+e+++ +++
  gene1602|gene1602|rna1602|rna1602   3 RIQKSK-SKLSKAALLTLQKQLSALLERQKQLIRRKNELDNEIYKYETE 50 
                                        555555.4667778889999*********************99987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1273  (0.0710023); expected 358.6 (0.02)
Passed bias filter:                      594  (0.0331307); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.57u 0.38s 00:00:00.95 Elapsed: 00:00:00.56
# Mc/sec: 506.69
//
Query:       gene1603|gene1603|rna1603|rna1603  [L=118]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    8.2e-14   51.1   0.0    1.1e-13   50.7   0.0    1.2  1  RNA_pol_L_2  RNA polymerase Rpb3/Rpb11 dimerisation domain


Domain annotation for each model (and alignments):
>> RNA_pol_L_2  RNA polymerase Rpb3/Rpb11 dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.7   0.0   6.1e-18   1.1e-13       2      68 ..      32      99 ..      31     106 .. 0.91

  Alignments for each domain:
  == domain 1  score: 50.7 bits;  conditional E-value: 6.1e-18
                                       EEEEEES--HHHHHHHHHHHTTSTTEEEEEEECSSTTTSEEEEEEEEST..SS-HHHHHHHHHHHHHHH CS
                        RNA_pol_L_2  2 ltfeingEDhTLgnlLrhlllknpsVefagYkipHPlepkmnlriqtks..snnpleaLkkalkdlldi 68
                                        t+ i+ EDhTL+n++++ l++ p + +agY ipH +e+ ++l i  k+  + n  + L +alkdl+++
  gene1603|gene1603|rna1603|rna1603 32 TTIRIAHEDHTLMNVVQYFLMQRPFI-IAGYVIPHLSEDVVELSIVGKDdmKGNVFDWLCDALKDLEAM 99
                                       599*********************87.68*****************9986677*************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       416  (0.0232026); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 792.97
//
Query:       gene1604|gene1604|rna1604|rna1604  [L=889]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (889 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       648  (0.0361426); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.70u 0.26s 00:00:00.96 Elapsed: 00:00:00.45
# Mc/sec: 5885.16
//
Query:       gene1605|gene1605|rna1605|rna1605  [L=1179]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.9e-31  107.1   7.2    3.8e-18   65.7   0.2    4.6  4  C2        C2 domain
     0.0002   20.8   3.1      0.047   13.2   0.9    2.9  3  SMP_LBD   Synaptotagmin-like mitochondrial-lipid-binding doma
  ------ inclusion threshold ------
      0.057   13.8   0.0       0.65   10.4   0.0    2.5  2  JmjC      JmjC domain, hydroxylase


Domain annotation for each model (and alignments):
>> C2  C2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.0   1.3e-05      0.08      17      74 ..     376     431 ..     340     456 .. 0.78
   2 !   26.8   0.1   8.2e-10   4.9e-06      36      95 ..     595     653 ..     590     659 .. 0.89
   3 ?    1.6   0.1     0.058   3.4e+02      57      90 ..     735     767 ..     730     781 .. 0.78
   4 !   65.7   0.2   6.4e-22   3.8e-18       1      88 [.    1041    1127 ..    1041    1135 .. 0.97

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.3e-05
                                        STTSSCEEEEEEEEECEEEEEE-SCSSSSSSEEEEEEEEEESCHTTSEEEEEEEEECS CS
                                 C2  17 dkkgssdpyvkvsldgkqkakTrviknslnPvWnekftfevaeleeakLeveVfdndr 74 
                                        d ++ ++ y+++++dg + +kT+  +  +  v+ne f++ v++  ++++ v+  +  +
  gene1605|gene1605|rna1605|rna1605 376 DNTSDMSCYAEIDVDGRRLYKTE-RREGTRIVYNEYFYVVVHN-RDDTVNVTFTSTAV 431
                                        44667899***************.6666599************.88888887666555 PP

  == domain 2  score: 26.8 bits;  conditional E-value: 8.2e-10
                                        EEE-SCSSSSSSEEEEEEEEEESCHTTSEEEEEEEEECSSSTEEEEEEEEEEGHHHHTTH CS
                                 C2  36 akTrviknslnPvWnekftfevaeleeakLeveVfdndrlskddfiGkveiplstllsge 95 
                                        ++T+ +  + +P ++ekf++ +++ ++++L ++V d++  s++++iG+v +pl+++ +g+
  gene1605|gene1605|rna1605|rna1605 595 GRTHRVMETRSPFFDEKFEVFCRNIQKDVLYLTVVDQQE-SENEVIGTVDVPLRDVYDGT 653
                                        68886666669****************************.*************9977765 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.058
                                        ESCHTTSEEEEEEEEECSSSTEEEEEEEEEEGHH CS
                                 C2  57 vaeleeakLeveVfdndrlskddfiGkveiplst 90 
                                        v+ +e+++L++ +f ++  +++dfiG+ ++++ +
  gene1605|gene1605|rna1605|rna1605 735 VPAEEDDRLRIFLFRENF-NESDFIGEGTVDVVN 767
                                        445679999999999777.********9999876 PP

  == domain 4  score: 65.7 bits;  conditional E-value: 6.4e-22
                                         TEEEEEEEEEESSSSSSTTSSCEEEEEEEEECEEEEEE-SCSSSSSSEEEEEEEEEESCHTTSEEEEEEEEECS CS
                                 C2    1 gklevtvieAknLpnkdkkgssdpyvkvsldgkqkakTrviknslnPvWnekftfevaeleeakLeveVfdndr 74  
                                         g+lev+++ A+++   +k++ sdpyvk++l++++++kT++i+n++nP +ne+f  +v+   ++++++ V d++r
  gene1605|gene1605|rna1605|rna1605 1041 GYLEVRILGATKVRGVEKNSMSDPYVKAYLNNTKVYKTKTIQNTVNPSFNESFFCKVNI-MTDVIRFDVIDWNR 1113
                                         68**************9******************************************.************** PP

                                         SSTEEEEEEEEEEG CS
                                 C2   75 lskddfiGkveipl 88  
                                         ++ d++i  veipl
  gene1605|gene1605|rna1605|rna1605 1114 IETDQLISFVEIPL 1127
                                         ************98 PP

>> SMP_LBD  Synaptotagmin-like mitochondrial-lipid-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.6   0.0   0.00083         5       3      64 ..     150     212 ..     148     232 .. 0.79
   2 !   13.2   0.9   7.9e-06     0.047     101     179 ..     274     354 ..     253     355 .. 0.86
   3 ?   -2.7   0.0      0.58   3.5e+03     102     124 ..     455     479 ..     444     484 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.00083
                                        B--HHHHHHHHHHHHHHHHHHHHHHHHTHHHHHH.TT-GGGTTEEEEEEE--SS--EEEEEEE CS
                            SMP_LBD   3 eraewlnktvkhmwpficqfieklfretiepavr.ganthlstfsftkvdvgqqplringvkv 64 
                                        e  ew+n +v+++w +i   + k +   ++p +   + ++ls +++++  +g  p  ++g+  
  gene1605|gene1605|rna1605|rna1605 150 ESVEWINFAVERVWKIIEAEVSKEVFRVVNPILAeKCPSFLSQLALSEFTLGSLPPTLKGISF 212
                                        789**************999988777788998761567799***********99999999865 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 7.9e-06
                                        EEEEEEEEEEEEEE--B-SST.TSB-EEEEEESS--EEEEEEESHH..HHCTSTTTTT--HHHHHHHHHHHTBTT- CS
                            SMP_LBD 101 vksiqihgtmrvilepligdm.plvgalsifflrkplleinwtglt..nlldipglnglsdtiildiisnylvlpn 173
                                        v+++   g mr+il      + plv ++ + fl  p ++ +   l   +l+++pgl  +  t+i   + + lv pn
  gene1605|gene1605|rna1605|rna1605 274 VRNLSFAGRMRIILTLAKSLVtPLV-SVELCFLSAPQIDFDLCPLKsiDLMNMPGLSTFIHTLIDSNLQKMLVDPN 348
                                        7788899******987666551565.67899**********999863379************************** PP

                                        -EEEES CS
                            SMP_LBD 174 ritvpl 179
                                         +t+ l
  gene1605|gene1605|rna1605|rna1605 349 SLTIDL 354
                                        **9976 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 0.58
                                        EEEEE..EEEEEEEE--B-SSTTSB CS
                            SMP_LBD 102 ksiqi..hgtmrvilepligdmplv 124
                                        + i+i  +gt+r +le  i   p+v
  gene1605|gene1605|rna1605|rna1605 455 QDIKIwrKGTIRAVLETDIKYYPVV 479
                                        555553379*******999999987 PP

>> JmjC  JmjC domain, hydroxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00011      0.65      18      64 ..     147     193 ..     141     198 .. 0.92
   2 ?   -0.4   0.0      0.25   1.5e+03      77     111 ..     391     425 ..     372     427 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00011
                                        GG-EEEEEEEEES-EEEEEE-GGGHHHHHHHHHHHHHCCSTTGCCTT CS
                               JmjC  18 qglySinylhfgapkvWyiipeekkeklekvlskknskeqpdllrhk 64 
                                        ++l S+ + +f  ++vW+ii+ e ++++ +v+++  ++++p++l+++
  gene1605|gene1605|rna1605|rna1605 147 CELESVEWINFAVERVWKIIEAEVSKEVFRVVNPILAEKCPSFLSQL 193
                                        67899******************************99*****98875 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.25
                                        T---EEEEE-TT-EEEE-TT-EEEEEESSSEEEEE CS
                               JmjC  77 gipvyrfvqkpgefVfvfpgayHsvfnlgfniaea 111
                                        g + y+++ ++g  ++ + + y +v+n +++++++
  gene1605|gene1605|rna1605|rna1605 391 GRRLYKTERREGTRIVYNEYFYVVVHNRDDTVNVT 425
                                        5578999999999999999************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1179 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1184  (0.0660383); expected 358.6 (0.02)
Passed bias filter:                      711  (0.0396564); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.92u 0.33s 00:00:01.25 Elapsed: 00:00:00.49
# Mc/sec: 7273.56
//
Query:       gene1606|gene1606|rna1606|rna1606  [L=209]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1314  (0.0732891); expected 358.6 (0.02)
Passed bias filter:                      660  (0.0368119); expected 358.6 (0.02)
Passed Vit filter:                        76  (0.00423894); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.38
# Mc/sec: 1630.95
//
Query:       gene1607|gene1607|rna1607|rna1607  [L=903]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.5e-31  107.3   6.4      2e-30  106.2   1.4    2.9  3  Coatomer_WDAD  Coatomer WD associated region
    4.9e-29  100.0   7.6    2.4e-08   34.5   0.0    6.2  7  WD40           WD domain, G-beta repeat
      5e-08   32.6   1.9    1.6e-06   27.7   1.1    2.6  2  WD40_like      WD40-like domain
    4.7e-07   30.0   0.0       0.36   11.2   0.0    5.0  5  ANAPC4_WD40    Anaphase-promoting complex subunit 4 WD40 doma
    8.7e-07   28.0   0.7    1.4e-06   27.3   0.7    1.2  1  COPI_C         Coatomer (COPI) alpha subunit C-terminus
    6.3e-05   22.9   1.6      0.026   14.4   0.1    3.0  4  eIF2A          Eukaryotic translation initiation factor eIF2A
    0.00089   18.0   0.5       0.85    8.2   0.0    2.3  2  Nup160         Nucleoporin Nup120/160
  ------ inclusion threshold ------
      0.071   13.2   2.0       0.22   11.6   0.0    2.9  4  GHD            Beta-sandwich domain in beta galactosidase


Domain annotation for each model (and alignments):
>> Coatomer_WDAD  Coatomer WD associated region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0     0.099   2.2e+02      32     105 ..      54     130 ..      39     138 .. 0.73
   2 ?    0.7   0.1     0.092   2.1e+02      37     146 ..     142     257 ..     127     298 .. 0.67
   3 !  106.2   1.4   8.9e-34     2e-30      36     432 ..     314     679 ..     286     682 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.099
                                        XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.....XXXXXXXXXXXXXX.XXXXXX.XXXXXXX CS
                      Coatomer_WDAD  32 eiypqslshnpngrfvlVcgdgeyiiytalalrnkaygkgld.....fvwvssnrfavles.sksvkifknfkekk 101
                                        +  ++s++++p++ +++  gd++y  ++  a r++ + kg++     + + +++ f +  s  ++vki  nf++kk
  gene1607|gene1607|rna1607|rna1607  54 DGPVRSIQFHPQNDIFVSGGDDQYVRIWDYASRTNVKLKGHTdyircVRFHQNEPFLLSASdDRTVKI-WNFQSKK 128
                                        567899*****9999999******99997777777666665311111334445558888888999999.9999888 PP

                                        XXXX CS
                      Coatomer_WDAD 102 tksi 105
                                          +i
  gene1607|gene1607|rna1607|rna1607 129 --KI 130
                                        ..55 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.092
                                        XXXXXXXXXXXXXXXXXXXXXXX......XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXX CS
                      Coatomer_WDAD  37 slshnpngrfvlVcgdgeyiiyt......alalrnkaygkgldfvwvssnrfavlessksvkifknfkekktksik 106
                                          ++ +++r+v V  d+++ + +      ++     +  ++l+ ++++ ++fa+++ s + +i k f++  +++ +
  gene1607|gene1607|rna1607|rna1607 142 CAEFLHDKRVVSVSLDQTIRVWNiddgtsEIVEAHDKGINALSLLFNN-GSFAIFTGSDDRSI-KMFNSDLVSTDS 215
                                        555666788888877777777777776665566667777888888887.99****99999999.888888877777 PP

                                        XXXXXXXXXX....XXXXXXXXXX.XXXXXXXXXXXXXXXXXXX CS
                      Coatomer_WDAD 107 leyqvdkifg....GalLgvksegsvsfYDweqgklvrridvkk 146
                                         +y  + +++      + + + e+++ f  ++++k  rri+ + 
  gene1607|gene1607|rna1607|rna1607 216 FNYHSKAVTAlltfNKVVISCGEDGLLF--VNENKKTRRIEREG 257
                                        7777777766666777777777775555..56667777777665 PP

  == domain 3  score: 106.2 bits;  conditional E-value: 8.9e-34
                                        XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXX CS
                      Coatomer_WDAD  36 qslshnpngrfvlVcgdgeyiiytalalrnkaygkgldfvwvssnrfavlessksvkifknfkekktksikleyqv 111
                                        ++ s+  +g +++V+  +++++y+a++ r     +g+ + ++      v  ++++      + + ++k  ++ + +
  gene1607|gene1607|rna1607|rna1607 314 EAKSICSQGDMLIVNYAHRFEVYKARDQRLCWSETGNAAFFND---LIVCSNKGEFHT--YLLNGQVKDECIFFLA 384
                                        5556778889999999999999999998888888888788765...666665555555..3344444677777778 PP

                                        XXXXX..XXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXX......... CS
                      Coatomer_WDAD 112 dkifg..GalLgvksegsvsfYDweqgklvrridvkkvknVvwsddgelvalvs.kdtvyilsynleaveeedeee 184
                                         +++g   a +++++++ +++ + + ++   ++    v+nV+ s++ e v++v+ ++++ il+ +le         
  gene1607|gene1607|rna1607|rna1607 385 GRVVGfkTAFFVLNEKK-IVMVNAKYERKSTSVPFV-VTNVYYSEKPEPVCVVTgRNDLAILDNELE--------- 449
                                        88888855656666666.999999999999999988.7**********9999965899*********......... PP

                                        ....XXXXXXX.XXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXX.XXX..XXXXXXXXXXXXX CS
                      Coatomer_WDAD 185 gvedafevlhelsesiksgaWvgdvfiYttsnnrlkylvngevgiikhldktlyilg.ykgkenklylldkdgnvv 259
                                             +   ++  ++i s++  +  ++Ytt++ +l y+     g+i +l++ +y+++ yk+ e+ + ll  d++ v
  gene1607|gene1607|rna1607|rna1607 450 ----IVRHTND-MTRILSVVISDGLVFYTTEK-QLRYVFRYSEGVICSLNS-FYLARmYKKDERDMCLLVNDAQTV 518
                                        ....99999**.9*******9999********.****88888888888765.666662677778899999****** PP

                                        XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.......XXXXXXXXXXXXXXXX-GGGSS-HHHHHHHHHHTT- CS
                      Coatomer_WDAD 260 sleidlselefktavlrkdleevlkiiaasnllpeipkeegqkiirfLekkgypelAlqlvqDpetkFdLAlelgn 335
                                          e++l+e++fk+avl++d +++++ i   nl        g ++++fL+  g  ++Al ++++  +kF L l++g+
  gene1607|gene1607|rna1607|rna1607 519 EREVNLDEIKFKLAVLNNDSDAIASHIG--NLP-------GMAVVNFLRINGRGDIALPFIHERAQKFKLYLSMGD 585
                                        *********************9777766..777.......************************************ PP

                                        HHHHHHHHHHH--HHHHHH..HHHHHHHTT-HHHHHHHHHHTT-HHHHHHHHHHHT-HHHHHHHHHHHHHTT-HHH CS
                      Coatomer_WDAD 336 LelAlelakelddeekWkk..LgdaAlsqgniklaeeayqkakdfdkLllLylstgnkekLkkLakiaekkgdyni 409
                                        +  A+e+a++ d+ ++  +  + ++ l   n++++e + q++kd  kL+++yl+tgn ekL+ +      + d+n+
  gene1607|gene1607|rna1607|rna1607 586 IANAYEIANDPDEYAQIYQagMKNVELIDKNYEVIEGCVQRMKDERKLFMFYLVTGNDEKLRAM-----VADDLNV 656
                                        ********8888655433312456677789**********************************.....4569*** PP

                                        HHHHHHHHT-HHHHHHHHHHTT- CS
                      Coatomer_WDAD 410 afqaalllgdvekcvdlLiksgr 432
                                        ++   ++l+d++  +++L + g+
  gene1607|gene1607|rna1607|rna1607 657 RLLRCVYLDDKNGVMEMLRDGGN 679
                                        ******************98775 PP

>> WD40  WD domain, G-beta repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0         8   1.8e+04      13      26 ..      15      28 ..      11      40 .. 0.66
   2 !   28.7   0.4   7.1e-10   1.6e-06       4      38 .]      47      82 ..      44      82 .. 0.92
   3 !   34.5   0.0   1.1e-11   2.4e-08       6      38 .]      90     123 ..      86     123 .. 0.91
   4 !   20.0   0.0   4.2e-07   0.00093       2      38 .]     128     164 ..     127     164 .. 0.90
   5 !   14.1   0.0   2.9e-05     0.064       7      38 .]     173     207 ..     169     207 .. 0.85
   6 ?    1.0   0.0      0.41   9.2e+02      10      34 ..     219     242 ..     212     244 .. 0.72
   7 ?   -2.8   0.0       6.4   1.4e+04      21      36 ..     267     280 ..     260     282 .. 0.55

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 8
                                       EEEEEEETTSSEEE CS
                               WD40 13 vtslafspdgawla 26
                                       v s++f+++ + ++
  gene1607|gene1607|rna1607|rna1607 15 VKSVCFHRSRPVVL 28
                                       88999999888753 PP

  == domain 2  score: 28.7 bits;  conditional E-value: 7.1e-10
                                       EEEEESS.SSEEEEEEETTSSEEEEEETTSEEEEEE CS
                               WD40  4 lrtltGH.ssvtslafspdgawlasGsdDgtvriWd 38
                                       ++++  H ++v+s++f+p ++ ++sG+dD+ vriWd
  gene1607|gene1607|rna1607|rna1607 47 IHKFLDHdGPVRSIQFHPQNDIFVSGGDDQYVRIWD 82
                                       688889*888*************************9 PP

  == domain 3  score: 34.5 bits;  conditional E-value: 1.1e-11
                                        EEESS.SSEEEEEEETTSSEEEEEETTSEEEEEE CS
                               WD40   6 tltGH.ssvtslafspdgawlasGsdDgtvriWd 38 
                                        +l+GH + +++++f+++ ++l+s+sdD+tv+iW+
  gene1607|gene1607|rna1607|rna1607  90 KLKGHtDYIRCVRFHQNEPFLLSASDDRTVKIWN 123
                                        589**555*************************8 PP

  == domain 4  score: 20.0 bits;  conditional E-value: 4.2e-07
                                        EEEEEEESS.SSEEEEEEETTSSEEEEEETTSEEEEEE CS
                               WD40   2 qclrtltGH.ssvtslafspdgawlasGsdDgtvriWd 38 
                                        +++rtl GH + v +  f +d++ ++  s D+t+r+W+
  gene1607|gene1607|rna1607|rna1607 128 KKIRTLAGHtNYVMCAEFLHDKRVVS-VSLDQTIRVWN 164
                                        6799*****888************85.677*******8 PP

  == domain 5  score: 14.1 bits;  conditional E-value: 2.9e-05
                                        EESS.SSEEEEE.EETTSSE.EEEEETTSEEEEEE CS
                               WD40   7 ltGH.ssvtsla.fspdgaw.lasGsdDgtvriWd 38 
                                         ++H +++++l+    +g++ +++GsdD+++++++
  gene1607|gene1607|rna1607|rna1607 173 VEAHdKGINALSlLFNNGSFaIFTGSDDRSIKMFN 207
                                        579*999****998888888556*********987 PP

  == domain 6  score: 1.0 bits;  conditional E-value: 0.41
                                        S.SSEEEEEEETTSSEEEEEETTSEE CS
                               WD40  10 H.ssvtslafspdgawlasGsdDgtv 34 
                                        H + vt+l     ++ ++s+++Dg +
  gene1607|gene1607|rna1607|rna1607 219 HsKAVTAL--LTFNKVVISCGEDGLL 242
                                        86679988..555566889999*976 PP

  == domain 7  score: -2.8 bits;  conditional E-value: 6.4
                                        TSSEEEEEETTSEEEE CS
                               WD40  21 dgawlasGsdDgtvri 36 
                                        ++  +++G+ D +  i
  gene1607|gene1607|rna1607|rna1607 267 ENV-IVAGH-DESFVI 280
                                        444.45698.766655 PP

>> WD40_like  WD40-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.3   0.0    0.0048        11       3      62 ..      57     115 ..      55     116 .. 0.88
   2 !   27.7   1.1   7.2e-10   1.6e-06       9     187 ..     104     284 ..      98     309 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0048
                          WD40_like   3 iYsidiskkgslilyGgkddkctvlkleslesvsivesfedSvifvklldddlilvvtlD 62 
                                        + si++ +++++++ Gg+d+ +++ +  s + v + ++ +d +  v++ +++ +l  + D
  gene1607|gene1607|rna1607|rna1607  57 VRSIQFHPQNDIFVSGGDDQYVRIWDYASRTNVKL-KGHTDYIRCVRFHQNEPFLLSASD 115
                                        679999*************************9986.788999*99999999988876655 PP

  == domain 2  score: 27.7 bits;  conditional E-value: 7.2e-10
                          WD40_like   9 skkgslilyGgkddkctvlkleslesvsivesfedSvifvklldddlilvvtlDGtillsllenee..evenek.i 81 
                                         ++  ++l  ++d ++++ +++s++++  +++ ++ v+ +++l+d+ ++ v+lD ti    +  +   +ve ++  
  gene1607|gene1607|rna1607|rna1607 104 HQNEPFLLSASDDRTVKIWNFQSKKKIRTLAGHTNYVMCAEFLHDKRVVSVSLDQTIRVWNIDDGTseIVEAHDkG 179
                                        55666777788999*******************************************9999998877555554413 PP

                          WD40_like  82 eedistvkvidd.klliGtnkGsiyvfskdlqleevllgqsseIkeikiennkiysLsesafivfdlfsqnieyki 156
                                         +++s   + +   +  G++  si +f+ dl +   +  +s  +  + + n ++ s  e+ ++  +   +n+++++
  gene1607|gene1607|rna1607|rna1607 180 INALSLLFNNGSfAIFTGSDDRSIKMFNSDLVSTDSFNYHSKAVTALLTFNKVVISCGEDGLLFVN---ENKKTRR 252
                                        46666654443326777999*****************************************99884...4455555 PP

                          WD40_like 157 svkdiktfeii.enkdilligtegeililkkn 187
                                          ++++      +++++++ g++++++i+k +
  gene1607|gene1607|rna1607|rna1607 253 IEREGRFWCLArNSENVIVAGHDESFVIFKLK 284
                                        5566665555557899************8743 PP

>> ANAPC4_WD40  Anaphase-promoting complex subunit 4 WD40 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0     0.023        50      36      76 ..      10      50 ..       2      54 .. 0.87
   2 !    8.1   0.0    0.0015       3.3      36      71 ..      52      87 ..      47      96 .. 0.89
   3 !   11.2   0.0   0.00016      0.36      37      89 ..      94     145 ..      88     148 .. 0.87
   4 ?   -2.6   0.0       3.2   7.1e+03      28      64 ..     161     205 ..     149     226 .. 0.53
   5 ?   -0.7   0.0      0.78   1.8e+03      40      79 ..     419     458 ..     394     466 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.023
                        ANAPC4_WD40 36 kedsevrsLaWkpdgklLavaysdgevrlldaesgkvvhsl 76
                                        ++ +v+s++++ +  +   a ++ge+r +d      +h++
  gene1607|gene1607|rna1607|rna1607 10 IKSPRVKSVCFHRSRPVVLLALHNGEIRAYDYTLSSFIHKF 50
                                       56678**************************9999999987 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0015
                        ANAPC4_WD40 36 kedsevrsLaWkpdgklLavaysdgevrlldaesgk 71
                                       ++d+ vrs++++p++ +++ + +d  vr+ d  s +
  gene1607|gene1607|rna1607|rna1607 52 DHDGPVRSIQFHPQNDIFVSGGDDQYVRIWDYASRT 87
                                       57899*************************988765 PP

  == domain 3  score: 11.2 bits;  conditional E-value: 0.00016
                        ANAPC4_WD40  37 edsevrsLaWkpdgklLavaysdgevrlldaesgkvvhslsvksekavtclgW 89 
                                        +   +r++++++++ +L  a +d +v++ + +s+k +++l  +++  v+c ++
  gene1607|gene1607|rna1607|rna1607  94 HTDYIRCVRFHQNEPFLLSASDDRTVKIWNFQSKKKIRTLAGHTN-YVMCAEF 145
                                        66789*********************************9987777.5888665 PP

  == domain 4  score: -2.6 bits;  conditional E-value: 3.2
                        ANAPC4_WD40  28 rvwtl........eedkedsevrsLaWkpdgklLavaysdgevrl 64 
                                        rvw++        e+++++ +  sL +++    +  + +d ++++
  gene1607|gene1607|rna1607|rna1607 161 RVWNIddgtseivEAHDKGINALSLLFNNGSFAIFTGSDDRSIKM 205
                                        556654444443222233333333333333333334444445554 PP

  == domain 5  score: -0.7 bits;  conditional E-value: 0.78
                        ANAPC4_WD40  40 evrsLaWkpdgklLavaysdgevrlldaesgkvvhslsvk 79 
                                         v+++ ++++ +  +v++  + + +ld e + v h+ +++
  gene1607|gene1607|rna1607|rna1607 419 VVTNVYYSEKPEPVCVVTGRNDLAILDNELEIVRHTNDMT 458
                                        5888999999999999999999999999988777776655 PP

>> COPI_C  Coatomer (COPI) alpha subunit C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   0.7   6.4e-10   1.4e-06     190     307 ..     733     838 ..     719     850 .. 0.80

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 6.4e-10
                                        HHHHHHHHHHHT-HHHHHHHHHHHHHHGGG----SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-SSHHHHHHHH CS
                             COPI_C 190 rLkaaYklttegkfseavekfrsillsipllvvdskqevdevkeLieicreYivgLrmEikRkelkksddqkrqaE 265
                                        +  +a   + +gk ++a++++ +i++s++         +de k  + i   Y+ gL+ E kRk+ +   d kr+ E
  gene1607|gene1607|rna1607|rna1607 733 EFDSAMACIDAGKAKDALKTLYTIFYSLA-------DSLDEKKRFL-I-GRYVAGLESERKRKKET---DVKRMLE 796
                                        55667777788888888888888777764.......3344444433.3.46******999999888...9****** PP

                                        HHHHHHHS---HHHHHHHHHHHHHHHHHHTBHHHHHHHHHHH CS
                             COPI_C 266 laAYfthcnlqpvHliLaLrsAlnlffKlknfktaasfarrL 307
                                         a +f h +l p H+++  ++ + + +K  n+++a+  a +L
  gene1607|gene1607|rna1607|rna1607 797 RAHFFYHLELLPKHRKIQTENYVAVSYKNGNYTSAKLAAEQL 838
                                        ********************************9887766665 PP

>> eIF2A  Eukaryotic translation initiation factor eIF2A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.0    0.0014       3.1      56     149 ..      51     142 ..      34     162 .. 0.81
   2 !   14.4   0.1   1.2e-05     0.026      28     119 ..     147     237 ..     136     254 .. 0.90
   3 ?   -3.4   0.0       3.3   7.5e+03       3      22 ..     335     354 ..     334     381 .. 0.76
   4 ?   -3.4   0.0       3.3   7.5e+03      23      54 ..     404     435 ..     391     445 .. 0.48

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0014
                                        EESSS.EEEEEE-TTSS-EEEEESSSSCEEEEEEC..SCEEEEEEEEES--EEEE-TTSSEEEEE-TTSSS-EEEE CS
                              eIF2A  56 lkkegpihdvaWspkskefaviyGkmpakvslfdl..kvkviskleeqkrNtiffspkgklvllaGfgnlaGelei 129
                                        l+++gp+  ++  p+++ f  + G  ++ v ++d   + +v+ k ++++  ++ f++++ ++l a    +   ++i
  gene1607|gene1607|rna1607|rna1607  51 LDHDGPVRSIQFHPQNDIF--VSGGDDQYVRIWDYasRTNVKLKGHTDYIRCVRFHQNEPFLLSASDDRT---VKI 121
                                        8999*********999877..6888899999988744699999999******************997777...*** PP

                                        EETTTTEEEEEEE.-TT--EE CS
                              eIF2A 130 wdvkkkkkiakae.aanatlv 149
                                        w+ ++kkki ++  ++n +++
  gene1607|gene1607|rna1607|rna1607 122 WNFQSKKKIRTLAgHTNYVMC 142
                                        ****99999986426666666 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 1.2e-05
                                        --TT-CEEEEEEEEEESSSTT--EEECCEESSS.EEEEEE-TTSS-EEEEESSSSCEEEEEECSCEEEEEEEEES- CS
                              eIF2A  28 vdktnksyygetelyliklkkkksevvelkkegpihdvaWspkskefaviyGkmpakvslfdlkvkviskleeqkr 103
                                        +dk   s+   +++ + +++++ se+ve + +g i +++   ++  fa+  G  ++++++f++++  + +++ +++
  gene1607|gene1607|rna1607|rna1607 147 HDKRVVSVSLDQTIRVWNIDDGTSEIVEAHDKG-INALSLLFNNGSFAIFTGSDDRSIKMFNSDLVSTDSFNYHSK 221
                                        68888899999999999***************9.*****************************************9 PP

                                        -EEEE-TTSSEEEEE- CS
                              eIF2A 104 NtiffspkgklvllaG 119
                                               ++k+v+ +G
  gene1607|gene1607|rna1607|rna1607 222 AVTALLTFNKVVISCG 237
                                        9999999999999998 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 3.3
                                        ESSECEEEEEE-TTTTEEEE CS
                              eIF2A   3 ffkadkvklkWnkkGtsllv 22 
                                        ++ka + +l W+++G++  +
  gene1607|gene1607|rna1607|rna1607 335 VYKARDQRLCWSETGNAAFF 354
                                        57888899999999987665 PP

  == domain 4  score: -3.4 bits;  conditional E-value: 3.3
                                        EEE.E--TT-CE.EEEEEEEEESSSTT--EEEC CS
                              eIF2A  23 lvstevdktnks.yygetelyliklkkkksevv 54 
                                        +v+++++++ +s     t++y+  +k ++++vv
  gene1607|gene1607|rna1607|rna1607 404 MVNAKYERKSTSvPFVVTNVYYS-EKPEPVCVV 435
                                        33333333333313344444444.333334433 PP

>> Nup160  Nucleoporin Nup120/160
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.0   0.00038      0.85     222     255 ..      97     132 ..      78     139 .. 0.85
   2 !    7.9   0.2   0.00047       1.1     227     250 ..     144     168 ..     133     173 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00038
                                        ET.......TTTEEEEEETT-EEEEEETTTTEEEEE CS
                             Nup160 222 avavvei..gqtylfalsrdgkLrvWnlltgkclat 255
                                        ++++v+   ++ +l+++s d+++++Wn +++k ++t
  gene1607|gene1607|rna1607|rna1607  97 YIRCVRFhqNEPFLLSASDDRTVKIWNFQSKKKIRT 132
                                        577888887899*******************99987 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.00047
                                        ...TTTEEEEEETT-EEEEEETTTT CS
                             Nup160 227 ei.gqtylfalsrdgkLrvWnlltg 250
                                        e  +++ ++++s+d+++rvWn+++g
  gene1607|gene1607|rna1607|rna1607 144 EFlHDKRVVSVSLDQTIRVWNIDDG 168
                                        445778899*************987 PP

>> GHD  Beta-sandwich domain in beta galactosidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       4.5     1e+04      30      55 ..     242     266 ..     237     275 .. 0.78
   2 ?   -2.4   0.1       2.4   5.3e+03      30      53 ..     289     313 ..     262     321 .. 0.65
   3 ?   -3.3   0.1       4.4   9.8e+03      29      51 ..     394     416 ..     389     418 .. 0.61
   4 ?   11.6   0.0   9.7e-05      0.22       7      52 ..     488     532 ..     484     534 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 4.5
                                GHD  30 FlvNndkkkdatvtFrgssyeLpakS 55 
                                        ++vN +kk+  +++ +g+ + L++ S
  gene1607|gene1607|rna1607|rna1607 242 LFVNENKKTR-RIEREGRFWCLARNS 266
                                        6788888877.888888888777776 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 2.4
                                GHD  30 FlvNndkkkdatvtFrgssy.eLpa 53 
                                        F  N   +++ +v++r++++ +L +
  gene1607|gene1607|rna1607|rna1607 289 FDENYVIRDSRVVNYRNERVvDLKK 313
                                        5566667788899999876415554 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 4.4
                                GHD  29 aFlvNndkkkdatvtFrgssyeL 51 
                                         F+ N +k  +++ +++ +s ++
  gene1607|gene1607|rna1607|rna1607 394 FFVLNEKKIVMVNAKYERKSTSV 416
                                        34557766667777777666555 PP

  == domain 4  score: 11.6 bits;  conditional E-value: 9.7e-05
                                GHD   7 ktvslgksveatvfekkkgkcvaFlvNndkkkdatvtFrgssyeLp 52 
                                           sl+  + a++++k++    ++lvN  ++ + +v++++ +++L+
  gene1607|gene1607|rna1607|rna1607 488 VICSLNSFYLARMYKKDE-RDMCLLVNDAQTVEREVNLDEIKFKLA 532
                                        567999***********9.79**********************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (903 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       650  (0.0362541); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.79u 0.30s 00:00:01.09 Elapsed: 00:00:00.48
# Mc/sec: 5675.57
//
Query:       gene1608|gene1608|rna1608|rna1608  [L=315]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.6e-05   24.7   8.4    0.00023   20.9   8.4    2.4  1  RabGAP-TBC  Rab-GTPase-TBC domain


Domain annotation for each model (and alignments):
>> RabGAP-TBC  Rab-GTPase-TBC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   8.4   1.3e-08   0.00023      41     194 ..      44     258 ..      10     276 .. 0.51

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 1.3e-08
                         RabGAP-TBC  41 seeske.lsqIkkDvprtfpesesfknkqgqnqLeriLkaysiynpevgYcqGmndivapll.............. 101
                                        + +s++ l+ Ik Dv+rt+     +  ++    L++ L+ + i+ p  +Y+qGmnd++a+l               
  gene1608|gene1608|rna1608|rna1608  44 AVKSQDdLNVIKMDVERTYF----DYGDKDVTLLRKELFNLLIRIP-FEYVQGMNDVAAVLVyfyaesesmdeval 114
                                        33444459**********99....3334556778888888889999.8**************55555555555554 PP

                         RabGAP-TBC 102 ..........................................................lvsldeeeaFwcfvsLle 119
                                                                                                  +++   +    + +++l 
  gene1608|gene1608|rna1608|rna1608 115 nsidtkdcadddsdsdrgviyrckngqfvpsstpneydntvdqkifedvteyeditnlMNNATRRRMLTAVYHIL- 189
                                        444444444444444444444444444444444444444444433333333333333222222222555555555. PP

                         RabGAP-TBC 120 kyklrdlytsslpglkrklkvleellkkkdpklykhlkeegldlelfaikwfltlflrefpletvlrlwDllleg 194
                                        k+k  +l++++++   ++ kv+ ++l+k  ++++    +e++ ++ +++ wf  +++r    + v  ++ +++e+
  gene1608|gene1608|rna1608|rna1608 190 KDKYLCLVQNEFKVYLAMNKVMLNMLNKEQKSVS---VNESIRFMNYTLTWFSRILKRR---DDVYFIFKIIIEE 258
                                        5555555555553333333334344333333332...2345666666666666666544...4455555555654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (315 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       892  (0.0497518); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 2142.59
//
Query:       gene1609|gene1609|rna1609|rna1609  [L=590]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.9e-45  154.6   0.0      3e-43  148.8   0.0    2.0  2  DAO            FAD dependent oxidoreductase
    3.2e-32  111.1   0.2    6.6e-32  110.0   0.2    1.6  1  DAO_C          C-terminal domain of alpha-glycerophosphate ox
    5.1e-13   48.9   2.1    6.2e-12   45.3   2.1    2.0  1  FAD_binding_2  FAD binding domain
    2.5e-06   27.1   2.2    0.00011   21.7   2.2    2.2  2  FAD_oxidored   FAD dependent oxidoreductase
    2.6e-06   26.8   0.9    0.00024   20.3   0.3    2.3  2  GIDA           Glucose inhibited division protein A
    2.6e-05   23.6   0.0    4.9e-05   22.7   0.0    1.5  1  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
    0.00027   19.8   0.5     0.0005   18.9   0.5    1.4  1  HI0933_like    HI0933-like protein
     0.0022   17.3   0.0       0.64    9.2   0.1    2.1  2  FAD_binding_3  FAD binding domain
     0.0026   17.9   0.3      0.034   14.4   0.6    2.3  2  NAD_binding_8  NAD(P)-binding Rossmann-like domain
      0.007   15.7   0.0      0.015   14.5   0.0    1.5  1  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase
  ------ inclusion threshold ------
      0.014   14.7   0.1       0.04   13.2   0.0    1.8  2  Thi4           Thi4 family
      0.026   14.4   0.7      0.037   13.9   0.0    1.6  2  3HCDH_N        3-hydroxyacyl-CoA dehydrogenase, NAD binding d
      0.031   13.3   0.1        0.3   10.1   0.1    2.0  2  Lycopene_cycl  Lycopene cyclase protein
      0.048   14.2   0.3        0.2   12.2   0.1    2.2  2  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase


Domain annotation for each model (and alignments):
>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  148.8   0.0   2.3e-46     3e-43       1     331 [.      62     417 ..      62     419 .. 0.75
   2 !    5.5   0.0    0.0085        11     192     271 ..     412     505 ..     395     549 .. 0.61

  Alignments for each domain:
  == domain 1  score: 148.8 bits;  conditional E-value: 2.3e-46
                                        EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSSGGGSSEEEEESSSSTHHSTH.....HHHHHHHHHHHHHH CS
                                DAO   1 dvviiGGGiiGlstAyeLarrg..VtllekgdiagsgaSgrnsgllhsglrylpeas.....elarlslealeelr 69 
                                        dv++iGGG  G+++A+++a+rg  V+ +e+g ++++++S+++++llh+g+ryl++a        ++l+leal+e++
  gene1609|gene1609|rna1609|rna1609  62 DVLVIGGGASGSGCALDAATRGlkVAMVESG-DFACETSSKSTKLLHGGVRYLEKAVksldlSNLQLVLEALRERK 136
                                        8******************************.6666******************9889999944599*******96 PP

                                        HHHHHHSSTTS.EEEEEEEEEES...SHHHHHHHHHHHHHH...HHTTTTEEEEEHHHHHHHSTT..STTTSEEEE CS
                                DAO  70 eleeelgidid.yrrtGllslaa...deeelealdkllall...leagldaelldaeevrelepa..lpgllgalf 136
                                         + +   i+    +   +l++++    +  l +l k+++     +++g   + ++ +e+++ +p+  l+gl+g+++
  gene1609|gene1609|rna1609|rna1609 137 YVIDA--IPYMaKPIALMLPVYSklmVPYFLVGL-KMYDYFswnKSLGGS-HHISVKETLQHFPNikLDGLKGSIV 208
                                        66653..443314445555554322211123334.666665776556765.4689988******97666******* PP

                                        ETTEEEEEHHHHHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEE.....EECTEEEE..EEEEEEE--GGGHH CS
                                DAO 137 ypdtgqvdpakltaalaraaealGveilegtevtgleeedgkvwgve.....rttpgend..aadavVnaaGawsd 205
                                        y+d g+ d+ +    +a +a+   +++l++++vt l ++dg v+g           ge++  +a++v+ ++G+++d
  gene1609|gene1609|rna1609|rna1609 209 YYD-GIHDDSRTNLMIALTAAYYNADVLNYSPVTQLVKNDGAVVGAVckdmiG---GEEFniRAKCVISTTGPFTD 280
                                        ***.999****************************977788888887765543...4443224566********** PP

                                        HH.HTT.CTTTSEEEEEEEEEEEEEECCTHSTGSGCSEEEEEEEETTTTEEEEEETTSEEEEEESSEEETTCSSTS CS
                                DAO 206 ll.gll.keldlpispvrgqvlvlkplseklvspaailpvpetdddgrgvyvtprkdgrvlvGgtadeesgdddpe 279
                                        ++ +l+ ++ +  ++p  g ++v+ p++   +   +i p   ++ d+r+++++p++ +++++G t+ + +   +p+
  gene1609|gene1609|rna1609|rna1609 281 QTkELAnPKSQSLVVPSSGVHIVV-PKEYGANDMGLINP---NTSDNRVLFFIPWL-NKTIIGCTDKPCKVQKEPK 351
                                        99555554447889**********.65554444446666...88999********9.779998888666666669* PP

                                        CSHHHHHHHHHHHHHHSGG...G..CGEEEEEEEEEE...E...TTSSEEEEEEE....TEEEEEEE CS
                                DAO 280 vdeedidellealrklfPq...l..gdvlrkwaGlrp...l...pdglpligetp....gvkglyla 331
                                        + +++i ++l+++++++ +   l  +d+++ w+G+rp   +   +d+  l  + +      ++l+++
  gene1609|gene1609|rna1609|rna1609 352 PKDDEITYILKEANRFLKEdkiLkkSDISSVWCGIRPlvkNparRDTKSLARN-HitylTEENLLVL 417
                                        *****************8866525699**********6542332355555444.2344444566555 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0085
                                        EEEEEEE--GGGHH..HH.HTTCTT.....T.SEEEEEEEEEEEEEECCT.HSTGSGCSEEEEEEEETTTTEEEEE CS
                                DAO 192 aadavVnaaGawsd..ll.gllkel.....d.lpispvrgqvlvlkplse.klvspaailpvpetdddgrgvyvtp 257
                                        + + +V+a G w++  ++ + + +l     +  pi+p+   ++ +   ++ + + +a i  +++ ++d+  +++t+
  gene1609|gene1609|rna1609|rna1609 412 E-NLLVLAGGKWTTyrKMaEDAIDLavkkfHlNPIRPCVTNYIKMLGSHNyTKQLSADIQRELDLNEDESTHFITR 486
                                        3.569*******98754432223335554335799**999999994444423444446666664555444445555 PP

                                        ETTSEEEEEESSE.....E CS
                                DAO 258 rkdgrvlvGgtad.....e 271
                                        + d ++++    d     +
  gene1609|gene1609|rna1609|rna1609 487 YGDRSLIFQNYKDrkaplK 505
                                        5655666665544555443 PP

>> DAO_C  C-terminal domain of alpha-glycerophosphate oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.0   0.2   5.2e-35   6.6e-32       1     125 [.     448     569 ..     448     570 .. 0.94

  Alignments for each domain:
  == domain 1  score: 110.0 bits;  conditional E-value: 5.2e-35
                                        --TTS---TT--.......TT-STTHT--HHHHHHHHHHHGGGHHHHHHHHHHTH...HHHHHTTS-HHHHHHHHH CS
                              DAO_C   1 crTkklpLvGaenwsknlaaelaqeygldeevaehLaerYGsraeevlelakedekpelaerlspelpyieaevvY 76 
                                        c+T+ ++++G++n++k+l+a++++e+ l+e+++ h ++rYG+r        + ++++   ++l++++ y+e ev Y
  gene1609|gene1609|rna1609|rna1609 448 CVTNYIKMLGSHNYTKQLSADIQRELDLNEDESTHFITRYGDRSLIFQ---NYKDRKAPLKKLHSDYMYTEEEVYY 520
                                        9******************************************97765...33333469***************** PP

                                        HHHHS---SHHHHHHTTS-HHHH-HHHHHHHHHHHHHHHHHHTT--HHH CS
                              DAO_C  77 avrhEmartlvDvlaRRtrlafldadaalealpevaelmaeelgWdear 125
                                        a++hEma++++Dvl+RR+rl fld++a ++al++v+++++++++W++a+
  gene1609|gene1609|rna1609|rna1609 521 AIDHEMACKPADVLTRRMRLGFLDVKACEKALEKVMKIFKKRMSWSAAK 569
                                        **********************************************987 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.3   2.1   4.8e-15   6.2e-12       1     213 [.      62     288 ..      62     300 .. 0.73

  Alignments for each domain:
  == domain 1  score: 45.3 bits;  conditional E-value: 4.8e-15
                                        SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGGGG-....-S-EE-TT..SSGGSTC.CHHHHHHHHH.HH CS
                      FAD_binding_2   1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefggataws....qGgidavlspeqkkagikdspelhrtdt.lk 71 
                                        Dv+ViG+G++G  +Al aa +Glkva+ve ++    ++  s     Gg+  +        +   s++l   ++ l+
  gene1609|gene1609|rna1609|rna1609  62 DVLVIGGGASGSGCALDAATRGLKVAMVESGDFACETSSKStkllHGGVRYLE-------KAVKSLDLSNLQLvLE 130
                                        9******************************9854444444111255555555.......2235666655554055 PP

                                        HTTT-S.-HHHHHHHHHTHHHHHHHHHHTT----B........................CCTS..SB-EEE-TT-S CS
                      FAD_binding_2  72 aldela.dqplveafveaapeavdeLeelgvpfsr........................tedg..pvdvrelGgls 120
                                        al+e+    +++ ++++  + ++    +l vp++                         +     ++   +l gl+
  gene1609|gene1609|rna1609|rna1609 131 ALRERKyVIDAIPYMAKPIALMLPVYSKLMVPYFLvglkmydyfswnkslggshhisvkE--TlqHFPNIKLDGLK 204
                                        667777788888888888888888888888888887776676777666555444443322..03466666666666 PP

                                        STEEEE-.STT-......HHHHHHHHHHHHHHTCTEEEEESEEEEEEEECTTEEEEEEEEETTTTCEEEEEESEEE CS
                      FAD_binding_2 121 atartlhdaadarretlvtghallarlvesarkagvdfqerteadeLivedgrvtGavvenpesgrevrirakavv 196
                                            +  +  d       +  +l+ +l +++  ++ d+++  ++++L+ +dg v+Gav++++ +g+e+ irak v+
  gene1609|gene1609|rna1609|rna1609 205 GSIVYYDGIHDD------SRTNLMIALTAAY--YNADVLNYSPVTQLVKNDGAVVGAVCKDMIGGEEFNIRAKCVI 272
                                        665444555555......7788888888888..89***************************************** PP

                                        E-----GG......... CS
                      FAD_binding_2 197 latgGfgrallkellga 213
                                         +tg f  ++ kel+++
  gene1609|gene1609|rna1609|rna1609 273 STTGPFT-DQTKELANP 288
                                        ******9.566665544 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   2.2   8.9e-08   0.00011       1      33 [.      62      94 ..      62      95 .. 0.96
   2 ?    3.2   0.0     0.035        45      85     144 ..     215     276 ..     182     277 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 8.9e-08
                       FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLveergv 33
                                       Dv+V+GGg++G  +A+ Aa +G kv++ve  ++
  gene1609|gene1609|rna1609|rna1609 62 DVLVIGGGASGSGCALDAATRGLKVAMVESGDF 94
                                       9****************************9876 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.035
                       FAD_oxidored  85 epevakavleemlaeagvtvllntrlvevekegkriesvtveske.g.rktirAkvfiDATg 144
                                        + +  + ++    a ++ +vl  + +++ +k+++ + + ++++   g + +irAk++i  Tg
  gene1609|gene1609|rna1609|rna1609 215 DDSRTNLMIALTAAYYNADVLNYSPVTQLVKNDGAVVGAVCKDMIgGeEFNIRAKCVISTTG 276
                                        555555555666678999*************99899999999988779**********9987 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.3   1.9e-07   0.00024       1      37 [.      62      97 ..      62     131 .. 0.71
   2 ?    4.7   0.0      0.01        13     118     155 ..     240     282 ..     226     292 .. 0.67

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 1.9e-07
                                       CEEEE-SSHHHHHHHHHHHHTT--EEEEES-GGGTT- CS
                               GIDA  1 dviViGgGhAGceAAlaaarlGakvlLithkldtiae 37
                                       dv ViGgG +G+ +Al aa +G+kv+++ ++ d  +e
  gene1609|gene1609|rna1609|rna1609 62 DVLVIGGGASGSGCALDAATRGLKVAMV-ESGDFACE 97
                                       79*************************9.33333222 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.01
                                        EEEEEECTTEEEEEEETT.....S-EEEECEEEE--TT-BT-E CS
                               GIDA 118 veeliveekkvkgvvted.....getikakavviatGtflkgk 155
                                        v++l+ +++ v g v +d     +  i+ak+v+ +tG+f +++
  gene1609|gene1609|rna1609|rna1609 240 VTQLVKNDGAVVGAVCKDmiggeEFNIRAKCVISTTGPFTDQT 282
                                        566655555555544333222116678899*********9876 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.0   3.8e-08   4.9e-05       1      48 [.      61     107 ..      61     141 .. 0.82

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 3.8e-08
                                        CSEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHHHCHHHH CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        Pyr_redox_2   1 kdvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcllskallg 48 
                                        +dv+viGgG+ G  +al++a+ g+kv++v + g +  ++ + s++ll+
  gene1609|gene1609|rna1609|rna1609  61 YDVLVIGGGASGSGCALDAATRGLKVAMV-ESGDFACETSSKSTKLLH 107
                                        69***************************.666677777666665554 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.5   3.9e-07    0.0005       1      32 [.      61      92 ..      61      98 .. 0.93

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 3.9e-07
                                       -SEEEE--SHHHHHHHHHHHHTT--EEEE-SS CS
                        HI0933_like  1 kdviviGgGaAGlmaAisaakrgkrVllleka 32
                                       +dv+viGgGa+G  +A+ aa+rg +V+++e++
  gene1609|gene1609|rna1609|rna1609 61 YDVLVIGGGASGSGCALDAATRGLKVAMVESG 92
                                       59***************************987 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.1    0.0005      0.64       2      39 ..      61      98 ..      60     120 .. 0.83
   2 !    6.0   0.0    0.0047         6     131     255 ..     244     364 ..     169     385 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0005
                                       EEEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCS CS
                      FAD_binding_3  2 tdVlIVGaGpaGlmlallLseaGvrvvlvekrsttvvl 39
                                       +dVl++G+G +G   al  +++G +v +ve  + + ++
  gene1609|gene1609|rna1609|rna1609 61 YDVLVIGGGASGSGCALDAATRGLKVAMVESGDFACET 98
                                       79***************************987655555 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0047
                                        CEECCCCCCCEEEECCTTEEEEEEEEEEEE--GTT-HHHHHHTGGEEEEEEEEEEEEEEEEEEC-SCCCTTC..CE CS
                      FAD_binding_3 131 leqdeegvtaevrdketgeeetvrakYlvGaDGgrStvrktlgiefegeetvyeagvldvlfdadlsdivep..lv 204
                                        +++d+  v a+ +d   gee ++rak ++   G  +   k+l  + ++++ v+++  + +++ ++    +++  l 
  gene1609|gene1609|rna1609|rna1609 244 VKNDGAVVGAVCKDMIGGEEFNIRAKCVISTTGPFTDQTKELANP-KSQSLVVPSSGVHIVVPKEYG--ANDmgLI 316
                                        478999999***************************999999966.666666555555555444444..3343466 PP

                                        EEEECCTTEEEEEECCETEEEEEEEEECCE-GGGSCCCHHHHHHHHHHHHH CS
                      FAD_binding_3 205 lilsaesrgvmviPlentlerfyvqvearaekeersekfteeevkarlrei 255
                                            +++r++ +iP+ n   + ++ ++ ++ k ++++k +++e++ +l+e+
  gene1609|gene1609|rna1609|rna1609 317 NPNTSDNRVLFFIPWLN---KTIIGCTDKPCKVQKEPKPKDDEITYILKEA 364
                                        6677788899*******...7899999999999999999999999998876 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.6   2.7e-05     0.034       1      29 [.      65      93 ..      65     113 .. 0.90
   2 ?    0.3   0.0      0.67   8.6e+02      32      65 ..     419     453 ..     417     456 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.7e-05
                                       EE--SHHHHHHHHHHHCCTEEEEEE-SSS CS
                      NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrd 29
                                       ++G+G+sG+ +A  +a +g++v  +e++d
  gene1609|gene1609|rna1609|rna1609 65 VIGGGASGSGCALDAATRGLKVAMVESGD 93
                                       8*************************997 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.67
                                        SGGG-EECE.TTCEECTS---EEETTHHHHCHHHH CS
                      NAD_binding_8  32 GGraasyev.pgvrvdygahifhgsgyypnvrrll 65 
                                        GG++++y+   + ++d+ +  fh     p v++++
  gene1609|gene1609|rna1609|rna1609 419 GGKWTTYRKmAEDAIDLAVKKFHLNPIRPCVTNYI 453
                                        9******98778999*9999999876677777665 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   1.2e-05     0.015     158     206 ..      55     101 ..      42     133 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.2e-05
                        Pyr_redox_3 158 efhkyagqkvvViGgknSavDaAlelvrkgaeVtvvtrgseiekeesdp 206
                                        ++ k++  +v+ViGg+ S+   Al+ + +g +V +v +g+   +++ + 
  gene1609|gene1609|rna1609|rna1609  55 NM-KTKYYDVLVIGGGASGSGCALDAATRGLKVAMVESGDFACETS-SK 101
                                        33.6677899*************************99998655443.33 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   3.1e-05      0.04      17      49 ..      60      91 ..      49     147 .. 0.92
   2 ?   -2.6   0.0         2   2.6e+03     156     167 ..     265     276 ..     225     281 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.1e-05
                                       EEEEEEE--SHHHHHHHHHHHHCTTS-EEEEES CS
                               Thi4 17 esDvvivGaGssGLtaayylakkpdlkvailer 49
                                         Dv+++G+G+sG  +a   a++ +lkva++e+
  gene1609|gene1609|rna1609|rna1609 60 YYDVLVIGGGASGSGCALDAATR-GLKVAMVES 91
                                       47*********************.*******96 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2
                                        EEEEEEEEE--G CS
                               Thi4 156 virakvvvdatG 167
                                         irak v+++tG
  gene1609|gene1609|rna1609|rna1609 265 NIRAKCVISTTG 276
                                        578888888887 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   2.9e-05     0.037       2      44 ..      63     105 ..      62     146 .. 0.67
   2 ?   -3.9   0.1       8.5   1.1e+04      32      54 ..     549     571 ..     544     583 .. 0.45

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.9e-05
                                        EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHH CS
                            3HCDH_N   2 vaviGaGtmGagiaavfasagleVvlvdiseealekalekiek 44 
                                        v viG G  G+g a  +a +gl+V +v+  + a e++ ++ + 
  gene1609|gene1609|rna1609|rna1609  63 VLVIGGGASGSGCALDAATRGLKVAMVESGDFACETSSKSTKL 105
                                        78*************************9977777766655543 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 8.5
                                        HHHHHHHHHHHHHHHHCCTTTTS CS
                            3HCDH_N  32 eealekalekieksleklvekgk 54 
                                        e+alek+++  +k+++  ++k k
  gene1609|gene1609|rna1609|rna1609 549 EKALEKVMKIFKKRMSWSAAKTK 571
                                        33344444444443333333333 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.1   0.00024       0.3       1      36 [.      62      95 ..      62     119 .. 0.88
   2 ?    1.0   0.0      0.14   1.8e+02     104     146 ..     235     288 ..     206     328 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00024
                      Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvlieaspsl 36
                                       Dv+viG+G+ g   A     a  glkv ++e+++  
  gene1609|gene1609|rna1609|rna1609 62 DVLVIGGGASGSGCALDA--ATRGLKVAMVESGDFA 95
                                       9**************999..99*********99865 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.14
                      Lycopene_cycl 104 lleakvesveeeeageslvvleg...gr..kirarlvvdarglaslk......k 146
                                        l  + v++ ++++ + + +v+++   g+  +ira++v+  +g +  +      +
  gene1609|gene1609|rna1609|rna1609 235 LNYSPVTQLVKNDGAVVGAVCKDmigGEefNIRAKCVISTTGPFTDQtkelanP 288
                                        4456677777777767778887533255789***********555555555544 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       9.9   1.3e+04      52      66 ..       4      18 ..       2      34 .. 0.80
   2 ?   12.2   0.1   0.00016       0.2       2      33 ..      63      94 ..      62     108 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 9.9
                                       HTTEEEECSEEEEEE CS
                          Pyr_redox 52 kngievllntkveei 66
                                       k +i +l++t+v + 
  gene1609|gene1609|rna1609|rna1609  4 KSKIALLTGTVVLSY 18
                                       668999999998765 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00016
                                       EEEECSSHHHHHHHHHHHHTTSEEEEEESSSS CS
                          Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdk 33
                                       v+v+GgG +g  +A  +a  g kV +ve +d 
  gene1609|gene1609|rna1609|rna1609 63 VLVIGGGASGSGCALDAATRGLKVAMVESGDF 94
                                       89**************************9885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (590 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       720  (0.0401584); expected 358.6 (0.02)
Passed bias filter:                      573  (0.0319594); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.71u 0.29s 00:00:01.00 Elapsed: 00:00:00.47
# Mc/sec: 3780.85
//
Query:       gene161|gene161|rna161|rna161  [L=316]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.8e-65  219.3   0.0    6.8e-65  219.1   0.0    1.0  1  Pkinase         Protein kinase domain
    4.4e-34  117.9   0.1      6e-34  117.5   0.1    1.1  1  Pkinase_Tyr     Protein tyrosine kinase
      3e-07   30.1   0.0    2.7e-05   23.6   0.0    2.1  2  Kinase-like     Kinase-like
    1.5e-05   24.2   0.5    2.7e-05   23.3   0.5    1.3  1  Haspin_kinase   Haspin like kinase domain
  ------ inclusion threshold ------
      0.032   13.0   0.1      0.046   12.5   0.1    1.2  1  Pkinase_fungal  Fungal protein kinase
      0.067   12.8   0.7       0.26   10.9   0.0    2.0  2  RIO1            RIO1 family
       0.07   13.0   0.0       0.11   12.4   0.0    1.3  1  APH             Phosphotransferase enzyme family


Domain annotation for each model (and alignments):
>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  219.1   0.0   2.6e-68   6.8e-65       3     264 .]       6     279 ..       4     279 .. 0.91

  Alignments for each domain:
  == domain 1  score: 219.1 bits;  conditional E-value: 2.6e-68
                                    EEEEEEEESSEEEEEEEETTTTEEEEEEEEECHCHCHHHHHHHHHHHHHHHHHSCTTB--EEEEEEESSEEEEEEE--TT CS
                        Pkinase   3 kleklGeGsfGkVykaveketgkivAvKkikkekakkkkekkvlrEikilkklkhpnivrlyevfeekdelylvleyveg 82 
                                    + + +GeG+fGkVy a +++t+ +vAvKkik ek+  +    ++rE+kilk +++++i++lye++  + ++y+vley++ 
  gene161|gene161|rna161|rna161   6 NAQMIGEGTFGKVYVANDTKTNTKVAVKKIKLEKNGVSLI--TIRELKILKLCNSQHIIKLYECYIADGSFYMVLEYLPF 83 
                                    6789******************************999876..9************************************8 PP

                                    EBHHHHHHHHSS--HHHHHHHHHHHHHHHHHHHHTTEE-SS-SGGGEEEETTTEEEE-SGTTSEESSSSCSBCTTTSCGG CS
                        Pkinase  83 geladllerkgslseeeakkiakqilegleylHskgiiHrDlKpeNiLidekgelKitDFGlakelessskltsfvgtse 162
                                    + l  l   k  +s++++k++++q+l+gl+ylH++giiHrD+K++NiL+ ++g lKi+DFGl+k   +  ++t++v+t +
  gene161|gene161|rna161|rna161  84 D-LSALFLSKYRFSDDQIKNLTYQLLHGLSYLHERGIIHRDVKSSNILLTHDGLLKIADFGLSKYECR--DMTNQVCTLW 160
                                    8.6666667899***************************************************98666..48******** PP

                                    GS-HHHH.TTSCBSHHHHHHHHHHHHHHHHHSS-STTTSSHHHHHHHHHHTHHHHHHHCT......SHH...HHHTTS.. CS
                        Pkinase 163 YlAPEvl.keneyskkvDvWslGvilyelltgkppfsgekgkekvekeldqlekilkilg......etkeklpeasei.. 233
                                    Y+APE+l +en+y++ vD Ws+G+il+e+   +p+fs   +++    e+ q+ +i+k+lg      +++  +++++ +  
  gene161|gene161|rna161|rna161 161 YRAPELLlGENNYDNRVDTWSVGCILLEFKVLNPVFS---ENN----EVLQIARIFKLLGaplrtyKYSSLFEQEKYVve 233
                                    *******9*****************************...444....78888889999998777543344444444449* PP

                                    ...............-HHHHHHHHHHT-SSGCCSTTHHHHHTSGGG CS
                        Pkinase 234 ...............seeakdllkkllkkdpkkRltaeellqhpyl 264
                                                    ++++ l+  ll+ d ++R++++++++ p +
  gene161|gene161|rna161|rna161 234 lpwgeiiernfgryfHPDFLYLIGLLLNLDFSERISCTDAMKLPIF 279
                                    ****************************************998865 PP

>> Pkinase_Tyr  Protein tyrosine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.5   0.1   2.3e-37     6e-34       4     198 ..       7     189 ..       4     209 .. 0.89

  Alignments for each domain:
  == domain 1  score: 117.5 bits;  conditional E-value: 2.3e-37
                                    EEEEEEESSEEEEEEEEETTTTSSEEEEEEEEESTTSSHHHHHHHHHHHHHHHTS-BTTB--EEEEEESSSSEEEEEE-- CS
                    Pkinase_Tyr   4 gkklGeGafGkVvegtlkgekekkevkVavKtlkeeateeekeelleeakimkklkhpnivkllgvctkeepllivteyv 83 
                                     + +GeG+fGkV+ ++ +    k+++kVavK++k e++   +   ++e+ki+k ++ ++i+kl+ +++ +++ ++v+ey+
  gene161|gene161|rna161|rna161   7 AQMIGEGTFGKVYVANDT----KTNTKVAVKKIKLEKNGV-SLITIRELKILKLCNSQHIIKLYECYIADGSFYMVLEYL 81 
                                    578**********99888....999********8887777.677899********************************* PP

                                    TTEBHHHHHHHTCTTTSBHHHHHHHHHHHHHHHHHHHHTTEEEST-SGGGEEEEETTEEEE-STTTHEETTTSSEEEETT CS
                    Pkinase_Tyr  84 kgGdLlkfLrkkekekltlkdllsfalqvAkGmeyLeskklvHrdlaarNvLlsenkvvkisDfGLardiekddeyvkke 163
                                    +      fL k    +++ +++ ++++q+ +G++yL+++ ++Hrd+ + N+Ll+++ + ki+DfGL++        ++ +
  gene161|gene161|rna161|rna161  82 PFDLSALFLSKY---RFSDDQIKNLTYQLLHGLSYLHERGIIHRDVKSSNILLTHDGLLKIADFGLSKYE-----CRDMT 153
                                    *96666677666...9***************************************************987.....55555 PP

                                    SSTSGGGGS-HHHHH.HSEEEHHHHHHHHHHHHHHH CS
                    Pkinase_Tyr 164 eaklpvkWmapEslk.ekkftsksDvWsfGvllwEi 198
                                    ++ + + + apE l  e+++  + D Ws G +l E 
  gene161|gene161|rna161|rna161 154 NQVCTLWYRAPELLLgENNYDNRVDTWSVGCILLEF 189
                                    666666666***9762667**************996 PP

>> Kinase-like  Kinase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.3   0.0     0.008        21      17      49 ..       7      39 ..       3      85 .. 0.82
   2 !   23.6   0.0   1.1e-08   2.7e-05     148     241 ..     102     187 ..      91     213 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.008
                    Kinase-like 17 gellkkgdrsvvfevkdqetgeplavkvfllps 49
                                    +++++g +++v+ ++d +t+ ++avk   l++
  gene161|gene161|rna161|rna161  7 AQMIGEGTFGKVYVANDTKTNTKVAVKKIKLEK 39
                                   689***********************9877765 PP

  == domain 2  score: 23.6 bits;  conditional E-value: 1.1e-08
                    Kinase-like 148 llTlqlirlaanLqakglvhgkftvdnllldekgglmlggftaLvragtkvvlseve.kgfaPpEllgsrggytrknktk 226
                                     lT ql+    +L+++g++h ++++ n+ll ++g l++ +f+ L ++  +   ++v+   +  pEll   + y +     
  gene161|gene161|rna161|rna161 102 NLTYQLLHGLSYLHERGIIHRDVKSSNILLTHDGLLKIADFG-LSKYECRDMTNQVCtLWYRAPELLLGENNYDN----- 175
                                    59999************************************7.99999999999999567899999887666655..... PP

                    Kinase-like 227 mthkldaWqlGlviy 241
                                        +d+W +G   +
  gene161|gene161|rna161|rna161 176 ---RVDTWSVGCILL 187
                                    ...788888887665 PP

>> Haspin_kinase  Haspin like kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.5   1.1e-08   2.7e-05     109     280 ..      11     173 ..       2     179 .. 0.75

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 1.1e-08
                  Haspin_kinase 109 seklssevyqtke..kdkevvlKviplevledvtiskelslkelkslklvkgtypglllllqdkvlkekpdfyseqqlfl 186
                                    +e+ +++vy +++  ++++v++K+i l    + +   ++ + elk lkl++ +   +++ l + ++ +   f     +  
  gene161|gene161|rna161|rna161  11 GEGTFGKVYVANDtkTNTKVAVKKIKL----EKNGVSLITIRELKILKLCNSQ---HIIKLYECYIADG-SF---YMVLE 79 
                                    89999****998877899*********....3344458899*********998...6666666666555.12...22333 PP

                  Haspin_kinase 187 vlllkdkGtdLeevklkswkqalsifwqivkiLyvaEtkfeFEHRdLhldniLvdknlnvtlidlklsRle..ssegkvl 264
                                    +l ++ +   L++ ++++ +q++++ +q ++ L+   ++    HRd +  niL+ + +   + d+ ls++e  + +++v+
  gene161|gene161|rna161|rna161  80 YLPFDLSALFLSKYRFSD-DQIKNLTYQLLHGLSYLHER-GIIHRDVKSSNILLTHDGLLKIADFGLSKYEcrDMTNQVC 157
                                    444555555555555544.7*************988766.678***************************9875556665 PP

                  Haspin_kinase 265 ytrlddpllFqGggDy 280
                                          p+l  G+++y
  gene161|gene161|rna161|rna161 158 TLWYRAPELLLGENNY 173
                                    5555577777777776 PP

>> Pkinase_fungal  Fungal protein kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   1.8e-05     0.046     317     342 ..     109     133 ..     100     175 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.8e-05
                 Pkinase_fungal 317 kghrsLflkagiLHrDiSenNilitd 342
                                     g+  L+ + gi+HrD+   Nil+t 
  gene161|gene161|rna161|rna161 109 HGLSYLH-ERGIIHRDVKSSNILLTH 133
                                    6788899.****************93 PP

>> RIO1  RIO1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.1      0.36   9.3e+02       1      21 [.      17      38 ..      17      49 .. 0.79
   2 ?   10.9   0.0    0.0001      0.26      93     149 ..      85     142 ..      44     147 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.36
                                   EEEEEEE.TTTEEEEEEEE-S- CS
                           RIO1  1 nVyhavs.edgkevaiKiykts 21
                                   +Vy+a++ +++++va+K  k++
  gene161|gene161|rna161|rna161 17 KVYVANDtKTNTKVAVKKIKLE 38
                                   5999999455669999987765 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.0001
                                    EEGGBHHHCG.-HHHHHHHHHHHHHHHHHHHHTSTEEESS-STTSEEEETT.EEEE--G CS
                           RIO1  93 vaapklkdve.eeeeaeelyeevleemrklykeaglvHaDLSeyNvlvded.kvviIDv 149
                                    + a  l++++ +++++++l +++l+ +  l  e g++H D+   N+l+++d  + i D+
  gene161|gene161|rna161|rna161  85 LSALFLSKYRfSDDQIKNLTYQLLHGLSYLH-ERGIIHRDVKSSNILLTHDgLLKIADF 142
                                    555667778867999**********877665.****************99944445565 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   4.3e-05      0.11     162     198 ..     110     147 ..      87     152 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4.3e-05
                                    S...SS-EEEE-SS-SGGGEEEC..TTEEEEE---TT-EE CS
                            APH 162 g...elptvllHgDlhpgNllvdpddgrvtGviDfedagl 198
                                    g     +++++H+D ++ N+l++  ++ +  + Df+++++
  gene161|gene161|rna161|rna161 110 GlsyLHERGIIHRDVKSSNILLT--HDGLLKIADFGLSKY 147
                                    45556799***************..444447888888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (316 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       595  (0.0331865); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 2373.82
//
Query:       gene1610|gene1610|rna1610|rna1610  [L=56]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (56 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       679  (0.0378716); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.28s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 408.85
//
Query:       gene1611|gene1611|rna1611|rna1611  [L=94]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       665  (0.0370907); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 742.18
//
Query:       gene1612|gene1612|rna1612|rna1612  [L=141]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       624  (0.0348039); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1024.04
//
Query:       gene1613|gene1613|rna1613|rna1613  [L=650]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.031   14.5   0.0      0.078   13.2   0.0    1.7  1  Ricin_B_lectin  Ricin-type beta-trefoil lectin domain


Domain annotation for each model (and alignments):
>> Ricin_B_lectin  Ricin-type beta-trefoil lectin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   4.3e-06     0.078      31      90 ..      84     143 ..      36     170 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.3e-06
                                        -TSCCGGGEEEEE...TTSEEEETT.TTEEEEES.SSSTTSBEEEEETTTTSGGGCEEEETTTT CS
                     Ricin_B_lectin  31 ChgskgkQlwtlt...kdgeirskaqselCldvs.staegakvvlakChkgkgnqrWefdkdgt 90 
                                        C+++ +  +w+++   +++ i++  + + Cl+vs +++++ ++++++C  +++  +W++ + + 
  gene1613|gene1613|rna1613|rna1613  84 CTDEHA-VRWKIYregEKNYIKN--DYDGCLKVSkRNENDHNIKVRRCY-DNSMFHWDIINAHG 143
                                        555533.5677663312222333..577777777777777777777777.66677777544444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (650 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1219  (0.0679904); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.62u 0.26s 00:00:00.88 Elapsed: 00:00:00.42
# Mc/sec: 4644.03
//
Query:       gene1614|gene1614|rna1614|rna1614  [L=177]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.079   12.0   1.9       0.11   11.4   1.9    1.2  1  Histidinol_dh   Histidinol dehydrogenase
       0.17   11.9   4.9        1.1    9.3   4.8    2.2  1  DUF1803         Domain of unknown function (DUF1803)
       0.19   12.0   1.1       0.44   10.8   1.1    1.9  1  Retrotrans_gag  Retrotransposon gag protein


Domain annotation for each model (and alignments):
>> Histidinol_dh  Histidinol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   1.9   1.9e-05      0.11      16     100 ..      67     149 ..      57     160 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 1.9e-05
                                        HHHHHHHHHHCHHHHHHHHHHCCSS.S.SG.GCCEE-HHHHHHHHHCS-HHHHHHHHHHHHHHHHHHHCC----EE CS
                      Histidinol_dh  16 keiledvreeGdealleytekFDkv.k.kl.eslrvseeeieealekldeelkealeeaaenirkfheaqkeseee 88 
                                         ei +  +++ ++ l+ey e+F ++ + ++ ++ ++++ e +++++k d+++    +ea+++ +k  ++q+++   
  gene1614|gene1614|rna1614|rna1614  67 VEIYQYLQKKDKTLLREYVERFKQMdTcDKgTDRKIKRVEKKKMVDKTDKRI---KREAIKRANKCVRQQRDE--R 137
                                        579999999999**********988532223555666666555565555555...455666666666666643..3 PP

                                        EEEECTTEEEEE CS
                      Histidinol_dh  89 vketepgvvlgq 100
                                        ++++e+  +++ 
  gene1614|gene1614|rna1614|rna1614 138 IETKEKLKIFTA 149
                                        333444444444 PP

>> DUF1803  Domain of unknown function (DUF1803)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   4.8   0.00019       1.1      13      61 ..      65     117 ..      53     149 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00019
                            DUF1803  13 lFkeLieyLaehddviLRelkkeFadqkkldrlldeli....daglikRenkr 61 
                                        +  e+ +yL+++d+++LRe  + F++ +  d+  d  i    +++++ + +kr
  gene1614|gene1614|rna1614|rna1614  65 FIVEIYQYLQKKDKTLLREYVERFKQMDTCDKGTDRKIkrveKKKMVDKTDKR 117
                                        4468899*****************99888776666555111156677777776 PP

>> Retrotrans_gag  Retrotransposon gag protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   1.1   7.4e-05      0.44      35      78 ..      52      95 ..       9     150 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 7.4e-05
                     Retrotrans_gag 35 aflktflpserkdqleeelsslrQ.gtesvreYvtrfktladqld 78
                                       +f kt+  s++     e  + l++ ++  +reYv+rfk++ d +d
  gene1614|gene1614|rna1614|rna1614 52 RFIKTYMRSAHPVFIVEIYQYLQKkDKTLLREYVERFKQM-DTCD 95
                                       899999999999999998888999777779********84.6666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1837  (0.10246); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1330.24
//
Query:       gene1615|gene1615|rna1615|rna1615  [L=413]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.039   13.7   0.0       0.58    9.9   0.0    2.3  2  DUF3950   Domain of unknown function (DUF3950)


Domain annotation for each model (and alignments):
>> DUF3950  Domain of unknown function (DUF3950)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0     0.022     4e+02      14      20 ..     167     173 ..     166     176 .. 0.85
   2 ?    9.9   0.0   3.2e-05      0.58      11      26 ..     260     275 ..     257     276 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.022
                            DUF3950  14 sqNFSAW 20 
                                        s NFS W
  gene1615|gene1615|rna1615|rna1615 167 SDNFSLW 173
                                        78***99 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 3.2e-05
                            DUF3950  11 seksqNFSAWVkeACR 26 
                                         e++qN+SA V + CR
  gene1615|gene1615|rna1615|rna1615 260 NEGTQNYSALVLNRCR 275
                                        59*************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (413 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1210  (0.0674884); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.44
# Mc/sec: 2846.04
//
Query:       gene1616|gene1616|rna1616|rna1616  [L=1474]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   2.1e-123  412.4   1.6   2.1e-123  412.4   1.6    1.8  2  DNA_topoisoIV    DNA gyrase/topoisomerase IV, subunit A
    4.9e-53  178.8   0.7    1.4e-52  177.3   0.7    1.9  1  TOPRIM_C         C-terminal associated domain of TOPRIM
    1.9e-19   69.8   0.6    4.9e-19   68.5   0.6    1.6  1  DNA_gyraseB      DNA gyrase B
    3.3e-10   40.4   0.0    8.2e-10   39.2   0.0    1.7  1  HATPase_c        Histidine kinase-, DNA gyrase B-, and HSP90-
    2.3e-09   37.4   0.0    7.2e-09   35.8   0.0    1.9  1  Toprim           Toprim domain
  ------ inclusion threshold ------
       0.21   11.6   1.8       0.51   10.3   1.8    1.6  1  tRNA_NucTran2_2  tRNA nucleotidyltransferase domain 2 putativ


Domain annotation for each model (and alignments):
>> DNA_topoisoIV  DNA gyrase/topoisomerase IV, subunit A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.2      0.38   1.1e+03     307     360 ..     392     444 ..     224     514 .. 0.74
   2 !  412.4   1.6  6.9e-127  2.1e-123       1     425 [.     723    1131 ..     723    1132 .. 0.97

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.38
                      DNA_topoisoIV 307 eilkeflevrlevyerrk.eyllekleerleilegllkalnkidevievirkskk 360
                                        ++ ++f+++++ +++ r  +  l+k++++l++ +    + +ki  ++++ ++++ 
  gene1616|gene1616|rna1616|rna1616 392 TLSDDFVKHTVALLSDRVlSQALAKMSKQLKKTD--GSKSSKITGIEKLSDANLA 444
                                        3445566666666655531445566666666666..3444555555555555554 PP

  == domain 2  score: 412.4 bits;  conditional E-value: 6.9e-127
                      DNA_topoisoIV    1 RaiPsvrDGlKPvqRriLyamfkllnldkkekKvaqlvGev..lgkYhPHGdaslydaivrlaqdfvg..nipl 70  
                                         R+iPsv+DG+KP+qR+++y +fk +nl k+e+KvaqlvG+v  +++Yh HG+ sl+++i++la+dfvg  ni+l
  gene1616|gene1616|rna1616|rna1616  723 RSIPSVVDGFKPGQRKVMYCCFK-RNL-KSEIKVAQLVGYVaeHSAYH-HGEVSLQQTIIKLAHDFVGsnNINL 793 
                                         9**********************.999.********************.************************* PP

                      DNA_topoisoIV   71 ldpqGnfGsildgdkd.AaaRYietrLskiarellkeidketvdyqenyDgsekEPevlppiiPnlLvnGaeGI 143 
                                         l+p+G+fG++l+g+kd A+aRYi+t+L++i+r+++ e d+ +++y ++ D+ ++EP +++pi+P++LvnGa+GI
  gene1616|gene1616|rna1616|rna1616  794 LMPEGQFGTRLQGGKDaASARYIFTNLASITRKIFVESDDALLNYITE-DNMKIEPSFYVPIVPMVLVNGADGI 866 
                                         ************************************************.************************* PP

                      DNA_topoisoIV  144 avGmatkipphnlkeiidaliallkgeeaellelvlgPdfptgggiigkeeikeayetgrGkikvrakveieek 217 
                                         ++G+ tkip+++l eiid+++ ll+++e+   +  + P++++++g+i++ +  ++y+ + G + v ++      
  gene1616|gene1616|rna1616|rna1616  867 GTGWLTKIPNYDLLEIIDNIKLLLDDQEM---N-TMVPFYRGFKGEIEDLG-GKKYRIS-GIYDVDGD------ 928 
                                         ***************************65...5.79***********7777.899***9.*******9...... PP

                      DNA_topoisoIV  218 tivitElPigvntskliekieelvkkkkikisdirde.sdrgvrivielkrgaseekvleklykktkLessisv 290 
                                         +++itElP++++t++++e++e+ ++k+ +k  ++r++ ++r+v+++++l+       v +++ kk++L+s   +
  gene1616|gene1616|rna1616|rna1616  929 NLTITELPVKIWTQTYKEFLEKKIEKGDVK--EFREYhTERSVHFEVNLA-------VSGEIDKKFSLSSINIF 993 
                                         8*************************9999..*****9999*******99.......677799******9999* PP

                      DNA_topoisoIV  291 nnlvlfdk.k..pkylslkeilkeflevrlevyerrkeyllekleerleilegllkalnkidevievirkskk. 360 
                                         nn v+fd+ +  +ky s++eil+ef++ rle+y+ rk ++l+ lee+l++l+      nk+++++ev++++++ 
  gene1616|gene1616|rna1616|rna1616  994 NNFVCFDRhGkiKKYESAEEILREFYSIRLEFYNLRKAHMLNTLEEQLKRLH------NKVRFIKEVVNGTLVv 1061
                                         *******9648*****************************************......**************** PP

                      DNA_topoisoIV  361 ekkakkeLieelse.......eqaeyllemrlrrLtkeeveklekeieelekeikelekllaklkklikeel 425 
                                         +k++k+++i+el++       + ++yll+m + +Lt e++e+l++e+++++ e +el  ++ak  +l++ +l
  gene1616|gene1616|rna1616|rna1616 1062 SKRKKTDIIAELERkeyykieDTYDYLLNMAILSLTLEKIERLNEEYRNTQREYDELLGKSAK--ELWIYDL 1131
                                         ***********999999999988****************************************..9999887 PP

>> TOPRIM_C  C-terminal associated domain of TOPRIM
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  177.3   0.7   4.7e-56   1.4e-52       1     128 []     568     721 ..     568     721 .. 0.94

  Alignments for each domain:
  == domain 1  score: 177.3 bits;  conditional E-value: 4.7e-56
                           TOPRIM_C   1 FitPivkvtkkk..ke........................eisffslpeyeewkestenlkkwkikYYkGLgtsts 50 
                                        FitPiv+vtk+k  ++                        +i+ff++peye+wk+st++ k+w++kYYkGLgtsts
  gene1616|gene1616|rna1616|rna1616 568 FITPIVRVTKTKgsRTsrsnseddsdehtntpassdpvgtVIDFFTIPEYEDWKNSTPDIKNWTVKYYKGLGTSTS 643
                                        9********9954411445677888999999999***9999*********************************** PP

                           TOPRIM_C  51 keakeyfsnldkhlkefkleeeedkeaielaFskkkaderkewlkklepgtyldkkkkkisysdFvnkeLilfsma 126
                                        k+ak+yfsnl+kh+k+f+l ++ed+++i+laF+kkkad+rk wlk+++pgt+ld++ +ki+++dF+nkeLilfsma
  gene1616|gene1616|rna1616|rna1616 644 KDAKQYFSNLEKHVKSFTLLTTEDQSLIDLAFNKKKADDRKLWLKNCVPGTFLDHSAHKIPIRDFINKELILFSMA 719
                                        **************************************************************************** PP

                           TOPRIM_C 127 dn 128
                                        dn
  gene1616|gene1616|rna1616|rna1616 720 DN 721
                                        *8 PP

>> DNA_gyraseB  DNA gyrase B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.5   0.6   1.6e-22   4.9e-19       3     167 ..     275     422 ..     266     428 .. 0.81

  Alignments for each domain:
  == domain 1  score: 68.5 bits;  conditional E-value: 1.6e-22
                        DNA_gyraseB   3 kdfveelnkdkkelikevlsvegekaveevievevalqwtssysenilsFvNniatpeGGtHvdgfksaltktlne 78 
                                        k++v+ + +d        ++v +e  v+e++ev+v l   s+++ +++sFvN+i t +GGtHv+++ ++l++ + e
  gene1616|gene1616|rna1616|rna1616 275 KQYVSLYLGD-------DVKVVHEV-VNERWEVAVVL---SDEQFQQVSFVNSICTIKGGTHVNHVLDQLVEPVIE 339
                                        5666666666.......23333444.46669999999...66777******************************* PP

                        DNA_gyraseB  79 yakkkkllkkkeekisgediregltavvsvkipepqFeGQTKekLgnsevksivekvvseeleafleenkeeakki 154
                                         ++kk++    +  i++  +r++++++v+  i++  F++QTKe+L+ + ++   + ++s+ + +        ++++
  gene1616|gene1616|rna1616|rna1616 340 RVQKKDK----NLVIKPFFVRNSIFIFVNALIENAAFDSQTKETLTLRVSSFGSRCTLSDDFVKHTVA--LLSDRV 409
                                        **99885....448*********************************999988888888887665444..567777 PP

                        DNA_gyraseB 155 lekaveaakarea 167
                                        l++a++++ ++++
  gene1616|gene1616|rna1616|rna1616 410 LSQALAKMSKQLK 422
                                        7777777776664 PP

>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.2   0.0   2.8e-13   8.2e-10       4     110 ..      87     230 ..      84     232 .. 0.72

  Alignments for each domain:
  == domain 1  score: 39.2 bits;  conditional E-value: 2.8e-13
                                        HHHHHHHHHHHHHHHHH...HSTTTEEEEEEEEEETEEEEEEEESSSSSTTHHHT........GTCSTTCH..... CS
                          HATPase_c   4 krLrqiisnlvdNavkf...atkageieveikaseddlvisveDnGiGipkedlk........klfekfsq..... 63 
                                        ++L++i+++++ Na+++    ++++++ v i       +isv++nG+G+p +++k        ++f+ + +     
  gene1616|gene1616|rna1616|rna1616  87 PGLYKIFDEILVNAADNkirDPSMSKLCVDIA----GDKISVWNNGKGVPIKMHKkenvyvpeLIFGQLLTssnyd 158
                                        78999**********99766568889999999....789************************9998666668898 PP

                                        HCSTCHTSTSSSHHHHHHHH.HHHH......TTTEEEE..........EEET........TTEEEEEEEEES CS
                          HATPase_c  64 ddstkrggggtGlGlsivkk.lvel......mgGeiwv..........esep........grGttftftlpl 110
                                        d+++k++gg++G+G+++++   +e        + +i++          ++ep        +  t++tft++l
  gene1616|gene1616|rna1616|rna1616 159 DKEKKVTGGRNGYGAKLCNIfSSEFiietadSKENITYyqrysdnmskREEPvitkqrvrESFTKITFTPDL 230
                                        89999*************884444323332211244445555555554222233333344557888888877 PP

>> Toprim  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.8   0.0   2.4e-12   7.2e-09       2      89 ..     454     553 ..     453     564 .. 0.82

  Alignments for each domain:
  == domain 1  score: 35.8 bits;  conditional E-value: 2.4e-12
                                        EEEESSHHHHHHHHHTHT...STEEEEEEESSSSEEEHS.TTEEEEE..ECTTTHHHHHH......HHHHHHHHSE CS
                             Toprim   2 lvivEgpsdaktiakalg...sgfqavtaslGhildlet.efkpvye..eiedkkkvlka......lkelakrade 65 
                                        l++ Eg+s+   + + l+   ++++ v++++G++l++ + + k+++e  e+++ kk+l+          +++r+ +
  gene1616|gene1616|rna1616|rna1616 454 LILTEGDSAKTLAISGLSvvgRDYYGVFPLRGKLLNVREaNHKQIMEneELNNLKKILALqhhkdyTSTESLRYGH 529
                                        899999996555555555777******************76666666988888888887788888788888***** PP

                                        EEEECSSSHHHHHHHHHHHHHHTH CS
                             Toprim  66 iilatDpDreGeaiawellevlke 89 
                                        +i++tD D +G++i+ +++++++ 
  gene1616|gene1616|rna1616|rna1616 530 VIIMTDQDHDGSHIKGLIINFFDH 553
                                        *******************99874 PP

>> tRNA_NucTran2_2  tRNA nucleotidyltransferase domain 2 putative
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   1.8   0.00017      0.51      24     105 ..    1037    1128 ..    1029    1134 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00017
                    tRNA_NucTran2_2   24 arsfLkswkfsnklikavtallkllekrk.........naeltkl......elykageealllaeelaqaqgqa 82  
                                          ++ Lk +    ++ik+v++   +++krk                      + y++ ++++ l + l ++++ +
  gene1616|gene1616|rna1616|rna1616 1037 LEEQLKRLHNKVRFIKEVVNGTLVVSKRKktdiiaeleR-----KeyykieDTYDYLLNMAILSLTLEKIERLN 1105
                                         678899999999****************98777444432.....322323466********************* PP

                    tRNA_NucTran2_2   83 edlqaldeiyqaLpIkskkeLai 105 
                                         e+ ++ +  y++L  ks keL i
  gene1616|gene1616|rna1616|rna1616 1106 EEYRNTQREYDELLGKSAKELWI 1128
                                         ********************977 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1474 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       715  (0.0398795); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.86u 0.35s 00:00:01.21 Elapsed: 00:00:00.52
# Mc/sec: 8567.62
//
Query:       gene1617|gene1617|rna1617|rna1617  [L=397]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-15   57.3  42.1    7.2e-12   45.8  11.5    3.5  4  MgtE      Divalent cation transporter


Domain annotation for each model (and alignments):
>> MgtE  Divalent cation transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0      0.24   4.4e+03      47      61 ..      31      45 ..      10      66 .. 0.48
   2 !   45.8  11.5     4e-16   7.2e-12       2     123 ..      65     193 ..      64     194 .. 0.74
   3 ?    1.4   6.3     0.022     4e+02      42      95 ..     208     266 ..     195     268 .. 0.55
   4 !   23.9   6.3   2.3e-09   4.1e-05       2     123 ..     270     386 ..     269     387 .. 0.71

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.24
                                       HHHHHHHHHHHHHHH CS
                               MgtE 47 gvilgllifllalll 61
                                       +++++l+ f +a ++
  gene1617|gene1617|rna1617|rna1617 31 SLLISLVGFTIAGIY 45
                                       333333333333332 PP

  == domain 2  score: 45.8 bits;  conditional E-value: 4e-16
                                        HHHHHHHHHHHHHHHHHHHHHHHTT.......SS-GGH.....HHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-.C CS
                               MgtE   2 PvilglgGnlgaqlasristalhlg.......elekkl.....kkvllkelrvvlllgvilgllifllalllgwsl 65 
                                        ++il+++Gn++ ++a+ +s+  ++             +     + v++++++++l +gv+ + +++l+   +   +
  gene1617|gene1617|rna1617|rna1617  65 TCILSFKGNIELIFAMHLSSISNVYnpvieyaR----FaidnsCMVVVQSIMIGLSVGVVGMSVVILR---FDDAF 133
                                        6799*******************8644332221....1122227777777777777777766666666...66677 PP

                                        TSHHHHHHHHHHHHHHHHHH.....HHHHHHHHHHTTS-GGGSHHHHHHHHHHHHHHHHHH CS
                               MgtE  66 llalvvglalvlvllaaall...ilgvllplllwklglDPdnaaiPlltalgDllgtlllv 123
                                          a++  ++ ++ +l+++l+   i   + +ll+++l+++Pdn+++P ++a++D +++l l+
  gene1617|gene1617|rna1617|rna1617 134 RYAVITLCSCLVSCLVSTLVvllI-LLAAVLLFKNLQINPDNVVLPSIAAFSDYFTVLSLI 193
                                        777777888888888888887844.444448**************************9986 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.022
                                        HHHHHHHHHHHHHHHHHHHHT-.......CTSHHHHHHHHHHHHHHHHHH...HHHHHHHH CS
                               MgtE  42 vvlllgvilgllifllalllgw......slllalvvglalvlvllaaall.ilgvllplll 95 
                                         + ++++il+++ f++++           ++ ++++ +++vl  ++ +l+ ++  + p+l+
  gene1617|gene1617|rna1617|rna1617 208 CATTILLILVVVPFIMQVS--RrspailPIQSLTLLVITFVLSSISGMLIeYFSLMYPFLA 266
                                        2333344444444444333..1335555555555677777777777777788888888775 PP

  == domain 4  score: 23.9 bits;  conditional E-value: 2.3e-09
                                        HHHHHHHHHHHHHHHHHHHHHHHTTSS-GGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-.CTSHHHHHHHHHH CS
                               MgtE   2 PvilglgGnlgaqlasristalhlgelekklkkvllkelrvvlllgvilgllifllalllgwslllalvvglalvl 77 
                                        Pv++gl G++  + + r  t+l +++ ++k k  l      +l++++ ++l  +++  +l++   l  ++++ +++
  gene1617|gene1617|rna1617|rna1617 270 PVFCGLTGSTSFIYLNRKLTSLYTKQPHNK-KASL----FSLLIISLAMSLTYIIILNTLFE--RLPSTFSFLFIV 338
                                        9************************99666.3434....44444444444444444223233..344455666666 PP

                                        HHHHHHHH.....HHHHHHHHHHTTS-GGGSHHHHHHHHHHHHHHHHHH CS
                               MgtE  78 vllaaall...ilgvllplllwklglDPdnaaiPlltalgDllgtlllv 123
                                        ++l+ +ll   ++ ++l ++ +++++   ++a+P++t+ +D++g ++lv
  gene1617|gene1617|rna1617|rna1617 339 CFLVDVLLlieVVDYVLSHFQRSVEM-AGVVALPVITSTADFFGSSFLV 386
                                        66666666678889999999999998.5688****************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (397 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1179  (0.0657594); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.63u 0.29s 00:00:00.92 Elapsed: 00:00:00.45
# Mc/sec: 2667.63
//
Query:       gene1618|gene1618|rna1618|rna1618  [L=260]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
       0.17   11.9   0.1       0.23   11.4   0.1    1.2  1  Pyrid_oxidase_2  Pyridoxamine 5'-phosphate oxidase


Domain annotation for each model (and alignments):
>> Pyrid_oxidase_2  Pyridoxamine 5'-phosphate oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   1.3e-05      0.23      37      79 ..     104     146 ..      82     163 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 1.3e-05
                                        EEEEE-BSSSTT---S--EEEE-TTSHHHHHHHH--EEEEEEE CS
                    Pyrid_oxidase_2  37 anvvsisdgaaddstGnpylllvdidstaqniqknsklsltis 79 
                                          +  + +  + +s+Gn+++++++  +t+q++  n ++ +ti 
  gene1618|gene1618|rna1618|rna1618 104 FTMLMYTMMSFSKSPGNILFFMTKRHTTVQDAVFNVNVLFTIV 146
                                        455566666788*************************999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1471  (0.0820458); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 1780.47
//
Query:       gene1619|gene1619|rna1619|rna1619  [L=76]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.2e-06   26.6   2.2      5e-06   26.0   2.2    1.3  1  Sgf11     Sgf11 (transcriptional regulation protein)


Domain annotation for each model (and alignments):
>> Sgf11  Sgf11 (transcriptional regulation protein)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   2.2   2.8e-10     5e-06       5      28 ..      52      75 ..      50      76 .] 0.94

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 2.8e-10
                                       EE-TTTSSEEEGGGHHHHHHHHCH CS
                              Sgf11  5 vtCpnCgRqiaasRFApHLekClg 28
                                       ++C  Cg++  a RF +H+e+C+ 
  gene1619|gene1619|rna1619|rna1619 52 IKCHKCGKYAPAKRFTSHMERCMK 75
                                       68*********************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       770  (0.0429472); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 551.90
//
Query:       gene162|gene162|rna162|rna162  [L=167]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-07   32.4   0.1     0.0074   16.8   0.0    2.3  2  Ribosomal_L6e  Ribosomal protein L6e


Domain annotation for each model (and alignments):
>> Ribosomal_L6e  Ribosomal protein L6e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   4.1e-07    0.0074       1      46 [.      79     125 ..      79     131 .. 0.88
   2 !   14.6   0.0   1.9e-06     0.035      69     108 ..     125     164 ..     119     167 .] 0.86

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 4.1e-07
                  Ribosomal_L6e   1 lNgvPLrRvnqryVIatstkvdlsgvd.ekipeklndeyFkkekkkk 46 
                                    +N++PL  +++r+++ tst +++s+ d + ++e + d  +++e+ ++
  gene162|gene162|rna162|rna162  79 INSIPLFSIDERFLLKTSTILKISDYDlKDVKECSMDVNYENEDVET 125
                                    7**************************99999999999888876554 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 1.9e-06
                  Ribosomal_L6e  69 rkadqkavDkallaaikkekllkkYLkskFsLrkgdyphe 108
                                      +  + ++  ll++i k k+++ YLk+ F+  ++d+p +
  gene162|gene162|rna162|rna162 125 TSELEQRIEGDLLKEIAKIKFMRTYLKTPFKAPENDHPLA 164
                                    5667889999*********************999998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       754  (0.0420548); expected 358.6 (0.02)
Passed bias filter:                      534  (0.0297841); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1200.52
//
Query:       gene1620|gene1620|rna1620|rna1620  [L=297]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-23   84.1   0.4    1.5e-23   83.6   0.4    1.2  1  Y_phosphatase    Protein-tyrosine phosphatase
    2.5e-07   30.9   0.2    8.6e-07   29.2   0.1    1.9  2  PTPlike_phytase  Inositol hexakisphosphate
      5e-07   29.6   0.1    1.1e-06   28.5   0.0    1.6  2  DSPc             Dual specificity phosphatase, catalytic doma
     0.0027   17.7   0.1     0.0046   16.9   0.0    1.5  2  Y_phosphatase3   Tyrosine phosphatase family
  ------ inclusion threshold ------
      0.066   13.1   0.1       0.13   12.1   0.1    1.4  1  Haemagg_act      haemagglutination activity domain


Domain annotation for each model (and alignments):
>> Y_phosphatase  Protein-tyrosine phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.6   0.4   4.2e-27   1.5e-23      30     233 ..     109     291 ..      91     293 .. 0.76

  Alignments for each domain:
  == domain 1  score: 83.6 bits;  conditional E-value: 4.2e-27
                                        EEEEEEEECTEEEEEEEEE---GGGHHHHHHHHHHTT--EEEEESBSEETTEESS---S-SSTSSEEEETT..EEE CS
                      Y_phosphatase  30 InAnyikgykkekkyIatQgPlkstvedFWrmvwqekvkvivmLtsleekgrekcaqYwpeeeeesleygk..ikv 103
                                        InA++i+++    +yIa+Q P  +  ++F +   ++ + +iv+L++++e        Y+  ++  s+  +    +v
  gene1620|gene1620|rna1620|rna1620 109 INASFIRTEF--VTYIACQRPKVKYYQKFVEF-ANHASDLIVCLCNDQED-------YFTGSTCSSTADEGagTTV 174
                                        9*****6665..89*******99******987.57789***********6.......9996666655555512444 PP

                                        EEE.EEEEEESSEEEEEEEEEETTTTEEEEEEEEEEESSS-SSSSG..SCCHHHHHHHHHHHHHHSTTSS-EEEEC CS
                      Y_phosphatase 104 tlkekekedekeyvlrelevkkkkeeseerevkqlqytnWpdhgvp..esaksllklirkvekskeaksgpvvVhC 177
                                        ++  k+ ++++e v+   +++         ++k +++  W+d +vp  e+  ++ +   ++ ks     +pv+VhC
  gene1620|gene1620|rna1620|rna1620 175 QTD-KQDTNKDERVYVIEQIN---------NTKRIKFLRWEDFDVPnrEDFAQFYDAYVSMDKSD----KPVIVHC 236
                                        444.33323323333323333.........235678**********5555555556666666555....******* PP

                                        SSSSHHHHHHHHHHHHHHHHHHHSEEEHHHHHHHHHTTSTTSS-SHHHHHHHHHHH CS
                      Y_phosphatase 178 saGvgRtgtfvaldillqqleaeeevdvlqivkelrkqRpgmvqtleqyiflyevi 233
                                        +aGvgRtgtf++ d+l+++ + ++ev + +++ ++r+qR+ mv + +q+++l +++
  gene1620|gene1620|rna1620|rna1620 237 KAGVGRTGTFILYDVLVRMKNVTKEVFIDELC-KMREQRNFMVFNGAQLKWLANIF 291
                                        *****************999999999997765.69**************9998876 PP

>> PTPlike_phytase  Inositol hexakisphosphate
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       0.6   2.2e+03     110     139 ..     124     153 ..      85     166 .. 0.81
   2 !   29.2   0.1   2.4e-10   8.6e-07      74     154 ..     172     252 ..     149     254 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.6
                                        TS---HHHHHHHHHHHHTS-TT-EEEEE-S CS
                    PTPlike_phytase 110 ekapeeedfdalvsilkeapektalvfnCq 139
                                        ++ p+ ++ +++v++ ++a++  ++++n q
  gene1620|gene1620|rna1620|rna1620 124 CQRPKVKYYQKFVEFANHASDLIVCLCNDQ 153
                                        677888888888888888876666666655 PP

  == domain 2  score: 29.2 bits;  conditional E-value: 2.4e-10
                                        S-............EE-H.HHHHHHTT-EEEEEEE-TTS---HHHHHHHHHHHHTS.-TT-EEEEE-SSSSHHHHH CS
                    PTPlike_phytase  74 ktlqevweevetpeevye.relaeelslrYaRipitdekapeeedfdalvsilkea.pektalvfnCqmGrgRTTt 147
                                         t+q  +++ ++ e+vy  ++++ + ++++ R   +d   p+ edf +++++  ++ +++++++++C++G+gRT t
  gene1620|gene1620|rna1620|rna1620 172 TTVQTDKQDTNKDERVYViEQINNTKRIKFLRW--EDFDVPNREDFAQFYDAYVSMdKSDKPVIVHCKAGVGRTGT 245
                                        2444444444567777777************96..8*****************999888***************99 PP

                                        HHHHHHH CS
                    PTPlike_phytase 148 amviatL 154
                                        ++    L
  gene1620|gene1620|rna1620|rna1620 246 FILYDVL 252
                                        9876555 PP

>> DSPc  Dual specificity phosphatase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       1.8   6.3e+03      37      59 ..     116     139 ..      88     153 .. 0.54
   2 !   28.5   0.0   3.1e-10   1.1e-06      48     128 ..     205     288 ..     167     291 .. 0.76

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 1.8
                                        TTTSEEEEEC.CESSTTSCCGGGH CS
                               DSPc  37 kseieklrip.vedehetkiskyl 59 
                                        ++  +++ ++  + ++ +k+ ++ 
  gene1620|gene1620|rna1620|rna1620 116 TEFVTYIACQrPKVKYYQKFVEFA 139
                                        444444444422224444444444 PP

  == domain 2  score: 28.5 bits;  conditional E-value: 3.1e-10
                                        ESSTTSCCGGGHHHHHHHHHHHHHTT-EEEEEESSSSSHHHHHHHH.HHHHHHTSCHHHHHHHH...HHHSTT-SS CS
                               DSPc  48 edehetkiskyleeavefidkakqkgkkvlVHCqaGisRSatliia.Ylmktknlslneayefl...kerrpaisp 119
                                        e + +   ++++ +  +   ++ ++ k v+VHC+aG+ R++t+i+   l + kn++ + +++ l   +e+r+ ++ 
  gene1620|gene1620|rna1620|rna1620 205 E-DFDVPNREDFAQFYDAYVSMDKSDKPVIVHCKAGVGRTGTFILYdVLVRMKNVTKEVFIDELckmREQRNFMVF 279
                                        3.46677788899999999999********************9985257788888988888888777899988888 PP

                                        THHHHHHHH CS
                               DSPc 120 nagfirqLl 128
                                        n  ++++L 
  gene1620|gene1620|rna1620|rna1620 280 NGAQLKWLA 288
                                        888888875 PP

>> Y_phosphatase3  Tyrosine phosphatase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       1.7   6.1e+03      84     104 ..      29      49 ..       9      71 .. 0.49
   2 !   16.9   0.0   1.3e-06    0.0046     106     139 ..     211     248 ..     127     273 .. 0.76

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 1.7
                     Y_phosphatase3  84 eekeeeeaeetlaelYrelle 104
                                        +++ +e++++++a++Y++ ++
  gene1620|gene1620|rna1620|rna1620  29 QNTPKEAEDRNIASIYAKNPK 49 
                                        223333333444444443333 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 1.3e-06
                     Y_phosphatase3 106 akkayrkvfealad.ee...pvlfHCtaGKDRTGvlaa 139
                                        +++ ++++ +a  + ++   pv++HC aG  RTG ++ 
  gene1620|gene1620|rna1620|rna1620 211 NREDFAQFYDAYVSmDKsdkPVIVHCKAGVGRTGTFIL 248
                                        45677777776666544568**************8754 PP

>> Haemagg_act  haemagglutination activity domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   3.7e-05      0.13      11      50 ..     175     214 ..     166     232 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.7e-05
                                        EEC-EE..EETCS-ECCEEEEEETTSEEEEEECE--B-TTEE CS
                        Haemagg_act  11 tnvkak..kagngvpivniatpqkggnsfnsfseFnvpeggv 50 
                                        ++ k++  k +  ++i++i   +++ + f ++++F+vp+ + 
  gene1620|gene1620|rna1620|rna1620 175 QTDKQDtnKDERVYVIEQIN--NTKRIKFLRWEDFDVPNRED 214
                                        33333300344555666666..****************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (297 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       907  (0.0505884); expected 358.6 (0.02)
Passed bias filter:                      488  (0.0272185); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.37
# Mc/sec: 2381.27
//
Query:       gene1621|gene1621|rna1621|rna1621  [L=135]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.5e-21   76.8   0.3      2e-21   76.4   0.3    1.2  1  HSF_DNA-bind  HSF-type DNA-binding


Domain annotation for each model (and alignments):
>> HSF_DNA-bind  HSF-type DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.4   0.3   1.1e-25     2e-21       1      96 []      16     107 ..      16     107 .. 0.93

  Alignments for each domain:
  == domain 1  score: 76.4 bits;  conditional E-value: 1.1e-25
                                        HHHHHHHHHCTTTT..SEESSSSSEEEES-HHHHHHHTHHHHSTT--HHHHHHHHHHTTEEE---SSBTTB--TTS CS
                       HSF_DNA-bind   1 FlkkLyklledeel..isWsedgksfvvkdkeefakevlpkyfkhsnfssFvrqLnlYgFrkvkrkeekkkkkskv 74 
                                        F+ +Ly  ++d ++  + Ws++++sf++ dke+f+++vlp + k+++fs F+rqLn YgF+k +      + + +v
  gene1621|gene1621|rna1621|rna1621  16 FIIRLYAAIDDPNVtsVIWSRHETSFLILDKEHFQHHVLPMISKTTEFSGFIRQLNAYGFKKRN------NIDPSV 85 
                                        999******9966666**********************************************66......456788 PP

                                        EEEEESS--XXXXXXXXXXXXX CS
                       HSF_DNA-bind  75 weFshenFkrgkpelLkkikrk 96 
                                         e++h+nF +++ +lL+k+ r+
  gene1621|gene1621|rna1621|rna1621  86 REYAHPNFIKNRFDLLTKLSRR 107
                                        9*****************9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       274  (0.0152825); expected 358.6 (0.02)
Passed bias filter:                      220  (0.0122706); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 935.27
//
Query:       gene1622|gene1622|rna1622|rna1622  [L=73]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (73 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1753  (0.0977746); expected 358.6 (0.02)
Passed bias filter:                      740  (0.0412739); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 537.00
//
Query:       gene1623|gene1623|rna1623|rna1623  [L=61]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0041   17.2   0.1     0.0043   17.2   0.1    1.0  1  UPF0242          Uncharacterised protein family (UPF0242) N-t
  ------ inclusion threshold ------
      0.018   15.5   0.7      0.026   15.0   0.7    1.5  1  ICMT             Isoprenylcysteine carboxyl methyltransferase
      0.033   14.2   0.0      0.033   14.2   0.0    1.1  1  Phage_holin_3_6  Putative Actinobacterial Holin-X, holin supe
      0.089   12.9   0.0       0.13   12.3   0.0    1.3  1  ETRAMP           Malarial early transcribed membrane protein 


Domain annotation for each model (and alignments):
>> UPF0242  Uncharacterised protein family (UPF0242) N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.1   9.6e-07    0.0043       9      65 ..       2      58 ..       1      61 [] 0.82

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 9.6e-07
                            UPF0242  9 iflYllPllllaiysiqllseqksWs.llsiGlllaaaGsLlllllllkwekalkekl 65
                                       ++l+++P++++++    l++eq+s    ls++ll ++ G ++l++  ++ e+++++kl
  gene1623|gene1623|rna1623|rna1623  2 VLLFSAPVIMMSVLTK-LFPEQESIMgALSVALLFVILGLICLFVHRIECEEEEEKKL 58
                                       678999**99998875.56666665449*****************9999999888876 PP

>> ICMT  Isoprenylcysteine carboxyl methyltransferase (ICMT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.7   5.7e-06     0.026      63      90 ..      25      53 ..       2      59 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 5.7e-06
                               ICMT 63 lcnakltalvllalvalllf.vRikeEek 90
                                       ++ a  +al++++l ++ lf +Ri++Ee+
  gene1623|gene1623|rna1623|rna1623 25 IMGALSVALLFVILGLICLFvHRIECEEE 53
                                       567889**************9****9997 PP

>> Phage_holin_3_6  Putative Actinobacterial Holin-X, holin superfamily III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   7.3e-06     0.033      46      88 ..       2      47 ..       1      60 [. 0.78

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 7.3e-06
                    Phage_holin_3_6 46 lallalllllvalalalaa....lwlaalivaavllvlagvlalvgl 88
                                       ++l++++++++ ++  l +    + ++al va+++++l++++++v +
  gene1623|gene1623|rna1623|rna1623  2 VLLFSAPVIMMSVLTKL-FpeqeSIMGALSVALLFVILGLICLFVHR 47
                                       67888888888887544.233589999***************99866 PP

>> ETRAMP  Malarial early transcribed membrane protein (ETRAMP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   2.9e-05      0.13       4      32 ..      29      57 ..      26      61 .] 0.83

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.9e-05
                             ETRAMP  4 tkvllffafLlavnlltpeslcdevnkkk 32
                                         v+l+f++L +++l++  + c+e+++kk
  gene1623|gene1623|rna1623|rna1623 29 LSVALLFVILGLICLFVHRIECEEEEEKK 57
                                       5789*******************999654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1117  (0.0623013); expected 358.6 (0.02)
Passed bias filter:                      744  (0.041497); expected 358.6 (0.02)
Passed Vit filter:                        97  (0.00541023); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 443.34
//
Query:       gene1624|gene1624|rna1624|rna1624  [L=822]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.7e-39  134.9   0.1    2.7e-33  115.2   0.0    2.2  2  CPSase_L_D2    Carbamoyl-phosphate synthase L chain, ATP bind
    7.9e-16   58.6   0.0    1.6e-15   57.6   0.0    1.5  1  Biotin_carb_N  Biotin carboxylase, N-terminal domain
    4.1e-13   49.4   0.1    1.3e-12   47.8   0.0    1.9  2  Biotin_carb_C  Biotin carboxylase C-terminal domain
     0.0018   18.3   0.0       0.62   10.1   0.0    2.5  2  ATP-grasp_3    ATP-grasp domain
  ------ inclusion threshold ------
       0.05   13.4   0.0      0.086   12.6   0.0    1.3  1  ATPgrasp_Ter   ATP-grasp in the biosynthetic pathway with Ter


Domain annotation for each model (and alignments):
>> CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   6.3e-07    0.0022       2      64 ..     114     171 ..     113     172 .. 0.74
   2 !  115.2   0.0   7.6e-37   2.7e-33      73     207 ..     407     538 ..     388     541 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 6.3e-07
                                        HHHHHHHHHHTT-BBSSEECSSBSSHHHHHHHHHHH-SSEEEEETTCCTTTTEEEESSHHHHH CS
                        CPSase_L_D2   2 kesakealkkinvpvvpssaapvetleealaiakeigyPviikaafglGGkGmrvarneeela 64 
                                        k  +++ ++  +vp++p ++     ++e +++ + +  Pv+ik++ ++GGkG  v+++ee+l+
  gene1624|gene1624|rna1624|rna1624 114 KIMSNRFAESRGVPCIPYTTD----EDEFVRFYRAH-APVLIKSSDSGGGKGIEVVETEEQLV 171
                                        555555566666666665544....77777776655.6**********************985 PP

  == domain 2  score: 115.2 bits;  conditional E-value: 7.6e-37
                                        HHHHHHSTS-EEEEE--SSSEEEEEEEEEETTS-EEEEEEEEECCECTCCCCEEEES-SS--HHHHHHHHHHHHHH CS
                        CPSase_L_D2  73 eakaafgnkqvlvekslkgpkeiEvevlrDakgnvitvcerenslqlrtqkvievAPsqtLtdeerqalreaavkv 148
                                         +++  +++ v++ k +k+ ++iE+++lrD+++n++ +++r++ lq+r+qk+ie+ P+ +L++  ++++++ a  +
  gene1624|gene1624|rna1624|rna1624 407 LTSTPSTRNDVFMTKIIKNARHIELQMLRDNHNNTVLLGTRDCTLQRRHQKIIEEGPA-MLSPTMYERMKRCAEVL 481
                                        233455799************************************************9.69*************** PP

                                        HHHHT-EEEEEEEEEEETTTTEEEEEEEESS--CCHHHHHHHHS--HHHHHHHHHTT-- CS
                        CPSase_L_D2 149 vrevgvvgagtveflldpkskeyyviEvNtRlsvesalaekaTGldlvkeaakialgek 207
                                        +++ g+vg +tvefl+ +    +y++EvNtR++ve++++e   G+++ + ++ +a+ ++
  gene1624|gene1624|rna1624|rna1624 482 LHDAGYVGVATVEFLVAR--PYFYFLEVNTRIQVEHPVTEFNAGVNIPELQLGVAMDKN 538
                                        ****************96..99******************************9998765 PP

>> Biotin_carb_N  Biotin carboxylase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.6   0.0   4.4e-19   1.6e-15       2     110 .]       5     108 ..       4     108 .. 0.91

  Alignments for each domain:
  == domain 1  score: 57.6 bits;  conditional E-value: 4.4e-19
                                        --EEEE---HHHHHHHHHHHHHTT-EEEEEEEGGGTTSH..HHHHSSEEEEEESSTTCCGGG-HHHHHHHHHHTT- CS
                      Biotin_carb_N   2 ikkvlianrGeiAvriiravrelgietvavyseedansl..hvreadeavelgpasasesYlniekivkaakesga 75 
                                        ++k+lian++ +A+++i +++  +i+++ +++++d +s   +v++ d++v +        Y  +++i++aa   + 
  gene1624|gene1624|rna1624|rna1624   5 TTKILIANNSLAATKFIISLTAHNITFLGMVTTHDLHSNqlYVTYLDRYVIVR------DY-GVDEILRAAAYFQP 73 
                                        579*****************************997655433899999999995......45.69************ PP

                                        SEEE--SSTTTT-HHHHHHHHHTT-EESSS-HHHH CS
                      Biotin_carb_N  76 davhpGyGflsEnaefaeaveeagivfiGPsaeal 110
                                        d v+pG+G+ sEn  ++ +++++g  fiGP+++a+
  gene1624|gene1624|rna1624|rna1624  74 DYVWPGWGHSSENYVLPMMLRQHGYQFIGPDEHAM 108
                                        ********************************998 PP

>> Biotin_carb_C  Biotin carboxylase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.1       1.8   6.4e+03      74     107 ..      19      51 ..       7      52 .. 0.68
   2 !   47.8   0.0   3.6e-16   1.3e-12       2     107 ..     612     713 ..     611     714 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1.8
                                        T-EEESS-BSHHHHHHHHH-HHHHHT---TTTCC CS
                      Biotin_carb_C  74 elrieGvktnieflrailedeefakgeldtkfle 107
                                        ++ i+  ++ni fl  ++ ++++++++l +++l+
  gene1624|gene1624|rna1624|rna1624  19 KFIISLTAHNITFLGMVT-THDLHSNQLYVTYLD 51 
                                        556777788999987666.456677777777776 PP

  == domain 2  score: 47.8 bits;  conditional E-value: 3.6e-16
                                        EEEESEETTTTTEE--CE-SEEE---STTEEEEE---TT-EE-TTS-SEEEEEEEEESSHHHHHHHHHHHHHT-EE CS
                      Biotin_carb_C   2 aRinaEdpeknflpssGkvtelelpegpgvRvdsgveegsevspyyDsllaKlivhgetreealarlrraLaelri 77 
                                        aRi+aEd   +f p++G+v+   lp  p++  + +v +g +++++ Ds +++++++g++r+ea+a+l +aL +++i
  gene1624|gene1624|rna1624|rna1624 612 ARITAEDC--QFNPQTGRVSVAYLP-TPNTLAYFSVLNG-QITEQNDSQFGHVFAYGRHRKEAIANLITALMNIKI 683
                                        8******5..69*************.6666677777766.799999****************************** PP

                                        ESS-BSHHHHHHHHH-HHHHHT---TTTCC CS
                      Biotin_carb_C  78 eGvktnieflrailedeefakgeldtkfle 107
                                        +G+ + ++ + +il+++ fa+ ++ t+ le
  gene1624|gene1624|rna1624|rna1624 684 TGIDSPVPRVLDILRSRFFADYDFYTDTLE 713
                                        ***************************998 PP

>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.8   0.0    0.0038        13       3      55 ..     113     169 ..     111     172 .. 0.74
   2 !   10.1   0.0   0.00017      0.62     117     159 ..     467     512 ..     400     514 .. 0.70

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0038
                                        SHHHHHHHHTTT.S--.-.......-EESS--SSSEEEEESS-------B--SS--T CS
                        ATP-grasp_3   3 dKlktykkLkeagvkv.P...tkleaeeleeeekklvvKprdGaggesvrvveekee 55 
                                        dK+ + ++ + +gv++ P   ++ e  ++ ++  ++ +K +d++gg+++ vve +e+
  gene1624|gene1624|rna1624|rna1624 113 DKIMSNRFAESRGVPCiPyttDEDEFVRFYRAHAPVLIKSSDSGGGKGIEVVETEEQ 169
                                        7888888888888886464333334444556699******************99977 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00017
                                        HHHHHHHHHHHHTTSTT--EEEE...EEEEESS.SEEEEEEESS-- CS
                        ATP-grasp_3 117 keevvelaeevvekleglaGyvG...vDlvlkdeepyviEvNPRlt 159
                                        +  ++e +++  e l   aGyvG   v+++++    y++EvN R++
  gene1624|gene1624|rna1624|rna1624 467 SPTMYERMKRCAEVLLHDAGYVGvatVEFLVARPYFYFLEVNTRIQ 512
                                        34455555555555555555555111677799999*********98 PP

>> ATPgrasp_Ter  ATP-grasp in the biosynthetic pathway with Ter operon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   2.4e-05     0.086      55     117 ..     480     543 ..     456     554 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.4e-05
                       ATPgrasp_Ter  55 rlaeefgldglvnvQvrededgpkLLEiNpRasGGlgys.alaGvnlpylalklllgleteeve 117
                                         l +  g  g+  v +   +   + LE+N+R++    ++ + aGvn+p+l l  ++++++   +
  gene1624|gene1624|rna1624|rna1624 480 VLLHDAGYVGVATVEFLVARPYFYFLEVNTRIQVEHPVTeFNAGVNIPELQLGVAMDKNMGWLK 543
                                        5555566666666667777777899*********998873568*********999997555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (822 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       492  (0.0274416); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.60u 0.25s 00:00:00.85 Elapsed: 00:00:00.39
# Mc/sec: 6269.39
//
Query:       gene1625|gene1625|rna1625|rna1625  [L=317]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.9e-44  152.1   0.7    2.2e-44  151.9   0.7    1.0  1  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
    4.6e-20   72.1   0.3    6.8e-17   61.7   0.0    2.1  2  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase
    3.4e-12   46.7   4.5    2.9e-11   43.7   0.8    2.5  3  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
    0.00021   20.5   0.3          5    6.1   0.0    4.0  4  GIDA           Glucose inhibited division protein A
    0.00023   20.5   2.8    0.00039   19.8   0.2    2.4  3  Thi4           Thi4 family
    0.00082   18.6   0.1       0.42    9.7   0.0    2.5  2  K_oxygenase    L-lysine 6-monooxygenase (NADPH-requiring)
     0.0046   16.1   1.3      0.035   13.2   0.2    2.8  4  FAD_binding_2  FAD binding domain
     0.0054   15.5   0.6        2.5    6.7   0.1    3.2  4  HI0933_like    HI0933-like protein
     0.0073   16.5   0.0      0.019   15.2   0.0    1.7  1  NAD_binding_8  NAD(P)-binding Rossmann-like domain
     0.0079   15.8   2.0        0.1   12.2   0.7    2.3  2  DAO            FAD dependent oxidoreductase
  ------ inclusion threshold ------
       0.11   11.7   0.3       0.27   10.5   0.1    1.7  2  FAD_binding_3  FAD binding domain


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  151.9   0.7   1.3e-47   2.2e-44       1     294 []       7     299 ..       7     299 .. 0.86

  Alignments for each domain:
  == domain 1  score: 151.9 bits;  conditional E-value: 1.3e-47
                                        CSEEEE--SHHHHHHHHHHHHHTS-EEEEE...TTHCHHHCSHHHHCHHHHHHHHHHHHH.........HHHHCHH CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxx.........xxxxxxx RF
                        Pyr_redox_2   1 kdvvviGgGpAGlaaaltlaqagakvtlve...legtclnggcllskallgvaedaeias.........evvkkln 64 
                                        +dv++iG+GpA+++aal+l+   +kv+++e    +++ ++g+   ++++ ++++ ++ ++         ++v++ n
  gene1625|gene1625|rna1625|rna1625   7 YDVIIIGSGPAAYSAALYLQD--YKVLVLEggiVGNNGPGGQLTTTTVVDNYPGYPNGITgpelmmimkKQVESKN 80 
                                        69*****************99..88888877899*************************9*999977754433333 PP

                                        HHCCCCHCCTCEEEEESCEEEEETEEECTCEEEEEESEEEE---EEE-BCTCTTC.TTBEECCSECHHHHHHCCSS CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        Pyr_redox_2  65 qgielllgeevvkidpgkkkvklekkkegdeekiaydklvlAtGssprdlgipGvaenvgklvrtldsaealklkl 140
                                           ++  +++++++   ++++    +++    ++ + ++v+AtG+++++l +pG a+ ++k+++t++ +++     
  gene1625|gene1625|rna1625|rna1625  81 LC-TKEETATALSV-SSEGRFFNVCTRQ---GDYVAYSIVIATGAQAKRLCVPGTATFWQKGISTCAVCDGHLFLD 151
                                        22.22333245555.4446888855554...46999*********************************9975554 PP

                                        -TSEEEEES-SHHHHHHHHHHHHHT-EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTE.. CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
                        Pyr_redox_2 141 lpkrivvvGgGyiGvElAaalaklgkevtlveardrllraldkelsaaleealekeGvevklgtsvkeidgnge.. 214
                                            ++v+GgG  ++E + +la ++ +v+l+++rd++      + +++l+++ +++++e+   +  +e++g++   
  gene1625|gene1625|rna1625|rna1625 152 E--VVAVIGGGDSAMEESLYLAGIARKVYLIHRRDTFR-----SRKDMLMRVEKNKKIEIIRSSILVEAKGEKLls 220
                                        4..59********************************8.....5688888888999*****999999999999888 PP

                                        ..EEE.EEETTSCEEEESEEEE-S-EEES-HHCSHCCT-EEEETTEEE--TTSBESSTTEEE-GGGCTECCSS--H CS
                                        ..xxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        Pyr_redox_2 215 ..kle.vvledgeeidadlvvvavGvrpstelleeklglelderggivvdeflrtnvpgiyaiGDvaggkggpela 287
                                           ++ vv+++  e+++d +++avG  p+t+++ +k  +e+ + g+i++d+ +rt+ +g++a+GDv+  ++++++a
  gene1625|gene1625|rna1625|rna1625 221 siVVKnVVNDELCELAVDGLFFAVGHLPNTDFI-KKGFVEM-DEGYIKTDSLMRTSRKGVFACGDVQ--DRIYRQA 292
                                        76666788888888*******************.*******.99***********************..9****** PP

                                        HHHHHHH CS
                                        xxxxxxx RF
                        Pyr_redox_2 288 qaAvqqG 294
                                         +A ++G
  gene1625|gene1625|rna1625|rna1625 293 NTAAASG 299
                                        ***9887 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.2   0.00055      0.89       1      34 [.      10      40 ..      10      43 .. 0.93
   2 !   61.7   0.0   4.2e-20   6.8e-17      83     305 .]      68     282 ..      46     282 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00055
                        Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkgnign 34
                                       iIiG GPa  +aa+ l++ ++   l+lE g +gn
  gene1625|gene1625|rna1625|rna1625 10 IIIGSGPAAYSAALYLQDYKV---LVLEGGIVGN 40
                                       8*****************998...8****99987 PP

  == domain 2  score: 61.7 bits;  conditional E-value: 4.2e-20
                        Pyr_redox_3  83 aleYlrevaksfelpiklfe.eVesvkkedegfevetsketyeAkkviiAtGefdkPnklnipGeek...lvkhys 154
                                        ++  +++ ++s++l  k+++ +  sv++e++ f+v t++++y A +++iAtG   + ++l +pG      + + + 
  gene1625|gene1625|rna1625|rna1625  68 LMMIMKKQVESKNLCTKEETaTALSVSSEGRFFNVCTRQGDYVAYSIVIATGA--QAKRLCVPGTATfwqKGISTC 141
                                        5555667778888877776614689***************************9..89999****995444788999 PP

                        Pyr_redox_3 155 kvkefhkyagqkvvViGgknSavDaAlelvrkgaeVtvvtrgseiekeesdpsyslkpdienrleelvkeekikvl 230
                                         v + h + ++ v+ViGg++Sa++  l l+    +V +++r+++ +++ +d+ ++++   + ++ +  ++  +++ 
  gene1625|gene1625|rna1625|rna1625 142 AVCDGHLFLDEVVAVIGGGDSAMEESLYLAGIARKVYLIHRRDTFRSR-KDMLMRVEKNKKIEIIR--SSILVEAK 214
                                        999***************************************977776.46666665544444433..33357788 PP

                        Pyr_redox_3 231 fnaevkeikekeeeykvktedgkkvevkddvvlatGykpdlsflkkslfeldedgrpvlteeteetnvpglflaG 305
                                         ++ + +i  k++   v+  +  ++ v d  ++a+G  p+++f+kk  +e  ++g+++ t++ + t  +g+f +G
  gene1625|gene1625|rna1625|rna1625 215 GEKLLSSIVVKNV---VND-ELCELAV-DGLFFAVGHLPNTDFIKKGFVEM-DEGYIK-TDSLMRTSRKGVFACG 282
                                        8877888776532...343.3356666.78899************766666.666665.678899*******998 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.1     0.049        80       2      22 ..       9      29 ..       8      37 .. 0.89
   2 ?   -2.6   0.0       5.3   8.7e+03      37      54 ..      63      80 ..      48      96 .. 0.68
   3 !   43.7   0.8   1.8e-14   2.9e-11       2      79 ..     154     225 ..     153     231 .. 0.93

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.049
                                       EEEECSSHHHHHHHHHHHHTT CS
                          Pyr_redox  2 vvvvGgGyiglElAgalaelg 22
                                       v+++G+G  +  +A +l++++
  gene1625|gene1625|rna1625|rna1625  9 VIIIGSGPAAYSAALYLQDYK 29
                                       89***************9987 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 5.3
                                       TSSHHHHHHHHHHHHHTT CS
                          Pyr_redox 37 llDeeaskilqeklekng 54
                                         ++e+  i+++++e ++
  gene1625|gene1625|rna1625|rna1625 63 ITGPELMMIMKKQVESKN 80
                                       556777777888877775 PP

  == domain 3  score: 43.7 bits;  conditional E-value: 1.8e-14
                                        EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHT.TEEEECSEEEEEEEEETTSEEEE CS
                          Pyr_redox   2 vvvvGgGyiglElAgalaelgkkVtvversdkllrllDeeaskilqeklekn.gievllntkveeiegsedgvesv 76 
                                        v+v+GgG++++E+  +la ++ kV++++r+d+++       +k +  ++ekn +ie++ ++ ++e +g++  ++s+
  gene1625|gene1625|rna1625|rna1625 154 VAVIGGGDSAMEESLYLAGIARKVYLIHRRDTFR------SRKDMLMRVEKNkKIEIIRSSILVEAKGEKL-LSSI 222
                                        79********************************......*********9999**************8876.7888 PP

                                        EEE CS
                          Pyr_redox  77 klk 79 
                                        ++k
  gene1625|gene1625|rna1625|rna1625 223 VVK 225
                                        876 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0     0.014        22       1      21 [.       8      28 ..       8      35 .. 0.86
   2 !    6.1   0.0     0.003         5     101     151 ..      72     121 ..      67     140 .. 0.81
   3 ?    3.9   0.0     0.015        24       2      30 ..     154     188 ..     153     232 .. 0.79
   4 ?    1.7   0.0     0.068   1.1e+02     347     390 ..     266     312 ..     236     314 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.014
                                       CEEEE-SSHHHHHHHHHHHHT CS
                               GIDA  1 dviViGgGhAGceAAlaaarl 21
                                       dvi+iG G A + AAl +   
  gene1625|gene1625|rna1625|rna1625  8 DVIIIGSGPAAYSAALYLQDY 28
                                       8**************998765 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.003
                                        HHHHHHTSTTEEEEES-EEEEEECT.TEEEEEEETTS-EEEECEEEE--TT- CS
                               GIDA 101 vteklenepnleiieeeveelivee.kkvkgvvtedgetikakavviatGtf 151
                                        +++++e+ +nl   ee+++ l+v++ ++   v+t++g ++ a ++viatG+ 
  gene1625|gene1625|rna1625|rna1625  72 MKKQVES-KNLCTKEETATALSVSSeGRFFNVCTRQGDYV-AYSIVIATGAQ 121
                                        8899999.99999********9976689999999999877.678999***93 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.015
                                        EEEE-SSHHHHHHHHHHHHTT--EEEE......ES CS
                               GIDA   2 viViGgGhAGceAAlaaarlGakvlLi......th 30 
                                        v ViGgG + +e +l +a    kv Li        
  gene1625|gene1625|rna1625|rna1625 154 VAVIGGGDSAMEESLYLAGIARKVYLIhrrdtfRS 188
                                        89************************955555444 PP

  == domain 4  score: 1.7 bits;  conditional E-value: 0.068
                                        -T.TSBBSSSBTEEE-CGGGTB-SH...HHHHHHHHHHHHHHHHHHCT CS
                               GIDA 347 ln.tLetkkvkgLflAGqinGteGY...eEaaaqGllAGinaarkakg 390
                                        ++ +L   ++kg+f++G++     Y     aaa+G++A++ +  +++g
  gene1625|gene1625|rna1625|rna1625 266 KTdSLMRTSRKGVFACGDVQDRI-YrqaNTAAASGCIAALSVREYLNG 312
                                        44466667799999999999885.511145788******999988876 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.2   2.4e-07   0.00039      14      70 ..       3      54 ..       1      58 [. 0.86
   2 ?   -0.4   0.0      0.35   5.7e+02      17      49 ..     151     182 ..     138     187 .. 0.79
   3 ?   -1.7   0.1      0.88   1.4e+03     110     125 ..     213     228 ..     193     242 .. 0.54

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 2.4e-07
                                       HHTEEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TTTTTTSTTBSEEEEE CS
                               Thi4 14 kyaesDvvivGaGssGLtaayylakkpdlkvailersvspGGGawlGGqlfsaivvr 70
                                       + ++ Dv+i+G+G++  +aa yl      kv++le  +   G  + GGql ++ vv 
  gene1625|gene1625|rna1625|rna1625  3 ECMVYDVIIIGSGPAAYSAALYLQD---YKVLVLEGGI--VGNNGPGGQLTTTTVVD 54
                                       67899******************75...5******976..57788999999988886 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.35
                                        EEEEEEE--SHHHHHHHHHHHHCTTS-EEEEES CS
                               Thi4  17 esDvvivGaGssGLtaayylakkpdlkvailer 49 
                                        +  v+++G+G s +  + yla     kv ++ r
  gene1625|gene1625|rna1625|rna1625 151 DEVVAVIGGGDSAMEESLYLAGI-ARKVYLIHR 182
                                        5568899****999999999977.667777766 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 0.88
                                        STTEEEEESEEEEEEE CS
                               Thi4 110 lanvkllnavaveDli 125
                                          + kll +++v +++
  gene1625|gene1625|rna1625|rna1625 213 AKGEKLLSSIVVKNVV 228
                                        2233344444443333 PP

>> K_oxygenase  L-lysine 6-monooxygenase (NADPH-requiring)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.4   0.0    0.0027       4.3       2      25 ..       6      29 ..       5      35 .. 0.87
   2 !    9.7   0.0   0.00026      0.42     131     230 ..      98     188 ..      73     200 .. 0.66

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0027
                        K_oxygenase  2 ilDligiGiGpsnLsLailleevk 25
                                       ++D+i+iG Gp++ s a+ l++ k
  gene1625|gene1625|rna1625|rna1625  6 VYDVIIIGSGPAAYSAALYLQDYK 29
                                       79***************9999876 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00026
                        K_oxygenase 131 elltveskdaegeeeelearnlvlgvGtepk...iPevleklegkervvHsseylerkeellakkriaVvGsGqSa 203
                                        + ++v +     ++  + a ++v+++G ++k   +P +++  ++   +   +       +l   + +aV+G+G Sa
  gene1625|gene1625|rna1625|rna1625  98 RFFNVCT-----RQGDYVAYSIVIATGAQAKrlcVPGTATFWQK--GISTCAVCD---GHLFLDEVVAVIGGGDSA 163
                                        3555555.....56789999999999977643337877775552..232222222...23566789********** PP

                        K_oxygenase 204 aeifedllrrqkkvelklvtrsealep 230
                                         e    l+  ++  ++ l+ r++ ++ 
  gene1625|gene1625|rna1625|rna1625 164 MEESLYLAGIAR--KVYLIHRRDTFRS 188
                                        *97777766655..7788888877765 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.2   2.1e-05     0.035       1      30 [.       8      35 ..       8      41 .. 0.86
   2 ?   -1.9   0.0      0.82   1.3e+03     139     201 ..      64     120 ..      44     146 .. 0.56
   3 ?   -2.6   0.0       1.4   2.2e+03       2      36 ..     154     188 ..     154     190 .. 0.83
   4 ?   -0.2   0.0      0.25     4e+02     376     413 ..     265     296 ..     263     304 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.1e-05
                                       SEEEE--SHHHHHHHHHHHHTTT-EEEEES CS
                      FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvek 30
                                       Dvi+iGsG A ++AAl +  +  kv+v+e 
  gene1625|gene1625|rna1625|rna1625  8 DVIIIGSGPAAYSAALYL--QDYKVLVLEG 35
                                       9***************66..6778888876 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.82
                                        HHHHHHHHHHHHHHTCTEEEEESEEEEEEEECTTEEEEEEEEETTTTCEE.......EEEESEEEE---- CS
                      FAD_binding_2 139 tghallarlvesarkagvdfqerteadeLivedgrvtGavvenpesgrev.......rirakavvlatgG 201
                                        tg++l+  + +++++ +           L ++++ +t   v+  ++gr +        ++a  +v+atg+
  gene1625|gene1625|rna1625|rna1625  64 TGPELMMIMKKQVESKN-----------LCTKEETATALSVS--SEGRFFnvctrqgDYVAYSIVIATGA 120
                                        55555555555554444...........33333333333333..22222222222224555666666665 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 1.4
                                        EEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGS CS
                      FAD_binding_2   2 viViGsGlAGLaAAleaaeaGlkvavvekeqefgg 36 
                                        v ViG+G + +  +l +a   +kv ++   + f++
  gene1625|gene1625|rna1625|rna1625 154 VAVIGGGDSAMEESLYLAGIARKVYLIHRRDTFRS 188
                                        78*****9999999999998888988887777665 PP

  == domain 4  score: -0.2 bits;  conditional E-value: 0.25
                                        EEBETTSBESTTEEESSBTEEE-STCEESSSSTTS--T CS
                      FAD_binding_2 376 vetdengrvldadgqpipGLYAaGevaaggvhganrlg 413
                                        ++td  +r+        +G +A+G v   ++  an  +
  gene1625|gene1625|rna1625|rna1625 265 IKTDSLMRT------SRKGVFACGDVQDRIYRQANTAA 296
                                        567777777......889******99988888777655 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.7   0.1    0.0015       2.5       1      31 [.       7      35 ..       7      40 .. 0.87
   2 !    4.5   0.0     0.007        11     110     166 ..      67     122 ..      57     134 .. 0.83
   3 ?    0.0   0.0      0.17   2.7e+02       3      33 ..     154     184 ..     152     190 .. 0.86
   4 ?   -2.9   0.0       1.3   2.1e+03     365     386 ..     265     286 ..     249     286 .. 0.70

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0015
                                       -SEEEE--SHHHHHHHHHHHHTT--EEEE-S CS
                        HI0933_like  1 kdviviGgGaAGlmaAisaakrgkrVlllek 31
                                       +dvi+iG G+A   aA+ +  ++ +Vl+le 
  gene1625|gene1625|rna1625|rna1625  7 YDVIIIGSGPAAYSAALYL--QDYKVLVLEG 35
                                       59**********9999998..7788999886 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.007
                                        HHHHHHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE----SS CS
                        HI0933_like 110 divdallkelkeagvklrletevksvekeedgkfrvktkseeeleadklvlAtGGlS 166
                                        +++ +++k++++++   + et+ +   ++e+++f+v t  ++ + a ++v+AtG ++
  gene1625|gene1625|rna1625|rna1625  67 ELMMIMKKQVESKNLCTKEETATALSVSSEGRFFNVCT-RQGDYVAYSIVIATGAQA 122
                                        66778888999999888888877766678888899999.999************875 PP

  == domain 3  score: 0.0 bits;  conditional E-value: 0.17
                                        EEEE--SHHHHHHHHHHHHTT--EEEE-SSS CS
                        HI0933_like   3 viviGgGaAGlmaAisaakrgkrVlllekak 33 
                                        v+viGgG + +  ++ +a   ++V l+ + +
  gene1625|gene1625|rna1625|rna1625 154 VAVIGGGDSAMEESLYLAGIARKVYLIHRRD 184
                                        89*********99999999999999998766 PP

  == domain 4  score: -2.9 bits;  conditional E-value: 1.3
                                        B-TTT-BBTTSTTEEE-GGGBS CS
                        HI0933_like 365 vssktmeskkvpgLffaGEvlD 386
                                        ++ + ++  + +g+f +G v D
  gene1625|gene1625|rna1625|rna1625 265 IKTDSLMRTSRKGVFACGDVQD 286
                                        677778889999******9965 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   1.2e-05     0.019       1      41 [.      11      54 ..      11      74 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.2e-05
                                       EE--SHHHHHHHHHHHCCTEEEEEE-SS....SSSSGGG-EECE.T CS
                      NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekr....drlGGraasyev.p 41
                                       I+G+G ++ +aA +L++  ++vl+le +    +++GG++++ +v +
  gene1625|gene1625|rna1625|rna1625 11 IIGSGPAAYSAALYLQD--YKVLVLEGGivgnNGPGGQLTTTTVvD 54
                                       9***************8..7******85555489*****9998763 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.7   6.1e-05       0.1       1      33 [.       8      39 ..       8      62 .. 0.86
   2 ?    2.4   0.0     0.057        93     168     206 ..      87     125 ..      58     138 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 6.1e-05
                                       EEEEECTSHHHHHHHHHHHHTTEEEEESSSSTT CS
                                DAO  1 dvviiGGGiiGlstAyeLarrgVtllekgdiag 33
                                       dv+iiG+G +  s+A++L+  +V++le g i+g
  gene1625|gene1625|rna1625|rna1625  8 DVIIIGSGPAAYSAALYLQDYKVLVLEGG-IVG 39
                                       9*****************6667*****99.888 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.057
                                        CEEEEEEEE.TCEEEEEEECT.EEEEEEEEEEE--GGGHH.H CS
                                DAO 168 evtgleeed.gkvwgverttp.gendaadavVnaaGawsd.l 206
                                        ++t+l+  + g+  +v   t+ g  +a   +V+a+Ga+++ l
  gene1625|gene1625|rna1625|rna1625  87 TATALSVSSeGRFFNV--CTRqGDYVA-YSIVIATGAQAKrL 125
                                        4555544223777777..676686533.56********8744 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1   0.00016      0.27       2      30 ..       7      33 ..       6      36 .. 0.88
   2 ?   -3.3   0.0       2.4   3.9e+03       4      35 ..     154     185 ..     153     188 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00016
                                       EEEEEE--SHHHHHHHHHHHHTTHHEEEE CS
                      FAD_binding_3  2 tdVlIVGaGpaGlmlallLseaGvrvvlv 30
                                       +dV+I+G+Gpa  ++al L+ +  +v+++
  gene1625|gene1625|rna1625|rna1625  7 YDVIIIGSGPAAYSAALYLQDY--KVLVL 33
                                       69******************99..66666 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 2.4
                                        EEEE--SHHHHHHHHHHHHTTHHEEEEESSSS CS
                      FAD_binding_3   4 VlIVGaGpaGlmlallLseaGvrvvlvekrst 35 
                                        V+++G+G + +  +l L+    +v l+ +r+t
  gene1625|gene1625|rna1625|rna1625 154 VAVIGGGDSAMEESLYLAGIARKVYLIHRRDT 185
                                        78999998887777776655445777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (317 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       530  (0.029561); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 2072.20
//
Query:       gene1626|gene1626|rna1626|rna1626  [L=203]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-15   57.1   0.3    3.9e-15   55.5   0.1    1.9  2  XPA_C          XPA protein C-terminus
  ------ inclusion threshold ------
      0.045   14.0   0.6      0.092   12.9   0.3    1.7  2  Atg8           Autophagy protein Atg8 ubiquitin like
        6.3    6.6  12.1       0.18   11.6   3.8    2.6  2  A2L_zn_ribbon  A2L zinc ribbon domain


Domain annotation for each model (and alignments):
>> XPA_C  XPA protein C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.5   0.1   6.5e-19   3.9e-15       1      51 []      77     124 ..      77     124 .. 0.95
   2 ?   -1.6   0.0      0.47   2.8e+03      27      40 ..     170     183 ..     162     184 .. 0.67

  Alignments for each domain:
  == domain 1  score: 55.5 bits;  conditional E-value: 6.5e-19
                              XPA_C   1 kysLiTkTeakedYLLtdedLkdrelLkflkkkNPhnstwgdMkLYlklqV 51 
                                        k++Li kT  +++YLL +edLkd    k+l+++NP+++tw+dM+L+  +++
  gene1626|gene1626|rna1626|rna1626  77 KLRLINKTAIIKEYLLGNEDLKD---VKCLTRPNPKKGTWSDMQLFQLEEI 124
                                        789********************...********************87765 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.47
                              XPA_C  27 LkflkkkNPhnstw 40 
                                        ++   k N h+ t+
  gene1626|gene1626|rna1626|rna1626 170 IEDRMKINTHKHTF 183
                                        55556889999987 PP

>> Atg8  Autophagy protein Atg8 ubiquitin like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0      0.73   4.4e+03      55      55 ..      56      56 ..      26      83 .. 0.60
   2 ?   12.9   0.3   1.5e-05     0.092       4      72 ..     122     190 ..     120     200 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.73
                                       H CS
                               Atg8 55 r 55
                                       r
  gene1626|gene1626|rna1626|rna1626 56 R 56
                                       3 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 1.5e-05
                                        HHHHHHHHHSTTEEEEEEEE-TTSSS---S-SEEEEETTSBHHHHHHHHHHHTT--TTS-EEEEETTE- CS
                               Atg8   4 kesekirekypdriPvivekaekeklpeldkkkylvPedltvgqlvliirkrlqlepekalfllvnetl 72 
                                        +e e i+++    i  i +  e+ k   ldkkk  + + +   +  ++i  r++++++k  f+lv+ + 
  gene1626|gene1626|rna1626|rna1626 122 EEIETIAKRKWGSIENIENEKERRKELLLDKKKKKIRKRVKELRKCTLIEDRMKINTHKHTFILVDGVC 190
                                        5677788888888888877778888889*************99**********************9865 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   3.8   2.9e-05      0.18       3      30 ..      46      76 ..      45      77 .. 0.83
   2 ?   -1.7   1.2      0.42   2.5e+03       7      28 ..     191     195 ..     188     200 .. 0.57

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2.9e-05
                      A2L_zn_ribbon  3 lkvCsvCggngi...lnseqgylvCieCgas 30
                                       +k C++C+++ i   ++++ g+ vC+eC ++
  gene1626|gene1626|rna1626|rna1626 46 NKLCKYCDNPRIdfeVQQAFGISVCNECKYT 76
                                       789******86544489***********875 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.42
                      A2L_zn_ribbon   7 svCggngilnseqgylvCieCg 28 
                                        + C                eCg
  gene1626|gene1626|rna1626|rna1626 191 K-C----------------ECG 195
                                        3.3................333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1712  (0.0954878); expected 358.6 (0.02)
Passed bias filter:                      508  (0.028334); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1501.38
//
Query:       gene1627|gene1627|rna1627|rna1627  [L=202]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.7e-50  171.3   0.2    2.1e-50  171.0   0.2    1.1  1  CK_II_beta  Casein kinase II regulatory subunit


Domain annotation for each model (and alignments):
>> CK_II_beta  Casein kinase II regulatory subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  171.0   0.2   1.2e-54   2.1e-50       1     182 []      23     194 ..      23     194 .. 0.97

  Alignments for each domain:
  == domain 1  score: 171.0 bits;  conditional E-value: 1.2e-54
                         CK_II_beta   1 sWiswflslkgneyfvevdedfiedkfnltgLseevpnykealelildveeeeeleeseksevessaelLYgliHa 76 
                                        +Wi++f s+ +n+ ++ ++++f++dkfnl+gL + ++n ++ +++i +         +  s  +++++lLY l+H+
  gene1627|gene1627|rna1627|rna1627  23 TWITRFHSRAENSGLIVIHDSFLQDKFNLVGLMRYIANLSRSFDVIKN---------KMPSRNKKEETLLYYLVHQ 89 
                                        6*********************************************99.........45566778899******** PP

                         CK_II_beta  77 ryiltkkglakmlekykkkefgrCprvlCekqkvLPvGlsdkpgektvklyCpkCedvYspkssrsrsidGafFGt 152
                                        ryilt++g++kmle++ ++ +g C r+ Ce+ +++P+Gls++p+ ++vklyC +C++v+ p++s s ++dG+ FG+
  gene1627|gene1627|rna1627|rna1627  90 RYILTNTGMEKMLERVIQHFYGDCRRMGCEDIPLIPLGLSNNPKISSVKLYCYNCNNVFDPDNSLS-ELDGCSFGS 164
                                        ***************************************************************887.********* PP

                         CK_II_beta 153 tfphlllltypelepkkskekyepriyGfk 182
                                        +f+hll+lt++e  +kk+  +y pri+Gf+
  gene1627|gene1627|rna1627|rna1627 165 SFAHLLILTHKENFQKKKYGSYIPRIFGFR 194
                                        *****************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       686  (0.038262); expected 358.6 (0.02)
Passed bias filter:                      524  (0.0292264); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1461.26
//
Query:       gene1628|gene1628|rna1628|rna1628  [L=304]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.032   14.6   0.7      0.066   13.7   0.1    1.8  2  BAG       BAG domain


Domain annotation for each model (and alignments):
>> BAG  BAG domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   3.7e-06     0.066       3      49 ..     128     183 ..     127     186 .. 0.80
   2 ?   -3.4   0.1      0.77   1.4e+04      13      20 ..     284     291 ..     273     299 .. 0.52

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.7e-06
                                        HHHHHHHHH.HHHHHHHHHHH.........HHH..H...HHHHHHHHHHHHHTCEES CS
                                BAG   3 eilkevetllepeveafektv.......kkekeyly...lsElLlklLlkLDsieie 49 
                                        ++++ v++l e++v++ ++++        ++k+y +   + E+L k+ l LD ie +
  gene1628|gene1628|rna1628|rna1628 128 NVSAYVRKL-EKKVTTGIESIlkvifrrSVKKKYTFsneFIEMLKKEVLVLDRIEFN 183
                                        577788888.99988888888988899844666655679***************984 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 0.77
                                        HHHHHHHH CS
                                BAG  13 epeveafe 20 
                                        ++ v+++e
  gene1628|gene1628|rna1628|rna1628 284 KQLVREYE 291
                                        23333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (304 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       997  (0.0556082); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2160.99
//
Query:       gene1629|gene1629|rna1629|rna1629  [L=41]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (41 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       237  (0.0132188); expected 358.6 (0.02)
Passed bias filter:                      193  (0.0107647); expected 358.6 (0.02)
Passed Vit filter:                         7  (0.000390429); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.29u 0.24s 00:00:00.53 Elapsed: 00:00:00.36
# Mc/sec: 337.15
//
Query:       gene163|gene163|rna163|rna163  [L=347]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.5e-14   54.3   0.3    4.2e-14   53.5   0.3    1.3  1  Tau95       RNA polymerase III transcription factor (TF)IIIC 
  ------ inclusion threshold ------
      0.041   14.0   0.3       0.56   10.4   0.3    2.4  1  TFIIF_beta  TFIIF, beta subunit HTH domain


Domain annotation for each model (and alignments):
>> Tau95  RNA polymerase III transcription factor (TF)IIIC subunit HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.5   0.3   4.7e-18   4.2e-14      29     138 ..     134     250 ..      98     252 .. 0.74

  Alignments for each domain:
  == domain 1  score: 53.5 bits;  conditional E-value: 4.7e-18
                                    XXXXXXXXXX-----EE-.--S--TT-----......HHHHHHHHHHHHHHHH-SEEEHHHHHTTS-GGGT...TTHHHH CS
                          Tau95  29 kklvntsksrkkktivlk.Ptepeeelvkelkek...kelqkaveelkklfeerPiwtrraLknklekker...kklkla 101
                                    k++ n++k++k+++        +++elv++lk+    +e ++ ++e++ lfe + i   r +   +  + +    k+k++
  gene163|gene163|rna163|rna163 134 KNVTNSRKNKKRQREKHVlAGVERNELVNKLKKLygdEEYDEILKEVESLFETHKILRIRRFCRLIVHQLKyplVKIKKF 213
                                    444444444443333333355556666666665567688888899************988877766666656777***** PP

                                    GGGTEEEE-SSTTTTEEEETT--TTS-GGGGGG-EEE CS
                          Tau95 102 lpyvaYyfksGPWrdlwvrfGyDPrkdpeariYQtld 138
                                    lp+va+  + GPWr++w+++ yDPr++ ++   Q++ 
  gene163|gene163|rna163|rna163 214 LPLVAFFQRAGPWRRSWIKLNYDPREHFSSYRHQVII 250
                                    ******************************9999886 PP

>> TFIIF_beta  TFIIF, beta subunit HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.3   6.3e-05      0.56       6      58 ..     174     230 ..     153     235 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 6.3e-05
                     TFIIF_beta   6 qelldalfelFeeyqYWslkdLkae....trqPeayLkevLeeIAvlhrsGpfknkw 58 
                                    +e+l+++ +lFe ++  +++ +       ++ P + +k  L  +A+++r+Gp+   w
  gene163|gene163|rna163|rna163 174 DEILKEVESLFETHKILRIRRFCRLivhqLKYPLVKIKKFLPLVAFFQRAGPWRRSW 230
                                    57788888888888888888765546666999**********************999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (347 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       708  (0.0394891); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 2253.89
//
Query:       gene1630|gene1630|rna1630|rna1630  [L=43]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (43 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       196  (0.010932); expected 358.6 (0.02)
Passed bias filter:                      174  (0.00970495); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.44
# Mc/sec: 294.85
//
Query:       gene1631|gene1631|rna1631|rna1631  [L=225]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.1e-43  148.7   0.0    1.3e-43  148.4   0.0    1.1  1  UFD1        Ubiquitin fusion degradation protein UFD1
  ------ inclusion threshold ------
      0.039   13.7   0.0       0.07   12.9   0.0    1.4  1  CDC48_2     Cell division protein 48 (CDC48), domain 2


Domain annotation for each model (and alignments):
>> UFD1  Ubiquitin fusion degradation protein UFD1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  148.4   0.0   1.5e-47   1.3e-43       5     173 .]      17     186 ..      13     186 .. 0.95

  Alignments for each domain:
  == domain 1  score: 148.4 bits;  conditional E-value: 1.5e-47
                               UFD1   5 yrcysvsmkaereelekggkiiLPpsaLdeLtrlnieyPmlFelsnkkkkksthagVleFtaeegtvylPewmmen 80 
                                        +r +++++   ++ ++ ggk +LP+ ++++L++l+i  P++Fe+s++++ + +h gVleFta+  ++++Pew++++
  gene1631|gene1631|rna1631|rna1631  17 WRLIPTKY-PPNSPNNFGGKALLPQRVIEDLVNLQIPAPYTFEISHSNRLYVSHTGVLEFTARGEEIVVPEWLYQQ 91 
                                        67788888.6788999*****************************999999************************* PP

                               UFD1  81 lgleegdlveiesvslpkgkfvklqpqsedfldisdpkavLekaLrnfatLtkgdvieikynd.kvyelkvlevkp 155
                                        l++++  lv++++ +l  g+++kl p+++dfl+i+ pk  Lek L n+++Lt gd i +++ +   ++++v +++p
  gene1631|gene1631|rna1631|rna1631  92 LEMDQCGLVTVTYKQLMPGRSIKLLPHTTDFLEIESPKRELEKCLVNYQVLTCGDEIVCSFDEyGAMRFTVNQIEP 167
                                        *************************************************************762579********* PP

                               UFD1 156 es.avsiietdlevdfaeP 173
                                        ++ a++i++tdl v+f +P
  gene1631|gene1631|rna1631|rna1631 168 DDdAIYIVDTDLIVEFLPP 186
                                        988*************988 PP

>> CDC48_2  Cell division protein 48 (CDC48), domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   7.8e-06      0.07      14      53 ..     136     178 ..     126     186 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 7.8e-06
                                        CTT.EEE-TTEEEEECCT.CCCEEEEEEEECCCC.SCEEECTS CS
                            CDC48_2  14 Flg.rpvtkGdlvvfefk.gqeiklvVvstePkg.pvgitetT 53 
                                        + + +++t Gd +v +f   ++++++V  +eP + +  i++t+
  gene1631|gene1631|rna1631|rna1631 136 LVNyQVLTCGDEIVCSFDeYGAMRFTVNQIEPDDdAIYIVDTD 178
                                        555699*******99887789*************644666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (225 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       306  (0.0170673); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1650.22
//
Query:       gene1632|gene1632|rna1632|rna1632  [L=502]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      6e-16   59.3   0.1      6e-16   59.3   0.1    2.6  2  SET       SET domain


Domain annotation for each model (and alignments):
>> SET  SET domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   1.1     0.092   1.6e+03     122     133 ..     217     256 ..      63     326 .. 0.58
   2 !   59.3   0.1   3.3e-20     6e-16       1     168 [.     383     491 ..     383     492 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.092
                                        C............................GTTGGGCEEXS CS
                                        x............................xxxxxxxxxxx RF
                                SET 122 a............................gplarflNHsC 133
                                        +                            +++ + lN sC
  gene1632|gene1632|rna1632|rna1632 217 TpvltnkylyvyqkirknfnfncceltraFNFFSSLNLSC 256
                                        0333333333333333333333444444455555555555 PP

  == domain 2  score: 59.3 bits;  conditional E-value: 3.3e-20
                                        SCEEEESSXBXTTXEEEEEE.ECCEECHHHHHHHHHH......HTEEEEEXGGXXGGSXHHHHHHHTTSSHHHHHH CS
                                        xxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                                SET   1 GrGvfAtedIpkgeficeyp.eeiiltkdeadksele......aylfslpeapknlaftkelakasastllqklak 69 
                                        G+G+f+ +d+ k++f++ey+ e  i+t++ea++++l        ylf+l+                          
  gene1632|gene1632|rna1632|rna1632 383 GYGLFTVDDLSKDDFVIEYVgE--IITNEEAERRGLFyekrklSYLFDLS-------------------------- 430
                                        9*******************77..*************9*****9999998.......................... PP

                                        HHHHHHHHHHHHTHHHHHHHXTTTSXXXHCCCCCHCCCHEEEETEEEEEECCCGTTGGGCEEXSSSSEEEEEEEET CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                                SET  70 dqkqaekedtdaalkasskaesdlnaskpeagafsaiagysidaralksgngagplarflNHsCdpNcnltvqnvl 145
                                                                          s   + +id  a+k  n a    rf+NHs + N+ + ++ v 
  gene1632|gene1632|rna1632|rna1632 431 ---------------NL-----------------SDCTKETID--ATKIANKA----RFINHSKKANLIAKTVQVA 468
                                        ...............11.................233333499..77999999....***********9999988* PP

                                        TSSEEEEEESSXBXTTEEEEEXT CS
                                        xxxxxxxxxxxxxxxxxxxxxxx RF
                                SET 146 rgprvavfAtrdIkkGeEltidY 168
                                        + +r++++A++ I+ +eEl++dY
  gene1632|gene1632|rna1632|rna1632 469 GRKRIGFYAQKTIRRNEELFFDY 491
                                        *********************** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (502 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1224  (0.0682693); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.25s 00:00:00.80 Elapsed: 00:00:00.42
# Mc/sec: 3585.95
//
Query:       gene1633|gene1633|rna1633|rna1633  [L=126]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
       0.58   10.5   0.1       0.58   10.5   0.1    2.7  3  Sigma_reg_N  Sigma factor regulator N-terminal


Domain annotation for each model (and alignments):
>> Sigma_reg_N  Sigma factor regulator N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1   3.2e-05      0.58      50      84 ..      17      51 ..       5      56 .. 0.86
   2 ?    1.5   0.7      0.02   3.6e+02      22      48 ..      62      89 ..      61      97 .. 0.71
   3 ?   -0.9   0.3      0.11   2.1e+03      23      36 ..     109     123 ..     100     126 .] 0.50

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 3.2e-05
                        Sigma_reg_N 50 elaveitsPNvyvdsgsvsqsgffggeieyelskq 84
                                       ++  ++ +P + v++++++++++f+g+  + ++k+
  gene1633|gene1633|rna1633|rna1633 17 KSDTSVNKPASSVMTEYTQTEAIFSGNFDFLIFKM 51
                                       5567899*********************9999987 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.02
                        Sigma_reg_N 22 vlllifvil.vvtllylaekegnklrev 48
                                       vl++i +++ v+++ y++  +++ l ++
  gene1633|gene1633|rna1633|rna1633 62 VLFIIPPLIlVLLNFYFDYFNPMHLSFT 89
                                       5788888886777777788777777555 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 0.11
                        Sigma_reg_N  23 lllifvil.vvtlly 36 
                                        +l++f++  + t+ y
  gene1633|gene1633|rna1633|rna1633 109 ALVYFLVVgIATFFY 123
                                        344444444544444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       842  (0.046963); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 911.26
//
Query:       gene1634|gene1634|rna1634|rna1634  [L=402]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.011   15.1   0.2      0.046   13.1   0.1    2.1  2  DNA_pol_E_B   DNA polymerase alpha/epsilon subunit B
      0.071   13.2   0.8       0.24   11.5   0.0    2.3  3  DNA_pol_D_N   DNA polymerase delta subunit OB-fold domain
       0.69   10.6   4.9       0.65   10.7   0.2    2.8  2  HSF_DNA-bind  HSF-type DNA-binding


Domain annotation for each model (and alignments):
>> DNA_pol_E_B  DNA polymerase alpha/epsilon subunit B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   7.7e-06     0.046     116     154 ..     285     329 ..     251     345 .. 0.74
   2 ?   -0.8   0.0      0.14   8.3e+02     185     210 ..     342     367 ..     331     368 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 7.7e-06
                                        ........EEE--BSEEEEETTEEEEE--S-HHHH---EEESHHH CS
                        DNA_pol_E_B 116 k......elklvtNPsrielnsvevvltsddivkdlkreslkesn 154
                                               +l+ +tNPsri+l ++++++++d+i ++  + ++ ++n
  gene1634|gene1634|rna1634|rna1634 285 DikdkpsNLHPTTNPSRIQLHNMDIMVVKDEICAKKVQGTFFKEN 329
                                        04444448999********************99876665555555 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.14
                                        GGGGGB-GGG---SEEE---SS--EE CS
                        DNA_pol_E_B 185 wdkddalvleplPdvlvlpdelpeFa 210
                                        +++  +  ++++P +++++++ + F+
  gene1634|gene1634|rna1634|rna1634 342 YTYNFDIGFKEMPRLIFVGQNTRAFV 367
                                        33333344589********9999986 PP

>> DNA_pol_D_N  DNA polymerase delta subunit OB-fold domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       1.2     7e+03      55      59 ..      63      67 ..      33     104 .. 0.54
   2 ?   11.5   0.0   4.1e-05      0.24      81     130 .]     146     194 ..     118     194 .. 0.87
   3 ?   -1.1   0.0      0.32   1.9e+03      53      90 ..     221     271 ..     211     328 .. 0.60

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.2
                        DNA_pol_D_N 55 klkps 59
                                       +++  
  gene1634|gene1634|rna1634|rna1634 63 NERKY 67
                                       22222 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 4.1e-05
                        DNA_pol_D_N  81 sekdellLEDesgrvrLsgsgiesek.lvtGvvvavlGvetengdfeVedi 130
                                        ++ de ++ED+++ v++ ++ i+++  + +G+  ++ G   eng+fe+++i
  gene1634|gene1634|rna1634|rna1634 146 NKFDENVVEDDESVVKVRFN-IDEDLfIFDGMFFGAAGSN-ENGEFEIKRI 194
                                        557999*************9.66666488*********97.8*****9975 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 0.32
                        DNA_pol_D_N  53 emklkpsvlkeiak.............edesapqaerkkyvsekdellLED 90 
                                        +mkl  + l+ i+               ++++++++r   + ++d +++ D
  gene1634|gene1634|rna1634|rna1634 221 NMKLENETLDRIKAvecdilvltgkfnVKNISSAVTRFANTCKNDIIVMLD 271
                                        566666666666555555555555444222223333333333344444434 PP

>> HSF_DNA-bind  HSF-type DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.8      0.17     1e+03      22      61 ..      93     130 ..      39     164 .. 0.73
   2 ?   10.7   0.2   0.00011      0.65      23      58 ..     308     344 ..     292     368 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.17
                                        SEEEES-HHHHHHHTHHHHSTT--HH.HHHHHHHHTTEEE- CS
                       HSF_DNA-bind  22 ksfvvkdkeefakevlpkyfkhsnfs.sFvrqLnlYgFrkv 61 
                                          fv+   e+++k++   +f+ + f+  F   L+ Y F + 
  gene1634|gene1634|rna1634|rna1634  93 LNFVI---ERIEKSLTCDIFRLKGFEkEFSNDLERYYFLQS 130
                                        45666...667777777888888885268888888888663 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00011
                                        EEEES-HHHHHHHTHHHHSTT--HHHHHHH.HHHTTE CS
                       HSF_DNA-bind  23 sfvvkdkeefakevlpkyfkhsnfssFvrq.LnlYgF 58 
                                         ++v + e  ak+v  ++fk + ++sF+r  L+ Y +
  gene1634|gene1634|rna1634|rna1634 308 DIMVVKDEICAKKVQGTFFKENYYESFTRTfLSQYTY 344
                                        4555577889999****************86777744 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (402 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       866  (0.0483016); expected 358.6 (0.02)
Passed bias filter:                      486  (0.0271069); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.25s 00:00:00.82 Elapsed: 00:00:00.44
# Mc/sec: 2720.09
//
Query:       gene1635|gene1635|rna1635|rna1635  [L=1065]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.42   11.5   0.1       0.42   11.5   0.1    3.9  4  Vasculin  Vascular protein family Vasculin-like 1


Domain annotation for each model (and alignments):
>> Vasculin  Vascular protein family Vasculin-like 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   2.4e-05      0.42      19      79 ..      91     152 ..      77     158 .. 0.78
   2 ?   -3.1   0.2      0.83   1.5e+04      37      59 ..     358     380 ..     344     419 .. 0.69
   3 ?   -2.0   2.8      0.38   6.8e+03      31      95 ..     714     774 ..     699     778 .. 0.65
   4 ?   -1.8   2.0      0.32   5.7e+03      34      88 ..     926     982 ..     915    1007 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 2.4e-05
                           Vasculin  19 gwqeesendenylplTed.ElkEFkskseqlkknglgkngfllqsrsltlklsplrnstlka 79 
                                        gw + +  d+n +p  e+  + EF +++++l ++gl++++  +++  l+ ++ + r+s  ka
  gene1635|gene1635|rna1635|rna1635  91 GWMNGDKKDNNIAPSIENgGIEEFAAQTKKLDSDGLSRGNCPIEQSNLNTTSRKSRTSRKKA 152
                                        9**999999999996665279******************99887777777777777555555 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 0.83
                           Vasculin  37 ElkEFkskseqlkknglgkngfl 59 
                                        E+  F +++e + +n ++ +++l
  gene1635|gene1635|rna1635|rna1635 358 EVYSFFMSTEGMTSNEFRVKEVL 380
                                        56666677777777777655554 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 0.38
                           Vasculin  31 lplTedElkEFkskseqlkknglgkngfllqsrsltlklsplrnstlkaavnedsdsetsssetS 95 
                                        l   e+E kE  ++ e  k+++l  +  ++   +++ k     + t   ++ e++d   +s+ +S
  gene1635|gene1635|rna1635|rna1635 714 LKTAENEEKETTRNDEMRKQPTLPAEDAKQTGVAVQEKE----EGTDISRITEQNDMRKTSESSS 774
                                        556788999999999999999997777654444444433....3444455556666666666555 PP

  == domain 4  score: -1.8 bits;  conditional E-value: 0.32
                           Vasculin  34 TedElkEFkskseqlkknglgkngfllqsrsltlklsp..lrnstlkaavnedsdse 88 
                                        Te+E k +  +s   ++ g  + ++l  ++    + s+  ++ ++  ++ +++++s+
  gene1635|gene1635|rna1635|rna1635 926 TENERKKYLDSSSLSHRRGNYRSSYLSCNEYGREPCSNnsWNAQNQMKHSQRKQESS 982
                                        788888888777777777777777775555544444331144222222222222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1065 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1483  (0.0827152); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.74u 0.29s 00:00:01.03 Elapsed: 00:00:00.48
# Mc/sec: 6663.20
//
Query:       gene1636|gene1636|rna1636|rna1636  [L=231]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.4e-24   85.6   2.5    5.9e-22   78.6   0.0    2.1  2  Tub       Tub family


Domain annotation for each model (and alignments):
>> Tub  Tub family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.9   0.7   0.00026       4.7      22      88 ..      48     107 ..      31     116 .. 0.70
   2 !   78.6   0.0   3.3e-26   5.9e-22     142     238 ..     130     226 ..     109     228 .. 0.91

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.00026
                                Tub  22 ltstYhLylelekgkfLlaarkrrrsttseYlisldaedlsrdsesyiGklrsnflgtkftlydkgv 88 
                                         + +YhL l+++++ +++ a k    t   Y i + +++   ++   iG l+ n+ + +f+ly+++ 
  gene1636|gene1636|rna1636|rna1636  48 YSFSYHLELSERRELLVMNAYK----TLFGYNIYTFEKN---QKLRKIGWLKMNMKKNEFVLYEAER 107
                                        5668888888444444444444....3345666655553...33457****************9874 PP

  == domain 2  score: 78.6 bits;  conditional E-value: 3.3e-26
                                Tub 142 spedeeeslqeetkkeeesdllvlknksprwneqlqayvLnFrgRvtvaSvKNfqLvaaedeekvilqfGkvgkdv 217
                                          + e +s+ e+++++ee++++ l nk+pr+n++   y+Ln++++  ++S +NfqL++ +  +++ l+fG  +++ 
  gene1636|gene1636|rna1636|rna1636 130 IYTVEGDSVLERYRNNEEDKIIRLVNKKPRYNKDRDLYTLNYNNSSIMPSERNFQLTHPKIPSHINLSFGANSEND 205
                                        555567888899999************************************************************* PP

                                Tub 218 FtmDyryPlsalqAFaiclss 238
                                        + ++y++P  alqAFai+ls+
  gene1636|gene1636|rna1636|rna1636 206 YRLNYTFPWNALQAFAISLSA 226
                                        *******************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       531  (0.0296168); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1655.01
//
Query:       gene1637|gene1637|rna1637|rna1637  [L=145]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.1e-19   68.7   2.8    4.9e-19   68.1   2.6    1.5  2  dCMP_cyt_deam_1  Cytidine and deoxycytidylate deaminase zinc-
    4.3e-14   52.4   1.3    6.1e-14   51.9   1.3    1.3  1  MafB19-deam      MafB19-like deaminase


Domain annotation for each model (and alignments):
>> dCMP_cyt_deam_1  Cytidine and deoxycytidylate deaminase zinc-binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.1   2.6   5.5e-23   4.9e-19       4      93 ..       6      89 ..       3      96 .. 0.92
   2 ?   -2.3   0.0      0.48   4.3e+03      21      34 ..      96     109 ..      88     115 .. 0.69

  Alignments for each domain:
  == domain 1  score: 68.1 bits;  conditional E-value: 5.5e-23
                                       HHHHHHHHHHHHHHHHTTTSCSEEEEEEETTEEEEEEESBHHCCTGTTB-HHHHHHHHHHHHTSSCETTEEEEEEE-- CS
                    dCMP_cyt_deam_1  4 dekllelalkaakeaqkcsnfkVGavivkngeiistgyngepaggsktiHAEvnAilkaaknggsklegatlyvtleP 81
                                        +++++ a+++ak+a   ++++VG+v+v+ng+iis+ +n +++ +++ +HAE++ i++a+   + k  ++ +y t+eP
  gene1637|gene1637|rna1637|rna1637  6 VKYYMKEAINEAKKALIVDEVPVGCVFVRNGNIISKSHNLTNKLNDPLAHAEIVGIRSAC---C-K--NCDVYLTCEP 77
                                       689********************************************************9...3.4..4********* PP

                                       BHHHHHHHHHHT CS
                    dCMP_cyt_deam_1 82 CsmCakaiiqsg 93
                                       C mC  ++  ++
  gene1637|gene1637|rna1637|rna1637 78 CVMCFGVLKRLN 89
                                       *****9998765 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.48
                                        TTSCSEEEEEEETT CS
                    dCMP_cyt_deam_1  21 csnfkVGavivkng 34 
                                        c n+ +G+ +v++ 
  gene1637|gene1637|rna1637|rna1637  96 CFNPIFGCSLVETS 109
                                        55777888888843 PP

>> MafB19-deam  MafB19-like deaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.9   1.3   6.8e-18   6.1e-14       4     131 ..       7     124 ..       4     137 .. 0.76

  Alignments for each domain:
  == domain 1  score: 51.9 bits;  conditional E-value: 6.8e-18
                        MafB19-deam   4 ekafrkalaevekatkikedkigavivkdkkviargsnekelnakataHaEiaalqqAakklkskrlddatlyvtl 79 
                                        + ++++a++e++ka+ ++e+++g+v v ++++i + +n ++  ++++aHaEi  ++ A+ k+ +       +y t 
  gene1637|gene1637|rna1637|rna1637   7 KYYMKEAINEAKKALIVDEVPVGCVFVRNGNIISKSHNLTNKLNDPLAHAEIVGIRSACCKNCD-------VYLTC 75 
                                        6799******************************************************877655.......5**** PP

                        MafB19-deam  80 epCdmCagaivqaglkklvygagnpks.....lnkLkvkekngrvelveddckeilk 131
                                        epC mC      + lk+l+       +     +   +++e +++v l +++c ++lk
  gene1637|gene1637|rna1637|rna1637  76 EPCVMCF-----GVLKRLNCTIY---FgcfnpIFGCSLVETSDNVFLDNQECVDLLK 124
                                        ******6.....55555544333...1112335555555555555555555655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       703  (0.0392102); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 1093.39
//
Query:       gene1638|gene1638|rna1638|rna1638  [L=104]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.045   13.4   0.0       0.05   13.2   0.0    1.1  1  SARAF     SOCE-associated regulatory factor of calcium homoeo


Domain annotation for each model (and alignments):
>> SARAF  SOCE-associated regulatory factor of calcium homoeostasis
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   2.8e-06      0.05     160     232 ..       7      80 ..       1     101 [. 0.43

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.8e-06
                              SARAF 160 asllfvvlvllviayivykaflaaeee.reaeaeggrrgeggggggggggpgseeeqddpPppy...sltksqkps 231
                                        + ++ +v+ +l++++ +   f++++++ +++  eg+ +++g ++  gggg  s +++++pP      +++k++k++
  gene1638|gene1638|rna1638|rna1638   7 IIIIATVAAILLVGVPLLVHFMGKKDNsPSKDGEGNGEKGGMKSLFGGGG--S-KDDSKPPKDPakdDMNKCEKDD 79 
                                        33445566666667777777887777742222222222222222222222..1.2222333222233222222222 PP

                              SARAF 232 s 232
                                        +
  gene1638|gene1638|rna1638|rna1638  80 K 80 
                                        2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       825  (0.0460148); expected 358.6 (0.02)
Passed bias filter:                      631  (0.0351944); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 729.67
//
Query:       gene1639|gene1639|rna1639|rna1639  [L=103]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.1e-09   38.3   0.1    1.5e-09   37.9   0.1    1.2  1  Glutaredoxin  Glutaredoxin
      0.003   17.7   0.7     0.0041   17.3   0.7    1.2  1  DUF3276       Protein of unknown function (DUF3276)
  ------ inclusion threshold ------
      0.042   14.3   0.1      0.058   13.8   0.1    1.3  1  DUF836        Glutaredoxin-like domain (DUF836)
      0.062   13.7   0.0      0.077   13.4   0.0    1.1  1  GST_N_3       Glutathione S-transferase, N-terminal domain


Domain annotation for each model (and alignments):
>> Glutaredoxin  Glutaredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.9   0.1   3.4e-13   1.5e-09       3      60 .]      22      79 ..      20      79 .. 0.95

  Alignments for each domain:
  == domain 1  score: 37.9 bits;  conditional E-value: 3.4e-13
                                       EEESTSSHHHHHHHHHHHHTTGGEEEEEGCCSHHHHHHHHHHHTSSSSSEEEETTEEE CS
                       Glutaredoxin  3 lftkptCpyCkkakrlLkelgvkfeeidvdkdeeireelkelsgvrtvPqvfidgkhv 60
                                       + +kp C +Ckkak+lL+++ +++e++    ++++   ++e++++ ++P +f +g+++
  gene1639|gene1639|rna1639|rna1639 22 IIGKPDCIFCKKAKDLLDKNSLDYEYYSSCTESKYVRNIMEKLDYHKFPIIFYKGDFI 79
                                       7899*****************************9999999999************997 PP

>> DUF3276  Protein of unknown function (DUF3276)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.7   9.1e-07    0.0041      33      76 ..      44      87 ..      36      91 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 9.1e-07
                            DUF3276 33 kddyyltitEskkvtnddgsvsfekHkifLykEDfekFkeglee 76
                                         +yy + tEsk v n   ++ ++k  i  yk Df    + l+e
  gene1639|gene1639|rna1639|rna1639 44 DYEYYSSCTESKYVRNIMEKLDYHKFPIIFYKGDFIGGFTELNE 87
                                       569********************************765555555 PP

>> DUF836  Glutaredoxin-like domain (DUF836)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   1.3e-05     0.058       2      28 ..      20      46 ..      19      68 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.3e-05
                                       EEEEE-TT-HHHHHHHHHHHHHCCCTT CS
                             DUF836  2 ltLyskpgChlCeqakekLkelkleeg 28
                                       + +++kp C  C++ak++L + +l+ +
  gene1639|gene1639|rna1639|rna1639 20 IYIIGKPDCIFCKKAKDLLDKNSLDYE 46
                                       7899****************8777665 PP

>> GST_N_3  Glutathione S-transferase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   1.7e-05     0.077       2      52 ..      23      75 ..      22      88 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.7e-05
                                       ES-TTSHHHHHHHHHHHHHT--EEE.E---TTTTHHHHHHH-TT--SSEE.ET CS
                            GST_N_3  2 ygfpaSpyarrvrlaLnekglpvev.vevtpgehdeellaknplgkvPvL.ed 52
                                       +g p++ ++++++ +L+   l++e+  ++t+ +  +++++k  ++k+P++ ++
  gene1639|gene1639|rna1639|rna1639 23 IGKPDCIFCKKAKDLLDKNSLDYEYySSCTESKYVRNIMEKLDYHKFPIIfYK 75
                                       5789********************6488899999**************99433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       627  (0.0349713); expected 358.6 (0.02)
Passed bias filter:                      484  (0.0269954); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 740.93
//
Query:       gene164|gene164|rna164|rna164  [L=196]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       953  (0.0531541); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1388.96
//
Query:       gene1640|gene1640|rna1640|rna1640  [L=471]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.095   11.9   0.8        7.9    5.6   0.1    2.2  2  DXP_synthase_N  1-deoxy-D-xylulose-5-phosphate synthase


Domain annotation for each model (and alignments):
>> DXP_synthase_N  1-deoxy-D-xylulose-5-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.1   0.00093        17     161     207 ..     122     168 ..     117     199 .. 0.81
   2 ?    5.6   0.1   0.00044       7.9     168     230 ..     310     372 ..     284     382 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.00093
                     DXP_synthase_N 161 kkkllvilNdNemsisknvGalskylskllsskayeklkkevkkllk 207
                                        +++ ++i N  + s s  + +l +y+++++ +kaye +k++++++  
  gene1640|gene1640|rna1640|rna1640 122 SQNTVIIRNTYRNSLSFYMLSLVRYIQDVTFDKAYEMVKENMRNVEM 168
                                        578899************************************99875 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.00044
                     DXP_synthase_N 168 lNdNemsisknvGalskylskllsskayeklkkevkkllkkigkklaelakklkeslkellvp 230
                                        +N  + +isk vG  ++ l + l+ + y+k  + + +++ + +++++++++kl+++ k  ++ 
  gene1640|gene1640|rna1640|rna1640 310 FNGKSLVISKFVGNYNENLLNRLKGEGYSKDDAMIATIVANSSTEVNKVLQKLEKKEKPKISA 372
                                        5777889********************************9999***********999977665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (471 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       755  (0.0421105); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.28s 00:00:00.88 Elapsed: 00:00:00.49
# Mc/sec: 2889.85
//
Query:       gene1641|gene1641|rna1641|rna1641  [L=284]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.1e-16   59.5   7.8      4e-16   59.1   7.8    1.1  1  FH2       Formin Homology 2 Domain


Domain annotation for each model (and alignments):
>> FH2  Formin Homology 2 Domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.1   7.8   2.2e-20     4e-16      82     369 ..       7     276 ..       3     279 .. 0.86

  Alignments for each domain:
  == domain 1  score: 59.1 bits;  conditional E-value: 2.2e-20
                                        HHHHHHHHHHHHTS-HHHHHHHHHTTTTCCCTHHHHHHHHHHCGGHHHHHHHHCTCTSGTTB-HHHHHHHHHTTST CS
                                FH2  82 rsqniaIlLkklkltaeeiveaileldeealdlellenLlkmaPtkeelkklkeykgevseLseaeqFllelvkip 157
                                        r   ++I Lk+++++   ++++ l     +l le l+ + +++Pt+ee+k l ++k++   L + e+ +       
  gene1641|gene1641|rna1641|rna1641   7 RLFLVSISLKTFEKKQLVLQDQQL----ANLPLEDLTMINTIIPTDEEYKILCTHKKD---LNDIERRMI---VFY 72 
                                        555566666666333333333222....458899999999************877777...777776444...444 PP

                                        THHHHHHHHHHHHTHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHST..CSTTCS-SEE-GGGGG CS
                                FH2 158 rlekRleallfkstfeeeveelkrslealeaaseeLknskkfkklLeliLalGNymNd..gtrrgqAkGFkLssLl 231
                                         ++k +++l+f   f e+  +    +e ++++ + + +s + + lL+++L+lGN  N   g++r++A++F++ sL 
  gene1641|gene1641|rna1641|rna1641  73 PYKKLIRLLIFERRFFENKDSWIIGVENIKSVYDTILQSNNIRLLLKTVLELGNTINTnyGNSRKRASAFRICSLV 148
                                        57888**************************************************987336778************ PP

                                        GCCCSB-STTTSBHHHHHHHHHHTTSGGGGGHHHHTTTHHHCCTS-HHHHHHHHHHHHHHHHHHHHHHHHCCTTSS CS
                                FH2 232 kLsdvKstdnkttLLHylvkiireklpevldfsseLknvkkaakvnleslekevkklekglkklekelessekkee 307
                                          ++ K++ + ++LL +++++ r++   ++  +s+L++++++ + +l + ++ ++++  + +  ++ ++s +    
  gene1641|gene1641|rna1641|rna1641 149 LTKNYKGKRSDQSLLKFVAETARSR---LKSIKSDLETIESIRNDELGNYKEIINEYILEYRTSKEWMDSLSG--- 218
                                        ********************97665...566789*******99999999999999999999999999999999... PP

                                        TT-THHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--TTCCHHHHHHHHHHHHHH CS
                                FH2 308 psdkflevlkeflkeaeeklkkleeelkeakelvkelveYfgedkkevspeeffkilreFlk 369
                                           ++++ +k fl   ++ ++++++e++ea      + + fge +++ +++e+ +il +Flk
  gene1641|gene1641|rna1641|rna1641 219 ---ELRANMKAFLFFFSQFVRNFSNEYREAVIYSSIIKRKFGE-PENKNVKEIIAILYDFLK 276
                                        ...9**************************************8.7899************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (284 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       698  (0.0389313); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 2056.07
//
Query:       gene1642|gene1642|rna1642|rna1642  [L=490]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.5e-23   81.9   3.0    5.2e-23   80.9   1.1    2.2  2  Bromodomain      Bromodomain
    3.2e-06   27.4   0.3    4.5e-05   23.7   0.3    2.4  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    3.5e-05   23.7   0.5      0.015   15.2   0.0    2.5  2  Acetyltransf_10  Acetyltransferase (GNAT) domain
     0.0005   20.4   0.1    0.00094   19.6   0.1    1.4  1  Acetyltransf_7   Acetyltransferase (GNAT) domain


Domain annotation for each model (and alignments):
>> Bromodomain  Bromodomain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.24   1.1e+03      25      41 ..     143     159 ..     124     173 .. 0.81
   2 !   80.9   1.1   1.2e-26   5.2e-23       4      83 ..     275     354 ..     272     355 .. 0.96

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.24
                                        CSTTHHHH.SS---HHH CS
                        Bromodomain  25 efpdyyavikkPldLst 41 
                                        e+  y+++ k+P+ L  
  gene1642|gene1642|rna1642|rna1642 143 EYLSYPKRLKHPIYLMA 159
                                        6778999******9976 PP

  == domain 2  score: 80.9 bits;  conditional E-value: 1.2e-26
                                        HHHHBHTTTCGGGGCSTT-GCCSTTHHHH.SS---HHHHHHHHHTT--SSHHHHHHHHHHHHHHHHHHSHTTSHHH CS
                        Bromodomain   4 ilsellehklaepFlepvdpeefpdyyavikkPldLstIkkklesnkYksladfeadlkllfsNarkyngegsviy 79 
                                        i+s++ ++  a pFl+pv+++e+pdyy++ik P+d+s+I++++e+ kY+sl+ fe+d+ l+f+N++ yn + + ++
  gene1642|gene1642|rna1642|rna1642 275 IISDIRTDTHAWPFLQPVNEKEVPDYYQIIKTPMDISKIEQNVEDDKYESLEVFEQDFALIFKNCYIYNAPSTTYC 350
                                        889999999******************************************************************* PP

                                        HHHH CS
                        Bromodomain  80 elae 83 
                                        ++a+
  gene1642|gene1642|rna1642|rna1642 351 KCAH 354
                                        *995 PP

>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.3     1e-08   4.5e-05      19      92 ..      64     133 ..      48     174 .. 0.83

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 1e-08
                                        HHHHHHHHHHHSTTCEEEEEEETTEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHT CS
                     Acetyltransf_1  19 aseeefeesfsleaegllvaeedgeliGfisllkipdekggvayieslaVspeyrgkGlGsaLlealeeraree 92 
                                        +++ + +++ +++ + l  ++ dg+++G is+++ ++  +  +++ +la++++ + +G Gs+ ++ l e++++e
  gene1642|gene1642|rna1642|rna1642  64 KEYIIKQIFNEKHRNIL--CLIDGTIVGGISYRPFYE--QSFVELVFLAIDSNVQVNGHGSMIIDILKEHCKRE 133
                                        44555556644455555..55****************..89*****************************9998 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   3.3e-06     0.015      20      86 ..      65     135 ..      42     141 .. 0.79
   2 !    6.2   0.1    0.0021       9.3      88     108 ..     156     176 ..     139     185 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 3.3e-06
                    Acetyltransf_10  20 ealrerieegealllvaeeggkivGvielrdgs.....hisllfVdpeyrgqGigkaLleaveeeaekdgik 86 
                                        e + ++i ++++  +++  +g+ivG i++r        ++  l++d++ + +G g+++++ ++e+++ ++i+
  gene1642|gene1642|rna1642|rna1642  65 EYIIKQIFNEKHRNILCLIDGTIVGGISYRPFYeqsfvELVFLAIDSNVQVNGHGSMIIDILKEHCK-REIQ 135
                                        44555565999999*************7643333557899999***********************5.5455 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0021
                    Acetyltransf_10  88 eltvnaspyavpfYeklGFka 108
                                         l + a++ya++f++k+GF +
  gene1642|gene1642|rna1642|rna1642 156 YLMAYADNYAIGFFKKQGFST 176
                                        78899**************75 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.1   2.1e-07   0.00094       6      75 ..      79     175 ..      73     176 .. 0.69

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 2.1e-07
                                        EEEEETTEEEEEEEEEEES....TCTEEEEE-GGGTTSSHHHHHHHH........TTSEEE............... CS
                     Acetyltransf_7   6 fVaeddgkivGfialslld....aeitrlaVdpeyrgkGiGraLlea........aekgii............... 54 
                                        +++  dg ivG i++ +       e+ +la+d + + +G G+ ++++        +    +               
  gene1642|gene1642|rna1642|rna1642  79 ILCLIDGTIVGGISYRPFYeqsfVELVFLAIDSNVQVNGHGSMIIDIlkehckreI----Qnietdfleylsypkr 150
                                        44667899***99999998877666666******************6454444320....1344666666666666 PP

                                        EE.EEEE...THHHHHHHHHHTTEE CS
                     Acetyltransf_7  55 le.qlel...naekaikfYeklGFe 75 
                                        l+   +l   ++++ai+f++k GF 
  gene1642|gene1642|rna1642|rna1642 151 LKhPIYLmayADNYAIGFFKKQGFS 175
                                        33333444432239**********6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (490 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1218  (0.0679346); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.45
# Mc/sec: 3294.54
//
Query:       gene1643|gene1643|rna1643|rna1643  [L=108]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       245  (0.013665); expected 358.6 (0.02)
Passed bias filter:                      221  (0.0123264); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.55u 0.35s 00:00:00.90 Elapsed: 00:00:00.56
# Mc/sec: 581.67
//
Query:       gene1644|gene1644|rna1644|rna1644  [L=422]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      6e-17   61.8   2.4    2.4e-13   50.2   0.0    2.8  2  MMR_HSR1     50S ribosome-binding GTPase
    4.4e-12   46.3   0.3    1.3e-11   44.8   0.1    1.8  1  NGP1NT       NGP1NT (NUC091) domain
    1.2e-08   34.6   0.8     0.0001   21.8   0.0    2.4  2  FeoB_N       Ferrous iron transport protein B
    6.1e-07   29.5   0.3    1.5e-06   28.2   0.3    1.6  1  RsgA_GTPase  RsgA GTPase
    1.9e-05   24.3   0.2     0.0017   17.9   0.1    2.5  2  GTP_EFTU     Elongation factor Tu GTP binding domain
    0.00036   20.0   1.6       0.18   11.3   0.1    2.6  2  Arf          ADP-ribosylation factor family
     0.0019   17.8   0.2       0.34   10.5   0.1    2.4  2  cobW         CobW/HypB/UreG, nucleotide-binding domain
  ------ inclusion threshold ------
       0.03   13.8   0.4       0.18   11.2   0.0    2.3  2  SRPRB        Signal recognition particle receptor beta subuni
      0.037   14.1   6.4        1.5    8.9   0.1    3.7  3  Dynamin_N    Dynamin family
      0.046   13.9   0.9        3.5    7.9   0.0    2.7  2  Roc          Ras of Complex, Roc, domain of DAPkinase


Domain annotation for each model (and alignments):
>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.9   0.00027      0.48      70     114 .]     163     208 ..      55     208 .. 0.84
   2 !   50.2   0.0   1.3e-16   2.4e-13       2      64 ..     264     322 ..     263     386 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00027
                                        HHHHHC.TSEEEEEEETT.TTCSHHHHHHHHHHHHH.TTSEEEEEEES CS
                           MMR_HSR1  70 flalee.adlillvvdas.eeklkpldeeleellee.akkplilvlnk 114
                                        + ++ + +d+i++v+d++   k+  l +++ e+ ++ ++k++i+vlnk
  gene1644|gene1644|rna1644|rna1644 163 LYKVLDtSDVIVHVLDVRyP-KMF-LCKQVIEYVKQnEHKNMIIVLNK 208
                                        33444438********8842.222.223344443333899*******8 PP

  == domain 2  score: 50.2 bits;  conditional E-value: 1.3e-16
                                        EEEEESTTSSHHHHHHHHHTS.TEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSSHHHHHH CS
                           MMR_HSR1   2 vaivGrpNvGKStLinaltge.kaivsdkpgtTrdinegrvklkgkeielvDtpGliegaseek 64 
                                        v++vG+pN+GKS++in l+++  a+++  +g T++ ++ +++   k i+l D pG+i+   ++k
  gene1644|gene1644|rna1644|rna1644 264 VGFVGYPNTGKSSIINVLLNKkSAKTAPLAGETKNWQQVKLD---KGIHLFDSPGVID--VKDK 322
                                        89******************9668****************98...57********876..2222 PP

>> NGP1NT  NGP1NT (NUC091) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.8   0.1   7.3e-15   1.3e-11       1      86 [.      18      98 ..      18     113 .. 0.87

  Alignments for each domain:
  == domain 1  score: 44.8 bits;  conditional E-value: 7.3e-15
                             NGP1NT  1 mykegkakrdkkGkiikaaalqskeasksariepdrrWFgntrvisqeaLekfreeleekvkdpysvllkrnklPmsL 78
                                       my ++++k  + G+i+++a++qs++  k+a i p+ + F+ tr+i+ +++++      ek + +y+vl+k+ ++P+s+
  gene1644|gene1644|rna1644|rna1644 18 MY-NNRPKYSAYGEILRPAHFQSTRS-KVAVIPPNYKLFTSTRTINMNEITE------EKERSAYEVLIKKGQVPFSI 87
                                       89.99*******************99.******************9988875......566779************** PP

                             NGP1NT 79 ledkakk...k 86
                                       l++++ k   +
  gene1644|gene1644|rna1644|rna1644 88 LSERKGKvklE 98
                                       ***98873432 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.2   0.00014      0.25      77     134 ..     168     228 ..     157     247 .. 0.81
   2 !   21.8   0.0   5.9e-08    0.0001       2      62 ..     263     321 ..     262     341 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00014
                                        TSSSEEEEEEEGGGHHHHHHHHHHHHHT.....TSSEEEEEETHHHHHHTTEEE-HHHHHHHH CS
                             FeoB_N  77 eepdvvvnvvdatnlernLyLtlqllel.....gvpvvlalnmideaekkgieidlkkLsekL 134
                                        ++ dv+v+v+d      +++L  q++e      +++++++ln++d + ++ ++ +++ Ls+++
  gene1644|gene1644|rna1644|rna1644 168 DTSDVIVHVLDVRYP--KMFLCKQVIEYvkqneHKNMIIVLNKVDLVPTAVTKKNIDILSKHF 228
                                        6789*******9976..5899999998733332478***********9999999999998875 PP

  == domain 2  score: 21.8 bits;  conditional E-value: 5.9e-08
                                        EEEEEESTTSSHHHHHHHHHTTS.EEEEESTTSSSEEEEEEEEETTEEEEEEE----SSSSS CS
                             FeoB_N   2 tvalvGnpnvGkttlfnaltgak.qkvgNwpGvtvekkegklklkgkeveivDlPGiYslsa 62 
                                        +v +vG pn+Gk++++n l ++k  k +  +G t + +++kl+   k +++ D PG+ ++++
  gene1644|gene1644|rna1644|rna1644 263 SVGFVGYPNTGKSSIINVLLNKKsAKTAPLAGETKNWQQVKLD---KGIHLFDSPGVIDVKD 321
                                        6889*************9987663799*******999999988...99********988854 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.2   0.3   8.5e-10   1.5e-06      23     161 ..     175     316 ..     165     320 .. 0.62

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 8.5e-10
                                        EESTTTT--HHHHHHHHHHHHHTT-.EEEEEEE-GGG--HHH...HHHHHHHHHHHTTSEEEE--TT.....THTT CS
                        RsgA_GTPase  23 vslkepelslnlldrfLvlaeekgi.epvivlnKiDlleeee...eleelkeelealgyevllvsak.....tkeg 89 
                                          l+    ++ l ++++  +++++  +++ivlnK+Dl+ ++    +++ l++++ ++ +     s++      k++
  gene1644|gene1644|rna1644|rna1644 175 HVLDVRYPKMFLCKQVIEYVKQNEHkNMIIVLNKVDLVPTAVtkkNIDILSKHFPTVAM----HSKSlfnfyGKNN 246
                                        44444444445555555555555544899*********999833333333333333322....2221111112333 PP

                                        HHHHH...HHCTT.SEEE.EECSTTSSHHHHHHHHCTT-----S--------------SEEEEEETTTEEEESS-S CS
                        RsgA_GTPase  90 leelk...ellkd.ktsv.lvGqSGvGKStLinallpelelktgevseklgrGkhTTtavellelaegglliDtPG 160
                                        l +l    +++++  +sv +vG    GKS++in+ll+++++kt+ +  +       T++ + ++l++g  l D+PG
  gene1644|gene1644|rna1644|rna1644 247 LMNLLrqyKKIHKkTISVgFVGYPNTGKSSIINVLLNKKSAKTAPLAGE-------TKNWQQVKLDKGIHLFDSPG 315
                                        33333011233331334358888889******************99987.......89999999999999*****9 PP

                                        S CS
                        RsgA_GTPase 161 f 161
                                        +
  gene1644|gene1644|rna1644|rna1644 316 V 316
                                        8 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.1   9.5e-07    0.0017      86     150 ..     162     228 ..     153     257 .. 0.82
   2 ?    4.0   0.0     0.018        32       2      31 ..     260     289 ..     259     318 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 9.5e-07
                                        HHHHHHHT-SEEEEEEETTTBSTHHHHHHHHHHHHTTTE.EEEEEESCGST.HHHHHHHHHHHHHHH CS
                           GTP_EFTU  86 evirglrvlDgavlvvdaveGvepqteevlrlalkegvp.iivfiNKmDrl.kaelkeiveevkqkl 150
                                        e ++ l + D+ v v+d++   +   ++v++ +++++ + +i+++NK+D +  a  k+ ++ +++++
  gene1644|gene1644|rna1644|rna1644 162 ELYKVLDTSDVIVHVLDVRYPKMFLCKQVIEYVKQNEHKnMIIVLNKVDLVpTAVTKKNIDILSKHF 228
                                        677889999*************************999999***********7555666666555555 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.018
                                        CEEEEEEEESTTSSHHHHHHHHHHHTTSSC CS
                           GTP_EFTU   2 rirnigiighvDhGKtTLtdrLlyktgais 31 
                                        +++ +g++g  ++GK++++  Ll k++a +
  gene1644|gene1644|rna1644|rna1644 260 KTISVGFVGYPNTGKSSIINVLLNKKSAKT 289
                                        67899******************8877654 PP

>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   0.2    0.0016       2.8      72     136 ..     157     221 ..     154     237 .. 0.69
   2 !   11.3   0.1   9.9e-05      0.18       5      51 ..     251     298 ..     247     320 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0016
                                        GGGGGGGCT...TESEEEEEEETT-CTTHHHHHHHHHHHCTSGCCTTSEEEEEEE-TTS.TTSS-HHHH CS
                                Arf  72 RplWknYfe...ktdavifvvDsadreRleeakeeLkalleeeelkevallvlaNKqDl.pealseeel 136
                                        +++W++ ++   + d++++v+D+    ++  +k+ ++ + ++e   +  ++++ NK Dl p+a++++++
  gene1644|gene1644|rna1644|rna1644 157 KRIWNELYKvldTSDVIVHVLDVRYP-KMFLCKQVIEYVKQNE---HKNMIIVLNKVDLvPTAVTKKNI 221
                                        57788877622145788999998765.5667888877764443...45689999****83456666655 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 9.9e-05
                                        HHGGTT..TTEEEEEEEESTTSSHHHHHHHHHHSSCEECSSSSSEEEE CS
                                Arf   5 laklklk.kkelrilllGLDnaGKtTilkklkleelvttvPTigfnve 51 
                                        l+++k+  kk + + ++G  n+GK+ i++ l +++ ++t P  g + +
  gene1644|gene1644|rna1644|rna1644 251 LRQYKKIhKKTISVGFVGYPNTGKSSIINVLLNKKSAKTAPLAGETKN 298
                                        555554437889999**************************9997544 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.1   0.00019      0.34     110     162 ..     168     220 ..     151     234 .. 0.72
   2 !    5.0   0.0    0.0088        16       4      37 ..     265     297 ..     261     344 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00019
                                        CCECEEEEEEETTTH.CCHCCHHHHHHHHHHTSSE.EEEE-HHHHCHC..HHHH CS
                               cobW 110 ltldavvavvDaknleaeeekieekaedqlaaadl.lvlnKtDlldeeallekl 162
                                         t d++v v+D++  +    k+  ++ +q +  ++ +vlnK+Dl++++ + +k 
  gene1644|gene1644|rna1644|rna1644 168 DTSDVIVHVLDVRYPKMFLCKQVIEYVKQNEHKNMiIVLNKVDLVPTAVT-KKN 220
                                        46789999****777777788888888888877762579*******9944.333 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0088
                                        EEEESTTCCHHHHHHHHHCT--SS-EEEEESS-S CS
                               cobW   4 vltGflGsGKTtLlnhllenraglklavivNefg 37 
                                        +++G++ +GK++++n ll++ ++ k+a + +e +
  gene1644|gene1644|rna1644|rna1644 265 GFVGYPNTGKSSIINVLLNK-KSAKTAPLAGETK 297
                                        5788999********99965.6677777777754 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.1      0.34   6.1e+02      98     151 ..     185     237 ..     163     259 .. 0.69
   2 ?   11.2   0.0    0.0001      0.18       6      62 ..     264     319 ..     258     340 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.34
                                        HHHHHHHHHHHHTT---EEEEEE-TTSTT---HHHHHHHHHHHHHHHHHCHHHH CS
                              SRPRB  98 llyeilliteklkdavdiliACnKqelflakspklikdaLEkElnkiierrska 151
                                        +l + +++ +k++++ +++i  nK +l+ +   k+  d L k   ++   +sk+
  gene1644|gene1644|rna1644|rna1644 185 FLCKQVIEYVKQNEHKNMIIVLNKVDLVPTAVTKKNIDILSKHFPTVAM-HSKS 237
                                        6666677777888888888888998887555555544666666666543.3444 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.0001
                                        EEEE-STTSSHHHHHHHHHHSS---B---S.S-EEETTG...GGTT-SEEEETT-GCC CS
                              SRPRB   6 vllvGlsdsGKTslftrLttdsvkktvtSq.essaalkvksekgskltliDfPGhekl 62 
                                        v +vG  ++GK s+++ L++++  kt     e++  ++v  + ++ ++l D PG   +
  gene1644|gene1644|rna1644|rna1644 264 VGFVGYPNTGKSSIINVLLNKKSAKTAPLAgETKNWQQV--KLDKGIHLFDSPGVIDV 319
                                        6689*****************999998777688888888..677889999***97655 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.6      0.06   1.1e+02     119     168 .]     150     209 ..      95     209 .. 0.80
   2 ?    8.9   0.1   0.00082       1.5       1      22 [.     264     285 ..     264     304 .. 0.86
   3 ?    3.6   0.0     0.035        62      98     116 ..     303     321 ..     294     333 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.06
                                        S..........HHHHHHHSTTEEEEEEEETTS-CCC-CHHHHHHHHSTTBTTEEEEEE-C CS
                          Dynamin_N 119 q..........elvkeyikkadiilavtsanhdlsnsealflarevdpkgkrtivvltkl 168
                                                   + + + ++ +d+i++v++     +   ++ ++   ++++k++i+vl+k+
  gene1644|gene1644|rna1644|rna1644 150 AlrpgrskriwNELYKVLDTSDVIVHVLDVRYPKMFLCKQVIEYVKQNEHKNMIIVLNKV 209
                                        144455555557788889999999999999998887788888888888888899999985 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00082
                                        EEEEEBTTTTHHHHHHHHHTS- CS
                          Dynamin_N   1 iavvGsqSsGKSSvlnaLlged 22 
                                        + +vG  + GKSS++n Ll ++
  gene1644|gene1644|rna1644|rna1644 264 VGFVGYPNTGKSSIINVLLNKK 285
                                        678999************9987 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.035
                                        TTS-SEEEEE---B-SSSG CS
                          Dynamin_N  98 llvkgltlvDlPGldsvnk 116
                                         l+kg+ l+D+PG+++v++
  gene1644|gene1644|rna1644|rna1644 303 KLDKGIHLFDSPGVIDVKD 321
                                        57899*********99876 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.2     0.036        64      80     119 ..     170     210 ..     160     211 .. 0.65
   2 ?    7.9   0.0    0.0019       3.5       3      32 ..     265     293 ..     263     312 .. 0.72

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.036
                                        SCEEEEEEEGHHHH.CHHHHHHHHHHHCSSS-EEEEEE-TT CS
                                Roc  80 aalailvydsrsse.nlkeWlkelkkvagkspvilvgnkiD 119
                                        +++++ v+d r  +  l + + e  k+++++++i+v nk+D
  gene1644|gene1644|rna1644|rna1644 170 SDVIVHVLDVRYPKmFLCKQVIEYVKQNEHKNMIIVLNKVD 210
                                        66777777766433133333444445567789999*****9 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0019
                                        EEESSTTSSHHHHHHCHCT-CCC-EEETTT CS
                                Roc   3 vlvGdsgvGKtsllkrfvedkfsekeksti 32 
                                         +vG  ++GK+s+++ ++++k  + + +  
  gene1644|gene1644|rna1644|rna1644 265 GFVGYPNTGKSSIINVLLNKKSAK-TAPLA 293
                                        589***************777644.34444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (422 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1380  (0.0769703); expected 358.6 (0.02)
Passed bias filter:                      596  (0.0332422); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.78u 0.36s 00:00:01.14 Elapsed: 00:00:00.57
# Mc/sec: 2239.38
//
Query:       gene1645|gene1645|rna1645|rna1645  [L=175]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-08   35.3   1.5    4.7e-06   26.9   0.3    2.6  3  RNA_pol_Rbc25  RNA polymerase III subunit Rpc25
  ------ inclusion threshold ------
        0.1   12.9   0.1       0.17   12.3   0.1    1.4  1  SHS2_Rpb7-N    SHS2 domain found in N terminus of Rpb7p/Rpc25


Domain annotation for each model (and alignments):
>> RNA_pol_Rbc25  RNA polymerase III subunit Rpc25
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0      0.94   8.4e+03      63      73 ..      38      48 ..      16      53 .. 0.62
   2 !   26.9   0.3   5.2e-10   4.7e-06       2      76 ..      76     155 ..      76     159 .. 0.81
   3 !    8.0   0.0   0.00036       3.3     110     129 .]     156     175 .]     152     175 .] 0.91

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 0.94
                                       TTSEEEEEEEE CS
                      RNA_pol_Rbc25 63 vgeeirfrvee 73
                                        +e i +rv+e
  gene1645|gene1645|rna1645|rna1645 38 PNEGIGIRVKE 48
                                       45555555554 PP

  == domain 2  score: 26.9 bits;  conditional E-value: 5.2e-10
                                        STTSEEEEEEEEEETTCEEEEBTTBSEEEEECCCCSTTEEE......ECCCTCEEEEESSSEEEEE-TTSEEEEEE CS
                      RNA_pol_Rbc25   2 fvgevltgkiksstregikvslgffddifvpkelLfepsef......deeeqawvweveeeeelyldvgeeirfrv 71 
                                        f++e+++++i++++++gi +   ++++i v       + ++       e++ +w+w + ++ ++y+++g+ +r +v
  gene1645|gene1645|rna1645|rna1645  76 FKDEIVEATISKQDENGIYLMHPIVNTIHVKTLFPGTEKKYfvmkdsPEKHMCWCWTY-KNDNFYFKNGQFVRCKV 150
                                        799**************************97544333334423332246778******.8999************* PP

                                        EEEEE CS
                      RNA_pol_Rbc25  72 eeeif 76 
                                        +++++
  gene1645|gene1645|rna1645|rna1645 151 VHVSY 155
                                        *9987 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.00036
                                        -SCEEEEEB-STTTCECGCC CS
                      RNA_pol_Rbc25 110 spyevlgsiqedGlGlvsWw 129
                                        +p+ v + + ++GlG+  Ww
  gene1645|gene1645|rna1645|rna1645 156 NPFVVEARMDDNGLGPKEWW 175
                                        7899**************** PP

>> SHS2_Rpb7-N  SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   1.9e-05      0.17       2      52 ..       9      57 ..       8      73 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.9e-05
                                       EEEEE-GGGTTSTHHHHHHHHHHHHHTTBEETTTEEEEEEEEEEEECCEEE CS
                        SHS2_Rpb7-N  2 dtvrlePsylgstledallerllekyegkvvpslGvivavldiaeysegkv 52
                                       d++++ P   +   +++l  ++++ky ++++p+ G+ + v +i++++    
  gene1645|gene1645|rna1645|rna1645  9 DNISILPTSKD--HLTSLYTATNKKYTNRIIPNEGIGIRVKEIKKIYGKEL 57
                                       55666665544..5567789***********************88765444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (175 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       429  (0.0239277); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.31s 00:00:00.83 Elapsed: 00:00:00.53
# Mc/sec: 996.21
//
Query:       gene1646|gene1646|rna1646|rna1646  [L=115]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.2e-14   53.2   0.5    3.8e-14   52.9   0.5    1.0  1  mRNA_triPase  mRNA capping enzyme, beta chain
  ------ inclusion threshold ------
      0.012   15.5   0.3      0.014   15.2   0.3    1.1  1  DUF3284       Domain of unknown function (DUF3284)


Domain annotation for each model (and alignments):
>> mRNA_triPase  mRNA capping enzyme, beta chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.9   0.5   4.2e-18   3.8e-14     129     219 .]      14      92 ..       6      92 .. 0.89

  Alignments for each domain:
  == domain 1  score: 52.9 bits;  conditional E-value: 4.2e-18
                                        -EEEEEEEEEEEEEEEE-TTSSSEEEEEEEEEEE-SSSHHHCTTS--SEEEEEEEEEEEECCGTEEEEEEEESSS- CS
                       mRNA_triPase 129 evlkkieKeriadlniylPnsklDyriSinlElpvseskaklskktpvseRlkeRlSyihkksgiqfDLtkvekte 204
                                          +++i+Ker+a  ++++Pn  +D+ri+++ E+pv     +   k  ++ R++eR S+i ++  ++fD t      
  gene1646|gene1646|rna1646|rna1646  14 GKTTTIRKERVALYDVFIPNAVYDLRIALSREIPV-----TNVIKASTYRRERERESFIVDS--TRFDFTIT---- 78 
                                        45778*****************************4.....5667788999************..9***9987.... PP

                                        --S--EEEEEEEEEE CS
                       mRNA_triPase 205 ktkkteekyElEiEi 219
                                         ++ ++ +yE+E+E+
  gene1646|gene1646|rna1646|rna1646  79 -KSTNQVSYEIEVEL 92 
                                        .67899********6 PP

>> DUF3284  Domain of unknown function (DUF3284)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.3   1.6e-06     0.014      10      73 ..      22      91 ..      15      98 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.6e-06
                            DUF3284 10 saeefFdkliksvleDikqatgkelsrdql.kGfeYskqfknk.....eskakveIteleknkvYaikts 73
                                       +   ++d +i ++++D + a  +e++ +++ k  +Y+++ + +     +++++ +It+ +++ +Y+i+++
  gene1646|gene1646|rna1646|rna1646 22 ERVALYDVFIPNAVYDLRIALSREIPVTNViKASTYRREREREsfivdSTRFDFTITKSTNQVSYEIEVE 91
                                       55679*********************99999********99999***9******************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       515  (0.0287244); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 794.31
//
Query:       gene1647|gene1647|rna1647|rna1647  [L=153]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-05   25.1   0.0    2.6e-05   24.3   0.0    1.4  1  FeS_assembly_P  Iron-sulfur cluster assembly protein
     0.0083   15.0   0.0      0.014   14.3   0.0    1.3  1  DUF1679         Protein of unknown function (DUF1679)
  ------ inclusion threshold ------
      0.092   13.1   0.3        2.6    8.4   0.0    2.2  2  DUF4368         Domain of unknown function (DUF4368)


Domain annotation for each model (and alignments):
>> FeS_assembly_P  Iron-sulfur cluster assembly protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.0   4.4e-09   2.6e-05       3      54 ..      28      90 ..      26     102 .. 0.86

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 4.4e-09
                                       HHHHHHTT-B-TTTSSBCCCCT---E..EEE-T.........-EEEEEE--SSTT-TTHHHHH CS
                     FeS_assembly_P  3 avlaaLrtVtDPelgvdlvslglvre..idieg.........gkVsvditltypacslaeair 54
                                        v++ +r+++DPe++ +l  l++v    i+i++          +V v++++t+p+cs+a+ i 
  gene1647|gene1647|rna1647|rna1647 28 MVFELIRHIKDPEHPYSLEILNVVNLdsIEIKEisttygknlQQVVVHFQPTIPHCSMAAIIG 90
                                       599************8877777765444999999999999999**************999876 PP

>> DUF1679  Protein of unknown function (DUF1679)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   2.4e-06     0.014      10      46 ..     113     149 ..     112     153 .] 0.93

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.4e-06
                            DUF1679  10 eThvtleDvekaiqeqlgteaklgenkkltnigdlkG 46 
                                        +Thv+++ ++k++ ++ +t+a + + + l+ igd  G
  gene1647|gene1647|rna1647|rna1647 113 DTHVNWKTINKQLDDKDRTNAAFENTSILNLIGDCIG 149
                                        6*********************************988 PP

>> DUF4368  Domain of unknown function (DUF4368)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.0   0.00043       2.6      24      40 ..      20      36 ..       6      38 .. 0.88
   2 ?    2.5   0.1      0.03   1.8e+02      38      61 ..      54      77 ..      46      78 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00043
                            DUF4368 24 dieeLtpeilnelIekI 40
                                       d+++Lt+ ++ elI++I
  gene1647|gene1647|rna1647|rna1647 20 DPNKLTKGMVFELIRHI 36
                                       789*************9 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.03
                            DUF4368 38 ekIeVheaekkdgkrtqeieIyYn 61
                                       + Ie+ e   + gk+ q++ ++++
  gene1647|gene1647|rna1647|rna1647 54 DSIEIKEISTTYGKNLQQVVVHFQ 77
                                       6799***999999999*****995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       684  (0.0381505); expected 358.6 (0.02)
Passed bias filter:                      574  (0.0320152); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1028.53
//
Query:       gene1648|gene1648|rna1648|rna1648  [L=833]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.6e-65  220.0   5.4    9.3e-65  218.6   5.4    1.6  1  SNF2_N         SNF2 family N-terminal domain
    1.8e-20   73.4   0.1    1.4e-19   70.5   0.0    2.6  2  Helicase_C     Helicase conserved C-terminal domain
    1.6e-13   51.0   0.1    1.6e-13   51.0   0.1    2.7  2  ResIII         Type III restriction enzyme, res subunit
    3.4e-13   49.6   4.1    3.4e-13   49.6   4.1    2.8  3  SLIDE          SLIDE
      3e-08   33.6   0.0    7.8e-08   32.3   0.0    1.8  1  DEAD           DEAD/DEAH box helicase
  ------ inclusion threshold ------
      0.014   15.0   2.3        1.1    8.8   0.1    3.0  3  Fzo_mitofusin  fzo-like conserved region
      0.071   13.4   0.1       0.47   10.7   0.0    2.5  3  AAA_22         AAA domain
       0.16   12.5   3.5       0.44   11.0   3.5    1.8  1  MPP6           M-phase phosphoprotein 6
        2.6    8.8  15.3        0.1   13.3   6.8    3.0  3  HAND           HAND


Domain annotation for each model (and alignments):
>> SNF2_N  SNF2 family N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  218.6   5.4   4.7e-68   9.3e-65      49     349 ..      79     346 ..      67     347 .. 0.87

  Alignments for each domain:
  == domain 1  score: 218.6 bits;  conditional E-value: 4.7e-68
                                        HHHHHTT--EEE---TTS--HHHHHHHHH...HHTTTS---.......S-EEEE--HHHHHHHHHHHHHH-TTS-E CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SNF2_N  49 aeakqsvrGGiLaDemGLGKTvqvlalilaqrakeekdkekkrkdtlagptLivvPaslldqWeneierhvsssal 124
                                        ++ ++++ ++iLaDemGLGKT+q+++++    + +   k+        +p+L++vP+sll++W+ e++++++s +l
  gene1648|gene1648|rna1648|rna1648  79 ISMHEKNINCILADEMGLGKTLQTITFLG---YLKSFLKND-------TPHLLIVPKSLLHNWKAEFKKFLPSFRL 144
                                        56788999*********************...777777765.......8*************************** PP

                                        EE--SSHHHH-----------------EEEE-HHHHHHHT......TTS-S-S-SEEEES-GGGT--TTSHHHHHH CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SNF2_N 125 rvlvyggqkkmkkkntkvapklladydvvittYdvlsreaelqkkrsvlkqvewkrvvlDEghtlknstskaaeav 200
                                          ++ +  +  k+          ++ydvvittY++  + +      +v+++++w ++v+DE+h++kn++s ++++v
  gene1648|gene1648|rna1648|rna1648 145 FTFHASHVE-IKE---MEETMENTNYDVVITTYEMCISAK------KVFQRIQWCYLVIDEAHRIKNEASLLSKIV 210
                                        888777765.222...233444579************777......9***************************** PP

                                        HH---S-EEEE-S--SSS-HHHHHHHHHHH-TTTT--HHHHHHHTHHHHHHHHHHHHHHHHTT-STTEE---GGGT CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SNF2_N 201 skLstsnrwiltGTPiqnsledlygLlkfLreepfgekqtfdkllqrpieaqaekgrsrLlqllqrlmlrrakkdv 276
                                        + ++ ++r++ltGTP+qn++++l++Ll+fL ++ f++ + f+k++++  e+ ++ g+ +L+++lq + lrr k+dv
  gene1648|gene1648|rna1648|rna1648 211 RIFRCEHRLLLTGTPLQNNVHELWALLNFLDPKLFKDPEQFEKWITQM-ENDNKGGIDQLRKVLQLFFLRREKRDV 285
                                        ********************************************9875.5599*********************** PP

                                        --S---EEEEEEEEE--HHHHHHHH....................HHHHHH-HHH-HHHHHHHHHHHHH---X CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SNF2_N 277 eknlPpkteeiiflklskverksYnrllevlrkkalakllkrseaalkssskskekilelllelrqacnhpql 349
                                        ek l pk++  ++ +l++++r++Y+ +le   k+    l+kr   ++ks       +l+ + +lr++cnhp+l
  gene1648|gene1648|rna1648|rna1648 286 EKTLLPKKVINLYPQLTAMQRNLYKMILE---KDLTPLLHKR---EIKS------SLLNVVIQLRKCCNHPYL 346
                                        *************************3333...3333333333...3333......37**************98 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       1.7   3.4e+03      40      73 ..     141     172 ..     112     177 .. 0.66
   2 !   70.5   0.0   6.9e-23   1.4e-19       2     111 .]     368     481 ..     367     481 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.7
                                        TSTEEEEST.TSTHHHHHHHHHHHHTTSSSEEEES CS
                         Helicase_C  40 gikvavlhg.elpqnereeileqfnkgesdvLiat 73 
                                        +++  ++h+   + +e ee++e   + ++dv+i+t
  gene1648|gene1648|rna1648|rna1648 141 SFRLFTFHAsHVEIKEMEETME---NTNYDVVITT 172
                                        5666666662344445555555...5578898888 PP

  == domain 2  score: 70.5 bits;  conditional E-value: 6.9e-23
                                        HHHHHHHHH.HHTTTTSEEEEEESSHHHHHH.HHHHHHHTTSTEEEESTTSTHHHHHHHHHHHH..TTSSS.EEEE CS
                         Helicase_C   2 kleallell.kleeeggkilifvntidrlek.vklllekkgikvavlhgelpqnereeileqfn..kgesd.vLia 72 
                                        k+ +l +ll +++++++++lif++ +++l+   ++ ++ +++++ +++g++++ er e++++fn  + ++  +L++
  gene1648|gene1648|rna1648|rna1648 368 KMVYLDKLLtEMKRRNSRVLIFTQMTRMLDIlEDY-CTMREYEYRRIDGSTSAAERGEAIDDFNaeNSDVFvFLLS 442
                                        6778889988999****************874444.45668***********************5533444589** PP

                                        SGGGTSSSTSTTESEEEESSSSSSHHHHHHHHTTSSSTT CS
                         Helicase_C  73 tdvaerGidipkvnlVinfdlprnvtsyiqriGRtgRag 111
                                        t++++ Gi++  ++ Vi++d ++n++   q+ +R++R+g
  gene1648|gene1648|rna1648|rna1648 443 TRAGGLGINLATADIVIMYDSDWNPQIDLQAQDRAHRIG 481
                                        *************************************97 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.0   0.1   8.3e-17   1.6e-13       3     169 ..      66     225 ..      64     227 .. 0.85
   2 ?   -4.8   5.2         9   1.8e+04      98     122 ..     544     573 ..     493     742 .. 0.67

  Alignments for each domain:
  == domain 1  score: 51.0 bits;  conditional E-value: 8.3e-17
                                        EE-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S......-EEEEESSHHHHHHHHHHGGGG CS
                             ResIII   3 elreyQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkee.kflflvprkslleqtleefkkf 77 
                                        +lreyQ+e ++ l++    +++ + +++ + G GKTl  + +  +l++  k++   l++vp ksll  ++ efkkf
  gene1648|gene1648|rna1648|rna1648  66 TLREYQIEGVNWLISMH--EKNINCILADEMGLGKTLQTITFLGYLKSFLKNDtPHLLIVP-KSLLHNWKAEFKKF 138
                                        69********9999655..7899999*****************999999998855666666.799*********** PP

                                        TGG.........GEEEESSS-B--.......-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.T CS
                             ResIII  78 lseayke.....igkkvsgdkkkakekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakk 148
                                        l++ + +     + ++++ ++ +    ++tn ++++tt+++  +++       + ++r +  +++iDEaHr++ ++
  gene1648|gene1648|rna1648|rna1648 139 LPSFRLFtfhasHVEIKEMEETM----ENTNYDVVITTYEMCISAK-------KVFQRIQWCYLVIDEAHRIKNEA 203
                                        ***99889866444444444444....59*************9999.......899999999***********985 PP

                                        .TTHHHHHT---SEEEEEESS- CS
                             ResIII 149 .swreilekfkeavllglTATp 169
                                            +i++ f+   +l lT+Tp
  gene1648|gene1648|rna1648|rna1648 204 sLLSKIVRIFRCEHRLLLTGTP 225
                                        36777999*************9 PP

  == domain 2  score: -4.8 bits;  conditional E-value: 9
                                        ......-SEEEEEHHHHHHTH......... CS
                             ResIII  98 ekdstnkkilvttiqsldadseee.....e 122
                                         k+++++++ +++i ++ +++++      e
  gene1648|gene1648|rna1648|rna1648 544 DKEEKTAELNIEEIIKIGEEKTKIlntqlE 573
                                        444444444444444444444221222220 PP

>> SLIDE  SLIDE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.5       4.6   9.1e+03       6      42 ..     541     579 ..     539     594 .. 0.56
   2 ?   -0.4   0.4      0.58   1.1e+03      51      83 ..     669     701 ..     636     703 .. 0.75
   3 !   49.6   4.1   1.7e-16   3.4e-13       1     113 [.     722     828 ..     722     829 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 4.6
                              SLIDE   6 qIekgekkieklk..elkellkkkveqyknplqelkiky 42 
                                        +I  +e+k  +l+  e+ ++ ++k++ ++  l+ ++++ 
  gene1648|gene1648|rna1648|rna1648 541 NIFDKEEKTAELNieEIIKIGEEKTKILNTQLESVTLSE 579
                                        566666666654311444555566666666666666655 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.58
                              SLIDE  51 eyteeeDrfllvllakyGygnyekikkeiresp 83 
                                        ++t++     + +++ yG +n+e+ kk i +s+
  gene1648|gene1648|rna1648|rna1648 669 NWTKKDFLTFIKVTEMYGRDNFEEFKKHIDKSE 701
                                        456655566788889999999999999998876 PP

  == domain 3  score: 49.6 bits;  conditional E-value: 1.7e-16
                              SLIDE   1 ekiikqIekgekkieklkelkellkkkveqyknplqelkikyppsnkgkkeyteeeDrfllvlla.kyGygnyeki 75 
                                        +ki+++I kge++++k++ ++++lk+++e+ ++pl+  +i   ++ ++k+ +te+ D+++l  ++ +   +  +++
  gene1648|gene1648|rna1648|rna1648 722 DKILAHIAKGEQRQKKETVINTILKRIFED-NEPLRLKNI---VNVRSKN-FTEQIDMAILRGYYyRKDAEYLQNL 792
                                        79***************************9.888887775...5677776.**********954404455547*** PP

                              SLIDE  76 kkeiresplFrfDwflksrtpqelqkRcetLlklveke 113
                                         +e+++++l +f  f++++t +++qkR+++L ++++k+
  gene1648|gene1648|rna1648|rna1648 793 LMELKRKHLLNF--FVRTLTLNDIQKRLKALKSALCKS 828
                                        *********766..*********************996 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.3   0.0   3.9e-11   7.8e-08      12     149 ..      79     213 ..      68     233 .. 0.69

  Alignments for each domain:
  == domain 1  score: 32.3 bits;  conditional E-value: 3.9e-11
                                        H....TTCEEEEEESTTSSHHHH..HHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEE.E CS
                                        x....xxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.x RF
                               DEAD  12 l....gggdvlvaaeTGsGKTla..flipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvl.l 80 
                                        +    ++ ++++a e G GKTl    ++  l+++     k+ +  l+++P ++L ++   ++kkf+   +  +   
  gene1648|gene1648|rna1648|rna1648  79 IsmheKNINCILADEMGLGKTLQtiTFLGYLKSF----LKNDTPHLLIVP-KSLLHNWKAEFKKFLPSFR--LFtF 147
                                        44443455999**********9722444445555....455555677777.678899999*******855..4424 PP

                                        EETTSSHHHHHHHHHTT.CSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHS CS
                                        xxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               DEAD  81 iiggvaardqlskldng.vdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsdfinrilnql 149
                                          + v+ ++  ++++n+ +d+v++t +++++   ++ ++  q  +lV+DEa+r+ ++     +++i++ +
  gene1648|gene1648|rna1648|rna1648 148 HASHVEIKEMEETMENTnYDVVITTYEMCIS--AKKVFQRIQWCYLVIDEAHRIKNE--ASLLSKIVRIF 213
                                        567888888888888667************9..556677888899*********998..44444444444 PP

>> Fzo_mitofusin  fzo-like conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.1   0.00056       1.1      88     156 ..     146     214 ..     136     218 .. 0.91
   2 ?   -2.1   0.0       1.2   2.5e+03     102     139 ..     689     726 ..     687     748 .. 0.77
   3 ?    4.5   0.2     0.011        23      68     142 ..     745     822 ..     736     830 .. 0.68

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00056
                      Fzo_mitofusin  88 sancshqvqqelsstfarlcqqvdetekeleeeikelekeiekleevqkkakllrnkaslleseLekfe 156
                                        + + sh   +e+++t+++ + +v  t+ e+  + k++ ++i+    v+ +a+ ++n+asll++ ++ f+
  gene1648|gene1648|rna1648|rna1648 146 TFHASHVEIKEMEETMENTNYDVVITTYEMCISAKKVFQRIQWCYLVIDEAHRIKNEASLLSKIVRIFR 214
                                        557788889****************************************************99888885 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.2
                      Fzo_mitofusin 102 tfarlcqqvdetekeleeeikelekeiekleevqkkak 139
                                         f+++++++d++e+e++   +    +i++l+e  k + 
  gene1648|gene1648|rna1648|rna1648 689 NFEEFKKHIDKSEEEIRGYHRVFWGRIDELDEKDKILA 726
                                        57888999999999999988888888888888766554 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.011
                      Fzo_mitofusin  68 lKrQfveyatekLrlivsltsancshqvqqe.lsstfarlcqq.vdetekelee.eikelekeiekleevqkkakl 140
                                        lKr f +    +L+ iv++ s+n+ +q+    l  ++ r  ++  ++   el++ ++ +   +  +l+++qk++k+
  gene1648|gene1648|rna1648|rna1648 745 LKRIFEDNEPLRLKNIVNVRSKNFTEQIDMAiLRGYYYRKDAEyLQNLLMELKRkHLLNFFVRTLTLNDIQKRLKA 820
                                        89999999999****************9865134444333332134444555431345556666677777777777 PP

                      Fzo_mitofusin 141 lr 142
                                        l+
  gene1648|gene1648|rna1648|rna1648 821 LK 822
                                        76 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       4.2   8.3e+03      92     115 ..      86     112 ..      64     129 .. 0.57
   2 ?   10.7   0.0   0.00024      0.47      93     131 ..     189     225 ..     159     229 .. 0.78
   3 ?   -3.0   0.0       4.1   8.1e+03      66      91 ..     653     675 ..     633     704 .. 0.72

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 4.2
                             AAA_22  92 ielliiDEaqhlr...seealeeLrsl 115
                                        i +++ DE+       + + l +L+s+
  gene1648|gene1648|rna1648|rna1648  86 INCILADEMGLGKtlqTITFLGYLKSF 112
                                        466666666543222224444444555 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00024
                             AAA_22  93 elliiDEaqhlr.seealeeLrsllnlsrkgvqliLvGtp 131
                                          l+iDEa+++  ++ +l+++   + + r+  +l+L Gtp
  gene1648|gene1648|rna1648|rna1648 189 CYLVIDEAHRIKnEASLLSKI---VRIFRCEHRLLLTGTP 225
                                        579********4335555555...5555599999**9998 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 4.1
                             AAA_22  66 lelkaerlsseellealeqalrarav 91 
                                        ++   e +++eel+e+ ++++ +++ 
  gene1648|gene1648|rna1648|rna1648 653 EQ---ESKRKEELMEMGYRNWTKKDF 675
                                        22...445888888888888777655 PP

>> MPP6  M-phase phosphoprotein 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   3.5   0.00022      0.44      32     114 ..     636     751 ..     595     770 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00022
                               MPP6  32 kklkdssewvldnpekkkkkskiksevsnvgfedl.........essvifGRrsFggfnkeve..e.......... 86 
                                        + +k++ e++ + ++ ++++sk+k+e+  +g+ +          + + ++GR  F+ f+k+++  e          
  gene1648|gene1648|rna1648|rna1648 636 EIIKKENELYDQGEQLSEQESKRKEELMEMGYRNWtkkdfltfiKVTEMYGRDNFEEFKKHIDksEeeirgyhrvf 711
                                        56778888888999999999*****8888888888888888888889****************5425677777777 PP

                               MPP6  87 ............kkeeeeeeeekekeedvsdeelakrykk 114
                                                      +   + e+++k+e v  + l++++++
  gene1648|gene1648|rna1648|rna1648 712 wgrideldekdkILAHIAKGEQRQKKETVINTILKRIFED 751
                                        7666544433332222233333356666666666666655 PP

>> HAND  HAND
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.4         9   1.8e+04      81      85 ..     545     549 ..     508     572 .. 0.46
   2 ?   13.3   6.8   5.2e-05       0.1      18      68 ..     610     660 ..     595     703 .. 0.71
   3 ?   -3.7   0.0         9   1.8e+04      35      53 ..     708     726 ..     706     739 .. 0.70

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 9
                                        HHHHH CS
                               HAND  81 ekrke 85 
                                        +++k+
  gene1648|gene1648|rna1648|rna1648 545 KEEKT 549
                                        22222 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 5.2e-05
                                        --.--S--------GGC--S--CCHHHHHHHHHHHHHHCCT----CCCHTT CS
                               HAND  18 tkkpkapraPKqiniqdfqffpkeLkeLqekEqlaykKkigykvtlddkke 68 
                                        +++++  + PKq+ + +++f+pkeL+e+ +kE+  y +  +   + ++ ke
  gene1648|gene1648|rna1648|rna1648 610 RRNSSLFQRPKQLILPEYHFYPKELFEIIKKENELYDQGEQLSEQESKRKE 660
                                        455778899************************999887666644333333 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 9
                                        --S--CCHHHHHHHHHHHH CS
                               HAND  35 fqffpkeLkeLqekEqlay 53 
                                        ++ f  +++eL ek+++  
  gene1648|gene1648|rna1648|rna1648 708 HRVFWGRIDELDEKDKILA 726
                                        6667777888888887654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (833 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1333  (0.0743488); expected 358.6 (0.02)
Passed bias filter:                      452  (0.0252106); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.72u 0.30s 00:00:01.02 Elapsed: 00:00:00.46
# Mc/sec: 5439.13
//
Query:       gene1649|gene1649|rna1649|rna1649  [L=45]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (45 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       278  (0.0155056); expected 358.6 (0.02)
Passed bias filter:                      210  (0.0117129); expected 358.6 (0.02)
Passed Vit filter:                         7  (0.000390429); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.23s 00:00:00.57 Elapsed: 00:00:00.39
# Mc/sec: 348.42
//
Query:       gene165|gene165|rna165|rna165  [L=312]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    9.2e-11   42.1   9.4     0.0037   18.1   0.1    5.4  6  WD40       WD domain, G-beta repeat
    3.8e-06   26.5   1.8    0.00014   21.3   0.5    2.2  2  WD40_like  WD40-like domain
    6.4e-05   22.4   0.1    0.00014   21.2   0.0    1.5  1  NUP214     Nucleoporin or Nuclear pore complex subunit NUP214
    0.00013   21.7   7.0       0.75    9.8   0.2    4.9  5  PQQ        PQQ enzyme repeat
     0.0072   16.8   4.9       0.56   10.8   0.3    4.5  5  PQQ_3      PQQ-like domain
  ------ inclusion threshold ------
      0.038   13.5   0.1       0.36   10.3   0.0    2.6  4  HPS3_N     Hermansky-Pudlak syndrome 3


Domain annotation for each model (and alignments):
>> WD40  WD domain, G-beta repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.1   0.4    0.0073        22      13      38 .]      19      44 ..       7      44 .. 0.87
   2 ?    2.2   0.0      0.13     4e+02       9      36 ..      50      83 ..      47      85 .. 0.68
   3 !   16.9   0.1   2.9e-06    0.0085       3      38 .]      90     124 ..      88     124 .. 0.74
   4 ?   -0.9   0.0       1.2   3.7e+03      10      30 ..     176     196 ..     167     202 .. 0.54
   5 !   18.1   0.1   1.2e-06    0.0037       5      38 .]     211     251 ..     208     251 .. 0.86
   6 ?   -2.0   0.0       2.6   7.9e+03      12      31 ..     266     286 ..     254     288 .. 0.64

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0073
                                   EEEEEEETTSSEEEEEETTSEEEEEE CS
                           WD40 13 vtslafspdgawlasGsdDgtvriWd 38
                                   v+++a ++  + +a+ s+D++++ +d
  gene165|gene165|rna165|rna165 19 VSDIALHDTYDIFAATSWDCSIYYYD 44
                                   899999999****999******9776 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.13
                                   SSSSEEEEE......EETTSSEEEEEETTSEEEE CS
                           WD40  9 GHssvtsla......fspdgawlasGsdDgtvri 36
                                   GH+s t l+         dg+ +++G  +gt+++
  gene165|gene165|rna165|rna165 50 GHKSTTKLDapllsgSFFDGNKMVAGAVNGTLYV 83
                                   6655666666666665566666678999999987 PP

  == domain 3  score: 16.9 bits;  conditional E-value: 2.9e-06
                                    EEEEEESS.SSEEEEEEETTSSEEEEEETTSEEEEEE CS
                           WD40   3 clrtltGH.ssvtslafspdgawlasGsdDgtvriWd 38 
                                    ++ +++GH  ++  +    +++ +++Gs+D+++++Wd
  gene165|gene165|rna165|rna165  90 QVSEIKGHdLGIKKV--KVYNNIVITGSWDKKLKFWD 124
                                    567789995335544..336677*************9 PP

  == domain 4  score: -0.9 bits;  conditional E-value: 1.2
                                    S.SS.EEEEEEETTSSEEEEEET CS
                           WD40  10 H.ss.vtslafspdgawlasGsd 30 
                                      ++  +s++ s d+ ++  G+ 
  gene165|gene165|rna165|rna165 176 KlKWqLRSVCCSNDQVLV--GGV 196
                                    444445566666665553..655 PP

  == domain 5  score: 18.1 bits;  conditional E-value: 1.2e-06
                                    EEEESS.SS.....EEEEEEETTSSEE.EEEETTSEEEEEE CS
                           WD40   5 rtltGH.ss.....vtslafspdgawl.asGsdDgtvriWd 38 
                                    + ++GH +      +++++++p ++ l asG+ D++v i++
  gene165|gene165|rna165|rna165 211 HFYKGHrNAnvlyaINCIDVHPLNSSLiASGGNDNNVLIYN 251
                                    6799**97789********88888886269999******97 PP

  == domain 6  score: -2.0 bits;  conditional E-value: 2.6
                                    SEEEEEEETTSSE.EEEEETT CS
                           WD40  12 svtslafspdgaw.lasGsdD 31 
                                    +vt+ +f+++g++ + s ++D
  gene165|gene165|rna165|rna165 266 PVTAGRFNRNGQFyIYSTGED 286
                                    477667888998866555555 PP

>> WD40_like  WD40-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.5   4.6e-08   0.00014      92     231 ..      69     213 ..      62     228 .. 0.79
   2 !    4.4   0.1    0.0068        20       6      36 ..     228     259 ..     220     264 .. 0.78

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 4.6e-08
                      WD40_like  92 ddklliGtnkGsiyvfskdlqleevllgqsseIkeikiennkiysLsesa.fivfdlfsqnieykisvkdiktfeiienk 170
                                    ++k++ G+ +G++yv +   + +  + g+   Ik++k+ nn++ + s ++ +  +dl s+  +   ++ +      i+n 
  gene165|gene165|rna165|rna165  69 GNKMVAGAVNGTLYVVDVATNQVSEIKGHDLGIKKVKVYNNIVITGSWDKkLKFWDLRSNAPLFTHELANKVYAMDIKNG 148
                                    7899***********999988888999*****************99966515566************9998888778788 PP

                      WD40_like 171 di.lligtegeili....lkknvilqkidvegkPecillvddylivGgsfkyllliNiklnvntfk 231
                                    ++ l++++++ ++     ++++ il + +++ +   +  ++d ++vGg    + ++N+   + +f+
  gene165|gene165|rna165|rna165 149 NLaLALSNNTVVMHsigdFQRQRIL-RTKLKWQLRSVCCSNDQVLVGGVEGAIEVLNMSDVSDHFY 213
                                    8735666666555421222344455.3344445589999*******************98888886 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.0068
                      WD40_like   6 idisk.kgslilyGgkddkctvlkleslesvs 36 
                                    id+ + ++sli+ Gg+d+++ +++ ++ ++v 
  gene165|gene165|rna165|rna165 228 IDVHPlNSSLIASGGNDNNVLIYNKQQRIKVH 259
                                    566533899**************988877765 PP

>> NUP214  Nucleoporin or Nuclear pore complex subunit NUP214=Nup159
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0   4.7e-08   0.00014      73     169 ..      68     166 ..      58     183 .. 0.86

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 4.7e-08
                                    ETTE.EEEEESSEEEEEESSSTT.EEEEEE-SS-EE..EEETTEEEEEETTSEEEEEETT.......EEEECSEEEEEE- CS
                         NUP214  73 lndevvlvstksellsldleelseleeihklekdlvelkllkstlllldsnnqLsaldlskkel...kslaenvasfDvl 149
                                     ++++v  + +++l+ +d+   ++++ei+  +  ++++k++++ ++  + +++L+ +dl+ +     ++la++v ++D+ 
  gene165|gene165|rna165|rna165  68 DGNKMVAGAVNGTLYVVDVAT-NQVSEIKGHDLGIKKVKVYNNIVITGSWDKKLKFWDLRSNAPlftHELANKVYAMDIK 146
                                    456677777889999999988.78899********************************966547889************ PP

                                    SSEEEEEETTS-EEEEEEEE CS
                         NUP214 150 edkLvvllkdksvqvfelen 169
                                    + +L++ l++++v ++++  
  gene165|gene165|rna165|rna165 147 NGNLALALSNNTVVMHSIGD 166
                                    ******99999998877754 PP

>> PQQ  PQQ enzyme repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.9   0.3    0.0092        27       3      19 ..      30      47 ..      29      47 .. 0.91
   2 !    9.8   0.2   0.00025      0.75       1      21 [.      70      90 ..      70      91 .. 0.91
   3 !    6.9   0.0    0.0022       6.5       6      22 ..     134     150 ..     130     151 .. 0.83
   4 ?   -2.3   0.0       1.7   5.2e+03       8      16 ..     218     226 ..     215     226 .. 0.80
   5 ?   -3.1   0.0       3.2   9.5e+03       5      17 ..     293     305 ..     291     306 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.0092
                                   EEEE.ETTSEEEEEETTT CS
                            PQQ  3 vylg.sadGylyAlDadT 19
                                   ++++ s d  +y +Da++
  gene165|gene165|rna165|rna165 30 IFAAtSWDCSIYYYDAND 47
                                   89999***********97 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00025
                                   TEEEEEETTSEEEEEETTTCC CS
                            PQQ  1 gvvylgsadGylyAlDadTGk 21
                                   +++++g  +G+ly +D++T++
  gene165|gene165|rna165|rna165 70 NKMVAGAVNGTLYVVDVATNQ 90
                                   6899***************87 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.0022
                                    EETTSEEEEEETTTCCE CS
                            PQQ   6 gsadGylyAlDadTGkv 22 
                                    +   +++yA D+++G++
  gene165|gene165|rna165|rna165 134 HELANKVYAMDIKNGNL 150
                                    667799*********96 PP

  == domain 4  score: -2.3 bits;  conditional E-value: 1.7
                                    TTSEEEEEE CS
                            PQQ   8 adGylyAlD 16 
                                    + ++lyA++
  gene165|gene165|rna165|rna165 218 NANVLYAIN 226
                                    6789***98 PP

  == domain 5  score: -3.1 bits;  conditional E-value: 3.2
                                    EEETTSEEEEEET CS
                            PQQ   5 lgsadGylyAlDa 17 
                                    ++++++ ++ lD+
  gene165|gene165|rna165|rna165 293 ATQFPTSVCVLDV 305
                                    5578889999997 PP

>> PQQ_3  PQQ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.6      0.05   1.5e+02      10      40 .]      15      47 ..      11      47 .. 0.76
   2 !   10.8   0.3   0.00019      0.56       7      40 .]      55      88 ..      54      88 .. 0.87
   3 ?    0.1   0.0      0.42   1.2e+03      19      38 ..     106     125 ..      98     127 .. 0.82
   4 ?   -3.7   0.0         6   1.8e+04      31      39 ..     138     146 ..     133     147 .. 0.77
   5 ?   -2.6   0.0       3.1   9.3e+03      12      22 ..     232     242 ..     229     249 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.05
                          PQQ_3 10 pgpvnsspavdggl.vyvgtg.dGtlyAlDaet 40
                                   p +++s  a+ + + ++++t+ d ++y +Da++
  gene165|gene165|rna165|rna165 15 PNDTVSDIALHDTYdIFAATSwDCSIYYYDAND 47
                                   5566677777776667777778********975 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00019
                          PQQ_3  7 vqlpgpvnsspavdgglvyvgtgdGtlyAlDaet 40
                                   ++l++p+ s+  +dg++ ++g+ +Gtly +D +t
  gene165|gene165|rna165|rna165 55 TKLDAPLLSGSFFDGNKMVAGAVNGTLYVVDVAT 88
                                   66777888888899*****************988 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.42
                          PQQ_3  19 vdgglvyvgtgdGtlyAlDa 38 
                                    v++++v +g++d +l   D 
  gene165|gene165|rna165|rna165 106 VYNNIVITGSWDKKLKFWDL 125
                                    67899*******99866665 PP

  == domain 4  score: -3.7 bits;  conditional E-value: 6
                          PQQ_3  31 GtlyAlDae 39 
                                    +++yA D +
  gene165|gene165|rna165|rna165 138 NKVYAMDIK 146
                                    578998875 PP

  == domain 5  score: -2.6 bits;  conditional E-value: 3.1
                          PQQ_3  12 pvnsspavdgg 22 
                                    p+nss+ ++gg
  gene165|gene165|rna165|rna165 232 PLNSSLIASGG 242
                                    67888888887 PP

>> HPS3_N  Hermansky-Pudlak syndrome 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       1.7     5e+03      24      46 ..      23      47 ..       9      56 .. 0.64
   2 ?   -1.1   0.0      0.38   1.1e+03     153     208 ..     103     161 ..      96     163 .. 0.62
   3 ?   10.3   0.0   0.00012      0.36       7      45 ..     166     206 ..     159     229 .. 0.86
   4 ?   -1.8   0.0      0.62   1.9e+03      26      47 ..     241     264 ..     221     279 .. 0.54

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 1.7
                         HPS3_N 24 caagdk..Llvatesgc.vevydlee 46
                                     ++    ++ at+ +c +  yd + 
  gene165|gene165|rna165|rna165 23 ALHD-TydIFAATSWDCsIYYYDAND 47
                                   3444.235899999888888888544 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.38
                         HPS3_N 153 klslfrlkvktqdise.lkllDfeel..llllelkfvpkqvaicedyvAvmselevkvl 208
                                    k+++++  v t + ++ lk+ D+ +   l+ +el  ++  ++i ++ +A++ +++  v+
  gene165|gene165|rna165|rna165 103 KVKVYNNIVITGSWDKkLKFWDLRSNapLFTHELANKVYAMDIKNGNLALALSNNTVVM 161
                                    55566554444444444777777653225777777777777777777777777666665 PP

  == domain 3  score: 10.3 bits;  conditional E-value: 0.00012
                         HPS3_N   7 nFksqevvsveq..eptavcaagdkLlvatesgcvevydle 45 
                                     F+ q++++++   +  +vc+++d++lv+  +g +ev +++
  gene165|gene165|rna165|rna165 166 DFQRQRILRTKLkwQLRSVCCSNDQVLVGGVEGAIEVLNMS 206
                                    7*******999878999********************9875 PP

  == domain 4  score: -1.8 bits;  conditional E-value: 0.62
                         HPS3_N  26 ag.dk.Llvatesgcvevydleee 47 
                                    +g d+ +l+  +++++ v + +++
  gene165|gene165|rna165|rna165 241 GGnDNnVLIYNKQQRIKVHTERTN 264
                                    223334666666666666554443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (312 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       482  (0.0268838); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 2138.61
//
Query:       gene1650|gene1650|rna1650|rna1650  [L=447]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      6e-17   61.6  21.8    9.3e-17   61.0  21.8    1.3  1  MFS_1_like  MFS_1 like family
    0.00074   17.9   0.2     0.0024   16.2   0.0    1.9  1  OATP        Organic Anion Transporter Polypeptide (OATP) fami


Domain annotation for each model (and alignments):
>> MFS_1_like  MFS_1 like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.0  21.8     1e-20   9.3e-17       3     378 ..       7     391 ..       5     395 .. 0.84

  Alignments for each domain:
  == domain 1  score: 61.0 bits;  conditional E-value: 1e-20
                         MFS_1_like   3 slkilyFfffaalgsllPYltiylkskglkaseigiitlilpltsilsppiwgvlaDrfgkrkkvvilslllsavl 78 
                                        sl ++ Ff++a++ +++ ++    k++g+  ++   ++ +l ++++++  i+ +l Dr g++  +v+++++l  v+
  gene1650|gene1650|rna1650|rna1650   7 SLFMISFFLYASIYAVHNFMFQIVKETGVIDKKKYCLLQLLYIFKFAGVVIFCNLGDRKGIHRYLVAINVVLYSVS 82 
                                        667788********************************************************************** PP

                         MFS_1_like  79 flsllfippskerqeesklevsvaqdvdaektfwilfllvvlasfflaailvlldaatlkel...gedrkdyGrqr 151
                                         l+l+ ++              +   +  +k   +++l +v  ++f++++++lld++t++ l   g d ++ Gr+r
  gene1650|gene1650|rna1650|rna1650  83 ILALYNLS--------------SIASLRLRKA--FVILTIVSSYIFISGTFPLLDSLTYNYLeheGLDVRQSGRVR 142
                                        **999433..............4444445555..55667778899*****************6655667789**** PP

                         MFS_1_like 152 lfGsvGyaifafitGilidhysvnllp...........ysallyvlaallvisllvv..lilnetekesklkvtks 214
                                        + G++G + + ++ ++l   +s+ l +           +s  l++ a+  +i+ll++  ++l ++  +   k  k+
  gene1650|gene1650|rna1650|rna1650 143 MGGALGNMFVQVVCSLLQYCFSRRLRGegtknrenvinISCNLFFSAGTALIALLFApnYVLGKKVIHAPKKAWKV 218
                                        ******998888888877777887766********99955555555555555555531266666666655555555 PP

                         MFS_1_like 215 lqvllni..lknpeviifllvalilgmswgiienFlflYLkelgasntllGslvalgvvaeiplfffaeklleklG 288
                                        ++ ++ +  l np +++  l++l  g+  + i +Fl+ YL+++g  ++ + +l + +++ ei ++ +++++   lG
  gene1650|gene1650|rna1650|rna1650 219 KKIFTDLisLLNPLLVLYTLAVLGQGIDRAGISTFLSKYLENKGIERSYVHVLFFCRCIPEILIYGLSQQIESVLG 294
                                        555555511346777777777777889999********************************************** PP

                         MFS_1_like 289 hvklliiallayilrfllyaii.......enawlvlpievLhgisfgllwaaaveyvskiapksleatgqgllsgl 357
                                        + ++ ++++++   r + y+++       +   +++++e+++g+    +   + +  + +a++ + +  qg+++g+
  gene1650|gene1650|rna1650|rna1650 295 MNTMFLLSVIISSSRSFFYSSYnfnnspgTLKAITVIAEIFKGFYSSFFNYCGLRIFRSFATDDTLSLAQGIFNGT 370
                                        ***************9999998888777666789999************9************************** PP

                         MFS_1_like 358 yfglGralGsliGGllwdlks 378
                                        y  l  +  +++G +l d+++
  gene1650|gene1650|rna1650|rna1650 371 YNALSYFTFAFLGYFLVDYEK 391
                                        ****99999999977777765 PP

>> OATP  Organic Anion Transporter Polypeptide (OATP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   2.7e-07    0.0024     223     335 ..     150     271 ..     144     285 .. 0.69

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2.7e-07
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......x......xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               OATP 223 gvllllaaiplffFPkelpkkkeerakkkseeesa......e......kkeekkkkeksksseeeelkslkdfpka 286
                                        +++ ++++++ ++F ++l+++ ++++++  + + +      +      ++ +    +k  +   +++ ++k++++ 
  gene1650|gene1650|rna1650|rna1650 150 MFVQVVCSLLQYCFSRRLRGEGTKNRENVINISCNlffsagTaliallFAPNYVLGKKVIHAP-KKAWKVKKIFTD 224
                                        566778888888888888877777776665554445555441445555333333333333333.567889999999 PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               OATP 287 lkrllknpifllvilssvfeillvaGfitFlpkylEtqFslsaseAnll 335
                                        l +ll np+++l++l+   + +  aG++tFl+kylE++ ++++s+ ++l
  gene1650|gene1650|rna1650|rna1650 225 LISLL-NPLLVLYTLAVLGQGIDRAGISTFLSKYLENK-GIERSYVHVL 271
                                        99887.9*****************************97.5666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (447 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       618  (0.0344693); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 3146.74
//
Query:       gene1651|gene1651|rna1651|rna1651  [L=594]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
      0.055   13.6   0.5        1.7    8.7   0.0    3.0  3  TAN         Telomere-length maintenance and DNA damage repair
          1    9.7   4.1        1.7    9.0   0.2    3.4  4  His_kinase  Histidine kinase


Domain annotation for each model (and alignments):
>> TAN  Telomere-length maintenance and DNA damage repair
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.0   0.00019       1.7       9      63 ..      27      76 ..      19     109 .. 0.87
   2 ?    1.3   0.1     0.038   3.4e+02     105     145 ..     168     206 ..     144     210 .. 0.78
   3 ?   -3.2   0.0      0.93   8.3e+03      13      21 ..     520     528 ..     505     579 .. 0.54

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00019
                                TAN  9 ssskikeRnkaldeLkhllsskrnktslsdlkdkawheifeaLfklvekEkeayl 63
                                        ss +++R +a+++Lk+++ +++n     +++  ++++++e+++++v++++  +l
  gene1651|gene1651|rna1651|rna1651 27 ASSYLEDRVAAINSLKEIVEKSPN-----EVGIYSMASVIESMQHFVHRDHFEVL 76
                                       588899******************.....9*****************99886665 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.038
                                TAN 105 lldhitqllpgpdgelleplaldyikaLrsllsvpphvehL 145
                                        ++++i ++l  ++++ ++p+   ++  Lr+ ++v+ h   L
  gene1651|gene1651|rna1651|rna1651 168 IFESIFKML--HEHKHVKPCFSTISNLLRDSFEVQDHFYDL 206
                                        666777777..366889999999999999999998887666 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 0.93
                                TAN  13 ikeRnkald 21 
                                        i+eR kal+
  gene1651|gene1651|rna1651|rna1651 520 ITERCKALQ 528
                                        444444444 PP

>> His_kinase  Histidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.29   2.6e+03      38      48 ..      74      84 ..      37     125 .. 0.59
   2 ?   -3.7   0.0       1.8   1.6e+04      31      48 ..     180     197 ..     170     206 .. 0.64
   3 ?    9.0   0.2   0.00019       1.7      11      31 ..     219     236 ..     216     274 .. 0.73
   4 ?   -1.3   0.1      0.32   2.9e+03      40      64 ..     340     366 ..     335     367 .. 0.68

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.29
                         His_kinase 38 ekLskllrysl 48
                                       e Ls+++r s 
  gene1651|gene1651|rna1651|rna1651 74 EVLSSIFRSSN 84
                                       33333333333 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 1.8
                         His_kinase  31 eeaeemlekLskllrysl 48 
                                        + ++   + +s+llr s+
  gene1651|gene1651|rna1651|rna1651 180 KHVKPCFSTISNLLRDSF 197
                                        445556667788888777 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.00019
                         His_kinase  11 nPHFlfNtLnsiqslaeedpe 31 
                                        nPH++fN+L+s+      +++
  gene1651|gene1651|rna1651|rna1651 219 NPHYFFNVLESLLDT---RNT 236
                                        9**********9422...333 PP

  == domain 4  score: -1.3 bits;  conditional E-value: 0.32
                         His_kinase  40 Lskllrysl.eseee.vtLeeElelle 64 
                                         s+ll  sl  +++e  ++++E+++ e
  gene1651|gene1651|rna1651|rna1651 340 VSELLETSLkIKTDEqEPVQKEIDYSE 366
                                        578888888423333467****99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (594 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       945  (0.0527079); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.62u 0.25s 00:00:00.87 Elapsed: 00:00:00.45
# Mc/sec: 3992.23
//
Query:       gene1652|gene1652|rna1652|rna1652  [L=171]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.8e-15   57.2   8.0    3.2e-15   56.4   8.0    1.4  1  DUF4451      Domain of unknown function (DUF4451)
  ------ inclusion threshold ------
       0.36   11.2   9.3        1.7    9.1   1.0    3.3  3  zf-C2H2_jaz  Zinc-finger double-stranded RNA-binding
          1    9.5   8.6       0.98    9.5   0.3    3.1  3  zf-CW        CW-type Zinc Finger
        2.6    8.6   7.0         19    5.9   0.1    3.3  3  zf-H2C2_2    Zinc-finger double domain


Domain annotation for each model (and alignments):
>> DUF4451  Domain of unknown function (DUF4451)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.4   8.0   7.1e-19   3.2e-15       4     122 .]      73     169 ..      70     169 .. 0.85

  Alignments for each domain:
  == domain 1  score: 56.4 bits;  conditional E-value: 7.1e-19
                            DUF4451   4 ndlYeprvvrgekdknekkeglCpiCeeevekkekflklknssyekhlsfeHGvlsngslvpePillrskkrrkak 79 
                                        +++Y p+ v+g   k+  +eg C  C+       k+++lk+ssy++h++++HG++s+g ++p+P+l       +++
  gene1652|gene1652|rna1652|rna1652  73 KEMYRPKHVKG---KGILREGYCDSCN-------KWFRLKTSSYWYHMNYKHGINSKGKKYPQPYLR------EMY 132
                                        689********...999**********.......9*****************************997......333 PP

                            DUF4451  80 ekekegivCpkCneiievslsknkkekkvnellayfrHfkkch 122
                                        +  + +  C  C ++i + + + kk+      +a++rHf+k h
  gene1652|gene1652|rna1652|rna1652 133 N--RLESYCRMCDKWIFLCSASGKKSV----TYAWYRHFQKNH 169
                                        3..36678*******976655544443....489******998 PP

>> zf-C2H2_jaz  Zinc-finger double-stranded RNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.1         1   4.7e+03      19      24 ..      79      84 ..      78      85 .. 0.86
   2 ?    9.1   1.0   0.00037       1.7       3      11 ..      91      99 ..      91     100 .. 0.95
   3 ?    6.1   0.3    0.0031        14       3      10 ..     138     145 ..     136     146 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1
                                       CCTTSH CS
                        zf-C2H2_jaz 19 nHlkSK 24
                                       +H+k+K
  gene1652|gene1652|rna1652|rna1652 79 KHVKGK 84
                                       69**99 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00037
                                       BBTTTTBBB CS
                        zf-C2H2_jaz  3 YCvlCdKyF 11
                                       YC  C+K+F
  gene1652|gene1652|rna1652|rna1652 91 YCDSCNKWF 99
                                       9******** PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.0031
                                        BBTTTTBB CS
                        zf-C2H2_jaz   3 YCvlCdKy 10 
                                        YC  CdK+
  gene1652|gene1652|rna1652|rna1652 138 YCRMCDKW 145
                                        *******9 PP

>> zf-CW  CW-type Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.42   1.9e+03      27      35 ..      11      19 ..       3      25 .. 0.74
   2 ?    9.5   0.3   0.00022      0.98       5      17 ..      92     104 ..      91     112 .. 0.86
   3 ?    3.0   1.2     0.024   1.1e+02       5      16 ..     139     150 ..     138     164 .. 0.71

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.42
                              zf-CW 27 kWvCsmnps 35
                                        ++C ++++
  gene1652|gene1652|rna1652|rna1652 11 HFFCYDQNN 19
                                       799*99773 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00022
                              zf-CW   5 CdkClKWRrlpte 17 
                                        Cd+C KW rl+t+
  gene1652|gene1652|rna1652|rna1652  92 CDSCNKWFRLKTS 104
                                        *******999886 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.024
                              zf-CW   5 CdkClKWRrlpt 16 
                                        C  C KW  l +
  gene1652|gene1652|rna1652|rna1652 139 CRMCDKWIFLCS 150
                                        99*****66655 PP

>> zf-H2C2_2  Zinc-finger double domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.1    0.0043        19      16      24 ..      91      99 ..      77     100 .. 0.82
   2 ?    5.2   0.4    0.0068        31       2      22 ..     106     144 ..     105     146 .. 0.74
   3 ?   -1.2   0.1      0.77   3.4e+03       3       9 ..     162     169 ..     160     170 .. 0.72

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0043
                          zf-H2C2_2 16 eCplCdkaF 24
                                        C++C+k+F
  gene1652|gene1652|rna1652|rna1652 91 YCDSCNKWF 99
                                       6*******9 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0068
                          zf-H2C2_2   2 LrrHir.kHt....gek...py..........eCplCdk 22 
                                        +++H+  kH     g+k   py           C  Cdk
  gene1652|gene1652|rna1652|rna1652 106 YWYHMNyKHGinskGKKypqPYlremynrlesYCRMCDK 144
                                        89***7367787766666555688888889999999988 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 0.77
                          zf-H2C2_2   3 rrHirk.H 9  
                                         rH+ k H
  gene1652|gene1652|rna1652|rna1652 162 YRHFQKnH 169
                                        69997658 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       656  (0.0365888); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 1152.99
//
Query:       gene1653|gene1653|rna1653|rna1653  [L=547]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.1e-13   51.2   0.5    1.1e-13   51.2   0.5    2.4  3  MS_channel  Mechanosensitive ion channel
      0.004   17.0   0.2      0.037   14.0   0.2    2.7  1  EF-hand_6   EF-hand domain
  ------ inclusion threshold ------
      0.069   12.7   0.2      0.069   12.7   0.2    2.7  3  EF-hand_1   EF hand


Domain annotation for each model (and alignments):
>> MS_channel  Mechanosensitive ion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.2       0.3   1.8e+03       1      22 [.      36      57 ..      36      68 .. 0.85
   2 ?   -1.7   0.3      0.28   1.7e+03      24      40 ..     147     163 ..     141     167 .. 0.87
   3 !   51.2   0.5   1.8e-17   1.1e-13       2     148 ..     340     485 ..     339     540 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.3
                                       ..HHHHHHHHHHHHHHHHTTT- CS
                         MS_channel  1 kkilkiliivvgilivlsllgv 22
                                       kki+++ i+++g + ++ ++  
  gene1653|gene1653|rna1653|rna1653 36 KKIFNYAILICGSVYIFRYIFN 57
                                       589*************999865 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.28
                                        SCCHHHHHHHHHHHHHH CS
                         MS_channel  24 vsallavlGalglalgl 40 
                                        +s +l++ +++g+al++
  gene1653|gene1653|rna1653|rna1653 147 LSGILTGTAFTGVALAM 163
                                        7899***********97 PP

  == domain 3  score: 51.2 bits;  conditional E-value: 1.8e-17
                                        .HHHHHHHHHHHHHHHHTTT--SCCHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHTT-SS-TT-EEESSSEEEEEE CS
                         MS_channel   2 kilkiliivvgilivlsllgvnvsallavlGalglalglalkdlisnlvaGiillfekpfkiGDlveigdieGtVe 77 
                                        +il+i++  + il++l  +g++++ lla++   +l+l +a+  +  +l   +++l+++pf+iGD v i +  +tV 
  gene1653|gene1653|rna1653|rna1653 340 DILSIVVCGFLILAYLVIFGIPLKELLALALSSALVLNFAVSGMAVDLYFNFMVLLSHPFDIGDDVIIDNTNYTVY 415
                                        7999************************************************************************ PP

                                        EE-SSEEEEEETTSEEEEEEHHHHHTS-EEESSS.SSEEEEEEEEEE-TTS-...HHHHHHHHHHHHHH-T CS
                         MS_channel  78 diglrttkirtfdgrivtiPnsslvtsnieNlsresgtrrikvsigvtyssdvkklekvleelkealkekp 148
                                        +igl +t++  ++g  v   ns l++++ +N++r  +++ + +++++  + d +  +++ +++ + lk  +
  gene1653|gene1653|rna1653|rna1653 416 KIGLNSTSFLGRNGGKVKFLNSVLWKKTLINMTR-APEKVLLFTFKLSSDVDADVFRNLKSRIHQYLKTRK 485
                                        **********************************.899988999988888887788888888877776655 PP

>> EF-hand_6  EF-hand domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.2   6.2e-06     0.037       4      26 ..     292     314 ..     290     323 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 6.2e-06
                          EF-hand_6   4 eaFklfDkdgdGkidaeElrkal 26 
                                        +aF +fD ++d +++++E+++ +
  gene1653|gene1653|rna1653|rna1653 292 QAFAYFDANDDRTVSRKEFKDTI 314
                                        79*****************9965 PP

>> EF-hand_1  EF hand
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.6       1.7     1e+04      17      22 ..      13      18 ..      12      19 .. 0.86
   2 ?   -1.7   0.1      0.46   2.8e+03      17      26 ..     275     284 ..     274     285 .. 0.82
   3 ?   12.7   0.2   1.2e-05     0.069       4      25 ..     292     313 ..     289     317 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 1.7
                                       EEHHHH CS
                          EF-hand_1 17 IdfeEf 22
                                       Id eEf
  gene1653|gene1653|rna1653|rna1653 13 IDVEEF 18
                                       9****9 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.46
                                        EEHHHHHHHH CS
                          EF-hand_1  17 IdfeEfkell 26 
                                        ++f+Ef +++
  gene1653|gene1653|rna1653|rna1653 275 MSFNEFADIF 284
                                        699***9875 PP

  == domain 3  score: 12.7 bits;  conditional E-value: 1.2e-05
                                        HHHHHHTTTSSSEEEHHHHHHH CS
                          EF-hand_1   4 eiFrefDkDgdGkIdfeEfkel 25 
                                        ++F+ fD + d +++++Efk+ 
  gene1653|gene1653|rna1653|rna1653 292 QAFAYFDANDDRTVSRKEFKDT 313
                                        79*****************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (547 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       784  (0.043728); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.61u 0.27s 00:00:00.88 Elapsed: 00:00:00.46
# Mc/sec: 3538.05
//
Query:       gene1654|gene1654|rna1654|rna1654  [L=666]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   1.2e-111  371.8   3.3     2e-111  371.1   3.3    1.3  1  ERCC3_RAD25_C  ERCC3/RAD25/XPB C-terminal helicase
    4.3e-33  114.2   0.0    1.2e-32  112.7   0.0    1.7  2  Helicase_C_3   Helicase conserved C-terminal domain
      4e-15   56.2   0.9    1.3e-14   54.5   0.0    2.3  3  ResIII         Type III restriction enzyme, res subunit
    3.1e-12   46.8   0.2    1.5e-11   44.6   0.0    2.4  2  Helicase_C     Helicase conserved C-terminal domain
    1.1e-06   27.6   0.4      4e-06   25.8   0.4    1.8  2  SNF2_N         SNF2 family N-terminal domain
    8.1e-05   22.4   0.0    0.00019   21.2   0.0    1.7  1  DEAD           DEAD/DEAH box helicase
     0.0092   15.3   0.0      0.017   14.4   0.0    1.4  1  DUF3638        Protein of unknown function (DUF3638)


Domain annotation for each model (and alignments):
>> ERCC3_RAD25_C  ERCC3/RAD25/XPB C-terminal helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  371.1   3.3    8e-115    2e-111       1     241 [.     396     634 ..     396     645 .. 0.96

  Alignments for each domain:
  == domain 1  score: 371.1 bits;  conditional E-value: 8e-115
                      ERCC3_RAD25_C   1 LqekgylakvqcaevWcpmtaefykeylkakskkkkllyvmnpnkfracefLikyhekrgDkiivfsDnvfaLkey 76 
                                        L+ +g++a v c evWc mt++fy+ yl+++++k++++++mnp+kf++ ++Li++hekrgDkiivfsDnv+aLk+y
  gene1654|gene1654|rna1654|rna1654 396 LSMQGHIATVSCFEVWCSMTNHFYAAYLRQNMRKRRVIAIMNPTKFQTTQYLINMHEKRGDKIIVFSDNVHALKSY 471
                                        6789************************************************************************ PP

                      ERCC3_RAD25_C  77 akklkkpyiyGetseaerlkilqkfkknpkvntiflskvgDtsiDlPeanvliqisshfgsrrqeaqrlGriLrak 152
                                        a kl kpyiyG t ++er+kil++f++np +nt+flskvgDtsiDlPea++liqisshfgsrrqeaqrlGriLrak
  gene1654|gene1654|rna1654|rna1654 472 ALKLGKPYIYGPTGQQERMKILKQFQTNPMINTLFLSKVGDTSIDLPEATCLIQISSHFGSRRQEAQRLGRILRAK 547
                                        **************************************************************************** PP

                      ERCC3_RAD25_C 153 kksneeefnaffYsLvskDtkemaystkrqqflvdqGYafkviteleeleeeeelaystkeeqkellqkvlaakde 228
                                        ++ n+ +f+ +fYsLvskDt+em+ystkrqq+l+dqGY+fkv  ++ ++++ ++ +++tkeeqkell+++l a+++
  gene1654|gene1654|rna1654|rna1654 548 RR-NDPGFKVYFYSLVSKDTDEMYYSTKRQQYLIDQGYTFKVFDDM-KMDNFDNRVFKTKEEQKELLASILLASEN 621
                                        **.9**************************************9887.5777799********************99 PP

                      ERCC3_RAD25_C 229 eaeeeelekelke 241
                                        e e+e++e+++ +
  gene1654|gene1654|rna1654|rna1654 622 ELESEDAEETVVS 634
                                        9999888776643 PP

>> Helicase_C_3  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.7   0.0   4.8e-36   1.2e-32       1     124 [.      31     155 ..      31     157 .. 0.98
   2 ?   -2.9   0.1       2.7     7e+03      17      49 ..     607     639 ..     601     642 .. 0.78

  Alignments for each domain:
  == domain 1  score: 112.7 bits;  conditional E-value: 4.8e-36
                       Helicase_C_3   1 livqaDltillegdsplaeearaaLaafAelesrpehahtyrltplSlrrAldaGltaeeiiefLerlskypvPqa 76 
                                        ++v+ D+ i+le++spl ++a+++L+a++e++srp h+h+y++t++Sl++A+++Gl++e+i+  L+rlsk+ +P+ 
  gene1654|gene1654|rna1654|rna1654  31 FWVNYDGIIILETFSPLFKAATDFLIAISEPISRPKHIHEYKITSYSLYAAASVGLNTEDILFSLDRLSKNVIPKC 106
                                        69********************************************************************9***** PP

                       Helicase_C_3  77 leylirdvarryGklrlgl.easlvlrsddpalleelladkkiaklllr 124
                                        ++++i+ ++ +yGkl+l l e ++++++++ ++l+++l+d++i+++l++
  gene1654|gene1654|rna1654|rna1654 107 IRKFITACTLSYGKLKLILrESKYFMEIANGDVLKTVLKDPQISSALIQ 155
                                        ********************************************99886 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 2.7
                       Helicase_C_3  17 laeearaaLaafAelesrpehahtyrltplSlr 49 
                                         ++e+ a +   +e e ++e a +  ++++Slr
  gene1654|gene1654|rna1654|rna1654 607 EQKELLASILLASENELESEDAEETVVSQKSLR 639
                                        566777778888888888889999999999987 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.5   0.0   5.2e-18   1.3e-14       3     169 ..     217     370 ..     198     372 .. 0.83
   2 ?   -1.5   0.0      0.85   2.2e+03     109     146 ..     436     470 ..     418     502 .. 0.67
   3 ?   -3.0   0.2       2.4   6.1e+03      97     121 ..     606     630 ..     574     655 .. 0.57

  Alignments for each domain:
  == domain 1  score: 54.5 bits;  conditional E-value: 5.2e-18
                                        EE-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGT CS
                             ResIII   3 elreyQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkfl 78 
                                         +r yQe  ++++  +    r + g+i++++G+GKTlv + +i  +++      +l+l+ +   +eq++ ++k+f+
  gene1654|gene1654|rna1654|rna1654 217 VIRTYQEISLNKMFGN---GRGRSGIIVLPCGSGKTLVGITAICTIKR-----PTLVLCTSAVSVEQWKAQIKQFT 284
                                        5677777777777533...57789********************9999.....8********************** PP

                                        GG....GEEEESSS-B--.......-SEEEEEHHHHHHTH..........HHHTTT-S.EEEEETGGGTTS.TTTH CS
                             ResIII  79 seaykeigkkvsgdkkkakekdstnkkilvttiqsldadseee..eeeseellrdrfd.viiiDEaHrlgakkswr 151
                                        s ++++i  ++s++k+           ++++t+ +l  + ++    ++  ++ ++++  ++i DE+H + a + +r
  gene1654|gene1654|rna1654|rna1654 285 SVKDEDIACFTSERKDVC-------DAVIISTYTMLCFSGKRSyeAQKAIDYIKNTEWgLLILDEVHVVPA-QMFR 352
                                        ***999988888888888.......8888888888866664444433344444443335************.**** PP

                                        HHHHT---SEEEEEESS- CS
                             ResIII 152 eilekfkeavllglTATp 169
                                        ++l  +++ ++lglTAT+
  gene1654|gene1654|rna1654|rna1654 353 KVLGLVSHHCKLGLTATL 370
                                        *****************7 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.85
                                        EEHHHHHHTH........HHHTTT-SEEEEETGGGTTS CS
                             ResIII 109 ttiqsldadseeeeeeseellrdrfdviiiDEaHrlga 146
                                        ++  +++  +      + + +r+ + +++ D +H l++
  gene1654|gene1654|rna1654|rna1654 436 MNPTKFQTTQ---YLINMHEKRGDKIIVFSDNVHALKS 470
                                        4444444444...5556666777777888999998766 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 2.4
                                        .......-SEEEEEHHHHHHTH... CS
                             ResIII  97 kekdstnkkilvttiqsldadseee 121
                                        +e+++  ++il++++++l ++  ee
  gene1654|gene1654|rna1654|rna1654 606 EEQKELLASILLASENELESEDAEE 630
                                        2223334455555555555555443 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       3.1   7.9e+03      14      28 ..     286     300 ..     260     327 .. 0.57
   2 !   44.6   0.0     6e-15   1.5e-11       7     110 ..     445     546 ..     439     547 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 3.1
                                        TTTSEEEEEESSHHH CS
                         Helicase_C  14 eeggkilifvntidr 28 
                                        +++++i +f+  +++
  gene1654|gene1654|rna1654|rna1654 286 VKDEDIACFTSERKD 300
                                        344444444444442 PP

  == domain 2  score: 44.6 bits;  conditional E-value: 6e-15
                                        HHHH.HHTTTTSEEEEEESSHHHHHHHHHHHHHTTSTEEEESTTSTHHHHHHHHHHHH.TTSSSEEEESGGGTSSS CS
                         Helicase_C   7 lell.kleeeggkilifvntidrlekvklllekkgikvavlhgelpqnereeileqfn.kgesdvLiatdvaerGi 80 
                                         +l+  +e++g+ki++f+ ++  l+  ++ l k  +   +++g + q+er +il+qf+ +  ++ L  ++v+ ++i
  gene1654|gene1654|rna1654|rna1654 445 QYLInMHEKRGDKIIVFSDNVHALK--SYAL-K--LGKPYIYGPTGQQERMKILKQFQtNPMINTLFLSKVGDTSI 515
                                        44444579****************6..5552.3..444469****************9445556************ PP

                                        TSTTESEEEESSSS.SSHHHHHHHHTTSSST CS
                         Helicase_C  81 dipkvnlVinfdlp.rnvtsyiqriGRtgRa 110
                                        d+p+++++i+++    + ++  qr GR+ Ra
  gene1654|gene1654|rna1654|rna1654 516 DLPEATCLIQISSHfGSRRQEAQRLGRILRA 546
                                        ***********9994559************8 PP

>> SNF2_N  SNF2 family N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.34   8.7e+02     144     164 ..     208     228 ..     183     242 .. 0.81
   2 !   25.8   0.4   1.6e-09     4e-06      49     192 ..     229     349 ..     204     393 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.34
                                        --------EEEE-HHHHHHHT CS
                                        xxxxxxxxxxxxxxxxxxxxx RF
                             SNF2_N 144 pklladydvvittYdvlsrea 164
                                         ++  + ++vi tY+ +s ++
  gene1654|gene1654|rna1654|rna1654 208 INMELKNNIVIRTYQEISLNK 228
                                        56778899******9998665 PP

  == domain 2  score: 25.8 bits;  conditional E-value: 1.6e-09
                                        HHHHHTT--EEE---TTS--HHHHHHHHH...HHTTTS---.......S-EEEE--HHH.HHHHHHHHHHH-TTS- CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx RF
                             SNF2_N  49 aeakqsvrGGiLaDemGLGKTvqvlalilaqrakeekdkekkrkdtlagptLivvPasl.ldqWeneierhvsssa 123
                                        ++ +   r Gi+    G GKT+  ++ i                 t++ ptL+++ +++ ++qW+ +i++++s + 
  gene1654|gene1654|rna1654|rna1654 229 MFGNGRGRSGIIVLPCGSGKTLVGITAIC----------------TIKRPTLVLCTSAVsVEQWKAQIKQFTSVKD 288
                                        55556677888888888888888888888................45579*******55389**********9997 PP

                                        EEE--SSHHHH-----------------EEEE-HHHHHHHT..........TTS-S-S-SEEEES-GGGT--T CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SNF2_N 124 lrvlvyggqkkmkkkntkvapklladydvvittYdvlsreaelq....kkrsvlkqvewkrvvlDEghtlkns 192
                                         ++   ++++                  v+i tY +l +  +++    k ++ +k+ ew  ++lDE h +  +
  gene1654|gene1654|rna1654|rna1654 289 EDIACFTSER------------KDVCDAVIISTYTMLCFSGKRSyeaqKAIDYIKNTEWGLLILDEVHVVPAQ 349
                                        6666666643............346778*********98877777788********************99765 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0   7.5e-08   0.00019       3     170 ..     221     371 ..     219     377 .. 0.72

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 7.5e-08
                                        HHHHHHHHHH...TTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTST CS
                                        xxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               DEAD   3 iQaeaiplil...gggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyid 75 
                                        +Q+ +++ +    +g++ ++  + GsGKTl+ + +++ +        +  +l+++ +   +eq   ++k+f++  d
  gene1654|gene1654|rna1654|rna1654 221 YQEISLNKMFgngRGRSGIIVLPCGSGKTLVGITAIC-T-------IKRPTLVLCTSAVSVEQWKAQIKQFTSVKD 288
                                        5777777777655678999************777777.3.......45578**********************766 PP

                                        SEEEEEETTSSHHHHHHHHHTTCSEEEEEHHHHHHHH.HCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSH CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               DEAD  76 lrvlliiggvaardqlskldngvdivvgtpgrlddll.stgklnlsqvrflVlDEadrlldqgfsdfinrilnqlp 150
                                          + +++++++++   +++ +++ ++    +r  +      +++  +  +l+lDE++ +  q f++ +  + +++ 
  gene1654|gene1654|rna1654|rna1654 289 EDI-ACFTSERKDVCDAVIISTYTMLCFSGKRSYEAQkAIDYIKNTEWGLLILDEVHVVPAQMFRKVLGLVSHHC- 362
                                        333.4444444434444444556666666666666332344455777789***************9999988888. PP

                                        HHCTTSTTTSEEEEEESSBS CS
                                        xxxxxxxxxxxxxxxxxxxx RF
                               DEAD 151 qitcdgklqrqvivlSATlp 170
                                                    + l+ATl 
  gene1654|gene1654|rna1654|rna1654 363 -----------KLGLTATLL 371
                                        ...........577777775 PP

>> DUF3638  Protein of unknown function (DUF3638)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   6.7e-06     0.017      11      82 ..     206     277 ..     197     303 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 6.7e-06
                            DUF3638  11 ewLlleiesniliReeQaevAkemispssgensvlQLnmGeGKssvIvPivaaaladgkkLvrvivlkpllk 82 
                                        + + +e+ +ni+iR+ Q+   ++m  + +g++ ++ L  G GK+ v +  ++++ + +  L+   v  ++ k
  gene1654|gene1654|rna1654|rna1654 206 KEINMELKNNIVIRTYQEISLNKMFGNGRGRSGIIVLPCGSGKTLVGITAICTIKRPTLVLCTSAVSVEQWK 277
                                        56779*************999***********************9988888877766666666555544444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (666 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       976  (0.0544369); expected 358.6 (0.02)
Passed bias filter:                      472  (0.0263261); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.68u 0.32s 00:00:01.00 Elapsed: 00:00:00.50
# Mc/sec: 4014.58
//
Query:       gene1655|gene1655|rna1655|rna1655  [L=157]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-14   54.0   1.1      2e-14   53.4   1.1    1.3  1  SPC22     Signal peptidase subunit
  ------ inclusion threshold ------
       0.14   11.7   0.0       0.19   11.3   0.0    1.3  1  CopB      Copper resistance protein B precursor (CopB)


Domain annotation for each model (and alignments):
>> SPC22  Signal peptidase subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.4   1.1   2.2e-18     2e-14       2     157 ..       5     142 ..       4     153 .. 0.79

  Alignments for each domain:
  == domain 1  score: 53.4 bits;  conditional E-value: 2.2e-18
                              SPC22   2 lqRlnavlalaltvlavlvalialsslflk.l.skakskisnvkvsvaksvrdygsnrkkkdraklkfdldaDlss 75 
                                        ++R+ a++++++ + ++l+++i + +++ + + ++ + +i+++++    +++++          ++ f+ ++Dl++
  gene1655|gene1655|rna1655|rna1655   5 SSRIVALSSILFNATTILLFCICIFTYIADkRrAPCNLQIVSIQP---VTTHNV--------GKNVVFNPQIDLRE 69 
                                        68999****************999999777222244444544444...333333........34689********* PP

                              SPC22  76 lfnWNtKqlFvyltaeYetkknevNqvvlWDkIirskedaklklknvkskYslkdqeksLrgrkvtltLhwnvmPv 151
                                        +f+ N+Kq+Fvyl  + +++++     ++W +I+++++++++ +++  + Y+++d+ +   g+k+ ++L+  v P+
  gene1655|gene1655|rna1655|rna1655  70 YFHLNVKQIFVYLRMHNKNNSE-----MVWSEIVKKNDSKRF-YERLVNTYRFFDIAD---GAKIRFELRGCVFPY 136
                                        *************987555555.....9******99876655.55689********75...899************ PP

                              SPC22 152 vGllty 157
                                        vG++  
  gene1655|gene1655|rna1655|rna1655 137 VGIVQD 142
                                        **9865 PP

>> CopB  Copper resistance protein B precursor (CopB)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   2.2e-05      0.19     154     192 ..     118     156 ..     100     157 .] 0.90

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 2.2e-05
                               CopB 154 dvelglRLrYeisrefaPYiGvewerklGetadlaraeg 192
                                        d+  g+++r+e++  + PY+G+  ++ lG+  + ++++g
  gene1655|gene1655|rna1655|rna1655 118 DIADGAKIRFELRGCVFPYVGIVQDKLLGSVVTTVKRSG 156
                                        67789************************9888887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       863  (0.0481343); expected 358.6 (0.02)
Passed bias filter:                      537  (0.0299515); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.50
# Mc/sec: 936.49
//
Query:       gene1656|gene1656|rna1656|rna1656  [L=79]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       411  (0.0229238); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 519.68
//
Query:       gene1657|gene1657|rna1657|rna1657  [L=64]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.067   13.8   0.3      0.069   13.7   0.3    1.0  1  Phage_rep_O  Bacteriophage replication protein O
        0.1   12.9   0.7        1.4    9.3   0.0    2.0  2  DUF2492      Protein of unknown function (DUF2492)


Domain annotation for each model (and alignments):
>> Phage_rep_O  Bacteriophage replication protein O
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.3   7.7e-06     0.069      43      91 ..      14      63 ..       5      64 .] 0.88

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 7.7e-06
                        Phage_rep_O 43 fkkksdwisnsqlveltgisrtkvskalkeLirekviikeg.rkvgvnkn 91
                                       f+k+ + +++++l  +t++++ kv++ ++ L ++ vi+  +   v++n++
  gene1657|gene1657|rna1657|rna1657 14 FQKRFKMVEHKDLESTTDMNNMKVQSFITVLPQKYVIKASKaAFVARNSK 63
                                       99***********************************9998666677765 PP

>> DUF2492  Protein of unknown function (DUF2492)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.2     0.012     1e+02      49      67 ..       8      26 ..       2      33 .. 0.76
   2 ?    9.3   0.0   0.00015       1.4      42      75 ..      31      64 .]      28      64 .] 0.92

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.012
                            DUF2492 49 deLiefLlkkgKfvesedg 67
                                        +L +f++k+ K+ve++d 
  gene1657|gene1657|rna1657|rna1657  8 CRLNKFFQKRFKMVEHKDL 26
                                       56889*********99875 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00015
                            DUF2492 42 saedltadeLiefLlkkgKfvesedgftvnaeki 75
                                         +++++++ i+ L +k  + +s+++f+++++ki
  gene1657|gene1657|rna1657|rna1657 31 DMNNMKVQSFITVLPQKYVIKASKAAFVARNSKI 64
                                       679**************************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (64 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       875  (0.0488036); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.33u 0.25s 00:00:00.58 Elapsed: 00:00:00.38
# Mc/sec: 503.74
//
Query:       gene1658|gene1658|rna1658|rna1658  [L=546]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-51  176.0   4.1    3.3e-50  171.1   0.8    2.2  2  TruD      tRNA pseudouridine synthase D (TruD)


Domain annotation for each model (and alignments):
>> TruD  tRNA pseudouridine synthase D (TruD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.0   0.1   0.00024       4.3      11      56 ..      14      72 ..       7      92 .. 0.58
   2 !  171.1   0.8   1.9e-54   3.3e-50      45     283 ..     124     351 ..     104     369 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.00024
                               TruD 11 tegigGrlrespeDFiVeEieefsgeeeade..............geylvlrvekrnwdt 56
                                       ++ ++  +++ p DFiV+E+++ ++   +de              +e +   ve+++++ 
  gene1658|gene1658|rna1658|rna1658 14 KNKVNYMIKHLPSDFIVQEVHDHDDI-CDDEsdhldvsflkqfldDEIVKTIVELKEIED 72
                                       4467889*************887432.222211244445544444444555555555555 PP

  == domain 2  score: 171.1 bits;  conditional E-value: 1.9e-54
                               TruD  45 lvlrvekrnwdtldlvrelaralgisrkrvgfaGtKDkrAvTtQlisirkvepeelealeikdvelevvgrarrkl 120
                                          + ++k+n dt ++  +++r+l++  k++gfaG KD+rA+T Q isi++v  ++++       +l+ v r+r +l
  gene1658|gene1658|rna1658|rna1658 124 FSFVLRKENEDTVEACMRISRELNVPFKNIGFAGNKDRRAITYQRISISDVYYKDVK-------HLHCVRRERGHL 192
                                        456799*************************************************98.......7899******** PP

                               TruD 121 rlGdLaGNkFeirvrdvaeee..eaakraeeileele.ekggvPNyfGvQRFGsrrpvthlvGkaivkgdleeAve 193
                                        +lG+ +GN+F i vr  +e++  + + ++++ +++++ +++ +PN+fG+QRFG++   +hlvGk + ++++e+A++
  gene1658|gene1658|rna1658|rna1658 193 KLGRFKGNRFIILVRP-KEDPseTGTCSLDDAIRKMDvNTKKFPNFFGIQRFGRN-LDNHLVGKLLHQKKYEDAIN 266
                                        ***************9.4444222222333333333212336***********95.999****************8 PP

                               TruD 194 lyvgkpfeeesedtreareavaetgdleealeelpkslryErallkrLaekpkdykkAlealpknLqrlFvhAyqS 269
                                        l+    +e++ + ++ea++ +  ++++++a+ ++p+++  E+++++++ +    y++A+ +++++++ l++hAyqS
  gene1658|gene1658|rna1658|rna1658 267 LI-MMVKESDGDYVKEAKHSF-YNKEYDQAYAQFPRNCLAEKSICRNISK---GYRRAIFSIKEKIRILYLHAYQS 337
                                        65.567778999999**9999.79************************99...9********************** PP

                               TruD 270 ylFNrvlseRlerg 283
                                        y+FN+ ls+ l ++
  gene1658|gene1658|rna1658|rna1658 338 YIFNQELSKLLTEK 351
                                        ********999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (546 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       432  (0.024095); expected 358.6 (0.02)
Passed bias filter:                      254  (0.014167); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.41
# Mc/sec: 3951.25
//
Query:       gene1659|gene1659|rna1659|rna1659  [L=76]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    6.8e-05   22.8   5.7    6.8e-05   22.8   5.7    2.1  2  Sec61_beta  Sec61beta family
     0.0066   16.7   1.1     0.0073   16.6   1.1    1.0  1  DUF996      Protein of unknown function (DUF996)
  ------ inclusion threshold ------
       0.03   14.7   2.4      0.037   14.4   2.4    1.0  1  MgtE        Divalent cation transporter
       0.11   12.4   3.2       0.21   11.5   0.1    2.1  2  MadM        Malonate/sodium symporter MadM subunit
       0.14   12.0   5.2       0.17   11.8   5.2    1.1  1  DUF2975     Protein of unknown function (DUF2975)
       0.27   11.8   6.1        4.7    7.8   6.1    2.0  1  DUF2418     Protein of unknown function (DUF2418)


Domain annotation for each model (and alignments):
>> Sec61_beta  Sec61beta family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   5.7   2.3e-08   6.8e-05      18      41 .]      21      44 ..      19      44 .. 0.95
   2 ?    0.7   1.3      0.18   5.5e+02      30      39 ..      57      66 ..      54      68 .. 0.50

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 2.3e-08
                                       B-THHHHHHHHHHHHHHHHHTSS- CS
                         Sec61_beta 18 idPkvVlvlsvafiasVilLhila 41
                                       i+P++Vl++s++fi+ V++Lh++a
  gene1659|gene1659|rna1659|rna1659 21 ISPVHVLIISLLFIGTVFVLHLYA 44
                                       89*******************975 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.18
                                       HHHHHHHHTS CS
                         Sec61_beta 30 fiasVilLhi 39
                                       ++++V++L +
  gene1659|gene1659|rna1659|rna1659 57 VAFAVLILSV 66
                                       4455555554 PP

>> DUF996  Protein of unknown function (DUF996)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   1.1   2.4e-06    0.0073      23      92 ..       9      73 ..       4      76 .] 0.80

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 2.4e-06
                             DUF996 23 ekifsnaliafilsiialvvailalllvlgalatalelpgleeaaslilllllvliiayvlliisavflk 92
                                       ++++++ l +fi+s + ++++ l+++++++ l  +  +   ++     +l ++v +++++l +++++ l 
  gene1659|gene1659|rna1659|rna1659  9 KELMNSQLKPFIISPVHVLIISLLFIGTVFVLHLYARFSPGTT-----SLQMVVAFAVLILSVFASYQLN 73
                                       6889999***********************9999999997776.....4455555567777777777665 PP

>> MgtE  Divalent cation transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   2.4   1.2e-05     0.037      28      83 ..      11      69 ..       6      73 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.2e-05
                                       S-GG.HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-...CTSHHHHHHHHHHHHHHHH CS
                               MgtE 28 lekk.lkkvllkelrvvlllgvilgllifllalllgw..slllalvvglalvlvllaaa 83
                                       l ++ lk ++++++ v+++ ++++g++ +l  +  ++  +  l +vv++a++++ ++a+
  gene1659|gene1659|rna1659|rna1659 11 LMNSqLKPFIISPVHVLIISLLFIGTVFVLHLYARFSpgTTSLQMVVAFAVLILSVFAS 69
                                       433337999******************99997765556677777788888888877775 PP

>> MadM  Malonate/sodium symporter MadM subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.5     0.078   2.3e+02      11      24 ..      26      39 ..      20      44 .. 0.85
   2 ?   11.5   0.1   7.1e-05      0.21       9      33 ..      52      76 .]      48      76 .] 0.92

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.078
                               MadM 11 gLvtaFavvGllmw 24
                                        L+++++++G + +
  gene1659|gene1659|rna1659|rna1659 26 VLIISLLFIGTVFV 39
                                       599*******9876 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 7.1e-05
                               MadM  9 kngLvtaFavvGllmwvSyvlSkkl 33
                                       + ++v+aFav+ l +++Sy l k+l
  gene1659|gene1659|rna1659|rna1659 52 SLQMVVAFAVLILSVFASYQLNKRL 76
                                       568******************9987 PP

>> DUF2975  Protein of unknown function (DUF2975)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   5.2   5.6e-05      0.17      67     110 ..      27      68 ..      19      70 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 5.6e-05
                            DUF2975  67 iaaalllaagivalallaelelapgvvllllgvafaslvigllv 110
                                        ++++ll+++++++l+l a   ++pg++ l ++vafa+l++ +++
  gene1659|gene1659|rna1659|rna1659  27 LIISLLFIGTVFVLHLYAR--FSPGTTSLQMVVAFAVLILSVFA 68 
                                        5678999999999999999..89******************997 PP

>> DUF2418  Protein of unknown function (DUF2418)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   6.1    0.0016       4.7      23      53 ..      22      73 ..      10      75 .. 0.67

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0016
                            DUF2418 23 sPlhvlllvlll.....................sesvlktlllvvllslqly 53
                                       sP+hvl++ ll                       ++ + +l+l+v+ s+ql+
  gene1659|gene1659|rna1659|rna1659 22 SPVHVLIISLLFigtvfvlhlyarfspgttslqMVVAFAVLILSVFASYQLN 73
                                       6666666665445555555555555555544444488888889999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       965  (0.0538234); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.41u 0.31s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 508.84
//
Query:       gene166|gene166|rna166|rna166  [L=261]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.8e-33  114.1   0.0    1.6e-32  112.6   0.0    1.6  1  SHMT           Serine hydroxymethyltransferase
    0.00012   21.3   0.0    0.00016   21.0   0.0    1.1  1  Aminotran_1_2  Aminotransferase class I and II
  ------ inclusion threshold ------
      0.024   13.7   0.0      0.036   13.1   0.0    1.3  1  SelA           L-seryl-tRNA selenium transferase


Domain annotation for each model (and alignments):
>> SHMT  Serine hydroxymethyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.6   0.0   2.7e-36   1.6e-32     196     398 ..       1     185 [.       1     186 [. 0.91

  Alignments for each domain:
  == domain 1  score: 112.6 bits;  conditional E-value: 2.7e-36
                                    TT-EEEEE-GGGHHHHHTTSS--GCCTSSEEEEESSSTT-S-S-EEEEEC-SEEEEETTTEEEEHHHHHHHHHHHTTTT- CS
                           SHMT 196 vgayllvdmahiaGlvaagvipsPfeyadvvtttthktlrGprgglillrkgvksvdktgkevleelekkinsavfPglq 275
                                    vga+ll d++h +Gl++ g++ +Pf+y+dvvtt   kt+ Gpr+g+i+++          k+    +e+ i  a    l 
  gene166|gene166|rna166|rna166   1 VGAILLGDISHPSGLISHGLMNNPFKYCDVVTTVMQKTMGGPRAGIIYCK----------KK----YEQLIRDA-QTVLC 65 
                                    69************************************************..........22....33333333.23457 PP

                                    SS--HHHHHHHHHHHHHCTSHHHHHHHHHHHHHHHHHHHHHHHTT-EEGGGS-SSSEEEEEGGGGTS-HHHHHHHHHHTT CS
                           SHMT 276 GGPlnhviaakavalkealepefkvyqkqvlknakalaealkekgyklvsgGtdnhlvlvdlrekgldGkraekvlekvn 355
                                    G  ++h+i  +avalkeal++ + + + ++ +na+ l + l ++ ++     td+h++l+d+    ++  + e v + + 
  gene166|gene166|rna166|rna166  66 GNSHTHIILQVAVALKEALSEGHYELSLRIQSNARYLRKRLIDHQFDT--YTTDSHMILLDMG-CAIKACNFEIVADFLG 142
                                    889*****************************************9996..569********96.68999*********** PP

                                    EE-EEE--TTSSTTTT-SEEEEESHHHHHTT--HHHHHHHHHH CS
                           SHMT 356 itankntvPgdksalvtsGlrlGtpaltsrgfkeedlekvakf 398
                                    i+ ++ ++     a  ++G+rlGt+ +t+rg+++ +l+k++k+
  gene166|gene166|rna166|rna166 143 ISLDRVSLAIHPCACKPTGIRLGTTGVTRRGMGKRELKKIGKI 185
                                    ****************************************986 PP

>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   2.6e-08   0.00016     222     322 ..      38     136 ..      12     174 .. 0.79

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 2.6e-08
                                    TTSSGGG-EEEEEEEHHHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSTEEEEC CS
                  Aminotran_1_2 222 afGlaGeRvGyilgnaavvsqlrklsrpflsssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLaelglkvla 301
                                     +G  G R G+i++++++ + +r++++ ++  s++  ++  a+  ++   + + e   r+q+++++lr++L +  ++ ++
  gene166|gene166|rna166|rna166  38 TMG--GPRAGIIYCKKKYEQLIRDAQTVLCGNSHTHIILQVAVALKEALSEGHYELSLRIQSNARYLRKRLIDHQFDTYT 115
                                    555..667***********************77777777777776666677999*****************999****** PP

                                    CSCSSEEEEEETHHCHHHHHH CS
                  Aminotran_1_2 302 sqsgmflltdlsaetakelsk 322
                                     +s+m+ll  ++a +a  +  
  gene166|gene166|rna166|rna166 116 TDSHMILLDMGCAIKACNFEI 136
                                    ********9988875555554 PP

>> SelA  L-seryl-tRNA selenium transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0     6e-06     0.036     203     235 ..      27      59 ..       8      78 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 6e-06
                                    T-SEEEEETTSTT-SSS-EEEEE-HHHHHHHHH CS
                           SelA 203 GvdlvsfsGDkllGgpqaGiivGkkelieklkk 235
                                     +d+v+    k +Ggp+aGii  kk++ + ++ 
  gene166|gene166|rna166|rna166  27 YCDVVTTVMQKTMGGPRAGIIYCKKKYEQLIRD 59 
                                    49***********************99766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       694  (0.0387082); expected 358.6 (0.02)
Passed bias filter:                      589  (0.0328518); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.32s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 1603.23
//
Query:       gene1660|gene1660|rna1660|rna1660  [L=300]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (300 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1079  (0.0601818); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2159.89
//
Query:       gene1661|gene1661|rna1661|rna1661  [L=185]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00095   19.6   0.2     0.0038   17.6   0.2    1.8  1  SET              SET domain
  ------ inclusion threshold ------
      0.054   12.8   0.1      0.088   12.1   0.0    1.3  1  Methyltrans_RNA  RNA methyltransferase


Domain annotation for each model (and alignments):
>> SET  SET domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.2   4.3e-07    0.0038     116     167 ..      96     157 ..      32     157 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 4.3e-07
                                        EEEECCCGTTGGGCEEXSSSSEEEEEEEE..............TTSSEEEEEESSXBXTTEEEEEX CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxx..............xxxxxxxxxxxxxxxxxxxxxxx RF
                                SET 116 lksgngagplarflNHsCdpNcnltvqnv..............lrgprvavfAtrdIkkGeEltid 167
                                        +   n +     +    C++N+++++ ++              +++++v ++At++I+k+eEl+++
  gene1661|gene1661|rna1661|rna1661  96 FDQQNEI----NLAKRKCRNNVKIRIARNkeivfkkslngfvrTGNYKVLLIATQNISKDEELFLS 157
                                        4555555....6667789999988888889999999999999*********************985 PP

>> Methyltrans_RNA  RNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   9.9e-06     0.088      96     152 ..      29      91 ..      18     118 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 9.9e-06
                                        TTSSS...HHHHHHHHHHHHHHHHHHHHHHT-SS--EEEEEEEHHHHHHHCSCCEE......E CS
                    Methyltrans_RNA  96 ersvvkldekkkdkklerwqkilieAaeQsgrtrlpevkepislkelleelkeadl......k 152
                                        +++++k  + +  +k++rw+k l ++ +   +t++ e+k +i lk+ le+ k+ ++      +
  gene1661|gene1661|rna1661|rna1661  29 KNVIRKEAKARGFHKKQRWNKSLLAGEKCGFNTIICELKGHIMLKDELEQPKDGTVyfdpklN 91 
                                        567788889999**************99999*********************99774444442 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       580  (0.0323498); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1345.42
//
Query:       gene1662|gene1662|rna1662|rna1662  [L=348]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      1e-47  162.7   8.8    4.1e-45  154.2   8.8    2.9  1  Septin        Septin
    1.5e-05   25.1   0.4    3.9e-05   23.7   0.0    1.9  2  AAA_14        AAA domain
     0.0056   16.4   0.0      0.012   15.4   0.0    1.6  1  AAA_24        AAA domain
  ------ inclusion threshold ------
      0.012   15.0   0.1       0.02   14.3   0.1    1.3  1  FtsK_SpoIIIE  FtsK/SpoIIIE family
      0.058   13.9   0.4       0.19   12.3   0.0    2.2  2  AAA_18        AAA domain
      0.078   13.4   0.0       0.82   10.0   0.0    2.1  2  AAA_16        AAA ATPase domain


Domain annotation for each model (and alignments):
>> Septin  Septin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  154.2   8.8   1.4e-48   4.1e-45       3     276 ..      24     314 ..      22     319 .. 0.93

  Alignments for each domain:
  == domain 1  score: 154.2 bits;  conditional E-value: 1.4e-48
                                        EEEEEEEEEBTTSSCCCCCCTTSSSS----........................................------ CS
                             Septin   3 ieftlmvvGesglGkttlintlfetdliee........................................ekleea 38 
                                         +++l+++G+ glGktt++n l+++++ ++                                        e   ++
  gene1662|gene1662|rna1662|rna1662  24 HSYNLIIAGARGLGKTTFMNNLVRKKIFKQslylekkddglrelqfiendifsspkpyevgdeyirydegEGW-ST 98 
                                        578*************************999*********************************998753222.23 PP

                                        --------S-EEEEEEEEETTCEEEEEEEE---BSSSSSHHCCCHHHHHHHHHHHHHHHHHCTSS--SS-----EE CS
                             Septin  39 sekkkktveikkkkvvieedgvklnltviDtpgfGdavdnskswepiveyideqfeeylreesklkRkkivDkRvH 114
                                        +  ++++v ++ ++++i e+g+++n+  ++    Gd vdn++++ piv+yi+ +++ey ++e++ +R +i+D+R+H
  gene1662|gene1662|rna1662|rna1662  99 TWLEEHKVAFELTEAQIFERGIRVNFSALEVSNIGDCVDNTDAHIPIVDYINRKYKEYYENERNHRRDEIIDTRIH 174
                                        3467899********************************************************************* PP

                                        EEEEEE-TTSSSS-HHHHHHHHHHTTTS-EEEEESSGGGS-HHHHHHHHHHHHHHHHHTT--------SSSS-SCC CS
                             Septin 115 aclyfisPtghglkpldvelmkklsekvnliPviaKaDtltkeElkefKkkireeleeeeikiyklpdeeededee 190
                                        aclyf +P gh ++++d + + ++s+ + +iPv+a+ D++t eE + ++++ +++leee+i++yk     +     
  gene1662|gene1662|rna1662|rna1662 175 ACLYFFEPAGHWMREIDKKNISEISKICVVIPVVARGDIFTMEERELIRNNFQKTLEEEKINLYK-----H----- 240
                                        *****************************************************************.....2..... PP

                                        HHHHHHHHHHC-SEEB-SSSSEEEESSSEEEEEEETTEEEETT-TTT-SCCHHHHHHHHHCHHHHHHHHHHTHHHH CS
                             Septin 191 akelseklkeslPfaivgsneliekkgkkvrgRkypWGvvevenekhsdFlkLrklllkthledLkevteellYet 266
                                                 + +Pf i++    i++    v  R+y WG v+  n+  +d  +Lr+++++  +  ++e  ++ +Y  
  gene1662|gene1662|rna1662|rna1662 241 --------LQIVPFFIISN--HIDE-FGIVYERQYMWGSVQATNKYICDTEELRNVVIRDQMLYVIEECDK-FYRL 304
                                        ........2479*****74..4554.55899*************************************998.9*** PP

                                        HHHHHH-XXX CS
                             Septin 267 yRseklsklk 276
                                        yRs+ l+++ 
  gene1662|gene1662|rna1662|rna1662 305 YRSSILKDEL 314
                                        ****999765 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.0   1.3e-08   3.9e-05       5      72 ..      28      92 ..      24     114 .. 0.76
   2 ?   -2.3   0.1       1.4   4.2e+03      31      36 ..     312     317 ..     272     343 .. 0.54

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 1.3e-08
                             AAA_14  5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelilek..lkeekktylflDE 72
                                       l+i GaR  GKTt++++l+++++   ++ ly++ +d+ +++l+     ++ i+++   +e +++y+  DE
  gene1662|gene1662|rna1662|rna1662 28 LIIAGARGLGKTTFMNNLVRKKI--FKQSLYLEKKDDGLRELQFI---ENDIFSSpkPYEVGDEYIRYDE 92
                                       79*********************..899****9999988877743...3444443122223555555555 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.4
                             AAA_14  31 esilyi 36 
                                        ++ + +
  gene1662|gene1662|rna1662|rna1662 312 DELIKY 317
                                        222222 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   3.9e-06     0.012       2      44 ..      25      73 ..      24     115 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 3.9e-06
                             AAA_24  2 klkiliyGpsgiGKTtlakel......gpkplfidtekGlksldadkfp 44
                                       +++++i G  g GKTt++++l      +++  +   ++Gl++l++++ +
  gene1662|gene1662|rna1662|rna1662 25 SYNLIIAGARGLGKTTFMNNLvrkkifKQSLYLEKKDDGLRELQFIEND 73
                                       6899*****************7777744444444788899999988865 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1   6.6e-06      0.02      36      60 ..      22      46 ..      10      54 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 6.6e-06
                                       GGS-.SEEEE--TTSSHHHHHHHHH CS
                       FtsK_SpoIIIE 36 kkmashllvaGatgsGKStalntLi 60
                                       k++  +l++aGa g GK+t++n+L+
  gene1662|gene1662|rna1662|rna1662 22 KTHSYNLIIAGARGLGKTTFMNNLV 46
                                       44557******************98 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   6.2e-05      0.19       2      82 ..      29     149 ..      28     177 .. 0.69
   2 ?   -1.4   0.2       1.1   3.2e+03      88      88 ..     296     296 ..     217     339 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 6.2e-05
                             AAA_18   2 lltGtpGvGKttlakeLskrlgf.................................gvnlrdvakenglllevdpe 44 
                                        +++G+ G GKtt+ ++L ++  +                                 g++++ +   +g+++++ +e
  gene1662|gene1662|rna1662|rna1662  29 IIAGARGLGKTTFMNNLVRKK-IfkqslylekkddglrelqfiendifsspkpyevGDEYIRYDEGEGWSTTWLEE 103
                                        79***************8883.446677777777777888778888888888888888888888888888888888 PP

                             AAA_18  45 .....aldeskrldedkldklldaleenss....aleegknlvidgh 82 
                                             +l e ++++++   ++++ale ++     ++++++  ++d +
  gene1662|gene1662|rna1662|rna1662 104 hkvafELTEAQIFERGI-RVNFSALEVSNIgdcvDNTDAHIPIVDYI 149
                                        66544333333333333.44444444444445555555555555555 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.1
                             AAA_18  88 s 88 
                                        +
  gene1662|gene1662|rna1662|rna1662 296 E 296
                                        1 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00027      0.82      25      62 ..      26      63 ..      13      88 .. 0.78
   2 ?    0.6   0.0      0.21   6.4e+02      44      92 ..     282     325 ..     279     343 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00027
                             AAA_16 25 elvllsGesGvGKsslv.rellralekdggiflrgkcdq 62
                                        ++++ G++G GK++ + + +++ + k+  ++l+ k d 
  gene1662|gene1662|rna1662|rna1662 26 YNLIIAGARGLGKTTFMnNLVRKKIFKQ-SLYLEKKDDG 63
                                       5789*************66677788877.5666666555 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.21
                             AAA_16  44 llralekdggiflrgkcdqlesaipysalaqalareellrqlldeaesa 92 
                                        l++ + +d ++++ ++cd++     y  + + + ++el++ ++dea+ +
  gene1662|gene1662|rna1662|rna1662 282 LRNVVIRDQMLYVIEECDKF-----YRLYRSSILKDELIKYVKDEAKIK 325
                                        55555566688888999999.....66688888899******9994443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (348 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       684  (0.0381505); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 2423.32
//
Query:       gene1663|gene1663|rna1663|rna1663  [L=267]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.2e-72  242.6   0.5      8e-72  242.4   0.5    1.0  1  Cpn60_TCP1     TCP-1/cpn60 chaperonin family
    0.00063   20.0   0.0     0.0013   19.0   0.0    1.6  1  Phage_gp49_66  Phage protein (N4 Gp49/phage Sf6 gene 66) fami


Domain annotation for each model (and alignments):
>> Cpn60_TCP1  TCP-1/cpn60 chaperonin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  242.4   0.5   8.9e-76     8e-72     222     490 ..       1     265 [.       1     266 [. 0.98

  Alignments for each domain:
  == domain 1  score: 242.4 bits;  conditional E-value: 8.9e-76
                                        CCCCSCCHHHHHHHHHHHHHHHHHHHHHHTTECEEEESS-B-HHHHHHHHHCT-EEE-S--HHHHHHHHHHHT--E CS
                         Cpn60_TCP1 222 vvlsdaeeleklekaeekqleellekiiksgvnvvvcqkgiddlalhflakngilalrrvkkkdlerlakatGata 297
                                        v+l+++e+++++++ae+k ++++l+kii++g+nvv++   + d+a++++a+++i+++ rv k+dl r+++a+G+++
  gene1663|gene1663|rna1663|rna1663   1 VRLKSVEDYQAIVDAEWKLIRDKLDKIIDTGANVVLSSLPVGDYATQYFARKKIFCAGRVAKEDLFRVVNACGGKI 76 
                                        6899************************************************************************ PP

                                        BSCGGGGGCGC-EEEEEEEECCETTCCEEEEECESSSSXEEEEEEESTCCCHHHHHHHHHHHHHHHHHHHHHHEEE CS
                         Cpn60_TCP1 298 vssledltpeelGtakkveeekigsekttiieevksgkiatillrgatdtvldeieraiedAlnvvknaiedekvv 373
                                         +s   l+    Gt+  +ee+++g+ ++ ++++   +k+ t+++rg+ ++vl+e+er+++dA+ vvk++++++ vv
  gene1663|gene1663|rna1663|rna1663  77 YNSTNFLNT--CGTCTLFEEKQVGKLRYNYFSG-GTKKAYTLIIRGPGEDVLNEVERSVNDAVMVVKRTLRNNSVV 149
                                        ***988877..7********************9.8999************************************** PP

                                        ETTTCHHHHHHHHHHCCCCTSXCCHHHHHHHHHHHHTHHHHHHHHHCTSXHHHHHHHHHHHHHTTXTTEEEETTTT CS
                         Cpn60_TCP1 374 pGGGatelelakklkeyaksvsgeeqlaieafakALevipktLaeNaGldpievlaklraahnkgekelgidvesg 449
                                         GGG+te+el+++++e+ k++  + +l++ a+akA+evip++La+N G d+ie++++lr++h++++ + g+++++g
  gene1663|gene1663|rna1663|rna1663 150 TGGGSTEMELSRYIREEGKNIAMKSALVYIAVAKAFEVIPYQLAKNFGQDAIEIIQQLRYEHSNDKSHSGVNIKKG 225
                                        *************************************************************************999 PP

                                        CEEECCCCTXEEEHHHHHHHHHHHHHHHHHHHCEEEEEXXX CS
                         Cpn60_TCP1 450 eiidlveagvvDplkvkrqalksAteaastiLrideiikak 490
                                        + +d++e+gv++pl +k++++k+++ a+s +L++d +i+ k
  gene1663|gene1663|rna1663|rna1663 226 T-SDMLEDGVLEPLLIKTNMVKASFNAVSALLMVDTTIVSK 265
                                        8.6***********************************976 PP

>> Phage_gp49_66  Phage protein (N4 Gp49/phage Sf6 gene 66) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   1.5e-07    0.0013      23      79 ..     132     194 ..      94     196 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.5e-07
                      Phage_gp49_66  23 etdkltvcvlvLkNgftvtg.esacvdpenfdaeiGrkiakenav.....dkiWeLeGyllre 79 
                                         +d ++v++ +L+N+  vtg  s  ++ + + +e G++ia++ a       k +e+  y+l +
  gene1663|gene1663|rna1663|rna1663 132 VNDAVMVVKRTLRNNSVVTGgGSTEMELSRYIREEGKNIAMKSALvyiavAKAFEVIPYQLAK 194
                                        2489***************98999******************987666668999999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       673  (0.037537); expected 358.6 (0.02)
Passed bias filter:                      497  (0.0277205); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 1882.48
//
Query:       gene1664|gene1664|rna1664|rna1664  [L=230]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      2e-50  171.9   0.4    2.3e-50  171.7   0.4    1.0  1  Cpn60_TCP1  TCP-1/cpn60 chaperonin family


Domain annotation for each model (and alignments):
>> Cpn60_TCP1  TCP-1/cpn60 chaperonin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  171.7   0.4   1.3e-54   2.3e-50       1     203 [.      31     224 ..      31     229 .. 0.91

  Alignments for each domain:
  == domain 1  score: 171.7 bits;  conditional E-value: 1.3e-54
                                        HHHHHHCCSSTTXXEEEEEETTSEEEEEXSHHHHHHCSXXXSHHHHHHHHHHHHCCCCCTTCHHHHHHHHHHHHHH CS
                         Cpn60_TCP1   1 ladivkttlGPkGmdKmlvnkggkvvvTnDGatilkeleiehPaakllveaaesqdeevGDGTttvviLageLlee 76 
                                        +ad +kttlGP G+dKm    ++++ +TnDGatilk+++iehPa +ll++++esqd+evGDGTt+vv+La+ +le 
  gene1664|gene1664|rna1664|rna1664  31 IADSLKTTLGPYGRDKMFL-INDEILITNDGATILKNMKIEHPAGRLLAAISESQDKEVGDGTTSVVLLACGILEH 105
                                        799**************98.5669**************************************************** PP

                                        HHHHHHCTXXHHHHHHHHHHHHHHHHHHHHHHXEEBXSCSTT.HHHHHHHHHHCTTSSXXSTHHHHHHHHHHHHHC CS
                         Cpn60_TCP1  77 aekliaagvhpttiiegyekalekaleaLkeiaveisseekdreeLlkvartslsskltskeaeelsklvvdAvkl 152
                                         + l+++ ++++  ++ +++  ek+l++L+ +++ +++     +  +++a+tsl+sk+ ++++  ++k++vd +k 
  gene1664|gene1664|rna1664|rna1664 106 LKPLVKDSLDIKFMKNTLQEIQEKCLKKLEDCKIGFND-----DLFYSIAQTSLTSKILKYDKCSFAKMIVDTLKG 176
                                        *****************************999778875.....589****************************88 PP

                                        HCCCSEECSCCCEECCCCEECECTTSEEESEEEESS--SSTTSSCEEECEE CS
                         Cpn60_TCP1 153 ieenekeldlgrikvvkieggsledselveGlvldkgvlspdmpkklenak 203
                                        ie+     d   i+++k+ ggs++dse+v+G++++k ++++  +++ ++ +
  gene1664|gene1664|rna1664|rna1664 177 IEDI---DDTRLIGIKKVSGGSISDSEMVDGVAFEKCFTYAGYEQQPKKLQ 224
                                        8644...56667***************************995444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       531  (0.0296168); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 1708.06
//
Query:       gene1665|gene1665|rna1665|rna1665  [L=691]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.3e-51  173.7  13.9    5.3e-51  173.7  13.9    1.6  2  Sec6         Exocyst complex component Sec6
  ------ inclusion threshold ------
       0.14   11.7   0.1       0.74    9.4   0.0    2.3  2  Sigma70_r4   Sigma-70, region 4
       0.61   10.1   3.7        6.7    6.7   0.1    3.9  3  Prefoldin_2  Prefoldin subunit
        7.8    6.5   7.8        1.2    9.1   0.3    3.6  5  Sec20        Sec20


Domain annotation for each model (and alignments):
>> Sec6  Exocyst complex component Sec6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0      0.37   1.6e+03      39      92 ..     185     275 ..     182     276 .. 0.75
   2 !  173.7  13.9   1.2e-54   5.3e-51     144     561 ..     304     676 ..     297     688 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 0.37
                                        HHHHHHHHHHCCCCS.----TT--...............................................----- CS
                               Sec6  39 kiverEekeDeklealreltkkekdeedaanfr.....................................arrprn 77 
                                          +  Eek+D ++ + +     ++++ +++ f+                                     ar  r+
  gene1665|gene1665|rna1665|rna1665 185 SMIVYEEKKDVEALRAKRGRDGSNPTVEKEYFAlggtkfvidtdviagnerikstleydrafyyankslcARPVRK 260
                                        5677788888888887777777555555555556788888888888888888888888888888888888888999 PP

                                        HHHHHHHHHHHHHHH CS
                               Sec6  78 ykkkflealeesvee 92 
                                         k +fl+ + +++++
  gene1665|gene1665|rna1665|rna1665 261 LKLRFLKNVYKAISQ 275
                                        999999998888876 PP

  == domain 2  score: 173.7 bits;  conditional E-value: 1.2e-54
                                        HHHHHHHHHHHHHHTTS---HHHHHHHHHHHHHHHH.HTTTSSHHHC.CCC.---SS-HHHHHHHHHHHHHHHHHH CS
                               Sec6 144 kiYhnklhdllqelvsseleaedilailewvkkYskklsklnpelefkkke.lkpllldekkeeLledYlklivkk 218
                                         +Yh  l++ ++    s+lea+dil +l++ k Y++ l++         +  +   +lde  e+ ++ Yl+++++k
  gene1665|gene1665|rna1665|rna1665 304 VFYHAVLKSKIN---LSTLEAGDILNLLAFKKSYNTLLQA--------HSVtMTDDILDE--ERFIDRYLSVLQNK 366
                                        567777777663...566******************8888........344477778887..8************* PP

                                        HHHHHHHHHHHHHHHHHCT---..EESSSEE-CHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHH CS
                               Sec6 219 mkeWldnllktEvkkftereeppeededglyvlplpvdvfqmlaeqvdvaaeskqakilvgvleelsellksrqda 294
                                        ++ W+ n+++ Ev+  +er+++p+ de++l+ +++++ ++++++eq++ +  +  ++i++gv + +   ++++++a
  gene1665|gene1665|rna1665|rna1665 367 IALWISNITNLEVEMLKERSKAPPLDESNLFISTNFINLLKIIKEQLEPV--TFDERIFKGVSRFILDSVTDFKNA 440
                                        **************************************************..999********************* PP

                                        HHHHHHC-TTSTT.............HHHHHHHHHHHHHHHHH...HHHHHC.........---HHHHHHHHHHHH CS
                               Sec6 295 wqelleeelkkymsvknnereeskpglveyliAlaNdqlkcadyaeslsskylelvsskyeeriteefeelldgfv 370
                                        +   le e+k+ +s ++       pg+ ey i+++N+ lk+++y+ ++ +              + e++el ++f+
  gene1665|gene1665|rna1665|rna1665 441 IVLTLENEYKSAISLSS------TPGYEEYAIMIGNSGLKLTQYIANIPQCQ------------NVEISELGEIFI 498
                                        ************98888......7*************************998............89********** PP

                                        HHHHHHHHHHCHHHHCCTTCCCCHHHHTTTSSHHHHHHHHHHHHTTTTGGGS.S-HHHHHHHHHHHHHHHHHHHHH CS
                               Sec6 371 dlskeaisalleiifnDLkpalsklftkkWytgelmeqivetiedYlndykeylspelfevlleelldelvveYlr 446
                                        ++ k+  ++l++++++ Lkpa+++lft + y+++ ++qi++t++d+l dyke +++ +f +++++l+ e+   Y++
  gene1665|gene1665|rna1665|rna1665 499 SIVKSSNHFLIKFVLATLKPAIKELFTERYYAEKNLKQITATLKDFLDDYKECMNEYVFVTFVNDLAAEFSTVYFK 574
                                        **************************************************************************** PP

                                        HHCSS----SHHHHHHHHHHHHHHHHHHHHHHHHTT-..---CCCCTTHHHH...HHHH--SHHHHHHHHHHHHHS CS
                               Sec6 447 alrkkklkfaakkqkkfaekikrDaeklydffeklgseedaaylkqklraielllelleledpdavplevetlles 522
                                        +l kkk+ +    ++++ + i++D + +  +f  +++   ++++  +l++++    ll +++ d+++ e +++l  
  gene1665|gene1665|rna1665|rna1665 575 QLIKKKSLI----YQSLCDNIENDQDVMNRLFWPYVN---EDIV--NLTVLN---PLLVTRSVDTFIAETKNVLYT 638
                                        *********....************************...4454..578888...66667777***********76 PP

                                        -TT--HHHHHHHHHCCSS-STCHHHHHHHHTT---SS-- CS
                               Sec6 523 ypdisedhveavlkaRkDldksevkelveqlkeikkeve 561
                                        y  +++d+++ ++k R Dld +e+kel + ++ ++ +  
  gene1665|gene1665|rna1665|rna1665 639 Y-EFKKDFIKSLIKKRSDLDANEIKELTDAVNSVYVSDD 676
                                        5.79************************99998866544 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0      0.61   2.7e+03      21      30 ..       1      10 [.       1      11 [. 0.89
   2 ?    9.4   0.0   0.00017      0.74       1      30 [.     512     541 ..     512     542 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.61
                                       --HHHHHHHH CS
                         Sigma70_r4 21 lTleEIgerl 30
                                       ++l+E++++l
  gene1665|gene1665|rna1665|rna1665  1 MSLQELAKML 10
                                       79******98 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00017
                                        HHHHS-HHHHHHHHHHHTTT--HHHHHHHH CS
                         Sigma70_r4   1 aLasLpererevlelrfgeglTleEIgerl 30 
                                        +La+L +  +e ++ r++ + +l++I ++l
  gene1665|gene1665|rna1665|rna1665 512 VLATLKPAIKELFTERYYAEKNLKQITATL 541
                                        599***********************8876 PP

>> Prefoldin_2  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.1    0.0015       6.7      65      99 ..      27      61 ..      24      64 .. 0.92
   2 ?   -0.0   0.0      0.19   8.4e+02      30      54 ..     405     429 ..     401     449 .. 0.81
   3 ?    0.2   0.1      0.15   6.9e+02      55      90 ..     511     546 ..     510     554 .. 0.71

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0015
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        Prefoldin_2 65 eeLeerketlekeiktlekqleklekeleelkeel 99
                                       ++L++r+  ++k+i++++ ++ +++k+le+ ++ l
  gene1665|gene1665|rna1665|rna1665 27 PDLDARESAYNKKIESITGKILDIQKNLENTQSDL 61
                                       799***************************99987 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.19
                                        HHHHHHHHHHHS-TT--EEEEETTE CS
                        Prefoldin_2  30 elelvleelelldedtkvyklvGdv 54 
                                         l+ ++e le +  d++++k v + 
  gene1665|gene1665|rna1665|rna1665 405 LLKIIKEQLEPVTFDERIFKGVSRF 429
                                        578899**************99874 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.15
                                        EEEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        Prefoldin_2  55 lvkqdkeevkeeLeerketlekeiktlekqleklek 90 
                                        +v+ +++ +++eL ++  ++ek++k+++  l++   
  gene1665|gene1665|rna1665|rna1665 511 FVLATLKPAIKELFTERYYAEKNLKQITATLKDFLD 546
                                        677777777778888888888888888777776555 PP

>> Sec20  Sec20
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.3   0.00027       1.2       7      54 ..      57     104 ..      38     115 .. 0.82
   2 ?   -4.0   0.0       3.2   1.5e+04      38      54 ..     170     186 ..     166     186 .. 0.84
   3 ?   -1.4   0.0      0.51   2.3e+03      19      33 ..     307     321 ..     302     351 .. 0.73
   4 ?   -3.0   0.0       1.6   7.2e+03      30      47 ..     533     550 ..     530     554 .. 0.74
   5 ?   -1.9   0.1      0.73   3.3e+03      23      53 ..     656     686 ..     626     689 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00027
                              Sec20   7 TeslraisqllsqevqqSeenleeldastkslekleeeykqvedvlsr 54 
                                        T+s +  s+ l++ + + e n ++l ++ ++++kl+  +++++++ + 
  gene1665|gene1665|rna1665|rna1665  57 TQSDLGESRRLVARITRAESNFMDLISNYNQIKKLSTTFFNMKKTRRY 104
                                        555566788899999999999999999999999999999999887555 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 3.2
                              Sec20  38 lekleeeykqvedvlsr 54 
                                        l +  eey++ e+vls+
  gene1665|gene1665|rna1665|rna1665 170 LDDYGEEYFSRENVLSM 186
                                        677889****9999985 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.51
                              Sec20  19 qevqqSeenleelda 33 
                                        ++v++S++nl +l+a
  gene1665|gene1665|rna1665|rna1665 307 HAVLKSKINLSTLEA 321
                                        578899999998876 PP

  == domain 4  score: -3.0 bits;  conditional E-value: 1.6
                              Sec20  30 eldastkslekleeeykq 47 
                                        +l++ t +l++  ++yk+
  gene1665|gene1665|rna1665|rna1665 533 NLKQITATLKDFLDDYKE 550
                                        677778888888888876 PP

  == domain 5  score: -1.9 bits;  conditional E-value: 0.73
                              Sec20  23 qSeenleeldastkslekleeeykqvedvls 53 
                                          ++ ++el    +s++  +++ k+ +++++
  gene1665|gene1665|rna1665|rna1665 656 LDANEIKELTDAVNSVYVSDDGTKKKKSMFK 686
                                        3455666666666777777777777766666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (691 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       907  (0.0505884); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.58u 0.26s 00:00:00.84 Elapsed: 00:00:00.40
# Mc/sec: 5148.17
//
Query:       gene1666|gene1666|rna1666|rna1666  [L=335]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (335 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       945  (0.0527079); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2372.61
//
Query:       gene1667|gene1667|rna1667|rna1667  [L=402]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.8e-06   27.4   1.1    2.8e-05   24.2   1.1    2.3  1  PAP_assoc        Cid1 family poly A polymerase
    0.00024   21.3   0.0    0.00052   20.3   0.0    1.6  1  NTP_transf_2     Nucleotidyltransferase domain
  ------ inclusion threshold ------
      0.018   15.3   0.0      0.038   14.2   0.0    1.5  1  tRNA_NucTransf2  tRNA nucleotidyltransferase, second domain


Domain annotation for each model (and alignments):
>> PAP_assoc  Cid1 family poly A polymerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   1.1   4.7e-09   2.8e-05       1      33 [.     287     319 ..     287     334 .. 0.77

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 4.7e-09
                                        -HHHHHHHHHHHHHHT--TTTEEEECSST-EEE CS
                          PAP_assoc   1 sLGeLLigFFeyYgreFdyenvvisirtggilt 33 
                                        +L +L+++FFe+Yg+ F y++ +i+ +  ++ t
  gene1667|gene1667|rna1667|rna1667 287 NLSVLFMDFFEFYGQDFCYDKAAICSSGYKAKT 319
                                        799*********************986655443 PP

>> NTP_transf_2  Nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   8.7e-08   0.00052      11      74 ..     135     191 ..     127     240 .. 0.69

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 8.7e-08
                                        HTTTSEEEEEHHHHCTTSCTTSSEEEEEEESTTCHHHHHHEHHHHHHHHCCCEEECTTEEEEEE CS
                       NTP_transf_2  11 lepvakvvlfGSyarGtalkgSDiDllvvlpeevsrekkeegleklaeiikfleellglevdlv 74 
                                        ++p+ +v + GSya+G++l g D Dl ++++ee         lekl+ +  +  ++l + v ++
  gene1667|gene1667|rna1667|rna1667 135 KRPGNRVKCIGSYATGLYLAGGDTDLSLLTEEEDA-------LEKLSHFLRKSPLILRRSVIFI 191
                                        45578999*************************44.......4454444444444444444444 PP

>> tRNA_NucTransf2  tRNA nucleotidyltransferase, second domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   6.4e-06     0.038       3      93 ..     239     345 ..     237     362 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 6.4e-06
                                        HHHHHHHHHHTT-BSSSTTT-SB-HHHHHHHHHHHSSHHHHHHHHTT--TTEEE...E.................. CS
                    tRNA_NucTransf2   3 vrllKkflkgigvYGselkvkGfsGYlaEllvleygsfeevleaaakwkpkvvi...d....leekea........ 63 
                                        +  lK+flk  g+   e +  G+  Y   l+++++ +++ ++++  ++k ++ +   d                  
  gene1667|gene1667|rna1667|rna1667 239 ALFLKQFLKCRGL--NENRRGGLNSYAQLLMIISFLNLHPLVQNQVSIKANLSVlfmDffefY----Gqdfcydka 308
                                        5689*******99..699****************************99998888334343340....144455555 PP

                                        .......EEE..-SS-EEEETTEEEEETTTTS-HHHH CS
                    tRNA_NucTransf2  64 .......llkkfdeplvviDPvDpkRNvaaalslekl 93 
                                               ++k+ ++ l + DP+ ++  v+   ++ ++
  gene1667|gene1667|rna1667|rna1667 309 aicssgyKAKTSNSYLSIEDPTNSSYDVGCLSTKMNV 345
                                        566676577778999*******999998876555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (402 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       626  (0.0349155); expected 358.6 (0.02)
Passed bias filter:                      466  (0.0259914); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 2645.24
//
Query:       gene1668|gene1668|rna1668|rna1668  [L=171]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       525  (0.0292822); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 1106.38
//
Query:       gene1669|gene1669|rna1669|rna1669  [L=145]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.035   14.1   0.1      0.086   12.9   0.0    1.6  1  Tnp_22_dsRBD  L1 transposable element dsRBD-like domain


Domain annotation for each model (and alignments):
>> Tnp_22_dsRBD  L1 transposable element dsRBD-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   4.8e-06     0.086      15      48 ..     100     133 ..      93     141 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 4.8e-06
                                        HHHHHTT---EEETTTEEEEESSSSEEEESSHHH CS
                       Tnp_22_dsRBD  15 qiLkekkfqPrllYPakLsiiieGeikvfiDktk 48 
                                        +iL ek++q r+    k+ i  +G  k    k k
  gene1669|gene1669|rna1669|rna1669 100 KILEEKNCQVRVEVRNKVKICNNGSNKRVKAKDK 133
                                        69***********************998764443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1656  (0.0923643); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.28s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1037.72
//
Query:       gene167|gene167|rna167|rna167  [L=289]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.019   15.0   0.5      0.019   15.0   0.5    2.8  3  CtIP_N          Tumour-suppressor protein CtIP N-terminal dom
      0.055   13.3   0.9       0.11   12.4   0.2    1.8  2  RNA_pol_Rpb5_C  RNA polymerase Rpb5, C-terminal domain
       0.29   11.5   4.5        0.7   10.2   0.8    2.9  3  DUF2935         Domain of unknown function (DUF2935)
        3.5    8.3   7.1        6.4    7.5   0.1    3.5  4  Plk4_PB2        Polo-like Kinase 4 Polo Box 2
        4.2    5.9   9.7        3.6    6.1   0.4    2.1  2  FapA            Flagellar Assembly Protein A
        5.1    7.9  12.9        5.9    7.7   0.6    2.9  3  Occludin_ELL    Occludin homology domain


Domain annotation for each model (and alignments):
>> CtIP_N  Tumour-suppressor protein CtIP N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.5   6.2e-06     0.019      56     117 ..       3      76 ..       1      79 [. 0.84
   2 ?   -0.9   0.1      0.54   1.6e+03      30      65 ..      85     119 ..      69     128 .. 0.61
   3 ?   -0.4   0.8      0.37   1.1e+03      24      27 ..     259     262 ..     170     285 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 6.2e-06
                         CtIP_N  56 enikvlenrLraglC.drCavtqelakkkqqefessklqslqlitiLt...........nEmntLkeenkkLke 117
                                     +i vl+ + r  +C ++Cav+  + kk+++++ + + q++ li  +t           ++ + Lk +n+kL+e
  gene167|gene167|rna167|rna167   3 TKIYVLDAEVRLNQCtNKCAVLFSHYKKRRTNYKNINHQKIMLILLITlskampsdetlADLSGLKTNNEKLSE 76 
                                    57899**********779*************************9988877777777666677777788887776 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.54
                         CtIP_N  30 rcldaqrleelfsknqqlreqqkalkenikvlenrL 65 
                                     + d+++++el   ++ lr+ +  ++ + k +e++L
  gene167|gene167|rna167|rna167  85 TIADTKEIKELDLNDKILRDYNACMN-SSKDYEEKL 119
                                    45566666666666666666655443.334455554 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.37
                         CtIP_N  24 lelk 27 
                                    ++l+
  gene167|gene167|rna167|rna167 259 KDLN 262
                                    2222 PP

>> RNA_pol_Rpb5_C  RNA polymerase Rpb5, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       1.7   5.1e+03      26      47 ..      83     105 ..      73     110 .. 0.55
   2 ?   12.4   0.2   3.6e-05      0.11      18      60 ..     225     267 ..     214     277 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.7
                                    HTT--T.TCSS-EETTSHHHHCC CS
                 RNA_pol_Rpb5_C  26 klkike.eqLPkisksDpvaryl 47 
                                    +++i + +++ ++  +D ++r +
  gene167|gene167|rna167|rna167  83 QVTIADtKEIKELDLNDKILRDY 105
                                    44433314455555666666655 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 3.6e-05
                                    HHHHHHHHHTT--TTCSS-EETTSHHHHCCT--TTSEEEEEEE CS
                 RNA_pol_Rpb5_C  18 eekkellkklkikeeqLPkisksDpvarylglkkGdvvkItrk 60 
                                     e +++++++k   ++L ki+ sD +++++++++ d+ kI  +
  gene167|gene167|rna167|rna167 225 TELRRFVDHYKQILDHLSKILYSDGMIKEMQVENKDLNKISQD 267
                                    57788899*******************************9875 PP

>> DUF2935  Domain of unknown function (DUF2935)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       1.2   3.5e+03      70      94 ..      13      37 ..      10      60 .. 0.68
   2 ?    1.0   0.0      0.17     5e+02      30      79 ..     136     184 ..      69     188 .. 0.72
   3 ?   10.2   0.8   0.00024       0.7      26      91 ..     217     284 ..     212     287 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.2
                        DUF2935 70 kLneealkltreliqFkkellekvl 94
                                   +Ln+ + k++  + ++kk+ ++  +
  gene167|gene167|rna167|rna167 13 RLNQCTNKCAVLFSHYKKRRTNYKN 37
                                   5788888888888888888665433 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.17
                        DUF2935  30 kdlikeakefkkeFekllaeavelseglvrasseleeavakLneealklt 79 
                                    k ++ke + f+ + e++ ++ v l + + + +++l++++++L +++l+++
  gene167|gene167|rna167|rna167 136 KPVLKEIDFFNYDTEAFFKKLVGLFSFF-SERPDLTDKFSELFTDSLRVL 184
                                    4455666666666666666666666555.777777777777777777665 PP

  == domain 3  score: 10.2 bits;  conditional E-value: 0.00024
                        DUF2935  26 dpkekdlikeakefkkeFekllaea..velseglvrasseleeavakLneealkltreliqFkkelle 91 
                                    d+  k++  e+++f  +++++l +   + +s+g+++  + ++++++k+ ++++k+++ + + k++ l+
  gene167|gene167|rna167|rna167 217 DEDHKQFRTELRRFVDHYKQILDHLskILYSDGMIKEMQVENKDLNKISQDFMKELETFKSHKQQHLQ 284
                                    55567777777777666666665441134789999999999*******************99999876 PP

>> Plk4_PB2  Polo-like Kinase 4 Polo Box 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.1      0.47   1.4e+03      52      86 ..       5      39 ..       1      45 [. 0.75
   2 ?    2.2   0.1     0.097   2.9e+02      43      94 ..      78     131 ..      58     139 .. 0.55
   3 ?    7.5   0.1    0.0021       6.4      50      85 ..     209     244 ..     168     259 .. 0.76
   4 ?   -0.3   0.1      0.59   1.7e+03      51      81 ..     252     281 ..     243     286 .. 0.45

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.47
                       Plk4_PB2 52 sltleseeeleslsselkkllehaeeclkqclkle 86
                                    + l++e +l++++++   l++h+++ + +  +++
  gene167|gene167|rna167|rna167  5 IYVLDAEVRLNQCTNKCAVLFSHYKKRRTNYKNIN 39
                                   56677777788888888888888888888877776 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.097
                       Plk4_PB2  43 vkiieksg..ksltleseeeleslsselkkllehaeeclkqclklesalsslek 94 
                                    +k+i++ +  ++ ++++ +  +++  +++++++  ++  ++  +l ++l  +++
  gene167|gene167|rna167|rna167  78 IKLISQVTiaDTKEIKELDLNDKILRDYNACMNSSKDYEEKLNSLRKSLDDNKS 131
                                    555555532233334444444555555555555555555555555555555444 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.0021
                       Plk4_PB2  50 gksltleseeeleslsselkkllehaeeclkqclkl 85 
                                    gk+ ++e++e+ +++++el++ ++h+++ l++  k+
  gene167|gene167|rna167|rna167 209 GKNERIETDEDHKQFRTELRRFVDHYKQILDHLSKI 244
                                    46778888899********************99887 PP

  == domain 4  score: -0.3 bits;  conditional E-value: 0.59
                       Plk4_PB2  51 ksltleseeeleslsselkkllehaeeclkq 81 
                                    k++++e++ +l+++s+++ k le++++  +q
  gene167|gene167|rna167|rna167 252 KEMQVENK-DLNKISQDFMKELETFKSHKQQ 281
                                    34444444.4444444444444444444333 PP

>> FapA  Flagellar Assembly Protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   3.6    0.0072        21     341     417 ..      59     136 ..      35     143 .. 0.81
   2 ?    6.1   0.4    0.0012       3.6     305     408 ..     181     279 ..     164     287 .. 0.51

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.0072
                           FapA 341 eleeeleeleeeleklkkkikklpklkaekqlesekkeqlkklletkeklkeeleeleeelkelkeeleskkeea.ki 417
                                    e   +l  l+ + ekl + ik++++  + +  e + ++  +k+l+++++ +++ ++ ee+l++l ++l++ k+++   
  gene167|gene167|rna167|rna167  59 ETLADLSGLKTNNEKLSEFIKLISQVTIADTKEIKELDLNDKILRDYNACMNSSKDYEEKLNSLRKSLDDNKSKNgAK 136
                                    555667778888888888899999988888888889999999999999999999999999999999999985444344 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0012
                           FapA 305 ikalkevkakklGs.elgtkteiev.gldepelkeklkeleeeleeleeeleklkkkikklpklkaekqlesekkeqlkk 382
                                    +++l++ + +  G  + +t+t +++ g+ ++e +e  ++ ++   el++ ++ +k+ +++l+k+  ++        ++k+
  gene167|gene167|rna167|rna167 181 LRVLRHNSSPVEGDtKTTTNTILRFfGFGKNERIETDEDHKQFRTELRRFVDHYKQILDHLSKILYSDG-------MIKE 253
                                    555555555555554667888888888884444444466666666666666666666666666433332.......2222 PP

                           FapA 383 lletkeklkeeleeleeelkelkeel 408
                                    ++ + + l+++ ++ ++el++ k+  
  gene167|gene167|rna167|rna167 254 MQVENKDLNKISQDFMKELETFKSHK 279
                                    22222222222222222222222222 PP

>> Occludin_ELL  Occludin homology domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       2.5   7.6e+03      47      58 ..      27      38 ..      12      45 .. 0.53
   2 ?    7.7   0.6     0.002       5.9      35      79 ..      74     119 ..      64     132 .. 0.79
   3 ?    6.0   3.2    0.0064        19      14      75 ..     220     282 ..     211     287 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 2.5
                   Occludin_ELL 47 elkegskeykki 58
                                   ++k+++++yk+i
  gene167|gene167|rna167|rna167 27 HYKKRRTNYKNI 38
                                   333333333333 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.002
                   Occludin_ELL  35 skkfseLerelkelkegskeykkieeeilqeykklkk.dpeyqekk 79 
                                     ++f +L +++  +++++ ++ +++++il++y+ + + +++y ek 
  gene167|gene167|rna167|rna167  74 LSEFIKLISQVTIADTKEIKELDLNDKILRDYNACMNsSKDYEEKL 119
                                    578899999999998888899**************99666666653 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.0064
                   Occludin_ELL  14 kaeFnkeYkeYkelhaeleevskkfseLerelkelkegskeykkieeeilqeykklkk.dpey 75 
                                     ++F++e +++ + ++++ +  +k+   + ++ke++ ++k  +ki ++ ++e++ +k+ ++++
  gene167|gene167|rna167|rna167 220 HKQFRTELRRFVDHYKQILDHLSKILYSDGMIKEMQVENKDLNKISQDFMKELETFKShKQQH 282
                                    467888888888888888888888999999999999999999999999999999998855555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (289 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1442  (0.0804284); expected 358.6 (0.02)
Passed bias filter:                      479  (0.0267165); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 1921.59
//
Query:       gene1670|gene1670|rna1670|rna1670  [L=131]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       800  (0.0446204); expected 358.6 (0.02)
Passed bias filter:                      531  (0.0296168); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 856.93
//
Query:       gene1672|gene1672|rna1672|rna1672  [L=301]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (301 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1090  (0.0607954); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 2148.11
//
Query:       gene1673|gene1673|rna1673|rna1673  [L=775]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   4.2e-201  669.1   7.6   6.6e-201  668.5   7.6    1.2  1  Chitin_synth_2   Chitin synthase
    1.2e-15   58.0   0.0    1.1e-14   54.9   0.0    2.2  2  Glyco_tranf_2_3  Glycosyltransferase like family 2
    1.7e-14   54.2   3.5    1.7e-14   54.2   3.5    2.6  2  Glyco_trans_2_3  Glycosyl transferase family group 2
    8.2e-05   22.5   0.1       0.22   11.3   0.0    2.4  2  Glycos_transf_2  Glycosyl transferase family 2
  ------ inclusion threshold ------
      0.012   15.1   0.0       0.19   11.2   0.0    2.3  2  Glyco_transf_21  Glycosyl transferase family 21


Domain annotation for each model (and alignments):
>> Chitin_synth_2  Chitin synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  668.5   7.6  1.8e-204  6.6e-201      14     500 ..     257     719 ..     242     746 .. 0.93

  Alignments for each domain:
  == domain 1  score: 668.5 bits;  conditional E-value: 1.8e-204
                     Chitin_synth_2  14 lidkrslefqlkfticlvtaysegeeglrttldslastdyddkrklllvvcdGlikGsGndkstPeivldllkdav 89 
                                        li k+++ ++++  i+lvt+yse+ eg+++tldsl++ +y +  k++lv++dGl+kGsG++ +tP+i+++l++  v
  gene1673|gene1673|rna1673|rna1673 257 LIRKNRVANENLPCIMLVTCYSEDREGIKKTLDSLCNQNYLE--KVILVIADGLVKGSGSETTTPDIIIELMN--V 328
                                        56677788889999**************************75..89***************************..4 PP

                     Chitin_synth_2  90 spkedveplsyvavaeGskrhnkakvyaGfyeyeddstvpeekqqrvPlivvvkvGtpseasekkPGnrGkrdsqi 165
                                        ++    e+  y+++       n++ vy+G y++++         +   ++v+vkvG+++e+s  kPGnrGkrdsq+
  gene1673|gene1673|rna1673|rna1673 329 DK--RREAAEYKSLNG---TLNRGVVYSGTYNSDT---------NTCKMVVIVKVGREDERS--KPGNRGKRDSQV 388
                                        44..456778999965...4799*********997.........33689***********99..************ PP

                     Chitin_synth_2 166 ilmsflekvtfdermteleyelfkkikkviGvspdfyeivlmvdadtkvapdsltrlvaalvkdpeilglcGetki 241
                                        i+m f++k+ +++rm++l++e+++++k v+G++p ++e+++mvdadt v+pd+l ++ +a+v+dp+i+g+cGetki
  gene1673|gene1673|rna1673|rna1673 389 IIMGFFQKLLYQDRMSDLDFEIYEAFKDVMGMEPRHFEMIMMVDADTIVHPDALLHFNSAFVNDPKIMGMCGETKI 464
                                        **************************************************************************** PP

                     Chitin_synth_2 242 ankkeswvtaiqvfeyyishhlskafesvfGsvtclPGcfslyrikaakgadgkwvPilvspeiveeysenvvdtl 317
                                         nk  swvt+iqvfeyyishhl+k+fesvfG+vtclPGcf++yrik +++  +k+vPil+++ ++  ys ++++tl
  gene1673|gene1673|rna1673|rna1673 465 INKGASWVTMIQVFEYYISHHLTKTFESVFGGVTCLPGCFCIYRIKVKEN--DKYVPILANSFVLGPYSVTRTETL 538
                                        ***********************************************999..889********************* PP

                     Chitin_synth_2 318 hkknllllGedrylttlllktfpkrktvfvpqakcktvaPdtfkvllsqrrrwinstvhnllelvlvrdlcGtfcf 393
                                        h+knllllGedrylttlllktf +rk +f+p a+c+t +Pdtf+vllsqrrrwinstvhnl+elv v+ lcGtfc 
  gene1673|gene1673|rna1673|rna1673 539 HEKNLLLLGEDRYLTTLLLKTFYRRKLIFLPAATCRTYVPDTFSVLLSQRRRWINSTVHNLMELVSVNALCGTFCC 614
                                        **************************************************************************** PP

                     Chitin_synth_2 394 smrfvvfieligtvvlPvaiaftlylivasilksklvpviplvllaivlGlpailivltarkleyvawllvyllal 469
                                        sm+f v +el gt+vlPv+i+ft+ li  sil       ipl++la ++Glp ili++t+ kl+yv wl vy+l+l
  gene1673|gene1673|rna1673|rna1673 615 SMQFAVGVELAGTLVLPVSIIFTFVLIAVSILI--KPAWIPLIMLACIFGLPIILILVTSFKLQYVFWLFVYILSL 688
                                        ***************************999998..5679************************************* PP

                     Chitin_synth_2 470 PifnfvlPlyafwhlddfswGetrvveGekk 500
                                        P++n+vlP+yafwh+ddfswGetr+v+ +++
  gene1673|gene1673|rna1673|rna1673 689 PVWNLVLPVYAFWHFDDFSWGETRKVDNDDG 719
                                        **************************87654 PP

>> Glyco_tranf_2_3  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.14   4.8e+02       4      39 ..     270     306 ..     269     325 .. 0.77
   2 !   54.9   0.0     3e-18   1.1e-14      80     228 ..     411     592 ..     338     594 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.14
                    Glyco_tranf_2_3   4 lavlVptfneed.vlgevlesllaqeyprvevvvvvd 39 
                                        ++ lV+++ e++  + ++l+sl +q y +  + v++d
  gene1673|gene1673|rna1673|rna1673 270 CIMLVTCYSEDReGIKKTLDSLCNQNYLEKVILVIAD 306
                                        6789******9988999********995544444443 PP

  == domain 2  score: 54.9 bits;  conditional E-value: 3e-18
                    Glyco_tranf_2_3  80 nealravk......sdlvllvDdDtvvePdtlkrllqff.ltpkvgavgtpvfl.lnrstlvsalgalefaerhlr 147
                                        +ea++ v       ++++ +vD+Dt+v+Pd+l  ++ +f ++pk++ + +     + + ++v++ + +e+++ h+ 
  gene1673|gene1673|rna1673|rna1673 411 YEAFKDVMgmeprhFEMIMMVDADTIVHPDALLHFNSAFvNDPKIMGMCGETKIiNKGASWVTMIQVFEYYISHHL 486
                                        4444443355566689***********************87776666665554426799***************** PP

                    Glyco_tranf_2_3 148 flaarralg.vltlnGsgslirrevlkele.....................gldp.lflltdDyelglrlrr..ag 198
                                        +  +   +g v++l G ++ +r +v ++ +                     ++ + l ll++D  l+  l +  ++
  gene1673|gene1673|rna1673|rna1673 487 TKTFESVFGgVTCLPGCFCIYRIKVKENDKyvpilansfvlgpysvtrtetLHEKnLLLLGEDRYLTTLLLKtfYR 562
                                        ******998689999*********999999*******************96555589999***9988888885777 PP

                    Glyco_tranf_2_3 199 frtayvpgaavrevfpsslkayikqrnRwv 228
                                         +  ++p a++r++ p++++ +  qr+Rw+
  gene1673|gene1673|rna1673|rna1673 563 RKLIFLPAATCRTYVPDTFSVLLSQRRRWI 592
                                        77779************************7 PP

>> Glyco_trans_2_3  Glycosyl transferase family group 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.1      0.23   8.2e+02     157     193 ..     214     252 ..     190     272 .. 0.69
   2 !   54.2   3.5   4.8e-18   1.7e-14       2     171 ..     428     667 ..     427     703 .. 0.68

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.23
                    Glyco_trans_2_3 157 gylgsllwsalplhl..allllfsllalalvllllllla 193
                                         y+g+l  +++ +++  +ll+l+ +++++l++l ++l++
  gene1673|gene1673|rna1673|rna1673 214 CYFGKLGGKTYGCLVadILLYLSTVIIFSLIILKFVLAI 252
                                        566666555544433226777777777777765554443 PP

  == domain 2  score: 54.2 bits;  conditional E-value: 4.8e-18
                    Glyco_trans_2_3   2 illlDaDtvlppdclreiaaela.spevaivqgpvlv.mnvanwleelaalffaedhgkdilvrealgrvvpsvGs 75 
                                        i+++DaDt ++pd l+ +++ +  +p++  ++g + + + +a+w++ ++++++ ++h     + + +g+v+ ++G 
  gene1673|gene1673|rna1673|rna1673 428 IMMVDADTIVHPDALLHFNSAFVnDPKIMGMCGETKIiNKGASWVTMIQVFEYYISHHLTKTFESVFGGVTCLPGC 503
                                        899***************9966658*********8763789************9********************** PP

                    Glyco_trans_2_3  76 gaflrrsalq....................evggwdgdes.........svsEDfdmglrlqrkGyrv..rfvpes 120
                                         ++ r+++ +                    +        +          ++ED ++   l++  yr   +f p++
  gene1673|gene1673|rna1673|rna1673 504 FCIYRIKVKEndkyvpilansfvlgpysvtR--------TetlheknllLLGEDRYLTTLLLKTFYRRklIFLPAA 571
                                        *******999888777776666444443332........13344445669*******9999877765333****** PP

                    Glyco_trans_2_3 121 lvkekspltlraalrQrkRwayGc.....eleklil........................................ 151
                                         +++++p+t+   l Qr+Rw+        e     l                                        
  gene1673|gene1673|rna1673|rna1673 572 TCRTYVPDTFSVLLSQRRRWINSTvhnlmE-----Lvsvnalcgtfccsmqfavgvelagtlvlpvsiiftfvlia 642
                                        ***********************7554331.....02233444555556666666666666555555555444443 PP

                    Glyco_trans_2_3 152 ...lvrll..gylgsllwsalplhl 171
                                           l+++    ++++ + ++lp+ l
  gene1673|gene1673|rna1673|rna1673 643 vsiLIKPAwiPLIMLACIFGLPIIL 667
                                        3332222211222222333333333 PP

>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.0     6e-05      0.22       4      37 ..     274     307 ..     272     327 .. 0.93
   2 !    8.6   0.0   0.00042       1.5      82     165 ..     427     511 ..     413     514 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 6e-05
                                        EEESS-.TTTHHHHHHHHHHHGGCCEEEEEEEEES CS
                    Glycos_transf_2   4 iptyNe.ektlletlesllaqdpypdfeiivvDDg 37 
                                        +++y e  + +++tl+sl++q +y+++ i+v+ Dg
  gene1673|gene1673|rna1673|rna1673 274 VTCYSEdREGIKKTLDSLCNQ-NYLEKVILVIADG 307
                                        89*******************.*********9998 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00042
                                        EEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SSEEEECCHCC.CCHCCCCCCSTTCST CS
                    Glycos_transf_2  82 yilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiernkrvgenerlyfk.erkrslkgnlsfeig 156
                                         i+ +DaD++++pd l  +  a+ +d++ + +++  +i  +   +  + +v+e ++  +  ++  s +g++++  g
  gene1673|gene1673|rna1673|rna1673 427 MIMMVDADTIVHPDALLHFNSAFVNDPKIMGMCGETKIINKGASWVTMIQVFEYYISHHLtKTFESVFGGVTCLPG 502
                                        6899*********************777544444444444444444444444444444440445567788999999 PP

                                        CCCEEEEHH CS
                    Glycos_transf_2 157 saallrrea 165
                                        +++++r ++
  gene1673|gene1673|rna1673|rna1673 503 CFCIYRIKV 511
                                        999998876 PP

>> Glyco_transf_21  Glycosyl transferase family 21
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   5.4e-05      0.19      25     109 ..     419     508 ..     413     511 .. 0.82
   2 ?    1.2   0.0     0.064   2.3e+02     126     172 ..     546     592 ..     519     593 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 5.4e-05
                    Glyco_transf_21  25 aleaakydllvisDsdvrvkpdyLeellaaled.pkvglVtslpvgsdakglaaaleaafl.ntlagvlqa...kl 95 
                                        ++e    +++++ D+d++v pd+L ++  a+   pk+   ++     ++   + ++ ++f  ++ + +++     +
  gene1673|gene1673|rna1673|rna1673 419 GMEPRHFEMIMMVDADTIVHPDALLHFNSAFVNdPKIMGMCGETKIINKGASWVTMIQVFEyYISHHLTKTfesVF 494
                                        566677899******************99987559**999999999999999999999998556666666554356 PP

                    Glyco_transf_21  96 sglgfavGksmalr 109
                                        +g+ +  G ++++r
  gene1673|gene1673|rna1673|rna1673 495 GGVTCLPGCFCIYR 508
                                        89999999999987 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.064
                    Glyco_transf_21 126 LAeDyalgkllraa..GlkvvlspapiaqtsvprrsslrallaRqlrWa 172
                                        L eD  l++ll +     k+++ pa+ ++t vp+  +++ ll++  rW 
  gene1673|gene1673|rna1673|rna1673 546 LGEDRYLTTLLLKTfyRRKLIFLPAATCRTYVPD--TFSVLLSQRRRWI 592
                                        7899999999999977889999999999999996..99**********6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (775 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       919  (0.0512577); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.69u 0.31s 00:00:01.00 Elapsed: 00:00:00.45
# Mc/sec: 5140.46
//
Query:       gene1674|gene1674|rna1674|rna1674  [L=352]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-44  152.7   0.0    5.2e-44  150.6   0.0    1.8  1  Pkinase         Protein kinase domain
    9.3e-17   61.2   0.0    1.2e-12   47.7   0.0    2.1  2  Pkinase_Tyr     Protein tyrosine kinase
    2.6e-06   26.5   0.0    3.6e-06   26.0   0.0    1.1  1  Pkinase_fungal  Fungal protein kinase
     0.0019   18.2   0.0     0.0058   16.6   0.0    1.7  1  APH             Phosphotransferase enzyme family
  ------ inclusion threshold ------
      0.029   13.7   0.1      0.066   12.6   0.1    1.5  2  Kdo             Lipopolysaccharide kinase (Kdo/WaaP) family
      0.043   13.1   0.0        4.5    6.5   0.0    2.2  2  Kinase-like     Kinase-like
      0.047   13.2   0.0      0.087   12.3   0.0    1.4  1  YrbL-PhoP_reg   PhoP regulatory network protein YrbL
      0.097   12.2   0.2       0.17   11.4   0.2    1.3  1  Choline_kinase  Choline/ethanolamine kinase
       0.18   11.4   0.1        3.4    7.3   0.0    2.5  2  DUF3778         Protein of unknown function (DUF3778)


Domain annotation for each model (and alignments):
>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  150.6   0.0   2.6e-47   5.2e-44       1     264 []      19     348 ..      19     348 .. 0.85

  Alignments for each domain:
  == domain 1  score: 150.6 bits;  conditional E-value: 2.6e-47
                                        EEEEEEEEEESSEEEEEEEETT...TTEE...EEEEEEECHCHCHHHHHHHHHHHHHHHHHS.CTTB--EEEEEEE CS
                            Pkinase   1 yekleklGeGsfGkVykaveke...tgki...vAvKkikkekakkkkekkvlrEikilkklk.hpnivrlyevfee 69 
                                        y+++ + GeG+f++Vykav+ +   +++     A+K i   +a      +v++E+++lkkl+  + ++ l++v++ 
  gene1674|gene1674|rna1674|rna1674  19 YKVIARAGEGTFSTVYKAVDLNhteSDNSysnAAIKNITMTSAP----ARVAEELRFLKKLNgENGVIPLLNVLRF 90 
                                        6677888***********97541113333111455555555444....5899**********8888********** PP

                                        SSEEEEEEE--TTEBHHHHHHHHSS--HHHHHHHHHHHHHHHHHHHHTTEE-SS-SGGGEEEE.TTTEEEE-SGTT CS
                            Pkinase  70 kdelylvleyveggeladllerkgslseeeakkiakqilegleylHskgiiHrDlKpeNiLid.ekgelKitDFGl 144
                                        +d+++ v+ y e+ ++ ++le     +  ++k +++q++ +l++ H+++iiHrD+Kp+N+L++ e++   ++DFGl
  gene1674|gene1674|rna1674|rna1674  91 EDQVVAVFPYFECSDFREFLE---FCTIGDIKVYLRQLIIALKHTHDNHIIHRDIKPSNFLYNsEQQRGFLIDFGL 163
                                        ********************8...699************************************6667799****** PP

                                        SEESSSSCS........................................BCTTTSCGGGS-HHHH.TTSCBSHHHH CS
                            Pkinase 145 akelesssk........................................ltsfvgtseYlAPEvl.keneyskkvD 179
                                        a+e +s +                                         + ++ gt+ ++APEvl ++++ + ++D
  gene1674|gene1674|rna1674|rna1674 164 AQEEKSVQApdttparnaktkpsvmffnsvvsrstqppgyyqtdtrpvmKAQRAGTRGFRAPEVLfRNQNQTISID 239
                                        **9999888999************************************99999************999999***** PP

                                        HHHHHHHHHHHHHSS-STTTSSHHHHHHHHHHTHHHHHHHCTSHH...HHHTTS...................... CS
                            Pkinase 180 vWslGvilyelltgkppfsgekgkekvekeldqlekilkilgetkeklpeasei...................... 233
                                        +Ws+Gvi++ llt++ pf ++ +      +ld l++i+ i+g++++    ++                        
  gene1674|gene1674|rna1674|rna1674 240 IWSVGVIFLILLTKQYPFFNSLD------DLDALVEIACIFGNNEMRKLAKY-Hgrvwktnlssipneripferiv 308
                                        *******************4444......56666666666664222222222.12445555777899999****** PP

                                        .........-HHHHHHHHHHT-SSGCCSTTHHHHHTSGGG CS
                            Pkinase 234 .........seeakdllkkllkkdpkkRltaeellqhpyl 264
                                                 +++  dll ++l+  p+kR+taee+l+hp+l
  gene1674|gene1674|rna1674|rna1674 309 relnpscclDKHGYDLLYRMLELYPEKRITAEEALAHPFL 348
                                        **************************************97 PP

>> Pkinase_Tyr  Protein tyrosine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.7   0.0     6e-16   1.2e-12       5     155 ..      23     169 ..      19     197 .. 0.85
   2 !   11.6   0.0     6e-05      0.12     161     259 .]     212     311 ..     202     311 .. 0.69

  Alignments for each domain:
  == domain 1  score: 47.7 bits;  conditional E-value: 6e-16
                                        EEEEEESSEEEEEEEEET..TTTSSEEEEEEEEESTTSSHHHHHHHHHHHHHHHTS.-BTTB--EEEEEESSSSEE CS
                        Pkinase_Tyr   5 kklGeGafGkVvegtlkg..ekekkevkVavKtlkeeateeekeelleeakimkkl.khpnivkllgvctkeepll 77 
                                         + GeG+f++V+++   +  e++++  + a+K ++     +  +++ ee++++kkl   + ++ ll v   e++++
  gene1674|gene1674|rna1674|rna1674  23 ARAGEGTFSTVYKAVDLNhtESDNSYSNAAIKNITM---TSAPARVAEELRFLKKLnGENGVIPLLNVLRFEDQVV 95 
                                        5679**********87666788899999******44...444679***********556669********9***** PP

                                        EEEE--TTEBHHHHHHHTCTTTSBHHHHHHHHHHHHHHHHHHHHTTEEEST-SGGGEEEEETT.EEEE-STTTHEE CS
                        Pkinase_Tyr  78 ivteyvkgGdLlkfLrkkekekltlkdllsfalqvAkGmeyLeskklvHrdlaarNvLlsenk.vvkisDfGLard 152
                                         v+ y +  d+++fL+       t+ d+  +  q+  ++++ ++++++Hrd+   N L ++++    + DfGLa++
  gene1674|gene1674|rna1674|rna1674  96 AVFPYFECSDFREFLEFC-----TIGDIKVYLRQLIIALKHTHDNHIIHRDIKPSNFLYNSEQqRGFLIDFGLAQE 166
                                        ***************997.....9999********************************9755277899*****98 PP

                                        TTT CS
                        Pkinase_Tyr 153 iek 155
                                         ++
  gene1674|gene1674|rna1674|rna1674 167 EKS 169
                                        733 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 6e-05
                                        ETTSSTSGGGGS-HHHHHHSE.EEHHHHHHHHHHHHHHHHTTSSGTTTTSHHHHHHHHHHTTEES-BBTTSBHHHH CS
                        Pkinase_Tyr 161 kkeeaklpvkWmapEslkekk.ftsksDvWsfGvllwEiftlgespypglkneevleklkegkrlekpekcpeely 235
                                        +k ++     + apE+l++++  t + D+Ws Gv+   ++t+    +++l++ ++l  +      ++ +k  +   
  gene1674|gene1674|rna1674|rna1674 212 MKAQRAGTRGFRAPEVLFRNQnQTISIDIWSVGVIFLILLTKQYPFFNSLDDLDALVEIACIFGNNEMRKLAKYHG 287
                                        555666666789****99988356677********99999966655666677776666655555555555555556 PP

                                        HHHHHHT-SSGGGS--HHHHHHHH CS
                        Pkinase_Tyr 236 elmkkcweedpeeRptfselvekl 259
                                        ++ k+ +++ p+eR  f+++v++l
  gene1674|gene1674|rna1674|rna1674 288 RVWKTNLSSIPNERIPFERIVREL 311
                                        666777778888888888888765 PP

>> Pkinase_fungal  Fungal protein kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   0.0   1.8e-09   3.6e-06     312     388 ..     122     230 ..     107     252 .. 0.81

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 1.8e-09
                     Pkinase_fungal 312 lrDaIkghrsLflkagiLHrDiSenNilitdskkegerkglLiDLDlakelsddssesgare.............. 373
                                        lr+ I +++  + +  i+HrDi   N l +     ++++g+LiD+ la e++ +++ +                  
  gene1674|gene1674|rna1674|rna1674 122 LRQLIIALKHTH-DNHIIHRDIKPSNFLYN----SEQQRGFLIDFGLAQEEKSVQAPDTTPArnaktkpsvmffns 192
                                        789999****9*.***************99....5689**************988887542244566788888888 PP

                     Pkinase_fungal 374 .......................rtGTleFmaievlkg 388
                                                               r GT+ F a evl  
  gene1674|gene1674|rna1674|rna1674 193 vvsrstqppgyyqtdtrpvmkaqRAGTRGFRAPEVLFR 230
                                        88888888888888888888888999999999999865 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   2.9e-06    0.0058     151     196 ..      93     164 ..      51     165 .. 0.65

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 2.9e-06
                                        H............................HHHHHHHH--SSS-EEEE-SS-SGGGEEEC..TTEEEEE---TT- CS
                                APH 151 q............................vlaalaallpgelptvllHgDlhpgNllvdpddgrvtGviDfeda 196
                                        q                            +++ + al +   +  ++H+D++p N+l +++++r   +iDf++a
  gene1674|gene1674|rna1674|rna1674  93 QvvavfpyfecsdfreflefctigdikvyLRQLIIALKH-THDNHIIHRDIKPSNFLYNSEQQRG-FLIDFGLA 164
                                        455555555555555555555555555545555556666.48899**************666664.59****98 PP

>> Kdo  Lipopolysaccharide kinase (Kdo/WaaP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.0       3.3   6.5e+03      49      69 ..      56      76 ..      47      83 .. 0.72
   2 ?   12.6   0.1   3.3e-05     0.066     130     171 ..     128     166 ..     119     174 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 3.3
                                Kdo 49 yrfklgrtravrEfrllkrLe 69
                                        +++   +r+++E+r lk+L+
  gene1674|gene1674|rna1674|rna1674 56 ITMTSAPARVAEELRFLKKLN 76
                                       455556678889999999986 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 3.3e-05
                                Kdo 130 liaklhragvnHadlyaknillqqeeeeeaeiwliDldkarl 171
                                        + +  h+ ++ H+d+ + n+l + e+   ++  liD+  a++
  gene1674|gene1674|rna1674|rna1674 128 ALKHTHDNHIIHRDIKPSNFLYNSEQ---QRGFLIDFGLAQE 166
                                        66788******************998...9*******87765 PP

>> Kinase-like  Kinase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0      0.01        20     152     188 ..     124     161 ..     117     181 .. 0.76
   2 ?    6.5   0.0    0.0023       4.5     206     250 ..     221     257 ..     202     266 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.01
                        Kinase-like 152 qlirlaanLqakglvhgkftvdnllldek.gglmlggf 188
                                        qli    + +++ ++h ++++ n+l++ +  + +l +f
  gene1674|gene1674|rna1674|rna1674 124 QLIIALKHTHDNHIIHRDIKPSNFLYNSEqQRGFLIDF 161
                                        67777788999***************854144555555 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0023
                        Kinase-like 206 gfaPpEllgsrggytrknktkmthkldaWqlGlviyriwclklPl 250
                                        gf  pE+l         ++ + t+++d W +G+  + +   + P+
  gene1674|gene1674|rna1674|rna1674 221 GFRAPEVLF--------RNQNQTISIDIWSVGVIFLILLTKQYPF 257
                                        555555554........46789**********9888777777776 PP

>> YrbL-PhoP_reg  PhoP regulatory network protein YrbL
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   4.4e-05     0.087     125     166 ..     122     160 ..     110     182 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 4.4e-05
                      YrbL-PhoP_reg 125 keaLdefleelldnhivtndlsakNivvkknsegeeelvlvD 166
                                         ++L   l++  dnhi+ +d++++N +++ ++++    +l+D
  gene1674|gene1674|rna1674|rna1674 122 LRQLIIALKHTHDNHIIHRDIKPSNFLYNSEQQRG---FLID 160
                                        455555567789****************9888776...7777 PP

>> Choline_kinase  Choline/ethanolamine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.2   8.6e-05      0.17     141     171 ..     131     161 ..     100     167 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 8.6e-05
                                        HGG-EEEE-S--SGGGEEE.-CTTEEEE--G CS
                     Choline_kinase 141 lespvvfcHnDlqegNillnkeekklvlIDF 171
                                        + ++    H D+ ++N+l+n+e+++ +lIDF
  gene1674|gene1674|rna1674|rna1674 131 HTHDNHIIHRDIKPSNFLYNSEQQRGFLIDF 161
                                        34445566*********************** PP

>> DUF3778  Protein of unknown function (DUF3778)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.1      0.17   3.3e+02      40      50 ..      83      93 ..      69      95 .. 0.86
   2 ?    7.3   0.0    0.0017       3.4       5      41 ..     287     322 ..     284     328 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.17
                            DUF3778 40 GllvlLRFnde 50
                                        ll  LRF+d+
  gene1674|gene1674|rna1674|rna1674 83 PLLNVLRFEDQ 93
                                       57999****97 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0017
                            DUF3778   5 gwsldassllfpcssihvefviRVElrpsvrllsaGl 41 
                                        g+++++  +++p+ +i  e ++R El+ps  l   G 
  gene1674|gene1674|rna1674|rna1674 287 GRVWKTNLSSIPNERIPFERIVR-ELNPSCCLDKHGY 322
                                        689********************.9999988877775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (352 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       377  (0.0210274); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.55u 0.32s 00:00:00.87 Elapsed: 00:00:00.49
# Mc/sec: 2180.69
//
Query:       gene1675|gene1675|rna1675|rna1675  [L=351]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.098   12.8   0.2       0.37   11.0   0.2    1.9  2  Cass2     Integron-associated effector binding protein


Domain annotation for each model (and alignments):
>> Cass2  Integron-associated effector binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.2     2e-05      0.37      21      73 ..     169     226 ..     158     237 .. 0.72
   2 ?   -2.9   0.0      0.37   6.7e+03      86     113 ..     299     326 ..     284     327 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 2e-05
                                        CCH...HHHHHHHHHHHHH...HHCTTSBS..TEEEEEEEC-TT.-CCGEEEEEEEEE- CS
                              Cass2  21 eedlnkeigklwreflekg...rlkkikkd..krvfgiyhdyes.eenkfsyyagvevp 73 
                                         +d n++ +k++++f+ek+   r +k+k +   ++f +y+++ +  +++++++++   +
  gene1675|gene1675|rna1675|rna1675 169 STD-NTMHNKFFKDFNEKQqleRANKTKGQarIKMFYFYSSSSDsDDQGLTHVTCSHKE 226
                                        444.78889**********5554455555555556666666666899999999998665 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 0.37
                                        EE--EEEEEEEEESSSTT-HHHHHHHHH CS
                              Cass2  86 eiPggkYavftiegdfeedlaeaweaiy 113
                                         iP ++ +v++++ +f+  +++++e +y
  gene1675|gene1675|rna1675|rna1675 299 IIPVKHSLVHKLRSSFPSSFRKIMEMLY 326
                                        5777888888888888887777777666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (351 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       776  (0.0432818); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 2416.12
//
Query:       gene1676|gene1676|rna1676|rna1676  [L=633]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.6e-74  250.0   2.2    3.8e-74  249.4   2.2    1.3  1  tRNA-synt_1c    tRNA synthetases class I (E and Q), catalytic
    5.9e-22   78.4   0.8    3.5e-21   75.9   0.0    2.4  2  tRNA-synt_1c_C  tRNA synthetases class I (E and Q), anti-codo
  ------ inclusion threshold ------
      0.032   13.6   0.2      0.051   12.9   0.2    1.4  1  tRNA-synt_1e    tRNA synthetases class I (C) catalytic domain


Domain annotation for each model (and alignments):
>> tRNA-synt_1c  tRNA synthetases class I (E and Q), catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  249.4   2.2   6.4e-78   3.8e-74       4     313 ..     143     445 ..     140     446 .. 0.93

  Alignments for each domain:
  == domain 1  score: 249.4 bits;  conditional E-value: 6.4e-78
                                        EEE---SSSS-BHHHHHHHHHHHHHHHHTT-EEEEEE--SSCCC--HHHHHHHHHHHHHTT---SSEEEEGGGGHH CS
                       tRNA-synt_1c   4 tRfaPePtGyLHiGhakaallnylfAknnnGkfilRieDTdperekeeaeesiledlkwlgikwdekptyqsdrfd 79 
                                         Rf+PeP+GyLH+Gh kaalln  +A     ++i+R++DT++e+  e +e+ iledl++l++k  +++ ++sd+  
  gene1676|gene1676|rna1676|rna1676 143 CRFPPEPSGYLHLGHVKAALLNNSMAD----ELIVRFDDTNQEKGSELYEKIILEDLELLELKE-HRLSRTSDYYR 213
                                        6*********************99997....69*******************************.99********* PP

                                        HHHHHHHHHHHTTSEEEE-STHHHHHHHHCCSS.....HSS-TTTTS-HHHHHHHHHHHHHTTHSTTTS-EEEESS CS
                       tRNA-synt_1c  80 elkkyaeeLikkGkAYvcectkeeleeereeqe.....klgskerdrydeenlklfeeemkkgkaegekavvRlki 150
                                        ++   a+ Li++G+AY++++ +e++++er+e         +++ + r   ++ +l eee++ + +e e+++vR+ki
  gene1676|gene1676|rna1676|rna1676 214 TIVTCAQYLISEGLAYCDNTDQEQMNKERMEGIqsvkrDTKPVDNMRIFHRMIELGEEEKRGHGSEYEQYCVRAKI 289
                                        *****************************99655565556667777888899999999999999999********* PP

                                        BTTSS.GGGSSTEEEEEEESGGGSBTTTBTSTSEEE-HHHHHHHHHHHTT-SEEEEEGGGGCCHHHHHHHHHHTT- CS
                       tRNA-synt_1c 151 deess.vefrDlvrgriklepqeihdlvivksdiyPtYdfavvidDaleeithvlrteefldntpkyiwllealgl 225
                                            +  ++rD+v+ r k ++   h ++   s+ +PtYdfa++i+D++e++t vlrt+ef+d++++y+w+l+ l++
  gene1676|gene1676|rna1676|rna1676 290 SVDDKnKALRDPVIFRLKEKK---HGRTN--SRLSPTYDFACPIVDSVEGVTTVLRTNEFRDRNAQYFWFLNSLKM 360
                                        9998889***********999...88876..5679***************************************** PP

                                        S.-EEEEEE--EEETTSB-SHHHHHHHHHTTSSSSTT-TTSCBHHHHHHCTB-HHHHHHHHHHHCCCSSS.EEEEH CS
                       tRNA-synt_1c 226 evppfiheylrlnlekkklSKRklsllvdekqvkewddlreallnflrrlGwtpekerelftreeliksfdlnres 301
                                        +  p+i  ++rln+e++ lSKRkl ++++e+++  wdd+r +++++++rlG++++  +e + ++++ ++  + +++
  gene1676|gene1676|rna1676|rna1676 361 R-VPVIKDFSRLNFENTILSKRKLRTIIEEHDL-TWDDPRIPTIRGIMRLGLNINVLKEYIVMQGMRQKN-TINSW 433
                                        *.8999*********************777776.6*******************************9999.8899* PP

                                        HHHHHHHHHHHH CS
                       tRNA-synt_1c 302 ksleafdrkkLe 313
                                        ++++a+++k+Le
  gene1676|gene1676|rna1676|rna1676 434 DKIWAMNKKYLE 445
                                        *********997 PP

>> tRNA-synt_1c_C  tRNA synthetases class I (E and Q), anti-codon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.2      0.11   6.6e+02      82     130 ..     220     271 ..     172     310 .. 0.65
   2 !   75.9   0.0   5.8e-25   3.5e-21       2     174 .]     449     611 ..     448     611 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.11
                     tRNA-synt_1c_C  82 sgevtelkleydgesleearkkkg.iihWvsaeeaveaevrlYdrLfk..ee 130
                                        +  ++e  + +d+++ e+ +k+++  i+ v+ +++ + ++r + r+++  ee
  gene1676|gene1676|rna1676|rna1676 220 QYLISEGLAYCDNTDQEQMNKERMeGIQSVKRDTKPVDNMRIFHRMIElgEE 271
                                        4456666677788888888899988999999866555589999999875422 PP

  == domain 2  score: 75.9 bits;  conditional E-value: 5.8e-25
                     tRNA-synt_1c_C   2 pRymaVl.dpvkvtienlpeg....keeelevplhpknpelgtrkvpfskeiyiereDakrlkpgeevrLkelyni 72 
                                        +Ry  V  + vk+   + +++     e  l +p+++k+  +g+r+v f+++ +i+reDa+ l+++ee++L++++n+
  gene1676|gene1676|rna1676|rna1676 449 KRYSGVYgECVKICFVDCKDApaepLEAALMIPYNKKDLLMGQRTV-FTSNMVISREDAELLADNEEFTLMHIGNV 523
                                        56777766666666665533333356678899***********998.566788*********************** PP

                     tRNA-synt_1c_C  73 kveevekdesgevtelkleydgesleearkkkg.iihWvsaeeaveaevrlYdrLfkeeededfllnpdslkvlee 147
                                         v++ +     + + +  + dg ++    k+++ +i+Wvs e a ++++ +Y +L+ +       +n +s+++  +
  gene1676|gene1676|rna1676|rna1676 524 VVRNKQ----PDKILIMNKPDG-DV----KTTTnKITWVSLEGAHTVNLAVYGDLVVN-----GKFNTESKTI-IR 584
                                        **8874....233334456666.66....55555*********************753.....56999**987.6* PP

                     tRNA-synt_1c_C 148 glaepalanlkkgdivQfeRiGyfrvd 174
                                          ae+a++++k g+++QfeRiG++r d
  gene1676|gene1676|rna1676|rna1676 585 IHAEKAVEDVKCGEVIQFERIGFARRD 611
                                        ***********************9976 PP

>> tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.2   8.5e-06     0.051      71     144 ..     179     251 ..      14     276 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 8.5e-06
                                        -HHHHHHHHHHHHHHHHHHTT----SB--BGGGGHHHHHHHHHHHHHTTSEEE-TTS-EEE-GGG-TTTTTTTT CS
                       tRNA-synt_1e  71 svkelaekfieefkkdleaLnvlkptleprvsekvdeiielvekliekgyaYavsdgdvyfdvskkeeYgklsk 144
                                        ++++ +e +++   +dle L++++ +  +r s++   i+   + li++g aY  + ++++++++++e   ++++
  gene1676|gene1676|rna1676|rna1676 179 NQEKGSELYEKIILEDLELLELKE-HRLSRTSDYYRTIVTCAQYLISEGLAYCDNTDQEQMNKERMEGIQSVKR 251
                                        26677888999999*******988.6678**************************9**9999998887666654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (633 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       688  (0.0383736); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.66u 0.31s 00:00:00.97 Elapsed: 00:00:00.50
# Mc/sec: 3772.49
//
Query:       gene1677|gene1677|rna1677|rna1677  [L=218]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-17   64.9   3.0    1.3e-17   64.9   3.0    1.6  2  CDC37_N         Cdc37 N terminal kinase binding
     0.0031   17.8   5.9     0.0031   17.8   5.9    2.1  2  PGBA_C          Plasminogen-binding protein pgbA C-terminal
  ------ inclusion threshold ------
      0.011   15.6   0.1      0.029   14.3   0.0    1.7  1  Ferritin        Ferritin-like domain
      0.054   13.8   0.8       0.12   12.6   0.6    1.6  2  DUF5426         Family of unknown function (DUF5426)
      0.066   12.4   0.0      0.088   12.0   0.0    1.2  1  NAD_kinase      ATP-NAD kinase
        2.4    8.6   6.9       0.53   10.7   1.7    2.2  2  Ribosomal_L27e  Ribosomal L27e protein family


Domain annotation for each model (and alignments):
>> CDC37_N  Cdc37 N terminal kinase binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.9   3.0   4.2e-21   1.3e-17       9     128 ..      13     151 ..      10     152 .. 0.89
   2 ?   -2.1   0.0       2.3   6.9e+03      69      79 ..     179     189 ..     166     216 .. 0.49

  Alignments for each domain:
  == domain 1  score: 64.9 bits;  conditional E-value: 4.2e-21
                            CDC37_N   9 klELSDDsDievHPNVDk...rsfirwKqrdihekreqrkaeikklklereindkllkridkllealkekeveeee 81 
                                        ++ELS+Ds+ + HPN++k   r+++r+K+++ +e+++++ ++ikk+ +e +++ +l++r + l ++lk k ve+  
  gene1677|gene1677|rna1677|rna1677  13 EMELSSDSTEYEHPNIEKstlRRLVREKRKHDKEEWAKELDNIKKILSE-RYDPELENRKKFLEQKLKPKFVET-- 85 
                                        79****************9999**************************9.8***********************.. PP

                            CDC37_N  82 vvfkalnesleekkekedkpkae.............k......eeeqptydem.leklldqvkkelk 128
                                         +++++n+++ee++e+++ +++              +      + + +++de+ l++l +++k+ l+
  gene1677|gene1677|rna1677|rna1677  86 -STNMINNTVEERNEDDKFADYLlflggdptidnfiEfvedtkNINLERFDEFlLMNLSENIKEGLD 151
                                        .89*******999999999998877777776666550555553588999999989999999999887 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.3
                            CDC37_N  69 lealkekevee 79 
                                         ++lk++++++
  gene1677|gene1677|rna1677|rna1677 179 SDSLKDESKKH 189
                                        34444333333 PP

>> PGBA_C  Plasminogen-binding protein pgbA C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   5.9     1e-06    0.0031      27      82 ..      21      77 ..       7      79 .. 0.87
   2 ?    0.5   0.1      0.28   8.2e+02      26      48 ..     183     205 ..     169     215 .. 0.68

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1e-06
                             PGBA_C 27 kevnkpn.skeekrrlkeekkkakaeqrarefeqrarehqerdekeleerrkalean 82
                                        e + pn  k   rrl  ek+k   e+ a+e+++  +   er + ele+r+k le +
  gene1677|gene1677|rna1677|rna1677 21 TEYEHPNiEKSTLRRLVREKRKHDKEEWAKELDNIKKILSERYDPELENRKKFLEQK 77
                                       5777888447788*****************************************975 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.28
                             PGBA_C  26 kkevnkpnskeekrrlkeekkka 48 
                                        k e +k    ee r+  e+ k a
  gene1677|gene1677|rna1677|rna1677 183 KDESKKHIFDEECRKYYEDSKDA 205
                                        45555566667777777776665 PP

>> Ferritin  Ferritin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   9.8e-06     0.029      42     128 ..      94     189 ..      78     194 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 9.8e-06
                                        HHHHHHHHHHHHHHHHTTS....SHH.HHHH......C-SSSS.CS.SHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           Ferritin  42 eeerehadklaerilalGgtpvltra.elee......ieapke.fg.sveevleaalehekkvteslrelielaee 108
                                         eer+  dk+a+++l+lGg+p+++   e+ e      +e  +e    ++ e +++ l+    v+++l    ++ ++
  gene1677|gene1677|rna1677|rna1677  94 VEERNEDDKFADYLLFLGGDPTIDNFiEFVEdtkninLERFDEfLLmNLSENIKEGLDEAGMVISTLSLYFKYLKQ 169
                                        599999*************999875336666444433222222423466666666666666666666666666666 PP

                                        TT-HHHHHHHHHHHHHHHHH CS
                           Ferritin 109 egDpatadfledfleeqeeh 128
                                         g p ++ + + + +e  +h
  gene1677|gene1677|rna1677|rna1677 170 GGMPLLRKLSDSLKDESKKH 189
                                        66666666666666666666 PP

>> DUF5426  Family of unknown function (DUF5426)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.37   1.1e+03      91     126 ..      75     109 ..      53     112 .. 0.72
   2 ?   12.6   0.6   4.1e-05      0.12      59     129 ..      97     169 ..      81     172 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.37
                            DUF5426  91 eekeperifetvkleavvvlekeevlnsKLsDYfrl 126
                                        e+k + +++et   ++  ++e+    + K +DY  +
  gene1677|gene1677|rna1677|rna1677  75 EQKLKPKFVETSTNMINNTVEER-NEDDKFADYLLF 109
                                        55556678888888888888877.567788888655 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 4.1e-05
                            DUF5426  59 enafqklanivffietq..vnellgllleresikeekeperifetvkleavvvlekeevlnsKLsDYfrlFkd 129
                                        +n+ +k+a++ +f+  +  +++++  + ++++i+ e+ +e +     + ++ +l++  ++ s Ls Yf++ k+
  gene1677|gene1677|rna1677|rna1677  97 RNEDDKFADYLLFLGGDptIDNFIEFVEDTKNINLERFDEFLLMNLSENIKEGLDEAGMVISTLSLYFKYLKQ 169
                                        5666788888888854433**************************************************9985 PP

>> NAD_kinase  ATP-NAD kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   2.9e-05     0.088      65      98 ..      53     123 ..       9     128 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.9e-05
                                        ......................................EEECCC-TTTTTSSSEEEEEE-HHHHHHHHHHH CS
                         NAD_kinase  65 d.....................................dtrkaleafadagvdliivvGGDGTaldvarll 98 
                                        d                                     +++ + +++ d+++d ++++GGD T+    + +
  gene1677|gene1677|rna1677|rna1677  53 DnikkilserydpelenrkkfleqklkpkfvetstnmiNNTVEERNEDDKFADYLLFLGGDPTIDNFIEFV 123
                                        333333333333334444444444444444555566788889999999**************997666655 PP

>> Ribosomal_L27e  Ribosomal L27e protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   1.7   0.00018      0.53      36      84 ..      28      79 ..      20      80 .. 0.84
   2 ?   -0.0   0.3      0.39   1.2e+03      48      71 ..     180     203 ..     175     215 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00018
                     Ribosomal_L27e 36 vdvedlkelvkkealkdpakrkeakkevkkkfeery...ksgknkwffkkLr 84
                                       ++ + l+ lv ++  +d+++  +   ++kk+++ery    ++++k++ +kL+
  gene1677|gene1677|rna1677|rna1677 28 IEKSTLRRLVREKRKHDKEEWAKELDNIKKILSERYdpeLENRKKFLEQKLK 79
                                       5556788899999999999999**************99878889******96 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.39
                     Ribosomal_L27e  48 ealkdpakrkeakkevkkkfeery 71 
                                        ++lkd +k+    +e++k+ e++ 
  gene1677|gene1677|rna1677|rna1677 180 DSLKDESKKHIFDEECRKYYEDSK 203
                                        678888888888888888887764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1121  (0.0625244); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1498.51
//
Query:       gene1678|gene1678|rna1678|rna1678  [L=1658]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   6.4e-236  784.8   0.0   1.8e-235  783.3   0.0    1.8  1  Myosin_head      Myosin head (motor domain)
    3.7e-10   39.5   0.1    9.8e-10   38.1   0.1    1.8  1  Myosin_N         Myosin N-terminal SH3-like domain
    3.9e-06   26.7  30.1    3.9e-06   26.7  30.1    7.0  7  Filament         Intermediate filament protein
     0.0046   16.7   9.2     0.0046   16.7   9.2    9.8  9  DUF4201          Domain of unknown function (DUF4201)
     0.0047   16.9  13.2     0.0047   16.9  13.2    9.0  7  Wtap             WTAP/Mum2p family
  ------ inclusion threshold ------
      0.085   12.9   2.8       0.14   12.2   0.1    2.8  3  DUF4537          Domain of unknown function (DUF4537)
        1.3    8.9  11.5        1.1    9.2   0.0    4.0  4  Microtub_bd      Microtubule binding
        1.5    9.2   0.0        1.5    9.2   0.0    5.6  5  AAA_16           AAA ATPase domain
        2.6    8.2 164.9       0.26   11.5  19.4    9.1  9  ATG16            Autophagy protein 16 (ATG16)
        6.6    6.5   9.1       0.78    9.5   1.1    3.7  4  DUF3287          Protein of unknown function (DUF3287)


Domain annotation for each model (and alignments):
>> Myosin_head  Myosin head (motor domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  783.3   0.0  9.9e-239  1.8e-235       2     677 .]      68     716 ..      67     716 .. 0.98

  Alignments for each domain:
  == domain 1  score: 783.3 bits;  conditional E-value: 9.9e-239
                                        SBGCGSSS-SHHHHHHHHHHHHHTT--EEEETTEEEEE--SS--STSSHHHHHHHTTS-GGGSSSSHHHHHHHHHH CS
                        Myosin_head   2 edlveLsllneasvlenlkkRykkdliYtysglvlvavnPykklkiysedvikaykgkkreelpPHifaiadeayr 77 
                                        +dl+ Ls+lneasvl+nl++Ry++++iYtysgl+lva+nP+++l iy+e+v+k+y+ +k++el PHifa+a++ay 
  gene1678|gene1678|rna1678|rna1678  68 DDLAGLSYLNEASVLHNLHMRYTAHEIYTYSGLFLVALNPFRNLGIYTEKVMKKYSMNKKYELRPHIFAVANDAYT 143
                                        89************************************************************************** PP

                                        HHHHHTSEEEEEEESSTTSSHHHHHHHHHHHHHHHSSSSSCTCTTHHHHHHHHHHHHHHHHHEEEESSETTEESSE CS
                        Myosin_head  78 slledkenqsilisGEsGAGKteatKkvlqylasvaeskekveeeeleekilqsnPilEafGnAktvrndnssRFG 153
                                        s++ + +nqsili+GEsGAGKte+tK+ +++la+va+  ++++ +++e+ki+++nP+lEafGnA+t+rn nssRFG
  gene1678|gene1678|rna1678|rna1678 144 SMVMNGKNQSILITGESGAGKTENTKRAISFLAYVAQGCTASDGTSIEHKIVDTNPVLEAFGNAQTTRNYNSSRFG 219
                                        **************************************************************************** PP

                                        EEEEEEEETTSSEEEEEEEEECE-GGGGT---TT--SBHHHHHHHHCSTHHHHHHTT--.TCCGSTTTTTTSSSSB CS
                        Myosin_head 154 KfieiefdakgkiagakietYLLEksRvvkqakeERnyHiFYqllagaseeekkelkle.dvkdyaylsqsgeltv 228
                                        Kfi+i+f+  g+i+ga ie+YLLE+sRv +  ++ERnyHiFYqll+ga++ ++++l l+ +++dy++l + +  +v
  gene1678|gene1678|rna1678|rna1678 220 KFIKITFE-GGRITGAYIEKYLLERSRVTRPGPNERNYHIFYQLLKGADSALRSALCLTgTISDYKILRN-TPHSV 293
                                        *******7.69************************************************99********9.899** PP

                                        TTS-HHHHHHHHHHHHHHHT--HHHHHHHHHHHHHHHHHCTSSEEEECTTSSEEESSHHHHHHHHHHHTS-HHHHH CS
                        Myosin_head 229 dgiddseefketkkaldilglseeeqkeifrivaailhlGniefkkeakdeqavledeeklekaaellgvdaeele 304
                                        +g+dd++ef +t + +  lg++e+++++++rivaa+lhlGn++f ++   e+++l+d++ +e+a++ll +  ++l 
  gene1678|gene1678|rna1678|rna1678 294 PGVDDAKEFANTLRCMRSLGFDERTIEGVLRIVAAVLHLGNVSFVDTG--EKGELADRAPAEAACRLLSIPIASLV 367
                                        ********************************************9876..568999999***************** PP

                                        HHHHSEEEEETTEEEEEE-BHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSS-S-SEEEEEEEEE-B---SSB CS
                        Myosin_head 305 kalvkrriktgkevvskalnveqaevardalakaiyerlFdwlverinkslekkkeekksfiGvLDiaGFEifekn 380
                                        +++++++    +e+v+ + ++eqa+ ++dal + +ye +F+ +++ in+ +++     +++iGvLDiaGFEif+kn
  gene1678|gene1678|rna1678|rna1678 368 NSILSPTAVLSHETVTRNRSSEQAQRIVDALCRLLYEGVFEEVIRIINTCIRSPV--GSTYIGVLDIAGFEIFKKN 441
                                        *****************************************************99..99***************** PP

                                        -HHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHTTSSGCGS-GGGCCHHHHHHHHS.SSTSHHHHHHHHHTSTTS-H CS
                        Myosin_head 381 sFEqlcinyvnEkLqqlFnelvlklEqeeYvrEgiewkfidfgldnqaiidLiek.kplGilslLdeecllpkatd 455
                                        +FEq+ciny+nEkLqq+Fn+++++lEqe Y++E+iew++idfgld++++idLie+ +p+Gi++ +deec++p a++
  gene1678|gene1678|rna1678|rna1678 442 GFEQFCINYTNEKLQQFFNHHMFILEQEIYKKEQIEWNYIDFGLDLRPTIDLIERnNPIGIFAYIDEECVMPGADE 517
                                        ******************************************************989******************* PP

                                        HHHHHHHHHHHTTSTTEEETTSTTTTTEEEEEETTCEEEEE-TTHHHHHH----HHHHHHHHTSSSHHHHHHCCSH CS
                        Myosin_head 456 etfleklvkafskhakfeksrlkkgeakFiikHyAgkveYevegfleKnkDtlnedlvellksskkkllaelfkee 531
                                        +t+l+kl+ +  k ++fek r+   ++ F++kHyAg  eY v+g+l Knk++ +ed+ +l+ +s+++l+++l    
  gene1678|gene1678|rna1678|rna1678 518 RTLLHKLCTNL-KAPEFEKGRF---NDGFMLKHYAGVTEYAVDGWLAKNKEPYFEDIFALIVRSDDDLVRRLVARP 589
                                        ********997.6799****97...99*********************************************9983 PP

                                        CHB--.........CSSSECCCCCSBHHHHHHHHHHHHHHHHCTSEEEEEEEE-SSSS--TT---HHHHHHHHHHT CS
                        Myosin_head 532 ekeakaeakksekkkkkkkkkkkfktvgskfkeslaeLmktlestnphfvRCikpnekkkakkldeslvleqlrcl 607
                                        +               k +kk  f+tv++k+ke+la Lm++l++t phfvRCi pn +++a+++d++ +l+qlrc+
  gene1678|gene1678|rna1678|rna1678 590 T---------------KGEKKGFFRTVAQKHKEQLAYLMQQLRNTAPHFVRCILPNCRRSAAEFDNHFILHQLRCN 650
                                        3...............45677799**************************************************** PP

                                        THHHHHHHHHHSSSEEEEHHHHHHHHGGGSTTSS-SS.SSSHHHHHHHHHHHTTS-GCGEEECSSEEEET CS
                        Myosin_head 608 GvlegirirraGfpnRitfeefvqrYkllakkelkkllkedakkaveailkeleldkeeykiGktKiFfr 677
                                        Gvlegiri+r G+pnR+ f++fv+rY++++k+        d++  v+a+ ++  ++++ yk+G tK+Ff+
  gene1678|gene1678|rna1678|rna1678 651 GVLEGIRISRLGYPNRMDFKDFVERYRVIYKEFD--G--FDERAYVKALCDAQGVSADLYKLGLTKVFFK 716
                                        ******************************9884..5..599***************************8 PP

>> Myosin_N  Myosin N-terminal SH3-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.1   0.1   5.4e-13   9.8e-10       1      40 []      14      53 ..      14      53 .. 0.98

  Alignments for each domain:
  == domain 1  score: 38.1 bits;  conditional E-value: 5.4e-13
                                       SEEEEETTSTTS-EEEEEEEEESSEEEEEETTSEEEEEEG CS
                           Myosin_N  1 KklVWVpDpkegyvkGeIkeeeGdkvtVetedGktvtVkk 40
                                       Kkl+W pD++ +++ + I ee+G+ + V t+dG++++V+k
  gene1678|gene1678|rna1678|rna1678 14 KKLIWAPDKERAFILAQIREEDGEYYAVLTKDGEERRVRK 53
                                       9*************************************87 PP

>> Filament  Intermediate filament protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0      0.35   6.4e+02     153     185 ..     717     749 ..     709     767 .. 0.81
   2 ?   -6.3  32.9        10   1.8e+04     121     274 ..     791     949 ..     788     961 .. 0.75
   3 ?  -12.3  53.2        10   1.8e+04      11     272 ..     835    1106 ..     835    1122 .. 0.50
   4 ?  -16.7  37.2        10   1.8e+04      65     250 ..     974    1109 ..     962    1198 .. 0.35
   5 !   26.7  30.1   2.2e-09   3.9e-06      19     273 ..    1201    1458 ..    1199    1469 .. 0.76
   6 ?    2.6  13.2     0.047        85     155     286 ..    1419    1554 ..    1413    1563 .. 0.61
   7 ?    1.3   1.8      0.12   2.1e+02      26      86 ..    1588    1647 ..    1578    1656 .. 0.62

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.35
                                        XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                           Filament 153 eqvlvevdaarkldLteilkeiraqyeelaekn 185
                                        + vl e++++r+  L+e ++eira   + +  +
  gene1678|gene1678|rna1678|rna1678 717 QGVLAEIEEVRERALAELMREIRARIRAFVCVK 749
                                        67899******************9876666555 PP

  == domain 2  score: -6.3 bits;  conditional E-value: 10
                                        XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXX...XXXXXXXXXXXXXXXXX CS
                           Filament 121 dLekkvesLkeelaflkkvheeEvkelqkqvs.eqvlvevdaarkldLteilkeir...aqyeelaeknreeaeew 192
                                        d+ kk e  ke+l+  k++ e+E+ke +++++  ++ v +++++k +L++ l+  r   +  +el+   r+e +  
  gene1678|gene1678|rna1678|rna1678 791 DVTKKNELAKEQLSRIKQM-EQEMKECTQEIArLNAAVKTNQNEKDELAASLEKERllvEHKDELITAIRAERQ-S 864
                                        6677888888888888875.99********998899999**9**********9877443455677777777765.5 PP

                                        XXXXXXXXXXXXXXXXXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH...HHHHHHHHHHHHHHHH CS
                           Filament 193 ykskleelqeaaeknsealrsakeeitelrrqiqsleieleslkkqkasleaqlael...eerleaeleklqekls 265
                                         +++l+ +q++ +  +e+l++  +e ++  + + + ++e ++l++qk+ l ++   l     ++  ++++l++ ++
  gene1678|gene1678|rna1678|rna1678 865 MSEQLSAAQQEQHALQEQLKERARECAQNEQLLSTAQAEAQALRSQKDVLAQRYDALneeHRKMRVNRQSLEDRVN 940
                                        5889999999999999999999999999999999999999999999999887654440004444444455555555 PP

                                        HHHHHHHHH CS
                           Filament 266 eleeelaei 274
                                         l +e++ +
  gene1678|gene1678|rna1678|rna1678 941 ILTAEMQAM 949
                                        555555444 PP

  == domain 3  score: -12.3 bits;  conditional E-value: 10
                                         XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                           Filament   11 drlAsYidkVraLEqenkeLeakieeleekksaevsklkelyekeleelrkqldeltkerarlqleldnlreel 84  
                                         d lA+ ++k r L ++++eL + i++ ++  s++     ++ ++e + l++ql+e ++e a+ +  l+++++e+
  gene1678|gene1678|rna1678|rna1678  835 DELAASLEKERLLVEHKDELITAIRAERQSMSEQL----SAAQQEQHALQEQLKERARECAQNEQLLSTAQAEA 904 
                                         67999999*****9999999999999998853333....33444445555555555555555555555555555 PP

                                         XXXXXXXXXX..............XXXXXXXXXXXXXXX..........................XXXXXXXXX CS
                           Filament   85 edlrkkyeke..............lnkreevEaelkalr..........................kdldeatla 118 
                                         + lr++ +                  +r+++E+ ++ l                             l+++  +
  gene1678|gene1678|rna1678|rna1678  905 QALRSQKDVLaqrydalneehrkmRVNRQSLEDRVNILTaemqamsvknveqlvldkekelirtnNLLKQEEER 978 
                                         55554433320001111111111155555555555555533333333333333333333333333333333333 PP

                                         XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX....XXXXXXXXXXXXXXXXXXXXX. CS
                           Filament  119 rvdLekkvesLkeelaflkkvheeEvkelqkqvseqvlvevdaarkld....Lteilkeiraqyeelaeknre. 187 
                                         r  Le+++ + k                                   +    L+e l+e ra  e++a++n++ 
  gene1678|gene1678|rna1678|rna1678  979 RRALEEQLGTFK-----------------------------------EnvhvLEERLEEERARAEQQAAQNNAl 1017
                                         333333333333...................................234446666777777777666665541 PP

                                         XX.XXXXXXXXXXXXXXXXXXXXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH...HHHHHHH CS
                           Filament  188 ea.eewykskleelqeaaeknsealrsakeeitelrrqiqsleieleslkkqkasleaqlaele...erleael 257 
                                         +a  ++  ++++ l+ + +++++a+rs kee++++++ +   + + e+    +++l+++l+ l     r e+el
  gene1678|gene1678|rna1678|rna1678 1018 SAqSANNAQRVHALTMSCAQQESAVRSLKEELANANKALSIAKNDAEDGAVLNQKLREELRKLSgelRRKENEL 1091
                                         22023445566667777777777777777777777776666666666666666666666665551113445555 PP

                                         HHHHHHHHHHHHHHH CS
                           Filament  258 eklqeklseleeela 272 
                                         +++qe ++  ee+ a
  gene1678|gene1678|rna1678|rna1678 1092 QHAQELVHMEEEKSA 1106
                                         555555555555444 PP

  == domain 4  score: -16.7 bits;  conditional E-value: 10
                                         XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.......XXXXXXXXXXXXXXXXXXXXXX CS
                           Filament   65 eltkerarlqleldnlreeledlrkkyekelnkreevEaelkalr.......kdldeatlarvdLekkvesLke 131 
                                         + ++ r  l+ +l++ +e+++ l +++e+e ++ e++ a+ +al        + ++++t++ ++ e+ v sLke
  gene1678|gene1678|rna1678|rna1678  974 QEEERRRALEEQLGTFKENVHVLEERLEEERARAEQQAAQNNALSaqsannaQRVHALTMSCAQQESAVRSLKE 1047
                                         33333333444444444444444444444432222222222222222333334444444444444444444444 PP

                                         XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                           Filament  132 elaflkkvheeEvkelqkqvseqvlvevdaarkldLteilkeiraqyeelaeknreeaeewykskleelqeaae 205 
                                         ela   k     ++  ++ +++ ++  ++++ + +L +   e+r+                             
  gene1678|gene1678|rna1678|rna1678 1048 ELANANKA----LSIAKNDAEDGAV--LNQKLREELRKLSGELRR----------------------------- 1086
                                         44433222....2222333221111..222233333333333333............................. PP

                                         XXXXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           Filament  206 knsealrsakeeitelrrqiqsleieleslkkqkasleaqlaele 250 
                                                               +e el++ ++  +  e++ a l 
  gene1678|gene1678|rna1678|rna1678 1087 ----------------------KENELQHAQELVHMEEEKSAALA 1109
                                         ......................22222222222222222111111 PP

  == domain 5  score: 26.7 bits;  conditional E-value: 2.2e-09
                                         XXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                           Filament   19 kVraLEqenkeLeakieeleekksaevsklkelyekeleelrkqldeltkerarlqleldnlreeledlrkkye 92  
                                         +V  LE+en++L+a +ee+ ++ s+ +s+ +    +  +++r++l e  ++++ l++   +lr+ele l++++e
  gene1678|gene1678|rna1678|rna1678 1201 RVSRLEHENADLRASLEERIQEDSTGSSECNMSVLESERKVRDELREELAQQEDLNM---QLRNELEALHASFE 1271
                                         7999***************99977777755555555555666666665555555555...57889********* PP

                                         XXXXXXXXXXXXXXXXX...XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX... CS
                           Filament   93 kelnkreevEaelkalr...kdldeatlarvdLekkvesLkeelaflkkvheeEvkelqkqvseqvlvevd... 160 
                                         ke+++r+++ +elka       ++e++  r +L +   +L e l+  +  +++ +++ ++++   v +e d   
  gene1678|gene1678|rna1678|rna1678 1272 KEVGERDALINELKARAvnkIGMQELYALRRELKACQRALAEALSTCQGTFNTRIAKYKAEI---VALEQDgrd 1342
                                         *********99998654432569**************************************9...555554222 PP

                                         .XXXXXXXXXXXXXXXXXXXXXXXXXXX..XXXXXXXXXXXXXXXXXXXXXXXXXX-HHHHHHHHHHHHHHHHH CS
                           Filament  161 .aarkldLteilkeiraqyeelaeknre..eaeewykskleelqeaaeknsealrsakeeitelrrqiqsleie 231 
                                          +a++ +L++ l e+  q e +a++nr+  ++ + yk+  e++ e  + ++++l+++++e +elr ++ + +i+
  gene1678|gene1678|rna1678|rna1678 1343 lKAQNYELKNKLGEMSMQAEVHANTNRNleSSLAFYKKSAEDAAERLQAKDAELSKCRNEGAELRARLSNAHIK 1416
                                         2378889***************9988742155567888888899999999999999999999999999988887 PP

                                         HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           Filament  232 leslkkqkasleaqlaeleerleaeleklqeklseleeelae 273 
                                          e   k ++   + ++ + +  ea +++l+e+ls+  +e ++
  gene1678|gene1678|rna1678|rna1678 1417 HEYALKIAEERAKDVSGILADREARIAELNEQLSKFAQEFER 1458
                                         777777666666666665555555555555555555554443 PP

  == domain 6  score: 2.6 bits;  conditional E-value: 0.047
                                         XXXXXXXXXXXXXXXXXXXXXX...XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX-HHHHHHHHHHH CS
                           Filament  155 vlvevdaarkldLteilkeira...qyeelaeknreeaeewykskleelqeaaeknsealrsakeeitelrrqi 225 
                                           + + ++r  d++ il++  a   + +e+ +k  +e e+  ++ ++e  e+ +   e++r   +e ++l+ ++
  gene1678|gene1678|rna1678|rna1678 1419 YALKIAEERAKDVSGILADREAriaELNEQLSKFAQEFERL-SALIKESDEEKALRAENARL-SKECAQLHVEL 1490
                                         55566666777777777664431113344444444444433.33334444444444444433.35788888888 PP

                                         HHHHHHHHHHHHHHHHHHHHHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           Filament  226 qsleieleslkkqkasleaqlaeleerle...aeleklqeklseleeelaeireemarqlreYq 286 
                                          +l+++ + lk++ +  e+++ +le r +   +e e  +++++ +e+e+++ +++ a   +e q
  gene1678|gene1678|rna1678|rna1678 1491 HALTTDNDVLKEHINRCEQSVLDLESRCSalkKENELKRSMMQCKEQEISNWKAQCASAAKELQ 1554
                                         8888888888888888888888888876511145666678888888888888888888888776 PP

  == domain 7  score: 1.3 bits;  conditional E-value: 0.12
                                         XXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                           Filament   26 enkeLeakieeleekksaevsklkelyekeleelrkqldeltkerarlqleldnlreeled 86  
                                         en eL+a+++e+     ++ +  +++ + e++el+k+++ l+ ++++l+ el + +++ + 
  gene1678|gene1678|rna1678|rna1678 1588 ENGELKARVAERDGI-INALTDERDAIKGEVHELKKAVEILELKNKQLERELADEKDANKL 1647
                                         566666666666666.444444666666666666666666666666666666665555554 PP

>> DUF4201  Domain of unknown function (DUF4201)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -6.2  28.2        10   1.8e+04      27     176 ..     801     947 ..     788     948 .. 0.85
   2 ?   -3.6  22.1       4.6   8.2e+03      47     169 ..     858     983 ..     855     986 .. 0.80
   3 ?   -2.6  14.7       2.1   3.8e+03      67     175 ..     945    1056 ..     934    1062 .. 0.66
   4 ?   -5.8  20.1        10   1.8e+04      21     141 ..     985    1101 ..     970    1105 .. 0.77
   5 ?   -1.6  21.6       1.1   1.9e+03       2     139 ..    1071    1213 ..    1070    1218 .. 0.91
   6 !   16.7   9.2   2.6e-06    0.0046      24     140 ..    1240    1359 ..    1229    1362 .. 0.88
   7 !    5.6   2.1    0.0065        12      78     127 ..    1374    1423 ..    1360    1436 .. 0.82
   8 ?    4.4   5.4     0.015        27      93     171 ..    1442    1521 ..    1420    1524 .. 0.78
   9 ?    2.0   1.5     0.086   1.5e+02      90     136 ..    1593    1639 ..    1585    1656 .. 0.71

  Alignments for each domain:
  == domain 1  score: -6.2 bits;  conditional E-value: 10
                            DUF4201  27 eklekkeelgegL..tlidFeqlqienqalnkkIeernkeLkrlkkkttktvhalthlkeklhmleselselkkel 100
                                        e+l   +++  ++  ++++   l++ +++ +++ +e  + L++ ++ +  +   +t ++  ++ ++++ls++++e 
  gene1678|gene1678|rna1678|rna1678 801 EQLSRIKQMEQEMkeCTQEIARLNAAVKTNQNEKDELAASLEKERLLVEHKDELITAIRAERQSMSEQLSAAQQEQ 876
                                        3344444444444113466778999999999999****************************************** PP

                            DUF4201 101 kekeerlaklrkelykvklerdklrkqneklkqqggllrvPaLlkDYdktkekveekrksvkkLrrkvkilemrlk 176
                                        + ++e+l++  +e  + ++  + ++++ + l++q+       L + Yd   e+  ++r   ++L+ +v+il+  ++
  gene1678|gene1678|rna1678|rna1678 877 HALQEQLKERARECAQNEQLLSTAQAEAQALRSQKDV-----LAQRYDALNEEHRKMRVNRQSLEDRVNILTAEMQ 947
                                        *********************************9988.....8888***********************9998765 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 4.6
                            DUF4201  47 lqienqalnkkIeernkeLkrlkkkttktvhalthlkeklhmleselselkkelkekeerlaklrkelykvklerd 122
                                        +++e q++++++   ++e ++l+++ +    + +++ + l++ ++e ++l+++ + + +r ++l +e  k + +r+
  gene1678|gene1678|rna1678|rna1678 858 IRAERQSMSEQLSAAQQEQHALQEQLKERARECAQNEQLLSTAQAEAQALRSQKDVLAQRYDALNEEHRKMRVNRQ 933
                                        6789999999999999999999999999999999999999999999999999999999999999999999999999 PP

                            DUF4201 123 klrkqneklkqqggllrv...PaLlkDYdktkekveekrksvkkLrrkvk 169
                                         l+++ + l ++ + ++v   ++L  D +k+  + +++ k+ ++ rr ++
  gene1678|gene1678|rna1678|rna1678 934 SLEDRVNILTAEMQAMSVknvEQLVLDKEKELIRTNNLLKQEEERRRALE 983
                                        99999999999999987522256666666666666677666666666555 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 2.1
                            DUF4201   67 rlkkkttktvhalthlkeklh........mleselselkkelkekeerlaklrkelykvklerdklrkqneklk 132 
                                         +++ ++ k+v +l   kek+           e+  ++l+++l + +e+ + l+++l++ +++ ++  +qn+ l+
  gene1678|gene1678|rna1678|rna1678  945 EMQAMSVKNVEQLVLDKEKELirtnnllkQEEERRRALEEQLGTFKENVHVLEERLEEERARAEQQAAQNNALS 1018
                                         67778888888888888887766666544555555667788888899999999999999999999999999999 PP

                            DUF4201  133 qqggllrvPaLlkDYdktkekveekrksvkkLrrkvkilemrl 175 
                                         +q+++ ++  +      t++  +  +++v++L++++ +++++l
  gene1678|gene1678|rna1678|rna1678 1019 AQSAN-NAQRVHA---LTMSCAQ-QESAVRSLKEELANANKAL 1056
                                         88877.4444433...3333333.4455555555555555544 PP

  == domain 4  score: -5.8 bits;  conditional E-value: 10
                            DUF4201   21 qlakiqeklekkeelgegLtlidFeqlqienqalnkkIeernkeLkrlkkkttktvhalthlkeklhmlesels 94  
                                         ql+ ++e+++ +ee  e+ +    eq  ++n+al+ + ++  + +++l  +++++  a+  lke l   ++ ls
  gene1678|gene1678|rna1678|rna1678  985 QLGTFKENVHVLEERLEEER-ARAEQQAAQNNALSAQSANNAQRVHALTMSCAQQESAVRSLKEELANANKALS 1057
                                         55555555555555444432.23477888999999999999999999999999999999999999999999999 PP

                            DUF4201   95 elkkelkekeerlaklrkelykvklerdklrkqneklkqqggllrvP 141 
                                          +k++ ++     +klr+el k+  e   lr++ ++l+   +l++++
  gene1678|gene1678|rna1678|rna1678 1058 IAKNDAEDGAVLNQKLREELRKLSGE---LRRKENELQHAQELVHME 1101
                                         99999999999999999999988765...777777777777777775 PP

  == domain 5  score: -1.6 bits;  conditional E-value: 1.1
                            DUF4201    2 rkkrnelsklrlklislkhqlakiqeklekkeelgegLtlidFeqlqienqal.....nkkIeernkeLkrlkk 70  
                                         +k r+el kl+ +l ++++ l++ qe ++  ee + +L +   e l+ en+al       +Ie+ n+ Lk+  k
  gene1678|gene1678|rna1678|rna1678 1071 QKLREELRKLSGELRRKENELQHAQELVHMEEEKSAALAA-RVEVLKGENEALpapgtAAEIERLNERLKKAEK 1143
                                         6789*********************************976.6899******995555568************** PP

                            DUF4201   71 kttktvhalthlkeklhmlese.lselkkelkekeerlaklrkelykvklerdklrkqneklkqqggllr 139 
                                         +       ++ +k   + le+e  +++kk+l+e++ r a+l k   k++ er+ l  + ++l+ ++++lr
  gene1678|gene1678|rna1678|rna1678 1144 TNRELNESIAAEKAFFKRLEEErAAQHKKNLSEMQGRYAELLKDAAKTNSERKALSMRVSRLEHENADLR 1213
                                         ***************99887762678999****************************9999999998886 PP

  == domain 6  score: 16.7 bits;  conditional E-value: 2.6e-06
                            DUF4201   24 kiqeklekkeelgegLtlidFeqlqienqalnkkIeernkeLkrlkkkttkt..vhalthlkeklhmleselse 95  
                                         k++++l++     e+L+++  + l++  ++++k++ er++ +++lk ++ ++  +++l  l+  l++ ++ l+e
  gene1678|gene1678|rna1678|rna1678 1240 KVRDELREELAQQEDLNMQLRNELEALHASFEKEVGERDALINELKARAVNKigMQELYALRRELKACQRALAE 1313
                                         66667777777788889988899999999*******************9997558**************99988 PP

                            DUF4201   96 lkke.lkekeerlaklrkelykvklerdklrkqneklkqqggllrv 140 
                                         + +    + ++r+ak+++e+  ++++   l++qn +lk ++g++++
  gene1678|gene1678|rna1678|rna1678 1314 ALSTcQGTFNTRIAKYKAEIVALEQDGRDLKAQNYELKNKLGEMSM 1359
                                         7665157999**********************************98 PP

  == domain 7  score: 5.6 bits;  conditional E-value: 0.0065
                            DUF4201   78 althlkeklhmleselselkkelkekeerlaklrkelykvklerdklrkq 127 
                                          l+ +k+ +   ++ l+++  el+++ ++ a+lr++l++++ +++ + k 
  gene1678|gene1678|rna1678|rna1678 1374 SLAFYKKSAEDAAERLQAKDAELSKCRNEGAELRARLSNAHIKHEYALKI 1423
                                         588999999999999999********************999999976655 PP

  == domain 8  score: 4.4 bits;  conditional E-value: 0.015
                            DUF4201   93 lselkkelkekeerlaklrkelykvklerdklrkqneklkqqggllrvP..aLlkDYdktkekveekrksvkkL 164 
                                          +el+++l++  ++ ++l + + +   e + lr++n++l++++++l+v+  aL++D d  ke+++  ++sv  L
  gene1678|gene1678|rna1678|rna1678 1442 IAELNEQLSKFAQEFERLSALIKESD-EEKALRAENARLSKECAQLHVElhALTTDNDVLKEHINRCEQSVLDL 1514
                                         55677777777777777777666554.55689999999999999999976689999999999999999999999 PP

                            DUF4201  165 rrkvkil 171 
                                         + ++  l
  gene1678|gene1678|rna1678|rna1678 1515 ESRCSAL 1521
                                         8887766 PP

  == domain 9  score: 2.0 bits;  conditional E-value: 0.086
                            DUF4201   90 eselselkkelkekeerlaklrkelykvklerdklrkqneklkqqgg 136 
                                         ++ ++e+  +++ +++++++++ e++++k+  + l+ +n++l+++++
  gene1678|gene1678|rna1678|rna1678 1593 KARVAERDGIINALTDERDAIKGEVHELKKAVEILELKNKQLERELA 1639
                                         45555666666777777777777777777777777777777776654 PP

>> Wtap  WTAP/Mum2p family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?  -32.8  49.2        10   1.8e+04       8     150 ..     801    1064 ..     794    1067 .. 0.55
   2 !   16.9  13.2   2.6e-06    0.0047      56     149 ..    1071    1166 ..    1066    1172 .. 0.92
   3 !    7.4  13.4    0.0022         4      82     154 ..    1192    1268 ..    1168    1270 .. 0.73
   4 ?   -0.2   6.7      0.48   8.5e+02      55     152 ..    1297    1399 ..    1294    1403 .. 0.66
   5 ?   -6.8  14.5        10   1.8e+04       8     155 ..    1328    1503 ..    1321    1504 .. 0.66
   6 ?   -6.2  16.3        10   1.8e+04      56     129 ..    1470    1551 ..    1387    1559 .. 0.65
   7 ?   -0.1   1.4      0.45   8.1e+02     100     149 ..    1587    1638 ..    1581    1643 .. 0.82

  Alignments for each domain:
  == domain 1  score: -32.8 bits;  conditional E-value: 10
                               Wtap    8 lllarlsakeqelqelksslqelkqslqpps.ss.........................qlrqvllDPAvnlvf 55  
                                         + l+r+++ eqe++e+++++  l+ + ++++ ++                                        
  gene1678|gene1678|rna1678|rna1678  801 EQLSRIKQMEQEMKECTQEIARLNAAVKTNQnEKdelaaslekerllvehkdelitairA-------------- 860 
                                         567888999999999998888888777774422255666665555555444444444442.............. PP

                               Wtap   56 srlrkeleeaenkleeaqeeLqalkftpds............................................ 85  
                                              e ++++++l++aq+e+ al+ +                                               
  gene1678|gene1678|rna1678|rna1678  861 -----ERQSMSEQLSAAQQEQHALQEQLKErarecaqneqllstaqaeaqalrsqkdvlaqrydalneehrkmr 929 
                                         .....333333333333333333333333222233333333333333333355555556666666666666666 PP

                               Wtap   86 ....................................................................qtGkrL 91  
                                                                                                             ++  + 
  gene1678|gene1678|rna1678|rna1678  930 vnrqsledrvniltaemqamsvknveqlvldkekelirtnnllkqeeerrraleeqlgtfkenvhvleERLEEE 1003
                                         55555666666666666666665555666666666666666666666666666666666666666443333333 PP

                               Wtap   92 makcrvLeqENeELgkv..leegrvakLeselalqkkfveelkkaleeleelleeleeeve 150 
                                          a+  +   +N+ L ++  ++ +rv+ L++  a q++ v+ lk++l+++++ l+ +++++e
  gene1678|gene1678|rna1678|rna1678 1004 RARAEQQAAQNNALSAQsaNNAQRVHALTMSCAQQESAVRSLKEELANANKALSIAKNDAE 1064
                                         4566666666777765422555677777777777777777777777777777777777666 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 2.6e-06
                               Wtap   56 srlrkeleeaenkleeaqeeLqalk..ftpdsqtGkrLmakcrvLeqENeELgkvleegrvakLeselalqkkf 127 
                                         ++lr+el++ + +l+++++eLq  +     + ++  +L a++ vL+ ENe L +  + +++++L ++l++++k+
  gene1678|gene1678|rna1678|rna1678 1071 QKLREELRKLSGELRRKENELQHAQelVHMEEEKSAALAARVEVLKGENEALPAPGTAAEIERLNERLKKAEKT 1144
                                         89********************99834466689999************************************** PP

                               Wtap  128 veelkkaleeleelleeleeev 149 
                                         ++el+++ +  + + + leee+
  gene1678|gene1678|rna1678|rna1678 1145 NRELNESIAAEKAFFKRLEEER 1166
                                         *******************997 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.0022
                               Wtap   82 tpdsqtGkrLmakcrvLeqENeELgkvle....egrvakLeselal...qkkfveelkkaleeleelleeleee 148 
                                         +   ++ k+L +++ +Le+EN++L ++le    e+++ + e ++++   ++k+ +el+++l++ e+l+ +l++e
  gene1678|gene1678|rna1678|rna1678 1192 N---SERKALSMRVSRLEHENADLRASLEeriqEDSTGSSECNMSVlesERKVRDELREELAQQEDLNMQLRNE 1262
                                         3...3559***************98876522226777777766554222799********************** PP

                               Wtap  149 vevlqs 154 
                                         +e l+ 
  gene1678|gene1678|rna1678|rna1678 1263 LEALHA 1268
                                         **9876 PP

  == domain 4  score: -0.2 bits;  conditional E-value: 0.48
                               Wtap   55 fsrlrkeleeaenkleeaqeeLqalkftpd......sqtGkrLmakcrvLeqENeELgkvleegrvak.L.ese 120 
                                         +  lr+el++++++l+ea   L++++ t +       ++  +L +  r L+ +N EL++ l e +++  + ++ 
  gene1678|gene1678|rna1678|rna1678 1297 LYALRRELKACQRALAEA---LSTCQGTFNtriakyKAEIVALEQDGRDLKAQNYELKNKLGEMSMQAeVhANT 1367
                                         556888888888888874...55666666622233335555677778889999999988888888753231334 PP

                               Wtap  121 lalqkkfveelkkaleeleelleeleeevevl 152 
                                          + +++ ++++kk+ e++ e l+  ++e+++ 
  gene1678|gene1678|rna1678|rna1678 1368 NRNLESSLAFYKKSAEDAAERLQAKDAELSKC 1399
                                         44566678888888888888888888887765 PP

  == domain 5  score: -6.8 bits;  conditional E-value: 10
                               Wtap    8 lllarlsakeqelqelksslqelkqslqppsssqlrqvllDPAvnlvfsrlrkeleeaenkleeaqeeLqalkf 81  
                                          + a + a eq  ++lk+++ elk++l + s++      +   ++  +   +k+ e+a ++l+++ +eL++++ 
  gene1678|gene1678|rna1678|rna1678 1328 KYKAEIVALEQDGRDLKAQNYELKNKLGEMSMQAEVHANTNRNLESSLAFYKKSAEDAAERLQAKDAELSKCRN 1401
                                         56677788899999999999999999777654433344444445555666678888888888888888888877 PP

                               Wtap   82 tpds........................qtGkrLmakcrvLeqENeELgkvlee.grvakLesel...alqkkf 127 
                                                                          L  +  +  + Ne L k ++e +r++ L +e    +++++ 
  gene1678|gene1678|rna1678|rna1678 1402 EGAElrarlsnahikheyalkiaeerakDVSGILADREARIAELNEQLSKFAQEfERLSALIKESdeeKALRAE 1475
                                         77745555555555555566666655555555677788888888888888776646677665544111455666 PP

                               Wtap  128 veelkkaleeleelleeleeevevlqst 155 
                                         +++l k+ ++l+  l  l+++++vl++ 
  gene1678|gene1678|rna1678|rna1678 1476 NARLSKECAQLHVELHALTTDNDVLKEH 1503
                                         8889999999999999999999998875 PP

  == domain 6  score: -6.2 bits;  conditional E-value: 10
                               Wtap   56 srlrkeleeaenkleeaqeeLqalkftpd.........sqtGkrLmakcrvLeqENeELgkvleegrvakLese 120 
                                         + lr+e +  ++++++   eL al+++ d          q+   L ++c  L++EN EL++++ + + +++++ 
  gene1678|gene1678|rna1678|rna1678 1470 KALRAENARLSKECAQLHVELHALTTDNDvlkehinrcEQSVLDLESRCSALKKEN-ELKRSMMQCKEQEISNW 1542
                                         67788888888888888888888888888555555555588888888888888888.46666655555555555 PP

                               Wtap  121 lalqkkfve 129 
                                         +a   + ++
  gene1678|gene1678|rna1678|rna1678 1543 KAQCASAAK 1551
                                         555555555 PP

  == domain 7  score: -0.1 bits;  conditional E-value: 0.45
                               Wtap  100 qENeELgkvlee..grvakLeselalqkkfveelkkaleeleelleeleeev 149 
                                          EN EL++ + e  g +  L+ e  + k  v elkka e le  +++le e+
  gene1678|gene1678|rna1678|rna1678 1587 YENGELKARVAErdGIINALTDERDAIKGEVHELKKAVEILELKNKQLEREL 1638
                                         6899998766542377999999999999999999999999999999999986 PP

>> DUF4537  Domain of unknown function (DUF4537)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   7.6e-05      0.14      49     116 ..       2      66 ..       1      69 [. 0.94
   2 ?   -3.0   0.1         4   7.2e+03      88     116 ..     445     473 ..     439     475 .. 0.72
   3 ?   -1.6   0.0       1.4   2.6e+03      61     100 ..    1554    1593 ..    1528    1603 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 7.6e-05
                            DUF4537  49 edakehslkvgDkVLAlhdpeeqeYvPGiVlagpsakeeeltVrfydgkkakvpreevikiskelyek 116
                                        +d++e +++  Dk L   +++e  ++ ++++   ++++e ++V   dg++ +v++ + +k++++++++
  gene1678|gene1678|rna1678|rna1678   2 ADTMEEKIQQKDKKLIWAPDKERAFILAQIR---EEDGEYYAVLTKDGEERRVRKVDTQKVNPQKFDA 66 
                                        68999***********9999999********...89***************************99986 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 4
                            DUF4537  88 eltVrfydgkkakvpreevikiskelyek 116
                                        ++ +++ ++k ++  ++ ++ +++e+y+k
  gene1678|gene1678|rna1678|rna1678 445 QFCINYTNEKLQQFFNHHMFILEQEIYKK 473
                                        55677777777777777888888888876 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 1.4
                            DUF4537   61 kVLAlhdpeeqeYvPGiVlagpsakeeeltVrfydgkkak 100 
                                         + +Al++    e+ P +V ++p++ +e + V  y++ + k
  gene1678|gene1678|rna1678|rna1678 1554 QSIALEKVPVPEFTPVQVNSVPEQRNEVVDVITYENGELK 1593
                                         55677777777899999*9999999999998888776554 PP

>> Microtub_bd  Microtubule binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.0   0.00062       1.1      69      97 ..     139     165 ..      81     175 .. 0.79
   2 ?    4.8   0.4     0.013        24       4      74 ..     724     823 ..     721     833 .. 0.67
   3 ?   -0.7   0.7      0.69   1.2e+03       1      34 [.     972    1005 ..     972    1049 .. 0.70
   4 ?   -3.3   0.1       4.4   7.9e+03      44      81 ..    1340    1377 ..    1308    1381 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00062
                                        CCCHHHHHHHHTT--EEEEEEES...... CS
                        Microtub_bd  69 eeisqlvqsaldgynvcifaygqTGsGKt 97 
                                        +   +++ ++++g+n +i+ +g+ G+GKt
  gene1678|gene1678|rna1678|rna1678 139 N--DAYTSMVMNGKNQSILITGESGAGKT 165
                                        3..47899999*****************9 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.013
                                        HHHHHHHCHHHHHHHCTB-EEEEEEECCCS-T....EEEETTT.............................TTTE CS
                        Microtub_bd   4 eetlRrkleNtiqelkGniRvfarvrpelesek...akikfpe..........................eekkkkk 50 
                                        ee + r l   + e++  iR f+ v++++ +e+   a++  ++                          ++k++  
  gene1678|gene1678|rna1678|rna1678 724 EEVRERALAELMREIRARIRAFVCVKRTHIDERkrsAALALKKdvllhlalrrygwwrlyqivkplldvTKKNELA 799
                                        7889999******************999998765663333332344445555555556666666666664455555 PP

                                        EEE-SEEEECTTHCCCCCCCCHHH CS
                        Microtub_bd  51 efsFdrvfeseseqeevfeeisql 74 
                                        + ++ r+ + e+e +e ++ei+ l
  gene1678|gene1678|rna1678|rna1678 800 KEQLSRIKQMEQEMKECTQEIARL 823
                                        556667777777777777776665 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.69
                                         HHHHHHHHHHCHHHHHHHCTB-EEEEEEECCCS- CS
                        Microtub_bd    1 lekeetlRrkleNtiqelkGniRvfarvrpeles 34  
                                         l++ee +Rr le ++   k n+ v     +e++ 
  gene1678|gene1678|rna1678|rna1678  972 LKQEEERRRALEEQLGTFKENVHVLEERLEEERA 1005
                                         5799***********9999999998654444444 PP

  == domain 4  score: -3.3 bits;  conditional E-value: 4.4
                                         ...TTTEEEE-SEEEECTTHCCCCCCCCHHHHHHHHTT CS
                        Microtub_bd   44 eekkkkkefsFdrvfeseseqeevfeeisqlvqsaldg 81  
                                           + k++++++   + + s q+ev+ +++  ++s+l  
  gene1678|gene1678|rna1678|rna1678 1340 GRDLKAQNYELKNKLGEMSMQAEVHANTNRNLESSLAF 1377
                                         44567778888888888888888888877777777755 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.0   0.00081       1.5      18      39 ..     145     166 ..     133     204 .. 0.82
   2 ?   -5.5   7.7        10   1.8e+04      71     134 ..     836     894 ..     729     916 .. 0.70
   3 ?  -14.7  17.0        10   1.8e+04      87      87 ..    1082    1082 ..     970    1317 .. 0.70
   4 ?   -3.3   0.9       5.9   1.1e+04     115     128 ..    1435    1454 ..    1368    1485 .. 0.55
   5 ?   -2.6   1.0       3.5   6.2e+03      72     104 ..    1452    1482 ..    1417    1582 .. 0.59

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00081
                             AAA_16  18 rvrsgrpelvllsGesGvGKss 39 
                                        +v  g  +++l++GesG GK+ 
  gene1678|gene1678|rna1678|rna1678 145 MVMNGKNQSILITGESGAGKTE 166
                                        56666669************95 PP

  == domain 2  score: -5.5 bits;  conditional E-value: 10
                             AAA_16  71 alaqalareellrqlldeaesaeleawrekleealaavpelagaeasrllellkrllallsrde 134
                                         la  l++e+ll + +de+ +a +++ +    e+l+    +a +e ++l e+lk+ ++ ++++e
  gene1678|gene1678|rna1678|rna1678 836 ELAASLEKERLLVEHKDELITAIRAERQSM-SEQLS----AAQQEQHALQEQLKERARECAQNE 894
                                        366777777777777777555333333332.22222....233333555555555554444433 PP

  == domain 3  score: -14.7 bits;  conditional E-value: 10
                             AAA_16   87 d 87  
                                          
  gene1678|gene1678|rna1678|rna1678 1082 G 1082
                                         2 PP

  == domain 4  score: -3.3 bits;  conditional E-value: 5.9
                             AAA_16  115 ea......srllellkrlla 128 
                                         +a        l+e+l+++++
  gene1678|gene1678|rna1678|rna1678 1435 LAdreariAELNEQLSKFAQ 1454
                                         22333344333333333332 PP

  == domain 5  score: -2.6 bits;  conditional E-value: 3.5
                             AAA_16   72 laqalareellrqlldeaesaeleawrekleea 104 
                                         +aq ++r + l ++ de  +++l+a  ++l ++
  gene1678|gene1678|rna1678|rna1678 1452 FAQEFERLSALIKESDE--EKALRAENARLSKE 1482
                                         44444332222222222..22222222222222 PP

>> ATG16  Autophagy protein 16 (ATG16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2  17.2     0.049        88      99     172 ..     801     874 ..     789     875 .. 0.86
   2 ?   11.5  19.4   0.00014      0.26      69     151 ..     862     944 ..     856     950 .. 0.87
   3 ?    0.5  15.7      0.33   5.9e+02     100     174 ..     954    1028 ..     950    1032 .. 0.82
   4 ?    2.4  30.7     0.086   1.5e+02      33     184 ..     999    1148 ..     998    1151 .. 0.81
   5 ?    5.3  26.6     0.011        20      25     175 ..    1132    1278 ..    1128    1286 .. 0.75
   6 ?    3.1   2.5     0.055        99      73     139 ..    1294    1361 ..    1277    1371 .. 0.55
   7 ?    6.7  11.9    0.0042       7.5      32     155 ..    1341    1465 ..    1335    1469 .. 0.71
   8 ?    9.6   9.9   0.00054      0.96      82     166 ..    1468    1554 ..    1464    1561 .. 0.76
   9 ?    3.5   2.4      0.04        71     128     180 ..    1585    1637 ..    1571    1649 .. 0.55

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.049
                              ATG16  99 elaqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelrekeklvqdlqDElsaLqlqlnqaEe 172
                                        e  +r++++++e+++  +++ + +++++  ++e+ +l   l++ +  ++ k++l+ +++ E +++  ql+ a +
  gene1678|gene1678|rna1678|rna1678 801 EQLSRIKQMEQEMKECTQEIARLNAAVKTNQNEKDELAASLEKERLLVEHKDELITAIRAERQSMSEQLSAAQQ 874
                                        45579999999999999999999999999999999999999999999999999999999999999999998876 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00014
                              ATG16  69 nskqsakiqsleqklaqlreelaelyksrgelaqrllelneelqkleeklkedeerlaeleaeraaletklkdree 144
                                         ++ s+++++ +q+ ++l+e+l+e  +++++++q l ++++e q+l+++    ++r ++l++e+++++ +++++e+
  gene1678|gene1678|rna1678|rna1678 862 RQSMSEQLSAAQQEQHALQEQLKERARECAQNEQLLSTAQAEAQALRSQKDVLAQRYDALNEEHRKMRVNRQSLED 937
                                        346899999*********************************************************9999999999 PP

                              ATG16 145 elrekek 151
                                        +++ +++
  gene1678|gene1678|rna1678|rna1678 938 RVNILTA 944
                                        8876655 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.33
                              ATG16  100 laqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelrekeklvqdlqDElsaLqlqlnqaEek 173 
                                          +q +l++++el + ++ lk++eer ++le++  + ++++  +ee+l+e ++  +++    +aL  q   + ++
  gene1678|gene1678|rna1678|rna1678  954 VEQLVLDKEKELIRTNNLLKQEEERRRALEEQLGTFKENVHVLEERLEEERARAEQQAAQNNALSAQSANNAQR 1027
                                         57888999999999999999999999999999999999999999999999999998888888888887666665 PP

                              ATG16  174 l 174 
                                          
  gene1678|gene1678|rna1678|rna1678 1028 V 1028
                                         5 PP

  == domain 4  score: 2.4 bits;  conditional E-value: 0.086
                              ATG16   33 aleaenaklekaaasaks.sksskksakekeasasqsnskqsakiqsleqklaqlreelaelyksrgelaqrll 105 
                                          le+e+a++e++aa++++ s+        ++a+++q+  + + +++++e+++ +l+eela++ k+ +  ++   
  gene1678|gene1678|rna1678|rna1678  999 RLEEERARAEQQAAQNNAlSA--------QSANNAQRVHALTMSCAQQESAVRSLKEELANANKALSIAKNDAE 1064
                                         577777777766666554322........223333334456788****************************** PP

                              ATG16  106 elneelqkleeklkedeerlaeleaeraaletklkdreeelrekeklvqdlqDElsaL.....qlqlnqaEekl 174 
                                         +     qkl+e+l++ + +l++ e+e ++ ++ +   ee+ + +++ v+ l+ E +aL       + + + e+l
  gene1678|gene1678|rna1678|rna1678 1065 DGAVLNQKLREELRKLSGELRRKENELQHAQELVHMEEEKSAALAARVEVLKGENEALpapgtAAEIERLNERL 1138
                                         *********************************************************93333334666666888 PP

                              ATG16  175 rklekENkeL 184 
                                         +k ek N+eL
  gene1678|gene1678|rna1678|rna1678 1139 KKAEKTNREL 1148
                                         8999999998 PP

  == domain 5  score: 5.3 bits;  conditional E-value: 0.011
                              ATG16   25 nrLldrtsaleaenaklekaaasakssksskksakekeasasqsnskqsakiqsleqklaqlreelaelyksrg 98  
                                          rL +r ++ e+ n++l++++a++k+         ++++++++  ++ ++++++++ + a+l ++ a++  +r 
  gene1678|gene1678|rna1678|rna1678 1132 ERLNERLKKAEKTNRELNESIAAEKA-------FFKRLEEERA--AQHKKNLSEMQGRYAELLKDAAKTNSERK 1196
                                         46777777888888888666666554.......2222222222..3467899********************** PP

                              ATG16   99 elaqrllelneelqklee....klkedeerlaeleaeraaletklkd.reeelrekeklvqdlqDElsaLqlql 167 
                                          l+ r+ +l+ e ++l++    +++ed++   e + ++ + e+k++d ++eel+++e l+ +l+ El+aL+  +
  gene1678|gene1678|rna1678|rna1678 1197 ALSMRVSRLEHENADLRAsleeRIQEDSTGSSECNMSVLESERKVRDeLREELAQQEDLNMQLRNELEALHASF 1270
                                         *************998762222566677777777778888888888746899*******************999 PP

                              ATG16  168 nqaEeklr 175 
                                         ++   +++
  gene1678|gene1678|rna1678|rna1678 1271 EKEVGERD 1278
                                         87665555 PP

  == domain 6  score: 3.1 bits;  conditional E-value: 0.055
                              ATG16   73 sakiqsleqklaqlreelaelyksr.gelaqrllelneelqkleeklkedeerlaeleaeraaletkl 139 
                                          +++ +l  +l++++  lae++ ++ g++++r+ + ++e+ +le+  +  +++  el+++  +++ + 
  gene1678|gene1678|rna1678|rna1678 1294 MQELYALRRELKACQRALAEALSTCqGTFNTRIAKYKAEIVALEQDGRDLKAQNYELKNKLGEMSMQA 1361
                                         45555556666666666666655532555666666666666666555555555555555554444443 PP

  == domain 7  score: 6.7 bits;  conditional E-value: 0.0042
                              ATG16   32 saleaenaklekaaasakssksskksakekeasasq....snskqsakiqsleqklaqlreelaelyksrgela 101 
                                         + l+a+n +l+++  + + ++  +++++++++s+ +    s+++ ++++q+ +++l+++r+e ael    + l+
  gene1678|gene1678|rna1678|rna1678 1341 RDLKAQNYELKNKLGEMSMQAEVHANTNRNLESSLAfykkSAEDAAERLQAKDAELSKCRNEGAELR---ARLS 1411
                                         57899999999998888887777778888888888899999999********************993...4444 PP

                              ATG16  102 qrllelneelqkleeklkedeerlaeleaeraaletklkdreeelrekeklvqd 155 
                                         +  ++ + +l+  ee++k  +  la+ ea++a+l+++l++ ++e++ + +l+++
  gene1678|gene1678|rna1678|rna1678 1412 NAHIKHEYALKIAEERAKDVSGILADREARIAELNEQLSKFAQEFERLSALIKE 1465
                                         444555666666666666666666666666666666666666666555555543 PP

  == domain 8  score: 9.6 bits;  conditional E-value: 0.00054
                              ATG16   82 klaqlreelaelyksrgelaqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelr..ekeklv 153 
                                         + ++lr+e a l k++++l   l +l++  ++l+e +++ e+++ +le++++al+++ + ++  ++  e+e  +
  gene1678|gene1678|rna1678|rna1678 1468 EEKALRAENARLSKECAQLHVELHALTTDNDVLKEHINRCEQSVLDLESRCSALKKENELKRSMMQckEQEISN 1541
                                         55799*************************************************98755555555500444444 PP

                              ATG16  154 qdlqDElsaLqlq 166 
                                          + q + +a +lq
  gene1678|gene1678|rna1678|rna1678 1542 WKAQCASAAKELQ 1554
                                         4555555555555 PP

  == domain 9  score: 3.5 bits;  conditional E-value: 0.04
                              ATG16  128 leaeraaletklkdreeelrekeklvqdlqDElsaLqlqlnqaEeklrklekE 180 
                                         ++ e+ +l+ ++++r+  ++ ++   ++++ E+  L+ +++ +E k+++le+E
  gene1678|gene1678|rna1678|rna1678 1585 ITYENGELKARVAERDGIINALTDERDAIKGEVHELKKAVEILELKNKQLERE 1637
                                         45555555555555555555555555555555555555555555555555554 PP

>> DUF3287  Protein of unknown function (DUF3287)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.1       3.5   6.2e+03      80      95 ..     802     816 ..     794     821 .. 0.76
   2 ?    9.5   1.1   0.00044      0.78      58      96 ..     912     950 ..     896     965 .. 0.83
   3 ?   -2.2   0.0       1.7   3.1e+03      80     118 ..    1321    1359 ..    1313    1396 .. 0.84
   4 ?   -2.9   0.1       2.8   5.1e+03      66      98 ..    1464    1496 ..    1463    1503 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 3.5
                            DUF3287  80 tleaRiarveRklrel 95 
                                        +l  Ri ++e +++e 
  gene1678|gene1678|rna1678|rna1678 802 QL-SRIKQMEQEMKEC 816
                                        44.89********975 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00044
                            DUF3287  58 dkvvekHrrlcderqklgkkrqtleaRiarveRklrele 96 
                                        d ++++   l++e++k++  rq+le R+  +  +++ + 
  gene1678|gene1678|rna1678|rna1678 912 DVLAQRYDALNEEHRKMRVNRQSLEDRVNILTAEMQAMS 950
                                        5677888899******************99999999886 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 1.7
                            DUF3287   80 tleaRiarveRklreleseprdWeeleldevariPdsll 118 
                                         t + Ria+ + ++  le + rd +  + +  +++ ++ +
  gene1678|gene1678|rna1678|rna1678 1321 TFNTRIAKYKAEIVALEQDGRDLKAQNYELKNKLGEMSM 1359
                                         667899999999999999999988888888888777766 PP

  == domain 4  score: -2.9 bits;  conditional E-value: 2.8
                            DUF3287   66 rlcderqklgkkrqtleaRiarveRklrelese 98  
                                         + +de + l+    +l +  a++  +l+ l  +
  gene1678|gene1678|rna1678|rna1678 1464 KESDEEKALRAENARLSKECAQLHVELHALTTD 1496
                                         5789999***************99999998766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1658 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3030  (0.169); expected 358.6 (0.02)
Passed bias filter:                      712  (0.0397122); expected 358.6 (0.02)
Passed Vit filter:                       220  (0.0122706); expected 17.9 (0.001)
Passed Fwd filter:                       111  (0.00619109); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 3.72u 0.46s 00:00:04.18 Elapsed: 00:00:00.84
# Mc/sec: 5927.97
//
Query:       gene1679|gene1679|rna1679|rna1679  [L=508]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.5e-23   81.8   0.0    1.6e-22   80.5   0.0    1.6  1  ABC_tran         ABC transporter
      2e-08   34.0   0.0    4.1e-08   32.9   0.0    1.5  1  SMC_N            RecF/RecN/SMC N terminal domain
      2e-05   24.6   0.1      0.051   13.4   0.0    2.5  2  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
    0.00061   20.1   0.1     0.0018   18.6   0.1    1.8  1  AAA_22           AAA domain
     0.0024   17.8   1.2     0.0054   16.6   0.1    2.1  3  RsgA_GTPase      RsgA GTPase
      0.003   18.0   0.0     0.0049   17.3   0.0    1.3  1  AAA_16           AAA ATPase domain
     0.0038   17.2   0.1     0.0096   15.9   0.1    1.7  1  Rad17            Rad17 P-loop domain
     0.0042   17.0   0.1      0.018   15.0   0.0    2.1  2  ATPase_2         ATPase domain predominantly from Archaea
     0.0049   16.5   0.0     0.0094   15.5   0.0    1.4  1  AAA_25           AAA domain
  ------ inclusion threshold ------
      0.011   16.1   0.1      0.051   14.0   0.1    2.3  2  RNA_helicase     RNA helicase
      0.013   15.9   0.7      0.059   13.8   0.7    2.1  1  AAA              ATPase family associated with various cellul
      0.016   14.6  13.7      0.025   14.0  13.7    1.3  1  ABC2_membrane    ABC-2 type transporter
      0.018   15.5   0.3      0.038   14.5   0.3    1.5  1  AAA_23           AAA domain
       0.02   13.7   3.5      0.014   14.3   1.9    1.5  1  COX1             Cytochrome C and Quinol oxidase polypeptide 
      0.025   13.3   0.9       0.14   10.8   0.2    2.0  2  AAA_13           AAA domain
       0.04   13.8   0.2       0.92    9.4   0.0    2.3  2  NTPase_1         NTPase
       0.04   14.1   0.2       0.07   13.4   0.2    1.3  1  AAA_28           AAA domain
      0.054   13.2   1.6      0.085   12.6   0.2    2.0  2  AAA_29           P-loop containing region of AAA domain
      0.056   13.5   0.0       0.13   12.3   0.0    1.6  1  MMR_HSR1         50S ribosome-binding GTPase
      0.081   13.5   0.3       0.39   11.3   0.2    2.2  2  AAA_18           AAA domain
      0.083   12.6   0.1       0.17   11.6   0.1    1.5  1  Viral_helicase1  Viral (Superfamily 1) RNA helicase
       0.11   12.3   0.1       0.23   11.2   0.1    1.5  1  PduV-EutP        Ethanolamine utilisation - propanediol utili
       0.11   12.6   0.0        0.2   11.8   0.0    1.5  1  AAA_33           AAA domain
       0.13   12.5   0.1       0.68   10.2   0.1    2.3  1  SbcCD_C          Putative exonuclease SbcCD, C subunit
       0.16   11.7   0.0       0.29   10.8   0.0    1.4  1  AAA_24           AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.5   0.0   2.3e-25   1.6e-22      12     137 .]      37     172 ..      28     172 .. 0.93

  Alignments for each domain:
  == domain 1  score: 80.5 bits;  conditional E-value: 2.3e-25
                                        SEEEEEESTTSSHHHHHHHHTTSS--...SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH..... CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..... RF
                           ABC_tran  12 ekvaivGenGaGKStLlkllagllkp...teGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren..... 79 
                                         ++a++G++G+GK+tL+++lag +     t+G +l+++k+ ++   +++ +++g++ q++ +f++lt++e+     
  gene1679|gene1679|rna1679|rna1679  37 GLTAVMGPSGCGKTTLISTLAGRVPSstkTSGCVLYNEKERNS---SVWMNSVGFVDQDHAFFEGLTAYETvyyaa 109
                                        5789******************99777779****999888777...9***************************** PP

                                        .........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                        .........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ABC_tran  80 .........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                                 + + +i+k+ +kl+++++ + ++    + LSgG+++rv++a  l+++p++++lDEpt+
  gene1679|gene1679|rna1679|rna1679 110 rfklkgqnvNIETKIAKLFEKLRIIDIMNCKM----RILSGGERKRVMIAVELVSDPQIVFLDEPTS 172
                                        **999998888888************999998....*****************************96 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.9   0.0   5.7e-11   4.1e-08      22     199 ..      34     202 ..      25     219 .. 0.79

  Alignments for each domain:
  == domain 1  score: 32.9 bits;  conditional E-value: 5.7e-11
                                        TTSSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEE...SSSSS CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxx RF
                              SMC_N  22 fsksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfdnedkk...lkiek 94 
                                         ++++ta++Gp G+GK+ l+  +    G   +    s+k+s  + +++++++++    ++ f ++d++     +  
  gene1679|gene1679|rna1679|rna1679  34 ATQGLTAVMGPSGCGKTTLISTL---AGRVPS----STKTSGCVLYNEKERNSSVWMNSVGFVDQDHAffeGLTAY 102
                                        57899****************99...564444....6777777776577777777788888889999933323344 PP

                                        SCEEEEEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTT CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              SMC_N  95 eevsisrrvkrkgeseykingkevtkkevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaa 170
                                        e v+   r k kg+ ++ i+ k ++  e  +++  ++ ++  LSgGe++ v++a    ++ v+   +++lDe  + 
  gene1679|gene1679|rna1679|rna1679 103 ETVYYAARFKLKGQ-NVNIETKIAKLFEKLRIIDIMNCKMRILSGGERKRVMIA----VELVSDPQIVFLDEPTSG 173
                                        44555555555555.77788888888777777888888899********88876....55677778999******* PP

                                        S-HHHHHHHHHHHHHHCTTSEEEEE-SSH CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              SMC_N 171 LDeknvkkvaellkeksknaQfivislre 199
                                        LD+     ++ellke  ++  ++++s+++
  gene1679|gene1679|rna1679|rna1679 174 LDNDVAFSIVELLKEVAQEGKIVIMSIHQ 202
                                        ************************99976 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.0     0.002       1.5       1      20 [.      38      57 ..      38      77 .. 0.89
   2 !   13.4   0.0   7.1e-05     0.051     256     298 ..     160     202 ..     142     205 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.002
                             AAA_21  1 lnvliGpNgsGKSnLLdald 20
                                       l+++ Gp g+GK++L+ +l 
  gene1679|gene1679|rna1679|rna1679 38 LTAVMGPSGCGKTTLISTLA 57
                                       68999***********9994 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 7.1e-05
                             AAA_21 256 kkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHS 298
                                        + + ++++DEp +gL+  +  +++ellke +++g  vi++ H+
  gene1679|gene1679|rna1679|rna1679 160 SDPQIVFLDEPTSGLDNDVAFSIVELLKEVAQEGKIVIMSIHQ 202
                                        3349***********************9999966555776665 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.1   2.5e-06    0.0018       4      32 ..      35      63 ..      33      92 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 2.5e-06
                             AAA_22  4 tagilvvtGesGtGKTtllrrlleqldee 32
                                       t+g+++v+G+sG+GKTtl+ +l+ + +  
  gene1679|gene1679|rna1679|rna1679 35 TQGLTAVMGPSGCGKTTLISTLAGRVPSS 63
                                       799******************99887644 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.1   7.5e-06    0.0054      99     127 ..      36      64 ..       6      74 .. 0.83
   2 ?   -2.4   0.0       5.5   3.9e+03      20      41 ..     195     217 ..     191     236 .. 0.72
   3 ?   -2.9   0.1         8   5.7e+03      11      23 ..     377     389 ..     369     415 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 7.5e-06
                                        TSEEEEECSTTSSHHHHHHHHCTT----- CS
                        RsgA_GTPase  99 dktsvlvGqSGvGKStLinallpelelkt 127
                                        + +++++G+SG GK+tLi +l+++   +t
  gene1679|gene1679|rna1679|rna1679  36 QGLTAVMGPSGCGKTTLISTLAGRVPSST 64 
                                        56899****************99876555 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 5.5
                                        EEEEESTTTT--HHHH.HHHHHH CS
                        RsgA_GTPase  20 livvslkepelslnll.drfLvl 41 
                                        ++++s+++p+ +l+ll d+++++
  gene1679|gene1679|rna1679|rna1679 195 IVIMSIHQPDDRLSLLlDKIILM 217
                                        78999999998877651444443 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 8
                                        TTEES--EEEEEE CS
                        RsgA_GTPase  11 pkvaNvdqllivv 23 
                                        + ++N++++li++
  gene1679|gene1679|rna1679|rna1679 377 RLICNIEEVLIII 389
                                        5588999988765 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   6.8e-06    0.0049      25      52 ..      37      67 ..      20     128 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 6.8e-06
                             AAA_16 25 elvllsGesGvGKsslvrellralekd...g 52
                                       +l+ + G+sG+GK++l+ +l+ ++  +    
  gene1679|gene1679|rna1679|rna1679 37 GLTAVMGPSGCGKTTLISTLAGRVPSStktS 67
                                       7899*************99997666554432 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1   1.3e-05    0.0096      47     134 ..      38     123 ..       7     144 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.3e-05
                              Rad17  47 iLLisGPsGCgkstvvkvLskelgiklrewlnpvslkepdnqks...dfkgltekesrflsqiesfkeleLkdaky 119
                                        +  + GPsGCgk+t +  L+   +++  + +  v+++e + + s   +  g ++++  f   + +++ +   +a++
  gene1679|gene1679|rna1679|rna1679  38 LTAVMGPSGCGKTTLISTLAGR-VPSSTKTSGCVLYNEKERNSSvwmNSVGFVDQDHAFFEGLTAYETV-YYAARF 111
                                        66789**************975.5666677777777666553331114556666666666666666555.555555 PP

                              Rad17 120 lklqklGddlrtdkk 134
                                         kl+  G++++ + k
  gene1679|gene1679|rna1679|rna1679 112 -KLK--GQNVNIETK 123
                                        .444..555555544 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   2.5e-05     0.018       8     113 ..      24     131 ..      20     200 .. 0.71
   2 ?   -1.6   0.0       2.9   2.1e+03      82     114 ..     378     417 ..     345     426 .. 0.62

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.5e-05
                           ATPase_2   8 lkeleeilerepneiyfiYGpegsGKtaLlkeiienledkdk.yviyyialreesiskldefieeeeekkklekal 82 
                                        +  l++ +   ++    + Gp g+GKt+L+  ++ +  ++ k     +++ +e+++s   ++++  +++  + + l
  gene1679|gene1679|rna1679|rna1679  24 ITLLNKACGCATQGLTAVMGPSGCGKTTLISTLAGRVPSSTKtSGCVLYNEKERNSSVWMNSVGFVDQDHAFFEGL 99 
                                        55677777778888899*****************999444443444445555555555555556333333333333 PP

                           ATPase_2  83 .giavpkaeleeilkeksklvfkaiellleki 113
                                         + ++   ++   lk ++ +++ +i++l+ek+
  gene1679|gene1679|rna1679|rna1679 100 tAYETVYYAARFKLKGQNVNIETKIAKLFEKL 131
                                        22222222222233355556666666666665 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2.9
                           ATPase_2  82 l.......giavpkaeleeilkeksklvfkaielllekik 114
                                        l       +i +  ++++ +++++++++ + i+++   i 
  gene1679|gene1679|rna1679|rna1679 378 LicnieevLIIIIAFTFNSVFNSEQRNIRREISAYSYTIV 417
                                        1555555578888889999999888999999888877765 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   1.3e-05    0.0094      32      85 ..      35      81 ..      31     138 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.3e-05
                             AAA_25 32 agelallaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEdsede 85
                                        ++l++++G++g+GKttl + la  v +  +       + g Vly   E + + 
  gene1679|gene1679|rna1679|rna1679 35 TQGLTAVMGPSGCGKTTLISTLAGRVPSSTK-------TSGCVLYNEKERNSSV 81
                                       5789*******************99986553.......4455555555555544 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   7.1e-05     0.051       3      44 ..      41      82 ..      39     156 .. 0.73
   2 ?   -2.2   0.0       7.4   5.3e+03      65      86 ..     357     380 ..     345     385 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 7.1e-05
                       RNA_helicase  3 lyGpsgeGKStlakeLakallkkl.........klkkkdsvysrnpeddfw 44
                                       + Gpsg+GK+tl+ +La ++ ++          +         ++ ++++w
  gene1679|gene1679|rna1679|rna1679 41 VMGPSGCGKTTLISTLAGRVPSSTktsgcvlynE---------KERNSSVW 82
                                       78***************99997773334443331.........33333333 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 7.4
                       RNA_helicase  65 e..npsdlaelirlvsstpyplnm 86 
                                        +  + +d+  lir+v+ + ++l +
  gene1679|gene1679|rna1679|rna1679 357 SadKFDDVLALIRVVNWFVLRLIC 380
                                        222334899999999999888766 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.7   8.2e-05     0.059       3      26 ..      41     119 ..      39     214 .. 0.58

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 8.2e-05
                                        EESSTTSSHHHHHHHHHHHHTHE..................................................... CS
                                AAA   3 lyGppGtGKTllakavakelgve..................................................... 25 
                                        ++Gp G+GKT+l++ +a  + ++                                                     
  gene1679|gene1679|rna1679|rna1679  41 VMGPSGCGKTTLISTLAGRVPSStktsgcvlynekernssvwmnsvgfvdqdhaffegltayetvyyaarfklkgq 116
                                        78***************99632222233333333444444444444444444444444444444444444444444 PP

                                        ..E CS
                                AAA  26 ..f 26 
                                           
  gene1679|gene1679|rna1679|rna1679 117 nvN 119
                                        433 PP

>> ABC2_membrane  ABC-2 type transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0  13.7   3.5e-05     0.025       3     164 ..     309     486 ..     307     489 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.5e-05
                      ABC2_membrane   3 ikallkrefl.qrwrdpslgllwrliqplllalvfgtvfgn...lg.nsedglnr............pgllffsvl 61 
                                        i++l++r ++   +r ++ +l++ +i +++ ++ fg++      +  +s+d ++             + l++ +  
  gene1679|gene1679|rna1679|rna1679 309 IGVLINRRMKlDVFRMKTFILYAIIIAIMIAIFSFGVLDNFvfnVSdKSADKFDDvlalirvvnwfvLRLICNIEE 384
                                        67888888886889999888777777777777777755332222223455555337999****9999888888877 PP

                      ABC2_membrane  62 flafsaltsvapvferergvlerelvsplyslsayvlakvlvelpvsllqalifllivyflvgldls.rfflflll 136
                                         l ++++++  +vf +e++++ re ++  y+  +y l+ +++el++ l +++ +l+ +++   ++++  +++++  
  gene1679|gene1679|rna1679|rna1679 385 VLIIIIAFTFNSVFNSEQRNIRREISAYSYTIVSYHLSVLIFELIYHLPLITCYLCATLY--KYTPKqGIGFVIGC 458
                                        7788888888899*******************************************9999..88998555999*** PP

                      ABC2_membrane 137 llltalaasslgllisalapsfedasql 164
                                         ll +++++ +g+l++++++ ++  +++
  gene1679|gene1679|rna1679|rna1679 459 QLLRYWVIVNFGFLLISIFSGYKASIFF 486
                                        *****************99888777665 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.3   5.2e-05     0.038      18      37 ..      35      54 ..      19     135 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 5.2e-05
                             AAA_23 18 skgltlItGpNGaGKTTild 37
                                        +glt++ Gp G+GKTT++ 
  gene1679|gene1679|rna1679|rna1679 35 TQGLTAVMGPSGCGKTTLIS 54
                                       68****************96 PP

>> COX1  Cytochrome C and Quinol oxidase polypeptide I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   1.9   1.9e-05     0.014     141     246 ..     313     422 ..     305     433 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.9e-05
                                        HHHHHTT-CCGS-HHHHHHHHHHHHHHHHCHHHHHHHHHCHHHHHCT-SSSC...E-HHHHHHHHHHHHTHHH.HH CS
                               COX1 141 krrapgmtvaklplfvwavlatailillalpvlalalllllldrslgkffsp...gdplldqhlfWffgHpeV.yi 212
                                          r+ ++ v++++ f+ ++++ ai+i+++ +++   +++++ d s  kf ++   +  + + +l+ +    eV  i
  gene1679|gene1679|rna1679|rna1679 313 INRRMKLDVFRMKTFILYAIIIAIMIAIFSFGVLDNFVFNVSDKSADKFDDVlalIRVVNWFVLRLICNIEEVlII 388
                                        3455679999*******************************99998777776445555555555555555566555 PP

                                        HHHHHHHHHHHHHHHHHTSCCCTHHHHHHHHHHH CS
                               COX1 213 lilpalgivyyilpkfagrplfsyklsvlafili 246
                                        +i +++  v     + ++r++ +y+  +++  l 
  gene1679|gene1679|rna1679|rna1679 389 IIAFTFNSVFNSEQRNIRREISAYSYTIVSYHLS 422
                                        5555555555555566667776666666554443 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.25   1.8e+02      23     104 ..      43     130 ..      40     138 .. 0.60
   2 ?   10.8   0.2    0.0002      0.14     526     562 ..     161     194 ..     154     204 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.25
                             AAA_13  23 GwNGaGKTtLSrllrslelgetepkfangsieitngeeldirVf..NrdFvee..nls......eqgelkpvftLG 88 
                                        G  G GKTtL + l+      +++  ++g   + n++e +  V+  +  Fv++   ++      e  + ++ f L 
  gene1679|gene1679|rna1679|rna1679  43 GPSGCGKTTLISTLAGRV---PSSTKTSG-CVLYNEKERNSSVWmnSVGFVDQdhAFFegltayETVYYAARFKLK 114
                                        77899****988888842...33222333.3333444444444421556888754444565554445566667777 PP

                             AAA_13  89 eesiekqekieklkke 104
                                         +++++++ki+kl ++
  gene1679|gene1679|rna1679|rna1679 115 GQNVNIETKIAKLFEK 130
                                        7888888888887665 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.0002
                             AAA_13 526 kdkivviDDPvSSLDsnslfivfsliksrllkkkkak 562
                                          +iv++D P S LD ++ f+++ l+k+++   ++ k
  gene1679|gene1679|rna1679|rna1679 161 DPQIVFLDEPTSGLDNDVAFSIVELLKEVA---QEGK 194
                                        679************************998...4444 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.0    0.0013      0.92       4      39 ..      41      75 ..      39     101 .. 0.79
   2 ?    2.0   0.0      0.25   1.8e+02     114     143 ..     182     213 ..     151     232 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0013
                                       EE--TTSSHHHHHHHHHHHH...GGGEEEEEEEEE- CS
                           NTPase_1  4 iTGppGvGKtTlvkkvlellkssgvkvgGfyteevr 39
                                       + Gp+G GKtTl++ ++  + ss  k +G +  + +
  gene1679|gene1679|rna1679|rna1679 41 VMGPSGCGKTTLISTLAGRVPSS-TKTSGCVLYNEK 75
                                       67***************999666.677776655544 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.25
                                        HHHHHHHHHTTTSEEEEE--SS-..-SHHHHH CS
                           NTPase_1 114 fkeaveevLksekpvlavihrrk..dlalvee 143
                                        + e ++ev +++k+v++ ih+++   + l+++
  gene1679|gene1679|rna1679|rna1679 182 IVELLKEVAQEGKIVIMSIHQPDdrLSLLLDK 213
                                        568899999************98633344555 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.2   9.7e-05      0.07       3      22 ..      40      59 ..      38      83 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 9.7e-05
                             AAA_28  3 vitGgestGKTtlleaLaar 22
                                       +++G++++GKTtl++ La r
  gene1679|gene1679|rna1679|rna1679 40 AVMGPSGCGKTTLISTLAGR 59
                                       689**************966 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.2   0.00012     0.085      20      39 ..      34      53 ..      25      63 .. 0.86
   2 ?   -1.8   0.1       3.7   2.6e+03       1      10 [.     365     374 ..     365     377 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00012
                             AAA_29 20 dlkgatlltGpsGsGKSTll 39
                                        ++g t ++GpsG GK+Tl+
  gene1679|gene1679|rna1679|rna1679 34 ATQGLTAVMGPSGCGKTTLI 53
                                       56789**************9 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 3.7
                             AAA_29   1 LkrlqlvNWg 10 
                                        L+ +++vNW 
  gene1679|gene1679|rna1679|rna1679 365 LALIRVVNWF 374
                                        56799****6 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00018      0.13       3      33 ..      40      70 ..      38     104 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00018
                                       EEEESTTSSHHHHHHHHHTSTEEESSSTTSS CS
                           MMR_HSR1  3 aivGrpNvGKStLinaltgekaivsdkpgtT 33
                                       a++G +  GK+tLi++l g++   +++ g+ 
  gene1679|gene1679|rna1679|rna1679 40 AVMGPSGCGKTTLISTLAGRVPSSTKTSGCV 70
                                       89*****************988888888765 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.2   0.00054      0.39       3      22 ..      41      60 ..      40     133 .. 0.74
   2 ?   -1.9   0.0       6.5   4.7e+03      50      80 ..     172     199 ..     121     221 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00054
                             AAA_18  3 ltGtpGvGKttlakeLskrl 22
                                       ++G++G+GKttl   L+ r 
  gene1679|gene1679|rna1679|rna1679 41 VMGPSGCGKTTLISTLAGRV 60
                                       89**************7664 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 6.5
                             AAA_18  50 krldedkldklldaleenssaleegknlvid 80 
                                          ld d+  +++++l+e ++   egk ++++
  gene1679|gene1679|rna1679|rna1679 172 SGLDNDVAFSIVELLKEVAQ---EGKIVIMS 199
                                        55666777777777777653...55554444 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00024      0.17       3      39 ..      41      76 ..      39      94 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00024
                    Viral_helicase1  3 vhGvpGcGKStlirkllrtsliltvnrptaelltegk 39
                                       v G  GcGK+tli +l+   +  ++ ++ ++l++e  
  gene1679|gene1679|rna1679|rna1679 41 VMGPSGCGKTTLISTLAGR-VPSSTKTSGCVLYNEKE 76
                                       77888************88.77777888888888865 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00032      0.23       6      33 ..      41      68 ..      38      75 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00032
                          PduV-EutP  6 liGkvgsGKttLtqalkgeelkYkktqa 33
                                       ++G++g+GKttL  +l g+  + +kt  
  gene1679|gene1679|rna1679|rna1679 41 VMGPSGCGKTTLISTLAGRVPSSTKTSG 68
                                       79**************998777777765 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00028       0.2       2      25 ..      39      68 ..      38     131 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00028
                             AAA_33  2 vllvGlpGsGKstlaerllkklg......a 25
                                       + + G++G+GK+tl+  l+ + +      +
  gene1679|gene1679|rna1679|rna1679 39 TAVMGPSGCGKTTLISTLAGRVPsstktsG 68
                                       5689************99876655555554 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.1   0.00094      0.68      62      89 ..     160     187 ..     137     188 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00094
                            SbcCD_C  62 palrlvfLDEAFsklDeesiatllelle 89 
                                        +++++vfLDE  s+lD++ + +++ell+
  gene1679|gene1679|rna1679|rna1679 160 SDPQIVFLDEPTSGLDNDVAFSIVELLK 187
                                        5689***************999999987 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00041      0.29       6      23 ..      40      57 ..      38      91 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00041
                             AAA_24  6 liyGpsgiGKTtlakelg 23
                                       +++Gpsg GKTtl+++l 
  gene1679|gene1679|rna1679|rna1679 40 AVMGPSGCGKTTLISTLA 57
                                       79*************993 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (508 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1108  (0.0617993); expected 358.6 (0.02)
Passed bias filter:                      622  (0.0346924); expected 358.6 (0.02)
Passed Vit filter:                       103  (0.00574488); expected 17.9 (0.001)
Passed Fwd filter:                        25  (0.00139439); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              25  [number of targets reported over threshold]
# CPU time: 0.71u 0.33s 00:00:01.04 Elapsed: 00:00:00.49
# Mc/sec: 3087.22
//
Query:       gene168|gene168|rna168|rna168  [L=126]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.3e-49  167.2   9.1    1.4e-49  167.0   9.1    1.0  1  Mei5_like     Putative double-strand recombination repair-lik
  ------ inclusion threshold ------
      0.014   15.2   0.2      0.015   15.2   0.2    1.1  1  Mei5          Double-strand recombination repair protein
      0.061   12.6   1.3      0.073   12.4   0.9    1.3  1  SLATT_5       SMODS and SLOG-associating 2TM effector domain 
      0.099   12.7   0.2       0.11   12.5   0.2    1.1  1  Peptidase_C1  Papain family cysteine protease


Domain annotation for each model (and alignments):
>> Mei5_like  Putative double-strand recombination repair-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  167.0   9.1   3.2e-53   1.4e-49       1     118 []       1     118 [.       1     118 [. 0.99

  Alignments for each domain:
  == domain 1  score: 167.0 bits;  conditional E-value: 3.2e-53
                      Mei5_like   1 myftevpenekekyealevdekafyklkekksekkknrRySDqFkdplfiekdiyrKLkliekfkkknkdleeliekwke 80 
                                    myf +v+++e++ y++l+vd+ +fy++k++ +++kk+rRySDqF+++++++kdiyrKLk++ek+k++n+dl++l++kwke
  gene168|gene168|rna168|rna168   1 MYFLNVENDERHLYNTLQVDGITFYYYKNSGIDQKKKRRYSDQFRTCHLNYKDIYRKLKILEKHKDDNRDLDTLTTKWKE 80 
                                    9******************************************************************************* PP

                      Mei5_like  81 vieeciiiLkkefelkakevfkafdLkkygfdledyge 118
                                    +i++ci++Lk+efel+ake+fkaf+Lkkygf ledyge
  gene168|gene168|rna168|rna168  81 CIDKCITVLKNEFELPAKEIFKAFELKKYGFLLEDYGE 118
                                    ************************************96 PP

>> Mei5  Double-strand recombination repair protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.2   3.4e-06     0.015     124     180 ..      36      94 ..      13     116 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 3.4e-06
                                    HHHHHHHHHHH....HHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           Mei5 124 ekakLekqvre....keelLrrLklvkkyeskndlseLqllikkwrnasqklleeLqkala 180
                                    +k++   q+r      ++  r+Lk+ +k   k+d  +L++l  kw+++ +k + +L+ ++ 
  gene168|gene168|rna168|rna168  36 KKRRYSDQFRTchlnYKDIYRKLKILEK--HKDDNRDLDTLTTKWKECIDKCITVLKNEFE 94 
                                    5566666666555557888999999987..5999999*******************99875 PP

>> SLATT_5  SMODS and SLOG-associating 2TM effector domain family 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.9   1.6e-05     0.073      91     136 ..      41      85 ..      32      92 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.6e-05
                        SLATT_5  91 AekfhkcaleLselynelrllliseedlkekykeiskeYeeiLdky 136
                                    +++f+ c+l+ +++y++l+ l  + +d+++ ++++  + +e +dk+
  gene168|gene168|rna168|rna168  41 SDQFRTCHLNYKDIYRKLKILE-KHKDDNRDLDTLTTKWKECIDKC 85 
                                    89*****************966.999999999*9*******99999 PP

>> Peptidase_C1  Papain family cysteine protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.2   2.5e-05      0.11      74     160 ..      23     107 ..      19     123 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.5e-05
                                    HHHHHHHTEBEBTTTS--SSSCSSS-CGCGGGSEEBEESEEEEEESSBHHHHHHHHHH.HSSEEEEEECCSHHHHTEESS CS
                   Peptidase_C1  74 afeyikkggivtekdypYkakeggkCkkkkkkekvakikgygkvkenseealkkalak.ngPvsvaidaseedfqlYksG 152
                                    +f y k++gi+++k+  Y+++  ++C+ + k+ +  k k  +k k++ +++l +  +k ++ +  +i++ +++f+l  + 
  gene168|gene168|rna168|rna168  23 TFYYYKNSGIDQKKKRRYSDQF-RTCHLNYKDIY-RKLKILEKHKDD-NRDLDTLTTKwKECIDKCITVLKNEFELPAKE 99 
                                    5889999*************99.7*****88766.777777776665.55555544443568999999999999988888 PP

                                    EESSTSCE CS
                   Peptidase_C1 153 vyketecs 160
                                    ++k  e++
  gene168|gene168|rna168|rna168 100 IFKAFELK 107
                                    88876555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1087  (0.060628); expected 358.6 (0.02)
Passed bias filter:                      517  (0.028836); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 793.75
//
Query:       gene1680|gene1680|rna1680|rna1680  [L=63]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (63 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       386  (0.0215294); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 461.17
//
Query:       gene1681|gene1681|rna1681|rna1681  [L=68]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (68 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       585  (0.0326287); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.23s 00:00:00.57 Elapsed: 00:00:00.37
# Mc/sec: 547.99
//
Query:       gene1682|gene1682|rna1682|rna1682  [L=130]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       432  (0.024095); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 970.52
//
Query:       gene1683|gene1683|rna1683|rna1683  [L=348]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
        0.1   11.3   0.3       0.16   10.7   0.3    1.2  1  Nucleoporin_C  Non-repetitive/WGA-negative nucleoporin C-term


Domain annotation for each model (and alignments):
>> Nucleoporin_C  Non-repetitive/WGA-negative nucleoporin C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.3     9e-06      0.16     257     356 ..      12     111 ..       3     118 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 9e-06
                                        XXXX............XXXHHHHHHHHHHHHTSXHHHHHHHHHHHHH..HHHXSSSSXHHHH......HHHHHHHS CS
                      Nucleoporin_C 257 ayde.arkeqilkL..lsigkleeaielaekledfralvellleianklasdkgederkelyekaeelekrielyf 329
                                        a+++ +r  q+++L  ++ ++ e  + +a  ++ ++   ++ l         +++ +r+e++ k  e  kr  l f
  gene1683|gene1683|rna1683|rna1683  12 AFKKlNRSLQVQELkaIECKQPEYKFVIAYFFKELKNKTSIALMNK--FGV-RDDGNRQEFELKIIEEIKRSGLLF 84 
                                        4444466677777744455577777888888877766555544433..222.23678888888899999******* PP

                                        SSXXHHHHHHHHHHHHHTTXGGGGGGX CS
                      Nucleoporin_C 330 ekfgkaFayalYdwlisqgqqekLLdl 356
                                        ++  ++F y++Yd li+    + +L +
  gene1683|gene1683|rna1683|rna1683  85 RNIKNEFQYEFYDELINGPAGGVVLAM 111
                                        ****************98888888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (348 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       455  (0.0253779); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 2448.11
//
Query:       gene1684|gene1684|rna1684|rna1684  [L=1078]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1078 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1211  (0.0675442); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.76u 0.29s 00:00:01.05 Elapsed: 00:00:00.48
# Mc/sec: 6770.35
//
Query:       gene1685|gene1685|rna1685|rna1685  [L=1550]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1550 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       710  (0.0396006); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.85u 0.29s 00:00:01.13 Elapsed: 00:00:00.44
# Mc/sec: 10606.65
//
Query:       gene1686|gene1686|rna1686|rna1686  [L=79]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       507  (0.0282782); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 594.76
//
Query:       gene1687|gene1687|rna1687|rna1687  [L=513]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.055   13.8   0.1        0.2   12.0   0.1    1.9  1  Orf78     Orf78 (ac78)


Domain annotation for each model (and alignments):
>> Orf78  Orf78 (ac78)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   1.1e-05       0.2      31      89 ..     449     503 ..     435     511 .. 0.43

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.1e-05
                              Orf78  31 ndkaenkkekksaaeknditekesnaaekaqalnillisllavvcvlvllyviyYfvil 89 
                                        ++k+++ ++  ++++k ++++  ++  +ka++ + + i +++++c+l+++ + +   i 
  gene1687|gene1687|rna1687|rna1687 449 QTKNKKGST--ESRAKINSESVYQK-GTKAGKVKKI-IIVICILCLLIVVLAFLLTCIY 503
                                        222222222..22222222222222.2233333322.3345556666665555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (513 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1453  (0.0810419); expected 358.6 (0.02)
Passed bias filter:                      628  (0.0350271); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.28s 00:00:00.89 Elapsed: 00:00:00.43
# Mc/sec: 3580.13
//
Query:       gene1688|gene1688|rna1688|rna1688  [L=265]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    0.00058   20.1   1.4     0.0016   18.7   1.4    1.7  1  MADF_DNA_bdg   Alcohol dehydrogenase transcription factor Myb
  ------ inclusion threshold ------
       0.06   13.6   0.0       0.16   12.2   0.0    1.7  1  Catalase-rel   Catalase-related immune-responsive
       0.14   12.2   0.5       0.79    9.8   0.1    2.3  2  ArsC           ArsC family
        2.2    8.4   5.7       0.72   10.0   0.2    2.2  2  zf-C2H2_aberr  Aberrant zinc-finger


Domain annotation for each model (and alignments):
>> MADF_DNA_bdg  Alcohol dehydrogenase transcription factor Myb/SANT-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   1.4   3.5e-07    0.0016      18      80 ..      15      73 ..       9      76 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 3.5e-07
                       MADF_DNA_bdg 18 dyrnkekrekaweeiaeelnekvdveeckkkwknLRdryrrelrkkksseskekkkskwryfe 80
                                       + ++k+kr+  w+ iae++ e  d    ++ +++  +++++++++++    + k+++kw y++
  gene1688|gene1688|rna1688|rna1688 15 NSKDKKKRDLLWKNIAEKVDEVDDPSVAQTMFSYFMKSFNKKMKEAN----AGKSCKKWIYYD 73
                                       5689***************98888777999999**********9999....9*********98 PP

>> Catalase-rel  Catalase-related immune-responsive
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   3.6e-05      0.16      17      52 ..      16      51 ..      13      51 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 3.6e-05
                                       HS-HHHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHH CS
                       Catalase-rel 17 smseeekerlvnniafelskvedeeiqerqlehfak 52
                                       s ++++++ l +nia+ ++ v+d+ + + ++++f k
  gene1688|gene1688|rna1688|rna1688 16 SKDKKKRDLLWKNIAEKVDEVDDPSVAQTMFSYFMK 51
                                       668899***************************975 PP

>> ArsC  ArsC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.23     1e+03      10      35 ..      21      46 ..      20      48 .. 0.87
   2 ?    9.8   0.1   0.00018      0.79      10      49 ..     188     227 ..     108     244 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.23
                                       TTSHHHHHCTCCCTTSBHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               ArsC 10 krgttyreLnldkedlsedellelil 35
                                       kr+ ++++   +++++++ ++ + + 
  gene1688|gene1688|rna1688|rna1688 21 KRDLLWKNIAEKVDEVDDPSVAQTMF 46
                                       67778999999*********999996 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00018
                                        TTSHHHHHCTCCCTTSBHHHHHHHHHH-GGGB-S-EEEES CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               ArsC  10 krgttyreLnldkedlsedellelilenpsLirRPivvdg 49 
                                        kr +  +   l++ d s+ ++l+li e+ +L++R +++d+
  gene1688|gene1688|rna1688|rna1688 188 KRLKVHKDAALKFSDPSDVKILDLINERDMLVKRLLITDN 227
                                        6667778888999999******************888885 PP

>> zf-C2H2_aberr  Aberrant zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.2   0.00016      0.72      53     110 ..      66     123 ..      44     133 .. 0.83
   2 ?    0.3   1.1      0.15   6.6e+02      58     118 ..     152     219 ..     132     243 .. 0.51

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00016
                      zf-C2H2_aberr  53 ntelleehlekehaakllellkeleieikkteetekvnykgkivelkkedsvvnlsdv 110
                                         ++ ++  l k+++ +l++  +++  ei++++  ekv + +  ++ +++ ++ n+ + 
  gene1688|gene1688|rna1688|rna1688  66 CKKWIYYDLAKKYMPDLVASAEQTAREIENKNSAEKVLSGSCSANNNEKSNMTNIVQA 123
                                        567788999****************************999888888888888776544 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.15
                      zf-C2H2_aberr  58 eehlekehaakllellkeleieikkteet.ekvnykgkivelkkedsv........vnlsdvitendvlk 118
                                        +  lek+   ++ e  k+l +  +k +e+ +++++ +k  + +++d+         v++ d+i+e+d+l 
  gene1688|gene1688|rna1688|rna1688 152 KLELEKKAD-NVFEFGKNLSVSPQKHDEKeTNIDMPKKRLK-VHKDAAlkfsdpsdVKILDLINERDMLV 219
                                        444444433.5666666666655444433145555433333.2333330111111145556666666654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (265 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1836  (0.102404); expected 358.6 (0.02)
Passed bias filter:                      537  (0.0299515); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 1928.30
//
Query:       gene1689|gene1689|rna1689|rna1689  [L=468]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.6e-69  233.5   0.1    3.1e-69  232.6   0.1    1.5  1  SRP54       SRP54-type protein, GTPase domain
    5.2e-27   94.4   1.8    8.3e-27   93.7   0.4    2.0  2  SRP_SPB     Signal peptide binding domain
    1.7e-11   44.1   0.6      6e-11   42.4   0.6    2.0  1  SRP54_N     SRP54-type protein, helical bundle domain
    7.2e-07   29.0   1.6    9.8e-06   25.3   0.7    2.8  2  cobW        CobW/HypB/UreG, nucleotide-binding domain
    0.00069   18.7   0.1     0.0038   16.3   0.0    2.2  4  MeaB        Methylmalonyl Co-A mutase-associated GTPase MeaB
    0.00093   19.4   0.0     0.0045   17.2   0.0    2.0  2  AAA_33      AAA domain
     0.0087   16.4   0.0      0.022   15.2   0.0    1.7  1  AAA_16      AAA ATPase domain
  ------ inclusion threshold ------
      0.011   15.8   0.0       0.11   12.5   0.0    2.6  1  CbiA        CobQ/CobB/MinD/ParA nucleotide binding domain
      0.015   15.0   0.0      0.027   14.2   0.0    1.4  1  AAA_30      AAA domain
      0.028   14.3   0.0      0.075   12.9   0.0    1.7  1  MobB        Molybdopterin guanine dinucleotide synthesis prot
       0.03   14.1   0.2        3.2    7.7   0.0    3.4  4  POTRA_2     POTRA domain, ShlB-type
      0.035   14.4   0.0        0.1   12.9   0.0    1.9  1  AAA_22      AAA domain
      0.047   13.6   0.0       0.11   12.3   0.0    1.6  1  APS_kinase  Adenylylsulphate kinase
      0.086   12.9   0.2        0.5   10.5   0.2    2.2  1  MMR_HSR1    50S ribosome-binding GTPase
       0.18   12.2   1.4       0.36   11.2   0.1    2.2  2  AAA_17      AAA domain


Domain annotation for each model (and alignments):
>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  232.6   0.1   2.6e-72   3.1e-69       2     196 .]     100     293 ..      99     293 .. 0.98

  Alignments for each domain:
  == domain 1  score: 232.6 bits;  conditional E-value: 2.6e-72
                                        EEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTSSTTHHHHHHHHHHHTTEEEEESSTTSCHHHHHHHHHH CS
                              SRP54   2 nvillvGlqGaGKTttlaKLaallkkegkkvllvaaDtfRaaAveQLktlaeklgvpvikkkeeadpaavakeave 77 
                                        +vi++vGlqGaGKTtt+ K a+ +kk+g+k+ +v+aDtfRa+A++Q+k++a k++vp++++  + dp++va+e+ve
  gene1689|gene1689|rna1689|rna1689 100 QVIMFVGLQGAGKTTTVCKYANFYKKKGYKAGIVCADTFRAGAFDQIKQNALKINVPYFGSA-DPDPVKVASEGVE 174
                                        69*******************************************************99766.789********** PP

                                        HHHHTTSSEEEEEE--SSTTHHHHHHHHHHHHHHHSSSEEEEEEETTBHTHHHHHHHHHHHHSSCSEEEEESTTSS CS
                              SRP54  78 kakeekidvvlvDTaGrlqndkelmeelkkikkvvkpdevllvldattgqeavkqakaFkeavgitgviltklDgd 153
                                        k++++k++v+lvDT+Gr+ ++++l++e+++i  +vkp+++++v+da +gq+a +qa  Fke+v+++++iltk+Dg 
  gene1689|gene1689|rna1689|rna1689 175 KFRKDKFEVILVDTSGRHTQENDLFNEMEEIVGAVKPENIVFVMDAGIGQSAEHQAMGFKEKVNLGSIILTKVDGA 250
                                        **************************************************************************** PP

                                        SSTTHHHHHHHHHTS-EEEEE-SSSTTGEEE--HHHHHHHHHT CS
                              SRP54 154 akgGaalsiaaelklPikfigvGekiedleefdperlvsrllg 196
                                         k+G+a+s +a ++ Pi fig+Ge ++dl++f+p+r+++++lg
  gene1689|gene1689|rna1689|rna1689 251 EKAGGAISSVAITGCPIEFIGNGEGMDDLDVFSPRRFINKILG 293
                                        *****************************************95 PP

>> SRP_SPB  Signal peptide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.7   0.4     7e-30   8.3e-27       1      99 []     322     419 ..     322     419 .. 0.92
   2 ?   -0.3   0.1       1.4   1.6e+03      14      45 ..     419     448 ..     417     453 .. 0.66

  Alignments for each domain:
  == domain 1  score: 93.7 bits;  conditional E-value: 7e-30
                                        SSCTHHHHHHHHHHHCCCCCCHHHHCCC......H...CCCCCHHHHHHHHHTTSBHHHHHSGCG-..H..HHHHH CS
                            SRP_SPB   1 eftlrdlleqlqqikkmGplskllsmiPgmsae.akaeeeaekklkrieaiidSMTkeErdspekllke..sRkrR 73 
                                        ++tl+d+  qlqq++++Gplsk+++miPgm++     ++  e  l+++ +i+dSMT++E+ s++++lk+  +R++R
  gene1689|gene1689|rna1689|rna1689 322 KYTLKDFNLQLQQLMSLGPLSKVMEMIPGMGNLpI--SD--EGVLRKMVCIFDSMTEKELGSDGEILKKetTRVTR 393
                                        69***************************887743..33..579***********************9668***** PP

                                        HHHHTTS-HHHHHHHHHHHHHHHHHT CS
                            SRP_SPB  74 iArGsGtsvqevnellkqfeqmkkmm 99 
                                        iA+GsGt+ + v +l++qfe+m+++m
  gene1689|gene1689|rna1689|rna1689 394 IAKGSGTRPELVLQLVAQFEMMSNLM 419
                                        ***********************987 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.4
                                        HHCCCCCCHHHHCCC.....H...CCCCCHHH CS
                            SRP_SPB  14 ikkmGplskllsmiPgmsaeakaeeeaekklk 45 
                                        +kk+G+ + +++ + + +++++a+e  + klk
  gene1689|gene1689|rna1689|rna1689 419 MKKLGNNQGFMNLLNADTSKMSASE--KAKLK 448
                                        899********99997444443333..34444 PP

>> SRP54_N  SRP54-type protein, helical bundle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.4   0.6   5.1e-14     6e-11       1      75 []       5      81 ..       5      81 .. 0.94

  Alignments for each domain:
  == domain 1  score: 42.4 bits;  conditional E-value: 5.1e-14
                                       HHHHHHHHHHHHCCSSCGHHHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHCTTS....S-HHHHHHHHHHHH CS
                            SRP54_N  1 LgkklnsalkklsgkskideedleealkeleeaLleaDVgvkvvkklienvkkkavgekk....lkpkqqvkkivkde 74
                                       Lgk++ns+l++l +k+ ++++ +e+a+ke+ ++L++++Vg k v++l  n+   +++ ++    +++++ v+++++de
  gene1689|gene1689|rna1689|rna1689  5 LGKSINSTLQNLFKKD-VTDQGIEAAIKEIIRQLIQNNVGTKCVTQLKINLDS-KLKTEElkpgINKAKWVYNAIFDE 80
                                       89*********99996.8*********************************55.899777899999************ PP

                                       H CS
                            SRP54_N 75 L 75
                                       L
  gene1689|gene1689|rna1689|rna1689 81 L 81
                                       8 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.7   8.2e-09   9.8e-06       2     156 ..     101     253 ..     100     263 .. 0.79
   2 ?   -1.1   0.0      0.99   1.2e+03      38      61 ..     376     399 ..     363     421 .. 0.81

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 8.2e-09
                                        EEEEEESTTCCHHHHHHHHH..CT--SS-EEEEESS-SSCHCCCCCCHCCCT.EEEETTTTECCHCTT-HHHHHHH CS
                               cobW   2 vtvltGflGsGKTtLlnhll..enraglklavivNefgevsiDaellretgveivelenGciCctlredllkelea 75 
                                        v++++G  G+GKTt ++++    +++g+k  ++  +    +   + +++++ +i     G       + +++ +e+
  gene1689|gene1689|rna1689|rna1689 101 VIMFVGLQGAGKTTTVCKYAnfYKKKGYKAGIVCADTFRAGAFDQ-IKQNALKINVPYFGSADPDPVKVASEGVEK 175
                                        78999***************99999***********996655444.455534444444566555556666777777 PP

                                        HHHHHTT-SEEEEEECT.TTTHHHHHTT.SHHHHHCCCECEEEEEEETTTH.CCHCCHHHHHHHHHHTSSEEEEE- CS
                               cobW  76 leereerldviliEttG.laePapvaft.eeelksdltldavvavvDaknleaeeekieekaedqlaaadllvlnK 149
                                        + +++  ++vil+ t+G   + + + f+  ee+  +++ + +v+v+Da  + ++ e+++  ++++++  + ++l+K
  gene1689|gene1689|rna1689|rna1689 176 FRKDK--FEVILVDTSGrHTQENDL-FNeMEEIVGAVKPENIVFVMDA-GIGQSAEHQAMGFKEKVNLGS-IILTK 246
                                        76666..**********66666666.5559******************.666899999999999999987.789** PP

                                        HHHHCHC CS
                               cobW 150 tDlldee 156
                                        +D ++++
  gene1689|gene1689|rna1689|rna1689 247 VDGAEKA 253
                                        **99887 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.99
                                        SCHCCCCCCHCCCT.EEEETTTTE CS
                               cobW  38 evsiDaellretgveivelenGci 61 
                                        e++ D+e+l+++++ ++ +++G  
  gene1689|gene1689|rna1689|rna1689 376 ELGSDGEILKKETTRVTRIAKGSG 399
                                        5889********999999999975 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   3.1e-06    0.0038      25      66 ..      95     136 ..      90     148 .. 0.93
   2 ?   -2.8   0.0         2   2.4e+03     122     146 ..     181     205 ..     169     212 .. 0.77
   3 ?   -3.3   0.0       2.8   3.4e+03      78     112 ..     271     306 ..     259     307 .. 0.76
   4 ?   -3.6   0.0       3.7   4.4e+03     204     238 ..     391     425 ..     374     441 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 3.1e-06
                                        G-S-SEEEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE- CS
                               MeaB  25 kaGraqvvGltGvPGaGkstlvealglelrrrGkrvavlavD 66 
                                        k G++qv+ + G+ GaGk t+v + +  ++++G++ +++  D
  gene1689|gene1689|rna1689|rna1689  95 KRGKSQVIMFVGLQGAGKTTTVCKYANFYKKKGYKAGIVCAD 136
                                        679***********************************9987 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 2
                                        -SEEEEEEESSTTHHHHHHTT-SEE CS
                               MeaB 122 fDvvlietvGvGqsevdvaevvdtf 146
                                        f+v+l++t G    e d+ + ++ +
  gene1689|gene1689|rna1689|rna1689 181 FEVILVDTSGRHTQENDLFNEMEEI 205
                                        8999999999988888887766655 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 2.8
                                        ------HCCC.TSTTEEEEEE-----HHHHHHHHHH CS
                               MeaB  78 GDklRleela.vdegvfiRslpsrGalGGlaaktre 112
                                        G+   +++l+   +  fi  +  +G l Gla+k ++
  gene1689|gene1689|rna1689|rna1689 271 GNGEGMDDLDvFSPRRFINKILGKGDLEGLAEKIKD 306
                                        555567777734688899999999999999998765 PP

  == domain 4  score: -3.6 bits;  conditional E-value: 3.7
                                        --EEEEEBCCCTBSHHHHHHHHHHHHHHHHHTTHH CS
                               MeaB 204 rpkvlktsavegeGidelvdaieehrevlkktGll 238
                                         +++ k s+++ e + +lv++ e   + +kk G+ 
  gene1689|gene1689|rna1689|rna1689 391 VTRIAKGSGTRPELVLQLVAQFEMMSNLMKKLGNN 425
                                        45666777777777777777777777777776654 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   3.7e-06    0.0045       1      82 [.     101     192 ..     101     218 .. 0.68
   2 ?   -0.7   0.0       1.2   1.5e+03      17      48 ..     416     450 ..     386     467 .. 0.65

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 3.7e-06
                             AAA_33   1 lvllvGlpGsGKstlaerl...lkklg..avllssdtlrrrlfgtdqqskt.....dytrvldrlyqilnelarka 66 
                                        ++++vGl+G+GK+t + ++   +kk g  a ++  dt+r   f + +q+       +   + ++  +  +e ++k 
  gene1689|gene1689|rna1689|rna1689 101 VIMFVGLQGAGKTTTVCKYanfYKKKGykAGIVCADTFRAGAFDQIKQNALkinvpYFGSADPDPVKVASEGVEKF 176
                                        89*************9888555777778888899999999888744443333444333345555555666777777 PP

                             AAA_33  67 lsagrnvildatnlsr 82 
                                        ++ ++ vil  t  ++
  gene1689|gene1689|rna1689|rna1689 177 RKDKFEVILVDTSGRH 192
                                        7777777777665444 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.2
                             AAA_33  17 erllkklg.....avllssdtlrrrlfgtdqqsktdy 48 
                                         +l+kklg     + ll+ dt  +++ ++++ +++++
  gene1689|gene1689|rna1689|rna1689 416 SNLMKKLGnnqgfMNLLNADT--SKMSASEKAKLKQQ 450
                                        456666666666888888887..34444344444333 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   1.8e-05     0.022      18     142 ..      93     219 ..      78     225 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.8e-05
                             AAA_16  18 rvrsgrpelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqlldeaesae 93 
                                        +v++g +++++++G +G GK++ v + ++ ++k+     +     +         a+++ r + + q++++a + +
  gene1689|gene1689|rna1689|rna1689  93 KVKRGKSQVIMFVGLQGAGKTTTVCKYANFYKKK----GYKAGIVC---------ADTF-RAGAFDQIKQNALKIN 154
                                        5788999*********************999999....34444444.........5556.5577777777766666 PP

                             AAA_16  94 leawrekleeala................avpelagaea..srllellkrllallsrderplvlvlD 142
                                        ++++  + ++ ++                +  + +g +   ++l++++ +++   ++ e  +v+v+D
  gene1689|gene1689|rna1689|rna1689 155 VPYFGSADPDPVKvasegvekfrkdkfevILVDTSGRHTqeNDLFNEMEEIVGAVKP-EN-IVFVMD 219
                                        666666666666655555555666666553333333333669999999999977776.77.888888 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   9.3e-05      0.11       9      88 ..     109     251 ..     102     358 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 9.3e-05
                                        TSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH.............................. CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.............................. RF
                               CbiA   9 GvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep.............................. 54 
                                        G+GKTt++++ a   +++g++   v aD+ +  ++       +i++                              
  gene1689|gene1689|rna1689|rna1689 109 GAGKTTTVCKYANFYKKKGYKAGIVCADTFRAGAF------DQIKQnalkinvpyfgsadpdpvkvasegvekfrk 178
                                        89***************999999998888866655......22222345668899999999999999999999999 PP

                                        ........................................CCHCCCHHHHHHCHCHHHH..EEEEEEEEESS.. CS
                                        ........................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               CbiA  55 ........................................dlkrllellealgkkkalllkiagvvlnrvdgen 88 
                                                                                d+  +++++e+   +++ ++++ +++l++vdg +
  gene1689|gene1689|rna1689|rna1689 179 dkfevilvdtsgrhtqendlfnemeeivgavkpenivfvmDA-GIGQSAEHQAMGFKEKVNLGSIILTKVDGAE 251
                                        999999999999999999999999999999999999999966.5577777777777777777888888877763 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   2.3e-05     0.027      17      58 ..      98     140 ..      93     191 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.3e-05
                             AAA_30  17 gdrvavltGpAGtGKttalkalreaweaaggrv.iglAptgka 58 
                                        + +v + +G  G+GKtt++ ++++ ++++g++  i++A t +a
  gene1689|gene1689|rna1689|rna1689  98 KSQVIMFVGLQGAGKTTTVCKYANFYKKKGYKAgIVCADTFRA 140
                                        4569999**********************96642677777665 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   6.3e-05     0.075       1      33 [.     101     133 ..     101     146 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6.3e-05
                               MobB   1 vlgivgksgsGKTtLleklipelkarglrvgti 33 
                                        v+ +vg +g+GKTt + k  +  k++g++ g++
  gene1689|gene1689|rna1689|rna1689 101 VIMFVGLQGAGKTTTVCKYANFYKKKGYKAGIV 133
                                        689**************************9988 PP

>> POTRA_2  POTRA domain, ShlB-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.0    0.0027       3.2      18      50 ..       8      40 ..       3      48 .. 0.90
   2 ?   -3.4   0.0       7.5   8.9e+03      45      54 ..     121     130 ..     120     135 .. 0.79
   3 ?    1.2   0.0      0.27   3.3e+02       6      43 ..     168     205 ..     165     208 .. 0.90
   4 ?   -0.4   0.0      0.85     1e+03      25      46 ..     286     307 ..     273     311 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0027
                                       CHHHHHCCCSSSEEEHHHHHHHHHHHHHHHHHT CS
                            POTRA_2 18 eleallqpylgkclgladlnqlakeltnayiek 50
                                        ++++lq++  k+++ +++++++ke+  ++i++
  gene1689|gene1689|rna1689|rna1689  8 SINSTLQNLFKKDVTDQGIEAAIKEIIRQLIQN 40
                                       578999***********************9997 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 7.5
                                        HHHHHTT-TT CS
                            POTRA_2  45 nayiekGYvt 54 
                                        n+y +kGY  
  gene1689|gene1689|rna1689|rna1689 121 NFYKKKGYKA 130
                                        8999****65 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.27
                                        EEEESGCCSSHCCHHHHHCCCSSSEEEHHHHHHHHHHH CS
                            POTRA_2   6 ielegntllsleeleallqpylgkclgladlnqlakel 43 
                                        +  eg + + ++++e +l +  g+  + +dl++ + e+
  gene1689|gene1689|rna1689|rna1689 168 VASEGVEKFRKDKFEVILVDTSGRHTQENDLFNEMEEI 205
                                        66799**************************9988876 PP

  == domain 4  score: -0.4 bits;  conditional E-value: 0.85
                                        CCSSSEEEHHHHHHHHHHHHHH CS
                            POTRA_2  25 pylgkclgladlnqlakeltna 46 
                                         +++k lg +dl+ la ++ ++
  gene1689|gene1689|rna1689|rna1689 286 RFINKILGKGDLEGLAEKIKDL 307
                                        6789999999*****9999876 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   8.6e-05       0.1       4      38 ..      98     146 ..      95     231 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 8.6e-05
                             AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaee..............e 38 
                                        + ++++ +G  G+GKTt++ ++++ +++  + +                
  gene1689|gene1689|rna1689|rna1689  98 KSQVIMFVGLQGAGKTTTVCKYANFYKKKGYKAGivcadtfragafdqI 146
                                        568999*******************987666665666666666555552 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   9.5e-05      0.11       2      44 ..      99     141 ..      98     150 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 9.5e-05
                                        -EEEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHTTT CS
                         APS_kinase   2 gvvvwltGlsgsGKstianalekkLvekgisvylLdGdnvRhg 44 
                                        + v+++ Gl g+GK+t  ++ ++  ++kg+++ ++  d+ R g
  gene1689|gene1689|rna1689|rna1689  99 SQVIMFVGLQGAGKTTTVCKYANFYKKKGYKAGIVCADTFRAG 141
                                        789*****************************99999999987 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.2   0.00042       0.5       2      87 ..     102     224 ..     101     246 .. 0.53

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00042
                                        EEEEESTTSSHHHHHHHHHT.................STEEESSSTTSSSSEEEEEEEETTEE............. CS
                           MMR_HSR1   2 vaivGrpNvGKStLinaltg.................ekaivsdkpgtTrdinegrvklkgke............. 47 
                                        +++vG   +GK+t + +  +                 +       +g+  +i++        +             
  gene1689|gene1689|rna1689|rna1689 102 IMFVGLQGAGKTTTVCKYANfykkkgykagivcadtfR-------AGAFDQIKQ--------Nalkinvpyfgsad 162
                                        78899999999999988887554444433222222111.......111122222........12222233333334 PP

                                        ....................EEEEECGGCSSHHHHHH...HHHHHHHHHHCTSEEEEEEETT..T CS
                           MMR_HSR1  48 ....................ielvDtpGliegaseek...glgkaflaleeadlillvvdas..e 87 
                                                            ++lvDt G  +   +e+   ++ +++    + + i++v+da   +
  gene1689|gene1689|rna1689|rna1689 163 pdpvkvasegvekfrkdkfeVILVDTSG-RH--TQENdlfNEMEEIVGAVKPENIVFVMDAGigQ 224
                                        44555555555566666666********.55..344411445555555666799******77431 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00031      0.36       1     108 [.     105     217 ..     105     223 .. 0.71
   2 ?   -2.7   0.0       6.1   7.3e+03      49      69 ..     406     426 ..     379     455 .. 0.56

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00031
                                        EE-TTSSHHHHHHHHHHHHTEEEEEHHHHHHHHHHTTTSHSSHHHHC........TSHHHHHHHHHHHHHHHHHHH CS
                             AAA_17   1 lGgPGsGKgtqceklvekygfthlsaGdllreeakrgglakardemr........klpleekkelqkeaaekiaee 68 
                                        +G+ G+GK+t + k +  y+ + + aG +  ++ + g  ++ +++           ++ ++  ++  e  ek +++
  gene1689|gene1689|rna1689|rna1689 105 VGLQGAGKTTTVCKYANFYKKKGYKAGIVCADTFRAGAFDQIKQNALkinvpyfgSADPDPV-KVASEGVEKFRKD 179
                                        79*******9999***9999999999988888877776555444444222333223343333.4555666666654 PP

                                        HHSSEEEEEE-SEEEETTEEEESSHHHHHHHH..SEEEEE CS
                             AAA_17  69 akkkgvlvdghprikeqagfldglpkevleelkpdaiill 108
                                         k + +lvd+  r  ++++++ ++++ ++  +kp+ i+++
  gene1689|gene1689|rna1689|rna1689 180 -KFEVILVDTSGRHTQENDLFNEMEE-IVGAVKPENIVFV 217
                                        .66789*****999999999999995.7788999998886 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 6.1
                                        SHHHHHHHHHHHHHHHHHHHH CS
                             AAA_17  49 lpleekkelqkeaaekiaeea 69 
                                        l+l+ + e++ ++++k+ +++
  gene1689|gene1689|rna1689|rna1689 406 LQLVAQFEMMSNLMKKLGNNQ 426
                                        344445555555555555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (468 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       883  (0.0492498); expected 358.6 (0.02)
Passed bias filter:                      645  (0.0359752); expected 358.6 (0.02)
Passed Vit filter:                        95  (0.00529868); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.65u 0.33s 00:00:00.98 Elapsed: 00:00:00.50
# Mc/sec: 2840.66
//
Query:       gene169|gene169|rna169|rna169  [L=190]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-30  106.4   1.6    1.7e-30  106.0   1.6    1.1  1  TLD       TLD
  ------ inclusion threshold ------
      0.049   12.8   0.2      0.063   12.5   0.2    1.3  1  Tho2      Transcription factor/nuclear export subunit protein


Domain annotation for each model (and alignments):
>> TLD  TLD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.0   1.6   1.9e-34   1.7e-30       1     139 []      52     189 ..      52     189 .. 0.95

  Alignments for each domain:
  == domain 1  score: 106.0 bits;  conditional E-value: 1.9e-34
                            TLD   1 llyssskdgsslstllekie.nkgptlllikdekkyifGaflsqpwkssnkkfygdsesflfsl.spkfkvykstgknka 78 
                                    l+yss ++g+sl+t++ ++  ++ p++l+++++++++fG+f+++++  ++    g+ ++flf++ + ++kv+k +g+  +
  gene169|gene169|rna169|rna169  52 LVYSSVEHGFSLRTMVDNLSkSRPPFILICRENEGNTFGVFINDKICFKST-LSGKINTFLFKMeNGQVKVFKYSGNLPY 130
                                    68******************66699*********************65555.89**********999************* PP

                            TLD  79 ylntssdglgfGggqpkfsLwidsslekgtsrhsetfengllsgaseerfkikdiEVWglg 139
                                    ++++s +++gfG++++kf+L  +s+l +g+s+  +tf+n+ ls   +e+f +k+iEVW++g
  gene169|gene169|rna169|rna169 131 FCLCSPSFIGFGCSEGKFGLLFNSTLLTGSSSRVTTFNNEVLS--RKEKFAVKQIEVWTIG 189
                                    *******************************************..9************986 PP

>> Tho2  Transcription factor/nuclear export subunit protein 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.2     7e-06     0.063     136     178 ..      54      95 ..      26     122 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 7e-06
                           Tho2 136 helktpnFstldlldrlfkanliplifscTerEaenlgrFlne 178
                                     ++   +Fs+ +++d+l k+   p+i  c e+E + +g+F+n+
  gene169|gene169|rna169|rna169  54 YSSVEHGFSLRTMVDNLSKS-RPPFILICRENEGNTFGVFIND 95 
                                    5566689*************.9*******************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (190 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       389  (0.0216967); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 1275.59
//
Query:       gene1690|gene1690|rna1690|rna1690  [L=103]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.1e-22   77.7   1.3    6.3e-22   77.4   1.3    1.0  1  TFIID-18kDa  Transcription initiation factor IID, 18kD subuni
  ------ inclusion threshold ------
      0.074   13.3   0.1      0.086   13.1   0.1    1.2  1  Cas_Cmr5     CRISPR-associated protein (Cas_Cmr5)


Domain annotation for each model (and alignments):
>> TFIID-18kDa  Transcription initiation factor IID, 18kD subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.4   1.3     7e-26   6.3e-22       2      92 ..       8      96 ..       7      97 .. 0.97

  Alignments for each domain:
  == domain 1  score: 77.4 bits;  conditional E-value: 7e-26
                                       --CCCCHHHHHCTTS-SS--HHHHHHHHHHHHHHHHHHHHHHHC-XXXX...XXXXXXXXXXXXXXXXXXXXXXXXXX CS
                        TFIID-18kDa  2 lfrkelqsmlyalGdvkePlqetvqlledlvrgyliellqqaakvaklrgsrkitlEDllfliRkDkkKlnRlkells 79
                                       lf kel+ m+y++Gd   P ++tv++l d + gyl++ll+++ ++a+ +g  k + +Dll++++kD++K  R+k+ll 
  gene1690|gene1690|rna1690|rna1690  8 LFTKELKLMMYGFGDTIIPRNDTVDVLHDYLLGYLKNLLIKTQNMARIKG--KTKTDDLLYILKKDRRKYMRVKDLLL 83
                                       699********************************************995..67899********************* PP

                                       XXXXXXXXXXXXX CS
                        TFIID-18kDa 80 lkellkkakKqfd 92
                                       ++e+lk+a+K+fd
  gene1690|gene1690|rna1690|rna1690 84 TNEELKNARKAFD 96
                                       ***********98 PP

>> Cas_Cmr5  CRISPR-associated protein (Cas_Cmr5)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   9.6e-06     0.086      59     108 ..      32      82 ..       4      88 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 9.6e-06
                                        CHHHHHHHHHHHHHHHHC.TSS...STTTCHHHHHHHHSTHHHHHHHHHHH CS
                           Cas_Cmr5  59 edahkkllehlaewlkke.ksaskkkkgendllkelleadlseymratrea 108
                                        +  h +ll  l++ l k  + a  k+k++ d l ++l++d+ +ymr+ +  
  gene1690|gene1690|rna1690|rna1690  32 DVLHDYLLGYLKNLLIKTqNMARIKGKTKTDDLLYILKKDRRKYMRVKDLL 82 
                                        6668999999****9999899999**********************98755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       742  (0.0413855); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 743.41
//
Query:       gene1691|gene1691|rna1691|rna1691  [L=591]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.073   13.6   2.5       0.27   11.8   2.5    2.0  1  MRP-S32   Mitochondrial 28S ribosomal protein S32


Domain annotation for each model (and alignments):
>> MRP-S32  Mitochondrial 28S ribosomal protein S32
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   2.5   1.5e-05      0.27      25      83 ..     466     524 ..     457     530 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1.5e-05
                            MRP-S32  25 htkPlplleneeetseqvlkeekkleeklkkkkkepvreeLskltfttkhrWyprardk 83 
                                        h++ l + ++e+  ++  +k+++++++++++k++  +r  L+ + +ttkh  y ++  +
  gene1691|gene1691|rna1691|rna1691 466 HSRSLSTKKSENIFNSCHIKSSSSFKATKRRKSQRKKRILLESVSYTTKHMMYHQSNVR 524
                                        7777775555556666668888999999999999*******************998766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (591 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1501  (0.0837191); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.23s 00:00:00.81 Elapsed: 00:00:00.43
# Mc/sec: 4170.12
//
Query:       gene1692|gene1692|rna1692|rna1692  [L=38]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.052   13.0   0.1      0.053   13.0   0.1    1.0  1  ASFV_360  African swine fever virus multigene family 360 prot


Domain annotation for each model (and alignments):
>> ASFV_360  African swine fever virus multigene family 360 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   2.9e-06     0.053     171     196 ..       5      30 ..       2      36 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.9e-06
                           ASFV_360 171 amltsvknfnienlffcidlGadafe 196
                                         ml++++    +nlf+cid+ a ++ 
  gene1692|gene1692|rna1692|rna1692   5 GMLITLMGRFYNNLFVCIDFLATVIM 30 
                                        59*****************9998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (38 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       347  (0.0193541); expected 358.6 (0.02)
Passed bias filter:                      233  (0.0129957); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.42
# Mc/sec: 273.32
//
Query:       gene1693|gene1693|rna1693|rna1693  [L=358]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (358 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       843  (0.0470188); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 2538.44
//
Query:       gene1694|gene1694|rna1694|rna1694  [L=60]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (60 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       207  (0.0115455); expected 358.6 (0.02)
Passed bias filter:                      171  (0.00953762); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 439.39
//
Query:       gene1695|gene1695|rna1695|rna1695  [L=413]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.6e-43  145.7   3.6    2.4e-15   56.1   0.1    4.4  4  RRM_1          RNA recognition motif. (a.k.a. RRM, RBD, or RN
    7.1e-05   22.6   1.2       0.14   12.1   0.0    4.3  4  RRM_occluded   Occluded RNA-recognition motif
  ------ inclusion threshold ------
      0.095   12.7   0.1        2.6    8.0   0.0    2.5  2  LPD16          Large polyvalent protein-associated domain 16
        0.1   12.8   0.4        2.6    8.2   0.0    3.4  4  RRM_7          RNA recognition motif
        1.3    7.9   9.2       0.71    8.7   0.3    2.4  2  DNA_topoisoIV  DNA gyrase/topoisomerase IV, subunit A


Domain annotation for each model (and alignments):
>> RRM_1  RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.1   0.1   6.7e-19   2.4e-15       1      69 [.       3      71 ..       3      72 .. 0.98
   2 !   35.2   0.0   2.3e-12   8.1e-09       1      67 [.     111     175 ..     111     178 .. 0.90
   3 !   17.6   0.1   6.8e-07    0.0024      29      69 ..     279     316 ..     274     317 .. 0.86
   4 !   35.1   0.0   2.4e-12   8.5e-09       1      59 [.     337     395 ..     337     407 .. 0.88

  Alignments for each domain:
  == domain 1  score: 56.1 bits;  conditional E-value: 6.7e-19
                                       EEEESETTTSSHHHHHHHHHTTSCEEEEEEEEETTTSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEE CS
                              RRM_1  1 lfVgnLppdvteeeLkelFskfGpiksiklvrdetgkskgfafVeFeskedAekAlealngkklggrel 69
                                       l+V+nLpp +te+++k++F+++G  +++ l r +   +kg++f+ + ++e A++A+++ +g  +++r++
  gene1695|gene1695|rna1695|rna1695  3 LVVKNLPPKITENDIKAIFREYGTLTDVFLLRRNASLNKGVCFIGYSKEEYAKEAIKQRHGSYIENRKI 71
                                       79*****************************************************************97 PP

  == domain 2  score: 35.2 bits;  conditional E-value: 2.3e-12
                                        EEEESETTTSSHHHHHHHHHTTSCEEEEEEEEE.TTTSEEEEEEEEESSHHHHHHHHHHHTTEEETTE CS
                              RRM_1   1 lfVgnLppdvteeeLkelFskfGpiksiklvrd.etgkskgfafVeFeskedAekAlealngkklggr 67 
                                        l+++ Lp  v++e++  +Fs+++ ik+i++v d +tg+  g+a+V++++ e+A++A++  ++  l gr
  gene1695|gene1695|rna1695|rna1695 111 LYLTKLPVIVSKEDIVNYFSDCN-IKNIEMVLDeKTGNFYGHAIVTMDDIESAKRAIR--QKDVLLGR 175
                                        7999******************8.56********************************..55555555 PP

  == domain 3  score: 17.6 bits;  conditional E-value: 6.8e-07
                                        EEEEETTTSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEE CS
                              RRM_1  29 klvrdetgkskgfafVeFeskedAekAlealngkklggrel 69 
                                        ++      +sk+ a  eF s+edA+k  ++l+ k ++++ +
  gene1695|gene1695|rna1695|rna1695 279 NVKV---APSKCLALLEFRSEEDAKKVYDELQYKRVKDKAI 316
                                        4444...479***************************9988 PP

  == domain 4  score: 35.1 bits;  conditional E-value: 2.4e-12
                                        EEEESETTTSSHHHHHHHHHTTSCEEEEEEEEETTTSEEEEEEEEESSHHHHHHHHHHH CS
                              RRM_1   1 lfVgnLppdvteeeLkelFskfGpiksiklvrdetgkskgfafVeFeskedAekAleal 59 
                                        l+++n+p+ +++ee+k+++    + k+i+l+++++g +kg++fV+ +s+edA+   + +
  gene1695|gene1695|rna1695|rna1695 337 LIIKNVPFQANKEEIKRILTTQVKLKDIRLPKKRDGMHKGYCFVTLNSPEDAKIVYQYF 395
                                        68**************************************************9877755 PP

>> RRM_occluded  Occluded RNA-recognition motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.0   3.8e-05      0.14       6      70 ..       5      73 ..       2      82 .. 0.81
   2 ?    2.1   0.0     0.048   1.7e+02       2      51 ..     109     162 ..     108     168 .. 0.75
   3 ?    1.0   0.0      0.11   3.8e+02      32      67 ..     280     315 ..     247     318 .. 0.80
   4 ?    2.2   0.0     0.045   1.6e+02       6      37 ..     339     369 ..     335     388 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.8e-05
                       RRM_occluded  6 llplsDtvnkariralveekegeikkivLv.....pdheGAivefkdekiagkasLaLdgsefegkklrc 70
                                       + +l+ +++++ i+a++ e+ g +++++L       +++ +++ +++e+ a  a+ + +gs +e++k+ +
  gene1695|gene1695|rna1695|rna1695  5 VKNLPPKITENDIKAIFREY-GTLTDVFLLrrnasLNKGVCFIGYSKEEYAKEAIKQRHGSYIENRKIIV 73
                                       5699****************.******9972222135566999999999999999999999999999865 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.048
                       RRM_occluded   2 rtisllplsDtvnkariralveekegeikkivLvpdheG......Aivefkdekia 51 
                                        +++ l  l+  v+k+ i + +++   +ik+i +v d +       Aiv ++d ++a
  gene1695|gene1695|rna1695|rna1695 109 KSLYLTKLPVIVSKEDIVNYFSDC--NIKNIEMVLDEKTgnfyghAIVTMDDIESA 162
                                        5788899999999**999999999..999999999875323333477777776666 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.11
                       RRM_occluded  32 ivLvpdheGAivefkdekiagkasLaLdgsefegkk 67 
                                        + + p++  A++ef++e++a k+  +L+ ++ ++k 
  gene1695|gene1695|rna1695|rna1695 280 VKVAPSKCLALLEFRSEEDAKKVYDELQYKRVKDKA 315
                                        556677778999******999987777666666655 PP

  == domain 4  score: 2.2 bits;  conditional E-value: 0.045
                       RRM_occluded   6 llplsDtvnkariralveekegeikkivLvpd 37 
                                        + +++ + nk++i+++++++  ++k+i L  +
  gene1695|gene1695|rna1695|rna1695 339 IKNVPFQANKEEIKRILTTQ-VKLKDIRLPKK 369
                                        55778889************.99999988655 PP

>> LPD16  Large polyvalent protein-associated domain 16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.0   0.00073       2.6      24      68 ..      47      92 ..      44     104 .. 0.91
   2 ?    1.6   0.0     0.075   2.7e+02      41      72 ..     191     222 ..     179     229 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00073
                              LPD16 24 GydytlYdkd.yreldgGqldnpdltieeaadeiladedlkgkkae 68
                                       Gy  + Y k+ +++  g++++n ++++e ++d+ l+ +++++kk++
  gene1695|gene1695|rna1695|rna1695 47 GYSKEEYAKEaIKQRHGSYIENRKIIVEMVRDDKLKRLKMELKKIG 92
                                       899999*******************************999888765 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.075
                              LPD16  41 qldnpdltieeaadeiladedlkgkkaekvdl 72 
                                        +++    ++e++++ i+++e++++k++  +  
  gene1695|gene1695|rna1695|rna1695 191 YYSKLFFNFESVVESICSEEKITKKELLDLKD 222
                                        56666678899*********998887766555 PP

>> RRM_7  RNA recognition motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.0   0.00073       2.6       6      29 ..       5      28 ..       1      60 [. 0.87
   2 ?   -1.6   0.0      0.83     3e+03      48      69 ..     188     209 ..     158     225 .. 0.73
   3 ?   -0.9   0.1       0.5   1.8e+03      70      93 ..     295     318 ..     285     319 .. 0.77
   4 ?   -1.3   0.0       0.7   2.5e+03       3      35 ..     336     369 ..     334     395 .. 0.62

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00073
                              RRM_7  6 vGGlPiDiteeelkatfkefgkvl 29
                                       v  lP+ ite+++ka f+e+g+++
  gene1695|gene1695|rna1695|rna1695  5 VKNLPPKITENDIKAIFREYGTLT 28
                                       6679*****************875 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.83
                              RRM_7  48 aakgyvflvfedeksvkaLlea 69 
                                         ++ y+ l f+ e+ v+++ ++
  gene1695|gene1695|rna1695|rna1695 188 KKEYYSKLFFNFESVVESICSE 209
                                        3556778888888888877654 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 0.5
                              RRM_7  70 cteeeeelylklssrrlkskevqi 93 
                                        ++e+ +++y +l+ +r+k+k++ +
  gene1695|gene1695|rna1695|rna1695 295 SEEDAKKVYDELQYKRVKDKAIYV 318
                                        45666999*9********999865 PP

  == domain 4  score: -1.3 bits;  conditional E-value: 0.7
                              RRM_7   3 kvFvGGlPiDiteeelkatfkefgkvl.vdwPkk 35 
                                        k+ +  +P   ++ee+k+ + + +k++ +  Pkk
  gene1695|gene1695|rna1695|rna1695 336 KLIIKNVPFQANKEEIKRILTTQVKLKdIRLPKK 369
                                        5666667777777777777766666533555555 PP

>> DNA_topoisoIV  DNA gyrase/topoisomerase IV, subunit A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   3.5     0.018        66     202     276 ..      92     167 ..      54     280 .. 0.63
   2 ?    8.7   0.3    0.0002      0.71     211     274 ..     329     391 ..     305     404 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.018
                      DNA_topoisoIV 202 grGkikvrakveie.e.ktivitElPigvntskliekieelv.kkkkikisdirde.sdr.gvrivielkrgasee 272
                                        g G+   +++v++e + k++++t lP+ v+++++++  +++  k+  i+   + de + +   +  +++++ +s++
  gene1695|gene1695|rna1695|rna1695  92 GSGSNPEEEDVSVEvKsKSLYLTKLPVIVSKEDIVNYFSDCNiKN--IE--MVLDEkTGNfYGHAIVTMDDIESAK 163
                                        445555666666666559*****************9999998333..44..6666657776666666777644444 PP

                      DNA_topoisoIV 273 kvle 276
                                        + ++
  gene1695|gene1695|rna1695|rna1695 164 RAIR 167
                                        4433 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0002
                      DNA_topoisoIV 211 kveie.ektivitElPigvntskliekieelvkkkkikisdirdesdrgvrivielkrgaseekv 274
                                        k e e +++++i+++P++ n++++++ ++  vk k i++ + rd  ++g  +v +l++ ++++ v
  gene1695|gene1695|rna1695|rna1695 329 K-ELEfTNKLIIKNVPFQANKEEIKRILTTQVKLKDIRLPKKRDGMHKGYCFV-TLNSPEDAKIV 391
                                        2.4443599***********************999999999999999988875.34444455555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (413 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1021  (0.0569468); expected 358.6 (0.02)
Passed bias filter:                      523  (0.0291706); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.43
# Mc/sec: 2857.78
//
Query:       gene1696|gene1696|rna1696|rna1696  [L=163]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.9e-20   71.1   0.6    8.3e-20   70.4   0.6    1.4  1  Homeodomain  Homeodomain
     0.0016   18.3   0.4      0.015   15.2   0.0    2.4  2  Homeobox_KN  Homeobox KN domain
  ------ inclusion threshold ------
      0.036   14.2   0.7      0.079   13.1   0.1    1.8  2  DUF1510      Domain of unknown function (DUF1510)


Domain annotation for each model (and alignments):
>> Homeodomain  Homeodomain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.4   0.6   1.4e-23   8.3e-20       1      56 [.      37      92 ..      37      93 .. 0.98

  Alignments for each domain:
  == domain 1  score: 70.4 bits;  conditional E-value: 1.4e-23
                                       ST-SSSS-HHHHHHHHHHHHHSSS-SHHHHHHHHHHHTS-HHHHHHHHHHHHHHHH CS
                        Homeodomain  1 rrkRttftkeqleeLeklFeenrypsaeereeLAkklgLeerqVkvWFqNrRakek 56
                                       +r+Rt +t+eql++Le+ ++ n++ps+e +e  A+k+g++ ++V++WFqNrRak+k
  gene1696|gene1696|rna1696|rna1696 37 KRRRTKLTEEQLNILEESYRINHHPSSEIKEAVAAKIGIPIKNVQIWFQNRRAKDK 92
                                       79****************************************************99 PP

>> Homeobox_KN  Homeobox KN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.1      0.12   7.4e+02      21      31 ..      39      49 ..      37      50 .. 0.88
   2 !   15.2   0.0   2.5e-06     0.015      11      39 ..      61      89 ..      57      90 .. 0.95

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.12
                        Homeobox_KN 21 keTglsvkqit 31
                                       ++T+l+ +q++
  gene1696|gene1696|rna1696|rna1696 39 RRTKLTEEQLN 49
                                       689******97 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 2.5e-06
                        Homeobox_KN 11 PseedKeeLlkeTglsvkqitnWFINaRr 39
                                       Ps e Ke  +++ g+ +k ++ WF N R+
  gene1696|gene1696|rna1696|rna1696 61 PSSEIKEAVAAKIGIPIKNVQIWFQNRRA 89
                                       9*************************996 PP

>> DUF1510  Domain of unknown function (DUF1510)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   1.3e-05     0.079      13      67 ..      47     101 ..      35     122 .. 0.75
   2 ?   -1.0   0.1      0.34   2.1e+03      16      29 ..     130     143 ..     120     154 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.3e-05
                            DUF1510  13 qtgehtssydkgsvDwnEmekavskatglsednmivwwlgnggspqkaigtvssk 67 
                                        q +  ++sy  ++   +E+++av++ +g++ +n+++w+ +++ ++++ +  + ++
  gene1696|gene1696|rna1696|rna1696  47 QLNILEESYRINHHPSSEIKEAVAAKIGIPIKNVQIWFQNRRAKDKSIKEHIIAE 101
                                        44444788999999999*********************99998877755555433 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.34
                            DUF1510  16 ehtssydkgsvDwn 29 
                                        +h ++y+++  D++
  gene1696|gene1696|rna1696|rna1696 130 THHHDYNSSARDYS 143
                                        57788888888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1162  (0.0648112); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1214.76
//
Query:       gene1697|gene1697|rna1697|rna1697  [L=790]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.5e-48  162.8   1.0    3.7e-38  131.2   0.1    3.0  3  SNF2_N          SNF2 family N-terminal domain
    1.2e-19   70.6   1.4    1.1e-18   67.6   0.0    2.9  3  Helicase_C      Helicase conserved C-terminal domain
    6.2e-07   29.6   0.0    6.2e-07   29.6   0.0    2.3  3  ResIII          Type III restriction enzyme, res subunit
    8.2e-05   22.4   5.5    8.2e-05   22.4   5.5    2.3  1  zf-C3HC4_3      Zinc finger, C3HC4 type (RING finger)
    0.00034   19.9   0.1    0.00077   18.8   0.1    1.6  1  ERCC3_RAD25_C   ERCC3/RAD25/XPB C-terminal helicase
     0.0012   18.8   8.1     0.0012   18.8   8.1    2.7  1  zf-RING_5       zinc-RING finger domain
     0.0055   16.5   6.1     0.0055   16.5   6.1    2.4  2  zf-C3HC4_2      Zinc finger, C3HC4 type (RING finger)
     0.0095   15.9   2.5     0.0095   15.9   2.5    2.7  2  zf-RING_UBOX    RING-type zinc-finger
  ------ inclusion threshold ------
       0.16   12.0   4.7       0.25   11.3   1.5    2.7  2  Cytochrome_C7   Cytochrome c7 and related cytochrome c
       0.61   10.1   4.6        1.7    8.7   0.9    2.6  2  zf-C2HC5        Putative zinc finger motif, C2HC5-type
       0.79    9.5   4.4       0.46   10.3   0.1    2.7  3  Paired_CXXCH_1  Doubled CXXCH motif (Paired_CXXCH_1)
       0.85    9.4   5.6       0.11   12.2   0.6    2.3  2  zf-C2H2_10      C2H2 zinc-finger
        7.6    6.5  16.9      0.018   14.9   6.3    2.3  1  zf-C3HC4        Zinc finger, C3HC4 type (RING finger)


Domain annotation for each model (and alignments):
>> SNF2_N  SNF2 family N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0     0.099   1.4e+02       1      15 [.     110     124 ..     110     126 .. 0.89
   2 !  131.2   0.1   2.7e-41   3.7e-38      51     238 ..     122     314 ..     118     320 .. 0.83
   3 !   28.8   0.0   3.6e-10   4.9e-07     229     349 ..     335     456 ..     334     457 .. 0.77

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.099
                                        HHHHHHHHH...... CS
                                        xxxxxxxxxxxxxxx RF
                             SNF2_N   1 yQkeavkwmlkReqn 15 
                                        +Qk+++ wm   eq+
  gene1697|gene1697|rna1697|rna1697 110 HQKRGLDWMISCEQS 124
                                        9********998887 PP

  == domain 2  score: 131.2 bits;  conditional E-value: 2.7e-41
                                        HHHTT--EEE---TTS--HHHHHHHHH...HHTTTS---.......S-EEEE--HHHHHHHHHHHHHH-TTS-EEE CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SNF2_N  51 akqsvrGGiLaDemGLGKTvqvlalilaqrakeekdkekkrkdtlagptLivvPaslldqWeneierhvsssalrv 126
                                         +++v+GGiLaDemGLGKT+qvl+lil+              +++ +  L+++P   l+qW++ei +h+ + ++  
  gene1697|gene1697|rna1697|rna1697 122 EQSPVSGGILADEMGLGKTIQVLSLILT--------------GKMGETNLVIAPVVALNQWKDEIMKHTVGINV-- 181
                                        67899**********************3..............3445567**********************987.. PP

                                        --SSHHHH-----------------EEEE-HHHHHHHT...................................... CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................................xxx RF
                             SNF2_N 127 lvyggqkkmkkkntkvapklladydvvittYdvlsreaelq................................kkr 170
                                         v ++++   k ++        + +v++ +Y ++++   ++                                   
  gene1697|gene1697|rna1697|rna1697 182 -VSQDNQ---KLRN-------DQINVILSSYGKIESIYRRNkkstalgnpekeenensschqhvekneyhddmFLF 246
                                        .566653...2323.......3445555555554433322244455669999999999999999999999998889 PP

                                        TTS-S-S-SEEEES-GGGT--TTSHHHHHHHH---S-EEEE-S--SSS-HHHHHHHHHHH-TTTT--H CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SNF2_N 171 svlkqvewkrvvlDEghtlknstskaaeavskLstsnrwiltGTPiqnsledlygLlkfLreepfgek 238
                                        s++ +++ +rv+lDE+h +k s s++  a+s+L+ ++rw +tGTP+qn ++dly+L+kfL++ep+g++
  gene1697|gene1697|rna1697|rna1697 247 SKIYELHFQRVILDEAHAIKDSRSSTNAAISRLKCNKRWGVTGTPVQNRVSDLYSLIKFLKIEPLGQY 314
                                        9****************************************************************975 PP

  == domain 3  score: 28.8 bits;  conditional E-value: 3.6e-10
                                        HH-TTTT--HH..HHHHHTHHHHH.....HHHHHHHHHHHTT-STTEE---GGGT..--S---EEEEEEEEE--HH CS
                                        xxxxxxxxxxx..xxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxx RF
                             SNF2_N 229 fLreepfgekq..tfdkllqrpie.....aqaekgrsrLlqllqrlmlrrakkdv..eknlPpkteeiiflklskv 295
                                        f  ++ fg+ +  ++++ +++p++     + ++k  + +  + + ++lrr+k ++  e  lP k+  ii+  +sk+
  gene1697|gene1697|rna1697|rna1697 335 FCSCGHFGSLHfgWWNRKITTPVKyfgltSRNKKIFRLIKRITSHFILRRTKIKLekELGLPSKQLCIIRSYFSKE 410
                                        5678889998888************99955555555555666779**********55557**************** PP

                                        HHHHHH....................HHHHHH-HHH-HHHHHHHHHHHHH---X CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SNF2_N 296 erksYnrllevlrkkalakllkrseaalkssskskekilelllelrqacnhpql 349
                                        er +Y+ + ++   ++ a + + +            +i++l+++lr a nhp l
  gene1697|gene1697|rna1697|rna1697 411 ERDFYESIYKKTKLEFNAYIGQCDTSY--------VNIFSLIQKLRMAANHPFL 456
                                        ******555555555555554443222........4499999999999999976 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.1      0.49   6.7e+02      11      59 ..      65     108 ..       6     122 .. 0.68
   2 ?   -3.5   0.1       9.7   1.3e+04      32      56 ..     385     413 ..     361     428 .. 0.57
   3 !   67.6   0.0   8.1e-22   1.1e-18       2     111 .]     619     735 ..     618     735 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.49
                                        HHTTTTSEEEEEESSHHHHHHHHHHHHHTTSTEEEESTTSTHHHHHHHH CS
                         Helicase_C  11 kleeeggkilifvntidrlekvklllekkgikvavlhgelpqnereeil 59 
                                        k+ ee+ ki+ + ++ ++ e  k+++   + kv++++ e p+n r + l
  gene1697|gene1697|rna1697|rna1697  65 KKMEEEAKIYAVHKNLKQSE--KVFR---KKKVVPVNVEVPHNLRTKLL 108
                                        44445555555555555554..5552...34566666666666666665 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 9.7
                                        HHHHHHHT....TSTEEEESTTSTHHHHH CS
                         Helicase_C  32 vklllekk....gikvavlhgelpqnere 56 
                                        +k+ lek+    + + +++ +  +++er+
  gene1697|gene1697|rna1697|rna1697 385 TKIKLEKElglpSKQLCIIRSYFSKEERD 413
                                        23333444445566777777777777776 PP

  == domain 3  score: 67.6 bits;  conditional E-value: 8.1e-22
                                        HHHHHHHHH.....HHTTTTSEEEEEESSHHHHHHHHHHHHHTTSTEEEESTTSTHHHHHHHHHHHH.TTSSS.EE CS
                         Helicase_C   2 kleallell.....kleeeggkilifvntidrlekvklllekkgikvavlhgelpqnereeileqfn.kgesd.vL 70 
                                        k+e+l+ell     + + + +k++if+++++ le++++ le+ g+++++++g++p ++r++++e+f+ + +++ +L
  gene1697|gene1697|rna1697|rna1697 619 KIETLIELLykiqsNARTSSNKSIIFSQFVNFLEMLSWRLERAGFRCVKIYGSMPRSQRKASIESFQnDSNIKiFL 694
                                        7888889988888999999************9987788899*************************85677788** PP

                                        EESGGGTSSSTSTTESEEEESSSSSSHHHHHHHHTTSSSTT CS
                         Helicase_C  71 iatdvaerGidipkvnlVinfdlprnvtsyiqriGRtgRag 111
                                        i+ ++++  ++++++n+V+ +d+++n++   q+++R++R+g
  gene1697|gene1697|rna1697|rna1697 695 ISLKAGGLALNLTEANNVFLMDPWWNPAVEEQAMDRIHRIG 735
                                        ***************************************97 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6   0.0   4.5e-10   6.2e-07       3     169 ..     106     291 ..     104     293 .. 0.81
   2 ?   -2.5   0.0       3.1   4.3e+03      65      84 ..     417     436 ..     407     472 .. 0.70
   3 ?   -3.7   0.5       7.5     1e+04      96     106 ..     536     552 ..     511     584 .. 0.39

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 4.5e-10
                                        EE-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGT CS
                             ResIII   3 elreyQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkfl 78 
                                        +l ++Q++ ++ +++  +      g+++ + G GKT+  ++li   +     e  l+++p  +l +q+++e++k +
  gene1697|gene1697|rna1697|rna1697 106 KLLPHQKRGLDWMISCEQ-SPVSGGILADEMGLGKTIQVLSLILTGKMG---ETNLVIAPVVAL-NQWKDEIMKHT 176
                                        566777777777774433.66668999999************9876663...478999999997.79**9999988 PP

                                        GG....GEEEESSS-B--.......-SEEEEEHHHHHHTH.............................HHHTTT- CS
                             ResIII  79 seaykeigkkvsgdkkkakekdstnkkilvttiqsldadseee.....................eeeseellrdrf 133
                                                ++vs+d++k    ++++++++++++ ++ ++ +++                       e++e+ +d f
  gene1697|gene1697|rna1697|rna1697 177 VG-----INVVSQDNQKL---RNDQINVILSSYGKIESIYRRNkkstalgnpekeenensschqHVEKNEYHDDMF 244
                                        76.....45777777777...7999******999999998777889999999888888777777666666666666 PP

                                        S..........EEEEETGGGTTS..TTTHHHHHT---SEEEEEESS- CS
                             ResIII 134 d..........viiiDEaHrlgak.kswreilekfkeavllglTATp 169
                                        +           +i DEaH ++++ +s ++++  +k +++ g+T+Tp
  gene1697|gene1697|rna1697|rna1697 245 LfskiyelhfqRVILDEAHAIKDSrSSTNAAISRLKCNKRWGVTGTP 291
                                        699********************84466668999************9 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 3.1
                                        HHHHHHHHHGGGGTGG.... CS
                             ResIII  65 slleqtleefkkflseayke 84 
                                        s++++t+ ef+ ++ +++++
  gene1697|gene1697|rna1697|rna1697 417 SIYKKTKLEFNAYIGQCDTS 436
                                        67888888888888777665 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 7.5
                                        -.............-SE CS
                             ResIII  96 a......kekdstnkki 106
                                        +      + +d+t+ ++
  gene1697|gene1697|rna1697|rna1697 536 NnianleNGHDTTTYRL 552
                                        23334322222222222 PP

>> zf-C3HC4_3  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   5.5     6e-08   8.2e-05       3      47 ..     463     506 ..     461     508 .. 0.94

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 6e-08
                                        SB-TTTSSSBS-EEETTEEEEEE-HHHHHHHHHTT-B-TTT--B- CS
                         zf-C3HC4_3   3 eeCviClerprnvvllpCgHlvlCeeCaekllkrkkkCpiCrrpi 47 
                                         +C+ C+e+  + v  +CgH+ +C++ ae +   ++kCp+C+ +i
  gene1697|gene1697|rna1697|rna1697 463 LICSYCHEEVFEPVQSRCGHV-FCKKEAEMYFLDNRKCPVCHLKI 506
                                        68*******************.*********99********9888 PP

>> ERCC3_RAD25_C  ERCC3/RAD25/XPB C-terminal helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.1   5.5e-07   0.00077      58     132 ..     636     716 ..     604     777 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 5.5e-07
                      ERCC3_RAD25_C  58 krgDkiivfsDnvfaLkeyakklkkp.....yiyGetseaerlkilqkfkknpkvntifls.kvgDtsiDlPeanv 127
                                        + ++k i+fs  v  L+ ++ +l+++      iyG++++++r++ +++f+++++++  ++s k g  +++l ean 
  gene1697|gene1697|rna1697|rna1697 636 TSSNKSIIFSQFVNFLEMLSWRLERAgfrcvKIYGSMPRSQRKASIESFQNDSNIKIFLISlKAGGLALNLTEANN 711
                                        3479****************9998753222269***********************99999899**********98 PP

                      ERCC3_RAD25_C 128 liqis 132
                                        +  ++
  gene1697|gene1697|rna1697|rna1697 712 VFLMD 716
                                        76655 PP

>> zf-RING_5  zinc-RING finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   8.1   8.7e-07    0.0012       2      43 ..     465     503 ..     464     503 .. 0.95

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 8.7e-07
                          zf-RING_5   2 CnkCfeklskeekfyltsCgHifCekClkkllekeavCpiCr 43 
                                        C+ C+e++    +++  +CgH+fC+k +  ++  +++Cp+C+
  gene1697|gene1697|rna1697|rna1697 465 CSYCHEEV---FEPVQSRCGHVFCKKEAEMYFLDNRKCPVCH 503
                                        99999999...99*******************9********5 PP

>> zf-C3HC4_2  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.4       1.8   2.5e+03      22      26 ..     315     319 ..     307     326 .. 0.84
   2 !   16.5   6.1     4e-06    0.0055       2      40 .]     465     502 ..     464     502 .. 0.95

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.8
                         zf-C3HC4_2  22 fCqkC 26 
                                        fC+kC
  gene1697|gene1697|rna1697|rna1697 315 FCKKC 319
                                        9**** PP

  == domain 2  score: 16.5 bits;  conditional E-value: 4e-06
                         zf-C3HC4_2   2 CpiCldmlkdpsvvtpCgHvfCqkCilrsLeekneCPlC 40 
                                        C  C ++  +p v   CgHvfC+k    +  ++ +CP+C
  gene1697|gene1697|rna1697|rna1697 465 CSYCHEEVFEP-VQSRCGHVFCKKEAEMYFLDNRKCPVC 502
                                        999**999999.889**************99999***** PP

>> zf-RING_UBOX  RING-type zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   3.0       9.2   1.3e+04      20      35 ..     315     335 ..     314     340 .. 0.58
   2 !   15.9   2.5   6.9e-06    0.0095       1      23 [.     465     487 ..     465     500 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 9.2
                       zf-RING_UBOX  20 FCreCl.....welskslega 35 
                                        FC++C      w ++  ++g 
  gene1697|gene1697|rna1697|rna1697 315 FCKKCEcasfvWLNHGARRGF 335
                                        899885555554445544444 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 6.9e-06
                       zf-RING_UBOX   1 CpIClelftdPlv.lpCGHtFCre 23 
                                        C+ C e+  +P v   CGH+FC++
  gene1697|gene1697|rna1697|rna1697 465 CSYCHEEVFEP-VqSRCGHVFCKK 487
                                        999**8777**.8447******96 PP

>> Cytochrome_C7  Cytochrome c7 and related cytochrome c
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.1      0.61   8.4e+02      51      60 ..     228     237 ..     205     274 .. 0.74
   2 ?   11.3   1.5   0.00018      0.25      12      56 ..     461     505 ..     449     533 .. 0.73

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.61
                      Cytochrome_C7  51 gaCHdgknaf 60 
                                         +CH++ +++
  gene1697|gene1697|rna1697|rna1697 228 SSCHQHVEKN 237
                                        3455555444 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00018
                      Cytochrome_C7  12 tgykCtdCHsklfeskakkk.maemekgkskkaevesltCgaCHdg 56 
                                        ++  C+ CH+++fe  + ++  + + k++++    ++++C  CH +
  gene1697|gene1697|rna1697|rna1697 461 NALICSYCHEEVFEPVQ-SRcGHVFCKKEAEMYFLDNRKCPVCHLK 505
                                        6788********73333.333455666666667777799*****76 PP

>> zf-C2HC5  Putative zinc finger motif, C2HC5-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.1      0.11   1.6e+02      35      48 ..     463     476 ..     455     479 .. 0.75
   2 ?    8.7   0.9    0.0012       1.7      22      43 ..     479     505 ..     474     513 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.11
                           zf-C2HC5  35 kpCsfCgspllsse 48 
                                          Cs+C+++++++ 
  gene1697|gene1697|rna1697|rna1697 463 LICSYCHEEVFEPV 476
                                        37*******99865 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0012
                           zf-C2HC5  22 nCGkiiCakegls.....kpCsfCgsp 43 
                                         CG + C+ke+        +C+ C+ +
  gene1697|gene1697|rna1697|rna1697 479 RCGHVFCKKEAEMyfldnRKCPVCHLK 505
                                        7*********988899999*****865 PP

>> Paired_CXXCH_1  Doubled CXXCH motif (Paired_CXXCH_1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.3       2.6   3.5e+03      10      15 ..     228     233 ..     224     244 .. 0.74
   2 ?   10.3   0.1   0.00033      0.46      18      39 ..     451     471 ..     448     473 .. 0.90
   3 ?   -1.3   0.0       1.3   1.8e+03       6      13 ..     496     503 ..     494     520 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 2.6
                     Paired_CXXCH_1  10 lsCHnp 15 
                                        +sCH+ 
  gene1697|gene1697|rna1697|rna1697 228 SSCHQH 233
                                        578865 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00033
                     Paired_CXXCH_1  18 sdnpkllkkakgaalCysCHde 39 
                                        +++p+ll  +k+a +C  CH+e
  gene1697|gene1697|rna1697|rna1697 451 ANHPFLL-SKKNALICSYCHEE 471
                                        689****.9***********97 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 1.3
                     Paired_CXXCH_1   6 egeClsCH 13 
                                        +++C  CH
  gene1697|gene1697|rna1697|rna1697 496 NRKCPVCH 503
                                        56899999 PP

>> zf-C2H2_10  C2H2 zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.4       3.8   5.2e+03      16      22 ..     278     284 ..     277     284 .. 0.80
   2 ?   12.2   0.6   8.2e-05      0.11       1      11 [.     460     470 ..     460     471 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 3.8
                         zf-C2H2_10  16 RAkCekR 22 
                                        R kC+kR
  gene1697|gene1697|rna1697|rna1697 278 RLKCNKR 284
                                        7799998 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 8.2e-05
                         zf-C2H2_10   1 KnkitCSYChe 11 
                                        Kn  +CSYChe
  gene1697|gene1697|rna1697|rna1697 460 KNALICSYCHE 470
                                        8999******9 PP

>> zf-C3HC4  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   6.3   1.3e-05     0.018       1      41 []     465     502 ..     465     502 .. 0.96

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.3e-05
                                        -TTT-S--SS-E.E-TTS--B-CHHHHHHHHCTSSB--TTT CS
                           zf-C3HC4   1 CpiCleeakepnelleCkHsfCskCirkilksrkkvkCPlC 41 
                                        C+ C ee+ ep+  + C+H fC+k  + +     ++kCP+C
  gene1697|gene1697|rna1697|rna1697 465 CSYCHEEVFEPV-QSRCGHVFCKKEAEMYFL--DNRKCPVC 502
                                        9***********.***********9999999..8999**** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (790 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1036  (0.0577835); expected 358.6 (0.02)
Passed bias filter:                      472  (0.0263261); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.69u 0.32s 00:00:01.01 Elapsed: 00:00:00.48
# Mc/sec: 4928.38
//
Query:       gene1698|gene1698|rna1698|rna1698  [L=34]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (34 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       166  (0.00925874); expected 358.6 (0.02)
Passed bias filter:                      117  (0.00652574); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.25s 00:00:00.59 Elapsed: 00:00:00.42
# Mc/sec: 240.48
//
Query:       gene1699|gene1699|rna1699|rna1699  [L=274]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-16   60.9   0.1    1.9e-16   60.1   0.1    1.4  1  Polysacc_deac_1  Polysaccharide deacetylase


Domain annotation for each model (and alignments):
>> Polysacc_deac_1  Polysaccharide deacetylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.1   0.1   1.1e-20   1.9e-16       4     113 ..      38     151 ..      35     159 .. 0.89

  Alignments for each domain:
  == domain 1  score: 60.1 bits;  conditional E-value: 1.1e-20
                                        TTSTEEEEEEEESSCSCHHHHHHHHHHCT--EEEEE-HHHHCH-..HHHHHHHHHTTEEEEE--SS--EGGGSHHH CS
                    Polysacc_deac_1   4 kgkksvalTfDdgprdntteilpvLkkykvkatffvigglvedy..pdevremaasGveignHtinhsnlkrlsee 77 
                                         +  ++alTfD gp+ +t++il++L++++vkatf+++ +++ ++   + +re +++G+++g       n+ ++ + 
  gene1699|gene1699|rna1699|rna1699  38 VKAGMIALTFDEGPTGYTPAILEMLRDEDVKATFHFTIQNITRGniSEHMREAVEDGHTVGLRVNPTRNYDEMDSG 113
                                        56789**********************************977776799**************************** PP

                                        HHHHHHHHHHHHHHHHHS----EEE-GG..GEE-HHHH CS
                    Polysacc_deac_1  78 evrreierakdalrkalgreprlfryPy..gsasatvl 113
                                        e++++ie+  +a++++++ + +  r+P   g+ +a+v 
  gene1699|gene1699|rna1699|rna1699 114 EIKEDIEQQIKAIQNETETKIKFARAPVdaGETNADVY 151
                                        ***************************72244555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (274 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       846  (0.0471861); expected 358.6 (0.02)
Passed bias filter:                      541  (0.0301746); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 1901.15
//
Query:       gene17|gene17|rna17|rna17  [L=241]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.1e-76  254.0   3.4      9e-76  253.7   3.4    1.1  1  eIF-6     eIF-6 family


Domain annotation for each model (and alignments):
>> eIF-6  eIF-6 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  253.7   3.4     5e-80     9e-76       1     195 [.       4     200 ..       4     202 .. 0.98

  Alignments for each domain:
  == domain 1  score: 253.7 bits;  conditional E-value: 5e-80
                                .E-BTTB--HHHH-EE-SSEEEE-TTS-HHHHHHHHHHHT-EEEE--BTTBS-HHHH-EE-SSEEEEETT--HHHHHHHHHHHH CS
                      eIF-6   1 rlsiegsseiGvfarltnkyalvpegveeefvkaieeeLkvevvettiagsrlvGslvvgNsngllvpstvtdeeleklkeslk 84 
                                r+++egss+iG +a ltnky++v ++ +++f++ ++e+L++++vetti+++++vGsl++gN+ngllvpst+td+el +l++ l+
  gene17|gene17|rna17|rna17   4 RIDFEGSSDIGAYAILTNKYCIVGKSSSRNFYSYFQEHLDIPLVETTINSIKTVGSLCAGNKNGLLVPSTATDQELLHLRNLLP 87 
                                799***********************9999****************************************************** PP

                                ---..EEE--SS--HHHHEEE-SSEEEE-GGGGG.GHHHHHHHHTSEEEE--BTTBS-TTTSEEE-SSEEEE-TT--HHHHHHH CS
                      eIF-6  85 lev..erleekltAlGNvilaNDkvAlvhpdlsketveiiadvLgvevvrgtiagiktvGsaavvtnkgllvhpkateeeleel 166
                                +++  +r++e+l+AlGNvi++ND+vAlvh+d++ e+v+ i++vL v+v+r++++ +++vG++++++n+g+lvhp+++ ee+eel
  gene17|gene17|rna17|rna17  88 ENIkiKRINERLNALGNVIVCNDSVALVHSDVDAESVKNIEEVLMVDVFRHNVGCEPLVGTFSAMNNQGMLVHPRTSVEEIEEL 171
                                66666******************************************************************************* PP

                                HHHHT-SEEE--BTTTBS-GGGTEEE-SS CS
                      eIF-6 167 eellkveveagTvNrGsklvgsglvaNdk 195
                                 +ll v+v agTvN+Gs+++g+g+v+Nd+
  gene17|gene17|rna17|rna17 172 CNLLSVSVVAGTVNKGSSVIGGGMVVNDW 200
                                ****************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       489  (0.0272742); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1625.50
//
Query:       gene170|gene170|rna170|rna170  [L=1131]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1752  (0.0977188); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.73u 0.30s 00:00:01.03 Elapsed: 00:00:00.48
# Mc/sec: 7130.47
//
Query:       gene1700|gene1700|rna1700|rna1700  [L=305]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (305 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       892  (0.0497518); expected 358.6 (0.02)
Passed bias filter:                      555  (0.0309554); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 2248.33
//
Query:       gene1701|gene1701|rna1701|rna1701  [L=235]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.062   14.1   0.8      0.062   14.1   0.8    3.0  4  YMF19     Plant ATP synthase F0


Domain annotation for each model (and alignments):
>> YMF19  Plant ATP synthase F0
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.8   3.5e-06     0.062      15      65 ..       4      53 ..       1      73 [. 0.78
   2 ?   -2.0   0.0      0.36   6.5e+03      54      54 ..      93      93 ..      67     130 .. 0.58
   3 ?   -0.6   0.1      0.14   2.5e+03      67      75 ..     132     140 ..     101     171 .. 0.60
   4 ?   -0.5   0.5      0.12   2.2e+03      15      28 ..     202     215 ..     200     233 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.5e-06
                              YMF19 15 lclfFitlYivllknilpkiarilklrkkllsslssevsklkkeqknlivs 65
                                       ++l F ++Y+ +++++  +  + +kl+++ +s++  e++ l+++++  ++s
  gene1701|gene1701|rna1701|rna1701  4 SFLLFSLFYFTIISSMNTNKTKNVKLKENTSSNKT-EKNALQSDETPIRHS 53
                                       799**************************999966.566666665544444 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.36
                              YMF19 54 k 54
                                       k
  gene1701|gene1701|rna1701|rna1701 93 K 93
                                       1 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.14
                              YMF19  67 dsalanvsl 75 
                                        d+ +++++ 
  gene1701|gene1701|rna1701|rna1701 132 DTHTKRNMS 140
                                        333333322 PP

  == domain 4  score: -0.5 bits;  conditional E-value: 0.12
                              YMF19  15 lclfFitlYivllk 28 
                                        l l+F + Y+++l+
  gene1701|gene1701|rna1701|rna1701 202 LSLIFTVSYVIYLE 215
                                        67999999*98882 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1361  (0.0759105); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1708.99
//
Query:       gene1702|gene1702|rna1702|rna1702  [L=1567]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    9.4e-44  149.0   2.3    1.8e-43  148.1   2.3    1.5  1  DSHCT       DSHCT (NUC185) domain
    7.3e-18   64.9   0.0    3.5e-17   62.7   0.0    2.1  2  DEAD        DEAD/DEAH box helicase
    2.3e-06   27.7   2.0    2.8e-06   27.5   0.0    2.2  2  ResIII      Type III restriction enzyme, res subunit
    0.00014   22.2   0.0    0.00052   20.3   0.0    2.1  1  Helicase_C  Helicase conserved C-terminal domain
  ------ inclusion threshold ------
      0.026   14.8   0.0      0.066   13.5   0.0    1.7  1  AAA_22      AAA domain
        8.6    6.1  18.6        0.4   10.5   0.3    2.5  2  RR_TM4-6    Ryanodine Receptor TM 4-6


Domain annotation for each model (and alignments):
>> DSHCT  DSHCT (NUC185) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  148.1   2.3   5.9e-47   1.8e-43       2     164 .]    1227    1391 ..    1226    1391 .. 0.84

  Alignments for each domain:
  == domain 1  score: 148.1 bits;  conditional E-value: 5.9e-47
                              DSHCT    2 ntvtlkGrvaaeirsedeLlltellfsgvlddlepeelaAllsalvfeekredeeekepkl.seeleealeelk 74  
                                         n++t kGrva+e+++e+ L+ltel+f+g + +l++ e++++ls+lvf e+++ e ++ ++l + +l+e++    
  gene1702|gene1702|rna1702|rna1702 1227 NSITVKGRVACELNTEE-LVLTELIFNGHFLKLSVVEVVSVLSCLVFTEREDAEVSE-QSLrNYKLIEEV---- 1294
                                         899**********9998.******************************996554443.444444444443.... PP

                              DSHCT   75 eiaeriakvs........vesrl.dlglvevvyaWakgasfaellektdldeGdiVRllrrleellrqlakaak 139 
                                            +++ kv+        ve      +l++vv  Wa gasf+++++ t+++eG+iVR+l+rl+e+lrql+ aa+
  gene1702|gene1702|rna1702|rna1702 1295 --VHNVVKVMnqvglnvqVEDFAySNELMDVVRMWAAGASFESVTARTQVFEGSIVRCLKRLDEMLRQLSCAAR 1366
                                         ..3333333333444444666556899*********************************************** PP

                              DSHCT  140 vigneeLkkkaeeaielikRdiVfa 164 
                                         +ign e+++ + e i +ikRdiVf+
  gene1702|gene1702|rna1702|rna1702 1367 AIGNLEMERVFGEGISKIKRDIVFC 1391
                                         ***********************95 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.7   0.0   1.2e-20   3.5e-17       4     171 ..      86     228 ..      84     232 .. 0.82
   2 ?   -1.7   0.0       0.7   2.1e+03      63     105 ..     924     967 ..     889     974 .. 0.69

  Alignments for each domain:
  == domain 1  score: 62.7 bits;  conditional E-value: 1.2e-20
                                        HHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEE CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               DEAD   4 QaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvl 79 
                                        Q+ ++ ++ ++++vlv+a+T+sGKT+++  ++  ++     k++ ++++ +P ++L +q +++lk  ++ ++    
  gene1702|gene1702|rna1702|rna1702  86 QRISCIALERDENVLVCAHTASGKTAIAEYAIHLAL-----KRKQRVVYTSPIKALSNQKYRELKLKFDDVG---- 152
                                        555555566889*****************9999666.....88899******************99999544.... PP

                                        EEETTSSHHHHHHHHHTTCSEEEEEHHHHHHHH..HCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHC CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               DEAD  80 liiggvaardqlskldngvdivvgtpgrlddll..stgklnlsqvrflVlDEadrlldqgfsdfinrilnqlpqit 153
                                        li+g+++       l+ ++ ++v+t++ l ++l  s++   + +++f+++DE++ + d +++  +++++       
  gene1702|gene1702|rna1702|rna1702 153 LITGDST-------LNPKASVLVMTTEILRNMLyrSNEL--VGEIKFVIFDEIHYMTDRERGVVWEECIILS---- 215
                                        5666544.......44456667*********99544444..9*************************77666.... PP

                                        TTSTTTSEEEEEESSBSH CS
                                        xxxxxxxxxxxxxxxxxx RF
                               DEAD 154 cdgklqrqvivlSATlpk 171
                                         +     ++++lSATlp+
  gene1702|gene1702|rna1702|rna1702 216 -R----FNCVFLSATLPN 228
                                        .2....339*******93 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.7
                                        HHHHHHHHTTT.STSEEEEEETTSSHHHHHHHHHTTCSEEEEEH CS
                                        xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               DEAD  63 tlnnlkkfkky.idlrvlliiggvaardqlskldngvdivvgtp 105
                                         +n+++k+k + i+l ++  i + + +   ++l +++ +++gtp
  gene1702|gene1702|rna1702|rna1702 924 LYNRINKMKRKcIKLHEVRAIYDARVKISNKRLGRKYAVLYGTP 967
                                        45666666666666666655555566666666666677777777 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.5   0.0   9.3e-10   2.8e-06      22     169 ..      94     226 ..      45     228 .. 0.83
   2 ?   -4.9   1.4         6   1.8e+04      91     115 ..    1123    1148 ..    1100    1163 .. 0.40

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 9.3e-10
                                        .TTSEEEEEESTTSTHHHHH.HHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG....GEEEESSS-B-- CS
                             ResIII  22 krdkrglikmaTGtGKTlva.aklierllkkgkeekflflvprkslleqtleefkkflseaykeigkkvsgdkkka 96 
                                        +rd+++l+ + T +GKT +a +++  +l++k   ++++   p k+l +q ++e+k  +++      + ++gd+  +
  gene1702|gene1702|rna1702|rna1702  94 ERDENVLVCAHTASGKTAIAeYAIHLALKRK---QRVVYTSPIKALSNQKYRELKLKFDDV-----GLITGDSTLN 161
                                        8999****************55555555554...59******************9999874.....7788888777 PP

                                        .......-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.T...TTHHHHHT---SEEEEEESS- CS
                             ResIII  97 kekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakk...swreilekfkeavllglTATp 169
                                              ++++lv+t++ l + +     ++   l ++++++i+DE H +++ +    w+e++   +++  + l+AT+
  gene1702|gene1702|rna1702|rna1702 162 -----PKASVLVMTTEILRNML-----YRSNELVGEIKFVIFDEIHYMTDRErgvVWEECIIL-SRFNCVFLSATL 226
                                        .....79***************.....9999999****************8677899996544.567778888987 PP

  == domain 2  score: -4.9 bits;  conditional E-value: 6
                                         SS-B--...........-SEEEEEHHHHH CS
                             ResIII   91 gdkkka....kekdstnkkilvttiqsld 115 
                                         ++   +     +++ ++k+i  +++q+ d
  gene1702|gene1702|rna1702|rna1702 1123 EK---NhleiINERMNDKEISRVNVQETD 1148
                                         11...112232233333333333333333 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   1.8e-07   0.00052      11     111 .]     537     652 ..     509     652 .. 0.72

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 1.8e-07
                                        HHTTTTSEEEEEESSHHHHHH.......HHHHHHHT.....TSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESG CS
                         Helicase_C  11 kleeeggkilifvntidrlek.......vklllekk.....gikvavlhgelpqnereeileqfnkgesdvLiatd 74 
                                        + ee+++ +lif +  ++l         ++     +        + ++h+ l    +e i   f  + ++vL at 
  gene1702|gene1702|rna1702|rna1702 537 TAEEKERITLIFNRALETLRAedrtlspIQ-----SmlpllVRGIGIHHSGLLPVLKEIIEILFSLNLVKVLFATE 607
                                        455666667888888885533334433322.....123333667777999999999999999999999******** PP

                                        GGTSSSTSTTESEEEESSSS.......SSH...HHHHHHHTTSSSTT CS
                         Helicase_C  75 vaerGidipkvnlVinfdlp.......rnv...tsyiqriGRtgRag 111
                                          + G+++p +++V +  l        r +    +yiq++GR+gR g
  gene1702|gene1702|rna1702|rna1702 608 TFSIGLNMP-AKCVLFTTLFkfdgekmR-TitsGEYIQMSGRAGRRG 652
                                        ********9.666666555555455552.04559***********75 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   2.2e-05     0.066       7     117 ..      98     216 ..      93     231 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.2e-05
                             AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeakaeeerpevv...fvtlpsst...sskdllrellralglelkaerlsse 76 
                                         ++v++++ +GKT  ++   + + ++      + +vv    +++ s     ++k  + ++  ++g+++ ++ +s  
  gene1702|gene1702|rna1702|rna1702  98 NVLVCAHTASGKTAIAEYAIHLALKR------KQRVVytsPIKALSNQkyrELKLKFDDVGLITGDSTLNPKASVL 167
                                        679*******************9865......66666444333333332223333355566666655555666666 PP

                             AAA_22  77 ellealeqalrarav.....ielliiDEaqhlr...seealeeLrslln 117
                                         + + + +++  r+      i+++i DE+++++   +  ++ee+ +l+ 
  gene1702|gene1702|rna1702|rna1702 168 VMTTEILRNMLYRSNelvgeIKFVIFDEIHYMTdreRGVVWEECIILSR 216
                                        66666666666666678999***********977544999999977765 PP

>> RR_TM4-6  Ryanodine Receptor TM 4-6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4  12.5      0.54   1.6e+03      29     144 ..     329     458 ..     280     489 .. 0.38
   2 ?   10.5   0.3   0.00013       0.4      96     195 ..    1098    1204 ..    1037    1208 .. 0.53

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.54
                                        XXXXX...XXXXXXXXXXXXXXXXXX......XXXXXX....XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                           RR_TM4-6  29 edlaeaageeeeedllsdvfgldlkk......eggqykvva.kkseagLgDlseteaeesptpelkkklaeeeeae 97 
                                        +dl++  ++++ +d+  +v +l++k+      e+g +k    +++++  g +s+ + +e +t              
  gene1702|gene1702|rna1702|rna1702 329 RDLKTRGHDTRGDDTRGEVKNLKTKNpkkygkEKGIKKYNGkNENNDKHGKMSSRTRKEDKT-------------- 390
                                        45555555555555555555555544221221222222221111222222222222222222.............. PP

                                        XXXXXXXXXXXXX.XXXXXXXXXXXXXXXX.............................................. CS
                           RR_TM4-6  98 eekeeeeepeaeaeekadaengekeekeke......................................keeeekes 135
                                                         d++n++k ++e++                                      ke+ +k++
  gene1702|gene1702|rna1702|rna1702 391 -----------------DRKNSKKGKNENStcssddrlaggddkrsksgktrddpsgskrtfnrgrgrKEDGRKKR 449
                                        .................11111111111111111111121111111112112222222212222233222222222 PP

                                        ..XXXXXXX CS
                           RR_TM4-6 136 eeeeeekkk 144
                                        ++e  +kk 
  gene1702|gene1702|rna1702|rna1702 450 TNERSTKKV 458
                                        222222222 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00013
                                         XXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXX...................XXXXXXXXXXXXXXXXXXXXXXX CS
                           RR_TM4-6   96 aeeekeeeeepeaeaeekadaengekeekeke.........keeeekeseeeeeekkkkkkakskkkeeaeaee 160 
                                          e+e+  e+e+ +e+e++++ +n+e++++            ke ++ + +e + +++ + ++++++++++++++
  gene1702|gene1702|rna1702|rna1702 1098 GEDERIGEDEKDEEDERNEKGSNKEEKNH--LeiinermndKEISRVNVQETDRSNSTEDTSSAAEHTSPSSAG 1169
                                         33333333333333322222222222222..1234333322222223333333333344444444555555555 PP

                                         XX-HH.HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           RR_TM4-6  161 sellk.klevyqtkllnylARNFYnlrflALfvaFa 195 
                                         ++l      v ++k+l+yl  N Yn +   Lf+a  
  gene1702|gene1702|rna1702|rna1702 1170 TALQGtASPVLKRKILKYLN-NVYNAKNGDLFLASR 1204
                                         55555344588999999996.999999988888855 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1567 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1361  (0.0759105); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 1.09u 0.34s 00:00:01.43 Elapsed: 00:00:00.52
# Mc/sec: 8992.09
//
Query:       gene1703|gene1703|rna1703|rna1703  [L=272]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-39  136.4   0.6    1.6e-39  136.2   0.6    1.0  1  ATP_bind_1       Conserved hypothetical ATP binding protein
    1.6e-05   24.8   0.1    0.00019   21.3   0.0    2.1  2  CLP1_P           mRNA cleavage and polyadenylation factor CLP
    0.00053   19.5   0.0    0.00093   18.8   0.0    1.3  1  AAA_7            P-loop containing dynein motor region
    0.00084   19.1   0.0     0.0013   18.5   0.0    1.3  1  AAA_24           AAA domain
     0.0015   18.8   0.0     0.0026   18.1   0.0    1.3  1  AAA_22           AAA domain
     0.0028   17.6   1.2     0.0078   16.2   0.1    2.1  2  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
     0.0043   17.1   0.0     0.0092   16.0   0.0    1.5  1  AAA_14           AAA domain
     0.0063   16.6   0.0     0.0073   16.4   0.0    1.4  1  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
      0.007   16.8   0.0      0.011   16.2   0.0    1.3  1  AAA_16           AAA ATPase domain
     0.0073   16.0   0.0      0.012   15.3   0.0    1.2  1  SRP54            SRP54-type protein, GTPase domain
     0.0081   16.1   0.0      0.013   15.4   0.0    1.3  1  AAA_31           AAA domain
     0.0087   15.3   0.0      0.011   15.0   0.0    1.1  1  DUF2075          Uncharacterized conserved protein (DUF2075)
  ------ inclusion threshold ------
       0.01   16.2   0.0      0.021   15.2   0.0    1.6  1  RNA_helicase     RNA helicase
      0.014   15.9   0.1      0.032   14.8   0.0    1.6  2  AAA_18           AAA domain
      0.034   13.7   0.0      0.061   12.9   0.0    1.4  1  AAA_25           AAA domain
      0.035   14.0   0.0      0.053   13.4   0.0    1.3  1  NACHT            NACHT domain
      0.041   14.2   0.0      0.047   14.0   0.0    1.4  1  AAA_19           AAA domain
      0.061   13.2   0.1       0.23   11.4   0.0    2.0  2  RsgA_GTPase      RsgA GTPase
      0.068   12.9   0.0        0.1   12.3   0.0    1.3  1  Viral_helicase1  Viral (Superfamily 1) RNA helicase
      0.068   13.7   0.0       0.11   13.0   0.0    1.3  1  ABC_tran         ABC transporter
       0.08   13.1   0.0        0.1   12.7   0.0    1.3  1  AAA_33           AAA domain
      0.094   12.4   0.0       0.28   10.9   0.0    1.7  2  Sigma54_activat  Sigma-54 interaction domain
      0.097   12.4   0.0       0.18   11.5   0.0    1.3  1  PRK              Phosphoribulokinase / Uridine kinase family
       0.11   12.3   0.0       0.31   10.8   0.0    1.8  2  PduV-EutP        Ethanolamine utilisation - propanediol utili
       0.12   12.4   0.0       0.99    9.5   0.0    2.1  1  MMR_HSR1         50S ribosome-binding GTPase
       0.16   11.8   0.0       0.43   10.5   0.0    1.9  1  NTPase_1         NTPase


Domain annotation for each model (and alignments):
>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  136.2   0.6   2.2e-42   1.6e-39       1     239 [.      32     258 ..      32     260 .. 0.89

  Alignments for each domain:
  == domain 1  score: 136.2 bits;  conditional E-value: 2.2e-42
                         ATP_bind_1   1 vvGpaGsGKttfvgalseilelrgrsvavvNLDPAaeelpYeaavdirelitledvmedlglgpngalvvaleflr 76 
                                        v+G aG+GKttf+ +l+++l++ + ++ ++NLDP  +  +   + di  +it+++vme ++lgpn ++  a+ +++
  gene1703|gene1703|rna1703|rna1703  32 VIGSAGAGKTTFCLNLYDHLSTHNHNPTLINLDPSQQ-SNNTYHHDICTYITTQNVMEATDLGPNSSILKAFATMA 106
                                        89********************************987.5667889******************************* PP

                         ATP_bind_1  77 esldwldeelekeeddyllfDtPGQielfthseslakiveeLesefalvvvyLvDsqrltdptkfisgllsalsam 152
                                        ++l++++ e       y+++D+PGQie+f hses  k +  ++ +++ v+v+++D    +++  f+ + +s +  +
  gene1703|gene1703|rna1703|rna1703 107 DHLENVEIEG------YCVVDMPGQIEIFVHSESFLKTIAYFKGQGRCVIVNVFDFINFKSVERFLGNGVSMCMCV 176
                                        ***8776666......************************************************************ PP

                         ATP_bind_1 153 lrlelPhvvvlnkfDllkeklekeleffedvealslllekeeekykklaeaiaelleefalvlrflplssekeesi 228
                                         r+elP+++ ++k+Dl+ ++++ e +  ed e+l   + +    + k  +++ ++le  +   +f+ + + +ee++
  gene1703|gene1703|rna1703|rna1703 177 GRVELPFINLVSKCDLFLKDENDEDNLSEDDEDLCFDQLL---LRTKFHKDLYQFLEHNSVL-NFTRI-RYTEEGM 247
                                        ****************997765565666666555553333...3567888999999988877.88887.5689999 PP

                         ATP_bind_1 229 edllslideal 239
                                        +d++ ++d+ l
  gene1703|gene1703|rna1703|rna1703 248 TDVIYMLDSVL 258
                                        99999999876 PP

>> CLP1_P  mRNA cleavage and polyadenylation factor CLP1 P-loop
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0   2.8e-07   0.00019       1      36 [.      34      69 ..      34      86 .. 0.95
   2 ?    1.0   0.0      0.44   3.1e+02      80     130 ..      98     143 ..      89     153 .. 0.72

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 2.8e-07
                             CLP1_P  1 GpkdsGKSTlarlLlNyalrkgrkpvyvDlDvGqse 36
                                       G+  +GK+T++ +L + +  ++++p++++lD+ q++
  gene1703|gene1703|rna1703|rna1703 34 GSAGAGKTTFCLNLYDHLSTHNHNPTLINLDPSQQS 69
                                       78899****************************986 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.44
                             CLP1_P  80 ylalvkelareveekleenkkakasgliIntpGwvkgl.gaelllelieale 130
                                        +l++++ +a+++e ++e      ++ ++++ pG ++ +   e  l++i++++
  gene1703|gene1703|rna1703|rna1703  98 ILKAFATMADHLE-NVEI-----EGYCVVDMPGQIEIFvHSESFLKTIAYFK 143
                                        5666777777777.3333.....6899******9997734577777777776 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   1.3e-06   0.00093      34      79 ..      28      73 ..      16      77 .. 0.92

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.3e-06
                              AAA_7 34 kpvllvGptGtGKtviikdllkkldkekylsltinfsaqtsanqlq 79
                                       + vl++G++G GKt+ + +l ++l++ +++++ in+  + ++n++ 
  gene1703|gene1703|rna1703|rna1703 28 YTVLVIGSAGAGKTTFCLNLYDHLSTHNHNPTLINLDPSQQSNNTY 73
                                       579**********************************999999985 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   1.9e-06    0.0013       3      54 ..      28      88 ..      27     117 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.9e-06
                             AAA_24  3 lkiliyGpsgiGKTtlakel.......gpkplfidtekGlksldadkfpdie..swedfld 54
                                       + +l++G++g+GKTt++++l         +p +i+++ + +s +  + + ++  + +++++
  gene1703|gene1703|rna1703|rna1703 28 YTVLVIGSAGAGKTTFCLNLydhlsthNHNPTLINLDPSQQSNNTYHHDICTyiTTQNVME 88
                                       6799*********************999999999999988777776666555555555555 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   3.7e-06    0.0026       8      69 ..      30      86 ..      27     121 .. 0.66

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 3.7e-06
                             AAA_22  8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelk 69
                                       ++v+G +G+GKTt + +l + l  ++    ++p+++  ++++++   +  ++++  ++ ++ 
  gene1703|gene1703|rna1703|rna1703 30 VLVIGSAGAGKTTFCLNLYDHLSTHN----HNPTLINLDPSQQS-NNTYHHDICTYITTQNV 86
                                       689*******************7664....35555555555444.55555666555554443 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1   1.1e-05    0.0078      18      73 ..      25      79 ..       8     143 .. 0.77
   2 ?   -0.3   0.1       1.5     1e+03      67      83 ..     221     237 ..     214     253 .. 0.67

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.1e-05
                                       H.TEEEEEEESTTSSHHHHHHHHHHHTT------TTTTSEEEEEE..SSEEEEE-TT CS
                               TsaE 18 l.gdvilLeGdLGaGKTtlvrglakalgveevkSPTFtlveeYelekeglyHfDlYR 73
                                       l   ++l  G  GaGKTt++ +l  +l   + + PT   + + ++ +++ yH D+  
  gene1703|gene1703|rna1703|rna1703 25 LpMYTVLVIGSAGAGKTTFCLNLYDHLST-HNHNPTLINLDPSQQ-SNNTYHHDICT 79
                                       234459999******************65.678899888888755.45599999754 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.5
                                        EEEE-TT-SSTHHHHHC CS
                               TsaE  67 yHfDlYRledeeeleel 83 
                                        +H DlY++ +++++ ++
  gene1703|gene1703|rna1703|rna1703 221 FHKDLYQFLEHNSVLNF 237
                                        799***98665555444 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   1.3e-05    0.0092       5      60 ..      30      86 ..      27      99 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.3e-05
                             AAA_14  5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelilek.l 60
                                       +++ G   +GKTt++ +l+++l +++ +   inld  ++++++  +++ ++i  + +
  gene1703|gene1703|rna1703|rna1703 30 VLVIGSAGAGKTTFCLNLYDHLSTHNHNPTLINLDPSQQSNNTYHHDICTYITTQnV 86
                                       7899999************9988999*********9999887766688999888744 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   1.1e-05    0.0073       5      45 ..      33      81 ..      29     262 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.1e-05
                                       ESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEE..SSCCCCH......H CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxx......x RF
                               CbiA  5 stkGGvGKTtlaanLaralarrglrVllvDaDp..qannlai......l 45
                                        ++ G+GKTt+++nL   l+ ++++  l+ +Dp  q+nn+ +      +
  gene1703|gene1703|rna1703|rna1703 33 IGSAGAGKTTFCLNLYDHLSTHNHNPTLINLDPsqQSNNTYHhdictyI 81
                                       5788****************************95455666544444332 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   1.5e-05     0.011      26     115 ..      29     126 ..      18     155 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.5e-05
                             AAA_16  26 lvllsGesGvGKsslvrellralekd..ggiflrgkcdqlesaipysa.laqalareellrqlldeaesaeleawr 98 
                                         vl++G +G GK++    l+++l+++  +  +++ +  q +s+ +y + + +++++  ++++ +  ++s+ l a++
  gene1703|gene1703|rna1703|rna1703  29 TVLVIGSAGAGKTTFCLNLYDHLSTHnhNPTLINLDPSQ-QSNNTYHHdICTYITTQNVMEATDLGPNSSILKAFA 103
                                        69**********************994334445555555.588899888999999999999988888777776666 PP

                             AAA_16  99 ekleeala.......avpelagae 115
                                        +  +  l+       +v +++g++
  gene1703|gene1703|rna1703|rna1703 104 TMADH-LEnveiegyCVVDMPGQI 126
                                        63333.333555555555555555 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   1.7e-05     0.012       3      38 ..      29      64 ..      27      70 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.7e-05
                                       EEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEES CS
                              SRP54  3 villvGlqGaGKTttlaKLaallkkegkkvllvaaD 38
                                        +l++G  GaGKTt +  L ++l+++++++ l+ +D
  gene1703|gene1703|rna1703|rna1703 29 TVLVIGSAGAGKTTFCLNLYDHLSTHNHNPTLINLD 64
                                       5899****************************9998 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   1.9e-05     0.013      12      63 ..      37      90 ..      31     141 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.9e-05
                             AAA_31 12 GvGKTTtsvnlaaalaklgkkvLlvDlDp..Qanattglgiekneiektlyevl 63
                                       G GKTT ++nl   l++ ++   l++lDp  Q+n t + +i +  ++++++e+ 
  gene1703|gene1703|rna1703|rna1703 37 GAGKTTFCLNLYDHLSTHNHNPTLINLDPsqQSNNTYHHDICTYITTQNVMEAT 90
                                       99**************************87789999988887777777777763 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   1.6e-05     0.011       3      55 ..      29      81 ..      27     118 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.6e-05
                            DUF2075  3 vvlVtGvaGtGKtvvllnllaeleddeeertavylsvNhplvlvlrealakke 55
                                        vlV G aG+GKt   lnl   l++++++ t + l  +++ ++++ +++    
  gene1703|gene1703|rna1703|rna1703 29 TVLVIGSAGAGKTTFCLNLYDHLSTHNHNPTLINLDPSQQSNNTYHHDICTYI 81
                                       589********************999999999999999999999999997655 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.0   3.1e-05     0.021       1      54 [.      30      80 ..      30     113 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 3.1e-05
                       RNA_helicase  1 iwlyGpsgeGKStlakeLakallkklklkkkdsvysrnpeddfwdgYtgqevvv 54
                                       +++ G++g GK+t++ +L ++l+++    ++++++   p+++  + Y++  ++ 
  gene1703|gene1703|rna1703|rna1703 30 VLVIGSAGAGKTTFCLNLYDHLSTHN---HNPTLINLDPSQQSNNTYHHDICTY 80
                                       5789*******************777...4444555666666666665443333 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   4.6e-05     0.032       1      42 [.      30      70 ..      30     122 .. 0.61
   2 ?   -2.1   0.0       7.8   5.4e+03      42      42 ..     213     213 ..     185     265 .. 0.53

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 4.6e-05
                             AAA_18  1 IlltGtpGvGKttlakeLskrlgfgvnlrdvakenglllevd 42
                                       +l+ G +G+GKtt++ +L ++l +  n++ ++ + +++   +
  gene1703|gene1703|rna1703|rna1703 30 VLVIGSAGAGKTTFCLNLYDHL-STHNHNPTLINLDPSQQSN 70
                                       789***************9997.3333333333333333333 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 7.8
                             AAA_18  42 d 42 
                                        d
  gene1703|gene1703|rna1703|rna1703 213 D 213
                                        1 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   8.9e-05     0.061      26      59 ..      21      53 ..       8      69 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 8.9e-05
                             AAA_25 26 vkgllpagelallaGapgtGKttlaldlalavat 59
                                       ++  lp   ++l++G  g+GKtt++l+l  +++t
  gene1703|gene1703|rna1703|rna1703 21 IQKTLP-MYTVLVIGSAGAGKTTFCLNLYDHLST 53
                                       556665.7899*****************988876 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   7.6e-05     0.053       2      30 ..      29      57 ..      28     103 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 7.6e-05
                                       CEEEEC-TTTCHHHHHHHHHHHHCTS-SC CS
                              NACHT  2 lvilqGeaGsGKTtLlqklalawaegklp 30
                                       +v++ G aG GKTt+   l + + + + +
  gene1703|gene1703|rna1703|rna1703 29 TVLVIGSAGAGKTTFCLNLYDHLSTHNHN 57
                                       89***************999999887744 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   6.8e-05     0.047       7      41 ..      24      58 ..      18     213 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 6.8e-05
                             AAA_19  7 alkekvllvtaGpGtGKTrvlkhivallvelggvk 41
                                       +l+  ++lv++ +G GKT+       +l   ++ +
  gene1703|gene1703|rna1703|rna1703 24 TLPMYTVLVIGSAGAGKTTFCLNLYDHLSTHNHNP 58
                                       778889***************99999999887653 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00033      0.23      89     123 ..      17      56 ..       6     129 .. 0.68
   2 ?   -1.4   0.0       2.7   1.9e+03      48      82 ..     182     217 ..     148     234 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00033
                                        THHHHHHHCTTSEEEEECSTTSSHHHHHHHHCTT.....- CS
                        RsgA_GTPase  89 gleelkellkdktsvlvGqSGvGKStLinallpe.....l 123
                                        ++ ++++ l   t++++G+ G+GK+t+  +l  +     +
  gene1703|gene1703|rna1703|rna1703  17 KHLTIQKTLPMYTVLVIGSAGAGKTTFCLNLYDHlsthnH 56 
                                        556789999999**************98877776444440 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2.7
                                        EEEEEEE-GGG--HHH.HHHHHHHHHHHTTSEEEE- CS
                        RsgA_GTPase  48 epvivlnKiDlleeee.eleelkeelealgyevllv 82 
                                        + + +++K+Dl  ++e + ++l+e+ e+l ++ ll+
  gene1703|gene1703|rna1703|rna1703 182 PFINLVSKCDLFLKDEnDEDNLSEDDEDLCFDQLLL 217
                                        444567888987666635566666666665555555 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00015       0.1       2      45 ..      31      72 ..      30      88 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00015
                    Viral_helicase1  2 vvhGvpGcGKStlirkllrtsliltvnrptaelltegkpklpnl 45
                                       +v G +G+GK+t + +l+++ l+   ++pt + l ++  +++n 
  gene1703|gene1703|rna1703|rna1703 31 LVIGSAGAGKTTFCLNLYDH-LSTHNHNPTLINLDPSQ-QSNNT 72
                                       6889**************99.44444555444444443.33333 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   0.00016      0.11      13      90 ..      29     110 ..      23     142 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00016
                                        EEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH....HHHTC CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxx RF
                           ABC_tran  13 kvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren....esdee 84 
                                        +v ++G+ GaGK+t++  l+ +l+  + + +l + d ++q+ + +++ i ++  ++++ + + ++ n    ++ + 
  gene1703|gene1703|rna1703|rna1703  29 TVLVIGSAGAGKTTFCLNLYDHLSTHNHNPTLINLDPSQQSNNTYHHDICTYITTQNVMEATDLGPNssilKAFAT 104
                                        6789***************999998776666665555555666666666555555556555555555544444444 PP

                                        HHHHHH CS
                                        xxxxxx RF
                           ABC_tran  85 iekals 90 
                                        +++ l+
  gene1703|gene1703|rna1703|rna1703 105 MADHLE 110
                                        444444 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00015       0.1       2      24 ..      30      52 ..      29     153 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00015
                             AAA_33  2 vllvGlpGsGKstlaerllkklg 24
                                       vl++G +G+GK+t+  +l+ +l 
  gene1703|gene1703|rna1703|rna1703 30 VLVIGSAGAGKTTFCLNLYDHLS 52
                                       799************99986554 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00041      0.28      22      53 ..      27      58 ..       9      78 .. 0.70
   2 ?   -1.8   0.1       3.1   2.2e+03     147     163 ..     214     230 ..     211     234 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00041
                                       SS-EEEECSTTSSHHHHHHHHHHHSTTTTS-E CS
                    Sigma54_activat 22 dlsvlitGesGtGKellaraiheaskrkekpf 53
                                         +vl+ G  G+GK+++   ++++ + ++++ 
  gene1703|gene1703|rna1703|rna1703 27 MYTVLVIGSAGAGKTTFCLNLYDHLSTHNHNP 58
                                       379******************99655444432 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 3.1
                                        HHHHTTSS-HHHHHHHT CS
                    Sigma54_activat 147 eaveegkfredLyyrln 163
                                        + + ++kf +dLy  l+
  gene1703|gene1703|rna1703|rna1703 214 QLLLRTKFHKDLYQFLE 230
                                        5677899******8776 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00026      0.18       4      69 ..      32      97 ..      30     113 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00026
                                PRK  4 vagsSGaGkttvarklekifgrekvkaaeiegdsflrldraekdleleerkrakekevsflspean 69
                                       v gs GaGktt+  +l + +  ++ +++ i++d   + ++ +++  +     ++ +e + l+p+  
  gene1703|gene1703|rna1703|rna1703 32 VIGSAGAGKTTFCLNLYDHLSTHNHNPTLINLDPSQQSNNTYHHDICTYITTQNVMEATDLGPNSS 97
                                       679****************************99999999999988888888888888888888765 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00046      0.31       1      23 [.      27      49 ..      27      65 .. 0.86
   2 ?   -2.0   0.0         4   2.8e+03      41      61 ..     120     143 ..     111     198 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00046
                          PduV-EutP  1 mkkilliGkvgsGKttLtqalkg 23
                                       m  +l+iG+ g+GKtt + +l +
  gene1703|gene1703|rna1703|rna1703 27 MYTVLVIGSAGAGKTTFCLNLYD 49
                                       6689**************98866 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 4
                          PduV-EutP  41 iDtPGe...ylenrklysalivts 61 
                                        +D PG+   +++++++ ++++ + 
  gene1703|gene1703|rna1703|rna1703 120 VDMPGQieiFVHSESFLKTIAYFK 143
                                        667776444555555555555443 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0    0.0014      0.99       2      67 ..      30     138 ..      29     171 .. 0.56

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0014
                                        EEEEESTTSSHHHHHHHHHTSTEEESSST.TSSSSEEEEEEEETTEE............................. CS
                           MMR_HSR1   2 vaivGrpNvGKStLinaltgekaivsdkp.gtTrdinegrvklkgke............................. 47 
                                        v+++G   +GK+t+   l +  +  ++ p    +d+ +   ++   +                             
  gene1703|gene1703|rna1703|rna1703  30 VLVIGSAGAGKTTFCLNLYDHLSTHNHNPtLINLDPSQQSNNTY--Hhdictyittqnvmeatdlgpnssilkafa 103
                                        889999999***99999997533332222133334433322211..012333333344445555666677777777 PP

                                        .............EEEEECGGCSS..HHHHHHHHH CS
                           MMR_HSR1  48 .............ielvDtpGlie..gaseekglg 67 
                                                     + +vD+pG ie   +se+   +
  gene1703|gene1703|rna1703|rna1703 104 tmadhlenveiegYCVVDMPGQIEifVHSESFLKT 138
                                        77778888888889999999976543222333333 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00063      0.43       2      28 ..      30      56 ..      29     155 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00063
                                       EEEE--TTSSHHHHHHHHHHHH...GG CS
                           NTPase_1  2 vfiTGppGvGKtTlvkkvlellkssgv 28
                                       v++ G+ G GKtT++ ++++ l+ ++ 
  gene1703|gene1703|rna1703|rna1703 30 VLVIGSAGAGKTTFCLNLYDHLSTHNH 56
                                       7889*****************988775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (272 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       511  (0.0285013); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        89  (0.00496402); expected 17.9 (0.001)
Passed Fwd filter:                        26  (0.00145016); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              26  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 1897.82
//
Query:       gene1704|gene1704|rna1704|rna1704  [L=422]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0023   17.7   0.0     0.0052   16.6   0.0    1.8  1  Peptidase_C12  Ubiquitin carboxyl-terminal hydrolase, family 
  ------ inclusion threshold ------
        1.2    8.1  15.1        1.6    7.7  15.1    1.1  1  LAP1C          Lamina-associated polypeptide 1C (LAP1C)
        2.1    7.0  12.9        3.3    6.4  12.9    1.4  1  Presenilin     Presenilin
        4.2    5.8  19.3        5.2    5.5  19.3    1.1  1  Macoilin       Macoilin family


Domain annotation for each model (and alignments):
>> Peptidase_C12  Ubiquitin carboxyl-terminal hydrolase, family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   1.2e-06    0.0052     148     189 ..     366     408 ..     227     420 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.2e-06
                                        ..---SSTHH..HHS--EEEEEEEEETTEEEEE-TTS.S-EEEE CS
                      Peptidase_C12 148 segqteapee..eedvafHFiafvpvngklyeLDGlkegPidlg 189
                                        s+++++++ +  + +++ HFi fv+ +g+ly+LD  +++   + 
  gene1704|gene1704|rna1704|rna1704 366 STSRKAKN-SgyNININDHFILFVRRGGRLYRLDNENDFAAAVT 408
                                        32222222.245677899****************9988876655 PP

>> LAP1C  Lamina-associated polypeptide 1C (LAP1C)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7  15.1   0.00036       1.6      24     145 ..     157     275 ..     127     351 .. 0.63

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00036
                                        XXXXXXXXXXXXXXX................XXXXXXXXXXXXXX..XXXXXXXXXXXX..........XXXXXXX CS
                              LAP1C  24 eeaqtrkplsslkkdhqevetigsesadtedkseseqevnlseepkdetEeedsessqsgeeghklsseslgeekl 99 
                                         +++ ++ +s++ +d  e +++g+ s  +e +s+ e++   ++++kde  ++d++s +++ ++ +++s +   +++
  gene1704|gene1704|rna1704|rna1704 157 GSHKNKDEISESGRD--ERDSRGERSSRDERSSRDERNRRGEKSSKDERGSKDDRSNKDERSKRESKSSKD-GKSV 229
                                        344445555555555..555566655555555555555555666666666677777776444444444444.4678 PP

                                        XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXX.... CS
                              LAP1C 100 dsedsvsssdktgradaqleessaalseeasdrtaasqepsaadsq 145
                                        + ++sv+ ++k g+++ + +es  + +  +s+ ++++q+ s +d  
  gene1704|gene1704|rna1704|rna1704 230 KDGKSVKDGNKDGKSSKNQRESKHNNNSTRSSSSRINQRTSRKDLG 275
                                        8888888888888888888888888777777777777777765432 PP

>> Presenilin  Presenilin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4  12.9   0.00074       3.3     235     306 ..     182     256 ..     140     342 .. 0.51

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.00074
                         Presenilin 235 seeeeeaekkkeeasesskeeeseeesseksaqsse..................seeeseeesseaessaeessee 292
                                        ++e++++++++++ ++ssk+e+ +++  ++++++s+                  +          + +++ +ss  
  gene1704|gene1704|rna1704|rna1704 182 RDERSSRDERNRRGEKSSKDERGSKDDRSNKDERSKresksskdgksvkdgksvK----------DGNKDGKSS-- 245
                                        2222222222222222222222211111111111111111111111111111110..........111111111.. PP

                         Presenilin 293 keseessesseeee 306
                                           ++++es+++++
  gene1704|gene1704|rna1704|rna1704 246 ---KNQRESKHNNN 256
                                        ...11111111111 PP

>> Macoilin  Macoilin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5  19.3    0.0012       5.2     239     377 ..     142     279 ..      80     335 .. 0.51

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0012
                           Macoilin 239 hslnkkdsslklpeleyrekkksakssrsdskkkhehnesvdsklqekeymenkskskrlsksessgsesellvee 314
                                         ++ ++d++ ++  + ++++k + ++s+ d++ ++ + +s d++ ++ e   n+  +k ++ +  s++  + + e 
  gene1704|gene1704|rna1704|rna1704 142 IDHISTDTAYEVFSIGSHKNKDEISESGRDERDSRGERSSRDERSSRDE--RNRRGEKSSKDERGSKDDRSNKDER 215
                                        3333335555666665555555555555555555544444554444444..3333333332222222222222222 PP

                           Macoilin 315 svkskssssssssnknskkasags.agssnssskkhsessksvtsssssknskkqklpaGkssa 377
                                        s ++++ss+  +s k+ k+ + g+  g s+   ++ +++++s+ ssss+ n++  +   G +  
  gene1704|gene1704|rna1704|rna1704 216 SKRESKSSKDGKSVKDGKSVKDGNkDGKSSKNQRESKHNNNSTRSSSSRINQRTSRKDLGAKCD 279
                                        3333333444444444444444330333444445556666666666665555554444443322 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (422 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1619  (0.0903006); expected 358.6 (0.02)
Passed bias filter:                      512  (0.0285571); expected 358.6 (0.02)
Passed Vit filter:                       107  (0.00596798); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.77u 0.31s 00:00:01.08 Elapsed: 00:00:00.48
# Mc/sec: 2636.01
//
Query:       gene1705|gene1705|rna1705|rna1705  [L=164]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.4e-47  161.1   0.1    2.7e-47  161.0   0.1    1.0  1  Pro_isomerase  Cyclophilin type peptidyl-prolyl cis-trans iso


Domain annotation for each model (and alignments):
>> Pro_isomerase  Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  161.0   0.1   1.5e-51   2.7e-47       8     156 ..      16     161 ..       9     163 .. 0.86

  Alignments for each domain:
  == domain 1  score: 161.0 bits;  conditional E-value: 1.5e-51
                      Pro_isomerase   8 s..kGrivieLfadkaPktvenFlklvkeg....fYdgttFhRvikgfmvqgGdptgktsageqe.kkggesirai 76 
                                        +  +G+i+ieL +d +Pkt+enF++l+ +g     Y++++FhR+i gfm+qgGd+t+++  g++  +  g    ++
  gene1705|gene1705|rna1705|rna1705  16 KepLGTIKIELRSDVVPKTAENFRALC-TGekgyGYKNCSFHRIIAGFMIQGGDFTNNN--GTGGrSIYG---PKF 85 
                                        3458***********************.5568899*******************99984..443324444...58* PP

                      Pro_isomerase  77 pdEitsklkh.krGalamartgkepnsagsqFfItlkeaphldgkytvFGkVveGmdvvekiekvetdeerpkknv 151
                                        +dE+ ++lkh ++G+++ma++g  p+++gsqFfIt++ + +ld+k++vFG+VveGmdvv++i+++++d      +v
  gene1705|gene1705|rna1705|rna1705  86 DDEN-FELKHdSEGVVSMANAG--PHTNGSQFFITVARTAWLDNKHVVFGRVVEGMDVVKNISEMRQDT--NDYPV 156
                                        ****.89999899*******98..8***************************************98777..44456 PP

                      Pro_isomerase 152 kivsa 156
                                         i ++
  gene1705|gene1705|rna1705|rna1705 157 IIYDC 161
                                        67666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       349  (0.0194657); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.49
# Mc/sec: 999.40
//
Query:       gene1706|gene1706|rna1706|rna1706  [L=113]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-15   56.9   0.5    1.6e-15   56.6   0.5    1.1  1  LSM       LSM domain


Domain annotation for each model (and alignments):
>> LSM  LSM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.6   0.5   8.8e-20   1.6e-15       2      65 ..      43     105 ..      42     107 .. 0.97

  Alignments for each domain:
  == domain 1  score: 56.6 bits;  conditional E-value: 8.8e-20
                                        HHHHTTTSEEEEEETTSEEEEEEEEEEETTSEEEEEEEEEEETTETEEEEEEEEEEEGGGEEEE CS
                                LSM   2 flkklinkkvtvelkngrelrGtLkgfDqfmNlvLedveetlkdkkekrklglvliRGnnivli 65 
                                        flk+ ++k++++ lk++  ++GtL gfD++ N+  + v+e++++   + kl++++iR+nni ++
  gene1706|gene1706|rna1706|rna1706  43 FLKSRLGKRIRISLKWNVDYEGTLDGFDDNFNIEVSSVSEFVESR-MVGKLKKMVIRCNNIKSM 105
                                        9*******************************************9.***************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (113 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       384  (0.0214178); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.29s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 766.15
//
Query:       gene1707|gene1707|rna1707|rna1707  [L=440]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.2e-25   88.9   0.0    6.8e-25   87.8   0.0    1.7  1  IMS       impB/mucB/samB family
  ------ inclusion threshold ------
      0.074   13.2   0.2      0.074   13.2   0.2    1.6  2  Ntox15    Novel toxin 15


Domain annotation for each model (and alignments):
>> IMS  impB/mucB/samB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.8   0.0   7.6e-29   6.8e-25       1     106 [.     100     198 ..     100     297 .. 0.92

  Alignments for each domain:
  == domain 1  score: 87.8 bits;  conditional E-value: 7.6e-29
                                        EEETTHHHHHHHHHT.T-TTS-EEEEET....TEEEEE-HHHHTTT--TTSBHHHHHTTHTT-EEEEEE-HHHHHH CS
                                IMS   1 iDmdaFyasverardpeLkgkPvvvaqgsekrgiviavsyeArayGvkrgmrikeakklcpdlivvkvdlekyrra 76 
                                        iD+daFyasve++ +p   + P++v++     ++++av+y Ar+yG+++gm+  + + lcp l+++k ++e+y+ +
  gene1707|gene1707|rna1707|rna1707 100 IDIDAFYASVEMIVNP--VSGPLAVGSM----SMLAAVNYDARKYGIRSGMPGYQGRTLCPSLVIRKCNFELYNIF 169
                                        8***************..**********....******************************************** PP

                                        HHHHHHHHHHH-S..EEEEETTEEEEE-HH CS
                                IMS  77 skkileilkrfispkvekasiDEayldltg 106
                                        s++++ +l++f ++++e +++DE+ l + +
  gene1707|gene1707|rna1707|rna1707 170 SERVMGMLAKF-DENIEIYGLDECSLVMDE 198
                                        ***********.99**********997776 PP

>> Ntox15  Novel toxin 15
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.2   8.3e-06     0.074      13     100 ..       8      92 ..       4      97 .. 0.87
   2 ?   -3.1   0.1      0.83   7.4e+03      63      82 ..     254     273 ..     229     299 .. 0.50

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 8.3e-06
                             Ntox15  13 eQeeglnkltvdeylknrdkYkqqkraseaaaerrqakarqerevreelekkiveklvrdlkeekdqaekkaaeal 88 
                                        + e+ +nk++ ++++++   Y ++++a + + e+r    ++ r++++++++ki + + ++l+++   ++++ +  +
  gene1707|gene1707|rna1707|rna1707   8 REEDFINKISGSQLIAGNIVYYDEENAFDTKKEERI---EMTRTRARAIKEKIAQFTDNELRYAYKMVQIEKERLI 80 
                                        56889**************99999999888776665...789999******************9999999988888 PP

                             Ntox15  89 kslAAlHepDqi 100
                                         +  Al + D +
  gene1707|gene1707|rna1707|rna1707  81 RAWPALFDSDYM 92 
                                        888888888865 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 0.83
                             Ntox15  63 kkiveklvrdlkeekdqaek 82 
                                        +k  +k++ +  e+   ++k
  gene1707|gene1707|rna1707|rna1707 254 EKDAKKMQIKPNETYNDGKK 273
                                        33333333333333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (440 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       645  (0.0359752); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 3103.98
//
Query:       gene1709|gene1709|rna1709|rna1709  [L=65]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (65 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       274  (0.0152825); expected 358.6 (0.02)
Passed bias filter:                      213  (0.0118802); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 493.21
//
Query:       gene171|gene171|rna171|rna171  [L=161]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.024   14.6   0.1      0.059   13.3   0.1    1.6  1  Mu-transpos_C  Mu transposase, C-terminal


Domain annotation for each model (and alignments):
>> Mu-transpos_C  Mu transposase, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   3.3e-06     0.059      12      50 ..      14      52 ..      10      53 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.3e-06
                                   --TTTS--EEEEEE-.SHHHHSS-SEEEEEE-GGGTTEEE CS
                  Mu-transpos_C 12 vqrdGirlngnrYws.peLaglvgkkVvvryDPrdlsrvy 50
                                   +++ Gir+ + +Y+s +e + + +kk v++y+P   sr+y
  gene171|gene171|rna171|rna171 14 LRHYGIRIGNGWYFSlEE-ILYLKKKDVIAYHPLFASRIY 52
                                   6899***********755.55788888899*****99998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       953  (0.0531541); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.46
# Mc/sec: 1051.58
//
Query:       gene1710|gene1710|rna1710|rna1710  [L=133]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0075   16.3   0.0      0.011   15.9   0.0    1.3  1  DUF2973   Protein of unknown function (DUF2973)


Domain annotation for each model (and alignments):
>> DUF2973  Protein of unknown function (DUF2973)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   5.9e-07     0.011      36      67 ..      48      79 ..      19      80 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 5.9e-07
                            DUF2973 36 kkskksrtkkvtpHPELLDeaGklikEpLLvm 67
                                       ++s+   + ++++HPE +D +Gk++   LLv+
  gene1710|gene1710|rna1710|rna1710 48 GNSRYFTRYEKAIHPESFDGKGKMMTYSLLVL 79
                                       46666778899*******************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       202  (0.0112667); expected 358.6 (0.02)
Passed bias filter:                      185  (0.0103185); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 973.94
//
Query:       gene1711|gene1711|rna1711|rna1711  [L=46]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (46 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       157  (0.00875676); expected 358.6 (0.02)
Passed bias filter:                      149  (0.00831056); expected 358.6 (0.02)
Passed Vit filter:                         6  (0.000334653); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.45
# Mc/sec: 308.11
//
Query:       gene1712|gene1712|rna1712|rna1712  [L=53]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (53 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       458  (0.0255452); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.25s 00:00:00.60 Elapsed: 00:00:00.41
# Mc/sec: 390.31
//
Query:       gene1713|gene1713|rna1713|rna1713  [L=248]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (248 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 1874.01
//
Query:       gene1714|gene1714|rna1714|rna1714  [L=125]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0036   15.4   1.9     0.0041   15.2   1.9    1.0  1  Prominin  Prominin
     0.0069   16.4   1.7     0.0069   16.4   1.7    1.7  2  SNARE     SNARE domain
     0.0089   15.7   0.9      0.011   15.5   0.9    1.1  1  YkyA      Putative cell-wall binding lipoprotein
  ------ inclusion threshold ------
      0.017   14.9   1.0       0.02   14.6   1.0    1.1  1  Use1      Membrane fusion protein Use1
      0.022   15.0   1.5       0.03   14.6   1.5    1.1  1  Tup_N     Tup N-terminal
      0.056   13.5   6.6        1.3    9.1   6.6    2.2  1  ETRAMP    Malarial early transcribed membrane protein (ETRAMP


Domain annotation for each model (and alignments):
>> Prominin  Prominin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   1.9   1.4e-06    0.0041     360     432 ..      51     123 ..      40     125 .] 0.81

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.4e-06
                           Prominin 360 vvpdlkkalakgreqikklakkiprealdavisdlenterssktfddvvekyek.yrwliglivcsllllivvi 432
                                         +  lkk++++++++i ++++ + + + ++ +++ +n+ +  ++f++ +e + + yr+ i l +cs++++  ++
  gene1714|gene1714|rna1714|rna1714  51 ATIGLKKNIKDINNEITSQSTIL-EIIENKAVENAHNVVKARNKFEKAIESLKSdYRNFIILFLCSVIVILFIV 123
                                        55578999999999999999888.777788899999***************97537888888888887765554 PP

>> SNARE  SNARE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   1.3       2.7   8.2e+03      37      51 ..       2      16 ..       2      17 .. 0.65
   2 !   16.4   1.7   2.3e-06    0.0069       4      53 .]      74     123 ..      71     123 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 2.7
                                       XXXXXXXXXXXXXXX CS
                              SNARE 37 lkciillilviillv 51
                                       ++ +++l++  ++++
  gene1714|gene1714|rna1714|rna1714  2 WLLYTFLLVAQFICL 16
                                       667778887766665 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 2.3e-06
                                        HHHHHHHHHHHHHHHHHHHHHHHHHHHHCTXXXXXXXXXXXXXXXXXXXX CS
                              SNARE   4 DrIdtnVenaqsnveraqkeLkkavkyqksnRklkciillilviillvvl 53 
                                          I+++  +   nv +a+++  ka ++ ks  +  +i++l+ vi++l+++
  gene1714|gene1714|rna1714|rna1714  74 EIIENKAVENAHNVVKARNKFEKAIESLKSDYRNFIILFLCSVIVILFIV 123
                                        5577777777789999********************************97 PP

>> YkyA  Putative cell-wall binding lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.9   3.6e-06     0.011      74     127 ..      56     108 ..      43     111 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 3.6e-06
                               YkyA  74 kesieeakeefekikeeieeiedeelkkeaeelieameeryeaydklykaYkea 127
                                        k++i++ ++e+++ ++++e ie++ + ++a+++++a ++ ++a+++l ++Y + 
  gene1714|gene1714|rna1714|rna1714  56 KKNIKDINNEITSQSTILEIIENK-AVENAHNVVKARNKFEKAIESLKSDYRNF 108
                                        899******************766.99************************975 PP

>> Use1  Membrane fusion protein Use1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   1.0   6.6e-06      0.02     174     241 ..      54     124 ..      33     125 .] 0.83

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 6.6e-06
                               Use1 174 nLKenslaasqiikkDtetlsksekaadqnlaslkkeserlee..h.skskvkcllwlllfvvlvvFismv 241
                                         LK+n + +++ i +   +l+  e++a +n  +  k+ ++ e+  + +ks ++ +++l l+ v+v+ + ++
  gene1714|gene1714|rna1714|rna1714  54 GLKKNIKDINNEITSQSTILEIIENKAVENAHNVVKARNKFEKaiEsLKSDYRNFIILFLCSVIVILFIVI 124
                                        69*********************9999999999999998888754359999****9999998887755444 PP

>> Tup_N  Tup N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   1.5     1e-05      0.03      15      72 ..      46     104 ..      40     107 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1e-05
                              Tup_N  15 alsqeass.lkaqkdeyelkiqsqiqElqqirqtlyeLeeahrkikqqYEeeiarLkae 72 
                                        +l ++a++ lk++ +++++ i+sq   l+ i ++  e   +  k ++++E+ i+ Lk++
  gene1714|gene1714|rna1714|rna1714  46 ELLKDATIgLKKNIKDINNEITSQSTILEIIENKAVENAHNVVKARNKFEKAIESLKSD 104
                                        445555555999***********************9999999999***********986 PP

>> ETRAMP  Malarial early transcribed membrane protein (ETRAMP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   6.6   0.00043       1.3      23      72 ..      20     124 ..       1     125 [] 0.73

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00043
                             ETRAMP  23 slcdevnkkk.......................................................ekakkaikkid 43 
                                          c+ +  kk                                                        +  ka +k++
  gene1714|gene1714|rna1714|rna1714  20 EICNISFSKKlnllfhchgmeiktndellkdatiglkknikdinneitsqstileiienkavenaHNVVKARNKFE 95 
                                        333333334457777777777777778888888888888888888888888888888888888889999******* PP

                             ETRAMP  44 dkiekkkkkkKliiistiatalallvasa 72 
                                        + ie  k+  ++ ii  +++++++l+ ++
  gene1714|gene1714|rna1714|rna1714  96 KAIESLKSDYRNFIILFLCSVIVILFIVI 124
                                        ************************99765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2154  (0.120141); expected 358.6 (0.02)
Passed bias filter:                      921  (0.0513693); expected 358.6 (0.02)
Passed Vit filter:                        87  (0.00485247); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 905.95
//
Query:       gene1715|gene1715|rna1715|rna1715  [L=577]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
       0.13   11.8   0.1       0.33   10.5   0.0    1.6  2  NTP_transferase  Nucleotidyl transferase


Domain annotation for each model (and alignments):
>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   1.8e-05      0.33      23     137 ..      28     137 ..      21     155 .. 0.66
   2 ?   -3.0   0.1      0.24   4.4e+03      44      73 ..     401     430 ..     397     439 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 1.8e-05
                                        GGSEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGT.SEEEEEEESS--BGGHHHHHTHHHH CS
                    NTP_transferase  23 klvpvlgkerliqatlsrlansgieeiivvltqehsflveeqlkegskfg.vevlialepegkgtAdAvalaaell 97 
                                         l+p+ +  +li++ l+ l+++g++e  ++l       v e+lk+++  + ++++++      ++  ++  +++ +
  gene1715|gene1715|rna1715|rna1715  28 TLFPISNI-PLIEYILEMLSKNGFTE--IILAGSSTSVVLEYLKRTKYHKlLNISCLS-----NSHTSLGDILREI 95 
                                        57888888.*****************..566666667777777777644423333332.....3333444444444 PP

                                        TTSSE...EEEEETTEEEESTTHHHHHHHHHTHSSTT.SEEE CS
                    NTP_transferase  98 edeks.delvlvLggDhlikdayeeavkkaiekaakg.tvtf 137
                                        ++++   +++lv  ++ +++++++ +++++  +++k   v++
  gene1715|gene1715|rna1715|rna1715  96 DEKDWrVDNLLVYYANTFVNYDLRFVLDEHLRSKKKNrNVIL 137
                                        444444678999999999999999999999877666433333 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 0.24
                                        TT-SEEEEEEETTTHHHHHHHHTTSGGGTS CS
                    NTP_transferase  44 sgieeiivvltqehsflveeqlkegskfgv 73 
                                        ++  e +v++++e+  ++ +q++e+++ +v
  gene1715|gene1715|rna1715|rna1715 401 KNLSECLVISNDEDGIIYLNQIEETDESEV 430
                                        566788999999999999999999987663 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (577 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       548  (0.030565); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.26s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 3804.51
//
Query:       gene1716|gene1716|rna1716|rna1716  [L=335]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    9.3e-58  195.4   0.0    1.3e-57  194.9   0.0    1.2  1  ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-bindi


Domain annotation for each model (and alignments):
>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  194.9   0.0   7.3e-62   1.3e-57      17     213 .]       5     214 ..       2     214 .. 0.95

  Alignments for each domain:
  == domain 1  score: 194.9 bits;  conditional E-value: 7.3e-62
                                        EEEEESTTSSHHHHHHHHHHHSSTS...........S.EEEEEEESEEHHHHHHHHHHCHHSSGGGGEEEEEEETT CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxx...........x.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        ATP-synt_ab  17 tlipgafgvGktvisqslskqsnsd...........d.aiiyvgiGergnevaevleefpegtimkrtvlvantsn 80 
                                         l ++++g++++ +++++++q+              + ai+++++G ++++++ + ++f+ +++++rt l++n +n
  gene1716|gene1716|rna1716|rna1716   5 FLFLAGSGLPHNDVAAQICRQAGLVkkktvidtsdeNfAIVFAAMGVNMETARFFKSSFELSGALERTALFLNLAN 80 
                                        56678899999999999999975546778999998768************************************** PP

                                        S-HHHHHHHHHHHHHHHHHHHH.TTSEEEEEEETHHHHHHHHHHHHHHTTTSBEGGGSBTTHHHHHHHHHTTSEEE CS
                                        xxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        ATP-synt_ab  81 epvaareasiytgitlAEyfrd.qgknvlliadslsrwaeAlreislrlgempadqgypaylgaklaslyERagka 155
                                        +p+++r++++ +++t+AEy+++ ++k+vl+i++++s +a+Alre+s++ +e+p+++gyp+ ++++l+ lyERag++
  gene1716|gene1716|rna1716|rna1716  81 DPTIERIITPKLALTAAEYLAYeTEKHVLVILTDMSSYADALREVSAAREEVPGRRGYPGCMYTDLSMLYERAGRI 156
                                        *********************999**************************************************** PP

                                        TSSEEEEEEEEEEE-GGCSTTSHHHHHHHHHSSEEEEB-HHHHHTTBSSSBCTTTEEE CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        ATP-synt_ab 156 pdrtGsvtivaavspaggDfsdpvttatlgitdgfivLdkklaqrkhfPainvlvSvS 213
                                        + ++Gs+t++++++++++D+++p+++ t +it+g+i++d+++++r+++P+invl S+S
  gene1716|gene1716|rna1716|rna1716 157 DGKNGSITQIPILTMPNDDITHPIPDLTGYITEGQIYIDRQMHNRQIYPPINVLPSLS 214
                                        ********************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (335 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       534  (0.0297841); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2445.18
//
Query:       gene1717|gene1717|rna1717|rna1717  [L=181]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.16   11.5   0.3       0.16   11.5   0.3    1.8  2  KNOX2     KNOX2 domain


Domain annotation for each model (and alignments):
>> KNOX2  KNOX2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.2      0.36   6.5e+03      19      29 ..       3      14 ..       2      17 .. 0.63
   2 ?   11.5   0.3   8.7e-06      0.16      11      33 ..     131     153 ..     126     161 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 0.36
                              KNOX2 19 LvkYk.eeLtrp 29
                                         +Yk +eL+r+
  gene1717|gene1717|rna1717|rna1717  3 FNRYKlKELKRT 14
                                       567874578776 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 8.7e-06
                              KNOX2  11 FMeaYcdvLvkYkeeLtrpveEA 33 
                                        F+e+Y d+  kY ee+ + ++E 
  gene1717|gene1717|rna1717|rna1717 131 FLEHYSDLAEKYDEEFWKAFKEK 153
                                        ********************994 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       852  (0.0475208); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.22s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1433.01
//
Query:       gene1718|gene1718|rna1718|rna1718  [L=299]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.6e-05   22.7   3.9    8.6e-05   22.7   3.9    1.9  2  Ada3      Histone acetyltransferases subunit 3
  ------ inclusion threshold ------
       0.89    8.6   6.7       0.93    8.6   5.3    1.7  1  PDCD7     Programmed cell death protein 7


Domain annotation for each model (and alignments):
>> Ada3  Histone acetyltransferases subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.1      0.38   3.4e+03      19      38 ..     123     143 ..     110     150 .. 0.75
   2 !   22.7   3.9   9.6e-09   8.6e-05      48     108 ..     185     245 ..     175     269 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.38
                               Ada3  19 ilepeedad.kydgredDeva 38 
                                        ++++++++    ++r++D+++
  gene1718|gene1718|rna1718|rna1718 123 LMSENNEESfVTKNRYEDDIL 143
                                        455555666678999999997 PP

  == domain 2  score: 22.7 bits;  conditional E-value: 9.6e-09
                               Ada3  48 LrevsliNgarkarLlelvkermayqeyqtiledlDkqvqqaYlKrtrtlkkkkkkkrsga 108
                                        L+++  iN+ r+++L ++++++++   + + l+++Dk +++   Kr+++  kkk +++ ++
  gene1718|gene1718|rna1718|rna1718 185 LKKQIGINNGRRKNLSDILEKKLEVLSILKFLREIDKKIEKIAFKRIKNKRKKKSEDNIQQ 245
                                        99***********************************************999999966544 PP

>> PDCD7  Programmed cell death protein 7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   5.3    0.0001      0.93      43     111 ..     195     262 ..     191     269 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0001
                              PDCD7  43 raeelkkelqeklalLedaerleelkrklerrkkkRarrkrrkeerkeekkekeerraereakidkWrr 111
                                        r+++l + l++kl+ L+  ++l+e+ +k+e+++ kR ++kr+k+  +++ ++  e + er++  d++++
  gene1718|gene1718|rna1718|rna1718 195 RRKNLSDILEKKLEVLSILKFLREIDKKIEKIAFKRIKNKRKKKS-EDNIQQLLELIMERNQFYDAFKN 262
                                        56788999*********************************9998.55555555666677666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1704  (0.0950416); expected 358.6 (0.02)
Passed bias filter:                      477  (0.0266049); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.22s 00:00:00.68 Elapsed: 00:00:00.37
# Mc/sec: 2450.58
//
Query:       gene1719|gene1719|rna1719|rna1719  [L=353]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-11   44.5   0.9    1.3e-11   44.5   0.9    1.9  2  DNA_pol3_delta2  DNA polymerase III, delta subunit
    9.3e-05   22.9   1.5    0.00025   21.5   0.5    2.3  2  AAA              ATPase family associated with various cellul
     0.0077   16.6   0.7      0.034   14.6   0.1    2.3  3  Rep_fac_C        Replication factor C C-terminal domain
     0.0083   16.2   0.4      0.027   14.5   0.1    2.0  2  AAA_14           AAA domain
  ------ inclusion threshold ------
       0.01   16.2   0.1      0.027   14.8   0.1    1.9  1  RNA_helicase     RNA helicase
       0.01   15.2   0.0      0.074   12.4   0.0    2.1  2  FtsK_SpoIIIE     FtsK/SpoIIIE family
      0.022   15.0   0.0       0.06   13.6   0.0    1.7  1  AAA_22           AAA domain
       0.03   14.7   0.0      0.056   13.8   0.0    1.6  1  AAA_16           AAA ATPase domain
      0.045   13.5   0.2       0.14   11.8   0.1    1.9  1  Viral_helicase1  Viral (Superfamily 1) RNA helicase
      0.088   12.6   3.1       0.56   10.0   3.1    2.2  1  AAA_11           AAA domain
      0.094   12.6   0.0          2    8.3   0.0    2.4  2  NACHT            NACHT domain
       0.11   11.9   0.1        7.7    5.9   0.0    2.4  2  SMC_N            RecF/RecN/SMC N terminal domain


Domain annotation for each model (and alignments):
>> DNA_pol3_delta2  DNA polymerase III, delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.5   0.9   8.8e-15   1.3e-11      22     159 ..      36     185 ..      23     189 .. 0.73
   2 ?   -2.6   0.1       2.7   4.1e+03     134     159 ..     265     290 ..     257     293 .. 0.74

  Alignments for each domain:
  == domain 1  score: 44.5 bits;  conditional E-value: 8.8e-15
                    DNA_pol3_delta2  22 yLfeGdegigkkelalnlakallceeknetk.......pcgecksckkieqgkhpDvivieteeker.....sikl 85 
                                        ++++G+ g+gk +l  +++++l+ +++++++       + ++  ++  +e++++ +++  + + k++     +ik+
  gene1719|gene1719|rna1719|rna1719  36 LIVHGRPGCGKRTLVYAFINHLFGKQPKTHHrsievvsSSDKKITISYVESEEYVEICPSDYNFKDKdviqdVIKK 111
                                        5789***********************9987766544433444444444444444444443333322333335554 PP

                    DNA_pol3_delta2  86 .dqirelieelsrkpreskkkiiiiedaekmtksAaNalLktlEEPsenaifiLitsdtnklLktirSRcqelkf 159
                                          + + + + l  ++   k k+i+i++aekmtk A+ al +t+E   +n  +i+i +dt+ ++++i+SR+  l++
  gene1719|gene1719|rna1719|rna1719 112 mAETKPILS-LISRTKSEKLKLIVITKAEKMTKDAQAALRRTVETYVDNFRMIMICNDTTGIIDPIKSRMLCLRV 185
                                        233333333.33444456889*************************************************98875 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2.7
                    DNA_pol3_delta2 134 aifiLitsdtnklLktirSRcqelkf 159
                                        ++ +++ +++n +   irS   el +
  gene1719|gene1719|rna1719|rna1719 265 MVKMMVKEQSNTVVMNIRSHLNELLI 290
                                        56677788888888888888777765 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.5   1.6e-07   0.00025       2     124 ..      37     180 ..      36     188 .. 0.68
   2 ?   -1.2   0.0       1.7   2.5e+03      81      97 ..     257     273 ..     184     294 .. 0.56

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 1.6e-07
                                        EEESSTTSSHHHHHHHHHHHH..........THEEEEEETTTCSSS........................STTHHH CS
                                AAA   2 llyGppGtGKTllakavakel..........gvefleisgsellsk........................yvgese 43 
                                        +++G pG+GK +l+ a +++l          ++e+++ s ++++ +                              
  gene1719|gene1719|rna1719|rna1719  37 IVHGRPGCGKRTLVYAFINHLfgkqpkthhrSIEVVSSSDKKITISyveseeyveicpsdynfkdkdviqD----- 107
                                        89******************987666444333444444444444225777777777888855555555552..... PP

                                        HHHHHHHHHHHHTS............TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEE CS
                                AAA  44 kkirelfkeakeka............kpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvivig 107
                                             ++k++ e +            k + ++i  +++++k+            +++L + ++ + +   ++ +i+
  gene1719|gene1719|rna1719|rna1719 108 -----VIKKMAETKpilslisrtkseKLKLIVITKAEKMTKDA-----------QAALRRTVETYVD---NFRMIM 164
                                        .....33333222222222222224346899999999998888...........9999999999999...6***** PP

                                        EESSGGGSTHHHHSTTS CS
                                AAA 108 atnrpdkldpallrgRf 124
                                        ++n+   + +++  +R+
  gene1719|gene1719|rna1719|rna1719 165 ICNDTTGIIDPIK-SRM 180
                                        ****999999998.776 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.7
                                        HHHHHHHHHHHHHHHTT CS
                                AAA  81 eeervvnqLlteldgvk 97 
                                        e e+vv  +++++ +++
  gene1719|gene1719|rna1719|rna1719 257 EWETVVTDMVKMMVKEQ 273
                                        33444444444444444 PP

>> Rep_fac_C  Replication factor C C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       3.8   5.6e+03       6      19 ..     105     116 ..      91     140 .. 0.61
   2 ?   -1.5   0.0       2.4   3.6e+03       3      22 ..     210     228 ..     209     236 .. 0.81
   3 !   14.6   0.1   2.3e-05     0.034       2      86 ..     258     343 ..     257     345 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 3.8
                                        HHHHHHHHHHT-HH CS
                          Rep_fac_C   6 ieeileaclngdfe 19 
                                        i+++++++  ++ +
  gene1719|gene1719|rna1719|rna1719 105 IQDVIKKM--AETK 116
                                        44444444..2333 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.4
                                        HHHHHHHHHHHHHT-HHHHH CS
                          Rep_fac_C   3 pteieeileaclngdfeeay 22 
                                        ++++++i++   +g+f++a 
  gene1719|gene1719|rna1719|rna1719 210 EKTLKQIISDS-HGNFRRAL 228
                                        67889999999.99999997 PP

  == domain 3  score: 14.6 bits;  conditional E-value: 2.3e-05
                                        -HHHHHHHHHHHHH....T-HHHHHHHHHHHHHHC---HHHHHHHHHHHGCCS..S-HHHHHHHHHHHHHHHHHHH CS
                          Rep_fac_C   2 hpteieeileacln....gdfeeaykklrellvekGysaediltqlhrvvkeqeelpeaqkleilellgeiekrlv 73 
                                        ++t+++++++ + +      + ++++ l+ +l  k +++  il+ l++ +++   +++     +  l + ++ r++
  gene1719|gene1719|rna1719|rna1719 258 WETVVTDMVKMMVKeqsnTVVMNIRSHLN-ELLIKCIPPRLILKALFETLMST--VKQTEYHNLCTLTAKYDCRIT 330
                                        899*********77666677778888886.66666****************95..6776666666779******** PP

                                        CTH-HHHHHHHHH CS
                          Rep_fac_C  74 eGasehlqlsall 86 
                                         G+ +  +l+a +
  gene1719|gene1719|rna1719|rna1719 331 LGTKSIFHLEAYV 343
                                        *********9976 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.1   1.8e-05     0.027       5     118 ..      36     154 ..      33     164 .. 0.73
   2 ?   -2.7   0.0       3.7   5.5e+03      94     112 ..     202     219 ..     189     238 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.8e-05
                             AAA_14   5 lvitGaRrvGKTtllkqlikell..vkkesilyinldderdkkladpekllelilek...lkeekktylflDEiqe 75 
                                        l++ G   +GK tl++ +i++l+   +k +   i++ + +dkk++ +    e++ e     ++ k++ ++ D i++
  gene1719|gene1719|rna1719|rna1719  36 LIVHGRPGCGKRTLVYAFINHLFgkQPKTHHRSIEVVSSSDKKITISYVESEEYVEIcpsDYNFKDKDVIQDVIKK 111
                                        7899999************9999*97777888888888888776643212244444322223345566999***** PP

                             AAA_14  76 vpewekalkslvdeg.knldvivtGSnskllskeiatslagrva 118
                                        + e + +l  + +++ ++l++iv   + k+  k+++  l++ v+
  gene1719|gene1719|rna1719|rna1719 112 MAETKPILSLISRTKsEKLKLIVITKAEKMT-KDAQAALRRTVE 154
                                        *999999999999776889998887777777.556666666655 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 3.7
                             AAA_14  94 dvivtGSnskllskeiats 112
                                        dv + GS  k l++ i+ +
  gene1719|gene1719|rna1719|rna1719 202 DVECIGSDEKTLKQIIS-D 219
                                        66677888887755433.3 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.1   1.8e-05     0.027       2      48 ..      37      84 ..      36     146 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.8e-05
                       RNA_helicase  2 wlyGpsgeGKStlakeLakallkklklkkkdsvys.rnpeddfwdgYt 48
                                       +++G++g+GK tl++ ++++l +k  ++++ s+ +  ++++++  +Y 
  gene1719|gene1719|rna1719|rna1719 37 IVHGRPGCGKRTLVYAFINHLFGKQPKTHHRSIEVvSSSDKKITISYV 84
                                       79********************99977777777775556666666665 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0     5e-05     0.074      28      62 ..      18      56 ..       8      64 .. 0.77
   2 ?   -0.1   0.0      0.32   4.7e+02     163     187 ..     116     140 ..      92     160 .. 0.58

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 5e-05
                                       S-EEEEEGGGS-.....SEEEE--TTSSHHHHHHHHHHH CS
                       FtsK_SpoIIIE 28 gnplvldlkkma....shllvaGatgsGKStalntLilS 62
                                       ++++ ++lk+ +    +hl+v+G++g GK t + ++i  
  gene1719|gene1719|rna1719|rna1719 18 NRKHASNLKNFTlstiPHLIVHGRPGCGKRTLVYAFINH 56
                                       55666666666666667****************999965 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.32
                                        .............-----------B CS
                       FtsK_SpoIIIE 163 neritsLsnqgpsygvhvlvtagre 187
                                        ++   ++s   +++   +++t++ +
  gene1719|gene1719|rna1719|rna1719 116 KPILSLISRTKSEKLKLIVITKAEK 140
                                        4444444444455555555555444 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0     4e-05      0.06       7     117 ..      35     154 ..      31     169 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4e-05
                             AAA_22   7 ilvvtGesGtGK.Ttllrrlleqldeeakaee..................erpevvfvtlpsst.sskdllrellr 62 
                                        +l+v+G +G+GK T++++ + + + +++k  +                  e+ e+v+++++  + + kd+ +++ +
  gene1719|gene1719|rna1719|rna1719  35 HLIVHGRPGCGKrTLVYAFINHLFGKQPKTHHrsievvsssdkkitisyvESEEYVEICPSDYNfKDKDVIQDVIK 110
                                        79**********6777777777777766666699999999999999988888888899999988999999999999 PP

                             AAA_22  63 alglelkaerlsseellealeqalraravielliiDEaqhlrseealeeLrslln 117
                                        ++         +++ +l+++ +  +++ +  l++i  a+++ +++a   Lr+ ++
  gene1719|gene1719|rna1719|rna1719 111 KMA--------ETKPILSLISRTKSEKLK--LIVITKAEKM-TKDAQAALRRTVE 154
                                        988........455666666666666555..7777777777.5555555555554 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   3.8e-05     0.056      22      51 ..      31      60 ..      19     158 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.8e-05
                             AAA_16 22 grpelvllsGesGvGKsslvrellralekd 51
                                       ++ + ++++G +G+GK +lv ++ ++l ++
  gene1719|gene1719|rna1719|rna1719 31 STIPHLIVHGRPGCGKRTLVYAFINHLFGK 60
                                       445899**************9998888766 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   9.6e-05      0.14       2      29 ..      37      66 ..      36      94 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 9.6e-05
                    Viral_helicase1  2 vvhGvpGcGKStlirkllrts..liltvnr 29
                                       +vhG pGcGK tl+  ++++    + ++++
  gene1719|gene1719|rna1719|rna1719 37 IVHGRPGCGKRTLVYAFINHLfgKQPKTHH 66
                                       8**************999994443333333 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   3.1   0.00037      0.56       2      59 ..      17      71 ..      16     327 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00037
                             AAA_11  2 lndsqreai.ksalseseitliqGPPGtgKTktivellsqll......srrkseeeksakpriLv 59
                                       +n++ + ++ +++ls+    +++G PG+gK + + +++++l                  ++ i v
  gene1719|gene1719|rna1719|rna1719 17 FNRKHASNLkNFTLSTIPHLIVHGRPGCGKRTLVYAFINHLFgkqpktH----------HRSIEV 71
                                       566666666445566666789********************74444330..........222323 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.0    0.0013         2       3      30 ..      36      63 ..      35      78 .. 0.83
   2 ?    1.5   0.0      0.17   2.5e+02     106     147 ..     115     157 ..      93     165 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0013
                                       EEEEC-TTTCHHHHHHHHHHHHCTS-SC CS
                              NACHT  3 vilqGeaGsGKTtLlqklalawaegklp 30
                                       +i++G++G+GK tL+  ++  +  ++++
  gene1719|gene1719|rna1719|rna1719 36 LIVHGRPGCGKRTLVYAFINHLFGKQPK 63
                                       69*************9999888666554 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.17
                                        ...HHHHHCTTTTT--EEEEEEECCCHHH.HCTTSSCE..EEE CS
                              NACHT 106 rtlLselirkkllpeasllltvrpralrd.leeqleeaivlev 147
                                         + + +li+++   + +l+++++ ++  + ++  l+++  + v
  gene1719|gene1719|rna1719|rna1719 115 TKPILSLISRTKSEKLKLIVITKAEKMTKdAQAALRRTVETYV 157
                                        4456799999999999999999999887755555555555545 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0    0.0052       7.7      27      60 ..      36      70 ..      19     118 .. 0.77
   2 ?    3.5   0.1     0.028        43     179     210 ..     118     150 ..     112     158 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0052
                                       EEEEESTTSSHHHHHHH.HHHHCTT.TTTTTTCHC CS
                                       xxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxx RF
                              SMC_N 27 taivGpNGSGKsnlldA.ilFvLGersakklrsek 60
                                        ++ G+ G+GK  l+ A i +++G++ +++ rs +
  gene1719|gene1719|rna1719|rna1719 36 LIVHGRPGCGKRTLVYAfINHLFGKQPKTHHRSIE 70
                                       5789*********9999789****99887777643 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.028
                                        HHHHHH.HHCTTSEEEEE-SSHHHCCC-SCEEE CS
                                        xxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              SMC_N 179 vaellk.eksknaQfivislreemlekadklvg 210
                                        + +l+  +ks++  +ivi+  e+m+++a++ ++
  gene1719|gene1719|rna1719|rna1719 118 ILSLISrTKSEKLKLIVITKAEKMTKDAQAALR 150
                                        555565367888****************88765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (353 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1049  (0.0585086); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.56u 0.31s 00:00:00.87 Elapsed: 00:00:00.46
# Mc/sec: 2317.94
//
Query:       gene172|gene172|rna172|rna172  [L=39]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (39 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       168  (0.00937029); expected 358.6 (0.02)
Passed bias filter:                      159  (0.00886831); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.29s 00:00:00.63 Elapsed: 00:00:00.43
# Mc/sec: 271.75
//
Query:       gene1720|gene1720|rna1720|rna1720  [L=65]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (65 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       236  (0.013163); expected 358.6 (0.02)
Passed bias filter:                      155  (0.00864521); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.45
# Mc/sec: 431.77
//
Query:       gene1721|gene1721|rna1721|rna1721  [L=108]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
       0.52   10.9  10.1       0.72   10.5  10.1    1.4  1  Ribosomal_60s  60s Acidic ribosomal protein


Domain annotation for each model (and alignments):
>> Ribosomal_60s  60s Acidic ribosomal protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5  10.1     4e-05      0.72      37      82 ..      53      99 ..      23     107 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 4e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX..XX--SS CS
                      Ribosomal_60s 37 ellangaaklaaaaaaaaaaaaaaaaaaaaeekkkeeeee.Eeeddd 82
                                       e ++ +++ l +a+aaa  a+  ++aa+++e+k+kee +    ed d
  gene1721|gene1721|rna1721|rna1721 53 ERMEGIYSMLMQAPAAASEAVVTDGAAKKEEAKPKEEAAPaATEDVD 99
                                       45555555555777777777777777777777777777655444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       445  (0.0248201); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 809.35
//
Query:       gene1722|gene1722|rna1722|rna1722  [L=741]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
       0.02   14.8   0.1        0.1   12.5   0.1    2.3  2  UME          UME (NUC010) domain
      0.082   12.8   0.0       0.25   11.3   0.0    1.8  1  Macscav_rec  Macrophage scavenger receptor


Domain annotation for each model (and alignments):
>> UME  UME (NUC010) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0      0.86   7.7e+03      61      80 ..      15      34 ..      14      46 .. 0.82
   2 ?   12.5   0.1   1.1e-05       0.1      39      96 ..     351     407 ..     337     413 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 0.86
                                UME 61 aleidelrsaalsvWatlls 80
                                       +l +del+++ +++  ++++
  gene1722|gene1722|rna1722|rna1722 15 MLTEDELQTEIITCIPSFVH 34
                                       57889999999999888886 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 1.1e-05
                                UME  39 liklagssissalpqimacLqsaleidelrsaalsvWatllsnlededleplleqtfa 96 
                                        l +     ++++lpqi+ c  +a+++ +++++a++  ++l ++++ e+ e  l+  f+
  gene1722|gene1722|rna1722|rna1722 351 LAEQRFDDLAVCLPQIVKCCLIAIDK-DVNEDACQLLQVLSQQVDGEQYENELSFCFI 407
                                        44444455899**************9.6*****************9999987776665 PP

>> Macscav_rec  Macrophage scavenger receptor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   2.7e-05      0.25      15      43 ..     339     367 ..     337     370 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 2.7e-05
                        Macscav_rec  15 LidsehFqNfSvttdQrfndvLlQLstLv 43 
                                        Li+ + F+ +S   +Qrf+d+ + L  +v
  gene1722|gene1722|rna1722|rna1722 339 LIQKNAFWPLSRLAEQRFDDLAVCLPQIV 367
                                        8999****************987776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (741 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       673  (0.037537); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.65u 0.30s 00:00:00.95 Elapsed: 00:00:00.48
# Mc/sec: 4623.85
//
Query:       gene1723|gene1723|rna1723|rna1723  [L=42]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (42 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       308  (0.0171789); expected 358.6 (0.02)
Passed bias filter:                      195  (0.0108762); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.22s 00:00:00.59 Elapsed: 00:00:00.40
# Mc/sec: 316.35
//
Query:       gene1724|gene1724|rna1724|rna1724  [L=291]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.6e-66  222.3  13.0    9.4e-66  221.5  13.0    1.3  1  PTP2             Polar tube protein 2 from Microsporidia
  ------ inclusion threshold ------
      0.037   13.6   1.3       0.97    9.0   1.3    2.3  1  LmjF365940-deam  A distinct subfamily of CDD/CDA-like deamina
       0.57   10.3   5.6       0.11   12.6   1.2    2.1  2  DUF2673          Protein of unknown function (DUF2673)


Domain annotation for each model (and alignments):
>> PTP2  Polar tube protein 2 from Microsporidia
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  221.5  13.0   1.6e-69   9.4e-66       1     217 []      88     284 ..      88     284 .. 0.99

  Alignments for each domain:
  == domain 1  score: 221.5 bits;  conditional E-value: 1.6e-69
                               PTP2   1 CnnqfieGkkilgangvnanllkkeqpeeClkekkekkkaiealakelikkavkkkasknkqkkeCikkvskksqa 76 
                                        C++++++G+         +nl++k+ +eeC+k+k+ekk+++e+lakel+          ++++++C+ ++sk+s++
  gene1724|gene1724|rna1724|rna1724  88 CDPRGVDGN---------WNLINKQLQEECIKQKREKKERAEQLAKELT----------QPSQDDCKIRISKESMV 144
                                        999******.........9******************************..........9**************** PP

                               PTP2  77 CilkkvlkelinepeyavkvhgNvvelekkdklvamivneqikylvkkkkkkakfafvkkpnaevkfNelGdvlsk 152
                                        C+++kv++++i++++y++k +gNvve++ k+++v+m+v+e+++y++k+ kk+a +af+++p+a++kfN+lG +ls+
  gene1724|gene1724|rna1724|rna1724 145 CHARKVMNNVIKDAYYTIKLFGNVVEIIVKNQPVFMGVTERFRYNAKRLKKQAPNAFKNSPTATFKFNRLGGLLSQ 220
                                        **************************************************************************** PP

                               PTP2 153 egeppqrkkknpcaeClkslkekaqtvEgeldkCeneCdnssiltsisnnttkkesksekkkdkk 217
                                        +ge+pq+kk+npca+Cl++lkek+++vEg++++C ++Cd++ ++t+i+n++++ ++k+e+++d+k
  gene1724|gene1724|rna1724|rna1724 221 TGEVPQPKKNNPCAACLEMLKEKTNSVEGQANNC-GGCDSMLDITTIHNGQFRIQNKEENTTDSK 284
                                        **********************************.*************************99975 PP

>> LmjF365940-deam  A distinct subfamily of CDD/CDA-like deaminases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   1.3   0.00016      0.97     131     167 ..     205     243 ..      31     283 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00016
                    LmjF365940-deam 131 Ptsa...vRevalhsesq..tsarksnPLkPCGaCeewLkki 167
                                        Pt++    R  +l s++    +++k+n   PC aC e+Lk  
  gene1724|gene1724|rna1724|rna1724 205 PTATfkfNRLGGLLSQTGevPQPKKNN---PCAACLEMLKEK 243
                                        554444456667777766223444445...999999999854 PP

>> DUF2673  Protein of unknown function (DUF2673)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   1.2   1.9e-05      0.11       3      58 ..       4      57 ..       2      82 .. 0.84
   2 ?   -1.6   0.2      0.49   2.9e+03      68      76 ..     278     286 ..     274     288 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.9e-05
                            DUF2673  3 nllkilliiafanpvfassmqmpdpasvtttqihamstnaqqdwiasltanqynml 58
                                       n++  +l  a+a  v   s    +p s  +t   + s+na+qd  a l  n   ml
  gene1724|gene1724|rna1724|rna1724  4 NMFMCFLSYAYAATVVGQSAAPQQPQSSPSTTAFTASANAKQDQAANLQQNA--ML 57
                                       677788999***********9999***9999999************998664..44 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.49
                            DUF2673  68 enttdaqkq 76 
                                        enttd++k+
  gene1724|gene1724|rna1724|rna1724 278 ENTTDSKKK 286
                                        9****9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1656  (0.0923643); expected 358.6 (0.02)
Passed bias filter:                      505  (0.0281667); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2074.43
//
Query:       gene1725|gene1725|rna1725|rna1725  [L=46]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.13   11.4   0.1       0.13   11.4   0.1    1.0  1  DUF3413   Domain of unknown function (DUF3413)


Domain annotation for each model (and alignments):
>> DUF3413  Domain of unknown function (DUF3413)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   7.1e-06      0.13      91     121 ..      10      40 ..       3      46 .] 0.82

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 7.1e-06
                            DUF3413  91 tlglilLlvDtevfqqyklHLnpvvlellln 121
                                        t    +LlvD  vf++  +HL   v +++ +
  gene1725|gene1725|rna1725|rna1725  10 TSNYKALLVDNDVFDTESMHLIDNVCHIISK 40 
                                        555679*****************99999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (46 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       374  (0.0208601); expected 358.6 (0.02)
Passed bias filter:                      237  (0.0132188); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.27s 00:00:00.61 Elapsed: 00:00:00.42
# Mc/sec: 332.41
//
Query:       gene1726|gene1726|rna1726|rna1726  [L=129]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-10   41.2   0.0    1.4e-10   40.8   0.0    1.2  1  RRM_1     RNA recognition motif. (a.k.a. RRM, RBD, or RNP dom


Domain annotation for each model (and alignments):
>> RRM_1  RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.8   0.0   7.8e-15   1.4e-10       3      70 .]      43     114 ..      41     114 .. 0.93

  Alignments for each domain:
  == domain 1  score: 40.8 bits;  conditional E-value: 7.8e-15
                                        EESETTTSSHHHHHHHHHT.TSCE..EEEEEEEE.TTTSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE CS
                              RRM_1   3 VgnLppdvteeeLkelFsk.fGpi..ksiklvrd.etgkskgfafVeFeskedAekAlealngkklggrelk 70 
                                        + ++p ++ +eeL ++++  + +i  +si lv+d +t+ s+gfafV F++ ed + A++al +k++++++++
  gene1726|gene1726|rna1726|rna1726  43 IFGIPVSIAHEELVDFLKYhIPSIpyQSIHLVKDrQTNLSRGFAFVYFDTIEDSTLAKDALVNKEIHNKRVR 114
                                        56789999999999999998999888******************************************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       351  (0.0195772); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 915.83
//
Query:       gene1727|gene1727|rna1727|rna1727  [L=167]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.037   13.7   0.1      0.071   12.8   0.1    1.5  1  Herpes_teg_N  Herpesvirus tegument protein, N-terminal conser
       0.53   10.6   2.4       0.44   10.8   0.2    2.0  3  IF3_N         Translation initiation factor IF-3, N-terminal 


Domain annotation for each model (and alignments):
>> Herpes_teg_N  Herpesvirus tegument protein, N-terminal conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   7.9e-06     0.071      34      87 ..     100     152 ..      93     165 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 7.9e-06
                       Herpes_teg_N  34 stvlskealdeiLeeGakldallrksgelkveyaqltelPkvvrldavtvkirr 87 
                                        + v++ +++ +iL eGa++  +++ + +l   ++  +e+P  v++++++++   
  gene1727|gene1727|rna1727|rna1727 100 DVVIEDSEVGKILAEGAAT-RMKSDEADLVGVTMTNVEVPAAVMTEEWATETLD 152
                                        5688999************.55555666655588899***99*****9987655 PP

>> IF3_N  Translation initiation factor IF-3, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       1.2   1.1e+04      16      34 ..      12      28 ..       8      31 .. 0.71
   2 ?   -2.1   0.0      0.56     5e+03      12      20 ..      45      53 ..      37      61 .. 0.72
   3 ?   10.8   0.2     5e-05      0.44       4      45 ..      93     133 ..      90     143 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 1.2
                                       SS-EEEEEEHHHHHHHHHH CS
                              IF3_N 16 dGeqlGvistreAlrlaee 34
                                       +Ge  ++i+t  A ++a +
  gene1727|gene1727|rna1727|rna1727 12 EGE--SMITTGMAGQIASD 28
                                       466..56888888888876 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.56
                                       EE-SSS-EE CS
                              IF3_N 12 lvdedGeql 20
                                       lv e+Ge +
  gene1727|gene1727|rna1727|rna1727 45 LVRENGEAM 53
                                       788888844 PP

  == domain 3  score: 10.8 bits;  conditional E-value: 5e-05
                                        S--SSEEEEE-SSS-EEEEEEHHHHHHHHHHHTSEEEEEESS CS
                              IF3_N   4 qIrarevrlvdedGeqlGvistreAlrlaeekgldLVevspn 45 
                                         I ++++ +v ed e +G i  + A  ++++ + dLV v  +
  gene1727|gene1727|rna1727|rna1727  93 MILVPTIDVVIEDSE-VGKILAEGAATRMKSDEADLVGVTMT 133
                                        68899********77.*********************99854 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       578  (0.0322383); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 1259.37
//
Query:       gene1728|gene1728|rna1728|rna1728  [L=331]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (331 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       783  (0.0436723); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 2085.43
//
Query:       gene1729|gene1729|rna1729|rna1729  [L=174]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      3e-22   78.7   0.8    4.6e-22   78.1   0.1    1.6  2  eIF-5_eIF-2B  Domain found in IF2B/IF5
  ------ inclusion threshold ------
      0.044   13.4   1.0       0.06   12.9   1.0    1.3  1  DUF3053       Protein of unknown function (DUF3053)
      0.061   13.1   0.1      0.081   12.6   0.1    1.2  1  CT_C_D        Carboxyltransferase domain, subdomain C and D


Domain annotation for each model (and alignments):
>> eIF-5_eIF-2B  Domain found in IF2B/IF5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1      0.31   1.8e+03       6      32 ..      27      52 ..      22      69 .. 0.60
   2 !   78.1   0.1   7.7e-26   4.6e-22       5     102 ..      72     168 ..      68     174 .] 0.86

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.31
                                       SSSS--SSTT--EEEETT.EEEETTHH CS
                       eIF-5_eIF-2B  6 dkkerykmpklqvkvegkkktvivNfe 32
                                       +++e++km k  + ++ + +  ++N+ 
  gene1729|gene1729|rna1729|rna1729 27 KREEKLKMVKSVLVKKKE-TEHVQNLP 52
                                       556677776665555544.55666664 PP

  == domain 2  score: 78.1 bits;  conditional E-value: 7.7e-26
                                        CSSSS--SSTT--EEEETT.EEEETTHHHHHHHHTTSHHHHHHHHHHHHTSEEEESETTEEEESSSSSCCHHHHHH CS
                       eIF-5_eIF-2B   5 edkkerykmpklqvkvegkkktvivNfeeiakaLnrdpehvlkyllkelgtqgsidengrlilngkfeakklekll 80 
                                        ++++ ++k+p l+vk+e  +kt+i N+ eiak Lnrdp+h+ kyl++el+t+gs++ +g+l+++g+f +++++++l
  gene1729|gene1729|rna1729|rna1729  72 DNTQAKMKLP-LEVKREFGNKTTI-NLVEIAKILNRDPDHIKKYLFSELATSGSVNIEGKLLMKGNFLKAQIQDVL 145
                                        3455566666.6777776658887.*************************************************** PP

                                        HHHHHHHTSTSSSTS.TCEEECC CS
                       eIF-5_eIF-2B  81 dkyieeyVlCkeCks.petelek 102
                                        + yie++++C +C+   +t++++
  gene1729|gene1729|rna1729|rna1729 146 RLYIEHFIVCASCDAvLNTDIVR 168
                                        *************9746888776 PP

>> DUF3053  Protein of unknown function (DUF3053)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   1.0     1e-05      0.06      72     139 ..      24      90 ..      20     144 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1e-05
                            DUF3053  72 vetslepvvdalqsirspqdyltrrdelrqaagalneleqqlqnakaqadkaraaLkqpddlkavydk 139
                                        +++  e+++++++s+ +++   ++ ++l ++   +n l+  ++   +++d+++a++k+p ++k  + +
  gene1729|gene1729|rna1729|rna1729  24 FRKKREEKLKMVKSVLVKKKETEHVQNLPEELTYNNLLKRAMHIL-KSNDNTQAKMKLPLEVKREFGN 90 
                                        667778899999999**************9999988888877665.579**************98865 PP

>> CT_C_D  Carboxyltransferase domain, subdomain C and D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   1.4e-05     0.081      50     121 ..      44     115 ..      22     120 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.4e-05
                                        SEEEEEESCCCCHHHHHH.HHHHHHHH.---------EEEEEEEESTTT-TTHHHHHHHHTS-HHHHHHHHH CS
                             CT_C_D  50 rsllvefdpealdaaellaalkalleeaeeeaaeesrlveipvcYdgevgpDLeevaelnglsveevirlht 121
                                        ++ +v+  pe+l++++ll++  ++l+++++++a+ + ++e+   ++++ + +L e+a++++ +++++ + ++
  gene1729|gene1729|rna1729|rna1729  44 ETEHVQNLPEELTYNNLLKRAMHILKSNDNTQAKMKLPLEVKREFGNKTTINLVEIAKILNRDPDHIKKYLF 115
                                        566788889999***************99999999999***************************9988766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1023  (0.0570584); expected 358.6 (0.02)
Passed bias filter:                      505  (0.0281667); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 1358.03
//
Query:       gene173|gene173|rna173|rna173  [L=44]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (44 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       236  (0.013163); expected 358.6 (0.02)
Passed bias filter:                      176  (0.0098165); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.30u 0.27s 00:00:00.57 Elapsed: 00:00:00.40
# Mc/sec: 330.69
//
Query:       gene1730|gene1730|rna1730|rna1730  [L=401]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (401 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       863  (0.0481343); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 2691.67
//
Query:       gene1731|gene1731|rna1731|rna1731  [L=743]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (743 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       601  (0.0335211); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.43
# Mc/sec: 5160.36
//
Query:       gene1732|gene1732|rna1732|rna1732  [L=456]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.3e-11   42.1  19.5    0.00023   21.1   1.4    6.2  6  TPR_8     Tetratricopeptide repeat
    3.8e-06   26.6  11.9       0.15   12.3   0.4    4.9  4  TPR_2     Tetratricopeptide repeat
    1.5e-05   24.6  19.5     0.0094   15.7   1.2    4.8  5  TPR_1     Tetratricopeptide repeat
    0.00051   20.3   0.9        1.3    9.3   0.1    4.0  3  TPR_12    Tetratricopeptide repeat
     0.0036   17.2   0.2       0.15   12.2   0.0    3.3  2  TPR_7     Tetratricopeptide repeat
  ------ inclusion threshold ------
      0.047   13.7   0.1        0.1   12.6   0.1    1.5  1  DUF4980   Domain of unknown function (DUF4980)
        2.9    7.6  10.0        6.8    6.5   1.1    4.2  4  TPR_11    TPR repeat


Domain annotation for each model (and alignments):
>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       1.2   3.1e+03       3      11 ..      68      76 ..      67      80 .. 0.58
   2 ?   -1.0   0.1       1.1   2.8e+03      18      27 ..     103     112 ..     101     113 .. 0.86
   3 !   21.1   1.4   8.9e-08   0.00023       3      33 ..     217     247 ..     215     248 .. 0.95
   4 !   15.0   0.4   8.5e-06     0.022       3      29 ..     251     277 ..     249     278 .. 0.92
   5 !   10.3   0.2   0.00026      0.67       7      33 ..     289     315 ..     288     316 .. 0.95
   6 ?    4.2   0.0     0.024        61       6      27 ..     355     376 ..     349     378 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1.2
                                       HHHHHHHHH CS
                              TPR_8  3 ayynlgsiy 11
                                       +y++lg+i+
  gene1732|gene1732|rna1732|rna1732 68 IYLKLGNIL 76
                                       455666655 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.1
                                        HHHHHHHHHH CS
                              TPR_8  18 eeAkeyyeka 27 
                                        ++++eyy +a
  gene1732|gene1732|rna1732|rna1732 103 KKSIEYYLEA 112
                                        589****998 PP

  == domain 3  score: 21.1 bits;  conditional E-value: 8.9e-08
                                        HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                              TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                        +y+ lg+ yl+++++ eAk+++ +a+++d++
  gene1732|gene1732|rna1732|rna1732 217 SYLVLGYYYLSKKKHGEAKKCFYEAIKYDKQ 247
                                        7999************************986 PP

  == domain 4  score: 15.0 bits;  conditional E-value: 8.5e-06
                                        HHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                              TPR_8   3 ayynlgsiylklgdyeeAkeyyekale 29 
                                        +++ lg++y+ l++ e+A+++y++a +
  gene1732|gene1732|rna1732|rna1732 251 LWLFLGLAYSGLKECENAISCYKQAKQ 277
                                        799*********************965 PP

  == domain 5  score: 10.3 bits;  conditional E-value: 0.00026
                                        HHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                              TPR_8   7 lgsiylklgdyeeAkeyyekaleldpd 33 
                                        l++ y+k+ ++e+A  +y +a +++p+
  gene1732|gene1732|rna1732|rna1732 289 LAYEYHKMYNIEQASFFYLRAFKIKPE 315
                                        7999*********************97 PP

  == domain 6  score: 4.2 bits;  conditional E-value: 0.024
                                        HHHHHHHHTT-HHHHHHHHHHH CS
                              TPR_8   6 nlgsiylklgdyeeAkeyyeka 27 
                                        + +++ l +gd++ ++ ++ k+
  gene1732|gene1732|rna1732|rna1732 355 LVAYAFLFTGDLDRSEMFLDKC 376
                                        456999***************9 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       1.5     4e+03      18      27 ..     103     112 ..     100     114 .. 0.85
   2 !   12.3   0.4   5.7e-05      0.15       4      32 ..     218     246 ..     216     248 .. 0.91
   3 !    9.1   0.2   0.00058       1.5       3      30 ..     251     278 ..     249     280 .. 0.93
   4 !    9.5   0.4   0.00043       1.1       5      33 ..     287     315 ..     287     316 .. 0.96

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.5
                              TPR_2  18 eeAleafekA 27 
                                        ++ +e++ +A
  gene1732|gene1732|rna1732|rna1732 103 KKSIEYYLEA 112
                                        58899**999 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 5.7e-05
                              TPR_2   4 lynlGlayyklgdyeeAleafekAleldP 32 
                                        +  lG+ y+ ++++ eA+++f +A+++d 
  gene1732|gene1732|rna1732|rna1732 218 YLVLGYYYLSKKKHGEAKKCFYEAIKYDK 246
                                        5679**********************997 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.00058
                              TPR_2   3 alynlGlayyklgdyeeAleafekAlel 30 
                                        ++  lGlay  l++ e A+ ++++A +l
  gene1732|gene1732|rna1732|rna1732 251 LWLFLGLAYSGLKECENAISCYKQAKQL 278
                                        6999*********************887 PP

  == domain 4  score: 9.5 bits;  conditional E-value: 0.00043
                              TPR_2   5 ynlGlayyklgdyeeAleafekAleldPn 33 
                                        ++l++ y k+ + e+A  ++ +A ++ P+
  gene1732|gene1732|rna1732|rna1732 287 FYLAYEYHKMYNIEQASFFYLRAFKIKPE 315
                                        79************************996 PP

>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       2.3     6e+03      10      16 ..      68      74 ..      67      75 .. 0.80
   2 ?   -2.2   0.1       1.7   4.2e+03      19      27 ..     104     112 ..     103     113 .. 0.83
   3 !   15.7   1.2   3.7e-06    0.0094       3      31 ..     217     245 ..     215     247 .. 0.91
   4 !   12.9   0.7   2.9e-05     0.076       3      30 ..     251     278 ..     249     278 .. 0.92
   5 !    6.9   0.5    0.0022       5.7       6      33 ..     288     315 ..     287     316 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 2.3
                                       HHHHTT- CS
                              TPR_1 10 ayfklgk 16
                                       +y+klg+
  gene1732|gene1732|rna1732|rna1732 68 IYLKLGN 74
                                       7999997 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.7
                                        HHHHHHHHH CS
                              TPR_1  19 eAleyyekA 27 
                                        + +eyy +A
  gene1732|gene1732|rna1732|rna1732 104 KSIEYYLEA 112
                                        789***988 PP

  == domain 3  score: 15.7 bits;  conditional E-value: 3.7e-06
                                        HHHHHHHHHHHTT-HHHHHHHHHHHHHHS CS
                              TPR_1   3 alynlGnayfklgkydeAleyyekALeln 31 
                                        ++  lG+ y++++k+ eA +++ +A++ +
  gene1732|gene1732|rna1732|rna1732 217 SYLVLGYYYLSKKKHGEAKKCFYEAIKYD 245
                                        57889*********************987 PP

  == domain 4  score: 12.9 bits;  conditional E-value: 2.9e-05
                                        HHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                              TPR_1   3 alynlGnayfklgkydeAleyyekALel 30 
                                         +  lG+ay  l++ + A+ +y++A +l
  gene1732|gene1732|rna1732|rna1732 251 LWLFLGLAYSGLKECENAISCYKQAKQL 278
                                        6888*********************876 PP

  == domain 5  score: 6.9 bits;  conditional E-value: 0.0022
                                        HHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                              TPR_1   6 nlGnayfklgkydeAleyyekALelnPn 33 
                                         l++ y+k+ + ++A  +y +A ++ P+
  gene1732|gene1732|rna1732|rna1732 288 YLAYEYHKMYNIEQASFFYLRAFKIKPE 315
                                        6999**********************97 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.9   0.0    0.0059        15      45      76 ..     215     246 ..     209     247 .. 0.86
   2 !    9.3   0.1   0.00052       1.3       4      39 ..     250     285 ..     247     315 .. 0.83
   3 ?    0.5   0.0      0.29   7.4e+02       5      33 ..     351     380 ..     347     386 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0059
                             TPR_12  45 attlrnLgrlyralgryeeAlelleealaiae 76 
                                        + ++  Lg +y+  +++ eA + + ea++ ++
  gene1732|gene1732|rna1732|rna1732 215 SVSYLVLGYYYLSKKKHGEAKKCFYEAIKYDK 246
                                        6789999****9999******99999998665 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00052
                             TPR_12   4 talnnlaavlrrlgrydeAlellekaleiarrllGp 39 
                                        +++  l++++  l++++ A++++++a +++  ++ p
  gene1732|gene1732|rna1732|rna1732 250 NLWLFLGLAYSGLKECENAISCYKQAKQLMIGSYKP 285
                                        677679999999*************99998655554 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.29
                             TPR_12   5 alnn.laavlrrlgrydeAlellekaleia 33 
                                        ++n  +a + +  g++d ++ +l+k+ + +
  gene1732|gene1732|rna1732|rna1732 351 VYNLlVAYAFLFTGDLDRSEMFLDKCKRDW 380
                                        566437788888999999999999987655 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0      0.24   6.1e+02      15      29 ..     102     114 ..      95     122 .. 0.79
   2 !   12.2   0.0   5.7e-05      0.15       2      25 ..     252     275 ..     251     285 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.24
                              TPR_7  15 yeeAielyeqsLalt 29 
                                         ++ ie+y +  a+ 
  gene1732|gene1732|rna1732|rna1732 102 DKKSIEYYLE--AMV 114
                                        6899*****9..765 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 5.7e-05
                              TPR_7   2 LlnLarlysrlGdyeeAielyeqs 25 
                                        +l L+ +ys l + e+Ai++y+q+
  gene1732|gene1732|rna1732|rna1732 252 WLFLGLAYSGLKECENAISCYKQA 275
                                        689********************4 PP

>> DUF4980  Domain of unknown function (DUF4980)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   4.1e-05       0.1      33      76 ..      89     131 ..      69     153 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.1e-05
                            DUF4980  33 knnkavkelnvrLavdkvdYyvPldldeykgakevtldikvkge 76 
                                        k n+  +  ++rL +++++Yy+   +++y ++k+++++   + +
  gene1732|gene1732|rna1732|rna1732  89 KRNEDFTLADCRLDKKSIEYYLEAMVKKYVDRKNLLINAVES-D 131
                                        445567788**********************99988875444.3 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.41     1e+03      30      38 ..      68      76 ..      67      77 .. 0.84
   2 ?    6.5   1.1    0.0026       6.8       1      39 [.     222     260 ..     222     263 .. 0.92
   3 ?    4.2   0.4     0.014        35       7      21 ..     262     276 ..     256     278 .. 0.76
   4 ?   -0.8   0.1      0.51   1.3e+03       4      26 ..     293     315 ..     290     316 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.41
                             TPR_11 30 ayynLGlay 38
                                       +y++LG+++
  gene1732|gene1732|rna1732|rna1732 68 IYLKLGNIL 76
                                       9*****986 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0026
                             TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayy 39 
                                        G+ y ++ k  eA +++ +A+k+d +  ++++ LGlay 
  gene1732|gene1732|rna1732|rna1732 222 GYYYLSKKKHGEAKKCFYEAIKYDKQIGNLWLFLGLAYS 260
                                        667999******************************995 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.014
                             TPR_11   7 qGkyeeAieaYkkAl 21 
                                        + + e+Ai +Yk+A 
  gene1732|gene1732|rna1732|rna1732 262 LKECENAISCYKQAK 276
                                        56779********95 PP

  == domain 4  score: -0.8 bits;  conditional E-value: 0.51
                             TPR_11   4 yyeqGkyeeAieaYkkAlkldPd 26 
                                        y++  ++e+A   Y +A k++P+
  gene1732|gene1732|rna1732|rna1732 293 YHKMYNIEQASFFYLRAFKIKPE 315
                                        566667788888899**999995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (456 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       623  (0.0347482); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.45
# Mc/sec: 3021.79
//
Query:       gene1733|gene1733|rna1733|rna1733  [L=402]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    8.9e-27   92.7   0.0    8.9e-27   92.7   0.0    2.6  4  BING4CT      BING4CT (NUC141) domain
  ------ inclusion threshold ------
      0.014   15.7   0.0        7.4    7.0   0.0    3.2  2  ANAPC4_WD40  Anaphase-promoting complex subunit 4 WD40 domain
      0.022   14.0   0.0      0.039   13.2   0.0    1.5  1  RAB3GAP2_N   Rab3 GTPase-activating protein regulatory subuni


Domain annotation for each model (and alignments):
>> BING4CT  BING4CT (NUC141) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.1      0.75   4.5e+03      56      78 ..      22      44 ..      12      45 .. 0.73
   2 ?   -2.2   0.0      0.62   3.7e+03       5      21 ..     147     163 ..     144     172 .. 0.73
   3 ?   -3.8   0.0       1.9   1.2e+04      24      44 ..     207     227 ..     205     234 .. 0.79
   4 !   92.7   0.0   1.5e-30   8.9e-27       8      76 ..     303     371 ..     298     374 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.75
                            BING4CT 56 kkqrrereVrsLLeKlqpelItl 78
                                       +++++e++ ++LL+  + + I l
  gene1733|gene1733|rna1733|rna1733 22 AEAQKENKMNALLQTQERGCIVL 44
                                       46788999999998877777766 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.62
                            BING4CT   5 hklpgskieslrFvpfe 21 
                                        h  ++++++++ + p++
  gene1733|gene1733|rna1733|rna1733 147 HLSHERNVRQMVYLPHH 163
                                        56677888888888886 PP

  == domain 3  score: -3.8 bits;  conditional E-value: 1.9
                            BING4CT  24 lgvghskgissiivPGsGepn 44 
                                        + vg ++g+  +  P + ep 
  gene1733|gene1733|rna1733|rna1733 207 VLVGGTRGVVRFFSPNAKEPL 227
                                        678999999999999998885 PP

  == domain 4  score: 92.7 bits;  conditional E-value: 1.5e-30
                            BING4CT   8 pgskieslrFvpfeDvlgvghskgissiivPGsGepnfdaleanpfetkkqrrereVrsLLeKlqpelI 76 
                                        + ++i+s++F p+eD+l+vg+++g+s +ivPG+G+pn+d +e+ pf tkkqrrere+++L+eK++  +I
  gene1733|gene1733|rna1733|rna1733 303 TYQSINSIEFAPYEDILAVGTKNGLSHMIVPGAGDPNIDFYEDSPFLTKKQRREREIKKLMEKIPSSFI 371
                                        3568*************************************************************9988 PP

>> ANAPC4_WD40  Anaphase-promoting complex subunit 4 WD40 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0    0.0064        38      19      81 ..     135     194 ..     128     245 .. 0.79
   2 ?    7.0   0.0    0.0012       7.4      35      64 ..     301     330 ..     276     337 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.0064
                        ANAPC4_WD40  19 llvfRlngqrvwtleedkedsevrsLaWkpdgklLavaysdgevrlldaesgkvvhslsvkse 81 
                                        l ++  ng +v +l   +++++vr++ + p   lL+   ++  +r ld + gk v +l +k+ 
  gene1733|gene1733|rna1733|rna1733 135 LFIYNKNGLEVHHL---SHERNVRQMVYLPHHFLLVTLSDQPFIRYLDTSMGKEVAKLYIKEP 194
                                        55556666667777...7889999999999866665555556899999999999999887766 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0012
                        ANAPC4_WD40  35 dkedsevrsLaWkpdgklLavaysdgevrl 64 
                                        +++ ++++s+++ p + +Lav++++g  ++
  gene1733|gene1733|rna1733|rna1733 301 KETYQSINSIEFAPYEDILAVGTKNGLSHM 330
                                        566789*******************97665 PP

>> RAB3GAP2_N  Rab3 GTPase-activating protein regulatory subunit N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   6.5e-06     0.039      73     143 ..     201     301 ..     178     327 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 6.5e-06
                         RAB3GAP2_N  73 spdwtviavGlssGylrfytengel.Llsqllheepvlkikcv.............................ssqe 118
                                        + d  +++vG ++G++rf++ n +  L s l++ +++ +i  v                             +s++
  gene1733|gene1733|rna1733|rna1733 201 RRDDGIVLVGGTRGVVRFFSPNAKEpLCSLLVNSSKISSIA-VkknnfvcsslqgtnfydfrnlnepvyrlpKSEN 275
                                        467889***************99872556666779*****9.4456667888888888888888888888877777 PP

                         RAB3GAP2_N 119 keeseelsilypkaivv.idglslls 143
                                        ++ s+ l+  y++ i++ ++g++  +
  gene1733|gene1733|rna1733|rna1733 276 VSLSHVLAMSYKNRITTfLNGTEYVK 301
                                        78888888888888887777776555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (402 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       889  (0.0495845); expected 358.6 (0.02)
Passed bias filter:                      554  (0.0308997); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 2597.43
//
Query:       gene1734|gene1734|rna1734|rna1734  [L=87]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       460  (0.0256568); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.44
# Mc/sec: 595.94
//
Query:       gene1735|gene1735|rna1735|rna1735  [L=39]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (39 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1230  (0.0686039); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.27s 00:00:00.63 Elapsed: 00:00:00.43
# Mc/sec: 275.12
//
Query:       gene1736|gene1736|rna1736|rna1736  [L=399]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.4e-13   48.7  12.2    1.1e-12   48.1  12.2    1.2  1  Pescadillo_N    Pescadillo N-terminus
  ------ inclusion threshold ------
       0.64   10.4   6.0       0.16   12.3   1.4    2.4  2  Ribosomal_L27e  Ribosomal L27e protein family


Domain annotation for each model (and alignments):
>> Pescadillo_N  Pescadillo N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.1  12.2   1.2e-16   1.1e-12       8     261 ..       8     253 ..       3     268 .. 0.79

  Alignments for each domain:
  == domain 1  score: 48.1 bits;  conditional E-value: 1.2e-16
                       Pescadillo_N   8 akkyitrkqalkkLqlslkdFRrLCilKGiyPrepkkkkkankgstaaktyYyakdikfLlhepilekfrei..ka 81 
                                        +k +i+ ++a+ +L+++ ++F+ L i   i+    ++  k +    +    Y  kd++ + + ++ +++++   + 
  gene1736|gene1736|rna1736|rna1736   8 QKTHISMQKACEELKVTKEQFKELIIHLNIHAESVRSIYKLSC---SDANTYSLKDVNKIYNSKLYATIQKNnqRE 80 
                                        7889******************************999888877...3466799*************9997641134 PP

                       Pescadillo_N  82 fakklkkalakkekekakrleknkpkykldhiikeRYPtfidAlrdldDaLsliflfatlpktkkikekliekcer 157
                                        ++kk+ + +++   +++    +n   y   +ii  +Y +f dA+ dl ++L+ ++++ ++ ++ + +e + e  + 
  gene1736|gene1736|rna1736|rna1736  81 LEKKTWRRRNR---NDIADKMRN-LDYDYVNIISSKYRSFSDAVADLGETLTFLYVYQFFSSRINDEEGISEIIRA 152
                                        44444444333...333333333.4688899******************************999999999999999 PP

                       Pescadillo_N 158 laeefqayviksrslrkvFlSiKGiYyqaeikgqkvtWlvPykfaqklekdvdfkvmltflefYetllkfvnfkLy 233
                                          ++f++++i +  ++ v+   KG+    +i+  ++ + vP + +    +d++ + +l ++++Y+  l  vn ++ 
  gene1736|gene1736|rna1736|rna1736 153 ELAKFEKFMIDNTLIKSVYPTKKGLHVLLRINVVEILFFVPLNSN---FTDIKRNDFLPYIKLYMYHLMMVNCRMK 225
                                        99***************************************9765...5688888889****************97 PP

                       Pescadillo_N 234 kslnlkyppkldeekdekaaelealsle 261
                                        +    +  + +de++ e++++ ++ + e
  gene1736|gene1736|rna1736|rna1736 226 NVKIDTAKDVVDEREYENEDNGRENAKE 253
                                        6444444455554444444433333322 PP

>> Ribosomal_L27e  Ribosomal L27e protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.2      0.43   3.8e+03      45      65 ..      76      96 ..      56     102 .. 0.56
   2 ?   12.3   1.4   1.8e-05      0.16      13      72 ..     202     263 ..     196     283 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.43
                     Ribosomal_L27e 45 vkkealkdpakrkeakkevkk 65
                                        ++ +l++++ r++ ++++++
  gene1736|gene1736|rna1736|rna1736 76 NNQRELEKKTWRRRNRNDIAD 96
                                       334445555555555555555 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 1.8e-05
                     Ribosomal_L27e  13 krskikpFvKvvnynhlmpTRY...tvdvedlkelvkkealkdpakrkeakkevkkkfeeryk 72 
                                        kr+ + p++K + y hlm   +   +v++   k++v++ + ++ ++ +e  ke+kk    +++
  gene1736|gene1736|rna1736|rna1736 202 KRNDFLPYIKLYMY-HLMMVNCrmkNVKIDTAKDVVDEREYENEDNGRENAKETKKDSTYNHD 263
                                        8999*******988.88888885566677889*********9999888888888887776663 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (399 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1553  (0.0866194); expected 358.6 (0.02)
Passed bias filter:                      503  (0.0280551); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.48
# Mc/sec: 2522.86
//
Query:       gene1737|gene1737|rna1737|rna1737  [L=759]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.7e-19   68.1   0.1    3.2e-18   66.1   0.0    2.1  2  SMC_hinge     SMC proteins Flexible Hinge Domain
    3.3e-16   59.4  24.0    6.6e-16   58.4  23.8    1.8  1  SMC_N         RecF/RecN/SMC N terminal domain
  ------ inclusion threshold ------
       0.81    9.8   9.0       0.22   11.6   1.0    3.4  3  TLE_N         Groucho/TLE N-terminal Q-rich domain
          3    7.3  30.4        0.3   10.6   2.0    3.3  3  Exonuc_VII_L  Exonuclease VII, large subunit


Domain annotation for each model (and alignments):
>> SMC_hinge  SMC proteins Flexible Hinge Domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.1      0.88     4e+03      35      75 ..      86     128 ..      75     168 .. 0.61
   2 !   66.1   0.0   7.2e-22   3.2e-18       2     108 ..     174     278 ..     173     285 .. 0.96

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.88
                          SMC_hinge  35 vedeetakkiieflkkknagratflpldr..ikqknkadgand 75 
                                        ve+  + +k ie l+kk   + +++   +  i++ +++ ++n+
  gene1737|gene1737|rna1737|rna1737  86 VETVRSNTKEIERLEKKAERNKALMKGTKkrIDDLKQKVDENT 128
                                        6777777777788888754445554442222333333333333 PP

  == domain 2  score: 66.1 bits;  conditional E-value: 7.2e-22
                          SMC_hinge   2 kgvlGrladlievd.egyekAveaalgnrlqalvvedeetakkiieflkkknagratflpldrikqknkadgandk 76 
                                        +gv G l +l++v  ++y  ++e+ lg + q +v+ ++++a ++i++l+ k++ r+tf+p+d++k  nk+ ++ + 
  gene1737|gene1737|rna1737|rna1737 174 PGVRGKLKNLLTVNqSRYVLPIEVLLGYHSQVIVTNTKDEALRCINYLEVKRLCRLTFFPIDSMKRLNKRTEVIN- 248
                                        799*********************************************************************988. PP

                          SMC_hinge  77 nsgavplidlvevddelrkalryllgdtlvvd 108
                                          g v+++d++++ + l+++++ ++ d++v  
  gene1737|gene1737|rna1737|rna1737 249 --GFVRAMDCISYSPDLQNIFECVFNDCYVIL 278
                                        ..9*************************9975 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.4  23.8   1.5e-19   6.6e-16     135     216 ..     420     748 ..      42     751 .. 0.75

  Alignments for each domain:
  == domain 1  score: 58.4 bits;  conditional E-value: 1.5e-19
                                        T........................................................................... CS
                                        x........................................................................... RF
                              SMC_N 135 e........................................................................... 135
                                                                                                                    
  gene1737|gene1737|rna1737|rna1737 420 Irarenekknllaefsrvkreleheieelsakmnirnkekdiksnferinkelkdakavfeeqrsasdrivneina 495
                                        0444444444444444444444444444444444444444444445555555555555555555555577788888 PP

                                        ............................................................................ CS
                                        ............................................................................ RF
                              SMC_N 136 ............................................................................ 135
                                                                                                                    
  gene1737|gene1737|rna1737|rna1737 496 vnkellvikneteklenekeeilqlgileeimspddvdkhvvaegnikekeeelnslnmkieeiyatcssgtaenr 571
                                        88888888888888888888888888888999999999999999999999999999999999************** PP

                                        ............................................................................ CS
                                        ............................................................................ RF
                              SMC_N 136 ............................................................................ 135
                                                                                                                    
  gene1737|gene1737|rna1737|rna1737 572 netkelkelqkqyeekkkesidlraelrgvkksrlelfnegygrisdilhkifsffnqsaqltctnmaepylgeik 647
                                        **************************************************************************** PP

                                        ............CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCT........TSE CS
                                        ............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........xxx RF
                              SMC_N 136 ............lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksk........naQ 191
                                                     LSgGek+++ l +++A++k+  ap+y++Deid+aLD ++++ ++e+l ++++        n Q
  gene1737|gene1737|rna1737|rna1737 648 yyvlkdeykfydDLSGGEKSIALLCFILAVNKYFNAPFYFFDEIDSALDRTHMASLSEYLSSRNEgekddlfdNDQ 723
                                        ************************************************************965432222233289* PP

                                        EEEE-SSHHHCCC-SCEEEEEEEET CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxx RF
                              SMC_N 192 fivislreemlekadklvgvtkven 216
                                        fi+isl++e++++ad+l+gv+  ++
  gene1737|gene1737|rna1737|rna1737 724 FICISLKKEFFKNADSLIGVYRSDS 748
                                        *********************9543 PP

>> TLE_N  Groucho/TLE N-terminal Q-rich domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.2     0.062   2.8e+02      70      98 ..      41      68 ..      24     148 .. 0.78
   2 ?   -3.4   0.1       2.1   9.5e+03      20      34 ..     337     351 ..     327     368 .. 0.71
   3 ?   11.6   1.0     5e-05      0.22      23      55 ..     485     517 ..     470     523 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.062
                              TLE_N 70 niemhkqteiakrlnaiiaqvlpflsqeh 98
                                       ++++ k++ei  r+n+i  +   +l  e 
  gene1737|gene1737|rna1737|rna1737 41 EMDADKHAEIIERVNQIREDY-NILLYEF 68
                                       344558999999999987643.3344444 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 2.1
                              TLE_N  20 vlescdrikeefqfl 34 
                                        +le ++ ikee +++
  gene1737|gene1737|rna1737|rna1737 337 ILERIEEIKEENKIM 351
                                        567778888886665 PP

  == domain 3  score: 11.6 bits;  conditional E-value: 5e-05
                              TLE_N  23 scdrikeefqflqaqyhsLklecekLasektem 55 
                                        + dri +e++ +++++  +k e ekL +ek e+
  gene1737|gene1737|rna1737|rna1737 485 ASDRIVNEINAVNKELLVIKNETEKLENEKEEI 517
                                        67*****************************97 PP

>> Exonuc_VII_L  Exonuclease VII, large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   2.0   6.6e-05       0.3     150     223 ..      76     156 ..      28     223 .. 0.67
   2 ?    1.9   0.9      0.03   1.3e+02     213     274 ..     340     410 ..     311     430 .. 0.56
   3 ?    3.6  14.7    0.0088        40     140     255 ..     436     583 ..     418     629 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 6.6e-05
                       Exonuc_VII_L 150 eelerrlekaikrlleekkqrleklasrlkspeellerkrqrldeleerleralkkq...lkkkrerleelkerl. 221
                                         + er++++ + ++++++ +++e+l+++ +++++l++  ++r+d+l++++++++++    lk+++++l+e+  ++ 
  gene1737|gene1737|rna1737|rna1737  76 IKDERNIRNLV-ETVRSNTKEIERLEKKAERNKALMKGTKKRIDDLKQKVDENTSNDlvrLKNRETELNEILGQFl 150
                                        33333444444.4567788899999999999999999999999999999999888774444444455544444443 PP

                       Exonuc_VII_L 222 k....e 223
                                        +     
  gene1737|gene1737|rna1737|rna1737 151 RyksfI 156
                                        354442 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.03
                       Exonuc_VII_L 213 rleelkerlk..........ekleekkerlkklkerlelleekkerleeleeklealsplkvLkrGyaivrk 274
                                        r+ee+ke+ k          ++++e +++ ++++++   l+++  +++++ ++l+a++ +++L+ G++ +++
  gene1737|gene1737|rna1737|rna1737 340 RIEEIKEENKimcieqvaleNTINELRAHNETINSKNPYLNARFAEFDRQLKRLKAVKFKSILN-GFSSIEE 410
                                        2222221111222222222244444444444554445578999999999999999999999985.8887775 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.0088
                       Exonuc_VII_L 140 pdkaeleeqleelerrlekaikrlleekkqrleklasrlkspeellerkrqrldeleerleralkkq...lkkkre 212
                                        ++k+ele+++eel+++++  i+++ ++ k+++e+++++lk++++++e++r++ d++ +++++ ++k+   +k+++e
  gene1737|gene1737|rna1737|rna1737 436 RVKRELEHEIEELSAKMN--IRNKEKDIKSNFERINKELKDAKAVFEEQRSASDRIVNEINA-VNKEllvIKNETE 508
                                        244445555555554443..3334466677888999999*9***************999999.4444488888888 PP

                       Exonuc_VII_L 213 rleelkerl.k....................ekleekkerlkklkerle...........lleekkerleeleek 255
                                        +le+ ke++ +                     +++ek+e+l++l++++e           + ++++++l+el+++
  gene1737|gene1737|rna1737|rna1737 509 KLENEKEEIlQlgileeimspddvdkhvvaeGNIKEKEEELNSLNMKIEeiyatcssgtaENRNETKELKELQKQ 583
                                        888888888668888777777777666666655555666666665555555555544433122222222222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (759 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2480  (0.138323); expected 358.6 (0.02)
Passed bias filter:                      558  (0.0311228); expected 358.6 (0.02)
Passed Vit filter:                        89  (0.00496402); expected 17.9 (0.001)
Passed Fwd filter:                        42  (0.00234257); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 1.24u 0.37s 00:00:01.61 Elapsed: 00:00:00.58
# Mc/sec: 3913.84
//
Query:       gene1738|gene1738|rna1738|rna1738  [L=240]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.1e-10   38.2   0.0    4.9e-07   29.2   0.1    2.9  2  PAXNEB    PAXNEB protein


Domain annotation for each model (and alignments):
>> PAXNEB  PAXNEB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.2   0.1   2.7e-11   4.9e-07      22     128 ..      17     100 ..      13     128 .. 0.77
   2 !    5.0   0.0   0.00064        11     293     346 ..     184     230 ..     146     236 .. 0.78

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 2.7e-11
                             PAXNEB  22 GtpsLDklLgGGLplGsillieEdgttdfakvLlkyFlAeGvvqkhevlvlsldddpeewlreLPgpltdkeeeke 97 
                                        G+p LD+ L   +  G+++lie d  t+ +++  k+F+A+ + ++++v+v s+   p      +P++++       
  gene1738|gene1738|rna1738|rna1738  17 GIPLLDNTL--SIEPGTSILIEHDPDTNNHHIFEKLFVAQSIADGKKVTVRSF---P----FCIPATVS------- 76 
                                        89999**99..8999**************************************...3....34677774....... PP

                             PAXNEB  98 qrkeekkaeeekeendlkIAWRYekelpkvq 128
                                        + +e+       +++ + IAWRY +++++++
  gene1738|gene1738|rna1738|rna1738  77 RTEEQ-------KYRPMEIAWRYAQRSRPET 100
                                        11222.......3567*******99333333 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.00064
                             PAXNEB 293 palkseeyqGlLkihklpalnelavgmpetedlafklsrkkfvIekfhLPPels 346
                                        + +k++ y+GlL+i+k ++        p++  +   +sr   ++e+f+L+P+++
  gene1738|gene1738|rna1738|rna1738 184 NYAKENGYHGLLRIKKFTRK-------PDNLLYGYNISRYGVIMEQFSLAPDDE 230
                                        3345578*********9775.......566688999999999999999999885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (240 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       353  (0.0196888); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1712.71
//
Query:       gene1739|gene1739|rna1739|rna1739  [L=413]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.4e-05   22.8  36.5     0.0045   15.8  36.5    2.2  1  MAP65_ASE1    Microtubule associated protein (MAP65/ASE1 fami
  ------ inclusion threshold ------
      0.063   13.3   5.6        2.2    8.3   1.2    3.1  3  DUF1216       Protein of unknown function (DUF1216)
       0.13   12.2   0.4       0.13   12.2   0.4    4.2  4  DASH_Dad4     DASH complex subunit Dad4


Domain annotation for each model (and alignments):
>> MAP65_ASE1  Microtubule associated protein (MAP65/ASE1 family)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8  36.5   7.5e-07    0.0045      27     409 ..       1     388 [.       1     396 [. 0.80

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 7.5e-07
                                        HHHHHHHHHHHHHHHHHHHHHHST-----....-SS--SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MAP65_ASE1  27 ieqkilneIaelraeasglksiLheepvdvpqsekkelsLlqkkkkldtaleelrkekaerlaeflelleqlqklc 102
                                        +e++i+++I ++++ ++++ + L+   +d     +++  L +  +++ ++++  +++ +e+++e++++le++++ +
  gene1739|gene1739|rna1739|rna1739   1 MEENIISRIHSNIDKLNNTIHKLSP--ID-ELIVPSPNYLEEHFSNIAREIDTALERVQEKMREIENKLEKDKQEL 73 
                                        5778888888888888888777776..55.44456677899******************************99866 PP

                                        HHHTS---SS--TSS--HHHHHHHHHHHHHHHH....HHHHHHHHHHHHHHHHHHHHHHHT----SHHHHHHHCT- CS
                         MAP65_ASE1 103 eelgeeplsllidslpkleeleslrkhleelke....ekerRleeikelkkqIkslmeeLglepktsieedllkes 174
                                           g+  +  l+ +++k+e+l   r  +++ ++      +  +e++k + kqI+ +   L  + +  ++++ +   
  gene1739|gene1739|rna1739|rna1739  74 IVRGS--RIGLSVKFEKFENLMLDRLNVANERNriivLEKIMMEKVKFFSKQINDYHYDLYGTYSGYANNECS--- 144
                                        55555..556888999999987777777777776666445568999999********************9443... PP

                                        TTTS-....TSHHHHH..HHHHHHHHHHHHH..HHHHHHHHHHH.HHHHHHHHHS---HHHHHHH........TTT CS
                         MAP65_ASE1 175 ednskklkpltretik..kLkllkkeleeqk..sereeklkdlr.ekikeLWnrLqvpqeeqeaf........vre 237
                                         +n +++ +l++++ +  +L++ +++l ++k  + +++ ++d++  ++  L ++  + +e+ e+          r 
  gene1739|gene1739|rna1739|rna1739 145 LENLETVRKLHDKLVAdvNLRFNQRRLLKKKllKYKMKDIDDMKfFQMVALVKKITEQEEKEEKLkivlrrsiHRV 220
                                        4444557789999998334667777776666223467777888734899999999998888888866666664444 PP

                                        SSSSSHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT--.-HHHHHTC-TTSTSS-.SHHHHHHHHHH CS
                         MAP65_ASE1 238 nsslsqetidaleeEleRLeeLKkknlkklIedlRqeIeelWdklly.seeerkafipvfeele.deelLelhEle 311
                                           l+ ++  +l + le+L+ +      kl+e+ + + + + d +    +e ++ f  +f++l+ + e   l+ + 
  gene1739|gene1739|rna1739|rna1739 221 LDLLNRDNDVVLPNNLEKLKIIY----EKLLEEEKAQFDRIFDATEReFNEICSIFFVKFDKLKrTRESIILMKKI 292
                                        45555556666666666666665....56789999999999999975268999999999999999899999999** PP

                                        HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-GGGGTSSTSH..HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MAP65_ASE1 312 lkqLkeelesnKeilelvekfeslwedeeeLEakskDpsRlnnRGghkiLLkEEKeRkriskhlPkveqeLtekve 387
                                        +++L e+ e+  e+ el+ek++ ++ + e +E+ ++Dp+Rl   G+ + LL EE+ R+++  +l  +e+++  k++
  gene1739|gene1739|rna1739|rna1739 293 INDLTERKEHFVELKELIEKRARIIVEIELFEKTARDPNRLK--GSSLQLLHEERFRRKVIPSLLEMESRILGKLN 366
                                        *****************************************7..67777*************************** PP

                                        HHHHHCTS--EETTEEHHHHHH CS
                         MAP65_ASE1 388 aweeefgrpFlvdGeklleiie 409
                                         +++  ++pF++ +e+  e + 
  gene1739|gene1739|rna1739|rna1739 367 DYKQLYNEPFMYGDEDYEEKLR 388
                                        **************98777665 PP

>> DUF1216  Protein of unknown function (DUF1216)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0     0.003        18       3      63 ..      14      74 ..      13      78 .. 0.86
   2 ?    8.3   1.2   0.00036       2.2      40      91 ..     161     212 ..     148     217 .. 0.79
   3 ?   -1.8   0.0       0.5     3e+03      64      89 ..     234     259 ..     225     273 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.003
                            DUF1216  3 ekLkalmkasckvsst...dekeyvsdmkskagklseamavlasklsksgevkkslqeeqqevm 63
                                       +kL ++++ ++++ +    + + + ++ +  a ++  a++ +++   k  e++++l++++qe++
  gene1739|gene1739|rna1739|rna1739 14 DKLNNTIHKLSPIDELivpSPNYLEEHFSNIAREIDTALERVQE---KMREIENKLEKDKQELI 74
                                       6899999999999999996666667777888999********99...889************98 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00036
                            DUF1216  40 vlasklsksgevkkslqeeqqevmktlkelqsva.skivsekkskkegsltlt 91 
                                         ++ ++++   +kk+l +++++ ++ +k++q va  k ++e+++k e+ l++ 
  gene1739|gene1739|rna1739|rna1739 161 DVNLRFNQRRLLKKKLLKYKMKDIDDMKFFQMVAlVKKITEQEEK-EEKLKIV 212
                                        56778999999********************99734667766555.8888765 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 0.5
                            DUF1216  64 ktlkelqsvaskivsekkskkegslt 89 
                                        ++l++l+ +++k+  e+k + +    
  gene1739|gene1739|rna1739|rna1739 234 NNLEKLKIIYEKLLEEEKAQFDRIFD 259
                                        78999999999999998877665555 PP

>> DASH_Dad4  DASH complex subunit Dad4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.4   2.2e-05      0.13      10      30 ..       3      23 ..       1      30 [. 0.91
   2 ?    2.0   0.4     0.035   2.1e+02       6      36 ..      38      68 ..      34      72 .. 0.80
   3 ?   -3.2   0.1       1.4   8.5e+03      33      50 ..      96     113 ..      91     124 .. 0.61
   4 ?    1.5   0.1     0.049   2.9e+02      24      53 ..     283     312 ..     276     327 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.2e-05
                          DASH_Dad4 10 salLsRIiknvekLnesvvel 30
                                       ++++sRI +n++kLn+++++l
  gene1739|gene1739|rna1739|rna1739  3 ENIISRIHSNIDKLNNTIHKL 23
                                       689***************998 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.035
                          DASH_Dad4  6 eeqqsalLsRIiknvekLnesvvelnkelee 36
                                       ee+ s++ + I + +e++ e++ e++++le+
  gene1739|gene1739|rna1739|rna1739 38 EEHFSNIAREIDTALERVQEKMREIENKLEK 68
                                       566667777777889************9997 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 1.4
                          DASH_Dad4  33 eleeinkkNknvelvsql 50 
                                        +l+ +n++N+ + l + +
  gene1739|gene1739|rna1739|rna1739  96 RLNVANERNRIIVLEKIM 113
                                        455556666555544444 PP

  == domain 4  score: 1.5 bits;  conditional E-value: 0.049
                          DASH_Dad4  24 nesvvelnkeleeinkkNknvelvsqlwen 53 
                                         es++ ++k +++ +++ ++   +++l+e+
  gene1739|gene1739|rna1739|rna1739 283 RESIILMKKIINDLTERKEHFVELKELIEK 312
                                        566666666666666666666666665554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (413 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2072  (0.115567); expected 358.6 (0.02)
Passed bias filter:                      601  (0.0335211); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.66u 0.36s 00:00:01.02 Elapsed: 00:00:00.50
# Mc/sec: 2472.79
//
Query:       gene1740|gene1740|rna1740|rna1740  [L=286]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.5e-21   75.0   0.1      6e-20   71.1   0.1    2.3  2  TFIID-18kDa  Transcription initiation factor IID, 18kD subuni


Domain annotation for each model (and alignments):
>> TFIID-18kDa  Transcription initiation factor IID, 18kD subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.1   0.1   3.4e-24     6e-20       2      87 ..      27     112 ..      26     117 .. 0.95
   2 ?    1.3   0.0      0.02   3.5e+02      38      72 ..     130     164 ..     125     170 .. 0.79

  Alignments for each domain:
  == domain 1  score: 71.1 bits;  conditional E-value: 3.4e-24
                                        --CCCCHHHHHCTTS-SS--HHHHHHHHHHHHHHHHHHHHHHHC-XXXX...XXXXXXXXXXXXXXXXXXXXXXXX CS
                        TFIID-18kDa   2 lfrkelqsmlyalGdvkePlqetvqlledlvrgyliellqqaakvaklrgsrkitlEDllfliRkDkkKlnRlkel 77 
                                        l+ +e+++mly++Gd k+P  +t+q le ++++++   l  a+++   r  + i+lED+ f+iRkD+ Kl+Rl ++
  gene1740|gene1740|rna1740|rna1740  27 LYTNEIKAMLYSFGDSKNPSLQTAQYLESVLKTQIQRFLSAANNIRICRRGKLINLEDIGFVIRKDPFKLRRLLNF 102
                                        6999********************************************999************************* PP

                                        XXXXXXXXXX CS
                        TFIID-18kDa  78 lslkellkka 87 
                                        + +ke + k 
  gene1740|gene1740|rna1740|rna1740 103 IHFKEIKGKL 112
                                        *****99775 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.02
                                        HHHHHHHC-XXXX...XXXXXXXXXXXXXXXXXXX CS
                        TFIID-18kDa  38 ellqqaakvaklrgsrkitlEDllfliRkDkkKln 72 
                                         l++  ++     +s++ ++E  +f i  D+kK++
  gene1740|gene1740|rna1740|rna1740 130 PLCEDNVENKSDIDSNSAKIEPDIFKITNDEKKFS 164
                                        566666666666778999999999*********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       485  (0.0270511); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 2009.54
//
Query:       gene1741|gene1741|rna1741|rna1741  [L=258]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       996  (0.0555525); expected 358.6 (0.02)
Passed bias filter:                      532  (0.0296726); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 1620.81
//
Query:       gene1742|gene1742|rna1742|rna1742  [L=119]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.6e-15   56.6   0.1    2.1e-15   56.3   0.1    1.2  1  eIF-1a       Translation initiation factor 1A / IF-1
  ------ inclusion threshold ------
       0.02   14.5   0.0      0.025   14.2   0.0    1.1  1  TRF          Telomere repeat binding factor (TRF)
      0.081   13.6   0.0       0.14   12.8   0.0    1.4  1  Ground-like  Ground-like domain


Domain annotation for each model (and alignments):
>> eIF-1a  Translation initiation factor 1A / IF-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.3   0.1   3.5e-19   2.1e-15       2      64 .]      25      85 ..      24      85 .. 0.94

  Alignments for each domain:
  == domain 1  score: 56.3 bits;  conditional E-value: 3.5e-19
                                       EEEEEEEEEETTTEEEEEE.SSSSBEEEEE-HHHHCT----TT-EEEEEE-TT-TTEEEEES- CS
                             eIF-1a  2 evigkViealgnnlfrVelpdngkevlaeipgkfRnkiwikrGdyVlVelspydltkGrIvyr 64
                                        v+g++++a g+++f+V ++d + +++++++g + +++wi  +d+Vl++ +++ ++kG+I+++
  gene1742|gene1742|rna1742|rna1742 25 SVYGQITRAFGSGRFEVICSD-SSTRVCKVRGSMYKRVWIQANDIVLISNREE-DDKGDIMHK 85
                                       699****************85.****************************776.89****986 PP

>> TRF  Telomere repeat binding factor (TRF)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   4.2e-06     0.025     107     164 ..      39      95 ..      29     106 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.2e-06
                                        HHHHHHCTTSHHHHHHHHHHHHHHHHHHH.HHHHHTT-HHHHHHHHHHHSSSSTCCHH. CS
                                TRF 107 ldifcpenelgkllkpqgvLyleLktqay.isalkeaeerskeeiLddlfpddlediLl 164
                                        ++++c+++ + ++ k  g +y+ + +qa  i+ +++ ee +k +i+ ++fp+++++ L+
  gene1742|gene1742|rna1742|rna1742  39 FEVICSDS-STRVCKVRGSMYKRVWIQANdIVLISNREEDDKGDIMHKYFPYEIKQ-LK 95 
                                        8999*998.78999**************7699999*******************98.54 PP

>> Ground-like  Ground-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   2.4e-05      0.14      29      57 ..      26      55 ..      11      58 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.4e-05
                        Ground-like 29 iqkaleekfgs.sfevicsegdfsytifag 57
                                       ++++  + fgs +fevics+++  +  ++g
  gene1742|gene1742|rna1742|rna1742 26 VYGQITRAFGSgRFEVICSDSSTRVCKVRG 55
                                       677889999999********9987733555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       390  (0.0217525); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 842.50
//
Query:       gene1743|gene1743|rna1743|rna1743  [L=158]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
       0.99    8.7   8.3        1.2    8.5   8.3    1.0  1  FAM76         FAM76 protein


Domain annotation for each model (and alignments):
>> FAM76  FAM76 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   8.3   6.4e-05       1.2     138     239 ..       8     105 ..       2     134 .. 0.48

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 6.4e-05
                              FAM76 138 akeeeeekrskskkkkskskkskkskekskekkaskkkskkhkkrssrlevskleeeklaeekesnetskksldsn 213
                                        +kee +++++k+++ k+ ++ +++s++++ +k++s k+ + +++++++ + ++++  k      +++++++s  + 
  gene1743|gene1743|rna1743|rna1743   8 KKEEVRDEEPKQEEVKKDEQPEEQSQKEEPAKTESAKNVEPVEEKPEEAKQTEIHIPK---I--KSGKMQQSGVLM 78 
                                        3333333444444444444444444444444444444445556666666666665222...2..222222222222 PP

                              FAM76 214 ssd.hlvavtqLkeeiaslkkqleqkd 239
                                        ++d   v++ ++ e ++++k + + k+
  gene1743|gene1743|rna1743|rna1743  79 QNDiLTVQIDDIVEYVKNRKEMEKLKE 105
                                        233133555566666655555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2705  (0.150873); expected 358.6 (0.02)
Passed bias filter:                     1155  (0.0644208); expected 358.6 (0.02)
Passed Vit filter:                       175  (0.00976072); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.34s 00:00:00.89 Elapsed: 00:00:00.47
# Mc/sec: 1016.36
//
Query:       gene1744|gene1744|rna1744|rna1744  [L=428]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0087   16.5   6.5       0.62   10.5   0.5    3.3  2  Snapin_Pallidin  Snapin/Pallidin
  ------ inclusion threshold ------
      0.047   13.8   0.1       0.13   12.4   0.1    1.8  1  DUF2794          Protein of unknown function (DUF2794)
        0.1   13.1   3.3       0.43   11.0   0.5    3.0  3  SPG48            AP-5 complex subunit, vesicle trafficking


Domain annotation for each model (and alignments):
>> Snapin_Pallidin  Snapin/Pallidin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.5    0.0001      0.62      34      78 ..      23      67 ..       5      71 .. 0.89
   2 !    6.9   0.9    0.0014       8.3      39      74 ..     169     206 ..     163     221 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0001
                    Snapin_Pallidin 34 eqldrlnekLkeleeaqeaevlpdlkeyakKLvnikkrmsslner 78
                                       e++++  ekLk+ ++  e+++l +lk+y  +Lv++++ ++ ++  
  gene1744|gene1744|rna1744|rna1744 23 EEIKNKIEKLKNSRKSSEDAILCQLKQYEGRLVEVERLLHDIHPN 67
                                       789999999998888877999***************999999865 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0014
                    Snapin_Pallidin  39 lnekLkeleeaqe..aevlpdlkeyakKLvnikkrmss 74 
                                         ++++k+l+e+ +  +e+++d++ y+k + ++kk++  
  gene1744|gene1744|rna1744|rna1744 169 AKKEMKNLSEELSrfNEYFVDTPFYKKNIDELKKKVLV 206
                                        44555555554444667899999999999999998754 PP

>> DUF2794  Protein of unknown function (DUF2794)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   2.2e-05      0.13      35      64 ..      67      96 ..      60     116 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.2e-05
                            DUF2794 35 vavFsvFrraaeiplYriekdpalarrqga 64
                                        + F++F+++ +  lYriekd  +++ ++ 
  gene1744|gene1744|rna1744|rna1744 67 NVQFAIFKNKNNEVLYRIEKDAVASAENED 96
                                       578******************887777665 PP

>> SPG48  AP-5 complex subunit, vesicle trafficking
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.5   7.3e-05      0.43      43     118 .]     233     310 ..     205     310 .. 0.83
   2 ?   -0.6   0.0       0.3   1.8e+03      83     105 ..     305     327 ..     299     343 .. 0.81
   3 ?    1.1   0.0     0.091   5.4e+02      67     103 ..     348     385 ..     331     391 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 7.3e-05
                              SPG48  43 skarllLailqFfLnhgea.vavdaeavlktlftsvlseefadpvlaf.etvqflrenlekLlkstsllkqyfPnl 116
                                        +     L i++ ++n +++ ++  +++++ ++f +  s+++++++laf +++ f ++ ++ +   ++l +  f n+
  gene1744|gene1744|rna1744|rna1744 233 KDFLDALMIMENLINIDDIkIMKFVKQAIADFFDDKRSKTMHEKILAFsDAIYFTQQYKRDFYDANGLKEDVFSNI 308
                                        555557888899999999955556799********************96799*******99999998888888888 PP

                              SPG48 117 lK 118
                                         K
  gene1744|gene1744|rna1744|rna1744 309 VK 310
                                        76 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.3
                              SPG48  83 adpvlafetvqflrenlekLlks 105
                                         ++++  e+v+f ++nle +l++
  gene1744|gene1744|rna1744|rna1744 305 FSNIVKSEVVSFQQSNLEHFLND 327
                                        56778889999999999999876 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.091
                              SPG48  67 eavlktlftsvlseefadpvlafetvq.flrenlekLl 103
                                        +++lk+++++ l e f   vl+f+t++ f   nl+k++
  gene1744|gene1744|rna1744|rna1744 348 NDTLKEIYNDKLCESFVGYVLSFDTISeFDALNLTKIS 385
                                        678999999999************99536666766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (428 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2048  (0.114228); expected 358.6 (0.02)
Passed bias filter:                      592  (0.0330191); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.45
# Mc/sec: 2853.14
//
Query:       gene1745|gene1745|rna1745|rna1745  [L=197]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.012   15.1   0.5      0.024   14.2   0.0    1.7  2  DUF1974   Domain of unknown function (DUF1974)
       0.17   11.9   0.0       0.17   11.9   0.0    3.2  3  RNR_N     Ribonucleotide reductase N-terminal


Domain annotation for each model (and alignments):
>> DUF1974  Domain of unknown function (DUF1974)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   2.6e-06     0.024     220     270 ..       3      53 ..       1      67 [. 0.91
   2 ?   -1.4   0.1      0.15   1.3e+03     219     225 ..     138     144 ..     104     170 .. 0.48

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.6e-06
                            DUF1974 220 fkavlaaeplekklkkaikkgklkklkleelleealekgviteeeaellee 270
                                        f +v  +e+le+k+++ ++++ l+++ ++e +++a+++g+i ee+ ++l +
  gene1745|gene1745|rna1745|rna1745   3 FLNVKPMEDLEEKIRRKHQNDYLPQEVVDEYIRAAINHGLIVEEDLKQLPK 53 
                                        6778889****************************************9965 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.15
                            DUF1974 219 afkavla 225
                                         +k+vl+
  gene1745|gene1745|rna1745|rna1745 138 RLKNVLN 144
                                        2222222 PP

>> RNR_N  Ribonucleotide reductase N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   1.9e-05      0.17      37      71 ..       5      39 ..       1      43 [. 0.91
   2 ?    0.5   0.1     0.068   6.1e+02      36      61 ..      52      77 ..      44      95 .. 0.73
   3 ?    0.4   1.0     0.073   6.6e+02      41      62 ..     132     152 ..     121     162 .. 0.55

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.9e-05
                              RNR_N 37 ntvkfesleekldyLvendYyeeevlekYskefie 71
                                       n + +e+leek++   +ndY  +ev+++Y ++ i+
  gene1745|gene1745|rna1745|rna1745  5 NVKPMEDLEEKIRRKHQNDYLPQEVVDEYIRAAIN 39
                                       788899***********************999886 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.068
                              RNR_N 36 pntvkfesleekldyLvendYyeeev 61
                                       p++ +fe l+ kld   + ++++ ++
  gene1745|gene1745|rna1745|rna1745 52 PKQITFEGLKAKLDEFRHDNFFHGSF 77
                                       67888999999998888888877665 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.073
                              RNR_N  41 fesleekldyLvendYyeeevl 62 
                                         e+ e++l+    n Yye e++
  gene1745|gene1745|rna1745|rna1745 132 LEKKEQRLKNV-LNAYYEYEMM 152
                                        44444455443.3556665554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1598  (0.0891293); expected 358.6 (0.02)
Passed bias filter:                      601  (0.0335211); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 1348.81
//
Query:       gene1746|gene1746|rna1746|rna1746  [L=393]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
     0.0012   18.6   0.0     0.0035   17.2   0.0    1.7  1  VEFS-Box   VEFS-Box of polycomb protein
     0.0068   17.2   0.8     0.0068   17.2   0.8    2.3  2  zf-C2H2_4  C2H2-type zinc finger
  ------ inclusion threshold ------
      0.028   14.6   0.3      0.084   13.1   0.3    1.8  1  FYVE_2     FYVE-type zinc finger


Domain annotation for each model (and alignments):
>> VEFS-Box  VEFS-Box of polycomb protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   5.8e-07    0.0035      47      84 ..     296     333 ..     278     335 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 5.8e-07
                           VEFS-Box  47 ealrlkerqmldeftDvnegekelmklWnlfvkkqrvv 84 
                                           r  +++++ e+ D ne + +lmk+Wn f+  ++ v
  gene1746|gene1746|rna1746|rna1746 296 GEFRYFSAKRIGEIIDTNERKLRLMKMWNDFIIYKKSV 333
                                        5555667899*********************9887766 PP

>> zf-C2H2_4  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.7       2.3   1.4e+04       5      13 ..     121     127 ..     120     132 .. 0.58
   2 !   17.2   0.8   1.1e-06    0.0068       3      24 .]     207     228 ..     205     228 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 2.3
                          zf-C2H2_4   5 iCgksFssk 13 
                                        +C  sFs +
  gene1746|gene1746|rna1746|rna1746 121 YC--SFSGC 127
                                        46..66544 PP

  == domain 2  score: 17.2 bits;  conditional E-value: 1.1e-06
                          zf-C2H2_4   3 CpiCgksFsskkaLlrHlkthH 24 
                                        C +C k+Fss ++L++H++t+H
  gene1746|gene1746|rna1746|rna1746 207 CIFCFKNFSSFNSLNDHVNTMH 228
                                        ********************99 PP

>> FYVE_2  FYVE-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.3   1.4e-05     0.084      29      71 ..     179     221 ..     157     249 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.4e-05
                             FYVE_2  29 lgelkeklekekskrellgnqaklgethCilCleefkllvnsk 71 
                                         ++lke+ + e  + ellg++  l +++Ci C ++f  + + +
  gene1746|gene1746|rna1746|rna1746 179 WNSLKEQNDSEMCHIELLGERYVLDQNMCIFCFKNFSSFNSLN 221
                                        57899999****************************8776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (393 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       914  (0.0509789); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.21s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 3015.18
//
Query:       gene1747|gene1747|rna1747|rna1747  [L=193]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-08   34.7   0.0    1.9e-08   34.0   0.0    1.4  1  RRM_1     RNA recognition motif. (a.k.a. RRM, RBD, or RNP dom


Domain annotation for each model (and alignments):
>> RRM_1  RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.0   0.0   1.1e-12   1.9e-08       1      69 [.      35     103 ..      35     104 .. 0.90

  Alignments for each domain:
  == domain 1  score: 34.0 bits;  conditional E-value: 1.1e-12
                                        EEEESETTTSSHHHHHHHHHTTSCEEEEEEEEETTTSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEE CS
                              RRM_1   1 lfVgnLppdvteeeLkelFskfGpiksiklvrdetgkskgfafVeFeskedAekAlealngkklggrel 69 
                                        l++gnLp ++tee L ++F +    + i   + ++    gfafVeF ++ d +kA  a  +++++gr +
  gene1747|gene1747|rna1747|rna1747  35 LYIGNLPLSTTEERLWTVFADLPIRRIIMGLNRNNLLFCGFAFVEFYNHVDCRKACVASANMMIDGRSV 103
                                        8*********************766555555559******************************99975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (193 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       415  (0.0231469); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1531.98
//
Query:       gene1748|gene1748|rna1748|rna1748  [L=132]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.6e-09   36.8   0.7    0.00044   20.0   0.1    2.4  2  EF-hand_8        EF-hand domain pair
    1.2e-07   31.1   1.0     0.0019   18.0   0.1    4.1  4  EF-hand_6        EF-hand domain
    3.3e-07   30.6   1.5     0.0055   17.1   0.1    2.5  2  EF-hand_7        EF-hand domain pair
    7.4e-06   25.1   1.3      0.014   14.9   0.1    3.6  3  EF-hand_1        EF hand
     0.0026   17.8   0.3      0.015   15.4   0.2    2.1  2  Sigma70_r1_1     Sigma-70 factor, region 1.1
  ------ inclusion threshold ------
      0.072   12.9   0.4       0.46   10.3   0.0    2.1  2  COR              C-terminal of Roc, COR, domain
      0.081   13.0   1.3        4.2    7.5   0.3    2.4  2  EFhand_Ca_insen  Ca2+ insensitive EF hand


Domain annotation for each model (and alignments):
>> EF-hand_8  EF-hand domain pair
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0     6e-06     0.015      21      51 ..      14      45 ..       4      48 .. 0.88
   2 !   20.0   0.1   1.7e-07   0.00044       4      52 ..      89     131 ..      86     132 .] 0.88

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 6e-06
                          EF-hand_8 21 k.glseeevdilfrefDtdgdGkisfeEFcvl 51
                                       + ++s++e+d+ f++fD+ ++G+++ eE+ ++
  gene1748|gene1748|rna1748|rna1748 14 HpSMSDKEIDEKFKLFDFGEKGYLTPEEYKAF 45
                                       468*************************9875 PP

  == domain 2  score: 20.0 bits;  conditional E-value: 1.7e-07
                          EF-hand_8   4 kItreelrrilrilglkkglseeevdilfrefDtdgdGkisfeEFcvll 52 
                                        +It ++++++l++l     ++++++++++ +f  ++ G++s++EF+  +
  gene1748|gene1748|rna1748|rna1748  89 YITYDTMKKALAKLN----ITDDDIREMITYF--NEQGVLSYNEFVKIF 131
                                        79*********9885....************9..5689*******9766 PP

>> EF-hand_6  EF-hand domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.1   7.4e-07    0.0019       1      25 [.      21      45 ..      21      50 .. 0.90
   2 ?    0.4   0.0      0.33   8.5e+02      13      27 ..      57      71 ..      57      78 .. 0.87
   3 ?    4.4   0.0     0.017        43      12      28 ..      85     101 ..      79     114 .. 0.81
   4 ?    3.6   0.0      0.03        76      13      26 ..     118     131 ..     114     132 .] 0.85

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 7.4e-07
                          EF-hand_6  1 elreaFklfDkdgdGkidaeElrka 25
                                       e++e+FklfD+   G++++eE +++
  gene1748|gene1748|rna1748|rna1748 21 EIDEKFKLFDFGEKGYLTPEEYKAF 45
                                       6899*****************9886 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.33
                          EF-hand_6 13 gdGkidaeElrkalr 27
                                       ++++i+++++ ++++
  gene1748|gene1748|rna1748|rna1748 57 KSNQIHRNDIADICN 71
                                       6899*****999876 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.017
                          EF-hand_6  12 dgdGkidaeElrkalrk 28 
                                        d+  +i+++ ++kal k
  gene1748|gene1748|rna1748|rna1748  85 DNGKYITYDTMKKALAK 101
                                        4445**********984 PP

  == domain 4  score: 3.6 bits;  conditional E-value: 0.03
                          EF-hand_6  13 gdGkidaeElrkal 26 
                                          G ++++E++k++
  gene1748|gene1748|rna1748|rna1748 118 EQGVLSYNEFVKIF 131
                                        5699*******997 PP

>> EF-hand_7  EF-hand domain pair
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.1   2.1e-06    0.0055       2      70 ..      20      46 ..       1      72 [. 0.65
   2 !   12.6   0.3   5.7e-05      0.14      14      70 ..      85     131 ..      79     132 .] 0.81

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 2.1e-06
                          EF-hand_7  2 eklkeaFkelDtdgdgyldkeellrllrkifqgagegsklsdeelellfkefDtdkdGvisfdEFlkly 70
                                       +++ e+Fk++D    gyl++ee++                                          +++
  gene1748|gene1748|rna1748|rna1748 20 KEIDEKFKLFDFGEKGYLTPEEYK------------------------------------------AFC 46
                                       345555555555555555555555..........................................444 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 5.7e-05
                          EF-hand_7  14 dgdgyldkeellrllrkifqgagegsklsdeelellfkefDtdkdGvisfdEFlkly 70 
                                        d+  y++++ ++++l k         +++d+ +++++     +  Gv+s++EF+k++
  gene1748|gene1748|rna1748|rna1748  85 DNGKYITYDTMKKALAK--------LNITDDDIREMITY--FNEQGVLSYNEFVKIF 131
                                        77789999999988885........45677788888888..57788********997 PP

>> EF-hand_1  EF hand
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.1   5.6e-06     0.014       1      28 [.      21      48 ..      21      49 .. 0.93
   2 ?    1.6   0.0       0.1   2.6e+02      15      29 .]      88     102 ..      84     102 .. 0.82
   3 !    5.7   0.1    0.0047        12      14      26 ..     119     131 ..     108     132 .] 0.84

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 5.6e-06
                                       HHHHHHHHHTTTSSSEEEHHHHHHHHHH CS
                          EF-hand_1  1 elkeiFrefDkDgdGkIdfeEfkellkk 28
                                       e++e F++fD    G+++ eE+k+++ +
  gene1748|gene1748|rna1748|rna1748 21 EIDEKFKLFDFGEKGYLTPEEYKAFCYS 48
                                       79999*******************9876 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.1
                                        SEEEHHHHHHHHHHH CS
                          EF-hand_1  15 GkIdfeEfkellkkl 29 
                                         +I+++ +k++l+kl
  gene1748|gene1748|rna1748|rna1748  88 KYITYDTMKKALAKL 102
                                        69********99985 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.0047
                                        SSEEEHHHHHHHH CS
                          EF-hand_1  14 dGkIdfeEfkell 26 
                                         G ++++Ef++++
  gene1748|gene1748|rna1748|rna1748 119 QGVLSYNEFVKIF 131
                                        699*******987 PP

>> Sigma70_r1_1  Sigma-70 factor, region 1.1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.42   1.1e+03      16      24 ..      33      41 ..      31      68 .. 0.82
   2 !   15.4   0.2   5.7e-06     0.015      18      51 ..      88     121 ..      84     126 .. 0.95

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.42
                                       HHSCEEHHH CS
                       Sigma70_r1_1 16 kkGyLtyeE 24
                                       +kGyLt eE
  gene1748|gene1748|rna1748|rna1748 33 EKGYLTPEE 41
                                       799999888 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 5.7e-06
                                        SCEEHHHHHHHGCCSS--HHHHHHHHHHHHCCT- CS
                       Sigma70_r1_1  18 GyLtyeEindaLpddeldseqiediiemLedmgI 51 
                                        +y+ty+ + +aL + +++ + i ++i++++++g+
  gene1748|gene1748|rna1748|rna1748  88 KYITYDTMKKALAKLNITDDDIREMITYFNEQGV 121
                                        79*******************************8 PP

>> COR  C-terminal of Roc, COR, domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.1      0.18   4.6e+02      14      32 ..      54      72 ..      39      76 .. 0.73
   2 ?   10.3   0.0   0.00018      0.46      16      57 ..      85     125 ..      73     131 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.18
                                COR 14 ekkkekyisleeykeicke 32
                                       +k k+++i+ +++ +ic+e
  gene1748|gene1748|rna1748|rna1748 54 KKIKSNQIHRNDIADICNE 72
                                       6678899999999999987 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00018
                                COR  16 kkekyisleeykeickekglkdeeeqetllefLhdlGvvlyF 57 
                                        ++ kyi+++ +k+  ++ +++d++ +++++ ++++ Gv+ y 
  gene1748|gene1748|rna1748|rna1748  85 DNGKYITYDTMKKALAKLNITDDD-IREMITYFNEQGVLSYN 125
                                        5889*******************9.************99875 PP

>> EFhand_Ca_insen  Ca2+ insensitive EF hand
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0     0.015        39       5      28 ..      19      43 ..      16      64 .. 0.76
   2 ?    7.5   0.3    0.0016       4.2      12      63 ..      80     127 ..      72     131 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.015
                                       HHHHHCHHHHH.CTTSSSEEHHHHH CS
                    EFhand_Ca_insen  5 aeqveeaFral.aggKpYvTeedLr 28
                                         ++ e F+    g+K Y T e+ +
  gene1748|gene1748|rna1748|rna1748 19 DKEIDEKFKLFdFGEKGYLTPEEYK 43
                                       5677778888877888888888754 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0016
                                        HHHHCTTSSSEEHHHHHHH-TTCHH.HHHHCCSEEE-STT..S-TTEEECCCH CS
                    EFhand_Ca_insen  12 FralaggKpYvTeedLrrellpeqa.eylierMpeysgpegdavekayDYvsF 63 
                                        F  l+++ +Y+T   ++++l + ++ +  i++M +y +++     + + Y++F
  gene1748|gene1748|rna1748|rna1748  80 FEFLSDNGKYITYDTMKKALAKLNItDDDIREMITYFNEQ-----GVLSYNEF 127
                                        777899999*************999999999999998554.....55556666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1032  (0.0575604); expected 358.6 (0.02)
Passed bias filter:                      696  (0.0388198); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 982.85
//
Query:       gene1749|gene1749|rna1749|rna1749  [L=165]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.1e-30  103.5   0.9    5.9e-30  103.0   0.9    1.2  1  GSHPx     Glutathione peroxidase
    0.00017   21.5   0.1    0.00027   20.8   0.1    1.5  1  AhpC-TSA  AhpC/TSA family
     0.0034   17.1   0.0     0.0067   16.2   0.0    1.7  1  Redoxin   Redoxin


Domain annotation for each model (and alignments):
>> GSHPx  Glutathione peroxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.0   0.9   9.9e-34   5.9e-30       1     107 [.       8     114 ..       8     115 .. 0.96

  Alignments for each domain:
  == domain 1  score: 103.0 bits;  conditional E-value: 9.9e-34
                                        GGGBEEEBTTSSEEEGGGGTTSEEEEEEEESSSTTHH.HHHHHHHHHHHHGGGTEEEEEEEE-TTTT---S-GGGH CS
                              GSHPx   1 iyelsakdidgekvkleklrgkvvlivnvaskCglte.qykeleelqkrykdkglvilgfPCnqfgkqepgsdeei 75 
                                        +y+lsa+++dg++ k+e+l+g vvli+n a+kCg+++  +++l +l kry+dk l il fPC qf +qe ++ +ei
  gene1749|gene1749|rna1749|rna1749   8 FYALSAMKMDGKEYKFEELEGSVVLIINSATKCGMATtTFENLVALAKRYHDKNLKILIFPCSQFRNQELMDSNEI 83 
                                        799*******************************8766*************************************9 PP

                                        HHTSSHTTT-SSEEB--BBSSSTTB-HHHHHH CS
                              GSHPx  76 kkfrqgkyevtfellekievnGekedplykfl 107
                                         k  ++ y+ +f ++ek++v G++ +p++kfl
  gene1749|gene1749|rna1749|rna1749  84 MKNIEK-YSKEFIVFEKVDVKGDNIHPVFKFL 114
                                        998765.************************9 PP

>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.1   4.5e-08   0.00027       5      68 ..       8      70 ..       4     146 .. 0.75

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 4.5e-08
                                       ----EEESTTCEEEECHHHTTSEEEEEEESTST-CCHHHHHHHHHHCHHHCCCTTEEEEEEESS CS
                           AhpC-TSA  5 apdfelknadgetvslsdykgkpvvlffypkdwcpvCttelpalaklyeefkergvevigvsvd 68
                                       +   ++ + dg+++++++++g++v+  + ++  c  +tt  ++l +l+++++++++++++  + 
  gene1749|gene1749|rna1749|rna1749  8 FYALSAMKMDGKEYKFEELEGSVVL-IINSATKCGMATTTFENLVALAKRYHDKNLKILIFPCS 70
                                       5566777999***********5555.5555559************************9987554 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   1.1e-06    0.0067      12      69 ..      12      77 ..       3     162 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.1e-06
                                       CEETTCEEEEEHHHHTTSEEEEEEESTTT-HHHHHTHHHHHTHHHHHHCSTTTEEEE.........E CS
                            Redoxin 12 plaatdgnsvslsefkgkkvvvnfvpgafcPtCsaehpyleklaellkekgvdvvav.........v 69
                                         ++ dg++++ +e++g +v+++  ++  c++ ++    l  la+++++k+ ++++           
  gene1749|gene1749|rna1749|rna1749 12 SAMKMDGKEYKFEELEGSVVLIINSAT-KCGMATTTFENLVALAKRYHDKNLKILIFpcsqfrnqeL 77
                                       45789**************99988888.************************998875544444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       836  (0.0466284); expected 358.6 (0.02)
Passed bias filter:                      533  (0.0297284); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1146.27
//
Query:       gene175|gene175|rna175|rna175  [L=375]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.1e-06   26.4   0.9    1.8e-05   24.9   0.9    1.8  1  EB1       EB1-like C-terminal motif
     0.0016   18.6   0.0     0.0039   17.3   0.0    1.7  1  CH        Calponin homology (CH) domain


Domain annotation for each model (and alignments):
>> EB1  EB1-like C-terminal motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.9     2e-09   1.8e-05       1      32 [.     337     371 ..     337     373 .. 0.70

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 2e-09
                                    HHHHHHHHHHHHHHHHHHHHH....TT----HHHHH CS
                            EB1   1 LekERdFYFsKLRdIEilcqt....epeleedlpiv 32 
                                    Le+ER+FY++KL +IE ++ t    e+++++ l+i+
  gene175|gene175|rna175|rna175 337 LEEERNFYYEKLLEIEKIV-TlnnwENSKDTVLDIL 371
                                    89*****************.6444433333344444 PP

>> CH  Calponin homology (CH) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   4.4e-07    0.0039       4      96 ..      78     167 ..      75     177 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 4.4e-07
                                    HHHHHHHHHHHHTTSTTSSTTSCHHHHHTTSHHHHHHHHHHSTTTSSGGGSTTT...HHHHHHHHHHHHHHHHHHTTCHT CS
                             CH   4 kkellrWinshleeagpkvkvedfeedlrDGvlLckLlnklapglvdkkklnks...efkkleNinlaldvaekklgvpk 80 
                                    k +l+ ++  +l++++p++      e+l +Gv++++Ll kl+p+  + +++n +   e+++++N++ +   +  k+++  
  gene175|gene175|rna175|rna175  78 KSQLILFLSTVLNHSIPSI------ESLGSGVVYAQLLYKLYPDF-PIRSINENpktEQERFNNLKIVQRYLV-KMNIVV 149
                                    6677777777777777766......89****************87.88888877889*********9999999.999999 PP

                                    TSS-HHHHHT...TSHHHH CS
                             CH  81 vlieaedlve...gknksv 96 
                                    v   +e++v     +n +v
  gene175|gene175|rna175|rna175 150 VF-PVEKMVGcrlQDNLEV 167
                                    99.9999998444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (375 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1316  (0.0734006); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 2573.43
//
Query:       gene1750|gene1750|rna1750|rna1750  [L=179]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.076   12.7   3.0        0.5   10.0   0.2    2.1  2  IL17R_fnIII_D1  Interleukin-17 receptor, fibronectin-III-like


Domain annotation for each model (and alignments):
>> IL17R_fnIII_D1  Interleukin-17 receptor, fibronectin-III-like domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.3    0.0032        58      89     115 ..      38      65 ..      21      89 .. 0.72
   2 ?   10.0   0.2   2.8e-05       0.5      43      90 ..      89     136 ..      78     153 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.0032
                     IL17R_fnIII_D1  89 k.mrspakerWsfsvdklvvdPgqeYev 115
                                        +  ++ ++e+Ws  +++lv++ +++  v
  gene1750|gene1750|rna1750|rna1750  38 QyNKEVEHEEWSHLFNNLVIHIDNTKIV 65 
                                        3336678999*********998776433 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 2.8e-05
                     IL17R_fnIII_D1  43 LvPvlkieWklkdDasilyLkgaeLsvlklstneklCvkfefkeklkm 90 
                                        +  v+ i Wk+++   i++ + +e s+++++ ne + v+   +++ +m
  gene1750|gene1750|rna1750|rna1750  89 VGKVMAIRWKVEEKIQIKFYTEQESSLFHEKINEAVVVNLRNSSNERM 136
                                        55699******************************9997655544333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (179 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2170  (0.121033); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1346.21
//
Query:       gene1751|gene1751|rna1751|rna1751  [L=192]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (192 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       807  (0.0450109); expected 358.6 (0.02)
Passed bias filter:                      570  (0.0317921); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.22s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 1479.02
//
Query:       gene1752|gene1752|rna1752|rna1752  [L=168]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
       0.11   12.8   5.6       0.24   11.7   5.6    1.8  1  Mis14         Kinetochore protein Mis14 like
        0.2   11.2   0.2       0.23   11.0   0.2    1.1  1  Phosphodiest  Type I phosphodiesterase / nucleotide pyrophosp
       0.29   11.5   3.5       0.38   11.1   3.5    1.3  1  DUF5063       Domain of unknown function (DUF5063)


Domain annotation for each model (and alignments):
>> Mis14  Kinetochore protein Mis14 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   5.6   4.1e-05      0.24      49     101 ..      61     111 ..      42     161 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 4.1e-05
                                        HHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHCT--HHHHH--.......----- CS
                              Mis14  49 lEdltvevAqlRreaPrkiaeayakelkaeleeldeyleainelek.....qekkdpe 101
                                         ++ + ++A  Rre+P+k a  +++  k+ +e+l++   +i+e ++     +    + 
  gene1752|gene1752|rna1752|rna1752  61 RDQMVEKLAITRRELPAKCALQVEEHYKRLQEDLKQ---IIAEDDEeteveE----HV 111
                                        57888899****************************...8877777422332....22 PP

>> Phosphodiest  Type I phosphodiesterase / nucleotide pyrophosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.2   3.9e-05      0.23     256     346 ..      53     149 ..      25     158 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 3.9e-05
                                        EEEECBHHS.SSEEEEEESTEEE.CCCTTHHHHHHHHHHTCHHCCHST.HTT.TEEEEEGGGS-GGGCH....STT CS
                       Phosphodiest 256 hlkdegkggakaliainpkarelnrvaeaeaeevyaelkakleelrkk.ege.alavylkeaipkrlhy....kkr 325
                                        +l d++   ++ + ++    rel ++   ++ee y++l+++l+++    + e  ++ + k+ +p++++     ++ 
  gene1752|gene1752|rna1752|rna1752  53 ELADKEEIRDQMVEKLAITRRELPAKCALQVEEHYKRLQEDLKQIIAEdDEEtEVEEHVKDVLPADYTClkeiNEG 128
                                        555555556666666666655699999999***********999995534556888899999*****9998777** PP

                                        S-SEEEEE-TTEEEESSTTCS CS
                       Phosphodiest 326 apdlvlvadpgwsitskdkpd 346
                                        +p +++  ++  s+++++++ 
  gene1752|gene1752|rna1752|rna1752 129 VPNIICKFERAMSVVEEASKN 149
                                        ******777777777776666 PP

>> DUF5063  Domain of unknown function (DUF5063)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   3.5   6.3e-05      0.38      66     132 ..      65     150 ..       8     156 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 6.3e-05
                            DUF5063  66 ve.................EedyealrealarlLgekddYlevfdpdmky..sdtpiaasisedLadIyqdlkngl 122
                                        ve                 Ee y++l e l+++++e+d+  ev + +      d +  ++i e +  I+++ ++ +
  gene1752|gene1752|rna1752|rna1752  65 VEklaitrrelpakcalqvEEHYKRLQEDLKQIIAEDDEETEVEEHVKDVlpADYTCLKEINEGVPNIICKFERAM 140
                                        22333455556666668899********************9999988877445555559***************** PP

                            DUF5063 123 avyregneee 132
                                        +v++e++++e
  gene1752|gene1752|rna1752|rna1752 141 SVVEEASKNE 150
                                        ***9988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1703  (0.0949858); expected 358.6 (0.02)
Passed bias filter:                      711  (0.0396564); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 1219.68
//
Query:       gene1753|gene1753|rna1753|rna1753  [L=67]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (67 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       508  (0.028334); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.32u 0.26s 00:00:00.58 Elapsed: 00:00:00.40
# Mc/sec: 508.13
//
Query:       gene1754|gene1754|rna1754|rna1754  [L=81]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.025   13.9   1.0      0.024   13.9   1.0    1.0  1  FAM91_N          FAM91 N-terminus
       0.32   10.4   4.3       0.32   10.4   4.3    1.0  1  Ppx-GppA         Ppx/GppA phosphatase family
       0.78   10.6   4.1        1.6    9.6   4.0    1.7  1  Methyltransf_1N  6-O-methylguanine DNA methyltransferase, rib
        6.2    6.6  13.8         10    6.0  13.8    1.4  1  Sde2_N_Ubi       Silencing defective 2 N-terminal ubiquitin d


Domain annotation for each model (and alignments):
>> FAM91_N  FAM91 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   1.0   5.3e-06     0.024     143     196 ..      17      69 ..       1      80 [. 0.75

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.3e-06
                            FAM91_N 143 kvkkkvvkelLpakplssvelepwwivevgdvteedikelskeekelidklide 196
                                        k ++++ k+ L +   +  +l +ww + + d+t+e+ ke +k ek++ +++ +e
  gene1754|gene1754|rna1754|rna1754  17 KEEREAEKKRLEEMEKE-KQLAEWWLIGAKDYTKEKEKEAKKVEKQMRKEINEE 69 
                                        34455556667665555.99***************************9988654 PP

>> Ppx-GppA  Ppx/GppA phosphatase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   4.3   7.2e-05      0.32     162     225 ..      16      78 ..       3      81 .] 0.84

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 7.2e-05
                                        HHHHHHHHHHHCTTTHHHHCCCEHHCCCCCCCHCCHHCHHHHHHCT.SSCEEEHHHHHHHHHHH CS
                           Ppx-GppA 162 veaarkavekeleevkdevkkegewtrlvgtsgtisalaeltelhgekgyeitaeeleeliekl 225
                                         ++ r+a +k+lee+ +e + +  w  ++++ +t++   e +++ +++ +ei++e l++ ie+ 
  gene1754|gene1754|rna1754|rna1754  16 RKEEREAEKKRLEEMEKEKQLAE-WWLIGAKDYTKEKEKEAKKVEKQMRKEINEETLRKEIEQY 78 
                                        44567767788******988888.*********************************9988875 PP

>> Methyltransf_1N  6-O-methylguanine DNA methyltransferase, ribonuclease-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   4.0   0.00035       1.6      27      63 ..      43      79 ..      14      80 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00035
                                       EEEC-HHHCCHHHCCCTTTSCCHCCHHHHHHHHHHHH CS
                    Methyltransf_1N 27 dlldkdtselkelpkllkqdeelpalaelkqaleeYf 63
                                       +  d++++ +ke +k++kq +++ + ++l++++e+Y+
  gene1754|gene1754|rna1754|rna1754 43 GAKDYTKEKEKEAKKVEKQMRKEINEETLRKEIEQYT 79
                                       556677779***************************7 PP

>> Sde2_N_Ubi  Silencing defective 2 N-terminal ubiquitin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0  13.8    0.0022        10     112     160 ..      15      63 ..       2      70 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0022
                         Sde2_N_Ubi 112 nndscRdldGrRLrtvkeakalaeylaekperekkekearrkrleavve 160
                                             R+ + +RL  ++++k+lae+  + ++   keke++ k++e+ ++
  gene1754|gene1754|rna1754|rna1754  15 RRKEEREAEKKRLEEMEKEKQLAEWWLIGAKDYTKEKEKEAKKVEKQMR 63 
                                        3445689999******************999999999999999988665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (81 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3732  (0.208154); expected 358.6 (0.02)
Passed bias filter:                      810  (0.0451782); expected 358.6 (0.02)
Passed Vit filter:                        95  (0.00529868); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.43u 0.30s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 575.90
//
Query:       gene1755|gene1755|rna1755|rna1755  [L=46]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.033   14.4   1.0      0.033   14.4   1.0    1.1  1  ABC_tran_CTD  ABC transporter C-terminal domain
      0.035   14.1   0.6       0.04   13.9   0.6    1.0  1  P4Ha_N        Prolyl 4-Hydroxylase alpha-subunit, N-terminal 
      0.083   13.1   1.0      0.083   13.1   1.0    1.1  1  DUF2508       Protein of unknown function (DUF2508)
       0.12   11.9   0.1       0.12   11.9   0.1    1.0  1  HXXSHH        Protein of unknown function (DUF1552)


Domain annotation for each model (and alignments):
>> ABC_tran_CTD  ABC transporter C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   1.0   7.4e-06     0.033       4      34 ..       3      33 ..       1      43 [. 0.89

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 7.4e-06
                       ABC_tran_CTD  4 ykeqreleeleaeIeaLEeeiaeleaeladp 34
                                        ++q+ ++e e+ Ie  E++  +le++++d 
  gene1755|gene1755|rna1755|rna1755  3 SNDQQLIDEFEELIEDTEQRNDTLENAISDM 33
                                       688999**********************985 PP

>> P4Ha_N  Prolyl 4-Hydroxylase alpha-subunit, N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.6   8.9e-06      0.04      12      46 ..       5      39 ..       2      44 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 8.9e-06
                             P4Ha_N 12 ErelveeLesyieeeekkleklkrfleeleeehes 46
                                       +++l++e+e+ ie++e++ ++l+++++++ +++ s
  gene1755|gene1755|rna1755|rna1755  5 DQQLIDEFEELIEDTEQRNDTLENAISDMIKNKTS 39
                                       689************************99887644 PP

>> DUF2508  Protein of unknown function (DUF2508)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   1.0   1.9e-05     0.083      13      40 ..       3      30 ..       1      43 [. 0.86

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.9e-05
                            DUF2508 13 eedeeLleeIektkeelesakslfensv 40
                                       + d++L++e e++ e+ e+ ++++en++
  gene1755|gene1755|rna1755|rna1755  3 SNDQQLIDEFEELIEDTEQRNDTLENAI 30
                                       58************************96 PP

>> HXXSHH  Protein of unknown function (DUF1552)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   2.8e-05      0.12     182     218 ..       1      37 [.       1      45 [. 0.78

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.8e-05
                             HXXSHH 182 LgaadrqKLdeylesvreiekrlekaekwaptakaea 218
                                        ++++d+q +de+ e ++++e+r ++ e++ +   + +
  gene1755|gene1755|rna1755|rna1755   1 MNSNDQQLIDEFEELIEDTEQRNDTLENAISDMIKNK 37 
                                        5789*******************88888666554444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (46 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1694  (0.0944838); expected 358.6 (0.02)
Passed bias filter:                     1007  (0.056166); expected 358.6 (0.02)
Passed Vit filter:                       101  (0.00563333); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 360.71
//
Query:       gene1756|gene1756|rna1756|rna1756  [L=51]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (51 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1721  (0.0959897); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 386.82
//
Query:       gene1757|gene1757|rna1757|rna1757  [L=428]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-15   57.9   2.7    1.2e-15   57.9   2.7    3.6  4  Nuf2             Nuf2 family
    1.2e-07   31.9  41.0     0.0028   17.6   7.0    4.1  4  Laminin_II       Laminin Domain II
    0.00029   20.9  42.9      0.081   13.0   5.1    3.4  3  DHR10            Designed helical repeat protein 10 domain
    0.00045   20.8   0.3    0.00045   20.8   0.3    5.2  5  SlyX             SlyX
    0.00062   19.3  19.4    0.00062   19.3  19.4    3.1  3  Golgin_A5        Golgin subfamily A member 5
  ------ inclusion threshold ------
      0.035   14.2   7.7        4.3    7.5   0.4    4.7  4  MbeD_MobD        MbeD/MobD like
      0.047   10.9   1.9      0.059   10.5   1.9    1.1  1  Spike_torovirin  Torovirinae spike glycoprotein
      0.076   12.3  35.0        1.3    8.3  13.7    3.3  3  DUF3450          Protein of unknown function (DUF3450)
       0.14   12.7  54.3       0.32   11.5  23.1    4.0  4  APG6_N           Apg6 coiled-coil region
       0.18   12.0  39.9      0.074   13.3  13.0    3.1  3  ATG16            Autophagy protein 16 (ATG16)
        0.2   11.7  54.9       0.76    9.8  29.2    4.0  3  CENP-F_leu_zip   Leucine-rich repeats of kinetochore protein 
       0.38    9.8  44.7       0.44    9.6  22.8    2.4  2  Atg14            Vacuolar sorting 38 and autophagy-related su
       0.39   10.8  35.8      0.036   14.1   7.2    4.0  4  DUF1664          Protein of unknown function (DUF1664)
        1.3    9.5  23.2         13    6.3   0.1    6.3  6  LPP              Lipoprotein leucine-zipper
        1.4    9.4  46.7       0.45   10.9  11.9    3.0  2  Fez1             Fez1
        1.7    7.9  27.9       0.51    9.7  12.3    2.1  2  DUF4407          Domain of unknown function (DUF4407)
          2    7.9  10.2        1.1    8.8   1.2    3.2  4  BRI3BP           Negative regulator of p53/TP53
          6    5.4  48.0        0.1   11.2  19.9    2.8  3  AAA_13           AAA domain
        7.4    5.4  55.3      0.086   11.7  15.5    3.2  3  Spc7             Spc7 kinetochore protein


Domain annotation for each model (and alignments):
>> Nuf2  Nuf2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.9   2.7   1.2e-18   1.2e-15       3     137 ..      10     129 ..       9     131 .. 0.90
   2 ?   -1.9   0.2       3.5   3.3e+03      64      88 ..     216     245 ..     175     259 .. 0.55
   3 ?   -3.2   0.0       8.9   8.4e+03      70      70 ..     305     305 ..     270     330 .. 0.52
   4 ?   -2.0   0.1       3.9   3.6e+03     119     136 ..     360     377 ..     337     403 .. 0.76

  Alignments for each domain:
  == domain 1  score: 57.9 bits;  conditional E-value: 1.2e-18
                               Nuf2   3 sfplldvreIvaclqelgfevteedlakPtpefvqklyeqfleilmgiseedieqaaraaleeleepelyedslpl 78 
                                         +p ++++eI+++++e g+++ +++++kP+ + v ++y++++  ++     +i              ++ ++s  l
  gene1757|gene1757|rna1757|rna1757  10 LIPNFQPSEIISYFSEHGIPILQSEITKPSFQNVLRIYSSIIGLIYTN--SSIS-------------NDADESKFL 70 
                                        67999**************************************99544..5552.............234556679 PP

                               Nuf2  79 lillrslkrflkacgvedFslsDllkPdpkRtrriLSaliNFirFreerseifeellee 137
                                        lil+++ + +l+ +g++ F+l+Dll P  kR   +LS++ NF+ +r+++ e +e+ll e
  gene1757|gene1757|rna1757|rna1757  71 LILYKRTDMLLRRLGIDFFELKDLLTPSYKRNLNFLSTIYNFCIYRDSKKEYYEKLLLE 129
                                        *******************************************************9877 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 3.5
                               Nuf2  64 e.....eleepelyedslpllillrslkrf 88 
                                        +     +++++++++d  ++l l+  ++ +
  gene1757|gene1757|rna1757|rna1757 216 NlkqeiKEMKTQVIDDPSKMLSLIEEMQVL 245
                                        033333334455555555555555555555 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 8.9
                               Nuf2  70 e 70 
                                        e
  gene1757|gene1757|rna1757|rna1757 305 E 305
                                        2 PP

  == domain 4  score: -2.0 bits;  conditional E-value: 3.9
                               Nuf2 119 NFirFreerseifeelle 136
                                        N+ + r er + fe +++
  gene1757|gene1757|rna1757|rna1757 360 NYSKVRTERNDYFERIAN 377
                                        666666666666666655 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1  10.5   1.9e-05     0.018       4      99 ..     136     228 ..     133     230 .. 0.96
   2 !    9.1   0.8    0.0013       1.2      14      52 ..     234     272 ..     230     287 .. 0.84
   3 !   17.6   7.0     3e-06    0.0028      27      96 ..     288     358 ..     279     358 .. 0.91
   4 !   11.2   6.1   0.00029      0.27      16      81 ..     344     413 ..     342     417 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.9e-05
                                        XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHH CS
                         Laminin_II   4 laaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelk 79 
                                        l++e+n +++  +++l+ ++ + ++ +++  e++++v + +++vk++ k  r+  +sv +++++ ++  dkl++lk
  gene1757|gene1757|rna1757|rna1757 136 LLNEINVSINMAESKLKSMKDEAQKKEKENAELENKVGQLEDEVKSLCKEQRERANSVEEMKRERDEFYDKLSSLK 211
                                        7899************************************************************************ PP

                                        HHHHH...HHHHHHHHHHHH CS
                         Laminin_II  80 qleeassslsdniseikelI 99 
                                            +   l+++i+e+k ++
  gene1757|gene1757|rna1757|rna1757 212 LVCLN---LKQEIKEMKTQV 228
                                        **999...*********987 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0013
                                        XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                         Laminin_II  14 evleqlaplsqnlentkeklseinrsveetnekvkdank 52 
                                        + l+ ++++++ ++ +k++++e+n+++++t+e++++  +
  gene1757|gene1757|rna1757|rna1757 234 KMLSLIEEMQVLIKTEKASIEEFNKKIRHTTELIDKEEE 272
                                        678999**************************9986544 PP

  == domain 3  score: 17.6 bits;  conditional E-value: 3e-06
                                        XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH....HHHHHHHHH CS
                         Laminin_II  27 entkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqleeasss.lsdniseik 96 
                                        +n  + ++e++++v   ++ +k++++ai+  +r + +L k++  ++ k++ lk++ ++++  ls+n++++k
  gene1757|gene1757|rna1757|rna1757 288 KNKTKTANELQNEVTCLEKTIKSLSMAINVSNRRIDHLSKQISHIEGKIEVLKKKDQENAKeLSNNLNKLK 358
                                        56677899***********************************************9997779*****9987 PP

  == domain 4  score: 11.2 bits;  conditional E-value: 0.00029
                                        XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX....--TTTTTGGGHHHHHHH CS
                         Laminin_II  16 leqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkL....eklapqLldklkelkql 81 
                                        +e  ++ls+nl+++k+++s+++++ +   e + + +k i++ + +++++    +k + +L++kl elk+ 
  gene1757|gene1757|rna1757|rna1757 344 QENAKELSNNLNKLKDNYSKVRTERNDYFERIANNQKEIKEIEYKMVQImnqhQKDMHVLISKLTELKNA 413
                                        67889*******************99999**************999886322235578899***999985 PP

>> DHR10  Designed helical repeat protein 10 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1  10.7    0.0057       5.4      52     107 ..     144     200 ..     132     211 .. 0.89
   2 !   12.3  14.9   0.00014      0.13       5     107 ..     247     349 ..     243     352 .. 0.97
   3 !   13.0   5.1   8.5e-05     0.081      48     116 ..     343     411 ..     342     412 .. 0.95

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0057
                              DHR10  52 leeakkklkelrdaleekeielrelerkeerlqrqlen.aeeklerlreqaeekrea 107
                                         + a++klk+ +d+ ++ke+e +ele+k  +l+  +++  +e+ er+    e+kre 
  gene1757|gene1757|rna1757|rna1757 144 INMAESKLKSMKDEAQKKEKENAELENKVGQLEDEVKSlCKEQRERANSVEEMKRER 200
                                        467899*****************************98637999****9999999985 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00014
                              DHR10   5 aeekeelaelErkarelqakidalqvvekdlrsciklleeieaelakleeakkklkelrdaleekeielrelerke 80 
                                        + ek++++e  +k+r +++ id  ++ ++ ++s+ik++   +++++  +e + +++ l++++++++   +  +r++
  gene1757|gene1757|rna1757|rna1757 247 KTEKASIEEFNKKIRHTTELIDKEEEEKTRIQSAIKMAISQKNKTKTANELQNEVTCLEKTIKSLSMAINVSNRRI 322
                                        679************************************************************************* PP

                              DHR10  81 erlqrqlenaeeklerlreqaeekrea 107
                                        ++l +q+++ e k+e l+++ +e +++
  gene1757|gene1757|rna1757|rna1757 323 DHLSKQISHIEGKIEVLKKKDQENAKE 349
                                        ********************9998876 PP

  == domain 3  score: 13.0 bits;  conditional E-value: 8.5e-05
                              DHR10  48 elakleeakkklkelrdaleekeielrelerkeerlqrqlenaeeklerlreqaeekreaakarleelr 116
                                        +++  +e + +l++l+d++++ ++e++++  +++  q+ ++  e k+ +  +q+++ ++   ++l+el+
  gene1757|gene1757|rna1757|rna1757 343 DQENAKELSNNLNKLKDNYSKVRTERNDYFERIANNQKEIKEIEYKMVQIMNQHQKDMHVLISKLTELK 411
                                        67888999***************************************************9999999998 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   3.6     0.036        34       4      58 ..     136     190 ..     133     202 .. 0.84
   2 ?    6.0   2.5     0.019        18       6      51 ..     166     211 ..     162     237 .. 0.92
   3 ?    1.4   1.9      0.54   5.1e+02       5      53 ..     239     287 ..     235     296 .. 0.72
   4 !   20.8   0.3   4.8e-07   0.00045       6      57 ..     295     346 ..     291     353 .. 0.90
   5 ?    1.3   0.4      0.56   5.3e+02      28      52 ..     388     412 ..     373     417 .. 0.57

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.036
                                        HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXXXXXXX CS
                               SlyX   4 rleeLEiklafqedtieeLndvvaeqqqqidrlqrqlrllaerlkeleessgase 58 
                                         l+e+ + +   e  ++++ d+  + +++ ++l+ ++ +l++++k+l +++++  
  gene1757|gene1757|rna1757|rna1757 136 LLNEINVSINMAESKLKSMKDEAQKKEKENAELENKVGQLEDEVKSLCKEQRERA 190
                                        578888899999999*****************************99987776443 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.019
                                        HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXX CS
                               SlyX   6 eeLEiklafqedtieeLndvvaeqqqqidrlqrqlrllaerlkele 51 
                                         eLE k+  +ed +++L ++  e +  +++++r+ ++ +++l++l+
  gene1757|gene1757|rna1757|rna1757 166 AELENKVGQLEDEVKSLCKEQRERANSVEEMKRERDEFYDKLSSLK 211
                                        59***************************************98774 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.54
                                        HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXX CS
                               SlyX   5 leeLEiklafqedtieeLndvvaeqqqqidrlqrqlrllaerlkelees 53 
                                        +ee+++ +      iee n+ + +  + id+ +++  +++  +k + ++
  gene1757|gene1757|rna1757|rna1757 239 IEEMQVLIKTEKASIEEFNKKIRHTTELIDKEEEEKTRIQSAIKMAISQ 287
                                        6777777777788888888888888888888888877777777655554 PP

  == domain 4  score: 20.8 bits;  conditional E-value: 4.8e-07
                                        HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXXXXXX CS
                               SlyX   6 eeLEiklafqedtieeLndvvaeqqqqidrlqrqlrllaerlkeleessgas 57 
                                        +eL+ +++ +e+ti++L+ ++   +++id+l +q+ +++ +++ l+++++++
  gene1757|gene1757|rna1757|rna1757 295 NELQNEVTCLEKTIKSLSMAINVSNRRIDHLSKQISHIEGKIEVLKKKDQEN 346
                                        6899**************************************9888887644 PP

  == domain 5  score: 1.3 bits;  conditional E-value: 0.56
                                        HHHHHHHHHHHHHHHHHHT-XXXXX CS
                               SlyX  28 eqqqqidrlqrqlrllaerlkelee 52 
                                        +  q + + q+ +  l  +l el++
  gene1757|gene1757|rna1757|rna1757 388 KMVQIMNQHQKDMHVLISKLTELKN 412
                                        3344555666666666666666555 PP

>> Golgin_A5  Golgin subfamily A member 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0  10.7       2.1   1.9e+03      75     130 ..     131     186 ..     112     193 .. 0.39
   2 !   19.3  19.4   6.6e-07   0.00062      39     157 ..     183     303 ..     176     320 .. 0.87
   3 !    6.5  13.1    0.0051       4.8      45     143 ..     304     402 ..     291     419 .. 0.52

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 2.1
                          Golgin_A5  75 telqdleaqqqaeaeslreqlqeleeqleeerkakeeveaelerlkeelryleeel 130
                                         e + l ++ +  ++ ++ +l++++++ ++++k++ e+e+++ +l++e+++l +e+
  gene1757|gene1757|rna1757|rna1757 131 EEQESLLNEINVSINMAESKLKSMKDEAQKKEKENAELENKVGQLEDEVKSLCKEQ 186
                                        22222222223333333334444444444444444444444444444444443333 PP

  == domain 2  score: 19.3 bits;  conditional E-value: 6.6e-07
                          Golgin_A5  39 lesstalsaeldelkqerdllreelqklnqqieqlrtelqdleaqqqaeaeslreqlqeleeqleeerkakeevea 114
                                         + +++ +  ++e+k+erd + ++l +l+  + +l++e++++++q+  + +++   ++e++  +++e+++ ee+++
  gene1757|gene1757|rna1757|rna1757 183 CKEQRERANSVEEMKRERDEFYDKLSSLKLVCLNLKQEIKEMKTQVIDDPSKMLSLIEEMQVLIKTEKASIEEFNK 258
                                        45677788999***************************************************************** PP

                          Golgin_A5 115 elerlkeelryleeelvrskatlqsrikdrek..eieklrnqltt 157
                                        ++++++e ++  eee +r ++ ++  i +++k    ++l+n++t 
  gene1757|gene1757|rna1757|rna1757 259 KIRHTTELIDKEEEEKTRIQSAIKMAISQKNKtkTANELQNEVTC 303
                                        *********************999998776651156778888774 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.0051
                          Golgin_A5  45 lsaeldelkqerdllreelqklnqqieqlrtelqdleaqqqaeaeslreqlqeleeqleeerkakeeveaelerlk 120
                                        l++ + +l+   ++ +  + +l++qi+++  +++ l+++ q++a++l ++l++l+++ ++ r +++++ + +++ +
  gene1757|gene1757|rna1757|rna1757 304 LEKTIKSLSMAINVSNRRIDHLSKQISHIEGKIEVLKKKDQENAKELSNNLNKLKDNYSKVRTERNDYFERIANNQ 379
                                        3334444444444445555555555555555555555666666666666666666666666666666666666666 PP

                          Golgin_A5 121 eelryleeelvrskatlqsrikd 143
                                        +e++ +e  +v+  ++ q+ ++ 
  gene1757|gene1757|rna1757|rna1757 380 KEIKEIEYKMVQIMNQHQKDMHV 402
                                        66666655555554444444433 PP

>> MbeD_MobD  MbeD/MobD like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.4    0.0046       4.3      30      64 ..     151     185 ..     134     192 .. 0.81
   2 ?   -1.8   0.0       3.7   3.5e+03      45      65 ..     201     228 ..     184     230 .. 0.55
   3 ?    5.4   0.1     0.021        20      46      66 ..     317     337 ..     233     341 .. 0.80
   4 ?    1.8   0.1      0.27   2.5e+02       6      32 ..     348     374 ..     344     410 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0046
                          MbeD_MobD  30 faelqrmfeltqrenaaLseqvtgLsqQVesLseq 64 
                                         ++++   + +++ena L+++v +L   V+sL ++
  gene1757|gene1757|rna1757|rna1757 151 LKSMKDEAQKKEKENAELENKVGQLEDEVKSLCKE 185
                                        4556666677899******************9764 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 3.7
                          MbeD_MobD  45 a.......aLseqvtgLsqQVesLseqv 65 
                                                 L+  + +L q ++++  qv
  gene1757|gene1757|rna1757|rna1757 201 DefydklsSLKLVCLNLKQEIKEMKTQV 228
                                        2333333366666667777776666665 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.021
                          MbeD_MobD  46 aLseqvtgLsqQVesLseqvr 66 
                                          + ++++Ls+Q+ ++ ++++
  gene1757|gene1757|rna1757|rna1757 317 VSNRRIDHLSKQISHIEGKIE 337
                                        446788888888888888876 PP

  == domain 4  score: 1.8 bits;  conditional E-value: 0.27
                          MbeD_MobD   6 kqLLsAlEqLQqdYeqrlqeWesafae 32 
                                        k+L + l +L  +Y++ + e ++ f+ 
  gene1757|gene1757|rna1757|rna1757 348 KELSNNLNKLKDNYSKVRTERNDYFER 374
                                        788899999999999999998888875 PP

>> Spike_torovirin  Torovirinae spike glycoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   1.9   6.2e-05     0.059    1075    1230 ..     262     414 ..     190     419 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 6.2e-05
                    Spike_torovirin 1075 srtplisnvktpkttfn..vklsmpklpkastlstigs.vlssglsiaslglsifsiiedrrvieltqqqimal 1145
                                           t li + +  kt ++  +k+++ +  k+ t + + + v     +i sl ++i   + +rr+  l  +qi  +
  gene1757|gene1757|rna1757|rna1757  262 HTTELIDKEEEEKTRIQsaIKMAISQKNKTKTANELQNeVTCLEKTIKSLSMAI--NVSNRRIDHL-SKQISHI 332 
                                         456788887778887652267777777777777776541555566777777666..5778887666.578**** PP

                    Spike_torovirin 1146 edqitilagyttknfeeiqsslntlgqqvqdfsqtsalslqqlsngfeqitqqldksiyyvm..avqqyatyms 1217
                                         e +i +l     +n +e+ ++ln l ++   +       +++++n  ++i     k i y m   ++q+   m 
  gene1757|gene1757|rna1757|rna1757  333 EGKIEVLKKKDQENAKELSNNLNKLKDNYSKVRTERNDYFERIANNQKEI-----KEIEYKMvqIMNQHQKDMH 401 
                                         ************************99887777766666677777766665.....444443311467888999* PP

                    Spike_torovirin 1218 slvnqlnelsqav 1230
                                          l+ +l el +a 
  gene1757|gene1757|rna1757|rna1757  402 VLISKLTELKNAA 414 
                                         ********99886 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3  13.7    0.0013       1.3      12     136 ..     145     268 ..     139     274 .. 0.88
   2 ?    5.6   5.8    0.0092       8.7      22      94 ..     268     342 ..     259     347 .. 0.74
   3 ?    6.2   5.1    0.0059       5.5      54     118 ..     345     409 ..     340     416 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0013
                            DUF3450  12 galaatldqalkeaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeq 87 
                                        + ++++l+++++ea+k  ++ a+ ++k+ +l+de ++l +e r+  + +e+++ ++++  + ++s++    +l+++
  gene1757|gene1757|rna1757|rna1757 145 NMAESKLKSMKDEAQKKEKENAELENKVGQLEDEVKSLCKEQRERANSVEEMKRERDEFYDKLSSLKLVCLNLKQE 220
                                        445899********************************************************************** PP

                            DUF3450  88 ieeieeierelvpllekmidrLeqfveldlPflleeRqarlakLkelmd 136
                                        i+e++    +    ++++i++++ ++++      ee ++++++  el+d
  gene1757|gene1757|rna1757|rna1757 221 IKEMKTQVIDDPSKMLSLIEEMQVLIKTEKA-SIEEFNKKIRHTTELID 268
                                        *****99999999999999999999998875.56666666666666666 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0092
                            DUF3450  22 lkeaekavaaaaqsqkkidk..lddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeieei 94 
                                        +ke+e+ +++++++   i++   ++ ++el++e++ l++ ++sl++  +  +r ++++ ++i+ +e +ie +++ 
  gene1757|gene1757|rna1757|rna1757 268 DKEEEEKTRIQSAIKMAISQknKTKTANELQNEVTCLEKTIKSLSMAINVSNRRIDHLSKQISHIEGKIEVLKKK 342
                                        555555555555555555541155667789999999999999999999999999999999999999999987765 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.0059
                            DUF3450  54 ralkeeleslevyneqlerlvasqeqeiasleeqieeieeierelvpllekmidrLeqfveldlP 118
                                        +++ke  ++l++ +++++++ ++ +  ++++ ++++ei+eie ++v+++ +  ++++ ++ + + 
  gene1757|gene1757|rna1757|rna1757 345 ENAKELSNNLNKLKDNYSKVRTERNDYFERIANNQKEIKEIEYKMVQIMNQHQKDMHVLISKLTE 409
                                        56677778888888888888888888899999999999999999999999888888877776655 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5  23.1   0.00034      0.32      25     127 ..     120     229 ..     114     235 .. 0.73
   2 ?    4.8   5.5      0.04        38      65     129 ..     216     280 ..     209     284 .. 0.89
   3 ?    4.2  15.3     0.063        59      10     113 ..     238     358 ..     237     363 .. 0.80
   4 ?    5.1   2.5     0.033        31      11      63 ..     354     414 ..     352     428 .] 0.63

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00034
                             APG6_N  25 rdaYeeflkklkkekkeeek.......qdeeleeleeeleklekeeeelleeLkelekereeleaelaaleeelea 93 
                                        ++ Ye+ l + +++++  ++        +++l++ ++e +k eke +el+++  +le+e ++l +e ++ ++  e+
  gene1757|gene1757|rna1757|rna1757 120 KEYYEKLLLEKEEQESLLNEinvsinmAESKLKSMKDEAQKKEKENAELENKVGQLEDEVKSLCKEQRERANSVEE 195
                                        4455555555555544433377777777788888888888888888888888888888888888888888888888 PP

                             APG6_N  94 leeeeerfwreynelqlelleleeeldsleaqye 127
                                        +++e ++f  + ++l+l  l+l++e + +++q+ 
  gene1757|gene1757|rna1757|rna1757 196 MKRERDEFYDKLSSLKLVCLNLKQEIKEMKTQVI 229
                                        8888888888888888888888888888888875 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.04
                             APG6_N  65 elleeLkelekereeleaelaaleeelealeeeeerfwreynelqlelleleeeldsleaqyeha 129
                                        +l +e+ke++++  +  +++ +l ee + l + e++ ++e+n++ +  +el ++ +  +++++ a
  gene1757|gene1757|rna1757|rna1757 216 NLKQEIKEMKTQVIDDPSKMLSLIEEMQVLIKTEKASIEEFNKKIRHTTELIDKEEEEKTRIQSA 280
                                        5789999999999999999************************9999999999999999888865 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.063
                             APG6_N  10 LleeldkqleqaekerdaYeeflkklkkekkeeek.................qdeeleeleeeleklekeeeelle 68 
                                        L+ee++  +++ ++ ++++++  ++ ++  ++ee+                 + +  +el++e+  lek+ ++l  
  gene1757|gene1757|rna1757|rna1757 238 LIEEMQVLIKTEKASIEEFNKKIRHTTELIDKEEEektriqsaikmaisqknKTKTANELQNEVTCLEKTIKSLSM 313
                                        66666666666666666666666666555555555778888888888888877778899***************** PP

                             APG6_N  69 eLkelekereeleaelaaleeelealeeeeerfwreynelqlell 113
                                         ++   +  + l ++++ +e + e l+++ ++  +e ++   +l+
  gene1757|gene1757|rna1757|rna1757 314 AINVSNRRIDHLSKQISHIEGKIEVLKKKDQENAKELSNNLNKLK 358
                                        ************************************999766665 PP

  == domain 4  score: 5.1 bits;  conditional E-value: 0.033
                             APG6_N  11 leeldkqleqaekerdaYeeflkklkkekkeeek........qdeeleeleeeleklekee 63 
                                        l++l+  +++++ er++Y e  ++ +ke ke e         +++++  l  +l +l+++ 
  gene1757|gene1757|rna1757|rna1757 354 LNKLKDNYSKVRTERNDYFERIANNQKEIKEIEYkmvqimnqHQKDMHVLISKLTELKNAA 414
                                        5778888888888888887777777777666543555555555555555555555555544 PP

>> ATG16  Autophagy protein 16 (ATG16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3  13.0   7.9e-05     0.074      76     164 ..     144     211 ..     121     231 .. 0.58
   2 ?   -0.7   2.8       1.5   1.4e+03     112     147 ..     240     275 ..     207     284 .. 0.54
   3 ?    3.0  18.0      0.11     1e+02      90     184 ..     287     385 ..     248     401 .. 0.58

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 7.9e-05
                              ATG16  76 iqsleqklaqlreelaelyksrgelaqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelrekek 151
                                        i+  e+kl+++++e ++  k+++el++++ +l++e++ l ++ +e++++++e+++er +  +kl++          
  gene1757|gene1757|rna1757|rna1757 144 INMAESKLKSMKDEAQKKEKENAELENKVGQLEDEVKSLCKEQRERANSVEEMKRERDEFYDKLSS---------- 209
                                        444555555555555555555555555555555555555555555555555555555555555544.......... PP

                              ATG16 152 lvqdlqDElsaLq 164
                                                   L+
  gene1757|gene1757|rna1757|rna1757 210 -----------LK 211
                                        ...........33 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.5
                              ATG16 112 qkleeklkedeerlaeleaeraaletklkdreeelr 147
                                        ++ +  +k+++++++e ++++++ ++ +++ eee  
  gene1757|gene1757|rna1757|rna1757 240 EEMQVLIKTEKASIEEFNKKIRHTTELIDKEEEEKT 275
                                        333444555555555555555555555555554433 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.11
                              ATG16  90 laelyksrgelaqrllelneelqkleeklkedeerlaeleaeraaletkl....kdreeelrekeklvqdlqDEls 161
                                        +++  k+ +el++ ++ l+++++ l   ++  ++r+++l+++++++e k+    k+ +e+ +e+ + +++l+D +s
  gene1757|gene1757|rna1757|rna1757 287 QKNKTKTANELQNEVTCLEKTIKSLSMAINVSNRRIDHLSKQISHIEGKIevlkKKDQENAKELSNNLNKLKDNYS 362
                                        3344566666666666666677777777777777777777776666666522223445556666666666777776 PP

                              ATG16 162 aLqlqlnqaEeklrklekENkeL 184
                                          + + n   e+  + +kE ke 
  gene1757|gene1757|rna1757|rna1757 363 KVRTERNDYFERIANNQKEIKEI 385
                                        66666666666666666665555 PP

>> CENP-F_leu_zip  Leucine-rich repeats of kinetochore protein Cenp-F/LEK1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8  29.2   0.00081      0.76       2     129 ..     148     286 ..     147     287 .. 0.94
   2 ?    8.0   3.0    0.0029       2.8      45     101 ..     285     341 ..     282     345 .. 0.89
   3 ?    9.3   3.5    0.0012       1.1      59     109 ..     345     395 ..     341     415 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00081
                     CENP-F_leu_zip   2 ekkklhvlekLKeserkadsLkdkvenLerelemseenqekvileaEtskaevetlkeeieelaeelreleldLva 77 
                                        e k ++++++ ++ e++++ L++kv +Le e++ + ++q +    +E+ k e  ++ +++  l+    +l++++++
  gene1757|gene1757|rna1757|rna1757 148 ESKLKSMKDEAQKKEKENAELENKVGQLEDEVKSLCKEQRERANSVEEMKRERDEFYDKLSSLKLVCLNLKQEIKE 223
                                        678999999**********************************************999999999999999999999 PP

                     CENP-F_leu_zip  78 lr...........sekeeLekelqkkqervseLeslnsslenlleekEqekvqmkeeskaave 129
                                        ++           s  ee++  +++++  ++e ++    +++l+ ++E+ek +++ + k a++
  gene1757|gene1757|rna1757|rna1757 224 MKtqviddpskmlSLIEEMQVLIKTEKASIEEFNKKIRHTTELIDKEEEEKTRIQSAIKMAIS 286
                                        9999999999999889999999**********************************9999986 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0029
                     CENP-F_leu_zip  45 leaEtskaevetlkeeieelaeelreleldLvalrsekeeLekelqkkqervseLes 101
                                        +   ++ +++++l++e+  l+++ + l++ ++   +  ++L k++ +   +++ L++
  gene1757|gene1757|rna1757|rna1757 285 ISQKNKTKTANELQNEVTCLEKTIKSLSMAINVSNRRIDHLSKQISHIEGKIEVLKK 341
                                        55677888999*****************************************99987 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.0012
                     CENP-F_leu_zip  59 eeieelaeelreleldLvalrsekeeLekelqkkqervseLeslnsslenl 109
                                        e+ +el+++l++l+ + +++r e+++  + + ++q++++e e   +++ n+
  gene1757|gene1757|rna1757|rna1757 345 ENAKELSNNLNKLKDNYSKVRTERNDYFERIANNQKEIKEIEYKMVQIMNQ 395
                                        66789*************************************988887775 PP

>> Atg14  Vacuolar sorting 38 and autophagy-related subunit 14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3  19.0     0.078        73      32     147 ..     149     267 ..     118     279 .. 0.75
   2 ?    9.6  22.8   0.00047      0.44      27     167 ..     263     412 ..     256     420 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.078
                              Atg14  32 aklksekeslkkkiekalegkeeaeqledkiknkkakleelksliadlrerlqelkdklsqlkkeieekkkklakl 107
                                         klks k++ +kk ++  e +++++qled++k++ +  +e  + +++ +++  e  dkls+lk    + k++++++
  gene1757|gene1757|rna1757|rna1757 149 SKLKSMKDEAQKKEKENAELENKVGQLEDEVKSLCKEQRERANSVEEMKRERDEFYDKLSSLKLVCLNLKQEIKEM 224
                                        5788999999999998888888999999999999999999999999999999999999999999999999999999 PP

                              Atg14 108 sdklkkRrsdleslqnele...errkkqiaklqdaikrieqkl 147
                                        + ++ +  s++ sl +e++   + +k++i+++ ++i+ +++ +
  gene1757|gene1757|rna1757|rna1757 225 KTQVIDDPSKMLSLIEEMQvliKTEKASIEEFNKKIRHTTELI 267
                                        9998855544444444443111556666666666666555554 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00047
                              Atg14  27 lrerlaklksekeslkkkiekalegke...eaeqledkiknkkakleelksliadlrerlqelkdklsqlkkeiee 99 
                                          e + k  +ek  +++ i+ a+++k+    a++l++++ ++ + +++l   i  +++r+  l++++s+   +ie 
  gene1757|gene1757|rna1757|rna1757 263 TTELIDKEEEEKTRIQSAIKMAISQKNktkTANELQNEVTCLEKTIKSLSMAINVSNRRIDHLSKQISHIEGKIEV 338
                                        555566667788889999999999999888889999**************************************** PP

                              Atg14 100 kkkklaklsdklkkRrsdleslqneleerrkkqiaklqdaikrieqk......lsslssktlesrsslcselak 167
                                         kkk +++ ++l+    +l+  +++++ +r++ ++++ ++ k+i++       +++ ++k ++  +s+++el +
  gene1757|gene1757|rna1757|rna1757 339 LKKKDQENAKELSNNLNKLKDNYSKVRTERNDYFERIANNQKEIKEIeykmvqIMNQHQKDMHVLISKLTELKN 412
                                        *************99999999**********9999999888866666555666556666666654444444433 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   2.8      0.01       9.7      76     122 ..     131     177 ..     120     186 .. 0.71
   2 ?    8.0   6.9     0.003       2.8      50     122 ..     154     226 ..     141     228 .. 0.86
   3 ?    6.1   9.1     0.012        11      51     123 ..     264     335 ..     233     336 .. 0.77
   4 ?   14.1   7.2   3.8e-05     0.036      35     123 ..     293     388 ..     292     389 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.01
                            DUF1664  76 deqkeiskeikeevtevredlseigedvesvkeavegleskleriee 122
                                        +eq+ + +ei+  ++ ++++l++++++ ++ ++   +le+k+ ++e+
  gene1757|gene1757|rna1757|rna1757 131 EEQESLLNEINVSINMAESKLKSMKDEAQKKEKENAELENKVGQLED 177
                                        66677777777777777777777777777777777777777777765 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.003
                            DUF1664  50 leqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskleriee 122
                                        +++  ++ ++   +L++++ ++++++++  + ++e ++ v+e++++ +e+ ++++s+k +  +l+++++++++
  gene1757|gene1757|rna1757|rna1757 154 MKDEAQKKEKENAELENKVGQLEDEVKSLCKEQRERANSVEEMKRERDEFYDKLSSLKLVCLNLKQEIKEMKT 226
                                        44444555666789*******************************************************9974 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.012
                            DUF1664  51 eqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeaveglesklerieek 123
                                        +++ ++ ++ k +++s i+ +  ++++ +++++e+++evt +++ +++++  ++  ++ + +l +++++ie+k
  gene1757|gene1757|rna1757|rna1757 264 TELIDKEEEEKTRIQSAIK-MAISQKNKTKTANELQNEVTCLEKTIKSLSMAINVSNRRIDHLSKQISHIEGK 335
                                        3333444566777777775.67778888899999************************************986 PP

  == domain 4  score: 14.1 bits;  conditional E-value: 3.8e-05
                            DUF1664  35 Tkrslsdavesvskqleqvseslaatkr...hLssridrvdkkld....eqkeiskeikeevtevredlseigedv 103
                                        T   l++ v+ + k ++++s +++   r   hLs++i +++ k++    + +e +ke+++++++++++ s+++++ 
  gene1757|gene1757|rna1757|rna1757 293 TANELQNEVTCLEKTIKSLSMAINVSNRridHLSKQISHIEGKIEvlkkKDQENAKELSNNLNKLKDNYSKVRTER 368
                                        66789999************999866543449***********98333345678899999**************** PP

                            DUF1664 104 esvkeaveglesklerieek 123
                                        +   e + + ++++++ie+k
  gene1757|gene1757|rna1757|rna1757 369 NDYFERIANNQKEIKEIEYK 388
                                        ******************87 PP

>> LPP  Lipoprotein leucine-zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.8      0.36   3.4e+02      11      32 ..     139     160 ..     130     167 .. 0.57
   2 ?    5.9   0.2     0.018        17       4      36 ..     167     199 ..     164     201 .. 0.80
   3 ?   -1.0   0.0       2.5   2.4e+03       9      30 ..     207     228 ..     200     230 .. 0.73
   4 ?    3.0   0.1      0.14   1.4e+02       3      27 ..     295     319 ..     293     322 .. 0.86
   5 ?    6.1   0.1     0.015        14       2      22 ..     322     342 ..     321     349 .. 0.81
   6 ?    6.3   0.1     0.014        13       3      36 ..     348     381 ..     346     384 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.36
                                LPP  11 qLkskvdqlssdvnsakaaaqa 32 
                                        + +  +++ +s+++s+k++aq+
  gene1757|gene1757|rna1757|rna1757 139 EINVSINMAESKLKSMKDEAQK 160
                                        3444455555555566555554 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.018
                                LPP   4 eLssqVsqLkskvdqlssdvnsakaaaqaakeE 36 
                                        eL + V qL+++v++l +++ + ++ +++ k E
  gene1757|gene1757|rna1757|rna1757 167 ELENKVGQLEDEVKSLCKEQRERANSVEEMKRE 199
                                        688899999999999999888888777777765 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 2.5
                                LPP   9 VsqLkskvdqlssdvnsakaaa 30 
                                        +s+Lk    +l+++++++k+++
  gene1757|gene1757|rna1757|rna1757 207 LSSLKLVCLNLKQEIKEMKTQV 228
                                        6777777778888888888765 PP

  == domain 4  score: 3.0 bits;  conditional E-value: 0.14
                                LPP   3 deLssqVsqLkskvdqlssdvnsak 27 
                                        +eL ++V  L++ +++ls  +n ++
  gene1757|gene1757|rna1757|rna1757 295 NELQNEVTCLEKTIKSLSMAINVSN 319
                                        789999999**99999999988765 PP

  == domain 5  score: 6.1 bits;  conditional E-value: 0.015
                                LPP   2 ldeLssqVsqLkskvdqlssd 22 
                                        +d Ls+q+s+ + k++ l+++
  gene1757|gene1757|rna1757|rna1757 322 IDHLSKQISHIEGKIEVLKKK 342
                                        899************999876 PP

  == domain 6  score: 6.3 bits;  conditional E-value: 0.014
                                LPP   3 deLssqVsqLkskvdqlssdvnsakaaaqaakeE 36 
                                        +eLs+++++Lk++ +++  + n+  + +++ ++E
  gene1757|gene1757|rna1757|rna1757 348 KELSNNLNKLKDNYSKVRTERNDYFERIANNQKE 381
                                        79***************99988877776666655 PP

>> Fez1  Fez1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4  30.4       5.8   5.4e+03      48     148 ..     131     250 ..     114     298 .. 0.50
   2 ?   10.9  11.9   0.00048      0.45      28     160 ..     296     423 ..     286     427 .. 0.68

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 5.8
                               Fez1  48 eekeeeikeleesleektlelevcenelqrkkseaellrekvekleeelkelreelselsleeeeaa......... 114
                                        ee+e+ ++e++ s++  + +l+ +++e q+k++e+  l++kv++le+e+k+l +e +e +++ ee++         
  gene1757|gene1757|rna1757|rna1757 131 EEQESLLNEINVSINMAESKLKSMKDEAQKKEKENAELENKVGQLEDEVKSLCKEQRERANSVEEMKrerdefydk 206
                                        3444445666666777777777777777777777777777777777777777555555444333333344444444 PP

                               Fez1 115 ..................................lesdeakaqrqeaeeleelkreverlraeLkeer 148
                                                                          +                        ++  +k+e+
  gene1757|gene1757|rna1757|rna1757 207 lsslklvclnlkqeikemktqviddpskmlslieE------------------------MQVLIKTEK 250
                                        45555555543322222222222222222222220........................222222222 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00048
                               Fez1  28 qklseivalkaqlrelrakleekeeeikeleesleektlelevcenelqrkkseaellrekvekleeelkelreel 103
                                        +  +e+  l  +++ l+ +++ ++++i++l++++++ + ++ev++++ q++    + l+++++kl+++ +++r+e 
  gene1757|gene1757|rna1757|rna1757 296 ELQNEVTCLEKTIKSLSMAINVSNRRIDHLSKQISHIEGKIEVLKKKDQENA---KELSNNLNKLKDNYSKVRTER 368
                                        3356777788888888888888888888888888888888887776655544...344455666666666666666 PP

                               Fez1 104 selsleeeeaalesdeakaqrqeaeeleelkreverlraeLkeerqkkeeqassFeq 160
                                        ++  ++ +++++e +e   + +  + +++ ++++  l ++L+e +++ ++  + Fe+
  gene1757|gene1757|rna1757|rna1757 369 NDYFERIANNQKEIKEI--EYKMVQIMNQHQKDMHVLISKLTELKNAANRYFMGFED 423
                                        66554444444444443..333456789999999************99999998875 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3  12.4      0.19   1.8e+02     126     236 ..     135     277 ..     118     282 .. 0.57
   2 ?    9.7  12.3   0.00054      0.51     112     235 ..     266     398 ..     256     404 .. 0.68

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.19
                            DUF4407 126 qlaaa.......ltaelaeleaqiaalqaeidaaearldalraeaqkeldgtk...gtgttgvaGkgpaake...k 188
                                        +l ++       ++++l+ ++++ ++ ++e +++e+++ +l++e+++ ++ ++   ++ ++ ++ + + +++    
  gene1757|gene1757|rna1757|rna1757 135 SLLNEinvsinmAESKLKSMKDEAQKKEKENAELENKVGQLEDEVKSLCKEQReraNSVEEMKRERDEFYDKlssL 210
                                        2222222224456777777777777777777777777777777777777765544322222222233333336663 PP

                            DUF4407 189 kaqldaaqaelaelkakld...................atarlaalraelaeleaerakeraasqaa 236
                                        k     +++e++e+k+++                    ++a +++ ++++   ++ ++ke++++++ 
  gene1757|gene1757|rna1757|rna1757 211 KLVCLNLKQEIKEMKTQVIddpskmlslieemqvliktEKASIEEFNKKIRHTTELIDKEEEEKTRI 277
                                        3344445555555555554655566667777778888888888888888888777777776666554 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00054
                            DUF4407 112 laeeqqeeakelkeqlaaa............ltaelaeleaqiaalqaeidaaearldalraeaqkeldgtkgtgt 175
                                        l+++ +ee++++++ ++ a            l++e++ le+ i++l+ +i+  ++r+d l ++   +++g+     
  gene1757|gene1757|rna1757|rna1757 266 LIDKEEEEKTRIQSAIKMAisqknktktaneLQNEVTCLEKTIKSLSMAINVSNRRIDHLSKQIS-HIEGKIEVL- 339
                                        55555555555555555444444444444457777777777777777777777777777777776.777766544. PP

                            DUF4407 176 tgvaGkgpaakekkaqldaaqaelaelkakld.atarlaalraelaeleaerakeraasqa 235
                                          ++ + ++ake  ++l++++ +  +++++++   +r+a++++e++e+e ++ ++ +++q+
  gene1757|gene1757|rna1757|rna1757 340 --KKKDQENAKELSNNLNKLKDNYSKVRTERNdYFERIANNQKEIKEIEYKMVQIMNQHQK 398
                                        ..55667777777777777777777777775577899999999999999999998888876 PP

>> BRI3BP  Negative regulator of p53/TP53
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.0   0.0       9.2   8.7e+03      39      57 ..      69      87 ..      67      96 .. 0.78
   2 ?    8.8   1.2    0.0011       1.1     151     179 ..     158     186 ..     147     187 .. 0.85
   3 ?    0.4   0.1      0.43   4.1e+02     148     176 ..     284     312 ..     281     317 .. 0.82
   4 ?    3.1   0.1     0.063        60     156     179 ..     320     343 ..     310     344 .. 0.80

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 9.2
                             BRI3BP 39 alevlarivtdlLdalGid 57
                                       +l +l++    lL+ lGid
  gene1757|gene1757|rna1757|rna1757 69 FLLILYKRTDMLLRRLGID 87
                                       6778888888889999988 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0011
                             BRI3BP 151 aksseesgasleakvrsLerqvrelnkrq 179
                                        a+++e+++a+le+kv +Le +v+ l k q
  gene1757|gene1757|rna1757|rna1757 158 AQKKEKENAELENKVGQLEDEVKSLCKEQ 186
                                        4566799*****************98876 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.43
                             BRI3BP 148 glyaksseesgasleakvrsLerqvreln 176
                                        +++ k+++++ ++l++ v  Le+ ++ l 
  gene1757|gene1757|rna1757|rna1757 284 AISQKNKTKTANELQNEVTCLEKTIKSLS 312
                                        5566777789999**********999986 PP

  == domain 4  score: 3.1 bits;  conditional E-value: 0.063
                             BRI3BP 156 esgasleakvrsLerqvrelnkrq 179
                                            +l +++ ++e++++ l+k+ 
  gene1757|gene1757|rna1757|rna1757 320 RRIDHLSKQISHIEGKIEVLKKKD 343
                                        56789***************9985 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6  10.6     0.011        10     400     468 ..     133     201 ..     114     214 .. 0.82
   2 ?   11.2  19.9   0.00011       0.1     317     454 ..     187     337 ..     182     342 .. 0.50
   3 ?    4.0  29.5     0.016        15     286     456 ..     219     392 ..     216     412 .. 0.63

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.011
                             AAA_13 400 elhlveeleseldeykkkykklekaieklekelkeeeaelkkleeeikeLekqlrdekpaaeeinkeLk 468
                                        + +l++e++  ++  ++k+k+++++++k eke +e e+++ +le+e+k L k+ r+  +++ee+ +e  
  gene1757|gene1757|rna1757|rna1757 133 QESLLNEINVSINMAESKLKSMKDEAQKKEKENAELENKVGQLEDEVKSLCKEQRERANSVEEMKRERD 201
                                        456778888888888999999999999999999999999999999999999999999999999987755 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00011
                             AAA_13 317 safeedkeelkaeaealeeqLkg...lqraleaKrkepfk........svel.esvkakiesikklvaeineliak 380
                                        ++ ++ +ee+k+e +++ ++L +   ++  l++ +ke+ +         ++l e+++  i+  k +++e+n+ i+ 
  gene1757|gene1757|rna1757|rna1757 187 RERANSVEEMKRERDEFYDKLSSlklVCLNLKQEIKEMKTqviddpskMLSLiEEMQVLIKTEKASIEEFNKKIRH 262
                                        4445555555555555555533322244445555544444100000004442244444445555555555555555 PP

                             AAA_13 381 hNekvanleeekeeakkklelhlveeleseld.eykkkykklekaieklekelkeeeaelkkleeeikeLekqlr 454
                                          e +++ eeek++++++++  + ++ + +   e+++++  lek+i++l  +++ +++++  l ++i+ +e +++
  gene1757|gene1757|rna1757|rna1757 263 TTELIDKEEEEKTRIQSAIKMAISQKNKTKTAnELQNEVTCLEKTIKSLSMAINVSNRRIDHLSKQISHIEGKIE 337
                                        555666666666666666666665555444333666666666666666666666666666666666666665543 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.016
                             AAA_13 286 erLekliekveskkselleklkav...sdeasensafeed.keelkaeaealeeqLkglqraleaKrkepfksvel 357
                                        +++++++++v  + s++l  ++++   ++++++ ++ +++ +   ++ +++ ee+ + +q+a++  + +  k+ + 
  gene1757|gene1757|rna1757|rna1757 219 QEIKEMKTQVIDDPSKMLSLIEEMqvlIKTEKASIEEFNKkIRHTTELIDKEEEEKTRIQSAIKMAISQKNKTKTA 294
                                        5566666666555555544444440004444444432222222222222333333333444444444444455667 PP

                             AAA_13 358 esvkakiesikklvaeineliakhNekvanleeekeeakkklelhlveeleseldeykkkykklekaieklekelk 433
                                        ++++++++ ++k ++++   i+  N++++ l ++ ++++ k+e     + +++ +e+ ++++kl+++ +k+ +e +
  gene1757|gene1757|rna1757|rna1757 295 NELQNEVTCLEKTIKSLSMAINVSNRRIDHLSKQISHIEGKIEVLKK-KDQENAKELSNNLNKLKDNYSKVRTERN 369
                                        88999999999999999999999999999999999999999998444.4445556777888888888888888888 PP

                             AAA_13 434 eeeaelkkleeeikeLekqlrde 456
                                        +  +++++ ++eike+e ++ ++
  gene1757|gene1757|rna1757|rna1757 370 DYFERIANNQKEIKEIEYKMVQI 392
                                        88888888888888888776655 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4  15.9     0.064        60     185     257 ..     128     200 ..     115     204 .. 0.53
   2 ?   -0.8  14.5       0.6   5.7e+02     171     261 ..     202     292 ..     194     296 .. 0.64
   3 ?   11.7  15.5   9.1e-05     0.086     145     256 ..     291     402 ..     287     412 .. 0.92

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.064
                               Spc7 185 klqeaaeelesidkeeLeelreelaelkaeieekkkelaelqeqleeleekieelkeqkseleeeiaeaervl 257
                                         ++e++e+l +  + +++ + ++l++ k e ++k+ke ael++++ +le+++++l ++ +e  + ++e +r +
  gene1757|gene1757|rna1757|rna1757 128 LEKEEQESLLNEINVSINMAESKLKSMKDEAQKKEKENAELENKVGQLEDEVKSLCKEQRERANSVEEMKRER 200
                                        4444444455555555555666666666666666666666666666666666555555555555555554444 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.6
                               Spc7 171 eleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelaelqeqleeleekieelkeqksel 246
                                        e+  + ++l+    +l+++ +e+++   ++  ++ + ++e ++ i+  k+ ++e ++++ + +e i++ +e+k+++
  gene1757|gene1757|rna1757|rna1757 202 EFYDKLSSLKLVCLNLKQEIKEMKTQVIDDPSKMLSLIEEMQVLIKTEKASIEEFNKKIRHTTELIDKEEEEKTRI 277
                                        4444555555555666666677666666666666677777777777777888888888888888888888888888 PP

                               Spc7 247 eeeiaeaervleeck 261
                                        +++i+ a + ++++k
  gene1757|gene1757|rna1757|rna1757 278 QSAIKMAISQKNKTK 292
                                        888876655555444 PP

  == domain 3  score: 11.7 bits;  conditional E-value: 9.1e-05
                               Spc7 145 eenlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkk 220
                                        +++ ++l+++ ++Lek  + l+ + +  +++ + l++++ +++ + e l++ d+e+ +el ++l++lk ++++ ++
  gene1757|gene1757|rna1757|rna1757 291 TKTANELQNEVTCLEKTIKSLSMAINVSNRRIDHLSKQISHIEGKIEVLKKKDQENAKELSNNLNKLKDNYSKVRT 366
                                        5788999********************************************************************* PP

                               Spc7 221 elaelqeqleeleekieelkeqkseleeeiaeaerv 256
                                        e ++  e++++ +++i+e++ ++ +++++ ++  +v
  gene1757|gene1757|rna1757|rna1757 367 ERNDYFERIANNQKEIKEIEYKMVQIMNQHQKDMHV 402
                                        *******************99999999998887666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (428 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      4198  (0.234146); expected 358.6 (0.02)
Passed bias filter:                      718  (0.0400469); expected 358.6 (0.02)
Passed Vit filter:                       197  (0.0109878); expected 17.9 (0.001)
Passed Fwd filter:                       102  (0.00568911); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 1.85u 0.37s 00:00:02.22 Elapsed: 00:00:00.63
# Mc/sec: 2051.77
//
Query:       gene1758|gene1758|rna1758|rna1758  [L=729]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
       0.11   12.3   0.1       0.11   12.3   0.1    5.4  5  KASH_CCD        Coiled-coil region of CCDC155 or KASH
       0.13   12.7   0.3       0.13   12.7   0.3    8.7  8  ZapB            Cell division protein ZapB
        2.7    8.3  69.2      0.025   14.8   5.3    7.2  7  TMF_TATA_bd     TATA element modulatory factor 1 TATA binding


Domain annotation for each model (and alignments):
>> KASH_CCD  Coiled-coil region of CCDC155 or KASH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   1.8e-05      0.11      73     124 ..      30      81 ..      21      99 .. 0.82
   2 ?    2.9   0.1     0.014        85     105     132 ..     215     242 ..     211     249 .. 0.78
   3 ?   -6.2  18.8         3   1.8e+04      11     149 ..     273     423 ..     265     460 .. 0.75
   4 ?   -0.1  20.4      0.12   7.1e+02      48     163 ..     456     566 ..     439     589 .. 0.66
   5 ?    0.6  16.8     0.073   4.3e+02      61     180 ..     595     726 ..     590     729 .] 0.64

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.8e-05
                           KASH_CCD  73 kalvkeleEkrarlkaqnkqlekenqsLiakiesLqeenikllaekdelkkk 124
                                        k++v ++  + +  + + ++++ en  L ++i++L++eni+ll+ ++++k+ 
  gene1758|gene1758|rna1758|rna1758  30 KKVVLTVHRRTNYYHFNYEKVKEENRNLWIQINNLKNENIRLLSKIEAVKRD 81 
                                        666666677777778888999**************************99975 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.014
                           KASH_CCD 105 esLqeenikllaekdelkkklkeLlkek 132
                                         +Lq+ + +l  e++ lk+k + L++e+
  gene1758|gene1758|rna1758|rna1758 215 INLQNTIYQLNRENNLLKEKNERLCREI 242
                                        5788888888888888888888888765 PP

  == domain 3  score: -6.2 bits;  conditional E-value: 3
                           KASH_CCD  11 adLqlnNkkLaeenskLkkav..etaeetnakLteeieeLkkkl.kst...QqalqkaklleeEleelkalvkele 80 
                                        +++   N +L++en k+k+++  e  +   +  +e  + L +++ + t     ++   + l++El+ +    k  e
  gene1758|gene1758|rna1758|rna1758 273 KNMCRLNDSLKNENIKVKASLilERKD-RENMVSEHKKTLSEQIaRLTrenTELVIVNERLSNELASAMDRCKLFE 347
                                        555666899999999999985324444.344566666777777523330003455667889999999999999999 PP

                           KASH_CCD  81 EkrarlkaqnkqlekenqsLiak..i.....esLqeenikllaekdelkkklkeLlkekaeLkkqlheleellaek 149
                                         ++++  ++ + +e en  L+ k  i      +L+e+n+ l++ +  l +k ke+ + ++ Lk + ++++++l++k
  gene1758|gene1758|rna1758|rna1758 348 RSNEECLNKCRFMEVENYDLKFKnnIyegleRKLDEKNFELQTYEYRLGEKDKEIERLRERLKDKDDKIHSMLVKK 423
                                        9999999999999999999976522333333478999999999999999999999999999999988888888776 PP

  == domain 4  score: -0.1 bits;  conditional E-value: 0.12
                           KASH_CCD  48 LkkklkstQq.alqkaklleeEleelkalvke.leEkrarlkaqnkqlekenqsLiakiesLqeenikllaekdel 121
                                        L +k+  + +    ++++++e  e l a+ k+  +E+ +r++   +ql + n+    +i  + +e++ l+ ++   
  gene1758|gene1758|rna1758|rna1758 456 LVEKMDEMSKtERANMRSIAESKEKLAAMYKDkADESLNRMERSDEQLRRCNE----RIRIMTVEIENLKKDEADA 527
                                        44444332220334456666666666655553145566666666666666554....5666667777777788888 PP

                           KASH_CCD 122 kkklkeLlkekaeLkkqlheleellaekealleektkqieeL 163
                                         +kl+e  +e+a+Lk+++   + ll++k++++++ + qi +L
  gene1758|gene1758|rna1758|rna1758 528 INKLNEVHEENANLKTKI---DGLLVQKNTFVKNNQSQIMKL 566
                                        899************999...99********98888877655 PP

  == domain 5  score: 0.6 bits;  conditional E-value: 0.073
                           KASH_CCD  61 kaklleeEleelkalvkeleEkrarlkaqnkq....le.kenqsLiakiesLqeenikllaekdelkkklkeLlke 131
                                        + k l + lee k+ v++le ++++++ + +q    +e    q L+   +++++ n k +       +k++eLl++
  gene1758|gene1758|rna1758|rna1758 595 NVKTLMKQLEESKNAVSSLENEKKNVNERFNQerarIEeYYTQELQNARAAIEDLNAKQQIYVTG-FEKIRELLQN 669
                                        679999**************998888766544211122123455554444444444554444333.3466777666 PP

                           KASH_CCD 132 kaeLkkqlheleel..........laekealleektkqieeLkltieEyssiieeLrae 180
                                           L +q++ +e+l           ++ + +l+ k++ ie++k +i  ++s++e++ + 
  gene1758|gene1758|rna1758|rna1758 670 S--LNTQVCDFEQLrevivglterCNKLDDELKTKERSIENFKGIILKLRSVNEKMLKK 726
                                        5..77777776665332222222145669999999999999999999999999987654 PP

>> ZapB  Cell division protein ZapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.2    0.0049        29      27      56 ..      47      76 ..      44      86 .. 0.56
   2 ?   12.7   0.3   2.2e-05      0.13      21      48 ..     215     242 ..     213     256 .. 0.89
   3 ?    2.4   3.5     0.035   2.1e+02      21      48 ..     309     336 ..     272     351 .. 0.78
   4 ?    4.1   3.1      0.01        62      17      66 ..     354     420 ..     344     422 .. 0.64
   5 ?   -1.1   1.8      0.45   2.7e+03      35      63 ..     483     511 ..     438     525 .. 0.64
   6 ?    3.7   7.8     0.014        83      18      57 ..     508     562 ..     491     583 .. 0.77
   7 ?    1.2   5.8     0.083     5e+02      20      53 ..     596     637 ..     591     653 .. 0.68
   8 ?    0.1   2.9      0.19   1.2e+03       8      52 ..     666     710 ..     662     729 .] 0.75

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0049
                               ZapB 27 ieeLkeeneelkeenreleeeneqlkeere 56
                                       +e++keen++l  ++++l+ en +l    e
  gene1758|gene1758|rna1758|rna1758 47 YEKVKEENRNLWIQINNLKNENIRLLSKIE 76
                                       455666666666666666655555443333 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 2.2e-05
                               ZapB  21 tlLqmeieeLkeeneelkeenreleeen 48 
                                          Lq+ i++L +en+ lke+n++l +e+
  gene1758|gene1758|rna1758|rna1758 215 INLQNTIYQLNRENNLLKEKNERLCREI 242
                                        579******************9998765 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.035
                               ZapB  21 tlLqmeieeLkeeneelkeenreleeen 48 
                                        ++L+++i++L +en el   n++l+ e+
  gene1758|gene1758|rna1758|rna1758 309 KTLSEQIARLTRENTELVIVNERLSNEL 336
                                        4566666666666666666666555544 PP

  == domain 4  score: 4.1 bits;  conditional E-value: 0.01
                               ZapB  17 idtitlLqmeieeLkeen.......eelkeenrele..........eeneqlkeereawqerlkkLL 66 
                                        +++++ +  e+++Lk +n       ++l e+n el+          +e+e+l+e  +   +++ ++L
  gene1758|gene1758|rna1758|rna1758 354 LNKCRFMEVENYDLKFKNniyegleRKLDEKNFELQtyeyrlgekdKEIERLRERLKDKDDKIHSML 420
                                        6677777788888888885554444555555555556666666666666666666666666666665 PP

  == domain 5  score: -1.1 bits;  conditional E-value: 0.45
                               ZapB  35 eelkeenreleeeneqlkeereawqerlk 63 
                                        + +k++++e     e+  e+    +er++
  gene1758|gene1758|rna1758|rna1758 483 AMYKDKADESLNRMERSDEQLRRCNERIR 511
                                        33455555555555555555555555555 PP

  == domain 6  score: 3.7 bits;  conditional E-value: 0.014
                               ZapB  18 dtitlLqmeieeLkeeneelkeenreleeeneqlk...............eerea 57 
                                        ++i+ +  eie Lk++ +   ++ +e+ een +lk               +++++
  gene1758|gene1758|rna1758|rna1758 508 ERIRIMTVEIENLKKDEADAINKLNEVHEENANLKtkidgllvqkntfvkNNQSQ 562
                                        6788889999999999999999999999999999866666666655555444444 PP

  == domain 7  score: 1.2 bits;  conditional E-value: 0.083
                               ZapB  20 itlLqmeieeLkeeneelkeenreleeeneqlk........e 53 
                                        +++L +++ee k  +++l++e+++++e  +q++        +
  gene1758|gene1758|rna1758|rna1758 596 VKTLMKQLEESKNAVSSLENEKKNVNERFNQERarieeyytQ 637
                                        567777888888888888888888887777777555555554 PP

  == domain 8  score: 0.1 bits;  conditional E-value: 0.19
                               ZapB   8 qLEskiqkaidtitlLqmeieeLkeeneelkeenreleeeneqlk 52 
                                         L+++ ++ +   ++L++ i  L e+ ++l +e +  e+++e++k
  gene1758|gene1758|rna1758|rna1758 666 LLQNSLNTQVCDFEQLREVIVGLTERCNKLDDELKTKERSIENFK 710
                                        588888888888999999999999999999999999998888877 PP

>> TMF_TATA_bd  TATA element modulatory factor 1 TATA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.1     0.081   4.8e+02      28      61 ..      47      80 ..      21      87 .. 0.80
   2 ?    4.1   0.0    0.0088        52      13      41 ..     213     241 ..     205     257 .. 0.88
   3 ?    2.2   1.5     0.033     2e+02      31      61 ..     297     327 ..     274     334 .. 0.78
   4 ?   14.8   5.3   4.1e-06     0.025      23     103 ..     331     411 ..     328     414 .. 0.97
   5 ?    8.2  12.9   0.00048       2.8      12     103 ..     455     547 ..     446     549 .. 0.84
   6 ?    1.4  13.4      0.06   3.6e+02      13      89 ..     555     633 ..     549     658 .. 0.79
   7 ?    1.6   0.8     0.054   3.2e+02      42      70 ..     678     706 ..     660     729 .] 0.52

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.081
                        TMF_TATA_bd 28 laslkeelerleaerdeareeivklmkeneelke 61
                                       ++++kee+ +l  + +++++e ++l+++ e++k+
  gene1758|gene1758|rna1758|rna1758 47 YEKVKEENRNLWIQINNLKNENIRLLSKIEAVKR 80
                                       5678999999999999999999999999998876 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.0088
                        TMF_TATA_bd  13 lverlsseirrlEgElaslkeelerleae 41 
                                        +v +l+ +i +l  E + lke++erl +e
  gene1758|gene1758|rna1758|rna1758 213 TVINLQNTIYQLNRENNLLKEKNERLCRE 241
                                        6779*********************9886 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.033
                        TMF_TATA_bd  31 lkeelerleaerdeareeivklmkeneelke 61 
                                         k++ + +++ +++++e+i++l++en el  
  gene1758|gene1758|rna1758|rna1758 297 RKDRENMVSEHKKTLSEQIARLTRENTELVI 327
                                        5677788899999999999999999988755 PP

  == domain 4  score: 14.8 bits;  conditional E-value: 4.1e-06
                        TMF_TATA_bd  23 rlEgElaslkeelerleaerdeareeivklmkeneelkelkkeleelekeleelqeryetlLellGeksEeveELr 98 
                                        rl +Elas++++++ +e++ +e  + +  +  en +lk +++ +e le++l+e + +++t    lGek+ e+e Lr
  gene1758|gene1758|rna1758|rna1758 331 RLSNELASAMDRCKLFERSNEECLNKCRFMEVENYDLKFKNNIYEGLERKLDEKNFELQTYEYRLGEKDKEIERLR 406
                                        7889************************************************************************ PP

                        TMF_TATA_bd  99 aDvaD 103
                                        + ++D
  gene1758|gene1758|rna1758|rna1758 407 ERLKD 411
                                        *9998 PP

  == domain 5  score: 8.2 bits;  conditional E-value: 0.00048
                        TMF_TATA_bd  12 qlverlsseirrlEgElaslkeelerleae.rdeareeivklmkeneelkelkkeleelekeleelqeryetlLel 86 
                                         lve++    +   + ++s+ e+ e+l+a  +d+a e + ++ ++ e+l++ +++++ ++ e+e+l++ +  +   
  gene1758|gene1758|rna1758|rna1758 455 ALVEKMDEMSKTERANMRSIAESKEKLAAMyKDKADESLNRMERSDEQLRRCNERIRIMTVEIENLKKDEADAINK 530
                                        577888877777778888888888888775266666667777788899**************************** PP

                        TMF_TATA_bd  87 lGeksEeveELraDvaD 103
                                        l e  Ee+  L+  ++ 
  gene1758|gene1758|rna1758|rna1758 531 LNEVHEENANLKTKIDG 547
                                        ************98875 PP

  == domain 6  score: 1.4 bits;  conditional E-value: 0.06
                        TMF_TATA_bd  13 lverlssei.rrlEgElaslkeelerleaerdear.eeivklmkeneelkelkkeleelekeleelqeryetlLel 86 
                                         v++ +s+i + lE+E ++ ++el++ ++  +++    iv++ + + +l+e+k+ +++le+e ++++er ++    
  gene1758|gene1758|rna1758|rna1758 555 FVKNNQSQImKLLEIERRENEKELQKYKKIAEDVDlGKIVNVKTLMKQLEESKNAVSSLENEKKNVNERFNQERAR 630
                                        4555566663789***************9988875379*******************************9987666 PP

                        TMF_TATA_bd  87 lGe 89 
                                        + e
  gene1758|gene1758|rna1758|rna1758 631 IEE 633
                                        655 PP

  == domain 7  score: 1.6 bits;  conditional E-value: 0.054
                        TMF_TATA_bd  42 rdeareeivklmkeneelkelkkeleele 70 
                                         +++re iv l++++++l+++ k+ e   
  gene1758|gene1758|rna1758|rna1758 678 FEQLREVIVGLTERCNKLDDELKTKERSI 706
                                        45666666666666655554444333322 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (729 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2506  (0.139774); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                        31  (0.00172904); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 1.22u 0.32s 00:00:01.54 Elapsed: 00:00:00.56
# Mc/sec: 3937.16
//
Query:       gene1759|gene1759|rna1759|rna1759  [L=154]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    7.3e-12   45.5  23.6      2e-06   28.0  10.0    2.1  2  ATP-synt_C  ATP synthase subunit C
     0.0049   16.0   0.0     0.0058   15.7   0.0    1.1  1  GIDA        Glucose inhibited division protein A
  ------ inclusion threshold ------
       0.11   12.2   0.1       0.21   11.3   0.1    1.4  1  DUF4239     Protein of unknown function (DUF4239)
        3.7    7.0   5.5          3    7.3   0.3    2.1  2  MS_channel  Mechanosensitive ion channel


Domain annotation for each model (and alignments):
>> ATP-synt_C  ATP synthase subunit C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   5.6     1e-08   4.5e-05       1      60 []       9      68 ..       9      68 .. 0.97
   2 !   28.0  10.0   4.5e-10     2e-06       2      60 .]      88     146 ..      87     146 .. 0.97

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 1e-08
                                       HHHHHHH.GGGHHHHHHHHHHHHHHHHHHHHSGHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         ATP-synt_C  1 lgaglavGlsalgsGigiGkagsagiravarnpklftksliilafaeaialygLivalil 60
                                       lg  l+ +l a+g+  g+  +  ++++++  npk+ +ksl++++++e   l g++++ ++
  gene1759|gene1759|rna1759|rna1759  9 LGSFLCFMLNAIGTTKGMLAISRTCAGSSIFNPKIGSKSLVGVIICEGNLLCGIVISYFI 68
                                       7899****************************************************9876 PP

  == domain 2  score: 28.0 bits;  conditional E-value: 4.5e-10
                                        HHHHHH.GGGHHHHHHHHHHHHHHHHHHHHSGHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         ATP-synt_C   2 gaglavGlsalgsGigiGkagsagiravarnpklftksliilafaeaialygLivalil 60 
                                         ag  +G  +++s +++G++++a++ + a+ pklf+k++    +a+++++ g+ +++++
  gene1759|gene1759|rna1759|rna1759  88 SAGTITGAVGFASSFATGIICAAICVMDAKEPKLFSKLVFYEFIAGSLGVMGIGIGFLI 146
                                        7999*****************************************************97 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   1.3e-06    0.0058     333     388 ..      61     116 ..      57     120 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.3e-06
                                        -EEEEEEEE-GGGB-T.TSBBSSSBTEEE-CGGGTB-SHHHHHHHHHHHHHHHHHHH CS
                               GIDA 333 Gyaieydyvdprqlln.tLetkkvkgLflAGqinGteGYeEaaaqGllAGinaarka 388
                                        G +i y ++++   ++ +L+      Lf AG i+G  G+  + a+G++ +   + +a
  gene1759|gene1759|rna1759|rna1759  61 GIVISYFIFNSIPYESkNLKDA-SYILFSAGTITGAVGFASSFATGIICAAICVMDA 116
                                        5566666666666665455544.6679********************9887666655 PP

>> DUF4239  Protein of unknown function (DUF4239)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   4.6e-05      0.21     131     186 ..      72     133 ..      69     138 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 4.6e-05
                            DUF4239 131 isdeavalppthflvlaalsllslvgfllea......lltflndsqkkallallvfsglval 186
                                        i +e  +l ++ +++ +a ++  +vgf+          + +++d ++++l++ lvf  ++a+
  gene1759|gene1759|rna1759|rna1759  72 IPYESKNLKDASYILFSAGTITGAVGFASSFatgiicAAICVMDAKEPKLFSKLVFYEFIAG 133
                                        567888999******************654377998777889**************999986 PP

>> MS_channel  Mechanosensitive ion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.8     0.025   1.1e+02       7      42 ..      59     100 ..      57     114 .. 0.74
   2 ?    7.3   0.3   0.00068         3      27      49 ..     131     153 ..     121     154 .] 0.84

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.025
                                        HHHHHHHHHHHHTTT--......SCCHHHHHHHHHHHHHHHH CS
                         MS_channel   7 liivvgilivlsllgvn......vsallavlGalglalglal 42 
                                        l+ +v+ + ++ ++ ++       s++l ++G++  a+g+a+
  gene1759|gene1759|rna1759|rna1759  59 LCGIVISYFIFNSIPYEsknlkdASYILFSAGTITGAVGFAS 100
                                        5566777777777776655555578999************97 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.00068
                                        HHHHHHHHHHHHHHHHCHHHHHH CS
                         MS_channel  27 llavlGalglalglalkdlisnl 49 
                                        +  +lG++g+++g+  k+ i+ +
  gene1759|gene1759|rna1759|rna1759 131 IAGSLGVMGIGIGFLIKERIKMF 153
                                        6679*************998866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       525  (0.0292822); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 1023.80
//
Query:       gene176|gene176|rna176|rna176  [L=73]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (73 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       702  (0.0391544); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 512.34
//
Query:       gene1760|gene1760|rna1760|rna1760  [L=138]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.015   15.3   0.1      0.025   14.6   0.1    1.5  1  Med10     Transcription factor subunit Med10 of Mediator comp
        0.1   12.3   0.0        0.1   12.3   0.0    1.5  2  BAG6      BCL2-associated athanogene 6


Domain annotation for each model (and alignments):
>> Med10  Transcription factor subunit Med10 of Mediator complex
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.1   2.7e-06     0.025      32      73 ..      61      98 ..      25     132 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.7e-06
                                       HHHHHHHHHHHHHHHHHHH..HH--EEEHHHHHHHHTTB-HH CS
                              Med10 32 aqklktlvesLqelsktaskllqdikiPlelieyvenGrNPd 73
                                       ++++k+l+++L +l++++     ++ +Pl +ie++++G+  d
  gene1760|gene1760|rna1760|rna1760 61 SKEMKELIDELLKLKRMEV----NMAVPLSVIEMLDDGKDFD 98
                                       6789999999999999988....7**************9755 PP

>> BAG6  BCL2-associated athanogene 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   1.1e-05       0.1      48      81 ..      32      65 ..      14      90 .. 0.82
   2 ?   -3.0   0.1      0.65   5.8e+03      31      45 ..     100     114 ..      96     123 .. 0.55

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.1e-05
                               BAG6 48 ldrvsEalhllshalhalSDlrldLsqpppRhLs 81
                                           s+a h++s  lhalS l+l+  + p+++++
  gene1760|gene1760|rna1760|rna1760 32 TSAFSDACHVISSKLHALSNLILEADRFPSKEMK 65
                                       45679******************98888877775 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 0.65
                               BAG6  31 tfeesdntegreeaq 45 
                                         f+e +++e  e+++
  gene1760|gene1760|rna1760|rna1760 100 IFNEREKEELEERKE 114
                                        455555555444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1337  (0.0745719); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 962.46
//
Query:       gene1761|gene1761|rna1761|rna1761  [L=85]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (85 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       538  (0.0300073); expected 358.6 (0.02)
Passed bias filter:                      218  (0.0121591); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.33u 0.25s 00:00:00.58 Elapsed: 00:00:00.39
# Mc/sec: 650.51
//
Query:       gene1762|gene1762|rna1762|rna1762  [L=300]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.8e-31  108.6   0.0    7.1e-31  108.3   0.0    1.1  1  Metallophos    Calcineurin-like phosphoesterase
     0.0045   17.2   0.0     0.0066   16.7   0.0    1.3  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d
     0.0067   16.8   0.1      0.013   15.9   0.1    1.4  1  STPPase_N      Serine-threonine protein phosphatase N-termina


Domain annotation for each model (and alignments):
>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.3   0.0   1.2e-34   7.1e-31       2     201 ..      42     233 ..      41     236 .. 0.87

  Alignments for each domain:
  == domain 1  score: 108.3 bits;  conditional E-value: 1.2e-34
                                        EEEEEESBTBTTCCTHHHHHHHHHHHHHHHTTE..SEEEEESTSSSSSHHHHHHHHH.HHHHHHHTSEEEEEC-TT CS
                        Metallophos   2 rilvigDlHlalgggqlddllkllddllreekp..dlvllaGDlvdrgdlekellel.laalvkypipvylllGNH 74 
                                        +i+++gD+H     gq+ dll++++++ ++ k+  +++l  GD+vdrg+ + e+l l l ++v+yp +  +l+GNH
  gene1762|gene1762|rna1762|rna1762  42 PITIVGDIH-----GQFFDLLNIFKKFGSP-KCtrYVFL--GDYVDRGVHSVETLSLlLIYKVMYPENMTILRGNH 109
                                        799******.....*************666.66447888..*******8888888887****************** PP

                                        S........CHHHHHHHHHHHHHHHHHHHEHHHCEEETSEEEEEETTEEEEEEEESE.CEEETHHHHHHHHHHHSC CS
                        Metallophos  75 e........gfeeellnkygylgifsepwrsdaevfnnlplaslgsgslkvlllhGg.spellvsldklgslnlel 141
                                        e        gf++e+  kyg+l+     +r ++evf++l l ++++g  +++++hGg s  +  +ld+ ++ +++ 
  gene1762|gene1762|rna1762|rna1762 110 EsskissiyGFSDEVRKKYGDLA----AYRAFCEVFEYLVLGCIVDG--RLFCVHGGiSSSI-INLDDFTKMPRFY 178
                                        ********************955....7799****************..********54444.5555555555555 PP

                                        HHHHCC...HHHHHHHHHHTTCSEEEEEESSESSCSSSCSCCHHHHHHHHHHTTESEEEEESS CS
                        Metallophos 142 eapepg...dewlkdlekrekadwvivlgHsplyrgsgylfgdealedllkkygvdlvisGHt 201
                                         ape+    d++++d        +   lg  p+ rg g+ +g++++ ++l  ++++ +i++H+
  gene1762|gene1762|rna1762|rna1762 179 HAPEKSkigDLLWSD--------PSQQLGFTPNVRGTGCAYGNDVVTKFLMVNQLQKIIRSHQ 233
                                        555555566******........***************************************7 PP

>> Metallophos_2  Calcineurin-like phosphoesterase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   1.1e-06    0.0066       3      81 ..      43     131 ..      42     183 .. 0.69

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.1e-06
                      Metallophos_2   3 laiiSDlHsnldaleavlealkevgvdaiihaGDleeeepevleellela........pvlaVrGNnD.....eev 65 
                                        + i+ D+H++++ l ++++++ + ++ + +++GD+ ++  +++e+l  l+         +++ rGN++     +  
  gene1762|gene1762|rna1762|rna1762  43 ITIVGDIHGQFFDLLNIFKKFGSPKCTRYVFLGDYVDRGVHSVETLSLLLiykvmypeNMTILRGNHEsskisS-- 116
                                        679*******************************955555567776666677788999**********654431.. PP

                      Metallophos_2  66 veedvlreaaelgtdl 81 
                                         +  +++e  +  +dl
  gene1762|gene1762|rna1762|rna1762 117 -IYGFSDEVRKKYGDL 131
                                        .333333333333333 PP

>> STPPase_N  Serine-threonine protein phosphatase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1   2.2e-06     0.013      22      45 ..      14      37 ..       5      38 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2.2e-06
                          STPPase_N 22 LseaEIrqlCakareiFLsQPtLL 45
                                       Ls +EI +lC+k+ +i+ ++P+ L
  gene1762|gene1762|rna1762|rna1762 14 LSAQEIDHLCTKVISILVNEPNIL 37
                                       99*******************988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (300 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       410  (0.022868); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1984.85
//
Query:       gene1763|gene1763|rna1763|rna1763  [L=964]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (964 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       667  (0.0372023); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.69u 0.29s 00:00:00.98 Elapsed: 00:00:00.46
# Mc/sec: 6249.85
//
Query:       gene1764|gene1764|rna1764|rna1764  [L=267]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.8e-24   84.9   0.7    5.8e-11   42.3   0.0    2.3  2  DEAD_2    DEAD_2
      3e-05   24.1   0.0    4.3e-05   23.6   0.0    1.2  1  ResIII    Type III restriction enzyme, res subunit
    0.00065   19.5   0.1    0.00098   18.9   0.1    1.2  1  DEAD      DEAD/DEAH box helicase
  ------ inclusion threshold ------
      0.049   13.1   0.0      0.068   12.6   0.0    1.1  1  PhoH      PhoH-like protein
        0.1   12.5   0.0       0.18   11.7   0.0    1.4  1  NACHT     NACHT domain


Domain annotation for each model (and alignments):
>> DEAD_2  DEAD_2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.9   0.3   4.3e-14   1.5e-10       1      84 [.      72     146 ..      72     156 .. 0.83
   2 !   42.3   0.0   1.6e-14   5.8e-11      87     139 ..     214     266 ..     186     267 .] 0.87

  Alignments for each domain:
  == domain 1  score: 40.9 bits;  conditional E-value: 4.3e-14
                                        EEESSHHHHHHHHHHHHHHHHHCHHHS---E..EEE--CCCC-SCHHCCCHHCCCCHHHHHHHHHCCHHCCHTTTT CS
                             DEAD_2   1 ycsRThsqleqvvkelkklesykkkkekvkv..viLgSRknlCineevkkekkekavneaCkelkkkkaeekeekC 74 
                                        yc+RT+++ e+++ elk l +y k++ kvk+  ++L+SRk+lC+ne+v+      +++  C++l +        +C
  gene1764|gene1764|rna1764|rna1764  72 YCTRTVQESEKTLVELKTLIAYVKQHVKVKYmgLGLTSRKHLCVNEDVQG-----NIEMSCRKLLSTG------NC 136
                                        9*********************999666665116789***********98.....78899***99998......59 PP

                                        TT-SCCCCHH CS
                             DEAD_2  75 sffenleelk 84 
                                        +++++  ++ 
  gene1764|gene1764|rna1764|rna1764 137 DYYDRIDHIL 146
                                        9998876554 PP

  == domain 2  score: 42.3 bits;  conditional E-value: 1.6e-14
                                        HHHHHHC---CHHHHHHHHHCT--HHHHHHHHHCCTSEEEEEHHHHTSCCCHH CS
                             DEAD_2  87 kkllleevvdiedlvelgeklklCPYylsrelledadiiilpYqyLldekire 139
                                        + + +++v+++e++++ g+  k+CPY+l+r++l++ +  il Y+y+ld+ki++
  gene1764|gene1764|rna1764|rna1764 214 QPFSFDGVYTFEQIKRKGQYFKFCPYFLTRKALSSSNFLILTYNYVLDPKIKK 266
                                        677899********************************************987 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.0   1.2e-08   4.3e-05       5      68 ..      18      79 ..      15     126 .. 0.73

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 1.2e-08
                                       -HHHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHH CS
                             ResIII  5 reyQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslle 68
                                        + Q + i++++++++     +++i+m+ G+GKT+++++++ +++  + e+ + f+  ++++ e
  gene1764|gene1764|rna1764|rna1764 18 SPEQLSYIKETIASFT--TTSNLFIEMPAGSGKTICILSAAVSYQLYHVEDDVRFVYCTRTVQE 79
                                       678999*********5..9999**************9777777777666666666666666654 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.1   2.7e-07   0.00098       5      80 ..      26     100 ..      22     127 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 2.7e-07
                                        HHHHHHHHTTCEEEEEESTTSSHHHHHHHHHH.HHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEE CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               DEAD   5 aeaiplilgggdvlvaaeTGsGKTlaflipvl.qivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvl 79 
                                        +e+i  + +  +++++++ GsGKT + l +++  ++y+   ++  + ++ + t +  e+tl +lk+++ y++  v+
  gene1764|gene1764|rna1764|rna1764  26 KETIASFTTTSNLFIEMPAGSGKTICILSAAVsYQLYH--VEDDVRFVYCTRTVQESEKTLVELKTLIAYVKQHVK 99 
                                        67899999999***************988877355665..99999***********************99874443 PP

                                        E CS
                                        x RF
                               DEAD  80 l 80 
                                        +
  gene1764|gene1764|rna1764|rna1764 100 V 100
                                        3 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   1.9e-05     0.068       8      68 ..      20      87 ..      16     109 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.9e-05
                                       HHHHHHHHHH....H-SEEEEE--TTSSTTHHHHHHHHHH..HHTTS-SEEEEEE-S-.-TT----SS CS
                               PhoH  8 eQkeylealk....kndivfaiGpaGtGKtylavalavea..lkkkkvkriiltrpav.eageelGfl 68
                                       eQ +y++       + + +f+  paG+GKt   +++av++  ++ ++  r+++   +v e+++ l  l
  gene1764|gene1764|rna1764|rna1764 20 EQLSYIKETIasftTTSNLFIEMPAGSGKTICILSAAVSYqlYHVEDDVRFVYCTRTVqESEKTLVEL 87
                                       5666655433344467788999********98888777641144455556676555552667776555 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0     5e-05      0.18       8      59 ..      43      92 ..      36     101 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 5e-05
                                       -TTTCHHHHHHHHHHHHCTS-SCCCC-SEEEEEETTTTTTS-....-HCHHHC CS
                              NACHT  8 eaGsGKTtLlqklalawaegklpqgafklvFflslrelsrsgna.rsladllf 59
                                       +aGsGKT+    + +a+ + +l++++ ++ F+ + r++++s+++   l++l++
  gene1764|gene1764|rna1764|rna1764 43 PAGSGKTIC---ILSAAVSYQLYHVEDDVRFVYCTRTVQESEKTlVELKTLIA 92
                                       79*****97...5666667777777789**************99988999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       549  (0.0306208); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1784.85
//
Query:       gene1765|gene1765|rna1765|rna1765  [L=493]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.7e-39  135.8   0.1    2.8e-39  135.0   0.1    1.3  1  Helicase_C_2  Helicase C-terminal domain
    5.4e-08   32.8   0.3     0.0028   17.4   0.0    2.4  2  HBB           Helical and beta-bridge domain
     0.0016   18.7   0.2      0.005   17.1   0.2    1.9  1  DUF3908       Protein of unknown function (DUF3908)


Domain annotation for each model (and alignments):
>> Helicase_C_2  Helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  135.0   0.1   4.6e-43   2.8e-39       2     162 ..     285     445 ..     284     448 .. 0.95

  Alignments for each domain:
  == domain 1  score: 135.0 bits;  conditional E-value: 4.6e-43
                       Helicase_C_2   2 lellevvpggvlvffpSyklleevverlkeeleskkieifvee.keesrekvleeyke..kkkkgaillavcrGkl 74 
                                         +l+++vp+g+++ffpSy +++e++++ +   ++ ++ if e+ + e++ + l +yk+  k+++gai+++v+rGk+
  gene1765|gene1765|rna1765|rna1765 285 KDLCDIVPDGMIIFFPSYVFMHEIISKCEFMIKKLHKLIFIETiNYEESINALMNYKRaiKHGRGAIMFCVARGKV 360
                                        689***************************999999999999888999999*******555*************** PP

                       Helicase_C_2  75 sEGidfsddllraviivglPfpnpkdpeveakreyldekgkknsgkewylpealravnQaiGRliRhkdDygaivl 150
                                        sEGidf+++++r+v+++g+Pf+ +++  ++++ ++l+++ +    + + + +alr   Q++GR++R k+Dyg +v+
  gene1765|gene1765|rna1765|rna1765 361 SEGIDFKNEEGRCVLLIGVPFAFTESVIIKERLKFLKQNIN---LNAFLQFDALRHALQCLGRVVRGKNDYGLMVM 433
                                        ************************************99887...99****************************** PP

                       Helicase_C_2 151 lDeRfakeeire 162
                                         D R+++ +++ 
  gene1765|gene1765|rna1765|rna1765 434 ADYRYNSYKYGD 445
                                        ******998875 PP

>> HBB  Helical and beta-bridge domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   4.7e-07    0.0028      44     122 ..      38      90 ..       6     110 .. 0.78
   2 !   13.2   0.0   8.6e-06     0.052     115     161 ..     149     195 ..     142     229 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 4.7e-07
                                        CHHHHHCHCHHHCHHHHHHHHHHHHHHHHHHHCCHHCCCTCC-SHHHHHHHHHHHHHHHTS.TTTEEEEEE.STT. CS
                                HBB  44 pdeileeavpglirsaehflsllkrlveygkarreekieksesPrsflsrlaefllawlssdeedYvrlvskeege 119
                                         + + ++  pg+ r+  h+ls+l+r+ e+++  +++++   ++P  f+ +l+                        
  gene1765|gene1765|rna1765|rna1765  38 LSTFNQKKWPGNLRKDVHVLSILRRILEFLRIKLKSTHLTINTPHNFVCSLE------------------------ 89 
                                        467889999***************************************9998........................ PP

                                        EEC CS
                                HBB 120 sLe 122
                                          +
  gene1765|gene1765|rna1765|rna1765  90 --N 90 
                                        ..3 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 8.6e-06
                                        .STT..EECCCCS-TCCHHHHHHHCHCCCCCCTS-SSHHHHHHHHT.. CS
                                HBB 115 keeg.esLeavcldPskalrflkerlssllmsgtltpleeysdiiGle 161
                                        +++  + ++++c d s+++    + +s +++sgtltp++ y +++G+ 
  gene1765|gene1765|rna1765|rna1765 149 NNSLsPKITLSCND-SRIAMSALKFRSIMVTSGTLTPFDVYMRLLGIT 195
                                        4443488999****.66666666666********************98 PP

>> DUF3908  Protein of unknown function (DUF3908)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.2   8.3e-07     0.005      12      87 ..     270     346 ..     265     368 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 8.3e-07
                            DUF3908  12 srardeedrkvveelkkvsiildendilliytkylfvdekklellfilkd.nkfvkv.giekekrvvieklkydki 85 
                                         r      r+++  +k+++ i+  + ++++++ y+f+ e + +  f++k+ +k++ +  i+ e+ ++  +    +i
  gene1765|gene1765|rna1765|rna1765 270 LRTSSSTVRNYATLIKDLCDIVP-DGMIIFFPSYVFMHEIISKCEFMIKKlHKLIFIeTINYEESINALMNYKRAI 344
                                        556666778*************8.78999*****************998659999983467777776433333456 PP

                            DUF3908  86 kn 87 
                                        k+
  gene1765|gene1765|rna1765|rna1765 345 KH 346
                                        65 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (493 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       589  (0.0328518); expected 358.6 (0.02)
Passed bias filter:                      464  (0.0258799); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.41
# Mc/sec: 3591.68
//
Query:       gene1766|gene1766|rna1766|rna1766  [L=40]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (40 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       302  (0.0168442); expected 358.6 (0.02)
Passed bias filter:                      150  (0.00836633); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.22s 00:00:00.57 Elapsed: 00:00:00.40
# Mc/sec: 303.27
//
Query:       gene1767|gene1767|rna1767|rna1767  [L=98]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.6e-09   36.5   0.3    5.6e-09   36.3   0.3    1.1  1  EnY2             Transcription factor e(y)2
  ------ inclusion threshold ------
      0.045   13.4   0.2      0.051   13.2   0.2    1.0  1  Rab3-GTPase_cat  Rab3 GTPase-activating protein catalytic sub
       0.15   11.9   0.1       0.25   11.2   0.1    1.3  1  MEF2_binding     MEF2 binding


Domain annotation for each model (and alignments):
>> EnY2  Transcription factor e(y)2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.3   0.3   9.3e-13   5.6e-09       4      82 ..      17      91 ..      15      93 .. 0.89

  Alignments for each domain:
  == domain 1  score: 36.3 bits;  conditional E-value: 9.3e-13
                                       HHHHHHHTTHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHH..HTSS.CHHHHHHHHHHHHHHHS-HHHHHHHHHHHH CS
                               EnY2  4 iqqkLvesGererlkelLrerLeesGWrdevkelckeiirekgleeevsveelveeitpkaralVPdevkkellqrIr 81
                                        +++L++   +++l +lL  +++ sG+ d++++ ++    +    e++++e l++ei + + a +P+ev+    +++r
  gene1767|gene1767|rna1767|rna1767 17 TSENLISEETKNKLLNLLDLHMKRSGFHDKIMQKMESLKIN----ENINIEALYKEIYDFMTANMPEEVQDAFFEDVR 90
                                       5789****************************997665444....55***********************99999888 PP

                                       H CS
                               EnY2 82 e 82
                                        
  gene1767|gene1767|rna1767|rna1767 91 R 91
                                       6 PP

>> Rab3-GTPase_cat  Rab3 GTPase-activating protein catalytic subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.2   8.5e-06     0.051      13      80 ..      10      77 ..       5      91 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 8.5e-06
                    Rab3-GTPase_cat 13 enltLletgeplyaPvtqeppplTedlleeraevleklgssaegselrarlqsekLlsDMeaFkaAnp 80
                                       + +++l+t+e+l++  t+++ +   dl+++r+ +  k+ ++ e+ +++++++ e+L+     F  An 
  gene1767|gene1767|rna1767|rna1767 10 PRVRMLQTSENLISEETKNKLLNLLDLHMKRSGFHDKIMQKMESLKINENINIEALYKEIYDFMTANM 77
                                       6789************************************************************9994 PP

>> MEF2_binding  MEF2 binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   4.1e-05      0.25       9      19 ..      22      32 ..      20      34 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 4.1e-05
                       MEF2_binding  9 ISEETKQKLKs 19
                                       ISEETK KL +
  gene1767|gene1767|rna1767|rna1767 22 ISEETKNKLLN 32
                                       9********77 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1130  (0.0630264); expected 358.6 (0.02)
Passed bias filter:                      511  (0.0285013); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 706.99
//
Query:       gene1768|gene1768|rna1768|rna1768  [L=667]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.9e-32  112.4  31.1    2.9e-32  112.4  31.1    2.0  2  PhoLip_ATPase_C  Phospholipid-translocating P-type ATPase C-t
    2.8e-11   44.1   0.7    1.3e-08   35.4   0.1    2.6  2  Hydrolase        haloacid dehalogenase-like hydrolase
    5.6e-07   29.6   0.1      8e-06   25.8   0.1    2.3  2  Cation_ATPase    Cation transport ATPase (P-type)
    0.00082   19.2   0.3      0.005   16.6   0.2    2.2  2  Hydrolase_3      haloacid dehalogenase-like hydrolase


Domain annotation for each model (and alignments):
>> PhoLip_ATPase_C  Phospholipid-translocating P-type ATPase C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   3.6       0.7   3.1e+03     181     235 ..       4      63 ..       1      76 [. 0.40
   2 !  112.4  31.1   6.6e-36   2.9e-32       2     240 ..     443     666 ..     442     667 .] 0.85

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.7
                    PhoLip_ATPase_C 181 iililgsillyflflllyssllpsssefygvleelfss.....psfwlvlllvvvvallp 235
                                        +i+il  ++l+  +++l+++l +++ e+yg+++   +       ++ l+  l+++  +++
  gene1768|gene1768|rna1768|rna1768   4 YIFILYFVILFASCTMLTTNLRKNEVEMYGIDNFSKQAlkltgTNYILYSYLIPLSLFVM 63 
                                        344444455555555666666666555554432222220001123333333333333333 PP

  == domain 2  score: 112.4 bits;  conditional E-value: 6.6e-36
                    PhoLip_ATPase_C   2 raSDyaiaqFrfLkrLLlvhGrwsyrRisklilyffyKnvvftlvqfwfqfyngfsgqslyeswlltlynllftsl 77 
                                         a D+ai  F++L++LL+ hG+++++R skl + +f+Kn++++  qf ++f ngfsg s +++++l  +n+lfts+
  gene1768|gene1768|rna1768|rna1768 443 LAGDFAIMSFHHLRKLLFHHGKNNLIRFSKLTINSFFKNIFLISFQFNYNFSNGFSGLSAFNYYFLNYFNILFTSF 518
                                        689************************************************************************* PP

                    PhoLip_ATPase_C  78 pvivlgifdq.....dvsaelllky.PelYklgqknklfnlktfllwileglyqsliifflsylvlddssfsdgkt 147
                                         +++++ifd+     +++++++ +   e Yk+ +  ++f++kt++  ++ ++++++++++ s+ +ld +       
  gene1768|gene1768|rna1768|rna1768 519 IPFTIAIFDRgkeqrEFQDQTADRLlLESYKETR--NYFSTKTIFCSMIFAIMKGCLLYWTSFGMLDWN------- 585
                                        **********777774445544444125677776..7************************99999754....... PP

                    PhoLip_ATPase_C 148 ndlqlfgtlvftalvlvvnlkvaletktwtliliililgsillyflflllyssllpsssefygvleelfsspsfwl 223
                                           +    +++++ + +v +++ l +++++++++i++ ++ l++ ++++ + +          v+++++++p f++
  gene1768|gene1768|rna1768|rna1768 586 -YAYVTTYFSYVVFISTVIFQISL-IEFFNIYTFISMAMTTLIFGIVMFGIDE----------VDYTIYGNPLFYF 649
                                        .23344444444445555555555.99************98788888877766..........477899******* PP

                    PhoLip_ATPase_C 224 vlllvvvvallpdllik 240
                                        +ll v+ + +  dl++k
  gene1768|gene1768|rna1768|rna1768 650 TLLAVMSINVGSDLIYK 666
                                        *************9997 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.6   0.1     0.002       8.8       1      18 [.      98     115 ..      98     120 .. 0.87
   2 !   35.4   0.1     3e-12   1.3e-08     106     208 ..     302     426 ..     191     428 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.002
                                        SSEEEEESBTTTBCHHHH CS
                                        xxxxxxxxxxxxxxxxxx RF
                          Hydrolase   1 iktvvfDkdGTLttgeps 18 
                                        i+ ++ Dk+GTLt+ ++ 
  gene1768|gene1768|rna1768|rna1768  98 IDIILSDKTGTLTENKMN 115
                                        7899*********99875 PP

  == domain 2  score: 35.4 bits;  conditional E-value: 3e-12
                                        HHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHHTT....GGGE.SEEEEHHCES...... CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxx.xxxxxxxxxx...... RF
                          Hydrolase 106 ralavftiadplkvkpeaaeavasLkaagievvlltgdnpetaeraanqlG....ddyf.daviasdiet...... 170
                                        +  +v  i+d   +  +++++v+ Lk agi+++++tgd +eta ++ + +G      y  d ++++ +e       
  gene1768|gene1768|rna1768|rna1768 302 EFAGVAYIEDR--IGFKVKDTVEDLKGAGIKIWMVTGDKKETALSCGRSVGitsnTAYKpDEIVDQLNENtslpmd 375
                                        66777777788..888899********************************9987444446666666666455555 PP

                                        STTT...............SHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHHH CS
                                        xxxx...............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          Hydrolase 171 vakp...............spegkvaaireLqgkpeevamVGDgvnDaaalaa 208
                                           +                p+ k  +++eL  ++  v+++GDg nD++++ a
  gene1768|gene1768|rna1768|rna1768 376 R--AvwmdtlpdtliiyraIPDKKAMVAKELVKRGLTVLAIGDGNNDVSMINA 426
                                        0..1455555566666666************988999*************876 PP

>> Cation_ATPase  Cation transport ATPase (P-type)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.1   1.8e-09     8e-06      36      87 ..     186     244 ..     145     247 .. 0.81
   2 ?    0.9   0.0      0.11   5.1e+02      15      29 ..     330     344 ..     320     370 .. 0.89

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 1.8e-09
                      Cation_ATPase  36 gldteelreetkkvqeipFnssrKrmsvvlkle.......pekkvrlyvKGApeiilkr 87 
                                        ++++e++  + k +++++Fns+r rms++++++       ++++v l++KG+ +++ ++
  gene1768|gene1768|rna1768|rna1768 186 KIEIENAVYDVKVLAVLEFNSERQRMSTLVQISsrnercvKNNEVYLFTKGSDQRLSAH 244
                                        56666677779999**************************************9999876 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.11
                      Cation_ATPase  15 devkllGnktEsALl 29 
                                        + + ++G+k E+AL 
  gene1768|gene1768|rna1768|rna1768 330 KIWMVTGDKKETALS 344
                                        56889********95 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.21   9.2e+02      19      55 ..     316     352 ..     310     358 .. 0.80
   2 !   16.6   0.2   1.1e-06     0.005     196     227 ..     401     432 ..     352     437 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.21
                                        HHHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCCC CS
                        Hydrolase_3  19 ktkeaikklkekgikvviATGRslravlpvleelgld 55 
                                        k k++++ lk +gik+   TG + +++l+  +++g++
  gene1768|gene1768|rna1768|rna1768 316 KVKDTVEDLKGAGIKIWMVTGDKKETALSCGRSVGIT 352
                                        77999999*************8888887777766665 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 1.1e-06
                                        HHHCT--GGGEEEEESSGGGHHHHHHSSEEEE CS
                        Hydrolase_3 196 akelnisleeviafGDgeNDieMLeaaglgvA 227
                                        akel      v+a+GDg+ND++M++a+ +gv 
  gene1768|gene1768|rna1768|rna1768 401 AKELVKRGLTVLAIGDGNNDVSMINASTVGVG 432
                                        55666666689****************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (667 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1054  (0.0587874); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.68u 0.27s 00:00:00.95 Elapsed: 00:00:00.46
# Mc/sec: 4376.45
//
Query:       gene1769|gene1769|rna1769|rna1769  [L=233]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      5e-18   64.6   4.4    9.2e-18   63.7   4.4    1.4  1  PhoLip_ATPase_N  Phospholipid-translocating ATPase N-terminal
    0.00077   19.0   0.8     0.0025   17.3   0.0    2.0  2  E1-E2_ATPase     E1-E2 ATPase


Domain annotation for each model (and alignments):
>> PhoLip_ATPase_N  Phospholipid-translocating ATPase N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.7   4.4     1e-21   9.2e-18      16      66 ..       5      55 ..       2      56 .. 0.96

  Alignments for each domain:
  == domain 1  score: 63.7 bits;  conditional E-value: 1e-21
                    PhoLip_ATPase_N 16 sNkIsTsKYtlltFlpknLfeqFrrvaNlYFLviailqliPqisplspvtt 66
                                       +NkI TsKYtl++Flp+nL+ qF++++N++F+v+++l liP++sp+ p+ +
  gene1769|gene1769|rna1769|rna1769  5 ENKIVTSKYTLASFLPLNLYRQFSKYSNVFFFVTLMLLLIPAVSPFPPYAY 55
                                       7***********************************************976 PP

>> E1-E2_ATPase  E1-E2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.5      0.11     1e+03     114     135 ..      26      47 ..      19      69 .. 0.48
   2 !   17.3   0.0   2.8e-07    0.0025      20      66 ..     123     181 ..     115     197 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.11
                                        HHHHHHHHHHHHHHHHHHHHHH CS
                       E1-E2_ATPase 114 kldklgkvlvpvvlliallvfl 135
                                        + +k+++v+++v l+++l+ ++
  gene1769|gene1769|rna1769|rna1769  26 QFSKYSNVFFFVTLMLLLIPAV 47 
                                        4444445544444444443322 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 2.8e-07
                                        GGG--TTSEEEEETT-B--SEEEEEE............E-SEEE-TTTS---S-EE-G- CS
                       E1-E2_ATPase  20 akelvpGDivllkagdrvpaDgrive............gsaevdesaLTGEslpvekek 66 
                                        +++l++G +++l++++ vp D+++++            + + +++s+L GE    +k+ 
  gene1769|gene1769|rna1769|rna1769 123 VEDLRVGNVIILRENEEVPSDIVLLNakvfdgkhlkcrSFCFIQTSSLDGETNLKKKQS 181
                                        789***********************999999999975556999999999999888864 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (233 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       796  (0.0443973); expected 358.6 (0.02)
Passed bias filter:                      508  (0.028334); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 1647.61
//
Query:       gene177|gene177|rna177|rna177  [L=157]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0072   16.1   0.8       0.18   11.5   0.0    2.0  2  Use1           Membrane fusion protein Use1
  ------ inclusion threshold ------
      0.076   12.9   0.0        0.1   12.4   0.0    1.2  1  Abhydrolase_3  alpha/beta hydrolase fold


Domain annotation for each model (and alignments):
>> Use1  Membrane fusion protein Use1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    2.9   0.7    0.0084        76      30      77 ..       5      54 ..       3      77 .. 0.59
   2 !   11.5   0.0     2e-05      0.18     164     239 ..      79     151 ..      71     157 .] 0.72

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.0084
                           Use1 30 kyvkaleemleeLkkesskpskevlk..eYse.kveaLkllleaeklsste 77
                                   + +++l ++le+L+++++  +k+ lk  +Y++  +  L+++l+ + ++s +
  gene177|gene177|rna177|rna177  5 HTIASLLTSLEQLSAQHT-HTKDDLKrlKYTKiALSVLAKQLKGPLNTSLQ 54
                                   667888888888888887.55555552235554555555555555554333 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 2e-05
                           Use1 164 laeemlsLarnLKenslaasqiikkDtetlsksekaadqnlaslkkeserleehskskvkcllwlllfvvlvvFis 239
                                    + +em   a++L+ ++      + +D+e ++k +  +  n+++++++   +ee+ +  ++c  w++  +v++v + 
  gene177|gene177|rna177|rna177  79 VLDEMKRYAKKLRAKAVEFDGCLERDKEHVDKLQMGMTYNVNRTEENVRGAEER-T--MECGGWFVGSFVVFVVVY 151
                                    469****************************************98766666654.3..444444444333332222 PP

>> Abhydrolase_3  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   1.1e-05       0.1     147     201 ..      42     101 ..       7     108 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.1e-05
                                    GGGGGSTTTSGGGC..S-...SST---EEEEEETT-TTHHHHHHHHHHHHHTT--EEEEE CS
                  Abhydrolase_3 147 eadrddplasplla..ed...lsglpptlvvvaefDplrdegeayaerlraagvevelie 201
                                     ++++ pl   l++  ++   l     t v+  ++D+  de ++ya++lra+ ve +   
  gene177|gene177|rna177|rna177  42 AKQLKGPLNTSLQShlQKyvnLPANTHTSVIKLKNDLVLDEMKRYAKKLRAKAVEFDGCL 101
                                    44444444333333211222255555699**********************999976555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1214  (0.0677115); expected 358.6 (0.02)
Passed bias filter:                      692  (0.0385967); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 1197.90
//
Query:       gene1770|gene1770|rna1770|rna1770  [L=445]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.3e-17   61.4   0.3    8.3e-17   61.4   0.3    1.9  2  RhoGAP    RhoGAP domain


Domain annotation for each model (and alignments):
>> RhoGAP  RhoGAP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.1      0.29   5.2e+03      58      86 ..     128     156 ..     101     172 .. 0.60
   2 !   61.4   0.3   4.7e-21   8.3e-17       4     145 ..     267     405 ..     264     409 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 0.29
                                        HHHHHHHHHSSSTTTTGGHHHHHHHHHTS CS
                             RhoGAP  58 slLKrfLrelpepLltkelyeelieaaks 86 
                                        +l K++ ++l e L+  el  + ++  k 
  gene1770|gene1770|rna1770|rna1770 128 KLSKLYEKNLNEMLIFSELKTTNVQHIKL 156
                                        45566777777777766666665554444 PP

  == domain 2  score: 61.4 bits;  conditional E-value: 4.7e-21
                                        HHHHHHHHHHHTTTSTTTTTS-S-HHHHHHHHHHHHHTGGGCTTTTTSCHHHHHHHHHHHHHHSSSTTTTGGHHHH CS
                             RhoGAP   4 vekcvefiekrgldtegiyRvsgskarvkelreafdkgkavdsdleeedvhavaslLKrfLrelpepLltkelyee 79 
                                        + +++++++ +g ++ gi+R+sg  ++v+++ +++++g++v  +l+ + v ++ slLK + r+  + + t++  + 
  gene1770|gene1770|rna1770|rna1770 267 IFSLINHLKMHGQREIGIFRLSGRLTNVQMVLNKIKAGQDV--NLSTYPVRDIVSLLKIYVRNNLDGICTRNVTKI 340
                                        6689*************************************..8******************************** PP

                                        HHHHHTSSSHHHHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHHHTHHHH---HHHHHHHHHHHHHT CS
                             RhoGAP  80 lieaaksedeeerlealkellekLPkenrdtLryLlehLkrvaenskenkMtaknLaivfaPtLlr 145
                                        l+++ +  + ++  ++lk l   +    r+++ +L+e++ ++++++  nkM+ + L  + aPt+++
  gene1770|gene1770|rna1770|rna1770 341 LLNIFQR-NTDTINKSLKYLPFIFYGDRRKLIISLFELFDEISSCEFHNKMSRQMLIRCTAPTFFS 405
                                        **76554.6666669************************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (445 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1132  (0.0631379); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 3071.37
//
Query:       gene1771|gene1771|rna1771|rna1771  [L=193]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.5e-12   46.5   0.1    4.2e-12   46.2   0.1    1.1  1  Bac_surface_Ag  Surface antigen


Domain annotation for each model (and alignments):
>> Bac_surface_Ag  Surface antigen
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.2   0.1   2.3e-16   4.2e-12     146     320 ..      21     188 ..       2     192 .. 0.79

  Alignments for each domain:
  == domain 1  score: 46.2 bits;  conditional E-value: 2.3e-16
                                        .TTSSS-EEEEEEEEEEEEESSTTSSSEEEEEEEEEEEEESSSS-.--GGG-B-BSSTTSSTEE-TT-BS-EEEEE CS
                     Bac_surface_Ag 146 llggdvsylkldakasyyvpltkekdlvlaarvalgyisgygtkdelpfyerFyaGGsnsvRGfesgglgprdesg 221
                                          ++++ ++kl++ ++  v l    ++   +r+ +g+i+g      ++ +e+F++G    vRG+   ++ p d  +
  gene1771|gene1771|rna1771|rna1771  21 GCFENSLFYKLTVLYKSMVMLP--FNFFHKLRMHAGVIHG----H-VHSSEKFFLGDH--VRGYVPMSISPLDM-N 86 
                                        4899999********9999998..3455677888888776....4.7788******99..***********887.* PP

                                        EE--BSEEEEEEEEEEEE-SSS-GGTTEEEEEEEEEEEEE-TT--TTTTTTS--TT..........TS-EEEEEEE CS
                     Bac_surface_Ag 222 dalGGdsyavaslElrfplpflkkqnsvrlalFfDaGnvwdkegqspsssrsasst..........aeirasvGvg 287
                                        + lGG+s ++ s  l +++      +s++l +F D+G+     +++++ +++++s+          + +++s+G+g
  gene1771|gene1771|rna1771|rna1771  87 EYLGGKSCIELSNALGYRF------RSMKLFVFNDFGFN----SRQNNLFETVKSSmlglllvhkpSCLGWSTGIG 152
                                        ******************9......47***********6....33333344445555888**************** PP

                                        EEEEE.....TTEEEEEEEEEEEE-STT--EESEEEEE CS
                     Bac_surface_Ag 288 Lrwqs.....PlGPlrfdyAiplkkedgdktqrFqFgi 320
                                        L++ +         + ++yAipl+++++  +q F+F i
  gene1771|gene1771|rna1771|rna1771 153 LTVGLhkykdITTNITMSYAIPLTEPQS--KQSFKFEI 188
                                        *987622221478999**********99..66676665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (193 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       351  (0.0195772); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 1288.73
//
Query:       gene1772|gene1772|rna1772|rna1772  [L=127]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       553  (0.0308439); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 941.78
//
Query:       gene1773|gene1773|rna1773|rna1773  [L=251]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.9e-44  149.4   0.2    1.1e-43  149.0   0.2    1.1  1  Proteasome    Proteasome subunit
  ------ inclusion threshold ------
      0.065   13.6   2.8        0.5   10.8   0.3    2.8  2  CW_binding_1  Putative cell wall binding repeat


Domain annotation for each model (and alignments):
>> Proteasome  Proteasome subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  149.0   0.2   1.2e-47   1.1e-43       3     188 ..      49     225 ..      48     227 .. 0.95

  Alignments for each domain:
  == domain 1  score: 149.0 bits;  conditional E-value: 1.2e-47
                                        HS-EEEEEEETTEEEEEEEEEEEETTEEEESSSSTSEEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHSSG CS
                         Proteasome   3 kGttvvGikgkdgvvlaadkratagskllskstveKifkiddhigvafaGlaaDartlvrraraeaqlyrlrygrp 78 
                                        kGtt++++ +k+g+++a+d+rat+gs++ +++tv+K+++++++++ ++aG aaD+ ++ +r+ a a+ly++++g++
  gene1773|gene1773|rna1773|rna1773  49 KGTTTLAFIFKEGIAIAVDSRATSGSYI-ASRTVHKVIRVNNYLLTTMAGGAADCLYWEKRMGAFAKLYEVTNGKR 123
                                        7***************************.6667******************************************* PP

                                        TCHHHHHHHHHHHHHHHHHHCTTTTTSEEEEEEEEETTTEEEEEEEETTSEEEEESSEEEESTTHHHHHHHHHHHH CS
                         Proteasome  79 ipverlvarvaaklqaytqrsgrrpfgvslliagvdeeggpeLyqidpsGsyieekdavaiGsgseaaktalekey 154
                                        +pv     +++++l + +  +  r + ++++++g+d++g p +y++d +G++++   ++++Gsgs+ a+++l+++y
  gene1773|gene1773|rna1773|rna1773 124 LPVP----AAVNYLRNCIVGR--RGLSIGTMVCGWDDKG-PNIYYLDNDGTMVKG-TVFSVGSGSTIAYGLLNSNY 191
                                        ****....7777777777765..99***********887.***************.5******************* PP

                                        STTBSHHHHHHHHHHHHHHHHHHBTTSCSSEEEE CS
                         Proteasome 155 kedltleeavelavkalkealerdklsgknieva 188
                                        + d++++e+++la+ a+  a++rd++sg+ ++++
  gene1773|gene1773|rna1773|rna1773 192 RYDMSRDEGLKLARDAIFYATYRDAYSGGFVNLY 225
                                        ****************************999987 PP

>> CW_binding_1  Putative cell wall binding repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.3   5.6e-05       0.5       9      19 .]     158     168 ..     154     168 .. 0.89
   2 ?    2.0   0.2     0.034   3.1e+02      11      17 ..     225     231 ..     223     237 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 5.6e-05
                                        EEEEETTTSEB CS
                       CW_binding_1   9 nWYYfdsdGkM 19 
                                        n YY+d+dG M
  gene1773|gene1773|rna1773|rna1773 158 NIYYLDNDGTM 168
                                        56*******99 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.034
                                        EEETTTS CS
                       CW_binding_1  11 YYfdsdG 17 
                                        Y++d++G
  gene1773|gene1773|rna1773|rna1773 225 YFMDNNG 231
                                        6667777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       418  (0.0233142); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1805.70
//
Query:       gene1774|gene1774|rna1774|rna1774  [L=236]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      3e-13   49.8   3.5      6e-11   42.3   1.4    2.2  2  RVT_1     Reverse transcriptase (RNA-dependent DNA polymerase
  ------ inclusion threshold ------
       0.14   12.3   0.9       0.39   10.9   0.1    2.0  2  DUF2703   Domain of unknown function (DUF2703)
       0.23    9.9   3.8       0.11   10.9   0.5    1.8  2  GerA      Bacillus/Clostridium GerA spore germination protein
       0.93    9.5   7.2        1.2    9.1   7.2    1.1  1  RAMPs     RAMP superfamily


Domain annotation for each model (and alignments):
>> RVT_1  Reverse transcriptase (RNA-dependent DNA polymerase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.5   0.0   0.00058       2.6      54      91 ..      70     107 ..      41     119 .. 0.82
   2 !   42.3   1.4   1.3e-14     6e-11     140     221 ..     131     203 ..     127     204 .. 0.95

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.00058
                                        ........HCCHTS--EEEEEEBCCGCCCSBB-GGGGG CS
                              RVT_1  54 avedllkalkkkkkaklllklDlkkaFdsvpleellrk 91 
                                        ++ ++ ++ +k + a +++ lD+k  F++++ +e ++k
  gene1774|gene1774|rna1774|rna1774  70 KISEIEEIFNKLHDAGYVTVLDMKERFFQIKIRERDKK 107
                                        337788889999********************999876 PP

  == domain 2  score: 42.3 bits;  conditional E-value: 1.3e-14
                                        HHHHHHHHHHHHTT-T......TEEECTTEEEEEESSHHHHHHHHHHHHHHHHHTT--BEGGG-EEE.....ESSE CS
                              RVT_1 140 PllfnlfmnellrelrkrakgvtllrYaDDililskskeelqelleaveewlkesglkinpeKtklvlftvkseev 215
                                         ++f+ +mn+ lr +       +   Y DD++i++k+ ee++++  ++ +++k+++lkin eK++l      ++e+
  gene1774|gene1774|rna1774|rna1774 131 SFIFQQIMNHELRGWTD----KNAQFYLDDVVIYAKTVEEHDKIFLKILDKFKKVKLKINLEKIQLK-----KKEI 197
                                        579*************9....5*********************************************.....9*** PP

                                        EETTEE CS
                              RVT_1 216 kyLGvt 221
                                        +++G +
  gene1774|gene1774|rna1774|rna1774 198 NFMGQI 203
                                        ****86 PP

>> DUF2703  Domain of unknown function (DUF2703)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.1      0.35   1.6e+03      31      56 ..      91     116 ..      59     137 .. 0.60
   2 ?   10.9   0.1   8.6e-05      0.39      20      70 ..     162     214 ..     158     234 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.35
                            DUF2703  31 elkeaLealgievelekvelseeela 56 
                                        ++ke++ ++ i+ + +k  +s+ e++
  gene1774|gene1774|rna1774|rna1774  91 DMKERFFQIKIRERDKKNSISKSEVR 116
                                        34444444444444445555555555 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 8.6e-05
                            DUF2703  20 eTgktleeavkelkeaLealgievelekvelseeelare..flesntilingr 70 
                                        +T ++ +++  ++ ++++++ ++++lek++l+++e++     ++ +ti++ + 
  gene1774|gene1774|rna1774|rna1774 162 KTVEEHDKIFLKILDKFKKVKLKINLEKIQLKKKEINFMgqIVNGKTIRMLES 214
                                        6888889999999**********************997666888888887654 PP

>> GerA  Bacillus/Clostridium GerA spore germination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.5   2.5e-05      0.11      30     123 ..       2     114 ..       1     120 [. 0.83
   2 ?    0.1   0.2     0.049   2.2e+02      62     102 ..     170     214 ..     130     229 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 2.5e-05
                               GerA  30 vyidglvdkelieesilkpllelkeeeeeeeee....................lellellekllpvaevkevedle 85 
                                        v+ +  ++k  ++++i k+l+e+k+++  ++++                    l+l  ++ k ++++e ++++++e
  gene1774|gene1774|rna1774|rna1774   2 VCAKPYTNKGSLKDKIEKELEEMKNKDYLRDSKsrwknpvkpilkkdgrirlcLNL--MTLKEITNNEEEKISEIE 75 
                                        5667788999999*******9999988777777899999*******9999854333..447889999********* PP

                               GerA  86 evveailsGktvllvdgldkallidtkgyekR.sveepe 123
                                        e+++++ +   v ++d  ++++ i++++ +k+ s++++e
  gene1774|gene1774|rna1774|rna1774  76 EIFNKLHDAGYVTVLDMKERFFQIKIRERDKKnSISKSE 114
                                        **************************9987651566555 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.049
                               GerA  62 e....lellellekllpvaevkevedleevveailsGktvllvdg 102
                                             l+  + ++ +++ ++++  ++  +++ +i++Gkt+ ++++
  gene1774|gene1774|rna1774|rna1774 170 IflkiLDKFKKVKLKINLEKIQLKKKEINFMGQIVNGKTIRMLES 214
                                        133333333445666666677777777777777777777776664 PP

>> RAMPs  RAMP superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   7.2   0.00027       1.2      40     153 ..      10     199 ..      10     230 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00027
                                        HHHHHHHHHHHHH.HHHTT-HHHHH.H....................................HHHHHH--S...S CS
                              RAMPs  40 kGalRsalekllgsekkekkdeysrkkekqrvkkgd...........................leeaiFGneeesk 88 
                                        kG+l+  +ek+l++ k+++  ++s+   k++vk ++                            +e+iF +     
  gene1774|gene1774|rna1774|rna1774  10 KGSLKDKIEKELEEMKNKDYLRDSKSRWKNPVKPILkkdgrirlclnlmtlkeitnneeekisEIEEIFNKL---H 82 
                                        9************************99******999************************************...* PP

                                        S--SEEEEE................................................................... CS
                              RAMPs  89 iagrvffeDarpvkipgqileeskqikstpsp............................................ 120
                                         ag v++ D +   ++ +i+e+ k++ +++s                                             
  gene1774|gene1774|rna1774|rna1774  83 DAGYVTVLDMKERFFQIKIRERDKKNSISKSEvrntnsiecrwdlknfsfifqqimnhelrgwtdknaqfylddvv 158
                                        ***********999999999999999999999*9999999999999999999999999999999999999999999 PP

                                        ......EEEEEEEEEEEEEEEEE--SSS-EEEEEE.....- CS
                              RAMPs 121 ......klsgselrelldhsterrtrvaidrktktngk..k 153
                                              +  ++++  +ld++++++ ++ +++ + ++++  +
  gene1774|gene1774|rna1774|rna1774 159 iyaktvEEHDKIFLKILDKFKKVKLKINLEKIQLKKKEinF 199
                                        99998888888888888888888888888887777766542 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1487  (0.0829383); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1668.47
//
Query:       gene1775|gene1775|rna1775|rna1775  [L=52]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (52 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       249  (0.0138881); expected 358.6 (0.02)
Passed bias filter:                      184  (0.0102627); expected 358.6 (0.02)
Passed Vit filter:                         7  (0.000390429); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.42
# Mc/sec: 369.38
//
Query:       gene1776|gene1776|rna1776|rna1776  [L=384]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.012   15.5   0.0      0.022   14.7   0.0    1.4  1  TMEM154        TMEM154 protein family
       0.15   12.6   0.0       0.39   11.3   0.0    1.7  1  DUF3899        Domain of unknown function (DUF3899)


Domain annotation for each model (and alignments):
>> TMEM154  TMEM154 protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   2.5e-06     0.022       8      83 ..     307     383 ..     303     384 .] 0.78

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.5e-06
                            TMEM154   8 gdtaletatleeesadatsaasteseslkqeeakeslssaelsne..sdqlelvlmiiiPlvllillllvviiliq 81 
                                        + +a +++++  +  +a+      +e+ k+ee+k   +s+++++   + + + + ++ i l +l+++ ++v+i+i 
  gene1776|gene1776|rna1776|rna1776 307 TASAAPKDGAAGKKKEASKSEEK-KEASKSEEKKGDGKSGDTEEGwfKKNRKPLFIVGIGLLALVVIAIIVVIVIR 381
                                        66788888888888888766666.77888888888889999988633455556999*******************6 PP

                            TMEM154  82 kk 83 
                                        +k
  gene1776|gene1776|rna1776|rna1776 382 MK 383
                                        65 PP

>> DUF3899  Domain of unknown function (DUF3899)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   4.3e-05      0.39      43      83 ..     326     374 ..     308     375 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 4.3e-05
                            DUF3899  43 k.skkddsyyeykek.......kkes..skkstrplliiGlllivlsivll 83 
                                        + +kk++s+ e+k+        +  +  +kk  +pl+i+G+ l++l ++ +
  gene1776|gene1776|rna1776|rna1776 326 SeEKKEASKSEEKKGdgksgdtE--EgwFKKNRKPLFIVGIGLLALVVIAI 374
                                        12333333333333355444333..266*****************998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (384 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1339  (0.0746835); expected 358.6 (0.02)
Passed bias filter:                      884  (0.0493056); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.63u 0.28s 00:00:00.91 Elapsed: 00:00:00.45
# Mc/sec: 2557.93
//
Query:       gene1777|gene1777|rna1777|rna1777  [L=204]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00032   19.5   0.1     0.0017   17.1   0.0    1.9  2  Nup160    Nucleoporin Nup120/160
     0.0022   16.6   0.1     0.0027   16.3   0.1    1.1  1  Rrn6      RNA polymerase I-specific transcription-initiation 


Domain annotation for each model (and alignments):
>> Nup160  Nucleoporin Nup120/160
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   1.8e-07    0.0017     229     274 ..       7      56 ..       1      68 [. 0.79
   2 ?    0.4   0.0     0.021   1.9e+02      83     153 ..     124     195 ..      97     200 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.8e-07
                                        TTTEEEEEETT-EEEEEETTTTEEEEEEE--.....-SSSTTS--SSEES CS
                             Nup160 229 gqtylfalsrdgkLrvWnlltgkclatidll....rdeeaqdessskstl 274
                                         + +l+++s d+kL+vWnl++ +c+   +l+    +  +++d+ ++ st 
  gene1777|gene1777|rna1777|rna1777   7 RNPFLYSISFDRKLKVWNLKDERCVFKVTLDvvplKIYIETDDFDCSSTA 56 
                                        5779*********************9999987777666666666666554 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.021
                                        S-SESSSESEEEEESSSEEEEEEEESSS-EEEEEEE.HHHHHSTT----S..TSBEEB-SSGT.TTS-EEEE CS
                             Nup160  83 ssllpscvsftdsesgdvlivivtttsvhlyvlrls.sdffrsskailndldewckidspsslstsskpgrl 153
                                        + l+++ + f + +s  + +v+ + +++++y +  s ++++   k++++  de+c  d  s + t+s  g+l
  gene1777|gene1777|rna1777|rna1777 124 KGLSVFDCKFEELKSILIGFVLDIQSNAQFYFVLASsRKLYILEKTSFEICDEYCDVDCFSIFGTNSIWGML 195
                                        556667777777777445567778888888877777799999999999999999999888888666666655 PP

>> Rrn6  RNA polymerase I-specific transcription-initiation factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.1     3e-07    0.0027     195     284 ..      83     161 ..      68     172 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 3e-07
                               Rrn6 195 lrksgsifdpeledlsseteldgwkrIlWvsdvntLlVcnrrklvlvdikgnsqeelvlaltlsrssewILDvkrs 270
                                          k+ +i d   +++ ++t  ++ k I W+ ++n++++ + + l+++d k ++  + +++++        LD++  
  gene1777|gene1777|rna1777|rna1777  83 HTKKQRIGDTYGSHKRKKTQMSNHKEICWSKNINRIIIGTSKGLSVFDCKFEE--LKSILIGFV------LDIQS- 149
                                        5667778778878888888*******************************999..999999977......99999. PP

                               Rrn6 271 pvnpshvfvLTste 284
                                          n ++ fvL s++
  gene1777|gene1777|rna1777|rna1777 150 --NAQFYFVLASSR 161
                                        ..889999998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       806  (0.0449551); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1547.72
//
Query:       gene1778|gene1778|rna1778|rna1778  [L=89]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       599  (0.0334096); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.29s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 589.81
//
Query:       gene1779|gene1779|rna1779|rna1779  [L=101]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      4e-12   46.2   6.7    4.8e-12   46.0   6.7    1.1  1  Sof1      Sof1-like domain
     0.0099   16.7   0.0      0.021   15.7   0.0    1.6  1  WD40      WD domain, G-beta repeat


Domain annotation for each model (and alignments):
>> Sof1  Sof1-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.0   6.7   5.4e-16   4.8e-12       4      70 ..      32      97 ..      30     101 .] 0.89

  Alignments for each domain:
  == domain 1  score: 46.0 bits;  conditional E-value: 5.4e-16
                               Sof1  4 seklgvlsaReraaleyreaLkekykhmpeikrIarhRhvPkaikkakkekremkeaekrKeenrrk 70
                                       sek   +s Re++ale ++ Lk+ky h+ +++rI +hR +Pk +k   + + e ++a +rK+++  +
  gene1779|gene1779|rna1779|rna1779 32 SEKE-NMSRREENALECNQMLKDKYYHVGDVRRIDKHRFLPKELKGRIRNEIEHHKAVERKKNRALT 97
                                       5554.5799*****************************************9999***9999987654 PP

>> WD40  WD domain, G-beta repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   2.3e-06     0.021      22      37 ..      12      27 ..       3      28 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.3e-06
                                       SSEEEEEETTSEEEEE CS
                               WD40 22 gawlasGsdDgtvriW 37
                                       +++++sGs+Dg+vr+W
  gene1779|gene1779|rna1779|rna1779 12 KRFILSGSEDGNVRLW 27
                                       35689*********** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       779  (0.0434492); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.43
# Mc/sec: 708.91
//
Query:       gene178|gene178|rna178|rna178  [L=48]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (48 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1068  (0.0595683); expected 358.6 (0.02)
Passed bias filter:                      656  (0.0365888); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.31s 00:00:00.71 Elapsed: 00:00:00.46
# Mc/sec: 313.26
//
Query:       gene1780|gene1780|rna1780|rna1780  [L=42]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (42 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       267  (0.0148921); expected 358.6 (0.02)
Passed bias filter:                      180  (0.0100396); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.24s 00:00:00.58 Elapsed: 00:00:00.39
# Mc/sec: 325.20
//
Query:       gene1781|gene1781|rna1781|rna1781  [L=36]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (36 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       225  (0.0125495); expected 358.6 (0.02)
Passed bias filter:                      139  (0.0077528); expected 358.6 (0.02)
Passed Vit filter:                         7  (0.000390429); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.27u 0.22s 00:00:00.49 Elapsed: 00:00:00.34
# Mc/sec: 313.67
//
Query:       gene1782|gene1782|rna1782|rna1782  [L=48]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (48 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       672  (0.0374812); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 358.48
//
Query:       gene1783|gene1783|rna1783|rna1783  [L=58]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (58 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       533  (0.0297284); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.26s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 435.50
//
Query:       gene1784|gene1784|rna1784|rna1784  [L=477]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.096   12.5   0.0       0.23   11.3   0.0    1.6  1  Transposase_1  Transposase (partial DDE domain)


Domain annotation for each model (and alignments):
>> Transposase_1  Transposase (partial DDE domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   1.3e-05      0.23      27      64 ..     256     292 ..     250     299 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 1.3e-05
                      Transposase_1  27 hekkvmltVwWsakgviyyeflppgetitsevYaqqle 64 
                                           ++ l ++++   vi y++l++++ti  +++++ l 
  gene1784|gene1784|rna1784|rna1784 256 DPGNFSLAFFFDRL-VITYQWLEKNQTILDTKFKESLG 292
                                        55667788899999.***************99999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (477 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       722  (0.04027); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 3394.32
//
Query:       gene1785|gene1785|rna1785|rna1785  [L=472]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (472 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       675  (0.0376485); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 2956.88
//
Query:       gene1786|gene1786|rna1786|rna1786  [L=96]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      4e-08   32.9   0.8    1.7e-07   30.9   0.8    1.7  1  vATP-synt_E  ATP synthase (E/31 kDa) subunit


Domain annotation for each model (and alignments):
>> vATP-synt_E  ATP synthase (E/31 kDa) subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.9   0.8   9.3e-12   1.7e-07     135     199 .]      19      92 ..       8      92 .. 0.73

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 9.3e-12
                                        CCCHHCCSSSS--SEEEEESSEB.........TTSSSEEEECCSSSCEEECCCHHHCHHHHHHHHHHCCCCCHC CS
                        vATP-synt_E 135 aeeykaktkkktvevagdeedfl.........edvlGGvvleaadgkikvnnTlearLelvleqllpeirkaLF 199
                                        +e +  + + +++ +a d++++           d lGG+++ ++dg + v+n+   rLe v+ q +p ++k+LF
  gene1786|gene1786|rna1786|rna1786  19 MEVVRDEKDVVVYVLARDRNRVNvrgeireleSDRLGGIIVMSKDGTVLVDNSYLTRLEKVRIQHMPTVSKELF 92 
                                        4444444444444444444444444555555599***************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       635  (0.0354175); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 696.47
//
Query:       gene1787|gene1787|rna1787|rna1787  [L=162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    0.00038   20.2   0.2      0.017   15.0   0.1    2.6  2  EF-hand_6  EF-hand domain
  ------ inclusion threshold ------
      0.016   15.6   0.3        0.5   10.9   0.0    2.3  2  EF-hand_7  EF-hand domain pair
      0.056   13.8   0.0       0.12   12.8   0.0    1.5  1  NuiA       Nuclease A inhibitor-like protein


Domain annotation for each model (and alignments):
>> EF-hand_6  EF-hand domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.1   2.9e-06     0.017       2      27 ..      26      51 ..      25      63 .. 0.92
   2 ?    2.5   0.0      0.03   1.8e+02      13      27 ..     100     115 ..      94     121 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.9e-06
                          EF-hand_6  2 lreaFklfDkdgdGkidaeElrkalr 27
                                       l+e+F+++D+  d kida++l ++l 
  gene1787|gene1787|rna1787|rna1787 26 LKEVFNMIDNPPDDKIDAADLNNFLP 51
                                       89********************9995 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.03
                          EF-hand_6  13 gdG.kidaeElrkalr 27 
                                        +d+ +++++El++ lr
  gene1787|gene1787|rna1787|rna1787 100 DDNvTVNKSELMNYLR 115
                                        444499********99 PP

>> EF-hand_7  EF-hand domain pair
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   8.3e-05       0.5       3      31 ..      25      53 ..      23      95 .. 0.80
   2 ?    3.0   0.0     0.024   1.4e+02      14      51 ..     100     129 ..      99     147 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 8.3e-05
                          EF-hand_7  3 klkeaFkelDtdgdgyldkeellrllrki 31
                                        lke+F+++D+  d ++d ++l ++l  i
  gene1787|gene1787|rna1787|rna1787 25 SLKEVFNMIDNPPDDKIDAADLNNFLPTI 53
                                       6899*****************99976544 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.024
                          EF-hand_7  14 dgdgyldkeellrllrkifqgagegsklsdeelellfk 51 
                                        d++  ++k+el+++lr      +e+ + +d  le++f 
  gene1787|gene1787|rna1787|rna1787 100 DDNVTVNKSELMNYLR------CEQLNGTD--LEYVFG 129
                                        66778999********......66666666..666665 PP

>> NuiA  Nuclease A inhibitor-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0     2e-05      0.12      23      94 ..      11      82 ..       9      87 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2e-05
                                       --EEEEESS-SSSSSTTHHHHHHT-TTTSSCEEE-HHHHTTCTT--SSTS-HHHHHHHHHHHHHHHHHTTHS CS
                               NuiA 23 pfeviswevdakeltkekllketghpadtpvesveldeflrnalteeewyeeeekeeaqrfqtlvklLksnL 94
                                       p +v+s+ ++++  + +++ + + +p+d ++  ++l++fl  ++++ + +e e+ e+   f +l++++ +++
  gene1787|gene1787|rna1787|rna1787 11 PSNVFSMLTQTQISSLKEVFNMIDNPPDDKIDAADLNNFLPTIVNQDQLHEFENLEKDIGFYALLAAISDKF 82
                                       667888888888899999999999***************************999999999999988887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       654  (0.0364772); expected 358.6 (0.02)
Passed bias filter:                      468  (0.026103); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1225.36
//
Query:       gene1788|gene1788|rna1788|rna1788  [L=43]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (43 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       231  (0.0128842); expected 358.6 (0.02)
Passed bias filter:                      176  (0.0098165); expected 358.6 (0.02)
Passed Vit filter:                         6  (0.000334653); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.31u 0.25s 00:00:00.56 Elapsed: 00:00:00.37
# Mc/sec: 344.77
//
Query:       gene1789|gene1789|rna1789|rna1789  [L=73]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.017   15.3   0.9      0.018   15.2   0.9    1.0  1  TMF_TATA_bd  TATA element modulatory factor 1 TATA binding
      0.032   14.4   0.7      0.033   14.4   0.7    1.0  1  Med30        Mediator complex subunit 30
      0.062   13.3   0.4      0.062   13.3   0.4    1.5  2  Holin_BhlA   BhlA holin family
      0.063   13.2   0.9      0.071   13.0   0.9    1.0  1  Sec34        Sec34-like family
      0.068   13.3   4.7        3.3    7.9   0.2    2.0  2  DUF148       Domain of unknown function DUF148
      0.069   13.5   4.1       0.18   12.2   3.6    2.0  1  FlaC_arch    Flagella accessory protein C (FlaC)
       0.18   12.1   1.8        0.2   11.9   1.8    1.0  1  zf-C4H2      Zinc finger-containing protein


Domain annotation for each model (and alignments):
>> TMF_TATA_bd  TATA element modulatory factor 1 TATA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.9   7.2e-06     0.018      35      98 ..       3      66 ..       1      69 [. 0.94

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 7.2e-06
                        TMF_TATA_bd 35 lerleaerdeareeivklmkeneelkelkkeleelekeleelqeryetlLellGeksEeveELr 98
                                       + ++++  +++++ + +l++  e+ ke  + ++e+++ +e+l++ +e l  ++   s+e++E +
  gene1789|gene1789|rna1789|rna1789  3 NDQFNEIEQNLQNVLSSLIEAFETIKEPYGGINEIKNAVESLKKVQEGLISVYENNSDENKEIK 66
                                       567889999*****************************************************98 PP

>> Med30  Mediator complex subunit 30
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.7   1.3e-05     0.033      42     106 ..       5      71 ..       1      73 [] 0.84

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.3e-05
                              Med30  42 qaqdrkkklqeqlrqlkvlfkkLrliYekckencqgleevp..iesLipyvdeekskreerkkseev 106
                                        q ++ +++lq+ l  l + f++++  Y  ++e  +++e+++   e Li + ++++ +++e k+++++
  gene1789|gene1789|rna1789|rna1789   5 QFNEIEQNLQNVLSSLIEAFETIKEPYGGINEIKNAVESLKkvQEGLISVYENNSDENKEIKTKDNY 71 
                                        556778999******************9999999999977776799***999998888888877766 PP

>> Holin_BhlA  BhlA holin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.4   2.4e-05     0.062      36      69 ..       5      45 ..       2      48 .. 0.77
   2 ?   -2.9   0.1       2.7     7e+03      31      34 ..      61      64 ..      52      71 .. 0.49

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.4e-05
                         Holin_BhlA 36 kqeerekkyqeiikkltekfeiv.......eeikkdvdeik 69
                                       + +e e+++q++++ l e fe++       +eik+ v+ +k
  gene1789|gene1789|rna1789|rna1789  5 QFNEIEQNLQNVLSSLIEAFETIkepyggiNEIKNAVESLK 45
                                       55788******************666666666666666655 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 2.7
                         Holin_BhlA 31 ekre 34
                                       e++e
  gene1789|gene1789|rna1789|rna1789 61 ENKE 64
                                       3333 PP

>> Sec34  Sec34-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.9   2.8e-05     0.071       3      70 ..       4      71 ..       3      73 .] 0.93

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.8e-05
                              Sec34  3 dqLeskeeecdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaeeieekLky 70
                                       dq+++ e++++++l+++ ea e+++e     +++++  +sl++  e l++  ++ ++ ++ei++k +y
  gene1789|gene1789|rna1789|rna1789  4 DQFNEIEQNLQNVLSSLIEAFETIKEPYGGINEIKNAVESLKKVQEGLISVYENNSDENKEIKTKDNY 71
                                       68899999******************************************************998655 PP

>> DUF148  Domain of unknown function DUF148
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.2    0.0013       3.3      46      70 ..       4      28 ..       2      29 .. 0.89
   2 ?    7.4   0.8    0.0018       4.5      54      85 ..      36      67 ..      34      71 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0013
                             DUF148 46 aqkeevkknvtavisnLssvqekle 70
                                       +q +e+++n ++v+s+L +++e ++
  gene1789|gene1789|rna1789|rna1789  4 DQFNEIEQNLQNVLSSLIEAFETIK 28
                                       6889****************99886 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0018
                             DUF148 54 nvtavisnLssvqekleaIldnkslTrkeqke 85
                                       ++++++++L++vqe l ++++n s  +ke k+
  gene1789|gene1789|rna1789|rna1789 36 EIKNAVESLKKVQEGLISVYENNSDENKEIKT 67
                                       67899******************999998876 PP

>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   3.6   7.1e-05      0.18       3      46 ..       7      57 ..       5      63 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 7.1e-05
                          FlaC_arch  3 delEnklsklst....eletvkk...eneelsksveelkenVkdllsLYEv 46
                                       +e+E+ l+++ +     +et+k+    ++e+++ ve lk+  + l+s+YE 
  gene1789|gene1789|rna1789|rna1789  7 NEIEQNLQNVLSslieAFETIKEpygGINEIKNAVESLKKVQEGLISVYEN 57
                                       789999998766567766667653336899********9999*******96 PP

>> zf-C4H2  Zinc finger-containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   1.8   7.8e-05       0.2      60     121 ..       5      67 ..       2      73 .] 0.89

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 7.8e-05
                            zf-C4H2  60 DinalEsvikeaeeekekslekakklyeeykklkeevnelrse.lglekledleeeeeellke 121
                                          n++E+ +++  ++  +++e++k+ y  ++++k+ v++l++   gl ++ +++++e++ +k+
  gene1789|gene1789|rna1789|rna1789   5 QFNEIEQNLQNVLSSLIEAFETIKEPYGGINEIKNAVESLKKVqEGLISVYENNSDENKEIKT 67 
                                        57999**********************************999889***999999999988875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (73 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1462  (0.0815439); expected 358.6 (0.02)
Passed bias filter:                      619  (0.0345251); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 528.49
//
Query:       gene179|gene179|rna179|rna179  [L=96]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
     0.0094   15.9   0.5       0.01   15.7   0.5    1.1  1  GP41        Retroviral envelope protein
  ------ inclusion threshold ------
      0.019   13.0   0.3       0.02   12.9   0.3    1.0  1  Prominin    Prominin
      0.058   13.4   0.1       0.11   12.6   0.1    1.5  1  SNARE       SNARE domain
      0.077   13.0   0.1      0.099   12.6   0.1    1.2  1  SYCP2_ARLD  Synaptonemal complex 2 armadillo-repeat-like doma
       0.33   11.4   2.6       0.22   11.9   0.8    1.8  2  FlaC_arch   Flagella accessory protein C (FlaC)


Domain annotation for each model (and alignments):
>> GP41  Retroviral envelope protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.5   2.9e-06      0.01     103     173 ..      17      93 ..       4      96 .] 0.65

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.9e-06
                                    HHHHHHHHHHHHHHH...HHHHHHHHHHHH.HHHHH.HHHHHHHHHH..HHHH.....HHHHHCHHHHHHHHHHHXXXXX CS
                           GP41 103 sydlaelhnliediq...nqqektldeldk.ldklaqslanwfkllnslWvky.....ivvilvglrivlivlsllPvvf 173
                                    + +++e+ +l+ di+   n q ++l+ +d+ ++  +++l+ +f  ++ +W +       +++ v++ ivli+l    v+f
  gene179|gene179|rna179|rna179  17 NTQITEIGQLMSDISmhiNIQGENLKRIDEvIERVDDNLFGGFREIEKVWNSVkgrrkSIGVFVAVWIVLILLY---VLF 93 
                                    445555555555554222445566666665268999***************97777665666666655555554...445 PP

>> Prominin  Prominin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.3   5.7e-06      0.02     349     433 ..       8      91 ..       1      94 [. 0.82

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5.7e-06
                       Prominin 349 ipekvknqtaevvpdlkkalakgreqikklakkiprealdavisdle.nterssktfddvvekyekyrwliglivcslll 427
                                    i+++    +++ ++++ + +++++ +i+ + +++  +++d+vi+ ++ n+    ++ ++v++ +   r+ ig+ v++ ++
  gene179|gene179|rna179|rna179   8 IKRQNYAMLNTQITEIGQLMSDISMHINIQGENL--KRIDEVIERVDdNLFGGFREIEKVWNSVKGRRKSIGVFVAVWIV 85 
                                    4444444556667777788888888888888888..99****************************************** PP

                       Prominin 428 livvil 433
                                    li++ +
  gene179|gene179|rna179|rna179  86 LILLYV 91 
                                    **9866 PP

>> SNARE  SNARE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1     3e-05      0.11       2      51 ..      40      89 ..      39      93 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3e-05
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTXXXXXXXXXXXXXXXXXX CS
                          SNARE  2 mvDrIdtnVenaqsnveraqkeLkkavkyqksnRklkciillilviillv 51
                                    + rId  +e++++n+ ++ +e+ k+ ++ k +Rk    ++ + ++++l+
  gene179|gene179|rna179|rna179 40 NLKRIDEVIERVDDNLFGGFREIEKVWNSVKGRRKSIGVFVAVWIVLILL 89
                                   578*******************************9877777777777765 PP

>> SYCP2_ARLD  Synaptonemal complex 2 armadillo-repeat-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   2.8e-05     0.099     132     169 ..      13      50 ..       3      52 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.8e-05
                     SYCP2_ARLD 132 iqlldsFllrlgalvtdkriniliqqealrtlNsiLdk 169
                                      +l++ ++++g+l+ d +++i iq e l+++  ++++
  gene179|gene179|rna179|rna179  13 YAMLNTQITEIGQLMSDISMHINIQGENLKRIDEVIER 50 
                                    469****************************9988876 PP

>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       2.3   8.2e+03      17      23 ..       6      12 ..       2      18 .. 0.68
   2 ?   11.9   0.8   6.2e-05      0.22       2      37 ..      20      55 ..      19      71 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 2.3
                      FlaC_arch 17 etvkken 23
                                   +t+k++n
  gene179|gene179|rna179|rna179  6 STIKRQN 12
                                   6777777 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 6.2e-05
                      FlaC_arch  2 idelEnklsklsteletvkkeneelsksveelkenV 37
                                   i e+ + +s++s+ ++   ++++ + + +e++++n 
  gene179|gene179|rna179|rna179 20 ITEIGQLMSDISMHINIQGENLKRIDEVIERVDDNL 55
                                   78999*****************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1262  (0.0703888); expected 358.6 (0.02)
Passed bias filter:                      854  (0.0476323); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 657.65
//
Query:       gene1790|gene1790|rna1790|rna1790  [L=62]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (62 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       519  (0.0289475); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 449.94
//
Query:       gene1791|gene1791|rna1791|rna1791  [L=180]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.065   12.8   2.5        0.2   11.2   2.5    2.1  1  DUF3452   Domain of unknown function (DUF3452)
       0.08   12.9   0.2       0.24   11.4   0.2    1.8  1  Cdc6_C    CDC6, C terminal winged helix domain


Domain annotation for each model (and alignments):
>> DUF3452  Domain of unknown function (DUF3452)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   2.5   2.2e-05       0.2      42      75 ..     120     152 ..       2     161 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 2.2e-05
                            DUF3452  42 lrqeieelernfsvttvifkkYrqiFeelFlspa 75 
                                         ++++eel+r fs + +i+++Yr i +++F+ + 
  gene1791|gene1791|rna1791|rna1791 120 NKTNLEELKRYFSYS-TIYQHYRSICKNIFKGKY 152
                                        67899*******986.69************9765 PP

>> Cdc6_C  CDC6, C terminal winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.2   2.7e-05      0.24      11      51 ..     126     166 ..     119     170 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 2.7e-05
                                        CSSS-EEHHHHHHHHHHHHHHTT-----HHHHHHHHHHHHH CS
                             Cdc6_C  11 sgkeevttgevyevYkslCesegvdpltqrevsdllseLem 51 
                                        + k++++ + +y+ Y+s+C+     +  ++e+s +++ L++
  gene1791|gene1791|rna1791|rna1791 126 ELKRYFSYSTIYQHYRSICKNIFKGKYRRQEISLVIRLLDS 166
                                        46899999************998888888888888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       734  (0.0409393); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1363.10
//
Query:       gene1792|gene1792|rna1792|rna1792  [L=600]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
        2.5    8.3   7.2        2.9    8.1   0.3    2.6  2  Furin-like_2  Furin-like repeat, cysteine-rich


Domain annotation for each model (and alignments):
>> Furin-like_2  Furin-like repeat, cysteine-rich
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.3   0.00016       2.9       5      71 ..     174     238 ..     170     271 .. 0.83
   2 ?    2.6   1.6    0.0081   1.5e+02      56      78 ..     569     591 ..     565     598 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00016
                       Furin-like_2   5 alcseenGclkckkklfllleregirqiGvc.lascpaGyfgvrnkevnrctkckaeecescfskdfc 71 
                                        + cs+  G l+  kkl l l+ +++ ++G+  +++c +  +++++ +++  t+ +    ++   ++ c
  gene1792|gene1792|rna1792|rna1792 174 SGCSDCYGVLRSLKKLTLKLKLDQLIRVGIIgIETCKNAGYELKSGDLSATTNEQQ---NTKHVRNGC 238
                                        67***********************999975399***9999999999887766544...344445555 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.0081
                       Furin-like_2  56 kckaeecescfskdfctkckegf 78 
                                        kck e+   cf k+f  + ++++
  gene1792|gene1792|rna1792|rna1792 569 KCKFESAYLCFYKNFSKRINKRI 591
                                        9**************99987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (600 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1438  (0.0802053); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.41
# Mc/sec: 4407.05
//
Query:       gene1793|gene1793|rna1793|rna1793  [L=697]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-27   97.2   0.0    2.2e-27   96.1   0.0    1.4  1  Peptidase_M24    Metallopeptidase family M24
    4.2e-26   92.0   3.8      6e-25   88.2   0.5    3.0  3  Creatinase_N_2   Creatinase/Prolidase N-terminal domain
    8.2e-15   54.6   0.4    8.2e-15   54.6   0.4    2.6  3  Peptidase_M24_C  C-terminal region of peptidase_M24
    1.1e-14   55.2   0.4    8.1e-13   49.2   0.1    2.9  2  Creatinase_N     Creatinase/Prolidase N-terminal domain
     0.0057   17.4   0.0       0.03   15.1   0.0    2.2  1  DUF4373          Domain of unknown function (DUF4373)
  ------ inclusion threshold ------
        0.1   12.5   0.1        8.6    6.3   0.0    3.2  2  GCV_H            Glycine cleavage H-protein


Domain annotation for each model (and alignments):
>> Peptidase_M24  Metallopeptidase family M24
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.1   0.0   7.2e-31   2.2e-27      40     205 ..     466     627 ..     448     629 .. 0.90

  Alignments for each domain:
  == domain 1  score: 96.1 bits;  conditional E-value: 7.2e-31
                                        HHTTTCEESSSSEEEEGGGGGSTTTBCSSSB--TTEEEEEEEEEEETTEEEEEEEEEECSSGSHHHHHHHHHHHHH CS
                      Peptidase_M24  40 krhgarglafppivasgenaavlhytpndrvlkegdlvlidagaeydgyasDitrTvlvGkftpeqrelyeavlea 115
                                        +++g+  ++f++i+++g+++a++h++++d+++ ++ l+lid+g ++   ++Di+rT+++G+++ eq   ++ vl++
  gene1793|gene1793|rna1793|rna1793 466 AKTGFLFPSFSTIIGYGKHGAIVHHSASDTTVDDKNLILIDCGSQFIFATTDISRTIHLGTPSSEQIHDFTNVLKG 541
                                        56778999****************************************************99999*********** PP

                                        HHHHHHC-ST.TSBHHHHHHHHHHHHHHTTBCCGBSSCSEEEES..SSSSEEEEEESSSTTCSSB--TTBEEEEEE CS
                      Peptidase_M24 116 qeaaikavkp.GvtlseidaaarevlesaglakffphglGHgvG..levhdegpsvsresndgrkleeGmvftiEp 188
                                        q    ++v p  + ++ i++  r +l+ +g  k++ hg+ HgvG  l vh++ p +      g ++e+ ++ftiEp
  gene1793|gene1793|rna1793|rna1793 542 QLLSKRLVGPkKNVGGLIQDLPRYYLWPEG--KNYEHGTSHGVGtaLYVHESPPEIR---F-GATIEAHQIFTIEP 611
                                        *9999*****77789999999999999764..488*********999***9955565...4.89************ PP

                                        EEEEETTTEEEEEBEEE CS
                      Peptidase_M24 189 giyfapgeggvriedtv 205
                                        g+y  ++++gvried v
  gene1793|gene1793|rna1793|rna1793 612 GYY-KEDNYGVRIEDAV 627
                                        ***.66778******88 PP

>> Creatinase_N_2  Creatinase/Prolidase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       0.6   1.8e+03      70      95 ..      52      75 ..      32     127 .. 0.69
   2 !   88.2   0.5     2e-28     6e-25      18     161 .]     198     323 ..     190     323 .. 0.89
   3 ?    3.1   0.0      0.03        91     138     159 ..     436     455 ..     387     457 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.6
                                       EEEES.S-EEEEE-GGG-..-HHHHH CS
                     Creatinase_N_2 70 aivtkdekatLFvdeeklteevkehl 95
                                       ++vtk +++ L++d++    +++++l
  gene1793|gene1793|rna1793|rna1793 52 VVVTK-TECALYTDSRYY-LQAQKEL 75
                                       56665.588889887753.2333333 PP

  == domain 2  score: 88.2 bits;  conditional E-value: 2e-28
                                        HSS-HHHHHHHHHHHHHHTT-SEEEE-SHHHHHHHTTEE--SBTTB----EEEEEES.S-EEEEE-GGG-..-HHH CS
                     Creatinase_N_2  18 aGesvaeKlerlrkelkkkkadalvlsaldeiAWllNlRGsDipynPvflsyaivtkdekatLFvdeeklteevke 93 
                                         G ++++K+  ++k l++   +a++ls+ld+iAWllNlRG Di+ n vf++y+++tkd ++++F+d + +      
  gene1793|gene1793|rna1793|rna1793 198 PGLTYSNKIGIVQKSLQE--NEAMILSSLDSIAWLLNLRGRDIANNTVFYAYVYITKD-RLVIFTDVK-V------ 263
                                        588999**********97..59*********************************975.*******66.3...... PP

                                        HHHHTTEEEE-GGGHHHHHHHHHHHH----EEE-TTSBHHHHHHH-GGGEEE-S-HHHHHHHC--HHH CS
                     Creatinase_N_2  94 hleengveikpyeevvsdlkalasaskkkvlldpsktsyalasalkekkvveeespiallKavKNevE 161
                                             ++e+++y+e++ +lk++++   ++v ++ +++++ +a+ l e++ +++++ +a lK+vKN  E
  gene1793|gene1793|rna1793|rna1793 264 ---PRDIELRKYSEFYMFLKRIEE---NTVYVS-DNVNASIADILGEDR-MKKNNLVAKLKSVKNRNE 323
                                        ...34599**************83...468887.99********97666.5889***********987 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.03
                                        H-GGGEEE-S-HHHHHHHC--H CS
                     Creatinase_N_2 138 lkekkvveeespiallKavKNe 159
                                        +  +k + ++sp++ +Ka KN+
  gene1793|gene1793|rna1793|rna1793 436 I--NKNMFSSSPVKSPKAAKNN 455
                                        2..3334568***********8 PP

>> Peptidase_M24_C  C-terminal region of peptidase_M24
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.1       2.4   7.1e+03      22      41 ..       7      27 ..       5      39 .. 0.65
   2 ?   -2.6   0.0         2     6e+03       7      19 ..     126     138 ..     122     139 .. 0.84
   3 !   54.6   0.4   2.8e-18   8.2e-15       6      61 ..     638     692 ..     635     694 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 2.4
                                       GS-HHHHHHHHHHH.HHHHHH CS
                    Peptidase_M24_C 22 lLtpeEiawLnaYh.akvrek 41
                                       lLt+   + L+aY  ++  e+
  gene1793|gene1793|rna1793|rna1793  7 LLTQLTLNNLDAYIlNHTDEH 27
                                       788888888888853344444 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2
                                        ES------STT-- CS
                    Peptidase_M24_C   7 tlTlvPidrklId 19 
                                        +l lvP + +l+d
  gene1793|gene1793|rna1793|rna1793 126 KLVLVPVENELVD 138
                                        5779*******98 PP

  == domain 3  score: 54.6 bits;  conditional E-value: 2.8e-18
                                        EES------STT--GGGS-HHHHHHHHHHHHHHHHHHHHHHHHT-H.HHHHHHHT- CS
                    Peptidase_M24_C   6 etlTlvPidrklIdvslLtpeEiawLnaYhakvreklsplLeeeneeleWLkraTr 61 
                                        +++T+vP++ +l+d slLt+eE+++Ln+Y+++vr+ l+++L +e +e+eWL ++Tr
  gene1793|gene1793|rna1793|rna1793 638 QNMTFVPLQLNLLDDSLLTDEEVEYLNKYNENVRNILGEYLYDE-KEKEWLINNTR 692
                                        789**************************************777.569*******8 PP

>> Creatinase_N  Creatinase/Prolidase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.2   0.1   2.7e-16   8.1e-13       5     122 ..       7     130 ..       4     140 .. 0.82
   2 ?    2.9   0.0     0.053   1.6e+02      15      55 ..     217     261 ..     209     370 .. 0.76

  Alignments for each domain:
  == domain 1  score: 49.2 bits;  conditional E-value: 2.7e-16
                                        HHHHHHHTT-SEEEEECC............HHHHHHHSS...-SSSEEEEEEESSCEEEEEECTTHHHHHHHH..T CS
                       Creatinase_N   5 lralmeekgldallvtsp............enlrYltGfatetgsrglalvvtadgalllvdalryteaaees.at 67 
                                        l + ++ ++lda+++ +              ++  ltGf   tgs+g+++ vt+ ++ l++d +ry  +a+++ ++
  gene1793|gene1793|rna1793|rna1793   7 LLTQLTLNNLDAYILNHTdehlsefisdadMRVKRLTGF---TGSNGTVV-VTKTECALYTD-SRYYLQAQKElIE 77 
                                        55566666777777777777777777777788888****...********.***********.7776666666699 PP

                                        TSEEEEESTHSSHHHHHHHHHHHHT-EEEE-TTSSBHHHHHHHHHHCTTSEEEET CS
                       Creatinase_N  68 veevveyddpvealadllkellesekrvgveldaltvafyealkealpdaelvda 122
                                        ++++++    +++l ++lk++++ e+rvgv l+ ++ ++y+++ +++++ +lv +
  gene1793|gene1793|rna1793|rna1793  78 PFKMMKIGV-DKSLLEFLKDTIK-EGRVGVSLRLISHERYKEMTKEFESTKLVLV 130
                                        999999985.99*********76.6**********************99888765 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.053
                                        SEEEEECCHHHHHHHSS........-SSSEEEEEEESSCEEEEEEC CS
                       Creatinase_N  15 dallvtspenlrYltGfa.....tetgsrglalvvtadgalllvda 55 
                                        +a++++s +++ +l + +     + t  + +++ +t+d+ ++++d 
  gene1793|gene1793|rna1793|rna1793 217 EAMILSSLDSIAWLLNLRgrdiaNNTVFYAYVY-ITKDRLVIFTDV 261
                                        689999999999999999998866666666666.899999999983 PP

>> DUF4373  Domain of unknown function (DUF4373)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0     1e-05      0.03      11      64 ..      36      88 ..      29     103 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1e-05
                            DUF4373 11 dekierleaeyglkGygvyvkllekiykekgyyiewdeeqlllladkaklevde 64
                                       d +++rl+   g +G  v+ k  +++y++  yy+++++e ++ +   +k +vd+
  gene1793|gene1793|rna1793|rna1793 36 DMRVKRLTGFTGSNGTVVVTKTECALYTDSRYYLQAQKELIEPFKM-MKIGVDK 88
                                       8899***********************************9988877.4566655 PP

>> GCV_H  Glycine cleavage H-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.51   1.5e+03      44      68 ..     305     329 ..     293     335 .. 0.82
   2 ?    6.3   0.0    0.0029       8.6      59      93 ..     410     444 ..     336     460 .. 0.69

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.51
                                        EE-TT-EEEEEEESS-EEEEE-SSS CS
                              GCV_H  44 kvkkgeslaavEsvKaasevyapvs 68 
                                        ++kk++ +a + svK+  e++  ++
  gene1793|gene1793|rna1793|rna1793 305 RMKKNNLVAKLKSVKNRNEIMGFFQ 329
                                        6789999********9999876655 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0029
                                        -EEEEE-SSSEEEEEE-GGGTT-TTHHHH-TTTTT CS
                              GCV_H  59 aasevyapvsGevvevNekleeepeliNkdpyeeg 93 
                                         +  v+  ++G+++e N+ l ++ + iNk+ + ++
  gene1793|gene1793|rna1793|rna1793 410 LTNLVFELFTGKLTEQNKSLLQNMARINKNMFSSS 444
                                        44557788899999999999999999999888665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (697 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       564  (0.0314574); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.62u 0.27s 00:00:00.89 Elapsed: 00:00:00.45
# Mc/sec: 4639.64
//
Query:       gene1794|gene1794|rna1794|rna1794  [L=527]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.1e-25   89.3   2.5    5.7e-25   88.4   2.5    1.4  1  HECT      HECT-domain (ubiquitin-transferase)
     0.0018   18.4   0.1     0.0052   17.0   0.1    1.7  1  AZUL      Amino-terminal Zinc-binding domain of ubiquitin lig


Domain annotation for each model (and alignments):
>> HECT  HECT-domain (ubiquitin-transferase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.4   2.5   6.3e-29   5.7e-25       2     156 ..     385     525 ..     384     527 .] 0.88

  Alignments for each domain:
  == domain 1  score: 88.4 bits;  conditional E-value: 6.3e-29
                                        HHHHHHT-GGGSSEEESSTTSSSEEE-TTHHHHS....HHHHHHHHHHHHHTT--BSS-B-HHHHHHHTT-.---T CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               HECT   2 llskelldpklglfeeesedsgtlypkpssseeellklfeflGkvlGkaiyeeilldlpfsraflkfllgeekitl 77 
                                        l+s+el++   +lf   + +++ l++++ + ++++   +e++Gk++G a+y++++l+lpf+ +++k  l+ +k++l
  gene1794|gene1794|rna1794|rna1794 385 LVSEELIHD-KFLF---TIQNNLLWFTEGK-KNSR---YEVVGKLIGVALYNDVVLNLPFPTFLFKIFLN-KKVEL 451
                                        678887775.5688...5789999999764.4456...9*******************************.6**** PP

                                        CHHHHH-HHHHHHHHHHH..HS-GGG...GT-BSEEEEETTEEEEEESSTTGGGSB--TTTHHHHHHHHHHHHHTG CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               HECT  78 edleeidpelakslkellslesnteevedlaLtFtipenagasatieLipnGanipVtnenkkeYiklyvnyllkk 153
                                        +dl ei+pe+ +slk++l++++++  + +l+  F i+    +++++eLip+G++i +t++nk++++++yv+yl++ 
  gene1794|gene1794|rna1794|rna1794 452 DDLMEIEPEICQSLKKILHMSDEE--LCALEQYFFITR---NDKSVELIPKGKSIMLTEKNKELFVEKYVEYLTYL 522
                                        ******************886665..989999999994...5779****************************987 PP

                                        GGH CS
                                        xxx RF
                               HECT 154 sve 156
                                        +++
  gene1794|gene1794|rna1794|rna1794 523 EMK 525
                                        766 PP

>> AZUL  Amino-terminal Zinc-binding domain of ubiquitin ligase E3A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.1   5.8e-07    0.0052       4      28 ..       6      30 ..       4      46 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 5.8e-07
                               AZUL  4 lveqYfyQLthGCgsknCtnptCas 28
                                       l   Y++QL  GC++++C+  +C+ 
  gene1794|gene1794|rna1794|rna1794  6 LQDLYVRQLYIGCDNSDCKMYFCRN 30
                                       5567*******************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (527 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       932  (0.0519828); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.48
# Mc/sec: 3328.91
//
Query:       gene1795|gene1795|rna1795|rna1795  [L=115]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.8e-35  120.7   0.1    9.5e-35  120.6   0.1    1.0  1  HECT      HECT-domain (ubiquitin-transferase)


Domain annotation for each model (and alignments):
>> HECT  HECT-domain (ubiquitin-transferase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.6   0.1   5.3e-39   9.5e-35     189     305 ..       2     113 ..       1     115 [] 0.95

  Alignments for each domain:
  == domain 1  score: 120.6 bits;  conditional E-value: 5.3e-39
                                        CSSS.--HHHHHHTEEEETT--TTSHHHHHHHHHHHHS-HHHHHHHHHHHHSSSS--TTCGGG-B--EEEEE-S.. CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               HECT 189 GedelidvedlrrnteykggynaesetiewlweilkefspeekrlfLqFvTgssrlPlgGfaelhpkftierkske 264
                                        G++ +i+v+ l++ ++y+g ++++s +++ +w+i++e+s e+k+++L+F+Tg +r+P++  ++   k+ i+r++  
  gene1795|gene1795|rna1795|rna1795   2 GSN-VINVSLLKKTAVYSG-FTEDSHIVKTFWKIFEEYSLEDKKKLLMFITGNERVPVTCTENW--KLIIVRNG-C 72 
                                        555.7************75.******************************************99..******88.9 PP

                                        -TTS--EEEGGGTEEEE---SSHHHHHHHHHHHHHHHH--X CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               HECT 265 detrLPtahTCfnlLklpdYsskeilkekLltAieetegFe 305
                                        d++rLP+++TCfn+L lp+Yss+e+lk+kL +Ai+ t+gF 
  gene1795|gene1795|rna1795|rna1795  73 DTDRLPSSQTCFNTLLLPEYSSEEKLKNKLGIAISMTKGFF 113
                                        ***************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       436  (0.0243181); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.30s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 769.32
//
Query:       gene1796|gene1796|rna1796|rna1796  [L=184]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.7e-08   32.3   1.0    1.1e-07   31.8   1.0    1.2  1  PLDc_2    PLD-like domain
  ------ inclusion threshold ------
      0.042   14.0   0.0      0.099   12.9   0.0    1.7  1  PLDc      Phospholipase D Active site motif


Domain annotation for each model (and alignments):
>> PLDc_2  PLD-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.8   1.0   1.3e-11   1.1e-07       3     127 ..      34     166 ..      31     172 .. 0.73

  Alignments for each domain:
  == domain 1  score: 31.8 bits;  conditional E-value: 1.3e-11
                             PLDc_2   3 qliksAkksidiatyyf...vsdreildallkaakrgvkvrilldskkddagavdeaslkelkellleagvevrvf 75 
                                        + ++   k++ i+t yf   + +rei+++++  ++++ +  +++d    +   ++e+ +  lke+ + + v  +  
  gene1796|gene1796|rna1796|rna1796  34 NNLRT-AKKVFIITLYFgnkQKTREIMEEIRIRKQKNLETMVIIDY---NRCKQNEQIFVLLKEY-QIEDVVCYAN 104
                                        55555.5778899999999999999********************8...4344444444444444.3333332322 PP

                             PLDc_2  76 et......ll......gslHaKlylidgktvivGSsNltkrgldlnlElnvviedkelakelee 127
                                         +       +        lH K+yl+d + vi+ ++Nl +++++ +l+  + i d+ela++l +
  gene1796|gene1796|rna1796|rna1796 105 -RksyfllPNcikelfFVLHVKMYLFD-SLVILSGANLEDKYFTNRLDRYFSINDSELAEYLMK 166
                                        .134443300444556799*******7.7*****************************999866 PP

>> PLDc  Phospholipase D Active site motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   1.1e-05     0.099       2      26 ..     119     142 ..     118     144 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.1e-05
                                        TBEE---EEEETTTEEEEE---SSH CS
                               PLDc   2 mgthHqKivivDdrvafvGgaNLcd 26 
                                        ++++H K++ +D   ++++gaNL d
  gene1796|gene1796|rna1796|rna1796 119 FFVLHVKMYLFDSL-VILSGANLED 142
                                        689***********.*******966 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1027  (0.0572815); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 1336.36
//
Query:       gene1797|gene1797|rna1797|rna1797  [L=181]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-08   34.4   0.4    2.3e-08   34.0   0.4    1.3  1  PLDc_2    PLD-like domain


Domain annotation for each model (and alignments):
>> PLDc_2  PLD-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.0   0.4   1.3e-12   2.3e-08      59     131 ..      75     152 ..      20     154 .. 0.73

  Alignments for each domain:
  == domain 1  score: 34.0 bits;  conditional E-value: 1.3e-12
                             PLDc_2  59 kelkellleagvevrvfetllgslHaKlyli.dgk..tvivGSsNltkrgldlnlElnvviedk..elakeleeeF 129
                                         ++k+  + +++++r f +++ s+H K+++   g+  ++++GSsN+++r+ +++ Eln+v+  k  +l+k++++e 
  gene1797|gene1797|rna1797|rna1797  75 YTIKTENILEKADLRTFYKKKASFHFKGIWAfAGDfaITVIGSSNFNERSYRKDKELNFVLVTKdeQLIKQFKQEI 150
                                        55555556778888888765689******987788446668**************999876555449*****9998 PP

                             PLDc_2 130 er 131
                                        ++
  gene1797|gene1797|rna1797|rna1797 151 KY 152
                                        86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       860  (0.047967); expected 358.6 (0.02)
Passed bias filter:                      440  (0.0245412); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1262.92
//
Query:       gene1798|gene1798|rna1798|rna1798  [L=415]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.9e-42  144.2   0.0    6.8e-42  143.0   0.0    1.7  1  AAA              ATPase family associated with various cellul
    6.6e-10   38.6   0.1    1.5e-09   37.5   0.1    1.6  1  AAA_lid_3        AAA+ lid domain
    2.2e-06   28.0   0.1     0.0088   16.3   0.0    3.0  3  AAA_22           AAA domain
      1e-05   25.6   0.2    9.5e-05   22.4   0.2    2.6  1  AAA_5            AAA domain (dynein-related subfamily)
    3.8e-05   24.1   0.0     0.0017   18.7   0.0    2.4  2  AAA_16           AAA ATPase domain
    3.8e-05   23.0   0.0    6.5e-05   22.2   0.0    1.3  1  DUF815           Protein of unknown function (DUF815)
    0.00014   22.0   0.0    0.00063   19.9   0.0    2.1  1  AAA_2            AAA domain (Cdc48 subfamily)
    0.00031   20.5   0.0      0.001   18.9   0.0    1.8  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
      0.002   18.4   0.0      0.005   17.1   0.0    1.8  1  AAA_28           AAA domain
     0.0021   18.6   0.0     0.0057   17.2   0.0    1.8  1  AAA_18           AAA domain
      0.003   17.7   0.0     0.0062   16.7   0.0    1.6  1  AAA_33           AAA domain
     0.0043   16.3   0.0      0.025   13.8   0.0    2.0  2  TIP49            TIP49 P-loop domain
     0.0072   16.7   0.0      0.043   14.2   0.0    2.1  2  RNA_helicase     RNA helicase
     0.0079   15.6   0.0       0.02   14.3   0.0    1.6  1  Mg_chelatase     Magnesium chelatase, subunit ChlI
     0.0081   15.9   0.1      0.034   13.9   0.1    2.0  1  AAA_24           AAA domain
     0.0096   15.7   0.0      0.018   14.8   0.0    1.4  1  IstB_IS21        IstB-like ATP binding protein
  ------ inclusion threshold ------
      0.011   15.8   0.1      0.056   13.5   0.0    2.1  2  AAA_14           AAA domain
      0.013   15.4   0.2       0.64    9.9   0.0    2.6  3  ATPase_2         ATPase domain predominantly from Archaea
      0.014   14.9   0.0      0.044   13.3   0.0    1.8  1  AAA_7            P-loop containing dynein motor region
      0.055   13.3   0.0       0.11   12.3   0.0    1.5  1  AAA_3            ATPase family associated with various cellul
      0.074   12.4   0.0       0.26   10.6   0.0    1.9  2  ATPase           KaiC
      0.076   12.7   0.0        0.2   11.3   0.0    1.7  1  Sigma54_activat  Sigma-54 interaction domain
      0.076   12.9   0.0        1.2    9.0   0.0    2.3  2  NACHT            NACHT domain
      0.097   11.7   0.0       0.17   10.9   0.0    1.3  1  Parvo_NS1        Parvovirus non-structural protein NS1
       0.12   12.0   0.1       0.53    9.8   0.0    2.0  2  AAA_25           AAA domain
       0.16   12.4   0.0        0.3   11.6   0.0    1.5  1  ABC_tran         ABC transporter


Domain annotation for each model (and alignments):
>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  143.0   0.0   9.8e-45   6.8e-42       1     131 [.     196     326 ..     196     327 .. 0.96

  Alignments for each domain:
  == domain 1  score: 143.0 bits;  conditional E-value: 9.8e-45
                                        EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH.T CS
                                AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksr.s 75 
                                        vllyGppGtGKTllakava+ +++ f+++ gsel++kyvge+++ +re+f+  ++k+  +++f+DE+da++++r  
  gene1798|gene1798|rna1798|rna1798 196 VLLYGPPGTGKTLLAKAVANRTNACFIRVIGSELIQKYVGEGARMVREIFELGRRKK-ACVIFFDEVDAFGGTRyA 270
                                        79**************************************************99887.8***************88 PP

                                        TCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
                                AAA  76 gseseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieie 131
                                        +s+++e +r++ +L+++ldg++++ +++ vi+atnrpd+ldpallr gR+drk+e++
  gene1798|gene1798|rna1798|rna1798 271 ESDDNEVQRTMLELINQLDGFDNR-GNIKVIMATNRPDTLDPALLRpGRLDRKVEFS 326
                                        8899999****************7.66***************************987 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.5   0.1   2.2e-12   1.5e-09       4      43 ..     352     391 ..     349     393 .. 0.93

  Alignments for each domain:
  == domain 1  score: 37.5 bits;  conditional E-value: 2.2e-12
                          AAA_lid_3   4 lkeLAerTeGySGADlaalcreAallAlrrgikeitmedf 43 
                                        ++ +A+++++ +GA+l ++c eA++ A+r+ +k+ t++df
  gene1798|gene1798|rna1798|rna1798 352 YELIARLCPNATGAELRSVCTEAGMFAIRERRKAATEKDF 391
                                        5679***********************************9 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   1.3e-05    0.0088       8      29 ..     196     217 ..     191     229 .. 0.86
   2 !    8.2   0.0     0.004       2.8      75     128 ..     237     302 ..     221     307 .. 0.77
   3 ?   -1.7   0.0       4.5   3.1e+03      47      91 ..     359     404 ..     346     409 .. 0.69

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.3e-05
                             AAA_22   8 lvvtGesGtGKTtllrrlleql 29 
                                        ++++G++GtGKT+l++ ++++ 
  gene1798|gene1798|rna1798|rna1798 196 VLLYGPPGTGKTLLAKAVANRT 217
                                        689***************9987 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.004
                             AAA_22  75 seellealeqalraravielliiDEaqhlr.....s.......eealeeLrsllnl.srkgvqliLv 128
                                          ++++ + +  r++++  ++  DE++ +      +        ++le + +l  + +r ++++i++
  gene1798|gene1798|rna1798|rna1798 237 GARMVREIFELGRRKKA-CVIFFDEVDAFGgtryaEsddnevqRTMLELINQLDGFdNRGNIKVIMA 302
                                        56777888888999999.***********88755515777888888888877766677999999975 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 4.5
                             AAA_22  47 lpsst..sskdllrellralglelkaerlsseellealeqalrarav 91 
                                        +p+ t  +++++++e   +  +e+ +  ++++++l+a+e+ ++ +a+
  gene1798|gene1798|rna1798|rna1798 359 CPNATgaELRSVCTEAGMFAIRERRK-AATEKDFLNAVEKVIQGYAK 404
                                        44555456666666655555555555.68999999999999888765 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.2   1.4e-07   9.5e-05       1      78 [.     195     265 ..     195     316 .. 0.63

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 1.4e-07
                                        EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------..G-SEEEEESG CS
                              AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar..egeilvlDEv 74 
                                        +vlL GppGtgK+ la+ +a ++n+ +  v +++      l++++  ++ + +++  +l   +r  +++++++DEv
  gene1798|gene1798|rna1798|rna1798 195 GVLLYGPPGTGKTLLAKAVANRTNACFIRVIGSE------LIQKYVGEGARMVREIFEL---GRrkKACVIFFDEV 261
                                        59**********************9998888876......7777773222223333333...33348999999999 PP

                                        GG-- CS
                              AAA_5  75 erae 78 
                                        +   
  gene1798|gene1798|rna1798|rna1798 262 DAFG 265
                                        8554 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   2.5e-06    0.0017      24      47 ..     193     216 ..     165     232 .. 0.83
   2 ?    2.9   0.0      0.19   1.3e+02     124     146 ..     242     269 ..     234     300 .. 0.67

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 2.5e-06
                             AAA_16  24 pelvllsGesGvGKsslvrellra 47 
                                        p  vll+G++G+GK+ l+++++++
  gene1798|gene1798|rna1798|rna1798 193 PKGVLLYGPPGTGKTLLAKAVANR 216
                                        489*****************9974 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.19
                             AAA_16 124 krllallsrderplvlvlDdlq......w 146
                                        +++++l +r ++  v+++D+++       
  gene1798|gene1798|rna1798|rna1798 242 REIFELGRR-KKACVIFFDEVDafggtrY 269
                                        445566777.777*********6666663 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0   9.4e-08   6.5e-05      16     116 ..     147     261 ..     139     283 .. 0.78

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 9.4e-08
                             DUF815  16 lepveevdevklddLvgidkqkealve.......nteqfle..glpannvLLwGarGtGKSslvkallneyaeegL 82 
                                        l  vee  +v+ +d+ g +++ e+++e       n e+f++    p + vLL+G  GtGK  l ka+ n++++  +
  gene1798|gene1798|rna1798|rna1798 147 LMQVEEKPNVTYEDIGGCKEEIEKIKEvveapllNPEKFVNlgIDPPKGVLLYGPPGTGKTLLAKAVANRTNACFI 222
                                        6677777778888887777766666553333444778888742368999*************************** PP

                             DUF815  83 rli..evekedlkelpklvellr...erperfilfvDDL 116
                                        r+i  e+ ++ + e  ++v+++    +r++ +++f D +
  gene1798|gene1798|rna1798|rna1798 223 RVIgsELIQKYVGEGARMVREIFelgRRKKACVIFFDEV 261
                                        ***77788899999888888776343678889***9976 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   9.1e-07   0.00063       6     123 ..     196     299 ..     191     310 .. 0.74

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 9.1e-07
                                        EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHH...HHHHTTT-HHHHTTSEEEEETGG CS
                              AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsr...ligappgyvgaeegGivllDEid 78 
                                        +ll gp g+Gkt+laka+a+  ++     +ir+  sel++     ++v +    + +     ++++  ++++DE+d
  gene1798|gene1798|rna1798|rna1798 196 VLLYGPPGTGKTLLAKAVANRTNA----CFIRVIGSELIQ-----KYVGEgarMVREIFELGRRKKACVIFFDEVD 262
                                        6899******************96....9****9***999.....44433000222222233445555******** PP

                                        G-------------HHHHHHHHHHHH--EE-------EE-TT-EE CS
                              AAA_2  79 KihpkessgadvSregVqrdLLqileggtltdkqgrkvdtknilf 123
                                              +  a+   ++Vqr +L ++ +    d+ g      ni +
  gene1798|gene1798|rna1798|rna1798 263 AFGG--TRYAESDDNEVQRTMLELINQLDGFDNRG------NIKV 299
                                        9999..667777789*********99877667777......4445 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       8.5   5.9e+03      89     103 ..      25      39 ..      19      41 .. 0.84
   2 !   18.9   0.0   1.5e-06     0.001      35      72 ..     195     233 ..     184     267 .. 0.70

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 8.5
                             RuvB_N  89 fideihrlsraveev 103
                                        + dei ++++ ++e 
  gene1798|gene1798|rna1798|rna1798  25 YTDEIQKIEKLINET 39 
                                        789*****9999986 PP

  == domain 2  score: 18.9 bits;  conditional E-value: 1.5e-06
                             RuvB_N  35 hvllyGpPGlGkttlakiiakelgvk.lkitsgPvleka 72 
                                         vllyGpPG Gkt lak +a+  ++  +++  +  ++k 
  gene1798|gene1798|rna1798|rna1798 195 GVLLYGPPGTGKTLLAKAVANRTNACfIRVIGSELIQKY 233
                                        69*******************998752566666666664 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   7.3e-06     0.005       2      39 ..     196     238 ..     195     287 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 7.3e-06
                             AAA_28   2 ivitGgestGKTtlleaLaar....gypvv.pEaareileekl 39 
                                        + + G+++tGKT l++a a+r     ++v+  E   +++ e++
  gene1798|gene1798|rna1798|rna1798 196 VLLYGPPGTGKTLLAKAVANRtnacFIRVIgSELIQKYVGEGA 238
                                        6799***************986555555666666666655544 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   8.3e-06    0.0057       1      29 [.     196     231 ..     196     301 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 8.3e-06
                             AAA_18   1 IlltGtpGvGKttlakeLskrl.gf......gvnlr 29 
                                        +ll G+pG+GKt lak++++r+ ++      ++ ++
  gene1798|gene1798|rna1798|rna1798 196 VLLYGPPGTGKTLLAKAVANRTnACfirvigSELIQ 231
                                        799******************956688777533333 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   8.9e-06    0.0062       2      39 ..     196     235 ..     196     287 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 8.9e-06
                             AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlfg 39 
                                        vll G+pG+GK+ la+ +++++   ++++   +l+++++g
  gene1798|gene1798|rna1798|rna1798 196 VLLYGPPGTGKTLLAKAVANRTNacFIRVIGSELIQKYVG 235
                                        7899***************999966666666666666665 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.81   5.6e+02      73     111 ..       9      47 ..       7      91 .. 0.81
   2 !   13.8   0.0   3.6e-05     0.025      51      90 ..     194     231 ..     187     246 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.81
                                        XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                              TIP49  73 elgedvpfvalsgsevyslevkktevltqalrksigvri 111
                                        elg+d       g + y+ e++k e l+++    ++v++
  gene1798|gene1798|rna1798|rna1798   9 ELGKDADEFLYYGQNYYTDEIQKIEKLINETFDRVNVKL 47 
                                        5677776667788999*********99877655555554 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 3.6e-05
                                        XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                              TIP49  51 ravLlaGpsgtGktalaiaiskelgedvpfvalsgsevys 90 
                                        ++vLl Gp+gtGkt la a+++  +    f+ + gse+ +
  gene1798|gene1798|rna1798|rna1798 194 KGVLLYGPPGTGKTLLAKAVANRTN--ACFIRVIGSELIQ 231
                                        89*******************9866..7899999999865 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       2.8     2e+03      49      65 ..     152     168 ..     144     182 .. 0.76
   2 !   14.2   0.0   6.2e-05     0.043       1      51 [.     196     237 ..     196     259 .. 0.71

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 2.8
                       RNA_helicase  49 gqevvvidDfgqvkdee 65 
                                        +++ v ++D+g +k+e 
  gene1798|gene1798|rna1798|rna1798 152 EKPNVTYEDIGGCKEEI 168
                                        678999*******9883 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 6.2e-05
                       RNA_helicase   1 iwlyGpsgeGKStlakeLakallkklklkkkdsvysrnpeddfwdgYtgqe 51 
                                        ++lyGp+g+GK++lak +a         ++++ +++r   ++  ++Y g+ 
  gene1798|gene1798|rna1798|rna1798 196 VLLYGPPGTGKTLLAKAVA---------NRTNACFIRVIGSELIQKYVGEG 237
                                        689**************44.........44455555666666666666555 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   2.9e-05      0.02      25      43 ..     196     214 ..     186     219 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.9e-05
                       Mg_chelatase  25 lllvGppGsGKtmlakrlp 43 
                                        +ll+GppG+GKt+lak+++
  gene1798|gene1798|rna1798|rna1798 196 VLLYGPPGTGKTLLAKAVA 214
                                        89*************9875 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.1   4.9e-05     0.034       5      23 ..     196     216 ..     193     276 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.9e-05
                             AAA_24   5 iliyGpsgiGKTtlakel..g 23 
                                        +l+yGp+g+GKT lak     
  gene1798|gene1798|rna1798|rna1798 196 VLLYGPPGTGKTLLAKAVanR 216
                                        89*************998433 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   2.7e-05     0.018      47      70 ..     193     216 ..     184     226 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.7e-05
                          IstB_IS21  47 kenivllGpsGvGKshlaialgve 70 
                                         ++++l Gp+G+GK+ la a++ +
  gene1798|gene1798|rna1798|rna1798 193 PKGVLLYGPPGTGKTLLAKAVANR 216
                                        57899***************9875 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       2.7   1.9e+03      69      79 ..      25      35 ..       6      46 .. 0.76
   2 ?   13.5   0.0   8.2e-05     0.056       5      76 ..     196     264 ..     193     303 .. 0.68

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 2.7
                             AAA_14 69 flDEiqevpew 79
                                       + DEiq+++++
  gene1798|gene1798|rna1798|rna1798 25 YTDEIQKIEKL 35
                                       45999999876 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 8.2e-05
                             AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkla..dpekllelileklkeekktylflDEiqev 76 
                                        +++ G+  +GKT l+k ++++         +i +   ++ ++   + +++ ++i+e+ +++k  ++f+DE+   
  gene1798|gene1798|rna1798|rna1798 196 VLLYGPPGTGKTLLAKAVANRTN-----ACFIRVIGSELIQKYvgEGARMVREIFELGRRKKACVIFFDEVDAF 264
                                        7899***********99996655.....4444444444432221133367888888744458888******876 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       7.6   5.2e+03       7      23 ..      28      44 ..      25      50 .. 0.71
   2 ?    9.9   0.0   0.00093      0.64      23      45 ..     196     218 ..     187     237 .. 0.81
   3 ?    2.2   0.0      0.21   1.4e+02     112     134 ..     246     266 ..     238     304 .. 0.72

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 7.6
                           ATPase_2  7 elkeleeilerepneiy 23
                                       e++++e++++++ +++ 
  gene1798|gene1798|rna1798|rna1798 28 EIQKIEKLINETFDRVN 44
                                       78888888877766665 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00093
                           ATPase_2  23 yfiYGpegsGKtaLlkeiienle 45 
                                        +++YGp g GKt L k ++++ +
  gene1798|gene1798|rna1798|rna1798 196 VLLYGPPGTGKTLLAKAVANRTN 218
                                        789*********99999999874 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.21
                           ATPase_2 112 kikkkgkkiiiiiDelqklidlg 134
                                        ++ +++k  +i++De+   +  g
  gene1798|gene1798|rna1798|rna1798 246 ELGRRKKACVIFFDEVDAFG--G 266
                                        5667888899****998777..4 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   6.3e-05     0.044      27      58 ..     187     218 ..     180     287 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 6.3e-05
                              AAA_7  27 elllknkkpvllvGptGtGKtviikdllkkld 58 
                                        +l ++  k vll+Gp GtGKt+++k + ++ +
  gene1798|gene1798|rna1798|rna1798 187 NLGIDPPKGVLLYGPPGTGKTLLAKAVANRTN 218
                                        566667789****************9988776 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00017      0.11       2      30 ..     196     224 ..     195     237 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00017
                              AAA_3   2 vllegvPGlaktllvkalakaldlefkri 30 
                                        vll g PG++ktll+ka+a+  ++ f r+
  gene1798|gene1798|rna1798|rna1798 196 VLLYGPPGTGKTLLAKAVANRTNACFIRV 224
                                        7999********************99998 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00038      0.26      14      37 ..     188     211 ..     166     217 .. 0.86
   2 ?   -2.0   0.0       2.7   1.9e+03     124     152 ..     257     289 ..     236     307 .. 0.59

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00038
                             ATPase  14 gGipegrvvlitGepGtGKtifal 37 
                                         Gi   + vl++G pGtGKt++a+
  gene1798|gene1798|rna1798|rna1798 188 LGIDPPKGVLLYGPPGTGKTLLAK 211
                                        577777889*************97 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2.7
                             ATPase 124 viDsitgl....ayeekeavaReilrqlvrvlk 152
                                          D ++++      e++++++ +++ +l+++l 
  gene1798|gene1798|rna1798|rna1798 257 FFDEVDAFggtrYAESDDNEVQRTMLELINQLD 289
                                        445554443212244556667777777776664 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0    0.0003       0.2      22      46 ..     193     217 ..     173     232 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0003
                                        SS-EEEECSTTSSHHHHHHHHHHHS CS
                    Sigma54_activat  22 dlsvlitGesGtGKellaraiheas 46 
                                        +  vl+ G  GtGK+lla+a+ +++
  gene1798|gene1798|rna1798|rna1798 193 PKGVLLYGPPGTGKTLLAKAVANRT 217
                                        5679***************997654 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.0    0.0018       1.2       3      22 ..     196     215 ..     194     219 .. 0.89
   2 ?    1.3   0.0       0.4   2.8e+02      57     115 ..     229     287 ..     214     290 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0018
                                        EEEEC-TTTCHHHHHHHHHH CS
                              NACHT   3 vilqGeaGsGKTtLlqklal 22 
                                        v+l G++G GKT L++ +a 
  gene1798|gene1798|rna1798|rna1798 196 VLLYGPPGTGKTLLAKAVAN 215
                                        799************99985 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.4
                                        HHCCCCTS--SSS-CCHHHHCCSCCCEEEEEE-STT-SS-TCH..........HHHHHCT CS
                              NACHT  57 llfsqlpepaapvsevwavllelperlLlilDglDelvtdlgq.kekqpvrtlLselirk 115
                                        l+ +   e a+ v+e + +l ++++  ++ +D +D +     + ++ ++v++ + eli++
  gene1798|gene1798|rna1798|rna1798 229 LIQKYVGEGARMVRE-IFELGRRKKACVIFFDEVDAFGGTRYAeSDDNEVQRTMLELINQ 287
                                        444445555666666.88899999999*********998777778999999999999986 PP

>> Parvo_NS1  Parvovirus non-structural protein NS1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00025      0.17     117     137 ..     196     216 ..     191     220 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00025
                          Parvo_NS1 117 vwfyGpantGktnlaeaIaka 137
                                        v++yGp+ tGkt la+a a+ 
  gene1798|gene1798|rna1798|rna1798 196 VLLYGPPGTGKTLLAKAVANR 216
                                        89***************9985 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   0.00077      0.53      36      52 ..     196     212 ..     170     217 .. 0.86
   2 ?   -1.0   0.0       1.6   1.1e+03     142     184 ..     252     300 ..     238     303 .. 0.63

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00077
                             AAA_25  36 allaGapgtGKttlald 52 
                                        +ll+G+pgtGKt la  
  gene1798|gene1798|rna1798|rna1798 196 VLLYGPPGTGKTLLAKA 212
                                        69***********9965 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.6
                             AAA_25 142 gvrlvviDplsralgg..densnsdv....galvealeriarrtgaavl 184
                                        ++ ++ +D ++++ g    e ++++v     +l+++l+ +  r ++ v+
  gene1798|gene1798|rna1798|rna1798 252 KACVIFFDEVDAFGGTryAESDDNEVqrtmLELINQLDGFDNRGNIKVI 300
                                        5667888888888777777777777531114566666666666666555 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00044       0.3       4      36 ..     186     218 ..     184     297 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00044
                                        EEEEEETTSEEEEEESTTSSHHHHHHHHTTSS- CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ABC_tran   4 vslklkegekvaivGenGaGKStLlkllagllk 36 
                                        v+l + + + v + G+ G+GK+ L+k++a+ ++
  gene1798|gene1798|rna1798|rna1798 186 VNLGIDPPKGVLLYGPPGTGKTLLAKAVANRTN 218
                                        7899999999*****************998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (415 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       738  (0.0411624); expected 358.6 (0.02)
Passed bias filter:                      652  (0.0363657); expected 358.6 (0.02)
Passed Vit filter:                        91  (0.00507558); expected 17.9 (0.001)
Passed Fwd filter:                        26  (0.00145016); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              26  [number of targets reported over threshold]
# CPU time: 0.62u 0.29s 00:00:00.90 Elapsed: 00:00:00.44
# Mc/sec: 2827.78
//
Query:       gene1799|gene1799|rna1799|rna1799  [L=315]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.7e-18   65.8  13.5      6e-09   35.5   0.3    4.0  3  ERO1      Endoplasmic Reticulum Oxidoreductin 1 (ERO1)


Domain annotation for each model (and alignments):
>> ERO1  Endoplasmic Reticulum Oxidoreductin 1 (ERO1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   1.4     0.013   2.2e+02       3      42 ..      23      61 ..      21      69 .. 0.85
   2 !   29.6   1.5   2.2e-11   3.9e-07      95     220 ..      73     174 ..      59     186 .. 0.80
   3 !   35.5   0.3   3.4e-13     6e-09     282     347 ..     205     261 ..     200     264 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.013
                               ERO1  3 rplLkeLvktdfFryfkvnldkeCpfweddeglCanraCa 42
                                       r +L+e++k++ F+  +++++++C f  +  + C+  +C 
  gene1799|gene1799|rna1799|rna1799 23 RRQLNEICKHRAFSRIEMDFSNTCLFP-ELMKECKLWECL 61
                                       6789**********************7.566999999996 PP

  == domain 2  score: 29.6 bits;  conditional E-value: 2.2e-11
                               ERO1  95 eeeeeavyvdLlenperfTgYkGesaervWkaiYeencfkeeseseeseekeleelclekrvfyrliSGlhasisi 170
                                        ++ e+   vdLl npe++TgYk  s +++W+ +   n                     +++++  ++SG+h+s++i
  gene1799|gene1799|rna1799|rna1799  73 KNGESRMIVDLLLNPESYTGYKKGS-SEIWEKLKGIN---------------------DSELYKIMLSGIHQSVNI 126
                                        44455789*************9887.89**9876443.....................346788899********* PP

                               ERO1 171 hlaaeylnqetgewepnlelfkervgkhperlenlYfnyalvlrAvakla 220
                                        h aa y+     ++ +n+ lf++  + + +++ n  +  +++l ++ kl+
  gene1799|gene1799|rna1799|rna1799 127 HKAAFYKPCG-YNFLKNVMLFRKTCR-NDAFIGNFKILRLFLLTSLKKLE 174
                                        *****99975.5899******77665.56899999999999999998875 PP

  == domain 3  score: 35.5 bits;  conditional E-value: 3.4e-13
                               ERO1 282 rerfrnisrimdCVgCekCrLwGKlqttGlgtAlkilfeeeekeeekklkLernevvALintlerl 347
                                         + +++  +i+ C  C kCrLw+ +q +Glg+A ki+  e+          +++++v +in l+r+
  gene1799|gene1799|rna1799|rna1799 205 SKDLEDAIDILSCMPCPKCRLWSTIQFKGLGVAAKIIAGEKI---------SQQDLVFFINFLNRI 261
                                        566777789****************************98854.........455666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (315 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       579  (0.032294); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.38
# Mc/sec: 2478.94
//
Query:       gene18|gene18|rna18|rna18  [L=506]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.5e-70  237.4   0.0    1.7e-70  237.2   0.0    1.0  1  Metalloenzyme  Metalloenzyme superfamily
    1.9e-57  194.2   0.3    3.1e-57  193.5   0.3    1.2  1  iPGM_N         BPG-independent PGAM N-terminus (iPGM_N)
    0.00013   21.4   0.0     0.0004   19.9   0.0    1.7  2  Sulfatase      Sulfatase
     0.0015   18.2   0.0     0.0034   17.0   0.0    1.5  2  Phosphodiest   Type I phosphodiesterase / nucleotide pyrophos


Domain annotation for each model (and alignments):
>> Metalloenzyme  Metalloenzyme superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  237.2   0.0   3.8e-74   1.7e-70       2     247 ..      16     491 ..      15     492 .. 0.98

  Alignments for each domain:
  == domain 1  score: 237.2 bits;  conditional E-value: 3.8e-74
                                EEEEEEETTBB----GGGTTHHHS--HHHHHHHHH.......SEEEEEESSSTT----HHHHHHHH.................. CS
                                xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.................. RF
              Metalloenzyme   2 kvvlvvlDGlGeapadelnaihvAktPtldkLkkeaPerwlikahgtavglpeddmgnsevgHlel.................. 67 
                                kv lv++DG+G++++++ nai+  +   ++ L  ++  ++l++a+gt+vglp d+mgns vgHl++                  
  gene18|gene18|rna18|rna18  16 KVCLVIIDGWGQRNEKKGNAIETTDCKWMKLLSSKY-SSYLLSASGTDVGLPADQMGNSMVGHLTIgagrvvlqpqkqidalia 98 
                                899**************************9998885.556******************************************** PP

                                .................................................................................... CS
                                .................................................................................... RF
              Metalloenzyme  68 .................................................................................... 67 
                                                                                                                    
  gene18|gene18|rna18|rna18  99 thklkeclenagvykesgrlhliglvsdggihshishlfalidllkdafseifvhfiadgrdtapqsavhyvrslqkeiaksen 182
                                ************************************************************************************ PP

                                .................................................................................... CS
                                .................................................................................... RF
              Metalloenzyme  68 .................................................................................... 67 
                                                                                                                    
  gene18|gene18|rna18|rna18 183 vkmasfagrwytmdrdknlerveeaylmmtdgkvidesidsyinkqydkqiydenippvllnqdgvilpndtllffnyradrmk 266
                                ************************************************************************************ PP

                                .................................................HHHHTT-----EEEEEEEE-S---SSHHHHHT--E CS
                                .................................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
              Metalloenzyme  68 .................................................lrisetvkfahvtffwnggrsgyfnpleereeips 102
                                                                                  +i+et+k+ahvt+f nggr+++f++ e+r+ i+s
  gene18|gene18|rna18|rna18 267 qiverfsrknrkiftltrydetfnfpfivhgenvpntlaetisrsgaaqSHIAETEKYAHVTYFLNGGREQPFEN-EKRFLINS 349
                                *************************************************99************************.******** PP

                                EEE--SHHSTT--HHHHHHHHHHHH.CC.-SEEEEEE-HHHHHHHTT-HHHHHHHHHHHHHHHHHHHTTS-TTTEEEEEE-SSB CS
                                xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
              Metalloenzyme 103 dtvitfdlqpemkavevaekaldailsgkfdlvvvniknaDmvGHtgdleatiaaieaaDeavkeildaieqvdgilvvtADHg 186
                                ++v  + l+pem+ ++++e+  ++++ +   ++v+n++n+DmvGHtg++eat +a+   De+++ + + + ++d ilvvtADHg
  gene18|gene18|rna18|rna18 350 PKVSSYHLKPEMSIYQIVEQCFKEMTAN-TPFIVLNFANPDMVGHTGNFEATCEAVLCTDECIGLVYEGCIENDYILVVTADHG 432
                                *************************666.99***************************************************** PP

                                --TTTSS........-----EEEEEESTT----S--SSHHHHTT-TTEEEEGGGHHHHHHH CS
                                xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
              Metalloenzyme 187 naedmvkrdkqplTsHtlepVPilivgkglapdkvkegakfrekggLanvaatllnllgle 247
                                nae m +++ + +T+Ht  +VP+++  + + p+k++ g  fr +g+L++va+t+l+llgle
  gene18|gene18|rna18|rna18 433 NAEIMEDENGNVVTKHTSSKVPLIVCARVVGPAKTEWG--FRGEGTLSDVAPTVLHLLGLE 491
                                ****************************9999555555..******************997 PP

>> iPGM_N  BPG-independent PGAM N-terminus (iPGM_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  193.5   0.3   6.9e-61   3.1e-57      11     214 ..      97     286 ..      91     295 .. 0.88

  Alignments for each domain:
  == domain 1  score: 193.5 bits;  conditional E-value: 6.9e-61
                                GG-HHHHHHHHHH..HHCTSEEEEEEE-SS--SS--CHHHHHHHHHHHHTT-SEEEEEEEE-SSSSTTT-HHHHHHHHHHHHHH CS
                     iPGM_N  11 fenealkeaieka..kkngkalHllGLlSdGgVHShidhllallelakeegvkkvvvhaflDGRDtapksaleyleeleeklke 92 
                                  +++lke++e+a   k++++lHl+GL+SdGg+HShi+hl+al++l k++   +++vh++ DGRDtap+sa++y+++l++++++
  gene18|gene18|rna18|rna18  97 IATHKLKECLENAgvYKESGRLHLIGLVSDGGIHSHISHLFALIDLLKDAFS-EIFVHFIADGRDTAPQSAVHYVRSLQKEIAK 179
                                55667777777762245789***************************99866.******************************* PP

                                CT--EEEEEEEHHHHT--SS-HHHHHHHHHHHCCSSSEEECTTHHHHHHHHHHTT--GGG---EEE...TCCGGS--TT-EEEE CS
                     iPGM_N  93 lgvgkiasvsGRyyaMDRdkrwervekaydalvkgegeskaesaveaieesyakgetDefveptviaeegkkegtikdgDavif 176
                                 ++ k+as  GR+y+MDRdk+ erve+ay ++++g+  +  es  ++i+++y+k++ De ++p+++    +++g i  +D+++f
  gene18|gene18|rna18|rna18 180 SENVKMASFAGRWYTMDRDKNLERVEEAYLMMTDGKVID--ESIDSYINKQYDKQIYDENIPPVLL----NQDGVILPNDTLLF 257
                                *999*****************************997644..58999********************....7889********** PP

                                ----CCCCHHHHHHHHSTTHHCC.--TT-EEEESS-S- CS
                     iPGM_N 177 fNFRaDRareltraltdkefkefekakklklvtmteYd 214
                                fN+RaDR++++++ +++k+ k         ++t+t+Yd
  gene18|gene18|rna18|rna18 258 FNYRADRMKQIVERFSRKNRK---------IFTLTRYD 286
                                ****************75444.........44444444 PP

>> Sulfatase  Sulfatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       0.5   2.2e+03     241     285 ..     254     301 ..     250     318 .. 0.68
   2 !   19.9   0.0   8.9e-08    0.0004     210     308 ..     396     489 ..     337     490 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.5
                                EEEEEE..ESSSSCCCG..HHTTSSSCTTCSSSHHHHBEEEEEEETTTS CS
                  Sulfatase 241 tlvvft..SDhgaslee..sngplrggkganayeggtrvPllvwwpgek 285
                                tl++f   +D   ++ e  s+++ ++    + y++ ++ P++v++ +  
  gene18|gene18|rna18|rna18 254 TLLFFNyrADRMKQIVErfSRKNRKIFTL-TRYDETFNFPFIVHGENVP 301
                                55555445666666666655555555555.7899999999999987765 PP

  == domain 2  score: 19.9 bits;  conditional E-value: 8.9e-08
                                HHHHHHHHHHHHHHHHHHHHHHHHHTTTGGGEEEEEEESSSS.CCCGHHTTSSSCTTCSSSHHHHBEEEEEEETTTSHCEEECS CS
                  Sulfatase 210 lleaylnsveyvDdligrvlaaLeenglldntlvvftSDhga.sleesngplrggkganayeggtrvPllvwwpgekaprvsee 292
                                + ea + +v ++D++ig v++        ++ ++v+t+Dhg  ++ e       +  + + + + +vPl+v      +++++++
  gene18|gene18|rna18|rna18 396 NFEATCEAVLCTDECIGLVYEGC----IENDYILVVTADHGNaEIME-----DENGNVVTKHTSSKVPLIVCARVVGPAKTEWG 470
                                5678899****************....**************713444.....2333335666777******************* PP

                                EEE...GGGHHHHHHHHTT CS
                  Sulfatase 293 lvs...hiDlfptildlag 308
                                +     ++D++pt+l+l+g
  gene18|gene18|rna18|rna18 471 FRGegtLSDVAPTVLHLLG 489
                                *99999***********99 PP

>> Phosphodiest  Type I phosphodiesterase / nucleotide pyrophosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0      0.76   3.4e+03     227     261 ..     122     158 ..     102     240 .. 0.58
   2 !   17.0   0.0   7.5e-07    0.0034     171     239 ..     376     439 ..     316     451 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.76
                                EEEES---.EEEHTTSEEEGGGTSTGGH...GEEEEECB CS
               Phosphodiest 227 ilvSDHGm.advsddkvielndlleekg...llhlkdeg 261
                                 lvSD G+ +++  ++++ l dll+++      h +++g
  gene18|gene18|rna18|rna18 122 GLVSDGGIhSHI--SHLFALIDLLKDAFseiFVHFIADG 158
                                566666652333..5555555555554444422333222 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 7.5e-07
                                SSESEEEEEECCCHHHHHHH-TTSHHHHHHHHHHHHHHHHHHHHHHHTTGTTTEEEEEEES---EEEH.T CS
               Phosphodiest 171 ekpdlllvyleetDtvgHkfGpdspevedalrrvDkaigdLlealderglsaetniilvSDHGmadvs.d 239
                                 ++ ++++++ ++D vgH  G + +++ +a+   D++ig  +e+  e+    ++ +++++DHG a++  d
  gene18|gene18|rna18|rna18 376 ANTPFIVLNFANPDMVGH-TG-NFEATCEAVLCTDECIGLVYEGCIEN----DYILVVTADHGNAEIMeD 439
                                67889*************.55.8889999******************9....***********9999755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (506 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       648  (0.0361426); expected 358.6 (0.02)
Passed bias filter:                      552  (0.0307881); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.63u 0.31s 00:00:00.94 Elapsed: 00:00:00.49
# Mc/sec: 3108.20
//
Query:       gene180|gene180|rna180|rna180  [L=167]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       814  (0.0454013); expected 358.6 (0.02)
Passed bias filter:                      586  (0.0326845); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.32s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1061.88
//
Query:       gene1800|gene1800|rna1800|rna1800  [L=32]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (32 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       155  (0.00864521); expected 358.6 (0.02)
Passed bias filter:                      106  (0.00591221); expected 358.6 (0.02)
Passed Vit filter:                         5  (0.000278878); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.43
# Mc/sec: 224.04
//
Query:       gene1801|gene1801|rna1801|rna1801  [L=305]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (305 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       845  (0.0471303); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 2165.48
//
Query:       gene1802|gene1802|rna1802|rna1802  [L=177]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.012   15.7   5.3      0.018   15.1   5.3    1.4  1  Rootletin    Ciliary rootlet component, centrosome cohesion
      0.016   15.5   3.7      0.016   15.5   3.7    1.5  2  Gp-FAR-1     Nematode fatty acid retinoid binding protein (Gp
      0.097   13.1   7.5       0.14   12.5   7.0    1.5  1  CENP-H       Centromere protein H (CENP-H)
      0.099   12.7   8.9       0.15   12.1   8.9    1.3  1  UPF0242      Uncharacterised protein family (UPF0242) N-termi
       0.16   11.0   5.2       0.16   11.0   5.2    1.1  1  Atg14        Vacuolar sorting 38 and autophagy-related subuni
       0.22   11.7   7.7        1.2    9.3   7.7    2.3  2  Cep57_CLD_2  Centrosome localisation domain of PPC89
       0.22   10.9   7.8        6.5    6.1   5.3    2.1  2  GBP_C        Guanylate-binding protein, C-terminal domain
       0.43   10.4   5.8       0.93    9.3   4.7    2.0  2  DUF2570      Protein of unknown function (DUF2570)
        1.5    9.1  10.0       0.83    9.9   1.0    3.2  3  HALZ         Homeobox associated leucine zipper


Domain annotation for each model (and alignments):
>> Rootletin  Ciliary rootlet component, centrosome cohesion
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   5.3   8.9e-06     0.018      68     126 ..      21      78 ..       3     102 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 8.9e-06
                          Rootletin  68 dleealakLeeErqrseklaqvnslLreqleearqaneaLtedlqkltkdwerlreele 126
                                        +  e+l+kL  E+    + +++n+ Lre++e  +++n++L++d+   +k++ r+++ +e
  gene1802|gene1802|rna1802|rna1802  21 NF-ELLEKLIKEKDNLVSQEKLNNSLREEVESLSKENRELKNDIIGKSKEIARIKKHSE 78 
                                        44.899*************************************9988999999888766 PP

>> Gp-FAR-1  Nematode fatty acid retinoid binding protein (Gp-FAR-1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   3.7   8.1e-06     0.016      28      92 ..       9      73 ..       2     125 .. 0.71
   2 ?   -2.9   0.0         4   7.9e+03      78      98 ..     145     165 ..     134     170 .. 0.55

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 8.1e-06
                           Gp-FAR-1 28 evvknykg.yknedellaalKkkspaLyekaeklqaklkekvdkLspeakeFvkkliakgrkleaq 92
                                       +++ ++++ +k   ell+ l k +++L ++ ekl++ l+e+v++Ls e +e+ +++i+k +++   
  gene1802|gene1802|rna1802|rna1802  9 DLILEMRNiNKLNFELLEKLIKEKDNLVSQ-EKLNNSLREEVESLSKENRELKNDIIGKSKEIARI 73
                                       556666665555567777776777888765.9**************************99999653 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 4
                           Gp-FAR-1  78 Fvkkliakgrkleaqvlagek 98 
                                        F   l++ ++  ++++++ ++
  gene1802|gene1802|rna1802|rna1802 145 FLRRLVDSIKDSHDNYIKMNQ 165
                                        444555555555555554444 PP

>> CENP-H  Centromere protein H (CENP-H)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   7.0   7.2e-05      0.14       6      82 ..       5      84 ..       2      92 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 7.2e-05
                             CENP-H  6 eqrdelssellklsqelrelqeeltevekenlrlkrknrelaaellelakekesek...eklkeelekleaelkksrq 80
                                       +++d+l++e+ ++++   el+e+l + + + ++ ++ n++l +e++ l+ke+++ k     +++e+++++++ + +++
  gene1802|gene1802|rna1802|rna1802  5 KRIDDLILEMRNINKLNFELLEKLIKEKDNLVSQEKLNNSLREEVESLSKENRELKndiIGKSKEIARIKKHSEVAIR 82
                                       689************************************************999997775589999999999988888 PP

                             CENP-H 81 rw 82
                                       r+
  gene1802|gene1802|rna1802|rna1802 83 RM 84
                                       76 PP

>> UPF0242  Uncharacterised protein family (UPF0242) N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   8.9   7.7e-05      0.15      66     147 ..      25     107 ..       4     117 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 7.7e-05
                            UPF0242  66 ekskleekeaklteldeglktkeealeelqeeeeeLkeeldakeeelerlkeenq.qLqekleaiae.dfeelkle 139
                                         ++ ++ek +++++++   +  +e++e l +e++eLk+ +  k++e++r k+  +  ++  +++ia     + ++e
  gene1802|gene1802|rna1802|rna1802  25 LEKLIKEKDNLVSQEK-LNNSLREEVESLSKENRELKNDIIGKSKEIARIKKHSEvAIRRMKHDIASeTCPKRRKE 99 
                                        3445555555555555.45567788888888888888888888888888887766466666666555145677777 PP

                            UPF0242 140 leeqLaek 147
                                        l e ++++
  gene1802|gene1802|rna1802|rna1802 100 LSESIDYE 107
                                        87777765 PP

>> Atg14  Vacuolar sorting 38 and autophagy-related subunit 14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   5.2   8.1e-05      0.16      59     137 ..      25     105 ..       3     164 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 8.1e-05
                              Atg14  59 edkiknkkakleelksliadlrerlqelkdklsqlkkeieekkkklakls..dklkkRrsdleslqneleerrkkq 132
                                         +k+ ++k++l ++ +l  +lre+++ l++  ++lk  i  k+k++a+ +  ++++ Rr +++ +++   +rrk++
  gene1802|gene1802|rna1802|rna1802  25 LEKLIKEKDNLVSQEKLNNSLREEVESLSKENRELKNDIIGKSKEIARIKkhSEVAIRRMKHDIASETCPKRRKEL 100
                                        3444444444555555555555555555555555555555555555432211333455555555555555555554 PP

                              Atg14 133 iaklq 137
                                         +++ 
  gene1802|gene1802|rna1802|rna1802 101 SESID 105
                                        44443 PP

>> Cep57_CLD_2  Centrosome localisation domain of PPC89
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   7.7   0.00061       1.2      19      64 ..      18      59 ..      13      71 .. 0.73
   2 ?   -2.9   0.0       3.7   7.3e+03      26      40 ..     135     149 ..     118     156 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00061
                        Cep57_CLD_2 19 lqvheeelkrLnkERdsalrqLgvAyeelneLkaevealrkELkeq 64
                                       +  ++e+l++L kE d+ ++q  +++  +n+L++eve+l kE++e 
  gene1802|gene1802|rna1802|rna1802 18 NKLNFELLEKLIKEKDNLVSQ--EKL--NNSLREEVESLSKENREL 59
                                       567899************997..333..456666666666666654 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 3.7
                        Cep57_CLD_2  26 lkrLnkERdsalrqL 40 
                                        +k +n   d +lr+L
  gene1802|gene1802|rna1802|rna1802 135 YKVVNDPKDDFLRRL 149
                                        455566677888887 PP

>> GBP_C  Guanylate-binding protein, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   5.3    0.0033       6.5     192     272 ..      28     109 ..      17     118 .. 0.85
   2 ?    5.3   0.0    0.0055        11      90     118 ..     138     166 ..     132     170 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0033
                              GBP_C 192 ilqtdkaltakekeieaeqakaeaaeaekelleekqkeeeqrmeakeksleehvkqLkekleeere.klleeqerl 266
                                        +++   +l+ +ek ++  +++ e++ +e+++l++    + ++++  +k+ e  ++++k+ + +e   k ++e  + 
  gene1802|gene1802|rna1802|rna1802  28 LIKEKDNLVSQEKLNNSLREEVESLSKENRELKNDIIGKSKEIARIKKHSEVAIRRMKHDIASETCpKRRKELSES 103
                                        45566789***************************************************99999876667777666 PP

                              GBP_C 267 lekklk 272
                                        ++ +lk
  gene1802|gene1802|rna1802|rna1802 104 IDYELK 109
                                        666655 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0055
                              GBP_C  90 fkdenqkFqkeLkeslekkkedflkknee 118
                                        ++d +++F ++L++s++  +++++k n+ 
  gene1802|gene1802|rna1802|rna1802 138 VNDPKDDFLRRLVDSIKDSHDNYIKMNQA 166
                                        7999*********************9986 PP

>> DUF2570  Protein of unknown function (DUF2570)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   4.7   0.00047      0.93      41      84 ..      16      62 ..       3      86 .. 0.74
   2 ?    0.6   0.3      0.25     5e+02      63      92 ..      66      95 ..      52     105 .. 0.65

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00047
                            DUF2570 41 eqqkanqrLteqLeqerqavekqqkianelkakvee...ekeevkti 84
                                       + +k n +L e+L +e+     q+k +n l+++ve    e+ e+k+ 
  gene1802|gene1802|rna1802|rna1802 16 NINKLNFELLEKLIKEKDNLVSQEKLNNSLREEVESlskENRELKND 62
                                       44677889************************998521145566654 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.25
                            DUF2570 63 qqkianelkakveeekeevktilkqesCak 92
                                       + k    +k++ e +  ++k  ++ e+C k
  gene1802|gene1802|rna1802|rna1802 66 KSKEIARIKKHSEVAIRRMKHDIASETCPK 95
                                       344445667777777777777777777765 PP

>> HALZ  Homeobox associated leucine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   1.0     0.079   1.6e+02      22      34 ..      26      38 ..      19      45 .. 0.80
   2 ?    9.9   1.0   0.00042      0.83      15      35 ..      43      63 ..      40      65 .. 0.86
   3 ?    0.6   0.1      0.35     7e+02       8      29 ..     144     165 ..     144     166 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.079
                               HALZ 22 dsLkkenekLkae 34
                                       + L ke+++L ++
  gene1802|gene1802|rna1802|rna1802 26 EKLIKEKDNLVSQ 38
                                       5899******998 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00042
                               HALZ 15 daLksdydsLkkenekLkael 35
                                       ++L+ +++sL ken++Lk+ +
  gene1802|gene1802|rna1802|rna1802 43 NSLREEVESLSKENRELKNDI 63
                                       589999999999999999865 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.35
                               HALZ   8 dvLKasYdaLksdydsLkkene 29 
                                        d L++  d+ k ++d+  k n+
  gene1802|gene1802|rna1802|rna1802 144 DFLRRLVDSIKDSHDNYIKMNQ 165
                                        5799999****99998666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1683  (0.0938703); expected 358.6 (0.02)
Passed bias filter:                      582  (0.0324614); expected 358.6 (0.02)
Passed Vit filter:                        88  (0.00490825); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 1323.47
//
Query:       gene1803|gene1803|rna1803|rna1803  [L=164]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-16   59.8   0.2    3.6e-16   58.8   0.2    1.5  1  Ribosomal_L11_N  Ribosomal protein L11, N-terminal domain
    8.7e-16   58.2   0.1    1.4e-15   57.6   0.1    1.3  1  Ribosomal_L11    Ribosomal protein L11, RNA binding domain


Domain annotation for each model (and alignments):
>> Ribosomal_L11_N  Ribosomal protein L11, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.8   0.2     4e-20   3.6e-16       5      64 ..      10      67 ..       6      68 .. 0.96

  Alignments for each domain:
  == domain 1  score: 58.8 bits;  conditional E-value: 4e-20
                    Ribosomal_L11_N  5 vkvvklrvpaGkAtpaPplGpaLGplGlnikkfckefnkaTkdkkglripVkitvyqdrs 64
                                       +k+v lr+ +G++ p+  l++++GplG+++k ++++++kaT d+k l+i V++ + +dr+
  gene1803|gene1803|rna1803|rna1803 10 IKYVSLRCVGGEV-PGATLAQKVGPLGIPAKVVGEDIKKATMDYKSLKINVRLAI-KDRK 67
                                       89***********.*****************************************.9997 PP

>> Ribosomal_L11  Ribosomal protein L11, RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.6   0.1   1.5e-19   1.4e-15       3      70 .]      74     142 ..      72     142 .. 0.91

  Alignments for each domain:
  == domain 1  score: 57.6 bits;  conditional E-value: 1.5e-19
                                        -SHHHHHHHHHTXSSXXSSTTTSXX..EEEEHHHHHHHHHHHGGGHTXS.SHHHHHHHHHHHHCTTTEEE CS
                      Ribosomal_L11   3 PptsylLkkaagiekgsgkpgketv..GtvslkqvyeIAkiKksdlnaalsleaavksilgtArsmGikV 70 
                                        P+t++l++ka++++++++k++k++   G+++l +v+eIA+++k  + ++ ++++++ ++lgt+ s+G+k+
  gene1803|gene1803|rna1803|rna1803  74 PSTATLILKALNEPPRDRKKEKNIKhtGSITLVDVVEIARAMKGRSLSN-EFKGTIMQVLGTCVSIGCKI 142
                                        9******************99973366****************655578.******************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       529  (0.0295053); expected 358.6 (0.02)
Passed bias filter:                      456  (0.0254337); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 1246.86
//
Query:       gene1804|gene1804|rna1804|rna1804  [L=242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (242 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       770  (0.0429472); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 1819.08
//
Query:       gene1805|gene1805|rna1805|rna1805  [L=238]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (238 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       376  (0.0209716); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1677.26
//
Query:       gene1806|gene1806|rna1806|rna1806  [L=222]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    7.2e-09   36.0   0.2    1.1e-08   35.4   0.2    1.2  1  HAD_2        Haloacid dehalogenase-like hydrolase
    0.00015   21.6   0.0       0.51   10.2   0.0    2.4  2  Acid_PPase   Acid Phosphatase
      0.002   18.5   0.0        1.1    9.4   0.0    2.1  2  Hydrolase    haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
      0.086   12.5   0.0       0.18   11.5   0.0    1.5  1  PNK3P        Polynucleotide kinase 3 phosphatase
       0.15   12.2   0.0       0.86    9.8   0.0    2.2  1  Hydrolase_6  Haloacid dehalogenase-like hydrolase
       0.16   12.4   0.0       0.32   11.4   0.0    1.6  1  HAD          haloacid dehalogenase-like hydrolase


Domain annotation for each model (and alignments):
>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.4   0.2   3.6e-12   1.1e-08       1     165 [.      30     194 ..      30     200 .. 0.66

  Alignments for each domain:
  == domain 1  score: 35.4 bits;  conditional E-value: 3.6e-12
                              HAD_2   1 iiFDlDgTlldteeliiqafnelleeygls.elseeelrkliglsl...rellrklgeseeeee..kieellrk.y 69 
                                        ++FDlD Tl+ te++i+  ++e + +y l+ ++ e++ r+l+   +   + +l+ l  +    +  +++e+ +  +
  gene1806|gene1806|rna1806|rna1806  30 LVFDLDSTLYQTENYIYRRIEECAIKY-LEiKFGEKKARNLMDSVSsisNSVLKGLLMT----NsiTYDEYHECiF 100
                                        58**********************999.4446666666666655440003444444443....2223444433202 PP

                              HAD_2  70 neekkkkevkpydgvkelLeeLkeagyklgivTsksreaveekleqlgiesyFd.vivtsedvekk..KPdpevie 142
                                           ++++ ++  d ++ lLe++   +  l i+++++++ v++ le lgie++F  v +++ d+++   KP+ + + 
  gene1806|gene1806|rna1806|rna1806 101 SMVNYEDLIRRDDRLIRLLENI---QKPLFIMSNGTKAHVKRVLEILGIEHLFRgVFYVGYDCGNYirKPSIRAFM 173
                                        2233335566666666666666...77**************************84568999999987798877665 PP

                              HAD_2 143 kaleklklkkeeviyvGDsptDi 165
                                        ++ + +   ++++ ++ D+++ i
  gene1806|gene1806|rna1806|rna1806 174 TVEKLT--RAKKIHFFDDKQRNI 194
                                        543333..334456666666555 PP

>> Acid_PPase  Acid Phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.0   0.00026      0.79       4      22 ..      28      46 ..      26      94 .. 0.81
   2 !   10.2   0.0   0.00017      0.51     123     151 ..     180     208 ..     101     217 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00026
                                       SEEEE-STTTSSSS-TTTS CS
                         Acid_PPase  4 klivFDLDyTLWpfevdtl 22
                                       +++vFDLD TL + e +++
  gene1806|gene1806|rna1806|rna1806 28 EILVFDLDSTLYQTENYIY 46
                                       579**********999987 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00017
                                        -GGGEEEEES-HHHHHHHHTTT-EEEE-S CS
                         Acid_PPase 123 eyedmlfFDdesrnievesrlgvtfvlvp 151
                                        + +++ fFDd++rni+  + l  + + v+
  gene1806|gene1806|rna1806|rna1806 180 RAKKIHFFDDKQRNIDIAALLKWVGYTVD 208
                                        678999*********99887776666664 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.0   0.00038       1.1       3      26 ..      29      52 ..      28      90 .. 0.79
   2 !    7.2   0.0    0.0018       5.4     130     204 ..     119     197 ..     106     201 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00038
                                       EEEEESBTTTBCHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx RF
                          Hydrolase  3 tvvfDkdGTLttgepsvedvivsa 26
                                        +vfD+d TL+++e+ + + i++ 
  gene1806|gene1806|rna1806|rna1806 29 ILVFDLDSTLYQTENYIYRRIEEC 52
                                       58************8777766665 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0018
                                        HHHTTEEEEEEESSEHHHHHHHHHHTT.GGGE.SEEEEHHCES..STTTSHHHHHHHHHHHTSTGGGEEEEESSHH CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxx.xxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          Hydrolase 130 LkaagievvlltgdnpetaeraanqlG.ddyf.daviasdiet..vakpspegkvaaireLqgkpeevamVGDgvn 201
                                        L     ++++++++ +++++r+++ lG ++ f  + + +++ +  + kps +++  + +  ++k+  + +++D   
  gene1806|gene1806|rna1806|rna1806 119 LENIQKPLFIMSNGTKAHVKRVLEILGiEHLFrGVFYVGYDCGnyIRKPSIRAFMTVEKLTRAKK--IHFFDDKQR 192
                                        44445579*******************99888777777777778888888877776666666666..777777655 PP

                                        ..HHH CS
                                        ..xxx RF
                          Hydrolase 202 ..Daa 204
                                          D+a
  gene1806|gene1806|rna1806|rna1806 193 niDIA 197
                                        24444 PP

>> PNK3P  Polynucleotide kinase 3 phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   5.9e-05      0.18       2     108 ..      29     177 ..      28     192 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 5.9e-05
                              PNK3P   2 iaaFDlDstliktksgkefakdaddwkllses........vlekLkklkeegykivifsNqggvvek.......kt 62 
                                        i +FDlDstl +t++    + ++   k+l+ +        +++++++  +   k ++++N     e         +
  gene1806|gene1806|rna1806|rna1806  29 ILVFDLDSTLYQTENYIYRRIEECAIKYLEIKfgekkarnLMDSVSSISNSVLKGLLMTNSITYDEYhecifsmVN 104
                                        889***********98777777777777666544555666777777777777888999998887776767755555 PP

                              PNK3P  63 kkslekfkekieallkeldvpllvyaatkk...........................dkyRKPetGmweelkk 108
                                         ++l +  +++ +ll++++ pl++     k                           + +RKP++  + +++k
  gene1806|gene1806|rna1806|rna1806 105 YEDLIRRDDRLIRLLENIQKPLFIMSNGTKahvkrvleilgiehlfrgvfyvgydcgNYIRKPSIRAFMTVEK 177
                                        5566666677888888889999988776667899999999999999999999998888999998876666655 PP

>> Hydrolase_6  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   0.00029      0.86      11      51 ..     104     144 ..      30     151 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00029
                                        ETTEE-TTHHHHHHHHHHTT-EEEEEE---SS-HHHHHHHH CS
                        Hydrolase_6  11 rgdkaipgaaealnalraagkpvvllTNnsskseeeyakkl 51 
                                        + +++i   +++++ l++ +kp+++++N+++ + + +++ l
  gene1806|gene1806|rna1806|rna1806 104 NYEDLIRRDDRLIRLLENIQKPLFIMSNGTKAHVKRVLEIL 144
                                        66778888899*******************99998888876 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00011      0.32       2     130 ..      31     152 ..      30     197 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00011
                                HAD   2 lfDfDgTLldgdsle..lllrfllrrgaprlwralreklllalfrellrldraglaelleallaglseelaaeler 75 
                                        +fD+D TL +++ ++   + +  ++  + + ++  ++ l+ ++ ++++ +       +l  ll   s   ++++e 
  gene1806|gene1806|rna1806|rna1806  31 VFDLDSTLYQTENYIyrRIEECAIKYLEIKFGEKKARNLMDSV-SSISNS-------VLKGLLMTNSITYDEYHEC 98 
                                        8**********66666766666666666666666666666666.555555.......3333333333333333333 PP

                                HAD  76 fvaevirpkl..ldpgalellaahraaGdrvvvvSgglrplvepllaelgadevlat 130
                                        ++  v  + l   d  + +ll+       ++ + S+g +  v+++l+ lg++++   
  gene1806|gene1806|rna1806|rna1806  99 IFSMVNYEDLirRDDRLIRLLE---NIQKPLFIMSNGTKAHVKRVLEILGIEHLFRG 152
                                        3322222223114458888888...77779********************8887666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       524  (0.0292264); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 1459.49
//
Query:       gene1807|gene1807|rna1807|rna1807  [L=225]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (225 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       281  (0.0156729); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1662.87
//
Query:       gene1808|gene1808|rna1808|rna1808  [L=149]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.6e-15   56.5   0.1      5e-15   56.0   0.1    1.1  1  HIT       HIT domain
    0.00079   19.9   0.0     0.0012   19.4   0.0    1.2  1  DcpS_C    Scavenger mRNA decapping enzyme C-term binding
     0.0024   17.7   0.0      0.003   17.4   0.0    1.1  1  CwfJ_C_1  Protein similar to CwfJ C-terminus 1


Domain annotation for each model (and alignments):
>> HIT  HIT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.0   0.1   8.3e-19     5e-15       6      95 ..      11      98 ..       8     101 .. 0.95

  Alignments for each domain:
  == domain 1  score: 56.0 bits;  conditional E-value: 8.3e-19
                                       CCEEEE-SSEEEEE-SS-SSSSEEEEEESSTGCSGGGCCHHHHHHHHHHHHHHHHHHHTCTTCCCEEEEEEESGGGT- CS
                                HIT  6 stvvyeddlvlafldidpkapghlLvipkkhlselhdlteeelakllsavkkvakalqkkfknkglrvvinngahagq 83
                                       +++v e+  +++f++ +p  + hlLv p + +  l d++e   a+l+ +++ ++ka++    +k ++++ ++g++agq
  gene1808|gene1808|rna1808|rna1808 11 EHIVAETASTFVFVNLRPFLKYHLLVSPIQPAISLRDMSEVQTADLFNTARICMKAFEF--YAKDFTMTLQDGEAAGQ 86
                                       68999****************************************************96..78999************ PP

                                       SSSS-EEEEEEC CS
                                HIT 84 svahlHiHvipr 95
                                       +v+h+HiH+ipr
  gene1808|gene1808|rna1808|rna1808 87 TVPHVHIHLIPR 98
                                       **********98 PP

>> DcpS_C  Scavenger mRNA decapping enzyme C-term binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   1.9e-07    0.0012      13     100 ..      10      96 ..       2     104 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 1.9e-07
                                        -B-EEEE-SSEEEEE-SS-SSSEEEEEEESS---SGGG--TTTTTHHHHHHHHHHHHHHHTT-T-EEEEE--SCCC CS
                             DcpS_C  13 pervvyedekfvvlkDikpkaklhllvipkrdikslrdLtkehlpllkemrekakkvieekynevdaeelrvgvhy 88 
                                        +e +v e+ ++ v+  ++p  k+hllv p +   slrd+++ +   l +  +   k+  e y +   + l+ g  +
  gene1808|gene1808|rna1808|rna1808  10 EEHIVAETASTFVFVNLRPFLKYHLLVSPIQPAISLRDMSEVQTADLFNTARICMKAF-EFYAKDFTMTLQDGEAA 84 
                                        4566889999*********************999999998777776666666666666.45656778999****** PP

                                        T--S-S--EEEE CS
                             DcpS_C  89 qPsvyhlHlHvi 100
                                         ++v h+H+H+i
  gene1808|gene1808|rna1808|rna1808  85 GQTVPHVHIHLI 96 
                                        **********98 PP

>> CwfJ_C_1  Protein similar to CwfJ C-terminus 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0     5e-07     0.003      23     108 ..       8      97 ..       3     112 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 5e-07
                                        --SS--S-B-SSEEEE---S-SSTT-EEEEESS--SSTTSS-H....HHHHHHHHHHHHHHHHHHHTT--EEEEEE CS
                           CwfJ_C_1  23 lekhlivsignkvYlalpkgpLssgHvliipieHisallslde....evldeirkfrkalvkmykkqdkdavvfEi 94 
                                         +++ iv+   ++++ +   p  ++H+l+ pi+ + +l+ ++e    ++ +  r  +ka+    k + + +   E 
  gene1808|gene1808|rna1808|rna1808   8 IPEEHIVAETASTFVFVNLRPFLKYHLLVSPIQPAISLRDMSEvqtaDLFNTARICMKAFEFYAKDFTMTLQDGEA 83 
                                        6778899999****************************99999633344444444444444444555555556688 PP

                                        -SSS-----EEEEE CS
                           CwfJ_C_1  95 ssersvHlaiqvip 108
                                        + +  +H++i++ip
  gene1808|gene1808|rna1808|rna1808  84 AGQTVPHVHIHLIP 97 
                                        89***********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       263  (0.014669); expected 358.6 (0.02)
Passed bias filter:                      241  (0.0134419); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 1144.76
//
Query:       gene1809|gene1809|rna1809|rna1809  [L=394]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.4e-15   56.6  14.1     0.0018   19.1   0.0    8.2  8  WD40       WD domain, G-beta repeat
    3.3e-09   36.5  19.4    0.00066   19.1   7.4    3.3  2  WD40_like  WD40-like domain
    0.00048   20.5   2.1         28    5.4   0.1    4.9  5  PQQ_3      PQQ-like domain
     0.0097   16.2   0.7      0.098   13.0   0.2    2.5  2  Ig_2       Immunoglobulin domain
  ------ inclusion threshold ------
      0.033   14.2   5.1        1.9    8.6   1.1    4.1  5  BBS2_Mid   Ciliary BBSome complex subunit 2, middle region
      0.041   14.4   0.3       0.12   12.9   0.3    1.8  1  NLE        NLE (NUC135) domain
       0.13   12.4   0.3         18    5.4   0.1    2.7  2  AMOP       AMOP domain


Domain annotation for each model (and alignments):
>> WD40  WD domain, G-beta repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       4.4   1.1e+04       7      16 ..      48      57 ..      43      73 .. 0.71
   2 !   14.9   0.4   1.5e-05     0.038       3      38 .]      87     121 ..      86     121 .. 0.91
   3 ?    1.9   0.0      0.19   4.8e+02      22      38 .]     145     161 ..     126     161 .. 0.72
   4 !   19.1   0.0   6.9e-07    0.0018       3      37 ..     166     199 ..     164     200 .. 0.84
   5 !    6.2   0.0     0.008        21       2      37 ..     211     244 ..     210     245 .. 0.78
   6 !    7.7   0.2    0.0028       7.2      12      33 ..     290     313 ..     249     322 .. 0.79
   7 !    6.9   0.0    0.0051        13      12      37 ..     331     354 ..     316     355 .. 0.70
   8 ?    0.8   0.0      0.42   1.1e+03      19      37 ..     375     393 ..     361     394 .] 0.72

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 4.4
                                       EESSSSE.EEE CS
                               WD40  7 ltGHssv.tsl 16
                                       ++GH  + ++l
  gene1809|gene1809|rna1809|rna1809 48 YSGH-IItNDL 57
                                       7899.333344 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 1.5e-05
                                        EEEEEESS.SSEEEEEEETTSSEEEEEETTSEEEEEE CS
                               WD40   3 clrtltGH.ssvtslafspdgawlasGsdDgtvriWd 38 
                                        c  +++GH s v ++a + +  + + G+ D tvr Wd
  gene1809|gene1809|rna1809|rna1809  87 CSSSFSGHeSAVLAVACDGNDVF-TVGG-DATVRKWD 121
                                        7899****888****99999999.66**.*******9 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.19
                                        SSEEEEEETTSEEEEEE CS
                               WD40  22 gawlasGsdDgtvriWd 38 
                                        ++++++G++D  v ++d
  gene1809|gene1809|rna1809|rna1809 145 NNMVFTGGMDAQVCVFD 161
                                        34489********9998 PP

  == domain 4  score: 19.1 bits;  conditional E-value: 6.9e-07
                                        EEEEEESS.SSEEEEEEETTSSE...EEEEETTSEEEEE CS
                               WD40   3 clrtltGH.ssvtslafspdgaw...lasGsdDgtvriW 37 
                                        +l t++GH +++t++     g     ++++s+D+tvr+W
  gene1809|gene1809|rna1809|rna1809 166 LLCTIRGHsNGITGI-----GEIeemIVTSSRDKTVRFW 199
                                        68899***8889999.....666777999********** PP

  == domain 5  score: 6.2 bits;  conditional E-value: 0.008
                                        EEEEEEESSSS.EEEEEEETTSSEEEEEETTSEEEEE CS
                               WD40   2 qclrtltGHss.vtslafspdgawlasGsdDgtvriW 37 
                                        +c++t+ +H++ v+++ ++ +  +  s s+D +v+i+
  gene1809|gene1809|rna1809|rna1809 211 ECVYTY-AHDGiVNGIYVHNSRIY--SYSKDSSVKIY 244
                                        799999.8*5558***77666666..6799*****98 PP

  == domain 6  score: 7.7 bits;  conditional E-value: 0.0028
                                        S.EEEEEEETTSSEEEEEE.TTSE CS
                               WD40  12 s.vtslafspdgawlasGs.dDgt 33 
                                        + ++s+++s++g ++a+Gs  ++t
  gene1809|gene1809|rna1809|rna1809 290 NlISSIDVSQNGIYFATGSfSKKT 313
                                        2588999***********722444 PP

  == domain 7  score: 6.9 bits;  conditional E-value: 0.0051
                                        SEEEEEEETTSSE....EEEEETTSEEEEE CS
                               WD40  12 svtslafspdgaw....lasGsdDgtvriW 37 
                                        sv+ +      ++    + s+s+D+t++i+
  gene1809|gene1809|rna1809|rna1809 331 SVYKV------KMvsymVYSSSKDKTIKIF 354
                                        45555......4433335699********7 PP

  == domain 8  score: 0.8 bits;  conditional E-value: 0.42
                                        ETTSSEEEEEETTSEEEEE CS
                               WD40  19 spdgawlasGsdDgtvriW 37 
                                        + +g  ++++++Dg v+++
  gene1809|gene1809|rna1809|rna1809 375 DLHGEKVVAACKDGRVYFF 393
                                        445555778899**99875 PP

>> WD40_like  WD40-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   7.4   2.6e-07   0.00066      56     214 ..     108     274 ..      69     287 .. 0.66
   2 !   18.1   3.8   5.2e-07    0.0013       3     107 ..     292     393 ..     290     394 .] 0.90

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 2.6e-07
                          WD40_like  56 ilvvtlDGtill..slleneeevenekieedistvkviddklliGtnkGsiyvfskdlqleevllgqsseIkeiki 129
                                        +  v  D t+ +   ++++++++++e+    i +vk++++ +  G+   ++ vf+kdl+l  ++ g+s  I  i  
  gene1809|gene1809|rna1809|rna1809 108 VFTVGGDATVRKwdFDMKLQKKISKEHT-HWIQVVKILNNMVFTGGMDAQVCVFDKDLNLLCTIRGHSNGITGIGE 182
                                        4555555555431145777777776654.579******************************************99 PP

                          WD40_like 130 ennkiysLsesafivf...dlfsqnieykisv....kdiktfeiienkdilligtegeililkknvilqkidvegk 198
                                        ++++i + s ++ + f     ++++iey+  +     +i +   ++n+ i   +++++++i+ k   +++i+++++
  gene1809|gene1809|rna1809|rna1809 183 IEEMIVTSSRDKTVRFwqkKDKNEKIEYECVYtyahDGIVNGIYVHNSRIYSYSKDSSVKIYEKMRYVTEIKTNSS 258
                                        9777777777777766211112222332221111102233333346777777777777777777777777777777 PP

                          WD40_like 199 PecillvddylivGgs 214
                                         +++   ++ + +G++
  gene1809|gene1809|rna1809|rna1809 259 INTLKAHEKDVYIGCE 274
                                        6666666666666665 PP

  == domain 2  score: 18.1 bits;  conditional E-value: 5.2e-07
                          WD40_like   3 iYsidiskkgslilyGgkddkctvlkleslesvsivesfedSvifvklldddlilvvtlDGtillslleneeeven 78 
                                        i sid+s++g +++ G+ ++k  v++++ +  +    +f dSv  vk+++  ++   + D ti    l+ +++v++
  gene1809|gene1809|rna1809|rna1809 292 ISSIDVSQNGIYFATGSFSKKTCVYTTDGDL-IAEYMHF-DSVYKVKMVSYMVY-SSSKDKTIKIFSLKTKKVVST 364
                                        669**********************998665.5444455.9********97655.7899***************** PP

                          WD40_like  79 ekieedistvkviddklliGtnkGsiyvf 107
                                           ++++   +  ++k++   + G +y f
  gene1809|gene1809|rna1809|rna1809 365 LICKDEVYDFDLHGEKVVAACKDGRVYFF 393
                                        ***************************99 PP

>> PQQ_3  PQQ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.1     0.011        28      17      37 ..     101     121 ..      85     123 .. 0.82
   2 ?    3.5   0.0     0.043   1.1e+02      22      38 ..     146     162 ..     143     163 .. 0.89
   3 ?    4.4   0.0     0.022        56      24      34 ..     269     279 ..     254     280 .. 0.87
   4 ?   -1.7   0.0       1.8   4.6e+03      22      34 ..     300     323 ..     291     324 .. 0.59
   5 ?    2.2   0.0      0.11   2.8e+02      20      36 ..     377     393 ..     359     394 .] 0.81

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.011
                              PQQ_3  17 pavdgglvyvgtgdGtlyAlD 37 
                                        +a dg+ v++++gd t++  D
  gene1809|gene1809|rna1809|rna1809 101 VACDGNDVFTVGGDATVRKWD 121
                                        4889************98776 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.043
                              PQQ_3  22 glvyvgtgdGtlyAlDa 38 
                                        + v++g++d  ++ +D 
  gene1809|gene1809|rna1809|rna1809 146 NMVFTGGMDAQVCVFDK 162
                                        68*************96 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.022
                              PQQ_3  24 vyvgtgdGtly 34 
                                        vy+g++dG++y
  gene1809|gene1809|rna1809|rna1809 269 VYIGCEDGSVY 279
                                        9*********9 PP

  == domain 4  score: -1.7 bits;  conditional E-value: 1.8
                              PQQ_3  22 glvyvgtg...........dGtly 34 
                                        + +y++tg           dG l 
  gene1809|gene1809|rna1809|rna1809 300 NGIYFATGsfskktcvyttDGDLI 323
                                        556777765555555555566665 PP

  == domain 5  score: 2.2 bits;  conditional E-value: 0.11
                              PQQ_3  20 dgglvyvgtgdGtlyAl 36 
                                         g +v++++ dG++y +
  gene1809|gene1809|rna1809|rna1809 377 HGEKVVAACKDGRVYFF 393
                                        57889999999999977 PP

>> Ig_2  Immunoglobulin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.31   7.9e+02      47      69 ..     198     220 ..     162     224 .. 0.72
   2 !   13.0   0.2   3.8e-05     0.098      34      66 ..     279     310 ..     274     318 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.31
                               Ig_2  47 finavsaedsgtYtCrarntkgg 69 
                                        f +++  + +  Y C++++ + g
  gene1809|gene1809|rna1809|rna1809 198 FWQKKDKNEKIEYECVYTYAHDG 220
                                        336677777778*****997755 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 3.8e-05
                               Ig_2  34 ykggevinsspnffinavsaedsgtYtCrarnt 66 
                                        yk+++vi ++ n +i+++ ++++g+Y+ + + +
  gene1809|gene1809|rna1809|rna1809 279 YKNNSVIAKQNN-LISSIDVSQNGIYFATGSFS 310
                                        9***********.**************998754 PP

>> BBS2_Mid  Ciliary BBSome complex subunit 2, middle region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.58   1.5e+03      39      67 ..     134     162 ..      95     170 .. 0.53
   2 ?    2.7   0.4     0.049   1.3e+02      14      78 ..     186     205 ..     135     223 .. 0.69
   3 ?    8.6   1.1   0.00073       1.9      13     103 ..     185     276 ..     174     281 .. 0.63
   4 ?    7.6   0.1    0.0015       3.8      19      62 ..     236     278 ..     222     300 .. 0.84
   5 ?    2.8   0.0     0.046   1.2e+02      21     105 ..     348     390 ..     305     394 .] 0.61

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.58
                           BBS2_Mid  39 tekvvslarlekerfayaleNGtvgvyek 67 
                                        + + ++++++ ++   ++     v v++k
  gene1809|gene1809|rna1809|rna1809 134 HTHWIQVVKILNNMVFTGGMDAQVCVFDK 162
                                        44444455554444444444445555544 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.049
                           BBS2_Mid  14 eLvvgsddfeirvfkeeelvaeitetekvvslarlekerfayaleNGtvgvyekkerlWrvkskn 78 
                                         +v +s d ++r +++++                                             kn
  gene1809|gene1809|rna1809|rna1809 186 MIVTSSRDKTVRFWQKKD---------------------------------------------KN 205
                                        344445555555555443.............................................33 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.00073
                           BBS2_Mid  13 neLvvgsddfeirvfkee....elvaeit...etekvvslarlekerfayaleNGtvgvyekkerlWrvksknevv 81 
                                        + +v +s d ++r ++++    ++  e+     ++ +v+ + ++++r+    +  +v++yek+  + ++k+++++ 
  gene1809|gene1809|rna1809|rna1809 185 EMIVTSSRDKTVRFWQKKdkneKIEYECVytyAHDGIVNGIYVHNSRIYSYSKDSSVKIYEKMRYVTEIKTNSSIN 260
                                        5566677888888876541111455554311245667777777888877777788888888888888888888887 PP

                           BBS2_Mid  82 alaaydingdgtkelivgwsnG 103
                                         l+a++ +      + +g+++G
  gene1809|gene1809|rna1809|rna1809 261 TLKAHEKD------VYIGCEDG 276
                                        77776654......44454444 PP

  == domain 4  score: 7.6 bits;  conditional E-value: 0.0015
                           BBS2_Mid  19 sddfeirvfkeeelvaeitetekvvslarlekerfayaleNGtv 62 
                                        s+d +++++++ + v+ei++++ + +l++  +++  ++ e G+v
  gene1809|gene1809|rna1809|rna1809 236 SKDSSVKIYEKMRYVTEIKTNSSINTLKAH-EKDVYIGCEDGSV 278
                                        899******************999999874.5566777787775 PP

  == domain 5  score: 2.8 bits;  conditional E-value: 0.046
                           BBS2_Mid  21 dfeirvfkeeelvaeitetekvvslarlekerfayaleNGtvgvyekkerlWrvksknevvalaaydingd...gt 93 
                                        d +i++                                              + k+k+ v  l++ d+  d     
  gene1809|gene1809|rna1809|rna1809 348 DKTIKI---------------------------------------------FSLKTKKVVSTLICKDEVYDfdlHG 378
                                        444444.............................................4444444444444433321111133 PP

                           BBS2_Mid  94 kelivgwsnGkl 105
                                        ++++ ++++G++
  gene1809|gene1809|rna1809|rna1809 379 EKVVAACKDGRV 390
                                        445555555554 PP

>> NLE  NLE (NUC135) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.3   4.8e-05      0.12       1      36 [.       9      40 ..       9      42 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 4.8e-05
                                NLE  1 vqvrFvtkdedeslavpgtplsvPasltrkqLselv 36
                                       v ++F + +  e++    ++++vP++++r qL el+
  gene1809|gene1809|rna1809|rna1809  9 VVIQFYDTST-ETT---SQSFQVPVKIRRTQLLELL 40
                                       789*****53.466...***************9987 PP

>> AMOP  AMOP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0     0.025        64      38      89 ..     119     170 ..     113     184 .. 0.81
   2 ?    5.4   0.1    0.0072        18      72     130 ..     301     367 ..     266     390 .. 0.72

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.025
                               AMOP  38 rfrpdleCdasrdkeciykkgavhcvrsvqssesgagqqCCYdeegklllta 89 
                                        ++  d++ +++ +ke ++  + v+ ++++  +  + +q+C +d++ +ll t 
  gene1809|gene1809|rna1809|rna1809 119 KWDFDMKLQKKISKEHTHWIQVVKILNNMVFTGGMDAQVCVFDKDLNLLCTI 170
                                        677778888888888888899999999999999999***********99774 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0072
                               AMOP  72 g........agqqCCYdeegkllltadslsggtptraheagtppyksaekvpelShflvDvlpfilC 130
                                        g        ++++C Y+++g l+  + ++ + +  +  ++ ++   + +++  +S  ++ v++ ++C
  gene1809|gene1809|rna1809|rna1809 301 GiyfatgsfSKKTCVYTTDGDLIAEYMHFDSVYKVKMVSYMVYSSSKDKTIKIFSLKTKKVVSTLIC 367
                                        244455555899***********88888888887777777777777888888888888888888888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (394 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       963  (0.0537119); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 2682.90
//
Query:       gene181|gene181|rna181|rna181  [L=190]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.049   14.0   0.0      0.073   13.4   0.0    1.3  1  RNA_pol_Rpb4  RNA polymerase Rpb4
        0.1   12.4   0.6       0.24   11.2   0.3    1.7  2  DUF3836       Family of unknown function (DUF3836)
       0.11   12.1   1.0        1.5    8.4   0.6    2.1  2  GXGXG         GXGXG motif


Domain annotation for each model (and alignments):
>> RNA_pol_Rpb4  RNA polymerase Rpb4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   1.2e-05     0.073      79     121 ..       2      76 ..       1      78 [. 0.87

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.2e-05
                                    HHHHHHHHHCSTSSHHHHHHHSTTGTT................................TSTSHHHHHHHHHHHH CS
                   RNA_pol_Rpb4  79 kaEklqlvnlkPesavelktlieelee................................rfedeqleeiLdelke 121
                                    k  +l+l+n+kP ++++l ++i ++ +                                  + ++ +eiL+ +++
  gene181|gene181|rna181|rna181   2 KDSVLNLINIKPANLDNLGSVITKCTYfsfdtflyalssgkiylndmrvclqsrrthqfSYQPDNYKEILSAVSD 76 
                                    56789*********************9999999999999999999999888888888666688999999998887 PP

>> DUF3836  Family of unknown function (DUF3836)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.25   1.5e+03      45      69 ..      40      65 ..      37      76 .. 0.63
   2 ?   11.2   0.3     4e-05      0.24      15      68 ..      77     130 ..      66     139 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.25
                                   EEEEEEEE.TTEEEEEEEEEEEEETT CS
                        DUF3836 45 sktvyked.gklLtnklkYeYkyddq 69
                                   s ++y +d    L+    ++++y  +
  gene181|gene181|rna181|rna181 40 SGKIYLNDmRVCLQSRRTHQFSYQPD 65
                                   56788888555677666666555433 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 4e-05
                                    XXXXXXXXXXXTTTTEECEEEEEEETTEEEEEEEEEEETTEEEEEEEEEEEEET CS
                        DUF3836  15 vllvtsltasaaaneknfiyneeeenglvvsktvykedgklLtnklkYeYkydd 68 
                                    + +v   ++ a++ ++ ++y+++++ + v++ +v+k+d k +++ +  e  y+ 
  gene181|gene181|rna181|rna181  77 ISVVDDHSFVARNLNTVILYDTRNDRSCVSTYEVFKADAKSVQRVCNLELVYER 130
                                    566666778888889999************************999988887776 PP

>> GXGXG  GXGXG motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0     0.026   1.5e+02      93     109 ..      32      48 ..      21      58 .. 0.87
   2 ?    8.4   0.6   0.00025       1.5      97     127 ..     142     172 ..     132     186 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.026
                                    SSTTTT--SEEEEESSB CS
                          GXGXG  93 nvvlygatgGklfirgk 109
                                    ++ ly+  +Gk++++++
  gene181|gene181|rna181|rna181  32 DTFLYALSSGKIYLNDM 48 
                                    799**********9986 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00025
                                    TT--SEEEEESSB--SSTTTT-SS-EEEESE CS
                          GXGXG  97 ygatgGklfirgkageRfavrnsgatavveg 127
                                     g  +G+ ++ g+ geR++v+ +g+  v++ 
  gene181|gene181|rna181|rna181 142 TGDFDGNFYVFGRDGERVSVKGEGVAKVIGC 172
                                    57789*******************9999975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (190 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       507  (0.0282782); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1318.83
//
Query:       gene1810|gene1810|rna1810|rna1810  [L=221]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      0.003   17.8   0.1     0.0045   17.2   0.1    1.2  1  Ricin_B_lectin  Ricin-type beta-trefoil lectin domain
  ------ inclusion threshold ------
      0.063   13.2   0.1        0.1   12.5   0.1    1.2  1  Big_2           Bacterial Ig-like domain (group 2)


Domain annotation for each model (and alignments):
>> Ricin_B_lectin  Ricin-type beta-trefoil lectin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.1     5e-07    0.0045      28      96 ..     100     173 ..      84     180 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 5e-07
                                        EEE-TSCCGG.GEEEEETT..SEEEETT.TTEEEEES.....SSSTTSBEEEEETTTTSGGGCEEEETTTTEEEET CS
                     Ricin_B_lectin  28 lydChgskgk.Qlwtltkd..geirskaqselCldvs.....staegakvvlakChkgkgnqrWefdkdgtqirhk 95 
                                        +  C+ +++k   wt+t++  ge+    ++++Cl+        +++g ++ ++kC+ + +n +W++ +   +i++ 
  gene1810|gene1810|rna1810|rna1810 100 VVACDIATNKnTEWTVTNKsgGEVIE--TDGFCLTKDeldtrMETRGYRLSVEKCS-KASNYMWKISEVDPMIYNG 172
                                        456777766679*****653344333..59****99899998999**********9.899******9999999997 PP

                                        T CS
                     Ricin_B_lectin  96 k 96 
                                        +
  gene1810|gene1810|rna1810|rna1810 173 N 173
                                        6 PP

>> Big_2  Bacterial Ig-like domain (group 2)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   1.1e-05       0.1       7      50 ..      84     125 ..      82     128 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.1e-05
                                        EEEC-CEEETT-EEEEEEEEESTT-S---EEEEECC-SSEEEET CS
                              Big_2   7 vsptevtvkkgatqqltvevtpssasdkkvtwtssngsvAtVsa 50 
                                        +  ++++ k g++ +++v  + +++++  ++wt++n+s ++V  
  gene1810|gene1810|rna1810|rna1810  84 IVNEKAICKAGENNDMVVACDIATNKN--TEWTVTNKSGGEVIE 125
                                        55678999****************887..*********999974 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       316  (0.0176251); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1658.68
//
Query:       gene1811|gene1811|rna1811|rna1811  [L=49]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (49 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       358  (0.0199677); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.25s 00:00:00.59 Elapsed: 00:00:00.40
# Mc/sec: 365.39
//
Query:       gene1812|gene1812|rna1812|rna1812  [L=889]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.2e-22   78.9   6.0    8.6e-11   41.8   0.0    4.6  5  PAH             Paired amphipathic helix repeat
    7.6e-14   51.6   0.4    3.4e-13   49.5   0.1    2.2  2  Sin3_corepress  Sin3 family co-repressor
    0.00047   20.0  14.7    0.00062   19.6   0.0    4.2  5  Sin3a_C         C-terminal domain of Sin3a protein


Domain annotation for each model (and alignments):
>> PAH  Paired amphipathic helix repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.22   1.3e+03      11      35 ..     157     192 ..     157     193 .. 0.78
   2 !   41.8   0.0   1.4e-14   8.6e-11       2      45 .]     194     237 ..     193     237 .. 0.98
   3 !   27.7   0.4   3.8e-10   2.3e-06       3      44 ..     353     392 ..     351     393 .. 0.95
   4 !    8.4   0.4   0.00039       2.3       2      23 ..     413     434 ..     412     453 .. 0.83
   5 ?   -3.2   0.0       1.7     1e+04      26      34 ..     749     757 ..     734     759 .. 0.73

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.22
                                PAH  11 hdyqke.qidske..........VyeqVskLFhdhp 35 
                                        +dyqk+  i++k             e V+  F+d+p
  gene1812|gene1812|rna1812|rna1812 157 NDYQKDfIINKKKedlnlndaisFLETVKTVFADDP 192
                                        689999877666667888888888888999999988 PP

  == domain 2  score: 41.8 bits;  conditional E-value: 1.4e-14
                                PAH   2 vYkeFLdiLhdyqkeqidskeVyeqVskLFhdhpdLlreFnqFL 45 
                                        +Y++FL++++dy+  +id  +V+     LF++ pd l++Fn FL
  gene1812|gene1812|rna1812|rna1812 194 IYDSFLEVMRDYKHGKIDAGGVVRAATTLFKGKPDILEGFNDFL 237
                                        8******************************************8 PP

  == domain 3  score: 27.7 bits;  conditional E-value: 3.8e-10
                                PAH   3 YkeFLdiLhdyqkeqidskeVyeqVskLFhdhpdLlreFnqF 44 
                                        YkeF++ L  yqk +   + V ++++k++ d+ dL++eF +F
  gene1812|gene1812|rna1812|rna1812 353 YKEFIEALTHYQKTK--DELVLAKIKKILGDNRDLIDEFLTF 392
                                        ************998..788********************99 PP

  == domain 4  score: 8.4 bits;  conditional E-value: 0.00039
                                PAH   2 vYkeFLdiLhdyqkeqidskeV 23 
                                        vY+eFL+ ++ ++++    ke+
  gene1812|gene1812|rna1812|rna1812 413 VYEEFLKAMNLFNQKLMEGKEL 434
                                        8************987666665 PP

  == domain 5  score: -3.2 bits;  conditional E-value: 1.7
                                PAH  26 qVskLFhdh 34 
                                         V++L+++h
  gene1812|gene1812|rna1812|rna1812 749 DVVDLLKGH 757
                                        588899888 PP

>> Sin3_corepress  Sin3 family co-repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0      0.91   5.5e+03      47      60 ..     405     418 ..     387     421 .. 0.73
   2 !   49.5   0.1   5.7e-17   3.4e-13       6      92 ..     482     563 ..     479     569 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.91
                     Sin3_corepress  47 sfkasrknqyeeal 60 
                                        +++ + kn yee l
  gene1812|gene1812|rna1812|rna1812 405 KKILEAKNVYEEFL 418
                                        3566789****987 PP

  == domain 2  score: 49.5 bits;  conditional E-value: 5.7e-17
                     Sin3_corepress   6 sYrlLpksyqqpkcsgrdelekevLNdewvsvptwasedsgsfkasrknqyeealfrcEderyelDmvieanrsti 81 
                                        sYr ++++      s++d+l+k+vLN+ + s+p  ase+++  +  ++++y e+l+r+Ederye++++ie+ +s i
  gene1812|gene1812|rna1812|rna1812 482 SYRIYKDKG---FRSNQDALSKQVLNHVCYSFPLYASEEED--VQFKRSAYMETLYRLEDERYEIELLIERGESLI 552
                                        555555552...3589*******************999994..666****************************** PP

                     Sin3_corepress  82 klleelakkie 92 
                                         ++e + ++ +
  gene1812|gene1812|rna1812|rna1812 553 FSFEVFLNSER 563
                                        99998877655 PP

>> Sin3a_C  C-terminal domain of Sin3a protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.1      0.14   8.2e+02      63      88 ..     187     212 ..     151     215 .. 0.66
   2 ?   -2.2   0.1      0.46   2.7e+03      63      82 ..     406     425 ..     331     434 .. 0.65
   3 ?   -0.7   0.1      0.16   9.5e+02      11      26 ..     728     743 ..     721     745 .. 0.90
   4 !   19.6   0.0     1e-07   0.00062      79     119 ..     751     793 ..     744     799 .. 0.85
   5 !    6.6   1.7   0.00091       5.4     198     285 ..     814     875 ..     794     876 .. 0.65

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.14
                            Sin3a_C  63 seeeeeeyYsqllelveklldGeidq 88 
                                           ++ ++Y+ +le+++++  G+id 
  gene1812|gene1812|rna1812|rna1812 187 VFADDPSIYDSFLEVMRDYKHGKIDA 212
                                        4567788999******9999999996 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.46
                            Sin3a_C  63 seeeeeeyYsqllelvekll 82 
                                        +  e++++Y+++l++++ + 
  gene1812|gene1812|rna1812|rna1812 406 KILEAKNVYEEFLKAMNLFN 425
                                        44677888888888875544 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.16
                            Sin3a_C  11 lrlfqiLyeRLlkikq 26 
                                        lr+f +L eRL +ik+
  gene1812|gene1812|rna1812|rna1812 728 LRYFYLLMERLAEIKD 743
                                        89***********985 PP

  == domain 4  score: 19.6 bits;  conditional E-value: 1e-07
                            Sin3a_C  79 eklldGeidq..sqfEdslRemfgikaYklfTldKliqalvkq 119
                                         +ll+G ++   + fE++lR +   +aYkl T+dKl+ ++ k 
  gene1812|gene1812|rna1812|rna1812 751 VDLLKGHLEApvNDFEEKLRIVSKAQAYKLATIDKLLDKINKR 793
                                        47889988864489*************************9885 PP

  == domain 5  score: 6.6 bits;  conditional E-value: 0.00091
                            Sin3a_C 198 eerwkeYvesYvlveptegv.ereklkkvfLkRnlkaerkeeekkeeeeqekaekeeeaekeleveekleiricln 272
                                        +++  eY e+Y+    t+++ ++    +vf++Rnl                       + +++ ++  ++++ic +
  gene1812|gene1812|rna1812|rna1812 814 KNEQDEYAEKYS----TNDIdNAFVRDRVFMNRNL-----------------------RDQRFCFSYRITVKICRK 862
                                        444455555555....2233123344455666666.......................2333445699******** PP

                            Sin3a_C 273 syklvyvpgtedv 285
                                        syk+ y ++  d+
  gene1812|gene1812|rna1812|rna1812 863 SYKIKYSEDEIDY 875
                                        *******999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (889 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       706  (0.0393775); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.66u 0.31s 00:00:00.97 Elapsed: 00:00:00.46
# Mc/sec: 5841.83
//
Query:       gene1813|gene1813|rna1813|rna1813  [L=343]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.9e-12   46.2   5.0    3.7e-05   23.3   3.7    2.2  2  UCH           Ubiquitin carboxyl-terminal hydrolase
      0.002   17.8   3.9       0.51    9.9   0.1    2.2  2  UCH_1         Ubiquitin carboxyl-terminal hydrolase
  ------ inclusion threshold ------
      0.039   13.6   0.9      0.039   13.6   0.9    2.3  2  Urotensin_II  Urotensin II


Domain annotation for each model (and alignments):
>> UCH  Ubiquitin carboxyl-terminal hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   3.7   6.2e-09   3.7e-05       1      56 [.     115     166 ..     115     247 .. 0.71
   2 !   22.7   0.1     1e-08     6e-05     192     257 .]     275     340 ..     183     340 .. 0.72

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 6.2e-09
                                        -EES-SSSTHHHHHHHHHHHTSHHHHHHHHTCHHCCSSTCCCCC-.TT.TTS.TTH CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                                UCH   1 tGlsNlGntCymnsvlQcLfsipelrdyllsleevkkesrnkkelnesnplgkkge 56 
                                        +Gl+N+ ++Cy+n+v+Q+Lfs +++ + ++  ++++k+ +  +el    ++++k++
  gene1813|gene1813|rna1813|rna1813 115 CGLVNFNAHCYINAVVQILFSSQKFVKCMQANAKKCKILHLLNEL----YMKMKNH 166
                                        7****************************9977777776666555....3333333 PP

  == domain 2  score: 22.7 bits;  conditional E-value: 1e-08
                                        BTTS-TCS-BEEEEEEEEEES.CTTSEEEEEEEECTTTTEEEEEETTEEEEE-HHCCCTT..CEEEEEE CS
                                        xxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxx RF
                                UCH 192 kkkkteekkkYeLiavvvHsG.slssGHYvayiknekngkWykydDetvkevkeeeevls..sayiLfY 257
                                         +  t ++ +Y+L +++     + ++ H +a++k  +n++W++++De v +++++ evl+  + y  fY
  gene1813|gene1813|rna1813|rna1813 275 CNVITIKNVRYKLLGILERVLnNFNGYHIIAFAK--RNNEWFMFNDECVLKINAN-EVLEnkETYYIFY 340
                                        3333344455*******9988799999******9..99***************77.7888898999898 PP

>> UCH_1  Ubiquitin carboxyl-terminal hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   1.3   0.00018       1.1       2      48 ..     116     160 ..     115     193 .. 0.82
   2 !    9.9   0.1   8.6e-05      0.51     271     320 .]     282     321 ..     198     321 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00018
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              UCH_1   2 GLEnhivnsYlNslLQvlyfipplrnlalshlakeckkehcLlcElg 48 
                                        GL n ++ +Y+N+++Q+l+  + + + +++ + k+ck    Ll El 
  gene1813|gene1813|rna1813|rna1813 116 GLVNFNAHCYINAVVQILFSSQKFVKCMQANA-KKCKI-LHLLNELY 160
                                        9999***************9999999888887.66665.35666665 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 8.6e-05
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              UCH_1 271 ikvYeLqsvvvhigdskesghLvslvkvaekelerdppesqWylFNDflV 320
                                         + Y+L ++  ++ ++ +  h ++++k           +++W++FND +V
  gene1813|gene1813|rna1813|rna1813 282 NVRYKLLGILERVLNNFNGYHIIAFAKR----------NNEWFMFNDECV 321
                                        578***********9988*********3..........368******876 PP

>> Urotensin_II  Urotensin II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.1      0.52   3.1e+03       2       6 ..     111     115 ..     110     115 .. 0.82
   2 ?   13.6   0.9   6.6e-06     0.039       3      10 ..     219     226 ..     218     226 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.52
                       Urotensin_II   2 gkpeC 6  
                                         +peC
  gene1813|gene1813|rna1813|rna1813 111 RNPEC 115
                                        59*** PP

  == domain 2  score: 13.6 bits;  conditional E-value: 6.6e-06
                       Urotensin_II   3 kpeCFWKY 10 
                                        + eCFWKY
  gene1813|gene1813|rna1813|rna1813 219 NQECFWKY 226
                                        679***** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (343 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       615  (0.034302); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 2650.33
//
Query:       gene1814|gene1814|rna1814|rna1814  [L=282]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-11   44.7   0.1    2.7e-11   43.7   0.1    1.4  1  Hexokinase_1     Hexokinase
    3.3e-11   43.1   0.6    4.5e-07   29.6   0.1    2.2  2  Hexokinase_2     Hexokinase
  ------ inclusion threshold ------
      0.099   12.6   1.2       0.19   11.7   1.2    1.4  1  Intein_splicing  Intein splicing domain


Domain annotation for each model (and alignments):
>> Hexokinase_1  Hexokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.7   0.1   4.6e-15   2.7e-11     128     197 ..       7      78 ..       2      79 .. 0.92

  Alignments for each domain:
  == domain 1  score: 43.7 bits;  conditional E-value: 4.6e-15
                                        -EEEEEEE-SSEE-SBTT--EE-S--TT---TT-T..TSBHHHHHHHHHHHTT-SEEEEEEE-HHHHHHHHH CS
                       Hexokinase_1 128 elplGftFSFPveqtsldegtlirwtKgfaikdve..gkdvvqllqealerkglpvkvvalvNDTvgtllsl 197
                                        ++  G+t S+P+++++l++g + +++K+f  k  +  ++++v+  ++a+++ + ++++  l+NDT++tl+s+
  gene1814|gene1814|rna1814|rna1814   7 NMTAGMTISYPIQHSALNNGYIREIGKDFPFKKINikKEELVENTTKAFQKYNINIHIKVLLNDTTATLASA 78 
                                        5789**************************988555699******************************985 PP

>> Hexokinase_2  Hexokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6   0.1   7.4e-11   4.5e-07       2      96 ..      87     169 ..      86     194 .. 0.85
   2 !   11.8   0.0     2e-05      0.12     155     236 ..     195     276 ..     193     280 .. 0.77

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 7.4e-11
                                        EEEEESSSEEEEEEEEGGG-GGGTTTS-TTSEEEEE--GGGTTTT-SS-..--HHHHHHHHH..SSSTTS-HHHHC CS
                       Hexokinase_2   2 iGlIlGtGtNacyleklsnieklegkkeksgemviNtEwgafgdegklpllrtkyDkeldee..spnpgeqlfEkm 75 
                                        iG++lGtGtN++  +k+  +   e       + +iNtE+ +f++e+     ++ yD +++e+  s+n+  ++++ m
  gene1814|gene1814|rna1814|rna1814  87 IGIVLGTGTNIAFNDKI--LY--E-------NQIINTEIASFDSEHL---RKNIYDMKIKEDilSSNKIYKPLDCM 148
                                        9************9998..22..2.......239********99544...3699*****999778*********** PP

                                        CSHHHHHHHHHHHHHHHHC.T CS
                       Hexokinase_2  76 iSGmYLGelvrlvlldlieek 96 
                                         +G+ L +l+ l++ d ++++
  gene1814|gene1814|rna1814|rna1814 149 LGGYQLVKLFNLAIKDQFDRE 169
                                        **************9988754 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 2e-05
                                        HHHHHHHHHHHHHCHHHHHHHHH-.....SSEEEEEESHHHHHSTTHHHHHHHHHHHHHT--S....-SEEEEE-- CS
                       Hexokinase_2 155 vceavsrRaarlvAagiaallkklgkeekekvtvgvdGslyekypkfrerlqealrellgeepe...kkvklklae 227
                                        v+ ++ +R  r+ A ++ ++l+  +   ++k+++  +G+++e+  +  + + + +r+l+ ++++   k+++++ + 
  gene1814|gene1814|rna1814|rna1814 195 VILSIKKRTMRILASMVFGILEAQEV--DSKIKIVLNGTVFEQDYDR-RIFIDEIRRLCADSTAykyKHFTFESIC 267
                                        566899****************8644..689***********65553.3445556677655544677999999999 PP

                                        -TTTHHHHH CS
                       Hexokinase_2 228 dGsgvGAAl 236
                                        d+ + G A 
  gene1814|gene1814|rna1814|rna1814 268 DATLRGIAR 276
                                        999999775 PP

>> Intein_splicing  Intein splicing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   1.2   3.2e-05      0.19      13     121 ..      29     133 ..      19     136 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.2e-05
                                        HHHCCECTTEEEEEETTTTEEEEEEEEEEEEEEEEEEEEEEETTS-EEEEET..T-EEEECCTTEEEEEECCC--T CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxx RF
                    Intein_splicing  13 eelvekegeevlslnledlklevksvkkliklklkelyeiklesgrkikaTp..eHkllvvrdegivEkradeLke 86 
                                        +e+   +++   ++n+++++l  ++ k++ k++++  +++ l+  +   a++     ++ +   giv  ++ ++  
  gene1814|gene1814|rna1814|rna1814  29 REI--GKDFPFKKINIKKEELVENTTKAFQKYNINIHIKVLLNDTTATLASAvrSDDVFYI---GIVLGTGTNIAF 99 
                                        555..356667789999********9*********88888888877776665226789999...9999******** PP

                                        T-EEEEEHSCEEEEEEEEEEEEECEEEEEEEEETT CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Intein_splicing  87 gdliavpdadvvwdkvksievedeeeyVYdltved 121
                                        +d i   +++++++++ s + e+ ++++Yd+++++
  gene1814|gene1814|rna1814|rna1814 100 NDKIL-YENQIINTEIASFDSEHLRKNIYDMKIKE 133
                                        ****9.6889*********************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (282 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       598  (0.0333538); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1847.38
//
Query:       gene1815|gene1815|rna1815|rna1815  [L=210]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      2e-09   37.7   0.0    2.4e-09   37.4   0.0    1.3  1  Hexokinase_1  Hexokinase
  ------ inclusion threshold ------
       0.06   12.9   0.0      0.084   12.4   0.0    1.3  1  FGGY_N        FGGY family of carbohydrate kinases, N-terminal
       0.13   11.9   0.0       0.21   11.2   0.0    1.3  1  TPMT          Thiopurine S-methyltransferase (TPMT)


Domain annotation for each model (and alignments):
>> Hexokinase_1  Hexokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.4   0.0   4.1e-13   2.4e-09      40     119 ..      91     170 ..      13     183 .. 0.79

  Alignments for each domain:
  == domain 1  score: 37.4 bits;  conditional E-value: 4.1e-13
                                        -EE----S.---S--EEEEEEEEESSSEEEEEEEEEESSS-EEEEEEE.EE--GGGGGSBHHHHHHHHHHHHHHHH CS
                       Hexokinase_1  40 mlptyvtr.lPtGkekGtylAlDlGgtnlRvllveLlgeskveitqek.ykipeelktgtaeeLFdfiakciaefl 113
                                         +  +v+   P+++ek ++lA+DlGg+ l+ +  +L++++ v+ tq k yki+++  + ++ ++Fd+ia + ++fl
  gene1815|gene1815|rna1815|rna1815  91 LIAKPVNLlCPSDREK-KVLAIDLGGSFLKLCVYKLRNDEIVSHTQLKkYKISKD-GSLSNVSMFDWIAAKTQDFL 164
                                        5556666546888888.99*******************999987777769***99.4458899************9 PP

                                        HHH... CS
                       Hexokinase_1 114 eeegee 119
                                          e +e
  gene1815|gene1815|rna1815|rna1815 165 MGEFKE 170
                                        766444 PP

>> FGGY_N  FGGY family of carbohydrate kinases, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   1.4e-05     0.084       2      52 ..     108     159 ..     107     185 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.4e-05
                                        EEEEEEESSEEEEEEEE.TTS-EEEEEEEE--EB-SSTT--EE-HHHHHHHH CS
                             FGGY_N   2 ilglDcGttstkaivld.ekgkvvasaqaelelsspkegwaeqdpeeiwqal 52 
                                        +l++D+G++++k  v+  ++ ++v++ q++   +s++ + ++ ++  +++a 
  gene1815|gene1815|rna1815|rna1815 108 VLAIDLGGSFLKLCVYKlRNDEIVSHTQLKKYKISKDGSLSNVSMFDWIAAK 159
                                        699**************************99999998888888887777664 PP

>> TPMT  Thiopurine S-methyltransferase (TPMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   3.6e-05      0.21      31     114 ..      72     160 ..      61     165 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 3.6e-05
                                        HT.T-S--EEEEEET-TT-H.....HHHHH-BTTEEEEEE-S-HHHHHHHHHHHTTSGGGGGEEEE--........ CS
                               TPMT  31 dalkakaglrvlvPlCGkal.....dlvwlAeqgrevvGvelselAvekffeeanlepkvkelsgvke.ysageie 100
                                        +++++ ++++++ P CG+al     +l   ++++++v++++l  + ++    +    +++ + ++ k+   +++ +
  gene1815|gene1815|rna1815|rna1815  72 SSSNLLEHEKTFEPSCGGALiakpvNLLCPSDREKKVLAIDLGGSFLKLCVYKLRN-DEIVSHTQLKKyKISKDGS 146
                                        44689999*********98533322666679************9999986555555.4455555555525566778 PP

                                        ....-TTT---SS- CS
                               TPMT 101 llcgdvFtlraeel 114
                                        l   ++F++ a++ 
  gene1815|gene1815|rna1815|rna1815 147 LSNVSMFDWIAAKT 160
                                        88999999988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       895  (0.0499191); expected 358.6 (0.02)
Passed bias filter:                      483  (0.0269396); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1410.22
//
Query:       gene1816|gene1816|rna1816|rna1816  [L=186]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.018   14.5   0.4      0.022   14.2   0.4    1.1  1  DUF599    Protein of unknown function, DUF599
      0.066   12.8   0.3      0.078   12.6   0.3    1.1  1  Pox_D3    Chordopoxvirinae D3 protein
       0.07   13.8   4.2        0.1   13.2   1.7    2.1  2  WBP-1     WW domain-binding protein 1
      0.076   12.8   1.5       0.11   12.3   1.5    1.2  1  DUF975    Protein of unknown function (DUF975)
      0.092   12.8   0.2        8.2    6.5   0.1    2.4  2  Tfb5      Transcription factor TFIIH complex subunit Tfb5


Domain annotation for each model (and alignments):
>> DUF599  Protein of unknown function, DUF599
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.4   6.3e-06     0.022      87     137 ..      20      71 ..       3     103 .. 0.65

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 6.3e-06
                             DUF599  87 d.klsdllkslpvfgatsealfelKlllllli...flvAFlkfvqsirlynhasf 137
                                        + +++   +++++++++ +  fe  ++++l++   f++ Fl+f +++r++n+++ 
  gene1816|gene1816|rna1816|rna1816  20 AvPAN---EQVQYIQSEIASFFETNFFSVLIFipyFILGFLCFGIAHRFFNYITT 71 
                                        22333...355666777777777665555553333*****************975 PP

>> Pox_D3  Chordopoxvirinae D3 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.3   2.2e-05     0.078      27     153 ..      25     152 ..       8     166 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.2e-05
                             Pox_D3  27 nhnefinkrlkklkekavfyaeYevspde.egsLelrlisSsvk.ikgryvnveefisagkairlcskkneliksl 100
                                        +++++i+  + +  e   f++  + +p    g L+  + +  ++ i ++y+n  +  sa +   +  ++n +++sl
  gene1816|gene1816|rna1816|rna1816  25 EQVQYIQSEIASFFET-NFFSVLIFIPYFiLGFLCFGIAHRFFNyITTKYINFRKPASASYSSPSALNENVINDSL 99 
                                        6788999999999887.7888888888751579999999999877******************************* PP

                             Pox_D3 101 dskdklliydilvleaakvkrilliqcpqilkvekesvltnpflvkdnrklfk 153
                                        ds+  ++ ++i   ++ ++   ll++  q  ++++e+   +p l     ++f 
  gene1816|gene1816|rna1816|rna1816 100 DSEHIFISRAIGPCNHSTMENGLLVESLQNNNETNENENRDPPLYTADAQCFE 152
                                        **55555578888899999**************99999999988877776665 PP

>> WBP-1  WW domain-binding protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.21   7.5e+02      24      42 ..      44      64 ..      31     105 .. 0.58
   2 ?   13.2   1.7   2.9e-05       0.1      50     104 .]     135     182 ..     103     182 .. 0.59

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.21
                              WBP-1 24 fwlvwt..llil.lsCicalak 42
                                        +l+++  ++ l ++C+ + ++
  gene1816|gene1816|rna1816|rna1816 44 SVLIFIpyFI-LgFLCFGIAHR 64
                                       3455554233.34888876665 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 2.9e-05
                              WBP-1  50 eqqerqreinlvay...reaknsaslvldlrllaslklPsyeevlkaarpetPpPpYs 104
                                        e+++r+           +   ++ +   +l l++ + lP y+e    a p++PpPpYs
  gene1816|gene1816|rna1816|rna1816 135 ENENRD-------PplyTADAQCFEQINQLPLFKIVTLPDYDEA---AYPQQPPPPYS 182
                                        222222.......122322233333334677899999****998...67999*****7 PP

>> DUF975  Protein of unknown function (DUF975)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   1.5     3e-05      0.11     201     236 ..      42      76 ..      29      82 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3e-05
                             DUF975 201 fvLdLsfiGWliLviltlgiallyLlpYietakaiF 236
                                        f+  L fi+ +iL +l +gia   +  Yi+t +++F
  gene1816|gene1816|rna1816|rna1816  42 FFSVLIFIPYFILGFLCFGIAHR-FFNYITTKYINF 76 
                                        566799***************55.568********9 PP

>> Tfb5  Transcription factor TFIIH complex subunit Tfb5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0     0.012        43      46      66 ..      24      44 ..      13      46 .. 0.86
   2 ?    6.5   0.1    0.0023       8.2      29      47 ..      91     109 ..      83     134 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.012
                               Tfb5 46 eevveelkkeleellekntye 66
                                       +e+v+++++e++++ e n ++
  gene1816|gene1816|rna1816|rna1816 24 NEQVQYIQSEIASFFETNFFS 44
                                       689**************9886 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0023
                               Tfb5  29 sqkfiiedLDethlfvkee 47 
                                        ++++i   LD +h+f++  
  gene1816|gene1816|rna1816|rna1816  91 NENVINDSLDSEHIFISRA 109
                                        67899999********865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       590  (0.0329076); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.42u 0.30s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1268.35
//
Query:       gene1817|gene1817|rna1817|rna1817  [L=360]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0086   16.0   0.6        1.2    9.1   0.2    2.8  2  HTH_15           Helix-turn-helix domain of alkylmercury lyas
  ------ inclusion threshold ------
      0.025   14.4   0.1          6    6.7   0.0    3.0  3  TMV_coat         Virus coat protein (TMV like)
      0.033   14.5   3.1       0.11   12.7   0.4    2.2  2  FANCI_S2         FANCI solenoid 2
       0.16   12.8   1.6       0.71   10.7   0.6    2.5  2  DUF4359          Domain of unknown function (DUF4359)
       0.16   12.4   4.6      0.074   13.5   1.3    2.2  2  DUF4600          Domain of unknown function (DUF4600)
        1.3    9.4   7.9         20    5.6   0.2    3.4  3  DUF3852          Protein of unknown function (DUF3852)
        1.6    9.2   6.6       0.49   10.9   0.8    2.4  3  DUF3597          Domain of unknown function (DUF3597)
        3.4    7.7   6.8        5.1    7.1   0.0    2.7  3  DDE_Tnp_1_3      Transposase DDE domain
        4.8    6.0  11.8       0.58    9.0   2.6    2.4  2  Phage_min_cap2   Phage minor capsid protein 2
        6.9    7.8  10.1         45    5.2   0.1    3.9  4  RNase_J_C        Ribonuclease J C-terminal domain


Domain annotation for each model (and alignments):
>> HTH_15  Helix-turn-helix domain of alkylmercury lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.2   0.00069       1.2      23      74 .]      48      99 ..      44      99 .. 0.96
   2 ?    4.2   0.0     0.022        40      39      73 ..     227     261 ..     214     262 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00069
                             HTH_15 23 lrpLlrlLakGepVtveeLAaatgrsveevrqaLaalpstEydedGrvvGfG 74
                                       l pLl+++++G     ++L  ++ ++ + +  +++ +  +E  e   vvG G
  gene1817|gene1817|rna1817|rna1817 48 LKPLLDVIVEGCEALDTNLTSIVTQTGDDISTIITNTTAVEMKEIQDVVGNG 99
                                       689**********99***********************************98 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.022
                             HTH_15  39 eeLAaatgrsveevrqaLaalpstEydedGrvvGf 73 
                                        ++L + + + +e++++ ++ + + E+d++  ++  
  gene1817|gene1817|rna1817|rna1817 227 DDLVKLVTKLLEQIKAEIQKTEDYELDKEKSIIDA 261
                                        6788888999*****************99888865 PP

>> TMV_coat  Virus coat protein (TMV like)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0       0.7   1.3e+03      30      55 ..     146     171 ..     134     176 .. 0.75
   2 ?    6.7   0.0    0.0034         6      35     100 ..     181     258 ..     176     266 .. 0.74
   3 ?    3.3   0.2     0.037        66      78     106 ..     289     317 ..     276     331 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.7
                                        TTS-TTSCCCCHHHHHHCCCT-B--S CS
                           TMV_coat  30 raikfsvassrsvvaealaalgrdlp 55 
                                        +ai++ v s+ s++++++ +  +d +
  gene1817|gene1817|rna1817|rna1817 146 QAIQALVDSANSQIKNLVDNHTNDEF 171
                                        67777788888888888777666666 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0034
                                        TSCCCCHHHHHHCCCT-B--S.BTTC-SS...S.TT.........SSSEEEEHHHHHHHHHHHCHHHS....S-SC CS
                           TMV_coat  35 svassrsvvaealaalgrdlpvsvterFpgartslG.........dkeflllldkrvtaalsrladaad...dekn 98 
                                        + ++  +++++ la   +++p+ ++ +Fp + t            + + + l++k ++++  ++++  d   d+ +
  gene1817|gene1817|rna1817|rna1817 181 ENQTIYTQIQNILADPTNTSPIIPQLKFPDPATIANsivpgknqlNDDLVKLVTKLLEQIKAEIQKTEDyelDKEK 256
                                        5677789**********************99998877777777776666666677777777777666556555555 PP

                                        CC CS
                           TMV_coat  99 rv 100
                                         +
  gene1817|gene1817|rna1817|rna1817 257 SI 258
                                        55 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.037
                                        HHHHHHHHHHHCHHHS.S-SCCCCCCCCS CS
                           TMV_coat  78 ldkrvtaalsrladaaddeknrvvelnka 106
                                          ++vt+ l +la++  + kn +v l+k 
  gene1817|gene1817|rna1817|rna1817 289 SSTVVTSLLASLAANNLEMKNSIVDLTKK 317
                                        56889999****77777*******99975 PP

>> FANCI_S2  FANCI solenoid 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.1      0.11   1.9e+02      45     109 ..      99     164 ..      55     172 .. 0.61
   2 ?   12.7   0.4   6.4e-05      0.11       5     128 ..     229     358 ..     226     359 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.11
                           FANCI_S2  45 gsqiLlelfkvhesarseiieqllsriitkseeevsqyiklLse....lvksapltllesssklkelld 109
                                        g ++ ++      +a+ + i  l++ i+ ++e e    ++lL+e    lv++ ++ +++  s++k+l d
  gene1817|gene1817|rna1817|rna1817  99 GNTLYVSNLTDLFQATAKTITDLINTITGSEEAE---TSTLLKEketaLVQAIQALVDSANSQIKNLVD 164
                                        4444444444444455555666677776665553...34455432333777777777777777777666 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 6.4e-05
                           FANCI_S2   5 lvqlgfaLldsagpkkvvgvksaeas......aaksktvaqaaaklgsqiLlelfkvhesarseiieqllsriitk 74 
                                        lv+l   Ll+  +++ +++++  e +       a ++  + ++ ++ ++iL+ + k  ++++s+++  ll  ++++
  gene1817|gene1817|rna1817|rna1817 229 LVKLVTKLLEQIKAE-IQKTEDYELDkeksiiDAGTTSYVDKLNTIRADILVGVQKITDDVSSTVVTSLLASLAAN 303
                                        566666666666543.32222222223445555666888899999******************************* PP

                           FANCI_S2  75 seeevsqyiklLselvksapltllesssk.lkelldylsflpletatallkAllP 128
                                        + e  + +++l +++ + a++ + e ++  +++l   ++ +++e+a++++  l P
  gene1817|gene1817|rna1817|rna1817 304 NLEMKNSIVDLTKKMDQDASAYVIEVTNLeINNLAPLITEYNQEIAKQIIPNLKP 358
                                        ****************999998888877558888888899999999998877766 PP

>> DUF4359  Domain of unknown function (DUF4359)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       1.9   3.3e+03      45      64 ..      67      86 ..      49      88 .. 0.73
   2 ?   10.7   0.6   0.00039      0.71      39      78 ..     139     182 ..     107     193 .. 0.71

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1.9
                            DUF4359 45 kelvdsakpqikelieestq 64
                                       +++v+++ ++i ++i+++t 
  gene1817|gene1817|rna1817|rna1817 67 TSIVTQTGDDISTIITNTTA 86
                                       44899999999999999996 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00039
                            DUF4359  39 k....lkseCkelvdsakpqikelieestqrqNfilfSiyttel 78 
                                        +    l +  ++lvdsa++qik+l++++t+ +  +l S+ +te 
  gene1817|gene1817|rna1817|rna1817 139 EketaLVQAIQALVDSANSQIKNLVDNHTNDEFTGLESLIKTEN 182
                                        212345566788******************99999999999985 PP

>> DUF4600  Domain of unknown function (DUF4600)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.1       1.8   3.2e+03      35      59 ..     139     163 ..     103     191 .. 0.60
   2 ?   13.5   1.3   4.1e-05     0.074      22      88 ..     239     326 ..     222     352 .. 0.71

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.8
                            DUF4600  35 gnpsdrlasirvleklteeelnqll 59 
                                        ++++   + i++l +  ++++++l+
  gene1817|gene1817|rna1817|rna1817 139 EKETALVQAIQALVDSANSQIKNLV 163
                                        3333333344444444444444443 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 4.1e-05
                            DUF4600  22 qiailkeklekirgnpsdrlasirv.......................leklteeelnqllkqLekekkslenqlk 74 
                                        qi+ + +k e+     +++ ++i++                       +++++++ + +ll  L  +  +++n + 
  gene1817|gene1817|rna1817|rna1817 239 QIKAEIQKTEDYE--LDKEKSIIDAgttsyvdklntiradilvgvqkiTDDVSSTVVTSLLASLAANNLEMKNSIV 312
                                        4444444444444..2222233333333333333333337777888889*************************** PP

                            DUF4600  75 dlelrleqEsKayh 88 
                                        dl  +++q++ ay 
  gene1817|gene1817|rna1817|rna1817 313 DLTKKMDQDASAYV 326
                                        ************95 PP

>> DUF3852  Protein of unknown function (DUF3852)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.4      0.13   2.4e+02      25      51 ..      72      98 ..      55     111 .. 0.77
   2 ?    5.6   0.2     0.011        20      29      51 ..     143     165 ..     131     168 .. 0.85
   3 ?    4.2   0.1     0.029        53      42     102 ..     278     340 ..     261     342 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.13
                            DUF3852 25 Aasgdvagaiestwkeaksqiktvvnn 51
                                        +  d+++ i++t       i+ vv n
  gene1817|gene1817|rna1817|rna1817 72 QTGDDISTIITNTTAVEMKEIQDVVGN 98
                                       234689999*99999999999999977 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.011
                            DUF3852  29 dvagaiestwkeaksqiktvvnn 51 
                                         + +ai+  +++a+sqik++v+n
  gene1817|gene1817|rna1817|rna1817 143 ALVQAIQALVDSANSQIKNLVDN 165
                                        56789****************98 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.029
                            DUF3852  42 ksqiktvvnnvvfpvidvilavllfvklat..ayldYrkhgqlefaapailfagLvfsltApl 102
                                           +++++++v   v+  +la l    l++  + +d  k+ + + +a +i ++ L +  +Apl
  gene1817|gene1817|rna1817|rna1817 278 LVGVQKITDDVSSTVVTSLLASLAANNLEMknSIVDLTKKMDQDASAYVIEVTNLEINNLAPL 340
                                        556899*****************9999877336799999999999999999999999988886 PP

>> DUF3597  Domain of unknown function (DUF3597)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       5.5   9.9e+03       6      30 ..     122     146 ..     118     166 .. 0.51
   2 ?    0.6   0.1      0.42   7.6e+02      35      75 ..     215     260 ..     182     273 .. 0.62
   3 ?   10.9   0.8   0.00027      0.49      56      85 ..     294     323 ..     279     327 .. 0.77

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 5.5
                                        HHHHT--..-SS-TTTT-------S CS
                            DUF3597   6 lskifgkaaaaaaapaasaapaata 30 
                                        +++i g+++a++++  +++++a  +
  gene1817|gene1817|rna1817|rna1817 122 INTITGSEEAETSTLLKEKETALVQ 146
                                        5566666555554444444333333 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.42
                                        S.---------SS..EE.-HHHHHHHHHH....HSS---TTT-HHH CS
                            DUF3597  35 aaaaaPaaaaaaaaavd.veavlealaak....sgeklnwrtSivD 75 
                                        a++  P +++ ++  v  v++ le++ a+    ++ +l+  +Si+D
  gene1817|gene1817|rna1817|rna1817 215 ANSIVPGKNQLNDDLVKlVTKLLEQIKAEiqktEDYELDKEKSIID 260
                                        3556677777766666535556666654400004456666788888 PP

  == domain 3  score: 10.9 bits;  conditional E-value: 0.00027
                                        HHHHHHHHSS---TTT-HHHHHHHT----S CS
                            DUF3597  56 lealaaksgeklnwrtSivDLlkllglDss 85 
                                         + la+ ++++l+ ++SivDL k ++ D+s
  gene1817|gene1817|rna1817|rna1817 294 TSLLASLAANNLEMKNSIVDLTKKMDQDAS 323
                                        33456667889***************9998 PP

>> DDE_Tnp_1_3  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   1.5     0.065   1.2e+02      49     145 ..      67     163 ..      63     170 .. 0.76
   2 ?    7.1   0.0    0.0028       5.1      98     136 ..     223     261 ..     201     277 .. 0.85
   3 ?   -2.0   0.1       1.7   3.1e+03     109     142 ..     301     335 ..     280     342 .. 0.55

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.065
                        DDE_Tnp_1_3  49 hliindkGeilavkltpgnvdDrepveelakellgklfaDkgyiskklaeelleegielitklrknmkkkllslld 124
                                          i+ ++G+ +++ +t++   + + +++++ +     +++ + + ++ a+++ ++ i+ it   +  +++ll+  +
  gene1817|gene1817|rna1817|rna1817  67 TSIVTQTGDDISTIITNTTAVEMKEIQDVVGNGNTLYVSNLTDLFQATAKTI-TDLINTITGSEEAETSTLLKEKE 141
                                        5678888888888888888888888887777755555555666666666655.56788899999999999999999 PP

                        DDE_Tnp_1_3 125 kllLrk.rslietvndelknis 145
                                         +l++  ++l+++ n ++kn++
  gene1817|gene1817|rna1817|rna1817 142 TALVQAiQALVDSANSQIKNLV 163
                                        9998753799*********986 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0028
                        DDE_Tnp_1_3  98 eelleegielitklrknmkkkllslldkllLrkrsliet 136
                                        ++l+ + ++l+tkl +++k+++ ++ d  l + +s+i++
  gene1817|gene1817|rna1817|rna1817 223 NQLNDDLVKLVTKLLEQIKAEIQKTEDYELDKEKSIIDA 261
                                        6899999*****************************985 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 1.7
                        DDE_Tnp_1_3 109 tklrknmkkkllslldkllLr.krslietvndelk 142
                                        +    +mk++++ l+ k+      ++ie  n e+ 
  gene1817|gene1817|rna1817|rna1817 301 AANNLEMKNSIVDLTKKMDQDaSAYVIEVTNLEIN 335
                                        34445577777666666543313455555555555 PP

>> Phage_min_cap2  Phage minor capsid protein 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   2.6   0.00032      0.58      57     134 ..      90     166 ..      50     195 .. 0.56
   2 ?    1.9   1.9     0.047        84      57     131 ..     238     311 ..     214     357 .. 0.47

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00032
                     Phage_min_cap2  57 reilkliskltgksekelrkllkeagdkaiksddkelaiykeaglepkplekseelqqlveaylkqtegelkNltn 132
                                        +ei++++ +      ++l +l++ +++  i +  + +   +ea+ ++   ek+++l q+++a+++ +++++kNl+ 
  gene1817|gene1817|rna1817|rna1817  90 KEIQDVVGNGNTLYVSNLTDLFQATAK-TITDLINTITGSEEAETSTLLKEKETALVQAIQALVDSANSQIKNLVD 164
                                        344444444444444444555544433.333333344444555544444666666777777777777777776664 PP

                     Phage_min_cap2 133 tt 134
                                          
  gene1817|gene1817|rna1817|rna1817 165 NH 166
                                        32 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.047
                     Phage_min_cap2  57 reilkliskltgksekelrkllkeagdkaiksddkelaiykeaglepkplekseelqqlveaylkqtegelkNlt 131
                                        ++i+  i+k++++  ++ ++++ +ag+ ++ ++ + ++++  +g+++++ + s+++   + a l+  + e+kN +
  gene1817|gene1817|rna1817|rna1817 238 EQIKAEIQKTEDYELDKEKSII-DAGTTSYVDKLNTIRADILVGVQKITDDVSSTVVTSLLASLAANNLEMKNSI 311
                                        3333444444333333333332.3444444444444444444444444444444444444444444444444433 PP

>> RNase_J_C  Ribonuclease J C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.1     0.025        45      10      52 ..     102     144 ..      94     152 .. 0.84
   2 ?    5.0   0.1      0.03        53      16      66 ..     149     203 ..     142     205 .. 0.72
   3 ?    2.5   0.4      0.17   3.1e+02      15      58 ..     226     269 ..     221     274 .. 0.80
   4 ?   -2.2   0.1       5.1   9.1e+03      38      51 ..     301     314 ..     281     331 .. 0.54

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.025
                          RNase_J_C  10 vyvkeseeLieeakkvvretieealeekesdwnelkrkireal 52 
                                         yv + ++L+++++k++++ i+++ +++e+++++l ++  +al
  gene1817|gene1817|rna1817|rna1817 102 LYVSNLTDLFQATAKTITDLINTITGSEEAETSTLLKEKETAL 144
                                        5888999*******************99999998877666665 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.03
                          RNase_J_C  16 eeLieeakkvvretieealeek....esdwnelkrkirealkkflykktkrrPmI 66 
                                        + L+++a++++++ ++++ +++    es  ++ ++ i +++++ l + t+ +P+I
  gene1817|gene1817|rna1817|rna1817 149 QALVDSANSQIKNLVDNHTNDEftglESLIKTENQTIYTQIQNILADPTNTSPII 203
                                        6777888888888888777775222245555557889999999999999999998 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.17
                          RNase_J_C  15 seeLieeakkvvretieealeekesdwnelkrkirealkkflyk 58 
                                        +++L++ ++k+++++  e++++++++ ++ k+ i   +++++ k
  gene1817|gene1817|rna1817|rna1817 226 NDDLVKLVTKLLEQIKAEIQKTEDYELDKEKSIIDAGTTSYVDK 269
                                        56788888888888888888888899999999998888888865 PP

  == domain 4  score: -2.2 bits;  conditional E-value: 5.1
                          RNase_J_C  38 esdwnelkrkirea 51 
                                         +++ e+k++i + 
  gene1817|gene1817|rna1817|rna1817 301 AANNLEMKNSIVDL 314
                                        34444555555443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (360 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1357  (0.0756874); expected 358.6 (0.02)
Passed bias filter:                      535  (0.0298399); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.54u 0.31s 00:00:00.85 Elapsed: 00:00:00.44
# Mc/sec: 2438.92
//
Query:       gene1818|gene1818|rna1818|rna1818  [L=441]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      7e-42  143.6   0.2    1.8e-41  142.2   0.2    1.6  1  Pkinase      Protein kinase domain
    1.2e-15   57.6   0.0    2.8e-15   56.3   0.0    1.6  2  Pkinase_Tyr  Protein tyrosine kinase
    9.8e-08   31.6   0.0    1.3e-06   27.9   0.0    2.3  2  Kinase-like  Kinase-like
     0.0084   15.7   1.3        1.3    8.6   0.3    2.5  2  FTA2         Kinetochore Sim4 complex subunit FTA2
     0.0097   15.3   0.1      0.017   14.5   0.1    1.3  1  Kdo          Lipopolysaccharide kinase (Kdo/WaaP) family


Domain annotation for each model (and alignments):
>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  142.2   0.2   5.1e-45   1.8e-41       4     264 .]      32     377 ..      29     377 .. 0.86

  Alignments for each domain:
  == domain 1  score: 142.2 bits;  conditional E-value: 5.1e-45
                                        EEEEEEESSEEEEEEEETTTTEEEEEEEEECHCHCHHHHHHHHHHHHHHHHHS..CTTB--EEEEEEESSEEEEEE CS
                            Pkinase   4 leklGeGsfGkVykaveketgkivAvKkikkekakkkkekkvlrEikilkklk..hpnivrlyevfeekdelylvl 77 
                                        +  lG G+f+ Vyk+ +  +++++A+K++k      k     ++E  +lkkl+   ++ v +ye f  k+++++v 
  gene1818|gene1818|rna1818|rna1818  32 QDYLGCGTFADVYKIEDLYSNNQFAIKIFKSGTCYLK---VGMNEAFLLKKLRnyRNHFVIFYEEFFYKQHFCIVE 104
                                        5679*************************99876664...569********999877777777777779******* PP

                                        E--TTEBHHHHHH..HHSS--HHHHHHHHHHHHHHHHHHHHTTEE-SS-SGGGEEEETTTE....EEE-SGTTSEE CS
                            Pkinase  78 eyveggeladlle..rkgslseeeakkiakqilegleylHskgiiHrDlKpeNiLidekge....lKitDFGlake 147
                                        ++++++ l ++++  +++ ++++ +k+ia q+l++l  l  +gi H D+KpeNi +d+ ++    +Ki+D+G +  
  gene1818|gene1818|rna1818|rna1818 105 QLLSNN-LYEFIKytNHQGFDHDMTKNIAIQLLNALFILQMEGITHGDIKPENICLDKIDDksfkIKIIDLGSSFT 179
                                        ***977.889988877778**************************************53334789*******9866 PP

                                        SSSSCSBCTTTSCGGGS-HHHHTTSCBSHHHHHHHHHHHHHHHHHSS-STTTSSHHHHHHHHHHTHHHHHHHCT.S CS
                            Pkinase 148 lessskltsfvgtseYlAPEvlkeneyskkvDvWslGvilyelltgkppfsgekgkekvekeldqlekilkilg.e 222
                                          ++   + ++ +++Y+APE + + +y++ +D+WslG+++ye++tg p+f+g+++ke + + +      +k+lg +
  gene1818|gene1818|rna1818|rna1818 180 QPKK--NSFYIQSRYYRAPETILGLNYGHGIDLWSLGCVIYEVFTGVPLFPGKSNKE-QIMRY------TKLLGiP 246
                                        6554..588999***************************************555554.33333......4444442 PP

                                        HH...HHHTTS................................................................. CS
                            Pkinase 223 tkeklpeasei................................................................. 233
                                            l++ +++                                                                 
  gene1818|gene1818|rna1818|rna1818 247 PIAMLENGKNVqlyfykkddetakscstwhnfydknedtfgivtnkenktdllgntagfghpgksndykmcysdan 322
                                        22333333333344455556667777999999******************************************** PP

                                        ........................-HHHHHHHHHHT-SSGCCSTTHHHHHTSGGG CS
                            Pkinase 234 ........................seeakdllkkllkkdpkkRltaeellqhpyl 264
                                                                + ++ d+l ++lk+ p++R+ +e+l++hpyl
  gene1818|gene1818|rna1818|rna1818 323 dekdyltmpgfrksitsrsknktdNANLMDFLLSILKMHPMERPIIEDLKEHPYL 377
                                        *****************************************************97 PP

>> Pkinase_Tyr  Protein tyrosine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.3   0.0   7.8e-19   2.8e-15       4     215 ..      32     236 ..      29     246 .. 0.83
   2 ?   -2.3   0.0       0.6   2.2e+03     226     257 ..     342     373 ..     331     374 .. 0.79

  Alignments for each domain:
  == domain 1  score: 56.3 bits;  conditional E-value: 7.8e-19
                                        EEEEEEESSEEEEEEEEETTTTSSEEEEEEEEESTTSSHHHHHHHHHHHHHHHTS..-BTTB--EEEEEESSSSEE CS
                        Pkinase_Tyr   4 gkklGeGafGkVvegtlkgekekkevkVavKtlkeeateeekeelleeakimkkl..khpnivkllgvctkeepll 77 
                                        ++ lG G+f++V++ +       ++ + a+K++k+++     +  ++ea ++kkl    ++ v ++     +++ +
  gene1818|gene1818|rna1818|rna1818  32 QDYLGCGTFADVYKIEDL----YSNNQFAIKIFKSGTCYL--KVGMNEAFLLKKLrnYRNHFVIFYEEFFYKQHFC 101
                                        6789*********98877....68889******8887766..8899********9754577889999888777777 PP

                                        EEEE--TTEBHHHHHHHTCTTTSBHHHHHHHHHHHHHHHHHHHHTTEEEST-SGGGEEEEE....TTEEEE-STTT CS
                        Pkinase_Tyr  78 ivteyvkgGdLlkfLrkkekekltlkdllsfalqvAkGmeyLeskklvHrdlaarNvLlse....nkvvkisDfGL 149
                                        iv +++ +++L +f++ ++++ ++ + + ++a+q+ +++  L+ + + H d+   N+ l++    + ++ki D G 
  gene1818|gene1818|rna1818|rna1818 102 IVEQLL-SNNLYEFIKYTNHQGFDHDMTKNIAIQLLNALFILQMEGITHGDIKPENICLDKiddkSFKIKIIDLGS 176
                                        766665.679*************************************************98776567999999998 PP

                                        HEETTTSSEEEETTSSTSGG.GGS-HHHHHHSEEEHHHHHHHHHHHHHHHHTTSSGTTTTSHHHHHH CS
                        Pkinase_Tyr 150 ardiekddeyvkkeeaklpv.kWmapEslkekkftsksDvWsfGvllwEiftlgespypglkneevl 215
                                        + +        kk++  +    + apE++   ++ +  D Ws G +++E+ft g   +pg +n+e +
  gene1818|gene1818|rna1818|rna1818 177 SFTQ------PKKNSFYIQSrYYRAPETILGLNYGHGIDLWSLGCVIYEVFT-GVPLFPGKSNKEQI 236
                                        8776......33333444440466****************************.98889998665543 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.6
                                        BBTTSBHHHHHHHHHHT-SSGGGS--HHHHHH CS
                        Pkinase_Tyr 226 kpekcpeelyelmkkcweedpeeRptfselve 257
                                        k+++ +++l++++ + ++ +p eRp +++l e
  gene1818|gene1818|rna1818|rna1818 342 KNKTDNANLMDFLLSILKMHPMERPIIEDLKE 373
                                        45556778999999999999999999988875 PP

>> Kinase-like  Kinase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0     0.056     2e+02      12      47 ..      27      62 ..      21      86 .. 0.88
   2 !   27.9   0.0   3.8e-10   1.3e-06     134     244 ..     116     221 ..      79     238 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.056
                        Kinase-like 12 rtlvrgellkkgdrsvvfevkdqetgeplavkvfll 47
                                        ++++++ l+ g +  v++++d + ++++a+k+f +
  gene1818|gene1818|rna1818|rna1818 27 NKFIVQDYLGCGTFADVYKIEDLYSNNQFAIKIFKS 62
                                       5778899999999*******************9975 PP

  == domain 2  score: 27.9 bits;  conditional E-value: 3.8e-10
                        Kinase-like 134 rsethkkletiarlllTlqlirlaanLqakglvhgkftvdnllld....ekgglmlggftaLvragtkvvlsevek 205
                                        ++++h+   +   + + +ql++    Lq +g+ hg+++++n++ld    + +++++ ++++ +++ +k       +
  gene1818|gene1818|rna1818|rna1818 116 KYTNHQGFDHDMTKNIAIQLLNALFILQMEGITHGDIKPENICLDkiddKSFKIKIIDLGSSFTQPKKNSFYIQSR 191
                                        45668888888889999***************************7333368***************9999888889 PP

                        Kinase-like 206 gfaPpEllgsrggytrknktkmthkldaWqlGlviyriw 244
                                         +  pE++           +++ h++d W lG viy + 
  gene1818|gene1818|rna1818|rna1818 192 YYRAPETILG---------LNYGHGIDLWSLGCVIYEVF 221
                                        ******9876.........89***************986 PP

>> FTA2  Kinetochore Sim4 complex subunit FTA2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.6   0.2    0.0029        10      22      85 ..      27      87 ..      12      98 .. 0.69
   2 !    8.6   0.3   0.00036       1.3     154     210 ..     108     164 ..      78     169 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0029
                               FTA2 22 kdiefleyLgkglhsiVlkvk..irgkeYALKlFrfleaeeleeaeedlkiprealkelasysdpf 85
                                       +++   +yLg g+ + V+k++  + ++++A+K+F+  +  +l    +    + + lk+l++y ++f
  gene1818|gene1818|rna1818|rna1818 27 NKFIVQDYLGCGTFADVYKIEdlYSNNQFAIKIFKSGTC-YL----KVGMNEAFLLKKLRNYRNHF 87
                                       56677899************9667888*******98733.22....23333344444444444433 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00036
                               FTA2 154 krpiraIVKelellkeqeelevsqlpkllrdlkklhklgIvvrDlkeenyidgkLvD 210
                                        ++ ++ ++K  + +  ++ ++ +++ +ll+ l +l+ +gI + D+k+en++ +k+ D
  gene1818|gene1818|rna1818|rna1818 108 SNNLYEFIKYTNHQGFDHDMTKNIAIQLLNALFILQMEGITHGDIKPENICLDKIDD 164
                                        45555566665555667888999999************************9888866 PP

>> Kdo  Lipopolysaccharide kinase (Kdo/WaaP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.1   4.6e-06     0.017     111     169 ..     119     177 ..      92     186 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4.6e-06
                                Kdo 111 kwaelaeelkrallkavgrliaklhragvnHadlyaknillqqeeeeeaeiwliDldka 169
                                        +++ +++ +++++  ++  +   l   g+ H+d+ + ni l++ +++ ++i +iDl  +
  gene1818|gene1818|rna1818|rna1818 119 NHQGFDHDMTKNIAIQLLNALFILQMEGITHGDIKPENICLDKIDDKSFKIKIIDLGSS 177
                                        334488888888888887777788889****************************9765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (441 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       504  (0.0281109); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.41
# Mc/sec: 3199.02
//
Query:       gene1819|gene1819|rna1819|rna1819  [L=99]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
       0.12   12.6   0.0       0.13   12.5   0.0    1.1  1  Ricin_B_lectin  Ricin-type beta-trefoil lectin domain


Domain annotation for each model (and alignments):
>> Ricin_B_lectin  Ricin-type beta-trefoil lectin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   7.5e-06      0.13      54     106 ..       5      52 ..       1      71 [. 0.81

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 7.5e-06
                                        TTEEEEESSSSTTSBEEEEETTTTSG.GGCEEEETTTTEEEETTTSEEEEESTT CS
                     Ricin_B_lectin  54 selCldvsstaegakvvlakChkgkg.nqrWefdkdgtqirhkksgkCLdvkga 106
                                        ++lCl       g++v+l +   +k+  + W+f + +++   + s++CL+v++ 
  gene1819|gene1819|rna1819|rna1819   5 KKLCLV-----GGDQVTLCNPY-DKSvLDDWRFVETSKGTSLRTSNMCLTVSMT 52 
                                        789995.....69999995544.44459****999999999999******9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       256  (0.0142785); expected 358.6 (0.02)
Passed bias filter:                      223  (0.0124379); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.29s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 654.80
//
Query:       gene182|gene182|rna182|rna182  [L=189]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.046   13.7   0.8      0.076   13.0   0.2    1.7  2  SapB_1    Saposin-like type B, region 1


Domain annotation for each model (and alignments):
>> SapB_1  Saposin-like type B, region 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0      0.73   1.3e+04      30      36 ..      34      40 ..      33      41 .. 0.74
   2 ?   13.0   0.2   4.3e-06     0.076       2      23 ..      84     105 ..      83     109 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 0.73
                                   HHHHHHH CS
                         SapB_1 30 LekvCsk 36
                                   ++++C++
  gene182|gene182|rna182|rna182 34 IHQECAL 40
                                   6889986 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 4.3e-06
                                    HHHHHHHHHHHHHHHH-SS--H CS
                         SapB_1   2 eCdlCefvVkeveklLkdNkTe 23 
                                    +C lC+fv + v + +++N+ e
  gene182|gene182|rna182|rna182  84 MCVLCTFVAHFVLNAMGENEIE 105
                                    8******************876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (189 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       888  (0.0495287); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 1150.12
//
Query:       gene1820|gene1820|rna1820|rna1820  [L=216]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
       0.19   12.0   0.6       0.48   10.7   0.0    1.8  2  Ricin_B_lectin  Ricin-type beta-trefoil lectin domain


Domain annotation for each model (and alignments):
>> Ricin_B_lectin  Ricin-type beta-trefoil lectin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.1      0.16   2.8e+03     100     117 ..      10      23 ..       7      31 .. 0.55
   2 ?   10.7   0.0   2.7e-05      0.48      28      78 ..     104     159 ..      90     169 .. 0.53

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.16
                                        EEEESTTSSTTTBEEEEE CS
                     Ricin_B_lectin 100 CLdvkgasksneklilkk 117
                                        CLd+++++     li++k
  gene1820|gene1820|rna1820|rna1820  10 CLDLTQQK----WLIVSK 23 
                                        55555553....455554 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 2.7e-05
                                        EEE-TSCCGG.GEEEEE.TTSEEEETT.TTEEEEES.....SSSTTSBEEEEETTTTS CS
                     Ricin_B_lectin  28 lydChgskgk.Qlwtlt.kdgeirskaqselCldvs.....staegakvvlakChkgk 78 
                                        +++C+g ++k  lw+++ + + +++  ++++Cl ++       a++ +v l +C+ ++
  gene1820|gene1820|rna1820|rna1820 104 VAPCDGPSNKeSLWRIDeNSNGFKI-ITGDMCLRLTttdskLYAKTLSVGLDECD-DD 159
                                        4555555555555655544444444.33555555544333223334444444444.34 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (216 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       322  (0.0179597); expected 358.6 (0.02)
Passed bias filter:                      240  (0.0133861); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.22s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1651.95
//
Query:       gene1821|gene1821|rna1821|rna1821  [L=311]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0047   16.7   6.6      0.043   13.6   0.1    3.8  4  partial_CstF     Partial cleavage stimulation factor domain
  ------ inclusion threshold ------
      0.018   14.6   0.9      0.026   14.1   0.9    1.4  1  Exonuc_VII_L     Exonuclease VII, large subunit
      0.021   14.9   0.1       0.35   11.0   0.0    2.5  2  Mating_N         Mating-type protein beta 1
       0.17   12.0   3.8          2    8.5   0.1    3.5  3  IKKbetaNEMObind  I-kappa-kinase-beta NEMO binding domain
        1.1    9.4   4.9        2.5    8.1   2.0    2.8  2  IL3Ra_N          IL-3 receptor alpha chain N-terminal domain
        2.9    7.8   8.8          1    9.3   0.2    3.3  3  Shugoshin_N      Shugoshin N-terminal coiled-coil region
        9.9    5.8  19.5        2.3    8.0   5.0    2.3  2  DUF445           Protein of unknown function (DUF445)


Domain annotation for each model (and alignments):
>> partial_CstF  Partial cleavage stimulation factor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.49   1.3e+03      37      54 ..      70      87 ..      66      93 .. 0.85
   2 ?    3.0   0.2     0.034        87       2      33 ..     105     138 ..     104     143 .. 0.83
   3 ?   -0.0   0.1       0.3   7.7e+02       7      23 ..     162     178 ..     157     197 .. 0.78
   4 !   13.6   0.1   1.7e-05     0.043       6      45 ..     232     271 ..     227     273 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.49
                       partial_CstF 37 edmtsWpsEqkqqVLSIq 54
                                       +++  W   +  ++LS +
  gene1821|gene1821|rna1821|rna1821 70 NKVSRWEYAETDKILSYK 87
                                       57889**********966 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.034
                       partial_CstF   2 kiddllsgvepaeeaLVdeViknkd..iLqnilk 33 
                                        ki++++ + ++aee+ ++++i++++  i + i +
  gene1821|gene1821|rna1821|rna1821 105 KIKKTVYTFNQAEEEDIEAIIRKENqkICTQIEQ 138
                                        67888888899**********9988788888866 PP

  == domain 3  score: -0.0 bits;  conditional E-value: 0.3
                       partial_CstF   7 lsgvepaeeaLVdeVik 23 
                                         s v+ ++++L +e+ k
  gene1821|gene1821|rna1821|rna1821 162 ASIVSSDKPKLLEEIKK 178
                                        47789999999999976 PP

  == domain 4  score: 13.6 bits;  conditional E-value: 1.7e-05
                       partial_CstF   6 llsgvepaeeaLVdeViknkdiLqnilkskpedmtsWpsE 45 
                                        + s+++  +  LV+ + +n ++L+   ++k  +mt+ ++E
  gene1821|gene1821|rna1821|rna1821 232 VCSATNKESRTLVESIYRNYSLLEEFITIKASEMTKNTEE 271
                                        4599999****************************96665 PP

>> Exonuc_VII_L  Exonuclease VII, large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.9     1e-05     0.026     139     288 ..      33     229 ..      24     283 .. 0.63

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1e-05
                       Exonuc_VII_L 139 vpdkaeleeqleelerrlekaikrlleekkqrleklasrl.....kspeellerkrqrldeleerleralkkqlkk 209
                                        +  k+e++e++++ ++ l+ ++ + +ee+ + + ++ +++     ++ +++l+ k ++l+   e l + +++++kk
  gene1821|gene1821|rna1821|rna1821  33 LTLKSEIHETINDGNEALKLEFLHVFEEATKSIIEYINKVsrweyAETDKILSYKCSELTTNIECLIKDVSNKIKK 108
                                        5556777778877777777777777777766665555444333333445555555555555555555545555544 PP

                       Exonuc_VII_L 210 krerleelkerl.kekleekk.........................................erlkklkerle.ll 242
                                           ++++++e+  ++ +++++                                         + l+++k+ ++  +
  gene1821|gene1821|rna1821|rna1821 109 TVYTFNQAEEEDiEAIIRKENqkictqieqilcdthnfdpiipqlvfpdpahiasivssdkpKLLEEIKKLMNqFI 184
                                        4444444443222211111112233333444444555556666666666665555555555422333333344346 PP

                       Exonuc_VII_L 243 eekkerleeleeklealsplkvLkrGyaivrkedgkvvtsakdlkk 288
                                        ee+k +++ ++e+le+ + +k++ +G a+v+++ +++v ++ dl +
  gene1821|gene1821|rna1821|rna1821 185 EEAKLEIS-QIEELELHDQKKIMDKGVAMVMNALEEIVYETLDLIE 229
                                        66666665.7789******************977888887766655 PP

>> Mating_N  Mating-type protein beta 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.23   5.9e+02      12      44 ..      26      59 ..      17      72 .. 0.78
   2 ?   11.0   0.0   0.00014      0.35       9      65 ..     216     273 ..     210     279 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.23
                           Mating_N 12 edvrqtLdalrkdFfssLrgesea.lstFlsaws 44
                                       ++  + L +l+++  + +++++ea   +Fl  ++
  gene1821|gene1821|rna1821|rna1821 26 CEMEKLLLTLKSEIHETINDGNEAlKLEFLHVFE 59
                                       66677788999999999999*9997788887665 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00014
                           Mating_N   9 esDedvrqtLdalrkdFfssLrgesea.lstFlsawskfdellqschdsLseeTleli 65 
                                          +e+v +tLd ++k+  s+ ++es++ +++ ++++s ++e++    ++ ++ T e i
  gene1821|gene1821|rna1821|rna1821 216 ALEEIVYETLDLIEKKVCSATNKESRTlVESIYRNYSLLEEFITIKASEMTKNTEEII 273
                                        3399***************************************999999999997766 PP

>> IKKbetaNEMObind  I-kappa-kinase-beta NEMO binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.1     0.067   1.7e+02       6      29 ..      27      50 ..      23      52 .. 0.86
   2 ?    8.5   0.1   0.00079         2       5      21 ..     127     143 ..     125     145 .. 0.92
   3 ?   -1.4   0.1         1   2.6e+03       3      14 ..     172     183 ..     171     192 .. 0.60

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.067
                    IKKbetaNEMObind  6 EnqnyLsqLtslmqettkeqdsSl 29
                                       E +++L  L s ++et+ ++++ l
  gene1821|gene1821|rna1821|rna1821 27 EMEKLLLTLKSEIHETINDGNEAL 50
                                       6789999**********9998776 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00079
                    IKKbetaNEMObind   5 eEnqnyLsqLtslmqet 21 
                                        +Enq+ ++q + ++ +t
  gene1821|gene1821|rna1821|rna1821 127 KENQKICTQIEQILCDT 143
                                        6*************998 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 1
                    IKKbetaNEMObind   3 LleEnqnyLsqL 14 
                                        LleE  ++ +q+
  gene1821|gene1821|rna1821|rna1821 172 LLEEIKKLMNQF 183
                                        555555555554 PP

>> IL3Ra_N  IL-3 receptor alpha chain N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   2.0   0.00098       2.5      11      60 ..      82     146 ..      78     147 .. 0.77
   2 ?   -1.0   0.0       0.7   1.8e+03      19      31 ..     267     279 ..     233     306 .. 0.66

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00098
                            IL3Ra_N  11 rrLtWDlkenvteieCvlsskeesk..............ie.kkvaekntyCqFenlslheganl 60 
                                        + L+  ++e +t+ieC++++ +++               ie    +e++++C+  +  l+++ n+
  gene1821|gene1821|rna1821|rna1821  82 KILSYKCSELTTNIECLIKDVSNKIkktvytfnqaeeedIEaIIRKENQKICTQIEQILCDTHNF 146
                                        679999************99887556788888888877766455566666688888888888887 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.7
                            IL3Ra_N  19 envteieCvlssk 31 
                                        +n+ ei C ++  
  gene1821|gene1821|rna1821|rna1821 267 KNTEEIICEITRL 279
                                        3333444444333 PP

>> Shugoshin_N  Shugoshin N-terminal coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.2    0.0004         1      17      36 ..      82     101 ..      79     106 .. 0.88
   2 ?   -1.5   0.2      0.95   2.4e+03      14      25 ..     127     138 ..     125     139 .. 0.82
   3 ?    2.4   0.3     0.057   1.5e+02      19      37 ..     258     276 ..     256     283 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0004
                        Shugoshin_N  17 salslkirelekevseLlsE 36 
                                        ++ls k++el++ +++L++ 
  gene1821|gene1821|rna1821|rna1821  82 KILSYKCSELTTNIECLIKD 101
                                        689**************986 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.95
                        Shugoshin_N  14 KsNsalslkire 25 
                                        K N++++++i +
  gene1821|gene1821|rna1821|rna1821 127 KENQKICTQIEQ 138
                                        899999999965 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.057
                        Shugoshin_N  19 lslkirelekevseLlsEN 37 
                                        +++k +e++k  +e++ E+
  gene1821|gene1821|rna1821|rna1821 258 ITIKASEMTKNTEEIICEI 276
                                        68999***********996 PP

>> DUF445  Protein of unknown function (DUF445)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   6.5     0.024        62     251     343 ..      31     130 ..       4     135 .. 0.60
   2 ?    8.0   5.0   0.00088       2.3     145     244 ..     171     270 ..     159     284 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.024
                             DUF445 251 lwealkdlllkdlneeesllrerisklleklge.......................klaedpklreklnkflenaa 303
                                        l   lk+ +++ +n+ + +l+                                   ++ae +k+++++  +l +++
  gene1821|gene1821|rna1821|rna1821  31 LLLTLKSEIHETINDGNEALK-----------LeflhvfeeatksiieyinkvsrwEYAETDKILSYKCSELTTNI 95 
                                        333344444444444332222...........12222222222244446666666799999999999999999999 PP

                             DUF445 304 akvlekyrldiskiveetvnafdaeeleelIelivgkeLq 343
                                        + ++++    +s  +++tv +f+++e ee Ie i++ke q
  gene1821|gene1821|rna1821|rna1821  96 ECLIKD----VSNKIKKTVYTFNQAE-EEDIEAIIRKENQ 130
                                        999998....8888888888888877.6678888888866 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.00088
                             DUF445 145 dlldriknllkdeevkekikelidelieeesgklvlesivsmflreltsilekvksdpdhllreeedkkvreliad 220
                                        +ll++ik+l++++ +++k++    e +e + +k + ++ v+m++++l++i+ +  +  ++ +  + +k+ r+l+++
  gene1821|gene1821|rna1821|rna1821 171 KLLEEIKKLMNQFIEEAKLEISQIEELELHDQKKIMDKGVAMVMNALEEIVYETLDLIEKKVCSATNKESRTLVES 246
                                        46777777777766666666666666666666777***************************************** PP

                             DUF445 221 llndpelaakveklkkkklsdlev 244
                                        +  + +l +++ ++k + + + ++
  gene1821|gene1821|rna1821|rna1821 247 IYRNYSLLEEFITIKASEMTKNTE 270
                                        999999999999999888876655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1881  (0.104914); expected 358.6 (0.02)
Passed bias filter:                      579  (0.032294); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.63u 0.29s 00:00:00.92 Elapsed: 00:00:00.48
# Mc/sec: 1931.23
//
Query:       gene1822|gene1822|rna1822|rna1822  [L=318]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
        7.9    6.4   7.0       0.95    9.4   1.1    2.2  2  Intein_splicing  Intein splicing domain


Domain annotation for each model (and alignments):
>> Intein_splicing  Intein splicing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.2     0.088   1.6e+03      49      73 ..      40      63 ..      29      78 .. 0.63
   2 ?    9.4   1.1   5.3e-05      0.95       3      76 ..     211     285 ..     205     305 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.088
                                       EEEEEETTS-EEEEETT-EEEECCT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Intein_splicing 49 lyeiklesgrkikaTpeHkllvvrd 73
                                         e++ ++ +++ +   Hkl+ v +
  gene1822|gene1822|rna1822|rna1822 40 TKELRKTKTYNVEIFTIHKLMKV-N 63
                                       34555555666666666777666.3 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 5.3e-05
                                        ECTTCEE.EEHHHHCC..ECTTEEEEEETTTTEEEEEEEEEEEEEEEEEEEEEEETTS-EEEEETT-EEEECCT.T CS
                                        xxxxxxx.xxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.x RF
                    Intein_splicing   3 ledgeek.vkieelve..kegeevlslnledlklevksvkkliklklkelyeiklesgrkikaTpeHkllvvrd.e 74 
                                        +ed+e+   ++    +  +eg +++ +n+e+lk++   v        +++ +i ++ ++ i+ T   +l  +++  
  gene1822|gene1822|rna1822|rna1822 211 FEDKEITnIEMC---DisREGITEQHYNMEELKIKTLMVLDKYTDIGRKIKKIITKDNTVIIHTVCDNLVFLNQnL 283
                                        566555534444...3559*******************9999988888********99999999766665553324 PP

                                        EE CS
                                        xx RF
                    Intein_splicing  75 gi 76 
                                        +i
  gene1822|gene1822|rna1822|rna1822 284 EI 285
                                        44 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (318 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1033  (0.0576162); expected 358.6 (0.02)
Passed bias filter:                      466  (0.0259914); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2267.78
//
Query:       gene1823|gene1823|rna1823|rna1823  [L=183]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.062   13.4   1.2      0.068   13.3   0.2    1.5  2  Mod_r     Modifier of rudimentary (Mod(r)) protein


Domain annotation for each model (and alignments):
>> Mod_r  Modifier of rudimentary (Mod(r)) protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.2   3.8e-06     0.068      55     110 ..      31      89 ..      19      96 .. 0.80
   2 ?   -2.4   0.0      0.25   4.5e+03      63      63 ..     157     157 ..     122     178 .. 0.59

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.8e-06
                              Mod_r  55 eleelrselqekle...elkelekefeekeqeldellqkfspdallarLqtavaeaeee 110
                                        e+++ ++ ++e+     el+el+k + e+ +  d+l+++f++  l + L t ++e ee+
  gene1823|gene1823|rna1823|rna1823  31 EVRNDKEIVNESVGrslELDELKKLWSEYCSIVDDLCDEFNLRVLNMELDTIISELEEM 89 
                                        555555555555432127**************************************996 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.25
                              Mod_r  63 l 63 
                                        l
  gene1823|gene1823|rna1823|rna1823 157 L 157
                                        2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       770  (0.0429472); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:02.37
# Mc/sec: 233.72
//
Query:       gene1824|gene1824|rna1824|rna1824  [L=283]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.4e-45  154.0   0.7    5.5e-45  153.7   0.7    1.1  1  ParA            NUBPL iron-transfer P-loop NTPase
      3e-08   33.8   0.0    3.6e-08   33.5   0.0    1.2  1  CbiA            CobQ/CobB/MinD/ParA nucleotide binding domain
    2.3e-07   30.9   3.3    2.5e-06   27.5   3.3    2.0  1  AAA_31          AAA domain
    0.00057   19.8   0.5      0.093   12.5   0.1    2.2  2  AAA_26          AAA domain
    0.00063   19.5   0.0      0.077   12.7   0.0    2.1  2  RuvB_N          Holliday junction DNA helicase RuvB P-loop do
     0.0021   17.3   1.0      0.016   14.4   0.3    2.4  3  ArsA_ATPase     Anion-transporting ATPase
      0.003   16.9   0.2     0.0054   16.1   0.2    1.6  1  MipZ            ATPase MipZ
      0.008   16.1   0.2       0.07   13.0   0.0    2.2  2  RsgA_GTPase     RsgA GTPase
  ------ inclusion threshold ------
      0.012   14.8   1.3      0.025   13.8   1.3    1.6  1  NB-ARC          NB-ARC domain
      0.015   15.0   0.0      0.023   14.4   0.0    1.3  1  AAA_24          AAA domain
       0.03   13.9   0.1      0.069   12.7   0.1    1.6  1  AAA_25          AAA domain
      0.031   14.7   0.5      0.077   13.4   0.5    1.8  1  RNA_helicase    RNA helicase
      0.041   14.1   1.7        0.1   12.8   1.7    1.7  1  zinc_ribbon_16  Zinc-ribbon like family
       0.11   12.4   0.2       0.22   11.4   0.1    1.6  2  NTPase_1        NTPase
       0.11   12.7   0.0       0.18   11.9   0.0    1.4  1  AAA_33          AAA domain
       0.11   12.9   0.1        0.2   12.1   0.1    1.4  1  AAA             ATPase family associated with various cellula
       0.23   10.6   0.1       0.32   10.1   0.1    1.1  1  DAP3            Mitochondrial ribosomal death-associated prot


Domain annotation for each model (and alignments):
>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  153.7   0.7   5.2e-48   5.5e-45       3     223 ..      48     263 ..      46     281 .. 0.92

  Alignments for each domain:
  == domain 1  score: 153.7 bits;  conditional E-value: 5.2e-48
                               ParA   3 kkviavlSgKGGVGKStvavnlAlaLakkglkvgllDaDiyGpsiprllgveeekpeqsekkliPvea..kgikvm 76 
                                        kk+iav+SgKGGVGKSt+ +++A aL+    k ++lD D+ Gpsi+++ g+e++ +++ +++++Pv++  + i v+
  gene1824|gene1824|rna1824|rna1824  48 KKIIAVMSGKGGVGKSTMCMQIAHALK----KCCVLDFDVSGPSIAKMSGTENAIITNVQDTFVPVHVhgTCIGVV 119
                                        79************************5....79********************99999999*******555699** PP

                               ParA  77 SigfllesedeavvwrGpmkskaikqllkdvewgelDyLiiDlPPGtgDeqltvaqklplagaviVttpqevalad 152
                                        S   + e ++   +++ + +s+++ ++l+++++++   ++iD+PPG +De+l + + ++ a +v+V+tp  +a++d
  gene1824|gene1824|rna1824|rna1824 120 SAYHVNEWHSVEQLYQPSFISSFLINVLSNCNFDTYTHVVIDTPPGITDEHLIISNYVD-AVCVLVSTPGVLAVND 194
                                        ******9999999********************************************97.789************* PP

                               ParA 153 vkkaiemfkkvkvkvlGvveNmsgfvcpkcgekteifgkgggeklaeelgvpllgeipldpeireasdegk 223
                                          ++i++++++ vkvlGvveNm  fvc+ cg     +g+  +++++ + gv++lg +   +++   +d g 
  gene1824|gene1824|rna1824|rna1824 195 LVRQIDFCERAGVKVLGVVENMREFVCE-CGCV-VPMGTVDVREVCLRRGVRYLGGLQCVKAVGMFADGGM 263
                                        ***************************8.7755.6789******************999999888888776 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.5   0.0   3.5e-11   3.6e-08       1      82 [.      51     215 ..      51     276 .. 0.87

  Alignments for each domain:
  == domain 1  score: 33.5 bits;  conditional E-value: 3.5e-11
                                        EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH...................... CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...................... RF
                               CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep...................... 54 
                                        ia++s+kGGvGK+t++  +a al++      ++D+D+ +++ a   g+en i +                      
  gene1824|gene1824|rna1824|rna1824  51 IAVMSGKGGVGKSTMCMQIAHALKK----CCVLDFDVSGPSIAKMSGTENAIITnvqdtfvpvhvhgtcigvvsay 122
                                        89**********************9....9***********99899999999889999999999999999999999 PP

                                        .......................................................................CCHCC CS
                                        .......................................................................xxxxx RF
                               CbiA  55 .......................................................................dlkrl 59 
                                                                                                               dl r 
  gene1824|gene1824|rna1824|rna1824 123 hvnewhsveqlyqpsfissflinvlsncnfdtythvvidtppgitdehliisnyvdavcvlvstpgvlavnDLVRQ 198
                                        9999999999999999999999999999999999999999999999999999999999999888877777766666 PP

                                        CHHHHHHCHCHHHH..EEEEEEE CS
                                        xxxxxxxxxxxxxxxxxxxxxxx RF
                               CbiA  60 lellealgkkkalllkiagvvln 82 
                                        + ++e+ g      +k++gvv n
  gene1824|gene1824|rna1824|rna1824 199 IDFCERAG------VKVLGVVEN 215
                                        66666666......446666655 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.5   3.3   2.4e-09   2.5e-06       2     162 ..      49     197 ..      48     210 .. 0.69

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 2.4e-09
                             AAA_31   2 kvIaianqKGGvGKTTtsvnlaaalaklgkkvLlvDlDpQanattglgiekneiektlyevlieeknikeaiiktk 77 
                                        k+Ia++  KGGvGK+T ++++a al    kk  + D+D  + +  +++ ++n i +++ ++++  ++++ + i   
  gene1824|gene1824|rna1824|rna1824  49 KIIAVMSGKGGVGKSTMCMQIAHAL----KKCCVLDFDVSGPSIAKMSGTENAIITNVQDTFV-PVHVHGTCI--- 116
                                        9*******************99998....7899******999888887777777777777755.333444444... PP

                             AAA_31  78 venldlips..sidLaeaeielvelekkeeilkellekvk.deYDyiiiDcpPsLglltenaLvasdsv.iipvqa 149
                                              ++s  +++  +   +l + +   + l ++l++ + d+Y  ++iD+pP    +t+  L++s++v  + v  
  gene1824|gene1824|rna1824|rna1824 117 ----G-VVSayHVNEWHSVEQLYQPSFISSFLINVLSNCNfDTYTHVVIDTPPG---ITDEHLIISNYVdAVCVLV 184
                                        ....2.3340134444445567777777888999999998466**********6...6899999999873233333 PP

                             AAA_31 150 eayaleGleqllk 162
                                        +   +  +++l++
  gene1824|gene1824|rna1824|rna1824 185 STPGVLAVNDLVR 197
                                        3333333444444 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0     0.012        13       5      37 ..      53      86 ..      49     106 .. 0.73
   2 !   12.5   0.1   8.8e-05     0.093     127     186 ..     177     247 ..     164     255 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.012
                             AAA_26  5 vtgtdtgvGKTvvslgLvralkr.kgvkvgyfKP 37
                                       v +   gvGK++ ++ +++alk+ +   +++  P
  gene1824|gene1824|rna1824|rna1824 53 VMSGKGGVGKSTMCMQIAHALKKcCVLDFDVSGP 86
                                       6677789**************9844555555555 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 8.8e-05
                             AAA_26 127 lgapvilVargglgtinqllltiealrqknvrvlGvilNkvrnp..e..........nvetlekksgipvlG 186
                                         +a  +lV ++g  ++n+l+ +i+++ + +v+vlGv+ N  r+   e          +v++++   g++ lG
  gene1824|gene1824|rna1824|rna1824 177 VDAVCVLVSTPGVLAVNDLVRQIDFCERAGVKVLGVVENM-REFvcEcgcvvpmgtvDVREVCLRRGVRYLG 247
                                        57888********************************997.3333313344444445777777777777666 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.0   7.3e-05     0.077      29      84 ..      43     104 ..      25     110 .. 0.73
   2 ?    4.7   0.0     0.021        23      32      79 ..     154     199 ..     139     223 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 7.3e-05
                             RuvB_N  29 reealdhv..llyGpPGlGkttlakiiakelgvklki...tsgPvleka.gdlaalltnlee 84 
                                        r++a   +  +++G  G+Gk+t+++ ia+ l+  +      sgP + k  g   a++tn+++
  gene1824|gene1824|rna1824|rna1824  43 RNTAGKKIiaVMSGKGGVGKSTMCMQIAHALKKCCVLdfdVSGPSIAKMsGTENAIITNVQD 104
                                        4444444412689******************98765422379***99862667899999987 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.021
                             RuvB_N  32 aldhvllyGpPGlGkttlakiiakelgvklkitsgPvlekagdlaall 79 
                                        +  hv++  pPG+       ii++ +++ +   s+P +   +dl+  +
  gene1824|gene1824|rna1824|rna1824 154 TYTHVVIDTPPGITDEH--LIISNYVDAVCVLVSTPGVLAVNDLVRQI 199
                                        668********996665..59***************999999998665 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.3   1.5e-05     0.016       4      25 ..      52      73 ..      48      82 .. 0.83
   2 ?   -3.8   0.0       5.3   5.6e+03     260     280 ..      91     111 ..      85     113 .. 0.77
   3 ?    0.8   0.1      0.21   2.2e+02     116     136 ..     146     165 ..     139     223 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.5e-05
                                       EEEEESTTSSHHHHHHHHHHHH CS
                        ArsA_ATPase  4 ilvgGKGGVGKttvsaatavkl 25
                                        +++GKGGVGK+t+   +a  l
  gene1824|gene1824|rna1824|rna1824 52 AVMSGKGGVGKSTMCMQIAHAL 73
                                       479***********99888776 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 5.3
                                        HHHHHHHHHHHHHHHTTTSEE CS
                        ArsA_ATPase 260 rkkiqkkylkeieelfedlev 280
                                           ++++ +++++++f +++v
  gene1824|gene1824|rna1824|rna1824  91 MSGTENAIITNVQDTFVPVHV 111
                                        556778889999999999987 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.21
                                        HHHHHHCSSSSEEEEESBSCC CS
                        ArsA_ATPase 116 llkyvkeeeydvvvlDtaPTG 136
                                        +l  ++ ++y  vv+Dt+P G
  gene1824|gene1824|rna1824|rna1824 146 VLSNCNFDTYTHVVIDTPP-G 165
                                        5555566778889999988.3 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.2   5.1e-06    0.0054       2      53 ..      50      97 ..      49     200 .. 0.68

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 5.1e-06
                                       EEEE--SSTTSSHHHHHHHHHHHHHTTT--EEEEE--TTT-HHHHHHHHHHH CS
                               MipZ  2 vivlgnekGGsGksttavhvavaLlkkGarvaaidldlrqrtlarylenraa 53
                                       +i +   kGG Gkst+++ +a aL k      ++d+d+   ++a+  +   a
  gene1824|gene1824|rna1824|rna1824 50 IIAVMSGKGGVGKSTMCMQIAHALKK----CCVLDFDVSGPSIAKMSGTENA 97
                                       7888899****************975....5677777777777766554444 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.0   6.6e-05      0.07      90     122 ..      38      72 ..       8      84 .. 0.75
   2 ?    0.6   0.0      0.43   4.5e+02      15      50 ..     176     210 ..     152     217 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 6.6e-05
                                        HHHHHHHCTT..SEEEEECSTTSSHHHHHHHHCTT CS
                        RsgA_GTPase  90 leelkellkd..ktsvlvGqSGvGKStLinallpe 122
                                         ++++++ ++   ++v+ G+ GvGKSt+  +++  
  gene1824|gene1824|rna1824|rna1824  38 KSRIARNTAGkkIIAVMSGKGGVGKSTMCMQIAHA 72 
                                        445666655532468999**********9888765 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.43
                                        S--EEEEEEESTTTT--HHHHHHHHHHHHHTT-EEE CS
                        RsgA_GTPase  15 NvdqllivvslkepelslnlldrfLvlaeekgiepv 50 
                                         vd ++++vs+    l +n l r + ++e++g++++
  gene1824|gene1824|rna1824|rna1824 176 YVDAVCVLVSTP-GVLAVNDLVRQIDFCERAGVKVL 210
                                        489999999988.88999999999999999988876 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   1.3   2.4e-05     0.025      18      52 ..      47      82 ..      34     157 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.4e-05
                                       SCSEEEEEEESTTSSHHHHHHHHCCSHCCCCC.CBT CS
                             NB-ARC 18 lqslvvalvGmgGvGKttlakqilnksdeveg.rFd 52
                                        ++++  ++G+gGvGK+t+  qi + +++     Fd
  gene1824|gene1824|rna1824|rna1824 47 GKKIIAVMSGKGGVGKSTMCMQIAHALKKCCVlDFD 82
                                       455777789***************998876655666 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   2.2e-05     0.023       4      73 ..      51     162 ..      48     171 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.2e-05
                             AAA_24   4 kiliyGpsgiGKTtlakel...gpkplfidtekGlksldadkfpdieswedfldevvel................. 59 
                                          ++ G+ g+GK+t++ ++    +k  ++d++ +  s+    + +   ++++ d++v +                 
  gene1824|gene1824|rna1824|rna1824  51 IAVMSGKGGVGKSTMCMQIahaLKKCCVLDFDVSGPSIAKMSGTENAIITNVQDTFVPVhvhgtcigvvsayhvne 126
                                        56778**************9999*********97666666666655555555555555566677777777777778 PP

                             AAA_24  60 ......................aaeladyktlviDt 73 
                                                              +++ ++y  +viDt
  gene1824|gene1824|rna1824|rna1824 127 whsveqlyqpsfissflinvlsNCNFDTYTHVVIDT 162
                                        888888888889999999999999999999999998 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   6.5e-05     0.069      27      57 ..      43      73 ..      31      86 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 6.5e-05
                             AAA_25 27 kgllpagelallaGapgtGKttlaldlalav 57
                                       ++   ++ +a+  G +g+GK+t+++++a+a+
  gene1824|gene1824|rna1824|rna1824 43 RNTAGKKIIAVMSGKGGVGKSTMCMQIAHAL 73
                                       566677889999****************986 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.5   7.3e-05     0.077       2      42 ..      53     105 ..      52     174 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 7.3e-05
                       RNA_helicase   2 wlyGpsgeGKStlakeLakallkkl............klkkkdsvysrnpedd 42 
                                        +++G+ g+GKSt++ ++a+al k              k+  +++ ++ n++d+
  gene1824|gene1824|rna1824|rna1824  53 VMSGKGGVGKSTMCMQIAHALKKCCvldfdvsgpsiaKMSGTENAIITNVQDT 105
                                        689*************9999987656666666666664444444444455555 PP

>> zinc_ribbon_16  Zinc-ribbon like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   1.7   9.6e-05       0.1      22     109 ..      49     130 ..      17     139 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 9.6e-05
                     zinc_ribbon_16  22 aavssaGgakfldksksslcprcskplpkcavcglslGtsdvtnkdskrksvvkevssskkrfekwlsfclscghg 97 
                                        + ++   g+   ++ ks++c + ++ l kc+v  + +    +++    +++++ +v+++   ++       +c  +
  gene1824|gene1824|rna1824|rna1824  49 KIIAVMSGKG--GVGKSTMCMQIAHALKKCCVLDFDVSGPSIAKMSGTENAIITNVQDTFVPVH----VHGTCIGV 118
                                        2222222222..45677*******************99888**999999999999998765544....33456677 PP

                     zinc_ribbon_16  98 ahashakewfst 109
                                        + a h +ew s 
  gene1824|gene1824|rna1824|rna1824 119 VSAYHVNEWHSV 130
                                        778888888775 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   0.00021      0.22       3      25 ..      53      75 ..      51     103 .. 0.85
   2 ?   -3.4   0.0       7.6     8e+03      22      34 ..     201     213 ..     189     221 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00021
                                       EEE--TTSSHHHHHHHHHHHH.. CS
                           NTPase_1  3 fiTGppGvGKtTlvkkvlellks 25
                                       +++G+ GvGK+T++ +++++lk+
  gene1824|gene1824|rna1824|rna1824 53 VMSGKGGVGKSTMCMQIAHALKK 75
                                       578******************86 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 7.6
                                        HH...GGGEEEEE CS
                           NTPase_1  22 llkssgvkvgGfy 34 
                                         +++ gvkv G++
  gene1824|gene1824|rna1824|rna1824 201 FCERAGVKVLGVV 213
                                        3444555555543 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00017      0.18       3      33 ..      53      87 ..      51     137 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00017
                             AAA_33  3 llvGlpGsGKstlaerllkklg.avllssdt...l 33
                                       ++ G  G+GKst   +++ +l+ +++l+ d+    
  gene1824|gene1824|rna1824|rna1824 53 VMSGKGGVGKSTMCMQIAHALKkCCVLDFDVsgpS 87
                                       799*******************9999998875553 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   0.00019       0.2       3      43 ..      54      96 ..      52     116 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00019
                                       EESSTTSSHHHHHHHHHHHHT...HEEEEEETTTCSSSSTTHHH CS
                                AAA  3 lyGppGtGKTllakavakelg...vefleisgsellskyvgese 43
                                       ++G  G+GK++++ ++a+ l+   v  + +sg+++  k+ g  +
  gene1824|gene1824|rna1824|rna1824 54 MSGKGGVGKSTMCMQIAHALKkccVLDFDVSGPSIA-KMSGTEN 96
                                       7899***************98554444788888888.5555444 PP

>> DAP3  Mitochondrial ribosomal death-associated protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.1    0.0003      0.32      18      50 ..      44      75 ..      30     103 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0003
                                       -SSS---EEEEE-SSSSSTTTTHHHHHHHGGGS CS
                               DAP3 18 dkkkkvkrlvltGekgsGKSvlLlqalayAlek 50
                                       + ++k+   v++G+ g+GKS++ +q+  +Al+k
  gene1824|gene1824|rna1824|rna1824 44 NTAGKKIIAVMSGKGGVGKSTMCMQIA-HALKK 75
                                       5667777789***********999965.56655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (283 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       660  (0.0368119); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); expected 358.6 (0.02)
Passed Vit filter:                        80  (0.00446204); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 1831.25
//
Query:       gene1825|gene1825|rna1825|rna1825  [L=1004]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.6e-36  124.5   0.8    3.5e-29  102.1   0.2    2.9  4  RIBIOP_C        40S ribosome biogenesis protein Tsr1 and BMS1
    6.1e-08   32.6   0.1    6.1e-08   32.6   0.1    3.4  3  AARP2CN         AARP2CN (NUC121) domain
    0.00082   19.0   0.8     0.0027   17.3   0.8    1.9  1  GTP_EFTU        Elongation factor Tu GTP binding domain
  ------ inclusion threshold ------
       0.18   11.7   0.2        1.2    9.0   0.0    2.3  3  Flavi_NS2B      Flavivirus non-structural protein NS2B
       0.87   10.0   4.0        4.5    7.8   4.0    2.2  1  G0-G1_switch_2  G0/G1 switch protein 2
          1    9.3   3.3          3    7.8   3.3    1.8  1  DUF4446         Protein of unknown function (DUF4446)
        9.9    6.2  12.3       0.17   11.8   1.0    3.3  4  DUF3439         Domain of unknown function (DUF3439)


Domain annotation for each model (and alignments):
>> RIBIOP_C  40S ribosome biogenesis protein Tsr1 and BMS1 C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.4   1.4       3.8   9.9e+03      25      47 ..      18      43 ..       3      70 .. 0.49
   2 !   30.0   0.0   1.4e-10   3.5e-07      40     202 ..     470     640 ..     453     647 .. 0.66
   3 !  102.1   0.2   1.4e-32   3.5e-29     191     291 ..     712     812 ..     692     813 .. 0.94
   4 ?   -5.1   1.6       6.5   1.7e+04      14      38 ..     960     984 ..     952     997 .. 0.45

  Alignments for each domain:
  == domain 1  score: -4.4 bits;  conditional E-value: 3.8
                           RIBIOP_C 25 sewdpken...lpeeyarifefenfk 47
                                        + + ke+    +  y++    +n++
  gene1825|gene1825|rna1825|rna1825 18 RKGNIKEKkkvIKGMYKNEPMDNNYD 43
                                       33333333333344444444444444 PP

  == domain 2  score: 30.0 bits;  conditional E-value: 1.4e-10
                           RIBIOP_C  40 ifefenfketkkrvlkeale..............eregveg....Gtyvrleiknvpeelveeknfdekkplivfg 97 
                                         ++f++ +++  ++l+++ +               +         G+y+++ +k   +++++    ++++ li+  
  gene1825|gene1825|rna1825|rna1825 470 KLSFQELRKNALQKLTNNHNkkqnstnpsttnhpIQ----NvfipGNYIEILVK---TTFNH----SPDSILIIAP 534
                                        444444443333333322222222333333223222....23444888888776...33444....3455555555 PP

                           RIBIOP_C  98 llphEekvsvvnvrikrhreyekpikskdplifsvGfRrfqakPifsqedtknnkhklerylkpght.cvatfygp 172
                                        +    +  +++++++ r++++ + ++s dp+++s G+ rf + P+f         h ++ yl+ +   c+a  ygp
  gene1825|gene1825|rna1825|rna1825 535 IDY--TAHALIKASFLRTKHFIHFVRSDDPIVVSAGWQRFITFPVFYRRL-----HGMNVYLRSSVDgCMACYYGP 603
                                        544..5668999**********************************9998.....6777777766667******** PP

                           RIBIOP_C 173 itfpntpvlafkel.........sskeasfrlvatGsvl 202
                                        ++ +   v++++++         ++   +fr+v+tG + 
  gene1825|gene1825|rna1825|rna1825 604 VCRGG--VVMVRRVcedgesnrdNNFFYNFRIVGTGRIN 640
                                        *9775..56666556677777777778899999999875 PP

  == domain 3  score: 102.1 bits;  conditional E-value: 1.4e-32
                           RIBIOP_C 191 asfrlvatGsvlevdpsriivkrivLtGhpfkihkktaviryMFfnpedvawFkpveLrTksGrrGhIkeslgthG 266
                                        ++ + + t ++l++++++ + k+++L+G+ + i+ +ta++r+MF+++++v+ F  + ++T sG+rG+Ik++l ++G
  gene1825|gene1825|rna1825|rna1825 712 TPTNTISTTTTLNTNNDHLMYKKLKLIGNAYAIKGNTAFVRNMFNTNLEVNRFLHAGIKTTSGIRGIIKKALDKNG 787
                                        566788999******************************************************************* PP

                           RIBIOP_C 267 yfkatFddklkqsDiVlmslYkrvf 291
                                         f+a F++++ + D+V++++++r+ 
  gene1825|gene1825|rna1825|rna1825 788 SFRASFEGEIVEGDTVILNTFVRMS 812
                                        **********************986 PP

  == domain 4  score: -5.1 bits;  conditional E-value: 6.5
                           RIBIOP_C  14 akyrglkslrtsewdpkenlpeeya 38 
                                        ak+++++++ ++e ++++ l +e++
  gene1825|gene1825|rna1825|rna1825 960 AKRKEMQRIAQQEKENEQRLRKEEE 984
                                        3444444444444433333222222 PP

>> AARP2CN  AARP2CN (NUC121) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.3       3.2   8.3e+03      37      64 ..      14      41 ..       5      42 .. 0.59
   2 !   32.6   0.1   2.4e-11   6.1e-08       3      86 .]     259     330 ..     257     330 .. 0.93
   3 ?   -2.1   0.2       1.6   4.1e+03      31      57 ..     972     997 ..     956     999 .. 0.64

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 3.2
                            AARP2CN 37 seskeeeskedrtlsveGyvrGsplsan 64
                                       +++k++ + ++++ +++G+ +  p+++n
  gene1825|gene1825|rna1825|rna1825 14 KDKKRKGNIKEKKKVIKGMYKNEPMDNN 41
                                       2222334444555667899999888877 PP

  == domain 2  score: 32.6 bits;  conditional E-value: 2.4e-11
                            AARP2CN   3 lnllrfisvqkfrplswReqrpyiladrveiltdseskeeeskedrtlsveGyvrGsplsanqlvHipglGDfqie 78 
                                        + ll  ++v k rpls++++++y+++d v+++ d                 GyvrG+++ a+  + +pg+GD+++ 
  gene1825|gene1825|rna1825|rna1825 259 RMLLNCVAVFKSRPLSFKCENAYVVVDCVRVERDGMRM------------RGYVRGKRMMAGACFYVPGVGDVKVG 322
                                        66888999********************9998877666............9************************* PP

                            AARP2CN  79 kieklpdP 86 
                                         i +++dP
  gene1825|gene1825|rna1825|rna1825 323 GIVRVKDP 330
                                        ******99 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 1.6
                            AARP2CN  31 veiltdseske...eeskedrtlsveGyvr 57 
                                        ++  ++    +   ee+ke++ ++ eG+++
  gene1825|gene1825|rna1825|rna1825 972 EKENEQ----RlrkEEEKERQRIKREGIIK 997
                                        222222....14448889999999999875 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.8     1e-06    0.0027      86     135 ..     184     235 ..     178     289 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1e-06
                                        HHHHHHHT-SEEEEEEETTTBSTHHHHHHHHHHHHTTTE..EEEEEESCGST CS
                           GTP_EFTU  86 evirglrvlDgavlvvdaveGvepqteevlrlalkegvp..iivfiNKmDrl 135
                                        ++i +++++D+avlvv  ++G++    e + l+++ g+p  ++ + + +D+ 
  gene1825|gene1825|rna1825|rna1825 184 QMIDAAKIADLAVLVVNGTDGICKEHVEFITLLNAFGMPkvVVYVATRVDNK 235
                                        799************************************8666666788865 PP

>> Flavi_NS2B  Flavivirus non-structural protein NS2B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.0   0.00045       1.2      18      60 ..     205     247 ..     189     261 .. 0.90
   2 ?   -1.6   0.0      0.87   2.2e+03      21      38 ..     596     613 ..     584     622 .. 0.75
   3 ?   -2.9   0.0       2.3     6e+03      23      48 ..     791     816 ..     771     859 .. 0.54

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00045
                         Flavi_NS2B  18 llkedvnllGPlivGGllialvvvaGrvddlelkklaevswee 60 
                                        + ke v+++  l + G+  ++v va rvd+  lk + +v w+e
  gene1825|gene1825|rna1825|rna1825 205 ICKEHVEFITLLNAFGMPKVVVYVATRVDNKTLKHVKKVVWKE 247
                                        67999************************************98 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.87
                         Flavi_NS2B  21 edvnllGPlivGGllial 38 
                                         +  + GP+  GG++++ 
  gene1825|gene1825|rna1825|rna1825 596 CMACYYGPVCRGGVVMVR 613
                                        577889*******99975 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 2.3
                         Flavi_NS2B  23 vnllGPlivGGllialvvvaGrvddl 48 
                                         ++ G ++ G  +i+   v  +v++l
  gene1825|gene1825|rna1825|rna1825 791 ASFEGEIVEGDTVILNTFVRMSVNEL 816
                                        34555555555555555555555555 PP

>> G0-G1_switch_2  G0/G1 switch protein 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   4.0    0.0018       4.5      44      96 ..     941     992 ..     934    1002 .. 0.59

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0018
                     G0-G1_switch_2  44 etvcspFssesrlreeeeavaklqaar.ekeaeekeeelvlekekakelalaqR 96 
                                        +tv+spF +e+ + e+e ++++++ +r +++++e+e++l  e+ek+++    +R
  gene1825|gene1825|rna1825|rna1825 941 NTVLSPFLKEDLVLEKEIKAKRKEMQRiAQQEKENEQRLRKEEEKERQ--RIKR 992
                                        69*********7666655544444444044444444445555555544..4444 PP

>> DUF4446  Protein of unknown function (DUF4446)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   3.3    0.0012         3      42      87 ..     953     998 ..     935    1000 .. 0.92

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0012
                            DUF4446  42 sleellkekleeveelkeeseelekeieeleeklkkslqkvglvrY 87 
                                         le+ +k k +e++++ ++++e+e+++++ eek ++ +++ g+++ 
  gene1825|gene1825|rna1825|rna1825 953 VLEKEIKAKRKEMQRIAQQEKENEQRLRKEEEKERQRIKREGIIKH 998
                                        589****************************************996 PP

>> DUF3439  Domain of unknown function (DUF3439)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.9      0.44   1.1e+03      34      73 ..     432     473 ..     411     477 .. 0.59
   2 ?   -1.1   0.0      0.68   1.7e+03      13      49 ..     477     513 ..     468     527 .. 0.75
   3 ?   11.8   1.0   6.8e-05      0.17      41      75 ..     698     733 ..     671     754 .. 0.76
   4 ?   -2.7   0.0       2.1   5.5e+03      48      61 ..     906     919 ..     873     935 .. 0.66

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.44
                            DUF3439  34 sgsgkpvrsiicptttttt..ttttttmpttttlptttkmsm 73 
                                         gs +   s   p tt+    tt+    p+t  +  t k+s+
  gene1825|gene1825|rna1825|rna1825 432 HGSNNRCNSNFIPPTTSPIppTTSPVNSPSTNPITKTNKLSF 473
                                        466666666555545544411444456677777777778775 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.68
                            DUF3439  13 kknskivkakssavdpdsakcsgsgkpvrsiicpttt 49 
                                        +kn+ +  +++++ +++s++ s + +p++ +  p   
  gene1825|gene1825|rna1825|rna1825 477 RKNALQKLTNNHNKKQNSTNPSTTNHPIQNVFIPGNY 513
                                        5666666677778999999999999999999999654 PP

  == domain 3  score: 11.8 bits;  conditional E-value: 6.8e-05
                            DUF3439  41 rsiicpttt.tttttttttmpttttlptttkmsmvk 75 
                                        + i  p t  t ttt t t+ ttttl t     m k
  gene1825|gene1825|rna1825|rna1825 698 KIISTPNTNpTLTTTPTNTISTTTTLNTNNDHLMYK 733
                                        445567665255777799**********98877766 PP

  == domain 4  score: -2.7 bits;  conditional E-value: 2.1
                            DUF3439  48 tttttttttttmpt 61 
                                         t +tt t  t+p 
  gene1825|gene1825|rna1825|rna1825 906 NTISTTNTNITIPN 919
                                        34455555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1004 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1944  (0.108428); expected 358.6 (0.02)
Passed bias filter:                      519  (0.0289475); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.87u 0.29s 00:00:01.15 Elapsed: 00:00:00.46
# Mc/sec: 6568.83
//
Query:       gene1826|gene1826|rna1826|rna1826  [L=616]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.7e-15   55.4   0.0    6.3e-14   51.8   0.0    2.7  2  CRM1_repeat_3    CRM1 / Exportin repeat 3
    2.3e-09   36.8   0.2    6.9e-09   35.2   0.2    1.8  1  CRM1_repeat_2    CRM1 / Exportin repeat 2
  ------ inclusion threshold ------
      0.035   14.4   0.1       0.19   12.1   0.1    2.3  1  Ca_bind_SSO6904  Calcium binding protein SSO6904


Domain annotation for each model (and alignments):
>> CRM1_repeat_3  CRM1 / Exportin repeat 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.8   0.0   1.1e-17   6.3e-14       4      50 ..      66     112 ..      63     113 .. 0.92
   2 ?   -0.2   0.0      0.19   1.1e+03      30      45 ..     137     152 ..     134     156 .. 0.83

  Alignments for each domain:
  == domain 1  score: 51.8 bits;  conditional E-value: 1.1e-17
                      CRM1_repeat_3   4 eWswnnlnkLCWAiGSISgamseedEkrfLvtvikdLLnLceekrgk 50 
                                        e +  +ln++CW +G+I ga+s edE  f v v+kdLL+Lce ++ k
  gene1826|gene1826|rna1826|rna1826  66 EMNTGTLNTMCWTVGCIQGALSAEDEDPFYVDVLKDLLTLCENRHRK 112
                                        567789************************************99987 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.19
                      CRM1_repeat_3  30 krfLvtvikdLLnLce 45 
                                         +fL tv k+L++++ 
  gene1826|gene1826|rna1826|rna1826 137 TNFLRTVAKKLFEFMR 152
                                        68*********98875 PP

>> CRM1_repeat_2  CRM1 / Exportin repeat 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.2   0.2   1.2e-12   6.9e-09      20      52 ..       1      33 [.       1      41 [. 0.92

  Alignments for each domain:
  == domain 1  score: 35.2 bits;  conditional E-value: 1.2e-12
                      CRM1_repeat_2 20 MakPeEVliveneeGeivretvkdtdtialYkt 52
                                       M++P EVlivene+Geivre+v+ t+++++ ++
  gene1826|gene1826|rna1826|rna1826  1 MPRPIEVLIVENEDGEIVREKVEGTENLEFGRM 33
                                       9**************************997555 PP

>> Ca_bind_SSO6904  Calcium binding protein SSO6904
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   3.2e-05      0.19      21      72 ..      96     149 ..      93     165 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.2e-05
                                        HHHHHHHHHHHHHHHHHSS-..HHHHHHHHHHHTHHHHHHTHHHHHHHHHHHHH CS
                    Ca_bind_SSO6904  21 veevekileeieedlrksnn..ikssiifvyanhveevkknkefydliskilek 72 
                                        v++++++l+  e+  rk ++  i s i++v  ++ +++++n +f   ++k l  
  gene1826|gene1826|rna1826|rna1826  96 VDVLKDLLTLCENRHRKEDKaiIASNIMYVVGKYYQFLRRNTNFLRTVAKKLFE 149
                                        5789999*****99999764448999******************9999887755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (616 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       704  (0.039266); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.61u 0.28s 00:00:00.89 Elapsed: 00:00:00.46
# Mc/sec: 4040.35
//
Query:       gene1827|gene1827|rna1827|rna1827  [L=698]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (698 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       955  (0.0532657); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.68u 0.31s 00:00:00.99 Elapsed: 00:00:00.47
# Mc/sec: 4437.95
//
Query:       gene1828|gene1828|rna1828|rna1828  [L=224]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.036   13.6   2.7       0.59    9.7   0.3    2.5  2  Fzo_mitofusin  fzo-like conserved region
       0.09   12.8   0.3       0.16   12.0   0.3    1.5  1  DUF226         Borrelia family of unknown function DUF226
       0.18   12.2   2.7       0.25   11.7   2.7    1.5  1  Gp-FAR-1       Nematode fatty acid retinoid binding protein (


Domain annotation for each model (and alignments):
>> Fzo_mitofusin  fzo-like conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.2    0.0058        35     112     155 ..      26      69 ..       5      99 .. 0.62
   2 ?    9.7   0.3   9.9e-05      0.59      77     111 ..     188     222 ..     183     224 .] 0.89

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.0058
                      Fzo_mitofusin 112 etekeleeeikelekeiekleevqkkakllrnkaslleseLekf 155
                                        +   ++ e+i++++++ ++le++ k  k   + a++l + +++ 
  gene1828|gene1828|rna1828|rna1828  26 KKLVKVVENIETMHNSNDALEKLRKMDKNTIKNAQKLYNTFQTC 69 
                                        22223334444444444444444444444445555555555554 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 9.9e-05
                      Fzo_mitofusin  77 tekLrlivsltsancshqvqqelsstfarlcqqvd 111
                                        t k+  iv ++s+n++  v qels+    l++q +
  gene1828|gene1828|rna1828|rna1828 188 TCKMCEIVPTHSENVERTVSQELSHHEGSLTHQNH 222
                                        568999*******************9999998865 PP

>> DUF226  Borrelia family of unknown function DUF226
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.3   2.6e-05      0.16      55     133 ..      52     128 ..      18     132 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.6e-05
                             DUF226  55 vkkekngvkksyalkklyyiefrFkkGsvfcYlkslarllkkekentkyykalleklkklekkvykFYnkklpegG 130
                                         k+++++ +k y   ++   ef    G ++cY++++a  l+   +n + + ++++++k+++ +vy+  +  ++++ 
  gene1828|gene1828|rna1828|rna1828  52 DKNTIKNAQKLYNTFQTCRNEFASSSGDLKCYIRTVACALDL--VNLTKQLVTVSEIKDVDLTVYDVLKTTFRDKK 125
                                        34455556677888888889*****************99976..55566778999**********99888888877 PP

                             DUF226 131 iik 133
                                        ++ 
  gene1828|gene1828|rna1828|rna1828 126 VLA 128
                                        765 PP

>> Gp-FAR-1  Nematode fatty acid retinoid binding protein (Gp-FAR-1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   2.7   4.2e-05      0.25      21      66 ..      23      68 ..      15     154 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 4.2e-05
                           Gp-FAR-1 21 eekaqlkevvknykgyknedellaalKkkspaLyekaeklqaklke 66
                                       +  ++l++vv+n +++ n +++l+ l k   +  ++a+kl++++++
  gene1828|gene1828|rna1828|rna1828 23 TISKKLVKVVENIETMHNSNDALEKLRKMDKNTIKNAQKLYNTFQT 68
                                       55689**************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1383  (0.0771376); expected 358.6 (0.02)
Passed bias filter:                      568  (0.0316805); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 1415.50
//
Query:       gene1829|gene1829|rna1829|rna1829  [L=211]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1423  (0.0793686); expected 358.6 (0.02)
Passed bias filter:                      606  (0.0338); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1489.84
//
Query:       gene183|gene183|rna183|rna183  [L=143]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.5e-34  115.5   0.0    1.1e-33  115.1   0.0    1.1  1  TAFII28   hTAFII28-like protein conserved region


Domain annotation for each model (and alignments):
>> TAFII28  hTAFII28-like protein conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.1   0.0   6.2e-38   1.1e-33       2      85 ..      43     126 ..      42     127 .. 0.98

  Alignments for each domain:
  == domain 1  score: 115.1 bits;  conditional E-value: 6.2e-38
                        TAFII28   2 LlenfdeeqlnRYevfrrsklnkaavkklvnsvlsqsvsqnvaivvaglaKvFvgeiveeArevqeeweesgplqpehlr 81 
                                    ++++++e ql+RYe+frrs + k ++kklvn+vl+q+++ n++i+v+g+aKvFvge+v +A+evq++w++sgpl+p+h++
  gene183|gene183|rna183|rna183  43 IVDQMTEPQLHRYESFRRSGFLKVNIKKLVNNVLNQACNPNFIIAVSGVAKVFVGEMVCKAKEVQDRWGDSGPLMPAHVH 122
                                    689***************************************************************************** PP

                        TAFII28  82 eayr 85 
                                    eayr
  gene183|gene183|rna183|rna183 123 EAYR 126
                                    **98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       587  (0.0327403); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.35s 00:00:00.95 Elapsed: 00:00:00.56
# Mc/sec: 769.43
//
Query:       gene1830|gene1830|rna1830|rna1830  [L=257]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.013   15.5   0.7       0.11   12.5   0.2    2.4  2  HisKA_2    Histidine kinase
      0.023   14.4   0.1      0.038   13.7   0.1    1.3  1  IFT46_B_C  Intraflagellar transport complex B protein 46 C te
       0.05   13.8   2.6        2.5    8.3   0.1    2.3  2  DUF1033    Protein of unknown function (DUF1033)
      0.057   13.6   0.6       0.17   12.1   0.6    1.9  1  DUF2258    Uncharacterized protein conserved in archaea (DUF2


Domain annotation for each model (and alignments):
>> HisKA_2  Histidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.13   5.8e+02      34      55 ..      62      84 ..      43     101 .. 0.74
   2 ?   12.5   0.2   2.6e-05      0.11      27      70 ..     146     189 ..     134     195 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.13
                            HisKA_2 34 resqnRvlsialiheeLykse.d 55
                                       + s+++++s  +++e+ yk   +
  gene1830|gene1830|rna1830|rna1830 62 ETSNEKIISCLMVYERNYKHMfN 84
                                       67889999999999998887543 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 2.6e-05
                            HisKA_2  27 eevkealresqnRvlsialiheeLyksedletvdfseylekLve 70 
                                         + +e++ e+++ ++s  ++ ++  + e++++ +f+ey+ +L +
  gene1830|gene1830|rna1830|rna1830 146 MSYREVMAEIEQNINSTKTVFDTVANYENFSNANFAEYVAELNK 189
                                        45689***********************************9965 PP

>> IFT46_B_C  Intraflagellar transport complex B protein 46 C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   8.6e-06     0.038     133     204 ..     142     213 ..     107     217 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 8.6e-06
                                        -TT----SS----TTGGGS---HHHHHHHTT----TT-TT--HHHHHHHHHHHHT----THHHHHHHHHHHH CS
                          IFT46_B_C 133 ppptveyskkmpdieelmqewpeefeealkkvklpsaeldlsLeeyvkiicaildiPveksliesLhlLFtl 204
                                          +t++y++ m +ie+ ++  ++ f+++++  ++ +a+    ++e+ ki  +il   +++++ie+++++F+l
  gene1830|gene1830|rna1830|rna1830 142 ARQTMSYREVMAEIEQNINSTKTVFDTVANYENFSNANFAEYVAELNKIFHSILLFKTKSEKIEAVKIFFDL 213
                                        5799******************************************************************98 PP

>> DUF1033  Protein of unknown function (DUF1033)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.4    0.0041        18      39      96 ..      74     128 ..      52     137 .. 0.69
   2 ?    8.3   0.1   0.00056       2.5      35      94 ..     143     202 ..     132     213 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0041
                            DUF1033  39 yykkeWqklkeeyksiksksnllaafWeeedkrWceecdedlqqykslallkdkqeip 96 
                                        +y+++++++ +     k  s  +  +++     Wc + ++ l q ++++l +d ++++
  gene1830|gene1830|rna1830|rna1830  74 VYERNYKHMFNV---KKVGSAKFEKLFNLLSFIWCTDEQNTLEQVRAMLLCRDDRKLV 128
                                        555555544333...333333344455666678****************999887765 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00056
                            DUF1033  35 ealkyykkeWqklkeeyksiksksnllaafWeeedkrWceecdedlqqykslallkdkqe 94 
                                             y++  ++++++ +s+k+  +++a + + ++ ++ e  +e  + ++s++l+k k+e
  gene1830|gene1830|rna1830|rna1830 143 RQTMSYREVMAEIEQNINSTKTVFDTVANYENFSNANFAEYVAELNKIFHSILLFKTKSE 202
                                        5567899***********************************************987654 PP

>> DUF2258  Uncharacterized protein conserved in archaea (DUF2258)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.6   3.7e-05      0.17      28      67 ..     171     210 ..     134     216 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.7e-05
                                        HTTSS.HHHHHHHHHHHHHHHHHHHHCCTT--TTSEEEEE CS
                            DUF2258  28 kkkkeekkeiaraiaeLNkklYevlveklkidKldvvrir 67 
                                        + ++ ++ + a+ +aeLNk  +++l  k k +K + v+i 
  gene1830|gene1830|rna1830|rna1830 171 NYENFSNANFAEYVAELNKIFHSILLFKTKSEKIEAVKIF 210
                                        4455667788999*************************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1232  (0.0687155); expected 358.6 (0.02)
Passed bias filter:                      516  (0.0287802); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.68u 0.37s 00:00:01.05 Elapsed: 00:00:00.59
# Mc/sec: 1306.28
//
Query:       gene1831|gene1831|rna1831|rna1831  [L=34]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (34 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       246  (0.0137208); expected 358.6 (0.02)
Passed bias filter:                      191  (0.0106531); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.47
# Mc/sec: 216.03
//
Query:       gene1832|gene1832|rna1832|rna1832  [L=150]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-06   27.8   0.0    2.7e-06   27.7   0.0    1.3  1  MutS_III  MutS domain III


Domain annotation for each model (and alignments):
>> MutS_III  MutS domain III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7   0.0   1.5e-10   2.7e-06      32      81 ..       1      50 [.       1     148 [. 0.79

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 1.5e-10
                                       HHHHHHHHHHH--BS-HHHHHHHHHHHHHT..TT.HHHHHHHHTT---HH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           MutS_III 32 mGaRlLrewllqPltdleeInaRldaVeeleneelreelrellrrlpDle 81
                                       mG  lL++++l P+t  eeI +R+ a+e l +++l  ++ ++l+++ D++
  gene1832|gene1832|rna1832|rna1832  1 MGYQLLKNNILFPFTGSEEIVQRQAAIEHLIDRKLTGKISHSLKNCIDID 50
                                       9****************************779999*********977765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       697  (0.0388756); expected 358.6 (0.02)
Passed bias filter:                      454  (0.0253221); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1047.71
//
Query:       gene1833|gene1833|rna1833|rna1833  [L=98]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 711.00
//
Query:       gene1834|gene1834|rna1834|rna1834  [L=157]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.2e-10   38.8  11.3    4.2e-10   38.5  11.3    1.0  1  HSP70       Hsp70 protein
  ------ inclusion threshold ------
      0.063   13.4   9.2       0.08   13.0   9.2    1.1  1  UPF0242     Uncharacterised protein family (UPF0242) N-termin
       0.24   10.8   7.8        0.3   10.5   7.8    1.1  1  PBP_sp32    Proacrosin binding protein sp32
        2.5    5.9   6.6          3    5.7   6.6    1.0  1  V_ATPase_I  V-type ATPase 116kDa subunit family


Domain annotation for each model (and alignments):
>> HSP70  Hsp70 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.5  11.3   9.4e-14   4.2e-10     483     594 ..      13     125 ..      11     129 .. 0.93

  Alignments for each domain:
  == domain 1  score: 38.5 bits;  conditional E-value: 9.4e-14
                                        EEETTTCCEEEEEEECCSS.SBHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.GGGSTHHH CS
                              HSP70 483 akdketgkeeeitieaseg.lseeeiekmvkdaeesaeedkkkkeaieakneaeelvyslekkleee.aekvseae 556
                                        a++k+++k+e++t+++s++  + e+ e+m k+++e++e+d+kkke++ ak e e+++y+l++k+ e   ++v+++ 
  gene1834|gene1834|rna1834|rna1834  13 AREKGSNKSEKLTVSNSNRkTTPEQLEEMHKKHKEFEEADRKKKENVSAKIEYEAMLYQLNEKVGEVpDQNVKSNL 88 
                                        7899*************998999********************************************888999999 PP

                                        HHHHHHHHHHHHCHTTSSCHHHHHHHHHHHHHHHHHHH CS
                              HSP70 557 kekvesaieeLkeeleeeekeeieakteelkkvvekia 594
                                        ++++++++e+L+++  +++kee+ +k++el  +++++a
  gene1834|gene1834|rna1834|rna1834  89 ESSLKQHQEWLDTH-PNADKEEYMNKKNELMGLLQQVA 125
                                        9************9.5899999****999999988876 PP

>> UPF0242  Uncharacterised protein family (UPF0242) N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   9.2   1.8e-05      0.08      68     173 ..      15     119 ..       3     124 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.8e-05
                            UPF0242  68 skleekeaklteldeglktkeealeelqeeeeeLkeeldakeeelerlkeenqqLqekleaiaedf..eelklele 141
                                        +k ++k +klt  + + kt  e+lee+ ++++e +e   +k+e++    e ++ L  +l++ + ++  +++k +le
  gene1834|gene1834|rna1834|rna1834  15 EKGSNKSEKLTVSNSNRKTTPEQLEEMHKKHKEFEEADRKKKENVSAKIEYEAMLY-QLNEKVGEVpdQNVKSNLE 89 
                                        55678888999888899*****************9987777776666666555554.6666666542266789999 PP

                            UPF0242 142 eqLaekqellqeyqetieeqrsvlekrqdqie 173
                                        + L++ qe l++  +   ++ + ++k+++  +
  gene1834|gene1834|rna1834|rna1834  90 SSLKQHQEWLDTHPN--ADKEEYMNKKNELMG 119
                                        99**99999998765..477778888877655 PP

>> PBP_sp32  Proacrosin binding protein sp32
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   7.8   6.6e-05       0.3     137     227 ..      20     116 ..      11     131 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 6.6e-05
                           PBP_sp32 137 evevsaevsslsaetPivteatstekeafqpwperllnnvee.......llksslslggkekapeakpkeeqllek 205
                                        + e  ++  s   +tP   e     ++ f+    ++++nv         l++ ++ + g++   + k + e  l++
  gene1834|gene1834|rna1834|rna1834  20 KSEKLTVSNSNRKTTPEQLEEMHKKHKEFEEADRKKKENVSAkieyeamLYQLNEKV-GEVPDQNVKSNLESSLKQ 94 
                                        56667778888999**999999999999*999999999998788899999*******.677777779999999*** PP

                           PBP_sp32 206 kqeqleehkteekkkqeeqeee 227
                                        +qe l+ h++++k++  ++++e
  gene1834|gene1834|rna1834|rna1834  95 HQEWLDTHPNADKEEYMNKKNE 116
                                        ***********99987776655 PP

>> V_ATPase_I  V-type ATPase 116kDa subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   6.6   0.00066         3      62     162 ..      22     125 ..       9     131 .. 0.62

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.00066
                         V_ATPase_I  62 sleapeekeldeleeelekleeelkelnenleklkkelnelvelkavlekakefleee.eeeeeeeeseeeeeeke 136
                                        ++ + ++++ ++  e+le+++++ ke++e  +k k++++  +e++a+l + +e + e  +++ +++ +++ ++++e
  gene1834|gene1834|rna1834|rna1834  22 EKLTVSNSNRKTTPEQLEEMHKKHKEFEEADRKKKENVSAKIEYEAMLYQLNEKVGEVpDQNVKSNLESSLKQHQE 97 
                                        3444455666777889999999999999999999999999999999999999999877544444444444333333 PP

                         V_ATPase_I 137 eeeeeeseeeeeeelleeeee....lsfva 162
                                          ++++++++ee   +++++e    l+ va
  gene1834|gene1834|rna1834|rna1834  98 WLDTHPNADKEE--YMNKKNElmglLQQVA 125
                                        333333332222..2222222233344555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2490  (0.138881); expected 358.6 (0.02)
Passed bias filter:                      783  (0.0436723); expected 358.6 (0.02)
Passed Vit filter:                        89  (0.00496402); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 1098.01
//
Query:       gene1835|gene1835|rna1835|rna1835  [L=551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     4e-150  500.9   0.5    2.5e-94  316.6   0.0    2.4  2  HSP70           Hsp70 protein
    9.7e-10   37.8   0.1    7.2e-05   21.8   0.0    3.2  3  MreB_Mbl        MreB/Mbl protein
     0.0003   20.6   0.1    0.00077   19.2   0.1    1.7  1  FGGY_C          FGGY family of carbohydrate kinases, C-termin
    0.00035   21.0   0.1       0.52   10.8   0.0    3.1  2  FtsA            Cell division protein FtsA
     0.0044   16.3   0.0        2.7    7.2   0.0    2.7  2  Hydantoinase_A  Hydantoinase/oxoprolinase
  ------ inclusion threshold ------
      0.014   14.1   0.0      0.022   13.4   0.0    1.2  1  GDA1_CD39       GDA1/CD39 (nucleoside phosphatase) family
      0.032   13.5   0.0       0.46    9.7   0.0    2.3  2  StbA            StbA protein
      0.057   12.4   0.1          9    5.2   0.0    2.6  3  DDR             Diol dehydratase reactivase ATPase-like domai


Domain annotation for each model (and alignments):
>> HSP70  Hsp70 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  316.6   0.0   1.1e-97   2.5e-94       1     317 [.      13     356 ..      13     369 .. 0.89
   2 !  181.6   0.7   8.5e-57   1.9e-53     318     482 ..     384     549 ..     368     551 .] 0.93

  Alignments for each domain:
  == domain 1  score: 316.6 bits;  conditional E-value: 1.1e-97
                                        EEEEEEXSSEEEEEEEETTEEEEEXXTTSXSSEESEEEEXTT.SEEETHHHHHCTTTTGGGEEEXGGGTTTXBTTS CS
                              HSP70   1 viGiDLGttnsvvavmeggkievianeegnrttPsvvaFtkk.erlvGeaAkrqavtnpkntvfsvKrliGrkfsd 75 
                                        +iGiDLGtt+s+v   ++g+ evi neeg+r+tPs+vaF+++ + ++G+aA ++ ++np+++v++vKrliGr ++ 
  gene1835|gene1835|rna1835|rna1835  13 AIGIDLGTTYSCVCAYRNGELEVISNEEGARITPSIVAFDEEgNIVIGTAAEHRLTSNPDKVVYDVKRLIGRGYDS 88 
                                        59****************************************99******************************** PP

                                        HHHHHHHTTXSSEEEEETT...............SBEEEEEEETTE..EEEHHHHHHHHHHHHHHHHHHHHTSBEE CS
                              HSP70  76 pevqkeikelpykvvkken...............gkavveveaage..kftpeqisamvLkklketaeaylgkkvt 134
                                        p +++ ik++p++vv+ +n               +++ +e+   g+   + p +is+ vL  lk+ aea+l+  vt
  gene1835|gene1835|rna1835|rna1835  89 PILESSIKKWPFRVVRWDNerncptdrparpdavDNIRIEIVKGGKttYYDPMEISGYVLGFLKRAAEAVLNSGVT 164
                                        ***************98772222222222222223456777777889889************************** PP

                                        EEEEEEXTTXXHHHHHHHHHHHHHTTXEEEEEEEHHHHHHHHHHTCCSS.....SCEEEEEEEEXSSXEEEEEEEE CS
                              HSP70 135 davitvPaYfndaqRqatkdAgkiAGLnvlRivNepTAaalaYGldkkd.....kernvlvyDlGggtfdvSilel 205
                                         avitvPa+fnd+q++ tk A++iAG++ +R++NepTAaal+Y  dk       ke++vlv+DlGggtfdvSil++
  gene1835|gene1835|rna1835|rna1835 165 TAVITVPAHFNDNQKEKTKMAAEIAGFKNVRLLNEPTAAALSYAYDKMRrkeanKEETVLVFDLGGGTFDVSILKF 240
                                        ***********************************************9989999********************** PP

                                        E....TT.EEEEEEEEEETTXSHHHHHHHHHHHHHHHHHHHHSXXGGG..SHHHHHHHHHHHHHHHHHTTTSSCSE CS
                              HSP70 206 e....kG.vfevkaTagDthlGGedfDealvehlveefkkkegidlsk..dkkalqrlkeaaekaKkeLSsskqte 274
                                        e    +G + ev++T gDt lGG dfD+al eh+++ f k++    ++  +++a +rl+ a+ekaK++LS+    +
  gene1835|gene1835|rna1835|rna1835 241 EppseSGaIAEVLNTEGDTFLGGVDFDNALFEHCLALFLKQNPSVKKEdiKDRAKRRLRMACEKAKRNLSA--MYS 314
                                        8666566467***************************988754433331146899****************..677 PP

                                        EEEEEEEEETTTEEEEEEEEHHHHHHHHHHHHHHTHHHHHHHH CS
                              HSP70 275 inleietvdedgkdlseklsRakfeelvedllertlepvekal 317
                                        +++eie++++ +  l ++++Ra f++l+++ ++r+++ v+ +l
  gene1835|gene1835|rna1835|rna1835 315 TTIEIECLHS-DLGLCTNITRALFNNLCMKHFRRCMDRVKGCL 356
                                        7888999999.99************************999876 PP

  == domain 2  score: 181.6 bits;  conditional E-value: 8.5e-57
                                        HHCTEEGGGCSEEEEESGGGGSHHHHHHHHHHTT.CHHBSSSHTTTHHHHHHHHHHHHHCTC..GCSH.CCEEEEB CS
                              HSP70 318 kdaklkkeeidevvlvGGstRiPkvqelvkelfg.kepsktvnpDeavaiGAAvqagvlsge..eevk.dllllDv 389
                                        +da     +id v++vGGs+Ri k++e++ e+fg +++  +v+pDea+a+GAA qa++ sg    +v+ +llllD+
  gene1835|gene1835|rna1835|rna1835 384 NDA---IAQIDRVIVVGGSSRIIKIREMLAEIFGeHKLDFSVHPDEAIARGAAYQAALISGGtsLDVEcPLLLLDT 456
                                        444...468*************************999***********************98554554489***** PP

                                        ESS-EEEEETTTEEEEEESTTCBSSEEEEEEEEESSTTSSSEEEEEEESSSSBGGGSEEEEEEEEECESSCSTTCS CS
                              HSP70 390 tpLslgietlggvmtkliernttiptkksqvfstaadnqtaveievlqgerelvkdnkllgsfeldgippaprGvp 465
                                        +pL ++ietlggv+t++i++nt+ipt k++vfsta+dnqt+v+i++++g  e+v++n+l+gsf+l gi+pa rGvp
  gene1835|gene1835|rna1835|rna1835 457 VPLNISIETLGGVATTIIKKNTVIPTAKTEVFSTASDNQTSVTINIFEGLGEMVEHNNLIGSFNLCGITPARRGVP 532
                                        **************************************************************************** PP

                                        EEEEEEEEETTSCEEEE CS
                              HSP70 466 qieVtfdidanGiltvs 482
                                        qieVt d+d nGil v+
  gene1835|gene1835|rna1835|rna1835 533 QIEVTCDVDNNGILVVT 549
                                        **************997 PP

>> MreB_Mbl  MreB/Mbl protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.0   0.00033      0.73       2      57 ..      12      74 ..      11      79 .. 0.75
   2 !   21.8   0.0   3.2e-08   7.2e-05      94     164 ..     164     240 ..     137     260 .. 0.81
   3 ?    3.5   0.0     0.012        26     274     316 ..     391     433 ..     380     440 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00033
                                       SEEEEEE-SSEEEE..EETTTEEEEE.E......ES-EEEETTT--EEEESHHHHTTTTS-GTTE CS
                           MreB_Mbl  2 kdlgiDLGtantlv..yvkgkgivln.e......psvvAikkktkkvlavGeeAkkmlgktpgni 57
                                       k +giDLGt+   v  y +g+  v++ e      ps+vA++++ + v  +G+ A++ l   p+++
  gene1835|gene1835|rna1835|rna1835 12 KAIGIDLGTTYSCVcaYRNGELEVISnEegaritPSIVAFDEEGNIV--IGTAAEHRLTSNPDKV 74
                                       789*******9988668888876664235666669*****9987754..7888888777777665 PP

  == domain 2  score: 21.8 bits;  conditional E-value: 3.2e-08
                                        -EEEEEE-SS--HHHHHHHHHHHHHTT-SEEEEEEHHHHHHHHTT--......TTSSS-EEEEEE-SS-EEEEEEE CS
                           MreB_Mbl  94 prvvicvPsgiteverrAvkeaakkaGarevllieeplaAAiGaglp......veepsgnmvvdiGggttevavis 163
                                        ++ vi+vP + ++ +++  k aa+ aG ++v l++ep aAA+    +       ++ +  +v d+Gggt +v+++ 
  gene1835|gene1835|rna1835|rna1835 164 TTAVITVPAHFNDNQKEKTKMAAEIAGFKNVRLLNEPTAAALSYAYDkmrrkeANKEETVLVFDLGGGTFDVSILK 239
                                        5789**************************************9776521111145566789*************96 PP

                                        T CS
                           MreB_Mbl 164 l 164
                                        +
  gene1835|gene1835|rna1835|rna1835 240 F 240
                                        5 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.012
                                        HH-EEEESGGGGSBTHHHHHHHHHS.S-EEE-SSTTTHHHHHHH CS
                           MreB_Mbl 274 drgivltGGgallkgldkllseetg.lpvkvaedpltcvakGtg 316
                                        dr ++++GG++ +  ++++l e +g  +   + +p +++a+G++
  gene1835|gene1835|rna1835|rna1835 391 DR-VIVVGGSSRIIKIREMLAEIFGeHKLDFSVHPDEAIARGAA 433
                                        44.5666***************9963678999999999999986 PP

>> FGGY_C  FGGY family of carbohydrate kinases, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.1   3.5e-07   0.00077     145     196 ..     377     438 ..     319     439 .. 0.72

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 3.5e-07
                             FGGY_C 145 d........sgkpldrlavdGGgskndllmqllAdilg.vpVe.rpktaeatalGaAilAav 196
                                                   +++dr++v+GG s+   ++++lA+i+g  +++  ++++ea a GaA+ Aa+
  gene1835|gene1835|rna1835|rna1835 377 AantsaindAIAQIDRVIVVGGSSRIIKIREMLAEIFGeHKLDfSVHPDEAIARGAAYQAAL 438
                                        0444444335788*************************9555514555************96 PP

>> FtsA  Cell division protein FtsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.4   0.1    0.0052        12       1      35 [.      14      46 ..      14      63 .. 0.81
   2 !   10.8   0.0   0.00023      0.52       2     101 ..     225     437 ..     224     438 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0052
                                       EEEEE-SSSEEEEEEETTEEEEEEEES-.-HHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxx RF
                               FtsA  1 alvDiGagktdvavaedgalvhlrvigv.ggngitk 35
                                       +++D+G++ ++v  +++g    l+vi   +g  it 
  gene1835|gene1835|rna1835|rna1835 14 IGIDLGTTYSCVCAYRNG---ELEVISNeEGARITP 46
                                       58***************9...677776666666665 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00023
                                        EEEE-SSSEEEEEEETTEEEE....EEEES--HHHHHHH..............................HHHHHT- CS
                                        xxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxx..............................xxxxxxx RF
                               FtsA   2 lvDiGagktdvavaedgalvh....lrvigvggngitkd..............................iakalrt 43 
                                        + D+G+g+ dv++++ + +       +v++++g+ +  +                              +++ lr+
  gene1835|gene1835|rna1835|rna1835 225 VFDLGGGTFDVSILKFEPPSEsgaiAEVLNTEGDTFLGGvdfdnalfehclalflkqnpsvkkedikdrAKRRLRM 300
                                        5699************9988888888888885555555555555599999999999999999999999999999** PP

                                        -HHHHHHHHHHH--S--EEEEEHHHHH................................................. CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxx................................................. RF
                               FtsA  44 aveeAerikikyGsalaekeigrkels................................................. 70 
                                        a e+A+r      sa+ + +i+ + l+                                                 
  gene1835|gene1835|rna1835|rna1835 301 ACEKAKRNL----SAMYSTTIEIECLHsdlglctnitralfnnlcmkhfrrcmdrvkgcllglakikpdytsegfl 372
                                        ****99999....888866666544557777777777888878888888888888889999999999999999999 PP

                                        .........................GGGGSTTHHHHHHHHH.........T-..HH.HT-GGGHHH CS
                                        .........................xxxxxxxxxxxxxxxx.........xxxxxx.xxxxxxxxx RF
                               FtsA  71 .........................ggsalpnleelaeral.........spklee.vsdpeyasa 101
                                                                 g+s + +++e++++++          p +e+ +++ +y +a
  gene1835|gene1835|rna1835|rna1835 373 taasaantsaindaiaqidrvivvgGSSRIIKIREMLAEIFgehkldfsvHP-DEAiARGAAYQAA 437
                                        9999999999999999999999999999999999999999754444444333.4555666666665 PP

>> Hydantoinase_A  Hydantoinase/oxoprolinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.1   0.1    0.0026       5.8      74     109 ..       6      41 ..       1      56 [. 0.83
   2 !    7.2   0.0    0.0012       2.7      74      97 ..     216     239 ..     195     254 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0026
                     Hydantoinase_A  74 klagekkvItfDmGGTstDvslikdgevevsletei 109
                                        ++++ +k+I++D+G T   v+++++ge ev +++e 
  gene1835|gene1835|rna1835|rna1835   6 TKQETSKAIGIDLGTTYSCVCAYRNGELEVISNEEG 41 
                                        4566779**********************9888874 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0012
                     Hydantoinase_A  74 klagekkvItfDmGGTstDvslik 97 
                                        + ++e+ v++fD+GG ++Dvs +k
  gene1835|gene1835|rna1835|rna1835 216 EANKEETVLVFDLGGGTFDVSILK 239
                                        56678899*************987 PP

>> GDA1_CD39  GDA1/CD39 (nucleoside phosphatase) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   9.8e-06     0.022     142     286 ..     204     341 ..     201     367 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 9.8e-06
                          GDA1_CD39 142 aiNYllGkfnkeapevskqetvgvlDlGGaStQia...fepq.eeseiaekvedieelklqekledkkyklyvtsf 213
                                        a+ Y++ k+ ++  e++k+etv v+DlGG+   +    fep  e+++iae   +  e  + +   d +  l+ +  
  gene1835|gene1835|rna1835|rna1835 204 ALSYAYDKMRRK--EANKEETVLVFDLGGGTFDVSilkFEPPsESGAIAEV-LNT-EGDTFLGGVDFDNALFEHCL 275
                                        788999999999..89**************987643349999555666554.444.24566677788889999998 PP

                          GDA1_CD39 214 LgyGanealrkklaklikkaseevlkdpClprglektvevkdlefkqfaikgtgnyeqCrksikellnknakC 286
                                          + +++   k  +++ik   +  l+  C + + +    ++++   + +   +++   C++ ++ l+n+   C
  gene1835|gene1835|rna1835|rna1835 276 ALFLKQNPSVK--KEDIKDRAKRRLRMACEKAKRNLSAMYSTT---IEIECLHSDLGLCTNITRALFNN--LC 341
                                        88876665554..457888888889999999888888888777...44555677888899999999884..33 PP

>> StbA  StbA protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0   0.00021      0.46     140     180 ..     192     238 ..     176     263 .. 0.76
   2 ?    1.0   0.0      0.09     2e+02     269     286 ..     387     404 ..     373     426 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00021
                               StbA 140 kkvkvlPeslPagfealke......ldeleslLiiDlGGttLDvakv 180
                                        k+v+ l e   a+ +   +       ++ e +L+ DlGG t Dv+ +
  gene1835|gene1835|rna1835|rna1835 192 KNVRLLNEPTAAALSYAYDkmrrkeANKEETVLVFDLGGGTFDVSIL 238
                                        566666666666554332222333489999**************965 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.09
                               StbA 269 fsgythvmvvGGGaelia 286
                                        ++++ +v+vvGG + +i+
  gene1835|gene1835|rna1835|rna1835 387 IAQIDRVIVVGGSSRIIK 404
                                        456789*********995 PP

>> DDR  Diol dehydratase reactivase ATPase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0    0.0066        15     132     153 ..     220     241 ..     154     289 .. 0.89
   2 ?    5.2   0.0     0.004         9     268     301 ..     383     416 ..     362     420 .. 0.83
   3 ?   -3.0   0.0       1.2   2.7e+03     279     297 ..     438     456 ..     427     459 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.0066
                                DDR 132 ekplailDlGaGstDaalieee 153
                                        e+ + + DlG+G+ D ++++ e
  gene1835|gene1835|rna1835|rna1835 220 EETVLVFDLGGGTFDVSILKFE 241
                                        567899***********99755 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.004
                                DDR 268 ptgnirdidfvvlvGgsalDfEipelvtdalaey 301
                                         ++ i +id v++vGgs+    i e++++ + e+
  gene1835|gene1835|rna1835|rna1835 383 INDAIAQIDRVIVVGGSSRIIKIREMLAEIFGEH 416
                                        456699*********************9987665 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 1.2
                                DDR 279 vlvGgsalDfEipelvtda 297
                                         + Gg++lD E p l+ d+
  gene1835|gene1835|rna1835|rna1835 438 LISGGTSLDVECPLLLLDT 456
                                        6789*******99988775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (551 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       504  (0.0281109); expected 358.6 (0.02)
Passed bias filter:                      441  (0.024597); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.68u 0.31s 00:00:00.99 Elapsed: 00:00:00.49
# Mc/sec: 3388.02
//
Query:       gene1836|gene1836|rna1836|rna1836  [L=111]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (111 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       862  (0.0480785); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 805.73
//
Query:       gene1837|gene1837|rna1837|rna1837  [L=95]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       278  (0.0155056); expected 358.6 (0.02)
Passed bias filter:                      236  (0.013163); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.30s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 676.15
//
Query:       gene1838|gene1838|rna1838|rna1838  [L=523]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        6.4    6.7   7.5        1.4    8.9   3.5    1.9  2  MSA-2c    Merozoite surface antigen 2c


Domain annotation for each model (and alignments):
>> MSA-2c  Merozoite surface antigen 2c
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   3.5   7.9e-05       1.4       6      95 ..     312     410 ..     309     421 .. 0.76
   2 ?   -3.1   0.1      0.37   6.6e+03      47      71 ..     484     508 ..     452     517 .. 0.65

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 7.9e-05
                             MSA-2c   6 kakdtlkaLkkvkalikeeapfetslfdaevleelstkddee..llkallesikg.....mkiileklnkf..lke 72 
                                        k kd + +L+ ++++ik+   ++ +l ++e +  l   d+e+  l++a++  i       mki ++    f  l+e
  gene1838|gene1838|rna1838|rna1838 312 KCKDLHVTLQRIETIIKQALKMNIKLNNTELMASLIQLDNEQsaLFNAFIAHISAendlfMKIFVNMRIVFssLNE 387
                                        5789999***************************99988887557*****99975333336666554333322566 PP

                             MSA-2c  73 lrknsdkleeDkekvvkYykkhi 95 
                                          ++   + ++ +k++kY  +++
  gene1838|gene1838|rna1838|rna1838 388 NVRDNLNVMDEMNKIRKYVYDDV 410
                                        55555556666689999988877 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 0.37
                             MSA-2c  47 ellkallesikgmkiileklnkflk 71 
                                        + +k l+  i  ++ i e+ln+ l+
  gene1838|gene1838|rna1838|rna1838 484 DEYKKLVSLICTLNEICEHLNTILN 508
                                        3456666666666777777776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (523 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1162  (0.0648112); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.32s 00:00:00.90 Elapsed: 00:00:00.49
# Mc/sec: 3180.01
//
Query:       gene1839|gene1839|rna1839|rna1839  [L=190]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-26   93.2   0.0    1.8e-26   92.9   0.0    1.2  1  Carboxyl_trans  Carboxyl transferase domain


Domain annotation for each model (and alignments):
>> Carboxyl_trans  Carboxyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.9   0.0     1e-30   1.8e-26     295     431 ..       3     146 ..       1     185 [. 0.83

  Alignments for each domain:
  == domain 1  score: 92.9 bits;  conditional E-value: 1e-30
                                        EEEEEEE--SEEETTEE-HHHHHHHHHHHHHHHHTT--EEEEE-BSEE--SHHHHHTTHHHHHHHHHHHHHT--S- CS
                     Carboxyl_trans 295 pvGvvAnetrveaGqvlfidsavKaarfirlcdaenlPlviladvrGflvGqrqeyggilkhGaklvdalaeakvP 370
                                        pvG++      +   vl+  s++K + fi  ++aenl l+i+a+ +Gf++G  ++++gilk+G+k++++l++ k  
  gene1839|gene1839|rna1839|rna1839   3 PVGIIYAYE-NGTC-VLDAPSSEKFSTFIDQINAENLNLIIMANFKGFSGGDTDMKNGILKQGSKIIESLKTFKNK 76 
                                        788885542.3444.8************************************************************ PP

                                        EEEEE-T..EEEHHHHHTTTGGGSTTTTEEETTT-EEESS-HHHHHHHHSHHHHHHHHHHH.......HH CS
                     Carboxyl_trans 371 kitvilr..kayGGayvvmdskingadlvaawptariaVlgpegaveilfrkekaaaemer.......kd 431
                                        +++++    + +GG +v +d  in++  v+     ri+++ p+g++e++f+++   +  er       k+
  gene1839|gene1839|rna1839|rna1839  77 IFVYVGCgwQVRGGTFVILDKFINERIRVFVSMHGRIGIMQPSGLSEVKFKDKCRIKVLERnglvvndKN 146
                                        ****9888******************8889999********************99998777555543322 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (190 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       485  (0.0270511); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 1182.57
//
Query:       gene184|gene184|rna184|rna184  [L=415]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.7e-41  141.7   0.0    3.5e-41  141.3   0.0    1.1  1  Pkinase      Protein kinase domain
    5.2e-24   84.9   0.0    6.8e-24   84.5   0.0    1.1  1  Pkinase_Tyr  Protein tyrosine kinase
    0.00028   20.3   0.0    0.00047   19.6   0.0    1.3  1  Kdo          Lipopolysaccharide kinase (Kdo/WaaP) family
    0.00031   20.2   0.0     0.0005   19.5   0.0    1.4  1  Kinase-like  Kinase-like
  ------ inclusion threshold ------
      0.014   15.3   0.0        5.2    6.9   0.0    2.1  2  APH          Phosphotransferase enzyme family
      0.043   14.0   1.7        5.6    7.2   0.3    2.7  2  Tat          Transactivating regulatory protein (Tat)
       0.19   10.7   0.0       0.24   10.3   0.0    1.2  1  GRAS         GRAS domain family


Domain annotation for each model (and alignments):
>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  141.3   0.0   1.4e-44   3.5e-41       1     202 [.     148     364 ..     148     409 .. 0.86

  Alignments for each domain:
  == domain 1  score: 141.3 bits;  conditional E-value: 1.4e-44
                                    EEEEEEEEEESSEEEEEEEETTTTEEEEEEEEECHCHCHHHH...HHHHHHHHHHHHHS..CTTB--EEEEEEESSEEEE CS
                        Pkinase   1 yekleklGeGsfGkVykaveketgkivAvKkikkekakkkke...kkvlrEikilkklk..hpnivrlyevfeekdelyl 75 
                                    y++++ lGeG +++Vy++++ +t++ vA+K+  k  +  ++    ++ +r  +ilk+    +pniv+++++ e+ ++ ++
  gene184|gene184|rna184|rna184 148 YKTVRVLGEGRYATVYEGINCATNQRVAIKITCKMLMAGTNPhfiSNERRTYEILKNNArySPNIVQFVDFKEDRENAFF 227
                                    78899***************************99999999884555555556677776689******************* PP

                                    EEE--TTEBHHHHHH......HHSS--HHHHHHHHHHHHHHHHHHHHTTEE-SS-SGGGEEEETTTEEEE-SGTTSEESS CS
                        Pkinase  76 vleyveggeladlle......rkgslseeeakkiakqilegleylHskgiiHrDlKpeNiLidekgelKitDFGlakele 149
                                    ++ey +g +l++++       ++ +l+++e k ++ qi  +l++lH+  i+H DlKpeNi++  ++ +K++DFG +   +
  gene184|gene184|rna184|rna184 228 IMEYFDGFTLQRVVYeslnnkEREKLTDSERKGFLMQIGDALQFLHALDIFHGDLKPENIIVR-RQLIKLCDFGCSIVSS 306
                                    *********99998878888777789999**********************************.999********99998 PP

                                    SSCS...BCTTTSCGGGS-HHHH..TTSCBSHHHHHHHHHHHHHHHHHSS-STTTSSH CS
                        Pkinase 150 sssk...ltsfvgtseYlAPEvl..keneyskkvDvWslGvilyelltgkppfsgekg 202
                                     +        + gt+ Y +PEvl  ++    +  D W++++++y l++g +pf++++ 
  gene184|gene184|rna184|rna184 307 DRMCaakRLVYNGTPGYAPPEVLdmGGMVNLEDLDTWAYACVIYYLYSGVQPFAKDNL 364
                                    887777677899***********644445599**********************4443 PP

>> Pkinase_Tyr  Protein tyrosine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.5   0.0   2.7e-27   6.8e-24       3     218 ..     150     371 ..     148     409 .. 0.85

  Alignments for each domain:
  == domain 1  score: 84.5 bits;  conditional E-value: 2.7e-27
                                    EEEEEEEESSEEEEEEEEETTTTSSEEEEEEEEESTTSSHHHHHHHHHHHHHHHTS..-BTTB--EEEEEESSSSEEEEE CS
                    Pkinase_Tyr   3 lgkklGeGafGkVvegtlkgekekkevkVavKtlkeeateeekeelleeakimkkl..khpnivkllgvctkeepllivt 80 
                                    + + lGeG++++V+eg    ++++  +k+  K+l ++++ +  ++  + ++i+k+     pniv+++ +  ++e+ ++++
  gene184|gene184|rna184|rna184 150 TVRVLGEGRYATVYEGINCATNQRVAIKITCKMLMAGTNPHFISNERRTYEILKNNarYSPNIVQFVDFKEDRENAFFIM 229
                                    5689*************99999999999999999999999999999999****9987789******************** PP

                                    E--TTEBHHHHHHHT....CTTTSBHHHHHHHHHHHHHHHHHHHHTTEEEST-SGGGEEEEETTEEEE-STTTHEETTTS CS
                    Pkinase_Tyr  81 eyvkgGdLlkfLrkk....ekekltlkdllsfalqvAkGmeyLeskklvHrdlaarNvLlsenkvvkisDfGLardiekd 156
                                    ey +g +L+  + ++    e+eklt ++   f +q+ +++++L++ ++ H dl   N++++ ++++k++DfG +   +++
  gene184|gene184|rna184|rna184 230 EYFDGFTLQRVVYESlnnkEREKLTDSERKGFLMQIGDALQFLHALDIFHGDLKPENIIVR-RQLIKLCDFGCSIVSSDR 308
                                    ******99876554444449****************************************9.889*********998666 PP

                                    SEEEETTSSTSGGGGS-HHHHHHSE..EEHHHHHHHHHHHHHHHHTTSSGTTTTSHHHHHHHHH CS
                    Pkinase_Tyr 157 deyvkkeeaklpvkWmapEslkekk..ftsksDvWsfGvllwEiftlgespypglkneevlekl 218
                                        k+   +    + +pE+l+ +     +  D W+++ +++ +++ g +p+++ +  +++++l
  gene184|gene184|rna184|rna184 309 MCAAKRLVYNGTPGYAPPEVLDMGGmvNLEDLDTWAYACVIYYLYS-GVQPFAKDNLCRTFQNL 371
                                    66788888899999*******987633667889************9.99999876655555554 PP

>> Kdo  Lipopolysaccharide kinase (Kdo/WaaP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   1.9e-07   0.00047      91     155 ..     224     293 ..     193     306 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1.9e-07
                            Kdo  91 rAlllterlegaqdLedllakwae.....laeelkrallkavgrliaklhragvnHadlyaknillqqee 155
                                     A+ ++e  +g+    +++++ ++     l ++ ++  l+++g + + lh++++ H+dl + ni ++ + 
  gene184|gene184|rna184|rna184 224 NAFFIMEYFDGFTLQRVVYESLNNkerekLTDSERKGFLMQIGDALQFLHALDIFHGDLKPENIIVRRQL 293
                                    688888888888765555555444445578999999******************************9885 PP

>> Kinase-like  Kinase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0     2e-07    0.0005     112     253 ..     224     362 ..     199     395 .. 0.77

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 2e-07
                    Kinase-like 112 nallllpaas.vdleilnkvlqkrsethkkletiarlllTlqlirlaanLqakglvhgkftvdnllldekgglmlggfta 190
                                    na++++       l++++ +  ++ ++++kl +  r+   +q+    + L+a+ ++hg+++++n++  ++  ++l +f+ 
  gene184|gene184|rna184|rna184 224 NAFFIMEYFDgFTLQRVVYESLNN-KEREKLTDSERKGFLMQIGDALQFLHALDIFHGDLKPENIIVRRQ-LIKLCDFGC 301
                                    556666554323444444333333.33566777777766689999999*****************98766.699****98 PP

                    Kinase-like 191 Lvragtkvvlseve.....kgfaPpEllgsrggytrknktkmthkldaWqlGlviyriwclklPltla 253
                                     +   +++ +++        g+aPpE+l   g      +      ld+W+   viy++++ + P+ ++
  gene184|gene184|rna184|rna184 302 SIVSSDRMCAAKRLvyngtPGYAPPEVLDMGGM----VN---LEDLDTWAYACVIYYLYSGVQPFAKD 362
                                    77777777654433466679********99444....23...358*****************999876 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0    0.0032       8.1      32     108 ..     187     275 ..     150     277 .. 0.78
   2 ?    6.9   0.0     0.002       5.2     169     196 ..     278     302 ..     277     306 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0032
                                    S-HHHHHHHHHHHHHHHHTT-B--B-CTTBS-EEETTEEEEEEE----EE-SS............HHHHHHHHHHHHHHH CS
                            APH  32 raaeeirrevallrlLakagvpvPevlagdtddeeigllfalieyvpgrsllr............klsaaqlpellealg 99 
                                     ++ +i++e + +  L ++  + P ++ +    e+++  f+++ey +g +l r            kl++++++ +l ++g
  gene184|gene184|rna184|rna184 187 TNPHFISNERRTYEILKNNARYSPNIVQFVDFKEDRENAFFIMEYFDGFTLQRvvyeslnnkereKLTDSERKGFLMQIG 266
                                    4677999**********99889999999888888888899*********9999999999999999999999999999999 PP

                                    HHHCCHHCH CS
                            APH 100 eflaalhqv 108
                                    ++l  lh++
  gene184|gene184|rna184|rna184 267 DALQFLHAL 275
                                    999999987 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.002
                                    E-SS-SGGGEEEC..TTEEEEE---TT- CS
                            APH 169 lHgDlhpgNllvdpddgrvtGviDfeda 196
                                     HgDl+p N++v+    +++ + Df+++
  gene184|gene184|rna184|rna184 278 FHGDLKPENIIVR--R-QLIKLCDFGCS 302
                                    7***********9..3.33356777765 PP

>> Tat  Transactivating regulatory protein (Tat)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.3    0.0022       5.6      10      29 ..      52      71 ..      46      78 .. 0.86
   2 ?    5.0   0.1     0.011        28      12      28 ..      94     110 ..      86     117 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0022
                                   GGS-B-S-SS---S--SCCH CS
                            Tat 10 wkhpgsqpktactncyckkc 29
                                   ++h  s p +ac nc c + 
  gene184|gene184|rna184|rna184 52 FNHYFSSPLSACSNCPCLRF 71
                                   578899***********885 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.011
                                    S-B-S-SS---S--SCC CS
                            Tat  12 hpgsqpktactncyckk 28 
                                    h  + p +ac nc c +
  gene184|gene184|rna184|rna184  94 HVFNSPLSACSNCSCLQ 110
                                    6667899********76 PP

>> GRAS  GRAS domain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   9.5e-05      0.24     192     294 ..     164     265 ..     147     324 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 9.5e-05
                                    HHCT--TTSEEEEEEES.GGCSS-SSSSCCC..HHHHHHHHHHHC--SEEEEEEESS-S.SSHHHHHHHHHHHHHHHHHH CS
                           GRAS 192 eqLrvkpgEalaVnlvlqlhrlldesvsles..erdefLklvkslsPkvvvvveqeanhnsesFlerflealeyysalfd 269
                                    e +++ ++  +a+++  ++     +++ +++  ++ e+Lk   + sP++v +v+   +++++ F+ +  + +    ++++
  gene184|gene184|rna184|rna184 164 EGINCATNQRVAIKITCKMLMAGTNPHFISNerRTYEILKNNARYSPNIVQFVDFKEDRENAFFIMEYFDGFTLQRVVYE 243
                                    6677888888898888888888777777666447789******************************************* PP

                                    HHHHHS-TT-HHHHHHHHHTHHHHH CS
                           GRAS 270 sleaklpreseerikveeellgrei 294
                                    sl++k   e e+ +  e++ +  +i
  gene184|gene184|rna184|rna184 244 SLNNK---EREKLTDSERKGFLMQI 265
                                    **888...34444444554444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (415 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       648  (0.0361426); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 2657.42
//
Query:       gene1840|gene1840|rna1840|rna1840  [L=521]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.7e-97  325.3   0.8    1.9e-96  323.8   0.8    1.7  1  RtcB      tRNA-splicing ligase RtcB


Domain annotation for each model (and alignments):
>> RtcB  tRNA-splicing ligase RtcB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  323.8   0.8  1.1e-100   1.9e-96       1     412 []      61     521 .]      61     521 .] 0.88

  Alignments for each domain:
  == domain 1  score: 323.8 bits;  conditional E-value: 1.1e-100
                                        HHHHHTTSTTB-S-EEEEEEEE--SSS-EEEEEEE--EE-HHHC-SST.-EEEEEEEEEEHHHHGGGHHHHHHHHH CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               RtcB   1 qlknvaslpgivkhvaamPDvHlGkgapiGsViatkgviiPaaVGvDI.CGvrllktnltaeeleeklkelvkele 75 
                                        q+  v++lp ++  v+ +PD+HlG+ +piGsV+   g+++P++VG DI CGvr+++t  +  ++   + e++++l+
  gene1840|gene1840|rna1840|rna1840  61 QMLAVTRLPQVYT-VVGLPDIHLGYAFPIGSVVGA-GIVVPEGVGSDInCGVRMVRTRTNCRNV--DIAEVARQLF 132
                                        6778999***998.899***************985.9**************************9..58******** PP

                                        HHS-----......................--------H.HHHHHHHHHTHHHHHHTTSS-GGGGGGBGGGG--TT CS
                                        xxxxxxxx......................xxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               RtcB  76 kavpvglg......................skkkvklsk.keleevleegakwaveeglgeeedlekieeegalke 128
                                        + +p+g+g                      s+k++ +++ k ++e+++eg ++ v+ g+  +e  ++ie+ g++ +
  gene1840|gene1840|rna1840|rna1840 133 DVIPSGIGadtanatvseiaeqlnknvadtSNKEMVFTDlKVINEICNEGIDFLVKYGIVGDE-RDRIEKGGRFPG 207
                                        *******98999999999999998877765333333332489999999999999999988777.489999999999 PP

                                        --GGGS-HHHHHHHGGGTT---STT-EEEEEEEEEES-HHHHHHHT--TTEEEEEEEE--HHHHHHHHHHHHHHHH CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               RtcB 129 adlekvskkakerarkqlGtlGsGNHFiEvqlveeildeeaakalgleegqvvvmlHsGSRglGhqiaedylkiak 204
                                         d++  s+kak+++ kqlG+lG+GNHF+E+q v e+ d++     g e +++v+m+H+GSRglG +++e   ++a+
  gene1840|gene1840|rna1840|rna1840 208 -DSRMLSQKAKAKGLKQLGSLGAGNHFLELQRVVEVHDND----AGFEIDELVFMIHTGSRGLGFEVCESASQVAT 278
                                        .7999****************************9999976....58999***********************9999 PP

                                        .......CCHHHCT---SS.................................GGG--EETTSHHHHHHHHHHHHHH CS
                                        .......xxxxxxxxxxxx.................................xxxxxxxxxxxxxxxxxxxxxxxx RF
                               RtcB 205 .......kalkkkgiklpd.................................rdLaylpagseegqaYlkamqaaa 240
                                               +       ++ d                                 ++L+y+++  +e ++Y+ +m +aa
  gene1840|gene1840|rna1840|rna1840 279 smrsiskS-------EIGDesheirqvkqamglyendettvssvnssqlgsfENLSYFEI--HESEDYILEMGCAA 345
                                        44444440.......344444455556666677777788888888888888888888887..6799********** PP

                                        HHHHHHHHHHHHHHHHHHHHT.T--HHHH--EEEEEEESEEEEEEEE.TEEEEEEEES-EE-............TT CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............xx RF
                               RtcB 241 nyAkaNRqvitervreilekvlkkekedlelelvvdvaHNiakkEehedekvlVhRKGAtrA............kv 304
                                        n+A++NR++i ++v+++l+++       +++elv+dv HN  +kE+ ++++++VhRKGA rA            + 
  gene1840|gene1840|rna1840|rna1840 346 NFAFCNRAIISKKVENVLKNWN------IKCELVYDVGHNSLHKENIDGKELFVHRKGAARAlppnhpelrsnrEN 415
                                        **************99998765......6789***************9**************************** PP

                                        --EEEE--STTS-EEEEE--HHHHSSSEE---S-----------------TTTTTCCCT-EEEE------------ CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               RtcB 305 gqpviipGsmgtkSyivkGkgnaesfgStsHGAGRlmsRakakkkfkleevkkdleeqgigvearkkegvleEape 380
                                        gqp+ i Gsmgt+Sy++ ++++++s+ S+ HGAGR++sR+ka+k +++e++k+ +   ++++++++++g +eEap 
  gene1840|gene1840|rna1840|rna1840 416 GQPIPIGGSMGTSSYLLYAQDTKKSLFSSPHGAGRRISRSKARKLITMEQLKQMMG--NTVLMSKSEKGAIEEAPI 489
                                        *************************************************7766554..4457889999******** PP

                                        ------HHHHHHHHCTS-EEEEEEEEEEEEE- CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               RtcB 381 aYKdideVveaqaeaglvevvarlkpvlvvkg 412
                                         YKdi++Vv+a+ e glv++v++l+p++v+kg
  gene1840|gene1840|rna1840|rna1840 490 VYKDIEDVVNAAVELGLVKKVVKLEPLAVIKG 521
                                        *******************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (521 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       805  (0.0448993); expected 358.6 (0.02)
Passed bias filter:                      640  (0.0356964); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.66u 0.27s 00:00:00.93 Elapsed: 00:00:00.44
# Mc/sec: 3585.50
//
Query:       gene1841|gene1841|rna1841|rna1841  [L=89]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       426  (0.0237604); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 697.62
//
Query:       gene1842|gene1842|rna1842|rna1842  [L=295]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (295 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       811  (0.045234); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 2080.61
//
Query:       gene1843|gene1843|rna1843|rna1843  [L=239]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (239 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1087  (0.060628); expected 358.6 (0.02)
Passed bias filter:                      497  (0.0277205); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 1795.16
//
Query:       gene1844|gene1844|rna1844|rna1844  [L=924]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    6.2e-11   41.5   3.0    1.1e-10   40.8   3.0    1.4  1  Adaptin_N  Adaptin N terminal region


Domain annotation for each model (and alignments):
>> Adaptin_N  Adaptin N terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.8   3.0     6e-15   1.1e-10      34     179 ..      43     187 ..      12     321 .. 0.88

  Alignments for each domain:
  == domain 1  score: 40.8 bits;  conditional E-value: 6e-15
                                        HHCT---GHHHHHHHCCCCSS-CHHHHHHHHHHHHHCTTSCCHHCCCCHHHHHHCCSSSHHHHHHHHHHHCCC--C CS
                          Adaptin_N  34 ialGedvsflffevvklvaskdfelKrlvYlylellaeesedlalLvtnslqkDlkdpnqlirglALrvLssirvp 109
                                         ++ edvs ++ +v++ + + ++ +K l+  yl ++ ++ +  ++L++n+  kDl+d n++++   Lrv ++i+ +
  gene1844|gene1844|rna1844|rna1844  43 KMHTEDVSSYLTKVIRHIDTPNLFIKSLINYYLINIKHNTTV-LMLIINTTLKDLSD-NDYFKIQGLRVATNIKNS 116
                                        477899*****************************9999998.99**********87.89**************** PP

                                        CCHHHHHHHHHHHHT-SSHHHHHHHHHHHHHCCCCCHHCCCCC.HHHHHHHCTT-SSHHHHHHHHHHHHHH CS
                          Adaptin_N 110 elaedlapaikkllkdrspyvrkkAalailklykkdpdllrkq.lveeikellsdkdpgvvlaAvalleei 179
                                        ++ + ++  i kl++dr+ +vr  +++a++ +++++ d + +  + e++   + d+   v  ++++++   
  gene1844|gene1844|rna1844|rna1844 117 DIQQFFVARIHKLMSDRNFVVRLCSVIASISIFEQNYDKFMEYkFGEQLMRMMGDSVLAVRECVLMAISTT 187
                                        ***********************************9999988899************99999999999877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (924 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       773  (0.0431145); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.64u 0.28s 00:00:00.92 Elapsed: 00:00:00.43
# Mc/sec: 6471.46
//
Query:       gene1845|gene1845|rna1845|rna1845  [L=468]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-06   27.3  22.9    5.9e-06   25.0  22.9    2.0  1  Sec3_C           Exocyst complex component Sec3
  ------ inclusion threshold ------
      0.024   14.2   1.6       0.23   11.0   0.4    2.6  2  Chlor_dismutase  Chlorite dismutase
          2    7.8   6.6       0.75    9.2   0.9    2.7  2  UCH              Ubiquitin carboxyl-terminal hydrolase


Domain annotation for each model (and alignments):
>> Sec3_C  Exocyst complex component Sec3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0  22.9   9.9e-10   5.9e-06      58     349 ..      10     342 ..       2     387 .. 0.77

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 9.9e-10
                             Sec3_C  58 veLstlsedieyIEsqnngLQvksaNqklLykeLeellstvslsesdleaLkeaelssanglealeealeaLfkAl 133
                                        ++L+ ls ++e + + nn+ + + +N+ +L + L+el+  ++++e+  +  ++ +  +a  + ++ee+l  +f+++
  gene1845|gene1845|rna1845|rna1845  10 YKLNRLSAELEDVQNMNNTYETEINNKEKLRDALSELVRMLEIDEKYFSYFENDNYGDAMVMSRIEESL-YMFDCV 84 
                                        68**********************************************************888888777.689999 PP

                             Sec3_C 134 taIdsdlk.....dlesdlgemravkerrerYekvsssFlrrlveflekkfksaekelgkdldsatkkklslekhl 204
                                           ++d++     +l +d  ++++  e ++r   v+++F +++ +f  kk +s ++          k+k +l+ h+
  gene1845|gene1845|rna1845|rna1845  85 LGCQKDDHrvyayNL-NDF-NLKVANEFKKRILDVKKTFYKKFGHFFTKKLNSYKS----------KSKGELKIHK 148
                                        999999999*97444.444.7******************************66633..........45789999** PP

                             Sec3_C 205 evlnlLliYsgLilflKevdaekfeallqqYnasiskvYereikeffeslkkslkkssgseeseslssssseekkt 280
                                         ++++ ++Y++++           ++ +++Y+++++k+Y  e+++ +es+   lk+ ++ + s +l+   ++    
  gene1845|gene1845|rna1845|rna1845 149 DIYDEVIKYKSFMT----------QEYVEIYIKCMKKLYSHEFRYHLESVFDILKRKKNVTLSVNLNVIFQSLLLI 214
                                        ***********997..........566889********************99999777777777777777888888 PP

                             Sec3_C 281 eglalrksrkltlkssktganlsekaaqkktsgrlkpdeafaevLdel...eplilveQnFiidfFhlssl..... 348
                                         +  +   rk + ks++t+++    ++++++s++   ++ fa+ ++++    +++++ Q F+ d++ l+++     
  gene1845|gene1845|rna1845|rna1845 215 RECEYDFIRKISKKSTETHEQ----KNDEQSSEDETNSVYFATHFKDMdifDDVVIMIQTFLADLYELDRFqtiia 286
                                        889999999999999999944....5556666677777777777777622268****************9976777 PP

                             Sec3_C 349 .......................................................e 349
                                                                                                
  gene1845|gene1845|rna1845|rna1845 287 lgdsiqhyrektkeelrsgfyerflesvlnnyknlrkdfvrlaiskykgenkkktI 342
                                        77777777766776665555555555555555555555544444444444444433 PP

>> Chlor_dismutase  Chlorite dismutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0     0.037   2.2e+02      50      89 ..      39      74 ..      10     100 .. 0.74
   2 ?   11.0   0.4   3.8e-05      0.23     100     153 ..     385     439 ..     352     443 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.037
                                       HHHHHHHSTGGGGEEEEEEEEEEEEEESSSSS-GGGHHHC CS
                    Chlor_dismutase 50 aerelrrtalgkvlepaysyvsvtelseYkeedeenkshv 89
                                       ++ +l  ++l ++le  + y+s++e  +Y   d++  s +
  gene1845|gene1845|rna1845|rna1845 39 LRDAL--SELVRMLEIDEKYFSYFENDNY--GDAMVMSRI 74
                                       33333..56999*****************..444444444 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 3.8e-05
                                        SSEEEEEEEEE-EEGGGS-HHH.HHHHHHHHHHHHHGCTTEEEEEEE-TTTSSSS CS
                    Chlor_dismutase 100 kkyvcvYPmsksreWYllpeee.RrelmaeHgeigrkYgkVrqiitgsfGldDyE 153
                                        +k+ cvYP+ k  ++Y l  ee  + +++e   +  +Y ++++++ + + +dD E
  gene1845|gene1845|rna1845|rna1845 385 RKFECVYPIRKCTDYYFLLVEEmKKIIIDEMFAVELDYVRIKKNVGYIMRMDDEE 439
                                        7899**********77666665155567888899999********9999999988 PP

>> UCH  Ubiquitin carboxyl-terminal hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.5     0.046   2.8e+02      45     117 ..      27     108 ..       7     186 .. 0.61
   2 ?    9.2   0.9   0.00012      0.75       8      64 ..     200     258 ..     195     453 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.046
                                        -.TT.TTS.TTHHHHHHHHHHHHHH.......SH-CCEE--HHHHHHHHHHSGGGT..SSSTCEHHHHHHHHHHHH CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxx RF
                                UCH  45 lnesnplgkkgelakalkdlfkell.......kskskavsPkklkktlsklaksfs..gykqqDaqEflaflLdql 111
                                        +  + ++++k++l +al++l++ l          ++ ++   ++++ ++++  +f    + q+D + + a+ L+++
  gene1845|gene1845|rna1845|rna1845  27 NTYETEINNKEKLRDALSELVRMLEidekyfsYFENDNYGDAMVMSRIEESLYMFDcvLGCQKDDHRVYAYNLNDF 102
                                        2233445566678888888887777665444422233444455555555555555565666777777777777776 PP

                                        HHHHCC CS
                                        xxxxxx RF
                                UCH 112 hedlnr 117
                                        + ++ +
  gene1845|gene1845|rna1845|rna1845 103 NLKVAN 108
                                        666666 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00012
                                        STHHHHHHHHHHHTSHHHH.HHHHTCHHCCSSTCCCCC-.TT.TTS.TT.HHHHHHHHH CS
                                        xxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx RF
                                UCH   8 ntCymnsvlQcLfsipelr.dyllsleevkkesrnkkelnesnplgkkg.elakalkdl 64 
                                         +  +n + Q+L+ i+e   d++++++++++e++++k+ ++s++ +++   +a+++kd+
  gene1845|gene1845|rna1845|rna1845 200 LSVNLNVIFQSLLLIRECEyDFIRKISKKSTETHEQKNDEQSSEDETNSvYFATHFKDM 258
                                        55568**************9999998888888877776654444444444777766654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (468 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1726  (0.0962686); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.39
# Mc/sec: 3587.59
//
Query:       gene1846|gene1846|rna1846|rna1846  [L=175]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00022   20.8   0.1     0.0007   19.2   0.1    1.7  1  MTS              Methyltransferase small domain
     0.0052   16.2   0.0     0.0065   15.9   0.0    1.1  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
     0.0057   16.6   0.3      0.019   14.9   0.2    1.8  2  Methyltransf_18  Methyltransferase domain
  ------ inclusion threshold ------
      0.018   14.9   0.0      0.031   14.2   0.0    1.4  1  UPF0146          Uncharacterised protein family (UPF0146)
      0.042   13.1   0.0      0.063   12.6   0.0    1.2  1  Meth_synt_2      Cobalamin-independent synthase, Catalytic do
      0.072   13.8   0.0       0.12   13.1   0.0    1.3  1  Methyltransf_25  Methyltransferase domain
      0.075   12.8   0.0       0.15   11.8   0.0    1.3  1  N6-adenineMlase  Probable N6-adenine methyltransferase
       0.19   10.9   0.1       0.26   10.4   0.1    1.1  1  Methyltransf_33  Histidine-specific methyltransferase, SAM-de


Domain annotation for each model (and alignments):
>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.1   3.1e-07    0.0007      22     110 ..      13      91 ..       9     100 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 3.1e-07
                                        HHHHHCHCC..TCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTTTSTT CS
                                MTS  22 lLletlpke..lsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasdvleevee 95 
                                         Ll+t+ ++  +++ ++ +G+G   +  +l++ +      ++d++ +Al+ a         ++++++s++l+++++
  gene1846|gene1846|rna1846|rna1846  13 TLLDTIRAQelKNKVIVEIGTGSATIINTLLQYNH---CIATDINPYALKNA---------KCDAIQSNLLDNLQQ 76 
                                        57777777765566678888888777666666443...56888888888755.........4778999******** PP

                                        S-EEEEEE---STTT CS
                                MTS  96 kkfdlivsNPPfhag 110
                                          +d+i+ NPP+ ++
  gene1846|gene1846|rna1846|rna1846  77 TGIDVIIFNPPYLNE 91 
                                        ***********9766 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   2.9e-06    0.0065     153     213 ..      16      70 ..       9      98 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2.9e-06
                               PrmA 153 ealeklvkegeevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkveakl 213
                                         ++ ++  +++ ++ +GtGS+  +i   +L  ++ +a+Di++ A+k ak  a    ++++l
  gene1846|gene1846|rna1846|rna1846  16 DTIRAQELKNKVIVEIGTGSA--TIINTLLQYNHCIATDINPYALKNAKCDA----IQSNL 70 
                                        44445556667778******9..799******************98776543....33333 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.2   8.5e-06     0.019      13      68 ..      23      75 ..      13      83 .. 0.82
   2 ?   -1.1   0.0      0.74   1.7e+03       1      21 [.      89     108 ..      89     113 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 8.5e-06
                    Methyltransf_18 13 ekgsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagledkie 68
                                        k+++++ iGt  + +   l++ +   ++ia+Din+ +l++ak ++ +++l d+++
  gene1846|gene1846|rna1846|rna1846 23 LKNKVIVEIGTGSATIINTLLQYN---HCIATDINPYALKNAKCDAIQSNLLDNLQ 75
                                       46889****************755...56**************9999988877655 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.74
                    Methyltransf_18   1 lskRLkaiaslvekgsrvaDi 21 
                                        l++R+ ++ ++v+ +++++Di
  gene1846|gene1846|rna1846|rna1846  89 LNERIVRCEQMVP-CEKCLDI 108
                                        679999999***9.9999998 PP

>> UPF0146  Uncharacterised protein family (UPF0146)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   1.4e-05     0.031       9      62 ..      20      72 ..      13     107 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.4e-05
                                       HHHS-SSEEEEET-TT--HHHHHHHHHS-EEEEE-SS-S.....STTEE---SSS CS
                            UPF0146  9 aeenargkvvEvGiGrkldvaealakrgvdlvatDikekkak.egvrivrDDvtd 62
                                       a+e +++ +vE+G G  + +  +l+      +atDi++   k  ++ +++ ++ d
  gene1846|gene1846|rna1846|rna1846 20 AQELKNKVIVEIGTGSATIINTLLQYN--HCIATDINPYALKnAKCDAIQSNLLD 72
                                       556667789********9999988877..89*******97776777777776665 PP

>> Meth_synt_2  Cobalamin-independent synthase, Catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   2.8e-05     0.063     108     184 ..      13      95 ..       7     105 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.8e-05
                                        STHHHHHHTTS-SS-BEEEEE-HHHHHHTSEE-.....TTS-HHHHHHHHHHHHHHHHH.HHHHTT-SEEEEE-TT CS
                        Meth_synt_2 108 tvkesalaqsltdkpvkglltGpvtilnwsfvr.....ddvdraeaaaqialalrdevk.dLeaaGikviQiDepa 177
                                        t+  ++ aq l++k + ++ tG  ti+n           d++  +  +    a++ ++  +L++ Gi vi +  p 
  gene1846|gene1846|rna1846|rna1846  13 TLLDTIRAQELKNKVIVEIGTGSATIINTLLQYnhciaTDINPYALKNAKCDAIQSNLLdNLQQTGIDVIIFNPPY 88 
                                        56678899*******************9765443444478887777777778888887769*************** PP

                                        SSTT--S CS
                        Meth_synt_2 178 lreGlpl 184
                                        l e ++ 
  gene1846|gene1846|rna1846|rna1846  89 LNERIVR 95 
                                        *998875 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   5.1e-05      0.12       1      46 [.      28      70 ..      28      87 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 5.1e-05
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT CS
                    Methyltransf_25  1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl 46
                                       ++++G+G+ +++  l++     + +++Di++ +l++a+  a +++l
  gene1846|gene1846|rna1846|rna1846 28 IVEIGTGSATIINTLLQY---NHCIATDINPYALKNAKCDAIQSNL 70
                                       799*************88...7***************987766554 PP

>> N6-adenineMlase  Probable N6-adenine methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   6.9e-05      0.15      73     106 ..      56      96 ..      42     133 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 6.9e-05
                    N6-adenineMlase  73 Ydlnnpe..elpeel.....kgkfdviviDPPFlseeclkk 106
                                        Y l+n +   ++++l     +  +dvi++ PP+l+e +++ 
  gene1846|gene1846|rna1846|rna1846  56 YALKNAKcdAIQSNLldnlqQTGIDVIIFNPPYLNERIVRC 96 
                                        555555543344333344468899************99765 PP

>> Methyltransf_33  Histidine-specific methyltransferase, SAM-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.1   0.00012      0.26      41     108 ..       7      64 ..       3      83 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00012
                    Methyltransf_33  41 ptrtEiaiLqehaaeiaaaipaatlvelGsGsseKtrlLLealeaaekeltYvplDvseeaLeealea 108
                                        p ++ +++L++  a+   +++++++ve+G Gs++ +++LL+  +        ++ D++  aL++a  +
  gene1846|gene1846|rna1846|rna1846   7 PSEDTYTLLDTIRAQ---ELKNKVIVEIGTGSATIINTLLQYNH-------CIATDINPYALKNAKCD 64 
                                        555555555554433...345789****************9985.......69999999999987543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (175 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       477  (0.0266049); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1304.32
//
Query:       gene1847|gene1847|rna1847|rna1847  [L=206]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       763  (0.0425568); expected 358.6 (0.02)
Passed bias filter:                      522  (0.0291148); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1645.92
//
Query:       gene1848|gene1848|rna1848|rna1848  [L=533]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (533 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1062  (0.0592336); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.56u 0.25s 00:00:00.81 Elapsed: 00:00:00.43
# Mc/sec: 3694.68
//
Query:       gene1849|gene1849|rna1849|rna1849  [L=187]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       869  (0.048469); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.48
# Mc/sec: 1169.44
//
Query:       gene185|gene185|rna185|rna185  [L=225]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
       0.13   12.1   1.8       0.35   10.8   1.8    1.7  1  SF3a60_bindingd  Splicing factor SF3a60 binding domain


Domain annotation for each model (and alignments):
>> SF3a60_bindingd  Splicing factor SF3a60 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   1.8   1.9e-05      0.35      11      21 ..      90     100 ..      89     100 .. 0.96

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 1.9e-05
                SF3a60_bindingd  11 FYkrLkeIKdy 21 
                                    F+++LkeIK+y
  gene185|gene185|rna185|rna185  90 FFEQLKEIKEY 100
                                    9*********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (225 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       830  (0.0462937); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1619.66
//
Query:       gene1850|gene1850|rna1850|rna1850  [L=248]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.036   14.2   0.4      0.077   13.1   0.4    1.5  1  TssO            Type VI secretion system, TssO
      0.041   14.0   0.0      0.058   13.4   0.0    1.3  1  Neur_chan_memb  Neurotransmitter-gated ion-channel transmembr
       0.08   13.2   0.3       0.08   13.2   0.3    2.1  3  Orf78           Orf78 (ac78)


Domain annotation for each model (and alignments):
>> TssO  Type VI secretion system, TssO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.4   1.3e-05     0.077       4      61 ..      47     105 ..      45     109 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.3e-05
                               TssO   4 kErrsgflyflllFlvtvlllflivffffkssplqekeil.lkelerkkkfeekqkelk 61 
                                        +E  + fl f ++F++  ll+++++ ++ ++ p +++e++ + e+ +++++++ + +++
  gene1850|gene1850|rna1850|rna1850  47 REMSMVFLMFSVMFIIWFLLMYFCLTKTPYQQPDTHSEQEyVVEIGENNSLMSLNSNQE 105
                                        788999********************997777777776666999999998888777665 PP

>> Neur_chan_memb  Neurotransmitter-gated ion-channel transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   9.8e-06     0.058      59     160 ..      52     148 ..      48     217 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 9.8e-06
                                        HHHHHHHHHHHHHHHHHHHHHHHHHH-S-S---HHHHHHHTTHHHHHHC--------------............. CS
                     Neur_chan_memb  59 kYLlftmvfvtlsivetvfVlnvhhrsprthtmpawvrkvfldklprllfmkrpsevkdnekkl............ 122
                                         +L+f  +f +  ++ + +   + +++p th+ ++ v ++  +    l+ ++ ++e++++++++            
  gene1850|gene1850|rna1850|rna1850  52 VFLMFSVMFIIWFLLMYFCLTKTPYQQPDTHSEQEYVVEIGENNS--LMSLNSNQENNARPQSEasvdghhvdspl 125
                                        589999999999999999999999999999999999988776644..44444444444444433233444444333 PP

                                        .....-------------------------------------- CS
                     Neur_chan_memb 123 .....ssgasseaeelilskskseskkaklseeqgsekastck 160
                                             +                    +++l ee +s ++s  +
  gene1850|gene1850|rna1850|rna1850 126 sydrnN--------------------DEDLYEEIPSTESSSFS 148
                                        333220....................33333333333333333 PP

>> Orf78  Orf78 (ac78)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.3   1.3e-05      0.08      40      95 ..      22      78 ..      14      89 .. 0.67
   2 ?   -1.9   0.1      0.72   4.3e+03      30      37 ..     104     111 ..      91     140 .. 0.53
   3 ?   -2.9   0.0       1.5   8.7e+03      37      48 ..     196     207 ..     182     228 .. 0.47

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.3e-05
                              Orf78 40 kksaaeknditekesn.aaekaqalnillisllavvcvlvllyviyYfvilrerqks 95
                                       ++++ ++ ++ +++ n  ++++++   + +++l++ +++++ ++++Yf +++   ++
  gene1850|gene1850|rna1850|rna1850 22 TNNILQEPQAAQMNCNvYQNENAFRREMSMVFLMFSVMFIIWFLLMYFCLTKTPYQQ 78
                                       4445555555555555445667788899999999999***********999873332 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.72
                              Orf78  30 dndkaenk 37 
                                        ++++a+ +
  gene1850|gene1850|rna1850|rna1850 104 QENNARPQ 111
                                        22221111 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 1.5
                              Orf78  37 kkekksaaeknd 48 
                                        +++++++ ++ +
  gene1850|gene1850|rna1850|rna1850 196 ADDDNAQITSPR 207
                                        222222333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (248 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1016  (0.056668); expected 358.6 (0.02)
Passed bias filter:                      574  (0.0320152); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 1790.06
//
Query:       gene1851|gene1851|rna1851|rna1851  [L=197]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.14   12.2   0.5       0.63   10.0   0.1    2.1  3  ApoO      Apolipoprotein O


Domain annotation for each model (and alignments):
>> ApoO  Apolipoprotein O
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.1   3.5e-05      0.63      51      99 ..      20      70 ..       4      74 .. 0.77
   2 ?   -0.8   0.0     0.077   1.4e+03      52      75 ..     106     129 ..      94     130 .. 0.82
   3 ?   -2.7   0.0       0.3   5.5e+03      48      55 ..     164     171 ..     143     188 .. 0.52

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 3.5e-05
                               ApoO 51 svtdtiasLkepp.edllPrlgyilvagLaGsila.rrrsilkRvlyPlal 99
                                       +v++++++  e + + l+P l+++ v  ++G+i+  rr   ++++ yP  l
  gene1851|gene1851|rna1851|rna1851 20 NVSTELDTCVERSgPYLIPFLLAVFVIFILGLIFIiRRTKKFLKFSYPESL 70
                                       55666666666666899***************9972566789*****9765 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.077
                               ApoO  52 vtdtiasLkeppedllPrlgyilv 75 
                                        v + ++++ + p  + P++ yi+v
  gene1851|gene1851|rna1851|rna1851 106 VDSIFDQIEHNPSYFAPSSNYITV 129
                                        567788888889999999999987 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 0.3
                               ApoO  48 aeqsvtdt 55 
                                        +eq   + 
  gene1851|gene1851|rna1851|rna1851 164 LEQEYVSR 171
                                        23333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1008  (0.0562218); expected 358.6 (0.02)
Passed bias filter:                      640  (0.0356964); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1317.09
//
Query:       gene1852|gene1852|rna1852|rna1852  [L=229]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
       0.35   10.6   2.8        0.7    9.6   2.8    1.4  1  MotA_ExbB  MotA/TolQ/ExbB proton channel family


Domain annotation for each model (and alignments):
>> MotA_ExbB  MotA/TolQ/ExbB proton channel family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   2.8   3.9e-05       0.7      48     113 ..     111     173 ..      98     176 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 3.9e-05
                                        HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTSSSGGCTHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          MotA_ExbB  48 ilatigslaPllGLlGTVlGlieafqaladagsadlakvapgiaeALiaTalGlvvAipavlaynk 113
                                        il+   ++ ++l Ll TV+ + +a++ +++   ++ ++ a+ i  AL+  ++ l++ i +++  n+
  gene1852|gene1852|rna1852|rna1852 111 ILSLYYTYNTALCLLTTVILMCNALNMMSK---NNREVYATLIVNALYCGLMVLFTIIALMFQLNR 173
                                        677888899999*****************9...45589**************99998888777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (229 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1174  (0.0654805); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 1550.74
//
Query:       gene1853|gene1853|rna1853|rna1853  [L=237]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
       0.19   11.3   5.4       0.32   10.6   0.1    2.9  3  DUF716      Family of unknown function (DUF716)
       0.53   10.2   8.0      0.049   13.6   1.5    2.3  3  DUF679      Protein of unknown function (DUF679)
       0.79   10.0   9.2         23    5.3   4.0    2.6  2  DUF1772     Domain of unknown function (DUF1772)
        1.1    8.7  10.5        2.3    7.6   3.8    2.3  2  Ceramidase  Ceramidase
        4.6    6.5  14.9       0.17   11.2   0.9    3.0  3  DUF3810     Protein of unknown function (DUF3810)
        6.9    6.6   8.9       0.81    9.6   0.3    3.2  4  CAAD        CAAD domains of cyanobacterial aminoacyl-tRNA syn


Domain annotation for each model (and alignments):
>> DUF716  Family of unknown function (DUF716)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.2      0.57   1.7e+03      40      53 ..      30      43 ..      21      65 .. 0.47
   2 ?    2.0   0.2     0.049   1.5e+02      14      54 ..      73     113 ..      59     135 .. 0.74
   3 ?   10.6   0.1   0.00011      0.32       3      61 ..     168     226 ..     166     231 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.57
                             DUF716 40 vvalsllsalleal 53
                                       + ++sl ++++ ++
  gene1853|gene1853|rna1853|rna1853 30 MLLASLTMCVIATI 43
                                       23333333333333 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.049
                             DUF716  14 qelllfhfhskdhsglegrvhlLLvlvvalsllsalleall 54 
                                        +e +++   +++++ +++ +   L+++++++++ +++++  
  gene1853|gene1853|rna1853|rna1853  73 VEKYILGTNKTNKDSVNAFLMYGLIIIATVAVIYTFINCYE 113
                                        56677777888899999999999999999999999999974 PP

  == domain 3  score: 10.6 bits;  conditional E-value: 0.00011
                             DUF716   3 llkllaalaffqelllfhfhskdhsglegrvhlLLvlvvalsllsalleallpksflle 61 
                                         l  l  +af+++ + f +   d+++ +  v + L lv+al +++ ++ +l++++++ +
  gene1853|gene1853|rna1853|rna1853 168 TLSFLIVVAFGIKSVFFKSTDDDKKKKDEGVLKYLTLVIALIAAVLFMYTLVNSELYYD 226
                                        5678899*****************************************99999887665 PP

>> DUF679  Protein of unknown function (DUF679)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.6      0.23   6.8e+02      26      48 ..      80     102 ..      19     114 .. 0.59
   2 ?    0.1   0.1      0.23   6.8e+02      26      51 ..      80     105 ..      55     137 .. 0.74
   3 ?   13.6   1.5   1.6e-05     0.049      35     128 ..     140     232 ..     112     237 .] 0.78

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.23
                             DUF679  26 tneGeCetvnrlltaaLlallav 48 
                                        tn+ + ++vn +l+  L+++ +v
  gene1853|gene1853|rna1853|rna1853  80 TNKTNKDSVNAFLMYGLIIIATV 102
                                        33444444555555555544444 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.23
                             DUF679  26 tneGeCetvnrlltaaLlallavscv 51 
                                        tn+ + ++vn +l+  L+++ +v+ +
  gene1853|gene1853|rna1853|rna1853  80 TNKTNKDSVNAFLMYGLIIIATVAVI 105
                                        55666667777888877776665543 PP

  == domain 3  score: 13.6 bits;  conditional E-value: 1.6e-05
                             DUF679  35 nrlltaaLlallavscvllsfTDsivgedgkvyYgvatlkglkvfnkeke.deeeklekyrlrllDfvhAflsvvv 109
                                        + ++ +aLl+l+++++++ + T s+   +g++ + ++++ g+k +  +++ d+++k+++  l+ l +v A++++v 
  gene1853|gene1853|rna1853|rna1853 140 SLMVNIALLLLCGFAAFVQAKT-SYE-ITGTLSFLIVVAFGIKSVFFKSTdDDKKKKDEGVLKYLTLVIALIAAVL 213
                                        5567788888888887777666.665.89**********9998654444437778999999*************** PP

                             DUF679 110 FlavalsdknvvkClfpea 128
                                        F+   + ++   + lf ++
  gene1853|gene1853|rna1853|rna1853 214 FMYTLVNSELYYDALFSQK 232
                                        *988877777777776665 PP

>> DUF1772  Domain of unknown function (DUF1772)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   4.0    0.0078        23      11      82 ..      27     108 ..       9     117 .. 0.56
   2 ?    4.5   3.1     0.013        39       7      83 ..     140     219 ..      87     235 .. 0.72

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0078
                            DUF1772  11 vPallslpassslllkqwrrlfkrgkavfpplallsalafa.yla............araasrgarllylaaaall 73 
                                         P++l ++ +   +++ w  l    +++f ++ +++++a++ y+             +  +++ ++ l++++ +++
  gene1853|gene1853|rna1853|rna1853  27 LPIMLLASLTMCVIATIWGDLH--TNKLFETTFIVVSIATFaYIIfvevekyilgtnKTNKDSVNAFLMYGLIIIA 100
                                        4444444433333666666655..4455555444444444436667788888888774444444444443544443 PP

                            DUF1772  74 llsivpyTl 82 
                                        + + v+yT+
  gene1853|gene1853|rna1853|rna1853 101 T-VAVIYTF 108
                                        3.2455666 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.013
                            DUF1772   7 slfvvPallslpassslllkqwrrlfkrgkavfpplallsalafayla.........araasrgarllylaaaall 73 
                                        sl+v  all l   +  ++ q ++++     + ++l++l+++af+  +         ++++++g  ++++++ al+
  gene1853|gene1853|rna1853|rna1853 140 SLMVNIALLLLCGFA--AFVQAKTSY----EITGTLSFLIVVAFGIKSvffkstdddKKKKDEGVLKYLTLVIALI 209
                                        555555555555444..556666666....5557777777777773337899999965555555555554444444 PP

                            DUF1772  74 llsivpyTll 83 
                                        +++++ yTl+
  gene1853|gene1853|rna1853|rna1853 210 AAVLFMYTLV 219
                                        4445556665 PP

>> Ceramidase  Ceramidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   3.8   0.00077       2.3     110     189 ..      25     107 ..       5     133 .. 0.69
   2 ?    5.3   0.5    0.0038        11      22      76 ..     161     218 ..     139     229 .. 0.51

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.00077
                         Ceramidase 110 vllgvll...talavvvtllylvlkepvlhqvafalltvlvllrsiyliekkvdksdeaakkevkklallgliifl 182
                                         +l+++l   ++++v+ t++  ++ +  +  +   + +++ ++ +++++ek +  +++++k++v++++++glii++
  gene1853|gene1853|rna1853|rna1853  25 FMLPIMLlasLTMCVIATIWGDLHTNKLFETTFIVVSIATFAYIIFVEVEKYILGTNKTNKDSVNAFLMYGLIIIA 100
                                        4445444111344444455555555566666666666667777777777888877788999999999999999888 PP

                         Ceramidase 183 lgfliWn 189
                                        +  +i++
  gene1853|gene1853|rna1853|rna1853 101 TVAVIYT 107
                                        7666655 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0038
                         Ceramidase  22 yiAEfvNTlsnllfillallgi..ynaa.kkklekrfllaylglalvGlgSalFHaTL 76 
                                         + E+  Tls l++++++++ +  +++  +kk++   +l yl+l++  + ++lF  TL
  gene1853|gene1853|rna1853|rna1853 161 TSYEITGTLSFLIVVAFGIKSVffKSTDdDKKKKDEGVLKYLTLVIALIAAVLFMYTL 218
                                        3345555555555555555555321222122222444445555555555555555554 PP

>> DUF3810  Protein of unknown function (DUF3810)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.1      0.17     5e+02      49      88 ..      15      54 ..       7      57 .. 0.79
   2 ?    1.1   4.3     0.067     2e+02      27      76 ..      56     108 ..      51     123 .. 0.55
   3 ?   11.2   0.9   5.8e-05      0.17      26      90 ..     164     232 ..     116     236 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.17
                            DUF3810 49 rkkkkkrllkvllrvllvllvvyflftllwglnYyrepls 88
                                        +  k++llk++l ++l++++ +++    wg ++ ++ ++
  gene1853|gene1853|rna1853|rna1853 15 SGWDKATLLKFMLPIMLLASLTMCVIATIWGDLHTNKLFE 54
                                       5566789999999999999999999999999888777665 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.067
                            DUF3810  27 llivllillvilylvlai...klkkrkkkkkrllkvllrvllvllvvyflftl 76 
                                         +iv++i+ +++++++ +   +l + k +k ++  +l+  l+++++v +++t+
  gene1853|gene1853|rna1853|rna1853  56 TFIVVSIATFAYIIFVEVekyILGTNKTNKDSVNAFLMYGLIIIATVAVIYTF 108
                                        46677777777777777777533333334344444444444444444444443 PP

  == domain 3  score: 11.2 bits;  conditional E-value: 5.8e-05
                            DUF3810  26 ellivllillvilylvlai....klkkrkkkkkrllkvllrvllvllvvyflftllwglnYyreplser 90 
                                        e++ +l++l+v+++ ++ +    +   +kkk++ +lk+l+ v++++++v+f++tl+   +Yy   +s++
  gene1853|gene1853|rna1853|rna1853 164 EITGTLSFLIVVAFGIKSVffksTDDDKKKKDEGVLKYLTLVIALIAAVLFMYTLVNSELYYDALFSQK 232
                                        4555555556666655555777666778999999****************************9999886 PP

>> CAAD  CAAD domains of cyanobacterial aminoacyl-tRNA synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.1      0.91   2.7e+03      14      27 ..      57      71 ..      40      82 .. 0.58
   2 ?    9.6   0.3   0.00027      0.81      15      46 ..      90     121 ..      75     126 .. 0.78
   3 ?   -1.9   0.2         1   3.1e+03      22      37 ..     154     169 ..     144     183 .. 0.56
   4 ?    1.1   0.0      0.12   3.5e+02      11      34 ..     196     219 ..     187     221 .. 0.66

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.91
                               CAAD 14 lkvigli.laaival 27
                                       ++v+ ++ +a i+++
  gene1853|gene1853|rna1853|rna1853 57 FIVVSIAtFAYIIFV 71
                                       333333323444444 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00027
                               CAAD  15 kviglilaaivalklalavldaiddiPllppl 46 
                                        + ++++l+ i ++ ++ ++++  +++Pllp +
  gene1853|gene1853|rna1853|rna1853  90 AFLMYGLIIIATVAVIYTFINCYEQLPLLPAF 121
                                        45667788888899999************986 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 1
                               CAAD  22 aaivalklalavldai 37 
                                        aa+v  k +  +  ++
  gene1853|gene1853|rna1853|rna1853 154 AAFVQAKTSYEITGTL 169
                                        5555555544444443 PP

  == domain 4  score: 1.1 bits;  conditional E-value: 0.12
                               CAAD  11 erklkviglilaaivalklalavl 34 
                                        e  lk ++l++a+i a+ ++ +++
  gene1853|gene1853|rna1853|rna1853 196 EGVLKYLTLVIALIAAVLFMYTLV 219
                                        445777777777777777766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (237 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1167  (0.0650901); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.71u 0.36s 00:00:01.06 Elapsed: 00:00:00.56
# Mc/sec: 1276.79
//
Query:       gene1854|gene1854|rna1854|rna1854  [L=130]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.7e-08   34.2   0.7    3.9e-08   33.7   0.7    1.3  1  Histone        Core histone H2A/H2B/H3/H4
     0.0044   17.1   0.0     0.0085   16.2   0.0    1.5  1  Apo-CII        Apolipoprotein C-II
     0.0072   16.6   0.0      0.013   15.8   0.0    1.4  1  CBFD_NFYB_HMF  Histone-like transcription factor (CBF/NF-Y) a
  ------ inclusion threshold ------
      0.041   12.2   0.6      0.044   12.1   0.6    1.1  1  CDC45          CDC45-like protein


Domain annotation for each model (and alignments):
>> Histone  Core histone H2A/H2B/H3/H4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.7   0.7   8.7e-12   3.9e-08      34     130 ..       5     101 ..       1     102 [. 0.81

  Alignments for each domain:
  == domain 1  score: 33.7 bits;  conditional E-value: 8.7e-12
                                        SB--TTT-XTTHHHHHHHHHHHHXXSXXSXHHHHHHHHHHHH.TTSSSXEEXHHHHHHHHHHHHHHHHHHHHHHHH CS
                            Histone  34 kkkkkrryrpgtvalkeirkyqkstdlliqklpfaRvvreivksekedlrisaeavlalqealEallvelfeeAnl 109
                                        k++ +++ + +++  +  r++   + l++ +l+ + v r ++++ k+++ is+ av++l +++ +++  + ++A+ 
  gene1854|gene1854|rna1854|rna1854   5 KSTDPKQKAEDKEHSQRTRRRTNPKNLESSALYKSSVKRLVRERLKDNYTISSAAVTILSSIAFDFFNMIGTTAGD 80 
                                        44455555555566666666666777777777777777777778889***************************** PP

                                        HHHHTTXSEEXHHHHHHHHHH CS
                            Histone 110 lakhaKRvTitpkDiqlArrl 130
                                        l+k  ++ T+ + ++++A+rl
  gene1854|gene1854|rna1854|rna1854  81 LSKSVNKLTVGATEVKSAIRL 101
                                        ********************8 PP

>> Apo-CII  Apolipoprotein C-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   1.9e-06    0.0085      33      68 ..      34      69 ..      27      77 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.9e-06
                            Apo-CII 33 qdLYkktylptvdekirdmYskstaAvstYagiltD 68
                                         LYk ++   v e+++d Y+ s+aAv++   i  D
  gene1854|gene1854|rna1854|rna1854 34 SALYKSSVKRLVRERLKDNYTISSAAVTILSSIAFD 69
                                       579**************************9999776 PP

>> CBFD_NFYB_HMF  Histone-like transcription factor (CBF/NF-Y) and archaeal histone
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   2.9e-06     0.013       6      65 .]      39      99 ..      35      99 .. 0.95

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2.9e-06
                                       HHHHHHHHCC.TTXS-B-HHHHHHHHHHHHHHHHHHHHHHHHHHCCTTSSCE-HHHHHHHH CS
                      CBFD_NFYB_HMF  6 arvkkImksd.pdarkiakdAkeliaecveefieelaseAaeickkekrKtikaehiklAv 65
                                       + vk+++++  +d+ +i+++A  +++ ++  f + + + A ++ k  ++ t+ a  +k+A+
  gene1854|gene1854|rna1854|rna1854 39 SSVKRLVRERlKDNYTISSAAVTILSSIAFDFFNMIGTTAGDLSKSVNKLTVGATEVKSAI 99
                                       68****************************************************9999996 PP

>> CDC45  CDC45-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.6   9.9e-06     0.044     174     247 ..       6      80 ..       1      97 [. 0.78

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 9.9e-06
                              CDC45 174 ksdeeeesddddersrkrrrsepsakklrrq...lkkerrkyeavlekyysqgtsygesvsslmYsLaselgredn 246
                                        ++d +++ +d+++++r rrr++p  k+l+++   + + +r  +++l+++y+  +  ++  ss+ ++  +++g +  
  gene1854|gene1854|rna1854|rna1854   6 STDPKQKAEDKEHSQRTRRRTNP--KNLESSalyKSSVKRLVRERLKDNYTISSAAVTILSSIAFDFFNMIGTTAG 79 
                                        33444446666677777777774..4444444578888999999**********************9999998766 PP

                              CDC45 247 d 247
                                        d
  gene1854|gene1854|rna1854|rna1854  80 D 80 
                                        5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1083  (0.0604049); expected 358.6 (0.02)
Passed bias filter:                      568  (0.0316805); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.58u 0.37s 00:00:00.95 Elapsed: 00:00:00.55
# Mc/sec: 709.38
//
Query:       gene1855|gene1855|rna1855|rna1855  [L=250]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       691  (0.0385409); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.65u 0.33s 00:00:00.98 Elapsed: 00:00:00.56
# Mc/sec: 1344.80
//
Query:       gene1856|gene1856|rna1856|rna1856  [L=717]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.2e-23   82.9   2.7    4.3e-21   75.5   0.1    2.9  3  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
  ------ inclusion threshold ------
       0.35    9.0  15.7        0.5    8.5  15.7    1.1  1  Nop14            Nop14-like family


Domain annotation for each model (and alignments):
>> Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.5   0.1   4.8e-25   4.3e-21       4     165 ..     250     396 ..     247     416 .. 0.81
   2 !    6.7   0.0   0.00057       5.1     169     199 ..     482     512 ..     469     513 .. 0.78
   3 ?   -3.7   0.1      0.86   7.7e+03     158     190 ..     528     558 ..     524     561 .. 0.63

  Alignments for each domain:
  == domain 1  score: 75.5 bits;  conditional E-value: 4.8e-25
                                        H---TT-E.EEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CTCCHHHHCC. CS
                    Methyltr_RsmB-F   4 Lapqeeet.ilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDarkidkvlgge 78 
                                        L+ +++   +lDlcaaPG+K th++e   n+ t++A+d++ +R   v++    ++     +++a +  +++     
  gene1856|gene1856|rna1856|rna1856 250 LKTRKGALqVLDLCAAPGSKSTHMLE---NNITLTANDVSLKRCFVVQHRSAHMPKL---LTNANGLSFPRPAVP- 318
                                        5555555449*************976...699***************9999999988...999999999998886. PP

                                        .EEEEEEEE--CCGGGTTT-TCHHHH--HHHHHHHHHHHHHHHHHHCCCEEEEEEEEEEES--STTTTHHHHHHHH CS
                    Methyltr_RsmB-F  79 lfDriLlDaPCsgtgvirrdpdvklrrkekdiaqlaklqkellsaaidllkkgGvlvYsTCsvlveEneevieeaL 154
                                         +D +L+DaPCsg g+ r+++ v     +k++     l ++l+  a+ ++  +G++vYsTC+v + Ene+v++++ 
  gene1856|gene1856|rna1856|rna1856 319 -YDAVLVDAPCSGDGTFRKNRVV---VGDKNVR----LMRALVIKALSMV-GDGYVVYSTCAVDPVENEWVVQSVR 385
                                        .*******************999...4455554....4455555555544.79********************998 PP

                                        HH-TTEEEESS CS
                    Methyltr_RsmB-F 155 kkredvelvet 165
                                         + e v ++e+
  gene1856|gene1856|rna1856|rna1856 386 DECEVVSVDEV 396
                                        87777766655 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.00057
                                        TSTTSSECEECTSEEE-TTTTSS-SEEEEEE CS
                    Methyltr_RsmB-F 169 epkglklgeeagtlrllPhtenkdgffiakl 199
                                        e k  ++ e ++ +r++P+ +n  +ffia l
  gene1856|gene1856|rna1856|rna1856 482 EYKSENYHELKKCMRFYPQDNNSGAFFIAIL 512
                                        44556666666889***************88 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 0.86
                                        TTEEEESSBSTTSTTSSECEECTSEEE-TTTTS CS
                    Methyltr_RsmB-F 158 edvelvetelsepkglklgeeagtlrllPhten 190
                                        ed+++++t++++ k+ ++++ +   +l Ph+ +
  gene1856|gene1856|rna1856|rna1856 528 EDAKIENTRVKDVKIEHNKVSS--HNLTPHHTS 558
                                        5666777777776555555555..677788765 PP

>> Nop14  Nop14-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5  15.7   5.5e-05       0.5     318     438 ..      92     206 ..      49     238 .. 0.36

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 5.5e-05
                              Nop14 318 dldddfvleeeeeeeefglgkgl..ka....taeeeeeededdfeedddlveseseeeeeeeeedeeeeedeeeee 387
                                        + + + v+e   +e+e  +gkg   k     +     e++   ++e+++++e e+  ++++ee+ +e   d+    
  gene1856|gene1856|rna1856|rna1856  92 ENERGSVVE---NERESVVGKGGggKGsmtgE-----EREGVTENEKNEENEMEDALDKKKEENGKEGVLDK---- 155
                                        233333444...33444455555322122221.....11111111111112222222222222222222222.... PP

                              Nop14 388 eeeededdlsdleseeeeeedeleeel..leeekkaaeekkekkkkkkkseek 438
                                        e e+  d+++++++e  + e+e ++++  + +++k++e++++++  +k+++e+
  gene1856|gene1856|rna1856|rna1856 156 ERESVLDNDKEEKHEITNTENETTNKEtiNIKNTKENETTNKEN--TKDKNEQ 206
                                        22223333333333333333333333312222222222222222..2222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (717 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1957  (0.109153); expected 358.6 (0.02)
Passed bias filter:                      513  (0.0286129); expected 358.6 (0.02)
Passed Vit filter:                        77  (0.00429472); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.93u 0.38s 00:00:01.31 Elapsed: 00:00:00.57
# Mc/sec: 3778.38
//
Query:       gene1857|gene1857|rna1857|rna1857  [L=202]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.7e-16   59.8   0.2    2.7e-16   59.1   0.2    1.4  1  RRM_1        RNA recognition motif. (a.k.a. RRM, RBD, or RNP 
    1.3e-07   31.9   0.0    2.3e-07   31.1   0.0    1.4  1  CSTF2_hinge  Hinge domain of cleavage stimulation factor subu
  ------ inclusion threshold ------
      0.018   15.1   0.0       0.03   14.4   0.0    1.4  1  RRM_7        RNA recognition motif
      0.085   12.5   0.0       0.14   11.8   0.0    1.4  1  CSTF_C       Transcription termination and cleavage factor C-
      0.096   13.2   0.4        6.4    7.3   0.1    3.0  3  HMA          Heavy-metal-associated domain


Domain annotation for each model (and alignments):
>> RRM_1  RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.1   0.2   7.6e-20   2.7e-16       1      64 [.       7      70 ..       7      76 .. 0.93

  Alignments for each domain:
  == domain 1  score: 59.1 bits;  conditional E-value: 7.6e-20
                                       EEEESETTTSSHHHHHHHHHTTSCEEEEEEEEE.TTTSEEEEEEEEESSHHHHHHHHHHHTTEEE CS
                              RRM_1  1 lfVgnLppdvteeeLkelFskfGpiksiklvrd.etgkskgfafVeFeskedAekAlealngkkl 64
                                       +fVgn+ +dv ee+L e ++ +G+++s+++v+d +t+kskg++f+e+e+ke A+ A+++ln   +
  gene1857|gene1857|rna1857|rna1857  7 VFVGNIDFDVPEEKLIEQLGTIGRVVSFRMVYDhKTKKSKGYGFCEYETKEIAQLAVKSLN-ISF 70
                                       8*********************************************************998.444 PP

>> CSTF2_hinge  Hinge domain of cleavage stimulation factor subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.1   0.0   6.5e-11   2.3e-07      17      78 ..      92     152 ..      80     155 .. 0.87

  Alignments for each domain:
  == domain 1  score: 31.1 bits;  conditional E-value: 6.5e-11
                        CSTF2_hinge  17 aIsktLsslppeqllellsqlKalaqqnpsqarelLkqnpqLayAllqalllmglvdpdvvt 78 
                                        +I  +L+++++ +ll++l++lK++a +n  ++r+lL++       ++ +l+ +glvd++ v 
  gene1857|gene1857|rna1857|rna1857  92 KIEDVLKKMDKVNLLDVLKYLKTMAVNNTGELRRLLRN-EHFCALVVGVLVKLGLVDEEGVC 152
                                        899*********************************85.5566669999********98765 PP

>> RRM_7  RNA recognition motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   8.3e-06      0.03       2      68 ..       5      64 ..       4      90 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 8.3e-06
                              RRM_7  2 rkvFvGGlPiDiteeelkatfkefgkvlvdwPkkaeskkkaaenskaakgyvflvfedeksvkaLle 68
                                       + vFvG +  D+ ee+l++ +++ g+v v +   + +k+k++      kgy f  +e+++  +  ++
  gene1857|gene1857|rna1857|rna1857  5 CSVFVGNIDFDVPEEKLIEQLGTIGRV-VSFRMVYDHKTKKS------KGYGFCEYETKEIAQLAVK 64
                                       78***********************96.78888888877654......6999999988775555554 PP

>> CSTF_C  Transcription termination and cleavage factor C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   3.9e-05      0.14       4      38 ..     164     198 ..     161     201 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.9e-05
                             CSTF_C   4 ekaeLlqQVLqLseeqIaaLPpdqRrsImiLrqQl 38 
                                        +k+  l+  Lq  ee + +  +  R+ Im+L++ l
  gene1857|gene1857|rna1857|rna1857 164 GKEHVLMHILQVKEEELGMYDEHTRERIMLLKNML 198
                                        78899***************************865 PP

>> HMA  Heavy-metal-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.23   8.1e+02      39      57 ..      11      26 ..       9      30 .. 0.80
   2 ?    7.3   0.1    0.0018       6.4      25      48 ..      62      86 ..      55     102 .. 0.70
   3 ?    2.6   0.1     0.054   1.9e+02      14      27 ..      91     104 ..      87     123 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.23
                                HMA 39 tVegdaestklrkiieaie 57
                                       ++++d+++   +k+ie++ 
  gene1857|gene1857|rna1857|rna1857 11 NIDFDVPE---EKLIEQLG 26
                                       68999999...99999876 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0018
                                HMA 25 gVesvkvdlatktvtVegdaes.tk 48
                                        V+s ++++++++v +++ + + + 
  gene1857|gene1857|rna1857|rna1857 62 AVKSLNISFNNRQVKINYAENDmKR 86
                                       699***************8887443 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.054
                                HMA  14 akvekvLselpgVe 27 
                                         k+e+vL++++ V+
  gene1857|gene1857|rna1857|rna1857  91 WKIEDVLKKMDKVN 104
                                        69********9995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1094  (0.0610185); expected 358.6 (0.02)
Passed bias filter:                      541  (0.0301746); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1418.57
//
Query:       gene1858|gene1858|rna1858|rna1858  [L=149]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.8e-25   88.6   5.4    5.5e-25   87.6   5.4    1.5  1  Ribosomal_L26  Ribosomal proteins L26 eukaryotic, L24P archae
     0.0047   17.8   0.6     0.0092   16.9   0.6    1.4  1  CSN5_C         Cop9 signalosome subunit 5 C-terminal domain
  ------ inclusion threshold ------
      0.032   13.8   1.9      0.045   13.3   1.9    1.2  1  Poxvirus_B22R  Poxvirus B22R protein
      0.076   13.0   2.3       0.15   12.0   2.3    1.5  1  KOW            KOW motif
      0.098   12.3   0.0       0.19   11.4   0.0    1.4  1  TRAM1          TRAM1-like protein


Domain annotation for each model (and alignments):
>> Ribosomal_L26  Ribosomal proteins L26 eukaryotic, L24P archaeal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.6   5.4   1.5e-28   5.5e-25       1      81 [.      33     145 ..      33     146 .. 0.99

  Alignments for each domain:
  == domain 1  score: 87.6 bits;  conditional E-value: 1.5e-28
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................................x RF
                      Ribosomal_L26   1 sssrrkqrKahfnapshirrklmsapLskeLrekygvrslpir................................g 44 
                                        sssrrkqrK+hfna+s    k m+apLsk L+e+ g++++p+r                                g
  gene1858|gene1858|rna1858|rna1858  33 SSSRRKQRKRHFNAQSTDLTKQMTAPLSKALKEELGIKRIPVRpndtvmvrvgkykktegkvvrvnrvarkicieG 108
                                        89************************************************************************** PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Ribosomal_L26  45 vtrekangttvpvgihpSkvvItklklDkdrkkiLer 81 
                                        v+ +k++g+  ++g+hpS++ I++l+++kdr++++e+
  gene1858|gene1858|rna1858|rna1858 109 VSITKKDGAVRYLGVHPSNLSIVRLSMEKDRNRMIEK 145
                                        ***********************************96 PP

>> CSN5_C  Cop9 signalosome subunit 5 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.6   2.6e-06    0.0092       8      73 ..      10     107 ..       8     110 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2.6e-06
                             CSN5_C   8 NrdYatkqisDLaeKlekaessvsrsrsaagtlseeaseaeekkk............................... 52 
                                        Nr+++t+ i D ++K  k ++++s+sr+++ + + +a++++ +k+                               
  gene1858|gene1858|rna1858|rna1858  10 NRSFITQNIFDPSKKKMKLNKNISSSRRKQRKRHFNAQSTDLTKQmtaplskalkeelgikripvrpndtvmvrvg 85 
                                        9**************************9998777776666665556778888888888888888888888888888 PP

                             CSN5_C  53 .kkkedsqLakvvkdstkiase 73 
                                          kk++ ++ +v + ++ki +e
  gene1858|gene1858|rna1858|rna1858  86 kYKKTEGKVVRVNRVARKICIE 107
                                        7778888888888888888877 PP

>> Poxvirus_B22R  Poxvirus B22R protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   1.9   1.2e-05     0.045     117     181 ..      28      95 ..      14     107 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.2e-05
                      Poxvirus_B22R 117 skkkeeakeRkrRsdeeekeeekppvppkkdlveklkeeLgik..pvIprkvselQvGas.gsdgsVv 181
                                         +k++++  Rk+R  + + ++++   + +  l + lkeeLgik  pv p+++  + vG + +++g+Vv
  gene1858|gene1858|rna1858|rna1858  28 LNKNISSSRRKQRKRHFNAQSTDLTKQMTAPLSKALKEELGIKriPVRPNDTVMVRVGKYkKTEGKVV 95 
                                        3445666677777776666666666667799************99999**********9967788887 PP

>> KOW  KOW motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   2.3   4.3e-05      0.15       1      24 [.      76      99 ..      76     100 .. 0.95

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 4.3e-05
                                       TTSEEEESSSTTTTCEEEEEEEET CS
                                KOW  1 pGdhVkVvsGphkGktGkVvkvdq 24
                                       p d+V+V  G++k  +GkVv+v++
  gene1858|gene1858|rna1858|rna1858 76 PNDTVMVRVGKYKKTEGKVVRVNR 99
                                       78********************97 PP

>> TRAM1  TRAM1-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   5.3e-05      0.19      38      62 ..       6      30 ..       2      31 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 5.3e-05
                              TRAM1 38 vftflRaflmeyvlrPlarrlgikk 62
                                       v ++ R+f+++ +++P  +++++ k
  gene1858|gene1858|rna1858|rna1858  6 VGSWNRSFITQNIFDPSKKKMKLNK 30
                                       56788*****************988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1120  (0.0624686); expected 358.6 (0.02)
Passed bias filter:                      545  (0.0303977); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1022.28
//
Query:       gene1859|gene1859|rna1859|rna1859  [L=44]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (44 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       222  (0.0123822); expected 358.6 (0.02)
Passed bias filter:                      173  (0.00964917); expected 358.6 (0.02)
Passed Vit filter:                         7  (0.000390429); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.33u 0.25s 00:00:00.58 Elapsed: 00:00:00.40
# Mc/sec: 330.87
//
Query:       gene186|gene186|rna186|rna186  [L=100]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       814  (0.0454013); expected 358.6 (0.02)
Passed bias filter:                      555  (0.0309554); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 722.43
//
Query:       gene1860|gene1860|rna1860|rna1860  [L=356]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.1e-43  144.8  11.4    1.9e-10   41.2   0.0    7.5  7  RCC1      Regulator of chromosome condensation (RCC1) repeat
    3.4e-16   58.6  19.5    0.00024   20.8   0.1    8.0  7  RCC1_2    Regulator of chromosome condensation (RCC1) repeat


Domain annotation for each model (and alignments):
>> RCC1  Regulator of chromosome condensation (RCC1) repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.2   0.0   5.6e-11     5e-07       4      50 .]       3      50 ..       2      50 .. 0.96
   2 !   41.2   0.0   2.1e-14   1.9e-10       1      50 []      52      97 ..      52      97 .. 0.98
   3 !   13.8   0.2   7.7e-06     0.069       1      48 [.     100     147 ..     100     148 .. 0.82
   4 !    4.5   0.1     0.006        54       2      14 ..     152     164 ..     151     207 .. 0.82
   5 !   21.9   0.1   2.3e-08   0.00021       2      50 .]     211     256 ..     210     256 .. 0.89
   6 !   15.2   0.0   2.7e-06     0.024       3      27 ..     261     285 ..     259     304 .. 0.77
   7 !   19.2   0.1   1.6e-07    0.0014       1      49 [.     307     353 ..     307     354 .. 0.75

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 5.6e-11
                                       EEEEE--GGGTTSSSS-.--EEEEEE-GGGTTS-EEEEEEETTEEEEE CS
                               RCC1  4 VysWGrndyGqLGlgtt.esvlvPtkveglsgnrvvkvacGddhtval 50
                                       Vy++G+n   qLG+g++  s+++P +++ +++ +v k++cG+ ht+ l
  gene1860|gene1860|rna1860|rna1860  3 VYTFGSNLLSQLGTGDEpGSSSTPLELPAFTDLKVDKACCGSLHTLIL 50
                                       9*****************9999*********99************975 PP

  == domain 2  score: 41.2 bits;  conditional E-value: 2.1e-14
                                       TTEEEEEE--GGGTTSSSS---EEEEEE-GGGTTS-EEEEEEETTEEEEE CS
                               RCC1  1 dGrVysWGrndyGqLGlgttesvlvPtkveglsgnrvvkvacGddhtval 50
                                       +G+Vys+G+nd+  LG+  +e+v  P +v++++  r++++ +G++ ++++
  gene1860|gene1860|rna1860|rna1860 52 EGSVYSFGCNDEFALGREGDENV--PIRVQLPE--RITHIGAGQSASFCI 97
                                       7**********************..********..*************97 PP

  == domain 3  score: 13.8 bits;  conditional E-value: 7.7e-06
                                        TTEEEEEE..--GGGTTSSSS---E.EEEEE-GGGTTS.-EEEEEEETTEEE CS
                               RCC1   1 dGrVysWG..rndyGqLGlgttesv.lvPtkveglsgn.rvvkvacGddhtv 48 
                                        +G++y+WG  r+  G  G +++++   vP+ +     + +v + a G++h++
  gene1860|gene1860|rna1860|rna1860 100 SGKLYGWGtfRDKGGVIGFKPNKKFqKVPVVL----HRgPVRQLAVGSNHVL 147
                                        59********************5552556555....444***********86 PP

  == domain 4  score: 4.5 bits;  conditional E-value: 0.006
                                        TEEEEEE--GGGT CS
                               RCC1   2 GrVysWGrndyGq 14 
                                        G+Vy+ G n++G 
  gene1860|gene1860|rna1860|rna1860 152 GEVYAIGANEFGE 164
                                        99********996 PP

  == domain 5  score: 21.9 bits;  conditional E-value: 2.3e-08
                                        TEEEEEE--GGGTTSSSS-...--EEEEEE-GGGTTS-EEEEEEETTEEEEE CS
                               RCC1   2 GrVysWGrndyGqLGlgtt...esvlvPtkveglsgnrvvkvacGddhtval 50 
                                        G+ +++G+n + qLGlg+t    s+   +kv++    +v+++++G  ht+++
  gene1860|gene1860|rna1860|rna1860 211 GDAFAFGQNANAQLGLGNThggISK---RKVPLD---DVQSISSGELHTLFV 256
                                        899****************999666...788774...8***********985 PP

  == domain 6  score: 15.2 bits;  conditional E-value: 2.7e-06
                                        EEEEEE--GGGTTSSSS---EEEEE CS
                               RCC1   3 rVysWGrndyGqLGlgttesvlvPt 27 
                                         +y+ G n +GqLG+g++ +++v t
  gene1860|gene1860|rna1860|rna1860 261 ALYAVGHNMFGQLGTGDNADRHVLT 285
                                        69****************7776533 PP

  == domain 7  score: 19.2 bits;  conditional E-value: 1.6e-07
                                        TTEEEEEE--GGGTTSSSS-.--EEEEEE-GGGTTS-EEEEEEETTEEEE CS
                               RCC1   1 dGrVysWGrndyGqLGlgtt.esvlvPtkveglsgnrvvkvacGddhtva 49 
                                        d+  ysWG+n++G +G   +  s   P+++e+   ++vv    G+d++v+
  gene1860|gene1860|rna1860|rna1860 307 DDGMYSWGFNSHGECGYAGQdSSA--PKRMETQF-DDVVCFDVGHDFCVV 353
                                        6789*************6662555..*9997732.377777778888876 PP

>> RCC1_2  Regulator of chromosome condensation (RCC1) repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0      0.12     1e+03      20      26 ..       3       9 ..       3      13 .. 0.87
   2 !   12.4   0.3   1.2e-05       0.1       4      27 ..      40      62 ..      37      64 .. 0.88
   3 !    7.8   0.4   0.00031       2.8       2      24 ..      85     107 ..      84     111 .. 0.88
   4 !    4.6   0.0    0.0033        30       1      29 [.     136     163 ..     136     164 .. 0.74
   5 !    7.7   0.1   0.00035       3.1       6      29 ..     199     222 ..     197     223 .. 0.90
   6 !   20.8   0.1   2.7e-08   0.00024       1      30 []     243     272 ..     243     272 .. 0.95
   7 !   11.9   0.1   1.7e-05      0.15       4      29 ..     295     319 ..     292     320 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.12
                             RCC1_2 20 VlcWGsN 26
                                       V+++GsN
  gene1860|gene1860|rna1860|rna1860  3 VYTFGSN 9 
                                       9*****9 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 1.2e-05
                             RCC1_2  4 vsaGdyHscaLtedGeVlcWGsNs 27
                                        ++G+ H++ ++++G V+++G+N+
  gene1860|gene1860|rna1860|rna1860 40 ACCGSLHTL-ILAEGSVYSFGCND 62
                                       579******.9999********96 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.00031
                             RCC1_2   2 ksvsaGdyHscaLtedGeVlcWG 24 
                                        +++ aG + s+ + ++G++++WG
  gene1860|gene1860|rna1860|rna1860  85 THIGAGQSASFCIGSSGKLYGWG 107
                                        67889999999999********* PP

  == domain 4  score: 4.6 bits;  conditional E-value: 0.0033
                             RCC1_2   1 VksvsaGdyHscaLtedGeVlcWGsNsdG 29 
                                        V++++ G++H +     GeV++ G N++G
  gene1860|gene1860|rna1860|rna1860 136 VRQLAVGSNHVL-YNVRGEVYAIGANEFG 163
                                        667788888876.4447899999999888 PP

  == domain 5  score: 7.7 bits;  conditional E-value: 0.00035
                             RCC1_2   6 aGdyHscaLtedGeVlcWGsNsdG 29 
                                        +G+  s+ ++e G+ +++G+N + 
  gene1860|gene1860|rna1860|rna1860 199 CGAGTSFMVSERGDAFAFGQNANA 222
                                        89999****************875 PP

  == domain 6  score: 20.8 bits;  conditional E-value: 2.7e-08
                             RCC1_2   1 VksvsaGdyHscaLtedGeVlcWGsNsdGQ 30 
                                        V s+s+G  H++++t+++++++ G+N +GQ
  gene1860|gene1860|rna1860|rna1860 243 VQSISSGELHTLFVTRNNALYAVGHNMFGQ 272
                                        679***********************9998 PP

  == domain 7  score: 11.9 bits;  conditional E-value: 1.7e-05
                             RCC1_2   4 vsaGdyHscaLtedGeVlcWGsNsdG 29 
                                         s  +++s+a t+dG +++WG Ns+G
  gene1860|gene1860|rna1860|rna1860 295 ASTKGFFSVAYTDDG-MYSWGFNSHG 319
                                        577899*********.********99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (356 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       217  (0.0121033); expected 358.6 (0.02)
Passed bias filter:                      197  (0.0109878); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.21s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 2679.94
//
Query:       gene1861|gene1861|rna1861|rna1861  [L=136]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.5e-19   68.9   0.2    3.5e-19   68.5   0.2    1.2  1  Ribosomal_S19  Ribosomal protein S19


Domain annotation for each model (and alignments):
>> Ribosomal_S19  Ribosomal protein S19
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.5   0.2     2e-23   3.5e-19       1      81 []      43     119 ..      43     119 .. 0.87

  Alignments for each domain:
  == domain 1  score: 68.5 bits;  conditional E-value: 2e-23
                                        .HHHSS.TTCCCHHHHHHHHHHTS-----EEES-TT-B--GGGTT-EEEEE-SSSEEEEE--CCCTTSBCGGGT-S CS
                      Ribosomal_S19   1 rslkkg.pfvqesllkkvrkakaekkkevikthsRdstIlPemvgltvgVynGktfvpveikeemvGhkLgEFspT 75 
                                        r++++g + ++ +l+k++++ +       ikt +R+++IlP m+g +vgV+nG +fv++++k+em+G ++ + +pT
  gene1861|gene1861|rna1861|rna1861  43 RHINRGfSEEEYTLIKQCERNE-----PDIKTKCRNMMILPVMIGQVVGVHNGCNFVEIDVKPEMIGRRFKDLVPT 113
                                        5678887777777777664443.....458********************************************** PP

                                        S----S CS
                      Ribosomal_S19  76 rkpvkh 81 
                                        ++ + h
  gene1861|gene1861|rna1861|rna1861 114 KTSKAH 119
                                        **9988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       326  (0.0181828); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 988.21
//
Query:       gene1862|gene1862|rna1862|rna1862  [L=414]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    0.00056   19.4   0.3     0.0012   18.3   0.3    1.7  1  Adap_comp_sub  Adaptor complexes medium subunit family
  ------ inclusion threshold ------
      0.013   15.6   0.2      0.037   14.1   0.2    1.8  1  PH_3           PH domain


Domain annotation for each model (and alignments):
>> Adap_comp_sub  Adaptor complexes medium subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.3   1.3e-07    0.0012      12      86 ..     208     295 ..     198     364 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.3e-07
                                        X-EEEEEEEEEEEEEE-TTS-EEEEEEEEEEEEEE---TT-EEEEEE-SS-EE...........--S..SEESEEE CS
                      Adap_comp_sub  12 kneiyldviErvsvlvdkkGkilksevqGtiacksklsgmpelklgLndklnk...........ekk..ielddvs 74 
                                        + +++l ++Er+s++vdk+G+  + e++G++++ +k +   ++++ +  +              +kk     + + 
  gene1862|gene1862|rna1862|rna1862 208 SKKVQLLITERLSLVVDKEGNKKSGEITGDMTMYIKDERFKDISIEIRAPHPVkyspnlqkdsaKKKvlKAKKSFP 283
                                        6789999****************************************99887767777777765333433334455 PP

                                        EETT-B-TTHHH CS
                      Adap_comp_sub  75 fHqcVnldkfes 86 
                                        +++cV l k+ +
  gene1862|gene1862|rna1862|rna1862 284 VKKCVALVKWTR 295
                                        667777766665 PP

>> PH_3  PH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.2   4.1e-06     0.037      26      73 ..     207     253 ..     196     280 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4.1e-06
                               PH_3  26 farkRqllltdgPrLiyvDpekmekkGeIplskelkvevknskkFlih 73 
                                         ++k qll+t++   ++vD+e ++k+GeI+ + ++ ++ + +k+  i 
  gene1862|gene1862|rna1862|rna1862 207 PSKKVQLLITERLS-LVVDKEGNKKSGEITGDMTMYIKDERFKDISIE 253
                                        48*********954.579************999999999988887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (414 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1321  (0.0736795); expected 358.6 (0.02)
Passed bias filter:                      657  (0.0366445); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.43
# Mc/sec: 2876.18
//
Query:       gene1863|gene1863|rna1863|rna1863  [L=1107]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.7e-05   22.0   0.1    0.00016   21.2   0.1    1.4  1  Nucleoside_tran  Nucleoside transporter
  ------ inclusion threshold ------
       0.24   11.5   0.9         47    4.2   0.0    3.6  4  PAC3             Proteasome assembly chaperone 3
        1.5    8.8   0.0        1.5    8.8   0.0    4.5  4  Neur_chan_memb   Neurotransmitter-gated ion-channel transmemb


Domain annotation for each model (and alignments):
>> Nucleoside_tran  Nucleoside transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.1   2.7e-08   0.00016      59     133 ..       2      76 ..       1      82 [. 0.77

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 2.7e-08
                    Nucleoside_tran  59 kesallYFivsivvvivcvilllvlkklefykeykqlklegslletkeelrqekeeeseskvkltaekskegeen 133
                                        k+sa +Y + +i+vv++ ++l+ +++k ++y+   ++k  + l e +ee ++++e++++++ +   ++++ ++en
  gene1863|gene1863|rna1863|rna1863   2 KKSAHIYTFYGIAVVVLLLVLYVFVHKKAVYNPVVEMKRSAMLDELEEEKKKKEEKQKDEEQWKDGDRKDAEKEN 76 
                                        799*********************************997776666666666555555544566666666555554 PP

>> PAC3  Proteasome assembly chaperone 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0    0.0095        57      17      40 ..     308     331 ..     298     334 .. 0.90
   2 ?    4.2   0.0    0.0079        47      16      40 ..     329     353 ..     324     356 .. 0.87
   3 ?    2.5   0.0     0.027   1.6e+02      16      40 ..     351     375 ..     345     377 .. 0.87
   4 ?   -0.7   0.0      0.28   1.7e+03      12      40 ..     438     471 ..     434     473 .. 0.64

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.0095
                               PAC3  17 pdsksdelseptytvrvllGkddd 40 
                                        +d+k++e+++p++t  ++lG+d+d
  gene1863|gene1863|rna1863|rna1863 308 KDKKEEENVSPSFTGITVLGNDKD 331
                                        5999*****************987 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.0079
                               PAC3  16 tpdsksdelseptytvrvllGkddd 40 
                                         +d+k++e+++p++t  ++lG+d+d
  gene1863|gene1863|rna1863|rna1863 329 DKDKKKEESVSPSFTGITVLGNDKD 353
                                        5799******************987 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.027
                               PAC3  16 tpdsksdelseptytvrvllGkddd 40 
                                         +d+k++e+++p++t  + lG+d+d
  gene1863|gene1863|rna1863|rna1863 351 DKDKKKEESVSPSFTGITALGNDKD 375
                                        5799******************987 PP

  == domain 4  score: -0.7 bits;  conditional E-value: 0.28
                               PAC3  12 lvsvtpdsksdelsep.....tytvrvllGkddd 40 
                                        +v+++ d+k +++++      ++t +  lGkdd+
  gene1863|gene1863|rna1863|rna1863 438 VVHTSDDKKDKKKKDEnsilpSLTGTSALGKDDK 471
                                        56666444444444434455599********764 PP

>> Neur_chan_memb  Neurotransmitter-gated ion-channel transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0   0.00025       1.5      64     123 ..       7      90 ..       5     205 .. 0.66
   2 ?   -9.0  16.6         3   1.8e+04     122     220 ..     507     639 ..     435     662 .. 0.41
   3 ?   -0.5   0.5      0.17     1e+03      85     165 ..     744     864 ..     739     909 .. 0.54
   4 ?   -0.1   3.7      0.13     8e+02      86     168 ..     946    1053 ..     918    1097 .. 0.40

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00025
                                        HHHHHHHHHHHHHHHHHHHH.H-S-S---HHHHHHHTTHHHHHHC--------------................. CS
                     Neur_chan_memb  64 tmvfvtlsivetvfVlnvhh.rsprthtmpawvrkvfldklprllfmkrpsevkdnekkl................ 122
                                        ++ f  +++v+   Vl+v+  ++   + + + +r+++ld+l++ +  k+++++ ++++k                 
  gene1863|gene1863|rna1863|rna1863   7 IYTFYGIAVVVLLLVLYVFVhKKAVYNPVVEMKRSAMLDELEEEKKKKEEKQKDEEQWKDgdrkdaekenteragn 82 
                                        567889999999999999873666779999************9999888877777777666665555555554444 PP

                                        .......- CS
                     Neur_chan_memb 123 .......s 123
                                               +
  gene1863|gene1863|rna1863|rna1863  83 mdggistP 90 
                                        44444441 PP

  == domain 2  score: -9.0 bits;  conditional E-value: 3
                                        ...............................................----------------------------- CS
                     Neur_chan_memb 122 l..............................................ssgasseaeelilskskseskkaklseeq 151
                                        +                                                    + e+ + +++++ ++++   +++
  gene1863|gene1863|rna1863|rna1863 507 KkdeksilpspffntsildkdkdekkkkkdeksilpspffntsildkD-----KDEKKKKKDENNTLPFSIFGTKH 577
                                        144455555555544444444333333333333333333332111110.....22222222222222222222222 PP

                                        ---------SS---TTGGG--..........-----TTTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     Neur_chan_memb 152 gsekastckckckegeeaspstqlsk.....eelspelkkavegvkyiadhlraededksvkedwkyvamviDr 220
                                        ++ ++++ + ++ ++++        +      ++s++ ++ +++ ++   +  +++++k+ k+       v+Dr
  gene1863|gene1863|rna1863|rna1863 578 SQTESNNRNETSPSSQD--------RmsgtgTKASDRTDSSTKESNVPMASNDKTKDKKQKKD----EQPVVDR 639
                                        22222221111111111........12222233333333333333333222222222222222....2233333 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.17
                                        -S-S.---HHHHHHHTTHHHHHHC--------------...................................... CS
                     Neur_chan_memb  85 sprt.htmpawvrkvfldklprllfmkrpsevkdnekkl..................................... 122
                                        +p++ ++ + ++ k fld    +  +   +++k++  ++                                     
  gene1863|gene1863|rna1863|rna1863 744 TPNRkQKDEGRTDKKFLDSYDLFSSIDDAKKDKRDSTETvgdkydvpgevpvksdtlltnggiikpenslstgnep 819
                                        5554133344566777777777777777777666666668888888888888888888888887777666666666 PP

                                        ..--------------------------------------SS--- CS
                     Neur_chan_memb 123 ..ssgasseaeelilskskseskkaklseeqgsekastckckcke 165
                                          ssg++s+++++   ++k+  +++  ++++  +   t + k+k+
  gene1863|gene1863|rna1863|rna1863 820 egSSGQPSKSQKTGNLSNKNRISANYTESTPIFRDLPTYTNKNKK 864
                                        666666666655555555554333322222222222222222222 PP

  == domain 4  score: -0.1 bits;  conditional E-value: 0.13
                                         S-S---HHHHHHHTTHHHHHHC--------------.........------------------........... CS
                     Neur_chan_memb   86 prthtmpawvrkvfldklprllfmkrpsevkdnekkl........ssgasseaeelilsksks........... 140 
                                         p+t+t +++   v++ + p +   k+p+ + ++  k+        +           ++k+++           
  gene1863|gene1863|rna1863|rna1863  946 PSTNTSSDAPAVVVTPEHPTVNQEKNPEVTLTAIPKKrvhrrikhK-----------SHKKRKnappkksepvv 1008
                                         4444444444444444444444444444444333332222222110...........11111111122222233 PP

                                         .................--------------------SS---TTG CS
                     Neur_chan_memb  141 .................eskkaklseeqgsekastckckckegee 168 
                                                          + k++  +++++++k ++++  ++e ++
  gene1863|gene1863|rna1863|rna1863 1009 neqgffdffmpgtntegDNKDQGERTSHKHHKGKKKHKVSQEISN 1053
                                         333322222222221111222222222222222222222212222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1583  (0.0882927); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 1.12u 0.34s 00:00:01.46 Elapsed: 00:00:00.56
# Mc/sec: 5950.03
//
Query:       gene1864|gene1864|rna1864|rna1864  [L=95]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.015   15.1   0.8      0.027   14.3   0.8    1.4  1  zf-C3HC4_3   Zinc finger, C3HC4 type (RING finger)
      0.039   13.8   1.0       0.06   13.2   1.0    1.3  1  Prok-RING_4  Prokaryotic RING finger family 4
       0.04   14.3   6.2      0.072   13.4   6.2    1.4  1  zf-RING_2    Ring finger domain


Domain annotation for each model (and alignments):
>> zf-C3HC4_3  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.8   4.5e-06     0.027      24      48 ..       1      25 [.       1      27 [. 0.89

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.5e-06
                                       EE-HHHHHHHHHTT-B-TTT--B-- CS
                         zf-C3HC4_3 24 vlCeeCaekllkrkkkCpiCrrpie 48
                                       v+C  C+ ++   +  Cp+C r ++
  gene1864|gene1864|rna1864|rna1864  1 VFCWPCVYHWSTTSSFCPVCMRRMT 25
                                       58********99********98876 PP

>> Prok-RING_4  Prokaryotic RING finger family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   1.0     1e-05      0.06      19      42 ..       1      26 [.       1      30 [. 0.79

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1e-05
                        Prok-RING_4 19 lvCkeCfdsk..dlssCPlCqrrisk 42
                                       ++C  C  ++   +s CP+C rr+ +
  gene1864|gene1864|rna1864|rna1864  1 VFCWPCVYHWstTSSFCPVCMRRMTE 26
                                       58999*9999545559******9865 PP

>> zf-RING_2  Ring finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   6.2   1.2e-05     0.072      24      43 ..       1      20 [.       1      21 [. 0.95

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.2e-05
                          zf-RING_2 24 vfhreClerwlrssstCPlC 43
                                       vf++ C+ +w ++ss CP+C
  gene1864|gene1864|rna1864|rna1864  1 VFCWPCVYHWSTTSSFCPVC 20
                                       6*************99**** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       689  (0.0384294); expected 358.6 (0.02)
Passed bias filter:                      522  (0.0291148); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 651.19
//
Query:       gene1865|gene1865|rna1865|rna1865  [L=36]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (36 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       292  (0.0162865); expected 358.6 (0.02)
Passed bias filter:                      197  (0.0109878); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.28s 00:00:00.67 Elapsed: 00:00:00.45
# Mc/sec: 240.64
//
Query:       gene1866|gene1866|rna1866|rna1866  [L=400]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.4e-29  101.3   0.8    8.2e-29  100.1   0.3    1.9  2  V-ATPase_H_C  V-ATPase subunit H
    1.5e-10   40.9   1.5    3.5e-10   39.7   1.5    1.6  1  V-ATPase_H_N  V-ATPase subunit H
  ------ inclusion threshold ------
      0.033   14.1   0.0      0.088   12.8   0.0    1.7  1  L27_1         L27_1


Domain annotation for each model (and alignments):
>> V-ATPase_H_C  V-ATPase subunit H
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       1.9   1.1e+04      61      69 ..     247     255 ..     234     273 .. 0.69
   2 !  100.1   0.3   1.4e-32   8.2e-29       2     117 .]     285     399 ..     284     399 .. 0.98

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 1.9
                       V-ATPase_H_C  61 avalnDige 69 
                                         v ++Di +
  gene1866|gene1866|rna1866|rna1866 247 LVTCHDIIN 255
                                        577888765 PP

  == domain 2  score: 100.1 bits;  conditional E-value: 1.4e-32
                       V-ATPase_H_C   2 ltsfdeYlaElesgkLewspvHksekFWkenaekleeknfkllkkLiklleeskdktvlavalnDigelvkllpeg 77 
                                        ++sf++Yl+El sgkLe++p+H s+ FW+ n+++l e +++++++L+k+l +s  ++  +va+nD++++vk +pe 
  gene1866|gene1866|rna1866|rna1866 285 TSSFQNYLRELFSGKLENTPYHFSDVFWSMNMNSLIEYKIEIIRALKKYL-KSGCTQHKCVAANDLYRFVKACPEI 359
                                        79*********************************9999***********.5788999****************** PP

                       V-ATPase_H_C  78 kkvleklkaKekimellehedeevkyeALkavqkllvqnw 117
                                         +++ek++ K+++++l+e++++++++ AL++++ +++q+w
  gene1866|gene1866|rna1866|rna1866 360 VRIVEKFDLKTELFKLCESTNDDLRFYALQSLSVCIFQEW 399
                                        ***************************************9 PP

>> V-ATPase_H_N  V-ATPase subunit H
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.7   1.5   5.8e-14   3.5e-10     211     315 .]     185     278 ..     160     278 .. 0.86

  Alignments for each domain:
  == domain 1  score: 39.7 bits;  conditional E-value: 5.8e-14
                       V-ATPase_H_N 211 iQlqYqvllclWlLsFekkiaeelvkkkelipllvdilrdsvKEKvtRvilatlrNllekaeksskelaavmvqvk 286
                                         ++qY++  +lW +sF+k+ +e++  +  ++p+l+++l++   EK +R +++++rNll++       +  ++  ++
  gene1866|gene1866|rna1866|rna1866 185 RNVQYNASIILWYVSFSKETIEYF--EL-IVPHLLHLLKTRECEKMVRTTFFIIRNLLKNGF-----FFSLVTCHD 252
                                        579********************9..66.99***************************9998.....777666666 PP

                       V-ATPase_H_N 287 llkllenLeerkfsDeditedleyLkeeL 315
                                        +++ + n    k++De+++  ++++   L
  gene1866|gene1866|rna1866|rna1866 253 IINDTAN---MKYEDEELKSTIDQVARVL 278
                                        6666665...59***********998765 PP

>> L27_1  L27_1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   1.5e-05     0.088      23      46 ..     261     284 ..     246     285 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.5e-05
                              L27_1  23 keedeeLrqalerviniFksqLfq 46 
                                        k edeeL++++++v +++ks+L +
  gene1866|gene1866|rna1866|rna1866 261 KYEDEELKSTIDQVARVLKSRLLK 284
                                        469*******************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (400 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       858  (0.0478554); expected 358.6 (0.02)
Passed bias filter:                      527  (0.0293937); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2867.44
//
Query:       gene1867|gene1867|rna1867|rna1867  [L=208]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      3e-21   76.2  20.5    3.5e-21   76.0  20.5    1.1  1  HlyIII    Haemolysin-III related
  ------ inclusion threshold ------
        9.4    6.0   9.3         33    4.2   5.7    2.6  2  DUF2157   Predicted membrane protein (DUF2157)


Domain annotation for each model (and alignments):
>> HlyIII  Haemolysin-III related
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.0  20.5   3.9e-25   3.5e-21       4     223 ..       3     198 ..       1     199 [. 0.88

  Alignments for each domain:
  == domain 1  score: 76.0 bits;  conditional E-value: 3.9e-25
                             HlyIII   4 hnEtlniwtHllgailfivlailllslaevkensklakvvvlvfllgallcllcSalyHtlsihseeklrkffakl 79 
                                        ++++l++ +H +++i+++v +il+l+++  ++     +   l+ l + +++++ S++yH+ s+++  ++++f ++l
  gene1867|gene1867|rna1867|rna1867   3 QKPILRGRIHQIAFIISFVSLILYLVYSLFTNL----HSGTLIILTTQCILYGTSSFYHLTSFKHT-RTERFAQRL 73 
                                        5789999**********9999999999988886....7899999*******************999.********* PP

                             HlyIII  80 DysgIslliagsylplilyalakapkagllylslilalgvlgiisklvplfsrpearplravlfillgllgvipll 155
                                        D++ I+l+ia    + + ++l  +  ++ l+l++++++ +lg    +++    + ++ + +vl+i+ gl+ +i+l 
  gene1867|gene1867|rna1867|rna1867  74 DHMCIFLFIASV-HSSMALTL--KLMYTKLILTTTWMIFILGATKIFLTE---KIIESIDVVLYIVHGLSILIFLR 143
                                        *******99754.44555555..367889999999999999998887777...999************99888876 PP

                             HlyIII 156 hlllvltqlgeaaelalvllvlggvlylvGavfYalrvPErlkpgkfdivghsHqiFHvfvvlgalfh 223
                                             l ++         +l lgg+ly+vG+++++l+     kp+ +++v+++H++FH ++vl+ +++
  gene1867|gene1867|rna1867|rna1867 144 F--ESLRSVY------RMVLPLGGLLYVVGGIVFGLE-----KPDLVPTVYGYHELFHTLTVLANICF 198
                                        5..6666444......78899****************.....***********************996 PP

>> DUF2157  Predicted membrane protein (DUF2157)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   4.2      0.16   1.4e+03      50      72 ..      78     100 ..      12     119 .. 0.64
   2 ?    4.2   5.7    0.0037        33      44     112 ..     130     204 ..      75     206 .. 0.73

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.16
                            DUF2157  50 lilfvAanWqglsrlvkfllllv 72 
                                        ++lf+A++  ++  ++k++   +
  gene1867|gene1867|rna1867|rna1867  78 IFLFIASVHSSMALTLKLMYTKL 100
                                        55666666666666666554333 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.0037
                            DUF2157  44 lllglGlilfvAanWqglsrlvkfllllvllllslllgavlwrdr......rvpprlgeallllaalllgaaial 112
                                        l ++ Gl +++   +++l  + +++l l+ ll +++++++ ++++       +++ l + l +la +++++ i++
  gene1867|gene1867|rna1867|rna1867 130 LYIVHGLSILIFLRFESLRSVYRMVLPLGGLLYVVGGIVFGLEKPdlvptvYGYHELFHTLTVLANICFLIPIIM 204
                                        456667777777777888888888888888888888886666556677777666677777777777777766666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1012  (0.0564449); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1378.76
//
Query:       gene1868|gene1868|rna1868|rna1868  [L=397]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-34  118.2   1.3    1.8e-34  118.2   1.3    2.5  2  Cyclin_N  Cyclin, N-terminal domain
    1.5e-17   63.8   0.2    2.9e-17   62.9   0.2    1.5  1  Cyclin_C  Cyclin, C-terminal domain
  ------ inclusion threshold ------
       0.44   11.2   3.0         48    4.7   0.6    3.5  2  RAWUL     RAWUL domain RING finger- and  WD40-associated ubiq
       0.91   10.3   2.8        2.1    9.1   0.1    2.0  2  TbpB_A    N-Lobe handle Tf-binding protein B


Domain annotation for each model (and alignments):
>> Cyclin_N  Cyclin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.2   1.3     4e-38   1.8e-34      10     127 .]     156     271 ..     149     271 .. 0.96
   2 ?    1.2   1.2     0.062   2.8e+02      43     109 ..     284     347 ..     276     362 .. 0.73

  Alignments for each domain:
  == domain 1  score: 118.2 bits;  conditional E-value: 4e-38
                                        HCHTS-STTCTTCTSSS-HHHHHHHHHHHHHHHHHTT--TTHHHHHHHHHHHHHHHS---CCCHHHHHHHHHHHHH CS
                           Cyclin_N  10 elkflpkpdyldqqpelnpemRailidwlvevaekfkltpetlflavnyldRflskksvpkdklqlvgatcLllAa 85 
                                        ++k l ++dy+  q+el+++mR+il+dwl++v+ ++ l+petlfl+v+++dRfls + v+k+klqlvg+t+L++Aa
  gene1868|gene1868|rna1868|rna1868 156 DQKVLINHDYMVYQQELTWRMRTILVDWLIDVHWQLGLHPETLFLTVDLIDRFLSLRTVSKNKLQLVGVTALMVAA 231
                                        557899*****99999************************************************************ PP

                                        HHHSSS---HHHHHHHTTTSS-HHHHHHHHHHHHHHTTT--- CS
                           Cyclin_N  86 KveeisppkledlvyitdeafteeeilemErliLetLnfdls 127
                                        K+ee+++p  + + ++++  ++ ++++++Er++L tL+f+l+
  gene1868|gene1868|rna1868|rna1868 232 KYEEVECPLFSTFRMLIN--CDTSDLMNAERYLLMTLDFNLN 271
                                        ****************87..9*******************96 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.062
                                        HHTT--TTHHHHHHHHHHHHHHHS---CCCHHHHHHHHHHHHHHHHSSS---HHHHHHHTTTSS-HH CS
                           Cyclin_N  43 ekfkltpetlflavnyldRflskksvpkdklqlvgatcLllAaKveeisppkledlvyitdeaftee 109
                                         + + + +t +la  +l+ +l ++++  ++++  ++++ + A K+ e++  +   ++ ++    +++
  gene1868|gene1868|rna1868|rna1868 284 IVNNYEVKTRVLAKYILELMLLNEQFIIYNAHIKACAAFYTARKILEMDNFSNLFFMLACT---DKK 347
                                        5555666788899999999999999999999999**********99998665555555554...333 PP

>> Cyclin_C  Cyclin, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.9   0.2   6.4e-21   2.9e-17       2     118 ..     274     386 ..     273     387 .. 0.95

  Alignments for each domain:
  == domain 1  score: 62.9 bits;  conditional E-value: 6.4e-21
                                        -HHHHHHHHHCCSSHT.-HCCHHCHHCHHHHHHCSCCHCCS-HHHHHHHHHHHCCHHHHS--S-HHHHHHC---HH CS
                           Cyclin_C   2 tplsFlrrflkaadasedselrtlakylleltlldydflsyppSliAaaalllarstlnspewtetlehytgyske 77 
                                         pl+F+rr++ ++++  + ++r laky+lel+ll+ +f+ y   + A aa++ ar++l+  ++++ +  +   +k+
  gene1868|gene1868|rna1868|rna1868 274 SPLCFVRRLSIVNNY--EVKTRVLAKYILELMLLNEQFIIYNAHIKACAAFYTARKILEMDNFSNLFFMLACTDKK 347
                                        69**********777..889*********************************************999999***** PP

                                        HHHHHHHHHHHHHHHHHGSS--HHCCCCTCGGGCCCGGS-S CS
                           Cyclin_C  78 dlkpcvelilellssapssklqavrrkyssskfhkvstlse 118
                                         +k cv+ il +l  a+  ++ +v+rky  +++++vs+++e
  gene1868|gene1868|rna1868|rna1868 348 TIKGCVNDILVML--AKPIRYDSVKRKYGVDRMMRVSAFVE 386
                                        *************..7889******************9876 PP

>> RAWUL  RAWUL domain RING finger- and  WD40-associated ubiquitin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.6     0.011        48      29      46 ..     273     322 ..     197     340 .. 0.50
   2 ?    3.3   0.1      0.03   1.4e+02       9      18 ..     388     397 .]     385     397 .] 0.89

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.011
                                        H................................GGGEEEEEEE..TTSEE CS
                              RAWUL  29 e................................ekqytiyiveilyegef 46 
                                                                         ++q++iy++ i +  +f
  gene1868|gene1868|rna1868|rna1868 273 LsplcfvrrlsivnnyevktrvlakyilelmllNEQFIIYNAHIKACAAF 322
                                        04444444444444444444444444444444455688888887777666 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.03
                                        SBHHHHHHHH CS
                              RAWUL   9 atVdhLsKyL 18 
                                        ++V+hLsKyL
  gene1868|gene1868|rna1868|rna1868 388 FRVKHLSKYL 397
                                        78*******9 PP

>> TbpB_A  N-Lobe handle Tf-binding protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.1   0.00047       2.1      30      88 ..       5      63 ..       2      70 .. 0.81
   2 ?    1.2   0.3      0.13   5.9e+02      39     102 ..      89     151 ..      79     169 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00047
                             TbpB_A 30 prrniapkdeegeeevpls.eediekvedellkipkekevkkksdekesfvhshdgskks 88
                                       + rni +kde   +e+ +  e+ ++ ++de+ +i   ++  k+ +ek+++ + +d ++++
  gene1868|gene1868|rna1868|rna1868  5 VLRNITNKDEG-RKEDGTReEQKWKCTDDERANITCMADCGKYGQEKDRRCDFVDTTSPE 63
                                       6799*999965.55555553888899999*******************999999988765 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.13
                             TbpB_A  39 eegeeevplseediekvedellkipkekevkkksdekesfvhshdgskksrkrdyqYVrsGyvl 102
                                          +++ +pl e+d+++ e + lk +++  + +  de+ sf     +   +   +++Y ++ +++
  gene1868|gene1868|rna1868|rna1868  89 SGKKHAEPLAEKDVNAPEKKILKEESRVGQSTLTDEERSFY-EIMEMDAQSDITMEYGYAEHFF 151
                                        44556889999999999998888888888555555555554.4455666666666766666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (397 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       598  (0.0333538); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 2773.35
//
Query:       gene1869|gene1869|rna1869|rna1869  [L=396]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.022   14.2   0.0      0.055   12.9   0.0    1.7  1  eIF-6          eIF-6 family
       0.22   11.7   2.0       0.25   11.5   0.4    1.9  2  Binary_toxB_3  Clostridial binary toxin B/anthrax toxin PA do


Domain annotation for each model (and alignments):
>> eIF-6  eIF-6 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   6.1e-06     0.055      57     148 ..     200     296 ..     157     309 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6.1e-06
                                        H-EE-SSEEEEETT-...-HHHHHHHH.HHHH---EEE--SS--HHHHEEE-.SSEEEE-GGGGG.GHHHHHHHHT CS
                              eIF-6  57 lvvgNsngllvpstv...tdeeleklk.eslkleverleekltAlGNvilaN.DkvAlvhpdlsketveiiadvLg 127
                                        ++v N++ +l+++ +   ++ +l++++ e ++ +++r e  +   GN++l+N D v + +++ +k+t+   ++vL+
  gene1869|gene1869|rna1869|rna1869 200 IMVINEKLILISNKTgilKEIDLNTFEiEDIRTNIKRFERGFYVQGNIFLVNkDIVLFLNEKYQKRTIYHFENVLD 275
                                        67888888888886522234444444423345999*****************4445568999************** PP

                                        SEEEE--BTTBS-TTTSEEE- CS
                              eIF-6 128 vevvrgtiagiktvGsaavvt 148
                                        ++  +g++  ++  G ++v  
  gene1869|gene1869|rna1869|rna1869 276 IKFLEGKFYFLNSCGFFIVQD 296
                                        ****99999888888877765 PP

>> Binary_toxB_3  Clostridial binary toxin B/anthrax toxin PA domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.1   0.1         2   1.8e+04      76      90 ..       2      16 ..       2      19 .. 0.79
   2 ?   11.5   0.4   2.8e-05      0.25      56      95 ..     116     155 ..     106     161 .. 0.85

  Alignments for each domain:
  == domain 1  score: -4.1 bits;  conditional E-value: 2
                                       -HHHHHHHHHHHHTT CS
                      Binary_toxB_3 76 drrtekkikkeleel 90
                                       d+++ +++kk + +l
  gene1869|gene1869|rna1869|rna1869  2 DKKARRNVKKSVTDL 16
                                       678899999998876 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 2.8e-05
                                        -SSSS-EETTEEGGGEEEEE-HHHHHHHHHHHHTTT-SST CS
                      Binary_toxB_3  56 eekeklsykdesidevdfifdrrtekkikkeleelkakni 95 
                                        ee++  + kd + d++++i++++ e ki+++l   +++ i
  gene1869|gene1869|rna1869|rna1869 116 EEHDLHYLKDREQDDLNVIYEEKKEAKIQNKLFRCNTRII 155
                                        6777788899**********************98888766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (396 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       872  (0.0486363); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 2636.00
//
Query:       gene187|gene187|rna187|rna187  [L=848]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.1e-97  326.8   0.0    5.6e-95  318.8   0.0    2.2  1  Topoisom_bac    DNA topoisomerase
    1.2e-19   70.1  18.6    1.3e-10   41.2   2.9    2.7  2  zf-GRF          GRF zinc finger
    2.9e-15   56.3   0.0    7.1e-15   55.1   0.0    1.7  1  Toprim          Toprim domain
      0.008   16.6   0.0      0.027   14.9   0.0    1.9  1  Toprim_4        Toprim domain
  ------ inclusion threshold ------
        4.3    7.2   7.1       0.35   10.7   1.5    2.0  2  zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger


Domain annotation for each model (and alignments):
>> Topoisom_bac  DNA topoisomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  318.8   0.0   1.6e-98   5.6e-95       2     412 ..     152     595 ..     151     596 .. 0.91

  Alignments for each domain:
  == domain 1  score: 318.8 bits;  conditional E-value: 1.6e-98
                   Topoisom_bac   2 inenlvdaaeaRrelDwliGinlsrlltkklkg.kkvlsaGRVqtptLaliveRereienFvpeeyweveatl.kkekke 79 
                                    i++++ d++ aR elD++iG++++rl+t++l   k+v+s+G +q+ptL+++veR  e+++Fv e+++++++ + k+++++
  gene187|gene187|rna187|rna187 152 IDMRQCDSVAARMELDLRIGASFTRLQTLNLAAhKNVVSYGSCQIPTLGFVVERALEHKKFVAEKFFTLKICIvKDRHTN 231
                                    79999************************6666689**********************************9875655555 PP

                   Topoisom_bac  80 kekkkkkkkerikdkeeaeaileklkkk..eakvesvekkekkkppplpfdtttLqkeasrklglsakktlsiaqkLYek 157
                                        +++++++++dk+++  ++  l ++    +v+ vekk  ++++plp++t+++qk  sr   + +++++++a+ LY++
  gene187|gene187|rna187|rna187 232 ---IFSWTRGNVFDKNCVLYFFRYLTDElaGTVVTGVEKKSVTRYRPLPLRTVDMQKILSRS--MPSHRIMQVAETLYQR 306
                                    ...48********************88554678999*************************6..***************7 PP

                   Topoisom_bac 158 aglitYpRTdstrlseeaelkailealakkygkeylefaekllkktkkksvvknkkveaHeAIrPteelpklkelsddek 237
                                     g+i+YpRT+++ +++++e + i++ + k  g   ++ a++++  +++    +n++  aH +I+P ++     +l+ dek
  gene187|gene187|rna187|rna187 307 -GIISYPRTETDCFPRNFEYNRIKTEILKA-G--RHNVANTAFRGPRSG---RNND-FAHLPIYPLKNP---ANLTADEK 375
                                    .****************99*********95.4..355566666655544...4556.8********774...489***** PP

                   Topoisom_bac 238 klYelIvrrflaslmkdakyeettvkleveeeefkasgktilekGfkkvykeekkeeeeeelpelkegee.......... 307
                                    k+Y++I++rf+as+++da  ee+ v l+ ++e+f ++g++++++Gf+k+y++++  e++  ++ + ege+          
  gene187|gene187|rna187|rna187 376 KVYNFIADRFIASVSEDALLEEHVVHLRMKDEHFVLKGTKVVKHGFLKFYHHDRVGEKD--ISVFREGERfelskieric 453
                                    **************************************************999999875..7777777777777777777 PP

                   Topoisom_bac 308 ....................................vkvkeveleekkTkppkryteasLikamekagiGtpaTraeiie 351
                                                                        ++ + + +++++Tkpp+++te++Li++m+++giGt+aT++e+i+
  gene187|gene187|rna187|rna187 454 slgedekdkpgndrddasedviivneapgtlrdehrMNKNCIFVNDGTTKPPNYLTESELIALMDRNGIGTDATIHEHIK 533
                                    7777788999999999999999999999999888777777777************************************* PP

                   Topoisom_bac 352 klvergYverkkkslvptelGkalvellekf.kdlvspelTaeleekLdeIaegkadakevl 412
                                    k+++r+Yv ++ k+lvpt+lG +l+  ++++  +l  p+++++le++L++I++g  d+ +v+
  gene187|gene187|rna187|rna187 534 KILDRKYVSKRTKYLVPTNLGYSLICCYKTLgLNLERPHYRRDLEKSLKDIEQGVVDRMNVV 595
                                    **********87*****************9*9**********************99998887 PP

>> zf-GRF  GRF zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.8   7.9   7.1e-12   2.5e-08       1      42 [.     750     789 ..     750     791 .. 0.94
   2 !   41.2   2.9   3.6e-14   1.3e-10       2      44 ..     804     844 ..     803     845 .. 0.92

  Alignments for each domain:
  == domain 1  score: 33.8 bits;  conditional E-value: 7.1e-12
                         zf-GRF   1 plCkcgrlavlltvrktgpNkGRkFYkCpkgkekqCgFFkWa 42 
                                    ++C c + a+ + v+ +g+Nk ++FY C+k+ +  C+FF+W 
  gene187|gene187|rna187|rna187 750 VFCDCREKAKANFVK-KGKNKDKEFYSCAKFPD-GCNFFQWK 789
                                    58************5.****************8.8******6 PP

  == domain 2  score: 41.2 bits;  conditional E-value: 3.6e-14
                         zf-GRF   2 lCkcgrlavlltvrktgpNkGRkFYkCpkgkekqCgFFkWade 44 
                                     C cg   + l+++ t +N+G++FYkC+k+    C+FF W+de
  gene187|gene187|rna187|rna187 804 KCLCGAGVRKLISN-TDKNRGKAFYKCNKRYR-PCNFFMWEDE 844
                                    6****999999997.*************9986.8********8 PP

>> Toprim  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.1   0.0     2e-18   7.1e-15       3     103 .]       5     137 ..       3     137 .. 0.84

  Alignments for each domain:
  == domain 1  score: 55.1 bits;  conditional E-value: 2e-18
                                    EEESSHHHHHHHHHTHT.....................STEEEEEEESSSSEEEHS.............TTEEEEE.ECT CS
                         Toprim   3 vivEgpsdaktiakalg.....................sgfqavtaslGhildlet.............efkpvye.eie 47 
                                     i+E+ps ak+i ++                       s+    t++lGh++++e+              f + ++  i+
  gene187|gene187|rna187|rna187   5 NIAEKPSVAKSITRTIAssasaartkykytpvhkftynSDAHLFTSVLGHLYTQEFtdnrkwtecdpltLFTADITeYIK 84 
                                    59*************9999*******************99****************777777755555544433335666 PP

                                    TTHHHHHH.HHHHHHHHSEEEEECSSSHHHHHHHHHHHHHHTHHHTTTEEEEEESSS CS
                         Toprim  48 dkkkvlka.lkelakradeiilatDpDreGeaiawellevlkellenkigrvefsei 103
                                    d+ k+lk+ l +l+  +d+++++tD+DreGe ia+e+     +ll++k+ r++fs i
  gene187|gene187|rna187|rna187  85 DEFKALKEnLLHLSTGVDKVVIWTDCDREGEYIALEIQ----KLLNRKCWRARFSAI 137
                                    666666666777779***********************....677788999999876 PP

>> Toprim_4  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   7.5e-06     0.027      43      88 ..      91     132 ..      78     133 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 7.5e-06
                       Toprim_4  43 ktenlveaekkvkevilaldgDaeGeataerlaellleegvkvtrl 88 
                                    k+ nl++    v++v++++d D eGe  a+++ +ll   + k++r+
  gene187|gene187|rna187|rna187  91 KE-NLLHLSTGVDKVVIWTDCDREGEYIALEIQKLL---NRKCWRA 132
                                    33.566677889**********************88...8888885 PP

>> zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   1.5   9.9e-05      0.35      13      34 ..     763     787 ..     756     789 .. 0.78
   2 ?   -2.8   0.3       1.6   5.8e+03      18      32 ..     822     838 ..     814     843 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 9.9e-05
                                    EEE-SSS..EEEEESST.T.----E CS
                 zf-C4_Topoisom  13 lkrgkkG..kFvGCsnYPe.Ckftk 34 
                                    +k+gk++  +F++C  +P+ C+f  
  gene187|gene187|rna187|rna187 763 VKKGKNKdkEFYSCAKFPDgCNFFQ 787
                                    466666669*********9788765 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.6
                                    SS.EEEEES.ST.T--- CS
                 zf-C4_Topoisom  18 kG.kFvGCs.nYPeCkf 32 
                                    +G  F+ C+ +Y  C+f
  gene187|gene187|rna187|rna187 822 RGkAFYKCNkRYRPCNF 838
                                    34489999724555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (848 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       721  (0.0402142); expected 358.6 (0.02)
Passed bias filter:                      531  (0.0296168); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.71u 0.30s 00:00:01.01 Elapsed: 00:00:00.47
# Mc/sec: 5398.40
//
Query:       gene1870|gene1870|rna1870|rna1870  [L=785]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (785 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       870  (0.0485247); expected 358.6 (0.02)
Passed bias filter:                      440  (0.0245412); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.65u 0.26s 00:00:00.91 Elapsed: 00:00:00.44
# Mc/sec: 5401.19
//
Query:       gene1871|gene1871|rna1871|rna1871  [L=96]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.8e-11   41.6  10.6    1.3e-10   41.2  10.6    1.1  1  bZIP_1           bZIP transcription factor
    3.2e-06   27.1  13.2      4e-06   26.8  13.2    1.1  1  bZIP_2           Basic region leucine zipper
     0.0021   17.8   0.9     0.0028   17.4   0.9    1.3  1  DivIC            Septum formation initiator
      0.005   16.8   2.3     0.0059   16.6   2.3    1.1  1  Ax_dynein_light  Axonemal dynein light chain
  ------ inclusion threshold ------
      0.016   15.4   3.5      0.025   14.8   3.5    1.4  1  HALZ             Homeobox associated leucine zipper
      0.025   14.7   1.5      0.048   13.8   1.5    1.5  1  NYD-SP28_assoc   Sperm tail C-terminal domain


Domain annotation for each model (and alignments):
>> bZIP_1  bZIP transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.2  10.6   4.2e-14   1.3e-10       5      63 ..      16      74 ..      13      75 .. 0.96

  Alignments for each domain:
  == domain 1  score: 41.2 bits;  conditional E-value: 4.2e-14
                                       XXXXXX--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             bZIP_1  5 KrekrkqkNReaArrsRqRKqaeieeLerrvkaLekeNksLkseleelkkevekLkskv 63
                                       K+ k +  NR +Ar+s +RK+ +ie+Le++ + L  eN ++k++le+++k+ + ++ k+
  gene1871|gene1871|rna1871|rna1871 16 KKRKLMVVNRASARKSALRKKLYIEALEKENQSLRDENNEMKNKLENYRKMFAVMLGKN 74
                                       999**************************************************999887 PP

>> bZIP_2  Basic region leucine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8  13.2   1.3e-09     4e-06       1      53 [.      12      65 ..      12      66 .. 0.95

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 1.3e-09
                                       .XXXXXXXXX.XXXXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             bZIP_2  1 kddeyrerRr.kNreAarrsRekkkakeeeleervkeLeeeNaqLrqkveqLek 53
                                       +dde++++ +  Nr++ar+s  +kk++ e le+++++L+ eN++ ++k+e+++k
  gene1871|gene1871|rna1871|rna1871 12 TDDEKKRKLMvVNRASARKSALRKKLYIEALEKENQSLRDENNEMKNKLENYRK 65
                                       5899999999****************************************9876 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.9   9.5e-07    0.0028      21      52 ..      34      65 ..      20      71 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 9.5e-07
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHCC-XX CS
                              DivIC 21 qlkqeiaalqaelaklkaeneeLeaevkdLks 52
                                       ++k  i+al++e+++l++en+e++ +++++++
  gene1871|gene1871|rna1871|rna1871 34 RKKLYIEALEKENQSLRDENNEMKNKLENYRK 65
                                       67788***********************9974 PP

>> Ax_dynein_light  Axonemal dynein light chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   2.3     2e-06    0.0059     116     167 ..      25      78 ..      10      83 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 2e-06
                    Ax_dynein_light 116 qaeqgkselekk..ikeLeeekeelekqvaelkaklealekrekerrqeeekkh 167
                                         a  +ks l+kk  i++Le+e+++l+++++e+k+kle+ +k ++  + ++++ h
  gene1871|gene1871|rna1871|rna1871  25 RASARKSALRKKlyIEALEKENQSLRDENNEMKNKLENYRKMFAVMLGKNTNSH 78 
                                        455778888888999************************999988888777776 PP

>> HALZ  Homeobox associated leucine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   3.5   8.4e-06     0.025      21      42 ..      39      60 ..      32      61 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 8.4e-06
                               HALZ 21 ydsLkkenekLkaelqeLkekl 42
                                        ++L+ken++L+ e +e+k+kl
  gene1871|gene1871|rna1871|rna1871 39 IEALEKENQSLRDENNEMKNKL 60
                                       69*******************9 PP

>> NYD-SP28_assoc  Sperm tail C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   1.5   1.6e-05     0.048      36      59 ..      40      63 ..      27      63 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.6e-05
                     NYD-SP28_assoc 36 aklieetesLekqNeeLrnlLkqy 59
                                       ++l +e++sL+ +N+e++n L++y
  gene1871|gene1871|rna1871|rna1871 40 EALEKENQSLRDENNEMKNKLENY 63
                                       67999****************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1930  (0.107647); expected 358.6 (0.02)
Passed bias filter:                      768  (0.0428356); expected 358.6 (0.02)
Passed Vit filter:                       102  (0.00568911); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 663.28
//
Query:       gene1872|gene1872|rna1872|rna1872  [L=183]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.7e-10   40.1   5.7    6.5e-08   32.9   1.8    2.8  2  EF-hand_7       EF-hand domain pair
    6.6e-10   38.1   6.9       0.01   15.7   0.0    4.8  5  EF-hand_6       EF-hand domain
    1.4e-09   36.8  11.1    2.1e-05   23.7   0.1    5.1  5  EF-hand_1       EF hand
      0.001   18.9   3.1      0.069   13.0   0.3    3.7  3  EF-hand_8       EF-hand domain pair
  ------ inclusion threshold ------
       0.03   13.8   0.5        4.9    6.8   0.0    3.2  3  EF-hand_5       EF hand
      0.086   12.5   0.9       0.12   12.1   0.2    1.7  2  DBD_Tnp_Hermes  Hermes transposase DNA-binding domain
      0.094   12.7   1.9       0.46   10.5   0.2    2.6  3  EF-hand_4       Cytoskeletal-regulatory complex EF hand
       0.13   12.2   0.0       0.28   11.2   0.0    1.5  1  Synapsin_N      Synapsin N-terminal


Domain annotation for each model (and alignments):
>> EF-hand_7  EF-hand domain pair
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.1    0.0016       3.5      16      70 ..      40      89 ..      16      90 .. 0.90
   2 !   32.9   1.8   2.9e-11   6.5e-08       1      68 [.      98     167 ..      98     169 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0016
                          EF-hand_7 16 dgyldkeellrllrkifqgagegsklsdeelellfkefDtdkdGvisfdEFlkly 70
                                       +gy+++ +l+ +++k+f + ge + ++      lf+ ++ ++  +i+f+E+l +y
  gene1872|gene1872|rna1872|rna1872 40 SGYMTEKDLQLIFKKLFPF-GECNRFTV----ILFRTINISGTKTIDFNELLIAY 89
                                       6999999999888888866.88888888....9*****************99888 PP

  == domain 2  score: 32.9 bits;  conditional E-value: 2.9e-11
                          EF-hand_7   1 eeklkeaFkelDtdgdgyldkeellrllrkifqgagegsklsdeelellfkefD..tdkdGvisfdEFlk 68 
                                        +ekl+++F+++D+d dg + k+e+ ++++++ +++g  +++  +  + +++ fD   +k+G ++fd+F+ 
  gene1872|gene1872|rna1872|rna1872  98 FEKLRWIFRLYDCDSDGVVGKDEMIKVVKAFLDMIGASFDVNVDVGRFISNIFDdlENKSGFLTFDDFKI 167
                                        79*********************888*******998888888888999999997334889********85 PP

>> EF-hand_6  EF-hand domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.3   0.0    0.0098        22      13      28 ..      39      54 ..      32      60 .. 0.86
   2 !    7.9   0.0    0.0014       3.2       5      27 ..      68      90 ..      66      95 .. 0.89
   3 !   15.7   0.0   4.6e-06      0.01       5      27 ..     104     126 ..     102     133 .. 0.92
   4 !    8.9   0.9   0.00068       1.5       5      24 ..     149     167 ..     145     178 .. 0.84
   5 ?   -2.1   0.0       2.3   5.1e+03       3      10 ..     176     183 .]     174     183 .] 0.72

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0098
                          EF-hand_6 13 gdGkidaeElrkalrk 28
                                        +G+ + ++l+ +++k
  gene1872|gene1872|rna1872|rna1872 39 PSGYMTEKDLQLIFKK 54
                                       59***********994 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0014
                          EF-hand_6  5 aFklfDkdgdGkidaeElrkalr 27
                                       +F+ +  +g+ +id++El  a++
  gene1872|gene1872|rna1872|rna1872 68 LFRTINISGTKTIDFNELLIAYS 90
                                       68999999**********99876 PP

  == domain 3  score: 15.7 bits;  conditional E-value: 4.6e-06
                          EF-hand_6   5 aFklfDkdgdGkidaeElrkalr 27 
                                        +F+l+D d dG + ++E++k+ +
  gene1872|gene1872|rna1872|rna1872 104 IFRLYDCDSDGVVGKDEMIKVVK 126
                                        7*******************987 PP

  == domain 4  score: 8.9 bits;  conditional E-value: 0.00068
                          EF-hand_6   5 aFklfDkdgdGkidaeElrk 24 
                                        +F+ +  +++G++++++++ 
  gene1872|gene1872|rna1872|rna1872 149 IFDDL-ENKSGFLTFDDFKI 167
                                        56666.89**********96 PP

  == domain 5  score: -2.1 bits;  conditional E-value: 2.3
                          EF-hand_6   3 reaFklfD 10 
                                         ++F+ fD
  gene1872|gene1872|rna1872|rna1872 176 LQIFEVFD 183
                                        57888888 PP

>> EF-hand_1  EF hand
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0     0.044        98      14      29 .]      40      55 ..      40      55 .. 0.93
   2 ?    4.2   0.0     0.017        38       6      24 ..      69      87 ..      67      91 .. 0.82
   3 !   23.7   0.1   9.3e-09   2.1e-05       2      28 ..     101     127 ..     100     128 .. 0.93
   4 !    9.2   0.3   0.00042      0.94      12      24 ..     155     167 ..     146     171 .. 0.85
   5 ?   -0.1   0.1      0.38   8.5e+02       1      10 [.     174     183 .]     174     183 .] 0.86

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.044
                                       SSEEEHHHHHHHHHHH CS
                          EF-hand_1 14 dGkIdfeEfkellkkl 29
                                       +G+++ ++++ ++kkl
  gene1872|gene1872|rna1872|rna1872 40 SGYMTEKDLQLIFKKL 55
                                       7************986 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.017
                                       HHHHTTTSSSEEEHHHHHH CS
                          EF-hand_1  6 FrefDkDgdGkIdfeEfke 24
                                       Fr +   g+ +Idf+E++ 
  gene1872|gene1872|rna1872|rna1872 69 FRTINISGTKTIDFNELLI 87
                                       7777788999******975 PP

  == domain 3  score: 23.7 bits;  conditional E-value: 9.3e-09
                                        HHHHHHHHTTTSSSEEEHHHHHHHHHH CS
                          EF-hand_1   2 lkeiFrefDkDgdGkIdfeEfkellkk 28 
                                        l++iFr++D D dG + ++E+++++k+
  gene1872|gene1872|rna1872|rna1872 101 LRWIFRLYDCDSDGVVGKDEMIKVVKA 127
                                        899********************9997 PP

  == domain 4  score: 9.2 bits;  conditional E-value: 0.00042
                                        TSSSEEEHHHHHH CS
                          EF-hand_1  12 DgdGkIdfeEfke 24 
                                        +++G+++f++fk 
  gene1872|gene1872|rna1872|rna1872 155 NKSGFLTFDDFKI 167
                                        9**********96 PP

  == domain 5  score: -0.1 bits;  conditional E-value: 0.38
                                        HHHHHHHHHT CS
                          EF-hand_1   1 elkeiFrefD 10 
                                        e+ +iF++fD
  gene1872|gene1872|rna1872|rna1872 174 EVLQIFEVFD 183
                                        5779*****9 PP

>> EF-hand_8  EF-hand domain pair
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.1     0.072   1.6e+02       2      47 ..      40      84 ..      39      89 .. 0.54
   2 !   13.0   0.3   3.1e-05     0.069       5      52 ..      80     125 ..      76     127 .. 0.76
   3 ?    2.4   0.0     0.061   1.4e+02      39      49 ..     156     166 ..     154     182 .. 0.73

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.072
                          EF-hand_8  2 kgkItreelrrilrilglkkglseee..vdilfrefDtdgdGkisfeE 47
                                       +g++t  +l+ i ++l  +  ++e +    ilfr++ + g  +i+f+E
  gene1872|gene1872|rna1872|rna1872 40 SGYMTEKDLQLIFKKL-FP--FGECNrfTVILFRTINISGTKTIDFNE 84
                                       5677777777766443.12..333333234566666666666666666 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 3.1e-05
                          EF-hand_8   5 ItreelrrilrilglkkglseeevdilfrefDtdgdGkisfeEFcvll 52 
                                        I++ el  +++il +      e+++++fr+ D d dG+++++E + ++
  gene1872|gene1872|rna1872|rna1872  80 IDFNELLIAYSILRKG--SIFEKLRWIFRLYDCDSDGVVGKDEMIKVV 125
                                        6666666666666544..445789*******************88766 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.061
                          EF-hand_8  39 gdGkisfeEFc 49 
                                        ++G ++f++F 
  gene1872|gene1872|rna1872|rna1872 156 KSGFLTFDDFK 166
                                        56666666664 PP

>> EF-hand_5  EF hand
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       1.6   3.5e+03      15      21 ..      79      85 ..      79      86 .. 0.81
   2 ?    6.8   0.0    0.0022       4.9       5      24 ..     105     124 ..     102     126 .. 0.90
   3 ?    3.5   0.0     0.024        53      11      22 ..     155     166 ..     154     169 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.6
                                       CE-HHHH CS
                          EF-hand_5 15 kIskeEL 21
                                       +I++ EL
  gene1872|gene1872|rna1872|rna1872 79 TIDFNEL 85
                                       5999998 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0022
                                        HHHH-SS-SSCE-HHHHHHH CS
                          EF-hand_5   5 FqaiDlNgDGkIskeELktl 24 
                                        F+  D + DG + k+E  ++
  gene1872|gene1872|rna1872|rna1872 105 FRLYDCDSDGVVGKDEMIKV 124
                                        9999************9876 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.024
                                        S-SSCE-HHHHH CS
                          EF-hand_5  11 NgDGkIskeELk 22 
                                        N++G+++++ +k
  gene1872|gene1872|rna1872|rna1872 155 NKSGFLTFDDFK 166
                                        9********998 PP

>> DBD_Tnp_Hermes  Hermes transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       2.4   5.4e+03      16      33 ..      15      32 ..      11      37 .. 0.73
   2 ?   12.1   0.2   5.4e-05      0.12       4      60 ..      84     143 ..      81     149 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 2.4
                                       HHHHHHHHHHHTT--GGG CS
                     DBD_Tnp_Hermes 16 aiekctqWvvrDcrpfsa 33
                                        ++k++ +   D + +sa
  gene1872|gene1872|rna1872|rna1872 15 TVKKFSHFNESDIKKWSA 32
                                       577887777777777776 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 5.4e-05
                                        --B---HHHHHHHHHHHHHHHHH..TT--GGGGG-HHHHHHHHHHHH.HHHHH-S-B-HH CS
                     DBD_Tnp_Hermes   4 eLkivseedkkeaiekctqWvvr..DcrpfsavtGaGfkklvkfflk.igavYGeqvdve 60 
                                        eL i   + +k +i    +W+ r  Dc +  +v     +k+vk fl  iga++  +vdv 
  gene1872|gene1872|rna1872|rna1872  84 ELLIAYSILRKGSIFEKLRWIFRlyDCDSDGVVGKDEMIKVVKAFLDmIGASFDVNVDVG 143
                                        6666666677777766678997766********************9659*****999996 PP

>> EF-hand_4  Cytoskeletal-regulatory complex EF hand
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0      0.18   4.1e+02      52      70 ..      72      90 ..      19      95 .. 0.72
   2 ?   10.5   0.2    0.0002      0.46      43      79 ..      99     135 ..      88     149 .. 0.85
   3 ?   -1.3   0.0      0.94   2.1e+03      14      30 ..     148     164 ..     139     175 .. 0.68

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.18
                          EF-hand_4 52 adidedgkldfeefciamr 70
                                        +i    ++df+e+ ia  
  gene1872|gene1872|rna1872|rna1872 72 INISGTKTIDFNELLIAYS 90
                                       4566777899999998865 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.0002
                          EF-hand_4  43 dklekiwdladidedgkldfeefciamrlifdlvnge 79 
                                        +kl  i+ l d d+dg +  +e++ +++  +d++  +
  gene1872|gene1872|rna1872|rna1872  99 EKLRWIFRLYDCDSDGVVGKDEMIKVVKAFLDMIGAS 135
                                        68999****************************9765 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 0.94
                          EF-hand_4  14 eifsglkpednkltgdk 30 
                                        +if  l++++  lt d 
  gene1872|gene1872|rna1872|rna1872 148 NIFDDLENKSGFLTFDD 164
                                        46666666666665543 PP

>> Synapsin_N  Synapsin N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00012      0.28      12      25 ..      33      48 ..      31      49 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00012
                         Synapsin_N 12 sFlanLPnGYls..DL 25
                                        F an P+GY++  DL
  gene1872|gene1872|rna1872|rna1872 33 EFNANYPSGYMTekDL 48
                                       589********95555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       407  (0.0227007); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1197.26
//
Query:       gene1873|gene1873|rna1873|rna1873  [L=62]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (62 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       347  (0.0193541); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.40
# Mc/sec: 461.07
//
Query:       gene1874|gene1874|rna1874|rna1874  [L=207]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
     0.0021   18.3   0.2     0.0042   17.4   0.2    1.4  1  zf-Di19     Drought induced 19 protein (Di19), zinc-binding
  ------ inclusion threshold ------
      0.013   15.9   3.1      0.046   14.2   3.1    2.0  1  Zn-C2H2_12  Autophagy receptor zinc finger-C2H2 domain


Domain annotation for each model (and alignments):
>> zf-Di19  Drought induced 19 protein (Di19), zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.2   4.6e-07    0.0042       4      24 ..     110     130 ..     108     133 .. 0.94

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 4.6e-07
                            zf-Di19   4 tCPyCgkeltvkeLveHvede 24 
                                         CP+C+k+++v+++ +Hv++e
  gene1874|gene1874|rna1874|rna1874 110 ECPFCSKKIDVNSFERHVKEE 130
                                        6*****************986 PP

>> Zn-C2H2_12  Autophagy receptor zinc finger-C2H2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   3.1   5.1e-06     0.046       1      24 [.     109     128 ..     109     129 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 5.1e-06
                         Zn-C2H2_12   1 KeCPlCseqFpknvdqdeFeeHVe 24 
                                        KeCP Cs+     +d++ Fe+HV 
  gene1874|gene1874|rna1874|rna1874 109 KECPFCSK----KIDVNSFERHVK 128
                                        9*****85....7**********6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1104  (0.0615762); expected 358.6 (0.02)
Passed bias filter:                      669  (0.0373138); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1484.58
//
Query:       gene1875|gene1875|rna1875|rna1875  [L=46]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (46 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       310  (0.0172904); expected 358.6 (0.02)
Passed bias filter:                      195  (0.0108762); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.23s 00:00:00.57 Elapsed: 00:00:00.39
# Mc/sec: 354.03
//
Query:       gene1876|gene1876|rna1876|rna1876  [L=347]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (347 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       788  (0.0439511); expected 358.6 (0.02)
Passed bias filter:                      453  (0.0252663); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 2435.42
//
Query:       gene1877|gene1877|rna1877|rna1877  [L=542]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.2e-12   45.7  17.5    8.2e-07   29.1   4.8    2.5  2  zf-B_box  B-box zinc finger
  ------ inclusion threshold ------
        4.6    7.6  18.1       0.83    9.9   4.1    3.2  3  IBR       IBR domain, a half RING-finger domain


Domain annotation for each model (and alignments):
>> zf-B_box  B-box zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   4.8   1.4e-08   0.00012       2      36 ..     278     320 ..     277     326 .. 0.85
   2 !   29.1   4.8   9.1e-11   8.2e-07       5      40 ..     334     371 ..     330     373 .. 0.89

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 1.4e-08
                           zf-B_box   2 eetkCpeHknkpatlfCedCqqplCeeCstgeHr........g 36 
                                        + ++C+++++++a+ fC   ++ +C+eC+++ H+        +
  gene1877|gene1877|rna1877|rna1877 278 KSNMCERCQKREANMFCVAERASFCKECDQKLHYdfftrrhlR 320
                                        6789*****************************9777764444 PP

  == domain 2  score: 29.1 bits;  conditional E-value: 9.1e-11
                           zf-B_box   5 kCpeHknkpatlfCedCqqplCeeC.stgeHrg.Hevv 40 
                                        +C+eH++    +fC++C+ plC +C ++g+H   H ++
  gene1877|gene1877|rna1877|rna1877 334 NCEEHPETVVDYFCKECKIPLCTQCrLKGSHPSdHALI 371
                                        7*************************9****8548765 PP

>> IBR  IBR domain, a half RING-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.38   3.4e+03      10      22 ..     203     215 ..     197     231 .. 0.83
   2 ?    9.9   4.1   9.3e-05      0.83      21      60 ..     282     313 ..     263     316 .. 0.71
   3 ?    4.4   3.2     0.005        45      39      57 ..     345     364 ..     324     368 .. 0.70

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.38
                                IBR  10 kslesdpnlkwCp 22 
                                        k++++++n+++C 
  gene1877|gene1877|rna1877|rna1877 203 KTVNNNENVRQCL 215
                                        5689999999997 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 9.3e-05
                                IBR  21 CprpdCeaiieksegcksvtCskCgfefCfnCkkewHegl 60 
                                        C    C+      + ++++ C   + +fC +C ++ H+++
  gene1877|gene1877|rna1877|rna1877 282 CE--RCQ------KREANMFCVAERASFCKECDQKLHYDF 313
                                        22..222......3344599*****************986 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.005
                                IBR  39 vtCskCgfefCfnCk.kewH 57 
                                          C++C+   C++C+ k  H
  gene1877|gene1877|rna1877|rna1877 345 YFCKECKIPLCTQCRlKGSH 364
                                        46************944456 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (542 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1064  (0.0593452); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.63u 0.27s 00:00:00.90 Elapsed: 00:00:00.50
# Mc/sec: 3285.24
//
Query:       gene1878|gene1878|rna1878|rna1878  [L=200]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.11   12.6   0.0        0.2   11.7   0.0    1.4  1  DUF5415   Family of unknown function (DUF5415)


Domain annotation for each model (and alignments):
>> DUF5415  Family of unknown function (DUF5415)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   1.1e-05       0.2      28      52 ..      74      99 ..      66     105 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 1.1e-05
                            DUF5415 28 ke.vlekvqfdllrGkdkdleeyiyq 52
                                       +e vl+    dllr  d d+ +yiy 
  gene1878|gene1878|rna1878|rna1878 74 QEiVLNDQHNDLLRTTDIDFRNYIYE 99
                                       5526788889***************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       647  (0.0360868); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1355.88
//
Query:       gene1879|gene1879|rna1879|rna1879  [L=595]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (595 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       613  (0.0341904); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 4044.48
//
Query:       gene188|gene188|rna188|rna188  [L=117]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       627  (0.0349713); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 858.46
//
Query:       gene1880|gene1880|rna1880|rna1880  [L=52]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (52 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       230  (0.0128284); expected 358.6 (0.02)
Passed bias filter:                      193  (0.0107647); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.26s 00:00:00.61 Elapsed: 00:00:00.41
# Mc/sec: 384.39
//
Query:       gene1881|gene1881|rna1881|rna1881  [L=57]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
      0.044   14.6   0.0      0.065   14.0   0.0    1.4  1  Connexin50  Gap junction alpha-8 protein (Cx50)


Domain annotation for each model (and alignments):
>> Connexin50  Gap junction alpha-8 protein (Cx50)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   3.6e-06     0.065       4      26 ..      14      36 ..      12      53 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.6e-06
                         Connexin50  4 akGYklLeEeKevshfyPLaEvg 26
                                       a GY +++EeK+v  +  L Ev 
  gene1881|gene1881|rna1881|rna1881 14 AHGYNKIDEEKIVNTYIQLREVN 36
                                       89***************999996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (57 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       715  (0.0398795); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.25s 00:00:00.60 Elapsed: 00:00:00.41
# Mc/sec: 413.62
//
Query:       gene1882|gene1882|rna1882|rna1882  [L=90]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       403  (0.0224776); expected 358.6 (0.02)
Passed bias filter:                      221  (0.0123264); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.28s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 654.31
//
Query:       gene1883|gene1883|rna1883|rna1883  [L=321]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      6e-16   58.5   0.1    2.3e-13   50.2   0.0    2.3  2  MMR_HSR1     50S ribosome-binding GTPase
    6.7e-10   38.7   0.0    8.7e-05   22.1   0.0    2.4  2  FeoB_N       Ferrous iron transport protein B
    8.6e-05   22.5   0.0    0.00018   21.5   0.0    1.4  1  RsgA_GTPase  RsgA GTPase
     0.0063   15.9   1.9      0.041   13.2   1.9    2.0  1  DUF3388      Protein of unknown function (DUF3388)
  ------ inclusion threshold ------
      0.073   12.6   0.2       0.86    9.1   0.1    2.3  2  GTP_EFTU     Elongation factor Tu GTP binding domain
      0.097   12.9   0.8       0.74   10.0   0.1    2.6  2  Roc          Ras of Complex, Roc, domain of DAPkinase
       0.12   13.0   0.0        1.9    9.0   0.0    2.4  2  AAA_18       AAA domain


Domain annotation for each model (and alignments):
>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.3   0.0    0.0039        10      73     114 .]      90     126 ..      70     126 .. 0.72
   2 !   50.2   0.0   8.9e-17   2.3e-13       3      65 ..     181     241 ..     179     305 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0039
                                        HHCTSEEEEEEETTTTCSHHHHHHHHHHHHHTTSEEEEEEES CS
                           MMR_HSR1  73 leeadlillvvdaseeklkpldeeleelleeakkplilvlnk 114
                                         + +d i++vvd+++ ++   +eel e+     kp+il++nk
  gene1883|gene1883|rna1883|rna1883  90 TDVCDYICVVVDSRNVGFF-FEEELLEMG----KPVILIMNK 126
                                        3449********7744443.447777775....8*******8 PP

  == domain 2  score: 50.2 bits;  conditional E-value: 8.9e-17
                                        EEEESTTSSHHHHHHHHHTS.TEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCS.SHHHHHHH CS
                           MMR_HSR1   3 aivGrpNvGKStLinaltge.kaivsdkpgtTrdinegrvklkgkeielvDtpGli.egaseekg 65 
                                        a +G+pNvGKS+Li+++++  k ++s++pg+T+ ++ ++++    +i ++D+pGl+ +++s+e+ 
  gene1883|gene1883|rna1883|rna1883 181 AMIGYPNVGKSSLIKTISNHvKIKISSTPGKTKFVQSYQFT----DILFLDVPGLVfKRHSREEL 241
                                        89******************889*****************8....6********86322222222 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   8.2e-06     0.021      74     119 ..      88     131 ..      74     136 .. 0.87
   2 !   22.1   0.0   3.4e-08   8.7e-05       2      77 ..     179     250 ..     178     282 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 8.2e-06
                                        HHCTSSSEEEEEEEGGGHHHHHHHHHHHHHTTSSEEEEEETHHHHH CS
                             FeoB_N  74 lleeepdvvvnvvdatnlernLyLtlqllelgvpvvlalnmideae 119
                                        ++++  d +  vvd+ n+   +++  +lle+g+pv+l++n++d  +
  gene1883|gene1883|rna1883|rna1883  88 IATDVCDYICVVVDSRNV--GFFFEEELLEMGKPVILIMNKYDLCN 131
                                        5677899*********98..599*******************9865 PP

  == domain 2  score: 22.1 bits;  conditional E-value: 3.4e-08
                                        EEEEEESTTSSHHHHHHHHHTT.SEEEEESTTSSSEEEEEEEEETTEEEEEEE----SSSSSSSHHHHHHHHHHHC CS
                             FeoB_N   2 tvalvGnpnvGkttlfnaltga.kqkvgNwpGvtvekkegklklkgkeveivDlPGiYslsayseeekvardflle 76 
                                        + a++G pnvGk++l+ ++++  k k++  pG+t   ++ +++    ++ ++D+PG   ++ +s+ee +  +++  
  gene1883|gene1883|rna1883|rna1883 179 KYAMIGYPNVGKSSLIKTISNHvKIKISSTPGKTKFVQSYQFT----DILFLDVPGL-VFKRHSREELLIYNIINV 249
                                        5799***************985278********9888887777....9********7.578899999888887765 PP

                                        T CS
                             FeoB_N  77 e 77 
                                        +
  gene1883|gene1883|rna1883|rna1883 250 D 250
                                        4 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0   6.9e-08   0.00018      47     160 ..     118     230 ..     109     233 .. 0.67

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 6.9e-08
                                        -EEEEEEE-GGG--HHH.....HHHHHHHHHHHTTSEEEE--TT.THTTHHHHHHHCTT..SEEEEECSTTSSHHH CS
                        RsgA_GTPase  47 iepvivlnKiDlleeee.....eleelkeelealgyevllvsak.tkegleelkellkd..ktsvlvGqSGvGKSt 114
                                         ++++++nK Dl++ +       +++  + + ++ +++++ s+  ++ ++e l+ l ++  +  +++G   vGKS+
  gene1883|gene1883|rna1883|rna1883 118 KPVILIMNKYDLCNGNVpddnnFFRNRFKFVDRI-FKIFKFSNVdQHVNIEFLEFLKSQgnRKYAMIGYPNVGKSS 192
                                        568899*******988877554444444555555.66776555405556665554433345899************ PP

                                        HHHHHCTT-----S--------------SEEEEEETTTEEEESS-S CS
                        RsgA_GTPase 115 LinallpelelktgevseklgrGkhTTtavellelaegglliDtPG 160
                                        Li+++ ++ ++k++++  k       T+ v+ +++  + l  D PG
  gene1883|gene1883|rna1883|rna1883 193 LIKTISNHVKIKISSTPGK-------TKFVQSYQFT-DILFLDVPG 230
                                        ********88877665544.......5555555555.555555555 PP

>> DUF3388  Protein of unknown function (DUF3388)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   1.9   1.6e-05     0.041      29     157 ..     153     290 ..     146     313 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.6e-05
                            DUF3388  29 ktfrfvreelgllvdflaellkkeghkliGirGmPrvGktesivaasvcank.......rwlflsstllkqtvrsq 97 
                                        k f+f   +  + ++fl e+lk +g++   + G P vGk+  i + s + +        +  f+ s  + +++  +
  gene1883|gene1883|rna1883|rna1883 153 KIFKFSNVDQHVNIEFL-EFLKSQGNRKYAMIGYPNVGKSSLIKTISNHVKIkisstpgKTKFVQSYQFTDILFLD 227
                                        78999999999*****9.999******************9877555544332011111145566665555444333 PP

                            DUF3388  98 ...liedeynednifiidgivsarranekhlqlireimr.lpavkvvehPdifvketeytlddf 157
                                           l+ + ++++++ +i  i+ + +++  + +l   +++ + +++++eh  i + +t++tld++
  gene1883|gene1883|rna1883|rna1883 228 vpgLVFKRHSREEL-LIYNIINVDQSKIDYEKLFELLLQkISMIQIIEHFKIKLLNTNCTLDEL 290
                                        11133333444444.455677777777777777776665157899****************985 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.1   0.00034      0.86      91     153 ..      90     148 ..      86     202 .. 0.67
   2 ?    1.3   0.0     0.081   2.1e+02       4      32 ..     178     206 ..     175     228 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00034
                                        HHT-SEEEEEEETTTBSTHHHHHHHHHHHHTTTEEEEEEESCGSTHHHHHHHHHHHHHHHHHH CS
                           GTP_EFTU  91 lrvlDgavlvvdaveGvepqteevlrlalkegvpiivfiNKmDrlkaelkeiveevkqklsrk 153
                                        + v+D+ ++vvd++  v    ee    +l++g p+i+++NK D ++ ++    +  +++++ +
  gene1883|gene1883|rna1883|rna1883  90 TDVCDYICVVVDSR-NVGFFFEEE---LLEMGKPVILIMNKYDLCNGNVPDDNNFFRNRFKFV 148
                                        67889999999887.455555544...467899************777777777666666443 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.081
                                        EEEEEEESTTSSHHHHHHHHHHHTTSSCH CS
                           GTP_EFTU   4 rnigiighvDhGKtTLtdrLlyktgaisk 32 
                                        r+ ++ig  + GK++L+ ++  + ++  +
  gene1883|gene1883|rna1883|rna1883 178 RKYAMIGYPNVGKSSLIKTISNHVKIKIS 206
                                        56678888888999999888766655433 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.33   8.5e+02     108     119 ..     117     128 ..      93     129 .. 0.82
   2 ?   10.0   0.1   0.00029      0.74       1      34 [.     179     211 ..     179     223 .. 0.75

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.33
                                        SS-EEEEEE-TT CS
                                Roc 108 kspvilvgnkiD 119
                                         +pvil++nk+D
  gene1883|gene1883|rna1883|rna1883 117 GKPVILIMNKYD 128
                                        579*******99 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00029
                                        EEEEESSTTSSHHHHHHCHCT-CCC-EEETTTTE CS
                                Roc   1 KvvlvGdsgvGKtsllkrfvedkfsekekstigv 34 
                                        K  ++G  +vGK+sl+k +  ++++ k +st g 
  gene1883|gene1883|rna1883|rna1883 179 KYAMIGYPNVGKSSLIKTIS-NHVKIKISSTPGK 211
                                        6689************9877.6666666666665 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0      0.14   3.5e+02      46      99 ..      69     122 ..      30     130 .. 0.74
   2 ?    9.0   0.0   0.00075       1.9       4      30 ..     183     222 ..     181     302 .. 0.77

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.14
                             AAA_18  46 ldeskrldedkldklldaleenssaleegknl..vidghlaeleseaakdikk..vvL 99 
                                          +++ + e++++++l+ + + +     ++ +  v+d++ + +++e+     +  v+L
  gene1883|gene1883|rna1883|rna1883  69 AWQNNTVAEMNRNVWLQFWIATDV----CDYIcvVVDSRNVGFFFEEELLEMGkpVIL 122
                                        355566667777889999999876....888888999999999966554333235555 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00075
                             AAA_18   4 tGtpGvGKttlakeLskrlgf.............gvnlrd 30 
                                         G+p vGK++l k +s++ ++             +++ +d
  gene1883|gene1883|rna1883|rna1883 183 IGYPNVGKSSLIKTISNHVKIkisstpgktkfvqSYQFTD 222
                                        69**************997666676776655555444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (321 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       811  (0.045234); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 2246.84
//
Query:       gene1884|gene1884|rna1884|rna1884  [L=258]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.9e-61  207.2   0.0    3.6e-61  206.8   0.0    1.1  1  Pkinase        Protein kinase domain
    1.3e-32  113.2   0.0    1.7e-32  112.8   0.0    1.3  1  Pkinase_Tyr    Protein tyrosine kinase
    3.4e-06   26.3   0.2    2.9e-05   23.2   0.2    1.9  1  Haspin_kinase  Haspin like kinase domain
    0.00073   18.9   0.0     0.0059   16.0   0.0    1.9  2  Kinase-like    Kinase-like
    0.00095   19.1   0.0      0.094   12.6   0.0    2.2  2  APH            Phosphotransferase enzyme family
      0.002   17.5   0.1     0.0065   15.8   0.0    1.7  2  Kdo            Lipopolysaccharide kinase (Kdo/WaaP) family
  ------ inclusion threshold ------
      0.087   12.4   0.4       0.29   10.7   0.4    1.8  1  RIO1           RIO1 family
       0.16   11.4   0.1       0.49    9.9   0.0    1.7  2  YrbL-PhoP_reg  PhoP regulatory network protein YrbL


Domain annotation for each model (and alignments):
>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  206.8   0.0   1.6e-64   3.6e-61       1     258 [.       4     252 ..       4     254 .. 0.86

  Alignments for each domain:
  == domain 1  score: 206.8 bits;  conditional E-value: 1.6e-64
                                        EEEEEEEEEESSEEEEEEEETTTTEEEEEEEEECHCHCHHHHHHHHHHHHHHHHHSCTTB--EEEEEEESSEEEEE CS
                            Pkinase   1 yekleklGeGsfGkVykaveketgkivAvKkikkekakkkkekkvlrEikilkklkhpnivrlyevfeekdelylv 76 
                                        y +++ lG+G+++kVy+av +++++ +A+Kki+  +++ +  +++lrEi+ilk+l+hpni+ l+ev+++++ l+lv
  gene1884|gene1884|rna1884|rna1884   4 YIQKRFLGSGTYSKVYEAV-DHNNNRFALKKIRLFEEEGTP-STALREISILKTLHHPNIIILVEVVHTPSFLTLV 77 
                                        567899*************.589999********9888755.7********************************* PP

                                        EE--TTEBHHHHHHHHSS--HHHHHHHHHHHHHHHHHHHHTTEE-SS-SGGGEEEETTTEEEE-SGTTSEESSSSC CS
                            Pkinase  77 leyveggeladllerkgslseeeakkiakqilegleylHskgiiHrDlKpeNiLidekgelKitDFGlakelesss 152
                                        +ey++ + l+++++ +  +s+    ++++q+++g++y+H+++++HrDlKp+NiL++ ++++Ki+DFGla+ l  + 
  gene1884|gene1884|rna1884|rna1884  78 FEYMDFD-LNTFIT-HYGFSM----DLFEQVIKGISYIHAMKVVHRDLKPQNILVNLERQVKIADFGLARSLAVTI 147
                                        *****77.999996.455655....6899********************************************999 PP

                                        S.BCTTTSCGGGS-HHHH.TTSCBSHHHHHHHHHHHHHHHHHSS-STTTSSHHHHHHHHHHT.HHHHHHHCTSHH. CS
                            Pkinase 153 k.ltsfvgtseYlAPEvl.keneyskkvDvWslGvilyelltgkppfsgekgkekvekeldq.lekilkilgetke 225
                                        + l+s+v+t +Y++PE+l + ++y   vD+Ws+G+il+e+ltg+ +f+g +++e + +++++ + + ++     + 
  gene1884|gene1884|rna1884|rna1884 148 PvLSSEVVTLWYRSPELLsNMQDYNYFVDMWSVGCILFEMLTGCVLFKGGSSNE-QLAIIHNaVGHRRRF---FEY 219
                                        99****************8889**************************777777.444444412222222...233 PP

                                        ..HHHTTS....-HHHHHHHHHHT-SSGCCSTTHHHH CS
                            Pkinase 226 klpeasei....seeakdllkkllkkdpkkRltaeel 258
                                         ++    +    +    +++  +l+++ ++Rl a e+
  gene1884|gene1884|rna1884|rna1884 220 LID----VlgpgNTFYVEIIMGCLDMNVNQRLNAYEI 252
                                        344....24554888999*************998775 PP

>> Pkinase_Tyr  Protein tyrosine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.8   0.0   7.4e-36   1.7e-32       4     213 ..       7     202 ..       4     256 .. 0.83

  Alignments for each domain:
  == domain 1  score: 112.8 bits;  conditional E-value: 7.4e-36
                                        EEEEEEESSEEEEEEEEETTTTSSEEEEEEEEESTTSSHHHHHHHHHHHHHHHTS-BTTB--EEEEEESSSSEEEE CS
                        Pkinase_Tyr   4 gkklGeGafGkVvegtlkgekekkevkVavKtlkeeateeekeelleeakimkklkhpnivkllgvctkeeplliv 79 
                                        ++ lG+G+++kV+e+  +     ++ + a+K+++   +e + +  l+e++i+k+l+hpni+ l+ v+   + l +v
  gene1884|gene1884|rna1884|rna1884   7 KRFLGSGTYSKVYEAVDH-----NNNRFALKKIRLFEEEGTPSTALREISILKTLHHPNIIILVEVVHTPSFLTLV 77 
                                        577************999.....88899*****9999999999*************************9999**** PP

                                        EE--TTEBHHHHHHHTCTTTSBHHHHHHHHHHHHHHHHHHHHTTEEEST-SGGGEEEEETTEEEE-STTTHEETTT CS
                        Pkinase_Tyr  80 teyvkgGdLlkfLrkkekekltlkdllsfalqvAkGmeyLeskklvHrdlaarNvLlsenkvvkisDfGLardiek 155
                                        +ey++  dL++f+++           +++  qv kG++y++++k+vHrdl  +N+L++ +++vki+DfGLar++  
  gene1884|gene1884|rna1884|rna1884  78 FEYMDF-DLNTFITHY-------GFSMDLFEQVIKGISYIHAMKVVHRDLKPQNILVNLERQVKIADFGLARSL-- 143
                                        ****98.9*****997.......44567889*******************************************.. PP

                                        SSEEEETTSSTSGGGGS-HHHHHHSE.EEHHHHHHHHHHHHHHHHTTSSGTTTTS.HHHH CS
                        Pkinase_Tyr 156 ddeyvkkeeaklpvkWmapEslkekk.ftsksDvWsfGvllwEiftlgespypgl.knee 213
                                          +  + +++ + + + +pE l++++ ++   D+Ws G +l+E++t     ++g  +ne+
  gene1884|gene1884|rna1884|rna1884 144 AVTIPVLSSEVVTLWYRSPELLSNMQdYNYFVDMWSVGCILFEMLTG-CVLFKGGsSNEQ 202
                                        56666777778888888******9988*******************5.444544414444 PP

>> Haspin_kinase  Haspin like kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.2   1.3e-08   2.9e-05     109     282 ..      11     173 ..       2     177 .. 0.70

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 1.3e-08
                      Haspin_kinase 109 seklssevyqtke.kdkevvlKviplevledvtiskelslkelkslklvkgtypglllllqdkvlkekpdfyseqq 183
                                        + + +s+vy++ + +++  +lK+i l   e+ t s  + l e   lk ++   p++ ++l + v          + 
  gene1884|gene1884|rna1884|rna1884  11 GSGTYSKVYEAVDhNNNRFALKKIRL-FEEEGTPS--TALREISILKTLHH--PNI-IILVEVVH---------TP 71 
                                        55667777776665667777777777.44444444..44444444443332..233.33333333.........33 PP

                      Haspin_kinase 184 lflvlllkdkGtdLeevklkswkqalsifwqivkiLyvaEtkfeFEHRdLhldniLvdknlnvtlidlklsRle.. 257
                                         fl l+++++  dL+++ ++ +   + +f q++k ++    + +  HRdL+ +niLv+ + +v + d+ l+R    
  gene1884|gene1884|rna1884|rna1884  72 SFLTLVFEYMDFDLNTF-ITHYGFSMDLFEQVIKGISYIH-AMKVVHRDLKPQNILVNLERQVKIADFGLARSLav 145
                                        58999*********998.778999999*******999885.58999**************************9866 PP

                      Haspin_kinase 258 ...ssegkvlytrlddpllFqGggDyqf 282
                                             +++v+      p+l  + +Dy++
  gene1884|gene1884|rna1884|rna1884 146 tipVLSSEVVTLWYRSPELLSNMQDYNY 173
                                        6663344444444458899999999987 PP

>> Kinase-like  Kinase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.12   2.7e+02      13      49 ..       3      38 ..       2      51 .. 0.82
   2 !   16.0   0.0   2.6e-06    0.0059     152     243 ..     101     187 ..      83     201 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.12
                        Kinase-like 13 tlvrgellkkgdrsvvfevkdqetgeplavkvfllps 49
                                       t++++  l+ g  s+v+e+ d + ++ +a+k   l +
  gene1884|gene1884|rna1884|rna1884  3 TYIQKRFLGSGTYSKVYEAVDHN-NNRFALKKIRLFE 38
                                       5789999**************99.8889988765544 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 2.6e-06
                        Kinase-like 152 qlirlaanLqakglvhgkftvdnllldekgglmlggftaLvragtkvvl..seve.kgfaPpEllgsrggytrknk 224
                                        q+i+ + +++a  +vh +++++n+l + + ++++ +f+  +      ++  sev    +  pEll++         
  gene1884|gene1884|rna1884|rna1884 101 QVIKGISYIHAMKVVHRDLKPQNILVNLERQVKIADFGLARSLAVTIPVlsSEVVtLWYRSPELLSNM-------- 168
                                        899999*******************************98888888887774444435689*****993........ PP

                        Kinase-like 225 tkmthkldaWqlGlviyri 243
                                          + + +d W +G   + +
  gene1884|gene1884|rna1884|rna1884 169 QDYNYFVDMWSVGCILFEM 187
                                        3577799999999999987 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0     0.014        32       3      47 ..       8      56 ..       7      83 .. 0.75
   2 !   12.6   0.0   4.2e-05     0.094     168     197 ..     114     141 ..     109     148 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.014
                                       EEE--.SSCEEEEEEETT.--EEEEEE-TT...S-HHHHHHHHHHHHHH CS
                                APH  3 relsggasnrtylvttpa.gryvlrrnppa...raaeeirrevallrlL 47
                                       r+l++g+++++y+ ++ +  r++l+ ++      ++ ++ re  +l+ L
  gene1884|gene1884|rna1884|rna1884  8 RFLGSGTYSKVYEAVDHNnNRFALKKIRLFeeeGTPSTALREISILKTL 56
                                       799*************9988***99977653335556666666666555 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 4.2e-05
                                        EE-SS-SGGGEEEC...TTEEEEE---TT-E CS
                                APH 168 llHgDlhpgNllvd.pddgrvtGviDfedag 197
                                        ++H+Dl+p+N+lv+ +++ +   + Df++a+
  gene1884|gene1884|rna1884|rna1884 114 VVHRDLKPQNILVNlERQVK---IADFGLAR 141
                                        79************444444...89999885 PP

>> Kdo  Lipopolysaccharide kinase (Kdo/WaaP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.45     1e+03      56      76 ..      44      64 ..      30      71 .. 0.79
   2 !   15.8   0.0   2.9e-06    0.0065     122     166 ..      97     137 ..      76     144 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.45
                                Kdo 56 travrEfrllkrLeeagvavp 76
                                        +a rE+++lk L++  + ++
  gene1884|gene1884|rna1884|rna1884 44 STALREISILKTLHHPNIIIL 64
                                       6899*********99888776 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 2.9e-06
                                Kdo 122 allkavgrliaklhragvnHadlyaknillqqeeeeeaeiwliDl 166
                                         l+++v + i+ +h+++v H+dl ++nil++ e     ++ + D+
  gene1884|gene1884|rna1884|rna1884  97 DLFEQVIKGISYIHAMKVVHRDLKPQNILVNLER----QVKIADF 137
                                        567899999**********************998....5555555 PP

>> RIO1  RIO1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.4   0.00013      0.29     108     150 ..      96     138 ..       7     144 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00013
                                        HHHHHHHHHHHHHHHHTSTEEESS-STTSEEEETT.EEEE--GT CS
                               RIO1 108 eelyeevleemrklykeaglvHaDLSeyNvlvded.kvviIDvs 150
                                         +l+e+v++ +   ++ +++vH DL   N+lv+ + +v i D++
  gene1884|gene1884|rna1884|rna1884  96 MDLFEQVIKGI-SYIHAMKVVHRDLKPQNILVNLErQVKIADFG 138
                                        56788888864.455699***************99888888885 PP

>> YrbL-PhoP_reg  PhoP regulatory network protein YrbL
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       1.1   2.4e+03       6      19 ..       7      20 ..       5      56 .. 0.67
   2 ?    9.9   0.0   0.00022      0.49     111     157 ..      85     131 ..      75     143 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.1
                      YrbL-PhoP_reg  6 ekllakGteRlvya 19
                                       +++l++Gt  +vy+
  gene1884|gene1884|rna1884|rna1884  7 KRFLGSGTYSKVYE 20
                                       56777777777775 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00022
                      YrbL-PhoP_reg 111 LedlvkkeeltaelkeaLdefleelldnhivtndlsakNivvkknse 157
                                        L++++ + ++  +l e++ + + ++   ++v +dl+++Ni+v+ +++
  gene1884|gene1884|rna1884|rna1884  85 LNTFITHYGFSMDLFEQVIKGISYIHAMKVVHRDLKPQNILVNLERQ 131
                                        88899999999999999999*********************987766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       460  (0.0256568); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 1845.87
//
Query:       gene1885|gene1885|rna1885|rna1885  [L=467]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (467 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       747  (0.0416643); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 3084.95
//
Query:       gene1886|gene1886|rna1886|rna1886  [L=542]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.1e-11   42.8   0.1    5.5e-07   29.8   0.0    2.4  2  ABC1         ABC1 family
    0.00027   20.4   7.3     0.0061   16.0   2.6    3.6  3  Pkinase      Protein kinase domain
     0.0027   17.0   3.6      0.045   13.0   1.8    3.0  3  Pkinase_Tyr  Protein tyrosine kinase
     0.0035   17.0   0.3        0.3   10.7   0.1    2.4  2  RIO1         RIO1 family


Domain annotation for each model (and alignments):
>> ABC1  ABC1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.0   0.00011      0.51      10      30 ..     121     141 ..     116     148 .. 0.86
   2 !   29.8   0.0   1.2e-10   5.5e-07      34     115 ..     190     271 ..     185     275 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00011
                               ABC1  10 iFaefdeePiAaASiaqVhrA 30 
                                        +F+   ++Pi+++S+aqV++ 
  gene1886|gene1886|rna1886|rna1886 121 LFHFVTHKPIGSGSVAQVYKV 141
                                        6888899************95 PP

  == domain 2  score: 29.8 bits;  conditional E-value: 1.2e-10
                               ABC1  34 sgeeVavKvqrpgvkkriksDlellkllakllkkflkelrldleelvdefskslleEldferEAknaekfrenfak 109
                                         +++ a+K+ +p+ +k + +D ++l  +ak+l+ ++    l+++e + +f++++l+++d++ E +n++ +r+ ++ 
  gene1886|gene1886|rna1886|rna1886 190 GHKTLAIKIIHPNTTKDVYLDCQILTNAAKVLSVIPALSCLNINEQILHFQNEILKQIDLTGEERNMKVMRHLTRY 265
                                        46799*************************9999998888********************************9999 PP

                               ABC1 110 lkevkv 115
                                        +k++ +
  gene1886|gene1886|rna1886|rna1886 266 DKNILI 271
                                        988765 PP

>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.1   0.0    0.0054        24       2      23 ..     125     146 ..     124     153 .. 0.82
   2 !   16.0   2.6   1.4e-06    0.0061     106     153 ..     350     397 ..     184     407 .. 0.88
   3 ?   -2.0   0.1      0.42   1.9e+03      39      80 ..     429     470 ..     421     491 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.0054
                                        EEEEEEEEESSEEEEEEEETTT CS
                            Pkinase   2 ekleklGeGsfGkVykaveket 23 
                                        ++++ +G+Gs+++Vyk++ +++
  gene1886|gene1886|rna1886|rna1886 125 VTHKPIGSGSVAQVYKVIINDE 146
                                        57899***********996655 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 1.4e-06
                                        HHHHHHHHHHHTTEE-SS-SGGGEEEETTTEEEE-SGTTSEESSSSCS CS
                            Pkinase 106 qilegleylHskgiiHrDlKpeNiLidekgelKitDFGlakelesssk 153
                                         +   ++ l+ +++iH Dl p N+ + ++++l + DFGl k l++ ++
  gene1886|gene1886|rna1886|rna1886 350 ALTFFVKSLFYNEFIHTDLHPGNVSVTKSNKLILYDFGLTKFLSHAEH 397
                                        555557889999*****************************9998764 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 0.42
                                        HHHHHHHHHHHHHHHHHSCTTB--EEEEEEESSEEEEEEE-- CS
                            Pkinase  39 kkkekkvlrEikilkklkhpnivrlyevfeekdelylvleyv 80 
                                        + ++kk++ Ei+ l +   ++++r+ +  +++d +++  ey 
  gene1886|gene1886|rna1886|rna1886 429 NVDKKKFRGEINELINHYFKQVLRMNGNSTRNDAYMITKEYG 470
                                        445577899999999999999999999999999999998885 PP

>> Pkinase_Tyr  Protein tyrosine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0      0.64   2.9e+03       4      21 ..     127     144 ..     125     149 .. 0.83
   2 !   13.0   1.8   9.9e-06     0.045      51     156 ..     255     395 ..     238     402 .. 0.70
   3 ?    1.9   0.0     0.024   1.1e+02      42      82 ..     429     469 ..     418     481 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.64
                                        EEEEEEESSEEEEEEEEE CS
                        Pkinase_Tyr   4 gkklGeGafGkVvegtlk 21 
                                        +k +G+G+ ++V++  ++
  gene1886|gene1886|rna1886|rna1886 127 HKPIGSGSVAQVYKVIIN 144
                                        6889*********98776 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 9.9e-06
                                        HHHHHHTS.-BTTB--EEEEEESSSSEEEEEE--TTEBHHHHHHHT.............................. CS
                        Pkinase_Tyr  51 eakimkkl.khpnivkllgvctkeepllivteyvkgGdLlkfLrkk.............................. 95 
                                        ++k+m++l + ++ + +   ++ + + ++++ey++g ++ +   +                               
  gene1886|gene1886|rna1886|rna1886 255 NMKVMRHLtRYDKNILIAEPIM-ATKNVLIMEYLEGESIVSRSGRMsnqidnnrtnnektglplhdtknesskefs 329
                                        6778888874444444444444.34568899998887766654444556777799999999999999999999998 PP

                                        ..CTTTSBHHHHHHHHHHHHHH...HHHHHHTTEEEST-SGGGEEEEETTEEEE-STTTHEETTTS CS
                        Pkinase_Tyr  96 ..ekekltlkdllsfalqvAkG...meyLeskklvHrdlaarNvLlsenkvvkisDfGLardiekd 156
                                          ++ ++ l ++ + +l v +    ++ L  ++++H dl   Nv ++++++  + DfGL++ +++ 
  gene1886|gene1886|rna1886|rna1886 330 knKNMNFGLFKKQNHSLSVTALtffVKSLFYNEFIHTDLHPGNVSVTKSNKLILYDFGLTKFLSHA 395
                                        774444444444444444444300134466689***************************988554 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.024
                                        HHHHHHHHHHHHHHHTS-BTTB--EEEEEESSSSEEEEEE- CS
                        Pkinase_Tyr  42 eeekeelleeakimkklkhpnivkllgvctkeepllivtey 82 
                                        + +k+++  e++ + +   ++++++ g  t+++ ++i  ey
  gene1886|gene1886|rna1886|rna1886 429 NVDKKKFRGEINELINHYFKQVLRMNGNSTRNDAYMITKEY 469
                                        345899************************99998888887 PP

>> RIO1  RIO1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.1   6.6e-05       0.3      56      92 ..     253     291 ..     236     313 .. 0.73
   2 !    4.0   0.0    0.0075        33     120     152 ..     356     389 ..     322     406 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 6.6e-05
                                        HHHHHHHHHHHHTT..--S--EEEEETTEEEEE--EETT CS
                               RIO1  56 ekEfrnLkrleeag..vpvPkpielkrhvlvmefigedg 92 
                                        e+ ++ ++ l + +  + + +pi   ++vl+me+++ + 
  gene1886|gene1886|rna1886|rna1886 253 ERNMKVMRHLTRYDknILIAEPIMATKNVLIMEYLEGES 291
                                        4555555555443322999***************99544 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.0075
                                        HHHHTSTEEESS-STTSEEEETT.EEEE--GTTE CS
                               RIO1 120 klykeaglvHaDLSeyNvlvded.kvviIDvsQa 152
                                        k +  ++ +H DL   Nv v++  k+++ D++  
  gene1886|gene1886|rna1886|rna1886 356 KSLFYNEFIHTDLHPGNVSVTKSnKLILYDFGLT 389
                                        33446899**********9999889***999755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (542 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       505  (0.0281667); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.41
# Mc/sec: 3994.84
//
Query:       gene1887|gene1887|rna1887|rna1887  [L=593]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.5e-15   56.6   0.8    5.3e-15   55.5   0.8    1.5  1  MS_channel  Mechanosensitive ion channel


Domain annotation for each model (and alignments):
>> MS_channel  Mechanosensitive ion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.5   0.8     3e-19   5.3e-15       7     174 ..     370     533 ..     362     557 .. 0.80

  Alignments for each domain:
  == domain 1  score: 55.5 bits;  conditional E-value: 3e-19
                                        HHHHHHHHHHHHT.TT--SCCHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHTT-SS-TT-EEESSSEEEEEEEE-S CS
                         MS_channel   7 liivvgilivlsl.lgvnvsallavlGalglalglalkdlisnlvaGiillfekpfkiGDlveigdieGtVedigl 81 
                                        lii+v+il  + l l +++ +l     +l ++    lkd++ ++   i++++++pf+ GD++ i + +  V++i+l
  gene1887|gene1887|rna1887|rna1887 370 LIILVIILSLSPLlLKMKIPYLRIPTPMLLFGFLAILKDPLTSF---IFIIYSHPFDSGDRIVIRGDTHMVQKINL 442
                                        45555555544431445577777777777777777777777766...699************************** PP

                                        SEEEEEETTSEEEEEEHHHHHTS-EEESSS.SSEEEEEEEEEE-TTS-...HHHHHHHHHHHHHH-TTB-TTS-EE CS
                         MS_channel  82 rttkirtfdgrivtiPnsslvtsnieNlsresgtrrikvsigvtyssdvkklekvleelkealkekpevlkdkell 157
                                          t++++++g+++ i n+ l++   +N++r s +++ ++ + ++ +++v+k++++ ++ k  +k+++++ ++ +  
  gene1887|gene1887|rna1887|rna1887 443 YNTTLQKWNGELISISNKWLANHITKNYRR-SEAQKWEIFVIIASNTPVSKIDELKKKFKSLAKKHRDDYPSIT-C 516
                                        ******************************.99999999999*************************9997333.3 PP

                                        EEEEEE-SSSEEEEEEE CS
                         MS_channel 158 vvldefgdsslnfevrv 174
                                        +v++    + +++ v+v
  gene1887|gene1887|rna1887|rna1887 517 NVVGIENSNKMKLVVYV 533
                                        44455555555544444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (593 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       996  (0.0555525); expected 358.6 (0.02)
Passed bias filter:                      468  (0.026103); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.27s 00:00:00.87 Elapsed: 00:00:00.44
# Mc/sec: 4087.61
//
Query:       gene1888|gene1888|rna1888|rna1888  [L=56]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (56 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       340  (0.0189637); expected 358.6 (0.02)
Passed bias filter:                      230  (0.0128284); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.42
# Mc/sec: 395.79
//
Query:       gene1889|gene1889|rna1889|rna1889  [L=123]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (123 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       439  (0.0244855); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.29s 00:00:00.63 Elapsed: 00:00:00.42
# Mc/sec: 886.21
//
Query:       gene189|gene189|rna189|rna189  [L=682]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.098   12.9   0.1         23    5.2   0.1    3.1  2  HdeA      HdeA/HdeB family


Domain annotation for each model (and alignments):
>> HdeA  HdeA/HdeB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.1    0.0013        23      12      49 ..     406     443 ..     399     458 .. 0.78
   2 ?    3.7   0.0    0.0038        68      59      90 ..     561     592 ..     552     593 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0013
                                    XXXXXXXGGG.XSCCS-GGG-BHHHHHTS-GGGHHHHH CS
                           HdeA  12 lsssAlAqkaaakakkdlskmtCedFldldeeskpkvi 49 
                                    ++++++A+++  ++k  + + tC+dFld + ++ ++v+
  gene189|gene189|rna189|rna189 406 IAQNGIAPDNFSDNKGIICTRTCRDFLDFEMAANDVVL 443
                                    677888888844556566799******99988888776 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.0038
                                    CSGCCCCSHHHHHHHHHHHHHHHHHHTTTSBG CS
                           HdeA  59 gkkgdavvdeegiekvtpkvveyCkknpkkkl 90 
                                     ++++av++++ + ++t+++  y +k+p+  +
  gene189|gene189|rna189|rna189 561 CERETAVIEVDIFNQITNEILLYVSKKPSIDF 592
                                    5789******************9999998665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (682 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       838  (0.0467399); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.62u 0.30s 00:00:00.92 Elapsed: 00:00:00.64
# Mc/sec: 3223.70
//
Query:       gene1890|gene1890|rna1890|rna1890  [L=359]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.011   16.0   0.4        7.6    6.9   0.1    2.7  2  P22_AR_N  P22_AR N-terminal domain
      0.016   15.0   0.2       0.34   10.8   0.0    2.9  3  Csm1_B    Csm1 subunit domain B
       0.19   11.9   2.9        4.4    7.6   0.2    3.2  3  SRI       SRI (Set2 Rpb1 interacting) domain
       0.29   12.0   0.2       0.29   12.0   0.2    2.4  3  Ntox50    Bacterial toxin 50
        3.8    7.9   8.3       0.43   10.9   2.1    2.6  3  GAT       GAT domain
          4    8.4   9.5        3.6    8.6   0.5    3.3  3  CSN5_C    Cop9 signalosome subunit 5 C-terminal domain


Domain annotation for each model (and alignments):
>> P22_AR_N  P22_AR N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.1    0.0025       7.6      77     107 ..      81     113 ..      47     119 .. 0.84
   2 ?    6.7   0.0     0.003       8.9      84     109 ..     233     258 ..     193     263 .. 0.91

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0025
                           P22_AR_N  77 LakInpnk..vkpelrekviaYqeecaevLady 107
                                        L  I+ +k  ++++l++k+ +Y +e a++L+d+
  gene1890|gene1890|rna1890|rna1890  81 LSDIESEKnyISQDLKDKLKNYGKELANILKDK 113
                                        667775553378******************986 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.003
                           P22_AR_N  84 kvkpelrekviaYqeecaevLadywt 109
                                        + + +l + ++++ +ec++ L+++++
  gene1890|gene1890|rna1890|rna1890 233 QLSLSLTDVLNKFENECQDYLTNEFR 258
                                        5567899****************997 PP

>> Csm1_B  Csm1 subunit domain B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       1.2   3.5e+03      56      75 ..      94     113 ..      90     126 .. 0.78
   2 ?   -0.0   0.0      0.26   7.8e+02      58      77 ..     239     258 ..     233     261 .. 0.88
   3 ?   10.8   0.0   0.00011      0.34      12      89 ..     266     345 ..     260     347 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.2
                                        HHHHHHHHHHHHHHHHCCCC CS
                             Csm1_B  56 kvkekleeiekelnewllke 75 
                                        + k+kl+++ kel ++l ++
  gene1890|gene1890|rna1890|rna1890  94 DLKDKLKNYGKELANILKDK 113
                                        56889999999999888766 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.26
                                        HHHHHHHHHHHHHHCCCCTS CS
                             Csm1_B  58 kekleeiekelnewllkefk 77 
                                         ++l+++e+e+++ l++ef+
  gene1890|gene1890|rna1890|rna1890 239 TDVLNKFENECQDYLTNEFR 258
                                        6889************9996 PP

  == domain 3  score: 10.8 bits;  conditional E-value: 0.00011
                                        HHHHHHHHHHHHHHHHHHHHTT--CCCEE..EEETTEEEEEEE--HHHHHHHHHHHHHHHHHCCCCTSSS-EEEEE CS
                             Csm1_B  12 gRSfylellleeivdelleklelsranll..YagGGhfylLlpntekvkekleeiekelnewllkefkgkLylala 85 
                                        +R   l+  ++++v+++++klel  a+    +++ G++ ++l nt+ + + ++  ek+   w+  + +g++++  +
  gene1890|gene1890|rna1890|rna1890 266 ARHETLNAQIDHVVRNIISKLELVGAKFSseFTSKGQIRFFLYNTDANSKPVTFEEKKYTPWFNFDSNGNINVYAK 341
                                        66666777789************988764449**********************9********9998998888777 PP

                                        EEEE CS
                             Csm1_B  86 yvel 89 
                                          ++
  gene1890|gene1890|rna1890|rna1890 342 KRPF 345
                                        6665 PP

>> SRI  SRI (Set2 Rpb1 interacting) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.2    0.0015       4.4       7      47 ..      56     114 ..      51     136 .. 0.76
   2 ?   -1.8   0.0       1.2   3.6e+03      19      36 ..     188     211 ..     165     218 .. 0.62
   3 ?    3.3   0.1     0.031        92      12      40 ..     234     265 ..     223     286 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0015
                                SRI   7 kfkkelakvVvnvlnkYrkklk..................kedfKklakeltkklvekE 47 
                                         ++++++   +n l+ + + +                   k+++K++ kel+++l +k 
  gene1890|gene1890|rna1890|rna1890  56 AWQNKFSRETANELKTFTNLMHrdvlsdieseknyisqdlKDKLKNYGKELANILKDKS 114
                                        5666666666666666666655566667777777777999**************98885 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.2
                                SRI  19 vlnkYrkklk......kedfKkla 36 
                                        ++n+  kk+k       e++K+l 
  gene1890|gene1890|rna1890|rna1890 188 LVNPLDKKIKdalgstMEQLKELN 211
                                        444444444444444445555444 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.031
                                SRI  12 lakvVvnvlnkYrkklk...kedfKklakelt 40 
                                        l+     vlnk++++++   + +f++l   l+
  gene1890|gene1890|rna1890|rna1890 234 LSLSLTDVLNKFENECQdylTNEFRYLKSNLV 265
                                        56667789********9999888888766554 PP

>> Ntox50  Bacterial toxin 50
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.2       5.3   1.6e+04      11      31 ..      85     107 ..      83     117 .. 0.50
   2 ?   12.0   0.2   9.6e-05      0.29       7      49 ..     125     169 ..     120     187 .. 0.83
   3 ?   -1.7   0.2       1.7   5.2e+03      42      70 ..     200     228 ..     164     254 .. 0.55

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 5.3
                             Ntox50  11 kghknYee..gkSyllidskeaq 31 
                                        +++knY++   k +l +  ke  
  gene1890|gene1890|rna1890|rna1890  85 ESEKNYISqdLKDKLKNYGKELA 107
                                        55566655333444444444444 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 9.6e-05
                             Ntox50   7 gkHikghknYee..gkSyllidskeaqellkkyagtgevvkdrkg 49 
                                        +kH++  +nY +   +S+ + + k++++l +k++gt +v  ++++
  gene1890|gene1890|rna1890|rna1890 125 EKHMPAINNYFDvrIRSKAYFNLKKPEDLENKIQGTVNVQHSHRQ 169
                                        7*********99555699999*****************9988443 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 1.7
                             Ntox50  42 evvkdrkgkwrnkevvdfgevigvvvdke 70 
                                          ++ ++ k  n+++ + +  i +  d++
  gene1890|gene1890|rna1890|rna1890 200 LGSTMEQLKELNEKILQAEPSITKTADEQ 228
                                        33333333333444444444444444433 PP

>> GAT  GAT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.1       3.2   9.7e+03      55      67 ..      25      37 ..      23      37 .. 0.84
   2 ?   -0.9   0.0      0.68     2e+03      13      45 ..      83     111 ..      61     120 .. 0.66
   3 ?   10.9   2.1   0.00014      0.43      21      70 ..     202     248 ..     177     255 .. 0.75

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 3.2
                                GAT 55 aelLqlNDeLnnv 67
                                       ael  +N +++++
  gene1890|gene1890|rna1890|rna1890 25 AELVAVNNKISQA 37
                                       6899999999985 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.68
                                GAT  13 stepdeellenellkeLyetckamqpriqklie 45 
                                          e     ++n + ++L +++k+  + + +++ 
  gene1890|gene1890|rna1890|rna1890  83 DIE----SEKNYISQDLKDKLKNYGKELANILK 111
                                        333....34666677777777777666666655 PP

  == domain 3  score: 10.9 bits;  conditional E-value: 0.00014
                                GAT  21 lenellkeLyetckamqpriqklieetadeedllaelLqlNDeLnnvler 70 
                                        + +e lkeL+e++ +++p+i+k ++e +  e   +  L+l D Ln+  + 
  gene1890|gene1890|rna1890|rna1890 202 STMEQLKELNEKILQAEPSITKTADEQNKAE---QLSLSLTDVLNKFENE 248
                                        5699**********************44444...4567777777776555 PP

>> CSN5_C  Cop9 signalosome subunit 5 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.3      0.11   3.2e+02      70      87 ..      82      99 ..      24     122 .. 0.64
   2 ?    2.3   0.2      0.11   3.3e+02      14      67 ..     148     199 ..     139     205 .. 0.59
   3 ?    8.6   0.5    0.0012       3.6      13      43 ..     204     234 ..     201     280 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.11
                             CSN5_C 70 iaseaqhGLiaqelKdkl 87
                                         +e ++  i+q+lKdkl
  gene1890|gene1890|rna1890|rna1890 82 SDIESEKNYISQDLKDKL 99
                                       456777777777777776 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.11
                             CSN5_C  14 kqisDLaeKlekaessvsrsrsaagtlseeaseaeekkkkkkedsqLakvvkds 67 
                                        k+ +DL++K++ + + v++s+++ +t + ++ ++  + ++ +  ++L+k +kd+
  gene1890|gene1890|rna1890|rna1890 148 KKPEDLENKIQGTVN-VQHSHRQDETPEINK-SELLQVTDPNLVNPLDKKIKDA 199
                                        666899999987654.444444443333222.2333344667777777777776 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.0012
                             CSN5_C  13 tkqisDLaeKlekaessvsrsrsaagtlsee 43 
                                         +q+++L+eK+ +ae s++++  +++++++ 
  gene1890|gene1890|rna1890|rna1890 204 MEQLKELNEKILQAEPSITKTADEQNKAEQL 234
                                        68******************99888776654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (359 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1441  (0.0803726); expected 358.6 (0.02)
Passed bias filter:                      508  (0.028334); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.57u 0.31s 00:00:00.87 Elapsed: 00:00:00.49
# Mc/sec: 2211.98
//
Query:       gene1891|gene1891|rna1891|rna1891  [L=57]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (57 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       279  (0.0155614); expected 358.6 (0.02)
Passed bias filter:                      200  (0.0111551); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.54u 0.34s 00:00:00.88 Elapsed: 00:00:00.56
# Mc/sec: 308.78
//
Query:       gene1892|gene1892|rna1892|rna1892  [L=216]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (216 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       376  (0.0209716); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.61u 0.32s 00:00:00.93 Elapsed: 00:00:00.55
# Mc/sec: 1188.25
//
Query:       gene1893|gene1893|rna1893|rna1893  [L=34]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (34 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       369  (0.0205812); expected 358.6 (0.02)
Passed bias filter:                      218  (0.0121591); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.51u 0.36s 00:00:00.87 Elapsed: 00:00:00.56
# Mc/sec: 183.12
//
Query:       gene1894|gene1894|rna1894|rna1894  [L=892]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (892 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       584  (0.0325729); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.85u 0.33s 00:00:01.18 Elapsed: 00:00:00.58
# Mc/sec: 4669.96
//
Query:       gene1895|gene1895|rna1895|rna1895  [L=284]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      0.007   16.3   0.9      0.044   13.7   0.2    2.1  2  TraS      Plasmid conjugative transfer entry exclusion protei
  ------ inclusion threshold ------
      0.024   13.4   0.4       0.04   12.7   0.4    1.2  1  Tektin    Tektin family
      0.058   13.9   0.1       0.13   12.7   0.1    1.5  1  Goodbye   fungal STAND N-terminal Goodbye domain
       0.22   11.6   1.3       0.26   11.4   0.1    1.6  2  Ada3      Histone acetyltransferases subunit 3


Domain annotation for each model (and alignments):
>> TraS  Plasmid conjugative transfer entry exclusion protein TraS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0     0.083   3.7e+02      97     115 ..      62      80 ..      14     100 .. 0.69
   2 !   13.7   0.2   9.8e-06     0.044      54     107 ..     159     215 ..     141     223 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.083
                               TraS  97 sgcisikewvkcqlddqyd 115
                                        + +i+i+e+ +c+l d +d
  gene1895|gene1895|rna1895|rna1895  62 NEVITINEYDQCELYDLFD 80 
                                        4679999999999999988 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 9.8e-06
                               TraS  54 nisdef....kfskgiwyvimpvcsllspllslmifiggtlyelrrvsgcisikewvk 107
                                        +isd f    kf+k     +m  cs +s ++s++     t +++  + gc+si ew  
  gene1895|gene1895|rna1895|rna1895 159 KISDYFnkknKFTKRK-TKLMKTCSAISLFFSIIQNTLQTNFDVDEMVGCLSITEWSA 215
                                        4555552222566654.5689***********************************76 PP

>> Tektin  Tektin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.4   8.9e-06      0.04      38     102 ..     132     196 ..     126     198 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 8.9e-06
                             Tektin  38 kktqadsnkrLeeRiediefwkeeLekeleelkeeieaLeeekrrlekalealeeplhiaqecle 102
                                        ++ ++ +n+rL     +i++  ++L++++++  ++ +++++ k++l k+++a++  ++i+q+ l+
  gene1895|gene1895|rna1895|rna1895 132 QNIHKSTNDRLVSTFLEIRHIMDKLDMKISDYFNKKNKFTKRKTKLMKTCSAISLFFSIIQNTLQ 196
                                        455678999***************************************************99887 PP

>> Goodbye  fungal STAND N-terminal Goodbye domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   2.9e-05      0.13      10      77 ..     136     199 ..     128     206 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.9e-05
                            Goodbye  10 keTgkdlkdealkelssvedllkqieaekdkfeefrekkeklkealkkilspiqllggiaaqgasmaF 77 
                                        k+T+ +l     +++ ++  ++++++ + +   ++++k  k k  l+k++s i+l+ +i+++ +++ F
  gene1895|gene1895|rna1895|rna1895 136 KSTNDRL----VSTFLEIRHIMDKLDMKISDYFNKKNKFTKRKTKLMKTCSAISLFFSIIQNTLQTNF 199
                                        4444444....8888999999999*99999888889999***********************999988 PP

>> Ada3  Histone acetyltransferases subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.1         1   4.6e+03      64      83 ..      84     103 ..      61     104 .. 0.68
   2 ?   11.4   0.1   5.8e-05      0.26      72     103 ..     146     177 ..     131     199 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1
                               Ada3  64 elvkermayqeyqtiledlD 83 
                                        + +k+ + +qe++  ++++D
  gene1895|gene1895|rna1895|rna1895  84 SEIKNMIDFQEIRMFMDQMD 103
                                        34566677777777777766 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 5.8e-05
                               Ada3  72 yqeyqtiledlDkqvqqaYlKrtrtlkkkkkk 103
                                        + e+++i+++lD  + +++ K+++  k+k k 
  gene1895|gene1895|rna1895|rna1895 146 FLEIRHIMDKLDMKISDYFNKKNKFTKRKTKL 177
                                        689*********************88877775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (284 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       938  (0.0523175); expected 358.6 (0.02)
Passed bias filter:                      454  (0.0253221); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.58u 0.31s 00:00:00.88 Elapsed: 00:00:00.53
# Mc/sec: 1605.63
//
Query:       gene1896|gene1896|rna1896|rna1896  [L=33]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (33 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       186  (0.0103743); expected 358.6 (0.02)
Passed bias filter:                      139  (0.0077528); expected 358.6 (0.02)
Passed Vit filter:                         5  (0.000278878); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.24s 00:00:00.58 Elapsed: 00:00:00.40
# Mc/sec: 247.41
//
Query:       gene1897|gene1897|rna1897|rna1897  [L=104]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.063   12.6   0.1      0.064   12.6   0.1    1.1  1  AAL_decarboxy  Alpha-acetolactate decarboxylase


Domain annotation for each model (and alignments):
>> AAL_decarboxy  Alpha-acetolactate decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   3.6e-06     0.064      45     103 ..       2      60 ..       1      90 [. 0.90

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3.6e-06
                      AAL_decarboxy  45 ldgkvYqlksdgsvrevddeektPFavvtkfepektvklkealskeeleealeellpsk 103
                                        ++ + Y+++++  +++v+++e tPF++ ++ +++ +  ++++ ++e ++e+l+++++ k
  gene1897|gene1897|rna1897|rna1897   2 VNVEPYNADNSTLLEHVTHDEYTPFISYHTTKHRIDLPYDNRNNYEYIDEHLTRRIRAK 60 
                                        56788***********************************99**********9998665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       727  (0.0405488); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 764.90
//
Query:       gene1898|gene1898|rna1898|rna1898  [L=473]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0064   15.7   0.1      0.012   14.8   0.1    1.4  1  UPF0565   Uncharacterised protein family UPF0565


Domain annotation for each model (and alignments):
>> UPF0565  Uncharacterised protein family UPF0565
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.1   6.7e-07     0.012     186     220 ..     104     183 ..      55     202 .. 0.58

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 6.7e-07
                            UPF0565 186 a.............................................relnldksklvLiGFSkGCvVLnqllyElk 216
                                                                                      ++    k+k++L+G  +G +VLn+llyE++
  gene1898|gene1898|rna1898|rna1898 104 SnqpmqytapsrergvalfnlyameqccyetctstkepffrwyannNSFFTPKEKMILLGQVRGLSVLNNLLYEIT 179
                                        122223334444444445555555566666666665555555543322456799********************98 PP

                            UPF0565 217 eakt 220
                                          + 
  gene1898|gene1898|rna1898|rna1898 180 FKRL 183
                                        7665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (473 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       628  (0.0350271); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 3443.81
//
Query:       gene1899|gene1899|rna1899|rna1899  [L=327]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.1e-19   70.8   0.0    1.1e-18   68.5   0.0    1.9  1  4HBT_3         Thioesterase-like superfamily
    3.2e-07   30.3   0.1    5.1e-05   23.1   0.3    2.5  2  Acyl_CoA_thio  Acyl-CoA thioesterase
  ------ inclusion threshold ------
       0.28   11.1   2.2          1    9.2   0.2    2.4  2  eIF-5_eIF-2B   Domain found in IF2B/IF5


Domain annotation for each model (and alignments):
>> 4HBT_3  Thioesterase-like superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.5   0.0   1.8e-22   1.1e-18       4     248 .]      19     323 ..      16     323 .. 0.70

  Alignments for each domain:
  == domain 1  score: 68.5 bits;  conditional E-value: 1.8e-22
                                        GGECTTC...-HHHHHHHHHHHHHHT..-S.SSEEEEEEE-S---SE.EEEEEEEEEE--SS-EEEEEEEEETTEE CS
                             4HBT_3   4 pwtpgga.g.yGGyvlAlalraaqrtv.pdprlhslhvyFlrpgdag.pviyhvervrdGrsfstrtvelsqggrp 75 
                                        +w p    + +GG +++l+l  a+    ++p   s+h yFl pg++g p+ ++v+ +++G +   + v+ +q +r 
  gene1899|gene1899|rna1899|rna1899  19 LWPPFPSyPaFGGHLVSLFLLSAMLFRnTKP--TSVHTYFLSPGEVGvPMNFEVTMLKEGQTSKFVNVKGYQSKRL 92 
                                        6777777777*********999997753566..6****************************************** PP

                                        EEEEEEEEE---T...................................---EE-------.GGGE---.--SSGGG CS
                             4HBT_3  76 iftatasfgraes...............................tgwelepaaapppvpppdeaalaadeaplplf 120
                                        ++t  + ++++++                               t+  l + a++  +p+       +++++++  
  gene1899|gene1899|rna1899|rna1899  93 VVTSDCLMCNTADgaviyqddievyddvyvhlsthftnlwrigkTSNHLNNVATNDTLPK------NSNKTQYDTL 162
                                        **********99989999999999998888888777755544332211222222233333......2223333333 PP

                                        S.GG..TEEEE-HHT---S.............S-EEEEEEEETTTS-SSHHHH.HHHHTT-.-GGGGTSS-..... CS
                             4HBT_3 121 r.rvpgflepfeprpaegg......kpdspagpkrvrqWvrlreggepahlaa.LaylsDsfpvprvhglrld... 185
                                           v++ ++ +e  + +           +p+g kr+   ++     ++  ++  +a+++D f  ++ +  + +   
  gene1899|gene1899|rna1899|rna1899 163 HsNVDDIIKKIEENYKKLDkyfsiyI-GRPNGVKRQ---FKIVLKTKNINFSVlVAFITDLFL-SNSSLAWIRnky 233
                                        33333333333333332222222211.123344444...4444345678877669******86.666666655567 PP

                                        .................................SB--EEEEEEEE-S--S-...EEEEEE-SEEETTEEEEEEEEE CS
                             4HBT_3 186 .......................aea......sgwmpsldltiyfhrepaedeWllleaetpwagdgrglvearlw 232
                                                                 +      s   +sld+ i+fh +   ++ l + ++++ +g+  +l e++l+
  gene1899|gene1899|rna1899|rna1899 234 tmktysnsdlkivriqnehewnhM-DtvinmdSIQRMSLDHKIHFHCNK-FHDELIFVTKCQFIGEKKVLFEGKLL 307
                                        777787777777777666555550.156666667779*********953.46899********************* PP

                                        -TTS-EEEEEEEEEET CS
                             4HBT_3 233 dedGrlvAtstQeglv 248
                                        +++G+lvA++tQeg++
  gene1899|gene1899|rna1899|rna1899 308 SREGVLVASVTQEGII 323
                                        *************986 PP

>> Acyl_CoA_thio  Acyl-CoA thioesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.5   0.0     0.005        30      79     126 ..      51      95 ..      33     107 .. 0.76
   2 !   23.1   0.3   8.6e-09   5.1e-05      56     131 ..     241     321 ..     228     322 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.005
                                        EEEEEEE-S--BTTS-EEEEEEEEEEETTEEEEEECCEEECTTEEEEE CS
                      Acyl_CoA_thio  79 ldHsvyFlrpgdlnewilydvespsasggrgLrqGriFstqdgklias 126
                                          H+ yFl pg++  ++ ++v   +  +  ++++ +   +q+++l+ +
  gene1899|gene1899|rna1899|rna1899  51 SVHT-YFLSPGEVGVPMNFEVTMLKEGQTSKFVNVKG--YQSKRLVVT 95 
                                        4599.*****************944444444444444..599988876 PP

  == domain 2  score: 23.1 bits;  conditional E-value: 8.6e-09
                                        TTSSSGGGGGGGGT.......TTSTTEEE.EEEEEEEE-S--BTTS-EEEEEEEEEEETTEEEEEECCEEECTTEE CS
                      Acyl_CoA_thio  56 SDltllltalttHe.......lledslqv.sldHsvyFlrpgdlnewilydvespsasggrgLrqGriFstqdgkl 123
                                        SDl+++  +++ He       + +ds+q  sldH ++F+   ++++++++ ++ +   +++ L +G+   +++g l
  gene1899|gene1899|rna1899|rna1899 241 SDLKIV-RIQNEHEwnhmdtvINMDSIQRmSLDHKIHFHCN-KFHDELIFVTKCQFIGEKKVLFEGKLL-SREGVL 313
                                        555544.45566665555766678999999*********75.788899999999899999*********.****** PP

                                        EEEEEEEE CS
                      Acyl_CoA_thio 124 iasvqqeG 131
                                        +asv qeG
  gene1899|gene1899|rna1899|rna1899 314 VASVTQEG 321
                                        *******9 PP

>> eIF-5_eIF-2B  Domain found in IF2B/IF5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.2   0.00017         1      23      70 ..     158     205 ..     139     219 .. 0.81
   2 ?    0.6   0.1     0.081   4.8e+02       8      70 ..     240     305 ..     233     310 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00017
                                        T.EEEETTHHHHHHHHTTSHHHHHHHHHHHHTSEEEESETTEEEESSS CS
                       eIF-5_eIF-2B  23 kkktvivNfeeiakaLnrdpehvlkyllkelgtqgsidengrlilngk 70 
                                        +  t+  N+++i k+++ + +++ ky++  +g    ++ + +++l+ k
  gene1899|gene1899|rna1899|rna1899 158 QYDTLHSNVDDIIKKIEENYKKLDKYFSIYIGRPNGVKRQFKIVLKTK 205
                                        23799**************************99999977777777654 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.081
                                        SS--SSTT--EEEETT.EEEETTHHHHHH.HHTTSHHHHHHHHHHHHTSEEEES..ETTEEEESSS CS
                       eIF-5_eIF-2B   8 kerykmpklqvkvegkkktvivNfeeiak.aLnrdpehvlkyllkelgtqgsid..engrlilngk 70 
                                        ++ +k+ ++q ++e ++  ++ N+++i + +L+ + +  ++ +  el   ++++  ++++++++gk
  gene1899|gene1899|rna1899|rna1899 240 NSDLKIVRIQNEHEWNHMDTVINMDSIQRmSLDHKIHFHCNKFHDELIFVTKCQfiGEKKVLFEGK 305
                                        556788888888888886666699999762466666666777777777666655546666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (327 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1262  (0.0703888); expected 358.6 (0.02)
Passed bias filter:                      607  (0.0338558); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 2294.21
//
Query:       gene19|gene19|rna19|rna19  [L=1132]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.4e-47  161.2  49.6    7.3e-47  159.6  49.6    2.0  1  SMC_N           RecF/RecN/SMC N terminal domain
      7e-25   87.6   0.1    2.9e-24   85.6   0.1    2.2  1  SMC_hinge       SMC proteins Flexible Hinge Domain
    1.3e-12   48.2   9.6    4.2e-07   30.1   3.5    3.2  2  AAA_21          AAA domain, putative AbiEii toxin, Type IV TA
    1.4e-07   31.1   0.1    2.9e-07   30.1   0.1    1.5  1  AAA_29          P-loop containing region of AAA domain
    1.2e-06   28.5  24.6    1.2e-06   28.5  24.6    4.8  3  AAA_15          AAA ATPase domain
     0.0079   16.2   1.6      0.028   14.4   1.6    2.0  1  tRNA-synt_2b    tRNA synthetase class II core domain (G, H, P
  ------ inclusion threshold ------
       0.05   13.8   0.0       0.14   12.4   0.0    1.7  1  SbcCD_C         Putative exonuclease SbcCD, C subunit
       0.34   11.0   5.1       0.64   10.1   0.9    3.4  2  KorB            KorB domain


Domain annotation for each model (and alignments):
>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  159.6  49.6   3.2e-50   7.3e-47       3     216 ..      15    1118 ..      13    1121 .. 0.99

  Alignments for each domain:
  == domain 1  score: 159.6 bits;  conditional E-value: 3.2e-50
                                 EEEEEESETTEECEEEEEETTSSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEE CS
                                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      SMC_N    3 krleienFksyagktvilpfsksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfd 84  
                                 + +++ nFksy+g++ i ++s+ ft +vG+NGSGKsn++dA+lF++G  sakk+r++  s li+k       ++++vei f+
  gene19|gene19|rna19|rna19   15 TDITLYNFKSYEGHHRISNISN-FTTVVGSNGSGKSNIIDAVLFLFGY-SAKKMRHKVNSGLINK-----GKDSCYVEIKFT 89  
                                 6899********9999999987.************************6.788************8.....789********* PP

                                 ETTEESSSSSSCEEEEEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STT............................... CS
                                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............................... RF
                      SMC_N   85 nedkklkiekeevsisrrvkrkgeseykingkevtkkevsellesagiske............................... 135 
                                  ++++       +s++r++++ g+s y+in+kev+ +ev++ ++  +++ e                               
  gene19|gene19|rna19|rna19   90 ASNDQ-------FSVKRELIK-GRSLYYINDKEVNVAEVRDKMKYYNVDLEhnrflilqgeieaiammkpkdeknvgileyl 163 
                                 99999.......****99986.667************************999****************************** PP

                                 .................................................................................. CS
                                 .................................................................................. RF
                      SMC_N  136 .................................................................................. 135 
                                                                                                                   
  gene19|gene19|rna19|rna19  164 ediigtnvyhdeiqvleqqlsalkekedvmkssfkfqekefnfvraknesneqllneraewlkekirlnyleeikearvrdk 245 
                                 ********************************************************************************** PP

                                 .................................................................................. CS
                                 .................................................................................. RF
                      SMC_N  136 .................................................................................. 135 
                                                                                                                   
  gene19|gene19|rna19|rna19  246 lmkenkslenelskiknnddveqikmlegelvkhksalsrkereflsckqevnrinreilrresdyemlvrtekmavqeyen 327 
                                 ********************************************************************************** PP

                                 .................................................................................. CS
                                 .................................................................................. RF
                      SMC_N  136 .................................................................................. 135 
                                                                                                                   
  gene19|gene19|rna19|rna19  328 tireqkmnqieveaiktekdenmreidvfekklrakedelvrlrqnckhgdkiralkklmdryekdilnlnekksrirlnqt 409 
                                 ********************************************************************************** PP

                                 .................................................................................. CS
                                 .................................................................................. RF
                      SMC_N  136 .................................................................................. 135 
                                                                                                                   
  gene19|gene19|rna19|rna19  410 qqdevvlrnkileceknlnilkgldrnictdmrvlknniqateqeleskkeqlreakqqnttrkteseligrlkgvegfigr 491 
                                 ********************************************************************************** PP

                                 .................................................................................. CS
                                 .................................................................................. RF
                      SMC_N  136 .................................................................................. 135 
                                                                                                                   
  gene19|gene19|rna19|rna19  492 lgdlgrvnskydiaitaaskgklnnivvksvesaencikiintnglkrtsflvmdrlvdeplkkdkdfvycvdlidckekyk 573 
                                 ********************************************************************************** PP

                                 .................................................................................. CS
                                 .................................................................................. RF
                      SMC_N  136 .................................................................................. 135 
                                                                                                                   
  gene19|gene19|rna19|rna19  574 kafsfvlkdtilcndldeatsvafdrkirrrtvslqgdlieksgimsrmkvtgsmntqvdteklekklarieaaksnmenll 655 
                                 ********************************************************************************** PP

                                 .................................................................................. CS
                                 .................................................................................. RF
                      SMC_N  136 .................................................................................. 135 
                                                                                                                   
  gene19|gene19|rna19|rna19  656 kekeeqiravksildgrkeanecindleqkmgrmidsyckltnksrtddlnalfrddneemraldekvnelkneikgvrkei 737 
                                 ********************************************************************************** PP

                                 .................................................................................. CS
                                 .................................................................................. RF
                      SMC_N  136 .................................................................................. 135 
                                                                                                                   
  gene19|gene19|rna19|rna19  738 edlegneikgrtcdkqlltdqinlfikrnqdldekmnrillldtqsklknvdntlkdarrkmkeiesmdeikkecnsktklc 819 
                                 ********************************************************************************** PP

                                 .................................................................................. CS
                                 .................................................................................. RF
                      SMC_N  136 .................................................................................. 135 
                                                                                                                   
  gene19|gene19|rna19|rna19  820 meletvyeneqdeirrlceqindlknvteelmqkeleirnrieknlekmkkksmkndhmdelkvfkrlgyrfddimgsendd 901 
                                 ********************************************************************************** PP

                                 .................................................................................. CS
                                 .................................................................................. RF
                      SMC_N  136 .................................................................................. 135 
                                                                                                                   
  gene19|gene19|rna19|rna19  902 niskkvvdyktidnteldnligetqfkiqkldknekidfelvheyknkkieyenvkneynrfmntfdtivkqfsdlknkrhe 983 
                                 ********************************************************************************** PP

                                 ........................................................CS-HHHHHHHHHHHHHHHHCCS--SE CS
                                 ........................................................xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      SMC_N  136 ........................................................lLSgGektLvalaLlfAiqkvkpapl 161 
                                                                                         +LSgGektL++laL+fA++ ++p+p+
  gene19|gene19|rna19|rna19  984 efmngfaiinkhlkeiyqtitfggnaelelvdytdpfsegvvlsvmppkktwnkvsSLSGGEKTLASLALVFALHTYSPSPF 1065
                                 ********************************************************************************** PP

                                 EEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCCC-SCEEEEEEEET CS
                                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      SMC_N  162 yllDeidaaLDeknvkkvaellkeksknaQfivislreemlekadklvgvtkven 216 
                                 y++DeidaaLD++nv+ va+l+ke++   Qf+vislr++m+e adklvgv+k+e 
  gene19|gene19|rna19|rna19 1066 YVMDEIDAALDFRNVSLVANLIKEQK--GQFLVISLRNDMFELADKLVGVYKNEG 1118
                                 ************************99..************************654 PP

>> SMC_hinge  SMC proteins Flexible Hinge Domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.6   0.1   1.3e-27   2.9e-24       2     116 ..     486     595 ..     485     596 .. 0.96

  Alignments for each domain:
  == domain 1  score: 85.6 bits;  conditional E-value: 1.3e-27
                  SMC_hinge   2 kgvlGrladlievdegyekAveaalgnrlqalvvedeetakkiieflkkknagratflpldrikqknkadgandknsgavplid 85 
                                +g++Grl+dl +v ++y++A+ aa  ++l+++vv++ e+a+ +i+ + ++ ++r++fl++dr+ +++ +++++      v+++d
  gene19|gene19|rna19|rna19 486 EGFIGRLGDLGRVNSKYDIAITAASKGKLNNIVVKSVESAENCIKIINTNGLKRTSFLVMDRLVDEPLKKDKD-----FVYCVD 564
                                799************************************************************9999999984.....79**** PP

                  SMC_hinge  86 lvevddelrkalryllgdtlvvdsldeAeel 116
                                l++++++++ka+ ++l+dt+++++ldeA+ +
  gene19|gene19|rna19|rna19 565 LIDCKEKYKKAFSFVLKDTILCNDLDEATSV 595
                                ****************************976 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.1   3.5   1.9e-10   4.2e-07       1     203 [.      37     261 ..      37     271 .. 0.86
   2 !   20.0   0.2   2.2e-07   0.00049     165     296 ..     994    1098 ..     900    1098 .. 0.73

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 1.9e-10
                     AAA_21   1 lnvliGpNgsGKSnLLdaldllarl....................drdvegltdelsggggirkipslldlydpeipfefeiee 64 
                                ++ ++G NgsGKSn++da  +l+++                        +  t +++ ++  r+ ++   ly+++ + +   e 
  gene19|gene19|rna19|rna19  37 FTTVVGSNGSGKSNIIDAVLFLFGYsakkmrhkvnsglinkgkdsCYVEIKFTASNDQFSVKRELIKGRSLYYINDKEVNVAE- 119
                                799*****************************************977777888888888888888888888888888888888. PP

                     AAA_21  65 flsqgvryryglrlersqv.eeklssvetllesgllldkrsleeedvfnpeargirggvsvfslkelsvsepndlqfgkaltdi 147
                                + ++++ y+  l+ +r+ + +  + +  + + + +      ++ ed    ++++  ++v + +l +l  +e+  + ++k+  + 
  gene19|gene19|rna19|rna19 120 VRDKMKYYNVDLEHNRFLIlQGEIEAIAMMKPKDEKNVGILEYLEDIIGTNVYHDEIQVLEQQLSALKEKEDVMKSSFKFQEKE 203
                                9******************96666666666666666666666666666778888888999999999999999999999999999 PP

                     AAA_21 148 tsrawsllllldglrke..rigllnifadyfgfakekrllqrlvrslklveielsdlg 203
                                +++ +  +++++ l++e  +++   i  +y+ + ke r +++l+++ k  e+els+++
  gene19|gene19|rna19|rna19 204 FNFVRAKNESNEQLLNEraEWLKEKIRLNYLEEIKEARVRDKLMKENKSLENELSKIK 261
                                999999999999999999************************************9996 PP

  == domain 2  score: 20.0 bits;  conditional E-value: 2.2e-07
                     AAA_21  165 rigllnifadyfgfakekrllqrlvrslklveielsdlgegeeliasvderlrergvvflengdgqelparelSdGtkrll. 245 
                                 +++   ++  +fg++ e++l++   + +  v + ++  ++ +++                         +++lS G k l+ 
  gene19|gene19|rna19|rna19  994 KHLKEIYQTITFGGNAELELVDYTDPFSEGVVLSVMPPKKTWNK-------------------------VSSLSGGEKTLAs 1050
                                 56666666666666666666666666666666666666655555.........................4578*******87 PP

                     AAA_21  246 .alltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltT 296 
                                  al+ al+   ++ ++++ DE+++ L+ + ++ ++ l+ke +    Q+++ +
  gene19|gene19|rna19|rna19 1051 lALVFALHTYSPS-PFYVMDEIDAALDFRNVSLVANLIKEQKG---QFLVIS 1098
                                 7999999999999.************************99866...988765 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.1   0.1   1.3e-10   2.9e-07       2      46 ..      15      59 ..      14      72 .. 0.83

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 1.3e-10
                     AAA_29  2 krlqlvNWgtfdg.htieidlkgatlltGpsGsGKSTllDAiqalL 46
                               + + l+N  +++g h+i+ + +++t ++G +GsGKS ++DA+ +l+
  gene19|gene19|rna19|rna19 15 TDITLYNFKSYEGhHRIS-NISNFTTVVGSNGSGKSNIIDAVLFLF 59
                               6899*********55554.45679******************9987 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.5  24.6   5.4e-10   1.2e-06       2     254 ..      13     262 ..      13     289 .. 0.61
   2 ?  -35.6  49.1         8   1.8e+04      88     247 ..     571     790 ..     286     810 .. 0.60
   3 ?  -13.5  39.6         8   1.8e+04      54     256 ..     774    1003 ..     755    1075 .. 0.66

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 5.4e-10
                     AAA_15   2 kIkkikikNFRslkd.vei.dlseeltvliGkNnsGKSsilealdlFlnnkekknkkvikiekedleifeniseskdikIdvef 83 
                                k++ i++ NF+s++    i ++s+ +t+++G N+sGKS+i++a  +++  +   +k+ +k+++  +++    + s  ++I+++ 
  gene19|gene19|rna19|rna19  13 KMTDITLYNFKSYEGhHRIsNISN-FTTVVGSNGSGKSNIIDAVLFLFGYS--AKKMRHKVNSGLINKG---KDSCYVEIKFTA 90 
                                5789**********9777724555.***********************966..3344555555555554...444444444444 PP

                     AAA_15  84 aekekakeyektlkskekkkadlllkkkesdlkktikdkklklkknelsdekisvekkks..............kkelpkekee 153
                                     +++ ++ +++  k  +            ++i+dk+ ++ + +++ + ++v+ + +              +k  ++++  
  gene19|gene19|rna19|rna19  91 -----SNDQFSVKRELIKGRSL-----------YYINDKEVNVAEVRDKMKYYNVDLEHNrflilqgeieaiamMKPKDEKNVG 158
                                .....22222333322222222...........222222222222222222222222222223333433334444444445555 PP

                     AAA_15 154 klekekeelkid..kedlkklikkleeslkkeeelknvlksaiiklllisakRnvsdedsekkssllgklkekil.eealqekl 234
                                 le  ++ + ++   ++++ l ++l+  ++ke+++k+++k + +++ +  ak+++++++ ++  ++l ++++  + ee+++ + 
  gene19|gene19|rna19|rna19 159 ILEYLEDIIGTNvyHDEIQVLEQQLSALKEKEDVMKSSFKFQEKEFNFVRAKNESNEQLLNERAEWLKEKIRLNYlEEIKEARV 242
                                555555555555548888888888888888888************************999999999888887655055544444 PP

                     AAA_15 235 eeelteklkeiqeklkeidk 254
                                +++l ++ k+++++l++i++
  gene19|gene19|rna19|rna19 243 RDKLMKENKSLENELSKIKN 262
                                66666666666666666654 PP

  == domain 2  score: -35.6 bits;  conditional E-value: 8
                     AAA_15  88 kakeyektlkskekkkadlllkkkesdlkktikdkklklkknelsdekisvekkkskkelpkekeeklekekeelkidkedlkk 171
                                k k+ +++  ++ + ++d l + ++ +++  i+ ++  l+ + + ++ i   +k          +eklek+ + ++  k+++++
  gene19|gene19|rna19|rna19 571 KYKKAFSFVLKDTILCND-LDEATSVAFDRKIRRRTVSLQGDLIEKSGIMSRMKVTGSMNTQVDTEKLEKKLARIEAAKSNMEN 653
                                333333333333333333.33333333333333333333333333333333333333333333455555555555555666666 PP

                     AAA_15 172 likkleeslkkee..............................................................elknvlksa 193
                                l+k+ ee++   +                                                              e+k v k+ 
  gene19|gene19|rna19|rna19 654 LLKEKEEQIRAVKsildgrkeanecindleqkmgrmidsyckltnksrtddlnalfrddneemraldekvnelknEIKGVRKEI 737
                                666555555555544444444444444444444444444444444444444444444444444444433332223333333333 PP

                     AAA_15 194 iiklllisakRnvsdedsekkssllgklkekileealqekleeelteklkeiqe 247
                                 ++     + R+ ++++ + + +l++k  +++ e +++  l +++++klk++++
  gene19|gene19|rna19|rna19 738 EDLEGNEIKGRTCDKQLLTDQINLFIKRNQDLDE-KMNRILLLDTQSKLKNVDN 790
                                3333444444444445555544444444444433.2333333333333333333 PP

  == domain 3  score: -13.5 bits;  conditional E-value: 8
                     AAA_15   54 n.......................kkvikiekedleifeniseskdikIdvefaekekakeyektlkskekkkadlllkkke 112 
                                 n                       k++  +  ++++++ n +++ +++++  + e+e+++++  +++ ++ k  + +l++ke
  gene19|gene19|rna19|rna19  774 NrillldtqsklknvdntlkdarrKMKEIESMDEIKKECNSKTKLCMELETVY-ENEQDEIRRLCEQINDLKNVTEELMQKE 854 
                                 15555555555557777888887655556666777777788899999999999.55777777777777777777779***** PP

                     AAA_15  113 sdlkktikdkklklkknelsdekisvekkks....kkelpkekeeklekekeelkidkedlkklikkleeslkkee..elkn 188 
                                  ++ ++i+++  k kk+  +++  +  k  +    +     + + +  +++++++++  d k + ++   +l +e   ++++
  gene19|gene19|rna19|rna19  855 LEIRNRIEKNLEKMKKKSMKNDHMDELKVFKrlgyR-----FDDIMGSENDDNISKKVVDYKTIDNTELDNLIGETqfKIQK 931 
                                 *************99777777766644444444443.....44444444444444444444444444444444444445555 PP

                     AAA_15  189 vlksaiiklllisakRnvsdedsekkssl..lgklkekileealqekl..eeelteklkeiqeklkeidkkl 256 
                                 + k++ i+++l ++ +n + e +++k+++  ++++++ i+++ ++ k   +ee    +  i++ lkei++++
  gene19|gene19|rna19|rna19  932 LDKNEKIDFELVHEYKNKKIEYENVKNEYnrFMNTFDTIVKQFSDLKNkrHEEFMNGFAIINKHLKEIYQTI 1003
                                 667777777777766665554444444332256666666665544333557777777777788888877776 PP

>> tRNA-synt_2b  tRNA synthetase class II core domain (G, H, P, S and T)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   1.6   1.3e-05     0.028      81     166 ..     874     991 ..     803     996 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.3e-05
                                HHHHHHHHHHHHHTT.SCEEEEEEGTTSC.............................BTTSEEEEEEEEETTTSEEEEEEEEE CS
                                xxxxxxxxxxxxxxxxxxxxxxxxxxxxx.............................xxxxxxxxxxxxxxxxxxxxxxxxxx RF
               tRNA-synt_2b  81 rdlikaisriferlglefraiielmsaks.............................adykdkkefeavsesltkgieigtiq 135
                                ++  ++  ++f+rlg  f  i+++ ++ +                             +d ++k +fe+v e  +k+ie   ++
  gene19|gene19|rna19|rna19 874 KNDHMDELKVFKRLGYRFDDIMGSENDDNiskkvvdyktidnteldnligetqfkiqkLDKNEKIDFELVHEYKNKKIEYENVK 957
                                33344455799999999999999944444678999************************************************* PP

                                EEETHHHHHTTE...EEECTTSSEEEEEEEEEEE CS
                                xxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxx RF
               tRNA-synt_2b 136 klgtrlserlga...tvldennreksvimicaai 166
                                + ++r+ +++++   ++ d +n++++ +m ++ai
  gene19|gene19|rna19|rna19 958 NEYNRFMNTFDTivkQFSDLKNKRHEEFMNGFAI 991
                                ***********97777888888888888888774 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   6.3e-05      0.14      26      53 ..    1034    1060 ..    1013    1088 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 6.3e-05
                    SbcCD_C   26 lsrssgtlSGGekqflaylalaaalaal 53  
                                 + +++++lSGGek +la+lal++al+ +
  gene19|gene19|rna19|rna19 1034 TWNKVSSLSGGEK-TLASLALVFALHTY 1060
                                 567899*******.**********9865 PP

>> KorB  KorB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.9   0.00029      0.64      33      87 ..     429     483 ..     381     485 .. 0.87
   2 ?    0.6   0.2      0.27     6e+02      40      75 ..     811     847 ..     797     874 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00029
                       KorB  33 lrelydseviadirtLyeLrraaekhpaevrafvaengeagltrsavrrflkslk 87 
                                + + +d++++ d r+L +  +a e++ +  ++ ++e+++++ tr++ ++++ +lk
  gene19|gene19|rna19|rna19 429 ILKGLDRNICTDMRVLKNNIQATEQELESKKEQLREAKQQNTTRKTESELIGRLK 483
                                345589************99******9**********************999998 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.27
                       KorB  40 eviadirtLyeLrraaekhpaevrafvaenge.aglt 75 
                                e  + +++  eL  + e++ +e+r+++++  + +++t
  gene19|gene19|rna19|rna19 811 ECNSKTKLCMELETVYENEQDEIRRLCEQINDlKNVT 847
                                4556778888999999999999999994433314444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2699  (0.150538); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        77  (0.00429472); expected 17.9 (0.001)
Passed Fwd filter:                        39  (0.00217525); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 1.51u 0.39s 00:00:01.90 Elapsed: 00:00:00.62
# Mc/sec: 5541.23
//
Query:       gene190|gene190|rna190|rna190  [L=68]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (68 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       122  (0.00680462); expected 358.6 (0.02)
Passed bias filter:                      102  (0.00568911); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.43
# Mc/sec: 471.86
//
Query:       gene1900|gene1900|rna1900|rna1900  [L=323]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.5e-15   57.4   4.8    3.1e-13   49.8   4.8    2.5  1  Choline_kinase  Choline/ethanolamine kinase
    2.2e-07   31.1   0.0    2.7e-06   27.5   0.0    2.2  1  APH             Phosphotransferase enzyme family
     0.0013   18.1   2.3     0.0037   16.6   2.1    1.7  1  EcKinase        Ecdysteroid kinase


Domain annotation for each model (and alignments):
>> Choline_kinase  Choline/ethanolamine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.8   4.8   5.2e-17   3.1e-13      28     199 ..      60     204 ..      41     217 .. 0.67

  Alignments for each domain:
  == domain 1  score: 49.8 bits;  conditional E-value: 5.2e-17
                                        HHHHHTTSSS-EEEEETTEEEEE--TCEE--TTGGGCHHHHHHHHHHHHHHTTCHH.TTSSSS-HHHHHHHHHHHC CS
                     Choline_kinase  28 allserglgpklygifenGrieefiesrtlstedlrepeiskkiAkklaelHsleleseskespslwktmqkwlln 103
                                        ++l+  +  pk+y + ++ rieef+  +     d++     k iA+ la++H+++++ + + +++l k + +    
  gene1900|gene1900|rna1900|rna1900  60 EILKYVN-VPKIYEMKSGYRIEEFLRHE---VPDFKR--DIKLIATALAQFHNTDVPGIESFEDMLIKLVLEN--- 126
                                        4443333.37888888888888887543...333333..4567888888888888866666666666666555... PP

                                        CS.TT..ECHHGGCCHCCCTHHHHHHHHHTHHHHHHCHGG-EEEE-S--SGGGEEE.-CTTEEEE--GTT-EEEEH CS
                     Choline_kinase 104 keaqtkakkekkkkqlklinledlekelekleklleelespvvfcHnDlqegNillnkeekklvlIDFEYagynyr 179
                                           qt +++e            ++ +  +kl+ ll e +s   + H Dlq gN+l+   ++ + lIDFEY++   +
  gene1900|gene1900|rna1900|rna1900 127 ---QTLKHNE------------SITNVYNKLKYLL-EDKSMDGLIHMDLQVGNMLK--IDNLVRLIDFEYSCTGSI 184
                                        ...2222222............3333344444444.333334566***********..99**************** PP

                                        HHHHHHHHHHTTEEHHHCST CS
                     Choline_kinase 180 gfDlanhfiEwagdyeeeea 199
                                          D+an+f+E++ +y+++++
  gene1900|gene1900|rna1900|rna1900 185 ILDIANFFCETMTNYQHDSI 204
                                        ***************99875 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.5   0.0   4.5e-10   2.7e-06       9     209 ..      31     192 ..      25     228 .. 0.80

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 4.5e-10
                                        SSCEEEEEEETT--EEEEEE-TTS-HHHHHHHHHHHHHHHHTT-B--B-CTTBS-EEETTEEEEEEE----EE-SS CS
                                APH   9 asnrtylvttpagryvlrrnpparaaeeirrevallrlLakagvpvPevlagdtddeeigllfalieyvpgrsllr 84 
                                        +sn +y++ + + ry+l+++  +    e ++e+++l++     v vP+++        +g  +++ e++  ++++ 
  gene1900|gene1900|rna1900|rna1900  31 YSNLVYQILSNRNRYILKLYINR----ERSNEFEILKY-----VNVPKIYE-----MKSG--YRIEEFLRHEVPDF 90 
                                        89********99*******9999....99*********.....999*****.....7788..67778888888877 PP

                                        HHHHHHHHHHHHHHHHHHCCHHCH..-STTTB-SHHCHTCCHHHHHHCHHHCCCGCCTCCHHHHHHHHHHHHHHHH CS
                                APH  85 klsaaqlpellealgeflaalhqvd.paalpladflaqdlellrqlesatarllaselldlleeleeqvlaalaal 159
                                               ++ +  ++ +la++h++d p    ++d+l       ++l+ +  ++    ++     ++  v+++l+ l
  gene1900|gene1900|rna1900|rna1900  91 -------KRDIKLIATALAQFHNTDvPGIESFEDML-------IKLVLE--NQTLKHNE----SITN-VYNKLKYL 145
                                        .......67889999*********655544444444.......555555..22222222....3556.99999999 PP

                                        --SSS-EEEE-SS-SGGGEEEC..TTEEEEE---TT-EEEECCHHHHCCH CS
                                APH 160 lpgelptvllHgDlhpgNllvdpddgrvtGviDfedaglgpplyDlavll 209
                                        l   +  +l+H Dl  gN+l    d+ v  +iDfe++++g ++ D+a + 
  gene1900|gene1900|rna1900|rna1900 146 LEDKSMDGLIHMDLQVGNMLKI--DNLV-RLIDFEYSCTGSIILDIANFF 192
                                        999999**************99..5555.59***************9876 PP

>> EcKinase  Ecdysteroid kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   2.1   6.2e-07    0.0037     172     266 ..     113     197 ..      97     205 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 6.2e-07
                           EcKinase 172 kaalealreelpelekeaekleklkenlferllelveekeeefnvlnHGDlwvnNimfkydeegepedvilvDFQl 247
                                        +++ ++l + +   e+++ k ++ ++n++++l+ l+  +++ +  l H Dl v N++ k d+      v+l+DF +
  gene1900|gene1900|rna1900|rna1900 113 ESFEDMLIKLVL--ENQTLKHNESITNVYNKLKYLL--EDKSMDGLIHMDLQVGNML-KIDN-----LVRLIDFEY 178
                                        455555522222..2244666777789999999999..888999***********87.6774.....49******* PP

                           EcKinase 248 srygSpalDLlyflytste 266
                                        s  gS++lD++ f+   ++
  gene1900|gene1900|rna1900|rna1900 179 SCTGSIILDIANFFCETMT 197
                                        ************9986665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (323 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       916  (0.0510904); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 2174.06
//
Query:       gene1901|gene1901|rna1901|rna1901  [L=145]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       428  (0.0238719); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 1021.30
//
Query:       gene1902|gene1902|rna1902|rna1902  [L=519]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.14   12.5   0.0       0.36   11.2   0.0    1.6  1  Orf78     Orf78 (ac78)


Domain annotation for each model (and alignments):
>> Orf78  Orf78 (ac78)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0     2e-05      0.36      35      85 ..     466     516 ..     461     518 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 2e-05
                              Orf78  35 enkkekksaaeknditekesnaaekaqalnillisllavvcvlvllyviyY 85 
                                        +n ++++ + +k+d + ++ ++++++++ + +++ ll ++ +++ +++ yY
  gene1902|gene1902|rna1902|rna1902 466 KNGSNDTVVDPKKDQQVDNGTSQKNMSVAKKMFLLLLLLILIILTIIAFYY 516
                                        455666677777777777777666677777777666666666666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (519 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1061  (0.0591779); expected 358.6 (0.02)
Passed bias filter:                      686  (0.038262); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.65u 0.32s 00:00:00.97 Elapsed: 00:00:00.47
# Mc/sec: 3336.43
//
Query:       gene1903|gene1903|rna1903|rna1903  [L=372]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (372 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2307  (0.128674); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); expected 358.6 (0.02)
Passed Vit filter:                       107  (0.00596798); expected 17.9 (0.001)
Passed Fwd filter:                        36  (0.00200792); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 1.01u 0.41s 00:00:01.42 Elapsed: 00:00:00.56
# Mc/sec: 2016.05
//
Query:       gene1904|gene1904|rna1904|rna1904  [L=239]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    9.8e-09   34.9   0.1    4.4e-05   23.2   0.0    2.5  2  RRM_1        RNA recognition motif. (a.k.a. RRM, RBD, or RNP 
  ------ inclusion threshold ------
      0.023   13.7   0.1      0.038   13.0   0.1    1.4  1  AFOR_C       Aldehyde ferredoxin oxidoreductase, domains 2 & 
      0.045   13.8   0.2       0.11   12.5   0.2    1.7  1  Nup35_RRM_2  Nup53/35/40-type RNA recognition motif
       0.19   12.2   1.5       0.43   11.0   1.5    1.6  1  Toxin_6      BmTXKS1/BmP02 toxin family


Domain annotation for each model (and alignments):
>> RRM_1  RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.0   9.8e-09   4.4e-05       1      48 [.       3      43 ..       3      68 .. 0.88
   2 !    9.6   0.0   0.00017      0.78      37      69 ..     146     178 ..     127     179 .. 0.89

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 9.8e-09
                                       EEEESETTTSSHHHHHHHHHTTSCEEEEEEEEETTTSEEEEEEEEESS CS
                              RRM_1  1 lfVgnLppdvteeeLkelFskfGpiksiklvrdetgkskgfafVeFes 48
                                       l+++++p++++ +eL+++F ++G+i+++++ ++       +++  +++
  gene1904|gene1904|rna1904|rna1904  3 LIIKDIPSELSYDELYDYFTEYGRINDFRIKYN-------YGYLCYNN 43
                                       689****************************95.......77766666 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00017
                                        SEEEEEEEEESSHHHHHHHHHHHTTEEETTEEE CS
                              RRM_1  37 kskgfafVeFeskedAekAlealngkklggrel 69 
                                        +s  +++VeF s e+ e+Al+ l++ ++++ ++
  gene1904|gene1904|rna1904|rna1904 146 QSGQHGIVEFGSIEAKEDALRILDNVTFKNMQI 178
                                        68899***********************99876 PP

>> AFOR_C  Aldehyde ferredoxin oxidoreductase, domains 2 & 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   8.4e-06     0.038      23      80 ..      24      86 ..       5     110 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 8.4e-06
                                       H-GGGHHHHHHHTT---BTTTTBS-..-TTGGGGSH.....HHHHHHTEEEE.E-TT-SS--EEE CS
                             AFOR_C 23 yGTaelvnianetgalptknfqegt..fekaekisg.....ealeekylvknegCfsCpiaCgre 80
                                       yG  +   i  ++g l  +n   ++  f++++k+sg     +++++  +  +e+C  Cp++Cg +
  gene1904|gene1904|rna1904|rna1904 24 YGRINDFRIKYNYGYLCYNNADVERrvFNTYHKVSGyklnvDKAAQ--NETMERCSHCPVHCGGR 86
                                       5555555566677778888877744479999999997744333333..344445********854 PP

>> Nup35_RRM_2  Nup53/35/40-type RNA recognition motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.2   2.5e-05      0.11      16      46 ..      16      44 ..       8      49 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.5e-05
                        Nup35_RRM_2 16 lVlehFasfGeIvkhyvpkevsvmyvkfese 46
                                       + +++F ++G+I+++ +  + ++ y+++ + 
  gene1904|gene1904|rna1904|rna1904 16 ELYDYFTEYGRINDFRI--KYNYGYLCYNNA 44
                                       6799**********999..58*******875 PP

>> Toxin_6  BmTXKS1/BmP02 toxin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   1.5   9.7e-05      0.43       3      13 ..      76      86 ..      75      89 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 9.7e-05
                            Toxin_6  3 CeeCpihCkgq 13
                                       C  Cp hC+g+
  gene1904|gene1904|rna1904|rna1904 76 CSHCPVHCGGR 86
                                       99*******97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (239 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       607  (0.0338558); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.42u 0.29s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1685.94
//
Query:       gene1905|gene1905|rna1905|rna1905  [L=322]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-29  102.8  15.4    1.6e-29  102.8  15.4    2.8  2  PTPLA     Protein tyrosine phosphatase-like protein, PTPLA
  ------ inclusion threshold ------
      0.024   15.2   0.3      0.035   14.6   0.3    1.2  1  bZIP_Maf  bZIP Maf transcription factor


Domain annotation for each model (and alignments):
>> PTPLA  Protein tyrosine phosphatase-like protein, PTPLA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   3.1      0.78     7e+03      88      88 ..      49      49 ..       3      84 .. 0.54
   2 !  102.8  15.4   1.8e-33   1.6e-29       1     161 [.     174     309 ..     174     312 .. 0.94

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 0.78
                              PTPLA 88 t 88
                                       t
  gene1905|gene1905|rna1905|rna1905 49 T 49
                                       1 PP

  == domain 2  score: 102.8 bits;  conditional E-value: 1.8e-33
                              PTPLA   1 QtlavlEvlhallglvrspvlttamQvasRllvvwgvvelfpelqtkspavtllllaWsvtEviRYsfyalklslg 76 
                                        Q++ vlE+l++l+ + r+++++t +Q +sRl+++w++++ ++   t+  +v ++ll W v++ +RY fy+ +    
  gene1905|gene1905|rna1905|rna1905 174 QSFYVLEILNILVNVSRARLFPTCVQLSSRLFIIWYICYRYNF--TD-AVVHIMLLCWFVSDTVRYVFYFSRR--- 243
                                        9999************************************976..55.89**********************9... PP

                              PTPLA  77 kvpklltwlRYtlfivLYPlGvasElvliyaalpvlkeskklsielpnklnfsfsykyflllllllyvpglyvlyt 152
                                           + +++lRY+lfivLYPlG ++E+vl+ +   +                    +kyfl +++l+y+pg+ +ly 
  gene1905|gene1905|rna1905|rna1905 244 ---GTVKFLRYNLFIVLYPLGTLCEIVLVSRVERICT----------------GVLKYFLRIVMLCYIPGFSFLYV 300
                                        ...79***********************988777655................579******************** PP

                              PTPLA 153 hmlkqRrkv 161
                                        hm+++Rr++
  gene1905|gene1905|rna1905|rna1905 301 HMIRRRRRT 309
                                        *******97 PP

>> bZIP_Maf  bZIP Maf transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.3   3.9e-06     0.035      26      48 ..     300     322 .]     293     322 .] 0.90

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.9e-06
                           bZIP_Maf  26 verLKqrRRrlKNrgyakscrkr 48 
                                        v  +++rRR+ KN+g a++++++
  gene1905|gene1905|rna1905|rna1905 300 VHMIRRRRRTSKNKGVAQRKKDK 322
                                        7789***************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (322 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1123  (0.062636); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.31s 00:00:00.90 Elapsed: 00:00:00.48
# Mc/sec: 2013.79
//
Query:       gene1906|gene1906|rna1906|rna1906  [L=351]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (351 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       726  (0.0404931); expected 358.6 (0.02)
Passed bias filter:                      201  (0.0112109); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 2291.65
//
Query:       gene1907|gene1907|rna1907|rna1907  [L=154]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.1e-17   64.1   0.0    1.4e-17   63.8   0.0    1.1  1  Proteasome  Proteasome subunit
  ------ inclusion threshold ------
      0.093   13.2   0.0       0.16   12.4   0.0    1.3  1  PNPase      Polyribonucleotide nucleotidyltransferase, RNA bi


Domain annotation for each model (and alignments):
>> Proteasome  Proteasome subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.8   0.0   1.6e-21   1.4e-17      60     190 .]       2     133 ..       1     133 [. 0.92

  Alignments for each domain:
  == domain 1  score: 63.8 bits;  conditional E-value: 1.6e-21
                                        HHHHHHHHHHHHHHHHSSGTCHHHHHHHHHHHHHHHHHHC.....TTTTTSEEEEEEEEETTTEEEEEEEETTSEE CS
                         Proteasome  60 lvrraraeaqlyrlrygrpipverlvarvaaklqaytqrs.....grrpfgvslliagvdeeggpeLyqidpsGsy 130
                                        +v++ r+ +  + ++y++  +v  +++r++a+ ++   r+       rpfgvs+lia +   ++p+Ly ++psGsy
  gene1907|gene1907|rna1907|rna1907   2 IVEKSRMYMMGRMMQYDECSSVVGILKRLCAQSLKFGERDpnkkiFSRPFGVSILIAAFE--DAPKLYLLEPSGSY 75 
                                        678888889999999999999999*********99999876655567************9..77************ PP

                                        EEESSEEEESTTHHHHHHHHHHHHSTTBSHHHHHHHHHHHHHHHHHHBTTSCSSEEEEEE CS
                         Proteasome 131 ieekdavaiGsgseaaktalekeykedltleeavelavkalkealerdklsgknievavi 190
                                         + + a +iGs+ +a+ + l ++y e ++ +++v+l    lke+++ dk+s++n+e  v+
  gene1907|gene1907|rna1907|rna1907  76 KQFR-AKSIGSAYQAVDNELLERYDEQMSHDDTVRLSYTLLKEVMR-DKISKENVETMVV 133
                                        ***5.****************************************9.99******98876 PP

>> PNPase  Polyribonucleotide nucleotidyltransferase, RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   1.8e-05      0.16      23      77 ..      76     128 ..      71     129 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.8e-05
                                        HHHHHHHHHHHHHHHHHHHH...HHSTTS-HHHHHHHHHHHHHHHHHHHHHHTS- CS
                             PNPase  23 KqeRyaaldeikekvveafaaeleeedeedekeikeifkalekkvvRsrildegv 77 
                                        Kq R + + + +++v ++++++++e  + ++ +   + ++l k+v+R +i +e+v
  gene1907|gene1907|rna1907|rna1907  76 KQFRAKSIGSAYQAVDNELLERYDE--QMSHDDTVRLSYTLLKEVMRDKISKENV 128
                                        999*****************99866..899999*****************98875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       637  (0.035529); expected 358.6 (0.02)
Passed bias filter:                      454  (0.0253221); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1122.29
//
Query:       gene1908|gene1908|rna1908|rna1908  [L=76]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.1e-11   42.4   0.0    6.8e-11   41.6   0.0    1.4  1  Proteasome_A_N  Proteasome subunit A N-terminal signature
    4.3e-10   39.4   0.4    6.1e-10   38.9   0.4    1.2  1  Proteasome      Proteasome subunit


Domain annotation for each model (and alignments):
>> Proteasome_A_N  Proteasome subunit A N-terminal signature
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.6   0.0   7.6e-15   6.8e-11       2      23 .]       4      25 ..       4      25 .. 0.96

  Alignments for each domain:
  == domain 1  score: 41.6 bits;  conditional E-value: 7.6e-15
                     Proteasome_A_N  2 DrslttFSPdGRLfQVEYAmkA 23
                                       D  ++ +SP+GR++Q+EYAmkA
  gene1908|gene1908|rna1908|rna1908  4 DHKVNSYSPEGRIYQIEYAMKA 25
                                       78999****************9 PP

>> Proteasome  Proteasome subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.9   0.4   6.8e-14   6.1e-10       1      53 [.      26      76 .]      26      76 .] 0.97

  Alignments for each domain:
  == domain 1  score: 38.9 bits;  conditional E-value: 6.8e-14
                                       HHHS-EEEEEEETTEEEEEEEEEEEETTEEEESSSSTSEEEEETTEEEEEEES CS
                         Proteasome  1 vkkGttvvGikgkdgvvlaadkratagskllskstveKifkiddhigvafaGl 53
                                       +++G t+v+++++  vv+ ++k++   skl+ +s+++K fkidd+ig+af+G+
  gene1908|gene1908|rna1908|rna1908 26 MNHGVTTVALATTQSVVISSEKKIL--SKLQVTSSATKHFKIDDRIGLAFSGD 76
                                       79***********************..99999*******************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       714  (0.0398237); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.28s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 534.58
//
Query:       gene1909|gene1909|rna1909|rna1909  [L=413]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.7e-10   40.3   0.1    6.3e-10   39.1   0.1    1.6  1  Peptidase_M48  Peptidase family M48


Domain annotation for each model (and alignments):
>> Peptidase_M48  Peptidase family M48
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.1   0.1   3.5e-14   6.3e-10      32     192 ..     244     411 ..     223     413 .] 0.79

  Alignments for each domain:
  == domain 1  score: 39.1 bits;  conditional E-value: 3.5e-14
                                        GGGT-EEEEESSS-EEEEEEHHHH-SSB-HHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHTT-SHH CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Peptidase_M48  32 spkrNAFalgggknkrivltdgLlkqllseeelaaVlGHElGHikhrhsvvslivsllasillllglallisraee 107
                                        ++++NA  +g gk  r+ ++        ++++l  V+ HE+GH+k +  ++++i++    i+ ll ++ ++ + + 
  gene1909|gene1909|rna1909|rna1909 244 GSEKNAALIGYGKGARMEIYGNFT--ETDQDQLFSVFLHEIGHAKENTLMRKTIIYIALLIIELLFMLYIYDTIST 317
                                        344599999999999999999988..99*******************99999888777766666655555544433 PP

                                        HHHTT--S---HHHHHHHHHHTT...........HHHHHHHHHHHHHHHHTTT.HHHHHHHHHHHHHHTT--S--- CS
                                        xxxxxxxxxxxxxxxxxxxxxxx...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Peptidase_M48 108 daagafldalavliglliillfl...........alSRkrEyqADeagvellkrakdlvraliklakdlerqdvsa 172
                                        +    +  +  ++++ll ++  +             S ++E ++D ++++  +  ++l+++l +++ d++ + + +
  gene1909|gene1909|rna1909|rna1909 318 KFTTEI-ISVFTAFVLLVFIYRAllrqwllmiykIASQQSEINSDMFAKQHDY-GRELAETLFNIVIDANDFLKPT 391
                                        333333.34444444444443337888******99******************.********************** PP

                                        HHHHHHS-SS--HHHHHHHH CS
                                        xxxxxxxxxxxxxxxxxxxx RF
                      Peptidase_M48 173 slrsellstHPplleRiqal 192
                                        + ++ l s HP +  Ri  l
  gene1909|gene1909|rna1909|rna1909 392 AVYNFLRSGHPAIYARIDYL 411
                                        ****************9866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (413 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1246  (0.0694963); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.45
# Mc/sec: 2762.09
//
Query:       gene191|gene191|rna191|rna191  [L=36]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (36 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       197  (0.0109878); expected 358.6 (0.02)
Passed bias filter:                      163  (0.00909142); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.28s 00:00:00.63 Elapsed: 00:00:00.44
# Mc/sec: 248.19
//
Query:       gene1910|gene1910|rna1910|rna1910  [L=391]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-06   28.0   6.3     0.0032   17.1   1.4    2.9  3  Hexapep          Bacterial transferase hexapeptide (six repea
    0.00034   19.7   0.2    0.00053   19.0   0.2    1.3  1  Fucokinase       L-fucokinase
     0.0043   15.3   1.5     0.0043   15.3   1.5    1.6  2  DUF4954          Domain of unknown function (DUF4954)
     0.0086   15.7   0.0      0.015   14.9   0.0    1.2  1  NTP_transferase  Nucleotidyl transferase
  ------ inclusion threshold ------
      0.037   14.4   1.3      0.067   13.6   1.3    1.4  1  DUF3795          Protein of unknown function (DUF3795)


Domain annotation for each model (and alignments):
>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.1   0.00012      0.41      12      29 ..     313     330 ..     301     335 .. 0.86
   2 !   17.1   1.4   8.8e-07    0.0032       2      30 ..     315     348 ..     314     349 .. 0.74
   3 !   17.1   3.5   9.4e-07    0.0034       1      27 [.     337     362 ..     331     366 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00012
                                        TTEEEETTEEE-TTEEEE CS
                            Hexapep  12 pfaviggnVkIGdnvkIg 29 
                                        ++a++g++++IGd + ++
  gene1910|gene1910|rna1910|rna1910 313 KNATVGNDCEIGDETLVE 330
                                        489999999999988765 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 8.8e-07
                                        EEEETTEEE-T.....TEEEETTEEE-TTEEEET CS
                            Hexapep   2 tvIGsnvlIgp.....faviggnVkIGdnvkIga 30 
                                        +++G+++ Ig       +++ +nVkIG+ +kI +
  gene1910|gene1910|rna1910|rna1910 315 ATVGNDCEIGDetlveDSIVFNNVKIGNSCKIRR 348
                                        566777777776666666666***********98 PP

  == domain 3  score: 17.1 bits;  conditional E-value: 9.4e-07
                                        TEEEETTEEE-TTEEEETTEEE-TTEE CS
                            Hexapep   1 stvIGsnvlIgpfaviggnVkIGdnvk 27 
                                        +++IG+ ++I+  + ig+nV+I d+++
  gene1910|gene1910|rna1910|rna1910 337 NVKIGNSCKIR-RCLIGSNVTICDGCV 362
                                        45666666666.777777777777776 PP

>> Fucokinase  L-fucokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.2   1.5e-07   0.00053     270     317 ..     295     370 ..     238     384 .. 0.59

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.5e-07
                         Fucokinase 270 k............................kesavvinSvlessvsvgegsviehsslkgnvsigsnsivsgleles 317
                                                                      ++ +v +S++ ++v++g+++ i  + +++nv+i  ++++ +++++s
  gene1910|gene1910|rna1910|rna1910 295 PddknivgrflttgksylknatvgndceiGDETLVEDSIVFNNVKIGNSCKIRRCLIGSNVTICDGCVLMDCKVTS 370
                                        1334444555552222222223333444456666667777777777777777777777777777777777776665 PP

>> DUF4954  Domain of unknown function (DUF4954)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.1      0.48   1.7e+03      71     102 ..     257     287 ..     232     293 .. 0.65
   2 !   15.3   1.5   1.2e-06    0.0043     201     267 ..     308     370 ..     297     387 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 0.48
                            DUF4954  71 linceigdnvlienvknyianYeigdeviien 102
                                        l++ e+ d +   + ++y+ nY++ ++ +i++
  gene1910|gene1910|rna1910|rna1910 257 LHSAELHDLTEH-EKHKYVMNYNLQNKNFIFK 287
                                        555555554443.3468999999998888876 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 1.2e-06
                            DUF4954 201 gasklengtinSskeapveiGegViledfiissGskikdgavisrcfvGqavklkkqfsaedsllfa 267
                                        g s l+n+t+     +  eiG++  +ed+i+ +  ki ++ +i rc++G +v++  +  + d+ + +
  gene1910|gene1910|rna1910|rna1910 308 GKSYLKNATVG----NDCEIGDETLVEDSIVFNNVKIGNSCKIRRCLIGSNVTICDGCVLMDCKVTS 370
                                        55666666664....4578**********************************99998888876655 PP

>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0     4e-06     0.015       9     144 ..      13     140 ..      10     147 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 4e-06
                                        --GGGTTCCTTSSGGG.SEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGTSEEEEEEESS- CS
                    NTP_transferase   9 sGtRLwPLtrtlakkl.vpvlgkerliqatlsrlansgieeiivvltqehsflveeqlkegskfgvevlialepeg 83 
                                          t L P+    ++k  +p+l++ +l+ + l   ++   +eiiv+  ++ +++v+e ++e  + + +++++     
  gene1910|gene1910|rna1910|rna1910  13 PSTELNPICTVKYPKFtLPILNE-PLLLHNLR-WMDGVSTEIIVIGLERYKERVHEIVAESMCKS-KITFIGLLHY 85 
                                        56889999888887762666666.****9986.566788889****************9998666.9****999** PP

                                        -BGGHHHHHTHHHHTTSSE..EEEEETTEEEESTTHHHHHHHHHTHSSTTSEEEEEEESS- CS
                    NTP_transferase  84 kgtAdAvalaaelledeksdelvlvLggDhlikdayeeavkkaiekaakgtvtfgivpvee 144
                                        +gt + ++++++ ++ ++    +++  gD++   +++e+v+ + +++    v ++++++++
  gene1910|gene1910|rna1910|rna1910  86 DGTYHNLKKIIKDIKTTH----IIITKGDIISFVKLKEIVNAFLKRKT--GVFVILKRDAD 140
                                        *****9999998888777....9***********************99..67776666654 PP

>> DUF3795  Protein of unknown function (DUF3795)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   1.3   1.9e-05     0.067      55      83 ..     341     369 ..     312     371 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.9e-05
                            DUF3795  55 aeeCkirkCakekglefCaeCeefpCekl 83 
                                         ++Ckir+C    +++ C  C  ++C+ +
  gene1910|gene1910|rna1910|rna1910 341 GNSCKIRRCLIGSNVTICDGCVLMDCKVT 369
                                        345***********************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (391 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       712  (0.0397122); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 2681.46
//
Query:       gene1911|gene1911|rna1911|rna1911  [L=222]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.2e-10   39.7   0.4    4.8e-09   36.3   0.0    2.6  3  Glutaredoxin  Glutaredoxin
     0.0068   16.5   0.0      0.014   15.5   0.0    1.6  1  SH3BGR        SH3-binding, glutamic acid-rich protein
  ------ inclusion threshold ------
      0.083   12.3   0.5       0.15   11.5   0.1    1.7  2  DUF562        Protein of unknown function (DUF562)


Domain annotation for each model (and alignments):
>> Glutaredoxin  Glutaredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.13   7.5e+02      25      52 ..      57      84 ..      45      87 .. 0.81
   2 ?   -2.4   0.0      0.95   5.7e+03      16      24 ..      99     107 ..      91     120 .. 0.58
   3 !   36.3   0.0     8e-13   4.8e-09       1      59 [.     126     193 ..     126     194 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.13
                                       GEEEEEGCCSHHHHHHHHHHHTSSSSSE CS
                       Glutaredoxin 25 kfeeidvdkdeeireelkelsgvrtvPq 52
                                       ++ +++++  + ++e  ++   v+++P 
  gene1911|gene1911|rna1911|rna1911 57 EYIIVNLSISPVLKERFMKTYSVEKLPI 84
                                       4889999999999999999999999885 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.95
                                        HHHHHHTTG CS
                       Glutaredoxin  16 krlLkelgv 24 
                                         ++Lke++v
  gene1911|gene1911|rna1911|rna1911  99 DAYLKERKV 107
                                        344444444 PP

  == domain 3  score: 36.3 bits;  conditional E-value: 8e-13
                                        EEEEES.....TSSHHHHHHHHHHHHTTGG....EEEEEGCCSHHHHHHHHHHHTSSSSSEEEETTEE CS
                       Glutaredoxin   1 vvlftk.....ptCpyCkkakrlLkelgvk....feeidvdkdeeireelkelsgvrtvPqvfidgkh 59 
                                        v++f k     p C + k  +  ++el +k    + ++++  d + r  lk++++++t+Pq++id  +
  gene1911|gene1911|rna1911|rna1911 126 VMVFIKgspdkPECKFTKELISHFDELQLKngkdYSYFNIKLDNKTRNRLKKRNNWPTFPQIYIDKLF 193
                                        7888888877777777777777777777444555******************************9765 PP

>> SH3BGR  SH3-binding, glutamic acid-rich protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   2.4e-06     0.014      54      96 ..     171     213 ..     125     214 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.4e-06
                                        T-CCCS-SSSS--S-EEEETTEEEEEHHHHHHHHTTT-HHHHH CS
                             SH3BGR  54 apeekkpengkplPPqifnedeYcGDydaffeakeentleefL 96 
                                        + +  k +n+ p+ Pqi+ ++ ++G  d+f + ke+ ++++ L
  gene1911|gene1911|rna1911|rna1911 171 TRNRLKKRNNWPTFPQIYIDKLFVGGLDTFKKMKEKKIVQKML 213
                                        345556788999***************************9876 PP

>> DUF562  Protein of unknown function (DUF562)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.1      0.51   3.1e+03      51      62 ..      33      44 ..      12      64 .. 0.60
   2 ?   11.5   0.1   2.5e-05      0.15      15      68 ..     123     179 ..      91     184 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.51
                             DUF562 51 ylNifsvksest 62
                                       y Ni++ +++++
  gene1911|gene1911|rna1911|rna1911 33 YTNIIAHENDEQ 44
                                       555555555443 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 2.5e-05
                             DUF562  15 eknvvVvlndsklgkesleeeslsklieeLee...sgYSylNifsvksestivkeRr 68 
                                        ek+v+V ++ s  ++e +  ++l     eL+    ++YSy+Ni   ++ +  +k+R+
  gene1911|gene1911|rna1911|rna1911 123 EKKVMVFIKGSPDKPECKFTKELISHFDELQLkngKDYSYFNIKLDNKTRNRLKKRN 179
                                        8899999998877777665555555555665312379******87777778888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       889  (0.0495845); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1479.75
//
Query:       gene1912|gene1912|rna1912|rna1912  [L=307]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.12   12.7   1.1       0.23   11.8   0.1    1.9  2  Orf78     Orf78 (ac78)


Domain annotation for each model (and alignments):
>> Orf78  Orf78 (ac78)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.2      0.33   5.9e+03      36      53 ..      32      49 ..      16      62 .. 0.49
   2 ?   11.8   0.1   1.3e-05      0.23      14      82 ..     236     297 ..     225     303 .. 0.44

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.33
                              Orf78 36 nkkekksaaeknditeke 53
                                       n +e+k+++ +n+i+e++
  gene1912|gene1912|rna1912|rna1912 32 NMREAKESTCNNKISETD 49
                                       233333333344444433 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 1.3e-05
                              Orf78  14 vdyIPLKLAlndldnddndkaenkkekksaaeknditekesnaaekaqalnillisllavvcvlvllyv 82 
                                          y P+ +  n+    + d++   k+ +++++++  +e++++++++ ++ ++    +l+v+c l+++y+
  gene1912|gene1912|rna1912|rna1912 236 SMYNPIGIGTNK----KVDDQ---KTCENVKAESTEEENTKKNMNTYTKFKVAAGIFLVVFCCLLMVYI 297
                                        333333333333....22222...222222333333333333344455555566667778888888886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (307 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1473  (0.0821574); expected 358.6 (0.02)
Passed bias filter:                      659  (0.0367561); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 2004.21
//
Query:       gene1913|gene1913|rna1913|rna1913  [L=170]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.4e-06   27.4   0.1    3.6e-06   26.8   0.1    1.3  1  PUA              PUA domain
  ------ inclusion threshold ------
      0.069   12.8   0.2        3.7    7.1   0.1    2.1  2  Proton_antipo_C  NADH-dehyrogenase subunit F, TMs, (complex I
      0.076   13.3   0.1       0.14   12.5   0.1    1.5  1  UPF0113          UPF0113 PUA domain


Domain annotation for each model (and alignments):
>> PUA  PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8   0.1   6.1e-10   3.6e-06       1      60 [.      80     143 ..      80     156 .. 0.84

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 6.1e-10
                                        CEEEE-HHHHHHHHTT-EEEGGGEEEEETT-....-TTSEEEEEETTSCEEEEEEESS-HHHHH CS
                                PUA   1 grvvvddgAvkallsgasLlapGvvevegdf....eegdvVaivdedgelvavGlanysseela 60 
                                        + v+vd+gA + ll+g+++++pGv ++++ +     ++dvV+i   +  + ++++a+   +e+ 
  gene1913|gene1913|rna1913|rna1913  80 PSVWVDEGARQPLLRGSDIFVPGVYKYKEMIdrefVKNDVVVINIVGYGIFGLAVALIGYKEMS 143
                                        579***********************98766555599******999888888888888888885 PP

>> Proton_antipo_C  NADH-dehyrogenase subunit F, TMs, (complex I) C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.1   0.00062       3.7     185     229 ..      19      63 ..      13      74 .. 0.86
   2 ?    3.9   0.0    0.0058        35     152     182 ..     111     144 ..     103     168 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.00062
                    Proton_antipo_C 185 qnldlinsfvkkgpkrilldkiinviynWSynrgYiDvfYekvlv 229
                                        q+ ++ +++ +  p+++ l+k++n i   S n +Yi + Y+   +
  gene1913|gene1913|rna1913|rna1913  19 QKKKIEKEIGQALPQDTYLHKCKNKIKLLSHNNSYIMFCYNDRWI 63 
                                        56778889999999**************************97655 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.0058
                    Proton_antipo_C 152 wyefltnaifSvsia...lfGifiAsllYkpvys 182
                                          ef++n ++ + i    +fG+ +A++ Yk++  
  gene1913|gene1913|rna1913|rna1913 111 DREFVKNDVVVINIVgygIFGLAVALIGYKEMSA 144
                                        4699999998888862226666799999998765 PP

>> UPF0113  UPF0113 PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   2.3e-05      0.14       2      40 ..      82     123 ..      81     154 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.3e-05
                            UPF0113   2 vvvkekaeklFLYGrdvlkesilkitesvk....enqvvvVln 40 
                                        v+v+e a + +L G d++  ++ k++e ++    +n+vvv+ n
  gene1913|gene1913|rna1913|rna1913  82 VWVDEGARQPLLRGSDIFVPGVYKYKEMIDrefvKNDVVVI-N 123
                                        8*************************766622214555554.4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       520  (0.0290033); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1217.22
//
Query:       gene1914|gene1914|rna1914|rna1914  [L=241]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.047   14.2   3.5        0.9   10.1   0.2    2.3  2  HD-ZIP_N  HD-ZIP protein N terminus


Domain annotation for each model (and alignments):
>> HD-ZIP_N  HD-ZIP protein N terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.2     5e-05       0.9      44      79 ..      15      55 ..       2      78 .. 0.72
   2 ?    4.9   0.4     0.002        37      19      78 ..     113     173 ..      84     193 .. 0.53

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 5e-05
                           HD-ZIP_N 44 lsWnelfssskreaaeaasdvrsflrgidvNraps.....r 79
                                         ++++fs+s+ e+++a+++ + +l +i vN+        +
  gene1914|gene1914|rna1914|rna1914 15 FYFSDIFSTSEDEETNANQENNMLLNTISVNQSHNvrdicS 55
                                       356899****999******************9988433331 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.002
                           HD-ZIP_N  19 eeeesslrlnlaPssslssssslfslsWnelfssskreaaeaasdvr..sflrgidvNraps 78 
                                        +++++  + n  P +sl+s +s+f  + +el s+s +++a++a++ +     + i++N   s
  gene1914|gene1914|rna1914|rna1914 113 HKNDDVNSENDSPCTSLPSYESVFVDNTTELPSMS-TNNARCAKENKllIQTKRIQININTS 173
                                        22223344455555555555555544434444444.66777777777544446677776666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       905  (0.0504769); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1713.99
//
Query:       gene1915|gene1915|rna1915|rna1915  [L=231]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.3e-53  181.2   7.9    3.8e-53  181.0   7.9    1.0  1  Actin_micro  Putative actin-like family
  ------ inclusion threshold ------
       0.53   11.3   0.2       0.53   11.3   0.2    2.9  3  zf-C2H2_4    C2H2-type zinc finger


Domain annotation for each model (and alignments):
>> Actin_micro  Putative actin-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  181.0   7.9   4.2e-57   3.8e-53     200     369 .]       2     231 .]       1     231 [] 0.97

  Alignments for each domain:
  == domain 1  score: 181.0 bits;  conditional E-value: 4.2e-57
                        Actin_micro 200 tnlsl.adeedfvdefrkleelkekkefsCkvCdvkfevekiseHllkkHii........................ 250
                                        +n++l ++ee+fvdef+++ee+k +k+f+C+vC+++f+ e +++H+ kkHi+                        
  gene1915|gene1915|rna1915|rna1915   2 SNITLfRAEEEFVDEFDSWEEFKLDKTFRCDVCGTWFVREGVFMHVVKKHIKngkcecrksknskseevtgvkerc 77 
                                        5788779********************************************************************* PP

                        Actin_micro 251 ................................................kehvkehiteyknkhkdviekigkrlra 278
                                                                                        k+hvk hit y++k+++v++kig++++ 
  gene1915|gene1915|rna1915|rna1915  78 tdehehssnnahelsagdaaehpfnrsegsvsflnvetiknanindsiKQHVKGHIT-YIFKGRSVYDKIGHFIKV 152
                                        *********************************************************.****************** PP

                        Actin_micro 279 klsklerlkkinskvifidldnvtiselkeklafetanvvpeiieeakessilrgakvlkelevsKelWlTDkEWn 354
                                        +l+k erlkkin++ ++   d+ tis++ke+  f+ +++v+ i +    +s++rgak+l++++v+KelW+TDkEWn
  gene1915|gene1915|rna1915|rna1915 153 YLTK-ERLKKINTI-VT---DEGTISKMKEH--FNNFTYVD-IGK----ASAWRGAKDLMRIDVAKELWMTDKEWN 216
                                        ****.*******99.44...799*******9..99******.666....789************************ PP

                        Actin_micro 355 svrlRvLKeKvLFyl 369
                                        ++rlRvLKeK+LFyl
  gene1915|gene1915|rna1915|rna1915 217 ATRLRVLKEKLLFYL 231
                                        *************97 PP

>> zf-C2H2_4  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.2     6e-05      0.53       1      24 []      29      51 ..      29      54 .. 0.75
   2 ?   -2.8   0.5       1.9   1.7e+04       5      13 ..      58      66 ..      56      68 .. 0.64
   3 ?   -0.8   0.0      0.46   4.1e+03      15      23 ..     124     132 ..     121     133 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 6e-05
                          zf-C2H2_4  1 fkCpiCgksFsskkaLlrHlkthH 24
                                       f+C++Cg++F  ++++  H+ + H
  gene1915|gene1915|rna1915|rna1915 29 FRCDVCGTWF-VREGVFMHVVKKH 51
                                       89********.5555566766666 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.9
                          zf-C2H2_4  5 iCgksFssk 13
                                        C+ks +sk
  gene1915|gene1915|rna1915|rna1915 58 ECRKSKNSK 66
                                       687776665 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 0.46
                          zf-C2H2_4  15 aLlrHlkth 23 
                                        ++++H+k h
  gene1915|gene1915|rna1915|rna1915 124 SIKQHVKGH 132
                                        5789*9988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1084  (0.0604607); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1705.49
//
Query:       gene1916|gene1916|rna1916|rna1916  [L=215]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.5e-65  221.8   1.1    1.7e-65  221.6   1.1    1.0  1  Actin_micro  Putative actin-like family


Domain annotation for each model (and alignments):
>> Actin_micro  Putative actin-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  221.6   1.1   9.5e-70   1.7e-65       1     192 [.      11     212 ..      11     215 .] 0.90

  Alignments for each domain:
  == domain 1  score: 221.6 bits;  conditional E-value: 9.5e-70
                        Actin_micro   1 ieqIttanKnitsffmrsdnSyfvkekeryaaYrkdedrvliv.vvedkliisekevetddyfykselnkeeeegl 75 
                                        +++IttanKni+sffmr+d Syfvke+e+y+aY+kd+drvl++ +v+d+++++e+e+++ddy+y+ e      +g+
  gene1916|gene1916|rna1916|rna1916  11 VHTITTANKNIHSFFMRTDISYFVKESECYPAYKKDDDRVLVLrMVDDEIEVHECEDSNDDYEYEGEPE----DGA 82 
                                        69**************************************************************98766....555 PP

                        Actin_micro  76 ieeg...........kiaknikkvsldklfktikeivysLesevl...lkeelk.pkdiFvslvfkdtlnrseila 136
                                          e+           +iak + k ++d+lf+   ++   + s  l   l+++l+ +kd Fv+lvfkdtl+rse+l+
  gene1916|gene1916|rna1916|rna1916  83 EVESnaeaynnlcnlRIAKSVSKYRVDGLFEG--NVLAPVSSTQLlfkLYNNLPcLKDAFVCLVFKDTLRRSELLF 156
                                        555555667999999****************4..444433322223569*****9********************* PP

                        Actin_micro 137 lvdlflnisgfkGilllPesLalclglgiqsaiviseyekhttvslveDyvlldsf 192
                                        l+ ++ln++++kG+lllPesLa+c++l++q+a+vi+++ + t++s+veDyvl++++
  gene1916|gene1916|rna1916|rna1916 157 LIHVMLNHKSGKGMLLLPESLAVCMSLTLQNALVIHNQGDATYISVVEDYVLTEVK 212
                                        *****************************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (215 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       372  (0.0207485); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1605.86
//
Query:       gene1917|gene1917|rna1917|rna1917  [L=302]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.8e-40  136.4   0.1    9.6e-40  136.1   0.1    1.1  1  Proteasome      Proteasome subunit
    5.3e-07   29.2   0.0    1.1e-06   28.2   0.0    1.5  1  Proteasome_A_N  Proteasome subunit A N-terminal signature
  ------ inclusion threshold ------
       0.15   12.4   0.4         17    5.7   0.1    2.7  2  PAS_9           PAS domain


Domain annotation for each model (and alignments):
>> Proteasome  Proteasome subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  136.1   0.1   1.6e-43   9.6e-40       1     189 [.      93     276 ..      93     277 .. 0.94

  Alignments for each domain:
  == domain 1  score: 136.1 bits;  conditional E-value: 1.6e-43
                                        HHHS-EEEEEEETTEEEEEEEEEEEETTEEEESSSSTSEEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHS CS
                         Proteasome   1 vkkGttvvGikgkdgvvlaadkratagskllskstveKifkiddhigvafaGlaaDartlvrraraeaqlyrlryg 76 
                                        v++++t++G++++dg+vl + + +  ++ ++s++  eKi++i+  i+++++G ++D+ +++++ar  aq+y +r+g
  gene1917|gene1917|rna1917|rna1917  93 VSNAGTTLGLTCTDGIVLLGITTTN-KNHIISRN--EKIYRITGSIYCTISGIFSDGLQIISMARFIAQEYLYRNG 165
                                        67899***************97777.56665777..8*************************************** PP

                                        SGTCHHHHHHHHHHHHHHHHHHCTTTTTSEEEEEEEEETTTEEEEEEEETTSEEEEESSEEEESTTHHHHHHHHHH CS
                         Proteasome  77 rpipverlvarvaaklqaytqrsgrrpfgvslliagvdeeggpeLyqidpsGsyieekdavaiGsgseaaktalek 152
                                         ++++ +lv++va ++q  tq +g+rpfgvs+l+a v  ++   Ly++dp+Gs+ +++ a a G++++++ +al++
  gene1917|gene1917|rna1917|rna1917 166 VEMSIGYLVEEVAMRMQYFTQGGGMRPFGVSFLFAQVRGDE-CLLYSTDPAGSCNRWR-AKAFGQKEDSINNALQS 239
                                        **************************************555.9**************5.*****99********** PP

                                        HHSTTBSHHHHHHHHHHHHHHHHHHBTTSCSSEEEEE CS
                         Proteasome 153 eykedltleeavelavkalkealerdklsgknievav 189
                                        +     tlee+v+   k++ +  e  +++  n+ev  
  gene1917|gene1917|rna1917|rna1917 240 NADRQFTLEEGVRECFKVVMQKQEITESNAANYEVLF 276
                                        *************999999999999999999999865 PP

>> Proteasome_A_N  Proteasome subunit A N-terminal signature
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.2   0.0   1.8e-10   1.1e-06       5      22 ..      74      91 ..      73      91 .. 0.95

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 1.8e-10
                     Proteasome_A_N  5 lttFSPdGRLfQVEYAmk 22
                                       ++tF+ +GR++QVEYA+k
  gene1917|gene1917|rna1917|rna1917 74 TNTFNEEGRILQVEYAIK 91
                                       79**************98 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0    0.0084        50       3      25 ..     112     133 ..     105     138 .. 0.80
   2 ?    5.7   0.1    0.0028        17      16      90 ..     218     299 ..     205     302 .] 0.58

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.0084
                              PAS_9   3 gilidnpdgrilyaNeaalrllG 25 
                                        gi  +n+++ i++ Ne+  r++G
  gene1917|gene1917|rna1917|rna1917 112 GITTTNKNH-IISRNEKIYRITG 133
                                        455577777.************9 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0028
                              PAS_9  16 aNeaalrllGyspeevlgks....itdlfvtdpeanerlraaleqgrk...kerevevvlirkngetfwvlltasp 84 
                                        +N+  ++ +G++++ + +       +++   ++  +e ++ +++  +    ++ ++ev +i+k++++f+    + +
  gene1917|gene1917|rna1917|rna1917 218 CNRWRAKAFGQKEDSINNALqsnaDRQFT-LEEGVRECFKVVMQKQEItesNAANYEVLFITKDRSYFLKSEDVKR 292
                                        66666666665544433311111112222.3344444444444444448999***************997766655 PP

                              PAS_9  85 v.kdddg 90 
                                        + +d++g
  gene1917|gene1917|rna1917|rna1917 293 IiRDTKG 299
                                        5344455 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       618  (0.0344693); expected 358.6 (0.02)
Passed bias filter:                      489  (0.0272742); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 2125.10
//
Query:       gene1918|gene1918|rna1918|rna1918  [L=675]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.073   13.2   0.0        1.1    9.5   0.0    2.4  2  FYRC      F/Y rich C-terminus


Domain annotation for each model (and alignments):
>> FYRC  F/Y rich C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0     0.037   6.6e+02      59      76 ..     422     439 ..     404     440 .. 0.87
   2 ?    9.5   0.0   6.1e-05       1.1      49      77 ..     537     565 ..     522     566 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.037
                               FYRC  59 sepaivrlieslpgaekc 76 
                                         +p+i++++ s+p  +k+
  gene1918|gene1918|rna1918|rna1918 422 EHPTIIQCVASMPTLRKL 439
                                        59***********98876 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 6.1e-05
                               FYRC  49 sisGeemfGLsepaivrlieslpgaekct 77 
                                        +is + +fG+++  i+ lie lpg  +++
  gene1918|gene1918|rna1918|rna1918 537 NISKLTLFGFNDRMITSLIEILPGLTTLQ 565
                                        678889******************98775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (675 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       872  (0.0486363); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.25s 00:00:00.82 Elapsed: 00:00:00.41
# Mc/sec: 4934.22
//
Query:       gene1919|gene1919|rna1919|rna1919  [L=184]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.6e-16   60.1   1.2    1.6e-16   60.1   1.2    1.7  2  zf-DBF       DBF zinc finger
     0.0091   16.2   0.1      0.015   15.5   0.1    1.4  1  Dfp1_Him1_M  Dfp1/Him1, central region
  ------ inclusion threshold ------
      0.032   13.6   0.2      0.045   13.1   0.2    1.3  1  NotI         Restriction endonuclease NotI


Domain annotation for each model (and alignments):
>> zf-DBF  DBF zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       1.6   9.4e+03      24      31 ..      21      28 ..      20      31 .. 0.69
   2 !   60.1   1.2   2.7e-20   1.6e-16       1      44 [.      63     106 ..      63     107 .. 0.96

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 1.6
                             zf-DBF 24 kHrkFaen 31
                                       kH+ F ++
  gene1919|gene1919|rna1919|rna1919 21 KHQPFYKE 28
                                       78888754 PP

  == domain 2  score: 60.1 bits;  conditional E-value: 2.7e-20
                             zf-DBF   1 kksGYCEnCrvkfedleeHlksekHrkFaenssnfeelDelisk 44 
                                        +k G+CE+C +k+ +++ H++++ Hr+Fa +s n++++D++i++
  gene1919|gene1919|rna1919|rna1919  63 RKGGFCEICYQKYVSYDAHVRERSHREFALDSRNYKDIDDIIDS 106
                                        589***************************************86 PP

>> Dfp1_Him1_M  Dfp1/Him1, central region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.1   2.5e-06     0.015      73     101 ..       3      30 ..       1      54 [. 0.78

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.5e-06
                        Dfp1_Him1_M  73 kdlhyFkgpyvlveDleqelrpiivreyk 101
                                        k+++ F++py+l+eD++ +++p+  +ey 
  gene1919|gene1919|rna1919|rna1919   3 KKYVIFSKPYILIEDIKGKHQPF-YKEYD 30 
                                        67999*****************7.58883 PP

>> NotI  Restriction endonuclease NotI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.2   7.6e-06     0.045      18      50 ..      40      73 ..      25     114 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 7.6e-06
                               NotI 18 raeekqCPfldeksekctkskadvslGvCsi.kg 50
                                       r+  + CPfl++k  k tk +++   G C i ++
  gene1919|gene1919|rna1919|rna1919 40 RSPALCCPFLKNKRFKSTKRRKERKGGFCEIcYQ 73
                                       566778*************************643 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       506  (0.0282224); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 1313.20
//
Query:       gene192|gene192|rna192|rna192  [L=251]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0017   17.3   6.1     0.0042   16.0   5.0    2.0  2  HECT_2    HECT-like Ubiquitin-conjugating enzyme (E2)-binding
  ------ inclusion threshold ------
      0.023   14.6   0.2      0.053   13.5   0.2    1.5  1  KH_7      KH domain
       0.11   12.4   4.8       0.13   12.2   1.3    2.4  2  DUF3797   Domain of unknown function (DUF3797)


Domain annotation for each model (and alignments):
>> HECT_2  HECT-like Ubiquitin-conjugating enzyme (E2)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   5.0   7.1e-07    0.0042     121     154 ..      70      99 ..      55     158 .. 0.70
   2 ?   -0.5   0.0     0.072   4.3e+02     305     333 ..     184     212 ..     147     235 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 7.1e-07
                         HECT_2 121 knvllksrkikrwkdLPSenwaemmdfWhCHkpd 154
                                    ++++    +++ +  LPS nw+e +d W CH+ +
  gene192|gene192|rna192|rna192  70 NKTI----NYQSLSLLPSHNWHEYIDLWSCHNSE 99 
                                    4444....6788999****************988 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.072
                         HECT_2 305 sssssleaqramKvlYkdeieeedaekll 333
                                     ++++ +   a+Kv +k++++ e + +l+
  gene192|gene192|rna192|rna192 184 GDTKNGRMYPALKVGFKSVKSIERESELM 212
                                    5678889999*******666655555444 PP

>> KH_7  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.2   8.9e-06     0.053      14      56 ..      23      63 ..      19      65 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 8.9e-06
                           KH_7 14 klPkevkitdveFEGPelViYtknpklfaengdlirklAkelr 56
                                    +P+  k+ +ve  G ++ViYt + ++++ +++li  lA++++
  gene192|gene192|rna192|rna192 23 LIPERFKVIHVETSG-NIVIYTIEREYVI-SEQLIVDLASHIK 63
                                   689999*****9999.8***********9.789999***9998 PP

>> DUF3797  Domain of unknown function (DUF3797)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.1     0.086   5.2e+02      31      47 ..      54      70 ..      50      73 .. 0.77
   2 ?   12.2   1.3   2.2e-05      0.13       7      37 ..     121     151 ..     116     160 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.086
                        DUF3797 31 viieddtfyreCkCgfn 47
                                   +i++  ++ +e  C++n
  gene192|gene192|rna192|rna192 54 LIVDLASHIKEIYCSCN 70
                                   67888888888777776 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 2.2e-05
                        DUF3797   7 vkLdekYvqCPeCgNnkvlNsegkviieddt 37 
                                    + +++k ++C +C  +++  +e ++ i++d 
  gene192|gene192|rna192|rna192 121 FMISDKHIYCCKCYKDRIFYNEVNMSISNDD 151
                                    67899********************998874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       790  (0.0440627); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.32s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 1562.88
//
Query:       gene1920|gene1920|rna1920|rna1920  [L=541]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.9e-43  147.8   4.1    5.7e-43  147.3   4.1    1.2  1  UCH       Ubiquitin carboxyl-terminal hydrolase
    2.9e-19   69.8  16.5    2.1e-18   67.0  12.8    2.8  2  UCH_1     Ubiquitin carboxyl-terminal hydrolase


Domain annotation for each model (and alignments):
>> UCH  Ubiquitin carboxyl-terminal hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  147.3   4.1   6.3e-47   5.7e-43       2     257 .]     242     538 ..     241     538 .. 0.91

  Alignments for each domain:
  == domain 1  score: 147.3 bits;  conditional E-value: 6.3e-47
                                        EES-SSSTHHHHHHHHHHHTSHHHHHHHHTCHHCCSSTCCCCC-.TT.TTS.TTHHHHHHHHHHHHHHSH-CCEE- CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                                UCH   2 GlsNlGntCymnsvlQcLfsipelrdyllsleevkkesrnkkelnesnplgkkgelakalkdlfkellkskskavs 77 
                                        G++NlGntCy+ns+lQ++f++  l++ + ++ ++k   +n+k             +++alk+++ e ++  ++ + 
  gene1920|gene1920|rna1920|rna1920 242 GIINLGNTCYINSILQVFFNTGILKKCFFDTMHEKVLCKNEK------------CIVCALKNMYMECYN-LHSLIV 304
                                        99***********************99999655555555553............489*******99996.899*** PP

                                        -HHHHHHHHHHSGGGTSSSTCEHHHHHHHHHHHHHHHHCCHCCCHHH..HHHCCCTTSHHHHHH-EEEEE...... CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxx...... RF
                                UCH  78 PkklkktlsklaksfsgykqqDaqEflaflLdqlhedlnrevaeekw..kkhlkrndslitdlfegqlks...... 145
                                        P++++ +l ++++   +++q Da+Ef+  l + lh+++  + +++    +++  + +++i+++f g l+s      
  gene1920|gene1920|rna1920|rna1920 305 PNEFLYILWSISSVHYSSRQFDAHEFFLDLCELLHKNFFTDPDRQVLgnENTVVKCKCVIHRVFCGVLNStltclk 380
                                        **************999***********************87777779999************************* PP

                                        ......................................................EEEEEEB-SEEEEEEESEEETE CS
                                        ......................................................xxxxxxxxxxxxxxxxxxxxxx RF
                                UCH 146 ......................................................klklkrlPeiLiihlkRfsyns 167
                                                                                              ++++ + P+iL++hlkRf++n+
  gene1920|gene1920|rna1920|rna1920 381 cgcksvkeenfysisigirnqksvndalahffteeslgesvlcqhcerkepflkEMSVASQPPILVLHLKRFQMNK 456
                                        **************************************************************************99 PP

                                        E.EEE--SEEB--SEEE-GGGBSS-BTTS-TCS-BEEEEEEEEEESCTTSEEEEEEEECTTTTEEEEEETTEEEEE CS
                                        x.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                                UCH 168 s.ksKlntkvefpeeldlssylaeekkkkteekkkYeLiavvvHsGslssGHYvayiknekngkWykydDetvkev 242
                                        +   K nt ++f + +++    +     k ++++ Y+L+++v+H G+l++GHY+++ +   ++ W ++dDe+++  
  gene1920|gene1920|rna1920|rna1920 457 NdAVKDNTVLNFSHLVECC---T---L-KSNDSRVYRLFGMVCHVGTLEYGHYFTFLR--VENTWKRFDDERITDA 523
                                        9888888888888555554...3...2.2244567***********************..8899************ PP

                                        -HHCCCTT.CEEEEEE CS
                                        xxxxxxxx.xxxxxxx RF
                                UCH 243 keeeevls.sayiLfY 257
                                        +e++     s+yiLfY
  gene1920|gene1920|rna1920|rna1920 524 NENDMC-DcSPYILFY 538
                                        *88555.45******* PP

>> UCH_1  Ubiquitin carboxyl-terminal hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    2.8   0.1     0.008        72      38     228 ..      37      63 ..      13     179 .. 0.70
   2 !   67.0  12.8   2.4e-22   2.1e-18       7     317 ..     247     517 ..     242     520 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.008
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              UCH_1  38 kkehcLlcElgflfdmldkakglncqasnFlralssipeasalglileeeeetekssaislssliqsfnrflldql 113
                                        +   cL+cE+ f                                                                
  gene1920|gene1920|rna1920|rna1920  37 NIHMCLVCERMF---------------------------------------------------------------- 48 
                                        233455555555................................................................ PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              UCH_1 114 ekelketkknsseeesaieqllgtkaettirclkCgseksrksstlvldlkyPkpsnekkeakvtfasilkssler 189
                                                                                                                    
  gene1920|gene1920|rna1920|rna1920   - ----------------------------------------------------------------------------   -
                                        ............................................................................ PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              UCH_1 190 ekttrawCekCkryqpteqrktvknlPpvLalnakleee 228
                                                                 +P+ La ++++++e
  gene1920|gene1920|rna1920|rna1920  49 ------------------------CFPDHLAHDCGVDKE 63 
                                        ........................555555555555544 PP

  == domain 2  score: 67.0 bits;  conditional E-value: 2.4e-22
                                        xxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              UCH_1   7 ivnsYlNslLQvlyfipplr..nlalshlakeckkehcLlcElgflfdmldkakglncqasnFlralssipeasal 80 
                                         +++Y+Ns+LQv++ +  l    +++ h +  ck+e+c++c l  +++m+     + +  ++Fl  l si+   ++
  gene1920|gene1920|rna1920|rna1920 247 GNTCYINSILQVFFNTGILKkcFFDTMHEKVLCKNEKCIVCALK-NMYMECYNLHSLIVPNEFLYILWSIS---SV 318
                                        589*************9999755678888889*********998.78888888888999999******999...33 PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              UCH_1  81 glileeeeetekssaislssliqsfnrflldqlekelketkknsseeesaieqllgtkaettirclkCgseksrks 156
                                        +   ++ ++   ++++ +  l + +++ ++ +  ++   ++++  + +  i++++   +++t++clkCg ++++++
  gene1920|gene1920|rna1920|rna1920 319 HY--SS-RQF--DAHEFFLDLCELLHKNFFTDPDRQVLGNENTVVKCKCVIHRVFCGVLNSTLTCLKCGCKSVKEE 389
                                        33..22.122..34556788899888888888888888888888999999************************** PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              UCH_1 157 stlvldlkyPkpsnekkeakvtfasilksslerektt.rawCekCkryqpteqrktvknlPpvLalnakleeeeel 231
                                        +++++++           +++++++ l++++++e+      C++C+r++p+ ++ +v + Pp+L+l++k+++ ++ 
  gene1920|gene1920|rna1920|rna1920 390 NFYSISIGI--------RNQKSVNDALAHFFTEESLGeSVLCQHCERKEPFLKEMSVASQPPILVLHLKRFQMNKN 457
                                        *****9944........345789**********88762678*****************************988878 PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              UCH_1 232 elwktknwlpleiklsldedknleeklkeerekakaekeikvYeLqsvvvhigdskesghLvslvkvaekelerdp 307
                                        +  k++++l+ +  ++           +       ++++++vY L+++v+h+g + e gh+ ++ +v+        
  gene1920|gene1920|rna1920|rna1920 458 DAVKDNTVLNFSHLVECC---------T------LKSNDSRVYRLFGMVCHVG-TLEYGHYFTFLRVE-------- 509
                                        888888888866655222.........2......2345789************.766**********3........ PP

                                        xxxxxxxxxx RF
                              UCH_1 308 pesqWylFND 317
                                          + W  F+D
  gene1920|gene1920|rna1920|rna1920 510 --NTWKRFDD 517
                                        ..45888888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (541 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       790  (0.0440627); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.27s 00:00:00.86 Elapsed: 00:00:00.46
# Mc/sec: 3541.91
//
Query:       gene1921|gene1921|rna1921|rna1921  [L=559]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   2.5e-146  488.4   0.0   2.9e-146  488.2   0.0    1.0  1  G_glu_transpept  Gamma-glutamyltranspeptidase


Domain annotation for each model (and alignments):
>> G_glu_transpept  Gamma-glutamyltranspeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  488.2   0.0  1.6e-150  2.9e-146       2     511 ..      43     553 ..      42     554 .. 0.96

  Alignments for each domain:
  == domain 1  score: 488.2 bits;  conditional E-value: 1.6e-150
                                        HHHHTT--HHHHHHHHHHHHHHHSTTT-STTSEEEEEEEETT.SCEEEEEEE--BB-TT--TTTTTSCBCCHHHHS CS
                    G_glu_transpept   2 evLrkGGnAvDAavAaalclgvvepqssGiGGGgfllvydak.tkkvealdaretAPaaatkdmfdkegdsklskt 76 
                                        e++r GGnAvDAavA+a+c+g+++ +ssG+GGGgf+l++  + +++v ++d+retAP +++ d +  ++++++sk+
  gene1921|gene1921|rna1921|rna1921  43 EMIRMGGNAVDAAVASAICVGIINSFSSGLGGGGFMLIKLPGnQNEVVTVDFRETAPWKVNVDDY--KTKKDMSKK 116
                                        799***********************************987515677799***************..********* PP

                                        SGGG-BB--HHHHHHHHHHHH-SS-HHHHHHHHHHHHHH-EE--HHHHHHHHHCHHHHHTSHHHHHHHEETTSE-- CS
                    G_glu_transpept  77 galavgVPGevagleeahkkyGklpwadllepaiklareGfpvsealaralaeaeerlkkdpelaklFlpegevlk 152
                                        g++a+gVPGe++gl+++h kyGklpw+ lle  +++a++ f+vs++l+r l++ ++ + +dp+l+++++++g+ ++
  gene1921|gene1921|rna1921|rna1921 117 GGRAIGVPGEIKGLYHTHLKYGKLPWKFLLEKNAEIAEN-FEVSDQLHRRLKKLKKYIFRDPGLSSIYIRNGDLVQ 191
                                        *************************************86.************************************ PP

                                        TTSEE--HHHHHHHHHHHHHTTHHHHSSHHHHHHHHHHHHTT-S--HHHHHH---EEES-EEEEETTCEEEEE-TT CS
                    G_glu_transpept 153 agellkqpalAktLerlaeeGaeaFYkGelAeklvaelqkagGiltaeDLanykvevreplsadyrggytvyeppp 228
                                        +g++++++++A+tL++la + +e+FY+G +A+++va +q +gG l+++D+ +y+++  +pl+ +y +++ v++++ 
  gene1921|gene1921|rna1921|rna1921 192 PGDMIQRKNYAQTLRTLALD-PESFYRGAIARQIVAAVQSQGGRLSMQDMIKYEIKTPKPLQSTY-KDNLVFTTNL 265
                                        ******************85.89******************************************.9********* PP

                                        CSHHHHHHHHHHHHCTTTGGGCTTTC.....HHHHHHHHHHHHHHHHHHHHH-SSTTTSSSGHCHHHHHT-HHHHH CS
                    G_glu_transpept 229 ssggivllqiLnilegfdlkslssns.....aetlhllvEamklayadRsrylgDpdfvknptelveellskeyak 299
                                        ++ g+ l+++Lnile+fdlk+l+           +hllvE +k++ a+R + lgDp fv++++e++e+l+ske+ak
  gene1921|gene1921|rna1921|rna1921 266 PTAGPLLIEALNILESFDLKELQGIGtehgiFPEYHLLVEIFKFMSAKRGE-LGDPAFVPEAQEIAERLISKEHAK 340
                                        ******************5555433244599999*****************.************************ PP

                                        HHHTT.BTTB..SGGGCSCGGCSCG.TTEEEEEEEEETTS-EEEEEEEESSTTTTSEBETTTTEBE--GGGGSBS. CS
                    G_glu_transpept 300 eraklIkdkaatpsseyykaaeaaeesggTthlsvvDregnaVSltstinllFGsgvvvpgtGilLnnemddfst. 374
                                        ++++ Ik +++    + y+ ++a +e++gTthl+  D++g++V ltstinl+FG++ +   tGi++nne ddf   
  gene1921|gene1921|rna1921|rna1921 341 KVSETIKFDRTLS-IQEYGYENAFTEDHGTTHLNAYDEQGMMVLLTSTINLEFGAKYMDLVTGIIFNNEIDDFYVp 415
                                        ************9.899999******************************************************** PP

                                        TS..TTSCSTTSTTB--TT----B----EEEEETTEEEEEEEEESGGGHHHHHHHHHHHHHTT-S-HHHHHHS--E CS
                    G_glu_transpept 375 gvenafgldpspanaiePgkRplssmaPtivlkdgkpvlvlGaaGGsriisavlqvlvnvldlgldlqeavdapri 450
                                         v+naf+l++s+an i+PgkRp+ss aP++++k  +  l+lGaaGG+ri+++++ ++++ l lg+ l+eav++pr+
  gene1921|gene1921|rna1921|rna1921 416 FVKNAFDLPESQANIIKPGKRPFSSAAPLLLIK-PNQILALGAAGGTRIPTSIISTIFH-LELGKTLSEAVAEPRL 489
                                        ********************************9.8899*******************97.58************** PP

                                        EESSSSTEEEESTTS.HHHHHHHHHTTSEEEESSSTCCCEEEEEEEE...TTTEEEEEE-TTTT CS
                    G_glu_transpept 451 hhqllpdkvevEegfseevveeLearGhkvkevedsssvvaavavak...ekgvleaasDprkd 511
                                        hhq++p ++++E +++ +vv+ L++ G ++ke++++s +++++  +     + ++ea sD+rk 
  gene1921|gene1921|rna1921|rna1921 490 HHQMIPYVTYIEYNLNHDVVNYLAKIGNEIKESSTNSIFTSVQGMIVrknPEIEIEAYSDKRKG 553
                                        **************************************99998887766778899*******96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (559 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       381  (0.0212505); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.32s 00:00:00.88 Elapsed: 00:00:00.47
# Mc/sec: 3547.52
//
Query:       gene1922|gene1922|rna1922|rna1922  [L=209]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.018   15.2   0.5      0.041   14.1   0.1    1.7  2  FMP23     Found in mitochondrial proteome
       0.22   12.2   3.8       0.85   10.3   3.8    2.0  1  BLI1      BLOC-1 interactor 1


Domain annotation for each model (and alignments):
>> FMP23  Found in mitochondrial proteome
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.32   2.9e+03      35      66 ..      29      62 ..      25      72 .. 0.69
   2 ?   14.1   0.1   4.6e-06     0.041      65     115 ..      97     150 ..      73     175 .. 0.71

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.32
                              FMP23 35 yiekfydeleafsnef.l.ekqlkksyadfedeP 66
                                       ++e+  + l++++ne+ l +++++  ++d    P
  gene1922|gene1922|rna1922|rna1922 29 FLEETQESLNKLKNECwLyKEHINTFFSDSGSYP 62
                                       6777788888888887331445566677766555 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 4.6e-06
                              FMP23  65 ePeelvfqlekyielqiiPkyseeaaeksderaal..iqlksl.sdklvieryl 115
                                        + e l+f+++k +e ++iP +s++a++  ++ ++l   +++ l  +k+ +e + 
  gene1922|gene1922|rna1922|rna1922  97 HLETLIFEMKKILECEVIPDHSNSATKYISHLQNLlsGTVELLtEEKICVEGFN 150
                                        5689*******************8887665544444444554414678888774 PP

>> BLI1  BLOC-1 interactor 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   3.8   9.5e-05      0.85      40      98 ..      41     105 ..      15     112 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 9.5e-05
                               BLI1  40 enekWl..eeikekyk....lkdedelkalkalkkkklkkleelekkveyyeklldeleefqdel 98 
                                        +ne Wl  e i++ ++       ++el + ++lk  k+k  e  e+k+ yye+++  le +  e+
  gene1922|gene1922|rna1922|rna1922  41 KNECWLykEHINTFFSdsgsYPSHQELGDESTLKLYKVKYCELNEEKLGYYERIISHLETLIFEM 105
                                        577777434566666411113467899999*****************************998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       887  (0.0494729); expected 358.6 (0.02)
Passed bias filter:                      531  (0.0296168); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 1350.44
//
Query:       gene1923|gene1923|rna1923|rna1923  [L=413]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.5e-39  135.8   1.3    2.3e-39  135.3   1.3    1.1  1  GSH_synth_ATP  Eukaryotic glutathione synthase, ATP binding d
    1.7e-13   50.9   0.7    2.8e-12   47.0   0.0    2.4  2  GSH_synthase   Eukaryotic glutathione synthase
  ------ inclusion threshold ------
        0.2   12.0   6.0        2.3    8.5   0.1    2.8  3  Ta0938         Ta0938


Domain annotation for each model (and alignments):
>> GSH_synth_ATP  Eukaryotic glutathione synthase, ATP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  135.3   1.3   3.8e-43   2.3e-39      34     374 ..      18     411 ..       8     411 .. 0.84

  Alignments for each domain:
  == domain 1  score: 135.3 bits;  conditional E-value: 3.8e-43
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      GSH_synth_ATP  34 sesathapvtLlPspfprklfeeAvevqkayneLyakvasdeefLeevleevikvDeFtakLweiyekvkkeglvq 109
                                        +++++ + vt  Ps+fp++   eA ++qk++n L+ k  +d++     + e++++De  + L++    +k+++ ++
  gene1923|gene1923|rna1923|rna1923  18 TNNFVPINVTRHPSKFPADKVVEALKLQKVMNILLYKAIKDHA-----TYEISTMDEIYNMLVK----MKRTNNKK 84 
                                        556666777899*********************9999999874.....6788889987766665....56666778 PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........xxxxxx.....xxxxx RF
                      GSH_synth_ATP 110 klslglfRsDYllheeeekeelslkqvEfNtisssfgglsskvselhryllk........kekkkk.....sllks 172
                                        kl+l  +R+DYll+++     + lkqvE+Ntis++f  l  +++++h+  +k             k     +l ++
  gene1923|gene1923|rna1923|rna1923  85 KLTLIYMRTDYLLNKD-----YVLKQVEINTISVAFVELNPRLNKVHSVEHKnvwlpenmP----KfvqmvTLVRD 151
                                        9*************94.....68************************99888666653331....24554333344 PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxx................................................... RF
                      GSH_synth_ATP 173 nelpenealeelaeglakAhkaysk................................................... 197
                                        + + +n   + +a  l +  +   +                                                   
  gene1923|gene1923|rna1923|rna1923 152 SFIETNGYNDVIALLLDDNTSLQ-Sanffekknlifelaakgitmlhvtakdieikgvfendkfiydgkcvffvyl 226
                                        43444444444444444444444.34788889999999************************************** PP

                                        ............................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      GSH_synth_ATP 198 ............................PsiatqLagtKkvqqvLakpgvLerfleekeeveklretFaglysLdk 245
                                                                    Psi++q+ g K  q +  +++vL+++l ++++v+++ + F +  +++ 
  gene1923|gene1923|rna1923|rna1923 227 ryfynydhhddnimelrrriensdavtlPSIELQIIGLKMFQVIFESKDVLRKYL-SDAQVKSIYDHFGDFKNIK- 300
                                        ******************************************************6.5589999999999988883. PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      GSH_synth_ATP 246 desegkeavklaleepekyVLKPqrEGGGnNiYgedipefLkklkeeersaYILMelieppavknvlvraegevek 321
                                                 +  + ++++y+LK  rEGG n i  ed ++ ++     e ++Y LM++i++ +v+n       e   
  gene1923|gene1923|rna1923|rna1923 301 ---------DYQTGDENTYILKSMREGG-NTIITEDFQNYIN-----EPDKYFLMKKIDSITVSNRFYT---EKDD 358
                                        .........234567889********75.8898999888876.....5679**************9999...4578 PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      GSH_synth_ATP 322 eevisELGiygtilfkkeevlvneeaGyllRtKasssdegGVaaGfgvlDspl 374
                                         ++i ELG+ gt++  + +v+ ne +G+++R+K++ s+e GV   +g lDs++
  gene1923|gene1923|rna1923|rna1923 359 VDMILELGVLGTLIEYDGNVILNEPSGFICRSKKKGSNECGVTCNYGGLDSVY 411
                                        99*************************************************97 PP

>> GSH_synthase  Eukaryotic glutathione synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.1     0.054   3.2e+02      58      73 ..      78      98 ..      24     129 .. 0.65
   2 !   47.0   0.0   4.6e-16   2.8e-12      11     102 ..     175     261 ..     163     262 .. 0.94

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.054
                                       T.....EEEEEEEECS-SSGG CS
                       GSH_synthase 58 k.....kevsvvYfRagYapk 73
                                       k     k+ + +Y+R+ Y  +
  gene1923|gene1923|rna1923|rna1923 78 KrtnnkKKLTLIYMRTDYLLN 98
                                       133333788889999888654 PP

  == domain 2  score: 47.0 bits;  conditional E-value: 4.6e-16
                                        -TTHHHHHHHHHHHHHCC-EEEEE-HHHHHHHEEE...TT-EEEETTTEEEEEEEECS-SSGGG--SHHHHHHHHH CS
                       GSH_synthase  11 ernvfDqrlleyellekhikvirvtleelkeetkleekekkkllldkkkevsvvYfRagYapkdypseeeweaRll 86 
                                          n+f+++ l +el  k+i++++vt ++++ +  +   e++k ++d+ k v  vY+R++Y+ ++  + +++e+R++
  gene1923|gene1923|rna1923|rna1923 175 SANFFEKKNLIFELAAKGITMLHVTAKDIEIKGVF---ENDKFIYDG-KCVFFVYLRYFYNYDHHDD-NIMELRRR 245
                                        579*****************************977...789999**9.9****************88.6******* PP

                                        HHHSSSEEET-HHHHH CS
                       GSH_synthase  87 lErssaikcPsiayqL 102
                                        +E+s+a+ +Psi+ q+
  gene1923|gene1923|rna1923|rna1923 246 IENSDAVTLPSIELQI 261
                                        **************98 PP

>> Ta0938  Ta0938
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.1    0.0024        14      45      84 ..      68     107 ..      61     122 .. 0.86
   2 ?    8.5   0.1   0.00038       2.3      42      76 ..     322     356 ..     319     363 .. 0.90
   3 ?   -3.6   0.3       2.3   1.4e+04      12      23 ..     390     401 ..     385     404 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0024
                                        S-TTS-THHHHHHHHHHHS---EE---TTT-S--EEEE-- CS
                             Ta0938  45 kefvnllnevkkrtglskideleingnyykgrnveaksge 84 
                                         e+ n+l ++k+  +++k+  + ++ +y   ++ ++k+ e
  gene1923|gene1923|rna1923|rna1923  68 DEIYNMLVKMKRTNNKKKLTLIYMRTDYLLNKDYVLKQVE 107
                                        4789*************************99999888765 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00038
                                        SSSS-TTS-THHHHHHHHHHHS---EE---TTT-S CS
                             Ta0938  42 icakefvnllnevkkrtglskideleingnyykgr 76 
                                        i +++f n +ne  k + ++kid ++++  +y+ +
  gene1923|gene1923|rna1923|rna1923 322 IITEDFQNYINEPDKYFLMKKIDSITVSNRFYTEK 356
                                        67899************************999866 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 2.3
                                        SGGGS-SS---S CS
                             Ta0938  12 tkekgcalcgat 23 
                                        +k+kg   cg t
  gene1923|gene1923|rna1923|rna1923 390 SKKKGSNECGVT 401
                                        788999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (413 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       987  (0.0550505); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.49
# Mc/sec: 2523.86
//
Query:       gene1924|gene1924|rna1924|rna1924  [L=62]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.024   14.7   0.3      0.042   13.9   0.3    1.4  1  DUF1192   Protein of unknown function (DUF1192)


Domain annotation for each model (and alignments):
>> DUF1192  Protein of unknown function (DUF1192)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.3   2.3e-06     0.042      27      47 ..      40      60 ..      37      62 .] 0.88

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.3e-06
                            DUF1192 27 erIalLeaEIaRleaaiakkk 47
                                       + I +L++EI+R+++ i kk 
  gene1924|gene1924|rna1924|rna1924 40 AEIDELKSEIERVSKIINKKP 60
                                       5699**************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (62 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1415  (0.0789224); expected 358.6 (0.02)
Passed bias filter:                      678  (0.0378158); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.29s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 431.92
//
Query:       gene1925|gene1925|rna1925|rna1925  [L=106]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-15   56.2   0.4    2.9e-15   55.7   0.4    1.3  1  LSM       LSM domain
     0.0071   16.0   0.1      0.013   15.1   0.1    1.4  1  Hfq       Hfq protein


Domain annotation for each model (and alignments):
>> LSM  LSM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.7   0.4   3.3e-19   2.9e-15       6      66 ..      14      76 ..       9      77 .. 0.94

  Alignments for each domain:
  == domain 1  score: 55.7 bits;  conditional E-value: 3.3e-19
                                       TTTSEEEEEETTSEEEEEEEEEEETTSEEEEEEEEEEETTET..EEEEEEEEEEEGGGEEEEE CS
                                LSM  6 linkkvtvelkngrelrGtLkgfDqfmNlvLedveetlkdkk..ekrklglvliRGnnivlis 66
                                       ++++ v++ l +gr   G+L++fDqf N+ Le+++ ++   +   +r+lgl +iRG+ni+li+
  gene1925|gene1925|rna1925|rna1925 14 FLDNHVVIYLHDGRYMYGILRSFDQFNNITLEQTVCRIFIDDeyAERRLGLHVIRGENIILIG 76
                                       6899*********************************9999999*****************97 PP

>> Hfq  Hfq protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.1   1.5e-06     0.013      14      37 ..      17      40 ..      15      51 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.5e-06
                                       -EEEEEETTS-EEEEEEEEE-SSE CS
                                Hfq 14 ipvtifLvnGiklkGviksfDnft 37
                                       ++v+i+L  G  + G+++sfD+f 
  gene1925|gene1925|rna1925|rna1925 17 NHVVIYLHDGRYMYGILRSFDQFN 40
                                       579********************5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       351  (0.0195772); expected 358.6 (0.02)
Passed bias filter:                      250  (0.0139439); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 676.46
//
Query:       gene1926|gene1926|rna1926|rna1926  [L=122]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.3e-29  101.3   0.0    5.7e-29  101.2   0.0    1.0  1  PGK       Phosphoglycerate kinase
  ------ inclusion threshold ------
        0.1   12.2   0.3       0.19   11.3   0.3    1.4  1  SH3_1     SH3 domain


Domain annotation for each model (and alignments):
>> PGK  Phosphoglycerate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.2   0.0   6.4e-33   5.7e-29     273     377 ..       7     109 ..       1     110 [. 0.93

  Alignments for each domain:
  == domain 1  score: 101.2 bits;  conditional E-value: 6.4e-33
                                        EEEECCG--TT-EEEEE-HHHHHHHHHHHCC-SEEEEES-SS-TTSGCCCHHHHHHHHHHHHHCH.TSEEEEESHH CS
                                PGK 273 kvveveaipedemalDigpktielfaeaikeaktvvwnGpmGvfeiekfakGTkaiakalaeatk.galsivGGgd 347
                                        + + v++i++++m++Digp++++++++ ++++++++wnGp+G+fe ek a+GT+++++ l  a+k g +++vGGg+
  gene1926|gene1926|rna1926|rna1926   7 QYKVVNRIDDGWMGVDIGPESLKELERLVNNSQSIFWNGPVGMFEDEKCANGTEKLVRLLEMAQKkGKYVLVGGGE 82 
                                        5566899*****************************************************99888799******** PP

                                        HHHHHHHTT-GGGSSEEESSSHHHHHHHCT CS
                                PGK 348 saaaveklgladkvshvStGGgAsLelLeg 377
                                        +a a++++g+   ++ vStGGgA+L+++eg
  gene1926|gene1926|rna1926|rna1926  83 TAYAARMFGH---LENVSTGGGALLSYMEG 109
                                        *********7...6789************9 PP

>> SH3_1  SH3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.3   2.1e-05      0.19      17      34 ..       3      20 ..       2      24 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 2.1e-05
                                       STTEEEEEEEECSSSEEE CS
                              SH3_1 17 kkGDviivleksedgWwk 34
                                       k GD+++v+++ +dgW+ 
  gene1926|gene1926|rna1926|rna1926  3 KNGDQYKVVNRIDDGWMG 20
                                       78**************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       436  (0.0243181); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 882.93
//
Query:       gene1927|gene1927|rna1927|rna1927  [L=216]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-31  110.1   0.0    1.5e-31  109.8   0.0    1.1  1  PGK       Phosphoglycerate kinase


Domain annotation for each model (and alignments):
>> PGK  Phosphoglycerate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.8   0.0   8.1e-36   1.5e-31       2     226 ..       9     215 ..       8     216 .] 0.82

  Alignments for each domain:
  == domain 1  score: 109.8 bits;  conditional E-value: 8.1e-36
                                        GGS--TT-EEEEEE-----EECTTEES--HHHHHHHHHHHHHHHTT-E.EEEEE--S--TTS-..........GGG CS
                                PGK   2 kdldlkgkrvlvRvDfNvplkkegkitddtriraalpTikyllekgak.vvllsHlgrpkgek..........ekl 66 
                                         d+ lk k+v++ +DfNvp+ + g+i d+ ri+++lpTi y+l+++   +v+++Hlgrp+ ++             
  gene1927|gene1927|rna1927|rna1927   9 YDVPLKHKKVVLYADFNVPIVE-GEIADTFRIEKTLPTIIYVLSQEPDlLVIMTHLGRPDIHEkkcfvegkgkLAN 83 
                                        6999****************86.**********************99889*********65332233333333566 PP

                                        -SHHHHHHHHHHHTT-EEEESSTTSHHHHHHHHT-TTT-EEEES-GGGSTTTTTT-HHHHHHHHHT-SEEEE--GG CS
                                PGK  67 slkpvaerLsellgkeVkfvedvvgeeveeaiaelkegevllLeNvrfykeEekndeelakklasladvyVnDAFg 142
                                        +l pv   Ls+ ++  ++fv+d+     +   +  +++  +lLeN+r y++       + ++l  ++d+ + D+Fg
  gene1927|gene1927|rna1927|rna1927  84 TLLPVYTWLSQRIN--IEFVRDL-----D---NLYEKKGTVLLENTRLYEKA-----YIINRL-YFIDLVIFDGFG 143
                                        68888888888886..8888552.....2...334566789*******9776.....466666.578********* PP

                                        GTTS--TTTTHHHHCSEEEE-HHHHHHHHHHHHHHHS--SSEEEEEEES-HHHCHHHHHHHTTT-SEEEEETCHHH CS
                                PGK 143 tahrahaStvgiakvlsaaaGllmekElealskvlenperplvailGGakvsdkikvienLlekvdkliigGgman 218
                                        +ahr       i+k  + +aGllm++Ele   + ++      ++i+GG+k+ dk+++i++L  k+ +++ gGgm++
  gene1927|gene1927|rna1927|rna1927 144 VAHRP----LIIPKNKKVYAGLLMRAELERRLDNFD------LVIMGGRKITDKMALIKHL--KFKNIFFGGGMCF 207
                                        ****6....568888877**********87766665......9*****************9..7889********* PP

                                        HHHHHTT- CS
                                PGK 219 tFlkaqgl 226
                                          lk +++
  gene1927|gene1927|rna1927|rna1927 208 SILKQKKY 215
                                        ****9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (216 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       279  (0.0155614); expected 358.6 (0.02)
Passed bias filter:                      247  (0.0137766); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1543.18
//
Query:       gene1928|gene1928|rna1928|rna1928  [L=351]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.7e-20   73.0   0.1      4e-20   71.8   0.1    1.7  1  Ribosomal_L10  Ribosomal protein L10
    5.6e-20   71.1   0.3    9.3e-20   70.4   0.3    1.4  1  RL10P_insert   Insertion domain in 60S ribosomal protein L10P
  ------ inclusion threshold ------
        0.1   12.0   0.0       0.17   11.2   0.0    1.4  1  DUF1186        Protein of unknown function (DUF1186)


Domain annotation for each model (and alignments):
>> Ribosomal_L10  Ribosomal protein L10
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.8   0.1   6.8e-24     4e-20       2      98 ..      96     190 ..      95     192 .. 0.97

  Alignments for each domain:
  == domain 1  score: 71.8 bits;  conditional E-value: 6.8e-24
                                        SCCCHCCCCCCCCCCCTTSSEEEEEE-TTS-HHHHHHCCCHHHHHGCEEEEESCCCCCCCCHCCTSS.SSCGCCSS CS
                      Ribosomal_L10   2 tkekKeelvkelkellkkyksvvvvdyegltvaqlqelRkklrengaelkvvKntlmrrAleetgeeeklkellkg 77 
                                         ke+K+ l+++ k+ + +y+++++v ++++t++qlq  ++++ ++ ae+ ++Knt +++Al++ g++ ++ + + g
  gene1928|gene1928|rna1928|rna1928  96 PKERKQLLFSRTKDYFTQYSQFIIVGLNNVTSSQLQSAKQAWHGK-AEFLFGKNTTVKKALRDMGHD-DIVSRIFG 169
                                        69******************************************9.********************9.8******* PP

                                        SEEEEEESS-TCHHHHCCCCC CS
                      Ribosomal_L10  78 pvalvftnedpvalakvleef 98 
                                        +va++ftn+d+ +++ ++e++
  gene1928|gene1928|rna1928|rna1928 170 NVAFIFTNGDVREIKHIVEDN 190
                                        *******************98 PP

>> RL10P_insert  Insertion domain in 60S ribosomal protein L10P
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.4   0.3   1.6e-23   9.3e-20       1      71 []     196     265 ..     196     265 .. 0.99

  Alignments for each domain:
  == domain 1  score: 70.4 bits;  conditional E-value: 1.6e-23
                       RL10P_insert   1 AraGtiAtedviipagplelaPgsiepeLrklglptklkkGkivleedylvckkGetltseqaqlLklLgi 71 
                                        A++G+iA+ dv+i+++ +++ P+++ +++++lg+ tk++kGk+++ ++ +  ++Ge++t++qa+lL +++i
  gene1928|gene1928|rna1928|rna1928 196 AKVGAIAQTDVWIEKKVTNMGPDKT-SFFQALGISTKITKGKVEIIQNSKALTAGEKVTPSQANLLAIMDI 265
                                        9************************.******************************************998 PP

>> DUF1186  Protein of unknown function (DUF1186)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   2.9e-05      0.17      95     144 ..     162     211 ..     148     248 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 2.9e-05
                            DUF1186  95 DvvteDlerilasvsdGnvepikeLieneevneyvrgaalksllvLlaee 144
                                        D+v   ++ +    ++G+v  ik+++e+++ n++ ++ a+    v + ++
  gene1928|gene1928|rna1928|rna1928 162 DIVSRIFGNVAFIFTNGDVREIKHIVEDNKRNTFAKVGAIAQTDVWIEKK 211
                                        6666667777777789************************8877666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (351 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       591  (0.0329634); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 2296.81
//
Query:       gene1929|gene1929|rna1929|rna1929  [L=334]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.5e-61  204.8   0.4    7.7e-61  204.3   0.4    1.2  1  Gp_dh_C       Glyceraldehyde 3-phosphate dehydrogenase, C-ter
    8.6e-23   80.6   0.0    2.6e-22   79.1   0.0    1.8  1  Gp_dh_N       Glyceraldehyde 3-phosphate dehydrogenase, NAD b
  ------ inclusion threshold ------
      0.044   13.1   0.1       0.11   11.9   0.0    1.6  2  AIG1          AIG1 family
      0.073   12.4   0.0       0.15   11.4   0.0    1.5  1  2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, 


Domain annotation for each model (and alignments):
>> Gp_dh_C  Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  204.3   0.4   1.7e-64   7.7e-61       1     158 []     156     312 ..     156     312 .. 0.97

  Alignments for each domain:
  == domain 1  score: 204.3 bits;  conditional E-value: 1.7e-64
                                        HHHHHHHHHHHHEEEEEEEEEEEECTTTSBSSSS--.SSTTTTSBTTCSSEEEE-THHHHHHHHSGGGTTTEEEEE CS
                            Gp_dh_C   1 LaplakvlndkfgikkglmttvhaytndQkllDgpskkdlrraraaaeniiptstgaakavglVlpelkgkldglA 76 
                                        Lap+ak+++d+f i++glm t+ha+t++Qk++D++skk+ r +r   +niip+stgaakavg+V+p+l+gkl+g+A
  gene1929|gene1929|rna1929|rna1929 156 LAPIAKAIHDEFVIVEGLMSTIHAATATQKVVDTVSKKNRRLSR-SFSNIIPSSTGAAKAVGKVIPDLNGKLTGMA 230
                                        8**********************************965555555.679**************************** PP

                                        EEESSSSEEEEEEEEEESSTS-HHHHHHHHHHHHHTTTTTTEEEEHSHHHGGGGTTGCSSEEEEGGGCEEETTTEE CS
                            Gp_dh_C  77 vrVPtpnvsvvdlvvelekevtveevnaalkeaaegalkgilsyteeelvssDlvgdphssifdaketivveenlv 152
                                        +rVP++nvsvvdl+v+++ke t e++n+ +++aaeg++kgi++yt+ee+vssD++g+++ss++d+k++i+++++++
  gene1929|gene1929|rna1929|rna1929 231 FRVPVMNVSVVDLTVRTQKECTLEQINECIRKAAEGRMKGIVAYTDEEIVSSDINGSEYSSVYDSKAGIQLNKTFF 306
                                        **************************************************************************** PP

                                        EEEEEE CS
                            Gp_dh_C 153 kvvawy 158
                                        kvv+wy
  gene1929|gene1929|rna1929|rna1929 307 KVVSWY 312
                                        *****9 PP

>> Gp_dh_N  Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.1   0.0   5.8e-26   2.6e-22       2     100 ..       6     104 ..       5     105 .. 0.95

  Alignments for each domain:
  == domain 1  score: 79.1 bits;  conditional E-value: 5.8e-26
                                        EEEEESTSHHHHHHHHHHHHHTTCEEEEEE-.TS-HHHHHHHHHEETTTEC-SS-EEEETTEEEETTEEEEEE--S CS
                            Gp_dh_N   2 kvainGfGRIGrlvlralleekelevvaind.ltdletlayllkyDsvhgrfkgeveaeeealvvngkkikvlaek 76 
                                         v+inGfGRIG++v+r++ + +  ++  ind ++d+ t+ay l yDsv  + ++ v++ e+++   g++ kv+++ 
  gene1929|gene1929|rna1929|rna1929   6 IVGINGFGRIGKIVYRVMRQ-RGHKIPLINDpAIDACTAAYALTYDSVTPQKERAVKTGENEFKYLGETTKVTTHC 80 
                                        59**************8765.589*******99******************************************* PP

                                        SGGGS-CHHHTSSEEEE-SSS--S CS
                            Gp_dh_N  77 dpeelpwkelgvdlVvestGvftd 100
                                        +p+ +pw+++gv++V+e++G+f +
  gene1929|gene1929|rna1929|rna1929  81 EPKLIPWRDHGVEVVIEASGFFLE 104
                                        *********************975 PP

>> AIG1  AIG1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   2.4e-05      0.11      22     104 ..      63     146 ..      60     153 .. 0.83
   2 ?   -3.2   0.0      0.99   4.4e+03      64      83 ..     247     266 ..     235     278 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.4e-05
                                        TS--SS--TTTS---SS-EEEEEEETTEEEE.EEE--SCCCTTCCHHCHHHHHHHHHHHCTT-ESEEEEEEETTB- CS
                               AIG1  22 gkkaFesklsaqsvtkkcqkksrtwdgkkin.ViDTPglfdlsvsadkiskeivrclllseegihalllvlslgrf 96 
                                        g++ F+   ++++vt++c+ k   w+++ ++ Vi++ g f  +++  + +k   + + +++++++a ++v+ +++ 
  gene1929|gene1929|rna1929|rna1929  63 GENEFKYLGETTKVTTHCEPKLIPWRDHGVEvVIEASGFFLEHEKCMAHIKAGAKKVVITAPSPDAKMFVMGVNEN 138
                                        7889999999*****************99973589***9777777666777777789**************99966 PP

                                        SHHHHHHH CS
                               AIG1  97 teedekal 104
                                        + + e+++
  gene1929|gene1929|rna1929|rna1929 139 DYNGEEVV 146
                                        65555555 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 0.99
                                        CCHHCHHHHHHHHHHHCTT- CS
                               AIG1  64 vsadkiskeivrclllseeg 83 
                                        ++++ + ++i +c+  ++eg
  gene1929|gene1929|rna1929|rna1929 247 TQKECTLEQINECIRKAAEG 266
                                        34455556666666666655 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   3.4e-05      0.15      39      68 ..       7      36 ..       2      57 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3.4e-05
                                       EEEES-SHHHHHHHHHHHHTT-EEEEESSS CS
                       2-Hacid_dh_C 39 vGiiGlGrIGqavakrlkafgmkviaydrs 68
                                       vGi G+GrIG+ v +++++ g k+  ++  
  gene1929|gene1929|rna1929|rna1929  7 VGINGFGRIGKIVYRVMRQRGHKIPLINDP 36
                                       9******************99999766654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (334 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       742  (0.0413855); expected 358.6 (0.02)
Passed bias filter:                      554  (0.0308997); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 2357.71
//
Query:       gene193|gene193|rna193|rna193  [L=357]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-20   73.5   0.1      2e-20   72.8   0.1    1.3  1  Acyltransferase  Acyltransferase
  ------ inclusion threshold ------
      0.025   14.7   1.1      0.058   13.5   1.1    1.7  1  Acyltransf_C     Acyltransferase C-terminus


Domain annotation for each model (and alignments):
>> Acyltransferase  Acyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.8   0.1   2.2e-24     2e-20       8     132 ..      79     232 ..      73     235 .. 0.82

  Alignments for each domain:
  == domain 1  score: 72.8 bits;  conditional E-value: 2.2e-24
                Acyltransferase   8 enlpekgpailvaNHqsylDvlllwlllyksn.gprnvviiakkellsipllgflmrllgfifidRksnaraagslenis 86 
                                    +++ +k+++++++NHq+++D+l++  +l+k + + r+v i++k +l++ip++g +m+++g++fi+R s +++ ++l++ +
  gene193|gene193|rna193|rna193  79 KQILQKKRCLVISNHQTNYDWLIILIVLQKFDmY-RDVCILVKSSLAQIPIFGSAMKAFGYVFIKR-SWSEDLNTLKKSL 156
                                    455668**********************999966.*******************************.7777778888877 PP

                Acyltransferase  87 e.lleegkl.vviFPEGtrsre.........................gellpfkkGlvrlaakak...kgvpivPv 132
                                    + l  ++kl  +iFPEGt +                             l p   G  ++  ++k   +g+++v++
  gene193|gene193|rna193|rna193 157 NyLHTKSKLfFLIFPEGTILVPsthsksitysqkmnvklrdtsfspqNVLIPRTSGTNMIYNELKdtmEGIIDVTL 232
                                    7666666888*******99888777777888888888888877776444478888888887777777777777776 PP

>> Acyltransf_C  Acyltransferase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   1.1   6.5e-06     0.058      30      55 ..     273     307 ..     267     340 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 6.5e-06
                   Acyltransf_C  30 aeWlhelfeeKDklleeFyktgtFe.........p 55 
                                    + Wl+e+fe+K+ l+e++++  + +          
  gene193|gene193|rna193|rna193 273 KDWLYEIFEKKEILIEKYKQSCQLFksiedvndfT 307
                                    68*****************9655553555444442 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (357 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       672  (0.0374812); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 2381.40
//
Query:       gene1930|gene1930|rna1930|rna1930  [L=136]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       490  (0.02733); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 998.96
//
Query:       gene1931|gene1931|rna1931|rna1931  [L=100]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       582  (0.0324614); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 699.09
//
Query:       gene1932|gene1932|rna1932|rna1932  [L=138]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       657  (0.0366445); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.44
# Mc/sec: 949.65
//
Query:       gene1933|gene1933|rna1933|rna1933  [L=58]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (58 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       465  (0.0259356); expected 358.6 (0.02)
Passed bias filter:                      227  (0.0126611); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.29s 00:00:00.69 Elapsed: 00:00:00.45
# Mc/sec: 385.70
//
Query:       gene1934|gene1934|rna1934|rna1934  [L=694]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.5e-30  103.8   0.0    2.5e-29  102.1   0.0    1.9  1  E1-E2_ATPase  E1-E2 ATPase
    1.3e-24   87.7   0.0      2e-24   87.1   0.0    1.3  1  Hydrolase     haloacid dehalogenase-like hydrolase
    1.9e-05   25.0   0.2    4.7e-05   23.8   0.2    1.7  1  HMA           Heavy-metal-associated domain
  ------ inclusion threshold ------
      0.011   15.9   0.1      0.026   14.6   0.1    1.6  1  Hydrolase_6   Haloacid dehalogenase-like hydrolase
       0.16   12.3   0.0       0.61   10.5   0.0    1.9  2  HAD           haloacid dehalogenase-like hydrolase


Domain annotation for each model (and alignments):
>> E1-E2_ATPase  E1-E2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.1   0.0   6.9e-33   2.5e-29      16     179 ..     191     346 ..     172     348 .. 0.90

  Alignments for each domain:
  == domain 1  score: 102.1 bits;  conditional E-value: 6.9e-33
                                        EEEEGGG--TTSEEEEETT-B--SEEEEEEE-SEEE-TTTS---S-EE-G-TTEE-TT-EEEE-EEEEEEEE-TTT CS
                       E1-E2_ATPase  16 eeidakelvpGDivllkagdrvpaDgrivegsaevdesaLTGEslpvekekgdmvfsGtvvvsgeakavVtatged 91 
                                        ++ + +e++ G ++++++++ +  Dg+++eg + vdes+LTGE +  ek+kgd ++s t ++ g++++ V ++ge+
  gene1934|gene1934|rna1934|rna1934 191 KNLNYEEIKEGHVIVVEKEKHILFDGIVMEGASYVDESSLTGEIKLKEKKKGDHIHSDTYNKTGRIIVHVRRVGEE 266
                                        348899********************************************************************** PP

                                        STTTTTSTTS--------HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTTSSTTHHHHHHHHHHHHHS-TTHHHHH CS
                       E1-E2_ATPase  92 telgkiarlveeakskktplqkkldklgkvlvpvvlliallvflialllgkslaeallralallvaaiPcaLplav 167
                                        t lgk+ +++  +       + + +++++ +++++++ +  ++l a  l+ +la+a+  +l+ll++a+PcaL +  
  gene1934|gene1934|rna1934|rna1934 267 TSLGKLLKQIDHS------SVSNTNEITGLFIFIIFVTIGSFMLCA--LNTPLAQAIETSLSLLIIACPCALNISE 334
                                        ***********98......577889999999999998888888887..5566679********************* PP

                                        HHHHHHHHHHHH CS
                       E1-E2_ATPase 168 plalalgarrla 179
                                        pl++++g+++l 
  gene1934|gene1934|rna1934|rna1934 335 PLTILIGTKKLF 346
                                        *********996 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.1   0.0   5.6e-28     2e-24       3     208 ..     366     601 ..     364     603 .. 0.77

  Alignments for each domain:
  == domain 1  score: 87.1 bits;  conditional E-value: 5.6e-28
                                        EEEEESBTTTBCHHHHHHHHHHHHCHHHHHHHHHH......HHCHHHHHHHHHHHHH......HHHHHHHHH..ET CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxx......xxxxxxxxx..xx RF
                          Hydrolase   3 tvvfDkdGTLttgepsvedvivsaalalaaaletg......sehpigkalvaaakar......sgaltgfat..fi 64 
                                        ++++Dk+GTLt+g+  v+d+i+   l+++ +  ++      s hpi+  l++++         +    ++    ++
  gene1934|gene1934|rna1934|rna1934 366 VLFIDKTGTLTDGTFIVKDFINTSSLDISTVKTLVhtlerrSYHPIASTLTEYCMVSamgevlK---YEMMSngIK 438
                                        799*********************66666666666779999*************9999643320...222222233 PP

                                        TTE.......HHHHTHHHHHHHH...........HCHHHHHHHHHHHHHHCHHHHHH................... CS
                                        xxx.......xxxxxxxxxxxxx...........xxxxxxxxxxxxxxxxxxxxxxx................... RF
                          Hydrolase  65 grg.......ayaigkpewltal...........dippdlgaaigsaqsqgrtvall................... 103
                                        gr         ++ig+  +l a+                                 +                   
  gene1934|gene1934|rna1934|rna1934 439 GRVryrnahyDVQIGNDGLLSANikngrcfetnrS------------------IKDEnyetdnvpkrindknyaly 496
                                        34488888888888888888888444443322220..................22222223333444445566667 PP

                                        .............TTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHHTTGGGESEEEEH CS
                                        .............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          Hydrolase 104 .............qaralavftiadplkvkpeaaeavasLkaagievvlltgdnpetaeraanqlGddyfdavias 166
                                                     ++++  vf ++d+  +  +a  a++ L++++i +++ltgd+ ++a+r+a++l+          
  gene1934|gene1934|rna1934|rna1934 497 tpdedlisvyvivNDELTCVFYLEDK--IVNGASSALKLLNEQNITTIMLTGDSYRNAMRIAHRLN---------- 560
                                        7777777778888*************..**************************************.......... PP

                                        HCES.STTTSHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHHH CS
                                        xxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          Hydrolase 167 diet.vakpspegkvaaireLqgkpeevamVGDgvnDaaalaa 208
                                         i++  a     +k  +i+ +  k++ v mVGDg+nD +a+a 
  gene1934|gene1934|rna1934|rna1934 561 -ISKvYANKTAIHKSNIIQNY-RKGHVVGMVGDGINDYSAIAH 601
                                        .66669999************.89999*************997 PP

>> HMA  Heavy-metal-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.2   1.3e-08   4.7e-05       1      58 [.       7      66 ..       7      70 .. 0.84

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 1.3e-08
                                HMA  1 tvrvsgmhCagCaakvekvLselpgVesvkvdlatktvtVeg..daestklrkiieaiek 58
                                       t+++ +++C++C  k++k L +l+ V++vk++  tk+v+ e    ++s+k++ i++a+ +
  gene1934|gene1934|rna1934|rna1934  7 TLKIANITCGSCIPKIQKCLRGLEYVNDVKINIFTKEVQLEMhtLIDSAKIKHIKRALNE 66
                                       6899************************************99874444555667777655 PP

>> Hydrolase_6  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.1   7.4e-06     0.026       8      64 ..     516     572 ..     512     587 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 7.4e-06
                                        TSEETTEE-TTHHHHHHHHHHTT-EEEEEE---SS-HHHHHHHHHHTT----GGGEE CS
                        Hydrolase_6   8 vLwrgdkaipgaaealnalraagkpvvllTNnsskseeeyakkleklgvditeeqvv 64 
                                        v++ +dk+++ga  al+ l+++++++++lT  s ++   +a++l+   v +++  + 
  gene1934|gene1934|rna1934|rna1934 516 VFYLEDKIVNGASSALKLLNEQNITTIMLTGDSYRNAMRIAHRLNISKVYANKTAIH 572
                                        78999*******************************999999997766666555444 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       2.3   8.2e+03     136     165 ..      36      67 ..      25      72 .. 0.73
   2 ?   10.5   0.0   0.00017      0.61      89     136 ..     526     573 ..     500     601 .. 0.77

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 2.3
                                HAD 136 d..rltgelglegkpvrgegkvaalrewlaae 165
                                        +   +t+e+ le +   +++k++++++ l ++
  gene1934|gene1934|rna1934|rna1934  36 KinIFTKEVQLEMHTLIDSAKIKHIKRALNEN 67 
                                        14489999999999999999999999955444 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00017
                                HAD  89 galellaahraaGdrvvvvSgglrplvepllaelgadevlatelevdd 136
                                        ga  +l+   ++++++++++g   +++ +++ +l++  v+a++ + ++
  gene1934|gene1934|rna1934|rna1934 526 GASSALKLLNEQNITTIMLTGDSYRNAMRIAHRLNISKVYANKTAIHK 573
                                        6777777777*****************************999666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (694 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       760  (0.0423894); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.60u 0.29s 00:00:00.88 Elapsed: 00:00:00.43
# Mc/sec: 4835.19
//
Query:       gene1935|gene1935|rna1935|rna1935  [L=40]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (40 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       297  (0.0165653); expected 358.6 (0.02)
Passed bias filter:                      165  (0.00920297); expected 358.6 (0.02)
Passed Vit filter:                         5  (0.000278878); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.43
# Mc/sec: 280.53
//
Query:       gene1936|gene1936|rna1936|rna1936  [L=502]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.066   12.9   0.8       0.12   12.0   0.8    1.3  1  FAM176     FAM176 family
       0.15   11.5   0.0       0.64    9.4   0.0    1.8  2  Rax2       Cortical protein marker for cell polarity


Domain annotation for each model (and alignments):
>> FAM176  FAM176 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.8   1.3e-05      0.12      43      86 ..     424     470 ..     420     484 .. 0.48

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.3e-05
                             FAM176  43 iriscrkdle...rlkkkkkklkeesekasededeeeeeeeedsses 86 
                                         r+ c+++ +   ++++ +k+++++++k+ e+e +eeeeeee+++++
  gene1936|gene1936|rna1936|rna1936 424 CRVLCKPQPKmiaKKEPVRKTTRDRKKKKVEEESSEEEEEEETHNKK 470
                                        67778877765555555555555444444222222222222222222 PP

>> Rax2  Cortical protein marker for cell polarity
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.1       0.1   9.3e+02      23      82 ..      23      86 ..      15     100 .. 0.72
   2 ?    9.4   0.0   7.2e-05      0.64     143     171 ..     457     485 ..     431     501 .. 0.70

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.1
                               Rax2 23 pvtsftladsdisqlwvagkss.ngssf..llkydgskWssiddinlgesttirglqvlslt..n 82
                                        ++++ ++++   ++ v+gk +  ++s   + k ++s++ ++ +   +++t++ + +++ ++   
  gene1936|gene1936|rna1936|rna1936 23 DINEMQPVTDIKVDYFVNGKQKsLDDSCikVQKCKDSSYDTVIS-GCRSETSFASSSIIRVKffA 86
                                       67777777777778888888776555552467899999999985.59999999999888887542 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 7.2e-05
                               Rax2 143 ksnsfssssdlkkkkkklsrgfVVlIgLA 171
                                        +s + + +++ +kkkkklsrg+V++I+ +
  gene1936|gene1936|rna1936|rna1936 457 SSEEEEEEETHNKKKKKLSRGVVIGISCC 485
                                        444445556677**************977 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (502 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1862  (0.103854); expected 358.6 (0.02)
Passed bias filter:                     1026  (0.0572257); expected 358.6 (0.02)
Passed Vit filter:                       151  (0.00842211); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.71u 0.30s 00:00:01.01 Elapsed: 00:00:00.44
# Mc/sec: 3461.03
//
Query:       gene1937|gene1937|rna1937|rna1937  [L=598]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (598 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1075  (0.0599587); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.43
# Mc/sec: 4170.21
//
Query:       gene1938|gene1938|rna1938|rna1938  [L=51]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (51 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       642  (0.0358079); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.25s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 380.13
//
Query:       gene1939|gene1939|rna1939|rna1939  [L=77]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       980  (0.05466); expected 358.6 (0.02)
Passed bias filter:                      681  (0.0379832); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.31s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 499.95
//
Query:       gene194|gene194|rna194|rna194  [L=219]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      9e-20   72.0   2.1    1.3e-19   71.5   2.1    1.3  1  AAA_23       AAA domain
    2.2e-16   60.0   0.3    2.5e-16   59.8   0.3    1.1  1  SMC_N        RecF/RecN/SMC N terminal domain
    1.7e-12   47.8   8.7    2.1e-12   47.5   8.7    1.1  1  AAA_15       AAA ATPase domain
    4.1e-09   36.0   0.0    8.2e-09   35.1   0.0    1.5  1  AAA_29       P-loop containing region of AAA domain
    5.8e-06   26.0   0.1    9.8e-06   25.3   0.1    1.4  1  AAA_27       AAA domain
    4.4e-05   23.5   0.6    4.4e-05   23.5   0.6    1.4  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    0.00061   20.3   0.1    0.00085   19.8   0.1    1.6  1  ABC_tran     ABC transporter
     0.0013   17.5   0.4     0.0038   15.9   0.0    1.8  2  AAA_13       AAA domain
     0.0013   18.7   0.0     0.0038   17.2   0.0    1.7  1  RsgA_GTPase  RsgA GTPase
     0.0023   17.9   0.2        2.2    8.1   0.0    2.2  2  Rad17        Rad17 P-loop domain
  ------ inclusion threshold ------
      0.017   14.4   0.1      0.038   13.3   0.0    1.6  2  Zeta_toxin   Zeta toxin
      0.027   15.0   0.1      0.066   13.8   0.1    1.9  1  AAA_18       AAA domain
      0.031   14.0   0.0      0.071   12.8   0.0    1.6  1  PRK          Phosphoribulokinase / Uridine kinase family
      0.043   12.9   0.2      0.083   12.0   0.0    1.5  2  FH2          Formin Homology 2 Domain
      0.068   13.6   0.0       0.15   12.4   0.0    1.6  1  AAA          ATPase family associated with various cellular a
      0.069   12.7   0.0        7.4    6.0   0.0    2.3  2  AAA_7        P-loop containing dynein motor region
       0.09   13.1   0.0       0.13   12.7   0.0    1.6  1  AAA_16       AAA ATPase domain
       0.15   12.1   0.0        0.5   10.4   0.0    1.8  2  AAA_5        AAA domain (dynein-related subfamily)
       0.17   10.9   0.0       0.25   10.4   0.0    1.2  1  T2SSE        Type II/IV secretion system protein


Domain annotation for each model (and alignments):
>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.5   2.1   1.4e-22   1.3e-19       1     170 [.      12     168 ..      12     218 .. 0.62

  Alignments for each domain:
  == domain 1  score: 71.5 bits;  conditional E-value: 1.4e-22
                         AAA_23   1 kLkienfrsfrdqeidFskgltlItGpNGaGKTTildAiklaLygetprlsrksgrgfeksdveiesegkvkayveltfe 80 
                                    +L+++nf+ ++d+++dF++ l+ I GpNG+GK+Ti +Ai ++++g t+ ls+ ++      d+  +++ ++++y+e++++
  gene194|gene194|rna194|rna194  12 SLQLHNFQTYSDVKFDFHPRLNFIAGPNGSGKSTIANAIAFIFGGSTKVLSKAKD----LMDFI-KFD-TNDSYIEIKIK 85 
                                    69*******************************************9999988765....33443.333.56789*****9 PP

                         AAA_23  81 nkdgrytrsiererelskkkgkttkkak.lelleideleqfisellgskkiilnlilflgqerfeefelkdkkerleele 159
                                    ++++   ++i  +r l   k+++  + +  +  +i+  +q+ +el   k +i+n++ +l+qe+ +ef + +++e  + ++
  gene194|gene194|rna194|rna194  86 YTGKV--TTI--RRALVPLKNSSLWFLNgCSTPYIK-IQQMYNEL---KININNICNYLPQEKVAEFTRFSPEELFRTFI 157
                                    99993..333..444444444455444404444444.45666654...33478999999999977777766666555555 PP

                         AAA_23 160 keleeledekk 170
                                    + + e++ ++k
  gene194|gene194|rna194|rna194 158 ETYHEQNIVDK 168
                                    55444433332 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.8   0.3   2.7e-19   2.5e-16       2     135 ..      10     130 ..       9     202 .. 0.81

  Alignments for each domain:
  == domain 1  score: 59.8 bits;  conditional E-value: 2.7e-19
                                    EEEEEEESETTEECEEEEEETTSSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N   2 lkrleienFksyagktvilpfsksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaevei 81 
                                    + +l+++nF++y  + v+ +f++++++i GpNGSGKs + +Ai F++G +++   ++++l d i+       ++  ++ei
  gene194|gene194|rna194|rna194  10 IISLQLHNFQTY--SDVKFDFHPRLNFIAGPNGSGKSTIANAIAFIFGGSTKVLSKAKDLMDFIKF-----DTNDSYIEI 82 
                                    66899*******..69********************************876655688889999987.....677888888 PP

                                    EEEETTEESSSSSSCEEEEEEEE.TTSEEEEEETTEEE-HHHHHHHHHCTT-STT CS
                                    xxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N  82 tfdnedkklkiekeevsisrrvk.rkgeseykingkevtkkevsellesagiske 135
                                     ++ ++k        ++i+r ++  k++s +++ng +  + +++++ ++ +i+++
  gene194|gene194|rna194|rna194  83 KIKYTGKV-------TTIRRALVpLKNSSLWFLNGCSTPYIKIQQMYNELKININ 130
                                    88889998.......89999876256778999********************998 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.5   8.7   2.2e-15   2.1e-12       3     176 ..      10     173 ..       9     217 .. 0.68

  Alignments for each domain:
  == domain 1  score: 47.5 bits;  conditional E-value: 2.2e-15
                         AAA_15   3 IkkikikNFRslkdveidlseeltvliGkNnsGKSsilealdlFlnnkekknkkvikiekedleifeniseskdikIdve 82 
                                    I ++++ NF  ++dv+ d+ + l+++ G+N+sGKS+i++a+ +++  +     kv+ ++k+ ++  + + ++  i+I+++
  gene194|gene194|rna194|rna194  10 IISLQLHNFQTYSDVKFDFHPRLNFIAGPNGSGKSTIANAIAFIFGGS----TKVLSKAKDLMDFIKFDTNDSYIEIKIK 85 
                                    678999****************************************99....7899999999999999999999999999 PP

                         AAA_15  83 f....................aekekakeyektlkskekkkadlllkkkesdlkktikdkklklkknelsdekisvekkk 142
                                    +                                               ++     +ik ++++++ + ++++++++  ++
  gene194|gene194|rna194|rna194  86 YtgkvttirralvplknsslwF--------------------------LNGCSTPYIKIQQMYNELKININNICNYLPQE 139
                                    9333333333333222222220..........................22333456667777777777777777777777 PP

                         AAA_15 143 skkelpkekeeklekekeelkidkedlkklikkl 176
                                    +  e+  ++ e+l     e+ +++++++k+   +
  gene194|gene194|rna194|rna194 140 KVAEFTRFSPEELFRTFIETYHEQNIVDKINTLI 173
                                    7777777777777777777777777777765533 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.1   0.0   8.7e-12   8.2e-09       3      51 ..      12      59 ..      10      63 .. 0.92

  Alignments for each domain:
  == domain 1  score: 35.1 bits;  conditional E-value: 8.7e-12
                         AAA_29  3 rlqlvNWgtfdghtieidlkgatlltGpsGsGKSTllDAiqalLvpakk 51
                                   +lql N +t+++ +++++++   +++Gp+GsGKST+  Ai++++ +++k
  gene194|gene194|rna194|rna194 12 SLQLHNFQTYSDVKFDFHPRL-NFIAGPNGSGKSTIANAIAFIFGGSTK 59
                                   69****************996.********************9988875 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.1     1e-08   9.8e-06       3      52 ..      10      55 ..       9      77 .. 0.90

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 1e-08
                         AAA_27  3 lerLdLeryGkftdrsldfsaeeadlhliyGpNEAGKstalrAisdllfG 52
                                   + +L+L+ +  ++d ++df+   ++l +i GpN +GKst+ +Ai  ++fG
  gene194|gene194|rna194|rna194 10 IISLQLHNFQTYSDVKFDFH---PRLNFIAGPNGSGKSTIANAIA-FIFG 55
                                   6689***************8...9*******************96.5555 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.6   4.6e-08   4.4e-05       1      31 [.      32      56 ..      32      93 .. 0.73
   2 ?   -3.5   0.0       7.4     7e+03     168     185 ..     152     169 ..     135     188 .. 0.53

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 4.6e-08
                         AAA_21  1 lnvliGpNgsGKSnLLdaldllarldrdveg 31
                                   ln++ GpNgsGKS++  a+ ++++      g
  gene194|gene194|rna194|rna194 32 LNFIAGPNGSGKSTIANAIAFIFG------G 56
                                   79*******************964......2 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 7.4
                         AAA_21 168 llnifadyfgfakekrll 185
                                    l++ f+++++++++ + +
  gene194|gene194|rna194|rna194 152 LFRTFIETYHEQNIVDKI 169
                                    333333333333333333 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.1   9.1e-07   0.00085      13      35 ..      32      54 ..      21     191 .. 0.74

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 9.1e-07
                                   EEEEEESTTSSHHHHHHHHTTSS CS
                                   xxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran 13 kvaivGenGaGKStLlkllagll 35
                                   +  i G+nG+GKSt+++++a   
  gene194|gene194|rna194|rna194 32 LNFIAGPNGSGKSTIANAIAFIF 54
                                   55799*************98665 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0     4e-06    0.0038      16      39 ..      30      53 ..      16      84 .. 0.83
   2 ?   -0.7   0.1      0.43     4e+02     294     346 ..     159     209 ..     139     217 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 4e-06
                         AAA_13 16 kriNliYGwNGaGKTtLSrllrsl 39
                                    r N+i G NG+GK+t++++++ +
  gene194|gene194|rna194|rna194 30 PRLNFIAGPNGSGKSTIANAIAFI 53
                                   599******************986 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.43
                         AAA_13 294 kveskkselleklkavsdeasensafeedkeelkaeaealeeqLkglqralea 346
                                    ++ ++  ++++k+++++d + ++     d e++  ++ a+e+ + g++r +e+
  gene194|gene194|rna194|rna194 159 TYHEQ--NIVDKINTLIDMEGFYDSLSGDLEKILCNKMAIEKVISGMSRDIEK 209
                                    44444..5777777778877777777777777777777777777777777654 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0     4e-06    0.0038      80     150 ..      11     101 ..       6     107 .. 0.70

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 4e-06
                                    EE--TTTHTTHHHHHHHCTTSEEEEECSTTSSHHHHHHHHCTT.....................-----S---------- CS
                    RsgA_GTPase  80 llvsaktkegleelkellkdktsvlvGqSGvGKStLinallpe.....................lelktgevseklgrGk 138
                                    + ++ ++ ++++++k  ++ ++ +++G+ G GKSt+ na++                       ++ +  e++ k  +Gk
  gene194|gene194|rna194|rna194  11 ISLQLHNFQTYSDVKFDFHPRLNFIAGPNGSGKSTIANAIAFIfggstkvlskakdlmdfikfdTNDSYIEIKIK-YTGK 89 
                                    5566677789999**************************987655666666666666666554333333344332.4566 PP

                                    ----SEEEEEET CS
                    RsgA_GTPase 139 hTTtavellela 150
                                     TT ++ l++l+
  gene194|gene194|rna194|rna194  90 VTTIRRALVPLK 101
                                    666666666666 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.0    0.0024       2.2      46      73 ..      31      58 ..      15      91 .. 0.85
   2 !    7.8   0.3    0.0029       2.8      71     142 ..     123     195 ..     108     215 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0024
                          Rad17 46 riLLisGPsGCgkstvvkvLskelgikl 73
                                   r+  i+GP G gkst+ + ++ ++g + 
  gene194|gene194|rna194|rna194 31 RLNFIAGPNGSGKSTIANAIAFIFGGST 58
                                   5778************999998887665 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0029
                          Rad17  71 iklrewlnpvslkepdnqksdfkgltekesrflsqiesfkeleLkdakylklqklG..ddlrtdkklilvedlP 142
                                     +l+ ++n +    p+ ++ +f   +  e+ f + ie+++e ++ d  +  +++ G  d l +d++ il + + 
  gene194|gene194|rna194|rna194 123 NELKININNICNYLPQEKVAEFTR-FSPEELFRTFIETYHEQNIVDKINTLIDMEGfyDSLSGDLEKILCNKMA 195
                                    345566777776778999999975.666777******************9999999778999999999987765 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0     4e-05     0.038      14      37 ..      28      51 ..      17      65 .. 0.87
   2 ?   -3.8   0.0       6.8   6.4e+03     159     177 ..     196     214 ..     192     216 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4e-05
                     Zeta_toxin 14 erPklillgGqpGAGKselaellk 37
                                    +P l +++G  G+GKs++a++++
  gene194|gene194|rna194|rna194 28 FHPRLNFIAGPNGSGKSTIANAIA 51
                                   5899****************9986 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 6.8
                     Zeta_toxin 159 hdeafeglresvealeeek 177
                                    ++++ +g+++ +e+++e+k
  gene194|gene194|rna194|rna194 196 IEKVISGMSRDIEKVKEKK 214
                                    5677788888888888876 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1     7e-05     0.066       2      21 ..      34      53 ..      34     169 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 7e-05
                         AAA_18  2 lltGtpGvGKttlakeLskr 21
                                   +++G+ G+GK+t+a++++  
  gene194|gene194|rna194|rna194 34 FIAGPNGSGKSTIANAIAFI 53
                                   69*************99644 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   7.6e-05     0.071       4      51 ..      35      83 ..      34      95 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 7.6e-05
                            PRK  4 vagsSGaGkttvarklekifgre.kvkaaeiegdsflrldraekdlele 51
                                   +ag+ G+Gk+t+a+++  ifg+  kv ++  +++ f+++d  +  +e++
  gene194|gene194|rna194|rna194 35 IAGPNGSGKSTIANAIAFIFGGStKVLSKAKDLMDFIKFDTNDSYIEIK 83
                                   89******************97614556666888888888777666665 PP

>> FH2  Formin Homology 2 Domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   8.8e-05     0.083     319     366 ..     107     158 ..      89     162 .. 0.80
   2 ?   -3.0   0.0       3.1   2.9e+03     279     297 ..     194     212 ..     170     217 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 8.8e-05
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHT.T--TT...CCHHHHHHHHHHH CS
                            FH2 319 flkeaeeklkkleeelkeakelvkelveYf.gedkk...evspeeffkilre 366
                                    fl+ +++ + k++++++e+k + +++++Y+ +e+     ++spee+f+++ e
  gene194|gene194|rna194|rna194 107 FLNGCSTPYIKIQQMYNELKININNICNYLpQEKVAeftRFSPEELFRTFIE 158
                                    999***************************6444444556677777776654 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 3.1
                                    HHHHHHHHHHHHHHHHHHH CS
                            FH2 279 eslekevkklekglkklek 297
                                     ++ek ++ ++++++k+++
  gene194|gene194|rna194|rna194 194 MAIEKVISGMSRDIEKVKE 212
                                    4556666666666666665 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00016      0.15       3      23 ..      35      55 ..      34      97 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00016
                                   EESSTTSSHHHHHHHHHHHHT CS
                            AAA  3 lyGppGtGKTllakavakelg 23
                                   + Gp G GK+++a+a+a  +g
  gene194|gene194|rna194|rna194 35 IAGPNGSGKSTIANAIAFIFG 55
                                   68***************8875 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0     0.027        26      38      52 ..      35      49 ..      29      76 .. 0.88
   2 ?    6.0   0.0    0.0078       7.4     114     144 ..     157     187 ..     150     202 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.027
                          AAA_7 38 lvGptGtGKtviikd 52
                                   + Gp G+GK++i++ 
  gene194|gene194|rna194|rna194 35 IAGPNGSGKSTIANA 49
                                   78**********987 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0078
                          AAA_7 114 kekygaqppiellRqlldyggwYdrkklefk 144
                                     e+y +q+ +  +  l+d++g+Yd    +++
  gene194|gene194|rna194|rna194 157 IETYHEQNIVDKINTLIDMEGFYDSLSGDLE 187
                                    69**********************8554444 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00013      0.13      23      48 ..      29      54 ..      13     192 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00013
                         AAA_16 23 rpelvllsGesGvGKsslvrellral 48
                                    p+l ++ G+ G+GKs+++++++  +
  gene194|gene194|rna194|rna194 29 HPRLNFIAGPNGSGKSTIANAIAFIF 54
                                   567889**************998544 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00053       0.5       3      28 ..      34      59 ..      33      69 .. 0.83
   2 ?   -1.7   0.0       2.8   2.6e+03     117     117 ..     157     157 ..      87     179 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00053
                                   EEE--SSSSHHHHHHHGGGGBS--EE CS
                          AAA_5  3 lLvGppGtgKselaerlaaalnreve 28
                                   ++ Gp G+gKs++a  +a  ++ ++ 
  gene194|gene194|rna194|rna194 34 FIAGPNGSGKSTIANAIAFIFGGSTK 59
                                   578***************99966655 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2.8
                                    E CS
                          AAA_5 117 i 117
                                    i
  gene194|gene194|rna194|rna194 157 I 157
                                    2 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00026      0.25     134     165 ..      35      66 ..      28      97 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00026
                          T2SSE 134 vsGgTgsGKttllyallkeinksderivtvED 165
                                    ++G+ gsGK+t+++a+  ++  s++ +  + D
  gene194|gene194|rna194|rna194  35 IAGPNGSGKSTIANAIAFIFGGSTKVLSKAKD 66 
                                    89*************98877777666655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       775  (0.0432261); expected 358.6 (0.02)
Passed bias filter:                      514  (0.0286686); expected 358.6 (0.02)
Passed Vit filter:                        87  (0.00485247); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 1387.16
//
Query:       gene1940|gene1940|rna1940|rna1940  [L=60]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (60 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       461  (0.0257125); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); expected 358.6 (0.02)
Passed Vit filter:                         5  (0.000278878); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 453.05
//
Query:       gene1941|gene1941|rna1941|rna1941  [L=304]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (304 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       573  (0.0319594); expected 358.6 (0.02)
Passed bias filter:                      466  (0.0259914); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 2177.18
//
Query:       gene1942|gene1942|rna1942|rna1942  [L=109]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-39  134.5  10.7    1.3e-39  134.3  10.7    1.0  1  DUF5101   Domain of unknown function (DUF5101)
     0.0047   16.5   1.2     0.0047   16.5   1.2    2.1  3  PikAIV_N  Narbonolide/10-deoxymethynolide synthase PikA4 N-te


Domain annotation for each model (and alignments):
>> DUF5101  Domain of unknown function (DUF5101)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  134.3  10.7   1.4e-43   1.3e-39       1      98 [.       1      98 [.       1      99 [. 0.99

  Alignments for each domain:
  == domain 1  score: 134.3 bits;  conditional E-value: 1.4e-43
                            DUF5101  1 mrlkleektneekkevkkkkkkklsdkekvleylkevkaktkdysLkYDlskCiEileGkEnqevvelkealeevleE 78
                                       mr++l+ek++++k+++++k++k+l+dk++vl++l++v+++t+d+sLkYDl+kC+E++eGkEn+e+velk+al+e+leE
  gene1942|gene1942|rna1942|rna1942  1 MRIPLSEKNTRSKQSQMHKQHKQLTDKQRVLNFLCDVTNTTNDHSLKYDLMKCVETIEGKENVEYVELKGALREALEE 78
                                       9***************************************************************************** PP

                            DUF5101 79 nEklvkekvdLiaeleilke 98
                                       nE+l ++kv+L++e+e+lke
  gene1942|gene1942|rna1942|rna1942 79 NERLEQDKVKLMCENEYLKE 98
                                       *******************8 PP

>> PikAIV_N  Narbonolide/10-deoxymethynolide synthase PikA4 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0      0.58   5.2e+03      22      29 ..      19      26 ..      19      26 .. 0.78
   2 !   16.5   1.2   5.3e-07    0.0047       9      22 ..      71      84 ..      70      86 .. 0.92
   3 ?   -1.7   0.0      0.25   2.2e+03      16      22 ..      92      98 ..      90      98 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 0.58
                           PikAIV_N 22 qqNrrLtA 29
                                       +q+ +Lt+
  gene1942|gene1942|rna1942|rna1942 19 KQHKQLTD 26
                                       58999985 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 5.3e-07
                           PikAIV_N  9 ALRaSLkEnERLRq 22
                                       ALR++L EnERL q
  gene1942|gene1942|rna1942|rna1942 71 ALREALEENERLEQ 84
                                       9***********77 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 0.25
                           PikAIV_N 16 EnERLRq 22
                                       EnE L++
  gene1942|gene1942|rna1942|rna1942 92 ENEYLKE 98
                                       9999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1586  (0.08846); expected 358.6 (0.02)
Passed bias filter:                      477  (0.0266049); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 867.62
//
Query:       gene1943|gene1943|rna1943|rna1943  [L=296]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      0.008   16.3   0.0      0.013   15.6   0.0    1.5  1  DUF1080   Domain of Unknown Function (DUF1080)
  ------ inclusion threshold ------
      0.079   12.8   0.1       0.18   11.7   0.1    1.5  1  Monellin  Monellin
       0.15   12.8   3.2       0.59   10.9   3.2    2.0  1  DUF4829   Domain of unknown function (DUF4829)


Domain annotation for each model (and alignments):
>> DUF1080  Domain of Unknown Function (DUF1080)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   2.2e-06     0.013     106     173 ..      84     196 ..      42     218 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.2e-06
                                        TSBTTT.........................BTTB--SSS--S--TTSEEEEEEEEETTEEEEEETTEEEEEEETT CS
                            DUF1080 106 Gslyde.........................eskqvkpkakaakppgeWntyeiivkgdrvtvwlNGvlvldftdl 156
                                        G+ +d+                         + +q ++++  +k+ +++ ++++++++d+++ w+NGv  +d++ +
  gene1943|gene1943|rna1943|rna1943  84 GKAFDVffklnivdncqlklilylkyknmsfDYRQSSNSKALDKNLKKYGECTVECDKDEIKKWHNGVHFVDYALK 159
                                        55555555555555555555555555555553345567788889999999************************99 PP

                                        SHHHHHH....................SSBEEEEECC CS
                            DUF1080 157 daetekg....................kkgpIaLqdh 173
                                        +  + +                     +  +IaL+ +
  gene1943|gene1943|rna1943|rna1943 160 KHSEPNIikrflelfepdppeiyglkaHVSYIALEEQ 196
                                        9876555666777776666666666666666666655 PP

>> Monellin  Monellin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   2.9e-05      0.18       2      24 ..     249     272 ..     248     274 .. 0.95

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.9e-05
                           Monellin   2 Eikiieiqly.vYAsdkLfkadvd 24 
                                        E++++ i  + vY s+k++  d++
  gene1943|gene1943|rna1943|rna1943 249 EWNGYKINIFnVYTSEKIGTVDIS 272
                                        9*********9************9 PP

>> DUF4829  Domain of unknown function (DUF4829)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   3.2   9.9e-05      0.59      36     108 ..      90     162 ..      60     165 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 9.9e-05
                            DUF4829  36 fenlenskliniseeseekqklkyikylkgeennvkaenvkiy.kVefdlkykkkvspvesgkqewffiLvred 108
                                        f++l+  +  + ++    k k+++  y +++  +  ++n+k+y + +++   k++++++ +g + +++ L++ +
  gene1943|gene1943|rna1943|rna1943  90 FFKLNIVDNCQLKLILYLKYKNMSFDYRQSSNSKALDKNLKKYgECTVEC-DKDEIKKWHNGVHFVDYALKKHS 162
                                        45555555555555557889999999*999999999****9993456666.5677777*************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (296 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       659  (0.0367561); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.66u 0.33s 00:00:00.99 Elapsed: 00:00:00.57
# Mc/sec: 1561.76
//
Query:       gene1944|gene1944|rna1944|rna1944  [L=39]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.084   12.7   0.0       0.09   12.6   0.0    1.0  1  PhoQ_Sensor  PhoQ Sensor


Domain annotation for each model (and alignments):
>> PhoQ_Sensor  PhoQ Sensor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0     5e-06      0.09      32      58 ..       7      33 ..       4      36 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5e-06
                        PhoQ_Sensor 32 lvsfdkttyrllrgesnlfyslaqwed 58
                                        +s+dk t ++lr+e   +  laq+e+
  gene1944|gene1944|rna1944|rna1944  7 NISYDKDTINFLRNEQHHYNLLAQYEK 33
                                       58**********************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (39 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       551  (0.0307323); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.37s 00:00:00.86 Elapsed: 00:00:00.53
# Mc/sec: 219.68
//
Query:       gene1945|gene1945|rna1945|rna1945  [L=261]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.9e-24   84.9   1.3    4.3e-24   84.3   1.3    1.3  1  dCMP_cyt_deam_1  Cytidine and deoxycytidylate deaminase zinc-
    7.1e-17   61.4   0.1      1e-16   60.9   0.1    1.2  1  MafB19-deam      MafB19-like deaminase
  ------ inclusion threshold ------
      0.079   13.0   0.6       0.16   12.1   0.5    1.6  1  Bd3614-deam      Bd3614-like deaminase


Domain annotation for each model (and alignments):
>> dCMP_cyt_deam_1  Cytidine and deoxycytidylate deaminase zinc-binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.3   1.3   7.3e-28   4.3e-24       3      99 ..     118     233 ..     116     235 .. 0.95

  Alignments for each domain:
  == domain 1  score: 84.3 bits;  conditional E-value: 7.3e-28
                                        HHHHHHHHHHHHHHHHHTTTSCSEEEEEEETTEEEEEEESBHHCCTG.......................TTB-HH CS
                    dCMP_cyt_deam_1   3 kdekllelalkaakeaqkcsnfkVGavivkngeiistgyngepaggs.......................ktiHAE 55 
                                        ++ +++++a  ++ ++ +c + +VGav+vk ++i+stgyng++ g                          ++HAE
  gene1945|gene1945|rna1945|rna1945 118 WETYFMDIATFVSHRS-ACAKRNVGAVLVKGNRIVSTGYNGTAMGTLncidggcprccsgtpsgsnldlcVCLHAE 192
                                        889*************.*************99**********98877***************************** PP

                                        HHHHHHHHHHTSSCETTEEEEEEE--BHHHHHHHHHHT-SEEEE CS
                    dCMP_cyt_deam_1  56 vnAilkaaknggsklegatlyvtlePCsmCakaiiqsgikkvvv 99 
                                         +A++ ++++   +l g+ lyvtl+PC  Cak iiq++ik+v++
  gene1945|gene1945|rna1945|rna1945 193 ESAMMGVVSE---RLSGCDLYVTLFPCMLCAKKIIQAQIKRVIF 233
                                        ********66...7899*************************98 PP

>> MafB19-deam  MafB19-like deaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.9   0.1   1.7e-20     1e-16       3     113 ..     118     254 ..     116     258 .. 0.94

  Alignments for each domain:
  == domain 1  score: 60.9 bits;  conditional E-value: 1.7e-20
                        MafB19-deam   3 kekafrkalaevekatkikedkigavivkdkkviargsn.......................ekelnakataHaEi 55 
                                        +e +f+ ++  v++++ + ++ +gav vk+++++ +g+n                         +l+  +  HaE 
  gene1945|gene1945|rna1945|rna1945 118 WETYFMDIATFVSHRSACAKRNVGAVLVKGNRIVSTGYNgtamgtlncidggcprccsgtpsGSNLDLCVCLHAEE 193
                                        899**********************************************************999************ PP

                        MafB19-deam  56 aalqqAakklkskrlddatlyvtlepCdmCagaivqaglkklvygagnpks.......lnkLkvk 113
                                         a++       s rl+++ lyvtl pC+ Ca+ i+qa++k+++++  +  s       l++Lk++
  gene1945|gene1945|rna1945|rna1945 194 SAMMGV----VSERLSGCDLYVTLFPCMLCAKKIIQAQIKRVIFKNYYCASdvesrklLEELKIE 254
                                        *99976....8899*****************************9988877777888888888875 PP

>> Bd3614-deam  Bd3614-like deaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.5   2.6e-05      0.16      77     115 ..     206     241 ..     192     246 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.6e-05
                        Bd3614-deam  77 garllvtlqcCkmCAalvvaaadapgrevllkvvYleed 115
                                        g  l+vtl +C +CA  +++a     ++v+ k +Y   d
  gene1945|gene1945|rna1945|rna1945 206 GCDLYVTLFPCMLCAKKIIQAQI---KRVIFKNYYCASD 241
                                        789***************99877...6777888887766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       661  (0.0368676); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.60u 0.35s 00:00:00.95 Elapsed: 00:00:00.54
# Mc/sec: 1443.03
//
Query:       gene1946|gene1946|rna1946|rna1946  [L=322]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-33  116.0   0.6    1.9e-33  115.6   0.6    1.1  1  adh_short        short chain dehydrogenase
    1.2e-19   70.8   0.3    1.5e-19   70.5   0.3    1.1  1  adh_short_C2     Enoyl-(Acyl carrier protein) reductase
    0.00011   22.1   0.4    0.00017   21.5   0.4    1.3  1  KR               KR domain
     0.0082   15.3   0.2       0.01   15.0   0.2    1.3  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
  ------ inclusion threshold ------
      0.041   14.2   0.2      0.093   13.0   0.2    1.6  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
       0.13   11.6   0.3        2.5    7.5   0.0    2.2  2  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas


Domain annotation for each model (and alignments):
>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.6   0.6   6.2e-37   1.9e-33       2     189 ..      75     253 ..      74     258 .. 0.92

  Alignments for each domain:
  == domain 1  score: 115.6 bits;  conditional E-value: 6.2e-37
                                        EEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSS CS
                          adh_short   2 vvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgk 77 
                                        ++++tGa++GIG+++a  lak+  ++++v+r++ekl+++ +e+ ++ ++   i +D + +++ ++++       ++
  gene1946|gene1946|rna1946|rna1946  75 WIMITGATDGIGKEMALILAKMRQNIIIVGRNAEKLAATQAEISKL-TQCKSILMDFAVEQSFDDVIT------DN 143
                                        799*****************************************97.8999******97777777765......67 PP

                                        ESEEEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHHHHH CS
                          adh_short  78 ldvLvnNAGitgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYsAsK 153
                                        + +L+nNAG++   +   ++ee++ ++i+vN   +++lt++vl++m+  +   I+n++S ++  p +  ++Y+AsK
  gene1946|gene1946|rna1946|rna1946 144 IGMLINNAGVSSEYTKDFVDEERITQIINVNNLNAIKLTQSVLKKMD--KYSYIINIGSKVADFPCPLHVVYAASK 217
                                        **********7777777777777**********************99..8889*********************** PP

                                        HHHHHHHHHHHHHHGGGTEEEEEEEESSBSSHHHHH CS
                          adh_short 154 aavagltrslakelaptgirvnavaPGlvdTdmake 189
                                          +++++ sla el+ + i v  + P +v+T+m k 
  gene1946|gene1946|rna1946|rna1946 218 RMLKSWSVSLAYELNHRYIHVEYISPHFVATKMSKI 253
                                        *********************************975 PP

>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.5   0.3   5.1e-23   1.5e-19       1     181 [.      80     253 ..      80     272 .. 0.90

  Alignments for each domain:
  == domain 1  score: 70.5 bits;  conditional E-value: 5.1e-23
                                        TTTTSHHHHHHHHHHHTT-EEEEEESSGGH.HHHHHHHHHHTTSEEEE--TTSHHHHHHHHHHHHHHHSSEEEEEE CS
                       adh_short_C2   1 GaasgIGraiAkalaeeGaevvltdlneea.kkrveelaeelgaevlecDVtdeeqvealveevvekfgklDilvn 75 
                                        Ga  gIG+++A  la+   +++++ +n e+ +++ +e+ + ++ + + +D + e++ ++++       +++ +l+n
  gene1946|gene1946|rna1946|rna1946  80 GATDGIGKEMALILAKMRQNIIIVGRNAEKlAATQAEISKLTQCKSILMDFAVEQSFDDVIT------DNIGMLIN 149
                                        899***************************77777777777777788898887777777765......4899**** PP

                                        -----EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHHHCTSCCEEEEEEEGGGTSBSTTTTHHHHHHHHHHHH CS
                       adh_short_C2  76 nagiapklkgpfletsreefdraldvnlyslfllakaalplmkeggsivnlssvgaervvpnynaygaaKaaleal 151
                                        nag++ + +++f+  ++e + ++++vn   +++l++ +l+ m + + i+n+ s  a    p + +y+a+K  l++ 
  gene1946|gene1946|rna1946|rna1946 150 NAGVSSEYTKDFV--DEERITQIINVNNLNAIKLTQSVLKKMDKYSYIINIGSKVADFPCPLHVVYAASKRMLKSW 223
                                        *******777765..6899********************************************************* PP

                                        HHHHHHHHGGGTEEEEEEEE--BHCTGGGG CS
                       adh_short_C2 152 trylAvelgpkgiRvNavspgpikTlaasg 181
                                        + +lA+el ++ i v  +sp +++T++++ 
  gene1946|gene1946|rna1946|rna1946 224 SVSLAYELNHRYIHVEYISPHFVATKMSKI 253
                                        **************************9764 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.4   5.8e-08   0.00017       4      61 ..      77     129 ..      75     226 .. 0.74

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 5.8e-08
                                        EEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE---- CS
                                 KR   4 litGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaD 61 
                                        +itG++ g+G+e+a  la+  ++++++++R+a++ ++ +a+i++l++     + + +D
  gene1946|gene1946|rna1946|rna1946  77 MITGATDGIGKEMALILAK-MRQNIIIVGRNAEKLAATQAEISKLTQC----KSILMD 129
                                        8*************88875.689********99999999999999874....344444 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.2   3.4e-06      0.01       1      74 [.      76     141 ..      76     241 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3.4e-06
                                        EEEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT CS
                    Polysacc_synt_2   1 vlvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekale 74 
                                        +++tGa+  iG+e+   il+k  ++ii++ r+  kl + + e+++ ++         +++ d + +++ +++++
  gene1946|gene1946|rna1946|rna1946  76 IMITGATDGIGKEMAL-ILAKMRQNIIIVGRNAEKLAATQAEISKLTQC-------KSILMDFAVEQSFDDVIT 141
                                        8************976.66667789999999999999999998543333.......345666666666666655 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.2   3.1e-05     0.093       1      78 [.      76     152 ..      76     160 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.1e-05
                                        EEEE--.SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHH.TTTCEEEEE--TTTHHHHHHHHHTTS.SEE CS
                    Sacchrp_dh_NADP   1 vliiGa.GsvGqavaellarhfdvdaeitvadrskeklealaaka.lgvrfeaialdaenyeavLaallkeg.dlv 73 
                                        ++i Ga  ++G+ +a  la+  +   +i++++r+ ekl+a+ a++ + +++++i +d + +++  + +++++ +++
  gene1946|gene1946|rna1946|rna1946  76 IMITGAtDGIGKEMALILAKMRQ---NIIIVGRNAEKLAATQAEIsKLTQCKSILMDFAVEQS-FDDVITDNiGML 147
                                        567788889***********987...6**************9999777778888888888888.999999988888 PP

                                        EE-SS CS
                    Sacchrp_dh_NADP  74 vnlsp 78 
                                        +n ++
  gene1946|gene1946|rna1946|rna1946 148 INNAG 152
                                        88665 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.0   0.00082       2.5      30      82 ..      67     117 ..      44     132 .. 0.77
   2 ?    2.1   0.1     0.036   1.1e+02     109     127 ..     181     199 ..     159     201 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.00082
                                        SBS-GTTSEEEEES-S.HHHHHHHHHHHHTT-EEEEESSSHHHHHCHHHHTCEE CS
                       2-Hacid_dh_C  30 lgkelsgktvGiiGlG.rIGqavakrlkafgmkviaydrskkkeeeeeelgvel 82 
                                          k+++g+ + i G+   IG+++a +l++++ ++i++ r+ +k +   ++++e 
  gene1946|gene1946|rna1946|rna1946  67 VWKNIKGRWIMITGATdGIGKEMALILAKMRQNIIIVGRNAEKLA---ATQAEI 117
                                        567889999999997626*********************977554...333332 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.036
                                        BSHHHHHCSTTTEEEEESS CS
                       2-Hacid_dh_C 109 inaeelakmkkgailiNta 127
                                        ++++ l+km k +++iN++
  gene1946|gene1946|rna1946|rna1946 181 LTQSVLKKMDKYSYIINIG 199
                                        67889************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (322 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1046  (0.0583412); expected 358.6 (0.02)
Passed bias filter:                      502  (0.0279993); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 2222.52
//
Query:       gene1947|gene1947|rna1947|rna1947  [L=880]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        3.2    7.6   9.4        4.9    7.0   0.7    4.4  4  LRR_8     Leucine rich repeat


Domain annotation for each model (and alignments):
>> LRR_8  Leucine rich repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.1    0.0049        89       3      32 ..     380     409 ..     371     424 .. 0.85
   2 ?   -1.4   0.0      0.11     2e+03      23      34 ..     523     534 ..     519     541 .. 0.80
   3 ?    7.0   0.7   0.00027       4.9      23      56 ..     631     666 ..     617     668 .. 0.87
   4 ?   -2.0   0.2      0.17   3.1e+03      15      32 ..     723     739 ..     707     740 .. 0.44

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.0049
                                        -SEEE-TTS--SEE-TTSSTT-TT--EEE- CS
                              LRR_8   3 LtsLdLsnNrltslddeaFkglsnLkvLdL 32 
                                         ++LdL+  +l + d e+ ++l nL+vL+L
  gene1947|gene1947|rna1947|rna1947 380 ISVLDLTGCSLCDRDLEVIRDLANLEVLHL 409
                                        567888888888888888888999998887 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.11
                                        T-TT--EEE--S CS
                              LRR_8  23 glsnLkvLdLsn 34 
                                        gl+nL+vL+  +
  gene1947|gene1947|rna1947|rna1947 523 GLPNLEVLSFHE 534
                                        799999998765 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.00027
                                        T..-TT--EEE--SS---GGGGGGGTT--S-.EEE- CS
                              LRR_8  23 g..lsnLkvLdLsnNllttlspgafsgLpsLrsLdL 56 
                                        +  ++ L++L++s N+ +   +  +++L++L+s+++
  gene1947|gene1947|rna1947|rna1947 631 SeqMKDLEELEISGNSFSNGYQLDIDNLTNLTSINI 666
                                        3359***************999**********9986 PP

  == domain 4  score: -2.0 bits;  conditional E-value: 0.17
                                        EE-TTSSTT-TT--EEE- CS
                              LRR_8  15 slddeaFkglsnLkvLdL 32 
                                        s ++  F   +nLk+L L
  gene1947|gene1947|rna1947|rna1947 723 SFKKNLFL-AKNLKYLTL 739
                                        34444444.355666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (880 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       615  (0.034302); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.67u 0.24s 00:00:00.91 Elapsed: 00:00:00.46
# Mc/sec: 5779.00
//
Query:       gene1948|gene1948|rna1948|rna1948  [L=218]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       597  (0.033298); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.29s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1571.81
//
Query:       gene1949|gene1949|rna1949|rna1949  [L=228]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (228 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       519  (0.0289475); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 1563.84
//
Query:       gene195|gene195|rna195|rna195  [L=286]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
        0.5   11.0  16.0        3.1    8.5   7.9    2.6  2  HIP1_clath_bdg  Clathrin-binding domain of Huntingtin-interac
       0.82   10.1  12.5        0.5   10.8   1.5    3.5  4  FlaC_arch       Flagella accessory protein C (FlaC)
        1.5    8.7  13.3       0.86    9.4   0.8    3.1  3  DivIC           Septum formation initiator
        1.7    9.2  25.0    1.2e+02    3.1   1.7    3.0  2  APG6_N          Apg6 coiled-coil region
        1.8    7.1  22.8        2.9    6.4   5.9    2.2  2  FapA            Flagellar Assembly Protein A
        3.7    8.1   9.0       0.43   11.1   0.5    3.0  2  TipAS           TipAS antibiotic-recognition domain
        4.8    7.9  10.5        6.7    7.5   4.1    2.5  2  DUF2203         Uncharacterized conserved protein (DUF2203)


Domain annotation for each model (and alignments):
>> HIP1_clath_bdg  Clathrin-binding domain of Huntingtin-interacting protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   7.9    0.0012       3.1      10      97 ..      23     114 ..      15     115 .. 0.75
   2 ?    6.8   1.0    0.0041        10      57      97 ..     133     173 ..     127     175 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0012
                 HIP1_clath_bdg  10 evtkqlsvarqaqeeverekkeleeelerlk.eeaerkle...eqkeelekLkreleakraelarlkssLesseqsgeql 85 
                                    + +k+    +  q+e+    ++++ + ++ + +++ rkl+   + +  le++ + +e+ ++e +++k  L+s+e+++e  
  gene195|gene195|rna195|rna195  23 NSVKIEGEIKTIQKEMSEYDNKIKSSSDSKEaKDHARKLAdikQNNVALERFAERIENYMHEKEKIKVDLKSNEKKKECA 102
                                    556666666667777777666666655443212233444345477889******************************** PP

                 HIP1_clath_bdg  86 ssqlaaLqaEke 97 
                                     ++++aL++E+ 
  gene195|gene195|rna195|rna195 103 LEKVDALEMERR 114
                                    **********95 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0041
                 HIP1_clath_bdg  57 LkreleakraelarlkssLesseqsgeqlssqlaaLqaEke 97 
                                    +++++ + ++e+ +lk+ L++  ++g ++ss++++L + k+
  gene195|gene195|rna195|rna195 133 VNKDFDKMEQEMMELKQELAELYKQGCKISSEVEELTRKKN 173
                                    67888999999**********************99998775 PP

>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.3     0.011        27      11      31 ..      26      46 ..      20      51 .. 0.86
   2 ?    0.5   2.2      0.32   8.1e+02       2      18 ..      31      47 ..      30      98 .. 0.73
   3 ?   -1.2   0.2       1.1   2.7e+03      11      34 ..      87     110 ..      75     121 .. 0.58
   4 ?   10.8   1.5   0.00019       0.5       3      35 ..     138     170 ..     137     178 .. 0.92

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.011
                      FlaC_arch 11 klsteletvkkeneelsksve 31
                                   k++ e++t++ke++e  ++++
  gene195|gene195|rna195|rna195 26 KIEGEIKTIQKEMSEYDNKIK 46
                                   68899*********9998886 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.32
                      FlaC_arch  2 idelEnklsklstelet 18
                                   i+++++++s+ + ++++
  gene195|gene195|rna195|rna195 31 IKTIQKEMSEYDNKIKS 47
                                   44555555555555444 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 1.1
                      FlaC_arch  11 klsteletvkkeneelsksveelk 34 
                                    k+++ l++ +k+ e   ++v+ l+
  gene195|gene195|rna195|rna195  87 KIKVDLKSNEKKKECALEKVDALE 110
                                    445566666655555555555544 PP

  == domain 4  score: 10.8 bits;  conditional E-value: 0.00019
                      FlaC_arch   3 delEnklsklsteletvkkeneelsksveelke 35 
                                    d++E+++ +l+ el+ + k+  ++s++veel +
  gene195|gene195|rna195|rna195 138 DKMEQEMMELKQELAELYKQGCKISSEVEELTR 170
                                    79****************************975 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   2.6     0.007        18      19      71 ..      17      67 ..       9      70 .. 0.84
   2 ?    2.4   1.2      0.05   1.3e+02      23      50 ..      51      78 ..      43      95 .. 0.80
   3 ?    9.4   0.8   0.00033      0.86      20      55 ..     138     173 ..     133     178 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.007
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-XXXXXXXXXXXXXXXXXXXXX CS
                          DivIC 19 ykqlkqeiaalqaelaklkaeneeLeaevkdLksdedyieerARselglvkpg 71
                                   y  lk++ ++++ e++++++e  e + ++k   sd    +  AR +l  +k++
  gene195|gene195|rna195|rna195 17 YLILKANSVKIEGEIKTIQKEMSEYDNKIKSS-SDSKEAKDHAR-KLADIKQN 67
                                   66788999999*********************.78888899999.66655555 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.05
                                   HHHHHHHHHHHHHHHHHHHHHHHHHCC- CS
                          DivIC 23 kqeiaalqaelaklkaeneeLeaevkdL 50
                                    +e ++  ++la +k+ n +Le+  ++ 
  gene195|gene195|rna195|rna195 51 SKEAKDHARKLADIKQNNVALERFAERI 78
                                   5788889999999999999999887776 PP

  == domain 3  score: 9.4 bits;  conditional E-value: 0.00033
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-XXXXX CS
                          DivIC  20 kqlkqeiaalqaelaklkaeneeLeaevkdLksded 55 
                                     +++qe+ +l++ela+l ++  +  +ev++L+  ++
  gene195|gene195|rna195|rna195 138 DKMEQEMMELKQELAELYKQGCKISSEVEELTRKKN 173
                                    678999999**********99999999999976555 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   1.7     0.048   1.2e+02      63      97 ..      24      58 ..       9      75 .. 0.50
   2 ?   -0.3  23.8      0.57   1.5e+03      16     120 ..      59     173 ..      24     202 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.048
                         APG6_N 63 eeelleeLkelekereeleaelaaleeelealeee 97
                                     + + e+k ++ke +e ++++++ +  +ea+++ 
  gene195|gene195|rna195|rna195 24 SVKIEGEIKTIQKEMSEYDNKIKSSSDSKEAKDHA 58
                                   44444455555555555555555544444444433 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.57
                         APG6_N  16 kqleqaekerdaYeeflkklkkekkeeek.......qdeeleeleeeleklekeeeelleeLkele...kereeleaela 85 
                                    ++l++ ++   a+e+f ++++++  e+ek       ++++ e + e++++le e+++ +e+L+  +   k   +++++  
  gene195|gene195|rna195|rna195  59 RKLADIKQNNVALERFAERIENYMHEKEKikvdlksNEKKKECALEKVDALEMERRNNIEKLEGFKlpsKPSMSVNKDFD 138
                                    57777888888888888888888777777888866655555555555666777777666666655433356678888888 PP

                         APG6_N  86 aleeelealeeeeerfwreynelqlelleleeeld 120
                                    + e+e  +l++e ++  ++  + + e++el  +++
  gene195|gene195|rna195|rna195 139 KMEQEMMELKQELAELYKQGCKISSEVEELTRKKN 173
                                    88888888888888888888888888888877654 PP

>> FapA  Flagellar Assembly Protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1  12.0    0.0055        14     337     415 ..      22      99 ..       9     106 .. 0.85
   2 ?    6.4   5.9    0.0011       2.9     354     419 ..     111     176 ..      96     224 .. 0.65

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.0055
                           FapA 337 eklkeleeeleeleeeleklkkkikklpklkaekqlesekkeqlkklletkeklkeeleeleeelkelkeeleskkeea 415
                                    ++  ++e e++ +++e+ ++++kik+ ++ ++e +  ++k+ ++k+   ++e++ e++e+ ++e++++k  l+s ++++
  gene195|gene195|rna195|rna195  22 ANSVKIEGEIKTIQKEMSEYDNKIKSSSD-SKEAKDHARKLADIKQNNVALERFAERIENYMHEKEKIKVDLKSNEKKK 99 
                                    555689999********************.667778999999999999999********************99994443 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0011
                           FapA 354 eklkkkikklpklkaekqlesekkeqlkklletkeklkeeleeleeelkelkeeleskkeeakikv 419
                                    ++ +++i+kl+  k +++ ++   ++++k+++++ +lk+el+el ++  ++++e+e+ +++++++v
  gene195|gene195|rna195|rna195 111 MERRNNIEKLEGFKLPSKPSMSVNKDFDKMEQEMMELKQELAELYKQGCKISSEVEELTRKKNLIV 176
                                    333344777777777777778888888888888888888888888888888888888843333332 PP

>> TipAS  TipAS antibiotic-recognition domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   2.5      0.52   1.3e+03      58      71 ..      53      66 ..      20     129 .. 0.58
   2 ?   11.1   0.5   0.00017      0.43      28      64 ..     135     170 ..     127     246 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.52
                                   XXXXXXXXXXXXXX CS
                          TipAS 58 eaqelaeehralie 71
                                   ea++ a+++ ++ +
  gene195|gene195|rna195|rna195 53 EAKDHARKLADIKQ 66
                                   33333333333333 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00017
                                    XXXXXXXXXXXXXXXXXXXX..XXXXXXXXXXXXXXX CS
                          TipAS  28 edweelkaelkelfaklaaalaagkdpdseeaqelae 64 
                                    +d++++++e++el ++la+++++g +  s e+ el +
  gene195|gene195|rna195|rna195 135 KDFDKMEQEMMELKQELAELYKQGCKI-SSEVEELTR 170
                                    7999*********************65.556777766 PP

>> DUF2203  Uncharacterized conserved protein (DUF2203)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   4.1    0.0026       6.7      15      79 ..      31      95 ..      21     101 .. 0.66
   2 ?    3.6   0.5     0.042   1.1e+02      35      76 ..     119     161 ..      97     173 .. 0.57

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0026
                        DUF2203 15 lkelleelralrkeleeleeeleeakaeaekseaaeleaeleeleaeieelveeieelGvevkdl 79
                                   +k + +e+ +  +++++ +++ e++ ++++  + ++++ +le+ +++ie++++e e+++v++k+ 
  gene195|gene195|rna195|rna195 31 IKTIQKEMSEYDNKIKSSSDSKEAKDHARKLADIKQNNVALERFAERIENYMHEKEKIKVDLKSN 95
                                   44444555555555555554444444444444488888888888889999999988888888875 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.042
                        DUF2203  35 eleeakaeaekse.aaeleaeleeleaeieelveeieelGvev 76 
                                    +le  k  ++ s   +++  ++e+ ++e+++ ++e+ + G+++
  gene195|gene195|rna195|rna195 119 KLEGFKLPSKPSMsVNKDFDKMEQEMMELKQELAELYKQGCKI 161
                                    3333333322222455556666666666666677777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2343  (0.130682); expected 358.6 (0.02)
Passed bias filter:                      470  (0.0262145); expected 358.6 (0.02)
Passed Vit filter:                        73  (0.00407162); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.54u 0.31s 00:00:00.85 Elapsed: 00:00:00.44
# Mc/sec: 1943.84
//
Query:       gene1950|gene1950|rna1950|rna1950  [L=303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        0.7    9.7   5.0       0.84    9.4   0.3    2.7  3  RB_A      Retinoblastoma-associated protein A domain


Domain annotation for each model (and alignments):
>> RB_A  Retinoblastoma-associated protein A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.1     0.027   4.8e+02     106     152 ..     120     166 ..     101     168 .. 0.81
   2 ?    0.1   0.2     0.033   5.9e+02     114     145 ..     174     205 ..     170     215 .. 0.82
   3 ?    9.4   0.3   4.7e-05      0.84     100     126 ..     217     243 ..     200     265 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.027
                               RB_A 106 lskllsnevfhrsLlacclevvlfayksetlsFpwilevlklkafdf 152
                                        + ++l+ + + r +l++  e ++     e   +   le+l++ a+df
  gene1950|gene1950|rna1950|rna1950 120 VLNMLNANHLKRLVLIVRPESIISNMFNELYYYFQALETLEIRAYDF 166
                                        5688999999999999999988888777777888899999**99999 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.033
                               RB_A 114 vfhrsLlacclevvlfayksetlsFpwilevl 145
                                        vf+r+   c ++v  ++ +s++ sF  +++ +
  gene1950|gene1950|rna1950|rna1950 174 VFLRCFTKCGVKVLSITCQSPHESFGTVISQF 205
                                        799***********999999888999998765 PP

  == domain 3  score: 9.4 bits;  conditional E-value: 4.7e-05
                               RB_A 100 rlsskdlskllsnevfhrsLlacclev 126
                                         + + ++++llsn++f +sL+ +c+ +
  gene1950|gene1950|rna1950|rna1950 217 EIYTYNFKQLLSNDKFSNSLFRLCISL 243
                                        467789****************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (303 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       569  (0.0317363); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2206.63
//
Query:       gene1951|gene1951|rna1951|rna1951  [L=1518]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.061   13.3   0.5       0.18   11.8   0.5    1.7  1  Inhibitor_I24  PinA peptidase inhibitor


Domain annotation for each model (and alignments):
>> Inhibitor_I24  PinA peptidase inhibitor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.5     1e-05      0.18      15      88 ..     377     455 ..     368     463 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1e-05
                      Inhibitor_I24  15 lcnyw..pelsagtvfkvrelvkeceddiepdtgiieielsdgkiiniydkpi...tywclwntesvengeieevv 85 
                                        +c  w  p+     vfk  e+ k+c+ +i      i+i  s g i   y + i    ++  w  e v+ng++ e +
  gene1951|gene1951|rna1951|rna1951 377 ICCNWtlPDTLEDVVFKKVEVEKNCKLNIGRACKQINITDSIGMIFIPYIHEIfvpQFFLNWSVELVQNGDVVEKL 452
                                        5555545888999*******************************99888777733447888*********998866 PP

                      Inhibitor_I24  86 ert 88 
                                          +
  gene1951|gene1951|rna1951|rna1951 453 TVS 455
                                        554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1518 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       622  (0.0346924); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.84u 0.31s 00:00:01.14 Elapsed: 00:00:00.49
# Mc/sec: 9267.90
//
Query:       gene1952|gene1952|rna1952|rna1952  [L=120]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.025   14.5   0.0       0.05   13.5   0.0    1.5  1  DUF3746   Protein of unknown function (DUF3746)


Domain annotation for each model (and alignments):
>> DUF3746  Protein of unknown function (DUF3746)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   2.8e-06      0.05       8      26 ..       6      24 ..       5      26 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.8e-06
                            DUF3746  8 LkvttsskKktCkKhifdN 26
                                       Lk+t s++ ++C+K+++ +
  gene1952|gene1952|rna1952|rna1952  6 LKDTLSCGSSYCRKAVYQG 24
                                       9****************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       515  (0.0287244); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 880.60
//
Query:       gene1953|gene1953|rna1953|rna1953  [L=1263]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-93  314.4  12.2    1.9e-93  313.6   6.3    3.8  2  RNA_pol_Rpb2_6  RNA polymerase Rpb2, domain 6
    1.3e-35  122.8   0.4    4.2e-23   81.9   0.1    2.3  2  RNA_pol_Rpb2_1  RNA polymerase beta subunit
    1.9e-23   82.7   1.1    6.1e-23   81.0   0.1    2.4  2  RNA_pol_Rpb2_7  RNA polymerase Rpb2, domain 7
    1.8e-17   63.3   0.2    6.3e-17   61.5   0.2    2.0  1  RNA_pol_Rpb2_3  RNA polymerase Rpb2, domain 3
    9.3e-11   41.9   1.8    1.4e-10   41.3   0.4    2.1  2  RNA_pol_Rpb2_4  RNA polymerase Rpb2, domain 4
     0.0028   18.2   2.6     0.0028   18.2   2.6    2.9  2  RNA_pol_Rpb2_5  RNA polymerase Rpb2, domain 5
     0.0028   17.3   2.4      0.011   15.4   0.2    2.7  3  RNA_pol_Rpb2_2  RNA polymerase Rpb2, domain 2
  ------ inclusion threshold ------
       0.23   10.2   0.5       0.38    9.5   0.5    1.3  1  Presenilin      Presenilin
        3.2    7.7   5.2        3.1    7.7   0.3    3.4  4  TrbM            TrbM


Domain annotation for each model (and alignments):
>> RNA_pol_Rpb2_6  RNA polymerase Rpb2, domain 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.3       1.5   2.9e+03     153     195 ..     274     317 ..     269     324 .. 0.63
   2 !  313.6   6.3   9.5e-97   1.9e-93       2     390 .]     725    1177 ..     724    1177 .. 0.79

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 1.5
                                        -SS-EEETT-EEE---..B-----...-----------...-B- CS
                     RNA_pol_Rpb2_6 153 rvgaevkegdilvgkvtkgeteltpeekllraifgekare.vkd 195
                                         ++++++++ i+v   t + +++t+e k  +++  ++++  vk+
  gene1953|gene1953|rna1953|rna1953 274 LIQEQLSKNRIIVTNETSTVSSFTSERKSRTTVIRKNNNYfVKN 317
                                        57888888888888877666677766555444444444334444 PP

  == domain 2  score: 313.6 bits;  conditional E-value: 9.5e-97
                                         HHT-SS-TTB-HHHHHHHHHHGGGB-S---TTTTT---SSEEEESS----SSB-S.TTTTTS........GGGS CS
                     RNA_pol_Rpb2_6    2 aklapvvehvqspriiiqaamekqalgiyslnkfkrsnqktyllcinqkPlvktgdkveagqvldgpatekgel 75  
                                         a+ +p++eh+qspr+++q+am+kq++gi+++n+ +r+++ +++ ++ q+P+        +          + e+
  gene1953|gene1953|rna1953|rna1953  725 ATTIPFPEHNQSPRNTYQCAMGKQSMGIACFNYKQRFDNVLFINYYVQRPVTYGD----Y----------VPEV 784 
                                         7889**********************************************86655....2..........3578 PP

                                         -SEEEEEBBBS--TTTTTTT-EEEBCHHHHTTTT-EEEEEE..EEE--SSSS---.-S--..--SS-GGGS-TT CS
                     RNA_pol_Rpb2_6   76 alGqnavVAvmsyeGYniEDaiilnerlvdrdvftsihikeyeveardtklgeeeitrdipnvseealkkLded 149 
                                          +Gqn++VAvms +GY+iEDai+ln++++dr++++ +++k+y+v + ++  g++++++  ++           d
  gene1953|gene1953|rna1953|rna1953  785 LSGQNVMVAVMSLSGYDIEDAIVLNRNSLDRGMARVTVYKSYSVGIGRYGDGSSDVIMPFKEC----------D 848 
                                         89***************************************9999988887776666555332..........4 PP

                                         SB--SS-EEETT-EEE---..B-----...-----------..-B---EE--TT-EEEEEEEEE.......... CS
                     RNA_pol_Rpb2_6  150 GivrvgaevkegdilvgkvtkgeteltpeekllraifgekarevkdtslrvksgeegvVdkvkvfsr....... 216 
                                         G v+ g+ v+++   v+  t ++t+   ++   +++  ++++e k+t +++  +ee   dk +  +r       
  gene1953|gene1953|rna1953|rna1953  849 GDVCQGQGVEKKRKSVKDAT-SNTKGRGNDDWDKNKRMNDETEEKNTEMEMYGEEERQNDKEMKNKRenynega 921 
                                         44444444444444444432.22222222333333444444444555555555544444444443335555566 PP

                                         ......................................................EE-TT--EEEEEEEEEEE-- CS
                     RNA_pol_Rpb2_6  217 ..................................................ekgdelkagvnklvkvyvaqkRkl 240 
                                                                                               ++     +l+k++++++R++
  gene1953|gene1953|rna1953|rna1953  922 rkcnhnptnstssnltmndgircvgeivkndilinkyspkgvfnglfhkkLAIVDTVVITDTLIKIKMRETRTP 995 
                                         66666666666777777777777777*********************865333444455689************ PP

                                         -TT-BEEETTS---BBEEEB-TTTSEEETTS---SEEE-GGGCHHH-BTTHHHHHHHHHCCCSSSS--B--TT- CS
                     RNA_pol_Rpb2_6  241 qvGDKfasrhGqKGvvslilpqeDmPfledGivvDivlNPlgvPSRmtigqllEtllgkaaalegkkvdatvFd 314 
                                          +GDKf+srhGqKGvv++i++  D+Pf e Giv+D+++NP+g+PSRmt+g++ E+++gk++ l g++++ ++++
  gene1953|gene1953|rna1953|rna1953  996 VIGDKFSSRHGQKGVVGRIIRAVDLPFNERGIVPDLIMNPHGFPSRMTLGKIKEVVAGKVGVLLGRRMECSAYS 1069
                                         ********************************************************************999988 PP

                                         ..................................-.HHHHHHHHHTTS-TT-EE-EEETTTS-B-SS-EEB-EE CS
                     RNA_pol_Rpb2_6  315 g....................ak...........e.eeikelLeeagleasGkevlydGrtGekleaeifvGvi 356 
                                                               k           + e+ +  L++ g+++sGke++y+G+tG+++ +++f+G++
  gene1953|gene1953|rna1953|rna1953 1070 FneyddkcsvadngddidsdgDKyftcndkktlkTiEDYCMVLQSLGYSYSGKETFYSGMTGKPIPTHVFFGPV 1143
                                         855666666655555555555004555555555435778999******************************** PP

                                         EEEEBS--CCCS----SS--B-TTT--B-SCGGG CS
                     RNA_pol_Rpb2_6  357 YylkLkhlvedKihaRstGpyslltqQPlgGkaq 390 
                                         Yy++Lkh+vedKihaR++G+ ++lt+QP++G+++
  gene1953|gene1953|rna1953|rna1953 1144 YYQRLKHMVEDKIHARNIGKRTVLTRQPTEGRSR 1177
                                         ********************************86 PP

>> RNA_pol_Rpb2_1  RNA polymerase beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.9   0.1   2.1e-26   4.2e-23       1     144 [.      12     145 ..      12     170 .. 0.93
   2 !   38.9   0.0   3.3e-13   6.5e-10     131     193 ..     254     452 ..     247     463 .. 0.95

  Alignments for each domain:
  == domain 1  score: 81.9 bits;  conditional E-value: 2.1e-26
                                        CTTHHHHHHHHHHHHTHHHHHCTTSSECCHCSSSHCSSSCEEEEEEEEEEESCSSECTTSCEEES.HHHHHHCTSB CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     RNA_pol_Rpb2_1   1 gLvsqqldSFnkfveqdlekiikeeaaieseeeiqssgeelelkfvsirlgkPvvdesdasereiyPkearlrnlt 76 
                                        gL + +l S+n+f+ +dl++i k +++i s+ +++     +++k+ +ir++kP + + +++ r+++P+e+rlr+l+
  gene1953|gene1953|rna1953|rna1953  12 GLFRHHLTSYNHFITTDLKNILKVNNTILSDIDPS-----FHMKMSNIRVNKPNIID-NMVVRDVLPEECRLRDLS 81 
                                        58899****************************97.....****************9.9***************** PP

                                        XEEEEEEEEEEEECCCCTCCEEEEEEEEEEEEEXBTTSTTSSSTTS..HHHHHHTTS.TTS..SSEEET CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxx RF
                     RNA_pol_Rpb2_1  77 YsaplyvklklvvyekdnkeeikeeevyiGelPlMlrskacvlsea.seeelvelkEcpldqGGyFiin 144
                                        Y + + v++++ v     ++ + +++v iG++P+M+ s  c+l  a ++ee+  +kEc ld  G  i+n
  gene1953|gene1953|rna1953|rna1953  82 YLGDIVVDVEYCV----CRKINVRKDVVIGKMPVMVGSILCHLGSAgEDEEMGWMKECILDGNGN-IVN 145
                                        *************....5899999*******************98835678*********98886.555 PP

  == domain 2  score: 38.9 bits;  conditional E-value: 3.3e-13
                                        TS.TTS..SSEEETTCEEEEXEEEE................................................... CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxx................................................... RF
                     RNA_pol_Rpb2_1 131 kEcpldqGGyFiinGtekvivaqek................................................... 155
                                         Ecpld G yFii+G e+ i+ qe+                                                   
  gene1953|gene1953|rna1953|rna1953 254 RECPLDEGAYFIIKGVERAILIQEQlsknriivtnetstvssftserksrttvirknnnyfvknnvftedvplivl 329
                                        7*************************************************************************** PP

                                        ............................................................................ CS
                                        ............................................................................ RF
                     RNA_pol_Rpb2_1 156 ............................................................................ 155
                                                                                                                    
  gene1953|gene1953|rna1953|rna1953 330 lknygveeheivslgcslndlridvhaylksvckgregfmdeivlpnvkrevkgfylltmarlierkgtfsdldfl 405
                                        **************************************************************************** PP

                                        ......XHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTSS...SSSHH CS
                                        ......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxx RF
                     RNA_pol_Rpb2_1 156 ......laGeLlaslfrvllkklerdvkerlqkslekld...dlmlq 193
                                              l G Ll  lf+++lk++++++k+ ++k l k +   ++++ 
  gene1953|gene1953|rna1953|rna1953 406 gnkrfeLSGSLLCLLFEDALKRFNEEIKKGIDKILSKRMraqEFQPL 452
                                        **********************************9998844445555 PP

>> RNA_pol_Rpb2_7  RNA polymerase Rpb2, domain 7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.1       1.6   3.1e+03      29      55 ..    1087    1114 ..    1085    1122 .. 0.83
   2 !   81.0   0.1   3.1e-26   6.1e-23       1      85 [.    1179    1259 ..    1179    1261 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 1.6
                                         TTTEEEEEEESSSSSCCCEE.EBTTTTC CS
                     RNA_pol_Rpb2_7   29 kSDavevdvcgrckllaaan.eCkivks 55  
                                         +SD  +   c++ k+l++++ +C++++s
  gene1953|gene1953|rna1953|rna1953 1087 DSDGDKYFTCNDKKTLKTIEdYCMVLQS 1114
                                         7999999999999999987679999876 PP

  == domain 2  score: 81.0 bits;  conditional E-value: 3.1e-26
                                         BBEEEEHHHHHHHHHHTBHHHHHHHHTTTTTEEEEEEESSSSSCCCEEEBTTTTCSSSEEEEEEEHHHHHHHHH CS
                     RNA_pol_Rpb2_7    1 GGlrfGEMErdaliayGaaalLkerltikSDavevdvcgrckllaaaneCkivkseekiekveipeafklLlqe 74  
                                         GGlr+GEMErd+l+++Gaa++L++rl+ +SDav+v vc+rc +++   +   +    ++ +v++p+a+klL+ e
  gene1953|gene1953|rna1953|rna1953 1179 GGLRVGEMERDCLVGHGAAEMLRDRLLFSSDAVDVGVCDRCYVVKD--RGGAC--CGRVVDVKMPYACKLLFVE 1248
                                         9****************************************99999..33344..45688999*********** PP

                                         HHHTTBEEEEE CS
                     RNA_pol_Rpb2_7   75 Lqslgialkll 85  
                                         L+++gi ++++
  gene1953|gene1953|rna1953|rna1953 1249 LMAMGIYPRIK 1259
                                         ******99985 PP

>> RNA_pol_Rpb2_3  RNA polymerase Rpb2, domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.5   0.2   3.1e-20   6.3e-17       3      68 .]     490     552 ..     488     552 .. 0.96

  Alignments for each domain:
  == domain 1  score: 61.5 bits;  conditional E-value: 3.1e-20
                     RNA_pol_Rpb2_3   3 ldrlnplselshlrrvsslrgglskerkttevRdlhpshwGriCpveTPEGencGlvksLallarv 68 
                                        l rl++l++++ l+rv s    ++k+rk + +R lh s +G +Cp++TPEGe+cGlvk L++l+++
  gene1953|gene1953|rna1953|rna1953 490 LSRLSYLNTVNTLTRVVSQ---FEKTRKIAGPRSLHTSCFGVLCPCDTPEGESCGLVKTLSMLTEI 552
                                        789**************88...****************************************9987 PP

>> RNA_pol_Rpb2_4  RNA polymerase Rpb2, domain 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       6.8   1.3e+04      14      31 ..     213     231 ..     208     240 .. 0.65
   2 !   41.3   0.4   6.8e-14   1.4e-10       1      60 [.     579     634 ..     579     635 .. 0.94

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 6.8
                                        HCCHHHHHHHHCCTTS.S- CS
                     RNA_pol_Rpb2_4  14 pkklvetlRelRRkgk.is 31 
                                        +k+ v+ lR+ +R++  ++
  gene1953|gene1953|rna1953|rna1953 213 KKRAVSGLRTKKRNETqMN 231
                                        6778889999999644233 PP

  == domain 2  score: 41.3 bits;  conditional E-value: 6.8e-14
                                        EECTT-BEEE-S-HCCHHHHHHHHCCTTSS-TT-EEEE-TTT--EEEE-SSEEB-EEEEE CS
                     RNA_pol_Rpb2_4   1 VfvNGrllGvtrdpkklvetlRelRRkgkiseevsivlnekqkevkiatDgGRvcRPlii 60 
                                        Vf+NG  +G +++   +ve+l ++RR+g i++ vs+++   +  v ++tDgGR+cRPl++
  gene1953|gene1953|rna1953|rna1953 579 VFLNGCPVGSCNE--CIVERLVRMRRAGTIDKYVSVSRT--DTFVFVSTDGGRICRPLLV 634
                                        9*********986..69*******************987..578**************97 PP

>> RNA_pol_Rpb2_5  RNA polymerase Rpb2, domain 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   2.6   1.4e-06    0.0028       3      57 ..     680     716 ..     679     717 .. 0.79
   2 ?   -3.9   3.0         9   1.8e+04      16      43 ..     889     925 ..     887     937 .. 0.61

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.4e-06
                                        HHHHTTSEEEEEHHHHTT--EESSTTTCSST-SSTTTSS--TTSSSST-SEEES- CS
                     RNA_pol_Rpb2_5   3 dLlregvvEylDaeEEetamIamtpedleksreekealeekenskshtyTHcEIh 57 
                                        dL+++gvvEylD++E  +a+I +  +  +k+                  TH E+h
  gene1953|gene1953|rna1953|rna1953 680 DLVHKGVVEYLDINEQCNALISLRHRYSTKH------------------THYELH 716
                                        9********************9987665444..................555555 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 9
                                        HHHTT--EESSTTTCSST.-SSTTTSS-........- CS
                     RNA_pol_Rpb2_5  16 eEEetamIamtpedleks.reekealee........k 43 
                                         EE ++   m+ e+ +++ +e+k++ e+        +
  gene1953|gene1953|rna1953|rna1953 889 TEEKNTEMEMYGEEERQNdKEMKNKRENynegarkcN 925
                                        5777777777777766666888877666555555441 PP

>> RNA_pol_Rpb2_2  RNA polymerase Rpb2, domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.2   5.5e-06     0.011       6      74 ..     274     345 ..     271     363 .. 0.76
   2 ?   -0.2   0.0      0.32   6.4e+02     154     188 ..     378     409 ..     364     411 .. 0.78
   3 ?   -1.9   0.0       1.1   2.1e+03      70     106 ..     667     702 ..     665     712 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 5.5e-06
                                        EEEE-SSSSSE.....SSSCCEECCCEEEEECCCCSTSCEEEEECTTSSSEEEHHHHHHHTT--STTHHHHHHT CS
                     RNA_pol_Rpb2_2   6 yvekekdknki.....satvtsslisqrgsvlklekdgktliwtriskkrkipivivlkAlglvsdreIleric 74 
                                        + + + +kn+i      +tv+s ++++++ +++++k+ +++++ +   ++++p++++lk  g+  ++eI++  c
  gene1953|gene1953|rna1953|rna1953 274 LIQEQLSKNRIivtneTSTVSSFTSERKSRTTVIRKNNNYFVKNN-VFTEDVPLIVLLKNYGV-EEHEIVSLGC 345
                                        566777888888998666777777777777777777777777776.6777************6.99***98655 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.32
                                        H...HHHHHHHHHHHHHHHHTTSSSS--TTSGGGEE CS
                     RNA_pol_Rpb2_2 154 kr.lkaqdilymidrLlslklgrrevDDiDhlgnkR 188
                                        kr +k +++l m+ rL++ k   +++ D D lgnkR
  gene1953|gene1953|rna1953|rna1953 378 KReVKGFYLLTMA-RLIERK---GTFSDLDFLGNKR 409
                                        4558999999997.688877...999*********9 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 1.1
                                        HHHHTSSSTTHHHHHHHHHHHHHHCTSSSCHHHHHHH CS
                     RNA_pol_Rpb2_2  70 lericydsedsqlleelleeleekeeiqtqeealdyi 106
                                        l+r +y +e+ ++++++ +   e+ +i +q +al  +
  gene1953|gene1953|rna1953|rna1953 667 LQRTVY-NEYMSMHDLVHKGVVEYLDINEQCNALISL 702
                                        788888.899999999**************9999876 PP

>> Presenilin  Presenilin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.5   0.00019      0.38     238     366 ..     858     985 ..     837     995 .. 0.55

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00019
                         Presenilin 238 eeeaekkkeeasesskeeeseeesseksaqsseseeeseeesseaessaeesseekeseessesseeeeeeeeeee 313
                                        e+++++ k+++s+++ + +++++++++++ ++e+++++ e   e+e++++++ ++k+++ ++ +++ +++ +++++
  gene1953|gene1953|rna1953|rna1953 858 EKKRKSVKDATSNTKGRGNDDWDKNKRMNDETEEKNTEMEMYGEEERQNDKEMKNKRENYNEGARKCNHNPTNSTS 933
                                        4455555555555555555555544444444433333333333333322222222222222222222222223333 PP

                         Presenilin 314 eseseergvkLGLGDFiFYSvLvgkAalsgdlntvvacfvailiGLclTLllL 366
                                        ++ + ++g++   G  +   +L+ k + +g +n ++   +ai+  +++T +l+
  gene1953|gene1953|rna1953|rna1953 934 SNLTMNDGIR-CVGEIVKNDILINKYSPKGVFNGLFHKKLAIVDTVVITDTLI 985
                                        3333557998.589999999999999999999999999999988888776555 PP

>> TrbM  TrbM
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.1       1.4   2.7e+03      44     106 ..     246     308 ..     238     322 .. 0.65
   2 ?   -1.3   0.0      0.96   1.9e+03      50      68 ..     580     599 ..     574     644 .. 0.67
   3 ?    7.7   0.3    0.0016       3.1      58      99 ..     905     943 ..     881     982 .. 0.78
   4 ?   -1.7   0.0       1.3   2.5e+03      76     125 ..    1064    1117 ..    1052    1133 .. 0.57

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.4
                               TrbM  44 veaRrnFLklCPvseedpem.aelvdaisrgagkCdaeylnstlevkavkeiegerriraveie 106
                                        v+ R ++ + CP +e    + +   +ai+ + ++   + +  t+e+ +v + ++er+ r++ i+
  gene1953|gene1953|rna1953|rna1953 246 VTKRPAYRRECPLDEGAYFIiKGVERAILIQ-EQLSKNRIIVTNETSTVSSFTSERKSRTTVIR 308
                                        5678889999999996554404455556555.44455555566666666777777777666554 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.96
                               TrbM  50 FLklCPvse.edpemaelvd 68 
                                        FL+ CPv++ ++  ++ lv+
  gene1953|gene1953|rna1953|rna1953 580 FLNGCPVGScNECIVERLVR 599
                                        9******9855555555554 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.0016
                               TrbM  58 eedpemaelvdaisrgagkCdaeylnstlevkavkeiegerr 99 
                                        ++d em++++++  +ga+kC+ +  nst ++ ++++   + r
  gene1953|gene1953|rna1953|rna1953 905 QNDKEMKNKRENYNEGARKCNHNPTNSTSSNLTMND---GIR 943
                                        4789***********************999888653...333 PP

  == domain 4  score: -1.7 bits;  conditional E-value: 1.3
                               TrbM   76 kCdaeylnstlevkavkeiegerriraveie......tviedklPayCvayeahay 125 
                                         +C a ++n+   +  v   +++  i++   +      + + +++ +yC+++++  y
  gene1953|gene1953|rna1953|rna1953 1064 ECSAYSFNEYDDKCSVA--DNGDDIDSDGDKyftcndKKTLKTIEDYCMVLQSLGY 1117
                                         56666666543333322..2222222222222333346777778888888876555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1247  (0.0695521); expected 358.6 (0.02)
Passed bias filter:                      623  (0.0347482); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 1.01u 0.30s 00:00:01.31 Elapsed: 00:00:00.47
# Mc/sec: 8041.90
//
Query:       gene1954|gene1954|rna1954|rna1954  [L=155]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-34  117.9  10.9    3.1e-34  117.7  10.9    1.0  1  ORMDL     ORMDL family
     0.0054   16.5   4.8      0.011   15.4   4.8    1.5  1  Rer1      Rer1 family


Domain annotation for each model (and alignments):
>> ORMDL  ORMDL family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.7  10.9   3.5e-38   3.1e-34       2     136 .]      19     147 ..      18     147 .. 0.99

  Alignments for each domain:
  == domain 1  score: 117.7 bits;  conditional E-value: 3.5e-38
                              ORMDL   2 kntewvnskglwviyiviilllkllllalpgvseevawtltnlvhnlvtyillHwikGtPfetadqgeydeltlWE 77 
                                        +n++w+ +kg+++++i+++++ + +l++   +++e+a++lt l++n++t++++H+i G+Pf+     +++++++WE
  gene1954|gene1954|rna1954|rna1954  19 QNVAWTVHKGSFIAHISVVMIGHSILRFA--FTKEIAYQLTPLLYNVLTFVFFHLIVGDPFDP----RFNNHSFWE 88 
                                        79*************************99..*******************************9....********* PP

                              ORMDL  78 QidegeqytptrkfLtvvPivLfllsthytkydlelfvinlivllvvvipKlpfmhrvR 136
                                        Q++e+  y++t  f++v+Piv+f++ +h++ ++++lf++ +++l++vv+pKl+fmhr+R
  gene1954|gene1954|rna1954|rna1954  89 QMVEQIGYSSTTIFFMVFPIVMFIVINHLVVWNVYLFYLTILSLILVVVPKLGFMHRKR 147
                                        *********************************************************98 PP

>> Rer1  Rer1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   4.8   1.3e-06     0.011      97     150 ..      76     131 ..      74     139 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.3e-06
                               Rer1  97 PfirrlpEfkfWlsatkailialvltffevfdvpVfwpi..Llvyfivlfvltmrr 150
                                        Pf  r++   fW ++++ i  + ++ ff vf +  f  i  L+v+ + lf+lt+ +
  gene1954|gene1954|rna1954|rna1954  76 PFDPRFNNHSFWEQMVEQIGYSSTTIFFMVFPIVMFIVInhLVVWNVYLFYLTILS 131
                                        9999********************************988889**********9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1017  (0.0567237); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 1060.16
//
Query:       gene1955|gene1955|rna1955|rna1955  [L=822]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.032   14.8   0.3       0.17   12.4   0.3    2.3  1  PCI       PCI domain


Domain annotation for each model (and alignments):
>> PCI  PCI domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.3   9.6e-06      0.17      15      88 ..     439     514 ..     427     515 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 9.6e-06
                                        HHHHHHHHHHHHHHHHHHTTHHH..HHHHHHHHHHHHHHHHHHHCESEEEHHHHHHHHTSSH..HHHHHHHHHHHH CS
                                PCI  15 lsgfseelkdleeelladdglaq..llesLekkvrerllrqvskiyssislerlaklldlsv..devEkilvklIr 86 
                                        +  +   l+ +  ++++++ + +   +e + + ++ +ll  +sk+  ++ +++++k+l l++  ++v+ki+ k I 
  gene1955|gene1955|rna1955|rna1955 439 VFFALDVLRTY--RVFDKQVIDKclKMETVDHLAYDTLLGNISKKTARFAFKKIEKTLMLFSndENVQKIIKKIID 512
                                        55555566777..67777777775556789999****************************************999 PP

                                        TT CS
                                PCI  87 dg 88 
                                        +g
  gene1955|gene1955|rna1955|rna1955 513 KG 514
                                        87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (822 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1493  (0.0832729); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.67u 0.32s 00:00:00.99 Elapsed: 00:00:00.46
# Mc/sec: 5325.88
//
Query:       gene1956|gene1956|rna1956|rna1956  [L=811]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00016   21.9   0.2       0.16   12.2   0.0    4.1  4  ANAPC4_WD40     Anaphase-promoting complex subunit 4 WD40 dom
  ------ inclusion threshold ------
      0.081   12.9   0.2        6.5    6.8   0.0    2.5  2  Ribosomal_S28e  Ribosomal protein S28e
       0.13   13.2   0.1      1e+02    4.0   0.0    4.0  3  WD40            WD domain, G-beta repeat


Domain annotation for each model (and alignments):
>> ANAPC4_WD40  Anaphase-promoting complex subunit 4 WD40 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.48   2.8e+03      35      70 ..     122     156 ..     112     165 .. 0.76
   2 ?   -2.1   0.0      0.81   4.9e+03      52      76 ..     252     276 ..     248     295 .. 0.70
   3 ?    3.9   0.0     0.011        65      39      85 ..     471     516 ..     456     523 .. 0.80
   4 !   12.2   0.0   2.7e-05      0.16      42      82 ..     604     644 ..     571     675 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.48
                        ANAPC4_WD40  35 dkedsevrsLaWkpdgklLavaysdgevrlldaesg 70 
                                         +++++v  ++  ++g +L v+  d++vr+ +  +g
  gene1956|gene1956|rna1956|rna1956 122 RAHNESVLRVKMLENGIVLSVGR-DSTVRMSSFRDG 156
                                        56778888899999999999985.778888777766 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.81
                        ANAPC4_WD40  52 lLavaysdgevrlldaesgkvvhsl 76 
                                        +++ + + g+++ ++ ++ k+v+  
  gene1956|gene1956|rna1956|rna1956 252 FIVTVSERGTINTFSTKKRKIVKRT 276
                                        5666667777777777777777654 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.011
                        ANAPC4_WD40  39 sevrsLaWkpdgklLavaysdg.evrlldaesgkvvhslsvksekavt 85 
                                         +v++   ++d+++L v   d+ e++++d++  kvv +l+ ++   + 
  gene1956|gene1956|rna1956|rna1956 471 FKVSCADSNEDNSVLFVCNYDSyEINIVDIKRSKVVDTLKLSAM--IR 516
                                        566666778899999998777769*************9998766..55 PP

  == domain 4  score: 12.2 bits;  conditional E-value: 2.7e-05
                        ANAPC4_WD40  42 rsLaWkpdgklLavaysdgevrlldaesgkvvhslsvksek 82 
                                        +s +   dg+ L+ + + +e++++d e+g v+++l+ +++k
  gene1956|gene1956|rna1956|rna1956 604 TSCSLTYDGTTLVCGAQANEIKIVDLETGCVIQTLKLSRNK 644
                                        66677789***************************998875 PP

>> Ribosomal_S28e  Ribosomal protein S28e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.0    0.0011       6.5      36      55 ..     276     295 ..     264     299 .. 0.82
   2 ?    3.4   0.1     0.013        78      34      62 ..     716     744 ..     708     745 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0011
                                        -EEEEEEES---TT-EEEES CS
                     Ribosomal_S28e  36 riiiRnVkGPvreGDiLtLl 55 
                                          + RnV  ++r+GD L Ll
  gene1956|gene1956|rna1956|rna1956 276 TFLDRNVRHACRKGDQLFLL 295
                                        4678*************998 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.013
                                        -S-EEEEEEES---TT-EEEES--S--TT CS
                     Ribosomal_S28e  34 kgriiiRnVkGPvreGDiLtLlEterEAr 62 
                                        k++  +R   G++     ++++E+ rE r
  gene1956|gene1956|rna1956|rna1956 716 KEHRFVRALLGSINLKSKIMIKECIRETR 744
                                        567789999******************87 PP

>> WD40  WD domain, G-beta repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0     0.017     1e+02       5      36 ..     119     150 ..     115     150 .. 0.81
   2 ?    3.8   0.0      0.02   1.2e+02      16      35 ..     391     409 ..     374     409 .. 0.83
   3 ?   -1.2   0.0      0.76   4.5e+03      13      32 ..     603     622 ..     597     628 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.017
                                        EEEESS.SSEEEEEEETTSSEEEEEETTSEEEE CS
                               WD40   5 rtltGH.ssvtslafspdgawlasGsdDgtvri 36 
                                        + +++H  sv  ++   +g  l+ G  D tvr+
  gene1956|gene1956|rna1956|rna1956 119 GDIRAHnESVLRVKMLENGIVLSVGR-DSTVRM 150
                                        56789*777999*9999999997666.****96 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.02
                                        EEEETTSSEEEEEETTSEEE CS
                               WD40  16 lafspdgawlasGsdDgtvr 35 
                                        ++fs +++ ++s+  D+tv+
  gene1956|gene1956|rna1956|rna1956 391 VDFSENNDIMLSCA-DNTVH 409
                                        459********999.***95 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 0.76
                                        EEEEEEETTSSEEEEEETTS CS
                               WD40  13 vtslafspdgawlasGsdDg 32 
                                         ts++   dg+ l++G   +
  gene1956|gene1956|rna1956|rna1956 603 CTSCSLTYDGTTLVCGAQAN 622
                                        57888899999999987555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (811 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1323  (0.0737911); expected 358.6 (0.02)
Passed bias filter:                      497  (0.0277205); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.75u 0.32s 00:00:01.07 Elapsed: 00:00:00.49
# Mc/sec: 4937.23
//
Query:       gene1957|gene1957|rna1957|rna1957  [L=283]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
       0.72    8.9   5.4       0.93    8.5   5.4    1.1  1  ABC2_membrane_3  ABC-2 family transporter protein


Domain annotation for each model (and alignments):
>> ABC2_membrane_3  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   5.4   5.2e-05      0.93      13     134 ..      10     146 ..       9     201 .. 0.66

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 5.2e-05
                    ABC2_membrane_3  13 ilvlllglifsnsveddentpiavvdedn......sslsqqlvealeaspsvelvyevdseeeakkalkngdidgi 82 
                                        +++ l+++++s+s++  +++ + ++++ +       +l +q+++++e++++     e+++ + +k+++++  ++ +
  gene1957|gene1957|rna1957|rna1957  10 LFISLFITFCSASSAGESDQVVPILNDFHvvkiqlETLIEQMNSIIEQTGQE---TEINNFTLLKHHVRQLFVNVL 82 
                                        6899999999****99***************766655555666666666554...59******************* PP

                    ABC2_membrane_3  83 lvipkgfskdll....kgesatvtvlinssnlnss.........kailnalns.llqqlnasalv.......l 134
                                        + i+++ ++d +    k         ++++ l +          ++i++  n  ++ + ++++          
  gene1957|gene1957|rna1957|rna1957  83 IEIENDTENDEQklifK---------YYKQLLDILgndlfihltMIIYKPANRdMIDEVLRHNIEvkksnelF 146
                                        *******9986644443.........44444444444555555577777777655555554443344333321 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (283 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1277  (0.0712254); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 2079.85
//
Query:       gene1958|gene1958|rna1958|rna1958  [L=301]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      2e-35  123.2   0.0    2.8e-35  122.7   0.0    1.1  1  Metallophos  Calcineurin-like phosphoesterase
     0.0021   18.5   0.2     0.0067   16.9   0.2    1.9  1  STPPase_N    Serine-threonine protein phosphatase N-terminal 


Domain annotation for each model (and alignments):
>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.7   0.0   3.2e-39   2.8e-35       2     201 ..      43     234 ..      42     236 .. 0.95

  Alignments for each domain:
  == domain 1  score: 122.7 bits;  conditional E-value: 3.2e-39
                                        EEEEEESBTBTTCCTHHHHHHHHHHHH..HHHTTESEEEEESTSSSSS..HHHHHHHHHHHHHHHHTSEEEEEC-T CS
                        Metallophos   2 rilvigDlHlalgggqlddllkllddl..lreekpdlvllaGDlvdrg..dlekellellaalvkypipvylllGN 73 
                                        +i+++gD+H     gq++dl++l++    +++  ++l++  GD+vdrg  ++e+ +  +l+  +kyp+++ +l+GN
  gene1958|gene1958|rna1958|rna1958  43 PITICGDIH-----GQFYDLMELFKVGgmPPD-TNYLFM--GDFVDRGfhSVET-FSLMLCLRLKYPNRITILRGN 109
                                        799******.....**********88764555.889999..*******888888.8888***************** PP

                                        TS........CHHHHHHHHHHHHHHHHHHHEHHHCEEETSEEEEEETTEEEEEEEESE.CEEETHHHHHHHHHHHS CS
                        Metallophos  74 He........gfeeellnkygylgifsepwrsdaevfnnlplaslgsgslkvlllhGg.spellvsldklgslnle 140
                                        He        gf++e+ +kyg+    s++w+ +++ f++lpla+++++   ++++hGg sp   +++d+++++n+ 
  gene1958|gene1958|rna1958|rna1958 110 HEsrqitqvyGFYDECVRKYGS----SMVWKEFTDLFDYLPLAAIVNN--SFFCCHGGlSPTV-DTIDQIHKINRV 178
                                        *********************8....99********************..********88888.************ PP

                                        CHHHHCC...HHHHHHHHHHTTCSEEEEEESSESSCSSSCSCCHHHHHHHHHHTTESEEEEESS CS
                        Metallophos 141 leapepg...dewlkdlekrekadwvivlgHsplyrgsgylfgdealedllkkygvdlvisGHt 201
                                         e+p++g   d++++d        ++  +g    +rg+g +fg ++++++ k +g+ +v+++H+
  gene1958|gene1958|rna1958|rna1958 179 VEVPHEGsmcDLLWSD--------PDERIGFGSSPRGAGFTFGKDVTARFNKTNGLSMVCRAHQ 234
                                        ****************........999999999999***************************7 PP

>> STPPase_N  Serine-threonine protein phosphatase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.2   7.4e-07    0.0067       1      46 [.       2      39 ..       2      41 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 7.4e-07
                          STPPase_N  1 vDdiIerLlevrgkpggkkvq.LseaEIrqlCakareiFLsQPtLLe 46
                                       +D+ Ie+L           +q L+e+E++qlC k ++++ ++P+   
  gene1958|gene1958|rna1958|rna1958  2 IDEFIEKLFR---------CQcLTEEEVKQLCEKGKDVLSREPNVVS 39
                                       5666666665.........333*********************9665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (301 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       541  (0.0301746); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 2289.22
//
Query:       gene1959|gene1959|rna1959|rna1959  [L=463]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.11   12.4   0.0       0.51   10.3   0.0    2.1  2  DUF5605   Domain of unknown function (DUF5605)


Domain annotation for each model (and alignments):
>> DUF5605  Domain of unknown function (DUF5605)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   2.8e-05      0.51      31      63 ..      21      53 ..       3      56 .. 0.85
   2 ?   -3.5   0.0      0.54   9.7e+03      25      40 ..     213     228 ..     209     231 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 2.8e-05
                            DUF5605 31 egsrykveviDtWnmtieelpgvfegkvrveLP 63
                                       e+s+ ++ +  + n+ti ++++ f gk+r+eLP
  gene1959|gene1959|rna1959|rna1959 21 ENSKANIHITKAENVTISNCNELFAGKFRLELP 53
                                       66789999999*********************9 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 0.54
                            DUF5605  25 refelpegsrykvevi 40 
                                        r  +l+++ +y v++ 
  gene1959|gene1959|rna1959|rna1959 213 RVAKLDNKPTYDVKIT 228
                                        6667888888888874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (463 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       642  (0.0358079); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.23s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 3478.18
//
Query:       gene196|gene196|rna196|rna196  [L=161]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
     0.0066   16.1   0.7     0.0066   16.1   0.7    1.8  2  RE_Bpu10I    Bpu10I restriction endonuclease
  ------ inclusion threshold ------
      0.013   15.3   3.3      0.014   15.2   2.7    1.4  1  DUF19        Domain of unknown function (DUF19)
       0.54   10.8   9.4        7.5    7.1   9.4    2.1  1  ECM11        Extracellular mutant protein 11
        1.8    8.8  13.4       0.86    9.8   4.2    2.2  2  TMF_TATA_bd  TATA element modulatory factor 1 TATA binding


Domain annotation for each model (and alignments):
>> RE_Bpu10I  Bpu10I restriction endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.7   1.5e-06    0.0066     131     197 ..      12      77 ..       8     100 .. 0.79
   2 ?   -1.0   0.1      0.25   1.1e+03     163     184 ..     129     149 ..      96     159 .. 0.57

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.5e-06
                      RE_Bpu10I 131 cEwLdltpvslaktdiDevlilRkakrlssniRkeyatvegrqkkreeyveyldknpfapdvfqrll 197
                                    +  Ld++++ ++k d+Dev i +k+  +++ + + y ++++ +  +  +   ++++  +++ f+++ 
  gene196|gene196|rna196|rna196  12 SALLDFSSIPVTKNDVDEVSIFKKTSFVKMAVNNTYLAIKKNKYDHRDF-TIIENKLRKVNLFNKFT 77 
                                    5679********************************9998655444444.45666666777777775 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.25
                      RE_Bpu10I 163 Rkeyatvegrqkkreeyveyld 184
                                    Rk y  +e ++++re+ ++ ++
  gene196|gene196|rna196|rna196 129 RKIY-EYERKVAHRERLIDEIK 149
                                    2222.23334444555544444 PP

>> DUF19  Domain of unknown function (DUF19)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   2.7   3.2e-06     0.014      16      73 ..      82     138 ..      68     160 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 3.2e-06
                          DUF19  16 vsrlkellektdelelkdkkelkkfkksCeslksCfkslkCkeeeeakeakkkiekac 73 
                                    ++ l++ le+++++ + +++ +k+  ++ e+lksCf++++ ++ +e+k+++ ++e++ 
  gene196|gene196|rna196|rna196  82 LATLEKKLEEIEDKRVRNQSVYKEKLENVEKLKSCFQKIQATR-DEEKRKIYEYERKV 138
                                    456777889999999*************************998.44444444455444 PP

>> ECM11  Extracellular mutant protein 11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   9.4    0.0017       7.5      11     124 ..      46     157 ..      39     161 .] 0.63

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0017
                          ECM11  11 syseLekepFdhdpaa...........ppaelppsl.dtsetleekleelknlnekeqheffsslsideWeeaGdwlldq 78 
                                    +y  ++k+++dh + +               ++ +  d+ +tle+klee+++++ ++q+ + ++l          + +++
  gene196|gene196|rna196|rna196  46 TYLAIKKNKYDHRDFTiienklrkvnlF---NKFTPhDELATLEKKLEEIEDKRVRNQSVYKEKL----------ENVEK 112
                                    6777777777777766543333322111...1111114444455555555554444444444444..........57899 PP

                          ECM11  79 fsellkklkeaRrakrktaaefeaeierReeavrkkgeeldrkLee 124
                                    +++ ++k++++R + ++++ e+e+++++Re+ +  + ++l+ +Le+
  gene196|gene196|rna196|rna196 113 LKSCFQKIQATRDEEKRKIYEYERKVAHRERLI-DEIKDLEIQLER 157
                                    *****************************8765.567777777776 PP

>> TMF_TATA_bd  TATA element modulatory factor 1 TATA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   4.2   0.00019      0.86      63      98 ..      79     114 ..      74     118 .. 0.93
   2 ?    4.7   3.7    0.0075        34      30      76 ..     112     158 ..     111     161 .] 0.91

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00019
                    TMF_TATA_bd  63 kkeleelekeleelqeryetlLellGeksEeveELr 98 
                                    ++el++lek+lee++++      +++ek E+ve L+
  gene196|gene196|rna196|rna196  79 HDELATLEKKLEEIEDKRVRNQSVYKEKLENVEKLK 114
                                    57899*****************************98 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.0075
                    TMF_TATA_bd  30 slkeelerleaerdeareeivklmkeneelkelkkeleelekeleel 76 
                                    +lk+  ++++a rde ++ i +  +++   ++l +e+++le +le  
  gene196|gene196|rna196|rna196 112 KLKSCFQKIQATRDEEKRKIYEYERKVAHRERLIDEIKDLEIQLERS 158
                                    5788899**********************************999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2340  (0.130515); expected 358.6 (0.02)
Passed bias filter:                      574  (0.0320152); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 1104.74
//
Query:       gene1960|gene1960|rna1960|rna1960  [L=177]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       829  (0.0462379); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 1343.17
//
Query:       gene1961|gene1961|rna1961|rna1961  [L=301]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.3e-17   62.7   0.0    6.3e-17   61.8   0.0    1.4  1  RhoGAP    RhoGAP domain


Domain annotation for each model (and alignments):
>> RhoGAP  RhoGAP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.8   0.0   3.5e-21   6.3e-17       3     147 ..     112     254 ..     111     258 .. 0.94

  Alignments for each domain:
  == domain 1  score: 61.8 bits;  conditional E-value: 3.5e-21
                                        HHHHHHHHHHHHTTTSTTTTTS-S-HHHHHHHHHHHHHTGGGCTTTTTSCHHHHHHHHHHHHHHSSSTTTTGGHHH CS
                             RhoGAP   3 ivekcvefiekrgldtegiyRvsgskarvkelreafdkgkavdsdleeedvhavaslLKrfLrelpepLltkelye 78 
                                        ++ k+++fi+ +  +  gi+R sg+ ++  +l e+f +g+    dl+ +dv  + + +K +L++  + ++++++++
  gene1961|gene1961|rna1961|rna1961 112 FIFKIMDFIKTKRANYHGIFRCSGDYRASTRLYERFIAGDVF--DLNTTDVRNIVAFFKIYLKKKVNGIFSFDILD 185
                                        67899************************************9..8******************************* PP

                                        HHHHHHTSSSHHHHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHHHTHHHH---HHHHHHHHHHHHHT-T CS
                             RhoGAP  79 elieaaksedeeerlealkellekLPkenrdtLryLlehLkrvaenskenkMtaknLaivfaPtLlrpk 147
                                        +l+e+ak+++       l  l   +   +r+ L  L++++k++ +++ en M + nL  ++aP+L+++ 
  gene1961|gene1961|rna1961|rna1961 186 TLYETAKHRSSPSINYLLFYLPFCFVGDKRRFLIGLIDMFKEIDQHKNENDMPIPNLVRCIAPSLFPDT 254
                                        ***9988877777777777777899999**************************************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (301 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       448  (0.0249875); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 2191.86
//
Query:       gene1963|gene1963|rna1963|rna1963  [L=85]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.1e-15   56.4   0.5    3.3e-15   56.3   0.5    1.0  1  dsDNA_bind  Double-stranded DNA-binding domain


Domain annotation for each model (and alignments):
>> dsDNA_bind  Double-stranded DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.3   0.5   1.8e-19   3.3e-15      35     110 ..       4      78 ..       1      80 [. 0.89

  Alignments for each domain:
  == domain 1  score: 56.3 bits;  conditional E-value: 1.8e-19
                                        --SSHHHHTTS--HHHHHHHHHHTTT-HHHHHHHHHHHHHHHH--SS-----HHHHHHHHHHHS---XXXXX..XX CS
                         dsDNA_bind  35 eeakqaiLsqiLepeAreRLsrirlvkperaeavenrLiqlaqsGqlrskvteeqLkeLLeqvaekkketkivisr 110
                                        + +  ++L++iLep   +R +ri+l +++ra+++en Li+l++sG+++++++e+++ e  +++ +++   +iv+ r
  gene1963|gene1963|rna1963|rna1963   4 QPNTDQLLASILEPASLTRFNRIKLYNKDRAKKIENELIRLYKSGRVQRQINEDEFEEFVSNLCKENA-PRIVVMR 78 
                                        556789*****************************************************999988665.5565555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (85 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       676  (0.0377043); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.26s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 650.58
//
Query:       gene1964|gene1964|rna1964|rna1964  [L=347]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (347 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       666  (0.0371465); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 2403.80
//
Query:       gene1965|gene1965|rna1965|rna1965  [L=261]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.5e-16   60.6  26.8    1.5e-16   60.6  26.8    3.9  3  zf-CHY         CHY zinc finger
    2.2e-12   46.8   6.1    2.2e-12   46.8   6.1    4.1  4  zinc_ribbon_6  Zinc-ribbon
    9.9e-08   32.2   5.6    9.9e-08   32.2   5.6    5.1  5  zf-RING_2      Ring finger domain
    6.1e-06   26.2   0.7    6.1e-06   26.2   0.7    4.5  5  zf-RING_UBOX   RING-type zinc-finger
    1.4e-05   25.0   6.7    1.4e-05   25.0   6.7    6.4  6  zf-RING_5      zinc-RING finger domain
    2.9e-05   23.8   5.4    2.9e-05   23.8   5.4    6.0  6  zf-C3HC4_2     Zinc finger, C3HC4 type (RING finger)
    7.4e-05   22.5   3.6    7.4e-05   22.5   3.6    5.6  6  zf-C3HC4_3     Zinc finger, C3HC4 type (RING finger)


Domain annotation for each model (and alignments):
>> zf-CHY  CHY zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.6  26.8   5.8e-20   1.5e-16       1      75 []      23      96 ..      23      96 .. 0.99
   2 ?   -5.1  19.7         7   1.8e+04      12      72 ..     112     189 ..      99     192 .. 0.59
   3 ?   -5.7  15.0         7   1.8e+04      17      73 ..     181     248 ..     167     255 .. 0.54

  Alignments for each domain:
  == domain 1  score: 60.6 bits;  conditional E-value: 5.8e-20
                             zf-CHY  1 CkHykravvairapcCkklyaCreCHeeledhelerlevkevlcllCeteqekavlCkkCkkefaeyfCpiCkll 75
                                       CkHy+r+ + i + cCk++y+Cr CH++ edh++ r+++k +lcl C + q +++ C  Ck ++a+yfC++Ck++
  gene1965|gene1965|rna1965|rna1965 23 CKHYRRK-CLIITDCCKRTYPCRLCHDHNEDHRMIRHRTKYMLCLCCGMIQGASQFCIMCKVKMANYFCKTCKFW 96
                                       *******.****************************************************************985 PP

  == domain 2  score: -5.1 bits;  conditional E-value: 7
                             zf-CHY  12 rapcCkklyaCreCH.....eeledhelerlevkevlcllCeteqekavl...CkkCkk..........efaeyfC 69 
                                        r+   + +++C  C      e l++h+  + + k  +c  C +   ++v+     +C++          + ++++C
  gene1965|gene1965|rna1965|rna1965 112 RVGNKNAFFHCSDCNaclprELLNNHNHVENTLK-STCPICAEFMFESVNdvvLLNCGHsihfacfkvyKESSFQC 186
                                        4455577999999998888533667766666655.56999987653333212244566655555333444444589 PP

                             zf-CHY  70 piC 72 
                                        p+C
  gene1965|gene1965|rna1965|rna1965 187 PVC 189
                                        999 PP

  == domain 3  score: -5.7 bits;  conditional E-value: 7
                             zf-CHY  17 kklyaCreCHeeledhelerlevkevlcllCeteq.....ekavlCkkCkk...efaey.....fCpiCk 73 
                                        ++ ++C  C ++  + ++ + +++ +l ++ + +       ++v C  C++   ++  y     +C +C 
  gene1965|gene1965|rna1965|rna1965 181 ESSFQCPVCLKSAGNTKVLNERIDCILNSNVNLNAkrqnyMCQVSCFDCQSvskTI--YtflynKCVKCG 248
                                        45799****96555544444444433333222221100124555677787765422..233544688886 PP

>> zinc_ribbon_6  Zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -9.8   9.4         7   1.8e+04      31      53 ..      45      68 ..      24      70 .. 0.63
   2 ?   -5.5   6.6         7   1.8e+04      28      54 ..      86     112 ..      79     117 .. 0.68
   3 ?   -1.6   3.3       1.1   2.7e+03      27      37 ..     117     127 ..     111     129 .. 0.75
   4 !   46.8   6.1   8.6e-16   2.2e-12       8      59 .]     201     253 ..     194     253 .. 0.89

  Alignments for each domain:
  == domain 1  score: -9.8 bits;  conditional E-value: 7
                      zinc_ribbon_6 31 lCnDCekkse.vkfhvlglkCkeC 53
                                       lC+D ++  + ++ +  ++ C  C
  gene1965|gene1965|rna1965|rna1965 45 LCHDHNEDHRmIRHRTKYMLCLCC 68
                                       355554444434445555556555 PP

  == domain 2  score: -5.5 bits;  conditional E-value: 7
                      zinc_ribbon_6  28 vkilCnDCekksevkfhvlglkCkeCg 54 
                                        ++ +C+ C+  ++    +   +Ck C+
  gene1965|gene1965|rna1965|rna1965  86 ANYFCKTCKFWTDSLGVFHCKQCKVCR 112
                                        555677777666666666667777775 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 1.1
                      zinc_ribbon_6  27 kvkilCnDCek 37 
                                         +  +C DC++
  gene1965|gene1965|rna1965|rna1965 117 NAFFHCSDCNA 127
                                        55668999985 PP

  == domain 4  score: 46.8 bits;  conditional E-value: 8.6e-16
                      zinc_ribbon_6   8 raldaeiaeqp.mpeeyknkkvkilCnDCekksevkfhvlglkCkeCgSYNTr 59 
                                        +++d +++++  ++++ +n++++++C DC++ s++ + +l++kC +CgSYNTr
  gene1965|gene1965|rna1965|rna1965 201 ERIDCILNSNVnLNAKRQNYMCQVSCFDCQSVSKTIYTFLYNKCVKCGSYNTR 253
                                        678888888766999*************************************7 PP

>> zf-RING_2  Ring finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?  -10.1  16.8         7   1.8e+04      13      30 ..      28      47 ..      14      69 .. 0.52
   2 ?  -13.5  23.5         7   1.8e+04       3      44 .]      65     112 ..      63     128 .. 0.75
   3 ?    1.4  10.7      0.16     4e+02       2      43 ..     107     151 ..     106     152 .. 0.57
   4 !   32.2   5.6   3.9e-11   9.9e-08       2      43 ..     147     189 ..     146     190 .. 0.86
   5 ?   -1.7   2.4       1.5   3.9e+03      21      30 ..     222     230 ..     205     248 .. 0.56

  Alignments for each domain:
  == domain 1  score: -10.1 bits;  conditional E-value: 7
                          zf-RING_2 13 adsvlllpCgHv.f.hreCl 30
                                       ++++++++C++  + +r C 
  gene1965|gene1965|rna1965|rna1965 28 RKCLIITDCCKRtYpCRLCH 47
                                       23444445554334466665 PP

  == domain 2  score: -13.5 bits;  conditional E-value: 7
                          zf-RING_2   3 CpICleelssadsvlllpCgH...v.fhreClerwlrssst.....CPlCr 44 
                                        C +C   ++ a++ +++ C+      f+++C + w+ s        C +Cr
  gene1965|gene1965|rna1965|rna1965  65 CLCC-GMIQGASQFCIM-CKVkmaNyFCKTC-KFWTDSLGVfhckqCKVCR 112
                                        5556.568888888899.98345545*****.5675555555544588887 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.16
                          zf-RING_2   2 eCpICleelssadsvlllpCgHvfhreCl.erwlrssst........CPlC 43 
                                        +C +C   + +++      C+   +  Cl +++l+++++        CP+C
  gene1965|gene1965|rna1965|rna1965 107 QCKVCR--VGNKNAFFH--CSD--CNACLpRELLNNHNHventlkstCPIC 151
                                        899996..555455442..433..55566433444444455558899**** PP

  == domain 4  score: 32.2 bits;  conditional E-value: 3.9e-11
                          zf-RING_2   2 eCpICleel.ssadsvlllpCgHvfhreClerwlrssstCPlC 43 
                                        +CpIC e + +s ++v+ll CgH++h+ C++ + +ss +CP+C
  gene1965|gene1965|rna1965|rna1965 147 TCPICAEFMfESVNDVVLLNCGHSIHFACFKVYKESSFQCPVC 189
                                        7****655567777788889************9999999**** PP

  == domain 5  score: -1.7 bits;  conditional E-value: 1.5
                          zf-RING_2  21 CgHvfhreCl 30 
                                        C  v +++C 
  gene1965|gene1965|rna1965|rna1965 222 C-QVSCFDCQ 230
                                        6.45666773 PP

>> zf-RING_UBOX  RING-type zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -6.0   4.6         7   1.8e+04       4       6 ..      37      39 ..      21      51 .. 0.59
   2 ?   -4.7   4.9         7   1.8e+04      20      26 ..      89      96 ..      88     122 .. 0.67
   3 ?   -1.3   0.7      0.92   2.4e+03      21      25 ..     125     129 ..     108     145 .. 0.63
   4 !   26.2   0.7   2.4e-09   6.1e-06       1      39 []     148     187 ..     148     187 .. 0.83
   5 ?   -3.3   0.1       3.8   9.6e+03      23      34 ..     204     218 ..     204     222 .. 0.45

  Alignments for each domain:
  == domain 1  score: -6.0 bits;  conditional E-value: 7
                       zf-RING_UBOX  4 Cle 6 
                                       C+ 
  gene1965|gene1965|rna1965|rna1965 37 CKR 39
                                       333 PP

  == domain 2  score: -4.7 bits;  conditional E-value: 7
                       zf-RING_UBOX 20 FCreCl.w 26
                                       FC+ C  w
  gene1965|gene1965|rna1965|rna1965 89 FCKTCKfW 96
                                       78887533 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 0.92
                       zf-RING_UBOX  21 CreCl 25 
                                        C  Cl
  gene1965|gene1965|rna1965|rna1965 125 CNACL 129
                                        55666 PP

  == domain 4  score: 26.2 bits;  conditional E-value: 2.4e-09
                       zf-RING_UBOX   1 CpIClelft....dPlv.lpCGHtFCreClwelskslegafkCP 39 
                                        CpIC e +     d +v l+CGH+++  C    +  +e +f+CP
  gene1965|gene1965|rna1965|rna1965 148 CPICAEFMFesvnD-VVlLNCGHSIHFACF---KVYKESSFQCP 187
                                        ******77745434.4636***********...999*******9 PP

  == domain 5  score: -3.3 bits;  conditional E-value: 3.8
                       zf-RING_UBOX  23 eCl..w.elsksleg 34 
                                        +C+     + + +++
  gene1965|gene1965|rna1965|rna1965 204 DCIlnSnVNLNAKRQ 218
                                        688541433344444 PP

>> zf-RING_5  zinc-RING finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?  -21.3  25.3         7   1.8e+04      24      43 ..      64      82 ..      21      95 .. 0.61
   2 ?   -3.2   6.7       3.5   8.9e+03      23      43 ..      88     112 ..      86     113 .. 0.72
   3 ?   -3.2  12.8       3.4   8.7e+03      25      43 ..     125     152 ..     104     153 .. 0.72
   4 !   25.0   6.7   5.3e-09   1.4e-05       2      42 ..     148     189 ..     147     191 .. 0.94
   5 ?   -2.3   1.4       1.8   4.7e+03      35      42 ..     222     229 ..     204     231 .. 0.56
   6 ?   -4.4   5.1         7   1.8e+04      28      42 ..     226     247 ..     218     249 .. 0.49

  Alignments for each domain:
  == domain 1  score: -21.3 bits;  conditional E-value: 7
                          zf-RING_5 24 fCekClkkllekeavCpiCr 43
                                       +C  C + +  +++ C +C+
  gene1965|gene1965|rna1965|rna1965 64 LCLCCGMIQG-ASQFCIMCK 82
                                       3443333333.555555554 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 3.5
                          zf-RING_5  23 ifCekClkkll....ekeavCpiCr 43 
                                        +fC++C           +++C +Cr
  gene1965|gene1965|rna1965|rna1965  88 YFCKTCKFWTDslgvFHCKQCKVCR 112
                                        5788886666666777788888887 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 3.4
                          zf-RING_5  25 CekClkkll.........ekeavCpiCr 43 
                                        C++Cl ++l         + + +CpiC 
  gene1965|gene1965|rna1965|rna1965 125 CNACLPRELlnnhnhvenTLKSTCPICA 152
                                        89999999999999**9999*******5 PP

  == domain 4  score: 25.0 bits;  conditional E-value: 5.3e-09
                          zf-RING_5   2 CnkCfekl.skeekfyltsCgHifCekClkkllekeavCpiC 42 
                                        C++C e + ++  +++l++CgH+++ +C+k ++e++++Cp+C
  gene1965|gene1965|rna1965|rna1965 148 CPICAEFMfESVNDVVLLNCGHSIHFACFKVYKESSFQCPVC 189
                                        ******99888888**************************** PP

  == domain 5  score: -2.3 bits;  conditional E-value: 1.8
                          zf-RING_5  35 keavCpiC 42 
                                         ++ C  C
  gene1965|gene1965|rna1965|rna1965 222 CQVSCFDC 229
                                        33444445 PP

  == domain 6  score: -4.4 bits;  conditional E-value: 7
                          zf-RING_5  28 Clkkll.......ekeavCpiC 42 
                                        C++ ++         +++C  C
  gene1965|gene1965|rna1965|rna1965 226 CFDCQSvsktiytFLYNKCVKC 247
                                        3333333335555445556555 PP

>> zf-C3HC4_2  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.9   4.5         7   1.8e+04      16      27 ..      21      31 ..      13      46 .. 0.60
   2 ?   -7.7   8.4         7   1.8e+04       2      15 ..      43      56 ..      42      81 .. 0.51
   3 ?   -9.5  11.3         7   1.8e+04      21      30 ..      76      85 ..      63     105 .. 0.65
   4 ?   -0.8   4.2      0.56   1.4e+03       1      34 [.     107     137 ..     107     139 .. 0.72
   5 !   23.8   5.4   1.2e-08   2.9e-05       2      40 .]     148     189 ..     147     189 .. 0.76
   6 ?   -3.4   2.7       3.6   9.3e+03       2      10 ..     222     231 ..     221     250 .. 0.50

  Alignments for each domain:
  == domain 1  score: -4.9 bits;  conditional E-value: 7
                         zf-C3HC4_2 16 tpCgHvfCqkCi 27
                                       + C+H   +kC+
  gene1965|gene1965|rna1965|rna1965 21 FGCKHY-RRKCL 31
                                       567773.34443 PP

  == domain 2  score: -7.7 bits;  conditional E-value: 7
                         zf-C3HC4_2  2 CpiCldmlkdpsvv 15
                                       C +C d  +d  ++
  gene1965|gene1965|rna1965|rna1965 43 CRLCHDHNEDHRMI 56
                                       66666666654333 PP

  == domain 3  score: -9.5 bits;  conditional E-value: 7
                         zf-C3HC4_2 21 vfCqkCilrs 30
                                       +fC +C  ++
  gene1965|gene1965|rna1965|rna1965 76 QFCIMCKVKM 85
                                       4555555443 PP

  == domain 4  score: -0.8 bits;  conditional E-value: 0.56
                         zf-C3HC4_2   1 kCpiCldmlkdpsvvtpCgHvfCqkCilr.sLeek 34 
                                        +C++C    k++   + C  + C+ C+ r  L+++
  gene1965|gene1965|rna1965|rna1965 107 QCKVCRVGNKNA--FFHC--SDCNACLPReLLNNH 137
                                        699998888885..8888..469999888445554 PP

  == domain 5  score: 23.8 bits;  conditional E-value: 1.2e-08
                         zf-C3HC4_2   2 CpiCldmlkdp...svvtpCgHvfCqkCilrsLeekneCPlC 40 
                                        CpiC +++ +    +v+ +CgH+ +  C++ + e++ +CP+C
  gene1965|gene1965|rna1965|rna1965 148 CPICAEFMFESvndVVLLNCGHSIHFACFKVYKESSFQCPVC 189
                                        ****99765431114666*************855555***** PP

  == domain 6  score: -3.4 bits;  conditional E-value: 3.6
                         zf-C3HC4_2   2 Cpi.Cldmlk 10 
                                        C++ C+d  +
  gene1965|gene1965|rna1965|rna1965 222 CQVsCFDCQS 231
                                        5555555433 PP

>> zf-C3HC4_3  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -5.6  13.8         7   1.8e+04       4      29 ..      42      68 ..      21      70 .. 0.78
   2 ?    3.2  12.1     0.032        83       4      47 ..      42      85 ..      39      88 .. 0.80
   3 ?   -1.2  10.4      0.75   1.9e+03       4      44 ..      77     112 ..      74     116 .. 0.63
   4 ?    1.3  13.2      0.12   3.1e+02       3      44 ..     106     152 ..     104     154 .. 0.84
   5 !   22.5   3.6   2.9e-08   7.4e-05       3      45 ..     146     191 ..     144     195 .. 0.90
   6 ?    2.2   2.4     0.065   1.7e+02      22      45 ..     222     249 ..     214     254 .. 0.82

  Alignments for each domain:
  == domain 1  score: -5.6 bits;  conditional E-value: 7
                                       B-TTTSSSBS-EEETT..EEEEEE-HHH CS
                         zf-C3HC4_3  4 eCviClerprnvvllp..CgHlvlCeeC 29
                                       +C +C++ ++++ +++  ++++ lC  C
  gene1965|gene1965|rna1965|rna1965 42 PCRLCHDHNEDHRMIRhrTKYM-LCLCC 68
                                       7999999877766654337888.88888 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.032
                                       B-TTTSSSBS-EEETT..EEEEEE-HHHHHHHHHTT-B-TTT--B- CS
                         zf-C3HC4_3  4 eCviClerprnvvllp..CgHlvlCeeCaekllkrkkkCpiCrrpi 47
                                       +C +C++ ++++ +++  ++++ lC  C       ++ C +C+ ++
  gene1965|gene1965|rna1965|rna1965 42 PCRLCHDHNEDHRMIRhrTKYM-LCLCCGMIQ-GASQFCIMCKVKM 85
                                       7******988876664349999.**9888777.789******9875 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 0.75
                                        B-TTTSSSBS-EEETTEEEEEE-HHHHHHHHH....TT-B-TTT- CS
                         zf-C3HC4_3   4 eCviClerprnvvllpCgHlvlCeeCaekllk....rkkkCpiCr 44 
                                         C++C+ + +n ++  C+ +           +    + k+C +Cr
  gene1965|gene1965|rna1965|rna1965  77 FCIMCKVKMANYFCKTCKFW---------TDSlgvfHCKQCKVCR 112
                                        57777777777777777655.........3223335667777777 PP

  == domain 4  score: 1.3 bits;  conditional E-value: 0.12
                                        SB-TTTSSSBS-EEETTEEEEEE-HHHHHHHHH.........TT-B-TTT- CS
                         zf-C3HC4_3   3 eeCviClerprnvvllpCgHlvlCeeCaekllk.........rkkkCpiCr 44 
                                        ++C++C   ++n+++    H+  C++C+ + l           k +CpiC 
  gene1965|gene1965|rna1965|rna1965 106 KQCKVCRVGNKNAFF----HCSDCNACLPRELLnnhnhventLKSTCPICA 152
                                        68*************....88899999976544478889999999*****6 PP

  == domain 5  score: 22.5 bits;  conditional E-value: 2.9e-08
                                        SB-TTTSS....SBS-EEETTEEEEEE-HHHHHHHHHTT-B-TTT-- CS
                         zf-C3HC4_3   3 eeCviCle....rprnvvllpCgHlvlCeeCaekllkrkkkCpiCrr 45 
                                        ++C+iC e    +  +vvll+CgH  +  +C++ +++++ +Cp+C +
  gene1965|gene1965|rna1965|rna1965 146 STCPICAEfmfeSVNDVVLLNCGHS-IHFACFKVYKESSFQCPVCLK 191
                                        68****9988766888*********.99*******99********76 PP

  == domain 6  score: 2.2 bits;  conditional E-value: 0.065
                                        EEEE-HHHHHHHHH....TT-B-TTT-- CS
                         zf-C3HC4_3  22 HlvlCeeCaekllk....rkkkCpiCrr 45 
                                        ++v C +C +  +       +kC  C +
  gene1965|gene1965|rna1965|rna1965 222 CQVSCFDCQSVSKTiytfLYNKCVKCGS 249
                                        6788999998887788899999999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1253  (0.0698868); expected 358.6 (0.02)
Passed bias filter:                      266  (0.0148363); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.56u 0.25s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 1597.53
//
Query:       gene1966|gene1966|rna1966|rna1966  [L=305]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.8e-57  192.6   2.3    9.8e-57  192.6   2.3    1.8  2  Fumble    Fumble


Domain annotation for each model (and alignments):
>> Fumble  Fumble
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.1     0.024   4.3e+02       2      14 ..      17      29 ..      16      32 .. 0.89
   2 !  192.6   2.3   5.5e-61   9.8e-57      69     328 ..      50     297 ..      29     299 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.024
                             Fumble  2 iavDiGgsLaKlv 14
                                       i++D GgsL+K++
  gene1966|gene1966|rna1966|rna1966 17 IGIDFGGSLIKCI 29
                                       89*********75 PP

  == domain 2  score: 192.6 bits;  conditional E-value: 5.5e-61
                             Fumble  69 kskekekkkktikaTGGGaykyaelikeelgvevekedemeclikGlkfllteipkevftyseekpkkavekkese 144
                                        k+  k+kk+  ++ TGGG+yky+ +  +++        eme+l  G k+l+++  ++ +ty+  + +k+++    +
  gene1966|gene1966|rna1966|rna1966  50 KEMLKRKKHARLTLTGGGSYKYNFTPCKNI------LPEMEALYLGYKYLIRHNAQQFYTYTP-TDMKQIQI---K 115
                                        222233344489**********87766555......78************************5.34444444...3 PP

                             Fumble 145 eiyPylLvniGSGvsilkvegeekfervgGtslgGgtfwGLlslLtgaksfdellelaekGdnskvDmlvgDiyGe 220
                                        +   ++LvniGSG+si+k ++  +fer+gGt +gGgtf GL +l++g ++ d + ++a+ G+n  vD+ ++DiyG+
  gene1966|gene1966|rna1966|rna1966 116 PSNECILVNIGSGISIVKLTKT-RFERLGGTTIGGGTFTGLGRLICGETDVDTMFHMASLGNNFGVDLSINDIYGN 190
                                        33459**************987.8***************************************************8 PP

                             Fumble 221 ..dyekiglksdliassfgkvfkkkkkkeeeekeDiarslLyaisnnigqiaylqaklhnlkriyFgGsfirgheq 294
                                          + + +gl +dl+assfgkv  ++  ++e +k+Di  slL  i+nn + +a+ +a+++n +ri+F+G f ++ ++
  gene1966|gene1966|rna1966|rna1966 191 cdTQQMLGLAGDLVASSFGKVSLSS--DTEYNKNDILSSLLSLIVNNACLMAISHAEKQNQQRIVFSGCFSSQ-AI 263
                                        7567778***************988..4555568************************************766.59 PP

                             Fumble 295 tmktlsyaikfwskgelkalFlrHegylGavGaf 328
                                          + + y ++   k +++ +F+   g+lGa G++
  gene1966|gene1966|rna1966|rna1966 264 VRERIVYCFHALKKTSIQPVFIAQAGFLGAFGCI 297
                                        99******************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (305 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       601  (0.0335211); expected 358.6 (0.02)
Passed bias filter:                      500  (0.0278878); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.45
# Mc/sec: 2035.34
//
Query:       gene1967|gene1967|rna1967|rna1967  [L=323]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (323 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1017  (0.0567237); expected 358.6 (0.02)
Passed bias filter:                      536  (0.0298957); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 1983.68
//
Query:       gene1968|gene1968|rna1968|rna1968  [L=582]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (582 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       603  (0.0336327); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.72u 0.28s 00:00:01.00 Elapsed: 00:00:00.53
# Mc/sec: 3308.21
//
Query:       gene1969|gene1969|rna1969|rna1969  [L=107]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       954  (0.0532099); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.30u 0.25s 00:00:00.55 Elapsed: 00:00:00.39
# Mc/sec: 820.80
//
Query:       gene197|gene197|rna197|rna197  [L=35]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.076   12.0   0.1      0.076   12.0   0.1    1.0  1  DUF684    Protein of unknown function (DUF684)


Domain annotation for each model (and alignments):
>> DUF684  Protein of unknown function (DUF684)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   4.3e-06     0.076       6      33 ..       3      30 ..       1      35 [] 0.86

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 4.3e-06
                         DUF684  6 lkkklkkLsdkmsekfddLkafiveqeF 33
                                   l++ +  ++ k+ ++f+dLk+f + +e+
  gene197|gene197|rna197|rna197  3 LNDMICDVDAKIRAEFEDLKSFTTDTEI 30
                                   778899999**************99885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (35 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       333  (0.0185733); expected 358.6 (0.02)
Passed bias filter:                      253  (0.0141112); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.43
# Mc/sec: 243.40
//
Query:       gene1970|gene1970|rna1970|rna1970  [L=49]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (49 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       513  (0.0286129); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.30u 0.23s 00:00:00.53 Elapsed: 00:00:00.38
# Mc/sec: 386.28
//
Query:       gene1971|gene1971|rna1971|rna1971  [L=46]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0053   16.3   0.0     0.0053   16.3   0.0    1.0  1  RVT_1           Reverse transcriptase (RNA-dependent DNA poly
  ------ inclusion threshold ------
      0.025   14.4   0.0      0.028   14.3   0.0    1.1  1  PEGA            PEGA domain
      0.065   12.5   0.0      0.065   12.5   0.0    1.0  1  RE_NgoFVII      NgoFVII restriction endonuclease
       0.11   11.6   0.0       0.11   11.5   0.0    1.0  1  Lipoprotein_18  NlpB/DapX lipoprotein


Domain annotation for each model (and alignments):
>> RVT_1  Reverse transcriptase (RNA-dependent DNA polymerase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   1.2e-06    0.0053      62     100 ..       5      43 ..       1      46 [] 0.86

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.2e-06
                                        HCCHTS--EEEEEEBCCGCCCSBB-GGGGGGG-EEET.. CS
                              RVT_1  62 lkkkkkaklllklDlkkaFdsvpleellrkltafkvptk 100
                                        +++k ++  l+ lDlk ++ +++ ee ++ +ta+ +  +
  gene1971|gene1971|rna1971|rna1971   5 VEAKIGSSNLTVLDLKEGYYQIEIEEADKHKTALEFGNN 43 
                                        5567888899***********************999855 PP

>> PEGA  PEGA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   6.2e-06     0.028      19      42 ..       6      30 ..       3      39 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 6.2e-06
                               PEGA 19 GkylGkTPvtls.leaGnyslrvek 42
                                       + ++G++++t+  l++G+y++++e 
  gene1971|gene1971|rna1971|rna1971  6 EAKIGSSNLTVLdLKEGYYQIEIEE 30
                                       5689******************984 PP

>> RE_NgoFVII  NgoFVII restriction endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   1.4e-05     0.065      92     134 ..       3      43 ..       1      46 [] 0.79

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.4e-05
                                        TEEEEEEESXXSXXTTSXXXSBXEEEEEE.HHHHHHHHHHHHH CS
                         RE_NgoFVII  92 kplsAliGSANlssnglrtrqrEtlvdldtedafkeldeyiqs 134
                                        ++++A iGS Nl+++ l++ ++ + ++  ++d+ k+  e+ ++
  gene1971|gene1971|rna1971|rna1971   3 RIVEAKIGSSNLTVLDLKEGYYQIEIE--EADKHKTALEFGNN 43 
                                        6899******************99887..46666666666655 PP

>> Lipoprotein_18  NlpB/DapX lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   2.5e-05      0.11     267     297 ..       8      42 ..       4      45 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 2.5e-05
                                        HHTSXX...XXXXSEEEEEEEEEET.TEEEEEEEX CS
                     Lipoprotein_18 267 slgake...ldlkegeYrlqlgdlg.nrtsitllD 297
                                        ++g+++   ldlkeg Y++ +++ + ++t++ + +
  gene1971|gene1971|rna1971|rna1971   8 KIGSSNltvLDLKEGYYQIEIEEADkHKTALEFGN 42 
                                        5777778889**************9455*999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (46 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       435  (0.0242624); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 306.39
//
Query:       gene1972|gene1972|rna1972|rna1972  [L=148]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.4e-09   35.9   1.7    1.4e-07   31.3   1.7    2.2  1  PAP2      PAP2 superfamily
  ------ inclusion threshold ------
       0.48   10.5   8.0        2.4    8.2   8.0    2.1  1  MARVEL    Membrane-associating domain
        1.4    9.1   5.4       0.86    9.8   1.0    2.1  2  DUF2178   Predicted membrane protein (DUF2178)


Domain annotation for each model (and alignments):
>> PAP2  PAP2 superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.3   1.7   2.4e-11   1.4e-07       9     125 ..      36     134 ..      31     144 .. 0.80

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 2.4e-11
                               PAP2   9 lalaalltsvlKdlvgrpRPfflaeetkldtqvstletseskeakesfPSgHsafafalalllalllrrkrkkigl 84 
                                        +al  +++++lK +++  RP  +++  +        +     + ++ fPS+Hs+f +  +      + ++  +   
  gene1972|gene1972|rna1972|rna1972  36 IALCFIVSNILKLYFRMDRPGDVNRGYIRGIVDNGIYI---FTSNYAFPSTHSVFYTQYF------MYNMSVF--- 99 
                                        7888999******************9999998555554...4678999999998766544......4455555... PP

                               PAP2  85 vllalillllavlvalsRlylgvHflsDvlaGlliGialaa 125
                                              ++l  ++ +++R++ ++H++ +v++Gl++++++ +
  gene1972|gene1972|rna1972|rna1972 100 ------TFLIGLFGIFTRVFYNHHTPQQVFFGLCFALFMEI 134
                                        ......5566678999********************99866 PP

>> MARVEL  Membrane-associating domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   8.0    0.0004       2.4      29      75 ..      65     124 ..       2     134 .. 0.68

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0004
                             MARVEL  29 a............kldqllgspssalnfavfvavfsflyalfllvlylfk.nsaftsilw 75 
                                        +            +++   +s   ++ f+  ++vf+fl+ lf+++  +f+ + + ++ ++
  gene1972|gene1972|rna1972|rna1972  65 GivdngiyiftsnYAFPSTHSVFYTQYFMYNMSVFTFLIGLFGIFTRVFYnHHTPQQVFF 124
                                        05555555555556677888899999***********************96555444444 PP

>> DUF2178  Predicted membrane protein (DUF2178)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.2     0.059   3.5e+02      81     106 .]      24      49 ..       2      49 .. 0.69
   2 ?    9.8   1.0   0.00014      0.86      64     100 ..      96     131 ..      93     137 .. 0.73

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.059
                            DUF2178  81 lksdfpeytrvgfllafsallllilY 106
                                         +s +   + + ++l+f+++ +l lY
  gene1972|gene1972|rna1972|rna1972  24 RRSVYHSNQIIRIALCFIVSNILKLY 49 
                                        44555556889999999999888777 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00014
                            DUF2178  64 lqillfliallgvvlivlksdfpeytrvgfllafsal 100
                                        + +++fli+l g++  v+ +++   ++v f l+f+++
  gene1972|gene1972|rna1972|rna1972  96 MSVFTFLIGLFGIFTRVFYNHH-TPQQVFFGLCFALF 131
                                        789**************66654.44566666666644 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       647  (0.0360868); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 924.67
//
Query:       gene1973|gene1973|rna1973|rna1973  [L=202]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.1e-13   48.6   0.3    1.9e-12   47.0   0.1    1.9  2  Med26     TFIIS helical bundle-like domain


Domain annotation for each model (and alignments):
>> Med26  TFIIS helical bundle-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0      0.21   3.7e+03       3       3 ..     109     109 ..      95     120 .. 0.49
   2 !   47.0   0.1     1e-16   1.9e-12       1      50 [.     144     193 ..     144     195 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.21
                                        H CS
                              Med26   3 L 3  
                                        L
  gene1973|gene1973|rna1973|rna1973 109 L 109
                                        3 PP

  == domain 2  score: 47.0 bits;  conditional E-value: 1e-16
                                        HHHHHS---....HHHHHHSHHHHHHHHHH-TTS-HHHHHHHHHHHHHHH CS
                              Med26   1 kiLaqLeklpittetLkstgIGkvVnalrkhkhetaevktlAksLvekWk 50 
                                        +iL+ L k+ +t+++L ++ IGk+V +++ ++het+e+++l k+Lv+kW 
  gene1973|gene1973|rna1973|rna1973 144 EILSFLLKTSVTRDQLVESEIGKIVYFYSLNNHETSEIRNLSKQLVKKWT 193
                                        59999****99******************999*****************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       858  (0.0478554); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.31s 00:00:00.87 Elapsed: 00:00:00.53
# Mc/sec: 1156.48
//
Query:       gene1975|gene1975|rna1975|rna1975  [L=195]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       621  (0.0346366); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.42
# Mc/sec: 1385.98
//
Query:       gene1976|gene1976|rna1976|rna1976  [L=211]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.7e-15   55.3   1.1    1.9e-08   33.6   0.2    3.1  2  ORC2      Origin recognition complex subunit 2
  ------ inclusion threshold ------
        1.1    9.5   8.1       0.14   12.3   3.1    2.1  2  Mg296     Mg296 protein


Domain annotation for each model (and alignments):
>> ORC2  Origin recognition complex subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.1   2.5e-07    0.0023      31      71 ..       2      41 ..       1      63 [. 0.84
   2 !   33.6   0.2   2.1e-12   1.9e-08     172     318 ..      79     195 ..      73     203 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2.5e-07
                                       HHHHHHHHGGGHHHHHHHHHTT-EEEE--SS--HHHHHHHH CS
                               ORC2 31 kekLeklhkklfpqwlfeLeqGFslllyGvGSKrklleeFa 71
                                       k+kL++ h +  p++l+ L+  F++l+yG+G K  ll+e  
  gene1976|gene1976|rna1976|rna1976  2 KKKLKDFHISCVPEYLTFLK-TFNILFYGYGDKSVLLREMF 41
                                       57888888889999888765.6***************9865 PP

  == domain 2  score: 33.6 bits;  conditional E-value: 2.1e-12
                                        EEEEE--STTHHHH.--HHHHTTS-EEE---------GGGGGG--.-TT---.--.----HHHHHHHHHHS-HHHH CS
                               ORC2 172 hliasiDhinapll.wdssklsqfnfvfhdvtTfapysaElsfedevlellgrskrrvggkegakfVLkSLtenar 246
                                        ++++  D+++   + +  + l+ fnf++ d+tT+ py  E  fe               g+  +k  L+ +++++r
  gene1976|gene1976|rna1976|rna1976  79 NVVCVLDTMDPTAInFCDEDLEDFNFIMKDLTTYVPY--ENVFEV-----D-------KGEADLKNLLNNVPKRSR 140
                                        5778888887655415555669***************..444443.....2.......37899************* PP

                                        HHHHHHHHHHHT--------------------BHHHHHHHHHHS--SSSGGGHHHHHHHHTTTTSS-B---- CS
                               ORC2 247 klfklLveeqLekkeseekkekskkgseeagveykelynkareefivssemalrtlLkEFkDHklikskkda 318
                                        +l+k+ ++ +                  ++   + el+n a++e + ++  ++ +lL EF+DH +ik ++d+
  gene1976|gene1976|rna1976|rna1976 141 NLLKIFINLCE-----------------NNFALITELLNVAKKELFITNTKTIYQLLGEFVDHRIIKYREDK 195
                                        *****998542.................3444578999*****************************99886 PP

>> Mg296  Mg296 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.1       0.3   2.7e+03      46      64 ..      30      48 ..      23      50 .. 0.88
   2 ?   12.3   3.1   1.6e-05      0.14      12     112 ..      64     165 ..      52     183 .. 0.69

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.3
                                       --S-HHHHHHHHHHHHHHH CS
                              Mg296 46 yeeidffeksieselfyvk 64
                                       y +++ +++ +  ++++++
  gene1976|gene1976|rna1976|rna1976 30 YGDKSVLLREMFPNANFIN 48
                                       8899999999*99999996 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 1.6e-05
                                        HHHHHTS-HHHH.HHHHHHHHHHHHT-SSGGGSS---S-HHHHHHHHHHHHHHHHHHH---.....---------- CS
                              Mg296  12 keilekvdlekl.iqnynlileretstlliyedddyeeidffeksieselfyvksklvkelndhiedllkvkvddd 86 
                                        k  l   d ek+ ++n   +l+    t + + d+d e+ +f +k + +   yv  + v e++    dl + + + +
  gene1976|gene1976|rna1976|rna1976  64 KFDLTSTDPEKFpKNNVVCVLDTMDPTAINFCDEDLEDFNFIMKDLTT---YVPYENVFEVDKGEADLKNLLNNVP 136
                                        5567778889993456667799999*******************9976...6666777777444445444444445 PP

                                        -...--HHHHHHHHHHHSHHHHHHHHHHT CS
                              Mg296  87 k...gdlkilhdsfyealtllisalaltk 112
                                        k     lki  +   + ++l+++ l ++k
  gene1976|gene1976|rna1976|rna1976 137 KrsrNLLKIFINLCENNFALITELLNVAK 165
                                        51104456655555566666666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       694  (0.0387082); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.42
# Mc/sec: 1515.04
//
Query:       gene1977|gene1977|rna1977|rna1977  [L=188]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
        0.1   13.0   3.4       0.42   11.0   0.1    2.2  2  DUF3048_C  Protein of unknown function (DUF3048) C-terminal d
       0.26   11.5   2.6       0.48   10.6   2.6    1.5  1  BCOR       BCL-6 co-repressor, non-ankyrin-repeat region


Domain annotation for each model (and alignments):
>> DUF3048_C  Protein of unknown function (DUF3048) C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.6     0.012   1.1e+02      12      36 ..      33      57 ..      22      78 .. 0.77
   2 ?   11.0   0.1   4.6e-05      0.42       9      51 ..      77     122 ..      65     180 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.012
                                       EEEETTTTEEEEEETTEE-B-TTTS CS
                          DUF3048_C 12 feYdaedglYlryqdgephideetg 36
                                        +Y++++ +Y+r  +++ + +++  
  gene1977|gene1977|rna1977|rna1977 33 PNYNEARREYRRMCKNKHTYNQNAR 57
                                       57**********9998888776654 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 4.6e-05
                                        S.EEEEEETTTTEEEEEETTEE-B-T..TTSSB--BSEEEEEE-.. CS
                          DUF3048_C   9 k.stfeYdaedglYlryqdgephide..etgeqlavkNvivlevev 51 
                                        +  ++ ++ ++ + +r  ++++++ e  + ++  a +Nv+++ v +
  gene1977|gene1977|rna1977|rna1977  77 QlRYYIWSRKRSKHDRTIYEDENVSEkrKRKSACASDNVVLMRVFH 122
                                        3589********************995556667999******9843 PP

>> BCOR  BCL-6 co-repressor, non-ankyrin-repeat region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   2.6   5.4e-05      0.48     161     205 ..      43      88 ..      41     117 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 5.4e-05
                               BCOR 161 KRpCKTKHlslqerrrelsktkeeatelekaegkvtverra....rkrp 205
                                        +R CK KH+ +q++rr+l + k    ++ +a+ ++  + r     rkr+
  gene1977|gene1977|rna1977|rna1977  43 RRMCKNKHTYNQNARRILGLGKV---KIVNAKRDKIKQLRYyiwsRKRS 88 
                                        59**************9998886...44455444444444334556664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       862  (0.0480785); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.31s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 1160.13
//
Query:       gene1978|gene1978|rna1978|rna1978  [L=197]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.6e-06   26.4   7.4    8.3e-06   25.6   7.4    1.4  1  PHD          PHD-finger
  ------ inclusion threshold ------
      0.018   15.6   1.5      0.039   14.5   1.4    1.7  1  ING          Inhibitor of growth proteins N-terminal histone-
      0.021   14.8   0.5       0.03   14.3   0.5    1.3  1  Swm2         Nucleolar protein Swm2
      0.032   14.3   1.9      0.052   13.7   1.2    1.7  1  DMAP1_like   Putative DMAP1-like
      0.037   13.6   3.7      0.066   12.8   3.7    1.5  1  PHD_2        PHD-finger
      0.043   13.3   0.2       0.06   12.8   0.2    1.2  1  Latexin      Latexin
       0.12   12.2   3.8        5.1    6.8   0.0    2.6  3  Rep_fac-A_C  Replication factor-A C terminal domain
        1.1    9.6   8.9       0.46   10.8   4.6    2.4  2  zf-HC5HC2H   PHD-like zinc-binding domain


Domain annotation for each model (and alignments):
>> PHD  PHD-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   7.4   3.7e-09   8.3e-06       1      51 [.     145     191 ..     145     192 .. 0.88

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 3.7e-09
                                        SBTTTTSTTSTTSCEEEET..TTSC.EEETTTSSSTHSHHSHHSSTBSSTTTHT CS
                                PHD   1 rCavCkkksdeeeelvqCd..gCkr.wfHqkClkppleseekpegewlCekCke 51 
                                        +C +C++   + ++++ Cd  gCk  w+H +C+++  +    p+g+w+C++Ck+
  gene1978|gene1978|rna1978|rna1978 145 YC-LCRA--SAFGDMIRCDdpGCKVlWYHFECVGLVHT----PKGNWYCSTCKK 191
                                        69.9*99..89*******9556*976**********77....7889******96 PP

>> ING  Inhibitor of growth proteins N-terminal histone-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   1.4   1.7e-05     0.039       4      64 ..      21      85 ..      18     108 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.7e-05
                                       HHHTSGGGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTS..S-HHHHHHHHH....HHHH CS
                                ING  4 dyldsvenLPlelqrnltelreiDakvqellkeidskiekflkngslqknekeeels....riqe 64
                                       ++l++v   Pl+ q++l  +++iD+k+ + +++++++ +  lk ++++ n++ +++     ++++
  gene1978|gene1978|rna1978|rna1978 21 KLLNDVHLYPLDAQHQLVTIQDIDNKIVNYTRKLHKYFKGSLKLSRKTYNKQIKKCLasisHLNR 85
                                       678899999*************************9999999933333333333332221223333 PP

>> Swm2  Nucleolar protein Swm2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.5   1.3e-05      0.03       4      75 ..      40     111 ..      37     143 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.3e-05
                               Swm2   4 ltdlekipkeysplLspyye.aiakdeelkkkalkkCkevfekweekddavdkevvkrcldlwlvlkgkeYkl 75 
                                        ++d+++   +y+  L +y++ + + +++  +k +kkC   ++++++k++a  + ++++  +++  ++ + Y  
  gene1978|gene1978|rna1978|rna1978  40 IQDIDNKIVNYTRKLHKYFKgSLKLSRKTYNKQIKKCLASISHLNRKRKAAMSIIMECTREIYADMQKE-YPE 111
                                        6788777889*********9568899999********************99999999999**9998765.765 PP

>> DMAP1_like  Putative DMAP1-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   1.2   2.3e-05     0.052      35      87 ..      39      88 ..      17      96 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.3e-05
                         DMAP1_like 35 eledkelkikeiinkkqsypnvfLaSslgfskstwnkkvekiLkkf.gldkklk 87
                                       +++d++   ++i+n ++++++ f + sl++s++t+nk+++k L  + +l++k k
  gene1978|gene1978|rna1978|rna1978 39 TIQDID---NKIVNYTRKLHKYFKG-SLKLSRKTYNKQIKKCLASIsHLNRKRK 88
                                       344444...5666667777776666.59***************98746777765 PP

>> PHD_2  PHD-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   3.7     3e-05     0.066       4      36 .]     156     190 ..     153     190 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3e-05
                              PHD_2   4 llsCd..kCsva.VHasCYGvskesdgeeWlCrrCe 36 
                                        ++ Cd  +C+v   H +C G++  ++g  W+C+ C+
  gene1978|gene1978|rna1978|rna1978 156 MIRCDdpGCKVLwYHFECVGLVHTPKG-NWYCSTCK 190
                                        78899889998537*************.*******5 PP

>> Latexin  Latexin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.2   2.7e-05      0.06      51      99 ..      61     107 ..      32     122 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.7e-05
                                        EEEEEEEETTT---EEEEEEEEEE--TT-----EEEEEESS------HH CS
                            Latexin  51 dlefsveeyiseeelgkCsAevlfkkqkprpaievkctvegelkkrqqe 99 
                                        +l++s ++y  +++++kC A++ + ++k + a+++ ++++ e+  + q+
  gene1978|gene1978|rna1978|rna1978  61 SLKLSRKTY--NKQIKKCLASISHLNRKRKAAMSIIMECTREIYADMQK 107
                                        455555555..567******************99988888877766665 PP

>> Rep_fac-A_C  Replication factor-A C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0         1   2.3e+03     113     127 ..      61      75 ..      33      90 .. 0.58
   2 ?    6.8   0.0    0.0023       5.1      78     127 ..      93     142 ..      87     152 .. 0.88
   3 ?    5.5   0.7    0.0059        13      31      47 ..     177     193 ..     162     196 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1
                                        EEEEE---------- CS
                        Rep_fac-A_C 113 rlrvkeesyndesrv 127
                                         l+   ++yn + ++
  gene1978|gene1978|rna1978|rna1978  61 SLKLSRKTYNKQIKK 75 
                                        355566666665544 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0023
                                        HHHSS-HHHHHHHCCC-HHHHHHHHHHTTT-EEEEEEEEE---------- CS
                        Rep_fac-A_C  78 kllglsaeelkklkeedeeefekiiekvklkeflfrlrvkeesyndesrv 127
                                         ++ ++ e + ++++e +ee+++ i + + ++ +f+ rv +e  n++ ++
  gene1978|gene1978|rna1978|rna1978  93 IIMECTREIYADMQKEYPEELKSSIGDPSKNPSVFKTRVSKEDVNNNIKQ 142
                                        688999999******************************99999987765 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.0059
                                        EEETTTEEEETTTTEEE CS
                        Rep_fac-A_C  31 veeedgewrCekCdkev 47 
                                        v++ +g+w+C +C+k+ 
  gene1978|gene1978|rna1978|rna1978 177 VHTPKGNWYCSTCKKNR 193
                                        566789********985 PP

>> zf-HC5HC2H  PHD-like zinc-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.1       1.2   2.7e+03       4      25 ..      76      95 ..      63     109 .. 0.51
   2 ?   10.8   4.6    0.0002      0.46      29      66 ..     135     174 ..     119     193 .. 0.72

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 1.2
                         zf-HC5HC2H  4 Calwipevvfeeekeiemeeie 25
                                       C+  i+++  +++    m+ i+
  gene1978|gene1978|rna1978|rna1978 76 CLASISHLNRKRKAA--MSIIM 95
                                       444444443333222..33333 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.0002
                         zf-HC5HC2H  29 kikkerkklkCylCkkk.vGaciqCskkkCkk.afHvtCa 66 
                                        +++++ k+ k +lC+ +  G +i+C+ + Ck   +H+ C 
  gene1978|gene1978|rna1978|rna1978 135 DVNNNIKQPKYCLCRASaFGDMIRCDDPGCKVlWYHFECV 174
                                        3444445555567775559***********97479****6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1345  (0.0750181); expected 358.6 (0.02)
Passed bias filter:                      670  (0.0373696); expected 358.6 (0.02)
Passed Vit filter:                        78  (0.00435049); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 1256.39
//
Query:       gene1979|gene1979|rna1979|rna1979  [L=98]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-28   97.8   9.7    2.9e-28   97.7   9.7    1.0  1  Med31     SOH1


Domain annotation for each model (and alignments):
>> Med31  SOH1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.7   9.7   1.6e-32   2.9e-28       2      93 ..       3      95 ..       2      97 .. 0.95

  Alignments for each domain:
  == domain 1  score: 97.7 bits;  conditional E-value: 1.6e-32
                                       HHHHHHHHHHHHHCSHHHHHHTTSSSSSSSTHHHHHHHGGGGGSTTCCCTT--CHHHHHHHHHHSSTT.CCCCTCTCH CS
                              Med31  2 krFeleleFvqsLanpaYlshLaqekyledeafiaYLkYLeywkepeYakfltyPqcLkaLellqeee.frkelkkpe 78
                                       ++Fe eleFvq L+np+Yl++L+q+ky++d++f ++LkYLeywke++Y + l yPq+L +L+ l+++e f ++l +++
  gene1979|gene1979|rna1979|rna1979  3 TKFEKELEFVQLLCNPYYLQYLYQNKYFDDPDFRKFLKYLEYWKEKPYRNLLIYPQSLAILDALNNNEeFVSKLDDEK 80
                                       69**************************************************************87655********* PP

                                       HHHHHHHHHHHH-XX CS
                              Med31 79 vvealekqqllewqk 93
                                       ++e++++q    w +
  gene1979|gene1979|rna1979|rna1979 81 ILEFVDEQLRFYWLH 95
                                       ********9998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       645  (0.0359752); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.24s 00:00:00.58 Elapsed: 00:00:00.37
# Mc/sec: 793.25
//
Query:       gene198|gene198|rna198|rna198  [L=299]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-07   31.2  10.9      2e-07   30.7  10.9    1.3  1  SMC_N            RecF/RecN/SMC N terminal domain
  ------ inclusion threshold ------
      0.039   13.4  13.4      0.059   12.8  13.4    1.3  1  Golgin_A5        Golgin subfamily A member 5
      0.063   12.5   4.8      0.027   13.7   2.2    1.6  2  Glyco_transf_11  Glycosyl transferase family 11
      0.082   12.0  11.9       0.51    9.4   7.1    2.5  2  Atg14            Vacuolar sorting 38 and autophagy-related su
       0.28   11.2  10.0       0.33   11.0   7.6    2.2  2  DUF1043          Protein of unknown function (DUF1043)
        1.5    7.6  18.4        1.8    7.3  18.4    1.1  1  CALCOCO1         Calcium binding and coiled-coil domain (CALC
        3.6    8.2  16.6       0.33   11.6   4.9    2.4  2  ING              Inhibitor of growth proteins N-terminal hist
        4.1    6.7  12.3        6.7    6.0  12.3    1.3  1  FAM76            FAM76 protein


Domain annotation for each model (and alignments):
>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.7  10.9     9e-11     2e-07      76     198 ..      30     262 ..       5     281 .. 0.74

  Alignments for each domain:
  == domain 1  score: 30.7 bits;  conditional E-value: 9e-11
                                    EEEEEEEE.EETTEESSSSSSCEEEEEEEETTSEEEEEE...TTEEE-HHHHHHHHHCTT-STT................ CS
                                    xxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxx................ RF
                          SMC_N  76 kaeveitf.dnedkklkiekeevsisrrvkrkgeseyki...ngkevtkkevsellesagiske................ 135
                                    + +v+  f d+e ++ k + ++++++  ++++++ +y     ++ e  +k++++ l++  +                   
  gene198|gene198|rna198|rna198  30 ELNVQKAFlDKERENKKRKISKIKTELVKYTTEQMSYVTelpEDIESLEKQIASELAKITFLNAdkkvlkdykekeklln 109
                                    55555555333333344455555555555555555554422223333345555555555555446777777777777777 PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                          SMC_N 136 ................................................................................ 135
                                                                                                                    
  gene198|gene198|rna198|rna198 110 dfhlkelemenkrkvsnqdinnlredlinslnekvavvndnfanffqklsfdgkveletenmkaskwklnilvrfrkeeq 189
                                    77777777777777777777777777777788899999999999999999999999999999999999999999999999 PP

                                    .......CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHH...HHCTTSEEEEE-SS CS
                                    .......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxx RF
                          SMC_N 136 .......lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellk...eksknaQfivislr 198
                                             SgGe++++ + +l+++ ++ pap+ l+Dei++ +D  n ++v +ll    +++++ Qf++++ +
  gene198|gene198|rna198|rna198 190 mqqlcsyIQSGGERSVSTIIFLLSLLEATPAPFRLVDEINQGMDSYNERIVHNLLVdliRNKNSPQFFIVTPK 262
                                    999999999****************************************9999887443455568****9955 PP

>> Golgin_A5  Golgin subfamily A member 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8  13.4   2.6e-05     0.059      45     162 ..      24     143 ..       3     159 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.6e-05
                      Golgin_A5  45 lsaeldelkqerdllreelqklnqqieqlrtelqdleaqqqaeaeslreqlqeleeqleeerkake..eveaelerlkee 122
                                     + +++el+ ++  l +e ++ + +i++++tel +  ++q + + +l e +++le+q+++e ++    ++++++ +  +e
  gene198|gene198|rna198|rna198  24 DKHKIEELNVQKAFLDKERENKKRKISKIKTELVKYTTEQMSYVTELPEDIESLEKQIASELAKITflNADKKVLKDYKE 103
                                    567899*****************************************************998887622566777788899 PP

                      Golgin_A5 123 lryleeelvrskatlqsrikdrekeieklrnqlttkslss 162
                                     + l ++ + +  +++++ k  +++i++lr++l ++ +++
  gene198|gene198|rna198|rna198 104 KEKLLNDFHLKELEMENKRKVSNQDINNLREDLINSLNEK 143
                                    9999*****************************9987765 PP

>> Glyco_transf_11  Glycosyl transferase family 11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   2.2   1.2e-05     0.027      16     114 ..      34     130 ..      18     136 .. 0.78
   2 ?   -1.4   0.0      0.47     1e+03      29      82 ..     172     229 ..     143     277 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.2e-05
                Glyco_transf_11  16 qaawalkiqklks.kkglftvnlngrlgnqkgeyatllalakllgrlafipasmeeiLaPfritlkvlakevklrkilsn 94 
                                    q a+  k +  k+ k+ +  ++l ++   q+    t l ++  +++l++  as+ + ++ ++ ++kvl+   ++ k+l++
  gene198|gene198|rna198|rna198  34 QKAFLDKERENKKrKISKIKTELVKYTTEQMSYV-TELPED--IESLEKQIASELAKITFLNADKKVLKDYKEKEKLLND 110
                                    4445445444444488888888888888877544.444566..99999999999999999******************** PP

                Glyco_transf_11  95 yhlkdfleeeYralrgetvk 114
                                    +hlk+++ e+ r++++++++
  gene198|gene198|rna198|rna198 111 FHLKELEMENKRKVSNQDIN 130
                                    *********99999988765 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.47
                Glyco_transf_11  29 kkglftvnlngrl..gnqkgeyatllalak..llgrlafipasmeeiLaPfritlkvl 82 
                                    k  ++  n+ +r+    q++++ + +       +    f++   e++ aPfr    + 
  gene198|gene198|rna198|rna198 172 KASKWKLNILVRFrkEEQMQQLCSYIQSGGerSVSTIIFLLSLLEATPAPFRLVDEIN 229
                                    4456666666665223566776666654322245555556666666666666555544 PP

>> Atg14  Vacuolar sorting 38 and autophagy-related subunit 14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   7.1   0.00023      0.51      79     155 ..       3      86 ..       1      88 [. 0.88
   2 ?    6.6   0.6    0.0016       3.5      37     142 ..      73     203 ..      67     299 .] 0.60

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00023
                          Atg14  79 lrerlqelkdklsqlkkeieekkkklaklsdklk.......kRrsdleslqneleerrkkqiaklqdaikrieqklssls 151
                                    ++e+l+  +d +++lk ++e  k+k+++l+ + +        ++++++++++el ++ ++q++ +++    ie   +++ 
  gene198|gene198|rna198|rna198   3 IQEKLRSFMDEIRNLKIRLELDKHKIEELNVQKAfldkereNKKRKISKIKTELVKYTTEQMSYVTELPEDIESLEKQIA 82 
                                    68999999**********************9988******98888888**************999988888888877777 PP

                          Atg14 152 sktl 155
                                    s+++
  gene198|gene198|rna198|rna198  83 SELA 86 
                                    7765 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0016
                          Atg14  37 ekeslkkkiekalegke...eaeqledkiknkkakleelksliadlrerlqelkdklsqlkke.ieekkkklaklsdklk 112
                                    + esl+k+i  +l++ +   + ++  ++ k k + l++   +  + +++ +  ++++ +l++  i+   +k+a  +d+ +
  gene198|gene198|rna198|rna198  73 DIESLEKQIASELAKITflnADKKVLKDYKEKEKLLNDFHLKELEMENKRKVSNQDINNLREDlINSLNEKVAVVNDNFA 152
                                    55889999999999888777555566666666666666666666666666666666666665326666666666666666 PP

                          Atg14 113 .................kRrsdleslqneleerrkkqiaklqdaik....r 142
                                                      ++++  +l+  ++ r+++q+++l ++i+    r
  gene198|gene198|rna198|rna198 153 nffqklsfdgkveleteNMKASKWKLNILVRFRKEEQMQQLCSYIQsggeR 203
                                    777777799999999998888888888888999999999999999966552 PP

>> DUF1043  Protein of unknown function (DUF1043)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   7.6   0.00015      0.33      27      93 ..      36     103 ..      25     135 .. 0.81
   2 ?   -0.6   1.6      0.54   1.2e+03      28      78 ..     117     157 ..      98     194 .. 0.56

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00015
                        DUF1043  27 kklekelekakaeleeqkqeledHfaqsaelLetlaedyqkLyqhlaksseeLlp.eleeqelfqqkk 93 
                                    + l ke e++k ++++ k el ++ ++ ++ +++l ed + L +++a++  ++++ +++++ l+  k+
  gene198|gene198|rna198|rna198  36 AFLDKERENKKRKISKIKTELVKYTTEQMSYVTELPEDIESLEKQIASELAKITFlNADKKVLKDYKE 103
                                    458899**********************************************9776666665544333 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.54
                        DUF1043  28 klekelekakaeleeqkqeledHfaqsaelLetlaedyqkLyqhlakssee 78 
                                    ++e++ + +++ +++ +++l           ++l+e+   +++++a+  ++
  gene198|gene198|rna198|rna198 117 EMENKRKVSNQDINNLREDLI----------NSLNEKVAVVNDNFANFFQK 157
                                    334444444444444444443..........44444444444444443333 PP

>> CALCOCO1  Calcium binding and coiled-coil domain (CALCOCO1) like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3  18.4   0.00082       1.8      74     237 ..       6     173 ..       1     191 [. 0.81

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.00082
                       CALCOCO1  74 erkelesrveelkeelkesrekveeleekq....kelerlseelaeeksalleakeesearirELEeDiktltqralekE 149
                                    + + + +++ +lk  l+  ++k+eel+ ++    ke e+ + ++++ k+ l++ + e+ + + EL eDi++l ++     
  gene198|gene198|rna198|rna198   6 KLRSFMDEIRNLKIRLELDKHKIEELNVQKafldKERENKKRKISKIKTELVKYTTEQMSYVTELPEDIESLEKQIASEL 85 
                                    455666788999999999999999998774444489999999******************************88877666 PP

                       CALCOCO1 150 teLeRlkerakkalaqrkeeeaerkqlqakleqseeelrslskelqelrnslae.rdtqvlqLqdtittltqkLttAqrk 228
                                    +++  l +  kk+l+  ke+e+  ++++ k  + e+  +  ++++++lr+ l +  + +v  ++d+ ++  qkL+   + 
  gene198|gene198|rna198|rna198  86 AKITFL-NADKKVLKDYKEKEKLLNDFHLKELEMENKRKVSNQDINNLREDLINsLNEKVAVVNDNFANFFQKLSFDGKV 164
                                    666555.56788999999888888887755555555555567899**99877551577889999***********99999 PP

                       CALCOCO1 229 eaenEallk 237
                                    e+e+E++++
  gene198|gene198|rna198|rna198 165 ELETENMKA 173
                                    999999875 PP

>> ING  Inhibitor of growth proteins N-terminal histone-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   3.8      0.14   3.1e+02      13      68 ..       4      58 ..       2      63 .. 0.82
   2 ?   11.6   4.9   0.00015      0.33       1      82 [.      66     149 ..      66     159 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.14
                                   HHHHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHTS..S-HHHHHHHHHHHHHHHHH CS
                            ING 13 PlelqrnltelreiDakvqellkei.dskiekflkngslqknekeeelsriqeelke 68
                                   +++l+  ++e+r++  +++  +++i + +++k +   +++ ++k++++s+i+ el +
  gene198|gene198|rna198|rna198  4 QEKLRSFMDEIRNLKIRLELDKHKIeELNVQKAF--LDKERENKKRKISKIKTELVK 58
                                   5678899999999999999999999555677777..5789999********999865 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00015
                                    HHHHHHTSGGGHHHHHHHHHHHHH..HHHHHHHHHHHHHHHHHHHHHTS..S-HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            ING   1 yLedyldsvenLPlelqrnltelr..eiDakvqellkeidskiekflkngslqknekeeelsriqeelkeaqelldeKiq 78 
                                    y+ ++ +++e+L +++   l ++   + D+kv + +ke ++ +++f  ++ + +n+++ + ++i++  ++++++l+eK++
  gene198|gene198|rna198|rna198  66 YVTELPEDIESLEKQIASELAKITflNADKKVLKDYKEKEKLLNDFHLKELEMENKRKVSNQDINNLREDLINSLNEKVA 145
                                    67778899***************9334699****************9555555566666666****************** PP

                                    HHHH CS
                            ING  79 laqq 82 
                                    ++++
  gene198|gene198|rna198|rna198 146 VVND 149
                                    *986 PP

>> FAM76  FAM76 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0  12.3     0.003       6.7     185     292 ..      30     144 ..       4     154 .. 0.55

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.003
                          FAM76 185 rlevskle.eeklaeekesnetskksldsnssdhlvavtqLkeeiaslkkqleqkdqel..lekdkkitelkaellekek 261
                                    +l+v+k+  ++++ ++k + +++k++l + +++++  vt+L e+i+sl+kq+++   ++  l+ dkk+ +   e+++  +
  gene198|gene198|rna198|rna198  30 ELNVQKAFlDKERENKKRKISKIKTELVKYTTEQMSYVTELPEDIESLEKQIASELAKItfLNADKKVLKDYKEKEKLLN 109
                                    23333333223333334444455557888899********************9765443226777766443333333333 PP

                          FAM76 262 el...reklkelekeakekieklekk.irellkev 292
                                    +    +  +++ +k +++ i++l++  i++l  +v
  gene198|gene198|rna198|rna198 110 DFhlkELEMENKRKVSNQDINNLREDlINSLNEKV 144
                                    32000223444445555555565543244444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2038  (0.113671); expected 358.6 (0.02)
Passed bias filter:                      490  (0.02733); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.63u 0.31s 00:00:00.94 Elapsed: 00:00:00.49
# Mc/sec: 1829.45
//
Query:       gene1980|gene1980|rna1980|rna1980  [L=353]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.1e-11   44.5   2.8    8.4e-11   41.6   2.8    2.3  1  DNA_pol_E_B  DNA polymerase alpha/epsilon subunit B
    1.5e-11   44.5   0.0      7e-11   42.3   0.0    1.9  2  DNA_pol_D_N  DNA polymerase delta subunit OB-fold domain
  ------ inclusion threshold ------
      0.058   13.7   0.0       0.16   12.4   0.0    1.8  1  EF-hand_14   EF-hand domain
      0.067   13.4   0.0       0.14   12.4   0.0    1.6  1  DUF3692      CRISPR-associated protein


Domain annotation for each model (and alignments):
>> DNA_pol_E_B  DNA polymerase alpha/epsilon subunit B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.6   2.8   1.9e-14   8.4e-11      32     202 ..     172     310 ..     145     317 .. 0.78

  Alignments for each domain:
  == domain 1  score: 41.6 bits;  conditional E-value: 1.9e-14
                                        --SEEEEES-SSBTTSHHHHHT---S--SSHHHHHHHHTHHHHTTS-TTSEEEEE--TTBTT-S-SBSB----TTT CS
                        DNA_pol_E_B  32 ppdvlilaGnfvdaahkaiasskvstdekkenfdalalllsilesllekttvvlvPgpnDpanstvlPqqPlprll 107
                                        +++ l+++G  +d             + +ken d la++l+++      ++ +++P++nDp+n+ +lPqqP+    
  gene1980|gene1980|rna1980|rna1980 172 KVTDLVIIGDIFD-------------EVTKENADLLAQFLEDFG-----ADAFIIPNINDPTNK-LLPQQPI---- 224
                                        5555555555555.............235666666776666665.....5669***********.*******.... PP

                                        TT--TTT...EEE--BSEEEEETTEEEEE--S-HHHH---EEESHHHHHS-HHHHHHHHHHHHTBS---SS.--B- CS
                        DNA_pol_E_B 108 lsrikrvfkelklvtNPsrielnsvevvltsddivkdlkreslkesntdverlrklvktildqrhlaPlap.tlrp 182
                                         +ri  +  ++ +++ P  +e+ + +++++   +++d+k +   +         +++k +++ rh++P+ap t+ +
  gene1980|gene1980|rna1980|rna1980 225 SNRIIDY--NCLFLPSPALFEV-GAKMLFIPPVVINDIKLYGEPSAI-------NIMKMLVKIRHICPTAPdTVGC 290
                                        5667777..68999***99998.6789999999******99888777.......7********************* PP

                                        GGGGGGGB-GGG---SEEE- CS
                        DNA_pol_E_B 183 vswdkddalvleplPdvlvl 202
                                        v+++  d+++l+++P++++ 
  gene1980|gene1980|rna1980|rna1980 291 VPYNGEDPFILYEMPNYVFT 310
                                        ***************98875 PP

>> DNA_pol_D_N  DNA polymerase delta subunit OB-fold domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.3   0.0   1.6e-14     7e-11       1     120 [.      10     119 ..      10     128 .. 0.86
   2 ?   -0.4   0.0      0.25   1.1e+03      28      56 ..     160     188 ..     148     229 .. 0.70

  Alignments for each domain:
  == domain 1  score: 42.3 bits;  conditional E-value: 1.6e-14
                        DNA_pol_D_N   1 QYaniYfaRleqlkprlleaakekwskeelkvnrildlkeg.eecivvGtiykemklkpsvlkeiakedesapqae 75 
                                        QY+++Y +Rle++++++   ++ ++ +   +++++ + +++   +  ++ +y+++ +k ++++e   +   +++++
  gene1980|gene1980|rna1980|rna1980  10 QYNQTYVTRLEKMRSLINLDVHDDT-T---ILSNLSEASSAsGPVAFIALLYVDCANKETIFDEAGLI---KKEKN 78 
                                        **********************999.5...99*****9988689999*****************9944...45555 PP

                        DNA_pol_D_N  76 rkkyvsekdellLEDesgrvrLsgsgieseklvtGvvvavlGvet 120
                                         k y  e+ ++++EDes rv+++++   ++ +vtG v+++  + +
  gene1980|gene1980|rna1980|rna1980  79 VKPY--ENFTYFVEDESCRVEVIFE--PKDLFVTGQVLGFIAERN 119
                                        5555..5668**************7..9999********987664 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.25
                        DNA_pol_D_N  28 eelkvnrildlkegeecivvGtiykemkl 56 
                                         +++++ i + k+  + +++G i+ e+ +
  gene1980|gene1980|rna1980|rna1980 160 LNVITDYISNSKKVTDLVIIGDIFDEVTK 188
                                        45566777777888899999999988743 PP

>> EF-hand_14  EF-hand domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   3.5e-05      0.16      34      90 .]     149     209 ..     135     209 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.5e-05
                         EF-hand_14  34 dDpRLkellkklkkvekekseaeesetleldretFkkcveenivLiakaLkn....qlvIP 90 
                                         D+R+++ +++l+ + +  s+++++++l +  + F ++ +en+ L+a+ L++     ++IP
  gene1980|gene1980|rna1980|rna1980 149 ADLRIRNSMSELNVITDYISNSKKVTDLVIIGDIFDEVTKENADLLAQFLEDfgadAFIIP 209
                                        59**********************************************9974222256666 PP

>> DUF3692  CRISPR-associated protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   3.1e-05      0.14       9      65 ..     163     221 ..     158     287 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.1e-05
                                        SHHHHHS-SSHHHHHHHHHHHHHHHHH...HHHHHHHHT-GGGEEES--TT-HHHHHHTS CS
                            DUF3692   9 VqefIaaaRktrDlWagSyllSylawk...aikelvekyGpdvliyPslrgnplvdawll 65 
                                        + ++I++++k+ Dl +   ++ +++++   ++ ++ e +G+d++i P++++ p  + + +
  gene1980|gene1980|rna1980|rna1980 163 ITDYISNSKKVTDLVIIGDIFDEVTKEnadLLAQFLEDFGADAFIIPNIND-PTNKLLPQ 221
                                        7899********************9872226678889***********954.55555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (353 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       372  (0.0207485); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 2682.67
//
Query:       gene1981|gene1981|rna1981|rna1981  [L=606]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    6.5e-74  248.4   2.1    1.5e-73  247.2   2.1    1.6  1  XRN_N      XRN 5'-3' exonuclease N-terminus
    6.9e-47  160.4  19.5    8.5e-33  114.0   2.2    3.0  3  XRN_M      Xrn1 helical domain
  ------ inclusion threshold ------
      0.031   14.4   2.7      0.054   13.6   2.7    1.4  1  zf-CCHC    Zinc knuckle
       0.08   12.9   0.2       0.36   10.8   0.1    2.1  2  FBA_3      F-box associated domain
       0.55   10.3   4.6        1.1    9.3   4.6    1.4  1  zf-CCHC_3  Zinc knuckle


Domain annotation for each model (and alignments):
>> XRN_N  XRN 5'-3' exonuclease N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  247.2   2.1   4.3e-77   1.5e-73       1     241 [.       1     295 [.       1     296 [. 0.91

  Alignments for each domain:
  == domain 1  score: 247.2 bits;  conditional E-value: 4.3e-77
                                        XXX-HHHHHHHHHSGGGEEE------SSSS-EEEEEEETHHHHHHHHS-SSS-......--SSHHHHHHHHHHHHH CS
                              XRN_N   1 mGvpklfrwlserypkivkevieeeeeeekefdnLYlDmNgiihkcshkedkeekelskkpkteeeifkkifkyid 76 
                                        mGvp+lfrwl+++yp+i+++++    +++  +d LY+D+N+iih ++ +      ++  +p +e+e++++i k+id
  gene1981|gene1981|rna1981|rna1981   1 MGVPSLFRWLTKKYPQIIEKAT----PKN-PTDILYIDFNAIIHISCTP------SDGPTPVNEDEMMNNIEKNID 65 
                                        9*****************9997....233.79***************66......56779**************** PP

                                        HHHHHH-EEEEEEEE------HHHHHHHHHHHHHHHHHHHHHHH...HHHHHHHHHHHHT-BB-............ CS
                              XRN_N  77 rlvkivrprkllylavDGvaPraKmnqqRsRRfrsakeakeeke...ekeelkeelekeekeee............ 137
                                        ++v+++ prk++++++DGvaPraK+nqqR+RR+rs  ea e ++   e +++  ++ +++ke+             
  gene1981|gene1981|rna1981|rna1981  66 SIVSKCLPRKMIVISTDGVAPRAKLNQQRARRYRSIIEALELSKksfE-NTKGANFVEKTKEKIqklaktptikde 140
                                        **************************************9999552231.222222222222222466777789999 PP

                                        ........................................................-------GGGSSTTSHHHHH CS
                              XRN_N 138 ........................................................eeeekfdsnvitpGtefmek 157
                                                                                                +e+e+fd+n+itpGt+fm++
  gene1981|gene1981|rna1981|rna1981 141 ykvdfvglmenstsdektgvvdetnnekkeedneledveidgfekhpsdlleesslTEDEAFDKNAITPGTRFMYD 216
                                        99************************************************************************** PP

                                        HHHHHHHHHHHHHHH-GGGGG-EEEEE-TTS-S-HHHHHHHHHHHHHTSTTS-TT-EEEEE---THHHHHHHHHT- CS
                              XRN_N 158 lsealkafikkklkedpawknlkvilsdaevpGEGEhKimefirkqrskpeydpntrhviyglDaDLillsLathe 233
                                        l++++++fi+++l ++p +knl  i+s+ ++ GEGE+Kim+ irk++     ++n +h iy+ DaDLi+l+ ++h 
  gene1981|gene1981|rna1981|rna1981 217 LEKRMDKFIRERLANNPMYKNLCFIYSNGRRAGEGEQKIMTLIRKMK-----NRNLKHTIYSPDADLIFLGTSLHG 287
                                        ***********************************************.....9*********************** PP

                                        SSEEEEEE CS
                              XRN_N 234 pniliLre 241
                                        +n++i+re
  gene1981|gene1981|rna1981|rna1981 288 RNVKIMRE 295
                                        *******9 PP

>> XRN_M  Xrn1 helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   2.4      0.25   8.8e+02      87     165 ..      94     172 ..      74     189 .. 0.41
   2 !   57.9   0.9   2.5e-19     9e-16       2      95 ..     353     446 ..     352     453 .. 0.94
   3 !  114.0   2.2   2.4e-36   8.5e-33     169     313 ..     456     590 ..     448     594 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.25
                              XRN_M  87 edrkekklakeeeaskedaaneeaavaeeklseskvak.saeaeaeaeaeaeaeakaekekrekaekeleeseeee 161
                                        ++r+ +++++  e sk++ +n++ a+  ek+ ++k++k  ++ + + e++++     e+++ ++ +  ++e+++e+
  gene1981|gene1981|rna1981|rna1981  94 RARRYRSIIEALELSKKSFENTKGANFVEKT-KEKIQKlAKTPTIKDEYKVDFVGLMENSTSDEKTGVVDETNNEK 168
                                        2233333333333333333333333333332.22222212233333333333333333333333222222222222 PP

                              XRN_M 162 eeeD 165
                                        +eeD
  gene1981|gene1981|rna1981|rna1981 169 KEED 172
                                        2222 PP

  == domain 2  score: 57.9 bits;  conditional E-value: 2.5e-19
                              XRN_M   2 fdleriiDDfvFlcFFvGNDFLPhlPsLeiregaidlllkvYkkelkklggyltdngevkldrveklvslvgkvee 77 
                                        ++++r+ DD++ ++F  GNDFLP l ++++r +ai+ l k+ ++ +++++ y+t +ge+++   +++   ++++e+
  gene1981|gene1981|rna1981|rna1981 353 YEFNRMADDWILMSFLAGNDFLPTLQCFDVRFEAIEILTKLLAENFNRTKKYITYKGEIDFAVLKNFFRILAHYED 428
                                        799************************************************************************* PP

                              XRN_M  78 kifrkrkeredrkekkla 95 
                                        +++ k+k+    ++++++
  gene1981|gene1981|rna1981|rna1981 429 HLYIKKKKLLTDTRRRFQ 446
                                        ***999998877776654 PP

  == domain 3  score: 114.0 bits;  conditional E-value: 2.4e-36
                              XRN_M 169 LgeeGykeRYYkekfevsseeieqrrevvqkYveGLcWvlrYYyqGvaSWkWfyPyhyaPFaSDlknladlkikFe 244
                                        L ++  k+RYY  k++++se+  ++  v ++Y+ GL Wv++YY +G + W+WfyPy yaPFa D+ n+ ++    +
  gene1981|gene1981|rna1981|rna1981 456 LETTYGKTRYYDTKLHLKSER--EVITVCREYILGLSWVFKYYVKGATNWEWFYPYDYAPFACDIANVRSMPYLNK 529
                                        5555559********997765..56789*******************************************9999* PP

                              XRN_M 245 kgspfkpleqLmavlPaaskkalPkayqkLmtdpdSpiidlypedfeidlnGkrvaWqgvaklPfidek 313
                                        +++p+  l+q m v+P++sk  +Pk           pi+d +p++++id+  k + Wqgva lP id +
  gene1981|gene1981|rna1981|rna1981 530 RTEPLDCLQQQMLVMPPQSKGLVPKE--------MHPIFDSFPTEIKIDMFDKLLPWQGVAILPIIDME 590
                                        ************************85........458*****************************965 PP

>> zf-CCHC  Zinc knuckle
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   2.7   1.5e-05     0.054       3      17 ..     308     322 ..     307     323 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.5e-05
                                        TSSSSSSSSTTTTST CS
                            zf-CCHC   3 CynCGepGHiardCp 17 
                                        C +CG+ GH++  C 
  gene1981|gene1981|rna1981|rna1981 308 CEKCGKKGHLSTYCN 322
                                        **************6 PP

>> FBA_3  F-box associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.41   1.5e+03      29      62 ..     294     329 ..     291     373 .. 0.68
   2 ?   10.8   0.1   9.9e-05      0.36      20      63 ..     375     417 ..     353     470 .. 0.75

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.41
                              FBA_3  29 sEkfkfiklp.eeklesl.lsktLinYkGklavvek 62 
                                         E+++f+ l+ ++ +e++ ++  L  Y  kla++++
  gene1981|gene1981|rna1981|rna1981 294 REDLEFVYLQrQHFCEKCgKKGHLSTYCNKLALFSC 329
                                        678888888754444444145578999999998654 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 9.9e-05
                              FBA_3  20 lvivsFDvrsEkfkfiklpeeklesllsktLinYkGklavvekk 63 
                                         ++ +FDvr E +++++      + +  k+ i YkG + ++  k
  gene1981|gene1981|rna1981|rna1981 375 PTLQCFDVRFEAIEILTKL-LAENFNRTKKYITYKGEIDFAVLK 417
                                        5788***********9994.77788888999*****99874443 PP

>> zf-CCHC_3  Zinc knuckle
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   4.6    0.0003       1.1       4      18 ..     305     320 ..     303     324 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0003
                          zf-CCHC_3   4 saaCQkClkkGHw.tY 18 
                                        + +C kC+kkGH+ tY
  gene1981|gene1981|rna1981|rna1981 305 QHFCEKCGKKGHLsTY 320
                                        679**********555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (606 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       973  (0.0542696); expected 358.6 (0.02)
Passed bias filter:                      549  (0.0306208); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 4189.16
//
Query:       gene1982|gene1982|rna1982|rna1982  [L=128]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1130  (0.0630264); expected 358.6 (0.02)
Passed bias filter:                      474  (0.0264376); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.46
# Mc/sec: 831.63
//
Query:       gene1983|gene1983|rna1983|rna1983  [L=328]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.4e-25   87.9  34.7    2.4e-21   76.3  34.7    3.0  1  Zip       ZIP Zinc transporter
  ------ inclusion threshold ------
       0.58   10.5   0.0       0.58   10.5   0.0    2.5  3  2TM       2TM domain


Domain annotation for each model (and alignments):
>> Zip  ZIP Zinc transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.3  34.7   2.7e-25   2.4e-21       7     332 ..       7     322 ..       3     323 .. 0.85

  Alignments for each domain:
  == domain 1  score: 76.3 bits;  conditional E-value: 2.7e-25
                                Zip   7 aiiaililsllgllgpllvpkiskllsklllslllafavGvllgtaflhLlPealealeesqleee.hth...... 75 
                                        ++ +i+i+sl+ +l+p  +++i     k+++  ++ fa+G +l+  +l+ +P++ + +++  + ++ ++h      
  gene1983|gene1983|rna1983|rna1983   7 LSTLIFITSLILCLIPRSLSRID--NIKKFYPHITVFAAGFMLAMLLLDFIPHVAGICKHGNSPHNsAHHsiseck 80 
                                        45567777777777777777776..55999999***************************999998555599**** PP

                                Zip  76 .........................................plagllvllGflllllveklltmivekksshkekt 110
                                                                                  l +l++ ++f++ll +++++ + ++         
  gene1983|gene1983|rna1983|rna1983  81 nplkcdlhkndehtsgnegnkhdehhhhdhghdhssgffgqNLGFLIAGCAFIFLLSIDSIVLHHSH--------- 147
                                        ****************************************999999**************9997544......... PP

                                Zip 111 pkkasssssesaakksvsndkveeseekedhvaeadtdadskeelrngkqeksesekeqaseeedkeklaslkvra 186
                                                        ++ndk+ ++ ++ +h+a             +g++++++++ +    + +  k +++k+ a
  gene1983|gene1983|rna1983|rna1983 148 ----------------CDNDKIVQMNDGLNHGA-------------HGHSHTHDQIGTC---NTSAIKETKSKIQA 191
                                        ................45666666666655322.............2233333333332...3356666778999* PP

                                Zip 187 iilllglilHsfidGLAlGvssssstgislfiAvllHelpeelglgaiLlkaglsrkkavllnllfaltaplGili 262
                                        ii++l+l+lHs+++GLA+    +  t+ +  + +++H+++e ++lg  + +a++s  + ++l++++++++plG++i
  gene1983|gene1983|rna1983|rna1983 192 IIFILALSLHSLFEGLAIN---KQRTFGIFEVGIIVHKMLESFALGFTVHMAEFSFAYTIVLITVYSMLTPLGMAI 264
                                        ******************7...77788888899******************************************* PP

                                Zip 263 GilvrsisessgaeivsgillalsaGtflYvalvellphEllnekgssslkqsllqllglllGfalmlll 332
                                        + +       + ++++++  ++l+ G  l +  ve++p  +++++        + +++ l  G+++ +++
  gene1983|gene1983|rna1983|rna1983 265 AYF------LPFNKMLNTACNGLALGSILFIVCVEMIPPNFHSKS------SDFIKIASLASGYVITAII 322
                                        ***......9****************************9999999......4889999999999998887 PP

>> 2TM  2TM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   6.5e-05      0.58       5      30 ..      26      51 ..      23      68 .. 0.81
   2 ?   -3.4   0.2       1.4   1.3e+04      15      31 ..     121     137 ..     118     147 .. 0.62
   3 ?   -2.9   2.4         1     9e+03      13      25 ..     235     247 ..     188     292 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 6.5e-05
                                2TM  5 krvkeikgFyrhlvvYlivniflili 30
                                       +r++ ik+Fy h++v+++  ++ +l+
  gene1983|gene1983|rna1983|rna1983 26 SRIDNIKKFYPHITVFAAGFMLAMLL 51
                                       799**************988744443 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 1.4
                                2TM  15 rhlvvYlivniflilin 31 
                                        ++l+  ++  +f++l++
  gene1983|gene1983|rna1983|rna1983 121 QNLGFLIAGCAFIFLLS 137
                                        55666666666666654 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 1
                                2TM  13 FyrhlvvYlivni 25 
                                        F  h++ + ++ +
  gene1983|gene1983|rna1983|rna1983 235 FTVHMAEFSFAYT 247
                                        3344433333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (328 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       864  (0.0481901); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 2367.97
//
Query:       gene1984|gene1984|rna1984|rna1984  [L=661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.6e-12   46.7   0.1    6.2e-12   45.5   0.1    1.7  2  GTP_EFTU   Elongation factor Tu GTP binding domain
    0.00014   21.3   0.5    0.00042   19.7   0.0    2.0  2  Septin     Septin
     0.0014   18.4   0.2       0.11   12.2   0.1    2.9  2  PduV-EutP  Ethanolamine utilisation - propanediol utilisation
     0.0027   17.8   0.3       0.29   11.2   0.1    3.1  2  Dynamin_N  Dynamin family
     0.0089   16.1   0.3      0.025   14.7   0.1    1.9  2  MMR_HSR1   50S ribosome-binding GTPase
  ------ inclusion threshold ------
      0.011   16.0   0.2       0.06   13.6   0.0    2.5  2  Roc        Ras of Complex, Roc, domain of DAPkinase


Domain annotation for each model (and alignments):
>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.5   0.1   2.1e-15   6.2e-12       2     145 ..      73     210 ..      72     260 .. 0.80
   2 ?   -3.3   0.0       1.8   5.4e+03      38      64 ..     399     425 ..     386     445 .. 0.72

  Alignments for each domain:
  == domain 1  score: 45.5 bits;  conditional E-value: 2.1e-15
                                        CEEEEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHSTHCHSHHHHHHTSCSSCEEEEEE...TTCSSEEEEE CS
                           GTP_EFTU   2 rirnigiighvDhGKtTLtdrLlyktgaiskkgekaeeervlDtlkeErergiTiksaaisle...ketkkylinl 74 
                                        ri+n++++g+  +GKtT++++L  + ga ++ g+ +     +  +  E++ +iT  ++  +     ++++++ +++
  gene1984|gene1984|rna1984|rna1984  73 RILNVVVLGDKSSGKTTFIEHLNLS-GACRSVGSAR-----V-HTLYEKKFCITTRISPSTNLyadSRGRSKIVTF 141
                                        799*******************955.5544433322.....2.3557889999999876543336569******** PP

                                        EEESSSGGGHHHHHHHHHT-SEEEEEEETTTBSTHHHHHHHHHHHHTTTEEEEEEESCGST.HHHHHHHHHH CS
                           GTP_EFTU  75 iDtPGHvdFskevirglrvlDgavlvvdaveGvepqteevlrlalkegvpiivfiNKmDrl.kaelkeivee 145
                                        iDtPGH dF+k   +  + +   v+ v ++   ep +  + +l +k g +ii++i+K+D + ++  + +v+ 
  gene1984|gene1984|rna1984|rna1984 142 IDTPGHSDFIKFHRNLFKFTTNFVITVNCT---EPFSTYHDYLFRKIGSNIILVITKIDLIiDNGADFMVKR 210
                                        *****************************9...68888999*******************964444444444 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 1.8
                                        HHHSTHCHSHHHHHHTSCSSCEEEEEE CS
                           GTP_EFTU  38 eeervlDtlkeErergiTiksaaisle 64 
                                        ++er+lD +  E ++ ++++ ++is++
  gene1984|gene1984|rna1984|rna1984 399 TGERYLDHMLWELKNIMSVDFTVISVF 425
                                        347889999999999999999999987 PP

>> Septin  Septin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   1.4e-07   0.00042       5      80 ..      75     156 ..      72     169 .. 0.78
   2 ?   -2.1   0.1      0.62   1.9e+03     142     166 ..     187     211 ..     183     219 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1.4e-07
                                        EEEEEEEBTTSSCCCCCCTTSSSS----....--------------S-EEEEEEEEET.TCEEEEEEEE---BSSS CS
                             Septin   5 ftlmvvGesglGkttlintlfetdliee....ekleeasekkkktveikkkkvvieed.gvklnltviDtpgfGda 75 
                                        ++++v G+++ Gktt+i+ l  +   ++    + ++  ++k   t++i+ ++++  +  g    +t iDtpg+ d+
  gene1984|gene1984|rna1984|rna1984  75 LNVVVLGDKSSGKTTFIEHLNLSGACRSvgsaRVHTLYEKKFCITTRISPSTNLYADSrGRSKIVTFIDTPGHSDF 150
                                        79******************999998887765666666668889999996666555542777779*********** PP

                                        SSH.HC CS
                             Septin  76 vdn.sk 80 
                                        +   ++
  gene1984|gene1984|rna1984|rna1984 151 IKFhRN 156
                                        986344 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.62
                                        S-EEEEESSGGGS-HHHHHHHHHHH CS
                             Septin 142 vnliPviaKaDtltkeElkefKkki 166
                                         n+i vi+K D + ++  + + k+i
  gene1984|gene1984|rna1984|rna1984 187 SNIILVITKIDLIIDNGADFMVKRI 211
                                        59*********99998777766666 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0     0.029        86       3      22 ..      76      95 ..      74      99 .. 0.88
   2 !   12.2   0.1   3.7e-05      0.11      39     105 ..     140     202 ..     115     230 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.029
                          PduV-EutP  3 killiGkvgsGKttLtqalk 22
                                       +++++G   sGKtt  ++l+
  gene1984|gene1984|rna1984|rna1984 76 NVVVLGDKSSGKTTFIEHLN 95
                                       5899**********998886 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 3.7e-05
                          PduV-EutP  39 eviDtPGeylenrklysalivtsaeadvialvqdateeesvfppgfasvfnkeviGiitkidlaede 105
                                        ++iDtPG     + + + l  ++++    ++ +++te+ s++ + + + +  ++i +itkidl  d+
  gene1984|gene1984|rna1984|rna1984 140 TFIDTPGHSDFIK-FHRNLFKFTTN---FVITVNCTEPFSTYHDYLFRKIGSNIILVITKIDLIIDN 202
                                        689***9754444.77788777765...457789****************************98655 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   0.1   9.6e-05      0.29       1      18 [.      77      94 ..      77      99 .. 0.94
   2 ?    3.0   0.0     0.033        97      98     120 ..     134     156 ..     109     212 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 9.6e-05
                                       EEEEEBTTTTHHHHHHHH CS
                          Dynamin_N  1 iavvGsqSsGKSSvlnaL 18
                                       ++v+G+ SsGK++++++L
  gene1984|gene1984|rna1984|rna1984 77 VVVLGDKSSGKTTFIEHL 94
                                       79**************98 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.033
                                        TTS-SEEEEE---B-SSSGTTSH CS
                          Dynamin_N  98 llvkgltlvDlPGldsvnkrdqe 120
                                           k +t++D+PG  +  k + +
  gene1984|gene1984|rna1984|rna1984 134 GRSKIVTFIDTPGHSDFIKFHRN 156
                                        456679*******9987777763 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.1   8.2e-06     0.025       1      56 [.      76     147 ..      76     197 .. 0.65
   2 ?   -2.6   0.0       1.9   5.7e+03      54      86 ..     524     563 ..     499     593 .. 0.53

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 8.2e-06
                                        EEEEEESTTSSHHHHHHHHHTS..TEEESSSTTSSSSEEEEEEEETTEE..............EEEEECGGC CS
                           MMR_HSR1   1 evaivGrpNvGKStLinaltge..kaivsdkpgtTrdinegrvklkgke..............ielvDtpGl 56 
                                        +v+++G   +GK+t+i  l  +     v++    T+  +++ ++++ ++              ++++DtpG 
  gene1984|gene1984|rna1984|rna1984  76 NVVVLGDKSSGKTTFIEHLNLSgaCRSVGSARVHTLYEKKFCITTRISPstnlyadsrgrskiVTFIDTPGH 147
                                        589***************9543214467777777777777777633111333444444555559*******3 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.9
                                        GGCS....S.HHHHHH.HHHHHHHHHHC.TSEEEEEEETT CS
                           MMR_HSR1  54 pGli....e.gaseek.glgkaflalee.adlillvvdas 86 
                                        +G++    e +++e+k  ++k++ +  e  + i++v + +
  gene1984|gene1984|rna1984|rna1984 524 AGIVnltiElSENEDKqIISKELTNSFElYNRIIYVYNYK 563
                                        5542222223222222133333333333335566665544 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0     2e-05      0.06       2     119 ..      77     197 ..      76     198 .. 0.61
   2 ?   -2.7   0.0       2.1   6.4e+03      11      24 ..     640     653 ..     638     660 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2e-05
                                        EEEESSTTSSHHHHHHCHCT-CCC-EEETTTTEEEEE......EECGGSGGCTTBTTTTCEEEEEEEE-SGGCTTT CS
                                Roc   2 vvlvGdsgvGKtsllkrfvedkfsekekstigvdflt......kevtkikgvendkkvkkvklniWDtaGqerfrs 71 
                                        vv++Gd+++GKt++++++  +   ++  s    ++++      ++++  +++  d++ ++  + + Dt G+ +f +
  gene1984|gene1984|rna1984|rna1984  77 VVVLGDKSSGKTTFIEHLNLSGACRSVGSARVHTLYEkkfcitTRISPSTNLYADSRGRSKIVTFIDTPGHSDFIK 152
                                        89**************99765554443333333333300000123333345566778888889999********99 PP

                                        T-HHHHCTSCEEEEEEE.GHHHHCHHHHHHHHHHHCSSS-EEEEEE-TT CS
                                Roc  72 lhplylreaalailvyd.srssenlkeWlkelkkvagkspvilvgnkiD 119
                                         h+  ++    +++ ++ ++ +++ +++l   +k    s++ilv++kiD
  gene1984|gene1984|rna1984|rna1984 153 FHRNLFKFTTNFVITVNcTEPFSTYHDYLF--RKI--GSNIILVITKID 197
                                        987666655555555542667777766653..222..346778888887 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2.1
                                        SHHHHHHCHCT-CC CS
                                Roc  11 GKtsllkrfvedkf 24 
                                        GKt  ++r++++  
  gene1984|gene1984|rna1984|rna1984 640 GKTRKVQRLMQEVL 653
                                        9********99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (661 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       825  (0.0460148); expected 358.6 (0.02)
Passed bias filter:                      501  (0.0279436); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.68u 0.35s 00:00:01.03 Elapsed: 00:00:00.53
# Mc/sec: 3741.94
//
Query:       gene1985|gene1985|rna1985|rna1985  [L=255]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.1e-05   22.4   3.2    6.1e-05   22.4   3.2    2.3  2  Zip       ZIP Zinc transporter
  ------ inclusion threshold ------
      0.098   12.9   0.5      0.098   12.9   0.5    2.3  2  DUF2871   Protein of unknown function (DUF2871)
        5.6    7.7  13.2         21    5.9   4.5    3.4  2  PrgI      PrgI family protein


Domain annotation for each model (and alignments):
>> Zip  ZIP Zinc transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    3.2   2.4    0.0069        41      14      64 ..      10      57 ..       5      81 .. 0.73
   2 !   22.4   3.2     1e-08   6.1e-05     186     331 ..     102     244 ..      76     252 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.0069
                                Zip 14 lsllgllgpllvpkiskllsklllslllafavGvllgtaflhLlPealeal 64
                                       l+l+ l++ +l+p+ ++l  +    +l +fa G++l+   + +lP  ++++
  gene1985|gene1985|rna1985|rna1985 10 LFLFHLVVTMLFPNPKRLQIN---YFLQFFAHGMILSMMVVCILPNIFQNC 57
                                       445555555555544444333...366789***************999876 PP

  == domain 2  score: 22.4 bits;  conditional E-value: 1e-08
                                Zip 186 aiilllglilHsfidGLAlGvssssstgislfiAvllHelpeelglgaiLlkaglsrkkavllnllfaltaplGil 261
                                          i++l+++lH f+d + l+  + +++++   +   + + +e   + ++++ ++++++ a+ ++ ++al ap+G+l
  gene1985|gene1985|rna1985|rna1985 102 NVIFILAIFLHTFSDTICLA-DVPDTSMLKFGVGYGIQKSLESSLVAIFIYLTDIKMPIAYSIAYIYALCAPAGML 176
                                        56899***************.44455555555666789***99999999*************************** PP

                                Zip 262 iGilvrsisessgaeivsgillalsaGtflYvalvellp.....hEllnekgssslkqsllqllglllGfalmll 331
                                        +Gi +r++  s  ++++   l ++s G++    + ell+     +++l+ek      +  +++l+  lGf  m +
  gene1985|gene1985|rna1985|rna1985 177 LGIYIRNH-TSINDLNLKCGLTGVSFGLLFFNFVSELLSggiqhQDILHEK------YDRSSILAYGLGFFAMTV 244
                                        ****8873.4678999999*******************8666667888888......677778888888877765 PP

>> DUF2871  Protein of unknown function (DUF2871)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   1.0     0.076   4.5e+02      50      88 ..       9      47 ..       6      58 .. 0.73
   2 ?   12.9   0.5   1.6e-05     0.098       8      86 ..     167     244 ..     157     250 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.076
                            DUF2871 50 vvfLlvllleklfklseekkfkkffivYniglvltvvmm 88
                                       ++fL+ l+++ lf   ++ +++ f+ ++  g++l ++++
  gene1985|gene1985|rna1985|rna1985  9 ILFLFHLVVTMLFPNPKRLQINYFLQFFAHGMILSMMVV 47
                                       677777777777777788888889999998887765544 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 1.6e-05
                            DUF2871   8 alvylilgllsGvfyReftklneftgktqLsvvHtHllvLGfvvfLlvllleklfklseekkfkkffivYniglvl 83 
                                         ++++ +g+l G++ R+ t +n+ + k  L+ v   ll + fv  Ll   ++++  l+ ek  +  +  Y +g   
  gene1985|gene1985|rna1985|rna1985 167 YALCAPAGMLLGIYIRNHTSINDLNLKCGLTGVSFGLLFFNFVSELLSGGIQHQDILH-EKYDRSSILAYGLGFFA 241
                                        34556689*****************************************999997766.56666668889888877 PP

                            DUF2871  84 tvv 86 
                                        ++v
  gene1985|gene1985|rna1985|rna1985 242 MTV 244
                                        665 PP

>> PrgI  PrgI family protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   4.5    0.0036        21      24      65 ..      35      76 ..      32      81 .. 0.90
   2 ?    5.5   0.7    0.0048        29       3      31 ..      82     118 ..      80     194 .. 0.65

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0036
                               PrgI 24 flvlallvaiglylllrafleelasvlvillavPvaalgfyk 65
                                       f++ ++++++ ++ +l++++++ + v +i++ +P+++l +++
  gene1985|gene1985|rna1985|rna1985 35 FFAHGMILSMMVVCILPNIFQNCTFVPIICTFLPFILLSLFE 76
                                       77888999*****************************98886 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0048
                               PrgI   3 pkDiseyeekiffg.LtlRQliflvlall.......v 31 
                                        ++D+s+ e + f + L+ RQ ++++la++       +
  gene1985|gene1985|rna1985|rna1985  82 NEDVSDAERSAFTKkLNHRQNVIFILAIFlhtfsdtI 118
                                        579999888888888*****99999998844444440 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       787  (0.0438954); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1687.28
//
Query:       gene1986|gene1986|rna1986|rna1986  [L=855]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
     0.0074   16.4   0.0      0.058   13.5   0.0    2.2  2  Rv2175c_C  Rv2175c C-terminal domain of unknown function


Domain annotation for each model (and alignments):
>> Rv2175c_C  Rv2175c C-terminal domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.0   3.3e-06     0.058       6      45 ..     210     249 ..     206     255 .. 0.90
   2 ?   -0.1   0.0     0.055   9.9e+02      11      28 ..     256     273 ..     254     278 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.3e-06
                          Rv2175c_C   6 GtltvLrDgGfddeeilrWLFteDesLpgrPidALregrk 45 
                                         ++++ + gG++d++ ++ LF ++ +L+ +P d L+ ++ 
  gene1986|gene1986|rna1986|rna1986 210 TLISLYQNGGYKDDDTMNQLFFNNLTLKKSPNDKLKRNHS 249
                                        5789999****************************99875 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.055
                          Rv2175c_C  11 LrDgGfddeeilrWLFte 28 
                                        L D+Gf++++ ++ ++ +
  gene1986|gene1986|rna1986|rna1986 256 LVDQGFSRNKYVKLMLRQ 273
                                        78********99988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (855 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1218  (0.0679346); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.70u 0.29s 00:00:00.99 Elapsed: 00:00:00.48
# Mc/sec: 5383.57
//
Query:       gene1987|gene1987|rna1987|rna1987  [L=304]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.2e-07   29.0   0.5     0.0002   21.1   0.2    2.3  2  Cyclin_N  Cyclin, N-terminal domain


Domain annotation for each model (and alignments):
>> Cyclin_N  Cyclin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.2   1.1e-08    0.0002      39     125 ..      39     126 ..      14     128 .. 0.79
   2 !    6.1   0.0    0.0005       8.9      72     102 ..     170     236 ..     156     278 .. 0.70

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 1.1e-08
                                        HHHHHHTT--TTHHHHHHHHHHHHHHHS.---CCCHHHHHHHHHHHHHHHHSSS---HHHHHHHT....TTSS-HH CS
                           Cyclin_N  39 vevaekfkltpetlflavnyldRflskk.svpkdklqlvgatcLllAaKveeisppkledlvyit....deaftee 109
                                        +++++ + l+++t++++vn++ R+l ++ +++     ++ ++ +ll++K+ e     ++ ++ ++    +++  ++
  gene1987|gene1987|rna1987|rna1987  39 MKLSRAMALKRSTFIMSVNLFYRMLITRpDLK---SDTLKCSVILLSCKIMENF-RGISFITEAAknylKSVPGRK 110
                                        78999********************9552444...445567889******8874.333333333322226699*** PP

                                        HHHHHHHHHHHHTTT- CS
                           Cyclin_N 110 eilemErliLetLnfd 125
                                        ei+  E+ i etLnfd
  gene1987|gene1987|rna1987|rna1987 111 EIIHTELIISETLNFD 126
                                        ***************8 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0005
                                        CHHHHHHHHHHHHHHH....................................HSSS---HHHHHHHT CS
                           Cyclin_N  72 klqlvgatcLllAaKv....................................eeisppkledlvyit 102
                                        k++ v+++c++lA Kv                                     ++s+p +++l++ +
  gene1987|gene1987|rna1987|rna1987 170 KRRNVALACIFLALKVlkpgafkskknvetdcsnqeiaavittgmkisidsnDRDSTPAVQNLAIES 236
                                        56789***********888888888887777777777777777777777766666667777766666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (304 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       647  (0.0360868); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 2251.92
//
Query:       gene1988|gene1988|rna1988|rna1988  [L=242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.3e-10   40.2   0.0    7.7e-10   39.4   0.0    1.4  1  RNase_PH  3' exoribonuclease family, domain 1


Domain annotation for each model (and alignments):
>> RNase_PH  3' exoribonuclease family, domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.4   0.0   4.3e-14   7.7e-10      18     131 ..      57     157 ..      53     158 .. 0.84

  Alignments for each domain:
  == domain 1  score: 39.4 bits;  conditional E-value: 4.3e-14
                                        EEEEEECCEEEEEEEEEEEEEE-TCCG--CCEEEECCCCECCCCEC-C...S...HHHHHHHHHHHHHHCCTC-CC CS
                           RNase_PH  18 SaylelGdtkvlasvtgpieerpseerddaegaldveveyapfasgerrregrpsdeeielsrlleralrpsille 93 
                                        S ++++G tk+ +s+ gp+++    +  +++  l++ v +   a +e+   +  ++ + +  ++l++ ++  ++l+
  gene1988|gene1988|rna1988|rna1988  57 SIVYTQGLTKIRVSIAGPKPK---ST--KFN--LNITVSINRSARTEI---NEWGRLADDHKHRLHNLFKTILILK 122
                                        77899**************87...33..345..555555556677777...446788888899***********88 PP

                                        GCCTCEEEEEEEEEECCCS-CHHHCHHHHHHHHHCTCE CS
                           RNase_PH  94 kkpkstididitvlssdggslldalinaaslALadagi 131
                                          p s +didi vl+++g sl++a++n++s+ +a agi
  gene1988|gene1988|rna1988|rna1988 123 --PASSVDIDILVLEDNG-SLYSAMVNSVSVCCAYAGI 157
                                        ..77**************.**************99998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (242 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       354  (0.0197445); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1592.12
//
Query:       gene1989|gene1989|rna1989|rna1989  [L=80]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.9e-24   84.5   4.8    4.4e-24   84.3   4.8    1.0  1  Elf1           Transcription elongation factor Elf1 like
  ------ inclusion threshold ------
      0.031   13.6   3.0      0.031   13.6   3.0    1.7  2  zf-TFIIB       Transcription factor zinc-finger
      0.053   13.2   1.1      0.054   13.1   1.1    1.1  1  DpnI           Dam-replacing family
      0.089   13.0   0.3      0.089   13.0   0.3    1.9  2  C1_4           TFIIH C1-like domain
       0.45   10.5   6.5        0.8    9.7   6.5    1.5  1  Zn_Tnp_IS1595  Transposase zinc-ribbon domain
          1    9.3  12.5        6.1    6.8   4.7    2.4  2  zf-HIT         HIT zinc finger


Domain annotation for each model (and alignments):
>> Elf1  Transcription elongation factor Elf1 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.3   4.8   1.5e-27   4.4e-24       1      77 [.       2      79 ..       2      80 .] 0.88

  Alignments for each domain:
  == domain 1  score: 84.3 bits;  conditional E-value: 1.5e-27
                               Elf1  1 gkRkk.kakkrkkkkkkklptkFdCpfCnheksvevkldkkekiaevsCkvCgesfetkvnalsepvDvYskwiDace 77
                                       g++k+ +++ +  k k +++t+F+Cp+Cn+e++v+++++++ +i+++ C+ C+++++++ n+l++p+DvYs wiD ++
  gene1989|gene1989|rna1989|rna1989  2 GRKKTrRSQVKSVKAKFRMETRFNCPRCNNEQAVRCTVERSAGIGIAYCTLCEAKYKCRSNNLTTPIDVYSSWIDDID 79
                                       566664555555666666*********************************************************976 PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   3.0     1e-05     0.031       1      26 [.      25      54 ..      25      54 .. 0.86
   2 ?   -2.7   0.0       1.3   3.9e+03       4      10 ..      58      65 ..      58      69 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1e-05
                           zf-TFIIB  1 kCPkCqd.ele..eser.ggveidyCpqCr 26
                                       +CP+C++ + +  ++er  g+ i yC+ C+
  gene1989|gene1989|rna1989|rna1989 25 NCPRCNNeQAVrcTVERsAGIGIAYCTLCE 54
                                       6*****944669*9999888********96 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.3
                           zf-TFIIB  4 kCqd.ele 10
                                       kC++ +l+
  gene1989|gene1989|rna1989|rna1989 58 KCRSnNLT 65
                                       68763554 PP

>> DpnI  Dam-replacing family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   1.1   1.8e-05     0.054      14      72 ..       6      66 ..       1      78 [. 0.75

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.8e-05
                                       TT-TTHHHHHHHHHHHHH---TTT--SS-EE------..--EEE-TTT--EEEEEEEESS- CS
                               DpnI 14 ksksqkaRvltEkWvaknlyCpkCgskklsefennkp..vaDfyCesckeefeLkskkskl 72
                                       + +sq+  v +   +++ + Cp C++++  + + ++   +   yC+ c+ +++ +s++ + 
  gene1989|gene1989|rna1989|rna1989  6 TRRSQVKSVKAKFRMETRFNCPRCNNEQAVRCTVERSagIGIAYCTLCEAKYKCRSNNLTT 66
                                       5566766666777788999*******99888776665115678**********99988654 PP

>> C1_4  TFIIH C1-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.3     3e-05     0.089      10      41 ..       8      39 ..       1      40 [. 0.77
   2 ?    0.2   0.2       0.3     9e+02       2      11 ..      50      59 ..      47      71 .. 0.58

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3e-05
                               C1_4 10 pklakkkkdeeltssryrCekCkndFCiDCDv 41
                                        +++k++k +  +++r++C++C+n+  + C v
  gene1989|gene1989|rna1989|rna1989  8 RSQVKSVKAKFRMETRFNCPRCNNEQAVRCTV 39
                                       4555666667799***********99999965 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.3
                               C1_4  2 CygCqkkfpk 11
                                       C  C  k++ 
  gene1989|gene1989|rna1989|rna1989 50 CTLCEAKYKC 59
                                       4444444433 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   6.5   0.00027       0.8      12      41 ..      17      60 ..      12      61 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00027
                      Zn_Tnp_IS1595 12 alrWpngfvCPhCgsrkayrikt..............rglfqCk 41
                                       ++r  ++f CP+C +++a r +                 +++C+
  gene1989|gene1989|rna1989|rna1989 17 KFRMETRFNCPRCNNEQAVRCTVersagigiayctlcEAKYKCR 60
                                       5677889*********6655554448886666666666666665 PP

>> zf-HIT  HIT zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   3.8    0.0031       9.2      12      24 ..      22      50 ..      17      52 .. 0.71
   2 ?    6.8   4.7     0.002       6.1       8      20 ..      50      63 ..      33      66 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0031
                                       -SEE-TTT--E................ES CS
                             zf-HIT 12 akYkCpkCntr................yC 24
                                        + +Cp+Cn                  yC
  gene1989|gene1989|rna1989|rna1989 22 TRFNCPRCNNEqavrctversagigiaYC 50
                                       6889*****87777666666666666666 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.002
                                       T-S.B-SEE-TTT- CS
                             zf-HIT  8 Cgf.pakYkCpkCn 20
                                       C+  +akYkC+  n
  gene1989|gene1989|rna1989|rna1989 50 CTLcEAKYKCRSNN 63
                                       9999******9877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       916  (0.0510904); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 534.15
//
Query:       gene199|gene199|rna199|rna199  [L=103]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.3e-23   82.0  17.6    3.3e-23   82.0  17.6    1.5  2  Ribosomal_L44  Ribosomal protein L44


Domain annotation for each model (and alignments):
>> Ribosomal_L44  Ribosomal protein L44
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.8       0.7   1.3e+04      53      59 ..       8      14 ..       5      15 .. 0.70
   2 !   82.0  17.6   1.8e-27   3.3e-23       2      75 ..      17      90 ..      16      91 .. 0.98

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 0.7
                                   EEEETTT CS
                  Ribosomal_L44 53 rleCteC 59
                                   r  C++C
  gene199|gene199|rna199|rna199  8 RTYCKKC 14
                                   5668888 PP

  == domain 2  score: 82.0 bits;  conditional E-value: 1.8e-27
                                   EEEEEEEE-------SSSHHHHHHHH.H-SSSGGGGS----.--SSBB--EEEEETTT--EEE----BBS--EE CS
                  Ribosomal_L44  2 HtehkveqykkgkdselaqgkRrydrkqsgygGqtkpvfkkkaKttKKivlrleCteCkkkrlkalkRakkfel 75
                                   ++e+k + +kkgk+++ +qg+Rry+rkq+g++Gqtkp++++kaK tKK+vl+leCt+Ck+ +lk + Rak++e+
  gene199|gene199|rna199|rna199 17 YQEKKQSLAKKGKENPRRQGARRYKRKQKGCHGQTKPILRRKAKITKKLVLKLECTKCKQVELKVCRRAKHVEF 90
                                   7999*********************************************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1395  (0.0778069); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 800.15
//
Query:       gene1990|gene1990|rna1990|rna1990  [L=728]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      3e-14   53.1   4.3      3e-09   37.1   0.1    3.8  4  XPG_I     XPG I-region
    1.1e-11   45.1   0.3    7.4e-11   42.4   0.1    2.6  2  XPG_N     XPG N-terminal domain


Domain annotation for each model (and alignments):
>> XPG_I  XPG I-region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.1       1.5   1.3e+04      58      82 ..     274     298 ..     257     305 .. 0.64
   2 ?   -2.8   0.1      0.93   8.3e+03      48      48 ..     347     347 ..     316     381 .. 0.52
   3 !   15.4   0.0   1.9e-06     0.017       2      23 ..     525     546 ..     524     551 .. 0.91
   4 !   37.1   0.1   3.3e-13     3e-09      26      94 .]     582     638 ..     556     638 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 1.5
                                        ..EEECEEEEEEHHHHHHHHT--HH CS
                              XPG_I  58 kekekkkvevidlekvlkelgltre 82 
                                        k+++k+  ++++lek  k+++ +++
  gene1990|gene1990|rna1990|rna1990 274 KKEDKEAFDIFTLEKEVKQVESNKD 298
                                        5566777788888777777665555 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 0.93
                                        S CS
                              XPG_I  48 n 48 
                                        +
  gene1990|gene1990|rna1990|rna1990 347 Q 347
                                        1 PP

  == domain 3  score: 15.4 bits;  conditional E-value: 1.9e-06
                                        HHT--EEE-SS-HHHHHHHHHH CS
                              XPG_I   2 lmgipyvvApgEAEAqcayLqk 23 
                                         +gipy++Ap+E ++q+ yL++
  gene1990|gene1990|rna1990|rna1990 525 ILGIPYIDAPYESDSQLGYLNN 546
                                        589*****************87 PP

  == domain 4  score: 37.1 bits;  conditional E-value: 3.3e-13
                                        SSSEEE-SSSHHHHTT-SEEEESTT.ECECTT..EEECEEEEEEHHHHHHHHT--HHHHHHHHHHHCET CS
                              XPG_I  26 lvdaviseDsDlllFGapkvlrnlskkkskkkkekekkkvevidlekvlkelgltreqlidlaillgcD 94 
                                        +vda+i+eD D++lFGa++v+++++     k+       ++ +++++++++l+l+re+li+l+++lg+D
  gene1990|gene1990|rna1990|rna1990 582 KVDAIITEDNDVFLFGANRVYKDYF-----KC-------PKLYTMQNIRDKLNLNREDLIKLSVFLGND 638
                                        4***********************9.....56.......799*************************98 PP

>> XPG_N  XPG N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.4   0.1   8.3e-15   7.4e-11       1      99 [.       1      85 [.       1      87 [. 0.89
   2 ?   -2.1   0.0      0.61   5.4e+03      19      50 ..     382     413 ..     370     430 .. 0.68

  Alignments for each domain:
  == domain 1  score: 42.4 bits;  conditional E-value: 8.3e-15
                                       X--TTHHHHHHHH-GEEEEEGGGGTTEEEEEEHHHHHHHHHHHSE.ETTEE-BS-HHHHHHHHHHHHHHHTTEEEEEE CS
                              XPG_N  1 MGikgLlkllkevaairsvsiealegkklaiDaslwlyrfliavreqlgnalentshlmglfsrllrlldfgikPifV 78
                                       MG+kgL+kll+e +        +  +++laiDas+wly+          +++ +t+ +  +++r+++ll+ + +  fV
  gene1990|gene1990|rna1990|rna1990  1 MGVKGLWKLLEECH-----TADTPRNQRLAIDASIWLYKY---------KNVPQTNMIYSFVKRIIMLLYHKNSLFFV 64
                                       *************9.....5666679************96.........34445678889****************** PP

                                       E--S--GGGHHHHHHHHHHHH CS
                              XPG_N 79 Fdgkapdlkkeelekrserrq 99
                                       Fd kap  k ++++kr+e+r 
  gene1990|gene1990|rna1990|rna1990 65 FDSKAPAEKIKTIAKRNEIRL 85
                                       *****************9985 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.61
                                        EEGGGGTTEEEEEEHHHHHHHHHHHSE.ETTE CS
                              XPG_N  19 vsiealegkklaiDaslwlyrfliavreqlgn 50 
                                         ++e+ ++  l +D +   y+  +  ++++ +
  gene1990|gene1990|rna1990|rna1990 382 KEPEESKNVYLSVDKNSVFYKNECYGQSENRM 413
                                        46788889999999999999876655555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (728 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1560  (0.0870099); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.63u 0.27s 00:00:00.90 Elapsed: 00:00:00.43
# Mc/sec: 5031.96
//
Query:       gene1991|gene1991|rna1991|rna1991  [L=182]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
        4.4    7.4   6.6       0.41   10.7   1.3    1.9  2  DUF3568         Protein of unknown function (DUF3568)


Domain annotation for each model (and alignments):
>> DUF3568  Protein of unknown function (DUF3568)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   1.3   2.3e-05      0.41      48      99 ..      13      63 ..       6      67 .. 0.89
   2 ?   -1.6   0.3      0.15   2.7e+03      65      79 ..     145     161 ..     123     180 .. 0.47

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 2.3e-05
                            DUF3568 48 kkvykAtlkaiedlnvlsvvekskdsssatieakaaedktvfiklekldkns 99
                                        +++kAtlk++++l+  +  +k++d +  +ie k+++d t + +++k+  n+
  gene1991|gene1991|rna1991|rna1991 13 LNAMKATLKVLNELE-AKNFNKKNDVTISDIEKKKKNDITCKTRVFKKRRNK 63
                                       5789***********.888899999999****************99998876 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.15
                            DUF3568  65 svvekskdss..satie 79 
                                        s +++sk+ss  + t+e
  gene1991|gene1991|rna1991|rna1991 145 SKDDNSKRSSfrKKTVE 161
                                        33333333322222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2059  (0.114842); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1240.19
//
Query:       gene1992|gene1992|rna1992|rna1992  [L=260]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.9e-30  104.0  18.9    4.1e-25   88.7   2.9    2.0  2  Zip       ZIP Zinc transporter
  ------ inclusion threshold ------
      0.057   13.3   0.1        2.5    8.0   0.0    2.4  2  DUF1418   Protein of unknown function (DUF1418)


Domain annotation for each model (and alignments):
>> Zip  ZIP Zinc transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   5.5   6.4e-10   5.8e-06      11     109 ..       8      95 ..       3     104 .. 0.77
   2 !   88.7   2.9   4.5e-29   4.1e-25     176     330 ..      95     248 ..      89     251 .. 0.90

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 6.4e-10
                                Zip  11 ililsllgllgpllvpkiskl.lsklllslllafavGvllgtaflhLlPealealeesqleeehthplagllvllG 85 
                                        +++ls++ +++ ll+++ ++   + ++ s+ ++fa+G++l+t ++h++P+++++  +          l +l+  ++
  gene1992|gene1992|rna1992|rna1992   8 LFFLSVFLFFFTLLFSFSYRFfKNLKISSYSKCFAGGIILSTLIFHIFPDVYQSNCG---------YLGQLFSGIS 74 
                                        6777777777777777777663555666899*********************95544.........799******* PP

                                Zip  86 flllllveklltmivekksshkek 109
                                        fl+l+ ++kl  ++++    +++ 
  gene1992|gene1992|rna1992|rna1992  75 FLILFSIDKLYLYVSDN---ENDS 95 
                                        ***********999888...3333 PP

  == domain 2  score: 88.7 bits;  conditional E-value: 4.5e-29
                                Zip 176 keklaslkvraiilllglilHsfidGLAlGvssssstgislfiAvllHelpeelglgaiLlkaglsrkkavllnll 251
                                        + +   +k+ a+i++++l+lHsf++GL + + +  ++++  ++ +l H+ +e+++l + +  +g+  k +  l ++
  gene1992|gene1992|rna1992|rna1992  95 SLPKNVSKAQAFIFIIALSLHSFMEGLGIPA-KEGKSLMWYSLGLLGHKWIEAFALSVSVHTSGFETKIVCALLTF 169
                                        45555567779*******************5.55555666899********************************* PP

                                Zip 252 faltaplGiliGilvrs.isessgaeivsgillalsaGtflYvalvellphEllnekgssslkqsllqllglllGf 326
                                        +++++plG+liG+++++  ++++  + +++il+++s+G f Y+ + e+l  E++++ +    +++ +++l++++Gf
  gene1992|gene1992|rna1992|rna1992 170 YSFLTPLGTLIGMGLIKvLENNKHYDDLTSILNGISCGSFFYIEFIEMLNSEFDKQGM-IARRKNGKKVLAIFVGF 244
                                        ******************9999999************************99****994.7789999********** PP

                                Zip 327 alml 330
                                        +lm 
  gene1992|gene1992|rna1992|rna1992 245 VLMT 248
                                        ***6 PP

>> DUF1418  Protein of unknown function (DUF1418)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0     0.012   1.1e+02      26      53 ..      87     114 ..      56     126 .. 0.84
   2 ?    8.0   0.0   0.00028       2.5      45      65 ..     236     256 ..     224     259 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.012
                            DUF1418  26 yLsvndylsLPgplsskeaaivmiflGv 53 
                                        y+s n+  sLP+++s+ +a i +i l +
  gene1992|gene1992|rna1992|rna1992  87 YVSDNENDSLPKNVSKAQAFIFIIALSL 114
                                        667778889************9998766 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.00028
                            DUF1418  45 aivmiflGvllllPaavalvw 65 
                                        +++ if+G +l+  aa+a  w
  gene1992|gene1992|rna1992|rna1992 236 KVLAIFVGFVLMTSAAIAFHW 256
                                        6889*************9988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       854  (0.0476323); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1775.40
//
Query:       gene1993|gene1993|rna1993|rna1993  [L=402]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.2e-57  193.7   0.2    5.6e-57  192.9   0.1    1.4  2  ThiF             ThiF family
     0.0001   22.3   2.3     0.0044   17.0   0.5    2.3  2  UBA_e1_thiolCys  Ubiquitin-activating enzyme active site
    0.00091   19.6   0.1     0.0025   18.2   0.0    1.7  2  NAD_binding_7    Putative NAD(P)-binding
      0.004   17.4   0.1      0.013   15.8   0.1    1.9  2  TrkA_N           TrkA-N domain
     0.0059   16.9   0.1      0.077   13.3   0.0    2.3  2  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
  ------ inclusion threshold ------
       0.01   15.9   0.0       0.02   14.9   0.0    1.5  1  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
      0.032   13.4   1.0      0.049   12.8   1.0    1.2  1  CoiA             Competence protein CoiA-like family
      0.057   14.0   0.2       0.14   12.7   0.2    1.7  1  Pyr_redox        Pyridine nucleotide-disulphide oxidoreductas
      0.069   12.8   0.0       0.12   12.0   0.0    1.4  1  ApbA             Ketopantoate reductase PanE/ApbA
        0.1   12.2   0.4       0.24   11.0   0.2    1.7  2  UDPG_MGDP_dh_N   UDP-glucose/GDP-mannose dehydrogenase family


Domain annotation for each model (and alignments):
>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  192.9   0.1   3.1e-60   5.6e-57      20     218 ..       4     301 ..       1     315 [. 0.96
   2 ?   -3.3   0.0       2.5   4.6e+03     114     146 ..     347     382 ..     335     396 .. 0.72

  Alignments for each domain:
  == domain 1  score: 192.9 bits;  conditional E-value: 3.1e-60
                                        EEEEE--SHHHHHHHHHHHHHTTTEEEEEESSB--GGGGGTBTTS-GGGTTSBHHHHHHHHHHHT-TTSEEEEEES CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               ThiF  20 kvllvGaGglGsellknLalsGvgkltlvDnDkielsNlnRqflfreediGkpKaevaaealqeinpdveveavte 95 
                                         vl+vG+Gg+G+ellk+L+l Gv+++t+vDnD+ie++NlnRqf f++ d+Gk Ka+v +   +++ +d+ ++ +te
  gene1993|gene1993|rna1993|rna1993   4 NVLVVGCGGIGCELLKLLILKGVKRVTVVDNDTIEITNLNRQFFFTKTDVGKFKADVTKSYYEKMVSDATITSYTE 79 
                                        79************************************************************************** PP

                                        -CCGCCS-HHHHTT-SEEEEESSSHHHHHHHHHHHHHHT-EEEEEEEETTEEEEEEEEECCS-ECTSS-TGGS.EE CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               ThiF  96 ritdetvleellesvDlVvdalDniearrlvnracvkkgiplieagtlgfegqvvviipgktgcyeCldpsstedp 171
                                        ++ ++++  e+++++ +V ++lDniear +vn +c+   ipl+++g +g+ gq +v++  k++cy+C++     ++
  gene1993|gene1993|rna1993|rna1993  80 NVINTKFDLEFFKNFEIVYNCLDNIEARSYVNLRCRLACIPLVDGGSAGYLGQSMVFF--KNECYDCTP-----KA 148
                                        ****99988************************************************9..89******5.....79 PP

                                        CCCCEEHHH................................................................... CS
                                        xxxxxxxxx................................................................... RF
                               ThiF 172 tekkvplct................................................................... 180
                                        +++++p+ct                                                                   
  gene1993|gene1993|rna1993|rna1993 149 QDQSFPICTirgkpdnfthciayakeyaytsiretlskyrkfqnvykflfpgnecgreapkivkklmkyhaklkkk 224
                                        9999************************************************************************ PP

                                        ......................................HHHCT.E-B-HHHHHHHHHHHHHHHHHHHTTBCGGGCC CS
                                        ......................................xxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               ThiF 181 ......................................siagn.ipaiatttavvaglaalellkllsgkeklens 217
                                                                              +i++n ip++ tt+a va+l+   + kll++   + n+
  gene1993|gene1993|rna1993|rna1993 225 nfpifnkdnktvvkfiyymalvrahnyniapenffeaeRIIKNiIPSVCTTNAAVASLMLISARKLLHSYFLTKNK 300
                                        ******************************************************************9776644444 PP

                                        E CS
                                        x RF
                               ThiF 218 l 218
                                        +
  gene1993|gene1993|rna1993|rna1993 301 K 301
                                        4 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 2.5
                                        EEESSS..HHHHHHHHHHHH.HHT-EEEEEEEETTE CS
                                        xxxxxx..xxxxxxxxxxxx.xxxxxxxxxxxxxxx RF
                               ThiF 114 vdalDn..iearrlvnracv.kkgiplieagtlgfe 146
                                        ++a+Dn  ++a++ v ++ v +++i ++++g + f+
  gene1993|gene1993|rna1993|rna1993 347 ILAVDNrfYDAQKDVGELNVsHNSIMIVKSGLESFK 382
                                        567777777788888887776777777777776665 PP

>> UBA_e1_thiolCys  Ubiquitin-activating enzyme active site
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.7   0.2    0.0066        12       1      58 [.     162     217 ..     162     227 .. 0.65
   2 !   17.0   0.5   2.4e-06    0.0044     195     250 ..     211     260 ..     201     262 .. 0.71

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0066
                    UBA_e1_thiolCys   1 PneieHtieWArdkFeglFekkpeevnkflkdkekfleelekekeeekletlekvlkl 58 
                                        P +  H+i++A+++  + ++++ ++++kf +   kfl   ++  ++e+ ++++k++k+
  gene1993|gene1993|rna1993|rna1993 162 PDNFTHCIAYAKEYAYTSIRETLSKYRKFQNV-YKFLFPGNE-CGREAPKIVKKLMKY 217
                                        8899*********9999999999999999854.344332222.233333455555555 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 2.4e-06
                    UBA_e1_thiolCys 195 aeeleklakkesslalklkpieFeKDddtnfhidfitaasNlRArnYkIkeadrlk 250
                                         ++l k  +k ++     +   F+KD++t   ++fi+ ++ +RA nY+I + + ++
  gene1993|gene1993|rna1993|rna1993 211 VKKLMKYHAKLKK----KNFPIFNKDNKT--VVKFIYYMALVRAHNYNIAPENFFE 260
                                        4444443333333....3455699**999..8*****************9988765 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   1.4e-06    0.0025       9      83 ..       4     115 ..       2     123 .. 0.69
   2 ?   -3.2   0.0       6.7   1.2e+04      59      78 ..     221     240 ..     205     257 .. 0.53

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.4e-06
                      NAD_binding_7   9 kvlvvGgGevAarkvrklleag.akvtvvapevkeele.................elvklaeeelekd........ 58 
                                        +vlvvG G ++ + ++ l+ +g ++vtvv++++ e+++                 +   ++++++ek         
  gene1993|gene1993|rna1993|rna1993   4 NVLVVGCGGIGCELLKLLILKGvKRVTVVDNDTIEITNlnrqffftktdvgkfkaD---VTKSYYEKMvsdatits 76 
                                        79****************9999788*******655444777777777767543330...34444444444445555 PP

                      NAD_binding_7  59 ..............legadlviaatddrelneriaeaak 83 
                                                      ++++++v+ + d+ e ++ +   ++
  gene1993|gene1993|rna1993|rna1993  77 ytenvintkfdlefFKNFEIVYNCLDNIEARSYVNLRCR 115
                                        555555555666667788899999999888888777776 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 6.7
                      NAD_binding_7  59 legadlviaatddrelneri 78 
                                        l++  + i   d++ + + i
  gene1993|gene1993|rna1993|rna1993 221 LKKKNFPIFNKDNKTVVKFI 240
                                        33333333333444444444 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.1   7.2e-06     0.013       1      41 [.       5      46 ..       5      63 .. 0.85
   2 ?   -2.3   0.0       2.8     5e+03      13      37 ..     210     239 ..     203     294 .. 0.53

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 7.2e-06
                                       EEEES-SHHHHHHHHHHHH.TTEEEEEEESSHHHHHHHHHTT CS
                             TrkA_N  1 iiiiGlGrvGrslaeeLse.ggkdvvvidkdeerveelreeg 41
                                       ++++G+G +G +l++ L   g k+v+v+d+d   + +l +++
  gene1993|gene1993|rna1993|rna1993  5 VLVVGCGGIGCELLKLLILkGVKRVTVVDNDTIEITNLNRQF 46
                                       68****************955589*******98888887776 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 2.8
                                        HHHHHHHTT.....EEEEEEESSHHHHHHH CS
                             TrkA_N  13 laeeLsegg.....kdvvvidkdeerveel 37 
                                        ++++L++++     k++ +  kd ++v ++
  gene1993|gene1993|rna1993|rna1993 210 IVKKLMKYHaklkkKNFPIFNKDNKTVVKF 239
                                        555555544455554455555555555444 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.0   4.3e-05     0.077       1      67 [.       5      69 ..       5     106 .. 0.72
   2 ?    1.1   0.0      0.25   4.5e+02      88     126 ..     167     225 ..     160     228 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.3e-05
                                       EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHH..TTTCEEEEE--TTTHHHHHHHHH CS
                    Sacchrp_dh_NADP  1 vliiGaGsvGqavaellarhfdvdaeitvadrskeklealaaka..lgvrfeaialdaenyeavLaall 67
                                       vl++G+G++G  +++ll  ++    ++tv+d +  +  +l  +   +++++ + + d    ++  ++++
  gene1993|gene1993|rna1993|rna1993  5 VLVVGCGGIGCELLKLLILKGVK--RVTVVDNDTIEITNLNRQFffTKTDVGKFKAD--VTKSYYEKMV 69
                                       89*****************9977..***********999988886644444333333..3333333333 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.25
                                        HHHHHT-EEEESS-....................BCGCCSCHCCSHHHHHTHHHHHHCT CS
                    Sacchrp_dh_NADP  88 aCietgvhyvdtsi....................skeertnyalreavlklkekakeag 126
                                         Ci+    y  tsi                    ++  r+++++ ++++k+++k k+++
  gene1993|gene1993|rna1993|rna1993 167 HCIAYAKEYAYTSIretlskyrkfqnvykflfpgNECGREAPKIVKKLMKYHAKLKKKN 225
                                        56666666666777777777777777777777766677999999999999999999875 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   1.1e-05      0.02      14      56 ..       4      46 ..       1      82 [. 0.85

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.1e-05
                                       EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHH CS
                       Shikimate_DH 14 kvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeel 56
                                       +vl++G G ++ +++k L+ kgvk+v+v+  +     +l +++
  gene1993|gene1993|rna1993|rna1993  4 NVLVVGCGGIGCELLKLLILKGVKRVTVVDNDTIEITNLNRQF 46
                                       89**************************988777777777766 PP

>> CoiA  Competence protein CoiA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   1.0   2.8e-05     0.049     190     288 ..     166     274 ..     145     313 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.8e-05
                               CoiA 190 yfiltfektkaftlsnikliskaklrelfk.......espdkesfqsslyeklarlrrkpftieakeinrrrewvy 258
                                         +++++ k+ a+t++  +l++  k+++++k          + +++ ++l++  a+l++k f+i +k  +   +++y
  gene1993|gene1993|rna1993|rna1993 166 THCIAYAKEYAYTSIRETLSKYRKFQNVYKflfpgneCGREAPKIVKKLMKYHAKLKKKNFPIFNKDNKTVVKFIY 241
                                        7********************************99975566678888899888899*****999998888777887 PP

                               CoiA 259 llkl...yekgqviqkllsiavfpqylaveitv 288
                                        ++ l   ++  + ++++++++  ++ +  ++ +
  gene1993|gene1993|rna1993|rna1993 242 YMALvraHNYNIAPENFFEAERIIKNIIPSVCT 274
                                        765411134456778888887777666555444 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.2   7.9e-05      0.14       1      30 [.       4      34 ..       4      44 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 7.9e-05
                                       EEEEECSSHHHHHHHHHHHHTT.SEEEEEES CS
                          Pyr_redox  1 kvvvvGgGyiglElAgalaelg.kkVtvver 30
                                       +v+vvG G ig+El + l   g k+Vtvv++
  gene1993|gene1993|rna1993|rna1993  4 NVLVVGCGGIGCELLKLLILKGvKRVTVVDN 34
                                       599***************77665899**987 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   6.6e-05      0.12       1      61 [.       5      67 ..       5      90 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 6.6e-05
                                       EEEES-SHHHHHHHHHHHHHTHC.EEEE-SCH.HHHHHHHHCEEEEETTCEEEEEECEEECCH CS
                               ApbA  1 iailGaGaiGsllaakLakagad.vtlilrsr.rlealkknGlrltseggeeilrppealsae 61
                                       ++++G+G+iG+ l   L  +g + vt+++++  ++ +l+++ +  +++ g++++ +++++ ++
  gene1993|gene1993|rna1993|rna1993  5 VLVVGCGGIGCELLKLLILKGVKrVTVVDNDTiEITNLNRQFFFTKTDVGKFKADVTKSYYEK 67
                                       68*********9999997766665********9999999999988888888888777776666 PP

>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.2   0.00013      0.24       2      42 ..       4      45 ..       3      74 .. 0.91
   2 ?   -3.4   0.0       3.3     6e+03      38      56 ..     220     238 ..     219     247 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00013
                                       EEEEE--STTHHHHHHHHHHCT.SEEEEE-S-HHHHHHHCTT CS
                     UDPG_MGDP_dh_N  2 kisviGlGYvGlvtaavlaeig.hevigvDideekvdklnsg 42
                                       ++ v+G G +G     +l  +g + v++vD+d+  + +ln++
  gene1993|gene1993|rna1993|rna1993  4 NVLVVGCGGIGCELLKLLILKGvKRVTVVDNDTIEITNLNRQ 45
                                       688******************9789**************986 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 3.3
                                        HHCTTS-SS--TTHHHHHH CS
                     UDPG_MGDP_dh_N  38 klnsgkipiyepgLeelvk 56 
                                        kl+++++pi++++ +++vk
  gene1993|gene1993|rna1993|rna1993 220 KLKKKNFPIFNKDNKTVVK 238
                                        7999999999999999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (402 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       885  (0.0493614); expected 358.6 (0.02)
Passed bias filter:                      484  (0.0269954); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.49
# Mc/sec: 2471.13
//
Query:       gene1994|gene1994|rna1994|rna1994  [L=81]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (81 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       905  (0.0504769); expected 358.6 (0.02)
Passed bias filter:                      541  (0.0301746); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 567.65
//
Query:       gene1995|gene1995|rna1995|rna1995  [L=26]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.022   14.9   0.0      0.027   14.6   0.0    1.2  1  EZH2_WD-Binding  WD repeat binding protein EZH2


Domain annotation for each model (and alignments):
>> EZH2_WD-Binding  WD repeat binding protein EZH2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   1.5e-06     0.027      13      23 ..       7      17 ..       3      20 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.5e-06
                    EZH2_WD-Binding 13 ekteiLNeeWk 23
                                        ++++LNe+W+
  gene1995|gene1995|rna1995|rna1995  7 PRLKVLNEDWS 17
                                       5899******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (26 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       166  (0.00925874); expected 358.6 (0.02)
Passed bias filter:                      104  (0.00580066); expected 358.6 (0.02)
Passed Vit filter:                         5  (0.000278878); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.29s 00:00:00.69 Elapsed: 00:00:00.49
# Mc/sec: 159.95
//
Query:       gene1996|gene1996|rna1996|rna1996  [L=210]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       808  (0.0450667); expected 358.6 (0.02)
Passed bias filter:                      456  (0.0254337); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.63u 0.38s 00:00:01.01 Elapsed: 00:00:00.60
# Mc/sec: 1056.12
//
Query:       gene1997|gene1997|rna1997|rna1997  [L=51]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.091   13.2   0.0        0.1   13.0   0.0    1.0  1  DUF2781   Protein of unknown function (DUF2781)


Domain annotation for each model (and alignments):
>> DUF2781  Protein of unknown function (DUF2781)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   5.8e-06       0.1       3      50 ..       3      48 ..       2      50 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 5.8e-06
                            DUF2781  3 vyllyflihipitllvDlqvllpaslfphflsklrewyiatnnDplll 50
                                       ++ + +++ ++ t++vD   ++      h+ ++l++wy++ ++D+l++
  gene1997|gene1997|rna1997|rna1997  3 FLHVMLFLNLIRTVFVDGRHEIDY--AHHSGRNLERWYFEDSDDKLFK 48
                                       66789999***********77654..3478999************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (51 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       242  (0.0134977); expected 358.6 (0.02)
Passed bias filter:                      209  (0.0116571); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.30s 00:00:00.70 Elapsed: 00:00:00.46
# Mc/sec: 332.77
//
Query:       gene1998|gene1998|rna1998|rna1998  [L=265]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.3e-10   39.2  34.7    1.9e-09   36.7  30.0    2.9  2  TFIIF_alpha  Transcription initiation factor IIF, alpha subun
  ------ inclusion threshold ------
      0.086   12.9   1.2      0.091   12.9   0.1    1.7  2  Amidase_6    Putative amidase domain


Domain annotation for each model (and alignments):
>> TFIIF_alpha  Transcription initiation factor IIF, alpha subunit (TFIIF-alpha)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.7  30.0   2.1e-13   1.9e-09      64     244 ..      49     214 ..      23     215 .. 0.63
   2 ?    0.3   2.5     0.022     2e+02     459     504 ..     213     255 ..     207     261 .. 0.78

  Alignments for each domain:
  == domain 1  score: 36.7 bits;  conditional E-value: 2.1e-13
                                        XXXXXXXXXXXXXGGGCCSXXEEEEEEEXXCTTSXEEEEESSTTS..EEEEEEEXSSSSSSEEEEEEEEETTSEEE CS
                        TFIIF_alpha  64 kesgaGsefnralREearrkkyGiiskkyrlddqPWiLevggkeggqkkfrGireGgvsenasyyvltkapdgafe 139
                                        k++ + se  +   E++++            + qP iLe  + eg  + f+G ++   + + +y+v+++ + +af+
  gene1998|gene1998|rna1998|rna1998  49 KNTKKKSETIEYVDEKYKKL--------SEEESQPLILE--DTEG--RGFKGRLQTVENTQNNYFVFIN-TGKAFK 111
                                        44444444444444444333........34699******..7777..99********************.8888** PP

                                        EEEEEEEEEEEEGGCSTXXSSTTTHHHHHHHXSSSXSHHHHHHXXXXXX........XXXXXXX..XXXXXX..XX CS
                        TFIIF_alpha 140 AypvneWynFnpvaryktLtleeAEeeferRkktlngfslmlkkalkkgeaa...vgdedeeeek.kkgggG..rs 209
                                         +pv++Wy+F++ ++y tLtleeAE ++++     +   ++++++ k++e +     +  +++++ + +  G   +
  gene1998|gene1998|rna1998|rna1998 112 VIPVSKWYKFTQRINYDTLTLEEAESKMGKDD---D---RWMMHKKKEEEVEeidYEEVFDDDDGeEAHVTGyeEK 181
                                        ****************************9754...4...4444444444443000444444455543333441144 PP

                                        XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                        TFIIF_alpha 210 kdLkikdkegddeedsdesdkgdededeekkkkKk 244
                                        k+L  + k  + ++   + ++++e +d+++k++Kk
  gene1998|gene1998|rna1998|rna1998 182 KQLSTSGK--ELKKFLRSLEESEERDDKGQKEEKK 214
                                        45555555..4444445555555555555555553 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.022
                                        XXX-SS--HHHHHHHHHHS-B-HHHHHHHTSHHHHSS-HHHHHHHH CS
                        TFIIF_alpha 459 nkadggvtEeavrryLmrkplTtkeLlkkfkakktglsseelveal 504
                                         k+ +++ E ++ +++m   + +keLl+++k +    + +e  ++l
  gene1998|gene1998|rna1998|rna1998 213 KKEMMKLSEGDLVQMIMNEEMSIKELLSRIKLR---FKIDEYTKKL 255
                                        566678899999999***************999...6666555555 PP

>> Amidase_6  Putative amidase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.2      0.93   8.3e+03      81     102 ..      36      57 ..      33      66 .. 0.58
   2 ?   12.9   0.1     1e-05     0.091      70     117 ..     186     233 ..     139     245 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 0.93
                          Amidase_6  81 sskkatpiakgsleekvktksk 102
                                        +++ka++ ++++++++ k+++ 
  gene1998|gene1998|rna1998|rna1998  36 REEKAEQPETETYKNTKKKSET 57 
                                        5555555556666655555544 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 1e-05
                          Amidase_6  70 agaeefknylssskkatpiakgsleekvktksklklGdvvqyekngdg 117
                                        ++ +e+k++l s +++++  ++ ++e+ k+  kl+ Gd+vq+ +n+++
  gene1998|gene1998|rna1998|rna1998 186 TSGKELKKFLRSLEESEERDDKGQKEEKKEMMKLSEGDLVQMIMNEEM 233
                                        56789********99999999999999999**************9887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (265 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2552  (0.142339); expected 358.6 (0.02)
Passed bias filter:                      583  (0.0325172); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 1858.50
//
Query:       gene1999|gene1999|rna1999|rna1999  [L=134]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.7e-16   59.1   1.5    8.3e-16   58.5   1.5    1.2  1  HIT       HIT domain
    8.8e-09   35.8   1.8    1.3e-08   35.3   1.8    1.3  1  DcpS_C    Scavenger mRNA decapping enzyme C-term binding
    3.7e-05   23.6   2.0      6e-05   22.9   2.0    1.5  1  CwfJ_C_1  Protein similar to CwfJ C-terminus 1
  ------ inclusion threshold ------
       0.19   11.7   0.0       0.22   11.4   0.0    1.1  1  YHYH      YHYH protein


Domain annotation for each model (and alignments):
>> HIT  HIT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.5   1.5   1.8e-19   8.3e-16       6      95 ..      15      98 ..      12     101 .. 0.93

  Alignments for each domain:
  == domain 1  score: 58.5 bits;  conditional E-value: 1.8e-19
                                       CCEEEE-SSEEEEE-SS-SSSSEEEEEESSTGCSGGGCCHHHHHHHHHHHHHHHHHHHTCTTCCCEEEEEEESGGGT- CS
                                HIT  6 stvvyeddlvlafldidpkapghlLvipkkhlselhdlteeelakllsavkkvakalqkkfknkglrvvinngahagq 83
                                        +v+y+d +v+++ldi+p ++ghlLvip kh + l + +ee++++ ++++ k++++l+     k ++++ nng    q
  gene1999|gene1999|rna1999|rna1999 15 MNVLYKDARVFVILDIRPLSQGHLLVIPIKHGEFLYENDEEDVSHAMRTIWKIVRVLGI----KKFNILQNNGH--IQ 86
                                       689*******************************************************9....47889998885..7* PP

                                       SSSS-EEEEEEC CS
                                HIT 84 svahlHiHvipr 95
                                       sv+h+H+H++p 
  gene1999|gene1999|rna1999|rna1999 87 SVPHVHFHIVPY 98
                                       **********96 PP

>> DcpS_C  Scavenger mRNA decapping enzyme C-term binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.3   1.8     3e-12   1.3e-08       1     109 [.       4     105 ..       4     109 .. 0.81

  Alignments for each domain:
  == domain 1  score: 35.3 bits;  conditional E-value: 3e-12
                                        T-HHHHHHTTSS-B-EEEE-SSEEEEE-SS-SSSEEEEEEESS---SGGG--TTTTTHHHHHHHHHHHHHHHTT-T CS
                             DcpS_C   1 kwvfnilakgkepervvyedekfvvlkDikpkaklhllvipkrdikslrdLtkehlpllkemrekakkvieekyne 76 
                                        k+vf++++ ++   +v+y+d ++ v+ Di+p ++ hllvip ++ + l++   ++ + + + ++++ k+++   ++
  gene1999|gene1999|rna1999|rna1999   4 KCVFCKIYTQNM--NVLYKDARVFVILDIRPLSQGHLLVIPIKHGEFLYE---NDEEDVSHAMRTIWKIVRVLGIK 74 
                                        79****999966..***************************776666555...55666778888888888887866 PP

                                        -EEEEE--SCCCT--S-S--EEEEE........ CS
                             DcpS_C  77 vdaeelrvgvhyqPsvyhlHlHvisldfespgl 109
                                         + + l+   h+ +sv h+H+H++    + ++l
  gene1999|gene1999|rna1999|rna1999  75 -KFNILQNNGHI-QSVPHVHFHIVPYVDQVNCL 105
                                        .77777777776.6*********9766666655 PP

>> CwfJ_C_1  Protein similar to CwfJ C-terminus 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   2.0   1.3e-08     6e-05      12     109 ..       3      99 ..       1     121 [. 0.77

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 1.3e-08
                                        HH-S----SS---SS--S-B-SSEEEE---S-SSTT-EEEEESS--SSTTSS-H.HHHHHHHHHHHHHHHHHHHTT CS
                           CwfJ_C_1  12 dsClfClsnpklekhlivsignkvYlalpkgpLssgHvliipieHisallslde.evldeirkfrkalvkmykkqd 86 
                                        d+C fC  +  +++ +++    +v++ l   pLs+gH+l+ipi+H + l + de +v   +r   k ++ +   ++
  gene1999|gene1999|rna1999|rna1999   3 DKCVFCKIY--TQNMNVLYKDARVFVILDIRPLSQGHLLVIPIKHGEFLYENDEeDVSHAMRTIWKIVRVL-GIKK 75 
                                        678888444..4556777788899999*99*******************8877737778888877755554.4444 PP

                                        --EEEEEE-SSS-----EEEEE.- CS
                           CwfJ_C_1  87 kdavvfEissersvHlaiqvip.v 109
                                         +++      ++ +H++ +++p v
  gene1999|gene1999|rna1999|rna1999  76 FNILQNNGHIQSVPHVHFHIVPyV 99 
                                        445555666899999999999944 PP

>> YHYH  YHYH protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0     5e-05      0.22      47      80 ..      56      97 ..      40     125 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 5e-05
                               YHYH 47 g........wkvdalaaverlgldtangHvqptgaYHyHgtp 80
                                       +        wk+  +  ++++ + ++ngH q+  + H+H++p
  gene1999|gene1999|rna1999|rna1999 56 DvshamrtiWKIVRVLGIKKFNILQNNGHIQSVPHVHFHIVP 97
                                       234445556999888899*********************887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       585  (0.0326287); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.39u 0.28s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 942.71
//
Query:       gene2|gene2|rna2|rna2  [L=1364]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.8e-62  208.2   0.3    3.8e-61  206.1   0.3    2.2  1  RNA_pol_Rpb1_2  RNA polymerase Rpb1, domain 2
    2.4e-51  174.7   0.5      5e-51  173.7   0.0    1.8  2  RNA_pol_Rpb1_5  RNA polymerase Rpb1, domain 5
    5.3e-23   81.7   0.0    1.3e-22   80.4   0.0    1.7  1  RNA_pol_Rpb1_3  RNA polymerase Rpb1, domain 3
    2.4e-16   59.6   0.2    1.1e-15   57.5   0.2    2.2  1  RNA_pol_Rpb1_4  RNA polymerase Rpb1, domain 4
    1.2e-15   57.7  12.7    7.9e-14   51.7   0.9    3.4  3  RNA_pol_Rpb1_1  RNA polymerase Rpb1, domain 1


Domain annotation for each model (and alignments):
>> RNA_pol_Rpb1_2  RNA polymerase Rpb1, domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  206.1   0.3   1.1e-64   3.8e-61       1     163 [.     429     592 ..     429     595 .. 0.92

  Alignments for each domain:
  == domain 1  score: 206.1 bits;  conditional E-value: 1.1e-64
                            SEEESSEEEEEEEEESSS-TTEEEEEHHHHTTSEEEEE-STTTHHHHHHHHHHTTTSSSSEEEEESTTSSEEETTTT-SC...HHCCT CS
         RNA_pol_Rpb1_2   1 GkrvdysaRsvispdpnlkldevgvPisvakkltvpeivtelnikklrklvengpevyPgasyvkredgsekklkakkrk...lakel 85 
                            Gkrv+y+aR+vispdp +++de+g+P+++a  lt+pe+vt++n+++l+++v+ngp v Pga+ +  e+g +++lk+ k++   +++ l
  gene2|gene2|rna2|rna2 429 GKRVNYTARTVISPDPYIATDEIGIPMHIACRLTFPERVTPFNRRRLERCVINGP-VFPGAECI-VENGVKRSLKYVKNRravAKTLL 514
                            9*****************************************************9.78****77.56788889988877435345556 PP

                            TTTSEEEEE--TTSEEEEE-SSTTSGGGEEEEEEEEESSSSEEEEGGGHCCCT--SSS-EEEEE--SSHHHHHHHHHC CS
         RNA_pol_Rpb1_2  86 ekgdiverhvkdgdvvllNRqPsLhklsimahrvkvlekktlrlnlsvttayNaDFDGDemnlhlpqseearaEaeel 163
                            +  ++v+rh+++gd+vl+NRqP+Lhk s+m+hrv++l+ kt+r++++++++yNaDFDGDemn+hl+q  +araE + l
  gene2|gene2|rna2|rna2 515 KNSTVVHRHMQHGDMVLVNRQPTLHKPSLMSHRVRILNDKTIRMHYVNCNSYNADFDGDEMNIHLAQGLMARAENAYL 592
                            677799********************************************************************8877 PP

>> RNA_pol_Rpb1_5  RNA polymerase Rpb1, domain 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.1      0.66   2.4e+03     155     155 ..     310     310 ..     213     569 .. 0.67
   2 !  173.7   0.0   1.4e-54     5e-51       1     130 [.     971    1170 ..     971    1228 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.66
                            E CS
                            x RF
         RNA_pol_Rpb1_5 155 i 155
                            +
  gene2|gene2|rna2|rna2 310 K 310
                            1 PP

  == domain 2  score: 173.7 bits;  conditional E-value: 1.4e-54
                             B--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTEEEETTSEEEETTS-EEESSGGGTS.................... CS
                             xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.................... RF
         RNA_pol_Rpb1_5    1 GLkvkefffhtmggReGLiDtAvkTaesGYlqRrlvkaledvvvkyddtvrnsggeivqflygedg.................... 66  
                             GL+ + fffh+ +gReGLiDtAvkT++sGYlqR++vk++e+ vv+yd +vr  +g ++q +ygedg                    
  gene2|gene2|rna2|rna2  971 GLSLSSFFFHCQAGREGLIDTAVKTSRSGYLQRCIVKMMEGTVVEYDMSVR--DGMLIQYVYGEDGkdpnrmvnerfmtmngglir 1054
                             999***********************************************7..5889***************************** PP

                             .....................................................B--TT-BHHHHHHHHHHHHHHCCCSSTTSSTCS CS
                             .....................................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
         RNA_pol_Rpb1_5   67 .....................................................lvepGeavGiiaaQSiGePgTQltlnTFHfaGv 99  
                                                                                   ++pGe+vG+iaaQ+iGeP+TQ+tlnTFH+aG 
  gene2|gene2|rna2|rna2 1055 dgsndkdrcrgsndknrdddrgddkdknkdkdtnintntnantnpintnyinqRIHPGESVGMIAAQAIGEPSTQMTLNTFHLAGC 1140
                             *************************************************************************************9 PP

                             STSSSSSSHHHHHHHHTT-SS-SS-EEEEEB CS
                             xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
         RNA_pol_Rpb1_5  100 asknvtlGvprlkeilnvskniksksltvll 130 
                             a +nvtlG+prlkeil++ ++  ++ ++ ++
  gene2|gene2|rna2|rna2 1141 A-TNVTLGMPRLKEILMIGNKSINTVIKGKI 1170
                             7.689**********8874444444444444 PP

>> RNA_pol_Rpb1_3  RNA polymerase Rpb1, domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.4   0.0   3.7e-26   1.3e-22       7     156 ..     602     760 ..     600     761 .. 0.93

  Alignments for each domain:
  == domain 1  score: 80.4 bits;  conditional E-value: 3.7e-26
                            TTEESSS--THHHHHHHHHSSTTEEEEHHHHHHHHHHSSSCCSSSSSSSSSBESSSEBEEHHHHHHCCCHC...CCCEEEE.SSSS.. CS
         RNA_pol_Rpb1_3   7 sgkPvigivQDsllGvyllTkedvfidreeaqqllykgvgsdsktvtlrpailkpkelwtgkqtfsrilpn...einyerk.neek.. 88 
                            +gkPv g+vQD +++++ +T +d f++r+e+++ll    +   +     +ail+pk+l+tgkq++ ++l     +inye   ++ +  
  gene2|gene2|rna2|rna2 602 NGKPVRGLVQDYVVSMFSITLKDRFFSRAEINELLIASRK--LNFTITSAAILRPKQLYTGKQLIAMLLSAydlRINYEHAnKI-Stl 686
                            8**********************************99943..3577999*******************************8433.358 PP

                            .......STSEEECSSEEEES--SHHHHSSSSTTSHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHCEB-TGGG CS
         RNA_pol_Rpb1_3  89 .......dgkvlikngelikGvidkkvvgkksqgslihvlakeygiketvrfldslqrlgfkyllqsgftigigD 156
                                   +++v + ng  ++Gv+dk+ vg  s+++l+h++    g   + ++l +l r++ +yl  +g  +gi+D
  gene2|gene2|rna2|rna2 687 ywkehreESTVRFHNGYYVHGVLDKSEVG-PSKNGLVHCIGMLKGYFVCNDVLTALGRMVSRYLVCYGQPLGISD 760
                            89999999*********************.9*************************************9999999 PP

>> RNA_pol_Rpb1_4  RNA polymerase Rpb1, domain 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.5   0.2   3.1e-19   1.1e-15      16     107 ..     875     963 ..     864     964 .. 0.81

  Alignments for each domain:
  == domain 1  score: 57.5 bits;  conditional E-value: 3.1e-19
                            HCHHHHHHHHHHHHHHHHHHHHHHHHHHCSTTTSHHHHHHHCTSSS-HHHHHHHHTB-EEEEBTTBSS--SSTSCSSTTSSSSESSTT CS
         RNA_pol_Rpb1_4  16 ksleelfeakinkilnkardkagkiaskslaasNsiliMvksGaKGsiinisqiagclGqqnvegkripkgfsgrtlphfkkidespe 103
                             +l+++ ++++ ++ +++ d   k +++  + sN++  ++ sGaKGsi+n+sqi+g+lGqq++eg r+p + +gr+l +f     s  
  gene2|gene2|rna2|rna2 875 INLDNTIKKEMHTVTSQVSDLLIKGIETPFP-SNKMANIILSGAKGSIVNFSQISGLLGQQSLEGGRVPLMSNGRSLCSFL--KSSVL 959
                            4567777777777777777777777777766.6*********************************************998..45555 PP

                            TSSE CS
         RNA_pol_Rpb1_4 104 srGF 107
                            s GF
  gene2|gene2|rna2|rna2 960 SGGF 963
                            5555 PP

>> RNA_pol_Rpb1_1  RNA polymerase Rpb1, domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.7   0.9   2.2e-17   7.9e-14      19     254 ..      16     229 ..      13     235 .. 0.85
   2 ?   -3.8   5.4       1.8   6.3e+03     126     152 ..     286     337 ..     228     384 .. 0.45
   3 !   12.1   0.0   2.4e-05     0.088     259     312 .]     381     427 ..     373     427 .. 0.86

  Alignments for each domain:
  == domain 1  score: 51.7 bits;  conditional E-value: 2.2e-17
                            HH-SBB--STTSTCSTSSSSBBSSSSSSSSS-SSSSSTSTTTSSTTTT-----EEEEEECEEE-HHHHHHHHHHCTTCETTTTEBSS- CS
                            xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
         RNA_pol_Rpb1_1  19 kwSvvevtkaetieekslkPeegGllDerlgtidkdleCetCgkkkkeCeghfGhieLakPvfhigffklilkilecvckecskllld 106
                            k+++ e+  ++t++   + P +gGl D  lg   ++++C+ C+ ++  C+ghfG i+L++ +++   fk    i++  c +c++  + 
  gene2|gene2|rna2|rna2  16 KVAEHEIFIPQTLDSL-NIPIQGGLQDTMLGPQPHETQCAKCHLNYFACPGHFGEIALQTMIINPLLFKDLFMIVRLGCTKCHRFRIP 102
                            5677899999999988.59********************************************************************* PP

                            TTSH....HHHHHHCSSSCCCCHHHHHHHHCCS-BE-SSSSB-EEEEEETTEEEEEESSSSTSCEEEE-HHHHHHHHHCSTHHHHHHT CS
                            xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
         RNA_pol_Rpb1_1 107 eekkkllsklkkrekleelkkrlkaieelckkinlcekCgavqpkleeegeklkaalkkskeeekeklsaekvkkllkriededvevl 194
                            ++ ++ + k+  ++    +    +++e+ c        C       ++  +kl+ ++ +  +     +++ +v ++++ +   + e  
  gene2|gene2|rna2|rna2 103 TNAREHVLKNTGERL---VAAMKENVEDRC------PYCT-----SRSRLSKLNLKIVSGTQ----YVQPFRVYRIVRALF--ENERS 170
                            *98833333333322...222234444444......4444.....26677788888877776....8999**********9..67888 PP

                            TSBTTTB-GGGCCECCEEE--GGGS-BEESSSSSEEBECCCCHHHHHHHHHHHHHHHHHS CS
                            xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
         RNA_pol_Rpb1_1 195 gfkssgsrPewliltvlPVpPpeiRPsvqldggrrsedDlteklrdiikrNnrLkkaeee 254
                             f+  +   + + ++ + V+P++ RP+ +++  +  e+  +  l++i+k+N+ Lk ++e+
  gene2|gene2|rna2|rna2 171 FFERMRVDYKAFFMHKVFVLPNKFRPLNRMND-KIFESAHNIHLSRIVKINQVLKDEIER 229
                            999999************************99.88899*****************98775 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 1.8
                            C.......CCHHHHHHHHCCS-BE-..................SSSSB-EEE CS
                            x.......xxxxxxxxxxxxxxxxx..................xxxxxxxxx RF
         RNA_pol_Rpb1_1 126 k.......krlkaieelckkinlce..................kCgavqpkl 152
                            +       + +k+++  +++ n+++                  +C+++q+  
  gene2|gene2|rna2|rna2 286 RtenklksEDVKRVKGRLEEENKIKgrveeertgnklknkerpACKNEQGIN 337
                            1112222222222232333333222333333333333333333565555444 PP

  == domain 3  score: 12.1 bits;  conditional E-value: 2.4e-05
                            TCHHHHHHHHHHHHHHCC-TTSSSSSEEBSTTSSS--THHHHHTSSSSCCCCCT CS
                            xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
         RNA_pol_Rpb1_1 259 liieeekelLQehvatlfdneisglkpatqkskrplkslsqrLkGKeGrfRgnL 312
                            ++++  ++ LQ +v+ +fd+           skr+  +++q+L  KeG fR+n+
  gene2|gene2|rna2|rna2 381 SVLNGLINALQCAVQYYFDSTEYP-------SKRKPPGFKQALEKKEGLFRQNM 427
                            6788999************98733.......799999***************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1364 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1246  (0.0694963); expected 358.6 (0.02)
Passed bias filter:                      547  (0.0305092); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.92u 0.31s 00:00:01.23 Elapsed: 00:00:00.48
# Mc/sec: 8627.92
//
Query:       gene20|gene20|rna20|rna20  [L=123]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
       0.99    8.1  12.9       0.98    8.1  12.9    1.0  1  SAPS            SIT4 phosphatase-associated protein
        9.4    4.9   6.0         11    4.7   6.0    1.2  1  Otopetrin       Otopetrin


Domain annotation for each model (and alignments):
>> SAPS  SIT4 phosphatase-associated protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1  12.9   0.00011      0.98     239     339 ..      14     114 ..       1     123 [] 0.61

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00011
                       SAPS 239 nekkgeeivkerDevrerlleeltseeealedvsdeaskeesaesedltdkdedvsleesksakd.....enkesdesesdtae 317
                                 ++k eei k+r + re++ +++++++e  ++ s +++ + +++++d++d+++++ + +++++k+     +     +s+ + + 
  gene20|gene20|rna20|rna20  14 IRRKKEEISKQRRKRREKMDDRKKESKEDRTERSLRKARKMKKKADDVKDTNTKTCEMKQEKHKKkrgrpS-----NSKIELNP 92 
                                456899**************999888888888888888888888899988888887777777777455542.....22222222 PP

                       SAPS 318 esseededdasseesalaeete 339
                                 +s+++++ +s   + ++++ e
  gene20|gene20|rna20|rna20  93 IKSKSEMKADSCVIEKKTKKIE 114
                                2222222222222222222222 PP

>> Otopetrin  Otopetrin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   6.0    0.0013        11      89     152 ..      12      77 ..       6     121 .. 0.49

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.0013
                  Otopetrin  89 vlvkeskkeitaylekeesaeeassssssarida..lrkakkvltkstakekiisarleqrtaste 152
                                ++++ +k+ei+++ +k+++++++ +++s++  ++  lrka+k+++k    ++  ++++e ++++++
  gene20|gene20|rna20|rna20  12 MVIRRKKEEISKQRRKRREKMDDRKKESKEDRTErsLRKARKMKKKADDVKDTNTKTCEMKQEKHK 77 
                                789999999999999996555555555444444300344443332222222222222222222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (123 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3351  (0.186904); expected 358.6 (0.02)
Passed bias filter:                      603  (0.0336327); expected 358.6 (0.02)
Passed Vit filter:                       132  (0.00736237); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.33s 00:00:00.89 Elapsed: 00:00:00.48
# Mc/sec: 762.93
//
Query:       gene200|gene200|rna200|rna200  [L=351]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-17   63.0   0.0    3.1e-17   62.5   0.0    1.2  1  Acyltransferase  Acyltransferase


Domain annotation for each model (and alignments):
>> Acyltransferase  Acyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.5   0.0   1.7e-21   3.1e-17       6     132 ..      76     230 ..      71     233 .. 0.79

  Alignments for each domain:
  == domain 1  score: 62.5 bits;  conditional E-value: 1.7e-21
                Acyltransferase   6 glenlpekgpailvaNHqsylDvlllwlllyksn.gprnvviiakkellsipllgflmrllgfifidRksnaraagslen 84 
                                    + +++ +k+++++v+NH ++lD++++ ++l + + + +++ ii+k +l ++p+ g +m+ +++if++R  +++ +   + 
  gene200|gene200|rna200|rna200  76 N-KEILKKKRCLIVSNHLTNLDWIFIVVILNELGmY-EELCIIMKYSLSKLPIYGYGMKCFDYIFLKRRWQEDIHILSQG 153
                                    4.445557**********************999966.*******************************777777777777 PP

                Acyltransferase  85 iselleegkl.vviFPEGtrsre.........................gellpfkkGlvrlaakak...kgvpivPv 132
                                    ++++ ++++  +++FPEGt + +                         + l p  kG+ ++ + +    +gv+++++
  gene200|gene200|rna200|rna200 154 LEKMKKKENFyLLFFPEGTILDSetyeksqkygrdlnmtidgrlynpqFCLIPRVKGINKIYEVLQeeiDGVIDITL 230
                                    76655555666**********99888888888888888888777765555577777777776666566666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (351 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       519  (0.0289475); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.68u 0.34s 00:00:01.02 Elapsed: 00:00:00.59
# Mc/sec: 1778.93
//
Query:       gene2000|gene2000|rna2000|rna2000  [L=401]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.092   13.1   0.2        1.1    9.7   0.1    2.8  2  TbpB_C    C-lobe handle domain of Tf-binding protein B
        1.3    9.9  10.2         33    5.6   0.4    5.4  3  LRR_1     Leucine Rich Repeat
        4.9    7.0   9.7        5.9    6.7   0.3    4.0  4  LRR_8     Leucine rich repeat


Domain annotation for each model (and alignments):
>> TbpB_C  C-lobe handle domain of Tf-binding protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.25   1.5e+03       6      40 ..     212     248 ..     208     268 .. 0.71
   2 ?    9.7   0.1   0.00018       1.1      10      35 ..     270     298 ..     261     331 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.25
                                        EEEEETT-SSEEE-B--S-TTEEEETTEEE..ES--- CS
                             TbpB_C   6 aekldlkklekkeldnFgnaakLvidgkei..pLlpe 40 
                                         +  dl++ +++ l+   n + Lvid   +  +L+++
  gene2000|gene2000|rna2000|rna2000 212 LVGCDLDEENIEVLKELVNLQTLVIDCAFFecDLVKN 248
                                        556677888889999999999****987542256666 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00018
                                        ET...T-SSEEE-B--S-TTEEEETTEEE CS
                             TbpB_C  10 dl...kklekkeldnFgnaakLvidgkei 35 
                                        dl   + ++++el++++n+++L++dg  i
  gene2000|gene2000|rna2000|rna2000 270 DLcslDFKTVQELKKYENIKHLILDGSII 298
                                        4444366789****************877 PP

>> LRR_1  Leucine Rich Repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.4    0.0055        33       1      15 [.     103     117 ..     103     133 .. 0.77
   2 ?    5.5   0.9     0.006        36       1      13 [.     206     218 ..     206     276 .. 0.89
   3 ?   -0.1   0.1      0.39   2.3e+03       1      17 [.     287     309 ..     287     316 .. 0.68

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0055
                              LRR_1   1 nLrhLdLsnnpllgl 15 
                                        nLr Ld+ +n++   
  gene2000|gene2000|rna2000|rna2000 103 NLRQLDIAYNFNNEC 117
                                        8********998322 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.006
                              LRR_1   1 nLrhLdLsnnpll 13 
                                        +L++L+L ++ l+
  gene2000|gene2000|rna2000|rna2000 206 KLKYLNLVGCDLD 218
                                        7*********993 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.39
                              LRR_1   1 nLrhLdLsnnpl......lglpp 17 
                                        n +hL L + ++      ++lp+
  gene2000|gene2000|rna2000|rna2000 287 NIKHLILDGSIIgyesifDCLPI 309
                                        67999998888755555555554 PP

>> LRR_8  Leucine rich repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.3   0.00099       5.9      23      56 ..     100     133 ..      98     135 .. 0.81
   2 ?    3.1   1.1     0.014        83      25      61 .]     182     217 ..     172     217 .. 0.80
   3 ?    2.6   0.3     0.019   1.1e+02      26      37 ..     206     217 ..     199     237 .. 0.45
   4 ?   -3.1   0.0       1.1   6.9e+03      48      56 ..     376     384 ..     373     395 .. 0.54

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.00099
                                        T-TT--EEE--SS---GGGGGGGTT--S-.EEE- CS
                              LRR_8  23 glsnLkvLdLsnNllttlspgafsgLpsLrsLdL 56 
                                        +l+nL+ Ld+ +N  +   ++ +s +  L++L++
  gene2000|gene2000|rna2000|rna2000 100 SLENLRQLDIAYNFNNECFNQNLSKCVDLEYLTV 133
                                        699**********555555699999999999987 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.014
                                        TT--EEE--SS.---GGGGGGGTT--S-.EEE--SS-- CS
                              LRR_8  25 snLkvLdLsnN.llttlspgafsgLpsLrsLdLsgNrL 61 
                                         + +vL+L+ N   + +   +f   ++L++L+L g++L
  gene2000|gene2000|rna2000|rna2000 182 GSINVLNLKMNiFFNEIF--TFNIRNKLKYLNLVGCDL 217
                                        567888888888888887..8888899******99987 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.019
                                        T--EEE--SS-- CS
                              LRR_8  26 nLkvLdLsnNll 37 
                                        +Lk+L+L    l
  gene2000|gene2000|rna2000|rna2000 206 KLKYLNLVGCDL 217
                                        344444433333 PP

  == domain 4  score: -3.1 bits;  conditional E-value: 1.1
                                        --S-.EEE- CS
                              LRR_8  48 LpsLrsLdL 56 
                                        +++L+ L L
  gene2000|gene2000|rna2000|rna2000 376 FNKLDDLVL 384
                                        444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (401 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       551  (0.0307323); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 2666.55
//
Query:       gene2001|gene2001|rna2001|rna2001  [L=693]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-16   60.5   0.2    2.6e-16   60.5   0.2    2.8  2  SET       SET domain


Domain annotation for each model (and alignments):
>> SET  SET domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.7   3.2         1   1.8e+04      91      91 ..     448     448 ..     312     538 .. 0.63
   2 !   60.5   0.2   1.4e-20   2.6e-16       1     169 []     564     670 ..     564     670 .. 0.84

  Alignments for each domain:
  == domain 1  score: -4.7 bits;  conditional E-value: 1
                                        T CS
                                        x RF
                                SET  91 s 91 
                                        +
  gene2001|gene2001|rna2001|rna2001 448 N 448
                                        1 PP

  == domain 2  score: 60.5 bits;  conditional E-value: 1.4e-20
                                        SCEEEESSXBXTTXEEEEEEECCEECHHHHHHHHHH........HTEEEEEXGGXXGGSXHHHHHHHTTSSHHHHH CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                                SET   1 GrGvfAtedIpkgeficeypeeiiltkdeadksele........aylfslpeapknlaftkelakasastllqkla 68 
                                        G G+fA+++Ipkg++i+ey+  i + +  adk e+e         ylf l+                         
  gene2001|gene2001|rna2001|rna2001 564 GNGLFASKPIPKGSMIIEYQG-IKIGNMMADKLENEyqqnninsIYLFRLD------------------------- 613
                                        77*****************94.34444444444444455567779999999......................... PP

                                        HHHHHHHHHHHHHTHHHHHHHXTTTSXXXHCCCCCHCCCHEEEETEEEEEECCCGTTGGGCEEXSSSSEEEEEEEE CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                                SET  69 kdqkqaekedtdaalkasskaesdlnaskpeagafsaiagysidaralksgngagplarflNHsCdpNcnltvqnv 144
                                                                                ++id  a+ +gn a    rf+NHsCdpN++++v   
  gene2001|gene2001|rna2001|rna2001 614 --------------------------------------KDLIID--ATVYGNKA----RFINHSCDPNAEARVTLH 645
                                        ......................................7789**..77******....***********9999999 PP

                                        TTSSEEEEEESSXBXTTEEEEEXTT CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxx RF
                                SET 145 lrgprvavfAtrdIkkGeEltidYg 169
                                        ++ +++ ++A++dI  ++E+t+ Y+
  gene2001|gene2001|rna2001|rna2001 646 DKQRKLLIYALKDILVNQEITMYYN 670
                                        **********************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (693 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1263  (0.0704445); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.33s 00:00:00.92 Elapsed: 00:00:00.46
# Mc/sec: 4505.16
//
Query:       gene2002|gene2002|rna2002|rna2002  [L=181]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0048   17.0   0.1     0.0096   16.0   0.1    1.5  1  DnaJ           DnaJ domain
  ------ inclusion threshold ------
      0.038   13.9   0.0      0.057   13.3   0.0    1.2  1  TMEM52         Transmembrane 52
      0.089   12.9   0.0       0.13   12.4   0.0    1.3  1  Trp_repressor  Trp repressor protein


Domain annotation for each model (and alignments):
>> DnaJ  DnaJ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.1   1.6e-06    0.0096       1      62 [.      32      90 ..      32      91 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.6e-06
                                       HHHHHHTSSTTG-HHHHHHHHHHHHHHH..STTTSCCHH.HHHHHHHHHHHHHHHHTSHHHHHHH CS
                               DnaJ  1 dyYeiLgvskdasedeIkkaYrklalky..HPDknpkdp.eaeekFkeineAyevLsdpekRkqY 62
                                       ++Ye+  v+++ + + I+++++kl+++    PD n   p   +e  k i+e y++L+    +++Y
  gene2002|gene2002|rna2002|rna2002 32 TFYEMFDVKENTDIKIIRSKFYKLVKESkpFPDLN--IPkGVAE--KIITEGYNILNR--HKQEY 90
                                       58***********************9762266777..4424444..799999999987..45555 PP

>> TMEM52  Transmembrane 52
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   9.5e-06     0.057      16      76 ..     107     169 ..      98     172 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 9.5e-06
                             TMEM52  16 vsLwyvwLilvivlllLlCgltasCvrfCclrkqqkaeeesppa..rkpyevtvialDsDstl 76 
                                           +yv L++ + ++ Ll  l+   +rf   r++ ++ ++++ +  r++ ++ v +lD+  t+
  gene2002|gene2002|rna2002|rna2002 107 RTFFYVNLVVFVLFVALLSDLLVCLIRFLVNRRRYEGVDKAQEKklRRRGDIEVFSLDRMYTI 169
                                        5789*******************99***99999887766555431267889999999986665 PP

>> Trp_repressor  Trp repressor protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   2.2e-05      0.13       5      86 ..      16      96 ..      12      98 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.2e-05
                      Trp_repressor  5 allelilkleneeeleellelllTpdEreal.aqRlqvvkeLLkeelsqreIaeelgvSiAtItRvsrsLktgsdeyk 81
                                        +l+ i++l+++ +   + e++  ++E +++ + R + +k L ke++++ +++   gv    It + + L+  ++ey+
  gene2002|gene2002|rna2002|rna2002 16 NILKSIQTLHKKTKFRTFYEMFD-VKENTDIkIIRSKFYK-LVKESKPFPDLNIPKGVAEKIITEGYNILNRHKQEYD 91
                                       57899999***999999999875.5555555268******.************************************* PP

                      Trp_repressor 82 avLkr 86
                                       a L+ 
  gene2002|gene2002|rna2002|rna2002 92 ALLRS 96
                                       *9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       847  (0.0472419); expected 358.6 (0.02)
Passed bias filter:                      497  (0.0277205); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1268.91
//
Query:       gene2003|gene2003|rna2003|rna2003  [L=213]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       416  (0.0232026); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.22s 00:00:00.60 Elapsed: 00:00:00.36
# Mc/sec: 1760.21
//
Query:       gene2004|gene2004|rna2004|rna2004  [L=117]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       863  (0.0481343); expected 358.6 (0.02)
Passed bias filter:                      566  (0.031569); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 907.10
//
Query:       gene2005|gene2005|rna2005|rna2005  [L=189]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (189 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       828  (0.0461822); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1434.06
//
Query:       gene2007|gene2007|rna2007|rna2007  [L=497]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-20   73.6   4.0      1e-19   70.5   4.2    2.4  2  ProRS-C_1       Prolyl-tRNA synthetase, C-terminal
    4.7e-19   69.1   0.0    1.5e-18   67.4   0.0    1.8  2  tRNA-synt_2b    tRNA synthetase class II core domain (G, H, P
    1.1e-13   51.2   0.1    4.4e-13   49.2   0.1    2.0  2  HGTP_anticodon  Anticodon binding domain


Domain annotation for each model (and alignments):
>> ProRS-C_1  Prolyl-tRNA synthetase, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.24   1.5e+03      24      40 ..     260     277 ..     249     288 .. 0.81
   2 !   70.5   4.2   1.7e-23     1e-19       1      69 []     419     497 .]     419     497 .] 0.98

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.24
                                        HHHHHHHHH.S-EEEEEE CS
                          ProRS-C_1  24 cEekIkeet.gakslcip 40 
                                        +Ee++ +++ g +++ci 
  gene2007|gene2007|rna2007|rna2007 260 NEEYVYQNSwGLTTRCIG 277
                                        67788777789*****95 PP

  == domain 2  score: 70.5 bits;  conditional E-value: 1.7e-23
                                        HHHHHHHHHTT-EEEEEESSGHHHHHHHHHHH...........S-EEEEEESSB-SSCCCSB-TTT-SB-SEEEEE CS
                          ProRS-C_1   1 weefkealekkgfvlapWcgeeecEekIkeet...........gakslcipfdqepseegtkCivcgkpakkwvlf 65 
                                        we fk +l+ ++++++p+cg+ ecEe Ikeet           gakslc+pf++ +++++ +Ci cg+  ++++lf
  gene2007|gene2007|rna2007|rna2007 419 WEHFKCELSCNNLIMIPFCGRIECEEVIKEETtvrkngcveqqGAKSLCVPFEN-NERKSLQCIKCGEACDRYTLF 493
                                        9***************************************************96.78999**************** PP

                                        E-B- CS
                          ProRS-C_1  66 grsY 69 
                                        grsY
  gene2007|gene2007|rna2007|rna2007 494 GRSY 497
                                        **** PP

>> tRNA-synt_2b  tRNA synthetase class II core domain (G, H, P, S and T)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0         1     6e+03      86     102 ..      22      43 ..      12      71 .. 0.64
   2 !   67.4   0.0   2.5e-22   1.5e-18       9     176 ..     112     280 ..     104     283 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 1
                                        HHHHHHHHTT.SC.....EEEE CS
                                        xxxxxxxxxxxxx.....xxxx RF
                       tRNA-synt_2b  86 aisriferlglef.....raii 102
                                          s+++++l ++      + i+
  gene2007|gene2007|rna2007|rna2007  22 NFSEWYQQLVIKSelleyYDIK 43 
                                        4566676665543222224444 PP

  == domain 2  score: 67.4 bits;  conditional E-value: 2.5e-22
                                        EEEEE-SSSHHHHHHHHHHHEEEB.GGSSEEEEEEEEEEBTTTSTBCTTTB-SEEEEEEEEEEES.GGGHHHHHHH CS
                                        xxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx RF
                       tRNA-synt_2b   9 reyiLkPtneetfvelirdevlrs.krLPlklyqiqtkyRdEksdsrGLlRvreFhqkdgyvfha.easlddslrd 82 
                                        +  +++Pt+e+ ++  ++++ l s ++LPlkl q + + R E +++ + +R+reF +++g+     ++ +++++ +
  gene2007|gene2007|rna2007|rna2007 112 EPVAIRPTSEAVMYPYFKKW-LFShRDLPLKLNQWCNVLRWEVKSTLPFIRGREFLWQEGHTAYYeKEGAEQEVLQ 186
                                        56789*************99.655377*****************788**************98886788******* PP

                                        HHHHHHHHHHHTT.SCEEEEEE.GTTSC.BTTSEEEEEEEEETTTSEEEEEEEEEEEETHHHHHTTEEEECTTSSE CS
                                        xxxxxxxxxxxxxxxxxxxxxx.xxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2b  83 likaisriferlglefraiiel.msaks.adykdkkefeavsesltkgieigtiqklgtrlserlgatvldennre 156
                                        ++ ++++i+ +l+  + +i++  +++++   +++++ +ea  + ++k+++ +t ++lg+++s+  +++++d+ n+e
  gene2007|gene2007|rna2007|rna2007 187 ILDLYEKIYTDLL-AVPVIKGRkTENEKfGGAEYTTTIEAFIPVSGKAVQAATSHFLGKNFSKMYDVKIVDRCNNE 261
                                        ***********97.4456666652222314578899**************************************** PP

                                        EEEEEEEEEEEHHHHHHHHH CS
                                        xxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2b 157 ksvimicaaigveRllsail 176
                                        + v+    ++  +R +++++
  gene2007|gene2007|rna2007|rna2007 262 EYVYQNSWGLT-TRCIGIAV 280
                                        ***87777776.89888765 PP

>> HGTP_anticodon  Anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.2   0.1   7.3e-17   4.4e-13       1      93 [.     299     392 ..     299     393 .. 0.95
   2 ?   -1.6   0.0      0.51     3e+03      48      73 ..     429     454 ..     406     465 .. 0.81

  Alignments for each domain:
  == domain 1  score: 49.2 bits;  conditional E-value: 7.3e-17
                                        SEEEEESSSSHHHHHHHHHHHHHHHHTTTSEEEEES.SSSTHHHHHHHHHHTT-SEEEEE-HHHHHHTEEEEEETT CS
                     HGTP_anticodon   1 qvvviplnekaeeleeyakklaeeLraagirveldd.snesigkkireadllgipfavvvGekelekgtvtvrdrd 75 
                                        q v++p+++ + ++  y  ++++e ++ g+rv ldd +n   g+k+++++l+g+p++ ++G +++++++v v +r+
  gene2007|gene2007|rna2007|rna2007 299 QLVIVPCGSLNGDVCAYIARIKKEVEDRGVRVFLDDrKNVLSGFKFNHWELKGVPLRMEIGMNDYNNNEVVVVTRM 374
                                        789*****9988899*********************8888889********************************* PP

                                        TCEEEEEETTHHHHHHHH CS
                     HGTP_anticodon  76 treqervsldelveklke 93 
                                        +r + rvs  ++++++ +
  gene2007|gene2007|rna2007|rna2007 375 NRCKKRVSSTNIADYVVN 392
                                        *************99976 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.51
                                        HHHTT-SEEEEE-HHHHHHTEEEEEE CS
                     HGTP_anticodon  48 adllgipfavvvGekelekgtvtvrd 73 
                                         +l+ ipf+  +  +e+ k++ tvr+
  gene2007|gene2007|rna2007|rna2007 429 NNLIMIPFCGRIECEEVIKEETTVRK 454
                                        56788999999999999999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (497 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       871  (0.0485805); expected 358.6 (0.02)
Passed bias filter:                      512  (0.0285571); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.44
# Mc/sec: 3356.96
//
Query:       gene2008|gene2008|rna2008|rna2008  [L=323]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    7.8e-39  134.3   0.2      1e-38  133.9   0.2    1.2  1  Metallophos  Calcineurin-like phosphoesterase
    1.6e-16   60.5   1.6    2.5e-16   59.9   0.9    1.8  2  STPPase_N    Serine-threonine protein phosphatase N-terminal 


Domain annotation for each model (and alignments):
>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  133.9   0.2   1.1e-42     1e-38       2     201 ..      57     248 ..      56     251 .. 0.92

  Alignments for each domain:
  == domain 1  score: 133.9 bits;  conditional E-value: 1.1e-42
                                        EEEEEESBTBTTCCTHHHHHHHHHHHH..HHHTTESEEEEESTSSSSSHHHHHHHHH.HHHHHHHTSEEEEEC-TT CS
                        Metallophos   2 rilvigDlHlalgggqlddllkllddl..lreekpdlvllaGDlvdrgdlekellel.laalvkypipvylllGNH 74 
                                        +i ++gD+H     gq++dllkl+d    +++ +++l+l  GD+vdrg  + e++ l +a+++kyp++++ll+GNH
  gene2008|gene2008|rna2008|rna2008  57 PIKICGDIH-----GQYRDLLKLFDFGgfPPD-NNYLFL--GDYVDRGKQSLETICLlFAYKIKYPQNIFLLRGNH 124
                                        6889*****.....**********77763555.899999..*******77777777779***************** PP

                                        S........CHHHHHHHHHHHHHHHHHHHEHHHCEEETSEEEEEETTEEEEEEEESE.CEEETHHHHHHHHHHHSC CS
                        Metallophos  75 e........gfeeellnkygylgifsepwrsdaevfnnlplaslgsgslkvlllhGg.spellvsldklgslnlel 141
                                        e        gf +e++++        ++w+++++ fn+lp++++++   ++l++hGg spel ++ld+++++++++
  gene2008|gene2008|rna2008|rna2008 125 EcasinkiyGFFDECKRRHS-----IRIWKNFTDSFNCLPISAIVGE--RILCMHGGiSPEL-KNLDQIRKIKRPT 192
                                        *****999999999999966.....9*********************..********88888.************* PP

                                        HHHHCC...HHHHHHHHHHTTCSEEEEEESSESSCSSSCSCCHHHHHHHHHHTTESEEEEESS CS
                        Metallophos 142 eapepg...dewlkdlekrekadwvivlgHsplyrgsgylfgdealedllkkygvdlvisGHt 201
                                        ++p++g   d+++ d       +   + g+  + rg + +fg ++++++l+ +++dl++++H+
  gene2008|gene2008|rna2008|rna2008 193 DVPDDGllcDILWGD-------PEPSISGWGENDRGVSVTFGADVVKEFLDSNDLDLICRAHQ 248
                                        ***************.......888888888888****************************8 PP

>> STPPase_N  Serine-threonine protein phosphatase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.9   0.9   2.8e-20   2.5e-16       1      47 [.       8      54 ..       8      55 .. 0.96
   2 ?   -2.9   0.0       1.1   9.6e+03      22      32 ..     235     245 ..     232     246 .. 0.83

  Alignments for each domain:
  == domain 1  score: 59.9 bits;  conditional E-value: 2.8e-20
                          STPPase_N  1 vDdiIerLlevrgkpggkkvqLseaEIrqlCakareiFLsQPtLLeL 47
                                       vD+iI++Ll+v++++ gk+v+Lse+EI +lC k +ei LsQP+LL +
  gene2008|gene2008|rna2008|rna2008  8 VDKIISKLLSVKNSRLGKNVHLSESEILFLCEKTKEIHLSQPMLLHI 54
                                       8************8888****************************87 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.1
                          STPPase_N  22 LseaEIrqlCa 32 
                                        L ++++ ++C+
  gene2008|gene2008|rna2008|rna2008 235 LDSNDLDLICR 245
                                        88999999**7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (323 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       324  (0.0180713); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2287.41
//
Query:       gene2009|gene2009|rna2009|rna2009  [L=36]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (36 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       309  (0.0172346); expected 358.6 (0.02)
Passed bias filter:                      231  (0.0128842); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.27s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 260.99
//
Query:       gene201|gene201|rna201|rna201  [L=182]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1103  (0.0615204); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1265.99
//
Query:       gene2010|gene2010|rna2010|rna2010  [L=415]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-29  103.4   1.5    3.7e-28   98.6   0.1    3.1  3  AAA              ATPase family associated with various cellul
    1.5e-05   25.0   0.5    0.00022   21.2   0.1    2.7  2  AAA_5            AAA domain (dynein-related subfamily)
    3.5e-05   24.1   0.1    9.3e-05   22.7   0.1    1.8  1  AAA_22           AAA domain
    4.2e-05   22.8   2.3    0.00063   19.0   2.4    2.2  1  DUF815           Protein of unknown function (DUF815)
    6.1e-05   22.8   0.1    0.00013   21.8   0.1    1.6  1  AAA_24           AAA domain
    6.2e-05   23.2   0.1    0.00015   21.9   0.1    1.7  1  AAA_2            AAA domain (Cdc48 subfamily)
    8.9e-05   22.1   0.3    0.00022   20.8   0.3    1.7  1  AAA_7            P-loop containing dynein motor region
    0.00015   21.2   0.0    0.00026   20.5   0.0    1.5  1  Mg_chelatase     Magnesium chelatase, subunit ChlI
    0.00036   20.9   0.0    0.00093   19.6   0.0    1.7  1  AAA_16           AAA ATPase domain
     0.0012   18.1   1.3     0.0038   16.5   0.2    1.9  2  TIP49            TIP49 P-loop domain
     0.0024   17.7   0.0     0.0052   16.5   0.0    1.6  1  IstB_IS21        IstB-like ATP binding protein
     0.0085   15.2   0.3      0.015   14.4   0.3    1.5  1  MCM              MCM P-loop domain
     0.0089   16.0   0.4       0.04   13.8   0.1    2.2  2  NACHT            NACHT domain
       0.01   16.2   0.2      0.061   13.7   0.0    2.5  2  RNA_helicase     RNA helicase
  ------ inclusion threshold ------
      0.016   14.6   0.2      0.047   13.0   0.2    1.9  1  ATPase           KaiC
      0.024   14.6   0.1      0.054   13.5   0.1    1.5  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
      0.026   14.3   0.0      0.066   12.9   0.0    1.7  1  Sigma54_activat  Sigma-54 interaction domain
      0.032   14.4   0.2         13    6.0   0.1    2.8  2  Roc              Ras of Complex, Roc, domain of DAPkinase
      0.045   14.1   0.0       0.11   12.9   0.0    1.6  1  AAA_19           AAA domain
      0.047   12.9   0.0      0.091   12.0   0.0    1.5  1  DUF2075          Uncharacterized conserved protein (DUF2075)
      0.057   13.2   0.7       0.13   12.0   0.0    2.0  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
      0.057   13.3   0.0       0.19   11.6   0.0    1.9  1  AAA_3            ATPase family associated with various cellul
      0.063   13.8   0.9       0.98   10.0   0.2    3.1  2  EF-G-binding_N   Elongation factor G-binding protein, N-termi
      0.083   12.3   0.8        0.2   11.0   0.3    1.9  2  TniB             Bacterial TniB protein
       0.11   12.1   0.2       0.24   11.0   0.0    1.6  1  AAA_25           AAA domain
       0.22   11.5   4.3       0.65   10.0   4.3    1.8  1  ResIII           Type III restriction enzyme, res subunit
        3.1    8.3   8.1        5.6    7.4   5.4    2.4  2  FeoB_associated  FeoB-associated Cys-rich membrane protein


Domain annotation for each model (and alignments):
>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0      0.77   5.1e+02      98     129 ..      92     124 ..      75     126 .. 0.77
   2 !   98.6   0.1   5.6e-31   3.7e-28       1     130 [.     145     309 ..     145     311 .. 0.84
   3 ?    0.2   0.0       1.4   9.2e+02      24      57 ..     330     363 ..     318     395 .. 0.72

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.77
                                        TSSSTEEEEEEESS..GGGSTHHHHSTTSSEEEE CS
                                AAA  98 kkeskvivigatnr..pdkldpallrgRfdrkie 129
                                        k  ++ +v  atn+   +++ + l+ gR++r+i+
  gene2010|gene2010|rna2010|rna2010  92 KTINDPTVFSATNYfgKENIMETLV-GRITRIIN 124
                                        3355678999****99999******.***99987 PP

  == domain 2  score: 98.6 bits;  conditional E-value: 5.6e-31
                                        EEEESSTTSSHHHHHHHHHHHH............THEEEEEETTTCSSS.....................STTHHH CS
                                AAA   1 vllyGppGtGKTllakavakel............gvefleisgsellsk.....................yvgese 43 
                                        +llyG pGtGKTll+k +a  l            ++++ +++ s+ll k                     yvg +e
  gene2010|gene2010|rna2010|rna2010 145 ILLYGEPGTGKTLLVKKMAFLLdqnlkllklkksKIDIQKMKKSDLLAKlkrmkpcvrliavqpsslndrYVGGTE 220
                                        69*******************8443333333322244555555555544888888888888888888888****** PP

                                        HHHHHHHHHHHHTS..TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTS.SSTEEEEEEESSGGGST CS
                                AAA  44 kkirelfkeakeka..kpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkk.eskvivigatnrpdkld 116
                                        k+i++l++ a +++    +i+f+DEid+++++r++++se++++v +++l  ldg+++k ++++i+igatn p++ld
  gene2010|gene2010|rna2010|rna2010 221 KNIQKLWDFATKNKkhVITIVFMDEIDSFFSKRKEENSEHSSNVKSEFLCILDGLRSKlTDRLIFIGATNLPKTLD 296
                                        *********9888874449**************99********************9998788************** PP

                                        HHHHSTTSSEEEET CS
                                AAA 117 pallrgRfdrkiei 130
                                        +a+l +Rf  ki +
  gene2010|gene2010|rna2010|rna2010 297 EAFL-RRFHTKILF 309
                                        ****.7***99987 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 1.4
                                        HEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTS CS
                                AAA  24 vefleisgsellskyvgesekkirelfkeakeka 57 
                                         ++  ++  el++   g ++++i+ +f++a   +
  gene2010|gene2010|rna2010|rna2010 330 YRLSDVEINELVNACNGLTQSQIARIFSDAADYS 363
                                        5667788899999999999999999999986655 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.1   3.3e-07   0.00022       1      33 [.     144     176 ..     144     195 .. 0.88
   2 ?    0.8   0.0      0.66   4.4e+02     113     138 .]     278     303 ..     239     303 .. 0.74

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 3.3e-07
                                        EEEEE--SSSSHHHHHHHGGGGBS--EEEEE-- CS
                              AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqlt 33 
                                        ++lL G+pGtgK+ l++++a +l +++    l+
  gene2010|gene2010|rna2010|rna2010 144 NILLYGEPGTGKTLLVKKMAFLLDQNLKLLKLK 176
                                        689********************9998776665 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.66
                                        .....-EEEEEESS--.-TT-TTHHHHTT- CS
                              AAA_5 113 r....frviatanpldrslnelspalrsRf 138
                                        +    + +i+++n ++     l++a+++Rf
  gene2010|gene2010|rna2010|rna2010 278 KltdrLIFIGATNLPK----TLDEAFLRRF 303
                                        1444478888998888....9999999999 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.1   1.4e-07   9.3e-05       5     105 ..     142     256 ..     138     295 .. 0.62

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 1.4e-07
                             AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst...sskdllrellralglelka....erl 73 
                                        ++ ++++Ge+GtGKT+l+++++  ld+  k  + +++ + ++  +++      + ++  +r + ++ ++    + +
  gene2010|gene2010|rna2010|rna2010 142 KKNILLYGEPGTGKTLLVKKMAFLLDQNLKLLKLKKSKIDIQKMKKSdllAKLKRMKPCVRLIAVQPSSlndrYVG 217
                                        6789*********************987777775666564444444433344444566666666666668888555 PP

                             AAA_22  74 sseellealeqalrarav..ielliiDEaqhlr.....s 105
                                         +e  +++l++ + + ++  i ++  DE++ ++     +
  gene2010|gene2010|rna2010|rna2010 218 GTEKNIQKLWDFATKNKKhvITIVFMDEIDSFFskrkeE 256
                                        666666666666666666666799999999977554220 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   2.4   9.5e-07   0.00063      51      96 ..     140     184 ..     108     273 .. 0.68

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 9.5e-07
                             DUF815  51 lpannvLLwGarGtGKSslvkallneyaeegLrlievekedlkelp 96 
                                        ++ +n+LL+G+ GtGK  lvk +   + +++L+l++++k++++  +
  gene2010|gene2010|rna2010|rna2010 140 AAKKNILLYGEPGTGKTLLVKKMA-FLLDQNLKLLKLKKSKIDIQK 184
                                        33479****************986.577899*******99886433 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.1   1.9e-07   0.00013       2      83 ..     142     255 ..     141     290 .. 0.73

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 1.9e-07
                             AAA_24   2 klkiliyGpsgiGKTtlakelgpkplfidtekGlksldadkfpdie.........swedfldevvel......... 59 
                                        k++il+yG++g+GKT l+k++   ++++d +  l +l+  k++ i+         +++                  
  gene2010|gene2010|rna2010|rna2010 142 KKNILLYGEPGTGKTLLVKKM---AFLLDQNLKLLKLKKSKID-IQkmkksdllaKLKR-------Mkpcvrliav 206
                                        789******************...6677776666666666665.433533334442222.......2444444577 PP

                             AAA_24  60 .........................aaeladyktlviDtideleelcla 83 
                                                                 + +++ + +++ D id + +  ++
  gene2010|gene2010|rna2010|rna2010 207 qpsslndryvggtekniqklwdfatKNKKHVITIVFMDEIDSFFSKRKE 255
                                        7888888888888888888888888888888999999999999775544 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.1   2.2e-07   0.00015       3     105 ..     142     274 ..     140     298 .. 0.73

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 2.2e-07
                                        ---EEEE--TTSSHHHHHHHHHHHTT-...............-EEEEEGGG-------THHHHHHHHHTTT-HHHH CS
                              AAA_2   3 iisilllgptgvGktelakalaellfv...........kkekkliradaselleeeevehlvsrligappgyvgae 67 
                                        + +ill g+ g+Gkt+l k++a ll+             + +k+  +d  + l+   ++  v    ++p   + + 
  gene2010|gene2010|rna2010|rna2010 142 KKNILLYGEPGTGKTLLVKKMAFLLDQnlkllklkkskIDIQKMKKSDLLAKLK--RMKPCVRLIAVQPSSLNDRY 215
                                        5699************99999999997777676553322223333333333333..44555555555555555555 PP

                                        TTS.....................EEEEETGGG----.---------HHHHHHHHHHHH- CS
                              AAA_2  68 egG.....................ivllDEidKihpk.essgadvSregVqrdLLqileg 105
                                         gG                     iv++DEid   +k ++++++ S+ +V   +L il+g
  gene2010|gene2010|rna2010|rna2010 216 VGGtekniqklwdfatknkkhvitIVFMDEIDSFFSKrKEENSEHSS-NVKSEFLCILDG 274
                                        5559999*****************************96555555555.7*********98 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.3   3.3e-07   0.00022      14      69 ..     123     177 ..     116     199 .. 0.77

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 3.3e-07
                              AAA_7  14 VptvdtvrysyllelllknkkpvllvGptGtGKtviikdllkkldkekylsltinf 69 
                                        ++ ++    + l +++ ++kk++ll+G+ GtGKt+++k++   ld ++++ l+++ 
  gene2010|gene2010|rna2010|rna2010 123 INLIEKKNKKLLNSKMTAAKKNILLYGEPGTGKTLLVKKMAFLLD-QNLKLLKLKK 177
                                        5566667778888999***********************888777.6666665554 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   3.8e-07   0.00026      19      61 ..     139     181 ..     124     254 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 3.8e-07
                       Mg_chelatase  19 aaGgHnlllvGppGsGKtmlakrlpsllpplseeealevakia 61 
                                         a + n+ll+G pG+GKt+l k+++ ll +  +   l+ +ki 
  gene2010|gene2010|rna2010|rna2010 139 TAAKKNILLYGEPGTGKTLLVKKMAFLLDQNLKLLKLKKSKID 181
                                        46789**********************9887777666666665 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   1.4e-06   0.00093      22      88 ..     140     197 ..     115     269 .. 0.71

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1.4e-06
                             AAA_16  22 grpelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqllde 88 
                                            ++ll+Ge+G+GK+ lv++ +  l +++  +l+ k  +          +q  ++++ll++l+++
  gene2010|gene2010|rna2010|rna2010 140 AAKKNILLYGEPGTGKTLLVKKMA-FLLDQNLKLLKLKKSKI--------DIQKMKKSDLLAKLKRM 197
                                        34489***************9998.45555444454444444........45555555555555555 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.2   5.8e-06    0.0038      48     104 ..     140     196 ..     122     205 .. 0.86
   2 ?   -0.4   0.0       0.8   5.3e+02     215     262 ..     232     279 ..     211     284 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 5.8e-06
                                        XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                              TIP49  48 laGravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkktevltqalr 104
                                         a + +Ll G++gtGkt l   ++  l ++++  +l+ s++  +++kk+++l +  r
  gene2010|gene2010|rna2010|rna2010 140 AAKKNILLYGEPGTGKTLLVKKMAFLLDQNLKLLKLKKSKIDIQKMKKSDLLAKLKR 196
                                        35689*********************************************9987665 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.8
                                        S----XXXXXXXXXXXXXXXXXXXXXXXX....XXXXXXXXXXXXXXX CS
                              TIP49 215 ekkkevvqevtLhdlDvanarpqdllslllqllkskkteiteklreei 262
                                        + kk+v+  v + ++D   +++++  s   +++ks+   i + lr+++
  gene2010|gene2010|rna2010|rna2010 232 KNKKHVITIVFMDEIDSFFSKRKEENSEHSSNVKSEFLCILDGLRSKL 279
                                        67889999999999**99999999999998999998888888888765 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   7.9e-06    0.0052      30      68 ..     125     163 ..     110     198 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 7.9e-06
                          IstB_IS21  30 ldkrkvkeLatlsfiekkenivllGpsGvGKshlaialg 68 
                                        l ++k k+L + + +++k+ni+l G +G+GK+ l   ++
  gene2010|gene2010|rna2010|rna2010 125 LIEKKNKKLLNSKMTAAKKNILLYGEPGTGKTLLVKKMA 163
                                        66788899************************9987665 PP

>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.3   2.3e-05     0.015      37      84 ..     122     169 ..      83     210 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.3e-05
                                        HHHHH---EBBBSSSSBBCSS-EEEEEESSTSTHHHHHHHHHHHSSSE CS
                                MCM  37 llqlfggvkkkledktklrgdinvllvgdpgtaKsqlLkyveklapra 84 
                                        ++ l+   +kkl +++ + ++ n+ll g+pgt+K+ l+k+++ l++++
  gene2010|gene2010|rna2010|rna2010 122 IINLIEKKNKKLLNSKMTAAKKNILLYGEPGTGKTLLVKKMAFLLDQN 169
                                        56778888888888888999*******************998776665 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.1     6e-05      0.04       3      26 ..     145     168 ..     143     177 .. 0.90
   2 ?   -0.9   0.0         2   1.3e+03      78      78 ..     263     263 ..     216     358 .. 0.60

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 6e-05
                                        EEEEC-TTTCHHHHHHHHHHHHCT CS
                              NACHT   3 vilqGeaGsGKTtLlqklalawae 26 
                                        ++l Ge+G GKT L++k+a+++ +
  gene2010|gene2010|rna2010|rna2010 145 ILLYGEPGTGKTLLVKKMAFLLDQ 168
                                        799****************99876 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 2
                                        C CS
                              NACHT  78 e 78 
                                         
  gene2010|gene2010|rna2010|rna2010 263 N 263
                                        2 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.0   9.1e-05     0.061       1      27 [.     145     173 ..     145     201 .. 0.72
   2 ?   -2.4   0.0       9.5   6.3e+03      49      79 ..     350     381 ..     338     392 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 9.1e-05
                       RNA_helicase   1 iwlyGpsgeGKStlakeLakallkkl..k 27 
                                        i+lyG++g+GK++l+k++a  l ++l   
  gene2010|gene2010|rna2010|rna2010 145 ILLYGEPGTGKTLLVKKMAFLLDQNLklL 173
                                        789**************877766666432 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 9.5
                       RNA_helicase  49 gqevvvidDfgqvkdee.npsdlaelirlvss 79 
                                        +q + ++ D +  +d+   + d+++++ l ++
  gene2010|gene2010|rna2010|rna2010 350 SQIARIFSDAADYSDTLtYYADFNDIMILLNN 381
                                        56666788888888887666688888877776 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.2   7.1e-05     0.047      19      38 ..     142     161 ..     133     259 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 7.1e-05
                             ATPase  19 grvvlitGepGtGKtifalq 38 
                                        ++ +l++GepGtGKt+++++
  gene2010|gene2010|rna2010|rna2010 142 KKNILLYGEPGTGKTLLVKK 161
                                        6789*************975 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   8.2e-05     0.054      18      41 ..     138     164 ..     121     172 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 8.2e-05
                                        H...TEEEEEEESTTSSHHHHHHHHHH CS
                               TsaE  18 l...gdvilLeGdLGaGKTtlvrglak 41 
                                        +   ++ ilL+G+ G+GKT lv+++a 
  gene2010|gene2010|rna2010|rna2010 138 MtaaKKNILLYGEPGTGKTLLVKKMAF 164
                                        1333678****************9985 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   9.9e-05     0.066      16      44 ..     136     164 ..     120     194 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 9.9e-05
                                        HHHCTSSS-EEEECSTTSSHHHHHHHHHH CS
                    Sigma54_activat  16 kkvaktdlsvlitGesGtGKellaraihe 44 
                                        +k+++ + ++l+ Ge GtGK+ll +++  
  gene2010|gene2010|rna2010|rna2010 136 SKMTAAKKNILLYGEPGTGKTLLVKKMAF 164
                                        456677799**************998854 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.1      0.02        13       2      19 ..     145     162 ..     144     200 .. 0.81
   2 ?    5.4   0.0      0.03        20      56      83 ..     223     249 ..     201     271 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.02
                                        EEEESSTTSSHHHHHHCH CS
                                Roc   2 vvlvGdsgvGKtsllkrf 19 
                                        ++l G+ g+GKt l+k++
  gene2010|gene2010|rna2010|rna2010 145 ILLYGEPGTGKTLLVKKM 162
                                        7899***********986 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.03
                                        EEEEEEEE-SGGCTTTT-HHHHCTSCEE CS
                                Roc  56 vklniWDtaGqerfrslhplylreaala 83 
                                        +  ++WD+a +++ + ++ +++ e + +
  gene2010|gene2010|rna2010|rna2010 223 I-QKLWDFATKNKKHVITIVFMDEIDSF 249
                                        3.389**************999876655 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   0.00016      0.11       7      36 ..     139     168 ..     134     180 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00016
                             AAA_19   7 alkekvllvtaGpGtGKTrvlkhivallve 36 
                                        ++++k++l+ + pGtGKT ++k++  ll +
  gene2010|gene2010|rna2010|rna2010 139 TAAKKNILLYGEPGTGKTLLVKKMAFLLDQ 168
                                        57899*************999887666555 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00014     0.091       1      26 [.     142     173 ..     142     270 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00014
                            DUF2075   1 kavvlVtGvaGtGKtvvllnllael......e 26 
                                        k+ +l  G++GtGKt++  ++++ l       
  gene2010|gene2010|rna2010|rna2010 142 KKNILLYGEPGTGKTLLVKKMAFLLdqnlklL 173
                                        578999************99999884333330 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0    0.0002      0.13      31      63 ..     140     172 ..     105     203 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.0002
                             RuvB_N  31 ealdhvllyGpPGlGkttlakiiakelgvklki 63 
                                         a   +llyG PG Gkt l k +a  l+ +lk 
  gene2010|gene2010|rna2010|rna2010 140 AAKKNILLYGEPGTGKTLLVKKMAFLLDQNLKL 172
                                        456689************999999888888775 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00028      0.19       2      30 ..     145     173 ..     144     183 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00028
                              AAA_3   2 vllegvPGlaktllvkalakaldlefkri 30 
                                        +ll g PG++ktllvk++a  ld ++k +
  gene2010|gene2010|rna2010|rna2010 145 ILLYGEPGTGKTLLVKKMAFLLDQNLKLL 173
                                        799*******************9988765 PP

>> EF-G-binding_N  Elongation factor G-binding protein, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.2    0.0015      0.98      16      45 ..      86     123 ..      79     147 .. 0.73
   2 ?   -0.7   0.0       3.3   2.2e+03      29      50 ..     340     361 ..     331     383 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0015
                     EF-G-binding_N  16 qllnayrsvnDkkvveavkalaaekIlel........f 45 
                                        ++  ay+++nD+ v +a+    +e+I+e          
  gene2010|gene2010|rna2010|rna2010  86 KMQDAYKTINDPTVFSATNYFGKENIMETlvgritriI 123
                                        6789************************9444444432 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 3.3
                     EF-G-binding_N  29 vveavkalaaekIlelfpelse 50 
                                         v+a   l++++I  +f+++ +
  gene2010|gene2010|rna2010|rna2010 340 LVNACNGLTQSQIARIFSDAAD 361
                                        5677778888888888887654 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.3    0.0003       0.2      24      56 ..     131     163 ..     118     189 .. 0.79
   2 ?   -2.2   0.0       3.5   2.3e+03     147     147 ..     265     265 ..     232     309 .. 0.53

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0003
                               TniB  24 eeLleypkrkrmpnlllvGdsnnGKtmivekFa 56 
                                        ++Ll+       +n+ll+G++ +GKt +v+k a
  gene2010|gene2010|rna2010|rna2010 131 KKLLNSKMTAAKKNILLYGEPGTGKTLLVKKMA 163
                                        6788887778889*****************976 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 3.5
                               TniB 147 k 147
                                        k
  gene2010|gene2010|rna2010|rna2010 265 K 265
                                        2 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00036      0.24      28      55 ..     137     164 ..     121     179 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00036
                             AAA_25  28 gllpagelallaGapgtGKttlaldlal 55 
                                         + +a++ +ll+G pgtGKt l+  +a+
  gene2010|gene2010|rna2010|rna2010 137 KMTAAKKNILLYGEPGTGKTLLVKKMAF 164
                                        567788899*************988775 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   4.3   0.00098      0.65      16     137 ..     123     272 ..     112     273 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00098
                                        T.................TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHH.....HHGG CS
                             ResIII  16 leklks...........krdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtl.....eefk 75 
                                        ++ +++             +k++l+  + GtGKTl+  k++  l ++ k    l l  +k+ +++++      ++k
  gene2010|gene2010|rna2010|rna2010 123 INLIEKknkkllnskmtAAKKNILLYGEPGTGKTLLVKKMAFLLDQNLK---LLKLKKSKIDIQKMKksdllAKLK 195
                                        433333333566667768888999*********************9854...666666665555555444444444 PP

                                        GGTGG..................GEEEESSS-B--..............-SEEEE.EHHHHHHTH........HHH CS
                             ResIII  76 kflseayke..............igkkvsgdkkka.......kekdstnkkilvt.tiqsldadseeeeeeseell 129
                                        +++++ +                +       +k++       ++++++ + i+++ +i+s+ ++++ee++e+ ++ 
  gene2010|gene2010|rna2010|rna2010 196 RMKPCVRLIavqpsslndryvggT-------EKNIqklwdfaTKNKKHVITIVFMdEIDSFFSKRKEENSEHSSNV 264
                                        444444433555555422333332.......333345555556667888888887478999999988888888888 PP

                                        TTT-SEEE CS
                             ResIII 130 rdrfdvii 137
                                        +++f++i+
  gene2010|gene2010|rna2010|rna2010 265 KSEFLCIL 272
                                        88888775 PP

>> FeoB_associated  FeoB-associated Cys-rich membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0       1.4   9.2e+02      14      27 ..      41      57 ..      34      59 .. 0.62
   2 ?    7.4   5.4    0.0085       5.6       3      25 ..      65      86 ..      63      88 .. 0.75

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 1.4
                    FeoB_associated 14 afvirrlikk...kkkG 27
                                       ++v ++l++k   kkkG
  gene2010|gene2010|rna2010|rna2010 41 YLVGYNLFQKpkdKKKG 57
                                       45555555555549998 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0085
                    FeoB_associated  3 iIVgliiaaavafvirrlikkkk 25
                                       iI+g+ii+ +++ v++++i kkk
  gene2010|gene2010|rna2010|rna2010 65 IIIGAIIV-CLIGVMYKIISKKK 86
                                       56666666.66669*******99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (415 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1358  (0.0757432); expected 358.6 (0.02)
Passed bias filter:                      742  (0.0413855); expected 358.6 (0.02)
Passed Vit filter:                       108  (0.00602376); expected 17.9 (0.001)
Passed Fwd filter:                        27  (0.00150594); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              27  [number of targets reported over threshold]
# CPU time: 0.68u 0.30s 00:00:00.98 Elapsed: 00:00:00.45
# Mc/sec: 2754.35
//
Query:       gene2011|gene2011|rna2011|rna2011  [L=124]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    7.3e-20   70.7   0.1    1.1e-19   70.1   0.1    1.3  1  TFIID_30kDa  Transcription initiation factor TFIID 23-30kDa s
  ------ inclusion threshold ------
      0.035   14.1   0.0        1.4    9.0   0.0    2.1  1  Bromo_TP     Bromodomain associated


Domain annotation for each model (and alignments):
>> TFIID_30kDa  Transcription initiation factor TFIID 23-30kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.1   0.1   1.2e-23   1.1e-19       1      49 [.      34      82 ..      34      83 .. 0.99

  Alignments for each domain:
  == domain 1  score: 70.1 bits;  conditional E-value: 1.2e-23
                        TFIID_30kDa  1 PiIPDavtayyLekaGletsDprlarlvsLaaqKFisdiaadAyqyski 49
                                       P+IPD v +++Le++G+++ D++ ++ +sL aqKFi+d+a++++q++ki
  gene2011|gene2011|rna2011|rna2011 34 PLIPDIVLDHLLERSGVDCADKETKKAISLLAQKFITDVATSSFQFHKI 82
                                       9***********************************************9 PP

>> Bromo_TP  Bromodomain associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.0   0.00016       1.4      15      56 ..      44      85 ..      38     119 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00016
                                       HHHHHT-SEE-HHHHHHHHHHHHHHHHHHHHHHHHHHTTSS- CS
                           Bromo_TP 15 ileeaGfdsaeesaLEtLteiaqkYirelgeqaksfaehagR 56
                                       +le +G d+a+++   + + +aqk+i+ ++ +  +f  +  +
  gene2011|gene2011|rna2011|rna2011 44 LLERSGVDCADKETKKAISLLAQKFITDVATSSFQFHKIHQK 85
                                       788999999999999999999999999999887777655444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1000  (0.0557756); expected 358.6 (0.02)
Passed bias filter:                      653  (0.0364214); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 928.87
//
Query:       gene2012|gene2012|rna2012|rna2012  [L=228]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (228 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       572  (0.0319036); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.30s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1529.86
//
Query:       gene2013|gene2013|rna2013|rna2013  [L=786]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.2e-11   43.3   0.4    8.3e-10   38.7   0.1    2.9  2  Sec8_exocyst  Sec8 exocyst complex component specific domain


Domain annotation for each model (and alignments):
>> Sec8_exocyst  Sec8 exocyst complex component specific domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.7   0.1   4.7e-14   8.3e-10       3      81 ..       8      82 ..       6     133 .. 0.86
   2 ?    1.2   0.0     0.018   3.1e+02      36      79 ..     727     770 ..     719     779 .. 0.88

  Alignments for each domain:
  == domain 1  score: 38.7 bits;  conditional E-value: 4.7e-14
                       Sec8_exocyst  3 kevlnkikeeWpavlsddanpvelalsllDdssvGlahrlkefkqlkkqieeaLqevvnehhqaFnssiasYskilss 80
                                       + +l+++  +W ++++ d+np++ al+l Ddssv      ++f+++++++++a+ e++ + + +Fn+s+  Y+ i   
  gene2013|gene2013|rna2013|rna2013  8 NTILKELMVDWDDLAQADYNPLKNALELNDDSSVV----ATNFRNFYHKVDAAMAEIIRNKYRGFNDSVLIYTDINGL 81
                                       56899999*************************86....6789*****************************998765 PP

                       Sec8_exocyst 81 i 81
                                        
  gene2013|gene2013|rna2013|rna2013 82 Y 82
                                       5 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.018
                       Sec8_exocyst  36 vGlahrlkefkqlkkqieeaLqevvnehhqaFnssiasYskils 79 
                                        vG  h+l+ f +  k++ee Lq       ++F +s   ++ +l+
  gene2013|gene2013|rna2013|rna2013 727 VGNDHELRTFINDLKNMEEMLQGLSLGQVEGFDESFNFFEDVLN 770
                                        8999******99999*******9999999999999888887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (786 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       975  (0.0543812); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.63u 0.27s 00:00:00.90 Elapsed: 00:00:00.44
# Mc/sec: 5333.35
//
Query:       gene2014|gene2014|rna2014|rna2014  [L=329]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    8.8e-30  103.1   0.0      2e-29  101.9   0.0    1.7  1  JAB         JAB1/Mov34/MPN/PAD-1 ubiquitin protease
    1.6e-07   31.1   0.0    2.6e-07   30.4   0.0    1.3  1  Prok-JAB    Prokaryotic homologs of the JAB domain
    4.1e-06   27.2   0.6    8.9e-06   26.1   0.6    1.6  1  MitMem_reg  Maintenance of mitochondrial structure and functi
  ------ inclusion threshold ------
      0.058   13.4   0.2       0.21   11.6   0.2    2.0  1  UPF0172     Uncharacterised protein family (UPF0172)


Domain annotation for each model (and alignments):
>> JAB  JAB1/Mov34/MPN/PAD-1 ubiquitin protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.9   0.0   4.5e-33     2e-29       4     116 ..      52     160 ..      49     162 .. 0.94

  Alignments for each domain:
  == domain 1  score: 101.9 bits;  conditional E-value: 4.5e-33
                                        CEEEEEHHHHHHHHHHHHHHHHHTS--EEEEEEEESSSEEEEEEEEEEESEEEESSECEEEEEHHHHHHHHHHHHH CS
                                JAB   4 qavhleslvllkildhalrtekeeeevmGlliGelnddttveitnvfalpfeetekdvdavsldqeylekksellk 79 
                                        + ++++sl+llk+l+h + +     evmGl++Ge+ d+ t+++++vfa+p+++t  +v+av+++ +  +++++ l 
  gene2014|gene2014|rna2014|rna2014  52 EIIQISSLALLKMLKHGRAGIPM--EVMGLMLGEFVDEFTIKVVDVFAMPQSGTGVTVEAVDPVFQ--TQMMDTLA 123
                                        5689*******************..**************************************999..99999988 PP

                                        HHCTT.SEEEEEEEESSSS-SS--HHHHHHHHHHHHHS CS
                                JAB  80 klrgr.ervvGWYhshpditvwlsevdvrtqalyqrmd 116
                                         + gr e vvGWYhshp++++wls+vd++tq ++++++
  gene2014|gene2014|rna2014|rna2014 124 VT-GRnETVVGWYHSHPGFGCWLSNVDISTQSAFEQLN 160
                                        87.666***************************99987 PP

>> Prok-JAB  Prokaryotic homologs of the JAB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.4   0.0   5.8e-11   2.6e-07       4      91 ..      60     152 ..      57     177 .. 0.74

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 5.8e-11
                           Prok-JAB   4 vlsalvaharrahpeEtcGlllgkeseseevivvplvnewsn...rfeipdpedslarlkf...earerglevvgi 73 
                                        +l ++++h r+  p E  Gl+lg+  ++  + vv++  ++ +    +++++ +  ++++++   + + r+++vvg 
  gene2014|gene2014|rna2014|rna2014  60 ALLKMLKHGRAGIPMEVMGLMLGEFVDEFTIKVVDVF-AMPQsgtGVTVEAVDPVFQTQMMdtlAVTGRNETVVGW 134
                                        5789*********************555555555554.55555885555555555555555678************ PP

                           Prok-JAB  74 wHSHpggsarPSetDrrd 91 
                                        +HSHpg +   S  D+++
  gene2014|gene2014|rna2014|rna2014 135 YHSHPGFGCWLSNVDIST 152
                                        *****9887667766665 PP

>> MitMem_reg  Maintenance of mitochondrial structure and function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.6     2e-09   8.9e-06       4      93 ..     199     319 ..     196     327 .. 0.82

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 2e-09
                         MitMem_reg   4 ei..gvehllkpsiqdasstlstglnrqyyslki..................................lqerldli 43 
                                        e+  ++++ + ps++    +l++glnr+yys +i                                    ++ +l 
  gene2014|gene2014|rna2014|rna2014 199 EVtsNIGYYNSPSVI----ALLHGLNRSYYSFNIqyrktemeekmllnlhkkswtdnlrirgvrsedmSTKMKELT 270
                                        55569999999****....************************************************88899999* PP

                         MitMem_reg  44 kdYlkkveegelpvnhe.ilrnlqkllnllPhleteelekefnvetnDvll 93 
                                         +Ylk+vee++   ++e +l++++kl+ +  hl + + e++ n++t   ll
  gene2014|gene2014|rna2014|rna2014 271 VNYLKRVEEEKSLTKEElELYKMGKLDFRK-HLMD-TCEDVCNENTLHNLL 319
                                        *********997788888*********322.4443.344444444444444 PP

>> UPF0172  Uncharacterised protein family (UPF0172)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.2   4.7e-05      0.21       2     115 ..      54     169 ..      53     314 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 4.7e-05
                            UPF0172   2 vevssqAYvKlllHaaKyptqaVnGvLlgkkssskskvevtDa..vPLfH...ssltlspmlevAlaqvesyake. 71 
                                        +++ss A +K+l H       +V+G++lg+  ++ + ++v+D+  +P      +  ++ p+++    + ++ a + 
  gene2014|gene2014|rna2014|rna2014  54 IQISSLALLKMLKHGRAGIPMEVMGLMLGEFVDEFT-IKVVDVfaMPQSGtgvTVEAVDPVFQTQ--MMDTLAVTg 126
                                        6899**************************988885.*****72256555333334444555543..344444333 PP

                            UPF0172  72 kglvivGyYqanerlsdtelsslaekiadkiaenfsdavllvvd 115
                                        ++ ++vG+Y+++  ++   ls++  +  ++ ++ +++av++v+d
  gene2014|gene2014|rna2014|rna2014 127 RNETVVGWYHSHPGFGC-WLSNVDISTQSAFEQLNKRAVAVVID 169
                                        68999999999776662.23333444444444444455555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (329 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       889  (0.0495845); expected 358.6 (0.02)
Passed bias filter:                      527  (0.0293937); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.72u 0.34s 00:00:01.06 Elapsed: 00:00:00.58
# Mc/sec: 1708.55
//
Query:       gene2015|gene2015|rna2015|rna2015  [L=258]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.15   11.7   0.1        1.6    8.3   0.1    2.5  2  DisA_N    DisA bacterial checkpoint controller nucleotide-bin


Domain annotation for each model (and alignments):
>> DisA_N  DisA bacterial checkpoint controller nucleotide-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.1   8.8e-05       1.6      96     116 ..      73      93 ..      68      96 .. 0.87
   2 ?   -0.0   0.0     0.035   6.2e+02      52      66 ..     112     127 ..      98     139 .. 0.65

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 8.8e-05
                                        HSSSEEEEE-TTTS-EEEEET CS
                             DisA_N  96 etdalvivVSeetgkislakd 116
                                        +td+  ivVSe+tg++ +a++
  gene2015|gene2015|rna2015|rna2015  73 QTDEEYIVVSESTGNVLIARR 93 
                                        799999**********99986 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.035
                                        TTCSSEEEE.ETTEEE CS
                             DisA_N  52 plhDGAvii.rdgriv 66 
                                          hD Avi  ++ +i 
  gene2015|gene2015|rna2015|rna2015 112 LIHDSAVITaDNYKIR 127
                                        4577777764455554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       668  (0.0372581); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.63u 0.32s 00:00:00.95 Elapsed: 00:00:00.55
# Mc/sec: 1413.66
//
Query:       gene2016|gene2016|rna2016|rna2016  [L=287]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.8e-42  145.2   0.8    8.4e-27   94.5   0.2    2.5  2  ATP_bind_1       Conserved hypothetical ATP binding protein
     0.0006   19.9   0.0     0.0067   16.5   0.0    2.5  1  MMR_HSR1         50S ribosome-binding GTPase
     0.0012   18.7   0.0        3.1    7.7   0.0    3.0  3  RsgA_GTPase      RsgA GTPase
     0.0046   16.5   0.0       0.82    9.2   0.0    2.9  3  GTP_EFTU         Elongation factor Tu GTP binding domain
  ------ inclusion threshold ------
      0.047   13.4   0.0      0.099   12.4   0.0    1.5  1  AAA_29           P-loop containing region of AAA domain
      0.056   13.2   0.0      0.084   12.6   0.0    1.3  1  Sigma54_activat  Sigma-54 interaction domain
      0.073   12.8   0.0       0.11   12.2   0.0    1.3  1  AAA_30           AAA domain
      0.091   12.9   0.1       0.18   12.0   0.1    1.4  1  AAA_33           AAA domain
       0.12   12.8   0.0       0.24   11.8   0.0    1.6  2  AAA_16           AAA ATPase domain
       0.13   12.8   0.0       0.23   12.0   0.0    1.4  1  AAA_18           AAA domain
       0.17   12.4   0.0       0.36   11.4   0.0    1.6  2  ABC_tran         ABC transporter
       0.27   11.7   0.0       0.37   11.3   0.0    1.2  1  AAA_23           AAA domain


Domain annotation for each model (and alignments):
>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.5   0.2   5.6e-30   8.4e-27       1     120 [.      11     135 ..      11     141 .. 0.88
   2 !   48.4   0.0   6.7e-16     1e-12     123     240 ..     172     284 ..     168     285 .. 0.93

  Alignments for each domain:
  == domain 1  score: 94.5 bits;  conditional E-value: 5.6e-30
                         ATP_bind_1   1 vvGpaGsGKttfvgalseilelr...........grsvavvNLDPAaeelpYeaavdirelitledvmedlglgpn 65 
                                        +vG+aG GK+tf +al+ +++++           ++++  +NLDPA  +++ + ++dire++++e+vm+ +++gpn
  gene2016|gene2016|rna2016|rna2016  11 IVGMAGTGKSTFSQALYTWISAKyppiidpqsclNTNITAINLDPATLKVKMPLDLDIREYFDYENVMQTYNIGPN 86 
                                        79****************9987644444444444788999************************************ PP

                         ATP_bind_1  66 galvvaleflresldwldeelekeeddyllfDtPGQielfthseslakiveeLes 120
                                        ga+++ ++++  +    d ++     d++++DtPGQie f +s++++ +ve+Le+
  gene2016|gene2016|rna2016|rna2016  87 GAVTTIINLFLMRW---DVKI---TGDFVIIDTPGQIEAFVWSNAGKVLVEKLEH 135
                                        **********9999...5666...56***************************96 PP

  == domain 2  score: 48.4 bits;  conditional E-value: 6.7e-16
                         ATP_bind_1 123 alvvvyLvDsqrltdptkfisgllsalsamlrlelPhvvvlnkfDllkeklekeleffedvealslllekeeekyk 198
                                        +++ +yLvDs  +++p+ f+ ++++al   lr ++P ++v+nk+Dl +      +e+++d e+++   +++    +
  gene2016|gene2016|rna2016|rna2016 172 SVILLYLVDSMECRKPSVFMCNMVYALILRLRFNIPILIVFNKVDL-S---PVPVEWLTDYEKFMDDVNDD-TMCN 242
                                        57899*****************************************.4...79**********99977765.7789 PP

                         ATP_bind_1 199 klaeaiaelleefalvlrflplssekeesiedllslidealq 240
                                        +l  ++a ++ee+++  + + +ss ++ + +++++ i+ +++
  gene2016|gene2016|rna2016|rna2016 243 SLLGSMALYFEEYYRSFNYVGVSSVTGAGRDAFFERIERIVD 284
                                        9************************************99886 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   4.5e-06    0.0067       2      57 ..       9     130 ..       8     214 .. 0.58

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 4.5e-06
                                        EEEEESTTSSHHHHHHHHHT..........STEEESSSTTSSSSEEEEEEEETTEE.................... CS
                           MMR_HSR1   2 vaivGrpNvGKStLinaltg..........ekaivsdkpgtTrdinegrvklkgke.................... 47 
                                        ++ivG+  +GKSt+ +al            +       p+  +++n   ++l+                       
  gene2016|gene2016|rna2016|rna2016   9 FLIVGMAGTGKSTFSQALYTwisakyppiiD-------PQSCLNTNITAINLDPATlkvkmpldldireyfdyenv 77 
                                        579***************8644433332221.......34444444444442221133444455566667777777 PP

                                        ..............................EEEEECGGC.............S CS
                           MMR_HSR1  48 ..............................ielvDtpGl.............i 57 
                                                                      ++++DtpG              +
  gene2016|gene2016|rna2016|rna2016  78 mqtynigpngavttiinlflmrwdvkitgdFVIIDTPGQieafvwsnagkvlV 130
                                        788888888888888888888888888888********723333333333330 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.0    0.0021       3.1     100     121 ..       7      28 ..       2      51 .. 0.87
   2 ?    1.0   0.0      0.23   3.4e+02     149     160 ..     104     115 ..      77     121 .. 0.85
   3 !    6.4   0.0    0.0053       7.9      38      63 ..     197     222 ..     172     279 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0021
                                        SEEEEECSTTSSHHHHHHHHCT CS
                        RsgA_GTPase 100 ktsvlvGqSGvGKStLinallp 121
                                        kt ++vG  G GKSt+  al  
  gene2016|gene2016|rna2016|rna2016   7 KTFLIVGMAGTGKSTFSQALYT 28 
                                        8899************998865 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.23
                                        ETTTEEEESS-S CS
                        RsgA_GTPase 149 laegglliDtPG 160
                                        +  + ++iDtPG
  gene2016|gene2016|rna2016|rna2016 104 ITGDFVIIDTPG 115
                                        566789*****9 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.0053
                                        HHHHHHHTT-EEEEEEE-GGG--HHH CS
                        RsgA_GTPase  38 fLvlaeekgiepvivlnKiDlleeee 63 
                                        +L+l  + +i+++iv+nK+Dl     
  gene2016|gene2016|rna2016|rna2016 197 ALILRLRFNIPILIVFNKVDLSPVPV 222
                                        577777889************87655 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0     0.057        85       4      25 ..       7      28 ..       4      36 .. 0.84
   2 ?    0.9   0.0      0.19   2.8e+02      72      82 ..     108     118 ..      88     123 .. 0.85
   3 !    9.2   0.0   0.00055      0.82     117     190 ..     200     281 ..     174     285 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.057
                                       EEEEEEESTTSSHHHHHHHHHH CS
                           GTP_EFTU  4 rnigiighvDhGKtTLtdrLly 25
                                        ++ i+g   +GK+T++ +L +
  gene2016|gene2016|rna2016|rna2016  7 KTFLIVGMAGTGKSTFSQALYT 28
                                       5789************999975 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.19
                                        EEEEEESSSGG CS
                           GTP_EFTU  72 inliDtPGHvd 82 
                                        + +iDtPG ++
  gene2016|gene2016|rna2016|rna2016 108 FVIIDTPGQIE 118
                                        789*****865 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.00055
                                        HHHHTTTEEEEEEESCGST......HHHHHHHHHHHHHHHHHH..HHHHHHHHHTTTTTEEEEEEBTTTTBTHHHH CS
                           GTP_EFTU 117 lalkegvpiivfiNKmDrl......kaelkeiveevkqklsrk..eeklekygekgekevpvvfgSalkgegvktl 184
                                        l l+ ++pi ++ NK+D         +++++  ++v+++   +   +++  y e+  + ++ v +S+++g g +++
  gene2016|gene2016|rna2016|rna2016 200 LRLRFNIPILIVFNKVDLSpvpvewLTDYEKFMDDVNDDTMCNslLGSMALYFEEYYRSFNYVGVSSVTGAGRDAF 275
                                        55677899**********9999999899999999999888665665555555555557899999999999999999 PP

                                        HHHHHH CS
                           GTP_EFTU 185 lealve 190
                                        +e + +
  gene2016|gene2016|rna2016|rna2016 276 FERIER 281
                                        988766 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   6.6e-05     0.099      22      44 ..       6      28 ..       1      34 [. 0.79

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 6.6e-05
                             AAA_29 22 kgatlltGpsGsGKSTllDAiqa 44
                                         ++l++G  G+GKST+  A+ +
  gene2016|gene2016|rna2016|rna2016  6 TKTFLIVGMAGTGKSTFSQALYT 28
                                       4579************9877765 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   5.6e-05     0.084      23      54 ..       7      38 ..       1      53 [. 0.81

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.6e-05
                                       S-EEEECSTTSSHHHHHHHHHHHSTTTTS-EE CS
                    Sigma54_activat 23 lsvlitGesGtGKellaraiheaskrkekpfv 54
                                        + li+G  GtGK+++++a+++  + k  p++
  gene2016|gene2016|rna2016|rna2016  7 KTFLIVGMAGTGKSTFSQALYTWISAKYPPII 38
                                       678******************98887776665 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   7.6e-05      0.11      15      43 ..       3      31 ..       1      42 [. 0.80

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 7.6e-05
                             AAA_30 15 tsgdrvavltGpAGtGKttalkalreawe 43
                                       +++ ++ +++G AGtGK+t  +al   + 
  gene2016|gene2016|rna2016|rna2016  3 HKPTKTFLIVGMAGTGKSTFSQALYTWIS 31
                                       56677899***********9998866555 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   0.00012      0.18       3      20 ..      10      27 ..       9      33 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00012
                             AAA_33  3 llvGlpGsGKstlaerll 20
                                       l+vG++G+GKst+++ l+
  gene2016|gene2016|rna2016|rna2016 10 LIVGMAGTGKSTFSQALY 27
                                       78************9885 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00016      0.24      25      51 ..       7      33 ..       1      75 [. 0.85
   2 ?   -3.2   0.0       6.5   9.7e+03     107     127 ..     263     283 ..     236     285 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00016
                             AAA_16 25 elvllsGesGvGKsslvrellralekd 51
                                          l++G++G+GKs+  ++l++ ++++
  gene2016|gene2016|rna2016|rna2016  7 KTFLIVGMAGTGKSTFSQALYTWISAK 33
                                       788************999998766655 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 6.5
                             AAA_16 107 avpelagaeasrllellkrll 127
                                         v++++ga++ +++e + r++
  gene2016|gene2016|rna2016|rna2016 263 GVSSVTGAGRDAFFERIERIV 283
                                        466777777788888777776 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00016      0.23       2      18 ..      10      26 ..      10      71 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00016
                             AAA_18  2 lltGtpGvGKttlakeL 18
                                       l+ G++G+GK+t++++L
  gene2016|gene2016|rna2016|rna2016 10 LIVGMAGTGKSTFSQAL 26
                                       699************99 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00024      0.36       9      34 ..       4      29 ..       1      59 [. 0.85
   2 ?   -3.2   0.0       7.5   1.1e+04      17      32 ..      83      97 ..      80     119 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00024
                                       ETTSEEEEEESTTSSHHHHHHHHTTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ABC_tran  9 kegekvaivGenGaGKStLlkllagl 34
                                       k+ ++  ivG  G+GKSt+ ++l+  
  gene2016|gene2016|rna2016|rna2016  4 KPTKTFLIVGMAGTGKSTFSQALYTW 29
                                       5678899*************999875 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 7.5
                                       EESTTSSHHHHHHHHT CS
                                       xxxxxxxxxxxxxxxx RF
                           ABC_tran 17 vGenGaGKStLlklla 32
                                       +G+nGa  +t+++l++
  gene2016|gene2016|rna2016|rna2016 83 IGPNGA-VTTIINLFL 97
                                       688998.567776665 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00025      0.37      21      41 ..       8      28 ..       5      88 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00025
                             AAA_23 21 ltlItGpNGaGKTTildAikl 41
                                        +lI+G+ G+GK+T+ +A+  
  gene2016|gene2016|rna2016|rna2016  8 TFLIVGMAGTGKSTFSQALYT 28
                                       79*************999854 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       399  (0.0222544); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        89  (0.00496402); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.63u 0.35s 00:00:00.98 Elapsed: 00:00:00.54
# Mc/sec: 1605.21
//
Query:       gene2017|gene2017|rna2017|rna2017  [L=672]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.037   14.5   0.8      0.037   14.5   0.8    2.6  3  DUF1765   Protein of unknown function (DUF1765)


Domain annotation for each model (and alignments):
>> DUF1765  Protein of unknown function (DUF1765)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.1      0.28   5.1e+03      12      42 ..      42      72 ..      36      79 .. 0.69
   2 ?   14.5   0.8     2e-06     0.037      72     119 ..     211     256 ..     200     258 .. 0.92
   3 ?   -2.2   0.1       0.3   5.4e+03      58      74 ..     561     577 ..     556     637 .. 0.51

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.28
                            DUF1765 12 tslydsnavfllldlleefinileeneksel 42
                                       +   ++ +v + +dl+ e+i  l+  ek ++
  gene2017|gene2017|rna2017|rna2017 42 IRTKEMMKVLFACDLTAEMIVKLFIEEKIRC 72
                                       5556667788888888888888777666555 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 2e-06
                            DUF1765  72 sflfniwdlipedeerkkklfldlLlseevfeklflhwsplVRsyyir 119
                                         ++++++++i+  ++r++ +f++ L+s++  + ++++ +++V++yy +
  gene2017|gene2017|rna2017|rna2017 211 NLIYECYKMIK--NCRLEYNFIKELFSSDNEHIMMMKIKEMVKIYYRT 256
                                        579*******6..*********************************65 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 0.3
                            DUF1765  58 mlesdnvqsllrtlsfl 74 
                                        +++s +++ +l++l +l
  gene2017|gene2017|rna2017|rna2017 561 VISSAHANWQLEVLNVL 577
                                        55666666666665554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (672 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1271  (0.0708907); expected 358.6 (0.02)
Passed bias filter:                      490  (0.02733); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.78u 0.35s 00:00:01.12 Elapsed: 00:00:00.55
# Mc/sec: 3682.48
//
Query:       gene2018|gene2018|rna2018|rna2018  [L=509]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-14   54.2   0.0    2.3e-14   53.5   0.0    1.4  1  Exo_endo_phos  Endonuclease/Exonuclease/phosphatase family
    3.6e-10   39.9   6.2    3.7e-06   27.2   1.2    2.6  2  LRR_4          Leucine Rich repeats (2 copies)
    4.3e-10   39.2  11.2    1.9e-06   27.5   2.6    2.5  2  LRR_8          Leucine rich repeat
    0.00038   20.6   3.6        5.8    7.9   0.1    4.9  4  LRR_1          Leucine Rich Repeat
  ------ inclusion threshold ------
        1.1    9.5   5.2        3.8    7.8   0.1    2.9  3  LRR_6          Leucine Rich repeat


Domain annotation for each model (and alignments):
>> Exo_endo_phos  Endonuclease/Exonuclease/phosphatase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.5   0.0   6.4e-18   2.3e-14       1     233 []     186     486 ..     186     486 .. 0.81

  Alignments for each domain:
  == domain 1  score: 53.5 bits;  conditional E-value: 6.4e-18
                                        EEEEESTG...........CHHHHTHHHHHHHHHHHHHHCTTSEEEEEEEBSCTCHHHHHHHHH...........T CS
                                        xxxxxxxx...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...........x RF
                      Exo_endo_phos   1 ltwNvngq...........aspalgssrrsdrladlltaydaDvlgLQEvdddelsriplllal...........g 54 
                                        +++N+++            +s+ l + +r+  + +++ +y+ Dvlg+QE+  ++  ++   +++            
  gene2018|gene2018|rna2018|rna2018 186 ASYNILSPhyatsqlfgyvPSWVLHWENRKEMIFQEIVSYNLDVLGIQEMETYSFIENFKDQLDhrcnydslfypS 261
                                        68999999999999999999*****************************999998887777766887766433330 PP

                                        TCEEEEECCH.....ECSSSTTSSEEEEEECSTEEEEEEEEEEETSSSSGCEEEEEEEEEEEEEEE.......... CS
                                        xxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......... RF
                      Exo_endo_phos  55 gflgasstsp.....tgggggggnggavlsrfpltslfrrtfiefndlvaalrreplaakleqlni.......... 115
                                                               +g+a+++++  ++l+  +++ f dlv +++r   +++  + n           
  gene2018|gene2018|rna2018|rna2018 262 ---------GrsqslPESQKMSVDGCATFWKRHKFTLIDQQCVKFSDLVFTDERFCKNEDIMNRNSgkdnialitv 328
                                        .........13444677888******************************************************** PP

                                        ................CCCHHGHHHHHHHHHHHHHHHHHHH.HHTTSEEEEEEE-SSSTSGGGBSCGHHHHHHCTT CS
                                        ................xxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Exo_endo_phos 116 ................ashrdhdlvrdlqllalllqvealn.adrgapvivaGDfNarpsdddsrvlrtrglalap 174
                                                        + ++ +++v   q ++l  +v+ +  + + a +i++GDfN+  ++ ++ ++ +++  ++ 
  gene2018|gene2018|rna2018|rna2018 329 lektngglliisnahiHWNPEYKDVKLFQTIILIEAVQKFKeKYPMAGIILLGDFNSMKNSAVYDLIVNGRIYPFN 404
                                        *************66544444444444444444444444431334457888***************9988887765 PP

                                        THH...................SSCESCETTTTTTTTTTTEB-BEEEEEECHHHCCEEEEEEECCHHEEC.....T CS
                                        xxx...................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....x RF
                      Exo_endo_phos 175 apv...................glyllgggptptyvtraggsrlDrilaspalalfrsgvlppplalvrr.....e 226
                                          +                     ++  ++ + t+ t  + + lD+i+ +++l l ++++ ++ + +v+r      
  gene2018|gene2018|rna2018|rna2018 405 IDFslynykpfstdgflhdlsvKDAYREQELELTNFTAHFKGVLDYIFHNDRLILCSTLSSIDNE-YVHRmvglpS 479
                                        5525555666677778889999*******************************999999999875.4444577777 PP

                                        SSCSSSB CS
                                        xxxxxxx RF
                      Exo_endo_phos 227 altlSDH 233
                                         + +SDH
  gene2018|gene2018|rna2018|rna2018 480 IHFPSDH 486
                                        7777777 PP

>> LRR_4  Leucine Rich repeats (2 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2   1.2     1e-09   3.7e-06       3      43 ..      55      92 ..      53      93 .. 0.89
   2 !   14.8   0.3   7.8e-06     0.028       2      42 ..     100     141 ..      99     143 .. 0.87

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 1e-09
                                       --EEE--SS---E-S-.HHH-TT--EEE-.-S-----GGGGX CS
                              LRR_4  3 LevLdLsnNqltdipl.leklpnLkeLdLsgNnlitdldeLk 43
                                       L++L+L+nN lt ip  +  l nL++Ld+s+N    +l+ L+
  gene2018|gene2018|rna2018|rna2018 55 LKELHLQNNELTFIPKgITELRNLEVLDVSDN----KLTFLP 92
                                       99**************8667*********999....777666 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 7.8e-06
                                        S--EEE--SS---E-S-.HHH-TT--EEE-.-S-----GGGG CS
                              LRR_4   2 nLevLdLsnNqltdipl.leklpnLkeLdLsgNnlitdldeL 42 
                                        +L++L L +N l+ ip  l+ l +L+++++ +N+l++++ +L
  gene2018|gene2018|rna2018|rna2018 100 KLKILKLDDNFLSFIPMeLGTLYQLETFSVDNNPLLEPFATL 141
                                        8****************8888*********777777887665 PP

>> LRR_8  Leucine rich repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.5   2.6   5.2e-10   1.9e-06       6      61 .]      35      88 ..      33      88 .. 0.97
   2 !   24.9   1.5   3.5e-09   1.3e-05       1      61 []      76     134 ..      76     134 .. 0.97

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 5.2e-10
                                       EE-TTS--SEE-TTSSTT-TT--EEE--SS---GGGGGGGTT--S-.EEE--SS-- CS
                              LRR_8  6 LdLsnNrltslddeaFkglsnLkvLdLsnNllttlspgafsgLpsLrsLdLsgNrL 61
                                       LdL +  ++ l++  F+ l+ Lk+L+L nN+lt++ p+ +  L++L+ Ld+s+N+L
  gene2018|gene2018|rna2018|rna2018 35 LDLVSQGIKFLSKCLFT-LKFLKELHLQNNELTFI-PKGITELRNLEVLDVSDNKL 88
                                       899999***********.*****************.9*****************98 PP

  == domain 2  score: 24.9 bits;  conditional E-value: 3.5e-09
                                        TT-SEEE-TTS--SEE-TTSSTT-TT--EEE--SS---GGGGGGGTT--S-.EEE--SS-- CS
                              LRR_8   1 pnLtsLdLsnNrltslddeaFkglsnLkvLdLsnNllttlspgafsgLpsLrsLdLsgNrL 61 
                                        +nL++Ld+s+N+lt l++e  + + +Lk+L+L +N l+++ p  +  L +L+   +++N+L
  gene2018|gene2018|rna2018|rna2018  76 RNLEVLDVSDNKLTFLPKELGR-MIKLKILKLDDNFLSFI-PMELGTLYQLETFSVDNNPL 134
                                        79******************99.*****************.9*****************97 PP

>> LRR_1  Leucine Rich Repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.1     0.011        40       2      18 ..      55      70 ..      54      75 .. 0.79
   2 !    7.9   0.1    0.0016       5.8       1      16 [.      77      92 ..      77      97 .. 0.81
   3 ?    3.3   0.1     0.053   1.9e+02       1      17 [.     100     115 ..     100     121 .. 0.82
   4 ?    0.6   0.0      0.39   1.4e+03       2      13 ..     124     135 ..     123     154 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.011
                              LRR_1  2 LrhLdLsnnpllglppn 18
                                       L++L+L nn l+ ++p 
  gene2018|gene2018|rna2018|rna2018 55 LKELHLQNNELT-FIPK 70
                                       9*********95.5554 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0016
                              LRR_1  1 nLrhLdLsnnpllglp 16
                                       nL++Ld+s+n l+ lp
  gene2018|gene2018|rna2018|rna2018 77 NLEVLDVSDNKLTFLP 92
                                       8***********6444 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.053
                              LRR_1   1 nLrhLdLsnnpllglpp 17 
                                        +L+ L L +n+l +++p
  gene2018|gene2018|rna2018|rna2018 100 KLKILKLDDNFL-SFIP 115
                                        7**********9.5555 PP

  == domain 4  score: 0.6 bits;  conditional E-value: 0.39
                              LRR_1   2 LrhLdLsnnpll 13 
                                        L++  + nnpll
  gene2018|gene2018|rna2018|rna2018 124 LETFSVDNNPLL 135
                                        99999*****93 PP

>> LRR_6  Leucine Rich repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.2     0.027        96       4      16 ..      54      66 ..      51      66 .. 0.88
   2 ?    7.8   0.1    0.0011       3.8       3      16 ..      76      89 ..      74      89 .. 0.90
   3 ?   -3.2   0.0       3.5   1.3e+04       4      13 ..     100     109 ..      99     109 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.027
                              LRR_6  4 hLteLdLsgNdIg 16
                                        L+eL+L+ N+++
  gene2018|gene2018|rna2018|rna2018 54 FLKELHLQNNELT 66
                                       69********986 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0011
                              LRR_6  3 thLteLdLsgNdIg 16
                                       ++L+ Ld+s+N+++
  gene2018|gene2018|rna2018|rna2018 76 RNLEVLDVSDNKLT 89
                                       79*********986 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 3.5
                              LRR_6   4 hLteLdLsgN 13 
                                        +L+ L L +N
  gene2018|gene2018|rna2018|rna2018 100 KLKILKLDDN 109
                                        6999999988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (509 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       473  (0.0263818); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.70u 0.36s 00:00:01.06 Elapsed: 00:00:00.57
# Mc/sec: 2704.65
//
Query:       gene2019|gene2019|rna2019|rna2019  [L=112]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       356  (0.0198561); expected 358.6 (0.02)
Passed bias filter:                      228  (0.0127168); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.48
# Mc/sec: 698.93
//
Query:       gene202|gene202|rna202|rna202  [L=487]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (487 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1251  (0.0697752); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 3100.34
//
Query:       gene2020|gene2020|rna2020|rna2020  [L=46]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (46 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       368  (0.0205254); expected 358.6 (0.02)
Passed bias filter:                      210  (0.0117129); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.31s 00:00:00.71 Elapsed: 00:00:00.49
# Mc/sec: 284.69
//
Query:       gene2021|gene2021|rna2021|rna2021  [L=167]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      3e-11   43.4   4.8    5.8e-10   39.2   4.8    2.0  1  Ribosomal_S7e  Ribosomal protein S7e
  ------ inclusion threshold ------
      0.088   12.9   1.0       0.39   10.8   1.0    2.0  2  KH_5           NusA-like KH domain


Domain annotation for each model (and alignments):
>> Ribosomal_S7e  Ribosomal protein S7e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.2   4.8   6.5e-14   5.8e-10      11     182 ..       4     164 ..       1     166 [. 0.81

  Alignments for each domain:
  == domain 1  score: 39.2 bits;  conditional E-value: 6.5e-14
                                        -HHHHHHHH...HHHHHHHHTSSCHHHHTT--ECEEEEEEETSSCEEEEEEEEHHHHHHTTTCHHHHHHHHHHHC. CS
                      Ribosomal_S7e  11 teleeqvaq...alldleanssdlkaelrelqissakevevkkkkkaivifvpvpllkafqkiqqrlvreLeKkfs 83 
                                        t+ e++v++   +l+  ++n +++k++l++++i  ++e e  + + a++i +p+++l   ++  +   ++L   f+
  gene2021|gene2021|rna2021|rna2021   4 TTSEKKVSNlihSLFSAQMN-DKVKNSLENIKIRMVQESEE-ETQAAMIIIMPIKVLDIIHQNFTLFRKNLANIFK 77 
                                        55677777611145555666.99***************998.999******************************9 PP

                                        SSEEEEEEE-----SSCG.TTSTSS--TTSSHHHHHHHHHHHHCTTS-EEEEEEEE-SSS-EEE.EEEEESCTCCC CS
                      Ribosomal_S7e  84 gkhvvfvaqRrilkkptrrskkkqkrprsrtltaVhdaiLedlvyPseivGkrirvrldgskll.kvfLdkkdqnn 158
                                        + +v+ v +  + +k ++   +          ++V+++ + dl+yP+e+  + ++++  g+ l+ kv+L++k  + 
  gene2021|gene2021|rna2021|rna2021  78 NYNVFCVRE-PLYNKLSK---S--------INKNVQEQWIFDLCYPAEVQCRMTEIKDGGKVLIeKVMLERKC-DF 140
                                        989887743.23333333...2........23579**********************9999877588888765.67 PP

                                        HHHHHHHHHHHHHHHHS-BEEEEE CS
                      Ribosomal_S7e 159 veekldtfsavykkLtgkdvvFef 182
                                        ++e ++ +++ y++Lt+k+v + +
  gene2021|gene2021|rna2021|rna2021 141 LQEDFKIMENAYRTLTDKTVIYAL 164
                                        7889****************9976 PP

>> KH_5  NusA-like KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   1.0   4.3e-05      0.39      31      67 ..      24      60 ..      19      62 .. 0.92
   2 ?   -1.5   0.0       0.3   2.7e+03      52      66 ..     102     116 ..      94     116 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 4.3e-05
                               KH_5 31 kavsseLkgekidvvewseDlaefianalsPaevlsV 67
                                        +v++ L++ ki+ v++se  ++ +  ++ P +vl++
  gene2021|gene2021|rna2021|rna2021 24 DKVKNSLENIKIRMVQESEEETQAAMIIIMPIKVLDI 60
                                       689*******************************998 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.3
                               KH_5  52 aefianalsPaevls 66 
                                        ++ i ++ +Paev++
  gene2021|gene2021|rna2021|rna2021 102 EQWIFDLCYPAEVQC 116
                                        567888999999975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1580  (0.0881254); expected 358.6 (0.02)
Passed bias filter:                      677  (0.0377601); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1069.51
//
Query:       gene2022|gene2022|rna2022|rna2022  [L=235]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.075   12.8   0.0        7.4    6.3   0.0    2.3  2  DNA_pol3_delta  DNA polymerase III, delta subunit


Domain annotation for each model (and alignments):
>> DNA_pol3_delta  DNA polymerase III, delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0   0.00041       7.4      33      64 ..      95     126 ..      86     148 .. 0.91
   2 ?    4.2   0.0    0.0019        34     146     172 ..     197     223 ..     195     224 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.00041
                                        EE-STTS-HHH.HTTTSTTTTSSSSEEEEEEE CS
                     DNA_pol3_delta  33 ikfdlnedwiddvleecetlpffsdkrivvlk 64 
                                        + fd n + +++ le+c t ++  d++iv+ +
  gene2022|gene2022|rna2022|rna2022  95 VHFDCNIKTYQEYLECCRTTSLSIDEKIVLEE 126
                                        67999***********************9855 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.0019
                                        E-HHHHHHHHHHHTT-HHHHHHHHHHH CS
                     DNA_pol3_delta 146 iekealelLlelvennlsaikqelekL 172
                                        ++++  ++L++++e n s++++ +e++
  gene2022|gene2022|rna2022|rna2022 197 LKEKIRSFLCKMSETNYSTVYNVVEMI 223
                                        6788899***************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       797  (0.0444531); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.32s 00:00:00.88 Elapsed: 00:00:00.54
# Mc/sec: 1320.94
//
Query:       gene2023|gene2023|rna2023|rna2023  [L=139]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    4.4e-09   36.5   0.3    7.4e-09   35.8   0.3    1.4  1  KH_6       KH domain
  ------ inclusion threshold ------
       0.14   11.3   0.0       0.14   11.2   0.0    1.1  1  SatRNA_48  Satellite RNA 48 kDa protein


Domain annotation for each model (and alignments):
>> KH_6  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.8   0.3   8.3e-13   7.4e-09       1      45 [.      74     120 ..      74     121 .. 0.95

  Alignments for each domain:
  == domain 1  score: 35.8 bits;  conditional E-value: 8.3e-13
                               KH_6   1 GmlfeVslslvrRll..nhvLeeLgkagpfeiavGlNGriWvksesp 45 
                                        G++fe+  + v+ l     +L+ +g ++++ +a+GlNG+iW++++++
  gene2023|gene2023|rna2023|rna2023  74 GWVFEIEAWAVKTLFvrKNILSDIGRDYKYKVALGLNGMIWIDGKNV 120
                                        99*************998888**********************9986 PP

>> SatRNA_48  Satellite RNA 48 kDa protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   1.6e-05      0.14      13      86 ..      23     100 ..      12     134 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 1.6e-05
                          SatRNA_48  13 esillaqkiqnstfksrgkvtlsqeklplvnrfqellle...kelleeveestpfvvndkraqhlfckk.verkvg 84 
                                        + illaq   nst + r kv + ++ l  + r  ++ +    +e l  +e    f ++    + lf++k +   +g
  gene2023|gene2023|rna2023|rna2023  23 KGILLAQAFLNSTKRNRPKVNIGDFLLCRIIRVGDVVFVsccEEGLGVLEGGWVFEIEAWAVKTLFVRKnILSDIG 98 
                                        679*************************999999887641114556667777888888888888877553667777 PP

                          SatRNA_48  85 rr 86 
                                        r 
  gene2023|gene2023|rna2023|rna2023  99 RD 100
                                        75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       375  (0.0209158); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 1035.59
//
Query:       gene2024|gene2024|rna2024|rna2024  [L=513]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.8e-18   65.1   0.0    1.3e-17   64.0   0.0    1.6  1  Lipase_3       Lipase (class 3)
    0.00012   21.6   0.0    0.00027   20.5   0.0    1.5  1  DUF676         Putative serine esterase (DUF676)
     0.0013   19.3   0.0     0.0019   18.8   0.0    1.2  1  Abhydrolase_6  Alpha/beta hydrolase family
     0.0065   16.1   0.0      0.013   15.2   0.0    1.5  1  Abhydrolase_1  alpha/beta hydrolase fold
  ------ inclusion threshold ------
      0.011   15.5   0.0      0.023   14.4   0.0    1.5  1  PGAP1          PGAP1-like protein
      0.012   15.2   0.0      0.024   14.2   0.0    1.5  1  DUF2974        Protein of unknown function (DUF2974)
      0.046   13.0   0.0       0.09   12.0   0.0    1.5  1  Hydrolase_4    Serine aminopeptidase, S33
       0.11   12.2   0.0       0.27   11.0   0.0    1.6  1  Abhydrolase_5  Alpha/beta hydrolase family


Domain annotation for each model (and alignments):
>> Lipase_3  Lipase (class 3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.0   0.0   5.7e-21   1.3e-17       1     139 [.     277     401 ..     277     404 .. 0.93

  Alignments for each domain:
  == domain 1  score: 64.0 bits;  conditional E-value: 5.7e-21
                                        EEEE----------------EEE-HHHH-GTT-EEEHHHHHHHHS-HHHHHHHHHHHHHHHTT-EEEEEEEETHHH CS
                           Lipase_3   1 vvafRGtesakdwltdldfslteakellekeggkvhsgfleayeeslreqvlkelkrllekypeysivvtGHSLGg 76 
                                        vv+fRGtesa+d+l+d+ +  +e+ +      g+ h+g+le+++ ++ e+ ++ ++  ++  +  +iv++GHSLGg
  gene2024|gene2024|rna2024|rna2024 277 VVSFRGTESAEDILADVSCDYVEFLD------GYAHRGILELAK-KFLEEHENVINCYMKTMKLKKIVFVGHSLGG 345
                                        79***************999988876......89**********.9999*************************** PP

                                        HHHHHHHHHHHHTT-SS---EEEEEES----B-HHHHHHHHT-TTEEEEEEEETT--GGG-S- CS
                           Lipase_3  77 alAlLaaldlvengenekkkvtvvtfGqPrvgnkefaklvdsqlnkkvlrvvntnDivPrlpp 139
                                        a+A+L+++ l +++ +   +++v++f++P   ++++ak+++    + v  +v   D+ Prl++
  gene2024|gene2024|rna2024|rna2024 346 AIASLVSILLTIKNCT--YPTSVMSFSSPPFLSYNLAKRFN----S-VRIFVLGSDVFPRLSY 401
                                        **************88..**********************9....3.5567999999999876 PP

>> DUF676  Putative serine esterase (DUF676)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   1.2e-07   0.00027      53     125 ..     306     372 ..     299     399 .. 0.77

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 1.2e-07
                             DUF676  53 fkgidvlgerlaeevlevvkkkkdk..nkkiSfvghSlGgliaraaiaklkekemtlkeaikglepvtfitlasP 125
                                        + gi +l+++ +ee  +v++ + ++   kki fvghSlGg ia+ +  +l  k+          +p   ++++sP
  gene2024|gene2024|rna2024|rna2024 306 HRGILELAKKFLEEHENVINCYMKTmkLKKIVFVGHSLGGAIASLVSILLTIKNC--T------YPTSVMSFSSP 372
                                        67888888888888777777666666678**************988777776654..3......66777777775 PP

>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   8.6e-07    0.0019      32      92 ..     278     358 ..     266     466 .. 0.68

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 8.6e-07
                                        E--TTSTS-GGCS--HHHC.HHHHHHHCCTT...........................TTSEEEEEETCHHHHHHH CS
                      Abhydrolase_6  32 pDlpGhGrsdpppldledl.adlaalldelaa.........................gggpvvlvGHSlGGalala 81 
                                        ++++G+   +++ + l+d+  d++++ld+ a+                           +++v vGHSlGGa+a++
  gene2024|gene2024|rna2024|rna2024 278 VSFRGT---ESAEDILADVsCDYVEFLDGYAHrgilelakkfleehenvincymktmKLKKIVFVGHSLGGAIASL 350
                                        556666...44444444433777888888877888888888888999999999999999****************9 PP

                                        HHHCC..EEEE CS
                      Abhydrolase_6  82 aaplalvvgvl 92 
                                           + ++ ++ 
  gene2024|gene2024|rna2024|rna2024 351 ---VSILLTIK 358
                                        ...55222222 PP

>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   5.6e-06     0.013      58      90 ..     319     351 ..     263     384 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 5.6e-06
                                        HHHHHHHHHHHHCTTSSEEEEEETHHHHHHHHH CS
                      Abhydrolase_1  58 svaddldrildalgddkltlvGhSmGGmialay 90 
                                         ++++++  +   +++k++ vGhS+GG+ia+ +
  gene2024|gene2024|rna2024|rna2024 319 EHENVINCYMKTMKLKKIVFVGHSLGGAIASLV 351
                                        57888889999*******************976 PP

>> PGAP1  PGAP1-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0     1e-05     0.023      80     113 ..     324     356 ..     300     376 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1e-05
                              PGAP1  80 lslysssekeptsviliGHSmGGivaraaltlkn 113
                                        ++ y  ++ + ++++ +GHS+GG +a ++ +l +
  gene2024|gene2024|rna2024|rna2024 324 INCY-MKTMKLKKIVFVGHSLGGAIASLVSILLT 356
                                        4455.57778899*************98876655 PP

>> DUF2974  Protein of unknown function (DUF2974)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   1.1e-05     0.024      34     124 ..     271     374 ..     254     388 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.1e-05
                            DUF2974  34 leedtlvvaFRGTddtlvgWkedfnmafrsev..paqesAlkYlnkileeseg............kiylgGhSkGG 95 
                                        +++++lvv+FRGT ++  +   d+  ++ +     a++  l+  +k+lee+e+            ki+ +GhS GG
  gene2024|gene2024|rna2024|rna2024 271 IHKNKLVVSFRGT-ESAEDILADVSCDYVEFLdgYAHRGILELAKKFLEEHENvincymktmklkKIVFVGHSLGG 345
                                        568999*******.7778888899998887542268888888889999999989999*******88********** PP

                            DUF2974  96 nlAvyaamnaeddlqeriskiysfDgpGf 124
                                         +A ++++ +  +     + ++sf +p f
  gene2024|gene2024|rna2024|rna2024 346 AIASLVSILLTIKNCTYPTSVMSFSSPPF 374
                                        ****9998866666666666677766665 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0     4e-05      0.09      48     149 ..     306     411 ..     302     439 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 4e-05
                        Hydrolase_4  48 krghvpsfddyvdDlaafvekvkeehpelplfllGhSmGGliallyl.....lrypdkvaglilsaPalkikaklk 118
                                        +rg ++  +++++  + +++   ++ + ++++ +GhS+GG+ia l+      +++    + + +s+P +   +   
  gene2024|gene2024|rna2024|rna2024 306 HRGILELAKKFLEEHENVINCYMKTMKLKKIVFVGHSLGGAIASLVSilltiKNCTYPTSVMSFSSPPFLSYNL-- 379
                                        56666667778888888888888888899**************9887665554444455667777776655544.. PP

                        Hydrolase_4 119 appllkl.llkllgkllpklqvsnnlkadsls 149
                                        a+++  + +  l + ++p+l+  + l++++l+
  gene2024|gene2024|rna2024|rna2024 380 AKRFNSVrIFVLGSDVFPRLSYGSVLDFKYLT 411
                                        45555442334445677777776666666665 PP

>> Abhydrolase_5  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00012      0.27      50      74 ..     327     351 ..     310     371 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00012
                      Abhydrolase_5  50 ikeapklekfvvgGhslGGvvasrf 74 
                                          ++ kl+k v  GhslGG++as +
  gene2024|gene2024|rna2024|rna2024 327 YMKTMKLKKIVFVGHSLGGAIASLV 351
                                        44577899**************965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (513 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       750  (0.0418317); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.42
# Mc/sec: 3658.33
//
Query:       gene2025|gene2025|rna2025|rna2025  [L=194]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-06   27.4   1.6    4.3e-06   26.5   1.6    1.5  1  KH_1      KH domain
  ------ inclusion threshold ------
      0.055   13.3   0.1       0.15   11.9   0.1    1.7  1  KH_4      KH domain


Domain annotation for each model (and alignments):
>> KH_1  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   1.6   4.8e-10   4.3e-06       9      65 ..     107     155 ..     103     156 .. 0.87

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 4.8e-10
                                        GHHHHHHTGGGHHHHHHHHHH.T-EEEEESSTT...T.-EEEEEESHHHHHHHHHHHH CS
                               KH_1   9 slvgriIGkgGsnIkeIreet.gakIkvpksedegsderevtisGspeavekAkelie 65 
                                        + +griIG+ G++   I+  t g+ + +         e+e+ + G++e+++kAke i+
  gene2025|gene2025|rna2025|rna2025 107 RAIGRIIGREGKVKSAIEH-TmGVCMLIK--------EDEIFMLGDEEGIKKAKESIS 155
                                        679****************.88***9965........3567777**********9886 PP

>> KH_4  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   1.7e-05      0.15      39      57 ..     108     126 ..      99     137 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.7e-05
                               KH_4  39 dlGrvIGkrGrtldAlqyl 57 
                                         +Gr+IG++G++ +A+ + 
  gene2025|gene2025|rna2025|rna2025 108 AIGRIIGREGKVKSAIEHT 126
                                        58**********9999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       394  (0.0219756); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1379.59
//
Query:       gene2026|gene2026|rna2026|rna2026  [L=322]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.058   13.7   0.4       0.29   11.5   0.1    2.2  3  Phage_int_SAM_5  Phage integrase SAM-like domain


Domain annotation for each model (and alignments):
>> Phage_int_SAM_5  Phage integrase SAM-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.21   3.7e+03      66      78 ..      24      36 ..      15      53 .. 0.70
   2 ?   -2.4   0.0      0.35   6.2e+03      63      79 ..      88     104 ..      72     108 .. 0.55
   3 ?   11.5   0.1   1.6e-05      0.29      39      76 ..     244     278 ..     215     281 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.21
                                       HHHHHHHHHHHHH CS
                    Phage_int_SAM_5 66 entiskyfkklka 78
                                        nti+ y ++l+ 
  gene2026|gene2026|rna2026|rna2026 24 INTIREYKEHLRD 36
                                       4566666555554 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.35
                                        ---HHHHHHHHHHHHHH CS
                    Phage_int_SAM_5  63 glsentiskyfkklkav 79 
                                        ++ en +s  f+++ ++
  gene2026|gene2026|rna2026|rna2026  88 PNVENAVSDIFQNFEKF 104
                                        44455555555555554 PP

  == domain 3  score: 11.5 bits;  conditional E-value: 1.6e-05
                                        S---TTT--HHHHHHHHHHHHHTS---HHHHHHHHHHH CS
                    Phage_int_SAM_5  39 kditfeeidkefleeFedYLkkkkglsentiskyfkkl 76 
                                        + i+ +ei+ + +e+F++YL   +   ++++++y+k +
  gene2026|gene2026|rna2026|rna2026 244 NIIRPKEITITKIEKFQQYL---QLTIQSSAGTYIKEF 278
                                        5599****************...777888888888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (322 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       669  (0.0373138); expected 358.6 (0.02)
Passed bias filter:                      456  (0.0254337); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2282.21
//
Query:       gene2027|gene2027|rna2027|rna2027  [L=343]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   6.2e-128  425.4   0.1   2.5e-125  416.9   0.0    2.0  2  Rad51     Rad51
    2.1e-12   47.1   0.1    2.9e-12   46.6   0.1    1.1  1  RecA      recA bacterial DNA recombination protein
    9.1e-10   38.4   0.0    1.5e-09   37.7   0.0    1.2  1  AAA_25    AAA domain
    1.7e-07   30.8   0.0    2.6e-07   30.2   0.0    1.4  1  ATPase    KaiC
    5.2e-07   30.2   0.1      3e-06   27.7   0.0    2.4  2  HHH_5     Helix-hairpin-helix domain
     0.0026   17.1   0.1       0.36   10.1   0.0    2.3  2  DnaB_C    DnaB-like helicase C terminal domain
     0.0053   17.0   0.1      0.022   15.0   0.0    1.9  2  AAA_22    AAA domain
  ------ inclusion threshold ------
      0.064   13.0   0.2        3.5    7.4   0.0    2.4  2  CobS_N    Cobaltochelatase CobS subunit N terminal
       0.07   13.0   0.1       0.25   11.2   0.1    1.9  1  DUF3173   Domain of unknown function (DUF3173)
       0.11   11.6   0.0       0.27   10.3   0.0    1.7  1  PAXNEB    PAXNEB protein
       0.14   12.6   0.0       0.41   11.1   0.0    1.9  2  HhH-GPD   HhH-GPD superfamily base excision DNA repair protei
       0.17   11.6   0.0       0.39   10.4   0.0    1.6  1  AAA_24    AAA domain


Domain annotation for each model (and alignments):
>> Rad51  Rad51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.7   0.0    0.0025       3.8      14      43 ..      16      45 ..       5      51 .. 0.87
   2 !  416.9   0.0  1.7e-128  2.5e-125       1     254 [.      87     340 ..      87     341 .. 0.99

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0025
                                       HSS-EE--S-HHHHHHHTSSEESSSEEEEE CS
                              Rad51 14 sellqlttGskklDelLgGGietgsiteif 43
                                       +e +qlttG  ++Del + Gi +g i+ ++
  gene2027|gene2027|rna2027|rna2027 16 REEIQLTTGPISVDELKNCGIAAGDIARLC 45
                                       45689********************99887 PP

  == domain 2  score: 416.9 bits;  conditional E-value: 1.7e-128
                                        -S-EBHHHHHHHHHSS-EE--S-HHHHHHHTSSEESSSEEEEEESTTSSHHHHHHHHHHHTTS-TTTS--SSEEEE CS
                              Rad51   1 lgfvsavellekrsellqlttGskklDelLgGGietgsiteifGefrsGktqlchtlcvtvqlplelgGgegkavy 76 
                                        +gf +a+++ +kr++++ +ttGs++lD+lL+GGietgsiteifGefr+Gktqlchtl+vt+ql+ e+gGg gka+y
  gene2027|gene2027|rna2027|rna2027  87 MGFSTATSYFQKRNNIVFITTGSQELDKLLKGGIETGSITEIFGEFRTGKTQLCHTLAVTCQLDRENGGGSGKALY 162
                                        79************************************************************************** PP

                                        EESSS---GGGGHHHHHHTT--HHHHGGGEEEEE--STTHHHHHHHHTHHHHHHS-EEEEEEETTTGGGCH----- CS
                              Rad51  77 idtegtfrperlveiaerykldkeevlenvayaRaytiehqeellqqaaallaedkfallivDsvtalyRtdfsgr 152
                                        idtegtfrper +++a+r++ld+++vlen++yaRay+++hq++ll qaaa+l+e++++l+ivDs++alyRtdfsgr
  gene2027|gene2027|rna2027|rna2027 163 IDTEGTFRPERCIAVAQRFGLDSDQVLENISYARAYNSDHQSQLLVQAAAMLSESNYSLIIVDSAMALYRTDFSGR 238
                                        **************************************************************************** PP

                                        --THHHHHHHHHHHHHHHHHHHHH--EEEEEEE-------.------------HHHHHHHH-SEEEEEEE-STTEE CS
                              Rad51 153 gelakRqqklgkllrtLrkladefevavvitnqvvaqvdgqaalfsadpkkPigGlvlahasttRlalrkgkgeeR 228
                                        gel +Rq +l+++lr+L +ladef+vavvitnqvva+vdg+aa+f+adpkkP gG+++ahasttRl+lrkg+ge+R
  gene2027|gene2027|rna2027|rna2027 239 GELGARQIHLARFLRMLLRLADEFSVAVVITNQVVASVDGAAAMFNADPKKPAGGHIIAHASTTRLYLRKGRGETR 314
                                        **************************************************************************** PP

                                        EEEEES-SSS-S-EEEEEEETTEEE- CS
                              Rad51 229 ivkvvdsPnlpeleavfaigeeGied 254
                                        i+k++dsP+lpe+eavfai+ +G+ d
  gene2027|gene2027|rna2027|rna2027 315 ICKIYDSPCLPESEAVFAITANGVDD 340
                                        ************************98 PP

>> RecA  recA bacterial DNA recombination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.6   0.1     2e-15   2.9e-12      27     221 ..      98     308 ..      76     317 .. 0.77

  Alignments for each domain:
  == domain 1  score: 46.6 bits;  conditional E-value: 2e-15
                                        .-----EE--S-HHHHHHTSSSSEETTSEEEEEESTTSSHHHH..HHHHHHHHHHTT....--EEEEESS----HH CS
                               RecA  27 eklkvetissGslaldialGiGGlpkGriieiyGpessGkttl..alhaiaeaqkkg....gvaafidaehaldpk 96 
                                        +++++  i++Gs  ld  l  GG+  G i+ei+G   +Gkt l  +l + ++  +++    g a +id+e ++ p+
  gene2027|gene2027|rna2027|rna2027  98 KRNNIVFITTGSQELDKLLK-GGIETGSITEIFGEFRTGKTQLchTLAVTCQLDRENgggsGKALYIDTEGTFRPE 172
                                        4578999*********9987.********************984457777887776522235799********997 PP

                                        ....HHHHTT--GGG-E..EE.....--SSHHHHHHHHHHHHTTT--SEEEEE-TTT---ST.T-----------H CS
                               RecA  97 ....yakklGvdidell..vs.....qpdtGeqaleiadalvrsgaidlivvdsvaalvpka.eieGemgdskvgl 160
                                             a+++G+d d++l  +s     + d+  q l  a a++  +   li+vds  al   +    Ge+g  ++ l
  gene2027|gene2027|rna2027|rna2027 173 rciaVAQRFGLDSDQVLenISyarayNSDHQSQLLVQAAAMLSESNYSLIIVDSAMALYRTDfSGRGELGARQIHL 248
                                        33335899*****9998555533333468888888888888888999**********9754313457888877765 PP

                                        HHHHHHHHHHHHHHHHTTT--EEEEEEE-----...-----.-------HHHHHHH-SEEEEEEE CS
                               RecA 161 qarlmsqalrkltgaisksntvvifinqireki...Gvmfg.npetttGGralkfyasvrldvrr 221
                                         ar+    lr l    ++  ++v+  nq+   +     mf  +p+  +GG+ +   ++ rl +r+
  gene2027|gene2027|rna2027|rna2027 249 -ARF----LRMLLRLADEFSVAVVITNQVVASVdgaAAMFNaDPKKPAGGHIIAHASTTRLYLRK 308
                                        .555....666666777888999999**998874333566548******************9998 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.7   0.0   9.9e-13   1.5e-09      17     188 ..     107     271 ..      97     273 .. 0.80

  Alignments for each domain:
  == domain 1  score: 37.7 bits;  conditional E-value: 9.9e-13
                             AAA_25  17 apppprrwlvkgllpagelallaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEdsedelrrRlra 92 
                                        +  +++++l+kg +  g+++ ++G   tGKt l+  la+++ ++++  g      gk ly+++E++    ++R  a
  gene2027|gene2027|rna2027|rna2027 107 TGSQELDKLLKGGIETGSITEIFGEFRTGKTQLCHTLAVTCQLDRENGG----GSGKALYIDTEGTF--RPERCIA 176
                                        5678899***********************************9996544....89***********9..7899999 PP

                             AAA_25  93 vgealrddarllvldlagveslpLfakdrggtlltadvdaleaaieevegvrlvviDplsralggdensnsd.... 164
                                        v + + +d++  + ++      + + +d++++ll ++    +a + e  ++ l+++D+  ++++ d     +    
  gene2027|gene2027|rna2027|rna2027 177 VAQRFGLDSDQVLENISYA---RAYNSDHQSQLLVQA----AAMLSE-SNYSLIIVDSAMALYRTDFSGRGElgar 244
                                        9999866666655555443...456667777775444....455556.569*********9999977766666666 PP

                             AAA_25 165 .v..galvealeriarrtgaavllvhH 188
                                         +  ++++ +l r+a+++ +av+++ +
  gene2027|gene2027|rna2027|rna2027 245 qIhlARFLRMLLRLADEFSVAVVITNQ 271
                                        6456******************99865 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.2   0.0   1.8e-10   2.6e-07       2     133 ..     106     231 ..     105     317 .. 0.76

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 1.8e-10
                             ATPase   2 ktgIeglDeilkgGipegrvvlitGepGtGKtifalqFlikgaekygepg......vfvtveepa..edlrenaks 69 
                                         tg ++lD++lkgGi  g+++ i Ge  tGKt ++ + +++   +  e+g      +++ +e +   e  +  a++
  gene2027|gene2027|rna2027|rna2027 106 TTGSQELDKLLKGGIETGSITEIFGEFRTGKTQLCHTLAVTCQLDR-ENGggsgkaLYIDTEGTFrpERCIAVAQR 180
                                        7999***********************************9976553.3222333449*****975559******** PP

                             ATPase  70 lGwdlekleeegklaiidasesaeesaeekdkedleelieelaeaikeikakrvviDsitglay 133
                                        +G d +++ e+  + +  a++s+++          ++l+ + a +++e + + +++Ds  +l y
  gene2027|gene2027|rna2027|rna2027 181 FGLDSDQVLEN--ISYARAYNSDHQ----------SQLLVQAAAMLSESNYSLIIVDSAMAL-Y 231
                                        *********99..777777776554..........677777788888888888888887777.3 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7   0.0     2e-09     3e-06      15      56 ..      41      82 ..      31      83 .. 0.92
   2 ?   -2.1   0.0       4.1   6.1e+03      29      48 ..     296     315 ..     281     320 .. 0.81

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 2e-09
                                       HHHHHTTT--SHHHHHHS-HHHHHTSTTS-HHHHHHHHHHHH CS
                              HHH_5 15 AlallsaGiesvedlaaadveeLakipGiGkktAeriilelk 56
                                       + +l++aG+ +ve+la   +++L +++G+++ +Ae+i+ e+ 
  gene2027|gene2027|rna2027|rna2027 41 IARLCEAGYHTVEALAFTPKKQLMTVKGFSEAKAEKILKEAA 82
                                       5689**********************************9986 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 4.1
                                        HHHS-HHHHHTSTTS-HHHH CS
                              HHH_5  29 laaadveeLakipGiGkktA 48 
                                        +a+a++ +L   +G G+ + 
  gene2027|gene2027|rna2027|rna2027 296 IAHASTTRLYLRKGRGETRI 315
                                        89999999998888888665 PP

>> DnaB_C  DnaB-like helicase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0      0.01        15       2      44 ..     105     148 ..     105     166 .. 0.87
   2 !   10.1   0.0   0.00024      0.36     115     182 ..     204     276 ..     184     287 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.01
                                        BXSSTHHHHHHCT.SBXTTXEEEEEEXTTSSHHHHHHHHHHHHH CS
                                        xxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             DnaB_C   2 lstgfkdLDklts.GlqkgdliiiAarpsmGktalalniaenaa 44 
                                        ++tg ++LDkl++ G++ g ++ i +   +Gkt l+ ++a ++ 
  gene2027|gene2027|rna2027|rna2027 105 ITTGSQELDKLLKgGIETGSITEIFGEFRTGKTQLCHTLAVTCQ 148
                                        68999****9986279********************99997665 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00024
                                        HHHHHHHHHHHHHTTEEEEEEEE.GGGTBTS.CS...SSCCCHHHHHHHHHHHHHHHHCTSXEEEEEEXSGGG CS
                                        xxxxxxxxxxxxxxxxxxxxxxx.xxxxxxx.xx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             DnaB_C 115 seirskarrlkkekglgliviDy.Lqlmegs.ee...kenreqevseisrsLkalakelnvpvialsqLsrav 182
                                        s++  +a  + +e++ +li++D  + l +++ +       r+  +++  r L  la e++v v++  q+  +v
  gene2027|gene2027|rna2027|rna2027 204 SQLLVQAAAMLSESNYSLIIVDSaMALYRTDfSGrgeLGARQIHLARFLRMLLRLADEFSVAVVITNQVVASV 276
                                        56667777788899********734555533322443559**************************9987776 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       1.6   2.5e+03     114     137 .]      95     116 ..      71     116 .. 0.73
   2 !   15.0   0.0   1.5e-05     0.022       4     127 ..     122     268 ..     120     271 .. 0.72

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 1.6
                             AAA_22 114 sllnlsrkgvqliLvGtpelrkll 137
                                         +++  r ++ +i  G +el+kll
  gene2027|gene2027|rna2027|rna2027  95 YFQK--RNNIVFITTGSQELDKLL 116
                                        3445..999999999999999986 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 1.5e-05
                             AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelka......... 70 
                                        t +i+ ++Ge  tGKT l+ +l+ + + + +    +++ +++  +++t + + + ++++ +gl+ +          
  gene2027|gene2027|rna2027|rna2027 122 TGSITEIFGEFRTGKTQLCHTLAVTCQLDRENGG-GSGKALYIDTEGTFRPERCIAVAQRFGLDSDQvlenisyar 196
                                        788999*****************99865544444.55555444555555778899999999999999999999999 PP

                             AAA_22  71 ..erlsseell.ealeqalraravielliiDEaqhlr....s............eealeeLrsllnlsrkgvqliL 127
                                          + + +++ll +a +  +++ +   l+i+D a  l     s            ++ l+ L +l++  +++v++++
  gene2027|gene2027|rna2027|rna2027 197 ayNSDHQSQLLvQAAAMLSESNYS--LIIVDSAMALYrtdfSgrgelgarqihlARFLRMLLRLAD--EFSVAVVI 268
                                        995555555551555555555555..******9998776662556677777777777777777777..88887775 PP

>> CobS_N  Cobaltochelatase CobS subunit N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0     0.052        78      22      30 ..      64      72 ..      64      74 .. 0.90
   2 ?    7.4   0.0    0.0023       3.5       6      21 ..     171     186 ..     168     188 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.052
                             CobS_N 22 meVpAFser 30
                                       m+V++Fse+
  gene2027|gene2027|rna2027|rna2027 64 MTVKGFSEA 72
                                       9******97 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0023
                             CobS_N   6 PDtkvsvRevFGIDsD 21 
                                        P + + v + FG+DsD
  gene2027|gene2027|rna2027|rna2027 171 PERCIAVAQRFGLDSD 186
                                        888999*********9 PP

>> DUF3173  Domain of unknown function (DUF3173)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00017      0.25       5      28 ..      60      84 ..      57     103 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00017
                            DUF3173  5 kkdLikl.GfkehtArdiIrqaKki 28
                                       kk+L+   Gf+e  A++i+++a k+
  gene2027|gene2027|rna2027|rna2027 60 KKQLMTVkGFSEAKAEKILKEAAKL 84
                                       7999*999*************9665 PP

>> PAXNEB  PAXNEB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00018      0.27      14      41 ..     100     127 ..      95     143 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00018
                             PAXNEB  14 dgqlltStGtpsLDklLgGGLplGsill 41 
                                        ++ +++ tG+++LDklL GG+  Gsi  
  gene2027|gene2027|rna2027|rna2027 100 NNIVFITTGSQELDKLLKGGIETGSITE 127
                                        5668999******************975 PP

>> HhH-GPD  HhH-GPD superfamily base excision DNA repair protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00028      0.41      18      67 ..      41     118 ..      36     263 .. 0.72
   2 ?   -1.2   0.0       1.9   2.8e+03       8      37 ..     245     277 ..     239     281 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00028
                                        HHHHHHHHSHCSHHHHHHSHHHHHHHHHTTSTTHHHHHHHHHHHHHHHH........................... CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........................... RF
                            HhH-GPD  18 ierlferfgfptpedladadeekLrelirelGfyrrKakyikelArilv........................... 66 
                                        i+rl+e+ g  t+e+la  + ++L++     Gf++ Ka+ i + A +l+                           
  gene2027|gene2027|rna2027|rna2027  41 IARLCEA-GYHTVEALAFTPKKQLMTV---KGFSEAKAEKILKEAAKLIpmgfstatsyfqkrnnivfittgsqel 112
                                        5788888.699****************...9**********99999999899999999998666555555555555 PP

                                        .....S CS
                                        .....x RF
                            HhH-GPD  67 .....g 67 
                                             g
  gene2027|gene2027|rna2027|rna2027 113 dkllkG 118
                                        555550 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.9
                                        TS-HHHHHHHHHHHHHHHS...HCSHHHHHHSH CS
                                        xxxxxxxxxxxxxxxxxxx...xxxxxxxxxxx RF
                            HhH-GPD   8 qtsderanriierlferfg...fptpedladad 37 
                                        q++ +r  r+  rl+++f     +t + +a++d
  gene2027|gene2027|rna2027|rna2027 245 QIHLARFLRMLLRLADEFSvavVITNQVVASVD 277
                                        888899999999999998877767777777665 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00026      0.39       7      79 ..     128     232 ..     124     235 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00026
                             AAA_24   7 iyGpsgiGKTtlakel.............gpkplfidtekGlksldadkfpdie.....swedfldevvel..... 59 
                                        i+G+  +GKT l+ +l               k+l+idte+ ++    + +           +++l+ + +      
  gene2027|gene2027|rna2027|rna2027 128 IFGEFRTGKTQLCHTLavtcqldrengggSGKALYIDTEGTFRPERCIAV---AqrfglDSDQVLENISYArayns 200
                                        89**************6666666666666666666666664422222222...24456655555555555577777 PP

                             AAA_24  60 ............aaeladyktlviDtidelee 79 
                                                       +++y+ +++D++  l++
  gene2027|gene2027|rna2027|rna2027 201 dhqsqllvqaaaMLSESNYSLIIVDSAMALYR 232
                                        77777777776645566688888888777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (343 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       423  (0.0235931); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.52u 0.31s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 2150.72
//
Query:       gene2028|gene2028|rna2028|rna2028  [L=191]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.3e-39  133.8   0.1      5e-39  133.6   0.1    1.1  1  Ribosomal_S8e  Ribosomal protein S8e


Domain annotation for each model (and alignments):
>> Ribosomal_S8e  Ribosomal protein S8e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  133.6   0.1   2.8e-43     5e-39      20     137 .]      30     190 ..       3     190 .. 0.90

  Alignments for each domain:
  == domain 1  score: 133.6 bits;  conditional E-value: 2.8e-43
                                        XSSXXXCCSBXXXXXXXEE...........SSHEEEEEEETTCEEEE............................. CS
                      Ribosomal_S8e  20 llrkkrkielgrkekatkl...........gaervkvvrvrgGkrkk............................. 55 
                                          +  ++i+ +rke+a+k+           + e+++vv   +Gk++                              
  gene2028|gene2028|rna2028|rna2028  30 GKELSHEIKERRKEAAAKYsvpipriaglsEVETFNVV--TTGKKRGkhwkrmvvkpcfvgdnftrktpkyerfir 103
                                        44445699***********9999999866448899999..66655556899************************* PP

                                        .EEESESEEEEEETTTTEEEEEEEEEEECSSSTCHHHHTTC--TTEEEEEESHHHHHHHHTTEEE....EEEESEH CS
                      Ribosomal_S8e  56 .ralrlkkanvthpeekvtkklkIlgVkknpsnneyvrlgvltKgaiievdvseLgevtqsgkvv....AqvtsrP 126
                                         +alr+kka+vthpe+k+t++l+Ilg k np++++y++lgvltKg+iiev+vseLg v q+g+vv    Aqvt++P
  gene2028|gene2028|rna2028|rna2028 104 pMALRFKKAHVTHPELKTTFCLPILGLKTNPHSHLYTSLGVLTKGTIIEVNVSELGIVEQNGRVVwgkyAQVTNNP 179
                                        **************************************************************************** PP

                                        HHHSSEEEEEE CS
                      Ribosomal_S8e 127 gqdGcvnavlL 137
                                        + dGcvnavlL
  gene2028|gene2028|rna2028|rna2028 180 EYDGCVNAVLL 190
                                        **********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (191 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       377  (0.0210274); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1305.07
//
Query:       gene2029|gene2029|rna2029|rna2029  [L=703]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      1e-38  133.3   0.2    1.4e-38  132.9   0.2    1.2  1  Sec23_trunk     Sec23/Sec24 trunk domain
    9.7e-15   54.3   6.4    2.1e-14   53.3   6.4    1.6  1  zf-Sec23_Sec24  Sec23/Sec24 zinc finger
    9.3e-14   51.1   0.1    1.7e-13   50.2   0.1    1.5  1  Sec23_helical   Sec23/Sec24 helical domain
    4.5e-10   40.1   0.0      9e-10   39.2   0.0    1.5  1  Sec23_BS        Sec23/Sec24 beta-sandwich domain
    2.5e-06   27.3   0.2    1.3e-05   25.0   0.2    2.2  1  Gelsolin        Gelsolin repeat
  ------ inclusion threshold ------
      0.037   13.8   1.4      0.069   12.9   1.4    1.4  1  zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal


Domain annotation for each model (and alignments):
>> Sec23_trunk  Sec23/Sec24 trunk domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  132.9   0.2   4.7e-42   1.4e-38       3     242 ..     118     364 ..     116     365 .. 0.93

  Alignments for each domain:
  == domain 1  score: 132.9 bits;  conditional E-value: 4.7e-42
                                        --EEEEEEE-SHHHHHHTHHHHHHHHHHHHCTTSSTSTT-EEEEEEESSSEEEEETSTTS......SSSEEEEECH CS
                        Sec23_trunk   3 ppvflFviDvsleaikegelkalkeslkqsLdllPeepralvglitfdsvvhffelksel......rqpkelvvsd 72 
                                         p+f+Fv+D++     e+  ++l++ ++   d lP  +++ +glit+++ +++f+++se       ++++++ ++ 
  gene2029|gene2029|rna2029|rna2029 118 QPTFFFVVDMCTF--DEQRYNLLIDGIRITYDGLP--DECTIGLITYGTNINLFDFQSEIkrtfifSGERNYDKKT 189
                                        599********98..899*****************..*********************999*************** PP

                                        TTSCCSSTS..SSSSEE.TTTTHHHHHHHHHHHHH.HSTT-TTC-----HHHHHHHHHHHHCHCT..S-EEEEEEE CS
                        Sec23_trunk  73 lqdvflpla..drlLvp.lseseavledlLeelpe.mfavtagkrperalgpalkaavellkave..tggkiivfv 142
                                        l+  f   +  +++L     +    ++d+++ +++ +f+v +g r+ r++g+al+ av+ll++v   ++ ki++f 
  gene2029|gene2029|rna2029|rna2029 190 LEGYFKDENanSQFLSFvFTKKTVDVNDFVKMMERdPFPVRSGLRQIRCTGSALSFAVSLLESVVhdAAIKIFLFT 265
                                        *****665553666654146667789************************************99888999****** PP

                                        SS---SSTTTSS-SBTTS...CCTSSTTCHHCHSCSSSCHHHHHHHHHHHCTEEEEEEEECSS--SHHHHTHHHHT CS
                        Sec23_trunk 143 gslptvgaggklksrede...slldidkekaklvkkadkfYkkLakecvkqgisvDlFlfsldyvdlaelkqlael 215
                                         ++ t g+g+  + +++e   s  di + kak+vk++++ +++Lak++++ g+s+D+  ++l+ ++l e+++l ++
  gene2029|gene2029|rna2029|rna2029 266 EGPITFGPGTMASLNLKEnirSGNDILRGKAKYVKTSKSYFDALAKRMANLGMSIDILSATLNDIGLYEMQSLIDM 341
                                        *********9999999998888999*************************************************** PP

                                        TT-EEEEETTTCCHHHHHHHHHHHHHH CS
                        Sec23_trunk 216 tgGqvvlydsFsaekdasklkqdlkrv 242
                                        tgG vv+++ F     ++++ ++ +++
  gene2029|gene2029|rna2029|rna2029 342 TGGLVVMAQDFD----HEIFTTSCAKN 364
                                        ***********9....88998887776 PP

>> zf-Sec23_Sec24  Sec23/Sec24 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.3   6.4   7.1e-18   2.1e-14       1      39 []      52      90 ..      52      90 .. 0.99

  Alignments for each domain:
  == domain 1  score: 53.3 bits;  conditional E-value: 7.1e-18
                     zf-Sec23_Sec24  1 PirCrrCraylNpfckidfggkrwiCnfCnhknevppeY 39
                                       Pi C +Cr++lNp++++d+++k w+C fCn+kn++pp+Y
  gene2029|gene2029|rna2029|rna2029 52 PIFCLTCRSILNPYTTVDYNTKEWTCIFCNKKNHLPPHY 90
                                       99************************************9 PP

>> Sec23_helical  Sec23/Sec24 helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.2   0.1   5.8e-17   1.7e-13       1     102 [.     473     567 ..     473     568 .. 0.93

  Alignments for each domain:
  == domain 1  score: 50.2 bits;  conditional E-value: 5.8e-17
                                        -HHHHHHHHHHHHHHHTTTS-HHHHHHHHHHHHHHHHHHHHHH-------------GGGTTHHHHHHHHHTSTTTS CS
                      Sec23_helical   1 DqeavtvllakqaidkalesgladarealdtslvdllsayrkvgasgsspsqlqlpeslklLPlyilallKspafr 76 
                                        Dqea+++l a+     +  ++  d+++ +d+sl+++++++++        + l+l++s+ l+P +i+ l++s  ++
  gene2029|gene2029|rna2029|rna2029 473 DQEAALILQARIFTFGTHIEEDLDLVRRIDRSLIRFIRKFGESN------NHLKLSSSMALYPNFIYFLRRSL-LV 541
                                        9****************9888889999*****************......66*********************.77 PP

                                        -.-TT--HHHHHHHHHHHHH--HHHHH CS
                      Sec23_helical  77 g.gnsvpaDervfalslllslpvdqll 102
                                        +  +++p De++++++++ ++pv++ +
  gene2029|gene2029|rna2029|rna2029 542 QtETNSP-DETSYYRNIVAREPVTNAM 567
                                        7588888.***************9987 PP

>> Sec23_BS  Sec23/Sec24 beta-sandwich domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.2   0.0     3e-13     9e-10       2      93 ..     376     460 ..     375     463 .. 0.86

  Alignments for each domain:
  == domain 1  score: 39.2 bits;  conditional E-value: 3e-13
                                        EEEEEEEEE-TTEEEEEEESSSEECSTBESSEESECSESEEEEEEEETT--EEEEEEESSBTCTTSEEEEEEEEEE CS
                           Sec23_BS   2 fnatlevrtSkelkvsgliGncvslsnvsekeiGeggtsewklcsldpdstlavyfdideklksgkqayiQfatlY 77 
                                        fna+++v+ +k+l  ++ iG  + l n ++      +   wkl+sl+++s++++ fd +++   ++  y+Q++t+Y
  gene2029|gene2029|rna2029|rna2029 376 FNAKFKVQ-TKGLTYKSGIGLGSPLLNQKN------EEIGWKLGSLHRNSNIGFIFDAKANKRDDEIGYVQIITQY 444
                                        78888887.589999999999998843433......3336*******************9*999************ PP

                                        EETTSEEEEEEEEEEE CS
                           Sec23_BS  78 thssgerrlRVttval 93 
                                        ++s+++  +RVtt a+
  gene2029|gene2029|rna2029|rna2029 445 QQSDRKLITRVTTAAR 460
                                        *************987 PP

>> Gelsolin  Gelsolin repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.2   4.4e-09   1.3e-05       3      44 ..     581     623 ..     580     669 .. 0.71

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 4.4e-09
                                        EEEEEBSSSGGGEETTSEEEEEESSEEEEEEHTT.SHHHHHHH CS
                           Gelsolin   3 vlpkvvklsssslesgdcyLLdngftiflWiGke.ssqeeknf 44 
                                        ++ k+v+++ +sl+++ ++LLd++ ++ +W+G++ +++ +++ 
  gene2029|gene2029|rna2029|rna2029 581 DETKPVPMDAKSLQPDIILLLDTFHNVLIWRGEHiNQWIQEGY 623
                                        5789*********************999999999988887764 PP

>> zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   1.4   2.3e-05     0.069      22      54 .]      52      84 ..      46      84 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.3e-05
                     zinc_ribbon_10 22 alICskChshnGlapkeeleevkyrCpkCgaln 54
                                       ++ C +C+s  + +++ ++++ ++ C +C+ +n
  gene2029|gene2029|rna2029|rna2029 52 PIFCLTCRSILNPYTTVDYNTKEWTCIFCNKKN 84
                                       788***************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (703 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       523  (0.0291706); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.65u 0.26s 00:00:00.91 Elapsed: 00:00:00.45
# Mc/sec: 4716.81
//
Query:       gene203|gene203|rna203|rna203  [L=259]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.5e-06   27.6  15.5    0.00087   19.6   1.3    2.8  2  zf-C2H2        Zinc finger, C2H2 type
      5e-06   26.7  14.9    3.8e-05   23.9   5.4    3.6  3  zf-H2C2_2      Zinc-finger double domain
    0.00033   21.2  11.1      0.012   16.4   1.0    2.8  2  zf-C2H2_4      C2H2-type zinc finger
     0.0025   18.4   2.3       0.51   11.0   0.0    2.9  3  FOXP-CC        FOXP coiled-coil domain
     0.0088   16.7   1.5      0.024   15.3   1.5    1.7  1  zf-TRAF        TRAF-type zinc finger
  ------ inclusion threshold ------
       0.02   15.2   2.9      0.046   14.0   2.9    1.6  1  zf-C2H2_8      C2H2-type zinc ribbon
      0.054   12.6   1.0      0.086   11.9   1.0    1.2  1  DREV           DREV methyltransferase
      0.062   13.4   0.8      0.062   13.4   0.8    2.2  2  Polbeta        Polymerase beta, Nucleotidyltransferase
       0.22   11.6   3.1        1.9    8.6   0.2    2.9  3  BCNT           Bucentaur or craniofacial development
        0.4   10.4   2.5        0.4   10.3   0.6    2.0  2  zf_C2H2_ZHX    Zinc-fingers and homeoboxes C2H2 finger domain
        4.9    7.7  11.3       0.71   10.4   3.3    3.0  2  zf-C2HE        C2HE / C2H2 / C2HC zinc-binding finger


Domain annotation for each model (and alignments):
>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   4.3   1.6e-05     0.025       1      23 []     184     208 ..     184     208 .. 0.97
   2 !   19.6   1.3   5.4e-07   0.00087       1      23 []     214     238 ..     214     238 .. 0.98

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.6e-05
                                    EEET..TTTEEESSHHHHHHHHHCC CS
                        zf-C2H2   1 ykCp..dCgksFkrksnLkrHirtH 23 
                                    ++C    C+  Fkr ++LkrH+r+H
  gene203|gene203|rna203|rna203 184 FVCQykNCSSAFKRFEHLKRHYRIH 208
                                    89**********************9 PP

  == domain 2  score: 19.6 bits;  conditional E-value: 5.4e-07
                                    EEET..TTTEEESSHHHHHHHHHCC CS
                        zf-C2H2   1 ykCp..dCgksFkrksnLkrHirtH 23 
                                    +kC+  +C k+F r++nL +H+++H
  gene203|gene203|rna203|rna203 214 FKCKypGCFKKFARSDNLSQHLKIH 238
                                    89*********************99 PP

>> zf-H2C2_2  Zinc-finger double domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.5     0.059        97      13      26 .]     182     197 ..     172     197 .. 0.87
   2 !   23.9   5.4   2.3e-08   3.8e-05       1      25 [.     200     226 ..     200     227 .. 0.91
   3 ?    3.7   0.0     0.056        91       1      10 [.     230     239 ..     230     246 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.059
                      zf-H2C2_2  13 kpyeCp..lCdkaFkt 26 
                                    +p+ C    C+ aFk+
  gene203|gene203|rna203|rna203 182 RPFVCQykNCSSAFKR 197
                                    699999989*****96 PP

  == domain 2  score: 23.9 bits;  conditional E-value: 2.3e-08
                      zf-H2C2_2   1 nLrrHirkHtgekpyeCp..lCdkaFk 25 
                                    +L+rH r Htge+p++C+   C k+F+
  gene203|gene203|rna203|rna203 200 HLKRHYRIHTGERPFKCKypGCFKKFA 226
                                    79****************766999997 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.056
                      zf-H2C2_2   1 nLrrHirkHt 10 
                                    nL++H++ H 
  gene203|gene203|rna203|rna203 230 NLSQHLKIHN 239
                                    8********7 PP

>> zf-C2H2_4  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   3.4    0.0019       3.1       1      23 [.     184     208 ..     184     209 .. 0.94
   2 !   16.4   1.0   7.4e-06     0.012       1      23 [.     214     238 ..     214     239 .. 0.97

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0019
                      zf-C2H2_4   1 fkCpi..CgksFsskkaLlrHlkth 23 
                                    f C +  C+  F++ ++L+rH + h
  gene203|gene203|rna203|rna203 184 FVCQYknCSSAFKRFEHLKRHYRIH 208
                                    7899999***************998 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 7.4e-06
                      zf-C2H2_4   1 fkCpi..CgksFsskkaLlrHlkth 23 
                                    fkC++  C k F ++++L++Hlk h
  gene203|gene203|rna203|rna203 214 FKCKYpgCFKKFARSDNLSQHLKIH 238
                                    89*********************99 PP

>> FOXP-CC  FOXP coiled-coil domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       3.3   5.3e+03      14      34 ..      10      30 ..       8      33 .. 0.78
   2 ?    6.0   0.1     0.011        18       6      27 ..     185     206 ..     183     211 .. 0.91
   3 !   11.0   0.0   0.00031      0.51       6      28 ..     215     237 ..     213     245 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 3.3
                        FOXP-CC 14 kvledveeflkhlnseHaldd 34
                                   +v++d+ e  k+l++e + +d
  gene203|gene203|rna203|rna203 10 QVFKDLLEIAKKLQNECKEGD 30
                                   688888999999998877666 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.011
                        FOXP-CC   6 vCkWPgCekvledveeflkhln 27 
                                    vC+  +C+++++ +e++ +h +
  gene203|gene203|rna203|rna203 185 VCQYKNCSSAFKRFEHLKRHYR 206
                                    7******************975 PP

  == domain 3  score: 11.0 bits;  conditional E-value: 0.00031
                        FOXP-CC   6 vCkWPgCekvledveeflkhlns 28 
                                     Ck PgC k +  ++++ +hl+ 
  gene203|gene203|rna203|rna203 215 KCKYPGCFKKFARSDNLSQHLKI 237
                                    5*******************974 PP

>> zf-TRAF  TRAF-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   1.5   1.5e-05     0.024       8      60 .]     182     234 ..     179     234 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.5e-05
                                    SEEE-TT--S-BEEET.TTCCCCCCTTSTTS--XXSSXXXXSXXXXXHH.HHHHT CS
                        zf-TRAF   8 apvpCpnecckkkilR.kdlkdHlekdCkkaevkCkfkevGCkekvkre.alqkH 60 
                                     p  C+++ c  +  R ++lk H++    +++ kCk+   GC +k+ r+ +l +H
  gene203|gene203|rna203|rna203 182 RPFVCQYKNCSSAFKRfEHLKRHYRIHTGERPFKCKY--PGCFKKFARSdNLSQH 234
                                    5778****9*9*9*99889******************..***9999875267776 PP

>> zf-C2H2_8  C2H2-type zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   2.9   2.8e-05     0.046      30      89 ..     178     238 ..     155     247 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.8e-05
                      zf-C2H2_8  30 slegklfrcstascaetfpsmqelvahtklhykpnryfkce..ncllrfrthrslfkhlhvc 89 
                                     l  + f c  + c+ +f  ++ l  h ++h   +r fkc+   c+ +f     l +hl++ 
  gene203|gene203|rna203|rna203 178 DLSSRPFVCQYKNCSSAFKRFEHLKRHYRIHT-GERPFKCKypGCFKKFARSDNLSQHLKIH 238
                                    566788************************96.689****8446******999*****9875 PP

>> DREV  DREV methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   1.0   5.3e-05     0.086      76     173 ..      10     107 ..       7     119 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 5.3e-05
                           DREV  76 eqfrkllaiekespasdqedkklldlGaGdGeitkrvaptfeevyatelsetmrdrlkkkkynv.lsalelqetdvkldl 154
                                    + f+ ll i k+  +  +e  ++ dl   + ++  ++ +  +e+y+ e   ++  +l     ++ ls+ e+++ +vk++ 
  gene203|gene203|rna203|rna203  10 QVFKDLLEIAKKLQNECKEGDNVADLNPYNIDLKLKIIKEGNEIYTREEDYNIFIQLFLESIDItLSVEEFAQKKVKFKG 89 
                                    56999******999999*****************************************999997467777********** PP

                           DREV 155 ilclnlldrcfdplklled 173
                                    i  +nl d   d + ll++
  gene203|gene203|rna203|rna203  90 INYVNLSDLK-DEFSLLNE 107
                                    *****99965.56788876 PP

>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.8   3.8e-05     0.062      43      93 .]      10      59 ..       4      59 .. 0.89
   2 ?    0.3   0.3      0.45   7.3e+02      33      78 ..      71     116 ..      68     138 .. 0.45

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.8e-05
                                   --HHHHHHHHHHHHHH.SSSEEEEEETTTS-HHHHHHHHHS-EEEES-SHH CS
                        Polbeta 43 ldleeelelaaelediklgkkvDlvdlneapplllyeilkegkllyskdee 93
                                   + +++ le+a++l++   ++   + dln  +++l+ +i+keg+ +y ++e+
  gene203|gene203|rna203|rna203 10 QVFKDLLEIAKKLQNE-CKEGDNVADLNPYNIDLKLKIIKEGNEIYTREED 59
                                   568999*********9.888999999**999****************9985 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.45
                                    EEEEEEESS-.........--HHHHHHHHHHHHHH.SSSEEEEEETTTS-HHHHH CS
                        Polbeta  33 iDlavllkek.........ldleeelelaaelediklgkkvDlvdlneappllly 78 
                                    iD+ + ++e                   + +l+d+  ++++ l++  + + ++++
  gene203|gene203|rna203|rna203  71 IDITLSVEEFaqkkvkfkgI-------NYVNLSDL--KDEFSLLNEANDEDEIAF 116
                                    56666666663322222221.......22223333..344444442222233333 PP

>> BCNT  Bucentaur or craniofacial development
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.2       2.6   4.2e+03      31      43 ..      12      24 ..       2      31 .. 0.47
   2 ?    8.6   0.2    0.0012       1.9      31      66 ..      92     141 ..      83     147 .. 0.77
   3 ?    2.3   0.0      0.11   1.8e+02      29      51 ..     223     245 ..     221     250 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 2.6
                           BCNT 31 ykdkegikeeLea 43
                                   +kd  +i ++L+ 
  gene203|gene203|rna203|rna203 12 FKDLLEIAKKLQN 24
                                   3333334555555 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0012
                           BCNT  31 ykdkegikeeLeahnkgke..............gYlerqdFLqRvddrke 66 
                                    y++ +++k+e +  n +++              +Yl+++ FL + ++++ 
  gene203|gene203|rna203|rna203  92 YVNLSDLKDEFSLLNEANDedeiafkkiktndlNYLDKKPFLGKNEQKEA 141
                                    566666777777777666666777777777788***********999975 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.11
                           BCNT  29 eaykdkegikeeLeahnkgkegY 51 
                                    +++  + ++++ L+ hn g+++Y
  gene203|gene203|rna203|rna203 223 KKFARSDNLSQHLKIHNTGQGNY 245
                                    67888999***********9999 PP

>> zf_C2H2_ZHX  Zinc-fingers and homeoboxes C2H2 finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.6   0.00025       0.4       5      35 ..     184     215 ..     182     218 .. 0.85
   2 ?   -2.3   0.1       2.3   3.7e+03      18      23 ..     229     234 ..     221     242 .. 0.60

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00025
                    zf_C2H2_ZHX   5 FvCv..eCsfsakkfegLalHNarsHpgetnft 35 
                                    FvC   +Cs   k+fe L+ H  r H+ge  f+
  gene203|gene203|rna203|rna203 184 FVCQykNCSSAFKRFEHLKRH-YRIHTGERPFK 215
                                    7885448**************.79****99887 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 2.3
                    zf_C2H2_ZHX  18 egLalH 23 
                                    ++L++H
  gene203|gene203|rna203|rna203 229 DNLSQH 234
                                    566666 PP

>> zf-C2HE  C2HE / C2H2 / C2HC zinc-binding finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   3.3   0.00044      0.71      24      61 ..     171     208 ..      92     211 .. 0.82
   2 ?    1.3   1.0       0.3   4.8e+02      36      61 ..     212     238 ..     209     240 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00044
                        zf-C2HE  24 lseeqskelilktpLkCtr..CganfgnkfpkLKeHLeee 61 
                                    +++ + + l  ++p+ C +  C+ + ++ f +LK+H   +
  gene203|gene203|rna203|rna203 171 RKKSKGTDL-SSRPFVCQYknCS-SAFKRFEHLKRHYRIH 208
                                    233333335.999****9777**.************6655 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.3
                        zf-C2HE  36 tpLkCtrCganfgnkfp...kLKeHLeee 61 
                                    +p+kC + g   ++kf+   +L +HL+ +
  gene203|gene203|rna203|rna203 212 RPFKCKYPG--CFKKFArsdNLSQHLKIH 238
                                    7999*9988..556665233688898877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1182  (0.0659267); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1772.50
//
Query:       gene2030|gene2030|rna2030|rna2030  [L=50]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (50 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       572  (0.0319036); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.32u 0.26s 00:00:00.58 Elapsed: 00:00:00.38
# Mc/sec: 391.81
//
Query:       gene2031|gene2031|rna2031|rna2031  [L=50]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (50 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       310  (0.0172904); expected 358.6 (0.02)
Passed bias filter:                      240  (0.0133861); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.44
# Mc/sec: 339.08
//
Query:       gene2032|gene2032|rna2032|rna2032  [L=658]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.9e-23   83.0   0.0    1.2e-13   51.5   0.0    2.4  2  AAA_11           AAA domain
    2.4e-18   66.5   2.9    7.7e-18   64.8   2.9    1.9  1  AAA_12           AAA domain
    2.9e-16   59.9   4.3    2.8e-06   27.3   0.2    3.5  3  Viral_helicase1  Viral (Superfamily 1) RNA helicase
    3.3e-09   36.8   0.0    9.1e-09   35.3   0.0    1.8  2  AAA_30           AAA domain
    2.1e-07   31.4   0.0      1e-06   29.1   0.0    2.1  2  AAA_19           AAA domain
    1.1e-06   28.4   0.0    2.8e-06   27.0   0.0    1.7  1  UvrD_C_2         UvrD-like helicase C-terminal domain
    0.00028   20.9   2.2    0.00045   20.3   0.1    2.3  3  ResIII           Type III restriction enzyme, res subunit
    0.00069   19.5   0.0     0.0014   18.5   0.0    1.5  1  Helicase_RecD    Helicase
     0.0044   17.3   0.4       0.28   11.5   0.1    3.1  2  AAA_22           AAA domain
  ------ inclusion threshold ------
      0.015   15.7   0.0      0.077   13.4   0.0    2.1  2  AAA_16           AAA ATPase domain
      0.017   14.4   0.0       0.32   10.2   0.0    2.4  2  DUF2075          Uncharacterized conserved protein (DUF2075)
      0.019   14.4   0.9      0.045   13.1   0.8    1.8  1  UvrD_C           UvrD-like helicase C-terminal domain
      0.022   15.2   0.6        6.7    7.2   0.0    3.5  3  RNA_helicase     RNA helicase
      0.042   13.0   0.1        2.8    7.0   0.1    2.5  2  NB-ARC           NB-ARC domain
       0.11   13.0   0.1       0.84   10.2   0.0    2.5  3  AAA_18           AAA domain
       0.14   12.7   0.0        8.4    6.9   0.0    3.0  2  ABC_tran         ABC transporter


Domain annotation for each model (and alignments):
>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.6   0.0   2.4e-10   2.7e-07       2      96 ..     279     360 ..     278     382 .. 0.78
   2 !   51.5   0.0   1.1e-16   1.2e-13     165     260 ..     354     446 ..     343     447 .. 0.82

  Alignments for each domain:
  == domain 1  score: 30.6 bits;  conditional E-value: 2.4e-10
                             AAA_11   2 lndsqreaiksalseseitliqGPPGtgKTktivellsqllsrrkseeeksakpriLvCapSNaAvDellerllrg 77 
                                        lnd q+ a++++l+++e++ i+G PGtgK+k+i+ l++ l           +++ +L+   +N ++ ++l+rl   
  gene2032|gene2032|rna2032|rna2032 279 LNDGQKIALEKCLTTKEFCSIHGMPGTGKSKVIALLIKIL---------LFHGRSVLLVCYTNLSIFNVLKRLNY- 344
                                        8***************************************.........78899999999999999999999876. PP

                             AAA_11  78 lldsegekykpkivRvgne 96 
                                           s ++  + k  R+ ++
  gene2032|gene2032|rna2032|rna2032 345 ---SYYRAGSFKQERINSK 360
                                        ...4444444444444444 PP

  == domain 2  score: 51.5 bits;  conditional E-value: 1.1e-16
                             AAA_11 165 qerrklkkerkelskeleeaeesleeevldeaeivltTlsgagsklleklakkfdvviIDEAaqavEpstliPlrl 240
                                        qer ++k+  +++ ++ + +++  e +   e + v++T+   + +++++    fd++iIDEA+q   + +liP++ 
  gene2032|gene2032|rna2032|rna2032 354 QERINSKSREDNVFTDKKVHKSVKEWKEYFEQSFVVSTCYNFKDPVFKER--TFDYLIIDEASQQHLLLSLIPISI 427
                                        5555555555555555555555556677888999****************..7*********************99 PP

                             AAA_11 241 gakkvvLvGDpkQLpatvis 260
                                          +k+vLvGDp QL +  +s
  gene2032|gene2032|rna2032|rna2032 428 S-RKFVLVGDPLQLYPLAKS 446
                                        9.*************98876 PP

>> AAA_12  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.8   2.9   6.9e-21   7.7e-18      17     198 ..     459     638 ..     451     639 .. 0.85

  Alignments for each domain:
  == domain 1  score: 64.8 bits;  conditional E-value: 6.9e-21
                             AAA_12  17 vvlLdtqYRmhpeIsrfpsklfYkgkLkdaesvkkreleaqealeepleplvfidvekseeekekke......... 83 
                                        + +L+ qYRm+++I+++++++fY+g+++++ +   + +  ++ +++  +++++ ++ k+++  ++++         
  gene2032|gene2032|rna2032|rna2032 459 TCVLNKQYRMKRSIMQISNEMFYEGRMETDLEGDGEVEL-IDITDHNCKEIAMKNCMKDRTYVNQENrftdgffad 533
                                        578*************************99987777766.666666677788899988888877777788889999 PP

                             AAA_12  84 ..ksyiNeeEaelvvklvekllkkgseeerkkigvitpYraqvellkkklkekeeeksekeievntvdgfQGrekd 157
                                          k+++ ++  ++++k +ek+ + ++e+  ++  +++ ++  ve++++  ++          +v+t+d++QG e d
  gene2032|gene2032|rna2032|rna2032 534 flKKLNGSCGKSMLLKNIEKIAQIIHERYDENTTILCYFNVTVEIVRRIDNR---------YKVSTIDKYQGCESD 600
                                        9899999999999999999999999999889999999999999988765542.........68************* PP

                             AAA_12 158 viilslVRsnekkeigflkderrlNValTRAkskliivGnk 198
                                         +il +       + ++++++ rlNValTR +++lii++++
  gene2032|gene2032|rna2032|rna2032 601 NVILLIYPFV---NNAIMNSRERLNVALTRSRNRLIIICEE 638
                                        9999876553...33579********************975 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.1   0.00068      0.76       3      21 ..     299     317 ..     297     367 .. 0.78
   2 !   23.3   0.0   4.1e-08   4.6e-05      23     100 ..     364     440 ..     348     482 .. 0.82
   3 !   27.3   0.2   2.5e-09   2.8e-06     118     234 .]     501     636 ..     494     636 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00068
                    Viral_helicase1   3 vhGvpGcGKStlirkllrt 21 
                                        +hG+pG GKS++i  l++ 
  gene2032|gene2032|rna2032|rna2032 299 IHGMPGTGKSKVIALLIKI 317
                                        9***********9887765 PP

  == domain 2  score: 23.3 bits;  conditional E-value: 4.1e-08
                    Viral_helicase1  23 liltvnrptaelltegk.pklpnlsvrtvdsflmalvkstkgkililDEylllhaGyill.laalskaklvilfGD 96 
                                         ++ ++++  + ++e+k  ++++  v+t+  f  +  k+ ++++li+DE+ ++h   +ll l+ +s ++ ++l+GD
  gene2032|gene2032|rna2032|rna2032 364 DNVFTDKKVHKSVKEWKeYFEQSFVVSTCYNFKDPVFKERTFDYLIIDEASQQH---LLLsLIPISISRKFVLVGD 436
                                        444556666888999997778888899************99*************...5555*************** PP

                    Viral_helicase1  97 plQi 100
                                        plQ 
  gene2032|gene2032|rna2032|rna2032 437 PLQL 440
                                        ***5 PP

  == domain 3  score: 27.3 bits;  conditional E-value: 2.5e-09
                    Viral_helicase1 118 lshrvgrrttyllpsdvaeilsak.................vgteveversgel.kvetepkgqe.kvlvyltftq 174
                                        ++h  +   ++ + +d++++++++                 +g+++ +++ ++  ++++e ++++ ++l+y   t 
  gene2032|gene2032|rna2032|rna2032 501 TDHNCKEIAMKNCMKDRTYVNQENrftdgffadflkklngsCGKSMLLKNIEKIaQIIHERYDENtTILCYFNVTV 576
                                        5666677777778888888888888888888777744444444444444433335444444444346888888899 PP

                    Viral_helicase1 175 alkealgvr.evttvhevqGltfdkVtlvllketdlelisesrenllvAlTRhrkslvilt 234
                                        + +++   r +v+t    qG + d+V+l++  +  +++i +sre l vAlTR+r++l+i++
  gene2032|gene2032|rna2032|rna2032 577 EIVRRIDNRyKVSTIDKYQGCESDNVILLIY-PFVNNAIMNSRERLNVALTRSRNRLIIIC 636
                                        999988888**********************.7777778889****************985 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.3   0.0   8.1e-12   9.1e-09       2     133 ..     279     445 ..     278     497 .. 0.74
   2 ?   -3.0   0.0       4.5   5.1e+03      30      43 ..     543     556 ..     542     654 .. 0.51

  Alignments for each domain:
  == domain 1  score: 35.3 bits;  conditional E-value: 8.1e-12
                             AAA_30   2 lnaeQaaavealltsgdrvavltGpAGtGKttalkalreaweaaggrviglAptgkaA.kvLa............. 63 
                                        ln++Q+ a+e+ lt+++ ++ ++G +GtGK+ +++ l +++  +g++v+++  t+    +vL+             
  gene2032|gene2032|rna2032|rna2032 279 LNDGQKIALEKCLTTKE-FCSIHGMPGTGKSKVIALLIKILLFHGRSVLLVCYTNLSIfNVLKrlnysyyragsfk 353
                                        99**************7.*******************************999998654155666667777777776 PP

                             AAA_30  64 .........eelgieastiakllkrlk.................grarlepg.tllivDEagmvdtkqlaallkaa 112
                                                 e+  ++ + ++k +k++k                   +  e+  + li+DEa+    + l +l+ + 
  gene2032|gene2032|rna2032|rna2032 354 qerinsksrEDNVFTDKKVHKSVKEWKeyfeqsfvvstcynfkdP-VFKERTfDYLIIDEASQQ--HLLLSLIPIS 426
                                        655555444344467778888888888***************973.2334446********975..4455555544 PP

                             AAA_30 113 ekagakvilvGDerQlasVea 133
                                           + k +lvGD+ Ql +  +
  gene2032|gene2032|rna2032|rna2032 427 I--SRKFVLVGDPLQLYPLAK 445
                                        3..379**********98766 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 4.5
                             AAA_30  30 GKttalkalreawe 43 
                                        GK+++lk ++++++
  gene2032|gene2032|rna2032|rna2032 543 GKSMLLKNIEKIAQ 556
                                        66666666554443 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1   0.0   9.3e-10     1e-06       7     142 ..     291     441 ..     283     445 .. 0.70
   2 ?   -1.2   0.0       2.1   2.3e+03      22     122 ..     543     651 ..     540     656 .. 0.42

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 9.3e-10
                             AAA_19   7 alkekvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerlaalgaeatTiHrlal..... 77 
                                         ++++ + + + pGtGK++v+   +++l+  g    +++llv++t+ +  ++ +rl+    +a  + +  +     
  gene2032|gene2032|rna2032|rna2032 291 LTTKEFCSIHGMPGTGKSKVIALLIKILLFHG----RSVLLVCYTNLSIFNVLKRLNYSYYRAGSFKQERInsksr 362
                                        56778899*********************999....89******************77777766665443355666 PP

                             AAA_19  78 .......ldfddlltealelle........eaeeekklqeee..llivDEfqdvdelqyrLlkallgek.kklllv 135
                                                ++++ ++e+ e++e        ++ ++  ++e++  +li+DE+++   l  +L+         k++lv
  gene2032|gene2032|rna2032|rna2032 363 ednvftdKKVHKSVKEWKEYFEqsfvvstcYNFKDPVFKERTfdYLIIDEASQQH-LLLSLIPIS---IsRKFVLV 434
                                        66666554444555555555557777778743444444444348*******9643.334444444...3456**** PP

                             AAA_19 136 GDpdQli 142
                                        GDp Ql 
  gene2032|gene2032|rna2032|rna2032 435 GDPLQLY 441
                                        *****86 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 2.1
                             AAA_19  22 GKTrvlkhivallvelggvkpeeillvaftgrAakelrerlaalgaeatTiHrlalldfddlltealelle..... 92 
                                        GK+ +lk i ++++ ++++  e+ +++++ +  ++ +r r+     + +Ti +    + d+ +     +++     
  gene2032|gene2032|rna2032|rna2032 543 GKSMLLKNIEKIAQIIHERYDENTTILCYFNVTVEIVR-RI-DNRYKVSTIDKYQGCESDNVILLIYPFVNnaimn 616
                                        66666666555555555554455555544433332222.22.2233455555554444444444444444444444 PP

                             AAA_19  93 .....eaeeekklqeee..llivDEfqdvd.elqyrLl 122
                                             +       ++++  ++i  E  + + el  +Ll
  gene2032|gene2032|rna2032|rna2032 617 srerlN---VALTRSRNrlIIICEENEMKNvELFAALL 651
                                        432221...11111222214444555555566666665 PP

>> UvrD_C_2  UvrD-like helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   0.0   2.5e-09   2.8e-06       4      52 .]     588     635 ..     587     635 .. 0.94

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 2.5e-09
                           UvrD_C_2   4 altihkaQGsefpaVivfdpdlaaarmgelrrrlLYtavTRAreklilv 52 
                                        ++ti k QG e ++Vi+    + +    + +r+ L +a+TR+r +li++
  gene2032|gene2032|rna2032|rna2032 588 VSTIDKYQGCESDNVILLIYPFVNNA-IMNSRERLNVALTRSRNRLIII 635
                                        68***************9999***99.667*****************96 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.1       2.8   3.2e+03     103     118 ..     136     151 ..      83     215 .. 0.60
   2 !   20.3   0.1     4e-07   0.00045       3     141 ..     278     413 ..     276     417 .. 0.75
   3 ?   -1.6   0.0         2   2.3e+03      37      79 ..     544     591 ..     513     639 .. 0.58

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 2.8
                                        .-SEEEEEHHHHHHTH CS
                             ResIII 103 nkkilvttiqsldads 118
                                        + k+lvtt + +++  
  gene2032|gene2032|rna2032|rna2032 136 DEKVLVTTAEIISRTD 151
                                        3444444444444444 PP

  == domain 2  score: 20.3 bits;  conditional E-value: 4e-07
                                        EE-HHHHHHHHHHT......TTSEEE.EEESTTSTHHHHHHHHHHHH-S.....-EEEEESSH....HHHHHHHHH CS
                             ResIII   3 elreyQeeaienlleklkskrdkrgl.ikmaTGtGKTlvaaklierllkkgkeekflflvprk....slleqtlee 73 
                                        +l++ Q+ a+e+ l        k+++ i+   GtGK+ v+a li+ ll +g+   +l+++ ++    ++l+++   
  gene2032|gene2032|rna2032|rna2032 278 SLNDGQKIALEKCL------TTKEFCsIHGMPGTGKSKVIALLIKILLFHGR--SVLLVCYTNlsifNVLKRLNYS 345
                                        67888888888887......3455555********************98766..9*****9998888888888877 PP

                                        GGGGTGG....GEEEESSS-B--..........-SEEEEEHHHHHHTH........HHHTTT-SEEEEETG CS
                             ResIII  74 fkkflseaykeigkkvsgdkkka...kekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEa 141
                                        + +  s ++++i+ k ++d+       +k+ +++k ++++   ++      + ++  +++ +fd++iiDEa
  gene2032|gene2032|rna2032|rna2032 346 YYRAGSFKQERINSKSREDNVFTdkkVHKSVKEWKEYFEQSFVVSTCY---NFKDPVFKERTFDYLIIDEA 413
                                        766666666665555555555555443356677777777776666666...6677779999*********8 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 2
                                        HHHHH..HHHHHHH-S.....-EEEEESSH...HHHHHHHHHGGGGTG CS
                             ResIII  37 KTlva..aklierllkkgkeekflflvprk...slleqtleefkkfls 79 
                                        K++++  ++ i+++ ++++ e++ +l+  +   +++ +  +++k  + 
  gene2032|gene2032|rna2032|rna2032 544 KSMLLknIEKIAQIIHERYDENTTILCYFNvtvEIVRRIDNRYKVSTI 591
                                        444443334444444444444444444322222344444444433333 PP

>> Helicase_RecD  Helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   1.3e-06    0.0014       2     101 ..     299     415 ..     298     429 .. 0.68

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.3e-06
                      Helicase_RecD   2 ltAdRGRGKSaalGlalaaliaegksnilvtapskenvktlfeflakglealglke......eekkkkaekaelrv 71 
                                        + + +G+GKS +++l+++ l+ +g+s +lv+ ++ +  + l +   +  +a ++k+      +      ++ ++ +
  gene2032|gene2032|rna2032|rna2032 299 IHGMPGTGKSKVIALLIKILLFHGRSVLLVCYTNLSIFNVLKRLNYSYYRAGSFKQerinskS------REDNVFT 368
                                        67889********************98888888888888777777777888888776554331......2222222 PP

                      Helicase_RecD  72 r.......kqrieyiapdellklkeqa..........dllvvDEAAa 101
                                        +       k+  ey++ + +++++ +           d l++DEA++
  gene2032|gene2032|rna2032|rna2032 369 DkkvhksvKEWKEYFEQSFVVSTCYNFkdpvfkertfDYLIIDEASQ 415
                                        2244555644444555554444443335555555555********97 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.1   0.00025      0.28       4      51 ..     293     334 ..     290     443 .. 0.79
   2 ?    2.3   0.0      0.17   1.9e+02      16      47 ..     542     574 ..     541     652 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00025
                             AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst 51 
                                        t+ ++ ++G +GtGK+ +++ l + l        ++++v++v+ ++++
  gene2032|gene2032|rna2032|rna2032 293 TKEFCSIHGMPGTGKSKVIALLIKILLF------HGRSVLLVCYTNLS 334
                                        678999***************9998853......47777777776665 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.17
                             AAA_22  16 tGKTtllrrlleqldeeakaee.erpevv..fvtl 47 
                                        +GK++ll+++ + ++  + +e+  + +++  ++++
  gene2032|gene2032|rna2032|rna2032 542 CGKSMLLKNIEKIAQ--IIHERyDENTTIlcYFNV 574
                                        7*********99984..455555444444234433 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   6.9e-05     0.077      25      50 ..     295     320 ..     284     370 .. 0.81
   2 ?   -1.1   0.0         2   2.2e+03      34      63 ..     541     565 ..     539     588 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 6.9e-05
                             AAA_16  25 elvllsGesGvGKsslvrellralek 50 
                                        e + ++G++G+GKs+++  l + l  
  gene2032|gene2032|rna2032|rna2032 295 EFCSIHGMPGTGKSKVIALLIKILLF 320
                                        7899*************999886655 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 2
                             AAA_16  34 GvGKsslvrellralekdggiflrgkcdql 63 
                                         +GKs l++ + + + +     + +++d++
  gene2032|gene2032|rna2032|rna2032 541 SCGKSMLLKNIEK-IAQI----IHERYDEN 565
                                        69******88885.3333....56666666 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00028      0.32       2      97 ..     295     413 ..     294     429 .. 0.63
   2 ?    1.4   0.1      0.13   1.5e+02     342     362 ..     617     637 ..     610     638 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00028
                            DUF2075   2 avvlVtGvaGtGKtvvllnllael................eddeeertavylsvNhp.lvlvlrealakke..ekk 58 
                                        + + ++G +GtGK+ v   l+  l                  + ++r +   ++ ++  ++ + ++ ++++  ++k
  gene2032|gene2032|rna2032|rna2032 295 EFCSIHGMPGTGKSKVIALLIKILlfhgrsvllvcytnlsIFNVLKRLNYSYYRAGSfKQERINSKSREDNvfTDK 370
                                        6789**********77655555445767777777766665222233333333333330344555555555566667 PP

                            DUF2075  59 kkkeafeklssfinnlsef....kkaeekkeepkedvvivDEA 97 
                                        k  +++++ +++ ++        + +    +e+++d +i+DEA
  gene2032|gene2032|rna2032|rna2032 371 KVHKSVKEWKEYFEQSFVVstcyNFKDPVFKERTFDYLIIDEA 413
                                        7777777777766665433666666666778999999999999 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.13
                            DUF2075 342 lkNayrVLLtRGrkGlyiyae 362
                                         + +++V LtR r+ l+i +e
  gene2032|gene2032|rna2032|rna2032 617 SRERLNVALTRSRNRLIIICE 637
                                        5789**************997 PP

>> UvrD_C  UvrD-like helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.8   4.1e-05     0.045     237     348 ..     547     638 ..     325     639 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.1e-05
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             UvrD_C 237 klenlreLysllkelekkeeeeeveeklneileiatLseseleeskkkekipiiTiHqAKGlEFdvVflagleegt 312
                                         l+n++++ +++ e  +  e++     l  ++ +  +    +      ++ +++Ti +  G+E d+V+l+      
  gene2032|gene2032|rna2032|rna2032 547 LLKNIEKIAQIIHERYD--ENTT---ILCYFNVTVEIVRRID------NRYKVSTIDKYQGCESDNVILLI----- 606
                                        67777777777777777..3322...2566666665555444......88899*****************8..... PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             UvrD_C 313 fPsyrskkekrleEEkRlfYVaiTRAkkrLfisysk 348
                                        +P + ++   +    +  + Va+TR ++rL+i++ +
  gene2032|gene2032|rna2032|rna2032 607 YP-FVNNAIMNS---RERLNVALTRSRNRLIIICEE 638
                                        **.666666444...44577************9876 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.1       2.6   2.9e+03      34      93 ..     121     174 ..     101     182 .. 0.68
   2 ?    7.2   0.0    0.0059       6.7       3      25 ..     299     321 ..     297     389 .. 0.83
   3 ?    4.1   0.0     0.052        58       9      80 ..     542     613 ..     539     632 .. 0.72

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 2.6
                       RNA_helicase  34 vys.rnpeddfwdgYtgqevvvidDfgqvkdeenpsdlaelirlvsstpyplnmasleekg 93 
                                        + +  ++++ f++ Y+++  v   ++ +++d+        ++rl   ++++l+   +eek 
  gene2032|gene2032|rna2032|rna2032 121 CNAfDASDNAFVNIYDEKVLVTTAEIISRTDS-------LKLRLNHYYNFKLKNIYIEEKS 174
                                        44445566666677777777777777766666.......7788888888888888888875 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0059
                       RNA_helicase   3 lyGpsgeGKStlakeLakallkk 25 
                                        ++G +g+GKS ++  L+k ll +
  gene2032|gene2032|rna2032|rna2032 299 IHGMPGTGKSKVIALLIKILLFH 321
                                        89***************999844 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.052
                       RNA_helicase   9 eGKStlakeLakallkkl..klkkkdsvys.rnpeddfwdgYt.gqevvvidDfgqvkdeenpsdlaelirlvsst 80 
                                        +GKS+l k+ ++++++ +   ++++ ++ +  n++ +++   + + +v  id    ++++   + +  +   v+++
  gene2032|gene2032|rna2032|rna2032 542 CGKSMLLKN-IEKIAQIIheRYDENTTILCyFNVTVEIVRRIDnRYKVSTIDKYQGCESD---NVILLIYPFVNNA 613
                                        9*******9.67777555443444445555579999999999977788888888888777...6666665555554 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.1    0.0025       2.8      15      37 ..     289     311 ..     282     318 .. 0.78
   2 ?    3.2   0.0     0.039        43      29      57 ..     540     568 ..     538     632 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0025
                                        TTTSCSEEEEEEESTTSSHHHHH CS
                             NB-ARC  15 kdelqslvvalvGmgGvGKttla 37 
                                        k+   + + +++Gm+G GK+ ++
  gene2032|gene2032|rna2032|rna2032 289 KCLTTKEFCSIHGMPGTGKSKVI 311
                                        555566799**********9654 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.039
                                        TTSSHHHHHHHHCCSHCCCCCCBTEEEEE CS
                             NB-ARC  29 gGvGKttlakqilnksdevegrFdsvawv 57 
                                        g +GK+ l+k+i +  + +++r+d    +
  gene2032|gene2032|rna2032|rna2032 540 GSCGKSMLLKNIEKIAQIIHERYDENTTI 568
                                        669*********999666666**965544 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00075      0.84       3      70 ..     299     401 ..     298     441 .. 0.58
   2 ?   -1.6   0.0       3.4   3.8e+03      26      68 ..     474     517 ..     461     542 .. 0.63
   3 ?   -2.0   0.0       4.5     5e+03       9      54 ..     542     584 ..     540     632 .. 0.58

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00075
                             AAA_18   3 ltGtpGvGKttlakeLskrlgf...........gvnlrdvakenglllevdpe.........aldeskrldedkld 58 
                                        + G+pG+GK+ +   L k l f              +++++ ++  + ++ +          + +e +++ ++k++
  gene2032|gene2032|rna2032|rna2032 299 IHGMPGTGKSKVIALLIKILLFhgrsvllvcytN-LSIFNVLKRLNYSYYRAGsfkqerinsKSREDNVFTDKKVH 373
                                        67**************888755766666666642.22333333333333333335556666666666666666655 PP

                             AAA_18  59 klldaleenss................a 70 
                                        k +++++e  +                +
  gene2032|gene2032|rna2032|rna2032 374 KSVKEWKEYFEqsfvvstcynfkdpvfK 401
                                        5555444444355555555555555554 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 3.4
                             AAA_18  26 vnlrdvakenglllevdpe.aldeskrldedkldklldaleens 68 
                                        ++++++++e++++++ + + +++  ++ d +  + ++++ ++ +
  gene2032|gene2032|rna2032|rna2032 474 QISNEMFYEGRMETDLEGDgEVELIDITDHNCKEIAMKNCMKDR 517
                                        56777788888887777777555555555555555555555543 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 4.5
                             AAA_18   9 vGKttlakeLskrlgfgvnlrdvakenglllevdpealdeskrlde 54 
                                        +GK+ l k+++k     +++ +   en + l++++  ++  +r+d 
  gene2032|gene2032|rna2032|rna2032 542 CGKSMLLKNIEKIA---QIIHERYDENTTILCYFNVTVEIVRRIDN 584
                                        68888888887764...33333333334444444443444444444 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.0    0.0075       8.4       8      35 ..     291     318 ..     286     397 .. 0.86
   2 ?    2.2   0.0      0.22   2.4e+02      22      37 ..     542     557 ..     538     590 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0075
                                        EETTSEEEEEESTTSSHHHHHHHHTTSS CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ABC_tran   8 lkegekvaivGenGaGKStLlkllagll 35 
                                        l   e   i G  G+GKS +++ll++ l
  gene2032|gene2032|rna2032|rna2032 291 LTTKEFCSIHGMPGTGKSKVIALLIKIL 318
                                        56678899***************99865 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.22
                                        SSHHHHHHHHTTSS-- CS
                                        xxxxxxxxxxxxxxxx RF
                           ABC_tran  22 aGKStLlkllagllkp 37 
                                        +GKS Llk + +  + 
  gene2032|gene2032|rna2032|rna2032 542 CGKSMLLKNIEKIAQI 557
                                        8********9987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (658 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       925  (0.0515924); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.71u 0.34s 00:00:01.05 Elapsed: 00:00:00.52
# Mc/sec: 3807.07
//
Query:       gene2033|gene2033|rna2033|rna2033  [L=428]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-10   41.2   0.3    2.8e-09   37.1   0.1    2.7  2  Dna2      DNA replication factor Dna2
  ------ inclusion threshold ------
      0.019   14.9   0.1       0.21   11.5   0.1    2.1  1  PDDEXK_1  PD-(D/E)XK nuclease superfamily


Domain annotation for each model (and alignments):
>> Dna2  DNA replication factor Dna2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.1   0.1   3.2e-13   2.8e-09       5     158 ..     128     303 ..     126     309 .. 0.82
   2 ?    1.5   0.0     0.024   2.2e+02     182     200 ..     302     320 ..     300     322 .. 0.92

  Alignments for each domain:
  == domain 1  score: 37.1 bits;  conditional E-value: 3.2e-13
                               Dna2   5 eekktvvLrddWaetsvekgdiihi.........................vgkfeeek.............iiidn 42 
                                        ++   v+L ++W + ++ +g+ i+i                                +             ++i+n
  gene2033|gene2033|rna2033|rna2033 128 GDDTVVYLYGEWDHEMYAPGMCIRIiecrccstnatniyenclaqnkiavC------AslsktkddsakkvFTITN 197
                                        567789*******************77776666666665555555555550......0555555566667788888 PP

                               Dna2  43 esnllIlhPdlLvsaTsvanslsClRravLqerlkvsge..sskamliGtilHelfqkalleeeldkekleelldk 116
                                        ++++l l     +s T + + ++C  + + +er+++ +     + +++G+++H ++q+ +            ++d 
  gene2033|gene2033|rna2033|rna2033 198 TNKYLLLVETPTLSVTNLISGMECALQPLFNERIESLNFlyDDRRVILGKLFHVMLQRDI------------TIDA 261
                                        8886666666667*********************88877679999************988............589* PP

                               Dna2 117 lleknleelyalglteeeakeeikekleeiekwakkyvkksn 158
                                        ll+++  ely+ +lte+eak++i + l++i ++ kk+  k++
  gene2033|gene2033|rna2033|rna2033 262 LLNEHSLELYTSNLTENEAKKRILDDLPKIINFRKKICGKNE 303
                                        ************************************998876 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.024
                               Dna2 182 iEEniwspkyGLKGkiDat 200
                                         EE i s  + +KG iD++
  gene2033|gene2033|rna2033|rna2033 302 NEEYIYSALLQMKGIIDIV 320
                                        6****************86 PP

>> PDDEXK_1  PD-(D/E)XK nuclease superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   2.3e-05      0.21       1     176 [.     209     346 ..     209     358 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 2.3e-05
                           PDDEXK_1   1 rlSvsrletfleCplrfflr.yllglreeeeleapdlGtlvHaaleefyewkkldkedleelleeaveelwpelll 75 
                                        +lSv+ l   +eC+l+  ++ +++ l+  ++ ++  lG l+H +l++            ++ll+e+  el  + l 
  gene2033|gene2033|rna2033|rna2033 209 TLSVTNLISGMECALQPLFNeRIESLNFLYDDRRVILGKLFHVMLQRDIT--------IDALLNEHSLELYTSNLT 276
                                        58999999999999986654145555446666666999999999985554........555554333333333222 PP

                           PDDEXK_1  76 eeeilessarlrylaeklkevleklverlaeeleakrgfrpvalelefggekvrLkGriDrvddkegelriiDyKt 151
                                        e          +  +++  + l k ++  ++   +++++++ al        +++kG+iD vd  +g   ii+ Kt
  gene2033|gene2033|rna2033|rna2033 277 E----------NEAKKRILDDLPKIINFRKKICGKNEEYIYSAL--------LQMKGIIDIVD--NG---IIEIKT 329
                                        2..........222333333333332222222223333222222........5699*****98..78...9***** PP

                           PDDEXK_1 152 gsappkskelaelkeglQlllYlla 176
                                        g+ ++k+ +        Q+llY l+
  gene2033|gene2033|rna2033|rna2033 330 GNFNTKDVA--------QVLLYYLV 346
                                        996555555........88888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (428 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       856  (0.0477439); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 2627.68
//
Query:       gene2034|gene2034|rna2034|rna2034  [L=196]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.3e-27   95.5   0.0    2.2e-26   93.1   0.0    1.8  1  Glucosamine_iso  Glucosamine-6-phosphate isomerases/6-phospho
  ------ inclusion threshold ------
      0.062   13.4   0.0      0.097   12.8   0.0    1.3  1  SKI              Shikimate kinase


Domain annotation for each model (and alignments):
>> Glucosamine_iso  Glucosamine-6-phosphate isomerases/6-phosphogluconolactonase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.1   0.0   2.5e-30   2.2e-26      19     192 ..      15     165 ..       3     181 .. 0.77

  Alignments for each domain:
  == domain 1  score: 93.1 bits;  conditional E-value: 2.5e-30
                                        HHHHH..HHS-EEEEE--SHCHHHHHHHHHCSG.GGGGS-GGGEEEEESEEESS-TTSTT-HHHHHHHHTGGGS-- CS
                    Glucosamine_iso  19 eeala..ergraslalsGGstpkalyealaeeeeaaaaldwskvhvflgDERfVpaddpdsNaklareallskvki 92 
                                        +++l+  + + a+++++GGs+ k l +a  +      +++ +k++v+++DER+ ++  +d N+ +  + +l++  +
  gene2034|gene2034|rna2034|rna2034  15 HQILKeyDGKAANIVIAGGSLLKLLDNADFT------KMKTDKWNVYYADERITNTV-QDLNHYQ-SQIFLQH--V 80 
                                        33333114578*********98877665442......5899***********98555.5555554.4678887..3 PP

                                        -GGGEE-S-TTSSTHHHHHHHHHHHHHHHHCCSSSSSESEEEE---TTS-BTTB-TTCHHHHCSSSSEEEESSBST CS
                    Glucosamine_iso  93 peanvhpikesaaeapeaaaaayeeelkellakelpvfDlvlLGmGpDGHtaSLFPgspeleetdrlvvavedspk 168
                                        +++  + i        e+  + ye+   e      +++Dl+lLG+G+DGH+aSLFPg++ l ++++ ++ +edspk
  gene2034|gene2034|rna2034|rna2034  81 EAKATLLI--------EQNIHLYEKLFDE------KTIDLALLGIGEDGHIASLFPGKKSL-DSNDYICYIEDSPK 141
                                        33344444........678999*999997......67***********************6.66688999****** PP

                                        SSS-EEEE-HHHHTTCSEEEEEEE CS
                    Glucosamine_iso 169 pppeRitlTlpvlnsarevlflva 192
                                        ppp R+tlT+++ln+ r+++f++ 
  gene2034|gene2034|rna2034|rna2034 142 PPPCRLTLTIRALNKVRNLYFFIP 165
                                        *********************985 PP

>> SKI  Shikimate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   1.1e-05     0.097      42     134 ..       5      98 ..       1     108 [. 0.80

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.1e-05
                                        HHHHHHHHHHHHHHHHHCCCSSEEEEE-TTGGGSHHHHHHHH...HHSEEEEEE--HHHHHHHHHHTTSSGGGCSC CS
                                SKI  42 egeegFrelEsevlkelleeeglViatGGGavlseenrellk...ekgiviyLdvsleellerlkadkeRPllqek 114
                                        +  ++Fr+  +++lke+  +   ++  GG+     +n ++ k   +k  v y d  ++++++ l++ ++ ++lq+ 
  gene2034|gene2034|rna2034|rna2034   5 KHTSNFRDVIHQILKEYDGKAANIVIAGGSLLKLLDNADFTKmktDKWNVYYADERITNTVQDLNHYQSQIFLQHV 80 
                                        56789************9999777777899888888888888777788899***********************99 PP

                                        HHHHHHHHHHHHHHHHHCCS CS
                                SKI 115 skeeelleelaereplyeea 134
                                        +   + +  +++  +lye++
  gene2034|gene2034|rna2034|rna2034  81 EA--KATLLIEQNIHLYEKL 98 
                                        99..3333333567888883 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       709  (0.0395449); expected 358.6 (0.02)
Passed bias filter:                      523  (0.0291706); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1257.14
//
Query:       gene2035|gene2035|rna2035|rna2035  [L=75]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-05   24.2   0.0    2.1e-05   24.2   0.0    1.1  1  dUTPase   dUTPase


Domain annotation for each model (and alignments):
>> dUTPase  dUTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.0   1.2e-09   2.1e-05      37     106 ..       4      73 ..       1      75 [] 0.79

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 1.2e-09
                                        EEEEE--TTEEEEEEE-HHHHH.HHEEEEEEEEETTBTS...EEEEEEEE-SSS-EEE-TT-EEEEEEEEEBEC CS
                            dUTPase  37 disiklpdglaalilpRSglaa.kglivvpgvidsdyrG...evkvvlfnltkkdvkikkgdRiAqLifarilt 106
                                        + +i+lp+++   +  RSgla+ kgl vv+    + y G   ev v + n++++  +  kgdRi q++f ++lt
  gene2035|gene2035|rna2035|rna2035   4 GFKIDLPEDVLINLYMRSGLALrKGLSVVG---KRIY-GsneEVCVEIRNYSEEVYRASKGDRIVQMVFHEVLT 73 
                                        5677888888888999*****725666666...3333.3355899************************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       349  (0.0194657); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 586.49
//
Query:       gene2036|gene2036|rna2036|rna2036  [L=62]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
      0.019   14.4   0.6      0.021   14.3   0.6    1.0  1  V-ATPase_C  V-ATPase subunit C
      0.031   13.8   0.0      0.031   13.8   0.0    1.0  1  DUF3087     Protein of unknown function (DUF3087)


Domain annotation for each model (and alignments):
>> V-ATPase_C  V-ATPase subunit C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.6   2.3e-06     0.021      91     146 ..       3      59 ..       1      61 [. 0.89

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.3e-06
                         V-ATPase_C  91 ng.kslesYltkFqWdeakypvkqslkelvdiiskevtqidedlktksaaYnelkss 146
                                        n+ + l+++  kF++ ++ y+++q+l +++d +  + +++ ++lk+   +Y   k+s
  gene2036|gene2036|rna2036|rna2036   3 NDyQALRKFAFKFKFKRKGYKMDQNLIDICDELVIRYAKVRKKLKKYRIRYDPEKTS 59 
                                        55478999**************************************99999877765 PP

>> DUF3087  Protein of unknown function (DUF3087)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   3.4e-06     0.031     105     159 ..       2      57 ..       1      62 [] 0.89

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.4e-06
                            DUF3087 105 egdenAlkilrFyyqglkqlyqLddNtltl.selekeieqlkelieelgltleaed 159
                                        ++d +Al+   F ++ +++ y++d+N + + +el    +++++++++++++ + e+
  gene2036|gene2036|rna2036|rna2036   2 ANDYQALRKFAFKFKFKRKGYKMDQNLIDIcDELVIRYAKVRKKLKKYRIRYDPEK 57 
                                        689*************************974789999******9999999888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (62 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       831  (0.0463495); expected 358.6 (0.02)
Passed bias filter:                      453  (0.0252663); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.35u 0.26s 00:00:00.61 Elapsed: 00:00:00.41
# Mc/sec: 455.66
//
Query:       gene2037|gene2037|rna2037|rna2037  [L=153]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       882  (0.049194); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1057.52
//
Query:       gene2038|gene2038|rna2038|rna2038  [L=271]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    7.3e-09   36.2   0.0    3.2e-06   27.6   0.0    2.2  1  Hydrolase  haloacid dehalogenase-like hydrolase
      1e-07   32.2   0.2    1.6e-07   31.5   0.2    1.3  1  HAD_2      Haloacid dehalogenase-like hydrolase
     0.0055   16.2   0.5       0.46    9.9   0.0    2.5  2  DUF2608    Protein of unknown function (DUF2608)


Domain annotation for each model (and alignments):
>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   0.0   5.4e-10   3.2e-06       3     205 ..      53     224 ..      51     229 .. 0.72

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 5.4e-10
                                        EEEEESBTTTBCHHHHHHHHHHHHCHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHETTTE..HHHHTHHHH CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxx RF
                          Hydrolase   3 tvvfDkdGTLttgepsvedvivsaalalaaaletgsehpigkalvaaakarsgaltgfatfigrg..ayaigkpew 76 
                                        ++v D+d+TL++ +  ved+i++                    lv++   ++ + ++  + + r   +y       
  gene2038|gene2038|rna2038|rna2038  53 LIVCDIDNTLYHPSAGVEDLIDKK-------------------LVEYLTTVTSSQEEALACKNRYddVYGLTVYGA 109
                                        79**********************...................555555553333333333333333666666666 PP

                                        HHHHHCHHHHHHHHHHHHHHCHHHHHHTTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHH CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          Hydrolase  77 ltaldippdlgaaigsaqsqgrtvallqaralavftiadplkvkpeaaeavasLkaagievvlltgdnpetaeraa 152
                                        l++l       +   +  s+  t  ++    ++++  +dp      +++++++L  +    + lt+++   a+ ++
  gene2038|gene2038|rna2038|rna2038 110 LAEL-------DVELDFYSKYITKTIN----YEEYLKKDP-----VLRDVLNRLDCR---KICLTNGDTIQAKGIL 166
                                        6666.......1111223333333333....344444444.....555667777755...55************** PP

                                        HHTT.GGGESEEEEHHCES...STTTSHHHHHHHHHHHTST.GGGEEEEESSHHHHHH CS
                                        xxxx.xxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx RF
                          Hydrolase 153 nqlG.ddyfdaviasdiet...vakpspegkvaaireLqgk.peevamVGDgvnDaaa 205
                                        + lG  ++f+av+++d  +   + kp +e ++ + + ++++ p++v++++D++  ++ 
  gene2038|gene2038|rna2038|rna2038 167 DALGlTECFEAVVTIDAAVpffIHKPTKESYQFVDELFGVSsPKNVLFFDDNIKNIEQ 224
                                        *********99999999999*******************555***********98875 PP

>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.5   0.2   2.8e-11   1.6e-07       1     170 [.      54     227 ..      54     232 .. 0.76

  Alignments for each domain:
  == domain 1  score: 31.5 bits;  conditional E-value: 2.8e-11
                              HAD_2   1 iiFDlDgTlldteeliiqafnelleey........gls.elseeelrkliglslrellrklgeseeeeekieellr 67 
                                        i+ D+D+Tl+  +  + + + + l ey        + +    ++ ++ ++gl+   +l +l ++ +    + +++ 
  gene2038|gene2038|rna2038|rna2038  54 IVCDIDNTLYHPSAGVEDLIDKKLVEYlttvtssqE-EaLACKNRYDDVYGLTVYGALAELDVELD---FYSKYIT 125
                                        56799***********99999999999444444321.11233444566777777777777777655...5666644 PP

                              HAD_2  68 kyneekkkkevkpydgvkelLeeLkeagyklgivTsksreaveekleqlgiesyFdvivtsed...vekkKPdpev 140
                                        k  +  +++++k  + ++++L+ L  +++   + T++++ +++  l++lg+++ F+ +vt +    ++ +KP  e+
  gene2038|gene2038|rna2038|rna2038 126 KTIN--YEEYLKKDPVLRDVLNRLDCRKI---CLTNGDTIQAKGILDALGLTECFEAVVTIDAavpFFIHKPTKES 196
                                        4443..33669999**********66555...77*************************98862226789****** PP

                              HAD_2 141 iekaleklklk.keeviyvGDsptDieaakk 170
                                        ++ + e ++++ +++v+++ D+++ ie a +
  gene2038|gene2038|rna2038|rna2038 197 YQFVDELFGVSsPKNVLFFDDNIKNIEQALA 227
                                        ********9853899***********98865 PP

>> DUF2608  Protein of unknown function (DUF2608)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.0   7.7e-05      0.46       9      34 ..      42      67 ..      29     120 .. 0.70
   2 !    4.1   0.1    0.0045        27     179     200 ..     208     226 ..     204     236 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 7.7e-05
                            DUF2608  9 anaiekadentLvvfDiDdtLltste 34
                                       ++ i+   ++tL+v DiD+tL  +  
  gene2038|gene2038|rna2038|rna2038 42 KQIITPLGNETLIVCDIDNTLYHPSA 67
                                       4455555789***********98753 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.0045
                            DUF2608 179 epksviFiDDkkknlasveeal 200
                                        +pk+v+F DD+ kn+   e+al
  gene2038|gene2038|rna2038|rna2038 208 SPKNVLFFDDNIKNI---EQAL 226
                                        79*******966665...5555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (271 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       517  (0.028836); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.63u 0.33s 00:00:00.96 Elapsed: 00:00:00.54
# Mc/sec: 1503.70
//
Query:       gene2039|gene2039|rna2039|rna2039  [L=232]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.2e-08   33.3  11.0    7.2e-08   32.2  11.0    1.6  1  zf-C3HC4_2       Zinc finger, C3HC4 type (RING finger)
    3.6e-08   33.6  10.2    7.2e-08   32.6  10.2    1.5  1  zf-RING_2        Ring finger domain
    6.5e-07   29.5  11.7    3.1e-06   27.4  11.7    2.1  1  zf-rbx1          RING-H2 zinc finger domain
    1.4e-06   27.9   5.5    3.7e-06   26.6   5.5    1.8  1  zf-RING_11       RING-like zinc finger
    1.4e-05   24.9  11.3    3.4e-05   23.6  11.3    1.7  1  zf-C3HC4         Zinc finger, C3HC4 type (RING finger)
    0.00028   20.8   9.5    0.00094   19.2   9.4    2.0  2  zf-RING_UBOX     RING-type zinc-finger
     0.0091   15.6   7.9      0.017   14.7   7.9    1.4  1  Zn_ribbon_17     Zinc-ribbon, C4HC2 type
  ------ inclusion threshold ------
      0.011   15.7  13.6      0.021   14.8  13.6    1.5  1  zf-RING_5        zinc-RING finger domain
      0.012   15.4  11.0      0.012   15.4  11.0    1.7  2  zf-C3HC4_3       Zinc finger, C3HC4 type (RING finger)
      0.018   15.1   8.9      0.067   13.2   9.0    1.9  2  zf-ANAPC11       Anaphase-promoting complex subunit 11 RING-H
      0.019   15.0   6.3      0.039   14.0   6.3    1.6  1  zf-C3H2C3        Zinc-finger
      0.042   14.2   0.5      0.042   14.2   0.5    2.3  2  C1_2             C1 domain
       0.22   11.4   7.8       0.49   10.2   7.8    1.6  1  zf-Nse           Zinc-finger of the MIZ type in Nse subunit
          1    9.4   8.8       0.23   11.5   4.2    1.9  2  rRNA_processing  rRNA processing
        1.1    9.6   9.4       0.24   11.7   5.6    1.9  2  zf-HC5HC2H       PHD-like zinc-binding domain
        5.2    7.3  10.7        2.1    8.6   6.4    2.2  2  zinc_ribbon_16   Zinc-ribbon like family


Domain annotation for each model (and alignments):
>> zf-C3HC4_2  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.2  11.0   6.4e-11   7.2e-08       2      40 .]     181     219 ..     180     219 .. 0.94

  Alignments for each domain:
  == domain 1  score: 32.2 bits;  conditional E-value: 6.4e-11
                         zf-C3HC4_2   2 CpiCldmlkdpsvvtpCgHvfCqkCilrsLeekneCPlC 40 
                                        C iC++ +k  ++  +C+H+f+ +Ci r+    n CPlC
  gene2039|gene2039|rna2039|rna2039 181 CSICFEKIKGMMYNLKCKHTFHMDCIFRWVYTCNLCPLC 219
                                        *********877777************************ PP

>> zf-RING_2  Ring finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.6  10.2   6.4e-11   7.2e-08       3      44 .]     181     220 ..     179     220 .. 0.89

  Alignments for each domain:
  == domain 1  score: 32.6 bits;  conditional E-value: 6.4e-11
                          zf-RING_2   3 CpICleelssadsvlllpCgHvfhreClerwlrssstCPlCr 44 
                                        C+IC+e+++    +  l+C+H+fh +C+ rw+ +++ CPlC+
  gene2039|gene2039|rna2039|rna2039 181 CSICFEKIK--GMMYNLKCKHTFHMDCIFRWVYTCNLCPLCK 220
                                        ********6..4666678***********************7 PP

>> zf-rbx1  RING-H2 zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4  11.7   2.8e-09   3.1e-06      14      55 .]     181     220 ..     176     220 .. 0.80

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 2.8e-09
                            zf-rbx1  14 cieckapgdeecpvvlGeCgHaFHlhCiskWlktrkvCPlcr 55 
                                        c  c ++ +  ++  l +C+H+FH++Ci +W+ t + CPlc+
  gene2039|gene2039|rna2039|rna2039 181 CSICFEKIKG-MMYNL-KCKHTFHMDCIFRWVYTCNLCPLCK 220
                                        5556555555.55566.9***********************6 PP

>> zf-RING_11  RING-like zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   5.5   3.3e-09   3.7e-06       2      29 .]     181     206 ..     181     206 .. 0.95

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 3.3e-09
                         zf-RING_11   2 CsICLeefkpgqalfilpCsHtFHfkCI 29 
                                        CsIC e++k   +++ l+C+HtFH +CI
  gene2039|gene2039|rna2039|rna2039 181 CSICFEKIKG--MMYNLKCKHTFHMDCI 206
                                        ********66..899************9 PP

>> zf-C3HC4  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6  11.3   3.1e-08   3.4e-05       1      41 []     181     219 ..     181     219 .. 0.94

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 3.1e-08
                                        -TTT-S--SS-E.E-TTS--B-CHHHHHHHHCTSSB--TTT CS
                           zf-C3HC4   1 CpiCleeakepnelleCkHsfCskCirkilksrkkvkCPlC 41 
                                        C+iC+e++k  +  l+CkH+f+ +Ci +++   + + CPlC
  gene2039|gene2039|rna2039|rna2039 181 CSICFEKIKGMMYNLKCKHTFHMDCIFRWVY--TCNLCPLC 219
                                        *******************************..5556***9 PP

>> zf-RING_UBOX  RING-type zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   9.4   8.4e-07   0.00094       1      39 []     181     222 ..     181     222 .. 0.79
   2 ?   -2.1   1.7       3.7   4.1e+03       1       7 [.     216     222 ..     216     228 .. 0.77

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 8.4e-07
                       zf-RING_UBOX   1 CpIClelftdPlv.lpCGHtFCreCl..welskslegafkCP 39 
                                        C+IC+e  +  +  l+C HtF+ +C+  w ++ +l +  kCP
  gene2039|gene2039|rna2039|rna2039 181 CSICFEKIKGMMYnLKCKHTFHMDCIfrWVYTCNLCPLCKCP 222
                                        ********86655669**********8776666666666666 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 3.7
                       zf-RING_UBOX   1 CpIClel 7  
                                        Cp C+ +
  gene2039|gene2039|rna2039|rna2039 216 CPLCKCP 222
                                        8888764 PP

>> Zn_ribbon_17  Zinc-ribbon, C4HC2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   7.9   1.6e-05     0.017       4      47 ..     178     218 ..     175     225 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.6e-05
                       Zn_ribbon_17   4 lksCayCelavkgrvvlcgvCeHvlHasCarewfenddlaeCps 47 
                                        +  C++C  ++kg + +  +C+H  H +C+  w  + +   Cp 
  gene2039|gene2039|rna2039|rna2039 178 NAICSICFEKIKGMM-YNLKCKHTFHMDCIFRWVYTCN--LCPL 218
                                        667********9965.689**************55544..3553 PP

>> zf-RING_5  zinc-RING finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8  13.6   1.8e-05     0.021       2      43 ..     181     220 ..     180     221 .. 0.95

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.8e-05
                          zf-RING_5   2 CnkCfeklskeekfyltsCgHifCekClkkllekeavCpiCr 43 
                                        C++Cfek+  +  +y ++C+H+f+ +C+ +    ++ Cp+C+
  gene2039|gene2039|rna2039|rna2039 181 CSICFEKI--KGMMYNLKCKHTFHMDCIFRWVYTCNLCPLCK 220
                                        ********..99******************9999999****8 PP

>> zf-C3HC4_3  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       5.8   6.5e+03       7      16 ..     112     121 ..     111     122 .. 0.77
   2 ?   15.4  11.0   1.1e-05     0.012       2      47 ..     178     223 ..     177     225 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 5.8
                                        TTSSSBS-EE CS
                         zf-C3HC4_3   7 iClerprnvv 16 
                                        iC + +rn +
  gene2039|gene2039|rna2039|rna2039 112 ICADVQRNSI 121
                                        8999888865 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 1.1e-05
                                        GSB-TTTSSSBS-EEET.TEEEEEE-HHHHHHHHHTT-B-TTT--B- CS
                         zf-C3HC4_3   2 deeCviClerprnvvll.pCgHlvlCeeCaekllkrkkkCpiCrrpi 47 
                                        + +C+iC+e+ + +++  +C+H+ +  +C  ++    + Cp+C+ pi
  gene2039|gene2039|rna2039|rna2039 178 NAICSICFEKIKGMMYNlKCKHT-FHMDCIFRWVYTCNLCPLCKCPI 223
                                        678*******998766449****.*********99*********998 PP

>> zf-ANAPC11  Anaphase-promoting complex subunit 11 RING-H2 finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       1.7   1.9e+03      21      34 ..     178     191 ..     166     196 .. 0.72
   2 ?   13.2   9.0     6e-05     0.067      51      78 ..     196     220 ..     178     226 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.7
                                        SSB-TTT-SBTTS- CS
                         zf-ANAPC11  21 ddvcGicrvsfdGt 34 
                                        + +c ic  + +G 
  gene2039|gene2039|rna2039|rna2039 178 NAICSICFEKIKGM 191
                                        56799997776665 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 6e-05
                                        TTS-EEEHHHHHHHHHHHSTSSB-TTTS CS
                         zf-ANAPC11  51 kckhnfhlhcilkwletetskglcpmcr 78 
                                        kckh+fh+ ci++w+ t    +lcp+c+
  gene2039|gene2039|rna2039|rna2039 196 KCKHTFHMDCIFRWVYTC---NLCPLCK 220
                                        7**************875...6899997 PP

>> zf-C3H2C3  Zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   6.3   3.5e-05     0.039       1      35 []     181     220 ..     181     220 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.5e-05
                          zf-C3H2C3   1 CdnCglkLdypfvaysCkHlvHakCa.....deevCPkCk 35 
                                        C +C  k++  +   +CkH +H +C      + + CP+Ck
  gene2039|gene2039|rna2039|rna2039 181 CSICFEKIKGMMYNLKCKHTFHMDCIfrwvyTCNLCPLCK 220
                                        99999999*99**************5455567899****7 PP

>> C1_2  C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.5   3.7e-05     0.042      16      47 .]     176     206 ..     168     206 .. 0.90
   2 ?   -1.5   2.0       2.9   3.2e+03      19      24 ..     211     216 ..     207     223 .. 0.61

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.7e-05
                               C1_2  16 sesfnCsaCgrkidgffYsCseCdfslhvrCa 47 
                                        +e+  Cs+C +ki+g++Y+  +C+ ++h++C+
  gene2039|gene2039|rna2039|rna2039 176 EENAICSICFEKIKGMMYNL-KCKHTFHMDCI 206
                                        56778*************97.9*********6 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.9
                               C1_2  19 fnCsaC 24 
                                        ++C++C
  gene2039|gene2039|rna2039|rna2039 211 YTCNLC 216
                                        345555 PP

>> zf-Nse  Zinc-finger of the MIZ type in Nse subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   7.8   0.00044      0.49      12      55 ..     179     220 ..     165     223 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00044
                                        SB-TTTSSB-SSEEEESSS--EEEHHHHHHHCTTTS-EE-SCCC CS
                             zf-Nse  12 lkCPltlqpfeePvtskkCpHvFEreaIlelikrkktvkCPvag 55 
                                          C + +++++  + + kC+H+F  + I++ +   ++  CP+  
  gene2039|gene2039|rna2039|rna2039 179 AICSICFEKIKGMMYNLKCKHTFHMDCIFRWV--YTCNLCPLCK 220
                                        5699999999999*******************..8888899854 PP

>> rRNA_processing  rRNA processing
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   4.2    0.0002      0.23      36     109 ..      11      84 ..       3      99 .. 0.82
   2 ?   -0.1   0.1      0.77   8.6e+02     111     128 ..     140     157 ..     127     167 .. 0.49

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.0002
                    rRNA_processing  36 lkkegleeeekvakeaekskneeeeskkskkeareeeeklkfkerkeivkerkeekreekleavqeklerikal 109
                                        l+++  +++ek   + +++++++++s +s+ e   + e+ + +e++++++er +ek e++ ea++++ er  ++
  gene2039|gene2039|rna2039|rna2039  11 LNDDSSDTSEKDIVSMSQQTQDDDSSMESIVEVVLSLEESDCREAERQARERVREKAEKEAEARRKRIERDIQM 84 
                                        677777777787777888888888888888888888888***************************99997555 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.77
                    rRNA_processing 111 kkkkerekrkkkLskkTk 128
                                         +   r+k  + L+kk k
  gene2039|gene2039|rna2039|rna2039 140 DSDDTRKKSPDILQKKQK 157
                                        223333333333333333 PP

>> zf-HC5HC2H  PHD-like zinc-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.1       5.4   6.1e+03      25      31 ..      38      44 ..      16      71 .. 0.59
   2 ?   11.7   5.6   0.00021      0.24       9      73 ..     149     213 ..     145     221 .. 0.73

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 5.4
                         zf-HC5HC2H 25 edvekik 31
                                       e++ ++ 
  gene2039|gene2039|rna2039|rna2039 38 ESIVEVV 44
                                       3333333 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00021
                         zf-HC5HC2H   9 pevvfeeekeiemeeiedvekikk..erkklkCylCkkk.vGaciqCskkkCkkafHvtCakeaglll 73 
                                        p++ ++++k++ +  +++++ +++   +++  C++C +k +G++    + kCk++fH+ C ++  +++
  gene2039|gene2039|rna2039|rna2039 149 PDILQKKQKKVGNTVLDKISVVPQivPEENAICSICFEKiKGMM---YNLKCKHTFHMDCIFRWVYTC 213
                                        67778888887777777777666522467889*****9934444...4678*********99866655 PP

>> zinc_ribbon_16  Zinc-ribbon like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.1       1.1   1.2e+03      54      81 ..      43      70 ..       6      77 .. 0.69
   2 ?    8.6   6.4    0.0019       2.1      88     119 ..     191     222 ..     171     225 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 1.1
                     zinc_ribbon_16 54 cglslGtsdvtnkdskrksvvkevsssk 81
                                         lsl +sd  + +++ ++ v+e  +++
  gene2039|gene2039|rna2039|rna2039 43 VVLSLEESDCREAERQARERVREKAEKE 70
                                       4577777777777777777777766655 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0019
                     zinc_ribbon_16  88 lsfclscghgahashakewfsthsicpvadcn 119
                                        + + l+c+h+ h +   +w  t ++cp+ +c 
  gene2039|gene2039|rna2039|rna2039 191 MMYNLKCKHTFHMDCIFRWVYTCNLCPLCKCP 222
                                        56889***********************9995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1795  (0.100117); expected 358.6 (0.02)
Passed bias filter:                      660  (0.0368119); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.67u 0.32s 00:00:00.99 Elapsed: 00:00:00.54
# Mc/sec: 1298.91
//
Query:       gene204|gene204|rna204|rna204  [L=143]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-17   64.2   8.9    1.6e-17   64.1   8.9    1.0  1  DUF572           Family of unknown function (DUF572)
  ------ inclusion threshold ------
      0.025   15.1   3.4      0.028   14.9   0.1    2.5  3  Zn_ribbon_recom  Recombinase zinc beta ribbon domain
      0.079   12.4   0.6        3.3    7.2   0.2    2.4  2  Mu-like_Com      Mu-like prophage protein Com
       0.11   12.6   0.1       0.19   11.9   0.1    1.5  1  hGDE_N           N-terminal domain from the human glycogen de


Domain annotation for each model (and alignments):
>> DUF572  Family of unknown function (DUF572)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.1   8.9   3.6e-21   1.6e-17      20     148 ..      18     140 ..       2     143 .] 0.77

  Alignments for each domain:
  == domain 1  score: 64.1 bits;  conditional E-value: 3.6e-21
                         DUF572  20 rlknrqlvvRlmaPfnmrCktCgeyIykGvkFNarKekVgnetYlgipIfrFyikCtrClneitfkTDPkntdYvveeGa 99 
                                    +++ ++  vR+ +Pf+++C+ Cg++  kG k Na K+k g    ++   f F i+C +C+ne+ ++TDP +  Y+   G+
  gene204|gene204|rna204|rna204  18 KKNSKTNCVRISLPFTIKCTFCGTFAFKGSKHNALKKKAGT--QMNADSFVFFIRCGKCNNEMMIQTDPLQGKYTEYGGC 95 
                                    32358889*******************************99..9******************************988888 PP

                         DUF572 100 tRnfkaekleeeeakreekekeeeeaedamkklEkrtkdskkemeales 148
                                    +   ++++ +++ ++r+e+  ++   +  ++kl  + k +  e+e++++
  gene204|gene204|rna204|rna204  96 KA-LNEKEKTDDYVERSERIPSA---SSVIQKLKMNKKLEDVEKEITNE 140
                                    88.54444466666777777666...55555555444444444444444 PP

>> Zn_ribbon_recom  Recombinase zinc beta ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1      0.69   3.1e+03      24      40 ..       6      26 ..       2      31 .. 0.62
   2 ?   -0.7   0.1      0.47   2.1e+03       6      20 ..      34      49 ..      33      59 .. 0.65
   3 ?   14.9   0.1   6.3e-06     0.028       6      35 ..      69     101 ..      65     118 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.69
                Zn_ribbon_recom 24 r....hyYrCstyrrkgkkCs 40
                                   +     yY+   ++++++ C 
  gene204|gene204|rna204|rna204  6 KsfieKYYKFALKKNSKTNCV 26
                                   345567888877777774475 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.47
                Zn_ribbon_recom  6 lrCgeCGsp.mtrrkr 20
                                   ++C  CG   ++++k+
  gene204|gene204|rna204|rna204 34 IKCTFCGTFaFKGSKH 49
                                   6899999753455555 PP

  == domain 3  score: 14.9 bits;  conditional E-value: 6.3e-06
                Zn_ribbon_recom   6 lrCgeCGspmtrrkrk..gkr.hyYrCstyrrk 35 
                                    +rCg+C++ m  ++    gk+ +y  C++ ++k
  gene204|gene204|rna204|rna204  69 IRCGKCNNEMMIQTDPlqGKYtEYGGCKALNEK 101
                                    9************98888777366589876655 PP

>> Mu-like_Com  Mu-like prophage protein Com
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.2   0.00074       3.3      23      33 ..      32      42 ..      25      56 .. 0.87
   2 ?    3.2   0.0     0.013        59       5      11 ..      69      75 ..      68      85 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.00074
                    Mu-like_Com 23 ltiKCPRCGtL 33
                                    tiKC  CGt 
  gene204|gene204|rna204|rna204 32 FTIKCTFCGTF 42
                                   69********7 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.013
                    Mu-like_Com  5 lRCGeCa 11
                                   +RCG+C 
  gene204|gene204|rna204|rna204 69 IRCGKCN 75
                                   79****6 PP

>> hGDE_N  N-terminal domain from the human glycogen debranching enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   4.2e-05      0.19      22      71 ..       2      55 ..       1      84 [. 0.75

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 4.2e-05
                                   -SSSS---TT--EEEE----SS.....S-EEEEEEE-S-CEEEEEEEEE-TTSS. CS
                         hGDE_N 22 PeegkeFeRdkfrelklkssfe.....kdiyidipitkaGaFafyftydeeeele 71
                                   P ++k+F  +k++++ lk++++      ++ ++i++t +G+Faf  + +++ +++
  gene204|gene204|rna204|rna204  2 PRKRKSFI-EKYYKFALKKNSKtncvrISLPFTIKCTFCGTFAFKGSKHNALKKK 55
                                   66666666.789******9999777766777888899999999988877765554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       976  (0.0544369); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.58u 0.33s 00:00:00.90 Elapsed: 00:00:00.54
# Mc/sec: 802.32
//
Query:       gene2040|gene2040|rna2040|rna2040  [L=59]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       279  (0.0155614); expected 358.6 (0.02)
Passed bias filter:                      226  (0.0126053); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.53u 0.35s 00:00:00.88 Elapsed: 00:00:00.54
# Mc/sec: 327.72
//
Query:       gene2041|gene2041|rna2041|rna2041  [L=962]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.069   13.3   1.2        2.2    8.5   0.1    2.9  2  Pentapeptide_4  Pentapeptide repeats (9 copies)


Domain annotation for each model (and alignments):
>> Pentapeptide_4  Pentapeptide repeats (9 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.1   0.00012       2.2      12      58 ..     150     196 ..     147     208 .. 0.90
   2 ?    2.3   0.1     0.011   1.9e+02      36      72 ..     829     867 ..     804     870 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00012
                     Pentapeptide_4  12 klsnvnFsearlrdcnFtecrlsnvnFdecnlsdvdfaevdlkrasF 58 
                                        +l n+nF +++  + n+ +c++s  nF++ +l + +++ ++l ++++
  gene2041|gene2041|rna2041|rna2041 150 DLQNTNFIQFYRVEENIYSCKMSGINFSDELLVSHKIRTAQLVNSRL 196
                                        689*********************************99999988765 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.011
                     Pentapeptide_4  36 vnFdecnlsdvdfaevdlkrasFsgcnlknvnf.sd.kl 72 
                                        v F+ +  +d+df + + k++++ + +l + ++ ++ k+
  gene2041|gene2041|rna2041|rna2041 829 VDFSISADEDIDFKKRNAKNMNLVNLRLHGLVIiNMdKF 867
                                        567777777888888888888888888888777665466 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (962 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       652  (0.0363657); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.83u 0.34s 00:00:01.17 Elapsed: 00:00:00.55
# Mc/sec: 5269.88
//
Query:       gene2042|gene2042|rna2042|rna2042  [L=528]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (528 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       795  (0.0443416); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.72u 0.34s 00:00:01.06 Elapsed: 00:00:00.55
# Mc/sec: 2916.08
//
Query:       gene2043|gene2043|rna2043|rna2043  [L=49]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (49 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       485  (0.0270511); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.51u 0.34s 00:00:00.85 Elapsed: 00:00:00.55
# Mc/sec: 269.45
//
Query:       gene2044|gene2044|rna2044|rna2044  [L=84]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.067   13.0   0.1      0.078   12.8   0.1    1.1  1  Phage-tail_1  Baseplate structural protein, domain 1


Domain annotation for each model (and alignments):
>> Phage-tail_1  Baseplate structural protein, domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   4.3e-06     0.078      52      94 ..      11      53 ..       4      67 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4.3e-06
                                       ESS-GTTT--S--EEEE.EE-BSS-TTS-EEEEEEEEEEEEE-- CS
                       Phage-tail_1 52 dsknihtkmdgneiiqi.svanandinnvktriygckhfsvsvd 94
                                       ++kni++ +    i +i s    ndi+n+k+ i  ck fs   d
  gene2044|gene2044|rna2044|rna2044 11 NTKNIKSLLS-RRIEEIqSYNIKNDIENMKSEIRDCKPFSAPDD 53
                                       6788877665.3455551445579***************98665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (84 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       883  (0.0492498); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.38s 00:00:00.91 Elapsed: 00:00:00.56
# Mc/sec: 453.02
//
Query:       gene2045|gene2045|rna2045|rna2045  [L=74]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00022   21.2   0.0    0.00023   21.2   0.0    1.0  1  Pam16     Pam16
    0.00077   19.5   0.0       0.33   11.1   0.0    2.3  2  DnaJ      DnaJ domain
  ------ inclusion threshold ------
      0.025   14.4   0.1       0.18   11.7   0.1    2.1  2  ANTAR     ANTAR domain


Domain annotation for each model (and alignments):
>> Pam16  Pam16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0   3.8e-08   0.00023      54     112 ..      15      72 ..       3      74 .] 0.85

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 3.8e-08
                                        XX-HHHHHHHHT--G--SHHHHHHHHHHHHHHT-CCCTS-HHHHHHHHHHHHHHHHHHH CS
                              Pam16  54 GisleeslkilnveedlnreevekryehlfevndkskGGslylqskvfrakerldeelk 112
                                         +slee+  iln        ++   ++ l+ +n  + GGs +l +k+  ak+ l + ++
  gene2045|gene2045|rna2045|rna2045  15 RMSLEEAHSILNTPS-KRYIDISTAHKNLLMINHPDMGGSPFLAAKINEAKDLLMKKYR 72 
                                        68**********988.5666899999*************************98877665 PP

>> DnaJ  DnaJ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.5   0.0    0.0015         9      45      59 ..      17      31 ..       3      33 .. 0.77
   2 !   11.1   0.0   5.5e-05      0.33      16      55 ..      34      69 ..      32      73 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0015
                                       HHHHHHHHHTSHHHH CS
                               DnaJ 45 eineAyevLsdpekR 59
                                        ++eA+++L++p+kR
  gene2045|gene2045|rna2045|rna2045 17 SLEEAHSILNTPSKR 31
                                       799***********9 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 5.5e-05
                                       HHHHHHHHHHHHHSTTTSCCHHHHHHHHHHHHHHHHHHTS CS
                               DnaJ 16 eIkkaYrklalkyHPDknpkdpeaeekFkeineAyevLsd 55
                                       +I  a+++l +  HPD   ++p  +    +ineA + L++
  gene2045|gene2045|rna2045|rna2045 34 DISTAHKNLLMINHPDMG-GSPFLAA---KINEAKDLLMK 69
                                       6999************99.8884444...58888888776 PP

>> ANTAR  ANTAR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.0      0.14   8.1e+02      25      36 ..      15      26 ..      14      31 .. 0.78
   2 ?   11.7   0.1     3e-05      0.18      13      27 ..      60      74 .]      56      74 .] 0.90

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.14
                                       T--HHHHHHHHH CS
                              ANTAR 25 glsedeAfrlLr 36
                                       ++s +eA+  L 
  gene2045|gene2045|rna2045|rna2045 15 RMSLEEAHSILN 26
                                       578899999886 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 3e-05
                                       HHHHHHHHHHHHT-- CS
                              ANTAR 13 ieqAkgiLmerygls 27
                                       i+ Ak++Lm++y+++
  gene2045|gene2045|rna2045|rna2045 60 INEAKDLLMKKYRMT 74
                                       999**********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (74 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       287  (0.0160076); expected 358.6 (0.02)
Passed bias filter:                      237  (0.0132188); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.33s 00:00:00.90 Elapsed: 00:00:00.60
# Mc/sec: 369.44
//
Query:       gene2046|gene2046|rna2046|rna2046  [L=423]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-05   24.9   0.0    4.6e-05   23.6   0.0    1.8  1  CTP_transf_like  Cytidylyltransferase-like
  ------ inclusion threshold ------
       0.14   12.5   0.3        2.7    8.4   0.0    2.3  2  DUF4124          Domain of unknown function (DUF4124)


Domain annotation for each model (and alignments):
>> CTP_transf_like  Cytidylyltransferase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.0   5.2e-09   4.6e-05       2      51 ..     279     330 ..     278     414 .. 0.71

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 5.2e-09
                                        EEE--TT--HHHHHHHHHHHHHSSESEEEEEESSTHCSST-.SCSS.THHHH CS
                    CTP_transf_like   2 agGtFDpiHlGHlrlleqakklleedlivgvpsdeppkkkk.kpla.saeeR 51 
                                        +gGtFD +H GH  ll  a+ l + +l +g+++++   +kk  +++ s+++R
  gene2046|gene2046|rna2046|rna2046 279 LGGTFDRFHEGHVLLLSTALLLTSDELTIGLTTKRLQTNKKyNTIIeSYNTR 330
                                        79**********************99********988888765555044444 PP

>> DUF4124  Domain of unknown function (DUF4124)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.1     0.035   3.2e+02      11      19 ..     102     110 ..      98     112 .. 0.88
   2 ?    8.4   0.0    0.0003       2.7      17      29 ..     127     139 ..     126     158 .. 0.92

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.035
                            DUF4124  11 aaevYkWvD 19 
                                        a++v+kW D
  gene2046|gene2046|rna2046|rna2046 102 AGDVWKWCD 110
                                        89*****99 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0003
                            DUF4124  17 WvDanGvvhysdq 29 
                                        ++D+nG+ h+s+ 
  gene2046|gene2046|rna2046|rna2046 127 CKDENGTKHFSEK 139
                                        9**********85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (423 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       705  (0.0393218); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.69u 0.34s 00:00:01.03 Elapsed: 00:00:00.56
# Mc/sec: 2285.89
//
Query:       gene2047|gene2047|rna2047|rna2047  [L=214]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-11   43.8   1.6    2.8e-11   43.1   1.6    1.4  1  FYRN      F/Y-rich N-terminus
     0.0023   18.0   0.1     0.0052   16.9   0.1    1.7  1  FYRC      F/Y rich C-terminus


Domain annotation for each model (and alignments):
>> FYRN  F/Y-rich N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.1   1.6   3.2e-15   2.8e-11       3      51 .]      67     120 ..      62     120 .. 0.97

  Alignments for each domain:
  == domain 1  score: 43.1 bits;  conditional E-value: 3.2e-15
                               FYRN   3 ltvlslGelvpds.pkfhteryIyPvGYkstRlYw....stkdprkrclYtceI 51 
                                        ++vl++Gel+ +s + + t++ +yP+++ s+R+Y+    ++++ +++++Y+c+I
  gene2047|gene2047|rna2047|rna2047  67 MSVLNVGELPKPSqKEYITPTIVYPINFISKRKYKkyngCPSKSKDKIFYICKI 120
                                        89************99*************************************9 PP

>> FYRC  F/Y rich C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.1   5.8e-07    0.0052      47      79 ..     153     184 ..     130     194 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 5.8e-07
                               FYRC  47 pesisGeemfGLsepaivrlieslpgaekctnY 79 
                                        +e+ s ee+fGL++p+ +r+ie+ +g +++t+Y
  gene2047|gene2047|rna2047|rna2047 153 SEYNSMEEFFGLKHPQLQRIIEE-KGTDELTEY 184
                                        4566779***************9.799999999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       579  (0.032294); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.62u 0.33s 00:00:00.95 Elapsed: 00:00:00.55
# Mc/sec: 1166.58
//
Query:       gene2048|gene2048|rna2048|rna2048  [L=210]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.048   13.2   0.2      0.067   12.7   0.2    1.2  1  Drf_GBD   Diaphanous GTPase-binding Domain


Domain annotation for each model (and alignments):
>> Drf_GBD  Diaphanous GTPase-binding Domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.2   3.7e-06     0.067       7      53 ..      39      86 ..      35     125 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.7e-06
                            Drf_GBD  7 eeidklFeelleelnlpeek.reallalpiekKwqlvvqdkkkkakke 53
                                       ++id  F+ +++e+ l+  + +  +++lpiekK +++ + +k+kak+ 
  gene2048|gene2048|rna2048|rna2048 39 DKIDTHFQIIMNEVGLDPVQmQYFIANLPIEKKMKMILSVSKRKAKTL 86
                                       789***********9887651566788**************9999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       602  (0.0335769); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1340.66
//
Query:       gene2049|gene2049|rna2049|rna2049  [L=598]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.048   13.8   0.7        4.6    7.3   0.0    2.8  2  TLE_N     Groucho/TLE N-terminal Q-rich domain
       0.11   12.6   2.6       0.15   12.2   0.6    2.3  2  SAS4      Something about silencing, SAS, complex subunit 4


Domain annotation for each model (and alignments):
>> TLE_N  Groucho/TLE N-terminal Q-rich domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.2    0.0072        65      17      59 ..      84     127 ..      74     129 .. 0.86
   2 ?    7.3   0.0   0.00051       4.6      18      52 ..     542     576 ..     527     594 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.0072
                              TLE_N  17 kftvlescdrikeef.qflqaqyhsLklecekLasektemqRhy 59 
                                         f+   +++ +k e+ ++l  q   L +e+  +  +kte  R++
  gene2049|gene2049|rna2049|rna2049  84 EFSKDKFLENVKREVkKYLADQSVRLAVELKEIERNKTEYIRVC 127
                                        677778899999998459*********************99976 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.00051
                              TLE_N  18 ftvlescdrikeefqflqaqyhsLklecekLasek 52 
                                        ++ +e +d+ik+ f++l++ y +L   + k   ek
  gene2049|gene2049|rna2049|rna2049 542 VMFMENIDHIKDRFDTLKESYAKLNSYLGKNVDEK 576
                                        56789*****************9987666666555 PP

>> SAS4  Something about silencing, SAS, complex subunit 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.1       1.1   9.5e+03      42      60 ..     303     321 ..     285     331 .. 0.52
   2 ?   12.2   0.6   1.7e-05      0.15      39      96 ..     509     565 ..     485     567 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 1.1
                               SAS4  42 ekLqgqdwlrvlgkitkin 60 
                                        +k  ++d + ++ k+ k++
  gene2049|gene2049|rna2049|rna2049 303 KKFTENDFVPFIRKVEKVK 321
                                        4444444444444444444 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 1.7e-05
                               SAS4  39 rllekLqgqdwlrvlgkitkindpkdkkelerkreltikeieallekferwkkeekkl 96 
                                         +  +L   ++ ++l+  +ki+  ++ + +e+k  +++++i+++ ++f+++k+   kl
  gene2049|gene2049|rna2049|rna2049 509 AINYDLLCVEYEEILALYSKIKG-NKYELIENKNVMFMENIDHIKDRFDTLKESYAKL 565
                                        55556677788999********9.****************************998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (598 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1069  (0.0596241); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.27s 00:00:00.88 Elapsed: 00:00:00.44
# Mc/sec: 4048.48
//
Query:       gene205|gene205|rna205|rna205  [L=49]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (49 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       346  (0.0192983); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.26s 00:00:00.61 Elapsed: 00:00:00.41
# Mc/sec: 357.45
//
Query:       gene2050|gene2050|rna2050|rna2050  [L=61]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       327  (0.0182386); expected 358.6 (0.02)
Passed bias filter:                      254  (0.014167); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 428.70
//
Query:       gene2051|gene2051|rna2051|rna2051  [L=42]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.14   12.4   0.0       0.14   12.4   0.0    1.0  1  AbiEi_2   Transcriptional regulator, AbiEi antitoxin, Type IV


Domain annotation for each model (and alignments):
>> AbiEi_2  Transcriptional regulator, AbiEi antitoxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   7.7e-06      0.14      97     127 ..       6      36 ..       4      42 .] 0.90

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 7.7e-06
                            AbiEi_2  97 rraFwrakkavgdieivpplliYaDLlaigd 127
                                        +r+F++ + +v++    + l +YaDLl+ + 
  gene2051|gene2051|rna2051|rna2051   6 IRTFYPRSLKVEKACQLSSLRLYADLLNAQR 36 
                                        689************************9864 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (42 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       153  (0.00853366); expected 358.6 (0.02)
Passed bias filter:                      128  (0.00713927); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.41
# Mc/sec: 308.81
//
Query:       gene2052|gene2052|rna2052|rna2052  [L=86]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       225  (0.0125495); expected 358.6 (0.02)
Passed bias filter:                      190  (0.0105974); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.30s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 611.33
//
Query:       gene2053|gene2053|rna2053|rna2053  [L=33]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (33 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       191  (0.0106531); expected 358.6 (0.02)
Passed bias filter:                      170  (0.00948185); expected 358.6 (0.02)
Passed Vit filter:                         7  (0.000390429); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.27s 00:00:00.62 Elapsed: 00:00:00.42
# Mc/sec: 236.96
//
Query:       gene2054|gene2054|rna2054|rna2054  [L=86]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       456  (0.0254337); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.43
# Mc/sec: 602.04
//
Query:       gene2055|gene2055|rna2055|rna2055  [L=177]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1212  (0.0676); expected 358.6 (0.02)
Passed bias filter:                      514  (0.0286686); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1221.80
//
Query:       gene2056|gene2056|rna2056|rna2056  [L=302]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 2020.89
//
Query:       gene2057|gene2057|rna2057|rna2057  [L=341]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.057   13.4  10.6       0.11   12.5  10.6    1.6  1  Rootletin       Ciliary rootlet component, centrosome cohesio
       0.12   11.3   1.5        0.2   10.5   1.0    1.6  2  tRNA-synt_1f    tRNA synthetases class I (K)
        0.3   11.4   2.8          1    9.7   0.2    2.6  2  DIMCO_N         Dinitrogenase iron-molybdenum cofactor, N-ter
       0.33   10.7   6.6        0.2   11.5   3.6    1.9  2  MCPsignal       Methyl-accepting chemotaxis protein (MCP) sig
       0.54    9.8   6.4       0.85    9.1   6.4    1.4  1  Exonuc_VII_L    Exonuclease VII, large subunit
       0.77   10.1   5.0       0.65   10.3   2.6    2.1  2  DUF2935         Domain of unknown function (DUF2935)
        1.1    9.2   7.1        4.9    7.1   3.2    2.1  2  DUF2400         Protein of unknown function (DUF2400)
        1.1    9.2   6.3       0.39   10.6   2.3    2.3  2  GIT_CC          GIT coiled-coil Rho guanine nucleotide exchan
        1.2    9.7  14.8        1.2    9.7  12.3    2.2  2  APG6_N          Apg6 coiled-coil region
        1.4    9.2  14.1        1.6    9.0   6.1    2.8  2  TMF_TATA_bd     TATA element modulatory factor 1 TATA binding
        1.4    9.1  12.8        1.5    9.0   2.4    2.5  2  Fib_alpha       Fibrinogen alpha/beta chain family
        2.3    8.6  16.9        6.9    7.1  10.7    2.6  2  CENP-H          Centromere protein H (CENP-H)
        2.8    8.6  10.6         44    4.7   0.1    2.7  2  Syntaxin-6_N    Syntaxin 6, N-terminal
        3.1    8.5  12.8    2.4e+02    2.4  12.8    3.2  1  YabA            Initiation control protein YabA
        3.8    7.6  17.3         20    5.2   0.5    2.6  3  UPF0242         Uncharacterised protein family (UPF0242) N-te
        5.7    7.3   9.8        8.6    6.8   8.1    2.2  2  Uso1_p115_C     Uso1 / p115 like vesicle tethering protein, C
        6.6    7.1  12.5         23    5.3   0.2    3.4  3  DUF948          Bacterial protein of unknown function (DUF948
        7.6    6.6  14.8         28    4.8  12.3    2.5  2  Mod_r           Modifier of rudimentary (Mod(r)) protein
        8.8    6.7  12.6         38    4.7   0.1    2.7  2  KxDL            Uncharacterized conserved protein
         10    6.7  17.0        7.1    7.2  12.7    2.9  2  ZapB            Cell division protein ZapB


Domain annotation for each model (and alignments):
>> Rootletin  Ciliary rootlet component, centrosome cohesion
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5  10.6   0.00012      0.11       6     137 ..     146     273 ..     129     319 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00012
                          Rootletin   6 ayqeaqqrqaqLvskLqaKvlqYkkrcseleqrllektselektkltlll...........ssareleeeesadle 70 
                                        + + a  + a+Lv+k ++ v +   r++e+++ +++             +            s +++++e ++  +
  gene2057|gene2057|rna2057|rna2057 146 QTRAAHAECAALVNKVHENVRDSTYRMQEMNAVINTV------------CshlgierdeltLSIQQIANEYTTLKQ 209
                                        3344444555555555555555555555555555553............033333332222456888888888888 PP

                          Rootletin  71 ealakLeeErqrseklaqvnslLreqleearqaneaLtedlqkltkdwerlreeleqkekewreeee 137
                                        +a+++ ++    +++laq+n+ L+  l++ +++n +++++l  l++++ + ++  +q  +++ ++++
  gene2057|gene2057|rna2057|rna2057 210 NARIEFDN---TNKNLAQENERLKSALKALKTENTEIRNELVILSNEFYKSKQLTKQTTQTLAKQKR 273
                                        99998886...5788999*******************************999999998888877765 PP

>> tRNA-synt_1f  tRNA synthetases class I (K)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.82   7.4e+02     322     348 ..     194     224 ..     189     243 .. 0.66
   2 ?   10.5   1.0   0.00023       0.2     128     170 ..     248     291 ..     214     297 .. 0.71

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.82
                       tRNA-synt_1f 322 dleilrlvdeYdklerkyf....aeqeeeee 348
                                         l+i+++ +eY +l++++     +++++ ++
  gene2057|gene2057|rna2057|rna2057 194 TLSIQQIANEYTTLKQNARiefdNTNKNLAQ 224
                                        4568999999999988887666522232233 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00023
                       tRNA-synt_1f 128 fisatelYksglydeaikealenrekikeilekyrgee.reety 170
                                        +i ++e+Yks ++++++++ l ++++i +il++ ++   re +y
  gene2057|gene2057|rna2057|rna2057 248 VILSNEFYKSKQLTKQTTQTLAKQKRIIDILQEKLTLTgRETNY 291
                                        46689***************************998877344444 PP

>> DIMCO_N  Dinitrogenase iron-molybdenum cofactor, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.2    0.0012         1      46      85 ..     204     242 ..     172     246 .. 0.64
   2 ?    0.8   0.2      0.71   6.3e+02      22      64 ..     272     316 ..     264     325 .. 0.63

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0012
                            DIMCO_N  46 vtdLktalasadgeeeeldigveseaLkeAvrlLkGegee 85 
                                         t Lk+     + ++++ + ++e+e+Lk+A+++Lk e+ e
  gene2057|gene2057|rna2057|rna2057 204 YTTLKQNA-RIEFDNTNKNLAQENERLKSALKALKTENTE 242
                                        45677766.55666666677799************99876 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.71
                            DIMCO_N  22 aqLlevLqerlgeplteekLakltvtdLktala..sadgeeeeld 64 
                                        ++++++Lqe+l ++  e++ + +   + ++al     dge ++++
  gene2057|gene2057|rna2057|rna2057 272 KRIIDILQEKLTLTGRETNYTIVDDLRFRIALLrsRIDGEVDGEK 316
                                        678888888887666666555444444444444666676666655 PP

>> MCPsignal  Methyl-accepting chemotaxis protein (MCP) signalling domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   3.6   0.00022       0.2      75     142 ..     138     209 ..     134     238 .. 0.69
   2 ?    0.7   1.0      0.44     4e+02      97     153 ..     196     253 ..     187     277 .. 0.52

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00022
                                        HHHHHHHHHHHHHHHHHHHHH..............HHHHHHHHHHHHHHHHHCC....HHHHHHHHHHHHHH CS
                          MCPsignal  75 dEVrkLAersaqaakeiealiieiqkeindsvesleetrqrveegselveetge....alkeiveavaevad 142
                                        +E r+L e++  a  e +al+ ++++++ ds+  ++e +  +++  +     ++    ++++i+++ + +++
  gene2057|gene2057|rna2057|rna2057 138 QELRALVEQTRAAHAECAALVNKVHENVRDSTYRMQEMNAVINTVCSHLGIERDeltlSIQQIANEYTTLKQ 209
                                        89***********************************99999987776544433001134555555544443 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.44
                                        .............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHH.HHHHHHHHH CS
                          MCPsignal  97 eiqkeindsvesleetrqrveegselveetgealkeiveavaevadlv.qeiaaasee 153
                                         iq+  n+ ++  +++r + +++ +  ++ +e lk+  +a +  ++++ +e+   s+e
  gene2057|gene2057|rna2057|rna2057 196 SIQQIANEYTTLKQNARIEFDNTNKNLAQENERLKSALKALKTENTEIrNELVILSNE 253
                                        5555566666666666666666666666655555555554443333331233333333 PP

>> Exonuc_VII_L  Exonuclease VII, large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   6.4   0.00095      0.85     150     263 ..     173     282 ..     105     317 .. 0.47

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00095
                       Exonuc_VII_L 150 eelerrlekaikrlleekkqrleklasrlk.speellerkrqrldeleerleralkkqlkkkrerleelkerlkek 224
                                        +e+++ +++   ++l  ++ +l+   ++++ + ++l +++r ++d+++++l +  +++lk++ ++l++ +++++++
  gene2057|gene2057|rna2057|rna2057 173 QEMNAVINTVC-SHLGIERDELTLSIQQIAnEYTTLKQNARIEFDNTNKNLAQ-ENERLKSALKALKTENTEIRNE 246
                                        11111111111.11122222222222233212222222334444444444444.3333333333333333333222 PP

                       Exonuc_VII_L 225 leekkerlkklkerle....lleekkerleeleeklealsplk 263
                                        l   ++++            l+++++++l+++++ ++ l+ + 
  gene2057|gene2057|rna2057|rna2057 247 LVILSNEF-------YkskqLTKQTTQTLAKQKRIIDILQEKL 282
                                        22222222.......1222223333333333333333333333 PP

>> DUF2935  Domain of unknown function (DUF2935)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.1       1.6   1.4e+03      30      70 ..     141     177 ..     133     213 .. 0.57
   2 ?   10.3   2.6   0.00073      0.65      22      79 ..     212     268 ..     192     335 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 1.6
                            DUF2935  30 kdlikeakefkkeFekllaeavelseglvrasseleeavak 70 
                                        ++l+++ ++ + e+ +l ++++e     vr s+   +++++
  gene2057|gene2057|rna2057|rna2057 141 RALVEQTRAAHAECAALVNKVHE----NVRDSTYRMQEMNA 177
                                        44555555555555555555554....22333333333333 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00073
                            DUF2935  22 ealldpkekdlikeakefkkeFekllaeavelseglvrasseleeavakLneealklt 79 
                                        +  +d+++k+l++e +++k ++++l +e+ e+ + lv + s+++ + ++L++++ + +
  gene2057|gene2057|rna2057|rna2057 212 RIEFDNTNKNLAQENERLKSALKALKTENTEIRNELV-ILSNEFYKSKQLTKQTTQTL 268
                                        6679********************************6.34444444444444444333 PP

>> DUF2400  Protein of unknown function (DUF2400)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.1      0.05        45      54     136 ..     103     182 ..      74     195 .. 0.73
   2 ?    7.1   3.2    0.0055       4.9      68     136 ..     203     271 ..     186     278 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.05
                            DUF2400  54 eeeeekdlkelekfkyRffnsedllallkalkelleksgsLeeaflkaeeeeeeleealeafreaflekekrtrkl 129
                                        +  + +d+k++  +++R+ +s ++   +k+ +++    + L++++ +++++++e+ + +++++e++ ++++r +++
  gene2057|gene2057|rna2057|rna2057 103 NVGKLEDAKQI--LRFRTCKSGRVERWCKS-ERMRCCVQELRALVEQTRAAHAECAALVNKVHENVRDSTYRMQEM 175
                                        44444444444..45799999999998876.455566778999999988899999999999999999988888887 PP

                            DUF2400 130 eflipsp 136
                                        +++i + 
  gene2057|gene2057|rna2057|rna2057 176 NAVINTV 182
                                        7777655 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0055
                            DUF2400  68 kyRffnsedllallkalkelleksgsLeeaflkaeeeeeeleealeafreaflekekrtrkleflipsp 136
                                        +y + +++  +++ ++ k+l ++++ L++a+++ ++e++e++++l  ++++f+++++ t+++++ ++++
  gene2057|gene2057|rna2057|rna2057 203 EYTTLKQNARIEFDNTNKNLAQENERLKSALKALKTENTEIRNELVILSNEFYKSKQLTKQTTQTLAKQ 271
                                        59999999999**********************99*******************888888877777776 PP

>> GIT_CC  GIT coiled-coil Rho guanine nucleotide exchange factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.1       3.5   3.1e+03      35      52 ..     158     175 ..     138     181 .. 0.71
   2 ?   10.6   2.3   0.00043      0.39      36      65 ..     216     245 ..     205     246 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 3.5
                             GIT_CC  35 LlkvNtslsdelrlLQsk 52 
                                        + kv ++  d   ++Q++
  gene2057|gene2057|rna2057|rna2057 158 VNKVHENVRDSTYRMQEM 175
                                        457777777877888876 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00043
                             GIT_CC  36 lkvNtslsdelrlLQskvqkLqaeNaqlrd 65 
                                         + N++l +e ++L s ++ L++eN+++r+
  gene2057|gene2057|rna2057|rna2057 216 DNTNKNLAQENERLKSALKALKTENTEIRN 245
                                        578************************997 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.3      0.63   5.7e+02      76     104 ..     139     167 ..     125     199 .. 0.62
   2 ?    9.7  12.3    0.0013       1.2       9     117 ..     156     280 ..     152     291 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.63
                             APG6_N  76 ereeleaelaaleeelealeeeeerfwre 104
                                        e ++l ++ +a+++e++al ++ ++ +r+
  gene2057|gene2057|rna2057|rna2057 139 ELRALVEQTRAAHAECAALVNKVHENVRD 167
                                        33444444555555555554444444443 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0013
                             APG6_N   9 lLleeldkqleqaekerdaYeeflkklkkekkeeek................qdeeleeleeeleklekeeeelle 68 
                                         L++++ + +++++  ++++++  +++ ++   e++                +++ + e ++  ++l +e e+l +
  gene2057|gene2057|rna2057|rna2057 156 ALVNKVHENVRDSTYRMQEMNAVINTVCSHLGIERDeltlsiqqianeyttlKQNARIEFDNTNKNLAQENERLKS 231
                                        567778888888888888888888888877666655777777777776666667777888888************* PP

                             APG6_N  69 eLkelekereeleaelaaleeelealeeeeerfwreynelqlellelee 117
                                         Lk+l++e+ e+++el  l++e  + ++  ++  +   ++++    l+e
  gene2057|gene2057|rna2057|rna2057 232 ALKALKTENTEIRNELVILSNEFYKSKQLTKQTTQTLAKQKRIIDILQE 280
                                        **********************999999999998888887765555555 PP

>> TMF_TATA_bd  TATA element modulatory factor 1 TATA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.9     0.056        50      33      74 ..     138     180 ..     129     210 .. 0.76
   2 ?    9.0   6.1    0.0018       1.6      22      91 ..     220     289 ..     213     312 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.056
                        TMF_TATA_bd  33 eelerleaerdeareeivklmken.eelkelkkeleelekele 74 
                                        +el  l ++ ++a +e+++l++++ e+++++  +++e+++ ++
  gene2057|gene2057|rna2057|rna2057 138 QELRALVEQTRAAHAECAALVNKVhENVRDSTYRMQEMNAVIN 180
                                        7889999999999999999996652667777777887777554 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0018
                        TMF_TATA_bd  22 rrlEgElaslkeelerleaerdeareeivklmkeneelkelkkeleelekeleelqeryetlLellGeks 91 
                                        + l  E + lk+ l+ l++e  e+r+e+v l++e  + k+l k+ +++ ++ + + + +++ L+l G  +
  gene2057|gene2057|rna2057|rna2057 220 KNLAQENERLKSALKALKTENTEIRNELVILSNEFYKSKQLTKQTTQTLAKQKRIIDILQEKLTLTGRET 289
                                        567789999******************************9999999999998888888888888888766 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   2.4    0.0017       1.5      35     111 ..     135     211 ..     129     232 .. 0.88
   2 ?    3.2   5.3       0.1        93      38      91 ..     227     278 ..     214     333 .. 0.49

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0017
                                        HHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHHHHH CS
                          Fib_alpha  35 kdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqesnirvLqnv 110
                                          +++l+  +e+ +  + e   lv+++++ +r+     ++ + vi+ + ++l  e  +l  +i++  ++   L+++
  gene2057|gene2057|rna2057|rna2057 135 CCVQELRALVEQTRAAHAECAALVNKVHENVRDSTYRMQEMNAVINTVCSHLGIERDELTLSIQQIANEYTTLKQN 210
                                        5699***********************************99***********999999999998888888888876 PP

                                        H CS
                          Fib_alpha 111 l 111
                                         
  gene2057|gene2057|rna2057|rna2057 211 A 211
                                        5 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.1
                                        CCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC CS
                          Fib_alpha  38 ekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeil 91 
                                        e+l++ l+ ++ +++e+++  + +++   + ++ +k++++++ k ++ ++  il
  gene2057|gene2057|rna2057|rna2057 227 ERLKSALKALKTENTEIRNELVILSNEFYKSKQLTKQTTQTLAKQKRIID--IL 278
                                        55555555555555555444444443333333333323333333333333..22 PP

>> CENP-H  Centromere protein H (CENP-H)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.3     0.052        46      39      89 ..     129     179 ..     115     186 .. 0.71
   2 ?    7.1  10.7    0.0077       6.9       7      87 ..     189     280 ..     184     289 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.052
                             CENP-H  39 lkrknrelaaellelakekesekeklkeelekleaelkksrqrwrvvknva 89 
                                         +++ r +++el+ l +++++   + ++ ++k+++++++s  r++ +  v+
  gene2057|gene2057|rna2057|rna2057 129 KSERMRCCVQELRALVEQTRAAHAECAALVNKVHENVRDSTYRMQEMNAVI 179
                                        566777778888777777777777777778888888877777766665554 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0077
                             CENP-H   7 qrdelssellklsqelrelqeel.tevekenlrlkrknrelaaellelakekesek..........eklkeelekl 71 
                                        +rdel ++++++++e+++l+++   e    n++l ++n+ l + l  l+ e+ + +           k k+  ++ 
  gene2057|gene2057|rna2057|rna2057 189 ERDELTLSIQQIANEYTTLKQNArIEFDNTNKNLAQENERLKSALKALKTENTEIRnelvilsnefYKSKQLTKQT 264
                                        79*************99987765268999999999******99997777777777779999987776688889999 PP

                             CENP-H  72 eaelkksrqrwrvvkn 87 
                                         + l k+++ + ++++
  gene2057|gene2057|rna2057|rna2057 265 TQTLAKQKRIIDILQE 280
                                        9999999999999886 PP

>> Syntaxin-6_N  Syntaxin 6, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.1     0.049        44      17      82 ..     133     194 ..     124     202 .. 0.77
   2 ?    4.5   8.2     0.058        52      10      94 ..     193     281 ..     189     284 .. 0.69

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.049
                       Syntaxin-6_N  17 aeslyrrwerlledtssstseeldetrteLrkalrsiewdledLeetvriveknpskfkidekels 82 
                                        ++  +++ + l e+t+++   e+  + +++++++r+  + +++++ ++++v +   + +i+ +el+
  gene2057|gene2057|rna2057|rna2057 133 MRCCVQELRALVEQTRAA-HAECAALVNKVHENVRDSTYRMQEMNAVINTVCS---HLGIERDELT 194
                                        555666666666666654.8999999**********************88876...4777777765 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.058
                       Syntaxin-6_N  10 Vqkslnkaeslyrrwerlledtss..stseeldetrteLrkalrsiewdledLeetvriveknpsk....fkidek 79 
                                           s++++++ y++ ++  +   +  +t+++l + ++ L++al+ ++++  ++++   i++++ +k     k + +
  gene2057|gene2057|rna2057|rna2057 193 LTLSIQQIANEYTTLKQNARI--EfdNTNKNLAQENERLKSALKALKTENTEIRNELVILSNEFYKskqlTKQTTQ 266
                                        555666666666666542222..244689999999****************9999998887754443013556667 PP

                       Syntaxin-6_N  80 elsrrrafveevree 94 
                                        +l++++++++ ++e+
  gene2057|gene2057|rna2057|rna2057 267 TLAKQKRIIDILQEK 281
                                        888888888877766 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4  12.8      0.26   2.4e+02      12      53 ..     192     245 ..     129     282 .. 0.74

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.26
                                        HHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHHHHHHHH...........X CS
                               YabA  12 eleeqleelleeleelkeela.elleenaeLeleneklrerl...........e 53 
                                        el+ +++++ +e ++lk++   e  + n++L  ene+l++ l           +
  gene2057|gene2057|rna2057|rna2057 192 ELTLSIQQIANEYTTLKQNARiEFDNTNKNLAQENERLKSALkalktenteirN 245
                                        566677777777777777664255566777777777777777333333332220 PP

>> UPF0242  Uncharacterised protein family (UPF0242) N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.1      0.13   1.2e+02     108     159 ..     129     180 ..       8     187 .. 0.87
   2 ?    5.2   0.5     0.023        20      85     140 ..     156     211 ..      98     217 .. 0.69
   3 ?    3.8  13.8      0.06        54      92     158 ..     213     282 ..     189     285 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.13
                            UPF0242 108 keeelerlkeenqqLqekleaiaedfeelkleleeqLaekqellqeyqetie 159
                                        k+e ++   +e   L e++ a+ ++ ++l  ++ e+++  + ++qe+++ i+
  gene2057|gene2057|rna2057|rna2057 129 KSERMRCCVQELRALVEQTRAAHAECAALVNKVHENVRDSTYRMQEMNAVIN 180
                                        6677777888888999999999999999999999999999999999988887 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.023
                            UPF0242  85 ktkeealeelqeeeeeLkeeldakeeelerlkeenqqLqekleaiaedfeelklel 140
                                        +  ++  e++++ + +++e  +  ++   +l  e  +L    ++ia+++  lk+++
  gene2057|gene2057|rna2057|rna2057 156 ALVNKVHENVRDSTYRMQEMNAVINTVCSHLGIERDELTLSIQQIANEYTTLKQNA 211
                                        33333446777777788887888888888888899999999999999999888875 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.06
                            UPF0242  92 eelqeeeeeLkeeldakeeelerlkeenqqLqekleaiaedfeelkl...eleeqLaekqellqeyqeti 158
                                         e  + +++L++e +  +++l+ lk en +++ +l   +++f ++k+   +  ++La+++  ++ +qe++
  gene2057|gene2057|rna2057|rna2057 213 IEFDNTNKNLAQENERLKSALKALKTENTEIRNELVILSNEFYKSKQltkQTTQTLAKQKRIIDILQEKL 282
                                        35667789999999999********************999998877611155578999999999999875 PP

>> Uso1_p115_C  Uso1 / p115 like vesicle tethering protein, C terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.1      0.66   5.9e+02      25      75 ..     159     211 ..     133     216 .. 0.56
   2 ?    6.8   8.1    0.0096       8.6      18      70 ..     191     242 ..     179     288 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.66
                        Uso1_p115_C  25 qslskalesleqk......eakkaaesqakeleaenkklekeleklraelkeekeke 75 
                                        ++  ++++           e ++ ++++ ++l  e+++l+  ++++  e+ + k+++
  gene2057|gene2057|rna2057|rna2057 159 NKVHENVR----DstyrmqEMNAVINTVCSHLGIERDELTLSIQQIANEYTTLKQNA 211
                                        22222222....123334444556677777777777777778888888888888877 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0096
                        Uso1_p115_C  18 eklkaelqslskalesleqkeakkaaesqakeleaenkklekeleklraelke 70 
                                         +l  ++q+ +++++ l+q  a  + ++ +k+l +en++l+++l++l+ e  e
  gene2057|gene2057|rna2057|rna2057 191 DELTLSIQQIANEYTTLKQN-ARIEFDNTNKNLAQENERLKSALKALKTENTE 242
                                        57777889999999999999.88899999999999999999999988877655 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.2     0.026        23      33      77 ..     138     182 ..     130     188 .. 0.75
   2 ?    3.2   1.7      0.12   1.1e+02      24      78 ..     186     237 ..     178     245 .. 0.77
   3 ?    5.0   0.5     0.034        30      43      67 ..     258     282 ..     255     290 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.026
                             DUF948  33 atieelekqvdpilkevedllakvnelledvneklekvdplteav 77 
                                        + ++ l +q+++   e ++l++kv e + d + ++++++++++ v
  gene2057|gene2057|rna2057|rna2057 138 QELRALVEQTRAAHAECAALVNKVHENVRDSTYRMQEMNAVINTV 182
                                        556777788888888888888888888888888888888777665 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.12
                             DUF948  24 lkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteava 78 
                                        l+   de++ +i+++ ++ + + ++++   +++n+   ++ ++ e++++  +a++
  gene2057|gene2057|rna2057|rna2057 186 LGIERDELTLSIQQIANEYTTLKQNARIEFDNTNK---NLAQENERLKSALKALK 237
                                        55566999999***********************9...66666666666666665 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.034
                             DUF948  43 dpilkevedllakvnelledvnekl 67 
                                        ++++k+++++lak +++ + ++ekl
  gene2057|gene2057|rna2057|rna2057 258 KQLTKQTTQTLAKQKRIIDILQEKL 282
                                        689*************999999987 PP

>> Mod_r  Modifier of rudimentary (Mod(r)) protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.4      0.16   1.5e+02       7      72 ..     139     209 ..     133     213 .. 0.65
   2 ?    4.8  12.3     0.031        28      33     102 ..     210     280 ..     184     290 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.16
                              Mod_r   7 eLqelledee....klealvktl.pevkqlkeekeellaeneslaeknlslepeleelrselqekleelke 72 
                                        eL++l+e+         alv+++ ++v++ + + +e+ a +  + ++   +++el+   +++++++ +lk+
  gene2057|gene2057|rna2057|rna2057 139 ELRALVEQTRaahaECAALVNKVhENVRDSTYRMQEMNAVINTVCSHLGIERDELTLSIQQIANEYTTLKQ 209
                                        55555555442222556677777555888888888885555555555555577888888888888887765 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.031
                              Mod_r  33 eekeellaeneslaeknlslepeleelrselqekleelkelekefeekeqeldellqkfspd.allarLqt 102
                                        +++ e  ++n++la++n  l+  l+ l+ e +e ++el  l++ef + +q  ++  q + ++  + + Lq+
  gene2057|gene2057|rna2057|rna2057 210 NARIEFDNTNKNLAQENERLKSALKALKTENTEIRNELVILSNEFYKSKQLTKQTTQTLAKQkRIIDILQE 280
                                        345567789****************************************9999999887766345555555 PP

>> KxDL  Uncharacterized conserved protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.1     0.042        38      28      79 ..     129     180 ..     106     183 .. 0.88
   2 ?    3.6   7.8     0.088        79      20      79 ..     224     283 ..     210     285 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.042
                               KxDL  28 knreLlelnalsqerlaklrarfkqgtkllkevkkdLesifkkirslkakla 79 
                                        k++++  + +++ + ++++ra  ++ + l+++v ++ + ++ +++ ++a ++
  gene2057|gene2057|rna2057|rna2057 129 KSERMRCCVQELRALVEQTRAAHAECAALVNKVHENVRDSTYRMQEMNAVIN 180
                                        788888999999999********************************99886 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.088
                               KxDL  20 qtsgrlnkknreLlelnalsqerlaklrarfkqgtkllkevkkdLesifkkirslkakla 79 
                                        q   rl++  + L++ n++  ++l  l+++f + ++l k++ + L + ++ i+ l++kl+
  gene2057|gene2057|rna2057|rna2057 224 QENERLKSALKALKTENTEIRNELVILSNEFYKSKQLTKQTTQTLAKQKRIIDILQEKLT 283
                                        5567888889999999***************************************99985 PP

>> ZapB  Cell division protein ZapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.1       2.2     2e+03      30      47 ..     140     153 ..     129     178 .. 0.47
   2 ?    7.2  12.7    0.0079       7.1       7      62 ..     191     247 ..     191     283 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 2.2
                               ZapB  30 Lkeeneelkeenreleee 47 
                                        L+    +l e+ r+  +e
  gene2057|gene2057|rna2057|rna2057 140 LR----ALVEQTRAAHAE 153
                                        22....222222222222 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0079
                               ZapB   7 eqLEskiqkaidtitlLqmeie.eLkeeneelkeenreleeeneqlkeereawqerl 62 
                                        ++L  +iq+  +++t+L++  + e    n++l++en++l++ +++lk+e +++++ l
  gene2057|gene2057|rna2057|rna2057 191 DELTLSIQQIANEYTTLKQNARiEFDNTNKNLAQENERLKSALKALKTENTEIRNEL 247
                                        6889999**********8766548999999**********99999999998887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (341 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1847  (0.103017); expected 358.6 (0.02)
Passed bias filter:                      549  (0.0306208); expected 358.6 (0.02)
Passed Vit filter:                        78  (0.00435049); expected 17.9 (0.001)
Passed Fwd filter:                        25  (0.00139439); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.67u 0.28s 00:00:00.95 Elapsed: 00:00:00.44
# Mc/sec: 2304.05
//
Query:       gene2058|gene2058|rna2058|rna2058  [L=150]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.2e-09   36.8   0.2      8e-09   35.5   0.2    1.6  1  DnaJ      DnaJ domain


Domain annotation for each model (and alignments):
>> DnaJ  DnaJ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.5   0.2   4.5e-13     8e-09       1      62 [.       6      66 ..       6      66 .. 0.93

  Alignments for each domain:
  == domain 1  score: 35.5 bits;  conditional E-value: 4.5e-13
                                       HHHHHHTSSTT..G-HHHHHHHHHHHHHHHSTTTSCCHHHHHHHHHHHHHHHHHHTSHHHHHHH CS
                               DnaJ  1 dyYeiLgvskd..asedeIkkaYrklalkyHPDknpkdpeaeekFkeineAyevLsdpekRkqY 62
                                       dy+ +L+++++   +++++k +Y+++a++yHP        ++++F  +++Ay++L+++ kR+ Y
  gene2058|gene2058|rna2058|rna2058  6 DYFTLLNLPHTffIDKQTLKHNYYTQAKRYHPSMT---GGNDNMFVGLKKAYDTLNNDLKRALY 66
                                       799********6569999***************99...55679******************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       682  (0.0380389); expected 358.6 (0.02)
Passed bias filter:                      453  (0.0252663); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 955.28
//
Query:       gene2059|gene2059|rna2059|rna2059  [L=543]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (543 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1904  (0.106197); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.76u 0.29s 00:00:01.05 Elapsed: 00:00:00.49
# Mc/sec: 3359.22
//
Query:       gene206|gene206|rna206|rna206  [L=66]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0056   17.0   0.3     0.0065   16.8   0.3    1.1  1  TSNAXIP1_N       Translin-associated factor X-interacting N-t
  ------ inclusion threshold ------
      0.011   15.6   2.1      0.013   15.4   2.1    1.0  1  Sec34            Sec34-like family
      0.024   15.1   0.4      0.026   14.9   0.4    1.1  1  DASH_Dad2        DASH complex subunit Dad2
      0.026   14.2   2.7       0.12   12.1   1.2    1.6  1  YkyA             Putative cell-wall binding lipoprotein
       0.03   14.1   0.9      0.035   13.9   0.9    1.0  1  TACC_C           Transforming acidic coiled-coil-containing p
      0.033   13.7   0.3      0.038   13.5   0.3    1.1  1  DegS             Sensor protein DegS
      0.033   14.6   1.5      0.035   14.5   1.5    1.0  1  Snapin_Pallidin  Snapin/Pallidin
      0.033   13.6   0.1      0.037   13.5   0.1    1.0  1  adh_short        short chain dehydrogenase
      0.042   13.9   0.3      0.049   13.7   0.3    1.2  1  Prefoldin_3      Prefoldin subunit
      0.044   14.4   0.7      0.067   13.8   0.7    1.4  1  Anti-adapt_IraP  Sigma-S stabilisation anti-adaptor protein
      0.045   13.8   0.7      0.047   13.7   0.7    1.1  1  Laminin_II       Laminin Domain II
      0.056   13.2   0.2      0.056   13.2   0.2    1.0  1  DUF2857          Protein of unknown function (DUF2857)
      0.061   13.1   0.1       0.33   10.7   0.0    1.8  2  GlutR_N          Glutamyl-tRNAGlu reductase, N-terminal domai
       0.26   10.8   3.6       0.28   10.7   3.6    1.0  1  Tsc35            Testis-specific protein 35
       0.66    9.8   4.1        1.5    8.7   0.8    2.2  2  DASH_Dam1        DASH complex subunit Dam1


Domain annotation for each model (and alignments):
>> TSNAXIP1_N  Translin-associated factor X-interacting N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.3   5.5e-06    0.0065       5      54 ..       6      54 ..       2      63 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 5.5e-06
                     TSNAXIP1_N  5 ekelqklkctedgpqekrlqvyrevFedlieefkaYkdlLseIKkEYely 54
                                    ++l +l ++++++  ++l+ +   F+++  +fk   ++L ++Kk ++ly
  gene206|gene206|rna206|rna206  6 LDKLSEL-NEDSKELLDKLNQFNASFDTVTLNFKNMEQILGQVKKAFDLY 54
                                   5667777.778889999*******************************99 PP

>> Sec34  Sec34-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   2.1   1.1e-05     0.013      19      77 ..       2      60 ..       1      64 [. 0.91

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.1e-05
                          Sec34 19 tdealeqLeeleekfksvsektsslheaceqlleeqkrleelaeeieekLkyFeeldpi 77
                                   t+e+l++L+el+e+ k+  +k ++++++ ++++ + k++e++  ++++  + ++e+  +
  gene206|gene206|rna206|rna206  2 TQELLDKLSELNEDSKELLDKLNQFNASFDTVTLNFKNMEQILGQVKKAFDLYKEVTVL 60
                                   68999********************************************9999998765 PP

>> DASH_Dad2  DASH complex subunit Dad2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.4   2.2e-05     0.026      11      55 ..       6      50 ..       2      65 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.2e-05
                      DASH_Dad2 11 LeaLkqlrdlsdslakqleeLeeklstladgteavasVlanWqnv 55
                                   L++L +l++ s++l ++l++++  ++t++ + +  +++l++ ++ 
  gene206|gene206|rna206|rna206  6 LDKLSELNEDSKELLDKLNQFNASFDTVTLNFKNMEQILGQVKKA 50
                                   899**********************************99876665 PP

>> YkyA  Putative cell-wall binding lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   1.2   9.9e-05      0.12     146     177 ..       3      34 ..       1      43 [. 0.86

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 9.9e-05
                           YkyA 146 eeleeqiekiNesyeevkeaneqFneatkkyn 177
                                    +el ++++++Ne ++e+ ++ +qFn +++++ 
  gene206|gene206|rna206|rna206   3 QELLDKLSELNEDSKELLDKLNQFNASFDTVT 34 
                                    78999*********************998875 PP

>> TACC_C  Transforming acidic coiled-coil-containing protein (TACC), C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.9     3e-05     0.035      68     118 ..       7      57 ..       2      62 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3e-05
                         TACC_C  68 keiqkvleekeqlladlnsveksfsdlfkryekqkevlegykkneeslkkc 118
                                     +++++ e+ ++ll +ln+ + sf+ +   ++++ + l + kk  + +k++
  gene206|gene206|rna206|rna206   7 DKLSELNEDSKELLDKLNQFNASFDTVTLNFKNMEQILGQVKKAFDLYKEV 57 
                                    56889999**********************************998888875 PP

>> DegS  Sensor protein DegS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.3   3.2e-05     0.038      28      78 ..       8      58 ..       2      62 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.2e-05
                           DegS 28 everlkkeleelkeevsevikevdklekkerkarkrLaeVskdFkkyseee 78
                                    +++l+++ +el +++++  ++ d+++ + +++ + L +V k F+ y+e +
  gene206|gene206|rna206|rna206  8 KLSELNEDSKELLDKLNQFNASFDTVTLNFKNMEQILGQVKKAFDLYKEVT 58
                                   5678999999**************************************976 PP

>> Snapin_Pallidin  Snapin/Pallidin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   1.5     3e-05     0.035      16      80 ..       3      65 ..       1      66 [] 0.91

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3e-05
                Snapin_Pallidin 16 deldeklkelrqsQeeLleqldrlnekLkeleeaqeaevlpdlkeyakKLvnikkrmsslnerlq 80
                                   +el +kl+el +  +eLl++l++ n++++ +  + +   ++++   +kK   + k+++ l +++ 
  gene206|gene206|rna206|rna206  3 QELLDKLSELNEDSKELLDKLNQFNASFDTVTLNFK--NMEQILGQVKKAFDLYKEVTVLINKSD 65
                                   577899***********************9887777..8*******************9998875 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   3.1e-05     0.037      33      83 ..      12      62 ..       5      64 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.1e-05
                                   CHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSSESEEEE CS
                      adh_short 33 seekleevakelkeegakalaiqvDvtdreevealvekavkklgkldvLvn 83
                                    +e+ +e++++l++ +a++ +++++ +++e++   v+ka + ++++ vL+n
  gene206|gene206|rna206|rna206 12 LNEDSKELLDKLNQFNASFDTVTLNFKNMEQILGQVKKAFDLYKEVTVLIN 62
                                   56888999*****99***********************************9 PP

>> Prefoldin_3  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.3   4.1e-05     0.049      15      61 ..       3      49 ..       2      65 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.1e-05
                    Prefoldin_3 15 dglkeeisalkeeddateedllriardfegslvtekEveeilGekqg 61
                                   ++l +++s+l+e+++   ++l + +  f+   ++ k +e+ilG+ ++
  gene206|gene206|rna206|rna206  3 QELLDKLSELNEDSKELLDKLNQFNASFDTVTLNFKNMEQILGQVKK 49
                                   578899999*99999999*************************9775 PP

>> Anti-adapt_IraP  Sigma-S stabilisation anti-adaptor protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.7   5.6e-05     0.067       7      70 ..       4      65 ..       1      66 [] 0.82

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 5.6e-05
                Anti-adapt_IraP  7 elLvklakkeeeskeLtaqVealelllsallltlskekvqeliesvekainsalessdevlksd 70
                                   elL kl++ +e+skeL  + +  +  +   +l++  ++++++ ++v+ka++  +e +  ++ksd
  gene206|gene206|rna206|rna206  4 ELLDKLSELNEDSKELLDKLNQFNASFDTVTLNF--KNMEQILGQVKKAFDLYKEVTVLINKSD 65
                                   89*******************9998888777666..479999******9987777665555555 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.7   3.9e-05     0.047      27      71 ..       3      47 ..       1      65 [. 0.58

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.9e-05
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTT CS
                     Laminin_II 27 entkeklseinrsveetnekvkdankairdArrsvkkLeklapqL 71
                                   +++ +klse+n++ +e  +k++++n   + +  + k++e+ + q+
  gene206|gene206|rna206|rna206  3 QELLDKLSELNEDSKELLDKLNQFNASFDTVTLNFKNMEQILGQV 47
                                   455566666666666666666666666666666666666655443 PP

>> DUF2857  Protein of unknown function (DUF2857)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.2   4.7e-05     0.056      28      71 ..       7      50 ..       1      63 [. 0.79

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.7e-05
                        DUF2857 28 eeldaLkqlsledlhalsnsrvsvlkvsvdhealrrlLkqaree 71
                                   ++l +L++ s e l +l ++++s+ +v+++ ++++++L q+++ 
  gene206|gene206|rna206|rna206  7 DKLSELNEDSKELLDKLNQFNASFDTVTLNFKNMEQILGQVKKA 50
                                   345555666677789999**********************9875 PP

>> GlutR_N  Glutamyl-tRNAGlu reductase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.31   3.7e+02      11      33 ..       4      27 ..       1      39 [. 0.67
   2 ?   10.7   0.0   0.00028      0.33     105     123 ..      41      59 ..      38      64 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.31
                        GlutR_N 11 elreklafseeelkellkelee.k 33
                                   el++kl+  +e+ kell++l++ +
  gene206|gene206|rna206|rna206  4 ELLDKLSELNEDSKELLDKLNQfN 27
                                   677888888888888888883323 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00028
                        GlutR_N 105 dqIlgQvkeayelakeagt 123
                                    +qIlgQvk+a++l ke  +
  gene206|gene206|rna206|rna206  41 EQILGQVKKAFDLYKEVTV 59 
                                    6***********9998765 PP

>> Tsc35  Testis-specific protein 35
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   3.6   0.00023      0.28      48     109 ..       1      64 [.       1      66 [] 0.86

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00023
                          Tsc35  48 vtkelknelrevreelkekmeeikqikdimdkdfdklkefveimkemqkdmd..ekmdvliniq 109
                                    +t+el ++l e+ e+ ke ++ + q     d     +k++ +i+ +++k  d    + vlin  
  gene206|gene206|rna206|rna206   1 MTQELLDKLSELNEDSKELLDKLNQFNASFDTVTLNFKNMEQILGQVKKAFDlyKEVTVLINKS 64 
                                    7******************************999999999999999999776225677777765 PP

>> DASH_Dam1  DASH complex subunit Dam1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   1.6    0.0027       3.3       7      36 ..       4      30 ..       2      32 .. 0.68
   2 ?    8.7   0.8    0.0012       1.5       2      30 ..      20      48 ..      19      52 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0027
                      DASH_Dam1  7 eLaDsletLdknledLqqihesLsdfNeSF 36
                                   eL D+l++L++  +   ++ ++L++fN SF
  gene206|gene206|rna206|rna206  4 ELLDKLSELNEDSK---ELLDKLNQFNASF 30
                                   56666666665554...4568999999998 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0012
                      DASH_Dam1  2 epafaeLaDsletLdknledLqqihesLs 30
                                    +++++++ s +t++ n+++++qi  +++
  gene206|gene206|rna206|rna206 20 LDKLNQFNASFDTVTLNFKNMEQILGQVK 48
                                   68999999*************99977665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (66 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1333  (0.0743488); expected 358.6 (0.02)
Passed bias filter:                      664  (0.037035); expected 358.6 (0.02)
Passed Vit filter:                       106  (0.00591221); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 510.00
//
Query:       gene2061|gene2061|rna2061|rna2061  [L=434]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-69  233.9   0.0    2.6e-69  233.4   0.0    1.2  1  Tubulin          Tubulin/FtsZ family, GTPase domain
    2.5e-48  163.4   0.1    3.8e-48  162.8   0.1    1.3  1  Tubulin_C        Tubulin C-terminal domain
    0.00051   19.8   0.0    0.00099   18.8   0.0    1.5  1  Tubulin_3        Tubulin domain
  ------ inclusion threshold ------
      0.098   13.0   0.0       0.18   12.1   0.0    1.4  1  Misat_Tub_SegII  Misato Segment II tubulin-like domain


Domain annotation for each model (and alignments):
>> Tubulin  Tubulin/FtsZ family, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  233.4   0.0   5.8e-73   2.6e-69       1     196 [.       3     210 ..       3     211 .. 0.99

  Alignments for each domain:
  == domain 1  score: 233.4 bits;  conditional E-value: 5.8e-73
                                        EEEEEEEHHHHHHHHHHHHH...HHHCH.............HHHT.....TTEEEEE....EEESBHHHHHTS-GS CS
                            Tubulin   1 eiivigvGqcGnqignelwellakehgiqsdg.........dslesfFsesgkveyiprsvaidtdpqvlneikag 67 
                                        eii i++Gq+G+qign++wel++kehgiq+dg         ds  sfFses +++y+pr+v+id++p v++++++g
  gene2061|gene2061|rna2061|rna2061   3 EIISIHIGQAGVQIGNACWELYCKEHGIQPDGrpdenfgrnDSCLSFFSESCENTYVPRTVMIDLEPGVIESVQKG 78 
                                        79***************************999******************************************** PP

                                        ........EEEE--CCCCTTC--TT-HHHHHHHHHHTHHHHHHHHTT-SE.SEEEEEEETTSSHHHHHHHHHHHHH CS
                            Tubulin  68 s..elfnpnklllgkegagnngaggypevgkeaaeeileeirkevekcdslqgffitaslgGGTGSGlgpvilevl 141
                                        +  +lf+p++l+ gke+a+nn+a+g+++vgke+ +e+l++irk +e+c+ lqgf+i++s+gGGTGSG+g++++++l
  gene2061|gene2061|rna2061|rna2061  79 PfkKLFHPEQLIHGKEDAANNYARGHYTVGKEILDESLDRIRKLTENCEGLQGFLIFHSFGGGTGSGFGALLMDRL 154
                                        **************************************************************************** PP

                                        HHTSTTSEEEEEEEE--.GG.G-HHHHHHHHHHHHHHHHT-SEEEEEEHHHHHCCS CS
                            Tubulin 142 keeypkalvvtvvvlPs.efsevvvepynailalkelieesdavividNdaLlkil 196
                                           y k+ ++ ++v+P  ++s+ vvepyn+il++++  ++sd+ +++dN+a+++++
  gene2061|gene2061|rna2061|rna2061 155 TSVYGKKSKLEFSVYPApKISTAVVEPYNSILTTHTTLDHSDCSFLVDNEAIYDMC 210
                                        ******************************************************98 PP

>> Tubulin_C  Tubulin C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  162.8   0.1   8.5e-52   3.8e-48       1     125 [.     259     388 ..     259     389 .. 0.99

  Alignments for each domain:
  == domain 1  score: 162.8 bits;  conditional E-value: 8.5e-52
                                        TTC-EEEEEEESSSCTTTTTCS-HHHHHHHHHTCSGGGBSSSTSTTTSSEEEEEEEEEESSSHHHHHHHHHHHHHT CS
                          Tubulin_C   1 PrlhFlltsyaPlvsaekaavektsvqdvtrallepknimvkvdprkgkylaiallirGdvepkevnkavqrikek 76 
                                        Pr+hF+l++y+P++s+eka++e++svq++t+a++++kn+mvk++p++gky+a++ll+rGdv+pk+vn+a    k+k
  gene2061|gene2061|rna2061|rna2061 259 PRIHFPLVAYSPMLSREKASHEQLSVQEITSACFDSKNQMVKCNPQNGKYMACCLLFRGDVNPKDVNQATLIAKTK 334
                                        9*************************************************************************** PP

                                        TTS-BSTTSTTTEEEEEEECECT-TTTS.....SCEEEEEEEEGGGHHHHHHHH CS
                          Tubulin_C  77 kkaqfveWiptgikvalnkkspyvkkqs.....kvsvlmlaNttsiaelfkrll 125
                                        +++qfveW+ptg+k+++nk+ p+v ++      k++v+ml+Ntt+iae++ rl+
  gene2061|gene2061|rna2061|rna2061 335 RSSQFVEWCPTGFKIGMNKREPTVLDGGamapvKRAVCMLSNTTAIAEAWARLN 388
                                        **************************999**********************986 PP

>> Tubulin_3  Tubulin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   2.2e-07   0.00099      58     107 ..     114     163 ..      80     190 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 2.2e-07
                          Tubulin_3  58 dlldrdlrpfaeecdqlrglqvftgvddaWG.Gfaakylerlrdeygkksi 107
                                        + ldr +r++ e+c+ l+g+ +f +     G Gf+a  ++rl   ygkks 
  gene2061|gene2061|rna2061|rna2061 114 ESLDR-IRKLTENCEGLQGFLIFHSFGGGTGsGFGALLMDRLTSVYGKKSK 163
                                        34666.8******************99887769***************985 PP

>> Misat_Tub_SegII  Misato Segment II tubulin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0     4e-05      0.18       1      71 [.       2      73 ..       2     111 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 4e-05
                    Misat_Tub_SegII  1 rEivtlqlGnyaNyvgtHfWNt..QesyftydeeeeesevdhdvlfregetkqgqvtytPRllivDlkgslgs 71
                                       rEi+++ +G+    +g   W +  +e+ ++ d + + ++  ++ +  +  +++ + ty+PR++++Dl+ ++ +
  gene2061|gene2061|rna2061|rna2061  2 REIISIHIGQAGVQIGNACWELycKEHGIQPDGRPD-ENFGRNDSCLSFFSESCENTYVPRTVMIDLEPGVIE 73
                                       799999999999999999998633677776666555.5553333333434567899**********9876654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (434 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       340  (0.0189637); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.22s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 3226.61
//
Query:       gene2062|gene2062|rna2062|rna2062  [L=285]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.9e-15   55.0   0.0    1.1e-09   37.5   0.0    2.7  3  Actin           Actin
  ------ inclusion threshold ------
       0.13   11.7   0.0       0.21   11.1   0.0    1.2  1  BcrAD_BadFG     BadF/BadG/BcrA/BcrD ATPase family
       0.14   12.4   0.1       0.29   11.3   0.1    1.5  2  Condensin2nSMC  Condensin II non structural maintenance of ch
       0.16   12.1   2.7        5.5    7.2   0.1    2.7  2  DUF3896         Protein of unknown function (DUF3896)


Domain annotation for each model (and alignments):
>> Actin  Actin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.11   4.7e+02       6      23 ..      18      35 ..      15      39 .. 0.82
   2 !   14.2   0.0   2.8e-06     0.013     113     166 ..      82     135 ..      69     139 .. 0.86
   3 !   37.5   0.0   2.3e-13   1.1e-09     273     404 ..     153     278 ..     141     280 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.11
                              Actin  6 avVlDnGssttraGyage 23
                                        +++D G+s+ ++G +  
  gene2062|gene2062|rna2062|rna2062 18 IFIIDIGTSFYKMGHSLR 35
                                       689***********9765 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 2.8e-06
                              Actin 113 alEivfEkfkvpalylaksavlsafasgkstglvvDsGasvtsvvpVldGyvLk 166
                                        +l  +fEk  v++++++++ v+ ++a+gk++g+++++  s    +++ d +v++
  gene2062|gene2062|rna2062|rna2062  82 VLSNLFEKRLVQGIMFVDDRVMDLYAAGKNNGIIINVSGSGVECAAICDSLVVE 135
                                        44557*******************************988888889999988875 PP

  == domain 3  score: 37.5 bits;  conditional E-value: 2.3e-13
                              Actin 273 geeRfkvpEiLFdpsligsesaleeekskllgiselivaainacdvdlrpeLlanivvtGGnsllpglteRlekel 348
                                        ge++f + E     ++++++ +++ +++ l  i + + + in+++++++++Llaniv++GG +  p lte +   l
  gene2062|gene2062|rna2062|rna2062 153 GEDKFVFKETFNYLEESKNTLEEKVKQKVLNDIEKAMNDLINKIKPEMKNSLLANIVLCGGYAKPPSLTEKIYDVL 228
                                        56666777766555556666565556888999*****************************************999 PP

                              Actin 349 aqlaskgvkvkiiapeeerkysaWiGGSiLAslgtfqqlwvskqEYeEqGssvver 404
                                        ++   +  ++k++++    ++s+++G  iL++l+++    +  ++YeE+G++v ++
  gene2062|gene2062|rna2062|rna2062 229 SK---EHKNIKVTKEL--DIFSTYTGCDILSRLDDLD-YFIGMKDYEEYGANVLDK 278
                                        99...55678888876..89**************997.568999*******99876 PP

>> BcrAD_BadFG  BadF/BadG/BcrA/BcrD ATPase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   4.7e-05      0.21     185     251 ..     168     239 ..     155     250 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 4.7e-05
                                        HHTT--HHHHHHHHHHHHHHHHHHHHHTT---SS......EEEESGGGG-HHHHHHH.....HHHH-S-EE- CS
                        BcrAD_BadFG 185 lsggekaedIlaglhraialrvialisrsggvtde.....vtltGGvakneaavkelrklvkenygevkini 251
                                        +s+++  e++ +++ ++i++ ++ li++++ + ++     ++l GG ak   + +++ + +++++ + k+  
  gene2062|gene2062|rna2062|rna2062 168 ESKNTLEEKVKQKVLNDIEKAMNDLINKIKPEMKNsllanIVLCGGYAKPPSLTEKIYDVLSKEHKNIKVTK 239
                                        6788888888899999999999999999999888889999***********************999877654 PP

>> Condensin2nSMC  Condensin II non structural maintenance of chromosomes subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       1.9   8.7e+03      95     108 ..      80      93 ..      61     103 .. 0.71
   2 ?   11.3   0.1   6.5e-05      0.29      10     113 ..     138     244 ..     132     255 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 1.9
                     Condensin2nSMC  95 rkvLsafhskkkek 108
                                        r+vLs++ +k+  +
  gene2062|gene2062|rna2062|rna2062  80 RRVLSNLFEKRLVQ 93 
                                        66676666666554 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 6.5e-05
                     Condensin2nSMC  10 kteeGrkflafvlt..ldtklikeilkaiksqipkleksvleaygeilfraWkkasgelkeeieesciqdlmeaal 83 
                                        k  +G+++ a++l+   d+ ++ke ++ +++    le++v +++ + + +a ++  +++k e+++s++ +++ +  
  gene2062|gene2062|rna2062|rna2062 138 KIYDGKEIDAWILKdgEDKFVFKETFNYLEESKNTLEEKVKQKVLNDIEKAMNDLINKIKPEMKNSLLANIVLCGG 213
                                        5567888888888874444556889999999999999999888888888899999999****************** PP

                     Condensin2nSMC  84 hakrkklakklrkvLsafhsk.kkekeveem 113
                                        +ak ++l +k+ +vLs+ h++ k +ke++ +
  gene2062|gene2062|rna2062|rna2062 214 YAKPPSLTEKIYDVLSKEHKNiKVTKELDIF 244
                                        **************************99865 PP

>> DUF3896  Protein of unknown function (DUF3896)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.1    0.0012       5.5      38      55 ..      49      66 ..      43      69 .. 0.90
   2 ?    4.0   0.5     0.013        57       8      34 ..     160     186 ..     155     209 .. 0.68

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0012
                            DUF3896 38 lkleidnyeyilnlvemn 55
                                       + +ei++ye  lnl+e n
  gene2062|gene2062|rna2062|rna2062 49 VDKEINDYETYLNLIESN 66
                                       568*************88 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.013
                            DUF3896   8 natkkyleekkqqlCkklssltlskke 34 
                                        + t  ylee k  l +k+++  l + e
  gene2062|gene2062|rna2062|rna2062 160 KETFNYLEESKNTLEEKVKQKVLNDIE 186
                                        456667777777777666665555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (285 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1138  (0.0634726); expected 358.6 (0.02)
Passed bias filter:                      678  (0.0378158); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.59u 0.33s 00:00:00.92 Elapsed: 00:00:00.52
# Mc/sec: 1660.24
//
Query:       gene2063|gene2063|rna2063|rna2063  [L=75]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       505  (0.0281667); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 524.14
//
Query:       gene2064|gene2064|rna2064|rna2064  [L=100]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       499  (0.027832); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 767.14
//
Query:       gene2065|gene2065|rna2065|rna2065  [L=871]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (871 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       397  (0.0221429); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.62u 0.30s 00:00:00.92 Elapsed: 00:00:00.48
# Mc/sec: 5446.69
//
Query:       gene2066|gene2066|rna2066|rna2066  [L=46]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (46 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       285  (0.015896); expected 358.6 (0.02)
Passed bias filter:                      213  (0.0118802); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.45
# Mc/sec: 306.77
//
Query:       gene2067|gene2067|rna2067|rna2067  [L=151]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.1e-16   58.3   0.0    8.5e-16   57.8   0.0    1.2  1  dUTPase   dUTPase


Domain annotation for each model (and alignments):
>> dUTPase  dUTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.8   0.0   4.7e-20   8.5e-16      18     129 .]      43     150 ..      33     150 .. 0.94

  Alignments for each domain:
  == domain 1  score: 57.8 bits;  conditional E-value: 4.7e-20
                                        EE-SSSEEEETTEEEEEEEEEEEE--TTEEEEEEE-HHHHHHHEEEEEEEEETTBTSEEEEEEEE-SSS-EEE-TT CS
                            dUTPase  18 lsaakdltvkpgetvlvptdisiklpdglaalilpRSglaakglivvpgvidsdyrGevkvvlfnltkkdvkikkg 93 
                                        l a++ + +k+++t l+p++++ + p ++  +i+   +     l++++gvidsdyrGe+++++ n +++dv++++g
  gene2067|gene2067|rna2067|rna2067  43 LFAPQSTSIKAHQTALLPLGLKTAFPSEYFLFITTTRS----PLVSTGGVIDSDYRGELGLIVCNAGDCDVTVERG 114
                                        678999**********************9999986544....699999**************************** PP

                                        -EEEEEEEEEBECGEEEEESSTTTESSBTTXTTTTX CS
                            dUTPase  94 dRiAqLifariltaeleevetlkatergeggfgssg 129
                                        +++   +f +i+ + ++ ve l+++ rg+ gfgs+g
  gene2067|gene2067|rna2067|rna2067 115 ECVGEGVFFKIVVPVFDVVEVLDDSVRGSDGFGSTG 150
                                        *********************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       254  (0.014167); expected 358.6 (0.02)
Passed bias filter:                      237  (0.0132188); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1096.71
//
Query:       gene2068|gene2068|rna2068|rna2068  [L=942]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (942 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       728  (0.0406046); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.66u 0.28s 00:00:00.94 Elapsed: 00:00:00.44
# Mc/sec: 6435.84
//
Query:       gene2069|gene2069|rna2069|rna2069  [L=128]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
      0.012   15.4   0.2      0.013   15.2   0.2    1.1  1  Cactin_mid  Conserved mid region of cactin
       0.05   14.0   0.0      0.062   13.7   0.0    1.1  1  DUF4199     Protein of unknown function (DUF4199)


Domain annotation for each model (and alignments):
>> Cactin_mid  Conserved mid region of cactin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.2   1.5e-06     0.013      75     146 ..      16      87 ..       1      97 [. 0.68

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.5e-06
                         Cactin_mid  75 glsleeleeleediksylelekseknaefWkallvvckdeleklkkkeeekeaaeeaeesgihasveadikk 146
                                        +l+l+ ++++ +  ++  ++ ++++   + k ll+ ckdel+++ k++++ ++ e +++ ++  +++++i++
  gene2069|gene2069|rna2069|rna2069  16 DLTLRSIKNIVKRYNKQRKVTQTDTSPTYLKLLLTSCKDELKEMSKNKKRITSMEIEKMMSLIGEISQEIND 87 
                                        245555555555555555556679999****************99998885554555666666677777765 PP

>> DUF4199  Protein of unknown function (DUF4199)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   6.9e-06     0.062      97     167 ..      42     123 ..      34     124 .. 0.55

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6.9e-06
                            DUF4199  97 pdfienyiaeilekleeakeesaeeenaemseeeikeale...sls.............piiv.alqsflgnliiG 155
                                        p++++ ++++ +++l+e+ ++ +       +  ei+++++   ++s                  + + + + ++i+
  gene2069|gene2069|rna2069|rna2069  42 PTYLKLLLTSCKDELKEMSKNKKR-----ITSMEIEKMMSligEISqeindlgkicgveK-KRnTRMVYYSLFVIC 111
                                        555555555555555555444433.....4444444444433322233334445555531.333788888888888 PP

                            DUF4199 156 lilsliiAlilk 167
                                        +i+++++++i+k
  gene2069|gene2069|rna2069|rna2069 112 IIVGVVVGAIVK 123
                                        888888888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2344  (0.130738); expected 358.6 (0.02)
Passed bias filter:                     1061  (0.0591779); expected 358.6 (0.02)
Passed Vit filter:                       105  (0.00585643); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 885.42
//
Query:       gene207|gene207|rna207|rna207  [L=201]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.1e-40  137.7   0.7    3.5e-40  137.5   0.7    1.0  1  Proteasome     Proteasome subunit
  ------ inclusion threshold ------
      0.057   12.7   0.0      0.071   12.3   0.0    1.1  1  SabA_adhesion  SabA N-terminal extracellular adhesion domain


Domain annotation for each model (and alignments):
>> Proteasome  Proteasome subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  137.5   0.7   3.9e-44   3.5e-40       3     190 .]       7     186 ..       5     186 .. 0.96

  Alignments for each domain:
  == domain 1  score: 137.5 bits;  conditional E-value: 3.9e-44
                                    HS-EEEEEEETTEEEEEEEEEEEETTEEEESSSSTSEEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHSSGTCHH CS
                     Proteasome   3 kGttvvGikgkdgvvlaadkratagskllskstveKifkiddhigvafaGlaaDartlvrraraeaqlyrlrygrpipve 82 
                                    +Gtt+v++k+++gv++aad+r+++g++++++ + +K+ k+ ++i+++ +G  + ++++++++ ++ +l  ++++r++ v+
  gene207|gene207|rna207|rna207   7 TGTTIVAMKFEGGVIMAADSRTSMGNYVVNRVS-NKLTKLAPKIYCCRSGRSSHTQAVAEYVASRTNLIAYTNEREPLVR 85 
                                    7***************************99996.********************************************** PP

                                    HHHHHHHHHHHHHHHHCTTTTTSEEEEEEEEETTTEEEEEEEETTSEEEEESSEEEES.TTHHHHHHHHHHHHSTTBSHH CS
                     Proteasome  83 rlvarvaaklqaytqrsgrrpfgvslliagvdeeggpeLyqidpsGsyieekdavaiG.sgseaaktalekeykedltle 161
                                         +a+++ a  +++   ++ +s+++ag+dee++ ++y+i+  Gs+++ +   a+G sgs + ++++++ y++d++ e
  gene207|gene207|rna207|rna207  86 ----DAANLIRAVVYYN--PMLTASIIVAGYDEEDKGSVYSINLGGSLLKRE--WAMGgSGSAFLYGYCDSMYRSDMSFE 157
                                    ....9999999999999..6799****************************8..67766********************* PP

                                    HHHHHHHHHHHHHHHHBTTSCSSEEEEEE CS
                     Proteasome 162 eavelavkalkealerdklsgknievavi 190
                                    e +el +k ++ a++rd++sg+ i+++vi
  gene207|gene207|rna207|rna207 158 EKFELTKKLVQLAIKRDNMSGGCIRMTVI 186
                                    *************************9997 PP

>> SabA_adhesion  SabA N-terminal extracellular adhesion domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   7.9e-06     0.071     152     229 ..      27     104 ..      11     125 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 7.9e-06
                  SabA_adhesion 152 kgeklevnvtkenrrtadinrekftatngkevsvkesngkskkatvkldvtnnAenLLkqAatilqvLktqcPllrak 229
                                    ++  +   v++ +++ ++   + +   +g+   ++ +     + t  + +tn+ e L++ Aa++++ +  + P+l+a+
  gene207|gene207|rna207|rna207  27 RTSMGNYVVNRVSNKLTKLAPKIYCCRSGRSSHTQAVAEYVASRTNLIAYTNEREPLVRDAANLIRAVVYYNPMLTAS 104
                                    44455555556566666666688899999999999999999*********************************9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (201 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       540  (0.0301188); expected 358.6 (0.02)
Passed bias filter:                      485  (0.0270511); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1363.46
//
Query:       gene2070|gene2070|rna2070|rna2070  [L=120]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.07   13.7   0.8         31    5.9   0.1    3.0  2  TMP       TMP repeat


Domain annotation for each model (and alignments):
>> TMP  TMP repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.1    0.0017        31       2      11 .]      72      81 ..      72      81 .. 0.92
   2 ?    5.3   0.0    0.0027        48       3      10 ..      84      91 ..      83      92 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0017
                                TMP  2 egIksffsga 11
                                       e+I++ffsg+
  gene2070|gene2070|rna2070|rna2070 72 ENISNFFSGI 81
                                       79******97 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0027
                                TMP  3 gIksffsg 10
                                       gIk+ff++
  gene2070|gene2070|rna2070|rna2070 84 GIKKFFKK 91
                                       9*****96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1557  (0.0868425); expected 358.6 (0.02)
Passed bias filter:                      490  (0.02733); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 927.24
//
Query:       gene2071|gene2071|rna2071|rna2071  [L=352]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (352 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       565  (0.0315132); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 2434.12
//
Query:       gene2072|gene2072|rna2072|rna2072  [L=188]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0089   15.8   0.4      0.028   14.2   0.4    1.8  1  LRR_8     Leucine rich repeat


Domain annotation for each model (and alignments):
>> LRR_8  Leucine rich repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.4   1.6e-06     0.028      24      61 .]     130     167 ..     127     167 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.6e-06
                                        -TT--EEE--SS---GGGGGGGTT--S-.EEE--SS-- CS
                              LRR_8  24 lsnLkvLdLsnNllttlspgafsgLpsLrsLdLsgNrL 61 
                                        l  Lk L+L++N+++   +  +  L++L+++ + +N++
  gene2072|gene2072|rna2072|rna2072 130 LGELKKLELKENKMKNYQRLNMKKLEALTKIKIVNNKI 167
                                        778*********************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       906  (0.0505327); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 1317.13
//
Query:       gene2073|gene2073|rna2073|rna2073  [L=47]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.056   13.4   0.0      0.056   13.4   0.0    1.0  1  UCR_14kD  Ubiquinol-cytochrome C reductase complex 14kD subun


Domain annotation for each model (and alignments):
>> UCR_14kD  Ubiquinol-cytochrome C reductase complex 14kD subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   3.1e-06     0.056      32      75 ..       3      46 ..       1      47 [] 0.91

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.1e-06
                           UCR_14kD 32 seenedvqeALrrLpeeeaydRvfRlkrAlqlslkhklLPkeew 75
                                       ++  + ++ AL    ++e+ dR  Rl+  +  +lk  +LPk+ w
  gene2073|gene2073|rna2073|rna2073  3 EDTMPGIKDALPINGQSESADRHSRLRYDTRAELKLLVLPKNVW 46
                                       556788999999999***************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (47 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       148  (0.00825478); expected 358.6 (0.02)
Passed bias filter:                      135  (0.0075297); expected 358.6 (0.02)
Passed Vit filter:                         3  (0.000167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.33u 0.22s 00:00:00.55 Elapsed: 00:00:00.39
# Mc/sec: 363.78
//
Query:       gene2074|gene2074|rna2074|rna2074  [L=35]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (35 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       332  (0.0185175); expected 358.6 (0.02)
Passed bias filter:                      219  (0.0122148); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.31u 0.29s 00:00:00.60 Elapsed: 00:00:00.41
# Mc/sec: 254.82
//
Query:       gene2075|gene2075|rna2075|rna2075  [L=255]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       473  (0.0263818); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1833.71
//
Query:       gene2076|gene2076|rna2076|rna2076  [L=327]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.8e-17   62.2   1.6    9.3e-17   61.3   1.6    1.5  1  RhoGAP    RhoGAP domain


Domain annotation for each model (and alignments):
>> RhoGAP  RhoGAP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.3   1.6   5.2e-21   9.3e-17       1     147 [.      91     250 ..      91     255 .. 0.92

  Alignments for each domain:
  == domain 1  score: 61.3 bits;  conditional E-value: 5.2e-21
                                        BHHHHHHHHHHHHHTTTSTTTTTS-S-HHHHHHHHHHHHHTGGGCT.......TTTTSCHHHHHHHHHHHHHHSSS CS
                             RhoGAP   1 PiivekcvefiekrgldtegiyRvsgskarvkelreafdkgkavds.......dleeedvhavaslLKrfLrelpe 69 
                                        Pi ++ ++e+i  + l++ g++R+s++ + ++++ + ++ +++ +        +l  +++ +++ + Kr + +++ 
  gene2076|gene2076|rna2076|rna2076  91 PIEFNCIMEAILTKNLNESGLFRKSANISDLERCFSLINDKETRQMyrleiinRLLPFNIITLTVVYKRLFDNYEM 166
                                        7888999*******************************999999889***************************** PP

                                        TTTTGGHHHHHHHHHTSSSHHHHHHHHHHHHTTS-HHHHHHHHHHHHHHHH....HHHTHHH..H---HHHHHHHH CS
                             RhoGAP  70 pLltkelyeelieaaksedeeerlealkellekLPkenrdtLryLlehLkr....vaenske..nkMtaknLaivf 139
                                        pL+++++++ l+++ak e++ e++  lk +l   Pk nr++  ++ +++      v++++k+   +M+++  a+v+
  gene2076|gene2076|rna2076|rna2076 167 PLIPHSYLKILLNVAKLENKYEQIVILKYVLYMIPKSNRNMVDSITQFFALmrylVTNYNKKptHNMDLHGFAVVI 242
                                        ************************************************975222266666657799********** PP

                                        HHHHHT-T CS
                             RhoGAP 140 aPtLlrpk 147
                                        +P ++ ++
  gene2076|gene2076|rna2076|rna2076 243 MPKIFLKP 250
                                        ***99776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (327 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       701  (0.0390987); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 2301.60
//
Query:       gene2077|gene2077|rna2077|rna2077  [L=54]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      7e-05   23.0   0.0    7.6e-05   22.8   0.0    1.1  1  Spindle_Spc25  Chromosome segregation protein Spc25


Domain annotation for each model (and alignments):
>> Spindle_Spc25  Chromosome segregation protein Spc25
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.0   4.2e-09   7.6e-05      28      72 ..       2      44 ..       1      45 [. 0.89

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 4.2e-09
                      Spindle_Spc25 28 dvsedtyevlecsPkLedeeleelleeLnetndlgkFlkevRkaF 72
                                       d+++d  +v+e+ P + +  le++ +  n ++d++ Fl++vR  F
  gene2077|gene2077|rna2077|rna2077  2 DFKDDMESVTEIWPCVVS--LEKINSVQNMSDDFYDFLRRVRGIF 44
                                       66777678*******776..**********************999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (54 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       416  (0.0232026); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 377.81
//
Query:       gene2078|gene2078|rna2078|rna2078  [L=208]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.9e-05   21.7  20.2     0.0001   21.3  20.2    1.1  1  Spc7             Spc7 kinetochore protein
    0.00011   21.7  10.5    0.00014   21.3  10.5    1.1  1  DUF4407          Domain of unknown function (DUF4407)
    0.00033   20.5   5.4    0.00035   20.5   4.4    1.5  1  Bacillus_HBL     Bacillus haemolytic enterotoxin (HBL)
    0.00067   19.6  13.8    0.00067   19.6  13.8    2.9  3  TMF_DNA_bd       TATA element modulatory factor 1 DNA binding
     0.0014   18.8  13.3     0.0014   18.8  13.3    2.7  3  TMF_TATA_bd      TATA element modulatory factor 1 TATA bindin
     0.0038   15.9  17.6     0.0044   15.6  17.6    1.1  1  Macoilin         Macoilin family
     0.0081   15.6  18.0        0.1   12.0   3.9    2.2  2  DUF4618          Domain of unknown function (DUF4618)
  ------ inclusion threshold ------
      0.013   14.1  16.8      0.018   13.7  16.8    1.1  1  AAA_13           AAA domain
      0.014   15.5  19.6       0.45   10.7   4.2    2.4  2  Fib_alpha        Fibrinogen alpha/beta chain family
      0.026   12.4  12.7      0.036   12.0  12.7    1.2  1  V_ATPase_I       V-type ATPase 116kDa subunit family
      0.029   14.6  14.9      0.092   13.0  14.9    1.8  1  DUF5082          Domain of unknown function (DUF5082)
      0.029   14.0  23.6       0.36   10.4   7.1    2.1  2  Filament         Intermediate filament protein
      0.034   13.1  18.8      0.047   12.6  18.8    1.2  1  DUF812           Protein of unknown function (DUF812)
      0.045   11.3  18.2      0.062   10.8  18.2    1.1  1  DUF3584          Protein of unknown function (DUF3584)
       0.14   11.6  26.3        1.2    8.6  13.2    2.0  2  HMMR_N           Hyaluronan mediated motility receptor N-term
       0.14   12.2  15.3        0.1   12.6   8.2    2.3  2  Laminin_II       Laminin Domain II
       0.19   11.8  13.1       0.13   12.3   6.9    2.3  3  DUF1664          Protein of unknown function (DUF1664)
        0.2   11.7  16.2       0.32   11.0   2.8    2.3  2  FlxA             FlxA-like protein
       0.27    9.1  12.6       0.36    8.7  12.6    1.1  1  Prominin         Prominin
       0.28   11.2   4.0        7.1    6.7   4.0    2.2  1  Baculo_PEP_C     Baculovirus polyhedron envelope protein, PEP
       0.31   10.6  15.2        0.4   10.2  15.2    1.1  1  Exonuc_VII_L     Exonuclease VII, large subunit
       0.43   10.6  23.5        1.5    8.9   1.7    3.0  2  TPR_MLP1_2       TPR/MLP1/MLP2-like protein
       0.58   10.4   9.9        1.2    9.3   0.6    3.1  3  SpmSyn_N         S-adenosylmethionine decarboxylase N -termin
       0.97    8.8   9.3        1.2    8.5   9.3    1.1  1  Tam41_Mmp37      Phosphatidate cytidylyltransferase, mitochon
       0.99    8.2  10.7        1.3    7.7  10.7    1.2  1  ALMT             Aluminium activated malate transporter
        1.1    8.4  17.9         13    5.0  17.8    2.0  1  TMPIT            TMPIT-like protein
        1.2    9.5  18.4       0.22   11.9   2.1    3.2  3  Csm1_N           Csm1 N-terminal domain
        1.7    8.7  27.0        5.2    7.1  27.0    1.8  1  CENP-F_leu_zip   Leucine-rich repeats of kinetochore protein 
        1.8    9.0  23.6        1.9    9.0  12.0    2.3  2  CENP-H           Centromere protein H (CENP-H)
        2.1    8.4  18.4       0.38   10.7  11.7    2.1  2  DUF1043          Protein of unknown function (DUF1043)
        2.1    6.1  18.7        2.7    5.7  18.7    1.1  1  Nup88            Nuclear pore component
        2.5    7.8   5.9        2.6    7.7   5.0    1.4  1  DUF3492          Domain of unknown function (DUF3492)
        2.6    7.3  17.8        1.5    8.1   6.3    2.1  2  DUF3450          Protein of unknown function (DUF3450)
        2.8    7.7  23.1       0.65    9.8   8.9    2.1  2  DUF724           Protein of unknown function (DUF724)
        2.9    7.9  26.5          3    7.9   3.9    2.3  2  UPF0242          Uncharacterised protein family (UPF0242) N-t
        3.2    8.3  15.2       0.31   11.5   7.3    2.7  4  Snapin_Pallidin  Snapin/Pallidin
        3.4    7.2  22.7        4.2    7.0  13.1    2.2  2  PI3K_P85_iSH2    Phosphatidylinositol 3-kinase regulatory sub
        3.5    7.5  20.3       0.21   11.5   5.4    2.3  2  Phage_Mu_Gam     Bacteriophage Mu Gam like protein
        3.5    8.0  23.4        6.4    7.2  23.4    1.4  1  Fez1             Fez1
        3.7    7.6  13.4         91    3.0  13.4    2.0  1  DUF87            Helicase HerA, central domain
        3.8    6.3  24.5        1.2    8.0   9.7    2.1  2  CALCOCO1         Calcium binding and coiled-coil domain (CALC
        4.4    7.4   9.7        4.7    7.3   3.2    2.7  2  Bcr-Abl_Oligo    Bcr-Abl oncoprotein oligomerisation domain
        4.6    7.4  12.5        4.2    7.5   6.7    2.6  2  DUF2730          Protein of unknown function (DUF2730)
        4.9    7.5  22.8    6.3e+02    0.7  22.8    2.4  1  OmpH             Outer membrane protein (OmpH-like)
          5    6.9   8.1        3.4    7.4   2.9    2.4  2  Lectin_N         Hepatic lectin, N-terminal domain
          5    6.7  14.1         11    5.6   5.1    2.0  2  DUF2968          Protein of unknown function (DUF2968)
        5.1    6.9  23.1        0.5   10.2   3.8    3.3  3  DivIC            Septum formation initiator
        5.3    6.9  22.4        4.6    7.1  19.7    1.9  2  DASH_Spc19       Spc19
        5.7    7.0  24.6        6.4    6.8   9.1    2.1  2  ADIP             Afadin- and alpha -actinin-Binding
          6    7.6  20.7        3.5    8.3  12.5    2.9  3  YabA             Initiation control protein YabA
        6.6    6.5  28.6        1.2    8.9  12.8    2.0  2  ERM              Ezrin/radixin/moesin family
        9.2    6.8  28.0    3.2e+02    1.8  28.0    2.5  1  APG6_N           Apg6 coiled-coil region
        9.2    6.9   6.8    1.6e+02    2.9   6.8    2.5  1  YtxH             YtxH-like protein
        9.7    6.7  14.4      3e+02    1.9   1.0    2.8  2  DUF4140          N-terminal domain of unknown function (DUF41
        9.9    5.8  13.1       0.31   10.7   5.5    2.0  2  WASH-7_C         WASH complex subunit 7, C-terminal


Domain annotation for each model (and alignments):
>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3  20.2   3.1e-07    0.0001     157     282 ..      42     163 ..      24     188 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 3.1e-07
                               Spc7 157 lLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelaelqeqleel 232
                                        lL+++ ++++e++   +e+k++l++ +++++++ ++    ++ee++ lr++l++lk ++++ ++el e   + + l
  gene2078|gene2078|rna2078|rna2078  42 LLSESVKKIKEVKYTRKEQKERLSHDIQMMRAEIKK----NEEEINRLRSNLEKLKHTLDKERNELLEAHHENDGL 113
                                        689999**************************7776....899********************************* PP

                               Spc7 233 eekieelkeqkseleeeiaeaervleeckgwsesevsrlkeevkaleelt 282
                                        +++++e +e+k++le  ++e er ++  +  +++e ++++++ k+le + 
  gene2078|gene2078|rna2078|rna2078 114 SKQMAEYDENKKNLERLVNEIERRVRGLQAQKANEMRSIEANEKKLEAEA 163
                                        **************999999999999999999999999888888888664 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3  10.5   4.3e-07   0.00014     115     230 ..      56     167 ..      25     174 .. 0.79

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 4.3e-07
                            DUF4407 115 eqqeeakelkeqlaaa...ltaelaeleaqiaalqaeidaaearldalraeaqkeldgtkgtgttgvaGkgpaake 187
                                        +++e++++l      +   ++ae++++e++i++l++++++++ +ld++r+e+ +  + + g   +++a + ++ k+
  gene2078|gene2078|rna2078|rna2078  56 TRKEQKERL----SHDiqmMRAEIKKNEEEINRLRSNLEKLKHTLDKERNELLEAHHENDG-LSKQMAEYDENKKN 126
                                        222222222....2225569********************************966666443.23447888888888 PP

                            DUF4407 188 kkaqldaaqaelaelkakldatarlaalraelaeleaeraker 230
                                         ++  +++++++  l+a+  ++ ++ + +a+ ++leae+++ r
  gene2078|gene2078|rna2078|rna2078 127 LERLVNEIERRVRGLQAQ--KANEMRSIEANEKKLEAEADQYR 167
                                        999999999999999999..99999999999999999998876 PP

>> Bacillus_HBL  Bacillus haemolytic enterotoxin (HBL)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   4.4   1.1e-06   0.00035      95     175 ..      50     135 ..      27     139 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 1.1e-06
                       Bacillus_HBL  95 v......dkkdkaellellekLqeeiqqnqkevkqlikeLkklklklakdsknFktdvdeltsilagdsgvisqlq 164
                                        +       k++k+ l+ +++ +++ei +n++e+++l  +L+klk  l+k+ +++ ++  e +  l+ + ++ ++ +
  gene2078|gene2078|rna2078|rna2078  50 IkevkytRKEQKERLSHDIQMMRAEIKKNEEEINRLRSNLEKLKHTLDKERNELLEAHHEND-GLSKQMAEYDENK 124
                                        2556677899*******************************************998875544.3666666666666 PP

                       Bacillus_HBL 165 neiedlqgkik 175
                                        +++e+l ++i+
  gene2078|gene2078|rna2078|rna2078 125 KNLERLVNEIE 135
                                        66666666664 PP

>> TMF_DNA_bd  TATA element modulatory factor 1 DNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   1.4       3.1   9.9e+02      39      55 ..      47      63 ..      24      70 .. 0.59
   2 !   19.6  13.8   2.1e-06   0.00067       3      72 ..      71     140 ..      69     142 .. 0.95
   3 ?   -0.1   0.2       2.9   9.4e+02      33      47 ..     147     161 ..     138     170 .. 0.45

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 3.1
                         TMF_DNA_bd 39 rkknkelekeikelkkk 55
                                        kk+ke  ++ ke+k++
  gene2078|gene2078|rna2078|rna2078 47 VKKIKEVKYTRKEQKER 63
                                       24444444444444444 PP

  == domain 2  score: 19.6 bits;  conditional E-value: 2.1e-06
                         TMF_DNA_bd   3 lekklkeKDeqIaqLmeEGekLskkelklnntikkLrkknkelekeikelkkkleklekeleeleerlke 72 
                                        +++ +k+ +e+I+ L++++ekL+++ +k++n + +   +n  l k+++e+++ +++le+ ++e+e+r ++
  gene2078|gene2078|rna2078|rna2078  71 MRAEIKKNEEEINRLRSNLEKLKHTLDKERNELLEAHHENDGLSKQMAEYDENKKNLERLVNEIERRVRG 140
                                        6788999**********************************************************99876 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 2.9
                         TMF_DNA_bd  33 ntikkLrkknkelek 47 
                                        n + +  + +k+le 
  gene2078|gene2078|rna2078|rna2078 147 NEMRSIEANEKKLEA 161
                                        223333333333333 PP

>> TMF_TATA_bd  TATA element modulatory factor 1 TATA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   1.0      0.58   1.9e+02      57     105 ..      23      72 ..      16      73 .. 0.59
   2 !   18.8  13.3   4.3e-06    0.0014      12      79 ..      66     133 ..      56     141 .. 0.88
   3 ?    0.4   0.6       2.2   7.1e+02      64      81 ..     147     164 ..     131     177 .. 0.48

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.58
                        TMF_TATA_bd  57 eelkelkkeleelekeleel.qeryetlLellGeksEeveELraDvaDlK 105
                                         +l+e ++  +el+k+++ l +e  +++ e+   ++E+ e L  D++ ++
  gene2078|gene2078|rna2078|rna2078  23 TNLHEIQSITSELRKKFSYLlSESVKKIKEVKYTRKEQKERLSHDIQMMR 72 
                                        55566666666666666543145556666666667777777777776665 PP

  == domain 2  score: 18.8 bits;  conditional E-value: 4.3e-06
                        TMF_TATA_bd  12 qlverlsseirrlEgElaslkeelerleaerdeareeivklmkeneelkelkkeleelekeleelqer 79 
                                        + ++ + +ei++ E E++ l+++le+l++  d+ r+e+++  +en+ l+++ +e++e +k+le l ++
  gene2078|gene2078|rna2078|rna2078  66 HDIQMMRAEIKKNEEEINRLRSNLEKLKHTLDKERNELLEAHHENDGLSKQMAEYDENKKNLERLVNE 133
                                        55889*******************************************99999999999988887654 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 2.2
                        TMF_TATA_bd  64 keleelekeleelqerye 81 
                                        +e++++e++ ++l+ + +
  gene2078|gene2078|rna2078|rna2078 147 NEMRSIEANEKKLEAEAD 164
                                        222222222222222222 PP

>> Macoilin  Macoilin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6  17.6   1.4e-05    0.0044     386     499 ..      49     163 ..      17     185 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.4e-05
                           Macoilin 386 slpnnqlskkdalvrLeadikkLkaeLqasrqteqelrskissltseerslkselqqlkkendllqtklhelvsak 461
                                         + + + ++k++ +rL +di+ ++ae++++ +  + lrs+++ l  +    ++el + ++end l +++ e  ++k
  gene2078|gene2078|rna2078|rna2078  49 KIKEVKYTRKEQKERLSHDIQMMRAEIKKNEEEINRLRSNLEKLKHTLDKERNELLEAHHENDGLSKQMAEYDENK 124
                                        455666799999*********************************999999************************* PP

                           Macoilin 462 qkdkqtlqqlekrLkeekearaslekqL.aeekkrkkee 499
                                        ++  + ++++e+r++  + ++a+  + + a+ekk   e+
  gene2078|gene2078|rna2078|rna2078 125 KNLERLVNEIERRVRGLQAQKANEMRSIeANEKKLEAEA 163
                                        **************9999888776555514555544333 PP

>> DUF4618  Domain of unknown function (DUF4618)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   9.8     0.002      0.65     158     229 ..      31     102 ..      13     106 .. 0.65
   2 !   12.0   3.9   0.00031       0.1     171     227 ..      93     150 ..      89     156 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.002
                            DUF4618 158 iqkkkekllkslaektlkatqeaLlqktlenqvlkkeiekfrefieeleeeipeLkaeveqLqaqaeeprev 229
                                        i  + +k ++ l  +++k+++e+   +  ++++l++ i+ +r +i++ eeei++L++++e+L++   + r+ 
  gene2078|gene2078|rna2078|rna2078  31 ITSELRKKFSYLLSESVKKIKEVKYTRKEQKERLSHDIQMMRAEIKKNEEEINRLRSNLEKLKHTLDKERNE 102
                                        333333344445556666667777777777788888888888888888888888888888888887776665 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00031
                            DUF4618 171 ektlkatqeaLlqktlenqvlkkeiekfrefieeleeeipeLkaeveqLqaqae.epr 227
                                        ++tl++ ++ Ll+   en  l+k+++++ e+ ++le  ++e+++ v  Lqaq + e+r
  gene2078|gene2078|rna2078|rna2078  93 KHTLDKERNELLEAHHENDGLSKQMAEYDENKKNLERLVNEIERRVRGLQAQKAnEMR 150
                                        6788999999****************************************99884555 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7  16.8   5.5e-05     0.018     317     469 ..      19     161 ..       6     167 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.5e-05
                             AAA_13 317 safeedkeelkaeaealeeqLkglqraleaKrkepfksvelesvkakiesikklvaeineliakhNekvanleeek 392
                                         + + + +e+++ +++l++++  l ++  +K+ke+      ++  ++ e+++++++ + + i+k+ e +++l ++ 
  gene2078|gene2078|rna2078|rna2078  19 TREFTNLHEIQSITSELRKKFSYLLSESVKKIKEVKY----TRK-EQKERLSHDIQMMRAEIKKNEEEINRLRSNL 89 
                                        4556778889999999999999988888888866654....443.344678999********************** PP

                             AAA_13 393 eeakkklelhlveeleseldeykkkykklekaieklekelkeeeaelkkleeeikeLekqlrdekpaaeeinkeLk 468
                                        e++k  l + + e     l e +++ ++l+k++ + ++++k+ e+ ++++e +++ L++q  +e +++e  +k+L+
  gene2078|gene2078|rna2078|rna2078  90 EKLKHTLDKERNE-----LLEAHHENDGLSKQMAEYDENKKNLERLVNEIERRVRGLQAQKANEMRSIEANEKKLE 160
                                        ***9999994443.....3345667899****************************************99999887 PP

                             AAA_13 469 a 469
                                        a
  gene2078|gene2078|rna2078|rna2078 161 A 161
                                        5 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   8.6    0.0031         1      46     119 ..      24      97 ..      15     106 .. 0.71
   2 ?   10.7   4.2    0.0014      0.45      38     102 ..     111     175 ..      94     182 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0031
                                        CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHHHHHHHHHHHHHH CS
                          Fib_alpha  46 eisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqesnirvLqnvlesneqkiq 119
                                        ++++ ++ ++el k+ +  l e  k+ k+ + + k+ +++l ++i+ ++++i+++e++i+ L+++le++++ + 
  gene2078|gene2078|rna2078|rna2078  24 NLHEIQSITSELRKKFSYLLSESVKKIKEVKYTRKEQKERLSHDIQMMRAEIKKNEEEINRLRSNLEKLKHTLD 97 
                                        44444455555556666666666666666667778888889999999999999999999999999888877654 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.0014
                                        CCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHH CS
                          Fib_alpha  38 ekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqes 102
                                        + l ++++e+ +++k+ e+lv+ei+  +r  q++k+++ + i+  +k+le e  ++++ +  ++s
  gene2078|gene2078|rna2078|rna2078 111 DGLSKQMAEYDENKKNLERLVNEIERRVRGLQAQKANEMRSIEANEKKLEAEADQYRKVLGINIS 175
                                        56899*******************************99************999999987766665 PP

>> V_ATPase_I  V-type ATPase 116kDa subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0  12.7   0.00011     0.036      23     148 ..      20     148 ..      13     197 .. 0.51

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00011
                         V_ATPase_I  23 rkfvk..evrrc.demerklrfleeeieklekavikeeeaeesleapeekeldeleeelekleeelkelnenlekl 95 
                                        r+f++  e++ +  e+ +k+++l +e  k + +++k+++  ++++++ +++++ + +e++k eee+++l++nlekl
  gene2078|gene2078|rna2078|rna2078  20 REFTNlhEIQSItSELRKKFSYLLSESVK-KIKEVKYTR--KEQKERLSHDIQMMRAEIKKNEEEINRLRSNLEKL 92 
                                        55554336665425788888888777777.555555555..66677777778888888888888888888888777 PP

                         V_ATPase_I  96 k....kelnelvelkavlekakefleee.eeeeeeeeseeeeee......keeeeeeeseeeee 148
                                        k    ke+nel+e+++     ++ ++e  e++++ e+  +e e+      +        ++ +e
  gene2078|gene2078|rna2078|rna2078  93 KhtldKERNELLEAHHENDGLSKQMAEYdENKKNLERLVNEIERrvrglqA--------QKANE 148
                                        611113445555555544444444433311111111111111111222111........11111 PP

>> DUF5082  Domain of unknown function (DUF5082)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0  14.9   0.00028     0.092       2     107 ..      58     159 ..      57     177 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00028
                            DUF5082   2 ktkisklqaqiaelrseiaaleekIerLkeaktklsdekeslkqkkkklekplnssesWkGkeennydgirsnles 77 
                                        k+++++l ++i  +r+ei+++ee I rL+   + l++ k++l++++++l +   +++ + ++  ++yd+   nle 
  gene2078|gene2078|rna2078|rna2078  58 KEQKERLSHDIQMMRAEIKKNEEEINRLR---SNLEKLKHTLDKERNELLEAHHENDGLSKQ-MAEYDENKKNLER 129
                                        5799************************6...688888888888888888888888777655.5567777888888 PP

                            DUF5082  78 syqtyvdkldelidaieeEIerLenqisea 107
                                         +++++++++ l+++  +E + +e   +++
  gene2078|gene2078|rna2078|rna2078 130 LVNEIERRVRGLQAQKANEMRSIEANEKKL 159
                                        888888888887777777777766554444 PP

>> Filament  Intermediate filament protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   7.1    0.0011      0.36     216     280 ..      30      91 ..      13      95 .. 0.68
   2 ?    8.5   9.8    0.0041       1.3     208     283 ..      93     164 ..      90     175 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0011
                                        HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           Filament 216 eeitelrrqiqsleieleslkkqkasleaqlaeleerleaeleklqeklseleeelaeireemar 280
                                        +  +elr++       l++  k+ + ++ + +e +erl++++++++++++++eee++++r+++++
  gene2078|gene2078|rna2078|rna2078  30 SITSELRKKFS---YLLSESVKKIKEVKYTRKEQKERLSHDIQMMRAEIKKNEEEINRLRSNLEK 91 
                                        33333333333...334555566667788889999999999999999999999999999998876 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0041
                                        XXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           Filament 208 sealrsakeeitelrrqiqsleieleslkkqkasleaqlaeleerleaeleklqeklseleeelaeireemarqlr 283
                                        +++l + ++e+ e++++ + l+ +++++ ++k++le+ ++e+e r+    ++  ++++++e++ +++ +e     +
  gene2078|gene2078|rna2078|rna2078  93 KHTLDKERNELLEAHHENDGLSKQMAEYDENKKNLERLVNEIERRVRGLQAQKANEMRSIEANEKKLEAE----AD 164
                                        567889999**********************************999877777777777777665544443....33 PP

>> DUF812  Protein of unknown function (DUF812)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6  18.8   0.00014     0.047     315     418 ..      38     144 ..      12     172 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00014
                             DUF812 315 a......kkaeteeelkkkreeeleelqeqieeleskieeleeeikklessikqveeeleeekeeneelekevklk 384
                                        +      +++++ +e+k  r+e+ e l+  i+ ++++i++ eeei++l+s++++++ +l++e++e  e   e++  
  gene2078|gene2078|rna2078|rna2078  38 KfsyllsESVKKIKEVKYTRKEQKERLSHDIQMMRAEIKKNEEEINRLRSNLEKLKHTLDKERNELLEAHHENDGL 113
                                        0223333689999999999999999******************************999988877766655555544 PP

                             DUF812 385 kktlellpdaeeniekLqalveasaqrlvelakq 418
                                         k +   ++ +en ++L++lv++ ++r+  l++q
  gene2078|gene2078|rna2078|rna2078 114 SKQM---AEYDENKKNLERLVNEIERRVRGLQAQ 144
                                        4433...456888888999999999998888766 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8  18.2   0.00019     0.062     374     512 ..      25     170 ..      15     185 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00019
                            DUF3584 374 hqdvqekydrrkqkikeeleeeleklkerleaireekdrl.......kaaieealealesqlrkqleaqkeelnee 442
                                         +++q+ + ++++k +  l e ++k+ke +   +e+k+rl       +a+i+++ e+++  lr++le+ k+ l +e
  gene2078|gene2078|rna2078|rna2078  25 LHEIQSITSELRKKFSYLLSESVKKIKEVKYTRKEQKERLshdiqmmRAEIKKNEEEIN-RLRSNLEKLKHTLDKE 99 
                                        44555555556666666666666666666555666666665556666777777777765.6888888888888888 PP

                            DUF3584 443 ekelesrlselklrldsatateEeleqieeadealekaqeelekaea.evealqaeeeqlrkkrdeadeal 512
                                        + el ++  e + +++++   +E ++++e  ++++e+  + l++ +a e ++ +a+e++l+++ d+  + l
  gene2078|gene2078|rna2078|rna2078 100 RNELLEAHHENDGLSKQMAEYDENKKNLERLVNEIERRVRGLQAQKAnEMRSIEANEKKLEAEADQYRKVL 170
                                        88888888888888888888888888888888888876666655554145667888888888888766655 PP

>> HMMR_N  Hyaluronan mediated motility receptor N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6  13.2    0.0036       1.2     206     287 ..      23     105 ..      15     110 .. 0.71
   2 ?    6.9   7.4     0.011       3.7     260     321 ..     109     170 ..     101     176 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0036
                             HMMR_N 206 aqLkeklvslekekieekseteklleyieelsnvseql.ekykldiaqleellkekndeiesLkssLeekeqelsk 280
                                        ++L e  + + +++++  +   + ++ i+e++ ++++  e+ + di+ ++  +k++++ei+ L+s+Le+ +++l+k
  gene2078|gene2078|rna2078|rna2078  23 TNLHEIQSITSELRKKFSYLLSESVKKIKEVKYTRKEQkERLSHDIQMMRAEIKKNEEEINRLRSNLEKLKHTLDK 98 
                                        5555544444444444444446667788888877654449999999999999999999999999999999999998 PP

                             HMMR_N 281 qvkdlne 287
                                        + ++l e
  gene2078|gene2078|rna2078|rna2078  99 ERNELLE 105
                                        8877755 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.011
                             HMMR_N 260 kndeiesLkssLeekeqelskqvkdlnekckllekekeelvreeeekeqtlsaEleelkekl 321
                                        +nd +++   + +e++++l++ v++ + +++ l+++k +++r  e +e++l+aE ++ ++ l
  gene2078|gene2078|rna2078|rna2078 109 ENDGLSKQMAEYDENKKNLERLVNEIERRVRGLQAQKANEMRSIEANEKKLEAEADQYRKVL 170
                                        45555555667789999999999999999999999999999999999999999998887766 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   1.3      0.13        42      65     100 ..      40      76 ..      15      78 .. 0.73
   2 ?   12.6   8.2   0.00031       0.1      13      91 ..      76     155 ..      73     175 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.13
                                        --TTTTTGGGHHHHHHHHHH....HHHHHHHHHHHHH CS
                         Laminin_II  65 eklapqLldklkelkqleeasss.lsdniseikelIa 100
                                          l+ + ++k+ke+k  +++++  ls++i+ +++ I+
  gene2078|gene2078|rna2078|rna2078  40 SYLLSESVKKIKEVKYTRKEQKErLSHDIQMMRAEIK 76 
                                        4455555789999998888877789999999998776 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.00031
                                        XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH.... CS
                         Laminin_II  13 kevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqleeasss. 87 
                                        k+ +e ++ l  nle++k  l + ++++ e +++ + ++k++++  ++ k+Le+l+++++ +++ l+ ++ ++   
  gene2078|gene2078|rna2078|rna2078  76 KKNEEEINRLRSNLEKLKHTLDKERNELLEAHHENDGLSKQMAEYDENKKNLERLVNEIERRVRGLQAQKANEMRs 151
                                        566889999*********************************************************9998885444 PP

                                        HHHH CS
                         Laminin_II  88 lsdn 91 
                                        + +n
  gene2078|gene2078|rna2078|rna2078 152 IEAN 155
                                        6665 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   6.9    0.0004      0.13      37     121 ..      37     121 ..      24     124 .. 0.89
   2 ?    6.9   3.5     0.019       6.1      48     101 ..      87     143 ..      83     165 .. 0.44
   3 ?    2.6   0.6      0.41   1.3e+02      44      81 ..     128     165 ..     122     186 .. 0.57

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.0004
                            DUF1664  37 rslsdavesvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeaveg 112
                                        + +s  +++  k++++v+ + +++k++Ls++i+ + +++++++e ++ ++++++++++ l++ ++++ + ++   g
  gene2078|gene2078|rna2078|rna2078  37 KKFSYLLSESVKKIKEVKYTRKEQKERLSHDIQMMRAEIKKNEEEINRLRSNLEKLKHTLDKERNELLEAHHENDG 112
                                        5556666667799999**************************************************9999999999 PP

                            DUF1664 113 lesklerie 121
                                        l +++++ +
  gene2078|gene2078|rna2078|rna2078 113 LSKQMAEYD 121
                                        999888765 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.019
                            DUF1664  48 kqleqvseslaatkrhLss...ridrvdkkldeqkeiskeikeevtevredlseige 101
                                        ++le+++++l + +++L +   + d + k++ e  e +k++++ v+e+++ ++ ++ 
  gene2078|gene2078|rna2078|rna2078  87 SNLEKLKHTLDKERNELLEahhENDGLSKQMAEYDENKKNLERLVNEIERRVRGLQA 143
                                        344444444444444443211123334444444444444444444444444444433 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.41
                            DUF1664  44 esvskqleqvseslaatkrhLssridrvdkkldeqkei 81 
                                        e++ +++e+    l+a+k + ++ i+  +kkl++ ++ 
  gene2078|gene2078|rna2078|rna2078 128 ERLVNEIERRVRGLQAQKANEMRSIEANEKKLEAEADQ 165
                                        34444555555566666666666666666666655544 PP

>> FlxA  FlxA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   2.8   0.00097      0.32      13      71 ..      26      81 ..      15      86 .. 0.69
   2 ?    6.3   7.7      0.03       9.6      14      89 ..      77     162 ..      76     169 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00097
                               FlxA 13 sgsasqiasLqkQikn.lqkqLkelsesdeltkeekkkqqqliqaQIqqlqaQIaqlqqq 71
                                        +++s +++L+k  +  l++++k+++e  + t   +k+q++ ++  Iq+++a+I++ +++
  gene2078|gene2078|rna2078|rna2078 26 HEIQSITSELRKKFSYlLSESVKKIKEV-KYT---RKEQKERLSHDIQMMRAEIKKNEEE 81
                                       4556666666666664246677777777.333...44899**************998765 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.03
                               FlxA  14 gsasqiasLqkQiknlqkqLkelses........deltkeekk..kqqqliqaQIqqlqaQIaqlqqqqaekaqek 79 
                                        +++++i++L+  +++l+  L++  ++        d l+k+  +  + ++ ++  ++ ++  ++ lq+q+a++ ++ 
  gene2078|gene2078|rna2078|rna2078  77 KNEEEINRLRSNLEKLKHTLDKERNElleahhenDGLSKQMAEydENKKNLERLVNEIERRVRGLQAQKANEMRSI 152
                                        567888888888888888888877777655655666666644477999***********************99988 PP

                               FlxA  80 qqsekeeksk 89 
                                        +++ek+ +++
  gene2078|gene2078|rna2078|rna2078 153 EANEKKLEAE 162
                                        8777766554 PP

>> Prominin  Prominin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7  12.6    0.0011      0.36     581     720 ..      23     171 ..      12     184 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0011
                           Prominin 581 vdlsnlelLteeerkdLeklresglskihsslyleqlckkltkvnletlaekleelanelsngk...knlkqslkn 653
                                         +l++++ +t+e rk+   l +  ++ki+  +y+ + +k+  + +++ + +++++  +e+++ +   ++lk+ l +
  gene2078|gene2078|rna2078|rna2078  23 TNLHEIQSITSELRKKFSYLLSESVKKIKEVKYTRKEQKERLSHDIQMMRAEIKKNEEEINRLRsnlEKLKHTLDK 98 
                                        58999999**************************************999999999999997776778888999999 PP

                           Prominin 654 eaqdlraiqqelvlp.......lessvkklkksvkkldeensdlqesikkllaaveraenflkkngseiinnes 720
                                        e ++l + ++e  +         +++ k+l++ v++++++ ++lq++  + ++++e+ e+ l+++++++ + ++
  gene2078|gene2078|rna2078|rna2078  99 ERNELLEAHHEN-DGlskqmaeYDENKKNLERLVNEIERRVRGLQAQKANEMRSIEANEKKLEAEADQYRKVLG 171
                                        998888887653.3300111113334445555555555588889999999999999999999988888765555 PP

>> Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   4.0     0.022       7.1      28      93 ..      85     155 ..      16     170 .. 0.65

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.022
                       Baculo_PEP_C  28 qnvqilaqlatlldaietqLnalsedlksllaeldt.............rldtlltnLtdalnalqdtlrneLtnl 90 
                                        + +++  +l+++ld+  ++L +  ++                       +l+ l++++++ +  lq +  ne+ ++
  gene2078|gene2078|rna2078|rna2078  85 LRSNL-EKLKHTLDKERNELLEAHHEND-------GlskqmaeydenkkNLERLVNEIERRVRGLQAQKANEMRSI 152
                                        22222.2333333333333333333333.......23334443666777777777777777777777777888887 PP

                       Baculo_PEP_C  91 nsi 93 
                                        +++
  gene2078|gene2078|rna2078|rna2078 153 EAN 155
                                        776 PP

>> Exonuc_VII_L  Exonuclease VII, large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2  15.2    0.0012       0.4     150     245 ..      29     155 ..      15     176 .. 0.50

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0012
                       Exonuc_VII_L 150 eelerrlekaikrll...........eekkqrleklasrlkspeellerkrqrldeleerleralkkqlkkkrerl 214
                                        ++++++l+k+++ ll            ++k++ e+l+++++  ++ ++++++++++l+++le+ lk++l+k+r++l
  gene2078|gene2078|rna2078|rna2078  29 QSITSELRKKFSYLLsesvkkikevkYTRKEQKERLSHDIQMMRAEIKKNEEEINRLRSNLEK-LKHTLDKERNEL 103
                                        333333334333333222222233335555555666666666777777777777777777777.777777777777 PP

                       Exonuc_VII_L 215 eelkerlk......ekleekkerlkklkerle...............lleek 245
                                         e++++        ++++e+k++l++l +++e               ++e++
  gene2078|gene2078|rna2078|rna2078 104 LEAHHENDglskqmAEYDENKKNLERLVNEIErrvrglqaqkanemrSIEAN 155
                                        7777444234544433333444443332222233334322111212223333 PP

>> TPR_MLP1_2  TPR/MLP1/MLP2-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   9.9     0.005       1.6      45      96 ..      55     105 ..      23     111 .. 0.52
   2 ?    8.9   1.7    0.0045       1.5      84     118 ..     110     144 ..     104     147 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.005
                         TPR_MLP1_2  45 Yerelvkhaedvkelqalreelnelkaeiaelkaeaesakaeleeseeswee 96 
                                        Y r  + ++  + ++q +r+e+++ ++ei+ l++++e++k++l+++++++ e
  gene2078|gene2078|rna2078|rna2078  55 YTRKEQ-KERLSHDIQMMRAEIKKNEEEINRLRSNLEKLKHTLDKERNELLE 105
                                        333322.233445556666666666666666666666666666665555443 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0045
                         TPR_MLP1_2  84 kaeleeseesweeqkeelekelselekriedlneq 118
                                        +  l+++ ++ +e k++le+ ++e+e+r+  l++q
  gene2078|gene2078|rna2078|rna2078 110 NDGLSKQMAEYDENKKNLERLVNEIERRVRGLQAQ 144
                                        6678999999***********************99 PP

>> SpmSyn_N  S-adenosylmethionine decarboxylase N -terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.1     0.069        23      61      90 ..      24      53 ..      15      58 .. 0.86
   2 ?    0.8   0.4       1.7   5.7e+02      52      79 ..      67      95 ..      62     107 .. 0.63
   3 ?    9.3   0.6    0.0038       1.2      54      88 ..     116     150 ..     104     155 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.069
                           SpmSyn_N 61 kaqevdkllnkveerlkellegsikrvkrl 90
                                       + +e++++ +++ +++  ll++s+k++k +
  gene2078|gene2078|rna2078|rna2078 24 NLHEIQSITSELRKKFSYLLSESVKKIKEV 53
                                       456899*********************975 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 1.7
                           SpmSyn_N 52 dlqsyeedekaq..evdkllnkveerlkel 79
                                       d+q +  + k++  e+++l +++e+ lk+ 
  gene2078|gene2078|rna2078|rna2078 67 DIQMMRAEIKKNeeEINRLRSNLEK-LKHT 95
                                       7777665544432488888888875.4433 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.0038
                           SpmSyn_N  54 qsyeedekaqevdkllnkveerlkellegsikrvk 88 
                                        q  e de+++++++l+n++e+r++ l  ++++ ++
  gene2078|gene2078|rna2078|rna2078 116 QMAEYDENKKNLERLVNEIERRVRGLQAQKANEMR 150
                                        77888999999**************9988877665 PP

>> Tam41_Mmp37  Phosphatidate cytidylyltransferase, mitochondrial
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   9.3    0.0038       1.2     185     300 ..      24     142 ..      15     158 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0038
                        Tam41_Mmp37 185 nknKvkniVekqleefrelYkplleelenvellekekekeeekkle.qdlspearaellrkLPkkl...rskllsk 256
                                        n + ++ i ++  ++f  l ++ ++++++v++++ke++++ ++ ++   ++ ++  e +++L ++l   +++l ++
  gene2078|gene2078|rna2078|rna2078  24 NLHEIQSITSELRKKFSYLLSESVKKIKEVKYTRKEQKERLSHDIQmMRAEIKKNEEEINRLRSNLeklKHTLDKE 99 
                                        6678999***************************999888886666444556666666666665551005555555 PP

                        Tam41_Mmp37 257 yekklskkkkdeeeflkkiakdeelaeevkkaikkivaksslkq 300
                                         +++l ++++++  + k++a+ +e ++++++ +++i ++    q
  gene2078|gene2078|rna2078|rna2078 100 -RNELLEAHHENDGLSKQMAEYDENKKNLERLVNEIERRVRGLQ 142
                                        .444457889999999*******99***9999999877655555 PP

>> ALMT  Aluminium activated malate transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7  10.7    0.0041       1.3     298     401 ..      49     156 ..      17     189 .. 0.62

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0041
                               ALMT 298 elqrvslesakvlrelaesvkkmkklsk.veellkevkvaaeeLqskldskskLlvnsekweaakkkekaeeveek 372
                                        ++++v     +  + l+++++ m+ + k  ee ++ +++ +e+L+++ld++ + l+++++++   +k+ ae  e+k
  gene2078|gene2078|rna2078|rna2078  49 KIKEVKYTRKEQKERLSHDIQMMRAEIKkNEEEINRLRSNLEKLKHTLDKERNELLEAHHENDGLSKQMAEYDENK 124
                                        3444444445555668888888887766578999999999999999999999989999988887777777777777 PP

                               ALMT 373 keeekeseskkeea.....eaveeaeseseksll 401
                                        k+ e+  ++ +++      +  +++e++s +   
  gene2078|gene2078|rna2078|rna2078 125 KNLERLVNEIERRVrglqaQ--KANEMRSIEANE 156
                                        66666555555554344321..222222221111 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0  17.8     0.038        13       7      74 ..      43     110 ..      36     185 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.038
                              TMPIT   7 lekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkee 74 
                                        l++++k+++e + + k++ e+ls+ ++ ++ eikk+++++++l+s+l+klk+++++e++e +e  +e+
  gene2078|gene2078|rna2078|rna2078  43 LSESVKKIKEVKYTRKEQKERLSHDIQMMRAEIKKNEEEINRLRSNLEKLKHTLDKERNELLEAHHEN 110
                                        78999***********************************************9884444443333222 PP

>> Csm1_N  Csm1 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.4       3.4   1.1e+03      48      61 ..      48      61 ..      22      69 .. 0.58
   2 ?    7.0   2.9     0.023       7.6      27      61 ..      66     100 ..      62     107 .. 0.82
   3 ?   11.9   2.1   0.00066      0.22      27      66 ..     108     147 ..     103     151 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 3.4
                             Csm1_N 48 eqlaeleekvkele 61
                                       ++++e++  +ke++
  gene2078|gene2078|rna2078|rna2078 48 KKIKEVKYTRKEQK 61
                                       22333333333333 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.023
                             Csm1_N  27 hENsvLsqkletkdqeiesLkeqlaeleekvkele 61 
                                        h  ++++ ++++ ++ei++L+ +l++l++ +++  
  gene2078|gene2078|rna2078|rna2078  66 HDIQMMRAEIKKNEEEINRLRSNLEKLKHTLDKER 100
                                        556788889999****************9988765 PP

  == domain 3  score: 11.9 bits;  conditional E-value: 0.00066
                             Csm1_N  27 hENsvLsqkletkdqeiesLkeqlaeleekvkeleerrkk 66 
                                        hEN  Ls+++  +d+  ++L++ ++e+e +v+ l+ ++++
  gene2078|gene2078|rna2078|rna2078 108 HENDGLSKQMAEYDENKKNLERLVNEIERRVRGLQAQKAN 147
                                        9*********************************998875 PP

>> CENP-F_leu_zip  Leucine-rich repeats of kinetochore protein Cenp-F/LEK1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1  27.0     0.016       5.2      21     136 ..      42     164 ..      24     168 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.016
                     CENP-F_leu_zip  21 sLkdkvenLerelemseenqekvileaEtskaevetlkeeieelaeelreleldLvalr.......sekeeLekel 89 
                                        +L + v++++  + + +e++e++  +    +ae+++ +eei++l+++l++l++ L++ r        e++ L k++
  gene2078|gene2078|rna2078|rna2078  42 LLSESVKKIKEVKYTRKEQKERLSHDIQMMRAEIKKNEEEINRLRSNLEKLKHTLDKERnelleahHENDGLSKQM 117
                                        6777788887777888888899999999999999999999999999999999888888877777777888888888 PP

                     CENP-F_leu_zip  90 qkkqervseLeslnsslenlleekEqekvqmkeeskaaveeLqtqlk 136
                                         +  e  ++Le+l  ++e+ ++ + ++k++++ + +a+ ++L+++  
  gene2078|gene2078|rna2078|rna2078 118 AEYDENKKNLERLVNEIERRVRGLQAQKANEMRSIEANEKKLEAEAD 164
                                        88888888888888888888888888888888887777777777765 PP

>> CENP-H  Centromere protein H (CENP-H)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   8.5     0.023       7.5      20      89 ..      23      96 ..      16      98 .. 0.76
   2 ?    9.0  12.0    0.0057       1.9      14      78 ..      81     162 ..      79     175 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.023
                             CENP-H 20 qelrelqeeltevekenlrlkrknrelaaell.elakekesek...eklkeelekleaelkksrqrwrvvknva 89
                                       ++l+e+q+  +e++k+   l  +++++++e+    +++ke+ +   + +++e++k e+e+++ r++ + +k+++
  gene2078|gene2078|rna2078|rna2078 23 TNLHEIQSITSELRKKFSYLLSESVKKIKEVKyTRKEQKERLShdiQMMRAEIKKNEEEINRLRSNLEKLKHTL 96
                                       5788999999999******************6355555555558884477777777777777777777777765 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0057
                             CENP-H  14 ellklsqelrelqeeltevekenlrlkrknrelaaellelakekesek.................eklkeelekle 72 
                                        e+ +l ++l++l+  l++ + e l+++++n  l ++++e  ++k++ +                  ++++++e+ e
  gene2078|gene2078|rna2078|rna2078  81 EINRLRSNLEKLKHTLDKERNELLEAHHENDGLSKQMAEYDENKKNLErlvneierrvrglqaqkANEMRSIEANE 156
                                        78999********************************877777777776887777777777643333344444444 PP

                             CENP-H  73 aelkks 78 
                                        ++l+++
  gene2078|gene2078|rna2078|rna2078 157 KKLEAE 162
                                        444444 PP

>> DUF1043  Protein of unknown function (DUF1043)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7  11.7    0.0012      0.38      17     102 ..      41     126 ..      38     137 .. 0.89
   2 ?    1.7   0.5      0.73   2.4e+02      21      47 ..     144     170 ..     136     184 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0012
                            DUF1043  17 rltnsklkkqkklekelekakaeleeqkqeledHfaqsaelLetlaedyqkLyqhlaksseeLlpeleeqelfqqk 92 
                                        +l+++++kk k+++ + +++k++l++  q +   ++++ e +++l ++ +kL+  l k+ +eLl + +e++  +++
  gene2078|gene2078|rna2078|rna2078  41 YLLSESVKKIKEVKYTRKEQKERLSHDIQMMRAEIKKNEEEINRLRSNLEKLKHTLDKERNELLEAHHENDGLSKQ 116
                                        688999*********************************************************9988888888877 PP

                            DUF1043  93 kleekkaeae 102
                                          e ++++++
  gene2078|gene2078|rna2078|rna2078 117 MAEYDENKKN 126
                                        7777776654 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.73
                            DUF1043  21 sklkkqkklekelekakaeleeqkqel 47 
                                        +k+++ +++e++ +k +ae +++++ l
  gene2078|gene2078|rna2078|rna2078 144 QKANEMRSIEANEKKLEAEADQYRKVL 170
                                        567788999999999999999999876 PP

>> Nup88  Nuclear pore component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7  18.7    0.0083       2.7     511     651 ..      46     177 ..      12     184 .. 0.73

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0083
                              Nup88 511 svsnpilsadkksskspkEclqllsratqvlReeylkkqelvreeiekrvkllkkqkeqqleelqsleeerkslse 586
                                        sv+       k+ + + kE  + ls+ +q++R e +kk+   +eei++    l+k k+   +e ++l e+ ++   
  gene2078|gene2078|rna2078|rna2078  46 SVK-----KIKEVKYTRKEQKERLSHDIQMMRAE-IKKN---EEEINRLRSNLEKLKHTLDKERNELLEAHHENDG 112
                                        333.....337778889999999*********99.5555...4788888888888888888888888887777666 PP

                              Nup88 587 raeklAekyeeikdkQeklvrrvkkvlkrlnsklpvlseaeremkkelekikekl.kslknalkqv 651
                                          +++Ae y+e k++ e lv+ +++ ++ l+++  + +++  + +k+le+  ++  k+l+ +++qv
  gene2078|gene2078|rna2078|rna2078 113 LSKQMAE-YDENKKNLERLVNEIERRVRGLQAQKANEMRSIEANEKKLEAEADQYrKVLGINISQV 177
                                        6677776.***********************99998887777778888776666515678888877 PP

>> DUF3492  Domain of unknown function (DUF3492)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   5.0     0.008       2.6      35     120 ..      27     113 ..      17     145 .. 0.62

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.008
                            DUF3492  35 avlfigsdeeeygelkyelPenVveveevylveeeeaskapasrkgekaaaetleellealkepeae....seell 106
                                        ++  i+s+ ++  ++ y l e V++++ev    +e++++  +  +  +a+ ++ ee +++l+++ ++     ++  
  gene2078|gene2078|rna2078|rna2078  27 EIQSITSELRK--KFSYLLSESVKKIKEVKYTRKEQKERLSHDIQMMRAEIKKNEEEINRLRSNLEKlkhtLDKER 100
                                        56678888777..9***************99999777776664444444444444444444444444222255555 PP

                            DUF3492 107 kelleelaekekkl 120
                                        +elle+ +e++ +l
  gene2078|gene2078|rna2078|rna2078 101 NELLEAHHEND-GL 113
                                        56666655555.22 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   6.3    0.0045       1.5      25      90 ..      47     112 ..      30     116 .. 0.84
   2 ?    6.6   7.3     0.013       4.3      16      89 ..      94     167 ..      92     175 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0045
                            DUF3450  25 aekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqiee 90 
                                         +k+ + +    +++++l+ + q + ae+++ +ee+++l+   e+l++ +++ ++e+ +   + + 
  gene2078|gene2078|rna2078|rna2078  47 VKKIKEVKYTRKEQKERLSHDIQMMRAEIKKNEEEINRLRSNLEKLKHTLDKERNELLEAHHENDG 112
                                        4566666666778999**************************************999887776665 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.013
                            DUF3450  16 atldqalkeaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqie 89 
                                        +tld+ ++e  +a+++    +k++ ++d++k++l++ ++++++++  l++++++  r++++ e++++    q  
  gene2078|gene2078|rna2078|rna2078  94 HTLDKERNELLEAHHENDGLSKQMAEYDENKKNLERLVNEIERRVRGLQAQKANEMRSIEANEKKLEAEADQYR 167
                                        578899999999***************************************************99998777665 PP

>> DUF724  Protein of unknown function (DUF724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   9.4      0.21        70     125     184 ..      36      92 ..      15     102 .. 0.57
   2 ?    9.8   8.9     0.002      0.65      89     168 ..      84     164 ..      82     183 .. 0.71

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.21
                             DUF724 125 krkleeeidelekkilelerqlallkekkeaadkeiarlkseaekleeeledveqeFeav 184
                                        ++k++  ++e  kki+e++  +   ke+ke+ +++i  +++e +k eee+++ +++ e++
  gene2078|gene2078|rna2078|rna2078  36 RKKFSYLLSESVKKIKEVKYTR---KEQKERLSHDIQMMRAEIKKNEEEINRLRSNLEKL 92 
                                        2334444445555555544444...46666666666666666666666666666665554 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.002
                             DUF724  89 alqsrlnkLlsl....kdeqtklleerkklekkieeeesekrkleeeidelekkilelerqlallkekkeaadkei 160
                                         l+s l+kL +     ++e  ++++e  +l k+++e +++k++le  ++e+e++++ l+ q+a   +  ea++k  
  gene2078|gene2078|rna2078|rna2078  84 RLRSNLEKLKHTldkeRNELLEAHHENDGLSKQMAEYDENKKNLERLVNEIERRVRGLQAQKANEMRSIEANEK-- 157
                                        5677777776541111334445667888999******************************9955544444444.. PP

                             DUF724 161 arlkseae 168
                                         +l++ea+
  gene2078|gene2078|rna2078|rna2078 158 -KLEAEAD 164
                                        .4444444 PP

>> UPF0242  Uncharacterised protein family (UPF0242) N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   3.9    0.0093         3      85     142 ..      19      77 ..       4      78 .. 0.80
   2 ?    6.0  16.7     0.036        12      83     163 ..      74     150 ..      72     168 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0093
                            UPF0242  85 ktkeealeelqeeeeeLkeeldak.eeelerlkeenqqLqekleaiaedfeelklelee 142
                                        + +  +l e q+ + eL++++++  +e +++ ke +   +e++e  ++d+++++ e+++
  gene2078|gene2078|rna2078|rna2078  19 TREFTNLHEIQSITSELRKKFSYLlSESVKKIKEVKYTRKEQKERLSHDIQMMRAEIKK 77 
                                        3344599*************99862566778888888999**************99986 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.036
                            UPF0242  83 glktkeealeelqeeeeeLkeeldakeeelerlkeenqqLqekleaiaedfeelkleleeqLaekqellqeyqeti 158
                                        ++k++ee+++ l+++ e+Lk+ ld+  +el + ++en  L++++ +    ++e k++le  ++e + ++  +q++ 
  gene2078|gene2078|rna2078|rna2078  74 EIKKNEEEINRLRSNLEKLKHTLDKERNELLEAHHENDGLSKQMAE----YDENKKNLERLVNEIERRVRGLQAQK 145
                                        57899************************************77655....77777777777777777666666543 PP

                            UPF0242 159 eeqrs 163
                                         +   
  gene2078|gene2078|rna2078|rna2078 146 ANEMR 150
                                        33322 PP

>> Snapin_Pallidin  Snapin/Pallidin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.2       2.9   9.4e+02      64      84 ..      42      62 ..      16      67 .. 0.46
   2 ?    3.6   1.8      0.27        88       7      49 ..      39      81 ..      33      89 .. 0.78
   3 ?   11.5   7.3   0.00096      0.31       9      82 ..      69     141 ..      68     149 .. 0.76
   4 ?    1.6   0.7       1.2   3.8e+02      31      66 ..     129     160 ..     121     173 .. 0.70

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 2.9
                    Snapin_Pallidin 64 KLvnikkrmsslnerlqklkk 84
                                        L++  k++++++ + ++ k+
  gene2078|gene2078|rna2078|rna2078 42 LLSESVKKIKEVKYTRKEQKE 62
                                       233444444444444444444 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.27
                    Snapin_Pallidin  7 llellepkldeldeklkelrqsQee.LleqldrlnekLkeleea 49
                                       ++ ll+ ++++++ ++k +r++Q+e L+++++ +++++k++ee+
  gene2078|gene2078|rna2078|rna2078 39 FSYLLSESVKKIK-EVKYTRKEQKErLSHDIQMMRAEIKKNEEE 81
                                       5666777777775.589999999755************999886 PP

  == domain 3  score: 11.5 bits;  conditional E-value: 0.00096
                    Snapin_Pallidin   9 ellepkldeldeklkelrqsQeeLleqldrlnekLkeleeaqe..aevlpdlkeyakKLvnikkrmsslnerlqkl 82 
                                        +++  ++++ +e+++ lr + e+L+++ld+++++L e+ ++++  ++++++ +e +k   n+++ +++++ r++ l
  gene2078|gene2078|rna2078|rna2078  69 QMMRAEIKKNEEEINRLRSNLEKLKHTLDKERNELLEAHHENDglSKQMAEYDENKK---NLERLVNEIERRVRGL 141
                                        688899*****************************9999999955555555555555...5555555555555554 PP

  == domain 4  score: 1.6 bits;  conditional E-value: 1.2
                    Snapin_Pallidin  31 eLleqldrlnekLkeleeaqeaevlpdlkeyakKLv 66 
                                         L ++++r  + L+ +++a+e   +  ++   kKL 
  gene2078|gene2078|rna2078|rna2078 129 RLVNEIERRVRGLQ-AQKANE---MRSIEANEKKLE 160
                                        56666777777776.666666...777777777764 PP

>> PI3K_P85_iSH2  Phosphatidylinositol 3-kinase regulatory subunit P85 inter-SH2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0  13.1     0.013       4.2      80     146 ..      37     103 ..      15     109 .. 0.83
   2 ?    4.0   6.0       0.1        34      90     148 ..      96     154 ..      92     163 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.013
                      PI3K_P85_iSH2  80 ehEieklqenleqlksrlkelhsskekLeedlkqqkeeereleReinalkpellqLqkrkdkylewL 146
                                        ++    l+e+++++k+   + +++ke+L++d++   +e ++ e ein+l+++l +L+ + dk  + L
  gene2078|gene2078|rna2078|rna2078  37 KKFSYLLSESVKKIKEVKYTRKEQKERLSHDIQMMRAEIKKNEEEINRLRSNLEKLKHTLDKERNEL 103
                                        4445568889999999999999**********************************99999876666 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.1
                      PI3K_P85_iSH2  90 leqlksrlkelhsskekLeedlkqqkeeereleReinalkpellqLqkrkdkylewLkt 148
                                        l++ ++ l e h + + L++++ +  e++++leR +n++   +  Lq +k + ++ ++ 
  gene2078|gene2078|rna2078|rna2078  96 LDKERNELLEAHHENDGLSKQMAEYDENKKNLERLVNEIERRVRGLQAQKANEMRSIEA 154
                                        55666778888999999**************************9999999887776655 PP

>> Phage_Mu_Gam  Bacteriophage Mu Gam like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   6.9      0.59   1.9e+02       7      54 ..      46      96 ..      40     110 .. 0.62
   2 ?   11.5   5.4   0.00065      0.21       6      59 ..     115     168 ..     110     173 .. 0.93

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.59
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHH...HHHHHHCHHHHHHHHHHHHHH CS
                       Phage_Mu_Gam  7 alrkiaelkreleeieaeaneeiaaik...ekleaeleplkkeieylesll 54
                                        ++ki+e+k   +e ++ +   i+ ++   +k e+e+++l ++ e+l+++l
  gene2078|gene2078|rna2078|rna2078 46 SVKKIKEVKYTRKEQKERLSHDIQMMRaeiKKNEEEINRLRSNLEKLKHTL 96
                                       567788776555555555555555555223345667777777777776665 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00065
                                        HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHH CS
                       Phage_Mu_Gam   6 walrkiaelkreleeieaeaneeiaaikekleaeleplkkeieylesllkqYae 59 
                                        + ++++ e k+ le++ +e++ ++  ++++ ++e+ +++++ ++le++  qY +
  gene2078|gene2078|rna2078|rna2078 115 KQMAEYDENKKNLERLVNEIERRVRGLQAQKANEMRSIEANEKKLEAEADQYRK 168
                                        5689************************************************76 PP

>> Fez1  Fez1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2  23.4      0.02       6.4      30     161 ..      25     162 ..      15     178 .. 0.58

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.02
                               Fez1  30 lseivalkaqlrelra.kleekeeeikeleesleektle....levcenelqrkkseaellrekvekleeelkelr 100
                                        l+ei ++ ++lr   +  l+e+ ++ike++ +++e+++     ++ + +e++++++e + lr ++ekl++ l + r
  gene2078|gene2078|rna2078|rna2078  25 LHEIQSITSELRKKFSyLLSESVKKIKEVKYTRKEQKERlshdIQMMRAEIKKNEEEINRLRSNLEKLKHTLDKER 100
                                        6777777777765544145566666666665554443322222666667777777777777777777777777777 PP

                               Fez1 101 eelselsleeeeaalesdeakaqrqe.aeeleelkreverlraeLkeerqkkeeqassFeqE 161
                                        +el e+++e++  ++++ e  +++++ ++ ++e +r+v  l+a+ ++e ++ e+++++ e E
  gene2078|gene2078|rna2078|rna2078 101 NELLEAHHENDGLSKQMAEYDENKKNlERLVNEIERRVRGLQAQKANEMRSIEANEKKLEAE 162
                                        77766665555555555554444444233455555556666665555555555555555555 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0  13.4      0.28        91      94     218 ..      14     184 ..       8     193 .. 0.63

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.28
                              DUF87  94 pwsldpeelldlleeddkpaaavqrsvleealdqakakeekeklssdepveklleelk.................. 151
                                        p++++ +e+ +l e+  ++ ++++r+ + ++l++ ++k ++ k++ +e  e+l ++++                  
  gene2078|gene2078|rna2078|rna2078  14 PRQMTTREFTNLHEI--QSITSELRKKFSYLLSESVKKIKEVKYTRKEQKERLSHDIQmmraeikkneeeinrlrs 87 
                                        666677777777777..55555544444444444444455555555555555555555444444455555555555 PP

                              DUF87 152 ..............................kekeelrklknqaiarlldkledllrkggsfsnsstdlialllekl 197
                                                                       e +e++k+ +++ ++++++++ l+ ++++ + s + ++++l+ ++
  gene2078|gene2078|rna2078|rna2078  88 nleklkhtldkernelleahhendglskqmAEYDENKKNLERLVNEIERRVRGLQAQKANEMRSIEANEKKLEAEA 163
                                        5555555555666666666666666666544556888888888888888888888888888888888888888888 PP

                              DUF87 198 ekegkitiidlsgvdelaqql 218
                                        ++ +k+  i++s+v ++++++
  gene2078|gene2078|rna2078|rna2078 164 DQYRKVLGINISQVCDSVLKI 184
                                        888888888888888877766 PP

>> CALCOCO1  Calcium binding and coiled-coil domain (CALCOCO1) like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   7.2     0.034        11     179     223 ..      52      97 ..      15      98 .. 0.64
   2 ?    8.0   9.7    0.0036       1.2      41     107 ..      98     163 ..      96     184 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.034
                           CALCOCO1 179 kleqseeel.rslskelqelrnslaerdtqvlqLqdtittltqkLt 223
                                        +++ +++e  ++ls+++q +r   ++ + ++ +L++++ +l+++L+
  gene2078|gene2078|rna2078|rna2078  52 EVKYTRKEQkERLSHDIQMMRAEIKKNEEEINRLRSNLEKLKHTLD 97 
                                        3445555541578888888888888888888888888888888886 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0036
                           CALCOCO1  41 reraeLlqaqeaanrqrekekeeykrdreeldrerkelesrveelkeelkesrekveeleekqkele 107
                                        +er+eLl a    n    k+  ey +++++l+r ++e+e+rv  l+++ ++    +e  e+k ++++
  gene2078|gene2078|rna2078|rna2078  98 KERNELLEA-HHENDGLSKQMAEYDENKKNLERLVNEIERRVRGLQAQKANEMRSIEANEKKLEAEA 163
                                        89******9.56778889999************************9986555555555554444333 PP

>> Bcr-Abl_Oligo  Bcr-Abl oncoprotein oligomerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   3.2     0.014       4.7      23      55 ..      72     104 ..      54     124 .. 0.78
   2 ?    4.1   0.4      0.14        47      38      69 ..     122     153 ..     106     158 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.014
                      Bcr-Abl_Oligo  23 LdsvedieqeLerCkaslrrLekelneekfkvi 55 
                                           ++  e+e++r + +l +L++ l +e+  ++
  gene2078|gene2078|rna2078|rna2078  72 RAEIKKNEEEINRLRSNLEKLKHTLDKERNELL 104
                                        456788899*******************97765 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.14
                      Bcr-Abl_Oligo  38 aslrrLekelneekfkviyLqtllakerksyD 69 
                                        ++ ++Le+ +ne   +v  Lq+  a e +s +
  gene2078|gene2078|rna2078|rna2078 122 ENKKNLERLVNEIERRVRGLQAQKANEMRSIE 153
                                        5567888889988889999****999999865 PP

>> DUF2730  Protein of unknown function (DUF2730)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   6.7     0.013       4.2      27      93 ..      53     117 ..      37     124 .. 0.92
   2 ?    3.3   0.6      0.27        90      40      83 ..     122     167 ..     113     179 .. 0.57

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.013
                            DUF2730  27 skYakredleklaekveendkrlteletkvenLPtakdlekLkllladlrgelkaleaevrqlshqv 93 
                                         kY+++e+ e+l + ++ ++  +++ e +++ L  +++lekLk +l + r el ++++e + ls+q+
  gene2078|gene2078|rna2078|rna2078  53 VKYTRKEQKERLSHDIQMMRAEIKKNEEEINRL--RSNLEKLKHTLDKERNELLEAHHENDGLSKQM 117
                                        59******************************9..789***************99999999999885 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.27
                            DUF2730  40 ekveendkrlteletkvenLPtak..dlekLkllladlrgelkale 83 
                                        e+ ++ ++ ++e+e +v  L  +k  ++ +++ + ++l++e ++ +
  gene2078|gene2078|rna2078|rna2078 122 ENKKNLERLVNEIERRVRGLQAQKanEMRSIEANEKKLEAEADQYR 167
                                        4444445555666666666655432266666666666666655554 PP

>> OmpH  Outer membrane protein (OmpH-like)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7  22.8       1.9   6.3e+02      18      93 ..      58     151 ..      18     181 .. 0.52

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 1.9
                                        HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTS...........................-HHHHHH... CS
                               OmpH  18 kaaqeqlekkfkklqaeleakekelqklqeelqkkakkl.e.........................keekeqe... 64 
                                        k+ +e+l  +++ ++ae+++ e+e+++l+ +l+k + +l +                         k     +   
  gene2078|gene2078|rna2078|rna2078  58 KEQKERLSHDIQMMRAEIKKNEEEINRLRSNLEKLKHTLdKernelleahhendglskqmaeydenK-----Knle 128
                                        3333444444455555555555555555555554444433354444446666666544443332211.....0211 PP

                                        .....HHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                               OmpH  65 .....lqkkeqelqqkqqqkaqelqkkqqellkp 93 
                                             ++++++            lq++++ ++++
  gene2078|gene2078|rna2078|rna2078 129 rlvneIERRVRG-----------LQAQKANEMRS 151
                                        222223333333...........33333333332 PP

>> Lectin_N  Hepatic lectin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   2.9      0.01       3.4      59     110 ..      34      89 ..      21     108 .. 0.74
   2 ?    2.3   1.4      0.41   1.3e+02      61      82 ..     124     145 ..      83     184 .. 0.48

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.01
                           Lectin_N  59 tLketfsnfssstlaeiqalss....qggslsekvtsleaklekkqqdlkadhsel 110
                                         L+++fs + s+   +i++++     q ++ls+ ++ ++a+++k++++++   s+l
  gene2078|gene2078|rna2078|rna2078  34 ELRKKFSYLLSESVKKIKEVKYtrkeQKERLSHDIQMMRAEIKKNEEEINRLRSNL 89 
                                        57888888777777777777666666788888899999999999999988888876 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.41
                           Lectin_N  61 ketfsnfssstlaeiqalssqg 82 
                                        k++++ + ++++  ++ l++q 
  gene2078|gene2078|rna2078|rna2078 124 KKNLERLVNEIERRVRGLQAQK 145
                                        2233333333333333333333 PP

>> DUF2968  Protein of unknown function (DUF2968)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   5.1     0.034        11     117     178 ..      56     117 ..      27     119 .. 0.85
   2 ?    5.4   2.0     0.039        13      96     124 ..     133     161 ..     118     170 .. 0.70

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.034
                            DUF2968 117 asearaerLqadlavarqQeqavaerQkqarkeaaaLeaqreaaqaqlralqrqirqLqaqq 178
                                        +++++ erL+ d++++r+  ++ +e+ + +r++ ++L++  ++ +++l +++++ + L +q 
  gene2078|gene2078|rna2078|rna2078  56 TRKEQKERLSHDIQMMRAEIKKNEEEINRLRSNLEKLKHTLDKERNELLEAHHENDGLSKQM 117
                                        56788899999999999999999999999999999999999999999999999888888776 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.039
                            DUF2968  96 eveirrikleaqkaqlerqiaasearaer 124
                                        e+e r   l+aqka   r i+a+e+++e+
  gene2078|gene2078|rna2078|rna2078 133 EIERRVRGLQAQKANEMRSIEANEKKLEA 161
                                        44545556899999999999999888765 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   3.8    0.0015       0.5      20      53 ..      55      88 ..      46      94 .. 0.87
   2 ?    4.0   6.0      0.13        43      13      72 ..      90     148 ..      87     149 .. 0.87
   3 ?    2.7   2.0      0.33   1.1e+02      27      51 ..     143     167 ..     137     170 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0015
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-XXX CS
                              DivIC 20 kqlkqeiaalqaelaklkaeneeLeaevkdLksd 53
                                       +  k++ ++l ++++ ++ae+++ e+e+++L+s+
  gene2078|gene2078|rna2078|rna2078 55 YTRKEQKERLSHDIQMMRAEIKKNEEEINRLRSN 88
                                       67899999**********************9876 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.13
                                        XXXXXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-XXXXXXXXXXXXXXXXXXXXXX CS
                              DivIC  13 kkgllaykqlkqeiaalqaelaklkaeneeLeaevkdLksdedyieerARselglvkpgE 72 
                                        +k  +++ + ++e+ +  +e++ l+++ +e +++ k+L+   + ie+r R  l+  k +E
  gene2078|gene2078|rna2078|rna2078  90 EKLKHTLDKERNELLEAHHENDGLSKQMAEYDENKKNLERLVNEIERRVR-GLQAQKANE 148
                                        667788999999**************************999*******99.776666666 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.33
                                        HHHHHHHHHHHHHHHHHHHHHCC-X CS
                              DivIC  27 aalqaelaklkaeneeLeaevkdLk 51 
                                        a++ +e+ ++ a +++Leae ++++
  gene2078|gene2078|rna2078|rna2078 143 AQKANEMRSIEANEKKLEAEADQYR 167
                                        78889999999*********99986 PP

>> DASH_Spc19  Spc19
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   1.2      0.16        52      59     100 ..      26      67 ..      16      74 .. 0.84
   2 ?    7.1  19.7     0.014       4.6      58     148 ..      57     146 ..      50     166 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.16
                                        HHTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH. CS
                         DASH_Spc19  59 eeiePqieellekaekeleklerreetLkaklelqegrlsna 100
                                        +ei+   +el +k +  l++  ++ ++ k +++ q+ rls++
  gene2078|gene2078|rna2078|rna2078  26 HEIQSITSELRKKFSYLLSESVKKIKEVKYTRKEQKERLSHD 67 
                                        688888899999999999999999999999999999999995 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.014
                                        HHHTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH......HHHHT-XXXXXXXXXXXX....XXXXXX CS
                         DASH_Spc19  58 aeeiePqieellekaekeleklerreetLkaklelqegrlsnaesskkeeeeseeskeeeeeeenkeeekskkklt 133
                                        ++e +  +++ ++ +++e++k e++ + L+++le++++ l+++ +++  e++ e++  +++ +e +e++k+ ++l 
  gene2078|gene2078|rna2078|rna2078  57 RKEQKERLSHDIQMMRAEIKKNEEEINRLRSNLEKLKHTLDKE-RNELLEAHHENDGLSKQMAEYDENKKNLERLV 131
                                        678889999999******************************5.55555555555555677778888888888866 PP

                                        XXXXXXXXXXXXXXX CS
                         DASH_Spc19 134 keelerlkkLkqkKe 148
                                        +e ++r++ L+++K 
  gene2078|gene2078|rna2078|rna2078 132 NEIERRVRGLQAQKA 146
                                        666666666666664 PP

>> ADIP  Afadin- and alpha -actinin-Binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   9.1      0.02       6.4      62     131 ..      25      95 ..      15     100 .. 0.74
   2 ?    4.3   9.3      0.12        39      60     120 ..     108     168 ..      94     176 .. 0.63

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.02
                               ADIP  62 irkleaeierlqskierlktqleqlerela.lvqakerqlekklktleqklknekeelqrlknalqqiktq 131
                                        ++++++  + l++k++ l  ++ ++ +e++ + ++++  l  +++   + +k+  ee++rl+++l+++k  
  gene2078|gene2078|rna2078|rna2078  25 LHEIQSITSELRKKFSYLLSESVKKIKEVKyTRKEQKERLSHDIQMMRAEIKKNEEEINRLRSNLEKLKHT 95 
                                        55566666677778887777777777777778888888888888888888888888888888888888765 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.12
                               ADIP  60 etirkleaeierlqskierlktqleqlerelalvqakerqlekklktleqklknekeelqr 120
                                         ++  l+  ++    + + l++ + + er++  +qa++++  +++++ e+kl  e+++ ++
  gene2078|gene2078|rna2078|rna2078 108 HENDGLSKQMAEYDENKKNLERLVNEIERRVRGLQAQKANEMRSIEANEKKLEAEADQYRK 168
                                        2222233333444444455555567788899999999999999999999999999998877 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   2.0      0.17        55       8      55 ..      30      78 ..      16      80 .. 0.73
   2 ?    8.3  12.5     0.011       3.5      14      79 ..      58     133 ..      47     134 .. 0.85
   3 ?    5.2   2.5       0.1        33       8      52 ..     125     170 ..     119     185 .. 0.68

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.17
                                       HHHHHHHHHHHHHH.HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHXXX CS
                               YabA  8 dkleeleeqleell.eeleelkeelaelleenaeLeleneklrerleee 55
                                       +  +el ++++ ll e+++++ke  ++  e+ ++L+ + + +r +++++
  gene2078|gene2078|rna2078|rna2078 30 SITSELRKKFSYLLsESVKKIKEVKYTRKEQKERLSHDIQMMRAEIKKN 78
                                       4455666666655415688899998999999999999999999988655 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.011
                                        HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH..........XXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                               YabA  14 eeqleelleeleelkeelaelleenaeLeleneklrerl..........eeeekkekekkkelsegkenLarlYee 79 
                                        +eq e+l+++++ +++e+++  ee ++L+ + ekl+++l          ++e++  +++ +e +e k+nL+rl +e
  gene2078|gene2078|rna2078|rna2078  58 KEQKERLSHDIQMMRAEIKKNEEEINRLRSNLEKLKHTLdkernelleaHHENDGLSKQMAEYDENKKNLERLVNE 133
                                        56778899999999999999999999999999999999999999999876677777889999999******99876 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.1
                                        HHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHHHHHHHHHH CS
                               YabA   8 dkleeleeqleelleeleelkee.laelleenaeLeleneklrerl 52 
                                        ++le+l +++e+ ++ l++ k++ + ++  ++++Le+e ++ r+ l
  gene2078|gene2078|rna2078|rna2078 125 KNLERLVNEIERRVRGLQAQKANeMRSIEANEKKLEAEADQYRKVL 170
                                        4556666666666666666666514555555678*********998 PP

>> ERM  Ezrin/radixin/moesin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9  12.8    0.0036       1.2      66     131 ..      43     108 ..      13     111 .. 0.80
   2 ?    7.2  18.4     0.012       3.8       3      87 ..      78     162 ..      77     170 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0036
                                ERM  66 lkesaekeeeekeklerklreaeleaarleeeserkeeeaerLkeeleeareaeeeakeklleals 131
                                        l es +k +e k+  +++ ++ +  ++ ++ e ++ eee +rL+++le+ ++++ +++++llea  
  gene2078|gene2078|rna2078|rna2078  43 LSESVKKIKEVKYTRKEQKERLSHDIQMMRAEIKKNEEEINRLRSNLEKLKHTLDKERNELLEAHH 108
                                        445666677778888888888999999999999999999999999999999999999999999876 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.012
                                ERM   3 aerekreleerLkqlqeeaekaqeaLreseetaelLaekarraeeeaelLeqkaaeaeeeiqrlkesaekeeeeke 78 
                                         e e ++l+  L++l+   +k +++L e++ + + L +++ +  e++++Le+  +e+e+  + l+ ++++e+++ e
  gene2078|gene2078|rna2078|rna2078  78 NEEEINRLRSNLEKLKHTLDKERNELLEAHHENDGLSKQMAEYDENKKNLERLVNEIERRVRGLQAQKANEMRSIE 153
                                        577889999***********************************************************99999988 PP

                                ERM  79 klerklrea 87 
                                        + e+kl++ 
  gene2078|gene2078|rna2078|rna2078 154 ANEKKLEAE 162
                                        888887654 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8  28.0      0.98   3.2e+02      36     126 ..      57     145 ..      15     171 .. 0.52

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.98
                             APG6_N  36 kkekkeeek..............qdeeleeleeeleklekeeeelleeLkelekereeleaelaaleeelealeee 97 
                                        +ke+ke  +              ++ee+++l+  lekl+ + ++  +eL e+ +e++ l +++a++ e +++le+ 
  gene2078|gene2078|rna2078|rna2078  57 RKEQKE--RlshdiqmmraeikkNEEEINRLRSNLEKLKHTLDKERNELLEAHHENDGLSKQMAEYDENKKNLERL 130
                                        222222..11112222222222234555555555555555555555555555555555555555555555555544 PP

                             APG6_N  98 eerfwreynelqlelleleeeldsleaqy 126
                                         +              e e + + l+aq 
  gene2078|gene2078|rna2078|rna2078 131 VN--------------EIERRVRGLQAQK 145
                                        44..............4444444444432 PP

>> YtxH  YtxH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   6.8      0.49   1.6e+02      24      69 ..      33     102 ..      30     170 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.49
                               YtxH  24 ketRkdlkekaddlkekakelleeakeka........................kekaedlkekvkekade 69 
                                        +e+Rk+ +  ++++ +k+ke++++ ke+                         +++ e+lk +++++ +e
  gene2078|gene2078|rna2078|rna2078  33 SELRKKFSYLLSESVKKIKEVKYTRKEQKerlshdiqmmraeikkneeeinrlRSNLEKLKHTLDKERNE 102
                                        699***********99999999999888888877777777777777666666666666666666665555 PP

>> DUF4140  N-terminal domain of unknown function (DUF4140)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1  14.0       8.1   2.6e+03      48      95 ..      49      96 ..      25     162 .. 0.88
   2 ?    1.9   1.0      0.91     3e+02      69      96 ..     133     160 ..     131     171 .. 0.58

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 8.1
                            DUF4140 48 tildvqvervpnreaeeeelkalraeleeledelaaledelaaaearl 95
                                       +i +v+++r++++e  +++++ +rae+++ e+e+++l++ l+ ++ +l
  gene2078|gene2078|rna2078|rna2078 49 KIKEVKYTRKEQKERLSHDIQMMRAEIKKNEEEINRLRSNLEKLKHTL 96
                                       577888888888888888888888888888888888888888777654 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.91
                            DUF4140  69 alraeleeledelaaledelaaaearla 96 
                                        +++++++ l++++a+  ++++a e++l+
  gene2078|gene2078|rna2078|rna2078 133 EIERRVRGLQAQKANEMRSIEANEKKLE 160
                                        5555666666666655555555555554 PP

>> WASH-7_C  WASH complex subunit 7, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   5.5   0.00094      0.31      99     169 ..      19      91 ..      15      97 .. 0.81
   2 ?   -0.5   1.3       2.6   8.6e+02     122     122 ..     130     130 ..      89     177 .. 0.50

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00094
                           WASH-7_C  99 eeeFdsLhWfesvkkkykkelekvkealaa..kekkkskkkedekllqtlkLtlkrleayqkEfelLeyslss 169
                                        ++eF +Lh  +s++++++k+ + + +++ +  ke k ++k+++e+l + +++++ +++ +++E++ L  +l+ 
  gene2078|gene2078|rna2078|rna2078  19 TREFTNLHEIQSITSELRKKFSYLLSESVKkiKEVKYTRKEQKERLSHDIQMMRAEIKKNEEEINRLRSNLEK 91 
                                        679***************9998875555440144445556668999*********************999875 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 2.6
                           WASH-7_C 122 v 122
                                        +
  gene2078|gene2078|rna2078|rna2078 130 L 130
                                        1 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3498  (0.195103); expected 358.6 (0.02)
Passed bias filter:                      980  (0.05466); expected 358.6 (0.02)
Passed Vit filter:                       216  (0.0120475); expected 17.9 (0.001)
Passed Fwd filter:                        90  (0.0050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              55  [number of targets reported over threshold]
# CPU time: 1.13u 0.40s 00:00:01.52 Elapsed: 00:00:00.57
# Mc/sec: 1095.52
//
Query:       gene2079|gene2079|rna2079|rna2079  [L=79]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00014   21.5   0.0    0.00023   20.8   0.0    1.4  1  UCH       Ubiquitin carboxyl-terminal hydrolase
  ------ inclusion threshold ------
       0.12   12.0   0.0       0.12   12.0   0.0    1.1  1  UCH_1     Ubiquitin carboxyl-terminal hydrolase


Domain annotation for each model (and alignments):
>> UCH  Ubiquitin carboxyl-terminal hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   2.5e-08   0.00023     197     242 ..      34      78 ..       3      79 .] 0.77

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 2.5e-08
                                        TCS-BEEEEEEEEEES.CTTSEEEEEEEECTTTTEEEEEETTEEEEE CS
                                        xxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                                UCH 197 eekkkYeLiavvvHsG.slssGHYvayiknekngkWykydDetvkev 242
                                         ++k+Y+L a++  +  + ++GH++++ k  + ++W+ ++De + ++
  gene2079|gene2079|rna2079|rna2079  34 FKNKTYNLRAIIRRKRkKNNKGHFYTIGK--RGNSWFEFNDEIIPQI 78 
                                        34556***********9*********999..7899*******88776 PP

>> UCH_1  Ubiquitin carboxyl-terminal hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   1.3e-05      0.12     270     317 ..      35      72 ..       4      75 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.3e-05
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              UCH_1 270 eikvYeLqsvvvhigdskesghLvslvkvaekelerdppesqWylFND 317
                                        + k+Y+L++++ + ++++++gh +++ k            ++W+ FND
  gene2079|gene2079|rna2079|rna2079  35 KNKTYNLRAIIRRKRKKNNKGHFYTIGKR----------GNSWFEFND 72 
                                        6689*******99998889*******994..........468*****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       626  (0.0349155); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.32s 00:00:00.71 Elapsed: 00:00:00.46
# Mc/sec: 517.34
//
Query:       gene208|gene208|rna208|rna208  [L=49]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (49 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       444  (0.0247643); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.42
# Mc/sec: 346.70
//
Query:       gene2080|gene2080|rna2080|rna2080  [L=188]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.2e-09   36.0   1.8    6.6e-09   35.6   1.4    1.3  1  UCH       Ubiquitin carboxyl-terminal hydrolase
  ------ inclusion threshold ------
      0.034   13.7   1.1      0.036   13.7   1.1    1.3  1  UCH_1     Ubiquitin carboxyl-terminal hydrolase


Domain annotation for each model (and alignments):
>> UCH  Ubiquitin carboxyl-terminal hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.6   1.4   7.4e-13   6.6e-09       1      69 [.      32     104 ..      32     123 .. 0.81

  Alignments for each domain:
  == domain 1  score: 35.6 bits;  conditional E-value: 7.4e-13
                                        -EES-SSSTHHHHHHHHHHHTSHHHHHHHHTCHHCCSSTCCCCC-....TT.TTS.TT.HHHHHHHHHHHHHH CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxx.xxxxxxxxxxxxxx RF
                                UCH   1 tGlsNlGntCymnsvlQcLfsipelrdyllsleevkkesrnkkel...nesnplgkkg.elakalkdlfkell 69 
                                        +Gl+N  n Cy+n+vlQ+Lfs+++++++l s+e+++    +  ++   + +n++  ++  l+++l+++ + l 
  gene2080|gene2080|rna2080|rna2080  32 CGLKNHHNVCYINAVLQSLFSCESFTTMLESIEPENGSVMYYIQNlwnDMKNNTLLNRlGLYRRLASMSNFLF 104
                                        7*******************************99998887777767875566666666689999999887776 PP

>> UCH_1  Ubiquitin carboxyl-terminal hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   1.1     4e-06     0.036       2      29 ..      33      60 ..      32     161 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4e-06
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              UCH_1  2 GLEnhivnsYlNslLQvlyfipplrnla 29
                                       GL nh + +Y+N++LQ l+ ++ ++ ++
  gene2080|gene2080|rna2080|rna2080 33 GLKNHHNVCYINAVLQSLFSCESFTTML 60
                                       9**************9998887777554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       859  (0.0479112); expected 358.6 (0.02)
Passed bias filter:                      499  (0.027832); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 1241.04
//
Query:       gene2081|gene2081|rna2081|rna2081  [L=616]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   2.5e-109  363.9   0.0   3.7e-109  363.3   0.0    1.3  1  ATP-synt_ab      ATP synthase alpha/beta family, nucleotide-b
    2.9e-45  153.0   0.1    6.1e-45  152.0   0.1    1.6  1  ATP-synt_ab_Xtn  ATPsynthase alpha/beta subunit N-term extens
    9.2e-12   45.3   0.5      2e-11   44.2   0.5    1.6  1  ATP-synt_ab_N    ATP synthase alpha/beta family, beta-barrel 


Domain annotation for each model (and alignments):
>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  363.3   0.0  6.2e-113  3.7e-109       1     213 []     245     466 ..     245     466 .. 0.98

  Alignments for each domain:
  == domain 1  score: 363.3 bits;  conditional E-value: 6.2e-113
                                        SSHHHHHHS-EBTT-EEEEEESTTSSHHHHHHHHHHHSSTSSEEEEEEESEEHHHHHHHHHHCHH.....SSGGGG CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxx RF
                        ATP-synt_ab   1 GirvlDalfpivqGqrtlipgafgvGktvisqslskqsnsddaiiyvgiGergnevaevleefpe.....gtimkr 71 
                                        G+r+lD+lfp+vqG++t+ipgafg+Gktvisqslsk+snsd +i+yvg+Gergne+aevl++fp+     ++imkr
  gene2081|gene2081|rna2081|rna2081 245 GQRILDSLFPCVQGGTTAIPGAFGCGKTVISQSLSKYSNSD-IIVYVGCGERGNEMAEVLMDFPQlkirgESIMKR 319
                                        9****************************************.***********************9888555**** PP

                                        EEEEEEETTS-HHHHHHHHHHHHHHHHHHHHTTSEEEEEEETHHHHHHHHHHHHHHTTTSBEGGGSBTTHHHHHHH CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        ATP-synt_ab  72 tvlvantsnepvaareasiytgitlAEyfrdqgknvlliadslsrwaeAlreislrlgempadqgypaylgaklas 147
                                        t+lvantsn+pvaareasiytgit+AEyfrdqg+nv+++ads+srwaeAlreis+rl empad+gypayl+akla 
  gene2081|gene2081|rna2081|rna2081 320 TILVANTSNMPVAAREASIYTGITIAEYFRDQGYNVSMMADSTSRWAEALREISGRLAEMPADSGYPAYLAAKLAF 395
                                        **************************************************************************** PP

                                        HHTTSEEE.....TSSEEEEEEEEEEE-GGCSTTSHHHHHHHHHSSEEEEB-HHHHHTTBSSSBCTTTEEE CS
                                        xxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        ATP-synt_ab 148 lyERagka.....pdrtGsvtivaavspaggDfsdpvttatlgitdgfivLdkklaqrkhfPainvlvSvS 213
                                        +yERagk      ++++Gsvtiv avsp+ggDfsdpvt atl+i+++f++LdkklaqrkhfP+in+  S+S
  gene2081|gene2081|rna2081|rna2081 396 FYERAGKCellgsDKKNGSVTIVGAVSPPGGDFSDPVTAATLAIVQVFWGLDKKLAQRKHFPSINWNLSYS 466
                                        ********999998889*****************************************************9 PP

>> ATP-synt_ab_Xtn  ATPsynthase alpha/beta subunit N-term extension
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  152.0   0.1     1e-48   6.1e-45       1     121 []     116     236 ..     116     236 .. 0.98

  Alignments for each domain:
  == domain 1  score: 152.0 bits;  conditional E-value: 1e-48
                                        EETTS-BHHHHHHHHTS.BE-TT----SS-SSS-EEEEESS-TT-EEETT-EEEEEECTTCEEEEEE--TT-EEEE CS
                    ATP-synt_ab_Xtn   1 yDGiqrpLekiaeksgs.fierGvkvpaldrekkwefkpkvkvgdkvsggdilGtvqeteliehkimvppkvegkv 75 
                                        +DGiqrpL++i  ++++ fi+rGv+vpaldr+kkw+f+p+vk gd v+ggdi+Gtv+e++l++hki+vpp+  gkv
  gene2081|gene2081|rna2081|rna2081 116 FDGIQRPLRDIFLEKKEiFIPRGVDVPALDRNKKWHFVPTVKIGDLVEGGDIFGTVDENTLVKHKILVPPDKAGKV 191
                                        9***********999999********************************************************** PP

                                        EEE--EEEE-TTSECEEECETT.ECEEEESSEEEETTS---ESEEE CS
                    ATP-synt_ab_Xtn  76 keiaeegeytvedtiaeveteegkekeltllqkwPvrkprpvkekl 121
                                        + i++eg+yt++dt++++ t++g e+ l++ ++w vr+prpvk+kl
  gene2081|gene2081|rna2081|rna2081 192 SFIVSEGDYTLKDTVMRLITKNG-EHMLKMSHEWSVRTPRPVKQKL 236
                                        *******************9996.9*******************97 PP

>> ATP-synt_ab_N  ATP synthase alpha/beta family, beta-barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.2   0.5   3.4e-15     2e-11       1      68 [.      38      99 ..      38     100 .. 0.96

  Alignments for each domain:
  == domain 1  score: 44.2 bits;  conditional E-value: 3.4e-15
                                       EEEEETTEEEEESSTSCETCTTEEEEECCETCSTEEEEEEEEEETTEEEEEESS-STTBBTTSEEEEE CS
                      ATP-synt_ab_N  1 ivqviGpvvdvefgigrlpgiynalevelvefgtlllgvalnlgedkVrvivmgstdGlsrGteVkrT 68
                                       i++v+Gpvv+ e++ g  +++ ++++v+      ++lg+++ ++ d++ ++v+++t+Gl++G++++++
  gene2081|gene2081|rna2081|rna2081 38 IYSVSGPVVIGEKMAG--CAMFELVKVG--T--IGILGEIIKIDKDRATIQVYEETSGLRVGDRIEPL 99
                                       789*************..**********..8..*******************************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (616 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       619  (0.0345251); expected 358.6 (0.02)
Passed bias filter:                      532  (0.0296726); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.63u 0.28s 00:00:00.91 Elapsed: 00:00:00.45
# Mc/sec: 4082.91
//
Query:       gene2082|gene2082|rna2082|rna2082  [L=194]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.011   15.1   4.3      0.016   14.5   4.1    1.4  1  NosD      Periplasmic copper-binding protein (NosD)
       0.12   12.6   0.0       0.23   11.7   0.0    1.4  1  DOG1      Seed dormancy control


Domain annotation for each model (and alignments):
>> NosD  Periplasmic copper-binding protein (NosD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   4.1   1.8e-06     0.016       2     101 ..      50     166 ..      49     183 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.8e-06
                               NosD   2 nnaisgdevlvsa.............rgngiqlensegseisnneisnsrdgi.lldnssnntitgntienlryGi 63 
                                        nn+ ++++ +v+              +g+ +++   +   is+  i n rd++ l+ + ++ ++++  ++++  Gi
  gene2082|gene2082|rna2082|rna2082  50 NNNFTKCTDTVFYkvicypdgiytigSGDMVHIFTRNTHMISKGMIFNLRDNVsLIVKRQSYKLKK-SLNSNIPGI 124
                                        66666766666666777434444444555566666688999************6666666666666.688889*** PP

                               NosD  64 hlenses..ntiedntlssnesGialmsss..nntlenNtis 101
                                        h++++++  ++++d  l++n +G +++s +   n l  N  +
  gene2082|gene2082|rna2082|rna2082 125 HVVEKDDvvVYVSDIMLDGNVKGTYIYSDNclINGLVSNLTN 166
                                        *******87788888889999*****9988443333344443 PP

>> DOG1  Seed dormancy control
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   2.6e-05      0.23      18      48 ..     157     188 ..     142     189 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.6e-05
                               DOG1  18 lrelvekvlahyeeyyraksaaa.kadvlhll 48 
                                        ++ lv+++ +++++yy+ k+ ++ ++d ++ll
  gene2082|gene2082|rna2082|rna2082 157 INGLVSNLTNNFQKYYKVKKSMSyEKDLFYLL 188
                                        6689**************9999989****997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       634  (0.0353617); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1414.11
//
Query:       gene2083|gene2083|rna2083|rna2083  [L=56]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (56 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       679  (0.0378716); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.27s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 417.75
//
Query:       gene2084|gene2084|rna2084|rna2084  [L=66]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.035   14.3   0.2      0.047   13.9   0.2    1.2  1  JIP_LZII       JNK-interacting protein  leucine zipper II
       0.11   11.2   0.2       0.12   11.0   0.2    1.0  1  Plexin_cytopl  Plexin cytoplasmic RasGAP domain
       0.19   11.7   0.0       0.24   11.3   0.0    1.2  1  OTOS           Otospiralin


Domain annotation for each model (and alignments):
>> JIP_LZII  JNK-interacting protein  leucine zipper II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.2   7.8e-06     0.047      29      56 ..      29      56 ..      27      65 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 7.8e-06
                           JIP_LZII 29 ddLIarvdeLtsereiLreEleslqkak 56
                                       +d++ rv+eL ++ e +  El+s+ k+ 
  gene2084|gene2084|rna2084|rna2084 29 NDILRRVEELDNDAEKMMLELSSIYKMI 56
                                       8********************9998765 PP

>> Plexin_cytopl  Plexin cytoplasmic RasGAP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.2   2.1e-05      0.12     497     549 ..       4      57 ..       2      60 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 2.1e-05
                                        HHHHHHHHHHHHHHHS---.-HHHHHHHHHHHHHHTTTTC-HHHHHHHHHHHHT CS
                      Plexin_cytopl 497 eYkeeveryYkdikklppi.sdqelnaalaeeskkhsnefntsaaLkeLykYvk 549
                                         Yke v++ Y+ + +++++ s  ++n+ l++  +  ++  + +  L+ +yk ++
  gene2084|gene2084|rna2084|rna2084   4 YYKESVKDLYSYVGNQQTVgSLPDMNDILRRVEELDNDAEKMMLELSSIYKMIH 57 
                                        59************999984568**************999**********9875 PP

>> OTOS  Otospiralin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0     4e-05      0.24      19      48 ..       4      33 ..       1      36 [. 0.91

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 4e-05
                               OTOS 19 yWPystsdfWnyveyfrslGaynqindlar 48
                                       y+  s  d+++yv   +++G+   +nd+ r
  gene2084|gene2084|rna2084|rna2084  4 YYKESVKDLYSYVGNQQTVGSLPDMNDILR 33
                                       778899*********************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (66 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       611  (0.0340789); expected 358.6 (0.02)
Passed bias filter:                      471  (0.0262703); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.34u 0.22s 00:00:00.56 Elapsed: 00:00:00.36
# Mc/sec: 555.75
//
Query:       gene2085|gene2085|rna2085|rna2085  [L=253]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.7e-14   53.1   2.5    5.7e-10   39.7   0.7    2.4  2  BIR       Inhibitor of Apoptosis domain
  ------ inclusion threshold ------
      0.072   13.4   0.2       0.18   12.1   0.2    1.6  1  DUF1922   Domain of unknown function (DUF1922)


Domain annotation for each model (and alignments):
>> BIR  Inhibitor of Apoptosis domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.7   0.7   6.4e-14   5.7e-10       1      72 [.       9      76 ..       9      77 .. 0.89
   2 !   13.0   0.0   1.3e-05      0.12      17      52 ..      95     130 ..      84     149 .. 0.81

  Alignments for each domain:
  == domain 1  score: 39.7 bits;  conditional E-value: 6.4e-14
                                BIR  1 RlatFkknWpeskkeakpsaeeLaeaGFyytptseskdnvqCfyCklaldgweedDdpleeHkkhspkCefl 72
                                       Rl+t++k   ++k+++k+++ + a  G+y++ + e++ +++C++C+++l+ w  dD p+ eH+k++++C++ 
  gene2085|gene2085|rna2085|rna2085  9 RLDTYEK---SKKNHRKTNSLDFALCGLYMYSS-ENHMTTTCYLCGKTLSYWLDDDIPFIEHLKRHKNCPLY 76
                                       8899966...455667788899*********99.8999*******************************975 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 1.3e-05
                                BIR  17 kpsaeeLaeaGFyytptseskdnvqCfyCklaldgw 52 
                                         +++++La+ GF+ +p ++ +  + C+ C+  ++++
  gene2085|gene2085|rna2085|rna2085  95 IVRKRKLAQRGFFAYPLKTGHIDLFCYKCGYYVNDF 130
                                        57789*************************998776 PP

>> DUF1922  Domain of unknown function (DUF1922)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.2     2e-05      0.18       8      29 ..      31      53 ..      28      55 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2e-05
                                       TS--EEEETT-SEEEE.TTTEEE CS
                            DUF1922  8 CGRvlYakegaktrkC.vCGkti 29
                                       CG  +Y+ e+  t +C  CGkt+
  gene2085|gene2085|rna2085|rna2085 31 CGLYMYSSENHMTTTCyLCGKTL 53
                                       ****************55***98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (253 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1106  (0.0616878); expected 358.6 (0.02)
Passed bias filter:                      688  (0.0383736); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1736.50
//
Query:       gene2086|gene2086|rna2086|rna2086  [L=421]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.3e-06   25.1   0.0    1.6e-05   24.3   0.0    1.3  1  Hydrolase_4    Serine aminopeptidase, S33
    5.7e-05   23.0   0.0    0.00011   22.1   0.0    1.6  1  Lipase_3       Lipase (class 3)
    0.00084   20.0   0.0     0.0012   19.6   0.0    1.2  1  Abhydrolase_6  Alpha/beta hydrolase family
     0.0077   15.9   0.1      0.015   14.9   0.1    1.4  1  Abhydrolase_1  alpha/beta hydrolase fold
  ------ inclusion threshold ------
       0.02   14.9   0.1       0.11   12.5   0.1    2.1  1  Cutinase       Cutinase
      0.047   13.3   0.0        0.2   11.2   0.0    1.8  1  DUF2974        Protein of unknown function (DUF2974)
      0.078   12.7   0.0       0.15   11.8   0.0    1.4  1  PGAP1          PGAP1-like protein


Domain annotation for each model (and alignments):
>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.0   6.3e-09   1.6e-05      58      96 ..     245     283 ..     242     293 .. 0.89

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 6.3e-09
                        Hydrolase_4  58 yvdDlaafvekvkeehpelplfllGhSmGGliallyllr 96 
                                        y++D+++++  vk++ p+ +++l GhSmG++ia +++  
  gene2086|gene2086|rna2086|rna2086 245 YLQDARQVYLDVKRRFPNNKIILTGHSMGAAIASAIGYI 283
                                        89*******************************988754 PP

>> Lipase_3  Lipase (class 3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   4.2e-08   0.00011      57      86 ..     255     284 ..     201     341 .. 0.89

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 4.2e-08
                                        HHHHHTT-EEEEEEEETHHHHHHHHHHHHH CS
                           Lipase_3  57 rllekypeysivvtGHSLGgalAlLaaldl 86 
                                        ++++++p+ +i++tGHS+G+a+A+ +++ +
  gene2086|gene2086|rna2086|rna2086 255 DVKRRFPNNKIILTGHSMGAAIASAIGYIY 284
                                        5678899999*************9877765 PP

>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   4.5e-07    0.0012      31      81 ..     208     279 ..     176     325 .. 0.73

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 4.5e-07
                                        EE--TTST..S-GGCS....................--HHHCHHH.HHHHCCTT..TTSEEEEEETCHHHHHHH CS
                      Abhydrolase_6  31 apDlpGhG..rsdppp....................ldledladl.aalldelaagggpvvlvGHSlGGalala 81 
                                        +p+l G+G  ++++++                    + l+d++++ +++ ++++   ++++l GHS+G+a+a+a
  gene2086|gene2086|rna2086|rna2086 208 SPSLLGYGngSTSTSDrifdniafdcnlspekvkrlFYLQDARQVyLDVKRRFP--NNKIILTGHSMGAAIASA 279
                                        688999954455555544444444444444444444555666666899999997..8889***********998 PP

>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.1   5.9e-06     0.015      36      98 ..     210     288 ..     197     291 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 5.9e-06
                                        EETTSTTSSSTTTGB.................CHHSHHHHHHHHHHHHHHCTTSSEEEEEETHHHHHHHHHHHHHG CS
                      Abhydrolase_1  36 DlrGvgySspapacin................ddygtasvaddldrildalgddkltlvGhSmGGmialayaaeyp 95 
                                         l+G+g +s++ + +                   + + + + ++  ++ ++++ k++l GhSmG +ia+a    y+
  gene2086|gene2086|rna2086|rna2086 210 SLLGYGNGSTSTSDRIfdniafdcnlspekvkRLFYLQDARQVYLDVKRRFPNNKIILTGHSMGAAIASAIGYIYN 285
                                        66777777777775444444444444444443333555555555688***********************999999 PP

                                        GGE CS
                      Abhydrolase_1  96 erV 98 
                                        e+V
  gene2086|gene2086|rna2086|rna2086 286 EYV 288
                                        988 PP

>> Cutinase  Cutinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   4.2e-05      0.11      63      94 ..     247     278 ..     245     394 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4.2e-05
                                        HHHHHHHHHHHHH-TT-EEEEEEETHHHHHHH CS
                           Cutinase  63 keaaalvqslaskCPdtkivlgGYSqGaqvid 94 
                                        ++a+++  +++ + P++ki+l G S Ga+++ 
  gene2086|gene2086|rna2086|rna2086 247 QDARQVYLDVKRRFPNNKIILTGHSMGAAIAS 278
                                        56777888899999***************975 PP

>> DUF2974  Protein of unknown function (DUF2974)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   7.9e-05       0.2      29      99 ..     191     278 ..     178     286 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 7.9e-05
                            DUF2974  29 aatfrleedtlvvaFRGTddtlvgWkedf.........nmafrsev.paqesAlkYlnkileeseg........ki 86 
                                         ++f++++ t v+a++GT  +l+g  +           n+af ++  p++ + l Yl+ + + + +        ki
  gene2086|gene2086|rna2086|rna2086 191 GIVFTVDH-TTVIAYKGTSPSLLGYGNGStstsdrifdNIAFDCNLsPEKVKRLFYLQDARQVYLDvkrrfpnnKI 265
                                        56677654.668999999999999966432222234457889888636777888899988888877888888878* PP

                            DUF2974  87 ylgGhSkGGnlAv 99 
                                        +l+GhS G+ +A 
  gene2086|gene2086|rna2086|rna2086 266 ILTGHSMGAAIAS 278
                                        *********9996 PP

>> PGAP1  PGAP1-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   5.8e-05      0.15      71     108 ..     245     280 ..     229     294 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 5.8e-05
                              PGAP1  71 ylndaIkyIlslysssekeptsviliGHSmGGivaraa 108
                                        yl+da +  l++   ++ +++++il GHSmG  +a a+
  gene2086|gene2086|rna2086|rna2086 245 YLQDARQVYLDVK--RRFPNNKIILTGHSMGAAIASAI 280
                                        5666655555554..88999*************99765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (421 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       813  (0.0453455); expected 358.6 (0.02)
Passed bias filter:                      505  (0.0281667); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.45
# Mc/sec: 2828.78
//
Query:       gene2087|gene2087|rna2087|rna2087  [L=266]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.8e-25   87.7   2.4    9.3e-25   86.8   2.4    1.4  1  PCNA_N    Proliferating cell nuclear antigen, N-terminal doma
    7.2e-19   68.2   2.3    2.4e-17   63.3   0.1    2.4  2  PCNA_C    Proliferating cell nuclear antigen, C-terminal doma
    1.1e-05   25.0   0.0    1.8e-05   24.3   0.0    1.4  1  Rad9      Rad9


Domain annotation for each model (and alignments):
>> PCNA_N  Proliferating cell nuclear antigen, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.8   2.4   1.6e-28   9.3e-25       7     122 ..      18     133 ..      14     136 .. 0.91

  Alignments for each domain:
  == domain 1  score: 86.8 bits;  conditional E-value: 1.6e-28
                                        SSHHHHHHHHHHHTTTCSEEEEEEETTEEEEEEE-TTSSEEEEEEEEGGGSSEEEESS-EEEEEEHHHHHHHHTTS CS
                             PCNA_N   7 eqasllkklleaikdlvneanfdcddsGislqalDsshvaLvslelrsegfekyrCDrnlalgvnlnslskilkca 82 
                                        +++s+++k++e+  d+v+++ ++ +d+G+s+q +D   va++ + l ++ f++yrCDr l+lg++++ +skilk  
  gene2087|gene2087|rna2087|rna2087  18 NRTSIFRKIVESAADIVDDVDIKLNDEGVSMQFMDAMNVAMMDVLLTKNMFDEYRCDRSLTLGLKIKEFSKILKGI 93 
                                        5789**********************************************************************88 PP

                                        TTT..SEEEEEEETTSSEEEEEEEECTSSEEEEEEEEEEEBG CS
                             PCNA_N  83 nne..dsvtlkaedeadtlalvfesekkdkiaeydlklklid 122
                                        + +   +  l+++d++dtl++vfe e    +++yd+kl++i 
  gene2087|gene2087|rna2087|rna2087  94 KLDtgTTFYLHCDDNPDTLNMVFEGE--AFVSNYDMKLQNIG 133
                                        6551157789*************976..57899999999885 PP

>> PCNA_C  Proliferating cell nuclear antigen, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.5   0.2     0.006        36      16      52 ..      21      57 ..       9     125 .. 0.65
   2 !   63.3   0.1     4e-21   2.4e-17       2     128 .]     139     262 ..     138     262 .. 0.95

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.006
                                       HHHHHHHHHHTTT-SEEEEEEETTEEEEEEEETTEEE CS
                             PCNA_C 16 sefaricrdlsqlsdsvvisvtkegvkfsasGdiGsa 52
                                       s f +i+   +++ d+v i++  egv  +    +  a
  gene2087|gene2087|rna2087|rna2087 21 SIFRKIVESAADIVDDVDIKLNDEGVSMQFMDAMNVA 57
                                       5599*********************976654443333 PP

  == domain 2  score: 63.3 bits;  conditional E-value: 4e-21
                                        ---SS-SEEEEEEHHHHHHHHHHHTTT-SEEEEEEETTEEEEEEEETTEEEEEEE--BEESSSGGGCBEEEESS-E CS
                             PCNA_C   2 ipdseydavvklpssefaricrdlsqlsdsvvisvtkegvkfsasGdiGsasivlkqvkdvdkeeeavklelkepv 77 
                                        ip++++ a  ++  s+f  + + + ++s+ + +++ k  ++fs +G+i  ++++ k  +        +kl+++e v
  gene2087|gene2087|rna2087|rna2087 139 IPQIDFTAEAEMKCSDFLYMRKAVGNFSEYIQMNACKTCINFSQKGEIIDSNMKFKAPE---TGKFDMKLNVTEDV 211
                                        9**************************************************99887654...4455689******* PP

                                        EEEEEHHHHHHHGGGGGC-SEEEEEEETTSEEEEEEEETTCEEEEEEE-BS CS
                             PCNA_C  78 tltfalkYlaeftkatsLservtlslssevPlvveykikdvgllayllakk 128
                                             +kY++ +tk++   ++v++ l +++P+ +e+ + d g+++y++a+k
  gene2087|gene2087|rna2087|rna2087 212 WVEIPMKYINCITKTAGFCQTVKICLGNNAPVFFEFMVGDYGHIRYYIAPK 262
                                        *************************************************97 PP

>> Rad9  Rad9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.0     3e-09   1.8e-05       1      74 [.      23      94 ..      23     187 .. 0.88

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 3e-09
                               Rad9  1 laralqclsrigdelyleisedglelrtvnssrSayalvtlkksfFdkyekevseqirckilvKsvlsvfrsls 74
                                       + +++++++ i d++ ++ +++g++++ +++ + a   v+l+k++Fd+y  + +  +++ +++K + +++++  
  gene2087|gene2087|rna2087|rna2087 23 FRKIVESAADIVDDVDIKLNDEGVSMQFMDAMNVAMMDVLLTKNMFDEY--RCDRSLTLGLKIKEFSKILKGIK 94
                                       5799*********************************************..77777777888899999998654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (266 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       796  (0.0443973); expected 358.6 (0.02)
Passed bias filter:                      544  (0.0303419); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 1818.33
//
Query:       gene2088|gene2088|rna2088|rna2088  [L=507]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
          7    4.6   9.8         12    3.9   9.8    1.2  1  DNA_pol_phi  DNA polymerase phi


Domain annotation for each model (and alignments):
>> DNA_pol_phi  DNA polymerase phi
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   9.8   0.00066        12     621     711 ..      69     162 ..      67     169 .. 0.51

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.00066
                        DNA_pol_phi 621 lldvLearenkegqaelfedededeeddeeeeeeddeededseeddde......eesdedeededdedvdeid.el 689
                                        +l+ L ++   + ++ +++d+d+d  ++ + ++    +d++++   ++       + d +++d++d+d++  d ++
  gene2088|gene2088|rna2088|rna2088  69 MLEKLVQESR-AAEECMVNDDDNDSNKNGNGMKHRMYNDDNND--GNNdngnggTTYDTNNNDDSDSDDNTSDcKF 141
                                        6666665544.45555553433333333333333333333333..22222356644444444444555555456** PP

                        DNA_pol_phi 690 reklaealgesgededdddsds 711
                                        ++ ++   g+++ d+  + sd+
  gene2088|gene2088|rna2088|rna2088 142 NNVIMSMYGTNN-DSTYNTSDE 162
                                        ************.444333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (507 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       800  (0.0446204); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.72u 0.37s 00:00:01.08 Elapsed: 00:00:00.58
# Mc/sec: 2650.52
//
Query:       gene2089|gene2089|rna2089|rna2089  [L=348]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.019   14.9   0.4      0.038   13.9   0.4    1.4  1  HSDR_N    Type I restriction enzyme R protein N terminus (HSD


Domain annotation for each model (and alignments):
>> HSDR_N  Type I restriction enzyme R protein N terminus (HSDR_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.4   2.1e-06     0.038     150     188 ..      69     108 ..      49     111 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.1e-06
                                        HH.HHTSS---.---SSSGGGGG--EEEEE-SS-EEEEE- CS
                             HSDR_N 150 in.QikryrkeksdvsipqlfrYlqfgvisngketrfyak 188
                                        ++ Qi+ry++ek+ + +++l  Y + +v++ng  t  ya 
  gene2089|gene2089|rna2089|rna2089  69 YQaQIRRYHREKKYNDLKRLIDYYATFVYTNGAGTISYAF 108
                                        4448*******87777****************99988875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (348 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       513  (0.0286129); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.64u 0.32s 00:00:00.96 Elapsed: 00:00:00.55
# Mc/sec: 1915.92
//
Query:       gene209|gene209|rna209|rna209  [L=181]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.5e-16   59.3   0.2      1e-15   58.1   0.2    1.6  1  TFIIS_M        Transcription factor S-II (TFIIS), central dom
    1.6e-13   50.2  10.4    1.6e-13   50.2  10.4    1.9  2  TFIIS_C        Transcription factor S-II (TFIIS)
  ------ inclusion threshold ------
        2.3    8.0   5.7        1.5    8.5   0.1    3.0  4  Baculo_LEF5_C  Baculoviridae late expression factor 5 C-termi


Domain annotation for each model (and alignments):
>> TFIIS_M  Transcription factor S-II (TFIIS), central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.1   0.2   1.8e-19     1e-15       1     110 [.      28     129 ..      28     131 .. 0.94

  Alignments for each domain:
  == domain 1  score: 58.1 bits;  conditional E-value: 1.8e-19
                                    -HHHHHHHHHHHHHTT---...-.--THHHHHHHHHHHHHHHT------HHHHHHHHHHHHHS-TT-HHHHHTSSSS--S CS
                        TFIIS_M   1 dkvRdkcrelLaealeedsseaeeeedveelaaeiEealfekekkstdkkykqkvrslvfNLkdkkNpeLrrrvlsgeis 80 
                                    d+ Rd+  +l++e++ +++++ + + ++++la ++E+++++      +k   +++rs ++NLkdk+N +L+  +++g i 
  gene209|gene209|rna209|rna209  28 DQSRDRTTSLFYEVFVSIINDVD-KLRAARLASDLEQEIYD------NKIVSSQIRSKYLNLKDKSN-DLCVGIYEGRIG 99 
                                    678****************8766.77***************......5679************9999.************ PP

                                    TTTTS---TTTSS-HHHHHHHHHHHHHHHH CS
                        TFIIS_M  81 peklvkmspeElaseelkeereklekeale 110
                                    + +++ ms +E++s+ +++ ++ l k ++e
  gene209|gene209|rna209|rna209 100 VHEFLLMSMDEMKSKARRSSDNDLIKSSIE 129
                                    ***********************9999987 PP

>> TFIIS_C  Transcription factor S-II (TFIIS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0      0.59   3.5e+03      14      20 ..      71      77 ..      70      78 .. 0.79
   2 !   50.2  10.4   2.8e-17   1.6e-13       2      39 .]     144     180 ..     143     180 .. 0.97

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.59
                        TFIIS_C 14 fqlQtRs 20
                                   +  Q+Rs
  gene209|gene209|rna209|rna209 71 VSSQIRS 77
                                   568***9 PP

  == domain 2  score: 50.2 bits;  conditional E-value: 2.8e-17
                        TFIIS_C   2 kCpkCgsreayffqlQtRsaDEpmtvfykCtkCghrWr 39 
                                     C kC++r++ + q+QtRsaDEpmt+++ C kCg++W+
  gene209|gene209|rna209|rna209 144 FCFKCKQRKCRYRQIQTRSADEPMTTYVFC-KCGNTWK 180
                                    6*****************************.******7 PP

>> Baculo_LEF5_C  Baculoviridae late expression factor 5 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       1.6   9.8e+03      18      26 ..      69      77 ..      61      77 .. 0.70
   2 ?    1.1   0.0     0.054   3.2e+02      24      32 ..     105     113 ..      98     119 .. 0.76
   3 ?   -2.9   0.2      0.92   5.5e+03      36      40 ..     144     148 ..     142     150 .. 0.78
   4 ?    8.5   0.1   0.00026       1.5      22      41 ..     158     176 ..     156     177 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 1.6
                  Baculo_LEF5_C 18 vtiEiQnRa 26
                                    ++ +Q R+
  gene209|gene209|rna209|rna209 69 KIVSSQIRS 77
                                   467789887 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.054
                  Baculo_LEF5_C  24 nRagDEivs 32 
                                    + ++DE+ s
  gene209|gene209|rna209|rna209 105 LMSMDEMKS 113
                                    569***977 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 0.92
                  Baculo_LEF5_C  36 yCskC 40 
                                     C kC
  gene209|gene209|rna209|rna209 144 FCFKC 148
                                    69999 PP

  == domain 4  score: 8.5 bits;  conditional E-value: 0.00026
                  Baculo_LEF5_C  22 iQnRagDEivsfvryCskCg 41 
                                    iQ+R+ DE    +  C kCg
  gene209|gene209|rna209|rna209 158 IQTRSADEPMTTYVFC-KCG 176
                                    8************999.787 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       730  (0.0407162); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.61u 0.32s 00:00:00.93 Elapsed: 00:00:00.55
# Mc/sec: 991.61
//
Query:       gene2090|gene2090|rna2090|rna2090  [L=236]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       181  (0.0100954); expected 358.6 (0.02)
Passed bias filter:                      144  (0.00803168); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.60u 0.32s 00:00:00.92 Elapsed: 00:00:00.55
# Mc/sec: 1300.91
//
Query:       gene2091|gene2091|rna2091|rna2091  [L=567]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.1e-28   97.7   1.5    1.4e-17   64.4   0.3    2.6  3  PI3_PI4_kinase  Phosphatidylinositol 3- and 4-kinase


Domain annotation for each model (and alignments):
>> PI3_PI4_kinase  Phosphatidylinositol 3- and 4-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0      0.37   6.6e+03     117     143 ..     110     138 ..     108     141 .. 0.86
   2 !   32.0   0.0   5.7e-12     1e-07       4      76 ..     318     386 ..     315     395 .. 0.93
   3 !   64.4   0.3   7.8e-22   1.4e-17     125     236 ..     397     502 ..     385     515 .. 0.78

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 0.37
                                        HHHHHHHHSSSHHHHHHH..HHHHHHHHH CS
                     PI3_PI4_kinase 117 llqeFvkkspsaeewlea..rkqFvrsla 143
                                        +++ F+  ++ ++ew++a  ++ +v++++
  gene2091|gene2091|rna2091|rna2091 110 VYNTFYLADNAEDEWGDAliYRGYVLECS 138
                                        678899999999****9999999999986 PP

  == domain 2  score: 32.0 bits;  conditional E-value: 5.7e-12
                                        EEEECSSCHHHHHHHHHHHHHHHHHHHHTTTTCCCT-------EEESSSSEEEEE--TTEEEHHHHHHHHHHH CS
                     PI3_PI4_kinase   4 giykvgddlrqdelivqvfklmdeelskennpkrrklalktysviplgrkcgiielvassetaaslldeklek 76 
                                        +i+k+gdd+rqd+l +q+++++ ++ ++ n+p      +++y vi++  +cg+ie++  + + ++  +ek ++
  gene2091|gene2091|rna2091|rna2091 318 LIFKAGDDCRQDQLALQLIQMFLNIFKESNLPIF----VYPYTVISTDYECGLIEVITDAISRDQMGREKINN 386
                                        79*******************************9....********************999999999998866 PP

  == domain 3  score: 64.4 bits;  conditional E-value: 7.8e-22
                                        SSSHHHHHHHHHHHHHHHHHHHHHHHHHT-TT--TTTEEEETTTSEEEESSTTTCCTCSHCSSSS-.SSSSSS-TH CS
                     PI3_PI4_kinase 125 spsaeewlearkqFvrslaklsvldyilgngDRhldNilvdktsgklihIDfGlilpdewkllpfpqekvPfrltr 200
                                        +++ +++ +a ++F++s+ ++s ++y l++ DRh++Ni++ +  g++ihIDfG++++ ++  l+ +   vP++ t+
  gene2091|gene2091|rna2091|rna2091 397 FKEGTAYKKAHRRFILSFVGYSLVTYFLNVKDRHNGNIMI-NGRGEMIHIDFGFMFDISPGGLNLE---VPLKITQ 468
                                        4555799999******************************.***************8888888876...******* PP

                                        HHHHHTSTTCCHHHHHHHHHHHHHHHHHTHHHHHHH CS
                     PI3_PI4_kinase 201 elvlaidpskdeglfresceealealrrdqnlltrl 236
                                        e+v+++ ++ + + +  + + ++++ rr +++++ +
  gene2091|gene2091|rna2091|rna2091 469 EIVELL-DDHMDEYVSLMIQGFFALRRRSKDIVL-M 502
                                        ******.455555555555555555555555444.3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (567 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       489  (0.0272742); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.73u 0.36s 00:00:01.08 Elapsed: 00:00:00.56
# Mc/sec: 3050.19
//
Query:       gene2092|gene2092|rna2092|rna2092  [L=314]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.055   12.7   0.1       0.12   11.6   0.0    1.5  2  Ploopntkinase2  P-loop Nucleotide Kinase2


Domain annotation for each model (and alignments):
>> Ploopntkinase2  P-loop Nucleotide Kinase2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   6.8e-06      0.12      22      70 ..      13      62 ..       7      76 .. 0.87
   2 ?   -3.4   0.0      0.25   4.5e+03     186     221 ..     201     236 ..     196     248 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 6.8e-06
                     Ploopntkinase2 22 fiewlrtklePeeleytvgd.ktrqfGlvfeelklvfvGqytvsnksgla 70
                                       ++++l+t +eP +  +t+     + f +  +++kl+fv qy +  ks+ +
  gene2092|gene2092|rna2092|rna2092 13 LMQHLKTMYEPLKSIFTISViGSIMFVIDNKDFKLLFVHQYHKQQKSDDS 62
                                       7899*************9862578899999*****************965 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 0.25
                     Ploopntkinase2 186 dekqdvlyksraannnevkkglvselkllsfdaplw 221
                                        ++ qd    s+ +n++ +++ + ++l  ls++  l 
  gene2092|gene2092|rna2092|rna2092 201 NKFQDASIASKPSNQQILTELVLNDLDSLSYERRLV 236
                                        455777777777888888888899999988887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (314 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       833  (0.046461); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.67u 0.31s 00:00:00.98 Elapsed: 00:00:00.55
# Mc/sec: 1724.45
//
Query:       gene2093|gene2093|rna2093|rna2093  [L=237]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (237 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       491  (0.0273858); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.63u 0.31s 00:00:00.94 Elapsed: 00:00:00.55
# Mc/sec: 1297.92
//
Query:       gene2094|gene2094|rna2094|rna2094  [L=71]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.075   13.5   0.0      0.087   13.3   0.0    1.1  1  C1ORF64   Steroid receptor-associated and regulated protein


Domain annotation for each model (and alignments):
>> C1ORF64  Steroid receptor-associated and regulated protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   4.8e-06     0.087      50      78 ..      12      40 ..       3      54 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.8e-06
                            C1ORF64 50 ilfcgenqprltqeislgggalaqardtL 78
                                       ++fcge++ +lt+e+ +g++ l++ +dt 
  gene2094|gene2094|rna2094|rna2094 12 VVFCGESNDKLTKETKYGKKILDEIQDTY 40
                                       8***********************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (71 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       908  (0.0506442); expected 358.6 (0.02)
Passed bias filter:                      560  (0.0312343); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.33s 00:00:00.92 Elapsed: 00:00:00.56
# Mc/sec: 382.62
//
Query:       gene2095|gene2095|rna2095|rna2095  [L=183]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       624  (0.0348039); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.61u 0.34s 00:00:00.95 Elapsed: 00:00:00.57
# Mc/sec: 966.90
//
Query:       gene2096|gene2096|rna2096|rna2096  [L=644]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.098   12.3   0.0       0.16   11.6   0.0    1.5  1  Ribosomal_L4  Ribosomal protein L4/L1 family


Domain annotation for each model (and alignments):
>> Ribosomal_L4  Ribosomal protein L4/L1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   9.1e-06      0.16     144     191 ..     544     588 ..     417     589 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 9.1e-06
                                        SSSSCHHHHHHTT-TTEEEEESTT--CHHHHHSSEEEEEHHHHHHHHH CS
                       Ribosomal_L4 144 sekdenlvlaarnlpgvevieveslnvydllkadkvvitksaveklee 191
                                        +  +e +v+ ++n+p+++  +v ++ +y+l+  +++ ++++a++kl +
  gene2096|gene2096|rna2096|rna2096 544 D--SESFVKFCANIPELDAETVIHVAIYQLIL-KHICCSQKALQKLVK 588
                                        3..589************************97.57999*****99976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (644 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       823  (0.0459033); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.75u 0.35s 00:00:01.10 Elapsed: 00:00:00.56
# Mc/sec: 3485.15
//
Query:       gene2097|gene2097|rna2097|rna2097  [L=1493]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        2.7    7.6  17.7        5.3    6.6   0.5    4.4  4  CAP_C     Adenylate cyclase associated (CAP) C terminal


Domain annotation for each model (and alignments):
>> CAP_C  Adenylate cyclase associated (CAP) C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.4   0.00089        16      39      77 ..     649     688 ..     614     693 .. 0.71
   2 ?    6.6   0.5   0.00029       5.3      32      59 ..     720     747 ..     711     769 .. 0.91
   3 ?   -1.8   0.4      0.11   2.1e+03      37      59 ..     807     829 ..     783     832 .. 0.48
   4 ?    6.0   0.5   0.00048       8.6      56     108 ..     904     954 ..     865     974 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.00089
                              CAP_C  39 CknstiqikgKvnaitldnckkv.svvvdsvvSsvevinc 77 
                                         + +t+++ + vn++ + nck v ++ + + v s+++  c
  gene2097|gene2097|rna2097|rna2097 649 VHGCTVSVANTVNNLEIYNCKGVfHIPILNHVLSLDIQDC 688
                                        3567777777777777777776524556666666666555 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.00029
                              CAP_C  32 qsvyifkCknstiqikgKvnaitldnck 59 
                                         s yi + + + +qi+gK+  + l++c+
  gene2097|gene2097|rna2097|rna2097 720 RSAYIRNVSGTCLQINGKCEHLYLEKCT 747
                                        5789***********************7 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 0.11
                              CAP_C  37 fkCknstiqikgKvnaitldnck 59 
                                        + ++ +++ ++  +  i++d+c+
  gene2097|gene2097|rna2097|rna2097 807 YISDGCILCLNSACDRISVDQCT 829
                                        22333333333334444444443 PP

  == domain 4  score: 6.0 bits;  conditional E-value: 0.00048
                              CAP_C  56 dnckkvsvvvdsvvSsvevincksvkvqvlgkvptisiDktdgvqiyLskesl 108
                                         +c+  +++v+ + ++++++++++++  +l  +p+i   ++  +  yL  e +
  gene2097|gene2097|rna2097|rna2097 904 ASCE--QLIVKRCTGTIDITKSAKITALTLADTPMIYNKEVHRAVTYLCLEHM 954
                                        4454..6899***************************9999999999976655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1493 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       508  (0.028334); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.85u 0.29s 00:00:01.13 Elapsed: 00:00:00.48
# Mc/sec: 9280.49
//
Query:       gene2098|gene2098|rna2098|rna2098  [L=65]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (65 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       521  (0.0290591); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.44
# Mc/sec: 438.94
//
Query:       gene2099|gene2099|rna2099|rna2099  [L=144]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       323  (0.0180155); expected 358.6 (0.02)
Passed bias filter:                      223  (0.0124379); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.45
# Mc/sec: 969.49
//
Query:       gene21|gene21|rna21|rna21  [L=121]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.3e-27   94.6   0.0    6.2e-27   94.4   0.0    1.0  1  Acetyltransf_15  Putative acetyl-transferase


Domain annotation for each model (and alignments):
>> Acetyltransf_15  Putative acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.4   0.0   3.4e-31   6.2e-27      95     210 .]       1     105 [.       1     105 [. 0.94

  Alignments for each domain:
  == domain 1  score: 94.4 bits;  conditional E-value: 3.4e-31
            Acetyltransf_15  95 eeslkelkknYkvdnelllaLHlnpkDksMnisfalYyslgFrkglfvksgPeelkkrlekiltfkdlvkvikkekrseekgky 178
                                +es++++ ++Y+++   ++aLHlnpkD++Mnisf++Y++lgF+++++v+ gP++l++ +eki t++d +      +  +  g+y
  gene21|gene21|rna21|rna21   1 MESTRKVCQRYNLT-RPIFALHLNPKDQMMNISFSFYVNLGFVNVAYVNDGPYDLQFDVEKISTKWDEI------QDRPASGRY 77 
                                68999*********.9*****************************************************......89999**** PP

            Acetyltransf_15 179 lamfckvndflnkkkiraeemkelgekLrkiL 210
                                lamfc ++ ++ +   +  +++e ge++r++L
  gene21|gene21|rna21|rna21  78 LAMFC-FDGLGTGV--KG-DFREVGENIRGKL 105
                                *****.9*999998..44.8899999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       358  (0.0199677); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.30s 00:00:00.73 Elapsed: 00:00:00.47
# Mc/sec: 780.59
//
Query:       gene210|gene210|rna210|rna210  [L=110]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       456  (0.0254337); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.29s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 766.03
//
Query:       gene2100|gene2100|rna2100|rna2100  [L=71]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-05   24.3   1.6    0.00037   20.3   0.4    2.5  2  UvrD_C_2         UvrD-like helicase C-terminal domain
    2.1e-05   22.7   0.1    2.1e-05   22.7   0.1    1.0  1  Herpes_Helicase  Helicase
     0.0082   15.9   0.0     0.0098   15.7   0.0    1.2  1  Viral_helicase1  Viral (Superfamily 1) RNA helicase


Domain annotation for each model (and alignments):
>> UvrD_C_2  UvrD-like helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.4   6.2e-08   0.00037       5      47 ..       1      37 [.       1      38 [. 0.80
   2 ?    2.3   0.0     0.024   1.5e+02      19      39 ..      45      66 ..      42      67 .. 0.67

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 6.2e-08
                           UvrD_C_2  5 ltihkaQGsefpaVivfdpdlaaarmgelrrrlLYtavTRAre 47
                                       +tihk+QG+ f+ V v    +++       +  LY+a++R r+
  gene2100|gene2100|rna2100|rna2100  1 MTIHKSQGQSFDEVGV--YLYSSIF----VHGQLYVALSRVRH 37
                                       7*************99..4454444....2678******9776 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.024
                           UvrD_C_2 19 ivfdpdlaaarmgel.rrrlLY 39
                                       iv+++d + a+++++ +++ +Y
  gene2100|gene2100|rna2100|rna2100 45 IVDNDDQSKADNNMVyTKNVVY 66
                                       4555559999988886666666 PP

>> Herpes_Helicase  Helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.1   3.5e-09   2.1e-05     734     778 ..       1      44 [.       1      67 [. 0.81

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 3.5e-09
                    Herpes_Helicase 734 mtiaksqGlslekvAicFgnhknlklssvYvalsRatdseflvmd 778
                                        mti ksqG s++ v +   ++      ++YvalsR+++++ l++ 
  gene2100|gene2100|rna2100|rna2100   1 MTIHKSQGQSFDEVGVYLYSS-IFVHGQLYVALSRVRHADGLKVY 44 
                                        9****************9999.667899**********9988764 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   1.6e-06    0.0098     186     227 ..       1      36 [.       1      45 [. 0.78

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.6e-06
                    Viral_helicase1 186 ttvhevqGltfdkVtlvllketdlelisesrenllvAlTRhr 227
                                        +t h  qG++fd+V ++l ++    ++ +   +l+vAl+R r
  gene2100|gene2100|rna2100|rna2100   1 MTIHKSQGQSFDEVGVYLYSS----IFVH--GQLYVALSRVR 36 
                                        699****************44....6654..789*****843 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (71 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       420  (0.0234257); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 526.96
//
Query:       gene2101|gene2101|rna2101|rna2101  [L=72]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.033   13.3   0.0      0.039   13.0   0.0    1.1  1  tRNA-synt_2  tRNA synthetases class II (D, K and N)


Domain annotation for each model (and alignments):
>> tRNA-synt_2  tRNA synthetases class II (D, K and N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   2.2e-06     0.039     254     309 ..      11      62 ..       4      65 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.2e-06
                                        HHHHHHCCHHSSSGGGGHHHH.HHHHCT--SEEEEEEEHHHHHHHHCT-SSGGGCSS CS
                                        xxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        tRNA-synt_2 254 eeklkskgldeeaeekfswyl.ealeyGapphgGlglGldRlvmlllgsesIrdvia 309
                                        +e+l++   +     ++ +y  + le  ++   G g+G +R++ +ll++e+I +v+a
  gene2101|gene2101|rna2101|rna2101  11 KEQLEKSSCS-----TITEYHkNILEDKCVYSIGGGIGQSRVMLFLLEKENIWEVQA 62 
                                        4444444444.....33333303334444566799*******************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (72 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       485  (0.0270511); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.28s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 531.34
//
Query:       gene2102|gene2102|rna2102|rna2102  [L=322]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-88  296.8   2.6    1.3e-88  296.6   2.6    1.0  1  AsnA             Aspartate-ammonia ligase
     0.0036   16.3   0.1     0.0053   15.7   0.1    1.2  1  Glyco_hydro_130  beta-1,4-mannooligosaccharide phosphorylase
  ------ inclusion threshold ------
      0.032   14.2   0.3      0.052   13.6   0.3    1.3  1  DUF2089          Protein of unknown function (DUF2089)
      0.085   11.9   0.4       0.12   11.5   0.4    1.1  1  tRNA-synt_2      tRNA synthetases class II (D, K and N)


Domain annotation for each model (and alignments):
>> AsnA  Aspartate-ammonia ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  296.6   2.6   2.9e-92   1.3e-88       1     226 [.      13     236 ..      13     237 .. 0.98

  Alignments for each domain:
  == domain 1  score: 296.6 bits;  conditional E-value: 2.9e-92
                                        HHHHHHHHHHHHHHHHHHC-EEE----SEEETTSS-S--TTST----EE--TSTT--EEE-S--TTHHHHHHHHTT CS
                               AsnA   1 qkaiklvkdlfeeelakelnltrvsaPllvekesglnDnLnGverpvsfkvkeleeeaevvhslakWkRlalkkyg 76 
                                        qkaik  k lfe++l+  l+l+++ +P+++++es  +D+L+G +rp++f++k+ +e+  + hslakWkR  l+kyg
  gene2102|gene2102|rna2102|rna2102  13 QKAIKIAKGLFEQKLSGVLHLEKIVSPIYIKDES-YHDTLDGAQRPIKFDFKN-GEHGMILHSLAKWKRAILSKYG 86 
                                        799***************************9876.89**************97.78899***************** PP

                                        --TT-EEEEEEEEE-TT-S--SS--SEEEEEEEEEE--TT--SHHHHHHHHHHHHHHHHHHHHHHHHHC.-----S CS
                               AsnA  77 fkvgeGlytdmnaiRkdeeldnlhsvyvdqwDwEkviekeernlefLketvkkiykalketekevaekypelkkkl 152
                                        +k geG++tdm aiR+de++++lhs+ vdqwDwE++i k++r+l+fL e+v+ki+++lke+e+e++ +yp+l+kkl
  gene2102|gene2102|rna2102|rna2102  87 YKDGEGIITDMLAIRRDEDISRLHSYLVDQWDWEMTIIKQKRTLDFLYEIVEKIFSVLKEVENEINMQYPTLSKKL 162
                                        **************************************************************************** PP

                                        -SS-EEEEHHHHHHHSTSS-HHHHHHHHHHHHSEEEEE--SSB-SSSSBSS---TTTB--SSEEEEEEEETTTT CS
                               AsnA 153 peeitfitseeledkyPdltpkeREeaivkeygavfligiGgklksgekhdgRapdYDdwsLngDilvynevld 226
                                        p++itfit++ele++yP++t++eRE++ivk+++avf+ +iGgkl sg+ h++RapdYDdw LngDi+vyne +d
  gene2102|gene2102|rna2102|rna2102 163 PNNITFITTQELENMYPEMTMDEREYEIVKKHKAVFISQIGGKLMSGKIHSVRAPDYDDWMLNGDIVVYNEKMD 236
                                        **********************************************************************9876 PP

>> Glyco_hydro_130  beta-1,4-mannooligosaccharide phosphorylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.1   1.2e-06    0.0053     122     190 ..     157     227 ..     145     238 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.2e-06
                                        SEEEEEEEESSSSSEEEE--SSSSSE..........EEEEE-SS-BTTBEEEEEESS...-S---EEEEEES CS
                    Glyco_hydro_130 122 gvrievattkdlltvkrleekialielkkdeislatkdgalfpkkikgkylmfsrvh...tvsekifLavsd 190
                                        + + ++ ++ +++t++ le+ ++++++ + e +++ k++a+f+ +i gk++   ++h    ++ + +++ +d
  gene2102|gene2102|rna2102|rna2102 157 TLSKKLPNNITFITTQELENMYPEMTMDEREYEIVKKHKAVFISQIGGKLMS-GKIHsvrAPDYDDWMLNGD 227
                                        56777788899***********************************999764.4555111556677777765 PP

>> DUF2089  Protein of unknown function (DUF2089)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.3   1.2e-05     0.052      51      98 ..     143     193 ..     120     213 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.2e-05
                            DUF2089  51 nlkevekelgisYpTvrnrldeileaLgyeeeeeeeee...eeerkeilek 98 
                                         lkeve+e+++ YpT+ ++l + ++ + ++e e+   e   +e++ ei++k
  gene2102|gene2102|rna2102|rna2102 143 VLKEVENEINMQYPTLSKKLPNNITFITTQELENMYPEmtmDEREYEIVKK 193
                                        59******************9999888888776622123345556666665 PP

>> tRNA-synt_2  tRNA synthetases class II (D, K and N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.4   2.6e-05      0.12     102     175 ..     102     185 ..      99     235 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 2.6e-05
                                        --S--BTTB-S-CEEEEEEEEET-SCHHHHHHHHHHHHHHHHHHHHCSCCCCCHTTTTTS............EE-S CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............xxxx RF
                        tRNA-synt_2 102 RaEdsrtdrhlaEFtqieaemsfieeedimqvleelikslvkevlessakdiefvirrns............kdlk 165
                                        R+Ed++  +      q + em +i++++ +++l e+++++++ + ++++++i+++  + s            ++l+
  gene2102|gene2102|rna2102|rna2102 102 RDEDISRLHSY-LVDQWDWEMTIIKQKRTLDFLYEIVEKIFSVL-KEVENEINMQYPTLSkklpnnitfittQELE 175
                                        78888777766.67899************************988.8899999999999994455555555555555 PP

                                        SS-EEEEHHH CS
                                        xxxxxxxxxx RF
                        tRNA-synt_2 166 kpfkrltyke 175
                                        + ++ +t++e
  gene2102|gene2102|rna2102|rna2102 176 NMYPEMTMDE 185
                                        5555555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (322 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       655  (0.036533); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 2217.90
//
Query:       gene2103|gene2103|rna2103|rna2103  [L=117]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.8e-16   60.0   3.1    2.6e-16   59.5   3.1    1.3  1  TFIIA_gamma_C  Transcription initiation factor IIA, gamma sub
      3e-15   56.0   0.0    4.2e-15   55.5   0.0    1.2  1  TFIIA_gamma_N  Transcription initiation factor IIA, gamma sub


Domain annotation for each model (and alignments):
>> TFIIA_gamma_C  Transcription initiation factor IIA, gamma subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.5   3.1   2.9e-20   2.6e-16       1      45 []      56      99 ..      56      99 .. 0.98

  Alignments for each domain:
  == domain 1  score: 59.5 bits;  conditional E-value: 2.9e-20
                      TFIIA_gamma_C  1 tfKgkLdtYrfcDdVWtFiiknvefklendetvkvdkvKIVACns 45
                                       +fKg +++Y+f+D+VW Fi +++ ++++n ++v++d vKIVAC++
  gene2103|gene2103|rna2103|rna2103 56 NFKGGVESYNFVDGVWNFITRDFVMTINN-KMVRCDYVKIVACDA 99
                                       8***************************9.*************96 PP

>> TFIIA_gamma_N  Transcription initiation factor IIA, gamma subunit, helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.5   0.0   4.7e-19   4.2e-15       2      44 ..       2      44 ..       1      47 [. 0.96

  Alignments for each domain:
  == domain 1  score: 55.5 bits;  conditional E-value: 4.7e-19
                      TFIIA_gamma_N  2 YelYRrstlGtaLtdaLDeliqegkIspqlamkVLeqFDksin 44
                                       Ye+YR+s +G+aL+d++++++++ +++p  a  +Le+FD+++ 
  gene2103|gene2103|rna2103|rna2103  2 YEFYRQSIIGKALQDTIEDMLSNSQLTPVQAKLILEKFDQAVP 44
                                       ****************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       525  (0.0292822); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.35u 0.27s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 878.02
//
Query:       gene2104|gene2104|rna2104|rna2104  [L=500]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-51  176.6  29.0    1.8e-51  176.1  29.0    1.2  1  Sec1      Sec1 family
  ------ inclusion threshold ------
       0.18   12.3   7.0      0.085   13.3   2.1    3.0  3  RSS_P20   Suppressor of RNA silencing P21-like N-terminal dom
        4.3    7.6   5.8         20    5.5   0.5    3.0  3  DUF3365   Protein of unknown function (DUF3365)


Domain annotation for each model (and alignments):
>> Sec1  Sec1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  176.1  29.0     3e-55   1.8e-51       2     574 ..      26     493 ..      25     493 .. 0.79

  Alignments for each domain:
  == domain 1  score: 176.1 bits;  conditional E-value: 3e-55
                                        EEEE-HHHHHHHHTT--HHHHHTTTEEETT..T.--S-.....BTTSEEEEEE-S-HHHHHHHHHHHHSS-SBS-E CS
                               Sec1   2 vLvlDkelskilssvlkvsdlleegVtkieklk.krepskrealphlkaiyflrptkenidrlakdfisarrykey 76 
                                        v v+ k++++il ++++ +++l++++ ++ +l+ +r+p     +   +aiyf++  ke+ +++ kd ++++ y +y
  gene2104|gene2104|rna2104|rna2104  26 VFVYNKSTARILTHIFTKTQILSNEILSMQRLElNRDP-----I-AYPAIYFVTYCKETYRAIKKD-VKNKIYTKY 94 
                                        67999*****************99***99999999999.....7.789****************76.57799**** PP

                                        EEEESS---HHHHHHHHH..SG.GGGEEEEE----SEEEETTEEE-STTHHHHSTTG.....GG.......--HHH CS
                               Sec1  77 hifftprlseslleglakadeevvkkvklkelnldfvplesdlfslnpelplsfrdlyldndnsaleeeieslldr 152
                                        +i+ t+ ++e   e++  +d     +++ k + ++fv+ ++++f++         d                +++ 
  gene2104|gene2104|rna2104|rna2104  95 YIIHTNEIKE--NEKII-GD-----NIFYKHVDINFVVMDERVFTC--L------D----------------SVED 138
                                        ********97..46777.66.....45578999***********98..2......2................2444 PP

                                        HHHHHHHHHHHH-..--EEEE-TT-HHHHHHHH..........HHHHTTT--SS--EEEEE-GGG-SSTTTS---B CS
                               Sec1 153 iakgLlsvllslekkiPiirykgsaasmvakkladelkekidskknfesessrqrpvLiIlDRsvDlvtpllhqwT 228
                                        + ++  s +l l++ + + r+           l ++l+++   ++  es s+  +++LiIlDRs+D++ pl+h + 
  gene2104|gene2104|rna2104|rna2104 139 AMRSFSS-ILKLRFNMVNLRADT--------ALFEQLRTN---DSMCESRSEYYNSDLIILDRSFDMIVPLIHFFN 202
                                        6777777.555532344555554........677888876...3444555789999******************** PP

                                        HHHHHHHHS--BTEEEEEE--SSSEEEEEE--TT..-TTHHHHTTSBHHHHHHHHHHHHHHHHHHHHTTT...-TT CS
                               Sec1 229 YqaliddllgglnnnnvvleeepkeekeaelvesssDeffaelrhlnfgevgeklkkeakeyqeenekkrngakes 304
                                        +++l++dl   l               +++ +   + ++++e+r+l++++ ++ l+++a+++ e + kk  + k++
  gene2104|gene2104|rna2104|rna2104 203 FESLLYDLN--L--------------CQSTTD---ESPLYREIRYLHIADTNSVLNNKAQKLVEGM-KKIDQ-KTD 257
                                        ********5..6..............222333...46***************************99.44433.359 PP

                                        HHHHHHHHHH-GGGHHHHHHHHHHHHHHHHHHHHS-HHH.HHHHHHHHHHHHSS--.B--..-HHHHHHHH.-TTS CS
                               Sec1 305 iadlkkfvaklpelqeekkklskHtnlaeellkevkkrkldellelEqdlatgesdkkikekkvieeliad.dept 379
                                        i++++k+v + pe  ++k+++   +nlae+ l+ ++k++l+ ++ +Eq++ tg+++k + +++ i+++ +  ++++
  gene2104|gene2104|rna2104|rna2104 258 INEIHKLVLEAPENIKLKESVNRYINLAEDTLNLFEKEQLNYIATFEQNISTGYDNKGSRYQNGIKDVFSVlNQKI 333
                                        ****************************************************664567777788888888876666 PP

                                        -H.HHHHHHHHHHHH...-B.-HT--GG....GGHHHHGGGGG........---.BGGG-------.......--- CS
                               Sec1 380 seledklRLlllyslvegglkekelkellrelvqsalygleylktlrsleklgllkkrkgkksskkksslklikee 455
                                        +  e+klRL+ll+  ++ +++++e+++l+ +l+  + + l   k+++   kl++++k+ +            +++e
  gene2104|gene2104|rna2104|rna2104 334 KR-ENKLRLVLLLLSTHYDFQANEVSKLKDKLML-TDQEL---KIFE---KLKVMRKNFN------------KRKE 389
                                        66.8************889999999999888877.54455...4445...4445533333............2223 PP

                                        ------S...TT-----HHHHHHHHHTTT-S-TTTS-BSS-GGGS--------------------------S-EEE CS
                               Sec1 456 edeesnydlsgvsryaPllvrlvealikgkklssespslskkdpsqeesssslrsakktnsaskesaekkkkqrvi 531
                                         ++  +y   ++sry Pll++l+ a ++ +k++  s+ ++ +  +      +++s +k++   +  ++k   ++++
  gene2104|gene2104|rna2104|rna2104 390 YNSKFTY---EISRYDPLLHDLLRAFVQ-NKNNRFSNLVKRETTE------KKESLRKSSFVFMRHETK---KKTL 452
                                        3333333...6899**************.7777777666655532......233444444444444444...77** PP

                                        EEEEEEE-HHHHHHHHHHT...TSSSEEEEEEEEE--HHHHHH CS
                               Sec1 532 VffvGGvTysEiralrllskqekknkeiiigttsilnpksfle 574
                                        V  +   Ty E+  ++++s+++  ++e++++t+++++pk++l+
  gene2104|gene2104|rna2104|rna2104 453 VLYIDVLTYPEMMLINQMSEKS--SYEVFVCTNQVVTPKEYLK 493
                                        ***************9999865..9***************985 PP

>> RSS_P20  Suppressor of RNA silencing P21-like N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.54   3.2e+03      43      66 ..      71      95 ..      37     111 .. 0.74
   2 ?   -2.7   0.0       1.4   8.3e+03      44      71 ..     154     181 ..     127     186 .. 0.53
   3 ?   13.3   2.1   1.4e-05     0.085       4      84 ..     228     308 ..     227     312 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.54
                            RSS_P20 43 Fvellk.lsdslKsdindsvkeked 66
                                       Fv+ +k +  ++K d++++  +k++
  gene2104|gene2104|rna2104|rna2104 71 FVTYCKeTYRAIKKDVKNKIYTKYY 95
                                       5555542457888888888777766 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.4
                            RSS_P20  44 vellklsdslKsdindsvkekedskksl 71 
                                        v+l ++ ++  +   ++ ++++ s++++
  gene2104|gene2104|rna2104|rna2104 154 VNLRADTALFEQLRTNDSMCESRSEYYN 181
                                        4445555555555556666666666665 PP

  == domain 3  score: 13.3 bits;  conditional E-value: 1.4e-05
                            RSS_P20   4 yfsveeyinli.sevtkllrrvfedsiglekgnlidsieeFvellklsdslKsdindsvkekedskkslKrrilkn 78 
                                        y+ + ++++ + +++ kl++ +++ +++++ +++ + + e  e++kl++s + +in + ++   ++k+  ++ +++
  gene2104|gene2104|rna2104|rna2104 228 YLHIADTNSVLnNKAQKLVEGMKKIDQKTDINEIHKLVLEAPENIKLKESVNRYINLAEDTLNLFEKE-QLNYIAT 302
                                        66777777765156999***************************************************.9****** PP

                            RSS_P20  79 ieenir 84 
                                        +e+ni+
  gene2104|gene2104|rna2104|rna2104 303 FEQNIS 308
                                        ****97 PP

>> DUF3365  Protein of unknown function (DUF3365)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0     0.023   1.4e+02      12      92 ..      27     107 ..      24     136 .. 0.68
   2 ?    5.5   0.5    0.0034        20      51     101 ..     252     309 ..     223     341 .. 0.70
   3 ?    0.3   0.1      0.13   7.8e+02      21      52 ..     362     420 ..     339     497 .. 0.48

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.023
                                        XXXXXXXXX--HHHHHHHHHHHHHHHHHHHHHHTTS-S...--GGGGS--SHHHHHHHHT-EEEEE-SS-SSGGGS CS
                            DUF3365  12 lslrsqkrqaeeealekarllaeqleavreyvakslkp.tivpayaareiaeefsekrkgysyketslnprnprnk 86 
                                        ++++++++ + +++ +k ++l +++ ++++ ++ + +p ++++ y+++   e ++  +k+++ k+++  ++   n+
  gene2104|gene2104|rna2104|rna2104  27 FVYNKSTARILTHIFTKTQILSNEILSMQR-LELNRDPiAYPAIYFVTYCKETYRAIKKDVKNKIYTKYYIIHTNE 101
                                        566777888999999999999999999988.444444433355566665555555555666667777666666666 PP

                                        --SHHH CS
                            DUF3365  87 pdefEk 92 
                                         +e Ek
  gene2104|gene2104|rna2104|rna2104 102 IKENEK 107
                                        666665 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0034
                                        .--GGGGS--SHHHHHHHHT-EEEEE-SS-SSGG.GS--SHHHHHHHHHEE....... CS
                            DUF3365  51 ivpayaareiaeefsekrkgysyketslnprnpr.nkpdefEkealeefkk......e 101
                                        i +++ ++ei++ + e  +++++ke  ++++n + ++ + fEke l+++++       
  gene2104|gene2104|rna2104|rna2104 252 IDQKTDINEIHKLVLEAPENIKLKESVNRYINLAeDTLNLFEKEQLNYIATfeqnisT 309
                                        45567778888888888889**************555599********9444433430 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.13
                                        --HHHHHHHHHHHHHHHHHHHHHHTTS-..S...........................- CS
                            DUF3365  21 aeeealekarllaeqleavreyvakslk..p....ti.....................v 52 
                                         +  ++++   ++e+l+ +r+ ++k+ +  +     i                     +
  gene2104|gene2104|rna2104|rna2104 362 DKLMLTDQELKIFEKLKVMRKNFNKRKEynSkftyEIsrydpllhdllrafvqnknnrF 420
                                        44555666666777777777766655553212222002223333333333333333331 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (500 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1375  (0.0766914); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.44
# Mc/sec: 3409.02
//
Query:       gene2105|gene2105|rna2105|rna2105  [L=93]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1361  (0.0759105); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        78  (0.00435049); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 631.81
//
Query:       gene2106|gene2106|rna2106|rna2106  [L=600]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (600 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       772  (0.0430587); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.59u 0.25s 00:00:00.84 Elapsed: 00:00:00.43
# Mc/sec: 4215.66
//
Query:       gene2107|gene2107|rna2107|rna2107  [L=216]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (216 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       659  (0.0367561); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1637.73
//
Query:       gene2108|gene2108|rna2108|rna2108  [L=200]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.7e-46  156.1   0.2    6.7e-46  155.8   0.2    1.0  1  Ras          Ras family
    8.2e-24   84.1   0.1    1.2e-23   83.6   0.1    1.2  1  Roc          Ras of Complex, Roc, domain of DAPkinase
    2.8e-11   43.2   0.1    3.5e-11   42.9   0.1    1.1  1  Arf          ADP-ribosylation factor family
    4.2e-05   23.2   0.1    0.00032   20.3   0.1    2.0  1  GTP_EFTU     Elongation factor Tu GTP binding domain
    0.00018   20.9   0.0    0.00025   20.5   0.0    1.2  1  Gtr1_RagA    Gtr1/RagA G protein conserved region
     0.0016   17.9   0.0     0.0024   17.4   0.0    1.2  1  SRPRB        Signal recognition particle receptor beta subuni
     0.0037   17.3   0.0     0.0054   16.8   0.0    1.3  1  MMR_HSR1     50S ribosome-binding GTPase
     0.0052   16.5   1.1      0.045   13.5   1.1    2.1  1  PduV-EutP    Ethanolamine utilisation - propanediol utilisati
     0.0054   16.7   0.6       0.18   11.7   0.0    2.6  3  RsgA_GTPase  RsgA GTPase


Domain annotation for each model (and alignments):
>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  155.8   0.2   3.4e-49   6.7e-46       1     161 [.      11     174 ..      11     175 .. 0.97

  Alignments for each domain:
  == domain 1  score: 155.8 bits;  conditional E-value: 3.4e-49
                                        EEEEEESTTSSHHHHHHHHHHSSCSSSCTTTSSEEEEEEEEEETTEEEEEEEEEETTSGGGHHHHHHHHTTESEEE CS
                                Ras   1 KlvlvGdsavGKtslllrfvkdkFkeeyesTigvdfytkeievdgkevkleiwDTAGqeefkslrelyyrdaegil 76 
                                        K+ ++G+++ GKts+llr ++d+F+++ e+Ti +++++ +i v++  ++l+iwDTAGqe+f+s+ +l y+++e ++
  gene2108|gene2108|rna2108|rna2108  11 KVTMIGSGQAGKTSILLRLIDDTFNKDCEPTI-FENKMITIVVEQVPISLHIWDTAGQEDFNSIIPLTYESTEIAI 85 
                                        899*****************************.******************************************* PP

                                        EEEETTBHHHHHTHH.HHHHHHHHHSTTTSEEEEEEETTTGGG...G-SS-HHHHHHHHHHHT.SEEEEEBTTTTC CS
                                Ras  77 lvyditsresfenvk.kwveeikrvaeenvpivLvGnKvDlee...kravsteegeelakelg.lkfletSAktne 147
                                        ++y+++++ s+e v+ kw +e++ + e nv+ivLv++K+Dl++     +++te+g++lak+++ ++f+e+SAk++ 
  gene2108|gene2108|rna2108|rna2108  86 ICYSVDDAYSYEAVTeKWENEVRYYSE-NVEIVLVATKIDLRNdgkASCLETEDGRRLAKQINaIAFFECSAKDSI 160
                                        **************9899999998888.7*************9888899**************9************ PP

                                        THHHHHHHHHHHHH CS
                                Ras 148 nveeafeellreil 161
                                        ++ e+f+ ++++i+
  gene2108|gene2108|rna2108|rna2108 161 GIPEIFNFVAKHIY 174
                                        ********999886 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.6   0.1   6.1e-27   1.2e-23       1     120 []      11     125 ..      11     125 .. 0.84

  Alignments for each domain:
  == domain 1  score: 83.6 bits;  conditional E-value: 6.1e-27
                                        EEEEESSTTSSHHHHHHCHCT-CCC-EEETTTTEEEEEEECGGSGGCTTBTTTTCEEEEEEEE-SGGCTTTT-HHH CS
                                Roc   1 KvvlvGdsgvGKtsllkrfvedkfsekekstigvdfltkevtkikgvendkkvkkvklniWDtaGqerfrslhply 76 
                                        Kv ++G +++GKts+l r+++d+f+++ ++ti  + + + v  ++      +   ++l+iWDtaGqe+f+s+ pl 
  gene2108|gene2108|rna2108|rna2108  11 KVTMIGSGQAGKTSILLRLIDDTFNKDCEPTIFENKMITIV--VE------Q-VPISLHIWDTAGQEDFNSIIPLT 77 
                                        89*****************************9655443322..22......2.3599******************* PP

                                        HCTSCEEEEEEE...GHHHHCH.HHHHHHHHHHCSSS-EEEEEE-TTT CS
                                Roc  77 lreaalailvyd...srssenl.keWlkelkkvagkspvilvgnkiDl 120
                                        +++ ++ai++y    + s+e + ++W +e++ ++++  ++lv++kiDl
  gene2108|gene2108|rna2108|rna2108  78 YESTEIAIICYSvddAYSYEAVtEKWENEVRYYSENVEIVLVATKIDL 125
                                        *********9974333355554389*********************95 PP

>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.9   0.1   1.7e-14   3.5e-11      12     174 ..       7     172 ..       1     173 [. 0.82

  Alignments for each domain:
  == domain 1  score: 42.9 bits;  conditional E-value: 1.7e-14
                                        TTEEEEEEEESTTSSHHHHHHHHHHSSCEE.CSSSSSEE.EEEEEE..TTEEEEEEEE-SSGGGGGGGGGGCTTES CS
                                Arf  12 kkelrilllGLDnaGKtTilkklkleelvt.tvPTigfn.veelei..knlkftvwDvGGqeklRplWknYfektd 83 
                                        +   ++ ++G  +aGKt il +l ++ +++   PTi  n + ++ +    +++++wD  Gqe   ++    +e+t+
  gene2108|gene2108|rna2108|rna2108   7 QIVSKVTMIGSGQAGKTSILLRLIDDTFNKdCEPTIFENkMITIVVeqVPISLHIWDTAGQEDFNSIIPLTYESTE 82 
                                        4457999********************987689**966623344442256899********************999 PP

                                        EEEEEEETT-CTTHHHHHHHHHHHCTSGCCTTSEEEEEEE-TTSTTSS-HHHHHHHTTGGGSSSSSSEEEEEEBTT CS
                                Arf  84 avifvvDsadreRleeakeeLkalleeeelkevallvlaNKqDlpealseeelrellgleelkgkrkleiqkcsav 159
                                          i +  + d    e   e+ ++ ++    ++v ++++a K+Dl+++ +++ l+++ g +  k+ + +  ++csa 
  gene2108|gene2108|rna2108|rna2108  83 IAIICYSVDDAYSYEAVTEKWENEVRY-YSENVEIVLVATKIDLRNDGKASCLETEDGRRLAKQINAIAFFECSAK 157
                                        888777777777777777777666554.567999****************99999999988888899********* PP

                                        TTBTHHHHHHHHHHH CS
                                Arf 160 kgeglkeglewlses 174
                                           g+ e ++ ++++
  gene2108|gene2108|rna2108|rna2108 158 DSIGIPEIFNFVAKH 172
                                        ******999988765 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.1   1.6e-07   0.00032      70     192 ..      57     173 ..       7     175 .. 0.75

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 1.6e-07
                                        EEEEEEEESSSGGGHHHHHHHHHT-SEEEEEEETTTB..STHHHHHHHHHHH..HTTTEEEEEEESCGSTHHHHHH CS
                           GTP_EFTU  70 ylinliDtPGHvdFskevirglrvlDgavlvvdaveG..vepqteevlrlal..kegvpiivfiNKmDrlkaelke 141
                                          +++ Dt G +dF++ +  +++ +++a++  ++++    e+ te+  + ++  +e+v+i+++ +K+D  ++    
  gene2108|gene2108|rna2108|rna2108  57 ISLHIWDTAGQEDFNSIIPLTYESTEIAIICYSVDDAysYEAVTEKWENEVRyySENVEIVLVATKIDLRNDGKAS 132
                                        458899*************************9999766655555555554441147899*********99555555 PP

                                        HHHHHH.HHHHHHHHHHHHHHHTTTTTEEEEEEBTTTTBTHHHHHHHHHHHS CS
                           GTP_EFTU 142 iveevk.qklsrkeeklekygekgekevpvvfgSalkgegvktllealvell 192
                                        + e+   ++l        k   +  + + ++ +Sa++  g+ ++++ + +++
  gene2108|gene2108|rna2108|rna2108 133 CLETEDgRRL-------AK---QI-NAIAFFECSAKDSIGIPEIFNFVAKHI 173
                                        5554440444.......22...22.3688999*******9999999999987 PP

>> Gtr1_RagA  Gtr1/RagA G protein conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   1.2e-07   0.00025       1     148 [.      11     150 ..      11     175 .. 0.74

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 1.2e-07
                          Gtr1_RagA   1 kvLLmGksgsGKtsmrsiiFdnylardtlrlgatidveksevrflgnltlnlwDcgGqeafveeylssqkeeifrn 76 
                                        kv ++G +++GKts+   + d +  +d+       ++    v     + l++wD  Gqe+f          +  ++
  gene2108|gene2108|rna2108|rna2108  11 KVTMIGSGQAGKTSILLRLIDDTFNKDCEPTIFENKMITIVV-EQVPISLHIWDTAGQEDFNSII---PLTYESTE 82 
                                        7889********************999865433333333333.234689***********98774...44445568 PP

                          Gtr1_RagA  77 vgvliyVfDvesreleedletlkeilealrqyspeakvfvlihKmDliqedereeifeerkeeireeiekle 148
                                        ++++ y +D    ++e   e++++   ++r ys+++++     K+Dl ++ + + + +e+ +++ ++i+ + 
  gene2108|gene2108|rna2108|rna2108  83 IAIICYSVDDA-YSYEAVTEKWEN---EVRYYSENVEIVLVATKIDLRNDGKASCLETEDGRRLAKQINAIA 150
                                        89999999877.567666666665...567789999999999999998877777777777777777777644 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   1.2e-06    0.0024       5      95 ..      11     102 ..       7     126 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.2e-06
                                        EEEEE-STTSSHHHHHHHHHHSS---B-.--S.S-EEETTG...GGTT-SEEEETT-GCCSHHHHHHHHHHGGEEE CS
                              SRPRB   5 avllvGlsdsGKTslftrLttdsvkktv.tSq.essaalkvksekgskltliDfPGheklrqklleklkaksslkg 78 
                                        +v ++G  ++GKTs++ rL  d+++k     + e+++ + v ++   +l++ D  G+e + + +  +  +++++  
  gene2108|gene2108|rna2108|rna2108  11 KVTMIGSGQAGKTSILLRLIDDTFNKDCePTIfENKMITIVVEQVPISLHIWDTAGQEDFNSIIPLT-YESTEIAI 85 
                                        6889******************987765145579999998889999**************9877665.78888999 PP

                                        EEEEEETTS-HHHHHHH CS
                              SRPRB  79 lvfvvDStidpkevkev 95 
                                        + + vD +     v+e 
  gene2108|gene2108|rna2108|rna2108  86 ICYSVDDAYSYEAVTEK 102
                                        9*****99888888775 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   2.7e-06    0.0054       2     114 .]      12     122 ..      11     146 .. 0.65

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 2.7e-06
                                        EEEEESTTSSHHHHHHHHHTS..TEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSSHHHHHHHHHHHHHHHHC CS
                           MMR_HSR1   2 vaivGrpNvGKStLinaltge..kaivsdkpgtTrdinegrvklkgkeielvDtpGliegaseekglgkaflalee 75 
                                        v  +G   +GK++++ +l+++  +   + + +  + i+   v+    +++++Dt+G  e  + +  +  ++++  e
  gene2108|gene2108|rna2108|rna2108  12 VTMIGSGQAGKTSILLRLIDDtfNKDCEPTIFENKMITIV-VEQVPISLHIWDTAG-QE--DFNSIIPLTYES-TE 82 
                                        7899***************973333333333333333333.33223679*******.44..344467777775.66 PP

                                        TSEEEEEEETTTTCSHHHHHHHHHHHHH..TTSEEEEEEES CS
                           MMR_HSR1  76 adlillvvdaseeklkpldeeleellee..akkplilvlnk 114
                                          +i++ vd +  +++++ e+ e+  +   ++ +++lv++k
  gene2108|gene2108|rna2108|rna2108  83 IAIICYSVDDA-YSYEAVTEKWENEVRYysENVEIVLVATK 122
                                        78899999844.33444433333333224445556666655 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   1.1   2.3e-05     0.045       2     141 ..      10     169 ..       9     171 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.3e-05
                          PduV-EutP   2 kkilliGkvgsGKttLtqalkg.............eelkYkktqaiefsdeviDtPGeylenrklysalivtsaea 64 
                                        +k+ +iG+ ++GKt++  +l +             ++++     ++ +s ++ Dt G+  e  +    l+  s+e 
  gene2108|gene2108|rna2108|rna2108  10 SKVTMIGSGQAGKTSILLRLIDdtfnkdceptifeNKMITIVVEQVPISLHIWDTAGQ--EDFNSIIPLTYESTEI 83 
                                        68999*********98888877688888865555544554555556666777899997..4444455666666666 PP

                          PduV-EutP  65 dvialvqdateeesvfppgfasvf.....nkeviGiitkidlaedee....nieaveelLksaGaekifevsavek 131
                                         +i   +d   +++  ++++ + +     n e++ + tkidl +d +    + e  ++l k+  a   fe sa ++
  gene2108|gene2108|rna2108|rna2108  84 AIICYSVDDAYSYEAVTEKWENEVryyseNVEIVLVATKIDLRNDGKasclETEDGRRLAKQINAIAFFECSAKDS 159
                                        6666555555555566666655442222246889999*****97754222234455667788888889******** PP

                          PduV-EutP 132 egieellkyl 141
                                        +gi e+++++
  gene2108|gene2108|rna2108|rna2108 160 IGIPEIFNFV 169
                                        ******9987 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.2     0.066   1.3e+02      94     122 ..       5      32 ..       1      71 [. 0.80
   2 ?    0.9   0.0      0.18   3.7e+02      53     101 ..      59     107 ..      33     109 .. 0.70
   3 !   11.7   0.0   9.1e-05      0.18      40     101 ..     107     173 ..      80     175 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.066
                                        HHHCTTSEEEEECSTTSSHHHHHHHHCTT CS
                        RsgA_GTPase  94 kellkdktsvlvGqSGvGKStLinallpe 122
                                        k+++ +k+ +++G+  +GK++++ +l+ +
  gene2108|gene2108|rna2108|rna2108   5 KKQIVSKV-TMIGSGQAGKTSILLRLIDD 32 
                                        44444444.57899999****99888765 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.18
                                        EE-GGG--HHHHHHHHHHHHHHTTSEEEE--TTTHTTHHHHHHHCTTSE CS
                        RsgA_GTPase  53 lnKiDlleeeeeleelkeelealgyevllvsaktkegleelkellkdkt 101
                                        l   D + +e+  + +  ++e++++++++ s+++  ++e+++e++++++
  gene2108|gene2108|rna2108|rna2108  59 LHIWDTAGQEDFNSIIPLTYESTEIAIICYSVDDAYSYEAVTEKWENEV 107
                                        3445666666644555678999999999999999999999999988865 PP

  == domain 3  score: 11.7 bits;  conditional E-value: 9.1e-05
                                        HHHHHTT-EEEEEEE-GGG--HHH....HHHHHHHHHHHTT.SEEEE--TTTHTTHHHHHHHCTTSE CS
                        RsgA_GTPase  40 vlaeekgiepvivlnKiDlleeee....eleelkeelealg.yevllvsaktkegleelkellkdkt 101
                                        v + ++++e+v+v +KiDl ++ +    e+e+ +   ++++ ++++ +sak++ g+ e+ + +++++
  gene2108|gene2108|rna2108|rna2108 107 VRYYSENVEIVLVATKIDLRNDGKasclETEDGRRLAKQINaIAFFECSAKDSIGIPEIFNFVAKHI 173
                                        567899****************9999887777777777777457889********999999888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       622  (0.0346924); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.45u 0.30s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 1401.57
//
Query:       gene2109|gene2109|rna2109|rna2109  [L=48]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (48 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       451  (0.0251548); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.33u 0.23s 00:00:00.56 Elapsed: 00:00:00.38
# Mc/sec: 383.66
//
Query:       gene211|gene211|rna211|rna211  [L=104]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       371  (0.0206927); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 788.88
//
Query:       gene2110|gene2110|rna2110|rna2110  [L=43]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (43 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       249  (0.0138881); expected 358.6 (0.02)
Passed bias filter:                      175  (0.00976072); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.25s 00:00:00.59 Elapsed: 00:00:00.41
# Mc/sec: 316.50
//
Query:       gene2111|gene2111|rna2111|rna2111  [L=898]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.4e-99  333.8   0.0    3.1e-52  177.7   0.0    2.2  2  DUF3591      Protein of unknown function (DUF3591)
    5.5e-20   71.2   0.0    1.5e-19   69.8   0.0    1.7  1  Bromodomain  Bromodomain
    5.7e-05   22.9   3.4    0.00012   21.8   3.4    1.5  1  zf-CCHC_6    Zinc knuckle


Domain annotation for each model (and alignments):
>> DUF3591  Protein of unknown function (DUF3591)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  153.8   0.0   9.3e-49   5.6e-45       1     183 [.     211     387 ..     211     395 .. 0.93
   2 !  177.7   0.0   5.3e-56   3.1e-52     189     389 ..     460     647 ..     453     685 .. 0.91

  Alignments for each domain:
  == domain 1  score: 153.8 bits;  conditional E-value: 9.3e-49
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........xxxxx RF
                            DUF3591   1 fnlsnDkaYealkenkqskvrstlgnlkveHSlpAlkLqlpfyktklskkelrsfHrprlkvk........kkakg 68 
                                        +n+snD++Ye+l      +v+s+lgnl ++HSlpAl+L + ++kt l+k+elr+fHrp+l++          ++  
  gene2111|gene2111|rna2111|rna2111 211 YNISNDRYYETL------SVKSNLGNLGMQHSLPALRLDMGLFKTFLTKEELRNFHRPALSLLeraekaifSRTLP 280
                                        8**********9......6899**************************************9988999998856778 PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DUF3591  69 keekellkktkDLslkdtskvvllEYseeyPpllsnvGMgsklinYYrkkkekDtsrpklelGetvvlepedksPF 144
                                        k++++++k+++ L+l+d++++ l+EYsee P+l++n GM s l++YY+ + +    +pk+ lG+++vle+e+ sPF
  gene2111|gene2111|rna2111|rna2111 281 KSSQQSIKSPSQLTLTDSASFALFEYSEEIPLLVQNRGMVSLLTTYYKNNGN----TPKKYLGKLTVLESEEPSPF 352
                                        89999******************************************86544....467789************** PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DUF3591 145 lnlGevepgetvqtlennliraPifkhkvkstDFLlirs 183
                                          + +++pg+++++l+nnl++a +fkh    tD+L+i +
  gene2111|gene2111|rna2111|rna2111 353 --IVDIKPGTCLTALTNNLFKACVFKHA--VTDYLMIVT 387
                                        ..9************************6..59***9976 PP

  == domain 2  score: 177.7 bits;  conditional E-value: 5.3e-56
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DUF3591 189 kkyylreidnlfvvGqtlPlveVpgphsrkvtnfsknrLkviiyrllrkskekrikvedikkafpdqselqiRkrL 264
                                         ky+lr+i++ f+vGqt+P+ eV +phsrk + f+knrLkv ++r ++++    ++++ i+  fp+ se + Rk L
  gene2111|gene2111|rna2111|rna2111 460 LKYFLRKINAAFTVGQTFPVEEVYSPHSRKLNIFCKNRLKVAAFREYQNNGL--LSASYIEDLFPQFSEGSKRKWL 533
                                        59********************************************998877..********************** PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DUF3591 265 kefaeyqrkgedsgvWklkeeerlpseeeirklvtPEdvcllesmqvgeqrlkdagyakeeeeeeedekkeeskle 340
                                        ke+ +  ++g+ + + +lk++ ++ +ee++r lvtPE+vc++e+m+++eqrl+d g++ +e+  ee          
  gene2111|gene2111|rna2111|rna2111 534 KEYSDSFKRGK-ETFYQLKKSATVLNEEDLRGLVTPENVCQYEAMLCAEQRLRDCGLEYKENVMEE---------- 598
                                        ****9888898.7899*****************************************998777755.......... PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DUF3591 341 leeqlapWnttknFlaAtqgkamlqlhGegDPtGrgegfsfvrtsmKeg 389
                                         e+ l pWn+++nF++ + g+ +l+++G gDPtG+gegfsfv+ + K+ 
  gene2111|gene2111|rna2111|rna2111 599 GELLLMPWNLSRNFINYVGGRGILEMKGPGDPTGIGEGFSFVKGNVKAA 647
                                        699****************************************999983 PP

>> Bromodomain  Bromodomain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.8   0.0   2.5e-23   1.5e-19      14      82 ..     797     865 ..     783     867 .. 0.94

  Alignments for each domain:
  == domain 1  score: 69.8 bits;  conditional E-value: 2.5e-23
                                        GGGGCSTT-GCCSTTHHHH.SS---HHHHHHHHHTT--SSHHHHHHHHHHHHHHHHHHSHTTSHHHHHH CS
                        Bromodomain  14 aepFlepvdpeefpdyyavikkPldLstIkkklesnkYksladfeadlkllfsNarkyngegsviyela 82 
                                        a++Fl+pv+ ++fpdy +v++ P+dL t+k+k +++kY ++ +f  dl+ +++N++ yng+++ + +la
  gene2111|gene2111|rna2111|rna2111 797 ASAFLRPVSAKKFPDYLKVVTDPIDLGTMKSKSKNHKYANFGEFVSDLRKMWQNCVAYNGVDHGLSKLA 865
                                        899**********************************************************99887777 PP

>> zf-CCHC_6  Zinc knuckle
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   3.4   2.1e-08   0.00012       2      24 ..     742     764 ..     741     776 .. 0.87

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 2.1e-08
                          zf-CCHC_6   2 vKCknCGAFGHtarSkrCPmkcw 24 
                                        ++C++CG  GH+ ++k CP  c+
  gene2111|gene2111|rna2111|rna2111 742 LRCGACGLVGHMKTNKSCPNFCA 764
                                        69*****************9885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (898 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       576  (0.0321267); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.66u 0.29s 00:00:00.95 Elapsed: 00:00:00.45
# Mc/sec: 5935.40
//
Query:       gene2112|gene2112|rna2112|rna2112  [L=526]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.3e-07   29.3   0.0    1.5e-06   28.4   0.0    1.5  1  XPG_I     XPG I-region


Domain annotation for each model (and alignments):
>> XPG_I  XPG I-region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4   0.0   8.4e-11   1.5e-06       4      94 .]     169     254 ..     166     254 .. 0.89

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 8.4e-11
                                        T--EEE-SS-HHHHHHHHHHTTSSSEEE-SSSHHHHTT.-SEEEESTT.ECECTT..EEECEEEEEEHHHHHHHHT CS
                              XPG_I   4 gipyvvApgEAEAqcayLqkkglvdaviseDsDlllFG.apkvlrnlskkkskkkkekekkkvevidlekvlkelg 78 
                                        +i ++ Ap+ A  qcay  ++++vd+v    +D ll+G ++kv+++++  +  k    ++  +e++  +++lk+l+
  gene2112|gene2112|rna2112|rna2112 169 RICCIRAPYSALGQCAYFLRNNVVDYVFGA-TDFLLYGnGEKVITEFN--FLCKD---REDRIEIFCRKDILKTLK 238
                                        6889***********************987.9*****94569****98..54333...5778************** PP

                                        --HHHHHHHHHHHCET CS
                              XPG_I  79 ltreqlidlaillgcD 94 
                                        l  ++++ +a++lgc+
  gene2112|gene2112|rna2112|rna2112 239 LPFSKFQMYALFLGCE 254
                                        **************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (526 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       498  (0.0277762); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 3401.09
//
Query:       gene2113|gene2113|rna2113|rna2113  [L=308]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.1e-05   25.3   1.9       0.18   11.8   0.0    3.4  3  HAT         HAT (Half-A-TPR) repeat
    0.00041   20.4   0.2      0.001   19.2   0.2    1.7  1  Suf         Suppressor of forked protein (Suf)
    0.00096   18.4   1.2        0.3   10.2   0.6    2.3  2  NRDE-2      NRDE-2, necessary for RNA interference
     0.0072   16.6   1.6       0.29   11.6   0.3    3.1  3  TPR_17      Tetratricopeptide repeat
  ------ inclusion threshold ------
      0.016   15.4   2.0       0.58   10.3   0.1    2.3  2  Coagulase   Staphylococcus aureus coagulase
       0.09   12.8   0.0       0.27   11.3   0.0    1.9  1  CaM_bdg_C0  Calmodulin-binding domain C0 of NMDA receptor NR1
        0.1   13.5   0.0         39    5.4   0.0    3.3  2  TPR_14      Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> HAT  HAT (Half-A-TPR) repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.77     2e+03      25      31 ..      31      37 ..      15      38 .. 0.87
   2 !   10.9   0.5   0.00014      0.35       2      30 ..      41      70 ..      40      72 .. 0.91
   3 !   11.8   0.0   7.2e-05      0.18       3      31 ..      76     105 ..      74     106 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.77
                                       HHHHHHH CS
                                HAT 25 kyArFEE 31
                                        yA FEE
  gene2113|gene2113|rna2113|rna2113 31 EYALFEE 37
                                       5999**9 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00014
                                       -HHHHHHHHHHHH.HHS--HHHHHHHHHHH CS
                                HAT  2 EidRAReiYeRFv.vVHpeVkNWikyArFE 30
                                       E +R R iYe  v + H + + W  yA FE
  gene2113|gene2113|rna2113|rna2113 41 EYNRSRTIYENAVaHNHSNTNLWKNYACFE 70
                                       889*******9886899**999*******9 PP

  == domain 3  score: 11.8 bits;  conditional E-value: 7.2e-05
                                        HHHHHHHHHHHHHHS.--HHHHHHHHHHHH CS
                                HAT   3 idRAReiYeRFvvVH.peVkNWikyArFEE 31 
                                        i+R R+i eR v     e+  W+ +A  EE
  gene2113|gene2113|rna2113|rna2113  76 INRCRSILERAVQMNpREISLWLFFAELEE 105
                                        99*************77************9 PP

>> Suf  Suppressor of forked protein (Suf)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.2   3.9e-07     0.001      63     146 ..      19      99 ..      12     128 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 3.9e-07
                                Suf  63 lKkFpedeefvlkYldyLislnddnnaRvlfekvvsklskekeakelykkfleyestfgdlssilklekRmeelfp 138
                                        +K+ p++ +   +Y  +   ln+ n+ R+++e++v++  +++   +l+k ++ +e ++ d++   ++ +R  ++ p
  gene2113|gene2113|rna2113|rna2113  19 IKTHPHNTAIHTEYALFEELLNEYNRSRTIYENAVAHNHSNT---NLWKNYACFELRQCDINRCRSILERAVQMNP 91 
                                        688999999999************************999988...9********************9999999988 PP

                                Suf 139 edskleqf 146
                                         + +l +f
  gene2113|gene2113|rna2113|rna2113  92 REISLWLF 99 
                                        87776665 PP

>> NRDE-2  NRDE-2, necessary for RNA interference
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.6   0.00012       0.3      47     132 ..       4      87 ..       1      88 [. 0.77
   2 !    9.1   0.0   0.00024      0.62       6      32 ..      83     109 ..      78     127 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00012
                             NRDE-2  47 aeiklsilekAlekn.ksnpdserLllelLklgseiwdseklakeWeellkenpnsvkLWreyldfrqsnfasfsv 121
                                        + +k++++++  +++ k++p+++ +  e+    + + + ++ ++ +e+++ +n ++++LW++y  f+++   +  +
  gene2113|gene2113|rna2113|rna2113   4 YAKKIQLIRNHYNHKiKTHPHNTAIHTEYALFEELLNEYNRSRTIYENAVAHNHSNTNLWKNYACFELR---QCDI 76 
                                        66777777777666514458888888888766666778888889999********************99...6678 PP

                             NRDE-2 122 ekvkelyekcl 132
                                        +++++++e+++
  gene2113|gene2113|rna2113|rna2113  77 NRCRSILERAV 87 
                                        88888887765 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00024
                             NRDE-2   6 lnraveenPedidaWlelvefQdells 32 
                                        l+rav+ nP++i++Wl ++e+ +++++
  gene2113|gene2113|rna2113|rna2113  83 LERAVQMNPREISLWLFFAELEEDMMN 109
                                        89********************98885 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.1     0.081   2.1e+02       3      32 ..      16      45 ..      14      47 .. 0.85
   2 !   11.6   0.3   0.00011      0.29       1      25 [.      48      72 ..      48      81 .. 0.88
   3 ?   -3.2   0.0       5.9   1.5e+04       2      11 ..      83      92 ..      82      97 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.081
                             TPR_17  3 lkaleldPnnadaynnLAelllknGdlmtA 32
                                          ++ +P n   ++++A + + ++++ + 
  gene2113|gene2113|rna2113|rna2113 16 NHKIKTHPHNTAIHTEYALFEELLNEYNRS 45
                                       5558999**************999999876 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00011
                             TPR_17  1 lylkaleldPnnadaynnLAelllk 25
                                       +y++a++++++n +++ n+A + l+
  gene2113|gene2113|rna2113|rna2113 48 IYENAVAHNHSNTNLWKNYACFELR 72
                                       5*******************99875 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 5.9
                             TPR_17  2 ylkaleldPn 11
                                       +++a++ +P 
  gene2113|gene2113|rna2113|rna2113 83 LERAVQMNPR 92
                                       6899999995 PP

>> Coagulase  Staphylococcus aureus coagulase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.3     0.012        31      69     133 ..      32      93 ..       5     109 .. 0.79
   2 ?   10.3   0.1   0.00023      0.58      18      69 ..     183     238 ..     170     258 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.012
                                        HHHHHHHHHHHHHHHHHHHHHHTT-S-TTS----TTT-------HHHHHHHHHHHHHHHHHHHHH CS
                          Coagulase  69 qyllekkkeeyekykklykkykkenpnsklkmkkfdkynledltmkeynelskslkdaveefkke 133
                                          l+e   +ey++ + +y+++  +n    ++++ +++y   +l+  + n  ++ l++av+   +e
  gene2113|gene2113|rna2113|rna2113  32 YALFEELLNEYNRSRTIYENAVAHNH---SNTNLWKNYACFELRQCDINRCRSILERAVQMNPRE 93 
                                        44677888999999999999886654...566778888888899999999999999998766555 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00023
                                        ----HHHHHHHHHHHHH..HHHHHHHHHH..-GGG-STTTHHHHHHHHHHHHHHHH CS
                          Coagulase  18 alisdsyywekiksles..qfaealdlle..eykygekeykdakdklmtrilgedq 69 
                                        ++++d+ y +++++le+  ++++a+ +++  +y++g k +kd   k+ t +++ed 
  gene2113|gene2113|rna2113|rna2113 183 ESMDDKTYVKIVDKLEKagRLQDAFIFVKrgKYRFGSKFFKDQYKKMSTGVVDEDD 238
                                        579999**********8445889988876448**********************95 PP

>> CaM_bdg_C0  Calmodulin-binding domain C0 of NMDA receptor NR1 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0    0.0001      0.27      10      22 ..     290     302 ..     282     303 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0001
                         CaM_bdg_C0  10 kqKqlELArhAaD 22 
                                        ++++l+LAr+++D
  gene2113|gene2113|rna2113|rna2113 290 RREKLQLARKTTD 302
                                        6789********9 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0     0.039     1e+02       6      42 ..      31      67 ..      26      69 .. 0.90
   2 ?    5.4   0.0     0.015        39      16      44 .]      75     103 ..      69     103 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.039
                             TPR_14  6 alaeallalGdpdeAiallrralalaPddaeawllla 42
                                       ++a +++ l ++ +++++++ a+a++ ++  +w  +a
  gene2113|gene2113|rna2113|rna2113 31 EYALFEELLNEYNRSRTIYENAVAHNHSNTNLWKNYA 67
                                       78999999*****************999999998886 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.015
                             TPR_14  16 dpdeAiallrralalaPddaeawlllaql 44 
                                        d  + + +l+ra++ +P +  +wl+ a+l
  gene2113|gene2113|rna2113|rna2113  75 DINRCRSILERAVQMNPREISLWLFFAEL 103
                                        55667889***************998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (308 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       793  (0.04423); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.53u 0.24s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 2143.39
//
Query:       gene2114|gene2114|rna2114|rna2114  [L=74]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
     0.0049   16.8   0.8     0.0049   16.8   0.8    1.8  2  HAT         HAT (Half-A-TPR) repeat
  ------ inclusion threshold ------
      0.027   14.9   0.1      0.029   14.8   0.1    1.0  1  RasGEF_N_2  Rapamycin-insensitive companion of mTOR RasGEF_N 


Domain annotation for each model (and alignments):
>> HAT  HAT (Half-A-TPR) repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.8   5.5e-07    0.0049       2      32 .]       7      38 ..       6      38 .. 0.95
   2 ?   -1.6   0.0      0.31   2.8e+03       2       6 ..      41      45 ..      40      49 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 5.5e-07
                                       -HHHHHHHHHHHHHHS.--HHHHHHHHHHHHH CS
                                HAT  2 EidRAReiYeRFvvVH.peVkNWikyArFEEe 32
                                       E  R R iYe+++     + + W+++  FEE+
  gene2114|gene2114|rna2114|rna2114  7 EKQRIRRIYEKYLEDRcMDARVWLQFIEFEES 38
                                       889************99**************7 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.31
                                       -HHHH CS
                                HAT  2 EidRA 6 
                                       E++RA
  gene2114|gene2114|rna2114|rna2114 41 EVERA 45
                                       89999 PP

>> RasGEF_N_2  Rapamycin-insensitive companion of mTOR RasGEF_N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.1   3.3e-06     0.029      13      76 ..       3      66 ..       1      73 [. 0.91

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3.3e-06
                         RasGEF_N_2 13 qLydqsrevvaaaleiLeeacddkeslevlvelkpslqhlgeigslLllkllstssGfkylqel 76
                                       ++ d+++ +++   ++Le+ c d +   +++e+++sl++++ ++ l+   l+  ++G++ ++e+
  gene2114|gene2114|rna2114|rna2114  3 RVLDEKQRIRRIYEKYLEDRCMDARVWLQFIEFEESLDEVERAEYLFRNALMILKNGVEIIEEE 66
                                       5679999*********************************8899999999********999775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (74 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       683  (0.0380947); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.28s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 535.26
//
Query:       gene2115|gene2115|rna2115|rna2115  [L=782]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.8e-19   69.8   2.1      1e-11   45.5   0.4    2.6  2  Hydrolase      haloacid dehalogenase-like hydrolase
    7.8e-07   29.1   0.0    1.8e-06   27.9   0.0    1.5  1  Cation_ATPase  Cation transport ATPase (P-type)
    1.3e-05   24.8   0.7    3.7e-05   23.3   0.7    1.8  1  E1-E2_ATPase   E1-E2 ATPase
  ------ inclusion threshold ------
      0.026   14.2   0.1      0.093   12.4   0.0    1.9  2  Flavodoxin_3   Flavodoxin domain
      0.081   12.4   0.0       0.17   11.3   0.0    1.5  1  Hint           Hint module


Domain annotation for each model (and alignments):
>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.5   0.4   2.8e-15     1e-11       2     160 ..     128     341 ..     127     360 .. 0.64
   2 !   23.1   0.1   2.1e-08   7.5e-05     167     210 .]     465     508 ..     447     508 .. 0.91

  Alignments for each domain:
  == domain 1  score: 45.5 bits;  conditional E-value: 2.8e-15
                                        SEEEEESBTTTBCHHHHHHHHHHHHCHHHHHHHHHH...........HHCHHHHHHHHHHHHHHHHHHHHHHETTT CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          Hydrolase   2 ktvvfDkdGTLttgepsvedvivsaalalaaaletg...........sehpigkalvaaakarsgaltgfatfigr 66 
                                        ++ +fDk+GTLt++e++v+ +++  +   a +l t                 g          + + + f+ ++ +
  gene2115|gene2115|rna2115|rna2115 128 DVACFDKTGTLTESEMVVHSIVAHDEHGVAGILSTChslledeqrrvV----GD---------PLEMSAFTYVNAQ 190
                                        6789****************9999966666666666555555533331....22.........2222233332222 PP

                                        E.........................................HHHHTHHHHHHHH..HCHHHHHHHHHHHHHHCHH CS
                                        x.........................................xxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxx RF
                          Hydrolase  67 g.........................................ayaigkpewltal..dippdlgaaigsaqsqgrt 99 
                                                                                  + ++g pe +++    +p+++++    a +  r 
  gene2115|gene2115|rna2115|rna2115 191 MvdectirtagmqydikkrfyfssalrrmcvvyregkkrvyrVGMKGAPETVRKFlaRVPEQYDEYRRYAAEGYRV 266
                                        2333333333343333333455566666666555566666667777777777777644444444444444444444 PP

                                        HHHH.................TTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHHTTGG CS
                                        xxxx.................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          Hydrolase 100 vall.................qaralavftiadplkvkpeaaeavasLkaagievvlltgdnpetaeraanqlGdd 158
                                         a l                 +++++ v  +  + kvk+e + +v +Lk ag+ vv++tgdn  ta ++a+ lG  
  gene2115|gene2115|rna2115|rna2115 267 LA-LagkhllsftesttresvEKDLVFVGFVLYKSKVKEESRAVVDALKGAGCAVVMITGDNALTAVAVAKCLG-- 339
                                        44.259999999999999999555555555555556**************************************.. PP

                                        GE CS
                                        xx RF
                          Hydrolase 159 yf 160
                                        ++
  gene2115|gene2115|rna2115|rna2115 340 IY 341
                                        33 PP

  == domain 2  score: 23.1 bits;  conditional E-value: 2.1e-08
                                        HCESSTTTSHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHHHTT CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          Hydrolase 167 dietvakpspegkvaaireLqgkpeevamVGDgvnDaaalaaAg 210
                                        d++++a ++p++k+++ir +++k+  ++m GDg nD+ al +A+
  gene2115|gene2115|rna2115|rna2115 465 DVSVFARADPKHKERLIRFYKAKGLVTLMCGDGTNDVGALNEAD 508
                                        46669*************************************98 PP

>> Cation_ATPase  Cation transport ATPase (P-type)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   0.0     5e-10   1.8e-06      13      85 ..     168     243 ..     159     248 .. 0.85

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 5e-10
                      Cation_ATPase  13 ekdevkllGnktEsALlvlaeklgldteelree...tkkvqeipFnssrKrmsvvlklepekkvrlyvKGApeiil 85 
                                        e++++ ++G++ E +   ++++++ d   +r     +++ + + F+s  +rm vv+++ ++ ++r+ +KGApe + 
  gene2115|gene2115|rna2115|rna2115 168 EDEQRRVVGDPLEMSAFTYVNAQMVDECTIRTAgmqYDIKKRFYFSSALRRMCVVYREGKKRVYRVGMKGAPETVR 243
                                        5678899*************99955554444433339999*********************************996 PP

>> E1-E2_ATPase  E1-E2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.7     1e-08   3.7e-05      79     179 ..      12     109 ..       8     111 .. 0.91

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 1e-08
                                        -EEEEEEEE-TTTSTTTTTSTTS--------HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTTSSTTHHHHHHHHH CS
                       E1-E2_ATPase  79 geakavVtatgedtelgkiarlveeakskktplqkkldklgkvlvpvvlliallvflialllgkslaeallralal 154
                                        ++++a V++tg  t+ gk++r + +    ++p   ++  +  +l ++++l +++v+ + + +gks  +++l+++ +
  gene2115|gene2115|rna2115|rna2115  12 KSVIAMVIETGFGTQQGKLIRKMMTN---TPPDNTEAYMFLLFLLIFAVLSSIIVLYQSIKMGKSNYKIMLEIILI 84 
                                        57899*******************98...6666777888889999999******************9********* PP

                                        HHHHS-TTHHHHHHHHHHHHHHHHH CS
                       E1-E2_ATPase 155 lvaaiPcaLplavplalalgarrla 179
                                        l+ ++P+ Lpl +++a+ +++ +l 
  gene2115|gene2115|rna2115|rna2115  85 LTNVVPPELPLELTIAVNAAVHKLL 109
                                        *******************999985 PP

>> Flavodoxin_3  Flavodoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   2.6e-05     0.093      26      76 ..     272     323 ..     261     332 .. 0.83
   2 ?   -2.7   0.0       1.2   4.3e+03      51      72 ..     519     540 ..     503     542 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.6e-05
                       Flavodoxin_3  26 keivsikeakek.veeadvvfvGfwvdkgtadeealkfletlknkkillfgT 76 
                                        k+++s+ e ++    e d+vfvGf  +k++  ee++ ++  lk+   ++++ 
  gene2115|gene2115|rna2115|rna2115 272 KHLLSFTESTTReSVEKDLVFVGFVLYKSKVKEESRAVVDALKGAGCAVVMI 323
                                        67778888877667799**************************987776665 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.2
                       Flavodoxin_3  51 dkgtadeealkfletlknkkil 72 
                                        +k+++++  + +l++l +kk+ 
  gene2115|gene2115|rna2115|rna2115 519 KKAQPESLREALLSELMDKKVN 540
                                        68999999999********996 PP

>> Hint  Hint module
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   4.8e-05      0.17      50     106 ..     240     296 ..     229     324 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 4.8e-05
                                        XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                               Hint  50 sevllfldrdseqraefveietengekltlTpaHLvfvsenekssseeeeavfaskv 106
                                        ++v  fl r +eq+ e+    +e  + l+l  +HL+  +e+++++s e++ vf   v
  gene2115|gene2115|rna2115|rna2115 240 ETVRKFLARVPEQYDEYRRYAAEGYRVLALAGKHLLSFTESTTRESVEKDLVFVGFV 296
                                        57899*****************************************99988887655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (782 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1068  (0.0595683); expected 358.6 (0.02)
Passed bias filter:                      545  (0.0303977); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.68u 0.28s 00:00:00.96 Elapsed: 00:00:00.43
# Mc/sec: 5425.67
//
Query:       gene2117|gene2117|rna2117|rna2117  [L=40]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (40 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       244  (0.0136092); expected 358.6 (0.02)
Passed bias filter:                      196  (0.010932); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.28s 00:00:00.67 Elapsed: 00:00:00.46
# Mc/sec: 263.82
//
Query:       gene2118|gene2118|rna2118|rna2118  [L=288]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-33  116.4   0.0    2.5e-33  115.9   0.0    1.2  1  GDPD      Glycerophosphoryl diester phosphodiesterase family
  ------ inclusion threshold ------
      0.079   13.1   0.8       0.13   12.4   0.8    1.5  1  DUF4852   Domain of unknown function (DUF4852)


Domain annotation for each model (and alignments):
>> GDPD  Glycerophosphoryl diester phosphodiesterase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.9   0.0   2.8e-37   2.5e-33       1     257 [.      14     277 ..      14     279 .. 0.82

  Alignments for each domain:
  == domain 1  score: 115.9 bits;  conditional E-value: 2.8e-37
                                        TTTTTTTSS.......TTSHHHHHHHHHTT-SEEEEEEEE-TTS-EEE-SSSBSTTTCSCCCH.BGGGS-HHHHHT CS
                               GDPD   1 HRGasgnlp.......EnTlesfakAaelGadyiEfDvqlTkDgvpVvlHDfnldrttdvagrldvkdltleelkr 69 
                                        HRG+++n+        EnT+esf+kA + Gad+iEfDv+lTkD vpV++H f + + ++ a    +++lt++e+ +
  gene2118|gene2118|rna2118|rna2118  14 HRGCGSNRAtniyncfENTIESFMKAHSSGADAIEFDVHLTKDYVPVIFHNFCVPVNGKNAF---IQNLTYAEFLN 86 
                                        *****************************************************999888887...**********9 PP

                                        ST.ECCTTCCCCSCCCSSGCCB....BHHHHHHH.HHHCCSEEEEEEECCCCCCCHHHHHHTCHHHCCCCCSCHHT CS
                               GDPD  70 ld.kiakenkaqlsenrvrlefpfp.tleevlkk.pqnvglnieikipmlseakeeeelqivkeilksvdeilkkv 142
                                        +  +  ++++ +l  n     + +p tle+v+k+ + ++ +n+e k+p ++e  e           ++++ i  kv
  gene2118|gene2118|rna2118|rna2118  87 AGkEFVSQERPHLDVNDH---RNVPgTLEDVFKHlNDGLVFNLELKYPTKDEMDEFNI-SETIPRETFIQHIM-KV 157
                                        994222333334433333...67877********888888888888888888777777.67777778888887.67 PP

                                        T..STTCSCEEEESTHHHHHHHHHTCTCTEEEEEEHHHHHHC-E....EECHCCCCCCCTCCCCHHCCCHCCCE.B CS
                               GDPD 143 lkkadkrkvifssfnpdilkllrekqpklpllflteggteaead...ssleraakfakadallgevsavaeglg.d 214
                                        ++  ++r+++fssf+ +il+ l++ +++  ++fl + + + + +    +  + ++ +  +++ g+v+ ++ + g  
  gene2118|gene2118|rna2118|rna2118 158 VYRYKNRRIFFSSFDISILISLKQYDTSAHIFFLKDFEYSGSLKdfvPLFSQELRICVLSGIDGIVFGSSTLNGdL 233
                                        888999*********************9999999775555555567856667888888888888888888777734 PP

                                        .CHHHHHHHTT-EEEEBSB-THSHHHHHHHHCCC.-SEEEES-H CS
                               GDPD 215 pdlVkraksrglvvhvytvnnedeeemkrlleag.vdgvitDfp 257
                                          l + ++s +l++  y+ + +d++ +k+++++  v g i+D++
  gene2118|gene2118|rna2118|rna2118 234 ALLFNFIRSLNLKIILYGERLKDRNFVKQVNDLHiVYGFIVDDV 277
                                        5678899999************9999999998853779999876 PP

>> DUF4852  Domain of unknown function (DUF4852)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.8   1.5e-05      0.13      18      76 ..     132     196 ..     125     283 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.5e-05
                            DUF4852  18 ekfeadeFelqel..raearkklekalrdvkleet....FtillearlseYdfdkqkFeieplst 76 
                                        +k e+deF++ e   r+   +++ k +   k++      F i   + l++Yd  + +F +++ + 
  gene2118|gene2118|rna2118|rna2118 132 TKDEMDEFNISETipRETFIQHIMKVVYRYKNRRIffssFDISILISLKQYDTSAHIFFLKDFEY 196
                                        7889*******975578999********9999998888899*****************9998755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (288 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       414  (0.0230911); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 2095.90
//
Query:       gene2119|gene2119|rna2119|rna2119  [L=228]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0083   15.1   0.1      0.013   14.4   0.1    1.3  1  FlgI      Flagellar P-ring protein
  ------ inclusion threshold ------
      0.056   13.7   0.1       0.11   12.8   0.1    1.5  1  TSCPD     TSCPD domain


Domain annotation for each model (and alignments):
>> FlgI  Flagellar P-ring protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.1   1.5e-06     0.013     203     261 ..      39      98 ..      33     132 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.5e-06
                               FlgI 203 vklpedleeerveflaevenlevep.dakarvvinertgtvVigenvrisevavshgnlt 261
                                        + +p+++++ r+  ++e+++  +++ +  + ++i++ tg v+ ++ +++++++vs+ +l+
  gene2119|gene2119|rna2119|rna2119  39 LVIPNNIQKVRLVNVSEMQKFFITVnELCKTLLIENSTGIVICNSPMNLEKIVVSQSSLS 98 
                                        678999999999999**********66778899***********************9986 PP

>> TSCPD  TSCPD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   1.2e-05      0.11       1      53 [.     116     166 ..     116     179 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.2e-05
                              TSCPD   1 YktkgvCsreieievddkliknvkfvgGCngnlkgiskLvegmkveevikklk 53 
                                        Y+ +g+  ++i ++++   + +++f  GC+ n+  i kL++++++++ + +l+
  gene2119|gene2119|rna2119|rna2119 116 YEFEGGQNEQICVHIK--NLCSLSFKHGCSNNIATIPKLMSDKTCDTSTLHLS 166
                                        5566666677777777..5799********************99988776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (228 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       472  (0.0263261); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1640.09
//
Query:       gene212|gene212|rna212|rna212  [L=139]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.6e-38  131.3   3.0    2.9e-38  131.2   3.0    1.0  1  Histone      Core histone H2A/H2B/H3/H4
    0.00046   20.8   3.8    0.00053   20.6   3.8    1.2  1  PAF          PCNA-associated factor histone like domain
     0.0023   18.3   0.0     0.0045   17.3   0.0    1.4  1  CENP-S       CENP-S protein
     0.0084   16.2   0.2      0.024   14.8   0.0    1.8  2  CENP-T_C     Centromere kinetochore component CENP-T histone 
  ------ inclusion threshold ------
      0.026   13.9   0.1      0.031   13.7   0.1    1.1  1  DUF1460      Protein of unknown function (DUF1460)
       0.12   12.5   0.0       0.29   11.2   0.0    1.7  2  TFIID-31kDa  Transcription initiation factor IID, 31kD subuni


Domain annotation for each model (and alignments):
>> Histone  Core histone H2A/H2B/H3/H4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  131.2   3.0   9.7e-42   2.9e-38       1     130 [.       1     132 [.       1     133 [. 0.97

  Alignments for each domain:
  == domain 1  score: 131.2 bits;  conditional E-value: 9.7e-42
                                    XXEESXEEEXXXXEEXXXXXXXXXXHT..TS-SSSSB--TTT-XTTHHHHHHHHHHHHXXSXXSXHHHHHHHHHHHH.TT CS
                        Histone   1 marekekarkesektapekkvsakker..kasskskkkkkrryrpgtvalkeirkyqkstdlliqklpfaRvvreivkse 78 
                                    mar+k++ark+++++ap+k++++k +r    + +s+ +kk ry+ g+valkeir+yqkst++  +k+pf+R+vr+++++ 
  gene212|gene212|rna212|rna212   1 MARTKQTARKSTGGKAPRKQLATKAARksAMQTSSQGVKKLRYKSGMVALKEIRRYQKSTETVVRKAPFQRMVRDVTSKI 80 
                                    9**************************97777888999****************************************** PP

                                    SSSXEEXHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTXSEEXHHHHHHHHHH CS
                        Histone  79 kedlrisaeavlalqealEallvelfeeAnllakhaKRvTitpkDiqlArrl 130
                                    ++d+r++a+++ al ea E++lv lfe+  l+a+haKRvT++p+Di l+ +l
  gene212|gene212|rna212|rna212  81 RDDMRYQAQCLSALHEAFENYLVGLFEDGLLAANHAKRVTVMPRDINLVGKL 132
                                    ***********************************************98776 PP

>> PAF  PCNA-associated factor histone like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   3.8   1.8e-07   0.00053       1      62 [.       1      59 [.       1      89 [. 0.79

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 1.8e-07
                            PAF  1 mVRTkAdvssarkavaakAprkslgassssssssssspkkkkkkyvGGNpvcpRptPaWQKp 62
                                   m RTk ++   rk  ++kAprk+l+++   +s+  +s+++ kk       v  +++   QK 
  gene212|gene212|rna212|rna212  1 MARTKQTA---RKSTGGKAPRKQLATKAARKSAMQTSSQGVKKLRYKSGMVALKEIRRYQKS 59
                                   99******...*************99888888777777665554444446667777777775 PP

>> CENP-S  CENP-S protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   1.5e-06    0.0045       8      70 ..      70     130 ..      65     133 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.5e-06
                         CENP-S   8 wysvgkiveeeaaekeveatkqfiaaltelvykqlenlakDLeaFakHAkRstittdDvlLla 70 
                                    + +v+ +++++  + ++++  q ++al e   + l  l +D  + a+HAkR t+ + D+ L+ 
  gene212|gene212|rna212|rna212  70 QRMVRDVTSKI--RDDMRYQAQCLSALHEAFENYLVGLFEDGLLAANHAKRVTVMPRDINLVG 130
                                    55555555554..566788899*************************************9986 PP

>> CENP-T_C  Centromere kinetochore component CENP-T histone fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.52   1.6e+03      16      25 ..      21      30 ..       5      62 .. 0.62
   2 !   14.8   0.0   7.9e-06     0.024      12      73 ..      68     129 ..      56     135 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.52
                       CENP-T_C 16 lakrfakasg 25
                                   la+++a++s+
  gene212|gene212|rna212|rna212 21 LATKAARKSA 30
                                   3333333322 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 7.9e-06
                       CENP-T_C  12 vvkklakrfakasgskaklekealkalekasdkffeqvgeDLeayakHagRKtidesDvilL 73 
                                      ++++++++++    ++ +++ l+al +a ++++  + eD    a+Ha+R t+   D+ l 
  gene212|gene212|rna212|rna212  68 PFQRMVRDVTSKIRDDMRYQAQCLSALHEAFENYLVGLFEDGLLAANHAKRVTVMPRDINLV 129
                                    557788888888778999***********************999**************9765 PP

>> DUF1460  Protein of unknown function (DUF1460)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1     1e-05     0.031      46     116 ..      26     100 ..      20     130 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1e-05
                                    HHBSSHHHHHHHHHHHHBGGG--STTTB--S.TT.THHHHH.HHT.SEEE-GGG-B-TT-EEE--EEEHHHHHHT CS
                        DUF1460  46 arssseeeFaknLkklRYkdgkvsflsRkHf.fs.dWiann.qkr.llrdvtaeisnkkaktlkalvtkkkkynq 116
                                    ar s+ ++  + +kklRYk g+v + + + +  s + + ++ + + ++rdvt +i+ +++ +++ l+  ++++++
  gene212|gene212|rna212|rna212  26 ARKSAMQTSSQGVKKLRYKSGMVALKEIRRYqKStETVVRKaPFQrMVRDVTSKIRDDMRYQAQCLSALHEAFEN 100
                                    4455567777889**********887644441344665554145579**********999888888888877776 PP

>> TFIID-31kDa  Transcription initiation factor IID, 31kD subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       1.3   3.9e+03      77      91 ..      14      28 ..       4      42 .. 0.61
   2 ?   11.2   0.0   9.6e-05      0.29      22      65 ..      85     128 ..      70     138 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.3
                    TFIID-31kDa 77 epppkelLlelAaer 91
                                   ++ p++ L   Aa++
  gene212|gene212|rna212|rna212 14 GKAPRKQLATKAARK 28
                                   455666666555544 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 9.6e-05
                    TFIID-31kDa  22 eyeerVvlqLldfayrytssvLedAkvlaehakkkevslddvrl 65 
                                     y+ + ++ L +   +y + ++ed ++ a+hak+ +v   d++l
  gene212|gene212|rna212|rna212  85 RYQAQCLSALHEAFENYLVGLFEDGLLAANHAKRVTVMPRDINL 128
                                    699999***********************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       783  (0.0436723); expected 358.6 (0.02)
Passed bias filter:                      456  (0.0254337); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1006.82
//
Query:       gene2120|gene2120|rna2120|rna2120  [L=925]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (925 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       613  (0.0341904); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.67u 0.32s 00:00:00.99 Elapsed: 00:00:00.49
# Mc/sec: 5682.63
//
Query:       gene2121|gene2121|rna2121|rna2121  [L=757]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.2e-14   52.0  18.9    1.4e-13   50.6  18.9    1.6  1  HSP90          Hsp90 protein
    1.5e-13   50.8   0.5    1.5e-13   50.8   0.5    2.3  3  HATPase_c_3    Histidine kinase-, DNA gyrase B-, and HSP90-li
    3.7e-08   33.9   0.3    7.8e-08   32.8   0.3    1.5  1  HATPase_c      Histidine kinase-, DNA gyrase B-, and HSP90-li
  ------ inclusion threshold ------
      0.056   13.5   0.6       0.16   12.0   0.1    2.0  2  DUF2433        Protein of unknown function (DUF2433)
       0.13   11.7   0.0        1.1    8.8   0.0    2.2  2  AA_permease_N  Amino acid permease N-terminal


Domain annotation for each model (and alignments):
>> HSP90  Hsp90 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.6  18.9     4e-17   1.4e-13      49     514 ..     217     665 ..     187     668 .. 0.72

  Alignments for each domain:
  == domain 1  score: 50.6 bits;  conditional E-value: 4e-17
                                        XXXXXXXXXXXXXX..XXXXXXXXXXEEEEEEESXXSXGGGSXGGGSXHHHHHHHHHHTTTT....TSXX..SEEE CS
                              HSP90  49 eeeeakveeeeeeeeekkktkkvketvkewellNkqkpiWlrkpkevteeeYkeFYkslskd....sedp..lavk 118
                                        ++ ++k e++  +++ek+  k+ ++  +e +++      W+ + +e   ++ +++Yks+       ++++  ++v 
  gene2121|gene2121|rna2121|rna2121 217 KKADTKKEKS--DDDEKDADKEPEKDAEEHKKVEL--FPWITSLDE---KKLEDYYKSIDGPgkilTSNKmrVTVA 285
                                        2333333333..33334455555555444444432..238886555...555556777765333444444114555 PP

                                        EEEEXS...SSXEEEEEEEXSSXXTTTTTTTTTSXXTTEEEEETTEEEESXXTTS..SXGGGTTXEEEEEESSSXS CS
                              HSP90 119 hfsaeg...evefkaiLfvPkrapsdlfekykkkkknnikLYvrrVfitdefedl..lPkyLsFvkGvvdsddLPL 189
                                        +  ++g   +v+f+ ++ +P+  + ++    + k k+   L+v     +++  dl  +P +L  ++ ++ s +  L
  gene2121|gene2121|rna2121|rna2121 286 QKDMDGkyqDVSFELLVVIPEFLDLRVLGMET-KGKH--YLFV-----NNQRVDLepIPAFLGPITFILKSSEAFL 353
                                        556666444699***************99633.3332..4555.....5554444449****************** PP

                                        SSTHHHHHTCH.HHHHHHHHHHHHHHHHHHTSXHHH..HHTHHHHHHHHHHHHHHHXGG.GHHHHHTTXEEEET.T CS
                              HSP90 190 NvsREtlqqnk.ilkvikkklvrKvlemlkklaeekeeykkfykefsknlklGiiedsa.nrkklakLlrfkss.k 262
                                           RE l ++k +   + + + +Kvl++++   +++   kk  k +   +k G +e ++ n++ la+L+      +
  gene2121|gene2121|rna2121|rna2121 354 VSTREKLLNSKdTCTALYNSIQKKVLQLIRAEMKKD--LKKVMKVYDFYIKTGYVESKKdNKSSLAELFAAVLPfN 427
                                        99***98665538999*************9877755..9****************998769*****9965332225 PP

                                        EEEEEEEHHHHHHHSXTTXXEEEEEEXSSHHHHHTSGGGHHHHHTTXXEEEEXSTTHHHHHHTXSEETTEEEEETT CS
                              HSP90 263 seeeltsLedYvermkekqksiYyiageskeevekspflerlkkkgyevlylvdpiDeyvvqqlkeyegkklvnva 338
                                        +++ l+ L+d+v+++  + + +Y   g+++  + +  +   +   +   +++   + e vv ++ ey+gkk+vn+ 
  gene2121|gene2121|rna2121|rna2121 428 TSDGLIMLQDFVDKLGADEDILYASIGHDTLDLPEGVYNPLFDGIKSPFILVSGLLEEQVV-SMFEYKGKKMVNIV 502
                                        5568************988888888899999988877766666666667777777777666.6789*********8 PP

                                        BSTXXXXXXHHHHHHHHHHHHHHHHHHHHHHHTTTTTESEEEEXSSXSSXSEEEEBXTTSXXHHHHHHHHHHHHHH CS
                              HSP90 339 kegleleeeeeekkkkeelkkkfeeltkllkevlkdkvekvkvserlvdsPcvlvtseygwsanmerimkaqalrd 414
                                         ++++        +k+ +     + ++ ++k  lk  v++v++s rlv++P+ l +++ ++s   ++++   ++++
  gene2121|gene2121|rna2121|rna2121 503 NKEFK--------NKEPAN---DDGFIAFCKRELKGVVDDVVMSVRLVNAPFFLKAKNAQFSQAHKHVIGEYTIKN 567
                                        76533........333333...4556777789******************************************** PP

                                        HSSTSSSSSXEEEEEXTTSHHHHHHHHHHHHTTTXHHHHHHHHHHHHHHHHHTTXXXSXHHHHHHHHHHHHTTTTH CS
                              HSP90 415 kskssymsskktleinprhpiikeLkkkveedkedeeakdlaellyetallesGfsledpasfakrierllklslg 490
                                        +  ++++++  +le+n +   +k++k+ +++d +  +a   a ++    + +  +  + + +f + i+ + ++ lg
  gene2121|gene2121|rna2121|rna2121 568 SAFKKTIETDIVLEVNTDSDEVKSIKELISNDYDRAVAALRAGVMAAGVICNMVY-NNTTVAFLNLIN-VQRNLLG 641
                                        *******************************976666555555554333333333.445556666554.5566677 PP

                                        XXSTTTTTTGGGXGGGXXXXXXXX CS
                              HSP90 491 idedeeveeeeeveeeeeeeeeee 514
                                        +++   v +e++ + e+e++++++
  gene2121|gene2121|rna2121|rna2121 642 MENVPIVVKEDDFDMEKEKKKTKN 665
                                        777777777777776666666554 PP

>> HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.8   0.5   4.1e-17   1.5e-13       7     116 ..      45     162 ..      39     175 .. 0.76
   2 ?   -3.4   0.0       2.2   7.9e+03      43      55 ..     185     197 ..     184     199 .. 0.89
   3 ?   -4.1   0.0       3.6   1.3e+04       5      16 ..     590     601 ..     586     608 .. 0.78

  Alignments for each domain:
  == domain 1  score: 50.8 bits;  conditional E-value: 4.1e-17
                        HATPase_c_3   7 laelvdNsldAdaen..............vkievnknrgktgeivieDdGkGmseeelknal.rlatsskeak.rk 66 
                                        l elv Ns+dA+ +               + ++++     ++ ++i D+G Gm+++el +++ +++ s ++a   +
  gene2121|gene2121|rna2121|rna2121  45 LRELVSNSMDANKKLvmaakqsdidtnkdIILTLK-----DNVFTISDNGIGMNKDELVSYIgTMGGSGTRALgDS 115
                                        78**********99855555544444433333333.....379*****************8734544444433268 PP

                        HATPase_c_3  67 stslGkkGiGlklAslslgkkltvitkkegesstltldvdkidkenekvl 116
                                        ++ +Gk+G+G + +++++++++ vitkk ge +t++l ++  +k  ++++
  gene2121|gene2121|rna2121|rna2121 116 KNFVGKFGVG-FYSVFVVADEVRVITKKYGENETYELVLKNGQK--TYTI 162
                                        999*******.*************************99986553..4444 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 2.2
                        HATPase_c_3  43 kGmseeelknalr 55 
                                        +G++e+elk++++
  gene2121|gene2121|rna2121|rna2121 185 TGLDEDELKKWMK 197
                                        79*********97 PP

  == domain 3  score: -4.1 bits;  conditional E-value: 3.6
                        HATPase_c_3   5 kAlaelvdNsld 16 
                                        k++ el+ N +d
  gene2121|gene2121|rna2121|rna2121 590 KSIKELISNDYD 601
                                        678999999998 PP

>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.8   0.3   2.2e-11   7.8e-08      10     109 ..      45     180 ..      41     182 .. 0.55

  Alignments for each domain:
  == domain 1  score: 32.8 bits;  conditional E-value: 2.2e-11
                                        HHHHHHHHHHH......HSTTTEE....EEEEEEEETEEEEEEEESSSSSTTHHHT....GTCSTTCH......HC CS
                          HATPase_c  10 isnlvdNavkf......atkagei....eveikaseddlvisveDnGiGipkedlk....klfekfsq......dd 65 
                                        +++lv+N++++      a+k+++i    ++ ++   +d+v++++DnGiG++k++l      +++   +      d 
  gene2121|gene2121|rna2121|rna2121  45 LRELVSNSMDAnkklvmAAKQSDIdtnkDIILT-L-KDNVFTISDNGIGMNKDELVsyigTMGG---SgtralgD- 114
                                        678888888887666764455555333333333.2.49******************75543333...12355333. PP

                                        STCHTSTSSSHHHHHH................HHHHHHTTTEEEE................EEETTTEEEEEEEEE CS
                          HATPase_c  66 stkrggggtGlGlsiv................kklvelmgGeiwv................esepgrGttftftlp 109
                                         +k+  g +G+G++ v                +          ++                +++ + Gtt++++l 
  gene2121|gene2121|rna2121|rna2121 115 -SKNFVGKFGVGFYSVfvvadevrvitkkygeN---------ETYelvlkngqktytidtiDDRGECGTTVQLKLS 180
                                        .33334666676776644577763333333331.........2223333333333344443333355888888775 PP

>> DUF2433  Protein of unknown function (DUF2433)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   4.5e-05      0.16      18      95 ..     357     430 ..     346     445 .. 0.76
   2 ?   -3.3   0.0       2.6   9.2e+03      22      45 ..     661     684 ..     644     693 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 4.5e-05
                            DUF2433  18 rsklakskakfaevwetvkkeveaaideaqrklLenalevvekiPtiakeeakkneastskekeesafknlWnfNL 93 
                                        r+kl +sk++ ++++++++k+v ++i  +++k L+++++v +   ++       ++++ +k++ ++ f  +  fN 
  gene2121|gene2121|rna2121|rna2121 357 REKLLNSKDTCTALYNSIQKKVLQLIRAEMKKDLKKVMKVYDFYIKTGY----VESKKDNKSSLAELFAAVLPFNT 428
                                        89**************************************996543333....22222334455555666666666 PP

                            DUF2433  94 cD 95 
                                        +D
  gene2121|gene2121|rna2121|rna2121 429 SD 430
                                        66 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 2.6
                            DUF2433  22 akskakfaevwetvkkeveaaide 45 
                                        +k+k++ + + e+v+++ ++++de
  gene2121|gene2121|rna2121|rna2121 661 KKTKNEIDGIKESVRGQDDESVDE 684
                                        466778888888888888888875 PP

>> AA_permease_N  Amino acid permease N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0    0.0003       1.1      23      46 ..     397     420 ..     393     442 .. 0.92
   2 ?   -0.3   0.0      0.22   7.9e+02      11      19 ..     452     460 ..     445     462 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0003
                      AA_permease_N  23 idfYrntasvsgaklsRPsLaeLH 46 
                                        +dfY  t+ v  +k ++ sLaeL 
  gene2121|gene2121|rna2121|rna2121 397 YDFYIKTGYVESKKDNKSSLAELF 420
                                        9*********************96 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.22
                      AA_permease_N  11 tfGhnTlDa 19 
                                          Gh+TlD 
  gene2121|gene2121|rna2121|rna2121 452 SIGHDTLDL 460
                                        57******6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (757 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1337  (0.0745719); expected 358.6 (0.02)
Passed bias filter:                      565  (0.0315132); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.77u 0.32s 00:00:01.09 Elapsed: 00:00:00.49
# Mc/sec: 4603.05
//
Query:       gene2122|gene2122|rna2122|rna2122  [L=153]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0095   16.5   7.1       0.48   11.0   0.1    2.6  3  PepSY_like      Putative beta-lactamase-inhibitor-like, PepSY
  ------ inclusion threshold ------
      0.069   13.0   0.0      0.097   12.5   0.0    1.2  1  DUF2345         Uncharacterized protein conserved in bacteria
        0.2   12.0   3.1       0.37   11.0   3.1    1.6  1  Inos-1-P_synth  Myo-inositol-1-phosphate synthase


Domain annotation for each model (and alignments):
>> PepSY_like  Putative beta-lactamase-inhibitor-like, PepSY-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.1     0.023   1.4e+02      42      73 ..      11      42 ..       7      47 .. 0.82
   2 !   11.0   0.1   8.1e-05      0.48      39      81 ..      35      82 ..      21      84 .. 0.79
   3 !    8.2   2.4   0.00062       3.7      11      71 ..      83     145 ..      74     152 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.023
                                       HHHHHHTTTEEEEEEEECSSEEEEEETTSEEE CS
                         PepSY_like 42 kaiknsypdekvtkierkkkeyeieleneiel 73
                                       ++ +  y+++kv + e + ++y   ++n +++
  gene2122|gene2122|rna2122|rna2122 11 TYARRGYNQDKVSNYELRGNNYGLNVQNHVQM 42
                                       444555999******************98876 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 8.1e-05
                                       HHHHHHHHH.TTT...EEEEEEEECSSEEEEEETT.SEEEEEETTS-E CS
                         PepSY_like 39 avlkaikns.ypd...ekvtkierkkkeyeielen.eielyfdedGnl 81
                                       +v+++++ + y     + ++ i  ++++y i+l   + el f+ +Gn 
  gene2122|gene2122|rna2122|rna2122 35 NVQNHVQMHsYETqnaSTIESISDTSTGYSIKLHArQGELDFRVEGNS 82
                                       78999998889886667777777888********99889999999985 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.00062
                                        EEEEE-TTS-EEEEE-TTSEESGGGS-HHHHHHHHHH.TTTEEEEEEEECS....SEEEEEETTSE CS
                         PepSY_like  11 teveFdkkGeWkeiegkkteiplsilpkavlkaikns.ypdekvtkierkk....keyeielenei 71 
                                          + F+k+ e +ei+   +++ ++++ +   + ++++ + d++ + + +      ++ ei++++++
  gene2122|gene2122|rna2122|rna2122  83 LFITFSKENEHMEIK---NQMRIDVINNDLHNFYAKEiHEDNDAYTVINLVfenpNGAEIKITKNF 145
                                        5589***********...999999999999999999977774444444333333799****99975 PP

>> DUF2345  Uncharacterized protein conserved in bacteria (DUF2345)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   1.6e-05     0.097      35      89 ..      29      83 ..      27     101 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.6e-05
                            DUF2345 35 genlaltagqdtqlaagkrllaaageaislfaqkagikliAakgkveiqAqsdal 89
                                       g+n  l  ++++q+ + ++  a+  e+is  + +  ikl+A +g+++ + + ++l
  gene2122|gene2122|rna2122|rna2122 29 GNNYGLNVQNHVQMHSYETQNASTIESISDTSTGYSIKLHARQGELDFRVEGNSL 83
                                       67788999**************************************998877766 PP

>> Inos-1-P_synth  Myo-inositol-1-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   3.1   6.2e-05      0.37      11      66 ..      10      71 ..       6     145 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 6.2e-05
                                       HHHHHTT-EEEEEEEEEEE-HHHHHHTTSHHHHHHHHHHHHHHHHHHHSS--EEE........ CS
                     Inos-1-P_synth 11 ellverglkvksivslNilGnnDgknlseeerfksKkisKssvvddivkanelly.......v 66
                                       ++++ rg + +++  +++ Gnn g+n++++ +++s +    s +++i +++ + y       +
  gene2122|gene2122|rna2122|rna2122 10 QTYARRGYNQDKVSNYELRGNNYGLNVQNHVQMHSYETQNASTIESISDTS-TGYsiklharQ 71
                                       67899****************************************997764.34445555540 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       946  (0.0527637); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 1000.12
//
Query:       gene2123|gene2123|rna2123|rna2123  [L=463]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    9.1e-28   95.6  18.4    5.9e-15   54.6   5.8    2.5  2  GATA          GATA zinc finger
  ------ inclusion threshold ------
       0.05   13.5   1.2       0.35   10.8   0.2    2.5  2  ADD_ATRX      Cysteine Rich ADD domain
        0.1   12.7   2.5         12    6.1   0.2    2.6  2  Zn-ribbon_8   Zinc ribbon domain
        0.1   13.2   0.5        0.1   13.2   0.5    3.0  4  Zn_ribbon_2   Putative zinc ribbon domain
        0.1   12.7   3.4        3.5    7.8   0.8    3.3  3  zf-piccolo    Piccolo Zn-finger
       0.16   12.0   6.1        4.7    7.3   6.1    2.5  1  DZR           Double zinc ribbon
        0.9    9.6   6.4       0.62   10.1   0.4    2.6  2  Zn_Tnp_IS91   Transposase zinc-binding domain
        1.4    8.5   8.1          2    8.0   0.9    2.7  2  TF_Zn_Ribbon  TFIIB zinc-binding


Domain annotation for each model (and alignments):
>> GATA  GATA zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.6   5.8   2.6e-18   5.9e-15       1      35 [.     133     167 ..     133     168 .. 0.98
   2 !   46.6   4.7   8.2e-16   1.8e-12       1      32 [.     191     221 ..     191     225 .. 0.95

  Alignments for each domain:
  == domain 1  score: 54.6 bits;  conditional E-value: 2.6e-18
                               GATA   1 CsnCgttkTplWRrgpdgnksLCnaCGlyykkkgl 35 
                                        CsnC tt+Tp WRr  dg+k LCnaCGly+k++g+
  gene2123|gene2123|rna2123|rna2123 133 CSNCVTTTTPSWRRSTDGKKLLCNACGLYQKLHGR 167
                                        *********************************97 PP

  == domain 2  score: 46.6 bits;  conditional E-value: 8.2e-16
                               GATA   1 CsnCgttkTplWRrgpdgnksLCnaCGlyykk 32 
                                        C nCgtt+T+ WRrg +g++ LCn+CGly++ 
  gene2123|gene2123|rna2123|rna2123 191 CGNCGTTETSFWRRGINGHP-LCNSCGLYFRD 221
                                        9*******************.*********96 PP

>> ADD_ATRX  Cysteine Rich ADD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.29   6.4e+02      10      18 ..     151     159 ..     145     166 .. 0.72
   2 ?   10.8   0.2   0.00016      0.35       9      50 ..     186     222 ..     178     227 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.29
                           ADD_ATRX  10 eivsCtaCg 18 
                                        +++ C aCg
  gene2123|gene2123|rna2123|rna2123 151 KKLLCNACG 159
                                        457888998 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00016
                           ADD_ATRX   9 eeivsCtaCgqqvnhfqkdslykHPvLkVLiCksCfkyyssd 50 
                                         ++++C  Cg     f +  +  HP     +C sC  y+ ++
  gene2123|gene2123|rna2123|rna2123 186 FDKIKCGNCGTTETSFWRRGINGHP-----LCNSCGLYFRDN 222
                                        5679*********************.....699999998876 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.1    0.0055        12       8      33 ..     133     159 ..     129     164 .. 0.81
   2 ?    6.1   0.2    0.0055        12       7      33 ..     190     216 ..     188     220 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0055
                        Zn-ribbon_8   8 CeeCghefe.vlqsisdapltaCPeCg 33 
                                        C +C ++ +  +++++d ++  C +Cg
  gene2123|gene2123|rna2123|rna2123 133 CSNCVTTTTpSWRRSTDGKKLLCNACG 159
                                        *****99996666666888888****9 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0055
                        Zn-ribbon_8   7 rCeeCghefevlqsisdapltaCPeCg 33 
                                        +C +Cg++ + + +   +  + C +Cg
  gene2123|gene2123|rna2123|rna2123 190 KCGNCGTTETSFWRRGINGHPLCNSCG 216
                                        7*****8877666666667788***98 PP

>> Zn_ribbon_2  Putative zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.5       6.5   1.5e+04      53      53 ..      28      28 ..       9      47 .. 0.45
   2 ?   -2.4   0.3       3.4   7.7e+03      37      61 ..      98     122 ..      85     145 .. 0.46
   3 ?   -3.6   0.2         8   1.8e+04       1       7 [.     154     160 ..     154     162 .. 0.84
   4 ?   13.2   0.5   4.6e-05       0.1       1      59 [.     211     271 ..     211     292 .. 0.77

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 6.5
                        Zn_ribbon_2 53 k 53
                                       k
  gene2123|gene2123|rna2123|rna2123 28 K 28
                                       1 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 3.4
                        Zn_ribbon_2  37 ftepdltmeemiekcvkklaeenke 61 
                                        f++++ +++   ++++ +++ + ++
  gene2123|gene2123|rna2123|rna2123  98 FQYNHNKFQGYDDYYTLRMNMRMHK 122
                                        5554445544444444444333322 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 8
                        Zn_ribbon_2   1 iCqsCGm 7  
                                        +C++CG+
  gene2123|gene2123|rna2123|rna2123 154 LCNACGL 160
                                        59***95 PP

  == domain 4  score: 13.2 bits;  conditional E-value: 4.6e-05
                        Zn_ribbon_2   1 iCqsCGmplkkeedlgteadgsksedYCky..CykdGeftepdltmeemiekcvkklaeen 59 
                                        +C+sCG+ +++++   +e++ s   ++ +y   ykdG f+e+++  +   + ++++++++ 
  gene2123|gene2123|rna2123|rna2123 211 LCNSCGLYFRDNTYKEKEKEMSHDANFASYadAYKDGGFKEKEMLRDPAFAPYTDMYKDDA 271
                                        5********9999999************994459*******88877777666666666554 PP

>> zf-piccolo  Piccolo Zn-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.3     0.083   1.9e+02      11      28 ..     121     138 ..     115     141 .. 0.77
   2 ?    7.8   0.8    0.0016       3.5      11      36 ..     135     160 ..     131     167 .. 0.84
   3 ?    2.1   0.1     0.098   2.2e+02      30      47 ..     211     228 ..     208     230 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.083
                         zf-piccolo  11 nvgskeppnyntCteCkk 28 
                                        +  sk +p  ++C++C +
  gene2123|gene2123|rna2123|rna2123 121 HKDSKRKPKMRVCSNCVT 138
                                        456788999*****9976 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0016
                         zf-piccolo  11 nvgskeppnyntCteCkkqvCnlCGF 36 
                                        n++++ +p ++  t+ kk +Cn+CG 
  gene2123|gene2123|rna2123|rna2123 135 NCVTTTTPSWRRSTDGKKLLCNACGL 160
                                        5567788999***************6 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.098
                         zf-piccolo  30 vCnlCGFnptphltekke 47 
                                        +Cn CG    +++ ++ke
  gene2123|gene2123|rna2123|rna2123 211 LCNSCGLYFRDNTYKEKE 228
                                        7*****988888877665 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   6.1    0.0021       4.7       1      49 []     133     216 ..     123     216 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0021
                                DZR   1 CpqCgee........lppdar.fCseCgtklkavaa....................edrCpsCgekvdpearf... 44 
                                        C++C +         ++ + +  C++Cg   k   +                    +++C +Cg+  ++ +r    
  gene2123|gene2123|rna2123|rna2123 133 CSNCVTTttpswrrsTDGK-KlLCNACGLYQKLHGRprpysttpegktkalksgfdKIKCGNCGTTETSFWRRgin 207
                                        7777777555555533333.34888888775433336688899*********************998888777778 PP

                                DZR  45 ....CpeCG 49 
                                            C++CG
  gene2123|gene2123|rna2123|rna2123 208 ghplCNSCG 216
                                        888899998 PP

>> Zn_Tnp_IS91  Transposase zinc-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   1.0      0.13     3e+02      56      78 ..     129     151 ..     115     163 .. 0.79
   2 ?   10.1   0.4   0.00028      0.62      33      79 ..     182     231 ..     176     238 .. 0.75

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.13
                        Zn_Tnp_IS91  56 ksrhCpsCqkkateewlekqqee 78 
                                        k r C++C + +t  w +++  +
  gene2123|gene2123|rna2123|rna2123 129 KMRVCSNCVTTTTPSWRRSTDGK 151
                                        77999999999999998766555 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00028
                        Zn_Tnp_IS91  33 aalGfaryeCeeCghekivyfsC...ksrhCpsCqkkateewlekqqeel 79 
                                         + Gf +++C +Cg +++++ +    ++  C+sC+   ++++ +++++e+
  gene2123|gene2123|rna2123|rna2123 182 LKSGFDKIKCGNCGTTETSFWRRginGHPLCNSCGLYFRDNTYKEKEKEM 231
                                        568**********97766555431114555*****999999998888877 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   1.1     0.018        41       2      27 ..     132     160 ..     131     161 .. 0.83
   2 ?    8.0   0.9   0.00089         2       2      36 ..     190     226 ..     189     230 .. 0.74

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.018
                                        EETTTTCEEC...HEETSTTCEEESSSSB CS
                       TF_Zn_Ribbon   2 kCPnCgstnl...veDpergelvCtdCGl 27 
                                        +C nC +t++    + ++   l+C +CGl
  gene2123|gene2123|rna2123|rna2123 132 VCSNCVTTTTpswRRSTDGKKLLCNACGL 160
                                        7999999887886666888899******7 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.00089
                                        EETTTTCEE.CHEETSTTCE.EESSSSBEEEECCCCC CS
                       TF_Zn_Ribbon   2 kCPnCgstn.lveDpergel.vCtdCGlVlednside 36 
                                        kC nCg+t+   +    + + +C +CGl   dn ++e
  gene2123|gene2123|rna2123|rna2123 190 KCGNCGTTEtSFWRRGINGHpLCNSCGLYFRDNTYKE 226
                                        8******88445565555555******9888886655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (463 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1489  (0.0830498); expected 358.6 (0.02)
Passed bias filter:                      518  (0.0288917); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.62u 0.24s 00:00:00.86 Elapsed: 00:00:00.45
# Mc/sec: 3082.76
//
Query:       gene2124|gene2124|rna2124|rna2124  [L=318]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.3e-71  239.3   0.2    4.2e-71  238.9   0.2    1.1  1  AOX       Alternative oxidase
  ------ inclusion threshold ------
      0.068   12.9   0.2       0.18   11.6   0.2    1.7  1  COQ7      Ubiquinone biosynthesis protein COQ7


Domain annotation for each model (and alignments):
>> AOX  Alternative oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  238.9   0.2   4.7e-75   4.2e-71       4     215 .]     107     307 ..     104     307 .. 0.98

  Alignments for each domain:
  == domain 1  score: 238.9 bits;  conditional E-value: 4.7e-75
                                AOX   4 eelesvklahrepktlsDkvaiglvkllRwlaDlvtrekkleltekkylhRaifLetvAgvpgmvaavlrhLrslr 79 
                                        ++l+ ++ +h  p+++sD++a+ +vk lR +aDl++++        +y++R+++LetvA++pgmv++++rhL+slr
  gene2124|gene2124|rna2124|rna2124 107 KSLDYESGKHFVPQSFSDTFAYLIVKGLRAFADLYFQK--------DYVRRVVVLETVAAIPGMVGGMFRHLYSLR 174
                                        567888999*****************************........****************************** PP

                                AOX  80 lmkrdkgwirtlleeaenermHllvllklaeptlleRllvllaqgvffniflllYllsPrvahrlvgyleEeavvt 155
                                         ++++ + i++l+ eaener Hll++l + +p++l R+l+ l q +ffn ++++Y+++Pr+ahr+vgyleEeav +
  gene2124|gene2124|rna2124|rna2124 175 NLEDNGEAIKKLVLEAENERQHLLTFLAVLKPNVLDRMLIKLGQFLFFNGYMVFYFVAPRTAHRFVGYLEEEAVRS 250
                                        **************************************************************************** PP

                                AOX 156 YtqliedideGkleewekvkaPeiAlqYwklqeeatlrdvilliRaDEakhrdvnhtlan 215
                                        Y+ + e+i  G+++   +v+aP+i+++Yw+l+eea+l dv++++RaDEa+hrdvnh++a+
  gene2124|gene2124|rna2124|rna2124 251 YDAFEEEILLGHIK---NVEAPRISKDYWNLPEEAMLIDVVRAVRADEAEHRDVNHKMAD 307
                                        **************...5****************************************96 PP

>> COQ7  Ubiquinone biosynthesis protein COQ7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.2     2e-05      0.18      83     143 ..     230     305 ..     171     315 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2e-05
                               COQ7  83 llGkeaamacteavEtvigeHYne........qlreleelee..........eedkelleiikqfrddEleHldtA 140
                                         + +++a+ ++   E++  + Y+         +++++e              +e++ l+++++ +r dE+eH+d+ 
  gene2124|gene2124|rna2124|rna2124 230 FVAPRTAHRFVGYLEEEAVRSYDAfeeeillgHIKNVE---ApriskdywnlPEEAMLIDVVRAVRADEAEHRDVN 302
                                        45566666666666666666666644444333444444...1456778889999********************87 PP

                               COQ7 141 ven 143
                                        ++ 
  gene2124|gene2124|rna2124|rna2124 303 HKM 305
                                        765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (318 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       488  (0.0272185); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 2237.79
//
Query:       gene2125|gene2125|rna2125|rna2125  [L=245]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    9.1e-36  121.5   5.9    2.8e-14   52.7   0.2    3.2  3  RRM_1         RNA recognition motif. (a.k.a. RRM, RBD, or RNP
    4.2e-07   29.7   0.1      0.093   12.6   0.0    3.3  3  RRM_occluded  Occluded RNA-recognition motif
    1.3e-06   28.4   0.1       0.24   11.5   0.0    3.4  2  RRM_7         RNA recognition motif
    1.8e-06   27.8   0.5       0.18   11.9   0.0    3.3  3  Nup35_RRM_2   Nup53/35/40-type RNA recognition motif
    3.2e-05   23.9   2.6       0.04   14.0   0.1    3.2  3  RRM_3         RNA binding motif
    7.3e-05   22.8   0.2       0.45   10.6   0.0    2.7  2  Limkain-b1    Limkain b1
     0.0018   18.3   0.8       0.67   10.0   0.2    3.6  3  RNA_bind      RNA binding domain
     0.0043   16.6   1.1      0.073   12.7   0.1    2.7  2  SET_assoc     Histone lysine methyltransferase SET associated
     0.0055   16.5   0.5        2.1    8.1   0.1    2.5  2  RRM_Rrp7      Rrp7 RRM-like N-terminal domain


Domain annotation for each model (and alignments):
>> RRM_1  RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.7   0.2   1.4e-17   2.8e-14       1      69 [.       4      74 ..       4      75 .. 0.96
   2 !   36.4   0.1   1.7e-12   3.3e-09       1      67 [.      86     147 ..      86     148 .. 0.90
   3 !   34.6   0.1   6.2e-12   1.2e-08       3      69 ..     175     233 ..     173     234 .. 0.90

  Alignments for each domain:
  == domain 1  score: 52.7 bits;  conditional E-value: 1.4e-17
                                       EEEESETTTSSHHHHHHHHHTTSCEEEEEEEEE..TTTSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEE CS
                              RRM_1  1 lfVgnLppdvteeeLkelFskfGpiksiklvrd..etgkskgfafVeFeskedAekAlealngkklggrel 69
                                       lfV+nLp ++t+ ++k++F  fGp ksik + +  +++++   af+e+ + +dA  A+++l +kk+ +r l
  gene2125|gene2125|rna2125|rna2125  4 LFVSNLPLNYTKTDIKQIFTAFGPLKSIKQYITpkKQESNIQSAFIEYVNNDDAVVAVKSLRNKKFYDRYL 74
                                       8****************************9999989999999************************99975 PP

  == domain 2  score: 36.4 bits;  conditional E-value: 1.7e-12
                                        EEEESETTTSSHHHHHHHHHTTSCEEEEEEEEETTTSEEEEEEEEESSHHHHHHHHHHHTTEEETTE CS
                              RRM_1   1 lfVgnLppdvteeeLkelFskfGpiksiklvrdetgkskgfafVeFeskedAekAlealngkklggr 67 
                                        l+VgnL   +t e+L+ +Fs++G+i  ++  ++     + +afV Fe+   Ae  +++   kk+gg+
  gene2125|gene2125|rna2125|rna2125  86 LYVGNLDDKITAEDLHSYFSDYGRIAAVQREKE-----NDYAFVVFEDAKVAEMLVNNHGVKKIGGN 147
                                        8************************88888886.....***************99995544888876 PP

  == domain 3  score: 34.6 bits;  conditional E-value: 6.2e-12
                                        EESETTTSSHHHHHHHHHTTSCEEEEEEEEETTTSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEE CS
                              RRM_1   3 VgnLppdvteeeLkelFskfGpiksiklvrdetgkskgfafVeFeskedAekAlealngkklggrel 69 
                                        V+n p++ t e+L ++F+++G +++i++ +       + afV F ++  A kA++  n+k+++gr+l
  gene2125|gene2125|rna2125|rna2125 175 VKNMPTT-TTEDLNAFFEDCGCVERIQMGS-------KKAFVVFRNELGALKAMKYKNKKEFNGRRL 233
                                        7777765.5578******************.......5***************************97 PP

>> RRM_occluded  Occluded RNA-recognition motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.2   0.0    0.0094        19       8      67 ..       8      73 ..       3      78 .. 0.71
   2 !   12.6   0.0   4.7e-05     0.093       6      51 ..      88     132 ..      84     139 .. 0.93
   3 !    8.1   0.0    0.0012       2.4       2      70 ..     171     235 ..     170     242 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0094
                       RRM_occluded  8 plsDtvnkariralveek......egeikkivLvpdheGAivefkdekiagkasLaLdgsefegkk 67
                                       +l+ + +k+ i+++++        ++ i+    +++ ++A++e+ ++ +a  a+ +L +++f ++ 
  gene2125|gene2125|rna2125|rna2125  8 NLPLNYTKTDIKQIFTAFgplksiKQYITPKKQESNIQSAFIEYVNNDDAVVAVKSLRNKKFYDRY 73
                                       566666788888888888333332233333345667799***********9999999999987765 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 4.7e-05
                       RRM_occluded   6 llplsDtvnkariralveekegeikkivLvpdheGAivefkdekia 51 
                                        + +l D+++ + + + ++++ g+i  ++ + ++  A+v+f+d+k a
  gene2125|gene2125|rna2125|rna2125  88 VGNLDDKITAEDLHSYFSDY-GRIAAVQREKENDYAFVVFEDAKVA 132
                                        669*****************.**********************987 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.0012
                       RRM_occluded   2 rtisllplsDtvnkariralveekegeikkivLvpdheGAivefkdekiagkasLaLdgsefegkklrc 70 
                                        r++++ +++ t +++ ++a++e+  g +++i++ +++  A+v+f++e  a ka+   + +ef+g++l +
  gene2125|gene2125|rna2125|rna2125 171 RSVCVKNMPTT-TTEDLNAFFEDC-GCVERIQMGSKK--AFVVFRNELGALKAMKYKNKKEFNGRRLAV 235
                                        77888888855.56789*******.*******99887..9*************999999******9975 PP

>> RRM_7  RNA recognition motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.0   0.00015       0.3       2      29 ..       2      29 ..       1      76 [. 0.77
   2 !   11.5   0.0   0.00012      0.24       3      74 ..      85     143 ..      83     168 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00015
                              RRM_7  2 rkvFvGGlPiDiteeelkatfkefgkvl 29
                                        k+Fv  lP + t++++k+ f +fg+++
  gene2125|gene2125|rna2125|rna2125  2 AKLFVSNLPLNYTKTDIKQIFTAFGPLK 29
                                       599**********************986 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00012
                              RRM_7   3 kvFvGGlPiDiteeelkatfkefgkvlvdwPkkaeskkkaaenskaakgyvflvfedeksvkaLleacteee 74 
                                        k++vG l   it e+l++ f+ +g+++         +      ++ ++ y+f+vfed k  + L+++   ++
  gene2125|gene2125|rna2125|rna2125  85 KLYVGNLDDKITAEDLHSYFSDYGRIAA-------VQ------REKENDYAFVVFEDAKVAEMLVNNHGVKK 143
                                        8889999999999999999999988753.......11......1223579********99999999865554 PP

>> Nup35_RRM_2  Nup53/35/40-type RNA recognition motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0      0.12   2.5e+02      30      53 .]      33      61 ..      16      61 .. 0.74
   2 !   10.6   0.1   0.00022      0.43      16      51 ..      99     134 ..      93     135 .. 0.88
   3 !   11.9   0.0   8.9e-05      0.18       2      52 ..     171     219 ..     170     228 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.12
                        Nup35_RRM_2 30 hyvp.....kevsvmyvkfesekdaekAL 53
                                       +y++     ++  ++++++ + +da  A+
  gene2125|gene2125|rna2125|rna2125 33 QYITpkkqeSNIQSAFIEYVNNDDAVVAV 61
                                       55556666677889**********98886 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00022
                        Nup35_RRM_2  16 lVlehFasfGeIvkhyvpkevsvmyvkfesekdaek 51 
                                        +   +F ++G+I     +ke  +++v fe+ k ae+
  gene2125|gene2125|rna2125|rna2125  99 DLHSYFSDYGRIAAVQREKENDYAFVVFEDAKVAEM 134
                                        5556**************************999885 PP

  == domain 3  score: 11.9 bits;  conditional E-value: 8.9e-05
                        Nup35_RRM_2   2 twvaVsGydtelielVlehFasfGeIvkhyvpkevsvmyvkfesekdaekA 52 
                                        + v+V   +t + e+  ++F+++G + ++ ++  +  ++v f++e  a kA
  gene2125|gene2125|rna2125|rna2125 171 RSVCVKNMPTTTTEDLNAFFEDCGCVERIQMG--SKKAFVVFRNELGALKA 219
                                        6789999999999999***************7..56677778899999998 PP

>> RRM_3  RNA binding motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0     0.013        26      13      60 ..      13      67 ..       4      81 .. 0.73
   2 !   14.0   0.1     2e-05      0.04       9      58 ..      91     140 ..      86     165 .. 0.86
   3 ?    3.8   0.1     0.028        57      11      60 ..     179     226 ..     172     242 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.013
                                       --HHHHHHHCHCCS...-E.CEEEE-TTSS...EEEEEESSHHHHHHHHHHHHHC CS
                              RRM_3 13 lsredikellsklg...ev.ayvdyekgdk...egevrFkedeeakkalekatea 60
                                        ++ dik+++ ++g   ++ +y+  +k ++   ++ + + ++++a  a++++ ++
  gene2125|gene2125|rna2125|rna2125 13 YTKTDIKQIFTAFGplkSIkQYITPKKQESniqSAFIEYVNNDDAVVAVKSLRNK 67
                                       67899*********55533358887776651225778888888888888887766 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 2e-05
                                        -SSS--HHHHHHHCHCCS-ECEEEE-TTSSEEEEEESSHHHHHHHHHHHH CS
                              RRM_3   9 lnkelsredikellsklgevayvdyekgdkegevrFkedeeakkalekat 58 
                                        l+++++ ed++  +s +g +a v  ek++  + v F++++ a+ ++++  
  gene2125|gene2125|rna2125|rna2125  91 LDDKITAEDLHSYFSDYGRIAAVQREKENDYAFVVFEDAKVAEMLVNNHG 140
                                        678999*********************************99998888765 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.028
                                        SS--HHHHHHHCHCCS-ECEEEE-TTSSEEEEEESSHHHHHHHHHHHHHC CS
                              RRM_3  11 kelsredikellsklgevayvdyekgdkegevrFkedeeakkalekatea 60 
                                          ++ ed+  +++  g v+ +  + g k++ v F ++  a ka++   ++
  gene2125|gene2125|rna2125|rna2125 179 PTTTTEDLNAFFEDCGCVERI--QMGSKKAFVVFRNELGALKAMKYKNKK 226
                                        4566999999******99977..6799*********99999998766554 PP

>> Limkain-b1  Limkain b1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.0   0.00054       1.1       5      68 ..       4      71 ..       1      84 [. 0.81
   2 !   10.6   0.0   0.00022      0.45       6      74 ..     174     236 ..     167     244 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00054
                         Limkain-b1  5 lvvsnLPtnrdk.lkkaikn...rLrrLsdncGGkvlsisgksavlrfanqeaaeralkrleneDvfG 68
                                       l+vsnLP n  k   k i      L+ + +    k ++   +sa + + n++ a  a+k l n   + 
  gene2125|gene2125|rna2125|rna2125  4 LFVSNLPLNYTKtDIKQIFTafgPLKSIKQYITPKKQESNIQSAFIEYVNNDDAVVAVKSLRNKKFYD 71
                                       89******99975334443312258999999999****9**********************9998875 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00022
                         Limkain-b1   6 vvsnLPtnrdklkkaiknrLrrLsdncGG.kvlsisgksavlrfanqeaaeralkrleneDvfGnritvs 74 
                                         v+n+Pt          + L+ ++++cG    +++  k a + f+n+  a +a+k  +  +  G r++v 
  gene2125|gene2125|rna2125|rna2125 174 CVKNMPTTTT-------EDLNAFFEDCGCvERIQMGSKKAFVVFRNELGALKAMKYKNKKEFNGRRLAVE 236
                                        4556665554.......779999****9632345566789******************99999*999986 PP

>> RNA_bind  RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.2   0.00033      0.67      12      68 ..       5      70 ..       2      86 .. 0.70
   2 ?    2.9   0.0     0.058   1.2e+02      22      61 ..      97     138 ..      90     145 .. 0.72
   3 ?    0.6   0.0      0.29   5.8e+02      22      62 ..     183     223 ..     176     233 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00033
                                       EEEE--TT--HHHHHHHTTTSEEE.....EEEEE....ETTEEEEEEEEE-HHHHHHHHHTT-SS- CS
                           RNA_bind 12 fyvtFPkeWktsDivqlFspfGsv.....yvsWl....ddtsAfvaLhrrdqasvvlktlkkeasy 68
                                       f    P ++ ++Di q F +fG       y+       + +sAf+   + d a v++k+l +++ y
  gene2125|gene2125|rna2125|rna2125  5 FVSNLPLNYTKTDIKQIFTAFGPLksikqYITPKkqesNIQSAFIEYVNNDDAVVAVKSLRNKKFY 70
                                       4556899999************752222255433221144699**999999999999999776655 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.058
                                        HHHHHHHTTTSEEEE.EEEE.ETTEEEEEEEEE-HHHHHHHH CS
                           RNA_bind  22 tsDivqlFspfGsvy.vsWl.ddtsAfvaLhrrdqasvvlkt 61 
                                         +D+ + Fs +G +  v+   ++  Afv  +  + a++ +++
  gene2125|gene2125|rna2125|rna2125  97 AEDLHSYFSDYGRIAaVQREkENDYAFVVFEDAKVAEMLVNN 138
                                        5799********975244431455688888888777777665 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.29
                                        HHHHHHHTTTSEEEEEEEEETTEEEEEEEEE-HHHHHHHHH CS
                           RNA_bind  22 tsDivqlFspfGsvyvsWlddtsAfvaLhrrdqasvvlktl 62 
                                        t+D+   F+  G v    + +  Afv   +   a  ++k  
  gene2125|gene2125|rna2125|rna2125 183 TEDLNAFFEDCGCVERIQMGSKKAFVVFRNELGALKAMKYK 223
                                        67999999999999988899999999998887776666654 PP

>> SET_assoc  Histone lysine methyltransferase SET associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.1     0.086   1.7e+02      36      47 ..     122     133 ..      92     144 .. 0.64
   2 !   12.7   0.1   3.7e-05     0.073      11      65 ..     180     235 ..     171     236 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.086
                          SET_assoc  36 yYivFndskeAe 47 
                                         ++vF+d k Ae
  gene2125|gene2125|rna2125|rna2125 122 AFVVFEDAKVAE 133
                                        589***999887 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 3.7e-05
                          SET_assoc  11 kvtvedlkkrLkkye.weriledktGyYivFndskeAerCfraedgtklftyrmvm 65 
                                        ++t edl++ ++  + +eri ++ +  ++vF++   A ++++  +++++ + r+ +
  gene2125|gene2125|rna2125|rna2125 180 TTTTEDLNAFFEDCGcVERIQMGSKKAFVVFRNELGALKAMKYKNKKEFNGRRLAV 235
                                        3567899999998862589******************************9999876 PP

>> RRM_Rrp7  Rrp7 RRM-like N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.1    0.0011       2.1      43      83 ..       3      43 ..       1      62 [. 0.84
   2 !    6.3   0.0    0.0039       7.8      34      72 ..     159     200 ..     147     213 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0011
                           RRM_Rrp7 43 slFlvNlPiettletlkkffqkvalgatiesvvsslltdeq 83
                                        lF+ NlP++ t   +k+ f        i+++++ ++++++
  gene2125|gene2125|rna2125|rna2125  3 KLFVSNLPLNYTKTDIKQIFTAFGPLKSIKQYITPKKQESN 43
                                       59*******************99888888888777766654 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0039
                           RRM_Rrp7  34 knndee....ssrslFlvNlPiettletlkkffqkvalgatie 72 
                                        k +  +     +rs+ + N+P  tt+e l  ff++  +  +i+
  gene2125|gene2125|rna2125|rna2125 159 KTESRKrqipYNRSVCVKNMPT-TTTEDLNAFFEDCGCVERIQ 200
                                        444333334489*********6.55688******999888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       789  (0.0440069); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 1636.41
//
Query:       gene2126|gene2126|rna2126|rna2126  [L=133]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-11   45.2   3.0    3.6e-11   43.4   3.0    1.8  1  Tim17     Tim17/Tim22/Tim23/Pmp24 family


Domain annotation for each model (and alignments):
>> Tim17  Tim17/Tim22/Tim23/Pmp24 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.4   3.0     2e-15   3.6e-11      10     109 ..      28     119 ..      10     121 .. 0.84

  Alignments for each domain:
  == domain 1  score: 43.4 bits;  conditional E-value: 2e-15
                              Tim17  10 vlGallGavfglvkgsrradtpapskerlreglrsvgkrgpslGknfgvvgglysgiecaleklRgkediwnsvaA 85 
                                        v+  ++G vfg++ g+ ++           + ++ + + + s+Gk+f ++g++y+g e ++e +Rgk d++n + A
  gene2126|gene2126|rna2126|rna2126  28 VANGAKGYVFGTLVGLLNSR----------KSIKCTLSDMHSSGKRFMMLGMIYTGSEALIETVRGKRDPLNVLGA 93 
                                        55666667777777765544..........45566777889*********************************** PP

                              Tim17  86 GaltGall..ragpqaaavgaiggaa 109
                                         a++G+l+  r+g+ +++ ga+g+ +
  gene2126|gene2126|rna2126|rna2126  94 SAIAGGLVmsRNGLGKSVLGAVGFSV 119
                                        *******7577************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       279  (0.0155614); expected 358.6 (0.02)
Passed bias filter:                      243  (0.0135535); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 932.43
//
Query:       gene2127|gene2127|rna2127|rna2127  [L=234]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.1e-33  116.9   1.4    3.3e-28   99.0   0.0    2.3  2  Gti1_Pac2  Gti1/Pac2 family
  ------ inclusion threshold ------
       0.03   14.9   0.1      0.065   13.8   0.0    1.5  1  TMC        TMC domain


Domain annotation for each model (and alignments):
>> Gti1_Pac2  Gti1/Pac2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.0   0.0   3.7e-32   3.3e-28       3      98 ..      19     113 ..      17     126 .. 0.89
   2 !   20.0   0.9   6.6e-08   0.00059     134     181 .]     104     151 ..      99     151 .. 0.75

  Alignments for each domain:
  == domain 1  score: 99.0 bits;  conditional E-value: 3.7e-32
                                        ES---SHHHHHHHHHHHHTTSS---SS---HHHHHHHSSTTEEEEEEHHHH--SS---S--B---EEETTEEEEEB CS
                          Gti1_Pac2   3 kgyiettkdalllieavlegilkrvtrRlkekErkeliksGsvFvfeeeesgikRWTDGvsWSpSrilgnfLvYre 78 
                                        +gy++t  +a l+++av+ g++k    Rl+ kEr+  i+sG++++f+e++  + RWTDG +WSpS+ilg+fL+Y+e
  gene2127|gene2127|rna2127|rna2127  19 RGYLHTYDEAFLMVHAVRLGLIKPYRERLSLKERD-DIRSGNIYIFIEDKTLMMRWTDGRTWSPSKILGSFLLYKE 93 
                                        69*********************************.9*************************************** PP

                                        -------------------- CS
                          Gti1_Pac2  79 ldkkrakkkkkkkkkkskes 98 
                                        + k+ +k+++ k+++++ e+
  gene2127|gene2127|rna2127|rna2127  94 VPKNLTKNATMKNRRNKMER 113
                                        *8888777777666555444 PP

  == domain 2  score: 20.0 bits;  conditional E-value: 6.6e-08
                                        ---------------------------EEEEEEEEEETTTEEEEEEE- CS
                          Gti1_Pac2 134 skslekdserslvgsltdsykfkkdgLvKkTisvtlkgkelhlisYyk 181
                                         k++++++er  + +l ++ +  k  L KkTis+++ ++++h+i+Y++
  gene2127|gene2127|rna2127|rna2127 104 MKNRRNKMERLKCTPLEKQLQQDKFLLHKKTISLSYGRETYHIIAYFQ 151
                                        34455566666666777777666667********************95 PP

>> TMC  TMC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   7.3e-06     0.065      34      79 ..     110     155 ..      89     171 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 7.3e-06
                                TMC  34 llvrklssa.llkllgkqefdiaknvldlvynqtlvwlGlffsPlLp 79 
                                         + ++l+++ l+k+l++ +f ++k++++l y++  + + ++f P++ 
  gene2127|gene2127|rna2127|rna2127 110 KM-ERLKCTpLEKQLQQDKFLLHKKTISLSYGRETYHIIAYFQPIFD 155
                                        33.33344469*********************************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       583  (0.0325172); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1664.21
//
Query:       gene2128|gene2128|rna2128|rna2128  [L=152]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.3e-37  126.4   0.0    7.4e-37  126.1   0.0    1.0  1  UQ_con    Ubiquitin-conjugating enzyme


Domain annotation for each model (and alignments):
>> UQ_con  Ubiquitin-conjugating enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.1   0.0   4.1e-41   7.4e-37       1     138 [.       7     141 ..       7     143 .. 0.95

  Alignments for each domain:
  == domain 1  score: 126.1 bits;  conditional E-value: 4.1e-41
                                        HHHHHHHHHHHSTTTTEEEEEEETTEECEEEEEEEB.TTSTTTTEEEEEEEE--TTTTTS--EEEESST-SCTTBE CS
                             UQ_con   1 rlqkelkelakkkpsgisaklvddenlfewkvlikgpedtpYeggvFklelefpedYPlkpPkvkfvtkifHPnvd 76 
                                        rl  e ++l+k+++ ++ a ++++ ++++w++ + gp+  +Y+g ++ ++l+f ++YP+kpP+vkfv+++fHPnv+
  gene2128|gene2128|rna2128|rna2128   7 RLLAEQANLKKERKYMFFARPSSK-DATKWDCGFPGPDTPLYKGSYYLVSLSFGRTYPFKPPNVKFVHRVFHPNVY 81 
                                        677889999**************6.*************************************************** PP

                                        TTSBB-CGGGSTTT--TTSHHHHHHHHHHHHHHS--TTS-SSHHHHHHHHHTHHHHHHHHHH CS
                             UQ_con  77 ksGevcldiLkeekWspaltlesvllsiqsLlaepnpesplnkeaakllkkdreeykkkvke 138
                                         sG+vcldiL +  W+p+ t++s+l ++q+Ll +pn +sp+n  a + + +++  y+k+v++
  gene2128|gene2128|rna2128|rna2128  82 LSGDVCLDILGSG-WKPSFTVSSILCALQQLLITPNVNSPANGPATRAYGNKE-VYEKEVRK 141
                                        ***********55.***********************************9665.89999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       325  (0.0181271); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1108.59
//
Query:       gene2129|gene2129|rna2129|rna2129  [L=88]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.2e-14   51.1   0.4    1.1e-13   50.6   0.4    1.2  1  LSM       LSM domain
  ------ inclusion threshold ------
       0.15   11.9   0.5       0.45   10.4   0.5    1.8  1  DUF2642   Protein of unknown function (DUF2642)


Domain annotation for each model (and alignments):
>> LSM  LSM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.6   0.4   1.3e-17   1.1e-13       2      66 ..       6      64 ..       5      65 .. 0.94

  Alignments for each domain:
  == domain 1  score: 50.6 bits;  conditional E-value: 1.3e-17
                                       HHHHTTTSEEEEEETTSEEEEEEEEEEETTSEEEEEEEEEEETTETEEEEEEEEEEEGGGEEEEE CS
                                LSM  2 flkklinkkvtvelkngrelrGtLkgfDqfmNlvLedveetlkdkkekrklglvliRGnnivlis 66
                                       fl+ l+ k++t+e+k  + ++GtL+ +D+ mN+ L++++ ++      + ++ ++iRG+++++++
  gene2129|gene2129|rna2129|rna2129  6 FLRTLKTKRLTIETKEKTIIKGTLTKIDKKMNIYLTNATIHN------EPVDSYFIRGTQVRYVI 64
                                       899***********************************9865......568************98 PP

>> DUF2642  Protein of unknown function (DUF2642)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.5     5e-05      0.45      11      38 ..       4      32 ..       2      64 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 5e-05
                            DUF2642 11 yqtlqsllgqevvvqttrgsv.rGiLkdv 38
                                       +q l++l+ ++++++t++ ++ +G+L+++
  gene2129|gene2129|rna2129|rna2129  4 IQFLRTLKTKRLTIETKEKTIiKGTLTKI 32
                                       799*************999988****998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       651  (0.0363099); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.37
# Mc/sec: 705.42
//
Query:       gene213|gene213|rna213|rna213  [L=83]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (83 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       347  (0.0193541); expected 358.6 (0.02)
Passed bias filter:                      180  (0.0100396); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.28s 00:00:00.67 Elapsed: 00:00:00.44
# Mc/sec: 568.43
//
Query:       gene2130|gene2130|rna2130|rna2130  [L=56]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (56 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1037  (0.0578393); expected 358.6 (0.02)
Passed bias filter:                      252  (0.0140554); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.25s 00:00:00.60 Elapsed: 00:00:00.41
# Mc/sec: 410.40
//
Query:       gene2131|gene2131|rna2131|rna2131  [L=726]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.6e-79  265.9   0.0    4.3e-79  265.1   0.0    1.4  1  LNS2         LNS2 (Lipin/Ned1/Smp2)
    3.3e-06   27.0   0.5    9.2e-06   25.6   0.5    1.8  1  Lipin_N      lipin, N-terminal conserved region
  ------ inclusion threshold ------
      0.013   15.6   0.4       0.16   12.1   0.0    2.9  2  Hydrolase_6  Haloacid dehalogenase-like hydrolase
      0.041   13.8   0.2      0.084   12.8   0.2    1.4  1  HemS         Haemin-degrading HemS.ChuX domain


Domain annotation for each model (and alignments):
>> LNS2  LNS2 (Lipin/Ned1/Smp2)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  265.1   0.0   9.6e-83   4.3e-79       3     226 .]     487     705 ..     485     705 .. 0.98

  Alignments for each domain:
  == domain 1  score: 265.1 bits;  conditional E-value: 9.6e-83
                               LNS2   3 lrltseqlkslnLkeGkneieFsvttklqgtaeveakiylwksddkivisdidgtitksdvlGhilpllgkdwthk 78 
                                         +l+s++l++l+L+ G+n++e+++      ++++e ++ylw+++dk+++sdidgtitksd++Ghi++l+gkdwth 
  gene2131|gene2131|rna2131|rna2131 487 RNLSSHDLHKLHLQCGRNTLEYKLAG---VDRRIEVSVYLWNESDKVIVSDIDGTITKSDLWGHIYDLVGKDWTHG 559
                                        5799*******************997...8899******************************************* PP

                               LNS2  79 gvaklyskikengYkilylsaraigqaeltreylksveqdgvkLPkgPvllspdrllsalkreviekkpeefkiac 154
                                        gva l++ki +n+Y+i+yls+ra+ ++  tr+yl++++q+g++LP+gP++lsp+++ls+l+ ev +++++ fki+c
  gene2131|gene2131|rna2131|rna2131 560 GVAALFTKIVNNNYRIIYLSNRAMPMYFRTRRYLSKIKQNGCTLPDGPIVLSPKSVLSSLYTEV-RNQSHIFKIDC 634
                                        ****************************************************************.5999******* PP

                               LNS2 155 LkdikklfpeeknpfyagfGnritdvisYkavgvpksriftinpkgelkeellkklkssyeslselvdkiFP 226
                                        L++i++lf   ++pf+agfGnri+d +sYk +g+ ks if+i+++g++ e +++k++ sy +l+++ ++iFP
  gene2131|gene2131|rna2131|rna2131 635 LQQIERLFC-GRRPFFAGFGNRISDLLSYKVLGIAKSMIFIIDRDGSICEGMKRKVSASYLTLNHFANTIFP 705
                                        *********.899**********************************************************9 PP

>> Lipin_N  lipin, N-terminal conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.5     2e-09   9.2e-06      31      88 ..       1      54 [.       1      63 [. 0.90

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 2e-09
                            Lipin_N 31 vveqedgelkcspfhvrFgklkvlrskekvvdievNgeevdlkmklgeaGeafFveet 88
                                       vv++++gel+++ f+v F + ++       v ++vNg  +d+ m+++e G+ fF  + 
  gene2131|gene2131|rna2131|rna2131  1 VVKDRQGELRSTKFYVCFDQSHFN----SSVYLIVNGVVTDIVMEVDEMGHCFFQVDY 54
                                       89*****************98774....569***********************8776 PP

>> Hydrolase_6  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.4      0.31   1.4e+03      24      91 ..     155     224 ..     121     234 .. 0.67
   2 ?   12.1   0.0   3.6e-05      0.16       2      83 ..     532     629 ..     531     639 .. 0.71

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.31
                                        HHHHHTT-EEEEEE---SS-HHHHHHHH.HHTT----GGGEEEHHHHHHHHHHHH.SXXXEEEEESXHHH CS
                        Hydrolase_6  24 nalraagkpvvllTNnsskseeeyakkl.eklgvditeeqvvtsataaaeylkkr.kadkkvlvigeegl 91 
                                        n+ ++++  +   T ++++s ++ +  l +k+++ ++e++++   ++a + l  + ++++k+ ++ +e++
  gene2131|gene2131|rna2131|rna2131 155 NQAENNQLAIKTGTAKNTSSMDDAMLALhKKIQMRMNENNILEDNQCANNALDFKlEDEEKCIMTDSEDD 224
                                        4444444555555666666666666666577888888888888888888877765444555555555555 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 3.6e-05
                                        EEESTTTSE...........ETTE.E-TTHHHHHHHHHHTT-EEEEEE---S...S-HHHHHHHHHHTT----GGG CS
                        Hydrolase_6   2 lfDidGvLw...........rgdk.aipgaaealnalraagkpvvllTNnss...kseeeyakkleklgvditeeq 62 
                                        ++DidG++             g++    g+a +++ + ++++++++l+N++       + y+ k+++ g+ + +  
  gene2131|gene2131|rna2131|rna2131 532 VSDIDGTITksdlwghiydlVGKDwTHGGVAALFTKIVNNNYRIIYLSNRAMpmyFRTRRYLSKIKQNGCTLPDGP 607
                                        7888888885555555555435551567899999****************6522245699*************977 PP

                                        EEEHHHHH.HHHHHHHSXXXEE CS
                        Hydrolase_6  63 vvtsataa.aeylkkrkadkkv 83 
                                        +v s +++ + +  + ++++ +
  gene2131|gene2131|rna2131|rna2131 608 IVLSPKSVlSSLYTEVRNQSHI 629
                                        7766555404444444666655 PP

>> HemS  Haemin-degrading HemS.ChuX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.2   1.9e-05     0.084      35      79 ..     149     195 ..     121     200 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.9e-05
                               HemS  35 evmalvrN..egavqektGpvenlkesghwglvldedidLrlfldqw 79 
                                        ++  +++   +    +ktG+ +n++ +++++l+l ++i++r++++++
  gene2131|gene2131|rna2131|rna2131 149 KILEITNQaeNNQLAIKTGTAKNTSSMDDAMLALHKKIQMRMNENNI 195
                                        4444444311335689***************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (726 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1073  (0.0598472); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.66u 0.33s 00:00:00.99 Elapsed: 00:00:00.50
# Mc/sec: 4375.81
//
Query:       gene2132|gene2132|rna2132|rna2132  [L=142]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       605  (0.0337442); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 949.23
//
Query:       gene2133|gene2133|rna2133|rna2133  [L=100]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       465  (0.0259356); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.47
# Mc/sec: 641.32
//
Query:       gene2134|gene2134|rna2134|rna2134  [L=81]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.014   16.2   3.6       0.02   15.7   3.4    1.4  1  HKR_ArcB_TM   Histidine kinase receptor ArcB trans-membrane d
       0.22   10.8   5.9       0.26   10.5   5.9    1.0  1  Peptidase_U4  Sporulation factor SpoIIGA


Domain annotation for each model (and alignments):
>> HKR_ArcB_TM  Histidine kinase receptor ArcB trans-membrane domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.7   3.4   2.2e-06      0.02      13      58 ..      25      70 ..      12      75 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.2e-06
                        HKR_ArcB_TM 13 lvlllivlalliqillslllsgeveiedllrsilfgllsaPwvlYF 58
                                       +++ +++ +++ +i++ l+l ++v ++    +i+fg++s+ w+++ 
  gene2134|gene2134|rna2134|rna2134 25 FFFKMVAGSFIAEIVVYLVLVKDVGWVRAWCAIFFGVFSVGWMVFL 70
                                       667778889999*******************************985 PP

>> Peptidase_U4  Sporulation factor SpoIIGA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   5.9   2.9e-05      0.26       7      77 ..       3      69 ..       2      76 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 2.9e-05
                       Peptidase_U4  7 lflvNllmdyllLlltakllklkikklrlllaAllGalyvvlvlflpklesillsillkilvsllmv.liaf 77
                                       l+++Nll+d+l Lll++kl  +++  ++++++++++++ v lvl ++     ++  ++ i++ ++ v +++f
  gene2134|gene2134|rna2134|rna2134  3 LLCTNLLLDLLRLLLVKKL--KNTFFFKMVAGSFIAEIVVYLVL-VKD--VGWVRAWCAIFFGVFSVgWMVF 69
                                       789***************9..457899************76655.542..3577777777777777655544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (81 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       744  (0.041497); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.30s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 525.23
//
Query:       gene2135|gene2135|rna2135|rna2135  [L=54]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (54 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       338  (0.0188521); expected 358.6 (0.02)
Passed bias filter:                      213  (0.0118802); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.32u 0.22s 00:00:00.54 Elapsed: 00:00:00.37
# Mc/sec: 441.67
//
Query:       gene2136|gene2136|rna2136|rna2136  [L=253]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (253 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       637  (0.035529); expected 358.6 (0.02)
Passed bias filter:                      559  (0.0311785); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 1977.07
//
Query:       gene2137|gene2137|rna2137|rna2137  [L=199]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1293  (0.0721178); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1393.21
//
Query:       gene2138|gene2138|rna2138|rna2138  [L=227]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-76  256.2   0.5    1.8e-76  256.0   0.5    1.0  1  MICSWaP   Spore wall protein


Domain annotation for each model (and alignments):
>> MICSWaP  Spore wall protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  256.0   0.5     1e-80   1.8e-76       1     193 []      32     224 ..      32     224 .. 0.99

  Alignments for each domain:
  == domain 1  score: 256.0 bits;  conditional E-value: 1e-80
                            MICSWaP   1 vinvkvyiseevrekYsdkgedleskvqkvaeelekalNkslkksnkeiriefdievsleipneieldkCgksvse 76 
                                        v+++++yis+++r +Y ++++++e+ vq+va ele+alN +l+ks+++++i+f++++ +eip+eieldkC++++ e
  gene2138|gene2138|rna2138|rna2138  32 VVRFHFYISPYARARYINENRKVEDLVQFVAAELERALNLYLEKSDRPVNITFVPIFVREIPPEIELDKCDTNMLE 107
                                        699************************************************************************* PP

                            MICSWaP  77 laslLnnvnnadsatsiIllltCeselyeevfisrglevpyvtqklsiecstrtaiFvEpeedkllsalanAlLka 152
                                        la++Lnn+n ++s+tsiI++l+C+s++ye vfi+rg+evpy+t++ls++c+trt+iF+E+ee+k+l+al++A+++a
  gene2138|gene2138|rna2138|rna2138 108 LATTLNNFNLETSDTSIIAVLSCDSRPYEGVFITRGQEVPYITHSLSSQCTTRTLIFLEIEEHKFLAALSTAMIRA 183
                                        **************************************************************************** PP

                            MICSWaP 153 agvpvnnpvkleevdggddGvkinirinketieellesecf 193
                                        agv+v np+ +eev++gd+Gv+++ir+n+et+++++e++cf
  gene2138|gene2138|rna2138|rna2138 184 AGVDVLNPLLFEEVINGDAGVRYDIRVNNETMDKIKENMCF 224
                                        ****************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (227 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       380  (0.0211947); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1617.12
//
Query:       gene2139|gene2139|rna2139|rna2139  [L=399]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    6.8e-13   49.0   0.6    1.8e-12   47.7   0.1    2.0  2  PCI         PCI domain
    3.3e-11   43.5   2.7    8.4e-09   35.8   0.2    2.4  2  RPN6_N      26S proteasome regulatory subunit RPN6 N-terminal
  ------ inclusion threshold ------
      0.031   13.8   5.0      0.037   13.6   2.5    2.3  2  ComR_TPR    ComR tetratricopeptide
      0.062   12.9   0.1       0.14   11.7   0.1    1.6  1  DDRGK       DDRGK domain
      0.081   13.6   0.3         17    6.1   0.0    2.4  2  DUF2853     Protein of unknown function (DUF2853)
       0.17   11.6   0.1       0.68    9.7   0.1    2.0  1  Get5_C      Get5 C-terminal domain
       0.28   11.6   2.8        5.2    7.5   0.1    3.0  3  RasGEF_N_2  Rapamycin-insensitive companion of mTOR RasGEF_N 
        0.3   11.4   4.4         14    6.1   0.1    3.2  3  TPR_12      Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> PCI  PCI domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       4.5     1e+04      64      85 ..      18      39 ..      16      59 .. 0.58
   2 !   47.7   0.1   8.1e-16   1.8e-12       8     104 ..     276     371 ..     271     372 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 4.5
                                       HHHHHHHTSSHHHHHHHHHHHH CS
                                PCI 64 erlaklldlsvdevEkilvklI 85
                                       e++ +  ++++d+ E+ + ++ 
  gene2139|gene2139|rna2139|rna2139 18 ETILQSTHVNNDDKESAIYEMA 39
                                       5555555555555555555443 PP

  == domain 2  score: 47.7 bits;  conditional E-value: 8.1e-16
                                        HHHHHTSHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHCESEEEHHHHHHHHTSSHHHHHHHHHH CS
                                PCI   8 kalrsgnlsgfseelkdleeelladdglaqllesLekkvrerllrqvskiyssislerlaklldlsvdevEkilvk 83 
                                        ++ + ++lsg++++ +++  e ++d ++  +l +L + +   ++ +++++y ++s++ la++l ++v+ +E  l k
  gene2139|gene2139|rna2139|rna2139 276 ESCKQRDLSGYDRIIREN-YETIKDNFILSHLAYLNDLLLDSNILKLIEPYLNVSISYLAEQLSFPVSAIEAKLRK 350
                                        5667889***********.9******************************************************** PP

                                        HHHTTSSSEEEETTTTEEEEC CS
                                PCI  84 lIrdgeirakidqesgivvfk 104
                                        lI dg+i++ +d  +g++v+ 
  gene2139|gene2139|rna2139|rna2139 351 LILDGRINGILDYYTGTLVMY 371
                                        ******************996 PP

>> RPN6_N  26S proteasome regulatory subunit RPN6 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.8   0.2   3.8e-12   8.4e-09      18     114 ..      19     109 ..      13     111 .. 0.88
   2 !    7.6   0.2    0.0021       4.7      30      74 ..     122     172 ..     114     197 .. 0.78

  Alignments for each domain:
  == domain 1  score: 35.8 bits;  conditional E-value: 3.8e-12
                             RPN6_N  18 eilskkskedeealreqeqalleLgelyrdqkkaeeLaelikesrsflssiaKaKtaKlvrtLldlfskipnslel 93 
                                        +il++++ +      ++e+a++e++++  +++  ++Lael ++ r++ s+++ a+++K++++++ l+   p+  +l
  gene2139|gene2139|rna2139|rna2139  19 TILQSTHVN----NDDKESAIYEMARIIISEQFYDKLAELCQSLRKLWSNLTGARASKIMKRIVGLIP--PQDFNL 88 
                                        555555544....459***************************************************9..667777 PP

                             RPN6_N  94 qievlkesiewakeekriFLr 114
                                         +    ++iew+++e   +L+
  gene2139|gene2139|rna2139|rna2139  89 ALLFEAKMIEWCQKEELKYLK 109
                                        7777889************98 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0021
                             RPN6_N  30 alreqeqalleLgelyrdqkkaeeLaelik....esrsf..lssiaKaKta 74 
                                        ++re+e++l ++gel ++ kk ++ a+li+    es+++  ++++++aK++
  gene2139|gene2139|rna2139|rna2139 122 EIREYEKCLENIGELSTELKKMNDKANLITlyiyESKTYyeMQNMSRAKAS 172
                                        689************999998888888876333345554448888888875 PP

>> ComR_TPR  ComR tetratricopeptide
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.52   1.2e+03      32      43 ..      42      53 ..      18      58 .. 0.65
   2 ?   13.6   2.5   1.6e-05     0.037     125     209 ..      97     181 ..      88     195 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.52
                                       HHHHHTGGGS-H CS
                           ComR_TPR 32 eifekyydnLPe 43
                                        i e++yd+L e
  gene2139|gene2139|rna2139|rna2139 42 IISEQFYDKLAE 53
                                       467999999987 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 1.6e-05
                                        TTTS-GGGHHHHHH.HHHHHHHHHHHTT--TTHHHHHHHHHHHHHHHT--TTHHHHHHHHHHHHHHTS--HHHHHH CS
                           ComR_TPR 125 eesleeedlfllrd.vllsaltvllklkeyeklekllkvlnkimektqdfqkkpivlmlewKyylkvkkdiekAke 199
                                        +e+ ++e+l  l+  +l++ +++l ++ eyek+ + + +l + ++k++d  + + ++++e K y    +++++Ak 
  gene2139|gene2139|rna2139|rna2139  97 IEWCQKEELKYLKLfFLTKRVGMLYEIREYEKCLENIGELSTELKKMNDKANLITLYIYESKTYY-EMQNMSRAKA 171
                                        55666666655554156778999*****************************************9.6788999999 PP

                                        HHHHHHHHHH CS
                           ComR_TPR 200 lYqkAilfak 209
                                        + ++A ++a 
  gene2139|gene2139|rna2139|rna2139 172 SLTSARALAV 181
                                        9999988874 PP

>> DDRGK  DDRGK domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   6.4e-05      0.14      73     148 ..     292     362 ..     279     375 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 6.4e-05
                                        XXXXXXXXXXXXXXXXXXXXXXXXXXXHHHHHHHHHHH-SEE-HHHHHHHH-S-HHHHHHHHHHHHHHSSS-EEE- CS
                              DDRGK  73 eeyeklksefvveeegtekesaeeeeklleefinyikekKvvlleelavkfklktqevierikeLeeqgsltGvlD 148
                                        e+ye +k++f++ + +  ++   +     +++++ i+    v +  la +++   + +  ++++L  +g+++G+lD
  gene2139|gene2139|rna2139|rna2139 292 ENYETIKDNFILSHLAYLNDLLLD-----SNILKLIEPYLNVSISYLAEQLSFPVSAIEAKLRKLILDGRINGILD 362
                                        566666666666666655555444.....67778888888899********************************9 PP

>> DUF2853  Protein of unknown function (DUF2853)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.1     0.018        40      35      90 ..      94     153 ..      89     161 .. 0.75
   2 ?    6.1   0.0    0.0076        17      19      77 ..     267     325 ..     252     329 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.018
                                        CCB--TT-HHHHHHHHHHIIIIIT--....-SSHHHHHHHHHHHHHH-TT-S--BHHHHH CS
                            DUF2853  35 aslVsasdksElervrenflkkkLgl....kdsdeldaaikevlekmgksnrnkyRavvY 90 
                                        a+++   +k+El+  +  fl+k+ g+    ++ +++ + i e  ++++k n +   +++Y
  gene2139|gene2139|rna2139|rna2139  94 AKMIEWCQKEELKYLKLFFLTKRVGMlyeiREYEKCLENIGELSTELKKMNDKANLITLY 153
                                        56677789*****************86554566667778888888888877544444444 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0076
                                        HHHHHHHHGCGGCSCCCCB--TT-HHHHHHHHHHIIIIIT---SSHHHHHHHHHHHHHH CS
                            DUF2853  19 lekvvkglgpaiynaDaslVsasdksElervrenflkkkLglkdsdeldaaikevlekm 77 
                                        + k+   lg + +++D s      ++  e++++nf+  +L+  ++  ld+ i + +e +
  gene2139|gene2139|rna2139|rna2139 267 IIKILVRLGESCKQRDLSGYDRIIRENYETIKDNFILSHLAYLNDLLLDSNILKLIEPY 325
                                        6678888888888888777777778999*************9999999*9999999876 PP

>> Get5_C  Get5 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.1    0.0003      0.68       6      16 ..     247     257 ..     247     274 .. 0.92

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0003
                             Get5_C   6 WndIeaLLknk 16 
                                        Wn+I aLLknk
  gene2139|gene2139|rna2139|rna2139 247 WNEINALLKNK 257
                                        **********8 PP

>> RasGEF_N_2  Rapamycin-insensitive companion of mTOR RasGEF_N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.1     0.075   1.7e+02      16      97 ..      30     110 ..      19     111 .. 0.69
   2 ?    7.5   0.1    0.0023       5.2      26      69 ..     117     160 ..     113     174 .. 0.87
   3 ?   -1.0   0.0         1   2.3e+03      21      52 ..     188     221 ..     181     256 .. 0.67

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.075
                         RasGEF_N_2  16 dqsrevvaaaleiLeeacddkeslevlvelkpslqhl.geigslLllkllst..ssGfkylqelnfveeeldkWie 88 
                                        d+++++ ++a  i+ e  +dk  +e + +l++  + l g ++s ++ ++     ++ f++       e ++ +W +
  gene2139|gene2139|rna2139|rna2139  30 DKESAIYEMARIIISEQFYDK-LAELCQSLRKLWSNLtGARASKIMKRIVGLipPQDFNLA---LLFEAKMIEWCQ 101
                                        667777777777777777775.556666666666667677788887777554225555533...577899999999 PP

                         RasGEF_N_2  89 kkneeYvkl 97 
                                        k++ +Y+kl
  gene2139|gene2139|rna2139|rna2139 102 KEELKYLKL 110
                                        999999876 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0023
                         RasGEF_N_2  26 leiLeeacddkeslevlvelkpslqhlgeigslLllkllstssG 69 
                                        + +L+e+ + +++le + el ++l++++++++l+ l ++++++ 
  gene2139|gene2139|rna2139|rna2139 117 VGMLYEIREYEKCLENIGELSTELKKMNDKANLITLYIYESKTY 160
                                        5689***9999****************999****9999988765 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 1
                         RasGEF_N_2  21 vvaaaleiLeea..cddkeslevlvelkpslqhl 52 
                                         ++a +e+L  +  c+d++++ ++ ++ ++l+  
  gene2139|gene2139|rna2139|rna2139 188 YIQAQIELLAGMylCEDRQYASAFSNFMEALDGF 221
                                        5666777776655688888888888888887544 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.1      0.61   1.4e+03       8      33 ..      37      62 ..      31      70 .. 0.55
   2 ?    4.9   0.1     0.014        32      37      74 ..     142     179 ..     114     181 .. 0.78
   3 ?    6.1   0.1    0.0062        14       4      34 ..     192     222 ..     187     233 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.61
                             TPR_12  8 nlaavlrrlgrydeAlellekaleia 33
                                       ++a +    + yd+  el++  + ++
  gene2139|gene2139|rna2139|rna2139 37 EMARIIISEQFYDKLAELCQSLRKLW 62
                                       55555555555555555555555555 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.014
                             TPR_12  37 lGpdhpltattlrnLgrlyralgryeeAlelleealai 74 
                                           d+++++t ++  + +y+++ +   A + l+ a a+
  gene2139|gene2139|rna2139|rna2139 142 KMNDKANLITLYIYESKTYYEMQNMSRAKASLTSARAL 179
                                        557999**************************999987 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.0062
                             TPR_12   4 talnnlaavl.rrlgrydeAlellekaleiar 34 
                                        ++   la ++ ++  +y+ A++++ +al+ ++
  gene2139|gene2139|rna2139|rna2139 192 QIE-LLAGMYlCEDRQYASAFSNFMEALDGFN 222
                                        555.456666488899***********99775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (399 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       884  (0.0493056); expected 358.6 (0.02)
Passed bias filter:                      540  (0.0301188); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 2455.96
//
Query:       gene214|gene214|rna214|rna214  [L=639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-27   96.5   0.5    3.5e-27   95.3   0.0    1.9  2  PolyA_pol        Poly A polymerase head domain
    0.00027   20.6   0.3    0.00075   19.2   0.1    1.9  2  PolyA_pol_RNAbd  Probable RNA and SrmB- binding site of polym


Domain annotation for each model (and alignments):
>> PolyA_pol  Poly A polymerase head domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.3   0.0   3.9e-31   3.5e-27       2     126 .]      32     164 ..      31     164 .. 0.88
   2 ?   -3.5   0.2       1.4   1.3e+04      55      83 ..     404     432 ..     386     438 .. 0.65

  Alignments for each domain:
  == domain 1  score: 95.3 bits;  conditional E-value: 3.9e-31
                                    EEETHHHHHHHTT---CEEEEEEC.S-HHHHHHHHHHHHT-EEEEETTTTCCCC.EECCEEEEECCEECEEEEEE---SS CS
                      PolyA_pol   2 ylvGGaVRDlllgkepkDvDlatd.aapeelakllrkkvkeallsgeefqtiav.lekkqllevatfRlekdesdarnpe 79 
                                    +++GG+VRD+llgk ++D+D++++  ++  +a+ ++k +         ++ i++  ek+++le+a +R+e  + d+ + +
  gene214|gene214|rna214|rna214  32 RIAGGWVRDKLLGKLSNDIDITINrISGYAFASGMQKYYGM----TGSVGQIKAnPEKSKHLETAVMRIEGVFVDFLSLR 107
                                    79**********************55667777777777766....5555555550555567******************* PP

                                    HHH............HHHHHHCTSSBGGGS-EEECTTTCEE-TTS.HHHHHHTTEE- CS
                      PolyA_pol  80 sekste.........sleeDlkrRDftiNalaynlnkgkvlDlfg.GikdLkskvir 126
                                    +e++ +         s++eD+ rRD+tiN+l+yn+ +++v+D++g G++dL+++vir
  gene214|gene214|rna214|rna214 108 TEEYFDtripvvkscSAQEDAFRRDLTINSLFYNIVEQRVEDFTGkGLSDLEQGVIR 164
                                    ****999************************************************97 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 1.4
                                    EECCEEEEECCEECEEEEEE---SSHHH. CS
                      PolyA_pol  55 lekkqllevatfRlekdesdarnpeseks 83 
                                     +++q l + + R+e++ +  +n+e +k 
  gene214|gene214|rna214|rna214 404 TKNEQPLTIEKRRTEQSDEIIANREYVKG 432
                                    33444478888888887777777766665 PP

>> PolyA_pol_RNAbd  Probable RNA and SrmB- binding site of polymerase A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       0.6   5.4e+03       5      22 ..      12      29 ..      12      31 .. 0.83
   2 !   19.2   0.1   8.3e-08   0.00075       2      58 ..     192     251 ..     191     256 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.6
                PolyA_pol_RNAbd  5 epeTaaairklaplLkki 22
                                   e++++  i+ +a+ L+ i
  gene214|gene214|rna214|rna214 12 EEKILTKIKTYAHTLQGI 29
                                   6788999******99876 PP

  == domain 2  score: 19.2 bits;  conditional E-value: 8.3e-08
                PolyA_pol_RNAbd   2 FtIepeTaaairklap...lLkkispeRifeEllKlLlsghpeaglelLretgLlkylfP 58 
                                    F+I+ + + a++  +    l kkis eRi  E+ K+L ++h  ++++   ++ L   +f 
  gene214|gene214|rna214|rna214 192 FKIADDLFMAFQNEHVrtnLHKKISNERIGQEMYKILGYEHFIHAFKVITQCELVPAIFK 251
                                    6677777777766554454669********************************999995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (639 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       703  (0.0392102); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.69u 0.31s 00:00:01.00 Elapsed: 00:00:00.53
# Mc/sec: 3601.19
//
Query:       gene2140|gene2140|rna2140|rna2140  [L=36]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (36 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       291  (0.0162307); expected 358.6 (0.02)
Passed bias filter:                      215  (0.0119917); expected 358.6 (0.02)
Passed Vit filter:                         6  (0.000334653); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.25s 00:00:00.59 Elapsed: 00:00:00.41
# Mc/sec: 262.96
//
Query:       gene2141|gene2141|rna2141|rna2141  [L=441]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-85  287.3  11.8      9e-60  202.8   3.8    2.0  2  TRM       N2,N2-dimethylguanosine tRNA methyltransferase


Domain annotation for each model (and alignments):
>> TRM  N2,N2-dimethylguanosine tRNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.5   1.3   1.3e-29   2.4e-25       8     101 ..       8     101 ..       2     115 .. 0.89
   2 !  202.8   3.8     5e-64     9e-60      95     376 .]     128     401 ..     102     401 .. 0.91

  Alignments for each domain:
  == domain 1  score: 89.5 bits;  conditional E-value: 1.3e-29
                                        ----SS--TT--SS--GGGHHHHHHHHHH....HHHHHHHH-S-EEEEESS-TTSHHHHHHHHH-S-EEEEEEE-S CS
                                TRM   8 edkevtvskkeeVFYNPvqefnRDlsvlvir.qlellkkklgekikvldaLsasGlRaiRfalEvpgvkevlaNDi 82 
                                        e++ ++++ +++ FYNP+qe+nRD+sv++i+ +l++ + k + ++ +++ +sa+GlR+iR+a+E++++ ++++NDi
  gene2141|gene2141|rna2141|rna2141   8 ENS-SIIKVTHKAFYNPAQEINRDISVMAINaFLDISNFK-EDNFCIFECMSATGLRGIRYAKEITEKCAIFMNDI 81 
                                        333.667788899*****************9999999999.799******************************** PP

                                        -HHHHHHHHHHHHHTT--.G CS
                                TRM  83 sekAvelikeNvklneve.e 101
                                         + Av  ikeN k+ne+  +
  gene2141|gene2141|rna2141|rna2141  82 DSDAVREIKENLKINEIRyD 101
                                        ****************9853 PP

  == domain 2  score: 202.8 bits;  conditional E-value: 5e-64
                                        HHTT--.GGEEEE-S-HHHHHC--SS-EEEEEE--SS--GGGHHHHHHHEEEEEEEEEEE--HHHHTTSSHHHHHH CS
                                TRM  95 klneve.eivvineddAnvllaekkkrfdviDlDPfGspapfldsavqsvkekglLlvTaTDtavLaGaspekclr 169
                                        + +e + + v   ++d n ++a++   f+viD+DPfG  ++ l  + +s+k++gl+++TaTDtavL+ +  +kc+r
  gene2141|gene2141|rna2141|rna2141 128 QAKETNtNGVILLNSDCNSVMASNCLFFHVIDVDPFGHFTKNLPFVFKSIKNHGLVCLTATDTAVLCTN-RNKCIR 202
                                        344443344555666****************************************************65.689*** PP

                                        HHSSB---STTHHHHHHHHHHHHHHHHHHTTTEEEEEEEEEEETTEEEEEEEEEE-HHHHHHHHTTEEEEEEETTT CS
                                TRM 170 kYgavalkselcHEvalRillkavareaakYekavepllslsadfYvrvfvkvktgaakvkkvleklglvlhCsgC 245
                                        kY+    k  ++ E+alR  l+++ar a  Y+  ++pllsls+dfYvr+fv+v++ +  vk++l+++++ + C  C
  gene2141|gene2141|rna2141|rna2141 203 KYDVLIRKVPYYGEMALRAALSTTARIAGMYDCGITPLLSLSVDFYVRLFVRVERRTSSVKASLNECAYYFICG-C 277
                                        **********************************************************************9985.5 PP

                                        .--EEEE--GGG--SB-TTT-SBEEEEEEEE-S-S--HHHHHHHHHHHCT..-TTS-HHHHHHHHHHHHHHS--SS CS
                                TRM 246 .lseekvkglakfkaecehcgaklhlaGPlwlgplkdkefveevleeaekekeeelkkrvkklLklikeElldapl 320
                                          + e+ +  ++++  c+ c +kl l GPlw g+l+d+ f+ ++ +++e+       krv ++L+lik+E     +
  gene2141|gene2141|rna2141|rna2141 278 gYTIEHGSKNTEISLFCPVCHNKLLLCGPLWKGKLNDSVFLSKLDNRTES-------KRVSEILRLIKQE-NTCFG 345
                                        4555777777788899***************************9999988.......8************.89999 PP

                                        -EEHHHHHHHHT-SS---HHHHHHH....TT-EE-TTSTTEEE-SS-HHHHHHHHH CS
                                TRM 321 yydlsqlasvlklsvpplkkvvsalkelgfevsrtHakpkaikTnapleavvevlr 376
                                        +y++  ++s lk++  p  k+vs+l++ g +vs tH++ ++ikT+ ++++++e++r
  gene2141|gene2141|rna2141|rna2141 346 FYHVPTVCSLLKTECIPIVKLVSELLNRGKKVSFTHCRANSIKTDCQYKEITEIIR 401
                                        *****************************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (441 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       905  (0.0504769); expected 358.6 (0.02)
Passed bias filter:                      440  (0.0245412); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.24s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 3135.06
//
Query:       gene2142|gene2142|rna2142|rna2142  [L=776]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (776 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       704  (0.039266); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.63u 0.31s 00:00:00.94 Elapsed: 00:00:00.47
# Mc/sec: 5006.41
//
Query:       gene2143|gene2143|rna2143|rna2143  [L=179]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.9e-05   21.9   0.9    8.3e-05   21.8   0.4    1.3  1  MMM1      Maintenance of mitochondrial morphology protein 1


Domain annotation for each model (and alignments):
>> MMM1  Maintenance of mitochondrial morphology protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.4   4.6e-09   8.3e-05      91     174 ..      49     132 ..      29     156 .. 0.88

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 4.6e-09
                                        HTTT--TTTS--B--HHHHHHHHHHHHHHHH-TTHHHHHHHHHHHHHHGGCS-TTEEEEEEEEEE--S---EEEEE CS
                               MMM1  91 ektyYdveshqpesLDWfnvLiaqtiaqfreealekdnilksLnealnseelpdyldkikvteidlGedfPifsnc 166
                                        +k  +  + h++  + Wfnv i +   ++ +   +kd i + + + ln  ++ + + ++ v +++l  + Pi+  +
  gene2143|gene2143|rna2143|rna2143  49 QKDIFRQSVHTTKDVAWFNVWIQRHWYELAHSYAHKDRISRIILKKLNVLKRRKIVKDVIVENLELSVEAPIIESV 124
                                        78889999******************************************************************** PP

                                        EE.EE-TT CS
                               MMM1 167 riikeske 174
                                        r+++ s+ 
  gene2143|gene2143|rna2143|rna2143 125 RVLTPSQY 132
                                        **854443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (179 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       636  (0.0354733); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1219.21
//
Query:       gene2144|gene2144|rna2144|rna2144  [L=89]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.9e-07   29.0   0.1    2.6e-06   27.2   0.1    2.0  1  zf-CCCH       Zinc finger C-x8-C-x5-C-x3-H type (and similar)
    7.9e-07   28.8   6.8    7.9e-07   28.8   6.8    2.1  3  zf-C3HC4      Zinc finger, C3HC4 type (RING finger)
    9.9e-07   28.7   5.3    2.2e-06   27.6   5.3    1.7  1  zf-RING_UBOX  RING-type zinc-finger
    1.3e-06   28.2   7.0    1.3e-06   28.2   7.0    1.7  2  zf-C3HC4_3    Zinc finger, C3HC4 type (RING finger)
    1.9e-06   27.7   2.1    6.5e-06   26.0   2.1    2.0  1  zf_CCCH_4     Zinc finger domain
    5.5e-06   26.1   9.0    5.5e-06   26.1   9.0    1.8  2  zf-C3HC4_2    Zinc finger, C3HC4 type (RING finger)
    1.8e-05   24.6   9.6    4.5e-05   23.3   9.6    1.7  1  zf-RING_5     zinc-RING finger domain
      2e-05   24.8   7.8      2e-05   24.8   7.8    2.1  2  zf-RING_2     Ring finger domain
    0.00036   20.3   5.0    0.00036   20.3   5.0    1.7  2  Prok-RING_4   Prokaryotic RING finger family 4
    0.00066   19.8   8.6    0.00066   19.8   8.6    1.8  2  zf-C3HC4_4    zinc finger of C3HC4-type, RING
     0.0064   16.3   1.1     0.0064   16.3   1.1    2.2  3  zf-CCCH_4     CCCH-type zinc finger
  ------ inclusion threshold ------
      0.016   14.9   2.2      0.016   14.9   2.2    2.4  2  zf-RING_11    RING-like zinc finger
       0.19   11.1   4.2       0.23   10.8   4.2    1.1  1  EURL          EURL protein
       0.55   10.1  14.8        2.3    8.1   3.2    2.3  2  zf-RING_4     RING/Ubox like zinc-binding domain


Domain annotation for each model (and alignments):
>> zf-CCCH  Zinc finger C-x8-C-x5-C-x3-H type (and similar)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2   0.1     2e-09   2.6e-06       5      25 ..      10      30 ..       9      32 .. 0.95

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 2e-09
                                       CBCHHHHHS--TTGGG-SSBS CS
                            zf-CCCH  5 lCrffmrtGyCkyGdrCkFaH 25
                                        C+ f++tG+C+y d Ck+ H
  gene2144|gene2144|rna2144|rna2144 10 VCKEFKETGTCRYKDECKYLH 30
                                       5******************** PP

>> zf-C3HC4  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.3       2.3     3e+03       4      10 ..      11      17 ..       7      27 .. 0.51
   2 !   28.8   6.8   6.2e-10   7.9e-07       1      41 []      40      77 ..      40      77 .. 0.93
   3 ?    0.6   0.3       0.4   5.2e+02      21      28 ..      73      80 ..      72      83 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 2.3
                                       T-S--SS CS
                           zf-C3HC4  4 Cleeake 10
                                       C+e  ++
  gene2144|gene2144|rna2144|rna2144 11 CKEFKET 17
                                       4444333 PP

  == domain 2  score: 28.8 bits;  conditional E-value: 6.2e-10
                                       -TTT-S--SS-E.E-TTS--B-CHHHHHHHHCTSSB--TTT CS
                           zf-C3HC4  1 CpiCleeakepnelleCkHsfCskCirkilksrkkvkCPlC 41
                                       C iC +e++e++ + +C+H+fC kC  + ++  k+  C +C
  gene2144|gene2144|rna2144|rna2144 40 CMICRKEYEEKV-VADCGHTFCLKCAFTEYQ--KSDLCYKC 77
                                       ************.*************99999..77779988 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.4
                                       B-CHHHHH CS
                           zf-C3HC4 21 fCskCirk 28
                                       +C+kC  +
  gene2144|gene2144|rna2144|rna2144 73 LCYKCKIN 80
                                       79999765 PP

>> zf-RING_UBOX  RING-type zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   5.3   1.7e-09   2.2e-06       1      26 [.      40      67 ..      40      84 .. 0.78

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 1.7e-09
                       zf-RING_UBOX  1 CpIClelftdPlvl.pCGHtFCreCl..w 26
                                       C IC+ ++++  v+  CGHtFC +C   +
  gene2144|gene2144|rna2144|rna2144 40 CMICRKEYEEK-VVaDCGHTFCLKCAftE 67
                                       9*******888.6559*********9531 PP

>> zf-C3HC4_3  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.5       2.4   3.1e+03      28      28 ..      13      13 ..       6      28 .. 0.57
   2 !   28.2   7.0   9.8e-10   1.3e-06       2      44 ..      37      78 ..      36      82 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 2.4
                                       H CS
                         zf-C3HC4_3 28 e 28
                                       e
  gene2144|gene2144|rna2144|rna2144 13 E 13
                                       2 PP

  == domain 2  score: 28.2 bits;  conditional E-value: 9.8e-10
                                       GSB-TTTSSSBS-EEETTEEEEEE-HHHHHHHHHTT-B-TTT- CS
                         zf-C3HC4_3  2 deeCviClerprnvvllpCgHlvlCeeCaekllkrkkkCpiCr 44
                                       d +C+iC ++ ++ v+ +CgH+ +C +Ca +  ++++ C  C+
  gene2144|gene2144|rna2144|rna2144 37 DVLCMICRKEYEEKVVADCGHT-FCLKCAFTEYQKSDLCYKCK 78
                                       789*******************.*******9999********8 PP

>> zf_CCCH_4  Zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   2.1   5.1e-09   6.5e-06       1      19 []      11      30 ..      11      30 .. 0.99

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 5.1e-09
                          zf_CCCH_4  1 Ckfflq.GtCkkGdkCrFaH 19
                                       Ck f++ GtC++ d C+++H
  gene2144|gene2144|rna2144|rna2144 11 CKEFKEtGTCRYKDECKYLH 30
                                       ******************** PP

>> zf-C3HC4_2  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.2       1.9   2.4e+03       4      12 ..      10      18 ..       9      28 .. 0.54
   2 !   26.1   9.0   4.3e-09   5.5e-06       2      40 .]      40      77 ..      39      77 .. 0.95

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.9
                         zf-C3HC4_2  4 iCldmlkdp 12
                                       +C ++ +++
  gene2144|gene2144|rna2144|rna2144 10 VCKEFKETG 18
                                       566655544 PP

  == domain 2  score: 26.1 bits;  conditional E-value: 4.3e-09
                         zf-C3HC4_2  2 CpiCldmlkdpsvvtpCgHvfCqkCilrsLeekneCPlC 40
                                       C iC  ++++  vv+ CgH+fC kC  +  ++++ C +C
  gene2144|gene2144|rna2144|rna2144 40 CMICRKEYEEK-VVADCGHTFCLKCAFTEYQKSDLCYKC 77
                                       *********96.****************99******888 PP

>> zf-RING_5  zinc-RING finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   9.6   3.5e-08   4.5e-05       2      43 ..      40      78 ..      39      79 .. 0.94

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 3.5e-08
                          zf-RING_5  2 CnkCfeklskeekfyltsCgHifCekClkkllekeavCpiCr 43
                                       C +C++++   e+ ++  CgH+fC kC+ ++ +k++ C  C+
  gene2144|gene2144|rna2144|rna2144 40 CMICRKEY---EEKVVADCGHTFCLKCAFTEYQKSDLCYKCK 78
                                       99******...777899**************99********7 PP

>> zf-RING_2  Ring finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.3      0.28   3.6e+02       5      23 ..      10      28 ..       9      35 .. 0.67
   2 !   24.8   7.8   1.6e-08     2e-05       3      44 .]      40      78 ..      39      78 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.28
                          zf-RING_2  5 ICleelssadsvl.llpCgH 23
                                       +C +e++++ +++ +++C++
  gene2144|gene2144|rna2144|rna2144 10 VC-KEFKETGTCRyKDECKY 28
                                       68.78888777773447973 PP

  == domain 2  score: 24.8 bits;  conditional E-value: 1.6e-08
                          zf-RING_2  3 CpICleelssadsvlllpCgHvfhreClerwlrssstCPlCr 44
                                       C+IC +e++  ++v+++ CgH+f+ +C+ +  ++s  C  C+
  gene2144|gene2144|rna2144|rna2144 40 CMICRKEYE--EKVVAD-CGHTFCLKCAFTEYQKSDLCYKCK 78
                                       *****9996..788887.*********7554666666*9996 PP

>> Prok-RING_4  Prokaryotic RING finger family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       3.7   4.7e+03      19      23 ..       9      13 ..       6      17 .. 0.74
   2 !   20.3   5.0   2.8e-07   0.00036       1      36 [.      40      77 ..      40      84 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 3.7
                        Prok-RING_4 19 lvCke 23
                                       lvCke
  gene2144|gene2144|rna2144|rna2144  9 LVCKE 13
                                       57875 PP

  == domain 2  score: 20.3 bits;  conditional E-value: 2.8e-07
                        Prok-RING_4  1 CvlCgeqekkailepCgHlvCkeC.fdskdls.sCPlC 36
                                       C++C+++ ++ +++ CgH +C +C f + + s  C  C
  gene2144|gene2144|rna2144|rna2144 40 CMICRKEYEEKVVADCGHTFCLKCaFTEYQKSdLCYKC 77
                                       ************************44444555455444 PP

>> zf-C3HC4_4  zinc finger of C3HC4-type, RING
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       6.7   8.5e+03       3       5 ..      10      12 ..       3      17 .. 0.62
   2 !   19.8   8.6   5.1e-07   0.00066       1      42 []      40      77 ..      40      79 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 6.7
                         zf-C3HC4_4  3 iCl 5 
                                       +C 
  gene2144|gene2144|rna2144|rna2144 10 VCK 12
                                       333 PP

  == domain 2  score: 19.8 bits;  conditional E-value: 5.1e-07
                         zf-C3HC4_4  1 CPiCldYLekPvsleCGhsfClsCisslqkepdgeqllCplC 42
                                       C iC++  e+ v  +CGh+fCl+C +   +++d     C+ C
  gene2144|gene2144|rna2144|rna2144 40 CMICRKEYEEKVVADCGHTFCLKCAFTEYQKSDL----CYKC 77
                                       99***999****************9887777754....4444 PP

>> zf-CCCH_4  CCCH-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   1.1     5e-06    0.0064       2      21 ..      10      30 ..      10      30 .. 0.98
   2 ?   -3.4   0.1       7.4   9.5e+03       3       4 ..      43      44 ..      42      45 .. 0.56
   3 ?   -3.4   0.1       7.2   9.2e+03      16      19 ..      62      65 ..      62      65 .. 0.47

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 5e-06
                          zf-CCCH_4  2 lCpyfa.kGsCrfGdnCrFsH 21
                                       +C++f  +G Cr+ d C+++H
  gene2144|gene2144|rna2144|rna2144 10 VCKEFKeTGTCRYKDECKYLH 30
                                       7******************** PP

  == domain 2  score: -3.4 bits;  conditional E-value: 7.4
                          zf-CCCH_4  3 Cp 4 
                                       C+
  gene2144|gene2144|rna2144|rna2144 43 CR 44
                                       55 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 7.2
                          zf-CCCH_4 16 nCrF 19
                                       +C F
  gene2144|gene2144|rna2144|rna2144 62 KCAF 65
                                       5654 PP

>> zf-RING_11  RING-like zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.2      0.78     1e+03       8      21 ..      13      27 ..      10      31 .. 0.66
   2 ?   14.9   2.2   1.2e-05     0.016       2      28 ..      40      63 ..      40      64 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.78
                         zf-RING_11  8 efk.pgqalfilpCs 21
                                       efk  g +++  +C+
  gene2144|gene2144|rna2144|rna2144 13 EFKeTGTCRYKDECK 27
                                       455368888888886 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 1.2e-05
                         zf-RING_11  2 CsICLeefkpgqalfilpCsHtFHfkC 28
                                       C+IC  e+++    +++ C+HtF +kC
  gene2144|gene2144|rna2144|rna2144 40 CMICRKEYEE---KVVADCGHTFCLKC 63
                                       99**999955...7899******9999 PP

>> EURL  EURL protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   4.2   0.00018      0.23       8      50 ..      30      74 ..      22      82 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00018
                               EURL  8 vsidlnddnicsvcklgtdketlsfch..vcfelnieGvpksdll 50
                                         id++dd +c +c+ + +++ ++ c    c++ +     ksdl 
  gene2144|gene2144|rna2144|rna2144 30 HIIDVDDDVLCMICRKEYEEKVVADCGhtFCLKCAFTEYQKSDLC 74
                                       358********************9995124666666777777775 PP

>> zf-RING_4  RING/Ubox like zinc-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   3.2    0.0018       2.3      19      48 .]      19      48 ..       8      48 .. 0.88
   2 ?    7.6   3.9    0.0025       3.1      19      44 ..      54      78 ..      51      82 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0018
                          zf-RING_4 19 eCgyqiClfCyhrileeeegrCPaCreeYk 48
                                       +C+y+  + ++h i  + +  C  Cr+eY+
  gene2144|gene2144|rna2144|rna2144 19 TCRYKDECKYLHIIDVDDDVLCMICRKEYE 48
                                       699998888888888899***********6 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0025
                          zf-RING_4 19 eCgyqiClfCyhrileeeegrCPaCr 44
                                       +Cg+ +Cl C      +++  C +C+
  gene2144|gene2144|rna2144|rna2144 54 DCGHTFCLKCAFTEY-QKSDLCYKCK 78
                                       6*********65444.5799*****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       825  (0.0460148); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.43
# Mc/sec: 624.66
//
Query:       gene2145|gene2145|rna2145|rna2145  [L=118]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
       0.02   15.2   6.6       0.03   14.7   6.6    1.3  1  zf-RING_2   Ring finger domain
       0.32   10.9   5.9       0.58   10.1   5.9    1.5  1  zf-C3HC4_3  Zinc finger, C3HC4 type (RING finger)
        1.3    9.0   8.3        2.1    8.3   8.3    1.4  1  zf-C3HC4_2  Zinc finger, C3HC4 type (RING finger)


Domain annotation for each model (and alignments):
>> zf-RING_2  Ring finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   6.6     5e-06      0.03       2      43 ..      69     107 ..      68     108 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 5e-06
                          zf-RING_2   2 eCpICleelssadsvlllpCgHvfhreCler.wlrssstCPlC 43 
                                        +C +C    +s++++ ++ C+H  +  C+ + ++++ ++CP+C
  gene2145|gene2145|rna2145|rna2145  69 QCHLCG---TSSHTLYRM-CQHPLDIPCAIKlYVTNGKKCPFC 107
                                        8999*6...455566678.*********98835777777**** PP

>> zf-C3HC4_3  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   5.9   9.8e-05      0.58       3      45 ..      68     109 ..      66     111 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 9.8e-05
                                        SB-TTTSSSBS-EEETTEEEEEE-HHHHHHHHH.TT-B-TTT-- CS
                         zf-C3HC4_3   3 eeCviClerprnvvllpCgHlvlCeeCaekllk.rkkkCpiCrr 45 
                                        e+C +C ++ + +++  C+H  l   Ca kl   + kkCp+C +
  gene2145|gene2145|rna2145|rna2145  68 EQCHLCGTS-SHTLYRMCQHP-LDIPCAIKLYVtNGKKCPFCDK 109
                                        689999976.4566778****.*********889********75 PP

>> zf-C3HC4_2  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   8.3   0.00035       2.1       1      40 []      69     107 ..      69     107 .. 0.91

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00035
                         zf-C3HC4_2   1 kCpiCldmlkdpsvvtpCgHvfCqkCilr.sLeekneCPlC 40 
                                        +C++C  +  +      C+H     C  + + +++++CP C
  gene2145|gene2145|rna2145|rna2145  69 QCHLCGTSSHT--LYRMCQHPLDIPCAIKlYVTNGKKCPFC 107
                                        79999998885..8899************8999999***** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       676  (0.0377043); expected 358.6 (0.02)
Passed bias filter:                      503  (0.0280551); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 791.71
//
Query:       gene2146|gene2146|rna2146|rna2146  [L=330]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.049   13.5   0.0       0.14   12.1   0.0    1.7  1  HSBP1     Heat shock factor binding protein 1


Domain annotation for each model (and alignments):
>> HSBP1  Heat shock factor binding protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   7.7e-06      0.14       6      41 ..     211     246 ..     209     247 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 7.7e-06
                              HSBP1   6 vVenlLqqlqdkFqtmsdqilsriDdMssriDdLEk 41 
                                        vV+nl   l++ F+t+  qi + ++ M + i +L +
  gene2146|gene2146|rna2146|rna2146 211 VVHNLVLSLKTYFDTLGCQIYEDMEAMHRAIQELGQ 246
                                        89*****************************99966 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (330 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       889  (0.0495845); expected 358.6 (0.02)
Passed bias filter:                      562  (0.0313459); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.24s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 2334.28
//
Query:       gene2147|gene2147|rna2147|rna2147  [L=169]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0014   18.4   0.4     0.0023   17.7   0.2    1.5  1  NIF       NLI interacting factor-like phosphatase


Domain annotation for each model (and alignments):
>> NIF  NLI interacting factor-like phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.2   1.3e-07    0.0023      25      76 ..     103     160 ..      57     167 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.3e-07
                                NIF  25 e....gekvevsvlkRpgldefLkelsklyevvi..fTasseeyaeavidildpekkl 76 
                                        +    +e++++ v++ p+ + fL+++ kl e  i  fT++ ++++++v+++ ++++kl
  gene2147|gene2147|rna2147|rna2147 103 RdwlrNENTQYKVIRVPFTKLFLEKIIKLSEFHIpnFTSEEKNTIKEVLNYDNQKNKL 160
                                        1445588899999999*************9999999*************997776664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (169 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       700  (0.0390429); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.21s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1277.72
//
Query:       gene2148|gene2148|rna2148|rna2148  [L=314]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.9e-63  213.1   0.0    5.6e-63  212.9   0.0    1.0  1  Dus       Dihydrouridine synthase (Dus)
  ------ inclusion threshold ------
       0.12   11.7   0.0       0.18   11.1   0.0    1.2  1  ThiG      Thiazole biosynthesis protein ThiG
       0.14   11.8   0.8       0.49   10.1   0.2    2.1  2  VraX      Family of unknown function


Domain annotation for each model (and alignments):
>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  212.9   0.0   9.4e-67   5.6e-63       1     284 [.      12     283 ..      12     305 .. 0.87

  Alignments for each domain:
  == domain 1  score: 212.9 bits;  conditional E-value: 9.4e-67
                                        EE---TTTS-HHHHHHHHHTT-SSEEEEEEEE-SSS---HHHHHHH-GGGGGTSCEEEEEE-S-HHHHHHHHHHHH CS
                                Dus   1 llaPmagvtdlpfRelvrefgataLvvtemvtakaivreekvrirmlseeeeetplavQlggsdpallaeaAklva 76 
                                        +laPm   + l++R+l+r++g++ L++temv+++++++  k + r l++  ++ pl+vQ++g+dp ++ +aA+   
  gene2148|gene2148|rna2148|rna2148  12 VLAPMYKNCGLAYRTLSRKYGTD-LCYTEMVHTQKFLQT-KNKKRWLDDFVDS-PLIVQICGNDPCVMRKAAEYFT 84 
                                        59*********************.*************98.4455555555555.9******************987 PP

                                        HTT-SCEEEEESSTTEEETTEEEGGGGGGSHHHHHHHHHHHHCCSSS-EEEEEESESSTTTC.HHHHHHHHHHCT- CS
                                Dus  77 dlgadeIdlNvGCPskkvtrggaGaaLlrkpdlvaqivkavvkaveiPvtvkirigiddeeenalelakiveaaGa 152
                                           a +Id+N+GCP+  ++rg++Ga L  +++l  +i+k +   +e Pvt kiri+ dd+   ++++++++e +G+
  gene2148|gene2148|rna2148|rna2148  85 G--ALAIDVNFGCPQLIAKRGNYGAYLQDDWQLTSEILKSLS-SLEQPVTCKIRIFDDDKR--TIDYVRMIEMSGC 155
                                        5..9***********************************996.69***********99655..6************ PP

                                        SEEEEESSECCCTT-C..G--CHHHHHHHHH-SS-EEEESS--SHHHHHHHHHHH--SEEEESCHHCCSTTHHHHH CS
                                Dus 153 qaltvHgRtraqnyeg..tadweaIkevkqavsipviaNGdIkdaedaqaileetGadgvmigrgalgnPwlfaes 226
                                        ++l+vHgRtr+q+ +    a+w++Ik vk++++ipvi NG+I  ++d+ ++l+ t +dgvm+++  l+nP +f   
  gene2148|gene2148|rna2148|rna2148 156 KMLAVHGRTREQRGQNtgLANWNTIKLVKEHLTIPVISNGNILCRRDVIDCLNFTKCDGVMVAETHLYNPLIFS-- 229
                                        *************999889******************************************************8.. PP

                                        HHHHHSC------HHHHHHHHHHHHHHCHHTTCCCCCCHHHHHHHHHHHHHHTTTTCH CS
                                Dus 227 tavktgeaepapplaeeaeiveehlkkleeelgedkglrkirkhlawylkglkkaael 284
                                          vk++   +   l+e+++++ e  +  e +++  k l k++ ++  y  +++ka ++
  gene2148|gene2148|rna2148|rna2148 230 -DVKKS---SFEVLREYFDLCGEATPIYEIKSHTYKILHKAFDQYDIYKCKIQKAGTF 283
                                        .55553...3344677777777777777777777777777777777776666655554 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0     3e-05      0.18     155     204 ..     168     218 ..     137     222 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 3e-05
                                        TTS----S-HHHHHHHHHH-SS-BEEES---SHHHHHHHHHTT.-SEEEES CS
                               ThiG 155 iGsglGllnkealkiiieeakvPvivDAGigspsdaaqamelG.adavlln 204
                                         G + Gl+n +++k++ e++++Pvi +  i    d++  +++  +d+v+++
  gene2148|gene2148|rna2148|rna2148 168 RGQNTGLANWNTIKLVKEHLTIPVISNGNILCRRDVIDCLNFTkCDGVMVA 218
                                        599***********************************9997549999986 PP

>> VraX  Family of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.32   1.9e+03      35      48 ..     116     129 ..     110     131 .. 0.80
   2 ?   10.1   0.2   8.2e-05      0.49      10      40 ..     248     274 ..     240     276 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.32
                               VraX  35 ktEiykLLsLLenD 48 
                                          Ei k Ls Le+ 
  gene2148|gene2148|rna2148|rna2148 116 TSEILKSLSSLEQP 129
                                        579******99975 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 8.2e-05
                               VraX  10 nGaPvYEiitktFktitikcDetFnktEiyk 40 
                                        + +P+YEi  +t+k +      +F++++iyk
  gene2148|gene2148|rna2148|rna2148 248 EATPIYEIKSHTYKIL----HKAFDQYDIYK 274
                                        789***********76....46777888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (314 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       539  (0.030063); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 2278.84
//
Query:       gene2149|gene2149|rna2149|rna2149  [L=256]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.7e-32  111.3   0.0    8.1e-32  110.8   0.0    1.2  1  NIF3      NIF3 (NGG1p interacting factor 3)


Domain annotation for each model (and alignments):
>> NIF3  NIF3 (NGG1p interacting factor 3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.8   0.0   4.5e-36   8.1e-32       2     243 ..      22     239 ..      21     243 .. 0.88

  Alignments for each domain:
  == domain 1  score: 110.8 bits;  conditional E-value: 4.5e-36
                               NIF3   2 ivevleelaplelaeswDnvGlqvg.dpekevkkvllaldlteevleeAiekgadliithHPlifkplkrlteddy 76 
                                        i+ ++++l pl++a swDnvG+++  + e++ kk ll++d+t++vl e iek++  +i++HP++f   ++      
  gene2149|gene2149|rna2149|rna2149  22 ILPFFQRLSPLSNAASWDNVGILIPsNIENNDKKYLLTIDFTPQVLRECIEKNIKKVISYHPVLFDAQRN------ 91 
                                        667899******************988899***********************************55444...... PP

                               NIF3  77 kkrllkkliknnislysaHtnlDaapgGvndwlakalglekieplepskeekkeeeeglgrigeleepvsleelak 152
                                        ++   + +i+n+is++s+Ht+lD++   +n +l  +lg  +ie  +            +  ig+  +   ++++++
  gene2149|gene2149|rna2149|rna2149  92 VSLFTAAIIENRISVFSPHTALDNV---MNRTLLSRLGCFDIETAD------------YMAIGNNGK--RMRDIID 150
                                        45568999****************9...5********988877655............456777665..899**** PP

                               NIF3 153 klkkklglekvrva....gdldkkvkkvaicaGsGaslieeakakgaDlliTGelkhhealdakekgiavidvgHy 224
                                         lk  ++++++r+a      +d+    ++   GsG   +      +  ++iTGe++hh+++++k+ + ++++v+H 
  gene2149|gene2149|rna2149|rna2149 151 LLKMTCNVKEIRLAlsdiHRMDSIPPYIYASVGSGR--F---SGGENSIIITGEMSHHNIMKLKKFN-TIMLVEHC 220
                                        **************877557788888**********..3...555667***************9998.99****** PP

                               NIF3 225 atErvflealaelLkeklk 243
                                        ++Er fl++l+  +++ ++
  gene2149|gene2149|rna2149|rna2149 221 RSERWFLNHLKVMMEDSIP 239
                                        **********998887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       547  (0.0305092); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 1599.50
//
Query:       gene215|gene215|rna215|rna215  [L=259]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.21   11.8   0.7       0.58   10.4   0.1    2.0  2  CotJB     CotJB protein


Domain annotation for each model (and alignments):
>> CotJB  CotJB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0      0.27   4.8e+03      46      55 ..     101     110 ..      85     122 .. 0.58
   2 ?   10.4   0.1   3.3e-05      0.58      19      59 ..     210     250 ..     208     253 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.27
                          CotJB  46 keYeekygPL 55 
                                    +++ e+y+ L
  gene215|gene215|rna215|rna215 101 RKFVENYEQL 110
                                    3444444444 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 3.3e-05
                          CotJB  19 LYLDthPddkealelfnkyskkrkelkkeYeekygPLtldg 59 
                                    L L+t  ++++a e+ +k  kk  ++kk+Yee   +Lt++g
  gene215|gene215|rna215|rna215 210 LQLNTKRKEEKANEKCKKKIKKICKAKKDYEELAFALTTFG 250
                                    5699999******************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2424  (0.1352); expected 358.6 (0.02)
Passed bias filter:                      860  (0.047967); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 1704.00
//
Query:       gene2150|gene2150|rna2150|rna2150  [L=262]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0034   17.2   0.3     0.0034   17.2   0.3    1.7  2  UPF0254   Uncharacterised protein family (UPF0254)


Domain annotation for each model (and alignments):
>> UPF0254  Uncharacterised protein family (UPF0254)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.3   1.9e-07    0.0034      44     148 ..       3     102 ..       1     118 [. 0.80
   2 ?   -3.2   0.1      0.35   6.2e+03      79      86 ..     229     236 ..     210     253 .. 0.46

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.9e-07
                                        EEEEEEEE--SHHHHHHHHT------..SSESSSEE-BHHHHHHHHHHHHHHHHHHHT-SEEEEEE-SEES-EEEE CS
                            UPF0254  44 vsvvaalFiPtlsgvksllkielPlepkelikgiKvYneeeDkevallmakavkkitnadigigttAGiGrGaiai 119
                                        v ++  +Fi   ++ +++ ++ +P+++++  ++i+  +ee   ++     + +  + n + +i  t  +G G+++i
  gene2150|gene2150|rna2150|rna2150   3 VGLLRKMFINCRKACRKIANFVAPSNNNK--DDIRSSEEE---RIVQRSKERIVGKRNREKSINKTESMGAGSVVI 73 
                                        6677889***************9999665..888765544...344555677778889999*************** PP

                                        E-SS-EEEE--S--EETTTT..TTHHHHH CS
                            UPF0254 120 vtdkkellttsdveadlrksdaeeilkRq 148
                                         +d ++++  s+ ++dlr + a + +k +
  gene2150|gene2150|rna2150|rna2150  74 DSDISSMSGISESKSDLRDERAAKTKKIK 102
                                        *****************998776554433 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 0.35
                                        E-BHHHHH CS
                            UPF0254  79 vYneeeDk 86 
                                         Y++ +++
  gene2150|gene2150|rna2150|rna2150 229 NYENSGEQ 236
                                        33332221 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (262 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2026  (0.113001); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 1948.95
//
Query:       gene2151|gene2151|rna2151|rna2151  [L=68]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.8e-08   33.1   0.4    5.9e-08   32.8   0.4    1.1  1  Glutaredoxin   Glutaredoxin
  ------ inclusion threshold ------
      0.025   15.0   0.0      0.028   14.8   0.0    1.1  1  GST_N_3        Glutathione S-transferase, N-terminal domain
       0.11   12.2   0.0       0.13   12.1   0.0    1.1  1  Thioredoxin_9  Thioredoxin


Domain annotation for each model (and alignments):
>> Glutaredoxin  Glutaredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.8   0.4   9.9e-12   5.9e-08       8      60 .]       3      55 ..       1      55 [. 0.97

  Alignments for each domain:
  == domain 1  score: 32.8 bits;  conditional E-value: 9.9e-12
                                       SSHHHHHHHHHHHHTTGGEEEEEGCCSHHHHHHHHHHHTSSSSSEEEETTEEE CS
                       Glutaredoxin  8 tCpyCkkakrlLkelgvkfeeidvdkdeeireelkelsgvrtvPqvfidgkhv 60
                                        C++C+ a +l+ke+++++++     ++ + +e++++ g +t+P +f+dg ++
  gene2151|gene2151|rna2151|rna2151  3 DCEDCVEAHKLMKEKNIDVKCACTQTNPILIDEIEKKHGHKTFPIIFVDGTFI 55
                                       7*************************************************997 PP

>> GST_N_3  Glutathione S-transferase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   4.8e-06     0.028       5      56 ..       2      54 ..       1      60 [. 0.83

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 4.8e-06
                                       TTSHHHHHHHHHHHHHT--EEEE---TTTT..HHHHHHH-TT--SSEEETTS-E CS
                            GST_N_3  5 paSpyarrvrlaLnekglpvevvevtpgeh..deellaknplgkvPvLeddgea 56
                                       +++  + +++ +++ek+++v+   +t+++    +e+ +k++++++P++  dg+ 
  gene2151|gene2151|rna2151|rna2151  2 KDCEDCVEAHKLMKEKNIDVKC-ACTQTNPilIDEIEKKHGHKTFPIIFVDGTF 54
                                       678888889999*********8.677777667****************766665 PP

>> Thioredoxin_9  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   2.1e-05      0.13      64     103 ..      11      50 ..       2      59 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.1e-05
                                        HHHHHH-TTEEEEEE-HHHHHHHTTTTTT.-SS--SSEEEE CS
                      Thioredoxin_9  64 akiaelnpnievkillrdenlelmdqylt.ngaraiPtlii 103
                                        +k+++++ ni+vk    + n+ l+d+  +  g+++ P++++
  gene2151|gene2151|rna2151|rna2151  11 HKLMKEK-NIDVKCACTQTNPILIDEIEKkHGHKTFPIIFV 50 
                                        6777777.8*******************9899999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (68 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       641  (0.0357521); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.35u 0.28s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 499.37
//
Query:       gene2152|gene2152|rna2152|rna2152  [L=448]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.8e-13   49.2   0.0      8e-13   48.5   0.0    1.3  1  Diphthamide_syn  Putative diphthamide synthesis protein


Domain annotation for each model (and alignments):
>> Diphthamide_syn  Putative diphthamide synthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.5   0.0   4.5e-17     8e-13     181     302 ..     264     382 ..     244     383 .. 0.91

  Alignments for each domain:
  == domain 1  score: 48.5 bits;  conditional E-value: 4.5e-17
                    Diphthamide_syn 181 skklt.eesydakkllrrRyaaiekakdakkvGiivgtlgvqgrlelverlkkllkeagkksylvlvgelnpakLa 255
                                        ++ l+  e++d  k+l  R ++++kakd+  +Gi +   + +   e + ++++ l ++gkk+y+ +++ ++ ++L 
  gene2152|gene2152|rna2152|rna2152 264 KDALNiIEEFDRVKFLISRLSRVQKAKDSTIFGIYFTNFKLE---EFAYKIREYLISKGKKTYMYYLRDISYERLT 336
                                        5555546899999***********************999876...6899*************************** PP

                    Diphthamide_syn 256 nfaeidafVlvaCprlsiddgkeFekPvltpyElevalgerewteey 302
                                         ++ i+++V+v C  +++ d +  + P++ p+El++a+++ ew++ y
  gene2152|gene2152|rna2152|rna2152 337 CMDGIECVVIVDCHYHTLFDIS-ISIPIVVPFELNLAFDDGEWDGMY 382
                                        **99****************98.9*******************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (448 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       705  (0.0393218); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 3200.93
//
Query:       gene2153|gene2153|rna2153|rna2153  [L=236]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.4e-19   68.9   1.8    1.7e-18   66.7   2.4    1.8  2  DCP2             Dcp2, box A domain
    1.9e-11   44.1   0.0    3.6e-11   43.2   0.0    1.4  1  NUDIX            NUDIX domain
  ------ inclusion threshold ------
      0.041   14.0   0.1        1.2    9.3   0.1    2.3  2  Leuk-A4-hydro_C  Leukotriene A4 hydrolase, C-terminal


Domain annotation for each model (and alignments):
>> DCP2  Dcp2, box A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.7   2.4   2.8e-22   1.7e-18       1      83 []       5      79 ..       5      79 .. 0.94
   2 ?   -2.4   0.0         1     6e+03      10      30 ..     187     207 ..     181     208 .. 0.74

  Alignments for each domain:
  == domain 1  score: 66.7 bits;  conditional E-value: 2.8e-22
                                       HHHHHHHHHHTTTS-HHHHTSHHHHHHHHHHHHHHHHHTHHHHTTTS----HHHHHHHHHCCSCCCHHCCCHCHHHHH CS
                               DCP2  1 eiLddlavrFilnlpeeeleslerlffqleeAhWfYeDfvreknpklpslklkeFaeklfekcpllkklkedvdeile 78
                                       ++Ld+l+vrF++nlp+++ es+erlff lee hW+Y+Df+ ++n      ++++F+  ++++++    ++ ++d++l+
  gene2153|gene2153|rna2153|rna2153  5 DVLDELTVRFLMNLPKQDYESVERLFFILEEVHWYYIDFMADDN-----KTFRTFVIDILSHINY---TQVEIDQCLK 74
                                       69**************************************9977.....48***********976...5689****** PP

                                       HHHHH CS
                               DCP2 79 efkeY 83
                                        f eY
  gene2153|gene2153|rna2153|rna2153 75 AFGEY 79
                                       **999 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1
                                        HTTTS-HHHHTSHHHHHHHHH CS
                               DCP2  10 Filnlpeeeleslerlffqle 30 
                                         i+    ++l+++ +++f+++
  gene2153|gene2153|rna2153|rna2153 187 DIMGKGANDLKQVRNVYFKIK 207
                                        555666788899999999985 PP

>> NUDIX  NUDIX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.2   0.0     6e-15   3.6e-11       6     120 ..      86     192 ..      82     203 .. 0.79

  Alignments for each domain:
  == domain 1  score: 43.2 bits;  conditional E-value: 6e-15
                                        EEEEEEETTSE.EEEEEESSSSTTTEESSEEECBTTSHHHHHHHHHHHHHHSEEE.EEEEEEEEEEEEEEEEEEEE CS
                              NUDIX   6 vgvvllnekge.vLlvrrskkpfpgWelPgGkvepgEtpeeAArREleEEtGlea.ellellgrlhylapydgpyg 79 
                                         g++++n +   +Ll +   ++ + + +P Gk  ++Et +++A+RE+ EE+G++  + +  ++          + +
  gene2153|gene2153|rna2153|rna2153  86 YGALIFNAQMDhILLNKGC-SKRAQFLFPRGKKFMNETGAQCAIREVYEEIGYDIsDKISKVA----------IRP 150
                                        5889999997768888877.5555568**********999*************7778887777..........444 PP

                                        E.EEEEEEEEE.EEECSGCSSTSTTTEEEEEEEEHHHHHHHHT CS
                              NUDIX  80 d.eheilyvfl.eevegelepndenevsevrwvpleellkekl 120
                                        + e++ ly+ +  +v+ + e + +ne++++rwv++ ++   k+
  gene2153|gene2153|rna2153|rna2153 151 SgERYTLYLIFnVPVNTRFECQTRNEIAAIRWVSVRDI-MGKG 192
                                        4466666777779999999999***************9.3333 PP

>> Leuk-A4-hydro_C  Leukotriene A4 hydrolase, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.1    0.0002       1.2      32      83 ..      39      90 ..       8      97 .. 0.76
   2 ?    2.7   0.0     0.021   1.3e+02      50      82 ..     103     135 ..      91     149 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0002
                                       TIIIT---HHHHHHHHHHHHHTT-GGGHHHHHHHTTT---HHHHHHHHHHHH CS
                    Leuk-A4-hydro_C 32 YklseskNaeirlrwlqlalkakyeeavpevaeflgsqGrmkfvrplYraLn 83
                                       Y ++ + +    +r + + + ++++ +  e+ ++l+  G  k+ +p+Y aL+
  gene2153|gene2153|rna2153|rna2153 39 YYIDFMADDNKTFRTFVIDILSHINYTQVEIDQCLKAFGEYKYDVPVYGALI 90
                                       55677777778899999999*****************************996 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.021
                                        HHHTT-GGGHHHHHHHTTT---HHHHHHHHHHH CS
                    Leuk-A4-hydro_C  50 alkakyeeavpevaeflgsqGrmkfvrplYraL 82 
                                          +++++  +p+ ++f++++G +  +r +Y+++
  gene2153|gene2153|rna2153|rna2153 103 GCSKRAQFLFPRGKKFMNETGAQCAIREVYEEI 135
                                        5567778889999*****************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       538  (0.0300073); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1590.45
//
Query:       gene2154|gene2154|rna2154|rna2154  [L=262]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.16   11.8   0.5       0.32   10.9   0.5    1.4  1  DUF1461   Protein of unknown function (DUF1461)


Domain annotation for each model (and alignments):
>> DUF1461  Protein of unknown function (DUF1461)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.5   1.8e-05      0.32      25      65 ..     129     173 ..     123     190 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 1.8e-05
                            DUF1461  25 plyekeikklnvkest....gmskedllentdelidYlkgkkkek 65 
                                        ++ye   kk++  ++     g+++e+++++++elidY+ ++ ++k
  gene2154|gene2154|rna2154|rna2154 129 KIYERLWKKYQHGNQRvyvkGFTAEQIMYQMKELIDYVIEEVEQK 173
                                        456666666666553334459*****************9997776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (262 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3992  (0.222656); expected 358.6 (0.02)
Passed bias filter:                      530  (0.029561); expected 358.6 (0.02)
Passed Vit filter:                        95  (0.00529868); expected 17.9 (0.001)
Passed Fwd filter:                        28  (0.00156172); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.89u 0.37s 00:00:01.26 Elapsed: 00:00:00.57
# Mc/sec: 1378.89
//
Query:       gene2155|gene2155|rna2155|rna2155  [L=400]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
      0.018   15.6   3.6      0.045   14.3   2.1    2.3  2  ING         Inhibitor of growth proteins N-terminal histone-b
       0.82    9.7  11.1       0.19   11.8   1.2    2.9  2  DHR10       Designed helical repeat protein 10 domain
        2.2    8.3   8.4         16    5.6   8.2    2.5  2  TMF_DNA_bd  TATA element modulatory factor 1 DNA binding


Domain annotation for each model (and alignments):
>> ING  Inhibitor of growth proteins N-terminal histone-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.74   4.4e+03      79      99 ..     251     271 ..     245     272 .. 0.82
   2 ?   14.3   2.1   7.5e-06     0.045      16      82 ..     282     347 ..     277     357 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.74
                                        HHHHHHHHHHHHHHHHHHCTX CS
                                ING  79 laqqaldlvdkhlrrLdqdle 99 
                                        l+   +++++++++ L+ +l+
  gene2155|gene2155|rna2155|rna2155 251 LSYREYEMIERRISFLEDELR 271
                                        6667799******99998876 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 7.5e-06
                                        HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTS..S-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                                ING  16 lqrnltelreiDakvqellkeidskiekflkngslqknekeeelsriqeelkeaqelldeKiqlaqq 82 
                                        ++++l+ l+e+D k++ l+++i++   +   + +lq  + e+ l+r ++  ++ + ++deK++ ++ 
  gene2155|gene2155|rna2155|rna2155 282 TNHLLSALQEKDTKLSVLMDQINKLTVNEH-RYKLQITTLEKDLTRANDRANAFKVIADEKVHCTTM 347
                                        6899*******************9999998.789*****************************8865 PP

>> DHR10  Designed helical repeat protein 10 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   1.2   3.2e-05      0.19      49     104 ..     286     341 ..     280     345 .. 0.93
   2 ?    2.0   2.6     0.034     2e+02      77     110 ..     346     379 ..     340     382 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.2e-05
                              DHR10  49 lakleeakkklkelrdaleekeielrelerkeerlqrqlenaeeklerlreqaeek 104
                                        l +l+e + kl+ l+d++++++ + + ++ +++ l++ l +a+++ +  +  a+ek
  gene2155|gene2155|rna2155|rna2155 286 LSALQEKDTKLSVLMDQINKLTVNEHRYKLQITTLEKDLTRANDRANAFKVIADEK 341
                                        568999***************************************99999888887 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.034
                              DHR10  77 erkeerlqrqlenaeeklerlreqaeekreaaka 110
                                        +++ e l+ qle  + k +rlr   +ek+ +a++
  gene2155|gene2155|rna2155|rna2155 346 TMENESLRDQLEFERSKNARLRSVLKEKESDARK 379
                                        678899**********************999875 PP

>> TMF_DNA_bd  TATA element modulatory factor 1 DNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   8.2    0.0027        16       2      70 ..     284     356 ..     283     374 .. 0.90
   2 ?    1.2   0.9     0.061   3.7e+02      20      51 ..     348     379 ..     339     384 .. 0.70

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0027
                         TMF_DNA_bd   2 slekklkeKDeqIaqLmeEGekLskkelklnntikkLrkknkelekeikelk....kkleklekeleeleerl 70 
                                        +l+  l eKD ++  Lm    kL  +e++ + +i  L k++  ++   +  k    +k+   ++e e+l++ l
  gene2155|gene2155|rna2155|rna2155 284 HLLSALQEKDTKLSVLMDQINKLTVNEHRYKLQITTLEKDLTRANDRANAFKviadEKVHCTTMENESLRDQL 356
                                        567789*************************************999999988888888888888888888876 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.061
                         TMF_DNA_bd  20 EGekLskkelklnntikkLrkknkelekeike 51 
                                        E e L+++   ++ +  +Lr+ +ke e++ ++
  gene2155|gene2155|rna2155|rna2155 348 ENESLRDQLEFERSKNARLRSVLKEKESDARK 379
                                        66777777777777777777777777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (400 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1309  (0.0730102); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 2542.86
//
Query:       gene2156|gene2156|rna2156|rna2156  [L=34]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (34 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       168  (0.00937029); expected 358.6 (0.02)
Passed bias filter:                      135  (0.0075297); expected 358.6 (0.02)
Passed Vit filter:                         6  (0.000334653); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.28s 00:00:00.64 Elapsed: 00:00:00.44
# Mc/sec: 231.74
//
Query:       gene2157|gene2157|rna2157|rna2157  [L=236]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.5e-12   47.4   2.3    4.9e-12   45.8   2.3    1.9  1  Bromodomain  Bromodomain


Domain annotation for each model (and alignments):
>> Bromodomain  Bromodomain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.8   2.3   2.7e-16   4.9e-12      12      75 ..      43     103 ..      32     106 .. 0.87

  Alignments for each domain:
  == domain 1  score: 45.8 bits;  conditional E-value: 2.7e-16
                                        TCGGGGCSTT-GCCSTTHHHH.SS---HHHHHHHHHTT--SSHHHHHHHHHHHHHHHHHHSHTT CS
                        Bromodomain  12 klaepFlepvdpeefpdyyavikkPldLstIkkklesnkYksladfeadlkllfsNarkyngeg 75 
                                        + + pFl pv+++e  +yy++ik+P+dL+t+ k+++   +   + f++dl+l+++N+++yn eg
  gene2157|gene2157|rna2157|rna2157  43 PYSIPFLYPVKKKEAYNYYDIIKHPMDLQTMLKRAD---IYDEQSFRHDLNLIYTNCITYNIEG 103
                                        46789**************************88875...566678****************876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       606  (0.0338); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.30s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1553.25
//
Query:       gene2158|gene2158|rna2158|rna2158  [L=73]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (73 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       281  (0.0156729); expected 358.6 (0.02)
Passed bias filter:                      186  (0.0103743); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.44
# Mc/sec: 498.68
//
Query:       gene2159|gene2159|rna2159|rna2159  [L=252]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       783  (0.0436723); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1800.94
//
Query:       gene216|gene216|rna216|rna216  [L=653]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.022   14.7   0.4      0.046   13.6   0.4    1.5  1  TarH         Tar ligand binding domain homologue
       0.16   11.7   0.9       0.29   10.8   0.9    1.3  1  DUF3685      Protein of unknown function (DUF3685)


Domain annotation for each model (and alignments):
>> TarH  Tar ligand binding domain homologue
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.4   5.1e-06     0.046      36     107 ..     352     418 ..     349     441 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5.1e-06
                                    HHHHCHHHHHHH.HHHHHHHHHHHHHHHHHHHHHHHHHHHTTTSSSSSSHHHHHHHHHHHHHHHHHHHHHTS CS
                           TarH  36 sndalrevytnrlqqqaaLaearvsllqaRltLnragiaaladeaedakellaraeeslaqseeawkaYlal 107
                                    ++++ ++vy++ l+qq+ L++ ++++l   ++Lnr  i +l++  +++++    + e l+  e++++++l++
  gene216|gene216|rna216|rna216 352 TQSNKKTVYNDTLEQQEFLTSLKQTMLHKENALNR--IKVLLSSLKKTRK---YVTEDLKLFEDNFENFLKA 418
                                    788999*****************************..5555555554433...3445666666666666655 PP

>> DUF3685  Protein of unknown function (DUF3685)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.9   3.2e-05      0.29      56     138 ..     358     440 ..     350     446 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 3.2e-05
                        DUF3685  56 elLnelaeveelkqnlykkellstReierfRNelswkyrlekyieepkaifEsryellvlkekgieklsiyapReqeLeq 135
                                    ++ n   e++e+ ++l ++ l     ++r++  ls+ ++++ky++e  ++fE+++e +  ++++++ +  +a  + eL +
  gene216|gene216|rna216|rna216 358 TVYNDTLEQQEFLTSLKQTMLHKENALNRIKVLLSSLKKTRKYVTEDLKLFEDNFENFLKASAEVSDVLSNADISPELYK 437
                                    56677778888888888888888999*********************************999999999999998888888 PP

                        DUF3685 136 Leg 138
                                    ++ 
  gene216|gene216|rna216|rna216 438 IDM 440
                                    765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (653 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2001  (0.111607); expected 358.6 (0.02)
Passed bias filter:                      509  (0.0283898); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.83u 0.33s 00:00:01.15 Elapsed: 00:00:00.51
# Mc/sec: 3856.85
//
Query:       gene2160|gene2160|rna2160|rna2160  [L=378]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.1e-17   61.8   0.3    8.1e-17   61.8   0.3    3.8  2  CDP-OH_P_transf  CDP-alcohol phosphatidyltransferase


Domain annotation for each model (and alignments):
>> CDP-OH_P_transf  CDP-alcohol phosphatidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.8   0.3   4.5e-21   8.1e-17       2      66 .]      60     134 ..      59     134 .. 0.84
   2 ?  -10.4  15.1         1   1.8e+04      15      42 ..     321     360 ..     141     362 .. 0.69

  Alignments for each domain:
  == domain 1  score: 61.8 bits;  conditional E-value: 4.5e-21
                                        -HHHHHHHHHHHHHHHHHGGGS-H.............HHHHHHHHHHHHHTTHHHHHHHHTT---HHHHHHHHHHH CS
                    CDP-OH_P_transf   2 lPnaiTllrlllsvlailllltyyp...........lvlailllliasltDalDGklARrlnqvstlGkllDslaD 66 
                                        +Pn+iT+++++++v+a+  +++yy            +++ +++l+i++++Da+DGk+ARr+++ s lG+l+D+++D
  gene2160|gene2160|rna2160|rna2160  60 APNLITVFGFIFIVFACA-VNVYYDyemvgaapsfvYYTNAVCLFIYMMFDAVDGKQARRTKTGSPLGQLFDHGID 134
                                        8****************5.6666666*********955555555566666***********99999********99 PP

  == domain 2  score: -10.4 bits;  conditional E-value: 1
                                        HHHHHGGGS-H..HHHHHHH............HHHHHHTT CS
                    CDP-OH_P_transf  15 vlailllltyyplvlailll............liasltDa 42 
                                        ++a+++++ty+ ++l  l+l            +i  ++Da
  gene2160|gene2160|rna2160|rna2160 321 MFAFCVYFTYRDIYLYGLFLfafisaclivfgIINEICDA 360
                                        2333333333333333333322222222222236666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (378 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       795  (0.0443416); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.22s 00:00:00.71 Elapsed: 00:00:00.39
# Mc/sec: 2877.43
//
Query:       gene2161|gene2161|rna2161|rna2161  [L=779]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.8e-13   50.1   1.1    9.5e-13   48.4   0.0    2.3  2  HA2          Helicase associated domain (HA2)
    2.1e-11   44.0   0.2    6.6e-11   42.4   0.1    1.9  2  OB_NTP_bind  Oligonucleotide/oligosaccharide-binding (OB)-fol
    3.8e-11   43.3   0.5    3.8e-11   43.3   0.5    2.6  3  Helicase_C   Helicase conserved C-terminal domain
    9.7e-08   32.0   0.0    5.1e-07   29.6   0.0    2.3  1  DEAD         DEAD/DEAH box helicase
  ------ inclusion threshold ------
      0.013   15.5   1.0      0.013   15.5   1.0    3.9  3  ResIII       Type III restriction enzyme, res subunit
      0.013   15.7   0.0      0.041   14.1   0.0    1.8  1  AAA_22       AAA domain
      0.023   14.6   0.0      0.083   12.8   0.0    2.0  1  NACHT        NACHT domain
        2.6    7.3  13.8        1.6    8.0   5.0    2.3  2  DltD         DltD protein


Domain annotation for each model (and alignments):
>> HA2  Helicase associated domain (HA2)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.3      0.89     2e+03      78      92 ..      72      89 ..      37     104 .. 0.49
   2 !   48.4   0.0   4.2e-16   9.5e-13       4      72 ..     545     611 ..     542     685 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.89
                                HA2 78 e...eekakkkrkeeeka 92
                                       +   ++k++kk++e +  
  gene2161|gene2161|rna2161|rna2161 72 KrpkKKKSEKKKNEGKST 89
                                       122223333333333332 PP

  == domain 2  score: 48.4 bits;  conditional E-value: 4.2e-16
                                HA2   4 lLvalgALdeegnlTelGrkmaelPlsprlakmLlaaaeleegcldevitivAalsveeifleeneeek 72 
                                         L +lg++d++ ++T+lG+k+ ++Pl++ ++k+Ll a+++  g+++ev+ i+++lsv+++f +  e +k
  gene2161|gene2161|rna2161|rna2161 545 KLLKLGCIDKDSKITQLGEKIHKIPLKVEMSKTLLKAIDY--GVFEEVAIICSVLSVKKLFYDDLEVRK 611
                                        6899*********************************888..*******************98876654 PP

>> OB_NTP_bind  Oligonucleotide/oligosaccharide-binding (OB)-fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0         5   1.1e+04      43      79 ..     289     325 ..     284     327 .. 0.74
   2 !   42.4   0.1     3e-14   6.6e-11       3      79 ..     694     765 ..     692     767 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 5
                                        T...TSSSEEEEEEEEESSSEEEEEEEEE-HHHHHHH CS
                        OB_NTP_bind  43 nekekepewvvytelvettklylrdltaidpawLllf 79 
                                        +e+++e+++++++ l ++    +  ++ i++++L +f
  gene2161|gene2161|rna2161|rna2161 289 HERKMEYDFIISYFLCKNLSKLVLMSATINSDQLTNF 325
                                        5778899999999888886666667777888888776 PP

  == domain 2  score: 42.4 bits;  conditional E-value: 3e-14
                                        HHHHHHHTTCEEEEEETTCCEEETT.TCEEEEE-TTSTTTTT...TSSSEEEEEEEEESSSEEEEEEEEE-HHHHH CS
                        OB_NTP_bind   3 aillaGlypqiarkdpskkdyktar.tktrvfihpsSvlaknekekepewvvytelvettklylrdltaidpawLl 77 
                                        ++ + G++ +ia  ++ k+ y +   ++++  ihpsS l++    ke ++++y+ l+ t+  y+ ++++++p +Ll
  gene2161|gene2161|rna2161|rna2161 694 QAFCEGYLLNIA--KKYKNFYLCIFnENEKLKIHPSSSLFD----KEANLIFYERLQYTNSFYMVNCCKVQPSTLL 763
                                        88999*******..4455559999779*************8....******************************* PP

                                        HH CS
                        OB_NTP_bind  78 lf 79 
                                        +f
  gene2161|gene2161|rna2161|rna2161 764 EF 765
                                        98 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.2       2.8   6.3e+03      10      47 ..      20      54 ..      12      77 .. 0.62
   2 !   43.3   0.5   1.7e-14   3.8e-11      10     110 ..     360     480 ..     352     481 .. 0.82
   3 ?   -3.0   0.2         4   8.9e+03      16      50 ..     653     687 ..     643     697 .. 0.62

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 2.8
                                       HHHTTTTSEEEEEESSHHHHHHHHHHHHHTTSTEEEES CS
                         Helicase_C 10 lkleeeggkilifvntidrlekvklllekkgikvavlh 47
                                       l ++e+++k++  +++++ le  +++  +k+i+v +++
  gene2161|gene2161|rna2161|rna2161 20 L-SKEIKEKVIRLLKRKEFLEVENIV--SKKISVQIFN 54
                                       3.466777777777777755434555..3334444444 PP

  == domain 2  score: 43.3 bits;  conditional E-value: 1.7e-14
                                        H...HHTTTTSEEEEEESSHHHHHH.HHHHHHHT....TSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGT CS
                         Helicase_C  10 l...kleeeggkilifvntidrlek.vklllekk....gikvavlhgelpqnereeileqfnkgesdvLiatdvae 77 
                                        +    +e e+g+il+f++  +++    + ++  +      k+++l+++ + +e+  i+e+   ++++v+++t++ae
  gene2161|gene2161|rna2161|rna2161 360 IsviCNETENGDILVFLPGMSDILAiEQQIR--NtvvkIPKIIKLYASVSYKEQMSIFEKC--DNRKVILSTNIAE 431
                                        23336889*************6632334442..244645799*******************..4678********* PP

                                        SSSTSTTESEEEESSSSSSH................HHHHHHHTTSSST CS
                         Helicase_C  78 rGidipkvnlVinfdlprnv................tsyiqriGRtgRa 110
                                         +i+++++++Vi+ +l ++                 +++ qr+GR+gR+
  gene2161|gene2161|rna2161|rna2161 432 SSITVNNLTYVIDSGLVKKQflrgnaesleivriskSQADQRAGRVGRI 480
                                        *****************7755678888899999999************7 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 4
                                        TSEEEEEESSHH.HHHHHHHHHHHT.TSTEEEESTTS CS
                         Helicase_C  16 ggkilifvntid.rlekvklllekk.gikvavlhgel 50 
                                        ++++li +n+i  +l+  +++++ + ++k+ ++  ++
  gene2161|gene2161|rna2161|rna2161 653 KRQSLIEANKILdQLK--RMFKKDNeKVKISKIAKNI 687
                                        5666777777654554..7775555567776665554 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6   0.0   2.3e-10   5.1e-07       5     172 ..     178     321 ..     175     325 .. 0.78

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 2.3e-10
                                        HHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEE CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               DEAD   5 aeaiplilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvll 80 
                                        +e+i  i +++  ++++eTG GKT+     +l        k  +k++i  P r  a ++++++++ +    +++  
  gene2161|gene2161|rna2161|rna2161 178 DEIIRKIRENKISIIEGETGCGKTTQIPKMLL--------KYYKKIIISLPRRMAAINIARRVSEELC---VKLGD 242
                                        689999999***************99766666........55679******************99988...56666 PP

                                        EETTSSHHHHHHHHHTTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCTTS CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               DEAD  81 iiggvaardqlskldngvdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsdfinrilnqlpqitcdg 156
                                        +ig + +    s+ +n++++++ t g l   + + +  ++q  ++VlDE ++   +   dfi +    +    c+ 
  gene2161|gene2161|rna2161|rna2161 243 LIGYKVRF--DSNYNNKTRVLFVTDGILSLECLSDS--IKQYDVIVLDEFHERKME--YDFIIS---YF---LCKN 306
                                        67754443..3445578************9776566..9*************8887..444444...22...2332 PP

                                        TTTSEEEEEESSBS.HH CS
                                        xxxxxxxxxxxxxx.xx RF
                               DEAD 157 klqrqvivlSATlp.kd 172
                                         +  +++++SAT++ ++
  gene2161|gene2161|rna2161|rna2161 307 LS--KLVLMSATINsDQ 321
                                        33..49*******9444 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   1.8      0.95   2.1e+03      65     101 ..      58      94 ..      28     147 .. 0.65
   2 ?   15.5   1.0   5.8e-06     0.013       8     170 ..     177     318 ..     152     319 .. 0.76
   3 ?    0.6   0.2      0.23   5.1e+02      60      97 ..     657     704 ..     614     744 .. 0.65

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.95
                                        HHHHHHHHHGGGGTGG....GEEEESSS-B--..... CS
                             ResIII  65 slleqtleefkkflseaykeigkkvsgdkkkakekds 101
                                        ++++++ e+   +++ ++k++++k+++++k+ +ek+ 
  gene2161|gene2161|rna2161|rna2161  58 EITKKMNENADLLTKRPKKKKSEKKKNEGKSTTEKSV 94 
                                        5566666666666666655544444444444422222 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 5.8e-06
                                        HHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG... CS
                             ResIII   8 QeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkflseayk 83 
                                        + e+i+++      +++k  +i+ +TG+GKT  + k+  +++k     k+++  pr+       +++++ l  +  
  gene2161|gene2161|rna2161|rna2161 177 EDEIIRKI------RENKISIIEGETGCGKTTQIPKMLLKYYK-----KIIISLPRRMAAINIARRVSEELCVKLG 241
                                        33333333......6889999***********99999999999.....6888888876665566555555555443 PP

                                        ..GEEEESSS-B--.......-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.TTTHHHHHT-. CS
                             ResIII  84 e.igkkvsgdkkkakekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakkswreilekf. 157
                                        + ig kv+ d++ +     +++++l++t   l+ +         + + +++dvi+ DE H  +   ++  i+ +f 
  gene2161|gene2161|rna2161|rna2161 242 DlIGYKVRFDSNYN-----NKTRVLFVTDGILSLEC-------LSDSIKQYDVIVLDEFHERKM--EYDFIISYFl 303
                                        34676777666666.....89999999998888888.......8999*************9988..8999999986 PP

                                        .--.SEEEEEESS-S CS
                             ResIII 158 .ke.avllglTATpe 170
                                         k+ ++l+ ++AT++
  gene2161|gene2161|rna2161|rna2161 304 cKNlSKLVLMSATIN 318
                                        533588999999986 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.23
                                        EESSHHHHHHHHHHGGGGTGG.....GEEEESSS-B--.......... CS
                             ResIII  60 lvprkslleqtleefkkflseayke.igkkvsgdkkka.........k 97 
                                        l+  +++l+q+++ fkk  ++ + + i k+++ ++ ++          
  gene2161|gene2161|rna2161|rna2161 657 LIEANKILDQLKRMFKKDNEKVKISkIAKNINYERIIQafcegyllnI 704
                                        455566777777777666665542233333333333335555544443 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   1.8e-05     0.041       4     102 ..     186     290 ..     182     322 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.8e-05
                             AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelka......... 70 
                                        + +i ++ Ge+G+GKTt + ++l ++           + + + lp  +   +++r++ ++l ++l +         
  gene2161|gene2161|rna2161|rna2161 186 ENKISIIEGETGCGKTTQIPKMLLKY----------YKKIIISLPRRMAAINIARRVSEELCVKLGDligykvrfd 251
                                        67899********************8..........4445555555555555555555555555555555556668 PP

                             AAA_22  71 erlsseellealeqalrarav.......ielliiDEaqh 102
                                        ++ +++  +  +++ + +            ++++DE++ 
  gene2161|gene2161|rna2161|rna2161 252 SNYNNKTRVLFVTDGILSLEClsdsikqYDVIVLDEFHE 290
                                        444444444455555555555556777778888888886 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   3.7e-05     0.083       2     132 ..     189     322 ..     188     341 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.7e-05
                                        CEEEEC-TTTCHHHHHHHHHHHHCTS-SCCCC-SEEEEEETTTTTTS-...-HCHHHCCCCTS--SSS-CCHHHHC CS
                              NACHT   2 lvilqGeaGsGKTtLlqklalawaegklpqgafklvFflslrelsrsgnarsladllfsqlpepaapvsevwavll 77 
                                        ++i++Ge G+GKTt + k+ l+  ++          +    r++  ++ ar++ + l+ +l ++++   + +    
  gene2161|gene2161|rna2161|rna2161 189 ISIIEGETGCGKTTQIPKMLLKYYKKI---------IISLPRRMAAINIARRVSEELCVKLGDLIGYKVR-FDSNY 254
                                        579***********9999988654443.........3334566666777789999999999999999999.99999 PP

                                        CSCCCEEEEEE-STT-SS-TCH......................HHHHHCTTTTT--EEEEEEECCCH CS
                              NACHT  78 elperlLlilDglDelvtdlgq.............kekqpvrtlLselirkkllpeasllltvrpral 132
                                         +++r+L++ Dg+  l+   +              ++k + +  +s  + k+l + + + +t+ +++l
  gene2161|gene2161|rna2161|rna2161 255 NNKTRVLFVTDGILSLECLSDSikqydvivldefhERKMEYDFIISYFLCKNLSKLVLMSATINSDQL 322
                                        9**********986665543334457777777776666666666666666666666666666666665 PP

>> DltD  DltD protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   5.0   0.00072       1.6     123     214 ..      19     105 ..       5     118 .. 0.76
   2 ?    4.2   1.5      0.01        23     101     167 ..     637     707 ..     623     753 .. 0.58

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00072
                                        HHHHHHHHHHHHH.-TT-T...THHHHHHHHTT----HHHHHHHHHHHHHHHHHHHHHTTC-HHHHHTTTHCT.TS CS
                               DltD 123 etkryiakrllelekskkskeelkkllkkyangkklsklqklllkikkallekedklksklkkkekkiekkak.kl 197
                                         ++++i++++++l    k ke     ++++ ++k   ++ ++ll+i k++ e+ d l++++kkk+ + +kk++ k 
  gene2161|gene2161|rna2161|rna2161  19 HLSKEIKEKVIRL-L--KRKEF--LEVENIVSKKISVQIFNTLLEITKKMNENADLLTKRPKKKK-SEKKKNEgKS 88 
                                        5778888888888.2..22222..2346677778788899999******************9544.4455555599 PP

                                        -SS--HHHHHHHHHHHH CS
                               DltD 198 pkeidwdelrkkaekeg 214
                                        ++e ++de++ ka+ ++
  gene2161|gene2161|rna2161|rna2161  89 TTEKSVDEEDIKADDIE 105
                                        99999999999998776 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.01
                                        HHHHH--HHHHHHHHHH--.SSHHHHHHHHHHHHH.-TT-T...THHHHHHHHTT----HHHHHHH.....H CS
                               DltD 101 aFaanfselqaykllknpkiseetkryiakrllelekskkskeelkkllkkyangkklsklqklll.....k 167
                                        aF++nfs+     ++ + + s    ++i ++l+++ k++++k +++k++k+++ +  ++++ + +l     k
  gene2161|gene2161|rna2161|rna2161 637 AFQQNFSQDFCKMYYMKRQ-SLIEANKILDQLKRMFKKDNEKVKISKIAKNINYERIIQAFCEGYLlniakK 707
                                        5666666654444444444.5555555555555554444445555666666666666666555555444431 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (779 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1849  (0.103129); expected 358.6 (0.02)
Passed bias filter:                      575  (0.0320709); expected 358.6 (0.02)
Passed Vit filter:                        73  (0.00407162); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.80u 0.30s 00:00:01.10 Elapsed: 00:00:00.46
# Mc/sec: 5039.26
//
Query:       gene2162|gene2162|rna2162|rna2162  [L=342]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        1.4    9.3   7.1       0.35   11.2   0.6    3.0  3  PriX      Primase X


Domain annotation for each model (and alignments):
>> PriX  Primase X
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.6     2e-05      0.35      25      89 ..       3      68 ..       1      75 [. 0.89
   2 ?   -1.2   0.1      0.14   2.6e+03      28      55 ..     181     209 ..     175     218 .. 0.76
   3 ?   -0.2   0.1     0.073   1.3e+03      14      24 ..     276     286 ..     242     315 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 2e-05
                                       HHHHHHTS---HHHHH.HHHHHHH....TTSSSS---HHHHHHHHHHHHHHT-----HHHHHHH-H CS
                               PriX 25 srYLvnvkklseeeal.kklkeflksckkkknlskiyeswirsvikgvkekglkpislkklkekdk 89
                                        +YL+n  ++ ++++     ++f + c ++ + ++ y s + + ++  k+ +l ++s+k l++ + 
  gene2162|gene2162|rna2162|rna2162  3 EKYLINYLNITQDHVDpTDYDNFAEECIEYVKNNRKYISLVLESLNIFKNDELLSMSYKILRNTNG 68
                                       68********99998625689999999999999999*************************99875 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.14
                                        HHHTS---HHHHHHHHHHHH.....TTSS CS
                               PriX  28 Lvnvkklseeealkklkefl.ksckkkkn 55 
                                        + n+  l  e++ + + +f  +sck++ +
  gene2162|gene2162|rna2162|rna2162 181 VCNLFSLLVEKVQQAIAQFKgESCKQQIQ 209
                                        56777778888899999999899988755 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.073
                                        STHHHHHHHTH CS
                               PriX  14 DgRkrlilyvi 24 
                                        +g ++ i + +
  gene2162|gene2162|rna2162|rna2162 276 NGDEKKIKETL 286
                                        22222222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (342 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       940  (0.052429); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 2337.75
//
Query:       gene2163|gene2163|rna2163|rna2163  [L=416]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.4e-30  105.9   0.1    5.6e-30  104.7   0.1    1.7  1  eIF2A          Eukaryotic translation initiation factor eIF2A
    6.2e-05   22.2   3.9      0.031   13.3   0.0    3.1  3  Coatomer_WDAD  Coatomer WD associated region


Domain annotation for each model (and alignments):
>> eIF2A  Eukaryotic translation initiation factor eIF2A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.7   0.1   6.3e-34   5.6e-30       5     194 .]     193     373 ..     184     373 .. 0.93

  Alignments for each domain:
  == domain 1  score: 104.7 bits;  conditional E-value: 6.3e-34
                                        SECEEEEEE-TTTTEEEEEEE.E--TT-CEEEEEEEEEESSSTT--EEECCEESSS.EEEEEE-TTSS-EEEEESS CS
                              eIF2A   5 kadkvklkWnkkGtsllvlvstevdktnksyygetelyliklkkkksevvelkkegpihdvaWspkskefaviyGk 80 
                                        k+d +++  + kG+ ll+ +    +++  sy g++el l + ++k+ ++++++  +          +  +av++  
  gene2163|gene2163|rna2163|rna2163 193 KVDAIDVRNSPKGNFLLLCTI---KTKVGSYFGAKELILFDFNSKSYHMLDVSSPN-----YFTFIKGGYAVCHSS 260
                                        788888999999999998887...567789***************99999998885.....456678899****** PP

                                        SSCEEEEEECSCEEEEEEEEES--EEEE-TTSSEEEEE-TTSSS-EEEEEETTTTEEEEEEE-TT--EEEE-TTSS CS
                              eIF2A  81 mpakvslfdlkvkviskleeqkrNtiffspkgklvllaGfgnlaGeleiwdvkkkkkiakaeaanatlvewspdgr 156
                                        +p+ vs++d   k i ++ +  rN i+++ +g++v++aGf nl+G +ei+d ++ + i++++   a++vewsp+g+
  gene2163|gene2163|rna2163|rna2163 261 QPSVVSIYDYSRKEIRRFPKGIRNRIYYNGHGNIVCFAGFDNLSGMIEIYDAQTSNLISSLKMLGASVVEWSPCGS 336
                                        **************************************************************************** PP

                                        EEEEEE-TTT-SSS-EEEEEETTTEEEEEEE-TTEEEE CS
                              eIF2A 157 yvlTattaprlrvdngfkiwsysGklvykkefdelyqv 194
                                        y+l a t   l+vdn + i+ y G+ +++k+f +l +v
  gene2163|gene2163|rna2163|rna2163 337 YFLVAITN-ALKVDNKVVIYDYFGRKINEKHFGNLINV 373
                                        *******9.9**********************999876 PP

>> Coatomer_WDAD  Coatomer WD associated region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.4   0.2    0.0009         8     118     166 ..      35      83 ..      15     112 .. 0.79
   2 !    4.1   0.1    0.0023        20     113     180 ..     120     197 ..      93     229 .. 0.76
   3 !   13.3   0.0   3.5e-06     0.031      71     179 ..     244     364 ..     198     390 .. 0.72

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0009
                                        XXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                      Coatomer_WDAD 118 alLgvksegsvsfYDweqgklvrridvkkvknVvwsddgelvalvskdt 166
                                        ++L+  + + +++YD+e++  +++i ++ vk++ +s d   + ++ +++
  gene2163|gene2163|rna2163|rna2163  35 NILCYYTGTHLIVYDLEKEVELSKIVMERVKKIEVSTDCWSIGVLLQNK 83 
                                        6788888888***********************9999876666655544 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.0023
                                        XXXX.....XXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX........ CS
                      Coatomer_WDAD 113 kifg.....GalLgvksegsvsfYDweqgklvrridvkkvknVvwsddgelvalvskdtvyilsynleavee.... 179
                                        +if       +lL  ++++ + ++  e+ k+ ++ + k+vk+ ++   g+++a++ ++ ++++ +n++++ e    
  gene2163|gene2163|rna2163|rna2163 120 DIFDfkmsdCYLLARSNKD-LRVFKAENSKFSHEESYKNVKDFYVH--GTVIAILDENGFFTVYKNQKKFFElfle 192
                                        5665666655667666666.9999999999999999999**99998..89*****999999999999988777665 PP

                                        ..... CS
                      Coatomer_WDAD 180 ....e 180
                                             
  gene2163|gene2163|rna2163|rna2163 193 kvdaI 197
                                        43332 PP

  == domain 3  score: 13.3 bits;  conditional E-value: 3.5e-06
                                        XXXXXXXXXXXXXXXXX.XXXXXX.XXXXXXXXXXXXXXXXXXXXXX...XXXXXXXX....XX.XXXXXXXXXXX CS
                      Coatomer_WDAD  71 gldfvwvssnrfavles.sksvkifknfkekktksikleyqvdkifg...GalLgvks....egsvsfYDweqgkl 138
                                         + f++++ + +av  s + sv+ + +++ k+++++      ++i++   G++ +       +g++ +YD ++ +l
  gene2163|gene2163|rna2163|rna2163 244 PNYFTFIK-GGYAVCHSsQPSVVSIYDYSRKEIRRFPKGI-RNRIYYnghGNIVCFAGfdnlSGMIEIYDAQTSNL 317
                                        55566665.7788888754455444888888878888776.789999999999988653333679*********** PP

                                        XXXXXXXXXXXXXXXXXXXXXXXX......XXXXXXXXXXXXX.... CS
                      Coatomer_WDAD 139 vrridvkkvknVvwsddgelvalv......skdtvyilsynleavee 179
                                        ++++++   + V ws+ g+++ ++       +++v+i++y  ++++e
  gene2163|gene2163|rna2163|rna2163 318 ISSLKMLGASVVEWSPCGSYFLVAitnalkVDNKVVIYDYFGRKINE 364
                                        *******99*********98655533665558999999887665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (416 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       672  (0.0374812); expected 358.6 (0.02)
Passed bias filter:                      466  (0.0259914); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.34s 00:00:00.88 Elapsed: 00:00:00.48
# Mc/sec: 2631.31
//
Query:       gene2164|gene2164|rna2164|rna2164  [L=25]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (25 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       119  (0.00663729); expected 358.6 (0.02)
Passed bias filter:                      107  (0.00596798); expected 358.6 (0.02)
Passed Vit filter:                         3  (0.000167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.29s 00:00:00.63 Elapsed: 00:00:00.43
# Mc/sec: 173.71
//
Query:       gene2165|gene2165|rna2165|rna2165  [L=178]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.7e-06   27.4   0.1    3.2e-06   27.2   0.1    1.2  1  Med18     Med18 protein


Domain annotation for each model (and alignments):
>> Med18  Med18 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2   0.1   1.8e-10   3.2e-06     110     175 ..      74     138 ..      31     157 .. 0.86

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 1.8e-10
                                        EEEE----SS-SSS-EEEEEEEEEE..ESS-HTHHHHHTTEEEEEEEEEEEEEEEETTEEEEEEEE CS
                              Med18 110 LqisDiPeagknqkvlvrtiyestlverkdsllqfledlGysvineYivkGvrFfhgdivielfkv 175
                                        L  +  P+  +n+ v++  i+ ++++e+  ++ +f++++Gy +  e ++ G+++++g+++i l kv
  gene2165|gene2165|rna2165|rna2165  74 LVNKSEPDHNRNRSVIACRINVMDIIEC-HNVNTFMQEMGYTYCEELVLDGYKYYKGNLTIDLLKV 138
                                        55566699999*************9665.6799******************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       607  (0.0338558); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 1373.42
//
Query:       gene2166|gene2166|rna2166|rna2166  [L=65]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.9e-10   39.3   0.4    8.6e-08   31.8   0.4    2.0  1  LSM       LSM domain
  ------ inclusion threshold ------
      0.099   12.3   0.0       0.12   12.0   0.0    1.2  1  Hfq       Hfq protein


Domain annotation for each model (and alignments):
>> LSM  LSM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.8   0.4   9.6e-12   8.6e-08       2      37 ..      11      46 ..      10      64 .. 0.82

  Alignments for each domain:
  == domain 1  score: 31.8 bits;  conditional E-value: 9.6e-12
                                       HHHHTTTSEEEEEETTSEEEEEEEEEEETTSEEEEE CS
                                LSM  2 flkklinkkvtvelkngrelrGtLkgfDqfmNlvLe 37
                                       ++k+++++kv + l++  +l+G+L gfD++mN+ L 
  gene2166|gene2166|rna2166|rna2166 11 LVKSYLEEKVCIYLRDRSKLEGVLCGFDEHMNVGLL 46
                                       5799****************************9875 PP

>> Hfq  Hfq protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   1.4e-05      0.12      15      37 ..      19      41 ..      10      50 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.4e-05
                                       EEEEEETTS-EEEEEEEEE-SSE CS
                                Hfq 15 pvtifLvnGiklkGviksfDnft 37
                                       +v i+L    kl+Gv+ +fD+++
  gene2166|gene2166|rna2166|rna2166 19 KVCIYLRDRSKLEGVLCGFDEHM 41
                                       799*****************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (65 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       199  (0.0110993); expected 358.6 (0.02)
Passed bias filter:                      192  (0.0107089); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.32u 0.26s 00:00:00.58 Elapsed: 00:00:00.39
# Mc/sec: 500.10
//
Query:       gene2167|gene2167|rna2167|rna2167  [L=406]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (406 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1576  (0.0879023); expected 358.6 (0.02)
Passed bias filter:                      508  (0.028334); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.67u 0.32s 00:00:00.99 Elapsed: 00:00:00.54
# Mc/sec: 2267.09
//
Query:       gene2168|gene2168|rna2168|rna2168  [L=210]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.4e-17   63.4   0.1      4e-17   62.6   0.1    1.4  1  Methyltransf_11  Methyltransferase domain
    1.9e-13   50.9   0.3    4.7e-13   49.7   0.3    1.7  1  Methyltransf_25  Methyltransferase domain
    2.1e-10   40.6   0.0      3e-10   40.1   0.0    1.3  1  Methyltransf_31  Methyltransferase domain
    2.5e-10   40.4   0.1    4.8e-10   39.5   0.1    1.4  1  Methyltransf_23  Methyltransferase domain
    4.3e-09   37.0   0.2    1.1e-08   35.7   0.2    1.7  1  Methyltransf_12  Methyltransferase domain
    2.5e-08   34.1   0.0    4.1e-08   33.3   0.0    1.4  1  Methyltransf_8   Hypothetical methyltransferase
    6.5e-08   31.9   0.0    9.2e-08   31.4   0.0    1.2  1  Methyltransf_9   Protein of unknown function (DUF1698)
    6.2e-05   22.4   0.0    0.00041   19.7   0.0    2.1  2  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    0.00083   19.0   0.0     0.0013   18.4   0.0    1.2  1  MetW             Methionine biosynthesis protein MetW


Domain annotation for each model (and alignments):
>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.6   0.1     2e-20     4e-17       1      96 []      46     133 ..      46     133 .. 0.96

  Alignments for each domain:
  == domain 1  score: 62.6 bits;  conditional E-value: 2e-20
                                        EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES-CCC-CC CS
                    Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvssevlhhved 76 
                                        Ld+GcG+Gr++          +g+D++ e+l  + ++a+++   + ++ +d++ lpf+d+sfD+v+s  v+hh+e+
  gene2168|gene2168|rna2168|rna2168  46 LDAGCGNGRHLSTTS------IGIDYTREFLYECVHAANKRA--LALMACDVSCLPFRDESFDAVLSCAVIHHLEN 113
                                        8********999888......9*********99999999998..789***************************** PP

                                        HHHHHHHHHHHEEEEEEEEE CS
                    Methyltransf_11  77 pekalkeiaRvLkpgGllvi 96 
                                         ++ +++++RvL+ gG ++i
  gene2168|gene2168|rna2168|rna2168 114 AREGVEQLYRVLRAGGSCMI 133
                                        *****************986 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.7   0.3   2.4e-16   4.7e-13       1      97 []      45     129 ..      45     129 .. 0.89

  Alignments for each domain:
  == domain 1  score: 49.7 bits;  conditional E-value: 2.4e-16
                                        EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGG CS
                    Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhh 76 
                                        +Ld+GcG+Gr++            +g+D++ e+l ++ + a+++   + ++ +d++ lpf d+sfD+v+s+ ++hh
  gene2168|gene2168|rna2168|rna2168  45 ILDAGCGNGRHLSTT--------SIGIDYTREFLYECVHAANKR--ALALMACDVSCLPFRDESFDAVLSCAVIHH 110
                                        8********765444........48***********99999554..79**********************877*** PP

                                        SSHHHHHHHHHHHHHHEEEEE CS
                    Methyltransf_25  77 lsdedlekalkeiarvLkpgG 97 
                                        l+  ++++ +++++rvL+ gG
  gene2168|gene2168|rna2168|rna2168 111 LE--NAREGVEQLYRVLRAGG 129
                                        98..6789************9 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.1   0.0   1.5e-13     3e-10       3     127 ..      41     150 ..      39     188 .. 0.78

  Alignments for each domain:
  == domain 1  score: 40.1 bits;  conditional E-value: 1.5e-13
                    Methyltransf_31   3 kglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDli 78 
                                        k++ +lD+GCG+G+ +             +GiD++ e +  +   a k  l    + ++d+  l+  + de+fD +
  gene2168|gene2168|rna2168|rna2168  41 KTKLILDAGCGNGRHLSTTS---------IGIDYTREFLYECVHAANKRALA---LMACDVSCLP--FRDESFDAV 102
                                        66779********9988777.........***************99999887...99********..********* PP

                    Methyltransf_31  79 lsnevlnaladpdkileeiervlkpggilliedprllaelpakveeesk 127
                                        ls +v+++l +  +  e++ rvl+ gg ++i      + +  + +++++
  gene2168|gene2168|rna2168|rna2168 103 LSCAVIHHLENAREGVEQLYRVLRAGGSCMIVVWA-VKAVHPHGSRKQN 150
                                        ******************************87665.4444444444444 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.5   0.1   2.4e-13   4.8e-10      14     164 ..      35     195 ..      22     196 .. 0.74

  Alignments for each domain:
  == domain 1  score: 39.5 bits;  conditional E-value: 2.4e-13
                    Methyltransf_23  14 erllpklraggrvLdiGcGtGillevlrengfsvt...gvDlspeaveiaekakkaqkdqfdeqeaaepqgkfdlI 86 
                                        e+l  ++++ + +Ld GcG G+ l+     g ++t   +++   +a++    +  a   +   ++ ++ +++fd +
  gene2168|gene2168|rna2168|rna2168  35 EFL--NRNKTKLILDAGCGNGRHLSTT-SIGIDYTrefLYECVHAANK----RALALMACD-VSCLPFRDESFDAV 102
                                        433..4899999*********776632.22333222223333333222....334444444.669999999***** PP

                    Methyltransf_23  87 vlrevlehvpdppellrqiatllkpgGylllseplasl................kedrllldwlylvpagrhisff 146
                                         +  v++h+++  e + q+++ l+ gG +++ ++++++                   + l dw+   ++ r  +++
  gene2168|gene2168|rna2168|rna2168 103 LSCAVIHHLENAREGVEQLYRVLRAGGSCMIVVWAVKAvhphgsrkqngkfvriRDSEYLVDWQGKGQM-RFYHLY 177
                                        *********************************999888866666555555544444445559999999.****** PP

                    Methyltransf_23 147 sarslkelleeaGlevve 164
                                          ++l el++  G++vv+
  gene2168|gene2168|rna2168|rna2168 178 EKDELVELVRSVGFRVVA 195
                                        ****************96 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.7   0.2   5.7e-12   1.1e-08       1      98 [.      46     130 ..      46     131 .. 0.83

  Alignments for each domain:
  == domain 1  score: 35.7 bits;  conditional E-value: 5.7e-12
                    Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvl 76 
                                        L+ GcG+G+ l+           +g+D+ ++++     + a ++++    +++  l   d+    sfD+v+++ v+
  gene2168|gene2168|rna2168|rna2168  46 LDAGCGNGRHLSTT--------SIGIDYTREFL-YECVHAANKRALALMACDVSCLPFRDE----SFDAVLSCAVI 108
                                        79999999655544........799********.666666666767777788888776654....*********** PP

                    Methyltransf_12  77 hhlkdirevldnirklLkpgGr 98 
                                        hhl++ re +++++++L+ gG 
  gene2168|gene2168|rna2168|rna2168 109 HHLENAREGVEQLYRVLRAGGS 130
                                        ********************96 PP

>> Methyltransf_8  Hypothetical methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.3   0.0   2.1e-11   4.1e-08      63     156 ..      33     133 ..       8     150 .. 0.73

  Alignments for each domain:
  == domain 1  score: 33.3 bits;  conditional E-value: 2.1e-11
                                        HHHHHCTS-TTS-EEEES-TT-HHH....HH--S-..EEEEESS-SSTT...EEES-TTS-S--TT-EEEEEEES- CS
                     Methyltransf_8  63 iirklkkkkdnlvvadlGcGeakia....eavrekekvrsfdlvavner...vvacdlakvPledesvdvavfcls 131
                                        + + l ++++ + + d GcG+ +        +  +++     ++a n+r   ++acd++ +P  des d ++ c  
  gene2168|gene2168|rna2168|rna2168  33 VTEFL-NRNKTKLILDAGCGNGRHLsttsIGIDYTREFLYECVHAANKRalaLMACDVSCLPFRDESFDAVLSCAV 107
                                        33334.56677889*******9965232112223333333456788887333579*******************98 PP

                                        --.SS-HHHHHHHHHHHEEEEEEEEE CS
                     Methyltransf_8 132 lm.gtnladflkeanrvlkvGGllkv 156
                                        +   +n ++ +++ +rvl+ GG  ++
  gene2168|gene2168|rna2168|rna2168 108 IHhLENAREGVEQLYRVLRAGGSCMI 133
                                        862699****************8776 PP

>> Methyltransf_9  Protein of unknown function (DUF1698)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.4   0.0   4.6e-11   9.2e-08     103     217 ..      29     133 ..      14     145 .. 0.85

  Alignments for each domain:
  == domain 1  score: 31.4 bits;  conditional E-value: 4.6e-11
                                        HHHHHGGGS.--TT-EEEEET-TTSHHHHHHHHCT-SEEEEE---HHHHHHHHHHHCCTTTTSSEEEE---GGGS- CS
                     Methyltransf_9 103 kWdrvlphlsdlkgrtildvGcgnGyhlwrmvgegaklvvGidPselfliqfeavrkllgedqrahllplgieqlp 178
                                         W  v++ l+  k + ild GcgnG hl       +++ +Gid ++ fl+  e v+   ++++   l+   +  lp
  gene2168|gene2168|rna2168|rna2168  29 PWPSVTEFLNRNKTKLILDAGCGNGRHL-------STTSIGIDYTREFLY--ECVHA--ANKRALALMACDVSCLP 93 
                                        49999********************998.......5789*********96..55553..345556677889999*9 PP

                                        T.---EEEEEEES-GGG-S-HHHHHHHHHCTEEEEEEEEE CS
                     Methyltransf_9 179 e.leafdtvfsmGvlyhrrsPldhllqlkdqlvkgGelvl 217
                                           e+fd+v+s  v++h +   + + ql   l++gG  ++
  gene2168|gene2168|rna2168|rna2168  94 FrDESFDAVLSCAVIHHLENAREGVEQLYRVLRAGGSCMI 133
                                        8789********************************8766 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   2.1e-07   0.00041      27     152 ..      22     134 ..       8     144 .. 0.72
   2 ?   -3.1   0.0         2   4.1e+03     201     217 ..     179     195 ..     175     199 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 2.1e-07
                                        HHTTTHHHHHHHHHHH--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEE CS
                    Ubie_methyltran  27 lslgihrlWkkfveklvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinief 102
                                        +s   h+ W + +e   +  + + +lD  +G g     l      + + +++D+  + L +  + ++   k  + +
  gene2168|gene2168|rna2168|rna2168  22 FSSTRHKPWPSVTE-FLNRNKTKLILDAGCGNGRH---L------STTSIGIDYTREFLYECVHAAN---KRALAL 84 
                                        56666666665443.44444556667777776642...1......2344567777777777655544...445678 PP

                                        EE--TTT-TTS-T-EEEEEEES-GGG-S-HHHHHHHHHHHEEEEEEEEEE CS
                    Ubie_methyltran 103 lqanaeeLpfeddsfDvvtvsfGlrnvtDklkaLkeayrvlkpGGrlvvl 152
                                        +  +   Lpf d+sfD v     +  + +  ++++++yrvl++GG  +++
  gene2168|gene2168|rna2168|rna2168  85 MACDVSCLPFRDESFDAVLSCAVIHHLENAREGVEQLYRVLRAGGSCMIV 134
                                        8999999***********99999**********************98765 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 2
                                        HHHHHHHHHHTTEEEEE CS
                    Ubie_methyltran 201 qetlkeliedaGfksve 217
                                        +++l el++  Gf+ v 
  gene2168|gene2168|rna2168|rna2168 179 KDELVELVRSVGFRVVA 195
                                        68899999999999875 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   6.5e-07    0.0013      16     103 ..      44     126 ..      31     139 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 6.5e-07
                               MetW  16 rvldlGcGdGellellkeekqvdgrGleldeegvaecvakGlsviqgdldkdlenfedksfdyvvlsqtlqatrnp 91 
                                         +ld GcG+G  l+    + ++d +  e   e+v ++ ++ l+++  d+      f+d+sfd v+    +  + n+
  gene2168|gene2168|rna2168|rna2168  44 LILDAGCGNGRHLSTT--SIGID-YTREFLYECVHAANKRALALMACDV--SCLPFRDESFDAVLSCAVIHHLENA 114
                                        489*******998876..34555.5667778888888899999998776..5678********9998888888888 PP

                               MetW  92 kevldellrigr 103
                                        +e +++l r+ r
  gene2168|gene2168|rna2168|rna2168 115 REGVEQLYRVLR 126
                                        877666655532 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       577  (0.0321825); expected 358.6 (0.02)
Passed bias filter:                      519  (0.0289475); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 1438.53
//
Query:       gene2169|gene2169|rna2169|rna2169  [L=143]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.1e-19   68.5   0.4    6.5e-19   67.8   0.4    1.3  1  SGS              SGS domain
     0.0061   15.5   0.1     0.0077   15.2   0.1    1.1  1  Tyr-DNA_phospho  Tyrosyl-DNA phosphodiesterase


Domain annotation for each model (and alignments):
>> SGS  SGS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.8   0.4   7.3e-23   6.5e-19       3      69 ..      75     141 ..      73     143 .] 0.93

  Alignments for each domain:
  == domain 1  score: 67.8 bits;  conditional E-value: 7.3e-23
                                SGS   3 WdklekelekeekeekkeeegeaalnklFkklYadadedtrrammKSyveSnGtvLstnWeevkkkk 69 
                                        W  l+ e+++e  ee+ e+e++++l+ l  klY+d+d+++rram KS+ eS+Gt+Lst+We vk kk
  gene2169|gene2169|rna2169|rna2169  75 WPCLTVETREEVCEEHVEDEKDDSLDGLLIKLYKDGDDEKRRAMDKSFRESGGTMLSTDWERVKGKK 141
                                        8888889999999999999********************************************9887 PP

>> Tyr-DNA_phospho  Tyrosyl-DNA phosphodiesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1   8.6e-07    0.0077     113     151 ..       3      41 ..       1      55 [. 0.79

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 8.6e-07
                                        TSEEEEEEESS-BSHHHHHSSB-EEEE---EEE...... CS
                    Tyr-DNA_phospho 113 ddslrvvihtaNlieaDwgnmtqgvwrspllpllesske 151
                                        d+ lr++  t N+  +Dw++ ++ +++ p++pl+ ++++
  gene2169|gene2169|rna2169|rna2169   3 DQPLRLIHKTKNMKLYDWHQSQTHIYINPHVPLTITQST 41 
                                        667899999***********************9333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       553  (0.0308439); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 976.42
//
Query:       gene217|gene217|rna217|rna217  [L=75]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.3e-08   32.7   0.3    5.4e-08   32.4   0.3    1.1  1  PIF1      PIF1-like helicase


Domain annotation for each model (and alignments):
>> PIF1  PIF1-like helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.4   0.3     3e-12   5.4e-08     328     364 .]       1      37 [.       1      37 [. 0.96

  Alignments for each domain:
  == domain 1  score: 32.4 bits;  conditional E-value: 3e-12
                                    SS-SCEEE-TT-EEEE-S--CTT-SC-TCEEEEEEEE CS
                           PIF1 328 lpnhvLkLkvGvpvmllrNldqsaGLcNGtrlivtql 364
                                    +p+h+L Lk G+ +mll Nld ++ L NGtrliv +l
  gene217|gene217|rna217|rna217   1 MPPHKLVLKRGTLIMLLPNLDLANDLLNGTRLIVDEL 37 
                                    79********************************886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       304  (0.0169558); expected 358.6 (0.02)
Passed bias filter:                      232  (0.0129399); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.23s 00:00:00.57 Elapsed: 00:00:00.37
# Mc/sec: 602.35
//
Query:       gene2170|gene2170|rna2170|rna2170  [L=294]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-25   90.0   2.1    1.1e-25   90.0   2.1    2.4  2  EIF_2_alpha     Eukaryotic translation initiation factor 2 al
  ------ inclusion threshold ------
      0.027   14.6   0.8      0.064   13.4   0.3    1.8  2  Acetyltransf_4  Acetyltransferase (GNAT) domain


Domain annotation for each model (and alignments):
>> EIF_2_alpha  Eukaryotic translation initiation factor 2 alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.0   2.1   1.2e-29   1.1e-25       1     115 [.      79     236 ..      79     237 .. 0.76
   2 ?   -3.1   0.1      0.89     8e+03      69      83 ..     245     259 ..     240     273 .. 0.58

  Alignments for each domain:
  == domain 1  score: 90.0 bits;  conditional E-value: 1.2e-29
                                        HHHCTHHHHTTTTS-HHHHHHHHHSTTH.HHHHTT......................................... CS
                        EIF_2_alpha   1 lyeevgwklyekyghaydaFklaitdee.vldkle......................................... 34 
                                        ly+++gw ++++yg++y++F  +++  +   d  +                                         
  gene2170|gene2170|rna2170|rna2170  79 LYDSFGWRKAREYGTLYNYFGQLMNALSrKTDGTRgtvngtvpedvhapdasiaadntdeklakhetkksnavkam 154
                                        79******************55555544244442233334444444455555555555556666666666666666 PP

                                        .........S-TTTHHHHHHCTHHHHHHT-EEEEEEEEEEE-STTHHHHHHHHHHHHST.S..TTSSSEEEEEEEE CS
                        EIF_2_alpha  35 .........ipeeveeaLveiikkklkpqkvkiradieltcftkdGveaIkeaLkageeasneeeveeeeevkikl 101
                                                 i++++++ Lve+ k k+++qkvkiradi+ltc +k G+eaIk+aL+        + ++++ +++++l
  gene2170|gene2170|rna2170|rna2170 155 atydelvkdIDPSFINILVEQTKLKYNIQKVKIRADIDLTCPAKGGIEAIKDALR--------SVKSVDDKIEVSL 222
                                        666666666**********************************************........3456779****** PP

                                        SSSSEEEEEEEES. CS
                        EIF_2_alpha 102 iapPeYvltvetld 115
                                        i+pP+Y +t+  +d
  gene2170|gene2170|rna2170|rna2170 223 IRPPTYAITLLLHD 236
                                        *********98877 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 0.89
                                        TTHHHHHHHHHHHHS CS
                        EIF_2_alpha  69 kdGveaIkeaLkage 83 
                                        k+G e++k+ +++ +
  gene2170|gene2170|rna2170|rna2170 245 KKGCEQVKKRIEELN 259
                                        567777777666333 PP

>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.3   7.2e-06     0.064      83     151 ..      35     102 ..      32     105 .. 0.88
   2 ?   -2.3   0.0      0.47   4.3e+03      37      56 ..     251     275 ..     243     287 .. 0.50

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 7.2e-06
                     Acetyltransf_4  83 ylaerdnnkeglgrelidaleqvlkeqnienllaeiasp.nensiqfhkalGFelvgifkkcikkngrwi 151
                                        y++  +++k++l++++ +  + + ++   +n++ + a++ n n i++++++G++++++   +++++g+  
  gene2170|gene2170|rna2170|rna2170  35 YID--LSRKKVLASDFDECYKRYCQNKIGHNIMVSAAKKmNVNVIELYDSFGWRKAREYGTLYNYFGQLM 102
                                        773..799********99999999888888888888877699************************9865 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.47
                     Acetyltransf_4  37 fekfleal.d..sek..eyvflvae 56 
                                        ++k++e+l +  +e+    v++v e
  gene2170|gene2170|rna2170|rna2170 251 VKKRIEELnGtyAEVneVKVYGVKE 275
                                        5555555522331112234444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (294 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       878  (0.0489709); expected 358.6 (0.02)
Passed bias filter:                      495  (0.0276089); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 2016.85
//
Query:       gene2171|gene2171|rna2171|rna2171  [L=63]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (63 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       443  (0.0247086); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.47
# Mc/sec: 402.17
//
Query:       gene2172|gene2172|rna2172|rna2172  [L=120]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.1e-12   45.7   1.4    5.1e-12   45.4   1.4    1.1  1  Ribosomal_L7Ae  Ribosomal protein L7Ae/L30e/S12e/Gadd45 famil


Domain annotation for each model (and alignments):
>> Ribosomal_L7Ae  Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.4   1.4   2.9e-16   5.1e-12      10      89 ..      24     102 ..      15     106 .. 0.92

  Alignments for each domain:
  == domain 1  score: 45.4 bits;  conditional E-value: 2.9e-16
                                        HHHHTEEEESHHHHHHHHHTTTESEEEEETTSSSGGHHHHHHHHHHHTTEEEEEESCHHHHHHHTTSSSECSEEEE CS
                     Ribosomal_L7Ae  10 akkagklvlGlkevtkalergeaklvilAedvepeekkkllealckekevpyvkvkskkeLGelvgkkrpvsalai 85 
                                         k  +k+++G k + ka++++++ + il  +++p +  ++l++lc+++ev+y++v+  + L ++ +  + ++++++
  gene2172|gene2172|rna2172|rna2172  24 LKTIKKVIRGRKACHKAIKSKKKGILILPFNISPCDLIAHLPMLCEDNEVKYCYVDR-EVLRRASNVDTLTCCVFV 98 
                                        556688***************************************************.*****************9 PP

                                        EEST CS
                     Ribosomal_L7Ae  86 kdeg 89 
                                        k++ 
  gene2172|gene2172|rna2172|rna2172  99 KKNA 102
                                        9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       553  (0.0308439); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 808.66
//
Query:       gene2173|gene2173|rna2173|rna2173  [L=56]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (56 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       155  (0.00864521); expected 358.6 (0.02)
Passed bias filter:                      150  (0.00836633); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 387.51
//
Query:       gene2174|gene2174|rna2174|rna2174  [L=181]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.1e-18   66.9   0.0      3e-18   65.5   0.0    1.7  2  RMMBL      Zn-dependent metallo-hydrolase RNA specificity dom
    1.4e-12   47.9   0.0    2.9e-12   46.9   0.0    1.6  1  Beta-Casp  Beta-Casp domain
  ------ inclusion threshold ------
       0.09   13.0   0.0       0.14   12.4   0.0    1.3  1  DRMBL      DNA repair metallo-beta-lactamase


Domain annotation for each model (and alignments):
>> RMMBL  Zn-dependent metallo-hydrolase RNA specificity domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0      0.64   3.8e+03      44      62 .]      21      38 ..      19      38 .. 0.66
   2 !   65.5   0.0     5e-22     3e-18       2      53 ..      63     118 ..      62     131 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.64
                              RMMBL 44 tsalarllkeeegidvfiP 62
                                       ++ +++l+ e+e++ v+iP
  gene2174|gene2174|rna2174|rna2174 21 LKIFKALC-EDEKNLVIIP 38
                                       56789999.6666666555 PP

  == domain 2  score: 65.5 bits;  conditional E-value: 5e-22
                              RMMBL   2 ipvkarieeidfSgHadknellelirklkprnvilvHGeeeatsalarllk....e 53 
                                        + +k+++ +i fS+Had +++l++i+k++prnv+lvHG+++ +++++r ++    +
  gene2174|gene2174|rna2174|rna2174  63 YTIKMQVRNIGFSAHADSSSILRFIAKIRPRNVVLVHGDKNRMAKFKRIIErmcsD 118
                                        579********************************************999544434 PP

>> Beta-Casp  Beta-Casp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.9   0.0   4.8e-16   2.9e-12      63     109 ..       3      49 ..       1      50 [. 0.95

  Alignments for each domain:
  == domain 1  score: 46.9 bits;  conditional E-value: 4.8e-16
                                        -SSEEEEES-TTSSSSHHHHHHHHHTTSTTSEEEESS---TTSHHHH CS
                          Beta-Casp  63 kgpkvilassgmlegGrsrellkklledprntvilvgyqaegTlgrk 109
                                        ++p ++++s+gml++G s +++k+l+ed++n+vi++gy+ ++Tl++ 
  gene2174|gene2174|rna2174|rna2174   3 DKPFIVFSSPGMLHTGNSLKIFKALCEDEKNLVIIPGYCMKNTLAEM 49 
                                        6899****************************************976 PP

>> DRMBL  DNA repair metallo-beta-lactamase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   2.3e-05      0.14      68     103 ..      57      96 ..      16      97 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.3e-05
                              DRMBL  68 s....ksrekisiyrvpYSeHSSfrELkefvkslkpkkii 103
                                        +    +++ k+++ ++ +S H   + + +f+  ++p++++
  gene2174|gene2174|rna2174|rna2174  57 VtlerEYTIKMQVRNIGFSAHADSSSILRFIAKIRPRNVV 96 
                                        133337899*****************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       495  (0.0276089); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.32s 00:00:00.85 Elapsed: 00:00:00.53
# Mc/sec: 1033.06
//
Query:       gene2175|gene2175|rna2175|rna2175  [L=256]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.5e-16   59.8   0.1    3.2e-16   59.4   0.1    1.1  1  Lactamase_B_2  Beta-lactamase superfamily domain
  ------ inclusion threshold ------
      0.076   12.9   0.0       0.85    9.5   0.0    2.0  2  Lactamase_B_3  Beta-lactamase superfamily domain
      0.078   13.2   0.6       0.15   12.3   0.6    1.4  1  DUF3586        Protein of unknown function (DUF3586)
       0.18   11.7   0.3        0.4   10.6   0.0    1.7  2  Bet_v_1        Pathogenesis-related protein Bet v I family


Domain annotation for each model (and alignments):
>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.4   0.1   7.3e-20   3.2e-16       3     199 ..      50     229 ..      48     230 .. 0.91

  Alignments for each domain:
  == domain 1  score: 59.4 bits;  conditional E-value: 7.3e-20
                                        EEES--TTHHHHHTCGGS--S.SS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHHHCCTTCGHH CS
                      Lactamase_B_2   3 iLiDagpdlrqqalralqPve.lrdelppidaVllthaHyDHlaglltlrelrpkklplyapkgvlavleanfvyl 77 
                                        iL+D+g  +  q +r+l   +   ++   i  +l+th H+D++ g++t   ++  k ++y +k +l+ +++   y 
  gene2175|gene2175|rna2175|rna2175  50 ILVDCGKHFYTQYNRYL---StYGNT--IIPELLITHPHADAIGGIDTYLMMCTGKKNVYSSKFTLDFIRKTNEYY 120
                                        9***********99998...324455..9999*******************998899******************9 PP

                                        HCHTT.....TTEEEEEE-TTSEEEECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEECTTEEEEEESS-S---H CS
                      Lactamase_B_2  78 aleee.....pavnvheldwgesfelgdggleitatparhksgrrldrnagdtlGlriegggkrvyyigDtgyipe 148
                                        + ++      +  + + l+ g+ +++g  g++++a+++ h++ +         l+++i+    +v+yi Dt  ++ 
  gene2175|gene2175|rna2175|rna2175 121 FVKPGdpehrGYFHPNVLAHGQITQIG--GIKVHAFEVDHGGIK--------SLAFLID---DKVLYISDTSDLH- 182
                                        9999888888888889999999999*9..899************........*******...7*********998. PP

                                        HHHHHHCT-SEEEEE-S-SSTTHHHHHHT---STSHHHHCTTSSSSEEEEE CS
                      Lactamase_B_2 149 eigerlggadllllditayeddemirhmgHltpeeaveaaadlgakrlvli 199
                                         i e+++  d+l++d+   +++      gHl++++  + a  l+++r++l+
  gene2175|gene2175|rna2175|rna2175 183 PIPEEFYHRDVLIIDCLTIDQHV----RGHLNLQDVKRYASILQPGRVILT 229
                                        67889999*******99888755....8*********************97 PP

>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0   0.00019      0.85      11     115 ..      42     179 ..      37     229 .. 0.76
   2 ?    2.7   0.1     0.023     1e+02      35      69 ..     194     225 ..     170     247 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00019
                      Lactamase_B_3  11 lletagarilvDPfka.nlgyeppaeeaDlvlisqaledHahletlkql........................... 58 
                                         ++++  +ilvD +k  +++y++   +    +i   l +H h++++ ++                           
  gene2175|gene2175|rna2175|rna2175  42 IINKGVSSILVDCGKHfYTQYNRYLSTYGNTIIPELLITHPHADAIGGIdtylmmctgkknvysskftldfirktn 117
                                        4455558999999999999999999999999999999999999999999999999*******************99 PP

                      Lactamase_B_3  59 ..............aenvkvleegeslevggleiravatshdavggsergenngflleqdgltiyhlGhla 115
                                                      +  ++vl++g+ +++gg+++ a++ +h +       +  +fl+++   ++++  +++
  gene2175|gene2175|rna2175|rna2175 118 eyyfvkpgdpehrgYFHPNVLAHGQITQIGGIKVHAFEVDHGGI------KSLAFLIDD---KVLYISDTS 179
                                        9999999999999988999********************99544......234455544...444444444 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.023
                      Lactamase_B_3  35 eeaDlvlisqaledHahletlkqlaenvkvleege 69 
                                          +D+++i q+   H +l+ +k+    + +l++g 
  gene2175|gene2175|rna2175|rna2175 194 LIIDCLTIDQHVRGHLNLQDVKR---YASILQPGR 225
                                        568999*****999999999999...555555554 PP

>> DUF3586  Protein of unknown function (DUF3586)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.6   3.4e-05      0.15      19      65 ..      13      59 ..      10      68 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3.4e-05
                            DUF3586 19 PsvtvtqtlCtdkgCrkgCkktvlptneClknggggSvvatCgaeev 65
                                       Ps+ +   +C   g  k C +t+ +    + n+g+ S++++Cg++  
  gene2175|gene2175|rna2175|rna2175 13 PSSGIPSLKCRLAGSCKVCDTTTRTNVSIIINKGVSSILVDCGKHFY 59
                                       566777789*****9*****9999999999*************9865 PP

>> Bet_v_1  Pathogenesis-related protein Bet v I family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.1         2   8.7e+03      94     111 ..     102     119 ..     100     123 .. 0.73
   2 ?   10.6   0.0     9e-05       0.4      36      71 ..     144     178 ..     134     186 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 2
                                        SSSS-EEEEEE-E-TTSS CS
                            Bet_v_1  94 eyksykvtlqvipksegs 111
                                        ++ s+k+tl++i k ++ 
  gene2175|gene2175|rna2175|rna2175 102 NVYSSKFTLDFIRKTNEY 119
                                        566788999999998875 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 9e-05
                                        TTEEEEEEEESSSSTT.-EEEEEEEETTEEEEEEEE CS
                            Bet_v_1  36 dkiqgvevhegewdshgsikiwtytvDgkvevlkek 71 
                                         +i g++vh  e d hg ik++ +++D+kv ++ ++
  gene2175|gene2175|rna2175|rna2175 144 TQIGGIKVHAFEVD-HGGIKSLAFLIDDKVLYISDT 178
                                        3799**********.88************9888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       475  (0.0264934); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1765.18
//
Query:       gene2176|gene2176|rna2176|rna2176  [L=500]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   5.1e-103  344.6   2.4    2.1e-88  296.6   2.4    2.1  2  Peptidase_M17    Cytosol aminopeptidase family, catalytic dom
  ------ inclusion threshold ------
       0.02   14.7   0.1      0.046   13.6   0.1    1.6  1  Peptidase_M17_N  Cytosol aminopeptidase family, N-terminal do


Domain annotation for each model (and alignments):
>> Peptidase_M17  Cytosol aminopeptidase family, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.1   0.0   4.2e-16   3.8e-12       1      74 [.     146     219 ..     146     228 .. 0.89
   2 !  296.6   2.4   2.3e-92   2.1e-88      75     311 .]     260     492 ..     250     492 .. 0.94

  Alignments for each domain:
  == domain 1  score: 46.1 bits;  conditional E-value: 4.2e-16
                                        HHHHHHHHS-TTTS-HHHHHHHHHH.HHTCCTEEEEEEEECHHHHHTT-HHHHHHHTTSSSS--EEEEEEEE-SS CS
                      Peptidase_M17   1 nlardlvntpaneltpeklaeeaee.lakeagkvevevldeeeleekgmgallaVgkgSeeepprlveleykgak 74 
                                        nlar l  tpan +tp+ + e++++ +a+ + +++++++d ++++e++m+++l+V+kgS+ e+p+l +l+y g++
  gene2176|gene2176|rna2176|rna2176 146 NLARFLSLTPANLMTPTLFTEYVKDvIAHLNLTISTQIYDSRAIAEMKMNLFLSVAKGSA-EEPKLAVLTYLGRD 219
                                        689*********************9546766689*************************5.5*********9876 PP

  == domain 2  score: 296.6 bits;  conditional E-value: 2.3e-92
                                        TTSEEEEEEEEEEEEEE-TTSS--HHHHTTGGGGGHHHHHHHHHHHHHHHHT-SSEEEEEEEEEEE--STTSTTTT CS
                      Peptidase_M17  75 ekekklalVGKGitfDtGGlslKpsasmeemkaDmgGAAavlgalkavaelklpvnvvavlplaeNmisgkavkpg 150
                                        ++e ++++VGKGitfD+GG+slKps++meemkaDm+G+A+v++ + a+a++kl+vnv++++pl+eN++sg+a kpg
  gene2176|gene2176|rna2176|rna2176 260 ASEYDVVMVGKGITFDSGGISLKPSKGMEEMKADMMGGAVVFASVVAAAQMKLRVNVKVIIPLCENLPSGHASKPG 335
                                        567899********************************************************************** PP

                                        EEEE-TTS-EEEES-TTGCHHHHHHHHHHHHHGCT--SEEEEEE---THHHHHHTTTSEEEEES-HHHHHHHHHHH CS
                      Peptidase_M17 151 dvitamnGktvevlnTDaEGRLvLADalayaeekekpdlivdvATLTgavvvalGkkaaglfsnddelaeelekag 226
                                        dvi  +nGk+ve++nTDaEGRL+LADal  a e+++ ++iv v+TLTga+v+alG+++ g++++dd l e++++ag
  gene2176|gene2176|rna2176|rna2176 336 DVIIGRNGKSVEINNTDAEGRLILADALNLA-EDFRTKAIVCVSTLTGACVIALGNEYYGVYTDDDGLFERIRTAG 410
                                        *******************************.689***************************************** PP

                                        HHHS-EEEE----HHHGGGG--SSSSEESS-SSSSTHHHHHHHHHHTTSSECGEEEEE-TTTTE.S.BTTB.S..E CS
                      Peptidase_M17 227 eeagervwrlpleeeykkqlkskvaDlknvgkkrragaitAalFLkefvketpWaHlDiagtal.kekealkkekg 301
                                         +++++ wr+pl+++y + ++s+vaD+kn g   +ag++tAa+FLk+fv+  +++HlDiag+   ++++  +   +
  gene2176|gene2176|rna2176|rna2176 411 YAVEDKGWRMPLDKKYMQCMESNVADMKNAGY--KAGSCTAAIFLKQFVTMNSFVHLDIAGMLGtEDTSLFA--GN 482
                                        *******************************9..99*************5488********97523333333..69 PP

                                        E--TTHHHHH CS
                      Peptidase_M17 302 atGvgvrtLv 311
                                         tG++ ++Lv
  gene2176|gene2176|rna2176|rna2176 483 ITGRPCAMLV 492
                                        9999999885 PP

>> Peptidase_M17_N  Cytosol aminopeptidase family, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   5.2e-06     0.046      67     120 ..      76     122 ..      71     128 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5.2e-06
                    Peptidase_M17_N  67 taealrkaagaaaralkgakvttiavalplegknsdekaeaaaegallglYrfd 120
                                        t  ++rkaa+ a +++k+ +v+++ +++        e+ eaaa g+ll+ +++d
  gene2176|gene2176|rna2176|rna2176  76 TYGNIRKAAALALKEMKKYGVENVRIDCG-------EFKEAAADGVLLAGFKYD 122
                                        6789*************************.......***************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (500 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       582  (0.0324614); expected 358.6 (0.02)
Passed bias filter:                      502  (0.0279993); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.48
# Mc/sec: 3136.10
//
Query:       gene2177|gene2177|rna2177|rna2177  [L=648]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      7e-30  104.0  11.0      7e-30  104.0  11.0    2.1  2  ABC2_membrane    ABC-2 type transporter
      4e-21   76.0   0.0    1.4e-20   74.2   0.0    1.9  1  ABC_tran         ABC transporter
    6.5e-06   26.2   3.0    0.00082   19.3   3.0    2.3  1  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
    8.7e-05   21.8  19.3    0.00016   20.9  19.3    1.4  1  ABC2_membrane_3  ABC-2 family transporter protein
     0.0033   17.3   1.8     0.0038   17.1   0.3    1.8  2  RsgA_GTPase      RsgA GTPase
  ------ inclusion threshold ------
      0.017   14.6   0.1      0.057   12.8   0.1    1.8  1  SMC_N            RecF/RecN/SMC N terminal domain
       0.02   15.4   0.1      0.033   14.7   0.1    1.4  1  AAA_23           AAA domain


Domain annotation for each model (and alignments):
>> ABC2_membrane  ABC-2 type transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.0  11.0   2.7e-33     7e-30       2     208 ..     385     595 ..     384     597 .. 0.94
   2 ?    1.2   0.7     0.081   2.1e+02     161     185 ..     618     642 ..     613     647 .. 0.63

  Alignments for each domain:
  == domain 1  score: 104.0 bits;  conditional E-value: 2.7e-33
                      ABC2_membrane   2 qikallkreflqrwrdpslgllwrliqplllalvfgtvfgnlgnsedgl.nr..pgllffsvlflafsaltsvapv 74 
                                        ++++l+ r+f+   +++ l  ++r+iq +++++++gt+++n+   +d++ +    gll+f+v++++f++ ++ ++ 
  gene2177|gene2177|rna2177|rna2177 385 EFLILTVRNFKMLSGNKLLC-FARVIQAIVTSVIIGTIYFNVSGADDFVyEKnaSGLLYFLVVNMMFTCSFGGVSA 459
                                        6899*******999999777.9*******************9977777744499********************** PP

                      ABC2_membrane  75 ferergvlerelvsplyslsayvlakvlvelpvsllqalifllivyflvgldls..rfflflllllltalaasslg 148
                                        f +++++ +re++ + y    y+l+k+l++lp+ +l  + ++++vy+l +l +s  ++++f+++ l+++ ++ ++g
  gene2177|gene2177|rna2177|rna2177 460 FYKDERLAYRETRGKKYGILCYYLSKLLADLPFVFLYPITVFTVVYLLANLSYSlkQIAFFYCTGLALSYLCHTVG 535
                                        ******************************************************966699999999999999**** PP

                      ABC2_membrane 149 llisalapsfedasqlaslvllpllllsGffipidsm.pkwlqwiaylnPltyavealrsn 208
                                        ll++a ++++ +  ++ + +++p++  sG ++++ds+ +   + ++y++P +ya++++++n
  gene2177|gene2177|rna2177|rna2177 536 LLFGAAFKDHSVTLIMLPTLITPIVTISGLMVNTDSLiE-PYKRMQYISPTRYAFNIVIKN 595
                                        *************************************95.5677*************9988 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.081
                      ABC2_membrane 161 asqlaslvllpllllsGffipidsm 185
                                        as++a lv++++ ++ G+f+ +++m
  gene2177|gene2177|rna2177|rna2177 618 ASFVALLVMILFCIVLGYFMLRWKM 642
                                        5566666666666666666666666 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.2   0.0   5.5e-24   1.4e-20       1     136 [.      20     218 ..      20     219 .. 0.90

  Alignments for each domain:
  == domain 1  score: 74.2 bits;  conditional E-value: 5.5e-24
                                        EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEE.................................. CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.................................. RF
                           ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGei.................................. 42 
                                        l+n++l +++++++ai+G +GaGK++Llk+l+g +  t+Gei                                  
  gene2177|gene2177|rna2177|rna2177  20 LENINLGIRKNKLTAIMGLSGAGKTSLLKVLSGYS--TNGEIlmkrslddgrvveisdgagvnsghdrgtygtsrs 93 
                                        78*******************************98..68***9999999999999999999999999999999999 PP

                                        .....................EET.TCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH.........HHHTCHHH CS
                                        .....................xxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.........xxxxxxxx RF
                           ABC_tran  43 .....................lld.gkdlkeqeleslrkeigvlpqepqlfpeltvren.........esdeeiek 87 
                                                              +d  +d ke + + +r+ ++ + q + l +  t+ e          e  + i++
  gene2177|gene2177|rna2177|rna2177  94 agstrdknrlikaneffaskyGIDmARDYKEVNDNYMRNISSLVYQSDVLPSWFTINEYltflcrlidEPLSSIDR 169
                                        9999888888888888888776665666666777888888888889999999999888899999999888888*** PP

                                        HHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ABC_tran  88 alsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                        +l+++++++ k+  +++++  +SgGq++r+++ + ll++p++l+lDEpt
  gene2177|gene2177|rna2177|rna2177 170 LLAEFDMSDRKHCLIGEQDGGISGGQRKRLSIIAELLSDPEILFLDEPT 218
                                        ************************************************9 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   3.0   3.2e-07   0.00082       1     299 [.      32     247 ..      32     249 .. 0.71

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 3.2e-07
                             AAA_21   1 lnvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfefeieeflsqgvryrygl 76 
                                        l+++ G  g+GK++LL+ l++ +           +     + + ++++  +++              +g   + g+
  gene2177|gene2177|rna2177|rna2177  32 LTAIMGLSGAGKTSLLKVLSGYST----------NGEILMKRSLDDGRVVEIS--------------DGAGVNSGH 83 
                                        68999999***********76632..........2222222222222222222..............223333333 PP

                             AAA_21  77 rlersqveeklssvetllesgllldkrsleeedvfnpeargirggvsvfslkelsvsepndlqfgkaltditsraw 152
                                        + +  +           ++ g ++dk  l++ ++f++ ++gi+  +++++                          
  gene2177|gene2177|rna2177|rna2177  84 DRGTYGT---------SRSAGSTRDKNRLIKANEFFASKYGIDMARDYKE-------------------------- 124
                                        3333333.........5555555777777888888888888888777654.......................... PP

                             AAA_21 153 sllllldglrke..rigllnifadyfgfakekrllqrlvrslklveielsdlgegeeliasvderlrergvvflen 226
                                            +++ +r+      + +   ++f+ ++ +++l rl+++++   ++l ++ ++++   + +  +++        
  gene2177|gene2177|rna2177|rna2177 125 ---VNDNYMRNIssLVYQSDVLPSWFTINEYLTFLCRLIDEPLSSIDRLLAEFDMSDRKHCLIGEQDG-------- 189
                                        ...55555666667888899999999999999999999999999999999999999999999999988........ PP

                             AAA_21 227 gdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHSp 299
                                                  +S G+++ l +++ ll+++    +l++DEp +gL+ +  +  ++ lk+ ++    ++lt H+p
  gene2177|gene2177|rna2177|rna2177 190 ---------GISGGQRKRLSIIAELLSDP---EILFLDEPTTGLDVRNASVMVKSLKNRKK---TIVLTIHQP 247
                                        .........89****************99...9*************888888777755444...777776666 PP

>> ABC2_membrane_3  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9  19.3   6.3e-08   0.00016     153     344 ..     434     635 ..     381     638 .. 0.72

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 6.3e-08
                    ABC2_membrane_3 153 eeelsnvasflvgliliilifitasfiavsi....veEkesrikelqlvsgvsplqywlskilgdf.lvyllqlll 223
                                        e+ +s+  +flv+ +++ ++f ++s   +++    +  +e+r k+  +++      y+lsk+l+d+ +v+l ++ +
  gene2177|gene2177|rna2177|rna2177 434 EKNASGLLYFLVVNMMFTCSFGGVS---AFYkderLAYRETRGKKYGILC------YYLSKLLADLpFVFLYPITV 500
                                        3333555555555554444444444...3333344778999999988888......**********4555556666 PP

                    ABC2_membrane_3 224 ill..lafglgipfgnlglll.llfllfglayialgyllsslfknsetaqilifivilllsgffgglfpledlpsa 296
                                        +++  l+ +l+++ +++ ++    + l +l+ + +g+l++++fk+++ + i+++ +i ++  ++g+++ +++l ++
  gene2177|gene2177|rna2177|rna2177 501 FTVvyLLANLSYSLKQIAFFYcTGLALSYLCHT-VGLLFGAAFKDHSVTLIMLPTLITPIVTISGLMVNTDSLIEP 575
                                        666333666467777888777577777777777.9***********9998855555555555555555599999** PP

                    ABC2_membrane_3 297 lkwifsiiPffapglgllrlitgdplwe............illsliilalfavvylllal 344
                                         k   +i P+ + ++  ++  +g    +            i  s+++l+++++++++l++
  gene2177|gene2177|rna2177|rna2177 576 YKRMQYISPTRYAFNIVIKNHFGKDVRDkmlkglvdgffsIEASFVALLVMILFCIVLGY 635
                                        ********************9888555588888888888655888888888888877765 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.3   1.5e-06    0.0038      85     123 ..      15      54 ..       2      87 .. 0.75
   2 ?   -1.9   0.1       1.1   2.7e+03      20      52 ..     239     271 ..     225     274 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.5e-06
                                        TTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT- CS
                        RsgA_GTPase  85 ktkegleelkellkd.ktsvlvGqSGvGKStLinallpel 123
                                        k +  le+++  +++ k+++++G SG+GK++L+++l +  
  gene2177|gene2177|rna2177|rna2177  15 KGNVVLENINLGIRKnKLTAIMGLSGAGKTSLLKVLSGYS 54 
                                        4455667777777776********************9863 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.1
                                        EEEEESTTTT--HHHHHHHHHHHHHTT-EEEEE CS
                        RsgA_GTPase  20 livvslkepelslnlldrfLvlaeekgiepviv 52 
                                         iv+++++p+ +l ++   L+++++k+i + i+
  gene2177|gene2177|rna2177|rna2177 239 TIVLTIHQPSSNLFFMFDDLIVLHDKRILMQIC 271
                                        68999999*****99999999999999988887 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   2.2e-05     0.057      24     199 ..      30     246 ..      21     261 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.2e-05
                                        SSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSCEEE CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              SMC_N  24 ksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfdnedkklkiekeevsi 99 
                                        +++tai+G  G+GK++ll  ++ +  + +    rs +  +++   +++a v++++   t+  + ++ ++++++  i
  gene2177|gene2177|rna2177|rna2177  30 NKLTAIMGLSGAGKTSLLKVLSGYSTNGEILMKRSLDDGRVVEI-SDGAGVNSGHDRGTYGTSRSAGSTRDKNRLI 104
                                        679****************9975555444433355555668886.99*************8888876676666666 PP

                                        EEEEETTSEEEEEE....TTEEE-H...HHHHHHHHCTT-STT................................. CS
                                        xxxxxxxxxxxxxx....xxxxxxx...xxxxxxxxxxxxxxx................................. RF
                              SMC_N 100 srrvkrkgeseyki....ngkevtk...kevsellesagiske................................. 135
                                        + + +    s+y i    + kev+    +++s+l+ ++    +                                 
  gene2177|gene2177|rna2177|rna2177 105 KANEFFA--SKYGIdmarDYKEVNDnymRNISSLVYQS----Dvlpswftineyltflcrlideplssidrllaef 174
                                        6555544..44666112133333321123444444444....25555***************************** PP

                                        ...............CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE- CS
                                        ...............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              SMC_N 136 ...............lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivis 196
                                                        +SgG+++ +  +++ A    +p+ l +lDe    LD +n + +++ lk+++k    iv +
  gene2177|gene2177|rna2177|rna2177 175 dmsdrkhcligeqdgGISGGQRKRL--SII-AELLSDPEIL-FLDEPTTGLDVRNASVMVKSLKNRKK---TIVLT 243
                                        *********************9844..444.6666677755.58***************999999994...56666 PP

                                        SSH CS
                                        xxx RF
                              SMC_N 197 lre 199
                                        +++
  gene2177|gene2177|rna2177|rna2177 244 IHQ 246
                                        655 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.1   1.3e-05     0.033      13      39 ..      21      50 ..       4     136 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.3e-05
                             AAA_23 13 qeidF...skgltlItGpNGaGKTTildAi 39
                                       ++i++   +++lt+I G  GaGKT++l  +
  gene2177|gene2177|rna2177|rna2177 21 ENINLgirKNKLTAIMGLSGAGKTSLLKVL 50
                                       4578899999****************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (648 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       903  (0.0503653); expected 358.6 (0.02)
Passed bias filter:                      578  (0.0322383); expected 358.6 (0.02)
Passed Vit filter:                        84  (0.00468515); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.75u 0.32s 00:00:01.07 Elapsed: 00:00:00.50
# Mc/sec: 3894.93
//
Query:       gene2178|gene2178|rna2178|rna2178  [L=273]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.1e-29  101.7   0.0    2.9e-28   99.2   0.0    1.8  2  CDC50     LEM3 (ligand-effect modulator 3) family / CDC50 fam


Domain annotation for each model (and alignments):
>> CDC50  LEM3 (ligand-effect modulator 3) family / CDC50 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.1     0.024   4.4e+02     245     276 ..      20      51 ..       5      55 .. 0.78
   2 !   99.2   0.0   1.6e-32   2.9e-28      40     269 ..      63     271 ..      57     273 .] 0.83

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.024
                              CDC50 245 lGgknpflgiaYlvvGgiclvlaivflvthli 276
                                        +G+ +  l  +Y++++  c+ l+i++ ++h++
  gene2178|gene2178|rna2178|rna2178  20 FGKPSLNLFPFYVLLSLACISLSIILGYIHIT 51 
                                        66667777789****************99987 PP

  == domain 2  score: 99.2 bits;  conditional E-value: 1.6e-32
                              CDC50  40 ftvpedlkapvyvyYeLtnfyQnhrryvkSrddsqlkgkaksslksssssdCepletakekkekkkiiyPCGliAn 115
                                        +tvp++++  + +y +  +f Qnh  y++S++ +ql+gk+    ++   ++C+p+ +     ++ +i+yPCGl++ 
  gene2178|gene2178|rna2178|rna2178  63 ITVPRKMT--LNLYIRFYDFSQNHILYARSISLDQLRGKKW---TD--LDRCKPIIR-----NEGTIVYPCGLVSD 126
                                        56666665..56788999**********************3...22..336****64.....33479********* PP

                              CDC50 116 slFNDtfslveessskltkvnltkkgIawksdkekkfknktkyealeevvkPpnWakk....pe...eteipelke 184
                                        +l  D  +l  ++     +++ +++gIa + +k kk k+ +  ++   v+kPp W ++     +   ++++++l+e
  gene2178|gene2178|rna2178|rna2178 127 TLPFDNVALIGSQ----GRIEPSTTGIAKNAHK-KKIKALM--TN-IPVTKPPSWPNRtgtlGSeqsDDQVIDLSE 194
                                        **99999665554....4688899******999.8999744..33.56899999*888765511667999****** PP

                              CDC50 185 nedfivWmrtAalptFrKlyrrindeedLkagtyevdiennfpvksFkGtKsivlsttswlGgknpflgiaYlvvG 260
                                        ne+f++W++ Aa+++F+Kl++r +d   L++g+y v ++++ +     G++s+vl ++ ++   +++l  +Yl+vG
  gene2178|gene2178|rna2178|rna2178 195 NERFVNWIQIAAFSRFKKLFGRFDD---LEKGDYDVVVDQKGE----LGRRSVVLREKRLVDVDSYWLP-VYLMVG 262
                                        **********************766...***********8766....59******************98.5***** PP

                              CDC50 261 giclvlaiv 269
                                        gi++++ ++
  gene2178|gene2178|rna2178|rna2178 263 GIFILFPVL 271
                                        ****99776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (273 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       355  (0.0198003); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 2081.39
//
Query:       gene2179|gene2179|rna2179|rna2179  [L=171]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.7e-12   46.3   1.8    9.4e-11   42.1   1.8    2.1  1  RNA_pol_Rpb8  RNA polymerase Rpb8
    0.00021   21.3   0.4    0.00041   20.4   0.3    1.5  1  RNA_pol_RpbG  DNA-directed RNA polymerase, subunit G


Domain annotation for each model (and alignments):
>> RNA_pol_Rpb8  RNA polymerase Rpb8
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.1   1.8     1e-14   9.4e-11       3     125 ..      54     156 ..      52     169 .. 0.88

  Alignments for each domain:
  == domain 1  score: 42.1 bits;  conditional E-value: 1e-14
                                        EEEEEEEE-..TT-SSEEEEEEEESS-S-EEEEEEETTTS---SS-EEEEEEES------------------GGS- CS
                       RNA_pol_Rpb8   3 iFevkdvdkdgkkfdrVsRieaeseslemeltlDintelyplkegdkltlvlasslsldgskdeeeakkswegeks 78 
                                        +++v+++dkd k f++ s+++   +   ++lt+D+++ l++ k +dk+++v+ + +  +               ++
  gene2179|gene2179|rna2179|rna2179  54 VYTVETIDKDKKIFNKLSKLYLADQ--AYKLTIDYHSLLFKPKINDKIEIVIYKGILAE---------------EE 112
                                        799******************9987..799************************99887...............34 PP

                                        CGGGSSEEEBEEEEEEEE-ST..T-EEEEEEBTTBEEEEEBSHHTTT CS
                       RNA_pol_Rpb8  79 ladkydYvmyGkvYkieeeeskeekvkvyvSfGGLlmaLegdakkls 125
                                        + + y+Yv+ G++Y+ +  +    k  + vSfGG+lm++  d+++++
  gene2179|gene2179|rna2179|rna2179 113 VPECYEYVLQGHCYRNKLADG---KRIIGVSFGGMLMEMIVDENDVN 156
                                        6789***********988885...77899*********999888776 PP

>> RNA_pol_RpbG  DNA-directed RNA polymerase, subunit G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.3   4.6e-08   0.00041      16      99 ..      67     154 ..      50     163 .. 0.76

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 4.6e-08
                       RNA_pol_RpbG  16 lkdlkivkikcqneeielDiiselnifkeedkveviisr...ekPeyldgkdFcghGylvtekeeenkiitliSlf 88 
                                        +++l    +  q +++++D +s l + k +dk+e++i +      e  + ++++ +G    +k  + k+i+ +S+ 
  gene2179|gene2179|rna2179|rna2179  67 FNKLSKLYLADQAYKLTIDYHSLLFKPKINDKIEIVIYKgilAEEEVPECYEYVLQGHCYRNKLADGKRIIGVSFG 142
                                        55566666677888**********************9773322344455677*******9****999********* PP

                       RNA_pol_RpbG  89 Gllvk.isskkd 99 
                                        G+l++ i  ++d
  gene2179|gene2179|rna2179|rna2179 143 GMLMEmIVDEND 154
                                        ****96555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       487  (0.0271627); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1266.61
//
Query:       gene218|gene218|rna218|rna218  [L=550]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.011   16.0   3.7        2.8    8.2   0.2    2.9  2  HALZ       Homeobox associated leucine zipper
      0.012   15.7  14.2       0.31   11.1   0.8    3.2  3  UPF0242    Uncharacterised protein family (UPF0242) N-terminu
      0.012   15.9   2.2        1.6    9.2   0.2    3.2  2  FlaC_arch  Flagella accessory protein C (FlaC)
        2.8    7.2   7.5        4.7    6.5   0.6    2.6  2  DUF4407    Domain of unknown function (DUF4407)


Domain annotation for each model (and alignments):
>> HALZ  Homeobox associated leucine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.3   0.00093       4.2      16      41 ..     435     458 ..     432     460 .. 0.86
   2 ?    8.2   0.2   0.00063       2.8       9      29 ..     524     544 ..     520     549 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00093
                           HALZ  16 aLksdydsLkkenekLkaelqeLkek 41 
                                    +L  +++ L++en  Lka + e k++
  gene218|gene218|rna218|rna218 435 KL--RNETLREENAHLKATISEIKAL 458
                                    55..5****************99987 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.00063
                           HALZ   9 vLKasYdaLksdydsLkkene 29 
                                    vLK +Yd Lk  +  L+ke++
  gene218|gene218|rna218|rna218 524 VLKGNYDMLKKTVAELLKERR 544
                                    8*****************987 PP

>> UPF0242  Uncharacterised protein family (UPF0242) N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   1.5   8.1e-05      0.37      66     129 ..     263     344 ..     240     360 .. 0.75
   2 ?   11.1   0.8   6.9e-05      0.31     142     186 ..     439     480 ..     410     484 .. 0.79
   3 ?    1.2   0.5     0.077   3.4e+02      82     119 ..     506     543 ..     480     550 .] 0.58

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 8.1e-05
                        UPF0242  66 ekskleekeaklteld..................eglktkeealeelqeeeeeLkeeldakeeelerlkeenqqLqekle 127
                                        ++ +  ++ e+d                  ++ +  +e+l+e ++++ +Lke++++ +  +++ + ++  L  + e
  gene218|gene218|rna218|rna218 263 HVISTDRQSPVINEQDaflrpisciddpagadhtQKGESSAENLKEQTNKTLQLKEHMKKENDYVQENTYDDDGLITQCE 342
                                    2233444555555555999888899998885554444555669*********************************9999 PP

                        UPF0242 128 ai 129
                                    a+
  gene218|gene218|rna218|rna218 343 AS 344
                                    85 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 6.9e-05
                        UPF0242 142 eqLaekqellqeyqetieeqrsvlekrqdqieqLeskVrDlnyEi 186
                                    e+L+e+     ++++ti+e ++ ++ ++++i+ Le +++ l +E 
  gene218|gene218|rna218|rna218 439 ETLREE---NAHLKATISEIKALIKMKNQNIGVLEQRINFLECEK 480
                                    333333...346789****************************95 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.077
                        UPF0242  82 eglktkeealeelqeeeeeLkeeldakeeelerlkeen 119
                                    e+++    ++e +++e+  Lk ++d  ++++++l +e 
  gene218|gene218|rna218|rna218 506 EEVRMFCRKMERVRQENTVLKGNYDMLKKTVAELLKER 543
                                    33333444566666666666666666666666665554 PP

>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.2    0.0082        37      17      38 ..     439     460 ..     431     479 .. 0.88
   2 ?    9.2   0.2   0.00036       1.6       8      42 ..     507     541 ..     503     541 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.0082
                      FlaC_arch  17 etvkkeneelsksveelkenVk 38 
                                    et+++en +l+ ++ e+k  +k
  gene218|gene218|rna218|rna218 439 ETLREENAHLKATISEIKALIK 460
                                    7899999999999999998776 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00036
                      FlaC_arch   8 klsklsteletvkkeneelsksveelkenVkdlls 42 
                                    ++  +  ++e v++en  l+ + ++lk++V +ll+
  gene218|gene218|rna218|rna218 507 EVRMFCRKMERVRQENTVLKGNYDMLKKTVAELLK 541
                                    555556699************************96 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.6    0.0011       4.7     180     254 ..     244     348 ..     200     355 .. 0.76
   2 ?    3.6   1.2    0.0081        36     125     226 ..     442     543 ..     424     550 .] 0.55

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0011
                        DUF4407 180 Gkgpaakekkaqldaaqaelaelkakld..............................atarlaalraelaeleaerake 229
                                    G+  +  ++++++ ++q+     +++ +                              ++++l+++ ++  +l++ ++ke
  gene218|gene218|rna218|rna218 244 GENGILNTNEENNIQKQQSHVISTDRQSpvineqdaflrpisciddpagadhtqkgesSAENLKEQTNKTLQLKEHMKKE 323
                                    444444444444444333333333333357777778888888888888888888888899******************** PP

                        DUF4407 230 raasqaaaaaddGllarlealdrlt 254
                                    ++  q+ + +ddGl+++ ea + l 
  gene218|gene218|rna218|rna218 324 NDYVQENTYDDDGLITQCEASEVLL 348
                                    ******************9977665 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.0081
                        DUF4407 125 eqlaaaltaelaeleaqiaalqaeidaaearldal..raeaqkeldgtkgtgttgvaGkgpaakekkaqldaaqaelael 202
                                    ++ +a+l+a+++e++a i+  +++i  +e+r++ l  ++++++  +g   +g + v +  ++++e  ++  ++ +++ + 
  gene218|gene218|rna218|rna218 442 REENAHLKATISEIKALIKMKNQNIGVLEQRINFLecEKKLRDTDHGMIENGLELVDRLKAVYQEEVRMFCRKMERVRQE 521
                                    34445577777777777777777777777777755114556666666557888888888888888433333333333333 PP

                        DUF4407 203 kakldatarlaalraelaeleaer 226
                                    ++    + + + l+++ ael +er
  gene218|gene218|rna218|rna218 522 NTV--LKGNYDMLKKTVAELLKER 543
                                    333..3333333333333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (550 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       994  (0.0554409); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.44
# Mc/sec: 3728.43
//
Query:       gene2180|gene2180|rna2180|rna2180  [L=153]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       277  (0.0154498); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 1045.32
//
Query:       gene2181|gene2181|rna2181|rna2181  [L=529]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.2e-40  138.5   9.4    1.2e-37  130.4   9.4    2.6  1  Sec1      Sec1 family
  ------ inclusion threshold ------
        0.1   12.7   2.2       0.17   12.0   2.2    1.3  1  UPF0242   Uncharacterised protein family (UPF0242) N-terminus
       0.12   12.4   0.5       0.21   11.7   0.5    1.4  1  DUF480    Protein of unknown function, DUF480


Domain annotation for each model (and alignments):
>> Sec1  Sec1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.4   9.4     2e-41   1.2e-37       4     483 ..     100     463 ..      97     525 .. 0.71

  Alignments for each domain:
  == domain 1  score: 130.4 bits;  conditional E-value: 2e-41
                                        EE-HHHHHHHHTT--HHHHHTTTEEETT..T.--S-.....BTTSEEEEEE-S-HHHHHHHHHHHHSS-SBS-EEE CS
                               Sec1   4 vlDkelskilssvlkvsdlleegVtkieklk.krepskrealphlkaiyflrptkenidrlakdfisarrykeyhi 78 
                                        ++D ++++ilss + ++  l+++++ +  l+ +r       ++ l +++f +pt +  +++++   ++++y++y +
  gene2181|gene2181|rna2181|rna2181 100 LFDSYTKPILSSHVPHTTFLKNEFFLFQMLTdTRCR-----MQGLTCVIFAQPT-SIYQIVCE--LREPKYGRYIV 167
                                        79******************99***66655445666.....*************.66677774..46689****** PP

                                        EESS---HHHHHHHHH..S.G.GGGEEEEE----SEEEETTEEE-STTHHHHSTTG.....GG.......--HHHH CS
                               Sec1  79 fftprlseslleglakade.evvkkvklkelnldfvplesdlfslnpelplsfrdlyldndnsaleeeieslldri 153
                                        fft+r++e+ le +a++d  +vv++v+  e+n+ +v l++ l+                +dn+             
  gene2181|gene2181|rna2181|rna2181 168 FFTSRVDEDVLEIMARSDTyAVVSEVY--EMNIGVVKLDDMLYRV--G-----------GDNR------------- 215
                                        ****************99889******..***********99988..3...........2444............. PP

                                        HHHHHHHHHHH-..--EEEE.-TT-HHHHHHHH..........HHHHTTT--SS--EEEEE-GGG-SSTTTS---B CS
                               Sec1 154 akgLlsvllslekkiPiiry.kgsaasmvakkladelkekidskknfesessrqrpvLiIlDRsvDlvtpllhqwT 228
                                         +g++ vl +l + +P+ ++  g   +   + + + + +  +   +       +r +Li l Rs+D++tpl+h+w 
  gene2181|gene2181|rna2181|rna2181 216 MDGIMCVLSTL-GICPKMIAtAG--MK---DTVTQIMVHA-S---K-----FANRGTLIMLNRSFDPYTPLVHEWR 276
                                        79*********.88***888355..55...3454444432.1...1.....246999******************* PP

                                        HHHHHHHHS--BTEEEEEE--SSSEEEEEE--TT..-TTHHHHTTSBHHHHHHHHHHHHHHHHHHHHTTT...-TT CS
                               Sec1 229 YqaliddllgglnnnnvvleeepkeekeaelvesssDeffaelrhlnfgevgeklkkeakeyqeenekkrngakes 304
                                        Yq +i+++lg   +n +v+++       ++ v++  D ff+ +++l ++ v+ +l++ + +  +            
  gene2181|gene2181|rna2181|rna2181 277 YQPMIYEYLG--SSNGIVTID-------RTYVLN--DAFFELNKFLDINTVSANLREFVTTTEKVP---------- 331
                                        *********9..778888876.......699999..************999999988887766544.......... PP

                                        HHHHHHHHHH-GGGHHHHHHHHHHHHHHHHHHHHS-HHH.HHHHHHHHHHHHSS--.B--..-HHHHHHHH-TTS- CS
                               Sec1 305 iadlkkfvaklpelqeekkklskHtnlaeellkevkkrkldellelEqdlatgesdkkikekkvieeliaddepts 380
                                          d    +++l + ++ k++l+kH++l ++++k+  ++k  e++e+E +++ +    ++ + k+ie+++++++  +
  gene2181|gene2181|rna2181|rna2181 332 -VD----LSALSTATKTKESLEKHLKLHNHIVKHCVDNK--EISEIEMKIIRD----NKMSSKQIEKVLSNEKL-T 395
                                        .22....34577789999*************99999887..9********953....2233367******9555.4 PP

                                        H.HHHHHHHHHHHH...-B.-H..T--GG......GGHHHHGGGGG........---.BGGG-------....... CS
                               Sec1 381 eledklRLlllyslvegglkek..elkellr..elvqsalygleylktlrsleklgllkkrkgkksskkksslkli 452
                                          e+k +L+++y l++ +   +   ++++ +  ++v++  ++ + + t+r+                         
  gene2181|gene2181|rna2181|rna2181 396 R-EQKCKLVMIYLLRNPHK-RNrpVFEKYTKaqQFVKKH-TN-AAVPTFREHV----------------------- 444
                                        5.6***********96332.2235444442211112211.11.1222222222....................... PP

                                        ---------S...TT-.----HHHHHHHHHTT CS
                               Sec1 453 keeedeesnydlsgvs.ryaPllvrlvealik 483
                                                     +++  y P ++ ++  ++k
  gene2181|gene2181|rna2181|rna2181 445 -------------DIKlAYEPVITSVLGRILK 463
                                        .............2344566666666666666 PP

>> UPF0242  Uncharacterised protein family (UPF0242) N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   2.2   2.8e-05      0.17      66     150 ..     312     395 ..     294     404 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.8e-05
                            UPF0242  66 ekskleekeaklteldeglktkeealeelqeeeeeLkeeldakeeelerlkeenqqLqekleaiaedfeelklele 141
                                        + ++++++ +  + + e++ +   al  +++ +e L+++l+  ++ +++   +n++++e   +i +d++++++++e
  gene2181|gene2181|rna2181|rna2181 312 DINTVSANLREFVTTTEKVPVDLSALSTATKTKESLEKHLKLHNHIVKHC-VDNKEISEIEMKIIRDNKMSSKQIE 386
                                        667777777777778889999999****************9988766655.56777888888899*********** PP

                            UPF0242 142 eqLaekqel 150
                                        + L ++++ 
  gene2181|gene2181|rna2181|rna2181 387 KVLSNEKLT 395
                                        ***998764 PP

>> DUF480  Protein of unknown function, DUF480
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.5   3.6e-05      0.21      17     104 ..     324     412 ..     311     443 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.6e-05
                                        HH-GGG-SEEHHHHHHHHT-SSS-SS-----HHHHHHHHHHHHHTTSEEEE..--SS.--EEEE-HHHHHT--HHH CS
                             DUF480  17 attPdqYPLslnalvaacNQkssRePvmelsesevqealdeLkkkklvseaseagsR.vekyehrleealklseae 91 
                                        +tt ++ P+ l al +a+  k s e  ++l+++ v++++d+ +  ++ ++  + ++  +++ e+ l+++   +e++
  gene2181|gene2181|rna2181|rna2181 324 VTTTEKVPVDLSALSTATKTKESLEKHLKLHNHIVKHCVDNKEISEIEMKIIRDNKMsSKQIEKVLSNEKLTREQK 399
                                        799************************************9987777666554444440445566666666667788 PP

                                        HHHHHHHHHH-SB CS
                             DUF480  92 lavlalllLRGpq 104
                                          ++ + lLR p 
  gene2181|gene2181|rna2181|rna2181 400 CKLVMIYLLRNPH 412
                                        8999999***986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (529 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1064  (0.0593452); expected 358.6 (0.02)
Passed bias filter:                      552  (0.0307881); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.66u 0.28s 00:00:00.94 Elapsed: 00:00:00.49
# Mc/sec: 3277.91
//
Query:       gene2182|gene2182|rna2182|rna2182  [L=184]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-30  105.9   1.6    2.1e-30  105.7   1.6    1.1  1  SPC25     Microsomal signal peptidase 25 kDa subunit (SPC25)
  ------ inclusion threshold ------
      0.066   13.3   0.4       0.11   12.6   0.4    1.6  1  UL41A     Herpesvirus UL41A


Domain annotation for each model (and alignments):
>> SPC25  Microsomal signal peptidase 25 kDa subunit (SPC25)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.7   1.6   2.3e-34   2.1e-30       2     160 ..      34     182 ..      33     184 .] 0.95

  Alignments for each domain:
  == domain 1  score: 105.7 bits;  conditional E-value: 2.3e-34
                              SPC25   2 lKntlDdalkeyltdl.gfkeshtltdvrLalGylavaiaavaflydykveFeeskpvlaiavvlYfilsgiltly 76 
                                        lK +++d l eylt++ g++++ht+td+++++G+++v++aa+++++++ ++Fe+ +++l++++++Yf ++++l + 
  gene2182|gene2182|rna2182|rna2182  34 LKVACNDLLIEYLTKEkGYRQKHTYTDMKIVVGLISVVCAALTCYMSMNYSFEDYRKALVVVLAVYFSFNFVLEIS 109
                                        8*************9999********************************************************** PP

                              SPC25  77 stfvekntifvgkrktgskriekitissslkklsptytltvsykdksnkgkslkakeleksvgewFdedGylveee 152
                                         +++ +nt+f+g++k+g     +i+i+   +  +  y+l ++++ k  +g      ++ ksv e+ de+G+l++e+
  gene2182|gene2182|rna2182|rna2182 110 LRLFARNTVFEGYNKEG-----SIRIDGFNRAVDTDYKLIIYKNGKAIPG------NFCKSVYELYDESGVLDHEA 174
                                        ***************99.....899999999999*********7777775......478899************** PP

                              SPC25 153 feqwlakl 160
                                        f +++a++
  gene2182|gene2182|rna2182|rna2182 175 FLREVAQV 182
                                        *****986 PP

>> UL41A  Herpesvirus UL41A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.4   1.2e-05      0.11      13      37 ..      57      81 ..      31     108 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.2e-05
                              UL41A 13 gyvdmnvcigmigvvcfvfgvfili 37
                                        y dm++++g+i vvc  +  ++ +
  gene2182|gene2182|rna2182|rna2182 57 TYTDMKIVVGLISVVCAALTCYMSM 81
                                       79**************998887654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       753  (0.041999); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 1442.18
//
Query:       gene2183|gene2183|rna2183|rna2183  [L=88]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       557  (0.031067); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.26s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 655.20
//
Query:       gene2184|gene2184|rna2184|rna2184  [L=217]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-07   30.9   0.0    3.7e-07   29.8   0.0    1.6  1  ECR1_N    Exosome complex exonuclease RRP4 N-terminal region


Domain annotation for each model (and alignments):
>> ECR1_N  Exosome complex exonuclease RRP4 N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8   0.0     2e-11   3.7e-07       2      37 ..       2      37 ..       1      38 [. 0.95

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 2e-11
                                       E-TT-EEEETTTSEE-TTEEEETTEEEESSSEEEEE CS
                             ECR1_N  2 VtPGevlttdeefmrGhGTYvrggtiyAsvaGtvev 37
                                        +PGe +++ e+ + +h+TY ++ +i++sv+Gt+++
  gene2184|gene2184|rna2184|rna2184  2 FIPGEKVCDIEDNIYSHNTYPHNTSIHSSVLGTLTR 37
                                       69*******************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       316  (0.0176251); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 1606.90
//
Query:       gene2185|gene2185|rna2185|rna2185  [L=1307]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.1e-13   49.3  14.4    8.3e-08   31.9   0.1    4.4  5  KH_1           KH domain
      0.004   17.0   1.6      0.014   15.2   0.2    2.6  3  HEPN-like_int  HEPN-like integron domain
  ------ inclusion threshold ------
       0.26   11.2   5.0       0.15   12.0   0.6    2.8  2  HATPase_c_5    GHKL domain


Domain annotation for each model (and alignments):
>> KH_1  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.1      0.41   2.4e+03      22      36 ..     100     114 ..      98     125 .. 0.75
   2 ?   -3.1   0.0       1.3   7.5e+03      44      61 ..     440     458 ..     433     459 .. 0.76
   3 ?   -0.3   0.0      0.16   9.4e+02       4      36 ..     481     514 ..     479     521 .. 0.76
   4 !   23.5   2.0   6.2e-09   3.7e-05       7      65 ..     516     569 ..     510     570 .. 0.83
   5 !   31.9   0.1   1.4e-11   8.3e-08       5      63 ..     579     642 ..     575     645 .. 0.71

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.41
                                        HHHHHHHHT-EEEEE CS
                               KH_1  22 IkeIreetgakIkvp 36 
                                        Ik+I e+t++ I + 
  gene2185|gene2185|rna2185|rna2185 100 IKKISEDTNVLIFLQ 114
                                        9********998854 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 1.3
                                        T.-EEEEEE.SHHHHHHHH CS
                               KH_1  44 derevtisG.speavekAk 61 
                                        + ++v ++G + + v+kA+
  gene2185|gene2185|rna2185|rna2185 440 TCTTVKLTGkNHKIVQKAI 458
                                        5689999998888788885 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.16
                                        EEEGGGHHHHHHTGGGHHHHHHHHHH.T-EEEEE CS
                               KH_1   4 ilvPsslvgriIGkgGsnIkeIreet.gakIkvp 36 
                                        ++++++  + +IGk+   I  ++ +   ++++++
  gene2185|gene2185|rna2185|rna2185 481 FIFKTHERSMVIGKKPGIIELLKYRDmYCHVQIE 514
                                        5677788899*****9999999954558888865 PP

  == domain 4  score: 23.5 bits;  conditional E-value: 6.2e-09
                                        GGGHHHHHHTGGGHHHHHHHHHHT-EEEEESSTT...T.-EEEEEESHHHHHHHHHHHH CS
                               KH_1   7 PsslvgriIGkgGsnIkeIreetgakIkvpksedegsderevtisGspeavekAkelie 65 
                                         ++l  ++ Gk++ +I++I ++tg+kI+++  +    +  ++ isG  ++v  A++++e
  gene2185|gene2185|rna2185|rna2185 516 SKELEEFLCGKKNGKINRIIKDTGTKINIM-VN----NVMTIYISGQSANVCVAIHAVE 569
                                        555566899*******************99.65....4689*****7777****99886 PP

  == domain 5  score: 31.9 bits;  conditional E-value: 1.4e-11
                                        EEGGGHHHHHHTGGGHHHHHHHHHHT-EEEEESSTT.....T.-EEEE...EESHHHHHHHHHH CS
                               KH_1   5 lvPsslvgriIGkgGsnIkeIreetgakIkvpksedeg..sderevti...sGspeavekAkel 63 
                                        ++  +++ riIG gG+nI++I+++ g++Ik++++ +++  + +  v++   + ++ea ek k++
  gene2185|gene2185|rna2185|rna2185 579 HLSERHHKRIIGFGGKNIQRIMKKHGVYIKFMSEYERRqnNYSGNVVVktpRKNREALEKMKNE 642
                                        667899*****************88*******64444468555555552144555555555555 PP

>> HEPN-like_int  HEPN-like integron domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0      0.61   3.6e+03      78      94 ..     506     522 ..     492     528 .. 0.76
   2 ?   -2.7   0.0      0.84     5e+03      32      59 ..     637     663 ..     623     668 .. 0.71
   3 !   15.2   0.2   2.4e-06     0.014      26     114 ..    1126    1214 ..    1110    1235 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.61
                      HEPN-like_int  78 rlltslpiElakelkel 94 
                                         +  ++ iEl kel+e+
  gene2185|gene2185|rna2185|rna2185 506 DMYCHVQIELSKELEEF 522
                                        56789999999999998 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 0.84
                      HEPN-like_int  32 evianellvlapseeslvayvalsrval 59 
                                        e++ ne+l+la ++e +  +v + r++l
  gene2185|gene2185|rna2185|rna2185 637 EKMKNEILQLADEKEYKREIVQI-RITL 663
                                        56677777777777777777777.6655 PP

  == domain 3  score: 15.2 bits;  conditional E-value: 2.4e-06
                      HEPN-like_int   26 dlieg.kevianellvlapseeslvayvalsrvalsnliigifklsEliEkkdrlltslpiElakelkelkkkf 98  
                                         +++++ ++++ n++  + ps  s    ++ls ++ + +i++++ +  l  +k+    ++    +k++k++   +
  gene2185|gene2185|rna2185|rna2185 1126 QYVNDeTMKMVNHINSIMPS-TSNISTISLSGICTKSMIMDVNDVVGLNSAKKEFYFDILGQKEKHIKKISPFY 1198
                                         66776699999*99777666.5777789*************************998888879999999997666 PP

                      HEPN-like_int   99 fledikeyRntyv.aHv 114 
                                         ++   k+yR ty+ aH+
  gene2185|gene2185|rna2185|rna2185 1199 YQ-IGKNYRCTYAfAHT 1214
                                         65.55*******83554 PP

>> HATPase_c_5  GHKL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.6   2.5e-05      0.15      42      90 ..     564     612 ..     538     620 .. 0.79
   2 ?   -1.3   0.3      0.35   2.1e+03      24      62 ..     808     846 ..     797     854 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.5e-05
                        HATPase_c_5  42 liisieNsyegekkklesskskkeehGiGlksireivkkykgnlsieae 90 
                                         i  +eN++ +e     s+ ++k+  G+G k+i++i+kk++  +++  e
  gene2185|gene2185|rna2185|rna2185 564 AIHAVENEFPEELAFHLSERHHKRIIGFGGKNIQRIMKKHGVYIKFMSE 612
                                        233589******99999999********************998887655 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.35
                        HATPase_c_5  24 ieeekrfIrltvrekkksliisieNsyegekkklessks 62 
                                         +e++++I+ +  +++++ + ++ N  e++ ++ ++ k+
  gene2185|gene2185|rna2185|rna2185 808 SREQSKEIHNEGVNDDGTAMAKCRNALEEHRHEQNEDKN 846
                                        445689999999999999999999999997654444333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1307 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1086  (0.0605723); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.81u 0.33s 00:00:01.14 Elapsed: 00:00:00.47
# Mc/sec: 8439.93
//
Query:       gene2186|gene2186|rna2186|rna2186  [L=290]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-18   67.5   0.1    2.9e-18   66.0   0.1    1.8  1  ArfGap    Putative GTPase activating protein for Arf
  ------ inclusion threshold ------
       0.25   11.5   1.4       0.64   10.2   1.4    1.6  1  UPF0767   UPF0767 family


Domain annotation for each model (and alignments):
>> ArfGap  Putative GTPase activating protein for Arf
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.0   0.1   3.3e-22   2.9e-18       3      75 ..      30     100 ..      28     104 .. 0.92

  Alignments for each domain:
  == domain 1  score: 66.0 bits;  conditional E-value: 3.3e-22
                                        HHHHHCCSCCCCB-TTT-SBS--EEETTTTEEE-HHHHHHHCCS.TTT--EEETTTS---HHHHHHHHHTCHH CS
                             ArfGap   3 alkellkepenkvCaDCgakeptWaslnlgvflCieCsgvHrslgvhiskvrsltldkwedeelellkalgNk 75 
                                         ++ l + pen+ C DC++++ptWa ln+gv+lC+ C+g Hr+   +  kvrsl  d+++d+e+  +  +gN 
  gene2186|gene2186|rna2186|rna2186  30 RISMLHTFPENAACNDCKSTNPTWANLNFGVLLCTACAGTHREN--KHYKVRSLLFDRLSDDEVLRVLVGGNG 100
                                        56778889**********************************98..7889******************99996 PP

>> UPF0767  UPF0767 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   1.4   7.1e-05      0.64      34      74 ..     159     203 ..     149     211 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 7.1e-05
                            UPF0767  34 llsdkytpy..eksisekReeRlleeelnkdvtqveslkek....kf 74 
                                        +++ k t +  +ksi+e R++R+ e    kd + v+++k++    + 
  gene2186|gene2186|rna2186|rna2186 159 IVKTKRTTKigSKSIEELRKKRESEG--MKDKAVVKEVKKQvvvkEV 203
                                        344555555689**********9965..5565666666655222244 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (290 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1164  (0.0649228); expected 358.6 (0.02)
Passed bias filter:                      497  (0.0277205); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2052.02
//
Query:       gene2187|gene2187|rna2187|rna2187  [L=1043]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-70  238.4   0.1    1.2e-49  169.0   0.0    3.7  3  AMP-binding    AMP-binding enzyme
    2.5e-14   54.0   0.2    6.3e-14   52.7   0.2    1.8  1  AMP-binding_C  AMP-binding enzyme C-terminal domain
    1.2e-11   44.3   0.2    2.6e-11   43.3   0.2    1.6  1  ACAS_N         Acetyl-coenzyme A synthetase N-terminus
  ------ inclusion threshold ------
      0.033   14.2   2.3       0.37   10.8   2.9    2.2  2  Mucin          Mucin-like glycoprotein


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  169.0   0.0   2.7e-53   1.2e-49       7     271 ..     180     531 ..     175     551 .. 0.87
   2 !   39.1   0.0   7.6e-14   3.4e-10     259     368 ..     678     786 ..     609     790 .. 0.85
   3 !   25.1   0.1   1.4e-09   6.2e-06     360     422 ..     861     923 ..     851     924 .. 0.84

  Alignments for each domain:
  == domain 1  score: 169.0 bits;  conditional E-value: 2.7e-53
                                        HST.TSEEEEE...CCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEEE CS
                        AMP-binding   7 ktp.dkvalvd...sgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvvpln 78 
                                        ++p d++al++   +g+  ++TY++ ++rv+ +A +L +lGv+ gd+V +++p++ + ++++la++++Gav+ ++ 
  gene2187|gene2187|rna2187|rna2187 180 RHPpDRTALIYdndDGTSVRYTYAQCKARVCVIAGALHALGVRMGDVVCVYMPMMDDTLFVALACARIGAVHNVVF 255
                                        5555*********9999*********************************************************** PP

                                        TTS-HHHHHHHHHHHTESEEE.....E.TCTCCC.HHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCSCTT CS
                        AMP-binding  79 ptltaeelayiledseakvli.....a.tvdsel.leklleaaakleavklvivldadellkeeelkeeeeseeka 147
                                         ++++e +   ++ds+akvl+     +  v++ +  + ++e+ + +  v++ +++d d+  k    +++ +  e +
  gene2187|gene2187|rna2187|rna2187 256 GGYSKESVVVRIKDSGAKVLVsvvegTrGVQRLNfYKVVEEIIK-EGGVSTALIIDGDCRGKG--GNGCRGRGERD 328
                                        *********************98866367777775555555555.678888999999998877..44444333333 PP

                                        S........................................................................... CS
                        AMP-binding 148 e........................................................................... 148
                                        +                                                                           
  gene2187|gene2187|rna2187|rna2187 329 Gkggneegrggndcegserdgnkdngkdngndkgkdngkdndsnpivnpttdpitnitnpnvnsknfakinflskm 404
                                        14567889999***************************************************************** PP

                                        ...-TSCCCS-BTTSEEEEEEE--SSSS-EEEEEEH.HHHHHHHHHHHHHHCSCCTTT-EEEESS-TTSCHHHHHH CS
                        AMP-binding 149 ...kpeeeeelkpddlayiiYTSGTTGkPKGVmlsh.rnlvanvaslkletrfklkeddvvlsilplahifglile 220
                                           ++ +  ++k++++++i+YTSG+TGkPKG+++s+ ++l+++  +   +++f++++++v++++++l +i+g+++ 
  gene2187|gene2187|rna2187|rna2187 405 nvnTDIPCTPVKAEHPLFILYTSGSTGKPKGIIHSTaGYLLYAHLT--TQHCFNTSSTSVFCCTADLGWITGHTYV 478
                                        ***4445667**************************7777777666..467799999******************* PP

                                        HHHHHHTT-EEEE-TTCGC.CHHHHHHHHHHHHT-SEEEEEHHHHHHHHH.CC CS
                        AMP-binding 221 lllallsGatvvllpkdaa.ldpklllelieklkvtviagvPrvlealle.sg 271
                                        l+++++ G+  v++ + ++ +d  ++++ +e+++vt+++++P++l+ l +  +
  gene2187|gene2187|rna2187|rna2187 479 LYGPMCIGMVSVVVGGLPTyPDVYRMWRIVERYGVTHFYTAPTLLRLLRKlVK 531
                                        *******************88899999*******************9955333 PP

  == domain 2  score: 39.1 bits;  conditional E-value: 7.6e-14
                                        EEHHHHHHHHHCCCHHCHHHHCCGTT-SEEEEESS-EBHHHHHHHHHHHTC.EEEEEEEEGGGSSECEECHCTTTC CS
                        AMP-binding 259 gvPrvleallesgalkaakkakdlsslrlvllggeplspellrffralfge.evlegYGlTEttgvvtvlpleedk 333
                                        +vP++ ++    g+   ++++++lssl+++ ++gep+++e+  +++++f + +v+++Y++TEt+g+v+++    d 
  gene2187|gene2187|rna2187|rna2187 678 TVPSLRNYKKT-GKH--KTTQYNLSSLQVLGSVGEPINKETYVWYSRTFNGrPVIDCYWQTETGGIVVCPVAYVDG 750
                                        55555554422.112..244569**************************9999**************884446667 PP

                                        TSTTS-BEE-TTEEEEEE.-TTTSCBEETTSEEEEE CS
                        AMP-binding 334 kklgsvGkplpgvevkiv.DeetgepvpdgeeGell 368
                                        +++  +G+ + g++v ++  +++g+  ++g+eG ++
  gene2187|gene2187|rna2187|rna2187 751 EVAECAGRGFLGIRVFVIrKDNDGKDGGKGNEGRVV 786
                                        788999*********999844558988999999875 PP

  == domain 3  score: 25.1 bits;  conditional E-value: 1.4e-09
                                        ETTSEEEEEEEET..TS-SEBTT-HHHHHHHEEETCCEEEEEEEEEEETTSEEEEEEECCCEEEE CS
                        AMP-binding 360 pdgeeGellvrgp..gvmkgYlkkpeataeafdsegrwlrTGDlgrldedGyleivgRkkdlikl 422
                                        +++e G +++ g   g+++  l+++++  ++++ + + + TGD g++  +G+l++ gR++d+i++
  gene2187|gene2187|rna2187|rna2187 861 QENELGLIVLYGSwpGMARTILNDHARFTSTYT-KHGVYYTGDEGVFY-RGRLFVRGRADDIINV 923
                                        4566699888887559****************9.646*********98.7*************98 PP

>> AMP-binding_C  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.7   0.2   1.4e-17   6.3e-14       8      76 .]     943    1007 ..     932    1007 .. 0.89

  Alignments for each domain:
  == domain 1  score: 52.7 bits;  conditional E-value: 1.4e-17
                                         SSTTEEEEEEE-----TTS---EEEEEE------HHHHHHHHHHHHT-TTTS-SEEEE-S---B-TTS- CS
                      AMP-binding_C    8 shpaVaeaaVvGvpdevkGealvafVvlkdgsealeeeLkahvrkelgpyavpkkvvfvdelpktrsGK 76  
                                         + + V e+a vG pde++G ++v fVv   ++   e  L+a++++++g++  p++v+fv++lpktr+GK
  gene2187|gene2187|rna2187|rna2187  943 EDERVVEVAMVGAPDEITGLCIVLFVVG--DV--CEGRLRAFLKRRIGAIINPRRVYFVKDLPKTRTGK 1007
                                         4567***********************7..54..459*******************************9 PP

>> ACAS_N  Acetyl-coenzyme A synthetase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.3   0.2   5.8e-15   2.6e-11       1      55 []     124     177 ..     124     177 .. 0.94

  Alignments for each domain:
  == domain 1  score: 43.3 bits;  conditional E-value: 5.8e-15
                                        HHHHHHHHHH-HHHHHHHHHCCS--SB--S-SECSTTTCT-EESTT-EE-HHHHH CS
                             ACAS_N   1 ykelykeSiedpeaFWaeqakeldWekpfdkvldgskgpfikWFeGGklNicyNc 55 
                                        y++ly++Si++p  F +++ ++l+W+k+++k  +  + ++ ++F++G+lN+cyN+
  gene2187|gene2187|rna2187|rna2187 124 YNALYNHSITNPTFFLEQAIDRLSWYKQPTKCTNN-NLQSLEYFSDGTLNACYNA 177
                                        89**********9888888899*********9998.899***************7 PP

>> Mucin  Mucin-like glycoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   2.9   8.3e-05      0.37      31      67 ..      66     101 ..      36     112 .. 0.83
   2 ?   -0.5   0.0      0.24   1.1e+03      28      71 ..     348     393 ..     205     419 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 8.3e-05
                              Mucin  31 sdaavveaaegqskltttttttkppttttttttastt 67 
                                        +d+ +ve+ +g++  ++tttt +++t++t+ tt   t
  gene2187|gene2187|rna2187|rna2187  66 EDSIGVEGVDGKDVVDSTTTTDTTTTAATANTTGN-T 101
                                        56778999999999999998888888877777543.3 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.24
                              Mucin  28 eGqsdaavveaa.egqsk.ltttttttkppttttttttasttittk 71 
                                        +G++d+ + +++ +g+++ ++  + ++  ptt  +t+ + + +++k
  gene2187|gene2187|rna2187|rna2187 348 DGNKDNGKDNGNdKGKDNgKDNDSNPIVNPTTDPITNITNPNVNSK 393
                                        4555444433321233321344555666666655555444444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1043 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1688  (0.0941491); expected 358.6 (0.02)
Passed bias filter:                      510  (0.0284455); expected 358.6 (0.02)
Passed Vit filter:                        76  (0.00423894); expected 17.9 (0.001)
Passed Fwd filter:                        22  (0.00122706); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.94u 0.32s 00:00:01.26 Elapsed: 00:00:00.50
# Mc/sec: 6243.86
//
Query:       gene2188|gene2188|rna2188|rna2188  [L=169]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (169 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       381  (0.0212505); expected 358.6 (0.02)
Passed bias filter:                      198  (0.0110436); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 1184.74
//
Query:       gene2189|gene2189|rna2189|rna2189  [L=121]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1236  (0.0689386); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 985.81
//
Query:       gene219|gene219|rna219|rna219  [L=270]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.6e-70  236.8   0.0    2.9e-70  236.7   0.0    1.0  1  Pkinase        Protein kinase domain
    1.7e-37  129.1   0.0      2e-37  128.9   0.0    1.0  1  Pkinase_Tyr    Protein tyrosine kinase
    2.6e-06   27.0   0.0    5.9e-06   25.8   0.0    1.5  2  Kinase-like    Kinase-like
    0.00035   20.2   0.0    0.00055   19.6   0.0    1.3  1  RIO1           RIO1 family
    0.00054   19.4   0.1    0.00082   18.8   0.1    1.2  1  Kdo            Lipopolysaccharide kinase (Kdo/WaaP) family
     0.0012   18.5   0.0       0.53    9.9   0.0    2.2  2  FTA2           Kinetochore Sim4 complex subunit FTA2
     0.0049   15.9   0.5      0.008   15.2   0.5    1.3  1  Haspin_kinase  Haspin like kinase domain
  ------ inclusion threshold ------
      0.036   14.4   0.0        1.3    9.4   0.0    2.5  2  PWI            PWI domain
       0.11   12.3   1.8        1.8    8.4   0.1    2.3  3  APH            Phosphotransferase enzyme family


Domain annotation for each model (and alignments):
>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  236.7   0.0   1.5e-73   2.9e-70       2     264 .]      10     261 ..       9     261 .. 0.93

  Alignments for each domain:
  == domain 1  score: 236.7 bits;  conditional E-value: 1.5e-73
                                    EEEEEEEEESSEEEEEEEETTTTEEEEEEEEECHCHCHHHH.HHHHHHHHHHHHHSCTTB--EEEEEEESSEEEEEEE-- CS
                        Pkinase   2 ekleklGeGsfGkVykaveketgkivAvKkikkekakkkke.kkvlrEikilkklkhpnivrlyevfeekdelylvleyv 80 
                                    e    lG G+fG+V  ++ek ++ i A+K+i k+  +k++  ++++rE++i+ kl++p+i+r+y+ f++k+++ylvley+
  gene219|gene219|rna219|rna219  10 ELGAPLGAGQFGQVWLVREKVRNYILALKIIPKSIVEKTDSyRQLRRELEIHTKLRSPYILRCYGHFHDKNNIYLVLEYA 89 
                                    56778*****************************99998889************************************** PP

                                    TTEBHHHHHHHHSS--HHHHHHHHHHHHHHHHHHHHTTEE-SS-SGGGEEEETTTEEEE-SGTTSEESSSSCSBCTTTSC CS
                        Pkinase  81 eggeladllerkgslseeeakkiakqilegleylHskgiiHrDlKpeNiLidekgelKitDFGlakelessskltsfvgt 160
                                    ++gel+++l +kg+++e++a ++++q+l++++ +Hs+++iHrDlKpeNiLi  +++l+i+DFG +     ++   +f+gt
  gene219|gene219|rna219|rna219  90 SNGELFHHLVEKGKFDEKTAANYIYQVLHAVRTMHSHKVIHRDLKPENILIGCDNKLRIADFGWSVCDVDQK-RGTFCGT 168
                                    ***************************************************************997666655.8****** PP

                                    GGGS-HHHHTTSCBSHHHHHHHHHHHHHHHHHSS-STTTSSHHHHHHHHHHTHHHHHHHCTSHH...HHHTTS-HHHHHH CS
                        Pkinase 161 seYlAPEvlkeneyskkvDvWslGvilyelltgkppfsgekgkekvekeldqlekilkilgetkeklpeaseiseeakdl 240
                                    +eYl PE++++n+y +kvD+W +G++ yell g++pf++ ++++  +  +++           +++++ ++ +se+a+++
  gene219|gene219|rna219|rna219 169 QEYLCPEIINKNQYNNKVDMWCIGILTYELLVGNTPFEAPDRTT--RDAYRK---------IRNLEYDLPKFLSENAQRF 237
                                    **************************************655554..444444.........34678899999******** PP

                                    HHHHT-SSGCCSTTHHHHHTSGGG CS
                        Pkinase 241 lkkllkkdpkkRltaeellqhpyl 264
                                    + +ll  + +kR+ ++e+l++p++
  gene219|gene219|rna219|rna219 238 IARLLVAESEKRPDVNEMLNDPWI 261
                                    ***********************7 PP

>> Pkinase_Tyr  Protein tyrosine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  128.9   0.0     1e-40     2e-37       2     256 ..      10     256 ..       9     258 .. 0.88

  Alignments for each domain:
  == domain 1  score: 128.9 bits;  conditional E-value: 1e-40
                                    EEEEEEEEESSEEEEEEEEETTTTSSEEEEEEEEESTTSSHHH..HHHHHHHHHHHHTS-BTTB--EEEEEESSSSEEEE CS
                    Pkinase_Tyr   2 elgkklGeGafGkVvegtlkgekekkevkVavKtlkeeateee..keelleeakimkklkhpnivkllgvctkeeplliv 79 
                                    elg  lG+G+fG+V+  + k     +++  a+K++ ++  e++   ++l +e++i +kl+ p i++++g   +++++++v
  gene219|gene219|rna219|rna219  10 ELGAPLGAGQFGQVWLVREK----VRNYILALKIIPKSIVEKTdsYRQLRRELEIHTKLRSPYILRCYGHFHDKNNIYLV 85 
                                    67889**********99999....666667777775543333222699******************************** PP

                                    EE--TTEBHHHHHHHTCTTTSBHHHHHHHHHHHHHHHHHHHHTTEEEST-SGGGEEEEETTEEEE-STTTHEETTTSSEE CS
                    Pkinase_Tyr  80 teyvkgGdLlkfLrkkekekltlkdllsfalqvAkGmeyLeskklvHrdlaarNvLlsenkvvkisDfGLardiekddey 159
                                    +ey+++G+L ++L +k   k++ k+  ++++qv ++++ ++s+k++Hrdl   N+L+  +++ +i+DfG +         
  gene219|gene219|rna219|rna219  86 LEYASNGELFHHLVEK--GKFDEKTAANYIYQVLHAVRTMHSHKVIHRDLKPENILIGCDNKLRIADFGWSVCD----VD 159
                                    **************98..9**************************************************98744....55 PP

                                    EETTSSTSGGGGS-HHHHHHSEEEHHHHHHHHHHHHHHHHTTSSGTTTTS..HHHHHHHHHHTTEES-BBTTSBHHHHHH CS
                    Pkinase_Tyr 160 vkkeeaklpvkWmapEslkekkftsksDvWsfGvllwEiftlgespypgl..kneevleklkegkrlekpekcpeelyel 237
                                    +k+++     +++ pE++++++++ k D+W+ G+l++E++  g++p++    +++++++k+++  + + p+  +e+ +++
  gene219|gene219|rna219|rna219 160 QKRGTFCGTQEYLCPEIINKNQYNNKVDMWCIGILTYELLV-GNTPFEAPdrTTRDAYRKIRN-LEYDLPKFLSENAQRF 237
                                    67777788999*****************************9.****87653367778888754.567789999******* PP

                                    HHHHT-SSGGGS--HHHHH CS
                    Pkinase_Tyr 238 mkkcweedpeeRptfselv 256
                                    + + + ++ e+Rp+ +e++
  gene219|gene219|rna219|rna219 238 IARLLVAESEKRPDVNEML 256
                                    **************99986 PP

>> Kinase-like  Kinase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0      0.89   1.8e+03      17      61 ..      12      56 ..       9      68 .. 0.69
   2 !   25.8   0.0     3e-09   5.9e-06     135     288 .]      99     249 ..      79     249 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.89
                    Kinase-like 17 gellkkgdrsvvfevkdqetgeplavkvfllpseaskkdlerlke 61
                                   g +l+ g+++ v++v+++ ++  la+k+           + +l++
  gene219|gene219|rna219|rna219 12 GAPLGAGQFGQVWLVREKVRNYILALKIIPKSIVEKTDSYRQLRR 56
                                   568888899999999999888888888765444445555555555 PP

  == domain 2  score: 25.8 bits;  conditional E-value: 3e-09
                    Kinase-like 135 set.hkkletiarlllTlqlirlaanLqakglvhgkftvdnllldekgglmlggftaLvragtkvvlseve..kgfaPpE 211
                                    +e+ ++ ++t+a  ++  q++  +  ++++ ++h +++++n+l   + +l + +f+  v + ++ +  + +  + +  pE
  gene219|gene219|rna219|rna219  99 VEKgKFDEKTAA-NYI-YQVLHAVRTMHSHKVIHRDLKPENILIGCDNKLRIADFGWSVCDVDQKR-GTFCgtQEYLCPE 175
                                    444344455555.555.599************************************9999888888.6666568999*** PP

                    Kinase-like 212 llgsrggytrknktkmthkldaWqlGlviyriwclklPltlateeakeew......kfklckkipekvkaLlkkfLqlsq 285
                                    ++++ +        ++  k+d W +G+  y +   + P++ +      ++      ++ l k  +e+ ++ ++++L  ++
  gene219|gene219|rna219|rna219 176 IINK-N--------QYNNKVDMWCIGILTYELLVGNTPFEAPDRTTRDAYrkirnlEYDLPKFLSENAQRFIARLLVAES 246
                                    **99.3........45669***************************99999999999*********************99 PP

                    Kinase-like 286 edR 288
                                    e+R
  gene219|gene219|rna219|rna219 247 EKR 249
                                    998 PP

>> RIO1  RIO1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   2.8e-07   0.00055      82     153 ..      83     155 ..      49     165 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 2.8e-07
                                    EEEEE--EETTEEGGBHHHCG-..HHHHHHHHHHHHHHHHHHHHTSTEEESS-STTSEEEETT.EEEE--GTTEE CS
                           RIO1  82 vlvmefigedgvaapklkdvee..eeeaeelyeevleemrklykeaglvHaDLSeyNvlvded.kvviIDvsQav 153
                                     lv+e+ + +g    +l +  +  e+ a+++ ++vl+++r +   ++++H DL   N+l+  d k+ i D++ +v
  gene219|gene219|rna219|rna219  83 YLVLEYAS-NGELFHHLVEKGKfdEKTAANYIYQVLHAVRTMH-SHKVIHRDLKPENILIGCDnKLRIADFGWSV 155
                                    58999998.6777777766664458889999999**9877766.*****************999******99887 PP

>> Kdo  Lipopolysaccharide kinase (Kdo/WaaP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.1   4.1e-07   0.00082     111     163 ..     100     148 ..      83     164 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 4.1e-07
                            Kdo 111 kwaelaeelkrallkavgrliaklhragvnHadlyaknillqqeeeeeaeiwl 163
                                    +  +++e+  ++ + +v  +++ +h+ +v H+dl + nil+  ++    ++ +
  gene219|gene219|rna219|rna219 100 EKGKFDEKTAANYIYQVLHAVRTMHSHKVIHRDLKPENILIGCDN----KLRI 148
                                    445588999999999*************************98877....3333 PP

>> FTA2  Kinetochore Sim4 complex subunit FTA2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.7   0.0    0.0025       4.9      22      98 ..       7      79 ..       1      92 [. 0.61
   2 !    9.9   0.0   0.00026      0.53     170     206 ..     105     141 ..      97     154 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0025
                           FTA2 22 kdiefleyLgkglhsiVlkvkirgkeY..ALKlFrfleaeeleeaeedlkiprealkelasysdpfasECRAfgRLkea 98
                                   +d+e+   Lg+g+ ++V+ v+ + + Y  ALK+  +       e+++++++ r+ l+  ++  +p+   C  +g +++ 
  gene219|gene219|rna219|rna219  7 DDFELGAPLGAGQFGQVWLVREKVRNYilALKIIPKS----IVEKTDSYRQLRRELEIHTKLRSPYILRC--YGHFHDK 79
                                   68899999**********9987777662266654443....32333333333333333333344544444..6666655 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00026
                           FTA2 170 qeelevsqlpkllrdlkklhklgIvvrDlkeenyidg 206
                                    +e++  +++ ++l+ ++ +h++ +++rDlk+en++ g
  gene219|gene219|rna219|rna219 105 DEKTAANYIYQVLHAVRTMHSHKVIHRDLKPENILIG 141
                                    577888999************************9744 PP

>> Haspin_kinase  Haspin like kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.5     4e-06     0.008     169     257 ..      67     157 ..      13     170 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 4e-06
                  Haspin_kinase 169 dkvlkekpdfyseqqlflvlllkdkGtdLeev...klkswkqalsifwqivkiLyvaEtkfeFEHRdLhldniLvdknln 245
                                     ++l+    f ++++++lvl+   +G+   ++      + k+a +  +q+++ +     + +  HRdL+ +niL+    +
  gene219|gene219|rna219|rna219  67 PYILRCYGHFHDKNNIYLVLEYASNGELFHHLvekGKFDEKTAANYIYQVLHAVRTMH-SHKVIHRDLKPENILIGCDNK 145
                                    3334444778899**************9999875423356778888899999888775.67999************9999 PP

                  Haspin_kinase 246 vtlidlklsRle 257
                                      + d+  s   
  gene219|gene219|rna219|rna219 146 LRIADFGWSVCD 157
                                    999999877666 PP

>> PWI  PWI domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0      0.11   2.2e+02      16      36 ..     103     123 ..      96     144 .. 0.69
   2 ?    9.4   0.0   0.00066       1.3      34      60 ..     215     241 ..     188     249 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.11
                            PWI  16 gfeDdvvieyvlnlLeeekel 36 
                                     f++ + ++y++++L+  +++
  gene219|gene219|rna219|rna219 103 KFDEKTAANYIYQVLHAVRTM 123
                                    6999***********543222 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00066
                            PWI  34 keldpkklqinltgfLekeaekFvkeL 60 
                                     + ++++l+ +l +fL ++a+ F+++L
  gene219|gene219|rna219|rna219 215 AYRKIRNLEYDLPKFLSENAQRFIARL 241
                                    6788999*****************998 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.1     0.033        65       4      49 ..      14      66 ..      12     127 .. 0.68
   2 ?    8.4   0.1   0.00092       1.8     166     186 ..     126     147 ..     109     158 .. 0.78
   3 ?   -3.5   0.0       4.1   8.1e+03     123     151 ..     213     232 ..     202     248 .. 0.41

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.033
                                   EE--.SSCEEEEEEETT--EE..EEEE-TT.....S-HHHHHHHHHHHHHHHH CS
                            APH  4 elsggasnrtylvttpagryv..lrrnppa.....raaeeirrevallrlLak 49
                                   +l++g+  +++lv ++ + y+  l+++p++     ++++++rre+++ + L+ 
  gene219|gene219|rna219|rna219 14 PLGAGQFGQVWLVREKVRNYIlaLKIIPKSivektDSYRQLRRELEIHTKLRS 66
                                   67888888999****99999966777777744444566666666665555543 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00092
                                    EEEE-SS-SGGGEEEC...TTE CS
                            APH 166 tvllHgDlhpgNllvd.pddgr 186
                                    + ++H+Dl+p N+l+  +++ r
  gene219|gene219|rna219|rna219 126 HKVIHRDLKPENILIGcDNKLR 147
                                    5589**********99555555 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 4.1
                                    CCHHHHHHCHHHCCCGCCTCCHHHHHHHH CS
                            APH 123 lellrqlesatarllaselldlleeleeq 151
                                    ++ +r++ +    ++ +++l        +
  gene219|gene219|rna219|rna219 213 RDAYRKIRNL--EYDLPKFLS-------E 232
                                    3333333333..333333333.......2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       451  (0.0251548); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 1975.51
//
Query:       gene2190|gene2190|rna2190|rna2190  [L=151]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.012   16.1   0.1      0.018   15.5   0.1    1.2  1  DUF3899          Domain of unknown function (DUF3899)
       0.02   14.8   0.1      0.035   14.1   0.1    1.3  1  DUF1310          Protein of unknown function (DUF1310)
      0.038   13.2   0.0      0.041   13.1   0.0    1.0  1  TipE             Na+ channel auxiliary subunit TipE
        0.1   13.2   0.1        0.1   13.2   0.1    1.9  2  OAD_gamma        Oxaloacetate decarboxylase, gamma chain
       0.12   12.0   0.1       0.13   11.9   0.1    1.1  1  Tetraspanin      Tetraspanin family
       0.15   12.5   0.2       0.27   11.7   0.2    1.4  1  FeoB_associated  FeoB-associated Cys-rich membrane protein
       0.16   12.2   0.1       0.26   11.5   0.1    1.4  1  MAP17            Membrane-associated protein 117 kDa, PDZK1-i


Domain annotation for each model (and alignments):
>> DUF3899  Domain of unknown function (DUF3899)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   0.1   7.1e-06     0.018       7      52 ..       3      49 ..       2      75 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 7.1e-06
                            DUF3899  7 lglllliigillivlnsGfFdgfsygfrklkklflkk.skkddsyye 52
                                       l +ll i+ +l++++  Gf  g++y+++k k+ +++  ++++++++ 
  gene2190|gene2190|rna2190|rna2190  3 LTMLLCIVVFLIFLIFVGFAAGYIYSVHKNKEEMNRLmDSQQAKKMG 49
                                       6799*****************************99889444444433 PP

>> DUF1310  Protein of unknown function (DUF1310)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   1.4e-05     0.035       2      42 ..      10      48 ..       6      68 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.4e-05
                            DUF1310  2 iivlvilvivilavGvkfyldeeklneEmvnvvkSdeakev 42
                                       +++l+ l+ v++a G +  ++++  +eEm +++ S++ak++
  gene2190|gene2190|rna2190|rna2190 10 VVFLIFLIFVGFAAGYIYSVHKN--KEEMNRLMDSQQAKKM 48
                                       45666677788888844444444..69***********986 PP

>> TipE  Na+ channel auxiliary subunit TipE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   1.6e-05     0.041     293     401 ..       2     119 ..       1     146 [. 0.69

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.6e-05
                               TipE 293 vfamaipipsfiisviylafayfviy....nedeeaalld.....kngeeediedelaetdegndnkidavnesea 359
                                        + +m + i  f+i +i++ fa   iy    n++e   l+d     k g + +++d l + de  +n    +  ++ 
  gene2190|gene2190|rna2190|rna2190   2 ILTMLLCIVVFLIFLIFVGFAAGYIYsvhkNKEEMNRLMDsqqakKMGLDSALQDYLVKKDEEVNNSFYGKPINNL 77 
                                        6789999************996666543335556566777433324455667777788888888777766666677 PP

                               TipE 360 avtanhinennvdtaGstiindasttattplqqllpnGtans 401
                                           a  i+++ +++aG +  ++++  + +  ++    G+an+
  gene2190|gene2190|rna2190|rna2190  78 YEKAGVIDKDTNKGAGGKGHGTDQQVKGSGKNEGNDKGAANK 119
                                        777888888888888888777777777776666666666665 PP

>> OAD_gamma  Oxaloacetate decarboxylase, gamma chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   4.1e-05       0.1       9      51 ..       7      46 ..       1      65 [. 0.75
   2 ?   -1.7   0.8       1.8   4.6e+03      39      39 ..     136     136 ..     103     151 .] 0.60

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.1e-05
                          OAD_gamma  9 lGmgvVFvvLilLslvislfskiikkkakkkkkkakaaaaaaa 51
                                       l+   + v+Li+L++v  + ++i +  ++k++++   ++++a+
  gene2190|gene2190|rna2190|rna2190  7 LC---IVVFLIFLIFVGFAAGYIYSVHKNKEEMNRLMDSQQAK 46
                                       33...45789999999999999999999999888777776665 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.8
                          OAD_gamma  39 k 39 
                                        +
  gene2190|gene2190|rna2190|rna2190 136 A 136
                                        1 PP

>> Tetraspanin  Tetraspanin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   5.1e-05      0.13      77     129 ..       4      54 ..       1      89 [. 0.68

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 5.1e-05
                                        XXXXXXXXXXXXXXXXXXXXXXXXX--HHH........HHHHHHHHHHHHHHH CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        Tetraspanin  77 cllltfsllllvlfllelaagilgfvfsdkargkvseiinnaievkyrddldl 129
                                        ++ll+ +++l++l+++ +aag +  v+++k  +++++ ++++  +k+  d+ l
  gene2190|gene2190|rna2190|rna2190   4 TMLLCIVVFLIFLIFVGFAAGYIYSVHKNK--EEMNRLMDSQQAKKMGLDSAL 54 
                                        467777788888888888888888888888..445555544444444444444 PP

>> FeoB_associated  FeoB-associated Cys-rich membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.2    0.0001      0.27       3      26 ..       9      35 ..       4      37 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.0001
                    FeoB_associated  3 iIVgliiaaavafv...irrlikkkkk 26
                                       i+V li ++ v+f+   i++++k+k++
  gene2190|gene2190|rna2190|rna2190  9 IVVFLIFLIFVGFAagyIYSVHKNKEE 35
                                       56666666777777787*******986 PP

>> MAP17  Membrane-associated protein 117 kDa, PDZK1-interacting protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1    0.0001      0.26      35     101 ..       6      68 ..       3      93 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.0001
                              MAP17  35 liAvvgFL.flvfvlllvnrvWcskaraedeeeetfrmeankeedvslskeekkeeekekkekkaake 101
                                        l  +v+FL fl+fv +++  ++  +   +++ee +  m +++++++ l+++ + +    kk+++ +++
  gene2190|gene2190|rna2190|rna2190   6 LLCIVVFLiFLIFVGFAAGYIYSVH---KNKEEMNRLMDSQQAKKMGLDSALQDY--LVKKDEEVNNS 68 
                                        66789998689***********998...333336889999999999998888888..33333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1434  (0.0799822); expected 358.6 (0.02)
Passed bias filter:                     1079  (0.0601818); expected 358.6 (0.02)
Passed Vit filter:                       156  (0.00870099); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 1106.75
//
Query:       gene2191|gene2191|rna2191|rna2191  [L=49]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (49 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       262  (0.0146132); expected 358.6 (0.02)
Passed bias filter:                      178  (0.00992805); expected 358.6 (0.02)
Passed Vit filter:                         6  (0.000334653); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.29u 0.24s 00:00:00.53 Elapsed: 00:00:00.36
# Mc/sec: 403.33
//
Query:       gene2192|gene2192|rna2192|rna2192  [L=366]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0047   16.9   0.1     0.0095   16.0   0.1    1.5  1  PspB             Phage shock protein B
      0.008   16.5   0.7      0.008   16.5   0.7    2.4  2  Ly49             Ly49-like protein, N-terminal region
  ------ inclusion threshold ------
      0.033   14.1   0.3      0.088   12.8   0.3    1.8  1  DUF3319          Protein of unknown function (DUF3319)
       0.12   12.4   0.0       0.27   11.3   0.0    1.5  1  Alpha_E3_glycop  Alphavirus E3 glycoprotein
       0.96    9.4   6.1       0.18   11.8   0.6    2.2  2  DUF4446          Protein of unknown function (DUF4446)
        2.1    8.0   3.3        3.1    7.4   3.2    1.5  1  Tetraspanin      Tetraspanin family
        4.4    5.6   6.6        1.8    6.9   0.3    2.1  2  SID-1_RNA_chan   dsRNA-gated channel SID-1


Domain annotation for each model (and alignments):
>> PspB  Phage shock protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.1   3.7e-06    0.0095       4      71 ..      68     138 ..      65     140 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 3.7e-06
                               PspB   4 flavpliifvlfVapiWLiLHYrs.kkkrskglsae...dekrLeellekAekleeRietLEriLdaespnw 71 
                                        f+++ + ++++ V+++++ ++ +s k++++++ls++   +e++L+++  + +kl+  i+ L + ++a +   
  gene2192|gene2192|rna2192|rna2192  68 FIIISV-VLFVTVVILGMKIYDNSqKRNTESSLSQKrtrNEQELKKIEVQQQKLSGKISMLKKKINATEDPA 138
                                        444445.5555555677777766637888999**9988899********************98777765554 PP

>> Ly49  Ly49-like protein, N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.7   3.1e-06     0.008      11      76 ..      68     144 ..      64     193 .. 0.60
   2 ?   -1.1   0.6      0.94   2.4e+03      67      67 ..     251     251 ..     214     305 .. 0.53

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 3.1e-06
                                        XXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX..HH........... CS
                               Ly49  11 lgILclllLvtvavLvtkifqysqekheleetlnlsqnysimqndinlkeelLrnkslecsilkd........... 75 
                                        + I+ ++l vtv++L++ki+  sq+++++    + + + ++  ++i+++++ L  k    ++  +           
  gene2192|gene2192|rna2192|rna2192  68 FIIISVVLFVTVVILGMKIYDNSQKRNTESSLSQKRTRNEQELKKIEVQQQKLSGKISMLKKKINatedparqvrp 143
                                        5689999**************9999887665554444444444455666666655554444333323333344555 PP

                                        H CS
                               Ly49  76 l 76 
                                        +
  gene2192|gene2192|rna2192|rna2192 144 K 144
                                        2 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.94
                                        X CS
                               Ly49  67 s 67 
                                         
  gene2192|gene2192|rna2192|rna2192 251 K 251
                                        1 PP

>> DUF3319  Protein of unknown function (DUF3319)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.3   3.4e-05     0.088      13      62 ..     103     152 ..      91     178 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.4e-05
                            DUF3319  13 satgatdiWkvkiknhvlsGsLsavkksidWwcdtaslidPkefealnek 62 
                                         + ++++  k+ ++++ lsG++s +kk i+   d a  + Pke + l + 
  gene2192|gene2192|rna2192|rna2192 103 RTRNEQELKKIEVQQQKLSGKISMLKKKINATEDPARQVRPKEGSILRDD 152
                                        4567788899********************************98777544 PP

>> Alpha_E3_glycop  Alphavirus E3 glycoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00011      0.27      33      53 ..     266     286 ..     255     290 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00011
                    Alpha_E3_glycop  33 ednvdrpgYydLLqaaLtCrs 53 
                                        e nv+++ Y dLL+ +L C +
  gene2192|gene2192|rna2192|rna2192 266 EKNVEKDCYADLLKDSLPCED 286
                                        67*****************65 PP

>> DUF4446  Protein of unknown function (DUF4446)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.6   7.1e-05      0.18       6      78 ..      68     134 ..      63     144 .. 0.69
   2 ?   -0.3   0.6      0.38   9.8e+02      39      77 ..     207     245 ..     186     267 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 7.1e-05
                            DUF4446   6 lavlvvillillivllvklkklkkkykklmkgkdgksleellkekleeveelkeeseelekeieeleeklkks 78 
                                        ++++ v+l++++++l +k+      y++ +k+++++sl ++  ++ +e+++++ ++++l+ +i+ l++k++++
  gene2192|gene2192|rna2192|rna2192  68 FIIISVVLFVTVVILGMKI------YDNSQKRNTESSLSQKRTRNEQELKKIEVQQQKLSGKISMLKKKINAT 134
                                        4556666666666666555......555566677788888888888888888888888888888888887765 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.38
                            DUF4446  39 dgksleellkekleeveelkeeseelekeieeleeklkk 77 
                                        +++   +++   +e+ +++++es+e++k i++ +++ ++
  gene2192|gene2192|rna2192|rna2192 207 EDNGHRSTIVVIIEREDDVSKESKENSKAINDDNNDKSN 245
                                        455555666667777777888888877777765555444 PP

>> Tetraspanin  Tetraspanin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   3.2    0.0012       3.1      80     129 ..      66     110 ..      56     267 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0012
                                        XXXXXXXXXXXXXXXXXXXXXX--HHH........HHHHHHHH.HHHHHHH CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxx RF
                        Tetraspanin  80 ltfsllllvlfllelaagilgfvfsdkargkvseiinnaievk.yrddldl 129
                                        +tf+++ +vlf++ +++g+ ++ +s+k+      + ++++++k  r+ ++l
  gene2192|gene2192|rna2192|rna2192  66 ATFIIISVVLFVTVVILGMKIYDNSQKR------NTESSLSQKrTRNEQEL 110
                                        4666666666666666666666666662......22222222201222222 PP

>> SID-1_RNA_chan  dsRNA-gated channel SID-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.3   0.00071       1.8     123     189 ..      67     131 ..      39     185 .. 0.49
   2 ?    1.8   1.3     0.025        64      61     105 ..     201     244 ..     191     272 .. 0.64

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.00071
                     SID-1_RNA_chan 123 vllvllvllsfllltllvvivekvresseekrvkessssesaseslesvssavrsesessveeesdy 189
                                        ++++++v+l +++++l + i+++++++++e+ +++++++++++ ++ +v+++  s + s +  ++++
  gene2192|gene2192|rna2192|rna2192  67 TFIIISVVLFVTVVILGMKIYDNSQKRNTESSLSQKRTRNEQELKKIEVQQQKLSGKISML--KKKI 131
                                        3333333333333333333333333333333333333333333333333332222222222..2222 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.025
                     SID-1_RNA_chan  61 aitvqkkefesgkffvvfvvkpedsaCstslkeknltknsnrtkk 105
                                        ++t++ ++  ++ + +v++++ ed+++++s+++++ +++ n+ k+
  gene2192|gene2192|rna2192|rna2192 201 DFTFKSEDNGHR-STIVVIIEREDDVSKESKENSKAINDDNNDKS 244
                                        677777776666.77888899999999998874444443333332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (366 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2370  (0.132188); expected 358.6 (0.02)
Passed bias filter:                      714  (0.0398237); expected 358.6 (0.02)
Passed Vit filter:                        92  (0.00513135); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.69u 0.30s 00:00:00.99 Elapsed: 00:00:00.46
# Mc/sec: 2394.75
//
Query:       gene2193|gene2193|rna2193|rna2193  [L=176]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-07   31.3   0.3    3.8e-07   30.4   0.3    1.5  1  SF3A2     Pre-mRNA-splicing factor SF3a complex subunit 2 (Pr
  ------ inclusion threshold ------
      0.033   14.4   3.5       0.21   11.8   0.4    2.1  2  DUF1492   Protein of unknown function (DUF1492)
       0.14   12.6   1.8       0.31   11.5   1.8    1.6  1  zf-met    Zinc-finger of C2H2 type
       0.68    8.5   6.3       0.86    8.1   6.3    1.1  1  FapA      Flagellar Assembly Protein A


Domain annotation for each model (and alignments):
>> SF3A2  Pre-mRNA-splicing factor SF3a complex subunit 2 (Prp11)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.4   0.3   8.6e-11   3.8e-07       3      77 ..      86     152 ..      85     166 .. 0.84

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 8.6e-11
                              SF3A2   3 rPgykvtkvrdpeteqvgllvevkypeikeevkPlhrimsaleqkleekpdkkvqyLliaaePYetiafkipske 77 
                                        +P+yk+ +vrd     +g+lv++k +  ++    +++i+ aleq++e   +++++yL++ +  Y++i+++++ +e
  gene2193|gene2193|rna2193|rna2193  86 QPKYKMYNVRDDV--YQGFLVKIKTK--HD---VMYKIVKALEQNVEL-VNQNYNYLVFKVREYDNIGLRVDVSE 152
                                        7**********65..78999999887..33...589***********7.*********************99655 PP

>> DUF1492  Protein of unknown function (DUF1492)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.4   4.7e-05      0.21      38      95 ..       9      67 ..       1      72 [. 0.78
   2 ?    3.6   0.2     0.016        72      20      51 ..      95     129 ..      81     141 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 4.7e-05
                            DUF1492 38 taeai..kkklelqrlidklensdsrsvLrmvyidkltvwqvidklnisrstyyrllrva 95
                                       t  +i  ++++ l++li++l++ +    Lr+ ++ k+   ++++  +  +s y   +   
  gene2193|gene2193|rna2193|rna2193  9 TPAIIkeNRRKRLKQLINRLHDLKNDKYLRINHLGKIEC-KLCYTTHTNESSYVIHRSST 67
                                       555552247789***********************9975.79999999999987666554 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.016
                            DUF1492  20 kddvyveLvv...akediekktaeaikkklelqrl 51 
                                        +ddvy  ++v   +k d+  k + a++++ el ++
  gene2193|gene2193|rna2193|rna2193  95 RDDVYQGFLVkikTKHDVMYKIVKALEQNVELVNQ 129
                                        799*9876442337999999999999999999765 PP

>> zf-met  Zinc-finger of C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   1.8   6.8e-05      0.31       2      25 .]      46      69 ..      45      69 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 6.8e-05
                             zf-met  2 yCelCnvtfnsesqlksHlqGKkH 25
                                       +C+lC +t+++es++  H  + +H
  gene2193|gene2193|rna2193|rna2193 46 ECKLCYTTHTNESSYVIHRSSTRH 69
                                       6*****************999888 PP

>> FapA  Flagellar Assembly Protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   6.3   0.00019      0.86     341     452 ..      16     131 ..       3     133 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00019
                               FapA 341 eleeeleeleeeleklkkk....ikklpklkaekqlesekkeqlkklletkeklkeeleeleeelk.elkeelesk 411
                                        + +++l++l ++l++lk++    i++l k++   +  + +  ++ +   + ++ ++  ++l +e++ + + +l+++
  gene2193|gene2193|rna2193|rna2193  16 NRRKRLKQLINRLHDLKNDkylrINHLGKIE---C--KLCYTTHTNESSYVIHRSSTRHQLLAEKQfKRDRMLNNQ 86 
                                        5567788888888888888765566666633...2..556677777777779999999998888888999999999 PP

                               FapA 412 keeakikvnkeiypgvkikig...kkkliikre.ysnttfvleeg 452
                                         + + ++v++ +y g  +ki+   + +++i +  ++n+ +v++++
  gene2193|gene2193|rna2193|rna2193  87 PKYKMYNVRDDVYQGFLVKIKtkhDVMYKIVKAlEQNVELVNQNY 131
                                        7777***********999999777777778777788888888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1188  (0.0662614); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1191.29
//
Query:       gene2195|gene2195|rna2195|rna2195  [L=177]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.3e-32  112.6   0.1    1.8e-32  112.2   0.1    1.2  1  Arf        ADP-ribosylation factor family
    2.2e-12   47.3   0.0    3.1e-12   46.7   0.0    1.2  1  Roc        Ras of Complex, Roc, domain of DAPkinase
    7.8e-12   45.0   1.0    1.8e-07   30.7   0.1    2.1  2  G-alpha    G-protein alpha subunit
    7.9e-11   41.8   0.0    1.3e-10   41.1   0.0    1.3  1  Ras        Ras family
    2.6e-10   40.4   0.0    3.9e-10   39.8   0.0    1.2  1  MMR_HSR1   50S ribosome-binding GTPase
    2.3e-05   23.9   0.0    3.1e-05   23.5   0.0    1.3  1  SRPRB      Signal recognition particle receptor beta subunit
    0.00036   20.0   0.1     0.0006   19.2   0.1    1.4  1  Gtr1_RagA  Gtr1/RagA G protein conserved region
    0.00055   19.5   0.0      0.061   12.8   0.0    2.1  2  GTP_EFTU   Elongation factor Tu GTP binding domain
  ------ inclusion threshold ------
      0.023   14.2   0.2      0.035   13.6   0.2    1.6  1  FeoB_N     Ferrous iron transport protein B
      0.081   12.9   0.0       0.14   12.2   0.0    1.5  1  TsaE       Threonylcarbamoyl adenosine biosynthesis protein T
       0.84    9.5   2.4        2.2    8.1   0.3    2.6  2  NOG1       Nucleolar GTP-binding protein 1 (NOG1)


Domain annotation for each model (and alignments):
>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.2   0.1   1.1e-35   1.8e-32       4     173 ..       6     166 ..       3     168 .. 0.89

  Alignments for each domain:
  == domain 1  score: 112.2 bits;  conditional E-value: 1.1e-35
                                        HHHGGTT.TTEEEEEEEESTTSSHHHHHHHHHHSSCEECSSSSSEEEEEEEETTEEEEEEEE-SSGGGGGGGGGGC CS
                                Arf   4 ilaklklkkkelrilllGLDnaGKtTilkklkleelvttvPTigfnveeleiknlkftvwDvGGqeklRplWknYf 79 
                                        +++++k+k+++l+ +++GLDn+GKtTi++++   +    +PT g+++ +  +kn ++t++D+GGqe lR++W+n++
  gene2195|gene2195|rna2195|rna2195   6 LVKQIKKKSNDLKFIVVGLDNSGKTTIINNILRIDAI-SSPTFGYTIYKNLYKNTNLTLFDIGGQEALRKYWSNFY 80 
                                        5678889999*******************98876655.58************************************ PP

                                        TTESEEEEEEETT-CTTHHHHHHHHHHHCTSGCCTTSEEEEEEE-TTSTTSS-HHHHHHHTTGGGSSSSSSEEEEE CS
                                Arf  80 ektdavifvvDsadreRleeakeeLkalleeeelkevallvlaNKqDlpealseeelrellgleelkgkrkleiqk 155
                                        e+ d+vifv D  d++ +     e++++  +e+l++ ++l+++NK+Dl     ++ l++    + +  +++++  +
  gene2195|gene2195|rna2195|rna2195  81 EDADGVIFVFDLFDTRDFV---GEFNRV--RETLADYPVLIYGNKIDLDRERGQSILEKVK--NGID-DESVNCYG 148
                                        **************98775...566664..6899**************9998887776654..4688.999***** PP

                                        EBTTTTBTHHHHHHHHHH CS
                                Arf 156 csavkgeglkeglewlse 173
                                        +s  +g+gl+eg++wl++
  gene2195|gene2195|rna2195|rna2195 149 VSGKMGTGLEEGMDWLID 166
                                        ****************87 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.7   0.0   1.9e-15   3.1e-12       1     120 []      18     123 ..      18     123 .. 0.90

  Alignments for each domain:
  == domain 1  score: 46.7 bits;  conditional E-value: 1.9e-15
                                        EEEEESSTTSSHHHHHHCHCT-CCC-EEETTTTEEEEEEECGGSGGCTTBTTTTCEEEEEEEE-SGGCTTTT-HHH CS
                                Roc   1 KvvlvGdsgvGKtsllkrfvedkfsekekstigvdfltkevtkikgvendkkvkkvklniWDtaGqerfrslhply 76 
                                        K ++vG  ++GKt+++++++  +++  +++t+g++++++ +            k+ +l ++D++Gqe  r+  + +
  gene2195|gene2195|rna2195|rna2195  18 KFIVVGLDNSGKTTIINNIL--RIDAISSPTFGYTIYKN-LY-----------KNTNLTLFDIGGQEALRKYWSNF 79 
                                        889*****************..7888999******9764.31...........34679****************** PP

                                        HCTSCEEEEEEEGHHHHCHHHHHHHHHHHCSSS-EEEEEE-TTT CS
                                Roc  77 lreaalailvydsrssenlkeWlkelkkvagkspvilvgnkiDl 120
                                        +++a+ +i+v+d  + +++   ++ +++   + pv++ gnkiDl
  gene2195|gene2195|rna2195|rna2195  80 YEDADGVIFVFDLFDTRDFVGEFNRVRETLADYPVLIYGNKIDL 123
                                        ************7777777778999*****************95 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.1   1.5e-05     0.024      18      45 ..      11      38 ..       4      42 .. 0.80
   2 !   30.7   0.1   1.1e-10   1.8e-07     186     235 ..      44      92 ..      35     112 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.5e-05
                                       XXE..EEEEEEEESTTSSHHHHHHHHHH CS
                            G-alpha 18 rkkkrevkllllGqseSGKsTilkqlkl 45
                                       +kk++++k++++G + SGK+Ti++++ +
  gene2195|gene2195|rna2195|rna2195 11 KKKSNDLKFIVVGLDNSGKTTIINNILR 38
                                       344679******************9865 PP

  == domain 2  score: 30.7 bits;  conditional E-value: 1.1e-10
                                        ----SEEEEEEECT-TEEEEEEEE-SSHHHHHGTCCCTTTECEEEEEEEG CS
                            G-alpha 186 lktvGisetkfevdsklefrivdvgGqrserkkWvpffddvdaiiFlvsl 235
                                         +t G + +k  ++ +++++++d+gGq + rk W +f++d+d +iF+  l
  gene2195|gene2195|rna2195|rna2195  44 SPTFGYTIYKNLYK-NTNLTLFDIGGQEALRKYWSNFYEDADGVIFVFDL 92 
                                        46899999999888.9*******************************876 PP

>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.1   0.0   8.2e-14   1.3e-10       1     157 [.      18     165 ..      18     169 .. 0.79

  Alignments for each domain:
  == domain 1  score: 41.1 bits;  conditional E-value: 8.2e-14
                                        EEEEEESTTSSHHHHHHHHHHSSCSSSCTTTSSEEEEEEEEEETTEEEEEEEEEETTSGGGHHHHHHHHTTESEEE CS
                                Ras   1 KlvlvGdsavGKtslllrfvkdkFkeeyesTigvdfytkeievdgkevkleiwDTAGqeefkslrelyyrdaegil 76 
                                        K+++vG  + GKt+++++  +   +  + +T g   y++      k+ +l+++D  Gqe  ++  +++y+da+g++
  gene2195|gene2195|rna2195|rna2195  18 KFIVVGLDNSGKTTIINNILRI--DAISSPTFGYTIYKNL----YKNTNLTLFDIGGQEALRKYWSNFYEDADGVI 87 
                                        89**************999864..5666799977766554....46789*************************** PP

                                        EEEETTBHHHHHTHHHHHHHHHHHSTTTSEEEEEEETTTGGGG-SS-.HHHHHHHHHHHTSEEEEEBTTTTCTHHH CS
                                Ras  77 lvyditsresfenvkkwveeikrvaeenvpivLvGnKvDleekravs.teegeelakelglkfletSAktnenvee 151
                                         v+d+ +++ f    + ++ ++++   ++p+++ GnK+Dl+++r  s  e++++  ++ +++ + +S k  +++ee
  gene2195|gene2195|rna2195|rna2195  88 FVFDLFDTRDFVG--E-FNRVRETLA-DYPVLIYGNKIDLDRERGQSiLEKVKNGIDDESVNCYGVSGKMGTGLEE 159
                                        *****99877643..2.233444444.699***********98865515677788888888888899988888888 PP

                                        HHHHHH CS
                                Ras 152 afeell 157
                                         ++ l+
  gene2195|gene2195|rna2195|rna2195 160 GMDWLI 165
                                        776665 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.8   0.0   2.4e-13   3.9e-10       2     110 ..      19     116 ..      18     120 .. 0.79

  Alignments for each domain:
  == domain 1  score: 39.8 bits;  conditional E-value: 2.4e-13
                                        EEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSSHHHHHHHHHHHHHHHHC.T CS
                           MMR_HSR1   2 vaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgkeielvDtpGliegaseekglgkaflalee.a 76 
                                        +++vG  N+GK+t+in +++  ai s + g T+  n ++ +    +++l D+ G  e       l+k + +  e a
  gene2195|gene2195|rna2195|rna2195  19 FIVVGLDNSGKTTIINNILRIDAISSPTFGYTIYKNLYKNT----NLTLFDIGG-QE------ALRKYWSNFYEdA 83 
                                        689********************************999654....7********.55......677777775555* PP

                                        SEEEEEEETT.....TTCSHHHHHHHHHHHHHTTSEEEE CS
                           MMR_HSR1  77 dlillvvdas.....eeklkpldeeleelleeakkplil 110
                                        d +++v+d+       +++++++e+l+++      p+++
  gene2195|gene2195|rna2195|rna2195  84 DGVIFVFDLFdtrdfVGEFNRVRETLADY------PVLI 116
                                        ********886544433466666666665......5555 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.0   1.9e-08   3.1e-05       5      84 ..      18      91 ..      14     132 .. 0.83

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 1.9e-08
                                       EEEEE-STTSSHHHHHHHHHHSS---B---SS-EEETTG...GGTT-SEEEETT-GCCSHHHHHHHHHHGGEEEEEEE CS
                              SRPRB  5 avllvGlsdsGKTslftrLttdsvkktvtSqessaalkvksekgskltliDfPGheklrqklleklkaksslkglvfv 82
                                       ++++vGl +sGKT++++ ++   + ++ t   +   + +   k+++ltl D+ G+e lr+  ++     + + g++fv
  gene2195|gene2195|rna2195|rna2195 18 KFIVVGLDNSGKTTIINNILRIDAISSPTFGYTIYKNLY---KNTNLTLFDIGGQEALRKYWSNF---YEDADGVIFV 89
                                       79***************9988766666555555555555...9****************988776...6778899999 PP

                                       EE CS
                              SRPRB 83 vD 84
                                        D
  gene2195|gene2195|rna2195|rna2195 90 FD 91
                                       88 PP

>> Gtr1_RagA  Gtr1/RagA G protein conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.1   3.7e-07    0.0006       1     122 [.      18     122 ..      18     150 .. 0.69

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 3.7e-07
                          Gtr1_RagA   1 kvLLmGksgsGKtsmrsiiFdnylardtlrlgatidveksevrflgnltlnlwDcgGqeafveeylssqkeeifrn 76 
                                        k + +G  +sGKt++ + i   + a    + g ti  +     +++n +l l+D+gGqea+ +       ++ +++
  gene2195|gene2195|rna2195|rna2195  18 KFIVVGLDNSGKTTIINNILR-IDAISSPTFGYTIYKN-----LYKNTNLTLFDIGGQEALRKY-----WSNFYED 82 
                                        5678999******99888864.5666667778887543.....478999*********987655.....4789999 PP

                          Gtr1_RagA  77 vgvliyVfDvesreleedletlkeilealrqyspeakvfvlihKmD 122
                                         + +i+VfD        d ++++  ++++r++  +  v +  +K+D
  gene2195|gene2195|rna2195|rna2195  83 ADGVIFVFDLF------DTRDFVGEFNRVRETLADYPVLIYGNKID 122
                                        *********98......33444444444444444445555555555 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.0   0.1    0.0098        16       5      25 ..      18      38 ..      14      46 .. 0.81
   2 !   12.8   0.0   3.8e-05     0.061      65     176 ..      54     152 ..      41     170 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.0098
                                       EEEEEESTTSSHHHHHHHHHH CS
                           GTP_EFTU  5 nigiighvDhGKtTLtdrLly 25
                                       +++++g  ++GKtT++ ++l 
  gene2195|gene2195|rna2195|rna2195 18 KFIVVGLDNSGKTTIINNILR 38
                                       688999999*********995 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 3.8e-05
                                        TTCSSEEEEEEEESSSGGGHHHHHHHHHT-SEEEEEEETTTBSTHHHHHHHHHHHHTTTEEEEEEESCGSTHHHHH CS
                           GTP_EFTU  65 ketkkylinliDtPGHvdFskevirglrvlDgavlvvdaveGvepqteevlrlalkegvpiivfiNKmDrlkaelk 140
                                        + +k+++++l D  G +   k  ++ ++ +Dg+++v+d  +      e +       + p+ +  NK+D  +++ +
  gene2195|gene2195|rna2195|rna2195  54 NLYKNTNLTLFDIGGQEALRKYWSNFYEDADGVIFVFDLFDTRDFVGEFNRVRETLADYPVLIYGNKIDLDRERGQ 129
                                        4789999*********************************99988888888888888999**************** PP

                                        HHHHHHHHHHHHHHHHHHHHHHTTTTTEEEEEEBTT CS
                           GTP_EFTU 141 eiveevkqklsrkeeklekygekgekevpvvfgSal 176
                                         i e+vk+ +  ++e++           +++ +S++
  gene2195|gene2195|rna2195|rna2195 130 SILEKVKNGI--DDESV-----------NCYGVSGK 152
                                        *******988..33333...........44444444 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.2   2.1e-05     0.035       2      61 ..      18      73 ..      17     159 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.1e-05
                                       EEEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEEEETTEEEEEEE----SSSS CS
                             FeoB_N  2 tvalvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegklklkgkeveivDlPGiYsls 61
                                       ++++vG  n+Gktt++n++   +   +   G t+ k+      k++++++ D+ G  +l 
  gene2195|gene2195|rna2195|rna2195 18 KFIVVGLDNSGKTTIINNILRIDAISSPTFGYTIYKNLY----KNTNLTLFDIGGQEALR 73
                                       5789***************99988888777888877643....34577777777766665 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   8.3e-05      0.14      23      58 ..      20      54 ..       3      89 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 8.3e-05
                                       EEEESTTSSHHHHHHHHHHHTT------TTT..TSEEE CS
                               TsaE 23 lLeGdLGaGKTtlvrglakalgveevkSPTF..tlvee 58
                                       +  G   +GKTt++ ++++    ++++SPTF  t+ ++
  gene2195|gene2195|rna2195|rna2195 20 IVVGLDNSGKTTIINNILRI---DAISSPTFgyTIYKN 54
                                       55555579*******99775...689****83344433 PP

>> NOG1  Nucleolar GTP-binding protein 1 (NOG1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.1       4.4   7.1e+03      37      53 ..       6      22 ..       5      22 .. 0.75
   2 ?    8.1   0.3    0.0013       2.2      17      58 .]      86     122 ..      82     122 .. 0.77

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 4.4
                               NOG1 37 Lleeikelfankpvivv 53
                                       L+++ik++ ++ ++ivv
  gene2195|gene2195|rna2195|rna2195  6 LVKQIKKKSNDLKFIVV 22
                                       77889988877777776 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0013
                               NOG1  17 vlFllDpseecgysleeQlsLleeikelfankpvivvlnKiD 58 
                                        v+F++D+  +  +     +  ++ ++e++a+ pv++  nKiD
  gene2195|gene2195|rna2195|rna2195  86 VIFVFDLFDTRDF-----VGEFNRVRETLADYPVLIYGNKID 122
                                        6666666666555.....334899*****************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       513  (0.0286129); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.49u 0.31s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1139.35
//
Query:       gene2196|gene2196|rna2196|rna2196  [L=304]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.069   12.6   5.5      0.098   12.1   5.5    1.1  1  Vac7      Vacuolar segregation subunit 7


Domain annotation for each model (and alignments):
>> Vac7  Vacuolar segregation subunit 7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   5.5   5.5e-06     0.098     121     262 ..      47     199 ..      39     217 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 5.5e-06
                               Vac7 121 glrsiaevldseksvagkksmKFsnttynssaldsdseesdegkkrsrgegsgrgtarhhhigrygrkaknghssl 196
                                         +rs     + e++ ++k+ m  snt   + + + +     e+++ s+ +g+g  +  h  +g  g++ +n    +
  gene2196|gene2196|rna2196|rna2196  47 VIRSEIRGKECENEYETKRGMIRSNTEDREPKYEYKRSFVRESRDMSARNGNGGINDVHVILGDKGQNGENDRVRM 122
                                        56887777888999************988888888888888888888888888777777888*****877877777 PP

                               Vac7 197 fd.eespftqaqksrakklsrqssrpksprssass.........srktasskkkkeeasydld.aegaddErtPLv 261
                                        f   +     +++ r+ ++ +++ +++  r ++ s         +r+++  ++++++++++ d  ++a+ E+tP+ 
  gene2196|gene2196|rna2196|rna2196 123 FIkGKETQCPSSRMRIVMNGTKTRNNENGREFTISgnregsieqNRRATIMRRNERNEAFNNDaLKHANSEKTPMN 198
                                        65144555566667888877777777777777777788999988778888899999999****88999******86 PP

                               Vac7 262 g 262
                                        g
  gene2196|gene2196|rna2196|rna2196 199 G 199
                                        5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (304 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       470  (0.0262145); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 2064.50
//
Query:       gene2197|gene2197|rna2197|rna2197  [L=923]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-26   92.6   3.6    2.4e-22   79.7   0.0    3.3  3  SIR2      Sir2 family


Domain annotation for each model (and alignments):
>> SIR2  Sir2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.7   0.0   1.4e-26   2.4e-22       1     134 [.      26     173 ..      26     191 .. 0.87
   2 !   11.4   0.0   1.3e-05      0.23     130     176 ..     403     451 ..     330     452 .. 0.79
   3 ?   -1.8   2.5      0.15   2.6e+03      50     120 ..     643     715 ..     614     741 .. 0.61

  Alignments for each domain:
  == domain 1  score: 79.7 bits;  conditional E-value: 1.4e-26
                                        -GGGGGGGT---SSSTTSHHHHSCHHHHSSHHHHHHHHHHHHH....HHHHHHHHHHCC..TSS--HHHHHHHHHH CS
                               SIR2   1 GAGiStesGipdfRskeGlyaklakeelaspealfskkllvee....vfyniarellae..eaepnaaHkalkkle 70 
                                        GAG+S+ s ipdfRs++Gl+a l+++     e++f+++ + e+    ++ +++ el +    a p+a H++l+ + 
  gene2197|gene2197|rna2197|rna2197  26 GAGLSVPSNIPDFRSTHGLFATLKQRYKIRGEHIFTYRFTIEKetrsTYLKVISELKRAvdAASPSAGHYFLNRMR 101
                                        9**********************99987777777777766665567789999988887777899************ PP

                                        HTTCEEEEEES-SSSHHHHTT-S.......SEEETTEEEEEEEETTTSBEEE.CCGGHCHHHCCTT.B-TTT CS
                               SIR2  71 kkgkllrliTQNiDgLekkaGsk.......kvvelHGslakakcvkcekkld.keelqeeieaekvpecekc 134
                                        + g+ lr++TQN+DgLe++aG++       +vv lHG+l+ + c+ c++++  + e  +  e+ ++ ece+c
  gene2197|gene2197|rna2197|rna2197 102 EIGRRLRVYTQNVDGLEERAGLRctgdcstEVVYLHGNLNVLVCSYCGYRCLfGGEHCDAFEKGCEVECERC 173
                                        *********************9988999899*****************987524566677777777888888 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 1.3e-05
                                        B-TTTCCBEEEEE--CTSB-S.HH.HHHHHHHHHH-SEEEEES--STST CS
                               SIR2 130 ecekcgkllkpdvvfFGealp.dk.lkkliekveeadlllviGtSlkVa 176
                                        + +  ++++ ++++ + +  p ++ + +l++  ++++lllv+GtSlkV+
  gene2197|gene2197|rna2197|rna2197 403 NRKLITGMMNTNIIHYYQVHPdSHyIASLTRRDSNCQLLLVMGTSLKVH 451
                                        44455679******99999987551555666999*************97 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 0.15
                                        HHHHCCTSS--..HHHHHHHHHHHTTCEEEEEES-SSSHHHHTT-SSEEETTEEEEEEEETTTSBEEECCGGH CS
                               SIR2  50 rellaeeaepn..aaHkalkklekkgkllrliTQNiDgLekkaGskkvvelHGslakakcvkcekkldkeelq 120
                                         +++ ++ ++n  ++H+   k e+ +k+  l T   D+L++k     + +   + ++++ ++c++k++    +
  gene2197|gene2197|rna2197|rna2197 643 DSKILQKLKYNkvTTHNNTPKQENINKQCLLSTCRNDDLHQKDCKGPLKDNAHKNESISINACDNKEKIRIRK 715
                                        3333444555511579999999999999999999999999998877666544455666666676666553322 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (923 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2386  (0.13308); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                       110  (0.00613531); expected 17.9 (0.001)
Passed Fwd filter:                        27  (0.00150594); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 1.29u 0.35s 00:00:01.64 Elapsed: 00:00:00.53
# Mc/sec: 5237.22
//
Query:       gene2198|gene2198|rna2198|rna2198  [L=914]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.5e-88  297.5   2.6      4e-66  223.7   0.2    3.1  3  RNA_pol_Rpb2_6  RNA polymerase Rpb2, domain 6
    2.8e-23   81.9   0.0    5.9e-23   80.8   0.0    1.6  1  RNA_pol_Rpb2_3  RNA polymerase Rpb2, domain 3
    1.6e-21   76.5   0.3    4.6e-21   75.0   0.3    1.8  1  RNA_pol_Rpb2_7  RNA polymerase Rpb2, domain 7


Domain annotation for each model (and alignments):
>> RNA_pol_Rpb2_6  RNA polymerase Rpb2, domain 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -5.4   4.4       2.7   1.6e+04     201     212 ..     387     398 ..     339     443 .. 0.40
   2 !   83.1   0.2   3.5e-27   2.1e-23       1     120 [.     452     555 ..     452     571 .. 0.92
   3 !  223.7   0.2   6.7e-70     4e-66     229     390 .]     601     825 ..     593     825 .. 0.93

  Alignments for each domain:
  == domain 1  score: -5.4 bits;  conditional E-value: 2.7
                                        -TT-EEEEEEEE CS
                     RNA_pol_Rpb2_6 201 ksgeegvVdkvk 212
                                         ++++ v++k++
  gene2198|gene2198|rna2198|rna2198 387 DNDHSNVINKIS 398
                                        222222222221 PP

  == domain 2  score: 83.1 bits;  conditional E-value: 3.5e-27
                                        HHHT-SS-TTB-HHHHHHHHHHGGGB-S---TTTTT---SSEEEESS----SSB-S.TTTTTS........GGGS- CS
                     RNA_pol_Rpb2_6   1 vaklapvvehvqspriiiqaamekqalgiyslnkfkrsnqktyllcinqkPlvktgdkveagqvldgpatekgela 76 
                                        va+ +p+++++qspr+++q++m+kqa+   +l++ +r+++k y+l+  q+Pl+kt      ++             
  gene2198|gene2198|rna2198|rna2198 452 VASTIPFADYNQSPRNMYQCQMAKQAMAYPTLTYNNRTDSKYYVLNNMQRPLIKTF-----LD-----------TL 511
                                        6999**************************************************99.....44...........57 PP

                                        SEEEEEBBBS--TTTTTTT-EEEBCHHHHTTTT-EEEEEE..EE CS
                     RNA_pol_Rpb2_6  77 lGqnavVAvmsyeGYniEDaiilnerlvdrdvftsihikeyeve 120
                                        lG+n+ +Av+sy++Y++EDa+++n+ +++r++f  +++ ++ +e
  gene2198|gene2198|rna2198|rna2198 512 LGTNVYIAVLSYTSYDMEDAMVINKCAIERGLFDGYVYVTKVIE 555
                                        8*************************************994443 PP

  == domain 3  score: 223.7 bits;  conditional E-value: 6.7e-70
                                        EEEEEEEEEE---TT-BEEETTS---BBEEEB-TTTSEEETTS---SEEE-GGGCHHH-BTTHHHHHHHHHCCCSS CS
                     RNA_pol_Rpb2_6 229 lvkvyvaqkRklqvGDKfasrhGqKGvvslilpqeDmPfledGivvDivlNPlgvPSRmtigqllEtllgkaaale 304
                                        l+ ++++ +R +q+GDKf+srhGqKGv+s+ ++  D+Pf e+G+v+D+++NP+++PSRmt+g+++E+l+g +a ++
  gene2198|gene2198|rna2198|rna2198 601 LAIITLRVRRSPQIGDKFCSRHGQKGVLSYRYRAVDLPFNEHGMVPDLIINPHAFPSRMTVGMMMEMLAGTVAVIK 676
                                        567999********************************************************************** PP

                                        SS--B--TT-.................................................................. CS
                     RNA_pol_Rpb2_6 305 gkkvdatvFdg...............................................................ak 317
                                        g++++ ++F++                                                               ++
  gene2198|gene2198|rna2198|rna2198 677 GERYACPPFKTygvknehdvendlgrnikndlsrnvknyldknvendlgrnikndldrnvendlhknvkhrmnnHT 752
                                        ***********9********99999999999999999999999999999998888888888777777666654333 PP

                                        -HHHHHHHHHTTS-TT-EE-EEETTTS-B-SS-EEB-EEEEEEBS--CCCS----SS--B-TTT--B-SCGGG CS
                     RNA_pol_Rpb2_6 318 eeeikelLeeagleasGkevlydGrtGekleaeifvGviYylkLkhlvedKihaRstGpyslltqQPlgGkaq 390
                                        +e+++e+L+  gl+++G+e+ly+G+tG+kl+a++f G++Yy++L+h+v+dK ++Rs Gp+++ t+QP++G+++
  gene2198|gene2198|rna2198|rna2198 753 HEHFCEQLRALGLNYYGNETLYSGITGHKLHARVFTGMCYYQRLRHMVSDKWQVRSVGPVQAQTRQPIKGRKR 825
                                        699********************************************************************86 PP

>> RNA_pol_Rpb2_3  RNA polymerase Rpb2, domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.8   0.0   9.8e-27   5.9e-23       2      67 ..     122     185 ..     121     186 .. 0.96

  Alignments for each domain:
  == domain 1  score: 80.8 bits;  conditional E-value: 9.8e-27
                     RNA_pol_Rpb2_3   2 vldrlnplselshlrrvsslrgglskerkttevRdlhpshwGriCpveTPEGencGlvksLallar 67 
                                        +++r+n +++lsh+ +++  rg++++  ktt vR l+p+++G++Cpv+TP+G++cGl+ ++a+ a 
  gene2198|gene2198|rna2198|rna2198 122 LAERINTYRFLSHFESIN--RGAFFAVLKTTGVRALRPESFGFLCPVHTPDGAPCGLIVHMAMDAI 185
                                        79****************..******************************************9885 PP

>> RNA_pol_Rpb2_7  RNA polymerase Rpb2, domain 7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.0   0.3   7.6e-25   4.6e-21       1      85 [.     827     911 ..     827     913 .. 0.96

  Alignments for each domain:
  == domain 1  score: 75.0 bits;  conditional E-value: 7.6e-25
                                        BBEEEEHHHHHHHHHHTBHHHHHHHHTTTTTEEEEEEESSSSSCCCEEEBTTTTCSSSEEEEEEEHHHHHHHHHHH CS
                     RNA_pol_Rpb2_7   1 GGlrfGEMErdaliayGaaalLkerltikSDavevdvcgrckllaaaneCkivkseekiekveipeafklLlqeLq 76 
                                        GG+rfGEMErdalia+G+a+lL +rl++ SD++  + c+rck++  +   + + + + ++ v++p+ fk L+ eL+
  gene2198|gene2198|rna2198|rna2198 827 GGVRFGEMERDALIAHGCAYLLYDRLMECSDKTAFEYCERCKTFLFVRDGTCLCGCRCVKVVYLPYVFKYLCTELM 902
                                        9*********************************************998888999999****************** PP

                                        HTTBEEEEE CS
                     RNA_pol_Rpb2_7  77 slgialkll 85 
                                        +++i ++++
  gene2198|gene2198|rna2198|rna2198 903 GMNIFVEVD 911
                                        ****99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (914 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1557  (0.0868425); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.80u 0.30s 00:00:01.10 Elapsed: 00:00:00.48
# Mc/sec: 5770.93
//
Query:       gene2199|gene2199|rna2199|rna2199  [L=417]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00024   19.8  20.0      0.001   17.7   1.3    3.2  3  MFS_2     MFS/sugar transport protein
     0.0019   18.2   2.7      0.012   15.6   0.6    2.9  2  DUF5316   Family of unknown function (DUF5316)
  ------ inclusion threshold ------
       0.86    9.5   5.9          2    8.3   0.1    2.9  3  DUF412    Protein of unknown function, DUF412


Domain annotation for each model (and alignments):
>> MFS_2  MFS/sugar transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   1.3   1.8e-07     0.001     265     330 ..      41     105 ..       4     116 .. 0.83
   2 !    6.9   1.3   0.00033         2     258     339 ..     121     225 ..     112     227 .. 0.84
   3 !    5.3   3.6     0.001       6.1     270     328 ..     286     345 ..     269     355 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.8e-07
                              MFS_2 265 llvvtisallgiplwqplakrlgkkntyllgalltivllvlvlllqpsnlllflvllviagfgvgv 330
                                        + +++is++l++++ + ++ ++g k++ ++ ++l +v+l ++++++ + +++++v++ + g +  +
  gene2199|gene2199|rna2199|rna2199  41 P-FFFISGFLASLVGPLFVEHFGEKTILIWDTVLDLVFLGCFFVIPNGRVAPLIVITCMHGASSSL 105
                                        3.47*****************************************999999999999999888444 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.00033
                              MFS_2 258 gsaasvfllvvtisallgiplwqplakrlgkk.ntyllgalltivllvlvlll......................q 310
                                        ++++s+f ++  +s++l++ + q l    + +  + ++++++t+  l+ +++l                       
  gene2199|gene2199|rna2199|rna2199 121 EKMYSTFNIIKRVSSILSSWIGQDLFYACSEYsPSLVVSIVSTACCLLTAFFLtgterkakesflntahmltrdtF 196
                                        5667777777777888888888888888887766778888888888888888899999999999999999999999 PP

                              MFS_2 311 psnlllflvllviagfgvgvaallpwsml 339
                                        ++n+++f vl +ia+++++++a++ +s++
  gene2199|gene2199|rna2199|rna2199 197 TRNYVFFGVLNIIASTIYISFAFYSASIF 225
                                        9***********************99986 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.001
                              MFS_2 270 isallgiplwqplakr..lgkkntyllgalltivllvlvlllqpsnlllflvllviagfgv 328
                                        i++ ++++l++ l +r  +  +++++l++ l++   v+++l++ +++l+   l++i+g ++
  gene2199|gene2199|rna2199|rna2199 286 IAK-IVSVLFSTLLTRtnYATRTLAYLCLFLVLCTIVCTFLMGYTSTLISSYLCFIVGATL 345
                                        344.44555555555512668999******************9999999988888888773 PP

>> DUF5316  Family of unknown function (DUF5316)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.6     2e-06     0.012      15      72 ..     160     217 ..     154     219 .. 0.85
   2 ?    0.8   0.1     0.086   5.1e+02       8      25 ..     279     296 ..     277     309 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2e-06
                            DUF5316  15 vfiliagllsGafvsgdriranytseskedrrkrfklsknllliglPNllaalllylf 72 
                                        ++   ++ll+  f +g++ +a     +  ++  r ++++n + +g+ N++a+ +++ f
  gene2199|gene2199|rna2199|rna2199 160 IVSTACCLLTAFFLTGTERKAKESFLNTAHMLTRDTFTRNYVFFGVLNIIASTIYISF 217
                                        444457788888**********999999************************999877 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.086
                            DUF5316   8 isGfvglvfiliagllsG 25 
                                        i G++ +++ ++++l+s 
  gene2199|gene2199|rna2199|rna2199 279 IFGYIDGIAKIVSVLFST 296
                                        678888888888888773 PP

>> DUF412  Protein of unknown function, DUF412
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.1   0.00034         2      16      48 ..      15      47 ..      10      67 .. 0.86
   2 ?    3.3   0.1     0.012        73      59      89 ..     229     263 ..     200     275 .. 0.71
   3 ?   -2.1   0.3      0.54   3.2e+03      34      57 ..     301     324 ..     293     345 .. 0.51

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00034
                             DUF412 16 PlekeLaalfpenrvikatrfaikvmpalavlt 48
                                       P  + ++++f e++ ik t f +kv+p++ +  
  gene2199|gene2199|rna2199|rna2199 15 PITPFITPFFVEKKQIKNTAFHNKVIPFFFISG 47
                                       7778899********************998755 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.012
                             DUF412  59 e....alpqailtalfllsLPlQGlywlGkraktp 89 
                                               ++a+  +l+ + LP+ +l +l  +a  p
  gene2199|gene2199|rna2199|rna2199 229 RkntnLASNAVGRVLYYVLLPFRALSFLIIKALAP 263
                                        1344344579999***************9888665 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 0.54
                             DUF412  34 trfaikvmpalavltlvlqlylag 57 
                                        t++a++++  l ++ ++++++++ 
  gene2199|gene2199|rna2199|rna2199 301 TNYATRTLAYLCLFLVLCTIVCTF 324
                                        444455555444444444443332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (417 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1047  (0.058397); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.26s 00:00:00.82 Elapsed: 00:00:00.44
# Mc/sec: 2860.63
//
Query:       gene22|gene22|rna22|rna22  [L=83]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-05   24.8   1.2    1.4e-05   24.7   1.2    1.1  1  Acetyltransf_15  Putative acetyl-transferase


Domain annotation for each model (and alignments):
>> Acetyltransf_15  Putative acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   1.2   7.7e-10   1.4e-05       1      47 [.      22      68 ..      22      78 .. 0.94

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 7.7e-10
            Acetyltransf_15  1 qpiksidqlkdilkevkkeFrnkrdeeeaitknenkydivqykkkee 47
                               +++ +++q  + ++evk eF + ++   ++t ++n+ydi++y+ kee
  gene22|gene22|rna22|rna22 22 NSFTHTSQALFAVNEVKPEFDKDQNDILKVTFYNNQYDIFYYRIKEE 68
                               57899**************************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (83 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       562  (0.0313459); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.43
# Mc/sec: 580.91
//
Query:       gene220|gene220|rna220|rna220  [L=241]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.1e-12   47.2   7.1    2.1e-12   47.2   7.1    2.1  2  zf-RING_2     Ring finger domain
      1e-10   41.1   5.8    2.7e-10   39.8   5.8    1.8  1  zf-RING_11    RING-like zinc finger
    1.7e-08   34.6   6.2    1.7e-08   34.6   6.2    2.0  2  zf-rbx1       RING-H2 zinc finger domain
      1e-07   31.7   6.8      1e-07   31.7   6.8    1.8  2  zf-C3HC4_2    Zinc finger, C3HC4 type (RING finger)
      1e-06   28.6   5.6      1e-06   28.6   5.6    1.9  2  zf-RING_5     zinc-RING finger domain
    1.7e-06   27.8   8.3    1.7e-06   27.8   8.3    1.8  2  zf-C3HC4      Zinc finger, C3HC4 type (RING finger)
      2e-05   24.5   2.0      2e-05   24.5   2.0    2.4  2  zf-RING_UBOX  RING-type zinc-finger
    5.4e-05   23.0   4.5    5.4e-05   23.0   4.5    1.9  2  zf-C3HC4_3    Zinc finger, C3HC4 type (RING finger)
    0.00049   19.9   6.4      0.001   18.9   6.4    1.5  1  Prok-RING_4   Prokaryotic RING finger family 4
     0.0042   17.2   9.7       0.19   11.9   9.7    2.6  1  FANCL_C       FANCL C-terminal domain
     0.0056   16.3   4.6     0.0056   16.3   4.6    2.2  2  Zn_ribbon_17  Zinc-ribbon, C4HC2 type
     0.0067   16.4   5.1       0.05   13.7   5.1    2.3  1  zf-ANAPC11    Anaphase-promoting complex subunit 11 RING-H2 f
     0.0098   14.5   5.2      0.013   14.1   5.2    1.1  1  MFS_2         MFS/sugar transport protein
  ------ inclusion threshold ------
       0.03   14.5   1.5      0.064   13.4   1.5    1.6  1  RANK_CRD_2    Receptor activator of the NF-KB cysteine-rich r
      0.093   12.6   1.0       0.24   11.3   1.0    1.6  1  zf-RING_6     zf-RING of BARD1-type protein
       0.78    9.8   7.6      0.083   12.9   2.4    2.1  2  zf-C3H2C3     Zinc-finger
        0.8    9.6   8.2        8.6    6.3   2.9    2.6  2  zf-C3HC4_5    Zinc finger, C3HC4 type (RING finger)
          2    8.7   6.7         11    6.3   6.8    2.3  2  zf-C3HC4_4    zinc finger of C3HC4-type, RING


Domain annotation for each model (and alignments):
>> zf-RING_2  Ring finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   1.1       2.1   2.1e+03      32      40 ..     120     128 ..     112     130 .. 0.53
   2 !   47.2   7.1   2.1e-15   2.1e-12       2      44 .]     188     230 ..     187     230 .. 0.97

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 2.1
                      zf-RING_2  32 rwlrssstC 40 
                                    +w+++++tC
  gene220|gene220|rna220|rna220 120 HWTQECKTC 128
                                    455555555 PP

  == domain 2  score: 47.2 bits;  conditional E-value: 2.1e-15
                      zf-RING_2   2 eCpICleelssadsvlllpCgHvfhreClerwlrssstCPlCr 44 
                                    +C+ICl e++ +d++ +lpC+H+fh +C+++w++    CPlC+
  gene220|gene220|rna220|rna220 188 NCSICLAEYNMNDKIKILPCNHHFHLNCIDEWFNIDDICPLCK 230
                                    6*****************************************7 PP

>> zf-RING_11  RING-like zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.8   5.8   2.7e-13   2.7e-10       1      29 []     188     216 ..     188     216 .. 0.98

  Alignments for each domain:
  == domain 1  score: 39.8 bits;  conditional E-value: 2.7e-13
                     zf-RING_11   1 eCsICLeefkpgqalfilpCsHtFHfkCI 29 
                                    +CsICL e+  ++++ ilpC+H FH++CI
  gene220|gene220|rna220|rna220 188 NCSICLAEYNMNDKIKILPCNHHFHLNCI 216
                                    7***************************9 PP

>> zf-rbx1  RING-H2 zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.4       7.1     7e+03      12      17 ..     123     128 ..     115     132 .. 0.56
   2 !   34.6   6.2   1.7e-11   1.7e-08      11      55 .]     186     230 ..     181     230 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 7.1
                        zf-rbx1  12 eaciec 17 
                                    ++c +c
  gene220|gene220|rna220|rna220 123 QECKTC 128
                                    333333 PP

  == domain 2  score: 34.6 bits;  conditional E-value: 1.7e-11
                        zf-rbx1  11 eeacieckapgdeecpvvlGeCgHaFHlhCiskWlktrkvCPlcr 55 
                                    +++c  c a+ + + ++++  C+H+FHl+Ci++W++  + CPlc+
  gene220|gene220|rna220|rna220 186 NANCSICLAEYNMNDKIKILPCNHHFHLNCIDEWFNIDDICPLCK 230
                                    667888888877776777789***********************6 PP

>> zf-C3HC4_2  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.5       5.2   5.2e+03      23      26 ..     125     128 ..     113     132 .. 0.66
   2 !   31.7   6.8     1e-10     1e-07       1      40 []     188     229 ..     188     229 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 5.2
                     zf-C3HC4_2  23 CqkC 26 
                                    C+ C
  gene220|gene220|rna220|rna220 125 CKTC 128
                                    4444 PP

  == domain 2  score: 31.7 bits;  conditional E-value: 1e-10
                     zf-C3HC4_2   1 kCpiCldmlkdpsvvt..pCgHvfCqkCilrsLeekneCPlC 40 
                                    +C iCl+++++   ++  pC+H f+ +Ci+++ +  + CPlC
  gene220|gene220|rna220|rna220 188 NCSICLAEYNMNDKIKilPCNHHFHLNCIDEWFNIDDICPLC 229
                                    5*******9988777777************************ PP

>> zf-RING_5  zinc-RING finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.6       2.6   2.6e+03      36      43 ..     122     129 ..     115     130 .. 0.64
   2 !   28.6   5.6     1e-09     1e-06       1      44 []     188     231 ..     188     231 .. 0.98

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 2.6
                      zf-RING_5  36 eavCpiCr 43 
                                     ++C +C+
  gene220|gene220|rna220|rna220 122 TQECKTCK 129
                                    46777776 PP

  == domain 2  score: 28.6 bits;  conditional E-value: 1e-09
                      zf-RING_5   1 hCnkCfeklskeekfyltsCgHifCekClkkllekeavCpiCrk 44 
                                    +C++C  +++ ++k+ +++C H f+ +C+++ ++ ++ Cp+C+k
  gene220|gene220|rna220|rna220 188 NCSICLAEYNMNDKIKILPCNHHFHLNCIDEWFNIDDICPLCKK 231
                                    6*****************************************97 PP

>> zf-C3HC4  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.7       7.8   7.8e+03      38      41 .]     125     128 ..     115     129 .. 0.56
   2 !   27.8   8.3   1.7e-09   1.7e-06       1      41 []     189     229 ..     189     229 .. 0.94

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 7.8
                                    -TTT CS
                       zf-C3HC4  38 CPlC 41 
                                    C +C
  gene220|gene220|rna220|rna220 125 CKTC 128
                                    3333 PP

  == domain 2  score: 27.8 bits;  conditional E-value: 1.7e-09
                                    -TTT-S--SS-E...E-TTS--B-CHHHHHHHHCTSSB--TTT CS
                       zf-C3HC4   1 CpiCleeakepn..elleCkHsfCskCirkilksrkkvkCPlC 41 
                                    C+iCl e+  ++  ++l+C+H f+ +Ci+++ +      CPlC
  gene220|gene220|rna220|rna220 189 CSICLAEYNMNDkiKILPCNHHFHLNCIDEWFN--IDDICPLC 229
                                    ********9999899******************..6677**** PP

>> zf-RING_UBOX  RING-type zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   2.0     2e-08     2e-05       1      26 [.     189     219 ..     189     225 .. 0.77
   2 ?   -0.3   0.6       1.2   1.2e+03       1       8 [.     226     233 ..     226     237 .. 0.85

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 2e-08
                   zf-RING_UBOX   1 CpIClelft..dPlv.lpCGHtFCreCl..w 26 
                                    C+ICl +++  d ++ lpC H F+ +C+  w
  gene220|gene220|rna220|rna220 189 CSICLAEYNmnDKIKiLPCNHHFHLNCIdeW 219
                                    ********965333447***********655 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.2
                   zf-RING_UBOX   1 CpIClelf 8  
                                    Cp C+ + 
  gene220|gene220|rna220|rna220 226 CPLCKKPI 233
                                    ****9876 PP

>> zf-C3HC4_3  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.3       1.5   1.5e+03      38      44 ..     123     129 ..     113     132 .. 0.58
   2 !   23.0   4.5   5.4e-08   5.4e-05       2      48 ..     186     234 ..     185     236 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 1.5
                                    -B-TTT- CS
                     zf-C3HC4_3  38 kkCpiCr 44 
                                    ++C  C+
  gene220|gene220|rna220|rna220 123 QECKTCK 129
                                    4555554 PP

  == domain 2  score: 23.0 bits;  conditional E-value: 5.4e-08
                                    GSB-TTTSSS...BS-EEETTEEEEEE-HHHHHHHHHTT-B-TTT--B-- CS
                     zf-C3HC4_3   2 deeCviCler...prnvvllpCgHlvlCeeCaekllkrkkkCpiCrrpie 48 
                                    +  C+iCl +   + ++ +lpC+H  +  +C +++ + ++ Cp+C++pi+
  gene220|gene220|rna220|rna220 186 NANCSICLAEynmNDKIKILPCNHH-FHLNCIDEWFNIDDICPLCKKPIN 234
                                    678******7766888*********.99********************96 PP

>> Prok-RING_4  Prokaryotic RING finger family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   6.4     1e-06     0.001       1      40 [.     189     233 ..     189     236 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1e-06
                    Prok-RING_4   1 CvlCgeq...ekkailepCgHlvCkeCfdsk.dls.sCPlCqrri 40 
                                    C +C  +   + k+ + pC+H +  +C d++ +    CPlC++ i
  gene220|gene220|rna220|rna220 189 CSICLAEynmNDKIKILPCNHHFHLNCIDEWfNIDdICPLCKKPI 233
                                    8999988888999******************766689*****987 PP

>> FANCL_C  FANCL C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   9.7   0.00019      0.19       2      42 ..     186     221 ..     185     238 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00019
                                    --S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHH CS
                        FANCL_C   2 eveCgiCyayrldsgevpdisCdnekCnkkfHsaCLkeWlr 42 
                                    + +C+iC+a+   ++++ +       Cn++fH +C+ eW++
  gene220|gene220|rna220|rna220 186 NANCSICLAEYNMNDKIKILP-----CNHHFHLNCIDEWFN 221
                                    579*******999**999986.....5789*********97 PP

>> Zn_ribbon_17  Zinc-ribbon, C4HC2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.1      0.57   5.6e+02       4      14 ..     122     132 ..     120     139 .. 0.79
   2 !   16.3   4.6   5.7e-06    0.0056       4      46 ..     186     227 ..     183     230 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.57
                   Zn_ribbon_17   4 lksCayCelav 14 
                                    +++C+ C++++
  gene220|gene220|rna220|rna220 122 TQECKTCKITA 132
                                    679****9986 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 5.7e-06
                   Zn_ribbon_17   4 lksCayCelavkgr.vvlcgvCeHvlHasCarewfenddlaeCp 46 
                                    + +C++C  + + +  +    C+H  H +C++ewf+ dd   Cp
  gene220|gene220|rna220|rna220 186 NANCSICLAEYNMNdKIKILPCNHHFHLNCIDEWFNIDD--ICP 227
                                    678999977765441444567******************..776 PP

>> zf-ANAPC11  Anaphase-promoting complex subunit 11 RING-H2 finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   5.1     5e-05      0.05      47      80 ..     202     232 ..     172     236 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5e-05
                                    EEEBTTS-EEEHHHHHHHHHHHSTSSB-TTTSSB CS
                     zf-ANAPC11  47 lvlGkckhnfhlhcilkwletetskglcpmcrqt 80 
                                    + +  c+h fhl ci +w++ +   + cp+c++ 
  gene220|gene220|rna220|rna220 202 IKILPCNHHFHLNCIDEWFNID---DICPLCKKP 232
                                    44557**************875...689999875 PP

>> MFS_2  MFS/sugar transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   5.2   1.3e-05     0.013     131     275 ..       6     162 ..       2     171 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.3e-05
                          MFS_2 131 eRtsltsvrsflsvlggvlaailafllvlilgg..............lkserkgylifaliialLmllgviivvlgtker 196
                                    +Rt+ +++++f++ l  + +    +++vli+++               ++++  + +f++++ +L+l+ +i+ +l  +e 
  gene220|gene220|rna220|rna220   6 QRTQTQRITRFMERLSALQCIKWFVVVVLIFKSlqviyntiilvvtmNQHTKAPFKLFISVYNVLVLVQIILFFLRHREY 85 
                                    6666667777777666666666666666666666667777777777789******************************9 PP

                          MFS_2 197 vemrkkekteqkeklslleqlkevfrnraflillllfllaalalgvlnglllYyltyvlgngsaasvfllvvtisallg 275
                                      +++  + ++++ lsl+ ++ + f+   f+ l  +  ++   +    +  lYy ty + +   + v++ ++ i  l++
  gene220|gene220|rna220|rna220  86 FRVTRLPDIQDNNELSLFSNFVDAFSL--FWCLTGFHWTQECKTCKITAPWLYYTTYAWSFLGIFVVISPLIAIVLLIF 162
                                    8889999999999***99999999986..55555555555555555566689*****9986555544444333333333 PP

>> RANK_CRD_2  Receptor activator of the NF-KB cysteine-rich repeat domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   1.5   6.4e-05     0.064      26      40 ..     115     129 ..     113     130 .. 0.95

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 6.4e-05
                     RANK_CRD_2  26 CtaGYHWsedcdcCr 40 
                                    C +G+HW ++c +C+
  gene220|gene220|rna220|rna220 115 CLTGFHWTQECKTCK 129
                                    9*************8 PP

>> zf-RING_6  zf-RING of BARD1-type protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   1.0   0.00024      0.24      18      52 ..     199     235 ..     184     239 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00024
                      zf-RING_6  18 repvclggcehifcsncisdcfg..sgcpvcytpawi 52 
                                     + + +  c+h f  nci + f     cp+c  p  i
  gene220|gene220|rna220|rna220 199 NDKIKILPCNHHFHLNCIDEWFNidDICPLCKKPINI 235
                                    55666778*************973257****999765 PP

>> zf-C3H2C3  Zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.2       6.2   6.2e+03      15      22 ..     113     120 ..     109     129 .. 0.48
   2 ?   12.9   2.4   8.4e-05     0.083      17      35 .]     207     230 ..     201     230 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 6.2
                      zf-C3H2C3  15 ysCkHlvH 22 
                                    + C+  +H
  gene220|gene220|rna220|rna220 113 FWCLTGFH 120
                                    55554444 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 8.4e-05
                      zf-C3H2C3  17 CkHlvHakCade.....evCPkCk 35 
                                    C+H +H +C de     ++CP+Ck
  gene220|gene220|rna220|rna220 207 CNHHFHLNCIDEwfnidDICPLCK 230
                                    *********997666668*****7 PP

>> zf-C3HC4_5  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   2.9    0.0086       8.6       3      39 ..     188     221 ..     186     222 .. 0.90
   2 ?    5.7   0.2     0.013        13       1       9 [.     223     231 ..     223     237 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0086
                     zf-C3HC4_5   3 iCPvCkssrYlnpdleflinpeCYhkmCesCvdRlFs 39 
                                     C +C ++  +n ++++l    C h+   +C+d  F+
  gene220|gene220|rna220|rna220 188 NCSICLAEYNMNDKIKIL---PCNHHFHLNCIDEWFN 221
                                    6***************99...6999999****99886 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.013
                     zf-C3HC4_5   1 deiCPvCks 9  
                                    d+iCP+Ck 
  gene220|gene220|rna220|rna220 223 DDICPLCKK 231
                                    8******95 PP

>> zf-C3HC4_4  zinc finger of C3HC4-type, RING
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.1       1.9   1.9e+03      21      26 ..     189     194 ..     182     204 .. 0.66
   2 ?    6.3   6.8     0.011        11      13      42 .]     204     229 ..     189     229 .. 0.70

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 1.9
                     zf-C3HC4_4  21 ClsCis 26 
                                    C  C+ 
  gene220|gene220|rna220|rna220 189 CSICLA 194
                                    555555 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.011
                     zf-C3HC4_4  13 sleCGhsfClsCisslqkepdgeqllCplC 42 
                                     l+C h f l+Ci+++ +   +    CplC
  gene220|gene220|rna220|rna220 204 ILPCNHHFHLNCIDEWFNID-D---ICPLC 229
                                    479************98766.3...48888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1280  (0.0713927); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); expected 17.9 (0.001)
Passed Fwd filter:                        23  (0.00128284); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 1522.76
//
Query:       gene2200|gene2200|rna2200|rna2200  [L=328]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.5e-61  206.5   0.2    7.7e-60  202.5   0.2    2.0  1  Pkinase        Protein kinase domain
    3.9e-29  101.7   0.2    5.5e-29  101.2   0.2    1.1  1  Pkinase_Tyr    Protein tyrosine kinase
    9.1e-06   24.8   0.1    1.3e-05   24.3   0.1    1.2  1  Haspin_kinase  Haspin like kinase domain
    7.7e-05   22.1   0.0     0.0001   21.7   0.0    1.3  1  Kinase-like    Kinase-like
  ------ inclusion threshold ------
      0.014   14.5   1.0      0.024   13.7   0.4    1.5  1  Seadorna_VP7   Seadornavirus VP7
      0.015   15.3   0.1      0.024   14.6   0.1    1.2  1  APH            Phosphotransferase enzyme family
      0.044   13.1   0.3       0.16   11.3   0.3    1.9  1  Kdo            Lipopolysaccharide kinase (Kdo/WaaP) family


Domain annotation for each model (and alignments):
>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  202.5   0.2     3e-63   7.7e-60       3     264 .]      12     302 ..      10     302 .. 0.88

  Alignments for each domain:
  == domain 1  score: 202.5 bits;  conditional E-value: 3e-63
                                        EEEEEEEESSEEEEEE...............EETTTTEEEEEEEEECHCHCHHHHHHHHHHHHHHHHHSCTTB--E CS
                            Pkinase   3 kleklGeGsfGkVyka...............veketgkivAvKkikkekakkkkekkvlrEikilkklkhpnivrl 63 
                                        +++klGeG++++Vy a                 ++   +vA+Kkik+ + +   + +++rEik +++++++++++l
  gene2200|gene2200|rna2200|rna2200  12 RQKKLGEGTYAVVYLAqmvqssgphkiiksiAANTHVSTVAIKKIKHYSSTTGIDLSTVREIKNMQRVQSKYVLTL 87 
                                        56788888888887652111111111111102234456899******999999999******************** PP

                                        EEEEEESSEEEEEEE--TTEBHHHHHH.HHSS--HHHHHHHHHHHHHHHHHHHHTTEE-SS-SGGGEEEETTTEEE CS
                            Pkinase  64 yevfeekdelylvleyveggeladlle.rkgslseeeakkiakqilegleylHskgiiHrDlKpeNiLidekgelK 138
                                        +evf +++++ + ley++ + l+++++ r+ ++ ++++k i+  +++g+  +H+k i+HrDlKp+NiL+d +g +K
  gene2200|gene2200|rna2200|rna2200  88 FEVFFHNNSVNMALEYAPYN-LEHIIKnRQLVIMPSDIKAIMLMVMKGVYAIHRKFIVHRDLKPNNILLDANGIVK 162
                                        ******************66.99999967777******************************************** PP

                                        E-SGTTSEESSSSCSBCTTTSCGGGS-HHHH.TTSCBSHHHHHHHHHHHHHHHHHSS-STTTSSHHHHHHHHHHTH CS
                            Pkinase 139 itDFGlakelessskltsfvgtseYlAPEvl.keneyskkvDvWslGvilyelltgkppfsgekgkekvekeldql 213
                                        i+DFGl++ l  +  +ts+v+t++Y+APE+l +++ y+ +vD+Ws+G+i++el+ + p f+   g++    +l+ql
  gene2200|gene2200|rna2200|rna2200 163 IADFGLSRDLGDN--MTSYVVTRWYRAPELLfGAKVYGFNVDMWSIGCIFAELFLRVPFFA---GEN----DLNQL 229
                                        **********995..7***************999***********************9999...443....78899 PP

                                        HHHHHHCT.SHH...HHHTTS.....................-HHHHHHHHHHT-SSGCCSTTHHHHHTSGGG CS
                            Pkinase 214 ekilkilg.etkeklpeasei.....................seeakdllkkllkkdpkkRltaeellqhpyl 264
                                          i++ lg +t+ ++p   ++                      ++a++ll+k+l  +p+kR++  ++l+h y+
  gene2200|gene2200|rna2200|rna2200 230 DVIFRALGtPTEHDWPGMCTLsnfvklpsyprvppktiftgaTDDAIELLEKMLVFEPQKRISSYNALKHAYF 302
                                        999999998889999999999999***********************************************98 PP

>> Pkinase_Tyr  Protein tyrosine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.2   0.2   2.1e-32   5.5e-29       4     200 ..      13     215 ..      11     232 .. 0.91

  Alignments for each domain:
  == domain 1  score: 101.2 bits;  conditional E-value: 2.1e-32
                                        EEEEEEESSEEEEEEEEET...........TTTSSEEEEEEEEESTTSSHHH.HHHHHHHHHHHHTS-BTTB--EE CS
                        Pkinase_Tyr   4 gkklGeGafGkVvegtlkg...........ekekkevkVavKtlkeeateee.keelleeakimkklkhpnivkll 67 
                                        +kklGeG+++ V+ +++ +             +++  +Va+K++k+ ++ +    + ++e+k m++++ + ++ l 
  gene2200|gene2200|rna2200|rna2200  13 QKKLGEGTYAVVYLAQMVQssgphkiiksiAANTHVSTVAIKKIKHYSSTTGiDLSTVREIKNMQRVQSKYVLTLF 88 
                                        689**************9999*****99988889999*******987777665788999***************** PP

                                        EEEESSSSEEEEEE--TTEBHHHHHHHTCTTTSBHHHHHHHHHHHHHHHHHHHHTTEEEST-SGGGEEEEETTEEE CS
                        Pkinase_Tyr  68 gvctkeepllivteyvkgGdLlkfLrkkekekltlkdllsfalqvAkGmeyLeskklvHrdlaarNvLlsenkvvk 143
                                         v  +++++ + +ey+++ +L++ ++++ +  +  +d+  ++l v kG+  +++k +vHrdl   N+Ll+ n +vk
  gene2200|gene2200|rna2200|rna2200  89 EVFFHNNSVNMALEYAPY-NLEHIIKNR-QLVIMPSDIKAIMLMVMKGVYAIHRKFIVHRDLKPNNILLDANGIVK 162
                                        *****************9.7*****999.9999******************************************* PP

                                        E-STTTHEETTTSSEEEETTSSTSGGGGS.-HHHHHHSE.EEHHHHHHHHHHHHHHHHT CS
                        Pkinase_Tyr 144 isDfGLardiekddeyvkkeeaklpvkWm.apEslkekk.ftsksDvWsfGvllwEift 200
                                        i+DfGL+rd+       ++ ++ +  +W+ apE l+  k +  + D+Ws G +  E+f 
  gene2200|gene2200|rna2200|rna2200 163 IADFGLSRDL------GDNMTSYVVTRWYrAPELLFGAKvYGFNVDMWSIGCIFAELFL 215
                                        **********......45555667778877****99776599**************996 PP

>> Haspin_kinase  Haspin like kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.1   5.2e-09   1.3e-05     109     284 ..      17     201 ..       5     203 .. 0.65

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 5.2e-09
                      Haspin_kinase 109 seklssevyqtke...kdkevvlKviplev.ledvtiskelslkelkslklvkgtypglllllqdkvlkekpdfys 180
                                        +e+ +  vy ++    +  + ++K i+ ++ ++ v i+k+        + l +    + ++++q+k++ +  +++ 
  gene2200|gene2200|rna2200|rna2200  17 GEGTYAVVYLAQMvqsSGPHKIIKSIAANThVSTVAIKKIKHYSSTTGIDLSTVREIKNMQRVQSKYVLTLFEVFF 92 
                                        6666666666655322334455555555431344444444444333333333333224446677777766644443 PP

                      Haspin_kinase 181 eqqlflvlllkdkGtdLeev....klksw.kqalsifwqivkiLyvaEtkfeFEHRdLhldniLvdknlnvtlidl 251
                                         +++++ + l+++  +Le++    +l  + ++++ i+  ++k +y+   kf   HRdL+ +niL+d+n+ v + d+
  gene2200|gene2200|rna2200|rna2200  93 -HNNSVNMALEYAPYNLEHIiknrQLVIMpSDIKAIMLMVMKGVYAIHRKFI-VHRDLKPNNILLDANGIVKIADF 166
                                        .45567788899999999998554333333789******************6.5********************** PP

                      Haspin_kinase 252 klsRle.ssegkvlytrld.dpllFqGggDyqfei 284
                                         lsR   ++    + tr    p+l  G + y f++
  gene2200|gene2200|rna2200|rna2200 167 GLSRDLgDNMTSYVVTRWYrAPELLFGAKVYGFNV 201
                                        ****8865555566666555777777877777765 PP

>> Kinase-like  Kinase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.0     4e-08    0.0001      87     238 ..      65     208 ..      16     228 .. 0.76

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 4e-08
                        Kinase-like  87 fdlvkiqkkkpfiqlkskesiywvvnallllpaasvdl....eilnkvlqkrsethkkletiarlllTlqlirlaa 158
                                        +dl ++ + k +++++sk  + ++   ++    +++ l      l +++++r+    +  + a  ++ l +++ + 
  gene2200|gene2200|rna2200|rna2200  65 IDLSTVREIKNMQRVQSK-YVLTLFEVFFHNNSVNMALeyapYNLEHIIKNRQLVIMPSDIKA--IM-LMVMKGVY 136
                                        677777777777666544.34446666666666666663333334444444444433333333..33.55789999 PP

                        Kinase-like 159 nLqakglvhgkftvdnllldekgglmlggftaLvragtkvvlsevekgfaPpEllgsrggytrknktkmthkldaW 234
                                         ++ k +vh +++++n+lld +g +++ +f+  +  g+++    v + +  pEll  ++         + +++d W
  gene2200|gene2200|rna2200|rna2200 137 AIHRKFIVHRDLKPNNILLDANGIVKIADFGLSRDLGDNMTSYVVTRWYRAPELLFGAKV--------YGFNVDMW 204
                                        9******************************9999999999666779******9877554........67788888 PP

                        Kinase-like 235 qlGl 238
                                         +G 
  gene2200|gene2200|rna2200|rna2200 205 SIGC 208
                                        8885 PP

>> Seadorna_VP7  Seadornavirus VP7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.4   9.4e-06     0.024     146     186 ..     127     165 ..     108     170 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 9.4e-06
                       Seadorna_VP7 146 iivaglkdLmdfhsestnllhGDcnpenlmcDknGylklvD 186
                                        i+++ +k +  +h   ++++h D +p+n++ D nG +k+ D
  gene2200|gene2200|rna2200|rna2200 127 IMLMVMKGVYAIH--RKFIVHRDLKPNNILLDANGIVKIAD 165
                                        5677789999999..789*********************99 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.1   9.4e-06     0.024     166     196 ..     141     169 ..     137     171 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 9.4e-06
                                        EEEE-SS-SGGGEEEC..TTEEEEE---TT- CS
                                APH 166 tvllHgDlhpgNllvdpddgrvtGviDfeda 196
                                        + ++H+Dl+p+N+l+d   + ++ + Df+++
  gene2200|gene2200|rna2200|rna2200 141 KFIVHRDLKPNNILLD--ANGIVKIADFGLS 169
                                        669*************..4555568888765 PP

>> Kdo  Lipopolysaccharide kinase (Kdo/WaaP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.3   6.3e-05      0.16      57     155 ..      68     159 ..      45     171 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 6.3e-05
                                Kdo  57 ravrEfrllkrLeeagvavpkpvaagavkvgle.yrAlllterlegaqdLedllakwaelaeelkrallkavgrli 131
                                          vrE+++++r +++ v ++  v++  + v+++   A    e++ + + L+ +  +         +a++  v + +
  gene2200|gene2200|rna2200|rna2200  68 STVREIKNMQRVQSKYVLTLFEVFFHNNSVNMAlEYAPYNLEHIIKNRQLVIMPSD--------IKAIMLMVMKGV 135
                                        55677777777777777777777776666666655555555555555555555444........566777788889 PP

                                Kdo 132 aklhragvnHadlyaknillqqee 155
                                          +hr  + H+dl + nill++++
  gene2200|gene2200|rna2200|rna2200 136 YAIHRKFIVHRDLKPNNILLDANG 159
                                        99*******************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (328 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       621  (0.0346366); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 2048.29
//
Query:       gene2201|gene2201|rna2201|rna2201  [L=360]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-36  125.5   0.0    3.6e-36  124.8   0.0    1.4  2  RVT_1     Reverse transcriptase (RNA-dependent DNA polymerase


Domain annotation for each model (and alignments):
>> RVT_1  Reverse transcriptase (RNA-dependent DNA polymerase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  124.8   0.0     2e-40   3.6e-36      23     221 ..       2     224 ..       1     225 [. 0.93
   2 ?   -4.1   0.0      0.52   9.3e+03      22      35 ..     292     305 ..     286     318 .. 0.68

  Alignments for each domain:
  == domain 1  score: 124.8 bits;  conditional E-value: 2e-40
                                        HCTB--...........-------HHHH................HCCHTS--EEEEEEBCCGCCCSBB-GGGGGGG CS
                              RVT_1  23 nkliakrLkdvl..ekllsenqpgfrpgrstldav...edllkalkkkkkaklllklDlkkaFdsvpleellrklt 93 
                                         +++a+rL+++   ek+l ++q g r+ + ++      ++++++ + k++a ++++lD++ka+d+vp+e ll kl+
  gene2201|gene2201|rna2201|rna2201   2 TRICADRLSNISerEKILIHEQAGSRKLEECVAHAtslYEIARQRSLKGRAPYAAFLDFSKAYDRVPHEGLLAKLK 77 
                                        6899*******999**************99988888998888887888999************************* PP

                                        -EEET.........................TEEEEESB--ST-TTHHHHHHHHHHHHHTT-T...........TEE CS
                              RVT_1  94 afkvptklinliksflstrsfsvrvngeeskgryekkglpqGsvlSPllfnlfmnellrelrkra.....kgvtll 164
                                        +++++ kl++l+ ++++ + +sv    ++s ++ ++ g++qG++ SP+lfnl++n+l+  ++  a      ++  l
  gene2201|gene2201|rna2201|rna2201  78 SYGFHGKLLRLLTAMYRRPCASVLTGDTRSAPFIYNIGVRQGCPASPILFNLYINDLFDGFSGVAiqpgvRSIPGL 153
                                        ****************88887777766699*********************************99*********** PP

                                        ECTTEEEEEESSHHHHHHHHHHHHHHHHHTT--BEGGG-EEE...................ESSEEETTEE CS
                              RVT_1 165 rYaDDililskskeelqelleaveewlkesglkinpeKtklvlft.............v.kseevkyLGvt 221
                                        ++aDD ++l++s +elq+ l+ +++w++++++++n eK+ lv+f+                  +++yLG++
  gene2201|gene2201|rna2201|rna2201 154 LFADDAVVLAESAHELQSNLQRISDWCERWRISLNIEKCGLVVFGpgearnmcyrgqsLpVVASYTYLGHP 224
                                        *********************************************99999998888643788899999986 PP

  == domain 2  score: -4.1 bits;  conditional E-value: 0.52
                                        HHCTB--....... CS
                              RVT_1  22 lnkliakrLkdvle 35 
                                        l+++i ++Lkd+l+
  gene2201|gene2201|rna2201|rna2201 292 LQRVIDHALKDILS 305
                                        67777777777653 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (360 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       319  (0.0177924); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.20s 00:00:00.67 Elapsed: 00:00:00.38
# Mc/sec: 2834.48
//
Query:       gene2202|gene2202|rna2202|rna2202  [L=286]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
        2.6    5.7   6.8        3.3    5.4   6.8    1.3  1  PI3K_1B_p101  Phosphoinositide 3-kinase gamma adapter protein


Domain annotation for each model (and alignments):
>> PI3K_1B_p101  Phosphoinositide 3-kinase gamma adapter protein p101 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   6.8   0.00018       3.3     324     397 ..     184     261 ..     106     284 .. 0.67

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.00018
                       PI3K_1B_p101 324 vdeeedleeee...eeeeedslarsstlstvsssskdsmlsllslsssslassvsslssgvdsdyv.edsdessss 395
                                         + ee++ +e+   e ee++ +++++  st + ss+ds+  ++ l+s+   + +ss+++ ++s++  ed   +s+s
  gene2202|gene2202|rna2202|rna2202 184 SHTEENVPSETirgEIEETQEVKEEENGSTTAVSSQDSINPVTDLTSKLALTPSSSVADITESHTNsEDHKRQSDS 259
                                        2233333332211133333444677788999999999999999999999999999999999996641444444444 PP

                       PI3K_1B_p101 396 sp 397
                                         +
  gene2202|gene2202|rna2202|rna2202 260 LS 261
                                        33 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       745  (0.0415528); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 1947.98
//
Query:       gene2203|gene2203|rna2203|rna2203  [L=89]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       309  (0.0172346); expected 358.6 (0.02)
Passed bias filter:                      224  (0.0124937); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.55u 0.34s 00:00:00.89 Elapsed: 00:00:00.55
# Mc/sec: 483.72
//
Query:       gene2204|gene2204|rna2204|rna2204  [L=94]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       583  (0.0325172); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.55u 0.34s 00:00:00.89 Elapsed: 00:00:00.54
# Mc/sec: 519.82
//
Query:       gene2205|gene2205|rna2205|rna2205  [L=1015]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-18   66.7   1.5      3e-17   63.1   1.3    2.3  2  CNH       CNH domain
    3.9e-16   59.8   3.0      9e-16   58.6   3.0    1.7  1  RhoGEF    RhoGEF domain
  ------ inclusion threshold ------
      0.015   15.3   0.1       0.04   13.9   0.1    1.7  1  DUF5402   Family of unknown function (DUF5402)


Domain annotation for each model (and alignments):
>> CNH  CNH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0     0.045   2.7e+02       5      19 ..     741     755 ..     738     757 .. 0.90
   2 !   63.1   1.3   5.1e-21     3e-17     135     272 ..     858     996 ..     812     999 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.045
                                CNH   5 tggqrlllGteeGly 19 
                                        +++q ll+Gt eGl+
  gene2205|gene2205|rna2205|rna2205 741 SDEQFLLFGTKEGLF 755
                                        5799**********9 PP

  == domain 2  score: 63.1 bits;  conditional E-value: 5.1e-21
                                CNH 135 fqvpaevfsisvlkpklcvgvakgFelvnldegaaeslldpedns..ldfaarkenlkplaviqisedefLlcyde 208
                                        + v   vf+i+++++kl+++ ++ Fe+v+ d+ ++++l+dp d    + f ++ +n+++l+v+ i++d fL+cyd 
  gene2205|gene2205|rna2205|rna2205 858 LFVGCLVFDIAFFNTKLVIA-CRDFEMVDSDTLKTQELVDPLDLCvpFYF-KELKNITALSVFTIESDVFLVCYDC 931
                                        555578999***********.789*****************999987555.999********************** PP

                                CNH 209 favyvdlqGrrsr.dseleWegkPesvaclepyllafhknfieirsvetgelvqeisgkklrfll 272
                                        ++++ d++Gr  r + ++ W   P ++ +++ yl+ ++++ + +++++t+++v   + + l+f++
  gene2205|gene2205|rna2205|rna2205 932 MGFFIDSYGRTIRqNVIFVWYIRPIKFKIYKEYLVCVSDQEVAVWDINTANMVYYTRQEHLMFVA 996
                                        **********7777**************************************9988888887775 PP

>> RhoGEF  RhoGEF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.6   3.0   1.5e-19     9e-16       2     181 ..      11     212 ..      10     213 .. 0.86

  Alignments for each domain:
  == domain 1  score: 58.6 bits;  conditional E-value: 1.5e-19
                                        HHHHHHHHHHHHHHHHHHHHHTHCCCHHCT..CCHHHHHH....HHCTTHHHHHHHHHHHHHHHHHHHH....... CS
                             RhoGEF   2 ikElleTErsYvrdLkvlvevylkplsele..vlseeeik....iiFsnieeilelhrsflleeLeerl....... 64 
                                        + E++e+E++Yv+dLk+  e + + l ++e  +   e+ +    ++F+n++ i++lh +++ +eL  r+       
  gene2205|gene2205|rna2205|rna2205  11 LSEIFESEKAYVSDLKIWGEDFKRYLFQSEtlT--IEKKHslskTLFINLDAIIALH-EQIAQELGRRNeyirein 83 
                                        68*********************9999888552..4443333448************.999999*99999999999 PP

                                        ...............HHHTTSS-S-SHHHHHHHHSTHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHTSGG CS
                             RhoGEF  65 ..............keseeqkeaqsigdvflkfadkfkkYseYcsnypnalkllkelskknkkfkafleeaeerpe 126
                                                      +++    +  +  +v+ k+++ f  Y  Y+s+ p ++  l+++ + n+ fk+ l +  ++++
  gene2205|gene2205|rna2205|rna2205  84 klptgdaykpivvnDDTAVMYKDLEYHSVYYKYLNRFGVYRYYVSRLPTVEFDLDKECNMNRFFKQELMDFFNERN 159
                                        99988888777665245555566788999*****99********************99999999999999887777 PP

                                        GTT--HHHHTTHHHHHHHHHHHHHHHHHHTS-TTSHHH.HHHHHHHHHHHHHHHHH CS
                             RhoGEF 127 cskldLeslLikPvqRlprYpLLLkellkntpeshpdy.ealkkaleaikevasei 181
                                          +l  ++++ +  q+l rY +L++++l +   ++p + e ++++++++ke+a+ +
  gene2205|gene2205|rna2205|rna2205 160 -IELGPKHFIYRASQKLARYAILWNAVLHYE--ENPVFiEGINETVQKLKEIARDV 212
                                        .68999*********************9998..556777*************9987 PP

>> DUF5402  Family of unknown function (DUF5402)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   6.7e-06      0.04      14      64 ..     907     957 ..     905     971 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 6.7e-06
                            DUF5402  14 kklqnllgkevfvsevdifalrcGcvGilievrGlevddveifkekilekl 64 
                                        k+l+n+++ +vf +e d+f +   c+G+ i+  G +++   if   i+   
  gene2205|gene2205|rna2205|rna2205 907 KELKNITALSVFTIESDVFLVCYDCMGFFIDSYGRTIRQNVIFVWYIRPIK 957
                                        789*******************************99999999977776555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1015 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1771  (0.0987785); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 1.02u 0.34s 00:00:01.36 Elapsed: 00:00:00.55
# Mc/sec: 5570.26
//
Query:       gene2206|gene2206|rna2206|rna2206  [L=390]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.1e-32  113.4   2.1    1.1e-32  113.4   2.1    2.1  2  RabGAP-TBC  Rab-GTPase-TBC domain
  ------ inclusion threshold ------
      0.021   15.2   0.0      0.061   13.7   0.0    1.7  1  DUF1689     Protein of unknown function (DUF1689)
       0.64    9.0   5.3        1.1    8.3   5.3    1.3  1  MMM1        Maintenance of mitochondrial morphology protein 1


Domain annotation for each model (and alignments):
>> RabGAP-TBC  Rab-GTPase-TBC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.2      0.14   8.5e+02     132     166 ..      51      84 ..      10      92 .. 0.59
   2 !  113.4   2.1   1.9e-36   1.1e-32       3     214 ..     105     352 ..     104     353 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.14
                         RabGAP-TBC 132 pglkrklkvleellkkkdpklykhlkeegldlelf 166
                                        + +++  ++ + + +++  k+y+h+ e +ld++ f
  gene2206|gene2206|rna2206|rna2206  51 NSTNTTANTTNYIEERIEYKIYSHISE-QLDISNF 84 
                                        233444444444444455555555544.5555555 PP

  == domain 2  score: 113.4 bits;  conditional E-value: 1.9e-36
                         RabGAP-TBC   3 lRgevWklllgyep..evkrlkksekkqeksekeksklekseeske..lsqIkkDvprtfp.......es...... 61 
                                        lR++ Wklllgy+p  + k+++  +++++ + ++++k +    ++     +I+kDv r +        ++      
  gene2206|gene2206|rna2206|rna2206 105 LRPKFWKLLLGYLPknKFKTEYHLKERRKLYHFYYEKANAVLMDNPgiDDAINKDVDRVCIlpvtvgvHDgsiaqk 180
                                        7*************774444444444444444444444444333333499*********99999999933445556 PP

                         RabGAP-TBC  62 ....esfknkqgqnqLeriLkaysiynpevgYcqGmndivaplllvsldeee..........aFwcfvsLlekykl 123
                                            +s  ++  +n+L+riL+++ + n  vgY+qGm+ ++ p++ v+  +++          aF+cf +L+    +
  gene2206|gene2206|rna2206|rna2206 181 csflDSCADRMHRNALKRILLTFKVTNSSVGYTQGMHMVLIPIYYVFSTSKDiddvryaeedAFFCFFNLM--SEI 254
                                        8777777889**********************************555555557777888888*********..556 PP

                         RabGAP-TBC 124 rdlytsslpg.....lkrklkvleellkkkdpklykhlkeegldlelfaikwfltlflrefpletvlrlwD.llle 193
                                         + ++s+ +      +++k+  + el++++d +ly  ++++++  ++f ++w+  l+++ef +e+vl lwD l++ 
  gene2206|gene2206|rna2206|rna2206 255 GEHFISEYDYdctvgIRKKMDSVLELVRRYDAELYAVMERKKISETMFHLRWVSLLLCSEFEIEQVLVLWDkLFAD 330
                                        666666553333444********************************************************99997 PP

                         RabGAP-TBC 194 ge..kfvllrvalailklleeel 214
                                         +  ++ ++++++ai+ l ++ +
  gene2206|gene2206|rna2206|rna2206 331 SYrfEM-VIYCCAAIIVLMKNAI 352
                                        776566.8889999998877765 PP

>> DUF1689  Protein of unknown function (DUF1689)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0     1e-05     0.061      15      91 ..     189     268 ..     184     306 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1e-05
                            DUF1689  15 daeDRleLakklqsiaraqllggwlgfsavflaptayrryktgaikgvkvpr.sfllGlvalv..vssqlaakyay 87 
                                        d+  R +L++ l +  ++++ +g++ ++ ++l+p++y   +++ i+ v+      ++ +++l+  +++++ ++y y
  gene2206|gene2206|rna2206|rna2206 189 DRMHRNALKRILLTFKVTNSSVGYTQGMHMVLIPIYYVFSTSKDIDDVRYAEeDAFFCFFNLMseIGEHFISEYDY 264
                                        677899******************************************9877645555555553467888888888 PP

                            DUF1689  88 kkkl 91 
                                        + ++
  gene2206|gene2206|rna2206|rna2206 265 DCTV 268
                                        7665 PP

>> MMM1  Maintenance of mitochondrial morphology protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   5.3   0.00018       1.1      41     109 ..      16      83 ..       2      97 .. 0.67

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00018
                                        XXX.XXXXXXXXXXXXXXXXXXXXX.XXXXX-HHH........HHHHHHHHTTT--TTTS--B--HHHH CS
                               MMM1  41 aaerlssskkklssvikkkkkekeessedleekkssnvveessakiesiLektyYdveshqpesLDWfn 109
                                        ++++ ++++++ +sv+++++++++++ ++++++++ n +++++++++ i e+  Y++ sh +e LD  n
  gene2206|gene2206|rna2206|rna2206  16 EENSVNMNNNNENSVTNTNSTNTNTNPTNTNTNPT-NSTNTTANTTNYIEERIEYKIYSHISEQLDISN 83 
                                        11223334455555555555566665555555555.6678889999********************877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (390 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1738  (0.0969379); expected 358.6 (0.02)
Passed bias filter:                      652  (0.0363657); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.65u 0.31s 00:00:00.96 Elapsed: 00:00:00.49
# Mc/sec: 2402.95
//
Query:       gene2207|gene2207|rna2207|rna2207  [L=1097]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.9e-29  101.1   0.7    1.4e-27   96.8   0.1    2.8  2  UCH            Ubiquitin carboxyl-terminal hydrolase
    9.9e-10   38.5   3.6    4.3e-06   26.5   0.7    2.6  2  UCH_1          Ubiquitin carboxyl-terminal hydrolase
     0.0039   16.6   0.1     0.0084   15.4   0.1    1.5  1  USP7_ICP0_bdg  ICP0-binding domain of Ubiquitin-specific prot


Domain annotation for each model (and alignments):
>> UCH  Ubiquitin carboxyl-terminal hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.1      0.55   3.3e+03      22      56 ..      71     105 ..      68     118 .. 0.71
   2 !   96.8   0.1   2.4e-31   1.4e-27       1     257 []     150     611 ..     150     611 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.55
                                        SHHHHHHHHTCHHCCSSTCCCCC-.TT.TTS.TTH CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                                UCH  22 ipelrdyllsleevkkesrnkkelnesnplgkkge 56 
                                         +++ +y+ ++  +++e+ +++++ ++n++++ ++
  gene2207|gene2207|rna2207|rna2207  71 YNRFDNYFGRYLFRNDEDGEHESNRDENNNTMGDR 105
                                        57889999998888888888888766666666553 PP

  == domain 2  score: 96.8 bits;  conditional E-value: 2.4e-31
                                        -EES-SSSTHHHHHHHHHHHTSHHHH.HHHHTCHHCCSSTCCCCC............................... CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxx............................... RF
                                UCH   1 tGlsNlGntCymnsvlQcLfsipelr.dyllsleevkkesrnkke............................... 44 
                                        +G++N+G+tCy+ns++Q+L++i+ +  +++ ++ + + ++  + +                               
  gene2207|gene2207|rna2207|rna2207 150 VGIRNMGATCYINSLVQVLYNINAFYnRVMSTPTQPEVNEGVA-Dkaltgkdfidegvasrtgkaltekgaptdln 224
                                        69************************55555554444444444.359***************************** PP

                                        .......................................................-..TT.TTS.TTHHHHHHHHH CS
                                        .......................................................x.xxxxxxxxxxxxxxxxxxx RF
                                UCH  45 .......................................................l.nesnplgkkgelakalkdl 64 
                                                                                               +  + +++ +++  +kal+++
  gene2207|gene2207|rna2207|rna2207 225 ekgaptdpnekdaptdpnekgaptdpnekdtlkntpkhealkntptdhedktptkVdARREEKRTNKYNLKALQQM 300
                                        **************************999999999999999999999888877762344555555566889***** PP

                                        HHHHHSH-CCEE--HHHHHHHHHHSGGGTSSSTCEHHHHHHHHHHHHHHHHCCHCCCHHHHHHCCCTTSHHHHHH- CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                                UCH  65 fkellkskskavsPkklkktlsklaksfsgykqqDaqEflaflLdqlhedlnrevaeekwkkhlkrndslitdlfe 140
                                        f++l  +++++v P+   + ls l +     + qD +E+ + lLd+l+++ ++               +  ++lf 
  gene2207|gene2207|rna2207|rna2207 301 FYKLR-TQQTEVHPDLTFRNLSLLGPL---DQHQDFHEYSKKLLDELEHETDD---------------QRFNSLFD 357
                                        ****9.69*******999999999999...99******************999...............33444555 PP

                                        EEEEE..........................................................EEEEEEB-SEEEE CS
                                        xxxxx..........................................................xxxxxxxxxxxxx RF
                                UCH 141 gqlks..........................................................klklkrlPeiLii 158
                                        g+l++                                                             + ++P+iL++
  gene2207|gene2207|rna2207|rna2207 358 GELTQyirascgctkesvekfndlqldvrhsikealdayfeedelcgdnkyrcdehglvdavkGQAIRKVPDILFV 433
                                        555555555555555555566666666666666666666666999999999***9***99999999********** PP

                                        EEESEEETEE...EEE--SEEB--SEEE-GGGBSS-BTTS-TCS-BEEEEEEEEEESCTTSEEEEEEEE..CTTTT CS
                                        xxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxx RF
                                UCH 159 hlkRfsynss...ksKlntkvefpeeldlssylaeekkkkteekkkYeLiavvvHsGslssGHYvayik..nekng 229
                                         +kRfs++ +     K+n   ef + l+++        +         L +vvvHsG +s+GHY++y++  +++  
  gene2207|gene2207|rna2207|rna2207 434 LIKRFSMDWEtneVVKNNGYCEFGDVLEING-------ER------LVLKGVVVHSGVSSDGHYYCYVRvaHDD-- 494
                                        *******88877889*********9999984.......22......57******************99965333.. PP

                                        E..........................................................................E CS
                                        x..........................................................................x RF
                                UCH 230 k..........................................................................W 231
                                        +                                                                          W
  gene2207|gene2207|rna2207|rna2207 495 StrdatgaenttrnttgaenttrdatdagnntrnktrdatdaenttrnatrdaagtawsksndhvvahdnragtvW 570
                                        245788899999999************************************************************* PP

                                        EEEETTEEEEE-HHCCCTT................CEEEEEE CS
                                        xxxxxxxxxxxxxxxxxxx................xxxxxxx RF
                                UCH 232 ykydDetvkevkeeeevls................sayiLfY 257
                                        +k++D+ v++v+e+ evl+                say LfY
  gene2207|gene2207|rna2207|rna2207 571 LKFNDHIVTRVSES-EVLEhnrggrhpyrraelpfSAYGLFY 611
                                        ************88.677667788888888888999999999 PP

>> UCH_1  Ubiquitin carboxyl-terminal hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.1   1.9e-05      0.11       1      31 [.     150     180 ..     150     189 .. 0.87
   2 !   26.5   0.7   7.2e-10   4.3e-06      71     306 ..     256     503 ..     251     578 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.9e-05
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              UCH_1   1 sGLEnhivnsYlNslLQvlyfipplrnlals 31 
                                        +G  n  +++Y+Nsl+Qvly i  ++n ++s
  gene2207|gene2207|rna2207|rna2207 150 VGIRNMGATCYINSLVQVLYNINAFYNRVMS 180
                                        7999999****************99987766 PP

  == domain 2  score: 26.5 bits;  conditional E-value: 7.2e-10
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxx................... RF
                              UCH_1  71 lssipeasalglileeeeetekssaislssliqs...fnrflldqlekelketkkns................... 124
                                        l+++p+ +al+    ++e+ ++ ++++ ++  ++    n   l+q+ ++l++++++                    
  gene2207|gene2207|rna2207|rna2207 256 LKNTPKHEALKNTPTDHED-KTPTKVDARREEKRtnkYNLKALQQMFYKLRTQQTEVhpdltfrnlsllgpldqhq 330
                                        6677777777775443333.33333444444433111333344444444444333336666666667777777777 PP

                                        ...............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              UCH_1 125 ...............seeesaieqllgtkaettirclkCgseksrksstlvldlkyPkpsnekkeakvtfasilks 185
                                                       +++++ +++l+  ++++ ir + Cg +k+  + +  l+l            ++++++ l +
  gene2207|gene2207|rna2207|rna2207 331 dfheyskklldelehETDDQRFNSLFDGELTQYIRAS-CGCTKESVEKFNDLQLD----------VRHSIKEALDA 395
                                        77777777777777766678899************99.99988888888888883..........46899999999 PP

                                        xxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              UCH_1 186 sler...ekttrawCekCkryqpteqrktvknlPpvLalnakleeeeelelwktknwlpleiklsldedknleekl 258
                                         +e+     ++++ C++ +      +++ ++++P++L +  k+++ +    w+t+++++++ + +  +        
  gene2207|gene2207|rna2207|rna2207 396 YFEEdelCGDNKYRCDE-HGLVDAVKGQAIRKVPDILFVLIKRFSMD----WETNEVVKNNGYCEFGD-------- 458
                                        99993333467777777.7789999******************9999....***99999999995444........ PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....x RF
                              UCH_1 259 keerekakaekeikvYeLqsvvvhigdskesghLvslvkvaekeler.....d 306
                                                 e +    +L +vvvh g s+  gh++++v+va+ +++r     +
  gene2207|gene2207|rna2207|rna2207 459 -------VLEINGERLVLKGVVVHSGVSS-DGHYYCYVRVAHDDSTRdatgaE 503
                                        .......234556678**********888.9***********99998655540 PP

>> USP7_ICP0_bdg  ICP0-binding domain of Ubiquitin-specific protease 7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1   1.4e-06    0.0084     156     219 ..     865     924 ..     851     941 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.4e-06
                      USP7_ICP0_bdg 156 pdakeyydfllnrveVtFkpkekpkdeeftleLskkmtYdqlaekvaekLkvdptklrfttvna 219
                                         +a+ ++++l +r+ + F +++    ++ftl L++++tY+++a+ v e+L +    +  ++ n 
  gene2207|gene2207|rna2207|rna2207 865 RSAALHLRYLSQRRCISFINRN----KSFTLFLKRTYTYNEVARIVREYLMDQKVAIAYFKGNV 924
                                        5677899************887....69**********************99998888887764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1097 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       735  (0.040995); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.80u 0.34s 00:00:01.14 Elapsed: 00:00:00.51
# Mc/sec: 6418.68
//
Query:       gene2208|gene2208|rna2208|rna2208  [L=400]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (400 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       653  (0.0364214); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 2636.37
//
Query:       gene2209|gene2209|rna2209|rna2209  [L=453]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (453 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       670  (0.0373696); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 2963.10
//
Query:       gene221|gene221|rna221|rna221  [L=416]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.2e-81  271.7   0.0    1.2e-80  271.3   0.0    1.1  1  Hist_deacetyl  Histone deacetylase domain


Domain annotation for each model (and alignments):
>> Hist_deacetyl  Histone deacetylase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  271.3   0.0   6.5e-85   1.2e-80       1     306 [.      22     312 ..      22     313 .. 0.94

  Alignments for each domain:
  == domain 1  score: 271.3 bits;  conditional E-value: 6.5e-85
                                    SCCGTHHHHHHHHHHHHT.THHHHCCE.EE-----HHHHTTTS-HHHHHHHHCHHHHCHHT.TTHCCHHHCCTSTSSSSS CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Hist_deacetyl   1 hpenpkRlsaileslaesvglldelelliqpseatkeellkvHskeYlelleslsnelkkkeeakekeleeiaskllddd 80 
                                    hp++p+R++ +++sl  +++l ++ +++++p  a+ e l+++Hs +Y+++l+s+s++  ++  +  k+l++ +   + dd
  gene221|gene221|rna221|rna221  22 HPMKPHRVR-MTHSLLVNYSLYKH-MDVFKPTMASFENLTNFHSIDYINFLQSVSQSNMDDM-I--KDLQKFN---VGDD 93 
                                    89*******.99****999*9866.557************************9886665554.3..3344444...5799 PP

                                    THCTTTCCHHHHHHHHHHHHHHHHHHTTSSSEEEETT.SS--TT-BTTB-BTTBSS-HHHHHHHHHHHCC-SS-EEEEE- CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Hist_deacetyl  81 tpvspktlkaallavgavleavdavlsgsvkaafvlv.rPpgHHakaseasGFClvNnvaiaikylqakhelkrvailDv 159
                                    +p++ +++++++ ++g++l a  ++ ++  +a+++++  ++ HHak++easGFC+vN+++++i +l + ++ +rv+++D+
  gene221|gene221|rna221|rna221  94 CPIFRGLYDYCRSTAGSSLCATYKLNTR--EADIAINwSGGLHHAKRGEASGFCYVNDIVLGILELLK-YN-ERVMYIDI 169
                                    **************************99..9***********************************99.44.7******* PP

                                    SSS--HHHHHHCTT-TTEEEEEEEE-CCTSTTSS--TT---SGGGTTSEEEEEE-TT-BHHHHHHHHHHCHHHHHCCH-- CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Hist_deacetyl 160 DvHhGnGteeafysdpdvltlSiHryegifyPgtgaledlgegkgkgfnlnvpleegtgdeeylkvfeeilrpvleefkP 239
                                    D HhG+G+eeafy +++v+t+S+H+y++ ++Pgtgal+d+g  +g+++++nvpl++g++d +y+++f+ i+ +++e f+P
  gene221|gene221|rna221|rna221 170 DCHHGDGVEEAFYTTDRVMTVSFHKYGE-YFPGTGALKDTGLLRGRNYAVNVPLKDGIDDFSYQSIFRPIVSRAVEMFRP 248
                                    *************************966.9************************************************** PP

                                    SEEEEEE-STTBTTSTT-S-BB-HHHHHHHHHHHCCCHGS-G.EEEEE-S---HHHHHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Hist_deacetyl 240 dlilvsaGfDalkgdplgelnlsvegykeltkklaeladkvkkvvllleGGYnlealaravtavlsa 306
                                     +i++++G+D+l+gd+lg +nl+ +g++e+++++++l     ++++l++GGY++++++r +t+ +++
  gene221|gene221|rna221|rna221 249 CAIVLQCGADSLAGDRLGCFNLTNKGHAECVRYVKNLQI---PLLVLGGGGYTIKNVSRTWTYETAI 312
                                    *************************************98...99******************99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (416 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       578  (0.0322383); expected 358.6 (0.02)
Passed bias filter:                      482  (0.0268838); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 2980.57
//
Query:       gene2210|gene2210|rna2210|rna2210  [L=551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (551 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       730  (0.0407162); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.47
# Mc/sec: 3499.10
//
Query:       gene2211|gene2211|rna2211|rna2211  [L=176]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-13   50.6   0.0    2.7e-13   50.0   0.0    1.3  1  RVT_1     Reverse transcriptase (RNA-dependent DNA polymerase


Domain annotation for each model (and alignments):
>> RVT_1  Reverse transcriptase (RNA-dependent DNA polymerase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.0   0.0   1.5e-17   2.7e-13      57     149 ..     108     175 ..      76     176 .] 0.83

  Alignments for each domain:
  == domain 1  score: 50.0 bits;  conditional E-value: 1.5e-17
                                        .....HCCHTS--EEEEEEBCCGCCCSBB-GGGGGGG-EEET.........................TEEEEESB- CS
                              RVT_1  57 dllkalkkkkkaklllklDlkkaFdsvpleellrkltafkvptklinliksflstrsfsvrvngeeskgryekkgl 132
                                        ++ + l+k ++ak+++ lD+k ++++++++e+++k+taf++                          +++ye +++
  gene2211|gene2211|rna2211|rna2211 108 EVDQVLEKLQGAKYFSVLDIKEGYFQINVREEDKKKTAFQIG-------------------------SRKYEFNRM 158
                                        334458899*********************************.........................99******* PP

                                        -ST-TTHHHHHHHHHHH CS
                              RVT_1 133 pqGsvlSPllfnlfmne 149
                                        p+G++++Pl+f+++mn+
  gene2211|gene2211|rna2211|rna2211 159 PMGFKNAPLIFQRIMNR 175
                                        ***************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       746  (0.0416086); expected 358.6 (0.02)
Passed bias filter:                      476  (0.0265492); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1356.99
//
Query:       gene2212|gene2212|rna2212|rna2212  [L=444]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.017   15.7   7.5      0.071   13.6   5.3    2.5  2  APG6_N           Apg6 coiled-coil region
      0.032   13.0   2.7      0.071   11.9   0.0    2.1  2  Peptidase_M29    Thermophilic metalloprotease (M29)
       0.13   10.8   7.1      0.076   11.6   3.5    2.0  2  FapA             Flagellar Assembly Protein A
       0.28   11.0   2.6       0.28   11.0   1.0    1.8  2  Peptidase_M41    Peptidase family M41
       0.39   11.4  11.7       0.26   11.9   5.7    2.4  2  HIP1_clath_bdg   Clathrin-binding domain of Huntingtin-intera
        4.2    7.2   6.9       0.24   11.2   1.4    1.8  2  ITAM_Cys-rich    Immunoreceptor tyrosine-based activation mot
        7.9    6.8  13.8          7    6.9   3.6    2.8  3  THOC7            Tho complex subunit 7


Domain annotation for each model (and alignments):
>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0      0.22   5.6e+02      72      98 ..     134     160 ..      87     180 .. 0.60
   2 ?   13.6   5.3   2.8e-05     0.071      26      92 ..     362     426 ..     347     442 .. 0.77

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.22
                             APG6_N  72 elekereeleaelaaleeelealeeee 98 
                                        e+++  ++le  +++l++  e++ +++
  gene2212|gene2212|rna2212|rna2212 134 EIDEVCKDLECFIRDLKANFEKIRNQN 160
                                        122222222222222222222222222 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 2.8e-05
                             APG6_N  26 daYeeflkklkkekkeeekqdeeleeleeeleklekeeeelleeLkelekereeleaelaaleeele 92 
                                        d+Y+   + +++e k++   +e  ++ e++l++  +e+++l+++L + +++ ++l++++++ ++e +
  gene2212|gene2212|rna2212|rna2212 362 DQYKIAGAAIDREVKDK--IEEINKKDENKLQQYTNERNALVKKLVAQKAKAQDLQKQIEEKRKEIQ 426
                                        45555555555443322..34455666777********************************99976 PP

>> Peptidase_M29  Thermophilic metalloprotease (M29)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   2.8e-05     0.071      81     145 ..     131     195 ..     126     214 .. 0.92
   2 ?    0.3   0.9     0.088   2.3e+02      73     133 ..     348     410 ..     338     427 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.8e-05
                                        HHHHHHHHHHTT-EEEEEE---GGGSTTS-HHHHHHHHHHHHHHHHHHHHHHHTTSS-B-BEE-- CS
                      Peptidase_M29  81 eaekleelveegaarlsilaedpkllkgvdpekiaaaqkarskalkeyreriasgklrWcvvavP 145
                                        ++++++e++++  ++++ l ++ + +++ ++ek++  ++  + + ++y ++i++g+++W    ++
  gene2212|gene2212|rna2212|rna2212 131 KKQEIDEVCKDLECFIRDLKANFEKIRNQNAEKLSYSEREFEIIVEKYGKEIKNGTFNWDAFVYS 195
                                        568899*****************************************************887776 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.088
                                        -TT---HHHHHHHHHHHHTT-EEEEEE--.-GGGSTTS-HHHHHHHHHHHHHHHHHH.HHHHH CS
                      Peptidase_M29  73 qleevpeweaekleelveegaarlsilae.dpkllkgvdpekiaaaqkarskalkey.reria 133
                                        +l+++ + +++ +++ ++ + a +  + + + + +++ d++k++++++ r+ + k++  ++++
  gene2212|gene2212|rna2212|rna2212 348 NLKYLYDQRVKSYTDQYKIAGAAIDREVKdKIEEINKKDENKLQQYTNERNALVKKLvAQKAK 410
                                        555555666666666666555555555555666667777777777776666666665233333 PP

>> FapA  Flagellar Assembly Protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.1     0.096   2.5e+02     334     374 ..     127     165 ..      94     187 .. 0.62
   2 ?   11.6   3.5     3e-05     0.076     315     414 ..     323     424 ..     297     436 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.096
                               FapA 334 elkeklkeleeeleeleeeleklkkkikklpklkaekqles 374
                                         lk+k +e++e  ++le  +++lk++++k+++ +a ++  s
  gene2212|gene2212|rna2212|rna2212 127 MLKDKKQEIDEVCKDLECFIRDLKANFEKIRNQNA-EK-LS 165
                                        55666666666666666666666666666666222.21.12 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 3e-05
                               FapA 315 klGselgtkteievgldepelkeklkeleeeleel.eeeleklkkk...ikklpklkaekqlesekkeqlkkllet 386
                                        +  s+l++kt++e  + + ++ ++ k+l+ ++ +  +++++++k +   i++  k  + ++++++ +++l++++++
  gene2212|gene2212|rna2212|rna2212 323 SYTSDLNQKTDLEHFFGFIHIYNS-KNLKYLYDQRvKSYTDQYKIAgaaIDREVK-DKIEEINKKDENKLQQYTNE 396
                                        556788999999987776666666.666666666544444444444546666666.66788999999********* PP

                               FapA 387 keklkeeleeleeelkelkeeleskkee 414
                                        +++l+++l + +++ ++l++++e+k++e
  gene2212|gene2212|rna2212|rna2212 397 RNALVKKLVAQKAKAQDLQKQIEEKRKE 424
                                        ***********************99544 PP

>> Peptidase_M41  Peptidase family M41
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       1.8   4.5e+03      98     150 ..       7      60 ..       3      89 .. 0.55
   2 ?   11.0   1.0   0.00011      0.28     115     181 ..     342     408 ..     334     418 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1.8
                                        HHHHHHTS--..-TTT-S--------..----.------SS-HHHHHHHHHHHHH CS
                      Peptidase_M41  98 arkmvtefGm..sdklGpvsleeeeeeevflgkelkkekelseetaeeideevke 150
                                        +++m+ ++ m  s+ l  ++  ++++  +++ +++++++++ ++++   d+e+++
  gene2212|gene2212|rna2212|rna2212   7 IKAMILSLFMylSNILSAFNSPRKAN-VAYNVQKSDQNNDFISQLKFYNDAELRN 60 
                                        55565555443355555555444444.4566677777777777777777777764 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00011
                                        -------..----.------SS-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHHS CS
                      Peptidase_M41 115 sleeeeeeevflgkelkkekelseetaeeideevkelveeayerakeileekreelealaeaLlekE 181
                                        ++ ++++ + ++ +++k+  +  +   ++id+evk+ +ee  ++ ++ l+++ +e +al+++L+ + 
  gene2212|gene2212|rna2212|rna2212 342 HIYNSKNLKYLYDQRVKSYTDQYKIAGAAIDREVKDKIEEINKKDENKLQQYTNERNALVKKLVAQK 408
                                        55555555555656666666666666789**********************************9875 PP

>> HIP1_clath_bdg  Clathrin-binding domain of Huntingtin-interacting protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.3     0.094   2.4e+02      23      54 ..     140     171 ..     127     184 .. 0.76
   2 ?   11.9   5.7    0.0001      0.26      27      80 ..     370     423 ..     355     428 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.094
                     HIP1_clath_bdg  23 eeverekkeleeelerlkeeaerkleeqkeel 54 
                                        +++e   ++l+ ++e++++++ +kl+  + e 
  gene2212|gene2212|rna2212|rna2212 140 KDLECFIRDLKANFEKIRNQNAEKLSYSEREF 171
                                        57788888999999999999999998444443 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.0001
                     HIP1_clath_bdg  27 rekkeleeelerlkeeaerkleeqkeelekLkreleakraelarlkssLesseq 80 
                                        +  +e+++++e+++++ e+kl++ + e ++L + l a++a+ + l++ +e++ +
  gene2212|gene2212|rna2212|rna2212 370 AIDREVKDKIEEINKKDENKLQQYTNERNALVKKLVAQKAKAQDLQKQIEEKRK 423
                                        55689999**************************************99999876 PP

>> ITAM_Cys-rich  Immunoreceptor tyrosine-based activation motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.4       4.2   1.1e+04       8      13 ..      12      17 ..      12      19 .. 0.80
   2 ?   11.2   1.4   9.2e-05      0.24       2      16 ..     426     440 ..     425     441 .. 0.93

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 4.2
                      ITAM_Cys-rich  8 LsvFRY 13
                                       Ls+F Y
  gene2212|gene2212|rna2212|rna2212 12 LSLFMY 17
                                       89**88 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 9.2e-05
                      ITAM_Cys-rich   2 rGcYRtLsvFRYkSR 16 
                                        +GcY    +FRYkSR
  gene2212|gene2212|rna2212|rna2212 426 QGCYPRQRIFRYKSR 440
                                        79************9 PP

>> THOC7  Tho complex subunit 7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.8    0.0054        14      74     113 ..     129     168 ..     127     177 .. 0.92
   2 ?   -2.9   0.0       2.9   7.5e+03      20      57 ..     231     263 ..     229     284 .. 0.49
   3 ?    6.9   3.6    0.0027         7      57     104 ..     376     424 ..     328     426 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0054
                              THOC7  74 eaekeeieseieavreeieelkaqLeearatranrkeyde 113
                                        +++k+ei++ +++++  i +lka  e+ r++ a +  y e
  gene2212|gene2212|rna2212|rna2212 129 KDKKQEIDEVCKDLECFIRDLKANFEKIRNQNAEKLSYSE 168
                                        789********************************99965 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 2.9
                              THOC7  20 tkrllklltslaesteeeleqlkedllldfaafelsie 57 
                                        +k +l+++t++      +  + k++  + +  f ++i+
  gene2212|gene2212|rna2212|rna2212 231 AKNFLSFITTK-----IAKYNEKDMWRTTYIWFGSQIR 263
                                        67777777773.....3333333333333433444433 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.0027
                              THOC7  57 e.rlqllakanerereryeaekeeieseieavreeieelkaqLeearat 104
                                        + +++ ++k  e + ++y++e++ + +++ a +++ ++l++q+ee+r++
  gene2212|gene2212|rna2212|rna2212 376 KdKIEEINKKDENKLQQYTNERNALVKKLVAQKAKAQDLQKQIEEKRKE 424
                                        45888888899999*******************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (444 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2168  (0.120921); expected 358.6 (0.02)
Passed bias filter:                      530  (0.029561); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.65u 0.29s 00:00:00.94 Elapsed: 00:00:00.47
# Mc/sec: 2847.86
//
Query:       gene2213|gene2213|rna2213|rna2213  [L=132]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.22   11.1   0.1        1.4    8.6   0.0    2.0  2  THB       Tri-helix bundle domain


Domain annotation for each model (and alignments):
>> THB  Tri-helix bundle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.0   7.6e-05       1.4       1      14 [.      40      53 ..      40      55 .. 0.93
   2 ?    0.0   0.0     0.037   6.7e+02       4      14 ..     100     110 ..      99     114 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 7.6e-05
                                THB  1 dvweiLrkakpkdY 14
                                       +v  iL+++++kdY
  gene2213|gene2213|rna2213|rna2213 40 EVARILSSVEKKDY 53
                                       6899********** PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.037
                                THB   4 eiLrkakpkdY 14 
                                        +iL ++++ dY
  gene2213|gene2213|rna2213|rna2213 100 NILYTSQKPDY 110
                                        69********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1017  (0.0567237); expected 358.6 (0.02)
Passed bias filter:                      568  (0.0316805); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.28s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 967.35
//
Query:       gene2214|gene2214|rna2214|rna2214  [L=551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.5e-32  111.5   0.1    1.6e-31  110.4   0.0    1.5  2  Metallophos   Calcineurin-like phosphoesterase
  ------ inclusion threshold ------
      0.031   14.0   0.1        3.1    7.4   0.0    2.4  2  Flavodoxin_3  Flavodoxin domain
          1    9.3   5.2       0.27   11.2   0.5    2.3  3  HisK_N        Histidine kinase N terminal


Domain annotation for each model (and alignments):
>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.4   0.0   2.7e-35   1.6e-31       4     202 ..     122     317 ..     120     319 .. 0.92
   2 ?   -3.9   0.0       2.8   1.7e+04     156     176 ..     328     354 ..     320     368 .. 0.59

  Alignments for each domain:
  == domain 1  score: 110.4 bits;  conditional E-value: 2.7e-35
                                        EEEESBTBTTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSSHHHHHHHHH.HHHHHHHTSEEEEEC-TTS... CS
                        Metallophos   4 lvigDlHlalgggqlddllkllddllreekpdlvllaGDlvdrgdlekellel.laalvkypipvylllGNHe... 75 
                                        +++gD+H     gq++dllk++++++ +++  +++  GD+vdrg++++e+  + +a +++yp++v+ll+GNHe   
  gene2214|gene2214|rna2214|rna2214 122 TIFGDIH-----GQYYDLLKIIKNINFDHETVVFV--GDYVDRGSFSSEVFLFlMALKLAYPKNVILLRGNHEsse 190
                                        589****.....*************9888888888..****************99******************998 PP

                                        .....CHHHHHHHHHHHHHHHHHHHEHHHCEEETSEEEEEETTEEEEEEEESE.CEEETHHHHHHHHHHHSCHHHH CS
                        Metallophos  76 .....gfeeellnkygylgifsepwrsdaevfnnlplaslgsgslkvlllhGg.spellvsldklgslnleleape 145
                                              f++e+  ky      ++ ++ + + f +lpl++ + +  k++++hGg sp+l +++++++++n++ e++ 
  gene2214|gene2214|rna2214|rna2214 191 mtryfSFKKECDIKYS-----NNMYKEFLSAFRALPLCAVVMK--KIFCVHGGiSPDL-KEIEDINRFNRFVEPTS 258
                                        8888777777777777.....6779999***********9999..********77777.**************999 PP

                                        CC...HHHHHHHHHHTTCSEEEEEESSESS.............CSSSCSCCHHHHHHHHHHTTESEEEEESSS CS
                        Metallophos 146 pg...dewlkdlekrekadwvivlgHsply.............rgsgylfgdealedllkkygvdlvisGHtH 202
                                        ++   d++++d               +p y             r+++y + + a++++l  +++  +++GH+ 
  gene2214|gene2214|rna2214|rna2214 259 NKtmlDLLWAD--------------PHPFYesletvyfapnknRRCSYFYTYLAVKEFLAANNLWCIVRGHEV 317
                                        99*********..............77777888888899999*****************************96 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 2.8
                                        HHTTCSEEEEEESSESS......CSSS CS
                        Metallophos 156 krekadwvivlgHsply......rgsg 176
                                          ++++ vi+++  p+y      rg+ 
  gene2214|gene2214|rna2214|rna2214 328 YIDDVPSVITIFSAPNYcdvyknRGAV 354
                                        555677788888888884443333333 PP

>> Flavodoxin_3  Flavodoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0    0.0064        38      87     124 ..      66     103 ..      60     118 .. 0.81
   2 ?    7.4   0.0   0.00053       3.1      38      67 ..     143     172 ..     122     218 .. 0.70

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.0064
                       Flavodoxin_3  87 kkilekvkalleknnevlgeflcqGkisekvrekyekl 124
                                        +kil+  k+ + ++  +  +f+ qGk+se++ +k++k 
  gene2214|gene2214|rna2214|rna2214  66 DKILRDQKKNCFDSDVIRIHFFNQGKLSESQASKITKA 103
                                        5788888888888899999***********99999885 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.00053
                       Flavodoxin_3  38 veeadvvfvGfwvdkgtadeealkfletlk 67 
                                        +++  vvfvG  vd+g++++e+  fl  lk
  gene2214|gene2214|rna2214|rna2214 143 FDHETVVFVGDYVDRGSFSSEVFLFLMALK 172
                                        78889*****************99999887 PP

>> HisK_N  Histidine kinase N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.2       1.6   9.6e+03     104     127 ..     133     154 ..     128     156 .. 0.68
   2 ?   -1.1   0.0      0.29   1.8e+03      34      47 ..     316     329 ..     314     337 .. 0.82
   3 ?   11.2   0.5   4.5e-05      0.27       5      76 ..     442     513 ..     438     518 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 1.6
                                        HHHHHHHHHHHHHHHHHHHHHHHH CS
                             HisK_N 104 elqllidkinefFDkflyyavskY 127
                                        +l ++i++in  FD+ ++  v  Y
  gene2214|gene2214|rna2214|rna2214 133 DLLKIIKNIN--FDHETVVFVGDY 154
                                        5667778777..777777777666 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.29
                                        HHHHHHHHHHHHHH CS
                             HisK_N  34 evkeNgealfelvi 47 
                                        ev+eNg++l++  i
  gene2214|gene2214|rna2214|rna2214 316 EVQENGYKLYKEYI 329
                                        89********8765 PP

  == domain 3  score: 11.2 bits;  conditional E-value: 4.5e-05
                                        HHHHHHCHHHHHHHHHCCS---TT-TTHH.HHHHHHHHHHHHHHHHHTTSS-GGGGHHHHHHHHHHHHHHT-- CS
                             HisK_N   5 vkyLeeekekfleewkkkilisdkDpyke.evkeNgealfelviellkeeiseedlkelaekiakeRveanvn 76 
                                         ++++ee   +  e  k ++++++D++ e ++k   +++f++ +  l++++s e++ + a+ i+ke  +a+ n
  gene2214|gene2214|rna2214|rna2214 442 NEFVDEESTDLSTENIKGVVVNEDDNFTEvKIKDIPNEVFKT-KDNLTKSMSIETVPSFAKDISKEVENADLN 513
                                        578888888898999999*********975899999999986.889********************9999988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (551 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       665  (0.0370907); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.31s 00:00:00.87 Elapsed: 00:00:00.47
# Mc/sec: 3547.50
//
Query:       gene2215|gene2215|rna2215|rna2215  [L=150]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.7e-27   94.9   1.7    4.5e-27   94.2   1.7    1.4  1  Ribosomal_S25  S25 ribosomal protein
  ------ inclusion threshold ------
      0.058   13.7   0.1      0.086   13.1   0.1    1.3  1  Pdase_M17_N2   M17 aminopeptidase N-terminal domain 2
      0.072   12.9   0.5       0.15   11.9   0.1    1.7  2  DUF5352        Family of unknown function (DUF5352)


Domain annotation for each model (and alignments):
>> Ribosomal_S25  S25 ribosomal protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.2   1.7   7.6e-31   4.5e-27       4      99 ..      30     125 ..      24     127 .. 0.87

  Alignments for each domain:
  == domain 1  score: 94.2 bits;  conditional E-value: 7.6e-31
                      Ribosomal_S25   4 kakkakaaaakaggkakkKKwskgkvkdklnnavlfdketydkllkevpkyklitpsvvserlkingslArraLre 79 
                                        ++k++k+a+ +++++++kKKw+ gk+kd+++++ ++d e++ k++k+vp++k+it+s+++e+++in+  + r+Lr 
  gene2215|gene2215|rna2215|rna2215  30 ESKASKEAKIAKSSSKEKKKWTTGKTKDEVSRQACVDPELLGKIVKDVPNMKMITRSTLVEKYNINLYSSIRVLRW 105
                                        33444444444555666*********************************************************** PP

                      Ribosomal_S25  80 leekgliklvskhraqviYt 99 
                                        l+e++++ +vs  r+ ++Y+
  gene2215|gene2215|rna2215|rna2215 106 LCENEIVGCVSAGRRLKVYC 125
                                        *******************7 PP

>> Pdase_M17_N2  M17 aminopeptidase N-terminal domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   1.4e-05     0.086      23      81 ..      23      77 ..       3      97 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.4e-05
                       Pdase_M17_N2 23 leaavaeliaevaeaktykavaaevsevasvtvavlptkaSRhNcpaRpdaitklVkaa 81
                                       ++a+ a+++++++eak+ k+   + +e  + t ++ ++++SR  c   p ++ k+Vk+ 
  gene2215|gene2215|rna2215|rna2215 23 SMAKKAPESKASKEAKIAKS---SSKEKKKWTTGKTKDEVSRQACVD-PELLGKIVKDV 77
                                       34444566666666666666...89999*****************65.99999999975 PP

>> DUF5352  Family of unknown function (DUF5352)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   2.5e-05      0.15      52     120 ..      27      95 ..       9      99 .. 0.74
   2 ?   -1.5   0.0      0.32   1.9e+03      88     107 ..     124     143 ..     119     145 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.5e-05
                            DUF5352  52 tnatkllvkaeksskkasklaelkkvkaddedpnaesCvDkvLRadvaeavkkatdnsCkgivnalvln 120
                                        +++     k++k +k++sk  ++ ++ +++++   + CvD++L   ++++v + +  +   +v+   +n
  gene2215|gene2215|rna2215|rna2215  27 KAPESKASKEAKIAKSSSKEKKKWTTGKTKDEVSRQACVDPELLGKIVKDVPNMKMITRSTLVEKYNIN 95 
                                        444445566677777777777777777888888999**************9998887777777766555 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.32
                            DUF5352  88 sCvDkvLRadvaeavkkatd 107
                                        +C  k ++++v+e+v k ++
  gene2215|gene2215|rna2215|rna2215 124 YCGSKFVKKEVVEDVTKKEE 143
                                        68888899999999988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1224  (0.0682693); expected 358.6 (0.02)
Passed bias filter:                      531  (0.0296168); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.30s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 987.17
//
Query:       gene2216|gene2216|rna2216|rna2216  [L=259]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      0.003   17.5   0.5       0.12   12.3   0.1    2.2  2  DinB             DinB family
  ------ inclusion threshold ------
      0.045   12.7   0.0      0.056   12.4   0.0    1.2  1  Herpes_DNAp_acc  Herpes DNA replication accessory factor
      0.057   13.9   0.0       0.16   12.4   0.0    1.8  1  DUF3922          Protein of unknown function (DUF3992)
        0.1   12.7   0.1       0.27   11.3   0.1    1.9  1  Spo0A_C          Sporulation initiation factor Spo0A C termin


Domain annotation for each model (and alignments):
>> DinB  DinB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0     0.014        61      35      59 ..       7      31 ..       2      35 .. 0.71
   2 !   12.3   0.1   2.7e-05      0.12      21      66 ..     101     145 ..      80     175 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.014
                                       --SSTTS--HHHHHHHHHHHHHHHH CS
                               DinB 35 aengegfqsvkqtlnHvldveelwl 59
                                       ++n+++   vk+++nH++++  l+l
  gene2216|gene2216|rna2216|rna2216  7 KQNARTREIVKKIVNHMTHSFLLFL 31
                                       5666666777888888888777775 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 2.7e-05
                                        HHHHHCT--CCCTT--SSTTS--HHHHHHHHHHHHHHHHHHHHH.. CS
                               DinB  21 tldaiaaLpdeelkaengegfqsvkqtlnHvldveelwlsrlegee 66 
                                        +l +++aL+ e+++ e  +  qsv  t+ H+l+ +++  ++l  ++
  gene2216|gene2216|rna2216|rna2216 101 LLILLNALS-EQYNTESEKIRQSVNSTVEHMLHIYHEICHALNDNF 145
                                        344556665.89****************************998733 PP

>> Herpes_DNAp_acc  Herpes DNA replication accessory factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   1.2e-05     0.056     207     255 ..     134     183 ..     116     228 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.2e-05
                                        -EE-SS-GGGSS-S.BSSTS-EEEESS-EEEEEEHHHHHHHHHHT-BTTT CS
                    Herpes_DNAp_acc 207 lkplelePaeaflg.vdkkgdvgvveadvvakVslesLiaAlglCkiPav 255
                                        ++ ++    + f+  ++k+ d++++ +   ak sl+ + + l lCk+P +
  gene2216|gene2216|rna2216|rna2216 134 YHEICHALNDNFDEvLEKSRDFSILLTSNKAKKSLKKIFQCLMLCKVPKF 183
                                        6677777888999989999*****************************76 PP

>> DUF3922  Protein of unknown function (DUF3992)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   3.6e-05      0.16       3      43 ..      92     133 ..      90     145 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.6e-05
                            DUF3922   3 ldkskkledyvnalqalreqyevetdkia.iieateeyylfl 43 
                                        +   k l+  + +l+al eqy+ e++ki   +++t e+ l +
  gene2216|gene2216|rna2216|rna2216  92 MASNKLLNRLLILLNALSEQYNTESEKIRqSVNSTVEHMLHI 133
                                        667788999999***************962578888877765 PP

>> Spo0A_C  Sporulation initiation factor Spo0A C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1     6e-05      0.27      11      69 ..      70     132 ..      62     175 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 6e-05
                            Spo0A_C  11 paklkGykylreaielv...ledpe.llesitkelypevAkkykttpsrVeraIrhaIevaWe 69 
                                        +++ +G++yl++ +el+   ++  +  l +    l ++++++y+t+++++ +++   +e++  
  gene2216|gene2216|rna2216|rna2216  70 TRHRRGFRYLCQTLELLdmlINMASnKLLNRLLILLNALSEQYNTESEKIRQSVNSTVEHMLH 132
                                        6899*******998875211333222444555567899*****************99999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1401  (0.0781416); expected 358.6 (0.02)
Passed bias filter:                      667  (0.0372023); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 1698.77
//
Query:       gene2217|gene2217|rna2217|rna2217  [L=133]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       562  (0.0313459); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.31s 00:00:00.73 Elapsed: 00:00:00.47
# Mc/sec: 858.18
//
Query:       gene2218|gene2218|rna2218|rna2218  [L=161]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.4e-50  169.3   0.1      4e-50  169.1   0.1    1.0  1  UQ_con     Ubiquitin-conjugating enzyme
      9e-05   22.2   0.0     0.0001   22.0   0.0    1.2  1  Prok-E2_B  Prokaryotic E2 family B
     0.0013   19.0   0.1     0.0017   18.6   0.1    1.3  1  RWD        RWD domain


Domain annotation for each model (and alignments):
>> UQ_con  Ubiquitin-conjugating enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  169.1   0.1   6.6e-54     4e-50       1     139 [.      16     152 ..      16     153 .. 0.98

  Alignments for each domain:
  == domain 1  score: 169.1 bits;  conditional E-value: 6.6e-54
                                        HHHHHHHHHHHSTTTTEEEEEEETTEECEEEEEEEB.TTSTTTTEEEEEEEE--TTTTTS--EEEESST-SCTTBE CS
                             UQ_con   1 rlqkelkelakkkpsgisaklvddenlfewkvlikgpedtpYeggvFklelefpedYPlkpPkvkfvtkifHPnvd 76 
                                        r+qke+++++ ++p+++sa++++de++++w+++i+gp++tpY++g+F le++fp++YP+ pPk+ f+t+ifH+n+ 
  gene2218|gene2218|rna2218|rna2218  16 RIQKEYMDMTLDPPENCSAGPISDEEFDKWEATIIGPHGTPYQDGIFILEIYFPPNYPYAPPKLMFKTQIFHCNI- 90 
                                        89*************************************************************************. PP

                                        TTSBB-CGGGSTTT--TTSHHHHHHHHHHHHHHS--TTS-SSHHHHHHHHHTHHHHHHHHHHH CS
                             UQ_con  77 ksGevcldiLkeekWspaltlesvllsiqsLlaepnpesplnkeaakllkkdreeykkkvkey 139
                                        k+G++cldiL+++ Wspalt+++vllsi sLl++pnp++plnk+aa+l+ +dr++y++ +k+y
  gene2218|gene2218|rna2218|rna2218  91 KDGHICLDILNTK-WSPALTISKVLLSISSLLSDPNPNDPLNKQAAELYMSDRQKYNRIAKDY 152
                                        59*********66.********************************************99887 PP

>> Prok-E2_B  Prokaryotic E2 family B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.0   1.7e-08    0.0001      34     119 ..      58     135 ..       5     153 .. 0.82

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 1.7e-08
                          Prok-E2_B  34 sggtvdlrlvypdsfpllppavflqdpeqlkllpHintfggaLClleeeldldewdpngsvadvleqlqqvLn.eg 108
                                        + g++ l++ +p+++p++pp+   +         H+n ++g +Cl        +w p+ ++ +vl +++ +L   +
  gene2218|gene2218|rna2218|rna2218  58 QDGIFILEIYFPPNYPYAPPKLMFKTQI-----FHCNIKDGHICL---DILNTKWSPALTISKVLLSISSLLSdPN 125
                                        578999**************98876444.....6***********...888899******************9888 PP

                          Prok-E2_B 109 isgdedaefag 119
                                        + +   + +a+
  gene2218|gene2218|rna2218|rna2218 126 PNDPL-NKQAA 135
                                        88877.33333 PP

>> RWD  RWD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.1   2.8e-07    0.0017      52      96 ..      59     104 ..       6     125 .. 0.72

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 2.8e-07
                                        CEEEEEEEEE-SSTTSS--EEEEEECC.SS-HHHHHHHHHHHHHHH CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxx RF
                                RWD  52 kpslkleiklpeeYPeeaPiislsste.nlpkeqvksleekleela 96 
                                        +  + lei +p++YP+ +P++ ++++    + ++ + + + l+ ++
  gene2218|gene2218|rna2218|rna2218  59 DGIFILEIYFPPNYPYAPPKLMFKTQIfHCNIKDGHICLDILNTKW 104
                                        55689******************99986333333334455555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       472  (0.0263261); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.30s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 1057.44
//
Query:       gene2219|gene2219|rna2219|rna2219  [L=159]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.071   13.2   1.3        4.1    7.6   0.1    2.4  2  SAS4      Something about silencing, SAS, complex subunit 4


Domain annotation for each model (and alignments):
>> SAS4  Something about silencing, SAS, complex subunit 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.1    0.0019        34      20      42 ..      15      37 ..       7      47 .. 0.88
   2 ?    7.6   0.1   0.00023       4.1      15      71 ..      90     146 ..      79     158 .. 0.73

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.0019
                               SAS4 20 krmrniekeraesEadrlerlle 42
                                       ++mrn+++e+++ +++ ++++++
  gene2219|gene2219|rna2219|rna2219 15 ESMRNNDIEQFQYNFNMVKHQYN 37
                                       58**************9999876 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.00023
                               SAS4  15 merqEkrmrniekeraesEadrlerllekLqgqdwlrvlgkitkindpkdkkelerk 71 
                                        m+ + ++++++   + ++    ++++++ L+++d +  +++i+++ +p +++ +++ 
  gene2219|gene2219|rna2219|rna2219  90 MTEENTALIKEQLGKYKEWDGCIHNIIKALENNDTKYKMEQISVVSKPAEHSPIQTI 146
                                        444444455555555544455678899********************9998877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1178  (0.0657036); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1205.19
//
Query:       gene222|gene222|rna222|rna222  [L=42]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (42 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       507  (0.0282782); expected 358.6 (0.02)
Passed bias filter:                      223  (0.0124379); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.31u 0.24s 00:00:00.55 Elapsed: 00:00:00.39
# Mc/sec: 322.48
//
Query:       gene2220|gene2220|rna2220|rna2220  [L=208]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.2e-29  101.3   1.2    4.9e-29  100.7   1.2    1.3  1  Rad10     Binding domain of DNA repair protein Ercc1 (rad10/S
     0.0059   15.9   1.0     0.0067   15.7   0.5    1.3  2  NUP214    Nucleoporin or Nuclear pore complex subunit NUP214=
  ------ inclusion threshold ------
       0.14   12.8   0.0       0.23   12.1   0.0    1.3  1  HHH_5     Helix-hairpin-helix domain


Domain annotation for each model (and alignments):
>> Rad10  Binding domain of DNA repair protein Ercc1 (rad10/Swi10)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.7   1.2   8.2e-33   4.9e-29       1     112 [.      15     122 ..      15     124 .. 0.95

  Alignments for each domain:
  == domain 1  score: 100.7 bits;  conditional E-value: 8.2e-33
                              Rad10   1 tilvserqkgnplLkslknvpwey.kdivpDyvigsttcvlflslkyhklhpeYieerlkklkkkyklrvlLvlvD 75 
                                        ti vs++q+gn++L++l++v+w y + +++D+ i++ ++vlflsl++h+ +peYi  rl++lk +yk+++lL++vD
  gene2220|gene2220|rna2220|rna2220  15 TIKVSTKQRGNNVLDHLNQVKWYYeDGLTTDFEIEHFISVLFLSLRFHSSKPEYIIARLNNLK-EYKTNILLIYVD 89 
                                        589*********************666999********************************9.99********** PP

                              Rad10  76 vedseevlkeLnkicilndltlllawsaeeaarylet 112
                                        ++++ee + e+ ++    +++++l++ ++eaa+yl++
  gene2220|gene2220|rna2220|rna2220  90 MHNYEEYMVEFVQF----ECQVFLCFGNDEAAKYLAA 122
                                        **********6655....99**************986 PP

>> NUP214  Nucleoporin or Nuclear pore complex subunit NUP214=Nup159
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.5   1.1e-06    0.0067      53     167 ..      41     161 ..      23     187 .. 0.76
   2 ?   -2.5   0.0      0.37   2.2e+03      50      75 ..     181     207 ..     167     208 .] 0.71

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.1e-06
                                        S-----SEEEE-TTE.EEEEEETTE..EEEEESSEEEEEESSSTT.EEEEEE-SS-EE..EEETTEEEEE....ET CS
                             NUP214  53 kaelefkwekeikdv.iavkflnde.vvlvstksellsldleelseleeihklekdlvelkllkstllll....ds 122
                                            +f+ e+ i+ + + ++f++++   ++++ ++l +++++ l  +  +h++e+ +ve+  ++ +++l     ++
  gene2220|gene2220|rna2220|rna2220  41 GLTTDFEIEHFISVLfLSLRFHSSKpEYIIARLNNLKEYKTNILLIYVDMHNYEEYMVEFVQFECQVFLCfgndEA 116
                                        45556666655554313478999998899999*************999******9999876655555544222223 PP

                                        TSEEEEEETT....EEEECSEEEEEE-SSEEEEEETTS-EEEEEE CS
                             NUP214 123 nnqLsaldlskkelkslaenvasfDvledkLvvllkdksvqvfel 167
                                         + L a+d+++++ +++ ++  sfD+ e k+  l k  +++ ++ 
  gene2220|gene2220|rna2220|rna2220 117 AKYLAAIDMNAHRSTEIIKHRYSFDLYERKIEFLAKIPKINKKDA 161
                                        45699999**9999*******************999888877665 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.37
                                        S..SS-----SEEEE-TTEEEEEEETT CS
                             NUP214  50 s.edkaelefkwekeikdviavkflnd 75 
                                        + ++++ l++k  + i++ + +kf+nd
  gene2220|gene2220|rna2220|rna2220 181 KaSNDVRLSTKKKESIEEYMNMKFTND 207
                                        334567788888889999999999887 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   3.9e-05      0.23       2      35 ..     148     184 ..     147     190 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.9e-05
                                        HHHHTSTT--HHHHHHHHTTT--S.....HHHHHHS-HH CS
                              HHH_5   2 eeLlsvsGiGpktAlallsaGies.....vedlaaadve 35 
                                        e L ++++i++k+A all +  ++     ++dl++++ +
  gene2220|gene2220|rna2220|rna2220 148 EFLAKIPKINKKDAAALLAG--KTclrtlFDDLMSKASN 184
                                        6899***************9..54444456899887654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       836  (0.0466284); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1548.47
//
Query:       gene2221|gene2221|rna2221|rna2221  [L=294]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.2e-05   24.2   7.9    2.3e-05   24.2   5.4    2.0  2  RabGAP-TBC  Rab-GTPase-TBC domain
  ------ inclusion threshold ------
      0.055   12.8   0.1       0.08   12.3   0.1    1.3  1  Foamy_BEL   Foamy virus BEL 1/2 protein
        5.5    7.1   6.6        1.1    9.3   2.5    2.1  2  ETRAMP      Malarial early transcribed membrane protein (ETRA


Domain annotation for each model (and alignments):
>> RabGAP-TBC  Rab-GTPase-TBC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   5.4   3.9e-09   2.3e-05      38     152 ..      31     150 ..       6     220 .. 0.68
   2 ?    0.0   0.2     0.093   5.6e+02      93     144 ..     199     252 ..     196     263 .. 0.58

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 3.9e-09
                         RabGAP-TBC  38 lekseeskelsqIkkDvprtfp...esesfknkqgqnqLeriLkaysiynpevgYcqGmndivaplllvsldeeea 110
                                        l   +++++l++I+ D++r fp   + + +k++  +n+L    k   ++ p v+Y+q m diva+l  ++l+e + 
  gene2221|gene2221|rna2221|rna2221  31 LDVGKNQNDLKTINVDINRNFPfyeHMADEKKPLFRNEL----KKTLLRLP-VSYVQSMCDIVAVLMYFYLSEMTE 101
                                        445566777*************55333555555555555....55556677.9**************888888887 PP

                         RabGAP-TBC 111 FwcfvsLlekyklrdlytssl..pg.....lkrklkvleellkkkdpkl 152
                                         + +vsL e+++  +  + +   +       +r+++++ ++lk+k+  l
  gene2221|gene2221|rna2221|rna2221 102 DNSLVSLAERENTASAINMNEddSLyddetYERMFRTIYNILKAKYVPL 150
                                        7888888833333333222221121333346666667777777544333 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.093
                         RabGAP-TBC  93 mndivapll.lvsldeeeaFwcfvsLl....ekyklrdlytsslpglkrklkvleel 144
                                        mndi  ++  ++s++++ +F ++v+      +k+k++ + ++    + + +k+ +e 
  gene2221|gene2221|rna2221|rna2221 199 MNDIYKIFAlIISCPTSVVFLLLVHYFdaieNKKKIKMNDNDI---MPKIIKLEKEF 252
                                        9999999863677799999999999884433333333333333...33333344444 PP

>> Foamy_BEL  Foamy virus BEL 1/2 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   1.3e-05      0.08     120     184 ..     147     215 ..     120     257 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.3e-05
                          Foamy_BEL 120 lfglldryykgylenpatfiv.wkftcqedpsgkrylgtq...fwvpplgqvniqfyknyqivifcdal 184
                                         + l+d  +k ylen ++fi  +k    e ps+k  + t+    w    ++   ++yk + ++i c + 
  gene2221|gene2221|rna2221|rna2221 147 YVPLIDDQFKTYLENNDIFIKmMKKRGVEIPSSKSLIYTNstlTWFSRSADSMNDIYKIFALIISCPTS 215
                                        45689**************8625677789*****9775542227888888889999*****99999653 PP

>> ETRAMP  Malarial early transcribed membrane protein (ETRAMP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.1         2   1.2e+04      34      48 ..      35      49 ..      30      50 .. 0.78
   2 ?    9.3   2.5   0.00019       1.1      11      75 ..     217     289 ..     202     294 .] 0.70

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 2
                             ETRAMP 34 kakkaikkiddkiek 48
                                       k+++++k i+ +i++
  gene2221|gene2221|rna2221|rna2221 35 KNQNDLKTINVDINR 49
                                       577888888888876 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00019
                             ETRAMP  11 afLlavnlltpeslcdevnkkk........ekakkaikkiddkiekkkkkkKliiistiatalallvasalGl 75 
                                        +fLl+v+++    ++++ + +         + +k  +   d+++    k   ++ii  +at+++++ a+++G+
  gene2221|gene2221|rna2221|rna2221 217 VFLLLVHYFDAIENKKKIKMNDndimpkiiKLEKEFLRLQDEQVASRPKVSNKAIIFGAATGAVIAGAVLFGI 289
                                        45555555554444444444447888888655555566667788888777777*******************5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (294 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       920  (0.0513135); expected 358.6 (0.02)
Passed bias filter:                      513  (0.0286129); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 2155.30
//
Query:       gene2222|gene2222|rna2222|rna2222  [L=149]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.049   12.8   4.7      0.055   12.7   4.7    1.1  1  Herpes_LMP1     Herpesvirus latent membrane protein 1 (LMP1)
       0.11   12.4  10.4       0.17   11.7   9.8    1.6  1  TatC            Sec-independent protein translocase protein (
       0.26   11.4   7.5       0.87    9.7   0.4    2.1  2  DHHC            DHHC palmitoyltransferase
       0.53    9.7   7.4       0.77    9.1   7.4    1.3  1  DUF373          Domain of unknown function (DUF373)
        2.8    7.6  13.3       0.84    9.4   2.0    2.1  2  DUF5381         Family of unknown function (DUF5381)
        3.4    7.5   9.6        2.6    7.8   2.2    2.5  2  DUF3188         Protein of unknown function (DUF3188)
        4.3    6.3  16.7      0.053   12.6   6.4    2.1  2  DUF973          Protein of unknown function (DUF973)


Domain annotation for each model (and alignments):
>> Herpes_LMP1  Herpesvirus latent membrane protein 1 (LMP1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   4.7   2.2e-05     0.055      59     139 ..      40     130 ..      13     147 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.2e-05
                                        XXXXXXXXXXXXX......XXXXXXXX....XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                        Herpes_LMP1  59 allliiiiliifi......frrdllcp....lgalcllllmitlllialwnlhgqalylgivlfifgcllvlglwi 124
                                        al++i+i  i f+      f r ++      +   +llllm  + l +  nl+  +l++  ++++f  + vlg+  
  gene2222|gene2222|rna2222|rna2222  40 ALIIIVIGSIFFLmggmlfFDRVMMMAgnivFSIGVLLLLMPQMSLNSSENLKSMSLFVAGIVLVFCGFAVLGFLF 115
                                        344444433333211111123322222111022234678889999999**********9888889999******** PP

                                        XXXXXXXXXXXXXXX CS
                        Herpes_LMP1 125 yllellwrlgatiwq 139
                                         l+ +l+ +   i  
  gene2222|gene2222|rna2222|rna2222 116 QLVSVLYTIRNKIPS 130
                                        ******998777655 PP

>> TatC  Sec-independent protein translocase protein (TatC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   9.8   6.5e-05      0.17      79     162 ..      24     122 ..      21     130 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 6.5e-05
                                        HHHCCCTTTTS---STTTHHHHHHHHHHHHHHHHHHHHTHHHHHHHHHT............TTTS...STTEEHHH CS
                               TatC  79 qlwafvapgLykherrlvlvfliaslllfllGaafayfvvlplvlkfll............seev...epllslse 139
                                        +++ f++pg++++ + +++ ++i s+++ ++G++f    v+ ++ ++++            s  +   e+l s+s 
  gene2222|gene2222|rna2222|rna2222  24 NIFDFLTPGMNERSESALIIIVIGSIFFLMGGMLFFDR-VMMMAGNIVFsigvllllmpqmS--LnssENLKSMSL 96 
                                        7899**********999888888887766666666554.55555555553455666666331..233355567777 PP

                                        HHHHHHHHHHHH...HHHTTHHHHHH CS
                               TatC 140 ylsfvlllllaf...giaFelPlvlv 162
                                        +++ ++l++ +f   g++F+l  vl+
  gene2222|gene2222|rna2222|rna2222  97 FVAGIVLVFCGFavlGFLFQLVSVLY 122
                                        77766666555522255566655554 PP

>> DHHC  DHHC palmitoyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.4   0.00034      0.87      79     124 ..      16      68 ..       1      72 [. 0.66
   2 ?    5.2   3.6    0.0082        21      61     123 ..      64     126 ..      62     142 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00034
                               DHHC  79 eekkseflavtllkk.......llsilllvlsllfllllgllllfhlylilrn 124
                                        +++k+ + +++ + +         +++++v+  +f+l+ g+l++ ++++++ n
  gene2222|gene2222|rna2222|rna2222  16 DHQKQLNMNIFDFLTpgmnersESALIIIVIGSIFFLMGGMLFFDRVMMMAGN 68 
                                        333333333333334777778767788899999999999**999999998766 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0082
                               DHHC  61 llilalvlllialvklveeekkseflavtllkkllsilllvlsllfllllgllllfhlylilr 123
                                        +++ ++v+++  l+ l+++++ ++ ++++ ++ +++ ++lv++ +++l +++ l+  ly+i++
  gene2222|gene2222|rna2222|rna2222  64 MMAGNIVFSIGVLLLLMPQMSLNSSENLKSMSLFVAGIVLVFCGFAVLGFLFQLVSVLYTIRN 126
                                        455566777777888888888888888887776666666666666666655555555555544 PP

>> DUF373  Domain of unknown function (DUF373)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   7.4    0.0003      0.77     148     262 ..      33     146 ..      24     149 .] 0.70

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0003
                             DUF373 148 lkdpelrktiLvplGlllliyalllllglpelalaiillllGlylllr.Gfgldelleelleklkesleegritfv 222
                                        +++   + +i++++G ++++++ +l+++ + ++++ i++ +G++lll   ++l++  +e l++++ ++    ++f 
  gene2222|gene2222|rna2222|rna2222  33 MNERSESALIIIVIGSIFFLMGGMLFFDRVMMMAGNIVFSIGVLLLLMpQMSLNS--SENLKSMSLFVAGIVLVFC 106
                                        788888999********************9************9988761456665..5666666665555444443 PP

                             DUF373 223 .tyvvallllligiisgyislesvss.asvssglltlilafi 262
                                         ++v+++l+ l+++++++ +  ++ s +s+  + +t+il+f+
  gene2222|gene2222|rna2222|rna2222 107 gFAVLGFLFQLVSVLYTIRN--KIPSfRSIVMNNITKILKFL 146
                                        13445555566666666555..33335566667777777776 PP

>> DUF5381  Family of unknown function (DUF5381)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   2.0   0.00033      0.84      30      76 ..      29      73 ..      20      74 .. 0.80
   2 ?    8.3   8.5   0.00071       1.8       9      77 ..      58     125 ..      55     144 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00033
                            DUF5381 30 lfeglkfeskysllyiiigiigtifgliillmvlpallkkGkvlfti 76
                                       l+ g++  s+ +l+ i+ig i+ + g +++    ++++  G+++f+i
  gene2222|gene2222|rna2222|rna2222 29 LTPGMNERSESALIIIVIGSIFFLMGGMLFFD--RVMMMAGNIVFSI 73
                                       56788889999999999999998888877765..667777*****99 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00071
                            DUF5381   9 kflrvllflatvglglaglfllfeglkfeskysl..lyiiigiigtifgliillmvlpallkkGkvlftik 77 
                                        +f rv+++ + +++ ++ l ll+  + ++s+  l  + ++++ i+++f+   +l +l  l++   vl+ti 
  gene2222|gene2222|rna2222|rna2222  58 FFDRVMMMAGNIVFSIGVLLLLMPQMSLNSSENLksMSLFVAGIVLVFCGFAVLGFLFQLVS---VLYTIR 125
                                        6789**********************999966553366777778889*************99...999994 PP

>> DUF3188  Protein of unknown function (DUF3188)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.9     0.018        46       1      15 [.      39      53 ..      39      61 .. 0.81
   2 ?    7.8   2.2     0.001       2.6       7      43 ..      72     110 ..      66     115 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.018
                            DUF3188  1 aAplLillgllilly 15
                                       +A+  i++g + +l 
  gene2222|gene2222|rna2222|rna2222 39 SALIIIVIGSIFFLM 53
                                       688899999999885 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.001
                            DUF3188   7 llgllillysqrq..gsdrlqslPallvGlgLivsgavg 43 
                                        ++g+l+ll  q +  +s++l s+ ++++G++L++ g ++
  gene2222|gene2222|rna2222|rna2222  72 SIGVLLLLMPQMSlnSSENLKSMSLFVAGIVLVFCGFAV 110
                                        7888888833332114556999999********999765 PP

>> DUF973  Protein of unknown function (DUF973)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   2.5      0.16   4.2e+02     133     150 ..      40      57 ..      22      61 .. 0.73
   2 ?   12.6   6.4   2.1e-05     0.053     102     162 ..      62     122 ..      58     146 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.16
                             DUF973 133 gviilligiilaliGqil 150
                                        ++ii++ig+i++l G +l
  gene2222|gene2222|rna2222|rna2222  40 ALIIIVIGSIFFLMGGML 57 
                                        566777777777777665 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 2.1e-05
                             DUF973 102 tliligaiiiiigvilaivsllslilslillgviilligiilaliGqillglsfyklGevY 162
                                        +++++g i+  igv+l+++  +sl++s+ l ++ + + gi+l++ G+ +lg+ f+ +   Y
  gene2222|gene2222|rna2222|rna2222  62 VMMMAGNIVFSIGVLLLLMPQMSLNSSENLKSMSLFVAGIVLVFCGFAVLGFLFQLVSVLY 122
                                        699***************9999******************************998776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1049  (0.0585086); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.58u 0.34s 00:00:00.92 Elapsed: 00:00:00.53
# Mc/sec: 844.67
//
Query:       gene2223|gene2223|rna2223|rna2223  [L=351]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.11   13.2   0.3    2.9e+02    2.7   0.0    4.8  3  LRR_1     Leucine Rich Repeat


Domain annotation for each model (and alignments):
>> LRR_1  Leucine Rich Repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0     0.017     3e+02       1      16 [.      97     112 ..      97     120 .. 0.88
   2 ?    1.3   0.0     0.048   8.5e+02       5      12 ..     166     173 ..     162     223 .. 0.65
   3 ?    2.7   0.0     0.016   2.9e+02       1      10 [.     286     295 ..     286     308 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.017
                              LRR_1   1 nLrhLdLsnnpllglp 16 
                                        +L++L + ++++++++
  gene2223|gene2223|rna2223|rna2223  97 SLKTLKIVDCCFFDFI 112
                                        69*********98765 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.048
                              LRR_1   5 LdLsnnpl 12 
                                        +dLs+n+ 
  gene2223|gene2223|rna2223|rna2223 166 IDLSRNFE 173
                                        56666652 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.016
                              LRR_1   1 nLrhLdLsnn 10 
                                        +L++L+L+n 
  gene2223|gene2223|rna2223|rna2223 286 HLKELNLENS 295
                                        69*****996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (351 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       379  (0.0211389); expected 358.6 (0.02)
Passed bias filter:                      220  (0.0122706); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.50
# Mc/sec: 2130.67
//
Query:       gene2224|gene2224|rna2224|rna2224  [L=273]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   2.2e-104  347.5   0.0   2.6e-104  347.3   0.0    1.0  1  Fibrillarin      Fibrillarin
    2.4e-05   24.1   0.0    5.1e-05   23.1   0.0    1.4  1  GCD14            tRNA methyltransferase complex GCD14 subunit
  ------ inclusion threshold ------
      0.081   13.0   0.0       0.11   12.6   0.0    1.3  1  FtsJ             FtsJ-like methyltransferase
       0.11   12.2   0.0       0.41   10.3   0.0    1.9  2  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F


Domain annotation for each model (and alignments):
>> Fibrillarin  Fibrillarin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  347.3   0.0  5.8e-108  2.6e-104       1     225 [.      42     269 ..      42     270 .. 0.99

  Alignments for each domain:
  == domain 1  score: 347.3 bits;  conditional E-value: 5.8e-108
                                        EEEECSSTTEEEEETTSSEEEEEE-SSTT--SSSSEEEEETTE....EEEEE-TTTSHHHHHHHTT-S--S--TTS CS
                        Fibrillarin   1 veeheklegvyivkekgdarlatknlvpgekvYgEklikveee....EyRvWnpfrsKlaaailkglkelpikkgs 72 
                                        ve+h+++ gvy+ ++k+d+ l+t n+vpg +vY+Ek+i+v++e    EyR+Wnp+rsKlaa++++g +++++ +gs
  gene2224|gene2224|rna2224|rna2224  42 VEKHARFPGVYVSRGKEDS-LCTLNMVPGMSVYNEKRITVDSEsekkEYRIWNPYRSKLAAGMVSGCEDIYMGPGS 116
                                        689************9999.*******************99888899***************************** PP

                                        EEEEESTTTSHHHHHHHHHHTTTSEEEEEESSHHHHHHHHHHHTTSTTEEEEES-TTSGGGGTTTS--EEEEEEES CS
                        Fibrillarin  73 kvLYlGaasGttvsHvsDivgeegvvyavefsprvlrelievakkRknivPileDArkPekYralvekvDvifaDv 148
                                        kvLYlGaasGttvsHvsD+vg++gvvyavefs+r++r+l+++akkR+ni+Pi++DAr+P++Yr+lv+ vD+if+Dv
  gene2224|gene2224|rna2224|rna2224 117 KVLYLGAASGTTVSHVSDLVGPSGVVYAVEFSQRSGRDLVNLAKKRPNIIPIIDDARYPQNYRMLVPIVDCIFSDV 192
                                        **************************************************************************** PP

                                        SSTTHHHHHHHHHHHHEEEEEEEEEEEEHHHHHSSSSHHHHHHHHHHHHHHTTEEEEEEEE-TTTSTTEEEEEEEE CS
                        Fibrillarin 149 aqpdqarilaknaklflkeggyllisikarsidvtkepeevfkeeveklkeeglkvleqvklepyekdhalvvgky 224
                                        aqpdqari+ +nak+flk+ g +++sika++id+tk++e+vf+eev+kl+++++k+ eqv+lep+ekdha+v+g y
  gene2224|gene2224|rna2224|rna2224 193 AQPDQARIVGLNAKYFLKNRGGVVMSIKANCIDSTKKAESVFAEEVNKLRKDEIKPREQVSLEPFEKDHAMVLGIY 268
                                        **************************************************************************99 PP

                                        E CS
                        Fibrillarin 225 k 225
                                        k
  gene2224|gene2224|rna2224|rna2224 269 K 269
                                        7 PP

>> GCD14  tRNA methyltransferase complex GCD14 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.0   1.1e-08   5.1e-05      38     173 ..     112     247 ..     107     255 .. 0.75

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 1.1e-08
                              GCD14  38 lkpGsvvvesGtGsgslshaiartvaPtGhlftfefheqraekareefrehelsqlvtvthrDvc.keGfdeevsg 112
                                        + pGs+v+  G+ sg+  + ++  v+P G ++++ef + r  + + ++ +++  +++ +   D+   + + + +  
  gene2224|gene2224|rna2224|rna2224 112 MGPGSKVLYLGAASGTTVSHVSDLVGPSGVVYAVEFSQ-RSGRDLVNLAKKRP-NIIPII-DDARyPQNY-RMLVP 183
                                        679**************99*****************75.66666666666553.444444.455426667.55669 PP

                              GCD14 113 kvDavfLDlPaPwea..ip.haakalkkeggrlCsf.sPCieqvqrtceaLrelgfteietlevl 173
                                         vD++f D+ +P++a  ++ +a+  lk++gg++ s  + Ci+  +++  +++e + ++++  e+ 
  gene2224|gene2224|rna2224|rna2224 184 IVDCIFSDVAQPDQAriVGlNAKYFLKNRGGVVMSIkANCIDSTKKAESVFAE-EVNKLRKDEIK 247
                                        *************9964443566667*****99998367**999887766665.56666655555 PP

>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   2.4e-05      0.11      20      97 ..     113     194 ..      87     254 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.4e-05
                                        -TT-EEEECT-TTSHHHHHHCCT.T.-SEEEEEESSSS.........HHHTTEEEECS-CCCSSHHHHHCHCHHHS CS
                               FtsJ  20 kpgktvvDlgaaPGgwsqvllqrlgakgkvvavDlqpm.........aplpgvttiqgditdpetiekikealser 86 
                                         pg +v+ lgaa G     ++  +g++g+v+av   +          +++p++  i  d + p++ +++ +     
  gene2224|gene2224|rna2224|rna2224 113 GPGSKVLYLGAASGTTVSHVSDLVGPSGVVYAVEFSQRsgrdlvnlaKKRPNIIPIIDDARYPQNYRMLVP----- 183
                                        48899******************************666599998887777999999***********9998..... PP

                                        SEEEEEE--S- CS
                               FtsJ  87 kvdlvvsDgap 97 
                                         vd++ sD+a 
  gene2224|gene2224|rna2224|rna2224 184 IVDCIFSDVAQ 194
                                        49******994 PP

>> Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   9.1e-05      0.41      10      51 ..     116     157 ..     111     193 .. 0.73
   2 ?   -1.3   0.0      0.31   1.4e+03      31      50 ..     228     247 ..     220     255 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 9.1e-05
                                        -EEEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHHHHH CS
                    Methyltr_RsmB-F  10 etilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvae 51 
                                         ++l l aa G   +h+++l+ ++g+v+Av+ +++  + +++
  gene2224|gene2224|rna2224|rna2224 116 SKVLYLGAASGTTVSHVSDLVGPSGVVYAVEFSQRSGRDLVN 157
                                        5689999************************98765544443 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.31
                                        TTTSEEEEEESSCCCHHHHH CS
                    Methyltr_RsmB-F  31 knkgtvvAvdankeRlkrva 50 
                                        k++  v+A ++nk R ++++
  gene2224|gene2224|rna2224|rna2224 228 KKAESVFAEEVNKLRKDEIK 247
                                        6788999******9999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (273 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       386  (0.0215294); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1798.12
//
Query:       gene2225|gene2225|rna2225|rna2225  [L=734]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00026   21.2   0.0    0.00073   19.8   0.0    1.7  1  GrpB             GrpB protein
  ------ inclusion threshold ------
      0.029   13.5   0.0        2.4    7.2   0.0    2.4  2  Glyco_hydro_2_C  Glycosyl hydrolases family 2, TIM barrel dom


Domain annotation for each model (and alignments):
>> GrpB  GrpB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   8.1e-08   0.00073      62     143 ..       8      89 ..       3      95 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 8.1e-08
                                        HHHHHHTT-EE.-TTTTSTTEEEEEE-SSS...--EEEEEEETT-HHHHHHHHHHHHHHH-HHHHHHHHHHHHHHH CS
                               GrpB  62 veaLeaagyellrgepgiperrlfvkgedee.ertvhlhvveagspelerhllfrdyLrahpearaeYaalKrela 136
                                        ++aL + ++e  +  + ++++++++++++ +   ++++hv++++s+ +++     d+L++ pe   +Y +l+++l 
  gene2225|gene2225|rna2225|rna2225   8 QDALDRNDFEE-MVAKIVQSQHFWCTDTELStFLVANIHVFKTRSEIMKKIEKTFDWLNECPECLIAYYKLRETLC 82 
                                        56788888887.56666788888888777665699***************************************** PP

                                        TT-SS-H CS
                               GrpB 137 akaeedi 143
                                        +k +edi
  gene2225|gene2225|rna2225|rna2225  83 RKDNEDI 89 
                                        *998885 PP

>> Glyco_hydro_2_C  Glycosyl hydrolases family 2, TIM barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0    0.0031        28      62     126 ..     460     525 ..     458     528 .. 0.85
   2 ?    7.2   0.0   0.00027       2.4      61      96 ..     627     672 ..     608     710 .. 0.70

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.0031
                                        HHHHHHHHHHT-EEEEE-S-B-TTSCCCCSHCT-.CCCCTTTSGGGHHHHHHHHHHHHHHHTT-TT CS
                    Glyco_hydro_2_C  62 eevyelcDeyGlyvidEanlethglaqklgeiep.synvladnpewlkavldrieelverdkNHps 126
                                        ++ +e++D+ G  + dE    ++ ++  + + +  s  v  ++ + l++vl++++  + r +N p+
  gene2225|gene2225|rna2225|rna2225 460 KKTLEIFDRNGEPLSDELCFYSLLIKSDFSTYDVqSLVVSENEQHALTHVLKKMNVYFDRFQNFPA 525
                                        678999*********************999777624455555677899****************98 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.00027
                                        SHHHHHHHHHHT-EEEEE-S-B-TTSCCCCSHCT-..........C CS
                    Glyco_hydro_2_C  61 qeevyelcDeyGlyvidEanlethglaqklgeiep..........s 96 
                                         +++ +l+D +G+++i+E++    +++ k++++++          s
  gene2225|gene2225|rna2225|rna2225 627 RTRIRNLADYFGIFLINESAKTENNVQPKVKRVKNvpnkfseevdS 672
                                        567889***********************99887755544333330 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (734 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1039  (0.0579508); expected 358.6 (0.02)
Passed bias filter:                      468  (0.026103); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.68u 0.26s 00:00:00.94 Elapsed: 00:00:00.45
# Mc/sec: 4918.14
//
Query:       gene2226|gene2226|rna2226|rna2226  [L=525]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.4e-59  200.1   0.7    4.8e-30  105.2   0.3    2.3  2  AAA_11           AAA domain
    4.4e-58  196.2   4.8    9.4e-58  195.1   3.1    2.1  2  AAA_12           AAA domain
    1.7e-12   47.5   0.0    2.7e-11   43.5   0.0    2.2  1  AAA_30           AAA domain
    1.8e-11   44.6   0.0    9.6e-11   42.2   0.0    2.0  2  AAA_19           AAA domain
    4.6e-10   39.6   0.0       0.05   13.3   0.0    3.4  3  Viral_helicase1  Viral (Superfamily 1) RNA helicase
    2.6e-09   37.1   0.7    1.8e-08   34.3   0.7    2.3  1  UvrD-helicase    UvrD/REP helicase N-terminal domain
    7.1e-06   26.1   0.0    1.9e-05   24.7   0.0    1.7  1  ResIII           Type III restriction enzyme, res subunit
    0.00027   21.3   0.2     0.0016   18.9   0.0    2.4  3  AAA              ATPase family associated with various cellul
     0.0019   18.5   0.0      0.011   16.0   0.0    2.3  1  AAA_22           AAA domain
     0.0019   17.6   0.4       0.11   11.9   0.1    2.3  2  UvrD_C           UvrD-like helicase C-terminal domain
     0.0091   15.8   0.0       0.02   14.7   0.0    1.6  1  UvrD_C_2         UvrD-like helicase C-terminal domain
  ------ inclusion threshold ------
      0.018   14.9   0.1       0.23   11.3   0.1    2.6  1  Helicase_RecD    Helicase
      0.052   13.9   0.0       0.74   10.2   0.0    2.6  2  RNA_helicase     RNA helicase
      0.071   12.3   0.1        1.6    7.9   0.0    2.5  3  DUF2075          Uncharacterized conserved protein (DUF2075)
       0.12   12.7   0.0        0.2   12.0   0.0    1.4  1  AAA_16           AAA ATPase domain


Domain annotation for each model (and alignments):
>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.5   0.0   7.6e-30   9.1e-27       2     122 ..      87     218 ..      86     232 .. 0.84
   2 !  105.2   0.3     4e-33   4.8e-30     184     260 ..     225     301 ..     211     302 .. 0.90

  Alignments for each domain:
  == domain 1  score: 94.5 bits;  conditional E-value: 7.6e-30
                             AAA_11   2 lndsqreaiksalsese.itliqGPPGtgKTktivellsqllsr......rkseeeksakpriLvCapSNaAvDel 70 
                                        ln sq+ aik+++++ + ++li+GPPGtgKTk+iv+l+++l s       +++    +++priL+CapSNaAvDel
  gene2226|gene2226|rna2226|rna2226  87 LNGSQQIAIKNVYTSAAfFSLIHGPPGTGKTKMIVSLIESLFSApiisalKSKMFITNREPRILICAPSNAAVDEL 162
                                        899**********999999**********************9666666554467899******************* PP

                             AAA_11  71 lerllrglldsegekykpkivRvgneeeriseavksvsleekvekrlekee......k 122
                                        ++r+ + l  +  e++k++++R+g ++ +i++++k ++l+ ++ek+le+++      +
  gene2226|gene2226|rna2226|rna2226 163 AKRIND-LRMKGREEEKLRVLRIGVQN-NIDDNLKMLTLDCIIEKELEERKnragltN 218
                                        ***999.6677778899**********.9******************99875555442 PP

  == domain 2  score: 105.2 bits;  conditional E-value: 4e-33
                             AAA_11 184 aeesleeevldeaeivltTlsgagsklleklakkfdvviIDEAaqavEpstliPlrlgakkvvLvGDpkQLpatvi 259
                                        ++ + + e+l+++++v++Tls+++++l++ ++ +fd+++IDEA+q+vE+stliPl++++ kvvLvGDpkQLp+tvi
  gene2226|gene2226|rna2226|rna2226 225 ERTKRKFELLKRSNVVCATLSSSAKELIKVANIDFDILVIDEACQSVETSTLIPLKFNPTKVVLVGDPKQLPPTVI 300
                                        344445689**********************99******************************************* PP

                             AAA_11 260 s 260
                                        s
  gene2226|gene2226|rna2226|rna2226 301 S 301
                                        9 PP

>> AAA_12  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.45   5.3e+02      86     141 ..     120     176 ..      83     212 .. 0.69
   2 !  195.1   3.1   7.9e-61   9.4e-58       1     198 [.     306     492 ..     306     493 .. 0.94

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.45
                             AAA_12  86 yiNeeEaelvvklvekllkkgsee.erkkigvitpYraqvellkkklkekeeeksek 141
                                        ++   E  + + ++++l +k+  +  + +i + +p +a v+ l k++++ + + +e+
  gene2226|gene2226|rna2226|rna2226 120 IVSLIESLFSAPIISALKSKMFITnREPRILICAPSNAAVDELAKRINDLRMKGREE 176
                                        444444444444555555444333566899999999999999999999755554443 PP

  == domain 2  score: 195.1 bits;  conditional E-value: 7.9e-61
                             AAA_12   1 lerSlferllkkekekvvlLdtqYRmhpeIsrfpsklfYkgkLkdaesvkkreleaqealeepleplvfidvekse 76 
                                        +e+Slf rl+k +  ++vlL++qYRmhp+I++fp+++fY+++L++++svkkre++    +++   p+ fi+v+++e
  gene2226|gene2226|rna2226|rna2226 306 YEQSLFVRLQKTY--QSVLLNVQYRMHPTIVEFPNQYFYDKRLQTHKSVKKRENP----YQNVVPPISFIQVNGEE 375
                                        79**********9..9***************************************....999999*******9888 PP

                             AAA_12  77 eekekkeksyiNeeEaelvvklvekllkkgsee.erkkigvitpYraqvellkkklkekeeeksekeievntvdgf 151
                                         +++    s++N +Ea+ + +++++l+k++++    +kig+itpY+aq++ +k+ l    +++    + vntvdgf
  gene2226|gene2226|rna2226|rna2226 376 RTDSY--FSFYNVAEARYIGNIISELMKNVKNYdLSNKIGIITPYKAQMKKIKEVLLG-IRKDILDFVCVNTVDGF 448
                                        88876..9**********************9998789******************995.45555667********* PP

                             AAA_12 152 QGrekdviilslVRsnekkeigflkderrlNValTRAkskliivGnk 198
                                        QG+ekdvi++s+V+s   k+igfl+d rr+NV++TRAk++lii+Gn+
  gene2226|gene2226|rna2226|rna2226 449 QGQEKDVILISTVKS---KNIGFLSDLRRINVSITRAKHSLIIIGNT 492
                                        **************9...79*************************97 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.5   0.0   2.3e-14   2.7e-11       2     130 ..      87     297 ..      86     331 .. 0.77

  Alignments for each domain:
  == domain 1  score: 43.5 bits;  conditional E-value: 2.3e-14
                             AAA_30   2 lnaeQaaavealltsgdrvavltGpAGtGKttalkalreaweaag...............grviglAptgkaAkvL 62 
                                        ln +Q+ a++++ ts + +++++Gp+GtGKt ++ +l e + +a                 r++++Ap+++a ++L
  gene2226|gene2226|rna2226|rna2226  87 LNGSQQIAIKNVYTSAAFFSLIHGPPGTGKTKMIVSLIESLFSAPiisalkskmfitnrePRILICAPSNAAVDEL 162
                                        899**********************************9999999889***************************** PP

                             AAA_30  63 a..................eelgieastiakllkrlk....................................... 81 
                                        a                                   +                                       
  gene2226|gene2226|rna2226|rna2226 163 AkrindlrmkgreeeklrvL----------------Rigvqnniddnlkmltldciiekeleerknragltnfevt 222
                                        *5554444444333222220................2233333444444444777777777777788888888888 PP

                             AAA_30  82 ..............................grarlepg.tllivDEagmvdtkqlaallkaaekagakvilvGDer 126
                                                                      +    + + ++l++DEa     +++   lk      +kv+lvGD++
  gene2226|gene2226|rna2226|rna2226 223 nsertkrkfellkrsnvvcatlsssakeliK--VANIDfDILVIDEACQSVETSTLIPLKFN---PTKVVLVGDPK 293
                                        8888888888888999999999999997652..2233459*******765444433333443...579******** PP

                             AAA_30 127 Qlas 130
                                        Ql++
  gene2226|gene2226|rna2226|rna2226 294 QLPP 297
                                        **97 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.2   0.0     8e-14   9.6e-11       7     143 ..     100     297 ..      91     299 .. 0.72
   2 ?   -0.7   0.0       1.3   1.6e+03      34      69 ..     403     442 ..     391     507 .. 0.68

  Alignments for each domain:
  == domain 1  score: 42.2 bits;  conditional E-value: 8e-14
                             AAA_19   7 alkekvllvtaGpGtGKTrvlkhivallvelggvkp...........eeillvaftgrAakelrerlaalgae... 68 
                                        ++++   l+ ++pGtGKT++++  ++ l ++  +++            +il++a+ + A++el++r++ l ++   
  gene2226|gene2226|rna2226|rna2226 100 TSAAFFSLIHGPPGTGKTKMIVSLIESLFSAPIISAlkskmfitnrePRILICAPSNAAVDELAKRINDLRMKgre 175
                                        4455567999******************9999888899999****9999******************999999666 PP

                             AAA_19  69 ...............atTiHrlal............................ldfddlltealelle......... 92 
                                                                                            +++ ++++ ++ell+         
  gene2226|gene2226|rna2226|rna2226 176 eeklrvlrigvqnniD-------DnlkmltldciiekeleerknragltnfeVTNSERTKRKFELLKrsnvvcatl 244
                                        6665555555555550.......05555555666677888888888888888666666667777777777777777 PP

                             AAA_19  93 .....eaeeekklqeeellivDEfqdvdelqyrLlkallgekkklllvGDpdQliy 143
                                             e  +  ++ + ++l++DE+ +      +L+   +++ +k++lvGDp+Ql++
  gene2226|gene2226|rna2226|rna2226 245 sssakELIKVANI-DFDILVIDEACQSV-ETSTLIPLKFNP-TKVVLVGDPKQLPP 297
                                        6654322233444.5559*****86543.345566655634.55**********97 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.3
                             AAA_19  34 lvelggvkpeeillvaftgrAakelrerlaalgae......a 69 
                                        +++   +  ++i ++++ +  +k+++e l ++ ++       
  gene2226|gene2226|rna2226|rna2226 403 VKNYD-L-SNKIGIITPYKAQMKKIKEVLLGIRKDildfvcV 442
                                        33333.2.2889999999999999999986666655554443 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.0   5.6e-05     0.066       2      22 ..     107     127 ..     106     169 .. 0.73
   2 !   13.3   0.0   4.2e-05      0.05      26     103 ..     217     298 ..     202     380 .. 0.72
   3 !    9.8   0.0   0.00052      0.62     183     233 ..     441     489 ..     397     490 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5.6e-05
                    Viral_helicase1   2 vvhGvpGcGKStlirkllrts 22 
                                        ++hG pG GK+++i++l+++ 
  gene2226|gene2226|rna2226|rna2226 107 LIHGPPGTGKTKMIVSLIESL 127
                                        79****************983 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 4.2e-05
                    Viral_helicase1  26 tvnrptaelltegk...pklpnlsvrtvdsflmalvks..tkgkililDEylllhaGyill.laalskaklvilfG 95 
                                        t    t+  +t++k    k  n  + t+ s  + l+k    +++il++DE+++    +    +  + +   v+l+G
  gene2226|gene2226|rna2226|rna2226 217 TNFEVTNSERTKRKfelLKRSNVVCATLSSSAKELIKVanIDFDILVIDEACQSV--ETSTlIPLKFNPTKVVLVG 290
                                        555666667777776555555555556666555555555678********98876..34443677889999***** PP

                    Viral_helicase1  96 DplQipfh 103
                                        Dp+Q p  
  gene2226|gene2226|rna2226|rna2226 291 DPKQLPPT 298
                                        ****9854 PP

  == domain 3  score: 9.8 bits;  conditional E-value: 0.00052
                    Viral_helicase1 183 revttvhevqGltfdkVtlvllketdlelisesrenllvAlTRhrkslvil 233
                                        + v+tv + qG++ d+  + + k+++   + ++     v +TR++ sl+i+
  gene2226|gene2226|rna2226|rna2226 441 C-VNTVDGFQGQEKDVILISTVKSKNIG-FLSDLRRINVSITRAKHSLIII 489
                                        5.99*********988888888776655.5556999************997 PP

>> UvrD-helicase  UvrD/REP helicase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.3   0.7   1.5e-11   1.8e-08      16     169 ..     106     357 ..      87     426 .. 0.66

  Alignments for each domain:
  == domain 1  score: 34.3 bits;  conditional E-value: 1.5e-11
                                        EEEEE-TTSSHHHHHHHHHHHHHHTSSSTGGG...........EEEEESSHHHHHHHHHHHHH.HHHHCCHHCTT- CS
                      UvrD-helicase  16 ilveAsAGsGKTfvlaerilrlikeeeiepdr...........ilvvTFTnkAaeElkeRiee.alkkaeqessdd 79 
                                         l+   +G+GKT+ ++++i  l  +  i++ +           il+    n+A +El +Ri+  ++k +e+e+++ 
  gene2226|gene2226|rna2226|rna2226 106 SLIHGPPGTGKTKMIVSLIESLFSAPIISALKskmfitnreprILICAPSNAAVDELAKRINDlRMKGREEEKLRV 181
                                        689999*************9999999888777788999999**********************7778888888888 PP

                                        HHHHHHHHHCTTSEEEEHHHHHHHHHHHHHGGTT...........SHTTTEEECHHHHHHCCHHHHHHHHHSCHSH CS
                      UvrD-helicase  80 erlrlalqnlseanisTlHsfcqkilkkeanrig...........ldpnfrildeedeedlkqqellkelleksad 144
                                         r+  + +  +++++ Tl+ +  k l++  nr+g            +++f++l+ ++ + +   +  kel+     
  gene2226|gene2226|rna2226|rna2226 182 LRIGVQNNIDDNLKMLTLDCIIEKELEERKNRAGltnfevtnserTKRKFELLKRSNVVCATLSSSAKELI----- 252
                                        8*********************************5555555555544555555544444444444444444..... PP

                                        TTTTHHHHHHHHHHHHHHCCCCCH.................................................... CS
                      UvrD-helicase 145 dslnldkkkleklikelsksrnik.................................................... 168
                                           ++++ +++ l++++  ++                                                       
  gene2226|gene2226|rna2226|rna2226 253 ---KVANIDFDILVIDEACQSVETstliplkfnptkvvlvgdpkqlpptvisnckpyeqslfvrlqktyqsvllnv 325
                                        ...4444444433333222222223445577777777777777777777777777777777777774444444444 PP

                                        ...............................H CS
                      UvrD-helicase 169 ...............................k 169
                                                                        
  gene2226|gene2226|rna2226|rna2226 326 qyrmhptivefpnqyfydkrlqthksvkkreN 357
                                        44444444444444444444444444444440 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.0   1.6e-08   1.9e-05       5     146 ..      88     272 ..      84     290 .. 0.78

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 1.6e-08
                                        -HHHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S..................-EEEEESSHHHH CS
                             ResIII   5 reyQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkee.............kflflvprksll 67 
                                        +  Q+ ai+n+  +         li+ + GtGKT ++++lie+l+++  ++             ++l+ +p+++ +
  gene2226|gene2226|rna2226|rna2226  88 NGSQQIAIKNVYTSA----AFFSLIHGPPGTGKTKMIVSLIESLFSAPIISalkskmfitnrepRILICAPSNAAV 159
                                        567888999997444....57899**********************99999************************* PP

                                        HHHHHHGGGGTGG.............GEEEESSS-B--..................-SEEEEEHHHHHHTH..... CS
                             ResIII  68 eqtleefkkflseayke.........igkkvsgdkkka...........kekdstnkkilvttiqsldadseee.. 121
                                        + + ++++++  + ++e         +++++++    +           ke ++ +++  +t+ +  +++++++  
  gene2226|gene2226|rna2226|rna2226 160 DELAKRINDLRMKGREEeklrvlrigVQNNIDD----NlkmltldciieKELEERKNRAGLTNFEVTNSERTKRkf 231
                                        *******99999888777777666552222222....133446666776777788888888888888888866688 PP

                                        .....................HHHTTT-SEEEEETGGGTTS CS
                             ResIII 122 ................eeeseellrdrfdviiiDEaHrlga 146
                                                         +e  +  +  fd+++iDEa  + +
  gene2226|gene2226|rna2226|rna2226 232 ellkrsnvvcatlsssAKELIKVANIDFDILVIDEACQSVE 272
                                        88888888888888777777788888888******977666 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   1.3e-06    0.0016       2      57 ..     107     177 ..     106     192 .. 0.73
   2 ?   -2.1   0.0       4.1   4.9e+03      48      67 ..     250     267 ..     220     274 .. 0.61
   3 ?   -2.7   0.0       6.1   7.3e+03      92     110 ..     444     462 ..     441     490 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.3e-06
                                        EEESSTTSSHHHHHHHHHHHH.THEEEEEETTTCS.SS.............STTHHHHHHHHHHHHHHHTS CS
                                AAA   2 llyGppGtGKTllakavakel.gvefleisgsell.sk.............yvgesekkirelfkeakeka 57 
                                        l++GppGtGKT ++ +++++l ++++++   s+++  +              v e +k+i++l  + +e++
  gene2226|gene2226|rna2226|rna2226 107 LIHGPPGTGKTKMIVSLIESLfSAPIISALKSKMFiTNreprilicapsnaAVDELAKRINDLRMKGREEE 177
                                        89******************856777666666655333566666667777777777777777766666555 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 4.1
                                        HHHHHHHHTSTSEEEEEETG CS
                                AAA  48 elfkeakekakpsilfiDEi 67 
                                        el+k a    +  il+iDE+
  gene2226|gene2226|rna2226|rna2226 250 ELIKVANI--DFDILVIDEA 267
                                        33333322..3489999996 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 6.1
                                        HHHHTTTSSSTEEEEEEES CS
                                AAA  92 eldgvkkkeskvivigatn 110
                                         +dg++ +e++vi+i + +
  gene2226|gene2226|rna2226|rna2226 444 TVDGFQGQEKDVILISTVK 462
                                        6788888888888887655 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0     9e-06     0.011       7      70 ..     105     176 ..     100     296 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 9e-06
                             AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeakaee........erpevvfvtlpsstsskdllrellralglelka 70 
                                        + +++G++GtGKT  +  l e+l  ++ +          +r + +++++ps    ++l++++      ++++
  gene2226|gene2226|rna2226|rna2226 105 FSLIHGPPGTGKTKMIVSLIESLFSAPIISAlkskmfitNREPRILICAPSNAAVDELAKRINDLRMKGREE 176
                                        669*******************95555444499999999888889999999999999998887665544444 PP

>> UvrD_C  UvrD-like helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.1     9e-05      0.11       3     109 ..     323     449 ..     321     465 .. 0.77
   2 ?    3.9   0.0     0.024        29     332     347 ..     476     491 ..     460     493 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 9e-05
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxx.............xxxxxxx.xxxxxxxxxxxxxxxxxxxxxx RF
                             UvrD_C   3 LekNyRStksLlkaankflenilnrrale.kek.............ktvekge.kivvleaeteeeEaekiaatik 63 
                                        L+  yR  +++++  n+++     ++ ++ k k               + +ge +   + +  +  Ea++i ++i 
  gene2226|gene2226|rna2226|rna2226 323 LNVQYRMHPTIVEFPNQYFYDKRLQTHKSvK-KrenpyqnvvppisFIQVNGEeRTDSYFSFYNVAEARYIGNIIS 397
                                        7888***************443333222232.2357889999999988888887888889999999********** PP

                                        xxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxx RF
                             UvrD_C  64 all...ekneklediavLvRsnkdadkiskaLkkeg...ipfnvvdeekfFk 109
                                        +l+   ++ +  ++i +++  +++ +ki++ L  ++   + f++v++ + F+
  gene2226|gene2226|rna2226|rna2226 398 ELMknvKNYDLSNKIGIITPYKAQMKKIKEVLLGIRkdiLDFVCVNTVDGFQ 449
                                        **97666666779*****************9977666666666666555555 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.024
                                        xxxxxxxxxxxxxxxx RF
                             UvrD_C 332 YVaiTRAkkrLfisys 347
                                         V iTRAk  L+i+ +
  gene2226|gene2226|rna2226|rna2226 476 NVSITRAKHSLIIIGN 491
                                        599**********965 PP

>> UvrD_C_2  UvrD-like helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   1.7e-05      0.02       2      52 .]     440     489 ..     439     489 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.7e-05
                           UvrD_C_2   2 ayaltihkaQGsefpaVivfdpdlaaarmgelrrrlLYtavTRAreklilv 52 
                                        +++ t+  +QG+e +++ +  +   +  ++    r + + +TRA++ li++
  gene2226|gene2226|rna2226|rna2226 440 VCVNTVDGFQGQEKDVILISTVKSKNI-GFLSDLRRINVSITRAKHSLIII 489
                                        6788*********99888866665554.47679***************996 PP

>> Helicase_RecD  Helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   0.00019      0.23       4     100 ..     110     268 ..     107     307 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00019
                      Helicase_RecD   4 AdRGRGKSaalGlalaaliaegk..............snilvtapskenvktlfeflakglealglke........ 57 
                                        + +G+GK+ ++  ++++l ++                 +il++aps+++v++l +++ + l+  g +e        
  gene2226|gene2226|rna2226|rna2226 110 GPPGTGKTKMIVSLIESLFSAPIisalkskmfitnrePRILICAPSNAAVDELAKRI-NDLRMKGREEeklrvlri 184
                                        566666666666665555544434444455566666699*****************9.555655555567888888 PP

                      Helicase_RecD  58 .....................................eekkkkaekaelrvr.................kqrieyi 79 
                                                                             +             +                   +    
  gene2226|gene2226|rna2226|rna2226 185 gvqnniddnlkmltldciiekeleerknragltnfevT-------------NsertkrkfellkrsnvvCAT---- 243
                                        88888888777777777777666544444333333321.............023221111122211122222.... PP

                      Helicase_RecD  80 apdellklkeqa...............dllvvDEAA 100
                                                                   d+lv+DEA 
  gene2226|gene2226|rna2226|rna2226 244 -----------LsssakelikvanidfDILVIDEAC 268
                                        ...........1223333344445556888888886 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00062      0.74       2      25 ..     107     130 ..     106     171 .. 0.81
   2 ?    0.2   0.1      0.79   9.4e+02      41      90 ..     378     426 ..     370     428 .. 0.54

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00062
                       RNA_helicase   2 wlyGpsgeGKStlakeLakallkk 25 
                                        +++Gp+g+GK+ ++ +L+++l ++
  gene2226|gene2226|rna2226|rna2226 107 LIHGPPGTGKTKMIVSLIESLFSA 130
                                        58***************9999754 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.79
                       RNA_helicase  41 ddfwdgYtgqevvvidDfgqvkdee.npsdlaelirlvsstpyplnmasle 90 
                                        d++++ Y+  e+  i  + +   ++ +  dl+++i+++  tpy+ +m++++
  gene2226|gene2226|rna2226|rna2226 378 DSYFSFYNVAEARYIGNIISELMKNvKNYDLSNKIGII--TPYKAQMKKIK 426
                                        55666666555544444444443321223666666665..56666666665 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.0    0.0013       1.6       5      41 ..     107     145 ..     104     189 .. 0.74
   2 ?    1.8   0.0     0.097   1.2e+02      52      99 ..     222     269 ..     210     355 .. 0.85
   3 ?   -3.6   0.0       4.2     5e+03     345     359 ..     474     488 ..     472     491 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0013
                            DUF2075   5 lVtGvaGtGKtvvllnllael..eddeeertavylsvNh 41 
                                        l++G +GtGKt + ++l+  l      +  ++++++ N+
  gene2226|gene2226|rna2226|rna2226 107 LIHGPPGTGKTKMIVSLIESLfsAPIISALKSKMFITNR 145
                                        89***********99999998652333444444444444 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.097
                            DUF2075  52 akkeekkkkkeafeklssfinnlsefkkaeekkeepkedvvivDEAhr 99 
                                        +++e+ k+k e +++++ +  +ls+  k+  k ++ ++d++++DEA  
  gene2226|gene2226|rna2226|rna2226 222 TNSERTKRKFELLKRSNVVCATLSSSAKELIKVANIDFDILVIDEACQ 269
                                        55666778888888888888888877777777788899*******965 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 4.2
                            DUF2075 345 ayrVLLtRGrkGlyi 359
                                        +++V +tR+ + l+i
  gene2226|gene2226|rna2226|rna2226 474 RINVSITRAKHSLII 488
                                        689********9998 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00017       0.2      28      51 ..     107     130 ..      94     233 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00017
                             AAA_16  28 llsGesGvGKsslvrellralekd 51 
                                        l++G++G+GK++++ +l ++l  +
  gene2226|gene2226|rna2226|rna2226 107 LIHGPPGTGKTKMIVSLIESLFSA 130
                                        8***********998888776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (525 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       836  (0.0466284); expected 358.6 (0.02)
Passed bias filter:                      546  (0.0304535); expected 358.6 (0.02)
Passed Vit filter:                        80  (0.00446204); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.72u 0.31s 00:00:01.03 Elapsed: 00:00:00.54
# Mc/sec: 2938.28
//
Query:       gene2227|gene2227|rna2227|rna2227  [L=230]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.6e-17   62.9   7.8    1.5e-13   51.0   7.8    2.8  1  LUC7         LUC7 N_terminus
  ------ inclusion threshold ------
       0.14   12.5   1.4        1.9    8.9   1.4    2.5  1  zf-C2H2_jaz  Zinc-finger double-stranded RNA-binding


Domain annotation for each model (and alignments):
>> LUC7  LUC7 N_terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.0   7.8   1.6e-17   1.5e-13       1     237 [.       3     201 ..       3     222 .. 0.81

  Alignments for each domain:
  == domain 1  score: 51.0 bits;  conditional E-value: 1.6e-17
                                        XXXXXXXXXXXXXXXXXXXXXXXXXXX-EEE--S--SSS-S--SSSS-S-EEEGGGHHHHHHHHHHHHHHHH-XXX CS
                               LUC7   1 daaralLdeLmGrnrnlapsekkkkvnfedpevCksylvkfCphdlfinTkadlGpCkkiHdeelkeeYeearksk 76 
                                        d ar+lLd L+G +r+l+++e ++    +d + C + l++fCp   +++T++d+G+C+   ++e+ ++Y + +k k
  gene2227|gene2227|rna2227|rna2227   3 DRARELLDRLLGPTRDLTEEEVEN---LRDTDNCIFLLAGFCPFKALEHTRMDIGQCPYSEHKEVPAKYMAPDKLK 75 
                                        789**************9998776...8*****************************************9995543 PP

                                        XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX....XXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                               LUC7  77 kklgyeeeflrfleklledvdrkiqkgkqrleltqeekeeeeeakakkqeqlkeleekiekllaeaeelgeeGkVd 152
                                            ye e+l  le +    +++ +k+                    k+++++ l  ++e++++ + + ++eGk d
  gene2227|gene2227|rna2227|rna2227  76 ---LYETELLGLLEMVAGLFENRRKKA---------------GI---KEQHVNLLAPNLEEKVKMIVSRAKEGKMD 130
                                        ...6******99998766665542222...............11...245788888889999999999999***** PP

                                        XXXXXXXXXXXXXXXXXXXXXXXXXX..XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                               LUC7 153 eaqklmkeveelkeekeeleqqyeaaaaneeseasqekkmkvCeiCGaflivgDaqqRiedHlmGKqHlGyaklre 228
                                        e+ +l +++e    e  ++          ++  +   +k + Ce+C a ++     +  + H++G++H +  ++r+
  gene2227|gene2227|rna2227|rna2227 131 ESLELAEKLEA---E--HVI---------SQPGNDGVNKTHFCEVCAATISNVVDSKEYKVHINGRLHQACVRMRT 192
                                        **998765543...2..222.........234566778999********9988888999***************** PP

                                        XXXXXX... CS
                               LUC7 229 aleelkekr 237
                                         l++l  k 
  gene2227|gene2227|rna2227|rna2227 193 FLAHLLLKY 201
                                        999886444 PP

>> zf-C2H2_jaz  Zinc-finger double-stranded RNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   1.4   0.00021       1.9       2      27 .]     157     185 ..     156     185 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00021
                                        CBBTTTTBBBSS...HHHHHCCTTSHHHH CS
                        zf-C2H2_jaz   2 fYCvlCdKyFks...enaldnHlkSKkHK 27 
                                        ++C++C+ + ++   ++ ++ H++++ H+
  gene2227|gene2227|rna2227|rna2227 157 HFCEVCAATISNvvdSKEYKVHINGRLHQ 185
                                        799999999986444899********996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       766  (0.0427241); expected 358.6 (0.02)
Passed bias filter:                      477  (0.0266049); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1563.96
//
Query:       gene2228|gene2228|rna2228|rna2228  [L=234]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      7e-30  104.1   0.0    1.4e-29  103.1   0.0    1.5  1  Ribosomal_L28e  Ribosomal L28e protein family
     0.0042   17.6   6.9     0.0042   17.6   6.9    2.1  2  Mak16           Mak16 protein C-terminal region


Domain annotation for each model (and alignments):
>> Ribosomal_L28e  Ribosomal L28e protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.1   0.0   1.6e-33   1.4e-29       2     115 .]      12     125 ..      12     125 .. 0.95

  Alignments for each domain:
  == domain 1  score: 103.1 bits;  conditional E-value: 1.6e-33
                     Ribosomal_L28e   2 iWelvrnnn...sFlvktrtsnkqtFsrepyNltglhsrkysglanskavtVreekkgvvlvtkkkerahkpakaw 74 
                                        iW+l+  +n   +F+  t+   +qt++++++N+tg++++++++l nsk++tVre +++++l++k++er + p +a+
  gene2228|gene2228|rna2228|rna2228  12 IWQLIGGKNnfcAFKLPTD---TQTLCKHENNVTGICEQSSCPLSNSKYATVREIDGRLYLFVKEPERVNLPVQAY 84 
                                        7****98887999999955...59**************************************************** PP

                     Ribosomal_L28e  75 ekvklsknsrkalkqiakllkky.rpdlrkaalaRlskitqs 115
                                        ek+ l+ ++ +alk+i++ lk y +p+ ++++++Rl k+tq+
  gene2228|gene2228|rna2228|rna2228  85 EKILLNAEYDEALKEIDEILK-YwDPWTIHKCKQRLGKLTQY 125
                                        ********************9.66***************996 PP

>> Mak16  Mak16 protein C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.27   2.4e+03      43      62 ..      78      97 ..      73     107 .. 0.67
   2 !   17.6   6.9   4.7e-07    0.0042       2      59 ..     146     209 ..     145     231 .. 0.71

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.27
                              Mak16 43 nveekafkkvlekeeeeeee 62
                                       n++ +a++k+l + e +e  
  gene2228|gene2228|rna2228|rna2228 78 NLPVQAYEKILLNAEYDEAL 97
                                       77888999999776633332 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 4.7e-07
                              Mak16   2 kKverRekrReeKAlaAAklekaIekeLleRLksgaYgd..iynveekafkkvlekeee....e 59 
                                        kK+ + e+ R  K +    +ek++++eLl RL++g Ygd   y++e +  k+ ++k+++    e
  gene2228|gene2228|rna2228|rna2228 146 KKALKIERGRGVKSMLRMDIEKEVKEELLLRLEEGLYGDelKYELERETEKENVRKRRRvfiaE 209
                                        788899999******************************7667766666666665554233321 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       765  (0.0426683); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1864.72
//
Query:       gene2229|gene2229|rna2229|rna2229  [L=604]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.8e-32  112.7   1.7    8.1e-15   55.5   0.0    3.4  3  ABC_tran      ABC transporter
    4.2e-10   39.5   5.6    0.00021   20.8   0.1    3.3  3  SMC_N         RecF/RecN/SMC N terminal domain
    9.4e-08   31.6   3.9    9.4e-08   31.6   3.9    2.6  2  Fer4          4Fe-4S binding domain
    1.8e-07   31.2  14.3       0.23   11.2   0.5    4.5  4  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    7.1e-07   28.9   6.3    7.1e-07   28.9   6.3    3.6  3  RLI           Possible Fer4-like domain in RNase L inhibitor,
    2.3e-06   28.1   0.0     0.0026   18.2   0.0    2.4  2  AAA_16        AAA ATPase domain
    2.8e-06   27.3  12.7      0.014   15.1   1.7    3.4  3  AAA_15        AAA ATPase domain
    4.8e-06   26.6   0.4     0.0061   16.5   0.0    2.5  2  RsgA_GTPase   RsgA GTPase
    7.8e-06   25.7  13.0    2.4e-05   24.2   3.9    2.8  2  Fer4_6        4Fe-4S binding domain
    8.7e-06   25.4   0.4       0.19   11.5   0.0    2.5  2  AAA_29        P-loop containing region of AAA domain
    0.00032   21.2  12.2    0.00093   19.7  12.2    1.9  1  Fer4_7        4Fe-4S dicluster domain
    0.00036   20.3   0.4       0.98    9.1   0.0    2.5  2  AAA_24        AAA domain
     0.0004   20.2   0.2       0.66    9.7   0.0    2.7  2  VirE          Virulence-associated protein E
    0.00044   20.3   3.2    0.00044   20.3   3.2    2.5  2  Fer4_21       4Fe-4S dicluster domain
    0.00067   20.2   5.1      0.041   14.4   0.0    2.6  2  AAA_23        AAA domain
    0.00081   19.5  14.8      0.002   18.3  14.8    1.7  1  Fer4_9        4Fe-4S dicluster domain
     0.0012   18.9   2.9     0.0012   18.9   2.9    2.2  2  Fer4_10       4Fe-4S dicluster domain
     0.0016   18.7   0.1       0.97    9.7   0.0    2.4  2  AAA_22        AAA domain
     0.0017   17.6   0.2       0.85    8.7   0.0    2.3  2  G-alpha       G-protein alpha subunit
     0.0025   18.7   0.7     0.0025   18.7   0.7    3.1  2  Fer4_16       4Fe-4S double cluster binding domain
     0.0032   17.4   0.3      0.041   13.8   0.1    2.3  2  Rad17         Rad17 P-loop domain
     0.0059   16.6   0.1        1.1    9.3   0.0    3.0  3  AAA_5         AAA domain (dynein-related subfamily)
      0.007   16.3   1.1       0.54   10.2   0.1    2.5  2  NACHT         NACHT domain
     0.0072   16.7   0.2          7    7.1   0.0    2.8  2  RNA_helicase  RNA helicase
     0.0086   16.1   1.4     0.0086   16.1   1.4    2.5  2  Fer4_2        4Fe-4S binding domain
  ------ inclusion threshold ------
      0.013   15.9   3.9      0.013   15.9   3.9    2.7  2  Fer4_4        4Fe-4S binding domain
      0.015   15.3   0.0        5.5    7.0   0.0    2.4  2  TsaE          Threonylcarbamoyl adenosine biosynthesis protei
      0.016   14.8   0.2        6.7    6.2   0.0    2.4  2  AAA_7         P-loop containing dynein motor region
      0.017   15.2   0.7        7.6    6.7   0.2    2.7  2  MMR_HSR1      50S ribosome-binding GTPase
      0.024   15.1   0.1        1.8    9.0   0.1    2.5  2  AAA           ATPase family associated with various cellular 
      0.024   13.8   0.3        1.4    8.0   0.1    2.2  2  NB-ARC        NB-ARC domain
      0.024   15.2   2.2         13    6.4   0.0    3.8  2  AAA_18        AAA domain
      0.053   12.7   0.2        6.8    5.8   0.1    2.3  2  DUF815        Protein of unknown function (DUF815)
       0.11   12.2   1.5        1.6    8.3   0.2    2.2  2  SRP54         SRP54-type protein, GTPase domain
        1.8    8.8   3.7        3.4    7.9   0.2    2.7  3  AAA_28        AAA domain
        3.2    8.4  12.5         53    4.5  12.7    2.5  1  Fer4_17       4Fe-4S dicluster domain
        3.7    8.7  15.7       0.13   13.2   4.1    3.1  2  Fer4_3        4Fe-4S binding domain
        9.1    6.8  13.5        0.8   10.2   3.2    2.2  2  Fer4_8        4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.5   0.0   1.7e-17   8.1e-15      13     136 ..     109     254 ..     105     255 .. 0.82
   2 !   24.3   0.4   7.5e-08   3.5e-05       8      51 ..     394     434 ..     391     456 .. 0.78
   3 !   31.1   0.0     6e-10   2.8e-07      87     137 .]     452     498 ..     421     498 .. 0.68

  Alignments for each domain:
  == domain 1  score: 55.5 bits;  conditional E-value: 1.7e-17
                                        EEEEEESTTSSHHHHHHHHTTSS--SEEEE...........EETTCEGGGB-HHHCCHCEEEE-SS..--S-TTSB CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...........xxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxx RF
                           ABC_tran  13 kvaivGenGaGKStLlkllagllkpteGei...........lldgkdlkeqeleslrkeigvlpqe..pqlfpelt 75 
                                        +va++G nG GKSt +k++++ lkp+ G             +++g +l+   ++ l+ +i++  +e    l p+  
  gene2229|gene2229|rna2229|rna2229 109 VVALIGTNGIGKSTTIKIMSNGLKPNLGIFknsvswqdiikNFKGSELHGYFIKMLEGKIKCAVKEqyIDLIPGE- 183
                                        79***********************99998777777777776667777767777777777776666555555555. PP

                                        HHHH..............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                        xxxx..............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ABC_tran  76 vren..............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                        ++++              ++d+  ++++++l+++ l d+ +     +LSgG+ qr ++ r+ ++k++ +++DEp+
  gene2229|gene2229|rna2229|rna2229 184 LKKKmkkdrllvqefikdKDDAYTKDLIERLNMHRLLDRDL----DELSGGELQRFCIFRTCMEKANSFFFDEPS 254
                                        33335677888888898777777******************....*****************************7 PP

  == domain 2  score: 24.3 bits;  conditional E-value: 7.5e-08
                                        EETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ABC_tran   8 lkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke 51 
                                        +k ge+v+++GenG GKSt+l+l+ g  +    +i++++ +lk+
  gene2229|gene2229|rna2229|rna2229 394 FKSGEIVVLLGENGMGKSTFLNLVKGVFSV---SIKYQKINLKY 434
                                        689*********************999876...55555555555 PP

  == domain 3  score: 31.1 bits;  conditional E-value: 6e-10
                                        HHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ABC_tran  87 kalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                        ++++ l+     d++++++  +LSgG+ qr++l  +l k+++++l+DEp+a
  gene2229|gene2229|rna2229|rna2229 452 ELMKDLE----IDKIMDNDVCKLSGGELQRLCLFICLSKNADIYLIDEPSA 498
                                        3333444....455566666*****************************75 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.1   4.5e-07   0.00021      23     188 ..     106     274 ..      94     282 .. 0.68
   2 ?    6.3   0.5     0.012       5.9      25      50 ..     398     423 ..     380     444 .. 0.79
   3 !   13.4   0.1     8e-05     0.038     119     197 ..     449     528 ..     424     545 .. 0.69

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 4.5e-07
                                        TSSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTT.CHCCCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSC. CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                              SMC_N  23 sksftaivGpNGSGKsnlldAilFvLGersakklr.seklsdlihkskekasvkkaeveitfdnedkklkiekee. 96 
                                         + + a++G NG GKs  +  ++  L  +    ++ s + +d+i++  ++++++   ++++  +   k  ++++  
  gene2229|gene2229|rna2229|rna2229 106 INCVVALIGTNGIGKSTTIKIMSNGLKPNLG-IFKnSVSWQDIIKN-FKGSELHGYFIKMLEGKI--KCAVKEQYi 177
                                        5668899************999888876555.555156889****9.555566655666642222..222222221 PP

                                        ....EEEEEEEETTSE..EEEEETTEEE-HHHHHHHHHCTT-...STTCS-HHHHHHHHHHHHHHHHCCS--SEEE CS
                                        ....xxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              SMC_N  97 ....vsisrrvkrkge..seykingkevtkkevsellesagi...skelLSgGektLvalaLlfAiqkvkpaplyl 163
                                             ++++++k++    +e+  ++ ++  k++ e l+++++   + ++LSgGe +      +f + + k +++ +
  gene2229|gene2229|rna2229|rna2229 178 dlipGELKKKMKKDRLlvQEFIKDKDDAYTKDLIERLNMHRLldrDLDELSGGELQRFC---IFRTCMEKANSF-F 249
                                        111133344444433354666668888888*********9984334679*****87553...566666666666.5 PP

                                        ECTTTTTS-HHHHHHHHHHHHHHCT CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxx RF
                              SMC_N 164 lDeidaaLDeknvkkvaellkeksk 188
                                        +De  + LD k++ +++++++ek++
  gene2229|gene2229|rna2229|rna2229 250 FDEPSSFLDVKQRIAISNVIREKRD 274
                                        9*********************984 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.012
                                        SEEEEEESTTSSHHHHHHHHHHHCTT CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              SMC_N  25 sftaivGpNGSGKsnlldAilFvLGe 50 
                                        ++ +++G+NG GKs +l+ ++ v++ 
  gene2229|gene2229|rna2229|rna2229 398 EIVVLLGENGMGKSTFLNLVKGVFSV 423
                                        578899********999888777764 PP

  == domain 3  score: 13.4 bits;  conditional E-value: 8e-05
                                        -HHHHHHHHHCTT-STT...CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSE CS
                                        xxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              SMC_N 119 tkkevsellesagiske...lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQ 191
                                        ++ e+++ le  +i  +    LSgGe +   l L   i   k a +yl+De  a LD   + +v++llk+   n Q
  gene2229|gene2229|rna2229|rna2229 449 NSVELMKDLEIDKIMDNdvcKLSGGELQ--RLCLF--ICLSKNADIYLIDEPSAYLDCDTRIRVSRLLKRFAVNKQ 520
                                        4444444444444443355579***965..44444..44567899************************8877766 PP

                                        ..EEEE-S CS
                                        ..xxxxxx RF
                              SMC_N 192 ..fivisl 197
                                          ++++ +
  gene2229|gene2229|rna2229|rna2229 521 kpLFIVEH 528
                                        33555555 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.3      0.64     3e+02      13      21 ..      28      36 ..      27      38 .. 0.89
   2 !   31.6   3.9     2e-10   9.4e-08       2      24 .]      53      75 ..      52      75 .. 0.95

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.64
                                       HHHHHSTTT CS
                               Fer4 13 aCvevCPvg 21
                                       +C + CPv+
  gene2229|gene2229|rna2229|rna2229 28 ECKKTCPVN 36
                                       599****98 PP

  == domain 2  score: 31.6 bits;  conditional E-value: 2e-10
                                       EEETTTSSS-THHHHHSTTTEEE CS
                               Fer4  2 videekCigCGaCvevCPvgAIt 24
                                       vi+e++Ci CG+Cv+ CP++AI+
  gene2229|gene2229|rna2229|rna2229 53 VIHENMCIDCGQCVKKCPFNAIE 75
                                       89********************6 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   2.1   0.00086      0.41       2      47 ..     110     149 ..     109     157 .. 0.79
   2 !   10.1   0.1     0.001      0.49     189     286 ..     172     273 ..     154     284 .. 0.83
   3 !   11.2   0.5   0.00048      0.23       1      26 [.     399     429 ..     399     453 .. 0.76
   4 ?    5.0   0.0     0.039        18     237     284 ..     470     514 ..     465     521 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00086
                             AAA_21   2 nvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkips 47 
                                         +liG Ng GKS+ ++++       + +++   ++ +++++++i++
  gene2229|gene2229|rna2229|rna2229 110 VALIGTNGIGKSTTIKIM------SNGLKPNLGIFKNSVSWQDIIK 149
                                        68****************......6667777777777777777665 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.001
                             AAA_21 189 vrslklveielsdlgegeeliasvderlrer.......gvvflengdgqelparelSdGtkrllalltallralkk 257
                                        v++   + i+ ++ ++++++  +v+e ++++        +  l + +  +++++elS G ++ ++++  + + + +
  gene2229|gene2229|rna2229|rna2229 172 VKEQYIDLIPGELKKKMKKDRLLVQEFIKDKddaytkdLIERLNMHRLLDRDLDELSGGELQRFCIFRTCMEKANS 247
                                        555556667777777778888888888888888888888889999999999***********************99 PP

                             AAA_21 258 gsllliDEpEngLHPkllrrllellkels 286
                                           +++DEp ++L+ k    +  +++e++
  gene2229|gene2229|rna2229|rna2229 248 ---FFFDEPSSFLDVKQRIAISNVIREKR 273
                                        ...*************9999999998775 PP

  == domain 3  score: 11.2 bits;  conditional E-value: 0.00048
                             AAA_21   1 lnvliGpNgsGKSnLLdaldllarl.....d 26 
                                        + vl G Ng GKS++L + ++++++      
  gene2229|gene2229|rna2229|rna2229 399 IVVLLGENGMGKSTFLNLVKGVFSVsikyqK 429
                                        679******************9988754431 PP

  == domain 4  score: 5.0 bits;  conditional E-value: 0.039
                             AAA_21 237 lSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellke 284
                                        lS G ++ l+l+  l   +   +++liDEp + L+     r+ +llk+
  gene2229|gene2229|rna2229|rna2229 470 LSGGELQRLCLFICLSKNA---DIYLIDEPSAYLDCDTRIRVSRLLKR 514
                                        5666666666666666666...9***********99877777777754 PP

>> RLI  Possible Fer4-like domain in RNase L inhibitor, RLI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.9   6.3   1.5e-09   7.1e-07       2      35 .]      11      41 ..      11      41 .. 0.95
   2 ?    0.4   0.0       1.3   6.1e+02      18      27 ..     230     238 ..     228     240 .. 0.81
   3 ?   -0.9   0.1       3.2   1.5e+03      18      26 ..     473     480 ..     471     484 .. 0.84

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 1.5e-09
                                       -EEEES---------TTHHHHHTTSEEEESS--S CS
                                RLI  2 rlAivdadqCdPKKCtgkkcarfcpvrlvrtgkk 35
                                       r A+v ++ C+P KC+  +c++ cpv  +++gkk
  gene2229|gene2229|rna2229|rna2229 11 RAAFVKPGLCKPHKCRL-ECKKTCPV--NNVGKK 41
                                       679**************.********..****97 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 1.3
                                        THHHHHTTSE CS
                                RLI  18 gkkcarfcpv 27 
                                        g +++rfc+ 
  gene2229|gene2229|rna2229|rna2229 230 G-ELQRFCIF 238
                                        6.9*****85 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 3.2
                                        THHHHHTTS CS
                                RLI  18 gkkcarfcp 26 
                                        g +++r+c+
  gene2229|gene2229|rna2229|rna2229 473 G-ELQRLCL 480
                                        6.9*****8 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.0      0.01       4.8      24      56 ..     106     140 ..      92     280 .. 0.69
   2 !   18.2   0.0   5.5e-06    0.0026      23     140 ..     396     526 ..     384     530 .. 0.69

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.01
                             AAA_16  24 p.elvllsGesGvGKsslvrellralekdggif.l 56 
                                          ++v l+G  G+GKs+ ++   + l+ + gif  
  gene2229|gene2229|rna2229|rna2229 106 InCVVALIGTNGIGKSTTIKIMSNGLKPNLGIFkN 140
                                        357899************98887777777444443 PP

  == domain 2  score: 18.2 bits;  conditional E-value: 5.5e-06
                             AAA_16  23 rpelvllsGesGvGKsslvrellralekdggif.lrgkcdqlesaipysa.laqalareellrqlldeaesaelea 96 
                                        ++e+v+l Ge G+GKs+ ++ ++       g+f ++ k+++   ++ y+  + +++ r + ++ ++ +++      
  gene2229|gene2229|rna2229|rna2229 396 SGEIVVLLGENGMGKSTFLNLVK-------GVFsVSIKYQKI--NLKYDKsVKSLIIRLKAINSVELMKDLEIDKI 462
                                        459********************.......455599999999..77886666666667666666666633322222 PP

                             AAA_16  97 wrekleeala..........................avpelagaeasrllellkrllallsrderplvlv 140
                                         +   +   +                          +++ l+++ + r+ +llkr++    ++++pl +v
  gene2229|gene2229|rna2229|rna2229 463 MDNDVC---KlsggelqrlclficlsknadiylidePSAYLDCDTRIRVSRLLKRFA---VNKQKPLFIV 526
                                        222222...133466668888888888888887777777777776666666666666...5557787776 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   1.7     3e-05     0.014      25     121 ..     109     208 ..      96     225 .. 0.57
   2 !   14.3   1.7   5.2e-05     0.024      25      55 ..     399     449 ..     380     470 .. 0.67
   3 ?    2.8   0.0      0.16        77     322     361 ..     486     525 ..     474     533 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3e-05
                             AAA_15  25 ltvliGkNnsGKSsilealdlFlnnkekkn...........kkvikiekedleifeniseskdikIdvef...... 83 
                                        +  liG+N++GKS+ ++++   l+     n           +               i+++k  ++  +f      
  gene2229|gene2229|rna2229|rna2229 109 VVALIGTNGIGKSTTIKIMSNGLKP----NlgifknsvswqD--------------IIKNFKGSELHGYFikmleg 166
                                        789**************99443333....3333344544432..............44444444444444333322 PP

                             AAA_15  84 ....aekekakeyektlkskekkkadlllkkkesdlkktikd 121
                                            a ke+ ++ +  + +k+ kk+ ll++++++d+++ +++
  gene2229|gene2229|rna2229|rna2229 167 kikcAVKEQYIDLIPGELKKKMKKDRLLVQEFIKDKDDAYTK 208
                                        222222245666666666666666666666666666554444 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 5.2e-05
                             AAA_15  25 ltvliGkNnsGKSsilealdlFlnnkekkn....................k 55 
                                        + vl G+N+ GKS++l++ +  ++ + k++                    +
  gene2229|gene2229|rna2229|rna2229 399 IVVLLGENGMGKSTFLNLVKGVFSVSIKYQkinlkydksvksliirlkaiN 449
                                        99************************8888666666444433333333332 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.16
                             AAA_15 322 eknvilliEEPEahLHpqaqkvlikllkelandnktQvii 361
                                        ++ +i+li+EP a+L  +    + +llk+ a ++++ ++i
  gene2229|gene2229|rna2229|rna2229 486 KNADIYLIDEPSAYLDCDTRIRVSRLLKRFAVNKQKPLFI 525
                                        4569***********9999999999999988887765555 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.1    0.0064         3     101     122 ..     109     130 ..      91     145 .. 0.82
   2 !   16.5   0.0   1.3e-05    0.0061      99     122 ..     396     420 ..     350     438 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0064
                                        EEEEECSTTSSHHHHHHHHCTT CS
                        RsgA_GTPase 101 tsvlvGqSGvGKStLinallpe 122
                                        +++l+G  G+GKSt i+ + + 
  gene2229|gene2229|rna2229|rna2229 109 VVALIGTNGIGKSTTIKIMSNG 130
                                        789***********99877665 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 1.3e-05
                                        T.SEEEEECSTTSSHHHHHHHHCTT CS
                        RsgA_GTPase  99 d.ktsvlvGqSGvGKStLinallpe 122
                                        + +++vl+G+ G+GKSt++n +++ 
  gene2229|gene2229|rna2229|rna2229 396 SgEIVVLLGENGMGKSTFLNLVKGV 420
                                        249*****************99884 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   1.7     0.027        13       2      22 ..      13      36 ..      12      38 .. 0.84
   2 !   24.2   3.9   5.2e-08   2.4e-05       2      24 .]      52      74 ..      51      74 .. 0.95

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.027
                             Fer4_6  2 veidpdkCi..gCgd.CvrvCPeg 22
                                       + ++p +C    C+  C + CP +
  gene2229|gene2229|rna2229|rna2229 13 AFVKPGLCKphKCRLeCKKTCPVN 36
                                       578999**9878*777******86 PP

  == domain 2  score: 24.2 bits;  conditional E-value: 5.2e-08
                             Fer4_6  2 veidpdkCigCgdCvrvCPegai 24
                                       ++i ++ Ci+Cg Cv+ CP++ai
  gene2229|gene2229|rna2229|rna2229 52 AVIHENMCIDCGQCVKKCPFNAI 74
                                       7899******************8 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.0    0.0004      0.19      12      44 ..      96     129 ..      93     145 .. 0.77
   2 !   11.4   0.1   0.00042       0.2      22      39 ..     396     414 ..     390     426 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.0004
                             AAA_29  12 fdghtieidlkg.atlltGpsGsGKSTllDAiqa 44 
                                        f+ h+++i   + ++ l+G++G GKST +  ++ 
  gene2229|gene2229|rna2229|rna2229  96 FKLHRLPIPKINcVVALIGTNGIGKSTTIKIMSN 129
                                        566888888778899************9865555 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00042
                             AAA_29  22 kg.atlltGpsGsGKSTll 39 
                                        +g +++l G++G GKST+l
  gene2229|gene2229|rna2229|rna2229 396 SGeIVVLLGENGMGKSTFL 414
                                        345899***********98 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7  12.2     2e-06   0.00093       4      52 .]      24      73 ..       4      73 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 2e-06
                             Fer4_7  4 gCg.aCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52
                                       +C+  C ++Cpv+ +  +  e+ ++   ++i++++C++Cg+Cv+ CP++a
  gene2229|gene2229|rna2229|rna2229 24 KCRlECKKTCPVNNVGKKCIEVTNTDSMAVIHENMCIDCGQCVKKCPFNA 73
                                       57778***********9987777776677899****************97 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.1    0.0023       1.1       4      22 ..     109     127 ..     106     141 .. 0.84
   2 !    9.1   0.0    0.0021      0.98       5      38 ..     400     441 ..     396     480 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0023
                             AAA_24   4 kiliyGpsgiGKTtlakel 22 
                                         ++++G +giGK+t++k +
  gene2229|gene2229|rna2229|rna2229 109 VVALIGTNGIGKSTTIKIM 127
                                        689*************988 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0021
                             AAA_24   5 iliyGpsgiGKTtlakel........gpkplfidtekGlksl 38 
                                        +++ G++g+GK+t+++          +++ + +  +k++ksl
  gene2229|gene2229|rna2229|rna2229 400 VVLLGENGMGKSTFLNLVkgvfsvsiKYQKINLKYDKSVKSL 441
                                        899************998666666666666666666666665 PP

>> VirE  Virulence-associated protein E
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.0    0.0045       2.1      47      74 ..     102     129 ..      81     210 .. 0.91
   2 !    9.7   0.0    0.0014      0.66      46      99 ..     390     443 ..     349     464 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0045
                               VirE  47 PgiKfDfvlvLvGkqgsgKstfleklge 74 
                                        P  K+  v+ L G  g+gKst+++++++
  gene2229|gene2229|rna2229|rna2229 102 PIPKINCVVALIGTNGIGKSTTIKIMSN 129
                                        777999*******************986 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0014
                               VirE  46 ePg.iKfDfvlvLvGkqgsgKstfleklgeewftdslksvedkdavekiqgvliv 99 
                                        +Pg  K  +++vL G+ g+gKstfl+ + +  f+ s+k ++ + ++ k  + li+
  gene2229|gene2229|rna2229|rna2229 390 RPGlFKSGEIVVLLGENGMGKSTFLNLV-KGVFSVSIKYQKINLKYDKSVKSLII 443
                                        56426999*****************855.55566666555555555555555554 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9  14.3   0.00019     0.088      13      58 ..      28      75 ..      13      76 .. 0.76
   2 !   20.3   3.2   9.4e-07   0.00044       1      26 [.      52      77 ..      52      89 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00019
                            Fer4_21 13 kCliaCedt..shqaieidaktvlkvv.edeCvGCnlCssvCPvedcie 58
                                       +C ++C+ +  + ++ie+++   ++v+ e+ C+ C  C++ CP  ++ie
  gene2229|gene2229|rna2229|rna2229 28 ECKKTCPVNnvGKKCIEVTNTDSMAVIhENMCIDCGQCVKKCPF-NAIE 75
                                       48888875422679**999888777764789************7.8886 PP

  == domain 2  score: 20.3 bits;  conditional E-value: 9.4e-07
                            Fer4_21  1 AridedkCigCgkCliaCedtshqai 26
                                       A+i+e++Ci+Cg+C++ C+ ++++ +
  gene2229|gene2229|rna2229|rna2229 52 AVIHENMCIDCGQCVKKCPFNAIEIM 77
                                       89*****************7666554 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   3.3     0.067        32      22     136 ..     110     239 ..     104     350 .. 0.66
   2 !   14.4   0.0   8.6e-05     0.041       9      41 ..     381     419 ..     380     459 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.067
                             AAA_23  22 tlItGpNGaGKTTildAiklaLygetprlsrks.....grgfeksdveiese.........gkvkayvelt..... 78 
                                        ++++G NG GK+T +  +  +L    + ++++       ++f+ s+ +  +          + +++y++l      
  gene2229|gene2229|rna2229|rna2229 110 VALIGTNGIGKSTTIKIMSNGLKPNLGIFKNSVswqdiIKNFKGSELHGYFIkmlegkikcAVKEQYIDLIpgelk 185
                                        6789**********99999999887766665547777644555555554444334444444455555555565532 PP

                             AAA_23  79 fenkdgrytrsiererelskkkgkttkkaklelleideleqfisellgskkiilnlil 136
                                         + k+    +++  + + ++k+  +tk+ +++l  ++ l++ ++el g + +++ ++ 
  gene2229|gene2229|rna2229|rna2229 186 KKMKK----DRLLVQEFIKDKDDAYTKDLIERLNMHRLLDRDLDELSGGELQRFCIFR 239
                                        22222....2333444444444444455555555556777888887777777554443 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 8.6e-05
                             AAA_23   9 sfrdqeidFskglt......lItGpNGaGKTTildAikl 41 
                                        +++++ ++  +gl+      ++ G+NG GK+T+l+ +k 
  gene2229|gene2229|rna2229|rna2229 381 KYENFVLNVRPGLFksgeivVLLGENGMGKSTFLNLVKG 419
                                        57777777755544444444**************98775 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3  14.8   4.2e-06     0.002       4      51 .]      24      74 ..      20      74 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 4.2e-06
                             Fer4_9  4 gCg.aCveaCpagvvvedaaerkarlraase..eaCigCgaCveaCpkgai 51
                                       +C+ +C + Cp + v +++ e ++   +a    + Ci+Cg+Cv++Cp +ai
  gene2229|gene2229|rna2229|rna2229 24 KCRlECKKTCPVNNVGKKCIEVTNTDSMAVIheNMCIDCGQCVKKCPFNAI 74
                                       58756**********99998888877665436699************9987 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0  16.6     9e-05     0.042      10      56 .]      23      70 ..      13      70 .. 0.89
   2 !   18.9   2.9   2.6e-06    0.0012       2      24 ..      52      75 ..      51     102 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 9e-05
                            Fer4_10 10 irCg.kCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                        +C+ +C+k CP+++ +++ ++ ++ +++  +    C++cg+Cv++CP
  gene2229|gene2229|rna2229|rna2229 23 HKCRlECKKTCPVNNVGKKCIEVTNTDSMAVIHENMCIDCGQCVKKCP 70
                                       47988********999999999999999999999*************9 PP

  == domain 2  score: 18.9 bits;  conditional E-value: 2.6e-06
                            Fer4_10  2 vvidddtCirCgkCvkaCPadl.t 24
                                       +vi ++ Ci Cg+Cvk CP+++ +
  gene2229|gene2229|rna2229|rna2229 52 AVIHENMCIDCGQCVKKCPFNAiE 75
                                       68999***************7651 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.0     0.021       9.7       8      29 ..     110     131 ..     108     151 .. 0.88
   2 !    9.7   0.0    0.0021      0.97       4      61 ..     396     446 ..     393     526 .. 0.66

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.021
                             AAA_22   8 lvvtGesGtGKTtllrrlleql 29 
                                        ++++G  G+GK+t+++ + + l
  gene2229|gene2229|rna2229|rna2229 110 VALIGTNGIGKSTTIKIMSNGL 131
                                        689************9877765 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0021
                             AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrell 61 
                                        +  i+v+ Ge G+GK+t l+ ++  +   +k +       +++l+ ++s k+l  +l 
  gene2229|gene2229|rna2229|rna2229 396 SGEIVVLLGENGMGKSTFLNLVKGVFSVSIKYQ-------KINLKYDKSVKSLIIRLK 446
                                        56799**************99998875432222.......555555555555544444 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1   0.1    0.0054       2.5      23      80 ..     107     165 ..      84     361 .. 0.67
   2 !    8.7   0.0    0.0018      0.85      26      80 ..     400     450 ..     371     567 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0054
                                        EEEEEEEESTTSSHHHHHHHHHHHCS--...--HHHHHCCHHHHHHHHHHHHHHHHHHHHH CS
                            G-alpha  23 evkllllGqseSGKsTilkqlkllykkg...fseeelatwraviqlnivrsiktileales 80 
                                        ++ + l+G+++ GKsT++k +    k++   f+++   +w+++i +   + ++  + ++ +
  gene2229|gene2229|rna2229|rna2229 107 NCVVALIGTNGIGKSTTIKIMSNGLKPNlgiFKNS--VSWQDIIKNFKGSELHGYFIKMLE 165
                                        46789****************97777777889999..899998877666666655555555 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0018
                                        EEEEESTTSSHHHHHHHHHHHCS----HHHHHC.CHHHHHHHHHHHHHHHHHHHHH CS
                            G-alpha  26 llllGqseSGKsTilkqlkllykkgfseeelat.wraviqlnivrsiktileales 80 
                                        ++llG+++ GKsT+l+ +k ++  +++ ++++  + + + + i+r     l+a++s
  gene2229|gene2229|rna2229|rna2229 400 VVLLGENGMGKSTFLNLVKGVFSVSIKYQKINLkYDKSVKSLIIR-----LKAINS 450
                                        789****************98888877776633355544444444.....333333 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   1.9      0.14        65       3      20 ..      23      41 ..       4      57 .. 0.76
   2 !   18.7   0.7   5.3e-06    0.0025       2      20 ..      59      77 ..      58     111 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.14
                            Fer4_16  3 gtCgk.CaevCPtnaikek 20
                                       ++C+  C ++CP+n + +k
  gene2229|gene2229|rna2229|rna2229 23 HKCRLeCKKTCPVNNVGKK 41
                                       4677668888888887777 PP

  == domain 2  score: 18.7 bits;  conditional E-value: 5.3e-06
                            Fer4_16  2 CgtCgkCaevCPtnaikek 20
                                       C++Cg+C++ CP nai+  
  gene2229|gene2229|rna2229|rna2229 59 CIDCGQCVKKCPFNAIEIM 77
                                       ****************854 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.1   8.8e-05     0.041      47      99 ..     109     163 ..      93     191 .. 0.83
   2 ?    1.1   0.0      0.68   3.2e+02      46      73 ..     398     425 ..     375     476 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 8.8e-05
                              Rad17  47 iLLisGPsGCgkstvvkvLskelgiklrewlnpvslke..pdnqksdfkglteke 99 
                                        ++ + G  G gkst++k++s  l ++l  + n+vs ++   +++ s+++g ++k 
  gene2229|gene2229|rna2229|rna2229 109 VVALIGTNGIGKSTTIKIMSNGLKPNLGIFKNSVSWQDiiKNFKGSELHGYFIKM 163
                                        667889*****************************99843456999999988875 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.68
                              Rad17  46 riLLisGPsGCgkstvvkvLskelgikl 73 
                                        +i+++ G  G gkst ++ +   +++++
  gene2229|gene2229|rna2229|rna2229 398 EIVVLLGENGMGKSTFLNLVKGVFSVSI 425
                                        489999*********9988766665554 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0      0.12        56       2      23 ..     110     131 ..     109     147 .. 0.84
   2 ?   -1.4   0.0       4.4   2.1e+03      51     107 ..     176     232 ..     162     248 .. 0.75
   3 !    9.3   0.0    0.0023       1.1       2      72 ..     400     494 ..     399     498 .. 0.74

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.12
                                        EEEE--SSSSHHHHHHHGGGGB CS
                              AAA_5   2 vlLvGppGtgKselaerlaaal 23 
                                        v L+G  G+gKs+ ++ ++  l
  gene2229|gene2229|rna2229|rna2229 110 VALIGTNGIGKSTTIKIMSNGL 131
                                        569***********99988766 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 4.4
                                        ......--------G-SEEEEESGGG--HHHHHHHHHHHHSSEEE..-SSSEEE--- CS
                              AAA_5  51 ttslvdsplvraaregeilvlDEveraesevlnsLlslleerrllleeggelvkakn 107
                                           l +++l++++++ ++lv + ++  +++ ++ L+  l+  rll  +++el + + 
  gene2229|gene2229|rna2229|rna2229 176 YIDLIPGELKKKMKKDRLLVQEFIKDKDDAYTKDLIERLNMHRLLDRDLDELSGGEL 232
                                        556778999999999999988888888888888888888888888777777766655 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.0023
                                        EEEE--SSSSHHHHHHHGGGGB..S--EEEEE--TT--HHHHH--B--.........--------........... CS
                              AAA_5   2 vlLvGppGtgKselaerlaaal..nreveyvqltrdtteedlkgrreikngttslvdsplvraar........... 64 
                                        v+L+G+ G gKs++   ++ ++    +++ ++l+ d + + l+ r++  n+ + ++d ++ + +            
  gene2229|gene2229|rna2229|rna2229 400 VVLLGENGMGKSTFLNLVKGVFsvSIKYQKINLKYDKSVKSLIIRLKAINSVELMKDLEIDKIMDndvcklsggel 475
                                        89*******************9877888888888888888888888877888777777776666666666665555 PP

                                        ...........G-SEEEEE CS
                              AAA_5  65 ...........egeilvlD 72 
                                                   +++i+++D
  gene2229|gene2229|rna2229|rna2229 476 qrlclficlskNADIYLID 494
                                        5555555555555555555 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.1     0.067        32       2      18 ..     109     125 ..     108     134 .. 0.83
   2 !   10.2   0.1    0.0011      0.54       2      18 ..     399     415 ..     398     421 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.067
                                        CEEEEC-TTTCHHHHHH CS
                              NACHT   2 lvilqGeaGsGKTtLlq 18 
                                        +v+l G +G+GK+t ++
  gene2229|gene2229|rna2229|rna2229 109 VVALIGTNGIGKSTTIK 125
                                        689**********9776 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0011
                                        CEEEEC-TTTCHHHHHH CS
                              NACHT   2 lvilqGeaGsGKTtLlq 18 
                                        +v+l Ge+G+GK+t+l 
  gene2229|gene2229|rna2229|rna2229 399 IVVLLGENGMGKSTFLN 415
                                        699************96 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.1     0.017       7.8       2      26 ..     111     135 ..     110     160 .. 0.74
   2 ?    7.1   0.0     0.015         7       1      23 [.     400     422 ..     400     457 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.017
                       RNA_helicase   2 wlyGpsgeGKStlakeLakallkkl 26 
                                         l G +g+GKSt++k +++ l  +l
  gene2229|gene2229|rna2229|rna2229 111 ALIGTNGIGKSTTIKIMSNGLKPNL 135
                                        589*************998887666 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.015
                       RNA_helicase   1 iwlyGpsgeGKStlakeLakall 23 
                                        ++l G++g GKSt+ + +   ++
  gene2229|gene2229|rna2229|rna2229 400 VVLLGENGMGKSTFLNLVKGVFS 422
                                        6899**********998554444 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   2.0       8.8   4.2e+03      13      21 ..      25      34 ..      11      35 .. 0.61
   2 !   16.1   1.4   1.8e-05    0.0086       4      21 ..      53      70 ..      50      71 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 8.8
                             Fer4_2 13 Cg.aCvsaCP 21
                                       C+  C + CP
  gene2229|gene2229|rna2229|rna2229 25 CRlECKKTCP 34
                                       5556667777 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 1.8e-05
                             Fer4_2  4 vvdtdrCigCgaCvsaCP 21
                                       v+ +++Ci Cg Cv+ CP
  gene2229|gene2229|rna2229|rna2229 53 VIHENMCIDCGQCVKKCP 70
                                       67799************* PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   2.7       2.6   1.2e+03       7      16 ..      25      35 ..      18      36 .. 0.76
   2 ?   15.9   3.9   2.9e-05     0.013       2      17 .]      57      72 ..      56      72 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 2.6
                             Fer4_4  7 Cg.sCvaaCPq 16
                                       C+  C  +CP+
  gene2229|gene2229|rna2229|rna2229 25 CRlECKKTCPV 35
                                       77459999997 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 2.9e-05
                             Fer4_4  2 erCigCgsCvaaCPqg 17
                                       + Ci+Cg+Cv  CP++
  gene2229|gene2229|rna2229|rna2229 57 NMCIDCGQCVKKCPFN 72
                                       68************85 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.0     0.012       5.5       6      44 ..      87     132 ..      82     152 .. 0.80
   2 ?    5.7   0.0      0.03        14      18      39 ..     393     417 ..     374     430 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.012
                                        HHHHHHHHHHHCH.......TEEEEEEESTTSSHHHHHHHHHHHTT CS
                               TsaE   6 etealgkklakal.......gdvilLeGdLGaGKTtlvrglakalg 44 
                                         t++ g++l k         + v++L G  G GK+t ++ + ++l+
  gene2229|gene2229|rna2229|rna2229  87 ITHRYGQNLFKLHrlpipkiNCVVALIGTNGIGKSTTIKIMSNGLK 132
                                        56777777777446666665667****************9999885 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.03
                                        H...TEEEEEEESTTSSHHHHHHHH CS
                               TsaE  18 l...gdvilLeGdLGaGKTtlvrgl 39 
                                        l   g++++L G+ G+GK+t+   +
  gene2229|gene2229|rna2229|rna2229 393 LfksGEIVVLLGENGMGKSTFLNLV 417
                                        2444788*************98654 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0     0.014       6.7      34      59 ..     108     133 ..     102     149 .. 0.85
   2 ?    6.1   0.0     0.015       7.3      29      74 ..     393     437 ..     369     447 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.014
                              AAA_7  34 kpvllvGptGtGKtviikdllkkldk 59 
                                          v l+G+ G GK+++ik + + l++
  gene2229|gene2229|rna2229|rna2229 108 CVVALIGTNGIGKSTTIKIMSNGLKP 133
                                        56889*************99999885 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.015
                              AAA_7  29 llknkkpvllvGptGtGKtviikdllkkldkekylsltinfsaqts 74 
                                        l+k++  v+l G+ G GK++ ++ +   ++  ++++ +in+++  s
  gene2229|gene2229|rna2229|rna2229 393 LFKSGEIVVLLGENGMGKSTFLNLVKGVFS-VSIKYQKINLKYDKS 437
                                        6788899************99875544444.666666666666555 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0      0.02       9.4       2      21 ..     110     129 ..     109     212 .. 0.79
   2 ?    6.7   0.2     0.016       7.6       2      21 ..     400     419 ..     399     446 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.02
                                        EEEEESTTSSHHHHHHHHHT CS
                           MMR_HSR1   2 vaivGrpNvGKStLinaltg 21 
                                        va++G    GKSt i+ +++
  gene2229|gene2229|rna2229|rna2229 110 VALIGTNGIGKSTTIKIMSN 129
                                        89*************99987 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.016
                                        EEEEESTTSSHHHHHHHHHT CS
                           MMR_HSR1   2 vaivGrpNvGKStLinaltg 21 
                                        v+++G    GKSt++n   g
  gene2229|gene2229|rna2229|rna2229 400 VVLLGENGMGKSTFLNLVKG 419
                                        799*************7655 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.1    0.0038       1.8       2      44 ..     111     166 ..     110     187 .. 0.72
   2 ?    3.6   0.0      0.18        85       1      23 [.     400     422 ..     400     501 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0038
                                        EEESSTTSSHHHHHHHHHHHHTHE.............EEEEETTTCSSSSTTHHHH CS
                                AAA   2 llyGppGtGKTllakavakelgve.............fleisgsellskyvgesek 44 
                                         l+G+ G+GK++++k + + l+ +             + +++gsel   +++  e 
  gene2229|gene2229|rna2229|rna2229 111 ALIGTNGIGKSTTIKIMSNGLKPNlgifknsvswqdiIKNFKGSELHGYFIKMLEG 166
                                        699*****************975544444445555556666666666555555555 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.18
                                        EEEESSTTSSHHHHHHHHHHHHT CS
                                AAA   1 vllyGppGtGKTllakavakelg 23 
                                        v+l G  G+GK+++ + v   ++
  gene2229|gene2229|rna2229|rna2229 400 VVLLGENGMGKSTFLNLVKGVFS 422
                                        6799*********9998877654 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.1     0.003       1.4      21      79 ..     108     167 ..      97     216 .. 0.77
   2 ?    3.7   0.0     0.062        29      21      40 ..     398     417 ..     383     466 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.003
                                        EEEEEEESTTSSHHHHHHHHCCSHCCCCCCBT.EEEEEEEESXXHHHHHHHXXHHHHHCC CS
                             NB-ARC  21 lvvalvGmgGvGKttlakqilnksdevegrFd.svawvvvsktdkseeiletilkeLsls 79 
                                         vval G  G+GK+t +k + n ++   g F  sv w  + k++k +e+    +k L+ +
  gene2229|gene2229|rna2229|rna2229 108 CVVALIGTNGIGKSTTIKIMSNGLKPNLGIFKnSVSWQDIIKNFKGSELHGYFIKMLEGK 167
                                        69***************9999999999999988999999999999999888877777544 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.062
                                        EEEEEEESTTSSHHHHHHHH CS
                             NB-ARC  21 lvvalvGmgGvGKttlakqi 40 
                                         +v l G  G+GK+t ++ +
  gene2229|gene2229|rna2229|rna2229 398 EIVVLLGENGMGKSTFLNLV 417
                                        3889***********76533 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0     0.027        13       1      28 [.     110     147 ..     110     224 .. 0.73
   2 ?    4.7   0.7     0.091        43      80     114 ..     481     515 ..     400     602 .. 0.64

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.027
                             AAA_18   1 IlltGtpGvGKttlakeLskrl.gf.........gvnl 28 
                                        ++l Gt G GK+t  k  s+ l  +         ++ +
  gene2229|gene2229|rna2229|rna2229 110 VALIGTNGIGKSTTIKIMSNGLkPNlgifknsvsWQDI 147
                                        6899*************998875446445554443333 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.091
                             AAA_18  80 dghlaeleseaakdikkvvLtaspeelleRlekRg 114
                                          +l+++ + +++d    +L++++ ++  Rl kR 
  gene2229|gene2229|rna2229|rna2229 481 FICLSKNADIYLIDEPSAYLDCDTRIRVSRLLKRF 515
                                        44444444444444444788888888888888874 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.1     0.015       6.8      56      77 ..     110     131 ..     105     137 .. 0.86
   2 ?    4.6   0.0     0.032        15      54      71 ..     398     415 ..     356     451 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.015
                             DUF815  56 vLLwGarGtGKSslvkallney 77 
                                        v L+G+ G GKS+++k + n +
  gene2229|gene2229|rna2229|rna2229 110 VALIGTNGIGKSTTIKIMSNGL 131
                                        5699************998765 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.032
                             DUF815  54 nnvLLwGarGtGKSslvk 71 
                                        + v+L G+ G+GKS+ + 
  gene2229|gene2229|rna2229|rna2229 398 EIVVLLGENGMGKSTFLN 415
                                        5689**********8644 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.2    0.0034       1.6       3      25 ..     109     131 ..     107     142 .. 0.86
   2 ?    2.7   0.1      0.18        86       3      18 ..     399     414 ..     397     428 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0034
                                        EEEEEESTTSSHHHHHHHHHHHH CS
                              SRP54   3 villvGlqGaGKTttlaKLaall 25 
                                        v++l+G++G+GK tt+  +++ l
  gene2229|gene2229|rna2229|rna2229 109 VVALIGTNGIGKSTTIKIMSNGL 131
                                        899************98887766 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.18
                                        EEEEEESTTSSHHHHH CS
                              SRP54   3 villvGlqGaGKTttl 18 
                                        +++l+G +G+GK t l
  gene2229|gene2229|rna2229|rna2229 399 IVVLLGENGMGKSTFL 414
                                        789**********986 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.2    0.0072       3.4       2      20 ..     110     128 ..     109     138 .. 0.88
   2 ?   -2.3   0.1        10   4.7e+03     120     148 ..     198     227 ..     193     228 .. 0.78
   3 ?    0.7   0.0       1.2   5.5e+02       2      18 ..     400     416 ..     399     425 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0072
                             AAA_28   2 ivitGgestGKTtlleaLa 20 
                                        ++++G+ + GK+t+++ ++
  gene2229|gene2229|rna2229|rna2229 110 VALIGTNGIGKSTTIKIMS 128
                                        89*************9876 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 10
                             AAA_28 120 ei.dddgeRredleereaiderlrealrel 148
                                        +i d+d++ ++dl er +++++l   l+el
  gene2229|gene2229|rna2229|rna2229 198 FIkDKDDAYTKDLIERLNMHRLLDRDLDEL 227
                                        456778888999999999999998887765 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 1.2
                             AAA_28   2 ivitGgestGKTtllea 18 
                                        +v++G  + GK+t l+ 
  gene2229|gene2229|rna2229|rna2229 400 VVLLGENGMGKSTFLNL 416
                                        89***********9975 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5  12.7      0.11        53      41      59 ..      54      72 ..      20      74 .. 0.56

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.11
                            Fer4_17 41 ekaslCieCgeCerkCPqg 59
                                          + Ci Cg+C++kCP +
  gene2229|gene2229|rna2229|rna2229 54 IHENMCIDCGQCVKKCPFN 72
                                       23378************65 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   3.8       6.1   2.9e+03       3      14 ..      24      36 ..      20      37 .. 0.79
   2 ?   13.2   4.1   0.00028      0.13       1      15 []      59      73 ..      59      73 .. 0.97

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 6.1
                             Fer4_3  3 gCg.aCvevCPvg 14
                                        C+  C + CPv+
  gene2229|gene2229|rna2229|rna2229 24 KCRlECKKTCPVN 36
                                       58756******97 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 0.00028
                             Fer4_3  1 CtgCgaCvevCPvgA 15
                                       C+ Cg+Cv+ CP +A
  gene2229|gene2229|rna2229|rna2229 59 CIDCGQCVKKCPFNA 73
                                       9***********998 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2  13.9      0.12        58       7      64 ..      24      72 ..      18      73 .. 0.87
   2 ?   10.2   3.2    0.0017       0.8       4      17 ..      58      71 ..      55      94 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.12
                             Fer4_8  7 eCg.aCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvg 64
                                       +C   C+++Cpv +  kk +  ++ + ++ v  e +         C  cg+C+++Cp +
  gene2229|gene2229|rna2229|rna2229 24 KCRlECKKTCPVNNVGKKCIEVTNTDSMA-VIHENM---------CIDCGQCVKKCPFN 72
                                       5654799****999999**9999999999.888777.........************75 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0017
                             Fer4_8  4 kCieCgaCqsaCpv 17
                                        Ci Cg C ++Cp+
  gene2229|gene2229|rna2229|rna2229 58 MCIDCGQCVKKCPF 71
                                       69999999999984 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (604 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       810  (0.0451782); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); expected 358.6 (0.02)
Passed Vit filter:                        95  (0.00529868); expected 17.9 (0.001)
Passed Fwd filter:                        38  (0.00211947); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              38  [number of targets reported over threshold]
# CPU time: 0.68u 0.31s 00:00:00.99 Elapsed: 00:00:00.44
# Mc/sec: 4150.05
//
Query:       gene223|gene223|rna223|rna223  [L=75]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       469  (0.0261587); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.33u 0.25s 00:00:00.58 Elapsed: 00:00:00.40
# Mc/sec: 565.91
//
Query:       gene2230|gene2230|rna2230|rna2230  [L=348]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.7e-11   43.9   7.0    1.7e-11   43.9   7.0    2.2  2  TFIIE_alpha     TFIIE alpha subunit
     0.0064   16.2   0.8      0.014   15.1   0.8    1.6  1  zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal
  ------ inclusion threshold ------
      0.019   14.5   1.5        2.9    7.6   0.1    2.7  2  zf_UBZ          Ubiquitin-Binding Zinc Finger
      0.021   15.1   3.4      0.021   15.1   3.4    1.8  2  TFIIE-A_C       C-terminal general transcription factor TFIIE
      0.058   13.4   0.9        8.9    6.4   0.1    2.4  2  PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
      0.078   13.1   0.5       0.21   11.8   0.5    1.7  1  Zn-ribbon_8     Zinc ribbon domain
       0.22   11.1   2.1          1    8.9   2.1    2.2  1  TF_Zn_Ribbon    TFIIB zinc-binding
        0.4   10.5   2.0        2.3    8.1   0.3    2.4  2  zf-C2H2_3       zinc-finger of acetyl-transferase ESCO


Domain annotation for each model (and alignments):
>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.9   7.0   7.4e-15   1.7e-11       2     103 ..      12     116 ..      11     118 .. 0.96
   2 ?   -0.8   0.1      0.61   1.4e+03      36      65 ..     159     187 ..     154     229 .. 0.57

  Alignments for each domain:
  == domain 1  score: 43.9 bits;  conditional E-value: 7.4e-15
                                        HHHHHHHHCS-HHHHHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEEEEEE...TTTEEEEEEE CS
                        TFIIE_alpha   2 llkevvrkfygeeavlvldvLlekgevteedlakelkidlnelrklLnrLyearlvkykrrrd...eekswykyyw 74 
                                        l++  +r fy  ++  ++d+L ek  + e+++   +k+  +e  kl+ +L+e++l+k   + +   ++ +  +  +
  gene2230|gene2230|rna2230|rna2230  12 LIRHTLRLFYQPHHCVIMDILSEKLLLRENEICSAMKMLSKEFNKLIVKLKEDKLIKQESKIEttiDGRQLLQQIY 87 
                                        7788899999*****************************************************9************ PP

                                        EEECCCHCCCHHHHHHHHHHHHHHHHCCC CS
                        TFIIE_alpha  75 rinyeklvdvvkrkleevvkkLeekleke 103
                                        +i+y+++ d++k+k+ ++  +++e+l+++
  gene2230|gene2230|rna2230|rna2230  88 YIDYREIKDIIKYKIYKMSTEINEHLREQ 116
                                        ************************99875 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.61
                                        HHTS-HHHHHHHH.HHHHHCTSEEEEEEEET CS
                        TFIIE_alpha  36 elkidlnelrklL.nrLyearlvkykrrrde 65 
                                        ++++d++el  l+ n+L++  ++++ ++ d+
  gene2230|gene2230|rna2230|rna2230 159 NTEVDPHELHTLMmNDLKD--IIDMLKQADN 187
                                        5666777776654145655..4666666663 PP

>> zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.8   6.1e-06     0.014      22      52 ..     121     152 ..     110     154 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 6.1e-06
                     zinc_ribbon_10  22 alICskChshnGlap.keeleevkyrCpkCga 52 
                                          +Cs+C++   + + ++  ++ +++Cp C+ 
  gene2230|gene2230|rna2230|rna2230 121 GYVCSECKTEYSVLEaQSLVKNYRFICPDCNI 152
                                        569***********978888888*******95 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.1    0.0013       2.9       3      18 ..     122     137 ..     121     138 .. 0.84
   2 ?    5.4   0.1    0.0061        14       3      15 ..     145     157 ..     144     161 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0013
                             zf_UBZ   3 ylCerCgkeipeselq 18 
                                        y+C++C++e ++ e q
  gene2230|gene2230|rna2230|rna2230 122 YVCSECKTEYSVLEAQ 137
                                        9*******99987766 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0061
                             zf_UBZ   3 ylCerCgkeipes 15 
                                        ++C++C+ e+ e+
  gene2230|gene2230|rna2230|rna2230 145 FICPDCNIELVEN 157
                                        89*****998765 PP

>> TFIIE-A_C  C-terminal general transcription factor TFIIE alpha
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.3       6.3   1.4e+04      24      31 ..     215     222 ..     200     233 .. 0.40
   2 ?   15.1   3.4   9.4e-06     0.021      30      77 ..     292     343 ..     241     347 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 6.3
                          TFIIE-A_C  24 seveeeee 31 
                                        ++ ++++e
  gene2230|gene2230|rna2230|rna2230 215 KTDDNMKE 222
                                        11223333 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 9.4e-06
                          TFIIE-A_C  30 eeeeeeee......addptvmVaGrpvslsevsqrpelvsqmtpeEkeaYikvg 77 
                                         ++ e +e      +d+ +v+V+G    +s v++  e  ++mt+eE e+Y +v 
  gene2230|gene2230|rna2230|rna2230 292 SDDLEKSEprpadvHDEIMVKVGGVAKVFSAVTE--EDKEKMTEEEYETYFEVF 343
                                        33334444667777899*****************..888***********9985 PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.1     0.004       8.9      20      29 ..     122     131 ..     111     132 .. 0.88
   2 ?    5.1   0.1    0.0095        21      17      26 ..     142     151 ..     137     154 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.004
                     PhnA_Zn_Ribbon  20 lvCpeCahEw 29 
                                        +vC+eC+ E 
  gene2230|gene2230|rna2230|rna2230 122 YVCSECKTEY 131
                                        8******997 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0095
                     PhnA_Zn_Ribbon  17 gallvCpeCa 26 
                                        +  ++Cp+C 
  gene2230|gene2230|rna2230|rna2230 142 NYRFICPDCN 151
                                        5569*****6 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.5   9.2e-05      0.21       6      33 ..     122     151 ..     121     157 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 9.2e-05
                        Zn-ribbon_8   6 YrCeeCghefevlqsis.daplta.CPeCg 33 
                                        Y C eC++e+ vl + s  ++    CP+C+
  gene2230|gene2230|rna2230|rna2230 122 YVCSECKTEYSVLEAQSlVKNYRFiCPDCN 151
                                        9**********99988886666667****7 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   2.1   0.00045         1       1      25 [.     122     150 ..     122     161 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00045
                                        EEETTTTCEE.CHEE....TSTTCEEESSS CS
                       TF_Zn_Ribbon   1 ykCPnCgstn.lveD....pergelvCtdC 25 
                                        y+C +C++++ + ++     ++  ++C+dC
  gene2230|gene2230|rna2230|rna2230 122 YVCSECKTEYsV-LEaqslVKNYRFICPDC 150
                                        89******9955.44366667777****** PP

>> zf-C2H2_3  zinc-finger of acetyl-transferase ESCO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.3     0.001       2.3       7      28 ..     116     136 ..     112     137 .. 0.75
   2 ?    2.2   0.0     0.073   1.6e+02       8      34 ..     137     165 ..     132     168 .. 0.68

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.001
                          zf-C2H2_3   7 gqksfgasqCkeCgMvYnpgsp 28 
                                         q+++g   C+eC+ +Y+  ++
  gene2230|gene2230|rna2230|rna2230 116 QQRQIGY-VCSECKTEYSVLEA 136
                                        5777665.6********98776 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.073
                          zf-C2H2_3   8 qksfgasq..CkeCgMvYnpgspeDeklH 34 
                                        q+  ++ +  C+ C+++ ++    ++  H
  gene2230|gene2230|rna2230|rna2230 137 QSLVKNYRfiCPDCNIELVENKNTEVDPH 165
                                        4555556678*****98877766666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (348 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1214  (0.0677115); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2530.32
//
Query:       gene2231|gene2231|rna2231|rna2231  [L=88]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0057   16.6   0.1     0.0059   16.5   0.1    1.0  1  TarH      Tar ligand binding domain homologue
  ------ inclusion threshold ------
        0.1   12.6   0.1       0.11   12.5   0.1    1.1  1  Raptor_N  Raptor N-terminal CASPase like domain


Domain annotation for each model (and alignments):
>> TarH  Tar ligand binding domain homologue
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.1   6.6e-07    0.0059      33     101 ..       3      70 ..       1      86 [. 0.90

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 6.6e-07
                                        HHHHHHHCHHHHHHH.HHHHHHHHHHHHHHHHHHHHHHHHHHHTTTSSSSSSHHHHHHHHHHHHHHHHH CS
                               TarH  33 lsrsndalrevytnrlqqqaaLaearvsllqaRltLnragiaaladeaedakellaraeeslaqseeaw 101
                                        +++ +++++ +  n +++++++a+++ +  + +l+L+  ++  l++e++  k+l+++a+++l++ ++ +
  gene2231|gene2231|rna2231|rna2231   3 IKKVQHNFEKMCLNYTTAIEDVAKVKPARIRISLNLYS-NTKQLLQEEDSFKDLMKNARNQLKDFNDLF 70 
                                        6778899999999999*********************8.************************999877 PP

>> Raptor_N  Raptor N-terminal CASPase like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   1.2e-05      0.11       9      53 ..      12      54 ..       4      85 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.2e-05
                           Raptor_N  9 vlclnigvdppdvvktkpcarleawidpsseleeiaknlqd..qyes 53
                                        +cln  +  +dv+k+kp ar+    +++s+   +++ lq+   ++ 
  gene2231|gene2231|rna2231|rna2231 12 KMCLNYTTAIEDVAKVKP-ARIRISLNLYSN---TKQLLQEedSFKD 54
                                       69****************.999999999993...3333333222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       988  (0.0551063); expected 358.6 (0.02)
Passed bias filter:                      525  (0.0292822); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 637.52
//
Query:       gene2232|gene2232|rna2232|rna2232  [L=74]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (74 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1080  (0.0602376); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 492.23
//
Query:       gene2233|gene2233|rna2233|rna2233  [L=209]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       574  (0.0320152); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1469.21
//
Query:       gene2234|gene2234|rna2234|rna2234  [L=255]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.3e-10   39.7   0.9    5.9e-10   38.8   0.9    1.4  1  FYRN      F/Y-rich N-terminus


Domain annotation for each model (and alignments):
>> FYRN  F/Y-rich N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.8   0.9   3.3e-14   5.9e-10       3      51 .]     129     179 ..     127     179 .. 0.93

  Alignments for each domain:
  == domain 1  score: 38.8 bits;  conditional E-value: 3.3e-14
                               FYRN   3 ltvlslGelvpds.pkfhteryIyPvGYkstRlYwstkdpr.krclYtceI 51 
                                        + +l++G +++ + ++f+++++IyP++Y+++R++  ++  +    +Ytc I
  gene2234|gene2234|rna2234|rna2234 129 FAILNIGVMPTAHqTDFYNRYFIYPINYRVERVFRGYRTDHsSLLVYTCVI 179
                                        679***********99*******************9998887999****87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1317  (0.0734564); expected 358.6 (0.02)
Passed bias filter:                      616  (0.0343577); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.83
# Mc/sec: 923.03
//
Query:       gene2235|gene2235|rna2235|rna2235  [L=642]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.8e-79  265.7   0.0    7.7e-79  265.2   0.0    1.2  1  AMP-binding  AMP-binding enzyme
  ------ inclusion threshold ------
      0.019   15.0   0.1       0.06   13.4   0.1    1.9  1  bPH_1        Bacterial PH domain


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  265.2   0.0   8.6e-83   7.7e-79      17     422 ..      59     527 ..      41     528 .. 0.82

  Alignments for each domain:
  == domain 1  score: 265.2 bits;  conditional E-value: 8.6e-83
                                        CCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEEETTS-HHHHHHHHHH CS
                        AMP-binding  17 sgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvvplnptltaeelayiled 92 
                                        +++ + +TY + ++rv+++ ++++ +++ +++ ++i++ n+ ew+++ +ail+a a+  pl++tl+ + +++i+++
  gene2235|gene2235|rna2235|rna2235  59 DNRVEYITYLDGYNRVRKIYSFIKGMNLDEEEIIGIFSVNREEWIISEQAILMADATSCPLYSTLGVDSIKHIINE 134
                                        5677899*****************99************************************************** PP

                                        HTESEEE.......................E.TCTCCC.HHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCC CS
                        AMP-binding  93 seakvli.......................a.tvdsel.leklleaaakleavklvivldadellkeeelkeeees 143
                                        +++++++                             +   ek+ ++ a       + v+  de+++++++k+ ++s
  gene2235|gene2235|rna2235|rna2235 135 TNMRIMFvsgekaeylyekilssdpnglevViS--YDHiSEKMVACFA----DLGISVYFFDEIYENSTEKDIKPS 204
                                        *******88888888888888776655432122..2222344444444....446667777778777777776666 PP

                                        SCTTS.................-TSCCCS-BTTSEEEEEEE--SSSS-EEEEEEHHHHHHHHHHHH.HHHC...SC CS
                        AMP-binding 144 eekae.................kpeeeeelkpddlayiiYTSGTTGkPKGVmlshrnlvanvaslk.letr...fk 198
                                        + ka+                 k + e++ kpdd++ i+YTSGT GkPKG+ml+ rn+v+++a+++  ++     +
  gene2235|gene2235|rna2235|rna2235 205 DLKAQnardvgdgfydsmkvlkKIRNESRSKPDDVVSICYTSGTCGKPKGAMLTNRNFVSSIAAFArGDDNgsvIE 280
                                        655536789999**********66667799**********************************987444445555 PP

                                        CTTT-EEEESS-TTSCHHHHHHHHHHHHTT-EEEE-TTCGCCHHHHHHHHHHHHT-SEEEEEHHHHHHH....... CS
                        AMP-binding 199 lkeddvvlsilplahifglilelllallsGatvvllpkdaaldpklllelieklkvtviagvPrvleal....... 267
                                        ++++ v++s+lplah+++  +++++++++ a++ ++ ++++     l ++i+ +++++++gvPrv++ +       
  gene2235|gene2235|rna2235|rna2235 281 VNNSVVYISYLPLAHAMEK-ICVYVIISVCARIAFYGGNPK----NLQQDIKIIRPSFLVGVPRVFNVFkekieek 351
                                        7679999***********6.*****************9977....3469********************5555555 PP

                                        ......HHCCCHHCHHHHC...................................CGTT.-SEEEEESS-EBHHHHH CS
                        AMP-binding 268 ......lesgalkaakkak...................................dlss.lrlvllggeplspellr 301
                                              l           +                                   ++++ +r+ l+g +pl+p++  
  gene2235|gene2235|rna2235|rna2235 352 vnergcL-----------TrfafymalkykkwkqrsgsvssyivdrfifkkiaaEFGGnIRFGLSGSAPLNPDVCS 416
                                        4444431...........03333444444467777788888899999999999999999***************** PP

                                        HHHHHHTCEEEEEEEEGGGSSECEECHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEETTSEEEEEEEETTS-SE CS
                        AMP-binding 302 ffralfgeevlegYGlTEttgvvtvlpleedkkklgsvGkplpgvevkivDeetgepvpdgeeGellvrgpgvmkg 377
                                        f++++f  +++egYG+TE++++ + l++++ +++ g+vG p+p + vk++  +    +pd+   e+l++g +v+kg
  gene2235|gene2235|rna2235|rna2235 417 FLQSVFSMKLYEGYGQTEALAANI-LKPPQ-CHTYGTVGIPFPSNMVKLIPSD----IPDQ--YEILLKGDNVFKG 484
                                        *******9*************988.77445.5788**************9655....3333..49*********** PP

                                        BTT-HHHHHHHEEETCCEEEEEEEEEEETTSEEEEEEECCCEEEE CS
                        AMP-binding 378 YlkkpeataeafdsegrwlrTGDlgrldedGyleivgRkkdlikl 422
                                        Y+k+pe+tae++d +++wl+TGDlg +  +G ++ivgR k+++k+
  gene2235|gene2235|rna2235|rna2235 485 YYKNPEKTAEVLD-SDGWLHTGDLGIVK-EGLFYIVGRRKEIFKT 527
                                        ************9.757**********9.9*************98 PP

>> bPH_1  Bacterial PH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   6.7e-06      0.06      17      57 ..      76     116 ..      68     139 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 6.7e-06
                                        CCHHHHGCGCGCT--EEEEEE-TSEEEEEESSEEEEEE--- CS
                              bPH_1  17 klekelgellidgEkilfafklirDevvFTnkrlilvdkqg 57 
                                        k+ + ++ + +d+E+i+ +f + r+e+++ ++++++ d+++
  gene2235|gene2235|rna2235|rna2235  76 KIYSFIKGMNLDEEEIIGIFSVNREEWIISEQAILMADATS 116
                                        56666788999***************************876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (642 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       603  (0.0336327); expected 358.6 (0.02)
Passed bias filter:                      490  (0.02733); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.63u 0.29s 00:00:00.92 Elapsed: 00:00:00.46
# Mc/sec: 4180.34
//
Query:       gene2236|gene2236|rna2236|rna2236  [L=432]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.8e-78  263.8   2.9    1.8e-78  263.8   2.9    1.5  2  Kinesin      Kinesin motor domain
      1e-16   61.2   2.5    1.4e-16   60.7   0.2    2.3  2  Microtub_bd  Microtubule binding


Domain annotation for each model (and alignments):
>> Kinesin  Kinesin motor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  263.8   2.9     2e-82   1.8e-78      32     333 .]      36     305 ..      10     305 .. 0.89
   2 ?   -2.8   0.1      0.26   2.4e+03     159     179 ..     363     381 ..     323     398 .. 0.55

  Alignments for each domain:
  == domain 1  score: 263.8 bits;  conditional E-value: 2e-82
                                        EEEECTTSCEEEEESEEEETTS-HHHHHHHHHHHHHHHHHTTSEEEEEEEESTTSSHHHHHTBCTTTSBSHHHHHH CS
                            Kinesin  32 kkenkeeeekkfkFdkvfdeeatqeevyeetakplvesvleGynatifaYGqtgsGKTyTmegkeeeeeGiipral 107
                                        +k ++++  + f ++kvf   +++  +y+e+++p ++ +++G++ t+faYGqtgsGKT+Tm+gk  ++ Gii r+l
  gene2236|gene2236|rna2236|rna2236  36 QKIEDDKFISYFCYKKVFY-MVDNCGLYKECIEPNIQPFVSGKSLTVFAYGQTGSGKTHTMTGK-PSDMGIIGRTL 109
                                        4445555567799999998.578999*************************************8.999******** PP

                                        HHHHHHHHHCTTTHEEEEEEEEEEEEEETTEEEETTSTTTTSTSSEBEEEECTTSCCEEETTS--EEESSHHHHHH CS
                            Kinesin 108 eelFesikkekeekekefsvkvsylEiYneeiyDLLeskkskkkkklkiredskkgevyvkgltevevksaeevle 183
                                        e++++s+++         ++ +sy+EiYne+i DL++++   +k   ++   ++  e++vkg++ + v+s+++ l+
  gene2236|gene2236|rna2236|rna2236 110 EDIYNSMDEA-------AECYISYFEIYNENIIDLINTN---NK--PRVFTYNN--ELIVKGIERTLVSSLDKSLR 171
                                        *******873.......4689****************98...23..47777777..49****************** PP

                                        HHHHHHHHHTSTTSSCTSHHCCSEEEEEEEEEEEETTTTTCEEEEEEEEEEEEEEECCCHHHHSSTCHHHHHHHHH CS
                            Kinesin 184 llekgeknrkvaetklneeSSRSHavftitleqknlkeeteekvkisklnLvDLAGsErasktgaaegerlkEaan 259
                                        l++ +e++rk+++t++n +SSRSH++f+++l+++n+         +s+++L+DLAGsE+as t+     r++E+  
  gene2236|gene2236|rna2236|rna2236 172 LIKGCEERRKTGQTQFNLRSSRSHTIFKLELQNTNS---------TSTMTLIDLAGSEKASGTS----LRIREGVY 234
                                        ********************************9983.........5899*********988777....479***** PP

                                        HHHHHHHHHHHHHHHHHTCCTSTSCGGGSHHHHHTGGGHSSSSEEEEEEEE-TBGGGHHHHHHHHHHHHHHCTT CS
                            Kinesin 260 iNkSLlaLgrvisaLaekkkskhipYRdSkLTrlLqdsLgGnsktlmivtvspssenleetlstlkfaerakei 333
                                        iNkSLlaLg+vi++L+++   ++  YR+SkLTr+Lq+s++Gn + + ++++sp++++l+e++stl+fa+r  +i
  gene2236|gene2236|rna2236|rna2236 235 INKSLLALGKVINSLNKN---EFTSYRESKLTRVLQSSMTGNVTLIALCMISPDRKCLDESISTLNFASRLCQI 305
                                        ***************999...9***********************************************98765 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 0.26
                                        CTTSCCEEETTS--EEESSHH CS
                            Kinesin 159 dskkgevyvkgltevevksae 179
                                        +++    ++ +l++++++s+e
  gene2236|gene2236|rna2236|rna2236 363 KNS--AEQIIQLQNKRIHSLE 381
                                        111..1234444444444444 PP

>> Microtub_bd  Microtubule binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.7   0.2   1.6e-20   1.4e-16      22     149 .]       5     138 ..       2     138 .. 0.87
   2 ?   -0.5   0.2      0.12   1.1e+03      49      87 ..     347     385 ..     292     413 .. 0.63

  Alignments for each domain:
  == domain 1  score: 60.7 bits;  conditional E-value: 1.6e-20
                                        -EEEEEEECCCS-T.EEEETTT................TTTEEEE-SEEEECTTHCCCCCCCCHHHHHHHHTT--E CS
                        Microtub_bd  22 iRvfarvrpelesekakikfpe.............eekkkkkefsFdrvfeseseqeevfeeisqlvqsaldgynv 84 
                                        + v++rvr++l++e ++ + +e             e++k    f + +vf    +     e i+  +q  ++g+  
  gene2236|gene2236|rna2236|rna2236   5 VNVYVRVRNKLTNE-LDGDQDElwflkdnllhqkiEDDKFISYFCYKKVFYMVDNCGLYKECIEPNIQPFVSGKSL 79 
                                        779******99998.44444434444456676666666777889********99999999999************* PP

                                        EEEEEES................ST-HCHHHHHHHHHHCCTSCCCCEEEEEEEEEEESS-EEETT CS
                        Microtub_bd  85 cifaygqTGsGKtyTmegeeeeagmipraveeifetiselkekgwkyeielqfveiynekvqDlL 149
                                        ++faygqTGsGKt+Tm+g+ ++ g i r++e i++ + e        e ++++ eiyne++ Dl+
  gene2236|gene2236|rna2236|rna2236  80 TVFAYGQTGSGKTHTMTGKPSDMGIIGRTLEDIYNSMDEA------AECYISYFEIYNENIIDLI 138
                                        **************************************99......67999************96 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.12
                                        TEEEE-SEEEECTTHCCCCCCCCHHHHHHHHTT--EEEE CS
                        Microtub_bd  49 kkefsFdrvfeseseqeevfeeisqlvqsaldgynvcif 87 
                                        +    F+ + +++ ++++ +e+i ql++  ++  +  i+
  gene2236|gene2236|rna2236|rna2236 347 SSAEDFTLMNPEKVKNKNSAEQIIQLQNKRIHSLESMII 385
                                        333333334444446666666666666666655555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (432 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       839  (0.0467957); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 2734.80
//
Query:       gene2237|gene2237|rna2237|rna2237  [L=389]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (389 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       741  (0.0413297); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2749.30
//
Query:       gene2238|gene2238|rna2238|rna2238  [L=153]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
      0.025   13.5   0.3      0.036   12.9   0.3    1.2  1  RAI16-like  Retinoic acid induced 16-like protein


Domain annotation for each model (and alignments):
>> RAI16-like  Retinoic acid induced 16-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.3     2e-06     0.036       8      51 ..      58      98 ..      51     101 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2e-06
                         RAI16-like  8 nkiletLctlgeadkpegvkkevlkfytkLlsklseplLphesv 51
                                       ++i   L+tl ++   +g+k ++  fyt L++k++++l++ ++v
  gene2238|gene2238|rna2238|rna2238 58 SEI---LTTLIKKILAKGMKIKMWLFYTLLIKKIRHDLMKTKNV 98
                                       444...56677889999***********************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1104  (0.0615762); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 981.20
//
Query:       gene2239|gene2239|rna2239|rna2239  [L=127]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.6e-48  162.2   7.8    5.2e-48  162.1   7.8    1.0  1  DUF5100   Domain of unknown function (DUF5100)
  ------ inclusion threshold ------
       0.21   11.6   2.1       0.72    9.9   0.4    2.6  3  HTH_45    Winged helix-turn-helix


Domain annotation for each model (and alignments):
>> DUF5100  Domain of unknown function (DUF5100)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  162.1   7.8   5.8e-52   5.2e-48       1     126 []       1     126 [.       1     126 [. 0.99

  Alignments for each domain:
  == domain 1  score: 162.1 bits;  conditional E-value: 5.8e-52
                            DUF5100   1 MsiesklekiekiLsikkdlenilesleslelileqkedeeeiflvPqeANfQLPnvFLrtkqlpecekfikskak 76 
                                        Ms+eskl+ki +iL+++++len++++les++l+l++++de+++f++P+eAN+QLPnvFLr+++l+ec++fikska+
  gene2239|gene2239|rna2239|rna2239   1 MSNESKLQKILHILNSSANLENYIDMLESIDLVLNVNDDEKDYFMCPEEANLQLPNVFLRQTKLLECKHFIKSKAN 76 
                                        9*************************************************************************** PP

                            DUF5100  77 kisveewneaidevldiLeeieleevefeeskkkipidqevleelvkkvl 126
                                        + ++e+++e+++e+ld+Le++el+e+ef+eskkk +id ++l+elvkk++
  gene2239|gene2239|rna2239|rna2239  77 NRIGEHFYENCREILDFLESVELQEPEFMESKKKPDIDVNLLRELVKKYI 126
                                        ************************************************96 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.4     8e-05      0.72      34      56 ..      18      43 ..       2      53 .. 0.79
   2 ?   -0.3   0.0      0.12   1.1e+03      42      72 ..      64      90 ..      48      95 .. 0.59
   3 ?   -0.6   0.0      0.15   1.3e+03      27      40 ..     113     126 ..      87     127 .] 0.61

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 8e-05
                             HTH_45 34 kllnkYLdmLvekgli...kkskekY 56
                                        +l++Y+dmL + +l+   +++++ Y
  gene2239|gene2239|rna2239|rna2239 18 ANLENYIDMLESIDLVlnvNDDEKDY 43
                                       6899***********87756677777 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.12
                             HTH_45 42 mLvekglikkskekYvlTekGlelleklkel 72
                                        L +k +ik + ++      G++++e+++e+
  gene2239|gene2239|rna2239|rna2239 64 LLECKHFIKSKANNR----IGEHFYENCREI 90
                                       566666665554442....255666666655 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.15
                             HTH_45  27 ykanLsykllnkYL 40 
                                         ++nL  +l++kY+
  gene2239|gene2239|rna2239|rna2239 113 IDVNLLRELVKKYI 126
                                        35677777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       779  (0.0434492); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.28s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 954.05
//
Query:       gene224|gene224|rna224|rna224  [L=490]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.8e-07   29.9   7.3    2.8e-07   29.9   7.3    3.1  2  APG9             Autophagy protein Apg9


Domain annotation for each model (and alignments):
>> APG9  Autophagy protein Apg9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   1.3     0.066   1.2e+03      40      58 ..      95     113 ..      41     163 .. 0.57
   2 !   29.9   7.3   1.6e-11   2.8e-07     246     356 ..     256     368 ..     235     468 .. 0.70

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.066
                           APG9  40 vfvvvfstfLllcvdyskl 58 
                                    + +v+f+t +   v+y + 
  gene224|gene224|rna224|rna224  95 LSMVLFITLFSITVNYLRT 113
                                    2233333333333333333 PP

  == domain 2  score: 29.9 bits;  conditional E-value: 1.6e-11
                           APG9 246 nlllaPfiviylllyfffryaeelkknpsslgsRrwsplAewklRefNELpHlfeaRlnrsyklAskYldqfpseklaii 325
                                     +l+aP++ + l++   +  +    ++ s++++ ++ pl+ + lR +  LpH++++ ++rs+k+A+++l+++ + + +++
  gene224|gene224|rna224|rna224 256 LALCAPIMCMLLFISRTVDMIR-TGSSLSHAFAYDYAPLSVVRLRRYGVLPHVYRTAVQRSRKHAQRMLRSYEHGVAHVL 334
                                    3466777666555555554444.5567788899*********************************************** PP

                           APG9 326 akfvafvagsiaavlvvlsll...deelllefei 356
                                    ak+v  v++++++vl+++ l     +  +l++ei
  gene224|gene224|rna224|rna224 335 AKCVLIVCSTVIFVLMLVLLKmfvYQRGILSLEI 368
                                    ***********99987754321234444445555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (490 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1414  (0.0788666); expected 358.6 (0.02)
Passed bias filter:                      653  (0.0364214); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.65u 0.29s 00:00:00.94 Elapsed: 00:00:00.45
# Mc/sec: 3240.57
//
Query:       gene2240|gene2240|rna2240|rna2240  [L=542]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.3e-31  109.7   2.8    5.5e-31  107.7   0.1    2.4  2  DEAD        DEAD/DEAH box helicase
    1.1e-24   87.0   0.2      2e-22   79.7   0.0    3.7  3  Helicase_C  Helicase conserved C-terminal domain
    3.5e-10   40.0   0.3    7.9e-10   38.8   0.3    1.6  1  DUF4217     Domain of unknown function (DUF4217)
    2.6e-07   30.8   1.2    4.8e-07   29.9   0.0    2.0  2  ResIII      Type III restriction enzyme, res subunit
     0.0099   15.2   0.1       0.83    8.9   0.0    2.7  2  SecA_DEAD   SecA DEAD-like domain
  ------ inclusion threshold ------
      0.063   13.3   0.0       0.14   12.1   0.0    1.6  1  Flavi_DEAD  Flavivirus DEAD domain


Domain annotation for each model (and alignments):
>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.7   0.1   1.9e-34   5.5e-31       1     174 [.      27     191 ..      27     193 .. 0.88
   2 ?    2.0   0.4     0.054   1.6e+02     108     155 ..     445     492 ..     383     502 .. 0.73

  Alignments for each domain:
  == domain 1  score: 107.7 bits;  conditional E-value: 1.9e-34
                                        -HHHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTS CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               DEAD   1 tdiQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidl 76 
                                        t+iQ  +i  +   +d++v+ +TG+GKTla+lip+++  ++ ++ ++  ali++PtreLa+q+ + l +++ +   
  gene2240|gene2240|rna2240|rna2240  27 TNIQTDVIRSFN--DDLIVESPTGTGKTLAYLIPIVDFYLK-NRPKRITALILVPTRELAQQVGSVLASLGVK--- 96 
                                        689999999998..9*********************88877.899999*******************999984... PP

                                        EEEEEETTSSHHHHHHHHHTTCSEEEEEHHHHHHHH........HCTSSH....CTTEEEEEEETHHHHHHTTTHH CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........xxxxxx....xxxxxxxxxxxxxxxxxxxxxx RF
                               DEAD  77 rvlliiggvaardqlskldngvdivvgtpgrlddll........stgkln....lsqvrflVlDEadrlldqgfsd 140
                                           +iigg++++ + +      +i+v+tpgr+ ++l        s+ +l+    l+++ flVlDEad+ll+ gf+ 
  gene2240|gene2240|rna2240|rna2240  97 -NTVIIGGTDEELNFE------EILVATPGRFNKILlnsrtvicSRTNLSlhtlLKKIDFLVLDEADKLLSLGFRS 165
                                        .4579***88855555......56**********888999999866666677889********************* PP

                                        HHHHHHHHSHHHCTTSTTTSEEEEEESSBSHHHH CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               DEAD 141 finrilnqlpqitcdgklqrqvivlSATlpkdvk 174
                                        ++ +i  q+       k  ++  ++SAT+++d+ 
  gene2240|gene2240|rna2240|rna2240 166 QLLSITGQI-------K-AKRNALFSATMNDDIA 191
                                        *********.......2.33589*******9886 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.054
                                        HHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCTT CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               DEAD 108 lddllstgklnlsqvrflVlDEadrlldqgfsdfinrilnqlpqitcd 155
                                        +dd  ++g ln ++++  V+D  d + +    + ++  ++++    c 
  gene2240|gene2240|rna2240|rna2240 445 IDDNQKEGLLNSENLQKSVFDDFDAMKKHLTDEILKLSVKAFVAHVCA 492
                                        34444788899***************9997777777777666555555 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.29   8.8e+02      41      65 ..      16      40 ..       4      47 .. 0.77
   2 ?    1.7   0.0      0.11   3.2e+02      10      74 ..      64     129 ..      51     149 .. 0.74
   3 !   79.7   0.0   6.6e-26     2e-22       2     110 ..     224     326 ..     223     327 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.29
                                       STEEEESTTSTHHHHHHHHHHHHTT CS
                         Helicase_C 41 ikvavlhgelpqnereeileqfnkg 65
                                        +  ++  ++p+n + +++++fn++
  gene2240|gene2240|rna2240|rna2240 16 ARLETISITTPTNIQTDVIRSFNDD 40
                                       6677788899************874 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.11
                                        HHHTTTTSEEEEEESSHHHHHHHHHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSS.EEEESG CS
                         Helicase_C  10 lkleeeggkilifvntidrlekvklllekkgikvavlhgelpqnereeileqfnkgesd.vLiatd 74 
                                        lk++ ++ ++li v+t++ +++v  +l + g+k +v+ g +  + + e +     g+++ +L+ ++
  gene2240|gene2240|rna2240|rna2240  64 LKNRPKRITALILVPTRELAQQVGSVLASLGVKNTVIIGGTDEELNFEEILVATPGRFNkILLNSR 129
                                        4777788888********888867776777888888888877776655444444777777777665 PP

  == domain 3  score: 79.7 bits;  conditional E-value: 6.6e-26
                                        HHHHHHHHHHHTTTTSEEEEEESSHHHHHH.HHHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGG CS
                         Helicase_C   2 kleallellkleeeggkilifvntidrlek.vklllekkgikvavlhgelpqnereeileqfnkgesdvLiatdva 76 
                                        kl++l++ +    +++k+++f  t+++++   +l++     ++a++hg+++q+er+++ e+f++    vL  td a
  gene2240|gene2240|rna2240|rna2240 224 KLKMLYDVI---MRNKKVICFFLTCNEVDYfYSLFTALGVKNIAKIHGKMKQEERNAVYENFKS----VLFGTDLA 292
                                        788899998...89**************76666665555799********************65....******** PP

                                        TSSSTSTTESEEEESSSSSSHHHHHHHHTTSSST CS
                         Helicase_C  77 erGidipkvnlVinfdlprnvtsyiqriGRtgRa 110
                                        +rGid+ +v++V++fd+p +++s+++r+GRtgR 
  gene2240|gene2240|rna2240|rna2240 293 SRGIDFLGVDVVVHFDIPLDPESFVHRSGRTGRN 326
                                        *********************************7 PP

>> DUF4217  Domain of unknown function (DUF4217)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.8   0.3   2.7e-13   7.9e-10      14      61 .]     477     524 ..     474     524 .. 0.96

  Alignments for each domain:
  == domain 1  score: 38.8 bits;  conditional E-value: 2.7e-13
                            DUF4217  14 dlkelAqkAfvsyvraYsvhlakeiFrvkkLdlealAksfGLleaPki 61 
                                        ++ +l++kAfv++v aY++h++++ +++k+L++++lAk   L ++Pk+
  gene2240|gene2240|rna2240|rna2240 477 EILKLSVKAFVAHVCAYKEHKLRFLLDFKELNFDSLAKLHFLMKIPKM 524
                                        6789*******************************************9 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.9   0.0   1.6e-10   4.8e-07      25     169 ..      39     186 ..      15     188 .. 0.80
   2 ?   -1.4   0.4      0.67     2e+03      85     109 ..     384     406 ..     327     460 .. 0.64

  Alignments for each domain:
  == domain 1  score: 29.9 bits;  conditional E-value: 1.6e-10
                                        SEEEEEESTTSTHHHHH.HHHHHHH-S......-EEEEESSHHHHHHHHHHGGGGTGG....GEEEESSS-B--.. CS
                             ResIII  25 krglikmaTGtGKTlva.aklierllkkgkee.kflflvprkslleqtleefkkflseaykeigkkvsgdkkkake 98 
                                          ++++ +TGtGKTl + + +++ +lk+++++  +l+lvp+++l +q  + ++++  +++  +    ++++     
  gene2240|gene2240|rna2240|rna2240  39 DDLIVESPTGTGKTLAYlIPIVDFYLKNRPKRiTALILVPTRELAQQVGSVLASLGVKNT--VIIGGTDEEL---- 108
                                        578999***********888999999988888999***************9999999875..3333333333.... PP

                                        .....-SEEEEEHHHHHHTH...............HHHTTT-SEEEEETGGGTTS....TTTHHHHHT---SEEEE CS
                             ResIII  99 kdstnkkilvttiqsldadseee.......eeeseellrdrfdviiiDEaHrlgak...kswreilekfkeavllg 164
                                           +  +ilv+t  ++++++ +        ++ s + l +++d+++ DEa +l +    ++  +i  ++k++    
  gene2240|gene2240|rna2240|rna2240 109 ---NFEEILVATPGRFNKILLNSrtvicsrTNLSLHTLLKKIDFLVLDEADKLLSLgfrSQLLSITGQIKAKRNAL 181
                                        ...4479************977799***9999******************99888533335555577777777777 PP

                                        EESS- CS
                             ResIII 165 lTATp 169
                                        ++AT+
  gene2240|gene2240|rna2240|rna2240 182 FSATM 186
                                        88876 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.67
                                        GEEEESSS-B--.......-SEEEE CS
                             ResIII  85 igkkvsgdkkkakekdstnkkilvt 109
                                        ++k+v+g+ +++  k++++ ++ ++
  gene2240|gene2240|rna2240|rna2240 384 ENKEVTGKLNNK--KKIDQQEMAIE 406
                                        333333333333..33333333333 PP

>> SecA_DEAD  SecA DEAD-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.0   0.00028      0.83      91     210 ..      39     159 ..      24     187 .. 0.76
   2 ?    3.0   0.0     0.018        53     132     182 ..     245     299 ..     238     308 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00028
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SecA_DEAD  91 egkiaemkTGEGKtlvatlpaylnaltgkgvhvvtvndYLakrdaewmgpvyeflGlsvgvieseleseerreaYe 166
                                        +  i+e  TG GKtl+  +p++   l++++  + +     ++  a+++g+v  +lG++  vi   +++e     + 
  gene2240|gene2240|rna2240|rna2240  39 DDLIVESPTGTGKTLAYLIPIVDFYLKNRPKRITALILVPTRELAQQVGSVLASLGVKNTVIIGGTDEELN---F- 110
                                        567999*********************999888777666666668999*********99999777665543...3. PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxx RF
                          SecA_DEAD 167 aditYgtnnelgfdyLrDnlalskeel.....vqrglnfaivDEvDsvL 210
                                         +i+ +t   +    L  + ++ +++      + ++++f ++DE+D +L
  gene2240|gene2240|rna2240|rna2240 111 EEILVATPGRFNKILLNSRTVICSRTNlslhtLLKKIDFLVLDEADKLL 159
                                        3677788888888888777544444333566566788888888888777 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.018
                                        xxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxx..xxxxxxxx.xxxxxxxx RF
                          SecA_DEAD 132 krdaewmgpvyeflGls.vgvieseleseerreaYe..aditYgtn.nelgfdyL 182
                                          + + + +++++lG++ +  i+ ++++eer+++Ye  + +++gt     g d+L
  gene2240|gene2240|rna2240|rna2240 245 CNEVDYFYSLFTALGVKnIAKIHGKMKQEERNAVYEnfKSVLFGTDlASRGIDFL 299
                                        5566777889999**9736889999**********94458999997234567776 PP

>> Flavi_DEAD  Flavivirus DEAD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   4.7e-05      0.14       9      60 ..      43      97 ..      38     128 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 4.7e-05
                                       EE--TTS-TTTTHHHHHHH...HHHHTT--EEEEESSHHHHHHHHHHTTTS-EEE CS
                         Flavi_DEAD  9 ldlhPGaGktrkvlpelvk...eaierrlrtlvLaPtrvvlaemeealkglevry 60
                                       ++   G+Gkt  +l  +v+   ++  +r+ +l+L+Ptr  ++ +   l+ l v+ 
  gene2240|gene2240|rna2240|rna2240 43 VESPTGTGKTLAYLIPIVDfylKNRPKRITALILVPTRELAQQVGSVLASLGVKN 97
                                       666679*******999997333566678899*************99999998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (542 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       865  (0.0482459); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.58u 0.26s 00:00:00.84 Elapsed: 00:00:00.51
# Mc/sec: 3208.96
//
Query:       gene2241|gene2241|rna2241|rna2241  [L=143]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.9e-17   64.1   0.2    2.6e-17   63.7   0.2    1.2  1  Ribosomal_L27A  Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27
  ------ inclusion threshold ------
       0.11   12.5   0.4       0.29   11.2   0.6    1.5  2  DUF5026         Domain of unknown function (DUF5026)


Domain annotation for each model (and alignments):
>> Ribosomal_L27A  Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.7   0.2   2.9e-21   2.6e-17       3     127 ..      28     140 ..      26     141 .. 0.86

  Alignments for each domain:
  == domain 1  score: 63.7 bits;  conditional E-value: 2.9e-21
                                        GGTSSTTTTTTTTT-..S--........S--.........---..GGG...---EEEEHHHHHHTTTTGTTS---- CS
                     Ribosomal_L27A   3 ktgGrGhkGqkkrsg..vkk.kpg.feGGqmplyrrlpkrGfk..nsk.fkkeykvvnlkdLdelideerlelade 71 
                                        ++gGrG+ G  ++++  ++k +p+ f  G+          G+k  ++k ++ + ++ n +dL  li ++++ + ++
  gene2241|gene2241|rna2241|rna2241  28 HPGGRGKCGGLTHHKtlFQKyHPDyF--GKR---------GIKifHRKtQALRFNITNTGDLFALIRHNEFVE-GQ 91 
                                        78********999999*999999988..999.........88855333134455****************965.59 PP

                                        --EEEGGGTTTTSSS....SE.EEE--S--..-.--EEEESEE-HHHHHHHHHTT-EEE CS
                     Ribosomal_L27A  72 aeeidleelaeaglikkkdgv.Kvlgkgel..tkklkvkaskfSkkAkekIeaaGGkve 127
                                        a+ id++++          g+ Kvlg+gel  +++l+v a++f+++Ak kIea+GG+v+
  gene2241|gene2241|rna2241|rna2241  92 APIIDCRAH----------GIhKVLGRGELslKQPLIVIAKQFTEEAKRKIEAVGGRVI 140
                                        *********..........*********6632677**********************97 PP

>> DUF5026  Domain of unknown function (DUF5026)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.6   3.2e-05      0.29      15      51 ..      15      51 ..       7      56 .. 0.87
   2 ?   -3.0   0.0      0.89     8e+03      23      33 ..      82      92 ..      69      97 .. 0.54

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 3.2e-05
                            DUF5026 15 ikkGdlvyakhrswpeGkaGfvtavtekelivqyhpG 51
                                       + +G+   +khr  p G++     + +k l  +yhp 
  gene2241|gene2241|rna2241|rna2241 15 VSHGHGRVGKHRKHPGGRGKCGGLTHHKTLFQKYHPD 51
                                       567777789*********999998999********95 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 0.89
                            DUF5026 23 akhrswpeGka 33
                                        +h  + eG+a
  gene2241|gene2241|rna2241|rna2241 82 IRHNEFVEGQA 92
                                       35555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       307  (0.0171231); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.47
# Mc/sec: 919.19
//
Query:       gene2242|gene2242|rna2242|rna2242  [L=773]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-15   57.2   0.3    1.3e-14   54.5   0.0    2.5  2  Helicase_C       Helicase conserved C-terminal domain
    1.3e-07   31.5   1.2    6.4e-07   29.3   1.2    2.0  1  DEAD             DEAD/DEAH box helicase
    1.8e-07   31.5   0.2    7.5e-07   29.5   0.1    2.1  2  AAA_22           AAA domain
    8.7e-06   26.0   0.3    6.7e-05   23.1   0.0    2.4  2  HA2              Helicase associated domain (HA2)
    9.4e-05   22.8   0.0    0.00027   21.3   0.0    1.7  1  AAA_19           AAA domain
     0.0025   17.9   4.9     0.0028   17.7   0.0    3.3  3  ResIII           Type III restriction enzyme, res subunit
     0.0043   17.2   0.0      0.016   15.3   0.0    2.0  1  AAA_33           AAA domain
     0.0057   16.6   0.7        1.1    9.2   0.0    2.8  2  RsgA_GTPase      RsgA GTPase
     0.0094   16.0   0.6      0.064   13.3   0.2    2.6  2  AAA_14           AAA domain
  ------ inclusion threshold ------
      0.017   15.1   0.0      0.037   14.0   0.0    1.5  1  Flavi_DEAD       Flavivirus DEAD domain
      0.034   14.5   0.0      0.083   13.3   0.0    1.7  1  OB_NTP_bind      Oligonucleotide/oligosaccharide-binding (OB)
      0.046   14.1   0.2       0.19   12.2   0.2    2.1  1  AAA              ATPase family associated with various cellul
      0.049   13.8   0.2       0.14   12.3   0.2    1.8  1  MukF_C           MukF C-terminal domain
       0.05   13.3   0.0      0.097   12.4   0.0    1.5  1  AAA_24           AAA domain
       0.05   13.4   0.0       0.25   11.1   0.0    2.1  2  AAA_29           P-loop containing region of AAA domain
      0.051   14.1   3.2       0.12   12.9   0.6    2.9  2  ABC_tran         ABC transporter
      0.074   12.6   0.0        0.2   11.1   0.0    1.7  1  AAA_7            P-loop containing dynein motor region
       0.13   12.0   0.8          5    6.8   0.0    2.8  3  Sigma54_activat  Sigma-54 interaction domain
       0.51    9.4   4.7          3    6.9   0.0    2.4  2  DUF815           Protein of unknown function (DUF815)
       0.56   10.1   5.5       0.12   12.3   1.4    2.1  1  Rad17            Rad17 P-loop domain
       0.59   10.6   0.0       0.59   10.6   0.0    3.8  4  AAA_23           AAA domain


Domain annotation for each model (and alignments):
>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.5   0.0   1.5e-17   1.3e-14       4     111 .]     377     496 ..     373     496 .. 0.87
   2 ?   -1.1   0.1       2.8   2.4e+03      51      76 ..     607     633 ..     568     659 .. 0.69

  Alignments for each domain:
  == domain 1  score: 54.5 bits;  conditional E-value: 1.5e-17
                                        HHHHHHHHHTTTTSEEEEEESSHHHHHH.HHHHHHHT....TSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESG CS
                         Helicase_C   4 eallellkleeeggkilifvntidrlek.vklllekk....gikvavlhgelpqnereeileqfnkgesdvLiatd 74 
                                        ++++e++  ++++g il+f+++++++++ ++ l   k    +i+ ++lh++lp ++++ i ++     +++++at+
  gene2242|gene2242|rna2242|rna2242 377 DRVVEIV--NKKEGSILVFLTSKTQIYSlIRSL---KgisdQIELIPLHASLPLKNQQMIYSNK----RKCVLATN 443
                                        5566665..899**************9554444...345579******************9887....459***** PP

                                        GGTSSSTSTTESEEEESSSSSSH................HHHHHHHTTSSSTT CS
                         Helicase_C  75 vaerGidipkvnlVinfdlprnv................tsyiqriGRtgRag 111
                                         ae+G++ip++++Vi++++ +n                 +s+ qr+GR+gR g
  gene2242|gene2242|rna2242|rna2242 444 YAETGLTIPGIKYVIDCGYEKNCvsngtlrsypvvpisrASAEQRKGRAGRTG 496
                                        ********************996689999999*******************86 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 2.8
                                        THHHHHHHHHHHH.TTSSSEEEESGGG CS
                         Helicase_C  51 pqnereeileqfn.kgesdvLiatdva 76 
                                          + r+e +e f  +++sd+Li  +++
  gene2242|gene2242|rna2242|rna2242 607 DIEIRREDFEHFYqNETSDLLIKAKII 633
                                        556777778888734444477766654 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.3   1.2   7.5e-10   6.4e-07       5     174 ..     166     313 ..     163     315 .. 0.81

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 7.5e-10
                                        HHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEE CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               DEAD   5 aeaiplilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvll 80 
                                        +e+i li ++  vl+ + TG GK++     +l    e   ++ + +l+  P r  +  + ++++  +++   +v  
  gene2242|gene2242|rna2242|rna2242 166 DEIISLIREKSVVLIIGSTGCGKSTQVPQMLL----E---NNFKGILMTQPRRISCVSISERINYETNE---QV-- 229
                                        5889999999*************998666666....3...45556999***********9999888884...22.. PP

                                        EETTSSHHHHHHHHHTTCSEEEEEHHHHHH.HHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCTT CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               DEAD  81 iiggvaardqlskldngvdivvgtpgrldd.llstgklnlsqvrflVlDEadrlldqgfsdfinrilnqlpqitcd 155
                                             + r + ++   +++i v t g l++ ++++    ls+++++++DE+++l  +   + +  +l++l qi +d
  gene2242|gene2242|rna2242|rna2242 230 --AAYRFRFNNNVT-PTTRIQVVTDGILLNeMIKDAM--LSKFNVIIVDEVHELTIN--LEILLPLLSRLVQIRKD 298
                                        ..334455555555.779************6667666..*****************9..77888889999999999 PP

                                        STTTSEEEEEESSBSHHHH CS
                                        xxxxxxxxxxxxxxxxxxx RF
                               DEAD 156 gklqrqvivlSATlpkdvk 174
                                         k    +i++SAT+++++ 
  gene2242|gene2242|rna2242|rna2242 299 LK----IILMSATPNDKIA 313
                                        88....********97765 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       5.1   4.3e+03      43     102 ..      54     111 ..      38     122 .. 0.67
   2 !   29.5   0.1   8.8e-10   7.5e-07       4     128 ..     174     304 ..     171     311 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 5.1
                             AAA_22  43 vfvtlpsst.sskdllrellralglelkaerlsseellealeqalraravielliiDEaqh 102
                                         + +++ +  + +  + +++r+ + +  + +  ++++ e+ ++ lr++++  l  ++E+qh
  gene2242|gene2242|rna2242|rna2242  54 NKADCSDKQgKKRRDYDKFVRDKNPKDGN-TYVKKHFCEKGQETLRSKDD--LEQLEEFQH 111
                                        46677777756666677777777744444.77777777777777777777..666666666 PP

  == domain 2  score: 29.5 bits;  conditional E-value: 8.8e-10
                             AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelka......... 70 
                                        ++++++++G +G+GK+t + ++l ++         + + +++t p   s  ++ +++  +++++  a         
  gene2242|gene2242|rna2242|rna2242 174 EKSVVLIIGSTGCGKSTQVPQMLLEN---------NFKGILMTQPRRISCVSISERINYETNEQVAAyrfrfnnnv 240
                                        7899***************9999999.........88888888888888888888888888887777888888888 PP

                             AAA_22  71 ......erlsseell.ealeqalraravielliiDEaqhlr.seealeeL.rsllnlsrkgvqliLv 128
                                              +  +   ll e++ +a+ +++   ++i+DE++ l+ + e+l  L ++l+   rk++++iL+
  gene2242|gene2242|rna2242|rna2242 241 tpttriQVVTDGILLnEMIKDAMLSKFN--VIIVDEVHELTiNLEILLPLlSRLVQ-IRKDLKIILM 304
                                        8777788888888998999999999999..**********6556666666244444.799****997 PP

>> HA2  Helicase associated domain (HA2)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.2       1.4   1.2e+03      52      87 ..      33      68 ..       7     106 .. 0.70
   2 !   23.1   0.0   7.8e-08   6.7e-05       3      78 ..     556     641 ..     554     678 .. 0.65

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 1.4
                                HA2 52 itivAalsveeifleeneeekeeeeeeeekakkkrk 87
                                       ++ +++   ++i+ +en++++++++ ++++ kk+r+
  gene2242|gene2242|rna2242|rna2242 33 ASTACCPPEQNILRNENSKRSNKADCSDKQGKKRRD 68
                                       455566666777877777666655432222222222 PP

  == domain 2  score: 23.1 bits;  conditional E-value: 7.8e-08
                                HA2   3 elLvalgALdeegnlTelGrkmaelPlsprlakmLlaaaeleegcldevitivAalsveeifleeneeekeeeee. 77 
                                        + L ++gA++ + ++T+lGr ++++P +prl+ +Ll         ++e+  i+++l  +  + +e++e+  ++e+ 
  gene2242|gene2242|rna2242|rna2242 556 KVLERIGAVK-NLKITKLGRLIVKYPFEPRLSVILLKY--D----FNEIKLIISILDSDIEIRREDFEHFYQNETs 624
                                        7899*****6.7**********************9988..4....5788888888884444444444333333335 PP

                                HA2  78 ................e 78 
                                                        +
  gene2242|gene2242|rna2242|rna2242 625 dllikakiilfcrdlnD 641
                                        56666655555544431 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0   3.2e-07   0.00027       4     126 ..     168     293 ..     165     303 .. 0.69

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 3.2e-07
                             AAA_19   4 ave.alkekvllvtaGpGtGKTrvlkhiv..allvelggvkpeeillvaftgrAakelrerlaalgae.....atT 71 
                                        +++   +++v+l+++  G+GK++ + +++  + ++ +   +p++i +v+  +r   e +e++aa+  +     + T
  gene2242|gene2242|rna2242|rna2242 168 IISlIREKSVVLIIGSTGCGKSTQVPQMLleNNFKGILMTQPRRISCVSISERINYETNEQVAAYRFRfnnnvTPT 243
                                        565567899************988877653345778888999******************9977776677764333 PP

                             AAA_19  72 iHrlalldfddlltealelleeaeeekklqeee.llivDEfqdvd...elqyrLlkall 126
                                          r+  + +d++l      l+e  ++  l +++ ++ivDE+ +++   e    Ll++l+
  gene2242|gene2242|rna2242|rna2242 244 T-RI-QVVTDGIL------LNEMIKDAML-SKFnVIIVDEVHELTinlEILLPLLSRLV 293
                                        3.34.23344444......4444456777.6666********99841223344555555 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   3.3e-06    0.0028     121     170 ..     247     309 ..     145     310 .. 0.69
   2 ?   -1.6   1.4       2.8   2.4e+03      94      94 ..     685     685 ..     609     737 .. 0.50
   3 ?   -1.2   0.2         2   1.7e+03      50      75 ..     698     734 ..     679     759 .. 0.67

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 3.3e-06
                                        ..............HHHTTT-SEEEEETGGGTTS......TTTHHHHHT---SEEEEEESS-S CS
                             ResIII 121 e........eeeseellrdrfdviiiDEaHrlgak.....kswreilekfkeavllglTATpe 170
                                        +        +e+ +++  ++f+vii+DE+H l+ +         ++++  k+ +++ ++ATp+
  gene2242|gene2242|rna2242|rna2242 247 QvvtdgillNEMIKDAMLSKFNVIIVDEVHELTINleillPLLSRLVQIRKDLKIILMSATPN 309
                                        0223333336668889999***************86555437777778888899********7 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2.8
                                        B CS
                             ResIII  94 k 94 
                                         
  gene2242|gene2242|rna2242|rna2242 685 L 685
                                        0 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 2
                                        S.....-EEEEESSHHHHHHHHHHG.............G CS
                             ResIII  50 kkgkeekflflvprkslleqtleef.............k 75 
                                        +  k+ k+lf+    +l+ +  +e+             k
  gene2242|gene2242|rna2242|rna2242 698 N--KIAKILFVTYHDHLCRRIHDEYyfngkqvhidrnsK 734
                                        2..234899999999999999888855554444443333 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   1.9e-05     0.016       1      75 [.     177     271 ..     177     278 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.9e-05
                             AAA_33   1 lvllvGlpGsGKstlaerllkklg..avllssdt....................lrrrlfgtdqqsktdytrvldr 54 
                                        +vl++G  G+GKst + ++l ++   ++l +++                     ++r  f++ ++++t+ + v+d 
  gene2242|gene2242|rna2242|rna2242 177 VVLIIGSTGCGKSTQVPQMLLENNfkGILMTQPRriscvsiserinyetneqvaAYRFRFNNNVTPTTRIQVVTDG 252
                                        89****************98777789********888888777777777777763333333444444333334444 PP

                             AAA_33  55 lyqilnelarkalsagrnvil 75 
                                        +   lne++++a+ +++nvi+
  gene2242|gene2242|rna2242|rna2242 253 IL--LNEMIKDAMLSKFNVII 271
                                        44..78999999999999776 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.0    0.0013       1.1      91     120 ..     166     196 ..     152     227 .. 0.83
   2 ?    4.8   0.0     0.028        24      26      69 ..     516     558 ..     512     573 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0013
                                        HHHHHHCTT.SEEEEECSTTSSHHHHHHHHC CS
                        RsgA_GTPase  91 eelkellkd.ktsvlvGqSGvGKStLinall 120
                                        +e+ +l+++ ++++++G++G GKSt + ++l
  gene2242|gene2242|rna2242|rna2242 166 DEIISLIREkSVVLIIGSTGCGKSTQVPQML 196
                                        5677778875777889*********886665 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.028
                                        TTTT--HHHHHHHHHHHHHTT-EEEEEEE-GGG--HHHHHHHHH CS
                        RsgA_GTPase  26 kepelslnlldrfLvlaeekgiepvivlnKiDlleeeeeleelk 69 
                                        ++p++++n ld fL+++ + +++  + +n+ D  + e+  +++ 
  gene2242|gene2242|rna2242|rna2242 516 NTPQVESNSLDHFLLVLFHFKVKHNVFINRPDNEKLER-SRKVL 558
                                        6899**************************99877666.33333 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.2   7.5e-05     0.064       3      98 ..     176     304 ..     174     318 .. 0.65
   2 ?   -2.2   0.0       4.6   3.9e+03      85     126 ..     381     420 ..     367     422 .. 0.55

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 7.5e-05
                             AAA_14   3 kilvitGaRrvGKTtllkqlikell......vkkesilyinldderd.............kkladpe......... 50 
                                         +++i G   +GK+t + q++ e+       +++++i  +++ +  +                   +         
  gene2242|gene2242|rna2242|rna2242 176 SVVLIIGSTGCGKSTQVPQMLLENNfkgilmTQPRRISCVSISERINyetneqvaayrfrF-----Nnnvtpttri 246
                                        689**************99877777799999888888888877766633333333322220.....1223333333 PP

                             AAA_14  51 kllelileklke................ekktylflDEiqev....pewekalkslvdegknldvivt 98 
                                        +                           +k ++++ DE++e+    + +   l +lv+ +k+l++i+ 
  gene2242|gene2242|rna2242|rna2242 247 Q----------VvtdgillnemikdamlSKFNVIIVDEVHELtinlEILLPLLSRLVQIRKDLKIILM 304
                                        1..........0333444444555577778999*******9865556666677777776677777765 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 4.6
                             AAA_14  85 slvdegknldviv.tGSnskllskeiatslagrvaeielypls 126
                                        ++v+++ ++ ++v   S+ ++    +  sl g  ++iel pl 
  gene2242|gene2242|rna2242|rna2242 381 EIVNKK-EGSILVfLTSKTQIY--SLIRSLKGISDQIELIPLH 420
                                        444444.333333033333333..3567888889999988885 PP

>> Flavi_DEAD  Flavivirus DEAD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   4.3e-05     0.037      13     137 ..     184     309 ..     172     318 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.3e-05
                                        TTS-TTTTHHHHHHHHHHHTT--EEEEESSH...HHHHHHHHHTTTS-EEE-------------SEEEEEHHHHHH CS
                         Flavi_DEAD  13 PGaGktrkvlpelvkeaierrlrtlvLaPtr...vvlaemeealkglevryktsavkeektgrelvdvmchatftk 85 
                                         G Gk  +v   l++++++  l t    P r   v ++e  +  ++ +v   +  ++++ t +  ++v+    + +
  gene2242|gene2242|rna2242|rna2242 184 TGCGKSTQVPQMLLENNFKGILMT---QPRRiscVSISERINYETNEQVAAYRFRFNNNVTPTTRIQVVTDGILLN 256
                                        577777766555555555554444...45551114444544555577888888888899999999*********** PP

                                        HHHHT------SEEEEETTT--SHHHHHHHHHHHHHHH.TTS-EEEEEESS-T CS
                         Flavi_DEAD  86 rllspvrkknyeliimDeahflDPasiaarGyletkae.egeaalilltatPP 137
                                         +++++   ++++ii+De h l  +       l+++++ +++ ++il++atP 
  gene2242|gene2242|rna2242|rna2242 257 EMIKDAMLSKFNVIIVDEVHELTINLEILLPLLSRLVQiRKDLKIILMSATPN 309
                                        ********************8887766667777777762467899******96 PP

>> OB_NTP_bind  Oligonucleotide/oligosaccharide-binding (OB)-fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   9.7e-05     0.083      32      76 ..     727     766 ..     700     768 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 9.7e-05
                                        EEE-TTSTTTTT...TSSSEEEEEEEEESSS.EEEEEEEEE-HHHH CS
                        OB_NTP_bind  32 vfihpsSvlaknekekepewvvytelvettk.lylrdltaidpawL 76 
                                        v+i  +S      k+  +e++v+++l e +  ly+ ++t++d++wL
  gene2242|gene2242|rna2242|rna2242 727 VHIDRNS------KDVISEYFVFQYLTERNGkLYAVNVTDVDKEWL 766
                                        4444444......335589********99766*************9 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.2   0.00022      0.19       1     111 [.     178     307 ..     178     323 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00022
                                        EEEESSTTSSHHHHHHHHHHHHT......HEEEEEETTTCSSS..........................STTHHHH CS
                                AAA   1 vllyGppGtGKTllakavakelg......vefleisgsellsk..........................yvgesek 44 
                                        vl++G  G+GK++ + ++  e +      ++  +is+ ++ +                            v     
  gene2242|gene2242|rna2242|rna2242 178 VLIIGSTGCGKSTQVPQMLLENNfkgilmTQPRRISCVSISERinyetneqvaayrfrfnnnvtpttriQVVTDGI 253
                                        799************9999996522233244566666666644777888999999999999999999877777778 PP

                                        HHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESS CS
                                AAA  45 kirelfkeakekakpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvivigatnr 111
                                         ++e++k+a  ++   ++++DE+++l+ +             + Ll+ l+++ + ++++ +i+++ +
  gene2242|gene2242|rna2242|rna2242 254 LLNEMIKDAMLSK-FNVIIVDEVHELTINL------------EILLPLLSRLVQIRKDLKIILMSAT 307
                                        9999999987665.79**********6554............4444444444444444555555555 PP

>> MukF_C  MukF C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.2   0.00016      0.14      22      85 ..     638     701 ..     634     728 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00016
                                        HHHHGGGS-EEEEEE----EEE--XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             MukF_C  22 sikdyfdepwlltvadaerlldlrdeelalrdeevtGelPeeleyeeleeieeqlaerieeala 85 
                                         ++dy +++++ ++  ++ + ++r e  a + ++  G++ + ley++l+e + +++e +e+++a
  gene2242|gene2242|rna2242|rna2242 638 DLNDYRENNHKERLNTNKNMFEMRKEVSANKTSNLRGKVKDLLEYDNLKEKKFNFTEDVENKIA 701
                                        5789*********************************************988888887777665 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00011     0.097       3      77 ..     176     278 ..     174     283 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00011
                             AAA_24   3 lkiliyGpsgiGKTtlakelgpkplfidtekGlksldadkfpdie...........swedfldevvel........ 59 
                                          +li+G+ g GK+t++ ++    l+ + +kG   ++++++ +++           +          +        
  gene2242|gene2242|rna2242|rna2242 176 SVVLIIGSTGCGKSTQVPQM----LLENNFKGILMTQPRRISCVSiserinyetneQ----------Vaayrfrfn 237
                                        5799************9999....9999999**********9998655554433331..........255556666 PP

                             AAA_24  60 .......................aaeladyktlviDtidel 77 
                                                               +a l++++++++D + el
  gene2242|gene2242|rna2242|rna2242 238 nnvtpttriqvvtdgillnemikDAMLSKFNVIIVDEVHEL 278
                                        7788888889999999999***9999**********99887 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0    0.0003      0.25      20      38 ..     172     191 ..     162     197 .. 0.77
   2 ?   -1.4   0.0       2.4     2e+03       6      23 ..     716     733 ..     714     737 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0003
                             AAA_29  20 dlkg.atlltGpsGsGKSTl 38 
                                         ++  ++l++G +G GKST 
  gene2242|gene2242|rna2242|rna2242 172 IREKsVVLIIGSTGCGKSTQ 191
                                        344449*************5 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2.4
                             AAA_29   6 lvNWgtfdghtieidlkg 23 
                                        + + ++f+g++++id+++
  gene2242|gene2242|rna2242|rna2242 716 IHDEYYFNGKQVHIDRNS 733
                                        567899********9765 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.1         4   3.4e+03      71     102 ..     115     169 ..      71     171 .. 0.60
   2 ?   12.9   0.6   0.00014      0.12       8      33 ..     172     197 ..     166     277 .. 0.70

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 4
                                        -TTSBHHHH.......................HHHTCHHHHHHHSTTGGTTCBGE CS
                                        xxxxxxxxx.......................xxxxxxxxxxxxxxxxxxxxxxx RF
                           ABC_tran  71 fpeltvren.......................esdeeiekalsklglkelkdtvv 102
                                        +++++ +en                       +++e+++++++kl +++ +d+++
  gene2242|gene2242|rna2242|rna2242 115 DNGSQYGENgtkssnevaeekdkaqiyggfcyNRREKVKRMREKLPIVYQEDEII 169
                                        3333344445555555555566666667776666666888888888888777665 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 0.00014
                                        EETTSEEEEEESTTSSHHHHHHHHTT CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ABC_tran   8 lkegekvaivGenGaGKStLlkllag 33 
                                        ++e ++v i+G++G+GKSt +  ++ 
  gene2242|gene2242|rna2242|rna2242 172 IREKSVVLIIGSTGCGKSTQVPQMLL 197
                                        678999*************7765554 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00024       0.2      29      56 ..     171     198 ..     166     222 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00024
                              AAA_7  29 llknkkpvllvGptGtGKtviikdllkk 56 
                                        l+++k  vl++G+tG+GK++ + ++l +
  gene2242|gene2242|rna2242|rna2242 171 LIREKSVVLIIGSTGCGKSTQVPQMLLE 198
                                        7899999*************99995543 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.1      0.14   1.2e+02     145     165 ..      13      33 ..       3      35 .. 0.76
   2 ?    6.8   0.0    0.0059         5      15      39 ..     168     192 ..     155     219 .. 0.82
   3 ?   -3.0   0.1       6.2   5.3e+03      96     110 ..     269     283 ..     266     291 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.14
                                        HHHHHHTTSS-HHHHHHHTSE CS
                    Sigma54_activat 145 leeaveegkfredLyyrlnvi 165
                                         e++ +++ +r+dLy r+n+ 
  gene2242|gene2242|rna2242|rna2242  13 YEDKRRKDALRSDLYKRINMA 33 
                                        455667889*********986 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0059
                                        HHHHCTSSS-EEEECSTTSSHHHHH CS
                    Sigma54_activat  15 ikkvaktdlsvlitGesGtGKella 39 
                                        i ++++ ++ vli G +G+GK++  
  gene2242|gene2242|rna2242|rna2242 168 IISLIREKSVVLIIGSTGCGKSTQV 192
                                        5567788999***********9755 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 6.2
                                        EEEEETGGGS-HHHH CS
                    Sigma54_activat  96 tlfLDeigelplelQ 110
                                        ++ +De++el+++l 
  gene2242|gene2242|rna2242|rna2242 269 VIIVDEVHELTINLE 283
                                        6789******99874 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.0    0.0035         3      55      83 ..     177     205 ..     165     224 .. 0.84
   2 ?    0.6   3.9      0.31   2.6e+02      85     181 ..     608     701 ..     605     703 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0035
                             DUF815  55 nvLLwGarGtGKSslvkallneyaeegLr 83 
                                         vL++G+ G+GKS+ v  +l e + +g+ 
  gene2242|gene2242|rna2242|rna2242 177 VVLIIGSTGCGKSTQVPQMLLENNFKGIL 205
                                        589*************9999888777755 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.31
                             DUF815  85 ievekedlkelpklvellrerperfilfvDDLsFeeeeeeyksLksvLeGsleakpenvliyaTsNrRhLlpekls 160
                                        ie+++ed +++ +  +     + ++ilf+ DL   +e+++   L +  + ++ +  ++v    TsN R  +++ l+
  gene2242|gene2242|rna2242|rna2242 608 IEIRREDFEHFYQNETSDLLIKAKIILFCRDLNDYRENNHKERLNT--NKNMFEMRKEVSANKTSNLRGKVKDLLE 681
                                        678888887776655555557899********97777777777776..5667888899**********99998765 PP

                             DUF815 161 dneeleeeeihaseaveekls 181
                                          ++l+e++ + +e ve+k++
  gene2242|gene2242|rna2242|rna2242 682 Y-DNLKEKKFNFTEDVENKIA 701
                                        4.4457999999999999986 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   1.4   0.00014      0.12      27     171 ..     158     304 ..     133     317 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00014
                              Rad17  27 kieevkewlkadvLesrkkriLLisGPsGCgkstvvkvLskelgiklr.....ewlnpvslkepdnqksdfkglte 97 
                                        k+  v +  +  +L ++ k ++Li G +GCgkst v  +  e  +k +       +  vs+ e  n +++ +    
  gene2242|gene2242|rna2242|rna2242 158 KLPIVYQEDEIISLIRE-KSVVLIIGSTGCGKSTQVPQMLLENNFKGIlmtqpRRISCVSISERINYETNEQVAAY 232
                                        55555555555566655.7899************996654443333220001134555666665555555544444 PP

                              Rad17  98 kesrflsqiesfkeleLkdakylklqklGddlrtdkklilvedlPnkfyrdsdalrevirkylrssealplilv 171
                                         +  f   +   + +++     l  ++  d + ++ ++i+v+++  +  ++++ l  ++ + +++++ l +il+
  gene2242|gene2242|rna2242|rna2242 233 RFR-FNNNVTPTTRIQVVTDGILLNEMIKDAMLSKFNVIIVDEVH-ELTINLEILLPLLSRLVQIRKDLKIILM 304
                                        443.65555555555554444444445556666777778887774.5677777788888888888887777665 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   4.7       2.9   2.5e+03      94     165 ..      46     116 ..       5     159 .. 0.67
   2 ?   10.6   0.0   0.00069      0.59      12      34 ..     166     190 ..     160     192 .. 0.84
   3 ?   -1.3   0.1       3.1   2.6e+03     154     170 ..     362     378 ..     210     429 .. 0.56
   4 ?   -1.1   4.3       2.6   2.3e+03     115     194 ..     613     702 ..     535     706 .. 0.55

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 2.9
                             AAA_23  94 relskkkgkttkkaklelleideleqfisellgskkiilnlilflgqerfeefelkdkkerleelekeleel 165
                                        r++++k +++ + +++++ + ++ ++f++++  ++ +      f+ ++++  ++ kd++e+lee++  ++++
  gene2242|gene2242|rna2242|rna2242  46 RNENSKRSNKADCSDKQGKKRRDYDKFVRDKNPKDGNTYVKKHFCEKGQE-TLRSKDDLEQLEEFQHPINDN 116
                                        44455555555666777777788888888877777776644445555553.345577788888888777765 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00069
                             AAA_23  12 dqeidF..skgltlItGpNGaGKTT 34 
                                        d+ i +  +k ++lI+G +G+GK+T
  gene2242|gene2242|rna2242|rna2242 166 DEIISLirEKSVVLIIGSTGCGKST 190
                                        45578888999*************9 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 3.1
                             AAA_23 154 rleelekeleeledekk 170
                                         l+ +++ ++e e +++
  gene2242|gene2242|rna2242|rna2242 362 HLNLYNRIKNETEIIDR 378
                                        22222222222222222 PP

  == domain 4  score: -1.1 bits;  conditional E-value: 2.6
                             AAA_23 115 deleqfisellgskkiilnlilflgqer.....feefelkdkkerleelekel......eeledekkllekleqek 179
                                        ++ e f +++ +   i  ++ilf+ + +     +++ e+ ++++ + e++ke       +   ++k+lle  + ++
  gene2242|gene2242|rna2242|rna2242 613 EDFEHFYQNETSDLLIKAKIILFCRDLNdyrenNHK-ERLNTNKNMFEMRKEVsanktsNLRGKVKDLLEYDNLKE 687
                                        333333333333334455566666555556554222.222233333333333211000022223333444444444 PP

                             AAA_23 180 ekekeleeleeelee 194
                                        +k +  e++e+++ +
  gene2242|gene2242|rna2242|rna2242 688 KKFNFTEDVENKIAK 702
                                        444444455555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (773 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1073  (0.0598472); expected 358.6 (0.02)
Passed bias filter:                      470  (0.0262145); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.75u 0.32s 00:00:01.07 Elapsed: 00:00:00.50
# Mc/sec: 4673.46
//
Query:       gene2243|gene2243|rna2243|rna2243  [L=922]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-19   70.7   5.2    1.3e-19   70.5   0.1    2.7  2  E1-E2_ATPase     E1-E2 ATPase
    7.5e-19   68.8   0.0    8.9e-10   39.2   0.0    2.6  2  Hydrolase        haloacid dehalogenase-like hydrolase
    6.4e-09   35.8  11.4    4.1e-06   26.6  11.0    3.4  4  Cation_ATPase_C  Cation transporting ATPase, C-terminus
    0.00017   21.4   0.1      0.013   15.2   0.1    2.8  2  Hydrolase_3      haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
        1.1    9.2   3.7          5    7.0   2.8    2.2  2  Tnp_DNA_bind     Transposase DNA-binding


Domain annotation for each model (and alignments):
>> E1-E2_ATPase  E1-E2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.5   0.1   3.5e-23   1.3e-19      18     181 .]     112     336 ..      81     336 .. 0.89
   2 ?    0.5   1.8       0.1   3.6e+02     124     163 ..     866     913 ..     833     914 .. 0.78

  Alignments for each domain:
  == domain 1  score: 70.5 bits;  conditional E-value: 3.5e-23
                                        EEGGG--TTSEEEEETT-B--SEEEEEEE-S.......EEE-TTTS---S-EE-...................... CS
                       E1-E2_ATPase  18 idakelvpGDivllkagdrvpaDgrivegsa.......evdesaLTGEslpvek...................... 64 
                                        + ++e+ +GDi+ l  gd++p D++++++s+       +v+es+LTGEs  v k                      
  gene2243|gene2243|rna2243|rna2243 112 VLTDEIGIGDIIHLSIGDKIPSDCILIDQSTfkttrflKVNESILTGESIGVIKkrskitledaflfydfccsnle 187
                                        8899************************55444445789************************************* PP

                                        .......................................G-TTEE-TT-EEEE-EEEEEEEE-TTTSTTTTTSTTS CS
                       E1-E2_ATPase  65 .......................................ekgdmvfsGtvvvsgeakavVtatgedtelgkiarlv 101
                                                                               + +   ++Gt+v++g+  a V+   ++ e+ ki +++
  gene2243|gene2243|rna2243|rna2243 188 vknsifmadieltksldkyderrrkrlvrilrrirrykrQDRRVFYGGTFVLQGTSLALVID--KSREVLKIQTSL 261
                                        *************************************988899999**********999986..677888999998 PP

                                        --------HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTTSSTTHHHHHHHHHHHHHS-TTHHHHHHHHHHHHHHH CS
                       E1-E2_ATPase 102 eeakskktplqkkldklgkvlvpvvlliallvflialllgkslaeallralallvaaiPcaLplavplalalgarr 177
                                         +    +++l+ +++k+ ++l+  +l i++++f++ ++lg+    +l    +l+v aiP++L l+v + l++ + +
  gene2243|gene2243|rna2243|rna2243 262 TNI---TSDLTSEVKKMQNILFSSILSICIALFIYCMVLGNM--STLKICTSLAVTAIPEGLELVVRINLSVIVFQ 332
                                        887...899999999999*****************9999998..68999***********************9988 PP

                                        HHHT CS
                       E1-E2_ATPase 178 lakk 181
                                        l+kk
  gene2243|gene2243|rna2243|rna2243 333 LKKK 336
                                        8876 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.1
                                        HHHHHHHHHHHHS-STTTSSTT.......HHHHH.HHHHHHHHS-TTH CS
                       E1-E2_ATPase 124 pvvlliallvflialllgksla.......eallr.alallvaaiPcaL 163
                                         +vl++++++ l++++++ +++       +  lr +l+l++ a P+ L
  gene2243|gene2243|rna2243|rna2243 866 HLVLAVFITITLLFIMTNSNAIswileveKVTLReFLSLALLAFPIIL 913
                                        578888888888888888888877788874444458888888888765 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.2   0.0   2.5e-13   8.9e-10       2     160 ..     353     618 ..     352     634 .. 0.76
   2 !   26.7   0.0   1.7e-09     6e-06     168     210 .]     667     708 ..     651     708 .. 0.86

  Alignments for each domain:
  == domain 1  score: 39.2 bits;  conditional E-value: 2.5e-13
                                        SEEEEESBTTTBCHHHHHHHHHHHH......................CHHHHHHHHHH........HHCHHHHHHH CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxx......................xxxxxxxxxxx........xxxxxxxxxx RF
                          Hydrolase   2 ktvvfDkdGTLttgepsvedvivsa......................alalaaaletg........sehpigkalv 47 
                                        + +v+Dk+GT+tt e+ + ++++ +                      + a+++a  +g         e   ++a+ 
  gene2243|gene2243|rna2243|rna2243 353 DMIVLDKTGTITTNEQIIDQIFEVVpvqtncpagvegkdfggedstsKGAESKAQGIGfkfkpvhiKENEMFQAVC 428
                                        789************8888888888777888888888888888887755555555555666666666666666665 PP

                                        HHHHHH..........HHHHHHHHHETTTE...........................HHHHTHHHHHHHH..HCHH CS
                                        xxxxxx..........xxxxxxxxxxxxxx...........................xxxxxxxxxxxxx..xxxx RF
                          Hydrolase  48 aaakar..........sgaltgfatfigrg...........................ayaigkpewltal..dipp 84 
                                        +   ++          + +++ f++++++                            ++++g pe + al   + +
  gene2243|gene2243|rna2243|rna2243 429 RHLSEVitvdgrtmgdPLDISMFEAVPDCKsellffktfccesmvtrgiielenkyyEILKGAPENVLALcrSYDS 504
                                        5555556777777765555577777777779999999999999888888888888887777777777777442222 PP

                                        HHHHHHHHHHHHCHHHHHH.................................................TTHHHHHH CS
                                        xxxxxxxxxxxxxxxxxxx.................................................xxxxxxxx RF
                          Hydrolase  85 dlgaaigsaqsqgrtvall.................................................qaralavf 111
                                        + ++ i                                                              + ++l+ +
  gene2243|gene2243|rna2243|rna2243 505 ENKESIK-----------IedkknilrnlkersiacaykklskryivervrnvtdmssgledkqlkkrNYKLLGFI 569
                                        2222222...........133333333555889999999************************9999999****** PP

                                        HHHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHHTT..GGGE CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxx RF
                          Hydrolase 112 tiadplkvkpeaaeavasLkaagievvlltgdnpetaeraanqlG..ddyf 160
                                        +++d+  ++++++e++++ ka+ i+v +ltgd+  t + ++n +G   d++
  gene2243|gene2243|rna2243|rna2243 570 AFKDT--LRKGVKECFNWCKANDIKVRILTGDSMLTTMNILNDIGvqGDFY 618
                                        *****..**************************************753333 PP

  == domain 2  score: 26.7 bits;  conditional E-value: 1.7e-09
                                        CESSTTTSHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHHHTT CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          Hydrolase 168 ietvakpspegkvaaireLqgkpeevamVGDgvnDaaalaaAg 210
                                         e++  +sp+ k+a+++ L g++++++m GDgvnD+ a+++A+
  gene2243|gene2243|rna2243|rna2243 667 FEVIYRASPSNKHAIVKYL-GRKNKILMTGDGVNDLLAIKQAD 708
                                        4556778************.88889*****************8 PP

>> Cation_ATPase_C  Cation transporting ATPase, C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.7       2.4   8.7e+03      97     120 ..      48      68 ..      47      84 .. 0.70
   2 ?   -0.5   0.3      0.24   8.5e+02      51      74 ..     275     298 ..     255     341 .. 0.71
   3 !   16.4   0.0   1.5e-06    0.0055       3      28 ..     778     803 ..     776     807 .. 0.91
   4 !   26.6  11.0   1.1e-09   4.1e-06      90     182 .]     831     921 ..     809     921 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 2.4
                    Cation_ATPase_C  97 tlvlsqifnalnlrsrreslfkfs 120
                                        +l l+q++ ++++ s   s+f f 
  gene2243|gene2243|rna2243|rna2243  48 FLLLLQLVSVFMVDS---SIFDFF 68 
                                        567778888888888...777743 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.24
                    Cation_ATPase_C  51 lrriliqgllqalvtllvffltll 74 
                                        + +il+ ++l++ ++l+++  +l 
  gene2243|gene2243|rna2243|rna2243 275 MQNILFSSILSICIALFIYCMVLG 298
                                        345666666666666666655554 PP

  == domain 3  score: 16.4 bits;  conditional E-value: 1.5e-06
                    Cation_ATPase_C   3 plsaiqiLwinLvtDllpalaLalep 28 
                                        +l++ q+L+inL+tD+lpa+ + +++
  gene2243|gene2243|rna2243|rna2243 778 ILNSKQLLFINLLTDGLPATLMCMNK 803
                                        7999****************999886 PP

  == domain 4  score: 26.6 bits;  conditional E-value: 1.1e-09
                    Cation_ATPase_C  90 aqtmaFitlvlsqifnalnlrsrreslfkfsglfsnkllllaillslllqvlivyvpglnavfgtaplsleewlia 165
                                          t  F+++v+++++n ln   +  sl+   + ++n  l+la++++++l+++++    + +++++++++l e+l +
  gene2243|gene2243|rna2243|rna2243 831 SKTKSFLFIVIGEMLNSLNNINLGISLLI--SCKQNLHLVLAVFITITLLFIMTNSNAISWILEVEKVTLREFLSL 904
                                        56889*****************9999987..999****************************************** PP

                    Cation_ATPase_C 166 lllalvvllvdelvKll 182
                                        +lla+ ++l+de++K +
  gene2243|gene2243|rna2243|rna2243 905 ALLAFPIILIDEVFKQF 921
                                        **************976 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0      0.02        71      17      55 ..     576     614 ..     569     626 .. 0.84
   2 !   15.2   0.1   3.7e-06     0.013     202     246 ..     687     731 ..     647     766 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.02
                                        -HHHHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCCC CS
                        Hydrolase_3  17 sektkeaikklkekgikvviATGRslravlpvleelgld 55 
                                         +  ke ++ +k+++ikv i TG s+ +++++l+++g++
  gene2243|gene2243|rna2243|rna2243 576 RKGVKECFNWCKANDIKVRILTGDSMLTTMNILNDIGVQ 614
                                        5667888888999*******************9999987 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 3.7e-06
                                        -GGGEEEEESSGGGHHHHHHSSEEEEETTS-HHHHHHSSEEE--G CS
                        Hydrolase_3 202 sleeviafGDgeNDieMLeaaglgvAmgnaseevkkaAdyvtksn 246
                                         +++++  GDg ND+  +++a++gv +g +s+  k+++d + ++ 
  gene2243|gene2243|rna2243|rna2243 687 RKNKILMTGDGVNDLLAIKQADVGVSLGEGSDLSKEVSDIILTDS 731
                                        57889999*******************************998765 PP

>> Tnp_DNA_bind  Transposase DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   2.8    0.0014         5       8      28 ..     201     221 ..     197     227 .. 0.84
   2 ?   -0.2   0.0      0.26   9.3e+02      11      25 ..     552     566 ..     549     573 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0014
                       Tnp_DNA_bind   8 gsadLgDkRltkRlvklaesl 28 
                                        +s+d +D+R++kRlv++++++
  gene2243|gene2243|rna2243|rna2243 201 KSLDKYDERRRKRLVRILRRI 221
                                        566779************987 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.26
                       Tnp_DNA_bind  11 dLgDkRltkRlvkla 25 
                                         L Dk l+kR +kl+
  gene2243|gene2243|rna2243|rna2243 552 GLEDKQLKKRNYKLL 566
                                        599********9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (922 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       960  (0.0535445); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.67u 0.30s 00:00:00.97 Elapsed: 00:00:00.45
# Mc/sec: 6139.44
//
Query:       gene2244|gene2244|rna2244|rna2244  [L=247]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      5e-10   39.3  20.8    0.00021   20.9   0.4    3.1  3  Tfb4            Transcription factor Tfb4
  ------ inclusion threshold ------
        0.1   12.7   0.0       0.22   11.7   0.0    1.6  1  Malt_amylase_C  Maltogenic Amylase, C-terminal domain


Domain annotation for each model (and alignments):
>> Tfb4  Transcription factor Tfb4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.4   2.4e-08   0.00021       4      57 ..      35      85 ..      32     114 .. 0.85
   2 !    8.2   0.2   0.00017       1.5     142     175 ..     126     159 ..      93     175 .. 0.85
   3 !   17.5  10.0   2.6e-07    0.0023     241     275 ..     207     239 ..     184     240 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 2.4e-08
                               Tfb4  4 ltvvldtnpkawaeleekltlsevlasllvflNahLalnaaNkvaviashsqka 57
                                       l vvld + ++wa+l++    +e+ +++lv++N+++ ++++Nk  vi  +sqk+
  gene2244|gene2244|rna2244|rna2244 35 LYVVLDLQRSSWAQLKDP---KELCNNILVLINTFIRMSYDNKAIVINNKSQKV 85
                                       89**************76...56689*********************9888774 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.00017
                               Tfb4 142 eklksRilvvsaskdsalqyipimNviFaaqklk 175
                                        ++ ++Ri+++s +++s+ +y+ ++ + F a++ +
  gene2244|gene2244|rna2244|rna2244 126 NTSNNRIIIISLTRESKNDYLKYLKSAFVAKRYS 159
                                        67799*************************9964 PP

  == domain 3  score: 17.5 bits;  conditional E-value: 2.6e-07
                               Tfb4 241 asCfchrkvvdiGfvCSvCLsilceispenkCktC 275
                                        + C ch++ +  G vC vCLsi c   p+  Ck C
  gene2244|gene2244|rna2244|rna2244 207 TKCNCHGREILYGLVCPVCLSIYCSLIPI--CKRC 239
                                        57************************998..9999 PP

>> Malt_amylase_C  Maltogenic Amylase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   2.4e-05      0.22      15      69 ..      65     124 ..      58     128 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.4e-05
                                        EEEEEETTEEEEEEEESS-EEEEE--G...GGTT-EEEETTTTEE-----SS..EEEEE- CS
                     Malt_amylase_C  15 aYlReyedetilvvaNrsaqaveldls...elagrvpvelfggeefpaigel..ytltLp 69 
                                        +++R + d++ +v++N+s++  + d++   +  ++v +++f  +    i+++  y lt++
  gene2244|gene2244|rna2244|rna2244  65 TFIRMSYDNKAIVINNKSQKVYDHDHPvvdQRDEKVITDIFAYNDIDSIANDigYALTIA 124
                                        69************************************************9999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       997  (0.0556082); expected 358.6 (0.02)
Passed bias filter:                      441  (0.024597); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1664.09
//
Query:       gene2245|gene2245|rna2245|rna2245  [L=51]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.065   13.2   0.1      0.081   12.9   0.1    1.3  1  MinC_N    Septum formation inhibitor MinC, N-terminal domain


Domain annotation for each model (and alignments):
>> MinC_N  Septum formation inhibitor MinC, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   4.5e-06     0.081      66      99 ..      17      51 .]       1      51 [] 0.86

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 4.5e-06
                             MinC_N 66 elisraglrivgvsgckdkaskee.imkagLpvLs 99
                                       e++ +++++iv +  c+d ++k+  + ++++ ++s
  gene2245|gene2245|rna2245|rna2245 17 EILVAFNVMIVTLQTCNDSYQKNVfLTQILFNIIS 51
                                       78899******************977888888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (51 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       403  (0.0224776); expected 358.6 (0.02)
Passed bias filter:                      203  (0.0113224); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.26s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 378.17
//
Query:       gene2246|gene2246|rna2246|rna2246  [L=231]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.1e-09   37.5   1.2    4.8e-09   36.9   1.2    1.2  1  ARS2         Arsenite-resistance protein 2
    5.3e-05   22.9   2.2    5.3e-05   22.9   2.2    2.1  2  DUF4187      Domain of unknown function (DUF4187)
     0.0061   17.3   9.9      0.049   14.5   3.0    3.6  3  zf-C2H2_4    C2H2-type zinc finger
     0.0064   16.7   0.2      0.045   13.9   0.1    2.0  2  CH           Calponin homology (CH) domain
     0.0076   16.5   9.6       0.45   10.9   0.3    3.4  3  zf-C2H2_jaz  Zinc-finger double-stranded RNA-binding
  ------ inclusion threshold ------
      0.013   15.9  10.2      0.033   14.5   2.0    2.3  2  zf-C2H2_2    C2H2 type zinc-finger (2 copies)
      0.016   15.7   3.2      0.016   15.7   3.2    3.5  3  zf-C2H2      Zinc finger, C2H2 type
      0.046   13.7   1.3      0.046   13.7   1.3    2.3  2  zf-C2H2_6    C2H2-type zinc finger
      0.049   13.5   2.1       0.67    9.8   0.2    2.4  2  PHD_Oberon   PHD - plant homeodomain finger protein
      0.068   13.5   1.8      0.081   13.3   0.4    1.9  2  PfUIS3       Plasmodium falciparum UIS3 membrane protein
       0.11   12.5   0.0        0.2   11.6   0.0    1.4  1  TetR_C_36    Tetracyclin repressor-like, C-terminal domain
        1.1    9.8   0.1        1.1    9.8   0.1    3.7  3  zf-H2C2_2    Zinc-finger double domain
        1.4    8.9   5.5         19    5.3   1.0    3.0  3  PyrI_C       Aspartate carbamoyltransferase regulatory chain,
        3.3    7.9  12.1         21    5.3   0.1    3.4  3  zf-met2      Zinc-binding


Domain annotation for each model (and alignments):
>> ARS2  Arsenite-resistance protein 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.9   1.2   3.8e-12   4.8e-09      37     109 ..     115     183 ..      97     188 .. 0.86

  Alignments for each domain:
  == domain 1  score: 36.9 bits;  conditional E-value: 3.8e-12
                               ARS2  37 eeeilklgkkdpekevEkfvqantqElakdKwlCplsGKkFkgpEFvrKHilnKHaekveevrkevefFnnyl 109
                                        e +   l+   pe+e+Ek+v      la   + C l  K F    +v+KHi+nKH+e   +v +e+e Fn +l
  gene2246|gene2246|rna2246|rna2246 115 ERNFNYLKTDSPETELEKYVVR----LADGVFRCDLCHKTFEQLVYVKKHIKNKHEELYSDVEQEIERFNCFL 183
                                        55567788899********965....7778899*************************************997 PP

>> DUF4187  Domain of unknown function (DUF4187)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   2.2   4.1e-08   5.3e-05      17      46 ..      61      90 ..      55      92 .. 0.95
   2 ?   -1.8   0.1       2.1   2.8e+03      10      37 ..     125     152 ..     119     160 .. 0.77

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 4.1e-08
                            DUF4187 17 klleyLReeylYCfwCgtkYedeedLeenC 46
                                       kl+++LR+ +lYC++C+  +++e ++ ++C
  gene2246|gene2246|rna2246|rna2246 61 KLITFLRHVFLYCYYCARVFDTEIEMIRKC 90
                                       899*************************99 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 2.1
                            DUF4187  10 eaeerLeklleyLReeylYCfwCgtkYe 37 
                                        ++e +Lek +  L +  + C  C  ++e
  gene2246|gene2246|rna2246|rna2246 125 SPETELEKYVVRLADGVFRCDLCHKTFE 152
                                        6788888888888888888888877765 PP

>> zf-C2H2_4  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.1       3.6   4.6e+03      15      21 ..      43      49 ..      34      51 .. 0.62
   2 ?    5.1   0.1     0.041        52       2      13 ..      72      83 ..      71      88 .. 0.82
   3 !   14.5   3.0   3.8e-05     0.049       1      24 []     142     165 ..     142     165 .. 0.97

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 3.6
                          zf-C2H2_4 15 aLlrHlk 21
                                        L++H k
  gene2246|gene2246|rna2246|rna2246 43 MLNKHYK 49
                                       2455665 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.041
                          zf-C2H2_4  2 kCpiCgksFssk 13
                                       +C +C ++F + 
  gene2246|gene2246|rna2246|rna2246 72 YCYYCARVFDTE 83
                                       7********875 PP

  == domain 3  score: 14.5 bits;  conditional E-value: 3.8e-05
                          zf-C2H2_4   1 fkCpiCgksFsskkaLlrHlkthH 24 
                                        f+C++C+k+F     +++H+k+ H
  gene2246|gene2246|rna2246|rna2246 142 FRCDLCHKTFEQLVYVKKHIKNKH 165
                                        89********************99 PP

>> CH  Calponin homology (CH) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.58   7.4e+02      58      81 ..      30      53 ..      16      74 .. 0.67
   2 !   13.9   0.1   3.5e-05     0.045      15      73 ..     121     187 ..     118     198 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.58
                                       HHHHHHHHHHHHHHHHHHTTCHTT CS
                                 CH 58 efkkleNinlaldvaekklgvpkv 81
                                       + k   N+++ + +++k+++ ++v
  gene2246|gene2246|rna2246|rna2246 30 RSKDSTNLRNIFHMLNKHYKTDLV 53
                                       667777888888888877766654 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 3.5e-05
                                        HTTSTTSSTTSCHHHHHTTSHHHHHHHHHHSTTTSSGGGSTTT........HHHHHHHHHHHHHHHH CS
                                 CH  15 leeagpkvkvedfeedlrDGvlLckLlnklapglvdkkklnks........efkkleNinlaldvae 73 
                                        l+ ++p ++ e+    l+DGv+ c+L +k   +lv +kk  k+         ++ +e++n +ld+++
  gene2246|gene2246|rna2246|rna2246 121 LKTDSPETELEKYVVRLADGVFRCDLCHKTFEQLVYVKKHIKNkheelysdVEQEIERFNCFLDMID 187
                                        5556667777888889**************999999988887789999999************9765 PP

>> zf-C2H2_jaz  Zinc-finger double-stranded RNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.69   8.8e+02       8      18 ..      45      55 ..      45      55 .. 0.86
   2 !   10.9   0.3   0.00035      0.45       2      16 ..      71      85 ..      71      88 .. 0.88
   3 !    8.2   1.9    0.0025       3.2       2      24 ..     142     164 ..     141     164 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.69
                                       TBBBSSHHHHH CS
                        zf-C2H2_jaz  8 dKyFksenald 18
                                       +K++k++ ++d
  gene2246|gene2246|rna2246|rna2246 45 NKHYKTDLVYD 55
                                       799**999886 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00035
                                       CBBTTTTBBBSSHHH CS
                        zf-C2H2_jaz  2 fYCvlCdKyFksena 16
                                       +YC +C++ F +e  
  gene2246|gene2246|rna2246|rna2246 71 LYCYYCARVFDTEIE 85
                                       6**********9976 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.0025
                                        CBBTTTTBBBSSHHHHHCCTTSH CS
                        zf-C2H2_jaz   2 fYCvlCdKyFksenaldnHlkSK 24 
                                        f C lC K+F+     ++H+k K
  gene2246|gene2246|rna2246|rna2246 142 FRCDLCHKTFEQLVYVKKHIKNK 164
                                        99********9777777777765 PP

>> zf-C2H2_2  C2H2 type zinc-finger (2 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   1.7    0.0097        12      12      66 ..      37      87 ..      28     126 .. 0.68
   2 ?   14.5   2.0   2.6e-05     0.033      37      94 ..     128     184 ..     103     189 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0097
                          zf-C2H2_2 12 veellehm.skkhgffipereylvdleglleylrekieekleClyCekefk.sleal 66
                                       + +++ hm +k+++ ++     + + ++l+++lr+       C+yC + f+ ++e +
  gene2246|gene2246|rna2246|rna2246 37 L-RNIFHMlNKHYKTDLV--YDCDNDDKLITFLRHVFLY---CYYCARVFDtEIEMI 87
                                       3.4455551444554444..788899*******998766...****99965255555 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 2.6e-05
                          zf-C2H2_2  37 eglleylrekieekleClyCekefkslealreHmkkkgHckineeeeeekkeiekfyd 94 
                                         +l +y+ +  +  ++C +C+k+f++l  +++H+k+k H ++  + e+e + ++ f d
  gene2246|gene2246|rna2246|rna2246 128 TELEKYVVRLADGVFRCDLCHKTFEQLVYVKKHIKNK-HEELYSDVEQEIERFNCFLD 184
                                        4566677777777899******************986.77775566666666666655 PP

>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.3       1.5   1.9e+03      14      22 ..      42      50 ..      41      50 .. 0.80
   2 ?    3.3   0.0      0.11   1.3e+02       2      12 ..      72      82 ..      71      88 .. 0.82
   3 ?   15.7   3.2   1.2e-05     0.016       1      23 []     142     165 ..     142     165 .. 0.97

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 1.5
                                       HHHHHHHHC CS
                            zf-C2H2 14 snLkrHirt 22
                                       ++L++H++t
  gene2246|gene2246|rna2246|rna2246 42 HMLNKHYKT 50
                                       589999886 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.11
                                       EETTTTEEESS CS
                            zf-C2H2  2 kCpdCgksFkr 12
                                       +C +C ++F +
  gene2246|gene2246|rna2246|rna2246 72 YCYYCARVFDT 82
                                       6********87 PP

  == domain 3  score: 15.7 bits;  conditional E-value: 1.2e-05
                                        EEETTTTEEESSHHHHHHHHHC.C CS
                            zf-C2H2   1 ykCpdCgksFkrksnLkrHirt.H 23 
                                        ++C+ C+k+F +    k+Hi+  H
  gene2246|gene2246|rna2246|rna2246 142 FRCDLCHKTFEQLVYVKKHIKNkH 165
                                        89*******************988 PP

>> zf-C2H2_6  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.3       1.5   1.9e+03       4      13 ..      73      82 ..      73      83 .. 0.85
   2 ?   13.7   1.3   3.6e-05     0.046       1      14 [.     141     154 ..     141     167 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.5
                          zf-C2H2_6  4 CsvCsksFps 13
                                       C +C ++F +
  gene2246|gene2246|rna2246|rna2246 73 CYYCARVFDT 82
                                       889****965 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 3.6e-05
                          zf-C2H2_6   1 vheCsvCsksFpsl 14 
                                        v++C+ C+k+F+ l
  gene2246|gene2246|rna2246|rna2246 141 VFRCDLCHKTFEQL 154
                                        7**********866 PP

>> PHD_Oberon  PHD - plant homeodomain finger protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.1      0.06        77      83     114 ..      47      75 ..      29      90 .. 0.68
   2 ?    9.8   0.2   0.00052      0.67      83     119 ..     135     171 ..     120     181 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.06
                         PHD_Oberon  83 sikldvefyCraCdkksellglvkkvlevake 114
                                        + k+d  +    Cd+  +l++++++v+  +  
  gene2246|gene2246|rna2246|rna2246  47 HYKTDLVY---DCDNDDKLITFLRHVFLYCYY 75 
                                        45555555...467777788888888877754 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00052
                         PHD_Oberon  83 sikldvefyCraCdkksellglvkkvlevakearsvd 119
                                        +  +d+ f+C  C+k+ e l +vkk ++  +e+   d
  gene2246|gene2246|rna2246|rna2246 135 VRLADGVFRCDLCHKTFEQLVYVKKHIKNKHEELYSD 171
                                        456799*******************999877665444 PP

>> PfUIS3  Plasmodium falciparum UIS3 membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0         6   7.6e+03      84      93 ..      40      49 ..      27      66 .. 0.54
   2 ?   13.3   0.4   6.3e-05     0.081       5      45 ..     160     200 ..     155     222 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 6
                                       HHHHHHHHHH CS
                             PfUIS3 84 lkyflkkvya 93
                                       + + l+k y 
  gene2246|gene2246|rna2246|rna2246 40 IFHMLNKHYK 49
                                       3333333332 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 6.3e-05
                                        -TSS--------S---HHHHHHHHHHHHHHHHHHHHHS-HH CS
                             PfUIS3   5 nlkkklkenkndvdvslkrynifvdivklaiqkhfedlsnd 45 
                                         +k+k  e   dv+  + r+n f+d++ + + ++f+ + n+
  gene2246|gene2246|rna2246|rna2246 160 HIKNKHEELYSDVEQEIERFNCFLDMIDINLLNYFDGIDNN 200
                                        577788888899************************99987 PP

>> TetR_C_36  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00016       0.2      41      87 ..      96     142 ..      94     152 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00016
                          TetR_C_36  41 kagevqrrvvaavaelleeevaageleppldlddlAyllvRiaEsfl 87 
                                        ++g+vqrrv +  ++++  e + ++l+ + + ++l   +vR+a+ ++
  gene2246|gene2246|rna2246|rna2246  96 RDGRVQRRVFDRKQKIITMERNFNYLKTDSPETELEKYVVRLADGVF 142
                                        68*****************************************9875 PP

>> zf-H2C2_2  Zinc-finger double domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   4.9       2.8   3.6e+03      15      26 .]      71      82 ..      42      82 .. 0.84
   2 ?    9.8   0.1   0.00085       1.1      15      25 ..     142     152 ..     132     153 .. 0.90
   3 ?    0.8   0.1       0.6   7.6e+02       3      10 ..     158     166 ..     156     181 .. 0.72

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 2.8
                          zf-H2C2_2 15 yeCplCdkaFkt 26
                                       + C +C+ +F t
  gene2246|gene2246|rna2246|rna2246 71 LYCYYCARVFDT 82
                                       58*****99975 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00085
                          zf-H2C2_2  15 yeCplCdkaFk 25 
                                        + C+lC+k+F 
  gene2246|gene2246|rna2246|rna2246 142 FRCDLCHKTFE 152
                                        89********6 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.6
                          zf-H2C2_2   3 rrHir.kHt 10 
                                        ++Hi+ kH 
  gene2246|gene2246|rna2246|rna2246 158 KKHIKnKHE 166
                                        799994475 PP

>> PyrI_C  Aspartate carbamoyltransferase regulatory chain, metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       2.5   3.3e+03      29      36 ..      49      56 ..      32      65 .. 0.60
   2 ?    5.3   1.0     0.015        19      32      46 ..      69      83 ..      64      84 .. 0.84
   3 ?    4.3   0.1     0.029        38      26      45 ..     134     153 ..     126     154 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 2.5
                                       TTTTEEEE CS
                             PyrI_C 29 kekvklkC 36
                                       k ++++ C
  gene2246|gene2246|rna2246|rna2246 49 KTDLVYDC 56
                                       55555555 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.015
                                       TEEEETTT--EEEHH CS
                             PyrI_C 32 vklkCkYCekeisee 46
                                       v l C YC ++++ e
  gene2246|gene2246|rna2246|rna2246 69 VFLYCYYCARVFDTE 83
                                       6789******99875 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.029
                                        EEETTTTEEEETTT--EEEH CS
                             PyrI_C  26 vedkekvklkCkYCekeise 45 
                                        v++  +++++C  C k++++
  gene2246|gene2246|rna2246|rna2246 134 VVRLADGVFRCDLCHKTFEQ 153
                                        56778899********9975 PP

>> zf-met2  Zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.1      0.44   5.6e+02       4      10 ..       9      15 ..       5      20 .. 0.88
   2 ?    5.3   0.1     0.017        21      21      34 ..      42      56 ..      34      58 .. 0.84
   3 ?    4.9   4.2     0.023        30       2      28 ..     144     167 ..     143     175 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.44
                            zf-met2  4 iCrqtFm 10
                                       iC  tF+
  gene2246|gene2246|rna2246|rna2246  9 ICVNTFI 15
                                       9*****9 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.017
                            zf-met2 21 HaenKHpK.dtveeC 34
                                       H  nKH K d v++C
  gene2246|gene2246|rna2246|rna2246 42 HMLNKHYKtDLVYDC 56
                                       999*****5557888 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.023
                            zf-met2   2 CkiCrqtFmcTtkevlLkeHaenKHpK 28 
                                        C  C  tF    + v  k H +nKH+ 
  gene2246|gene2246|rna2246|rna2246 144 CDLCHKTF---EQLVYVKKHIKNKHEE 167
                                        89999999...4567799*******87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       990  (0.0552178); expected 358.6 (0.02)
Passed bias filter:                      541  (0.0301746); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1502.49
//
Query:       gene2247|gene2247|rna2247|rna2247  [L=105]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-27   94.8   5.0    2.4e-27   94.7   5.0    1.0  1  CutA1     CutA1 divalent ion tolerance protein


Domain annotation for each model (and alignments):
>> CutA1  CutA1 divalent ion tolerance protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.7   5.0   1.4e-31   2.4e-27       1      97 [.       5     101 ..       5     103 .. 0.98

  Alignments for each domain:
  == domain 1  score: 94.7 bits;  conditional E-value: 1.4e-31
                                        EEEEEEESSHHHHHHHHHHHHHTTS-SEEEEEEEEEEEEEETTEEEEEEEEEEEEEEEGGGHHHHHHHHHHHSSSS CS
                              CutA1   1 vlvlvtapseeeakklaralveeklaACvnilpkieSvYrWkgkieedkEvllliktreekveelekrvkelhpye 76 
                                        v++++t+++e+ea+ + ++l+++kl+AC++ ++k+eS+Y+W+gkie+++E+++ + t +++v ++ +++ ++h+y+
  gene2247|gene2247|rna2247|rna2247   5 VIIFTTFKDENEANLILESLLRKKLIACAQKIQKVESMYVWNGKIETTEEIQVKMTTLNSCVLSIDNVISKMHSYQ 80 
                                        589************************************************************************* PP

                                        S-EEEEEEESEEEHHHHHHHH CS
                              CutA1  77 vpeiialpieagseaYlkWie 97 
                                        v ++ia+++e ++e+Y++W+ 
  gene2247|gene2247|rna2247|rna2247  81 VYQFIAVRLEYVNEKYIQWMW 101
                                        *******************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       816  (0.0455129); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 792.17
//
Query:       gene2248|gene2248|rna2248|rna2248  [L=60]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (60 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       336  (0.0187406); expected 358.6 (0.02)
Passed bias filter:                      263  (0.014669); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 448.08
//
Query:       gene2249|gene2249|rna2249|rna2249  [L=65]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (65 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       275  (0.0153383); expected 358.6 (0.02)
Passed bias filter:                      204  (0.0113782); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.26s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 482.57
//
Query:       gene225|gene225|rna225|rna225  [L=738]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.8e-07   29.7   9.4      0.017   15.2   0.4    4.7  4  TPR_2     Tetratricopeptide repeat
    5.5e-07   29.8   5.5       0.03   14.6   0.1    5.7  6  TPR_12    Tetratricopeptide repeat
    1.4e-05   24.7  14.0     0.0069   16.2   0.7    4.5  5  TPR_1     Tetratricopeptide repeat
    8.8e-05   22.9   1.0        2.2    8.8   0.0    4.4  4  TPR_19    Tetratricopeptide repeat
    0.00036   21.1   2.2       0.26   12.2   0.1    4.6  3  TPR_14    Tetratricopeptide repeat
     0.0006   19.8   7.6        5.5    7.5   0.7    5.6  5  TPR_8     Tetratricopeptide repeat
     0.0069   16.3   1.0        2.9    8.1   0.1    3.6  3  TPR_7     Tetratricopeptide repeat
     0.0073   15.5   0.7      0.017   14.3   0.5    1.7  2  TPR_15    Tetratricopeptide repeat
  ------ inclusion threshold ------
      0.015   15.2   2.0        5.6    7.0   0.0    3.9  3  TPR_10    Tetratricopeptide repeat
      0.017   14.8   5.8        1.1    8.9   1.5    2.7  2  TPR_11    TPR repeat
      0.047   14.4   0.2        2.2    9.0   0.2    2.6  2  TPR_16    Tetratricopeptide repeat
       0.46   11.0   8.1       0.59   10.6   0.2    4.2  4  TPR_17    Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0      0.13     2e+02       4      26 ..      74      96 ..      71      99 .. 0.89
   2 !   13.1   1.7   5.4e-05      0.08       8      34 .]     598     624 ..     594     624 .. 0.86
   3 ?   -2.7   0.0       6.3   9.4e+03      21      34 .]     643     656 ..     643     656 .. 0.88
   4 !   15.2   0.4   1.1e-05     0.017       2      32 ..     658     688 ..     657     690 .. 0.93

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.13
                          TPR_2  4 lynlGlayyklgdyeeAleafek 26
                                   l  +++++++l+ +  A+e++e+
  gene225|gene225|rna225|rna225 74 LLVRANVLIELDMLSAAEECLER 96
                                   5669*****************97 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 5.4e-05
                          TPR_2   8 GlayyklgdyeeAleafekAleldPnn 34 
                                    +l  +++++ye+Al+++++Ale++P n
  gene225|gene225|rna225|rna225 598 ALHRIRNKEYEKALALLKQALEHAPYN 624
                                    5566799*****************975 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 6.3
                          TPR_2  21 leafekAleldPnn 34 
                                    + +f + l++d nn
  gene225|gene225|rna225|rna225 643 ITYFLRILSIDSNN 656
                                    579*******9987 PP

  == domain 4  score: 15.2 bits;  conditional E-value: 1.1e-05
                          TPR_2   2 ealynlGlayyklgdyeeAleafekAleldP 32 
                                    e l n G+ y ++ +ye+A+ ++ +A +++ 
  gene225|gene225|rna225|rna225 658 ETLINTGNYYTEKEKYEDAVYFYTRAYKINK 688
                                    67899************************96 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0       1.2   1.8e+03      47      71 ..      73      97 ..      66     100 .. 0.71
   2 ?    1.2   0.0      0.32   4.7e+02      29      50 ..     250     271 ..     246     272 .. 0.83
   3 ?    0.1   0.0      0.68     1e+03       4      33 ..     345     374 ..     342     381 .. 0.79
   4 !    8.7   0.1    0.0014       2.1      14      32 ..     602     620 ..     590     626 .. 0.63
   5 !   14.6   0.1     2e-05      0.03      46      76 ..     658     688 ..     639     689 .. 0.89
   6 ?    0.5   0.0      0.49   7.4e+02       4      27 ..     691     714 ..     688     715 .. 0.74

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 1.2
                         TPR_12 47 tlrnLgrlyralgryeeAlelleea 71
                                    l   + ++ +l+ + +A+e le+ 
  gene225|gene225|rna225|rna225 73 NLLVRANVLIELDMLSAAEECLERY 97
                                   5666677777888888888888875 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.32
                         TPR_12  29 aleiarrllGpdhpltattlrn 50 
                                     +++  +++Gp+h ++a+++ +
  gene225|gene225|rna225|rna225 250 IVQLLIKSQGPEHVEYARAYLD 271
                                    567778999**********975 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.68
                         TPR_12   4 talnnlaavlrrlgrydeAlellekaleia 33 
                                    +++ ++a +++ +g+ +e +e le+ +e++
  gene225|gene225|rna225|rna225 345 RMHEKMAKCYLGMGKETEMIEELERMREMM 374
                                    577789999999999999999999887776 PP

  == domain 4  score: 8.7 bits;  conditional E-value: 0.0014
                         TPR_12  14 rrlgrydeAlellekalei 32 
                                     r ++y++Al+ll++ale 
  gene225|gene225|rna225|rna225 602 IRNKEYEKALALLKQALEH 620
                                    4455555555555555554 PP

  == domain 5  score: 14.6 bits;  conditional E-value: 2e-05
                         TPR_12  46 ttlrnLgrlyralgryeeAlelleealaiae 76 
                                    +tl+n g +y + ++ye+A++++++a++i +
  gene225|gene225|rna225|rna225 658 ETLINTGNYYTEKEKYEDAVYFYTRAYKINK 688
                                    589************************9976 PP

  == domain 6  score: 0.5 bits;  conditional E-value: 0.49
                         TPR_12   4 talnnlaavlrrlgrydeAlelle 27 
                                    ++l ++ ++l  +g+yde +++l 
  gene225|gene225|rna225|rna225 691 KVLKHVVTILEMAGKYDEIRKMLS 714
                                    566667788888999999988876 PP

>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0      0.11   1.7e+02       7      26 ..      77      96 ..      74      97 .. 0.92
   2 ?   -3.8   0.2       9.5   1.4e+04       8      16 ..     351     359 ..     350     359 .. 0.74
   3 !   12.6   0.8     6e-05      0.09      14      34 .]     604     624 ..     601     624 .. 0.92
   4 ?   -2.1   0.0       2.8   4.2e+03      21      34 .]     643     656 ..     643     656 .. 0.89
   5 !   16.2   0.7   4.6e-06    0.0069       2      32 ..     658     688 ..     657     689 .. 0.92

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.11
                                   HHHHHHHTT-HHHHHHHHHH CS
                          TPR_1  7 lGnayfklgkydeAleyyek 26
                                   ++n++ +l ++  A+e+ e+
  gene225|gene225|rna225|rna225 77 RANVLIELDMLSAAEECLER 96
                                   89***************997 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 9.5
                                    HHHHHHTT- CS
                          TPR_1   8 Gnayfklgk 16 
                                    + +y+ +gk
  gene225|gene225|rna225|rna225 351 AKCYLGMGK 359
                                    778888886 PP

  == domain 3  score: 12.6 bits;  conditional E-value: 6e-05
                                    TT-HHHHHHHHHHHHHHSTTH CS
                          TPR_1  14 lgkydeAleyyekALelnPnn 34 
                                    +++y++Al+  ++ALe+ P n
  gene225|gene225|rna225|rna225 604 NKEYEKALALLKQALEHAPYN 624
                                    79****************976 PP

  == domain 4  score: -2.1 bits;  conditional E-value: 2.8
                                    HHHHHHHHHHSTTH CS
                          TPR_1  21 leyyekALelnPnn 34 
                                    + y+ + L+++ nn
  gene225|gene225|rna225|rna225 643 ITYFLRILSIDSNN 656
                                    67999******998 PP

  == domain 5  score: 16.2 bits;  conditional E-value: 4.6e-06
                                    HHHHHHHHHHHHTT-HHHHHHHHHHHHHHST CS
                          TPR_1   2 kalynlGnayfklgkydeAleyyekALelnP 32 
                                    ++l n Gn y +++ky++A+ +y +A ++n 
  gene225|gene225|rna225|rna225 658 ETLINTGNYYTEKEKYEDAVYFYTRAYKINK 688
                                    678999********************99995 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.1     0.012        18      26      52 ..      72      98 ..      58     101 .. 0.80
   2 ?   -0.8   0.0       1.5   2.3e+03      31      50 ..     350     369 ..     345     373 .. 0.81
   3 !    8.8   0.0    0.0015       2.2       3      24 ..     603     624 ..     601     633 .. 0.83
   4 ?    2.8   0.0      0.12   1.7e+02       4      43 ..     670     708 ..     667     716 .. 0.69

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.012
                         TPR_19 26 earllLAeallalgqldeAealLdalp 52
                                   e +l  A++l++l  l +Ae++L+++ 
  gene225|gene225|rna225|rna225 72 ENLLVRANVLIELDMLSAAEECLERYK 98
                                   556778*****************9975 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.5
                         TPR_19  31 LAeallalgqldeAealLda 50 
                                    +A+++l +g  +e ++ L++
  gene225|gene225|rna225|rna225 350 MAKCYLGMGKETEMIEELER 369
                                    89******998887777776 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.0015
                         TPR_19   3 aegdyaeAlalleqalqedpkn 24 
                                     ++ y+ Alall+qal+++p n
  gene225|gene225|rna225|rna225 603 RNKEYEKALALLKQALEHAPYN 624
                                    5678999999999999999976 PP

  == domain 4  score: 2.8 bits;  conditional E-value: 0.12
                         TPR_19   4 egdyaeAlalleqalqedpknaearllLAeallalgqlde 43 
                                     ++y++A+ ++++a++ +  +a ++   + +l  +g +de
  gene225|gene225|rna225|rna225 670 KEKYEDAVYFYTRAYKINK-SAKVLKHVVTILEMAGKYDE 708
                                    5799**********99855.55555555666666666666 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.1      0.11   1.6e+02       3      27 ..      73      97 ..      71      99 .. 0.90
   2 !   12.2   0.1   0.00017      0.26      12      39 ..     602     629 ..     594     632 .. 0.83
   3 ?    0.9   0.0      0.75   1.1e+03       8      26 ..     697     715 ..     690     718 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.11
                         TPR_14  3 allalaeallalGdpdeAiallrra 27
                                    ll +a +l +l+ + +A+++l+r+
  gene225|gene225|rna225|rna225 73 NLLVRANVLIELDMLSAAEECLERY 97
                                   57889******************96 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00017
                         TPR_14  12 lalGdpdeAiallrralalaPddaeawl 39 
                                     ++ ++++A+all++al++aP + +++ 
  gene225|gene225|rna225|rna225 602 IRNKEYEKALALLKQALEHAPYNITLLH 629
                                    5899*****************9988775 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.75
                         TPR_14   8 aeallalGdpdeAiallrr 26 
                                    + +l+ +G++de +++l r
  gene225|gene225|rna225|rna225 697 VTILEMAGKYDEIRKMLSR 715
                                    5678999*********986 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0     0.098   1.5e+02       4      27 ..      74      97 ..      71     101 .. 0.85
   2 ?    3.7   0.1     0.058        87       3      26 ..     346     369 ..     344     369 .. 0.87
   3 ?    4.1   0.1     0.044        65      13      31 ..     603     621 ..     599     624 .. 0.85
   4 ?   -0.4   0.0       1.2   1.8e+03      19      34 .]     641     656 ..     635     656 .. 0.86
   5 !    7.5   0.7    0.0037       5.5       3      32 ..     659     688 ..     657     689 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.098
                                   HHHHHHHHHHTT-HHHHHHHHHHH CS
                          TPR_8  4 yynlgsiylklgdyeeAkeyyeka 27
                                   ++  ++++++l  + +A+e++e++
  gene225|gene225|rna225|rna225 74 LLVRANVLIELDMLSAAEECLERY 97
                                   5668999***************97 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.058
                                    HHHHHHHHHHHTT-HHHHHHHHHH CS
                          TPR_8   3 ayynlgsiylklgdyeeAkeyyek 26 
                                    ++ +++++yl +g+  e++e +e+
  gene225|gene225|rna225|rna225 346 MHEKMAKCYLGMGKETEMIEELER 369
                                    566899**************9985 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.044
                                    HTT-HHHHHHHHHHHHHHH CS
                          TPR_8  13 klgdyeeAkeyyekaleld 31 
                                      ++ye+A + +++ale +
  gene225|gene225|rna225|rna225 603 RNKEYEKALALLKQALEHA 621
                                    5799************955 PP

  == domain 4  score: -0.4 bits;  conditional E-value: 1.2
                                    HHHHHHHHHHHHHHH. CS
                          TPR_8  19 eAkeyyekaleldpdn 34 
                                    + + y+ + l++d +n
  gene225|gene225|rna225|rna225 641 NGITYFLRILSIDSNN 656
                                    6799*********986 PP

  == domain 5  score: 7.5 bits;  conditional E-value: 0.0037
                                    HHHHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                          TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldp 32 
                                     + n g+ y ++++ye A+ +y +a ++++
  gene225|gene225|rna225|rna225 659 TLINTGNYYTEKEKYEDAVYFYTRAYKINK 688
                                    66777999********************97 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       7.6   1.1e+04      16      24 ..      88      96 ..      78     105 .. 0.73
   2 !    8.1   0.1     0.002       2.9      14      35 ..     606     625 ..     598     626 .. 0.87
   3 ?    4.6   0.0     0.025        38       2      26 ..     660     684 ..     659     693 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 7.6
                          TPR_7 16 eeAielyeq 24
                                   + A+e++e+
  gene225|gene225|rna225|rna225 88 SAAEECLER 96
                                   678888887 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.002
                          TPR_7  14 dyeeAielyeqsLaltkdpeda 35 
                                    +ye+A+ l++q  al+ +p+++
  gene225|gene225|rna225|rna225 606 EYEKALALLKQ--ALEHAPYNI 625
                                    8**********..999999876 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.025
                          TPR_7   2 LlnLarlysrlGdyeeAielyeqsL 26 
                                    L n ++ y +  +ye+A+ +y+++ 
  gene225|gene225|rna225|rna225 660 LINTGNYYTEKEKYEDAVYFYTRAY 684
                                    6677999***************965 PP

>> TPR_15  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.0       4.2   6.3e+03     256     275 ..     128     147 ..     105     149 .. 0.79
   2 !   14.3   0.5   1.2e-05     0.017      12     135 ..     594     715 ..     583     732 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 4.2
                         TPR_15 256 DaleqagradeAwrlRrqvw 275
                                    D+ +++g++de+ r+ ++v 
  gene225|gene225|rna225|rna225 128 DVTYRNGEVDESRRVDKEVD 147
                                    89999999999999988875 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 1.2e-05
                         TPR_15  12 lkl.atllykqgdvkkAlevLkeaaqkaapskdteyWrtladLAwalqqedearkAyrqLlasgkaraedyerliel.ly 89 
                                    lkl a    ++++++kAl+ Lk+a+++a  + +   + + + L  al     +++   ++l+++  + e++ +  ++  +
  gene225|gene225|rna225|rna225 594 LKLeALHRIRNKEYEKALALLKQALEHA--PYNITLLHMTGCLETALHGN--GITYFLRILSIDSNNYETLINTGNYyTE 669
                                    555344456899*********9988888..78899999999998888755..5556678889999988888888889458 PP

                         TPR_15  90 daepkeaarlaekgwrrfrsprlLssalellerakdydriaellks 135
                                    ++++++a+     +++  +s ++L+  + +le a++yd+i+++l +
  gene225|gene225|rna225|rna225 670 KEKYEDAVYFYTRAYKINKSAKVLKHVVTILEMAGKYDEIRKMLSR 715
                                    899*****************************************88 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0      0.27     4e+02      25      37 ..      90     102 ..      87     104 .. 0.85
   2 ?    3.7   0.1     0.041        62      16      30 ..     605     619 ..     603     622 .. 0.64
   3 ?    7.0   0.0    0.0038       5.6       4      34 ..     659     689 ..     658     696 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.27
                         TPR_10  25 leealairrrllG 37 
                                    +ee+l++++r  G
  gene225|gene225|rna225|rna225  90 AEECLERYKRMIG 102
                                    79*******9766 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.041
                         TPR_10  16 grydeAealleeala 30 
                                    ++y++A+all++al+
  gene225|gene225|rna225|rna225 605 KEYEKALALLKQALE 619
                                    466666666666664 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.0038
                         TPR_10   4 slnNLanalrqrgrydeAealleealairrr 34 
                                    +l N +n++++  +y++A+ ++ +a+ i + 
  gene225|gene225|rna225|rna225 659 TLINTGNYYTEKEKYEDAVYFYTRAYKINKS 689
                                    67788********************999776 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.2     0.003       4.5       9      26 ..     606     623 ..     602     629 .. 0.82
   2 ?    8.9   1.5   0.00076       1.1       1      26 [.     664     689 ..     664     690 .. 0.93

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.003
                         TPR_11   9 kyeeAieaYkkAlkldPd 26 
                                    +ye+A++ +k+Al+  P 
  gene225|gene225|rna225|rna225 606 EYEKALALLKQALEHAPY 623
                                    8************96665 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00076
                         TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPd 26 
                                    G+ y+e+ kye+A+  Y +A k++ +
  gene225|gene225|rna225|rna225 664 GNYYTEKEKYEDAVYFYTRAYKINKS 689
                                    899*******************9975 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.2    0.0015       2.2       5      65 ..     599     622 ..     596     625 .. 0.53
   2 ?    2.2   0.0       0.2     3e+02      39      63 ..     662     686 ..     645     690 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0015
                         TPR_16   5 raalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraap 65 
                                    + ++r+++y++A+a+l++al+                                     +ap
  gene225|gene225|rna225|rna225 599 LHRIRNKEYEKALALLKQALE-------------------------------------HAP 622
                                    445555555555555555555.....................................555 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.2
                         TPR_16  39 llgdaalrqgrlaeAaalyraalra 63 
                                    + g+ + ++  +++A+ +y +a++ 
  gene225|gene225|rna225|rna225 662 NTGNYYTEKEKYEDAVYFYTRAYKI 686
                                    5688899999999999999999965 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       9.5   1.4e+04       2      33 ..      60      91 ..      60      92 .. 0.74
   2 ?   -2.4   0.1       5.9   8.8e+03      13      22 ..     565     574 ..     563     574 .. 0.83
   3 ?    2.7   0.0      0.14   2.1e+02       1      23 [.     613     635 ..     613     641 .. 0.85
   4 ?   10.6   0.2    0.0004      0.59       1      33 [.     645     677 ..     645     678 .. 0.94

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 9.5
                         TPR_17  2 ylkaleldPnnadaynnLAelllknGdlmtAr 33
                                   y++ +  + + ++ +  +A++l ++  l  A+
  gene225|gene225|rna225|rna225 60 YKNLILENIDKVENLLVRANVLIELDMLSAAE 91
                                   66777777778888899999998877766665 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 5.9
                         TPR_17  13 adaynnLAel 22 
                                    ++ yn+LAel
  gene225|gene225|rna225|rna225 565 VNTYNLLAEL 574
                                    789*****86 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.14
                         TPR_17   1 lylkaleldPnnadaynnLAell 23 
                                    l+++ale+ P n  ++++ + l 
  gene225|gene225|rna225|rna225 613 LLKQALEHAPYNITLLHMTGCLE 635
                                    5799************9998875 PP

  == domain 4  score: 10.6 bits;  conditional E-value: 0.0004
                         TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtAr 33 
                                    ++l+ l +d nn + + n ++++ ++ ++++A+
  gene225|gene225|rna225|rna225 645 YFLRILSIDSNNYETLINTGNYYTEKEKYEDAV 677
                                    5899**************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (738 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1732  (0.0966033); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.72u 0.32s 00:00:01.04 Elapsed: 00:00:00.49
# Mc/sec: 4537.84
//
Query:       gene2250|gene2250|rna2250|rna2250  [L=195]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-12   46.9   0.0    3.4e-12   46.3   0.0    1.3  1  RVT_1     Reverse transcriptase (RNA-dependent DNA polymerase
  ------ inclusion threshold ------
       0.12   12.2   0.2       0.17   11.7   0.2    1.2  1  DrrA_P4M  DrrA phosphatidylinositol 4-phosphate binding domai


Domain annotation for each model (and alignments):
>> RVT_1  Reverse transcriptase (RNA-dependent DNA polymerase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.3   0.0   3.8e-16   3.4e-12      83     201 ..       1     123 [.       1     154 [. 0.92

  Alignments for each domain:
  == domain 1  score: 46.3 bits;  conditional E-value: 3.8e-16
                                        SBB-GGGGGGG-EEET.........................TEEEEESB--ST-TTHHHHHHHHHHHHHTT-T... CS
                              RVT_1  83 vpleellrkltafkvptklinliksflstrsfsvrvngeeskgryekkglpqGsvlSPllfnlfmnellrelrkra 158
                                        vp+e+l+ kl+++++  k++n ik++++ +  sv+   + +k++y+k+ ++q +   P+lf l++n+ +  l    
  gene2250|gene2250|rna2250|rna2250   1 VPHERLFAKLQSYGICGKFLNPIKAIYRRPMGSVKTGDKCPKPFYYKTDVKQRCLAPPILFDLYINDQFDVLTGIK 76 
                                        89*****************************9999977778**************************999999976 PP

                                        .......TEEECTTEEEEEESSHHHHHHHHHHHHHHHHHTT--BEGG CS
                              RVT_1 159 ....kgvtllrYaDDililskskeelqelleaveewlkesglkinpe 201
                                            ++v  l++aDD+ +++++ ++ + ++  +++ +++ ++++n +
  gene2250|gene2250|rna2250|rna2250  77 vepkTSVPGLLFADDTGLFAEDYDKTKICIPRIKQECEKRKMELNIT 123
                                        99999***************************************965 PP

>> DrrA_P4M  DrrA phosphatidylinositol 4-phosphate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.2   1.9e-05      0.17      41      98 ..     117     174 ..     101     178 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 1.9e-05
                                        HHTT--SHHHHHHHHHHHHTSHHHHHHHS-SSHHHHHHT---HHHHHHHHHHHHHHHT CS
                           DrrA_P4M  41 kleeistkeeLeklvkefkkseeykilktgQglftrlfglkTssvkalekivkeaeke 98 
                                        k+e   t+  + ++ +e  ++ +yki++ +Q   +r ++l ++ + ++++i ++++++
  gene2250|gene2250|rna2250|rna2250 117 KMELNITEFGVMRFDTEATATIKYKIIEISQVSSYRCLRLPIDRKLNMNTITNDRKDR 174
                                        5555557777788999999**********************************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       436  (0.0243181); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1452.91
//
Query:       gene2251|gene2251|rna2251|rna2251  [L=148]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       286  (0.0159518); expected 358.6 (0.02)
Passed bias filter:                      199  (0.0110993); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 1059.99
//
Query:       gene2252|gene2252|rna2252|rna2252  [L=133]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       232  (0.0129399); expected 358.6 (0.02)
Passed bias filter:                      212  (0.0118244); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 967.20
//
Query:       gene2253|gene2253|rna2253|rna2253  [L=234]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       301  (0.0167884); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1653.86
//
Query:       gene2254|gene2254|rna2254|rna2254  [L=102]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       533  (0.0297284); expected 358.6 (0.02)
Passed bias filter:                      502  (0.0279993); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 693.72
//
Query:       gene2255|gene2255|rna2255|rna2255  [L=496]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0032   17.6   7.8     0.0032   17.6   7.8    3.3  4  EamA      EamA-like transporter family
  ------ inclusion threshold ------
      0.072   13.0   0.0      0.072   13.0   0.0    2.4  2  EOS1      N-glycosylation protein


Domain annotation for each model (and alignments):
>> EamA  EamA-like transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5  22.2     0.069   6.2e+02      18     134 ..      33     150 ..      19     151 .. 0.81
   2 ?    0.6   0.4     0.065   5.8e+02       3      24 ..     162     183 ..     160     189 .. 0.87
   3 ?   -3.5   0.1       1.2   1.1e+04      38      53 ..     339     354 ..     330     363 .. 0.61
   4 !   17.6   7.8   3.6e-07    0.0032      64     134 ..     419     488 ..     392     490 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.069
                               EamA  18 fvlskil...lrkvspltltfvrfliagillliiallkegklaklslkdwllllllgllgtvlafllffyalkkts 90 
                                        ++l k++   l +++++ l+ ++++i  +ll+++  +++ ++ +l+l+ +l+ +  ++  +vl+ +  + al+++s
  gene2255|gene2255|rna2255|rna2255  33 TLLNKHIttaLGFHPTFLLLLMQSVIIVALLVFLKTVNACSF-VLNLRCMLYWIPAAA-FMVLMIFSGLRALSHLS 106
                                        445555523255567778888999999999999999999999.999998888777776.567777899******** PP

                               EamA  91 asnaslitslePvftlilsvlllgekltlkqllgivlillGvll 134
                                         s  +l+ + ++++++++  +l+g  ++ ++++ +v+++++ +l
  gene2255|gene2255|rna2255|rna2255 107 ISMFTLFKNYSVIVIAVFELVLFGRAISRLSIMCFVMMIISGML 150
                                        *************************************9997555 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.065
                               EamA   3 gillallaalfwaiyfvlskil 24 
                                        g++++ + ++ +a+y ++ +++
  gene2255|gene2255|rna2255|rna2255 162 GYVWICINVIASAVYVIVLRMT 183
                                        899*************999876 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 1.2
                               EamA  38 fliagillliiallke 53 
                                         +++  +l++++l+++
  gene2255|gene2255|rna2255|rna2255 339 QILSIPFLFLLSLFFD 354
                                        4555555555555554 PP

  == domain 4  score: 17.6 bits;  conditional E-value: 3.6e-07
                               EamA  64 wllllllgllgtvlafllffyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvll 134
                                        ++l+++l+ ++++++ l  ++ l+++s+++ s++ ++  +++ + s ++lge++++++ ++i+++ l+ +l
  gene2255|gene2255|rna2255|rna2255 419 VFLFIVLSGVSVFFVALSTVWCLRSLSSTTLSMMGATNKIIVSM-SGVFLGERIGWIKAVSIAVGGLASIL 488
                                        4556777779999999***********************99988.55566************999887766 PP

>> EOS1  N-glycosylation protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   6.1       1.1     1e+04      14      73 ..      23      86 ..      19      97 .. 0.70
   2 ?   13.0   0.0     8e-06     0.072      38     165 ..     132     347 ..     108     353 .. 0.79

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 1.1
                               EOS1 14 saylayslldsLlvrWlvy.YsilaaliRllslqaiiwplvll..llsvlsad.keqplaaWiv 73
                                        +yl  sl+ +Ll++ + +   + ++ + ll  ++ii++l  +  +++++s+  + +++  Wi 
  gene2255|gene2255|rna2255|rna2255 23 PLYLLSSLVSTLLNKHITTaLGFHPTFLLLLMQSVIIVALLVFlkTVNACSFVlNLRCMLYWIP 86
                                       57999999999**999976267889999888888888877655124555555555667777775 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 8e-06
                               EOS1  38 aliRllslqaiiwplvllllsvlsadkeqplaaWivisttltlseivqswvt..Snladaeldsrevksrssaaer 111
                                        a+ Rl  +  +++ +  +l+ + ++  ++   +Wi i  ++++++++   +t   ++      s++++s+s  aer
  gene2255|gene2255|rna2255|rna2255 132 AISRLSIMCFVMMIISGMLVDYSETVVDRAGYVWICINVIASAVYVIVLRMTivHHIGVR--RSETEESTSHGAER 205
                                        7889999999999999999999999999*****************997766611455433..33333333444444 PP

                               EOS1 112 l........................................................................... 112
                                        +                                                                           
  gene2255|gene2255|rna2255|rna2255 206 Sgvngtgfagmnqtdkgllrkmlhgtiesrrageksddvgtaysdracttpvivfcseaarrvrnnriggyvrmfe 281
                                        4778999999999999999999999999999999****************************************** PP

                               EOS1 113 .............eskasslrqgksrhkrsvskseakkkrertsskrtldleeivvravvPvgvls 165
                                                      s++++++  +  + r+v+k++++k++++  + r  d+e++v   ++ + +l 
  gene2255|gene2255|rna2255|rna2255 282 gmgdrrpeqkpskGSTEENVQGVNVCDDRMVKKATERKTKRKNVKYRPNDFEHLVYSQILSIPFLF 347
                                        ***999988866533444444444556666666666777777777888888888888887776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (496 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1065  (0.059401); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.26s 00:00:00.86 Elapsed: 00:00:00.45
# Mc/sec: 3293.24
//
Query:       gene2256|gene2256|rna2256|rna2256  [L=95]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00026   20.8   0.0    0.00031   20.6   0.0    1.1  1  dCMP_cyt_deam_1  Cytidine and deoxycytidylate deaminase zinc-
     0.0014   18.4   0.0     0.0016   18.2   0.0    1.1  1  MafB19-deam      MafB19-like deaminase


Domain annotation for each model (and alignments):
>> dCMP_cyt_deam_1  Cytidine and deoxycytidylate deaminase zinc-binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   3.5e-08   0.00031      51     100 ..      16      66 ..       3      67 .. 0.88

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 3.5e-08
                                        TB-HHHHHHHHHHHHT.SSCETTEEEEEEE--BHHHHHHHHHHT-SEEEEE CS
                    dCMP_cyt_deam_1  51 tiHAEvnAilkaakng.gsklegatlyvtlePCsmCakaiiqsgikkvvvg 100
                                         +H  +nA++++ +++ ++  +g   +   ePC +C++a ++ +i++v+++
  gene2256|gene2256|rna2256|rna2256  16 LNHGILNAVTAVSQQQiNYLCTGLDAFLLNEPCVSCSMAFVHGRIRRVFYV 66 
                                        5799999**9999998898899*9************************996 PP

>> MafB19-deam  MafB19-like deaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   1.8e-07    0.0016      46     122 ..      12      91 ..       2      95 .] 0.75

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.8e-07
                        MafB19-deam  46 nakataHaEiaalqqAakklkskrlddatlyvtlepCdmCagaivqaglkklvygagnpks...lnkLkvkekngr 118
                                        + + ++H+  +a+   +++ ++    ++  +   epC  C  a v ++++++ y  +   +       ++k++n+r
  gene2256|gene2256|rna2256|rna2256  12 RDDILNHGILNAVTAVSQQQINYLCTGLDAFLLNEPCVSCSMAFVHGRIRRVFYVNNGTGTysrQRMHEFKKFNHR 87 
                                        4457778888888888888888888888889999*****************9987764433564444468999999 PP

                        MafB19-deam 119 velv 122
                                        + ++
  gene2256|gene2256|rna2256|rna2256  88 YAVF 91 
                                        9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       465  (0.0259356); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.48
# Mc/sec: 599.37
//
Query:       gene2257|gene2257|rna2257|rna2257  [L=142]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.7e-23   81.5   0.2    7.6e-23   81.3   0.2    1.0  1  Ribosomal_S9  Ribosomal protein S9/S16
  ------ inclusion threshold ------
      0.075   12.6   0.0       0.12   11.9   0.0    1.3  1  DLH           Dienelactone hydrolase family


Domain annotation for each model (and alignments):
>> Ribosomal_S9  Ribosomal protein S9/S16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.3   0.2   8.5e-27   7.6e-23       1     121 []       8     142 .]       8     142 .] 0.84

  Alignments for each domain:
  == domain 1  score: 81.3 bits;  conditional E-value: 8.5e-27
                                        EECTTEEEEEEEEESSS..EEEETTEECCHHSTTSCHHHHHCHHHHHTTTSS..SEEEEEEEESS-HHHHHHHHHH CS
                       Ribosomal_S9   1 GrrKesvArvwikegkg..kilvngksleeYfkeeaarekvleplkltgllg..kfdvfvkvkgGGlsgqaeAirl 72 
                                        G +K++ A+++ ++ ++  +++vn++  +  +++  +r+k+ e + ++g+++  ++ v+v+v+gGG+++q++A+r+
  gene2257|gene2257|rna2257|rna2257   8 GSKKHAKAHATTVPIQSpfSLTVNHVAHAL-IQDAFMRNKINELILTIGKENleNLCVNVSVRGGGHVSQVYAVRQ 82 
                                        789********9987651156777776666.799*********9999998776589******************** PP

                                        HHHHHHHHHHH.....HHHHHHC......TCCCTS-B--------TTSSCTTB----S-- CS
                       Ribosomal_S9  73 giaraLvalek.....eekkeLk......kaglltrDpRvvErkKtgkkkARkkyqwskR 121
                                        +ia+++va++      e+k+e++      ++  l++DpR+ E+kK+g + AR+ky++s+R
  gene2257|gene2257|rna2257|rna2257  83 AIAKGVVAFYGkfideEKKQEIQnrlmkfDKFTLVADPRRSEPKKYGGPSARAKYTKSYR 142
                                        *********855555333555555555788999*************************99 PP

>> DLH  Dienelactone hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   1.3e-05      0.12     108     138 ..      71     101 ..      62     113 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.3e-05
                                DLH 108 GGalalllaaevpevdaavafYGlspekele 138
                                        GG ++ ++a +++ ++++vafYG++ ++e +
  gene2257|gene2257|rna2257|rna2257  71 GGHVSQVYAVRQAIAKGVVAFYGKFIDEEKK 101
                                        99999******************44444333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       564  (0.0314574); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 940.33
//
Query:       gene2258|gene2258|rna2258|rna2258  [L=168]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-43  149.1   8.2    1.3e-43  148.9   8.2    1.1  1  Ribosomal_L13e  Ribosomal protein L13e


Domain annotation for each model (and alignments):
>> Ribosomal_L13e  Ribosomal protein L13e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  148.9   8.2   7.4e-48   1.3e-43       2     167 ..       7     161 ..       6     168 .] 0.84

  Alignments for each domain:
  == domain 1  score: 148.9 bits;  conditional E-value: 7.4e-48
                     Ribosomal_L13e   2 ipnnhfrKdwqrrvktwfdqparkkrRrearqakaakvaprpvekLrPvVrcptvrYntkvraGrGFtleElkaag 77 
                                        + +nhf K    + ktwfdqpa++++Rr+ar++ka+k  p pv+kL PvVr pt+r+n++vr+GrGFt +E+  ag
  gene2258|gene2258|rna2258|rna2258   7 LVSNHFNKGS-MKFKTWFDQPAKRQKRRAARREKAKKRYPIPVKKLLPVVRQPTQRHNYRVRLGRGFTEQEIVGAG 81 
                                        5689****76.679************************************************************** PP

                     Ribosomal_L13e  78 iskklArtiGIavDhRrknkseeslkaNveRLkeYkskLilfprkakkpkkgdaskeelkaakqvkvaavlpikke 153
                                        i+ ++A +iG++vD+Rrk++++e+ ++NveRLkeY +++ ++++   k  + d++k          + +++p+k+e
  gene2258|gene2258|rna2258|rna2258  82 IEVRYAMSIGVKVDKRRKDRNTETYERNVERLKEYLKHVKVYKNA--KEAREDNAK--------SFIGTIMPVKNE 147
                                        **************************************9988333..222223222........335557777766 PP

                     Ribosomal_L13e 154 akkekaraiteeek 167
                                        +  +k+ ++ + ++
  gene2258|gene2258|rna2258|rna2258 148 KPVTKFVNVADINS 161
                                        66666666655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1720  (0.095934); expected 358.6 (0.02)
Passed bias filter:                      809  (0.0451224); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 1047.70
//
Query:       gene2259|gene2259|rna2259|rna2259  [L=323]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.68    9.5   3.0         11    5.5   0.0    3.0  3  DUF3053   Protein of unknown function (DUF3053)


Domain annotation for each model (and alignments):
>> DUF3053  Protein of unknown function (DUF3053)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.1    0.0096   1.7e+02      75     123 ..      40      89 ..      30      98 .. 0.84
   2 ?    1.0   0.1     0.015   2.7e+02     119     144 ..     154     181 ..      98     197 .. 0.60
   3 ?    5.5   0.0   0.00064        11      66     110 ..     271     315 ..     264     320 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.0096
                            DUF3053  75 slepvvdalqsirspqdyltr.rdelrqaagalneleqqlqnakaqadka 123
                                        sl+pv d l++  +++++l++   +++  a++ +++ +++ + ++++d++
  gene2259|gene2259|rna2259|rna2259  40 SLRPVTDRLNKTPTQAELLEQiSANMQVYAENTERFMSSIYQSREHVDSS 89 
                                        78999999999999999999944678999999999999999999999875 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.015
                            DUF3053 119 qadkaraaLkqpd..dlkavydkayekt 144
                                         a+k  a Lk+    + k+vydk++  t
  gene2259|gene2259|rna2259|rna2259 154 LARKMAASLKKHIklEYKPVYDKIWCDT 181
                                        3667777777754115589999999654 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.00064
                            DUF3053  66 qqlnqavetslepvvdalqsirspqdyltrrdelrqaagalnele 110
                                        ++l++a+ + ++ +++++++i s ++ l+++  l+q +g l+ l+
  gene2259|gene2259|rna2259|rna2259 271 HRLTRAMIELVRSLFKMVNAIDSTANDLEKKAILQQHKGDLALLS 315
                                        67889999999****************************998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (323 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       966  (0.0538792); expected 358.6 (0.02)
Passed bias filter:                      582  (0.0324614); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.41
# Mc/sec: 2362.86
//
Query:       gene226|gene226|rna226|rna226  [L=198]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      4e-51  172.8   3.6    4.7e-51  172.6   3.6    1.0  1  Ras          Ras family
    1.4e-36  125.4   0.8    2.1e-36  124.8   0.8    1.3  1  Roc          Ras of Complex, Roc, domain of DAPkinase
    1.6e-17   63.5   1.2      2e-17   63.2   1.2    1.1  1  Arf          ADP-ribosylation factor family
    3.3e-08   33.2   2.1    4.2e-08   32.8   2.1    1.1  1  Gtr1_RagA    Gtr1/RagA G protein conserved region
    2.6e-07   30.7   0.3    4.6e-07   29.9   0.2    1.4  1  MMR_HSR1     50S ribosome-binding GTPase
    1.9e-06   27.5   0.7    3.8e-06   26.4   0.7    1.6  1  SRPRB        Signal recognition particle receptor beta subuni
    4.2e-05   23.2   2.7    5.2e-05   22.9   1.5    1.8  2  GTP_EFTU     Elongation factor Tu GTP binding domain
    0.00011   22.1   3.5    0.00047   20.1   0.1    2.2  2  RsgA_GTPase  RsgA GTPase
    0.00065   20.0   0.1     0.0031   17.8   0.0    2.1  2  AAA_22       AAA domain
     0.0013   18.3   0.1     0.0029   17.1   0.1    1.6  1  AAA_7        P-loop containing dynein motor region
     0.0076   16.7   0.0      0.014   15.8   0.0    1.5  1  AAA          ATPase family associated with various cellular a
     0.0096   15.5   2.1      0.033   13.7   1.8    2.0  2  FeoB_N       Ferrous iron transport protein B
  ------ inclusion threshold ------
      0.012   16.0   0.0      0.022   15.2   0.0    1.8  1  AAA_16       AAA ATPase domain
      0.012   15.0   0.1       0.26   10.7   0.0    2.3  2  TniB         Bacterial TniB protein
      0.019   15.5   0.5      0.054   14.0   0.5    1.8  1  ABC_tran     ABC transporter
       0.02   15.1   0.0      0.029   14.6   0.0    1.4  1  AAA_33       AAA domain
      0.024   14.2   0.3      0.032   13.8   0.3    1.3  1  PI-PLC-X     Phosphatidylinositol-specific phospholipase C, X
      0.027   13.8   2.6       0.14   11.4   2.5    2.0  1  AIG1         AIG1 family
      0.098   12.7   0.0       0.19   11.7   0.0    1.6  1  AAA_5        AAA domain (dynein-related subfamily)
       0.15   11.8   0.0       0.34   10.7   0.0    1.6  1  AAA_29       P-loop containing region of AAA domain
       0.21   10.9   0.1       0.43    9.9   0.0    1.5  2  DNA_pol_E_B  DNA polymerase alpha/epsilon subunit B


Domain annotation for each model (and alignments):
>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  172.6   3.6   5.5e-54   4.7e-51       1     160 [.       9     170 ..       9     172 .. 0.96

  Alignments for each domain:
  == domain 1  score: 172.6 bits;  conditional E-value: 5.5e-54
                                    EEEEEESTTSSHHHHHHHHHHSSCSSSCTTTSSEEEEEEEEEETTEEEEEEEEEETTSGGGHHHHHHHHTTESEEEEEEE CS
                            Ras   1 KlvlvGdsavGKtslllrfvkdkFkeeyesTigvdfytkeievdgkevkleiwDTAGqeefkslrelyyrdaegillvyd 80 
                                    K +l+G+s+vGKts+++r+v+++++e+y+sTigvdf++k+++ +gk+vkl+iwDTAGqe+f++++++yyr+a++i++v+d
  gene226|gene226|rna226|rna226   9 KTILIGNSGVGKTSIINRYVDETYTENYISTIGVDFKIKTLTRHGKTVKLQIWDTAGQERFRTITSSYYRGAHCIIVVFD 88 
                                    88****************************************************************************** PP

                                    TTBHHHHHTHHHHHHHHHHHSTTTSEEEEEEETTTGGGG-SS-HHHHHHHHHHHT...SEEEEEBTTTTCTHHHHHHHHH CS
                            Ras  81 itsresfenvkkwveeikrvaeenvpivLvGnKvDleekravsteegeelakelg...lkfletSAktnenveeafeell 157
                                    +t++esf++v++w+ e+++++ +++ ivL+GnK+D ++  av+++++ ++ + +      f  +SAk+n++++++fe+++
  gene226|gene226|rna226|rna226  89 VTEEESFSDVASWIAEVEKHKVNDTLIVLLGNKIDDQN-VAVKNDDVMKMIETYRldrSLFRYISAKENTDITTVFESIV 167
                                    ***********************************886.99*********9887733467*******************9 PP

                                    HHH CS
                            Ras 158 rei 160
                                    +++
  gene226|gene226|rna226|rna226 168 DKL 170
                                    987 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  124.8   0.8   2.4e-39   2.1e-36       1     119 [.       9     123 ..       9     124 .. 0.89

  Alignments for each domain:
  == domain 1  score: 124.8 bits;  conditional E-value: 2.4e-39
                                    EEEEESSTTSSHHHHHHCHCT-CCC-EEETTTTEEEEEEECGGSGGCTTBTTTTCEEEEEEEE-SGGCTTTT-HHHHCTS CS
                            Roc   1 KvvlvGdsgvGKtsllkrfvedkfsekekstigvdfltkevtkikgvendkkvkkvklniWDtaGqerfrslhplylrea 80 
                                    K +l+G+sgvGKts+++r+v+++++e++ stigvdf+ k++t        ++ k+vkl+iWDtaGqerfr+++++y+r+a
  gene226|gene226|rna226|rna226   9 KTILIGNSGVGKTSIINRYVDETYTENYISTIGVDFKIKTLT--------RHGKTVKLQIWDTAGQERFRTITSSYYRGA 80 
                                    789*********************************998873........235789************************ PP

                                    CEEEEEEE...GHHHHCHHHHHHHHHHHCSSS.-EEEEEE-TT CS
                            Roc  81 alailvyd...srssenlkeWlkelkkvagks.pvilvgnkiD 119
                                    +++i+v+d   ++s++++ +W+ e++k+  ++  ++l+gnkiD
  gene226|gene226|rna226|rna226  81 HCIIVVFDvteEESFSDVASWIAEVEKHKVNDtLIVLLGNKID 123
                                    ********7655567899*********98776256789****9 PP

>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.2   1.2   2.4e-20     2e-17      15     146 ..       8     144 ..       2     172 .. 0.83

  Alignments for each domain:
  == domain 1  score: 63.2 bits;  conditional E-value: 2.4e-20
                                    EEEEEEESTTSSHHHHHHHHHHSSCEE.CSSSSS..EEEEEEEE..TTEEEEEEEE-SSGGGGGGGGGGCTTESEEEEEE CS
                            Arf  15 lrilllGLDnaGKtTilkklkleelvt.tvPTig..fnveelei..knlkftvwDvGGqeklRplWknYfektdavifvv 89 
                                    ++ +l+G  + GKt i++++ +e  ++  + Tig  f++++l+   k++k+++wD  Gqe+ R + ++Y++  + +i v 
  gene226|gene226|rna226|rna226   8 FKTILIGNSGVGKTSIINRYVDETYTEnYISTIGvdFKIKTLTRhgKTVKLQIWDTAGQERFRTITSSYYRGAHCIIVVF 87 
                                    588999**************9998765488998755889999877799******************************** PP

                                    ETT-CTTHHHHHHHHHHHCTSGCCTTSEEEEEEE-TTSTT.SS-HHHHHHHTTGGGSS CS
                            Arf  90 DsadreRleeakeeLkalleeeelkevallvlaNKqDlpe.alseeelrellgleelk 146
                                    D++++e +++  + ++++ e++++++  +++l+NK+D ++ a++++++ ++++ ++l 
  gene226|gene226|rna226|rna226  88 DVTEEESFSDVASWIAEV-EKHKVNDTLIVLLGNKIDDQNvAVKNDDVMKMIETYRLD 144
                                    *************99996.677888999999*****8765388999999999998877 PP

>> Gtr1_RagA  Gtr1/RagA G protein conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.8   2.1   4.9e-11   4.2e-08       1     161 [.       9     168 ..       9     172 .. 0.72

  Alignments for each domain:
  == domain 1  score: 32.8 bits;  conditional E-value: 4.9e-11
                      Gtr1_RagA   1 kvLLmGksgsGKtsmrsi.iFdnylardtlrlgatidveksevrflgnltlnlwDcgGqeafveeylssqkeeifrnvgv 79 
                                    k +L+G+sg GKts+ +  + + y+ + + ++g+  +++  + r  + ++l++wD  Gqe+f + +     ++ +r    
  gene226|gene226|rna226|rna226   9 KTILIGNSGVGKTSIINRyVDETYTENYISTIGVDFKIKTLT-RHGKTVKLQIWDTAGQERFRTIT-----SSYYRGAHC 82 
                                    668***********8765166677778888899888887655.578899************98876.....77899999* PP

                      Gtr1_RagA  80 liyVfDvesreleedletlkeilealrqyspeakvfvli.hKmDliq.edereeifeerk.....eeireeieklekeei 152
                                    +i VfDv+    ee++++  + + ++ +++ + ++ vl+ +K+D  +   +++++++ ++     +++ + i+  e+++i
  gene226|gene226|rna226|rna226  83 IIVVFDVT---EEESFSDVASWIAEVEKHKVNDTLIVLLgNKIDDQNvAVKNDDVMKMIEtyrldRSLFRYISAKENTDI 159
                                    ********...577888899999999999999999998868999766333333444433300001333333445555577 PP

                      Gtr1_RagA 153 qffaTSiwd 161
                                    ++   Si d
  gene226|gene226|rna226|rna226 160 TTVFESIVD 168
                                    777777776 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.9   0.2   5.4e-10   4.6e-07       3     103 ..      11     108 ..       9     121 .. 0.63

  Alignments for each domain:
  == domain 1  score: 29.9 bits;  conditional E-value: 5.4e-10
                                    EEEESTTSSHHHHHHHHHTS.......TEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSSHHHHHHHHHHHHHHHHC CS
                       MMR_HSR1   3 aivGrpNvGKStLinaltge.......kaivsdkpgtTrdinegrvklkgkeielvDtpGliegaseekglgkaflalee 75 
                                    +++G++ vGK+++in+ ++e         i  d++ +T++   ++vk     ++++Dt+G  e   + + ++ ++ +   
  gene226|gene226|rna226|rna226  11 ILIGNSGVGKTSIINRYVDEtytenyiSTIGVDFKIKTLTRHGKTVK-----LQIWDTAG-QE---RFRTITSSYYR--G 79 
                                    79****************86332223222446666677776666665.....99******.54...23356666653..4 PP

                                    TSEEEEEEETT.TTCSHHHHHHHHHHHHH CS
                       MMR_HSR1  76 adlillvvdas.eeklkpldeeleellee 103
                                    a+ i++v+d++ ee+++++ + ++e+ ++
  gene226|gene226|rna226|rna226  80 AHCIIVVFDVTeEESFSDVASWIAEVEKH 108
                                    89*******88433555555555555433 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4   0.7   4.5e-09   3.8e-06       6     127 ..      10     128 ..       8     191 .. 0.80

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 4.5e-09
                                    EEEE-STTSSHHHHHHHHHHSS---B---S.S-EEETTG.....GGTT-SEEEETT-GCCSHHHHHHHHHHGGEEEEEEE CS
                          SRPRB   6 vllvGlsdsGKTslftrLttdsvkktvtSq.essaalkv..ksekgskltliDfPGheklrqklleklkaksslkglvfv 82 
                                     +l+G s  GKTs+++r   +++++ ++S     +  k+  +  k  kl++ D  G+e++r+  +    + + ++ ++ v
  gene226|gene226|rna226|rna226  10 TILIGNSGVGKTSIINRYVDETYTENYISTiGVDFKIKTltRHGKTVKLQIWDTAGQERFRTITSS---YYRGAHCIIVV 86 
                                    599**************************97666776664456677788999*********86555...588999***** PP

                                    EETTS-HHHHHHHHHHHHHHHHHHHHHTT---EEEEEE-.TTSTT- CS
                          SRPRB  83 vDStidpkevkevAEllyeilliteklkdavdiliACnK.qelfla 127
                                     D t ++    +vA ++ e+  +++  +d++ i++  nK ++  +a
  gene226|gene226|rna226|rna226  87 FDVT-EEESFSDVASWIAEVEKHKV--NDTL-IVLLGNKiDDQNVA 128
                                    **98.56789*******99977776..4444.44444551445555 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   1.5   6.1e-08   5.2e-05      54     191 ..      40     169 ..       7     173 .. 0.73
   2 ?    0.6   0.0      0.42   3.6e+02      17      53 ..     160     196 ..     159     197 .. 0.84

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 6.1e-08
                                    SCSSCEEEEEETTCSSEEEEEEEESSSGGGHHHHHHHHHT-SEEEEEEETTTB.STHHHHHHHHHHHHTTTE...EEEEE CS
                       GTP_EFTU  54 iTiksaaisleketkkylinliDtPGHvdFskevirglrvlDgavlvvdaveG.vepqteevlrlalkegvp...iivfi 129
                                    i ++ +  +l +++k+ ++++ Dt G + F   ++  +r +++ ++v+d++e    +     +  + k++v+   i+++ 
  gene226|gene226|rna226|rna226  40 IGVDFKIKTLTRHGKTVKLQIWDTAGQERFRTITSSYYRGAHCIIVVFDVTEEeSFSDVASWIAEVEKHKVNdtlIVLLG 119
                                    4444444444467*************************************987355677778888999999999788888 PP

                                    ESCGSTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTTEEEEEEBTTTTBTHHHHHHHHHHH CS
                       GTP_EFTU 130 NKmDrlkaelkeiveevkqklsrkeeklekygekgekevpvvfgSalkgegvktllealvel 191
                                    NK+D    ++    ++v  k+      +e y  +++    + ++Sa+++  ++t++e +v++
  gene226|gene226|rna226|rna226 120 NKIDDQ--NVAVKNDDVM-KM------IETYRLDRS---LFRYISAKENTDITTVFESIVDK 169
                                    ****76..3444444444.33......455555553...56778888888888888877765 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.42
                                    HHHHHHHHHHTTSSCHHHHHHHHHSTHCHSHHHHHHT CS
                       GTP_EFTU  17 tTLtdrLlyktgaiskkgekaeeervlDtlkeErerg 53 
                                    tT+ ++++ k+ + +k +  +ee+++ D   +Er r 
  gene226|gene226|rna226|rna226 160 TTVFESIVDKLIERHKLEDGDEENEFADIKIQERTRR 196
                                    89999999888888887777788999****9999985 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.1   5.5e-07   0.00047     102     124 ..      10      32 ..       8      82 .. 0.68
   2 ?    3.1   0.6     0.094        80      19      97 ..      83     166 ..      67     172 .. 0.65

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 5.5e-07
                                    EEEECSTTSSHHHHHHHHCTT-- CS
                    RsgA_GTPase 102 svlvGqSGvGKStLinallpele 124
                                    ++l+G+SGvGK+++in+ + e+ 
  gene226|gene226|rna226|rna226  10 TILIGNSGVGKTSIINRYVDETY 32 
                                    79***************999832 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.094
                                    EEEEEESTTTT--HHHHHHHHHHHHHTT-.EEEEEE..E-GGG--HHH...HHHHHHHHHHHTTSEEEE--TTTHTTHHH CS
                    RsgA_GTPase  19 llivvslkepelslnlldrfLvlaeekgi.epvivl..nKiDlleeee...eleelkeelealgyevllvsaktkeglee 92 
                                    +++v+ ++ +e s + +   ++++e++++ + +ivl  nKiD  + +    ++ ++ e+++     + ++sak+++++++
  gene226|gene226|rna226|rna226  83 IIVVFDVT-EEESFSDVASWIAEVEKHKVnDTLIVLlgNKIDDQNVAVkndDVMKMIETYRLDRSLFRYISAKENTDITT 161
                                    56777777.77778888889999999999434444456898876655523345555555554444455667777776666 PP

                                    HHHHC CS
                    RsgA_GTPase  93 lkell 97 
                                    + e +
  gene226|gene226|rna226|rna226 162 VFESI 166
                                    66655 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   3.6e-06    0.0031       8      61 ..      10     103 ..       9     126 .. 0.75
   2 ?   -1.4   0.0       3.2   2.7e+03      41      68 ..     146     174 ..     124     189 .. 0.70

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 3.6e-06
                         AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaee........................................erpevvfvtl 47 
                                    ++++G sG+GKT  ++r++++   e+++ +                                        ++  +v +++
  gene226|gene226|rna226|rna226  10 TILIGNSGVGKTSIINRYVDETYTENYISTigvdfkiktltrhgktvklqiwdtagqerfrtitssyyrgAHCIIVVFDV 89 
                                    589*****************997777777688888888888777777777777777766666666666444444446666 PP

                         AAA_22  48 psstsskdllrell 61 
                                    ++++s +d++++++
  gene226|gene226|rna226|rna226  90 TEEESFSDVASWIA 103
                                    66666666666665 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 3.2
                         AAA_22  41 evv.fvtlpsstsskdllrellralglel 68 
                                    +++ ++ +++ t+ +++++ ++ +l +++
  gene226|gene226|rna226|rna226 146 SLFrYISAKENTDITTVFESIVDKLIERH 174
                                    33347777777788888888887776655 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.1   3.4e-06    0.0029      36      71 ..      10      46 ..       7      57 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 3.4e-06
                          AAA_7 36 vllvGptGtGKtviikdllkkldkekyls.ltinfsa 71
                                   ++l+G++G+GKt+ii++++++  +e+y+s + + f+ 
  gene226|gene226|rna226|rna226 10 TILIGNSGVGKTSIINRYVDETYTENYIStIGVDFKI 46
                                   789**************88888888876514566655 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   1.6e-05     0.014       2      69 ..      11      92 ..      10     151 .. 0.59

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.6e-05
                                   EEESSTTSSHHHHHHHHHHHHT.HEEEEEETTTCSSS.............STTHHHHHHHHHHHHHHHTSTS.EEEEEETGG CS
                            AAA  2 llyGppGtGKTllakavakelg.vefleisgsellsk.............yvgesekkirelfkeakekakp.silfiDEid 68
                                   +l+G+ G+GKT++++  + e+   +++++ g ++  k             +  ++++++r + ++  + a +  i+++D  +
  gene226|gene226|rna226|rna226 11 ILIGNSGVGKTSIINRYVDETYtENYISTIGVDFKIKtltrhgktvklqiWDTAGQERFRTITSSYYRGA-HcIIVVFDVTE 91
                                   79******************74233333333333322233345566677788899999999999998888.62555566333 PP

                                   G CS
                            AAA 69 a 69
                                   +
  gene226|gene226|rna226|rna226 92 E 92
                                   3 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   1.8   3.9e-05     0.033       3      57 ..      10      66 ..       8     166 .. 0.85
   2 ?    0.3   0.1      0.52   4.4e+02      78     111 ..     130     163 ..     116     180 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.9e-05
                                   EEEEESTTSSHHHHHHHHHTTSEEEEES.TTSSSEEEEEEEEETT..EEEEEEE---- CS
                         FeoB_N  3 valvGnpnvGkttlfnaltgakqkvgNw.pGvtvekkegklklkg..keveivDlPGi 57
                                    +l+Gn  vGkt+++n+  + + +  N+ + + v+ k  +l+ +g   +++i D  G 
  gene226|gene226|rna226|rna226 10 TILIGNSGVGKTSIINRYVDET-YTENYiSTIGVDFKIKTLTRHGktVKLQIWDTAGQ 66
                                   689**************99865.56676467788888888777662255677787775 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.52
                                    SSSEEEEEEEGGGHHHHHHHHHHHHHTTSSEEEE CS
                         FeoB_N  78 epdvvvnvvdatnlernLyLtlqllelgvpvvla 111
                                    + d v++++++ +l+r+L+  +   e +  + + 
  gene226|gene226|rna226|rna226 130 KNDDVMKMIETYRLDRSLFRYISAKENTDITTVF 163
                                    5677889999999999998777766665555555 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.0   2.5e-05     0.022      28      55 ..      11      39 ..       9     195 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.5e-05
                         AAA_16 28 llsGesGvGKsslv.rellralekdggif 55
                                   +l+G+sGvGK+s++ r + + ++++++ +
  gene226|gene226|rna226|rna226 11 ILIGNSGVGKTSIInRYVDETYTENYIST 39
                                   799***********666666676664333 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0    0.0003      0.26      38      59 ..      10      31 ..       7      44 .. 0.86
   2 ?    2.2   0.0      0.12     1e+02      74     111 ..     150     187 ..     114     195 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0003
                           TniB 38 lllvGdsnnGKtmivekFarlh 59
                                    +l+G+s +GKt+i++++ ++ 
  gene226|gene226|rna226|rna226 10 TILIGNSGVGKTSIINRYVDET 31
                                   5799**************9875 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.12
                           TniB  74 vvqappkpdekrlyaaiLealgaplkararvskleqqv 111
                                    +++a ++ d    +++i+++l +++k ++  ++ e + 
  gene226|gene226|rna226|rna226 150 YISAKENTDITTVFESIVDKLIERHKLEDGDEENEFAD 187
                                    7899999999************9999988777766555 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.5   6.4e-05     0.054      14      99 ..      10     112 ..       8     192 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 6.4e-05
                                    EEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSB.HHHH............. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxx............. RF
                       ABC_tran  14 vaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpelt.vren............. 79 
                                    + ++G++G GK+++++    ++  te  i   g d+k ++l++  k ++    ++  +++ + + ++             
  gene226|gene226|rna226|rna226  10 TILIGNSGVGKTSIINRYVDETY-TENYISTIGVDFKIKTLTRHGKTVKLQIWDTAGQERFRtITSSyyrgahciivvfd 88 
                                    689*************9998876.89999888899988888888888877666633333333244446677777777777 PP

                                    ....HHHTCHHHHHHHSTTGGTTC CS
                                    ....xxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  80 ....esdeeiekalsklglkelkd 99 
                                        es ++++ ++++++ ++++d
  gene226|gene226|rna226|rna226  89 vteeESFSDVASWIAEVEKHKVND 112
                                    755444444555555555555444 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   3.3e-05     0.029       3     103 ..      11     116 ..      10     151 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.3e-05
                         AAA_33   3 llvGlpGsGKstlaerllkklg....avllssdtlrrrlfgtdqqsktdytrvldrlyqilnelarkalsagrnvil... 75 
                                    +l+G +G+GK+  + r++ ++       ++  d  +++l+  +++ k    +++d + q  ++++++   +g+++i+   
  gene226|gene226|rna226|rna226  11 ILIGNSGVGKTSIINRYVDETYtenyISTIGVDFKIKTLTRHGKTVK---LQIWDTAGQERFRTITSSYYRGAHCIIvvf 87 
                                    79***************988778776778888888888886655544...567777777778999999999***998655 PP

                         AAA_33  76 datnlsr.rerarflklarrlgvpvrivv 103
                                    d t  +  ++ a +++ +++++v+++++v
  gene226|gene226|rna226|rna226  88 DVTEEESfSDVASWIAEVEKHKVNDTLIV 116
                                    55544444555777777777777766655 PP

>> PI-PLC-X  Phosphatidylinositol-specific phospholipase C, X domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.3   3.8e-05     0.032      23     103 ..      36     129 ..      21     175 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.8e-05
                                    HHH---SS-HHHHHHTT--EEEEEE-...TT..............SEEEETTEEE.EEEHHHHHHHHHHHHHHSTT--EE CS
                       PI-PLC-X  23 lssessveayrnaLlrGcRcvEidvwdgedee.............pvvlhgytltkkikfrdvleaikdyafktselPvi 89 
                                      s+  v+  +++L r  + v +++wd + +e              +++    +t++ +f+dv + i ++ +++ + ++i
  gene226|gene226|rna226|rna226  36 YISTIGVDFKIKTLTRHGKTVKLQIWDTAGQErfrtitssyyrgaHCIIVVFDVTEEESFSDVASWIAEVEKHKVNDTLI 115
                                    456666777789999999************999***********97777778899************************* PP

                                    EEEEETTT-THHHH CS
                       PI-PLC-X  90 vsLevhcsaeqqek 103
                                    v L ++++ ++ ++
  gene226|gene226|rna226|rna226 116 VLLGNKIDDQNVAV 129
                                    ***99986654332 PP

>> AIG1  AIG1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   2.5   0.00017      0.14       3     126 ..      10     121 ..       8     178 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00017
                                    EEEESSTTSSHHHHHHHHHTS--SS--TTTS---SS-EEEEEEETTEEEEEEE--SCCCTTCCHHCHHHHHHHHHHHCTT CS
                           AIG1   3 ivlvGktgnGkSaTgNsilgkkaFesklsaqsvtkkcqkksrtwdgkkinViDTPglfdlsvsadkiskeivrclllsee 82 
                                     +l+G +g+Gk + +N  +++++ e  +s+ +v  k ++ +r  +  k+++ DT g            + i+        
  gene226|gene226|rna226|rna226  10 TILIGNSGVGKTSIINRYVDETYTENYISTIGVDFKIKTLTRHGKTVKLQIWDTAGQER--------FRTITS---SYYR 78 
                                    58**************************99**********99999999***99977322........222332...2234 PP

                                    -ESEEEEEEETTB-SHHHHHHHHHHHHHHCGGGGGGEEEEEEEG CS
                           AIG1  83 gihalllvlslgrfteedekalktlkelFGekilkylivvftrk 126
                                    g h +++v+++++ +   + +++ + e+  +k+ + liv++ +k
  gene226|gene226|rna226|rna226  79 GAHCIIVVFDVTEEE-SFSDVASWIAEVEKHKVNDTLIVLLGNK 121
                                    777777777765322.3345677777777777777777777665 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00022      0.19       2      23 ..      10      31 ..       9      84 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00022
                                   EEEE--SSSSHHHHHHHGGGGB CS
                          AAA_5  2 vlLvGppGtgKselaerlaaal 23
                                    +L+G++G+gK++++ r+   +
  gene226|gene226|rna226|rna226 10 TILIGNSGVGKTSIINRYVDET 31
                                   59************99986655 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00039      0.34      25      39 ..      10      24 ..       2      28 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00039
                         AAA_29 25 tlltGpsGsGKSTll 39
                                   t+l+G+sG+GK++++
  gene226|gene226|rna226|rna226 10 TILIGNSGVGKTSII 24
                                   89***********98 PP

>> DNA_pol_E_B  DNA polymerase alpha/epsilon subunit B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       3.6     3e+03      39      81 ..      13      53 ..      10      56 .. 0.62
   2 ?    9.9   0.0    0.0005      0.43      13      79 ..      92     172 ..      85     176 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 3.6
                                   ES-SSBTTSHHHHHT---S--SSHHHHHHHHTHHHHTTS-TTS CS
                    DNA_pol_E_B 39 aGnfvdaahkaiasskvstdekkenfdalalllsilesllekt 81
                                   +Gn+   ++  i+   v +++++en  +   ++ ++++l+ + 
  gene226|gene226|rna226|rna226 13 IGNSGVGKTSIIN-RYV-DETYTENYISTIGVDFKIKTLTRHG 53
                                   5555444444432.223.5788888888888888888888765 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0005
                                    ----HHHHHHHHHHH.HTT--SEEEEES-SSBTTSHHHHHT---..............S--SSHHHHHHHHTHHHHTTS- CS
                    DNA_pol_E_B  13 nrsleaLrkiLqgyapeesppdvlilaGnfvdaahkaiasskvs..............tdekkenfdalalllsilesll 78 
                                    ++s+     +++ +++++   ++++l+Gn +d ++ a ++ +v               ++++ken+d  + + si+++l 
  gene226|gene226|rna226|rna226  92 EESFSDVASWIAEVEKHKVNDTLIVLLGNKIDDQNVAVKNDDVMkmietyrldrslfrYISAKENTDITTVFESIVDKLI 171
                                    56788888999999988888899************9999999999****************************9999998 PP

                                    T CS
                    DNA_pol_E_B  79 e 79 
                                    e
  gene226|gene226|rna226|rna226 172 E 172
                                    6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (198 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       929  (0.0518155); expected 358.6 (0.02)
Passed bias filter:                      525  (0.0292822); expected 358.6 (0.02)
Passed Vit filter:                        85  (0.00474092); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.43
# Mc/sec: 1372.44
//
Query:       gene2260|gene2260|rna2260|rna2260  [L=232]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        0.1   12.5   0.0       0.23   11.4   0.0    1.6  1  CYTL1     Cytokine-like protein 1


Domain annotation for each model (and alignments):
>> CYTL1  Cytokine-like protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   1.3e-05      0.23      38      78 ..     178     218 ..     168     230 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 1.3e-05
                              CYTL1  38 klqksertescvevlPklyldihnscvlaklrdflaspkcr 78 
                                        +lq  +r ++c+e l k++ d+  +c l+ l d   +++ +
  gene2260|gene2260|rna2260|rna2260 178 SLQFKDRFKTCIEELDKVHTDVFAQCSLSSLFDSFDNEEWE 218
                                        57788899***********************9988776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       600  (0.0334653); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1657.59
//
Query:       gene2261|gene2261|rna2261|rna2261  [L=54]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (54 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       218  (0.0121591); expected 358.6 (0.02)
Passed bias filter:                      184  (0.0102627); expected 358.6 (0.02)
Passed Vit filter:                         6  (0.000334653); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.40
# Mc/sec: 408.26
//
Query:       gene2262|gene2262|rna2262|rna2262  [L=168]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      2e-30  104.8   5.6    3.3e-30  104.1   5.6    1.4  1  Ribosomal_L24e  Ribosomal protein L24e
  ------ inclusion threshold ------
       0.97    9.8   6.8       0.25   11.7   1.5    2.4  2  DUF2175         Uncharacterized protein conserved in archaea 


Domain annotation for each model (and alignments):
>> Ribosomal_L24e  Ribosomal protein L24e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.1   5.6   3.7e-34   3.3e-30       1      63 [.      14      76 ..      14      78 .. 0.98

  Alignments for each domain:
  == domain 1  score: 104.1 bits;  conditional E-value: 3.7e-34
                                       XXX-B-TTT-SB--SS--EEEE-TTS-EEEESSHHHHHHHHTT--GGGSTTSTTT-XXXXXXX CS
                     Ribosomal_L24e  1 mktekCsFsgykiyPGhGkrfvrnDgkvfrFlssKceklfkqkrnPrklkWTkayRrahkkel 63
                                       m++ekCsF+++++yPGhG +fvrnD+ vf+F++sKc+k+fk+k+nPr+++WTkayR  +kke+
  gene2262|gene2262|rna2262|rna2262 14 MRIEKCSFCSSSVYPGHGLTFVRNDSMVFTFCRSKCNKAFKRKWNPRRTRWTKAYRLYNKKEE 76
                                       9************************************************************97 PP

>> DUF2175  Uncharacterized protein conserved in archaea (DUF2175)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   1.5   2.7e-05      0.25       4      41 ..      18      55 ..      16      96 .. 0.83
   2 ?    0.3   0.3     0.094   8.4e+02      53      79 ..     131     158 ..     107     167 .. 0.47

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.7e-05
                            DUF2175  4 kCyiCgkeivegekFTft.kkgvvHyeClvekarkklke 41
                                       kC++C+ +++ g+  Tf+ ++++v   C ++k +k +k 
  gene2262|gene2262|rna2262|rna2262 18 KCSFCSSSVYPGHGLTFVrNDSMVFTFC-RSKCNKAFKR 55
                                       8*****************5666665555.6777776665 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.094
                            DUF2175  53 evlneeivklk.elerv.aedeevkkvle 79 
                                        + +++ i +++ +l +  +e  e+kk +e
  gene2262|gene2262|rna2262|rna2262 131 KDVDMNILRKHgHLLEEgKE-SESKKKME 158
                                        44444444433122222133.23333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1416  (0.0789782); expected 358.6 (0.02)
Passed bias filter:                      521  (0.0290591); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1150.56
//
Query:       gene2263|gene2263|rna2263|rna2263  [L=197]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.012   14.9   3.7      0.014   14.7   3.7    1.1  1  ORC6      Origin recognition complex subunit 6 (ORC6)
       0.24   10.0  10.1       0.03   12.9   4.9    1.8  2  FapA      Flagellar Assembly Protein A
       0.28   10.9   8.2       0.38   10.4   8.2    1.4  1  USP7_C2   Ubiquitin-specific protease C-terminal
       0.54    9.8   2.8        1.3    8.6   1.6    2.1  2  YvrJ      YvrJ protein family
        4.2    7.6  10.5        6.6    7.0  10.5    1.4  1  zf-C4H2   Zinc finger-containing protein


Domain annotation for each model (and alignments):
>> ORC6  Origin recognition complex subunit 6 (ORC6)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   3.7     4e-06     0.014     130     249 ..      56     183 ..      16     188 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 4e-06
                               ORC6 130 sksssplkrrrklaneedgeeeeed.apswvstsir....dsrpeisrtlspskslgdesilfndss....ddekk 196
                                         k  +   +  + ++e+++ e++ + +p+   ts+      +++++s++ ++sk++ +e++l+ +        +k+
  gene2263|gene2263|rna2263|rna2263  56 EKDATVEEIQMEEFDEQSDYEYNTSiVPDEHDTSYNpmydNTNQTNSHI-IESKPAVKERSLQSILIyastLLPKD 130
                                        5555666777788999999999999999999999999996555555555.67777766666655544666755566 PP

                               ORC6 197 seqksprk...llkkkkdkisdediielcnafelpaevlvkvletflarkrklvkk 249
                                        +++++ +k    l+++++++s  +i+++c+   +p++ +v +l +++  kr +v+k
  gene2263|gene2263|rna2263|rna2263 131 QKTQQNLKkivSLLYDQKEMSLNNIVTICK---VPKYRAVDILGKLSGAKRPIVSK 183
                                        666666665669999*************95...9*********9999999988876 PP

>> FapA  Flagellar Assembly Protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   4.9   8.4e-06      0.03     383     444 ..       1      63 [.       1      74 [. 0.87
   2 ?   -0.3   0.2      0.09   3.2e+02     349     402 ..      93     145 ..      67     169 .. 0.56

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 8.4e-06
                               FapA 383 lletkeklkeeleeleeelkelkeeleskkeea.kikvnkeiypgvkikigkkkliikreysn 444
                                        +l++++k+++ l e++++l++l+e  ++ k  + kik+ +e+++++ ++i + k++ +++ + 
  gene2263|gene2263|rna2263|rna2263   1 MLKKYQKINSLLVEIKTKLEKLQEHSNNLKLFNiKIKALNEAFKECSLTIENIKEEKDATVEE 63 
                                        57899************************77777*****************999998888544 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.09
                               FapA 349 leeeleklkkkikklpklkaekqlesekkeqlkklletkeklkeeleeleeelk 402
                                        + +++++ ++ i++ ++ +++++  + ++     ll + +k +++l+++   l 
  gene2263|gene2263|rna2263|rna2263  93 MYDNTNQTNSHIIESKP-AVKERSLQSILIYASTLLPKDQKTQQNLKKIVSLLY 145
                                        55555555555444444.344444444444444444444555555554444443 PP

>> USP7_C2  Ubiquitin-specific protease C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   8.2    0.0001      0.38      39     110 ..       2      74 ..       1     164 [. 0.87

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0001
                            USP7_C2  39 vpkngtvkdlleelqkkvklseeeskklrllevsnhkiqkvlke.dealeslndsttlraeeipedeleleed 110
                                        ++k ++++ ll e+++k++  +e+s++l+l++++ +   + +ke + ++e+++++++  +eei  +e + ++d
  gene2263|gene2263|rna2263|rna2263   2 LKKYQKINSLLVEIKTKLEKLQEHSNNLKLFNIKIKALNEAFKEcSLTIENIKEEKDATVEEIQMEEFDEQSD 74 
                                        68999*************99999*******************997789****************999988666 PP

>> YvrJ  YvrJ protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   1.6   0.00037       1.3      15      34 ..      11      30 ..      11      31 .. 0.95
   2 ?   -0.5   0.0      0.25     9e+02      19      31 ..      32      44 ..      32      47 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00037
                               YvrJ 15 LLvRiEkkLdeLtksIeeLs 34
                                       LLv i +kL++L+++ ++L+
  gene2263|gene2263|rna2263|rna2263 11 LLVEIKTKLEKLQEHSNNLK 30
                                       9***************9996 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.25
                               YvrJ 19 iEkkLdeLtksIe 31
                                       ++ k+++L+++ +
  gene2263|gene2263|rna2263|rna2263 32 FNIKIKALNEAFK 44
                                       6789****99865 PP

>> zf-C4H2  Zinc finger-containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0  10.5    0.0018       6.6       3      61 ..      13      71 ..      11     162 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0018
                            zf-C4H2  3 keirektleleklknklakevealekeekcleeykkelelLeqEkmaHveeLrlIhaDi 61
                                        ei++k+++l++ +n+l+     +++ ++  +e++ ++e++++Ek a vee+++ + D 
  gene2263|gene2263|rna2263|rna2263 13 VEIKTKLEKLQEHSNNLKLFNIKIKALNEAFKECSLTIENIKEEKDATVEEIQMEEFDE 71
                                       589****************9999*****************************9877664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2025  (0.112946); expected 358.6 (0.02)
Passed bias filter:                      641  (0.0357521); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.54u 0.32s 00:00:00.86 Elapsed: 00:00:00.51
# Mc/sec: 1156.24
//
Query:       gene2264|gene2264|rna2264|rna2264  [L=306]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (306 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1032  (0.0575604); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 2119.87
//
Query:       gene2265|gene2265|rna2265|rna2265  [L=685]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
       0.31   11.5   4.3        9.2    6.8   1.4    3.1  3  Snapin_Pallidin  Snapin/Pallidin


Domain annotation for each model (and alignments):
>> Snapin_Pallidin  Snapin/Pallidin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   1.4   0.00051       9.2      21      69 ..     462     511 ..     448     530 .. 0.84
   2 ?   -2.9   0.0      0.52   9.3e+03      70      88 ..     551     569 ..     547     570 .. 0.81
   3 ?    3.7   0.1    0.0045        81      45      79 ..     625     657 ..     620     662 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.00051
                    Snapin_Pallidin  21 klkelrqsQeeLleqldrlnekLkeleeaqe.aevlpdlkeyakKLvnik 69 
                                        +lk lr+  +  l ql++ +++Lk l+e++  ++++ +++e ++K+++i 
  gene2265|gene2265|rna2265|rna2265 462 SLKFLRDDNNLTLTQLEEYTKQLKLLQELTAfNQYIYNIHEFLDKITEIF 511
                                        455566666666899*******************************9985 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 0.52
                    Snapin_Pallidin  70 krmsslnerlqklkkRaek 88 
                                          m++++++++++  R++ 
  gene2265|gene2265|rna2265|rna2265 551 STMNEVSKVSSTAATRLSY 569
                                        5799999999999999875 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.0045
                    Snapin_Pallidin  45 eleeaqeaevlpdlkeya.kKLvnikkrmsslnerl 79 
                                        +++++++   +++l++ + k L+ni++++ +l++ +
  gene2265|gene2265|rna2265|rna2265 625 SCSREND---PQRLMSDHiKNLQNIRNDVLNLEKEM 657
                                        5666666...55665544388**********99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (685 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       824  (0.0459591); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.26s 00:00:00.86 Elapsed: 00:00:00.43
# Mc/sec: 4731.60
//
Query:       gene2266|gene2266|rna2266|rna2266  [L=142]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.011   15.3   0.0      0.015   14.9   0.0    1.2  1  RVT_1           Reverse transcriptase (RNA-dependent DNA poly
       0.12   12.2   0.0       0.22   11.4   0.0    1.3  1  YdaS_antitoxin  Putative antitoxin of bacterial toxin-antitox


Domain annotation for each model (and alignments):
>> RVT_1  Reverse transcriptase (RNA-dependent DNA polymerase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   1.6e-06     0.015     171     221 ..      23      87 ..       7      88 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.6e-06
                                        EEEESSHHHHHHHHHHHHHHHHHTT--BEGGG-EEE...................ESSEEETTEE CS
                              RVT_1 171 lilskskeelqelleaveewlkesglkinpeKtklvlft.............v.kseevkyLGvt 221
                                        +il++  +el++  +++++w+ +++++++  K+  ++f+             + + ++++yLG++
  gene2266|gene2266|rna2266|rna2266  23 VILAEFAHELESSQQKISDWCGRWRMSLSIGKCGTMVFGpkevhgicfkelpFpTIDSYTYLGLP 87 
                                        678888999*************************************999877689999****987 PP

>> YdaS_antitoxin  Putative antitoxin of bacterial toxin-antitoxin system, YdaS/YdaT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   2.4e-05      0.22      13      32 ..      27      45 ..      25      57 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 2.4e-05
                     YdaS_antitoxin 13 aLAealgvsqqaVsqWlkgk 32
                                       ++A++l+ sqq +s+W+ g+
  gene2266|gene2266|rna2266|rna2266 27 EFAHELESSQQKISDWC-GR 45
                                       79**************9.54 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       256  (0.0142785); expected 358.6 (0.02)
Passed bias filter:                      250  (0.0139439); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 989.23
//
Query:       gene2267|gene2267|rna2267|rna2267  [L=44]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0052   16.7   0.0     0.0071   16.2   0.0    1.2  1  DUF3746   Protein of unknown function (DUF3746)


Domain annotation for each model (and alignments):
>> DUF3746  Protein of unknown function (DUF3746)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   3.9e-07    0.0071       8      25 ..       6      23 ..       5      26 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 3.9e-07
                            DUF3746  8 LkvttsskKktCkKhifd 25
                                       Lk++ s++ ++C+K+++ 
  gene2267|gene2267|rna2267|rna2267  6 LKDVLSCGSRYCRKAAYE 23
                                       9***************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (44 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       271  (0.0151152); expected 358.6 (0.02)
Passed bias filter:                      190  (0.0105974); expected 358.6 (0.02)
Passed Vit filter:                         7  (0.000390429); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.25s 00:00:00.59 Elapsed: 00:00:00.40
# Mc/sec: 330.11
//
Query:       gene2268|gene2268|rna2268|rna2268  [L=1248]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-35  123.7  23.3      1e-35  123.7  23.3    2.9  3  PhoLip_ATPase_C  Phospholipid-translocating P-type ATPase C-t
    5.9e-12   45.1   7.2    1.7e-11   43.6   7.2    1.8  1  PhoLip_ATPase_N  Phospholipid-translocating ATPase N-terminal
    6.6e-10   39.6   3.8    0.00016   22.0   2.7    3.3  3  Hydrolase        haloacid dehalogenase-like hydrolase
    1.5e-09   37.8   0.0    1.8e-08   34.4   0.0    2.4  2  Cation_ATPase    Cation transport ATPase (P-type)
    9.4e-07   28.5  12.8    2.3e-06   27.2   0.1    3.2  2  E1-E2_ATPase     E1-E2 ATPase
  ------ inclusion threshold ------
      0.037   14.1   9.6       0.06   13.4   2.8    3.4  3  DUF1664          Protein of unknown function (DUF1664)
      0.038   13.4   2.5      0.087   12.2   2.5    1.5  1  TraF_2           F plasmid transfer operon, TraF, protein
      0.066   13.0   0.8       0.29   10.9   0.4    2.2  2  MCPsignal        Methyl-accepting chemotaxis protein (MCP) si
       0.11   12.8   2.9       0.24   11.7   0.5    2.9  2  DUF948           Bacterial protein of unknown function (DUF94
       0.16   12.0   3.5       0.11   12.5   0.6    2.2  2  Laminin_II       Laminin Domain II
       0.19   11.9   4.9      0.085   13.0   1.9    2.0  1  DUF211           Uncharacterized ArCR, COG1888
       0.27   11.7   4.3       0.48   10.9   1.8    2.9  2  FlaC_arch        Flagella accessory protein C (FlaC)
       0.51   10.8   9.9      0.065   13.7   2.2    2.8  3  NPV_P10          Nucleopolyhedrovirus P10 protein


Domain annotation for each model (and alignments):
>> PhoLip_ATPase_C  Phospholipid-translocating P-type ATPase C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   3.2       6.1   8.5e+03     181     224 ..      39      80 ..      22      89 .. 0.38
   2 ?    3.2   0.8     0.044        61     109     176 ..     525     582 ..     472     599 .. 0.59
   3 !  123.7  23.3   7.2e-39     1e-35       2     242 ..    1010    1234 ..    1009    1237 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 6.1
                    PhoLip_ATPase_C 181 iililgsi.llyflflllyssllpsssefygvleelfsspsfwlv 224
                                        +i+++  +  ++ ++++++s +     ++y  +  l+s++  w+ 
  gene2268|gene2268|rna2268|rna2268  39 FIVLFNQFkHFFNVYFFFISFSQL--IKTYR-VGPLISNIAPWFF 80 
                                        222222221122222222222111..22332.3344444444444 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.044
                    PhoLip_ATPase_C 109 lfnlktfllwileglyqsliifflsylvlddssfsdgktndlqlfgtlvftalvlvvnlkvaletktw 176
                                        ++n+ ++l  ++ +++ +++ +f+s ++         + +d++l+ +++++++v+ + lkv +++ ++
  gene2268|gene2268|rna2268|rna2268 525 EINYYSIL-LCVSSVIAACVFLFFSGIS---------SRFDVNLVRFIIIFSSVIPISLKVTIDVARM 582
                                        33433333.3344444444333332221.........2456666666666666666666666655544 PP

  == domain 3  score: 123.7 bits;  conditional E-value: 7.2e-39
                    PhoLip_ATPase_C    2 raSDyaiaqFrfLkrLLlvhGrwsyrRisklilyffyKnvvftlvqfwfqfyngfsgqslyeswlltlynllft 75  
                                          a+D++i +F+  + L ++hGr++y+ ++kli++++++ ++++++q +f+ +  fs   ly++++++ y  ++t
  gene2268|gene2268|rna2268|rna2268 1010 LAADFSILKFSDVTTLFFWHGRNCYKGTAKLIQFIIHRGTIISVMQGIFSAVFLFSPIALYQGFIMVGYVCVYT 1083
                                         69************************************************************************ PP

                    PhoLip_ATPase_C   76 slpvivlgifdqdvsaelllkyPelYklgqknklfnlktfllwileglyqsliifflsylvlddssfsdgktnd 149 
                                         ++p+ ++ i+d+dvs+ ++ kyPelYk+  + k+++ ++f  w l ++yq+ +i++ ++++++         ++
  gene2268|gene2268|rna2268|rna2268 1084 MCPMWCI-ILDRDVSKVNCFKYPELYKEMVHTKILSARSFASWNLISFYQGSVIMIATFFMFK---------HE 1147
                                         *****99.*****************************************************97.........56 PP

                    PhoLip_ATPase_C  150 lqlfgtlvftalvlvvnlkvaletktwtliliililgsillyflflllyssllps.ssefygvleelfsspsfw 222 
                                         l ++  ++f++lv+  +l v+l++++++ ++i++ ++s+++y+l+++++   l     +    ++++++s  + 
  gene2268|gene2268|rna2268|rna2268 1148 LLSIVSITFSCLVINELLVVLLMVSSINRWMILSQVVSLVAYVLSFIFLRDELRLpP-D----IKYFMGS--IA 1214
                                         99*************************************999999999888544321.1....2333333..33 PP

                    PhoLip_ATPase_C  223 lvlllvvvvallpdllikvl 242 
                                         l+ l+++++++  +l +k+l
  gene2268|gene2268|rna2268|rna2268 1215 LISLIAIAFSVAERLYFKYL 1234
                                         44444444444444544444 PP

>> PhoLip_ATPase_N  Phospholipid-translocating ATPase N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.6   7.2   1.2e-14   1.7e-11      11      59 ..      19      67 ..       5      75 .. 0.88

  Alignments for each domain:
  == domain 1  score: 43.6 bits;  conditional E-value: 1.2e-14
                    PhoLip_ATPase_N 11 kkkyasNkIsTsKYtlltFlpknLfeqFrrvaNlYFLviailqliPqis 59
                                       k+ y++N I+++KY++++F + +Lf+qF+++ N+YF++i+  qli + +
  gene2268|gene2268|rna2268|rna2268 19 KQAYPRNIIRNQKYSWYSFPFIVLFNQFKHFFNVYFFFISFSQLIKTYR 67
                                       568*****************************************98655 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       6.9   9.5e+03     115     145 ..     175     204 ..     103     242 .. 0.68
   2 !   22.0   2.7   1.2e-07   0.00016       3     149 ..     614     884 ..     612     889 .. 0.69
   3 !   14.5   0.0   2.4e-05     0.032     161     210 .]     945     995 ..     895     995 .. 0.75

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 6.9
                                        HTHHBHTTHHHHHHHHHHT.TEEEEEEESSEH CS
                                        xxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx RF
                          Hydrolase 115 dplkvkpeaaeavasLkaa.gievvlltgdnp 145
                                         +    +++a+++++ k++ g++ v+ + dn 
  gene2268|gene2268|rna2268|rna2268 175 ST--QVQDTAHLFKRSKEMtGLPSVMESLDNV 204
                                        33..5556666666666666666666555555 PP

  == domain 2  score: 22.0 bits;  conditional E-value: 1.2e-07
                                        EEEEESBTTTBCHHHHHHHHHHHH.............CHHHHHHHHHH.........HHCHHHHHHHHHHHHH... CS
                                        xxxxxxxxxxxxxxxxxxxxxxxx.............xxxxxxxxxxx.........xxxxxxxxxxxxxxxx... RF
                          Hydrolase   3 tvvfDkdGTLttgepsvedvivsa.............alalaaaletg.........sehpigkalvaaakar... 53 
                                         ++ Dk+GTLt+ e++ ++v v                                                      
  gene2268|gene2268|rna2268|rna2268 614 YLLSDKTGTLTRNEMEMRKVHVGTicyttelnseiteI---------IrkkmarkhrR--------------Srdl 666
                                        6789***************9999943333332222220.........12222211222..............1333 PP

                                        ..........HHHHHHHHHETTTE..HHHHTHHH......HHHHH....HCHHHHHHHHHHHHHHCHHHHHH.... CS
                                        ..........xxxxxxxxxxxxxx..xxxxxxxx......xxxxx....xxxxxxxxxxxxxxxxxxxxxxx.... RF
                          Hydrolase  54 ..........sgaltgfatfigrg..ayaigkpe......wltal....dippdlgaaigsaqsqgrtvall.... 103
                                                     +++++ +++ g   y+  +p+      w +a     +  ++ +               +    
  gene2268|gene2268|rna2268|rna2268 667 gsrvfelvraLAVCHNVTPVEEDGkhSYQASSPDeiaivqWCEAVgvllEKRTKDNV--------------Eiril 728
                                        333333233222234444444444555555555544444433333222211122222..............13444 PP

                                        ............................................................................ CS
                                        ............................................................................ RF
                          Hydrolase 104 ............................................................................ 103
                                                                                                                    
  gene2268|gene2268|rna2268|rna2268 729 edtvkryailhvfpftsdtkrmgvllrdedtdevlfvlkgadmvmrtiverndwldeevdnmareglrtlvigmkr 804
                                        4445555555778888888888888888888888889999999999999999999999999999999999999999 PP

                                        ....................................TTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESS CS
                                        ....................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          Hydrolase 104 ....................................qaralavftiadplkvkpeaaeavasLkaagievvlltgd 143
                                                                            + ++l++  ++d+  + + + + ++ L+ ag+++++ltgd
  gene2268|gene2268|rna2268|rna2268 805 lsteeheefeaafrqanlainnrneevqrvvcslerNLKLLGLTGVEDK--LQENVNQSLENLRNAGVKIWMLTGD 878
                                        99999999999999*********************999***********..************************* PP

                                        EHHHHH CS
                                        xxxxxx RF
                          Hydrolase 144 npetae 149
                                          eta 
  gene2268|gene2268|rna2268|rna2268 879 KVETAI 884
                                        ***996 PP

  == domain 3  score: 14.5 bits;  conditional E-value: 2.4e-05
                                        SEEEEHHCESSTTTSHHHHHHHHHHHT.STGGGEEEEESSHHHHHHHHHTT CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxx RF
                          Hydrolase 161 daviasdietvakpspegkvaaireLq.gkpeevamVGDgvnDaaalaaAg 210
                                        ++  + d +++    p +k  ++r L+    ++va +GDg nD++++ +A+
  gene2268|gene2268|rna2268|rna2268 945 KFAATLDAVVCCRCTPTQKALVARNLRmLTSHRVACIGDGGNDVSMITEAN 995
                                        4555555666777899**********9999****************99986 PP

>> Cation_ATPase  Cation transport ATPase (P-type)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.4   0.0   1.3e-11   1.8e-08       2      81 ..     679     770 ..     678     775 .. 0.82
   2 ?    0.1   0.0      0.62   8.6e+02      11      30 ..     867     886 ..     854     916 .. 0.82

  Alignments for each domain:
  == domain 1  score: 34.4 bits;  conditional E-value: 1.3e-11
                      Cation_ATPase   2 lcNsaafsensekdevkllGnktEsALlvlaeklgldteelree.............tkkvqeipFnssrKrmsvv 64 
                                        +c++ +   +++ +      +++E+A+++ +e++g   e+  ++             + +++++pF+s+ Krm+v+
  gene2268|gene2268|rna2268|rna2268 679 VCHNVTP-VEEDGKHSYQASSPDEIAIVQWCEAVGVLLEKRTKDnveiriledtvkrYAILHVFPFTSDTKRMGVL 753
                                        6887777.677888888899**************55555444445555566666666******************* PP

                      Cation_ATPase  65 lklepekkvrlyvKGAp 81 
                                        l+ e++ +v+ + KGA 
  gene2268|gene2268|rna2268|rna2268 754 LRDEDTDEVLFVLKGAD 770
                                        ***************96 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.62
                      Cation_ATPase  11 nsekdevkllGnktEsALlv 30 
                                        n+  + + l+G+k E+A+  
  gene2268|gene2268|rna2268|rna2268 867 NAGVKIWMLTGDKVETAISI 886
                                        66677899*********965 PP

>> E1-E2_ATPase  E1-E2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2   0.1   1.7e-09   2.3e-06       6      62 ..     107     168 ..     102     191 .. 0.83
   2 !    9.3   0.6   0.00053      0.73      73     170 ..     487     580 ..     474     588 .. 0.63

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 1.7e-09
                                        EEEEE-TTS-EEEEGGG--TTSEEEEETT-B--SEEEEEE.....E-SEEE-TTTS---S-E CS
                       E1-E2_ATPase   6 takvirdgteeeidakelvpGDivllkagdrvpaDgrive.....gsaevdesaLTGEslpv 62 
                                        + k++  + ++ ++++ l++GD+++l++++rvpaD++i++     g++ + + +L GE  + 
  gene2268|gene2268|rna2268|rna2268 107 EYKKVTREGVMVVPSSTLQVGDLIVLEKNQRVPADMVILKtfedeGQCFIRTDQLDGETDWK 168
                                        444444445889***************************98888788899999999998875 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00053
                                        T-EEEE-EEEEEEEE-TTTSTTTTTSTTS--------HHHHHHHHHHHH..HHHHHHHHHHHHHHS-STTTSSTTH CS
                       E1-E2_ATPase  73 GtvvvsgeakavVtatgedtelgkiarlveeakskktplqkkldklgkv..lvpvvlliallvflialllgkslae 146
                                         tv   + +++ V+ tg++t      r++ ++++ + ++ k+ +++  +  l +v+ +ia+ vfl++  +      
  gene2268|gene2268|rna2268|rna2268 487 NTVLATQGVIGCVIYTGKET------RAMMNTARPRNKFGKIEEEINYYsiLLCVSSVIAACVFLFFSGISSRFDV 556
                                        55555555556666666655......34444445555555555554444114455555555555555555555559 PP

                                        HHHHHHHHHHHHS-TTHHHHHHHH CS
                       E1-E2_ATPase 147 allralallvaaiPcaLplavpla 170
                                         l+r++ ++ ++iP+ L +++ +a
  gene2268|gene2268|rna2268|rna2268 557 NLVRFIIIFSSVIPISLKVTIDVA 580
                                        9****************9998877 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   2.8   4.3e-05      0.06      53     111 ..     197     254 ..     183     263 .. 0.79
   2 ?    2.1   0.0      0.14   1.9e+02      53      90 ..     264     301 ..     256     306 .. 0.90
   3 ?    0.1   0.1      0.57   7.8e+02      78     120 ..     802     845 ..     760     848 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.3e-05
                            DUF1664  53 vseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeave 111
                                        v+esl ++  +L++++d++d+++de+ +  + ++++v+e+ ++++e++++++ +++ v 
  gene2268|gene2268|rna2268|rna2268 197 VMESLDNV-GELNHDVDEIDHNVDEVDHQMNGMDHNVDEIDHNVDEVDHQMNRMDNNVD 254
                                        44555443.57889999999999999999999999999999999999999998888775 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.14
                            DUF1664  53 vseslaatkrhLssridrvdkkldeqkeiskeikeevt 90 
                                           ++++ k++L + id+  +++d   +   e+++ev 
  gene2268|gene2268|rna2268|rna2268 264 SNYEIENRKEELVEGIDHGPEEIDRALANNDETEKEVG 301
                                        566899***************************99996 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.57
                            DUF1664  78 qkeiskeikeevtev.redlseigedvesvkeavegleskleri 120
                                        +k++s+e +ee +++ r+   +i++  e+v+++v++le +l+ +
  gene2268|gene2268|rna2268|rna2268 802 MKRLSTEEHEEFEAAfRQANLAINNRNEEVQRVVCSLERNLKLL 845
                                        45555555555554414444578899999999999999999866 PP

>> TraF_2  F plasmid transfer operon, TraF, protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   2.5   6.3e-05     0.087      19      82 ..     192     253 ..     181     265 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 6.3e-05
                             TraF_2  19 glllplsvgvevgdvdnlvDkiDdlsdildgleaavnaasadetq.vdeaaddlnalLedlggdg 82 
                                        + +lp sv  ++ +v +l+ ++D+++ ++d+++ + n+++ +  + +d ++d+++ ++++++++ 
  gene2268|gene2268|rna2268|rna2268 192 T-GLP-SVMESLDNVGELNHDVDEIDHNVDEVDHQMNGMDHNV-DeIDHNVDEVDHQMNRMDNNV 253
                                        3.689.9999**********************99999999884.44***************9986 PP

>> MCPsignal  Methyl-accepting chemotaxis protein (MCP) signalling domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.4   0.00021      0.29     115     170 ..     196     251 ..     170     253 .. 0.85
   2 ?   -1.9   0.0       1.8   2.5e+03     124     149 ..     767     792 ..     757     796 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00021
                                        HHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          MCPsignal 115 rveegselveetgealkeiveavaevadlvqeiaaaseeqsasieevnqaveevak 170
                                         v e+++ v e ++++ ei ++v+ev+++++ +   ++e+ + ++ev + ++++++
  gene2268|gene2268|rna2268|rna2268 196 SVMESLDNVGELNHDVDEIDHNVDEVDHQMNGMDHNVDEIDHNVDEVDHQMNRMDN 251
                                        467788999999999************************************99986 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.8
                                        HHHCCHHHHHHHHHHHHHHHHHHHHH CS
                          MCPsignal 124 eetgealkeiveavaevadlvqeiaa 149
                                        + + +++++ive+ + ++++v+++a+
  gene2268|gene2268|rna2268|rna2268 767 KGADMVMRTIVERNDWLDEEVDNMAR 792
                                        567899*****************986 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.5   0.00018      0.24      31      72 ..     207     251 ..     193     263 .. 0.51
   2 ?   -1.7   0.1       2.5   3.5e+03      60      79 ..     847     867 ..     802     876 .. 0.51

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00018
                             DUF948  31 aaatieelekqvdpilkevedllakvne...lledvneklekvdp 72 
                                        +++ ++e+ ++vd++ ++++++ ++v e    +++v ++++++d+
  gene2268|gene2268|rna2268|rna2268 207 LNHDVDEIDHNVDEVDHQMNGMDHNVDEidhNVDEVDHQMNRMDN 251
                                        444444444444444444444444444411112224444444443 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2.5
                             DUF948  60 ledvnekl.ekvdplteavad 79 
                                        l +v++kl e+v++  e++++
  gene2268|gene2268|rna2268|rna2268 847 LTGVEDKLqENVNQSLENLRN 867
                                        245555542235555554444 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.6   8.2e-05      0.11       4      48 ..     210     254 ..     201     276 .. 0.87
   2 ?   -1.7   0.1         2   2.7e+03       8      60 ..     824     871 ..     814     877 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 8.2e-05
                                        XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                         Laminin_II   4 laaeanetakevleqlaplsqnlentkeklseinrsveetnekvk 48 
                                         ++e++  + ev +q+++++ n++++  ++ e++ ++++++++v+
  gene2268|gene2268|rna2268|rna2268 210 DVDEIDHNVDEVDHQMNGMDHNVDEIDHNVDEVDHQMNRMDNNVD 254
                                        578999999999999999999999999999999999888887775 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2
                                        XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                         Laminin_II   8 anetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrs 60 
                                        +n+  +ev++++  l+ nl+ +   l +++++    +e+v+++ + +r A+ +
  gene2268|gene2268|rna2268|rna2268 824 INNRNEEVQRVVCSLERNLKLL--GLTGVEDK---LQENVNQSLENLRNAGVK 871
                                        4555556666666666665433..34444444...666777777777777655 PP

>> DUF211  Uncharacterized ArCR, COG1888
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   1.9   6.2e-05     0.085      17      77 ..     191     251 ..     184     262 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 6.2e-05
                                        HHHHHHHHHTSTTEEEEEEEEEEE-SSEEEEEEEEEESSE-HHHHHHHHHCTT-EEEEEEE CS
                             DUF211  17 ivelakklaelegvdgvnitvkevDketenlkitieGenidyeeieeaieelggvihSiDe 77 
                                        ++ l + +++l++v   n  v e+D+++  ++ +++G + +++ei++ ++e++  +  +D+
  gene2268|gene2268|rna2268|rna2268 191 MTGLPSVMESLDNVGELNHDVDEIDHNVDEVDHQMNGMDHNVDEIDHNVDEVDHQMNRMDN 251
                                        5566778899****************************************99887777776 PP

>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   1.8   0.00035      0.48       2      40 ..     204     242 ..     203     253 .. 0.91
   2 ?   -1.9   0.0       3.4   4.7e+03      20      38 ..     825     843 ..     811     847 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00035
                          FlaC_arch   2 idelEnklsklsteletvkkeneelsksveelkenVkdl 40 
                                        ++el  ++++++ +++ v  +++ +  +v+e++ nV ++
  gene2268|gene2268|rna2268|rna2268 204 VGELNHDVDEIDHNVDEVDHQMNGMDHNVDEIDHNVDEV 242
                                        789999999999999999999999999999999999876 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 3.4
                          FlaC_arch  20 kkeneelsksveelkenVk 38 
                                         + nee++  v  l++n k
  gene2268|gene2268|rna2268|rna2268 825 NNRNEEVQRVVCSLERNLK 843
                                        4567778877777777765 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       6.3   8.7e+03      19      38 ..      90     109 ..      88     113 .. 0.75
   2 ?   13.7   2.2   4.7e-05     0.065      13      60 ..     204     255 ..     196     260 .. 0.67
   3 ?    0.9   0.2      0.47   6.5e+02      15      57 ..     823     868 ..     816     885 .. 0.70

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 6.3
                            NPV_P10  19 kVdalqqqvddvqenlpdvt 38 
                                         Vd lq  v d ++n+++ +
  gene2268|gene2268|rna2268|rna2268  90 AVDDLQRYVRDKEANSEEYK 109
                                        58899999999888887755 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 4.7e-05
                            NPV_P10  13 ikavddkVdalqqqvddvqenlp....dvtelnekLdaqsaqLaeletkven 60 
                                        + +++  Vd ++++vd+v+++++    +v+e+ +++d+   q++ ++++v++
  gene2268|gene2268|rna2268|rna2268 204 VGELNHDVDEIDHNVDEVDHQMNgmdhNVDEIDHNVDEVDHQMNRMDNNVDE 255
                                        5555555555555555555555322225667889999999999999999975 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.47
                            NPV_P10  15 avddkVdalqqqvddvqenlpd..vtelnekLd.aqsaqLaeletk 57 
                                        a++++ + +q  v +++ nl+   +t +++kL+ + +++L++l ++
  gene2268|gene2268|rna2268|rna2268 823 AINNRNEEVQRVVCSLERNLKLlgLTGVEDKLQeNVNQSLENLRNA 868
                                        6666777789999999999885225788888862467778888774 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1248 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1240  (0.0691617); expected 358.6 (0.02)
Passed bias filter:                      600  (0.0334653); expected 358.6 (0.02)
Passed Vit filter:                        78  (0.00435049); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.93u 0.30s 00:00:01.23 Elapsed: 00:00:00.46
# Mc/sec: 8197.74
//
Query:       gene2269|gene2269|rna2269|rna2269  [L=273]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (273 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       703  (0.0392102); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 1808.74
//
Query:       gene227|gene227|rna227|rna227  [L=528]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      5e-44  150.4   1.4    6.4e-44  150.1   0.3    1.7  2  Met_10           Met-10+ like-protein
    4.5e-07   29.6   0.0    7.8e-07   28.8   0.0    1.3  1  MTS              Methyltransferase small domain
      1e-05   25.1   0.0    1.8e-05   24.3   0.0    1.3  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
    1.1e-05   24.8   0.1    2.1e-05   23.9   0.1    1.4  1  TRM              N2,N2-dimethylguanosine tRNA methyltransfera
      6e-05   22.8   0.0    0.00011   21.9   0.0    1.3  1  Cons_hypoth95    Conserved hypothetical protein 95
    8.7e-05   22.3   0.1     0.0002   21.1   0.1    1.6  1  MethyltransfD12  D12 class N6 adenine-specific DNA methyltran
    0.00012   22.7   0.0    0.00031   21.4   0.0    1.7  1  Methyltransf_25  Methyltransferase domain
     0.0011   18.5   0.0     0.0026   17.3   0.0    1.6  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
     0.0011   18.7   0.1     0.0037   17.1   0.0    2.0  2  Methyltransf_31  Methyltransferase domain
  ------ inclusion threshold ------
      0.011   15.6   0.1      0.024   14.6   0.1    1.5  1  Methyltransf_18  Methyltransferase domain
      0.016   14.9   0.0      0.056   13.1   0.0    2.1  1  N6_N4_Mtase      DNA methylase
      0.039   14.6   0.0        0.1   13.3   0.0    1.7  1  Methyltransf_11  Methyltransferase domain


Domain annotation for each model (and alignments):
>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       2.9   4.3e+03      10      59 ..      93     143 ..      88     160 .. 0.56
   2 !  150.1   0.3   4.3e-47   6.4e-44       2     199 .]     275     472 ..     274     472 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 2.9
                                    EEEEB-TTSSHHHHHHHHHHHHHS.S-SCEEEE-S-SBTTTTB--EEEEEE CS
                         Met_10  10 vilnlreelkeykkvigevildkt.kvktvlrkvsevegefRtfelevlaG 59 
                                    + ++ ++ ++ +  ++ge +   + +v+ +++ +++ + ++ + e+  + G
  gene227|gene227|rna227|rna227  93 LSVKTEDAFDRFVVKVGERMKRENyDVEEICSMEDNGKKNYEKEEICSMEG 143
                                    555666666666666666655555566666665555444444444444444 PP

  == domain 2  score: 150.1 bits;  conditional E-value: 4.3e-47
                                    EEEEETTEEEEEB-TTSSHHHHHHHHHHHHHSS-SCEEEE-S-SBTTTTB--EEEEEES-.SEEEEEETTEEEEEETTTS CS
                         Met_10   2 kfeiiGdvvilnlreelkeykkvigevildktkvktvlrkvsevegefRtfelevlaGsdstetihkEngcrfklDvskv 81 
                                    +fe+ G ++ilnl+++ k+yk++i+e  +d  + kt++ k++ v+  +Rt+e+e+l G+ds  +   Eng++f + + +v
  gene227|gene227|rna227|rna227 275 SFEVLGKTLILNLSDDQKKYKTEIAEYFIDLGRYKTIFLKKDVVKEPYRTTEYELLLGEDSKDVLYVENGTKFAFNIGDV 354
                                    79****************************************************************************** PP

                                    ---GGGHHHHHHHHTT--TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-TTCEEEEES-GG CS
                         Met_10  82 yfsskleaErerlaklveegevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkvekvvkpileDgr 161
                                    yf+skl+  re+l++++++++vV d+f GiGp +i + k  ++  v+a+d+nP++++ +k+n+k N++  + ++ +eD++
  gene227|gene227|rna227|rna227 355 YFNSKLSGAREQLVNKFRKNDVVADLFCGIGPISIQALK--RGCYVIANDINPKAIESFKNNLKINRITARHEVHNEDAK 432
                                    **************************************9..*************************************** PP

                                    G---...TT-EEEEEE--TTTGGGGHHHHHHHEEEEEEEEE CS
                         Met_10 162 evir...eqladrvvmnlpksaieFldkvlaalkdggvihy 199
                                    +v+    + +++++v nlp+ +i F++ v +a ++  +++y
  gene227|gene227|rna227|rna227 433 DVLLsltDRVIEHFVFNLPELSIYFIKYV-KAFTNSELHCY 472
                                    **987888999***************876.55667778887 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.8   0.0   5.2e-10   7.8e-07      10      91 ..     354     433 ..     348     451 .. 0.80

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 5.2e-10
                                    STTTTS--HHHHHHHHHCHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC..EEEEE- CS
                            MTS  10 vFskdklDkGsklLletlpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle..vevvas 87 
                                    v+ + kl  + + L++++ k  ++ v+Dl cG+G+++++++k+     v + d++ +A+es k+nl+ n++    ev+++
  gene227|gene227|rna227|rna227 354 VYFNSKLSGAREQLVNKFRK--NDVVADLFCGIGPISIQALKRGCY--VIANDINPKAIESFKNNLKINRITarHEVHNE 429
                                    66777777777788888888..667*****************8877..99********************9977777776 PP

                                    STTT CS
                            MTS  88 dvle 91 
                                    d+ +
  gene227|gene227|rna227|rna227 430 DAKD 433
                                    6544 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.0   1.2e-08   1.8e-05     158     219 ..     370     430 ..     362     448 .. 0.84

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 1.2e-08
                           PrmA 158 lvkegeevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkveaklevalse 219
                                      ++++ v D+ +G G ++i a+k g   v+a Di++ A+++ k+N+++N+++a+ ev++++
  gene227|gene227|rna227|rna227 370 KFRKNDVVADLFCGIGPISIQALKRGC-YVIANDINPKAIESFKNNLKINRITARHEVHNED 430
                                    456778999***************997.799*************************997642 PP

>> TRM  N2,N2-dimethylguanosine tRNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.1   1.4e-08   2.1e-05      76     115 ..     397     436 ..     361     449 .. 0.84

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 1.4e-08
                                    EEEEE-S-HHHHHHHHHHHHHTT--GGEEEE-S-HHHHHC CS
                            TRM  76 evlaNDisekAvelikeNvklneveeivvineddAnvlla 115
                                     v+aNDi++kA+e+ k+N k+n +  + +++++dA+ +l 
  gene227|gene227|rna227|rna227 397 YVIANDINPKAIESFKNNLKINRITARHEVHNEDAKDVLL 436
                                    699**********************999*******98876 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.0   7.3e-08   0.00011      41     111 ..     373     442 ..     361     451 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 7.3e-08
                                    CC-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHCTS--SS CS
                  Cons_hypoth95  41 egarvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelkleeetaelkedaleallklakkk 111
                                    ++  v Dlf+G G +++ Al Rg+  +++ + +++a++  k+nl+  ++++++++++eda++ ll+l+ + 
  gene227|gene227|rna227|rna227 373 KNDVVADLFCGIGPISIQALKRGC-YVIANDINPKAIESFKNNLKINRITARHEVHNEDAKDVLLSLTDRV 442
                                    556688*****************7.6899********************************9999997654 PP

>> MethyltransfD12  D12 class N6 adenine-specific DNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.1   1.3e-07    0.0002      16      72 ..     368     423 ..     359     466 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 1.3e-07
                                    S-...--SEEEETT-TTSCCHHCS...SSCEEEEES-HHHHHHHHHHCCHSHHHHHHH CS
                MethyltransfD12  16 ipkd.kgktfvepFaGggaVffeakkqgkkvlinDinedlinlykaliknnveelike 72 
                                    + k  k+++++++F+G g ++++a+k+g  v++nDin++ i  +k+ +k  + +++ +
  gene227|gene227|rna227|rna227 368 VNKFrKNDVVADLFCGIGPISIQALKRGCYVIANDINPKAIESFKNNLK--INRITAR 423
                                    33445789**********************************9997666..4444444 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   2.1e-07   0.00031       1      58 [.     377     434 ..     377     459 .. 0.86

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 2.1e-07
                                    EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT..TEEEEESBCCGB CS
                Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl..nvefvqgdaedl 58 
                                    v dl cG G ++++++kr+  + v++ Di+++++e  +++++ +++  + e+++ da+d+
  gene227|gene227|rna227|rna227 377 VADLFCGIGPISIQALKRG--CYVIANDINPKAIESFKNNLKINRItaRHEVHNEDAKDV 434
                                    789***************5..********************9988888999999999984 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   1.7e-06    0.0026       3      76 ..     376     448 ..     374     453 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.7e-06
                Methyltransf_15   3 vilDlfsGaGGnviqfalvfekviaieinleklacaqhNaevYgvsdkitlvlgdvfellaklklekikvdlvf 76 
                                    v+ Dlf+G G  +iq  + ++ via +in++ ++  ++N ++  +  +  +   d +++l +l+ ++i   +vf
  gene227|gene227|rna227|rna227 376 VVADLFCGIGPISIQALKRGCYVIANDINPKAIESFKNNLKINRITARHEVHNEDAKDVLLSLTDRVI-EHFVF 448
                                    688***************************************99999998888888888888777776.55666 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       3.6   5.3e+03     101     114 ..     204     222 ..     191     259 .. 0.58
   2 !   17.1   0.0   2.5e-06    0.0037       2      68 ..     372     437 ..     371     508 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 3.6
                Methyltransf_31 101 lkpggilliedpr.....l 114
                                     k++g +++++++     +
  gene227|gene227|rna227|rna227 204 TKENGSFILDHFCigvgkI 222
                                    5778888888888533331 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 2.5e-06
                Methyltransf_31   2 dkglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgld.nveFeqgdiee.lek 68 
                                    +k+ +v Dl CG G +++++ ++   ++ v+  Di+++aie+ ++n++ + ++ + e++ +d+ + l +
  gene227|gene227|rna227|rna227 372 RKNDVVADLFCGIGPISIQALKR---GCYVIANDINPKAIESFKNNLKINRITaRHEVHNEDAKDvLLS 437
                                    58899****************76...567******************9999999999999999985543 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.1   1.6e-05     0.024       9      75 ..     368     432 ..     363     443 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.6e-05
                Methyltransf_18   9 aslvekgsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagledkievrlsdGl 75 
                                    ++  +k+++vaD  +  g ++i ++k+g +  via Din++++e+ k+n++ ++++ + ev+  d  
  gene227|gene227|rna227|rna227 368 VNKFRKNDVVADLFCGIGPISIQALKRGCY--VIANDINPKAIESFKNNLKINRITARHEVHNEDAK 432
                                    55667899*****************98876..***********************999999887765 PP

>> N6_N4_Mtase  DNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   3.7e-05     0.056     190     230 ..     372     412 ..     109     413 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.7e-05
                                    -TT-EEEETT-TTTHHHHHHHHTT-EEEEEESSHHHHHHHH CS
                    N6_N4_Mtase 190 kkgdivlDpFaGSGtTavaakelgrkfiGieieeeyvelae 230
                                    +k+d+v+D F+G G + + a++ g   i  +i+++++e+++
  gene227|gene227|rna227|rna227 372 RKNDVVADLFCGIGPISIQALKRGCYVIANDINPKAIESFK 412
                                    68*********************************999876 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   6.9e-05       0.1       3      59 ..     380     440 ..     378     460 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 6.9e-05
                                    ET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-..EEEETTEECCC..TSS-T CS
                Methyltransf_11   3 vGcGtGrlaealakrgarvvgvDlskemlklakekaseegl..kvefvvadaek..lpfed 59 
                                    + cG G ++ +  krg+ v++ D+++++++  k++ + +++  + e++ +da++  l + d
  gene227|gene227|rna227|rna227 380 LFCGIGPISIQALKRGCYVIANDINPKAIESFKNNLKINRItaRHEVHNEDAKDvlLSLTD 440
                                    569**********************************999888778899999884335555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (528 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       914  (0.0509789); expected 358.6 (0.02)
Passed bias filter:                      494  (0.0275531); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.64u 0.31s 00:00:00.95 Elapsed: 00:00:00.48
# Mc/sec: 3305.53
//
Query:       gene2270|gene2270|rna2270|rna2270  [L=519]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        1.9    8.9   8.1       0.28   11.6   1.6    2.6  2  Efg1      rRNA-processing protein Efg1
        3.9    7.3   6.9        2.1    8.2   1.3    2.4  2  CHD5      CHD5-like protein


Domain annotation for each model (and alignments):
>> Efg1  rRNA-processing protein Efg1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   1.6   3.1e-05      0.28      59     104 ..      70     114 ..      12     119 .. 0.70
   2 ?    0.2   0.6      0.11   9.5e+02      21      59 ..     278     316 ..     260     366 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 3.1e-05
                                        HHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHS CS
                               Efg1  59 fErkKatRklkrlkkqleeledeeekeelekkleelevdlnYvlyy 104
                                         E +K++R+++r k++l     ++++++le++l+ l ++++Y l +
  gene2270|gene2270|rna2270|rna2270  70 AEIRKLHRQIQRNKRELYGYA-QQNDQSLEESLHILFTNMEYFLVF 114
                                        699**************9875.56899***************9887 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.11
                                        HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                               Efg1  21 evreekereLkaleaeleeaekkekekklakkYhkvrFf 59 
                                        e  ++ + + k+ ++++ +++ ++ + k  +k + vr++
  gene2270|gene2270|rna2270|rna2270 278 EEGNTSNNTTKNAKSNATNNSLENLNTKTLEKDQHVRYT 316
                                        555555566667777777777777777777788888775 PP

>> CHD5  CHD5-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.4     0.024   2.1e+02      74     117 ..      72     115 ..       2     127 .. 0.72
   2 ?    8.2   1.3   0.00023       2.1      32     120 ..     280     368 ..     252     384 .. 0.75

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.024
                               CHD5  74 ldkleeeleklkkelsaskssfkkklkkvllvlttvpqlvlkfw 117
                                        + kl  ++++ k el    ++ ++ l+  l +l+t + ++l f+
  gene2270|gene2270|rna2270|rna2270  72 IRKLHRQIQRNKRELYGYAQQNDQSLEESLHILFTNMEYFLVFR 115
                                        56777777777777777777777777777777777777777666 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.00023
                               CHD5  32 kvssksakeqrklkkellklkeelnsisaqDefAkWaKlnRkldkleeeleklkkelsaskssfkkklkkvllvlt 107
                                          +s++++++ k ++  ++l++ ++++  +D+  +++   Rk d  +++ e l ++   +k+++++  ++    ++
  gene2270|gene2270|rna2270|rna2270 280 GNTSNNTTKNAKSNATNNSLENLNTKTLEKDQHVRYTADGRKSDVGNNKTEILGEKSFDKKNATHTSTQTRTIRVL 355
                                        23388999999999999**********************************9988888888877777776666666 PP

                               CHD5 108 tvpqlvlkfwyrk 120
                                        t  q + k++ r 
  gene2270|gene2270|rna2270|rna2270 356 TKNQNLTKVFVRE 368
                                        6666666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (519 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1641  (0.0915277); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.28s 00:00:00.88 Elapsed: 00:00:00.45
# Mc/sec: 3441.48
//
Query:       gene2271|gene2271|rna2271|rna2271  [L=403]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      5e-06   26.5   0.1    1.7e-05   24.8   0.1    1.9  2  LSM14     Scd6-like Sm domain
     0.0091   16.1   0.0      0.025   14.7   0.0    1.7  1  SM-ATX    Ataxin 2 SM domain
  ------ inclusion threshold ------
      0.017   14.8   0.1      0.044   13.5   0.1    1.7  1  LSM       LSM domain


Domain annotation for each model (and alignments):
>> LSM14  Scd6-like Sm domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.1   2.9e-09   1.7e-05      10      72 ..       8      72 ..       3      74 .. 0.84
   2 ?   -3.5   0.0         2   1.2e+04      13      22 ..     280     289 ..     279     291 .. 0.77

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 2.9e-09
                              LSM14 10 isksdirYeGilceinledstiaLqnvrsfGtegrkdneq..ippskevyeyivFrgsDikdLev 72
                                       +++ + +YeG+ ++ +  + ti L++vr+f  +  ++++   +++ + v+++ivF+ +  + Le+
  gene2271|gene2271|rna2271|rna2271  8 KTRIGNKYEGTFKSYDRLQGTIVLEDVRMFEHDTNTRENAvcVNADHRVFSFIVFKLNSLTYLEI 72
                                       5566779***********************98884444445799************999888887 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 2
                              LSM14  13 sdirYeGilc 22 
                                         + rYeG  c
  gene2271|gene2271|rna2271|rna2271 280 RSTRYEGFCC 289
                                        5679***876 PP

>> SM-ATX  Ataxin 2 SM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   4.1e-06     0.025      16      51 ..       5      39 ..       3      63 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 4.1e-06
                                       EEEEETTS-EEEEEEEEE-T..T--EEEEEEEETTS CS
                             SM-ATX 16 vevtvknGevyeGifstvslekdfsvvLkmarkvkk 51
                                       + v+++ G++yeG f++++   +  +vL+ +r  + 
  gene2271|gene2271|rna2271|rna2271  5 AIVKTRIGNKYEGTFKSYDR-LQGTIVLEDVRMFEH 39
                                       6799***************9.9**********9988 PP

>> LSM  LSM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   7.4e-06     0.044      12      50 ..       6      44 ..       3      71 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 7.4e-06
                                       EEEETTSEEEEEEEEEEET.TSEEEEEEEEEEETTETEEE CS
                                LSM 12 tvelkngrelrGtLkgfDq.fmNlvLedveetlkdkkekr 50
                                       +v+++ g +++Gt+k++D+ +  +vLedv ++ +d+ ++r
  gene2271|gene2271|rna2271|rna2271  6 IVKTRIGNKYEGTFKSYDRlQGTIVLEDVRMFEHDT-NTR 44
                                       599***************9445799*****999998.443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (403 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1088  (0.0606838); expected 358.6 (0.02)
Passed bias filter:                      544  (0.0303419); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.61u 0.28s 00:00:00.89 Elapsed: 00:00:00.49
# Mc/sec: 2480.23
//
Query:       gene2272|gene2272|rna2272|rna2272  [L=71]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (71 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       268  (0.0149478); expected 358.6 (0.02)
Passed bias filter:                      221  (0.0123264); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.27s 00:00:00.62 Elapsed: 00:00:00.42
# Mc/sec: 512.39
//
Query:       gene2273|gene2273|rna2273|rna2273  [L=407]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.3e-37  129.3   0.1    3.7e-36  124.5   0.0    2.1  2  DEAD        DEAD/DEAH box helicase
    2.6e-28   98.6   0.3      2e-27   95.7   0.1    2.4  3  Helicase_C  Helicase conserved C-terminal domain
     0.0015   18.5   0.0      0.003   17.6   0.0    1.5  1  ResIII      Type III restriction enzyme, res subunit
  ------ inclusion threshold ------
      0.013   15.2   0.3      0.032   13.9   0.3    1.6  1  AAA_30      AAA domain


Domain annotation for each model (and alignments):
>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  124.5   0.0   8.2e-40   3.7e-36       3     171 ..      52     213 ..      50     217 .. 0.95
   2 ?    2.7   0.0     0.022        96      44     104 ..     269     329 ..     257     344 .. 0.82

  Alignments for each domain:
  == domain 1  score: 124.5 bits;  conditional E-value: 8.2e-40
                                        HHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEE CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               DEAD   3 iQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrv 78 
                                        iQ+ ai  il+g+d+ ++a+ G+GKT+af+++ lq++ e  + +++++l+++ tre+aeq + ++++++k+++++v
  gene2273|gene2273|rna2273|rna2273  52 IQKTAIGPILQGRDIRAQAQSGTGKTGAFAVASLQRIDE--TLPATQVLVLCSTREIAEQNAARTTEIGKNMGVSV 125
                                        9************************************65..89999****************************** PP

                                        EEEETTSSHHHHHHHHHTTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCT CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               DEAD  79 lliiggvaardqlskldngvdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsdfinrilnqlpqitc 154
                                          + gg +  + +++l +++ iv gtpgr+++++stg l+++++ +l++DEad++l+ gf+d++++++ +l+    
  gene2273|gene2273|rna2273|rna2273 126 PFLAGGFNVGRTREELARNPPIVTGTPGRVLHMISTGDLKTDSIFLLIIDEADEMLKRGFKDQVREVFMSLN---- 197
                                        ****************999****************************************************3.... PP

                                        TSTTTSEEEEEESSBS.H CS
                                        xxxxxxxxxxxxxxxx.x RF
                               DEAD 155 dgklqrqvivlSATlp.k 171
                                        +  ++ qv ++SAT+  +
  gene2273|gene2273|rna2273|rna2273 198 R--EKIQVAMFSATWDkS 213
                                        2..5577*******9844 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.022
                                        TSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEEETTSSHHHHHHHHHTT.CSEEEEE CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxx RF
                               DEAD  44 gktgpkalivePtreLaeqtlnnlkkfkkyidlrvlliiggvaardqlskldng.vdivvgt 104
                                        +++  + +i + +r+ a+  ++ lk+ k +++  +++ +++++++d l++++ng ++++++t
  gene2273|gene2273|rna2273|rna2273 269 RSEVGQSVIFVNSRSKAKFLYEALKTHKFPCE-VIHSDLTQNERSDVLRRVRNGeCRCLIAT 329
                                        566678999999*************9999987.44477899999*******99999999988 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.48   2.1e+03      12      33 ..      90     115 ..      82     143 .. 0.64
   2 ?   -1.6   0.0      0.74   3.3e+03      11      30 ..     195     214 ..     169     236 .. 0.69
   3 !   95.7   0.1   4.5e-31     2e-27       2     111 .]     259     369 ..     258     369 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.48
                                        HTTTTSEEEEEESSHHHHHH....HH CS
                         Helicase_C  12 leeeggkilifvntidrlek....vk 33 
                                        ++    ++l+ + t++ +e+    ++
  gene2273|gene2273|rna2273|rna2273  90 ETLPATQVLVLCSTREIAEQnaarTT 115
                                        45577899999999996654443433 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.74
                                        HHTTTTSEEEEEESSHHHHH CS
                         Helicase_C  11 kleeeggkilifvntidrle 30 
                                        +l++e+ ++ +f+ t+d+ e
  gene2273|gene2273|rna2273|rna2273 195 SLNREKIQVAMFSATWDKSE 214
                                        44556666677777777554 PP

  == domain 3  score: 95.7 bits;  conditional E-value: 4.5e-31
                                        HHHHHHHHHHHTTTTSEEEEEESSHHHHHHHHHH...HHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESG CS
                         Helicase_C   2 kleallellkleeeggkilifvntidrlekvkll...lekkgikvavlhgelpqnereeileqfnkgesdvLiatd 74 
                                        k+e ll+++ +++e g+++ifvn++++++   +l   l+++++ + v+h++l+qner ++l++ ++ge+++Liat 
  gene2273|gene2273|rna2273|rna2273 259 KMEVLLDIY-RRSEVGQSVIFVNSRSKAK---FLyeaLKTHKFPCEVIHSDLTQNERSDVLRRVRNGECRCLIATG 330
                                        788999997.999*************994...4433345669********************************** PP

                                        GGTSSSTSTTESEEEESSSSSS..HHHHHHHHTTSSSTT CS
                         Helicase_C  75 vaerGidipkvnlVinfdlprn..vtsyiqriGRtgRag 111
                                         ++rGidi++++ V+nfdlp++   +syi+riGR+gR+g
  gene2273|gene2273|rna2273|rna2273 331 LMARGIDIQQLSIVFNFDLPKGldKSSYIHRIGRAGRFG 369
                                        ********************77446************86 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   6.7e-07     0.003      27     168 ..      66     209 ..      47     212 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 6.7e-07
                                        EEEEESTTSTHHHHH.HHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG........GEEEESSS-B--. CS
                             ResIII  27 glikmaTGtGKTlva.aklierllkkgkeekflflvprkslleqtleefkkflseayke....igkkvsgdkkkak 97 
                                        +  ++  GtGKT    ++  +r+ +  +  ++l+l+ ++++ eq   + +++ ++   +    +g++  g+++++ 
  gene2273|gene2273|rna2273|rna2273  66 IRAQAQSGTGKTGAFaVASLQRIDETLPATQVLVLCSTREIAEQNAARTTEIGKNMGVSvpflAGGFNVGRTREE- 140
                                        5567889*****988678889999999999*****************9999999987778888888888888888. PP

                                        ......-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS....TTTHHH.HHT---SEEEE.EESS CS
                             ResIII  98 ekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgak...kswrei.lekfkeavllg.lTAT 168
                                           + n  i+  t  ++   +      + +l+ d++ ++iiDEa  + +    +++re+ +  ++e+++++ ++AT
  gene2273|gene2273|rna2273|rna2273 141 --LARNPPIVTGTPGRVLHMI-----STGDLKTDSIFLLIIDEADEMLKRgfkDQVREVfMSLNREKIQVAmFSAT 209
                                        ..8889999999999988888.....78889999999999999999888655457777755555667777635787 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.3   7.2e-06     0.032       6     114 ..      53     198 ..      50     207 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 7.2e-06
                             AAA_30   6 QaaavealltsgdrvavltGpAGtGKt..talkalreaweaa.ggrviglAptgkaAkvLa............... 63 
                                        Q++a+  +l+++d    +++  GtGKt  +a+++l+++ e+    +v++l +t + A++ a               
  gene2273|gene2273|rna2273|rna2273  53 QKTAIGPILQGRD--IRAQAQSGTGKTgaFAVASLQRIDETLpATQVLVLCSTREIAEQNAartteigknmgvsvp 126
                                        8888888888887..77899*******44455666999999988***********999955344444433333333 PP

                             AAA_30  64 .eelgieastiakllkrlk................grarlepgtllivDEagmv....dtkqlaallkaaek 114
                                          + g++  ++ + l r+                 g  + ++  lli+DEa  +      +q+++++ ++++
  gene2273|gene2273|rna2273|rna2273 127 fLAGGFNVGRTREELARNPpivtgtpgrvlhmistGDLKTDSIFLLIIDEADEMlkrgFKDQVREVFMSLNR 198
                                        202223444444444444466677777777777675456666699999999755344333455555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (407 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       538  (0.0300073); expected 358.6 (0.02)
Passed bias filter:                      506  (0.0282224); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 2713.10
//
Query:       gene2274|gene2274|rna2274|rna2274  [L=55]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (55 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       844  (0.0470746); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.31s 00:00:00.79 Elapsed: 00:00:00.51
# Mc/sec: 321.89
//
Query:       gene2275|gene2275|rna2275|rna2275  [L=41]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (41 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       276  (0.0153941); expected 358.6 (0.02)
Passed bias filter:                      205  (0.011434); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.29s 00:00:00.68 Elapsed: 00:00:00.46
# Mc/sec: 266.48
//
Query:       gene2276|gene2276|rna2276|rna2276  [L=426]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.3e-58  198.7  36.1    1.9e-58  198.1  36.1    1.3  1  Aa_trans      Transmembrane amino acid transporter protein
    1.2e-09   37.7  14.8    1.2e-09   37.7  14.8    1.9  2  Trp_Tyr_perm  Tryptophan/tyrosine permease family


Domain annotation for each model (and alignments):
>> Aa_trans  Transmembrane amino acid transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  198.1  36.1   2.1e-62   1.9e-58       6     398 ..      44     412 ..      41     423 .. 0.89

  Alignments for each domain:
  == domain 1  score: 198.1 bits;  conditional E-value: 2.1e-62
                           Aa_trans   6 lsavlnlikaivGaGvLaLPyAfkqlGlivGlillllvallslytlllLvkcsktlasgkrnksYgdlgyrllGpk 81 
                                        ls+ +n++k+i+G+G+L +P+ fk+ G i  ++l+ l a ls+ +  + + c  +l+  +r+     l++    + 
  gene2276|gene2276|rna2276|rna2276  44 LSGYVNILKTIIGSGILYIPMLFKSYGAISTFFLMCLSATLSMVGQIIFLYCNAFLN--DRSTNITSLARESVPR- 116
                                        6899***************************************************96..8888888997777655. PP

                           Aa_trans  82 gkliidlailvqlfGvgvsyliligdllpaifesffdt.lllsnvyfilisaliiipLslipnlskLsylSllalv 156
                                         ++++d+  ++++fGv++syli+i +l+p++++++f++  l +  +  li+  +i p + +++l++L+y+S ++l+
  gene2276|gene2276|rna2276|rna2276 117 TRFLVDFFVFFKCFGVSTSYLIIIRELIPNLIQTVFGEsVLARPKVALLIFLCFISPITYFRQLKNLKYTSSIGLI 192
                                        9***********************************997777999999**************************** PP

                           Aa_trans 157 sslyyivilvlvvaelvklelkgvseetvkkasklkglflaigiivFAftghavlleiqnelkdpskfkkmtkvll 232
                                        ++ + i++++++++ +  + +  + +e++   +   +++  +g++vFAft+h +l+++qne+ d+s    m+k+++
  gene2276|gene2276|rna2276|rna2276 193 AISF-ILFFSMYNFIKHGSLEHVTLYEPI---T--IEWLKGLGTFVFAFTCHQNLISVQNEVVDNSP-DRMKKIVY 261
                                        **86.677777776665554445555554...2..47***************************999.88****** PP

                           Aa_trans 233 lsiilatvlyilvGlvGYltFGnevkgnillnlpkssilivivnlllvlhlilsfplqlhplrqvvenllikkeav 308
                                        ++++++ v+y+++G++ Y+ +  +  +n+l+++p+   ++ +  +l+v  + +s+plq+ p+r ++ nll  +   
  gene2276|gene2276|rna2276|rna2276 262 ATTATSLVIYMVFGFTNYALYATNMHDNVLKSYPNDH-ITLFLHFLYVCVMGFSYPLQINPARVYMYNLLGFN--- 333
                                        **********************************999.********************************875... PP

                           Aa_trans 309 agasekeapkskllrlvirlllvvityliAlsvpslakvlslvGatsstplsfilPalfhlkliktekksleklvk 384
                                              ++++++l++ vi++ll+++ty++ ++  +l+++ ++vGat+st++++i+P lf++ +    k   ++l+ 
  gene2276|gene2276|rna2276|rna2276 334 -----TKKRNNNLVHAVITTLLLASTYVLTITGLNLGEMYAFVGATASTMICLIFPLLFYYNMGLERK---RWLI- 400
                                        .....88888889***********************************************98644443...4444. PP

                           Aa_trans 385 kkildlicivlgll 398
                                          i+  i +v+g  
  gene2276|gene2276|rna2276|rna2276 401 --IFGCIGFVFGSC 412
                                        ..233444444444 PP

>> Trp_Tyr_perm  Tryptophan/tyrosine permease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.7  14.8   1.3e-13   1.2e-09       4     235 ..      42     274 ..      39     286 .. 0.82
   2 ?   -0.8   0.1     0.068   6.1e+02     342     359 ..     370     388 ..     324     404 .. 0.62

  Alignments for each domain:
  == domain 1  score: 37.7 bits;  conditional E-value: 1.3e-13
                       Trp_Tyr_perm   4 sllggvlliagtviGaGmlalPvatagagfipsllllilswvlmlasgllllEvllaake.easfttlakkllGkk 78 
                                        + l+g + i  t+iG+G+l +P+     g i + +l++ls+ l+++  +++l ++   +   +++t+la+++++++
  gene2276|gene2276|rna2276|rna2276  42 EYLSGYVNILKTIIGSGILYIPMLFKSYGAISTFFLMCLSATLSMVGQIIFLYCNAFLNDrSTNITSLARESVPRT 117
                                        5788999999********************************************999888799***********97 PP

                       Trp_Tyr_perm  79 gniivalvllfllyiLlvAyisggGsilselleeasg..ialsarlavliftlvlgalvvlstk.avdrinrvllf 151
                                         +++v + + f  +     y+  + +++ +l+++ +g  + + +++a lif  +++++  +       +++++ l+
  gene2276|gene2276|rna2276|rna2276 118 -RFLVDFFVFFKCFGVSTSYLIIIRELIPNLIQTVFGesVLARPKVALLIFLCFISPITYFRQLkNLKYTSSIGLI 192
                                        .667777788999999********************95455677899999*9999999999887688888887666 PP

                       Trp_Tyr_perm 152 lklvafvlllalllskvksdvLlsaksdtskvslvlsalPvlllsfGFhgivpsl.vkyldknvkkvkkailiGtl 226
                                        +  + ++++++ ++ + + +     +  t++    l+ l  ++ +f  h++  s+ ++++d++ +++kk +   t+
  gene2276|gene2276|rna2276|rna2276 193 AISFILFFSMYNFIKHGSLEHVTLYEPITIE---WLKGLGTFVFAFTCHQNLISVqNEVVDNSPDRMKKIVYATTA 265
                                        6666555666666655444444332333333...4778888999999999988882568899999*********** PP

                       Trp_Tyr_perm 227 iaLvlyllW 235
                                         +Lv+y++ 
  gene2276|gene2276|rna2276|rna2276 266 TSLVIYMVF 274
                                        ******985 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.068
                       Trp_Tyr_perm 342 yAG.laatilavilPalla 359
                                        + G +a t++++i+P l  
  gene2276|gene2276|rna2276|rna2276 370 FVGaTASTMICLIFPLLFY 388
                                        3355555666666665554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (426 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1045  (0.0582855); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.64u 0.27s 00:00:00.91 Elapsed: 00:00:00.46
# Mc/sec: 2799.02
//
Query:       gene2277|gene2277|rna2277|rna2277  [L=182]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-11   44.9   0.0    1.5e-11   44.5   0.0    1.2  1  Acetyltransf_1   Acetyltransferase (GNAT) family
      3e-09   36.9   0.0    4.3e-09   36.4   0.0    1.2  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    3.4e-09   37.0   0.1    4.7e-09   36.6   0.1    1.3  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
    3.3e-05   23.8   0.0    6.3e-05   22.9   0.0    1.5  1  FR47             FR47-like protein
     0.0019   18.3   0.0     0.0032   17.5   0.0    1.3  1  Acetyltransf_9   Acetyltransferase (GNAT) domain
  ------ inclusion threshold ------
      0.015   15.2   0.0      0.024   14.6   0.0    1.3  1  pPIWI_RE_REase   REase associating with pPIWI_RE
       0.74    9.2   5.8        5.4    6.4   3.0    2.4  2  Acetyltransf_15  Putative acetyl-transferase


Domain annotation for each model (and alignments):
>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.5   0.0     6e-15   1.5e-11      34     117 .]      52     134 ..      17     134 .. 0.83

  Alignments for each domain:
  == domain 1  score: 44.5 bits;  conditional E-value: 6e-15
                                        EEEEEEETTEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHTTESEEEEEEETTEHHHH CS
                     Acetyltransf_1  34 gllvaeedgeliGfisllkipdekggvayieslaVspeyrgkGlGsaLlealeerareegikkivlaveedndaai 109
                                        +  + ++  +++G+i +++        +++ sl ++p++r+ Gl++ L++ le    e++++ + l v+ +n +ai
  gene2277|gene2277|rna2277|rna2277  52 SSTCFLYTSKIVGYIIGKQERR-GVLSMHVSSLSIAPTHRKCGLATSLMRILEALGNERNAYFVDLFVRCSNFKAI 126
                                        2333457899**********99.67789999******************************99************* PP

                                        HHHHHTTE CS
                     Acetyltransf_1 110 rlYeklGF 117
                                        ++Yek G+
  gene2277|gene2277|rna2277|rna2277 127 AFYEKNGY 134
                                        *****998 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.4   0.0   1.7e-12   4.3e-09      38     109 ..      58     137 ..      34     141 .. 0.82

  Alignments for each domain:
  == domain 1  score: 36.4 bits;  conditional E-value: 1.7e-12
                    Acetyltransf_10  38 eggkivGviel.rdgs......hisllfVdpeyrgqGigkaLleaveeeaekdgikl.eltvnasp.yavpfYekl 104
                                           kivG+i + ++++      h+s l ++p +r+ G++++L+  +e+  ++++    +l v+ s+ +a++fYek 
  gene2277|gene2277|rna2277|rna2277  58 YTSKIVGYI-IgKQERrgvlsmHVSSLSIAPTHRKCGLATSLMRILEALGNERNAYFvDLFVRCSNfKAIAFYEKN 132
                                        3568*****.334444569******************************766666668****************** PP

                    Acetyltransf_10 105 GFkav 109
                                        G+ + 
  gene2277|gene2277|rna2277|rna2277 133 GYIKY 137
                                        **876 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.6   0.1   1.8e-12   4.7e-09      11      75 ..      49     135 ..      31     136 .. 0.68

  Alignments for each domain:
  == domain 1  score: 36.6 bits;  conditional E-value: 1.8e-12
                                        T..........TEEEEEEEEEEES.....TCTEEEEE-GGGTTSSHHHHHHHH.TT....SE.EEEEEEEE....T CS
                     Acetyltransf_7  11 d..........gkivGfialslld.....aeitrlaVdpeyrgkGiGraLlea.ae....kg.iileqlel....n 61 
                                        +           kivG+i+ + +       +   l ++p +r+ G+++ L+++ ++    ++ +  + + l    +
  gene2277|gene2277|rna2277|rna2277  49 EdlsstcflytSKIVGYIIGKQERrgvlsMHVSSLSIAPTHRKCGLATSLMRIlEAlgneRNaY--F-VDLfvrcS 121
                                        44555555555899**999888878765555555******************642223222212..2.22222333 PP

                                        HHHHHHHHHHTTEE CS
                     Acetyltransf_7  62 aekaikfYeklGFe 75 
                                        + kai+fYek+G++
  gene2277|gene2277|rna2277|rna2277 122 NFKAIAFYEKNGYI 135
                                        349**********7 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.0   2.5e-08   6.3e-05      24      81 ..      80     138 ..      58     142 .. 0.84

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 2.5e-08
                                        EEEEEE-GGG-SSSHHHHHHHHHHHHHHH.S-S-EEEEEETT-HHHHHHHHHHT-EEEE CS
                               FR47  24 lgalqvlpehrrrGlgsrlvkalakeiae.rgktvllvvvasNtpsirlyeklGfekie 81 
                                        +++l + p+hr+ Gl+++l + l +   e + + v l v+ sN ++i++yek G+ k++
  gene2277|gene2277|rna2277|rna2277  80 VSSLSIAPTHRKCGLATSLMRILEALGNErNAYFVDLFVRCSNFKAIAFYEKNGYIKYR 138
                                        57899***************999887777455667799******************985 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   1.3e-06    0.0032      31     125 ..      29     134 ..      15     136 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.3e-06
                                        HHHHHHHHHTTSEEEEEEETTEEEEEEEEEEEEE..EETT.EEEEE...EEEEEEEE-CCGTTS-HHHHHHHHHHH CS
                     Acetyltransf_9  31 ireyfrklleesrvlgaedngelvgqlallplel..nvpG.ktlka...agvtgVavapehrgrgvlskLlarale 100
                                        + +y+ + l+ s+ + + + ++l +++ l++ ++  ++ G ++ +      v++ + ap+hr+ g++++L++ + +
  gene2277|gene2277|rna2277|rna2277  29 LSYYLYYHLNFSDNMYIVKTEDLSSTCFLYTSKIvgYIIGkQERRGvlsMHVSSLSIAPTHRKCGLATSLMRILEA 104
                                        556666666777777777788888888888877733455634443312267888999******************* PP

                                        HHHHTT--EEEE--.....SSHHHHHTTT- CS
                     Acetyltransf_9 101 emreegqplsllfP.....ssipiYrrfGy 125
                                          +e+++ ++ lf       +i++Y++ Gy
  gene2277|gene2277|rna2277|rna2277 105 LGNERNAYFVDLFVrcsnfKAIAFYEKNGY 134
                                        *************9998865689**99999 PP

>> pPIWI_RE_REase  REase associating with pPIWI_RE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   9.3e-06     0.024      22      52 ..     147     179 ..     141     182 .] 0.93

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 9.3e-06
                     pPIWI_RE_REase  22 pelDayDllvefp.dg.tvwavDvKdytspelL 52 
                                        pe DayD+++ ++ dg ++++v vK   ++e+L
  gene2277|gene2277|rna2277|rna2277 147 PEEDAYDMRISLErDGdKRYMVPVKKPVHAENL 179
                                        899**********9888*************998 PP

>> Acetyltransf_15  Putative acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   3.0    0.0021       5.4     111     142 ..      11      45 ..       1      54 [. 0.74
   2 ?    3.7   0.0     0.014        37      73     103 ..      78     107 ..      47     172 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0021
                    Acetyltransf_15 111 lllaLHlnpkDk...sMnisfalYyslgFrkglfv 142
                                        ++++L l   D      ++s++lYy l+F + +++
  gene2277|gene2277|rna2277|rna2277  11 DIFSLDLVNLDSttdNYSLSYYLYYHLNFSDNMYI 45 
                                        5666666666641114689************9997 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.014
                    Acetyltransf_15  73 leiYtlyvsekyrgkGlakklLeeslkelkk 103
                                        + + +l + + +r+ Gla +l+ ++l++l +
  gene2277|gene2277|rna2277|rna2277  78 MHVSSLSIAPTHRKCGLATSLM-RILEALGN 107
                                        5566889999999999999865.45455533 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       367  (0.0204696); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1433.77
//
Query:       gene2278|gene2278|rna2278|rna2278  [L=312]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.019   14.8   7.4        1.1    9.1   7.4    2.5  1  CLTH      CTLH/CRA C-terminal to LisH motif domain


Domain annotation for each model (and alignments):
>> CLTH  CTLH/CRA C-terminal to LisH motif domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   7.4   6.3e-05       1.1       4      68 ..      94     156 ..      91     223 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 6.3e-05
                               CLTH   4 erqkIiklilegdlseaiewinenkpellesnsnLeFkLkllqfielirgktkdieealeyaren 68 
                                        ++++  ++i+++dl+e+   ++ nk  l+e +s+L  +Lk++ fi     + k++ ea++++r +
  gene2278|gene2278|rna2278|rna2278  94 KLKQKEENIRKNDLEELQIFCEANKVLLKELKSDLMENLKVRIFIIHCC-N-KEYSEAIQFVRAK 156
                                        56666789****************************************9.9.9**********83 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (312 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1320  (0.0736237); expected 358.6 (0.02)
Passed bias filter:                      484  (0.0269954); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 2200.51
//
Query:       gene2279|gene2279|rna2279|rna2279  [L=313]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (313 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       951  (0.0530426); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.20s 00:00:00.65 Elapsed: 00:00:00.37
# Mc/sec: 2503.83
//
Query:       gene228|gene228|rna228|rna228  [L=161]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.4e-44  149.0   0.0    7.2e-44  148.8   0.0    1.0  1  UQ_con    Ubiquitin-conjugating enzyme
     0.0061   16.8   0.0     0.0075   16.5   0.0    1.3  1  RWD       RWD domain


Domain annotation for each model (and alignments):
>> UQ_con  Ubiquitin-conjugating enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  148.8   0.0   8.1e-48   7.2e-44       2     137 ..       9     153 ..       8     156 .. 0.96

  Alignments for each domain:
  == domain 1  score: 148.8 bits;  conditional E-value: 8.1e-48
                                    HHHHHHHHHHSTTTTEEEEEEETTEECEEEEEEEB.TTSTTTTEEEEEEEE--TTTTTS--EEEESST-SCTTBETTSBB CS
                         UQ_con   2 lqkelkelakkkpsgisaklvddenlfewkvlikgpedtpYeggvFklelefpedYPlkpPkvkfvtkifHPnvdksGev 81 
                                    l+ke+k+  +k ++++s++lvd  n+++w+v+i gp++t+Ye+g+Fk+ ++fpe+YP +pPk++fv++++HPn+dk+G+v
  gene228|gene228|rna228|rna228   9 LHKEFKR--TKDNPSFSVGLVDG-NIYTWEVIILGPSNTLYENGIFKAIMQFPENYPDSPPKFRFVSDMWHPNIDKDGNV 85 
                                    6789995..899999*******7.******************************************************** PP

                                    -CGGGS............TTT--TTSHHHHHHHHHHHHHHS--TTS-SSHHHHHHHHHTHHHHHHHHH CS
                         UQ_con  82 cldiLk............eekWspaltlesvllsiqsLlaepnpesplnkeaakllkkdreeykkkvk 137
                                    c++iL+             e+W p+ + esv+lsi++Ll+ pn +sp+n +aa+++++d++ y+k+v 
  gene228|gene228|rna228|rna228  86 CISILHepgddlyeyecvAERWMPVRNPESVILSIVALLNWPNSDSPANLDAAREFREDKALYDKRVL 153
                                    *************99999888********************************************995 PP

>> RWD  RWD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   8.4e-07    0.0075      54      82 ..      50      78 ..       9     107 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 8.4e-07
                                   EEEEEEEE-SSTTSS--EEEEEECCSS-H CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            RWD 54 slkleiklpeeYPeeaPiislsstenlpk 82
                                    +k ++++pe+YP+++P++++ s  + p+
  gene228|gene228|rna228|rna228 50 IFKAIMQFPENYPDSPPKFRFVSDMWHPN 78
                                   678899*************9998875553 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       289  (0.0161191); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.28s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 1161.60
//
Query:       gene2280|gene2280|rna2280|rna2280  [L=281]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    7.8e-20   71.4  12.9    7.8e-20   71.4  12.9    2.3  2  DHHC         DHHC palmitoyltransferase
  ------ inclusion threshold ------
       0.47   11.1   3.5       0.91   10.2   3.5    1.4  1  IGFBP        Insulin-like growth factor binding protein
          2    9.0   7.6        0.3   11.7   3.3    1.7  2  PSI          Plexin repeat


Domain annotation for each model (and alignments):
>> DHHC  DHHC palmitoyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.8     0.021   1.3e+02      54      88 ..      43      77 ..       3      94 .. 0.68
   2 !   71.4  12.9   1.3e-23   7.8e-20       3     121 ..     132     243 ..     130     260 .. 0.71

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.021
                               DHHC 54 fllylllllilalvlllialvklveeekkseflav 88
                                       fl +ll l++++++l+ i+ ++ +   + s+   +
  gene2280|gene2280|rna2280|rna2280 43 FLTVLLCLTFYYVILYDIYALEKCALIRLSQLALM 77
                                       45555555555555555555555555555444443 PP

  == domain 2  score: 71.4 bits;  conditional E-value: 1.3e-23
                               DHHC   3 kelkfCstcniykpprskHcrvCnrcvlrfDHhCpwlnnciGerNykyFllfllylllllilalvlllialvklve 78 
                                        +++++C++c +++ +  +Hcr+C+ c  + DHhC w+n+ci e+N+++Fl+f+l+l+++++l++  ++++++  v 
  gene2280|gene2280|rna2280|rna2280 132 YNDDYCEKCLVIQRDFISHCRFCDVCLVNRDHHCAWFNKCIAENNFNVFLCFILSLTFSAFLIVSDTFQIFSAKVL 207
                                        7899*****************************************************9999998877777766555 PP

                               DHHC  79 eekkseflavtllkkllsilllvlsllfllllgllllfhlyli 121
                                         +  ++  ++        + ++++s+ +++l ++l l +l ++
  gene2280|gene2280|rna2280|rna2280 208 VKLSTFQIIIV-------VAIMLISMSLFVLSAILSLQYLLSL 243
                                        44443333222.......2222222223333333333333333 PP

>> IGFBP  Insulin-like growth factor binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   3.5   0.00015      0.91      15      49 ..     138     171 ..     128     175 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00015
                              IGFBP  15 esCpagvelvedgCgcCkvCarqegesCgvktgrC 49 
                                        e+C   ++    +C+ C vC+ +++ +C + + +C
  gene2280|gene2280|rna2280|rna2280 138 EKCLVIQRDFISHCRFCDVCLVNRDHHCAWFN-KC 171
                                        4676666666799****************996.99 PP

>> PSI  Plexin repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.1       1.6   9.4e+03       8      12 ..     137     141 ..     135     145 .. 0.80
   2 ?   11.7   3.3     5e-05       0.3       5      34 ..     151     177 ..     149     187 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1.6
                                        HHHHH CS
                                PSI   8 CssCl 12 
                                        C++Cl
  gene2280|gene2280|rna2280|rna2280 137 CEKCL 141
                                        99998 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 5e-05
                                        SSSHHHHHHSTCTTEEEETTTTEEEECTTS CS
                                PSI   5 yttCssCleardpgCgWCsdegrCieeskc 34 
                                         + C+ Cl +rd +C+W    ++Ci e+++
  gene2280|gene2280|rna2280|rna2280 151 CRFCDVCLVNRDHHCAWF---NKCIAENNF 177
                                        567**************9...899997765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1163  (0.064867); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 2108.94
//
Query:       gene2281|gene2281|rna2281|rna2281  [L=121]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00017   21.6   0.2    0.00022   21.2   0.2    1.2  1  ETRAMP          Malarial early transcribed membrane protein (
     0.0027   17.5   2.0     0.0036   17.1   0.3    1.9  2  Synaptobrevin   Synaptobrevin
      0.003   17.1   0.3      0.098   12.2   0.0    2.1  2  Baculo_11_kDa   Baculovirus 11 kDa family
     0.0047   16.7   0.5      0.021   14.6   0.2    1.9  2  ASFV_J13L       African swine fever virus J13L protein
  ------ inclusion threshold ------
       0.01   15.7   0.0      0.012   15.5   0.0    1.1  1  RIFIN           Rifin
      0.011   15.6   0.0      0.028   14.3   0.0    1.7  2  LRRC37AB_C      LRRC37A/B like protein 1 C-terminal domain
      0.012   15.4   0.5      0.017   14.9   0.5    1.4  1  DUF4448         Protein of unknown function (DUF4448)
      0.018   15.2   2.5        1.1    9.5   1.2    2.1  2  Pox_A14         Poxvirus virion envelope protein A14
      0.027   14.5   0.3      0.045   13.8   0.3    1.4  1  DUF4366         Domain of unknown function (DUF4366)
      0.039   13.9   0.0        2.2    8.2   0.0    2.2  2  TMEM154         TMEM154 protein family
      0.039   14.1   0.0      0.051   13.7   0.0    1.1  1  PIG-F           GPI biosynthesis protein family Pig-F
      0.046   13.7   0.6       0.68    9.9   0.0    2.2  2  Orthoreo_P10    Orthoreovirus membrane fusion protein p10
      0.079   12.6   0.5        1.6    8.3   0.0    1.9  2  SARAF           SOCE-associated regulatory factor of calcium 
       0.12   13.3   0.1       0.12   13.3   0.1    2.4  2  EphA2_TM        Ephrin type-A receptor 2 transmembrane domain
       0.25   11.6   2.0         13    6.2   0.0    2.2  2  Wzz             Chain length determinant protein
       0.63    9.9   3.5       0.96    9.3   3.5    1.3  1  Phage_Coat_Gp8  Phage major coat protein, Gp8
       0.66   10.6   0.0       0.66   10.6   0.0    2.6  2  OAD_gamma       Oxaloacetate decarboxylase, gamma chain
        3.3    7.8   7.4       0.37   10.8   1.5    2.3  2  DUF5316         Family of unknown function (DUF5316)
        5.3    8.1   8.6        6.9    7.7   0.0    2.5  2  DUF4834         Domain of unknown function (DUF4834)


Domain annotation for each model (and alignments):
>> ETRAMP  Malarial early transcribed membrane protein (ETRAMP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.2   2.3e-07   0.00022       3      74 ..       5     117 ..       3     121 .] 0.72

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 2.3e-07
                             ETRAMP   3 vtkv.llffafLlavnlltpeslcdevnkkk..........................................eka 35 
                                        +    +++++++l+ n+    + + +++k +                                          +k+
  gene2281|gene2281|rna2281|rna2281   5 FYHCaFFLIVLILLSNVYKIRCQSTVEKKDQnaendaggaspiaeevqgispdseekddggmgglfgkskdkdQKK 80 
                                        55553667777777888888888888877779**********************************9997655555 PP

                             ETRAMP  36 kkaikkiddkiekkkkkkKliiistiatalallvasalG 74 
                                        +k  k++++++  k   k  iii+++++++++ +++++G
  gene2281|gene2281|rna2281|rna2281  81 DKGSKSKNQSFFSK--YKTYIIIALVVIVVIVIAGVVFG 117
                                        55555555555555..44445566666666666666666 PP

>> Synaptobrevin  Synaptobrevin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.1       1.2   1.2e+03      69      81 ..       6      18 ..       2      25 .. 0.58
   2 !   17.1   0.3   3.8e-06    0.0036      53      86 ..      82     115 ..      76     118 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 1.2
                                       XXXXXXXXXXXXX CS
                      Synaptobrevin 69 iiililvvlilil 81
                                       + + ++++++++l
  gene2281|gene2281|rna2281|rna2281  6 YHCAFFLIVLILL 18
                                       5555555555544 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 3.8e-06
                                        HHHHHHHHHHHHTXXXXXXXXXXXXXXXXXXXXX CS
                      Synaptobrevin  53 qarklkrkmwwknmkliiililvvlililiiiiv 86 
                                        +  k k++  + ++k +ii++lvv+++i+i  +v
  gene2281|gene2281|rna2281|rna2281  82 KGSKSKNQSFFSKYKTYIIIALVVIVVIVIAGVV 115
                                        5678899********************9998766 PP

>> Baculo_11_kDa  Baculovirus 11 kDa family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0     0.078        74      41      62 ..       8      29 ..       6      41 .. 0.44
   2 !   12.2   0.0    0.0001     0.098      27      51 ..      86     111 ..      73     119 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.078
                      Baculo_11_kDa 41 cglvvfvvivlfilLlvvilkn 62
                                       c+++++v+i+l  +  +  +++
  gene2281|gene2281|rna2281|rna2281  8 CAFFLIVLILLSNVYKIRCQST 29
                                       5555555444433332222222 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.0001
                      Baculo_11_kDa  27 srNrsflrdF.vLvicglvvfvvivl 51 
                                        s+N+sf+  +   +i +lvv+vviv+
  gene2281|gene2281|rna2281|rna2281  86 SKNQSFFSKYkTYIIIALVVIVVIVI 111
                                        79*****9995467777777777775 PP

>> ASFV_J13L  African swine fever virus J13L protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0       0.5   4.7e+02      44      68 ..      11      35 ..       6      55 .. 0.80
   2 !   14.6   0.2   2.2e-05     0.021      20      49 ..      85     114 ..      79     121 .] 0.80

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.5
                          ASFV_J13L 44 iiivliylfssrkkkaaaaieeedi 68
                                        +ivli l    k ++ +++e++d 
  gene2281|gene2281|rna2281|rna2281 11 FLIVLILLSNVYKIRCQSTVEKKDQ 35
                                       4678888888888888888887775 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 2.2e-05
                          ASFV_J13L  20 svsapsffsthmytiliaivvliiiiivli 49 
                                             sffs +   i+ia+vv+++i+i  +
  gene2281|gene2281|rna2281|rna2281  85 KSKNQSFFSKYKTYIIIALVVIVVIVIAGV 114
                                        56678*******99******9999988643 PP

>> RIFIN  Rifin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   0.0   1.3e-05     0.012     217     293 ..      33     112 ..       5     116 .. 0.63

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.3e-05
                              RIFIN 217 akekekkeasskekikkkvekivekaekkaaaaaa...eaaaeataeaekaetaaveattaslqtaiiasivaivv 289
                                        + ++ ++ a  ++ i ++v+ i  + e+k +  +     +++++ ++  k + ++ ++ +++++t ii++ v+ivv
  gene2281|gene2281|rna2281|rna2281  33 KDQNAENDAGGASPIAEEVQGISPDSEEKDDGGMGglfGKSKDKDQKKDKGSKSKNQSFFSKYKTYIIIALVVIVV 108
                                        222333333333444444444444444444444336666777777788888899999999**************** PP

                              RIFIN 290 IvLi 293
                                        Iv+ 
  gene2281|gene2281|rna2281|rna2281 109 IVIA 112
                                        *985 PP

>> LRRC37AB_C  LRRC37A/B like protein 1 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       1.9   1.8e+03     127     142 ..      13      28 ..       8      45 .. 0.60
   2 ?   14.3   0.0     3e-05     0.028      91     136 ..      74     119 ..      47     120 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 1.9
                         LRRC37AB_C 127 miliiilcLieicshr 142
                                        ++li++  +++i+++ 
  gene2281|gene2281|rna2281|rna2281  13 IVLILLSNVYKIRCQS 28 
                                        3444444444444444 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 3e-05
                         LRRC37AB_C  91 aqseqkeqkskeltkevpeygynnklilaisvtvvvmiliiilcLi 136
                                        ++++qk+ k ++++++    +y+  +i+a+ v vv++i  ++++++
  gene2281|gene2281|rna2281|rna2281  74 KDKDQKKDKGSKSKNQSFFSKYKTYIIIALVVIVVIVIAGVVFGMF 119
                                        346677777777777777889*****************99999875 PP

>> DUF4448  Protein of unknown function (DUF4448)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.5   1.8e-05     0.017     130     179 ..      67     116 ..      19     121 .] 0.71

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.8e-05
                            DUF4448 130 GpkVsltkkedlkkledkeseegkkaekyalaialPvvvvvlvlgligfv 179
                                        G    ++k +d+kk++  +s++++  +ky+ +i + +vv+v++++  +++
  gene2281|gene2281|rna2281|rna2281  67 GGLFGKSKDKDQKKDKGSKSKNQSFFSKYKTYIIIALVVIVVIVIAGVVF 116
                                        55566777777777777888888888898888888887766655444333 PP

>> Pox_A14  Poxvirus virion envelope protein A14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.0     0.028        26      56      82 ..      10      36 ..       5      44 .. 0.76
   2 ?    9.5   1.2    0.0011       1.1      34      70 ..      86     121 .]      83     121 .] 0.82

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.028
                            Pox_A14 56 ivillglllfsmygrkCkatsskvvee 82
                                         +++ +ll ++y+ +C+ t++k++++
  gene2281|gene2281|rna2281|rna2281 10 FFLIVLILLSNVYKIRCQSTVEKKDQN 36
                                       556788899999*****9987766665 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0011
                            Pox_A14  34 skststtdkawralsivsFilgivillglllfsmygr 70 
                                        sk++s   + +++  i++ ++ +vi+++ ++f m+++
  gene2281|gene2281|rna2281|rna2281  86 SKNQS-FFSKYKTYIIIALVVIVVIVIAGVVFGMFKK 121
                                        45555.34589***********************975 PP

>> DUF4366  Domain of unknown function (DUF4366)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.3   4.8e-05     0.045      94     139 ..      47     120 ..      19     121 .] 0.52

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.8e-05
                            DUF4366  94 v.........................eepepekeaepeepeeepekksn....nglllvvlavaligggaayyfk 139
                                        +                          +++++k+ ++ +++++++  s+     +++lvv++v++i+g  + +fk
  gene2281|gene2281|rna2281|rna2281  47 IaeevqgispdseekddggmgglfgkSKDKDQKK-DKGSKSKNQSFFSKyktyIIIALVVIVVIVIAGVVFGMFK 120
                                        1444444444466666667777766422222222.2222222222222244447788888899999999999888 PP

>> TMEM154  TMEM154 protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0      0.05        48      69      99 ..      12      40 ..       8      62 .. 0.67
   2 ?    8.2   0.0    0.0023       2.2      52      81 ..      85     118 ..      69     121 .] 0.67

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.05
                            TMEM154 69 lillllvviiliqkkkrkrsKddekseaesd 99
                                       li+l+l+  +   +++++ +K d  ++ae+d
  gene2281|gene2281|rna2281|rna2281 12 LIVLILLSNVYKIRCQSTVEKKD--QNAEND 40
                                       55555555555448888877777..445555 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0023
                            TMEM154  52 esdqlel....vlmiiiPlvllillllvviiliq 81 
                                        +s ++++       iii lv++++++++++++ +
  gene2281|gene2281|rna2281|rna2281  85 KSKNQSFfskyKTYIIIALVVIVVIVIAGVVFGM 118
                                        4444444444445689999999999999999865 PP

>> PIG-F  GPI biosynthesis protein family Pig-F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   5.4e-05     0.051      29      82 ..      12     117 ..       4     119 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.4e-05
                              PIG-F  29 livlallqvlyvvlcl..................................................ekkkk..ksk 52 
                                        livl+ll  +y + c+                                                  +kk+k  ksk
  gene2281|gene2281|rna2281|rna2281  12 LIVLILLSNVYKIRCQstvekkdqnaendaggaspiaeevqgispdseekddggmgglfgkskdkdQKKDKgsKSK 87 
                                        67888999999999999*****************************999999999999998776542444467899 PP

                              PIG-F  53 kskivlallsllltlllatlllaillvlfG 82 
                                        +++++++ ++ ++++l++ ++++i+ v+fG
  gene2281|gene2281|rna2281|rna2281  88 NQSFFSKYKTYIIIALVVIVVIVIAGVVFG 117
                                        999999999999999999999999999998 PP

>> Orthoreo_P10  Orthoreovirus membrane fusion protein p10
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.4      0.28   2.7e+02      50      67 ..      10      27 ..       4      40 .. 0.61
   2 ?    9.9   0.0   0.00072      0.68      12      62 ..      66     116 ..      58     121 .] 0.87

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.28
                       Orthoreo_P10 50 gliviilllallycckak 67
                                        ++++++ll+ +y  + +
  gene2281|gene2281|rna2281|rna2281 10 FFLIVLILLSNVYKIRCQ 27
                                       567788888888754333 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00072
                       Orthoreo_P10  12 avsvfgnvhcqaakntaggdlqatssliaywpylaagggliviilllally 62 
                                        +  +fg+ + +  k   g   +  s +  y  y+ +   +iv+i++ ++++
  gene2281|gene2281|rna2281|rna2281  66 MGGLFGKSKDKDQKKDKGSKSKNQSFFSKYKTYIIIALVVIVVIVIAGVVF 116
                                        56789999999999999********************99999999988876 PP

>> SARAF  SOCE-associated regulatory factor of calcium homoeostasis
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.0    0.0017       1.6     165     236 ..      10      86 ..       2      93 .. 0.53
   2 ?    6.9   0.5    0.0044       4.2     132     180 ..      72     119 ..      66     121 .] 0.53

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0017
                              SARAF 165 vvlvllviayivykaflaaeeereaeaeggrrgegggggggggg..pgseeeqddpPppy....sltksqkpssss 234
                                        ++l++l+++  vyk+ ++++ e++ ++ ++ +g+ ++  ++ +g  p  +ee+dd    +    s+ k+qk+++ s
  gene2281|gene2281|rna2281|rna2281  10 FFLIVLILLSNVYKIRCQSTVEKKDQNAENDAGGASPIAEEVQGisP-DSEEKDDGGMGGlfgkSKDKDQKKDKGS 84 
                                        45667778889999999888887776777777777777666666432.2233344444444443222222222222 PP

                              SARAF 235 es 236
                                        +s
  gene2281|gene2281|rna2281|rna2281  85 KS 86 
                                        22 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0044
                              SARAF 132 ekkykkseeskkeeekkeevkkksssssasllfvvlvllviayivykaf 180
                                        ++k k+++++k +++k+++   ++ ++ + + +vv+v++via +v+ +f
  gene2281|gene2281|rna2281|rna2281  72 KSKDKDQKKDKGSKSKNQSFF-SKYKTYIIIALVVIVVIVIAGVVFGMF 119
                                        455555555444444444322.223333333367777777777777776 PP

>> EphA2_TM  Ephrin type-A receptor 2 transmembrane domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   0.00012      0.12      11      57 ..      11      99 ..       5      99 .. 0.50
   2 ?    0.8   7.2         1   9.6e+02       5      22 ..      99     116 ..      97     121 .] 0.73

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00012
                           EphA2_TM 11 llvilvilvlvlvrrrsknrkqksdl..................k......................skeekkeeens 48
                                       +l++l++l  v   r+++  ++k+++                  +                      +k++k++++++
  gene2281|gene2281|rna2281|rna2281 11 FLIVLILLSNVYKIRCQSTVEKKDQNaendaggaspiaeevqgiSpdseekddggmgglfgkskdkdQKKDKGSKSKN 88
                                       333333333343334444444444445677777777666655550555666677777777777655423333333333 PP

                           EphA2_TM 49 gk..kglktYv 57
                                       ++  +++ktY+
  gene2281|gene2281|rna2281|rna2281 89 QSffSKYKTYI 99
                                       334349****8 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 1
                           EphA2_TM   5 avaglvllvilvilvlvl 22 
                                        ++++lv++v++vi  +v+
  gene2281|gene2281|rna2281|rna2281  99 IIIALVVIVVIVIAGVVF 116
                                        678888888888887776 PP

>> Wzz  Chain length determinant protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0     0.014        13      31      61 ..      12      42 ..       6      61 .. 0.74
   2 ?    3.6   2.1     0.089        84      16      34 ..      98     116 ..      93     121 .] 0.77

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.014
                                       XXXXXXXXX-EEEEEEEES--CHHH.HHHHHH CS
                                Wzz 31 viyaflatpkYtataqilvpekkqv.easslt 61
                                       +i+++l++++Y+ + q +v++k+q+ e ++  
  gene2281|gene2281|rna2281|rna2281 12 LIVLILLSNVYKIRCQSTVEKKDQNaE-NDAG 42
                                       6888********************742.4433 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.089
                                        XXXXXXXXXXXXXXXXXXX CS
                                Wzz  16 kklIilvtllfallaviya 34 
                                         ++I+lv+++++++a+++ 
  gene2281|gene2281|rna2281|rna2281  98 YIIIALVVIVVIVIAGVVF 116
                                        5789999999999998875 PP

>> Phage_Coat_Gp8  Phage major coat protein, Gp8
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   3.5     0.001      0.96      25      47 ..      99     121 .]      90     121 .] 0.87

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.001
                                        HHHHHHHHHHHHHHHHHHHHHHH CS
                     Phage_Coat_Gp8  25 igyaWavVvvvvvAtlgIkLFKK 47 
                                        i  a  v+vv+v A+++  +FKK
  gene2281|gene2281|rna2281|rna2281  99 IIIALVVIVVIVIAGVVFGMFKK 121
                                        556677999*************9 PP

>> OAD_gamma  Oxaloacetate decarboxylase, gamma chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0    0.0007      0.66      17      62 ..      11      63 ..      10      67 .. 0.82
   2 ?   -0.1   0.2       1.5   1.5e+03      35      47 ..      73      85 ..      64      91 .. 0.42

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0007
                          OAD_gamma 17 vLilLslvislfskiikkkakkkkkkakaaaaaaaaaaaaa.......elddd 62
                                       +Li+L+l+ ++ +   +   +kk+++a+++a  a++ a+++       e++dd
  gene2281|gene2281|rna2281|rna2281 11 FLIVLILLSNVYKIRCQSTVEKKDQNAENDAGGASPIAEEVqgispdsEEKDD 63
                                       99***********9999999999999999999999888777777776655555 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1.5
                          OAD_gamma 35 kakkkkkkakaaa 47
                                        + k +kk k ++
  gene2281|gene2281|rna2281|rna2281 73 SKDKDQKKDKGSK 85
                                       2222222222222 PP

>> DUF5316  Family of unknown function (DUF5316)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0       1.2   1.1e+03      27      47 ..      18      38 ..       8      41 .. 0.69
   2 ?   10.8   1.5   0.00039      0.37       4      28 ..      96     120 ..      94     121 .] 0.93

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 1.2
                            DUF5316 27 fvsgdriranytseskedrrk 47
                                       + + ++ir   t e+k+   +
  gene2281|gene2281|rna2281|rna2281 18 LSNVYKIRCQSTVEKKDQNAE 38
                                       455678888888888887655 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00039
                            DUF5316   4 ltykisGfvglvfiliagllsGafv 28 
                                        +ty i   v +v+i+iag+++G f 
  gene2281|gene2281|rna2281|rna2281  96 KTYIIIALVVIVVIVIAGVVFGMFK 120
                                        799********************96 PP

>> DUF4834  Domain of unknown function (DUF4834)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.0    0.0073       6.9      14      46 ..      10      86 ..       4      98 .. 0.59
   2 ?   -0.1   7.1       2.1   1.9e+03       9      30 ..      98     119 ..      90     121 .] 0.72

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0073
                            DUF4834 14 ilviglsilsvilrtv............................................fglgsrkkssksaqkqf 46
                                        ++i+l++ls++++                                              fg+++ k ++k + +++
  gene2281|gene2281|rna2281|rna2281 10 FFLIVLILLSNVYKIRcqstvekkdqnaendaggaspiaeevqgispdseekddggmgglFGKSKDKDQKKDKGSKS 86
                                       45566666666666554556666667777777777777777777777777777777766677555544442222222 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 2.1
                            DUF4834   9 ifiiailviglsilsvilrtvf 30 
                                         +iia++vi++++++ ++  +f
  gene2281|gene2281|rna2281|rna2281  98 YIIIALVVIVVIVIAGVVFGMF 119
                                        5788888888888877766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1775  (0.0990016); expected 358.6 (0.02)
Passed bias filter:                      957  (0.0533772); expected 358.6 (0.02)
Passed Vit filter:                       157  (0.00875676); expected 17.9 (0.001)
Passed Fwd filter:                        23  (0.00128284); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.51u 0.32s 00:00:00.83 Elapsed: 00:00:00.45
# Mc/sec: 806.20
//
Query:       gene2282|gene2282|rna2282|rna2282  [L=62]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (62 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       636  (0.0354733); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.29s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 412.13
//
Query:       gene2283|gene2283|rna2283|rna2283  [L=35]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (35 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       410  (0.022868); expected 358.6 (0.02)
Passed bias filter:                      248  (0.0138323); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.28s 00:00:00.62 Elapsed: 00:00:00.42
# Mc/sec: 250.64
//
Query:       gene2284|gene2284|rna2284|rna2284  [L=131]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0018   18.5   0.0      0.018   15.3   0.0    1.9  2  TctB           Tripartite tricarboxylate transporter TctB fam
  ------ inclusion threshold ------
      0.038   13.4   0.0      0.081   12.3   0.0    1.5  2  DAG1           Dystroglycan (Dystrophin-associated glycoprote
      0.058   12.1   0.1      0.075   11.7   0.1    1.0  1  Prog_receptor  Progesterone receptor
      0.092   11.5   0.0        0.1   11.4   0.0    1.1  1  BatD           Oxygen tolerance
       0.12   12.4   0.7       0.12   12.4   0.7    2.4  3  Ferlin_C       Ferlin C-terminus
       0.13   12.6   0.8       0.13   12.6   0.8    1.4  2  DUF4212        Domain of unknown function (DUF4212)
       0.35   10.9   3.3        1.7    8.7   3.1    2.0  1  DUF4366        Domain of unknown function (DUF4366)
       0.43   10.3   1.1        0.6    9.8   1.1    1.2  1  TPR_21         Tetratricopeptide repeat-like domain
        2.5    7.9   5.8       0.16   11.8   1.0    1.4  2  Synaptobrevin  Synaptobrevin
        2.8    8.3   3.8       0.49   10.7   0.1    1.9  2  Orf78          Orf78 (ac78)
        4.7    7.6   5.9       0.87   10.0   0.5    2.3  2  DUF5383        Family of unknown function (DUF5383)
        7.5    7.6   5.7         65    4.6   0.0    2.3  2  DUF4834        Domain of unknown function (DUF4834)


Domain annotation for each model (and alignments):
>> TctB  Tripartite tricarboxylate transporter TctB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0      0.25   3.7e+02      39      49 ..      10      40 ..       2      66 .. 0.51
   2 !   15.3   0.0   1.2e-05     0.018      51      91 ..      86     126 ..      76     127 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.25
                               TctB 39 lallgllllv....................a 49
                                       l+l+ +l l+                    +
  gene2284|gene2284|rna2284|rna2284 10 LMLAVVLDLFlvpvgaevkvappkgeekesE 40
                                       2222222222566777666665555444330 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 1.2e-05
                               TctB  51 dgekeekearedwrkllklvlallaalllyallleplGfil 91 
                                        ++ ++++e +++w++  k+++ +l+++l+ +++l ++Gfil
  gene2284|gene2284|rna2284|rna2284  86 SEPEKGEENKSFWQRHKKTIIWCLVIFLVIIIALAVVGFIL 126
                                        4556677777888888889999899**************97 PP

>> DAG1  Dystroglycan (Dystrophin-associated glycoprotein 1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0         2     3e+03     122     144 ..      21      43 ..      15      44 .. 0.81
   2 ?   12.3   0.0   5.4e-05     0.081     131     174 ..      87     130 ..      81     131 .] 0.88

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 2
                                        XXXXXXXXXXXXXXXXXXXXXXX CS
                               DAG1 122 iPsevasteapeedaeksseddv 144
                                        +P  +   +ap ++ ek+se++v
  gene2284|gene2284|rna2284|rna2284  21 VPVGAEVKVAPPKGEEKESEGEV 43 
                                        67777778899999999999986 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 5.4e-05
                                        XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                               DAG1 131 apeedaeksseddvylhtvipavvvaailliagiiamicyrkkr 174
                                         pe++ e +s+ + + +t+i+ +v+  +++ia  ++   +++++
  gene2284|gene2284|rna2284|rna2284  87 EPEKGEENKSFWQRHKKTIIWCLVIFLVIIIALAVVGFILKRRK 130
                                        689999**************************988888777654 PP

>> Prog_receptor  Progesterone receptor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1     5e-05     0.075     112     179 ..      12      79 ..       8      84 .. 0.95

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 5e-05
                      Prog_receptor 112 ldsvldtllaPsgPgqskasPpaceatspwclfGpelPedprsapatqgvlaplmsrpegkaGdssgt 179
                                        l  vld  l P g +   a P   e  s   +  pe Pe  +  p t+  +ap   +  g +G ssg 
  gene2284|gene2284|rna2284|rna2284  12 LAVVLDLFLVPVGAEVKVAPPKGEEKESEGEVAKPEEPEKEKEEPETEDETAPTGDKGSGDSGKSSGS 79 
                                        7889**************************************************************96 PP

>> BatD  Oxygen tolerance
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0     7e-05       0.1     383     448 ..      47     129 ..      23     131 .] 0.36

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 7e-05
                               BatD 383 a...aaasspasstsaspaqkeevkllgkdir.....fik.geaslkkkgsff......lfw..lllllplllf.v 440
                                        +   +++++p+++ +++p+ ++    +gk+       f + + ++ ++++sf+       +w  +++l++++++ v
  gene2284|gene2284|rna2284|rna2284  47 EepeKEKEEPETEDETAPTGDKGSGDSGKSSGsvlgmF-SsEPEKGEENKSFWqrhkktIIWclVIFLVIIIALaV 121
                                        23333333333333333333333333333333333321.2122333333335556655555554222333333324 PP

                               BatD 441 vllllwrk 448
                                        v ++l r+
  gene2284|gene2284|rna2284|rna2284 122 VGFILKRR 129
                                        44444444 PP

>> Ferlin_C  Ferlin C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.2       1.4   2.1e+03     127     140 ..       8      21 ..       3      29 .. 0.62
   2 ?   -1.6   2.1       1.5   2.2e+03      27      43 ..      38      56 ..      25      77 .. 0.55
   3 ?   12.4   0.7   7.7e-05      0.12     117     142 ..      96     121 ..      89     127 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.4
                           Ferlin_C 127 iallilallalflv 140
                                        ++l++ ++l lflv
  gene2284|gene2284|rna2284|rna2284   8 LILMLAVVLDLFLV 21 
                                        34455555666654 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.5
                           Ferlin_C 27 ereerea..kkkkKkkkkr 43
                                       e e  +a  ++ +K+k++ 
  gene2284|gene2284|rna2284|rna2284 38 ESEGEVAkpEEPEKEKEEP 56
                                       3333333223333333333 PP

  == domain 3  score: 12.4 bits;  conditional E-value: 7.7e-05
                           Ferlin_C 117 fiWkkykkyiiallilallalflvll 142
                                         +W+++kk ii+ l+++l+ ++ +++
  gene2284|gene2284|rna2284|rna2284  96 SFWQRHKKTIIWCLVIFLVIIIALAV 121
                                        69***********9998876654444 PP

>> DUF4212  Domain of unknown function (DUF4212)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.1       9.7   1.4e+04      13      15 ..      12      14 ..       4      25 .. 0.50
   2 ?   12.6   0.8     9e-05      0.13       2      26 ..      95     119 ..      94     129 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 9.7
                            DUF4212 13 lil 15
                                       l++
  gene2284|gene2284|rna2284|rna2284 12 LAV 14
                                       222 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 9e-05
                            DUF4212   2 kaYwrenlrlililLviWfvvsfgl 26 
                                        k++w+++++ i+++Lvi++v+ + l
  gene2284|gene2284|rna2284|rna2284  95 KSFWQRHKKTIIWCLVIFLVIIIAL 119
                                        78****************9998773 PP

>> DUF4366  Domain of unknown function (DUF4366)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   3.1    0.0011       1.7      64     143 ..      50     129 ..      22     131 .] 0.52

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0011
                            DUF4366  64 eedeeaakeeeevcactekcaagkvntdcpv...eepepekeaepeepeeepekksnnglllvvlavaligggaay 136
                                        e+++e+ ++e e++ + +k + ++ +++++v      epek +e+++  + ++k+   +  lv+++v++i+  a++
  gene2284|gene2284|rna2284|rna2284  50 EKEKEEPETEDETAPTGDKGSGDSGKSSGSVlgmFSSEPEKGEENKSFWQRHKKT--IIWCLVIFLVIIIA-LAVV 122
                                        2333333444444444444444444444444888555666666664444444443..44444554554444.4444 PP

                            DUF4366 137 yfkvlkp 143
                                         f +++ 
  gene2284|gene2284|rna2284|rna2284 123 GFILKRR 129
                                        4444444 PP

>> TPR_21  Tetratricopeptide repeat-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   1.1    0.0004       0.6       1      25 [.      95     119 ..      95     123 .. 0.93

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0004
                             TPR_21   1 KawWkengklilvgvvlalvglaGw 25 
                                        K++W+++ k+i++ +v+ lv++++ 
  gene2284|gene2284|rna2284|rna2284  95 KSFWQRHKKTIIWCLVIFLVIIIAL 119
                                        89******************99986 PP

>> Synaptobrevin  Synaptobrevin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.3       8.2   1.2e+04      71      76 ..      10      15 ..       4      21 .. 0.46
   2 ?   11.8   1.0   0.00011      0.16      59      86 ..      94     121 ..      90     123 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 8.2
                                       XXXXXX CS
                      Synaptobrevin 71 ililvv 76
                                       ++ +vv
  gene2284|gene2284|rna2284|rna2284 10 LMLAVV 15
                                       222222 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00011
                                        HHHHHHTXXXXXXXXXXXXXXXXXXXXX CS
                      Synaptobrevin  59 rkmwwknmkliiililvvlililiiiiv 86 
                                        +k  w++ k +ii++lv++++i+i ++v
  gene2284|gene2284|rna2284|rna2284  94 NKSFWQRHKKTIIWCLVIFLVIIIALAV 121
                                        7889*********999999999998766 PP

>> Orf78  Orf78 (ac78)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.8       4.8   7.1e+03      67      81 ..       5      19 ..       1      22 [. 0.51
   2 ?   10.7   0.1   0.00033      0.49      52      91 ..      91     129 ..      27     131 .] 0.66

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 4.8
                              Orf78 67 lisllavvcvlvlly 81
                                         sl+ +++v++ l+
  gene2284|gene2284|rna2284|rna2284  5 HSSLILMLAVVLDLF 19
                                       445555555554444 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00033
                              Orf78  52 kesnaaekaqalnillisllavvcvlvllyviyYfvilre 91 
                                         e+ +++  q  +  +i  l+++ v+++  +++ f++ r+
  gene2284|gene2284|rna2284|rna2284  91 GEE-NKSFWQRHKKTIIWCLVIFLVIIIALAVVGFILKRR 129
                                        222.334444445555556666777777777777777765 PP

>> DUF5383  Family of unknown function (DUF5383)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.6      0.75   1.1e+03     100     119 ..       3      22 ..       1      26 [. 0.76
   2 ?   10.0   0.5   0.00058      0.87      67     114 ..      76     121 ..      33     130 .. 0.71

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.75
                            DUF5383 100 illillivllivvllivliP 119
                                        i+  +li++l vvl ++l+P
  gene2284|gene2284|rna2284|rna2284   3 IIHSSLILMLAVVLDLFLVP 22 
                                        67777888888888889999 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00058
                            DUF5383  67 akakelgLfseekesvkqsateqes..eeksnlLpillillivllivvll 114
                                        +  + lg+fs+e e     ++e++s  +++   + + l++++v++i++ +
  gene2284|gene2284|rna2284|rna2284  76 SSGSVLGMFSSEPEK----GEENKSfwQRHKKTIIWCLVIFLVIIIALAV 121
                                        555667788877665....6777777788889999999999999987644 PP

>> DUF4834  Domain of unknown function (DUF4834)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0     0.044        65      15      67 ..       8      60 ..       1     103 [. 0.54
   2 ?   -0.1   7.1       1.3   1.9e+03       8      27 ..     108     127 ..     102     130 .. 0.66

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.044
                            DUF4834 15 lviglsilsvilrtvfglgsrkkssksaqkqfgnstnsnqqksqsrsetkeeg 67
                                       l+++l+++  ++    g+  +    k ++k+++ +  ++++ +++++e ++e+
  gene2284|gene2284|rna2284|rna2284  8 LILMLAVVLDLFLVPVGAEVKVAPPKGEEKESEGEVAKPEEPEKEKEEPETED 60
                                       56666666666666666333333332222222222222222222222222111 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1.3
                            DUF4834   8 lifiiailviglsilsvilr 27 
                                         ++i+++++i+l+++++il+
  gene2284|gene2284|rna2284|rna2284 108 CLVIFLVIIIALAVVGFILK 127
                                        45566667777888888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1660  (0.0925874); expected 358.6 (0.02)
Passed bias filter:                     1147  (0.0639746); expected 358.6 (0.02)
Passed Vit filter:                       178  (0.00992805); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.41
# Mc/sec: 964.38
//
Query:       gene2285|gene2285|rna2285|rna2285  [L=180]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0019   18.2   1.5     0.0032   17.4   1.5    1.5  1  EFP_N     Elongation factor P (EF-P) KOW-like domain
  ------ inclusion threshold ------
       0.13   12.3   0.0       0.23   11.5   0.0    1.4  1  CARD      Caspase recruitment domain


Domain annotation for each model (and alignments):
>> EFP_N  Elongation factor P (EF-P) KOW-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   1.5   3.6e-07    0.0032       2      58 .]      25      85 ..      24      85 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 3.6e-07
                                       GGG--TT-EEEET...TEEEEEEEEEEEEET.TS--EEEEEEEETTTS-EEEEEEETT-EE CS
                              EFP_N  2 aselkkGlvieid...gklyvVlefehvkpG.kGqafvrvklknlrtGakvektfkagdkv 58
                                       a+ lk  +vi  d   ++ +++ ++  vk G  G+a v +  kn+rt+ k e +f +g kv
  gene2285|gene2285|rna2285|rna2285 25 ANTLKEKTVIVADadrKDYVRITSVTKVKTGkHGAAKVMISGKNIRTNLKAEMSFSGGSKV 85
                                       666777777776533356899********99458899*********************997 PP

>> CARD  Caspase recruitment domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   2.6e-05      0.23      35      68 ..     119     152 ..     116     157 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 2.6e-05
                                        HHHHHHTSSSHHHHHHHHHHHHHTSCHHHHHHHH CS
                               CARD  35 eeekikakttrlskareLldlvqkkgekacqafl 68 
                                        e+e+ +++   ++++  Lld++++ ge a + f 
  gene2285|gene2285|rna2285|rna2285 119 EMETLHCNEIEKDRVKLLLDTIKSAGEDAVIQFA 152
                                        899*************************998886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       522  (0.0291148); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1277.82
//
Query:       gene2286|gene2286|rna2286|rna2286  [L=309]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.6e-15   56.6   5.1    2.6e-11   43.6   0.5    3.0  3  DNA_pol3_delta2  DNA polymerase III, delta subunit
    7.4e-15   55.5   1.7    9.3e-15   55.2   0.3    1.8  2  AAA              ATPase family associated with various cellul
    1.5e-13   50.9   0.1    5.5e-12   45.9   0.0    2.6  2  Rep_fac_C        Replication factor C C-terminal domain
    2.8e-07   30.4   0.1    7.2e-07   29.1   0.1    1.7  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
      3e-07   30.5   1.3    1.8e-06   28.0   0.8    2.3  2  Rad17            Rad17 P-loop domain
    5.2e-05   23.7   0.0      0.046   14.1   0.0    2.3  2  AAA_16           AAA ATPase domain
    0.00014   21.7   1.2    0.00014   21.7   1.2    1.6  2  DNA_pol3_delta   DNA polymerase III, delta subunit
    0.00021   21.5   0.1     0.0012   19.2   0.0    2.2  2  AAA_assoc_2      AAA C-terminal domain
    0.00058   19.9   0.2     0.0015   18.6   0.1    1.6  2  AAA_14           AAA domain
     0.0006   19.3   0.1      0.021   14.2   0.0    2.5  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    0.00069   19.4   0.0      0.037   13.7   0.0    2.3  2  Sigma54_activat  Sigma-54 interaction domain
    0.00098   19.7   0.1     0.0033   18.0   0.0    1.9  2  AAA_18           AAA domain
      0.001   19.0   0.3      0.012   15.6   0.0    2.7  3  AAA_5            AAA domain (dynein-related subfamily)
     0.0028   18.0   1.7        2.5    8.4   0.0    3.0  3  AAA_22           AAA domain
     0.0031   17.6   0.2      0.036   14.2   0.0    2.3  2  Sigma54_activ_2  Sigma-54 interaction domain
      0.006   16.5   0.0      0.013   15.4   0.0    1.5  1  AAA_3            ATPase family associated with various cellul
     0.0065   15.7   0.2     0.0098   15.1   0.1    1.5  1  TIP49            TIP49 P-loop domain
     0.0069   16.8   0.2       0.03   14.7   0.0    2.2  2  RNA_helicase     RNA helicase
  ------ inclusion threshold ------
      0.013   14.6   0.1      0.024   13.7   0.1    1.5  1  T2SSE            Type II/IV secretion system protein
      0.018   14.9   1.5        2.7    7.9   0.1    2.3  2  NTPase_1         NTPase
      0.022   14.5   0.7      0.043   13.6   0.7    1.6  1  AAA_11           AAA domain
      0.024   15.0   0.5       0.13   12.6   0.5    2.3  1  AAA_19           AAA domain
      0.027   14.2   0.1      0.078   12.7   0.1    1.7  1  AAA_30           AAA domain
      0.027   13.9   0.2        4.2    6.7   0.0    2.3  2  TniB             Bacterial TniB protein
      0.042   14.2   1.1       0.39   11.1   0.0    2.8  3  Sec3_C_2         Sec3 exocyst complex subunit
      0.084   12.0   0.0       0.16   11.1   0.0    1.5  1  DUF815           Protein of unknown function (DUF815)
       0.11   12.7   0.0       0.33   11.1   0.0    1.8  1  Torsin           Torsin


Domain annotation for each model (and alignments):
>> DNA_pol3_delta2  DNA polymerase III, delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.0   6.5e-05     0.043       2      47 ..      27      71 ..      26      76 .. 0.92
   2 !   43.6   0.5   3.8e-14   2.6e-11      82     162 ..      82     161 ..      69     162 .. 0.89
   3 ?   -0.2   0.6       1.1   7.6e+02     106     139 ..     201     237 ..     173     247 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 6.5e-05
                    DNA_pol3_delta2  2 qeealkilskalksgrlahayLfeGdegigkkelalnlakallcee 47
                                       ++e+++ ++++l+ + + h +Lf+G+ g+gk ++a+ +a++++ ++
  gene2286|gene2286|rna2286|rna2286 27 NHETIESIQSILNANSMPH-LLFSGPPGTGKITVAKIIAEKIVNDK 71
                                       688999***********99.8********************99876 PP

  == domain 2  score: 43.6 bits;  conditional E-value: 3.8e-14
                    DNA_pol3_delta2  82 sikldqirelieelsrkpreskkkiiiiedaekmtksAaNalLktlEEPsenaifiLitsdtnklLktirSRcqel 157
                                        +  +d++r  i+++s +      k+ii+++++ mt +A+ a+ +t+E   ++  fiL+ ++ +k+ ++i+SRc ++
  gene2286|gene2286|rna2286|rna2286  82 ERGIDTVRTTIKNFSMRLS-TGLKVIILDECDSMTVAAQQAMRRTMETSTADCRFILVCNNIQKISEPIQSRCAIF 156
                                        4489**********98765.5689**************************************************** PP

                    DNA_pol3_delta2 158 kfspl 162
                                        +f+++
  gene2286|gene2286|rna2286|rna2286 157 TFNKI 161
                                        **986 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 1.1
                    DNA_pol3_delta2 106 iiiiedaekmtksAaNalLktlEEPsen...aifiLi 139
                                        i i++   + ++  +N +Lk+   Ps +   +i+iL+
  gene2286|gene2286|rna2286|rna2286 201 INILQSTLYSKEVNENVILKITGQPSPKlieSIIILL 237
                                        5555555555666778888888888875222345554 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.2   0.3   1.4e-17   9.3e-15       1     127 [.      46     156 ..      46     160 .. 0.86
   2 ?   -1.6   0.1         5   3.3e+03      80     111 ..     195     225 ..     179     242 .. 0.69

  Alignments for each domain:
  == domain 1  score: 55.2 bits;  conditional E-value: 1.4e-17
                                        EEEESSTTSSHHHHHHHHHHHH...THEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHH CS
                                AAA   1 vllyGppGtGKTllakavakel...gvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaks 73 
                                        +l++GppGtGK ++ak +a+++   + ++le+++s+ +   +      i+++  ++++    +++++DE d+++ +
  gene2286|gene2286|rna2286|rna2286  46 LLFSGPPGTGKITVAKIIAEKIvndKKYILELNASDER--GIDTVRTTIKNFSMRLSTG--LKVIILDECDSMTVA 117
                                        69*******************9877799**********..5555555555555555555..4***********999 PP

                                        HTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHSTTSSEE CS
                                AAA  74 rsgseseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallrgRfdrk 127
                                                    ++++ + ++  +    ++ +i+++n+++k+++++  +R+ + 
  gene2286|gene2286|rna2286|rna2286 118 A-----------QQAMRRTMETSTA---DCRFILVCNNIQKISEPIQ-SRCAIF 156
                                        9...........***********99...69*****************.9*9875 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 5
                                        HHHHHHHHHHHHHHHHTTTSSSTEEEEEEESS CS
                                AAA  80 eeeervvnqLlteldgvkkkeskvivigatnr 111
                                        ++ ++++n L + l   + +e+ vi+ ++++ 
  gene2286|gene2286|rna2286|rna2286 195 SDMRQAINILQSTLYSKEVNEN-VILKITGQP 225
                                        5667788888888888888655.555554444 PP

>> Rep_fac_C  Replication factor C C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.1       0.4   2.7e+02      37      71 ..     164     198 ..     136     203 .. 0.86
   2 !   45.9   0.0   8.3e-15   5.5e-12       1      86 [.     225     303 ..     225     304 .. 0.96

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.4
                                        HHHHHHHHHHGCCS...S-HHHHHHHHHHHHHHHHH CS
                          Rep_fac_C  37 ediltqlhrvvkeq.eelpeaqkleilellgeiekr 71 
                                        ed+ t l +++ ++  ++++++ + il  l++ ++r
  gene2286|gene2286|rna2286|rna2286 164 EDMKTRLNEIISDEnLNMSDEALNTILF-LSDSDMR 198
                                        567788889999988889*********5.9999999 PP

  == domain 2  score: 45.9 bits;  conditional E-value: 8.3e-15
                                        --HHHHHHHHHHHHHT-HHHHHHHHHHHHHHC---HHHHHHHHHHHGCCS..S-HHHHHHHHHHHHHHHHHHHCTH CS
                          Rep_fac_C   1 phpteieeileaclngdfeeaykklrellvekGysaediltqlhrvvkeqeelpeaqkleilellgeiekrlveGa 76 
                                        p p++ie+i+  +l++++eea +k++  ++ +Gy ++d+l  ++rv k+++        eil+ ++ ++ rl eG+
  gene2286|gene2286|rna2286|rna2286 225 PSPKLIESIIILLLKNKVEEALSKFD-CIWSDGYDPQDLLVSFFRVAKNMD------NYEILKCISKYQLRLFEGV 293
                                        78***********************7.**********************97......89***************** PP

                                        -HHHHHHHHH CS
                          Rep_fac_C  77 sehlqlsall 86 
                                         ++lq  +ll
  gene2286|gene2286|rna2286|rna2286 294 GSKLQFYSLL 303
                                        *****99886 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1   0.1   1.1e-09   7.2e-07       2     109 ..      17     127 ..      16     140 .. 0.67

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 1.1e-09
                             RuvB_N   2 rPksleeyigqekvkeklkifieaakkreealdhvllyGpPGlGkttlakiiakelgvklkitsgPvlekagdlaa 77 
                                        rP+++ + +g ++  e+++ +++a     +++ h+l++GpPG Gk t+akiia+++  + k       + ++ + +
  gene2286|gene2286|rna2286|rna2286  17 RPRKIGDVVGNHETIESIQSILNA-----NSMPHLLFSGPPGTGKITVAKIIAEKIVNDKKYILELNASDERGIDT 87 
                                        99**************99999887.....5789********************99877665544333333333333 PP

                             RuvB_N  78 lltnleek........dvlfideihrlsraveevlysame 109
                                        + t++++         +v+ +de   ++ a+++ +  +me
  gene2286|gene2286|rna2286|rna2286  88 VRTTIKNFsmrlstglKVIILDECDSMTVAAQQAMRRTME 127
                                        3333222100111112566666666666666666666666 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0   0.8   2.7e-09   1.8e-06       9      81 ..      12      81 ..       7     206 .. 0.81
   2 ?   -0.0   0.5       1.1   7.1e+02     115     172 ..     159     221 ..     131     232 .. 0.58

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 2.7e-09
                              Rad17  9 WfekykPekaeelavhkkkieevkewlkadvLesrkkriLLisGPsGCgkstvvkvLskelgi..klrewlnpvs 81
                                         eky+P k  ++    + ie ++  l+a+++++     LL sGP+G gk tv k+++ + +   k++  ln+  
  gene2286|gene2286|rna2286|rna2286 12 LTEKYRPRKIGDVVGNHETIESIQSILNANSMPH-----LLFSGPPGTGKITVAKIIAEKIVNdkKYILELNASD 81
                                       579*****************************97.....5*****************988775113444444444 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 1.1
                              Rad17 115 kdakylklqklGddlrtdkklilvedlPnk..fyrds..dalrevirkylrsseal.plilvi 172
                                        ++ k+  ++ + +++ +d +l + ++  n   f  ds  ++  ++++  l+s+e    +il i
  gene2286|gene2286|rna2286|rna2286 159 NKIKNEDMKTRLNEIISDENLNMSDEALNTilFLSDSdmRQAINILQSTLYSKEVNeNVILKI 221
                                        444555566666666666666666665543224444422444456666666666654555555 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.0     7e-05     0.046       3      54 ..      25      73 ..      23      85 .. 0.78
   2 !    7.9   0.0    0.0056       3.7     117     169 ..      86     137 ..      69     138 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 7e-05
                             AAA_16  3 vGReeeleqLlsalervrsgrpelvllsGesGvGKsslvrellralekdggi 54
                                       vG  e +e ++s+l++    + + +l+sG++G+GK ++++ +++ +  d+ +
  gene2286|gene2286|rna2286|rna2286 25 VGNHETIESIQSILNAN---SMPHLLFSGPPGTGKITVAKIIAEKIVNDKKY 73
                                       56667888888888844...4489***************9999998887544 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0056
                             AAA_16 117 srllellkrllallsrderplvlvlDdlqwadeaslqllaaLlrllesk.pllv 169
                                          ++ ++k++ ++ls++ +  v++lD+ +    a +q+++ ++++++++ ++++
  gene2286|gene2286|rna2286|rna2286  86 DTVRTTIKNFSMRLSTGLK--VIILDECDSMTVAAQQAMRRTMETSTADcRFIL 137
                                        6678899999999999777..*********************999988766665 PP

>> DNA_pol3_delta  DNA polymerase III, delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   1.2   2.1e-07   0.00014      57     170 ..     102     205 ..      90     206 .. 0.90
   2 ?   -2.7   0.0       6.4   4.3e+03      95     111 ..     233     249 ..     219     287 .. 0.63

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 2.1e-07
                                        SEEEEEEE--.....TT-S-TTHHHHHHHHTTT--SSEEEEEEES.S--HHHHHHHHHTTTEEEEEE----TTTHH CS
                     DNA_pol3_delta  57 dkrivvlknpklltkesklnekllkeLeeylsnlpedtlLiliapkklderkklvklLkkkatvveaktlkeeelk 132
                                        + ++++l+        ++ +   ++++ +++++  +d+ +il+++      +k+   ++++  ++++++ k+e++k
  gene2286|gene2286|rna2286|rna2286 102 GLKVIILDEC------DSMTVAAQQAMRRTMETSTADCRFILVCN----NIQKISEPIQSRCAIFTFNKIKNEDMK 167
                                        5577777777......45788899999******************....456899********************* PP

                                        HHHHHHHHHTT-EE-HHHHHHHHHHHTT-HHHHHHHHH CS
                     DNA_pol3_delta 133 kwiqkraqelglkiekealelLlelvennlsaikqele 170
                                        + +++++++++l++++eal+++l l+ ++++++ + l+
  gene2286|gene2286|rna2286|rna2286 168 TRLNEIISDENLNMSDEALNTILFLSDSDMRQAINILQ 205
                                        ********************************999887 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 6.4
                                        EEEEEES.S--HHHHHH CS
                     DNA_pol3_delta  95 lLiliapkklderkklv 111
                                        ++il +++k +e+ + +
  gene2286|gene2286|rna2286|rna2286 233 IIILLLKNKVEEALSKF 249
                                        45555555666665533 PP

>> AAA_assoc_2  AAA C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       3.4   2.3e+03       8      29 ..     118     139 ..     113     171 .. 0.77
   2 !   19.2   0.0   1.7e-06    0.0012       3      40 ..     177     214 ..     175     250 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 3.4
                                        XXXXXXXXXXXXXXXXXXXXXX CS
                        AAA_assoc_2   8 eddalealaeladGDaRkaLnl 29 
                                        +++a++  +e++  D+R +L +
  gene2286|gene2286|rna2286|rna2286 118 AQQAMRRTMETSTADCRFILVC 139
                                        5677888889999999988854 PP

  == domain 2  score: 19.2 bits;  conditional E-value: 1.7e-06
                                        X.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX. CS
                        AAA_assoc_2   3 kklkleddalealaeladGDaRkaLnlLElaaeaaeak 40 
                                        ++l+++d+al++++ l+d D+R+a+n+L+  + ++e +
  gene2286|gene2286|rna2286|rna2286 177 ENLNMSDEALNTILFLSDSDMRQAINILQSTLYSKEVN 214
                                        6899*************************877776654 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.1   2.2e-06    0.0015       5     110 ..      46     150 ..      42     154 .. 0.75
   2 ?   -2.2   0.0       5.8   3.9e+03      58      58 ..     180     180 ..     150     219 .. 0.51

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 2.2e-06
                             AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqevp.ew 79 
                                        l+ +G+  +GK t++k ++++   +k+ il++n  der  +   + ++ ++ ++ l++ + ++++lDE   ++  +
  gene2286|gene2286|rna2286|rna2286  46 LLFSGPPGTGKITVAKIIAEKIVNDKKYILELNASDERGIDTVRT-TIKNFSMR-LST-GLKVIILDECDSMTvAA 118
                                        56789999******877776665999999*******999765544.35555555.566.8999******8876267 PP

                             AAA_14  80 ekalkslvdeg.knldvivtGSnskllskeia 110
                                        ++a+++ ++++  ++++i+   n + +s+ i+
  gene2286|gene2286|rna2286|rna2286 119 QQAMRRTMETStADCRFILVCNNIQKISEPIQ 150
                                        88999999966688999988777777666665 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 5.8
                             AAA_14  58 e 58 
                                        +
  gene2286|gene2286|rna2286|rna2286 180 N 180
                                        1 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   3.2e-05     0.021       4      44 ..      23      65 ..      20      99 .. 0.77
   2 ?    2.0   0.0      0.17   1.1e+02     109     133 ..     105     129 ..      99     135 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.2e-05
                       Mg_chelatase  4 dvkGqeeakrale..iaaaGgHnlllvGppGsGKtmlakrlps 44
                                       dv+G++e+ + ++  + a    +ll+ GppG+GK  +ak +++
  gene2286|gene2286|rna2286|rna2286 23 DVVGNHETIESIQsiLNANSMPHLLFSGPPGTGKITVAKIIAE 65
                                       78888888777754356777889***************98864 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.17
                       Mg_chelatase 109 vLfLDElpefkrkvlevLRePledg 133
                                        v++LDE+  ++  + +++R+ +e+ 
  gene2286|gene2286|rna2286|rna2286 105 VIILDECDSMTVAAQQAMRRTMETS 129
                                        899*******************986 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.0   5.5e-05     0.037      10      59 ..      29      80 ..      21      85 .. 0.82
   2 ?    3.1   0.0       0.1        68      96     120 ..     105     129 ..      99     133 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.5e-05
                                       HHHHHHHHHCTSS..S-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETT CS
                    Sigma54_activat 10 elleqikkvaktd..lsvlitGesGtGKellaraiheaskrkekpfvavnca 59
                                       e++e+i+++ + +   ++l  G  GtGK ++a+ i e+  +++k ++++n +
  gene2286|gene2286|rna2286|rna2286 29 ETIESIQSILNANsmPHLLFSGPPGTGKITVAKIIAEKIVNDKKYILELNAS 80
                                       56777777776654478999******************99999999999976 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.1
                                        EEEEETGGGS-HHHHHHHHHHHHHS CS
                    Sigma54_activat  96 tlfLDeigelplelQekLlrvlqeg 120
                                        ++ LDe  ++++++Q+ + r +++ 
  gene2286|gene2286|rna2286|rna2286 105 VIILDECDSMTVAAQQAMRRTMETS 129
                                        689***************9999976 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0     5e-06    0.0033       3      66 ..      48     105 ..      46     143 .. 0.74
   2 ?   -1.3   0.0       4.5     3e+03      26      59 ..     168     199 ..     144     236 .. 0.56

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 5e-06
                             AAA_18   3 ltGtpGvGKttlakeLskrlgfgvnlrdvakenglllevdpealdeskrldedkldklldalee 66 
                                         +G+pG+GK t+ak ++++    vn ++++ e + ++e+  +     +   +++ ++l+++l+ 
  gene2286|gene2286|rna2286|rna2286  48 FSGPPGTGKITVAKIIAEK---IVNDKKYILELNASDERGID---TVRTTIKNFSMRLSTGLKV 105
                                        68*****************...68888888887777666555...4444444555555555555 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 4.5
                             AAA_18  26 vnlrdvakenglllevdpealdeskrldedkldk 59 
                                        ++l++++++++l  ++++   +  + l +  + +
  gene2286|gene2286|rna2286|rna2286 168 TRLNEIISDENLNMSDEAL--NTILFLSDSDMRQ 199
                                        3444444444444444444..3333333333333 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   1.8e-05     0.012       1      34 [.      45      79 ..      45     132 .. 0.89
   2 ?    0.1   0.0       1.1   7.4e+02      94     137 ..     108     152 ..      84     153 .. 0.54
   3 ?   -1.8   0.0       4.4   2.9e+03      79      86 ..     198     205 ..     158     245 .. 0.64

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.8e-05
                                       EEEEE--SSSSHHHHHHHGGGGB.S--EEEEE--T CS
                              AAA_5  1 dvlLvGppGtgKselaerlaaal.nreveyvqltr 34
                                       ++l  GppGtgK ++a+ +a+ + n++  +  l++
  gene2286|gene2286|rna2286|rna2286 45 HLLFSGPPGTGKITVAKIIAEKIvNDKKYILELNA 79
                                       68999******************988887777765 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 1.1
                                        EE..-SSSEEE---...........-EEEEEESS--.-TT-TTHHHHTT CS
                              AAA_5  94 llleeggelvkakndd.ller....frviatanpldrslnelspalrsR 137
                                        l+ +++ ++   ++    +e+     r+i  +n+ +    ++s++++sR
  gene2286|gene2286|rna2286|rna2286 108 LDECDSMTVAAQQAMRrTMETstadCRFILVCNNIQ----KISEPIQSR 152
                                        333333333333332222222556677777777777....666666666 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 4.4
                                        HHHHHHHH CS
                              AAA_5  79 sevlnsLl 86 
                                        ++++n+L+
  gene2286|gene2286|rna2286|rna2286 198 RQAINILQ 205
                                        33444444 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.0    0.0044       2.9       7      34 ..      45      72 ..      40      96 .. 0.69
   2 !    8.4   0.0    0.0038       2.5      76     128 ..      86     138 ..      72     145 .. 0.76
   3 ?   -0.3   0.2       1.8   1.2e+03      96     118 ..     174     195 ..     161     209 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0044
                             AAA_22  7 ilvvtGesGtGKTtllrrlleqldeeak 34
                                       +l+  G++GtGK t+++ ++e+ ++++k
  gene2286|gene2286|rna2286|rna2286 45 HLLFSGPPGTGKITVAKIIAEKIVNDKK 72
                                       78899***************99987533 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0038
                             AAA_22  76 eellealeqalrarav.ielliiDEaqhlrseealeeLrsllnlsrkgvqliLv 128
                                        + +++++ + + + ++  +++i+DE + + + +a +  r+ ++ s+ ++++iLv
  gene2286|gene2286|rna2286|rna2286  86 DTVRTTIKNFSMRLSTgLKVIILDECDSM-TVAAQQAMRRTMETSTADCRFILV 138
                                        4555666666666666889**********.888888888888889999999998 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 1.8
                             AAA_22  96 iiDEaqhlrseealeeLrsllnl 118
                                        i DE  ++ s+eal+++  l++ 
  gene2286|gene2286|rna2286|rna2286 174 ISDENLNM-SDEALNTILFLSDS 195
                                        55666666.99*****9999883 PP

>> Sigma54_activ_2  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   5.4e-05     0.036       6     107 ..      30     139 ..      25     151 .. 0.70
   2 ?    0.9   0.1      0.68   4.5e+02      56      78 ..     173     195 ..     150     232 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 5.4e-05
                                        HHHHHHHHHHHHHT-SS-EEEEEETT--HHHHHHCC--TTS-EE--SSTTHHHH-H.........HHHHHH..TTT CS
                    Sigma54_activ_2   6 aiqelkerLeqaaqsklpvfltGekGsgkelvArlLhknsgpwleifvverlaklp.........ldlleq..akg 70 
                                         i+ +++ L+  a+s+  ++  G++G+gk +vA++++++  ++ +   + + +++          ++++ +     
  gene2286|gene2286|rna2286|rna2286  30 TIESIQSILN--ANSMPHLLFSGPPGTGKITVAKIIAEKIVNDKKYILELNASDERgidtvrttiKNFSMRlsTGL 103
                                        5555555554..578889999****************998887665444333332244444444433333321355 PP

                                        SEEEEEE-TT--HHHHHHHHHHHHHHTTTT-EEEEEE CS
                    Sigma54_activ_2  71 gtLylkdiadlskaeqkeLlellakaeksslrlVsts 107
                                         +++l + +++  a+q+ +   ++ +   ++r++ ++
  gene2286|gene2286|rna2286|rna2286 104 KVIILDECDSMTVAAQQAMRRTMETS-TADCRFILVC 139
                                        68999******************999.9999999876 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.68
                                        HHHH-HHHHHHHTTTSEEEEEE- CS
                    Sigma54_activ_2  56 rlaklpldlleqakggtLylkdi 78 
                                          ++++l+++++a + +L+l d 
  gene2286|gene2286|rna2286|rna2286 173 IISDENLNMSDEALNTILFLSDS 195
                                        34578899999999999999884 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   1.9e-05     0.013       1      89 [.      45     129 ..      45     151 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.9e-05
                              AAA_3   1 hvllegvPGlaktllvkalakaldlefkriqftpdllPsdilGtevfeekekefefkkGpvfanllladeinrapp 76 
                                        h+l+ g PG++k +++k +a+++  + k i    +l  sd  G++ ++++ k+f+++    + ++++ de +  + 
  gene2286|gene2286|rna2286|rna2286  45 HLLFSGPPGTGKITVAKIIAEKIVNDKKYI---LELNASDERGIDTVRTTIKNFSMRLSTGL-KVIILDECDSMTV 116
                                        99********************99888766...6899*****************99987766.57777******** PP

                              AAA_3  77 ktqsalleameer 89 
                                         +q a+  +me +
  gene2286|gene2286|rna2286|rna2286 117 AAQQAMRRTMETS 129
                                        ******9999865 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.1   1.5e-05    0.0098      42     112 ..      37     106 ..       2     169 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.5e-05
                                        XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                              TIP49  42 likekklaGravLlaGpsgtGktalaiaiskelgedvpf.valsgsevyslevkktevltqalrksigvrik 112
                                        +++++ +    +L++Gp+gtGk  +a  i++++ +d ++   l++s+    +  +t +    +r s g+++ 
  gene2286|gene2286|rna2286|rna2286  37 ILNANSMP--HLLFSGPPGTGKITVAKIIAEKIVNDKKYiLELNASDERGIDTVRTTIKNFSMRLSTGLKVI 106
                                        55555555..79*******************99977666168**************9999999999999985 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   4.5e-05      0.03       2     106 ..      47     159 ..      46     160 .. 0.79
   2 ?   -2.0   0.0       7.2   4.8e+03      44      54 ..     253     264 ..     237     287 .. 0.64

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 4.5e-05
                       RNA_helicase   2 wlyGpsgeGKStlakeLakallkkl......klkkkdsvys.rnpeddfwdgYt.gqevvvidDfgqvkdeenpsd 69 
                                        +++Gp+g+GK t+ak +a+++ ++       +   +  + + r++ ++f    + g +v++ d+  +++  +++ +
  gene2286|gene2286|rna2286|rna2286  47 LFSGPPGTGKITVAKIIAEKIVNDKkyilelNASDERGIDTvRTTIKNFSMRLStGLKVIILDECDSMTVAAQQAM 122
                                        799******************9666678988555555666657788888766665889999999888876646667 PP

                       RNA_helicase  70 laelirlvsstpyplnmasleekgtlftSkvvivtsN 106
                                          ++      + ++l + ++++   +++S++ i t N
  gene2286|gene2286|rna2286|rna2286 123 RRTMETSTADCRFILVCNNIQKISEPIQSRCAIFTFN 159
                                        8888888888999999999998889999999888866 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 7.2
                       RNA_helicase  44 w.dgYtgqevvv 54 
                                        w dgY+ q+ +v
  gene2286|gene2286|rna2286|rna2286 253 WsDGYDPQDLLV 264
                                        448888665544 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   3.6e-05     0.024     107     168 ..      23      82 ..      11     129 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.6e-05
                              T2SSE 107 dlgaeealkekiaevlrkavrerglilvsGgTgsGKttllyallkeinksderivtvEDpvE 168
                                        d++ ++++ e i+++l++   +   +l+sG+ g+GK t++ ++ ++i ++++ i+ +  + E
  gene2286|gene2286|rna2286|rna2286  23 DVVGNHETIESIQSILNAN--SMPHLLFSGPPGTGKITVAKIIAEKIVNDKKYILELNASDE 82 
                                        5666677778999999998..8999********************99999999987766666 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.1    0.0041       2.7       1      25 [.      45      69 ..      45      74 .. 0.86
   2 ?    6.7   0.1    0.0095       6.3      73     154 ..      72     157 ..      68     174 .. 0.66

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0041
                                       EEEEE--TTSSHHHHHHHHHHHH.. CS
                           NTPase_1  1 kvfiTGppGvGKtTlvkkvlellks 25
                                       +++ +GppG+GK T+ k ++e++ +
  gene2286|gene2286|rna2286|rna2286 45 HLLFSGPPGTGKITVAKIIAEKIVN 69
                                       56789****************9965 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0095
                                        TEEE-HHHHHHHHHHHHHHHHHHH-........EEEE---STTGGG-HHHHHHHHHHHTTTSEEEEE--SS--SHH CS
                           NTPase_1  73 kyvvdvesfeelalealrkalsead........viviDEiGkmElkskkfkeaveevLksekpvlavihrrkdlal 140
                                        ky +++++ +e +++ +r+++++          vi++DE+ +m + +++  +   e+ + +  ++ v  +   +++
  gene2286|gene2286|rna2286|rna2286  72 KYILELNASDERGIDTVRTTIKNFSmrlstglkVIILDECDSMTVAAQQAMRRTMETSTADCRFILVCNNI--QKI 145
                                        677777777777777777777444444555566***********999877766666666677777777766..467 PP

                                        HHHHHT-TT-EEEE CS
                           NTPase_1 141 veeirerkdvkvfe 154
                                         e i++r    +f+
  gene2286|gene2286|rna2286|rna2286 146 SEPIQSR--CAIFT 157
                                        7777777..44443 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.7   6.4e-05     0.043       8     121 ..      32     166 ..      27     221 .. 0.56

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 6.4e-05
                             AAA_11   8 eaiksalsese..itliqGPPGtgKTktivellsqll.........................srrkseeeksakpr 56 
                                        e+i+s+l+ ++    l++GPPGtgK ++   + ++++                         +    +++ s++ +
  gene2286|gene2286|rna2286|rna2286  32 ESIQSILNANSmpHLLFSGPPGTGKITVAKIIAEKIVndkkyilelnasdergidtvrttikN---FSMRLSTGLK 104
                                        455555555554448**********86665555555555555555555444444333332220...3334444444 PP

                             AAA_11  57 iLv...CapSNaAvDellerllrglldsegekykpkivRvgneeeriseavksvsleekvekrlekee 121
                                        + +   C +  +A  + + r ++       ++ + +++ v n+ ++ise ++s +    ++k +++ +
  gene2286|gene2286|rna2286|rna2286 105 VIIldeCDSMTVAAQQAMRRTME------TSTADCRFILVCNNIQKISEPIQSRCAIFTFNKIKNEDM 166
                                        43333344444444445544444......444444555555554455555555555555555444444 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.5    0.0002      0.13       7     115 ..      40     146 ..      34     222 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.0002
                             AAA_19   7 alkekvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerlaalgaeatTiHrlalldfdd 82 
                                        a + ++ll  ++pGtGK +v k i + +v+ ++     + l a  +r  + +r+ ++++ ++ +T  ++ +ld  d
  gene2286|gene2286|rna2286|rna2286  40 ANSMPHLLFSGPPGTGKITVAKIIAEKIVNDKKY---ILELNASDERGIDTVRTTIKNFSMRLSTGLKVIILDECD 112
                                        55667889999********999999999988843...455678888999999999988888877766664544444 PP

                             AAA_19  83 llte.alelleeaeeekklqeee.llivDEfqdvd 115
                                         +t  a ++++++ e+++  ++  +l+   +q ++
  gene2286|gene2286|rna2286|rna2286 113 SMTVaAQQAMRRTMETSTA-DCRfILVCNNIQKIS 146
                                        4433033444444444444.444356656666665 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   0.00012     0.078      21     122 ..      46     138 ..      31     174 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00012
                             AAA_30  21 avltGpAGtGKttalkalreaweaa.ggrviglAptgkaAkvLaeelgieastiakllkrlkgrarlepg.tlliv 94 
                                         +  Gp+GtGK t+ k ++e + ++ ++ + + A+ ++  +++++       ti+++  rl       +g +++i 
  gene2286|gene2286|rna2286|rna2286  46 LLFSGPPGTGKITVAKIIAEKIVNDkKYILELNASDERGIDTVRT-------TIKNFSMRLS------TGlKVIIL 108
                                        5679**************766665538888888999988888884.......4555553333......23389999 PP

                             AAA_30  95 DEagmvdtkqlaallkaaeka..gakvilv 122
                                        DE   +  +  +a+ + +e++  + + ilv
  gene2286|gene2286|rna2286|rna2286 109 DECDSMTVAAQQAMRRTMETStaDCRFILV 138
                                        998666555545554444443005555555 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0    0.0064       4.2      21      55 ..      29      63 ..      25      83 .. 0.84
   2 ?    4.9   0.1     0.023        15     117     143 ..     100     126 ..      74     130 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0064
                               TniB 21 erLeeLleypkrkrmpnlllvGdsnnGKtmivekF 55
                                       e++e++ +  +++ mp+ll+ G++ +GK ++++  
  gene2286|gene2286|rna2286|rna2286 29 ETIESIQSILNANSMPHLLFSGPPGTGKITVAKII 63
                                       56777888889999**************9988755 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.023
                               TniB 117 elkvrvLiiDEihnllagsarkqrefl 143
                                        +++++v+i+DE +++  + +++ r+++
  gene2286|gene2286|rna2286|rna2286 100 STGLKVIILDECDSMTVAAQQAMRRTM 126
                                        5689***********999988888877 PP

>> Sec3_C_2  Sec3 exocyst complex subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0         2   1.3e+03      35      70 ..       9      43 ..       7      46 .. 0.74
   2 ?   11.1   0.0   0.00058      0.39      56      80 ..      83     107 ..      57     112 .. 0.79
   3 ?   -1.9   0.1       6.7   4.5e+03      42      55 ..     161     174 ..     144     206 .. 0.63

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 2
                           Sec3_C_2 35 eelaeekielkevkdilqdsilGCeslfstlnlysl 70
                                       e+l  ek + +++ d++ +     es+ s ln  s+
  gene2286|gene2286|rna2286|rna2286  9 ENLLTEKYRPRKIGDVVGNH-ETIESIQSILNANSM 43
                                       77777787778887777654.457899999998887 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00058
                           Sec3_C_2  56 lGCeslfstlnlyslelstvlndvi 80 
                                         G +++ +t+  +s+ lst l  +i
  gene2286|gene2286|rna2286|rna2286  83 RGIDTVRTTIKNFSMRLSTGLKVII 107
                                        699*****************98766 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 6.7
                           Sec3_C_2  42 ielkevkdilqdsi 55 
                                        i+ +++k  l++ i
  gene2286|gene2286|rna2286|rna2286 161 IKNEDMKTRLNEII 174
                                        44444444444433 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00023      0.16      41     108 ..      31      98 ..      18     142 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00023
                             DUF815  41 venteqfleglpannvLLwGarGtGKSslvkallneyaeegLrlievekedlkelpklvellrerper 108
                                        +e ++  l+ ++  ++L+ G  GtGK ++ k + +++ +++  ++e++ +d + ++++ +++++ ++r
  gene2286|gene2286|rna2286|rna2286  31 IESIQSILNANSMPHLLFSGPPGTGKITVAKIIAEKIVNDKKYILELNASDERGIDTVRTTIKNFSMR 98 
                                        566777888888999************************************99999999999977665 PP

>> Torsin  Torsin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0    0.0005      0.33      34      79 ..      27      69 ..       7      81 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0005
                                       HHHHHHHHHHHHT-SS-SS-EEEEEEE-TTSSHHHHHHHHHHHHST CS
                             Torsin 34 kklvvksvkaylenekpkkpLvlsfhGwtGtGknfvaeiiaenlyr 79
                                       ++  ++s+++ l+ ++      l f G +GtGk  va+iiae++ +
  gene2286|gene2286|rna2286|rna2286 27 NHETIESIQSILNANSMP---HLLFSGPPGTGKITVAKIIAEKIVN 69
                                       556667777776655433...35699****************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (309 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       899  (0.0501422); expected 358.6 (0.02)
Passed bias filter:                      521  (0.0290591); expected 358.6 (0.02)
Passed Vit filter:                        81  (0.00451782); expected 17.9 (0.001)
Passed Fwd filter:                        27  (0.00150594); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              27  [number of targets reported over threshold]
# CPU time: 0.64u 0.28s 00:00:00.92 Elapsed: 00:00:00.45
# Mc/sec: 2042.49
//
Query:       gene2287|gene2287|rna2287|rna2287  [L=303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
       0.59    8.3  20.1       0.62    8.2  20.1    1.0  1  Nop14       Nop14-like family


Domain annotation for each model (and alignments):
>> Nop14  Nop14-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2  20.1   3.5e-05      0.62     299     416 ..      93     211 ..      89     278 .. 0.46

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 3.5e-05
                              Nop14 299 deeeeeekkkkkkkeasaDdldddfvleeeeeeeefglgkglka.......taeeeeeededdfeedddlvesese 367
                                        d+++ ++++++k++    +d ddd++++++++ +   +++g ++                   + + +d  +  ++
  gene2287|gene2287|rna2287|rna2287  93 DSDSGKDRDSGKDR--DTNDKDDDNIRNSNNTYN-KEIKSGRRYkagyderG---------MVNLNGHDSRKGINN 156
                                        33444444444444..667777777777654444.33444443222333331.........222222222222222 PP

                              Nop14 368 eeeeeeeedeeeeedeeeeeeeeededdlsdlese..........eeeeedeleeelle 416
                                        ++ +++++d+++++d+++++++++d+ ++++ +++          +++++d+     ++
  gene2287|gene2287|rna2287|rna2287 157 DDGNNNDDDNDDNDDNDDNDDNNNDNINDDNINNNnsinsinnstNDNDSDNS----TN 211
                                        22223333333332222222222222222111111122333221111111111....11 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (303 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1120  (0.0624686); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.62u 0.27s 00:00:00.89 Elapsed: 00:00:00.41
# Mc/sec: 2242.63
//
Query:       gene2288|gene2288|rna2288|rna2288  [L=65]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (65 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       581  (0.0324056); expected 358.6 (0.02)
Passed bias filter:                      215  (0.0119917); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 481.94
//
Query:       gene2289|gene2289|rna2289|rna2289  [L=628]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.2e-31  106.5   0.0    1.3e-30  105.3   0.0    1.7  1  Radical_SAM_C    Radical_SAM C-terminal domain
    3.8e-19   69.7   0.2    1.5e-18   67.7   0.0    1.9  2  Radical_SAM      Radical SAM superfamily
    1.8e-07   31.4   0.2    8.1e-07   29.3   0.1    2.1  2  Acetyltransf_1   Acetyltransferase (GNAT) family
    6.5e-05   22.9   0.1    0.00013   21.8   0.1    1.5  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
     0.0093   16.4   0.1      0.024   15.1   0.1    1.6  1  Acetyltransf_7   Acetyltransferase (GNAT) domain


Domain annotation for each model (and alignments):
>> Radical_SAM_C  Radical_SAM C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.3   0.0   3.5e-34   1.3e-30       2      81 ..     303     382 ..     302     383 .. 0.98

  Alignments for each domain:
  == domain 1  score: 105.3 bits;  conditional E-value: 3.5e-34
                      Radical_SAM_C   2 dgvKlypllvikgTeLaelyksgeykplsleeyvdlvadilellppdirvhRltgdipkelliagpwhknlrelie 77 
                                        dg+K+yp+lvikgT+L+el+k++ yk +s++e+vd++a+il+l+pp++r++R+++dip++l+++g++ +n+rel++
  gene2289|gene2289|rna2289|rna2289 303 DGLKIYPTLVIKGTGLYELWKNKMYKNYSPDELVDFLARILMLVPPWTRIYRVQRDIPMPLVSSGVEYGNIRELAM 378
                                        8*************************************************************************99 PP

                      Radical_SAM_C  78 krlk 81 
                                        +++k
  gene2289|gene2289|rna2289|rna2289 379 AKIK 382
                                        9987 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.7   0.0   4.3e-22   1.5e-18       9     159 ..      97     286 ..      86     291 .. 0.84
   2 ?   -1.5   0.0      0.82   2.9e+03      28      67 ..     581     619 ..     572     621 .. 0.78

  Alignments for each domain:
  == domain 1  score: 67.7 bits;  conditional E-value: 4.3e-22
                                        S--TTTSCCTT...................HHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHH CS
                                        xxxxxxxxxxx...................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        Radical_SAM   9 lrCsfCarpet...................vrregrgrslsveeileevkelkaekgvkevilgggepllypdfve 65 
                                        + C++C+ + +                     r+++  +++    l+++++l + +++ e+i++gg+ l  +++++
  gene2289|gene2289|rna2289|rna2289  97 NICIYCPGGPDsefeystqsytgyeptsmrAIRNRYDPYMQSKTRLKQIESLGHIPDKVEFIIMGGTFLSLSNEYK 172
                                        34****************************5555555555555556666666556668888888888888766666 PP

                                        HHHHHHHTC..................CCTEEEEEEECSSCHG...HHHHHHHHHTT-SEEEEEEBSSSHHHHHHH CS
                                        xxxxxxxxx..................xxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        Radical_SAM  66 llerlakla..................vpgiritvetngtlpd...eeklerllelgvdrvslgleaaddekvlkl 120
                                          +  +  +                  + +i++  +t +t+pd   + ++ ++l +g++rv++g++++ +e v + 
  gene2289|gene2289|rna2289|rna2289 173 RDFVKKLHDslsghcsstleeaikfgeHGKIKCIGITIETRPDfcfRPHISEMLSYGCTRVEIGVQSIYEE-VARD 247
                                        6655555557899999999999*999*********************************************.**** PP

                                        HTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTSHHH CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        Radical_SAM 121 mnrghtfeevlealeklreagikrvvdrivglpGendee 159
                                        +nrght+++v  a+++++++g k v+++++ lp++ +++
  gene2289|gene2289|rna2289|rna2289 248 TNRGHTVSAVAFAFRMAKDSGYKIVSHMMPNLPNVDKRH 286
                                        *********************************988875 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.82
                                        HHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHH CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        Radical_SAM  28 slsveeileevkelkaekgvkevilgggepllypdfvell 67 
                                        ++ + e +++++e +++k +  +i+g g+  +y +f  +l
  gene2289|gene2289|rna2289|rna2289 581 TMLIAEAEKIAREEHHSK-KMAIISGVGTRKYYEKFGYWL 619
                                        567788888999996555.999999999999999888777 PP

>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       0.8   2.9e+03       3      53 ..     390     446 ..     388     459 .. 0.61
   2 !   29.3   0.1   2.3e-10   8.1e-07      65     117 .]     556     617 ..     524     617 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.8
                                        HHHHHHHHHTHHHHHHHHHHH...HHHHHHSTTC.EEEE.EEET..TEEEEEEEEEEE CS
                     Acetyltransf_1   3 dlvellvesffppnedaseee...feesfsleae.gllv.aeed..geliGfisllki 53 
                                        d+++ +v ++++ ++  + e+   ++++   +++ ++++  e++  + liG ++l+k 
  gene2289|gene2289|rna2289|rna2289 390 DVRSREVGIKRIAEGIVPKEIimvRRDY-VANNGwETFIsFEDIqnDILIGLLRLRKC 446
                                        5666666666666666666666655555.44444555553444443449999999886 PP

  == domain 2  score: 29.3 bits;  conditional E-value: 2.3e-10
                                        EEEE...........SGGGTTSSHHHHHHHHHHHHHHHT.TESEEEEEEETTEHHHHHHHHHTTE CS
                     Acetyltransf_1  65 slaV...........speyrgkGlGsaLlealeeraree.gikkivlaveedndaairlYeklGF 117
                                        +l+V           + ++++kG+G++L+ ++e++aree   kk+ +    + ++++++Yek+G+
  gene2289|gene2289|rna2289|rna2289 556 ELHVygvavpvdkqkNGSFQHKGYGTMLIAEAEKIAREEhHSKKMAI---ISGVGTRKYYEKFGY 617
                                        444444444888888889*********************66699866...699***********8 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.1   3.8e-08   0.00013      62     107 ..     573     618 ..     549     627 .. 0.90

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 3.8e-08
                    Acetyltransf_10  62 eyrgqGigkaLleaveeeaekdgikleltvnaspyavpfYeklGFk 107
                                        +++++G+g++L+ ++e+ a+++++++++ + +    +++Yek+G+ 
  gene2289|gene2289|rna2289|rna2289 573 SFQHKGYGTMLIAEAEKIAREEHHSKKMAIISGVGTRKYYEKFGYW 618
                                        69*****************9888888******************95 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.1   6.6e-06     0.024      34      74 ..     568     617 ..     538     617 .. 0.64

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 6.6e-06
                                        G....GGTTSSHHHHHHHH......TT...SEEEEEEEEETHH.......HHHHHHHHTTE CS
                     Acetyltransf_7  34 p....eyrgkGiGraLlea......ae...kgiileqlelnae.......kaikfYeklGF 74 
                                        +    +++ kG+G+ L++       +e   k           +        ++k+Yek+G+
  gene2289|gene2289|rna2289|rna2289 568 KqkngSFQHKGYGTMLIAEaekiarEEhhsK-----------KmaiisgvGTRKYYEKFGY 617
                                        4555579**********85233222102211...........122233346699******8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (628 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       515  (0.0287244); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.61u 0.30s 00:00:00.90 Elapsed: 00:00:00.47
# Mc/sec: 4006.72
//
Query:       gene229|gene229|rna229|rna229  [L=227]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.2e-20   70.9   0.9    1.5e-19   69.8   0.9    1.6  1  Ribosomal_S17    Ribosomal protein S17
    2.7e-18   66.1   1.8    7.3e-18   64.7   1.8    1.8  1  Ribosomal_S17_N  Ribosomal_S17 N-terminal


Domain annotation for each model (and alignments):
>> Ribosomal_S17  Ribosomal protein S17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.8   0.9   1.7e-23   1.5e-19       3      67 ..     142     209 ..     140     210 .. 0.98

  Alignments for each domain:
  == domain 1  score: 69.8 bits;  conditional E-value: 1.7e-23
                                    EEE--STTEEEEEEEEEEEETTTTEEEEEEEEEEEE-TTTS...--TT-EEEEEEECECSSSEEEEEE CS
                  Ribosomal_S17   3 VvsdkmdkTvvVrverlvkhpkykkyvkrrkkylahdenns...vkvGDiVrieecrPlSktkrfvvv 67 
                                    V ++k+ +T+++  +++++ +kyk+y++r+kk+ +h ++++   v+vGDiV ++  rPlSktkrfvvv
  gene229|gene229|rna229|rna229 142 VLKMKQVRTIICIKKYFFYVKKYKRYERRQKKFAVHFPPCFeglVNVGDIVNCALVRPLSKTKRFVVV 209
                                    999****************************************************************8 PP

>> Ribosomal_S17_N  Ribosomal_S17 N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.7   1.8   8.1e-22   7.3e-18       3      67 ..      80     136 ..      78     138 .. 0.89

  Alignments for each domain:
  == domain 1  score: 64.7 bits;  conditional E-value: 8.1e-22
                                    SSS----SS--------------....--------TT----GGGGS-----TTSSSSSS----S- CS
                Ribosomal_S17_N   3 erafqkQetvflnkkkskeekkkkkkkkryvknvglgfktPkeAiegtYiDkKCPFtGnvsirGr 67 
                                     + +++Q+++++n+k    +++    kkry+++vg g+++P++Ai+gtYiDk CPFtG v+  G+
  gene229|gene229|rna229|rna229  80 FKIYPQQPQIYNNPK----NEE----KKRYYRQVGYGITVPETAINGTYIDKNCPFTGSVRLYGK 136
                                    589************....222....369********************************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (227 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1138  (0.0634726); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 1421.36
//
Query:       gene2290|gene2290|rna2290|rna2290  [L=398]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (398 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       511  (0.0285013); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 2788.01
//
Query:       gene2291|gene2291|rna2291|rna2291  [L=107]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
        1.4    9.3  10.1        2.1    8.8   1.5    2.2  2  EBA-175_VI  Erythrocyte binding antigen 175


Domain annotation for each model (and alignments):
>> EBA-175_VI  Erythrocyte binding antigen 175
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   2.1    0.0011        19       5      27 ..       9      31 ..       4      48 .. 0.77
   2 ?    8.8   1.5   0.00011       2.1      18      51 ..      53      86 ..      36      88 .. 0.65

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0011
                         EBA-175_VI  5 eeiiklskknkCnnelslkyCds 27
                                        +i +  + nkC++++s + C  
  gene2291|gene2291|rna2291|rna2291  9 TKIDSYERINKCQDDCSKNVCAI 31
                                       46777788999999999999974 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00011
                         EBA-175_VI 18 nelslkyCdsikkkissgtCskekrknLCCsisd 51
                                       +++s +  +s +k+       k+ r  LCCsi d
  gene2291|gene2291|rna2291|rna2291 53 EKYSEHKHESTHKELCYTLNGKNTRTGLCCSIED 86
                                       444444444445555555557899999*****88 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       753  (0.041999); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 826.02
//
Query:       gene2292|gene2292|rna2292|rna2292  [L=507]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00095   19.6   0.0        3.8    8.1   0.0    3.9  5  PQQ_3     PQQ-like domain


Domain annotation for each model (and alignments):
>> PQQ_3  PQQ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.7   0.0    0.0026        46      20      37 ..      29      46 ..      17      49 .. 0.83
   2 ?   -3.1   0.0       0.7   1.3e+04      19      35 ..     183     202 ..     172     203 .. 0.70
   3 !    8.1   0.0   0.00021       3.8      20      38 ..     227     245 ..     215     246 .. 0.89
   4 ?   -2.7   0.0      0.53   9.6e+03      20      34 ..     265     279 ..     258     281 .. 0.64
   5 ?    1.3   0.0     0.029   5.2e+02      14      34 ..     298     318 ..     290     322 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.0026
                              PQQ_3 20 dgglvyvgtgdGtlyAlD 37
                                        +g v + + dG++y lD
  gene2292|gene2292|rna2292|rna2292 29 NNGFVIMCSRDGHVYFLD 46
                                       579999***********9 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 0.7
                              PQQ_3  19 vdggl...vyvgtgdGtlyA 35 
                                        + +g+   +y+ t +  +y 
  gene2292|gene2292|rna2292|rna2292 183 TKNGTsifLYCCTNNSFVYK 202
                                        55565555899999998885 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.00021
                              PQQ_3  20 dgglvyvgtgdGtlyAlDa 38 
                                        ++ +vyv++++G +y l a
  gene2292|gene2292|rna2292|rna2292 227 VDKYVYVSSSNGLVYKLSA 245
                                        699************9987 PP

  == domain 4  score: -2.7 bits;  conditional E-value: 0.53
                              PQQ_3  20 dgglvyvgtgdGtly 34 
                                        ++  +  g++dG ++
  gene2292|gene2292|rna2292|rna2292 265 VNTNILLGGTDGFIR 279
                                        444566677789875 PP

  == domain 5  score: 1.3 bits;  conditional E-value: 0.029
                              PQQ_3  14 nsspavdgglvyvgtgdGtly 34 
                                         +  a  + ++y+ ++d+tl+
  gene2292|gene2292|rna2292|rna2292 298 IFKIACRDQKLYTIGDDHTLR 318
                                        56678899**********996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (507 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       412  (0.0229795); expected 358.6 (0.02)
Passed bias filter:                      256  (0.0142785); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.20s 00:00:00.67 Elapsed: 00:00:00.36
# Mc/sec: 4194.73
//
Query:       gene2293|gene2293|rna2293|rna2293  [L=337]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.6e-24   86.4   9.7    6.8e-23   82.2   9.6    2.2  1  AAA_23    AAA domain
      1e-09   38.6  15.1    1.3e-09   38.3  15.1    1.1  1  AAA_15    AAA ATPase domain
    4.2e-07   29.6   0.1      8e-07   28.7   0.1    1.7  1  SMC_N     RecF/RecN/SMC N terminal domain
    8.8e-05   22.5   0.0    0.00014   21.8   0.0    1.3  1  AAA_21    AAA domain, putative AbiEii toxin, Type IV TA syste
      9e-05   22.1   0.0    0.00028   20.6   0.0    1.8  1  AAA_29    P-loop containing region of AAA domain
    0.00018   21.9   0.0     0.0003   21.2   0.0    1.5  1  AAA_16    AAA ATPase domain
     0.0021   17.8   1.0     0.0096   15.7   0.2    2.5  2  AAA_24    AAA domain
  ------ inclusion threshold ------
      0.013   15.8   0.1      0.051   13.9   0.0    2.1  2  AAA_22    AAA domain
      0.054   13.2   0.0       0.14   11.9   0.0    1.6  1  AAA_30    AAA domain
      0.059   13.9   4.2       0.62   10.7   0.0    3.3  3  DUF4046   Protein of unknown function (DUF4046)
       0.35   11.4   8.7        1.1    9.7   8.7    2.2  1  ABC_tran  ABC transporter


Domain annotation for each model (and alignments):
>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.2   9.6   4.1e-26   6.8e-23       1     198 [.       5     288 ..       5     306 .. 0.70

  Alignments for each domain:
  == domain 1  score: 82.2 bits;  conditional E-value: 4.1e-26
                             AAA_23   1 kLkienfrsf...rdqeidFskgltlItGpNGaGKTTildAiklaLygetprlsrksgrgfeksdveiesegkvka 73 
                                        kL i+++rs+       i+F  ++tlI G+NG+GKTTi++A+++a +g+ p++sr   +g++  d++++++++++a
  gene2293|gene2293|rna2293|rna2293   5 KLMIKGIRSYspsTSNVIQFF-PMTLILGENGTGKTTIIEALRYAITGDLPPMSR---GGAFVYDPTLSNSTDTNA 76 
                                        799*******65333449999.***************************999998...57899999999999**** PP

                             AAA_23  74 yvelt...................fenkdgry.....................................trsiere 93 
                                        +++l+                   +      +                                       + e+e
  gene2293|gene2293|rna2293|rna2293  77 QIKLKlcdryvvsrslslthrkskI------EqkntenvfsvivndsvsesygnnmenlcnndevgnvlGWKKEEE 146
                                        *****77777777777755554443......155555699999999999999999999999988866663333333 PP

                             AAA_23  94 relskkkgkttkkaklelleideleqfisellgskkiil.nlilflgqerfeefelkdkke............... 153
                                         + + k+++t++k k  + + ++ ++++   l+ +k+ l ++i+++++e+++++++ + ++               
  gene2293|gene2293|rna2293|rna2293 147 TNDRTKNTETKRKMKSLSGKAADIDKQMLMVLNTNKPLLdHVIFCHQEESTWPLSEPANFKkrmddifcstvyika 222
                                        3333344444444444444445556666668999999996666777777788888855555667788888887777 PP

                             AAA_23 154 .................rleelekeleeledekkllekleqekekek....eleeleeeleeilke 198
                                                         +l+el+ +l+ +++ k+ll +le+++e        +++l+++l+ ++++
  gene2293|gene2293|rna2293|rna2293 223 venlknvrkdknvqlkmKLQELNFALQAKKKHKELLARLERANEDFMnnsgVISNLQSKLQVLNEK 288
                                        776666666666666666666666666666666666666433332224455555555555555554 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.3  15.1   7.8e-13   1.3e-09       1     262 [.       1     293 [.       1     332 [. 0.67

  Alignments for each domain:
  == domain 1  score: 38.3 bits;  conditional E-value: 7.8e-13
                             AAA_15   1 MkIkkikikNFRslkdve...idlseeltvliGkNnsGKSsilealdlFlnnkekkn...kkvikiekedleifen 70 
                                        M+++k+ ik  Rs++  +   i++ + +t++ G+N++GK++i+eal + ++ +           ++ +  l+++ +
  gene2293|gene2293|rna2293|rna2293   1 MILNKLMIKGIRSYSPSTsnvIQFFP-MTLILGENGTGKTTIIEALRYAITGDL--PpmsRGGAFVYDPTLSNSTD 73 
                                        99************985412255555.*******************99999883..24465556677777777766 PP

                             AAA_15  71 iseskdikIdvefaekekakeyektlkskekkkadlllkkkesdlkktikdkklklkknelsdekisvekkks... 143
                                        ++  +++k+   +         +++      +k++++ k++e+ ++ +++d   + + n+  +   ++++      
  gene2293|gene2293|rna2293|rna2293  74 TNAQIKLKLCDRY----VVSRSLSLT----HRKSKIEQKNTENVFSVIVNDSVSESYGNNMENLC-NNDEV-Gnvl 139
                                        6666666666666....122222222....22333444555566666666665555544333333.32333.2357 PP

                             AAA_15 144 ..kkelpkekeeklekekeelkidkedlkklikkleeslkkee......................elknvlksaii 195
                                          kke +++ + k+++ k ++k  + ++ ++ k++   l+ ++                       +k+ + + + 
  gene2293|gene2293|rna2293|rna2293 140 gwKKEEETNDRTKNTETKRKMKSLSGKAADIDKQMLMVLNTNKplldhvifchqeestwplsepaNFKKRMDDIFC 215
                                        77788888888888888889999999999999999999999999999***************99999999999*** PP

                             AAA_15 196 klllisakRnvsdedsekkssllgklkekileealqekl......eeelteklkeiqeklkeidkklaeelk.... 261
                                         + +i+a+ n ++ +++k+  l++kl+e  +   +++k        e+ +e++ +    ++++++kl+   +    
  gene2293|gene2293|rna2293|rna2293 216 STVYIKAVENLKNVRKDKNVQLKMKLQELNFALQAKKKHkellarLERANEDFMNNSGVISNLQSKLQVLNEklca 291
                                        *************999999999999999998865544445566664444444444444444444444222223334 PP

                             AAA_15 262 .k 262
                                          
  gene2293|gene2293|rna2293|rna2293 292 rH 293
                                        32 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7   0.1   4.9e-10     8e-07       2      49 ..       3      50 ..       2     140 .. 0.88

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 4.9e-10
                                       EEEEEEESETTEECEEE.EEETTSSEEEEEESTTSSHHHHHHHHHHHCT CS
                                       xxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              SMC_N  2 lkrleienFksyagktv.ilpfsksftaivGpNGSGKsnlldAilFvLG 49
                                       l++l+i++ +sy  +t  +++f + +t i+G+NG GK+ +++A+++ + 
  gene2293|gene2293|rna2293|rna2293  3 LNKLMIKGIRSYSPSTSnVIQFFP-MTLILGENGTGKTTIIEALRYAIT 50
                                       899*********976551567777.9*******************9875 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.0   8.6e-08   0.00014       1      83 [.      27      87 ..      27     132 .. 0.75

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 8.6e-08
                             AAA_21  1 lnvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfefeieeflsqgvryryglrl 78
                                       ++++ G Ng+GK+++++al+++                      i++ l++ +  ++f++  ++ +s++++ +  l+l
  gene2293|gene2293|rna2293|rna2293 27 MTLILGENGTGKTTIIEALRYA----------------------ITGDLPPMSRGGAFVYDPTLSNSTDTNAQIKLKL 82
                                       699****************998......................7777777777777777777777777777777777 PP

                             AAA_21 79 ersqv 83
                                        ++ v
  gene2293|gene2293|rna2293|rna2293 83 CDRYV 87
                                       77777 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   1.7e-07   0.00028      24      48 ..      27      51 ..      16      54 .. 0.87

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 1.7e-07
                             AAA_29 24 atlltGpsGsGKSTllDAiqalLvp 48
                                       +tl+ G++G+GK+T++ A+ + +++
  gene2293|gene2293|rna2293|rna2293 27 MTLILGENGTGKTTIIEALRYAITG 51
                                       69*****************998886 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0   1.9e-07    0.0003      25      69 ..      26      76 ..      14     174 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 1.9e-07
                             AAA_16 25 elvllsGesGvGKsslvrellralekd......ggiflrgkcdqlesaipy 69
                                       +++l+ Ge G+GK++++++l+ a+++d      gg f++  + ++++++  
  gene2293|gene2293|rna2293|rna2293 26 PMTLILGENGTGKTTIIEALRYAITGDlppmsrGGAFVYDPTLSNSTDTNA 76
                                       799************************999998788888887777544433 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.2   5.9e-06    0.0096       4      92 ..      27     136 ..      25     210 .. 0.75
   2 ?   -1.8   0.0       1.4   2.2e+03     113     138 ..     221     248 ..     214     282 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 5.9e-06
                             AAA_24   4 kiliyGpsgiGKTtlakel....gpkplfi.....................dtekGlksldadkfpdie....... 47 
                                        + li G++g+GKTt++  l    +                           dt++  k                  
  gene2293|gene2293|rna2293|rna2293  27 MTLILGENGTGKTTIIEALryaiT-----GdlppmsrggafvydptlsnstDTNAQIKLKLC------Dryvvsrs 91 
                                        579****************44440.....244444455555555644444444444444444......34444447 PP

                             AAA_24  48 .swedfldevvelaaeladyktlviDtideleelclaevirqneka 92 
                                         s++  ++++++ ++e + ++++v D+++e +   ++++++++e++
  gene2293|gene2293|rna2293|rna2293  92 lSLTHRKSKIEQKNTE-NVFSVIVNDSVSESYGNNMENLCNNDEVG 136
                                        7777777777766555.55*************99999999999885 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.4
                             AAA_24 113 rllkklqelrk..nvifiahektrkded 138
                                        +++++l+++rk  nv + +++++ ++  
  gene2293|gene2293|rna2293|rna2293 221 KAVENLKNVRKdkNVQLKMKLQELNFAL 248
                                        5556666666666666666555554444 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   3.1e-05     0.051       7      60 ..      27      78 ..      26     132 .. 0.73
   2 ?   -1.1   0.1       1.3   2.1e+03      84      84 ..     263     263 ..     216     311 .. 0.50

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.1e-05
                             AAA_22  7 ilvvtGesGtGKTtllrrlleqldeeakaee....erpevvfvtlpsstsskdllrel 60
                                       ++++ Ge GtGKTt ++ l++  +           ++++ +fv+ p +++s+d   ++
  gene2293|gene2293|rna2293|rna2293 27 MTLILGENGTGKTTIIEALRYAIT------GdlppMSRGGAFVYDPTLSNSTDTNAQI 78
                                       689****************99863......1234455555555555555555554444 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.3
                             AAA_22  84 q 84 
                                        +
  gene2293|gene2293|rna2293|rna2293 263 R 263
                                        1 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   8.3e-05      0.14      20      43 ..      27      50 ..      24      63 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 8.3e-05
                             AAA_30 20 vavltGpAGtGKttalkalreawe 43
                                       ++++ G  GtGKtt+++alr a++
  gene2293|gene2293|rna2293|rna2293 27 MTLILGENGTGKTTIIEALRYAIT 50
                                       57899**************99876 PP

>> DUF4046  Protein of unknown function (DUF4046)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00038      0.62      24      55 ..      72     103 ..      60     129 .. 0.83
   2 ?   -0.2   0.4      0.94   1.5e+03      57      81 ..     233     258 ..     206     262 .. 0.61
   3 ?    2.2   0.3      0.16   2.6e+02      33      53 ..     288     308 ..     273     331 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00038
                            DUF4046  24 eeeevqhrlklclryvvlqklkikpqeillev 55 
                                        ++ + q +lklc ryvv + l +  +  ++e 
  gene2293|gene2293|rna2293|rna2293  72 TDTNAQIKLKLCDRYVVSRSLSLTHRKSKIEQ 103
                                        5678999************9999876655544 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.94
                            DUF4046  57 ksflikyklfyavykrqskg.lkell 81 
                                        k+  +k kl++  +  q+k+  kell
  gene2293|gene2293|rna2293|rna2293 233 KNVQLKMKLQELNFALQAKKkHKELL 258
                                        34556777777777777654145555 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.16
                            DUF4046  33 klclryvvlqklkikpqeill 53 
                                        klc r+ + + ++++++ +l+
  gene2293|gene2293|rna2293|rna2293 288 KLCARHAIKKEINVESEKLLV 308
                                        899999999999999988764 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   8.7    0.0007       1.1      13      36 ..      27      50 ..      22     310 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0007
                                       EEEEEESTTSSHHHHHHHHTTSS- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx RF
                           ABC_tran 13 kvaivGenGaGKStLlkllagllk 36
                                       ++ i+GenG+GK+t++++l    +
  gene2293|gene2293|rna2293|rna2293 27 MTLILGENGTGKTTIIEALRYAIT 50
                                       578*************98765443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (337 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1953  (0.10893); expected 358.6 (0.02)
Passed bias filter:                      623  (0.0347482); expected 358.6 (0.02)
Passed Vit filter:                        79  (0.00440627); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.62u 0.29s 00:00:00.90 Elapsed: 00:00:00.47
# Mc/sec: 2137.81
//
Query:       gene2294|gene2294|rna2294|rna2294  [L=422]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.034   14.7   5.3        3.5    8.2   0.3    3.6  2  EF-G-binding_N  Elongation factor G-binding protein, N-termin
       0.38   10.9   6.3       0.12   12.5   2.1    2.5  2  APC_N_CC        Coiled-coil N-terminus of APC, dimerisation d
       0.45   10.6   8.6       0.04   14.0   1.6    2.1  2  Mito_fiss_reg   Mitochondrial fission regulator


Domain annotation for each model (and alignments):
>> EF-G-binding_N  Elongation factor G-binding protein, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.6    0.0021        12      39      73 ..     161     195 ..     126     196 .. 0.83
   2 ?    8.2   0.3   0.00059       3.5      35      66 ..     352     383 ..     342     402 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0021
                     EF-G-binding_N  39 ekIlelfpelseeqkelLeqiddiktkekaeklLe 73 
                                        e+ +e++++ + +  e++eq+   k k ++e++L+
  gene2294|gene2294|rna2294|rna2294 161 EEKTEMVNNVHRNMDEYMEQVRMSKRKNEIERYLS 195
                                        555788999************************96 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.00059
                     EF-G-binding_N  35 alaaekIlelfpelseeqkelLeqiddiktke 66 
                                        ++++ekI e   e++ee kelL +i++ ++++
  gene2294|gene2294|rna2294|rna2294 352 DYVIEKIPEKEREKTEEYKELLIKIENDEKRT 383
                                        5899*********************9999775 PP

>> APC_N_CC  Coiled-coil N-terminus of APC, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.1         2   1.2e+04      11      24 ..      15      28 ..      13      47 .. 0.69
   2 ?   12.5   2.1   1.9e-05      0.12       6      47 ..     111     155 ..     107     159 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 2
                           APC_N_CC 11 EaLkkenthlrrEL 24
                                       E  kke  ++++E 
  gene2294|gene2294|rna2294|rna2294 15 ERVKKEFEKFKKEQ 28
                                       55677777777773 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 1.9e-05
                           APC_N_CC   6 LvrQvEaLkkenthlrrELedNSshL...skLEtetsgmKevlkq 47 
                                        +vr  EaL ke  +l   ++ NS+ +    k E ets++K+ + +
  gene2294|gene2294|rna2294|rna2294 111 IVRELEALCKEENNLEYAIKANSNAIkntKKSEFETSDLKAKMNE 155
                                        6999********************99444599********97665 PP

>> Mito_fiss_reg  Mitochondrial fission regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.8      0.11   6.5e+02      72     127 ..      10      60 ..       3      62 .. 0.62
   2 ?   14.0   1.6   6.7e-06      0.04      69     168 ..      87     185 ..      83     221 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.11
                      Mito_fiss_reg  72 fRselrkkleeekleffekllkrqdslpslrreekkvksdlkaneeAlkkiaaLed 127
                                         R++l++      ++ fek +k+q++ + +++ + +   ++k+  e +k i+aL++
  gene2294|gene2294|rna2294|rna2294  10 ARNDLERV-----KKEFEKFKKEQEKAERIKKMRDEYFYRKKVLFEDIKAISALQN 60 
                                        45555553.....3445555555555555555556667777788888898999886 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 6.7e-06
                      Mito_fiss_reg  69 yarfRselrkkleeekleffekllkrqdslpslrreekkvksdlkaneeAlkkiaaLedELakLRaQIAkIVaaqe 144
                                        y rfR+ l ++ +    e+  + ++  ++l+ l +ee++ + + kan++A+k + + e E + L+a   ++Va+ e
  gene2294|gene2294|rna2294|rna2294  87 YERFRQILIER-DGSMAEADDNHKRIVRELEALCKEENNLEYAIKANSNAIKNTKKSEFETSDLKAKMNELVALRE 161
                                        77888888875.66666777777888899999999***************************************** PP

                      Mito_fiss_reg 145 asnssaslelsdtpdllepksssa 168
                                        +++++ +  + ++ + +e+ + s+
  gene2294|gene2294|rna2294|rna2294 162 EKTEMVNNVHRNMDEYMEQVRMSK 185
                                        **9944444444444454444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (422 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2856  (0.159295); expected 358.6 (0.02)
Passed bias filter:                      615  (0.034302); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.70u 0.30s 00:00:01.00 Elapsed: 00:00:00.47
# Mc/sec: 2678.09
//
Query:       gene2295|gene2295|rna2295|rna2295  [L=499]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.3e-10   39.8   4.5    6.4e-10   38.8   4.5    1.5  1  SMC_N         RecF/RecN/SMC N terminal domain
    7.2e-05   22.7   3.6      8e-05   22.6   1.2    2.2  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
     0.0002   21.5   0.0    0.00051   20.2   0.0    1.7  1  SbcCD_C       Putative exonuclease SbcCD, C subunit
  ------ inclusion threshold ------
      0.017   15.3   0.2      0.047   13.8   0.2    1.7  1  zf-HC5HC2H_2  PHD-zinc-finger like domain
       0.02   14.7   2.2        7.4    6.5   0.1    4.0  3  DASH_Dam1     DASH complex subunit Dam1
       0.22   12.0   0.0       0.22   12.0   0.0    3.4  2  ABC_tran      ABC transporter
       0.28   11.5   2.3       0.35   11.1   0.3    2.2  2  zf-HC5HC2H    PHD-like zinc-binding domain
        3.7    7.9  13.8        2.2    8.6   7.1    3.4  2  DUF2935       Domain of unknown function (DUF2935)


Domain annotation for each model (and alignments):
>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.8   4.5   2.9e-13   6.4e-10      60     206 ..     197     473 ..     177     489 .. 0.88

  Alignments for each domain:
  == domain 1  score: 38.8 bits;  conditional E-value: 2.9e-13
                                        CCCCCC--BTTCSSTTEEEEEEEE..EETTEE.SSSSSSCEEEEEEEETTSEEEEEETTEEE-HHHHHHHHHCTT- CS
                                        xxxxxxxxxxxxxxxxxxxxxxxx..xxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              SMC_N  60 klsdlihkskekasvkkaeveitf..dnedkk.lkiekeevsisrrvkrkgeseykingkevtkkevsellesagi 132
                                        +l+++i+   ek++ +k +v  ++  ++e+++  +i++e + i+ +++rk +   +in++e + ke+ ++l+ +++
  gene2295|gene2295|rna2295|rna2295 197 DLNKVISD-YEKDKFMKNKVREYLkyQEEQQRiHTIKDEITGIKLSIQRKRQEILAINDSE-KIKEILSQLKLKDV 270
                                        68899998.788888889998877334555554556666688**********999999987.56788888888888 PP

                                        STT......................................................................... CS
                                        xxx......................................................................... RF
                              SMC_N 133 ske......................................................................... 135
                                        ++e                                                                         
  gene2295|gene2295|rna2295|rna2295 271 DIEdiikgvekeintregankqlaqnvkeytlqleekipnyseiythtkildvvlkdldksikaieksvlkyyenk 346
                                        88899*********************************************************************** PP

                                        ....................................................CS-HHHHHHHHHHHHHH..HHCCS CS
                                        ....................................................xxxxxxxxxxxxxxxxx..xxxxx RF
                              SMC_N 136 ....................................................lLSgGektLvalaLlfA..iqkvk 157
                                                                                              S G+k +++l +++A  i    
  gene2295|gene2295|rna2295|rna2295 347 ieelnrnlkylwsntykgndidkielkaeitnskysyklmmykndvelemrgRCSAGQKVIASLIFRLAlsITFSG 422
                                        *****************************************************************99995455555 PP

                                        --SEEEECTTTTTS-HHHHHHHHHHHH..HHCTTSEEEEE-SSHHHCCC-S CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxx RF
                              SMC_N 158 paplyllDeidaaLDeknvkkvaellk..eksknaQfivislreemlekad 206
                                           +  lDe   +LD+ n++ +a+ lk  e+ +n Q+++i+++ee+l+ ++
  gene2295|gene2295|rna2295|rna2295 423 NCNVLTLDEPTTNLDQCNIESLARTLKylERMSNLQLVIITHDEEFLNLVS 473
                                        566889*********************8888999************99873 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.1       1.1   2.4e+03     173     219 ..      57     103 ..      52     163 .. 0.63
   2 !   22.6   1.2   3.6e-08     8e-05     124     303 .]     178     470 ..     151     470 .. 0.70

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1.1
                             AAA_21 173 adyfgfakekrllqrlvrslklveielsdlgegeeliasvderlrer 219
                                         +  + ++e++ +++ +r++ +v+   + ++  +++i+   + lr++
  gene2295|gene2295|rna2295|rna2295  57 EKRKKLKDELQSIKQNMREIVDVRKIKEEIEGYNQEIKNLEVSLRQN 103
                                        55555555555566666666555555555555555555555544444 PP

  == domain 2  score: 22.6 bits;  conditional E-value: 3.6e-08
                             AAA_21 124 vfslkelsvsepndlqfgkaltditsrawsllllldglrkerigllnifadyfgfakekrllqrlvrslklveiel 199
                                        ++++ +++++e++ ++++ +l++++s++++ + ++++ r+ +  +++ +++  + ++e++ ++  + + ++  + +
  gene2295|gene2295|rna2295|rna2295 178 SEQATHHNLNEEEYYKKILDLNKVISDYEKDKFMKNKVRE-YLKYQEEQQRIHTIKDEITGIKLSIQRKRQEILAI 252
                                        5555555666666666666666666666653333333333.55555555555555555555554444444444444 PP

                             AAA_21 200 sdlgegeeliasvderlrer........................................................ 219
                                         d+++ +e       +l+ +                                                        
  gene2295|gene2295|rna2295|rna2295 253 NDSEKIKEILS----QLKLKdvdiediikgvekeintregankqlaqnvkeytlqleekipnyseiythtkildvv 324
                                        44432222221....1111133445566667777777777777777777777777777777777777777777777 PP

                             AAA_21 220 .........................................................gvvflengdgqelparel. 237
                                                                                                  + ++ ++++ el +r   
  gene2295|gene2295|rna2295|rna2295 325 lkdldksikaieksvlkyyenkieelnrnlkylwsntykgndidkielkaeitnskySYKLMMYKNDVELEMRGRc 400
                                        7777777777777777778888888888888888888888888889999999999999999999*********999 PP

                             AAA_21 238 SdGtkrllalltallralkkg...sllliDEpEngLHPkllrrllellkelsr.ngaQviltTHSpllld 303
                                        S G+k ++ l+  l+     +    +l +DEp ++L+   +++l++ lk+l+r  + Q+++ TH+ ++l+
  gene2295|gene2295|rna2295|rna2295 401 SAGQKVIASLIFRLALSITFSgncNVLTLDEPTTNLDQCNIESLARTLKYLERmSNLQLVIITHDEEFLN 470
                                        *******99999999988888999*****************************************98876 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   2.3e-07   0.00051      27      89 ..     394     449 ..     375     450 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 2.3e-07
                            SbcCD_C  27 srssgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatllelle 89 
                                         +++g+ S G+k ++a+l++ +al+  +s       ++ ++ LDE   +lD+ +i++l ++l+
  gene2295|gene2295|rna2295|rna2295 394 LEMRGRCSAGQK-VIASLIFRLALSITFSG------NCNVLTLDEPTTNLDQCNIESLARTLK 449
                                        47899*******.*****************......49*******************999875 PP

>> zf-HC5HC2H_2  PHD-zinc-finger like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.2   2.1e-05     0.047      53     105 ..      22      77 ..       4      82 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.1e-05
                       zf-HC5HC2H_2  53 rlkekCllCkkrkGaciqCs...kkeCktafHvtCalaaglvmeledlekklkvia 105
                                        r ++ C++C+ +kG+c+  +   +keCkt f  +   +++l  el++++++++ i+
  gene2295|gene2295|rna2295|rna2295  22 RDERFCSICRYSKGTCVDVKesvQKECKTWFYNILEKRKKLKDELQSIKQNMREIV 77 
                                        35778************875111567*********************999888776 PP

>> DASH_Dam1  DASH complex subunit Dam1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.1    0.0033       7.4       6      33 ..      60      90 ..      55      93 .. 0.72
   2 ?    4.8   0.1     0.011        24       7      34 ..     143     170 ..     141     174 .. 0.90
   3 ?   -0.7   0.0      0.57   1.3e+03       3      12 ..     345     354 ..     321     369 .. 0.57

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0033
                          DASH_Dam1  6 aeLaDsletLdknledLqq...ihesLsdfN 33
                                       ++L+D+l+ +++n++++ +   i+e++++ N
  gene2295|gene2295|rna2295|rna2295 60 KKLKDELQSIKQNMREIVDvrkIKEEIEGYN 90
                                       78*************9875111556666555 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.011
                          DASH_Dam1   7 eLaDsletLdknledLqqihesLsdfNe 34 
                                        +L+D+ ++L + +++++q++++L ++ e
  gene2295|gene2295|rna2295|rna2295 143 QLEDAKAALISETSKMNQLKQQLIQLEE 170
                                        699999*****************99877 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.57
                          DASH_Dam1   3 pafaeLaDsl 12 
                                        ++++eL+ +l
  gene2295|gene2295|rna2295|rna2295 345 NKIEELNRNL 354
                                        3333444333 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -7.8  13.1         8   1.8e+04      52      96 ..     206     269 ..      31     301 .. 0.69
   2 ?   12.0   0.0   9.9e-05      0.22      53     136 ..     331     433 ..     301     434 .. 0.65

  Alignments for each domain:
  == domain 1  score: -7.8 bits;  conditional E-value: 8
                                        B-HHHCCHCEE.EE-SS--S-TTSBHHHH..................HHHTCHHHHHHHSTTGG CS
                                        xxxxxxxxxxx.xxxxxxxxxxxxxxxxx..................xxxxxxxxxxxxxxxxx RF
                           ABC_tran  52 qeleslrkeig.vlpqepqlfpeltvren..................esdeeiekalsklglke 96 
                                        ++ ++++++++ +l+ +++ ++ +t++++                  +++e+i+++ls+l+lk+
  gene2295|gene2295|rna2295|rna2295 206 EKDKFMKNKVReYLKYQEEQQRIHTIKDEitgiklsiqrkrqeilaiNDSEKIKEILSQLKLKD 269
                                        2233333333212222233333333444466666666666666777777777777777777776 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 9.9e-05
                                        -HHHCCHCEEEE-SS..--S-TTSB.HHHH..........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHH CS
                                        xxxxxxxxxxxxxxx..xxxxxxxx.xxxx..........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ABC_tran  53 eleslrkeigvlpqe..pqlfpelt.vren..........esdeeiekalsklglkelkdtvvksspssLSgGqkq 115
                                        +++  +k++  + ++  ++l+++l+ + +n          e ++ei++   +++l   k++v  +     S Gqk+
  gene2295|gene2295|rna2295|rna2295 331 SIKAIEKSVLKYYENkiEELNRNLKyLWSNtykgndidkiELKAEITNSKYSYKLMMYKNDVELEMRGRCSAGQKV 406
                                        33333333333333334555555554444475555555555566666666666666666766666669*******9 PP

                                        ......HHHHHHHHHHTSSEEEEESTT CS
                                        ......xxxxxxxxxxxxxxxxxxxxx RF
                           ABC_tran 116 ......rvalarallkkpkllllDEpt 136
                                              r+al  ++  + ++l lDEpt
  gene2295|gene2295|rna2295|rna2295 407 iaslifRLALSITFSGNCNVLTLDEPT 433
                                        889999999*****************9 PP

>> zf-HC5HC2H  PHD-like zinc-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.3   0.00016      0.35      23      76 ..      12      67 ..       2      85 .. 0.74
   2 ?   -2.6   0.1         3   6.8e+03      28      41 ..     131     144 ..     109     156 .. 0.56

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00016
                         zf-HC5HC2H 23 eiedvekikkerkklkCylCkkkvGaciqCs...kkkCkkafHvtCakeagllleee 76
                                       ei+d+ k++  r +  C++C+ ++G c+  +   +k+Ck+ f  +  k+++l+ e +
  gene2295|gene2295|rna2295|rna2295 12 EIKDIGKVDY-RDERFCSICRYSKGTCVDVKesvQKECKTWFYNILEKRKKLKDELQ 67
                                       5666666654.56679*****999***9865222689*****988888877776655 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 3
                         zf-HC5HC2H  28 ekikkerkklkCyl 41 
                                        +   ++rk+l+C l
  gene2295|gene2295|rna2295|rna2295 131 NVKIAQRKELECQL 144
                                        22345666777765 PP

>> DUF2935  Domain of unknown function (DUF2935)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   7.1   0.00098       2.2      58     121 ..     111     196 ..       1     197 [. 0.79
   2 ?   -0.2   0.3      0.52   1.2e+03      31      59 ..     289     323 ..     245     364 .. 0.55

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00098
                            DUF2935  58 v.......................rasseleeavakLneealkltreliqFkkellekvlscklfsiiypllidHi 110
                                        v                        +++ele ++++     +++t ++ q+k++l++  +   +   +    ++H 
  gene2295|gene2295|rna2295|rna2295 111 VlresvkkmekrvakvkedknvkiAQRKELECQLEDAKAALISETSKMNQLKQQLIQLEEYLGVI-ENSEQATHHN 185
                                        255555566666666666666665999******************************99997776.89999***** PP

                            DUF2935 111 lrEaeyYlkll 121
                                        l+E+eyY k+l
  gene2295|gene2295|rna2295|rna2295 186 LNEEEYYKKIL 196
                                        ********998 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.52
                            DUF2935  31 dlikeakefkkeFekllaeavelseglv......r 59 
                                        ++ + a+++k+   +l+++  ++se  +       
  gene2295|gene2295|rna2295|rna2295 289 ANKQLAQNVKEYTLQLEEKIPNYSEIYThtkildV 323
                                        33344444444444444444444433334444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (499 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2996  (0.167104); expected 358.6 (0.02)
Passed bias filter:                      492  (0.0274416); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.78u 0.33s 00:00:01.11 Elapsed: 00:00:00.48
# Mc/sec: 3104.65
//
Query:       gene2296|gene2296|rna2296|rna2296  [L=657]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.1e-05   26.0   2.2        2.2    9.3   0.2    5.5  5  WD40         WD domain, G-beta repeat
  ------ inclusion threshold ------
        0.1   12.6   0.0       0.26   11.3   0.0    1.6  1  Nup35_RRM_2  Nup53/35/40-type RNA recognition motif
       0.41   10.8   1.6       0.85    9.8   0.0    2.3  3  DUF4145      Domain of unknown function (DUF4145)


Domain annotation for each model (and alignments):
>> WD40  WD domain, G-beta repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.7   0.0    0.0051        30       4      38 .]     122     157 ..     119     157 .. 0.90
   2 !    9.3   0.2   0.00037       2.2       3      36 ..     163     197 ..     161     199 .. 0.81
   3 ?    1.0   0.0      0.15   9.3e+02      18      37 ..     362     381 ..     346     382 .. 0.74
   4 ?    0.5   0.0      0.22   1.3e+03      12      28 ..     431     447 ..     420     456 .. 0.74
   5 ?    2.8   0.3     0.041   2.5e+02      23      35 ..     542     554 ..     529     554 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0051
                                        EEEEESS.SSEEEEEEETTSSEEEEEETTSEEEEEE CS
                               WD40   4 lrtltGH.ssvtslafspdgawlasGsdDgtvriWd 38 
                                        +++ + H + +t +   + +++++sG++ g +++++
  gene2296|gene2296|rna2296|rna2296 122 VKSMKEHdTAITTIFIERTNRYFLSGDEGGCIKLFN 157
                                        678899*777***********************987 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00037
                                        EEEEEESS.SSEEEEEEETTSSEEEEEETTSEEEE CS
                               WD40   3 clrtltGH.ssvtslafspdgawlasGsdDgtvri 36 
                                        ++r++  H ++++++ fs+ g++++s++  g v+i
  gene2296|gene2296|rna2296|rna2296 163 LIREFFLHfGGINDINFSHCGTYMISSDSGGCVKI 197
                                        56666669777*************99855998887 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.15
                                        EETTSSEEEEEETTSEEEEE CS
                               WD40  18 fspdgawlasGsdDgtvriW 37 
                                        f  d +++++   D+++r++
  gene2296|gene2296|rna2296|rna2296 362 FLNDDRYFITTATDNKLRVF 381
                                        5667777665444*****97 PP

  == domain 4  score: 0.5 bits;  conditional E-value: 0.22
                                        SEEEEEEETTSSEEEEE CS
                               WD40  12 svtslafspdgawlasG 28 
                                        ++t ++fs+dg  ++ +
  gene2296|gene2296|rna2296|rna2296 431 FITEISFSDDGYTFIVS 447
                                        49********9887654 PP

  == domain 5  score: 2.8 bits;  conditional E-value: 0.041
                                        SEEEEEETTSEEE CS
                               WD40  23 awlasGsdDgtvr 35 
                                        + l++GsdD++++
  gene2296|gene2296|rna2296|rna2296 542 SDLSTGSDDKSIK 554
                                        33699******97 PP

>> Nup35_RRM_2  Nup53/35/40-type RNA recognition motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   4.3e-05      0.26      15      33 ..     162     180 ..     152     205 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 4.3e-05
                        Nup35_RRM_2  15 elVlehFasfGeIvkhyvp 33 
                                        +l++e+F +fG I++++++
  gene2296|gene2296|rna2296|rna2296 162 NLIREFFLHFGGINDINFS 180
                                        89***************98 PP

>> DUF4145  Domain of unknown function (DUF4145)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.1      0.99   5.9e+03      39      57 ..      22      39 ..      13      45 .. 0.64
   2 ?   -2.9   0.0       1.3   7.9e+03      63      71 ..     393     401 ..     380     405 .. 0.74
   3 ?    9.8   0.0   0.00014      0.85      53      81 ..     548     577 ..     516     581 .. 0.75

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.99
                            DUF4145 39 nkiealvekgvipeklkel 57
                                       n+i +l++++ ++e+lkel
  gene2296|gene2296|rna2296|rna2296 22 NNIYSLTKEN-VEEALKEL 39
                                       5555666665.56666555 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.3
                            DUF4145  63 viGNdgaHe 71 
                                        v GN  aH+
  gene2296|gene2296|rna2296|rna2296 393 VNGNLLAHP 401
                                        469999998 PP

  == domain 3  score: 9.8 bits;  conditional E-value: 0.00014
                            DUF4145  53 klkelldairviGNdgaHe.lkditkedae 81 
                                        +  +++++ir++GN++ H+  + it ++ e
  gene2296|gene2296|rna2296|rna2296 548 SDDKSIKEIRTAGNRARHSaINVITDDNYE 577
                                        556899************747777777655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (657 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1391  (0.0775838); expected 358.6 (0.02)
Passed bias filter:                      564  (0.0314574); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.65u 0.27s 00:00:00.92 Elapsed: 00:00:00.45
# Mc/sec: 4415.22
//
Query:       gene2297|gene2297|rna2297|rna2297  [L=113]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.7e-05   24.2   0.0     0.0001   22.8   0.0    1.7  1  Trm112p     Trm112p-like protein
  ------ inclusion threshold ------
      0.069   13.3   0.0       0.34   11.0   0.0    1.9  2  zf-RRPl_C4  Putative ribonucleoprotein zinc-finger pf C4 type
       0.21   11.2   0.1         13    5.4   0.0    2.0  2  DUF2026     Protein of unknown function (DUF2026)


Domain annotation for each model (and alignments):
>> Trm112p  Trm112p-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.0   1.7e-08    0.0001       3      68 .]       4      93 ..       3      93 .. 0.66

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 1.7e-08
                                       GGCCC-B-TTTHH....C-.....................-HHHHHHHHHTT---S-SS----S.............. CS
                            Trm112p  3 lllniLaCpackg....pL.....................dwealvevaalglnelpkekpedy.............. 41
                                       ++ +iL+C+ c      +L                                                           
  gene2297|gene2297|rna2297|rna2297  4 FTFSILKCNSCDFtqklRLmptkvhkitpasefyrevdedT----------------------Leslrksfesvegiy 59
                                       68899999999877844445555555555444444443333......................144445555555555 PP

                                       .......CHHTTEECCCCEEEETTTTEEEEEETT CS
                            Trm112p 42 .......ellleldieegeLvCpncgraYpIkdG 68
                                                l+  +++eg++ C  cg  +pI+dG
  gene2297|gene2297|rna2297|rna2297 60 kleddtrMFLFGNVVDEGKIFCDGCGVYFPIEDG 93
                                       5555556678899********************9 PP

>> zf-RRPl_C4  Putative ribonucleoprotein zinc-finger pf C4 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.0      0.15   8.9e+02      57      77 ..      13      17 ..       5      60 .. 0.51
   2 ?   11.0   0.0   5.6e-05      0.34      16      43 ..      76     104 ..      71     112 .. 0.72

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.15
                         zf-RRPl_C4 57 kCkeknekekeircetfeeyl 77
                                       +C                   
  gene2297|gene2297|rna2297|rna2297 13 SCDF----------------T 17
                                       2221................1 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 5.6e-05
                         zf-RRPl_C4  16 netvyCeaCeiyfkvknekq.kvelvpik 43 
                                        + +++C+ C +yf ++++   +v+ v+++
  gene2297|gene2297|rna2297|rna2297  76 EGKIFCDGCGVYFPIEDGIVdFVNPVKVD 104
                                        568***********999864145556655 PP

>> DUF2026  Protein of unknown function (DUF2026)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0    0.0021        13     117     158 ..      15      56 ..       7      63 .. 0.86
   2 ?    5.2   0.0    0.0024        14      54     104 ..      58     106 ..      54     113 .] 0.79

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0021
                                        BEEEEGGG--SSTT---STT-EEEEE-HHHHHHHTTTGGG-H CS
                            DUF2026 117 mfqkkldsmaesindlkksGDffldpdlevteellkklaksl 158
                                         f +kl  m + +++++   +f+ + d + +e+l k++++ +
  gene2297|gene2297|rna2297|rna2297  15 DFTQKLRLMPTKVHKITPASEFYREVDEDTLESLRKSFESVE 56 
                                        58899*****************************99998865 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0024
                                        EEEETTE..EEEESB------B--SSTT-EEEEEETTEEEETTGGGTTTT- CS
                            DUF2026  54 aylldekkavlsfasleeDgqvkssedafhawveaDgwliDfmaPafsevl 104
                                        +y+l+++  +++f++++++g++  ++ +   +  +++ ++Df+ P   + +
  gene2297|gene2297|rna2297|rna2297  58 IYKLEDDTRMFLFGNVVDEGKIFCDGCGV--YFPIEDGIVDFVNPVKVDGN 106
                                        699999999***********988877665..555667799**999866655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (113 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       571  (0.0318478); expected 358.6 (0.02)
Passed bias filter:                      502  (0.0279993); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 814.10
//
Query:       gene2298|gene2298|rna2298|rna2298  [L=142]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-33  115.7   0.2    1.5e-33  115.4   0.2    1.0  1  Ribosomal_L14  Ribosomal protein L14p/L23e


Domain annotation for each model (and alignments):
>> Ribosomal_L14  Ribosomal protein L14p/L23e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.4   0.2   8.5e-38   1.5e-33       2     119 ..      22     139 ..      21     141 .. 0.95

  Alignments for each domain:
  == domain 1  score: 115.4 bits;  conditional E-value: 8.5e-38
                                        .CSS-EEE--SSSSBSEEEEEEETT-.....---EE-SSSEEEEEESSS-T...TTSSCEEEEEEEE-SS-EE-TT CS
                      Ribosomal_L14   2 iqlktrlkvaDNsgakevecikvlggk....krkaasvGdiivvsvkkakpkgkvkkgdvvkavvvrtkkevrrkd 73 
                                        iq++t+l +aDNsgak +++i v g +    + +aa++Gd+iv+sv k+kp     ++++v av +r+k+ +rr+d
  gene2298|gene2298|rna2298|rna2298  22 IQVGTILACADNSGAKMLKVIGVKGIRgrlnRLPAATLGDVIVCSVVKGKP---DLRKKIVLAVPIRQKQIIRRPD 94 
                                        89**********************988555455******************...899******************* PP

                                        S-EEEESS-EEEEB-TTS-BSS-.B-SBEEHHHHHH.-HHHHHTBS CS
                      Ribosomal_L14  74 GsvirfddnaaVllnkkgeplGtrifgpvarelrekkflkivslAp 119
                                         +++ f+dnaaVl+++k e++Gt+i+gpvare+ e  ++ki s A+
  gene2298|gene2298|rna2298|rna2298  95 AVHMYFEDNAAVLITNKCELRGTQINGPVAREACEL-WPKISSQAS 139
                                        ***********************************9.******997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       193  (0.0107647); expected 358.6 (0.02)
Passed bias filter:                      172  (0.0095934); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.28s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1044.48
//
Query:       gene2299|gene2299|rna2299|rna2299  [L=187]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       750  (0.0418317); expected 358.6 (0.02)
Passed bias filter:                      555  (0.0309554); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 1259.90
//
Query:       gene23|gene23|rna23|rna23  [L=283]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.7e-06   26.8   9.5     0.0018   18.6   1.2    2.8  2  zf-C2H2          Zinc finger, C2H2 type
    1.5e-05   25.2   9.6      0.039   14.4   0.3    2.5  2  zf-met           Zinc-finger of C2H2 type
      4e-05   24.1   6.1      0.065   14.1   1.1    2.9  2  zf-C2H2_4        C2H2-type zinc finger
    4.4e-05   23.7  11.5      0.044   14.1   0.5    2.5  2  zf-C2H2_jaz      Zinc-finger double-stranded RNA-binding
    4.5e-05   23.7   7.9     0.0004   20.7   2.9    2.4  2  zf-C2H2_2        C2H2 type zinc-finger (2 copies)
    0.00015   21.8   3.4    0.00023   21.2   1.8    2.2  2  DnaJ             DnaJ domain
  ------ inclusion threshold ------
       0.28   11.2   7.9        2.9    8.0   1.0    2.6  2  zf-C2H2_6        C2H2-type zinc finger
       0.92   10.3  12.8       0.41   11.4  10.3    1.6  1  MRNIP            MRN-interacting protein
        6.9    7.5  11.3      2e+02    2.8  11.5    2.6  1  zinc_ribbon_15   zinc-ribbon family
        7.2    7.2  14.7        5.6    7.6   0.3    3.3  3  zf-H2C2_2        Zinc-finger double domain


Domain annotation for each model (and alignments):
>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   1.6   0.00012      0.22       1      22 [.     174     195 ..     174     198 .. 0.92
   2 !   18.6   1.2     1e-06    0.0018       3      23 .]     263     283 .]     261     283 .] 0.97

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00012
                                EEETTTTEEESSHHHHHHHHHC CS
                    zf-C2H2   1 ykCpdCgksFkrksnLkrHirt 22 
                                ykC++C+k + +k  +  H++ 
  gene23|gene23|rna23|rna23 174 YKCTVCKKDYQQKTKYIEHMNG 195
                                9*******************85 PP

  == domain 2  score: 18.6 bits;  conditional E-value: 1e-06
                                ETTTTEEESSHHHHHHHHHCC CS
                    zf-C2H2   3 CpdCgksFkrksnLkrHirtH 23 
                                C+ C+k+F+++ +L+ H+++H
  gene23|gene23|rna23|rna23 263 CSLCDKKFPNRKELTLHLQKH 283
                                ********************9 PP

>> zf-met  Zinc-finger of C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   3.9   3.2e-05     0.057       1      25 []     174     198 ..     174     198 .. 0.98
   2 !   14.4   0.3   2.2e-05     0.039       2      21 ..     262     281 ..     261     283 .] 0.93

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.2e-05
                     zf-met   1 fyCelCnvtfnsesqlksHlqGKkH 25 
                                + C +C++ ++ ++ ++ H++G kH
  gene23|gene23|rna23|rna23 174 YKCTVCKKDYQQKTKYIEHMNGNKH 198
                                78*********************** PP

  == domain 2  score: 14.4 bits;  conditional E-value: 2.2e-05
                     zf-met   2 yCelCnvtfnsesqlksHlq 21 
                                +C+lC+++f +++ l  Hlq
  gene23|gene23|rna23|rna23 262 FCSLCDKKFPNRKELTLHLQ 281
                                8**************99998 PP

>> zf-C2H2_4  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.3   0.00021      0.37       1      21 [.     174     194 ..     174     195 .. 0.94
   2 !   14.1   1.1   3.6e-05     0.065       3      23 ..     263     283 .]     261     283 .] 0.95

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00021
                  zf-C2H2_4   1 fkCpiCgksFsskkaLlrHlk 21 
                                +kC++C+k +  k+++  H++
  gene23|gene23|rna23|rna23 174 YKCTVCKKDYQQKTKYIEHMN 194
                                8************99****95 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 3.6e-05
                  zf-C2H2_4   3 CpiCgksFsskkaLlrHlkth 23 
                                C++C+k F+++k+L  Hl++h
  gene23|gene23|rna23|rna23 263 CSLCDKKFPNRKELTLHLQKH 283
                                *************999***99 PP

>> zf-C2H2_jaz  Zinc-finger double-stranded RNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   4.7   3.7e-05     0.067       2      27 .]     174     199 ..     173     199 .. 0.97
   2 !   14.1   0.5   2.4e-05     0.044       3      22 ..     262     281 ..     261     283 .] 0.92

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.7e-05
                                CBBTTTTBBBSSHHHHHCCTTSHHHH CS
                zf-C2H2_jaz   2 fYCvlCdKyFksenaldnHlkSKkHK 27 
                                + C +C+K ++    + +H+++ kH+
  gene23|gene23|rna23|rna23 174 YKCTVCKKDYQQKTKYIEHMNGNKHR 199
                                89***********************7 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 2.4e-05
                                BBTTTTBBBSSHHHHHCCTT CS
                zf-C2H2_jaz   3 YCvlCdKyFksenaldnHlk 22 
                                +C lCdK F + + l  Hl 
  gene23|gene23|rna23|rna23 262 FCSLCDKKFPNRKELTLHLQ 281
                                8*****************85 PP

>> zf-C2H2_2  C2H2 type zinc-finger (2 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   2.9   2.2e-07    0.0004      13      77 ..     135     200 ..     126     213 .. 0.88
   2 ?    5.7   0.2     0.011        19      51      72 ..     261     282 ..     235     283 .] 0.84

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 2.2e-07
                  zf-C2H2_2  13 eellehm.skkhgffipereylvdleglleylrekieekleClyCekefkslealreHmkkkgHck 77 
                                 el++++ +k+ ++ +p+++y+++  + +++ + k e++++C +C+k+ +++ ++ eHm+ ++H++
  gene23|gene23|rna23|rna23 135 RELVKFLkQKEMTLLMPKAHYVKTEYKPVKKTKVKKEKTYKCTVCKKDYQQKTKYIEHMNGNKHRN 200
                                567777746788999*************************************************86 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.011
                  zf-C2H2_2  51 leClyCekefkslealreHmkk 72 
                                l C +C+k+f ++++l+ H++k
  gene23|gene23|rna23|rna23 261 LFCSLCDKKFPNRKELTLHLQK 282
                                5688888888888888888876 PP

>> DnaJ  DnaJ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   1.8   1.3e-07   0.00023       2      57 ..      35      87 ..      34      91 .. 0.94
   2 ?   -1.8   0.0       1.9   3.4e+03      13      28 ..     119     134 ..     107     135 .. 0.75

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 1.3e-07
                               HHHHHTSSTTG-HHHHHHHHHHHHHHHSTTTSCCHHHHHHHHHHHHHHHHHHTSHH CS
                       DnaJ  2 yYeiLgvskdasedeIkkaYrklalkyHPDknpkdpeaeekFkeineAyevLsdpe 57
                               +Y iL+++ + + ++I++aYrk+  +y   k++ d++ +++ ++i eAyev + +e
  gene23|gene23|rna23|rna23 35 PYTILQITDTDKYSTIRRAYRKQLFRY---KSTIDKDYSDMTRKILEAYEVIKRKE 87
                               7**************************...99999****************99876 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.9
                                -HHHHHHHHHHHHHHH CS
                       DnaJ  13 sedeIkkaYrklalky 28 
                                +e++I+  Y +  +ky
  gene23|gene23|rna23|rna23 119 DENNIRDVYSRFRMKY 134
                                7788999999998887 PP

>> zf-C2H2_6  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   1.0    0.0016       2.9       2      12 ..     174     184 ..     173     185 .. 0.87
   2 ?    6.5   0.9    0.0047       8.3       4      24 ..     263     283 .]     263     283 .] 0.88

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0016
                  zf-C2H2_6   2 heCsvCsksFp 12 
                                ++C+vC+k ++
  gene23|gene23|rna23|rna23 174 YKCTVCKKDYQ 184
                                9*******775 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0047
                  zf-C2H2_6   4 CsvCsksFpslqaLggHkksH 24 
                                Cs C+k Fp  ++L+ H+  H
  gene23|gene23|rna23|rna23 263 CSLCDKKFPNRKELTLHLQKH 283
                                *********999999998555 PP

>> MRNIP  MRN-interacting protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4  10.3   0.00023      0.41      14      89 ..     167     244 ..     161     257 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00023
                      MRNIP  14 qvkKskkwkCkvCnekqslkkvyg.sgsgkdcrqlVqklnlkkgekeeeed.eelkekkqeeeekeeseeeeklkedk 89 
                                 vkK+k++kC vC++  + k  y  +++g+  r+++++l ++ +  +e     ++ +++ ++ +ke +ee+++++++k
  gene23|gene23|rna23|rna23 167 KVKKEKTYKCTVCKKDYQQKTKYIeHMNGNKHRNKCRELGVELNIPDEICPqVKESRERGKSPKKECEEEHARIEKRK 244
                                689***********9988888888788888888888888877776666555122233333444444444444444333 PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8  11.5      0.11     2e+02      29      84 ..     166     218 ..     142     275 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.11
             zinc_ribbon_15  29 fkwkkkkpylacskCkslleaskelgkeiekkessekkeCknCgkeveeefkyCpk 84 
                                 k+kk ++ ++c+ Ck+ +++++++ ++++ ++  + ++C++ g e++   + Cp+
  gene23|gene23|rna23|rna23 166 TKVKK-EKTYKCTVCKKDYQQKTKYIEHMNGNK--HRNKCRELGVELNIPDEICPQ 218
                                45555.7889************96666665443..367788877777777777775 PP

>> zf-H2C2_2  Zinc-finger double domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   3.4    0.0065        12      10      24 ..     169     183 ..     164     184 .. 0.81
   2 ?    7.6   0.3    0.0031       5.6      15      24 ..     261     270 ..     248     272 .. 0.82
   3 ?   -2.3   0.3       4.2   7.6e+03       2       9 ..     276     283 .]     275     283 .] 0.78

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0065
                  zf-H2C2_2  10 tgekpyeCplCdkaF 24 
                                ++ek y+C +C+k +
  gene23|gene23|rna23|rna23 169 KKEKTYKCTVCKKDY 183
                                67889*******975 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0031
                  zf-H2C2_2  15 yeCplCdkaF 24 
                                + C+lCdk+F
  gene23|gene23|rna23|rna23 261 LFCSLCDKKF 270
                                57*******9 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 4.2
                  zf-H2C2_2   2 LrrHirkH 9  
                                L+ H+ kH
  gene23|gene23|rna23|rna23 276 LTLHLQKH 283
                                77799888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (283 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1589  (0.0886274); expected 358.6 (0.02)
Passed bias filter:                      441  (0.024597); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1826.56
//
Query:       gene2300|gene2300|rna2300|rna2300  [L=126]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       716  (0.0399353); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 863.91
//
Query:       gene2301|gene2301|rna2301|rna2301  [L=42]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.036   14.2   0.1      0.047   13.8   0.1    1.2  1  DUF1299   Protein of unknown function (DUF1299)


Domain annotation for each model (and alignments):
>> DUF1299  Protein of unknown function (DUF1299)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   2.6e-06     0.047      10      26 ..       2      18 ..       1      20 [. 0.88

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.6e-06
                            DUF1299 10 QEaYviLSDdEdNgTAP 26
                                       QE+Yv +SD+E  +  P
  gene2301|gene2301|rna2301|rna2301  2 QEEYVCISDNEVEDWSP 18
                                       9**********877666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (42 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       367  (0.0204696); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.46
# Mc/sec: 273.24
//
Query:       gene2302|gene2302|rna2302|rna2302  [L=97]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (97 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       424  (0.0236488); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 676.60
//
Query:       gene2303|gene2303|rna2303|rna2303  [L=482]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      3e-46  157.4   0.0    5.9e-46  156.4   0.0    1.5  1  DEAD           DEAD/DEAH box helicase
    4.8e-33  113.8   0.0    8.7e-32  109.8   0.1    2.6  3  Helicase_C     Helicase conserved C-terminal domain
    0.00025   20.4   0.4    0.00039   19.7   0.4    1.2  1  ERCC3_RAD25_C  ERCC3/RAD25/XPB C-terminal helicase
     0.0036   16.7   0.0     0.0081   15.5   0.0    1.5  1  CMS1           U3-containing 90S pre-ribosomal complex subuni
  ------ inclusion threshold ------
      0.018   15.3   0.1       0.11   12.7   0.0    2.3  2  AAA_22         AAA domain
      0.037   13.7   0.0      0.072   12.8   0.0    1.4  1  Helicase_C_4   C-terminal domain on Strawberry notch homologu
      0.056   13.4   0.0       0.13   12.2   0.0    1.6  1  ResIII         Type III restriction enzyme, res subunit


Domain annotation for each model (and alignments):
>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  156.4   0.0   2.3e-49   5.9e-46       2     176 .]     100     270 ..      99     270 .. 0.97

  Alignments for each domain:
  == domain 1  score: 156.4 bits;  conditional E-value: 2.3e-49
                                        HHHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHS...TTSTS-EEEEEESSHHHHHHHHHHHHHHTTTS CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               DEAD   2 diQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyet...kgktgpkalivePtreLaeqtlnnlkkfkkyi 74 
                                        +iQa+ +p +l+g+d+++ a+TGsGKT  f++p+l + + +   + ++gp ali++PtreL+ q+ + ++++  + 
  gene2303|gene2303|rna2303|rna2303 100 AIQAQGWPMALSGRDMVGIAQTGSGKTISFALPALVHAAAQvplRPNDGPIALILAPTRELCMQIQEVVEEYDRFF 175
                                        79*********************************9988889999******************************* PP

                                        TSEEEEEETTSSHHHHHHHHHTTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSH CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               DEAD  75 dlrvlliiggvaardqlskldngvdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsdfinrilnqlp 150
                                        ++r l+++ggv+a  q++++++gv+++v+tpgrl+dl+++g ++ls+v++lVlDEadr+ld+gf++++++i+ ++ 
  gene2303|gene2303|rna2303|rna2303 176 NMRSLAVYGGVSAFPQRQAIRRGVEVLVATPGRLIDLMEQGCIHLSRVTYLVLDEADRMLDMGFEPQLRSIIPRT- 250
                                        ************************************************************************999. PP

                                        HHCTTSTTTSEEEEEESSBSHHHHHH CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               DEAD 151 qitcdgklqrqvivlSATlpkdvkkl 176
                                              + +rq+++ SAT+p++v++l
  gene2303|gene2303|rna2303|rna2303 251 ------NPDRQTLMWSATWPQEVRDL 270
                                        ......56788*********999875 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.49   1.2e+03      19      72 ..     151     204 ..     138     209 .. 0.71
   2 ?   -1.1   0.0      0.93   2.4e+03      13      58 ..     250     296 ..     242     304 .. 0.73
   3 !  109.8   0.1   3.4e-35   8.7e-32       1     111 []     305     413 ..     305     413 .. 0.95

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.49
                                        EEEEESSHHHHHH.HHHHHHHT...TSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEE CS
                         Helicase_C  19 ilifvntidrlek.vklllekk...gikvavlhgelpqnereeileqfnkgesdvLia 72 
                                        +li ++t++ + +  ++++e     ++++++++g  ++  +++++++     + vL+a
  gene2303|gene2303|rna2303|rna2303 151 ALILAPTRELCMQiQEVVEEYDrffNMRSLAVYGGVSAFPQRQAIRRG----VEVLVA 204
                                        688899999664443444333244699999999999999999988876....445555 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.93
                                        TTTTSEEEEEESSHH.HHHHHHHHHHHTTSTEEEESTTSTHHHHHHH CS
                         Helicase_C  13 eeeggkilifvntid.rlekvklllekkgikvavlhgelpqnereei 58 
                                        ++ ++++l+ + t+  ++ ++ +   k+ i+v++   el++n +++ 
  gene2303|gene2303|rna2303|rna2303 250 TNPDRQTLMWSATWPqEVRDLAYSFMKNYIQVTIGEDELTSNRKIHQ 296
                                        56778888888888766655444444888999999999999998876 PP

  == domain 3  score: 109.8 bits;  conditional E-value: 3.4e-35
                                        HHHHHHHHHHHHTTTTSEEEEEESSHHHHHHHHHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGG CS
                         Helicase_C   1 dkleallellkleeeggkilifvntidrlekvklllekkgikvavlhgelpqnereeileqfnkgesdvLiatdva 76 
                                        dk++ l+ +l  +e++ k+++f+n++++++ +++ l k+ + + ++hg+ +q++r++++++f++g+ ++Liatdva
  gene2303|gene2303|rna2303|rna2303 305 DKVDNLVSFL--NENDMKVIVFCNKKRTCDTLEYELGKHRYYASAIHGDKSQQSRDRVINDFKSGRKNILIATDVA 378
                                        5778888887..89***************99888899999************************************ PP

                                        TSSSTSTTESEEEESSSSSSHHHHHHHHTTSSSTT CS
                         Helicase_C  77 erGidipkvnlVinfdlprnvtsyiqriGRtgRag 111
                                        +rG+d+++v+ Vinfd+p n +syi+riGRt+R++
  gene2303|gene2303|rna2303|rna2303 379 ARGLDVKDVQAVINFDFPPNCDSYIHRIGRTARGN 413
                                        *********************************85 PP

>> ERCC3_RAD25_C  ERCC3/RAD25/XPB C-terminal helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.4   1.5e-07   0.00039      40     154 ..     298     415 ..     266     427 .. 0.71

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1.5e-07
                      ERCC3_RAD25_C  40 vmnpnkfracefLikyhekrgDkiivfsDnvfaLkeyakklkkp.y....iyGetseaerlkilqkfkknpkvnti 110
                                        +   +    ++ L+++ ++ + k+ivf+++  +  ++  +l k+ y    i+G+ s++ r +++++fk+  + n +
  gene2303|gene2303|rna2303|rna2303 298 IRVCDERDKVDNLVSFLNENDMKVIVFCNKKRTCDTLEYELGKHrYyasaIHGDKSQQSRDRVINDFKSG-RKNIL 372
                                        333344467889*****************99999988888876422244499***************987.56888 PP

                      ERCC3_RAD25_C 111 flskvgDtsiDlPeanvliqisshfgsrrqeaqrlGriLrakkk 154
                                        +   v+   +D+ + + +i  ++          r+Gr  r  +k
  gene2303|gene2303|rna2303|rna2303 373 IATDVAARGLDVKDVQAVINFDFPPNCD-SYIHRIGRTARGNQK 415
                                        899***********99999887755443.345677776666555 PP

>> CMS1  U3-containing 90S pre-ribosomal complex subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   3.2e-06    0.0081     178     209 ..     199     230 ..     192     235 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 3.2e-06
                               CMS1 178 igiavGtpgRildLleeeslsvdeLkrivlDa 209
                                        + + v tpgR++dL+e+++++++ ++++vlD 
  gene2303|gene2303|rna2303|rna2303 199 VEVLVATPGRLIDLMEQGCIHLSRVTYLVLDE 230
                                        567799************************96 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   4.4e-05      0.11      11     113 ..     118     247 ..     115     269 .. 0.63
   2 ?   -1.9   0.0       1.5   3.8e+03     107     128 ..     305     324 ..     286     329 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.4e-05
                             AAA_22  11 tGesGtGKTtllrr..lleqldeeakaee...........erpevvfvtlpsst...sskdllrellralglelka 70 
                                        ++++G+GKT + +   l++ + +++   +           +            +     +++ +e  r+++ +  a
  gene2303|gene2303|rna2303|rna2303 118 IAQTGSGKTISFALpaLVHAAAQVPLRPNdgpialilaptR------------ElcmQIQEVVEEYDRFFNMRSLA 181
                                        57888999887665114444444444444333333333320............22356666666666666655555 PP

                             AAA_22  71 ....................erlsseellealeqalraravielliiDEaqh.lr.s.eealeeLr 113
                                                              ++  +l++++eq + + +++  l++DEa++ l+   e +l+ + 
  gene2303|gene2303|rna2303|rna2303 182 vyggvsafpqrqairrgvevLVATPGRLIDLMEQGCIHLSRVTYLVLDEADRmLDmGfEPQLRSII 247
                                        6666666666666666666666689999999****9999999**********66342455555554 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.5
                             AAA_22 107 ealeeLrsllnlsrkgvqliLv 128
                                        + + +L+s+ln  + ++++i++
  gene2303|gene2303|rna2303|rna2303 305 DKVDNLVSFLN--ENDMKVIVF 324
                                        34467888889..999998876 PP

>> Helicase_C_4  C-terminal domain on Strawberry notch homologue
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   2.8e-05     0.072      55     121 ..     362     420 ..     328     434 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.8e-05
                       Helicase_C_4  55 eaFmdgeKliaiiSeAastGiSlhadrraenqrrRvhitlelpwsadkaiqqlGrthRsnqasaPey 121
                                        + F +g+K+i+i ++ a+ G  ++  +          i ++ p + d+ i+ +Grt R nq ++   
  gene2303|gene2303|rna2303|rna2303 362 NDFKSGRKNILIATDVAARGLDVKDVQ--------AVINFDFPPNCDSYIHRIGRTARGNQKEGLAI 420
                                        68******************9776444........45779*********************987555 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   5.1e-05      0.13      31      84 ..     119     181 ..     111     265 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 5.1e-05
                                        ESTTSTHHHHHHHHHHHH-S............-EEEEESSHHHHHHHH...HHGGGGTGG.... CS
                             ResIII  31 maTGtGKTlvaaklierllkkgkee.......kflflvprkslleqtl...eefkkflseayke 84 
                                        + TG+GKT+ +++l + ++ +++          +l+l+p+++l+ q +   ee+ +f++    +
  gene2303|gene2303|rna2303|rna2303 119 AQTGSGKTI-SFALPALVHAAAQVPlrpndgpIALILAPTRELCMQIQevvEEYDRFFNMRSLA 181
                                        67******6.6777777777766668899999***************97776666666655444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (482 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       632  (0.0352502); expected 358.6 (0.02)
Passed bias filter:                      544  (0.0303419); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.46
# Mc/sec: 3178.41
//
Query:       gene2304|gene2304|rna2304|rna2304  [L=109]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0026   17.6   2.6      0.004   17.0   2.6    1.3  1  DUF5408   Family of unknown function (DUF5408)


Domain annotation for each model (and alignments):
>> DUF5408  Family of unknown function (DUF5408)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   2.6   2.2e-07     0.004       9      34 ..      45      70 ..      37      82 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 2.2e-07
                            DUF5408  9 AkRAvkiALvCvvitlllallslyvL 34
                                       A   + i +vC +i l++a l+l+++
  gene2304|gene2304|rna2304|rna2304 45 ASELIAIIVVCYFIFLIFASLNLWIV 70
                                       66678999*****************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       889  (0.0495845); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.77
# Mc/sec: 425.58
//
Query:       gene2305|gene2305|rna2305|rna2305  [L=230]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    4.7e-28   98.0   0.0    5.3e-28   97.8   0.0    1.1  1  Proteasome  Proteasome subunit


Domain annotation for each model (and alignments):
>> Proteasome  Proteasome subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.8   0.0     3e-32   5.3e-28       3     169 ..      30     188 ..      28     208 .. 0.87

  Alignments for each domain:
  == domain 1  score: 97.8 bits;  conditional E-value: 3e-32
                                        HS-EEEEEEETTEEEEEEEEEEEETTEEEESSSSTSEEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHSSG CS
                         Proteasome   3 kGttvvGikgkdgvvlaadkratagskllskstveKifkiddhigvafaGlaaDartlvrraraeaqlyrlrygrp 78 
                                        kG  ++G+ + dg vla+  + +  + l++ks+v+Ki  ++ ++g++++Gl++D+r+l++++ + ++ y++ yg+ 
  gene2305|gene2305|rna2305|rna2305  30 KGNLSIGLNAADGCVLASL-KPS--DRLIDKSKVTKIVPLSSNLGITYSGLQPDFRVLTNKLLKMVEGYNMVYGK- 101
                                        577789************7.444..6888********************************************96. PP

                                        TCHHHHHHHHHHHHHHHHHHCTTTTTSEEEEEEEEETTTEEEEEEEETTSEEEEESSEEEESTTHHHHHHHHHHHH CS
                         Proteasome  79 ipverlvarvaaklqaytqrsgrrpfgvslliagvdeeggpeLyqidpsGsyieekdavaiGsgseaaktalekey 154
                                        + v++lv+++++ +q+ tq +++rp+g+ ll++g   +++ +L+++dpsGs+ e   ++ iG++  + + ++e++ 
  gene2305|gene2305|rna2305|rna2305 102 MYVDTLVNKISREIQEFTQLGNMRPLGLLLLVCGTTFDNKTKLFSLDPSGSFQEVA-CAGIGKNYSESIRYMERRS 176
                                        77888*******************************9999***************5.******9999******987 PP

                                        STTBSHHHHHHHHHH CS
                         Proteasome 155 kedltleeavelavk 169
                                              e+ + +av 
  gene2305|gene2305|rna2305|rna2305 177 ---EGFEDNLSTAVC 188
                                        ...334444444555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       376  (0.0209716); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 1455.12
//
Query:       gene2306|gene2306|rna2306|rna2306  [L=205]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.6e-37  128.8   0.0    1.8e-37  128.7   0.0    1.0  1  Proteasome  Proteasome subunit


Domain annotation for each model (and alignments):
>> Proteasome  Proteasome subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  128.7   0.0     1e-41   1.8e-37       3     190 .]       8     190 ..       6     190 .. 0.97

  Alignments for each domain:
  == domain 1  score: 128.7 bits;  conditional E-value: 1e-41
                                        HS-EEEEEEETTEEEEEEEEEEEETTEEEESSSSTSEEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHSSG CS
                         Proteasome   3 kGttvvGikgkdgvvlaadkratagskllskstveKifkiddhigvafaGlaaDartlvrraraeaqlyrlrygrp 78 
                                         G++v++++gk+ +++++dkr+  +s+++s++  ++++k++d+++v+++  ++D+++lvr++r+e++l++++++r+
  gene2306|gene2306|rna2306|rna2306   8 YGGSVLALTGKHSAIIVSDKRLGNNSITVSTQ-HDRVYKMSDKVYVGMTLFVPDVQMLVRKLRMEVNLFEIEENRR 82 
                                        599********************888887777.7****************************************** PP

                                        TCHHHHHHHHHHHHHHHHHHCTTTTTSEEEEEEEEETTTEEEEEEEETTSEEEEESSEEEESTTHHHHHHHHHHHH CS
                         Proteasome  79 ipverlvarvaaklqaytqrsgrrpfgvslliagvdeeggpeLyqidpsGsyieekdavaiGsgseaaktalekey 154
                                        i ++    +++++l+ ++++ ++ p  v  ++ag+d +++p+++++d  G+     d++a+G++++  +++ e++y
  gene2306|gene2306|rna2306|rna2306  83 IDPD----EFSSLLSYTLYSHRFSPRFVDPVVAGIDAHDKPYICSMDLLGCQSTSNDFCAVGTAEDKLYGLAEALY 154
                                        ****....********************************************99999******************* PP

                                        STTBSHHHHHHHHHHHHHHHHHHBTTSCSSEEEEEE CS
                         Proteasome 155 kedltleeavelavkalkealerdklsgknievavi 190
                                         +d++++e++ +a ++  +a++rd+lsg+++e  +i
  gene2306|gene2306|rna2306|rna2306 155 VPDMNDDELFVTAMQIFLNAVDRDALSGWGAEAHII 190
                                        ******************************998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (205 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       442  (0.0246528); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1482.07
//
Query:       gene2307|gene2307|rna2307|rna2307  [L=78]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.022   14.2   0.8      0.023   14.1   0.8    1.1  1  DNA_primase_lrg  Eukaryotic and archaeal DNA primase, large s
      0.025   14.8   0.8      0.033   14.5   0.8    1.2  1  Med21            Subunit 21 of Mediator complex
       0.03   14.6   3.6      0.032   14.5   2.5    1.6  2  Mrx7             MIOREX complex component 7
      0.047   13.8   1.0       0.05   13.7   1.0    1.1  1  IFNGR1           Interferon gamma receptor (IFNGR1)
       0.16   11.3   0.0       0.17   11.2   0.0    1.1  1  DUF3482          Domain of unknown function (DUF3482)
       0.31   11.8   5.9          1   10.2   5.9    1.9  1  KMP11            Kinetoplastid membrane protein 11
        1.5    8.9   7.4        2.4    8.2   7.3    1.5  2  DUF3671          Protein of unknown function
        2.3    8.5  10.1       0.22   11.8   5.8    1.5  2  TPX2             Targeting protein for Xklp2 (TPX2)


Domain annotation for each model (and alignments):
>> DNA_primase_lrg  Eukaryotic and archaeal DNA primase, large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.8     1e-05     0.023      27      76 ..      21      70 ..       6      77 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1e-05
                                       EE-HHHHHHHHHHHHHHHHHH..........HHGGGSSS---HHHHHHHC CS
                    DNA_primase_lrg 27 ylpkeeleslllekfrkrlekalestkeslpeleeeikederekleelle 76
                                       +++k  ++ +++ +f  +++++++++ke++ +lee+i++ +++  +++ e
  gene2307|gene2307|rna2307|rna2307 21 IVKKFAAIDVIIDEFDTKIYEKINEIKEYRNNLEESIRKFKEKRNKKMRE 70
                                       68899999***********************9966666555544444433 PP

>> Med21  Subunit 21 of Mediator complex
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.8   1.5e-05     0.033      67     129 ..       9      72 ..       4      78 .] 0.78

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.5e-05
                              Med21  67 efaatqrelardlilkeqqIeyLIssLPg.igsseeeqeerikeLeeelreveeereekvkeke 129
                                        e +++ +  a+ +++k  +I+++I++  + i ++ +e +e  ++Lee +r+ +e+r++k++e  
  gene2307|gene2307|rna2307|rna2307   9 EREENGKGYATEIVKKFAAIDVIIDEFDTkIYEKINEIKEYRNNLEESIRKFKEKRNKKMREIY 72 
                                        567777889****************986425556666666667899999999999999999865 PP

>> Mrx7  MIOREX complex component 7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       1.1   2.6e+03      36      54 ..       9      27 ..       4      37 .. 0.61
   2 ?   14.5   2.5   1.4e-05     0.032      19      53 ..      37      69 ..      32      74 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1.1
                               Mrx7 36 ekqesellykptrrqklka 54
                                       e++e+++ y  +  +k+ a
  gene2307|gene2307|rna2307|rna2307  9 EREENGKGYATEIVKKFAA 27
                                       4555666666666666665 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 1.4e-05
                               Mrx7 19 rkihakvngiketeiseekqesellykptrrqklk 53
                                        ki++k+n+ike    ++ +es  ++k++r +k++
  gene2307|gene2307|rna2307|rna2307 37 TKIYEKINEIKEYR--NNLEESIRKFKEKRNKKMR 69
                                       79********9998..4567888999999999987 PP

>> IFNGR1  Interferon gamma receptor (IFNGR1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   1.0   2.2e-05      0.05      63     125 ..      17      77 ..       4      78 .] 0.78

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.2e-05
                                        -B-----EEEEE-XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             IFNGR1  63 vrtekskevCvpelvvslvdiyyiKkindlkrkkiilkksleskvksatsetkleskYslits 125
                                        + te  k+     ++  ++d+ +  kin++k+ ++ l++s+  k+k++ + +k+ + Y+++ s
  gene2307|gene2307|rna2307|rna2307  17 YATEIVKKFAAIDVIIDEFDTKIYEKINEIKEYRNNLEESIR-KFKEKRN-KKMREIYDIVSS 77 
                                        56666666555556778899999****************886.5666555.6999****9988 PP

>> DUF3482  Domain of unknown function (DUF3482)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   7.7e-05      0.17      11      65 ..      21      75 ..      17      78 .] 0.83

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 7.7e-05
                            DUF3482 11 avreFDavaaefee.elrLyesLatLleekreaLqrliealeeqrqarreeaaeli 65
                                       +v +F a+ + ++e   ++ye++++++e  r++L++ i++++e+r++ ++e   ++
  gene2307|gene2307|rna2307|rna2307 21 IVKKFAAIDVIIDEfDTKIYEKINEIKEY-RNNLEESIRKFKEKRNKKMREIYDIV 75
                                       677788888887775689********998.****************9998876666 PP

>> KMP11  Kinetoplastid membrane protein 11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   5.9   0.00045         1      42      69 ..      44      71 ..       5      76 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00045
                              KMP11 42 pemkehyekfekmikehtekfnkkmreh 69
                                        e+ke+ +++e  i++  ek nkkmre 
  gene2307|gene2307|rna2307|rna2307 44 NEIKEYRNNLEESIRKFKEKRNKKMREI 71
                                       699***********************95 PP

>> DUF3671  Protein of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       1.5   3.3e+03      33      46 ..      14      27 ..       6      32 .. 0.61
   2 ?    8.2   7.3    0.0011       2.4      12      44 ..      36      68 ..      23      76 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1.5
                            DUF3671 33 kkkfkkkvlkkygl 46
                                        k +   ++kk++ 
  gene2307|gene2307|rna2307|rna2307 14 GKGYATEIVKKFAA 27
                                       45555666777654 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0011
                            DUF3671 12 EKkiFdkidkidelakkknndkkkfkkkvlkky 44
                                       + ki++ki++i+e +++ + + +kfk+k+ kk+
  gene2307|gene2307|rna2307|rna2307 36 DTKIYEKINEIKEYRNNLEESIRKFKEKRNKKM 68
                                       67*****************************97 PP

>> TPX2  Targeting protein for Xklp2 (TPX2)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.1       3.6   8.2e+03      40      41 ..      10      11 ..       6      16 .. 0.44
   2 ?   11.8   5.8   9.9e-05      0.22      12      48 ..      34      70 ..      33      72 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 3.6
                               TPX2 40 ee 41
                                       +e
  gene2307|gene2307|rna2307|rna2307 10 RE 11
                                       11 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 9.9e-05
                               TPX2 12 eFdkkleekekakeaekeereakkkeeeeeeikqLRk 48
                                       eFd k+ ek ++ +++++++e+  +  +e+ +k++R 
  gene2307|gene2307|rna2307|rna2307 34 EFDTKIYEKINEIKEYRNNLEESIRKFKEKRNKKMRE 70
                                       9*************************99******995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2508  (0.139885); expected 358.6 (0.02)
Passed bias filter:                     1061  (0.0591779); expected 358.6 (0.02)
Passed Vit filter:                       136  (0.00758548); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.44u 0.31s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 525.05
//
Query:       gene2308|gene2308|rna2308|rna2308  [L=227]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00054   18.3   0.2    0.00064   18.1   0.2    1.0  1  Virul_Fac        Putative bacterial virulence factor
  ------ inclusion threshold ------
      0.052   13.1   3.6      0.062   12.8   3.6    1.1  1  UvrD-helicase    UvrD/REP helicase N-terminal domain
       0.12   12.6   5.3       0.07   13.3   3.2    1.6  2  RNase_H2-Ydr279  Ydr279p protein family (RNase H2 complex com


Domain annotation for each model (and alignments):
>> Virul_Fac  Putative bacterial virulence factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.2   1.1e-07   0.00064     610     750 ..      58     202 ..      45     222 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.1e-07
                          Virul_Fac 610 tlekaklfgelLkaLqvseetlrelylreeeveeeakeeaeaeavadeavaaaletaapaaa.ldlfsdaaaaaaa 684
                                         ++++  fg +L++++  ++++++ +l+ e v e+ ++++++   a  ++ ++++t  + +  +++ +  +++a  
  gene2308|gene2308|rna2308|rna2308  58 FKNRTLFFGVILANMCDMKKEVKKFILSCEPVFENFRKQENDCLSAVINTIDDFTTIMMRKLrYEVKESRENDALR 133
                                        4577889*********************888777777777766656666666666555444465555554444444 PP

                          Virul_Fac 685 aaa...paakaeeqarksaeeefaeavleeWiehLralsedaellaalglskeaveelvdElitaaeRl 750
                                          +   ++++++ +   +++++f e+ l++ +e + ++ +d+++++ + lsk  +e+lv+E+i  +e +
  gene2308|gene2308|rna2308|rna2308 134 YMKdifDSTQDTLEYIVKNKSRFEETSLNKLTECMNKVIDDKQMMKDIILSKVHAENLVEEIIKRVEQF 202
                                        433001344444455567789******************************************877654 PP

>> UvrD-helicase  UvrD/REP helicase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   3.6     1e-05     0.062      80     198 ..      87     211 ..      53     225 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1e-05
                                        H....HHHHHHHHCTTSEEEEHHHHHHHHHHHHHGGTTSHTTTEEECHHHHHHCCHHHHHHHHHSCHSHTTTTHHH CS
                      UvrD-helicase  80 e....rlrlalqnlseanisTlHsfcqkilkkeanrigldpnfrildeedeedlkqqellkelleksaddslnldk 151
                                        e     +r++++ +  a i T++ f+  +++k  ++++  ++ + l++ +     +q  l+ +++ ++   ++++ 
  gene2308|gene2308|rna2308|rna2308  87 EpvfeNFRKQENDCLSAVINTIDDFTTIMMRKLRYEVKESRENDALRYMKDIFDSTQDTLEYIVK-NKSRFEETSL 161
                                        2445588999****************************666666666666555566677777776.3333345555 PP

                                        HHHHHHHHHHHCCCCCH...HHHCCCHHHHHCHHHHHHHHHHHTTCCTTH CS
                      UvrD-helicase 152 kkleklikelsksrnik...keelslskskaeelrelvskakekqlspke 198
                                        +kl + + +++ ++++    +  ++ +++  ee+ + v+++k+  ++  +
  gene2308|gene2308|rna2308|rna2308 162 NKLTECMNKVIDDKQMMkdiILSKVHAENLVEEIIKRVEQFKQHIIKLSD 211
                                        55555545555555554566677888888888888888888887666555 PP

>> RNase_H2-Ydr279  Ydr279p protein family (RNase H2 complex component) wHTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0      0.61   3.6e+03      57      77 ..      69      87 ..      53     114 .. 0.65
   2 ?   13.3   3.2   1.2e-05      0.07      23      96 ..     135     209 ..     115     220 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.61
                    RNase_H2-Ydr279 57 laaiCdtveegdetmYrlsee 77
                                       la+ Cd ++e   + + ls+e
  gene2308|gene2308|rna2308|rna2308 69 LANMCDMKKE--VKKFILSCE 87
                                       6777887775..333444443 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 1.2e-05
                    RNase_H2-Ydr279  23 ldDlldslaessedlsellkler..sdiprslleerlaaiCdtve.egdetmYrlseekllefLlsKverladeag 95 
                                        ++D++ds+++    l+ + k+++   +++ + l e+++++ d ++   d  + ++  e l+e+++++ve++ +++ 
  gene2308|gene2308|rna2308|rna2308 135 MKDIFDSTQD---TLEYIVKNKSrfEETSLNKLTECMNKVIDDKQmMKDIILSKVHAENLVEEIIKRVEQFKQHII 207
                                        78********...9*****999987777888899999999999996669999*******************98875 PP

                    RNase_H2-Ydr279  96 .l 96 
                                         l
  gene2308|gene2308|rna2308|rna2308 208 kL 209
                                        43 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (227 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1561  (0.0870656); expected 358.6 (0.02)
Passed bias filter:                      518  (0.0288917); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1624.50
//
Query:       gene2309|gene2309|rna2309|rna2309  [L=101]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       921  (0.0513693); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 697.85
//
Query:       gene231|gene231|rna231|rna231  [L=307]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        4.3    6.6   9.1        1.1    8.5   3.0    2.2  2  UPF0014   Uncharacterised protein family (UPF0014)


Domain annotation for each model (and alignments):
>> UPF0014  Uncharacterised protein family (UPF0014)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   3.0   6.2e-05       1.1      30      91 ..      91     154 ..      85     184 .. 0.70
   2 ?    1.4   0.4    0.0092   1.6e+02      56     101 ..     221     268 ..     203     301 .. 0.64

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 6.2e-05
                        UPF0014  30 liaavrmvvQLllvGyvLklifalnsl..llvllillvmllvAaieaakrvkkklkklllivll 91 
                                    l+a++rm v  ll+ y+L ++f  + +  +++++ ll+++ +++    +  k+k  +++++  +
  gene231|gene231|rna231|rna231  91 LVATFRMDVPRLLIDYLLYFLFYYKLFvfWMIMITLLFIVQLSILRCNNNWKRKAIHFFMLPCI 154
                                    68********************988651155555566667777778888888777777773333 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.0092
                        UPF0014  56 lllvllillvmllvAai..eaakrvkkklkklllivllsllvstlltl 101
                                    +++ l+ ++++  vA+i  +  ++ +k+++++l  vl ++++ ++l  
  gene231|gene231|rna231|rna231 221 FIALLITVFMLDSVASIigTYLEKKGKSIQGMLSGVLSAIVLHYMLFR 268
                                    444444444445677765677788899999999999988888877643 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (307 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       911  (0.0508115); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 1949.87
//
Query:       gene2310|gene2310|rna2310|rna2310  [L=466]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.3e-15   56.3   0.1    9.4e-12   45.0   0.1    2.4  2  His_Phos_2  Histidine phosphatase superfamily (branch 2)
  ------ inclusion threshold ------
       0.15   11.7   0.0        3.1    7.4   0.0    2.4  2  His_Phos_1  Histidine phosphatase superfamily (branch 1)


Domain annotation for each model (and alignments):
>> His_Phos_2  Histidine phosphatase superfamily (branch 2)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.0   0.1     1e-15   9.4e-12       1     177 [.      40     213 ..      40     362 .. 0.72
   2 !    9.4   0.0   6.8e-05      0.61     352     383 .]     397     426 ..     373     426 .. 0.83

  Alignments for each domain:
  == domain 1  score: 45.0 bits;  conditional E-value: 1e-15
                                        EEEEEEEEEE--SBB-SHHHHHHHHHHHHHHHH.........HHCHHTGCCGGGGT..................-- CS
                         His_Phos_2   1 eLksvvvviRHGdRtPkqkvkksvtspiflsllkkhkeKlkqlktalekkghfpgtyrkv.........eveklql 67 
                                        +Lk+v+v+ RHGdR P ++  k+      ++            + a  ++ ++ ++ +           + +k+  
  gene2310|gene2310|rna2310|rna2310  40 KLKKVIVLHRHGDRMPLKTYGKEKGVCVRCDV----------RRRASRMNVDWAKDRNEPwyddrtdtySMQKCRI 105
                                        69******************965555555444..........58999999999999988899999999999***** PP

                                        SSSTTS.B-HHHHHHHHHHHHHHHHHCHTCCHTTSS--TTEEEEEESSHHHHHHHHHHHHHHCHCCC---S-TTST CS
                         His_Phos_2  68 ilkwggelthaGrkqaeelGrqfrqrYplgLlrlhltykdlkirassegRviaSAaafakGllglegeltdllskd 143
                                           ++g lt  G++q+++lGr ++  Y   L   +l   d+ +ra+  +R+  S   ++ G+++++  +  + ++ 
  gene2310|gene2310|rna2310|rna2310 106 SKCTDGTLTVKGYNQMRRLGRFIKDEYIPRLGHVRL--TDINFRATAVKRTHSSLSGVVSGMFEEDRMNVREEEVN 179
                                        ************************888735555555..9************************8888666444444 PP

                                        TGGG-TTTTCCCEEEHHHHCCCCHHCTTSHHTCH CS
                         His_Phos_2 144 kdllddsnaakdlldeakkklkelltegaeacpa 177
                                           ++ +n+  d+ +++++ l+   ++ +e+++ 
  gene2310|gene2310|rna2310|rna2310 180 AFSSWMENDGEDIGPDDDSPLNADGIQEREDTAY 213
                                        4444444444444444333333333333333333 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 6.8e-05
                                        .HCCCS-CT-EEEEEEEEETCTTTEEEEEEEC CS
                         His_Phos_2 352 saspelpymsqivfelyedssekkfyvrllls 383
                                        + ++ +p +s i++e++e  ++ ++yvr+l++
  gene2310|gene2310|rna2310|rna2310 397 RVIERPPLASAIFIEVWE--NKGDKYVRVLFN 426
                                        5567799***********..77779*****98 PP

>> His_Phos_1  Histidine phosphatase superfamily (branch 1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.0   0.00035       3.1      15      45 ..     103     133 ..      95     140 .. 0.86
   2 ?    1.4   0.0     0.025   2.2e+02      12      36 ..     187     211 ..     181     222 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.00035
                                        ....TT----B-HHHHHHHHHHHHHHTTS-- CS
                         His_Phos_1  15 grlqgrtdvpLteeGreqAealaerlagepi 45 
                                         r+++ td  Lt +G+ q+++l++++++e i
  gene2310|gene2310|rna2310|rna2310 103 CRISKCTDGTLTVKGYNQMRRLGRFIKDEYI 133
                                        5688999*******************99765 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.025
                                        B--....TT----B-HHHHHHHHHH CS
                         His_Phos_1  12 naegrlqgrtdvpLteeGreqAeal 36 
                                        n  + ++   d+pL+++G+++ e +
  gene2310|gene2310|rna2310|rna2310 187 NDGEDIGPDDDSPLNADGIQEREDT 211
                                        4444588899*********987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (466 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       604  (0.0336884); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 3062.70
//
Query:       gene2311|gene2311|rna2311|rna2311  [L=36]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (36 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       228  (0.0127168); expected 358.6 (0.02)
Passed bias filter:                      202  (0.0112667); expected 358.6 (0.02)
Passed Vit filter:                         7  (0.000390429); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.34s 00:00:00.82 Elapsed: 00:00:00.54
# Mc/sec: 201.84
//
Query:       gene2312|gene2312|rna2312|rna2312  [L=100]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-10   41.6   3.7    1.6e-10   41.5   3.7    1.1  1  Ribosomal_60s  60s Acidic ribosomal protein
  ------ inclusion threshold ------
      0.017   15.4   0.1      0.034   14.5   0.1    1.6  1  DUF1456        Protein of unknown function (DUF1456)
      0.058   11.4   0.1      0.059   11.3   0.1    1.1  1  MTTB           Trimethylamine methyltransferase (MTTB)
       0.22   11.2   0.1       0.75    9.5   0.0    1.8  2  HTH_33         Winged helix-turn helix


Domain annotation for each model (and alignments):
>> Ribosomal_60s  60s Acidic ribosomal protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.5   3.7   3.5e-14   1.6e-10       1      84 [.      16      95 ..      16     100 .] 0.80

  Alignments for each domain:
  == domain 1  score: 41.5 bits;  conditional E-value: 3.5e-14
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XX CS
                      Ribosomal_60s  1 eptaenikkvlkaagveveaarvkllvkalegkdieellangaaklaaaaaaaaaaaaaaaaaaaaeekkkeeeeeEe 78
                                       e+t+++i +++ +ag+e ++  v+ +++ l gk+i+e++a+g   ++++   + a  aa++++ + eek ke+++   
  gene2312|gene2312|rna2312|rna2312 16 EITKQSISELIRKAGAEPQDDEVENFLTKLDGKNIQEAIAEGLGMMQSV--ESRANPAAKEEEVEVEEKSKEPPKP-- 89
                                       69****************************************9997544..4555556677777777788887774.. PP

                                       --SS-- CS
                      Ribosomal_60s 79 edddmG 84
                                        d d  
  gene2312|gene2312|rna2312|rna2312 90 ADTDVD 95
                                       555544 PP

>> DUF1456  Protein of unknown function (DUF1456)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1   7.5e-06     0.034      12      49 ..      15      52 ..       4      63 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 7.5e-06
                            DUF1456 12 LdlkdedmveifklggvevtkeelsalLkkedeegyee 49
                                       L+++++ + e+++++g e + +e++++L+k d ++++e
  gene2312|gene2312|rna2312|rna2312 15 LEITKQSISELIRKAGAEPQDDEVENFLTKLDGKNIQE 52
                                       78999999999999999999999999999988888876 PP

>> MTTB  Trimethylamine methyltransferase (MTTB)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   1.3e-05     0.059      47      79 ..       7      39 ..       4      83 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 1.3e-05
                               MTTB 47 lriLeeiGiefldpealellkaaGakvegervr 79
                                         iL+e G+e+ ++++ el+++aGa+ +++ v+
  gene2312|gene2312|rna2312|rna2312  7 SLILNEAGLEITKQSISELIRKAGAEPQDDEVE 39
                                       569**********************99776653 PP

>> HTH_33  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0   0.00017      0.75       8      39 ..       3      34 ..       2      35 .. 0.93
   2 ?   -2.0   0.2      0.65   2.9e+03      44      54 ..      67      78 ..      62      82 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00017
                             HTH_33  8 arlaqlieerfgvsysvsgvyrlLkrlGfsyq 39
                                       a la li  + g++++++++++l +++G  +q
  gene2312|gene2312|rna2312|rna2312  3 AILASLILNEAGLEITKQSISELIRKAGAEPQ 34
                                       77999***********************9887 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.65
                             HTH_33 44 ra.pkqdpeaqe 54
                                       ra p + +e++e
  gene2312|gene2312|rna2312|rna2312 67 RAnPAAKEEEVE 78
                                       444777888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       935  (0.0521501); expected 358.6 (0.02)
Passed bias filter:                      663  (0.0369792); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.56u 0.37s 00:00:00.93 Elapsed: 00:00:00.54
# Mc/sec: 554.77
//
Query:       gene2313|gene2313|rna2313|rna2313  [L=101]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.13   12.4   3.2       0.98    9.6   0.1    2.3  2  HR1       Hr1 repeat


Domain annotation for each model (and alignments):
>> HR1  Hr1 repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.5    0.0048        86      20      52 ..       8      41 ..       7      48 .. 0.59
   2 ?    9.6   0.1   5.4e-05      0.98       7      25 ..      62      80 ..      59      98 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.0048
                                HR1 20 enllralesk.ktqnkkvrqeaeselsesnskie 52
                                       e++l+ le   ++ +  +r+ a+ +++  ++ki+
  gene2313|gene2313|rna2313|rna2313  8 EKMLESLEALlPKLSGVQRESAQYRIKMLKNKIS 41
                                       5666666655555555566666666666666664 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 5.4e-05
                                HR1  7 kklekElkireGAenllra 25
                                       +kl+kE++++eG ++++++
  gene2313|gene2313|rna2313|rna2313 62 QKLKKENNLIEGYNKIMSV 80
                                       89*************9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1296  (0.0722851); expected 358.6 (0.02)
Passed bias filter:                      515  (0.0287244); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.37s 00:00:00.92 Elapsed: 00:00:00.55
# Mc/sec: 554.16
//
Query:       gene2314|gene2314|rna2314|rna2314  [L=575]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      2e-57  194.5   0.0    2.9e-57  194.0   0.0    1.2  1  Pkinase         Protein kinase domain
      3e-37  128.3   0.0    4.9e-37  127.6   0.0    1.2  1  Pkinase_Tyr     Protein tyrosine kinase
    3.5e-10   39.6  23.1    4.8e-05   23.2   7.6    2.6  2  C1_1            Phorbol esters/diacylglycerol binding domain 
    0.00024   20.2   0.3    0.00038   19.5   0.3    1.2  1  Haspin_kinase   Haspin like kinase domain
     0.0015   17.9   0.0     0.0046   16.3   0.0    1.8  1  Kinase-like     Kinase-like
     0.0017   18.6  20.3      0.013   15.8   7.4    2.8  2  C1_2            C1 domain
  ------ inclusion threshold ------
      0.017   14.8   0.6      0.017   14.8   0.6    3.6  3  zf-RRN7         Zinc-finger of RNA-polymerase I-specific TFII
       0.63   10.1  20.0      0.035   14.1   7.2    2.6  2  DZR             Double zinc ribbon
        1.5    9.2  22.5        2.5    8.5   7.7    2.5  2  zf-RING-like    RING-like domain
          4    7.4  22.5        7.8    6.5   8.2    2.6  2  PHD             PHD-finger


Domain annotation for each model (and alignments):
>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  194.0   0.0   1.6e-60   2.9e-57       2     254 ..     292     533 ..     291     548 .. 0.89

  Alignments for each domain:
  == domain 1  score: 194.0 bits;  conditional E-value: 1.6e-60
                                        EEEEEEEEESSEEEEEEEETTTTEEEEEEEEECHCHCHHHH.HHHHHHHHHHHHHS...CTTB--EEEEEEESSEE CS
                            Pkinase   2 ekleklGeGsfGkVykaveketgkivAvKkikkekakkkke.kkvlrEikilkklk...hpnivrlyevfeekdel 73 
                                        + ++ lG+G+fGkV+ a+  +++  vA+K++kke + ++++ + +  E +ilk ++   hp++++++++f++++++
  gene2314|gene2314|rna2314|rna2314 292 SLVKVLGRGAFGKVMLAK--KNHTLVAMKILKKEVIVNSNNiHYLDLERHILKLVSeanHPFLMKMLYCFQDEQNV 365
                                        56799************9..7999**************999545556999999887778***************** PP

                                        EEEEE--TTEBHHHHHHHHSS--HHHHHHHHHHHHHHHHHHHHTTEE-SS-SGGGEEEETTTEEEE-SGTTSEESS CS
                            Pkinase  74 ylvleyveggeladllerkgslseeeakkiakqilegleylHskgiiHrDlKpeNiLidekgelKitDFGlakele 149
                                        y+ +e++ gg+l+++     ++++e++k ++ +il gle+lH+k+ii+rD+K +N+Li  +g++Ki+DFGl+k   
  gene2314|gene2314|rna2314|rna2314 366 YFGTEFLAGGDLFHYAA-THKFTHEQIKLYVCEILLGLEFLHAKNIIYRDMKLDNVLICADGHVKIADFGLCKDNI 440
                                        **************997.588***************************************************9877 PP

                                        SSCS.BCTTTSCGGGS-HHHHTTSCBSHHHHHHHHHHHHHHHHHSS-STTTSSHHHHHHHHHHTHHHHHHHCTSHH CS
                            Pkinase 150 sssk.ltsfvgtseYlAPEvlkeneyskkvDvWslGvilyelltgkppfsgekgkekvekeldqlekilkilgetk 224
                                           + + +f+gt + +APEv+ + +y+k +D+Ws Gv++ye++ ++ pf+g++++e +++e+ q            
  gene2314|gene2314|rna2314|rna2314 441 GPDTmTYTFCGTADTIAPEVILGGGYTKDADWWSFGVVIYEMYENECPFNGSTTEE-ISAEILQ------------ 503
                                        7666599*******************************************666655.2223333............ PP

                                        ...HHHTTS-HHHHHHHHHHT-SSGCCSTT CS
                            Pkinase 225 eklpeaseiseeakdllkkllkkdpkkRlt 254
                                           +  ++ ++ea+dl+ kll++dp++Rl+
  gene2314|gene2314|rna2314|rna2314 504 TMPKFTENTPSEAQDLILKLLTRDPSERLG 533
                                        356788899*******************98 PP

>> Pkinase_Tyr  Protein tyrosine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  127.6   0.0   2.7e-40   4.9e-37       3     249 ..     293     531 ..     291     534 .. 0.85

  Alignments for each domain:
  == domain 1  score: 127.6 bits;  conditional E-value: 2.7e-40
                                        EEEEEEEESSEEEEEEEEETTTTSSEEEEEEEEESTTSSHHH....HHHHHH.HHHHHHTS-BTTB--EEEEEESS CS
                        Pkinase_Tyr   3 lgkklGeGafGkVvegtlkgekekkevkVavKtlkeeateee....keelle.eakimkklkhpnivkllgvctke 73 
                                        l k lG+GafGkV+ ++ +      ++ Va+K+lk+e   ++      +l +  +k+ ++ +hp ++k+l +  +e
  gene2314|gene2314|rna2314|rna2314 293 LVKVLGRGAFGKVMLAKKN------HTLVAMKILKKEVIVNSnnihYLDLERhILKLVSEANHPFLMKMLYCFQDE 362
                                        7899***********9988......8999999998754332211113444442345556779************** PP

                                        SSEEEEEE--TTEBHHHHHHHTCTTTSBHHHHHHHHHHHHHHHHHHHHTTEEEST-SGGGEEEEETTEEEE-STTT CS
                        Pkinase_Tyr  74 epllivteyvkgGdLlkfLrkkekekltlkdllsfalqvAkGmeyLeskklvHrdlaarNvLlsenkvvkisDfGL 149
                                        +++++ te+++gGdL ++  ++   k+t +++  ++ ++  G+e+L++k+++ rd+   NvL++ + +vki+DfGL
  gene2314|gene2314|rna2314|rna2314 363 QNVYFGTEFLAGGDLFHYAATH---KFTHEQIKLYVCEILLGLEFLHAKNIIYRDMKLDNVLICADGHVKIADFGL 435
                                        ******************9998...9************************************************** PP

                                        HEETTTSSEEEETTSSTSGGGGS-HHHHHHSEEEHHHHHHHHHHHHHHHHTTSSGTTTTSHHHHHHHHHHTTEES- CS
                        Pkinase_Tyr 150 ardiekddeyvkkeeaklpvkWmapEslkekkftsksDvWsfGvllwEiftlgespypglkneevleklkegkrle 225
                                        ++d    d++  + +       +apE++  + +t+ +D WsfGv+++E+++  e p++g ++ee+ + + +    +
  gene2314|gene2314|rna2314|rna2314 436 CKDNIGPDTM--TYTFCGTADTIAPEVILGGGYTKDADWWSFGVVIYEMYE-NECPFNGSTTEEISAEILQT-MPK 507
                                        **99544444..34444566779***************************9.9***********99999654.345 PP

                                        BBTTSBHHHHHHHHHHT-SSGGGS CS
                        Pkinase_Tyr 226 kpekcpeelyelmkkcweedpeeR 249
                                          e++p+e ++l+ k +++dp+eR
  gene2314|gene2314|rna2314|rna2314 508 FTENTPSEAQDLILKLLTRDPSER 531
                                        66788****************999 PP

>> C1_1  Phorbol esters/diacylglycerol binding domain (C1 domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   7.5   6.7e-08   0.00012       5      50 ..     149     192 ..     145     195 .. 0.87
   2 !   23.2   7.6   2.7e-08   4.8e-05       5      52 ..     215     261 ..     211     262 .. 0.88

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 6.7e-08
                                        EE--SS--B-TTT-SB--SSSS-EEEETTT--EE-CCCCTTS-SBT CS
                               C1_1   5 hrnfkqptfCkhCgeflwgkekqglkCswCkllvHkkChekvpkec 50 
                                          ++  p +C+ C+++    ++ +++C  C++++HkkC + +   c
  gene2314|gene2314|rna2314|rna2314 149 NYKTITPFYCAVCNNIA--TFMDAYRCYKCRITCHKKCSNYILFYC 192
                                        55667889*********..********************9998888 PP

  == domain 2  score: 23.2 bits;  conditional E-value: 2.7e-08
                                        EE--SS--B-TTT-SB--SSSS-EEEETTT--EE-CCCCTTS-SBTTC CS
                               C1_1   5 hrnfkqptfCkhCgeflwgkekqglkCswCkllvHkkChekvpkecgc 52 
                                        + n++   +C+hCg  + +++  +  C+ C++++H+ C++ +pk+cg 
  gene2314|gene2314|rna2314|rna2314 215 DENASGFRYCNHCGTRI-RLGEMCKVCRKCNERFHETCASFLPKSCGI 261
                                        566667789********.9999************************85 PP

>> Haspin_kinase  Haspin like kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.3   2.1e-07   0.00038      90     262 ..     281     444 ..     261     452 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 2.1e-07
                      Haspin_kinase  90 lckikkilneadlasllndseklssevyqtkekdkevvlKviplevledvtiskelsl.kelkslklvkgtypgll 164
                                        +  ik+ + + +l+++l  +++ +++v  +k++++ v++K++  ev+ + +  +   l  e + lklv  +  +++
  gene2314|gene2314|rna2314|rna2314 281 KAAIKYEISDFSLVKVL--GRGAFGKVMLAKKNHTLVAMKILKKEVIVNSNNIHY--LdLERHILKLVSEA--NHP 350
                                        45566666555555444..8899******************99877755544444..445889*******9..9** PP

                      Haspin_kinase 165 lllqdkvlkekpdfyseqqlflvlllkdkGtdLeevklkswkqalsifwqivkiLyvaE..tkfeFEHRdLhldni 238
                                        +l++  +  ++     eq+++   ++  +G dL +   +   +  +i   + +iL   E   + +   Rd++ldn+
  gene2314|gene2314|rna2314|rna2314 351 FLMKMLYCFQD-----EQNVYFGTEFLAGG-DLFHYAATHKFTHEQIKLYVCEILLGLEflHAKNIIYRDMKLDNV 420
                                        ****9999998.....99999999997655.7888888888888899888999999999333446789******** PP

                      Haspin_kinase 239 LvdknlnvtlidlklsRlessegk 262
                                        L+ + ++v + d+ l++ +   ++
  gene2314|gene2314|rna2314|rna2314 421 LICADGHVKIADFGLCKDNIGPDT 444
                                        **************9987754444 PP

>> Kinase-like  Kinase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   2.6e-06    0.0046     159     288 .]     404     531 ..     376     531 .. 0.67

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 2.6e-06
                        Kinase-like 159 nLqakglvhgkftvdnllldekgglmlggftaLvrag.....tkvvlsevekgfaPpEllgsrggytrknktkmth 229
                                         L+ak ++  +++ dn+l   +g +++ +f+ L ++        +    ++ + aP  +lg   g        +t 
  gene2314|gene2314|rna2314|rna2314 404 FLHAKNIIYRDMKLDNVLICADGHVKIADFG-LCKDNigpdtMTYTFCGTADTIAPEVILGG--G--------YTK 468
                                        5788888888888888888888888888886.444321111123333444466666555554..4........667 PP

                        Kinase-like 230 kldaWqlGlviyriwclklPltlat.eeakeew...kfklckkipekvkaLlkkfLqlsqedR 288
                                          d W  G+viy ++  + P++  t ee++ e      k  ++ p + + L+ k+L ++  +R
  gene2314|gene2314|rna2314|rna2314 469 DADWWSFGVVIYEMYENECPFNGSTtEEISAEIlqtMPKFTENTPSEAQDLILKLLTRDPSER 531
                                        89******************9876515666663333222345788889999999999887665 PP

>> C1_2  C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   7.4   7.2e-06     0.013      17      47 .]     154     185 ..     142     185 .. 0.81
   2 !    7.7   5.0    0.0025       4.6      12      47 .]     215     252 ..     204     252 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 7.2e-06
                               C1_2  17 esfnCsaCgrkidgff..YsCseCdfslhvrCa 47 
                                          f C +C +    f+  Y+C +C+++ h++C+
  gene2314|gene2314|rna2314|rna2314 154 TPFYCAVCNNIA-TFMdaYRCYKCRITCHKKCS 185
                                        4599****9994.55568**************6 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0025
                               C1_2  12 gedssesfnCsaCgrk..idgffYsCseCdfslhvrCa 47 
                                        +e+ s+ + C+ Cg+     +++  C +C+  +h++Ca
  gene2314|gene2314|rna2314|rna2314 215 DENASGFRYCNHCGTRirLGEMCKVCRKCNERFHETCA 252
                                        56889999********754344499*99*********8 PP

>> zf-RRN7  Zinc-finger of RNA-polymerase I-specific TFIIB, Rrn7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.2      0.22   3.9e+02       7      13 ..     158     165 ..     156     167 .. 0.77
   2 ?   14.8   0.6   9.4e-06     0.017      18      30 ..     218     230 ..     215     231 .. 0.84
   3 ?   -1.3   0.8         1   1.8e+03       6      11 ..     239     244 ..     234     249 .. 0.59

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.22
                            zf-RRN7   7 CgvCgc.r 13 
                                        C+vC++  
  gene2314|gene2314|rna2314|rna2314 158 CAVCNNiA 165
                                        99999854 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 9.4e-06
                            zf-RRN7  18 ddGfyyCrrChtq 30 
                                        + Gf+yC++C+t 
  gene2314|gene2314|rna2314|rna2314 218 ASGFRYCNHCGTR 230
                                        78**********7 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 1
                            zf-RRN7   6 pCgvCg 11 
                                        +C  C+
  gene2314|gene2314|rna2314|rna2314 239 VCRKCN 244
                                        455555 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   4.9      0.24   4.2e+02      13      43 ..     156     185 ..     142     192 .. 0.79
   2 ?   14.1   7.2     2e-05     0.035       7      43 ..     216     252 ..     214     260 .. 0.78

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.24
                                DZR  13 rfCseCgtklkavaaedrCpsCgekvdpear 43 
                                         +C  C++      +++rC +C   ++++++
  gene2314|gene2314|rna2314|rna2314 156 FYCAVCNNIAT-FMDAYRCYKCRITCHKKCS 185
                                        58888887653.5558999999999888875 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 2e-05
                                DZR   7 elppdarfCseCgtklkavaaedrCpsCgekvdpear 43 
                                        e+ ++ r+C++Cgt+++  +  ++C +C+e  +++++
  gene2314|gene2314|rna2314|rna2314 216 ENASGFRYCNHCGTRIRLGEMCKVCRKCNERFHETCA 252
                                        68999***********976668888888888776664 PP

>> zf-RING-like  RING-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   7.7    0.0014       2.5       1      30 [.     158     187 ..     158     189 .. 0.87
   2 ?    6.1   6.9    0.0079        14       1      28 [.     224     252 ..     224     257 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0014
                       zf-RING-like   1 CeaCkeivt..qGvrCsnesCnvrlHvdCfqh 30 
                                        C++C++i+t   ++rC   +C++  H++C ++
  gene2314|gene2314|rna2314|rna2314 158 CAVCNNIATfmDAYRCY--KCRITCHKKCSNY 187
                                        *******9843599***..**********875 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0079
                       zf-RING-like   1 CeaCkeivtqGvrCs.nesCnvrlHvdCf 28 
                                        C+ C   +  G +C+  ++Cn r+H+ C+
  gene2314|gene2314|rna2314|rna2314 224 CNHCGTRIRLGEMCKvCRKCNERFHETCA 252
                                        999999999*****62479*********7 PP

>> PHD  PHD-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   6.4    0.0057        10       1      32 [.     157     187 ..     157     189 .. 0.92
   2 ?    6.5   8.2    0.0044       7.8       1      32 [.     223     254 ..     223     261 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0057
                                        SBTTTTSTTSTTSCEEEETTTSCEEETTTSSS CS
                                PHD   1 rCavCkkksdeeeelvqCdgCkrwfHqkClkp 32 
                                        +CavC++   +  +   C +C+ ++H+kC ++
  gene2314|gene2314|rna2314|rna2314 157 YCAVCNN-IATFMDAYRCYKCRITCHKKCSNY 187
                                        7******.8889999**************875 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0044
                                        SBTTTTSTTSTTSCEEEETTTSCEEETTTSSS CS
                                PHD   1 rCavCkkksdeeeelvqCdgCkrwfHqkClkp 32 
                                        +C+ C+ +   +e   +C +C++ fH +C ++
  gene2314|gene2314|rna2314|rna2314 223 YCNHCGTRIRLGEMCKVCRKCNERFHETCASF 254
                                        6999*996666777779************876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (575 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       788  (0.0439511); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.61u 0.27s 00:00:00.88 Elapsed: 00:00:00.46
# Mc/sec: 3737.26
//
Query:       gene2315|gene2315|rna2315|rna2315  [L=169]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (169 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       682  (0.0380389); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 1248.24
//
Query:       gene2316|gene2316|rna2316|rna2316  [L=241]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00065   19.3   1.2     0.0013   18.3   1.2    1.5  1  DUF3169          Protein of unknown function (DUF3169)
    0.00085   19.1   0.4     0.0016   18.2   0.1    1.6  2  Tetraspanin      Tetraspanin family
     0.0059   16.7   0.3     0.0059   16.7   0.3    2.0  2  GutM             Glucitol operon activator protein (GutM)
     0.0099   15.6   1.1      0.016   14.9   0.4    1.7  2  Vpu              Vpu protein
  ------ inclusion threshold ------
       0.02   15.2   2.3      0.064   13.6   0.4    2.2  2  Ly49             Ly49-like protein, N-terminal region
      0.069   12.3   0.8      0.089   11.9   0.8    1.2  1  ABC2_membrane_3  ABC-2 family transporter protein
      0.069   13.1   2.1       0.14   12.1   0.5    2.3  2  Holin_BhlA       BhlA holin family
      0.094   13.1   0.0       0.14   12.5   0.0    1.3  1  MacB_PCD         MacB-like periplasmic core domain
       0.12   12.2   2.1       0.36   10.6   1.2    2.1  2  Phi-29_GP16_7    Bacteriophage phi-29 early protein GP16.7
       0.13   12.3   0.0       0.26   11.4   0.0    1.4  1  Phage_holin_3_6  Putative Actinobacterial Holin-X, holin supe
       0.17   10.6   0.2       0.27    9.9   0.2    1.3  1  Sulfate_transp   Sulfate permease family
       0.23   11.2   0.8       0.35   10.6   0.8    1.3  1  ASFV_J13L        African swine fever virus J13L protein
       0.26   12.0   7.9      0.055   14.1   3.7    2.1  2  DUF3139          Protein of unknown function (DUF3139)


Domain annotation for each model (and alignments):
>> DUF3169  Protein of unknown function (DUF3169)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   1.2   9.2e-07    0.0013      52      98 ..       6      52 ..       1      65 [. 0.74

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 9.2e-07
                            DUF3169 52 ilpllli..iavlvviisvvflrkakkllkkwdeeddeeseeeyeqiek 98
                                       +l +l++  +a++ +i++v+ +++akk+ kk+ e+++e ++    q++ 
  gene2316|gene2316|rna2316|rna2316  6 YLIILIVgvVALVAIIVFVYGYSQAKKYEKKFMEQIEENYNS--IQAND 52
                                       344555575777777777********************9954..55554 PP

>> Tetraspanin  Tetraspanin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.1   1.1e-06    0.0016      81     136 ..       5      58 ..       3     109 .. 0.89
   2 ?   -2.2   0.0         2   2.7e+03      88     119 ..     176     207 ..     174     226 .. 0.66

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.1e-06
                                        XXXXXXXXXXXXXXXXXXXXX--HHH........HHHHHHHHHHHHHHHHHHTHHH CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        Tetraspanin  81 tfsllllvlfllelaagilgfvfsdkargkvseiinnaievkyrddldlkkcqnll 136
                                        +++++l+v +++++a++++++ +s+   +k+++++ ++ie++y++ + ++++++ +
  gene2316|gene2316|rna2316|rna2316   5 LYLIILIVGVVALVAIIVFVYGYSQA--KKYEKKFMEQIEENYNSIQANDSTKDIM 58 
                                        79999*********999999999999..89*************9998886654444 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2
                                        XXXXXXXXXXXXXX--HHH........HHHHH CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        Tetraspanin  88 vlfllelaagilgfvfsdkargkvseiinnai 119
                                        +lf+   ++g+  +   dka+gk++e+ + + 
  gene2316|gene2316|rna2316|rna2316 176 MLFIEAESIGASSYLIDDKAKGKFKENSKAKH 207
                                        55665666778888888888888887766555 PP

>> GutM  Glucitol operon activator protein (GutM)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.3   4.3e-06    0.0059       2     100 ..      11     109 ..       8     114 .. 0.72
   2 ?   -1.3   0.2       1.7   2.3e+03      76      95 ..     198     217 ..     197     227 .. 0.69

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 4.3e-06
                               GutM   2 lililliawllqillglfQiknfnkalkelrkk..gkvaiGrkkgrfragvivllavdedgiivearvmkGvTvfa 75 
                                        ++ +++++ ++ ++ g+ Q k+++k+++e  ++   ++    +++ + + v vll + + g      v kGv+   
  gene2316|gene2316|rna2316|rna2316  11 IVGVVALVAIIVFVYGYSQAKKYEKKFMEQIEEnyNSIQANDSTKDIMSEVKVLLFYKD-GANNGRIVVKGVSATG 85 
                                        56778888899999************999888845455556666666555544444433.333455679******* PP

                               GutM  76 rfkeleelegksleeieeeklkkkd 100
                                         fk+l++ + k+ e+  ++ +k+ +
  gene2316|gene2316|rna2316|rna2316  86 AFKDLKDQNMKKSEDFLKD-IKDAE 109
                                        *****99999888888776.66655 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.7
                               GutM  76 rfkeleelegksleeieeek 95 
                                        +fke ++ ++k ++++e++ 
  gene2316|gene2316|rna2316|rna2316 198 KFKENSKAKHKTFKSVEHKG 217
                                        68888888888887777663 PP

>> Vpu  Vpu protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.4   1.2e-05     0.016       1      47 [.       1      49 [.       1      60 [. 0.82
   2 ?   -2.7   0.0       3.8   5.3e+03      39      50 ..     157     168 ..     146     170 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.2e-05
                                Vpu  1 MlsleliglialivaliiaivvWtivyreykkikkq..keierlikrir 47
                                       M++l  +++ +++v+ ++ai+v  + y + kk  k+  ++ie+ ++ i+
  gene2316|gene2316|rna2316|rna2316  1 MKNLLYLIILIVGVVALVAIIVFVYGYSQAKKYEKKfmEQIEENYNSIQ 49
                                       677766777777777888***************9999999999999886 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 3.8
                                Vpu  39 ierlikrirera 50 
                                        i++l  ri+e+ 
  gene2316|gene2316|rna2316|rna2316 157 IKDLKARIKEID 168
                                        788888888875 PP

>> Ly49  Ly49-like protein, N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.4   4.6e-05     0.064      11      67 ..       9      63 ..       2     113 .. 0.74
   2 ?    1.1   0.1      0.34   4.7e+02      85     108 ..     201     223 ..     178     231 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.6e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXX.XXXXXXXXXXXXXXXXXXXXXXXX CS
                               Ly49 11 lgILclllLvtvavLvtkifqysqekheleetl.nlsqnysimqndinlkeelLrnks 67
                                       + I+ ++ Lv+++v+   ++ ysq k+ +++++ ++++ny+++q + + k+ + + k 
  gene2316|gene2316|rna2316|rna2316  9 ILIVGVVALVAIIVF---VYGYSQAKKYEKKFMeQIEENYNSIQANDSTKDIMSEVKV 63
                                       233333444444444...4567888888888888999*********999998866665 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.34
                                        HHHHHHHHTTTSXSXXXXXX-SCC CS
                               Ly49  85 krlysktktvlkslqntGklvekh 108
                                        ++   k+kt +ks++++Gk+v + 
  gene2316|gene2316|rna2316|rna2316 201 ENSKAKHKT-FKSVEHKGKKVTNM 223
                                        344456667.59999999998765 PP

>> ABC2_membrane_3  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.8   6.4e-05     0.089       4     122 ..       7     162 ..       5     238 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 6.4e-05
                    ABC2_membrane_3   4 liitlllPiilvlllglifsnsved..........................dentpiavvdednsslsqqlveale 53 
                                        lii ++ ++ lv+++++++++s ++                           +++++ + + d++++ + +v+ ++
  gene2316|gene2316|rna2316|rna2316   7 LIILIVGVVALVAIIVFVYGYSQAKkyekkfmeqieenynsiqandstkdiMSEVKVLLFYKDGANNGRIVVKGVS 82 
                                        7899999999***999999988885355666666666655555555555555555555555555666666666666 PP

                    ABC2_membrane_3  54 aspsve.........lvyevdseeeakkalkngdidgilvipkgfskdll..............kgesatvtvlin 106
                                        a++ ++            +++++++a+++++  d+++ l ++++ + + +              k           
  gene2316|gene2316|rna2316|rna2316  83 ATGAFKdlkdqnmkkSEDFLKDIKDAENLMNPDDTSAGLAFDADKIPSMSksqpalsgigsmfkK----------- 147
                                        5555555555555556667799*****************99999999877554443333333330........... PP

                    ABC2_membrane_3 107 ssnlnsskailnalns 122
                                          n+ s++++ + l++
  gene2316|gene2316|rna2316|rna2316 148 -FNVFSYNSVIKDLKA 162
                                        .333333333333333 PP

>> Holin_BhlA  BhlA holin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.5    0.0001      0.14       2      47 ..       2      48 ..       1      62 [. 0.82
   2 ?   -1.0   0.0       1.3   1.8e+03      54      66 ..     147     161 ..     141     169 .. 0.50

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.0001
                         Holin_BhlA  2 eqeilklaitqGiwavLfvvllvYilkkqekreekqeer.ekkyqei 47
                                       ++ ++ +++  G+ a+ +++++vY   +++k e+k  e+ e++y++i
  gene2316|gene2316|rna2316|rna2316  2 KNLLYLIILIVGVVALVAIIVFVYGYSQAKKYEKKFMEQiEENYNSI 48
                                       5556666777899**********************877747899987 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.3
                         Holin_BhlA  54 kfeiv..eeikkdvd 66 
                                        kf++   +++ kd++
  gene2316|gene2316|rna2316|rna2316 147 KFNVFsyNSVIKDLK 161
                                        555554434444333 PP

>> MacB_PCD  MacB-like periplasmic core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0    0.0001      0.14       3      46 ..       5      52 ..       4     124 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.0001
                           MacB_PCD  3 ltvLGiaiGvaaviaivslgeglqasvlsqisdl.....gnlvtvtpgk 46
                                       l ++ +++Gv a++ai++++ g +++ + + +       +n + ++ + 
  gene2316|gene2316|rna2316|rna2316  5 LYLIILIVGVVALVAIIVFVYGYSQAKKYEKK-FmeqieENYNSIQAND 52
                                       77899*****************9977666544.2222333333454443 PP

>> Phi-29_GP16_7  Bacteriophage phi-29 early protein GP16.7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   1.2   0.00026      0.36       4      55 ..       9      63 ..       6     107 .. 0.74
   2 ?   -2.7   0.0       3.6     5e+03      68      95 ..     169     195 ..     148     208 .. 0.60

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00026
                                       XXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX..XXXXXXXXXX CS
                      Phi-29_GP16_7  4 ilmigvlalc.vifllsgrnnkkkqeareledyledlnkrvvq..rtqilselne 55
                                       il++gv+al+ +i+++ g  + kk e + +e+  e+ n    +    +i+se++ 
  gene2316|gene2316|rna2316|rna2316  9 ILIVGVVALVaIIVFVYGYSQAKKYEKKFMEQIEENYNSIQANdsTKDIMSEVKV 63
                                       89******9724567889*************999999975443113357777765 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 3.6
                                        S-HHHHHHHHHHHHTT----HHHHHHHH CS
                      Phi-29_GP16_7  68 lsacevavldlyeqsniripsdiiedlv 95 
                                         + c  av+ + e   i   s +i+d  
  gene2316|gene2316|rna2316|rna2316 169 NTKCP-AVMLFIEAESIGASSYLIDDKA 195
                                        44443.4444556666666666666655 PP

>> Phage_holin_3_6  Putative Actinobacterial Holin-X, holin superfamily III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00019      0.26      69     104 ..       9      43 ..       3      50 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00019
                    Phage_holin_3_6  69 alivaavllvlagvlalvglkklkkakplpertiee 104
                                         li  +v++++a+++ + g++++kk ++++ + iee
  gene2316|gene2316|rna2316|rna2316   9 ILI-VGVVALVAIIVFVYGYSQAKKYEKKFMEQIEE 43 
                                        344.4889999999***********88867677776 PP

>> Sulfate_transp  Sulfate permease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.2    0.0002      0.27     187     244 ..       3      61 ..       1      66 [. 0.82

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0002
                     Sulfate_transp 187 kllvipapaelvavivatlvsaif.elkreagvkivgeipsglpelslpkvdwsllsal 244
                                        +ll++++ +  v+ +va++v ++  +++++++ k++ +i++++++++ ++ + +++s++
  gene2316|gene2316|rna2316|rna2316   3 NLLYLIILIVGVVALVAIIVFVYGySQAKKYEKKFMEQIEENYNSIQANDSTKDIMSEV 61 
                                        557777788888888888887777888999999****************9998888875 PP

>> ASFV_J13L  African swine fever virus J13L protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.8   0.00025      0.35      33      65 ..       8      43 ..       2      62 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00025
                          ASFV_J13L 33 tiliaivvliiiiivliylfssrkk...kaaaaiee 65
                                        ili  vv ++ iiv++y +s  kk   k    iee
  gene2316|gene2316|rna2316|rna2316  8 IILIVGVVALVAIIVFVYGYSQAKKyekKFMEQIEE 43
                                       57888899999**********998722144444544 PP

>> DUF3139  Protein of unknown function (DUF3139)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   3.7     4e-05     0.055       4      67 ..       6      72 ..       2      83 .. 0.65
   2 ?   -1.9   0.1       3.9   5.3e+03      28      28 ..     218     218 ..     187     241 .] 0.57

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4e-05
                            DUF3139  4 iiiililliillvivkvfl.glvgskpikk.ylan.kkldkylqekgykeddIksikpkydskkgsy 67
                                       ++iili+ ++ lv+++vf+ g+  +k+++k ++ + ++ ++ +q+++ ++d  ++ k    +k+g  
  gene2316|gene2316|rna2316|rna2316  6 YLIILIVGVVALVAIIVFVyGYSQAKKYEKkFMEQiEENYNSIQANDSTKDIMSEVKVLLFYKDGAN 72
                                       6788888888888888999889999999764555454555555666666655555565555555544 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 3.9
                            DUF3139  28 k 28 
                                        k
  gene2316|gene2316|rna2316|rna2316 218 K 218
                                        1 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1881  (0.104914); expected 358.6 (0.02)
Passed bias filter:                      975  (0.0543812); expected 358.6 (0.02)
Passed Vit filter:                       141  (0.00786435); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.60u 0.32s 00:00:00.92 Elapsed: 00:00:00.50
# Mc/sec: 1463.95
//
Query:       gene2317|gene2317|rna2317|rna2317  [L=59]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.017   14.9   0.5      0.019   14.7   0.5    1.2  1  MOZART1   Mitotic-spindle organizing gamma-tubulin ring assoc


Domain annotation for each model (and alignments):
>> MOZART1  Mitotic-spindle organizing gamma-tubulin ring associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.5   1.1e-06     0.019       5      35 ..      12      42 ..       8      54 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.1e-06
                            MOZART1  5 dilheiSqlLntgLDretLsicvkLienGVn 35
                                       ++l+eiS+ Ln+  + + + i + ++e G +
  gene2317|gene2317|rna2317|rna2317 12 ELLLEISDKLNITFNERMIDIALDMLEGGMS 42
                                       79*************************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       588  (0.032796); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 418.68
//
Query:       gene2318|gene2318|rna2318|rna2318  [L=213]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.6e-32  110.3  16.7    4.6e-32  110.3  16.7    1.7  2  zf-RRPl_C4   Putative ribonucleoprotein zinc-finger pf C4 typ
  ------ inclusion threshold ------
      0.012   15.9   4.6      0.012   15.9   4.6    1.6  2  DUF3795      Protein of unknown function (DUF3795)
      0.071   12.3   0.1      0.074   12.2   0.1    1.1  1  RPE65        Retinal pigment epithelial membrane protein


Domain annotation for each model (and alignments):
>> zf-RRPl_C4  Putative ribonucleoprotein zinc-finger pf C4 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.3  16.7   7.7e-36   4.6e-32       3     107 ..       4     106 ..       2     107 .. 0.98
   2 ?   -1.4   0.1      0.42   2.5e+03      71      90 ..     147     166 ..     129     184 .. 0.75

  Alignments for each domain:
  == domain 1  score: 110.3 bits;  conditional E-value: 7.7e-36
                         zf-RRPl_C4   3 kCkyClskklknlnetvyCeaCeiyfkvknekqkvelvpik.elekislrdkLCtkCkeknekekeircetfeeyl 77 
                                        +C++C++++l+++n+ +yC++C++y+k+kn++ +++++p+k + +++sl+d+LCtkCk++n++   ++c++f++++
  gene2318|gene2318|rna2318|rna2318   4 TCTFCTRSNLSTYNDLWYCPTCTVYLKQKNGRLFYHYIPSKiDGTIRSLNDILCTKCKTMNTT---VKCTNFDCFY 76 
                                        8*************************************************************9...********** PP

                         zf-RRPl_C4  78 kklklCkeCkervekvlkndfvknfllykk 107
                                        +k+++C++Ck+r+++vl+n+f+kn++++++
  gene2318|gene2318|rna2318|rna2318  77 RKVQYCDTCKARGYMVLRNNFYKNLPRCHR 106
                                        ***************************997 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.42
                         zf-RRPl_C4  71 etfeeylkklklCkeCkerv 90 
                                         +f +++ kl +C   + r 
  gene2318|gene2318|rna2318|rna2318 147 FNFLKFVMKLLICWALRDRC 166
                                        46778888888886655554 PP

>> DUF3795  Protein of unknown function (DUF3795)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.1       1.7     1e+04       8      48 ..       4      10 ..       2      17 .. 0.51
   2 ?   15.9   4.6   2.1e-06     0.012       8      76 ..      21      86 ..      19      89 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 1.7
                            DUF3795  8 dCeeCeayeakekeekkkkkkeafeelllaleeikCeGCre 48
                                       +C+ C                                  ++
  gene2318|gene2318|rna2318|rna2318  4 TCTFC----------------------------------TR 10
                                       34444..................................33 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 2.1e-06
                            DUF3795  8 dCeeCeayeakekeekkkkkk.eafeelllaleeikCeGCreeekkalaeeCkirkCakekglefCaeCe 76
                                       +C +C+ y ++++ +   +   ++ + +  +l++i C+ C++ +++++   C+  +C  +k +++C  C+
  gene2318|gene2318|rna2318|rna2318 21 YCPTCTVYLKQKNGRLFYHYIpSKIDGTIRSLNDILCTKCKTMNTTVK---CTNFDCFYRK-VQYCDTCK 86
                                       8*********98866554443588899999**************9986...******9876.99*****8 PP

>> RPE65  Retinal pigment epithelial membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   1.2e-05     0.074     194     244 ..     120     172 ..      34     196 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.2e-05
                                        S..------EEE-SSEEEEEE--EE..CHC.HCCCTCGGCEEE-TTS-EEEEE CS
                              RPE65 194 klkpayiHdfalTenyvvlvelplk..lnlkkgkksggdalewdpekptrfgv 244
                                         l + ++H   +T+n+v++v+  ++  +n++k   ++  +++ ++  + r++v
  gene2318|gene2318|rna2318|rna2318 120 ALLMLMMHQYTFTKNFVIFVDELYTrrFNFLKFVMKLLICWALRDRCNIRLLV 172
                                        34689****************87776777766433466666666666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       935  (0.0521501); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1512.60
//
Query:       gene2319|gene2319|rna2319|rna2319  [L=311]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1197  (0.0667633); expected 358.6 (0.02)
Passed bias filter:                      588  (0.032796); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.37
# Mc/sec: 2520.79
//
Query:       gene232|gene232|rna232|rna232  [L=45]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (45 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       288  (0.0160634); expected 358.6 (0.02)
Passed bias filter:                      155  (0.00864521); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.32u 0.25s 00:00:00.57 Elapsed: 00:00:00.38
# Mc/sec: 354.51
//
Query:       gene2320|gene2320|rna2320|rna2320  [L=212]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (212 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       831  (0.0463495); expected 358.6 (0.02)
Passed bias filter:                      635  (0.0354175); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1418.27
//
Query:       gene2321|gene2321|rna2321|rna2321  [L=402]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.2e-23   81.1   0.0    1.5e-22   80.2   0.0    1.4  1  ASF1_hist_chap  ASF1 like histone chaperone


Domain annotation for each model (and alignments):
>> ASF1_hist_chap  ASF1 like histone chaperone
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.2   0.0   8.2e-27   1.5e-22       4     119 ..       2     116 ..       1     134 [. 0.94

  Alignments for each domain:
  == domain 1  score: 80.2 bits;  conditional E-value: 8.2e-27
                                        EEEEEEEESS-SEETTS-EEEEEEEEESS--SS-EEEEEEEESSSSSGGGEEEEEEEEEES--SEEEEEEEEE--- CS
                     ASF1_hist_chap   4 vnvtnvkvlnnpakfsdpfkfeitfeclekLeedlewkliyvgsaeseeedqeLdsvlvGPikvGvnkFvfeadpp 79 
                                        ++++++k l+++ + +d++ feit+++  + ++d+e+++iy g +e++++dq L + +vGP+++G+  F++ a+p 
  gene2321|gene2321|rna2321|rna2321   2 ISIKSIKPLKQQFSTRDEIPFEITIDTDLD-NQDVEFSIIYCGDPEKDAHDQKLSEDIVGPLSKGRFGFTLCAEPV 76 
                                        8999*********************97655.689****************************************** PP

                                        -GGGSSSGGGSEEEEEEEEEEETTEEEEEEEEEEEEEETT CS
                     ASF1_hist_chap  80 dvskipkedvlgvtvilltasYkeqeFvrvGYyvnneyed 119
                                        d+ k+p+e v+gvt i++   +k+++Fvr G++vn +y +
  gene2321|gene2321|rna2321|rna2321  77 DIMKVPAEMVFGVTSIVIIGRFKGRQFVRAGFFVNVSYPG 116
                                        ************************************9965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (402 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1749  (0.0975515); expected 358.6 (0.02)
Passed bias filter:                      485  (0.0270511); expected 358.6 (0.02)
Passed Vit filter:                       108  (0.00602376); expected 17.9 (0.001)
Passed Fwd filter:                        35  (0.00195214); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 1.01u 0.37s 00:00:01.38 Elapsed: 00:00:00.54
# Mc/sec: 2223.20
//
Query:       gene2322|gene2322|rna2322|rna2322  [L=807]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0037   15.8   1.2     0.0061   15.1   1.2    1.2  1  ST7       ST7 protein
  ------ inclusion threshold ------
        6.5    7.2  10.6       0.12   12.7   2.1    2.6  3  RICH      RICH domain


Domain annotation for each model (and alignments):
>> ST7  ST7 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   1.2   6.8e-07    0.0061     216     281 ..     434     499 ..     417     511 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 6.8e-07
                                ST7 216 ekllkkalkvaealykrsqklqsksskeeavhrrdlnvlvyikrrlamcarklgrlkeavkmlrdl 281
                                         ++l  al v  +++   q+ +++s  ++ + +r ln  v++kr l+mc+  +gr++e +   rd 
  gene2322|gene2322|rna2322|rna2322 434 SNILTDALSVKVNVLTLRQQANDRSVANKLIDNRMLNERVHLKRLLSMCVVVMGRVREMLAADRDA 499
                                        35677888898899999999**************************************99999985 PP

>> RICH  RICH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   2.1   1.3e-05      0.12       9      56 ..     122     169 ..     119     196 .. 0.87
   2 ?   -3.7   0.1       1.8   1.6e+04      72      83 .]     359     370 ..     352     383 .. 0.58
   3 ?   -2.8   0.1      0.95   8.5e+03      39      56 ..     431     448 ..     417     462 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.3e-05
                               RICH   9 deVkeylekiLseikkqldKrkhtqnvaLikkLseIkteyLyelkvlk 56 
                                        +++++y++  + +  ++l+  k+ q  aL+ kL+ I++ y + +k+++
  gene2322|gene2322|rna2322|rna2322 122 KNISSYINDTIADTITKLKNIKNVQCCALFYKLNLIERAYQNAKKNSE 169
                                        579********9999*************************99999987 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 1.8
                               RICH  72 aeldaafekfkK 83 
                                        ++  aa+e++kK
  gene2322|gene2322|rna2322|rna2322 359 SDHAAAMEEVKK 370
                                        444455555554 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 0.95
                               RICH  39 kkLseIkteyLyelkvlk 56 
                                        k Ls+I t +L+ + ++ 
  gene2322|gene2322|rna2322|rna2322 431 KTLSNILTDALSVKVNVL 448
                                        569999999998655543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (807 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       943  (0.0525964); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.67u 0.29s 00:00:00.96 Elapsed: 00:00:00.47
# Mc/sec: 5163.57
//
Query:       gene2323|gene2323|rna2323|rna2323  [L=130]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    4.3e-33  114.2   0.0    4.8e-33  114.1   0.0    1.0  1  Arf        ADP-ribosylation factor family
    8.4e-11   41.6   3.5    4.6e-07   29.3   0.4    2.3  2  G-alpha    G-protein alpha subunit
    2.7e-10   40.5   0.0    3.6e-10   40.1   0.0    1.2  1  Roc        Ras of Complex, Roc, domain of DAPkinase
    3.9e-09   36.6   0.0    4.7e-09   36.3   0.0    1.1  1  MMR_HSR1   50S ribosome-binding GTPase
    8.9e-08   31.8   0.0      1e-07   31.6   0.0    1.1  1  SRPRB      Signal recognition particle receptor beta subunit
    7.5e-05   22.2   0.0    8.9e-05   21.9   0.0    1.1  1  Gtr1_RagA  Gtr1/RagA G protein conserved region
      8e-05   22.3   0.0    9.2e-05   22.1   0.0    1.1  1  Ras        Ras family
  ------ inclusion threshold ------
      0.027   14.7   0.1      0.054   13.7   0.1    1.5  1  WRKY       WRKY DNA -binding domain
      0.044   12.9   0.0      0.087   12.0   0.0    1.4  1  DAP3       Mitochondrial ribosomal death-associated protein 3
      0.053   13.1   0.1       0.13   11.8   0.1    1.7  1  FeoB_N     Ferrous iron transport protein B
        0.1   12.3   0.0       0.21   11.3   0.0    1.5  1  AAA_29     P-loop containing region of AAA domain
       0.12   13.0   0.0       0.17   12.4   0.0    1.5  1  AAA_18     AAA domain
       0.13   12.3   0.1       0.21   11.6   0.1    1.4  1  AAA_14     AAA domain


Domain annotation for each model (and alignments):
>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.1   0.0   3.5e-36   4.8e-33       7     119 ..       7     124 ..       1     129 [. 0.88

  Alignments for each domain:
  == domain 1  score: 114.1 bits;  conditional E-value: 3.5e-36
                                        GGTT.TTEEEEEEEESTTSSHHHHHHHHHHSSCEE......CSSSSSEEEEEEEETTEEEEEEEE-SSGGGGGGGG CS
                                Arf   7 klklkkkelrilllGLDnaGKtTilkklkleelvt......tvPTigfnveeleiknlkftvwDvGGqeklRplWk 76 
                                        +l    +e ++++lGLDn+GK+Til +l +   ++      + PT+gfn+++ ++kn k+++wD+ G++++R++Wk
  gene2323|gene2323|rna2323|rna2323   7 RLYY-YREKKVIILGLDNSGKSTILSQLLKYPKKRtirepyMPPTLGFNMQKTTFKNRKYSLWDLSGNNNIRKYWK 81 
                                        4444.7999****************998765444434457678********************************* PP

                                        GGCTTESEEEEEEETT-CTTHHHHHHHHHHHCTSGCCTTSEEE CS
                                Arf  77 nYfektdavifvvDsadreRleeakeeLkalleeeelkevall 119
                                        +Yf+  ++vifvvD+ad +R++e  + L +l+++eelk++a+ 
  gene2323|gene2323|rna2323|rna2323  82 CYFTGCNGVIFVVDTADIDRIDENLSILGELVSDEELKQAAIF 124
                                        **************************************99986 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.2   2.2e-05      0.03      24      47 ..      14      37 ..       7      47 .. 0.82
   2 !   29.3   0.4   3.3e-10   4.6e-07     187     276 ..      49     127 ..      37     130 .] 0.87

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.2e-05
                                       EEEEEEESTTSSHHHHHHHHHHHC CS
                            G-alpha 24 vkllllGqseSGKsTilkqlklly 47
                                        k+++lG + SGKsTil ql ++ 
  gene2323|gene2323|rna2323|rna2323 14 KKVIILGLDNSGKSTILSQLLKYP 37
                                       499****************97655 PP

  == domain 2  score: 29.3 bits;  conditional E-value: 3.3e-10
                                        ---SEEEEEEECT-TEEEEEEEE-SSHHHHHGTCCCTTTECEEEEEEEGGGTT-B-SS-TTSBHHHHHHHHHHCCC CS
                            G-alpha 187 ktvGisetkfevdsklefrivdvgGqrserkkWvpffddvdaiiFlvslsefdqvlyedekvnrleeslklFkeic 262
                                        +t+G++  k  ++ ++++ ++d+ G ++ rk W+ +f++ + +iF+v  +++d          r++e l++  e++
  gene2323|gene2323|rna2323|rna2323  49 PTLGFNMQKTTFK-NRKYSLWDLSGNNNIRKYWKCYFTGCNGVIFVVDTADID----------RIDENLSILGELV 113
                                        5899999999999.**********************************88886..........5777888888888 PP

                                        C-GGGTTSEEEEEE CS
                            G-alpha 263 nnkllkntpiiLfl 276
                                        + ++lk++ i+ f+
  gene2323|gene2323|rna2323|rna2323 114 SDEELKQAAIFSFF 127
                                        88888888887777 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.1   0.0   2.6e-13   3.6e-10       1      99 [.      15     106 ..      15     122 .. 0.76

  Alignments for each domain:
  == domain 1  score: 40.1 bits;  conditional E-value: 2.6e-13
                                        EEEEESSTTSSHHHHHHCHCT....-CC.C-EEETTTTEEEEEEECGGSGGCTTBTTTTCEEEEEEEE-SGGCTTT CS
                                Roc   1 KvvlvGdsgvGKtsllkrfve....dkf.sekekstigvdfltkevtkikgvendkkvkkvklniWDtaGqerfrs 71 
                                        Kv+++G  ++GK+++l+++++    +++ ++   +t+g ++ ++++            k+ k+++WD++G++++r+
  gene2323|gene2323|rna2323|rna2323  15 KVIILGLDNSGKSTILSQLLKypkkRTIrEPYMPPTLGFNMQKTTF------------KNRKYSLWDLSGNNNIRK 78 
                                        9******************973322122134456777777755433............344699************ PP

                                        T-HHHHCTSCEEEEEEEGHHHHCHHHHH CS
                                Roc  72 lhplylreaalailvydsrssenlkeWl 99 
                                          ++y+++ + +i+v+d+ + ++++e l
  gene2323|gene2323|rna2323|rna2323  79 YWKCYFTGCNGVIFVVDTADIDRIDENL 106
                                        *****************88777666544 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.3   0.0   3.4e-12   4.7e-09       1      98 [.      15     107 ..      15     126 .. 0.80

  Alignments for each domain:
  == domain 1  score: 36.3 bits;  conditional E-value: 3.4e-12
                                        EEEEEESTTSSHHHHHHHHHT...STEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSSHHHHHHHHHHHHHHH CS
                           MMR_HSR1   1 evaivGrpNvGKStLinaltg...ekaivsdkpgtTrdinegrvklkgkeielvDtpGliegaseekglgkaflal 73 
                                        +v+i+G  N+GKSt++++l++   ++ i + +   T+  n  + ++k++++ l+D+ G  +      +++k ++  
  gene2323|gene2323|rna2323|rna2323  15 KVIILGLDNSGKSTILSQLLKypkKRTIREPYMPPTLGFNMQKTTFKNRKYSLWDLSG-NN------NIRKYWKCY 83 
                                        699*****************8553488999***************99***********.33......455555544 PP

                                        HC.TSEEEEEEETTTTCSHHHHHHHH CS
                           MMR_HSR1  74 ee.adlillvvdaseeklkpldeele 98 
                                           ++ +++vvd +  +++++de+l 
  gene2323|gene2323|rna2323|rna2323  84 FTgCNGVIFVVDTA--DIDRIDENLS 107
                                        4459********44..5888888765 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.6   0.0   7.3e-11     1e-07       3     111 ..      13     121 ..      11     128 .. 0.78

  Alignments for each domain:
  == domain 1  score: 31.6 bits;  conditional E-value: 7.3e-11
                                        --EEEEE-STTSSHHHHHHHHHHSS---B---S....S-EEETTG...GGTT-SEEEETT-GCCSHHHHHHHHHHG CS
                              SRPRB   3 kpavllvGlsdsGKTslftrLttdsvkktvtSq....essaalkvksekgskltliDfPGheklrqklleklkaks 74 
                                        +++v+++Gl +sGK +++ +L++  +k+t           +  + ++ k+ k  l D+ G++++r+  + +    +
  gene2323|gene2323|rna2323|rna2323  13 EKKVIILGLDNSGKSTILSQLLKYPKKRTIREPymppTLGFNMQKTTFKNRKYSLWDLSGNNNIRKYWKCY---FT 85 
                                        689*******************996666655432200444445557889****************877665...78 PP

                                        GEEEEEEEEETTS-HHHHHHHHHHHHHHHHHHHHHTT CS
                              SRPRB  75 slkglvfvvDStidpkevkevAEllyeilliteklkd 111
                                           g++fvvD t+d  ++ e    l e++++ e+++ 
  gene2323|gene2323|rna2323|rna2323  86 GCNGVIFVVD-TADIDRIDENLSILGELVSDEELKQA 121
                                        89********.56777788888888888888887665 PP

>> Gtr1_RagA  Gtr1/RagA G protein conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.0   6.5e-08   8.9e-05       1     103 [.      15     114 ..      15     127 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 6.5e-08
                          Gtr1_RagA   1 kvLLmGksgsGKtsmrsiiFdnylardtl..rlgatidveksevrflgnltlnlwDcgGqeafveeylssqkeeif 74 
                                        kv+++G  +sGK+++ s + +    r ++  ++  t   + ++  +++n + +lwD+ G +++ +       ++ f
  gene2323|gene2323|rna2323|rna2323  15 KVIILGLDNSGKSTILSQLLKYPKKRTIRepYMPPTLGFNMQKT-TFKNRKYSLWDLSGNNNIRKY-----WKCYF 84 
                                        89****************98776666666334888999999888.678899********9987655.....4899* PP

                          Gtr1_RagA  75 rnvgvliyVfDvesre.leedletlkeile 103
                                        + ++ +i+V+D  + + ++e+l+ l e+++
  gene2323|gene2323|rna2323|rna2323  85 TGCNGVIFVVDTADIDrIDENLSILGELVS 114
                                        ************987668888888777665 PP

>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   6.6e-08   9.2e-05       1      85 [.      15     100 ..      15     124 .. 0.74

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 6.6e-08
                                        EEEEEESTTSSHHHHHHHHHH....SSCSSSCT.TTSSEEEEEEEEEETTEEEEEEEEEETTSGGGHHHHHHHHTT CS
                                Ras   1 KlvlvGdsavGKtslllrfvk....dkFkeeye.sTigvdfytkeievdgkevkleiwDTAGqeefkslrelyyrd 71 
                                        K++++G  + GK+++l +  k     + +e y  +T+g  f ++++++++++   ++wD  G ++ ++  + y+++
  gene2323|gene2323|rna2323|rna2323  15 KVIILGLDNSGKSTILSQLLKypkkRTIREPYMpPTLG--FNMQKTTFKNRK--YSLWDLSGNNNIRKYWKCYFTG 86 
                                        89*************98876422114566666525665..555566666655..578******************* PP

                                        ESEEEEEEETTBHH CS
                                Ras  72 aegillvyditsre 85 
                                        ++g++ v d  + +
  gene2323|gene2323|rna2323|rna2323  87 CNGVIFVVDTADID 100
                                        *****998877655 PP

>> WRKY  WRKY DNA -binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   3.9e-05     0.054       7      33 ..      63      88 ..      58     100 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.9e-05
                               WRKY  7 rKyGqkkikgskfprsYYrCthkkgCp 33
                                       rKy   +  g+++ r+Y++C ++ gC+
  gene2323|gene2323|rna2323|rna2323 63 RKYSLWDLSGNNNIRKYWKCYFT-GCN 88
                                       9********************95.997 PP

>> DAP3  Mitochondrial ribosomal death-associated protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   6.3e-05     0.087      23      46 ..      13      36 ..       4      41 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 6.3e-05
                                       --EEEEE-SSSSSTTTTHHHHHHH CS
                               DAP3 23 vkrlvltGekgsGKSvlLlqalay 46
                                        k++++ G + sGKS+ L+q+l y
  gene2323|gene2323|rna2323|rna2323 13 EKKVIILGLDNSGKSTILSQLLKY 36
                                       689*****************9987 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   9.2e-05      0.13       2      62 ..      15      78 ..      14     117 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 9.2e-05
                                       EEEEEESTTSSHHHHHHHHHTTSEE..E.EESTTSSSEEEEEEEEETTEEEEEEE----SSSSS CS
                             FeoB_N  2 tvalvGnpnvGkttlfnaltgakqk..v.gNwpGvtvekkegklklkgkeveivDlPGiYslsa 62
                                       +v+++G  n+Gk+t++ +l +  +k  +   +   t   +  k+++k++++++ Dl G  ++ +
  gene2323|gene2323|rna2323|rna2323 15 KVIILGLDNSGKSTILSQLLKYPKKrtIrEPYMPPTLGFNMQKTTFKNRKYSLWDLSGNNNIRK 78
                                       68999**************986443114246889999999999999999999999999877765 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00015      0.21      24      49 ..      15      38 ..       7      43 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00015
                             AAA_29 24 atlltGpsGsGKSTllDAiqalLvpa 49
                                        +++ G   sGKST+l   q l +p+
  gene2323|gene2323|rna2323|rna2323 15 KVIILGLDNSGKSTIL--SQLLKYPK 38
                                       5899***********9..55555555 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00012      0.17       1      42 [.      16      69 ..      16     128 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00012
                             AAA_18  1 IlltGtpGvGKttlakeL....skrlgf.........gvnlrdvakenglllevd 42
                                       +++ G   +GK+t+   L    +kr+ +         g+n +++ ++n+ +  +d
  gene2323|gene2323|rna2323|rna2323 16 VIILGLDNSGKSTILSQLlkypKKRT-IrepympptlGFNMQKTTFKNRKYSLWD 69
                                       79**************9966654442.3667778888777777777766665555 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00016      0.21       3      27 ..      14      38 ..      12      81 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00016
                             AAA_14  3 kilvitGaRrvGKTtllkqlikell 27
                                       k ++i G+  +GK+t+l ql+k   
  gene2323|gene2323|rna2323|rna2323 14 KKVIILGLDNSGKSTILSQLLKYPK 38
                                       6689****************97644 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       594  (0.0331307); expected 358.6 (0.02)
Passed bias filter:                      487  (0.0271627); expected 358.6 (0.02)
Passed Vit filter:                        81  (0.00451782); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 916.74
//
Query:       gene2324|gene2324|rna2324|rna2324  [L=75]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    0.00031   20.4   0.6    0.00039   20.1   0.6    1.1  1  ubiquitin    Ubiquitin family
     0.0064   16.3   1.7     0.0076   16.1   1.7    1.1  1  Rad60-SLD    Ubiquitin-2 like Rad60 SUMO-like
  ------ inclusion threshold ------
      0.021   14.8   0.0      0.023   14.7   0.0    1.2  1  ODC_AZ       Ornithine decarboxylase antizyme
      0.022   15.2   0.9      0.055   13.9   0.9    1.6  1  Ubiquitin_2  Ubiquitin-like domain


Domain annotation for each model (and alignments):
>> ubiquitin  Ubiquitin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.6   8.7e-08   0.00039       1      66 [.       3      70 ..       3      72 .. 0.91

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 8.7e-08
                                       EEEEE..TTSEEEEEEEETTSBHHHHHHHHHHHHTSSGGGEEEEETTEEE-TTSBHGGHTTSTTEEEE CS
                          ubiquitin  1 itvkt..ldgkkitleveesdtveelKekiaekegipaeqqrLiysGkvLedertleeygiqdgstlh 66
                                       itvk+    gk++ ++++ +  v++lK+k+    ++  +++ L  +  +++d+ +l+ y++ dg  ++
  gene2324|gene2324|rna2324|rna2324  3 ITVKCtdGLGKTVFVKIDDEVMVKDLKKKLGTMINVNDHRISLKKDNFIMRDHVKLSMYQVLDGQAIQ 70
                                       789984423679***************************************************98876 PP

>> Rad60-SLD  Ubiquitin-2 like Rad60 SUMO-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   1.7   1.7e-06    0.0076       3      70 ..       3      71 ..       1      72 [. 0.90

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.7e-06
                                       EEEEESSS-..-EEEEEETTSBHHHHHHHHHHHHT----TT-EEEETTEE--TTSBGGGSS--TTEEEEE CS
                          Rad60-SLD  3 iilkgkdgk..evkikVkptttvskLieayrkkkgipeeqkvrLiFDGeeLdpnstvedldiedgdtidv 70
                                       i++k+ dg   +v++k++ +  v++L++++ ++ ++    ++ L  D+  ++++  +  +++ dg  i++
  gene2324|gene2324|rna2324|rna2324  3 ITVKCTDGLgkTVFVKIDDEVMVKDLKKKLGTMINVND-HRISLKKDNFIMRDHVKLSMYQVLDGQAIQI 71
                                       89999997555*************************99.99*9999999999999999999999998886 PP

>> ODC_AZ  Ornithine decarboxylase antizyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   5.1e-06     0.023      22      59 ..       9      45 ..       3      64 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 5.1e-06
                             ODC_AZ 22 ekvqertlfvfldksvlsedlkegLvaLlelAeeklec 59
                                       +   ++t+fv++d++v+ +dlk+ L  ++++ +++++ 
  gene2324|gene2324|rna2324|rna2324  9 DG-LGKTVFVKIDDEVMVKDLKKKLGTMINVNDHRISL 45
                                       44.489***********************999987665 PP

>> Ubiquitin_2  Ubiquitin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.9   1.2e-05     0.055      18      80 ..      17      71 ..       2      72 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.2e-05
                                       EEEETTSBHHHHHHHHHHHH---TTCEEEEEE.-SSSSEEECSSGCCSBCCCCT--TTEEEEE CS
                        Ubiquitin_2 18 rrfsksltieelKekLelitGtspasmrLqlyddkkdnevsklddddalLgsYgvkdgmrihV 80
                                        +++ +  +++lK+kL ++  +++++ r++l+   kdn +   + d+ +L+ Y+v dg  i++
  gene2324|gene2324|rna2324|rna2324 17 VKIDDEVMVKDLKKKLGTM--INVNDHRISLK---KDNFI---MRDHVKLSMYQVLDGQAIQI 71
                                       68999999********977..79999999999...66665...569**************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       734  (0.0409393); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 548.69
//
Query:       gene2325|gene2325|rna2325|rna2325  [L=197]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       924  (0.0515366); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1390.27
//
Query:       gene2326|gene2326|rna2326|rna2326  [L=121]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.5e-08   32.9   0.8    1.2e-06   28.4   0.8    2.0  1  DIM1      Mitosis protein DIM1


Domain annotation for each model (and alignments):
>> DIM1  Mitosis protein DIM1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4   0.8   6.5e-11   1.2e-06      71     128 ..      56     112 ..       3     115 .. 0.77

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 6.5e-11
                                        TT-SSSEEEEEETTEEEEEE-SSS--SSB-S----HHHHHHHHHHHHHHHHHT-SEEE CS
                               DIM1  71 eledpvtilffyrnkhmkvDfgtgdnnKlnfvledkqelidiietiyrgakkgkglvv 128
                                        e ++   + f+y n  +kvD+g g+ + + + l+ ++++++ii+++y +a  g+ +v 
  gene2326|gene2326|rna2326|rna2326  56 EESELDGLQFYYDNCLIKVDCGIGNTEIIDYELT-RDQFVEIIKVVYMAAVNGRKVVF 112
                                        3334445779**************9998888885.688****************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       600  (0.0334653); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 862.01
//
Query:       gene2327|gene2327|rna2327|rna2327  [L=761]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.048   11.8   1.9       0.07   11.2   1.9    1.1  1  MSP1b     Major surface protein 1B
      0.096   12.4   0.4       0.18   11.5   0.4    1.4  1  GTP_CH_N  GTP cyclohydrolase N terminal


Domain annotation for each model (and alignments):
>> MSP1b  Major surface protein 1B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   1.9   7.8e-06      0.07     401     504 ..     534     632 ..     524     641 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 7.8e-06
                              MSP1b 401 nqkfeeinatlareatdiaqgvketyqsigdafgnafksvgdafksigdafksvndgiakwtaalagyasveqlee 476
                                         ++++e++a l ++  +i + vk ty+ + d f +  + v  ++  i d             +a+    ++ ++++
  gene2327|gene2327|rna2327|rna2327 534 RKQLKEVEA-LKKKEPEIYKAVKTTYDDVNDWFKEHGEKVETTYSNINDRKLDLMYT----ISAVRQDITIREMNK 604
                                        566777776.55666799999999999999998888888888888888865554444....467888899****** PP

                              MSP1b 477 akeadrvqaeqraeaqamtervaqeraa 504
                                        ake +r +a+++ae  a++++ a++ a 
  gene2327|gene2327|rna2327|rna2327 605 AKEKERLEAKKKAEEAALAKKKAEKTAV 632
                                        *******************999987765 PP

>> GTP_CH_N  GTP cyclohydrolase N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.4     2e-05      0.18     100     165 ..     566     631 ..     525     634 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 2e-05
                           GTP_CH_N 100 DpfghlvaevfkeelekgldirPtiavtkahlklpelkeavkkgrlkvDGkivlkskgevavtkva 165
                                          +g+ v+++++++ +++ld+  ti+  +  +++ e+++a +k+rl++  k   +  ++ +  k a
  gene2327|gene2327|rna2327|rna2327 566 KEHGEKVETTYSNINDRKLDLMYTISAVRQDITIREMNKAKEKERLEAKKKAEEAALAKKKAEKTA 631
                                        567999****************************************98877665555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (761 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2112  (0.117798); expected 358.6 (0.02)
Passed bias filter:                      519  (0.0289475); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.76u 0.28s 00:00:01.04 Elapsed: 00:00:00.46
# Mc/sec: 4946.48
//
Query:       gene2328|gene2328|rna2328|rna2328  [L=160]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       403  (0.0224776); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 1177.98
//
Query:       gene2329|gene2329|rna2329|rna2329  [L=197]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      2e-07   31.2   1.1      2e-07   31.2   1.1    2.3  2  ATP-synt_C  ATP synthase subunit C
     0.0084   15.8   0.4     0.0084   15.8   0.4    2.2  2  DUF1673     Protein of unknown function (DUF1673)
  ------ inclusion threshold ------
       0.65   10.2   8.6        1.2    9.4   4.7    2.2  2  DUF4293     Domain of unknown function (DUF4293)


Domain annotation for each model (and alignments):
>> ATP-synt_C  ATP synthase subunit C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   1.7     0.031   1.9e+02      35      59 ..      86     110 ..      57     111 .. 0.78
   2 !   31.2   1.1   3.3e-11     2e-07       1      59 [.     126     184 ..     126     185 .. 0.97

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.031
                                        HHHHHHHHHHHHHHHHHHHHHHHHH CS
                         ATP-synt_C  35 lftksliilafaeaialygLivali 59 
                                         ft ++  l f  +  +y Li+ ++
  gene2329|gene2329|rna2329|rna2329  86 EFTSVMAALCFLTTPVIYMLIIFFV 110
                                        5778888999999*********986 PP

  == domain 2  score: 31.2 bits;  conditional E-value: 3.3e-11
                                        HHHHHHH.GGGHHHHHHHHHHHHHHHHHHHHSGHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         ATP-synt_C   1 lgaglavGlsalgsGigiGkagsagiravarnpklftksliilafaeaialygLivali 59 
                                        l++++ +G ++ ++++ iG  ++  +   ++  k  +++ ++++f+e ++l++Liv+li
  gene2329|gene2329|rna2329|rna2329 126 LACCVITGWGCYFTAYTIGSMAKHVLVTKVKEKKFSGQFYLVFVFVEFVGLFALIVSLI 184
                                        689999****************************************************9 PP

>> DUF1673  Protein of unknown function (DUF1673)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.4   1.4e-06    0.0084     156     219 ..      54     122 ..      44     134 .. 0.79
   2 ?    1.1   1.7     0.046   2.8e+02     165     202 ..     150     186 ..     131     189 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.4e-06
                            DUF1673 156 lviflliavllillsyvesiagelqlge....vvssfisgllllllwliylqviywekkNkkti.vrkr 219
                                          ifl++  l  + + +++ a  +         + s ++ l +l++ +iy+++i++ +kNk++  +++ 
  gene2329|gene2329|rna2329|rna2329  54 SYIFLVVPALAGAGRGLKESAPGISSAAeikiEFTSVMAALCFLTTPVIYMLIIFFVFKNKQIAsFKDA 122
                                        56777777888888888888888876667777788888888888999**************99888876 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.046
                            DUF1673 165 llillsyvesiagelqlgevvssfisgllllllwliyl 202
                                        +l+ ++  ++++g+++l +v++ f+++ ++l++ li+l
  gene2329|gene2329|rna2329|rna2329 150 VLVTKVKEKKFSGQFYLVFVFVEFVGL-FALIVSLIFL 186
                                        555666677888899888888888888.7778888877 PP

>> DUF4293  Domain of unknown function (DUF4293)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.1     0.026   1.6e+02      57      80 ..       3      26 ..       1      31 [. 0.85
   2 ?    9.4   4.7    0.0002       1.2      16     131 ..      54     173 ..      48     185 .. 0.58

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.026
                            DUF4293 57 lvilllliailaliaIflyknRkl 80
                                       ++ l +l+ +  l+ I lyk Rk 
  gene2329|gene2329|rna2329|rna2329  3 ILYLHRLSLLSLLFHIYLYKTRKK 26
                                       677889999999**********96 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0002
                            DUF4293  16 maaflflplasivtedellsfyalgvstaeaetsvnvsvwvlvilllliailaliaIflyknRk........lQlr 83 
                                          +fl++p      +++ l+  a g+s+a++ +++++sv++ +++l+  +i  li  f +kn++        +   
  gene2329|gene2329|rna2329|rna2329  54 SYIFLVVPALA--GAGRGLKESAPGISSAAEIKIEFTSVMAALCFLTTPVIYMLIIFFVFKNKQiasfkdalV--- 124
                                        44455555554..34444666777778888888999***************************9555333333... PP

                            DUF4293  84 lclinllllvllyvllal.lllvnkanaaaeslgessl..kiglilplial 131
                                           +   ++++++ ++ + ++  +++    ++++e+++  +++l++ ++++
  gene2329|gene2329|rna2329|rna2329 125 --KLACCVITGWGCYFTAyTIGSMAKHVLVTKVKEKKFsgQFYLVFVFVEF 173
                                        ..3333333333333333223333333334444444440044455555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       932  (0.0519828); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1332.13
//
Query:       gene233|gene233|rna233|rna233  [L=207]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    6.2e-57  191.7   1.2    7.6e-57  191.4   1.2    1.1  1  Ras          Ras family
    1.1e-33  116.0   0.4    1.8e-33  115.3   0.4    1.4  1  Roc          Ras of Complex, Roc, domain of DAPkinase
    6.3e-16   58.3   0.4    8.1e-16   58.0   0.4    1.2  1  Arf          ADP-ribosylation factor family
    1.4e-06   28.3   0.4      3e-06   27.3   0.2    1.6  2  MMR_HSR1     50S ribosome-binding GTPase
    1.9e-06   27.9   0.1      0.013   15.4   0.0    2.2  2  RsgA_GTPase  RsgA GTPase
    1.3e-05   24.7   0.0    2.7e-05   23.6   0.0    1.5  1  Gtr1_RagA    Gtr1/RagA G protein conserved region
    3.8e-05   23.3   0.4     0.0021   17.6   0.4    2.7  1  GTP_EFTU     Elongation factor Tu GTP binding domain
    0.00013   21.4   0.4    0.00027   20.4   0.1    1.6  1  SRPRB        Signal recognition particle receptor beta subuni
     0.0021   18.4   0.0     0.0028   18.0   0.0    1.2  1  AAA_16       AAA ATPase domain
     0.0039   17.5   0.4       0.06   13.6   0.0    2.1  2  AAA_22       AAA domain
     0.0092   15.7   0.2      0.021   14.6   0.2    2.0  1  PduV-EutP    Ethanolamine utilisation - propanediol utilisati
  ------ inclusion threshold ------
      0.011   15.5   0.7      0.033   13.9   0.1    2.0  2  AAA_24       AAA domain
      0.017   14.7   0.2       0.41   10.2   0.0    2.2  2  cobW         CobW/HypB/UreG, nucleotide-binding domain
      0.021   15.1   0.1      0.097   12.9   0.1    2.1  2  AAA_28       AAA domain
      0.021   14.3   0.1      0.062   12.8   0.0    1.7  2  FeoB_N       Ferrous iron transport protein B
      0.024   14.2   0.0      0.054   13.0   0.0    1.6  1  AAA_7        P-loop containing dynein motor region
      0.036   13.4   0.2      0.088   12.1   0.1    1.7  2  Septin       Septin
      0.047   14.2   0.6      0.068   13.7   0.6    1.7  1  ABC_tran     ABC transporter
      0.058   14.0   0.2       0.14   12.7   0.0    1.8  2  AAA_18       AAA domain
      0.067   12.7   0.0       0.14   11.6   0.0    1.4  1  Pox_A32      Poxvirus A32 protein
      0.081   12.7   0.5       0.18   11.6   0.0    1.8  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
      0.084   12.9   0.1       0.14   12.1   0.1    1.8  1  AAA_5        AAA domain (dynein-related subfamily)
      0.087   12.7   0.0       0.25   11.2   0.0    1.7  2  NACHT        NACHT domain
        0.1   12.4   0.1       0.17   11.6   0.1    1.4  1  IstB_IS21    IstB-like ATP binding protein


Domain annotation for each model (and alignments):
>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  191.4   1.2     1e-59   7.6e-57       1     161 [.       9     170 ..       9     171 .. 0.99

  Alignments for each domain:
  == domain 1  score: 191.4 bits;  conditional E-value: 1e-59
                                    EEEEEESTTSSHHHHHHHHHHSSCSSSCTTTSSEEEEEEEEEETTEEEEEEEEEETTSGGGHHHHHHHHTTESEEEEEEE CS
                            Ras   1 KlvlvGdsavGKtslllrfvkdkFkeeyesTigvdfytkeievdgkevkleiwDTAGqeefkslrelyyrdaegillvyd 80 
                                    K+vl+Gds+vGKt+ll + ++++F+ e ++Tigv+f tk++++d+  +k +iwDTAGqe++++++++yyr++ g+l+vyd
  gene233|gene233|rna233|rna233   9 KIVLIGDSGVGKTNLLSQLTRKEFSAETKATIGVEFATKTFKIDSLVIKAQIWDTAGQERYRAITSAYYRGTLGALVVYD 88 
                                    9******************************************************************************* PP

                                    TTBHHHHHTHH.HHHHHHHHHSTTTSEEEEEEETTTGGGG-SS-HHHHHHHHHHHTSEEEEEBTTTTCTHHHHHHHHHHH CS
                            Ras  81 itsresfenvk.kwveeikrvaeenvpivLvGnKvDleekravsteegeelakelglkfletSAktnenveeafeellre 159
                                    it++++++n++ +w++++k++  e+++i+LvGnK+Dle++r+v+ + g++ ak+++l+fletSA +  nve+afeel+++
  gene233|gene233|rna233|rna233  89 ITRKSTLSNATkHWLTQLKEYSGEEIEIMLVGNKTDLEDERTVTVACGNDAAKSNNLNFLETSALDGSNVEKAFEELIKA 168
                                    *********9989*****************************************************************99 PP

                                    HH CS
                            Ras 160 il 161
                                    ++
  gene233|gene233|rna233|rna233 169 VY 170
                                    86 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.3   0.4   2.4e-36   1.8e-33       1     120 []       9     125 ..       9     125 .. 0.88

  Alignments for each domain:
  == domain 1  score: 115.3 bits;  conditional E-value: 2.4e-36
                                    EEEEESSTTSSHHHHHHCHCT-CCC-EEETTTTEEEEEEECGGSGGCTTBTTTTCEEEEEEEE-SGGCTTTT-HHHHCTS CS
                            Roc   1 KvvlvGdsgvGKtsllkrfvedkfsekekstigvdfltkevtkikgvendkkvkkvklniWDtaGqerfrslhplylrea 80 
                                    K+vl+GdsgvGKt ll+++++++fs ++k+tigv+f+tk++ ki+++        +k +iWDtaGqer+r++++ y+r+ 
  gene233|gene233|rna233|rna233   9 KIVLIGDSGVGKTNLLSQLTRKEFSAETKATIGVEFATKTF-KIDSL-------VIKAQIWDTAGQERYRAITSAYYRGT 80 
                                    9*************************************997.56553.......5889********************** PP

                                    CEEEEEEE.GHHH...HCHHHHHHHHHHHCSSS.-EEEEEE-TTT CS
                            Roc  81 alailvyd.srss...enlkeWlkelkkvagks.pvilvgnkiDl 120
                                      a++vyd +r+s   +  k+Wl++lk+++g++  ++lvgnk+Dl
  gene233|gene233|rna233|rna233  81 LGALVVYDiTRKStlsNATKHWLTQLKEYSGEEiEIMLVGNKTDL 125
                                    ********6333223256699********8865389*******95 PP

>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.0   0.4   1.1e-18   8.1e-16      15     174 ..       8     168 ..       1     169 [. 0.88

  Alignments for each domain:
  == domain 1  score: 58.0 bits;  conditional E-value: 1.1e-18
                                    EEEEEEESTTSSHHHHHHHHHHSSCEE.CSSSSS..EEEEEEEETT..EEEEEEEE-SSGGGGGGGGGGCTTESEEEEEE CS
                            Arf  15 lrilllGLDnaGKtTilkklkleelvt.tvPTig..fnveeleikn..lkftvwDvGGqeklRplWknYfektdavifvv 89 
                                    ++i+l+G  + GKt +l +l+ +e++  t+ Tig  f +++ +i    +k ++wD  Gqe+ R + + Y++ t + + v 
  gene233|gene233|rna233|rna233   8 FKIVLIGDSGVGKTNLLSQLTRKEFSAeTKATIGveFATKTFKIDSlvIKAQIWDTAGQERYRAITSAYYRGTLGALVVY 87 
                                    79*********************99754899998445677777765226789**************************** PP

                                    ETT-CTTHHHHHHHHHHHCTSGCCTTSEEEEEEE-TTSTTSS-HHHHHHHTTGGGSSSSSSEEEEEEBTTTTBTHHHHHH CS
                            Arf  90 DsadreRleeakeeLkalleeeelkevallvlaNKqDlpealseeelrellgleelkgkrkleiqkcsavkgeglkegle 169
                                    D + ++ l++a +   + l+e   +e+ +++++NK Dl++   e+ ++ + g +  k +++l+  ++sa+ g+++++++e
  gene233|gene233|rna233|rna233  88 DITRKSTLSNATKHWLTQLKEYSGEEIEIMLVGNKTDLED---ERTVTVACGNDAAK-SNNLNFLETSALDGSNVEKAFE 163
                                    ************99999999******************97...56788888888888.999******************* PP

                                    HHHHH CS
                            Arf 170 wlses 174
                                     l++ 
  gene233|gene233|rna233|rna233 164 ELIKA 168
                                    99875 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   0.2     4e-09     3e-06       1     114 []       9     122 ..       9     122 .. 0.64
   2 ?   -0.1   0.1       1.2   9.3e+02      23      23 ..     122     122 ..      90     201 .. 0.54

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 4e-09
                                    EEEEEESTTSSHHHHHHHHHTS..TEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSSHHHHHHHHHHHHHHHHCTSE CS
                       MMR_HSR1   1 evaivGrpNvGKStLinaltge..kaivsdkpgtTrdinegrvklkgkeielvDtpGliegaseekglgkaflaleeadl 78 
                                    +++++G + vGK+ L+++lt++   a+++++ g+   +++++++    + +++Dt+G  e   + + ++ a+ +   +  
  gene233|gene233|rna233|rna233   9 KIVLIGDSGVGKTNLLSQLTRKefSAETKATIGVEFATKTFKIDSLVIKAQIWDTAG-QE---RYRAITSAYYR--GTLG 82 
                                    689******************96556777776666666666666444789*******.54...34466777664..3567 PP

                                    EEEEEETT.TTCSHHHHHHHHHHHHH...TTSEEEEEEES CS
                       MMR_HSR1  79 illvvdas.eeklkpldeeleellee...akkplilvlnk 114
                                    +l+v d++ +++l++  ++    l+e   ++++++lv nk
  gene233|gene233|rna233|rna233  83 ALVVYDITrKSTLSNATKHWLTQLKEysgEEIEIMLVGNK 122
                                    7888887742233333333333333355556666666665 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1.2
                                    T CS
                       MMR_HSR1  23 k 23 
                                    k
  gene233|gene233|rna233|rna233 122 K 122
                                    1 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   1.8e-05     0.013     102     128 ..      10      37 ..       6      70 .. 0.82
   2 !   10.6   0.1   0.00053      0.39      30      97 ..      94     165 ..      82     171 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.8e-05
                                    EEEECSTTSSHHHHHHHHCTT-.----S CS
                    RsgA_GTPase 102 svlvGqSGvGKStLinallpel.elktg 128
                                    +vl+G SGvGK+ L+ +l+ ++ +++t+
  gene233|gene233|rna233|rna233  10 IVLIGDSGVGKTNLLSQLTRKEfSAETK 37 
                                    69****************9853244444 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00053
                                    --HHHHHHHHHHHHH...TT-EEEEEEE-GGG--HHH.HHHHHHHHHHHTTSEEEE--TTTHTTHHHHHHHC CS
                    RsgA_GTPase  30 lslnlldrfLvlaee...kgiepvivlnKiDlleeee.eleelkeelealgyevllvsaktkegleelkell 97 
                                    + +n  +  L++++e   ++ie+++v nK+Dl +e++ ++   +++ ++ ++++l +sa +++++e+  e+l
  gene233|gene233|rna233|rna233  94 TLSNATKHWLTQLKEysgEEIEIMLVGNKTDLEDERTvTVACGNDAAKSNNLNFLETSALDGSNVEKAFEEL 165
                                    555555555555444222789**************99777777888899999*******9999998766655 PP

>> Gtr1_RagA  Gtr1/RagA G protein conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.0   3.6e-08   2.7e-05       1     192 [.       9     186 ..       9     193 .. 0.72

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 3.6e-08
                      Gtr1_RagA   1 kvLLmGksgsGKtsmrsiiFdnylardtlrlgatidveksevrflg.nltlnlwDcgGqeafveeylssqkeeifrnvgv 79 
                                    k++L+G sg GKt + s +  +    +t   ++ ++   +++++ +  ++ ++wD  Gqe++ + +    +++   + g+
  gene233|gene233|rna233|rna233   9 KIVLIGDSGVGKTNLLSQLTRKEFSAETKA-TIGVEFATKTFKIDSlVIKAQIWDTAGQERYRAIT----SAYYRGTLGA 83 
                                    899***********9999887776666643.34445555666655514699*********998886....5555567788 PP

                      Gtr1_RagA  80 liyVfDvesreleedletlkeilealrqys.peakvfvlihKmDliqedereeifeerkeeireeieklekeeiqffaTS 158
                                    l+ V D++ ++     +  k+ l++l++ys +e+++    +K+Dl +e++   ++        ++++k  +++++f  TS
  gene233|gene233|rna233|rna233  84 LV-VYDITRKSTL--SNATKHWLTQLKEYSgEEIEIMLVGNKTDLEDERT--VTVA-----CGNDAAK--SNNLNFLETS 151
                                    87.99***55432..33456789999999945688888889999974433..2222.....2223333..34689999** PP

                      Gtr1_RagA 159 iwdes.lykAfssivqklipnldvleelLkklaea 192
                                      d s + kAf + ++ +  +++ l  ++k+++++
  gene233|gene233|rna233|rna233 152 ALDGSnVEKAFEELIKAVYRKRKALDPEFKEMLSR 186
                                    **98857799*999999999999999999988776 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.4   2.8e-06    0.0021      48     190 ..      34     167 ..       6     172 .. 0.71

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 2.8e-06
                                    HHHHHTSCSSCEEEEEETTCSSEEEEEEEESSSGGGHHHHHHHHHT-SEEEEEEETTTB..STHHHHHHHHHHHH...TT CS
                       GTP_EFTU  48 eErergiTiksaaisleketkkylinliDtPGHvdFskevirglrvlDgavlvvdaveG..vepqteevlrlalk...eg 122
                                    +E +  i ++ a+ +++ ++   + ++ Dt G + +   +++ +r + ga++v d+++     + t+  l ++++   e+
  gene233|gene233|rna233|rna233  34 AETKATIGVEFATKTFKIDSLVIKAQIWDTAGQERYRAITSAYYRGTLGALVVYDITRKstLSNATKHWLTQLKEysgEE 113
                                    4555555556665566545666778899****************************966557777887777777611156 PP

                                    TEEEEEEESCGSTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTTEEEEEEBTTTTBTHHHHHHHHHH CS
                       GTP_EFTU 123 vpiivfiNKmDrlkaelkeiveevkqklsrkeeklekygekgekevpvvfgSalkgegvktllealve 190
                                    ++i+++ NK D  +++   ++                   k+ ++ +++ +Sal+g +v++ +e l++
  gene233|gene233|rna233|rna233 114 IEIMLVGNKTDLEDERTVTVACGND-AA------------KS-NNLNFLETSALDGSNVEKAFEELIK 167
                                    77*********98776654443322.22............22.3678888888888888877777665 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.1   3.6e-07   0.00027       5     128 ..       9     129 ..       6     137 .. 0.76

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 3.6e-07
                                    EEEEE-STTSSHHHHHHHHHHSS-.--B---SS-EEETTG.....GGTT-SEEEETT-GCCSHHHHHHHHHHGGEEEEEE CS
                          SRPRB   5 avllvGlsdsGKTslftrLttdsv.kktvtSqessaalkv..ksekgskltliDfPGheklrqklleklkaksslkglvf 81 
                                    +++l+G s  GKT l+ +Lt +++  +t + +  ++a+k+   ++   k ++ D  G+e+ r   + +  ++ +l g + 
  gene233|gene233|rna233|rna233   9 KIVLIGDSGVGKTNLLSQLTRKEFsAETKATIGVEFATKTfkIDSLVIKAQIWDTAGQERYRAITSAY--YRGTL-GALV 85 
                                    589******************965157888886666665533344567899********999755554..55555.5555 PP

                                    EEETTS-HHHHHHHHHHHHHHHHHHHHHTT---EEEEEE-TTSTT-- CS
                          SRPRB  82 vvDStidpkevkevAEllyeilliteklkdavdiliACnKqelflak 128
                                    v D t ++   + +  +l+++   +    ++++i++  nK +l   +
  gene233|gene233|rna233|rna233  86 VYDITRKSTLSNATKHWLTQLKEYS---GEEIEIMLVGNKTDLEDER 129
                                    8999999888888999999875554...5999****99999987655 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   3.8e-06    0.0028      27     126 ..      10     168 ..       9     180 .. 0.63

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 3.8e-06
                         AAA_16  27 vllsGesGvGKsslvrellr.alekd.....ggiflrgkcdqlesaipy...salaqalareellrqllde......... 88 
                                    ++l+G+sGvGK+ l+ +l r +++++     g+ f++ +++    +  +   +++++++ + e +r++ ++         
  gene233|gene233|rna233|rna233  10 IVLIGDSGVGKTNLLSQLTRkEFSAEtkatiGVEFATKTFKID--S--LvikAQIWDTAGQ-ERYRAITSAyyrgtlgal 84 
                                    689************8888754444455666444455444444..1..1122557777744.777777666677666666 PP

                         AAA_16  89 .........aesaeleawrekleeala.....................................avpelagaeasrllel 122
                                             + s++  +w ++l+e  +                                     ++++l+g+  +  +e+
  gene233|gene233|rna233|rna233  85 vvyditrksTLSNATKHWLTQLKEYSGeeieimlvgnktdledertvtvacgndaaksnnlnflETSALDGSNVEKAFEE 164
                                    66777777766667777777777777777777777777777777777776666666666666666666666666555555 PP

                         AAA_16 123 lkrl 126
                                    l ++
  gene233|gene233|rna233|rna233 165 LIKA 168
                                    5555 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.0   8.1e-05      0.06       8      30 ..      10      32 ..       9      84 .. 0.78
   2 ?    2.3   0.1      0.25   1.9e+02      18      84 ..      92     171 ..      90     185 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 8.1e-05
                         AAA_22  8 lvvtGesGtGKTtllrrlleqld 30
                                   +v++G sG+GKT ll +l+++  
  gene233|gene233|rna233|rna233 10 IVLIGDSGVGKTNLLSQLTRKEF 32
                                   79****************99863 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.25
                         AAA_22  18 KTtllrrlleqldeeakaee..............erpevvfvtlpsst.sskdllrellralglelkaerlsseelleal 82 
                                    K+tl +  +++l++ ++                 e+ ++v+v + ++  +s +l     +al+ ++ +  +  eel++a+
  gene233|gene233|rna233|rna233  92 KSTLSNATKHWLTQLKEYSGeeieimlvgnktdlEDERTVTVACGNDAaKSNNLNFLETSALDGSNVE--KAFEELIKAV 169
                                    88899999999877666555888999999999999999999999999865555543334444443333..5555555555 PP

                         AAA_22  83 eq 84 
                                    ++
  gene233|gene233|rna233|rna233 170 YR 171
                                    55 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.2   2.8e-05     0.021       3      40 ..       9      48 ..       7     167 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.8e-05
                      PduV-EutP  3 killiGkvgsGKttLtqalkgeelkY..kktqaiefsdev 40
                                   ki+liG +g+GKt L  +l+ +e++   k t  +ef +++
  gene233|gene233|rna233|rna233  9 KIVLIGDSGVGKTNLLSQLTRKEFSAetKATIGVEFATKT 48
                                   89*****************999986411455566666555 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   4.5e-05     0.033       4      23 ..       9      34 ..       8      75 .. 0.79
   2 ?   -1.5   0.0       2.4   1.8e+03     107     132 ..     176     202 ..     156     205 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.5e-05
                         AAA_24  4 kiliyGpsgiGKTtlakel......g 23
                                   ki+++G+sg+GKT l+++l       
  gene233|gene233|rna233|rna233  9 KIVLIGDSGVGKTNLLSQLtrkefsA 34
                                   89****************96555554 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.4
                         AAA_24 107 laeefrrllkklqelrk.nvifiahek 132
                                    l +ef+++l + + +r+  +i i + k
  gene233|gene233|rna233|rna233 176 LDPEFKEMLSRTEPVRNkKIIQIKKKK 202
                                    567777777777777777777766655 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00056      0.41       3      48 ..      10      58 ..       8      70 .. 0.76
   2 ?    2.5   0.0      0.13        98     144     170 ..     117     143 ..      98     148 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00056
                                   EEEEESTTCCHHHHHHHHH.CT--SS-EEEEESS-SS..CHCCCCCCHC CS
                           cobW  3 tvltGflGsGKTtLlnhll.enraglklavivNefge..vsiDaellre 48
                                   +vl G  G GKT Ll++l+ ++ + +  a i  ef +  ++iD+ ++++
  gene233|gene233|rna233|rna233 10 IVLIGDSGVGKTNLLSQLTrKEFSAETKATIGVEFATktFKIDSLVIKA 58
                                   6899999************544455566777777765447777777766 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.13
                                    EEEEE-HHHHCHC..HHHHHHHHHHHH CS
                           cobW 144 llvlnKtDlldeeallekleerlrqln 170
                                    +lv nKtDl de++ + ++ +++ + n
  gene233|gene233|rna233|rna233 117 MLVGNKTDLEDERTVTVACGNDAAKSN 143
                                    7899*******9988788888877766 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   0.00013     0.097       1      25 [.       9      33 ..       9      74 .. 0.81
   2 ?    0.1   0.0       1.1   8.4e+02      68      85 ..     138     155 ..      91     191 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00013
                         AAA_28  1 kivitGgestGKTtlleaLaargyp 25
                                   kiv++G ++ GKT ll++L++++++
  gene233|gene233|rna233|rna233  9 KIVLIGDSGVGKTNLLSQLTRKEFS 33
                                   79******************87433 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 1.1
                         AAA_28  68 aaaaankvlfcDrglldt 85 
                                     aa++n++ f+++++ld 
  gene233|gene233|rna233|rna233 138 DAAKSNNLNFLETSALDG 155
                                    556788888888888875 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   8.2e-05     0.062       2      56 ..       9      65 ..       8      75 .. 0.81
   2 ?   -1.3   0.0       1.9   1.4e+03     107     121 ..     115     129 ..      87     164 .. 0.55

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 8.2e-05
                                   EEEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEEEETT..EEEEEEE--- CS
                         FeoB_N  2 tvalvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegklklkg..keveivDlPG 56
                                   +++l+G+  vGkt l+ +lt ++ +    + + ve ++ ++k+++   +++i D  G
  gene233|gene233|rna233|rna233  9 KIVLIGDSGVGKTNLLSQLTRKEFSAETKATIGVEFATKTFKIDSlvIKAQIWDTAG 65
                                   799******************999888888888888888888776445667777666 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.9
                                    SEEEEEETHHHHHHT CS
                         FeoB_N 107 pvvlalnmideaekk 121
                                    +++l+ n++d  +++
  gene233|gene233|rna233|rna233 115 EIMLVGNKTDLEDER 129
                                    333333444444444 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   7.2e-05     0.054      35      73 ..       9      48 ..       4      56 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 7.2e-05
                          AAA_7 35 pvllvGptGtGKtviikd.llkkldkekylsltinfsaqt 73
                                   +++l+G++G+GKt ++++ + k+++ e+  ++ ++f  +t
  gene233|gene233|rna233|rna233  9 KIVLIGDSGVGKTNLLSQlTRKEFSAETKATIGVEFATKT 48
                                   6899**************7778889999999999998876 PP

>> Septin  Septin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   0.00012     0.088       5      49 ..       8      52 ..       5      66 .. 0.81
   2 ?   -1.5   0.0       1.6   1.2e+03      63      89 ..     144     169 ..      92     196 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00012
                                   EEEEEEEBTTSSCCCCCCTTSSSS------------------S-E CS
                         Septin  5 ftlmvvGesglGkttlintlfetdlieeekleeasekkkktveik 49
                                   f ++++G+sg+Gkt l+  l +++   e+k +   e ++kt +i+
  gene233|gene233|rna233|rna233  8 FKIVLIGDSGVGKTNLLSQLTRKEFSAETKATIGVEFATKTFKID 52
                                   899******************999999887777777666776665 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.6
                                    EEEEEE---BSSSSSHHCCCHHHHHHH CS
                         Septin  63 nltviDtpgfGdavdnskswepiveyi 89 
                                    nl+ ++t    d  + +k++e +++ +
  gene233|gene233|rna233|rna233 144 NLNFLETSAL-DGSNVEKAFEELIKAV 169
                                    5555555554.4555566666666655 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.6   9.1e-05     0.068      13      42 ..       9      38 ..       8     197 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 9.1e-05
                                   EEEEEESTTSSHHHHHHHHTTSS--SEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran 13 kvaivGenGaGKStLlkllagllkpteGei 42
                                   k++++G++G GK+ Ll+ l++++  +e + 
  gene233|gene233|rna233|rna233  9 KIVLIGDSGVGKTNLLSQLTRKEFSAETKA 38
                                   579*****************9987655554 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00019      0.14       1      25 [.      10      41 ..      10      78 .. 0.75
   2 ?   -1.0   0.0       3.3   2.5e+03      83      83 ..     157     157 ..      92     203 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00019
                         AAA_18  1 IlltGtpGvGKttlakeLskrlgf........g 25
                                   I+l G +GvGKt l   L +++ f        g
  gene233|gene233|rna233|rna233 10 IVLIGDSGVGKTNLLSQLTRKE-FsaetkatiG 41
                                   89****************9884.5445555551 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 3.3
                         AAA_18  83 l 83 
                                     
  gene233|gene233|rna233|rna233 157 N 157
                                    1 PP

>> Pox_A32  Poxvirus A32 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00019      0.14      13      36 ..       7      30 ..       3      35 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00019
                        Pox_A32 13 pFrlalvGgsGsGktvyLlsLlrt 36
                                    F+++l+G sG Gkt  L +L r+
  gene233|gene233|rna233|rna233  7 LFKIVLIGDSGVGKTNLLSQLTRK 30
                                   59**************99988765 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00023      0.18       3      19 ..      11      27 ..       9      63 .. 0.81
   2 ?   -1.9   0.1       3.1   2.3e+03      80     105 ..     176     202 ..     149     205 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00023
                         AAA_21  3 vliGpNgsGKSnLLdal 19
                                   vliG+ g+GK+nLL  l
  gene233|gene233|rna233|rna233 11 VLIGDSGVGKTNLLSQL 27
                                   9************9755 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 3.1
                         AAA_21  80 rsqv.eeklssvetllesgllldkrsl 105
                                     +   +e+ls+ e+++ + +++ k+ +
  gene233|gene233|rna233|rna233 176 LDPEfKEMLSRTEPVRNKKIIQIKKKK 202
                                    222367888888888888888777765 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   0.00019      0.14       2      22 ..      10      30 ..       9     147 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00019
                                   EEEE--SSSSHHHHHHHGGGG CS
                          AAA_5  2 vlLvGppGtgKselaerlaaa 22
                                   ++L+G++G+gK+ l  +l + 
  gene233|gene233|rna233|rna233 10 IVLIGDSGVGKTNLLSQLTRK 30
                                   79*************999875 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00034      0.25       3      22 ..      10      29 ..       9      38 .. 0.90
   2 ?   -2.1   0.0       4.1   3.1e+03      39      79 ..     147     186 ..     131     190 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00034
                                   EEEEC-TTTCHHHHHHHHHH CS
                          NACHT  3 vilqGeaGsGKTtLlqklal 22
                                   ++l G++G+GKT Ll +l +
  gene233|gene233|rna233|rna233 10 IVLIGDSGVGKTNLLSQLTR 29
                                   799************99975 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 4.1
                                    EEETTTTTTS-...-HCHHHCCCCTS--SSS-CCHHHHCCS CS
                          NACHT  39 flslrelsrsgnarsladllfsqlpepaapvsevwavllel 79 
                                    fl+ ++l  s+ +  + +l+ +++ + +a  +e ++++l++
  gene233|gene233|rna233|rna233 147 FLETSALDGSNVEKAFEELIKAVYRKRKALDPE-FKEMLSR 186
                                    555666666666667777777777777777777.5555555 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00023      0.17      50     146 ..      10     119 ..       5     133 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00023
                      IstB_IS21  50 ivllGpsGvGKshlaialgveavragls....vlfvr....vedLveelkr..arrdgklaralkrllkvdl...lilDd 116
                                    ivl+G sGvGK+ l   l ++   a+++    v f +    ++ Lv + ++    +++++  + +++ + +l   ++ D 
  gene233|gene233|rna233|rna233  10 IVLIGDSGVGKTNLLSQLTRKEFSAETKatigVEFATktfkIDSLVIKAQIwdTAGQERYRAITSAYYRGTLgalVVYDI 89 
                                    89*************99998876544332222666442222566665544411344555666556665553333044444 PP

                      IstB_IS21 117 lgllpldqaeaellfeviekryerrsiiit 146
                                        +l++a ++ l ++ e   e   i++ 
  gene233|gene233|rna233|rna233  90 TRKSTLSNATKHWLTQLKEYSGEEIEIMLV 119
                                    445567777777777776666666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1172  (0.065369); expected 358.6 (0.02)
Passed bias filter:                      688  (0.0383736); expected 358.6 (0.02)
Passed Vit filter:                       101  (0.00563333); expected 17.9 (0.001)
Passed Fwd filter:                        24  (0.00133861); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              24  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 1345.12
//
Query:       gene2330|gene2330|rna2330|rna2330  [L=62]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (62 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       302  (0.0168442); expected 358.6 (0.02)
Passed bias filter:                      215  (0.0119917); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.25s 00:00:00.59 Elapsed: 00:00:00.40
# Mc/sec: 470.06
//
Query:       gene2331|gene2331|rna2331|rna2331  [L=96]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.053   12.8   0.0      0.054   12.8   0.0    1.1  1  7TM_GPCR_Srw  Serpentine type 7TM GPCR chemoreceptor Srw
      0.058   13.1   0.1      0.067   12.9   0.1    1.1  1  DUF4534       Protein of unknown function (DUF4534)


Domain annotation for each model (and alignments):
>> 7TM_GPCR_Srw  Serpentine type 7TM GPCR chemoreceptor Srw
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   6.1e-06     0.054     196     235 ..      37      76 ..      11      85 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6.1e-06
                       7TM_GPCR_Srw 196 egiiskiipsillpiltilLiieLrkakkkrkklssskkn 235
                                        +++i+ i+ s+l++++ i+L++++ k+kk + +l +  ++
  gene2331|gene2331|rna2331|rna2331  37 NAYIIGIFLSVLFIMVGIVLLFCMLKSKKLKHSLDKPGNK 76 
                                        56778999**********************9999866544 PP

>> DUF4534  Protein of unknown function (DUF4534)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   7.5e-06     0.067      44      79 ..      28      63 ..      10      67 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 7.5e-06
                            DUF4534 44 sevssfiicyskkivillsliTilvscllLysvyaq 79
                                       s+v   i  + + i i+ls++ i+v ++lL+++ ++
  gene2331|gene2331|rna2331|rna2331 28 SDVGMRIDPNAYIIGIFLSVLFIMVGIVLLFCMLKS 63
                                       5566667778899*******************8765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       990  (0.0552178); expected 358.6 (0.02)
Passed bias filter:                      709  (0.0395449); expected 358.6 (0.02)
Passed Vit filter:                        83  (0.00462937); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.28s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 742.39
//
Query:       gene2332|gene2332|rna2332|rna2332  [L=624]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.6e-31  107.3  13.2    1.8e-19   70.1   1.6    2.9  3  Peptidase_S8  Subtilase family
      1e-05   26.1   3.0    1.3e-05   25.8   0.2    2.6  2  Inhibitor_I9  Peptidase inhibitor I9
  ------ inclusion threshold ------
       0.12   11.3   0.4       0.19   10.8   0.4    1.2  1  SLC12         Solute carrier family 12


Domain annotation for each model (and alignments):
>> Peptidase_S8  Subtilase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.1      0.17     1e+03     158     171 ..      90     110 ..      66     132 .. 0.69
   2 !   44.1   0.9   2.5e-15   1.5e-11       1     121 [.     235     325 ..     235     339 .. 0.84
   3 !   70.1   1.6     3e-23   1.8e-19     123     281 ..     455     588 ..     422     601 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.17
                                        EEEE--SS-T-HH.......E CS
                                        xxxxxxxxxxxxx.......x RF
                       Peptidase_S8 158 vviSaGNngktgs.......s 171
                                        +v SaGN g + +       +
  gene2332|gene2332|rna2332|rna2332  90 FVLSAGNIGYESKsdelddkN 110
                                        789999999433344444333 PP

  == domain 2  score: 44.1 bits;  conditional E-value: 2.5e-15
                                        -TT-EEEEECS-B-TT-TTTGGGEEE..EEEE---TTSG.GGEETT-SS-TT-SC-SSS....HHHHHHHHHH-B. CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Peptidase_S8   1 gkgvlvavlDtGvdpshpdlsvttdgerklvdvideegagfngadsettstnwarddngnsieHGthvAGiaaana 76 
                                        gkg  v v+DtGv++shp+l+                g+ f ga+ +t   n +++  g    HGthvAG++a++ 
  gene2332|gene2332|rna2332|rna2332 235 GKGAQVYVIDTGVETSHPELQ----------------GRAFFGANFTTSGSNTDQN--G----HGTHVAGVIAGK- 287
                                        79999****************................3335555554444444444..5....************. PP

                                        .SSSSSB-SSTTSEEEEEE-SSTTSB-HH..HHHHHHHHHHHHCT CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Peptidase_S8  77 peegekngvapgakilsvkvldtsggsmetgteliraieeaaedk 121
                                              +g+a +a+i++vkvld+ g+ m   + +i +i+++++++
  gene2332|gene2332|rna2332|rna2332 288 -----TVGIARKAEIIAVKVLDKMGSGML--SSVIMGIDYVIRKH 325
                                        .....**********************96..78999998888765 PP

  == domain 3  score: 70.1 bits;  conditional E-value: 3e-23
                                        S....EEEE-EESCETTCHHCHHHHHHHHHHHH.CCT-EEEEE--SS-T-HHEEE-TTCEECTTTSTTCEEEEEES CS
                                        x....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Peptidase_S8 123 d....vinmslgestslpktgrsiealainravnkkgvlvviSaGNngktgsslqagspvgtpstsknvitvgayt 194
                                        +    ++nms+g + + +  +      a+++a+ + g+ + ++aGN++       + +++ +ps+sk ++t ga t
  gene2332|gene2332|rna2332|rna2332 455 QkpksIVNMSVG-GLKSKVLDY-----AVKYAT-DIGIHFSAAAGNDH------EDACEF-SPSSSKLAMTAGAST 516
                                        033359******.777777665.....899***.99************......777876.68889********** PP

                                        TTSSB-TT--B-TT.......-EEEE-S-CCCCCCCCCHHHTTTHHEEEE-SHHHCHHHHHHHHHHHHHHHTT--H CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Peptidase_S8 195 tegkiapfSsrGpssdgklkpdivapGgnivstwsrqsnnsaglssyqsmsGTSmAsPnaagaaAlllsalpkltp 270
                                          + ia fS++G ++      d+ apG++i s+w + +        y  +sGTSmA+P+++ga+Al l + +++tp
  gene2332|gene2332|rna2332|rna2332 517 ASDTIAFFSNYGQCV------DLYAPGVDIKSSWIKGE--------YRVVSGTSMAAPHVTGAMALYL-GEKEYTP 577
                                        **************9......6****************........**********************.6777*** PP

                                        HHHHHHHHCCS CS
                                        xxxxxxxxxxx RF
                       Peptidase_S8 271 etvraallntA 281
                                        +++ ++l n  
  gene2332|gene2332|rna2332|rna2332 578 AELIDMLKNDS 588
                                        **999999977 PP

>> Inhibitor_I9  Peptidase inhibitor I9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.2   2.2e-09   1.3e-05      46      81 ..      46      81 ..      13      82 .. 0.86
   2 ?   -1.4   0.2      0.67     4e+03      17      47 ..     171     200 ..     155     204 .. 0.54

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 2.2e-09
                                       SSSSSEEEEEE-GGGHHHHHTSTTEEEEEEEEEEEE CS
                       Inhibitor_I9 46 kilfnGfavklteeqaeklrkrpeVesVepDqsvrl 81
                                       ++l nGf + l ee+a++lr+++ V++Ve+D++v++
  gene2332|gene2332|rna2332|rna2332 46 NTLSNGFIGDLEEESAQRLRNNENVAYVEKDKEVSI 81
                                       3489*****************************986 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.67
                                        HHHHHHHH....HHHHTT..--EEEEEEESS CS
                       Inhibitor_I9  17 ssheswhqsllksvlkgedsakagilysYki 47 
                                        +s  +++ sll+++ +++++++ + ++sY +
  gene2332|gene2332|rna2332|rna2332 171 NSDIQKS-SLLRRTGENNKDTSRTRIQSYAH 200
                                        2222222.35666433337777777888876 PP

>> SLC12  Solute carrier family 12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.4   3.1e-05      0.19      67     222 ..      33     183 ..      24     236 .. 0.56

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 3.1e-05
                              SLC12  67 aLlqasGlgklkpnilllGyksdWqtcekeeleeYfnvihdafdlklavaiLrlkegldvs..ellqeeeeeeeek 140
                                        + + a G+g    n+l  G+  d ++ ++++l++  nv     d ++++  + ++ g+ +s  ++  e++++e ++
  gene2332|gene2332|rna2332|rna2332  33 SVFSALGIGDSVINTLSNGFIGDLEEESAQRLRNNENVAYVEKDKEVSIKDFTVEGGFVLSagNIGYESKSDELDD 108
                                        678899******************************************************9643333333333333 PP

                              SLC12 141 ekkeaeese..keeeekkkakkkklle.................ekskekeekekleekdsnlslseekkeeekek 197
                                        +++++   +  +++ee+++  ++++++                 +                   ++++  ++++  
  gene2332|gene2332|rna2332|rna2332 109 KNANR-GDKgnRNSEEDESGWDSNTRSklryvrgkgantnrspvT-------------------TNRRLGQTRSAP 164
                                        33322.222232222222222222222344444444433333220...................222222111111 PP

                              SLC12 198 kkekkkkkekkeklkkkekslllke 222
                                        k++++k+++ ++++       l ++
  gene2332|gene2332|rna2332|rna2332 165 KDKNRKNSDIQKSSL------LRRT 183
                                        111111111111111......1111 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (624 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       650  (0.0362541); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.42
# Mc/sec: 4458.89
//
Query:       gene2333|gene2333|rna2333|rna2333  [L=419]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
     0.0024   16.8   1.7      0.004   16.0   1.6    1.5  1  FBPase_glpX  Bacterial fructose-1,6-bisphosphatase, glpX-enco
  ------ inclusion threshold ------
       0.17   10.4  11.5       0.23   10.0  11.5    1.1  1  Macoilin     Macoilin family


Domain annotation for each model (and alignments):
>> FBPase_glpX  Bacterial fructose-1,6-bisphosphatase, glpX-encoded
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   1.6   4.5e-07     0.004     253     308 .]     236     290 ..     157     290 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 4.5e-07
                        FBPase_glpX 253 ltledLvkgddvifaatgvTdgelLkgvrfkgggarteslvmrsksgtvrfiesih 308
                                         t + ++  + v ++ t+vTdg++++ + ++++ ++t+s++ +s   tv++ +s h
  gene2333|gene2333|rna2333|rna2333 236 HTKNRIID-ETVKLCGTAVTDGAVIDSIAIQKNDTKTTSVTSTSMPSTVKKSKSAH 290
                                        44455555.8999*************************************998877 PP

>> Macoilin  Macoilin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0  11.5   2.5e-05      0.23     235     412 ..     160     400 ..     118     412 .. 0.57

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 2.5e-05
                           Macoilin 235 sknnhslnkk..dsslklpeleyrekkksakssrsdskkkhehn.................esvdsklqekeymen 291
                                        +++n + + +  + ++++ ++++ +   s + ++  +k +he                   ++    +++ + ++ 
  gene2333|gene2333|rna2333|rna2333 160 NDENVKAAVSteNDAKTVVDVHTAQ---SIETKKVAAKDQHEAVltgprtttmvntsmegrNNAAVSIDRRDALDA 232
                                        3222222221111122222222222...222222222222222233343333333333333334444444444444 PP

                           Macoilin 292 kskskrlsksessgsesellveesvkskssssssssnknskkasagsagssnssskkhsessksvtsssssknskk 367
                                         +++++    +++ +   + v++ +   s + +++++k+++ +s+++ ++++ s   hs+s+k  +++++++n+ k
  gene2333|gene2333|rna2333|rna2333 233 SLNHTKNRIIDETVKLCGTAVTDGAVIDSIAIQKNDTKTTSVTSTSMPSTVKKSKSAHSKSNKDLSNAKKTENKSK 308
                                        4444444444444555545554444444555555566899999999999999999999****99999999999999 PP

                           Macoilin 368 qklpaGkssa..alkdaaen.............................................slpnnqlskkd 396
                                        +kl + k ++    + +  n                                              +++ ++ kk+
  gene2333|gene2333|rna2333|rna2333 309 KKLQTAKRQRlsDDRRPRRNifsnfkptllhtptedeineyyadffiiknplksircgdspyvyyEVTEKKAVKKK 384
                                        9999999998433344444466666666666666666666666666666666666666666666555555667777 PP

                           Macoilin 397 alvrLeadikkLkaeL 412
                                          +rL ++ k +k eL
  gene2333|gene2333|rna2333|rna2333 385 ITIRLKGKKKSIKDEL 400
                                        7778888888777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (419 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2520  (0.140554); expected 358.6 (0.02)
Passed bias filter:                      669  (0.0373138); expected 358.6 (0.02)
Passed Vit filter:                        80  (0.00446204); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.67u 0.25s 00:00:00.92 Elapsed: 00:00:00.43
# Mc/sec: 2946.14
//
Query:       gene2334|gene2334|rna2334|rna2334  [L=44]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (44 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       371  (0.0206927); expected 358.6 (0.02)
Passed bias filter:                      178  (0.00992805); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.23s 00:00:00.57 Elapsed: 00:00:00.39
# Mc/sec: 339.98
//
Query:       gene2335|gene2335|rna2335|rna2335  [L=128]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.012   15.7   0.2      0.016   15.3   0.2    1.2  1  gp45-slide_C  gp45 sliding clamp, C terminal
      0.042   14.0   0.0       0.11   12.7   0.0    1.7  1  CheY-binding  CheY binding
      0.085   12.1   0.0       0.11   11.8   0.0    1.1  1  RAB3GAP2_N    Rab3 GTPase-activating protein regulatory subun


Domain annotation for each model (and alignments):
>> gp45-slide_C  gp45 sliding clamp, C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.2   2.6e-06     0.016      23      84 ..      45     110 ..      37     127 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.6e-06
                                        EEEE.EEETTEEEE...EEE-TTTSSSS-S-SEEEEEEE--SS--EEEEEEGGG----SS-EEEEE CS
                       gp45-slide_C  23 tiai.tveeGkivi...nGfnkvtdadlvrvkyslevgdydgeaefnflvnmanlkildddykvli 84 
                                        t+a+ t++ Gk+v+   n ++  t  d ++ kys + +d d +a + f +   n+ ++dd+y   i
  gene2335|gene2335|rna2335|rna2335  45 TLALgTTKSGKMVVlpsNYMEERTLKDEIDYKYSTNSSDHDITAIMCFGMVNGNMVFIDDEYEDAI 110
                                        566547899*****44444444455566889*****************9999**********8655 PP

>> CheY-binding  CheY binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   1.8e-05      0.11      34      54 ..      72      92 ..      64      98 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.8e-05
                       CheY-binding 34 slevtLettvseDDIvAVlcF 54
                                       +++   +t++s  DI+A++cF
  gene2335|gene2335|rna2335|rna2335 72 EIDYKYSTNSSDHDITAIMCF 92
                                       55666789************* PP

>> RAB3GAP2_N  Rab3 GTPase-activating protein regulatory subunit N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   1.8e-05      0.11       8      67 ..      38      96 ..      33     110 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1.8e-05
                         RAB3GAP2_N  8 slspdgellvlakeqk..avvlsskwssskeeneysiswrgsltedeeeeiItailclplss 67
                                       sl +dg++l+l+  ++  +vvl s+  ++ ++ + +i ++ s ++   ++ Itai+c+ +++
  gene2335|gene2335|rna2335|rna2335 38 SLLSDGSTLALGTTKSgkMVVLPSNYMEE-RTLKDEIDYKYSTNSS--DHDITAIMCFGMVN 96
                                       67899******976544499999888664.4444466666666666..455*******9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       702  (0.0391544); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.30s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 820.88
//
Query:       gene2336|gene2336|rna2336|rna2336  [L=332]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.012   16.0  29.7       0.02   15.3  29.7    1.3  1  DUF4604   Domain of unknown function (DUF4604)
       0.03   13.7  25.7      0.039   13.3  25.7    1.1  1  BUD22     BUD22


Domain annotation for each model (and alignments):
>> DUF4604  Domain of unknown function (DUF4604)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3  29.7   2.2e-06      0.02      86     163 ..     232     322 ..     197     327 .. 0.52

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.2e-06
                            DUF4604  86 eeegeeaeed...........iefkkpkkasikekasslaaksskkkkk.gkvvgeedeeeed............. 136
                                         +       d            e k++kk     ++s+ + k+++k+++ g+ +gee+ee++d             
  gene2336|gene2336|rna2336|rna2336 232 HK-------DdcdmhtdrcddDEDKDKKK----RRKSKDKKKGKRKRRRhGRRDGEEEEEDDDdstasysdedeye 296
                                        22.......12333332333211222222....2224444555666666799999999988889******887663 PP

                            DUF4604 137 kskakkkekekkkakkkkkkkkkkkkk 163
                                        + + +k+++++k +kkk+kk kk kkk
  gene2336|gene2336|rna2336|rna2336 297 S-RSEKRKDKDKRKKKKTKKTKKTKKK 322
                                        2.3332223333333333333333333 PP

>> BUD22  BUD22
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3  25.7   4.4e-06     0.039     173     279 ..     221     322 ..     179     331 .. 0.41

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.4e-06
                              BUD22 173 eesedsedeekeeseddeeeeeededdedaee.deedeeaeerelaqydglla.sddededeyneetdeesseesd 246
                                        + ++ ++d   + ++dd +  ++  dd+++++ +++ +++++++ ++  ++ +  d e+e+    e+d++s ++ +
  gene2336|gene2336|rna2336|rna2336 221 SCNKHKDD--CDGHKDDCDMHTDRCDDDEDKDkKKRRKSKDKKKGKRKRRRHGrRDGEEEE----EDDDDSTASYS 290
                                        22333333..222222222222222222222211111222222222222222233333333....12333333333 PP

                              BUD22 247 ssdssesasesesessekkkkkkkkkkkkakak 279
                                        ++d+ es se++++++++ kkkk+kk+kk+k+k
  gene2336|gene2336|rna2336|rna2336 291 DEDEYESRSEKRKDKDKR-KKKKTKKTKKTKKK 322
                                        333333333333333333.22333333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (332 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2846  (0.158737); expected 358.6 (0.02)
Passed bias filter:                      745  (0.0415528); expected 358.6 (0.02)
Passed Vit filter:                       212  (0.0118244); expected 17.9 (0.001)
Passed Fwd filter:                        55  (0.00306766); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.92u 0.35s 00:00:01.27 Elapsed: 00:00:00.49
# Mc/sec: 2032.58
//
Query:       gene2337|gene2337|rna2337|rna2337  [L=305]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.5e-55  185.7   0.0    1.2e-54  185.0   0.0    1.3  1  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
    3.8e-12   46.5   0.0    7.2e-12   45.6   0.0    1.5  1  Methyltr_RsmF_N  N-terminal domain of 16S rRNA methyltransfer
    0.00057   19.7   0.1    0.00089   19.1   0.1    1.3  1  Methyltransf_31  Methyltransferase domain
     0.0018   18.4   0.0     0.0029   17.7   0.0    1.4  1  FtsJ             FtsJ-like methyltransferase
  ------ inclusion threshold ------
      0.024   14.2   0.2      0.054   13.1   0.1    1.6  2  MTS              Methyltransferase small domain
      0.038   13.1   0.0      0.063   12.4   0.0    1.4  1  Fibrillarin      Fibrillarin
      0.097   12.5   0.1       0.19   11.6   0.1    1.4  1  SNO              SNO glutamine amidotransferase family


Domain annotation for each model (and alignments):
>> Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  185.0   0.0   4.6e-58   1.2e-54       2     198 ..     102     301 ..     101     303 .. 0.91

  Alignments for each domain:
  == domain 1  score: 185.0 bits;  conditional E-value: 4.6e-58
                                        HHH---TT-EEEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CTCCHHHHCC CS
                    Methyltr_RsmB-F   2 llLapqeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDarkidkvlgg 77 
                                        + L+ +e+  +lD+ca+PGgK t+iae+mkn+g ++ v++n eR++++  nl r+gv+n  v+++ +      +  
  gene2337|gene2337|rna2337|rna2337 102 MNLDVKEHMSVLDMCASPGGKSTFIAEMMKNTGMLYLVENNPERISSLSGNLLRMGVQNSVVINMNVLDL--EIE- 174
                                        67999**********************************************************9988766..444. PP

                                        ..EEEEEEEE--CCGGGTTT-TCHHHH--HHHHHHHHHHHHHHHHHHCCCEEEEEEEEEEES--STTTTHHHHHHH CS
                    Methyltr_RsmB-F  78 elfDriLlDaPCsgtgvirrdpdvklrrkekdiaqlaklqkellsaaidllkkgGvlvYsTCsvlveEneevieea 153
                                         ++Dr+LlDaPCsgtg+i++d ++k++ +e d++++++ qk+l+   +d+lk +G+++YsTCsvl +Ene v+e++
  gene2337|gene2337|rna2337|rna2337 175 -KVDRVLLDAPCSGTGTISKDGHAKTL-TEDDLKRYTEMQKKLILKGFDSLKGNGIMIYSTCSVLADENECVVEYL 248
                                        .6**********************988.789********************************************* PP

                                        HHH-TTEEEESSBSTTSTTSSECEEC...........TSEEE-TTTTSS-SEEEEE CS
                    Methyltr_RsmB-F 154 Lkkredvelvetelsepkglklgeea...........gtlrllPhtenkdgffiak 198
                                        L+kr+++++ e e + +k    g +a            ++r++Ph +n+dgff  k
  gene2337|gene2337|rna2337|rna2337 249 LRKRKNAKILECEGNVGK---KGFTAfrgmffdakmkYARRIFPHVHNMDGFFFVK 301
                                        *********999544433...333334457899998899**************987 PP

>> Methyltr_RsmF_N  N-terminal domain of 16S rRNA methyltransferase RsmF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.6   0.0   2.8e-15   7.2e-12       5      89 ..       9      97 ..       6      98 .. 0.89

  Alignments for each domain:
  == domain 1  score: 45.6 bits;  conditional E-value: 2.8e-15
                                       HHHHHHHHHGG.GHHHHHHHHH-----EEE--TTS..TTHHHH.HHH.-SS--B-TT-TTEEES---....TTSHHHH CS
                    Methyltr_RsmF_N  5 Fiekmkellge.eaeaflaaleeprkkglRvNtlKisveelek.lse.efelepvpwceeGfyleeeerp.gkhplhe 78
                                       F+ek+ ++++e e + fl+  e++r+  +RvNtlK++++el+k l + ++++e+ ++ +++  + +++ p g +p++ 
  gene2337|gene2337|rna2337|rna2337  9 FLEKIANMFNEeERAVFLEESEKKRPIVIRVNTLKATKKELAKnLLQrGMTVESLDFYSNCLTIYDSKVPvGATPEYL 86
                                       99*******99788899*******************9999987444479***********99877776666******* PP

                                       TTS-EE--TTT CS
                    Methyltr_RsmF_N 79 aGlyYiQEpSa 89
                                        G+yYiQ +S+
  gene2337|gene2337|rna2337|rna2337 87 DGWYYIQGASS 97
                                       **********9 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.1   3.5e-07   0.00089       3     119 ..     108     241 ..     106     276 .. 0.77

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 3.5e-07
                    Methyltransf_31   3 kglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDli 78 
                                        ++++vlD  +  G ++  +ae +   + ++++++++e i++   n+ + g++n  +   ++ +le  +e  k+D +
  gene2337|gene2337|rna2337|rna2337 108 EHMSVLDMCASPGGKSTFIAEMMKNTGMLYLVENNPERISSLSGNLLRMGVQNSVVINMNVLDLE--IE--KVDRV 179
                                        689*****************77777888*************************************..55..8**** PP

                    Methyltransf_31  79 lsnevl......................naladpdkileeiervlkpggilliedprllaelp 119
                                        l ++++                      ++   ++ il++ ++ lk +gi++ +++++la+  
  gene2337|gene2337|rna2337|rna2337 180 LLDAPCsgtgtiskdghaktlteddlkrYTEMQKKLILKG-FDSLKGNGIMIYSTCSVLADEN 241
                                        ***5555555555555555557777775555555555555.9999999999999999555443 PP

>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   1.1e-06    0.0029      20     132 ..     107     230 ..      91     278 .. 0.62

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.1e-06
                                        -TT-EEEECT-TTSHHHHHHCCT.T.-SEEEEEESSSSHHHTTEEEECS-CCCSSHHHHHCHCHHH.......... CS
                               FtsJ  20 kpgktvvDlgaaPGgwsqvllqrlgakgkvvavDlqpmaplpgvttiqgditdpetiekikealse.......... 85 
                                        k+ + v+D +a+PGg s ++++ ++++g+++ v  +p    ++++++ g+ +++ +++ +   ++           
  gene2337|gene2337|rna2337|rna2337 107 KEHMSVLDMCASPGGKSTFIAEMMKNTGMLYLVENNP----ERISSLSGNLLRMGVQNSVVINMNVldleiekvdr 178
                                        57788*******************8867777666666....55555555555555555443222223333311111 PP

                                        .......SSEEEEEE--S-SS-CHHHHHHHHHCCCCHHHHCCHCCCCECCCEEE CS
                               FtsJ  86 .......rkvdlvvsDgapdvsgvhdldeylqsqLllaalelalkllkpggtfv 132
                                               ++   +  Dg  ++    dl+ y++  + ++ +  +++ lk +g+++
  gene2337|gene2337|rna2337|rna2337 179 vlldapcSGTGTISKDGHAKTLTEDDLKRYTE--MQKKLILKGFDSLKGNGIMI 230
                                        11113444444555555544444455555554..34455555555566666555 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       2.3   5.8e+03      67      91 ..      41      67 ..      37      73 .. 0.68
   2 ?   13.1   0.1   2.1e-05     0.054      22     106 ..      99     184 ..      91     204 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 2.3
                                       HHHHHHHHHHHTTGC..EEEEE-STTT CS
                                MTS 67 Alesakenleankle..vevvasdvle 91
                                        l+++k+ l++n l+  ++v   d ++
  gene2337|gene2337|rna2337|rna2337 41 TLKATKKELAKNLLQrgMTVESLDFYS 67
                                       677788888888887655555556665 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 2.1e-05
                                        HHHHHCHCCTCSEEEEET-TTSHHHHHHHHHTTC.E.EEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTTTSTTS CS
                                MTS  22 lLletlpkelsgkvlDlGcGaGvlgaalakespeae.vtlvdvdarAlesakenleanklevevvasdvleeveek 96 
                                        l + +l+ +++ +vlD+++  G  ++ +a++ +++  + lv+++ + + s   nl + +++ +vv +  + ++e +
  gene2337|gene2337|rna2337|rna2337  99 LAVMNLDVKEHMSVLDMCASPGGKSTFIAEMMKNTGmLYLVENNPERISSLSGNLLRMGVQNSVVINMNVLDLEIE 174
                                        3467888888899*****************99998889***********************555555444455668 PP

                                        -EEEEEE--- CS
                                MTS  97 kfdlivsNPP 106
                                        k+d ++   P
  gene2337|gene2337|rna2337|rna2337 175 KVDRVLLDAP 184
                                        9999998777 PP

>> Fibrillarin  Fibrillarin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   2.4e-05     0.063      58     109 ..      97     147 ..      65     164 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.4e-05
                                        HHHTT-S--S--TTSEEEEESTTTSHHHHHHHHHHTTTSEEEEEESSHHHHH CS
                        Fibrillarin  58 ailkglkelpikkgskvLYlGaasGttvsHvsDivgeegvvyavefsprvlr 109
                                        +il  + +l +k+  +vL + a+ G     ++++++++g++y ve  p  + 
  gene2337|gene2337|rna2337|rna2337  97 SIL-AVMNLDVKEHMSVLDMCASPGGKSTFIAEMMKNTGMLYLVENNPERIS 147
                                        444.566799***********************************9887665 PP

>> SNO  SNO glutamine amidotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   7.3e-05      0.19      23     101 ..     102     174 ..      92     179 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 7.3e-05
                                        EEE-SGGGGCC-SEEEE-SS-HHHHHHHHHHTT-HHHHHHHHHTT.--EEEETHHHHHHCCEETTBSS-SS--CCE CS
                                SNO  23 ktvkrkedlaevdaliiPGGestamskliertglyedllefvknsekvvlGtCaGlillskelenelvktlellkv 98 
                                        +++  ke++  +d    PGG st ++ ++++tg    l+   +n+e++     +G  ll  +++n+ v ++++l++
  gene2337|gene2337|rna2337|rna2337 102 MNLDVKEHMSVLDMCASPGGKSTFIAEMMKNTG---MLYLVENNPERI--SSLSGN-LLRMGVQNSVVINMNVLDL 171
                                        5566678899999999*****************...566555666543..333443.4566777777777777777 PP

                                        EEE CS
                                SNO  99 kvk 101
                                        +++
  gene2337|gene2337|rna2337|rna2337 172 EIE 174
                                        765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (305 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       664  (0.037035); expected 358.6 (0.02)
Passed bias filter:                      550  (0.0306766); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 1962.00
//
Query:       gene2338|gene2338|rna2338|rna2338  [L=864]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.9e-81  274.0   3.8    7.2e-60  203.0   0.0    3.0  2  A_deaminase  Adenosine/AMP deaminase


Domain annotation for each model (and alignments):
>> A_deaminase  Adenosine/AMP deaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.8   3.5   1.1e-22     2e-18       2     106 ..     194     389 ..     193     406 .. 0.97
   2 !  203.0   0.0     4e-64   7.2e-60     115     327 ..     618     817 ..     605     818 .. 0.98

  Alignments for each domain:
  == domain 1  score: 66.8 bits;  conditional E-value: 1.1e-22
                                        S-EEEEEEECCCSS-HHHHHHHHHHHCHT..SS-SCCCCCCCCHCHCCHHHHCCHCCCHHCCCHHHT......... CS
                        A_deaminase   2 lpKvdlHvHldgclnpktllrlakkkgikeldekvveedeklltlqekfesLkeflydlsvdvlvlh......... 68 
                                        + Kvd H+H+++++n k+ll+++k+k + + d++v+++d+k  tl+e+f+ L+ + ++l ++  + h         
  gene2338|gene2338|rna2338|rna2338 194 VYKVDNHIHHSAAINCKHLLKFIKRKIKFNSDDVVYKKDGKTYTLREVFKHLNITVDELRIENIDTHshtdtfhrf 269
                                        569************************************************************************* PP

                                        ............................................................................ CS
                        A_deaminase  69 ............................................................................ 68 
                                                                                                                    
  gene2338|gene2338|rna2338|rna2338 270 drfnnkynllgqsllreiflkydnfidgrylaeltkelinyykenkyqnvelrisvygkskdefyklahwiesnkl 345
                                        **************************************************************************** PP

                                        ......CCCCCCHHHHHHCCCCCHCTTCCCCCCCCSHHHHHHH- CS
                        A_deaminase  69 ......wlievvrllavekakdlakdfvkylevifsPlfeatag 106
                                              w+++++rl+   k k  +k+f ++l++if+Plf+at  
  gene2338|gene2338|rna2338|rna2338 346 yskhikWVVQIPRLFPNLKEKYNIKSFGEMLQNIFDPLFKATEF 389
                                        *****************************************975 PP

  == domain 2  score: 203.0 bits;  conditional E-value: 4e-64
                                        HHCCCCCCCCCCHCCT-EEEEEECCETTTCCGHCCCHHHHHHCCCCCCCCCCCCC-TTSTTGGGHHHHHCCCCHTT CS
                        A_deaminase 115 vlkvvdgfdsvedeskvkerlilvksrkpeewseeinelasyyrdytvvnldllndekiepaslflklraeagkst 190
                                        +l  + gfd v+des   er  + k+++p+ew + +n+++syy +  ++n+++ln           + r+++  +t
  gene2338|gene2338|rna2338|rna2338 618 FLRNLGGFDTVDDESM-RERKYHQKFPSPDEWIHSENPPYSYYIYFLYTNIKMLN-----------DFRRSKKLNT 681
                                        566788*********9.**************************************...........********** PP

                                        -EEEEEESSSS-CHHHHHHHHCS--SCECE-GGGGGSHHHHHHHHHCT-EEEE-HHHHCCCSST-TTTT-CHHHHH CS
                        A_deaminase 191 llltpHaGEagglehvveAllllkaerigHGvrlrkdpvLqyllalaqiplevcPlSNvalgafleyaenPlkefl 266
                                        +++ pH+GE+g+ eh+v+++l+  a++i HGv+lrk   L yl++  qi+++++PlSN++l  f ++++nP+ +f+
  gene2338|gene2338|rna2338|rna2338 682 FKFIPHSGETGDYEHLVNTFLT--ADSICHGVQLRKCFPLTYLFYACQIGVTMSPLSNNSL--FIALEKNPFINFF 753
                                        **********************..*************************************..************* PP

                                        HTT-EEEE--BSCCCCT-S...HHHHHHHHHHHHT--HHHHHHHHHHHHHCSSS-HHHHHHHCH CS
                        A_deaminase 267 erglnvslntDDPlqfgtt...LieeYaiaaqvfklseedlaelarNsvkqsflsadekkklld 327
                                        + gln+sl+tDDPl f++t   L+eeY++++q +kls++d +elarNsv qs +s++ kk+ ++
  gene2338|gene2338|rna2338|rna2338 754 NIGLNLSLSTDDPLHFHFTrdpLMEEYSVISQLYKLSSVDQCELARNSVIQSNFSFEWKKEVIG 817
                                        ************************************************************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (864 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1197  (0.0667633); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.67u 0.29s 00:00:00.96 Elapsed: 00:00:00.45
# Mc/sec: 5814.99
//
Query:       gene2339|gene2339|rna2339|rna2339  [L=121]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.3e-13   50.4   1.3    2.4e-13   49.6   1.3    1.4  1  zf-U1        U1 zinc finger
  ------ inclusion threshold ------
       0.38   11.1   7.8        1.9    8.9   2.6    2.2  2  zf-C2H2_jaz  Zinc-finger double-stranded RNA-binding
       0.93   10.0   4.9         15    6.2   1.0    2.3  2  zf-met       Zinc-finger of C2H2 type


Domain annotation for each model (and alignments):
>> zf-U1  U1 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.6   1.3     4e-17   2.4e-13       1      38 []       6      43 ..       6      43 .. 0.99

  Alignments for each domain:
  == domain 1  score: 49.6 bits;  conditional E-value: 4e-17
                                       XXSEEETTTTEEESS-SHHHHHHHHTSHHHHHHHHHHH CS
                              zf-U1  1 mpkYyCdYCdiyLthDspsvRksHngGrkHkenvkdyy 38
                                       mpkY+C +Cdi L ++  ++Rk+H++G+kHk  +k+yy
  gene2339|gene2339|rna2339|rna2339  6 MPKYFCPFCDISLPNSLYRSRKTHISGKKHKLLKKAYY 43
                                       9************************************9 PP

>> zf-C2H2_jaz  Zinc-finger double-stranded RNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.2    0.0046        28       1      10 [.       8      17 ..       8      22 .. 0.83
   2 ?    8.9   2.6   0.00031       1.9      18      27 .]      27      36 ..      24      36 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0046
                                       ECBBTTTTBB CS
                        zf-C2H2_jaz  1 qfYCvlCdKy 10
                                       +++C+ Cd  
  gene2339|gene2339|rna2339|rna2339  8 KYFCPFCDIS 17
                                       69*****975 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00031
                                       HCCTTSHHHH CS
                        zf-C2H2_jaz 18 dnHlkSKkHK 27
                                       ++H+++KkHK
  gene2339|gene2339|rna2339|rna2339 27 KTHISGKKHK 36
                                       89*******9 PP

>> zf-met  Zinc-finger of C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.2     0.004        24       1      11 [.       9      19 ..       9      23 .. 0.87
   2 ?    6.2   1.0    0.0024        15      17      25 .]      27      35 ..      24      35 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.004
                             zf-met  1 fyCelCnvtfn 11
                                       ++C+ C++++ 
  gene2339|gene2339|rna2339|rna2339  9 YFCPFCDISLP 19
                                       89******986 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0024
                             zf-met 17 ksHlqGKkH 25
                                       k+H  GKkH
  gene2339|gene2339|rna2339|rna2339 27 KTHISGKKH 35
                                       89******* PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       641  (0.0357521); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.47
# Mc/sec: 775.89
//
Query:       gene234|gene234|rna234|rna234  [L=294]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.5e-14   54.2  14.2    1.5e-14   54.2  14.2    1.7  2  Syntaxin       Syntaxin
    3.3e-05   23.8   4.3    0.00014   21.8   4.3    2.2  1  SNARE          SNARE domain
     0.0057   15.9   0.9     0.0082   15.4   0.9    1.2  1  Lung_7-TM_R    Lung seven transmembrane receptor
  ------ inclusion threshold ------
      0.094   11.6   7.8       0.14   11.1   7.8    1.2  1  LMBR1          LMBR1-like membrane protein
       0.17   11.9   1.3       0.94    9.5   0.1    2.3  2  VitD-bind_III  Vitamin D binding protein, domain III
        0.3   11.6   2.7        8.6    7.0   0.1    3.6  3  YtxH           YtxH-like protein
       0.32   11.4  17.4        1.2    9.5   1.5    3.1  2  Syntaxin_2     Syntaxin-like protein
       0.49   10.7   0.1       0.49   10.7   0.1    4.0  4  Syntaxin-18_N  SNARE-complex protein Syntaxin-18 N-terminus
       0.59   10.6  10.4      0.034   14.6   3.0    2.4  3  ThiD2          ThiD2 family
        1.1    9.6   8.5        1.5    9.2   0.3    3.7  3  DUF948         Bacterial protein of unknown function (DUF948)
        1.5    8.5   7.9       0.18   11.5   0.8    2.2  2  DUF745         Protein of unknown function (DUF745)
        2.2    8.4  10.0       0.15   12.2   1.0    2.8  3  COG2           COG (conserved oligomeric Golgi) complex compo
        3.5    6.6  18.0       0.23   10.5   3.2    2.1  2  Atg14          Vacuolar sorting 38 and autophagy-related subu


Domain annotation for each model (and alignments):
>> Syntaxin  Syntaxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.2  14.2   1.1e-17   1.5e-14       1     188 [.       1     189 [.       1     199 [. 0.89
   2 ?   -0.8   0.3      0.72   9.9e+02      31      48 ..     208     226 ..     189     240 .. 0.44

  Alignments for each domain:
  == domain 1  score: 54.2 bits;  conditional E-value: 1.1e-17
                       Syntaxin   1 leeffkeveeikkeiekleeevkklkkqneeskts.traksvk.lkkrmesdikeikkraesvkarLeaLdksnkenekk 78 
                                    ++ef+   ++i++ei+kl++ ++klk   ++  +s  +  +   l +r+  + +  k++++ vk++L+ ++++nke   +
  gene234|gene234|rna234|rna234   1 MDEFLGRCKKIEDEIDKLRQYIHKLKVLSNRKANSiLSDREETeLDNRITVLNNMFKENSKRVKEKLKDMHEENKEISPE 80 
                                    899*********************997655444431333333349*******************************9988 PP

                       Syntaxin  79 sgegsavdRirksqtaaLrkklkevmteynelrekireeykerieRrlevtGkevseeeieelietgesevflqkllqeq 158
                                     +e +a++R ++   ++L++ l e+++ y++ + ++++e k+r++ ++ ++  +++e+e+ +l+++ e   +l+k ++ +
  gene234|gene234|rna234|rna234  81 DEEFEADTRNNRW--QVLTNYLAETIELYRTEQLNHTKEEKQRLKAQFLIAKPDATEDELHDLVNSSEGHKLLEKEFKPG 158
                                    8888888887765..58*************************************************************** PP

                       Syntaxin 159 .rgarealseieeRhkevlelekslkeLhql 188
                                     r+++  l+   eR+k+++++ +s++eL  l
  gene234|gene234|rna234|rna234 159 aRSSKGILKKAGERNKNIKNIVNSINELVSL 189
                                    9999***********************9665 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.72
                       Syntaxin  31 esktstraksvk.lkkrme 48 
                                    e+   +++k+vk  kk++e
  gene234|gene234|rna234|rna234 208 EIEIDVTRKTVKeAKKDLE 226
                                    2222333333333333322 PP

>> SNARE  SNARE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   4.3     1e-07   0.00014       2      52 ..     203     253 ..     202     262 .. 0.93

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 1e-07
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTXXXXXXXXXXXXXXXXXXX CS
                          SNARE   2 mvDrIdtnVenaqsnveraqkeLkkavkyqksnRklkciillilviillvv 52 
                                    +vD+I+ +++ ++  v++a+k L ka++yqk +   k  il i+ + + ++
  gene234|gene234|rna234|rna234 203 IVDNIEIEIDVTRKTVKEAKKDLEKARNYQKAAMYIKYVILFIFALAISFL 253
                                    79***********************************99999998887765 PP

>> Lung_7-TM_R  Lung seven transmembrane receptor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.9   5.9e-06    0.0082     209     256 ..     218     263 ..     174     273 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 5.9e-06
                    Lung_7-TM_R 209 LqktlrdlklkrnlvklklYrkftvvlvisvvasviivlvekillktv 256
                                     ++  +dl  +rn++k+ +Y k++++ ++++ +s++i+ v  ++l   
  gene234|gene234|rna234|rna234 218 VKEAKKDLEKARNYQKAAMYIKYVILFIFALAISFLIIGVILFAL--A 263
                                    5667899******************************99986654..3 PP

>> LMBR1  LMBR1-like membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   7.8   9.8e-05      0.14     209     378 ..      49     267 ..       8     286 .. 0.54

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 9.8e-05
                          LMBR1 209 aaklntekeeaereledllkevkklrksisesd............p.lrkyleeilk.................kvPeei 258
                                    +  ln+  +e+ ++++++lk++ + +k+is +d            + l +yl e ++                 k     
  gene234|gene234|rna234|rna234  49 ITVLNNMFKENSKRVKEKLKDMHEENKEISPEDeefeadtrnnrwQvLTNYLAETIElyrteqlnhtkeekqrlK----- 123
                                    333444444555777888888888888888777777777776555335555555555555555544444444440..... PP

                          LMBR1 259 aeklks..............................................nenkteeslaklekqlikalqkrertek 292
                                         +                                              ++nk+ ++++++ ++l + + + ++   
  gene234|gene234|rna234|rna234 124 -----AqfliakpdatedelhdlvnsseghkllekefkpgarsskgilkkagERNKNIKNIVNSINELVSLIDELHEMVM 198
                                    .....144444443333333334444666555555555555433333333332222222222222222222222222222 PP

                          LMBR1 293 qwkrllekalelediiknksskekefkssessrrgefakqgklkltptleyywaklllplvllilsiilvllsiiiilse 372
                                    +            +i++n + +    +++ ++ ++ + k ++    ++  +y++ ++l    +i+++++++l+i +il  
  gene234|gene234|rna234|rna234 199 NS----------RKIVDNIEIEIDVTRKTVKEAKKDLEKARN---YQKAAMYIKYVIL----FIFALAISFLIIGVILFA 261
                                    22..........344444444444444444455555555555...6778888888888....788888888888888877 PP

                          LMBR1 373 ltklle 378
                                    l kl++
  gene234|gene234|rna234|rna234 262 LAKLFF 267
                                    777775 PP

>> VitD-bind_III  Vitamin D binding protein, domain III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.1      0.46   6.3e+02       9      24 ..      54      69 ..      51      80 .. 0.82
   2 ?    9.5   0.1   0.00068      0.94      13      40 ..     117     144 ..     109     147 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.46
                  VitD-bind_III  9 ltFleyKkrlaeklkk 24
                                   + F e  kr++eklk 
  gene234|gene234|rna234|rna234 54 NMFKENSKRVKEKLKD 69
                                   78999999***99986 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00068
                  VitD-bind_III  13 eyKkrlaeklkkklPeaspeelkelvek 40 
                                    e K+rl+ ++  + P+a++ el++lv+ 
  gene234|gene234|rna234|rna234 117 EEKQRLKAQFLIAKPDATEDELHDLVNS 144
                                    569**********************985 PP

>> YtxH  YtxH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.1    0.0062       8.6      29      70 ..      10      74 ..       8      78 .. 0.65
   2 ?    5.0   1.6     0.025        35      29      53 ..      55      90 ..      50     237 .. 0.80
   3 ?   -1.9   0.0       3.7   5.2e+03       4      24 ..     253     273 ..     250     289 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0062
                           YtxH 29 dlkekaddlkekakelleeakeka.......................kekaedlkekvkekadel 70
                                   ++ ++ d+l++ + +l+   + ka                       ke+++ +kek+k+  +e 
  gene234|gene234|rna234|rna234 10 KIEDEIDKLRQYIHKLKVLSNRKAnsilsdreeteldnritvlnnmfKENSKRVKEKLKDMHEEN 74
                                   45555555555554444444444477888888888888888888888888888888888776664 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.025
                           YtxH 29 dlkekaddlkekakelleeakeka...........k 53
                                     ke+ + +kek+k+++ee ke +           +
  gene234|gene234|rna234|rna234 55 MFKENSKRVKEKLKDMHEENKEISpedeefeadtrN 90
                                   567888889999999988888777665555555550 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 3.7
                           YtxH   4 lliGaavGaaaglLlAPksGk 24 
                                    l+iG+++ a+a l+++   G+
  gene234|gene234|rna234|rna234 253 LIIGVILFALAKLFFSSWQGE 273
                                    677888888888888765554 PP

>> Syntaxin_2  Syntaxin-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   8.4     0.011        15       1      67 [.      11      88 ..      11     130 .. 0.69
   2 ?    9.5   1.5   0.00088       1.2       3      61 ..     174     233 ..     170     240 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.011
                     Syntaxin_2  1 issnlqkinsnvstleklvkq....Lgtkkdteelreklhelieeinelikktnellkklsqldnsssds.......q 67
                                   i++++ k+ + + +l+ l +     + ++++ +el++++  l +  +e +k+++e+lk++ +  +  s +       +
  gene234|gene234|rna234|rna234 11 IEDEIDKLRQYIHKLKVLSNRkansILSDREETELDNRITVLNNMFKENSKRVKEKLKDMHEENKEISPEdeefeadT 88
                                   5677888888888887776665445778899*****************************984444333345555552 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00088
                     Syntaxin_2   3 snlqkinsnvstleklvkqLgtk.kdteelreklhelieeinelikktnellkklsqldn 61 
                                    +n+++i +++++l +l++ L+    +++++ ++++  i+ +++++k+ +++l+k  ++++
  gene234|gene234|rna234|rna234 174 KNIKNIVNSINELVSLIDELHEMvMNSRKIVDNIEIEIDVTRKTVKEAKKDLEKARNYQK 233
                                    5777777777777777777777744799999*********************99988765 PP

>> Syntaxin-18_N  SNARE-complex protein Syntaxin-18 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   0.00036      0.49      42      66 ..       2      26 ..       1      45 [. 0.84
   2 ?   -0.3   0.9      0.92   1.3e+03      13      44 ..      62      84 ..      49     122 .. 0.45
   3 ?    2.5   0.3      0.13   1.8e+02      34      64 ..     165     192 ..     132     204 .. 0.53
   4 ?   -1.6   0.1       2.4   3.3e+03       8      16 ..     215     223 ..     194     238 .. 0.57

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00036
                  Syntaxin-18_N 42 deFikeAkeilkhItkLrkfLleir 66
                                   deF+ ++k+i   I+kLr+++++ +
  gene234|gene234|rna234|rna234  2 DEFLGRCKKIEDEIDKLRQYIHKLK 26
                                   89******************99875 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.92
                  Syntaxin-18_N 13 tvkasssskseekeakkrkkkrlkkskekdeF 44
                                    v         +++ k++++++++ s e++eF
  gene234|gene234|rna234|rna234 62 RV---------KEKLKDMHEENKEISPEDEEF 84
                                   33.........222233333333333333333 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.13
                  Syntaxin-18_N  34 rlkkskekdeFikeAkeilkhItkLrkfLle 64 
                                    +lkk  e+++ i   k+i+++I++L +++ e
  gene234|gene234|rna234|rna234 165 ILKKAGERNKNI---KNIVNSINELVSLIDE 192
                                    444444444333...3455555555444433 PP

  == domain 4  score: -1.6 bits;  conditional E-value: 2.4
                  Syntaxin-18_N   8 kasVktvka 16 
                                    +++Vk+ k+
  gene234|gene234|rna234|rna234 215 RKTVKEAKK 223
                                    344444421 PP

>> ThiD2  ThiD2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   3.0   2.5e-05     0.034      32     118 ..       6      94 ..       2     103 .. 0.85
   2 ?   -1.4   0.0       2.3   3.2e+03      44      71 ..     118     145 ..      92     153 .. 0.60
   3 ?   -0.3   0.2         1   1.4e+03      18      72 ..     191     216 ..     167     237 .. 0.42

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.5e-05
                          ThiD2  32 eelkelRhelaelekeleeaellaaRdtegDvgkelsteeekeresleevvaanlkRvqeslRvleEllklieael..aa 109
                                     ++k++  e+++l++ +++ ++l++R++++  + + +te +++ + l+++++ n+kRv+e l+ + E  k i++e    +
  gene234|gene234|rna234|rna234   6 GRCKKIEDEIDKLRQYIHKLKVLSNRKANSILSDREETELDNRITVLNNMFKENSKRVKEKLKDMHEENKEISPEDeeFE 85 
                                    57899999********999**********999999888888899999***********************9998874433 PP

                          ThiD2 110 ekvkkiRyr 118
                                    +  ++ R++
  gene234|gene234|rna234|rna234  86 ADTRNNRWQ 94 
                                    345555555 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2.3
                          ThiD2  44 lekeleeaellaaRdtegDvgkelstee 71 
                                     +++l+++ l+a+ d+++D  ++l +++
  gene234|gene234|rna234|rna234 118 EKQRLKAQFLIAKPDATEDELHDLVNSS 145
                                    2222456667777777777776665555 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 1
                          ThiD2  18 ediarfvlddeelteelkelRhelaelekeleeaellaaRdtegDvgkelsteee 72 
                                    +++   v++++++  ++                               e+  +++
  gene234|gene234|rna234|rna234 191 DELHEMVMNSRKIVDNI-----------------------------EIEIDVTRK 216
                                    33333333333333322.............................222221111 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.3      0.49   6.8e+02      23      47 ..      10      38 ..       4      88 .. 0.55
   2 ?    9.2   0.3    0.0011       1.5      22      78 ..     167     222 ..     151     231 .. 0.79
   3 ?    2.9   0.1     0.093   1.3e+02       4      21 ..     244     261 ..     241     288 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.49
                         DUF948 23 klkktldeaaatieele....kqvdpilk 47
                                   k+++ +d++++ i++l+    +++++il 
  gene234|gene234|rna234|rna234 10 KIEDEIDKLRQYIHKLKvlsnRKANSILS 38
                                   55666666666666665555533333332 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0011
                         DUF948  22 lklkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteava 78 
                                    +k+++  +++++ +++++ ++ ++++e+++++ ++++++++++ +++   + +++++
  gene234|gene234|rna234|rna234 167 KKAGERNKNIKNIVNSIN-ELVSLIDELHEMVMNSRKIVDNIEIEIDVTRKTVKEAK 222
                                    555555555555555554.677899*****************999999998888776 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.093
                         DUF948   4 lIaAiAFvvLviflivvl 21 
                                    +I+A+A+++L+i +i + 
  gene234|gene234|rna234|rna234 244 FIFALAISFLIIGVILFA 261
                                    799999999988777554 PP

>> DUF745  Protein of unknown function (DUF745)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   1.8      0.36   4.9e+02      83     132 ..      26      76 ..       8     125 .. 0.60
   2 ?   11.5   0.8   0.00013      0.18      85     174 ..     141     230 ..     120     237 .. 0.72

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.36
                         DUF745  83 kslqsseanakaaakaakqaqqqlealkallkaakenlen.aeqvaagaqq 132
                                    k l++ +an  +  +  ++  + +++l++++k+ ++++++ ++++ ++ ++
  gene234|gene234|rna234|rna234  26 KVLSNRKANSILSDREETELDNRITVLNNMFKENSKRVKEkLKDMHEENKE 76 
                                    456666667777777777778888888888877666554403444433333 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00013
                         DUF745  85 lqsseanakaaakaakqaqqqlealkallkaakenlenaeqvaagaqqelaektqlleaAkkRveeLkkqlkearkdlek 164
                                    l +s++  k+ +k  k   ++ + + +   + ++n++n+ +  ++  + ++e ++++++++k v++++ +++  rk  ++
  gene234|gene234|rna234|rna234 141 LVNSSEGHKLLEKEFKPGARSSKGILKKAGERNKNIKNIVNSINELVSLIDELHEMVMNSRKIVDNIEIEIDVTRKTVKE 220
                                    55555555555555554444444444444556677888888888888889999999999999999999999999999999 PP

                         DUF745 165 tkkaAykAac 174
                                     kk  +kA  
  gene234|gene234|rna234|rna234 221 AKKDLEKARN 230
                                    9998888864 PP

>> COG2  COG (conserved oligomeric Golgi) complex component, COG2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       1.1   1.5e+03      83     101 ..       9      27 ..       2      45 .. 0.62
   2 ?    0.5   0.6      0.42   5.8e+02      80     101 ..      58      76 ..      39     115 .. 0.51
   3 ?   12.2   1.0   0.00011      0.15      51     122 ..     173     244 ..     172     249 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1.1
                           COG2  83 kkvesvreklsereeeves 101
                                    kk+e+ ++kl + +++++ 
  gene234|gene234|rna234|rna234   9 KKIEDEIDKLRQYIHKLKV 27 
                                    5566666666655555554 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.42
                           COG2  80 aarkkvesvreklsereeeves 101
                                    +  k+   v+ekl++++ee ++
  gene234|gene234|rna234|rna234  58 ENSKR---VKEKLKDMHEENKE 76 
                                    22222...22222222222222 PP

  == domain 3  score: 12.2 bits;  conditional E-value: 0.00011
                           COG2  51 nedyadFvslSghLvglqeeleevesplaaarkkvesvreklsereeeveskleeakeleekrellklllkl 122
                                    n+++++ v+  ++Lv+l +el+e+  +  ++++++e  ++   ++ +e ++ le+a++ +++ +++k ++++
  gene234|gene234|rna234|rna234 173 NKNIKNIVNSINELVSLIDELHEMVMNSRKIVDNIEIEIDVTRKTVKEAKKDLEKARNYQKAAMYIKYVILF 244
                                    6777777777789****************************************************9998876 PP

>> Atg14  Vacuolar sorting 38 and autophagy-related subunit 14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   6.9     0.093   1.3e+02      83     196 ..       8     129 ..       5     133 .. 0.55
   2 ?   10.5   3.2   0.00017      0.23      35     115 ..     151     229 ..     144     239 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.093
                          Atg14  83 lqelkdklsqlkkeieekkkklaklsdklk......kRrsdleslqneleerrkkqiaklqdaik...rieqklsslssk 153
                                    +++++d +++l++ i + k    ++ +++       +   ++  l+n+ +e+ k+  +kl d+     +i+   ++++ +
  gene234|gene234|rna234|rna234   8 CKKIEDEIDKLRQYIHKLKVLSNRKANSILsdreetELDNRITVLNNMFKENSKRVKEKLKDMHEenkEISPEDEEFEAD 87 
                                    55666666666666555555444444443356666655555556777777777666666666666222444446666666 PP

                          Atg14 154 tlesr.sslcselaklyglrrtsyergkwvfskngeseesytIg 196
                                    t   r ++l   la+  +l rt+    + ++++++++++++ I+
  gene234|gene234|rna234|rna234  88 TRNNRwQVLTNYLAETIELYRTEQL--NHTKEEKQRLKAQFLIA 129
                                    6665513444556777777774333..34666666777777765 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00017
                          Atg14  35 ksekeslkkkiekalegkeeaeqledkiknkkakleelksliadlrerlqelkdklsqlkkeieekkkklaklsdklkkR 114
                                    +++ +  + + +k + +k   ++++++ikn  ++++el sli +l+e + + ++ +++   ei+ ++k++++ +++l k 
  gene234|gene234|rna234|rna234 151 LEKEFKPGARSSKGILKKA--GERNKNIKNIVNSINELVSLIDELHEMVMNSRKIVDNIEIEIDVTRKTVKEAKKDLEKA 228
                                    5555555566666666666..899**************************************************999743 PP

                          Atg14 115 r 115
                                    r
  gene234|gene234|rna234|rna234 229 R 229
                                    3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (294 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2958  (0.164984); expected 358.6 (0.02)
Passed bias filter:                      806  (0.0449551); expected 358.6 (0.02)
Passed Vit filter:                        93  (0.00518713); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.71u 0.28s 00:00:00.99 Elapsed: 00:00:00.45
# Mc/sec: 1953.84
//
Query:       gene2340|gene2340|rna2340|rna2340  [L=593]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.5e-30  106.4   0.0      6e-30  104.5   0.0    2.0  2  ABC_tran       ABC transporter
    4.6e-14   52.7  18.9    4.6e-14   52.7  18.9    1.6  2  ABC_membrane   ABC transporter transmembrane region
    2.2e-10   40.4   3.6    3.8e-07   29.8   0.3    2.5  2  SMC_N          RecF/RecN/SMC N terminal domain
    1.3e-07   31.8   3.6     0.0075   16.1   0.5    2.6  3  AAA_21         AAA domain, putative AbiEii toxin, Type IV TA 
     0.0035   17.1   9.6     0.0035   17.1   9.6    2.7  2  AAA_15         AAA ATPase domain
  ------ inclusion threshold ------
      0.023   14.4   0.0      0.054   13.2   0.0    1.6  1  AAA_24         AAA domain
      0.026   14.3   0.1       0.12   12.1   0.0    2.0  2  AAA_29         P-loop containing region of AAA domain
      0.046   13.6   0.0        0.1   12.5   0.0    1.7  1  RsgA_GTPase    RsgA GTPase
       0.14   12.0   0.4       0.45   10.4   0.1    2.1  2  Sec23_helical  Sec23/Sec24 helical domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       1.8   3.5e+03      79     122 ..     193     245 ..     171     248 .. 0.60
   2 !  104.5   0.0     3e-33     6e-30       2     137 .]     365     512 ..     364     512 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.8
                                        H......HHHTCHHHHHHHSTTGG.TTCBGESTTS..GGS-HHHHHHHHHHHH CS
                                        x......xxxxxxxxxxxxxxxxx.xxxxxxxxxx..xxxxxxxxxxxxxxxx RF
                           ABC_tran  79 n......esdeeiekalsklglke.lkdtvvkssp..ssLSgGqkqrvalara 122
                                        +      es++++ ++ls+++ +  +++++++  +  ++L   +k  v+l r+
  gene2340|gene2340|rna2340|rna2340 193 KlnlsinESNNKLIDILSNYESILaFNNQNLELYKydNKLATSEKHYVKLWRT 245
                                        14444557778888888887765445555554433447777777777777766 PP

  == domain 2  score: 104.5 bits;  conditional E-value: 3e-33
                                        EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHH CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvr 77 
                                        kn+s+++k+gek+a++G+nG GKS +lk+l++  +   G+i++d+++l +++  slr  i+++pq++ l +++ v+
  gene2340|gene2340|rna2340|rna2340 365 KNMSFEIKKGEKIALIGPNGIGKSNFLKMLLKFNE-YTGSIKIDDDELCTIDNYSLRDLISYVPQNSYLVSGT-VK 438
                                        8*******************************987.79*********************************99.** PP

                                        HH.......HHHTCHHHHHHHSTTGG.......TTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                        xx.......xxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ABC_tran  78 en.......esdeeiekalsklglke.......lkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                        en       + dee+ ++ ++l+ +e         +t ++++ s LSgG+kq+va+ara+lk+++++l+DEpta
  gene2340|gene2340|rna2340|rna2340 439 ENikygnlvATDEEMIELCRSLNFHEsfvrlssGYETCIGENNSVLSGGEKQKVAIARAMLKNAEIYLFDEPTA 512
                                        *********8888877777777777777777668899999999*****************************97 PP

>> ABC_membrane  ABC transporter transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.7  18.9   2.3e-17   4.6e-14      47     270 ..      68     288 ..      24     292 .. 0.91
   2 ?   -3.3   0.0       2.8   5.7e+03      79      94 ..     301     316 ..     298     317 .. 0.83

  Alignments for each domain:
  == domain 1  score: 52.7 bits;  conditional E-value: 2.3e-17
                                        HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCSTHHHHHHSCHHHHHHHHHHHHHHHHHHHCHHHHHH CS
                       ABC_membrane  47 llllglaqfilallqsyllnvtgerlskrlrrklfkkilrqpmsffdtnsvGellsrltndvsklrdglgeklglf 122
                                        ++++g+++++l  lq +++    +r+ ++  ++ ++  l ++ s f  +  Ge+++ + +  s ++++l  +++ +
  gene2340|gene2340|rna2340|rna2340  68 YMIVGILSSLLIELQGFIFKSSVQRAYRTALKSSLREYLLLNWSEFKMKGMGEITASIERRSSAVSEILDVFIINL 143
                                        899*******************************************************************999888 PP

                                        HH.HHHHHHHHHHHHHHHSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHTT CS
                       ABC_membrane 123 fq.slltfvgglivmfylgwkltlvllailpliilvsaviakilkklkkkeqkavakassvaeEslsgirtVkafg 197
                                        +  ++++f+++l ++ ++g   +l++l+ l+ +  v++ +a + ++++kk + +++++++ ++++ls+++ + af+
  gene2340|gene2340|rna2340|rna2340 144 LPvFFVLFLAVLKIYAIMGFTSSLIILISLITYTTVTIKMAVWRNEIRKKLNLSINESNNKLIDILSNYESILAFN 219
                                        87255678888999999*********************************************************** PP

                                        THHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSTHHHHHHHHHHHHHH CS
                       ABC_membrane 198 reeyflekfekaleeakkagikkaianglligitqllgllsyalalwfGttlvisgelsvgdlvvflslfail 270
                                        +++ +l k++++l + +k ++k  ++  ll+  ++++ ++ + +++++G+      +++++++v +ls++ il
  gene2340|gene2340|rna2340|rna2340 220 NQNLELYKYDNKLATSEKHYVKLWRTFYLLNFLQRFVLCVQTGMIIYVGMCN----KITSDQFVLYLSISKIL 288
                                        **********************************999999999998888764....47788888888877766 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 2.8
                                        HHHHHHHCSTHHHHHH CS
                       ABC_membrane  79 klfkkilrqpmsffdt 94 
                                        ++  +il++ msf dt
  gene2340|gene2340|rna2340|rna2340 301 RFTAAILNAKMSFLDT 316
                                        66789********996 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   0.5     9e-05      0.18      21      44 ..     370     394 ..     360     461 .. 0.78
   2 !   29.8   0.3   1.9e-10   3.8e-07     121     212 ..     451     555 ..     405     564 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 9e-05
                                        ETTSS.EEEEEESTTSSHHHHHHHH CS
                                        xxxxx.xxxxxxxxxxxxxxxxxxx RF
                              SMC_N  21 pfsks.ftaivGpNGSGKsnlldAi 44 
                                        +++k+   a++GpNG GKsn+l  +
  gene2340|gene2340|rna2340|rna2340 370 EIKKGeKIALIGPNGIGKSNFLKML 394
                                        4444314689***********9765 PP

  == domain 2  score: 29.8 bits;  conditional E-value: 1.9e-10
                                        HHHHHHHHCTT-STT.................CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHH CS
                                        xxxxxxxxxxxxxxx.................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              SMC_N 121 kevsellesagiske.................lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkv 179
                                        +e+ el +s +++++                 +LSgGek+ va+a      + k a +yl+De  a+LD+k  + +
  gene2340|gene2340|rna2340|rna2340 451 EEMIELCRSLNFHESfvrlssgyetcigennsVLSGGEKQKVAIA----RAMLKNAEIYLFDEPTANLDKKSEETF 522
                                        555555555555555666666666666666669*******99876....56899********************** PP

                                        HHHHHHHCTTSEEEEE-SSHHHCCC-SCEEEEE CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              SMC_N 180 aellkeksknaQfivislreemlekadklvgvt 212
                                         ++l e+++n  +ivi ++ e+l   d+++ ++
  gene2340|gene2340|rna2340|rna2340 523 FKRLAEDTQNKTVIVILHNLELLDYFDRIMFLQ 555
                                        *******************99999888877655 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.1       3.7   7.4e+03     140     160 ..     201     221 ..     186     243 .. 0.43
   2 !   16.1   0.5   3.8e-06    0.0075       3      19 ..     378     394 ..     377     416 .. 0.82
   3 !   15.8   0.0   4.6e-06    0.0091     234     303 .]     481     546 ..     421     546 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 3.7
                             AAA_21 140 fgkaltditsrawsllllldg 160
                                        ++  l+di s ++s+l  ++ 
  gene2340|gene2340|rna2340|rna2340 201 SNNKLIDILSNYESILAFNNQ 221
                                        222333333333333322222 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 3.8e-06
                             AAA_21   3 vliGpNgsGKSnLLdal 19 
                                        +liGpNg GKSn+L+ l
  gene2340|gene2340|rna2340|rna2340 378 ALIGPNGIGKSNFLKML 394
                                        79************988 PP

  == domain 3  score: 15.8 bits;  conditional E-value: 4.6e-06
                             AAA_21 234 arelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHSpllld 303
                                         + lS G k+  a++ a+l  +    ++l+DEp ++L+ k  +++++ l e ++ +  vi+  H+ +lld
  gene2340|gene2340|rna2340|rna2340 481 NSVLSGGEKQKVAIARAMLKNA---EIYLFDEPTANLDKKSEETFFKRLAEDTQ-NKTVIVILHNLELLD 546
                                        4567999999988888888888...9********************99988888.89****999999987 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.3      0.18   3.5e+02     166     200 ..     195     229 ..     165     295 .. 0.65
   2 !   17.1   9.6   1.8e-06    0.0035      15     104 ..     365     534 ..     363     592 .. 0.53

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.18
                             AAA_15 166 kedlkklikkleeslkkeeelknvlksaiikllli 200
                                        + ++++  +kl+ +l+ +e++  + ++++++++++
  gene2340|gene2340|rna2340|rna2340 195 NLSINESNNKLIDILSNYESILAFNNQNLELYKYD 229
                                        22222222222222222222222333333333332 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 1.8e-06
                             AAA_15  15 kdveidlsee.ltvliGkNnsGKSsilealdlFlnnkekknkkvikiekedleifeniseskdikIdvef...... 83 
                                        k+++ ++++     liG+N++GKS++l++l +F + +       iki++++l + +n+s    i            
  gene2340|gene2340|rna2340|rna2340 365 KNMSFEIKKGeKIALIGPNGIGKSNFLKMLLKFNEYT-----GSIKIDDDELCTIDNYSLRDLISYV--Pqnsylv 433
                                        5545555555599*****************9999966.....5677888888887666544433322..2224455 PP

                             AAA_15  84 ............................................................................ 83 
                                                                                                                    
  gene2340|gene2340|rna2340|rna2340 434 sgtvkenikygnlvatdeemielcrslnfhesfvrlssgyetcigennsvlsggekqkvaiaramlknaeiylfde 509
                                        5555555555666666555555555556666666666666666666666666655555555555555555555444 PP

                             AAA_15  84 ....aek.ekakeyektlkskekkka 104
                                              + +++++++k l+++ ++k+
  gene2340|gene2340|rna2340|rna2340 510 ptanL-DkKSEETFFKRLAEDTQNKT 534
                                        43321.12333334444444444433 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   2.7e-05     0.054       2      53 ..     374     423 ..     373     456 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.7e-05
                             AAA_24   2 klkiliyGpsgiGKTtlakelgpkplfidtekGlksldadkfpdie..swedfl 53 
                                        + ki+++Gp+giGK+ ++k+l    l ++   G+ ++d+d++ +i   s+ d++
  gene2340|gene2340|rna2340|rna2340 374 GEKIALIGPNGIGKSNFLKML----LKFNEYTGSIKIDDDELCTIDnySLRDLI 423
                                        569****************99....44444445556666665555555555555 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       1.2   2.3e+03       2      14 ..     103     115 ..     102     121 .. 0.79
   2 ?   12.1   0.0   6.1e-05      0.12      10      39 ..     362     391 ..     356     395 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.2
                             AAA_29   2 krlqlvNWgtfdg 14 
                                        ++  l+NW +f+ 
  gene2340|gene2340|rna2340|rna2340 103 REYLLLNWSEFKM 115
                                        566799***9985 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 6.1e-05
                             AAA_29  10 gtfdghtieidlkgatlltGpsGsGKSTll 39 
                                        + f++ ++ei+  + + l+Gp+G GKS +l
  gene2340|gene2340|rna2340|rna2340 362 YIFKNMSFEIKKGEKIALIGPNGIGKSNFL 391
                                        678999999*9666*************876 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   5.3e-05       0.1      71     127 ..     345     401 ..     283     456 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.3e-05
                                        HHHHTTSEEEE--TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT----- CS
                        RsgA_GTPase  71 elealgyevllvsaktkegleelkellkd.ktsvlvGqSGvGKStLinallpelelkt 127
                                        ++ ++  +v++   +++  +++++ ++k+ + ++l+G+ G+GKS ++++ll   +  t
  gene2340|gene2340|rna2340|rna2340 345 NILNTSNDVFTYAISDNYIFKNMSFEIKKgEKIALIGPNGIGKSNFLKMLLKF-NEYT 401
                                        55555667788888888889999999999899****************99875.3444 PP

>> Sec23_helical  Sec23/Sec24 helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       5.3     1e+04      60      80 ..     145     165 ..     129     166 .. 0.71
   2 ?   10.4   0.1   0.00023      0.45       5      48 ..     176     220 ..     173     291 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 5.3
                                        TTHHHHHHHHHTSTTTS--TT CS
                      Sec23_helical  60 klLPlyilallKspafrggns 80 
                                        + + ++ la+lK  a+ g++s
  gene2340|gene2340|rna2340|rna2340 145 PVFFVLFLAVLKIYAIMGFTS 165
                                        333366788888888888766 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00023
                                        HHHHHHHHHHHHTT.TS-HHHHHHHHHHHHHHHHHHHHHH----- CS
                      Sec23_helical   5 vtvllakqaidkal.esgladarealdtslvdllsayrkvgasgs 48 
                                         t++ +k+a+ + + +++l+  +++ +++l+d+ls+y +  a ++
  gene2340|gene2340|rna2340|rna2340 176 YTTVTIKMAVWRNEiRKKLNLSINESNNKLIDILSNYESILAFNN 220
                                        58899********9889**********************998752 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (593 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1133  (0.0631937); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.67u 0.29s 00:00:00.96 Elapsed: 00:00:00.47
# Mc/sec: 3758.70
//
Query:       gene2341|gene2341|rna2341|rna2341  [L=436]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.09   12.4   7.3      0.045   13.4   5.1    1.7  2  AIPR      AIPR protein


Domain annotation for each model (and alignments):
>> AIPR  AIPR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   5.1   2.5e-06     0.045     137     243 ..     151     282 ..     133     358 .. 0.68
   2 ?   -3.6   0.0      0.37   6.6e+03     215     253 ..     391     431 ..     379     435 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.5e-06
                               AIPR 137 r...eeqtkvfYerargefdnekafkpkskkitktdlakvlnalflqk.........Phqaskgkaklekkyekee 200
                                        +   ++ t + Y  +r+ f ++++ k +++++t+++ ++ ++ + ++k         P +a+k k+k         
  gene2341|gene2341|rna2341|rna2341 151 AavsDRITDFCYYPSREIFIEKSNNKFTVRQFTNREELNRYL-INNEKmffytsldsPWSAFKCKKK--------- 216
                                        255556678899999999999997777899999988888888.666667766666666666666666......... PP

                               AIPR 201 ekgskyekifkekltykkliasvilfkklekkikkelkegyk..........................a 243
                                            +yek f++ l++kkl ++ i+++ +e ++ k++k+ ++                          +
  gene2341|gene2341|rna2341|rna2341 217 ---LVYEKAFADHLSFKKLRYIRIIYEIVEAMVYKTQKNFVNramfailasricdelnesgiklelkfK 282
                                        ...79*******************************644443333333333333333333333333331 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 0.37
                               AIPR 215 tykkliasvilfkklekkikke..lkegykanivyyilaal 253
                                        +   ++ s+++fk lek    +  +++++ + i yy+  ++
  gene2341|gene2341|rna2341|rna2341 391 NSCIIVRSCLCFKNLEKFCGYKkyFDDAVVKRIRYYTDDIM 431
                                        35667788888888888888776555555566666665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (436 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       600  (0.0334653); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.33s 00:00:00.94 Elapsed: 00:00:00.53
# Mc/sec: 2467.02
//
Query:       gene2342|gene2342|rna2342|rna2342  [L=219]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.016   15.4   0.1       0.36   11.2   0.0    2.5  2  HEAT      HEAT repeat


Domain annotation for each model (and alignments):
>> HEAT  HEAT repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0      0.03   5.4e+02       4      30 ..     109     135 ..     106     136 .. 0.82
   2 ?   11.2   0.0     2e-05      0.36       6      24 ..     183     201 ..     181     201 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.03
                                        HHHHHHT-SSHHHHHHHHHHHHHHHHC CS
                               HEAT   4 lllkllsDpspeVReaAakaLgalaev 30 
                                         l  l++++s ++R+ +   + +l+++
  gene2342|gene2342|rna2342|rna2342 109 NLTVLIHHSSLRIRQRVSIIFKKLCRF 135
                                        56778899*******999999999976 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 2e-05
                                        HHHHT-SSHHHHHHHHHHH CS
                               HEAT   6 lkllsDpspeVReaAakaL 24 
                                        + +l+D++p+VR +A++a+
  gene2342|gene2342|rna2342|rna2342 183 IFALEDTDPQVRTNALNAI 201
                                        4569************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       798  (0.0445089); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 1500.25
//
Query:       gene2343|gene2343|rna2343|rna2343  [L=276]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.21   11.2   9.5       0.27   10.9   9.5    1.1  1  BSP_II    Bone sialoprotein II (BSP-II)


Domain annotation for each model (and alignments):
>> BSP_II  Bone sialoprotein II (BSP-II)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   9.5   1.5e-05      0.27     128     207 ..     118     199 ..      93     228 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 1.5e-05
                             BSP_II 128 ekatkeeesdeeeeeee.eeeneeeeaevdeneqgvngtstnsteaengngssggdngeeeeeesvteaeaeg.te 201
                                        ++a k+  +++ e+e++ e++ e +e++v++ e   ng ++ + + +++n  + g  g+e+  ++v + + e+ t 
  gene2343|gene2343|rna2343|rna2343 118 KRAIKKWSDKKAEDEDKkENNIEMNEKDVNDLERMQNGSNKGNVKDQSENDVDEGITGDEQAYNEVVDHHDENsTR 193
                                        3444433333333333323335678889999999999999999888888888887777766666666655444044 PP

                             BSP_II 202 veeeee 207
                                        v +e +
  gene2343|gene2343|rna2343|rna2343 194 VVSEVD 199
                                        444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (276 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1459  (0.0813765); expected 358.6 (0.02)
Passed bias filter:                      503  (0.0280551); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 2017.30
//
Query:       gene2344|gene2344|rna2344|rna2344  [L=40]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.089   12.5   0.2       0.15   11.8   0.1    1.4  2  Herpes_TK_C  Thymidine kinase from Herpesvirus C-terminal


Domain annotation for each model (and alignments):
>> Herpes_TK_C  Thymidine kinase from Herpesvirus C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       0.4   7.1e+03      21      24 ..      11      14 ..      10      15 .. 0.66
   2 ?   11.8   0.1   8.3e-06      0.15      11      24 ..      22      35 ..      22      37 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 0.4
                        Herpes_TK_C 21 pAIK 24
                                       ++IK
  gene2344|gene2344|rna2344|rna2344 11 GDIK 14
                                       5676 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 8.3e-06
                        Herpes_TK_C 11 teiYtqilkNpAIK 24
                                       ++iYtqi kN  I+
  gene2344|gene2344|rna2344|rna2344 22 GDIYTQISKNRRIR 35
                                       68********9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (40 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       190  (0.0105974); expected 358.6 (0.02)
Passed bias filter:                      157  (0.00875676); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.29s 00:00:00.63 Elapsed: 00:00:00.44
# Mc/sec: 275.85
//
Query:       gene2346|gene2346|rna2346|rna2346  [L=76]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       532  (0.0296726); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.32u 0.27s 00:00:00.59 Elapsed: 00:00:00.41
# Mc/sec: 560.03
//
Query:       gene2347|gene2347|rna2347|rna2347  [L=731]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.3e-16   60.0   0.1    1.3e-15   58.1   0.1    2.0  1  ABC_tran        ABC transporter
    5.7e-09   36.0   9.6    9.2e-09   35.3   9.6    1.3  1  ABC_membrane    ABC transporter transmembrane region
    5.4e-06   26.0   0.2     0.0012   18.3   0.0    2.5  2  SMC_N           RecF/RecN/SMC N terminal domain
    6.9e-05   22.7   0.0    0.00081   19.2   0.0    2.4  2  AAA_15          AAA ATPase domain
    0.00018   21.4   0.0     0.0004   20.3   0.0    1.5  1  AAA_21          AAA domain, putative AbiEii toxin, Type IV TA
     0.0012   19.4   0.4     0.0012   19.4   0.4    2.6  1  AAA_23          AAA domain
     0.0026   17.7   0.5      0.022   14.7   0.0    2.3  2  RsgA_GTPase     RsgA GTPase
     0.0032   17.2   0.0     0.0066   16.2   0.0    1.5  1  AAA_29          P-loop containing region of AAA domain
     0.0035   17.0   0.1      0.018   14.7   0.0    2.0  2  AAA_27          AAA domain
     0.0058   16.2   0.2      0.015   14.8   0.2    1.7  1  AAA_7           P-loop containing dynein motor region
     0.0075   16.3   0.0      0.021   14.9   0.0    1.8  1  MMR_HSR1        50S ribosome-binding GTPase
  ------ inclusion threshold ------
      0.022   13.9   0.1      0.085   12.0   0.0    1.9  2  DUF815          Protein of unknown function (DUF815)
      0.025   15.0   0.1       0.35   11.3   0.0    2.3  2  AAA             ATPase family associated with various cellula
      0.065   13.8   0.5       0.63   10.6   0.0    2.5  2  AAA_18          AAA domain
      0.097   12.9   0.1         27    5.1   0.1    2.8  2  SbcCD_C         Putative exonuclease SbcCD, C subunit
       0.13   12.5   0.1       0.47   10.7   0.0    2.0  2  Roc             Ras of Complex, Roc, domain of DAPkinase
       0.14   11.5   0.0       0.24   10.7   0.0    1.3  1  Mg_chelatase    Magnesium chelatase, subunit ChlI
       0.36   11.0   6.6      0.056   13.6   2.4    1.8  1  Laminin_EGF     Laminin EGF domain
       0.72    9.9   3.2          1    9.4   0.0    2.5  3  Dynamin_N       Dynamin family
        6.6    6.4   6.2        5.4    6.7   0.1    2.8  3  Cytidylate_kin  Cytidylate kinase


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.1   0.1   1.4e-18   1.3e-15       1     123 [.     416     537 ..     416     540 .. 0.78

  Alignments for each domain:
  == domain 1  score: 58.1 bits;  conditional E-value: 1.4e-18
                                        EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBH CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltv 76 
                                        l n+++++ +  kvaivG+nGaGKS+++k++++l+ p +G+i            ++ + ++ + +qepqlf ++ v
  gene2347|gene2347|rna2347|rna2347 416 LTNLTFNVAQYAKVAIVGPNGAGKSSIIKAILKLT-PYSGQI-----------QKIENTRLTYTSQEPQLFADT-V 478
                                        689******************************96.89****...........678999***************.6 PP

                                        HHH......HHHTC...HHHHHHHSTTGG......TTCBGESTTSGGS-HHHHHHHHHHHHH CS
                                        xxx......xxxxx...xxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ABC_tran  77 ren......esdee...iekalsklglke......lkdtvvksspssLSgGqkqrvalaral 123
                                          n      +   +   i +++ k+g ++         + +++++++LSgG++q++ l r +
  gene2347|gene2347|rna2347|rna2347 479 LYNvaygskA---KlrcIIAIAMKMGVHKdilrmrGYGSLLTENARNLSGGERQKITLLRNV 537
                                        6666986652...23345555555555444444443344455555*************9976 PP

>> ABC_membrane  ABC transporter transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.3   9.6     1e-11   9.2e-09       6     244 ..      27     260 ..      14     276 .. 0.90

  Alignments for each domain:
  == domain 1  score: 35.3 bits;  conditional E-value: 1e-11
                                        HHHHHHHHHHHHHHHHHHHHHHHHHSSTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       ABC_membrane   6 llailagvlsplfplvlgrildtlldkgdpetealnvysllllllglaqfilallqsyllnvtgerlskrlrrklf 81 
                                         ++il++ l++  +++l+ i + +    d++t  ++++++ l +++l+ ++++ ++ ++     +r+ ++  ++++
  gene2347|gene2347|rna2347|rna2347  27 TCIILSKYLKIYASSILKDIGQAI---EDSHT--VSRLIIKLGACYLLYAFFNEIYDFIAASPIQRAARHASNDFL 97 
                                        566666666666666666666666...45777..99**************************************** PP

                                        HHHHCSTHHHHHHSCHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHH.HSHHHHHHHHHHHHHHHH CS
                       ABC_membrane  82 kkilrqpmsffdtnsvGellsrltndvsklrdglgeklglffqslltfvgglivmfy.lgwkltlvllailpliil 156
                                        +++l   ++ ++  s+Ge+   l + +s ++d++  +l+ ++  l+tfv +l  m   +g   ++  + +l+++i+
  gene2347|gene2347|rna2347|rna2347  98 RNCLMERVRLYEC-SSGEVGRTLVRSASAVSDLIDITLLEILPLLITFVLALTEMYRkFGYAAFMYNVMMLIVYIV 172
                                        ****999999975.67777778888899999999999999999999999888866666****************** PP

                                        HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       ABC_membrane 157 vsaviakilkklkkkeqkavakassvaeEslsgirtVkafgreeyflekfekaleeakkagikkaianglligitq 232
                                        +++ i++  ++++++++ + ++a s   E ++++ t+  +   +++l+++++ +++++  + +   + +ll+ ++ 
  gene2347|gene2347|rna2347|rna2347 173 ITFAITRYRMRYRRRNNMYENRAHSKCLECIRNVDTITVYKTVQFELNQYDDINKKVQFYSSRQYQSLALLNLTQK 248
                                        **************************************************************************** PP

                                        HHHHHHHHHHHH CS
                       ABC_membrane 233 llgllsyalalw 244
                                        ++ +++++  l+
  gene2347|gene2347|rna2347|rna2347 249 VILYIFMVTYLY 260
                                        ******998765 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   1.4e-06    0.0012      27      45 ..     429     447 ..     417     490 .. 0.82
   2 ?    5.1   0.1     0.015        14     155     212 ..     643     700 ..     639     705 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.4e-06
                                        EEEEESTTSSHHHHHHHHH CS
                                        xxxxxxxxxxxxxxxxxxx RF
                              SMC_N  27 taivGpNGSGKsnlldAil 45 
                                         aivGpNG+GKs+++ Ail
  gene2347|gene2347|rna2347|rna2347 429 VAIVGPNGAGKSSIIKAIL 447
                                        68****************4 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.015
                                        CCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCCC-SCEEEEE CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              SMC_N 155 kvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivislreemlekadklvgvt 212
                                        k +p+ l+l+De  +a+D++    v e+l    +++ ++++ ++ ++l+  d+++ v 
  gene2347|gene2347|rna2347|rna2347 643 KNSPSILMLFDEATSAMDKSSEYDVIERLFDVCSECTVLMVIHNLTILHLFDTIIYVD 700
                                        678999********************99999999999999999999999888888776 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   2.3       2.1   1.9e+03     161     202 ..     358     397 ..     291     427 .. 0.59
   2 !   19.2   0.0     9e-07   0.00081      25     153 ..     428     634 ..     402     669 .. 0.68

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 2.1
                             AAA_15 161 elkidkedlkklikkleeslkkeeelknvlksaiiklllisa 202
                                        +   + ++ k++ +  ee+++ ++e kn ++++ + + +i+ 
  gene2347|gene2347|rna2347|rna2347 358 NSNNYAQKGKNICR--EENINTDQESKNDIQENGRAIPFINT 397
                                        22223444444444..44444444445555555555555544 PP

  == domain 2  score: 19.2 bits;  conditional E-value: 9e-07
                             AAA_15  25 ltvliGkNnsGKSsilealdlFlnnkekknkkvikiekedleifeniseskdikIdvef................. 83 
                                           ++G+N++GKSsi++a+ ++   + +          +++e+++ +++s++ ++                     
  gene2347|gene2347|rna2347|rna2347 428 KVAIVGPNGAGKSSIIKAILKLTPYSGQ---------IQKIENTRLTYTSQEPQLFADTvlynvaygskaklrcii 494
                                        578****************877775522.........223333333333333333222233333446666666666 PP

                             AAA_15  84 ......................................................................aekeka 89 
                                                                                                                +e++
  gene2347|gene2347|rna2347|rna2347 495 aiamkmgvhkdilrmrgygslltenarnlsggerqkitllrnvvygicacgdgvdcahcegcrdgsvqewSDEEER 570
                                        6666778888888888888888888888888888888888888888888888888888888888877654222667 PP

                             AAA_15  90 keyektlkskekkkadlllkkkesdlkktikdkklklkknelsdekisvekkkskkelpkekee 153
                                        ++ ++ ++++ + + + + + ++sd++ +  + + + ++n + d   + + ++ +  +++++++
  gene2347|gene2347|rna2347|rna2347 571 NVKISVADRESITQFNDDHQAFNSDFVPYEVTMQDDTYQNATEDRGSTTNYNMMYDVDEISSKN 634
                                        7777788888888888888888888888777777777777777777776666664444444333 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   4.5e-07    0.0004       3      57 ..     430     471 ..     429     481 .. 0.72

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 4.5e-07
                             AAA_21   3 vliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeip 57 
                                        +++GpNg+GKS++++a+                 + +g+i+ki++   +y   +p
  gene2347|gene2347|rna2347|rna2347 430 AIVGPNGAGKSSIIKAILK-------------LTPYSGQIQKIENTRLTYTSQEP 471
                                        79***************44.............45666666666666666655555 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.4   1.3e-06    0.0012      22      39 ..     429     446 ..     407     470 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 1.3e-06
                             AAA_23  22 tlItGpNGaGKTTildAi 39 
                                        ++I+GpNGaGK++i+ Ai
  gene2347|gene2347|rna2347|rna2347 429 VAIVGPNGAGKSSIIKAI 446
                                        58***************9 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.1      0.57   5.1e+02      47      93 ..     197     243 ..     167     255 .. 0.64
   2 !   14.7   0.0   2.4e-05     0.022      75     121 ..     401     448 ..     380     475 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.57
                                        -EEEEEEE-GGG--HHHHHHHHHHHHHHTTSEEEE--TTTHTTHHHH CS
                        RsgA_GTPase  47 iepvivlnKiDlleeeeeleelkeelealgyevllvsaktkegleel 93 
                                         + + ++  +D ++  ++++   +++ +++ +v + s+++ ++l+ l
  gene2347|gene2347|rna2347|rna2347 197 SKCLECIRNVDTITVYKTVQFELNQYDDINKKVQFYSSRQYQSLALL 243
                                        44444666677777777777777777777777777777766655544 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 2.4e-05
                                        TTSEEEE--TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCT CS
                        RsgA_GTPase  75 lgyevllvsaktkegleelkellkd.ktsvlvGqSGvGKStLinallp 121
                                        l+++ ++++ k++  l++l+ ++++   +++vG+ G+GKS++i+a+l 
  gene2347|gene2347|rna2347|rna2347 401 LQFQNVTIKHKNTPILTNLTFNVAQyAKVAIVGPNGAGKSSIIKAILK 448
                                        556777888888889999999999988999**************9976 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   7.3e-06    0.0066      24      45 ..     428     449 ..     415     456 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 7.3e-06
                             AAA_29  24 atlltGpsGsGKSTllDAiqal 45 
                                         + ++Gp+G+GKS+++ Ai  l
  gene2347|gene2347|rna2347|rna2347 428 KVAIVGPNGAGKSSIIKAILKL 449
                                        689*************999765 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       1.3   1.2e+03     141     160 ..     112     131 ..     110     134 .. 0.87
   2 !   14.7   0.0     2e-05     0.018      18      49 ..     418     449 ..     416     463 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1.3
                             AAA_27 141 egelgqlLfeasaGlaslre 160
                                        +ge+g++L+ +++++++l +
  gene2347|gene2347|rna2347|rna2347 112 SGEVGRTLVRSASAVSDLID 131
                                        79************998865 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 2e-05
                             AAA_27  18 sldfsaeeadlhliyGpNEAGKstalrAisdl 49 
                                        +l+f+ ++     i+GpN AGKs++++Ai +l
  gene2347|gene2347|rna2347|rna2347 418 NLTFNVAQYAKVAIVGPNGAGKSSIIKAILKL 449
                                        57788777777789***************988 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.2   1.6e-05     0.015       7      76 ..     401     469 ..     395     496 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.6e-05
                              AAA_7   7 akfseilVptvdtvrysyllelllknkkpvllvGptGtGKtviikdllkkldkekylsltinfsaqtsan 76 
                                        ++f++++++  +t  ++ l+   +++  +v +vGp G GK++iik +lk  + +  + ++ n   + +++
  gene2347|gene2347|rna2347|rna2347 401 LQFQNVTIKHKNTPILTNLT-FNVAQYAKVAIVGPNGAGKSSIIKAILKLTPYSGQIQKIENTRLTYTSQ 469
                                        67788888877777666654.55677788*****************999888555555554555555555 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   2.4e-05     0.021       1      22 [.     428     455 ..     428     489 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.4e-05
                                        EEEEEESTTSSHHHHHHHHHT......S CS
                           MMR_HSR1   1 evaivGrpNvGKStLinaltg......e 22 
                                        +vaivG   +GKS++i+a+++      +
  gene2347|gene2347|rna2347|rna2347 428 KVAIVGPNGAGKSSIIKAILKltpysgQ 455
                                        69*****************974333322 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       1.5   1.4e+03       9      47 ..     192     231 ..     186     243 .. 0.66
   2 ?   12.0   0.0   9.5e-05     0.085      33      76 ..     408     449 ..     380     470 .. 0.69

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.5
                             DUF815   9 ee.keegalepveevdevklddLvgidkqkealventeqf 47 
                                        e+ ++++ le++++vd++++ + v ++ ++ + ++   qf
  gene2347|gene2347|rna2347|rna2347 192 ENrAHSKCLECIRNVDTITVYKTVQFELNQYDDINKKVQF 231
                                        432667779*******999998888886554444444444 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 9.5e-05
                             DUF815  33 idkqkealventeqfleglpannvLLwGarGtGKSslvkallne 76 
                                        i+++++ +++n +  ++++   +v ++G  G+GKSs++ka+l+ 
  gene2347|gene2347|rna2347|rna2347 408 IKHKNTPILTNLTFNVAQY--AKVAIVGPNGAGKSSIIKAILKL 449
                                        4455555555554444333..468899**************975 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00039      0.35       2      48 ..     430     476 ..     429     511 .. 0.78
   2 ?    0.9   0.0      0.63   5.7e+02      43      90 ..     631     672 ..     615     696 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00039
                                        EEESSTTSSHHHHHHHHHHHH..THEEEEEETTTCSSSSTTHHHHHHHH CS
                                AAA   2 llyGppGtGKTllakavakel..gvefleisgsellskyvgesekkire 48 
                                         ++Gp G GK++++ka+ k +  + ++ +i+ ++l+  y ++ ++ +++
  gene2347|gene2347|rna2347|rna2347 430 AIVGPNGAGKSSIIKAILKLTpySGQIQKIENTRLT--YTSQEPQLFAD 476
                                        589***************997445778888888887..66666666555 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.63
                                        HHHHHHHHHHHHHTSTS.EEEEEETGGGHHHHHTTCCCHHHHHHHHHHH CS
                                AAA  43 ekkirelfkeakekakp.silfiDEidalaksrsgseseeeervvnqLl 90 
                                        ++k +e+f    +++ p   +++DE+ + + ++      +e +v++ L+
  gene2347|gene2347|rna2347|rna2347 631 SSKNEETFYPSAKNS-PsILMLFDEATSAMDKS------SEYDVIERLF 672
                                        556667777766666.8566789***9999888......4445555554 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.3       1.1     1e+03      12      69 ..     279     354 ..     279     397 .. 0.52
   2 ?   10.6   0.0    0.0007      0.63       1      44 [.     429     472 ..     429     497 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 1.1
                             AAA_18  12 ttlakeLskrlgf.............gvnlrdvakenglllevdpe......aldeskrldedkldklldaleens 68 
                                        +t+ +eLs++ g+                +rd+a  n++++            ++++  +   +++++ +++ee +
  gene2347|gene2347|rna2347|rna2347 279 STIIEELSNL-GCiyhrfskaivdlnTPFVRDMAETNQTYDRKPSVnlteepRTKRNTHVGNAVDQYHARGHEETN 353
                                        5666666665.45555555555555544555555555555444333333333344444444444444444444444 PP

                             AAA_18  69 s 69 
                                        +
  gene2347|gene2347|rna2347|rna2347 354 N 354
                                        3 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.0007
                             AAA_18   1 IlltGtpGvGKttlakeLskrlgfgvnlrdvakenglllevdpe 44 
                                        +++ G+ G+GK+++ k++ k++ ++ +++++   + ++++++p+
  gene2347|gene2347|rna2347|rna2347 429 VAIVGPNGAGKSSIIKAILKLTPYSGQIQKIENTRLTYTSQEPQ 472
                                        689***************99999999999999888888888887 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0     0.046        41      23      42 ..     513     532 ..     498     536 .. 0.79
   2 ?    5.1   0.1      0.03        27      64      85 ..     647     668 ..     636     673 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.046
                            SbcCD_C  23 ekelsrssgtlSGGekqfla 42 
                                         + l +++++lSGGe+q+++
  gene2347|gene2347|rna2347|rna2347 513 GSLLTENARNLSGGERQKIT 532
                                        455788999********987 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.03
                            SbcCD_C  64 lrlvfLDEAFsklDeesiatll 85 
                                          l+++DEA s +D+ s   ++
  gene2347|gene2347|rna2347|rna2347 647 SILMLFDEATSAMDKSSEYDVI 668
                                        447899********98766655 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00052      0.47       1      32 [.     428     459 ..     428     478 .. 0.78
   2 ?   -2.2   0.0       5.2   4.7e+03      79      90 ..     644     655 ..     566     686 .. 0.59

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00052
                                        EEEEESSTTSSHHHHHHCHCT-CCC-EEETTT CS
                                Roc   1 KvvlvGdsgvGKtsllkrfvedkfsekeksti 32 
                                        Kv +vG +g+GK+s++k +++ +  + + + i
  gene2347|gene2347|rna2347|rna2347 428 KVAIVGPNGAGKSSIIKAILKLTPYSGQIQKI 459
                                        89***************999876655555554 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 5.2
                                        TSCEEEEEEEGH CS
                                Roc  79 eaalailvydsr 90 
                                        ++  +++++d+ 
  gene2347|gene2347|rna2347|rna2347 644 NSPSILMLFDEA 655
                                        333445555544 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00027      0.24      22      62 ..     426     466 ..     412     479 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00027
                       Mg_chelatase  22 gHnlllvGppGsGKtmlakrlpsllpplseeealevakias 62 
                                          ++ +vGp G+GK+ ++k++ +l p   + + +e ++++ 
  gene2347|gene2347|rna2347|rna2347 426 YAKVAIVGPNGAGKSSIIKAILKLTPYSGQIQKIENTRLTY 466
                                        557889****************************9998764 PP

>> Laminin_EGF  Laminin EGF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   2.4   6.2e-05     0.056      17      43 ..     539     565 ..     530     570 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 6.2e-05
                                        TECESBTTTEESTTS-EE-TTEEEGTT CS
                        Laminin_EGF  17 tgqClCkenveGrkCdrCkpgyyglps 43 
                                         g C C ++v+  +C+ C++g +++ s
  gene2347|gene2347|rna2347|rna2347 539 YGICACGDGVDCAHCEGCRDGSVQEWS 565
                                        689******************998744 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.7       1.3   1.2e+03      29      86 ..     328     384 ..     322     420 .. 0.55
   2 ?    9.4   0.0    0.0012         1       1      20 [.     429     448 ..     429     484 .. 0.90
   3 ?   -3.1   0.0       7.6   6.8e+03      36      80 ..     599     642 ..     597     674 .. 0.66

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 1.3
                                        SS---S-EEEEECCT---CCS...SSEEEET-EB--CHHHHHHHHHHHHHHHT.SSSS- CS
                          Dynamin_N  29 nptTrrplelqlgeeeeaseravkeelkekekkledfsevreeieketekiag.ankgi 86 
                                        +p T r +++    +++ + ++  ee +++ ++ +++ +  ++i +e++ +++ + k++
  gene2347|gene2347|rna2347|rna2347 328 EPRTKRNTHVGNAVDQY-H-ARGHEETNNDGRNSNNYAQKGKNICREENINTDqESKND 384
                                        56677777777767777.4.344444444455555555555555555555543122222 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0012
                                        EEEEEBTTTTHHHHHHHHHT CS
                          Dynamin_N   1 iavvGsqSsGKSSvlnaLlg 20 
                                        +a+vG   +GKSS++ a+l+
  gene2347|gene2347|rna2347|rna2347 429 VAIVGPNGAGKSSIIKAILK 448
                                        79****************97 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 7.6
                                        EEEEECCT---CCS...SSEEEET-EB--CHHHHHHHHHHHHHHH CS
                          Dynamin_N  36 lelqlgeeeeaseravkeelkekekkledfsevreeieketekia 80 
                                         e++++++ + ++++++     +   ++d++e+  + e+ +  +a
  gene2347|gene2347|rna2347|rna2347 599 YEVTMQDDTY-QNATEDRGSTTNYNMMYDVDEISSKNEETFYPSA 642
                                        5667776666.3344444444447777777777777666655555 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       3.8   3.4e+03     135     149 ..      79      93 ..      75     100 .. 0.85
   2 ?    1.8   0.6      0.18   1.6e+02      30      80 ..     149     200 ..     141     241 .. 0.81
   3 ?    6.7   0.1    0.0061       5.4       1      18 [.     429     446 ..     429     453 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 3.8
                                        EEE--HHHHHHHHHH CS
                     Cytidylate_kin 135 fldAsveeRakRRlk 149
                                        f+ As+ +Ra+R ++
  gene2347|gene2347|rna2347|rna2347  79 FIAASPIQRAARHAS 93 
                                        99*********9865 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.18
                                        HHHHHHHHHHHHHTT--TT-HHHHHHHH.HT--EEEEEEEEEETTEE-TTGG CS
                     Cytidylate_kin  30 galYRalalaalrrkvdlldeaalvela.kevelsfeaekvllngedveeel 80 
                                         ++YR + +aa   +v +l +  ++++a ++ +++++ ++ +++++  ++ l
  gene2347|gene2347|rna2347|rna2347 149 TEMYRKFGYAAFMYNVMMLIVYIVITFAiTRYRMRYRRRNNMYENRAHSKCL 200
                                        68************99999999999986256789999998888887776655 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.0061
                                        EEEE-STTSSHHHHHHHH CS
                     Cytidylate_kin   1 iaiDGPagsGKssvaral 18 
                                        +ai GP g+GKss+ +a+
  gene2347|gene2347|rna2347|rna2347 429 VAIVGPNGAGKSSIIKAI 446
                                        7999**********9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (731 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1170  (0.0652574); expected 358.6 (0.02)
Passed bias filter:                      497  (0.0277205); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.74u 0.28s 00:00:01.02 Elapsed: 00:00:00.45
# Mc/sec: 4834.75
//
Query:       gene2348|gene2348|rna2348|rna2348  [L=326]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-18   67.7   1.6    7.6e-12   45.4   0.1    2.9  3  GCD14     tRNA methyltransferase complex GCD14 subunit


Domain annotation for each model (and alignments):
>> GCD14  tRNA methyltransferase complex GCD14 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   2.4e-08   0.00043       3      62 ..      62     120 ..      60     138 .. 0.89
   2 !   45.4   0.1   4.2e-16   7.6e-12      76     182 ..     196     302 ..     185     316 .. 0.85
   3 ?   -0.3   0.0     0.038   6.7e+02     235     246 ..     314     325 ..     307     326 .] 0.81

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 2.4e-08
                              GCD14   3 vyvlaptPeLWtlaLphrtqilytaDisliimkLelkpGsvvvesGtGsgslshaiartv 62 
                                        v +l+pt  L + +    tq+++  D s++ + + lk   v  e+G Gsg l+ ++ar v
  gene2348|gene2348|rna2348|rna2348  62 VTILRPTHYLISNT-ACSTQVIFDYDASFVCFVMGLKSTDVLFEAGFGSGVLTGSLARFV 120
                                        66788888887755.568***************************************987 PP

  == domain 2  score: 45.4 bits;  conditional E-value: 4.2e-16
                              GCD14  76 qraekareefrehel...sqlvtvthrDvckeGfdeevsgkvDavfLDlPaPweaiphaakalkkeggrlCsfsPC 148
                                        +r+++a  +  ++     +++v   hr  c+   ++ +++ vD + LD+P+Pw  ip +++ l k++  +C f   
  gene2348|gene2348|rna2348|rna2348 196 NRMHHAHTDVGQDTDggsEKMVESLHRKNCRISTKNVINKMVDGIVLDMPEPWLVIPTLKAIL-KRNKTMCVFVIS 270
                                        56666666665443323266899999999*9999999**************************.566678****** PP

                              GCD14 149 ieqvqrtceaLrelgfteietlevllrtyevrks 182
                                        i+qv +t +a+r   f++i++ e   r+y+++ks
  gene2348|gene2348|rna2348|rna2348 271 IQQVTKTLRAMRT--FKNIRVYENVGREYSMKKS 302
                                        ***********98..***************9986 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.038
                              GCD14 235 lkghtgyLtfat 246
                                           htgyL+f t
  gene2348|gene2348|rna2348|rna2348 314 QYMHTGYLIFGT 325
                                        567*******87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (326 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       891  (0.049696); expected 358.6 (0.02)
Passed bias filter:                      545  (0.0303977); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 2028.37
//
Query:       gene2349|gene2349|rna2349|rna2349  [L=86]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       595  (0.0331865); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 625.03
//
Query:       gene235|gene235|rna235|rna235  [L=472]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (472 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1567  (0.0874003); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.40
# Mc/sec: 3515.89
//
Query:       gene2350|gene2350|rna2350|rna2350  [L=162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       897  (0.0500307); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1150.77
//
Query:       gene2351|gene2351|rna2351|rna2351  [L=43]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (43 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       317  (0.0176809); expected 358.6 (0.02)
Passed bias filter:                      214  (0.011936); expected 358.6 (0.02)
Passed Vit filter:                         6  (0.000334653); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.31u 0.24s 00:00:00.55 Elapsed: 00:00:00.38
# Mc/sec: 342.84
//
Query:       gene2352|gene2352|rna2352|rna2352  [L=672]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (672 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       987  (0.0550505); expected 358.6 (0.02)
Passed bias filter:                      459  (0.025601); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.56u 0.26s 00:00:00.82 Elapsed: 00:00:00.38
# Mc/sec: 5275.94
//
Query:       gene2353|gene2353|rna2353|rna2353  [L=478]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
       0.07   12.9   0.2       0.31   10.8   0.1    2.0  1  N-glycanase_C  Peptide-N-glycosidase F, C terminal


Domain annotation for each model (and alignments):
>> N-glycanase_C  Peptide-N-glycosidase F, C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   1.7e-05      0.31      14      75 ..       6      66 ..       2     106 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 1.7e-05
                                       EEEESS-EEEEEEEEEEEEE--STTSTTTS---EEEEETTEEEEEE---BS-GGGGGGG-.. CS
                      N-glycanase_C 14 kfklpakakkvelkaiitgHGgenggdEfvkkshtvlvdgkevlefiparddlgsarrvneg 75
                                       kf + +++k  el ++i  HG +++ +Ef+ +   +l+d ++ ++    r+d  + +r +e 
  gene2353|gene2353|rna2353|rna2353  6 KFVFDNEYKAKELNLTINKHGISKDEKEFCDEIE-MLIDAEKNISDEDVRQDESCENRSAEE 66
                                       7888999999********************9875.667776666666999999999888743 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (478 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1854  (0.103408); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.27s 00:00:00.87 Elapsed: 00:00:00.46
# Mc/sec: 3093.31
//
Query:       gene2354|gene2354|rna2354|rna2354  [L=61]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       596  (0.0332422); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.42
# Mc/sec: 440.70
//
Query:       gene2355|gene2355|rna2355|rna2355  [L=207]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.5e-43  148.8   0.2    1.9e-43  148.5   0.2    1.0  1  Pro_isomerase  Cyclophilin type peptidyl-prolyl cis-trans iso
  ------ inclusion threshold ------
        0.1   12.6   0.0       0.18   11.8   0.0    1.4  1  Rad33          Rad33


Domain annotation for each model (and alignments):
>> Pro_isomerase  Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  148.5   0.2   2.1e-47   1.9e-43       9     157 ..      34     185 ..      28     186 .. 0.89

  Alignments for each domain:
  == domain 1  score: 148.5 bits;  conditional E-value: 2.1e-47
                      Pro_isomerase   9 kGrivieLfadkaPktvenFlklvkeg........fYdgttFhRvikgfmvqgGdptgktsageqe.kkggesira 75 
                                         +ri+ieLf++++Pkt++nF  ++ +g         Y++++FhR+i+gfm+qgGd+ +++  g+++ ++ g   ++
  gene2355|gene2355|rna2355|rna2355  34 TKRIIIELFDKDVPKTCDNFYSFI-KGcrvngqnlSYKNSIFHRIIDGFMIQGGDILNGN--GTGSiSSYG---KP 103
                                        579*********************.6678888899********************99984..454434444...59 PP

                      Pro_isomerase  76 ipdEitsklkh.krGalamartgkepnsagsqFfItlkeaphldgkytvFGkVv.eGmdvvekiekvetde.erpk 148
                                        ++dE+ +k+kh ++G+l+ma++g  p+++gsqFfIt++ +++ld+k++vFG+++ + ++ v  i+kv+tde +rp 
  gene2355|gene2355|rna2355|rna2355 104 FEDEN-FKYKHhQPGMLSMANSG--PDTNGSQFFITTAVTKWLDDKHVVFGQIInNTLQNVLDISKVPTDErHRPI 176
                                        *****.6666659*********8..8****************************98999999************** PP

                      Pro_isomerase 149 knvkivsae 157
                                        k v+i++++
  gene2355|gene2355|rna2355|rna2355 177 KSVVIKDCG 185
                                        *******97 PP

>> Rad33  Rad33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   2.1e-05      0.18      43      89 ..      38      84 ..      28      92 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.1e-05
                              Rad33 43 iPkcftkdieecidyyYelikskdvkidelnkkqeitlelieaytit 89
                                       i ++f kd+ ++ d +Y++ik   v+ ++l++k++i  ++i  + i 
  gene2355|gene2355|rna2355|rna2355 38 IIELFDKDVPKTCDNFYSFIKGCRVNGQNLSYKNSIFHRIIDGFMIQ 84
                                       6689*******************9*****************999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       555  (0.0309554); expected 358.6 (0.02)
Passed bias filter:                      471  (0.0262703); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1331.12
//
Query:       gene2356|gene2356|rna2356|rna2356  [L=353]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-12   48.1   0.4    1.9e-12   47.5   0.4    1.3  1  GCP_N_terminal  Gamma tubulin complex component N-terminal
  ------ inclusion threshold ------
      0.034   14.4   0.2          1    9.7   0.0    2.7  2  GIY-YIG         GIY-YIG catalytic domain


Domain annotation for each model (and alignments):
>> GCP_N_terminal  Gamma tubulin complex component N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.5   0.4   2.1e-16   1.9e-12     114     252 ..     195     316 ..     150     344 .. 0.77

  Alignments for each domain:
  == domain 1  score: 47.5 bits;  conditional E-value: 2.1e-16
                     GCP_N_terminal 114 wlqetllllrvLanlveevekanlkggallsllheaaqhgdpkvrkllsellervsrpflemlekWileGelsDpy 189
                                        +l+++++++ +L ++ +  +  ++   +  ++l  ++    +k  +l+ ++++++++ +   l+ W+ +G++ D  
  gene2356|gene2356|rna2356|rna2356 195 QLKPYIKTFILLDQINSHFQ--DT--KNPYNFLKFYSRDFFTKEDTLIYNIVSSCTKQLNINLNEWLVKGQFTDYA 266
                                        55555555555555555555..22..223444444444445566789999************************** PP

                     GCP_N_terminal 190 nEfFveenesvakeklkeddseklweekYtlrkemlPsflseelaekIletGkslnflrescg 252
                                         EfF+++n+++            +w  +Y ++  mlP f+s+e a+kIl +Gk  n+l ++++
  gene2356|gene2356|rna2356|rna2356 267 REFFITKNTND------------FW-LSYNVDTGMLPFFISAEIAQKILYIGKVSNLLVRISS 316
                                        *****887766............89.69******************************99833 PP

>> GIY-YIG  GIY-YIG catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0     0.043   3.9e+02      27      58 ..     209     245 ..     202     267 .. 0.67
   2 ?    9.7   0.0   0.00011         1       9      41 ..     296     328 ..     291     343 .. 0.72

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.043
                                        HHHHHHHHHHT--S-H.....S.STEEEEEEEE---- CS
                            GIY-YIG  27 lkqHnagkkakytrkk.....gkkpfeliileifptk 58 
                                        +++H++++k+ y+  k     ++++ + +i+ i ++ 
  gene2356|gene2356|rna2356|rna2356 209 INSHFQDTKNPYNFLKfysrdFFTKEDTLIYNIVSSC 245
                                        799***9999999988888884444444444444333 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00011
                                        ETTT--EEEEEESSHHHHHHHHHHHHHHT--S- CS
                            GIY-YIG   9 skenkliYvGstknlekRlkqHnagkkakytrk 41 
                                        ++++k++Y+G+ +nl  R+++  + + +k +++
  gene2356|gene2356|rna2356|rna2356 296 EIAQKILYIGKVSNLLVRISSVYEADYSKQATN 328
                                        5688999************66655555554444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (353 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       627  (0.0349713); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2559.77
//
Query:       gene2357|gene2357|rna2357|rna2357  [L=316]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    8.7e-13   48.7   0.1      2e-12   47.6   0.1    1.5  1  Rhodanese  Rhodanese-like domain


Domain annotation for each model (and alignments):
>> Rhodanese  Rhodanese-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.6   0.1   1.1e-16     2e-12      10     104 ..     204     296 ..     195     298 .. 0.84

  Alignments for each domain:
  == domain 1  score: 47.6 bits;  conditional E-value: 1.1e-16
                          Rhodanese  10 ekgkva..llDvRppeeYekghIpgAvnvskdtlsrakkseapllelpeellelgidnkktvvvycdgggr.aaaa 82 
                                        +k +v+  ++D+R+++eY+ ghI+ A+n+            ++ + l+ ++ +l    +  ++++c+ ++  a + 
  gene2357|gene2357|rna2357|rna2357 204 GKYNVKykIIDCRFDYEYNGGHIKDAINI------------DNVDSLIRSIPSL---CNHVLIFHCEFSSVrAPRI 264
                                        55566666*********************............8888899999998...9999********9977777 PP

                          Rhodanese  83 aallk........k..lGyknvsvldGGfkaw 104
                                        a+ l+        +  l +++++vl+GG+k++
  gene2357|gene2357|rna2357|rna2357 265 AKYLRnydrfnneYpsLDFPEIYVLEGGYKEF 296
                                        888887776666526699************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (316 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       623  (0.0347482); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 2128.63
//
Query:       gene2358|gene2358|rna2358|rna2358  [L=68]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (68 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1163  (0.064867); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.41
# Mc/sec: 502.63
//
Query:       gene2359|gene2359|rna2359|rna2359  [L=1082]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1082 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       913  (0.0509231); expected 358.6 (0.02)
Passed bias filter:                      624  (0.0348039); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.87u 0.27s 00:00:01.14 Elapsed: 00:00:00.47
# Mc/sec: 6963.76
//
Query:       gene236|gene236|rna236|rna236  [L=196]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    5.6e-12   45.9   3.6      3e-05   24.4   1.5    2.5  2  EF-hand_7  EF-hand domain pair
      6e-09   35.1   3.2      0.031   14.2   0.0    3.7  3  EF-hand_6  EF-hand domain
    1.3e-06   27.5  10.2      0.045   13.3   1.1    3.9  4  EF-hand_1  EF hand
     0.0049   16.7   2.9        4.7    7.1   0.2    3.5  3  EF-hand_8  EF-hand domain pair
  ------ inclusion threshold ------
      0.011   15.2   0.2       0.19   11.3   0.0    2.8  3  EF-hand_5  EF hand


Domain annotation for each model (and alignments):
>> EF-hand_7  EF-hand domain pair
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   8.7e-08   0.00031       3      30 ..      30      56 ..      28      88 .. 0.85
   2 !   24.4   1.5   8.3e-09     3e-05       4      70 ..     101     166 ..      99     167 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 8.7e-08
                      EF-hand_7  3 klkeaFkelDtdgdgyldkeellrllrk 30
                                    l+e+Fk+lD+  +gyl++++++ l+  
  gene236|gene236|rna236|rna236 30 LLYERFKMLDRQENGYLTYSDIM-LIPE 56
                                   69*******************99.7655 PP

  == domain 2  score: 24.4 bits;  conditional E-value: 8.3e-09
                      EF-hand_7   4 lkeaFkelDtdgdgyldkeellrllrkifqgagegsklsd....eelellfkefDtdkdGvisfdEFlkly 70 
                                    +k +F  +D + dg+l+ + l +++++       g+++s+     e+++l+   D+ + G +++++F+++y
  gene236|gene236|rna236|rna236 101 MKFVFSVFDLNEDGRLCSAVLSKIYEI-----VHGNEFSRdictREVDELLLFYDKKHKGFLDYNDFVNFY 166
                                    7899*******************9998.....5555555622225688888888***************98 PP

>> EF-hand_6  EF-hand domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   8.5e-06     0.031       2      23 ..      31      52 ..      30      56 .. 0.90
   2 !    9.0   0.0   0.00042       1.5       1      19 [.     100     118 ..     100     126 .. 0.82
   3 !    9.5   1.2   0.00028      0.99       4      26 ..     144     166 ..     141     172 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 8.5e-06
                      EF-hand_6  2 lreaFklfDkdgdGkidaeElr 23
                                   l+e Fk++D+  +G++++++++
  gene236|gene236|rna236|rna236 31 LYERFKMLDRQENGYLTYSDIM 52
                                   7899***************997 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00042
                      EF-hand_6   1 elreaFklfDkdgdGkida 19 
                                    +++ +F  fD + dG +  
  gene236|gene236|rna236|rna236 100 RMKFVFSVFDLNEDGRLCS 118
                                    5889***********9865 PP

  == domain 3  score: 9.5 bits;  conditional E-value: 0.00028
                      EF-hand_6   4 eaFklfDkdgdGkidaeElrkal 26 
                                    e+   +Dk + G++d++++++++
  gene236|gene236|rna236|rna236 144 ELLLFYDKKHKGFLDYNDFVNFY 166
                                    555679*************9987 PP

>> EF-hand_1  EF hand
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.0   0.00016      0.57       3      23 ..      32      52 ..      30      54 .. 0.87
   2 !    8.9   0.0   0.00033       1.2       2      17 ..     101     116 ..     100     119 .. 0.88
   3 !   13.3   1.1   1.3e-05     0.045       1      25 [.     141     165 ..     141     168 .. 0.92
   4 ?   -3.1   0.4       2.3   8.1e+03       8      14 ..     176     182 ..     172     182 .. 0.65

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00016
                                   HHHHHHHTTTSSSEEEHHHHH CS
                      EF-hand_1  3 keiFrefDkDgdGkIdfeEfk 23
                                    e F+++D+  +G++++++ +
  gene236|gene236|rna236|rna236 32 YERFKMLDRQENGYLTYSDIM 52
                                   578**************9876 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00033
                                    HHHHHHHHTTTSSSEE CS
                      EF-hand_1   2 lkeiFrefDkDgdGkI 17 
                                    +k +F++fD + dG++
  gene236|gene236|rna236|rna236 101 MKFVFSVFDLNEDGRL 116
                                    5889**********97 PP

  == domain 3  score: 13.3 bits;  conditional E-value: 1.3e-05
                                    HHHHHHHHHTTTSSSEEEHHHHHHH CS
                      EF-hand_1   1 elkeiFrefDkDgdGkIdfeEfkel 25 
                                    e++e+   +Dk + G++d+++f+++
  gene236|gene236|rna236|rna236 141 EVDELLLFYDKKHKGFLDYNDFVNF 165
                                    78999999**************986 PP

  == domain 4  score: -3.1 bits;  conditional E-value: 2.3
                                    HHTTTSS CS
                      EF-hand_1   8 efDkDgd 14 
                                    ++D D+d
  gene236|gene236|rna236|rna236 176 VIDFDHD 182
                                    4677766 PP

>> EF-hand_8  EF-hand domain pair
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0     0.015        53      32      48 ..      35      51 ..      24      52 .. 0.90
   2 ?    4.2   0.1     0.011        38      31      43 ..     104     116 ..     101     116 .. 0.88
   3 !    7.1   0.2    0.0013       4.7      27      53 ..     141     167 ..     121     169 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.015
                      EF-hand_8 32 frefDtdgdGkisfeEF 48
                                   f+ +D+ ++G++++ + 
  gene236|gene236|rna236|rna236 35 FKMLDRQENGYLTYSDI 51
                                   7889*********9986 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.011
                      EF-hand_8  31 lfrefDtdgdGki 43 
                                    +f+ fD+++dG++
  gene236|gene236|rna236|rna236 104 VFSVFDLNEDGRL 116
                                    79*********86 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.0013
                      EF-hand_8  27 evdilfrefDtdgdGkisfeEFcvlle 53 
                                    evd+l+   D +++G +++++F++++ 
  gene236|gene236|rna236|rna236 141 EVDELLLFYDKKHKGFLDYNDFVNFYL 167
                                    899999999**************9875 PP

>> EF-hand_5  EF hand
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       1.3   4.6e+03       5      10 ..      35      40 ..      32      48 .. 0.70
   2 ?   11.3   0.0   5.4e-05      0.19       4      17 ..     104     117 ..     101     119 .. 0.88
   3 ?    0.2   0.1      0.17   6.3e+02       7      23 ..     148     164 ..     142     166 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.3
                                   HHHH-S CS
                      EF-hand_5  5 FqaiDl 10
                                   F+++D 
  gene236|gene236|rna236|rna236 35 FKMLDR 40
                                   777775 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 5.4e-05
                                    HHHHH-SS-SSCE- CS
                      EF-hand_5   4 tFqaiDlNgDGkIs 17 
                                    +F+ +DlN DG++ 
  gene236|gene236|rna236|rna236 104 VFSVFDLNEDGRLC 117
                                    7**********985 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.17
                                    HH-SS-SSCE-HHHHHH CS
                      EF-hand_5   7 aiDlNgDGkIskeELkt 23 
                                      D+ + G+++   + +
  gene236|gene236|rna236|rna236 148 FYDKKHKGFLDYNDFVN 164
                                    5799999*999888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       605  (0.0337442); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1392.25
//
Query:       gene2360|gene2360|rna2360|rna2360  [L=383]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    4.9e-76  254.4   0.7    6.9e-76  253.9   0.7    1.2  1  MOZ_SAS     MOZ/SAS family
    9.3e-15   54.0   1.4    1.9e-14   53.0   0.7    1.9  2  zf-MYST     MYST family zinc finger domain
    1.3e-14   53.8   0.0    2.8e-14   52.7   0.0    1.6  1  Tudor-knot  RNA binding activity-knot of a chromodomain
  ------ inclusion threshold ------
       0.01   16.1   0.0      0.035   14.4   0.0    1.9  1  DUF2513     Hypothetical protein (DUF2513)


Domain annotation for each model (and alignments):
>> MOZ_SAS  MOZ/SAS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  253.9   0.7   1.5e-79   6.9e-76       1     178 [.     170     346 ..     170     347 .. 0.98

  Alignments for each domain:
  == domain 1  score: 253.9 bits;  conditional E-value: 1.5e-79
                            MOZ_SAS   1 ppGkeiYrkeklsvfevdGekeklycqnLcllaklFldhktlyydvepFlfYvlteadeegahivGyFskekesae 76 
                                        ppG+eiYrk++ls+fe+dG+ +k yc+nL+ll+klFldhktl+ydv+pF+fYvl++ +++g+hivGyFskek +++
  gene2360|gene2360|rna2360|rna2360 170 PPGNEIYRKDNLSFFELDGHIQKNYCRNLSLLSKLFLDHKTLFYDVDPFMFYVLCRLERDGYHIVGYFSKEKVCSQ 245
                                        8*************************************************************************** PP

                            MOZ_SAS  77 eynlaCilvlPpyqrkgyGklliefsYeLskrekkigtPekPlsdlgllsyrsywkeeilellkekekkkisieei 152
                                        + nlaC+l+lP  qr gyGk+li+fsY Lsk+e+ i++PekPlsdlgl+ y syw+e+ile+++  +++ is+eei
  gene2360|gene2360|rna2360|rna2360 246 GFNLACLLILPYEQRMGYGKILIDFSYLLSKKENVIASPEKPLSDLGLIGYLSYWREAILEVMQV-DSNGISVEEI 320
                                        *************************************************************9986.6799****** PP

                            MOZ_SAS 153 sektgikeeDiistleelkllkyakg 178
                                        s++t+i+ eD+++tl  +k++k ++g
  gene2360|gene2360|rna2360|rna2360 321 SSRTAITVEDVCNTLIYYKMVKFYDG 346
                                        *********************99875 PP

>> zf-MYST  MYST family zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.0   0.7   4.3e-18   1.9e-14       2      52 ..     116     164 ..     115     166 .. 0.95
   2 ?   -3.6   0.0       2.1   9.2e+03      34      43 ..     363     372 ..     363     375 .. 0.75

  Alignments for each domain:
  == domain 1  score: 53.0 bits;  conditional E-value: 4.3e-18
                            zf-MYST   2 kniekieiGeyeiktWYfSpYPeelankekLyvCefClkYmksakelerHk 52 
                                        k i+k++i +  i++WYfSpYPe+++    +y+C fCl Y+++++el+ H 
  gene2360|gene2360|rna2360|rna2360 116 KVIDKLHIKDKIIDAWYFSPYPEDIT--GIIYLCSFCLFYFRTKDELRVHD 164
                                        789**********************9..89******************995 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 2.1
                            zf-MYST  34 vCefClkYmk 43 
                                        v e Clk+  
  gene2360|gene2360|rna2360|rna2360 363 VDEKCLKWKG 372
                                        5789**9865 PP

>> Tudor-knot  RNA binding activity-knot of a chromodomain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.7   0.0   6.2e-18   2.8e-14       2      52 ..      13      65 ..      12      68 .. 0.90

  Alignments for each domain:
  == domain 1  score: 52.7 bits;  conditional E-value: 6.2e-18
                                       -TTTEEEEEE...TTSCEEEEEEEEEEETSSCEEEEEEETTS-CCC-EEEETTT CS
                         Tudor-knot  2 evgckvlvrk...kdgelrkAeilsirekkgkyeYYVHYeefNkRlDeWVsaer 52
                                        vg k+ v+k   +  e  kAeil i++k+ k+e+YVHY +fN+RlDeW +++ 
  gene2360|gene2360|rna2360|rna2360 13 GVGYKLCVKKdmgNGTENIKAEILGIKNKR-KKEFYVHYINFNRRLDEWLNGDS 65
                                       5899999999998888999*********97.78****************99875 PP

>> DUF2513  Hypothetical protein (DUF2513)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   7.8e-06     0.035      20      81 ..     313     375 ..     298     379 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 7.8e-06
                            DUF2513  20 keeslddeeekls.aidgyskeeiiyhlkllaeagLieaekkkakssiislvvkrLtweGhdF 81 
                                        +  s++  +++   +++++ +  i+y + +  + +Li +++++ k + +++  k L w+Gh F
  gene2360|gene2360|rna2360|rna2360 313 NGISVEEISSRTAiTVEDVCNTLIYYKMVKFYDGELIFVKDRNVKPRKYKVDEKCLKWKGHAF 375
                                        44444443333336888999999**************************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (383 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       826  (0.0460706); expected 358.6 (0.02)
Passed bias filter:                      549  (0.0306208); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.56u 0.26s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 2532.80
//
Query:       gene2361|gene2361|rna2361|rna2361  [L=223]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    6.7e-07   29.1   6.7    1.2e-06   28.3   6.7    1.4  1  PHD         PHD-finger
    7.7e-06   25.4   1.6    1.5e-05   24.4   1.6    1.5  1  PHD_2       PHD-finger
  ------ inclusion threshold ------
       0.02   15.1   2.2      0.059   13.6   2.2    1.9  1  zf-HC5HC2H  PHD-like zinc-binding domain
      0.055   13.4   0.2      0.079   12.9   0.2    1.2  1  XH          XH domain
      0.071   13.7   3.0       0.17   12.5   3.0    1.7  1  ING         Inhibitor of growth proteins N-terminal histone-b


Domain annotation for each model (and alignments):
>> PHD  PHD-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   6.7   3.4e-10   1.2e-06       2      51 ..     172     217 ..     171     218 .. 0.87

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 3.4e-10
                                        BTTTTSTTSTTSCEEEET..TTS.CEEETTTSSSTHSHHSHHSSTBSSTTTHT CS
                                PHD   2 CavCkkksdeeeelvqCd..gCk.rwfHqkClkppleseekpegewlCekCke 51 
                                        C  C+k  d + +++ Cd  +C+ +wfH +C+++++     p g+w+C++C++
  gene2361|gene2361|rna2361|rna2361 172 C-YCGK--DVNAKMIACDdpNCRiEWFHLSCIGISQP----PAGKWYCRECRK 217
                                        7.9999..899******9556*868**********66....7788******86 PP

>> PHD_2  PHD-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   1.6   4.3e-09   1.5e-05       4      36 .]     182     216 ..     179     216 .. 0.92

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 4.3e-09
                              PHD_2   4 llsCd..kCsva.VHasCYGvskesdgeeWlCrrCe 36 
                                        ++ Cd  +C++  +H sC G+s++++g +W+Cr C+
  gene2361|gene2361|rna2361|rna2361 182 MIACDdpNCRIEwFHLSCIGISQPPAG-KWYCRECR 216
                                        899*9999***769*************.*******6 PP

>> zf-HC5HC2H  PHD-like zinc-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   2.2   1.7e-05     0.059      28      66 ..     161     200 ..     138     219 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.7e-05
                         zf-HC5HC2H  28 ekikkerkklkCylCkkkvGaciqCskkkCk.kafHvtCa 66 
                                         +++k+r    Cy+ k+ +  +i C+ ++C+ + fH+ C 
  gene2361|gene2361|rna2361|rna2361 161 AHANKDRDGAPCYCGKDVNAKMIACDDPNCRiEWFHLSCI 200
                                        567788888899888888899*********9457*****6 PP

>> XH  XH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.2   2.2e-05     0.079      18     114 ..      30     128 ..      18     144 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.2e-05
                                 XH  18 klseeeaeekaaelcslWqeeikdpkwhPfkvvevdgkekevideddekLkeLkeeyGeevy..kaVtkallelne 91 
                                        ++++ +  +k + l  l++e+++  +++P kv ++  + k   ++ +++++++k+++  + +  +++++a+l l+e
  gene2361|gene2361|rna2361|rna2361  30 NFNNFNNFVKIQSLPMLFKESLESLEETPLKVQKTITNIKLLNNQSEDHINTIKQQIELDQCdlQKIVSAFLRLEE 105
                                        45566678888999999****************9999999999999*********88766552278********** PP

                                 XH  92 ynpsgryivselWnfkegrkAtl 114
                                         +++    ++ l nf +g+  t+
  gene2361|gene2361|rna2361|rna2361 106 NEKELNAHLHSLYNFIDGQTETV 128
                                        ***************99987766 PP

>> ING  Inhibitor of growth proteins N-terminal histone-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   3.0   4.7e-05      0.17       4      43 ..      49      88 ..      39     157 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4.7e-05
                                       HHHTSGGGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                                ING  4 dyldsvenLPlelqrnltelreiDakvqellkeidskiek 43
                                       + l+s+e+ Pl++q+ +t ++ + ++ +++++ i+++ie 
  gene2361|gene2361|rna2361|rna2361 49 ESLESLEETPLKVQKTITNIKLLNNQSEDHINTIKQQIEL 88
                                       4567777778888888888888888888888877777764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1287  (0.0717831); expected 358.6 (0.02)
Passed bias filter:                      519  (0.0289475); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1636.92
//
Query:       gene2362|gene2362|rna2362|rna2362  [L=365]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.4e-14   52.4   2.7    7.6e-14   51.6   2.7    1.4  1  Noc2      Noc2p family


Domain annotation for each model (and alignments):
>> Noc2  Noc2p family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.6   2.7   4.2e-18   7.6e-14     130     281 ..     220     356 ..     186     363 .. 0.86

  Alignments for each domain:
  == domain 1  score: 51.6 bits;  conditional E-value: 4.2e-18
                               Noc2 130 lrlhlirsLlrLsestgtfIPvaplllevLeskelkkkpkkkstlkpldfevtlkvpksylktrvyqdglieevve 205
                                        ++l++i+s lr+      +IP+a  l+e+++   +  k +k +  k++d  +++k++++yl++++ +  ++ee + 
  gene2362|gene2362|rna2362|rna2362 220 FHLKIIQSVLRI----PFYIPLARKLIELFKLG-IAIKDTK-TIGKKIDY-SKIKLTTEYLRSEELKGFILEESLA 288
                                        788888888887....58*************94.4444444.579****7.689********************** PP

                               Noc2 206 llleylallsksiaFPElvlpvvvqLkrflkstkneklrkqlkqLvekleenskfieekRekvefspkdreeveaf 281
                                        ll  +l+++s s +FPE+++ v+ +Lk++ ++      + +lk L+e++e+++++i++kR+ ++f  ++   +++f
  gene2362|gene2362|rna2362|rna2362 289 LLFAHLNSISDSLGFPEISYHVLKELKEINED------NIDLKDLIERIERQVDLITNKRKGIKFVSEKD--IREF 356
                                        ****************************9998......789***********************976543..4444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (365 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1534  (0.0855597); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 2364.13
//
Query:       gene2363|gene2363|rna2363|rna2363  [L=421]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.4e-10   39.0   0.1    2.4e-06   27.3   0.0    2.2  2  FAD_binding_1  FAD binding domain
    3.5e-08   33.8   0.6    8.2e-08   32.6   0.1    1.9  2  Flavodoxin_1   Flavodoxin
    7.3e-07   29.8   0.0    1.4e-06   28.9   0.0    1.5  1  NAD_binding_1  Oxidoreductase NAD-binding domain


Domain annotation for each model (and alignments):
>> FAD_binding_1  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.0   9.6e-05      0.57       4      55 ..      88     138 ..      86     160 .. 0.91
   2 !   27.3   0.0     4e-10   2.4e-06     131     222 .]     200     283 ..     168     283 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 9.6e-05
                                        BTTB-EEEEEEEEEE---.-SS--EEEEEEE-TTBT----TT-EEEE----- CS
                      FAD_binding_1   4 dakkvflakvlknreLtkpesernvihveldisdsglkYetGdhlgvypsNn 55 
                                        ++k+ + a++ ++  Lt+ ++ ++++ v l++++++  +e+Gd + +ypsN 
  gene2363|gene2363|rna2363|rna2363  88 KQKRLYDATIISKNMLTPCDHFQEILEVGLSVENYD-DFEPGDTIRIYPSNY 138
                                        578999****************************97.8*************6 PP

  == domain 2  score: 27.3 bits;  conditional E-value: 4e-10
                                        HHHHHHH-HHHHHTTTTT--HHHHHHHHHTT---TTS-HHHHHHHS-B---EEEEB-S-TTTTTTEEEEEEE--EE CS
                      FAD_binding_1 131 kLekLssdegakeykelklneartllevleefpsvklplefLlevlpqLkpRyYSiSssskvhpdevhltvvVvey 206
                                        ++  +s+d   + y + +   +rt+ evl++f  +klp++fL +++p+++pRy+ +   +     +  lt+++vey
  gene2363|gene2363|rna2363|rna2363 200 RIREMSTD--YELYFDYVKRPKRTFFEVLQDFA-LKLPFSFLKKIVPNIQPRYFTLTKRE----SSYYLTIALVEY 268
                                        45556666..667777788889**********6.89*******************98655....55689******* PP

                                        ---SSS--EE-HHHHH CS
                      FAD_binding_1 207 etdgegrirkGvcsny 222
                                        ++     +rkG+cs+y
  gene2363|gene2363|rna2363|rna2363 269 QN-SIKAKRKGLCSQY 283
                                        *8.88899******98 PP

>> Flavodoxin_1  Flavodoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.6   0.1   1.4e-11   8.2e-08      85     136 ..       9      60 ..       5      67 .. 0.89
   2 ?   -2.7   0.1       1.1   6.4e+03      98     112 ..     138     152 ..     137     153 .. 0.84

  Alignments for each domain:
  == domain 1  score: 32.6 bits;  conditional E-value: 1.4e-11
                                        TTTEEEEEEEEECTTSSSTTHHHHHHHHHHHHTTCEEESSSEEEETTSTHGH CS
                       Flavodoxin_1  85 lsgvrfavfglGdsayenFcaagkkldekleelGaerllkllegdednqegq 136
                                        l+ +++avfglGds+y +F+ a kkl + +++lGa+ +++ + g+ +++eg+
  gene2363|gene2363|rna2363|rna2363   9 LKSCNIAVFGLGDSSYAKFNFASKKLFKVFSKLGANLFVERGNGNVQDDEGY 60 
                                        78899**************************************999987665 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.1
                                        TTSSSTTHHHHHHHH CS
                       Flavodoxin_1  98 sayenFcaagkklde 112
                                        +++ +Fc+ ++ +d+
  gene2363|gene2363|rna2363|rna2363 138 YNWREFCDYIGNVDD 152
                                        67999*****99996 PP

>> NAD_binding_1  Oxidoreductase NAD-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.9   0.0   2.3e-10   1.4e-06       1     108 [.     311     403 ..     311     404 .. 0.85

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 2.3e-10
                                        EEEEGGGGHHHHHHHHHHHHHCTTCSEEEEEEEESSGC.GSTTHHHHHHHHHHCTTEEEEEEEESSCTTTSSSEES CS
                      NAD_binding_1   1 miagGtGiaPvrsvlraileeakdktkvvlvyGnrtee.dllyreeleelakklpgrlkvvavvsreeagweggkg 75 
                                        +i++GtGi+  r++++ ++++     ++v++yG+r+++ d ly ee+++     ++ +kvv++ sr      g++ 
  gene2363|gene2363|rna2363|rna2363 311 FICTGTGITLPRAFWNFFTDK-----NIVVFYGYRHDDkDRLYVEEMKKN----KN-VKVVYAPSRM-----GEEL 371
                                        7*************9988875.....8*********99999999998654....44.8999993333.....4568 PP

                                        SHHHHHHHHHHHHSSTTEEEEEECSHHHHHHHH CS
                      NAD_binding_1  76 rvqdalleellslkkeethvyvCGppgMikavr 108
                                        +vq+ + +++ + + ++ ++yv G+ ++ k vr
  gene2363|gene2363|rna2363|rna2363 372 YVQEIFYKYFHD-SIDQYLIYVSGRTRLNKEVR 403
                                        ******999999.89**********99999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (421 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       789  (0.0440069); expected 358.6 (0.02)
Passed bias filter:                      503  (0.0280551); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 2946.41
//
Query:       gene2364|gene2364|rna2364|rna2364  [L=87]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.6e-08   34.2   0.0    2.7e-08   34.1   0.0    1.0  1  Flavodoxin_1  Flavodoxin
  ------ inclusion threshold ------
      0.076   13.3   0.0      0.084   13.1   0.0    1.1  1  Flavodoxin_5  Flavodoxin domain


Domain annotation for each model (and alignments):
>> Flavodoxin_1  Flavodoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.1   0.0     3e-12   2.7e-08       1      72 [.       7      70 ..       7      86 .. 0.85

  Alignments for each domain:
  == domain 1  score: 34.1 bits;  conditional E-value: 3e-12
                                       EEEETSSSHHHHHHHHHHHHHHHTTTEEEEEEEEGTTSCGGGGGTHSEEEEEEEEETTTBEEGGGHHHHHHH CS
                       Flavodoxin_1  1 ilYgSetGnteklAkqlaeelgehgfnadvvslsdydeslseieeealllvvtsTfgnGdppengesffqdl 72
                                       i+Yg++ Gn+  + + ++ +l  h  ++ +v ++++   l+++ + +  ++v+sT+gnGd+p  ++     +
  gene2364|gene2364|rna2364|rna2364  7 IVYGTQSGNSLHVSQLIRSKLT-HY-TTHIVPVDEFL--LENFLNCNTFIFVCSTYGNGDFPFAAQ----YF 70
                                       89*******************9.55.47999999999..89*********************5544....33 PP

>> Flavodoxin_5  Flavodoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   9.4e-06     0.084       2      56 ..       7      60 ..       6      73 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 9.4e-06
                       Flavodoxin_5  2 ilYsSrdGqTkkiaeriaeelree.gelvdvedvekesedlesydavvigasvyyg 56
                                       i+Y ++ G++  + + i  +l++   ++v v++     e++ +++ ++++ s y +
  gene2364|gene2364|rna2364|rna2364  7 IVYGTQSGNSLHVSQLIRSKLTHYtTHIVPVDEF--LLENFLNCNTFIFVCSTYGN 60
                                       89********************999999999997..5799999********99975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       259  (0.0144459); expected 358.6 (0.02)
Passed bias filter:                      214  (0.011936); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.34u 0.26s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 668.19
//
Query:       gene2365|gene2365|rna2365|rna2365  [L=77]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1554  (0.0866752); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.43
# Mc/sec: 539.40
//
Query:       gene2366|gene2366|rna2366|rna2366  [L=59]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.5e-07   28.4   0.1      6e-07   28.3   0.1    1.0  1  Mpp10     Mpp10 protein


Domain annotation for each model (and alignments):
>> Mpp10  Mpp10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   0.1   3.3e-11     6e-07     349     399 ..       3      52 ..       1      53 [. 0.83

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 3.3e-11
                              Mpp10 349 kGEvtAkdRPenSLLeedleFdrtarpaPviTeettetLEdiIkqRIkdka 399
                                        kGE++A++RP nSLL  dleF +t r +   Te+  ++   ++k R ++k+
  gene2366|gene2366|rna2366|rna2366   3 KGEASARERPLNSLLGCDLEFKQT-RVVTKPTENDENETLMLVKTRLREKN 52 
                                        8********************886.667777776655555799***99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       317  (0.0176809); expected 358.6 (0.02)
Passed bias filter:                      229  (0.0127726); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.27s 00:00:00.62 Elapsed: 00:00:00.42
# Mc/sec: 422.99
//
Query:       gene2367|gene2367|rna2367|rna2367  [L=292]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (292 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       498  (0.0277762); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 2053.66
//
Query:       gene2368|gene2368|rna2368|rna2368  [L=118]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.9e-11   43.9   0.2    3.2e-11   43.1   0.2    1.4  1  Thioredoxin    Thioredoxin
    2.5e-08   34.4   0.0     0.0018   18.7   0.1    2.5  3  Thioredoxin_2  Thioredoxin-like domain
    0.00031   20.9   0.0    0.00085   19.5   0.0    1.7  1  Thioredoxin_7  Thioredoxin-like
     0.0015   18.5   0.0      0.002   18.0   0.0    1.2  1  AhpC-TSA       AhpC/TSA family
     0.0034   17.7   0.0        2.4    8.5   0.0    2.2  2  Thioredoxin_8  Thioredoxin-like
  ------ inclusion threshold ------
      0.059   13.1   0.1      0.096   12.4   0.1    1.3  1  Redoxin        Redoxin
      0.092   13.2   0.6       0.19   12.2   0.6    1.6  1  DUF836         Glutaredoxin-like domain (DUF836)
        0.1   13.1   0.0       0.16   12.4   0.0    1.4  1  DUF1717        Viral domain of unknown function (DUF1717)


Domain annotation for each model (and alignments):
>> Thioredoxin  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.1   0.2   1.4e-14   3.2e-11      11      97 ..      22     106 ..      14     112 .. 0.80

  Alignments for each domain:
  == domain 1  score: 43.1 bits;  conditional E-value: 1.4e-14
                                        HHHHTTTSSEEEEEEE-TTSHHHHCHHHHHHHHHHHCTT.TSEEEEEETTTSHHHHHHTT-SSSSEEEEEETTE.E CS
                        Thioredoxin  11 eeevakekklvlveFyApwCghCkalaPeleklaeelkd.kvklakvdvdenedlakkyevegiPtlklfkngk.e 84 
                                        ++  +++kk+++++F+A +C +Ck ++ el+k    +k+ ++ l+++dv e++dlak+++v+++P   l+ ++   
  gene2368|gene2368|rna2368|rna2368  22 KKIAKSTKKPLILKFTAVFCNPCKIMSEELKK----YKGrDIALLNIDVRESADLAKHFGVRAVPYCCLVDEECeV 93 
                                        444555899****************9988765....66669*************************9999887645 PP

                                        EEEEESS-HHHHH CS
                        Thioredoxin  85 vkkyegarekekl 97 
                                        v++ +g    +++
  gene2368|gene2368|rna2368|rna2368  94 VRDRSGLMYVDEF 106
                                        6666666555555 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       1.4   3.2e+03      77      87 ..       8      19 ..       2      24 .. 0.64
   2 !   18.7   0.1   8.2e-07    0.0018       1      34 [.      25      58 ..      25      69 .. 0.84
   3 !   13.4   0.0   3.5e-05     0.078      66     107 ..      66     108 ..      57     110 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.4
                      Thioredoxin_2 77 gvrgtPtiv.fl 87
                                       +++++Pti  + 
  gene2368|gene2368|rna2368|rna2368  8 EIQELPTITsLA 19
                                       578888876344 PP

  == domain 2  score: 18.7 bits;  conditional E-value: 8.2e-07
                      Thioredoxin_2  1 akgngkpvlvvftdpdCpyCkklkkelkelddvt 34
                                       ak+++kp+++ ft++ C  Ck + +elk++++  
  gene2368|gene2368|rna2368|rna2368 25 AKSTKKPLILKFTAVFCNPCKIMSEELKKYKGRD 58
                                       6899**************************4433 PP

  == domain 3  score: 13.4 bits;  conditional E-value: 3.5e-05
                      Thioredoxin_2  66 ieenvelarkygvrgtPtivfldgk.eivarlpGyvpaeelea 107
                                        + e+ +la+ +gvr++P+  + d++ e+v    G++  +e+e 
  gene2368|gene2368|rna2368|rna2368  66 VRESADLAKHFGVRAVPYCCLVDEEcEVVRDRSGLMYVDEFER 108
                                        568899********************999999***99999876 PP

>> Thioredoxin_7  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   3.8e-07   0.00085       6      82 ..      18      88 ..      14      89 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 3.8e-07
                                       HHHHHHHHHHHT--EEEEE--TT-HHHHHHHHHHHH-HHHHH.HH.HT-EEEEESS--S-GGG.-TT-...--SSEEE CS
                      Thioredoxin_7  6 ldealakaaergkpvlvffgaswcftCqalerdflsdeevkaala.ekfvllrvdvterdanilelde...qgvPvva 79
                                       l++ +  a++++kp+++ f+a  c +C+ + +      e+k+ ++  +++ll++dv e+ +     ++   + vP  +
  gene2368|gene2368|rna2368|rna2368 18 LADLKKIAKSTKKPLILKFTAVFCNPCKIMSE------ELKK-YKgRDIALLNIDVRESADLA---KHfgvRAVPYCC 85
                                       7788999*********************8865......5667.77789999999998888844...342234488777 PP

                                       EE- CS
                      Thioredoxin_7 80 fld 82
                                       ++d
  gene2368|gene2368|rna2368|rna2368 86 LVD 88
                                       776 PP

>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   8.9e-07     0.002      23      97 ..      24      96 ..       8     103 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 8.9e-07
                                       H...TTSEEEEEEESTST-CCHHHHHHHHHHCHHHCCCTTEEEEEEESSSCHHHHHHHHH-H.SSEEEE-TTSHHHHH CS
                           AhpC-TSA 23 y...kgkpvvlffypkdwcpvCttelpalaklyeefkergvevigvsvdspeshkkfiekeslnfpllsDeegkvaka 97
                                       +    +kp++l f++  +c +C+     ++++++++k r++ ++ + v + ++++k      +++  l Dee++v+++
  gene2368|gene2368|rna2368|rna2368 24 IaksTKKPLILKFTAV-FCNPCKI----MSEELKKYKGRDIALLNIDVRESADLAKHFGVRAVPYCCLVDEECEVVRD 96
                                       3432559*********.*****65....6777788999**********99999999999999************9986 PP

>> Thioredoxin_8  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.0    0.0011       2.4       2      27 ..      30      55 ..      29      60 .. 0.92
   2 !    7.1   0.0     0.003       6.8      69      95 .]      67      93 ..      57      93 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0011
                                       SEEEEEE--SSSHHHHHHHHHHHHHH CS
                      Thioredoxin_8  2 kvvlLyfgaswcppckaftpklkely 27
                                       k ++L f a +c pck + ++lk+++
  gene2368|gene2368|rna2368|rna2368 30 KPLILKFTAVFCNPCKIMSEELKKYK 55
                                       7899******************9975 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.003
                                       T-HHHHTT-S--TT-SEEEEE-TT-BE CS
                      Thioredoxin_8 69 kkrnklkkkynvkaiPtlvvldkngev 95
                                        ++  l+k+++v a+P   ++d + ev
  gene2368|gene2368|rna2368|rna2368 67 RESADLAKHFGVRAVPYCCLVDEECEV 93
                                       45789*****************88775 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   4.3e-05     0.096      22     100 ..      20      96 ..       4     107 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4.3e-05
                                        EHHH..HTTSEEEEEEESTTT-HHHHHTHHHHHTHHHHHHCSTTTEEEEEESSSHH..HHHHHHHTT-TSEEEE-T CS
                            Redoxin  22 slse..fkgkkvvvnfvpgafcPtCsaehpyleklaellkekgvdvvavvadndaf..vkefwgkeglkfpvlsDg 93 
                                        +l++     kk ++  +++ fc +C+      e+l++    kg d+  +++d ++     ++ g   +++  l+D+
  gene2368|gene2368|rna2368|rna2368  20 DLKKiaKSTKKPLILKFTAVFCNPCKIMS---EELKKY---KGRDIALLNIDVRESadLAKHFGVRAVPYCCLVDE 89 
                                        33333223355566666666*******88...666555...66677777777777766888889999999999999 PP

                                        TSHHHHH CS
                            Redoxin  94 saaftka 100
                                        + +++++
  gene2368|gene2368|rna2368|rna2368  90 ECEVVRD 96 
                                        9999886 PP

>> DUF836  Glutaredoxin-like domain (DUF836)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.6   8.5e-05      0.19       9      49 ..      40      79 ..      32      99 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 8.5e-05
                                       T-HHHHHHHHHHHHHCCCTTEEEEEEETTT-CCCHCCCCTT CS
                             DUF836  9 gChlCeqakekLkelkleegleleviDIakdeeleakYgle 49
                                        C  C+ ++e Lk+ k ++ + l+ iD+ ++ +l +++g++
  gene2368|gene2368|rna2368|rna2368 40 FCNPCKIMSEELKKYKGRD-IALLNIDVRESADLAKHFGVR 79
                                       7999*********886555.8****************9986 PP

>> DUF1717  Viral domain of unknown function (DUF1717)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   7.2e-05      0.16      29      74 ..      47      93 ..      41      97 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 7.2e-05
                            DUF1717 29 mieevlitkglsmv.ytsdfkemavlnrkygvngkmyctikgnhcel 74
                                       m ee+   kg  +     d +e a l +++gv    yc +  + ce+
  gene2368|gene2368|rna2368|rna2368 47 MSEELKKYKGRDIAlLNIDVRESADLAKHFGVRAVPYCCLVDEECEV 93
                                       667777777777641567***************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       541  (0.0301746); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 862.49
//
Query:       gene2369|gene2369|rna2369|rna2369  [L=76]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       214  (0.011936); expected 358.6 (0.02)
Passed bias filter:                      190  (0.0105974); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.27s 00:00:00.63 Elapsed: 00:00:00.42
# Mc/sec: 539.79
//
Query:       gene237|gene237|rna237|rna237  [L=358]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.8e-35  120.4   0.1    5.9e-35  119.3   0.1    1.6  1  YchF-GTPase_C  Protein of unknown function (DUF933)
    3.2e-23   82.0   0.0    1.1e-22   80.2   0.0    1.9  2  MMR_HSR1       50S ribosome-binding GTPase
    8.1e-09   35.2   0.1    2.6e-08   33.6   0.0    1.8  2  FeoB_N         Ferrous iron transport protein B
     0.0086   15.1   1.0      0.055   12.5   0.0    2.1  2  MeaB           Methylmalonyl Co-A mutase-associated GTPase Me
  ------ inclusion threshold ------
      0.016   15.3   0.0      0.046   13.8   0.0    1.8  1  TGS            TGS domain
      0.018   15.1   0.5        2.5    8.1   0.0    2.9  3  Dynamin_N      Dynamin family
      0.045   14.4   2.8        0.1   13.3   0.1    2.3  2  SecA_PP_bind   SecA preprotein cross-linking domain
      0.047   14.2   0.0       0.24   11.9   0.0    2.0  2  ABC_tran       ABC transporter


Domain annotation for each model (and alignments):
>> YchF-GTPase_C  Protein of unknown function (DUF933)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.3   0.1   2.6e-38   5.9e-35       1      84 []     268     351 ..     268     351 .. 0.99

  Alignments for each domain:
  == domain 1  score: 119.3 bits;  conditional E-value: 2.6e-38
                  YchF-GTPase_C   1 LitffTaGekevraWtikkgttapqaAgviHsDfekgFiraevikyedlvelgseaaakeagklrlegkdyvvqdgDiil 80 
                                    Li+ffT+G  ev++Wt+++gt+apqaA viHsDfek+Fi+aev++y+d++ +g+e+++k+ag++ ++g+dyvv+dg+iil
  gene237|gene237|rna237|rna237 268 LINFFTVGAPEVKSWTVREGTKAPQAAAVIHSDFEKNFIMAEVMEYKDIKLYGNEQNVKKAGRYLHKGRDYVVEDGNIIL 347
                                    89****************************************************************************** PP

                  YchF-GTPase_C  81 fkfN 84 
                                    fk+N
  gene237|gene237|rna237|rna237 348 FKIN 351
                                    **98 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.2   0.0   5.1e-26   1.1e-22       2     100 ..      16     133 ..      15     168 .. 0.82
   2 ?   -2.7   0.0       2.7     6e+03      74      91 ..     207     224 ..     179     241 .. 0.63

  Alignments for each domain:
  == domain 1  score: 80.2 bits;  conditional E-value: 5.1e-26
                                    EEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEE.................EEEEECGGCSSHHHHHH CS
                       MMR_HSR1   2 vaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgke.................ielvDtpGliegaseek 64 
                                    ++ivG pNvGKStL+nalt++ + ++++p++T++++egr+++ +++                 + ++D++Gli+gas++ 
  gene237|gene237|rna237|rna237  16 MGIVGLPNVGKSTLFNALTKRSVPAANYPFCTITPEEGRIEIPDERfeylvnlykpksvvpayLSVIDIAGLIKGASQGL 95 
                                    69***************************************7665577888888888999999***************** PP

                                    HHHHHHHHHHC.TSEEEEEEETT.TTCSHHHHHHHHHH CS
                       MMR_HSR1  65 glgkaflalee.adlillvvdas.eeklkpldeeleel 100
                                    glg++fl++++ +d i+ vv++  +e++ ++de++  l
  gene237|gene237|rna237|rna237  96 GLGNEFLENIRrTDGIFQVVRCFeDENIVHVDEDIDPL 133
                                    ********88879********99633455555555433 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2.7
                                    HCTSEEEEEEETTTTCSH CS
                       MMR_HSR1  74 eeadlillvvdaseeklk 91 
                                      ++ ++++ ++se++++
  gene237|gene237|rna237|rna237 207 LTTKEVVYLANISEDEYN 224
                                    335666666666644443 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.6   0.0   1.1e-11   2.6e-08       3      49 ..      16      62 ..      14      68 .. 0.91
   2 ?   -2.4   0.1       1.3     3e+03      70      86 ..     151     167 ..     138     188 .. 0.49

  Alignments for each domain:
  == domain 1  score: 33.6 bits;  conditional E-value: 1.1e-11
                                   EEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEEEETTEEE CS
                         FeoB_N  3 valvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegklklkgkev 49
                                   + +vG pnvGk+tlfnalt+ +   +N+p  t+  +eg++++ ++++
  gene237|gene237|rna237|rna237 16 MGIVGLPNVGKSTLFNALTKRSVPAANYPFCTITPEEGRIEIPDERF 62
                                   568*************************************9888766 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.3
                                    HHHHHHCTSSSEEEEEE CS
                         FeoB_N  70 ardflleeepdvvvnvv 86 
                                     ++ + +++ ++vv+v 
  gene237|gene237|rna237|rna237 151 ITKRIEKQKRETVVDVK 167
                                    33333333333333332 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.0   2.4e-05     0.055      21      51 ..       3      35 ..       1      41 [. 0.80
   2 ?    1.0   0.2     0.075   1.7e+02     175     208 ..     165     198 ..     145     210 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.4e-05
                                   HHGGG-S-SEE..EEEEE-TTSSHHHHHHHHHH CS
                           MeaB 21 rllakaGraqv..vGltGvPGaGkstlvealgl 51
                                    ++++ G+++   +G+ G+P +Gkstl +al+ 
  gene237|gene237|rna237|rna237  3 VMFSRPGKSHNlsMGIVGLPNVGKSTLFNALTK 35
                                   56778888875227****************986 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.075
                                    E---HHHHHHHHHHHHHHHHHCSTTBTTB--EEE CS
                           MeaB 175 nkaDkkeaekaarelraaleleeekekeWrpkvl 208
                                    +   kk  +++  +l+ +le+++++e+eW+p  +
  gene237|gene237|rna237|rna237 165 DVKKKKFETQTLDKLKEVLEVKWTNEAEWTPDEI 198
                                    4444555567788999**************9755 PP

>> TGS  TGS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   2.1e-05     0.046      11      56 ..     282     346 ..     273     349 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.1e-05
                                    EEEETTB-HHHHHHHHSTTHHHHEEEEEECS...................EEEETTSBB-SSEEE CS
                            TGS  11 pdlprgatveDfAykIhrslakkfiyAlVnG...................qrvgldhvLedgdvv 56 
                                     ++++g+ + ++A  Ih+++ k+fi A V                      + g d+v+edg ++
  gene237|gene237|rna237|rna237 282 WTVREGTKAPQAAAVIHSDFEKNFIMAEVMEykdiklygneqnvkkagryLHKGRDYVVEDGNII 346
                                    44899999*********************999999888888888888877788888888888776 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.0    0.0011       2.5       3      32 ..      18      47 ..      16      52 .. 0.78
   2 ?    3.8   0.0     0.024        54      85     138 ..      61     117 ..      46     129 .. 0.81
   3 ?   -0.5   0.4       0.5   1.1e+03      60      80 ..     143     163 ..     119     228 .. 0.63

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0011
                                   EEEBTTTTHHHHHHHHHTS--S---SSS-- CS
                      Dynamin_N  3 vvGsqSsGKSSvlnaLlgedilprgpnptT 32
                                   +vG  + GKS++ naL+++ +       +T
  gene237|gene237|rna237|rna237 18 IVGLPNVGKSTLFNALTKRSVPAANYPFCT 47
                                   7899999***********997655555555 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.024
                                    S--SS-EEEEEEETTS-SEEEEE---B-SSSGTTS...HHHHHHHSTTEEEEEEEET CS
                      Dynamin_N  85 giskkvillkilsllvkgltlvDlPGldsvnkrdq...elvkeyikkadiilavtsa 138
                                    ++   v l+k++s     l+++D  Gl++ + +     +   e i++ d i+ v+ +
  gene237|gene237|rna237|rna237  61 RFEYLVNLYKPKSVVPAYLSVIDIAGLIKGASQGLglgNEFLENIRRTDGIFQVVRC 117
                                    44445778999999999************9999988999999999999999999876 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.5
                                    -EB--CHHHHHHHHHHHHHHH CS
                      Dynamin_N  60 kkledfsevreeieketekia 80 
                                     +l+d++ +++ iek++++  
  gene237|gene237|rna237|rna237 143 LRLKDLQIITKRIEKQKRETV 163
                                    445555555555555554433 PP

>> SecA_PP_bind  SecA preprotein cross-linking domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.7       0.4     9e+02      22      50 ..     162     212 ..     140     242 .. 0.46
   2 ?   13.3   0.1   4.5e-05       0.1      24      88 ..     284     347 ..     264     351 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.4
                                    ECCCTTTSEEEESHHHHHHHHHCCT-........................SSS CS
                   SecA_PP_bind  22 yevdekkktveltekGvekvekllkv........................kee 50 
                                     +vd kkk+ e   + ++k++++l+v                        ke 
  gene237|gene237|rna237|rna237 162 TVVDVKKKKFE--TQTLDKLKEVLEVkwtneaewtpdeieylntlnllttKEV 212
                                    44555555433..4556666666666444333333333333333333332222 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 4.5e-05
                                    CCTTTSEEEESHHHHHHHHHCCT-SSSTTSCCHCCHHHHHHHHHHHHHCSTTTTTEEECTTCEEE CS
                   SecA_PP_bind  24 vdekkktveltekGvekvekllkvkeelydeenlelvhhvnqaLkAhtlferdvdYivkdgevii 88 
                                    v e +k  +     ++  ek + +  e+++ ++++l+ + +++ kA   +++ +dY+v+dg++i+
  gene237|gene237|rna237|rna237 284 VREGTKAPQAAAVIHSDFEKNFIM-AEVMEYKDIKLYGNEQNVKKAGRYLHKGRDYVVEDGNIIL 347
                                    555555555555556677888877.999**********************************987 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00011      0.24      14      44 ..      16      57 ..      11      88 .. 0.78
   2 ?   -0.6   0.1      0.76   1.7e+03      70      79 ..     157     166 ..     105     252 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00011
                                   EEEEESTTSSHHHHHHHHTTSS--...........SEEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxx...........xxxxxxx RF
                       ABC_tran 14 vaivGenGaGKStLlkllagllkp...........teGeill 44
                                   ++ivG    GKStL+++l++ + p           +eG+i++
  gene237|gene237|rna237|rna237 16 MGIVGLPNVGKSTLFNALTKRSVPaanypfctitpEEGRIEI 57
                                   79******************9988555555555555666555 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.76
                                    S-TTSBHHHH CS
                                    xxxxxxxxxx RF
                       ABC_tran  70 lfpeltvren 79 
                                     +++ tv + 
  gene237|gene237|rna237|rna237 157 KQKRETVVDV 166
                                    2222222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (358 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       869  (0.048469); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 2530.38
//
Query:       gene2370|gene2370|rna2370|rna2370  [L=160]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.5e-11   43.2   2.1    3.4e-11   42.7   2.1    1.2  1  Ribosomal_L7Ae   Ribosomal protein L7Ae/L30e/S12e/Gadd45 fami
    5.9e-07   29.3   0.0    2.9e-05   23.9   0.0    2.7  3  PELOTA_1         PELOTA RNA binding domain
  ------ inclusion threshold ------
      0.017   15.1   0.0      0.029   14.3   0.0    1.4  1  HRDC             HRDC domain
      0.023   14.5   0.3      0.026   14.3   0.3    1.3  1  Acetyltransf_16  GNAT acetyltransferase, Mec-17
      0.056   13.5   0.0       0.12   12.5   0.0    1.6  1  DUF1694          Protein of unknown function (DUF1694)


Domain annotation for each model (and alignments):
>> Ribosomal_L7Ae  Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.7   2.1   9.5e-15   3.4e-11       2      93 ..      42     132 ..      41     134 .. 0.93

  Alignments for each domain:
  == domain 1  score: 42.7 bits;  conditional E-value: 9.5e-15
                                        HHHHHHHHHHHHTEEEESHHHHHHHHHTTTESEEEEETTSSSGGHHHHHHHHHHHTTEEEEEESCHHHHHHHTTSS CS
                     Ribosomal_L7Ae   2 aieevlkkakkagklvlGlkevtkalergeaklvilAedvepeekkkllealckekevpyvkvkskkeLGelvgkk 77 
                                        ai ++lk ++  +kl++G+++vtk l r++ak++++++ ++++  +  +  l+k+ +vp+v ++s  eL+ ++++ 
  gene2370|gene2370|rna2370|rna2370  42 AITQTLKISSSNNKLKCGIRQVTKCLLRKNAKMIFISKEIDDKYRRI-VVGLAKKCSVPVVVIESGDELADMAQLG 116
                                        78999*************************************99999.**************************** PP

                                        SECSEEEEEESTTTHH CS
                     Ribosomal_L7Ae  78 rpvsalaikdegdskd 93 
                                        r++ a + k +++s +
  gene2370|gene2370|rna2370|rna2370 117 RTTLADVKKMPKCSAV 132
                                        9999888888888876 PP

>> PELOTA_1  PELOTA RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.13   4.5e+02      34      51 ..       7      24 ..       5      30 .. 0.82
   2 !   23.9   0.0     8e-09   2.9e-05       9      69 ..      42     104 ..      35     110 .. 0.83
   3 ?    0.6   0.0      0.14   5.2e+02       3      29 ..     119     145 ..     117     146 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.13
                           PELOTA_1 34 LRRvPekvlvrdeeepdl 51
                                       LRRv  k++ ++++++++
  gene2370|gene2370|rna2370|rna2370  7 LRRVFSKIFFSNPRNKKM 24
                                       9********999888665 PP

  == domain 2  score: 23.9 bits;  conditional E-value: 8e-09
                           PELOTA_1   9 riaeeygied.inliKPgigEaTRvlLRRvPekvlvrdeee.pdlahlllLakekgvpveevp 69 
                                        +i+++ +i++  n  K gi   T+ lLR+  + +++++e + +  + ++ Lak+ +vpv++++
  gene2370|gene2370|rna2370|rna2370  42 AITQTLKISSsNNKLKCGIRQVTKCLLRKNAKMIFISKEIDdKYRRIVVGLAKKCSVPVVVIE 104
                                        67888999761579**********************99766155566778*********9876 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.14
                           PELOTA_1   3 gaaaveriaeeygiedinliKPgigEa 29 
                                        + a+v+++ +  ++  ++++K ++g +
  gene2370|gene2370|rna2370|rna2370 119 TLADVKKMPKCSAVAVTDFVKCSVGRT 145
                                        56889999999999999*****99965 PP

>> HRDC  HRDC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   8.2e-06     0.029      14      60 ..      91     137 ..      86     139 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 8.2e-06
                                        HHHHHHTS-HHHHS-HHHHHHHHHH---SHHHHHTSTTT-HHHHHHH CS
                               HRDC  14 elAreedvppyvvfpdktLleiAeklPttleeLlqiegvgkrkleky 60 
                                         lA+++ vp  v+ + + L ++A+   ttl++++++++++   +  +
  gene2370|gene2370|rna2370|rna2370  91 GLAKKCSVPVVVIESGDELADMAQLGRTTLADVKKMPKCSAVAVTDF 137
                                        58************************************998877666 PP

>> Acetyltransf_16  GNAT acetyltransferase, Mec-17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.3   7.4e-06     0.026      22      84 ..      31      95 ..       9     153 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 7.4e-06
                                       .HTT-HHHHHEEHHEEHHHHHHHTT-SS-S--HHH..HHHS-EEEEEEEETTCCCT-EEEEEEEE CS
                    Acetyltransf_16 22 kaeeaqeklseiidelGkaSakaqglkkpiTsaek..lqssdhvlYllkdkeakgkgavvGllkv 84
                                          +++ +l++ i +  k S++ ++lk  i +++k  l+++ +++++ k+ + k + +vvGl k 
  gene2370|gene2370|rna2370|rna2370 31 PIIDDTFTLKDAITQTLKISSSNNKLKCGIRQVTKclLRKNAKMIFISKEIDDKYRRIVVGLAKK 95
                                       34445889999************************8777899********************996 PP

>> DUF1694  Protein of unknown function (DUF1694)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   3.4e-05      0.12      48      97 ..      59     108 ..      38     115 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.4e-05
                                        --HHHHHHHHC-SSEEEEEETTS-HHHHHHHHHHHHHTT--EEEE---SS CS
                            DUF1694  48 vykeleealkkkkalkllingkldedilskyiklakkenikftivndeea 97 
                                          +++++ l +k+a+ ++i++++d+++ + ++ lakk+++++ ++++ ++
  gene2370|gene2370|rna2370|rna2370  59 GIRQVTKCLLRKNAKMIFISKEIDDKYRRIVVGLAKKCSVPVVVIESGDE 108
                                        46789999999*******************************99988655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       789  (0.0440069); expected 358.6 (0.02)
Passed bias filter:                      543  (0.0302861); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 1025.82
//
Query:       gene2371|gene2371|rna2371|rna2371  [L=110]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.07   12.8   1.5       0.97    9.1   0.3    2.1  2  SMP_2     Bacterial virulence factor haemolysin


Domain annotation for each model (and alignments):
>> SMP_2  Bacterial virulence factor haemolysin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0    0.0036        65      62      88 ..       7      34 ..       1      44 [. 0.78
   2 ?    9.1   0.3   5.4e-05      0.97       5      37 ..      60      92 ..      56      97 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.0036
                              SMP_2 62 kllv.dnakeeklkelldqltkeslvlD 88
                                       ++++ ++a+ ekl e+ld  t ++ ++D
  gene2371|gene2371|rna2371|rna2371  7 STISsKEANIEKLLESLDDTTIDESIID 34
                                       444404555999**************99 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 5.4e-05
                              SMP_2  5 klkfrllltvivllclallvvllqgasqfslgs 37
                                       k+ + l    i+ lcl ++++l+ g + ++l+ 
  gene2371|gene2371|rna2371|rna2371 60 KMVKALRYGEIIFLCLIIMFMLVIGWNVVNLAR 92
                                       7788888999****************9999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       942  (0.0525406); expected 358.6 (0.02)
Passed bias filter:                      601  (0.0335211); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.29s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 741.04
//
Query:       gene2372|gene2372|rna2372|rna2372  [L=43]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (43 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       207  (0.0115455); expected 358.6 (0.02)
Passed bias filter:                      134  (0.00747392); expected 358.6 (0.02)
Passed Vit filter:                         3  (0.000167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.27s 00:00:00.61 Elapsed: 00:00:00.42
# Mc/sec: 308.63
//
Query:       gene2373|gene2373|rna2373|rna2373  [L=29]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (29 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       366  (0.0204139); expected 358.6 (0.02)
Passed bias filter:                      187  (0.01043); expected 358.6 (0.02)
Passed Vit filter:                         7  (0.000390429); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.47
# Mc/sec: 184.06
//
Query:       gene2374|gene2374|rna2374|rna2374  [L=373]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.092   13.0   3.2        1.4    9.2   0.4    2.2  2  FANCI_S2  FANCI solenoid 2


Domain annotation for each model (and alignments):
>> FANCI_S2  FANCI solenoid 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.4   7.8e-05       1.4      83     153 ..     139     212 ..     128     214 .. 0.76
   2 ?    4.2   0.2    0.0028        49      59     114 ..     243     300 ..     231     312 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 7.8e-05
                           FANCI_S2  83 iklLselvksapltllesssklkelldylsflpletatallkAl.....lPLlkvseslrdalilvLRKalfsrel 153
                                        ++ ++++++++ + l +++++lk++ + l ++  +  ++l++Al     +P+l+++ +l+ ++i++L  ++f + +
  gene2374|gene2374|rna2374|rna2374 139 FEYIKQIINTYDILLTNHQQTLKKMPN-LRVFLRN-ISKLIEALkrvvyMPVLNIEADLQKKIIMTLSLTMFYKAI 212
                                        567889999999999999999999655.5444333.345666664444679********************98766 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.0028
                           FANCI_S2  59 arseiieqllsrii..tkseeevsqyiklLselvksapltllesssklkelldylsfl 114
                                        ++s+  e l +r+   t+s e +++ i+  +  ++++  ++le s++lk+++dy  +l
  gene2374|gene2374|rna2374|rna2374 243 VESYTYEDLNERVCvkTNSLEYIMHTINETYLFIRKYESEFLEASTNLKKIIDYNLIL 300
                                        556666666666651144556677888888899********************96555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (373 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1001  (0.0558313); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2662.91
//
Query:       gene2375|gene2375|rna2375|rna2375  [L=113]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (113 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       675  (0.0376485); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.29s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 768.18
//
Query:       gene2376|gene2376|rna2376|rna2376  [L=307]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-60  205.0   0.0    1.6e-60  204.7   0.0    1.1  1  Pkinase         Protein kinase domain
    4.1e-32  111.5   0.0      5e-32  111.2   0.0    1.1  1  Pkinase_Tyr     Protein tyrosine kinase
     0.0018   17.2   0.0     0.0027   16.5   0.0    1.2  1  Pkinase_fungal  Fungal protein kinase
     0.0037   16.6   0.0     0.0059   16.0   0.0    1.3  1  Kinase-like     Kinase-like
  ------ inclusion threshold ------
        0.1   12.5   0.0       0.19   11.6   0.0    1.4  1  APH             Phosphotransferase enzyme family


Domain annotation for each model (and alignments):
>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  204.7   0.0   4.5e-64   1.6e-60       3     264 .]       9     255 ..       7     255 .. 0.93

  Alignments for each domain:
  == domain 1  score: 204.7 bits;  conditional E-value: 4.5e-64
                                        EEEEEEEESSEEEEEEEETTTTEEEEEEEEECHCHCHHHH.HHHHHHHHHHHHHS.CTTB--EEEEEEESSEEEEE CS
                            Pkinase   3 kleklGeGsfGkVykaveketgkivAvKkikkekakkkke.kkvlrEikilkklk.hpnivrlyevfeekdelylv 76 
                                         ++++G G+fG+Vy      + k +A+K ++++     k+ +++ +E k l +l  +++ v+l+ +f+++++++lv
  gene2376|gene2376|rna2376|rna2376   9 IIRTIGVGTFGRVYLTE--YNAKYYALKAVSTSTLLRLKQkDHLNEERKTLCELFfCKYFVKLIFSFKTSRSYFLV 82 
                                        6899**********988..799***********99888886899999****99999******************** PP

                                        EE--TTEBHHHHHHHHSS--HHHHHHHHHHHHHHHHHHHHTTEE-SS-SGGGEEEETTTEEEE-SGTTSEESSSSC CS
                            Pkinase  77 leyveggeladllerkgslseeeakkiakqilegleylHskgiiHrDlKpeNiLidekgelKitDFGlakelesss 152
                                        leyv ggel+ +l+++g ++ ++a+++a++i  +leyl+sk++++rDlKpeNiL+ ekg++K++D+G+ak+l++ +
  gene2376|gene2376|rna2376|rna2376  83 LEYVGGGELFYWLRKRGPFKLKDARFYAAEITLALEYLFSKNLLYRDLKPENILLTEKGHIKLVDLGFAKKLNTLT 158
                                        *************************************************************************976 PP

                                        SBCTTTSCGGGS-HHHHTTSCBSHHHHHHHHHHHHHHHHHSS-STTTSSHHHHHHHHHHTHHHHHHHCTSHH...H CS
                            Pkinase 153 kltsfvgtseYlAPEvlkeneyskkvDvWslGvilyelltgkppfsgekgkekvekeldqlekilkilgetkeklp 228
                                           + +gt+eY+APE lk+++y++++D+WslG+++ye+l g ppf+++      + +++      +il     ++p
  gene2376|gene2376|rna2376|rna2376 159 --FTLCGTPEYMAPEKLKSEGYGQSSDIWSLGILIYEMLKGIPPFYSKAP----YLIYQ------RIL----TDVP 218
                                        ..89******************************************2222....22333......344....469* PP

                                        HHTTS-HHHHHHHHHHT-SSGCCSTT.HHHHHTSGGG CS
                            Pkinase 229 easeiseeakdllkkllkkdpkkRlt.aeellqhpyl 264
                                        + s+++  a dl+++ll+kdpk+Rl+ ++ +++hp++
  gene2376|gene2376|rna2376|rna2376 219 NYSDMDLIAVDLIEQLLEKDPKRRLSdVNVIKEHPFF 255
                                        **************************8999999*998 PP

>> Pkinase_Tyr  Protein tyrosine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.2   0.0   1.4e-35     5e-32       1     251 [.       7     244 ..       7     251 .. 0.86

  Alignments for each domain:
  == domain 1  score: 111.2 bits;  conditional E-value: 1.4e-35
                                        EEEEEEEEEESSEEEEEEEEETTTTSSEEEEEEEEESTTS..SHHHHHHHHHHHHHHHTS.-BTTB--EEEEEESS CS
                        Pkinase_Tyr   1 lelgkklGeGafGkVvegtlkgekekkevkVavKtlkeea..teeekeelleeakimkkl.khpnivkllgvctke 73 
                                        l++ +++G G+fG+V+  +++          a+K ++ ++  + ++k++l ee k++++l   +  vkl+     +
  gene2376|gene2376|rna2376|rna2376   7 LKIIRTIGVGTFGRVYLTEYN------AKYYALKAVSTSTllRLKQKDHLNEERKTLCELfFCKYFVKLIFSFKTS 76 
                                        67899****************......4555666664433115667889999********99************** PP

                                        SSEEEEEE--TTEBHHHHHHHTCTTTSBHHHHHHHHHHHHHHHHHHHHTTEEEST-SGGGEEEEETTEEEE-STTT CS
                        Pkinase_Tyr  74 epllivteyvkgGdLlkfLrkkekekltlkdllsfalqvAkGmeyLeskklvHrdlaarNvLlsenkvvkisDfGL 149
                                        +++++v+eyv gG+L   Lrk+   +++lkd   +a+++  ++eyL sk+l+ rdl   N+Ll+e+ ++k+ D G 
  gene2376|gene2376|rna2376|rna2376  77 RSYFLVLEYVGGGELFYWLRKR--GPFKLKDARFYAAEITLALEYLFSKNLLYRDLKPENILLTEKGHIKLVDLGF 150
                                        *********************8..9*************************************************** PP

                                        HEETTTSSEEEETTSSTSGGGGS-HHHHHHSEEEHHHHHHHHHHHHHHHHTTSSGTTTTSHHHHHHHHHHTTEES- CS
                        Pkinase_Tyr 150 ardiekddeyvkkeeaklpvkWmapEslkekkftsksDvWsfGvllwEiftlgespypglkneevleklkegkrle 225
                                        a+++    + + + +     ++mapE lk++ + ++sD+Ws G+l++E+++ g  p+ +  +  +++++ ++  ++
  gene2376|gene2376|rna2376|rna2376 151 AKKL----N-TLTFTLCGTPEYMAPEKLKSEGYGQSSDIWSLGILIYEMLK-GIPPFYSKAPYLIYQRILTD--VP 218
                                        ****....3.33444555679*****************************9.*****999999999999654..34 PP

                                        BBTTSBHHHHHHHHHHT-SSGGGS-- CS
                        Pkinase_Tyr 226 kpekcpeelyelmkkcweedpeeRpt 251
                                        + +++     +l+++ +e+dp++R +
  gene2376|gene2376|rna2376|rna2376 219 NYSDMDLIAVDLIEQLLEKDPKRRLS 244
                                        44445555667788888888888865 PP

>> Pkinase_fungal  Fungal protein kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   7.6e-07    0.0027     318     389 ..     116     176 ..     111     188 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 7.6e-07
                     Pkinase_fungal 318 ghrsLflkagiLHrDiSenNilitdskkegerkglLiDLDlakelsddssesgarertGTleFmaievlkge 389
                                        +++ Lf  +++L rD   +Nil+t     ++ +  L+DL +ak+l++        +  GT+e+ma e lk e
  gene2376|gene2376|rna2376|rna2376 116 ALEYLF-SKNLLYRDLKPENILLT-----EKGHIKLVDLGFAKKLNT-----LTFTLCGTPEYMAPEKLKSE 176
                                        678899.9****************.....567889***********6.....45779********9998854 PP

>> Kinase-like  Kinase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   1.7e-06    0.0059     158     271 ..     118     222 ..      93     242 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.7e-06
                        Kinase-like 158 anLqakglvhgkftvdnllldekgglmlggftaLvragtkvvl.sevekgfaPpEllgsrggytrknktkmthkld 232
                                         +L +k l+  +++++n+ll ekg ++l +++   +  t       +++  aP  l ++  gy++        + d
  gene2376|gene2376|rna2376|rna2376 118 EYLFSKNLLYRDLKPENILLTEKGHIKLVDLGFAKKLNTLTFTlCGTPEYMAPEKLKSE--GYGQ--------SSD 183
                                        68999*************************99888888876644666677777666666..6666........88* PP

                        Kinase-like 233 aWqlGlviyriwclklPltlateeakeewkfklckkipe 271
                                         W lG+ iy +     P+  +++  + + ++  + + ++
  gene2376|gene2376|rna2376|rna2376 184 IWSLGILIYEMLKGIPPFYSKAPYLIYQRILTDVPNYSD 222
                                        ***********9999999888888877777777776665 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   5.2e-05      0.19     163     197 ..     120     152 ..      72     154 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 5.2e-05
                                        SS-EEEE-SS-SGGGEEEC..TTEEEEE---TT-E CS
                                APH 163 elptvllHgDlhpgNllvdpddgrvtGviDfedag 197
                                         +++ ll +Dl+p N+l++ ++g++  ++D+++a+
  gene2376|gene2376|rna2376|rna2376 120 LFSKNLLYRDLKPENILLT-EKGHI-KLVDLGFAK 152
                                        567889*************.88998.899999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (307 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       446  (0.0248759); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 2115.96
//
Query:       gene2377|gene2377|rna2377|rna2377  [L=952]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.019   14.9   0.0      0.077   13.0   0.0    2.0  1  RuBisCO_small  Ribulose bisphosphate carboxylase, small chain
      0.056   13.1   1.0       0.58    9.8   0.1    2.6  2  CENP-P         CENP-A-nucleosome distal (CAD) centromere subu


Domain annotation for each model (and alignments):
>> RuBisCO_small  Ribulose bisphosphate carboxylase, small chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   8.6e-06     0.077      40      91 ..     146     197 ..     114     199 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 8.6e-06
                                        T-S--EEES---TT---HHHHHHHHHHHHHHSTTSEEEEEEEETTTTEEEEE CS
                      RuBisCO_small  40 rnryWtmwklpmfdlkdaaevlaeleecrkaypeeyvrligfDnkkqsqvls 91 
                                        ++ y +++k  +++l+d+ e l+e+ e+ +++p+e++rl   D+ ++ +  s
  gene2377|gene2377|rna2377|rna2377 146 QKDYFDIFKYVFLHLDDNVELLSEMCESIQENPTEFLRLFENDSDEKARSNS 197
                                        569**************************************99999887666 PP

>> CENP-P  CENP-A-nucleosome distal (CAD) centromere subunit, CENP-P
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.1     0.046   4.1e+02      66      99 ..      38      71 ..      16      78 .. 0.70
   2 ?    9.8   0.1   6.5e-05      0.58      11      64 ..     365     418 ..     361     430 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.046
                             CENP-P 66 rslrsfaewcedrrrtfkhfkekypevvnlpeGa 99
                                        +++ f  + e+ + t khf     ++ ++ +G 
  gene2377|gene2377|rna2377|rna2377 38 TQMSRFITFLEQEKVTNKHFSVEQCNIDQIINGN 71
                                       2456788899999999999998888888877775 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 6.5e-05
                             CENP-P  11 lllfqlefqvleiqekeslsaaitdlsivvesveyselskfvsraeekkdlllf 64 
                                         l+f ++f+  eiq    ++  i+d   +++s+++ +ls+f  +  +  + l f
  gene2377|gene2377|rna2377|rna2377 365 YLKFTIDFKNNEIQPIRDMKVCISDDIYAINSTKFANLSRFTIQNVKFAQTLTF 418
                                        689**************************************8776665555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (952 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       907  (0.0505884); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.89u 0.36s 00:00:01.25 Elapsed: 00:00:00.59
# Mc/sec: 4832.35
//
Query:       gene2378|gene2378|rna2378|rna2378  [L=48]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (48 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       210  (0.0117129); expected 358.6 (0.02)
Passed bias filter:                      192  (0.0107089); expected 358.6 (0.02)
Passed Vit filter:                         4  (0.000223102); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.51u 0.33s 00:00:00.84 Elapsed: 00:00:00.53
# Mc/sec: 270.27
//
Query:       gene2379|gene2379|rna2379|rna2379  [L=70]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (70 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       269  (0.0150036); expected 358.6 (0.02)
Passed bias filter:                      174  (0.00970495); expected 358.6 (0.02)
Passed Vit filter:                         7  (0.000390429); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.37s 00:00:00.86 Elapsed: 00:00:00.53
# Mc/sec: 395.11
//
Query:       gene238|gene238|rna238|rna238  [L=42]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (42 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       198  (0.0110436); expected 358.6 (0.02)
Passed bias filter:                      144  (0.00803168); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.28s 00:00:00.67 Elapsed: 00:00:00.45
# Mc/sec: 278.21
//
Query:       gene2380|gene2380|rna2380|rna2380  [L=131]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       448  (0.0249875); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.49
# Mc/sec: 798.63
//
Query:       gene2381|gene2381|rna2381|rna2381  [L=86]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       339  (0.0189079); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 609.89
//
Query:       gene2382|gene2382|rna2382|rna2382  [L=90]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       348  (0.0194099); expected 358.6 (0.02)
Passed bias filter:                      213  (0.0118802); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 692.50
//
Query:       gene2383|gene2383|rna2383|rna2383  [L=301]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (301 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       514  (0.0286686); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 2132.39
//
Query:       gene2384|gene2384|rna2384|rna2384  [L=572]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-06   28.5   1.2      0.066   13.8   0.4    2.9  2  VCBS      Repeat domain in Vibrio, Colwellia, Bradyrhizobium 
  ------ inclusion threshold ------
        0.6   10.3   2.3        4.6    7.5   0.1    2.5  2  FG-GAP    FG-GAP repeat


Domain annotation for each model (and alignments):
>> VCBS  Repeat domain in Vibrio, Colwellia, Bradyrhizobium and Shewanella
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.4   7.4e-06     0.066      12      61 .]     139     194 ..     131     194 .. 0.69
   2 !   12.1   0.0   2.5e-05      0.22       1      53 [.     234     299 ..     234     299 .. 0.56

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 7.4e-06
                               VCBS  12 va..ndgglrvyrnng....dGtftdvtktslggsgggtgvavgDlDgDGdlDllv 61 
                                        ++  +  ++rv++ +g    + t + ++  +lg+ ++ ++ a +D+D+D ++D+l+
  gene2384|gene2384|rna2384|rna2384 139 FLirDGTHTRVLILRGnavdNQTVETWGGSALGSIMRDHTSAYVDVDNDSRADVLI 194
                                        4432344467777666336555666666778888999999*************985 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 2.5e-05
                               VCBS   1 DldgDGrlDlvva..ndgg......lrvyrnngdGtftdvtkt...slgg..sgggtgvavgDlDg 53 
                                        Dld DG+ Dl ++  n++g      ++ y+n++d  f++ tk+   +l++  + +   ++++DlD+
  gene2384|gene2384|rna2384|rna2384 234 DLDRDGKVDLCYVcaNSEGnhliihFNQYENENDVVFSSETKIrkiDLNEmfPEYDPVMRIADLDN 299
                                        9**********9877655524442222244444444554433222255555433333588999987 PP

>> FG-GAP  FG-GAP repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.1   0.00052       4.6       6      20 ..     180     194 ..     177     198 .. 0.89
   2 ?    1.7   0.3     0.034     3e+02       9      18 ..     234     243 ..     228     243 .. 0.93

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.00052
                                        EEESTSSSSS-EEEE CS
                             FG-GAP   6 avgDvNGDGyaDLav 20 
                                        a +Dv++D  aD+++
  gene2384|gene2384|rna2384|rna2384 180 AYVDVDNDSRADVLI 194
                                        668**********98 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.034
                                        STSSSSS-EE CS
                             FG-GAP   9 DvNGDGyaDL 18 
                                        D++ DG+ DL
  gene2384|gene2384|rna2384|rna2384 234 DLDRDGKVDL 243
                                        9******998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (572 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       870  (0.0485247); expected 358.6 (0.02)
Passed bias filter:                      581  (0.0324056); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.41
# Mc/sec: 4137.65
//
Query:       gene2385|gene2385|rna2385|rna2385  [L=571]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-32  110.3  13.3    9.4e-10   38.2   0.0    7.4  6  Arm       Armadillo/beta-catenin-like repeat
    4.1e-08   33.5   0.0     0.0054   17.2   0.0    4.2  4  HEAT_EZ   HEAT-like repeat
    2.5e-07   31.0   3.1      5e-07   30.1   3.1    1.4  1  IBB       Importin beta binding domain
    0.00051   20.1   4.6        1.8    9.0   0.0    5.2  7  HEAT      HEAT repeat
     0.0066   16.8   0.1        0.7   10.3   0.1    2.9  2  HEAT_2    HEAT repeats


Domain annotation for each model (and alignments):
>> Arm  Armadillo/beta-catenin-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   1.5   1.4e-08     5e-05       1      41 []      83     134 ..      83     134 .. 0.87
   2 !   38.2   0.0   2.6e-13   9.4e-10       1      40 [.     136     175 ..     136     176 .. 0.97
   3 !   20.5   0.6   9.8e-08   0.00035       2      39 ..     179     221 ..     178     221 .. 0.95
   4 !   14.4   0.0   8.2e-06     0.029      19      41 .]     243     265 ..     237     265 .. 0.89
   5 ?    2.8   0.0     0.037   1.3e+02      28      40 ..     345     357 ..     343     358 .. 0.89
   6 !    8.5   0.0    0.0006       2.2      24      40 ..     382     398 ..     361     399 .. 0.78

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 1.4e-08
                                        SHHHHHHHHHTTHHHHHHHHTT.......TSSHHHHH....HHHHHHHHHTT CS
                                Arm   1 nsenkdavieaGavppLvrLLs.......sedeevqe....eAawALsNLaa 41 
                                        ns++++ vi++G vp++v+LLs       + d +v++    eAawAL+N+a+
  gene2385|gene2385|rna2385|rna2385  83 NSPPIQSVIDSGLVPRFVELLSaecslykNADKRVVRsirmEAAWALTNIAS 134
                                        799**********************9999777766544444*********96 PP

  == domain 2  score: 38.2 bits;  conditional E-value: 2.6e-13
                                        SHHHHHHHHHTTHHHHHHHHTTTSSHHHHHHHHHHHHHHT CS
                                Arm   1 nsenkdavieaGavppLvrLLssedeevqeeAawALsNLa 40 
                                        +se+++a+ ++Ga+p + ++L+  de+++ +AawA +N+a
  gene2385|gene2385|rna2385|rna2385 136 TSEQTQAILDYGAIPLFADMLKENDEDLVDQAAWAFGNIA 175
                                        589************************************8 PP

  == domain 3  score: 20.5 bits;  conditional E-value: 9.8e-08
                                        HHHHHHHHHTTHHHHHHHHTT.....TSSHHHHHHHHHHHHHH CS
                                Arm   2 senkdavieaGavppLvrLLs.....sedeevqeeAawALsNL 39 
                                        ++ +da i++ ++++ ++L +     + + +v+++++w LsNL
  gene2385|gene2385|rna2385|rna2385 179 EKMRDAAINCDVLKIVINLATqllktNASLRVLKNCTWVLSNL 221
                                        5789**************************************9 PP

  == domain 4  score: 14.4 bits;  conditional E-value: 8.2e-06
                                        HHTTTSSHHHHHHHHHHHHHHTT CS
                                Arm  19 rLLssedeevqeeAawALsNLaa 41 
                                        +L++ +d+ev+ + +wALs++++
  gene2385|gene2385|rna2385|rna2385 243 HLIDYKDDEVLNDTLWALSYICD 265
                                        79999*****************6 PP

  == domain 5  score: 2.8 bits;  conditional E-value: 0.037
                                        HHHHHHHHHHHHT CS
                                Arm  28 vqeeAawALsNLa 40 
                                        +++e++w  sN+a
  gene2385|gene2385|rna2385|rna2385 345 LRKEICWIFSNIA 357
                                        789*********8 PP

  == domain 6  score: 8.5 bits;  conditional E-value: 0.0006
                                        SSHHHHHHHHHHHHHHT CS
                                Arm  24 edeevqeeAawALsNLa 40 
                                            ++ eA+wA++N+ 
  gene2385|gene2385|rna2385|rna2385 382 LQNYIKMEACWAITNMM 398
                                        5566899********86 PP

>> HEAT_EZ  HEAT-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0         5   1.8e+04      29      38 ..      95     104 ..      89     108 .. 0.73
   2 !   17.2   0.0   1.5e-06    0.0054       3      55 .]     121     174 ..     120     174 .. 0.91
   3 !    6.0   0.0    0.0048        17       3      55 .]     210     263 ..     208     263 .. 0.81
   4 !    5.0   0.0    0.0098        35       3      55 .]     345     397 ..     343     397 .. 0.73

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 5
                            HEAT_EZ  29 ilpaLlalLn 38 
                                        ++p ++ lL+
  gene2385|gene2385|rna2385|rna2385  95 LVPRFVELLS 104
                                        6777777774 PP

  == domain 2  score: 17.2 bits;  conditional E-value: 1.5e-06
                            HEAT_EZ   3 vRraAawaLGrlaggepellqp.lvpeilpaLlalLnddsdeVRaaAagaLgnl 55 
                                        +R  AawaL ++a+g +e+ q  l   ++p+++ +L+  + +   +Aa+a+gn+
  gene2385|gene2385|rna2385|rna2385 121 IRMEAAWALTNIASGTSEQTQAiLDYGAIPLFADMLKENDEDLVDQAAWAFGNI 174
                                        6889*****99********66658889*********99999999********98 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.0048
                            HEAT_EZ   3 vRraAawaLGr.laggepellqplvpeilpaLlalLnddsdeVRaaAagaLgnl 55 
                                        v  ++ w+L++   g +p+    + ++ l+ L  l   ++deV   +++aL+ +
  gene2385|gene2385|rna2385|rna2385 210 VLKNCTWVLSNlNRGRNPPPKLENMKASLDVLQHLIDYKDDEVLNDTLWALSYI 263
                                        55677888888777777777777888888888988899*************976 PP

  == domain 4  score: 5.0 bits;  conditional E-value: 0.0098
                            HEAT_EZ   3 vRraAawaLGrlaggepellqplvpeilpaLlalLnddsdeV....RaaAagaLgnl 55 
                                        +R   +w ++++a g +e+++ lv e + +Ll     + ++     +  A++a++n+
  gene2385|gene2385|rna2385|rna2385 345 LRKEICWIFSNIACGTKEHISSLVNENIMELL----YSTANLqnyiKMEACWAITNM 397
                                        78899999999999999999998877665555....144422244599999999886 PP

>> IBB  Importin beta binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.1   3.1   1.4e-10     5e-07       8      50 ..       8      48 ..       2      81 .. 0.74

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 1.4e-10
                                       XX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX... CS
                                IBB  8 kgkdaeelRrrReeeqvelRKqkreeqllKrRnvaaeaaaeee 50
                                       +++++e+ +++Ree+q+elR +kree l+K+R +++  +++++
  gene2385|gene2385|rna2385|rna2385  8 QNTSTENRKKQREEKQIELREKKREELLNKKRTMTV--CDAST 48
                                       45567888999***********************65..22222 PP

>> HEAT  HEAT repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.82   2.9e+03       1      13 [.      95     107 ..      95     113 .. 0.87
   2 !    5.8   0.1    0.0057        20      15      30 ..     120     135 ..     117     136 .. 0.90
   3 !    9.0   0.0    0.0005       1.8       2      28 ..     149     175 ..     148     178 .. 0.95
   4 ?   -2.4   0.0       2.4   8.8e+03      13      23 ..     178     188 ..     176     188 .. 0.81
   5 ?   -3.6   0.0         5   1.8e+04      12      27 ..     206     221 ..     196     221 .. 0.69
   6 ?   -0.7   0.0      0.67   2.4e+03       3      29 ..     239     265 ..     238     267 .. 0.78
   7 ?    1.7   0.0      0.11   4.1e+02      17      31 .]     387     401 ..     383     401 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.82
                                        HHHHHHHHHT-SS CS
                               HEAT   1 llPlllkllsDps 13 
                                        l+P +++lls ++
  gene2385|gene2385|rna2385|rna2385  95 LVPRFVELLSAEC 107
                                        79*******9986 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0057
                                        HHHHHHHHHHHHHHHC CS
                               HEAT  15 eVReaAakaLgalaev 30 
                                        ++R+ Aa+aL+++a++
  gene2385|gene2385|rna2385|rna2385 120 SIRMEAAWALTNIASG 135
                                        68************86 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.0005
                                        HHHHHHHHT-SSHHHHHHHHHHHHHHH CS
                               HEAT   2 lPlllkllsDpspeVReaAakaLgala 28 
                                        +Pl+  +l+ ++ +  + Aa+a+g++a
  gene2385|gene2385|rna2385|rna2385 149 IPLFADMLKENDEDLVDQAAWAFGNIA 175
                                        8************************98 PP

  == domain 4  score: -2.4 bits;  conditional E-value: 2.4
                                        SHHHHHHHHHH CS
                               HEAT  13 speVReaAaka 23 
                                        s + R+aA+++
  gene2385|gene2385|rna2385|rna2385 178 SEKMRDAAINC 188
                                        5677****998 PP

  == domain 5  score: -3.6 bits;  conditional E-value: 5
                                        SSHHHHHHHHHHHHHH CS
                               HEAT  12 pspeVReaAakaLgal 27 
                                         s +V +++ + L +l
  gene2385|gene2385|rna2385|rna2385 206 ASLRVLKNCTWVLSNL 221
                                        5667778888888765 PP

  == domain 6  score: -0.7 bits;  conditional E-value: 0.67
                                        HHHHHHHT-SSHHHHHHHHHHHHHHHH CS
                               HEAT   3 PlllkllsDpspeVReaAakaLgalae 29 
                                        ++l++l+  ++ eV   +++aL  ++ 
  gene2385|gene2385|rna2385|rna2385 239 DVLQHLIDYKDDEVLNDTLWALSYICD 265
                                        567777677999999999999999987 PP

  == domain 7  score: 1.7 bits;  conditional E-value: 0.11
                                        HHHHHHHHHHHHHCS CS
                               HEAT  17 ReaAakaLgalaevl 31 
                                         + A++a++++++++
  gene2385|gene2385|rna2385|rna2385 387 KMEACWAITNMMSHC 401
                                        677**********98 PP

>> HEAT_2  HEAT repeats
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.1   0.00019       0.7      46      86 ..     120     170 ..     107     192 .. 0.68
   2 ?    3.1   0.0     0.036   1.3e+02       6      59 ..     200     264 ..     195     285 .. 0.57

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00019
                             HEAT_2  46 avRraaaeaLgaig...dpe.........alpaLkellddddddvvReaAaea 86 
                                         +R++aa+aL  i+   + e         a+p+ +++l++ d+d+v +a a+a
  gene2385|gene2385|rna2385|rna2385 120 SIRMEAAWALTNIAsgtS-EqtqaildygAIPLFADMLKENDEDLVDQA-AWA 170
                                        467777777776642231.223445555577777777777777777764.444 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.036
                             HEAT_2   6 qalendpdpevrraairaLg....rignp........ealpaLvellededpavRraaaeaLgaig 59 
                                        q+l++ ++  v ++  ++L       +np         +l+ L  l++ +d +v     +aL+ i 
  gene2385|gene2385|rna2385|rna2385 200 QLLKTNASLRVLKNCTWVLSnlnrG-RNPppklenmkASLDVLQHLIDYKDDEVLNDTLWALSYIC 264
                                        5555555555555555556533321.1223444444445777777777777777777777777664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (571 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       855  (0.0476881); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.60u 0.28s 00:00:00.88 Elapsed: 00:00:00.48
# Mc/sec: 3593.27
//
Query:       gene2386|gene2386|rna2386|rna2386  [L=33]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (33 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       123  (0.00686039); expected 358.6 (0.02)
Passed bias filter:                      101  (0.00563333); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.21s 00:00:00.55 Elapsed: 00:00:00.38
# Mc/sec: 257.96
//
Query:       gene2387|gene2387|rna2387|rna2387  [L=51]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (51 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       359  (0.0200234); expected 358.6 (0.02)
Passed bias filter:                      208  (0.0116013); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.28s 00:00:00.63 Elapsed: 00:00:00.42
# Mc/sec: 365.71
//
Query:       gene2388|gene2388|rna2388|rna2388  [L=176]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.5e-11   41.5   0.1    1.6e-10   40.8   0.1    1.3  1  Peptidase_S24  Peptidase S24-like


Domain annotation for each model (and alignments):
>> Peptidase_S24  Peptidase S24-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.8   0.1   8.8e-15   1.6e-10       2      66 ..      56     120 ..      55     125 .. 0.92

  Alignments for each domain:
  == domain 1  score: 40.8 bits;  conditional E-value: 8.8e-15
                                        XXSSTTCCTXXTTXEEEEECTS---TTSEEEEEETTCE-EEEEEEEEETTEEEEE.SSTT.STEEE CS
                      Peptidase_S24   2 vpGdSMeptlldGdlilVdkfsepkrGdivvfrlpgeeeayiKrviglpgdrvllasnne.ypply 66 
                                        v ++SMep+++ Gd+++ +  ++++ Gd  vf+++++e+ +++r i++ g +vl++ +n+  +++ 
  gene2388|gene2388|rna2388|rna2388  56 VLSESMEPGFKRGDILFLS-PRSYDVGDMTVFQINKKEIPIVHRAIRKLGTKVLTKGDNNlRDDVP 120
                                        88****************9.5789********************************9996577664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       480  (0.0267723); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 1316.10
//
Query:       gene2389|gene2389|rna2389|rna2389  [L=172]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    0.00073   18.0   5.3    0.00082   17.9   5.3    1.1  1  MAD          Mitotic checkpoint protein
     0.0028   17.9   3.0     0.0028   17.9   3.0    2.3  2  Spc24        Spc24 subunit of Ndc80
     0.0049   17.1   3.0     0.0074   16.6   3.0    1.2  1  THOC7        Tho complex subunit 7
  ------ inclusion threshold ------
       0.36   10.8  10.1          1    9.4   1.5    2.4  2  Prefoldin_2  Prefoldin subunit
       0.41   10.5   7.9        5.5    6.8   0.3    2.4  2  DivIC        Septum formation initiator
        1.6    7.2   7.0        1.7    7.2   6.6    1.2  1  FapA         Flagellar Assembly Protein A
        4.3    7.5  11.2        2.4    8.3   1.8    3.0  3  bZIP_2       Basic region leucine zipper


Domain annotation for each model (and alignments):
>> MAD  Mitotic checkpoint protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   5.3   3.2e-07   0.00082     196     293 ..      33     134 ..      19     162 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 3.2e-07
                                MAD 196 laripelekelerlreenkklnelkenkelLkEevedlkkkLereE.kareelvkLelekekleqeLksWe....k 266
                                        +  + +l ++ + l+ ++++l++  +n+el+kE+ ++l  k + e  k+ + +v+Le + e l+ +L+ W+    k
  gene2389|gene2389|rna2389|rna2389  33 QPALDDLRENNKLLKRQIAQLQTEVKNNELVKEKNDGLFLKYNNERfKYAKRIVSLEKDIEDLKCKLEYWKeeevK 108
                                        5567789999999*************************999776544788899*****************744336 PP

                                MAD 267 laqdtgLnlrsPealsrkieqLqqeei 293
                                        l+ + +L +++P a    +e +   ++
  gene2389|gene2389|rna2389|rna2389 109 LQENICL-IKQPSANTLFLELMSGFNL 134
                                        7777777.7777776666665555555 PP

>> Spc24  Spc24 subunit of Ndc80
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   2.6     0.025        65      14      48 ..      30      62 ..      26      75 .. 0.69
   2 !   17.9   3.0   1.1e-06    0.0028       2     104 ..      74     170 ..      73     171 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.025
                              Spc24 14 sdleselesleselaelkeeleeleeeseekeser 48
                                       +d++ +l++l+++ + lk+++++l++e ++  +e+
  gene2389|gene2389|rna2389|rna2389 30 NDQQPALDDLRENNKLLKRQIAQLQTEVKN--NEL 62
                                       567778888899999999999999888777..222 PP

  == domain 2  score: 17.9 bits;  conditional E-value: 1.1e-06
                              Spc24   2 ldnekfriakelsdleselesleselaelkeeleeleeeseekeserve.detllklklYrsLGielekdvnkvli 76 
                                          ne+f+ ak + +le+++e+l+ +l+ +kee  +l+e+       +++  +++l l+l + + +++ k+  k+  
  gene2389|gene2389|rna2389|rna2389  74 YNNERFKYAKRIVSLEKDIEDLKCKLEYWKEEEVKLQENICL----IKQpSANTLFLELMSGFNLQFYKK--KCKA 143
                                        579***********************************9888....56669999*9*9999999888888..4444 PP

                              Spc24  77 rnkekgdvnvlnldd.klseffianyiWd 104
                                         n +k+  +v+++d   +    i+n +W 
  gene2389|gene2389|rna2389|rna2389 144 INVKKN--DVIEIDMeGMKNHEITNRVWR 170
                                        455554..788898889999999**9995 PP

>> THOC7  Tho complex subunit 7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   3.0   2.9e-06    0.0074      18     104 ..      10     105 ..       6     111 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 2.9e-06
                              THOC7  18 rltkrllklltsla..........esteeeleqlkedllldfaafelsierlqllakanerereryeaekeeiese 83 
                                         ltk++l+ +++++          +   ++l++  + l+ ++a+++++++  +l+ + n     +y++e+ +  + 
  gene2389|gene2389|rna2389|rna2389  10 DLTKSFLE-ADAVTynrippkndqQPALDDLRENNKLLKRQIAQLQTEVKNNELVKEKNDGLFLKYNNERFKYAKR 84 
                                        67888888.4444458888887766667788888888999************************************ PP

                              THOC7  84 ieavreeieelkaqLeearat 104
                                        i +++++ie+lk +Le  +++
  gene2389|gene2389|rna2389|rna2389  85 IVSLEKDIEDLKCKLEYWKEE 105
                                        ***************987765 PP

>> Prefoldin_2  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   1.5    0.0004         1       6      37 ..      35      66 ..      30      71 .. 0.85
   2 ?    6.0   1.7    0.0044        11      69      99 ..      83     113 ..      75     118 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0004
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        Prefoldin_2  6 kfqqlqqqlqqlaqqikqletqlkelelvlee 37
                                        + +l++  + l+ qi+ql+t++k++elv+e 
  gene2389|gene2389|rna2389|rna2389 35 ALDDLRENNKLLKRQIAQLQTEVKNNELVKEK 66
                                       56788899999******************985 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0044
                                        HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        Prefoldin_2  69 erketlekeiktlekqleklekeleelkeel 99 
                                        +r+ +lek i+ l+ +le+ ++e  +l+e++
  gene2389|gene2389|rna2389|rna2389  83 KRIVSLEKDIEDLKCKLEYWKEEEVKLQENI 113
                                        5667889999999999999999988888876 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   2.2    0.0026       6.6      28      53 ..      31      55 ..      28      69 .. 0.65
   2 ?    6.8   0.3    0.0022       5.5      18      50 ..      84     116 ..      80     122 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0026
                                       HHHHHHHHHHHHHHHHHHHHCC-XXX CS
                              DivIC 28 alqaelaklkaeneeLeaevkdLksd 53
                                       ++q  l+ l++ n+ L++++++L+ +
  gene2389|gene2389|rna2389|rna2389 31 DQQPALDDLRENNKLLKRQIAQLQ-T 55
                                       556666666667777776666663.2 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0022
                                        HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC- CS
                              DivIC  18 aykqlkqeiaalqaelaklkaeneeLeaevkdL 50 
                                        ++ +l+++i++l+ +l+  k+e+ +L++++ + 
  gene2389|gene2389|rna2389|rna2389  84 RIVSLEKDIEDLKCKLEYWKEEEVKLQENICLI 116
                                        678999********************9999777 PP

>> FapA  Flagellar Assembly Protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   6.6   0.00066       1.7     339     423 ..      36     113 ..      16     130 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.00066
                               FapA 339 lkeleeeleeleeeleklkkkikklpklkaekqlesekkeqlkklletkeklkeeleeleeelkelkeeleskkee 414
                                        l++l+e+ + l++++ +l+ ++k ++       ++++    + k+ +++ k+ +++ +le+++++lk +le   +e
  gene2389|gene2389|rna2389|rna2389  36 LDDLRENNKLLKRQIAQLQTEVKNNEL------VKEKNDGLFLKYNNERFKYAKRIVSLEKDIEDLKCKLEYW-KE 104
                                        355666666666666666666555554......4555669*******************************99.66 PP

                               FapA 415 akikvnkei 423
                                        +++k ++ i
  gene2389|gene2389|rna2389|rna2389 105 EEVKLQENI 113
                                        677777766 PP

>> bZIP_2  Basic region leucine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   1.8   0.00093       2.4      33      54 .]      35      56 ..      29      56 .. 0.86
   2 ?   -2.2   0.2       1.7   4.5e+03      11      17 ..      58      64 ..      57      67 .. 0.80
   3 ?    5.0   0.2      0.01        27      31      50 ..      82     101 ..      72     105 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00093
                                       HHHHHHHHHHHHHHHHHHHHHH CS
                             bZIP_2 33 rvkeLeeeNaqLrqkveqLeke 54
                                        + +L+e N  L+++++qL++e
  gene2389|gene2389|rna2389|rna2389 35 ALDDLRENNKLLKRQIAQLQTE 56
                                       5789****************98 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.7
                                       XXXXXXX CS
                             bZIP_2 11 kNreAar 17
                                       kN+e ++
  gene2389|gene2389|rna2389|rna2389 58 KNNELVK 64
                                       7999887 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.01
                                        HHHHHHHHHHHHHHHHHHHH CS
                             bZIP_2  31 eervkeLeeeNaqLrqkveq 50 
                                        ++r+ +Le++++ L++k+e 
  gene2389|gene2389|rna2389|rna2389  82 AKRIVSLEKDIEDLKCKLEY 101
                                        799**************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1224  (0.0682693); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1162.29
//
Query:       gene239|gene239|rna239|rna239  [L=81]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (81 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       382  (0.0213063); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.32s 00:00:00.74 Elapsed: 00:00:00.49
# Mc/sec: 502.01
//
Query:       gene2390|gene2390|rna2390|rna2390  [L=110]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       299  (0.0166769); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 782.69
//
Query:       gene2391|gene2391|rna2391|rna2391  [L=39]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (39 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       472  (0.0263261); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.41
# Mc/sec: 287.74
//
Query:       gene2392|gene2392|rna2392|rna2392  [L=123]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
       0.02   14.2   1.3      0.022   14.1   1.3    1.1  1  tRNA-synt_1b  tRNA synthetases class I (W and Y)
      0.044   13.8   0.1      0.082   12.9   0.1    1.5  1  Kazal_1       Kazal-type serine protease inhibitor domain


Domain annotation for each model (and alignments):
>> tRNA-synt_1b  tRNA synthetases class I (W and Y)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   1.3   2.5e-06     0.022     162     255 ..       6     106 ..       4     123 .] 0.77

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.5e-06
                                        HHHHHHHHHHHHHHHH..........STTSS-EEEEET.-BBSTTSSSBTTCETTCGC-BTTCCHHHHHHHHHHCH CS
                       tRNA-synt_1b 162 qnielgrdlarrfnkk..........evfkkpegltvp.lltgldGekKmSKSagnsaIfLddekesvkkkiqkav 226
                                        qn +l+r  a+++n++          ++ k++++ +++     ++ e  mSKS+++   ++ ++ es++  ++  +
  gene2392|gene2392|rna2392|rna2392   6 QNRTLTRRNAKKLNENttkkkrkipsTTAKNRVSRLNNiNYYEITSE-GMSKSKES---DYVKRLESPENSFRVKI 77 
                                        7889************8876666666555555555555644555555.6*******...***************** PP

                                        CSTTCSHHHHHHHHHTHHHCHHHHHHHHC CS
                       tRNA-synt_1b 227 tdsdeevekllklktelsnelierleavs 255
                                        +ds +  e++ +l+ e++ e++e    ++
  gene2392|gene2392|rna2392|rna2392  78 SDSFNWSEYDRYLREEIEQETYENECLIT 106
                                        ***************99997776655544 PP

>> Kazal_1  Kazal-type serine protease inhibitor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   9.1e-06     0.082      21      38 ..      96     121 ..      94     123 .] 0.89

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 9.1e-06
                                        SEEESSHHHH........HHHHHTTS CS
                            Kazal_1  21 gkTYsneCll........Caengkkg 38 
                                        + TY+neCl+        C+++++++
  gene2392|gene2392|rna2392|rna2392  96 QETYENECLIthaelfidCMKKMERE 121
                                        57**********9******9999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (123 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1432  (0.0798706); expected 358.6 (0.02)
Passed bias filter:                      452  (0.0252106); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.37
# Mc/sec: 986.05
//
Query:       gene2393|gene2393|rna2393|rna2393  [L=402]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.1e-39  133.5  34.0    1.1e-38  133.0  34.0    1.2  1  Aa_trans  Transmembrane amino acid transporter protein


Domain annotation for each model (and alignments):
>> Aa_trans  Transmembrane amino acid transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  133.0  34.0   6.4e-43   1.1e-38       2     408 ..       4     396 ..       3     397 .. 0.90

  Alignments for each domain:
  == domain 1  score: 133.0 bits;  conditional E-value: 6.4e-43
                           Aa_trans   2 tssalsavlnlikaivGaGvLaLPyAfkqlGlivGlillllvallslytlllLvkcsktlasgkrnksYgdlg... 74 
                                        + sa+++++ ++++++G GvL LP    +lG++ Gl+l ++va ++ +t++lL  ++ +  s++ + +Y  ++   
  gene2393|gene2393|rna2393|rna2393   4 NVSAIQGSILMMNTMFGVGVLYLPLIYYSLGWVQGLVLFVMVASVTALTMYLLGVAAIE--SEDPHPTYYSVCsrs 77 
                                        6799**************************************************99987..6799999999*9999 PP

                           Aa_trans  75 yrllGpkgkliidlailvqlfGvgvsyliligdllpaifesffdtlllsnvyfilisaliiipLslipnlskLsyl 150
                                         r +Gp      d ail+ +f+ +++yl +i++++   ++       + + ++++i+a+ +++L++ ++ls+L+++
  gene2393|gene2393|rna2393|rna2393  78 FRFMGP----CADIAILLCCFFCCMAYLTFITNTVHFEIKE-----AVPKPVITVIAAFLVFMLAVQKDLSSLKIA 144
                                        999999....9***********************9977776.....69**************************** PP

                           Aa_trans 151 SllalvsslyyivilvlvvaelvklelkgvseetvkkasklkglflaigiivFAftghavlleiqnelkdpskfkk 226
                                        S++++ s++y+ + +v++v+   +++ ++v   ++     +k++++ ++ + FA +++ +++ ++ +lkd s    
  gene2393|gene2393|rna2393|rna2393 145 SFVSVASIVYL-ACFVVYVF---VVNRENVTVLKF-----NKDYSTGVSGLLFALGCQQNMVAVYSQLKDGSR-AG 210
                                        ********984.33333333...334444444443.....36899*************************999.78 PP

                           Aa_trans 227 mtkvlllsiilatvlyilvGlvGYltFGnevkgnillnlpkss...............ilivivnlllvlhlilsf 287
                                        + kv + ++++  +ly+++Gl+GY+ FG+++ +nil  l  ++                 i +   l+++ l  sf
  gene2393|gene2393|rna2393|rna2393 211 VLKVAIGATLMGGLLYMAIGLFGYFGFGEAATTNILRLLTDRDsdlckmllkrnsvnkYAIRACDWLFIVTLSCSF 286
                                        9999999999999**************************999999****99999988777888888899******* PP

                           Aa_trans 288 plqlhplrqvvenllikkeavagasekeapkskllrlvirlllvvityliAlsvpslakvlslvGatsstplsfil 363
                                         +q hp+r +++n+l+k        +ke  +s++ r++++  +v+++ +iA +    +k+++ +Gat+   +++i 
  gene2393|gene2393|rna2393|rna2393 287 AFQSHPARVALNNILRKF----VGVKKEVLASNKYRYIATGTYVALICIIACFQVDCDKIVAYIGATCNNAICYIM 358
                                        ***************886....8888888899999***************************************** PP

                           Aa_trans 364 Palfhlkliktekksleklvkkkildlicivlglllvfyglavli 408
                                        Pal  + l k +   l+ +      +++++ lg++ ++y +a+ i
  gene2393|gene2393|rna2393|rna2393 359 PALAFIGLVKRST-VLRPI------AYAVVALGAIGMIYMVAMNI 396
                                        ***9999988873.33333......48999999999999998766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (402 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1215  (0.0677673); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.68u 0.37s 00:00:01.05 Elapsed: 00:00:00.57
# Mc/sec: 2118.95
//
Query:       gene2394|gene2394|rna2394|rna2394  [L=813]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.1e-36  123.4   0.1    1.7e-35  122.4   0.1    1.5  1  U6-snRNA_bdg    U6-snRNA interacting domain of PrP8
    1.2e-22   80.4   0.0    2.2e-22   79.5   0.0    1.3  1  U5_2-snRNA_bdg  U5-snRNA binding site 2 of PrP8
    1.3e-12   47.8   1.0    2.6e-12   46.9   1.0    1.4  1  RRM_4           RNA recognition motif of the spliceosomal PrP


Domain annotation for each model (and alignments):
>> U6-snRNA_bdg  U6-snRNA interacting domain of PrP8
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.4   0.1   2.8e-39   1.7e-35       6     154 ..     529     669 ..     524     672 .. 0.90

  Alignments for each domain:
  == domain 1  score: 122.4 bits;  conditional E-value: 2.8e-39
                       U6-snRNA_bdg   6 llksekfawtsarhdgkllnleryradviealGgveailehtlfkatsfksweglvwdkasgfeeslkakkltnaq 81 
                                        +   ++fa+++   dgkl++ +ry+ d++e +Gg e+i++++++++ s     + +w ++        + ++t+aq
  gene2394|gene2394|rna2394|rna2394 529 TG-DNPFAHFNSILDGKLWSTKRYKYDMTEFFGGPEHIISQSVLASISTAYDPQTLWRTT-------TYGTMTKAQ 596
                                        44.458999**********************************98776655556666664.......47789**** PP

                       U6-snRNA_bdg  82 rsGlsqiPnrrftlWWsPtinranvyvGfqvqldltGvfmhgklptlkisliqifrahlWqkihesvvmdllq 154
                                         sG    Pnrrf+++WsP in ++vyvG+ + +d++G++mhgkl++lk+s++++fr +lW ki e  v++l++
  gene2394|gene2394|rna2394|rna2394 597 LSGARLFPNRRFVFYWSPLINTSDVYVGYATVMDKSGIVMHGKLASLKMSYLKVFRDNLWMKICEEYVVELVR 669
                                        *****************************************************************99999976 PP

>> U5_2-snRNA_bdg  U5-snRNA binding site 2 of PrP8
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.5   0.0   3.7e-26   2.2e-22      27     123 ..     374     465 ..     359     472 .. 0.88

  Alignments for each domain:
  == domain 1  score: 79.5 bits;  conditional E-value: 3.7e-26
                     U5_2-snRNA_bdg  27 eiekfenrirqillssgsttftkiaakwntalialltyfreavvsteelldvlvkaetkiqtrvklglnskmpsrf 102
                                        +i  f  rir+i    +  +f +ia+kwn  l++l++ +re +  t+e ++++++ e++i + +k  +nskmp+rf
  gene2394|gene2394|rna2394|rna2394 374 SICPFVHRIRNI---NAFQSFLNIAEKWNMHLLSLVVTYREFL--TDEHVKTILRWENRILNLIKNHINSKMPTRF 444
                                        555566666665...45578*********************65..899999************************* PP

                     U5_2-snRNA_bdg 103 PpavfytPkelGGlGmlsagh 123
                                        P ++fy+P elGGlGm+s+g 
  gene2394|gene2394|rna2394|rna2394 445 PNVIFYAPVELGGLGMFSIGN 465
                                        ******************985 PP

>> RRM_4  RNA recognition motif of the spliceosomal PrP8
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.9   1.0   4.4e-16   2.6e-12       3      66 ..     241     304 ..     239     309 .. 0.94

  Alignments for each domain:
  == domain 1  score: 46.9 bits;  conditional E-value: 4.4e-16
                              RRM_4   3 idltllnrllrlivdknladyitaknnvvltykdmshvnsyGlirGlqfssfvvqyyglvldll 66 
                                        idl+ll+++l++ +d+n+++y++a+ n ++ ykd+++vn++G+ +G++fs ++++ y   +d+l
  gene2394|gene2394|rna2394|rna2394 241 IDLNLLQHVLSIFIDSNIVQYVIARVNSTVVYKDVNFVNRVGVSKGFEFSFLIYEAYYAAVDFL 304
                                        9*****************************************************9888888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (813 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       453  (0.0252663); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.78u 0.35s 00:00:01.12 Elapsed: 00:00:00.56
# Mc/sec: 4373.78
//
Query:       gene2395|gene2395|rna2395|rna2395  [L=280]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       555  (0.0309554); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.66u 0.32s 00:00:00.98 Elapsed: 00:00:00.54
# Mc/sec: 1548.72
//
Query:       gene2396|gene2396|rna2396|rna2396  [L=609]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.2e-12   46.0   0.0    1.9e-11   43.9   0.0    2.0  1  MutL_C       MutL C terminal dimerisation domain
    6.3e-09   35.8   0.2    1.4e-08   34.7   0.2    1.5  1  HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like
     0.0013   19.2   0.1     0.0047   17.4   0.1    1.9  1  HATPase_c    Histidine kinase-, DNA gyrase B-, and HSP90-like
  ------ inclusion threshold ------
       0.16   11.9   0.2       0.57   10.1   0.1    1.9  2  Phage_NinH   Phage NinH protein


Domain annotation for each model (and alignments):
>> MutL_C  MutL C terminal dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.9   0.0   4.3e-15   1.9e-11       4     147 .]     440     575 ..     439     575 .. 0.89

  Alignments for each domain:
  == domain 1  score: 43.9 bits;  conditional E-value: 4.3e-15
                                        EEEEEETTTEEEEEETTEEEEEEHHHHHHHHHHHHHHHHCCHSSB-EEEEEEEEEEE--HHHHHHHHHCHHHHHHC CS
                             MutL_C   4 kalgqvhgtyilaenedglvlvDqhaAherilyeklkeqlkeeelksQpLliPlvlelspeeaalleehkeeLakl 79 
                                        k++gq+++++ila  +  l++ Dqha +e +++e +k+ +k    ++Q+Ll P++l  ++  ++  ++    L ++
  gene2396|gene2396|rna2396|rna2396 440 KIIGQFNQGFILATLNGYLMIFDQHAVDEIYNFEMIKKGIKF---NKQSLLKPISLPSDSMLMSDDLSSPNRLDQA 512
                                        579**********************************99998...9***********9999999999999999888 PP

                                        T-EEEE..-STTEEEEEEEECCCTTTSHHHHHHHHHHHHCCCSS-H-HCCHHHHHHHHCTTSSSSSS--- CS
                             MutL_C  80 Gfelee..fgpnslivravPallrqqnleelirelleelaekgkesleekleellatmachssvkagrrl 147
                                         +   +  f+ +  +++a P++ ++ +  ++ rel+++ +        ++l + +a+ ac+ s+++g++l
  gene2396|gene2396|rna2396|rna2396 513 MLSSLNrsFEVKDDKITASPSFNKHLFNINDYRELVSTGEV-------SSLTNKIASKACRMSIMIGDKL 575
                                        77644446999999999999999999999999999999333.......4789999999****99999986 PP

>> HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.7   0.2     3e-12   1.4e-08       6     106 ..      57     149 ..      52     172 .. 0.74

  Alignments for each domain:
  == domain 1  score: 34.7 bits;  conditional E-value: 3e-12
                        HATPase_c_3   6 AlaelvdNsldAdaenvkievnknrgktgeivieDdGkGmseeelknalrlatsskeakrk..stslGkkGiGlkl 79 
                                         l elv+NsldA+a+++ i+++k      +i + D+G+Gm  e  +++++  ++++   ++   + +G kGi+  l
  gene2396|gene2396|rna2396|rna2396  57 ILKELVENSLDAKATRIIISISK------DIEVCDNGTGMVSE--IDYFKTNKETELVLSGtlTDYYGYKGIF--L 122
                                        689********************......59*********987..5667666666665554226669****99..5 PP

                        HATPase_c_3  80 Aslslgkkltvitkkegesstltldvd 106
                                        +s++   +l +itk+++e+ +  +d++
  gene2396|gene2396|rna2396|rna2396 123 SSVRDICDLVIITKTKEEKLARCIDYK 149
                                        566555567788888877776655554 PP

>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.1     1e-06    0.0047       7      87 ..      55     131 ..      52     171 .. 0.62

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1e-06
                                        HHHHHHHHHHHHHHHSTTTEEEEEEEEEETEEEEEEEESSSSSTTHHHTGTCS.TTCH...HCSTCHTS.TSSSHH CS
                          HATPase_c   7 rqiisnlvdNavkfatkageieveikaseddlvisveDnGiGipkedlkklfe.kfsq...ddstkrgg.ggtGlG 77 
                                        ++i+++lv+N++++  ka++i ++i+     + i+v DnG G+   +++  f+ +  +    ++t +++ g  G+ 
  gene2396|gene2396|rna2396|rna2396  55 TKILKELVENSLDA--KATRIIISIS-----KDIEVCDNGTGMVS-EID-YFKtNKETelvLSGTLTDYyGYKGIF 121
                                        579**********6..99******99.....479*********76.455.34333333466344444433777788 PP

                                        HHHHHHHHHH CS
                          HATPase_c  78 lsivkklvel 87 
                                        ls v+ +++l
  gene2396|gene2396|rna2396|rna2396 122 LSSVRDICDL 131
                                        8888777765 PP

>> Phage_NinH  Phage NinH protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.1   0.00013      0.57       4      40 ..     124     160 ..     122     168 .. 0.89
   2 ?   -2.4   0.0         1   4.5e+03      46      55 ..     452     461 ..     447     463 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00013
                         Phage_NinH   4 svktiPdlLvetyGnqtEvARrlkcsRatvRkYvrDk 40 
                                        sv+ i dl++ t+      AR ++ +R+tv k +r+ 
  gene2396|gene2396|rna2396|rna2396 124 SVRDICDLVIITKTKEEKLARCIDYKRGTVEKVARED 160
                                        7899****************************98864 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1
                         Phage_NinH  46 AivngvLmvh 55 
                                        A  ng Lm++
  gene2396|gene2396|rna2396|rna2396 452 ATLNGYLMIF 461
                                        778*****98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (609 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       716  (0.0399353); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.67u 0.28s 00:00:00.95 Elapsed: 00:00:00.50
# Mc/sec: 3653.40
//
Query:       gene2397|gene2397|rna2397|rna2397  [L=104]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.6e-14   52.9   8.4    6.1e-14   52.5   8.4    1.2  1  zinc_ribbon_15  zinc-ribbon family
    1.6e-05   24.8   5.2     0.0033   17.4   5.7    2.5  2  DZR             Double zinc ribbon
     0.0012   18.5   1.2     0.0012   18.5   1.2    3.1  3  zinc_ribbon_2   zinc-ribbon domain
     0.0059   16.7   2.1      0.017   15.2   0.5    2.2  2  NOB1_Zn_bind    Nin one binding (NOB1) Zn-ribbon like
     0.0066   15.8   1.2     0.0066   15.8   1.2    3.2  3  zf-ribbon_3     zinc-ribbon domain
  ------ inclusion threshold ------
      0.018   14.7   8.2        0.1   12.3   0.4    3.4  3  zf-NADH-PPase   NADH pyrophosphatase zinc ribbon domain
      0.042   14.3   6.5       0.62   10.6   6.5    2.1  1  zf-CHY          CHY zinc finger
        0.2   12.0  13.0        4.4    7.6  13.0    2.8  1  zf-LITAF-like   LITAF-like zinc ribbon domain
       0.28   11.7   2.9        2.6    8.5   0.1    2.2  2  Ribosomal_S26e  Ribosomal protein S26e
       0.28   11.8   5.1        1.7    9.3   2.0    2.6  2  Cript           Microtubule-associated protein CRIPT
       0.36   10.9   6.5       0.89    9.6   2.4    2.1  2  Zn_Tnp_IS91     Transposase zinc-binding domain
        1.1    9.6   8.8          5    7.5   0.1    2.7  2  zf-C6H2         zf-MYND-like zinc finger, mRNA-binding
        1.6    8.4   6.7        6.1    6.5   1.9    2.1  2  DUF2616         Protein of unknown function (DUF2616)


Domain annotation for each model (and alignments):
>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.5   8.4   4.5e-17   6.1e-14       1      86 []      18      91 ..      18      91 .. 0.96

  Alignments for each domain:
  == domain 1  score: 52.5 bits;  conditional E-value: 4.5e-17
                     zinc_ribbon_15  1 ilCpkCgklskaelvkkkkvlklffipvfkwkkkkpylacskCkslleaskelgkeiekkessekkeCknCgkeveee 78
                                       i+Cp C+++sk++   kk+++++++ip+f +k++ py+ c+kCk+ l++++             +++C+nC++++ ++
  gene2397|gene2397|rna2397|rna2397 18 IHCPICSRMSKTTKLVKKTYITFLMIPLFCVKTSAPYIGCDKCKYGLGMED-------------VMICDNCRNVIIDD 82
                                       68************************************************9.............*********98766 PP

                     zinc_ribbon_15 79 .fkyCpkCg 86
                                         ++C++Cg
  gene2397|gene2397|rna2397|rna2397 83 aDRFCSRCG 91
                                       589*****9 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   5.7   2.4e-06    0.0033      27      49 .]      37      91 ..      10      91 .. 0.62
   2 !   15.7   1.4   8.2e-06     0.011       1      23 [.      72      95 ..      72      99 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 2.4e-06
                                DZR 27 a...............................edrCpsCgek.vdpearfCpeCG 49
                                                                          C++C    +d  +rfC  CG
  gene2397|gene2397|rna2397|rna2397 37 YitflmiplfcvktsapyigcdkckyglgmedVMICDNCRNViIDDADRFCSRCG 91
                                       0555555555555555555555555555555599********9999********9 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 8.2e-06
                                DZR  1 CpqCgee.lppdarfCseCgtklk 23
                                       C +C++  +++ +rfCs+Cg k++
  gene2397|gene2397|rna2397|rna2397 72 CDNCRNViIDDADRFCSRCGFKVR 95
                                       888988756777779999998887 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.2      0.44   6.1e+02       9      19 ..      13      23 ..      11      25 .. 0.64
   2 ?    0.2   0.2       0.5   6.9e+02      14      22 ..      53      63 ..      48      67 .. 0.70
   3 !   18.5   1.2   8.7e-07    0.0012       2      22 ..      72      93 ..      71      94 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.44
                      zinc_ribbon_2  9 lqdnakFCpyC 19
                                       ++ ++  Cp C
  gene2397|gene2397|rna2397|rna2397 13 NPVENIHCPIC 23
                                       55556668877 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.5
                      zinc_ribbon_2 14 kF..CpyCGtp 22
                                       ++  C +C ++
  gene2397|gene2397|rna2397|rna2397 53 PYigCDKCKYG 63
                                       55558899554 PP

  == domain 3  score: 18.5 bits;  conditional E-value: 8.7e-07
                      zinc_ribbon_2  2 CpnCGael.qdnakFCpyCGtp 22
                                       C nC + + +d ++FC++CG++
  gene2397|gene2397|rna2397|rna2397 72 CDNCRNVIiDDADRFCSRCGFK 93
                                       99******899*********97 PP

>> NOB1_Zn_bind  Nin one binding (NOB1) Zn-ribbon like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.58     8e+02      24      31 ..      18      25 ..       9      43 .. 0.65
   2 !   15.2   0.5   1.3e-05     0.017       8      31 ..      69      92 ..      66      96 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.58
                       NOB1_Zn_bind 24 kFCpkCGn 31
                                         Cp C  
  gene2397|gene2397|rna2397|rna2397 18 IHCPICSR 25
                                       45666643 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 1.3e-05
                       NOB1_Zn_bind  8 vlrChaCfkvtkdmtkkFCpkCGn 31
                                       v+ C  C +v+ d   +FC++CG 
  gene2397|gene2397|rna2397|rna2397 69 VMICDNCRNVIIDDADRFCSRCGF 92
                                       789*******************95 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.7     0.023        32       2       8 ..      17      23 ..      16      24 .. 0.72
   2 ?    0.7   0.2      0.28   3.9e+02      19      24 ..      57      62 ..      55      64 .. 0.68
   3 !   15.8   1.2   4.8e-06    0.0066       5      25 ..      72      93 ..      69      94 .. 0.93

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.023
                        zf-ribbon_3  2 tvrCPnC 8 
                                        ++CP C
  gene2397|gene2397|rna2397|rna2397 17 NIHCPIC 23
                                       5778887 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.28
                        zf-ribbon_3 19 CpyCGt 24
                                       C +C +
  gene2397|gene2397|rna2397|rna2397 57 CDKCKY 62
                                       777766 PP

  == domain 3  score: 15.8 bits;  conditional E-value: 4.8e-06
                        zf-ribbon_3  5 CPnCGa.plssddnvCpyCGtk 25
                                       C nC + ++++ d++C  CG k
  gene2397|gene2397|rna2397|rna2397 72 CDNCRNvIIDDADRFCSRCGFK 93
                                       ******99************86 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.2     0.064        89      23      29 ..      19      25 ..      18      28 .. 0.82
   2 ?    3.0   0.2      0.06        83      22      29 ..      70      77 ..      69      79 .. 0.85
   3 ?   12.3   0.4   7.2e-05       0.1       4      12 ..      85      93 ..      83     104 .] 0.83

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.064
                      zf-NADH-PPase 23 vCpaCgl 29
                                       +Cp C +
  gene2397|gene2397|rna2397|rna2397 19 HCPICSR 25
                                       9****87 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.06
                      zf-NADH-PPase 22 rvCpaCgl 29
                                       + C++C++
  gene2397|gene2397|rna2397|rna2397 70 MICDNCRN 77
                                       89****98 PP

  == domain 3  score: 12.3 bits;  conditional E-value: 7.2e-05
                      zf-NADH-PPase  4 rFCgrCGap 12
                                       rFC+rCG +
  gene2397|gene2397|rna2397|rna2397 85 RFCSRCGFK 93
                                       9******65 PP

>> zf-CHY  CHY zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   6.5   0.00045      0.62      10      74 ..       8      77 ..       3      96 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00045
                             zf-CHY 10 airapcCkklyaCreCHeeledhelerlevke..vlcllCeteqekavlCkkCkk..efaeyf.CpiCkl 74
                                       +++++   +  +C  C + +++ +l +++  +  ++ l+C ++    + C kCk    +++ + C++C++
  gene2397|gene2397|rna2397|rna2397  8 KLETENPVENIHCPICSRMSKTTKLVKKTYITflMIPLFCVKTSAPYIGCDKCKYglGMEDVMiCDNCRN 77
                                       555555566678999998777666655544431155679*99999999*****99664555534888875 PP

>> zf-LITAF-like  LITAF-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6  13.0    0.0032       4.4       5      66 ..      17      79 ..      13      97 .. 0.62

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0032
                      zf-LITAF-like  5 qvdCpaCqqrvvTsveyksgkltwllalllclfgc...llc..cliPfcvdslkdvehyCpnCgall 66
                                       +++Cp+C++ + T+   k++ +t+l++ l+c+ +    ++c  c     +   ++    C nC++++
  gene2397|gene2397|rna2397|rna2397 17 NIHCPICSRMSKTTKLVKKTYITFLMIPLFCVKTSapyIGCdkC----KYGLGMEDVMICDNCRNVI 79
                                       79*********999888888888888844444444364333222....2222223334566665554 PP

>> Ribosomal_S26e  Ribosomal protein S26e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.1    0.0019       2.6      17      42 ..      14      39 ..       4      44 .. 0.87
   2 ?    3.4   0.7     0.075     1e+02      10      31 ..      59      80 ..      55      91 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0019
                                       ---EEE-TTT--EEES----EEEEEE CS
                     Ribosomal_S26e 17 hvkivrCsncarlvpkdKaikrfvvr 42
                                        v+ ++C  c+r+    K +k++++ 
  gene2397|gene2397|rna2397|rna2397 14 PVENIHCPICSRMSKTTKLVKKTYIT 39
                                       5889******************9985 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.075
                                       ----S-S---EEE-TTT--EEE CS
                     Ribosomal_S26e 10 rnkkgrghvkivrCsncarlvp 31
                                       + k g g + ++ C+nc  ++ 
  gene2397|gene2397|rna2397|rna2397 59 KCKYGLGMEDVMICDNCRNVII 80
                                       56889999*********98875 PP

>> Cript  Microtubule-associated protein CRIPT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.1      0.16   2.1e+02      71      87 ..      19      35 ..       7      37 .. 0.78
   2 ?    9.3   2.0    0.0012       1.7      45      68 ..      70      93 ..      47      97 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.16
                              Cript 71 iCamCGkklldtksskq 87
                                        C +C ++  +tk  k+
  gene2397|gene2397|rna2397|rna2397 19 HCPICSRMSKTTKLVKK 35
                                       58899888888887776 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0012
                              Cript 45 skCkiCktkveqkgakYCqkCaYk 68
                                       + C++C++ +  +  ++C++C +k
  gene2397|gene2397|rna2397|rna2397 70 MICDNCRNVIIDDADRFCSRCGFK 93
                                       469999999999899999999887 PP

>> Zn_Tnp_IS91  Transposase zinc-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.2     0.054        75      56      72 ..      16      32 ..      10      51 .. 0.69
   2 ?    9.6   2.4   0.00065      0.89      27      70 ..      54      97 ..      44     102 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.054
                        Zn_Tnp_IS91 56 ksrhCpsCqkkateewl 72
                                       ++ hCp C++ ++   l
  gene2397|gene2397|rna2397|rna2397 16 ENIHCPICSRMSKTTKL 32
                                       5789****987655433 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00065
                        Zn_Tnp_IS91 27 ilrCrtaalGfaryeCeeCghekivyfsCksrhCpsCqkkatee 70
                                       ++ C + ++G  +   + C++ + v     +r+C++C+ k +ee
  gene2397|gene2397|rna2397|rna2397 54 YIGCDKCKYGLGMEDVMICDNCRNVIIDDADRFCSRCGFKVREE 97
                                       677888888877776666666677999999********988776 PP

>> zf-C6H2  zf-MYND-like zinc finger, mRNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.1    0.0037         5       7      24 ..      12      29 ..       8      33 .. 0.81
   2 ?    3.7   4.3     0.058        80      12      35 ..      69      93 ..      46      96 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0037
                            zf-C6H2  7 gkeassLqCptClklgik 24
                                       +++ ++++Cp+C +++ +
  gene2397|gene2397|rna2397|rna2397 12 ENPVENIHCPICSRMSKT 29
                                       5778889*****998755 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.058
                            zf-C6H2 12 sLqCptClklgike.sfFCsqeCFk 35
                                        + C  C +  i++   FCs+  Fk
  gene2397|gene2397|rna2397|rna2397 69 VMICDNCRNVIIDDaDRFCSRCGFK 93
                                       489******9999999****98887 PP

>> DUF2616  Protein of unknown function (DUF2616)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.3     0.018        25     129     165 ..      13      49 ..       5      57 .. 0.79
   2 ?    6.5   1.9    0.0044       6.1      54      77 ..      71      94 ..      50     100 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.018
                            DUF2616 129 skvytvlsakclqcekklenteekilvkFdvklFCkk 165
                                        + v  ++   c  ++k+++ +++++++   + lFC k
  gene2397|gene2397|rna2397|rna2397  13 NPVENIHCPICSRMSKTTKLVKKTYITFLMIPLFCVK 49 
                                        4467788888999999999999998888889999976 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0044
                            DUF2616 54 kCefClevveeedklfCkkClfPl 77
                                        C+ C +v  ++++ fC++C f +
  gene2397|gene2397|rna2397|rna2397 71 ICDNCRNVIIDDADRFCSRCGFKV 94
                                       3*******9***********9866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       888  (0.0495287); expected 358.6 (0.02)
Passed bias filter:                      497  (0.0277205); expected 358.6 (0.02)
Passed Vit filter:                        77  (0.00429472); expected 17.9 (0.001)
Passed Fwd filter:                        23  (0.00128284); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 652.20
//
Query:       gene2398|gene2398|rna2398|rna2398  [L=241]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.5e-05   23.9   3.1       0.02   14.9   2.8    2.2  2  Lactamase_B    Metallo-beta-lactamase superfamily
  ------ inclusion threshold ------
      0.011   16.3   0.2      0.043   14.3   0.1    2.1  2  HAGH_C         Hydroxyacylglutathione hydrolase C-terminus
      0.019   14.5   0.1      0.028   14.0   0.1    1.3  1  Lactamase_B_2  Beta-lactamase superfamily domain


Domain annotation for each model (and alignments):
>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   2.8   3.3e-06      0.02      42      67 ..      65      90 ..      47     107 .. 0.83
   2 !    7.0   0.0   0.00086       5.2     122     197 .]     109     176 ..      99     176 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.3e-06
                                       GGGEEEEE-SBSSHHHHTTGGGCTTH CS
                        Lactamase_B 42 pkdvdavilTHlHlDHiGglgglvea 67
                                       ++++ av+ TH+H+DH  g+++++  
  gene2398|gene2398|rna2398|rna2398 65 DRKLLAVFTTHHHWDHSHGNDDVMLL 90
                                       68899***************999865 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.00086
                                        EEEHECTTSTSCCEEEEEETTCCEEEECTTTSSHHCCCCCC.TTCEEE-SHCHHHHHHHHHHHHHHHCHSEEEE.S CS
                        Lactamase_B 122 alyvtggpghghghgvveygggkvlftGDallagetgridltlrgaevrdpsdaekyldsllklaglkaevlvp.g 196
                                        +++v+   ++ h+  ++++ ++++l+ GD+ll    g++ +       + + d + + ++l+  ++ k+ev+++ g
  gene2398|gene2398|rna2398|rna2398 109 DFEVFALSTPCHTEDSYSFLIDDYLILGDTLLYLGCGKFFE-------GTAKDMKACFEKLK--KNVKPEVICCyG 175
                                        67899999************************998888877.......33333333333333..356777777777 PP

                                        S CS
                        Lactamase_B 197 H 197
                                        H
  gene2398|gene2398|rna2398|rna2398 176 H 176
                                        7 PP

>> HAGH_C  Hydroxyacylglutathione hydrolase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.66     4e+03       2      25 ..      20      43 ..      20      68 .. 0.66
   2 ?   14.3   0.1   7.1e-06     0.043      40      80 .]     202     238 ..     191     238 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.66
                             HAGH_C  2 YtlsNlkFalsvepdnealkkrlk 25
                                       Y++ N k+a +++  + ++ + + 
  gene2398|gene2398|rna2398|rna2398 20 YMVYNEKYAVAFDTTDVKILEHAL 43
                                       666677777777666555554443 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 7.1e-06
                             HAGH_C  40 stladEkktNpFLRldepevqkavgeevevfaaLRelKdnF 80 
                                         t ++E+++NpF+  ++  v +   ++++ +++LR  K+++
  gene2398|gene2398|rna2398|rna2398 202 LTFGEELAYNPFINFQK-LVDR---KAIKGLTELRTIKNRY 238
                                        5899***********76.3322...349***********97 PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   4.6e-06     0.028      26      52 ..      65      89 ..      49     126 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.6e-06
                                       --..SEEEEE-SS--HHHHGGGGCCCC CS
                      Lactamase_B_2 26 delppidaVllthaHyDHlaglltlre 52
                                       d+  ++ aV+ th H+DH +g +++  
  gene2398|gene2398|rna2398|rna2398 65 DR--KLLAVFTTHHHWDHSHGNDDVML 89
                                       44..889**************998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       531  (0.0296168); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 1470.96
//
Query:       gene2399|gene2399|rna2399|rna2399  [L=924]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
       0.03   14.4   0.0       0.11   12.6   0.0    2.0  1  PA28_alpha  Proteasome activator pa28 alpha subunit


Domain annotation for each model (and alignments):
>> PA28_alpha  Proteasome activator pa28 alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0     6e-06      0.11      15      44 ..     299     328 ..     292     335 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 6e-06
                         PA28_alpha  15 tkeAEeLvskffPkkiveLdeLLkspsfnv 44 
                                        +++A +++ k fP+ ++ L++L+  +s+n 
  gene2399|gene2399|rna2399|rna2399 299 FEKANNILRKHFPESVLYLESLINVESMNS 328
                                        799***********************9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (924 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       670  (0.0373696); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.65u 0.30s 00:00:00.95 Elapsed: 00:00:00.45
# Mc/sec: 6127.33
//
Query:       gene24|gene24|rna24|rna24  [L=197]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.8e-26   90.4   0.6    8.9e-26   89.6   0.1    1.7  2  RNA_pol_Rpb5_C   RNA polymerase Rpb5, C-terminal domain
    3.8e-14   53.0   1.2    8.7e-14   51.9   1.2    1.6  1  RNA_pol_Rpb5_N   RNA polymerase Rpb5, N-terminal domain
  ------ inclusion threshold ------
      0.016   15.3   0.0      0.025   14.6   0.0    1.3  1  Mrr_cat          Restriction endonuclease
      0.024   14.1   0.7       0.03   13.8   0.7    1.1  1  Glyco_tran_WbsX  Glycosyltransferase WbsX
      0.054   13.5   1.5       0.63   10.0   0.1    2.3  2  Pyr_excise       Pyrimidine dimer DNA glycosylase
       0.16   12.4   0.0       0.44   11.1   0.0    1.8  1  2OG-FeII_Oxy     2OG-Fe(II) oxygenase superfamily
       0.67   10.4   3.4        7.9    6.9   0.8    2.4  2  CRC_subunit      Chromatin remodelling complex Rsc7/Swp82 sub


Domain annotation for each model (and alignments):
>> RNA_pol_Rpb5_C  RNA polymerase Rpb5, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       2.6   6.6e+03      17      28 ..      67      77 ..      62      90 .. 0.52
   2 !   89.6   0.1   3.5e-29   8.9e-26       1      71 [.     124     194 ..     124     196 .. 0.99

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 2.6
                               HHHHHHHHHHTT CS
             RNA_pol_Rpb5_C 17 eeekkellkklk 28
                               +eek +l k++k
  gene24|gene24|rna24|rna24 67 DEEKMSL-KSVK 77
                               4444443.3333 PP

  == domain 2  score: 89.6 bits;  conditional E-value: 3.5e-29
                                ..-TSSSS--EEEEE-HHHHHHHHHHTT--TTCSS-EETTSHHHHCCT--TTSEEEEEEEETTTEEEEEEE CS
             RNA_pol_Rpb5_C   1 vnitkHelvPkhevlseeekkellkklkikeeqLPkisksDpvarylglkkGdvvkItrksetageavtYR 71 
                                +n+tkH+lv kh+++s eek++l+++ kikeeq+P+i+ +Dpva+ylg++kGdv++I r+setag+a ++R
  gene24|gene24|rna24|rna24 124 FNVTKHSLVFKHRIISVEEKERLMDEKKIKEEQMPRILITDPVAKYLGARKGDVLEIERESETAGSALYWR 194
                                7********************************************************************99 PP

>> RNA_pol_Rpb5_N  RNA polymerase Rpb5, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.9   1.2   3.4e-17   8.7e-14       7      89 .]       7      83 ..       2      83 .. 0.91

  Alignments for each domain:
  == domain 1  score: 51.9 bits;  conditional E-value: 3.4e-17
                               HHHHHCCCCCCCCCCCEE--CCCCT--CHHHHCCSB-SSSSB-GCCT-EEEESS.SS--EEEEEE-SSTTE-TCCCHHHCHHH CS
             RNA_pol_Rpb5_N  7 lfrirrTvleMlkdRgYlvaeeelnisleeFkekygdepkevdrekltisaskkddpseqilVfFpeekkvgvktikkyaerm 89
                                + +r+TvleMl+dRgY v+e ++n + ++F +ky +  k  d ++l+i ++k   ++e+++VfF++e+k++ k +k ++e+m
  gene24|gene24|rna24|rna24  7 QYLVRKTVLEMLSDRGYSVKEYQVN-DYDDFVNKYPNCVK--DTTNLRIIVQK---DKEMLFVFFSDEEKMSLKSVKILVENM 83
                               689********************98.79*******98755..99*******99...6799*****************999987 PP

>> Mrr_cat  Restriction endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   9.8e-06     0.025      13     111 ..      14     122 ..       6     124 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 9.8e-06
                                HHHHHHHHSSSEEE---B-TTSSB--EEEETTEEEE....EEEEEEE--......T..S-B-HHHHHHHHHHCTTS..SEEEEE CS
                    Mrr_cat  13 vaellealGykeveltgrsgDggiDliakkdplgse....rilvqaKry......k..nkvgvkeVqeligalkkrgadkgifv 84 
                                v e+l   Gy+ v+  +  +D+  D++ k  +  ++    ri+vq  +       +   k++ k V+ l+  ++k++ ++ i+v
  gene24|gene24|rna24|rna24  14 VLEMLSDRGYS-VKEYQ-VNDY-DDFVNKYPNCVKDttnlRIIVQKDKEmlfvffSdeEKMSLKSVKILVENMEKQNIKNLILV 94 
                                55666666666.44332.3333.244432222222233336666644444444441448999********************** PP

                                ESS-B-HHHHHHHHTT-.-EEEE-HHHH CS
                    Mrr_cat  85 ttsdftkaAreeaeeln.kieLldgdeL 111
                                   ++++aA ++a e+  +i++++ +eL
  gene24|gene24|rna24|rna24  95 LREGISPAANKFALECPmNITIFKEKEL 122
                                ***************8879*99999988 PP

>> Glyco_tran_WbsX  Glycosyltransferase WbsX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.7   1.2e-05      0.03     128     225 ..      26     125 ..      15     176 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.2e-05
            Glyco_tran_WbsX 128 qeygseeddkehfeyllpafkde...rYikvdgkpllliyrpekipklkevlelwrelakeegleglylvavesaeedlkelgf 208
                                +ey + +d++++++++ + +kd+   r i  ++k +l+++ +++ +   + ++++ e ++++++++l lv +e  +   ++  +
  gene24|gene24|rna24|rna24  26 KEY-QVNDYDDFVNKYPNCVKDTtnlRIIVQKDKEMLFVFFSDEEKMSLKSVKILVENMEKQNIKNLILVLREGISPAANKFAL 108
                                567.8899999999999999997444777789999999999999999999*********************9998744444444 PP

            Glyco_tran_WbsX 209 daavefptakelkkllk 225
                                +  +++  +ke++ l +
  gene24|gene24|rna24|rna24 109 ECPMNITIFKEKELLFN 125
                                44444422222222111 PP

>> Pyr_excise  Pyrimidine dimer DNA glycosylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.1   0.00025      0.63      66     102 ..      12      48 ..       5      62 .. 0.80
   2 ?    2.5   0.2     0.051   1.3e+02      41      91 ..     111     161 ..      73     192 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00025
                                HHHHHHHHHTT---S--S----TTS-GGGB------H CS
                 Pyr_excise  66 lllieEmlkRgynvneeekddisevekeyrgdwtpte 102
                                + ++e +++Rgy+v+e++ +d ++  ++y +  ++t 
  gene24|gene24|rna24|rna24  12 KTVLEMLSDRGYSVKEYQVNDYDDFVNKYPNCVKDTT 48 
                                567888899**************99999988887773 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.051
                                -SS--SSTTTTGGGTTBHHHHHHHHHHHHHHHHHTT---S--S----TTS- CS
                 Pyr_excise  41 pkhftlgtGHvtfFynkleyLrkrylllieEmlkRgynvneeekddiseve 91 
                                p ++t+ +  + +F+   + L   ++ +  E ++R +  ++ +++++ ++ 
  gene24|gene24|rna24|rna24 111 PMNITIFKEKELLFNVTKHSLVFKHRIISVEEKERLMDEKKIKEEQMPRIL 161
                                555666666778899999999999999999999998888777777665554 PP

>> 2OG-FeII_Oxy  2OG-Fe(II) oxygenase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00017      0.44       9      44 ..      33      75 ..      26     163 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00017
                               E......E-S---------EEEEEESSSEEEEEEE-.TT---E CS
               2OG-FeII_Oxy  9 y......ypphpdpevilglgahtdaslltillqdd.vgglev 44
                               y      yp++  +  +l++  ++d+++l ++++d+ ++ l+ 
  gene24|gene24|rna24|rna24 33 YddfvnkYPNCVKDTTNLRIIVQKDKEMLFVFFSDEeKMSLKS 75
                               55555558***666669******************98777643 PP

>> CRC_subunit  Chromatin remodelling complex Rsc7/Swp82 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.8    0.0031       7.9      63     100 ..      52      89 ..      16      94 .. 0.83
   2 ?    3.7   0.1     0.031        80      53      96 ..     112     158 ..     103     172 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0031
                CRC_subunit  63 lffkknpqllkllatqeekedLiergllpsslksrqik 100
                                ++++k +++l +  ++eek  L++ ++l +++++++ik
  gene24|gene24|rna24|rna24  52 IIVQKDKEMLFVFFSDEEKMSLKSVKILVENMEKQNIK 89 
                                678999**************************999886 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.031
                CRC_subunit  53 arllgfrdsylffk..knpqllkl.latqeekedLiergllpsslks 96 
                                ++++ f+++ l+f+  k++ ++k  +++ eeke L++++ ++++   
  gene24|gene24|rna24|rna24 112 MNITIFKEKELLFNvtKHSLVFKHrIISVEEKERLMDEKKIKEEQMP 158
                                555667755555542155556664268999*********99988655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1072  (0.0597914); expected 358.6 (0.02)
Passed bias filter:                      505  (0.0281667); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 1252.20
//
Query:       gene240|gene240|rna240|rna240  [L=387]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (387 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       570  (0.0317921); expected 358.6 (0.02)
Passed bias filter:                      511  (0.0285013); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 2701.61
//
Query:       gene2400|gene2400|rna2400|rna2400  [L=171]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.011   16.1   1.4      0.024   15.0   1.4    1.6  1  FeoB_associated  FeoB-associated Cys-rich membrane protein
      0.057   13.7   0.6      0.092   13.1   0.6    1.2  1  DPM2             Dolichol phosphate-mannose biosynthesis regu
       0.11   12.7   0.1       0.19   12.0   0.1    1.3  1  zf-LITAF-like    LITAF-like zinc ribbon domain


Domain annotation for each model (and alignments):
>> FeoB_associated  FeoB-associated Cys-rich membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   1.4     4e-06     0.024       5      38 ..      60      93 ..      56      95 .. 0.58

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 4e-06
                    FeoB_associated  5 Vgliiaaavafv.....irrlikkkkkGsCgggCsgCss 38
                                       V++i++++++ +     ++r   +k k      C +Cs 
  gene2400|gene2400|rna2400|rna2400 60 VIVILVVCMVGIlagliVWRRMYDKSKD-----CESCST 93
                                       4444443333333455577777777878.....999985 PP

>> DPM2  Dolichol phosphate-mannose biosynthesis regulatory protein (DPM2)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.6   1.5e-05     0.092      34      72 ..      45      80 ..      41      84 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.5e-05
                               DPM2 34 hvlhkyflpreyairipvillvvlllfvgtFiglvliks 72
                                       + + +y+l+ +y++ i +  +++++++vg+  gl++++ 
  gene2400|gene2400|rna2400|rna2400 45 S-VIEYVLAGDYTVFIVI--VILVVCMVGILAGLIVWRR 80
                                       4.779********99865..5566789999999999986 PP

>> zf-LITAF-like  LITAF-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   3.1e-05      0.19      24      63 ..      53      92 ..      42      94 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3.1e-05
                      zf-LITAF-like 24 gkltwllalllclfgcllccliPfcvdslkdvehyCpnCg 63
                                       g +t +++++++++++++++   ++++++ d+   C +C 
  gene2400|gene2400|rna2400|rna2400 53 GDYTVFIVIVILVVCMVGILAGLIVWRRMYDKSKDCESCS 92
                                       55566555444444443334445789*************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1081  (0.0602934); expected 358.6 (0.02)
Passed bias filter:                      699  (0.0389871); expected 358.6 (0.02)
Passed Vit filter:                        80  (0.00446204); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1129.69
//
Query:       gene2401|gene2401|rna2401|rna2401  [L=459]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.4e-07   30.7   0.0    1.8e-06   27.8   0.0    2.3  1  Polysacc_deac_1  Polysaccharide deacetylase
  ------ inclusion threshold ------
        0.2   11.9   3.6        0.4   10.9   0.4    2.7  3  Tn7_Tnp_TnsA_N   TnsA endonuclease N terminal
       0.25   11.1   0.9       0.77    9.5   0.9    1.8  1  DUF3464          Photosynthesis affected mutant 68
       0.36   11.3   6.0        6.3    7.2   5.5    2.2  2  RNA_pol_Rpc4     RNA polymerase III RPC4
          5    6.2  19.5       0.18   11.0   4.3    2.2  2  Astro_capsid_p   Turkey astrovirus capsid protein


Domain annotation for each model (and alignments):
>> Polysacc_deac_1  Polysaccharide deacetylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.8   0.0   5.1e-10   1.8e-06       8      62 ..      14      66 ..       8     117 .. 0.80

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 5.1e-10
                                       EEEEEEEESSCSCHHHHHHHHHHCT--EEEEE-HHHHCH-HHHHHHHHHTTEEEE CS
                    Polysacc_deac_1  8 svalTfDdgprdntteilpvLkkykvkatffvigglvedypdevremaasGveig 62
                                       ++++ fD gp++ t+++l++L+ y+++  f+v + +++d  d++++ma++ +eig
  gene2401|gene2401|rna2401|rna2401 14 VATISFDEGPSQHTDQLLQYLRYYNLPVCFHVDPYKINDK-DLITRMAEH-HEIG 66
                                       799************************************9.********9.8887 PP

>> Tn7_Tnp_TnsA_N  TnsA endonuclease N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.21   7.7e+02      48      70 ..      67      87 ..      54     117 .. 0.66
   2 ?   10.9   0.4   0.00011       0.4      27      72 ..     337     381 ..     321     390 .. 0.79
   3 ?   -2.4   0.2       1.5   5.5e+03      50      63 ..     397     410 ..     386     428 .. 0.52

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.21
                     Tn7_Tnp_TnsA_N 48 ellavevKyseeleeertrekle 70
                                         + +e+K++ ++++  +++k++
  gene2401|gene2401|rna2401|rna2401 67 LAITEEIKSEHDIDR--YIRKFK 87
                                       456789999999997..444444 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00011
                     Tn7_Tnp_TnsA_N  27 revpsvmtpDfLvtlkdstgeellavevKyseeleeertrekleie 72 
                                           ++ +t+ + + +++ ++++ +a e+K +e++++  +r+k+e e
  gene2401|gene2401|rna2401|rna2401 337 VHKDHSYTSSLRMPYNE-NNTKVFALEYKVEEDNDNLDVRKKFEEE 381
                                        44468899999999955.4559*********************987 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 1.5
                     Tn7_Tnp_TnsA_N  50 lavevKyseeleee 63 
                                        ++ e K+++ +e++
  gene2401|gene2401|rna2401|rna2401 397 EIKESKIKDTNEKK 410
                                        33344444444432 PP

>> DUF3464  Photosynthesis affected mutant 68
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.9   0.00021      0.77       7      60 ..     384     437 ..     375     456 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00021
                            DUF3464   7 pfepkkkrkkkpkkkkkskkakkeekekakeeekkdkeekeeaaiPevVskRmi 60 
                                         f++++k++k + + k+sk ++++ek++++++++kd+++ ++++i +  s+  +
  gene2401|gene2401|rna2401|rna2401 384 GFKRSTKSDKDKDEIKESKIKDTNEKKEESTKKEKDDNDTKAKEITKTQSNGCM 437
                                        566655555555555555555555556667777777777777788887776655 PP

>> RNA_pol_Rpc4  RNA polymerase III RPC4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0     0.059   2.1e+02      14      53 ..     192     230 ..     131     272 .. 0.56
   2 ?    7.2   5.5    0.0018       6.3      37      91 ..     388     442 ..     350     445 .. 0.54

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.059
                       RNA_pol_Rpc4  14 Pslkqkavsaaeddkseaesqsaekakaeeeskaekasga 53 
                                        P+++q a++++ d++s++++++ +++    e++ ++++++
  gene2401|gene2401|rna2401|rna2401 192 PKMEQ-ARDEDIDEESDHDESNGTEKGVVIEEEPTDEQEM 230
                                        44443.2222222222222222221111111111111111 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0018
                       RNA_pol_Rpc4  37 ekakaeeeskaekasgaeaeekkskkksskkkkkkkskalklkslpeGviGkLlv 91 
                                        ++++++++++ ++++ ++++ekk+++++++k+++++++++  k+  +G++ +L v
  gene2401|gene2401|rna2401|rna2401 388 STKSDKDKDEIKESKIKDTNEKKEESTKKEKDDNDTKAKEITKTQSNGCMNTLFV 442
                                        2222222222222223333333344444444444444444445555677777655 PP

>> Astro_capsid_p  Turkey astrovirus capsid protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   4.3   4.9e-05      0.18     206     284 ..     174     252 ..     169     255 .. 0.80
   2 ?    0.9   7.2     0.057     2e+02     192     266 ..     344     423 ..     323     434 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 4.9e-05
                                        EEEEESS--XXXX....XXXX......XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX..XXXXXXX CS
                     Astro_capsid_p 206 lfemkttvpqeralaegederktgaeeeisdpsdeedeevsdeetdtevesdeDeddevdrfDletsyeSeaeDdd 281
                                        lf+ ++++ + +  ++ +d++   a +e  d++++ de++ +e      e+ +De++ +++ D + +y+ e +Dd+
  gene2401|gene2401|rna2401|rna2401 174 LFHKNIKLLSFTR-FYAVDPKMEQARDEDIDEESDHDESNGTEKGVVIEEEPTDEQEMINEVDRKVEYKVERDDDK 248
                                        5666666666555.999999999999999999999996666666666668899**********************9 PP

                                        .XXX CS
                     Astro_capsid_p 282 .ven 284
                                          en
  gene2401|gene2401|rna2401|rna2401 249 nLEN 252
                                        6766 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.057
                                        TTTSSS---TT-EEEEEEESS--XXXX....XXXX............XXXXXXXXXX.XXXXXXXXXXXXXXXXXX CS
                     Astro_capsid_p 192 llhlitpppqavqllfemkttvpqeralaegederktg......aeeeisdpsdeed.eevsdeetdtevesdeDe 260
                                           l++p+ ++   +f ++ +v++ +  +++ ++++ +      +  + sd++++e  e+  ++  +++ es+  e
  gene2401|gene2401|rna2401|rna2401 344 TSSLRMPYNENNTKVFALEYKVEEDNDNLDVRKKFEEEgsgfkrS--TKSDKDKDEIkESKIKDTNEKKEESTKKE 417
                                        456899999999999999999999998887776666554445331..22222222222222333334445555556 PP

                                        XXXXXX CS
                     Astro_capsid_p 261 ddevdr 266
                                        +d+ d+
  gene2401|gene2401|rna2401|rna2401 418 KDDNDT 423
                                        655554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (459 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1908  (0.10642); expected 358.6 (0.02)
Passed bias filter:                      526  (0.0293379); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.68u 0.29s 00:00:00.97 Elapsed: 00:00:00.44
# Mc/sec: 3100.28
//
Query:       gene2402|gene2402|rna2402|rna2402  [L=627]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.9e-19   69.2   0.0    8.4e-19   68.4   0.0    1.4  1  ABC_tran      ABC transporter
    1.7e-12   47.2   0.0    3.2e-12   46.4   0.0    1.3  1  SMC_N         RecF/RecN/SMC N terminal domain
    7.3e-07   29.3   0.3      0.016   15.0   0.1    2.3  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    0.00019   21.9   0.0    0.00038   20.9   0.0    1.6  1  AAA_16        AAA ATPase domain
    0.00024   21.4   0.0     0.0006   20.1   0.0    1.7  1  AAA_22        AAA domain
      0.003   17.5   0.0     0.0095   15.8   0.0    1.8  2  RsgA_GTPase   RsgA GTPase
     0.0048   17.4   0.5      0.018   15.6   0.0    2.0  2  AAA_23        AAA domain
     0.0052   17.2   0.0      0.013   16.0   0.0    1.7  1  AAA_17        AAA domain
     0.0091   15.9   0.3     0.0091   15.9   0.3    2.1  1  ATPase_2      ATPase domain predominantly from Archaea
  ------ inclusion threshold ------
      0.016   14.4   0.0      0.036   13.2   0.0    1.6  1  NB-ARC        NB-ARC domain
      0.019   14.9   0.1      0.041   13.8   0.1    1.5  1  NACHT         NACHT domain
       0.02   14.0   0.0       0.14   11.3   0.0    2.1  2  PIF1          PIF1-like helicase
      0.026   14.9   1.8      0.041   14.3   0.1    2.2  2  AAA           ATPase family associated with various cellular 
      0.035   14.3   0.0       0.09   12.9   0.0    1.7  1  AAA_33        AAA domain
      0.039   13.9   0.1      0.092   12.7   0.1    1.5  1  Rad17         Rad17 P-loop domain
      0.049   13.4   0.0        0.1   12.4   0.0    1.4  1  AAA_29        P-loop containing region of AAA domain
       0.06   13.7   0.0       0.14   12.6   0.0    1.7  1  RNA_helicase  RNA helicase
      0.074   12.6   0.0       0.16   11.5   0.0    1.5  1  AAA_7         P-loop containing dynein motor region
      0.078   12.0   0.1       0.16   11.0   0.1    1.5  1  T2SSE         Type II/IV secretion system protein
      0.085   12.9   0.1       0.34   10.9   0.0    2.1  2  AAA_14        AAA domain
       0.13   11.8   0.1       0.72    9.4   0.0    2.2  2  AAA_25        AAA domain
       0.13   11.8   0.4       0.28   10.8   0.4    1.4  1  cobW          CobW/HypB/UreG, nucleotide-binding domain
       0.14   12.0   0.0        0.3   11.0   0.0    1.6  1  MobB          Molybdopterin guanine dinucleotide synthesis pr
       0.15   12.2   0.2        0.5   10.5   0.1    2.0  1  MMR_HSR1      50S ribosome-binding GTPase
       0.15   12.1   0.1       0.47   10.5   0.1    1.8  1  AAA_5         AAA domain (dynein-related subfamily)
        0.2   11.3   0.0        0.2   11.3   0.0    1.3  1  ATP-synt_ab   ATP synthase alpha/beta family, nucleotide-bind
       0.29   11.0   2.3       0.58   10.0   0.8    2.1  2  NTPase_1      NTPase
       0.38   11.1   1.8        1.7    9.0   1.8    2.0  1  AAA_19        AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.4   0.0   1.3e-21   8.4e-19      14     136 ..      39     171 ..      27     172 .. 0.91

  Alignments for each domain:
  == domain 1  score: 68.4 bits;  conditional E-value: 1.3e-21
                                        EEEEESTTSSHHHHHHHHTTSS--...SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH....... CS
                                        xxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....... RF
                           ABC_tran  14 vaivGenGaGKStLlkllagllkp...teGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren....... 79 
                                        +a+vG++G+GK+tLlk+++g+      t Gei + g++     le + k   +l q + l  ++t re        
  gene2402|gene2402|rna2402|rna2402  39 TAVVGPSGCGKTTLLKTILGKIPSkyvTTGEIVYCGEKR---VLENWTKITTYLDQSDALSGNITTREClyyaaaf 111
                                        799******************9878899****8886553...4589**********************9******* PP

                                        ...HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                        ...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ABC_tran  80 ...esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                            s++ei++ ++ l      ++++++++++LSgG+ +r+++a  l+ +++++l+DEpt
  gene2402|gene2402|rna2402|rna2402 112 nskRSESEINDNIDMLAERLYLTKILEHQMNKLSGGEVKRLKVAVELVINAPIILMDEPT 171
                                        999888889999999999999999999999*****************************9 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.4   0.0     5e-15   3.2e-12      18     199 ..      30     202 ..      24     212 .. 0.90

  Alignments for each domain:
  == domain 1  score: 46.4 bits;  conditional E-value: 5e-15
                                        EEEETTSSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEE.SSS CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxx RF
                              SMC_N  18 vilpfsksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfdnedkk.lki 92 
                                        v +++  +fta+vGp G+GK+ ll  i   LG+  +   +  ++ ++++  +++   +  +++ ++d++d+   +i
  gene2402|gene2402|rna2402|rna2402  30 VCGEIRAGFTAVVGPSGCGKTTLLKTI---LGKIPS---KYVTTGEIVYCGEKRVLENWTKITTYLDQSDALsGNI 99 
                                        5678999********************...**8877...6667788999877777788899*******99986899 PP

                                        SSSCEEEEEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTT CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              SMC_N  93 ekeevsisrrvkrkgeseykingkevtkkevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeid 168
                                        ++ e+     ++++++se +in++    +e   l +  + +++ LSgGe +     L +A++ v  ap+ l+De  
  gene2402|gene2402|rna2402|rna2402 100 TTRECLYYAAAFNSKRSESEINDNIDMLAERLYLTKILEHQMNKLSGGEVKR----LKVAVELVINAPIILMDEPT 171
                                        999*********************999999999999999999*******885....55666777789********* PP

                                        TTS-HHHHHHHHHHHHHHCTTSEEEEE-SSH CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              SMC_N 169 aaLDeknvkkvaellkeksknaQfivislre 199
                                          LD     +v+++lke  ++  +iv s+++
  gene2402|gene2402|rna2402|rna2402 172 TGLDSVLAYRVVQFLKEMAEHDTIIVCSIHQ 202
                                        **************************99976 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.1   2.5e-05     0.016       1      20 [.      38      57 ..      38      75 .. 0.85
   2 !   12.1   0.0    0.0002      0.13     234     295 ..     141     199 ..     110     204 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.5e-05
                             AAA_21  1 lnvliGpNgsGKSnLLdald 20
                                       +++++Gp g+GK++LL+++ 
  gene2402|gene2402|rna2402|rna2402 38 FTAVVGPSGCGKTTLLKTIL 57
                                       89****************94 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.0002
                             AAA_21 234 arelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQvilt 295
                                        +++lS G  + l++++ l   +   +++l DEp +gL+  l  r++++lke +++++ ++++
  gene2402|gene2402|rna2402|rna2402 141 MNKLSGGEVKRLKVAVELVINA---PIILMDEPTTGLDSVLAYRVVQFLKEMAEHDTIIVCS 199
                                        6677888888889999999999...************************9998866655555 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   5.9e-07   0.00038      25      76 ..      37      86 ..      20     214 .. 0.68

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 5.9e-07
                             AAA_16 25 elvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqal 76
                                       + + ++G+sG+GK++l++++l  +  +  ++++g+ + +++++ +  ++++ 
  gene2402|gene2402|rna2402|rna2402 37 GFTAVVGPSGCGKTTLLKTILGKIPSK--YVTTGEIVYCGEKRVLENWTKIT 86
                                       5789*********************99..77777777774443222233332 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   9.4e-07    0.0006       4      30 ..      35      61 ..      33     137 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 9.4e-07
                             AAA_22  4 tagilvvtGesGtGKTtllrrlleqld 30
                                       +ag+++v+G+sG+GKTtll+++l + +
  gene2402|gene2402|rna2402|rna2402 35 RAGFTAVVGPSGCGKTTLLKTILGKIP 61
                                       589******************998774 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   1.5e-05    0.0095      92     123 ..      29      60 ..       7     105 .. 0.83
   2 ?   -2.6   0.0         7   4.5e+03      19      41 ..     194     216 ..     188     222 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.5e-05
                                        HHHHHCTTSEEEEECSTTSSHHHHHHHHCTT- CS
                        RsgA_GTPase  92 elkellkdktsvlvGqSGvGKStLinallpel 123
                                        ++  +++  ++++vG+SG GK+tL++++l++ 
  gene2402|gene2402|rna2402|rna2402  29 DVCGEIRAGFTAVVGPSGCGKTTLLKTILGKI 60 
                                        55566788899*****************9874 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 7
                                        EEEEEESTTTT--HHHHHHHHHH CS
                        RsgA_GTPase  19 llivvslkepelslnlldrfLvl 41 
                                         +iv+s+++p+ ++ ll   ++l
  gene2402|gene2402|rna2402|rna2402 194 TIIVCSIHQPDDRTLLLFEQVML 216
                                        6899****999888777655555 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   2.8e-05     0.018      19      39 ..      36      56 ..      28     156 .. 0.84
   2 ?   -0.9   0.1       3.1     2e+03     149     165 ..     352     368 ..     243     375 .. 0.60

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.8e-05
                             AAA_23 19 kgltlItGpNGaGKTTildAi 39
                                        g+t+++Gp G+GKTT+l  i
  gene2402|gene2402|rna2402|rna2402 36 AGFTAVVGPSGCGKTTLLKTI 56
                                       799***************877 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 3.1
                             AAA_23 149 kdkkerleelekeleel 165
                                         + ++++++ e+++e++
  gene2402|gene2402|rna2402|rna2402 352 LKINQEINKTERQIEKE 368
                                        33333444444444443 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0     2e-05     0.013       1      31 [.      42      72 ..      42      96 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2e-05
                                       EE-TTSSHHHHHHHHHHHHTEEEEEHHHHHH CS
                             AAA_17  1 lGgPGsGKgtqceklvekygfthlsaGdllr 31
                                       +G+ G+GK+t+++++  k+  +++++G++++
  gene2402|gene2402|rna2402|rna2402 42 VGPSGCGKTTLLKTILGKIPSKYVTTGEIVY 72
                                       79**************************985 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.3   1.4e-05    0.0091      22     129 ..      38     172 ..      24     201 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.4e-05
                           ATPase_2  22 iyfiYGpegsGKtaLlkeiienledkdk...yviyyialre.esiskldefie......................e 71 
                                        +  + Gp g+GKt+Llk i+ +  +k     +++y  + r  e+ +k++++++                       
  gene2402|gene2402|rna2402|rna2402  38 FTAVVGPSGCGKTTLLKTILGKIPSKYVttgEIVYCGEKRVlENWTKITTYLDqsdalsgnittreclyyaaafnS 113
                                        66799***************99944333455666665544324445555555577777777777777777777766 PP

                           ATPase_2  72 eeekkklekalgiavpkaeleeilk.eksklvfkaielllekikkkgkkiiiiiDelqk 129
                                        +++++++++ +    ++  l +il+ + +kl    +++l+ +++     +ii++De   
  gene2402|gene2402|rna2402|rna2402 114 KRSESEINDNIDMLAERLYLTKILEhQMNKLSGGEVKRLKVAVELVINAPIILMDEPTT 172
                                        66666677777888888888888888888888889999999999999999999999554 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   5.7e-05     0.036      17      44 ..      33      60 ..      19     104 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 5.7e-05
                                       TSCSEEEEEEESTTSSHHHHHHHHCCSH CS
                             NB-ARC 17 elqslvvalvGmgGvGKttlakqilnks 44
                                       e+   + a+vG  G+GKttl+k il k 
  gene2402|gene2402|rna2402|rna2402 33 EIRAGFTAVVGPSGCGKTTLLKTILGKI 60
                                       45555889****************9884 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   6.5e-05     0.041       4      28 ..      40      64 ..      38      86 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 6.5e-05
                                       EEEC-TTTCHHHHHHHHHHHHCTS- CS
                              NACHT  4 ilqGeaGsGKTtLlqklalawaegk 28
                                       ++ G++G+GKTtLl+ +  ++ +++
  gene2402|gene2402|rna2402|rna2402 40 AVVGPSGCGKTTLLKTILGKIPSKY 64
                                       799**************98876666 PP

>> PIF1  PIF1-like helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00021      0.14       6      52 ..      19      66 ..      15      75 .. 0.82
   2 ?   -0.6   0.0       0.9   5.8e+02     242     273 ..     524     556 ..     504     576 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00021
                                       HHHHHHHH.......HCTS-EEEEESTTSSCHHHHHHHHHHCHCTCCC CS
                               PIF1  6 Qkkvfdaiieavln.ekgklfFvtGsgGtgKtflwkallkklrsegki 52
                                        ++v+++i+  v    ++++  v G +G gKt l+k++l k+ s+  +
  gene2402|gene2402|rna2402|rna2402 19 NRTVYEHILTDVCGeIRAGFTAVVGPSGCGKTTLLKTILGKIPSKYVT 66
                                       5889999999998735788999********************997544 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.9
                                        .HHCHCCS---S.S--...........EEEESS CS
                               PIF1 242 kieeivsevygd.llqeltdkeyleerailcpt 273
                                         + +i+ +vyg+ + +  +d++y + r+++c++
  gene2402|gene2402|rna2402|rna2402 524 ILPTIILRVYGNrIAKMKQDEDYTSIRTQVCTR 556
                                        56789999**996667777899*********97 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1   6.3e-05     0.041       3      28 ..      41      66 ..      39     100 .. 0.78
   2 ?   -2.5   0.0       9.8   6.2e+03      37      64 ..     309     335 ..     289     336 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 6.3e-05
                                       EESSTTSSHHHHHHHHHHHHTHEEEE CS
                                AAA  3 lyGppGtGKTllakavakelgvefle 28
                                       ++Gp G+GKT+l k +  ++ +++++
  gene2402|gene2402|rna2402|rna2402 41 VVGPSGCGKTTLLKTILGKIPSKYVT 66
                                       79***************998666554 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 9.8
                                        SSTTHHHHHHHHHHHHHHHTSTSEEEEE CS
                                AAA  37 kyvgesekkirelfkeakekakpsilfi 64 
                                        +++   e+++r +fk+a ++     +f+
  gene2402|gene2402|rna2402|rna2402 309 HIITICERELRITFKSAHKQT-FQLIFL 335
                                        566667899999999998876.677776 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   0.00014      0.09       4      26 ..      41      65 ..      39     138 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00014
                             AAA_33  4 lvGlpGsGKstlaerllkklg..av 26
                                       +vG++G+GK+tl++ +l k +  +v
  gene2402|gene2402|rna2402|rna2402 41 VVGPSGCGKTTLLKTILGKIPskYV 65
                                       79*************9988875444 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   0.00014     0.092      37      68 ..      28      60 ..      12      68 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00014
                              Rad17 37 advLesrkkriLLisGPsGCgkstvvk.vLske 68
                                       +dv  + +     + GPsGCgk+t +k +L k+
  gene2402|gene2402|rna2402|rna2402 28 TDVCGEIRAGFTAVVGPSGCGKTTLLKtILGKI 60
                                       555555555566789***********9445665 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00016       0.1      20      39 ..      35      53 ..      22      58 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00016
                             AAA_29 20 dlkgatlltGpsGsGKSTll 39
                                       + +g+t ++GpsG GK+Tll
  gene2402|gene2402|rna2402|rna2402 35 R-AGFTAVVGPSGCGKTTLL 53
                                       3.679**************9 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00022      0.14       3      36 ..      41      73 ..      39     132 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00022
                       RNA_helicase  3 lyGpsgeGKStlakeLakallkklklkkkdsvys 36
                                       ++Gpsg+GK+tl k++  ++ +k+  ++ + vy+
  gene2402|gene2402|rna2402|rna2402 41 VVGPSGCGKTTLLKTILGKIPSKY-VTTGEIVYC 73
                                       79*************988888777.333344444 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00024      0.16      37      63 ..      40      66 ..      19      91 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00024
                              AAA_7 37 llvGptGtGKtviikdllkkldkekyl 63
                                        +vGp+G+GKt+++k++l k++++ ++
  gene2402|gene2402|rna2402|rna2402 40 AVVGPSGCGKTTLLKTILGKIPSKYVT 66
                                       589******************955444 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   0.00026      0.16     130     156 ..      37      63 ..       4      74 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00026
                              T2SSE 130 glilvsGgTgsGKttllyallkeinks 156
                                        g   v G+ g GKttll ++l +i+++
  gene2402|gene2402|rna2402|rna2402  37 GFTAVVGPSGCGKTTLLKTILGKIPSK 63 
                                        555689******************987 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00053      0.34       5      35 ..      39      72 ..      36     108 .. 0.82
   2 ?   -2.9   0.0       9.8   6.3e+03      21      51 ..     184     213 ..     178     223 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00053
                             AAA_14  5 lvitGaRrvGKTtllkqlikell...vkkesily 35
                                        +++G+  +GKTtllk+++ +     v+  +i+y
  gene2402|gene2402|rna2402|rna2402 39 TAVVGPSGCGKTTLLKTILGKIPskyVTTGEIVY 72
                                       5799*************98665555555555555 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 9.8
                             AAA_14  21 qlikellvkkesilyinldderdkkladpek 51 
                                        q++ke   +++ i+  ++ +++d++l  +e+
  gene2402|gene2402|rna2402|rna2402 184 QFLKEMA-EHDTIIVCSIHQPDDRTLLLFEQ 213
                                        5665555.78889999999999988777653 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.0    0.0011      0.72      32      50 ..      35      53 ..      16      60 .. 0.90
   2 ?   -1.6   0.0       2.6   1.7e+03     114     147 ..     342     375 ..     315     376 .. 0.62

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0011
                             AAA_25 32 agelallaGapgtGKttla 50
                                       + ++++++G++g+GKttl+
  gene2402|gene2402|rna2402|rna2402 35 RAGFTAVVGPSGCGKTTLL 53
                                       6789*************97 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2.6
                             AAA_25 114 lpLfakdrggtlltadvdaleaaieevegvrlvv 147
                                        +p +  +    ++++++++ e++ie+ e++ +v 
  gene2402|gene2402|rna2402|rna2402 342 IPFTLRELLPLKINQEINKTERQIEKEEDLIVVF 375
                                        444444444455999***********77666665 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.4   0.00044      0.28       3      22 ..      39      58 ..      38      71 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00044
                                       EEEEESTTCCHHHHHHHHHC CS
                               cobW  3 tvltGflGsGKTtLlnhlle 22
                                       t ++G+ G GKTtLl+++l 
  gene2402|gene2402|rna2402|rna2402 39 TAVVGPSGCGKTTLLKTILG 58
                                       6799*************994 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00047       0.3       3      33 ..      40      70 ..      38     131 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00047
                               MobB  3 givgksgsGKTtLleklipelkarglrvgti 33
                                       ++vg sg+GKTtLl+ ++ ++ ++ ++ g i
  gene2402|gene2402|rna2402|rna2402 40 AVVGPSGCGKTTLLKTILGKIPSKYVTTGEI 70
                                       689*************999887776666655 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1   0.00079       0.5       3      23 ..      40      61 ..      38      88 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00079
                                       EEEESTTSSHHHHHHHHHTS.T CS
                           MMR_HSR1  3 aivGrpNvGKStLinaltge.k 23
                                       a+vG +  GK+tL+++++g+  
  gene2402|gene2402|rna2402|rna2402 40 AVVGPSGCGKTTLLKTILGKiP 61
                                       89****************9742 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1   0.00073      0.47       4      29 ..      41      66 ..      39      76 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00073
                                       EE--SSSSHHHHHHHGGGGBS--EEE CS
                              AAA_5  4 LvGppGtgKselaerlaaalnrevey 29
                                       +vGp+G+gK++l + ++  + +++++
  gene2402|gene2402|rna2402|rna2402 41 VVGPSGCGKTTLLKTILGKIPSKYVT 66
                                       69**************9999887765 PP

>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00031       0.2      13      53 ..      35      77 ..      27     542 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00031
                                       TT-EEEEEESTTSSHHHHHHHHHHHSSTS...S.EEEEEEESEEH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx...x.xxxxxxxxxxx RF
                        ATP-synt_ab 13 qGqrtlipgafgvGktvisqslskqsnsd...d.aiiyvgiGerg 53
                                       + + t+++g +g+Gkt+++++++ +  s+   +  i+y  +Ge++
  gene2402|gene2402|rna2402|rna2402 35 RAGFTAVVGPSGCGKTTLLKTILGKIPSKyvtTgEIVY--CGEKR 77
                                       5567899***************9998888543224454..45443 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.8   0.00091      0.58       4      31 ..      41      68 ..      39      87 .. 0.79
   2 ?   -1.0   0.0       2.3   1.5e+03     113     140 ..     181     208 ..     156     224 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00091
                                       EE--TTSSHHHHHHHHHHHH...GGGEE CS
                           NTPase_1  4 iTGppGvGKtTlvkkvlellkssgvkvg 31
                                       + Gp+G GKtTl+k +l ++ s+ v+ g
  gene2402|gene2402|rna2402|rna2402 41 VVGPSGCGKTTLLKTILGKIPSKYVTTG 68
                                       78******************88765544 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 2.3
                                        HHHHHHHHHHTTTSEEEEE--SS--SHH CS
                           NTPase_1 113 kfkeaveevLksekpvlavihrrkdlal 140
                                        ++ + ++e+ +++++++  ih+++d  l
  gene2402|gene2402|rna2402|rna2402 181 RVVQFLKEMAEHDTIIVCSIHQPDDRTL 208
                                        567888999999999******9974443 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   1.8    0.0026       1.7       7      38 ..      33      64 ..      28     204 .. 0.60

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0026
                             AAA_19  7 alkekvllvtaGpGtGKTrvlkhivallvelg 38
                                       +++++  +v+++ G+GKT++lk+i+  + +  
  gene2402|gene2402|rna2402|rna2402 33 EIRAGFTAVVGPSGCGKTTLLKTILGKIPSKY 64
                                       56788999***************998776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (627 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1173  (0.0654247); expected 358.6 (0.02)
Passed bias filter:                      566  (0.031569); expected 358.6 (0.02)
Passed Vit filter:                        92  (0.00513135); expected 17.9 (0.001)
Passed Fwd filter:                        29  (0.00161749); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              28  [number of targets reported over threshold]
# CPU time: 0.73u 0.31s 00:00:01.04 Elapsed: 00:00:00.46
# Mc/sec: 4101.84
//
Query:       gene2403|gene2403|rna2403|rna2403  [L=459]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.042   13.9   0.5       0.33   11.1   0.4    2.2  2  COP-gamma_platf  Coatomer gamma subunit appendage platform su
       0.16   11.8   0.1        3.9    7.4   0.0    3.0  3  DUF1508          Domain of unknown function (DUF1508)
       0.46   10.5   3.8        1.3    9.2   0.4    3.1  4  DUF5640          Family of unknown function (DUF5640)
        4.9    7.9   7.4        2.6    8.8   0.3    3.0  3  Cytochrom_B562   Cytochrome b562
        8.7    7.1   7.3         37    5.1   0.7    2.9  3  COMPASS-Shg1     COMPASS (Complex proteins associated with Se


Domain annotation for each model (and alignments):
>> COP-gamma_platf  Coatomer gamma subunit appendage platform subdomain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.4   9.1e-05      0.33      57     124 ..     199     262 ..     171     277 .. 0.74
   2 ?    0.1   0.0      0.22     8e+02      57      87 ..     275     304 ..     268     341 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 9.1e-05
                    COP-gamma_platf  57 tledqvLenvsvqlepeeeelfeevfiipiekLkynepgsvyvvlkrpseeeeklvsatfsntLkFtv 124
                                        tl++ + +    + ++     + +  i +i++L+ ++++ ++ +l+ ++++ ++  + tf+n+L+F +
  gene2403|gene2403|rna2403|rna2403 199 TLNNLIKQALAAAPKS----SIVDNLIAKIKQLAITAENAIFAALSLTEKNLSDFSTRTFTNMLQFNS 262
                                        5555544444333333....35555899******************9988888999999*******86 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.22
                    COP-gamma_platf  57 tledqvLenvsvqlepeeeelfeevfiipie 87 
                                        t  +++L+n  v+ ep ++ +f+++  i ++
  gene2403|gene2403|rna2403|rna2403 275 T-LETMLKNLYVKGEPPKKYNFKQKGLIMLD 304
                                        4.46899*****9999665577776666554 PP

>> DUF1508  Domain of unknown function (DUF1508)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.1       1.5   5.3e+03      30      45 ..     217     232 ..     196     233 .. 0.73
   2 ?    7.4   0.0    0.0011       3.9       6      23 ..     356     372 ..     355     378 .. 0.86
   3 ?    0.1   0.0      0.21   7.6e+02      12      26 ..     420     434 ..     418     438 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.5
                                        HHHHHHHHHHHTTTCC CS
                            DUF1508  30 aenGIesVkknapdae 45 
                                        ++n I+ +k  a +ae
  gene2403|gene2403|rna2403|rna2403 217 VDNLIAKIKQLAITAE 232
                                        4667777777776665 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0011
                                        EEEEEE-TTS-EEEEEEE CS
                            DUF1508   6 frFrLkaaNgevIatseg 23 
                                        +rF++k+ Ng++I++ eg
  gene2403|gene2403|rna2403|rna2403 356 PRFTFKS-NGQIILWEEG 372
                                        6999999.******9998 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.21
                                        -TTS-EEEEEEEBSS CS
                            DUF1508  12 aaNgevIatsegYss 26 
                                        +++g++I++  +++ 
  gene2403|gene2403|rna2403|rna2403 420 DSDGQIILSKNTFAQ 434
                                        579*****9887765 PP

>> DUF5640  Family of unknown function (DUF5640)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       1.6   5.9e+03      16      26 ..     291     301 ..     290     312 .. 0.77
   2 ?    9.2   0.4   0.00035       1.3      15      45 ..     317     348 ..     303     364 .. 0.86
   3 ?   -2.4   0.0       1.4     5e+03      17      30 ..     383     396 ..     368     400 .. 0.75
   4 ?    0.6   0.0      0.17     6e+02      11      28 ..     410     427 ..     402     436 .. 0.71

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.6
                                        EEEEE-SSS-E CS
                            DUF5640  16 ktYkFdedGtg 26 
                                        k Y+F+++G  
  gene2403|gene2403|rna2403|rna2403 291 KKYNFKQKGLI 301
                                        57999999965 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00035
                                        -EEEEE-SSS-EEEEEEETTEEE.EEE-SSSS CS
                            DUF5640  15 hktYkFdedGtgelelskaaykf.tYtieedq 45 
                                           +kF+ +Gt ++e+ ka++++ ++ti+++q
  gene2403|gene2403|rna2403|rna2403 317 TSWLKFEMKGTMSFENGKATMAYeKFTINGNQ 348
                                        5568****************77538***9997 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 1.4
                                        EEEE-SSS-EEEEE CS
                            DUF5640  17 tYkFdedGtgelel 30 
                                         Y+F+  Gt +l+ 
  gene2403|gene2403|rna2403|rna2403 383 GYSFRSYGTITLKT 396
                                        59999999988765 PP

  == domain 4  score: 0.6 bits;  conditional E-value: 0.17
                                        SSSS-EEEEE-SSS-EEE CS
                            DUF5640  11 tedshktYkFdedGtgel 28 
                                        t+ s+  Y+Fd dG   l
  gene2403|gene2403|rna2403|rna2403 410 TSVSYDGYRFDSDGQIIL 427
                                        5556778******97644 PP

>> Cytochrom_B562  Cytochrome b562
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.3   0.00071       2.6       9      70 ..      53     116 ..      49     135 .. 0.81
   2 ?    1.6   0.7      0.12   4.4e+02      19      70 ..     175     226 ..     152     251 .. 0.50
   3 ?    1.0   0.5      0.18   6.6e+02       9      50 ..     204     250 ..     201     283 .. 0.65

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00071
                     Cytochrom_B562   9 mkkalkqvakaddaeelkkalkelraaaedakeatpsklek.dseeqkdYqeGldkli.dqldk 70 
                                        +++ +k ++ a+++++++  ++++ +++++  ++ ++ l+k  see + +++   + i +qld+
  gene2403|gene2403|rna2403|rna2403  53 LGQDYKPFNPAATIAAVQRLVSNMAQVEQNYVKQSAAALQKgISEEIDRFEKVVTQTItTQLDA 116
                                        66789999999*******************9999999999999999999999875544145554 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.12
                     Cytochrom_B562  19 addaeelkkalkelraaaedakeatpsklekdseeqkdYqeGldklidqldk 70 
                                         ++++e  +al + +aa+e+ +++t ++l k++   +      d+li+++++
  gene2403|gene2403|rna2403|rna2403 175 NQTPAECVQALVKNHAASEQKSRSTLNNLIKQALAAAPKSSIVDNLIAKIKQ 226
                                        4444444444444444444444444444444333333333333444444443 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.18
                     Cytochrom_B562   9 mkkalkqvakaddaeelkkalkelraaaedakeatpsklek.....d 50 
                                        +k+al ++ k++ +++l +++k+l   ae+a  a  s  ek     +
  gene2403|gene2403|rna2403|rna2403 204 IKQALAAAPKSSIVDNLIAKIKQLAITAENAIFAALSLTEKnlsdfS 250
                                        67777777788888888888888888888887777655444444440 PP

>> COMPASS-Shg1  COMPASS (Complex proteins associated with Set1p) component shg1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.2     0.013        48      34      82 ..      67     117 ..      46     132 .. 0.72
   2 ?    5.1   0.7      0.01        37      18      81 ..     160     223 ..     156     239 .. 0.67
   3 ?   -1.0   0.1      0.84     3e+03      23      42 ..     263     282 ..     240     300 .. 0.66

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.013
                       COMPASS-Shg1  34 kkveeivesevkkdpsllfknrgkaaaliegeidrs..dvykkleegvdri 82 
                                        ++v+ +v+++ + ++++  +  + +++ i++eidr    v +++ +++d+i
  gene2403|gene2403|rna2403|rna2403  67 AAVQRLVSNMAQVEQNYVKQSAAALQKGISEEIDRFekVVTQTITTQLDAI 117
                                        679999999999999999999999999999999995211222222444444 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.01
                       COMPASS-Shg1  18 eiledfkeseaeqnlrkkveeivesevkkdpsllfknrgkaaaliegeidrsdvykkleegvdr 81 
                                        ++l+ +k   +  + +++  e v++ vk++     k r ++ +li++++    + + + + + +
  gene2403|gene2403|rna2403|rna2403 160 KCLKIIKGTSKTSKGNQTPAECVQALVKNHAASEQKSRSTLNNLIKQALAAAPKSSIVDNLIAK 223
                                        5666666666666666666777888888888777788999999999999987544433333333 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.84
                       COMPASS-Shg1  23 fkeseaeqnlrkkveeives 42 
                                        +k+++ +++l +++e++ ++
  gene2403|gene2403|rna2403|rna2403 263 LKQKDLQKDLATTLETMLKN 282
                                        34444445555555554444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (459 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1068  (0.0595683); expected 358.6 (0.02)
Passed bias filter:                      502  (0.0279993); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.43
# Mc/sec: 3240.51
//
Query:       gene2404|gene2404|rna2404|rna2404  [L=277]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (277 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1048  (0.0584528); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 1727.93
//
Query:       gene2405|gene2405|rna2405|rna2405  [L=327]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
       0.15   12.5   0.1       0.15   12.5   0.1    1.7  2  Spore_II_R  Stage II sporulation protein R (spore_II_R)


Domain annotation for each model (and alignments):
>> Spore_II_R  Stage II sporulation protein R (spore_II_R)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   8.2e-06      0.15      24      92 ..       2      70 ..       1      76 [. 0.89
   2 ?   -3.6   0.2      0.81   1.5e+04      76     118 ..     230     272 ..     214     280 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 8.2e-06
                         Spore_II_R 24 kvrdavleeleellkeakskeeaeelikenleeieeiaeevlekegvdykvkvelgkeyfpekeYgdlt 92
                                       k+ d++l++ e+ +k+++++++ + l+++    +    e+++ +++  y++ ++l+++yf+ek+Y++++
  gene2405|gene2405|rna2405|rna2405  2 KIVDRILKHREKIIKNMSRIKAITLLLATVALFFIIPYENTVYNKDSGYDYITNLNHVYFDEKTYDEFV 70
                                       78899*********999888888888888888888899***************************9976 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 0.81
                         Spore_II_R  76 velgkeyfpekeYgdltlpaGeYealrveiGegkGkNwWCvlf 118
                                         ++g+ y+   ++g +++ +  Y  + v  G+ + +  W +l+
  gene2405|gene2405|rna2405|rna2405 230 FTFGNRYWRMENFGPFVFFTALYFFVDVFYGTYQRRPPWILLY 272
                                        5567777777788888888888877777777766666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (327 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       958  (0.053433); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 2172.97
//
Query:       gene2406|gene2406|rna2406|rna2406  [L=347]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.6e-55  188.0  19.3    4.2e-55  187.4  19.3    1.3  1  CTP_transf_1  Cytidylyltransferase family


Domain annotation for each model (and alignments):
>> CTP_transf_1  Cytidylyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  187.4  19.3   2.3e-59   4.2e-55       3     266 .]      16     309 ..      14     309 .. 0.82

  Alignments for each domain:
  == domain 1  score: 187.4 bits;  conditional E-value: 2.3e-59
                                        HHHHHHHHHHHHHHTTTSH.HHHHHHHHHHHHHHHHHHHHTT--SHHHHHHHHH...HHHHHHHHHHTTTSSSHHH CS
                       CTP_transf_1   3 RvitalvlilivliilllgglvflllvavvvilalkElirlvrlkkrekrllllllslvlllllllflyleslial 78 
                                        R++++ ++++ vl i+l  ++++ l+v+v+ ++al+E+i +++++ r+k  +   l +++++++ lf+   ++  +
  gene2406|gene2406|rna2406|rna2406  16 RTYAGAIMFA-VLHIVLKDNVAVYLFVFVLKTFALNEVIGIKEENLRKKYRFKY-LLWYFVTVSDLFFSKSIARPF 89 
                                        5556666555.456677788**********************999887666555.788888888888776665555 PP

                                        HHHHHHHHHHHHHHH---...................HHHHHHHHHHHHHHHHHTHHHH.TTHHHHHHHHHHHHHH CS
                       CTP_transf_1  79 lklvlllvlvllllvlkvl................kskskklervilallallyvvlllqslllienikeglllvl 138
                                        +  +l l++ ++  +l  +                   +k++ +++++ +a++++ + +  + +++ni+ g ++++
  gene2406|gene2406|rna2406|rna2406  90 YIFLLSLDFPVTHAFLC-FslyilgivyfivnlrrGVLRKQFLQFSITHFAIMMINFPV--HCVFRNIRVGKFWFV 162
                                        55554444443333332.23455666677777654444455555555555555555555..99************* PP

                                        HHHHHHHHHHHHHHHHHHCH---B-S-TTS---BHHHHHHHHHHHHHHHHHHHHHHHCTS................ CS
                       CTP_transf_1 139 lllalvvaaDigaYffGklfGktkllpkiSPkKTveGfigGlvaavvvglllalvlskal................ 198
                                        ++++lv a+Di+aY++Gkl+G+t  l k+SPkKT eG+igG++++v+vg++++++ +++                 
  gene2406|gene2406|rna2406|rna2406 163 YPILLVAANDIFAYVTGKLIGRT-QLTKLSPKKTREGLIGGFIFTVIVGFFCIYLKCQFNiyegvydkailaktvt 237
                                        ***********************.*********************************988**************** PP

                                        ....---TTSHHHHHHHHHHHHHHHHHHHHHHHHHHT-SSS-S-SSSSS-HHHHHHHHHHHHHHHHHHHHHH CS
                       CTP_transf_1 199 ....alsllhllllslllslvavfGDLveSglKRafgiKDsGkliPGhGGilDRlDsllfaapvvylllelf 266
                                              ++lh+++l l++s+va+fG+L++S++KR f+ KD+++ +PGhGGi+DR+D+++++++++ ++l+ f
  gene2406|gene2406|rna2406|rna2406 238 rykiPAIYLHAIVLILFASFVAPFGGLLASAFKRLFKMKDFATYLPGHGGITDRIDCQILMGIFTRYYLSAF 309
                                        ***999************************************************************999765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (347 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       648  (0.0361426); expected 358.6 (0.02)
Passed bias filter:                      229  (0.0127726); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 2450.88
//
Query:       gene2407|gene2407|rna2407|rna2407  [L=260]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    4.3e-05   23.4   0.1    4.3e-05   23.4   0.1    2.7  3  SNARE       SNARE domain
  ------ inclusion threshold ------
      0.026   13.7   0.1      0.034   13.3   0.1    1.2  1  SatRNA_48   Satellite RNA 48 kDa protein
       0.31   11.4   9.4      0.066   13.6   4.0    2.3  3  Syntaxin_2  Syntaxin-like protein


Domain annotation for each model (and alignments):
>> SNARE  SNARE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.1      0.88   5.2e+03      17      34 ..     104     121 ..     103     124 .. 0.81
   2 !   23.4   0.1   7.1e-09   4.3e-05       1      26 [.     185     210 ..     185     212 .. 0.95
   3 ?   -3.3   4.8       1.6   9.3e+03      40      51 ..     226     237 ..     219     239 .. 0.50

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.88
                                        HHHHHHHHHHHHHHHCTX CS
                              SNARE  17 veraqkeLkkavkyqksn 34 
                                        ++++++ L+ ++++q+++
  gene2407|gene2407|rna2407|rna2407 104 AQNVHSLLVEYREMQQKY 121
                                        578889999999999885 PP

  == domain 2  score: 23.4 bits;  conditional E-value: 7.1e-09
                                        HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              SNARE   1 emvDrIdtnVenaqsnveraqkeLkk 26 
                                        +m+DrId+ V++a+sn++ a+ke+ k
  gene2407|gene2407|rna2407|rna2407 185 NMIDRIDYLVDEANSNLRMANKEIEK 210
                                        5**********************977 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 1.6
                                        XXXXXXXXXXXX CS
                              SNARE  40 iillilviillv 51 
                                        ++++ ++++ll+
  gene2407|gene2407|rna2407|rna2407 226 LLFITVCLLLLL 237
                                        344444444444 PP

>> SatRNA_48  Satellite RNA 48 kDa protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   5.7e-06     0.034      51      88 ..     127     164 ..      90     206 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5.7e-06
                          SatRNA_48  51 ekelleeveestpfvvndkraqhlfckkverkvgrrei 88 
                                        + + ++++e+++pf  n++++q+l+c+k +  +     
  gene2407|gene2407|rna2407|rna2407 127 NLQIFDDLEDTRPFQPNNNQSQQLICQKKQNDIESIRS 164
                                        2346799*********************9988865544 PP

>> Syntaxin_2  Syntaxin-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   4.0   1.1e-05     0.066      20      99 ..      50     127 ..      36     129 .. 0.87
   2 ?    5.3   1.5    0.0043        26      31      72 ..     103     152 ..      93     167 .. 0.79
   3 ?    0.1   0.3      0.18   1.1e+03      33      44 ..     188     199 ..     140     222 .. 0.49

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.1e-05
                         Syntaxin_2  20 kqLgtkkdteelreklhelieeinelikktnellkklsqldnsssdsqqklqkekLkkdfkealqeFqkiqrqyae 95 
                                        + L +    ++ re++++l +ei+ li + ++ lk+++ l+ ++    +k +k+  ++ + ++l e+ ++q++y +
  gene2407|gene2407|rna2407|rna2407  50 QCLPSFSKRKQKREEINKLKNEIRVLIVRLENYLKEINGLECTLV--LKKRMKDYFAQNVHSLLVEYREMQQKYLR 123
                                        446666677888****************************99996..78899**********************99 PP

                         Syntaxin_2  96 kekq 99 
                                        k k+
  gene2407|gene2407|rna2407|rna2407 124 KVKN 127
                                        9876 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0043
                         Syntaxin_2  31 lreklhelieeinelikktnellkklsqldnsssds........qqklqk 72 
                                        + +++h+l  e +e+ +k  +++k+l+  d+ ++++        +q l+ 
  gene2407|gene2407|rna2407|rna2407 103 FAQNVHSLLVEYREMQQKYLRKVKNLQIFDDLEDTRpfqpnnnqSQQLIC 152
                                        56899*************************99988888877766444444 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.18
                         Syntaxin_2  33 eklhelieeine 44 
                                        ++++ l++e+n 
  gene2407|gene2407|rna2407|rna2407 188 DRIDYLVDEANS 199
                                        333333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1927  (0.10748); expected 358.6 (0.02)
Passed bias filter:                      740  (0.0412739); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 1618.19
//
Query:       gene2408|gene2408|rna2408|rna2408  [L=448]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      1e-22   80.4   0.1      1e-22   80.4   0.1    2.8  3  V-ATPase_H_C  V-ATPase subunit H
    1.5e-09   37.6   9.7    9.8e-09   34.9   9.7    2.0  1  V-ATPase_H_N  V-ATPase subunit H
  ------ inclusion threshold ------
      0.075   13.0   0.1       0.38   10.8   0.1    2.2  2  KIX_2         KIX domain


Domain annotation for each model (and alignments):
>> V-ATPase_H_C  V-ATPase subunit H
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.1      0.12     7e+02      26      52 ..      85     112 ..      69     139 .. 0.81
   2 ?   -1.3   0.3      0.39   2.3e+03      41      73 ..     254     286 ..     243     317 .. 0.57
   3 !   80.4   0.1   1.7e-26     1e-22       2     115 ..     333     445 ..     332     447 .. 0.96

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.12
                       V-ATPase_H_C  26 ekFWkenaekl.eeknfkllkkLiklle 52 
                                        ++FW+   ++l +e+++++++ L+k+l+
  gene2408|gene2408|rna2408|rna2408  85 SSFWTFVRATLtTEEDHEIVNFLLKCLR 112
                                        6899998888878888999999999882 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.39
                       V-ATPase_H_C  41 fkllkkLiklleeskdktvlavalnDigelvkl 73 
                                        ++l+++L + ++++++++++ +a+  + +l ++
  gene2408|gene2408|rna2408|rna2408 254 VDLIEALENKIRKDTQDKIVRMACLVLMNLKEH 286
                                        556666666665555556666666555554444 PP

  == domain 3  score: 80.4 bits;  conditional E-value: 1.7e-26
                       V-ATPase_H_C   2 ltsfdeYlaElesgkLewspvHksekFWkenaekleeknfkllkkLiklleeskdktvlavalnDigelvkllpeg 77 
                                        ++s+d+Yl+El sg+Le + +H +e+FW+ n+ kl+ k+++++k++  +l+   +++++++alnD+ ++ ++  + 
  gene2408|gene2408|rna2408|rna2408 333 VSSVDNYLKELYSGHLEPTLYHFEESFWNVNLGKLQIKKHEIIKAIRLYLK-RGERQNVVMALNDLFMFHNVDASI 407
                                        79************************************************5.788899****************** PP

                       V-ATPase_H_C  78 kkvleklkaKekimellehedeevkyeALkavqkllvq 115
                                         +++e++++Ke+++el+ ++d e+++ AL+a  ++l q
  gene2408|gene2408|rna2408|rna2408 408 GRLIENYGVKEQLIELCGSNDGEIQFLALQAFLSVLNQ 445
                                        *******************************9988876 PP

>> V-ATPase_H_N  V-ATPase subunit H
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.9   9.7   1.6e-12   9.8e-09      81     312 ..      25     323 ..      22     326 .. 0.60

  Alignments for each domain:
  == domain 1  score: 34.9 bits;  conditional E-value: 1.6e-12
                       V-ATPase_H_N  81 dDllsedksrvelflslakkeeqdpwkpflkllnrqddfivllalrllakllvqgkkksnklv............. 143
                                        dD++s+++ +++    l+ +++  +++++l l n++d + + +++ ++ +  + +   +++++             
  gene2408|gene2408|rna2408|rna2408  25 DDIFSSEDLGKQHCYLLKMQNDI-LLDVLLGLCNKDDFYLKVKSIEIMSRRYSNALRDDPNSSfwtfvratlttee 99 
                                        56666666666655554443333.7777777888888888888888888777777777777333333433333333 PP

                       V-ATPase_H_N 144 .esaLnrllqlLss..qlss...........................................stnevieiavrll 173
                                         ++++n+ll+ L++  + ++                                           +            
  gene2408|gene2408|rna2408|rna2408 100 dHEIVNFLLKCLRNffL-ENlereqifpdlntavvfekqdrkdsdrkdqrenvgdtnpnnacaP------------ 162
                                        33333444444444321.1133344444444444444444444444444444444444444441............ PP

                       V-ATPase_H_N 174 qellrtkeyRelfveadgvstlisilr................................................. 200
                                                                                                                    
  gene2408|gene2408|rna2408|rna2408 163 --------------------------Dnqssktdtgtcsekdvddiniilkcskfipysqrydqrervesfrvhfv 212
                                        ..........................03333333333333333333333333333333333333333333333333 PP

                       V-ATPase_H_N 201 ....stvan.strvgiQlqYqvllclWlLsFekkiaeelvkkkelipllvdilrdsvKEKvtRvilatlrNlleka 271
                                            ++    s     +  Y++l+++WlLsF++k+ ++l+  + li  l + +r+ +  K++R++  +l Nl e  
  gene2408|gene2408|rna2408|rna2408 213 sdtaVQRRLlSFIETDDFCYNALFLIWLLSFTEKVFDKLSAVD-LIEALENKIRKDTQDKIVRMACLVLMNLKEHD 287
                                        3222111110122233689********************9999.****************************9998 PP

                       V-ATPase_H_N 272 eksskelaavmvqvkllkllenLeerkfsDeditedleyLk 312
                                              ++ +  ++++l++ +++ +rk +D + + d ++L+
  gene2408|gene2408|rna2408|rna2408 288 L-----FISLKNLHRMLNISKIMLNRKSEDLEYNHDKKELY 323
                                        8.....9999999*****************99998887776 PP

>> KIX_2  KIX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   6.4e-05      0.38       5      48 ..      92     136 ..      85     145 .. 0.92
   2 ?   -3.8   0.0       2.2   1.3e+04       9      24 ..     383     398 ..     380     403 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 6.4e-05
                              KIX_2   5 ratlspeeRqkivnkiletLkk.hlpvsgpeglnelkkiAvrFEe 48 
                                        ratl++ee ++ivn +l+ L++  l + + e++    + Av FE+
  gene2408|gene2408|rna2408|rna2408  92 RATLTTEEDHEIVNFLLKCLRNfFLENLEREQIFPDLNTAVVFEK 136
                                        99********************9999999999999999*****98 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 2.2
                              KIX_2   9 speeRqkivnkiletL 24 
                                        +  eRq++v  + + +
  gene2408|gene2408|rna2408|rna2408 383 KRGERQNVVMALNDLF 398
                                        5678999998876655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (448 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       853  (0.0475766); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.49
# Mc/sec: 2745.40
//
Query:       gene2409|gene2409|rna2409|rna2409  [L=374]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    6.3e-74  249.4   4.8    7.2e-74  249.2   4.8    1.0  1  Cpn60_TCP1  TCP-1/cpn60 chaperonin family


Domain annotation for each model (and alignments):
>> Cpn60_TCP1  TCP-1/cpn60 chaperonin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  249.2   4.8     4e-78   7.2e-74       2     336 ..      29     349 ..      28     371 .. 0.93

  Alignments for each domain:
  == domain 1  score: 249.2 bits;  conditional E-value: 4e-78
                                        HHHHHCCSSTTXXEEEEEETTSEEEEEXSHHHHHHCSXXXSHHHHHHHHHHHHCCCCCTTCHHHHHHHHHHHHHHH CS
                         Cpn60_TCP1   2 adivkttlGPkGmdKmlvnkggkvvvTnDGatilkeleiehPaakllveaaesqdeevGDGTttvviLageLleea 77 
                                          ++k+tlGP G++K+l    +k++vTnDGat+lk+l i+   a++l++a+ sqd e GDGTtt +iLa+ L+eea
  gene2409|gene2409|rna2409|rna2409  29 NTLIKSTLGPFGLTKLLT-CDDKIKVTNDGATLLKNLVIDSASARILINASVSQDWEEGDGTTTIAILASLLVEEA 103
                                        6789*************7.556****************************************************** PP

                                        HHHHHCTXXHHHHHHHHHHHHHHHHHHHHHHXEEBXSCSTT.HHHHHHHHHHCTTSSXXSTHHHHHHHHHHHHHCH CS
                         Cpn60_TCP1  78 ekliaagvhpttiiegyekalekaleaLkeiaveisseekdreeLlkvartslsskltskeaeelsklvvdAvkli 153
                                        +kl  +++hp++ii+gye+al++ale L+ ++  ++     +++++++a+t+l+sk+ + + +++++++v+A++li
  gene2409|gene2409|rna2409|rna2409 104 SKL--EEIHPIQIIKGYEMALARALEVLDGVCFVMK-----DDDMVTLAKTTLNSKILRCDLQRFAEICVNAINLI 172
                                        ***..9*************************44444.....479*****************************99* PP

                                        CCCSEECSCCCEECCCCEECECTTSEEESEEEESS--SSTTSSCEEECEEEEEESS-BS--HHCC.HHHCCCCSCC CS
                         Cpn60_TCP1 154 eenekeldlgrikvvkieggsledselveGlvldkgvlspdmpkklenakvllldvsLeiektet.kttvvlsdae 228
                                        ee+    dl+ i+v+k eg +l++s lv+G++ldk+v+ p    +l+n+++l+ ++s++++k ++  ++v+++++ 
  gene2409|gene2409|rna2409|rna2409 173 EER---DDLSLINVIKTEG-ELQHSYLVDGFILDKDVVVP----TLKNPRILVANTSMDTDKIKInGAQVNVRSVG 240
                                        988...8*********995.699****************9....79****************9984679******* PP

                                        HHHHHHHHHHHHHHHHHHHHH..HTTECEEEESS-B-HHHHHHHHHCT-EEE-S--HHHHHHHHHHHT--EBSCGG CS
                         Cpn60_TCP1 229 eleklekaeekqleellekii..ksgvnvvvcqkgiddlalhflakngilalrrvkkkdlerlakatGatavssle 302
                                        el ++e+ae++ ++e++eki+  + g +v+v+ + i d+ l+++++++++a+++++ + +erla+++Ga+++s+++
  gene2409|gene2409|rna2409|rna2409 241 ELSQIEDAERQRMQEKVEKIVgaENGIDVFVNRQIIYDYFLQLFREKNVVAVEHADFEGVERLANVLGAKIMSTFD 316
                                        ********************83366899***********************************************9 PP

                                        GGGCGC-EEEEEEEECCETTCCEEEEECESSSSX CS
                         Cpn60_TCP1 303 dltpeelGtakkveeekigsekttiieevksgki 336
                                        +l++ ++G ++++e+ ++g++ ++ +++ +++++
  gene2409|gene2409|rna2409|rna2409 317 SLND-CIGGCERMENVHVGEKVMVKFSGLRKARA 349
                                        9987.8********************98766554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (374 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       536  (0.0298957); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 2466.23
//
Query:       gene241|gene241|rna241|rna241  [L=128]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.4e-17   63.8   0.1    1.8e-17   63.4   0.1    1.1  1  Ribosomal_S8  Ribosomal protein S8
  ------ inclusion threshold ------
      0.073   13.1   0.0       0.09   12.8   0.0    1.2  1  Thg1          tRNAHis guanylyltransferase


Domain annotation for each model (and alignments):
>> Ribosomal_S8  Ribosomal protein S8
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.4   0.1   2.1e-21   1.8e-17       1     127 []       3     128 .]       3     128 .] 0.87

  Alignments for each domain:
  == domain 1  score: 63.4 bits;  conditional E-value: 2.1e-21
                                    -HHHHHHHHHHHHHHTT-SEEEE.E--HHHHHHHHHHHHCTSEEEEEEE.CCC..CCCEEEEE-BSSS-SBSSSEEEE-S CS
                   Ribosomal_S8   1 DpiadmltrirNaekakkeevev.pasklkeeilkvLkeeGyikdfeve.eek..kkkikielkynkkkksvikklkrvs 76 
                                    D++a+++t+i+Na++++ ++v + +   + ++ l++++  Gy++++++  +++  k +++++++ nk  ++++    +v+
  gene241|gene241|rna241|rna241   3 DKLAQACTTINNANQNQARQVIIrNINSVVRNFLNIMQAYGYLDEITYInDHRvgKAVVSLNGRLNK--CGAVCPRYDVQ 80 
                                    899********************89999********************8555444444777777777..9****999999 PP

                                    BTTC--EE-CCC---CGGGTSEEEEEETTEEEEHHHHHHCT--EEEEEEEE CS
                   Ribosomal_S8  77 kpgrrvYakvkelpkvlnglGiaivsTskGvmtdkeArkkkvGGevlayvw 127
                                     +  + Y ++  lp   + +G +ivsTskG++ ++e+  k++GG+vl + +
  gene241|gene241|rna241|rna241  81 IGEIERYRQS-ILP--ARQFGHLIVSTSKGILDHRECIVKGTGGKVLGFFY 128
                                    9999977653.344..578****************************9876 PP

>> Thg1  tRNAHis guanylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0     1e-05      0.09      36      77 ..      11      52 ..       3      81 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1e-05
                           Thg1 36 kfekPnDeralklmneaakelvkefedivlaYgqSDEislvl 77
                                    ++  n ++a +++ +  +++v++f +i+ aYg  DEi+ + 
  gene241|gene241|rna241|rna241 11 TINNANQNQARQVIIRNINSVVRNFLNIMQAYGYLDEITYIN 52
                                   5778999*******************************8765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       839  (0.0467957); expected 358.6 (0.02)
Passed bias filter:                      667  (0.0372023); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 909.32
//
Query:       gene2410|gene2410|rna2410|rna2410  [L=540]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.3e-08   33.5  11.9     0.0016   18.4   0.4    4.8  4  TPR_2       Tetratricopeptide repeat
    1.1e-05   25.6   3.5      3e-05   24.2   2.5    2.2  3  TPR_12      Tetratricopeptide repeat
    0.00018   21.2  13.6      0.014   15.2   0.8    4.4  3  TPR_1       Tetratricopeptide repeat
     0.0048   16.9   8.5       0.18   11.9   0.3    3.6  3  Fis1_TPR_C  Fis1 C-terminal tetratricopeptide repeat
  ------ inclusion threshold ------
       0.05   13.8   0.3       0.05   13.8   0.3    5.1  6  TPR_8       Tetratricopeptide repeat
      0.055   13.9   3.8         20    5.9   0.0    4.6  4  TPR_17      Tetratricopeptide repeat
       0.12   12.9   1.7        9.2    6.9   0.3    2.9  3  TPR_19      Tetratricopeptide repeat
       0.12   12.4   2.4          2    8.6   0.2    3.1  2  TPR_7       Tetratricopeptide repeat
       0.21   11.3   2.6       0.28   10.9   0.7    2.4  2  TPR_11      TPR repeat
        0.3   11.3  14.2        2.5    8.4   0.6    3.9  3  ANAPC3      Anaphase-promoting complex, cyclosome, subunit 3
        1.4    8.9   5.0          1    9.3   0.5    2.9  3  TPR_10      Tetratricopeptide repeat
        8.4    7.3   6.2    1.4e+02    3.4   0.1    4.7  5  TPR_6       Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.8   1.9e-06    0.0028       7      31 ..      45      69 ..      42      72 .. 0.90
   2 !   18.4   0.4   1.1e-06    0.0016       3      34 .]      79     110 ..      78     110 .. 0.94
   3 ?   -1.6   0.0       2.8   4.1e+03      11      24 ..     392     405 ..     390     406 .. 0.80
   4 ?    1.0   0.0      0.41   6.1e+02      11      27 ..     489     505 ..     483     508 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.9e-06
                              TPR_2  7 lGlayyklgdyeeAleafekAleld 31
                                        G+a+y++++y++Ale ++ Al++ 
  gene2410|gene2410|rna2410|rna2410 45 EGNAHYRNKEYAKALEKYNLALSYT 69
                                       79********************976 PP

  == domain 2  score: 18.4 bits;  conditional E-value: 1.1e-06
                              TPR_2   3 alynlGlayyklgdyeeAleafekAleldPnn 34 
                                        +l+n++l y+ l +yeeAl + ++ l+ld +n
  gene2410|gene2410|rna2410|rna2410  79 ILNNIALTYILLRNYEEALIYTNRFLALDRKN 110
                                        689**************************886 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 2.8
                              TPR_2  11 yyklgdyeeAleaf 24 
                                        ++++++y++A++ +
  gene2410|gene2410|rna2410|rna2410 392 LIHNKEYNRAEKVL 405
                                        678999*9999875 PP

  == domain 4  score: 1.0 bits;  conditional E-value: 0.41
                              TPR_2  11 yyklgdyeeAleafekA 27 
                                        y+ + + +e++++fe A
  gene2410|gene2410|rna2410|rna2410 489 YLMKRNDKECVKYFEMA 505
                                        66677888888888865 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   2.5     2e-08     3e-05      10      76 ..      46     108 ..      39     109 .. 0.89
   2 ?   -3.4   0.0       8.5   1.3e+04      10      24 ..     296     310 ..     290     312 .. 0.58
   3 ?   -1.9   0.0       2.9   4.4e+03      10      34 ..     487     510 ..     483     525 .. 0.64

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 2e-08
                             TPR_12  10 aavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76 
                                        +++++r ++y++Ale ++ al    r+ +++h   +++l+n++ +y +l +yeeAl + ++ la+++
  gene2410|gene2410|rna2410|rna2410  46 GNAHYRNKEYAKALEKYNLALSYT-RTCDEEH---LNILNNIALTYILLRNYEEALIYTNRFLALDR 108
                                        899******************999.5656666...89*********************999999887 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 8.5
                             TPR_12  10 aavlrrlgrydeAle 24 
                                        a++++  g+ + Al+
  gene2410|gene2410|rna2410|rna2410 296 ASIEHLKGNNERALS 310
                                        555555666665554 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 2.9
                             TPR_12  10 aavlrrlgrydeAlellekaleiar 34 
                                        ++ l+++ +  e+ +++e a+++  
  gene2410|gene2410|rna2410|rna2410 487 GNYLMKRND-KECVKYFEMARDMSG 510
                                        555555555.899999999988774 PP

>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   2.7    0.0004       0.6       8      29 ..      46      67 ..      43      68 .. 0.93
   2 !   15.2   0.8   9.4e-06     0.014       3      34 .]      79     110 ..      78     110 .. 0.91
   3 ?   -0.9   0.1       1.1   1.7e+03      11      27 ..     489     505 ..     483     507 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0004
                                       HHHHHHTT-HHHHHHHHHHHHH CS
                              TPR_1  8 GnayfklgkydeAleyyekALe 29
                                       Gna++++++y +Ale y+ AL+
  gene2410|gene2410|rna2410|rna2410 46 GNAHYRNKEYAKALEKYNLALS 67
                                       9*****************9995 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 9.4e-06
                                        HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                              TPR_1   3 alynlGnayfklgkydeAleyyekALelnPnn 34 
                                        +l+n++++y  l +y+eAl y ++ L l+ +n
  gene2410|gene2410|rna2410|rna2410  79 ILNNIALTYILLRNYEEALIYTNRFLALDRKN 110
                                        69*****************9999988888876 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 1.1
                                        HHHTT-HHHHHHHHHHH CS
                              TPR_1  11 yfklgkydeAleyyekA 27 
                                        y+ + + +e+++y+e A
  gene2410|gene2410|rna2410|rna2410 489 YLMKRNDKECVKYFEMA 505
                                        44555557778888776 PP

>> Fis1_TPR_C  Fis1 C-terminal tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   0.9     0.003       4.5      10      28 ..      48      66 ..      46      72 .. 0.87
   2 !   11.9   0.3   0.00012      0.18       6      35 ..      82     111 ..      78     115 .. 0.89
   3 ?   -0.9   0.0       1.2   1.8e+03      14      27 ..     395     408 ..     393     409 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.003
                                       HHHHHT-HHHHHHHHHHHH CS
                         Fis1_TPR_C 10 GhyklgeYseArryvdalL 28
                                       +hy+ +eY +A++  +  L
  gene2410|gene2410|rna2410|rna2410 48 AHYRNKEYAKALEKYNLAL 66
                                       8***********9887776 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00012
                                        HHHHHHHHHT-HHHHHHHHHHHHHHTTS-H CS
                         Fis1_TPR_C   6 ylAlGhyklgeYseArryvdalLeiEPenr 35 
                                         +Al ++ l++Y+eA+ y++++L+++ +n 
  gene2410|gene2410|rna2410|rna2410  82 NIALTYILLRNYEEALIYTNRFLALDRKNA 111
                                        68999999*****************99985 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 1.2
                                        HT-HHHHHHHHHHH CS
                         Fis1_TPR_C  14 lgeYseArryvdal 27 
                                         +eY++A + ++ l
  gene2410|gene2410|rna2410|rna2410 395 NKEYNRAEKVLKSL 408
                                        58*****9998875 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.4      0.26   3.8e+02       8      32 ..      46      70 ..      45      72 .. 0.86
   2 ?   13.8   0.3   3.4e-05      0.05       3      34 .]      79     110 ..      77     110 .. 0.92
   3 ?   -1.0   0.0       1.9   2.8e+03       4      22 ..     292     310 ..     291     313 .. 0.83
   4 ?   -2.5   0.1       5.8   8.7e+03      10      17 ..     360     367 ..     359     368 .. 0.84
   5 ?   -0.4   0.0       1.3   1.9e+03      21      32 ..     466     477 ..     448     479 .. 0.76
   6 ?   -2.8   0.0       7.3   1.1e+04       7      19 ..     486     497 ..     483     503 .. 0.54

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.26
                                       HHHHHHTT-HHHHHHHHHHHHHHHH CS
                              TPR_8  8 gsiylklgdyeeAkeyyekaleldp 32
                                       g+++   ++y +A e y+ al++ +
  gene2410|gene2410|rna2410|rna2410 46 GNAHYRNKEYAKALEKYNLALSYTR 70
                                       78899999*******9999999866 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 3.4e-05
                                        HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                              TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                        +++n++++y+ l +yeeA  y ++ l ld++n
  gene2410|gene2410|rna2410|rna2410  79 ILNNIALTYILLRNYEEALIYTNRFLALDRKN 110
                                        799********************999999986 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 1.9
                                        HHHHHHHHHHTT-HHHHHH CS
                              TPR_8   4 yynlgsiylklgdyeeAke 22 
                                        ++ ++si + +g+ e A +
  gene2410|gene2410|rna2410|rna2410 292 LFVKASIEHLKGNNERALS 310
                                        6789999999****99965 PP

  == domain 4  score: -2.5 bits;  conditional E-value: 5.8
                                        HHHHTT-H CS
                              TPR_8  10 iylklgdy 17 
                                        iylkl+d+
  gene2410|gene2410|rna2410|rna2410 360 IYLKLNDM 367
                                        9****998 PP

  == domain 5  score: -0.4 bits;  conditional E-value: 1.3
                                        HHHHHHHHHHHH CS
                              TPR_8  21 keyyekaleldp 32 
                                        ke + k+ eld+
  gene2410|gene2410|rna2410|rna2410 466 KEELTKCFELDK 477
                                        788899999997 PP

  == domain 6  score: -2.8 bits;  conditional E-value: 7.3
                                        HHHHHHHTT-HHH CS
                              TPR_8   7 lgsiylklgdyee 19 
                                        lg+ ++k +d+ e
  gene2410|gene2410|rna2410|rna2410 486 LGNYLMKRNDK-E 497
                                        55555555554.4 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.1       6.6   9.8e+03      20      34 .]      46      60 ..      46      60 .. 0.75
   2 ?    3.3   0.0      0.09   1.3e+02       8      33 ..      72      97 ..      71      98 .. 0.86
   3 ?    2.2   0.0      0.19   2.9e+02      10      33 ..     286     309 ..     278     310 .. 0.86
   4 ?    5.9   0.0     0.013        20       3      29 ..     470     496 ..     468     506 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 6.6
                             TPR_17 20 AelllknGdlmtArq 34
                                       ++++++n+++++A++
  gene2410|gene2410|rna2410|rna2410 46 GNAHYRNKEYAKALE 60
                                       677888888888875 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.09
                             TPR_17  8 ldPnnadaynnLAelllknGdlmtAr 33
                                       +d  + + +nn A ++  + ++++A+
  gene2410|gene2410|rna2410|rna2410 72 CDEEHLNILNNIALTYILLRNYEEAL 97
                                       56667789**************9995 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.19
                             TPR_17  10 PnnadaynnLAelllknGdlmtAr 33 
                                         +n+  ++ +A + + +G+ ++A+
  gene2410|gene2410|rna2410|rna2410 286 ETNSLTLFVKASIEHLKGNNERAL 309
                                        589******************996 PP

  == domain 4  score: 5.9 bits;  conditional E-value: 0.013
                             TPR_17   3 lkaleldPnnadaynnLAelllknGdl 29 
                                        +k+ eld++  ++y  L+++l k++d+
  gene2410|gene2410|rna2410|rna2410 470 TKCFELDKTFMKPYIVLGNYLMKRNDK 496
                                        799********************9996 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.3    0.0062       9.2       4      60 ..      52     112 ..      49     115 .. 0.86
   2 ?    2.4   0.0      0.15   2.2e+02      35      53 ..     392     410 ..     373     414 .. 0.83
   3 ?    3.8   0.1     0.054        81       3      66 ..     394     454 ..     392     456 .. 0.64

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0062
                             TPR_19   4 egdyaeAlalleqalqe....dpknaearllLAeallalgqldeAealLdalpeedpddar 60 
                                        ++ ya Al+ +  al++    d ++++++ + A  ++ l +++eA    ++ ++ d+++ar
  gene2410|gene2410|rna2410|rna2410  52 NKEYAKALEKYNLALSYtrtcDEEHLNILNNIALTYILLRNYEEALIYTNRFLALDRKNAR 112
                                        678999999999999999999999*********************9877777777777666 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.15
                             TPR_19  35 llalgqldeAealLdalpe 53 
                                        l+ +++++ Ae++L+ l  
  gene2410|gene2410|rna2410|rna2410 392 LIHNKEYNRAEKVLKSLKM 410
                                        78999*********99876 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.054
                             TPR_19   3 aegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddaryasLlA 66 
                                         ++ y +A + l+++   + +  ++  l +e ++  + +d+  al+d+ +++ + d+r+   +A
  gene2410|gene2410|rna2410|rna2410 394 HNKEYNRAEKVLKSL---KMETIALMSLACEFYFLIKKYDDVPALIDKMQRMSASDPRAYLFRA 454
                                        456667777777776...4455555556677777777777777777777777777777766665 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.2      0.18   2.7e+02       6      30 ..      46      68 ..      46      74 .. 0.79
   2 ?    8.6   0.2    0.0013         2       2      29 ..      80     107 ..      79     113 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.18
                              TPR_7  6 arlysrlGdyeeAielyeqsLaltk 30
                                       ++++ r  +y++A+e y    al +
  gene2410|gene2410|rna2410|rna2410 46 GNAHYRNKEYAKALEKYNL--ALSY 68
                                       688889999*******988..5544 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0013
                              TPR_7   2 LlnLarlysrlGdyeeAielyeqsLalt 29 
                                        L+n+a +y  l++yeeA+ +  + Lal+
  gene2410|gene2410|rna2410|rna2410  80 LNNIALTYILLRNYEEALIYTNRFLALD 107
                                        89***************98766666655 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.7   0.00018      0.28       1      25 [.      46      70 ..      46      87 .. 0.88
   2 ?   -3.8   0.0       7.3   1.1e+04      16      21 ..      92      97 ..      90      97 .. 0.53

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00018
                             TPR_11  1 GdayyeqGkyeeAieaYkkAlkldP 25
                                       G+a y   +y +A+e+Y+ Al ++ 
  gene2410|gene2410|rna2410|rna2410 46 GNAHYRNKEYAKALEKYNLALSYTR 70
                                       9*******************99865 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 7.3
                             TPR_11 16 aYkkAl 21
                                       +Y++Al
  gene2410|gene2410|rna2410|rna2410 92 NYEEAL 97
                                       555554 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   4.6    0.0062       9.3      31      76 ..      47      97 ..      20     103 .. 0.77
   2 ?   -3.0   0.0       6.2   9.2e+03      14      47 ..     280     313 ..     278     316 .. 0.63
   3 ?    8.4   0.6    0.0017       2.5      32      80 ..     391     437 ..     354     439 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0062
                                       HHHHHTT-HHHHHH.......HHHCTSHHHC-HHHHHHHHHHHHHTT-HHHHH CS
                             ANAPC3 31 lclylngqykrAye.......llrkaklnskslgcrylfAqcllkLkkyeeAi 76
                                        ++y+n++y +A+e       ++r++  ++++l+++  +A +++ L +yeeA+
  gene2410|gene2410|rna2410|rna2410 47 NAHYRNKEYAKALEkynlalsYTRTC--DEEHLNILNNIALTYILLRNYEEAL 97
                                       56777777666655222100055555..99**********************8 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 6.2
                                        HHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHH CS
                             ANAPC3  14 rllaaetespedayllAlclylngqykrAyellr 47 
                                        +++a++  ++  ++ +A    l g+ +rA+ l++
  gene2410|gene2410|rna2410|rna2410 280 KIYASKETNSLTLFVKASIEHLKGNNERALSLIK 313
                                        5555555555556666777777777778877776 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.0017
                                        HHHHTT-HHHHHHHHHCTSHHHC-HHHHHHHHHHHHHTT-HHHHHHHH- CS
                             ANAPC3  32 clylngqykrAyellrkaklnskslgcrylfAqcllkLkkyeeAiaaLe 80 
                                         l +n++y+rA ++l+++  + ++++   l+ + ++ +kky++  a+++
  gene2410|gene2410|rna2410|rna2410 391 DLIHNKEYNRAEKVLKSL--KMETIALMSLACEFYFLIKKYDDVPALID 437
                                        5789**************..666665555555666666***99766665 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.2      0.61   9.1e+02       9      23 ..      46      60 ..      46      70 .. 0.87
   2 ?    9.3   0.5   0.00068         1       2      22 ..      77      97 ..      76      99 .. 0.92
   3 ?   -3.1   0.0       5.7   8.5e+03       8      18 ..     486     496 ..     484     497 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.61
                             TPR_10  9 analrqrgrydeAea 23
                                       +na+++ ++y++A++
  gene2410|gene2410|rna2410|rna2410 46 GNAHYRNKEYAKALE 60
                                       799999999999986 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00068
                             TPR_10  2 AsslnNLanalrqrgrydeAe 22
                                       +++lnN+a ++  +++y+eA+
  gene2410|gene2410|rna2410|rna2410 77 LNILNNIALTYILLRNYEEAL 97
                                       689*****************8 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 5.7
                             TPR_10   8 Lanalrqrgry 18 
                                        L+n+l +r++ 
  gene2410|gene2410|rna2410|rna2410 486 LGNYLMKRNDK 496
                                        99***999986 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.1       0.2   3.1e+02       7      24 ..      46      63 ..      45      68 .. 0.83
   2 ?    3.4   0.1     0.097   1.4e+02       5      27 ..      82     104 ..      82     107 .. 0.89
   3 ?    0.0   0.1       1.2   1.7e+03       3      32 ..     354     382 ..     353     382 .. 0.77
   4 ?   -2.5   0.0       7.6   1.1e+04      22      26 ..     501     505 ..     489     522 .. 0.54
   5 ?   -1.9   0.0       4.8   7.2e+03      26      32 ..     531     537 ..     529     537 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.2
                                       HHHHHHHHHHHHHHHHHH CS
                              TPR_6  7 alsyrklgdtdkAleale 24
                                       + ++++ ++++kAle ++
  gene2410|gene2410|rna2410|rna2410 46 GNAHYRNKEYAKALEKYN 63
                                       67899988******9997 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.097
                                        HHHHHHHHHHHHHHHHHHHHHHH CS
                              TPR_6   5 klalsyrklgdtdkAlealerli 27 
                                        ++al y+ l ++++Al + +r++
  gene2410|gene2410|rna2410|rna2410  82 NIALTYILLRNYEEALIYTNRFL 104
                                        589*****99******9999987 PP

  == domain 3  score: 0.0 bits;  conditional E-value: 1.2
                                        HHHHHHHHHHHHHHHHHHHHHHHHHHH-TT CS
                              TPR_6   3 lyklalsyrklgdtdkAlealerlikeYPd 32 
                                        l+++ l y+kl +  + l+ l++ +++YP+
  gene2410|gene2410|rna2410|rna2410 354 LFYAMLIYLKL-NDMNYLTCLDKGLQSYPN 382
                                        89999999999.555677777777777876 PP

  == domain 4  score: -2.5 bits;  conditional E-value: 7.6
                                        HHHHH CS
                              TPR_6  22 alerl 26 
                                        ++e  
  gene2410|gene2410|rna2410|rna2410 501 YFEMA 505
                                        44443 PP

  == domain 5  score: -1.9 bits;  conditional E-value: 4.8
                                        HHHH-TT CS
                              TPR_6  26 likeYPd 32 
                                        ++keYPd
  gene2410|gene2410|rna2410|rna2410 531 CVKEYPD 537
                                        79****8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (540 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1016  (0.056668); expected 358.6 (0.02)
Passed bias filter:                      507  (0.0282782); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.65u 0.26s 00:00:00.91 Elapsed: 00:00:00.48
# Mc/sec: 3374.92
//
Query:       gene2411|gene2411|rna2411|rna2411  [L=121]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       483  (0.0269396); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 828.59
//
Query:       gene2412|gene2412|rna2412|rna2412  [L=606]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (606 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1468  (0.0818785); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.44
# Mc/sec: 4097.02
//
Query:       gene2413|gene2413|rna2413|rna2413  [L=246]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.9e-31  107.4   1.1    7.2e-31  106.1   1.1    1.7  1  KH_8      Krr1 KH1 domain
    1.7e-05   24.5   0.4     0.0064   16.3   0.0    2.4  2  KH_1      KH domain
  ------ inclusion threshold ------
      0.055   13.4   0.8       0.39   10.6   0.0    2.5  3  KH_4      KH domain


Domain annotation for each model (and alignments):
>> KH_8  Krr1 KH1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.1   1.1   1.2e-34   7.2e-31       1      81 []      16      96 ..      16      96 .. 0.99

  Alignments for each domain:
  == domain 1  score: 106.1 bits;  conditional E-value: 1.2e-34
                               KH_8  1 SsfevlfpkyrekylkeveekikklleekklklevdlkerslkvsTtekTrDPyiilkardlikLisrgvpleeakkv 78
                                       S+fe++++ + e+ lke+++ ik+ll+ek+++++++++er++++sTt+kTrDPy+i+k++d+i+L+++gvpl+ea+++
  gene2413|gene2413|rna2413|rna2413 16 SRFEIVYARHLESTLKENQKRIKALLKEKNVRIKINYDERVVQMSTTSKTRDPYVIIKSKDFITLVCKGVPLQEAERI 93
                                       89**************************************************************************** PP

                               KH_8 79 leD 81
                                       ++D
  gene2413|gene2413|rna2413|rna2413 94 FDD 96
                                       **9 PP

>> KH_1  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.1   0.3    0.0016       9.8      20      51 ..      35      60 ..      32      67 .. 0.78
   2 !   16.3   0.0   1.1e-06    0.0064      12      62 ..     120     162 ..     111     166 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0016
                                       HHHHHHHHHHT-EEEEESSTT...T.-EEEEE CS
                               KH_1 20 snIkeIreetgakIkvpksedegsderevtis 51
                                       ++Ik + +e++++Ik+  +     der+v++s
  gene2413|gene2413|rna2413|rna2413 35 KRIKALLKEKNVRIKI--NY----DERVVQMS 60
                                       78******99*****6..44....46888775 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 1.1e-06
                                        HHHHTGGGHHHHHHHHHHT-EEEEESSTT...T.-EEEEEESHHHHHHHHH CS
                               KH_1  12 griIGkgGsnIkeIreetgakIkvpksedegsderevtisGspeavekAke 62 
                                         r+IG++G ++k ++  t+++I  +  +      + v ++Gs ++v k ++
  gene2413|gene2413|rna2413|rna2413 120 NRLIGPNGDTLKALEMLTKTYIL-M-KS------KCVCVIGSFANVLKVEQ 162
                                        69**************9*****9.5.33......46777799999988876 PP

>> KH_4  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.1      0.13   7.6e+02       8      30 ..      37      58 ..      28      72 .. 0.67
   2 ?   10.6   0.0   6.6e-05      0.39      42      66 ..     121     145 ..     117     151 .. 0.85
   3 ?   -2.7   0.0      0.95   5.7e+03       6      19 ..     175     187 ..     174     196 .. 0.60

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.13
                               KH_4  8 lkalvddpeevevteeeeeeeve 30
                                       +kal+ ++++v+++++++e+ v+
  gene2413|gene2413|rna2413|rna2413 37 IKALL-KEKNVRIKINYDERVVQ 58
                                       45666.46677777776665555 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 6.6e-05
                               KH_4  42 rvIGkrGrtldAlqylvsaaankeg 66 
                                        r+IG +G tl+Al  l++ ++  ++
  gene2413|gene2413|rna2413|rna2413 121 RLIGPNGDTLKALEMLTKTYILMKS 145
                                        89***************99875555 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 0.95
                               KH_4   6 dilkalvddpeeve 19 
                                        ++lk+lv + +eve
  gene2413|gene2413|rna2413|rna2413 175 HLLKQLVAK-KEVE 187
                                        578888854.4444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1321  (0.0736795); expected 358.6 (0.02)
Passed bias filter:                      514  (0.0286686); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1688.99
//
Query:       gene2414|gene2414|rna2414|rna2414  [L=330]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.9e-46  157.6   0.2    3.2e-45  154.6   0.2    2.0  1  Septin    Septin


Domain annotation for each model (and alignments):
>> Septin  Septin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  154.6   0.2   1.8e-49   3.2e-45       1     278 [.      37     283 ..      37     286 .. 0.88

  Alignments for each domain:
  == domain 1  score: 154.6 bits;  conditional E-value: 1.8e-49
                                        XEEEEEEEEEEBTTSSCCCCCCTTSSSS------------------S-EEEEEEEEETTCEEEEEEEE---BSSSS CS
                             Septin   1 kgieftlmvvGesglGkttlintlfetdlieeekleeasekkkktveikkkkvvieedgvklnltviDtpgfGdav 76 
                                        kg++++++v G+ g G  tlin lf + + +++          +   ++++ +++ e+gv ln+ +  t     ++
  gene2414|gene2414|rna2414|rna2414  37 KGFSLNILVLGRRGSGTRTLINNLFLSPILSND----------RPDGLTTTCAQVTENGVCLNVRIS-TC---HEL 98 
                                        79**************************99885..........233567788999*********975.44...356 PP

                                        SHHCCCHHHHHHHHHHHHHHHHHCTSS--SS-----EEEEEEEE-TTSSSS-HHHHHHHHHHTTTS-EEEEESSGG CS
                             Septin  77 dnskswepiveyideqfeeylreesklkRkkivDkRvHaclyfisPtghglkpldvelmkklsekvnliPviaKaD 152
                                        d +++    +++i++   +y+++++ l  + + D RvH+cl+   Pt   l p +++lmk++ e  nliPvi+KaD
  gene2414|gene2414|rna2414|rna2414  99 DEDNT----IKFIKSTNFNYFEAQEGLM-EDTGDLRVHVCLFV-LPTD-TLLPGELKLMKRIGEYTNLIPVIGKAD 167
                                        66554....789999999***9999887.6789********65.5876.67899********************** PP

                                        GS-HHHHHHHHHHHHHHHHHTT--------SSSS-SCCHHHHHHHHHHC-SEEB-SSSSEEEESSSEEEEEEETTE CS
                             Septin 153 tltkeElkefKkkireeleeeeikiyklpdeeededeeakelseklkeslPfaivgsneliekkgkkvrgRkypWG 228
                                        t +++El   K ki+e l+e+++k++  p+e + e         + +++lP a+ +s++l++ +g++ rgR y+WG
  gene2414|gene2414|rna2414|rna2414 168 TYMQDELADRKAKITELLRENDVKMFV-PEELDGE---------NSTATLPMAVTASESLFKINGQTKRGRLYKWG 233
                                        **************************9.4333333.........34689*************************** PP

                                        EEETT-TTT-SCCHHHHHHHHHCHHHHHHHHHHTHHHHHHHHHH-XXXXX CS
                             Septin 229 vvevenekhsdFlkLrklllkthledLkevteellYetyRseklsklkek 278
                                         v+v++++ +dFl Lrk+l+ thle++k + e+++Ye++R e+l+ ++++
  gene2414|gene2414|rna2414|rna2414 234 FVDVNDTTCNDFLYLRKMLIGTHLEEIKRSFETNFYEEFRIEQLRMEEKR 283
                                        ********************************************988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (330 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       836  (0.0466284); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.38
# Mc/sec: 2582.92
//
Query:       gene2415|gene2415|rna2415|rna2415  [L=40]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (40 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       310  (0.0172904); expected 358.6 (0.02)
Passed bias filter:                      172  (0.0095934); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.25s 00:00:00.59 Elapsed: 00:00:00.42
# Mc/sec: 289.13
//
Query:       gene2416|gene2416|rna2416|rna2416  [L=310]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.4e-16   59.1   0.1    7.2e-16   58.5   0.1    1.3  1  rve             Integrase core domain
    1.2e-13   50.9   0.6    4.3e-13   49.1   0.5    2.0  2  Integrase_H2C2  Integrase zinc binding domain
    3.3e-06   27.2   2.8    4.4e-06   26.8   0.6    2.5  3  zf-H2C2         H2C2 zinc finger
  ------ inclusion threshold ------
      0.018   14.8   0.1      0.071   12.9   0.1    2.1  2  rve_3           Integrase core domain
      0.079   12.7   3.7       0.13   12.1   3.7    1.3  1  XRN1_D1         Exoribonuclease Xrn1 D1 domain


Domain annotation for each model (and alignments):
>> rve  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.5   0.1     2e-19   7.2e-16       2     117 ..      79     185 ..      78     187 .. 0.96

  Alignments for each domain:
  == domain 1  score: 58.5 bits;  conditional E-value: 2e-19
                                rve   2 trpgelwqvDvtvvripdgggkayllvvvddfsrlilaealsdemdastvlalleravarfggvepervlsDngse 77 
                                        trp e++ +D+++++      +  + +++d fsr i++  + ++  ++t+++ +++ v+  g   pe++++Dn +e
  gene2416|gene2416|rna2416|rna2416  79 TRPLEKVAIDIVKIK------EETVMIAIDYFSRIIWVRDVGNR-RKETIIEKMNELVEEWGV--PEMIITDNTKE 145
                                        7999********999......357********************.***************999..*********** PP

                                rve  78 ytskafrefladlgirvsftrpgrpqdnGkvErfhrtlkd 117
                                        +++ +++++  + +i ++ t + + ++nG+vEr +rt+++
  gene2416|gene2416|rna2416|rna2416 146 FVAIETKNWMTEARIIHEKTSVESHKSNGRVERVIRTVRE 185
                                        *************************************997 PP

>> Integrase_H2C2  Integrase zinc binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.1   0.5   1.2e-16   4.3e-13       3      57 ..      13      67 ..      11      68 .. 0.95
   2 ?   -2.1   0.0       1.2   4.4e+03      13      25 ..     202     217 ..     195     223 .. 0.67

  Alignments for each domain:
  == domain 1  score: 49.1 bits;  conditional E-value: 1.2e-16
                     Integrase_H2C2  3 kslrkeilkeaHdsagHlGiektlerlrrryyWpgmrkdvkkyvksCetCqrrkp 57
                                       k+ +++++ eaH +a   G e t+  l++ry+W gm++++ +++k+CetCq++++
  gene2416|gene2416|rna2416|rna2416 13 KENTEKLIIEAHLKANYRGLEPTYYELKERYHWLGMKRHITEIIKRCETCQQNNR 67
                                       677899***********************************************97 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.2
                     Integrase_H2C2  13 aHds...agHlGiekt 25 
                                        + d    + H+Gi+ t
  gene2416|gene2416|rna2416|rna2416 202 VEDRynkTYHAGIKCT 217
                                        4444555689998877 PP

>> zf-H2C2  H2C2 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8   0.6   1.2e-09   4.4e-06      15      39 .]      39      63 ..      35      63 .. 0.95
   2 ?   -3.0   0.0       2.5   8.9e+03       8      17 ..     122     131 ..     122     131 .. 0.86
   3 ?   -3.7   0.0       4.3   1.5e+04       3       9 ..     209     215 ..     208     216 .. 0.72

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 1.2e-09
                            zf-H2C2 15 larkYhwlgiketvseVissCkaCq 39
                                       l+++Yhwlg k+++ e+i++C +Cq
  gene2416|gene2416|rna2416|rna2416 39 LKERYHWLGMKRHITEIIKRCETCQ 63
                                       7899********************9 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 2.5
                            zf-H2C2   8 inkltallar 17 
                                        i+k+ +l+++
  gene2416|gene2416|rna2416|rna2416 122 IEKMNELVEE 131
                                        68*****986 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 4.3
                            zf-H2C2   3 ltHlGin 9  
                                        + H+Gi+
  gene2416|gene2416|rna2416|rna2416 209 TYHAGIK 215
                                        5599986 PP

>> rve_3  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       1.8   6.6e+03      14      28 ..     117     131 ..     112     142 .. 0.65
   2 ?   12.9   0.1     2e-05     0.071       7      55 ..     164     208 ..     158     210 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 1.8
                              rve_3  14 qqNglvEsfngtlrd 28 
                                         +   +E +n+ + +
  gene2416|gene2416|rna2416|rna2416 117 RKETIIEKMNELVEE 131
                                        455566666665544 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 2e-05
                              rve_3   7 yiapgkPqqNglvEsfngtlrdellneelfrslaearekleawredYNt 55 
                                         + + + + Ng vE++++t+r+ + ++el     e  +++++  ++YN+
  gene2416|gene2416|rna2416|rna2416 164 KTSVESHKSNGRVERVIRTVREAIEKMELN----EMGKAIKEVEDRYNK 208
                                        566777789*************99887665....999999999999996 PP

>> XRN1_D1  Exoribonuclease Xrn1 D1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   3.7   3.5e-05      0.13      78     183 ..     156     263 ..     147     277 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.5e-05
                                        EEEEEEEEE-SS-EEEEE-..SSSEEEEEE--THHHHHHHHHHHHHHHHHHHHHH..-EEES--S-EEEEEEEEEE CS
                            XRN1_D1  78 rEakvvavsdelfkyekelleekkkkvvsrphsekekkefkkkaerierkyskrl..gviigevevlvhveplkGL 151
                                         Ea++++ + +  +++++   e+  ++v++  ++ e +e  k  +++e++y+k++  g++    e+   ++ +  +
  gene2416|gene2416|rna2416|rna2416 156 TEARIIHEKTSVESHKSNGRVERVIRTVREAIEKMELNEMGKAIKEVEDRYNKTYhaGIKCTPEEAWKDITGIAAV 231
                                        55555555555555554445566667888899999999**************975449999*************** PP

                                        EE-TTS-EEEEE-SS-EE...EEGGG-BS--S CS
                            XRN1_D1 152 krteeGalvKeyeeeeeleteyalqlvveeva 183
                                        ++ ++G + K++++ +  +     q++v + +
  gene2416|gene2416|rna2416|rna2416 232 ENSKDGRYNKQFKKRKREKFAEGQQVIVAQKE 263
                                        *************99999999999**997643 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (310 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1426  (0.0795359); expected 358.6 (0.02)
Passed bias filter:                      614  (0.0342462); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 2126.96
//
Query:       gene2417|gene2417|rna2417|rna2417  [L=45]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    7.6e-06   26.2   0.0    7.6e-06   26.2   0.0    1.0  1  RT_RNaseH  RNase H-like domain found in reverse transcriptase


Domain annotation for each model (and alignments):
>> RT_RNaseH  RNase H-like domain found in reverse transcriptase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.0   4.2e-10   7.6e-06      54      90 ..       1      37 [.       1      45 [] 0.86

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 4.2e-10
                                       HHHHHHHHHHHHHHHTS--EEEE-SS--TTTTT---- CS
                          RT_RNaseH 54 llAivaalkkfrhylqgrkftvitDhknlkyllskks 90
                                       +lA+ + ++kf + l+ rk ++itDhk+l+ + +k +
  gene2417|gene2417|rna2417|rna2417  1 MLAVKWEIQKFSYELKARKSHLITDHKALEVIRNKPE 37
                                       69******************************97665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (45 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       295  (0.0164538); expected 358.6 (0.02)
Passed bias filter:                      221  (0.0123264); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.29s 00:00:00.70 Elapsed: 00:00:00.47
# Mc/sec: 290.26
//
Query:       gene2418|gene2418|rna2418|rna2418  [L=111]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    7.8e-14   51.5   0.0    1.1e-13   51.1   0.0    1.2  1  RT_RNaseH_2  RNase H-like domain found in reverse transcripta
    6.9e-05   23.1   0.0     0.0001   22.5   0.0    1.3  1  RT_RNaseH    RNase H-like domain found in reverse transcripta


Domain annotation for each model (and alignments):
>> RT_RNaseH_2  RNase H-like domain found in reverse transcriptase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.1   0.0   1.2e-17   1.1e-13       1      54 [.      53     106 ..      53     111 .] 0.95

  Alignments for each domain:
  == domain 1  score: 51.1 bits;  conditional E-value: 1.2e-17
                        RT_RNaseH_2   1 WteeqekafeklkealtsapvLahpdpdkpfiletDaSdtgigavLsqedddgk 54 
                                        W+e+ ++af +lk +l++a  L++ +++k+f+l+tDaS+tg+ avL+qed++gk
  gene2418|gene2418|rna2418|rna2418  53 WNEDMTEAFAELKLRLINARNLKLAEFEKKFTLKTDASNTGLVAVLLQEDKNGK 106
                                        ***************************************************887 PP

>> RT_RNaseH  RNase H-like domain found in reverse transcriptase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.0   1.2e-08    0.0001       2      29 ..      79     106 ..      78     111 .] 0.89

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 1.2e-08
                                        TTS-EEEEEEECTEEEEEEEEEETTE.. CS
                          RT_RNaseH   2 pskpfiletDAsddgigavLsqreedge 29 
                                        ++k+f+l+tDAs++g+ avL q++++g+
  gene2418|gene2418|rna2418|rna2418  79 FEKKFTLKTDASNTGLVAVLLQEDKNGK 106
                                        89********************998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (111 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       421  (0.0234815); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.45
# Mc/sec: 738.29
//
Query:       gene2419|gene2419|rna2419|rna2419  [L=72]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.1e-10   39.2   0.3    5.7e-10   39.1   0.3    1.0  1  RVT_1     Reverse transcriptase (RNA-dependent DNA polymerase


Domain annotation for each model (and alignments):
>> RVT_1  Reverse transcriptase (RNA-dependent DNA polymerase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.1   0.3   3.2e-14   5.7e-10     141     222 .]       1      70 [.       1      70 [. 0.94

  Alignments for each domain:
  == domain 1  score: 39.1 bits;  conditional E-value: 3.2e-14
                                        HHHHHHHHHHHTT-T......TEEECTTEEEEEESSHHHHHHHHHHHHHHHHHTT--BEGGG-EEE.....ESSEE CS
                              RVT_1 141 llfnlfmnellrelrkrakgvtllrYaDDililskskeelqelleaveewlkesglkinpeKtklvlftvkseevk 216
                                        ++f++++n++l +l      + l  Y+DDi+i++k+    ++l+++v ++l++++lk+n++K++ +     ++evk
  gene2419|gene2419|rna2419|rna2419   1 VIFQRVINQVLDRLIG----NGLESYMDDIIIHFKK---YDALVREVIKRLSRNKLKVNMKKVEYA-----RQEVK 64 
                                        59*************8....7*************99...667899*********************.....9**** PP

                                        ETTEEE CS
                              RVT_1 217 yLGvtl 222
                                         LGvt+
  gene2419|gene2419|rna2419|rna2419  65 LLGVTI 70 
                                        ****97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (72 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       970  (0.0541023); expected 358.6 (0.02)
Passed bias filter:                      584  (0.0325729); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 502.99
//
Query:       gene242|gene242|rna242|rna242  [L=838]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.1e-20   72.7   0.0    7.8e-20   71.4   0.0    1.7  1  DEAD             DEAD/DEAH box helicase
      6e-18   65.2   0.8    2.1e-15   57.0   0.0    3.2  3  Helicase_C       Helicase conserved C-terminal domain
    4.4e-14   52.9   6.4    4.4e-14   52.9   6.4    2.1  2  RecQ_Zn_bind     RecQ zinc-binding
    5.9e-12   45.4   0.0    1.2e-11   44.4   0.0    1.5  1  RQC              RQC domain
    2.3e-08   34.2   0.2    1.8e-07   31.4   0.0    2.2  2  ResIII           Type III restriction enzyme, res subunit
  ------ inclusion threshold ------
      0.063   13.5   0.6        5.4    7.3   0.1    3.3  3  SpmSyn_N         S-adenosylmethionine decarboxylase N -termin
      0.094   12.6   4.2       0.18   11.6   4.2    1.4  1  EspA             EspA-like secreted protein


Domain annotation for each model (and alignments):
>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.4   0.0   3.1e-23   7.8e-20       2     174 ..     345     513 ..     344     515 .. 0.81

  Alignments for each domain:
  == domain 1  score: 71.4 bits;  conditional E-value: 3.1e-23
                                    HHHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD   2 diQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvlli 81 
                                    + Q+e+i+++l+++dv+v ++TG GK+l++++p++         t++ +++++P+ +L+e+++++l ++    +l++++ 
  gene242|gene242|rna242|rna242 345 PNQEEIINAVLDEKDVFVLMPTGGGKSLCYFLPAV--------LTHNLTVVISPLLSLIEDQIQELLRLNIA-SLTLNSA 415
                                    78*********************************........57789******************999994.5666666 PP

                                    ETTSSHHHHHHHH.........HTTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHT..TTHHHHHHHHHHSH CS
                                    xxxxxxxxxxxxx.........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxx RF
                           DEAD  82 iggvaardqlskl.........dngvdivvgtpgrlddllstgklnlsqvrflVlDEadrlldq..gfsdfinrilnqlp 150
                                    ++  ++    ++l         +++++i++ tp+ l++    +++   ++  +V+DEa++++++  +f++++++ l+ ++
  gene242|gene242|rna242|rna242 416 MSARERGVVFRALregvrvgtaHKRIKILFLTPETLMQSDALQRMLKGNLARVVIDEAHCVSQWgnDFRPDYKK-LRMVK 494
                                    6655555555555444455554466************955445555789999************999******9.66664 PP

                                    HHCTTSTTTSEEEEEESSBSHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD 151 qitcdgklqrqvivlSATlpkdvk 174
                                    +         +v++l+AT+++ v+
  gene242|gene242|rna242|rna242 495 DVFG-----CTVMALTATATRRVE 513
                                    3322.....34********98876 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0     0.011        29      14      65 ..     380     431 ..     370     470 .. 0.78
   2 !   57.0   0.0   8.3e-19   2.1e-15      11     110 ..     562     660 ..     542     661 .. 0.85
   3 ?   -2.0   0.0       1.8   4.5e+03      20      65 ..     667     716 ..     663     724 .. 0.50

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.011
                                    TTTSEEEEEESSHHHHHH..HHHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTT CS
                     Helicase_C  14 eeggkilifvntidrlek..vklllekkgikvavlhgelpqnereeileqfnkg 65 
                                      ++ ++++++  + +e+   +ll  + +i +++l++ ++++er  ++++ ++g
  gene242|gene242|rna242|rna242 380 LTHNLTVVISPLLSLIEDqiQELL--RLNIASLTLNSAMSARERGVVFRALREG 431
                                    556667777777776665534555..668*******************999976 PP

  == domain 2  score: 57.0 bits;  conditional E-value: 8.3e-19
                                    HHTTTTSEEEEEESSHHHHHHHHHHHHHT.TSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSSTSTTESEEE CS
                     Helicase_C  11 kleeeggkilifvntidrlekvklllekk.gikvavlhgelpqnereeileqfnkgesdvLiatdvaerGidipkvnlVi 89 
                                    ++   ++  +i+v +++++e  ++ ++ + +i+++++h+ l+++er+++ +++  +e++v++at + ++Gi+  +v++Vi
  gene242|gene242|rna242|rna242 562 NTYYPRSPGIIYVISKREAE--EVSHKLNgHITSLYYHAGLTKKERNAVQRKWSTDEVRVIVATVAFGMGINKRNVRYVI 639
                                    55556666788888888887..444333448************************************************* PP

                                    ESSSSSSHHHHHHHHTTSSST CS
                     Helicase_C  90 nfdlprnvtsyiqriGRtgRa 110
                                    + ++p+++++y q  GR+gR 
  gene242|gene242|rna242|rna242 640 HHSMPYSLENYYQETGRAGRD 660
                                    ********************6 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 1.8
                                    EEEESSHH..HHHHHHHHHHHT.....TSTEEEESTTSTHHHHHHHHHHHHTT CS
                     Helicase_C  20 lifvntid..rlekvklllekk.....gikvavlhgelpqnereeileqfnkg 65 
                                    ++f  + d  rl+  +ll +++       +v+ +  + +   r+ il+ fn+ 
  gene242|gene242|rna242|rna242 667 ILFYSYADknRLN--NLL-KRQverdnLSRVVQYCENVTECRRKLILQYFNER 716
                                    5555555544443..333.1112332245555555556666666666666654 PP

>> RecQ_Zn_bind  RecQ zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -5.0   1.9         7   1.8e+04      58      63 ..     228     234 ..     202     246 .. 0.56
   2 !   52.9   6.4   1.7e-17   4.4e-14       2      66 .]     673     728 ..     672     728 .. 0.92

  Alignments for each domain:
  == domain 1  score: -5.0 bits;  conditional E-value: 7
                   RecQ_Zn_bind  58 eCgn.CD 63 
                                    +C n CD
  gene242|gene242|rna242|rna242 228 DCSNdCD 234
                                    4433344 PP

  == domain 2  score: 52.9 bits;  conditional E-value: 1.7e-17
                   RecQ_Zn_bind   2 qDvsrlrrlieqseesekekeaelekleamlaycentteCrrkllleyFgeeaaeeeCgnCDnCl 66 
                                    +D +rl++l+        ++++e+++l+++++ycen teCrrkl+l+yF+e+ +++ C  CDnC+
  gene242|gene242|rna242|rna242 673 ADKNRLNNLL--------KRQVERDNLSRVVQYCENVTECRRKLILQYFNERLTDS-CTGCDNCQ 728
                                    7888888998........6999*****************************98888.*******5 PP

>> RQC  RQC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.4   0.0   4.6e-15   1.2e-11       3      87 ..     734     817 ..     732     834 .. 0.87

  Alignments for each domain:
  == domain 1  score: 44.4 bits;  conditional E-value: 4.6e-15
                                    -EEE-HHHHHHHHHHHHHTTS-SBHHHHHHHHHT---CCCCCTTGGGSTTTTTTTTS-HHHHHHHHHHHHHTTSEEEE.. CS
                            RQC   3 etvDvteeaqkilscvyrtgqrfgaghivdvLrGsktkkirqlghdklstfGigkdlskkewrrlirqLiaegyLeedve 82 
                                     ++D+t++a++i ++v++  +r+ ++hiv+vLrGs++k +  +      ++G+++d+ ++ ++r++r ++ +g+L+e + 
  gene242|gene242|rna242|rna242 734 VQRDCTQCARAIARVVHEH-ERLSLTHIVNVLRGSRSKAVCAY--AGSACYGVLRDVRRSLLERVVRVMVGQGMLKEVHV 810
                                    689***************9.9********************98..9*****************************55544 PP

                                    ..SSSBE CS
                            RQC  83 ..eygvl 87 
                                      ++g++
  gene242|gene242|rna242|rna242 811 knRMGYV 817
                                    3633344 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.8      0.43   1.1e+03      43     118 ..      11     104 ..       9     144 .. 0.57
   2 !   31.4   0.0   6.9e-11   1.8e-07       3     169 ..     342     508 ..     340     510 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.43
                                    HHHHHH-S.....-E.EEEESSHHHHHHHH..HHGGGGTGG................GEEEESSS-B--........... CS
                         ResIII  43 klierllkkgkeekf.lflvprkslleqtl..eefkkflseayke............igkkvsgdkkka..........k 97 
                                    ++i ++ +k++  ++  ++ ++ +++eq +  ++++++ +e++ +            +       ++ +          +
  gene242|gene242|rna242|rna242  11 AAITEYNSKHSSTNVqHVISDSSDIIEQFIdsSDVRQYVNECDGRvnngkvnnfivsN-------GRVSdgrvnntninN 83 
                                    5677777777777662467788999999996666777777775444333322222211.......111122222223333 PP

                                    ......-SEEEEEHHHHHHTH CS
                         ResIII  98 ekdstnkkilvttiqsldads 118
                                     +d+ n ++  t+i+ ++++ 
  gene242|gene242|rna242|rna242  84 VNDNVNGRVSNTNINNVNNNV 104
                                    444444555555555555444 PP

  == domain 2  score: 31.4 bits;  conditional E-value: 6.9e-11
                                    EE-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG.. CS
                         ResIII   3 elreyQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkflseay 82 
                                    ++r+ Qee+i+++l      ++k +++ m+TG GK+l+++  +   ++      ++++ p +sl+e  ++e+ ++     
  gene242|gene242|rna242|rna242 342 SFRPNQEEIINAVL------DEKDVFVLMPTGGGKSLCYFLPAVLTHN-----LTVVISPLLSLIEDQIQELLRLNIASL 410
                                    589**********8......7899***************998888888.....69**************99966666654 PP

                                    ..GEEEESSS-B--.................-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS...... CS
                         ResIII  83 keigkkvsgdkkka..........kekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgak..... 147
                                    +  +  +s +++               + + +kil+ t ++l ++      + +++l+++   ++iDEaH +++      
  gene242|gene242|rna242|rna242 411 T-LNSAMSARERGVvfralregvrVGTAHKRIKILFLTPETLMQSD-----ALQRMLKGNLARVVIDEAHCVSQWgndfr 484
                                    3.333333333333445555566556677889**************.....9999999************9999777666 PP

                                    ...TTTHHHHHT---SEEEEEESS- CS
                         ResIII 148 ...kswreilekfkeavllglTATp 169
                                       k+ r +++ f  +++++lTAT 
  gene242|gene242|rna242|rna242 485 pdyKKLRMVKDVFG-CTVMALTATA 508
                                    55557777788887.999*****96 PP

>> SpmSyn_N  S-adenosylmethionine decarboxylase N -terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.1    0.0021       5.4      24      89 ..      57     121 ..      40     128 .. 0.86
   2 ?   -0.3   0.0      0.47   1.2e+03      65      85 ..     388     408 ..     381     414 .. 0.85
   3 ?    1.6   0.0      0.13   3.2e+02       6      31 ..     795     820 ..     790     825 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0021
                       SpmSyn_N  24 dhGylatyigkngsfaslriyphGlvlldlqsyeedekaqevdkllnkveerlkellegsikrvkr 89 
                                    ++G +  +i  ng+++  r+    +  ++   +++  ++++++++ n+v++++ ++++ +i+ +k+
  gene242|gene242|rna242|rna242  57 NNGKVNNFIVSNGRVSDGRVNNTNINNVN-DNVNGRVSNTNINNVNNNVNNKITNIVNPTITNTKQ 121
                                    56888899999999999999999999887.56778888889*******************999986 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.47
                       SpmSyn_N  65 vdkllnkveerlkellegsik 85 
                                    +  ll+ +e++++ell+ +i+
  gene242|gene242|rna242|rna242 388 ISPLLSLIEDQIQELLRLNIA 408
                                    6789************99987 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.13
                       SpmSyn_N   6 lqsifqeqemtetvhswedhGylaty 31 
                                    +  ++  q+m + vh  +  Gy+  y
  gene242|gene242|rna242|rna242 795 VVRVMVGQGMLKEVHVKNRMGYVNVY 820
                                    5567788***************9988 PP

>> EspA  EspA-like secreted protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   4.2   7.1e-05      0.18      64     135 ..      17      86 ..      11     107 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 7.1e-05
                           EspA  64 daqekaNemdaviAdltkddpkskeelppdVieYlrengIlvenktiddylkkngqvGegkldkgdLtavka 135
                                    +++  + ++++vi d +  d  ++   + dV +Y+ e +  v+n ++++++ +ng+v +g+++ ++++ v  
  gene242|gene242|rna242|rna242  17 NSKHSSTNVQHVISDSS--DIIEQFIDSSDVRQYVNECDGRVNNGKVNNFIVSNGRVSDGRVNNTNINNVND 86 
                                    67888889999999999..8777777799***********************************99998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (838 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1407  (0.0784762); expected 358.6 (0.02)
Passed bias filter:                      510  (0.0284455); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.73u 0.28s 00:00:01.01 Elapsed: 00:00:00.46
# Mc/sec: 5458.00
//
Query:       gene2420|gene2420|rna2420|rna2420  [L=46]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
     0.0014   18.2   0.0     0.0014   18.2   0.0    1.0  1  RVT_1       Reverse transcriptase (RNA-dependent DNA polymera
  ------ inclusion threshold ------
      0.021   14.2   0.0      0.021   14.2   0.0    1.0  1  RE_NgoFVII  NgoFVII restriction endonuclease


Domain annotation for each model (and alignments):
>> RVT_1  Reverse transcriptase (RNA-dependent DNA polymerase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   1.6e-07    0.0014      62     100 ..       5      43 ..       1      46 [] 0.87

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.6e-07
                                        HCCHTS--EEEEEEBCCGCCCSBB-GGGGGGG-EEET.. CS
                              RVT_1  62 lkkkkkaklllklDlkkaFdsvpleellrkltafkvptk 100
                                        ++++ +++ l+ lDlk ++ +++ ee ++ +taf +  +
  gene2420|gene2420|rna2420|rna2420   5 VEATIGSNNLTVLDLKEGYYQIEIEETDKHKTAFEFGNN 43 
                                        5567889999************************99865 PP

>> RE_NgoFVII  NgoFVII restriction endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   2.3e-06     0.021      92     128 ..       3      37 ..       1      46 [] 0.76

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.3e-06
                                        TEEEEEEESXXSXXTTSXXXSBXEEEEEE.HHHHHHH CS
                         RE_NgoFVII  92 kplsAliGSANlssnglrtrqrEtlvdldtedafkel 128
                                        ++++A iGS+Nl+++ l++ ++ + ++  + d+ k+ 
  gene2420|gene2420|rna2420|rna2420   3 RIVEATIGSNNLTVLDLKEGYYQIEIE--ETDKHKTA 37 
                                        689******************998777..34444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (46 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       492  (0.0274416); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.31u 0.27s 00:00:00.58 Elapsed: 00:00:00.39
# Mc/sec: 355.59
//
Query:       gene2421|gene2421|rna2421|rna2421  [L=107]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1797  (0.100229); expected 358.6 (0.02)
Passed bias filter:                      471  (0.0262703); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 770.00
//
Query:       gene2422|gene2422|rna2422|rna2422  [L=51]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (51 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       195  (0.0108762); expected 358.6 (0.02)
Passed bias filter:                      125  (0.00697194); expected 358.6 (0.02)
Passed Vit filter:                         4  (0.000223102); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.43
# Mc/sec: 353.20
//
Query:       gene2423|gene2423|rna2423|rna2423  [L=224]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.5e-26   90.5  40.5    1.7e-08   34.6   8.0    5.2  5  LRR_4     Leucine Rich repeats (2 copies)
    1.4e-23   82.4  50.7    3.3e-08   33.2   4.8    5.7  6  LRR_8     Leucine rich repeat
    1.6e-10   40.8  15.5    5.9e-07   29.2   5.3    2.8  3  LRR_9     Leucine-rich repeat
    1.9e-06   27.5  29.2       0.25   11.5   0.1    7.8  9  LRR_6     Leucine Rich repeat
     0.0045   17.3  31.9      0.046   14.3   0.8    7.4  6  LRR_1     Leucine Rich Repeat
  ------ inclusion threshold ------
       0.32   10.7   2.6          7    6.4   0.1    3.4  3  LRR_12    Leucine-rich repeat
        4.9    7.4  15.1        6.3    7.1   4.4    4.3  4  FNIP      FNIP Repeat


Domain annotation for each model (and alignments):
>> LRR_4  Leucine Rich repeats (2 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.3   1.4e-06    0.0035       4      33 ..      26      54 ..      23      54 .. 0.93
   2 !   34.6   8.0   6.8e-12   1.7e-08       1      43 [.      44      85 ..      44      87 .. 0.92
   3 !   20.8   3.9   1.5e-07   0.00039       3      42 ..      89     126 ..      89     128 .. 0.92
   4 !   30.3   2.7   1.5e-10   3.8e-07       2      43 ..     130     170 ..     129     171 .. 0.95
   5 !   18.4   1.1   8.1e-07    0.0021       1      33 [.     173     206 ..     173     215 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.4e-06
                                       -EEE--SS---E-S-HHH-TT--EEE-.-S CS
                              LRR_4  4 evLdLsnNqltdiplleklpnLkeLdLsgN 33
                                       +++ L +N++t+i   + lpn ++LdLs+N
  gene2423|gene2423|rna2423|rna2423 26 QSIILYHNKITSIRMTY-LPNVHSLDLSDN 54
                                       7889***********99.*********999 PP

  == domain 2  score: 34.6 bits;  conditional E-value: 6.8e-12
                                       SS--EEE--SS---E-S-HHH-TT--EEE-.-S-----GGGGX CS
                              LRR_4  1 pnLevLdLsnNqltdiplleklpnLkeLdLsgNnlitdldeLk 43
                                       pn  +LdLs+N +t+i+ le+lpnL++LdL g nl+t++ +L+
  gene2423|gene2423|rna2423|rna2423 44 PNVHSLDLSDNLITTIQDLENLPNLRTLDL-GYNLLTQIQNLS 85
                                       7999**************************.655999998875 PP

  == domain 3  score: 20.8 bits;  conditional E-value: 1.5e-07
                                        --EEE--SS---E-S-HHH-TT--EEE-.-S-----GGGG CS
                              LRR_4   3 LevLdLsnNqltdiplleklpnLkeLdLsgNnlitdldeL 42 
                                        L+ L L  N +  i++l+ +p+Lk LdL  +n+it++++L
  gene2423|gene2423|rna2423|rna2423  89 LTDLFLMCNDIERIENLG-IPSLKNLDL-ACNNITKIENL 126
                                        7889999999********.*********.8889****998 PP

  == domain 4  score: 30.3 bits;  conditional E-value: 1.5e-10
                                        S--EEE--SS---E-S-HHH-TT--EEE-.-S-----GGGGX CS
                              LRR_4   2 nLevLdLsnNqltdiplleklpnLkeLdLsgNnlitdldeLk 43 
                                        nLe+L+L+nN+++++++ e l +L++L+L ++n i+++d Lk
  gene2423|gene2423|rna2423|rna2423 130 NLEELYLGNNRIRTVENVEHLSKLHTLSL-QCNCIQRIDCLK 170
                                        9****************999*********.999*****9885 PP

  == domain 5  score: 18.4 bits;  conditional E-value: 8.1e-07
                                        SS--EEE--SS.---E-S-HHH-TT--EEE-.-S CS
                              LRR_4   1 pnLevLdLsnN.qltdiplleklpnLkeLdLsgN 33 
                                        +nL++L L +N +l+++++le l +L++Ld+s  
  gene2423|gene2423|rna2423|rna2423 173 KNLKYLLLDGNeKLQELENLECLRKLEYLDVSKT 206
                                        79*********99******************876 PP

>> LRR_8  Leucine rich repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       2.6   6.7e+03       6      16 ..       8      18 ..       6      20 .. 0.49
   2 !   33.2   4.8   1.3e-11   3.3e-08       2      61 .]      24      78 ..      23      78 .. 0.92
   3 !   27.1   5.7   9.8e-10   2.5e-06       1      52 [.      44      93 ..      44      99 .. 0.86
   4 !   24.0   1.8   9.4e-09   2.4e-05       1      41 [.     108     145 ..     108     148 .. 0.92
   5 !   27.9   4.6   5.6e-10   1.4e-06       2      59 ..     130     183 ..     129     184 .. 0.95
   6 !   21.1   2.6   7.7e-08    0.0002       1      59 [.     151     206 ..     151     208 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 2.6
                                       EE-TTS--SEE CS
                              LRR_8  6 LdLsnNrltsl 16
                                       L+L  ++l+ +
  gene2423|gene2423|rna2423|rna2423  8 LSLPYSNLKQI 18
                                       44555555544 PP

  == domain 2  score: 33.2 bits;  conditional E-value: 1.3e-11
                                       T-SEEE-TTS--SEE-TTSSTT-TT--EEE--SS---GGGGGGGTT--S-.EEE--SS-- CS
                              LRR_8  2 nLtsLdLsnNrltslddeaFkglsnLkvLdLsnNllttlspgafsgLpsLrsLdLsgNrL 61
                                       +++s++L +N++ts++ +    l+n+ +LdLs+Nl+tt+  + +++Lp+Lr LdL +N L
  gene2423|gene2423|rna2423|rna2423 24 EVQSIILYHNKITSIRMTY---LPNVHSLDLSDNLITTI--QDLENLPNLRTLDLGYNLL 78
                                       57899***********875...779**************..6****************87 PP

  == domain 3  score: 27.1 bits;  conditional E-value: 9.8e-10
                                       TT-SEEE-TTS--SEE-TTSSTT-TT--EEE--SS---GGGGGGGTT--S-. CS
                              LRR_8  1 pnLtsLdLsnNrltslddeaFkglsnLkvLdLsnNllttlspgafsgLpsLr 52
                                       pn++sLdLs+N +t ++d   ++l+nL++LdL++Nllt + + +f  L+ L 
  gene2423|gene2423|rna2423|rna2423 44 PNVHSLDLSDNLITTIQD--LENLPNLRTLDLGYNLLTQIQNLSFLPLTDLF 93
                                       789999999999999999..79999999999999999999888888886664 PP

  == domain 4  score: 24.0 bits;  conditional E-value: 9.4e-09
                                        TT-SEEE-TTS--SEE-TTSSTT-TT--EEE--SS---GGG CS
                              LRR_8   1 pnLtsLdLsnNrltslddeaFkglsnLkvLdLsnNllttls 41 
                                        p+L++LdL +N++t+++  +     nL++L+L+nN+++t++
  gene2423|gene2423|rna2423|rna2423 108 PSLKNLDLACNNITKIENLTCI---NLEELYLGNNRIRTVE 145
                                        78***************99988...8*************97 PP

  == domain 5  score: 27.9 bits;  conditional E-value: 5.6e-10
                                        T-SEEE-TTS--SEE-TTSSTT-TT--EEE--SS---GGGGGGGTT--S-.EEE--SS CS
                              LRR_8   2 nLtsLdLsnNrltslddeaFkglsnLkvLdLsnNllttlspgafsgLpsLrsLdLsgN 59 
                                        nL++L+L nNr+  ++    ++ls+L +L+L +N++++++  ++   ++L++L L+gN
  gene2423|gene2423|rna2423|rna2423 130 NLEELYLGNNRIRTVE--NVEHLSKLHTLSLQCNCIQRID--CLKLPKNLKYLLLDGN 183
                                        8*************97..5799*****************6..***************9 PP

  == domain 6  score: 21.1 bits;  conditional E-value: 7.7e-08
                                        TT-SEEE-TTS--SEE-TTSSTT-TT--EEE--SS.---GGGGGGGTT--S-.EEE--SS CS
                              LRR_8   1 pnLtsLdLsnNrltslddeaFkglsnLkvLdLsnN.llttlspgafsgLpsLrsLdLsgN 59 
                                        ++L++L+L++N ++ +d       +nLk+L L  N +l+ l+   +++L++L++Ld+s +
  gene2423|gene2423|rna2423|rna2423 151 SKLHTLSLQCNCIQRIDCLKLP--KNLKYLLLDGNeKLQELE--NLECLRKLEYLDVSKT 206
                                        589*************866666..9****************6..************9976 PP

>> LRR_9  Leucine-rich repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   2.1   4.7e-05      0.12      65     120 ..      24      73 ..      11      96 .. 0.59
   2 !   24.2   2.5   7.4e-09   1.9e-05      26     103 ..      94     166 ..      88     170 .. 0.84
   3 !   29.2   5.3   2.3e-10   5.9e-07      22     120 ..     111     203 ..     109     216 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 4.7e-05
                              LRR_9  65 rlktlllnnnrivriaegleevlPnleelvltnnelqeladldPlaslkklellsl 120
                                         +++++l  n+i+ i      +lPn+++l l++n ++ + dl+ l +l+ l+   l
  gene2423|gene2423|rna2423|rna2423  24 EVQSIILYHNKITSIRM---TYLPNVHSLDLSDNLITTIQDLENLPNLRTLD---L 73 
                                        35666666666666653...46777777777777777777755555544443...2 PP

  == domain 2  score: 24.2 bits;  conditional E-value: 7.4e-09
                              LRR_9  26 lrgykipvienlGatldqfdtidlsdndirkldgfPllkrlktlllnnnrivriaegleevlPnleelvltnnelq 101
                                        l  + i  ienlG     +  +dl+ n+i k++++  ++ l+ l+l nnri+ + e++ e l +l++l l+ n++q
  gene2423|gene2423|rna2423|rna2423  94 LMCNDIERIENLGIP--SLKNLDLACNNITKIENLTCIN-LEELYLGNNRIRTV-ENV-EHLSKLHTLSLQCNCIQ 164
                                        66788999****964..57789999**********9986.99********9766.566.6799************9 PP

                              LRR_9 102 el 103
                                        ++
  gene2423|gene2423|rna2423|rna2423 165 RI 166
                                        86 PP

  == domain 3  score: 29.2 bits;  conditional E-value: 2.3e-10
                              LRR_9  22 reldlrgykipvienlGatldqfdtidlsdndirkldgfPllkrlktlllnnnrivriaegleevlPnleelvltn 97 
                                        ++ldl  + i+ ienl      ++ + l +n ir ++++ +l +l+tl+l+ n i ri     +   nl+ l+l +
  gene2423|gene2423|rna2423|rna2423 111 KNLDLACNNITKIENLTC--INLEELYLGNNRIRTVENVEHLSKLHTLSLQCNCIQRID--CLKLPKNLKYLLLDG 182
                                        579************955..5789999*******************************5..4455568******99 PP

                              LRR_9  98 ne.lqeladldPlaslkklellsl 120
                                        ne lqel +l+ l +l+ l    +
  gene2423|gene2423|rna2423|rna2423 183 NEkLQELENLECLRKLEYL---DV 203
                                        9768888877766665555...44 PP

>> LRR_6  Leucine Rich repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0         7   1.8e+04      12      16 ..      32      36 ..      30      37 .. 0.81
   2 !    8.4   0.2   0.00097       2.5       3      16 ..      44      57 ..      42      58 .. 0.87
   3 !    8.0   0.5    0.0012       3.2       2      16 ..      65      79 ..      64      79 .. 0.86
   4 ?    0.1   0.0      0.43   1.1e+03       5      15 ..      89      99 ..      87     100 .. 0.85
   5 !   11.5   0.1   9.8e-05      0.25       3      16 ..     108     121 ..     106     122 .. 0.92
   6 ?    4.5   0.1     0.017        44       2      16 ..     128     142 ..     127     144 .. 0.88
   7 !    8.3   0.7     0.001       2.6       1      16 [.     149     164 ..     149     165 .. 0.90
   8 ?   -2.3   0.1       2.6   6.6e+03       4      14 ..     174     184 ..     173     189 .. 0.66
   9 ?    2.5   0.0     0.074   1.9e+02       3      13 ..     196     206 ..     194     209 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 7
                              LRR_6 12 gNdIg 16
                                       +N+I+
  gene2423|gene2423|rna2423|rna2423 32 HNKIT 36
                                       89997 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00097
                              LRR_6  3 thLteLdLsgNdIg 16
                                       +++ +LdLs+N I+
  gene2423|gene2423|rna2423|rna2423 44 PNVHSLDLSDNLIT 57
                                       6889*******998 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.0012
                              LRR_6  2 nthLteLdLsgNdIg 16
                                        ++L++LdL +N ++
  gene2423|gene2423|rna2423|rna2423 65 LPNLRTLDLGYNLLT 79
                                       589*********875 PP

  == domain 4  score: 0.1 bits;  conditional E-value: 0.43
                              LRR_6  5 LteLdLsgNdI 15
                                       Lt L L++NdI
  gene2423|gene2423|rna2423|rna2423 89 LTDLFLMCNDI 99
                                       788889****9 PP

  == domain 5  score: 11.5 bits;  conditional E-value: 9.8e-05
                              LRR_6   3 thLteLdLsgNdIg 16 
                                        ++L+ LdL++N+I+
  gene2423|gene2423|rna2423|rna2423 108 PSLKNLDLACNNIT 121
                                        68***********8 PP

  == domain 6  score: 4.5 bits;  conditional E-value: 0.017
                              LRR_6   2 nthLteLdLsgNdIg 16 
                                        + +L+eL L  N I 
  gene2423|gene2423|rna2423|rna2423 128 CINLEELYLGNNRIR 142
                                        789**********97 PP

  == domain 7  score: 8.3 bits;  conditional E-value: 0.001
                              LRR_6   1 snthLteLdLsgNdIg 16 
                                        + ++L +L+L++N+I+
  gene2423|gene2423|rna2423|rna2423 149 HLSKLHTLSLQCNCIQ 164
                                        5689**********96 PP

  == domain 8  score: -2.3 bits;  conditional E-value: 2.6
                              LRR_6   4 hLteLdLsgNd 14 
                                        +L++L L gN+
  gene2423|gene2423|rna2423|rna2423 174 NLKYLLLDGNE 184
                                        57777666664 PP

  == domain 9  score: 2.5 bits;  conditional E-value: 0.074
                              LRR_6   3 thLteLdLsgN 13 
                                        ++L++Ld+s  
  gene2423|gene2423|rna2423|rna2423 196 RKLEYLDVSKT 206
                                        79******975 PP

>> LRR_1  Leucine Rich Repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.3     0.045   1.2e+02       2      15 ..      46      59 ..      45      65 .. 0.73
   2 !   14.3   0.8   1.8e-05     0.046       1      21 [.      67      87 ..      67      89 .. 0.93
   3 ?    3.3   0.5     0.071   1.8e+02       1      16 [.     109     124 ..     109     128 .. 0.80
   4 !    7.7   2.7    0.0025       6.5       1      20 [.     130     163 ..     130     172 .. 0.74
   5 ?    1.5   1.0      0.27     7e+02       1      13 [.     174     186 ..     174     195 .. 0.79
   6 ?    0.9   0.0      0.44   1.1e+03       1       8 [.     197     204 ..     197     214 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.045
                              LRR_1  2 LrhLdLsnnpllgl 15
                                         +LdLs+n ++ +
  gene2423|gene2423|rna2423|rna2423 46 VHSLDLSDNLITTI 59
                                       579******99643 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 1.8e-05
                              LRR_1  1 nLrhLdLsnnpllglppnsfq 21
                                       nLr+LdL++n l+++++ sf 
  gene2423|gene2423|rna2423|rna2423 67 NLRTLDLGYNLLTQIQNLSFL 87
                                       8****************9997 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.071
                              LRR_1   1 nLrhLdLsnnpllglp 16 
                                        +L+ LdL  n+++ ++
  gene2423|gene2423|rna2423|rna2423 109 SLKNLDLACNNITKIE 124
                                        69*****999996555 PP

  == domain 4  score: 7.7 bits;  conditional E-value: 0.0025
                              LRR_1   1 nLrhLdLsnnpl..............lglppnsf 20 
                                        nL++L+L+nn++              l+l+ n++
  gene2423|gene2423|rna2423|rna2423 130 NLEELYLGNNRIrtvenvehlsklhtLSLQCNCI 163
                                        8**********97666666665555555555555 PP

  == domain 5  score: 1.5 bits;  conditional E-value: 0.27
                              LRR_1   1 nLrhLdLsnnpll 13 
                                        nL++L L +n  l
  gene2423|gene2423|rna2423|rna2423 174 NLKYLLLDGNEKL 186
                                        8******999854 PP

  == domain 6  score: 0.9 bits;  conditional E-value: 0.44
                              LRR_1   1 nLrhLdLs 8  
                                        +L++Ld+s
  gene2423|gene2423|rna2423|rna2423 197 KLEYLDVS 204
                                        7*****97 PP

>> LRR_12  Leucine-rich repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.2     0.071   1.8e+02       1      13 [.      68      80 ..      68      82 .. 0.84
   2 ?   -0.6   0.0      0.42   1.1e+03       1      11 [.     110     120 ..     108     122 .. 0.72
   3 ?    6.4   0.1    0.0027         7       1      11 [.     153     163 ..     153     165 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.071
                             LRR_12  1 LqtLhLqmNFInq 13
                                       L+tL+L+ N  +q
  gene2423|gene2423|rna2423|rna2423 68 LRTLDLGYNLLTQ 80
                                       9******997666 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.42
                             LRR_12   1 LqtLhLqmNFI 11 
                                        L++L+L  N I
  gene2423|gene2423|rna2423|rna2423 110 LKNLDLACNNI 120
                                        67888877766 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.0027
                             LRR_12   1 LqtLhLqmNFI 11 
                                        L+tL+Lq N I
  gene2423|gene2423|rna2423|rna2423 153 LHTLSLQCNCI 163
                                        9********88 PP

>> FNIP  FNIP Repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   1.5     0.074   1.9e+02      11      28 ..      44      82 ..       6      97 .. 0.61
   2 ?   -1.9   0.0       1.6     4e+03      33      41 ..     108     115 ..     100     117 .. 0.68
   3 ?    7.1   4.4    0.0024       6.3       2      39 ..     118     178 ..     118     183 .. 0.92
   4 ?    4.7   0.1     0.013        34       9      20 ..     170     181 ..     164     190 .. 0.72

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.074
                               FNIP 11 P.....................snleiLilgrdFnqkil 28
                                       P                     +nl  L lg++   +i+
  gene2423|gene2423|rna2423|rna2423 44 PnvhsldlsdnlittiqdlenlPNLRTLDLGYNLLTQIQ 82
                                       244444444444445555555566777777766666665 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.6
                               FNIP  33 PnSlkeLyF 41 
                                        P Slk L +
  gene2423|gene2423|rna2423|rna2423 108 P-SLKNLDL 115
                                        5.7777765 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.0024
                               FNIP   2 NqiikigeLP.......................snleiLilgrdFnqkiligsLPnSlkeL 39 
                                        N+i ki+ L+                       s l  L l  ++ q i    LP++lk+L
  gene2423|gene2423|rna2423|rna2423 118 NNITKIENLTcinleelylgnnrirtvenvehlSKLHTLSLQCNCIQRIDCLKLPKNLKYL 178
                                        8999*******99999999999999999999999999999999999999999999999999 PP

  == domain 4  score: 4.7 bits;  conditional E-value: 0.013
                               FNIP   9 eLPsnleiLilg 20 
                                         LP+nl++L l 
  gene2423|gene2423|rna2423|rna2423 170 KLPKNLKYLLLD 181
                                        599999999883 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       423  (0.0235931); expected 358.6 (0.02)
Passed bias filter:                      240  (0.0133861); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1465.07
//
Query:       gene2424|gene2424|rna2424|rna2424  [L=86]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.015   14.9   0.1       0.02   14.5   0.1    1.3  1  tRNA_int_endo_N  tRNA intron endonuclease, N-terminal domain
      0.046   13.0   0.0      0.046   13.0   0.0    1.0  1  PARG_cat         Poly (ADP-ribose) glycohydrolase (PARG)


Domain annotation for each model (and alignments):
>> tRNA_int_endo_N  tRNA intron endonuclease, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1   2.3e-06      0.02       4      36 ..      32      63 ..      30      74 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.3e-06
                                       EEETTEEEESSHHHHHHHHHTTT-SEECCTSSE CS
                    tRNA_int_endo_N  4 eLsgdrvlvedeeaakrlyekgfYGkplidepL 36
                                       eL++d+v++ de+  ++l+ k+++ ++  +++L
  gene2424|gene2424|rna2424|rna2424 32 ELRSDNVMIGDEKVENTLCYKNYF-ERVRGNKL 63
                                       89**********************.44555555 PP

>> PARG_cat  Poly (ADP-ribose) glycohydrolase (PARG)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   5.1e-06     0.046      56     110 ..       7      61 ..       1      79 [. 0.83

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 5.1e-06
                           PARG_cat  56 naFfclfprqernkseekklpsinfdrlfss.essseskaeklkcllhYFervtek 110
                                         +Ff ++p ++  + + +kl+++n+++l s      ++k+e   c+ +YFerv  +
  gene2424|gene2424|rna2424|rna2424   7 IMFFVVTPMDHL-TPSIQKLRNLNVKELRSDnVMIGDEKVENTLCYKNYFERVRGN 61 
                                        689999999655.8899***********998777889999************9843 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       383  (0.021362); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.31s 00:00:00.75 Elapsed: 00:00:00.50
# Mc/sec: 516.01
//
Query:       gene2425|gene2425|rna2425|rna2425  [L=58]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (58 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       332  (0.0185175); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 402.83
//
Query:       gene2426|gene2426|rna2426|rna2426  [L=73]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    4.3e-08   33.0   0.5    4.7e-08   32.8   0.5    1.0  1  MS_channel  Mechanosensitive ion channel


Domain annotation for each model (and alignments):
>> MS_channel  Mechanosensitive ion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.8   0.5   2.6e-12   4.7e-08      43     104 ..       6      66 ..       4      69 .. 0.93

  Alignments for each domain:
  == domain 1  score: 32.8 bits;  conditional E-value: 2.6e-12
                                        CHHHHHHHHHHHHHTT-SS-TT-EEESSSEEEEEEEE-SSEEEEEETTSEEEEEEHHHHHTS CS
                         MS_channel  43 kdlisnlvaGiillfekpfkiGDlveigdieGtVediglrttkirtfdgrivtiPnsslvts 104
                                        kd+i +++  + +l   pf+iGD +++++ eG Ve++ + ++ + + ++  ++iP+ ++ +s
  gene2426|gene2426|rna2426|rna2426   6 KDIIFSFFKTVYVLSFSPFRIGDKIRVNNKEGVVENMDMQFVVLSNKKN-KIFIPTGTVYNS 66 
                                        89*********************************************99.678999988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (73 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       522  (0.0291148); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.28s 00:00:00.63 Elapsed: 00:00:00.43
# Mc/sec: 504.08
//
Query:       gene2427|gene2427|rna2427|rna2427  [L=243]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
     0.0092   15.8   0.4     0.0092   15.8   0.4    2.6  3  SKA2       Spindle and kinetochore-associated protein 2
  ------ inclusion threshold ------
       0.17   11.8   1.3         17    5.4   0.2    2.6  2  Fanconi_A  Fanconi anaemia group A protein


Domain annotation for each model (and alignments):
>> SKA2  Spindle and kinetochore-associated protein 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.4     1e-06    0.0092      50      95 ..       7      52 ..       3      60 .. 0.88
   2 ?    0.9   0.1     0.043   3.8e+02      41      64 ..      77     100 ..      61     111 .. 0.77
   3 ?   -2.6   0.1      0.53   4.7e+03      38      40 ..     225     227 ..     203     239 .. 0.42

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1e-06
                               SKA2 50 vkeelqaLkeqceellaekkelidkirttlvanrellqqLqasael 95
                                       ++ e+q+L +++++l++e+kel +k++t++  + +ll  L  ++  
  gene2427|gene2427|rna2427|rna2427  7 LNGEFQNLLKEIKKLQNEQKELLTKLKTNICITEQLLMALLDRTHE 52
                                       56799**********************************9998843 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.043
                               SKA2  41 vkLlerlkkvkeelqaLkeqceel 64 
                                         kLl+ l+++++++++L +  e++
  gene2427|gene2427|rna2427|rna2427  77 TKLLHVLQQLRDRYNELLRLTENV 100
                                        689999999999999987766665 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 0.53
                               SKA2  38 eNp 40 
                                        +N 
  gene2427|gene2427|rna2427|rna2427 225 KNR 227
                                        222 PP

>> Fanconi_A  Fanconi anaemia group A protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.2    0.0019        17      27      58 ..      68      99 ..      40     101 .. 0.86
   2 ?    4.7   0.1    0.0031        27      24      50 ..     216     242 ..     210     243 .] 0.84

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0019
                          Fanconi_A 27 dslkalevcaeiLecLekrkvsWlvLFqltek 58
                                       +s+  + vc+++L++L++ +  +  L +lte+
  gene2427|gene2427|rna2427|rna2427 68 ESSPDITVCTKLLHVLQQLRDRYNELLRLTEN 99
                                       6677899***********99999999999995 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.0031
                          Fanconi_A  24 eavdslkalevcaeiLecLekrkvsWl 50 
                                        ++ + +k ++   e+L+ +e+ k+sWl
  gene2427|gene2427|rna2427|rna2427 216 KRFGRKKRVKNREEMLKKIEENKTSWL 242
                                        4567788888999*************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1633  (0.0910815); expected 358.6 (0.02)
Passed bias filter:                      548  (0.030565); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 1609.99
//
Query:       gene2428|gene2428|rna2428|rna2428  [L=79]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.083   12.2   0.0      0.097   12.0   0.0    1.1  1  PPV_E2_N  E2 (early) protein, N terminal


Domain annotation for each model (and alignments):
>> PPV_E2_N  E2 (early) protein, N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   5.4e-06     0.097      94     125 ..      21      52 ..      10      60 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 5.4e-06
                                        TTTTSHHHHCSSSTT-EEEEEEEEEEECTT-T CS
                           PPV_E2_N  94 LqdvsrerylaaPegtlKkkgktveviydgde 125
                                         q+ s++r + +Pe  lKk g ++   ydgd 
  gene2428|gene2428|rna2428|rna2428  21 TQQASANRVEFDPEYVLKKLGIEIRSAYDGDM 52 
                                        5899**************************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       491  (0.0273858); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.27s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 576.43
//
Query:       gene2429|gene2429|rna2429|rna2429  [L=332]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.4e-23   81.3  13.8    6.4e-23   81.3  13.8    2.4  2  DHHC            DHHC palmitoyltransferase
  ------ inclusion threshold ------
      0.041   13.8   3.2      0.085   12.8   3.2    1.5  1  Ribosomal_L40e  Ribosomal L40e family
        2.6    7.8  15.8       0.74    9.6   8.5    2.1  2  DUF975          Protein of unknown function (DUF975)


Domain annotation for each model (and alignments):
>> DHHC  DHHC palmitoyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   4.6     0.094   5.6e+02      51     128 ..      12      78 ..       1      84 [. 0.54
   2 !   81.3  13.8   1.1e-26   6.4e-23       3     130 ..     110     239 ..     108     243 .. 0.76

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.094
                               DHHC  51 Fllfllylllllilalvlllialvklveeekkseflavtllkkllsilllvlsllfllllgllllfhlylil.rnl 125
                                         ++  l+ +ll +  l+++++a+ +l+ ++  +            + ++l++ l+++++++++++ ++ ++  +++
  gene2429|gene2429|rna2429|rna2429  12 SIIKGLISSLLPFTLLYFYFTAIKVLCVDSLRF------------NSTSLYIYLIYTAMISYIIINYVRTMNdNKV 75 
                                        555555555555555555555555555544443............3445566666677777777666666663335 PP

                               DHHC 126 Tti 128
                                        Tt 
  gene2429|gene2429|rna2429|rna2429  76 TTF 78 
                                        655 PP

  == domain 2  score: 81.3 bits;  conditional E-value: 1.1e-26
                               DHHC   3 kelkfCstcniykpprskHcrvCnrcvlrfDHhCpwlnnciGerNykyFllfllylll...llilalv..lllial 73 
                                        k++ +C+ c +ykpprs Hc++C+rc l+   hC +l +ciG++N+k+F+l+l +l++   ++i+a++  l  + l
  gene2429|gene2429|rna2429|rna2429 110 KDKIVCEYCLVYKPPRSAHCKECGRCFLKRVSHCYFLETCIGFHNQKFFVLLLASLIVhgmAVIIAFIiaLKTTPL 185
                                        56779********************************************766555444110333333311223334 PP

                               DHHC  74 vklveeekkseflavtllkkllsilllvlsllfllllgllllfhlylilrnlTtiea 130
                                        +k+v  +k++e++ v+    +  i+++v++++ +l+ ++ l+fhlyli+rn T+ e+
  gene2429|gene2429|rna2429|rna2429 186 YKMVAVRKNQEYTLVFE---AHFIISIVIAFIEVLICTCYLVFHLYLIFRNETNLER 239
                                        45555555555554444...568******************************9987 PP

>> Ribosomal_L40e  Ribosomal L40e family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   3.2   1.4e-05     0.085       8      41 ..     104     135 ..      97     139 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.4e-05
                     Ribosomal_L40e   8 LAqKyncdKmiCrkCYArlpprAtnCrkkkCghs 41 
                                           K   dK +C  C    ppr+ +C+   Cg++
  gene2429|gene2429|rna2429|rna2429 104 VIDKQVKDKIVCEYCLVYKPPRSAHCK--ECGRC 135
                                        5678889*******************8..9**98 PP

>> DUF975  Protein of unknown function (DUF975)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.7     0.016        96      35      78 ..      26      72 ..       5      84 .. 0.48
   2 ?    9.6   8.5   0.00012      0.74      88     179 ..     149     236 ..     135     246 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.016
                             DUF975 35 llsflisiietilvssllel...livlllgtlltlsavfvviklvkr 78
                                       ll f    i+++ v+sl      l ++l++t++++ +++  ++ +++
  gene2429|gene2429|rna2429|rna2429 26 LLYFYFTAIKVLCVDSLRFNstsLYIYLIYTAMISYIIINYVRTMND 72
                                       22233333333333222111234555566666655555555555555 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00012
                             DUF975  88 lasfkeknfiklLvllllkelflllwsliallglliiiislslallsseieenlvvvllvlliilllivlilaiiv 163
                                         ++f      +++ +lll +l++  +++i+++++ +  + l+ ++   +++e ++v+   ++i++++  + + i  
  gene2429|gene2429|rna2429|rna2429 149 CIGF----HNQKFFVLLLASLIVHGMAVIIAFIIALKTTPLYKMVAVRKNQEYTLVFEAHFIISIVIAFIEVLICT 220
                                        4445....44677788888888888888888888888888888777889999999999999999888877777777 PP

                             DUF975 164 eyayslveyilveele 179
                                         y+ +  ++i+ +e++
  gene2429|gene2429|rna2429|rna2429 221 CYLVFHLYLIFRNETN 236
                                        7999999999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (332 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1411  (0.0786993); expected 358.6 (0.02)
Passed bias filter:                      538  (0.0300073); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 2110.59
//
Query:       gene243|gene243|rna243|rna243  [L=194]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.012   16.3   1.7      0.013   16.2   0.5    1.7  2  GRP       Glycine rich protein family


Domain annotation for each model (and alignments):
>> GRP  Glycine rich protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   16.2   0.5   7.2e-07     0.013      13      79 ..       2      73 ..       1      96 [. 0.61
   2 ?   -2.4   0.0      0.46   8.2e+03      30      36 ..     140     146 ..     112     170 .. 0.57

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 7.2e-07
                            GRP 13 laavlLissevaaael....skeeksekeeevkdekyggggkh.ggGgygggggggngGGGykgggGgyggg 79
                                   l+ vlL++se  + +     s++e + k   vk+ ++  +  + + G   gg  ++  G G ++g G  +g 
  gene243|gene243|rna243|rna243  2 LIYVLLVMSEHYEIHDddvvSRNEMKRKDLSVKQMEEEDNAGGgNDGNEDGGIEDRDRGNGSRDGNGSRDGS 73
                                   7899***99987766545664444444444444444433222313344444445667777877777777663 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.46
                            GRP  30 keeksek 36 
                                    +e k+++
  gene243|gene243|rna243|rna243 140 DEIKRNH 146
                                    2333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1402  (0.0781973); expected 358.6 (0.02)
Passed bias filter:                      486  (0.0271069); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.29s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1429.61
//
Query:       gene2430|gene2430|rna2430|rna2430  [L=100]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.3e-06   26.2   0.0    9.3e-06   25.8   0.0    1.2  1  CBFD_NFYB_HMF  Histone-like transcription factor (CBF/NF-Y) a
     0.0022   18.1   0.0     0.0031   17.6   0.0    1.2  1  TAF            TATA box binding protein associated factor (TA
  ------ inclusion threshold ------
      0.016   15.2   0.1      0.033   14.2   0.0    1.5  2  Bromo_TP       Bromodomain associated
       0.17   12.0   0.0        0.2   11.8   0.0    1.1  1  CENP-T_C       Centromere kinetochore component CENP-T histon


Domain annotation for each model (and alignments):
>> CBFD_NFYB_HMF  Histone-like transcription factor (CBF/NF-Y) and archaeal histone
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.0   2.1e-09   9.3e-06       6      61 ..      32      86 ..      27      90 .. 0.93

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 2.1e-09
                                       HHHHHHHHCCTTXS-B-HHHHHHHHHHHHHHHHHHHHHHHHHHCCTTSSCE-HHHH CS
                      CBFD_NFYB_HMF  6 arvkkImksdpdarkiakdAkeliaecveefieelaseAaeickkekrKtikaehi 61
                                        ++k++ ++  ++++++kd   +ia  + +f+e l + A e+c  ++rKt++  ++
  gene2430|gene2430|rna2430|rna2430 32 PAIKRLARKG-GVKRVSKDCYYVIATRAGFFLENLVRCAIEYCVVARRKTLSVCDV 86
                                       579*******.****************************************99887 PP

>> TAF  TATA box binding protein associated factor (TAF)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0     7e-07    0.0031       6      63 ..      31      88 ..      27      91 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 7e-07
                                       HHHHHHHHHHTT---B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHH CS
                                TAF  6 kesvkviAeslGitnLsdeaaalLaedveyrlkeivqeaakfmrhskRqkLtvaDvds 63
                                       k ++k +A   G++ +s++   ++a    + l + v+ a+ +  +++R++L+v Dv +
  gene2430|gene2430|rna2430|rna2430 31 KPAIKRLARKGGVKRVSKDCYYVIATRAGFFLENLVRCAIEYCVVARRKTLSVCDVMN 88
                                       568999*************************************************965 PP

>> Bromo_TP  Bromodomain associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       1.4   6.4e+03      53      64 ..      18      29 ..      14      39 .. 0.66
   2 ?   14.2   0.0   7.3e-06     0.033      39      74 ..      61      96 ..      55      98 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.4
                                       TSS-SS--HHHH CS
                           Bromo_TP 53 hagRseptlkDv 64
                                       + +R++p+ + +
  gene2430|gene2430|rna2430|rna2430 18 RHRRTTPKSFEL 29
                                       567888776655 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 7.3e-06
                                       HHHHHHHHHHHHHTTSS-SS--HHHHHHHHHHTT-- CS
                           Bromo_TP 39 YirelgeqaksfaehagRseptlkDvvltLqelgin 74
                                       ++++l ++a +++ +a+R + ++ Dv+++ + +g++
  gene2430|gene2430|rna2430|rna2430 61 FLENLVRCAIEYCVVARRKTLSVCDVMNGVKKMGVK 96
                                       788999****************************96 PP

>> CENP-T_C  Centromere kinetochore component CENP-T histone fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   4.6e-05       0.2      11      75 ..      32      91 ..      19      96 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 4.6e-05
                           CENP-T_C 11 avvkklakrfakasgskaklekealkalekasdkffeqvgeDLeayakHagRKtidesDvilLmk 75
                                        ++k+la++     g  ++++k+ + ++ +    f+e + +    y   a+RKt+   Dv+  +k
  gene2430|gene2430|rna2430|rna2430 32 PAIKRLARK-----GGVKRVSKDCYYVIATRAGFFLENLVRCAIEYCVVARRKTLSVCDVMNGVK 91
                                       455555543.....56679****************************************987666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       413  (0.0230353); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 699.51
//
Query:       gene2431|gene2431|rna2431|rna2431  [L=49]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (49 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       250  (0.0139439); expected 358.6 (0.02)
Passed bias filter:                      206  (0.0114898); expected 358.6 (0.02)
Passed Vit filter:                         6  (0.000334653); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.32u 0.24s 00:00:00.56 Elapsed: 00:00:00.39
# Mc/sec: 375.05
//
Query:       gene2432|gene2432|rna2432|rna2432  [L=148]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.8e-30  106.0   0.1    2.1e-30  105.8   0.1    1.0  1  Histone        Core histone H2A/H2B/H3/H4
    1.6e-06   28.7   0.1    1.7e-06   28.7   0.1    1.1  1  PAF            PCNA-associated factor histone like domain
    2.5e-06   27.6   0.0    4.6e-06   26.7   0.0    1.4  1  CENP-T_C       Centromere kinetochore component CENP-T histon
    0.00015   22.0   0.1    0.00031   20.9   0.0    1.6  2  CBFD_NFYB_HMF  Histone-like transcription factor (CBF/NF-Y) a
    0.00019   21.7   0.0    0.00035   20.9   0.0    1.4  1  CENP-S         CENP-S protein
     0.0026   17.7   0.0     0.0045   17.0   0.0    1.3  1  Bromo_TP       Bromodomain associated
  ------ inclusion threshold ------
       0.18   11.9   0.0       0.34   11.0   0.0    1.4  1  TFIID-18kDa    Transcription initiation factor IID, 18kD subu


Domain annotation for each model (and alignments):
>> Histone  Core histone H2A/H2B/H3/H4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.8   0.1   8.1e-34   2.1e-30       1     131 []       1     137 [.       1     137 [. 0.91

  Alignments for each domain:
  == domain 1  score: 105.8 bits;  conditional E-value: 8.1e-34
                                        XXEESXEEEXXXXEEXXXXXXXXXXHT...TS-SSSSB--TTT-XTTHHHH.HHHHHHHHXXSXXSXHHHHHHHHH CS
                            Histone   1 marekekarkesektapekkvsakker...kasskskkkkkrryrpgtval.keirkyqkstdlliqklpfaRvvr 72 
                                        mar+k++ark+++++ap+k ++ak +r     +  s++k+  ry+pg   l +ei+ky+ks d li++ pf+R v 
  gene2432|gene2432|rna2432|rna2432   1 MARTKQTARKSTGGKAPRKGLAAKAARktsAVDVGSATKRVSRYKPGNTLLfREIKKYSKSIDCLIPRQPFKRFVL 76 
                                        9************************999755556778888889999865554*********************887 PP

                                        .HHH..TTSSSXEEXHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTXSEEXHHHHHHHHHHT CS
                            Histone  73 .eivk.sekedlrisaeavlalqealEallvelfeeAnllakhaKRvTitpkDiqlArrlr 131
                                          + +   +++ r+ a +++alqealE+++v l e+A+l+++ha RvT++pkDi l++r++
  gene2432|gene2432|rna2432|rna2432  77 sALSEiGMRDSVRFKAGCLNALQEALENFIVTLCEDAYLCTRHAGRVTLMPKDINLVMRIK 137
                                        46777999***************************************************96 PP

>> PAF  PCNA-associated factor histone like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7   0.1   6.6e-10   1.7e-06       1      64 [.       1      63 [.       1     105 [. 0.87

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 6.6e-10
                                PAF  1 mVRTkAdvssarkavaakAprkslgass..ssssssssspkkkkkkyvGGNpvcpRptPaWQKpIt 64
                                       m RTk ++   rk  ++kAprk l+a+   + s+++  s++k  + y +GN    R++ +  K I+
  gene2432|gene2432|rna2432|rna2432  1 MARTKQTA---RKSTGGKAPRKGLAAKAarKTSAVDVGSATKRVSRYKPGNTLLFREIKKYSKSID 63
                                       99******...***********9987661145666667779999***************9999997 PP

>> CENP-T_C  Centromere kinetochore component CENP-T histone fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.7   0.0   1.8e-09   4.6e-06       8      78 ..      66     138 ..      58     141 .. 0.86

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 1.8e-09
                           CENP-T_C   8 lPaavvkklakrfakasg..skaklekealkalekasdkffeqvgeDLeayakHagRKtidesDvilLmkrqr 78 
                                        +P +  k+++ ++ ++ g   + + ++  l+al++a+++f+  ++eD    ++HagR t+  +D+ l m+ +r
  gene2432|gene2432|rna2432|rna2432  66 IPRQPFKRFVLSALSEIGmrDSVRFKAGCLNALQEALENFIVTLCEDAYLCTRHAGRVTLMPKDINLVMRIKR 138
                                        68888888888888887855567888999*****************************************887 PP

>> CBFD_NFYB_HMF  Histone-like transcription factor (CBF/NF-Y) and archaeal histone
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.1       5.5   1.4e+04      41      55 ..      22      29 ..      20      31 .. 0.50
   2 !   20.9   0.0   1.2e-07   0.00031      28      65 .]      97     134 ..      84     134 .. 0.92

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 5.5
                                       HHHHHHHHCCTTSSC CS
                      CBFD_NFYB_HMF 41 aseAaeickkekrKt 55
                                       a++A        rKt
  gene2432|gene2432|rna2432|rna2432 22 AAKA-------ARKT 29
                                       3444.......4444 PP

  == domain 2  score: 20.9 bits;  conditional E-value: 1.2e-07
                                        HHHHHHHHHHHHHHHHHHHHHCCTTSSCE-HHHHHHHH CS
                      CBFD_NFYB_HMF  28 liaecveefieelaseAaeickkekrKtikaehiklAv 65 
                                         ++e++e fi  l++ A+  + +++r t+++++i l++
  gene2432|gene2432|rna2432|rna2432  97 ALQEALENFIVTLCEDAYLCTRHAGRVTLMPKDINLVM 134
                                        69********************************9986 PP

>> CENP-S  CENP-S protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   1.4e-07   0.00035      15      71 ..      79     135 ..      69     139 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 1.4e-07
                             CENP-S  15 veeeaaekeveatkqfiaaltelvykqlenlakDLeaFakHAkRstittdDvlLlaR 71 
                                         +e+ ++ +v++    ++al e   + + +l++D  +  +HA+R t  ++D+ L++R
  gene2432|gene2432|rna2432|rna2432  79 LSEIGMRDSVRFKAGCLNALQEALENFIVTLCEDAYLCTRHAGRVTLMPKDINLVMR 135
                                        5677778889999999***************************************99 PP

>> Bromo_TP  Bromodomain associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   1.7e-06    0.0045      23      68 ..      89     134 ..      68     135 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1.7e-06
                                        EE-HHHHHHHHHHHHHHHHHHHHHHHHHHTTSS-SS--HHHHHHHH CS
                           Bromo_TP  23 saeesaLEtLteiaqkYirelgeqaksfaehagRseptlkDvvltL 68 
                                        +++++ L++L+e ++++i  l e+a     hagR +  +kD+ l++
  gene2432|gene2432|rna2432|rna2432  89 RFKAGCLNALQEALENFIVTLCEDAYLCTRHAGRVTLMPKDINLVM 134
                                        5899********************88888*************9887 PP

>> TFIID-18kDa  Transcription initiation factor IID, 18kD subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00013      0.34      25      65 ..      95     135 ..      85     141 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00013
                                        HHHHHHHHHHHHHHHHHHHHC-XXXX...XXXXXXXXXXXX CS
                        TFIID-18kDa  25 vqlledlvrgyliellqqaakvaklrgsrkitlEDllfliR 65 
                                        ++ l++ ++++++ l++ a   +++ g+  + + D+  ++R
  gene2432|gene2432|rna2432|rna2432  95 LNALQEALENFIVTLCEDAYLCTRHAGRVTLMPKDINLVMR 135
                                        56789999*******************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       340  (0.0189637); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 1053.22
//
Query:       gene2433|gene2433|rna2433|rna2433  [L=31]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (31 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                        84  (0.00468515); expected 358.6 (0.02)
Passed bias filter:                       77  (0.00429472); expected 358.6 (0.02)
Passed Vit filter:                         6  (0.000334653); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.51u 0.32s 00:00:00.83 Elapsed: 00:00:00.54
# Mc/sec: 172.54
//
Query:       gene2434|gene2434|rna2434|rna2434  [L=462]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00098   18.5   0.0      0.003   16.9   0.0    1.6  1  Nrap_D4   Nrap protein nucleotidyltransferase domain 4


Domain annotation for each model (and alignments):
>> Nrap_D4  Nrap protein nucleotidyltransferase domain 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   1.7e-07     0.003      88     122 ..     173     206 ..     163     240 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.7e-07
                                        EEEEEE---TTS-SSHHHHHHHHHHHHHHHHHHH. CS
                            Nrap_D4  88 dvvlqfEsSgkWPddleAiqkvKaAFllkiaeeLe 122
                                        +v l++E   kWP+d +Ai+ vK A+l +i +  +
  gene2434|gene2434|rna2434|rna2434 173 TVFLHMED-RKWPHDKQAIECVKSALLCHIYSHCK 206
                                        58888887.8******************9987665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (462 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       816  (0.0455129); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.64u 0.30s 00:00:00.94 Elapsed: 00:00:00.53
# Mc/sec: 2647.03
//
Query:       gene2435|gene2435|rna2435|rna2435  [L=72]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        0.2   11.0   0.0       0.22   10.8   0.0    1.1  1  IMD       IRSp53/MIM homology domain


Domain annotation for each model (and alignments):
>> IMD  IRSp53/MIM homology domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   1.2e-05      0.22      17      48 ..       2      33 ..       1      45 [. 0.87

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 1.2e-05
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                                IMD 17 skakklekalrtlvlaaeayldAlqKiaelAl 48
                                       +++++l k ++t   +ae+++d    ++ + +
  gene2435|gene2435|rna2435|rna2435  2 ALGTNLTKSFKTYLCVAEVFFDRRNNVGMRGV 33
                                       689*******************9888886665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (72 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       352  (0.019633); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 509.96
//
Query:       gene2436|gene2436|rna2436|rna2436  [L=456]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.1e-15   55.6   0.3    1.1e-14   55.0   0.3    1.3  1  Brix      Brix domain


Domain annotation for each model (and alignments):
>> Brix  Brix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.0   0.3   6.3e-19   1.1e-14       1     193 []      15     176 ..      15     176 .. 0.83

  Alignments for each domain:
  == domain 1  score: 55.0 bits;  conditional E-value: 6.3e-19
                                        BTT--HHHHHHHHHHHHHCTTSEEEEEE.ECT-TTTHHHHHHH-HHHHHHHH.HCTCSEEEEEE..SSTTEEEEEE CS
                               Brix   1 grktssrlrqllkdlrslmkphtasflk.rnsnklkdlvelagvthlellse.kndcslfvfelskkrPngptlef 74 
                                        +++ts+ ++ +lkdl +   p++++++k ++++++++l+++ +   l+++   k+ + + ++++      gp++e 
  gene2436|gene2436|rna2436|rna2436  15 SKNTSATHKYVLKDLVKFV-PNAIKESKcNGRKEIQELMSIHECDTLLYFECtKRRNTMWLVKS-----GGPSIEC 84 
                                        5789999************.99***9**866678999888888555555544388888999998.....99***** PP

                                        EEECECTGGGSTTTSTS-TT---EEEEES.....HHHHHHHHHHHHHH..SEEEG..-B-GG-SEEEEEEES.CCT CS
                               Brix  75 kvenyslmkdlkkakktefgsrPllvfng....kenfkllksllqdlFrvpkislkspklsglrrvvlftaaenqe 146
                                        +v+ + ++++lk   +t  +   +l+f+     + ++k lk++l+d+Fr +         + ++r +lf +++   
  gene2436|gene2436|rna2436|rna2436  85 NVDVMFSIDRLKFLVNTYLNVGHVLLFQPvfedNCELKALKNVLTDIFRRE--------DELCERAMLFAYED--- 149
                                        ***********99989999999999999666444445***********322........257********555... PP

                                        TTECEEEEEEEEEEE..STTTTECT..T..EEEEEEESEEEEEEEEE CS
                               Brix 147 tdktisfRhYaiklkksgkklpnlekekkerveLeEiGPrfdLklrk 193
                                         + ++++R+Y+++                   eL+EiGPr+++++rk
  gene2436|gene2436|rna2436|rna2436 150 -G-KVFLRNYKLD------------------DELQEIGPRMVFTVRK 176
                                        .5.8********4..................48***********986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (456 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1828  (0.101958); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.66u 0.25s 00:00:00.91 Elapsed: 00:00:00.46
# Mc/sec: 2975.62
//
Query:       gene2437|gene2437|rna2437|rna2437  [L=127]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.12   12.3   0.1       0.53   10.2   0.1    1.9  2  DUF3797   Domain of unknown function (DUF3797)
       0.48   10.8   3.9        1.3    9.4   0.2    2.6  3  DUF3621   Protein of unknown function (DUF3621)


Domain annotation for each model (and alignments):
>> DUF3797  Domain of unknown function (DUF3797)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.13   1.2e+03      20      36 ..      22      44 ..      13      50 .. 0.77
   2 ?   10.2   0.1   5.9e-05      0.53      21      47 ..      63      97 ..      60      98 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.13
                            DUF3797 20 gNnkvlNsegkv......iiedd 36
                                       +N+   N e +v      ii+dd
  gene2437|gene2437|rna2437|rna2437 22 KNEESSNHEQQVdlhlkpIISDD 44
                                       78888888888877777788887 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 5.9e-05
                            DUF3797 21 NnkvlNsegkv......iiedd..tfyreCkCgfn 47
                                       N+   N e ++      i++dd  t y++C+C+ +
  gene2437|gene2437|rna2437|rna2437 63 NEELSNHEQQIgtyperIVSDDesTIYQSCSCARD 97
                                       7778888888888888788776669*******865 PP

>> DUF3621  Protein of unknown function (DUF3621)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.2   0.00014       1.3      17      43 ..      21      47 ..      18      49 .. 0.82
   2 ?   -1.1   0.0      0.28   2.5e+03      16      29 ..      48      61 ..      45      65 .. 0.81
   3 ?    1.8   0.2     0.035   3.1e+02      20      29 ..      64      73 ..      60      78 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00014
                            DUF3621 17 qKkekqsEhEqqvakpvKtqKnEPqPY 43
                                        K+e  s hEqqv   +K+  ++ +P+
  gene2437|gene2437|rna2437|rna2437 21 SKNEESSNHEQQVDLHLKPIISDDKPF 47
                                       6999*********98888877776665 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.28
                            DUF3621 16 SqKkekqsEhEqqv 29
                                        +K++  s +E  v
  gene2437|gene2437|rna2437|rna2437 48 TCKRQIRSYPERIV 61
                                       69999999999866 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.035
                            DUF3621 20 ekqsEhEqqv 29
                                       e  s hEqq+
  gene2437|gene2437|rna2437|rna2437 64 EELSNHEQQI 73
                                       56689****7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       654  (0.0364772); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 822.32
//
Query:       gene2438|gene2438|rna2438|rna2438  [L=490]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.8e-29  102.3   0.4    7.9e-29  100.9   0.4    1.8  1  mRNA_cap_enzyme  mRNA capping enzyme, catalytic domain
    1.6e-11   44.8  11.3    2.4e-09   37.8  11.3    2.7  1  mRNA_cap_C       mRNA capping enzyme, C-terminal domain
  ------ inclusion threshold ------
        0.4   10.7  24.8       0.57   10.2  24.8    1.2  1  Asp-B-Hydro_N    Aspartyl beta-hydroxylase N-terminal region


Domain annotation for each model (and alignments):
>> mRNA_cap_enzyme  mRNA capping enzyme, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.9   0.4   1.3e-32   7.9e-29       3     195 .]      43     212 ..      41     212 .. 0.86

  Alignments for each domain:
  == domain 1  score: 100.9 bits;  conditional E-value: 1.3e-32
                                        EE--TTHHHHHHHS-EEEEEEESSEEEEEEEEECT..EEEEEEETTS-EEEESSST-BTTSSSSTCTSBGGSEEEE CS
                    mRNA_cap_enzyme   3 vSlerenlekLkqkkYvvseKaDGiRylmllteee..egvylidRenevyrvenlrfprekdkeklekvldetllD 76 
                                        v l r ++  L +++Y+++eK+DG+R l+++  e      ++idR++ +yr+ + + p+  d         + llD
  gene2438|gene2438|rna2438|rna2438  43 VTLLRRHIVDLVNRDYFACEKSDGMRALLYVICERgrSYFFFIDRKMCCYRILE-NEPVLLD--------GDYLLD 109
                                        788999************************977766577899**********94.4455554........467*** PP

                                        EEEEEEECTTCEEEEEEEEEEEEEETTEEGTTSBHHHHHHHHHHHTHHHHHHHHHTTCCCCTTSSSEEEE--EEET CS
                    mRNA_cap_enzyme  77 gElvidkveekkkelryliyDivaingvtvaeeplskRleilkkelikprneekktglletdkepfsvrlKefill 152
                                        gE++i   +    +  y ++D + +++ +v++ +l +Rl++ +k + +        +l++  ++ f+v +K++++ 
  gene2438|gene2438|rna2438|rna2438 110 GEVIITNED----KIEYSVFDTIIFQSNSVMQLNLLERLRLADKFIRH--------QLCH--LFSFKVLIKKMYKA 171
                                        ****96544....589***********************988776643........3333..479*********** PP

                                        THHHHHHHHCCCCCTTSTEEEEEEEESSSB--SEEEEEEEEE- CS
                    mRNA_cap_enzyme 153 eavaklleekfikklshesDGLIfqpvkepyvagrdsdllKwK 195
                                        +  a     ++  +l h +DGLIf++v+epyv+g++++l+KwK
  gene2438|gene2438|rna2438|rna2438 172 YGFAE--AYESRFSLGHGNDGLIFTCVEEPYVFGTCNNLYKWK 212
                                        *****..6666678****************************9 PP

>> mRNA_cap_C  mRNA capping enzyme, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.8  11.3     4e-13   2.4e-09      11     107 ..     353     466 ..     216     467 .. 0.79

  Alignments for each domain:
  == domain 1  score: 37.8 bits;  conditional E-value: 4e-13
                                        SSS--TTS--EEEEEEEES...TEEEEEEEB---HH...HHHHHHHT-...S--TTEEEEEEE-TTS......... CS
                         mRNA_cap_C  11 ekyedydakpkfellvleg...ekyekfaelylseeekeeweelksln...eeldgkIvEcsldeek......... 71 
                                        e++ed ++ +k ellv e+   +++e  ++l +++    +     ++n    ++++kI E++++e+k         
  gene2438|gene2438|rna2438|rna2438 353 EENEDVKEDNKNELLVEENengNRNEGHKRLKVNNTCLINN--HSESNnqiGKYHKKIGEFHFNENKksicmddys 426
                                        45566666666677776666667778888888887743333..2223324579***********885578888888 PP

                                        ....-EEEEEE-TT-SS--BHHHHHHHHHHHHTS--HHHH CS
                         mRNA_cap_C  72 ....rWkllriRdDKsepNhisvvekvleSIednvteeeL 107
                                            +W+llriR+DK++pN+++vv++++ S+++n+t e++
  gene2438|gene2438|rna2438|rna2438 427 ivkgKWELLRIREDKNTPNSFRVVTNIFLSMRENITYEDI 466
                                        87777*******************************9987 PP

>> Asp-B-Hydro_N  Aspartyl beta-hydroxylase N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2  24.8   9.5e-05      0.57      92     194 ..     277     375 ..     262     444 .. 0.52

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 9.5e-05
                      Asp-B-Hydro_N  92 laeekek.qkveeevkEqlkkvkeeivvkeeeeegieeepqleeekkllkedsderqeeleagkvkeev.Eeslkv 165
                                        ++++  k + ++e+vkE+ ++vkee + ++ e +g++e+++ +ee+  l+e++++ +ee+++++  ++v Ee+++ 
  gene2438|gene2438|rna2438|rna2438 277 HPTDGRKlNTAKENVKEENENVKEENENAK-ERNGKQENENVKEENVPLEEENENVKEENDVKEETNDVkEENVPL 351
                                        344433314578888888888888888887.666666666666677777777777666666655544431334444 PP

                      Asp-B-Hydro_N 166 eetvseeakkdmkekaseeenekskepve 194
                                        ee  +     d+ke  ++e   +++e  +
  gene2438|gene2438|rna2438|rna2438 352 EEENE-----DVKEDNKNELLVEENENGN 375
                                        33322.....2222222222222111111 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (490 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2173  (0.1212); expected 358.6 (0.02)
Passed bias filter:                      548  (0.030565); expected 358.6 (0.02)
Passed Vit filter:                        96  (0.00535445); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.72u 0.30s 00:00:01.02 Elapsed: 00:00:00.46
# Mc/sec: 3171.85
//
Query:       gene2439|gene2439|rna2439|rna2439  [L=51]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.7e-15   56.4  12.7    2.3e-15   55.9  12.7    1.2  1  Ribosomal_L39  Ribosomal L39 protein


Domain annotation for each model (and alignments):
>> Ribosomal_L39  Ribosomal L39 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.9  12.7   1.3e-19   2.3e-15       2      42 .]       9      49 ..       8      49 .. 0.99

  Alignments for each domain:
  == domain 1  score: 55.9 bits;  conditional E-value: 1.3e-19
                      Ribosomal_L39  2 KlrLaKalkqNrpvPaWvrlktdrkvrynpkrRhWRrtkLk 42
                                       K+rLaKalk+Nr++P W+r  +++k++ n+k+R+WRr+kLk
  gene2439|gene2439|rna2439|rna2439  9 KIRLAKALKKNRSIPPWKRELKHNKQEFNFKKRSWRRNKLK 49
                                       9***************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (51 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       458  (0.0255452); expected 358.6 (0.02)
Passed bias filter:                      201  (0.0112109); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.43
# Mc/sec: 355.93
//
Query:       gene244|gene244|rna244|rna244  [L=91]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       611  (0.0340789); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 624.88
//
Query:       gene2440|gene2440|rna2440|rna2440  [L=249]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-10   40.9   1.6    3.6e-08   33.0   0.5    2.2  2  LRR_8     Leucine rich repeat
    6.5e-09   35.9   3.5    2.6e-07   30.8   1.4    2.3  2  LRR_4     Leucine Rich repeats (2 copies)
    0.00018   21.3   3.8        3.8    7.8   0.2    3.4  3  LRR_6     Leucine Rich repeat
    0.00035   20.7   3.1       0.47   11.2   0.1    3.6  2  LRR_1     Leucine Rich Repeat
    0.00049   19.7   0.4    0.00078   19.0   0.4    1.3  1  LRR_9     Leucine-rich repeat


Domain annotation for each model (and alignments):
>> LRR_8  Leucine rich repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.0   0.5     1e-11   3.6e-08      23      61 .]      11      48 ..       5      52 .. 0.92
   2 !    6.8   0.0    0.0016       5.8       1      30 [.      59      87 ..      59      88 .. 0.87

  Alignments for each domain:
  == domain 1  score: 33.0 bits;  conditional E-value: 1e-11
                                       T-TT--EEE--SS---GGGGGGGTT--S-.EEE--SS-- CS
                              LRR_8 23 glsnLkvLdLsnNllttlspgafsgLpsLrsLdLsgNrL 61
                                       +l+nL++Ld s+N+l+ l p++fs L sL+ L+L++Nr+
  gene2440|gene2440|rna2440|rna2440 11 KLKNLESLDVSDNRLKEL-PDTFSALQSLTVLNLTNNRF 48
                                       599***************.9*****************85 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0016
                                       TT-SEEE-TTS--SEE-TTSSTT-TT--EE CS
                              LRR_8  1 pnLtsLdLsnNrltslddeaFkglsnLkvL 30
                                       ++L++L+L  N +++++ e+ + l+ L vL
  gene2440|gene2440|rna2440|rna2440 59 RTLHILSLEGNAINDVPVEVIR-LPYLSVL 87
                                       5799999999999999999999.8888887 PP

>> LRR_4  Leucine Rich repeats (2 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.8   1.4   7.3e-11   2.6e-07       1      38 [.      13      50 ..      13      55 .. 0.87
   2 ?    4.8   0.0     0.011        41       3      28 ..      61      87 ..      59      90 .. 0.80

  Alignments for each domain:
  == domain 1  score: 30.8 bits;  conditional E-value: 7.3e-11
                                       SS--EEE--SS---E-S-.HHH-TT--EEE-.-S----- CS
                              LRR_4  1 pnLevLdLsnNqltdipl.leklpnLkeLdLsgNnlitd 38
                                       +nLe+Ld s+N+l+++p  ++ l +L++L+L  Nn+ + 
  gene2440|gene2440|rna2440|rna2440 13 KNLESLDVSDNRLKELPDtFSALQSLTVLNL-TNNRFDE 50
                                       79****************9888*********.5556554 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.011
                                       --EEE--SS---E-S-..HHH-TT--EE CS
                              LRR_4  3 LevLdLsnNqltdipl..leklpnLkeL 28
                                       L +L+L +N + d+p   ++ lp L +L
  gene2440|gene2440|rna2440|rna2440 61 LHILSLEGNAINDVPVevIR-LPYLSVL 87
                                       88999999999999996655.7777666 PP

>> LRR_6  Leucine Rich repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.2    0.0011       3.8       3      15 ..      13      25 ..      11      26 .. 0.87
   2 !    6.6   0.2    0.0025         9       3      15 ..      36      48 ..      34      50 .. 0.88
   3 !    6.3   0.0    0.0033        12       3      18 ..      59      74 ..      58      78 .. 0.92

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0011
                              LRR_6  3 thLteLdLsgNdI 15
                                        +L++Ld+s+N +
  gene2440|gene2440|rna2440|rna2440 13 KNLESLDVSDNRL 25
                                       58*********87 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0025
                              LRR_6  3 thLteLdLsgNdI 15
                                       ++Lt L+L+ N +
  gene2440|gene2440|rna2440|rna2440 36 QSLTVLNLTNNRF 48
                                       79*********86 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.0033
                              LRR_6  3 thLteLdLsgNdIgDe 18
                                       ++L  L+L gN I+D+
  gene2440|gene2440|rna2440|rna2440 59 RTLHILSLEGNAINDV 74
                                       69************95 PP

>> LRR_1  Leucine Rich Repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   0.1   0.00013      0.47       1      23 []      14      35 ..      14      35 .. 0.89
   2 !    7.0   0.6     0.003        11       1      17 [.      37      52 ..      37      87 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00013
                              LRR_1  1 nLrhLdLsnnpllglppnsfqnL 23
                                       nL++Ld+s+n+l   +p++f+ L
  gene2440|gene2440|rna2440|rna2440 14 NLESLDVSDNRL-KELPDTFSAL 35
                                       8***********.7899988865 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.003
                              LRR_1  1 nLrhLdLsnnpllglpp 17
                                       +L++L+L+nn++ +  p
  gene2440|gene2440|rna2440|rna2440 37 SLTVLNLTNNRF-DEVP 52
                                       699*******99.3333 PP

>> LRR_9  Leucine-rich repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.4   2.2e-07   0.00078      42     122 ..      13      88 ..       8     100 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 2.2e-07
                              LRR_9  42 dqfdtidlsdndirkl.dgfPllkrlktlllnnnrivriaegleevlPnleelvltnnelqeladldPlaslkkle 116
                                          ++++d+sdn +++l d f  l+ l +l l nnr   +   +  ++ +l+ l l +n ++++      +++ +l 
  gene2440|gene2440|rna2440|rna2440  13 KNLESLDVSDNRLKELpDTFSALQSLTVLNLTNNRFDEVPR-IIGCIRTLHILSLEGNAINDVP-----VEVIRLP 82 
                                        567899*********9889*****************99865.5568999999999999998864.....3455555 PP

                              LRR_9 117 llsllk 122
                                        +ls+lk
  gene2440|gene2440|rna2440|rna2440  83 YLSVLK 88 
                                        555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       532  (0.0296726); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1845.20
//
Query:       gene2441|gene2441|rna2441|rna2441  [L=440]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.9e-11   42.9   0.3    4.9e-11   42.9   0.3    3.0  3  NOC3p          Nucleolar complex-associated protein
  ------ inclusion threshold ------
      0.042   13.5   0.1      0.071   12.8   0.1    1.4  1  Peptidase_C58  Yersinia/Haemophilus virulence surface antigen
      0.045   13.8   0.4      0.045   13.8   0.4    1.7  2  CBF            CBF/Mak21 family
        1.3    9.1  23.0       0.37   10.9   7.0    2.9  3  LicD           LicD family


Domain annotation for each model (and alignments):
>> NOC3p  Nucleolar complex-associated protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.9   0.3   1.1e-14   4.9e-11       4      94 .]      23     104 ..      20     104 .. 0.86
   2 ?    0.5   3.1      0.19   8.5e+02      64      89 ..     234     259 ..     229     263 .. 0.83
   3 ?   -2.8   0.0         2   8.9e+03      34      54 ..     323     341 ..     309     344 .. 0.72

  Alignments for each domain:
  == domain 1  score: 42.9 bits;  conditional E-value: 1.1e-14
                              NOC3p   4 eeiaslassiledPeenlsllkrllklaeskdsavtvrklallsllaVfkDiiPgYrIrsltekekeekvskevkk 79 
                                        ++ia ++++++ dP++nl ++  +++ +++        +++llsll +f+Di+P Y+I++l++   e k + + +k
  gene2441|gene2441|rna2441|rna2441  23 KKIALCSKQVIIDPKDNLLNVMYIFDHCHT------FPEVSLLSLLRIFLDIVPLYKIKTLSN---EVKDKTQLSK 89 
                                        5799999**********9888877776644......4589*******************9995...4467788999 PP

                              NOC3p  80 lrefEqkLlkvYkky 94 
                                        l+++Eq Ll +Y k+
  gene2441|gene2441|rna2441|rna2441  90 LNKWEQDLLMIYSKF 104
                                        ************998 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.19
                              NOC3p  64 ltekekeekvskevkklrefEqkLlk 89 
                                         +e+ k+ek+ k+v+ +r  E++++ 
  gene2441|gene2441|rna2441|rna2441 234 SKEERKQEKIRKQVESRRLEEEGIVD 259
                                        45777888**********99999986 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 2
                              NOC3p  34 kdsavtvrklallsllaVfkD 54 
                                        +  +++++ l +l++la++ D
  gene2441|gene2441|rna2441|rna2441 323 S--SAETKFLGILAVLALYED 341
                                        3..477888999999999988 PP

>> Peptidase_C58  Yersinia/Haemophilus virulence surface antigen
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   1.6e-05     0.071      46     105 ..     207     267 ..     196     317 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.6e-05
                                        HSTTS.HHHHHHHHHHHHHHH.HHHHHHHTT-SSHHHHHHH..HHHHHTT-EE-S--EEEE CS
                      Peptidase_C58  46 lyaggskgqsraaeiqslysi.kklqllsqrakaqdqqfqatdtwlkeaglepseeelklg 105
                                        +y++++k++++ ++ + l ++  k ++++++ k+++++ q+ + +l+e g++ +e+++kl+
  gene2441|gene2441|rna2441|rna2441 207 IYENEKKRRKDKKHADGLLNKdDKKKMSKEERKQEKIRKQVESRRLEEEGIVDKEKQKKLE 267
                                        68888999999999999877526899******************************99987 PP

>> CBF  CBF/Mak21 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.6       1.7   7.5e+03     102     122 ..     221     238 ..     200     265 .. 0.54
   2 ?   13.8   0.4     1e-05     0.045      30      79 ..     352     403 ..     332     427 .. 0.76

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 1.7
                                CBF 102 lkalleekfkdvkeeeeeekk 122
                                           ll+   kd k++ ++e++
  gene2441|gene2441|rna2441|rna2441 221 ADGLLN---KDDKKKMSKEER 238
                                        344555...222222222222 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 1e-05
                                CBF  30 aLYrkLldpelltsskra..lllnlly.kalkadkpvkrvaAFvKRllqlalh 79 
                                         LY +L +p+ l+ + ++  l  ++l    l + ++v++v+ F+KRl+ l+ +
  gene2441|gene2441|rna2441|rna2441 352 YLYDLL-EPRTLRLKSSEskLAAKALKhFFLTNKQSVTIVKMFIKRLMVLCSL 403
                                        699999.8887766664432555666555667888*************97754 PP

>> LicD  LicD family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   1.5   0.00021      0.96      57     169 ..       9     142 ..       1     182 [. 0.68
   2 ?   10.9   7.0   8.4e-05      0.37      91     183 ..     185     277 ..     174     299 .. 0.67
   3 ?   -2.1   0.7      0.78   3.5e+03      32      48 ..     421     437 ..     420     439 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00021
                               LicD  57 lreaekdknylenfaklldkntsiterkngngkn..................dsglyiDIfpldyvpkskllikkk 114
                                        +++a +d+n+ + ++k+   +++++   ++n  n                     +++DI pl +++  ++++k k
  gene2441|gene2441|rna2441|rna2441   9 NSYALSDENEDQVIKKIALCSKQVIIDPKDNLLNvmyifdhchtfpevsllsLLRIFLDIVPLYKIKTLSNEVKDK 84 
                                        3444567777777777776666666666666666678888889999999999999********8787655543333 PP

                               LicD 115 kekeklkkklalk....kslskkdkkelkkkillkkksfklkklnkkkklkkleklekk 169
                                          + ++ +k++++    +s++    +++++++++k   + lk+l++ ++ +kl  +  +
  gene2441|gene2441|rna2441|rna2441  85 T-QLSKLNKWEQDllmiYSKFVFLVTKDTNDVNYKCAAELLKELSHFNYVEKLVSFVLR 142
                                        3.222233333335667899999999999999999999999999999999998877666 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 8.4e-05
                               LicD  91 dsglyiDIfpldyvpkskll..ikkkkekeklkkklalkkslskkdkkelkkkillkkksfklkklnkkkklkkle 164
                                         + l iDIf ++ v+++     i+++++k++++kk+a  ++l +kd k+++ k ++k+++ +++  +++ + + + 
  gene2441|gene2441|rna2441|rna2441 185 SNFLDIDIFEFQAVKDKFFTgfIYENEKKRRKDKKHA--DGLLNKDDKKKMSKEERKQEKIRKQVESRRLEEEGIV 258
                                        7899***********9877787555554444444444..4677777777777766666666666556666666666 PP

                               LicD 165 klekkkeydlkkseyiavl 183
                                        ++ek+k+ +lk +++i  +
  gene2441|gene2441|rna2441|rna2441 259 DKEKQKKLELKICNCILRI 277
                                        6666657777777776655 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 0.78
                               LicD  32 DlqmprkdyerLaevfn 48 
                                        D+ m ++d++ +  +++
  gene2441|gene2441|rna2441|rna2441 421 DIDMVIDDFQEFSVYLK 437
                                        99*********987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (440 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1575  (0.0878465); expected 358.6 (0.02)
Passed bias filter:                      492  (0.0274416); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.61u 0.28s 00:00:00.89 Elapsed: 00:00:00.45
# Mc/sec: 2960.33
//
Query:       gene2442|gene2442|rna2442|rna2442  [L=63]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.041   13.4   1.1      0.043   13.3   1.1    1.0  1  DUF2764   Protein of unknown function (DUF2764)
       0.18   12.8   6.4       0.37   11.8   1.3    2.0  2  Spt5_N    Spt5 transcription elongation factor, acidic N-term


Domain annotation for each model (and alignments):
>> DUF2764  Protein of unknown function (DUF2764)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   1.1   4.8e-06     0.043      94     133 ..       5      44 ..       1      49 [. 0.71

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.8e-06
                            DUF2764  94 delpsylkdFlleylaeeaeerish.edrLaalyyeyamkc 133
                                        ++ ++y k+Fl++yl+++ae+++++ e rL + y  y + +
  gene2442|gene2442|rna2442|rna2442   5 EDADEYEKNFLKKYLTRKAEDKLNElEKRLKKRY-GYKKRT 44 
                                        56789*****************876155555555.444443 PP

>> Spt5_N  Spt5 transcription elongation factor, acidic N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   1.5    0.0042        38      59      80 ..       3      24 ..       1      29 [. 0.76
   2 ?   11.8   1.3   4.1e-05      0.37      59      87 ..      23      51 ..      20      59 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0042
                                       XXXXXXXXXXXXXXXXXXXXXX CS
                             Spt5_N 59 ededaeeiaealeeRYgrsskk 80
                                       + eda+e ++++ ++Y +++++
  gene2442|gene2442|rna2442|rna2442  3 KYEDADEYEKNFLKKYLTRKAE 24
                                       4499************985443 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 4.1e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             Spt5_N 59 ededaeeiaealeeRYgrsskkayrgeae 87
                                       ++ ++ e++++l++RYg ++++++  +++
  gene2442|gene2442|rna2442|rna2442 23 AEDKLNELEKRLKKRYGYKKRTNNGADGK 51
                                       457899***********977776666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (63 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1659  (0.0925317); expected 358.6 (0.02)
Passed bias filter:                      846  (0.0471861); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 484.63
//
Query:       gene2443|gene2443|rna2443|rna2443  [L=515]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.2e-43  149.2   0.0    1.8e-43  148.6   0.0    1.2  1  SNF2_N      SNF2 family N-terminal domain
    4.8e-09   36.4   0.0    1.1e-08   35.2   0.0    1.6  1  ResIII      Type III restriction enzyme, res subunit
     0.0014   19.0   1.3      0.026   14.9   0.0    3.3  3  Helicase_C  Helicase conserved C-terminal domain
  ------ inclusion threshold ------
      0.063   13.4   0.3       0.41   10.8   0.1    2.4  2  DUF3911     Protein of unknown function (DUF3911)
       0.07   12.3   0.2       0.34   10.0   0.0    2.0  2  HDA2-3      Class II histone deacetylase complex subunits 2 a


Domain annotation for each model (and alignments):
>> SNF2_N  SNF2 family N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  148.6   0.0     5e-47   1.8e-43      55     349 ..     133     409 ..     116     410 .. 0.83

  Alignments for each domain:
  == domain 1  score: 148.6 bits;  conditional E-value: 5e-47
                                        T--EEE---TTS--HHHHHHHHH...HHTTTS---.......S-EEEE--HHHHHHHHHHHHHH-TTS-EEE--SS CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SNF2_N  55 vrGGiLaDemGLGKTvqvlalilaqrakeekdkekkrkdtlagptLivvPaslldqWeneierhvsssalrvlvyg 130
                                         +GGiLaDemGLGKT+q++a++    +  +++          g++Li++P++ll+qW  ei+r  +  ++ +l+ +
  gene2443|gene2443|rna2443|rna2443 133 KHGGILADEMGLGKTIQAIAFLS---SLLHSN--------KIGGVLILCPTTLLEQWFLEIRRIYPFVRTIILHNS 197
                                        58*********************...433333........3689*********************99999888877 PP

                                        HHHH..--------------..---EEEE-HHHHHHHT......TTS-S-S-SEEEES-GGGT--TTSHHHHHHHH CS
                                        xxxx..xxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SNF2_N 131 gqkk..mkkkntkvapklla..dydvvittYdvlsreaelqkkrsvlkqvewkrvvlDEghtlknstskaaeavsk 202
                                          ++  ++  ++ ++ ++ +   + +v+ +Y+  +         +++  ++ + ++lDEgh++kn ++++ + +++
  gene2443|gene2443|rna2443|rna2443 198 FIESidKTLDQKIIDGRMGEnfRKTIVVASYEGFKIFF------NKIRGLNLDILILDEGHKIKNFNTQTFKYIKT 267
                                        6665542233333444444411578**********555......9******************************6 PP

                                        ---S-EEEE-S--SSS-HHHHHHHHHHH-TTTT--HHHHHHHTHHHHH............HHHHHHHHHHHTT-ST CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............xxxxxxxxxxxxxxxx RF
                             SNF2_N 203 LstsnrwiltGTPiqnsledlygLlkfLreepfgekqtfdkllqrpie............aqaekgrsrLlqllqr 266
                                        ++     iltGTP+qn+l++l++L++  +   +g+++ f++++++ i             +++ ++ + L +l+++
  gene2443|gene2443|rna2443|rna2443 268 YN-CLTYILTGTPVQNNLRELWSLFNITNKHLLGSYTDFHEQFEDVILkgtrrkadkkekENSAQRTAYLKSLIAP 342
                                        65.45689*************************************9999*******9887778888889******* PP

                                        TEE---GGGT--S---EEEEEEEEE--HHHHHHHH....................HHHHHH-HHH-HHHHHHHHHH CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SNF2_N 267 lmlrrakkdveknlPpkteeiiflklskverksYnrllevlrkkalakllkrseaalkssskskekilelllelrq 342
                                        ++lrr+kk +  nlP+k e+i f++++  + ++Y+   e+   k+++ + k      +       ++++ l  lr+
  gene2443|gene2443|rna2443|rna2443 343 YILRRTKKGT--NLPKKYEKIAFCPMTTDQISMYK---EFIESKTVSDIIKG-----S------RNVFYGLDVLRK 402
                                        *********9..***********************...33333333333222.....2......236777788888 PP

                                        HHH---X CS
                                        xxxxxxx RF
                             SNF2_N 343 acnhpql 349
                                        + nhp+l
  gene2443|gene2443|rna2443|rna2443 403 ITNHPSL 409
                                        8888765 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.2   0.0   3.2e-12   1.1e-08       5     169 ..     116     279 ..     113     281 .. 0.80

  Alignments for each domain:
  == domain 1  score: 35.2 bits;  conditional E-value: 3.2e-12
                                        -HHHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG CS
                             ResIII   5 reyQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkflse 80 
                                         + Q++a++ + + +   +++ g+++ + G GKT+ a+++  +ll+++k+  +l+l+p+ +lleq+  e++++++ 
  gene2443|gene2443|rna2443|rna2443 116 LPFQQTALTWFCSLF--MGKHGGILADEMGLGKTIQAIAFLSSLLHSNKIGGVLILCPT-TLLEQWFLEIRRIYPF 188
                                        577999999999877..6999*************************************8.699************9 PP

                                        ...........GEEEESSS-B--...........-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTT CS
                             ResIII  81 ayke.......igkkvsgdkkka....kekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlg 145
                                         ++        ++ +++ d+  +    +++++  k i+v++++ ++          ++ +  + d++i DE H+++
  gene2443|gene2443|rna2443|rna2443 189 VRTIilhnsfiESIDKTLDQ--KiidgRMGENFRKTIVVASYEGFKIFF-------NKIRGLNLDILILDEGHKIK 255
                                        99888866643222233333..2458899999***************99.......889999999**********9 PP

                                        S.TTTHHHHHT---..SEEEEEESS- CS
                             ResIII 146 akkswreilekfke..avllglTATp 169
                                             ++  +++k   ++   lT+Tp
  gene2443|gene2443|rna2443|rna2443 256 NF--NTQTFKYIKTynCLTYILTGTP 279
                                        94..3333444444225555578887 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.28   9.9e+02      43      62 ..      42      61 ..      14      88 .. 0.68
   2 ?   -0.5   0.1      0.43   1.5e+03      40      58 ..     205     223 ..     150     272 .. 0.60
   3 !   14.9   0.0   7.3e-06     0.026      15      69 ..     452     506 ..     443     509 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.28
                                       EEEESTTSTHHHHHHHHHHH CS
                         Helicase_C 43 vavlhgelpqnereeileqf 62
                                       +++l ge+++ e +e +++f
  gene2443|gene2443|rna2443|rna2443 42 FVYLLGEMNKTEPDERFTRF 61
                                       44455555555555555555 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.43
                                        TSTEEEESTTSTHHHHHHH CS
                         Helicase_C  40 gikvavlhgelpqnereei 58 
                                         +   +++g++  n r+ i
  gene2443|gene2443|rna2443|rna2443 205 TLDQKIIDGRMGENFRKTI 223
                                        3344445555555555533 PP

  == domain 3  score: 14.9 bits;  conditional E-value: 7.3e-06
                                        TTSEEEEEESSHHHHHHHHHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSSE CS
                         Helicase_C  15 eggkilifvntidrlekvklllekkgikvavlhgelpqnereeileqfnkgesdv 69 
                                          +k+lif+++ ++l+ ++ +  ++++ +++++g+++  er++ l+ f k+++ +
  gene2443|gene2443|rna2443|rna2443 452 PMNKVLIFSQSLEMLSIIESFIASNKYAYLRMDGTTSLMERKRRLDMFTKKDYFI 506
                                        5689***********88888878889**********************9887765 PP

>> DUF3911  Protein of unknown function (DUF3911)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   0.00012      0.41       3      25 ..       1      23 [.       1      36 [. 0.88
   2 ?   -1.5   0.0      0.79   2.8e+03      44      57 ..     195     208 ..     193     224 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00012
                            DUF3911  3 cvqikGtrkevvemlqlfdlmdt 25
                                       +vq++ tr+e+v+ l+l d m++
  gene2443|gene2443|rna2443|rna2443  1 MVQMEKTRQELVRSLRLVDEMEA 23
                                       59*******************86 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.79
                            DUF3911  44 hnefvasidlqane 57 
                                        hn f+ sid    +
  gene2443|gene2443|rna2443|rna2443 195 HNSFIESIDKTLDQ 208
                                        899*****965544 PP

>> HDA2-3  Class II histone deacetylase complex subunits 2 and 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.18   6.3e+02      48      67 ..     390     409 ..     338     410 .. 0.74
   2 ?   10.0   0.0   9.4e-05      0.34      90     153 ..     418     495 ..     412     504 .. 0.76

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.18
                                        HHHHHHHH.HHHHHHH-GGG CS
                             HDA2-3  48 ikslticlenlslvanHPsL 67 
                                           + + l+ l+ + nHPsL
  gene2443|gene2443|rna2443|rna2443 390 SRNVFYGLDVLRKITNHPSL 409
                                        55666778899999****98 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 9.4e-05
                                        -HHHHHHHHHHHHHTTSS..................EEEEEEE-STHHHHHHHHHHTTSSSEEEESSS--S--S-- CS
                             HDA2-3  90 SgKFkvlndlvnliierkrkss..............lnvlvvakskkeldLiEalllGkklkikrysgeklydekk 151
                                        SgK+++l  l++   e  ++                 +vl+ ++s   l +iE+++ ++k  + r++g++ + e k
  gene2443|gene2443|rna2443|rna2443 418 SGKMHMLAALLKKWYEGVKDDGlnaeprensdrmpmNKVLIFSQSLEMLSIIESFIASNKYAYLRMDGTTSLMERK 493
                                        7777777777766666554444566677777888878999999999999*******************98766665 PP

                                        -S CS
                             HDA2-3 152 kk 153
                                         +
  gene2443|gene2443|rna2443|rna2443 494 RR 495
                                        44 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (515 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       712  (0.0397122); expected 358.6 (0.02)
Passed bias filter:                      517  (0.028836); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.61u 0.30s 00:00:00.90 Elapsed: 00:00:00.47
# Mc/sec: 3311.12
//
Query:       gene2444|gene2444|rna2444|rna2444  [L=143]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       518  (0.0288917); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 956.39
//
Query:       gene2445|gene2445|rna2445|rna2445  [L=42]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (42 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       530  (0.029561); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.45
# Mc/sec: 281.41
//
Query:       gene2446|gene2446|rna2446|rna2446  [L=216]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.5e-13   49.8  26.0    2.4e-12   47.1   9.1    3.2  3  zf-CHY    CHY zinc finger
     0.0041   17.1  15.1       0.16   12.0   0.2    3.2  3  HypA      Hydrogenase/urease nickel incorporation, metallocha
  ------ inclusion threshold ------
      0.013   15.3   0.2      0.013   15.3   0.2    2.0  3  PocR      Sensory domain found in PocR


Domain annotation for each model (and alignments):
>> zf-CHY  CHY zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.7   1.2    0.0034        20      52      73 ..      41      62 ..      25      72 .. 0.72
   2 !    7.8   1.2    0.0008       4.8      39      74 ..      86     126 ..      74     131 .. 0.76
   3 !   47.1   9.1   4.1e-16   2.4e-12       1      54 [.     162     213 ..     162     215 .. 0.93

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0034
                             zf-CHY 52 ekavlCkkCkkefaeyfCpiCk 73
                                       +++v+Ck+C+++f+    ++C+
  gene2446|gene2446|rna2446|rna2446 41 TAQVVCKQCQRNFTINRSKQCQ 62
                                       4577888888877666666665 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0008
                             zf-CHY  39 vkevlcllCeteqekavlCkkCkk......efaeyfCpiCkl 74 
                                        ++  l+l C ++ e+   C +C++      +  e++C +C++
  gene2446|gene2446|rna2446|rna2446  86 MS-SLVLICFETPETILSCLNCGSyyhtkeKNVEFSCFNCNT 126
                                        44.457889988888889999999887766566678999986 PP

  == domain 3  score: 47.1 bits;  conditional E-value: 4.1e-16
                             zf-CHY   1 CkHykravvairapcCkklyaCreCHeeledhelerlevkevlcllCeteqeka 54 
                                        CkHy++++ + r+pcC+kl++C+eCH+e+ dhel+r+++  ++c lC +eq++a
  gene2446|gene2446|rna2446|rna2446 162 CKHYRKSFKWYRFPCCNKLFPCDECHNESVDHELKRASK--MICGLCAEEQNIA 213
                                        **********************************99875..59*******9875 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.2   2.7e-05      0.16      62      93 ..      35      64 ..      12      71 .. 0.77
   2 !   11.5   0.3   3.7e-05      0.22      64      95 ..      94     127 ..      75     134 .. 0.80
   3 ?    0.6   4.0     0.092   5.5e+02      71      95 ..     181     209 ..     156     214 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.7e-05
                                       EEEEEE--EEEETTTS-EEECHHHHHS-TTTS CS
                               HypA 62 LeieevpvkvrCreCgkefeleekalrCpkCg 93
                                       + +++  ++v C++C+++f+++++  +C+ C+
  gene2446|gene2446|rna2446|rna2446 35 IYMKSLTAQVVCKQCQRNFTINRS-KQCQ-CK 64
                                       5588999*************8864.3565.55 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 3.7e-05
                                        EEEE--EEEETTTS-EEECHHH..HHS-TTTSSS CS
                               HypA  64 ieevpvkvrCreCgkefeleek..alrCpkCgsa 95 
                                        +e+ +  + C +Cg+ ++++ek  +++C +C++ 
  gene2446|gene2446|rna2446|rna2446  94 FETPETILSCLNCGSYYHTKEKnvEFSCFNCNTF 127
                                        78889999*********977744899*****975 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.092
                                        EEETTTS-EEECHH..H..HHS-TTTSSS CS
                               HypA  71 vrCreCgkefelee..k..alrCpkCgsa 95 
                                        + C+eC++e   +e  +  ++ C+ C ++
  gene2446|gene2446|rna2446|rna2446 181 FPCDECHNESVDHElkRasKMICGLCAEE 209
                                        56999998877554442456789999876 PP

>> PocR  Sensory domain found in PocR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.2   2.2e-06     0.013      56     100 ..      46      85 ..      34      99 .. 0.83
   2 ?   -1.9   0.2      0.42   2.5e+03      47      78 ..      94     124 ..      87     130 .. 0.59
   3 ?   -3.3   0.9       1.1   6.6e+03      55      70 ..     182     197 ..     153     207 .. 0.62

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.2e-06
                               PocR  56 CrksdarggeeavksgkpyiykChaGLvdvavPIivegkllGaii 100
                                        C++++++        ++ +  +C+++L++  +PI+++++++G++ 
  gene2446|gene2446|rna2446|rna2446  46 CKQCQRNFT-----INRSKQCQCKNDLIYEFTPIFYHNNYVGRLE 85 
                                        777777776.....4577789*********************985 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.42
                               PocR  47 rstpegrkrCrksdarggeeavksgkpyiykC 78 
                                         +tpe+   C  + ++    + k+ +   + C
  gene2446|gene2446|rna2446|rna2446  94 FETPETILSCLNCGSYYHT-KEKNVEFSCFNC 124
                                        5566666667777666542.233335555555 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 1.1
                               PocR  55 rCrksdarggeeavks 70 
                                         C +++++  ++++k+
  gene2446|gene2446|rna2446|rna2446 182 PCDECHNESVDHELKR 197
                                        4666666666555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (216 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       862  (0.0480785); expected 358.6 (0.02)
Passed bias filter:                      252  (0.0140554); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1635.78
//
Query:       gene2447|gene2447|rna2447|rna2447  [L=184]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00017   21.3   0.1    0.00029   20.6   0.1    1.3  1  NUC153    NUC153 domain
  ------ inclusion threshold ------
      0.039   14.8   2.9      0.072   14.0   2.9    1.4  1  DUF1764   Eukaryotic protein of unknown function (DUF1764)
      0.048   13.1   0.1      0.056   12.9   0.1    1.2  1  DUF620    Protein of unknown function (DUF620)


Domain annotation for each model (and alignments):
>> NUC153  NUC153 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.1   4.9e-08   0.00029       1      23 [.     144     166 ..     144     170 .. 0.96

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 4.9e-08
                             NUC153   1 DpRFkalFedhdFaIDptspeFk 23 
                                        D+RF ++++d+ F ID ++p +k
  gene2447|gene2447|rna2447|rna2447 144 DSRFDKVYTDPSFYIDTSHPLYK 166
                                        9*******************999 PP

>> DUF1764  Eukaryotic protein of unknown function (DUF1764)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   2.9   1.2e-05     0.072      10      74 ..      75     140 ..      71     154 .. 0.64

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.2e-05
                            DUF1764  10 eideifseskkkkkekekeeeee...ekekkkkskkkkkkkkkkeeekkfedseskkrrktedGlpvY 74 
                                        ei++if +    +++ e  ee     + ek++k+++kk+++kk+++ek+ ++ e++ +rk +dG+ v+
  gene2447|gene2447|rna2447|rna2447  75 EIENIFLDCYFMDEKAELGEE-IfveKVEKVRKTNTKKSERKKQRKEKTKREIEERIKRKNADGF-VF 140
                                        666666554443333333322.1343667777777777777888888888888889999999998.44 PP

>> DUF620  Protein of unknown function (DUF620)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   9.3e-06     0.056      89     135 ..      69     115 ..      43     162 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 9.3e-06
                             DUF620  89 qGLdprstanlfseaacvgekkindedcfvLkleadkealkarsese 135
                                        + Ld + + n+f+++ ++ ek+  +e+ fv k+e  +++ +++se +
  gene2447|gene2447|rna2447|rna2447  69 DILDGQEIENIFLDCYFMDEKAELGEEIFVEKVEKVRKTNTKKSERK 115
                                        569999***************************99888877776644 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2586  (0.144236); expected 358.6 (0.02)
Passed bias filter:                      869  (0.048469); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 1260.39
//
Query:       gene2448|gene2448|rna2448|rna2448  [L=250]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.9e-23   81.1   0.0    8.4e-23   80.8   0.0    1.1  1  Proteasome      Proteasome subunit
     0.0037   16.9   0.0      0.007   16.0   0.0    1.5  1  Proteasome_A_N  Proteasome subunit A N-terminal signature


Domain annotation for each model (and alignments):
>> Proteasome  Proteasome subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.8   0.0   9.4e-27   8.4e-23       2     189 ..      39     221 ..      38     222 .. 0.90

  Alignments for each domain:
  == domain 1  score: 80.8 bits;  conditional E-value: 9.4e-27
                                        HHS-EEEEEEETTEEEEEEEEEEEETTEEEESSSSTSEEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHSS CS
                         Proteasome   2 kkGttvvGikgkdgvvlaadkratagskllskstveKifkiddhigvafaGlaaDartlvrraraeaqlyrlrygr 77 
                                        ++G+t++++k ++gv++a +k + ++ +++s++  ++i k+++++++a +Gl +D+  + + +++ +   + r   
  gene2448|gene2448|rna2448|rna2448  39 DNGSTCIALKNNNGVLIAIEKPIDSNLYIISED--KRIKKLTRNCVIAGTGLLSDMIFFNSLVQRDLIGLQ-RQTA 111
                                        68**********************888898888..8***************************99988666.4555 PP

                                        GTCHHHHHHHHHHHHHHHHHHCTTTTTSEEEEEEEEETTTEEEEEEEETTSEEEEESSEEEESTTHHHHHHHHHHH CS
                         Proteasome  78 pipverlvarvaaklqaytqrsgrrpfgvslliagvdeeggpeLyqidpsGsyieekdavaiGsgseaaktaleke 153
                                         +p  ++ + ++ + ++ t ++g rp+gv++l a  d  g++ Ly +d s +  e +   aiG+g+  akt lek 
  gene2448|gene2448|rna2448|rna2448 112 SLPANTVKKVISMHSSEFTRYYGCRPLGVNMLSAVND-FGTYTLYVTDTSSKTREVR-GYAIGKGAARAKTELEKI 185
                                        556664556666677778889999********99888.999***************5.****************** PP

                                        HSTTBSHHHHHHHHHHHHHHHHHHBTTSCSSEEEEE CS
                         Proteasome 154 ykedltleeavelavkalkealerdklsgknievav 189
                                          e+l+ + +++ av++l++ ++  k ++ ++e+++
  gene2448|gene2448|rna2448|rna2448 186 DIEELSHKRMIDNAVRILYKCFDPLKDKPFEVEIGI 221
                                        ***********************9999999999997 PP

>> Proteasome_A_N  Proteasome subunit A N-terminal signature
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   7.8e-07     0.007       7      22 ..      21      36 ..      17      36 .. 0.94

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 7.8e-07
                     Proteasome_A_N  7 tFSPdGRLfQVEYAmk 22
                                       +++P G + Q++YA+k
  gene2448|gene2448|rna2448|rna2448 21 IYTPTGNIAQIDYAQK 36
                                       89*************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       494  (0.0275531); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1719.09
//
Query:       gene2449|gene2449|rna2449|rna2449  [L=613]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (613 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       870  (0.0485247); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.59u 0.27s 00:00:00.86 Elapsed: 00:00:00.44
# Mc/sec: 4149.80
//
Query:       gene245|gene245|rna245|rna245  [L=148]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.19   10.9   2.1       0.25   10.5   2.1    1.2  1  DUF2465   Protein of unknown function (DUF2465)


Domain annotation for each model (and alignments):
>> DUF2465  Protein of unknown function (DUF2465)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   2.1   1.4e-05      0.25      92     171 ..       3      82 ..       1      95 [. 0.89

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 1.4e-05
                        DUF2465  92 lkskedrlkLlefLvsElqaarileskkekekekekkkkveeesetakelkeilktLglskppanitasqlfskieekik 171
                                    ++++e+++ L++ L + ++   ++ +  +++ ek ++k+ ++++++ +e k+i++t + + ++ ++t+++l++++++  +
  gene245|gene245|rna245|rna245   3 VSDEEQKMILINSLENQIKNISLIFNIIHDHIEKLEEKSRINQEPIKEECKDIISTFKTGTKTYSTTMKKLMDDVQDDQS 82 
                                    67899********************9998988888888889********************************9998655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1372  (0.0765241); expected 358.6 (0.02)
Passed bias filter:                      683  (0.0380947); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1025.95
//
Query:       gene2450|gene2450|rna2450|rna2450  [L=283]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    7.7e-05   22.1   4.9    0.00039   19.8   3.0    2.4  2  HAT_KAT11  Histone acetylation protein
  ------ inclusion threshold ------
       0.16   11.7   0.5       0.35   10.6   0.2    1.6  2  PAW        PNGase C-terminal domain, mannose-binding module P


Domain annotation for each model (and alignments):
>> HAT_KAT11  Histone acetylation protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   3.0   4.4e-08   0.00039      49     169 ..      15     125 ..       8     163 .. 0.77
   2 ?    0.9   0.0     0.025   2.2e+02     128     147 ..     188     207 ..     160     212 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 4.4e-08
                          HAT_KAT11  49 khflalsenddkeviifglevlvYitvfdeanerliFVSkaDstgylkllkvkvadivetllsylisikqreylrk 124
                                        k +++l +   +++ ++ + +   +   ++++ + +F+  +D+tg++++++++   +v++++ ++++    +yl+ 
  gene2450|gene2450|rna2450|rna2450  15 KELFMLLQRLTNDKGVLTVPIASLVI--ERDSMNGLFIESLDTTGLFQPRNLQ-TFYVQAFILFVVNLYDPDYLET 87 
                                        55666666666777777777776666..7788899**************6665.57999********999999876 PP

                          HAT_KAT11 125 vklsLFtraqdqYLFPnssknpkKHvLddkgLlkWWikvldkilr 169
                                             F  ++++ +F +ss  +k  +L +k+Llk W +v   +  
  gene2450|gene2450|rna2450|rna2450  88 -----FSHPKSELVFLKSSTAKK--ILAPKKLLKYWQNVFHMMYS 125
                                        .....5999**********9999..*************9887774 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.025
                          HAT_KAT11 128 sLFtraqdqYLFPnssknpk 147
                                        +L +r++++Y  Pn++k++k
  gene2450|gene2450|rna2450|rna2450 188 CLTARNAENYFVPNEKKIKK 207
                                        8999*************997 PP

>> PAW  PNGase C-terminal domain, mannose-binding module PAW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0      0.25   2.2e+03      24      54 ..     104     137 ..      94     181 .. 0.63
   2 ?   10.6   0.2   3.9e-05      0.35      21      77 ..     194     248 ..     184     251 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.25
                                        --EB---H.HHHHHTEEEEEEE..TTTTEEEECC CS
                                PAW  24 eyvfkpte.kekkekllelrYs..ivkDkYvrvs 54 
                                        + ++ p++  +  ++++++ Ys  +v+ +Y+r+s
  gene2450|gene2450|rna2450|rna2450 104 KKILAPKKlLKYWQNVFHMMYSnvMVHSNYHRTS 137
                                        4555555534445677888887223456666665 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 3.9e-05
                                        -----EB---HHHHHHTEEEEEEETTTTEEEECCGTTEEEESGGGG-SSEESEEEEE CS
                                PAW  21 kekeyvfkptekekkekllelrYsivkDkYvrvskneeeikgwesavfevenifrkv 77 
                                        +e+ +v + ++ +k +k++++ Y+i +D+Y   sk   ++ +++s ++ +e+i + v
  gene2450|gene2450|rna2450|rna2450 194 AENYFVPNEKKIKKLSKCFKIGYTIENDVYDFLSK--IRTGDYSSHIIASESIEKSV 248
                                        3344444555577789***************9999..77899999999999998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (283 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       489  (0.0272742); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 2085.04
//
Query:       gene2451|gene2451|rna2451|rna2451  [L=624]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-16   59.8   2.4    2.8e-16   59.8   2.4    2.1  2  UCH       Ubiquitin carboxyl-terminal hydrolase
     0.0018   17.9  14.7      0.003   17.2   7.6    3.3  2  UCH_1     Ubiquitin carboxyl-terminal hydrolase


Domain annotation for each model (and alignments):
>> UCH  Ubiquitin carboxyl-terminal hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.1      0.16   1.4e+03     113     142 ..     143     172 ..      52     228 .. 0.59
   2 !   59.8   2.4   3.1e-20   2.8e-16       1     257 []     337     620 ..     337     620 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.16
                                        HHHCCHCCCHHHHHHCCCTTSHHHHHH-EE CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                                UCH 113 edlnrevaeekwkkhlkrndslitdlfegq 142
                                        e++ ++  +++  ++  +++++i+d+fe++
  gene2451|gene2451|rna2451|rna2451 143 ESVFSDDYSQRQSSNFVSEQNNISDMFETK 172
                                        222222222222444444445555555544 PP

  == domain 2  score: 59.8 bits;  conditional E-value: 3.1e-20
                                        -EES-SSSTHHHHHHHHHHHTSHHHHHHHHTCHHCCSSTCCCCC-.TT.TTS.TTHHHHHHHHHHHHHHSH-CCEE CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                                UCH   1 tGlsNlGntCymnsvlQcLfsipelrdyllsleevkkesrnkkelnesnplgkkgelakalkdlfkellkskskav 76 
                                        tGl N   +C+ n+++Q+L++ +++ d+++s       ++ k +l            +++  +l++++lk+++k+v
  gene2451|gene2451|rna2451|rna2451 337 TGLPNKQSNCFFNASIQMLYASQSFVDFIKS-------DSLK-SL-----------CSMETLRLIHDMLKKNEKNV 393
                                        79*****************************.......3333.33...........56778889999998777777 PP

                                        --HHHHHHHHHHSGGGT.....SSSTCEHHHHHHHHHHHHHHHHCC.............................. CS
                                        xxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxx.............................. RF
                                UCH  77 sPkklkktlsklaksfs.....gykqqDaqEflaflLdqlhedlnr.............................. 117
                                          + ++k +++++k +        kq+Da +fl  l++++ +   +                              
  gene2451|gene2451|rna2451|rna2451 394 W-DVFLKLCASSKKLIPygnilEVKQHDAVDFLVDLFEEIWNMAGDksihleypfafisneisicatcqkptsikq 468
                                        7.589999999999866666769***************99988888899999999999999999999998887766 PP

                                        .......HCCCHHH.HHHCCCTTSHHHHHH-EEEEE.......................EEEEEEB-SEEEEEEES CS
                                        .......xxxxxxx.xxxxxxxxxxxxxxxxxxxxx.......................xxxxxxxxxxxxxxxxx RF
                                UCH 118 .......evaeekw.kkhlkrndslitdlfegqlks.......................klklkrlPeiLiihlkR 162
                                               + ++e   +++l   ++l          +                         +  ++P+ +ii ++R
  gene2451|gene2451|rna2451|rna2451 469 fencyvlDLKAEPSiNSQLVMFNCL----------EedirsgnikrckhvyscehtntiLKTCANVPKLIIIRIER 534
                                        6555555323333334444444444..........244444555559999999998887677899*********** PP

                                        EEETEE...EEE--SEEB--SEEE-GGGBSS-BTTS-TCS-BEEEEEEEEEESCTTSEEEEEEEECTTTTEEEEEE CS
                                        xxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                                UCH 163 fsynss...ksKlntkvefpeeldlssylaeekkkkteekkkYeLiavvvHsGslssGHYvayiknekngkWykyd 235
                                          ++s     +K+  +++ +e ++++              ++Y+L ++++H G+ + GH++a+++  k  kWy+ +
  gene2451|gene2451|rna2451|rna2451 535 NIFDSVlqkTKKNVAPIDTEEHITIN-------------TRDYRLKSFIMHFGEDNAGHFTAVVR--KGIKWYHVN 595
                                        ***99944444444455555444444.............234***********************..8899***** PP

                                        TTEEEEE-HHCCCTT...CEEEEEE CS
                                        xxxxxxxxxxxxxxx...xxxxxxx RF
                                UCH 236 Detvkevkeeeevls...sayiLfY 257
                                        D+ +  +++ +  l+     y+L+Y
  gene2451|gene2451|rna2451|rna2451 596 DDVIGLINDIHRFLKgnpYTYLLLY 620
                                        ****999976666668778888888 PP

>> UCH_1  Ubiquitin carboxyl-terminal hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.6     0.034     3e+02      62     138 ..      87     172 ..      43     231 .. 0.60
   2 !   17.2   7.6   3.3e-07     0.003       2     317 ..     338     596 ..     337     599 .. 0.72

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.034
                                        xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxx.........xxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxx.x RF
                              UCH_1  62 cqasnFlrals.sipeasalglileeeeete.........kssaislssliq.sfnrflldqlekelketkkns.s 125
                                        c +s+F ++ + ++pe   l+l  +++  +e         +  ++++ ++   s+  f+ + +++++++ ++++  
  gene2451|gene2451|rna2451|rna2451  87 CVSSEFHEQSQrNLPERGILRLQ-DSD--QEllsdmfetkRMYEQEYVPMPAtSLDSFIESVFSDDYSQRQSSNfV 159
                                        44444433322345554444442.221..11223344333333444444444345555555555555554444456 PP

                                        xxxxxxxxxxxxx RF
                              UCH_1 126 eeesaieqllgtk 138
                                        +e+++i+++++tk
  gene2451|gene2451|rna2451|rna2451 160 SEQNNISDMFETK 172
                                        7777788888665 PP

  == domain 2  score: 17.2 bits;  conditional E-value: 3.3e-07
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              UCH_1   2 GLEnhivnsYlNslLQvlyfipplrnlalshlakeckkehcLlcElgflfdmldkakglncqasnFlralssipea 77 
                                        GL n+ +n++ N+ +Q+ly  + +  +++s       k  c +  l ++ dml+k +++      Fl+   s+++ 
  gene2451|gene2451|rna2451|rna2451 338 GLPNKQSNCFFNASIQMLYASQSFVDFIKSDS----LKSLCSMETLRLIHDMLKKNEKNVW--DVFLKLCASSKKL 407
                                        999999****************9999999988....8888888888888899999875433..3466666655544 PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              UCH_1  78 salglileeeeetekssaislssliq.sfnrflldqlekelketkknsseeesaieqllgtkaettirclkCgsek 152
                                           g ile               + q     fl+d +e+ ++ + +    ++  +e  +++  ++ + c +C++ +
  gene2451|gene2451|rna2451|rna2451 408 IPYGNILE---------------VKQhDAVDFLVDLFEEIWNMAGD----KSIHLEYPFAFISNEISICATCQKPT 464
                                        44444433...............33424789999999999998765....566688899999999********988 PP

                                        ..xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxx RF
                              UCH_1 153 ..srksstlvldlkyPkpsnekkeakvtf.asilksslerekttrawCekCkryqpteqrktvk....nlPpvLal 221
                                          ++ ++ +vldlk+  +         ++ ++++  +  +e+   +  ++Ck+  + e+++t+     n+P+++++
  gene2451|gene2451|rna2451|rna2451 465 siKQFENCYVLDLKA--E--------PSInSQLVMFNCLEEDIRSGNIKRCKHVYSCEHTNTILktcaNVPKLIII 530
                                        6788899******77..2........234133333333334444578889988888888888777888******** PP

                                        xxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              UCH_1 222 nakle.eeeelelwktknwlpleiklsldedknleeklkeerekakaekeikvYeLqsvvvhigdskesghLvslv 296
                                          +++  ++         +l++  k  +          ++e   ++ + +++ Y L s+++h g ++++gh  ++v
  gene2451|gene2451|rna2451|rna2451 531 RIERNiFDS---------VLQKTKKN-VA-------PIDTE---EHITINTRDYRLKSFIMHFG-EDNAGHFTAVV 585
                                        **9865554.........44433222.11.......11122...224566889***********.555******** PP

                                        xxxxxxxxxxxxxx.xxxxxxx RF
                              UCH_1 297 kvaekelerdppes.qWylFND 317
                                        +   k        + +Wy  ND
  gene2451|gene2451|rna2451|rna2451 586 R---K--------GiKWYHVND 596
                                        *...3........338999999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (624 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       701  (0.0390987); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.66u 0.26s 00:00:00.92 Elapsed: 00:00:00.46
# Mc/sec: 4049.54
//
Query:       gene2452|gene2452|rna2452|rna2452  [L=297]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (297 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       775  (0.0432261); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1882.58
//
Query:       gene2453|gene2453|rna2453|rna2453  [L=94]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.015   15.5   0.4      0.018   15.3   0.4    1.1  1  VWD       von Willebrand factor type D domain
      0.059   13.6   0.5        0.1   12.8   0.5    1.5  1  DPM3      Dolichol-phosphate mannosyltransferase subunit 3 (D


Domain annotation for each model (and alignments):
>> VWD  von Willebrand factor type D domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.4     2e-06     0.018      56     103 ..      27      74 ..      16      93 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2e-06
                                VWD  56 sclksvkvrvgdveieltrrnkkvlvngqdvslplvnagkeveilksg 103
                                        ++++ + v v++ ++ ++  +  v++n++d+++++ +++++++++++ 
  gene2453|gene2453|rna2453|rna2453  27 IFTVVIDVFVFGFYVLMKSVFEAVVMNQTDIKNEVMEYNNKIKMTRER 74 
                                        56777889999*********************************9943 PP

>> DPM3  Dolichol-phosphate mannosyltransferase subunit 3 (DPM3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.5   1.1e-05       0.1      35      90 ..      23      80 ..       1      81 [. 0.78

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.1e-05
                               DPM3 35 devvpvlPlwalvlfGayslatlgyg..vltfndcpeaakeLqkeikeAkadLrkkGv 90
                                       +  ++++ ++ +++fG y l++ +++  v++  d +++  e +++ik  ++  ++k++
  gene2453|gene2453|rna2453|rna2453 23 QLNIIFTVVIDVFVFGFYVLMKSVFEavVMNQTDIKNEVMEYNNKIKMTRERIEQKNM 80
                                       3446667788899*******99887644788889*******************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1875  (0.104579); expected 358.6 (0.02)
Passed bias filter:                      562  (0.0313459); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 662.10
//
Query:       gene2454|gene2454|rna2454|rna2454  [L=290]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.085   13.2   0.0       0.22   11.9   0.0    1.7  2  ANAPC4_WD40  Anaphase-promoting complex subunit 4 WD40 domain


Domain annotation for each model (and alignments):
>> ANAPC4_WD40  Anaphase-promoting complex subunit 4 WD40 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   1.2e-05      0.22      20      78 ..      35      91 ..      30     113 .. 0.82
   2 ?   -3.3   0.0      0.66   1.2e+04      56      76 ..     210     230 ..     205     234 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.2e-05
                        ANAPC4_WD40 20 lvfRlngqrvwtleedkedsevrsLaWkpdgklLavaysdgevrlldaesgkvvhslsv 78
                                       lv   + +r++++ + +e ++++ ++W+++g+ L++ + d ev  ++++++k+   lsv
  gene2454|gene2454|rna2454|rna2454 35 LVRKNDYRRLYNF-TYDELQKIKFISWSEKGENLVICHTD-EVTAFNIYTKKTELRLSV 91
                                       4555577899999.678889**************997776.788899999988666655 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 0.66
                        ANAPC4_WD40  56 aysdgevrlldaesgkvvhsl 76 
                                         ys+ ++++++ +s  v+ +l
  gene2454|gene2454|rna2454|rna2454 210 CYSKKNLKIFEKHSDSVLLAL 230
                                        567777777777777776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (290 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       669  (0.0373138); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1995.56
//
Query:       gene2455|gene2455|rna2455|rna2455  [L=517]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.4e-15   55.8  11.8    1.6e-11   44.2   0.4    3.2  4  RVT_1           Reverse transcriptase (RNA-dependent DNA poly
      1e-05   25.7   5.1      1e-05   25.7   5.1    2.9  3  Telomerase_RBD  Telomerase ribonucleoprotein complex - RNA bi
  ------ inclusion threshold ------
       0.12   12.5   0.9        1.2    9.2   0.1    2.8  3  DUF3683         Protein of unknown function (DUF3683)


Domain annotation for each model (and alignments):
>> RVT_1  Reverse transcriptase (RNA-dependent DNA polymerase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.4   1.4e-07   0.00085       1      95 [.      72     161 ..      72     187 .. 0.70
   2 !   44.2   0.4   2.7e-15   1.6e-11     118     206 ..     240     326 ..     182     370 .. 0.77
   3 ?   -3.8   0.0       1.2   7.2e+03      22      38 ..     403     422 ..     399     438 .. 0.68
   4 ?   -2.1   0.2      0.38   2.2e+03     199     206 ..     476     483 ..     454     505 .. 0.49

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.4e-07
                                        EE-TT.S-EEE......-THHHHCTB--.........-------HHHH.............HCCHTS--EEEEEEB CS
                              RVT_1   1 ipKkgpgsyRpisllsvdykalnkliakrLkdvlekllsenqpgfrpgrstldavedllkalkkkkkaklllklDl 76 
                                        ipKk+  ++R+i   s ++k+      +++ +    ++ ++   +++g s +d ++  +++++   +a  +lk+D+
  gene2455|gene2455|rna2455|rna2455  72 IPKKD--GFRVIVNKSKRDKKG--KSENMILQS-AYHILTKEQELDHGNSFIDYTQIFNEFMRYDFSASFILKFDI 142
                                        78887..888875555555532..222222223.334555555788999999988889999999999********* PP

                                        CCGCCCSBB-GGGGGGG-E CS
                              RVT_1  77 kkaFdsvpleellrkltaf 95 
                                        k++Fds+p++ l   l +f
  gene2455|gene2455|rna2455|rna2455 143 KGCFDSIPHDNLQAILIDF 161
                                        **********998766555 PP

  == domain 2  score: 44.2 bits;  conditional E-value: 2.7e-15
                                        ......TEEEEESB--ST-TTHHHHHHHHHHHHHTT-T.......TEEECTTEEEEEESSHHHHHHHHHHHHHHHH CS
                              RVT_1 118 vngeeskgryekkglpqGsvlSPllfnlfmnellrelrkra.kgvtllrYaDDililskskeelqelleaveewlk 192
                                          g  ++++ ++kg+pqGs+lS +l++l++++l+ +l +++ k   + rY+DD+li+s s +e+ ++l+++ ++l+
  gene2455|gene2455|rna2455|rna2455 240 TFG--KEQYIQQKGIPQGSILSSILSSLYFQSLDTSLFNKIvKVGRIFRYVDDFLIVSPSLDEMLSILSSL-KYLE 312
                                        233..48999***************************999978889**********************998.59** PP

                                        HTT--BEGGG-EEE CS
                              RVT_1 193 esglkinpeKtklv 206
                                        + g++in +K++  
  gene2455|gene2455|rna2455|rna2455 313 KDGVTINYKKIESN 326
                                        **********9865 PP

  == domain 3  score: -3.8 bits;  conditional E-value: 1.2
                                        HHCTB--............- CS
                              RVT_1  22 lnkliakrLkdvl...ekll 38 
                                        +n+ ++k Lkd++   ++ +
  gene2455|gene2455|rna2455|rna2455 403 VNRFLKKILKDMYfvrRNAF 422
                                        67888888888876653333 PP

  == domain 4  score: -2.1 bits;  conditional E-value: 0.38
                                        EGGG-EEE CS
                              RVT_1 199 npeKtklv 206
                                         ++K kl+
  gene2455|gene2455|rna2455|rna2455 476 TEKKLKLI 483
                                        33333333 PP

>> Telomerase_RBD  Telomerase ribonucleoprotein complex - RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   5.1   1.7e-09     1e-05      83     133 ..       2      51 ..       1      52 [. 0.91
   2 ?   -3.6   0.0       1.9   1.1e+04      76      92 ..     117     133 ..      96     138 .. 0.72
   3 ?   -0.4   0.5      0.19   1.1e+03      88     113 ..     400     425 ..     390     467 .. 0.73

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 1.7e-09
                                        HHHHHHHHHHTCHHHHHHHH-EEEE--SSS-SEEEE-HHHHHHHHHHHHHH CS
                     Telomerase_RBD  83 lseflywlfdslliplirsfFYvTessktrnrlfyFrkdvWrkltkpalak 133
                                        ++++l+ +fd+l ipli++ FY Te   ++ ++fyF ++ W+ +tk +l++
  gene2455|gene2455|rna2455|rna2455   2 FCNLLFLIFDKLFIPLISTCFYSTEGF-QNFKVFYFTRKAWSFFTKIHLQE 51 
                                        6789999******************76.78****************99875 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 1.9
                                        HHHHHHHHHHHHHHHHH CS
                     Telomerase_RBD  76 aekrkellseflywlfd 92 
                                        +   +++++ef+ + f+
  gene2455|gene2455|rna2455|rna2455 117 FIDYTQIFNEFMRYDFS 133
                                        45567889999988765 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.19
                                        HHHHHTCHHHHHHHH-EEEE--SSS- CS
                     Telomerase_RBD  88 ywlfdslliplirsfFYvTessktrn 113
                                         + ++ +l ++++ +++v  + ++ +
  gene2455|gene2455|rna2455|rna2455 400 KYKVNRFLKKILKDMYFVRRNAFKYQ 425
                                        56677777777777777766554432 PP

>> DUF3683  Protein of unknown function (DUF3683)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.13   7.7e+02      59      86 ..     208     235 ..     204     248 .. 0.85
   2 ?   -3.1   0.0       1.4   8.3e+03      87     104 ..     338     355 ..     329     359 .. 0.66
   3 ?    9.2   0.1   0.00021       1.2      43      69 ..     403     429 ..     395     485 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.13
                            DUF3683  59 Rnpylqddlldnkkrrkalvealehrle 86 
                                         n  + dd+  + kr++ l+e++ + ++
  gene2455|gene2455|rna2455|rna2455 208 SNELIWDDVYVSYKRKECLIEEICKVIR 235
                                        5888999*************99987665 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 1.4
                            DUF3683  87 eiekrrereekveellea 104
                                        +i++ ++++e+v+ ll+a
  gene2455|gene2455|rna2455|rna2455 338 QIQNLSQNKEHVKMLLDA 355
                                        566666666667666665 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.00021
                            DUF3683  43 sarllyevlGdiwvvrRnpylqddlld 69 
                                          r+l ++l d++ vrRn++ +++l d
  gene2455|gene2455|rna2455|rna2455 403 VNRFLKKILKDMYFVRRNAFKYQNLYD 429
                                        5799*****************999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (517 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1161  (0.0647554); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.25s 00:00:00.84 Elapsed: 00:00:00.44
# Mc/sec: 3525.48
//
Query:       gene2456|gene2456|rna2456|rna2456  [L=153]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       997  (0.0556082); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 1039.78
//
Query:       gene2457|gene2457|rna2457|rna2457  [L=163]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.11   12.9   1.1       0.21   12.0   0.1    2.1  2  CLU_N     Mitochondrial function, CLU-N-term


Domain annotation for each model (and alignments):
>> CLU_N  Mitochondrial function, CLU-N-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   1.2e-05      0.21       7      30 ..      12      35 ..      11      72 .. 0.81
   2 ?   -1.7   0.0      0.21   3.8e+03      18      30 ..      94     107 ..      89     124 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.2e-05
                              CLU_N  7 dlrqvLselpstkylTnyhLkyen 30
                                       ++++vL+++p  ++lTn++L +++
  gene2457|gene2457|rna2457|rna2457 12 EITEVLNFVPMEEFLTNFSLQVDK 35
                                       6899****************7753 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.21
                              CLU_N  18 tkylTnyhLkye.n 30 
                                        ++ l + hL+y  n
  gene2457|gene2457|rna2457|rna2457  94 NNSLVCWHLNYAtN 107
                                        56778999988533 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       545  (0.0303977); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 1206.70
//
Query:       gene2458|gene2458|rna2458|rna2458  [L=517]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    4.2e-44  149.2   2.0    4.6e-24   84.7   0.1    2.7  2  CH          Calponin homology (CH) domain
      3e-09   36.6   0.3    3.8e-05   23.4   0.0    2.9  2  CAMSAP_CH   CAMSAP CH domain
     0.0022   18.1   0.5        0.2   11.8   0.0    2.8  2  CH_2        CH-like domain in sperm protein
  ------ inclusion threshold ------
       0.33   11.4   2.4         28    5.2   0.3    3.1  2  EF-hand_7   EF-hand domain pair
        3.1    8.2   6.6        5.5    7.4   0.9    3.6  4  Syntaxin_2  Syntaxin-like protein


Domain annotation for each model (and alignments):
>> CH  Calponin homology (CH) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.5   0.3     5e-21   1.8e-17       3     106 ..      20     121 ..      18     124 .. 0.94
   2 !   84.7   0.1   1.3e-27   4.6e-24       5     106 ..     138     238 ..     134     241 .. 0.95

  Alignments for each domain:
  == domain 1  score: 63.5 bits;  conditional E-value: 5e-21
                                        HHHHHHHHHHHHHTTSTTSSTTSCHHHHHTTSHHHHHHHHHHSTTTSSGGGSTTTHHHHHHHHHHHHHHHHHHTTC CS
                                 CH   3 qkkellrWinshleeagpkvkvedfeedlrDGvlLckLlnklapglvdkkklnksefkkleNinlaldvaekklgv 78 
                                        q k +++W+n++l+++ + + + +  +d++DG  L++Lln ++ + ++++k + sef++++Ni +a++++e + ++
  gene2458|gene2458|rna2458|rna2458  20 QVKSFTKWVNNQLQKK-HYPPIMSIVDDFCDGKTLINLLNVIYDEPIEHNKGKLSEFQRRDNIDKAIKFIE-SKNI 93 
                                        7799*********997.66779****************************9999*****************.**** PP

                                        HTTSS-HHHHHTTSHHHHHHHHHHHHHH CS
                                 CH  79 pkvlieaedlvegknksvltllaqLfra 106
                                        ++v i+a+ +++++ k++l++ ++L+++
  gene2458|gene2458|rna2458|rna2458  94 DLVSIDADHIFNKNVKLTLGMTWALILR 121
                                        *************************986 PP

  == domain 2  score: 84.7 bits;  conditional E-value: 1.3e-27
                                        HHHHHHHHHHHTTSTTSSTTSCHHHHHTTSHHHHHHHHHHSTTTSSGGGSTTTHHHHHHHHHHHHHHHHHHTTCHT CS
                                 CH   5 kellrWinshleeagpkvkvedfeedlrDGvlLckLlnklapglvdkkklnksefkkleNinlaldvaekklgvpk 80 
                                          ll+W++++++e+ ++v+++df+ +++DG+ + ++++++ap+lvd+ +l  s  ++ eN+++a+dvaek++++pk
  gene2458|gene2458|rna2458|rna2458 138 SILLKWCRDCTKEY-DNVDIKDFTHSWKDGLSFNAIIHHFAPHLVDYYSL--SGKNAKENLTNAFDVAEKNFNIPK 210
                                        679**********9.99*********************************..79********************** PP

                                        TSS-HHHHHT...TSHHHHHHHHHHHHHH CS
                                 CH  81 vlieaedlve...gknksvltllaqLfra 106
                                        +l ++edl e   +++ksv+t+++q +++
  gene2458|gene2458|rna2458|rna2458 211 LL-DPEDLTEsvvPDEKSVITYVSQYYLK 238
                                        **.**********************9976 PP

>> CAMSAP_CH  CAMSAP CH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.1   0.00014      0.51       3      68 ..      30      91 ..      28     106 .. 0.83
   2 !   23.4   0.0   1.1e-08   3.8e-05      11      83 ..     154     219 ..     146     221 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00014
                          CAMSAP_CH  3 serslplippvedllrdlsdGvaLaalihfYcPqliklediclkesmsladslyNiqllqefcerk 68
                                       ++ + ++ pp+  ++ d++dG  L +l++  + + i+    + k ++s ++  +Ni  + +f+e+k
  gene2458|gene2458|rna2458|rna2458 30 NQLQKKHYPPIMSIVDDFCDGKTLINLLNVIYDEPIEH---N-KGKLSEFQRRDNIDKAIKFIESK 91
                                       67788999**********************99999976...4.67799999999999888888776 PP

  == domain 2  score: 23.4 bits;  conditional E-value: 1.1e-08
                          CAMSAP_CH  11 ppvedllrdlsdGvaLaalihfYcPqliklediclkesmsladslyNiqllqefcerkLgnsvfhltleDlly 83 
                                          ++d++ +++dG+   a+ih + P+l++       +s+s +   +N+  +++++e+++ n +  l++eDl+ 
  gene2458|gene2458|rna2458|rna2458 154 VDIKDFTHSWKDGLSFNAIIHHFAPHLVDY------YSLSGKNAKENLTNAFDVAEKNF-NIPKLLDPEDLTE 219
                                        5689************************98......789*******************9.555555****986 PP

>> CH_2  CH-like domain in sperm protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.1     0.021        75       3      81 ..      26     105 ..      24     112 .. 0.73
   2 !   11.8   0.0   5.6e-05       0.2      13      88 ..     155     230 ..     140     237 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.021
                               CH_2   3 kWlqs.ldlsr..svknlkrdfsdGvlvAeilkkyypklvdlhnysngsslaaklnNWetLekvlkklgiklskel 75 
                                        kW+++ l+ ++  ++ ++  df+dG  + ++l+ +y +   +++ + + s  ++++N +   k+++ ++i+l + +
  gene2458|gene2458|rna2458|rna2458  26 KWVNNqLQKKHypPIMSIVDDFCDGKTLINLLNVIYDE--PIEHNKGKLSEFQRRDNIDKAIKFIESKNIDLVSID 99 
                                        8999875544411455899*****************99..555556666677777777777777777777777777 PP

                               CH_2  76 ieevas 81 
                                        ++++ +
  gene2458|gene2458|rna2458|rna2458 100 ADHIFN 105
                                        776666 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 5.6e-05
                               CH_2  13 svknlkrdfsdGvlvAeilkkyypklvdlhnysngsslaaklnNWetLekvlkklgiklskelieevasekpgaae 88 
                                         +k++++   dG+ +  i++++ p+lvd  + s +++ ++  n +++ ek ++  ++  +++l e+v+  ++ +++
  gene2458|gene2458|rna2458|rna2458 155 DIKDFTHSWKDGLSFNAIIHHFAPHLVDYYSLSGKNAKENLTNAFDVAEKNFNIPKLLDPEDLTESVVPDEKSVIT 230
                                        4678889999*************************************9*999887777777777777776666665 PP

>> EF-hand_7  EF-hand domain pair
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.1     0.014        49       6      21 ..     446     461 ..     441     470 .. 0.83
   2 ?    5.2   0.3    0.0079        28      52      71 .]     472     494 ..     468     494 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.014
                          EF-hand_7   6 eaFkelDtdgdgyldk 21 
                                          Fk +D+ ++ y+d+
  gene2458|gene2458|rna2458|rna2458 446 KLFKTYDSSDTKYIDE 461
                                        47************97 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0079
                          EF-hand_7  52 efDtdk...dGvisfdEFlklyr 71 
                                        ++Dtd+   dG+i +d+++++++
  gene2458|gene2458|rna2458|rna2458 472 NLDTDRdviDGRIHYDDYVQFVK 494
                                        56888844469*********985 PP

>> Syntaxin_2  Syntaxin-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0      0.38   1.4e+03      67      87 ..     187     207 ..     135     208 .. 0.80
   2 ?    0.4   0.1      0.24   8.4e+02      46      85 ..     248     282 ..     237     291 .. 0.73
   3 ?    7.4   0.9    0.0015       5.5      33      71 ..     341     379 ..     308     393 .. 0.81
   4 ?   -1.7   0.0       1.1   3.9e+03      36      63 ..     410     437 ..     383     458 .. 0.63

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.38
                         Syntaxin_2  67 qqklqkekLkkdfkealqeFq 87 
                                        + k +ke L++ f  a ++F+
  gene2458|gene2458|rna2458|rna2458 187 SGKNAKENLTNAFDVAEKNFN 207
                                        567899*******99999996 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.24
                         Syntaxin_2  46 ikktnellkklsqldnsssdsqqklqkekLkkdfkealqe 85 
                                        i+k +e+l k++++ +++ +       +kL+++f+ +lq+
  gene2458|gene2458|rna2458|rna2458 248 IEKGEEHLAKMDEWLRKNMG-----GYNKLAHEFSMLLQR 282
                                        55556677777777776643.....778999999998886 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.0015
                         Syntaxin_2  33 eklhelieeinelikktnellkklsqldnsssdsqqklq 71 
                                        ++l + ++e+++++++t  +lk+++q ++ +sd   ++ 
  gene2458|gene2458|rna2458|rna2458 341 NNLMNRMKETTDMLSRTRIKLKDIAQSIELNSDTLAYVD 379
                                        6889999**********************9999854443 PP

  == domain 4  score: -1.7 bits;  conditional E-value: 1.1
                         Syntaxin_2  36 helieeinelikktnellkklsqldnss 63 
                                        ++l + + +l+++  +llk+l++ ++ +
  gene2458|gene2458|rna2458|rna2458 410 NNLSSTVGKLCEEKLALLKDLDRHKEYE 437
                                        6667777777777777777777766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (517 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1121  (0.0625244); expected 358.6 (0.02)
Passed bias filter:                      534  (0.0297841); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.42
# Mc/sec: 3653.07
//
Query:       gene2459|gene2459|rna2459|rna2459  [L=482]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.9e-10   38.6   0.0    1.7e-09   37.5   0.0    1.5  1  Lactamase_B_2  Beta-lactamase superfamily domain
    3.4e-08   33.0   0.2      2e-06   27.4   0.0    2.9  3  Lactamase_B_4  tRNase Z endonuclease
      6e-05   23.1   0.2    0.00011   22.2   0.0    1.5  2  Lactamase_B    Metallo-beta-lactamase superfamily
    0.00073   19.0   0.1     0.0015   18.0   0.1    1.5  1  Lactamase_B_6  Metallo-beta-lactamase superfamily domain
  ------ inclusion threshold ------
      0.039   13.9   0.3       0.13   12.2   0.3    1.9  1  PBECR3         phage-Barnase-EndoU-ColicinE5/D-RelE like nucl


Domain annotation for each model (and alignments):
>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.5   0.0   4.8e-13   1.7e-09       3     144 ..     332     459 ..     331     471 .. 0.82

  Alignments for each domain:
  == domain 1  score: 37.5 bits;  conditional E-value: 4.8e-13
                                        EEES--TTHHHHHTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHH.....HCCTT CS
                      Lactamase_B_2   3 iLiDagpdlrqqalralqPvelrdelppidaVllthaHyDHlaglltlrelrpkklplyapkgvla.....vlean 73 
                                        +L+D+g d++ q  r    +  ++ l+++++++++h+H+DH  gl ++ +  ++k+ +++p++v       +l+a 
  gene2459|gene2459|rna2459|rna2459 332 YLLDCGEDTLSQIDRVY--G-DLRILEKLKLIFISHSHADHHLGLYFVLKKIQHKVVVLCPQKVKNflnlfDLDAT 404
                                        59*******99977777..3.355578*********************99556679999*****997777777777 PP

                                        CGHHHCHTTTTEEEEEE-TTSEEEECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEECTTEEEEEESS-S CS
                      Lactamase_B_2  74 fvylaleeepavnvheldwgesfelgdggleitatparhksgrrldrnagdtlGlriegggkrvyyigDtg 144
                                        f    ++++      e++   sf l+d  +++ + p+ h +           +G  ++ + ++++y+gD+ 
  gene2459|gene2459|rna2459|rna2459 405 FFVTDKNKK-----AEIT-YLSFNLNDKAIKVSICPVDHIGDS---------YGIKLQ-AAHSIAYSGDCR 459
                                        655555555.....3333.4579999999**********9999.........999999.9**********7 PP

>> Lactamase_B_4  tRNase Z endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   0.0   5.5e-10     2e-06      14      56 ..      15      56 ..       9      63 .. 0.89
   2 ?   -2.3   0.1       1.1   3.8e+03      37      56 ..     235     254 ..     233     259 .. 0.78
   3 ?    2.2   0.0     0.039   1.4e+02      16      56 ..     324     366 ..     317     372 .. 0.74

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 5.5e-10
                      Lactamase_B_4 14 lllLqldskrYlfGkvgEgtQRavneqkvrlsklesiFLtgkv 56
                                        llL+ ++k+YlfG   Eg QR  +e+++rl k+++++L++ +
  gene2459|gene2459|rna2459|rna2459 15 ALLLKQETKHYLFG-YYEGFQRHSIERNIRLPKITNVYLFEDH 56
                                       799**********6.56**********************9887 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.1
                      Lactamase_B_4  37 vneqkvrlsklesiFLtgkv 56 
                                        ++e + +l+k++  FL +k 
  gene2459|gene2459|rna2459|rna2459 235 FFELQKKLNKIDANFLLPKK 254
                                        566677999**999999875 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.039
                      Lactamase_B_4  16 lLqldskrYlfGkvgEgtQRavne..qkvrl.sklesiFLtgkv 56 
                                        + + d+  Yl+ ++gE t+  +      +r+  kl+ iF+++++
  gene2459|gene2459|rna2459|rna2459 324 IYEEDNCAYLL-DCGEDTLSQIDRvyGDLRIlEKLKLIFISHSH 366
                                        55667788999.99999887765544678877999999999988 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0   3.2e-08   0.00011       5      73 ..     319     385 ..     316     421 .. 0.91
   2 ?   -3.8   0.1         3   1.1e+04      56      68 ..     436     448 ..     435     455 .. 0.76

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 3.2e-08
                                        SSEEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEET CS
                        Lactamase_B   5 pvnsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvg 73 
                                        +v+s++ e d+ ++L D+G +t  +  +   +   + +++++ ++++H+H+DH  gl  + ++ + +v+
  gene2459|gene2459|rna2459|rna2459 319 NVSSIIYEEDNCAYLLDCGEDTLSQIDR--VYGDLRILEKLKLIFISHSHADHHLGLYFVLKKIQHKVV 385
                                        78999*********************98..89999999*******************999999888776 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 3
                                        HHHTTGGGCTTHH CS
                        Lactamase_B  56 DHiGglgglveat 68 
                                        DHiG+  g++ ++
  gene2459|gene2459|rna2459|rna2459 436 DHIGDSYGIKLQA 448
                                        9***999988766 PP

>> Lactamase_B_6  Metallo-beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.1   4.2e-07    0.0015       3      78 ..     326     395 ..     324     429 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 4.2e-07
                      Lactamase_B_6   3 eldnvkiLlDvGwdeskvslesalkelekviptvdliLLshatlehlGayallyakfksklllnipvyatlpvvkL 78 
                                        e dn+  LlD+G d    ++ + +    ++++++ li +sh+ ++h  ++ ++++k++    +++ v +++ v++ 
  gene2459|gene2459|rna2459|rna2459 326 EEDNCAYLLDCGEDTL-SQI-DRVYGDLRILEKLKLIFISHSHADHHLGLYFVLKKIQ----HKVVVLCPQKVKNF 395
                                        569999********86.445.45666667*************9986555556665554....56667777777665 PP

>> PBECR3  phage-Barnase-EndoU-ColicinE5/D-RelE like nuclease3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.3   3.6e-05      0.13      72     112 ..     207     242 ..     191     244 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 3.6e-05
                             PBECR3  72 kkeksieyvKkinngylvvvevdkkknelyvktmykikekk 112
                                        +    +++ K+++ng++v +e+   +ne++ k+++  ++k 
  gene2459|gene2459|rna2459|rna2459 207 RD--CLVLKKHYENGHFVLFEE---NNEIEYKSFFELQKKL 242
                                        43..78999999**********...***********99665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (482 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       630  (0.0351386); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 3102.16
//
Query:       gene246|gene246|rna246|rna246  [L=279]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-14   53.8   0.2    3.6e-14   53.1   0.2    1.3  1  Ran_BP1   RanBP1 domain
  ------ inclusion threshold ------
      0.063   13.2   0.0      0.063   13.2   0.0    2.1  2  DUF1125   Protein of unknown function (DUF1125)


Domain annotation for each model (and alignments):
>> Ran_BP1  RanBP1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.1   0.2     4e-18   3.6e-14       4     116 ..     148     263 ..     146     269 .. 0.93

  Alignments for each domain:
  == domain 1  score: 53.1 bits;  conditional E-value: 4e-18
                                    -SSTTEEEEEEEEEEEEEEETTTTEEEEEEEEEEEEEEETTTTEEEEEEEETTTTEEEEEEEE-TTS-EEESTTESSEEE CS
                        Ran_BP1   4 sgEEdEevlfkqraKLfrfdaekkewkeRGvGdiKilkkkddekvRllmRrdqvlkvcaNhvitkemklkplagsdrslv 83 
                                    + E d ++ fk   +Lf f++++   ++RG G i i   ++++ ++l m rd++ k+  Nh i +  kl+  ++s ++++
  gene246|gene246|rna246|rna246 148 NTEQDKNIHFKATCQLFMFSENTGAIEQRGDGIIYIKMVEKHKLYKLTMVRDRIYKLGCNHFILPIGKLHAHKTSANTFI 227
                                    57999*************************************************************************** PP

                                    EEE.EE-TTSSSEEE..EEEEEESSHHHHHHHHHHH CS
                        Ran_BP1  84 wta.adaadeeakle..qlaikfkkkeeadefkkkf 116
                                    w++  d  d++ k e  ++++kf+  e a++f++k+
  gene246|gene246|rna246|rna246 228 WHTkNDKCDDDVKSEkrTFVVKFGCGEDAERFESKY 263
                                    **9899999998765337**************9886 PP

>> DUF1125  Protein of unknown function (DUF1125)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.5       1.2   1.1e+04       6      23 ..       5      22 ..       2      23 .. 0.51
   2 ?   13.2   0.0     7e-06     0.063       5      30 ..     239     264 ..     238     272 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 1.2
                        DUF1125  6 kteknriivqfecGndie 23
                                   k  kn  +    c ++ie
  gene246|gene246|rna246|rna246  5 KEKKNEEVKAESCNENIE 22
                                   555555554445666665 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 7e-06
                        DUF1125   5 lkteknriivqfecGndieafscGfl 30 
                                    +k ek   +v+f cG+d e f   + 
  gene246|gene246|rna246|rna246 239 VKSEKRTFVVKFGCGEDAERFESKYG 264
                                    599*****************987665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (279 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       659  (0.0367561); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1785.12
//
Query:       gene2460|gene2460|rna2460|rna2460  [L=335]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.1e-19   68.3   8.4    9.1e-19   68.3   8.4    2.1  2  TAF4      Transcription initiation factor TFIID component TAF
  ------ inclusion threshold ------
      0.037   14.0   0.2       0.11   12.4   0.1    1.8  1  Ldh_1_C   lactate/malate dehydrogenase, alpha/beta C-terminal
          2    8.4   0.0          2    8.4   0.0    3.0  3  RST       RCD1-SRO-TAF4 (RST) plant domain
        3.5    8.0   6.4        7.8    6.8   0.2    2.8  2  PET117    PET assembly of cytochrome c oxidase, mitochondrial


Domain annotation for each model (and alignments):
>> TAF4  Transcription initiation factor TFIID component TAF4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.5   1.2         3   1.4e+04     149     159 ..      76      86 ..      67      93 .. 0.38
   2 !   68.3   8.4     2e-22   9.1e-19       1     272 [.      95     326 ..      95     331 .. 0.81

  Alignments for each domain:
  == domain 1  score: -4.5 bits;  conditional E-value: 3
                               TAF4 149 kdrskgedeee 159
                                        k+r+++ +e++
  gene2460|gene2460|rna2460|rna2460  76 KERESEPEEQQ 86 
                                        21111111111 PP

  == domain 2  score: 68.3 bits;  conditional E-value: 2e-22
                               TAF4   1 LnDvlasaGVdLkeEeerLlqssakeasrvseavravvrsekeepfLqknpLqkklaeiakkeglksidpDvlell 76 
                                        L+D++  aGV+LkeE e++ +   ++    + + +++ r++    +   ++  ++++ ia+k g+ ++d    + +
  gene2460|gene2460|rna2460|rna2460  95 LQDIIEYAGVNLKEEQENIGR---ENMIDQELEINEEDRRNSLDYLFDVEVFVQYVNFIARKRGM-EVDDSAYHAM 166
                                        89******************3...33344444566666777777999******************.8888888999 PP

                               TAF4  77 SlAveerLrgLltklivlskhRrrgekskkrtesltsdvrkqLrelaqkekeeeekrqakRieereglekaakdrs 152
                                         lA++  L ++++k++   + R++ +ks+  t+ + +d+r+qL  l+++e++e +k             k     +
  gene2460|gene2460|rna2460|rna2460 167 FLALKRKLTDMIEKMVKACEFRVDYIKSEVVTK-IENDIRRQLWVLEEQERKEMDKTLC----------K-----K 226
                                        9****************************9888.************9988888777666..........2.....3 PP

                               TAF4 153 kgedeeekklkaketakevqkeedekarhraANatAlaavgeprkKkyswmsagsg.sgggksgaskssssggkgl 227
                                         g+d +++k+k k   k+vq++ed  +++r +N  Alaa+g  ++K  swm+     ++ +k+++   +s+ ++  
  gene2460|gene2460|rna2460|rna2460 227 GGDDDDSQKKKLK---KNVQEREDLIIKKRLSNSVALAALG-IQRK--SWMTMDEAvGKPEKKSQF--QSLYSP-- 292
                                        4567777777777...789**********************.5544..799998874444444433..333333.. PP

                               TAF4 228 kgksgviserGknglrlrerergkritlrDllaaLEqerrtsksa 272
                                                    n+ ++++    +++ l D +++LE+++r  ks 
  gene2460|gene2460|rna2460|rna2460 293 -----------YNEKEMEKKIINRKVILDDFIYVLERDKRYNKSV 326
                                        ...........23345667778899***************99875 PP

>> Ldh_1_C  lactate/malate dehydrogenase, alpha/beta C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   2.6e-05      0.11      42      97 ..     223     273 ..     216     300 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.6e-05
                                        HHTTSTTSTHHHHHHHHHHHHHHHHHHHHHHTTSSSS-HHHHHHHHHHHHHHHTTH CS
                            Ldh_1_C  42 qvkellklsekqleeliervqnggdevvkakkGagsatlsmAvAgakfveallrdt 97 
                                         +k+  ++++ q+++l ++vq++ d ++k++    s   s+A A+  + ++ +  +
  gene2460|gene2460|rna2460|rna2460 223 LCKKGGDDDDSQKKKLKKNVQEREDLIIKKR---LS--NSVALAALGIQRKSWMTM 273
                                        577888899**********************...55..466666666666555555 PP

>> RST  RCD1-SRO-TAF4 (RST) plant domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.0   0.00044         2      17      54 ..       6      43 ..       3      45 .. 0.91
   2 ?   -4.3   0.8         4   1.8e+04      34      47 ..     237     250 ..     236     253 .. 0.66
   3 ?    1.9   0.2     0.046   2.1e+02      22      49 ..     280     307 ..     277     309 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00044
                                RST 17 skklpkskmdllqkhYedlkkkkIsreefvrklRsivG 54
                                        + l+ ++ ++++ +Y++ ++++Is ++f    + i G
  gene2460|gene2460|rna2460|rna2460  6 MNSLSLEQKKIIEINYKRAMNNEISPNDFFEECKRILG 43
                                       578899999********************999999887 PP

  == domain 2  score: -4.3 bits;  conditional E-value: 4
                                RST  34 dlkkkkIsreefvr 47 
                                        +lkk+   re+++ 
  gene2460|gene2460|rna2460|rna2460 237 KLKKNVQEREDLII 250
                                        67777777777764 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.046
                                RST  22 kskmdllqkhYedlkkkkIsreefvrkl 49 
                                        ++k ++ q++Y+ + +k++ ++   rk+
  gene2460|gene2460|rna2460|rna2460 280 PEKKSQFQSLYSPYNEKEMEKKIINRKV 307
                                        7888999************998777765 PP

>> PET117  PET assembly of cytochrome c oxidase, mitochondrial
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.2    0.0017       7.8      45      70 .]      73      96 ..      41      96 .. 0.87
   2 ?    2.4   1.9     0.043   1.9e+02      24      57 ..     212     249 ..     209     259 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0017
                             PET117 45 KerkrkenkaeleeqkelrkkyekvQ 70
                                       +   +ke+++e+eeq++++ k e+ Q
  gene2460|gene2460|rna2460|rna2460 73 H--AEKERESEPEEQQQKEIKTERLQ 96
                                       3..5679**********999999887 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.043
                             PET117  24 QrlerealrqGvir....DaerqaeKerkrkenkaele 57 
                                         ++er+++ ++  +    D+ +q++K++k+ + +++l 
  gene2460|gene2460|rna2460|rna2460 212 EEQERKEMDKTLCKkggdDDDSQKKKLKKNVQEREDLI 249
                                        68999999999976677699999999888777666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (335 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1853  (0.103352); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 2313.72
//
Query:       gene2462|gene2462|rna2462|rna2462  [L=170]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-41  143.1   1.8    3.1e-41  141.8   1.8    1.6  1  DUF5087   Domain of unknown function (DUF5087)
  ------ inclusion threshold ------
       0.15   11.8   0.1       0.44   10.3   0.0    1.8  2  BRCA2     BRCA2 repeat


Domain annotation for each model (and alignments):
>> DUF5087  Domain of unknown function (DUF5087)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  141.8   1.8   3.5e-45   3.1e-41     120     292 .]       2     158 ..       1     158 [. 0.88

  Alignments for each domain:
  == domain 1  score: 141.8 bits;  conditional E-value: 3.5e-45
                            DUF5087 120 ilsyqlaIdkklyknkklveflnkikenldLtassislkeellsliekfkvfdve.lieerindeife..nvasir 192
                                        +lsyq++I+k  +  +     + ki++++dL                 f+ fdv+ l+  ++ d+ f+  + as+r
  gene2462|gene2462|rna2462|rna2462   2 LLSYQVLIMKRTNDST---DIVSKIQDEMDL-----------------FEPFDVNgLCSTILADNEFShfKTASLR 57 
                                        5566666665544443...444556666666.................888999999*****9999997889**** PP

                            DUF5087 193 llchflDwdytYNefivevlypklketknpfyvlylgvlalnalksfgeeeSvekvidelkkvl.sekselsiasy 267
                                        ++c+f+Dw++tYN+f v++lyp+++e+ +p++++y+gv+++ ++k+fg++eSv++++de+k++l +e+ els++++
  gene2462|gene2462|rna2462|rna2462  58 IICSFMDWNWTYNIFTVQTLYPQFVESSRPILLFYMGVICTLGYKNFGMHESVQSIFDEIKTFLdKENHELSVIAC 133
                                        ****************************************************************999********* PP

                            DUF5087 268 lfvkqikkkasekwleknkeeisne 292
                                        +fvk+++ + + +w  kn+e+++n+
  gene2462|gene2462|rna2462|rna2462 134 SFVKNFDLDLAGQWCAKNREKYGNQ 158
                                        *********************9885 PP

>> BRCA2  BRCA2 repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   4.9e-05      0.44       2      16 ..      46      60 ..      45      60 .. 0.92
   2 ?   -2.3   0.0      0.41   3.7e+03      25      32 ..     110     117 ..     108     117 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 4.9e-05
                              BRCA2  2 dsfsgFkTAsGKkIr 16
                                       ++fs FkTAs++ I+
  gene2462|gene2462|rna2462|rna2462 46 NEFSHFKTASLRIIC 60
                                       89**********997 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.41
                              BRCA2  25 AkklFsei 32 
                                        + ++F+ei
  gene2462|gene2462|rna2462|rna2462 110 VQSIFDEI 117
                                        5689*996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       462  (0.0257683); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 1285.46
//
Query:       gene2463|gene2463|rna2463|rna2463  [L=231]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.8e-32  113.1   5.3    1.8e-32  113.1   5.3    2.1  2  DUF5087    Domain of unknown function (DUF5087)
  ------ inclusion threshold ------
      0.036   13.5   1.5      0.051   13.0   1.5    1.2  1  DIT1_PvcA  Pyoverdine/dityrosine biosynthesis protein
        5.1    7.5   9.7         29    5.1   7.4    2.1  2  AAA_23     AAA domain


Domain annotation for each model (and alignments):
>> DUF5087  Domain of unknown function (DUF5087)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    3.0   2.9      0.01        60     131     183 ..       2      55 ..       1      61 [. 0.66
   2 !  113.1   5.3     3e-36   1.8e-32       1     109 [.     116     224 ..     116     228 .. 0.98

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.01
                            DUF5087 131 lyknkklveflnkikenld.Ltassislkeellsliekfkvfdvelieerinde 183
                                        ++ + k++++ nkik+  + L+ ++i +k+ l  l  k  ++ ++ +e +i+++
  gene2463|gene2463|rna2463|rna2463   2 VHTDDKIKKYENKIKSLTKkLKYKKIIIKSLLHTLQRKKYKKRKNGLEMKIENN 55 
                                        678889*********976526556666666666666554444444566666665 PP

  == domain 2  score: 113.1 bits;  conditional E-value: 3e-36
                            DUF5087   1 FKtnfklkefvdyieneivlfsleekkkvklkkslkkyvktnlkkilkyllkniNtlelekicttlllisneleye 76 
                                        F++nfkl+e+v+y+++ +v++  ++k+++kl+k +  y+ktn+k ilk+++k+iNt+e+ek++t+l+++ +  +y+
  gene2463|gene2463|rna2463|rna2463 116 FRLNFKLDEYVEYTCSLFVPYVYDAKDDYKLSKLHLIYIKTNIKGILKHIFKDINTREVEKTWTLLFNLGCAQSYD 191
                                        899************************************************************************* PP

                            DUF5087  77 eklvilhDiilfledlskllfiisalfnnkeie 109
                                        ++++i+hD+++f++d+++++++++al++ k+++
  gene2463|gene2463|rna2463|rna2463 192 ALCMIVHDLFVFVDDFERVIYFSYALLHGKKLR 224
                                        ***************************998875 PP

>> DIT1_PvcA  Pyoverdine/dityrosine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   1.5   8.5e-06     0.051      77     169 ..       4     106 ..       1     123 [. 0.77

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 8.5e-06
                                        -HHHHHHHHHHHHHHHHHCT-TTEEEE-GGG-GGGGGG.......................TT-HHH.HHHHHHHH CS
                          DIT1_PvcA  77 ddeevdaYgeeLrelakekglediefvrlkdlleseeeaeeeseells.........eeeyleeaek.lrkeLlks 142
                                        +d+++++Y++++++l+k+ ++++i + +l + l+ ++ +++++   ++         +++  + ae+ +  e++++
  gene2463|gene2463|rna2463|rna2463   4 TDDKIKKYENKIKSLTKKLKYKKIIIKSLLHTLQRKKYKKRKNGLEMKiennlsvpiDSRADSVAEQvMEAEIEET 79 
                                        6999************************999997766666666666667899988886666666655144567777 PP

                                        H---HHHHHHHHTTSHHHHHHHHHHHH CS
                          DIT1_PvcA 143 fgedeeelrkeikededtlalYrgfsk 169
                                         g+++ +++   + +++  a+Y  + +
  gene2463|gene2463|rna2463|rna2463  80 GGDKKPDIDMIAAAHPESIATYSVLER 106
                                        777777887766699999999987766 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   7.4    0.0049        29     149     194 ..       9      54 ..       2      57 .. 0.85
   2 ?    2.7   0.0     0.025   1.5e+02      48     125 ..     105     182 ..      69     210 .. 0.61

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0049
                             AAA_23 149 kdkkerleelekeleeledekkllekleqekekekeleeleeelee 194
                                        k+ ++++++l+k+l+ ++ ++k l + +q+k+++k+ + le ++e+
  gene2463|gene2463|rna2463|rna2463   9 KKYENKIKSLTKKLKYKKIIIKSLLHTLQRKKYKKRKNGLEMKIEN 54 
                                        556679999999999999999999999***********99999986 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.025
                             AAA_23  48 prlsrksgrgfeksdveiesegkvkayvelt........fenkdgrytrsier.erelskkkgkttkkaklellei 114
                                        +r++r+++ ++++         k ++yve t        +  kd+   ++++      +k++ k + k +++ +++
  gene2463|gene2463|rna2463|rna2463 105 ERNNRTKEDKSFRLN------FKLDEYVEYTcslfvpyvYDAKDD---YKLSKlHLIYIKTNIKGILKHIFKDINT 171
                                        333333322222222......233344444444444432222222...3343336666677777777777777777 PP

                             AAA_23 115 deleqfisell 125
                                        +e e++++ l+
  gene2463|gene2463|rna2463|rna2463 172 REVEKTWTLLF 182
                                        77777776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1289  (0.0718947); expected 358.6 (0.02)
Passed bias filter:                      525  (0.0292822); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 1664.93
//
Query:       gene2465|gene2465|rna2465|rna2465  [L=181]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-06   29.2   0.6    2.2e-05   24.9   0.6    2.4  1  RNase_PH  3' exoribonuclease family, domain 1


Domain annotation for each model (and alignments):
>> RNase_PH  3' exoribonuclease family, domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.6   1.3e-09   2.2e-05       4     132 .]       4     115 ..       2     115 .. 0.85

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 1.3e-09
                                        EEEEEESSSSTTSEEEEEEECCEEEEEEEEEEEEEE-TCCG--CCEEEECCCCECCCCEC-C...S...HHHHHHH CS
                           RNase_PH   4 slsietgvlsqanGSaylelGdtkvlasvtgpieerpseerddaegaldveveyapfasgerrregrpsdeeiels 79 
                                        s++++ g++++a GS+ ++  +t+v++ v++   + ps + ++ +  ++v+ +  +  s ++     ++  e+  s
  gene2465|gene2465|rna2465|rna2465   4 SIDCSVGFMKNAMGSSSFQGMNTTVYCHVNVLPDV-PSCI-STLP-YIEVHWNEGSSRSLNT---YFAGVVEQIFS 73 
                                        899***************************98888.5556.6665.7999999886665555...56999****** PP

                                        HHHHHHHCCTC-CCGCCTCEEEEEEEEEECCCS-CHHHCHHHHHHHHHCTCEE CS
                           RNase_PH  80 rlleralrpsillekkpkstididitvlssdggslldalinaaslALadagip 132
                                        +++++ +r++++le +      +++ v      + l++++naa lAL+dag+p
  gene2465|gene2465|rna2465|rna2465  74 KIVKDDFRRVFVLELW------VGVGV-----RNALMCAFNAAVLALVDAGVP 115
                                        ************9988......44444.....27899**************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       421  (0.0234815); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1354.30
//
Query:       gene2466|gene2466|rna2466|rna2466  [L=61]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       274  (0.0152825); expected 358.6 (0.02)
Passed bias filter:                      229  (0.0127726); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 460.43
//
Query:       gene2467|gene2467|rna2467|rna2467  [L=359]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.5e-10   39.5   0.0    6.9e-10   38.8   0.0    1.3  1  Exo_endo_phos    Endonuclease/Exonuclease/phosphatase family
    0.00015   21.6   0.0        0.5   10.2   0.0    2.5  2  Exo_endo_phos_2  Endonuclease-reverse transcriptase


Domain annotation for each model (and alignments):
>> Exo_endo_phos  Endonuclease/Exonuclease/phosphatase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.8   0.0   7.7e-14   6.9e-10       1     233 []       6     326 ..       6     326 .. 0.76

  Alignments for each domain:
  == domain 1  score: 38.8 bits;  conditional E-value: 7.7e-14
                                        EEEEESTG.........CHHHHTHHHHHHHHHHHHHHCTTSEEEEEEEBSCTCHHHHHHHHH..TTCEEEEECCHE CS
                                        xxxxxxxx.........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxx RF
                      Exo_endo_phos   1 ltwNvngq.........aspalgssrrsdrladlltaydaDvlgLQEvdddelsriplllal..ggflgasstspt 65 
                                        +++Nvng                +++ +d+++d l+a+   +l++QE +++  s+ +  ++     f+        
  gene2467|gene2467|rna2467|rna2467   6 VSFNVNGLrsyskfiseR-----NTNINDYVRDRLKAT---ILCVQESRGSKSSLSEFYSLKdyIVFVS------A 67 
                                        59******8888655440.....444456688888888...******7777766665555544322222......3 PP

                                        CSSSTTSSEEEEEECSTEEEEEEEEEEETSSSSGCEEEEEEEEEEEEEEE...............CCCHHGHHHHH CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...............xxxxxxxxxxx RF
                      Exo_endo_phos  66 gggggggnggavlsrfpltslfrrtfiefndlvaalrreplaakleqlni...............ashrdhdlvrd 126
                                        ++++ g +g+a++++  ++      + e +++     r  l++ + ++                  ++ + ++   
  gene2467|gene2467|rna2467|rna2467  68 NRANSGKYGVATFIKKDFFCCGKQEVMEEFREYNGEGRFLLTRHGSFDILncyfpfvsesefrsdDEVCRKKVNNA 143
                                        5899**************555444444444444444444444444444446666999**99888888888888888 PP

                                        HHHHHHHHHHHHHHHHTTSEEEEEEE-SSSTSGGGBSCGHHHHHHCTTTH.......................... CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......................... RF
                      Exo_endo_phos 127 lqllalllqvealnadrgapvivaGDfNarpsdddsrvlrtrglalapap.......................... 176
                                        +++++++ q  ++n +     iv+GDfNa+ s  d+   +   l+   ++                          
  gene2467|gene2467|rna2467|rna2467 144 MRFYHYVEQYVNNNPN----TIVCGDFNAVYSLKDTYIYQQEFLRIQNRAmmidremdgivhaehvvqrddsehee 215
                                        8888888888877777....***********************************999999999999998888888 PP

                                        .............................H................................SSCESCETTTTTTT CS
                                        .............................x................................xxxxxxxxxxxxxx RF
                      Exo_endo_phos 177 .............................v................................glyllgggptptyv 191
                                                                                                      + ++ +++     +
  gene2467|gene2467|rna2467|rna2467 216 enetfdrgrfvnpiasptelpfffknekyLreyffelpsrkwlykmihecelidtyrmysnkEKVYSCWNSLLGLR 291
                                        8888888877777777666666666555505555566666667777788888888899999*************** PP

                                        TTTTEB-BEEEEEECHHHCCEEEEEEECCHHEEC.......TSSCSSSB CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxx RF
                      Exo_endo_phos 192 traggsrlDrilaspalalfrsgvlppplalvrr.......ealtlSDH 233
                                          + g r+D il+ +               +v +       +++++SDH
  gene2467|gene2467|rna2467|rna2467 292 KVNLGTRIDLILVHK--------------MYVKCvknadvmMNEYGSDH 326
                                        **************8..............888888888899******** PP

>> Exo_endo_phos_2  Endonuclease-reverse transcriptase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.0   5.6e-05       0.5      20      41 ..     149     168 ..     115     172 .. 0.78
   2 !    9.0   0.0   0.00013       1.2      87     119 .]     296     330 ..     254     330 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 5.6e-05
                    Exo_endo_phos_2  20 tlekllselkspkiiilGDfNa 41 
                                         +e+++++++  ++i++GDfNa
  gene2467|gene2467|rna2467|rna2467 149 YVEQYVNNNP--NTIVCGDFNA 168
                                        5566666666..9********8 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00013
                    Exo_endo_phos_2  87 sstiDltltsdnlals..kleleeedlgSDHrpil 119
                                         + iDl+l+ +  ++   + +   +++gSDH p++
  gene2467|gene2467|rna2467|rna2467 296 GTRIDLILVHKMYVKCvkNADVMMNEYGSDHCPVY 330
                                        688**********999988888999*******996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (359 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       559  (0.0311785); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2670.37
//
Query:       gene2468|gene2468|rna2468|rna2468  [L=73]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (73 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       387  (0.0215851); expected 358.6 (0.02)
Passed bias filter:                      237  (0.0132188); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 518.29
//
Query:       gene2469|gene2469|rna2469|rna2469  [L=127]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.7e-26   90.6   5.4    8.3e-26   90.3   5.4    1.0  1  Brr6_like_C_C  Di-sulfide bridge nucleocytoplasmic transport 


Domain annotation for each model (and alignments):
>> Brr6_like_C_C  Di-sulfide bridge nucleocytoplasmic transport domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.3   5.4   4.6e-30   8.3e-26       7     125 ..       5     121 ..       2     126 .. 0.95

  Alignments for each domain:
  == domain 1  score: 90.3 bits;  conditional E-value: 4.6e-30
                      Brr6_like_C_C   7 lfnlllvllllylvisfvltikkDiekkleekkaellaeieeCkkeYeeNkCdpetrvpaleekCeewekCmnrdp 82 
                                         fnlll+++l ++vi+++l +k+Di+ +++++ a+l++ ie+++++Ye+N+C   t +pa++++C+ w++ m++  
  gene2469|gene2469|rna2469|rna2469   5 QFNLLLIVILSFTVIKTFLVLKNDIRIRIDDEFANLQYLIEDSRYKYEINRCG-CTDIPAMRRDCMIWKSNMSKSR 79 
                                        59**************************************************6.5789***************997 PP

                      Brr6_like_C_C  83 eskverakvsaetlaeiinsfvepislktllfllllllivlfv 125
                                        +  +e +k+++ ++++i++ f+e+is+k ++f  +l++i+l++
  gene2469|gene2469|rna2469|rna2469  80 RD-IEVMKIVMDCFGDIVDRFLERISWKFFIFSACLTVIYLII 121
                                        77.*******************************999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       830  (0.0462937); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 866.07
//
Query:       gene247|gene247|rna247|rna247  [L=730]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (730 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1837  (0.10246); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.67u 0.25s 00:00:00.92 Elapsed: 00:00:00.42
# Mc/sec: 5228.61
//
Query:       gene2470|gene2470|rna2470|rna2470  [L=274]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.9e-66  222.0   0.5    1.1e-65  221.8   0.5    1.0  1  Septin           Septin
    3.3e-07   30.4   0.5    9.6e-05   22.3   0.0    2.4  2  RsgA_GTPase      RsgA GTPase
    4.6e-07   29.9   0.1    1.1e-06   28.7   0.1    1.8  1  MMR_HSR1         50S ribosome-binding GTPase
    3.5e-06   26.5   0.5    2.3e-05   23.8   0.0    2.1  2  AIG1             AIG1 family
    0.00079   19.1   0.4     0.0034   17.0   0.0    2.0  2  Ras              Ras family
      0.001   18.9   1.2     0.0014   18.4   1.2    1.3  1  AAA_15           AAA ATPase domain
     0.0013   18.9   0.9       0.55   10.3   0.0    2.9  3  Dynamin_N        Dynamin family
     0.0022   17.5   0.4       0.51    9.8   0.1    2.5  2  GTP_EFTU         Elongation factor Tu GTP binding domain
     0.0034   17.7   0.0      0.019   15.2   0.0    2.1  2  AAA_22           AAA domain
     0.0036   17.7   0.1      0.011   16.1   0.0    1.8  2  AAA              ATPase family associated with various cellul
     0.0078   15.6   1.5       0.11   11.8   1.5    2.3  1  Gtr1_RagA        Gtr1/RagA G protein conserved region
     0.0085   16.5   0.0      0.019   15.4   0.0    1.6  1  RNA_helicase     RNA helicase
     0.0087   16.3   0.1      0.024   14.9   0.0    1.8  2  Roc              Ras of Complex, Roc, domain of DAPkinase
  ------ inclusion threshold ------
      0.019   15.4   0.0      0.026   14.9   0.0    1.4  1  AAA_16           AAA ATPase domain
      0.022   14.3   0.0      0.066   12.7   0.0    1.9  1  FeoB_N           Ferrous iron transport protein B
      0.024   14.7   0.1       0.49   10.4   0.0    2.3  2  AAA_14           AAA domain
      0.029   13.9   0.0      0.049   13.2   0.0    1.3  1  AAA_7            P-loop containing dynein motor region
      0.029   13.8   0.0      0.063   12.7   0.0    1.5  1  SRPRB            Signal recognition particle receptor beta su
      0.029   13.5   0.0      0.053   12.7   0.0    1.5  1  NB-ARC           NB-ARC domain
      0.032   14.0   0.1      0.099   12.4   0.0    1.9  2  PduV-EutP        Ethanolamine utilisation - propanediol utili
      0.039   14.5   0.1      0.067   13.7   0.0    1.7  1  ABC_tran         ABC transporter
      0.049   13.4   0.0        0.1   12.3   0.0    1.5  1  Viral_helicase1  Viral (Superfamily 1) RNA helicase
       0.12   12.2   0.0       0.24   11.3   0.0    1.4  1  NACHT            NACHT domain
       0.14   11.8   0.2        0.8    9.3   0.0    2.1  2  cobW             CobW/HypB/UreG, nucleotide-binding domain


Domain annotation for each model (and alignments):
>> Septin  Septin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  221.8   0.5   1.4e-68   1.1e-65       5     275 ..       9     265 ..       5     270 .. 0.94

  Alignments for each domain:
  == domain 1  score: 221.8 bits;  conditional E-value: 1.4e-68
                                        EEEEEEEBTTSSCCCCCCTTSSSS------------------S-EEEEEEEEETTCEEEEEEEE---BSSSSSHHC CS
                             Septin   5 ftlmvvGesglGkttlintlfetdlieeekleeasekkkktveikkkkvvieedgvklnltviDtpgfGdavdnsk 80 
                                        ft m+vG  g Gkt++in+lf ++l+e +       +++k+  ++ + + ++ +g++ ++ ++Dtpg G +++ s 
  gene2470|gene2470|rna2470|rna2470   9 FTTMLVGPAGCGKTSFINSLFDQQLVEIS-------DTHKQEAFNVYVSDVDMEGLRRKISIVDTPGLGASMNDSY 77 
                                        99************************986.......33344567777888888999******************** PP

                                        CCHHHHHHHHHHHHHHHHHCTSS--.SS-----EEEEEEEE-TTSSSS-HHHHHHHHHHTTTS-EEEEESSGGGS- CS
                             Septin  81 swepiveyideqfeeylreesklkR.kkivDkRvHaclyfisPtghglkpldvelmkklsekvnliPviaKaDtlt 155
                                         ++ iv y+++qf ++l+ee+k++R  +  D+RvHa++yfi     gl+  d++++kk+++ vnli viaKaD+lt
  gene2470|gene2470|rna2470|rna2470  78 VHDSIVIYLRKQFCKFLTEETKINRnPNAEDTRVHALIYFIPSRCGGLRLSDIKFLKKVDKLVNLILVIAKADALT 153
                                        *************************9999*********************************************** PP

                                        HHHHHHHHHHHHHHHHHTT--------SSSS-SCCHHHHHHHHHHC-SEEB-SSSSEEEESSSEEEEEEETTEEEE CS
                             Septin 156 keElkefKkkireeleeeeikiyklpdeeededeeakelseklkeslPfaivgsneliekkgkkvrgRkypWGvve 231
                                         +Elk+fK++++++++++ei+i++ +d+e+ +d++      +l+++ Pf+i++ ++l      +v  R ypWG+  
  gene2470|gene2470|rna2470|rna2470 154 LNELKTFKENVKDQVRKNEIRIFN-FDKENLNDAD---VGFELQNKQPFTIISFDSL----KPEVTNRVYPWGTPG 221
                                        ************************.9999999888...8899**********86654....467999********* PP

                                        TT-TTT-SCCHHHHHHHHHCHHHHHHHHHHTHHHHHHHHHH-XX CS
                             Septin 232 venekhsdFlkLrklllkthledLkevteellYetyRseklskl 275
                                          n +h+dF++Lr+++l+++   L+e t+e lYe+yR+e ls+l
  gene2470|gene2470|rna2470|rna2470 222 TMNVDHCDFKILREIILSSYTDVLIEETSEELYENYRTEVLSTL 265
                                        ****************************************9976 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.0   1.3e-07   9.6e-05     100     161 ..       9      69 ..       1      73 [. 0.83
   2 ?    5.9   0.2     0.015        11      45      87 ..     138     183 ..     130     200 .. 0.75

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 1.3e-07
                                        SEEEEECSTTSSHHHHHHHHCTT-----S--------------SEEEEEETTTEEEESS-SS CS
                        RsgA_GTPase 100 ktsvlvGqSGvGKStLinallpelelktgevseklgrGkhTTtavellelaegglliDtPGf 161
                                         t++lvG+ G GK+++in+l  ++ ++++++ ++          v +  l ++  ++DtPG+
  gene2470|gene2470|rna2470|rna2470   9 FTTMLVGPAGCGKTSFINSLFDQQLVEISDTHKQEAFNVY-VSDVDMEGLRRKISIVDTPGL 69 
                                        5899******************988888888876655544.56899999999999*****98 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.015
                                        TT-EEEEEEE-GGG--HHH...HHHHHHHHHHHTTSEEEE--TTTH CS
                        RsgA_GTPase  45 kgiepvivlnKiDlleeee...eleelkeelealgyevllvsaktk 87 
                                        k +++++v+ K+D l+ +e     e++k+++++ +++++  ++++ 
  gene2470|gene2470|rna2470|rna2470 138 KLVNLILVIAKADALTLNElktFKENVKDQVRKNEIRIFNFDKENL 183
                                        56899*********99999665556777788888888888776654 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7   0.1   1.5e-09   1.1e-06       3      86 ..      12     121 ..      10     201 .. 0.63

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 1.5e-09
                                        EEEESTTSSHHHHHHHHHTS.TEEESSST.TSSSSEEEEEEEETT..EEEEEEECGGC.................. CS
                           MMR_HSR1   3 aivGrpNvGKStLinaltge.kaivsdkp.gtTrdinegrvklkg..keielvDtpGl.................. 56 
                                        ++vG    GK+++in+l+++  +++sd++ +   ++    v+++g  ++i +vDtpGl                  
  gene2470|gene2470|rna2470|rna2470  12 MLVGPAGCGKTSFINSLFDQqLVEISDTHkQEAFNVYVSDVDMEGlrRKISIVDTPGLgasmndsyvhdsiviylr 87 
                                        79*****************966777766525666666666775555689********7666666655555544433 PP

                                        ......SSHHHHHHH.....HHHHHHHHHCTSEEEEEEETT CS
                           MMR_HSR1  57 ......iegaseekg.....lgkaflaleeadlillvvdas 86 
                                              +              ++  ++  +++++++ + ++
  gene2470|gene2470|rna2470|rna2470  88 kqfckfL-------TeetkiNRNPNAEDTRVHALIYFIPSR 121
                                        3332221.......011111222222223345555555433 PP

>> AIG1  AIG1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.0   3.1e-08   2.3e-05       3      64 ..      11      75 ..       9     118 .. 0.79
   2 ?    0.7   0.2      0.36   2.7e+02     117     163 ..     140     181 ..     125     202 .. 0.73

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 3.1e-08
                                       EEEESSTTSSHHHHHHHHHTS--SS.--TTTS---SS-EEEEE.EETTEEEEEEE--SC.CCTTC CS
                               AIG1  3 ivlvGktgnGkSaTgNsilgkkaFe.sklsaqsvtkkcqkksr.twdgkkinViDTPgl.fdlsv 64
                                        +lvG  g+Gk + +Ns+ +++  e s +++q+  +   + +  +   +ki+++DTPgl  ++++
  gene2470|gene2470|rna2470|rna2470 11 TMLVGPAGCGKTSFINSLFDQQLVEiSDTHKQEAFNVYVSDVDmEGLRRKISIVDTPGLgASMND 75
                                       68*******************9977366666666666655555466779*********9444443 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.36
                                        GGEEEEEEEGGGGTTCCHHHHHHHHH-HHHHHHHHHTTTSEEEEETT CS
                               AIG1 117 kylivvftrkddleddsledylsksspeaLkevlkecgnRvvlfnnk 163
                                         +li+v+ ++d l  ++l+ + ++ + +     +++ + R+  f+ +
  gene2470|gene2470|rna2470|rna2470 140 VNLILVIAKADALTLNELKTFKENVKDQ-----VRKNEIRIFNFDKE 181
                                        4789999999999999988887754444.....66666666666654 PP

>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   4.5e-06    0.0034       3      59 ..      12      70 ..      10      87 .. 0.78
   2 ?   -0.4   0.1         1   7.5e+02     101     124 ..     136     159 ..     127     187 .. 0.58

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 4.5e-06
                                       EEEESTTSSHHHHHHHHHHSSCSSSCTTTS..SEEEEEEEEEETTEEEEEEEEEETTSG CS
                                Ras  3 vlvGdsavGKtslllrfvkdkFkeeyesTi..gvdfytkeievdgkevkleiwDTAGqe 59
                                       +lvG  ++GKts++++  +++  e +++     ++ y+++++++g + k++i DT G  
  gene2470|gene2470|rna2470|rna2470 12 MLVGPAGCGKTSFINSLFDQQLVEISDTHKqeAFNVYVSDVDMEGLRRKISIVDTPGLG 70
                                       69******************9987655443114778999****************9964 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1
                                        STTTSEEEEEEETTTGGGG-SS-H CS
                                Ras 101 aeenvpivLvGnKvDleekravst 124
                                        +++ v+++Lv  K+D  + ++++t
  gene2470|gene2470|rna2470|rna2470 136 VDKLVNLILVIAKADALTLNELKT 159
                                        445577777777777766333332 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   1.2   1.9e-06    0.0014      25     174 ..      10     202 ..       2     264 .. 0.61

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.9e-06
                             AAA_15  25 ltvliGkNnsGKSsilealdlFlnnkekkn.............................................. 54 
                                        +t l+G+ ++GK+s+++ l  F ++  + +                                              
  gene2470|gene2470|rna2470|rna2470  10 TTMLVGPAGCGKTSFINSL--FDQQLVEISdthkqeafnvyvsdvdmeglrrkisivdtpglgasmndsyvhdsiv 83 
                                        799****************..5555533334555677778888888888888666666666666666666666555 PP

                             AAA_15  55 ....kkvikiekedleifeniseskdikIdvef............................aek...ekakeyekt 95 
                                            k+                          f                              +   + + +++k+
  gene2470|gene2470|rna2470|rna2470  84 iylrKQ--------------------------FckflteetkinrnpnaedtrvhaliyfiP-SrcgGLRLSDIKF 132
                                        555533..........................144444444444444433333333333332.2466677777788 PP

                             AAA_15  96 lkskekkkadlllkkkesdlkktikdkklklkknelsdekisvekkkskkelpkekeeklekekeelkidkedlkk 171
                                        lk+ +k  + +l++ k ++l           ++ ++ +e+++++ +k++  ++++ +e+l+  +  ++++++  + 
  gene2470|gene2470|rna2470|rna2470 133 LKKVDKLVNLILVIAKADALTL---------NELKTFKENVKDQVRKNEIRIFNFDKENLNDADVGFELQNKQPFT 199
                                        8888888887777777775543.........333344444455555555555555555555555555555555555 PP

                             AAA_15 172 lik 174
                                        +i+
  gene2470|gene2470|rna2470|rna2470 200 IIS 202
                                        555 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.0   0.00073      0.55       3      27 ..      13      37 ..      12      49 .. 0.86
   2 ?    6.0   0.0     0.015        11      99     113 ..      57      71 ..      35      88 .. 0.81
   3 ?   -1.0   0.1       2.2   1.6e+03     108     126 ..     219     237 ..     141     269 .. 0.57

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00073
                                       EEEBTTTTHHHHHHHHHTS--S--- CS
                          Dynamin_N  3 vvGsqSsGKSSvlnaLlgedilprg 27
                                       +vG    GK+S++n+L  +++  ++
  gene2470|gene2470|rna2470|rna2470 13 LVGPAGCGKTSFINSLFDQQLVEIS 37
                                       79***************99976555 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.015
                                        TS-SEEEEE---B-S CS
                          Dynamin_N  99 lvkgltlvDlPGlds 113
                                        l+ ++++vD+PGl  
  gene2470|gene2470|rna2470|rna2470  57 LRRKISIVDTPGLGA 71 
                                        67899*******965 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 2.2
                                        ---B-SSSGTTSHHHHHHH CS
                          Dynamin_N 108 lPGldsvnkrdqelvkeyi 126
                                        +PG  +v++ d ++++e+i
  gene2470|gene2470|rna2470|rna2470 219 TPGTMNVDHCDFKILREII 237
                                        5555555555555555555 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0     0.014        11      48      79 ..      39      68 ..       7      71 .. 0.67
   2 !    9.8   0.1   0.00069      0.51     122     165 ..     139     181 ..     129     258 .. 0.74

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.014
                                       HHHHHTSCSSCEEEEEETTCSSEEEEEEEESS CS
                           GTP_EFTU 48 eErergiTiksaaisleketkkylinliDtPG 79
                                       + ++  + + ++ + +e  + +++i+++DtPG
  gene2470|gene2470|rna2470|rna2470 39 THKQEAFNVYVSDVDME--GLRRKISIVDTPG 68
                                       33344455666777777..8999999999998 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00069
                                        TTEEEEEEESCGST.HHHHHHHHHHHHHHHHHHHHHHHHHHHTTT CS
                           GTP_EFTU 122 gvpiivfiNKmDrl.kaelkeiveevkqklsrkeeklekygekge 165
                                         v++i++i K+D l  +elk  +e+vk++++++  +++ + +++e
  gene2470|gene2470|rna2470|rna2470 139 LVNLILVIAKADALtLNELKTFKENVKDQVRKN--EIRIFNFDKE 181
                                        4789**********999************9655..3333433333 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   2.5e-05     0.019       8      45 ..      11      47 ..       9      75 .. 0.75
   2 ?   -0.4   0.0       1.8   1.3e+03      88     113 ..     138     161 ..      85     178 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.5e-05
                             AAA_22  8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevvfv 45
                                       ++++G++G+GKT  ++ l++q   e++ ++ + e + v
  gene2470|gene2470|rna2470|rna2470 11 TMLVGPAGCGKTSFINSLFDQQLVEISDTH-KQEAFNV 47
                                       589******************866555444.3333333 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.8
                             AAA_22  88 aravielliiDEaqhlrseealeeLr 113
                                        +     +l+i  a+ l + + l++++
  gene2470|gene2470|rna2470|rna2470 138 KLVN-LILVIAKADAL-TLNELKTFK 161
                                        3333.67777777777.555555544 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   1.5e-05     0.011       2      41 ..      12      51 ..      11      73 .. 0.82
   2 ?   -2.1   0.1       6.3   4.7e+03      59      75 ..     141     158 ..     128     180 .. 0.57

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.5e-05
                                       EEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTH CS
                                AAA  2 llyGppGtGKTllakavakelgvefleisgsellskyvge 41
                                       +l+Gp G+GKT++++++  +  ve+  +   e ++ yv++
  gene2470|gene2470|rna2470|rna2470 12 MLVGPAGCGKTSFINSLFDQQLVEISDTHKQEAFNVYVSD 51
                                       79*****************987777777777777666654 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 6.3
                                        SEEEEEETGGGHHHHH.T CS
                                AAA  59 psilfiDEidalaksr.s 75 
                                          il+i  +dal+ ++ +
  gene2470|gene2470|rna2470|rna2470 141 NLILVIAKADALTLNElK 158
                                        356666666666666531 PP

>> Gtr1_RagA  Gtr1/RagA G protein conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   1.5   0.00015      0.11       3      73 ..      12      84 ..      10     192 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00015
                          Gtr1_RagA  3 LLmGksgsGKtsmrsiiFdnyl..ardtlrlgatidveksevrflgnl.tlnlwDcgGqeafveeylssqkeei 73
                                       +L+G+ g GKts  + +Fd+ l    dt + + + +v  s+v + g   +++++D +G  a +++++ +++  i
  gene2470|gene2470|rna2470|rna2470 12 MLVGPAGCGKTSFINSLFDQQLveISDTHK-QEAFNVYVSDVDMEGLRrKISIVDTPGLGASMNDSYVHDSIVI 84
                                       89****************986511456666.5568999999998886569*********999998766665555 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   2.5e-05     0.019       2      35 ..      12      45 ..      11      65 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.5e-05
                       RNA_helicase  2 wlyGpsgeGKStlakeLakallkklklkkkdsvy 35
                                       +l+Gp+g+GK++++++L ++ l ++ +++k++ +
  gene2470|gene2470|rna2470|rna2470 12 MLVGPAGCGKTSFINSLFDQQLVEISDTHKQEAF 45
                                       689**************99999888666655544 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   3.2e-05     0.024       3      80 ..      12      81 ..      10     104 .. 0.66
   2 ?   -2.2   0.0       6.2   4.6e+03      88     109 ..     150     171 ..     133     179 .. 0.57

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.2e-05
                                       EEESSTTSSHHHHHHCHCT-CCC-EEETTTTEEEEEEECGGSGGCTTBTTTTCEEEEEEEE-SGGCTTTT-HHHHCTS CS
                                Roc  3 vlvGdsgvGKtsllkrfvedkfsekekstigvdfltkevtkikgvendkkvkkvklniWDtaGqerfrslhplylrea 80
                                       +lvG +g GKts+++++ +++  e +++  +  f    v++++    +    + k++i Dt G     s++++y++++
  gene2470|gene2470|rna2470|rna2470 12 MLVGPAGCGKTSFINSLFDQQLVEISDTHKQEAFNV-YVSDVDM---E--GLRRKISIVDTPGLG--ASMNDSYVHDS 81
                                       89****************999976654444444332.2333222...2..223457777777753..35555555555 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 6.2
                                        EGHHHHCHHHHHHHHHHHCSSS CS
                                Roc  88 dsrssenlkeWlkelkkvagks 109
                                        d+ + ++lk+  +++k++++k+
  gene2470|gene2470|rna2470|rna2470 150 DALTLNELKTFKENVKDQVRKN 171
                                        3334456666666666655544 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   3.4e-05     0.026      27      48 ..      11      32 ..       4     152 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.4e-05
                             AAA_16 27 vllsGesGvGKsslvrellral 48
                                       ++l+G++G+GK+s +++l+++ 
  gene2470|gene2470|rna2470|rna2470 11 TMLVGPAGCGKTSFINSLFDQQ 32
                                       689***************9754 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   8.8e-05     0.066       2      57 ..      10      69 ..       9     103 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 8.8e-05
                                       EEEEEESTTSSHHHHHHHHHTTS.EEEEE...STTSSSEEEEEEEEETTEEEEEEE---- CS
                             FeoB_N  2 tvalvGnpnvGkttlfnaltgak.qkvgN...wpGvtvekkegklklkgkeveivDlPGi 57
                                       t +lvG   +Gkt+++n+l +++  +++         v  + + ++  +++++ivD PG 
  gene2470|gene2470|rna2470|rna2470 10 TTMLVGPAGCGKTSFINSLFDQQlVEISDthkQEAFNVYVSDVDMEGLRRKISIVDTPGL 69
                                       5789***************99884466652113445566666666666799999***996 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00066      0.49       6      34 ..      12      45 ..       9      77 .. 0.78
   2 ?    1.7   0.1      0.33   2.5e+02      23      46 ..     160     186 ..     153     209 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00066
                             AAA_14  6 vitGaRrvGKTtllkqlikell.....vkkesil 34
                                       +++G+  +GKT +++ l++++l     ++k++ +
  gene2470|gene2470|rna2470|rna2470 12 MLVGPAGCGKTSFINSLFDQQLveisdTHKQEAF 45
                                       789*****************99666554444444 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.33
                             AAA_14  23 ikell...vkkesilyinldderdkkl 46 
                                        +ke+    v+k++i  +n+d+e++ ++
  gene2470|gene2470|rna2470|rna2470 160 FKENVkdqVRKNEIRIFNFDKENLNDA 186
                                        5555566679999*******9988543 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   6.5e-05     0.049      35      56 ..      10      31 ..       5      54 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 6.5e-05
                              AAA_7 35 pvllvGptGtGKtviikdllkk 56
                                        ++lvGp+G+GKt+ i++l+++
  gene2470|gene2470|rna2470|rna2470 10 TTMLVGPAGCGKTSFINSLFDQ 31
                                       589***************5543 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   8.4e-05     0.063       6      58 ..      11      68 ..       7      79 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 8.4e-05
                                       EEEE-STTSSHHHHHHHHHHS...S---B---S.S-EEETTG....GGTT-SEEEETT CS
                              SRPRB  6 vllvGlsdsGKTslftrLttd...svkktvtSq.essaalkv.ksekgskltliDfPG 58
                                        +lvG+  +GKTs+++ L  +   ++ +t      +  + +v  +    k+ ++D PG
  gene2470|gene2470|rna2470|rna2470 11 TMLVGPAGCGKTSFINSLFDQqlvEISDTHKQEaFNVYVSDVdMEGLRRKISIVDTPG 68
                                       689***************9884333333333332233333443333457889999999 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   7.2e-05     0.053      16      65 ..       4      55 ..       1      95 [. 0.67

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 7.2e-05
                                       TTSCSEEEEEEESTTSSHHHHHHHHCCS.HCCCCCCBT.EEEEEEEESXXHH CS
                             NB-ARC 16 delqslvvalvGmgGvGKttlakqilnk.sdevegrFd.svawvvvsktdks 65
                                       +++q++   lvG +G+GKt  +++ + + + e+  +       v vs+ d++
  gene2470|gene2470|rna2470|rna2470  4 KKPQLFTTMLVGPAGCGKTSFINSLFDQqLVEISDTHKqEAFNVYVSDVDME 55
                                       67899999****************9987123344444435666777776554 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00013     0.099       4      27 ..      11      34 ..       9      69 .. 0.81
   2 ?   -2.3   0.0       4.3   3.2e+03      92     134 ..     142     183 ..     132     186 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00013
                          PduV-EutP  4 illiGkvgsGKttLtqalkgeelk 27
                                        +l+G+ g+GKt+  ++l +++l 
  gene2470|gene2470|rna2470|rna2470 11 TMLVGPAGCGKTSFINSLFDQQLV 34
                                       69****************998874 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 4.3
                          PduV-EutP  92 viGiitkidlaedeenieaveelLksaGaekifevsavekegi 134
                                        +i +i k+d   + +++++ +e +k    ++ +++ + +ke++
  gene2470|gene2470|rna2470|rna2470 142 LILVIAKADAL-TLNELKTFKENVKDQVRKNEIRIFNFDKENL 183
                                        46677777777.6677777777777666666666666666655 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   8.9e-05     0.067      14      36 ..      11      33 ..       7     173 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 8.9e-05
                                       EEEEESTTSSHHHHHHHHTTSS- CS
                                       xxxxxxxxxxxxxxxxxxxxxxx RF
                           ABC_tran 14 vaivGenGaGKStLlkllagllk 36
                                       + +vG+ G+GK+++++ l  +  
  gene2470|gene2470|rna2470|rna2470 11 TMLVGPAGCGKTSFINSLFDQQL 33
                                       789*************9987654 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00014       0.1       5      26 ..      15      37 ..      11      68 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00014
                    Viral_helicase1  5 GvpGcGKStlirkllrts..lilt 26
                                       G +GcGK++ i +l++++    ++
  gene2470|gene2470|rna2470|rna2470 15 GPAGCGKTSFINSLFDQQlvE-IS 37
                                       88*************996632.22 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00032      0.24       3      22 ..      11      30 ..      10      50 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00032
                                       EEEEC-TTTCHHHHHHHHHH CS
                              NACHT  3 vilqGeaGsGKTtLlqklal 22
                                        +l G+aG+GKT ++ +l +
  gene2470|gene2470|rna2470|rna2470 11 TMLVGPAGCGKTSFINSLFD 30
                                       6899***********99975 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0    0.0011       0.8       2      23 ..      10      31 ..       9      54 .. 0.86
   2 ?   -0.1   0.2      0.82   6.1e+02     145     171 ..     144     169 ..     125     184 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0011
                                       EEEEEESTTCCHHHHHHHHHCT CS
                               cobW  2 vtvltGflGsGKTtLlnhllen 23
                                       +t+l+G+ G GKT+++n+l ++
  gene2470|gene2470|rna2470|rna2470 10 TTMLVGPAGCGKTSFINSLFDQ 31
                                       689**************99844 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.82
                                        EEEE-HHHHCHC..HHHHHHHHHHHHT CS
                               cobW 145 lvlnKtDlldeeallekleerlrqlnp 171
                                        lv+ K+D l+ ++l ++++e +++  +
  gene2470|gene2470|rna2470|rna2470 144 LVIAKADALTLNEL-KTFKENVKDQVR 169
                                        56666666666644.455444444333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (274 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       673  (0.037537); expected 358.6 (0.02)
Passed bias filter:                      468  (0.026103); expected 358.6 (0.02)
Passed Vit filter:                        96  (0.00535445); expected 17.9 (0.001)
Passed Fwd filter:                        24  (0.00133861); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              24  [number of targets reported over threshold]
# CPU time: 0.55u 0.33s 00:00:00.88 Elapsed: 00:00:00.48
# Mc/sec: 1726.83
//
Query:       gene2471|gene2471|rna2471|rna2471  [L=278]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-30  105.8   8.7    1.8e-30  105.8   8.7    2.2  2  DHHC      DHHC palmitoyltransferase
  ------ inclusion threshold ------
       0.02   14.1  17.4       0.14   11.4   8.0    2.1  2  7tm_7     7tm Chemosensory receptor


Domain annotation for each model (and alignments):
>> DHHC  DHHC palmitoyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   3.0     0.015   1.3e+02      59     108 ..      10      57 ..       5      72 .. 0.67
   2 !  105.8   8.7     2e-34   1.8e-30       3     132 ..      78     203 ..      76     205 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.015
                               DHHC  59 llllilalvlllialvklveeekkseflavtllkkllsilllvlsllfll 108
                                        ++++il+l+l+l+++ +l+  +k + + +++l     +++ + + ++++l
  gene2471|gene2471|rna2471|rna2471  10 CVVIILTLTLHLVTMPVLLYGQKMNVYRILFLVF--HNFFAFWVYFFMIL 57 
                                        6667777777777777777777776666555543..45555555555554 PP

  == domain 2  score: 105.8 bits;  conditional E-value: 2e-34
                               DHHC   3 kelkfCstcniykpprskHcrvCnrcvlrfDHhCpwlnnciGerNykyFllfllylllllilalvlllialvklve 78 
                                        + +k+C  c+ ykp+r++Hc++C++cv ++DHhC+wl+nc+ + N  +F+ +lly +l+l+    ++++++v+  +
  gene2471|gene2471|rna2471|rna2471  78 EPNKYCILCDNYKPERAHHCSKCRQCVRKMDHHCMWLGNCVNNDNLGHFIRMLLYAVLSLLSLSAFSIYSIVRRDK 153
                                        6789**********************************************************99999999999888 PP

                               DHHC  79 eekkseflavtllkkllsilllvlsllfllllgllllfhlylilrnlTtieamk 132
                                         e  + f ++  +     ++++v+s l++l lg++l+ +++ +l+nlT  e ++
  gene2471|gene2471|rna2471|rna2471 154 FEPMFLFRTILVF----IVIIAVVSSLLFLALGFFLIERFIFVLKNLTYLESCN 203
                                        8888888777665....488888888889999999*************999987 PP

>> 7tm_7  7tm Chemosensory receptor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   1.9   0.00012       1.1     235     278 ..       7      54 ..       4      79 .. 0.73
   2 ?   11.4   8.0   1.5e-05      0.14      91     193 ..      96     198 ..      92     231 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00012
                              7tm_7 235 difglqlllillssfinitvlly....ylysslleesslftllvfvlw 278
                                        + f + ++l+l+ +++++ vlly    ++y++l +++++f  ++++ +
  gene2471|gene2471|rna2471|rna2471   7 KRFCVVIILTLTLHLVTMPVLLYgqkmNVYRILFLVFHNFFAFWVYFF 54 
                                        57999******************9996666666633333333333332 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 1.5e-05
                              7tm_7  91 qrrrlarllnellkldrrlkrlgnrrnkrrfnrllllllvliillllvtllgylllsqyftlvlllllyllpylvl 166
                                        +  + +++++++ +   +l  ++n++n  +f r ll+ ++ ++ l +++++ ++ ++ +  + l+ +++++  + +
  gene2471|gene2471|rna2471|rna2471  96 HCSKCRQCVRKMDHHCMWLGNCVNNDNLGHFIRMLLYAVLSLLSLSAFSIYSIVRRDKFEPMFLFRTILVFIVI-I 170
                                        6678899********************************************78888888888877777777777.9 PP

                              7tm_7 167 qlllllyfllllliy.ellrllnerLkq 193
                                         ++ +l fl+l++   e++ +++++L+ 
  gene2471|gene2471|rna2471|rna2471 171 AVVSSLLFLALGFFLiERFIFVLKNLTY 198
                                        99**********9999***999999975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (278 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1318  (0.0735122); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1801.34
//
Query:       gene2472|gene2472|rna2472|rna2472  [L=220]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.9e-11   42.3   0.2    1.6e-10   41.4   0.2    1.5  1  PIN_6         PIN domain of ribonuclease
    4.9e-09   36.2   2.5    1.2e-08   35.0   2.5    1.6  1  NOB1_Zn_bind  Nin one binding (NOB1) Zn-ribbon like
  ------ inclusion threshold ------
      0.025   14.5   2.0      0.037   13.9   0.1    2.1  2  MRP-S26       Mitochondrial ribosome subunit S26


Domain annotation for each model (and alignments):
>> PIN_6  PIN domain of ribonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.4   0.2   2.6e-14   1.6e-10       2      89 .]       4      87 ..       3      87 .. 0.92

  Alignments for each domain:
  == domain 1  score: 41.4 bits;  conditional E-value: 2.6e-14
                              PIN_6  2 VlDagaliknslsslqnlaeklyttpeVvaEirdkkarerlellplelevrePspesvkkvtefakktGDlsvLSktD 79
                                       V+D++ +i+++ls++    +k ++tp+++ E+r ++ ++ l+l   ++e+ +P+++++kkv +  k+ +    LS +D
  gene2472|gene2472|rna2472|rna2472  4 VIDTNIIIQRKLSEY--EFSKGFITPSILVEVRGEDLNSYLDLYAHKIEIVQPDEKYLKKVYDLQKEKN--LLLSVAD 77
                                       99******9966655..5788999****************************************99988..679**** PP

                              PIN_6 80 ievlALtyeL 89
                                       iev+ALt++L
  gene2472|gene2472|rna2472|rna2472 78 IEVVALTLQL 87
                                       ********98 PP

>> NOB1_Zn_bind  Nin one binding (NOB1) Zn-ribbon like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.0   2.5     2e-12   1.2e-08       5      59 ..     136     188 ..     133     195 .. 0.88

  Alignments for each domain:
  == domain 1  score: 35.0 bits;  conditional E-value: 2e-12
                       NOB1_Zn_bind   5 kswvlrChaCfkvtkdmtkkFCpkCGnktLkrvavsvdengelklhlkknfqlnl 59 
                                        + ++ rC +Cf+++++ +  FC+kC ++ ++rv+v  +eng++kl+lkk f++++
  gene2472|gene2472|rna2472|rna2472 136 RDFMFRCVSCFSLYEE-KLDFCKKCASNLITRVSVK-KENGKIKLFLKKGFKMKK 188
                                        89**********9975.789*************998.5679**********9876 PP

>> MRP-S26  Mitochondrial ribosome subunit S26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   6.2e-06     0.037     102     159 ..      53     120 ..      46     122 .. 0.74
   2 ?   -1.0   0.3      0.23   1.4e+03      84     121 ..     172     209 ..     156     219 .. 0.59

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 6.2e-06
                            MRP-S26 102 ekkeeilerieekeqkeeekkekaeeevlqek.........eesktFITeeNLdeaIee.aLdnpvnY 159
                                        + +e++l+++ + +++++     a+ ev ++          e+ + +IT+eN+de+Ie  +Ldn v++
  gene2472|gene2472|rna2472|rna2472  53 QPDEKYLKKVYDLQKEKNLLLSVADIEVVALTlqlngalrrERLSGWITKENIDEKIEClSLDNGVQH 120
                                        5667777777777777777777777777666666777777789999***********94367777766 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.23
                            MRP-S26  84 wNaelaelReerlkkeaeekkeeilerieekeqkeeek 121
                                        +N +++ + ++ +k ++ e k+++ + +++++q++ ++
  gene2472|gene2472|rna2472|rna2472 172 ENGKIKLFLKKGFKMKKTELKDKYGNILHSEDQNAYKM 209
                                        55555555555555555555555555555554444333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       794  (0.0442858); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1618.87
//
Query:       gene2473|gene2473|rna2473|rna2473  [L=57]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.14   12.6   0.9       0.35   11.3   0.5    1.7  2  GCK       GCK domain


Domain annotation for each model (and alignments):
>> GCK  GCK domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.5     2e-05      0.35      48      68 ..       6      28 ..       4      34 .. 0.77
   2 ?    1.4   0.0     0.024   4.3e+02      32      52 ..      25      45 ..      16      54 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 2e-05
                                GCK 48 kCmeahsdY..YePiLaaekaae 68
                                       kCm++h dY   + +L+++k  +
  gene2473|gene2473|rna2473|rna2473  6 KCMDDHTDYlvINHVLKEKKVLK 28
                                       9********76677887776554 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.024
                                GCK 32 kedlvekcaevtatlkkCmea 52
                                       k   + k  ++t+ ++ C+++
  gene2473|gene2473|rna2473|rna2473 25 KVLKTYKNTNLTDIFYLCVYT 45
                                       445556778888889999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (57 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       645  (0.0359752); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.26s 00:00:00.60 Elapsed: 00:00:00.41
# Mc/sec: 416.45
//
Query:       gene2474|gene2474|rna2474|rna2474  [L=250]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.2e-81  272.2  18.0      5e-81  271.9  18.0    1.1  1  DUF5095   Domain of unknown function (DUF5095)
  ------ inclusion threshold ------
      0.064   14.0   0.0       0.27   12.0   0.0    1.9  2  GST_N_4   Glutathione S-transferase N-terminal domain


Domain annotation for each model (and alignments):
>> DUF5095  Domain of unknown function (DUF5095)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  271.9  18.0   5.6e-85     5e-81       1     241 []      13     239 ..      13     239 .. 0.99

  Alignments for each domain:
  == domain 1  score: 271.9 bits;  conditional E-value: 5.6e-85
                            DUF5095   1 kdnPfdstslikkqketkeekkiaevvaeekelektkekskineddflkvLikkkkkekkekkilsng.Iynklki 75 
                                        +dnPf++t+++kkqk++++ek ++               +++n+d+f+k+L+k+++++k + k++s++ Iy+k+ki
  gene2474|gene2474|rna2474|rna2474  13 SDNPFRCTNVVKKQKINPSEKIRT---------------NQFNDDVFIKQLVKRDTSRKVTPKKCSTMnIYRKVKI 73 
                                        69******************9999...............6*************************9999******* PP

                            DUF5095  76 lskeeltkksvkyYkfPfthelkkeksdiyksiyveflsalkslFkeykkaneeFyvkykdellifstelkvskkl 151
                                        +sk+ l++k+v+y+kfPf++++kk++sd+y+ +y+e+l a++s++k+yk++neeFyvk+ d+++ifst+l++s+++
  gene2474|gene2474|rna2474|rna2474  74 VSKNVLEGKRVEYFKFPFNTNIKKDDSDLYNLVYMEWLLAITSVYKNYKNKNEEFYVKFFDKMFIFSTALYCSSAC 149
                                        **************************************************************************** PP

                            DUF5095 152 kklLesneiefveenselilsgkevalvlDlilNtklsstqalPfilSkykFensivyevrlkkkkavrskgkiky 227
                                        k++Le++e+e+++e+s+l++sg++valv+D+++N++++++++lPfilSk+kF+nsi+y++++ +++ vr++g +k+
  gene2474|gene2474|rna2474|rna2474 150 KEILEQLEVEYLNEGSFLKVSGIDVALVYDYVINYEFKPKDKLPFILSKHKFTNSISYDSKFVENQLVRDRGVLKH 225
                                        **************************************************************************** PP

                            DUF5095 228 ryiikGplitedfs 241
                                        +y+i+G+l+++dfs
  gene2474|gene2474|rna2474|rna2474 226 YYVIEGYLYGHDFS 239
                                        ************96 PP

>> GST_N_4  Glutathione S-transferase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.45     4e+03      44      67 ..      38      58 ..      16      71 .. 0.49
   2 ?   12.0   0.0     3e-05      0.27       9      58 ..     166     219 ..     164     226 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.45
                            GST_N_4 44 liadsefiieflkekgvdldaels 67
                                       +++d  fi + +k++    + +++
  gene2474|gene2474|rna2474|rna2474 38 QFNDDVFIKQLVKRDT---SRKVT 58
                                       4455333333333333...34444 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 3e-05
                            GST_N_4   9 yLrmagipyelepssne.mhaspkgklPfielngel...liadsefiieflkek 58 
                                        +L+++gi++ l+++     +  pk+klPfi  ++++      ds+f+ + l+++
  gene2474|gene2474|rna2474|rna2474 166 FLKVSGIDVALVYDYVInYEFKPKDKLPFILSKHKFtnsISYDSKFVENQLVRD 219
                                        8999999987776665223568**********9997777667888888888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       859  (0.0479112); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1824.15
//
Query:       gene2475|gene2475|rna2475|rna2475  [L=146]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.032   13.6   1.3      0.032   13.6   1.3    1.1  1  DltD             DltD protein
      0.051   14.2   0.0        0.1   13.3   0.0    1.5  1  RFX_DNA_binding  RFX DNA-binding domain
       0.23   11.1   4.4       0.28   10.8   4.4    1.2  1  Rota_NSP4        Rotavirus non structural protein
       0.23   11.3   2.6        1.4    8.7   0.6    2.1  2  Asp_Glu_race     Asp/Glu/Hydantoin racemase


Domain annotation for each model (and alignments):
>> DltD  DltD protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   1.3   7.1e-06     0.032     167     252 ..      54     140 ..       7     146 .] 0.75

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 7.1e-06
                                        HHHHHHHHHHHHHHTTC-HHHHHTTTHCT.TS-SS--HHHHHHHHHHHHHHCTTTTSSS--HHHHHHHTSTTCCTT CS
                               DltD 167 kikkallekedklksklkkkekkiekkak.klpkeidwdelrkkaekegkksttnNefgiknkyYkkrlkpklkkl 241
                                         i++ +l+++++l +++   ++ + k+++   +k+i +++ rk+   ++  +  +N+f +k++ +k++lk+  k+l
  gene2475|gene2475|rna2475|rna2475  54 IIEYITLRERNDLRKIICACDELLLKNSEeISLKDIVVKKKRKESIHQEIIHDLKNSFRVKDEAFKNYLKR-CKEL 128
                                        3567777777787777776666666666669999999999999999999999999***************9.7777 PP

                                        T.TTTTS---SS CS
                               DltD 242 k.gsqknlsyle 252
                                          +s ++ ++++
  gene2475|gene2475|rna2475|rna2475 129 NvDSLNRSDFTS 140
                                        767777777765 PP

>> RFX_DNA_binding  RFX DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   2.2e-05       0.1      17      47 ..     109     139 ..      98     144 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.2e-05
                    RFX_DNA_binding  17 dvsvprqevYaeYlsicsklklkplnaasFg 47 
                                        +++  ++e++++Yl+ c++l+++ ln ++F 
  gene2475|gene2475|rna2475|rna2475 109 NSFRVKDEAFKNYLKRCKELNVDSLNRSDFT 139
                                        56667999*********************96 PP

>> Rota_NSP4  Rotavirus non structural protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   4.4   6.4e-05      0.28      63     152 ..       4      94 ..       2     128 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 6.4e-05
                          Rota_NSP4  63 csykvvkycivtifntllklagy.keqittkdeiekqmdrvvkemrrqlemidklttreieqvellkriydkltvq 137
                                         syk  k  i+ti n ll  +     +  tk+ei + + + +   r   e+i+ +t re +++  +    d l ++
  gene2475|gene2475|rna2475|rna2475   4 FSYKAQKQKIITISNNLLFDSDLlIFKPYTKEEILHIVRKKLECERISDEIIEYITLRERNDLRKIICACDELLLK 79 
                                        59**************99655541345689*****9999999999999*************99999999******* PP

                          Rota_NSP4 138 ttgeidmtkeinqkn 152
                                         + ei +   + +k+
  gene2475|gene2475|rna2475|rna2475  80 NSEEISLKDIVVKKK 94 
                                        *****9865554443 PP

>> Asp_Glu_race  Asp/Glu/Hydantoin racemase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.6   0.00031       1.4     166     200 ..      47      82 ..      29      92 .. 0.75
   2 ?    3.5   0.1     0.012        55     139     181 ..      87     130 ..      79     135 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00031
                                        SH.HHHHHHHHHHHHH.TTT-SEEEE-STTHHHHHHH CS
                       Asp_Glu_race 166 ee.arrailkllerla.ergadaviLGCTelplllek 200
                                         e   ++i++++  l+ +++  ++i +C el l   +
  gene2475|gene2475|rna2475|rna2475  47 CErISDEIIEYIT-LReRNDLRKIICACDELLLKNSE 82 
                                        4456678999999.666**************975444 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.012
                                        EEE....T-CCCHHCCHCHHHHTT-.TTSHHHHHHHHHHHHHHT CS
                       Asp_Glu_race 139 evvvpseelqssvnqaiyeelkaGe.vteearrailkllerlae 181
                                        + +v ++++ +s++q i ++lk++  v++ea+++ lk +++l++
  gene2475|gene2475|rna2475|rna2475  87 KDIVVKKKRKESIHQEIIHDLKNSFrVKDEAFKNYLKRCKELNV 130
                                        44566677778888888889**5554999999999999997664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1190  (0.0663729); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.31s 00:00:00.80 Elapsed: 00:00:00.50
# Mc/sec: 884.82
//
Query:       gene2476|gene2476|rna2476|rna2476  [L=516]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (516 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       991  (0.0552736); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.63u 0.30s 00:00:00.93 Elapsed: 00:00:00.50
# Mc/sec: 3094.53
//
Query:       gene2477|gene2477|rna2477|rna2477  [L=198]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      5e-42  143.2   0.3      6e-42  143.0   0.3    1.1  1  Ras          Ras family
    3.8e-30  104.6   0.0    6.5e-30  103.8   0.0    1.3  1  Roc          Ras of Complex, Roc, domain of DAPkinase
    2.5e-17   62.9   0.4      3e-17   62.6   0.4    1.1  1  Arf          ADP-ribosylation factor family
    8.3e-08   32.3   0.1    1.3e-07   31.7   0.1    1.6  1  MMR_HSR1     50S ribosome-binding GTPase
    2.4e-06   27.1   0.1    3.1e-06   26.7   0.1    1.2  1  Gtr1_RagA    Gtr1/RagA G protein conserved region
      6e-06   25.9   1.0    4.2e-05   23.1   1.0    2.0  1  FeoB_N       Ferrous iron transport protein B
    0.00014   21.5   0.4     0.0039   16.8   0.1    2.2  2  GTP_EFTU     Elongation factor Tu GTP binding domain
    0.00047   20.1   0.2       0.93    9.4   0.1    2.2  2  RsgA_GTPase  RsgA GTPase
    0.00054   20.0   0.2    0.00076   19.6   0.2    1.1  1  DUF4340      Domain of unknown function (DUF4340)
    0.00062   20.1   0.1     0.0031   17.8   0.1    2.0  1  AAA_28       AAA domain
      0.002   18.0   0.2       0.15   11.8   0.1    2.1  2  ATP_bind_1   Conserved hypothetical ATP binding protein
     0.0021   17.5   0.1     0.0039   16.6   0.0    1.4  1  SRPRB        Signal recognition particle receptor beta subuni
     0.0059   16.1   0.0     0.0087   15.6   0.0    1.2  1  AAA_7        P-loop containing dynein motor region
     0.0089   14.9   0.1       0.01   14.7   0.1    1.3  1  DLIC         Dynein light intermediate chain (DLIC)
  ------ inclusion threshold ------
      0.031   14.2   1.5        0.1   12.5   0.1    2.2  2  ATPase_2     ATPase domain predominantly from Archaea
      0.038   13.8   0.2      0.087   12.6   0.0    1.6  2  PduV-EutP    Ethanolamine utilisation - propanediol utilisati
      0.049   13.9   0.1       0.43   10.8   0.1    2.2  1  AAA_22       AAA domain
       0.05   13.3   1.2       0.14   11.8   0.0    2.0  2  AAA_24       AAA domain
      0.051   13.6   0.2        0.1   12.6   0.1    1.7  1  AAA_14       AAA domain
      0.097   12.3   0.9        1.2    8.8   0.0    2.4  3  SRP54        SRP54-type protein, GTPase domain
        0.1   11.7   2.4        0.7    9.0   2.2    2.5  1  G-alpha      G-protein alpha subunit


Domain annotation for each model (and alignments):
>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  143.0   0.3     7e-45     6e-42       1     157 [.       6     166 ..       6     171 .. 0.92

  Alignments for each domain:
  == domain 1  score: 143.0 bits;  conditional E-value: 7e-45
                                        EEEEEESTTSSHHHHHHHHHHSSCSSSCTTTSSEEEEEEEEEETTEEEEEEEEEETTSGGGHHHHHHHHTTESEEE CS
                                Ras   1 KlvlvGdsavGKtslllrfvkdkFkeeyesTigvdfytkeievdgkevkleiwDTAGqeefkslrelyyrdaegil 76 
                                        K+v++G+++vGKt+l+ +f++++ +e+y++Tig+df+  +++++g+ev+l++wDTAGqe+f+s+ ++y r+a +++
  gene2477|gene2477|rna2477|rna2477   6 KIVFLGNQSVGKTTLISQFTNKEADENYHPTIGIDFTYLKVNLQGREVRLQLWDTAGQERFNSIIPNYTRGAYAAI 81 
                                        99************************************************************************** PP

                                        EEEETTBHHHHHTHHHHHHHHHHHST..TTSEEEEEEETTTGGG...G-SS-HHHHHHHHHHHTSEEEEEBTTTTC CS
                                Ras  77 lvyditsresfenvkkwveeikrvae..envpivLvGnKvDlee...kravsteegeelakelglkfletSAktne 147
                                        +v+d+++ +sfen+++w++++  + +  + ++iv+vGnK  l +   +++v+ + +e  ake++ k++et A + e
  gene2477|gene2477|rna2477|rna2477  82 IVFDLKHLNSFENIDHWIRDLVLINDpdRLTKIVIVGNKKELVDekeREEVKIRAVE-KAKEYNGKYIETCAMKYE 156
                                        *********************99999876789*******988774436667776655.799*************** PP

                                        THHHHHHHHH CS
                                Ras 148 nveeafeell 157
                                        +++e+++++ 
  gene2477|gene2477|rna2477|rna2477 157 DIRELVDHVN 166
                                        **99988775 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.8   0.0   7.6e-33   6.5e-30       1     119 [.       6     122 ..       6     123 .. 0.89

  Alignments for each domain:
  == domain 1  score: 103.8 bits;  conditional E-value: 7.6e-33
                                        EEEEESSTTSSHHHHHHCHCT-CCC-EEETTTTEEEEEEECGGSGGCTTBTTTTCEEEEEEEE-SGGCTTTT-HHH CS
                                Roc   1 KvvlvGdsgvGKtsllkrfvedkfsekekstigvdfltkevtkikgvendkkvkkvklniWDtaGqerfrslhply 76 
                                        K+v++G+++vGKt+l+++f++++ +e++++tig+df+  +v +++g       ++v+l++WDtaGqerf+s+ p y
  gene2477|gene2477|rna2477|rna2477   6 KIVFLGNQSVGKTTLISQFTNKEADENYHPTIGIDFTYLKV-NLQG-------REVRLQLWDTAGQERFNSIIPNY 73 
                                        9***********************************88776.5554.......689******************** PP

                                        HCTSCEEEEEEE...GHHHHCHHHHHHHHHHHCSSS...-EEEEEE-TT CS
                                Roc  77 lreaalailvyd...srssenlkeWlkelkkvagks...pvilvgnkiD 119
                                         r+a +ai+v+d    +s+en+++W+++l   ++ +   ++++vgnk +
  gene2477|gene2477|rna2477|rna2477  74 TRGAYAAIIVFDlkhLNSFENIDHWIRDLVLINDPDrltKIVIVGNKKE 122
                                        ************75555889********99887644244899*****86 PP

>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.6   0.4   3.5e-20     3e-17      13     172 ..       3     166 ..       1     169 [. 0.87

  Alignments for each domain:
  == domain 1  score: 62.6 bits;  conditional E-value: 3.5e-20
                                        TEEEEEEEESTTSSHHHHHHHHHHSSCEE.CSSSSSEEEEEEEE....TTEEEEEEEE-SSGGGGGGGGGGCTTES CS
                                Arf  13 kelrilllGLDnaGKtTilkklkleelvt.tvPTigfnveelei....knlkftvwDvGGqeklRplWknYfektd 83 
                                         +++i++lG  + GKtT++ +++++e ++   PTig +   l++    +++++++wD  Gqe+  ++  nY++   
  gene2477|gene2477|rna2477|rna2477   3 SKYKIVFLGNQSVGKTTLISQFTNKEADEnYHPTIGIDFTYLKVnlqgREVRLQLWDTAGQERFNSIIPNYTRGAY 78 
                                        579********************999876489****98887777667799************************** PP

                                        EEEEEEETT-CTTHHHHHHHHHHHCTSGC.CTTSEEEEEEE-TTSTTSS-HHHHHHHTTGGGSSSSSSEEEEEEBT CS
                                Arf  84 avifvvDsadreRleeakeeLkalleeee.lkevallvlaNKqDlpealseeelrellgleelkgkrkleiqkcsa 158
                                        a i v D  + + +e+  + ++ l+  ++  +  ++++++NK++l +  ++ee++   ++e+ k + + + ++++a
  gene2477|gene2477|rna2477|rna2477  79 AAIIVFDLKHLNSFENIDHWIRDLVLINDpDRLTKIVIVGNKKELVDEKEREEVKIR-AVEKAK-EYNGKYIETCA 152
                                        *********************9987665515567899***********999999755.555666.67778889999 PP

                                        TTTBTHHHHHHHHH CS
                                Arf 159 vkgeglkeglewls 172
                                        +k e++ e ++ + 
  gene2477|gene2477|rna2477|rna2477 153 MKYEDIRELVDHVN 166
                                        99999999998876 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.7   0.1   1.5e-10   1.3e-07       1      97 [.       6      99 ..       6     183 .. 0.78

  Alignments for each domain:
  == domain 1  score: 31.7 bits;  conditional E-value: 1.5e-10
                                       EEEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETT..EEEEEEECGGCSSHHHHHHHHHHHHHHHHCT CS
                           MMR_HSR1  1 evaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkg..keielvDtpGliegaseekglgkaflaleea 76
                                       +++++G+  vGK+tLi++ t+++a  + +p   +d ++ +v+l+g   +++l+Dt+G  e   + +++  ++ +   a
  gene2477|gene2477|rna2477|rna2477  6 KIVFLGNQSVGKTTLISQFTNKEADENYHPTIGIDFTYLKVNLQGreVRLQLWDTAG-QE---RFNSIIPNYTR--GA 77
                                       589***************************************887446689******.44...23355555554..35 PP

                                       SEEEEEEETT.TTCSHHHHHHH CS
                           MMR_HSR1 77 dlillvvdas.eeklkpldeel 97
                                        ++++v+d++  ++++++d+ +
  gene2477|gene2477|rna2477|rna2477 78 YAAIIVFDLKhLNSFENIDHWI 99
                                       5666666655322233333333 PP

>> Gtr1_RagA  Gtr1/RagA G protein conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.7   0.1   3.7e-09   3.1e-06       1     142 [.       6     142 ..       6     165 .. 0.86

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 3.7e-09
                          Gtr1_RagA   1 kvLLmGksgsGKtsmrsiiFdnylardtlrlgatidveksevrflg.nltlnlwDcgGqeafveeylssqkeeifr 75 
                                        k++++G+++ GKt++ s  F n  a +  + ++ id +  +v++ g ++ l+lwD  Gqe+f     +       r
  gene2477|gene2477|rna2477|rna2477   6 KIVFLGNQSVGKTTLISQ-FTNKEADENYHPTIGIDFTYLKVNLQGrEVRLQLWDTAGQERFNSIIPN-----YTR 75 
                                        799*************97.9******************99999886369************9887644.....445 PP

                          Gtr1_RagA  76 nvgvliyVfDvesreleedletlkeilealrqyspeakvfvlihKmDliqedereeifeerkeeire 142
                                           + i VfD ++ +  e+++++ + l  + + ++  k+ +  +K  l++e+eree+  +  e+ +e
  gene2477|gene2477|rna2477|rna2477  76 GAYAAIIVFDLKHLNSFENIDHWIRDLVLINDPDRLTKIVIVGNKKELVDEKEREEVKIRAVEKAKE 142
                                        5567788*****888888999999999999999999*******************998777666655 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   1.0   4.9e-08   4.2e-05       2     155 ..       6     164 ..       5     165 .. 0.82

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 4.9e-08
                                        EEEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEEEETTEEE..EEEE----SSSSSSSHH.HHHHHHHH CS
                             FeoB_N   2 tvalvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegklklkgkev..eivDlPGiYslsaysee.ekvardfl 74 
                                        +++++Gn+ vGkttl+ + t+++ +   +p + ++ +  k++l+g+ev  ++ D  G   ++++  +  + a   +
  gene2477|gene2477|rna2477|rna2477   6 KIVFLGNQSVGKTTLISQFTNKEADENYHPTIGIDFTYLKVNLQGREVrlQLWDTAGQERFNSIIPNyTRGAYAAI 81 
                                        7999*********************9999*******99999998865522789****9998776655245667777 PP

                                        HCTSSSEEEEEEEGGGHHHHHHHHHHHHHTTSSEEEEEE..THHHHHHTTEEE-HHHHHHHHTS-EEEEBTTTTBT CS
                             FeoB_N  75 leeepdvvvnvvdatnlernLyLtlqllelgvpvvlaln..mideaekkgieidlkkLsekLgvpvvktsakkkeg 148
                                        +  + + + +  +  +  r+L+L+ +   l++ v++     ++de e+++++i + + +++ + + ++t+a k e+
  gene2477|gene2477|rna2477|rna2477  82 IVFDLKHLNSFENIDHWIRDLVLINDPDRLTKIVIVGNKkeLVDEKEREEVKIRAVEKAKEYNGKYIETCAMKYED 157
                                        777777777777888999*****99988887766665322268999999999999999999*************** PP

                                        HHHHHHH CS
                             FeoB_N 149 ieellka 155
                                        i+el+++
  gene2477|gene2477|rna2477|rna2477 158 IRELVDH 164
                                        ***9987 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0     0.058        49       5      27 ..       6      28 ..       3      37 .. 0.82
   2 !   16.8   0.1   4.6e-06    0.0039      53     190 ..      36     167 ..      24     192 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.058
                                       EEEEEESTTSSHHHHHHHHHHHT CS
                           GTP_EFTU  5 nigiighvDhGKtTLtdrLlykt 27
                                       +i+++g    GKtTL+ + + k 
  gene2477|gene2477|rna2477|rna2477  6 KIVFLGNQSVGKTTLISQFTNKE 28
                                       588999999*******9988665 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 4.6e-06
                                        TSCSSCEEEEEETTCSSEEEEEEEESSSGGGHHHHHHHHHT-SEEEEEEETT.....TBSTHHHHHHHHHHHHTTT CS
                           GTP_EFTU  53 giTiksaaisleketkkylinliDtPGHvdFskevirglrvlDgavlvvdav.....eGvepqteevlrlalkegv 123
                                         i i+ +  +++ ++++ +++l Dt G + F++ + + +r +  a++v+d +     e + +  + ++ +    ++
  gene2477|gene2477|rna2477|rna2477  36 TIGIDFTYLKVNLQGREVRLQLWDTAGQERFNSIIPNYTRGAYAAIIVFDLKhlnsfENIDHWIRDLVLINDPDRL 111
                                        35555566666679**************************************777777788888888888888888 PP

                                        E.EEEEEESCGST.HHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTTEEEEEEBTTTTBTHHHHHHHHHH CS
                           GTP_EFTU 124 p.iivfiNKmDrl.kaelkeiveevkqklsrkeeklekygekgekevpvvfgSalkgegvktllealve 190
                                          i+++ NK   + ++e +e++  + +k          ++++g    + + ++a+k e +++l++ + +
  gene2477|gene2477|rna2477|rna2477 112 TkIVIVGNKKELVdEKEREEVKIRAVEKA---------KEYNG----KYIETCAMKYEDIRELVDHVND 167
                                        86777779988885555555555555555.........22233....4677777777777777666655 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.0    0.0017       1.4     102     123 ..       7      28 ..       2      40 .. 0.85
   2 !    9.4   0.1    0.0011      0.93      37      99 ..     100     167 ..      63     172 .. 0.63

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0017
                                        EEEECSTTSSHHHHHHHHCTT- CS
                        RsgA_GTPase 102 svlvGqSGvGKStLinallpel 123
                                        +v++G+  vGK+tLi ++++++
  gene2477|gene2477|rna2477|rna2477   7 IVFLGNQSVGKTTLISQFTNKE 28 
                                        79*************9998864 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0011
                                        HHHHHHHH..TT-EEEEEEE-GGG--HHH....HHHHHHHHHHHTTSEEEE--TTTHTTHHHHHHHCTT CS
                        RsgA_GTPase  37 rfLvlaee..kgiepvivlnKiDlleeee....eleelkeelealgyevllvsaktkegleelkellkd 99 
                                        r Lvl+++  +  ++viv nK +l++e+e    ++++++++ e  g + + + a + e+++el ++++d
  gene2477|gene2477|rna2477|rna2477 100 RDLVLINDpdRLTKIVIVGNKKELVDEKEreevKIRAVEKAKEYNG-KYIETCAMKYEDIRELVDHVND 167
                                        4455555411456999999*********976554555544444444.4444445557788888777765 PP

>> DUF4340  Domain of unknown function (DUF4340)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.2   8.9e-07   0.00076      93     177 ..      90     182 ..      73     186 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 8.9e-07
                            DUF4340  93 eslkkklsdwrdkdllqldsedvtkiel........vskegrtlelekkedget.tsakpegeeldtaklntllsa 159
                                        +s+  +++ w+   +l  d++++tki +        ++ke + +++++ e+ ++   ++ e+ +++ + + +l++ 
  gene2477|gene2477|rna2477|rna2477  90 NSFE-NIDHWIRDLVLINDPDRLTKIVIvgnkkelvDEKEREEVKIRAVEKAKEyNGKYIETCAMKYEDIRELVDH 164
                                        5544.8999*****************95433334456666777777777766668778888999999********* PP

                            DUF4340 160 lssLkisafveykasdea 177
                                        +++L i++f+e++++d++
  gene2477|gene2477|rna2477|rna2477 165 VNDLVIQDFAENDEEDKD 182
                                        **********98888875 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.1   3.6e-06    0.0031       1      47 [.       6      54 ..       6     164 .. 0.62

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 3.6e-06
                             AAA_28  1 kivitGgestGKTtlleaLaar..gypvvpEaareileeklakgedalp 47
                                       kiv++G +s GKTtl+++++++  + +++p ++ +++  k   ++++ +
  gene2477|gene2477|rna2477|rna2477  6 KIVFLGNQSVGKTTLISQFTNKeaDENYHPTIGIDFTYLKVNLQGREVR 54
                                       79******************77566677777777777766655555444 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0     0.031        27       2      26 ..      10      34 ..       9      40 .. 0.81
   2 !   11.8   0.1   0.00018      0.15      86     232 ..      48     185 ..      36     191 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.031
                         ATP_bind_1  2 vGpaGsGKttfvgalseilelrgrs 26
                                       +G  ++GKtt+++++++   +++++
  gene2477|gene2477|rna2477|rna2477 10 LGNQSVGKTTLISQFTNKEADENYH 34
                                       79999*********99877666555 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00018
                         ATP_bind_1  86 lekeeddyllfDtPGQielfthseslakiveeLesefalvvvyLvDsqrltd...ptkfisgllsalsamlrlelP 158
                                        l+ +e  + l Dt GQ ++  + +           ++a  ++ ++D + l++      +i    + l       + 
  gene2477|gene2477|rna2477|rna2477  48 LQGREVRLQLWDTAGQERFNSIIPNYT--------RGAYAAIIVFDLKHLNSfenIDHWIRD--LVLINDPDRLTK 113
                                        4333458999*****************........9***********999996544556666..344444555566 PP

                         ATP_bind_1 159 hvvvlnkfDllkeklekeleffedvealslllekeeekykklaeaiaelleefalvlrflplssekeesiedll 232
                                         v+v nk +l++ek+++e++    ve+ ++ + k  e  +   e+i+el++ ++   ++   + ++ee  +d++
  gene2477|gene2477|rna2477|rna2477 114 IVIVGNKKELVDEKEREEVKIRA-VEKAKEYNGKYIETCAMKYEDIRELVDHVNDL-VIQDFAENDEEDKDDVV 185
                                        78888*******88777877776.6677777777778999999*********9999.88888888888777776 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   4.6e-06    0.0039       3     133 ..       4     132 ..       2     145 .. 0.69

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 4.6e-06
                                        --EEEEE-STTSSHHHHHHHHHHSS---B---S.S-EEET.TG....GGTT-SEEEETT-GCCSHHHHHHHHHHGG CS
                              SRPRB   3 kpavllvGlsdsGKTslftrLttdsvkktvtSq.essaal.kv.ksekgskltliDfPGheklrqklleklkakss 75 
                                        k +++++G +  GKT+l+ + t++++ + +       +++ kv  + ++ +l+l D  G+e++ + + ++    + 
  gene2477|gene2477|rna2477|rna2477   4 KYKIVFLGNQSVGKTTLISQFTNKEADENYHPTiGIDFTYlKVnLQGREVRLQLWDTAGQERFNSIIPNY---TRG 76 
                                        66899*******************888888766444555414433556778899*********9877776...444 PP

                                        EEEEEEEEETTS-HHHHHHHHHHHHHHHHHHHHHTT---EEEEEE-TTSTT---HHHH CS
                              SRPRB  76 lkglvfvvDStidpkevkevAEllyeilliteklkdavdiliACnKqelflakspkli 133
                                        + + + v D        +++  ++ +++li+       +i+i  nK+el+  k+ + +
  gene2477|gene2477|rna2477|rna2477  77 AYAAIIVFDLK-HLNSFENIDHWIRDLVLIND-PDRLTKIVIVGNKKELVDEKEREEV 132
                                        44444455543.33455666677777777776.3445677888888887766655544 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0     1e-05    0.0087      31      65 ..       2      36 ..       1      49 [. 0.82

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1e-05
                              AAA_7 31 knkkpvllvGptGtGKtviikdllkkldkekylsl 65
                                       ++k+++++ G++ +GKt++i+++++k  +e+y ++
  gene2477|gene2477|rna2477|rna2477  2 RSKYKIVFLGNQSVGKTTLISQFTNKEADENYHPT 36
                                       67899*****************8888888888764 PP

>> DLIC  Dynein light intermediate chain (DLIC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.1   1.2e-05      0.01      24      81 ..       3      61 ..       1     152 [. 0.77

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.2e-05
                               DLIC 24 sgksvlvlGedgsGkttliaklqGv...eeekkGrGleylyldvkdedrddltrlnvwild 81
                                       s  +++ lG+++ Gkttli+++      e+++   G+++ yl+v+ + r+   rl+ w   
  gene2477|gene2477|rna2477|rna2477  3 SKYKIVFLGNQSVGKTTLISQFTNKeadENYHPTIGIDFTYLKVNLQGRE--VRLQLWDTA 61
                                       5567999*************997651115677889********9877664..566666555 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   0.00012       0.1      22      50 ..       7      34 ..       1     126 [. 0.79
   2 ?    0.9   0.2      0.42   3.6e+02     183     220 ..     144     185 ..     129     189 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00012
                           ATPase_2 22 iyfiYGpegsGKtaLlkeiienledkdky 50
                                       i+f  G +++GKt+L+ ++ ++  d +++
  gene2477|gene2477|rna2477|rna2477  7 IVF-LGNQSVGKTTLISQFTNKEADENYH 34
                                       444.5******************998885 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.42
                           ATPase_2 183 rhkyilvddldketalnflkegfkel..eel...skedfeeiy 220
                                          kyi+   +++e ++++++   ++l  +++    +ed+++++
  gene2477|gene2477|rna2477|rna2477 144 NGKYIETCAMKYEDIRELVDHV-NDLviQDFaenDEEDKDDVV 185
                                        4678888889999999998886.44434444666677777766 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0    0.0001     0.087       3      37 ..       6      42 ..       4      59 .. 0.83
   2 ?   -2.0   0.0       3.2   2.7e+03     119     141 ..     145     165 ..     116     167 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.0001
                          PduV-EutP  3 killiGkvgsGKttLtqalkgeel..kYkktqaiefs 37
                                       ki+++G+  +GKttL  +++++e   +Y+ t  i+f+
  gene2477|gene2477|rna2477|rna2477  6 KIVFLGNQSVGKTTLISQFTNKEAdeNYHPTIGIDFT 42
                                       89**************999997653368888888775 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 3.2
                          PduV-EutP 119 Gaekifevsavekegieellkyl 141
                                        G  k +e+ a++ e+i el++++
  gene2477|gene2477|rna2477|rna2477 145 G--KYIETCAMKYEDIRELVDHV 165
                                        3..44566667777777776665 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   0.00051      0.43       5      49 ..       4      50 ..       1     125 [. 0.65

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00051
                             AAA_22  5 agilvvtGesGtGKTtllrrlleqldeeakaee..erpevvfvtlps 49
                                       ++ +v  G   +GKTtl+ +++++   e+++ +   + ++++v+l++
  gene2477|gene2477|rna2477|rna2477  4 KYKIVFLGNQSVGKTTLISQFTNKEADENYHPTigIDFTYLKVNLQG 50
                                       66688899999*************86666555555333444444433 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00017      0.14       2      22 ..       4      24 ..       3      40 .. 0.88
   2 ?   -0.4   0.4      0.93   7.9e+02     125     143 ..     114     135 ..      90     186 .. 0.51

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00017
                             AAA_24  2 klkiliyGpsgiGKTtlakel 22
                                       k+ki+  G + +GKTtl++++
  gene2477|gene2477|rna2477|rna2477  4 KYKIVFLGNQSVGKTTLISQF 24
                                       89******************9 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.93
                             AAA_24 125 vifiahektrkdedpege...a 143
                                        +++++  k+  de++++e    
  gene2477|gene2477|rna2477|rna2477 114 IVIVGNKKELVDEKEREEvkiR 135
                                        4444444444444444441110 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   0.00012       0.1       5      42 ..       7      45 ..       3     139 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00012
                             AAA_14  5 lvitGaRrvGKTtllkqlikell.vkkesilyinldder 42
                                       +v  G   vGKTtl+ q+ +++   +   ++ i++   +
  gene2477|gene2477|rna2477|rna2477  7 IVFLGNQSVGKTTLISQFTNKEAdENYHPTIGIDFTYLK 45
                                       56679999**********999986444444444444433 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0    0.0014       1.2       3      34 ..       6      37 ..       4      43 .. 0.87
   2 ?   -3.6   0.0       8.3   7.1e+03      88      96 ..      57      65 ..      49      68 .. 0.75
   3 ?    1.1   0.7       0.3   2.6e+02      66     107 ..     146     189 ..     125     193 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0014
                                       EEEEEESTTSSHHHHHHHHHHHHHHTTS-EEE CS
                              SRP54  3 villvGlqGaGKTttlaKLaallkkegkkvll 34
                                        i+++G q +GKTt +++  ++  +e++++ +
  gene2477|gene2477|rna2477|rna2477  6 KIVFLGNQSVGKTTLISQFTNKEADENYHPTI 37
                                       589****************9999999887765 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 8.3
                                       EEEE--SST CS
                              SRP54 88 lvDTaGrlq 96
                                       l DTaG+ +
  gene2477|gene2477|rna2477|rna2477 57 LWDTAGQER 65
                                       789999865 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.3
                                        S..CHHHHHHHHHHHHHHTTSSEEEEEE--SSTTHHHHHHHHHH CS
                              SRP54  66 a..dpaavakeavekakeekidvvlvDTaGrlqndkelmeelkk 107
                                        +  ++ a+ +e +++  ++  d+v+ D a   ++dk+ + e+++
  gene2477|gene2477|rna2477|rna2477 146 KyiETCAMKYEDIRELVDHVNDLVIQDFAENDEEDKDDVVEIQA 189
                                        333677888999999999999****9999999988888887765 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   2.2   0.00081       0.7      23      44 ..       4      25 ..       1     176 [. 0.89

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00081
                                       EEEEEEEESTTSSHHHHHHHHH CS
                            G-alpha 23 evkllllGqseSGKsTilkqlk 44
                                       ++k+++lG+++ GK+T++ q+ 
  gene2477|gene2477|rna2477|rna2477  4 KYKIVFLGNQSVGKTTLISQFT 25
                                       68******************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (198 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1135  (0.0633053); expected 358.6 (0.02)
Passed bias filter:                      649  (0.0361983); expected 358.6 (0.02)
Passed Vit filter:                        95  (0.00529868); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.45
# Mc/sec: 1326.56
//
Query:       gene2478|gene2478|rna2478|rna2478  [L=389]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (389 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2056  (0.114675); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.66u 0.32s 00:00:00.98 Elapsed: 00:00:00.49
# Mc/sec: 2369.68
//
Query:       gene2479|gene2479|rna2479|rna2479  [L=55]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (55 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       428  (0.0238719); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.26s 00:00:00.60 Elapsed: 00:00:00.41
# Mc/sec: 400.21
//
Query:       gene248|gene248|rna248|rna248  [L=265]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.6e-11   41.8   8.9    1.4e-10   41.1   8.9    1.3  1  RINGv     RING-variant domain


Domain annotation for each model (and alignments):
>> RINGv  RING-variant domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.1   8.9   7.8e-15   1.4e-10       1      48 []      31      84 ..      31      84 .. 0.90

  Alignments for each domain:
  == domain 1  score: 41.1 bits;  conditional E-value: 7.8e-15
                                   ETTTTEE-SSSS...--B-SS--STCCCSB-HHHHHHHHHH...TCT-SB-TTT CS
                          RINGv  1 CriCleeeeese...plispCkCrGslklvHesClekWlde...keantqCeiC 48
                                   C+iC++ ++  +   +lispC C+Gs+k+vH++Cl  W  +    ++ ++Ce+C
  gene248|gene248|rna248|rna248 31 CKICYMYNNPIDstcDLISPCGCKGSIKYVHKTCLRLWRFKgknLREIKTCEQC 84
                                   ******999888899***********************988666667777**** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (265 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1170  (0.0652574); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1722.76
//
Query:       gene2480|gene2480|rna2480|rna2480  [L=896]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        1.9    9.0   9.1       0.45   11.0   0.2    3.3  2  DUF4367   Domain of unknown function (DUF4367)


Domain annotation for each model (and alignments):
>> DUF4367  Domain of unknown function (DUF4367)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   3.9      0.12   2.2e+03       4      75 ..      40     106 ..      37     142 .. 0.76
   2 ?   11.0   0.2   2.5e-05      0.45      11      77 ..     207     271 ..     193     284 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.12
                            DUF4367   4 ptylPeGykfkktnisedsesalleYkdengelisfsiskqskeesqklsidtedaevekieingikatyye 75 
                                        p  +P+      +  +++ +++++     ++e++  s +++++++  ++ ++ +d +ve+ ei +++a+  e
  gene2480|gene2480|rna2480|rna2480  40 PPDIPDEL---FEGYENEGSDFFVSM--SKDEKVENSDQNSEEKSYRQSVVAVDDQKVEEDEIIEQQAEPEE 106
                                        66677666...555577777777777..88888888878888888888888889999999999999987555 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 2.5e-05
                            DUF4367  11 ykfkktnisedsesalleYkdengelisfsiskqskeesqklsidtedaevekieingikatyyeke 77 
                                        y+f+k +i++++e ++ e +++++++ ++     + ++ +++s+ +ed +ve  +in   a++ye +
  gene2480|gene2480|rna2480|rna2480 207 YTFEKLHIQGTAEGFMAEEMSNANKKATIF--ADQSQDLKRVSVSNEDKTVESDQINDSFARVYERG 271
                                        67899999*************888888888..7899999**********************999975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (896 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1487  (0.0829383); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.72u 0.27s 00:00:00.99 Elapsed: 00:00:00.44
# Mc/sec: 6072.18
//
Query:       gene2481|gene2481|rna2481|rna2481  [L=111]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.026   14.6   0.0        1.6    8.9   0.0    2.2  2  Tautomerase_2  Tautomerase enzyme


Domain annotation for each model (and alignments):
>> Tautomerase_2  Tautomerase enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.0   8.7e-05       1.6      51      73 ..      18      40 ..      16      43 .. 0.89
   2 ?    3.6   0.0     0.004        71      15      39 ..      76      99 ..      68     110 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 8.7e-05
                                       HHHHHHHHHH---GGGEEEEEEE CS
                      Tautomerase_2 51 alaerlaaklgirpeDvfivlve 73
                                        +ae++++k+gi+pe  fi +++
  gene2481|gene2481|rna2481|rna2481 18 NIAEEIHEKTGIPPEKQFIHVTK 40
                                       69**************9999876 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.004
                                       E--T.....TS-TT-EEEEEEEES- CS
                      Tautomerase_2 15 viddtylgieRsddlvvieitlseg 39
                                       +++d y++ + +dd++ +eitl+++
  gene2481|gene2481|rna2481|rna2481 76 IFED-YMDDDDDDDITDLEITLKKE 99
                                       5665.9999************9965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (111 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       840  (0.0468515); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 723.61
//
Query:       gene2482|gene2482|rna2482|rna2482  [L=238]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (238 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1049  (0.0585086); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1633.18
//
Query:       gene2483|gene2483|rna2483|rna2483  [L=557]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.6e-09   37.4   7.0    2.8e-09   36.7   7.0    1.4  1  zf-C3HC4_3      Zinc finger, C3HC4 type (RING finger)
    6.7e-08   32.3   5.7    1.4e-07   31.3   5.7    1.5  1  Prok-RING_4     Prokaryotic RING finger family 4
      3e-06   27.1   8.0    6.3e-06   26.0   8.0    1.6  1  zf-RING_5       zinc-RING finger domain
    4.3e-06   26.5   9.4      1e-05   25.3   9.4    1.7  1  zf-C3HC4        Zinc finger, C3HC4 type (RING finger)
    7.7e-06   25.7   8.8    1.6e-05   24.6   8.8    1.6  1  zf-C3HC4_2      Zinc finger, C3HC4 type (RING finger)
    2.8e-05   24.0   3.0    8.5e-05   22.5   1.7    2.4  2  zf-RING_UBOX    RING-type zinc-finger
    3.2e-05   24.2   7.3    6.3e-05   23.2   7.3    1.5  1  zf-RING_2       Ring finger domain
     0.0018   18.1   3.8     0.0034   17.2   3.8    1.5  1  zf-RING_6       zf-RING of BARD1-type protein
  ------ inclusion threshold ------
      0.028   14.9   0.1      0.069   13.6   0.1    1.6  1  Zn-C2H2_12      Autophagy receptor zinc finger-C2H2 domain
      0.031   14.6   3.2      0.072   13.4   3.2    1.6  1  zf-rbx1         RING-H2 zinc finger domain
      0.059   13.3  12.7        1.3    9.0   0.0    6.4  5  Pox_A_type_inc  Viral A-type inclusion protein repeat
      0.065   13.5   0.2       0.36   11.1   0.0    2.3  2  TPR_5           Tetratrico peptide repeat
      0.072   13.2   8.0       0.12   12.5   6.5    2.2  2  zf-RING_10      zinc RING finger of MSL2
       0.36   11.0   6.9       0.85    9.8   6.9    1.7  1  zf-C3HC4_4      zinc finger of C3HC4-type, RING
        0.9    9.4   5.3          2    8.3   5.3    1.6  1  zf-RING_4       RING/Ubox like zinc-binding domain
          2    7.9   4.0        4.8    6.7   0.1    2.7  2  zf-ribbon_3     zinc-ribbon domain
        3.1    8.0   9.8      0.087   13.0   2.3    2.3  2  SMBP            Small metal-binding protein


Domain annotation for each model (and alignments):
>> zf-C3HC4_3  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.7   7.0   2.7e-12   2.8e-09       4      45 ..     504     545 ..     501     550 .. 0.92

  Alignments for each domain:
  == domain 1  score: 36.7 bits;  conditional E-value: 2.7e-12
                                        B-TTTSSSBS-EEETTEEEEEE-HHHHHHHHH.TT-B-TTT-- CS
                         zf-C3HC4_3   4 eCviClerprnvvllpCgHlvlCeeCaekllk.rkkkCpiCrr 45 
                                         C+ C ++ +++v+++C+H+ lC eC++  lk r++kCpiC +
  gene2483|gene2483|rna2483|rna2483 504 RCSTCDKNYKDTVIVKCMHV-LCRECVDGRLKmRSRKCPICGE 545
                                        7*******************.*******99988********86 PP

>> Prok-RING_4  Prokaryotic RING finger family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.3   5.7   1.3e-10   1.4e-07       1      43 [.     505     550 ..     505     552 .. 0.86

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 1.3e-10
                        Prok-RING_4   1 CvlCgeqekkailepCgHlvCkeCfdsk.dls..sCPlCqrrisks 43 
                                        C  C ++ k+ +++ C H++C+eC d+  ++    CP+C + +s++
  gene2483|gene2483|rna2483|rna2483 505 CSTCDKNYKDTVIVKCMHVLCRECVDGRlKMRsrKCPICGEGFSAT 550
                                        9*************************99733346*****9877665 PP

>> zf-RING_5  zinc-RING finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   8.0     6e-09   6.3e-06       1      43 [.     504     544 ..     504     545 .. 0.95

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 6e-09
                          zf-RING_5   1 hCnkCfeklskeekfyltsCgHifCekClkkll.ekeavCpiCr 43 
                                        +C+ C +++   ++ ++++C H++C +C++ +l  ++++CpiC+
  gene2483|gene2483|rna2483|rna2483 504 RCSTCDKNY---KDTVIVKCMHVLCRECVDGRLkMRSRKCPICG 544
                                        6********...999*****************9999*******7 PP

>> zf-C3HC4  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   9.4   9.8e-09     1e-05       1      41 []     505     543 ..     505     543 .. 0.98

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 9.8e-09
                                        -TTT-S--SS-E.E-TTS--B-CHHHHHHHHCTSSB--TTT CS
                           zf-C3HC4   1 CpiCleeakepnelleCkHsfCskCirkilksrkkvkCPlC 41 
                                        C+ C +++k+++ + +C+H +C++C++  lk  +++kCP+C
  gene2483|gene2483|rna2483|rna2483 505 CSTCDKNYKDTV-IVKCMHVLCRECVDGRLK-MRSRKCPIC 543
                                        9***********.******************.999****** PP

>> zf-C3HC4_2  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   8.8   1.5e-08   1.6e-05       1      40 []     504     543 ..     504     543 .. 0.95

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 1.5e-08
                         zf-C3HC4_2   1 kCpiCldmlkdpsvvtpCgHvfCqkCilrsLeekn.eCPlC 40 
                                        +C  C   +kd+ v+ +C Hv C++C++  L+  + +CP+C
  gene2483|gene2483|rna2483|rna2483 504 RCSTCDKNYKDT-VIVKCMHVLCRECVDGRLKMRSrKCPIC 543
                                        59*********7.999***************99999***** PP

>> zf-RING_UBOX  RING-type zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   1.7   8.1e-08   8.5e-05       1      39 []     505     541 ..     505     541 .. 0.89
   2 ?    3.1   0.1     0.094     1e+02       1       9 [.     540     548 ..     540     553 .. 0.86

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 8.1e-08
                       zf-RING_UBOX   1 CpIClelftdPlv.lpCGHtFCreClwelskslegafkCP 39 
                                        C+ C   ++d  v ++C H++CreC+    + + +++kCP
  gene2483|gene2483|rna2483|rna2483 505 CSTCDKNYKDT-ViVKCMHVLCRECV--DGRLKMRSRKCP 541
                                        999******99.5359**********..789999999999 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.094
                       zf-RING_UBOX   1 CpIClelft 9  
                                        CpIC e f+
  gene2483|gene2483|rna2483|rna2483 540 CPICGEGFS 548
                                        *****9996 PP

>> zf-RING_2  Ring finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   7.3     6e-08   6.3e-05       2      43 ..     504     543 ..     503     544 .. 0.84

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 6e-08
                          zf-RING_2   2 eCpICleelssadsvlllpCgHvfhreClerwlrssst.CPlC 43 
                                         C+ C ++++  d+v++ +C Hv +reC++  l+ +s+ CP+C
  gene2483|gene2483|rna2483|rna2483 504 RCSTCDKNYK--DTVIV-KCMHVLCRECVDGRLKMRSRkCPIC 543
                                        5999*98885..45554.4**********9999999999**** PP

>> zf-RING_6  zf-RING of BARD1-type protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   3.8   3.2e-06    0.0034       3      56 ..     498     553 ..     496     555 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 3.2e-06
                          zf-RING_6   3 rlekllrcsrctdilrepvclggcehifcsncisdcf...gsgcpvcytpawiqdvk 56 
                                        +  kllrcs c    ++ v +  c h++c +c+   +      cp+c       dvk
  gene2483|gene2483|rna2483|rna2483 498 KYRKLLRCSTCDKNYKDTVIV-KCMHVLCRECVDGRLkmrSRKCPICGEGFSATDVK 553
                                        678**********99999976.7**********876522256899997766666665 PP

>> Zn-C2H2_12  Autophagy receptor zinc finger-C2H2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   6.6e-05     0.069       1      14 [.     538     550 ..     538     554 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 6.6e-05
                         Zn-C2H2_12   1 KeCPlCseqFpknv 14 
                                        ++CP+C+e F++ +
  gene2483|gene2483|rna2483|rna2483 538 RKCPICGEGFSA-T 550
                                        8*********98.5 PP

>> zf-rbx1  RING-H2 zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   3.2   6.8e-05     0.072      14      54 ..     505     543 ..     499     544 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 6.8e-05
                            zf-rbx1  14 cieckapgdeecpvvlGeCgHaFHlhCiskWlkt.rkvCPlc 54 
                                        c +c+++ ++    v+ +C H+   +C++  lk  +++CP+c
  gene2483|gene2483|rna2483|rna2483 505 CSTCDKNYKD---TVIVKCMHVLCRECVDGRLKMrSRKCPIC 543
                                        8999999999...55568***************96778**** PP

>> Pox_A_type_inc  Viral A-type inclusion protein repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.0    0.0012       1.3       6      20 ..     188     202 ..     185     204 .. 0.92
   2 ?    1.7   0.3      0.25   2.6e+02       8      17 ..     240     249 ..     235     251 .. 0.80
   3 ?   -0.1   0.2      0.95     1e+03       7      14 ..     264     271 ..     263     275 .. 0.87
   4 ?   -0.0   0.1      0.86   9.1e+02      10      18 ..     310     318 ..     302     322 .. 0.83
   5 ?    4.1   0.1     0.043        45       6      18 ..     327     339 ..     326     340 .. 0.93

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0012
                     Pox_A_type_inc   6 lRsRIsDLErqLseC 20 
                                        l++++ DL ++L+ C
  gene2483|gene2483|rna2483|rna2483 188 LKRKVLDLNSSLANC 202
                                        9************** PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.25
                     Pox_A_type_inc   8 sRIsDLErqL 17 
                                         +I++L+++L
  gene2483|gene2483|rna2483|rna2483 240 KEIEELKKKL 249
                                        689****999 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.95
                     Pox_A_type_inc   7 RsRIsDLE 14 
                                        + +I DLE
  gene2483|gene2483|rna2483|rna2483 264 KKKIKDLE 271
                                        789****9 PP

  == domain 4  score: -0.0 bits;  conditional E-value: 0.86
                     Pox_A_type_inc  10 IsDLErqLs 18 
                                        + DL+++L+
  gene2483|gene2483|rna2483|rna2483 310 VKDLKQKLE 318
                                        57*****97 PP

  == domain 5  score: 4.1 bits;  conditional E-value: 0.043
                     Pox_A_type_inc   6 lRsRIsDLErqLs 18 
                                        l+++I DLE +L+
  gene2483|gene2483|rna2483|rna2483 327 LKEEIGDLEAELD 339
                                        89********996 PP

>> TPR_5  Tetratrico peptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00034      0.36      38      98 ..     189     249 ..     171     255 .. 0.89
   2 ?   -2.1   0.0       4.2   4.5e+03      40      73 ..     459     475 ..     449     508 .. 0.53

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00034
                              TPR_5  38 rratiqLassLRnlGeaeealaLLraeleapsdelddalaaflaLvLsdlgrereavsivl 98 
                                        +r ++ L ssL n Ge++   a+ + e + + del +a++a  +  + +l +e e ++  l
  gene2483|gene2483|rna2483|rna2483 189 KRKVLDLNSSLANCGETAPQKAVDKVEKDVNVDELMEAVEASKSEKMGELYKEIEELKKKL 249
                                        68899************************************99999988888888877655 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 4.2
                              TPR_5  40 atiqLassLRnlGeaeealaLLraeleapsdeld 73 
                                         ++ L s LR l +                 +++
  gene2483|gene2483|rna2483|rna2483 459 QQVRLESKLRMLSD-----------------DIS 475
                                        34555666665543.................222 PP

>> zf-RING_10  zinc RING finger of MSL2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       8.2   8.7e+03      51      66 ..     354     369 ..     352     372 .. 0.80
   2 ?   12.5   6.5   0.00011      0.12       2      44 ..     504     544 ..     503     554 .. 0.79

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 8.2
                         zf-RING_10  51 enkqlrlllqCYkklc 66 
                                        e+ +lr  l+ Yk+l 
  gene2483|gene2483|rna2483|rna2483 354 EELKLRKELNAYKNLK 369
                                        6778899999999986 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00011
                         zf-RING_10   2 sCvvCckLLvdPlepkekeCqHyvCrlCvgkkkklkp.sCsqCk 44 
                                         C+ C k  +d +     +C H +Cr Cv ++ k+++ +C+ C 
  gene2483|gene2483|rna2483|rna2483 504 RCSTCDKNYKDTVI---VKCMHVLCRECVDGRLKMRSrKCPICG 544
                                        57777777777654...58***************99846***97 PP

>> zf-C3HC4_4  zinc finger of C3HC4-type, RING
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   6.9   0.00081      0.85       1      42 []     505     543 ..     505     543 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00081
                         zf-C3HC4_4   1 CPiCldYLekPvsleCGhsfClsCisslqkepdgeqllCplC 42 
                                        C  C +  ++ v ++C h+ C +C++   k  +     Cp C
  gene2483|gene2483|rna2483|rna2483 505 CSTCDKNYKDTVIVKCMHVLCRECVDGRLKMRSR---KCPIC 543
                                        89999999******************99998866...59999 PP

>> zf-RING_4  RING/Ubox like zinc-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   5.3    0.0019         2       5      46 ..     505     546 ..     502     548 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0019
                          zf-RING_4   5 deeldetdkdlkpCeCgyqiClfCyhrileeeegrCPaCree 46 
                                        ++  d++ kd    +C + +C+ C +  l+  + +CP C e 
  gene2483|gene2483|rna2483|rna2483 505 CSTCDKNYKDTVIVKCMHVLCRECVDGRLKMRSRKCPICGEG 546
                                        55668888888999************999999*******765 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0      0.16   1.7e+02       4      15 ..     504     515 ..     502     518 .. 0.77
   2 ?    6.7   0.1    0.0046       4.8       3      15 ..     538     550 ..     536     553 .. 0.69

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.16
                        zf-ribbon_3   4 rCPnCGaplssd 15 
                                        rC+ C+++ ++ 
  gene2483|gene2483|rna2483|rna2483 504 RCSTCDKNYKDT 515
                                        8*****975665 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0046
                        zf-ribbon_3   3 vrCPnCGa.plssd 15 
                                        ++CP CG+   s+ 
  gene2483|gene2483|rna2483|rna2483 538 RKCPICGEgF-SAT 550
                                        4788888877.555 PP

>> SMBP  Small metal-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.9       8.5   8.9e+03      60      83 ..     138     167 ..     131     171 .. 0.39
   2 ?   13.0   2.3   8.3e-05     0.087      26     108 ..     215     302 ..     197     305 .. 0.78

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 8.5
                                        HHHH.........-------HHHHHHHHHH CS
                               SMBP  60 akaa......aekakeeekehldegikhLe 83 
                                         k+a      +++   + ++++++ i+++e
  gene2483|gene2483|rna2483|rna2483 138 KKNAagaendENECLDQHNDQIKKIIEQME 167
                                        333322111122222334444444455554 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 8.3e-05
                                        HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHH...-------HHHHHHHHHHHHHHHHHCT-HH...HHH CS
                               SMBP  26 hlaeAiehaeaAvahgkaghakalveHaeealkhakaaaekakeeekehldegikhLeeAIkhgkaghad...vAt 98 
                                          +  ++++ +Av+++k +++ +l ++ ee +k++ +  +k ++e+++  ++ ik Le+  k+ ++ + +    A+
  gene2483|gene2483|rna2483|rna2483 215 EKDVNVDELMEAVEASKSEKMGELYKEIEELKKKLLEN-AKVTGEGEDLSKKKIKDLEDVLKQVEERNCEllrDAQ 289
                                        6667788999*************************999.99*******************9999885544111344 PP

                                        HHH...HHHHHHH CS
                               SMBP  99 kaa...eeAlkhl 108
                                        k a   +eAl ++
  gene2483|gene2483|rna2483|rna2483 290 KNAvdfKEALDKM 302
                                        4332224555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (557 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2633  (0.146857); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); expected 358.6 (0.02)
Passed Vit filter:                        77  (0.00429472); expected 17.9 (0.001)
Passed Fwd filter:                        34  (0.00189637); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.89u 0.32s 00:00:01.21 Elapsed: 00:00:00.52
# Mc/sec: 3222.53
//
Query:       gene2484|gene2484|rna2484|rna2484  [L=328]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-34  118.9   0.0    2.9e-34  118.3   0.0    1.3  1  Transket_pyr     Transketolase, pyrimidine binding domain
    2.5e-33  114.6   0.0    4.2e-33  113.9   0.0    1.4  1  Transketolase_C  Transketolase, C-terminal domain
  ------ inclusion threshold ------
      0.011   16.0   0.0      0.021   15.1   0.0    1.4  1  PFOR_II          Pyruvate:ferredoxin oxidoreductase core doma


Domain annotation for each model (and alignments):
>> Transket_pyr  Transketolase, pyrimidine binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.3   0.0   4.8e-38   2.9e-34       3     176 ..       5     179 ..       3     181 .. 0.97

  Alignments for each domain:
  == domain 1  score: 118.3 bits;  conditional E-value: 4.8e-38
                                        EEHHHHHHHHHHHHHCTTTTEEEEESSTH..HHHTTCHCCHHEGGTTEGEEE--S-HHHHHHHHHHHHHHCTTEEE CS
                       Transket_pyr   3 iawrkaeaealaellkedpevvligaDva..ggtfsvrkgllhdqgegrvidsgisEqavlgfavGaalagpllvi 76 
                                        i+  +a++ al+e+++ +p++++ig++v+  gg ++++ +l+++ ge rv+ds+isE +++g a+Gaa ag l ++
  gene2484|gene2484|rna2484|rna2484   5 ITPIQAINIALDEEMEHNPKIFIIGEEVGvhGGAYGATLNLQKKYGEHRVVDSPISEIGFTGLAAGAAQAG-LHPV 79 
                                        556789*****************************************************************.9*** PP

                                        EEEEEHHHHGGG..HHGGHHHHHCHHHHHT--EEEEESBSGGGSTTGTTTSBSSHHHHHHTSTTEEEE--SSHHHH CS
                       Transket_pyr  77 veaqFgdFangA..qiyadqairsgeakgklkvgvvtrlpigvgedGpehqsaeleaflrlipglkvvrPsdpaet 150
                                        v  +  +Fa ++  +i++  a++ +++ g l++++v+r p g+     +++ +    ++ ++pglkvv+P+++ + 
  gene2484|gene2484|rna2484|rna2484  80 VDYMTWNFALQSidHIINTCAKSLYMSNGLLRTPIVFRGPNGFNYGVGAQHTQDFGCYYGAVPGLKVVAPYSARDH 155
                                        **************************************************************************** PP

                                        HHHHHHHHHSSS.SEEEEEE-SSEEC CS
                       Transket_pyr 151 khllrrairredrkPvvlrlpksllr 176
                                        +++lrra+r  d++Pv++++++ l++
  gene2484|gene2484|rna2484|rna2484 156 RGCLRRALR--DKNPVIFLENEVLYK 179
                                        *********..89*******999987 PP

>> Transketolase_C  Transketolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.9   0.0     7e-37   4.2e-33       2     124 .]     198     319 ..     197     319 .. 0.98

  Alignments for each domain:
  == domain 1  score: 113.9 bits;  conditional E-value: 7e-37
                                        EEEEEETTSSEEEEEETTHHHHHHHHHHHHHTTTTCEEEEE-SEEESHHHHHHHHHHHHHSEEEEEEEEESTTSHH CS
                    Transketolase_C   2 kaeilregkdvtlvayGsmveealeAaeeLekegisaeVvdlrtvkplDketilesvkktgrlvvveeavkrgGig 77 
                                        ka++++eg+d+tl++ + +v  +leAa++Le++gis+eV++l++++p+D +t+ esv+kt+rl++v++ ++ ++i+
  gene2484|gene2484|rna2484|rna2484 198 KAVVEKEGQDITLIGISLTVGICLEAAQALEEDGISVEVINLISIRPIDYATLVESVQKTRRLIIVDNSWPCFSIA 273
                                        7999************************************************************************ PP

                                        HHHHHHHHHCCCTTCSSEEEEEEE-SSSSSSGHHHHHHHTT-SHHHH CS
                    Transketolase_C  78 sevaaalaeeafdgldapvkrvggpdviepgsaeelekafgldaeki 124
                                        se++a + e++f  l+ pv+r+ + dv++p++  +le++ ++++e++
  gene2484|gene2484|rna2484|rna2484 274 SEISANIHEKMFSLLKMPVERINAEDVPTPYA-LNLEQLSLPSTENV 319
                                        ********************************.99*******99986 PP

>> PFOR_II  Pyruvate:ferredoxin oxidoreductase core domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0   3.6e-06     0.021       2      80 ..     207     282 ..     206     300 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.6e-06
                                        SEEEEE-STHHHHHHHHHHHHHHTT--EEEEEES--BS--HHHHHHHSTT-SEEEEEE-S--TT-G-HHHHHHHHH CS
                            PFOR_II   2 evvivamGsvagtaksavdelReegikvGllrlrtlrPFPeeelkellkkvkkvvvldrnisfgseGqlveevkaa 77 
                                        ++ ++++  ++g + +a+++l e+gi+v ++ l+++rP  ++ l e ++k+++++ +d +        +++e++a 
  gene2484|gene2484|rna2484|rna2484 207 DITLIGISLTVGICLEAAQALEEDGISVEVINLISIRPIDYATLVESVQKTRRLIIVDNSWPCF---SIASEISAN 279
                                        66788888889999********************************************998322...344444444 PP

                                        TGG CS
                            PFOR_II  78 lkk 80 
                                        +++
  gene2484|gene2484|rna2484|rna2484 280 IHE 282
                                        333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (328 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       594  (0.0331307); expected 358.6 (0.02)
Passed bias filter:                      550  (0.0306766); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 2257.43
//
Query:       gene2485|gene2485|rna2485|rna2485  [L=145]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.1e-10   40.1   0.2    7.4e-10   38.9   0.0    1.6  2  DUF5096   Domain of unknown function (DUF5096)


Domain annotation for each model (and alignments):
>> DUF5096  Domain of unknown function (DUF5096)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0      0.15   2.7e+03      95     121 ..      29      55 ..      22      62 .. 0.69
   2 !   38.9   0.0   4.1e-14   7.4e-10       1      39 [.      98     136 ..      98     143 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.15
                            DUF5096  95 nggiikkknresndvsIaladkkniev 121
                                        ng i  ++++ +  ++I ++  +n e+
  gene2485|gene2485|rna2485|rna2485  29 NGLIYVQEKNMQSLTQILFSHVENLEL 55 
                                        555666677777777777777777665 PP

  == domain 2  score: 38.9 bits;  conditional E-value: 4.1e-14
                            DUF5096   1 iseeqyksllseafnlyGPtkeefisiaalnllkllkni 39 
                                        +++eq+k+++ ea+++yGP++ee++siaa++++++lk+ 
  gene2485|gene2485|rna2485|rna2485  98 MTSEQRKNIIGEAYDNYGPSREEAASIAACYSINFLKTT 136
                                        689**********************************84 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       566  (0.031569); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1005.75
//
Query:       gene2486|gene2486|rna2486|rna2486  [L=171]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-48  165.1   0.5    1.9e-48  164.8   0.5    1.0  1  DUF5096   Domain of unknown function (DUF5096)
  ------ inclusion threshold ------
       0.12   12.3   0.0       0.15   12.0   0.0    1.2  1  TMEM52    Transmembrane 52


Domain annotation for each model (and alignments):
>> DUF5096  Domain of unknown function (DUF5096)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  164.8   0.5   2.1e-52   1.9e-48      34     192 .]       5     169 ..       2     169 .. 0.98

  Alignments for each domain:
  == domain 1  score: 164.8 bits;  conditional E-value: 2.1e-52
                            DUF5096  34 kllknif.....ssskkikiiiggddiyneIglilgRlllak.ktevlilcssknvkivrykfiyennggiikkkn 103
                                        +++kn+f     s+s+ki i+i++dd+ ++++++++Rll+a+ ++++li+ +++n+k+vr++fi++++++++k++ 
  gene2486|gene2486|rna2486|rna2486   5 QFFKNNFfgtkeSHSMKISIVIQKDDWHAQVAFNISRLLMAQgYYPELIMLCPVNCKTVRQLFISKKERQKKKDSL 80 
                                        79****************************************9********************************* PP

                            DUF5096 104 resndvsIaladkknievqekktaksvlflgvpenakeiknkigiffGvvpeefkkfkgelyliDvgfskklykky 179
                                        ++++d+sI+++d++ni +q+++++ +v+f+gvp+ +k+++++ +if+G++++e+k+f gel+++++gf+k++++++
  gene2486|gene2486|rna2486|rna2486  81 EGNYDLSIVACDNANILKQGSFESSNVVFIGVPNGTKSSSKMHAIFYGPYDAEYKNFGGELVFVNPGFGKRTLMRM 156
                                        **************************************************************************** PP

                            DUF5096 180 gldkefkksliki 192
                                        gld ++++++i++
  gene2486|gene2486|rna2486|rna2486 157 GLDYYPSCGYIVH 169
                                        **********986 PP

>> TMEM52  Transmembrane 52
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   1.6e-05      0.15      30      77 ..      52      98 ..      28     124 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.6e-05
                             TMEM52 30 llLlCgltasCvrfCclrkqqkaeeespparkpyevtvialDsDstlq 77
                                       l++lC + +  vr   ++k+++++++  + +  y+++++a D+   l+
  gene2486|gene2486|rna2486|rna2486 52 LIMLCPVNCKTVRQLFISKKERQKKKD-SLEGNYDLSIVACDNANILK 98
                                       89***********88888777666655.4489**********987665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       406  (0.0226449); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 1174.70
//
Query:       gene2487|gene2487|rna2487|rna2487  [L=170]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1050  (0.0585643); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1192.45
//
Query:       gene2488|gene2488|rna2488|rna2488  [L=473]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.7e-56  190.3  15.9    5.7e-56  190.0  15.9    1.1  1  SecY             SecY translocase
    1.4e-16   60.0   0.3    3.1e-16   58.9   0.3    1.7  1  Plug_translocon  Plug domain of Sec61p


Domain annotation for each model (and alignments):
>> SecY  SecY translocase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  190.0  15.9   6.3e-60   5.7e-56       1     305 [.      75     455 ..      75     456 .. 0.85

  Alignments for each domain:
  == domain 1  score: 190.0 bits;  conditional E-value: 6.3e-60
                                        BTTSSTCHHHHHHHHHHHHHHHHSSSSSSTS.-S.SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC......... CS
                               SecY   1 sifaLGImPyitasIilqLltvvipkleelk.ke.geegrkkinqitryltvvlalvqalgialslg......... 65 
                                        +++ LGI+P++t+s+i+q+l++    le+++ +   +e++ +++ + ++l+v+l++ q+++ + s+g         
  gene2488|gene2488|rna2488|rna2488  75 TLMDLGISPVVTSSMIMQMLSS----LEIVRvNSkVKEDQTLYSAASKLLAVLLTVGQSIVQV-STGfygptsdig 145
                                        89******************76....66666655599***********************965.445679****** PP

                                        .HH.HHHHHHHHHHHHHHHHHHHHHHH.HSSTTHHHHHHHHHHHHHHC.CHSS.................-HHHH. CS
                               SecY  66 .lalllivlqltagtvllmwLgEqite.kGiGnGisllifagivarlp.kals.................gliel. 120
                                          + ll+v+ql++ ++++++L+E++++ +G+G+G+ l+i+++++++++ kals                     l 
  gene2488|gene2488|rna2488|rna2488 146 iQVSLLLVIQLFFSGIIIILLDELLQKgYGLGSGVNLFIATNVCESIVwKALSpkmhttargiefegsliA---Lf 218
                                        96689*******************************************99999888777777777765441...24 PP

                                        ...........SS........THHHHHHHHHHHHHHHHHCHHHHBEEEECBBBSTT....S.S-EEEEETTCCCSC CS
                               SecY 121 ...........ale......gilallllllvtllvillvvyveeaerripvqyakrgrkggqssylPlklnyagvi 179
                                                   a        + l+++++l  tl++++lv+yv+ +++++  ++ +    +gq++++P+kl+y++ +
  gene2488|gene2488|rna2488|rna2488 219 hllfvrknklyA-LheaffrENLPNMMTLTSTLFIFALVIYVHGVRVNLRTESLQV---KGQQGNYPIKLLYSSTM 290
                                        444444444331.0345667569*****************************9955...59*************** PP

                                        HHHHHHHHHHHHHCCCCS.........................................TCCCSTHHHHHHHHHHH CS
                               SecY 180 PiIfassllalpstiaqfl........................................lallspsvlyvvlyvll 215
                                        PiI++  +++  st+ +fl                                        ++++  ++ly+++y+ +
  gene2488|gene2488|rna2488|rna2488 291 PIIVQNYIISHASTVSRFLyqkfpdvflvrllgvwtmrkngkmvpisgicyflfppdslMDIF-RKPLYFMVYTSI 365
                                        **********88888777788888888888888888888777777777776666665544444.557888888888 PP

                                        HHH....HHHHHHTCT.THHHHHHHCCHHTBSSSCTTTTCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS. CS
                               SecY 216 iif....Fayfyteit.fnpkevaenlkksggfipgirpgketakyLekvlsritliGalflaliavlpdllgasl 286
                                        +++    ++  ++ +t +n+++va+ l +   +i+g+ + +++a+ L +++++++++G+l++++i++l+++l++  
  gene2488|gene2488|rna2488|rna2488 366 VLLssafLSRAWIDMTeSNQNDVARSLINRRVTIKGVPE-RNLANKLGEYIPTAAFLGGLVIGFIVMLSNILDT-- 438
                                        88777879*****************************65.9*********************************.. PP

                                        TT.TTHHHHHHHHHHHHHH CS
                               SecY 287 igafggtslLivVgvalet 305
                                        ig  +gt + ++V+++ ++
  gene2488|gene2488|rna2488|rna2488 439 IG--SGTNIFLAVSIVWQY 455
                                        88..***********9987 PP

>> Plug_translocon  Plug domain of Sec61p
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.9   0.3   3.5e-20   3.1e-16       1      35 []      40      74 ..      40      74 .. 0.99

  Alignments for each domain:
  == domain 1  score: 58.9 bits;  conditional E-value: 3.5e-20
                                       HHHHHHCCSB-TT--SSS-TCCHTTTCCCCTSSTT CS
                    Plug_translocon  1 llYlvlsqiPLyGissssssDpfywlRaifAsnrG 35
                                       l+Ylv sq+PL+Gi +++s+Dpfyw+R+++AsnrG
  gene2488|gene2488|rna2488|rna2488 40 LIYLVSSQVPLFGILNTNSADPFYWMRMMMASNRG 74
                                       7*********************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (473 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       591  (0.0329634); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 3320.81
//
Query:       gene2489|gene2489|rna2489|rna2489  [L=33]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (33 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       147  (0.00819901); expected 358.6 (0.02)
Passed bias filter:                      124  (0.00691617); expected 358.6 (0.02)
Passed Vit filter:                         7  (0.000390429); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.31u 0.23s 00:00:00.54 Elapsed: 00:00:00.38
# Mc/sec: 258.10
//
Query:       gene249|gene249|rna249|rna249  [L=237]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (237 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       433  (0.0241508); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1708.83
//
Query:       gene2490|gene2490|rna2490|rna2490  [L=245]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.7e-81  271.9   0.0    5.7e-81  271.6   0.0    1.0  1  tRNA-synt_2d     tRNA synthetases class II core domain (F)
    5.2e-08   32.6   0.0      7e-08   32.2   0.0    1.1  1  tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM 
     0.0001   22.3   0.0    0.00013   22.0   0.0    1.2  1  tRNA-synt_2b     tRNA synthetase class II core domain (G, H, 
    0.00099   19.4   0.0      0.016   15.5   0.0    2.1  2  HBS1_N           HBS1 N-terminus
     0.0027   16.8   0.0     0.0097   15.0   0.0    1.8  2  tRNA-synt_2      tRNA synthetases class II (D, K and N)


Domain annotation for each model (and alignments):
>> tRNA-synt_2d  tRNA synthetases class II core domain (F)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  271.6   0.0   1.6e-84   5.7e-81      40     239 ..       4     232 ..       1     239 [. 0.96

  Alignments for each domain:
  == domain 1  score: 271.6 bits;  conditional E-value: 1.6e-84
                                        TTSEEEHHHHTSTTTSTTTSHHHCHTTSEBTCTSSS-..........................ECESEEE-SSTHH CS
                       tRNA-synt_2d  40 gpevesefynfdaLnvpqdhpaRdmqdtFylkkpeka..........................veekllLRthtta 89 
                                        +++ves+f+nfdaL++pq+hpaR+m+dtF+l +pek+                          ++ k++LRthtta
  gene2490|gene2490|rna2490|rna2490   4 SRYVESSFWNFDALFQPQNHPAREMHDTFFLANPEKTrltptsyservkdiheasykcewnpeESLKNVLRTHTTA 79 
                                        579***********************************************************99999********* PP

                                        HHHHHH......TTS-SSEEEEEEEEEEBSST-SSSB-SEEEEEEEEEEETT--HHHHHHHHHHHHHHHCTSTEEE CS
                       tRNA-synt_2d  90 vqirtl......ekkkppikiisigrvfRrdavDathlaeFhqveglvvdenvsladlkgvleellkklfgaevkv 159
                                         ++r+l      +++ +pik++si+rvfR+++vDathlaeFhq+eglv+++n+sl +l+g+l+ +++kl + + ++
  gene2490|gene2490|rna2490|rna2490  80 CSARMLyeigqnKDNLHPIKLFSIDRVFRNESVDATHLAEFHQIEGLVLGKNLSLGHLMGTLQGFYEKL-NLK-NI 153
                                        *********98777779****************************************************.888.9* PP

                                        EEEECEETTEEEEEEEEEEECCSSSSEEEEEEEEEE-HHHHHHTT-.TTSEEEEEEEEHHHHHHHHHT-SSGHHHH CS
                       tRNA-synt_2d 160 rfrpsyfpftePsaevdvylvekkkkwlEllgaGmvrpevleavgideevsgfafGlGveRlamlkygieDiRelv 235
                                        +f+p+++p+tePs+e+++++ ek +kw+E++++G++rpevle++gi+++ +++a+Gl++eR am+ky++++iR+l+
  gene2490|gene2490|rna2490|rna2490 154 KFKPAFNPYTEPSLEIFAFH-EKMNKWIEIGNSGIFRPEVLEPMGIKDDWRVIAWGLSLERPAMIKYNLDNIRDLL 228
                                        ********************.******************************************************9 PP

                                        TT.H CS
                       tRNA-synt_2d 236 endl 239
                                         + +
  gene2490|gene2490|rna2490|rna2490 229 GSKV 232
                                        9854 PP

>> tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.2   0.0   1.9e-11     7e-08      65     205 ..      64     200 ..      63     211 .. 0.86

  Alignments for each domain:
  == domain 1  score: 32.2 bits;  conditional E-value: 1.9e-11
                    tRNA_synthFbeta  65 nPlsedqsvlRtsLl...pglLevlarNlargnedvrlFEigkvflkd.seeelpeeerhlaivltgkreeeswse 136
                                        nP  + ++vlRt  +   + +L  +++N ++  + ++lF i +vf+++  + +  +e +++ +++ gk+       
  gene2490|gene2490|rna2490|rna2490  64 NPEESLKNVLRTHTTacsARMLYEIGQNKDNLHP-IKLFSIDRVFRNEsVDATHLAEFHQIEGLVLGKN------- 131
                                        566666778887765222689***********99.*************888899***************....... PP

                    tRNA_synthFbeta 137 karavdfydlkgivealleslgiekvefepaehpalhpgrsAeikvdgk......evGvlGelhpevleafdlkq 205
                                             +  +l g+++ + e+l++++++f+pa +p+ +p  s ei +  +      e+G  G + pevle +++k 
  gene2490|gene2490|rna2490|rna2490 132 ----LSLGHLMGTLQGFYEKLNLKNIKFKPAFNPYTEP--SLEIFAFHEkmnkwiEIGNSGIFRPEVLEPMGIKD 200
                                        ....**********************************..688877333367789*****************998 PP

>> tRNA-synt_2b  tRNA synthetase class II core domain (G, H, P, S and T)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.0   3.7e-08   0.00013      12     135 ..      72     186 ..      59     224 .. 0.77

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 3.7e-08
                                        EE-SSSHHHHHHHHHHHEEEBGG.SSEEEEEEEEEEBTTTSTBCTTTB-SEEEEEEEEEEESGGGHHHHHHHHHHH CS
                                        xxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2b  12 iLkPtneetfvelirdevlrskr.LPlklyqiqtkyRdEksdsrGLlRvreFhqkdgyvfhaeaslddslrdlika 86 
                                        +L+   ++  +++  + + ++ +  P+kl+ i +++R+E  d      + eFhq +g v +++     sl  l+ +
  gene2490|gene2490|rna2490|rna2490  72 VLRTHTTACSARMLYEIGQNKDNlHPIKLFSIDRVFRNESVDAT---HLAEFHQIEGLVLGKNL----SLGHLMGT 140
                                        5565555555666666666776646***************8443...478**********9988....7899999* PP

                                        HHHHHHHTT.SCEEEEEEGTTSCBTTSEEEEEEEEETTTSEEEEEEEEE CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2b  87 isriferlglefraiielmsaksadykdkkefeavsesltkgieigtiq 135
                                         + ++e+l l+  + +   +   +  ++++e+ a  e+++k ieig  +
  gene2490|gene2490|rna2490|rna2490 141 LQGFYEKLNLKNIKFKPAFN---PYTEPSLEIFAFHEKMNKWIEIGNSG 186
                                        *********99877766655...6799*****************99755 PP

>> HBS1_N  HBS1 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   4.5e-06     0.016      47      74 ..      51      78 ..      40      81 .. 0.89
   2 ?    1.5   0.0       0.1   3.7e+02      28      57 ..     220     244 ..     198     245 .] 0.75

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 4.5e-06
                             HBS1_N 47 ekqikeAlwkyyyDvekaldyllnkfkk 74
                                        k+i+eA +k++++ e++l+ +l+++++
  gene2490|gene2490|rna2490|rna2490 51 VKDIHEASYKCEWNPEESLKNVLRTHTT 78
                                       699*********************9986 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.1
                             HBS1_N  28 cldevrevLgeeaskvtvtekqikeAlwky 57 
                                         ld++r+ Lg      +v+ + ik++ + y
  gene2490|gene2490|rna2490|rna2490 220 NLDNIRDLLG-----SKVSLEFIKDSSMCY 244
                                        689*******.....445777777777755 PP

>> tRNA-synt_2  tRNA synthetases class II (D, K and N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   2.7e-06    0.0097      93     119 ..      99     124 ..      98     163 .. 0.91
   2 ?   -1.3   0.0      0.24   8.7e+02     287     307 ..     207     227 ..     206     228 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.7e-06
                                        EEEEEEEEE--S--BTTB-S-CEEEEE CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        tRNA-synt_2  93 rvfqiaraFRaEdsrtdrhlaEFtqie 119
                                        + f+i r+FR+E+++++ hlaEF qie
  gene2490|gene2490|rna2490|rna2490  99 KLFSIDRVFRNESVDAT-HLAEFHQIE 124
                                        68*************77.566*****9 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.24
                                        EEEEHHHHHHHHCT-SSGGGC CS
                                        xxxxxxxxxxxxxxxxxxxxx RF
                        tRNA-synt_2 287 lglGldRlvmlllgsesIrdv 307
                                        +gl+l+R  m+  ++++Ird+
  gene2490|gene2490|rna2490|rna2490 207 WGLSLERPAMIKYNLDNIRDL 227
                                        699****************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       366  (0.0204139); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.36
# Mc/sec: 2013.08
//
Query:       gene2491|gene2491|rna2491|rna2491  [L=437]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.018   14.4   0.0      0.047   13.0   0.0    1.7  1  DUF5066          Domain of unknown function (DUF5066)


Domain annotation for each model (and alignments):
>> DUF5066  Domain of unknown function (DUF5066)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   2.6e-06     0.047      50     110 ..      79     139 ..      64     147 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.6e-06
                            DUF5066  50 eslkallaydcdlkspygqkvleylvdsideegvilsyspdeeayygsgldiagvdledlm 110
                                         +   l+ay c+l +++++k  e  v++ +++ ++ s +pd +    + ++    ++e++ 
  gene2491|gene2491|rna2491|rna2491  79 SAKTFLVAYTCELEKSFDKKKRENNVEAQNNKCIVYSKQPDIKKKINVTYNGKRAEMENIF 139
                                        3344588************************************999999999999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (437 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2327  (0.12979); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.75u 0.36s 00:00:01.10 Elapsed: 00:00:00.57
# Mc/sec: 2310.08
//
Query:       gene2492|gene2492|rna2492|rna2492  [L=249]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-48  165.1   0.3    1.9e-48  164.9   0.3    1.1  1  FtsJ             FtsJ-like methyltransferase
    0.00099   18.8   0.2     0.0016   18.1   0.2    1.4  1  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
  ------ inclusion threshold ------
      0.046   13.6   0.1      0.094   12.6   0.1    1.5  1  UPF0146          Uncharacterised protein family (UPF0146)
      0.064   14.0   0.2       0.21   12.3   0.2    2.0  2  Methyltransf_25  Methyltransferase domain
      0.065   13.2   0.1       0.18   11.8   0.0    1.7  2  Herpes_UL55      Herpesvirus UL55 protein
       0.11   12.1   0.2       0.49   10.0   0.2    2.0  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase


Domain annotation for each model (and alignments):
>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  164.9   0.3   6.5e-52   1.9e-48       1     175 [.       7     184 ..       7     186 .. 0.97

  Alignments for each domain:
  == domain 1  score: 164.9 bits;  conditional E-value: 6.5e-52
                                        CCCCHHHHHHHHHHHHT-S-TT-EEEECT-TTSHHHHHHCCT.T.-SEEEEEESSSSHHHTTEEEECS-CCCSSHH CS
                               FtsJ   1 yrsRsayKLleidekfklfkpgktvvDlgaaPGgwsqvllqrlgakgkvvavDlqpmaplpgvttiqgditdpeti 76 
                                        yr+RsayK+++ide++k+++ ++tv+Dl+aaPGgw+q++++++   +kv+avD+q + p++gv +i+ dit+ +  
  gene2492|gene2492|rna2492|rna2492   7 YRARSAYKIQQIDEHYKILHGNTTVIDLCAAPGGWTQIIAEKC---TKVIAVDIQTILPIEGVVFIRDDITSDSCV 79 
                                        9*****************************************6...79**************************** PP

                                        HHHCHCHHH......SSEEEEEE--S-SS-CHHHHHHHHHCCCCHHHHCCHCCCCECCCEEEECCCHCCCHHHHHH CS
                               FtsJ  77 ekikealse......rkvdlvvsDgapdvsgvhdldeylqsqLllaalelalkllkpggtfvlkifrgeeteallk 146
                                        + ++e+++       +k+dlv++Dga+++sg+ d+d  +q ++l+aal+la k+ k   tfv k++r+ ++  +l+
  gene2492|gene2492|rna2492|rna2492  80 KSVLEHVHLlnnsenAKADLVLCDGASNTSGMLDVDVHVQHSILQAALKLAEKISKVCSTFVGKLYRNGDIGTVLR 155
                                        *999877668888889************************************************************ PP

                                        HHHCCEEEEEEEE-SS--CCG-EEEEEEE CS
                               FtsJ 147 qlkkfFekvsvvkPkssrsesseeflvcr 175
                                        q+++++e+v++vkPk srs+s e+f+++ 
  gene2492|gene2492|rna2492|rna2492 156 QFSEVYERVELVKPKCSRSQSIECFVIAM 184
                                        **************************986 PP

>> Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.2   5.5e-07    0.0016       8      42 ..      27      58 ..      24     119 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 5.5e-07
                                       TT-EEEESS-TTSHHHHHHHHHTTTTSEEEEEESS CS
                    Methyltr_RsmB-F  8 eeetilDlcaaPGgKTthiaelmknkgtvvAvdan 42
                                        + t++DlcaaPGg T  iae      +v+Avd++
  gene2492|gene2492|rna2492|rna2492 27 GNTTVIDLCAAPGGWTQIIAEK---CTKVIAVDIQ 58
                                       5789***************986...5678899876 PP

>> UPF0146  Uncharacterised protein family (UPF0146)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   3.2e-05     0.094      30      62 ..      43      75 ..      40      89 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3.2e-05
                                       HHHHHHS-EEEEE-SS-S....STTEE---SSS CS
                            UPF0146 30 ealakrgvdlvatDikekkakegvrivrDDvtd 62
                                       + +a++  +++a+Di+     egv ++rDD+t+
  gene2492|gene2492|rna2492|rna2492 43 QIIAEKCTKVIAVDIQTILPIEGVVFIRDDITS 75
                                       57899999*********9555**********98 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.2   7.1e-05      0.21       1      33 [.      31      61 ..      31     131 .. 0.71
   2 ?   -1.9   0.0       1.9   5.6e+03      56      91 ..     124     159 ..     102     162 .. 0.56

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 7.1e-05
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHH CS
                    Methyltransf_25  1 vLdlGcGtGrltlalakrlgkakvtgvDiseem 33
                                       v+dl++ +G +t+ +a+++   kv++vDi+  +
  gene2492|gene2492|rna2492|rna2492 31 VIDLCAAPGGWTQIIAEKC--TKVIAVDIQTIL 61
                                       89****************9..9*******8755 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.9
                                        CGBSSSTTTEEEEEEESTGGGSSHHHHHHHHHHHHH CS
                    Methyltransf_25  56 edlpfedgsfDlvvssgalhhlsdedlekalkeiar 91 
                                        ++    ++++  v+s+++  ++ + d+ ++l+++++
  gene2492|gene2492|rna2492|rna2492 124 QAALKLAEKISKVCSTFVGKLYRNGDIGTVLRQFSE 159
                                        332233446666666666555566666667666665 PP

>> Herpes_UL55  Herpesvirus UL55 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       1.3   3.9e+03      83     115 ..      81     113 ..      73     131 .. 0.71
   2 ?   11.8   0.0   6.2e-05      0.18      39      67 ..     159     187 ..     149     202 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.3
                        Herpes_UL55  83 sllnaervlreleekrsvdelCdaPfsaatild 115
                                        s l++ ++l + e+ ++   lCd    ++ +ld
  gene2492|gene2492|rna2492|rna2492  81 SVLEHVHLLNNSENAKADLVLCDGASNTSGMLD 113
                                        667777788888888777788887777777777 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 6.2e-05
                        Herpes_UL55  39 svakrsyllrakCesaedihaflfglrkd 67 
                                         v +r  l++ kC++++ i +f++++ k 
  gene2492|gene2492|rna2492|rna2492 159 EVYERVELVKPKCSRSQSIECFVIAMSKR 187
                                        5778999*******************443 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.2   0.00016      0.49       2     139 ..      29     162 ..      28     188 .. 0.60

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00016
                    Methyltransf_15   2 rvilDlfsGaGGnviqfalvfekviaieinleklacaqhNaevYgvsdkitlvlg..dvfellaklkleki.kvdl 74 
                                        ++++Dl++  GG +  +a++ +kvia++i++           v+ + d it   +  +v+e+++ l+ ++  k dl
  gene2492|gene2492|rna2492|rna2492  29 TTVIDLCAAPGGWTQIIAEKCTKVIAVDIQTI--LP--IEGVVF-IRDDITSDSCvkSVLEHVHLLNNSENaKADL 99 
                                        689************************99753..22..234455.6666665555224555555544333336777 PP

                    Methyltransf_15  75 vflSpPwGGpsYkkqekfdlkkklkplkleqllkeslklskniilf...LPrnsdlnqlaaltaevle 139
                                        v++     G s +    +d+  +++   l+  lk + k+sk    f   L rn d+  + +   ev+e
  gene2492|gene2492|rna2492|rna2492 100 VLCD----GAS-NTSGMLDVDVHVQHSILQAALKLAEKISKVCSTFvgkLYRNGDIGTVLRQFSEVYE 162
                                        7764....443.33455666557777766666666555544444432225566555544444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       539  (0.030063); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.59u 0.31s 00:00:00.89 Elapsed: 00:00:00.51
# Mc/sec: 1468.38
//
Query:       gene2493|gene2493|rna2493|rna2493  [L=245]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.8e-22   78.8   1.4    5.3e-22   78.4   1.4    1.1  1  ThiF      ThiF family


Domain annotation for each model (and alignments):
>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.4   1.4     3e-26   5.3e-22      44     227 ..       6     218 ..       5     237 .. 0.83

  Alignments for each domain:
  == domain 1  score: 78.4 bits;  conditional E-value: 3e-26
                                        EEEEEESSB--GGGGGTBTTS-GGGTTSBHHHHHHHHHHHT-TTSEEEEEES-CCGCCS-HHHHTT-SEEEEESSS CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               ThiF  44 kltlvDnDkielsNlnRqflfreediGkpKaevaaealqeinpdveveavteritdetvleellesvDlVvdalDn 119
                                        +lt+ DnD++ l++lnRqf+++++diG+pK++ ++e l +  + v ++ +++++ +         ++Dl + + Dn
  gene2493|gene2493|rna2493|rna2493   6 RLTVLDNDTVALTDLNRQFYYKQNDIGQPKVKILEEYLWQYHN-VRINIIHKDVFE-----VCDYEYDLMFCCFDN 75 
                                        69************************************99887.999999999944.....344689********* PP

                                        HHHHHHHHHHHHHHT-EEEEEEEETTEEEEEEE.EECCS-ECTSS-TGGS.EECCCCEEHHH.............. CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx.............. RF
                               ThiF 120 iearrlvnracvkkgiplieagtlgfegqvvvi.ipgktgcyeCldpsstedptekkvplct.............. 180
                                        +e+r+ +n + + + ip+i+ g +g++ +v  + +  + +c+ C++       t++ ++ ct              
  gene2493|gene2493|rna2493|rna2493  76 VESRMQLNYISYINNIPMIDLGIEGLQMHVKRVdFATNRACLYCMKE---LYGTKAAFNYCTlkntntrnreayiy 148
                                        *********************************644999******84...88889999999999999999999999 PP

                                        ...........................HHHCTE-B-HHHHHHHHHHHHHHHHHHHTTBCGGGCCEEEECCTTTT CS
                                        ...........................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               ThiF 181 ...........................siagnipaiatttavvaglaalellkllsgkeklenslltqvdlles 227
                                                                   ++ g    i +   ++a+l+a ++lk++++++    +    ++++e 
  gene2493|gene2493|rna2493|rna2493 149 slslkyesvedvvehfnavnavktdefEVRGIKENILPNACYIASLCASMALKMVDECKYDFIY----YNGYEK 218
                                        9**************99998888888733342346899999*************9655533333....333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       693  (0.0386525); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1657.20
//
Query:       gene2494|gene2494|rna2494|rna2494  [L=795]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.8e-26   92.9   0.1    1.8e-26   92.9   0.1    3.1  3  GTP_EFTU     Elongation factor Tu GTP binding domain
    7.7e-17   61.3   2.8    2.7e-16   59.6   2.8    2.0  1  IF-2         Translation-initiation factor 2
    1.2e-14   54.0   0.1    3.5e-14   52.4   0.1    1.9  1  GTP_EFTU_D4  Elongation factor Tu domain 4
    1.7e-11   44.4   2.6    2.1e-06   28.0   0.2    3.3  2  GTP_EFTU_D2  Elongation factor Tu domain 2
    3.2e-06   27.2   4.9    2.4e-05   24.4   0.0    3.6  3  MMR_HSR1     50S ribosome-binding GTPase
    0.00022   20.8   0.2     0.0038   16.8   0.0    3.0  3  FeoB_N       Ferrous iron transport protein B
    0.00031   20.9   0.0     0.0013   18.9   0.0    2.2  2  Roc          Ras of Complex, Roc, domain of DAPkinase
  ------ inclusion threshold ------
       0.02   14.5   0.0       0.15   11.6   0.0    2.6  1  Ras          Ras family


Domain annotation for each model (and alignments):
>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.2       1.3   2.8e+03      40      63 ..      31      54 ..      20      96 .. 0.59
   2 !   92.9   0.1   8.2e-30   1.8e-26       5     191 ..     214     419 ..     211     422 .. 0.75
   3 ?   -3.7   0.1       3.2   7.1e+03      57      76 ..     626     643 ..     599     662 .. 0.61

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.3
                                       HSTHCHSHHHHHHTSCSSCEEEEE CS
                           GTP_EFTU 40 ervlDtlkeErergiTiksaaisl 63
                                       ++v+D+++  +e+  T+  +  + 
  gene2494|gene2494|rna2494|rna2494 31 TAVIDKAAGNKEQDSTVVNKKENA 54
                                       445555555555555544333333 PP

  == domain 2  score: 92.9 bits;  conditional E-value: 8.2e-30
                                        EEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHSTHCHSHHHHHHTSCSSCEEEEEETTCSSEEEEEEEESSS CS
                           GTP_EFTU   5 nigiighvDhGKtTLtdrLlyktgaiskkgekaeeervlDtlkeErergiTiksaaisleketkkylinliDtPGH 80 
                                         ++i+ghvD+GKt ++d+L +++ +  ++g  +++  ++ +   E      ++ ++++++ + +   + +iDtPGH
  gene2494|gene2494|rna2494|rna2494 214 IVCILGHVDTGKTKILDKLRESNVQGGEAGGITQQIGATFFPYSE---L--VNKTNTKFDFDNDVPGLLVIDTPGH 284
                                        69******************8888877766655533233333333...2..34444444455999*********** PP

                                        GGGHHHHHHHHHT-SEEEEEEETTTBSTHHHHHHHHHHHHTTTEEEEEEESCGST...........HHHHHHHHHH CS
                           GTP_EFTU  81 vdFskevirglrvlDgavlvvdaveGvepqteevlrlalkegvpiivfiNKmDrl...........kaelkeivee 145
                                        + F +  +rg +++D+a+lvvd+ +  e qt e ++l++ +++p+ +++NK+Dr+           + +l+++ + 
  gene2494|gene2494|rna2494|rna2494 285 ETFANLRSRGSSMCDFAILVVDVLHALEKQTLESIELLKLRKTPFLIALNKIDRIykwrsetggfhNFDLQRQSSV 360
                                        *******************************************************777766666553344444444 PP

                                        HHHHHHHH..............HHHHHHHHHTTT.........TTEEEEEEBTTTTBTHHHHHHHHHHH CS
                           GTP_EFTU 146 vkqklsrk..............eeklekygekge.........kevpvvfgSalkgegvktllealvel 191
                                         k ++ +k              +          +         k+++++++Sa++geg+++l++ ++el
  gene2494|gene2494|rna2494|rna2494 361 TKAEFIEKsnhiilkfaemglnT----------RlfyenpderKFINIIPTSAITGEGLSDLVNKIIEL 419
                                        44444333555555555555433..........04444445558********************99985 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 3.2
                                        SCEEEEEETTCSSEEEEEEE CS
                           GTP_EFTU  57 ksaaisleketkkylinliD 76 
                                        +s++i+++  +++  +nliD
  gene2494|gene2494|rna2494|rna2494 626 ESQHIKIF--EAQIIYNLID 643
                                        34444444..4444444444 PP

>> IF-2  Translation-initiation factor 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.6   2.8   1.2e-19   2.7e-16       3     105 .]     540     646 ..     538     646 .. 0.90

  Alignments for each domain:
  == domain 1  score: 59.6 bits;  conditional E-value: 1.2e-19
                                        CHHHCCCSCS..SCCEEEEEESSHHHHHHHHHHHHCTT.SSTEEEECEEEESS.B-HHHHHHHHH..ST....EEE CS
                               IF-2   3 elfeeikeeg..kelnviikaDvqGsleAlkeaLekleseevkvkvihsgvGa.itesDvelasa..sn....aii 69 
                                        +++e+ike +  +++++ ++a+  GsleAl + +++      +++v ++g+G+ ++++Dv +++a  ++    +i+
  gene2494|gene2494|rna2494|rna2494 540 QVMEDIKELTnlEKVGIHLQASSLGSLEALIALVKNE-----RIPVASVGIGKnLSRKDVLKMKAikEKdahvGIM 610
                                        6788888777899*******************99997.....7*********769********99651157789** PP

                                        EEESSSCTHHHHHCCCCCTSEEEEESSHHHHHHHHH CS
                               IF-2  70 igFnvkvskkakklaekegvkirlynvIYkliddvk 105
                                        ++F++k++k++++lae++++ki+++++IY+lid++k
  gene2494|gene2494|rna2494|rna2494 611 LCFDTKIDKEMTDLAESQHIKIFEAQIIYNLIDKYK 646
                                        *********************************986 PP

>> GTP_EFTU_D4  Elongation factor Tu domain 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.4   0.1   1.6e-17   3.5e-14       2      86 .]     667     758 ..     666     758 .. 0.87

  Alignments for each domain:
  == domain 1  score: 52.4 bits;  conditional E-value: 1.6e-17
                                        -CEEEEEEEEEEETCCCEEEEEEEEEEEEETT-EEE...ETTE.EEEEEEEEEETTEEESEEETT-EEEEEEES.. CS
                        GTP_EFTU_D4   2 PgkikilpgvvfrrsdpaivGvevlgGvikpgvkli...kedGrevGeilqiqdkgkkleeakaGqevaisieg.. 72 
                                        P k++i+p++vf ++ p + Gve+l+G++k++++l    +++  ++G+++++  ++k++++a +G++++i ie   
  gene2494|gene2494|rna2494|rna2494 667 PCKLQIIPEYVFTKRSPLVLGVEILEGKLKTNMPLFvmhQDEIVQIGKVTSMIMEKKSVDVADKGSKLSIKIETtd 742
                                        99********************************852223445689**************************9643 PP

                                        ..S-TTTS--TT-EEE CS
                        GTP_EFTU_D4  73 ..kivGrqikegdily 86 
                                          k +Gr+ik  d +y
  gene2494|gene2494|rna2494|rna2494 743 apKLIGRDIKLTDLMY 758
                                        33569*****999887 PP

>> GTP_EFTU_D2  Elongation factor Tu domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0   0.2   9.4e-10   2.1e-06       3      71 ..     450     523 ..     448     526 .. 0.90
   2 !   14.9   0.2   1.2e-05     0.026       3      51 ..     685     731 ..     684     755 .. 0.82

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 9.4e-10
                                        EEEEEEEESEEETTEEEEEECTCTTSEEEEEEEEEEEEETEEESEE..........ETTSEEEEEEEESSCCSGSS CS
                        GTP_EFTU_D2   3 valgrvysGtlkkGdevrilgndtskkeivtrissletfhededea..........vaganaGvivaikgledaii 68 
                                        +++++v +Gtl ++d+++++g+d    +ivt ++sl+++ e+++e+           + a  G+++ + +le + i
  gene2494|gene2494|rna2494|rna2494 450 TVDAIVSNGTLSENDRIVLCGMDG---PIVTNVRSLLVP-EPLKELrvksvyknikCVKASLGIKIVANDLERT-I 520
                                        7999*****************653...9***********.99************99999999999999999996.8 PP

                                        TTC CS
                        GTP_EFTU_D2  69 vGd 71 
                                        +G+
  gene2494|gene2494|rna2494|rna2494 521 AGS 523
                                        886 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 1.2e-05
                                        EEEEEEEESEEETTEEEEEECTCTTSEE..EEEEEEEEEEETEEESEEETT CS
                        GTP_EFTU_D2   3 valgrvysGtlkkGdevrilgndtskke..ivtrissletfhededeavag 51 
                                        v ++ + +G+lk+++ + +  ++  ++e  ++++++s+ ++++ +d a +g
  gene2494|gene2494|rna2494|rna2494 685 VLGVEILEGKLKTNMPLFV--MH--QDEivQIGKVTSMIMEKKSVDVADKG 731
                                        67889**************..66..445569************99998555 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.7     0.099   2.2e+02      26      73 ..      55     105 ..      43     168 .. 0.57
   2 !   24.4   0.0   1.1e-08   2.4e-05       2     114 .]     215     335 ..     214     335 .. 0.69
   3 ?   -0.4   0.1      0.54   1.2e+03      70      97 ..     626     652 ..     582     670 .. 0.56

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.099
                                        ESSSTTSSSSEEEEEEE...ETTEEEEEEECGGC..............SSHHHHHHHHHHHHHHH CS
                           MMR_HSR1  26 vsdkpgtTrdinegrvk...lkgkeielvDtpGl..............iegaseekglgkaflal 73 
                                         +++p +T+d +e       +++++++ +D +G+              +              + 
  gene2494|gene2494|rna2494|rna2494  55 ENNEPVKTIDKKEDSTGakvENDQPVKKTDNAGVqpgsaqrrrpniafL--------------KQ 105
                                        4688888988877765444446699********6444444444443321..............21 PP

  == domain 2  score: 24.4 bits;  conditional E-value: 1.1e-08
                                        EEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEE......ETTEE............EEEEECGGCSSH CS
                           MMR_HSR1   2 vaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvk......lkgke............ielvDtpGlieg 59 
                                        v+i+G+  +GK+ ++ +l +++++ ++  g T++i    +       +                + ++DtpG  e 
  gene2494|gene2494|rna2494|rna2494 215 VCILGHVDTGKTKILDKLRESNVQGGEAGGITQQIGATFFPyselvnK---TntkfdfdndvpgLLVIDTPG-HE- 285
                                        89*****************99888888888888885544432233221...034455555555699999999.44. PP

                                        HHHHHHHHHHHHHHHC.TSEEEEEEETTTTCSHHHHHHHHHHHHHTTSEEEEEEES CS
                           MMR_HSR1  60 aseekglgkaflalee.adlillvvdaseeklkpldeeleelleeakkplilvlnk 114
                                              +++   +  + +d ++lvvd+  + l+++  e  ell+ +k p++++lnk
  gene2494|gene2494|rna2494|rna2494 286 -----TFANLRSRGSSmCDFAILVVDVL-HALEKQTLESIELLKLRKTPFLIALNK 335
                                        .....2333333222348********66.557777777777776689999*9*998 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.54
                                        HHHHHC...TSEEEEEEETTTTCSHHHHHHH CS
                           MMR_HSR1  70 flalee...adlillvvdaseeklkpldeel 97 
                                          ++++   a++i  ++d +   +k+  e+l
  gene2494|gene2494|rna2494|rna2494 626 ESQHIKifeAQIIYNLID-K---YKEYTENL 652
                                        222232222677777777.2...33333333 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   1.7e-06    0.0038       3     120 ..     215     341 ..     213     348 .. 0.85
   2 ?   -0.6   0.0      0.38   8.6e+02     136     156 .]     396     416 ..     391     416 .. 0.91
   3 ?   -2.9   0.1       1.9   4.2e+03      91     143 ..     691     743 ..     684     750 .. 0.69

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.7e-06
                                        EEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEEEE......TTEEEEE.EE----SSSSSSSHHHHHHH CS
                             FeoB_N   3 valvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegklkl......kgkevei.vDlPGiYslsayseeekvar 71 
                                        v+++G  ++Gkt ++++l +++ + g   G+t +   + + +      +++++++  D+PG   +++  +e     
  gene2494|gene2494|rna2494|rna2494 215 VCILGHVDTGKTKILDKLRESNVQGGEAGGITQQIGATFFPYselvnkTNTKFDFdNDVPGLLVIDTPGHETFANL 290
                                        7889****************************99999888774444323345554569********9999999999 PP

                                        HHHHCTSSSEEEEEEEGGG.HHHHHHHHHHHHHTT.SSEEEEEETHHHHHH CS
                             FeoB_N  72 dflleeepdvvvnvvdatn.lernLyLtlqllelg.vpvvlalnmideaek 120
                                        +   ++  d  + vvd  + le++ +  ++ll l+ +p+++aln+id + k
  gene2494|gene2494|rna2494|rna2494 291 RSRGSSMCDFAILVVDVLHaLEKQTLESIELLKLRkTPFLIALNKIDRIYK 341
                                        99999***********965399999999*****984799********9876 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.38
                                        S-EEEEBTTTTBTHHHHHHHH CS
                             FeoB_N 136 vpvvktsakkkegieellkai 156
                                        +++++tsa ++eg+++l+++i
  gene2494|gene2494|rna2494|rna2494 396 INIIPTSAITGEGLSDLVNKI 416
                                        689**************9886 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 1.9
                                        HHHHHHHHHHHHHTTSSEEEEEETHHHHHHTTEEE-HHHHHHHHTS-EEEEBT CS
                             FeoB_N  91 lernLyLtlqllelgvpvvlalnmideaekkgieidlkkLsekLgvpvvktsa 143
                                        le +L   + l+ ++++ ++ + ++  +  ++ ++d++   +kL +++ +t a
  gene2494|gene2494|rna2494|rna2494 691 LEGKLKTNMPLFVMHQDEIVQIGKVTSMIMEKKSVDVADKGSKLSIKIETTDA 743
                                        56666666677777777777777777777777777777777777777766655 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0     6e-07    0.0013       2     119 ..     215     337 ..     214     338 .. 0.75
   2 ?   -3.5   0.0       5.2   1.2e+04      32      52 ..     585     605 ..     572     630 .. 0.55

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 6e-07
                                        EEEESSTTSSHHHHHHCHCT-CCC-EE....ETTTTEEEEE.EECGGSGGCTTBTTTTCEEEEEEEE-SGGCTTTT CS
                                Roc   2 vvlvGdsgvGKtsllkrfvedkfseke....kstigvdflt.kevtkikgvendkkvkkvklniWDtaGqerfrsl 72 
                                        v+++G   +GKt++l+++ e++++  e    ++ ig++f+  +e+++ ++++ d + +   l + Dt G+e f +l
  gene2494|gene2494|rna2494|rna2494 215 VCILGHVDTGKTKILDKLRESNVQGGEaggiTQQIGATFFPySELVNKTNTKFDFDNDVPGLLVIDTPGHETFANL 290
                                        789*******************98765222368999999873334333333444444556799************* PP

                                        -HHHHCTSCEEEEEEEGHHHHCHHHHHHHHHHH.CSSS-EEEEEE-TT CS
                                Roc  73 hplylreaalailvydsrssenlkeWlkelkkv.agkspvilvgnkiD 119
                                        ++   +  + ailv+d  +  + k+ l++++    +k+p+++  nkiD
  gene2494|gene2494|rna2494|rna2494 291 RSRGSSMCDFAILVVDVLHALE-KQTLESIELLkLRKTPFLIALNKID 337
                                        ****************644333.3457777765246789999999999 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 5.2
                                        TTEEEEEEECGGSGGCTTBTT CS
                                Roc  32 igvdfltkevtkikgvendkk 52 
                                        ig ++++k+v k+k ++++++
  gene2494|gene2494|rna2494|rna2494 585 IGKNLSRKDVLKMKAIKEKDA 605
                                        455555555555555443332 PP

>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   6.7e-05      0.15      35     119 ..     261     355 ..     215     389 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 6.7e-05
                                        EEEEEEEEETTEEEEEEEEEETTSGGGHHHHHHHHTTESEEEEEEETTBHHHHHTHHHHHHHHHHHSTTTSEEEEE CS
                                Ras  35 dfytkeievdgkevkleiwDTAGqeefkslrelyyrdaegillvyditsresfenvkkwveeikrvaeenvpivLv 110
                                        +++++++++d+    l + DT G e f +lr+   + ++ ++lv d+ ++       + +e i+  + +++p+++ 
  gene2494|gene2494|rna2494|rna2494 261 NKTNTKFDFDNDVPGLLVIDTPGHETFANLRSRGSSMCDFAILVVDVLHALEK----QTLESIELLKLRKTPFLIA 332
                                        35556667778888999***************************999754322....2333333333334566666 PP

                                        EETTTGGG..............G CS
                                Ras 111 GnKvDlee..............k 119
                                         nK+D                 +
  gene2494|gene2494|rna2494|rna2494 333 LNKIDRIYkwrsetggfhnfdlQ 355
                                        67776544455555555555553 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (795 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2729  (0.152212); expected 358.6 (0.02)
Passed bias filter:                      640  (0.0356964); expected 358.6 (0.02)
Passed Vit filter:                       114  (0.00635841); expected 17.9 (0.001)
Passed Fwd filter:                        23  (0.00128284); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 1.04u 0.33s 00:00:01.37 Elapsed: 00:00:00.50
# Mc/sec: 4783.97
//
Query:       gene2495|gene2495|rna2495|rna2495  [L=245]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       655  (0.036533); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1720.78
//
Query:       gene2496|gene2496|rna2496|rna2496  [L=542]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.3e-09   36.2   0.0    9.4e-09   35.0   0.0    1.5  1  Glycos_transf_1  Glycosyl transferases group 1
    2.7e-06   27.9   0.0    4.4e-06   27.1   0.0    1.4  1  Glyco_trans_1_4  Glycosyl transferases group 1
     0.0015   18.9   0.0     0.0041   17.5   0.0    1.7  1  Glyco_trans_1_2  Glycosyl transferases group 1


Domain annotation for each model (and alignments):
>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.0   0.0   1.6e-12   9.4e-09      14     168 ..     311     487 ..     302     490 .. 0.90

  Alignments for each domain:
  == domain 1  score: 35.0 bits;  conditional E-value: 1.6e-12
                                        T-EEEEEESS-TTTTTHHHHHHHHHCCCCC..........HCSCEEEEEES............STTHHHHHHHHHH CS
                    Glycos_transf_1  14 kkkiilsvgrlekeKgvdllikafallkkq..........lnpnvklviaG...........ngeeekelkklaee 68 
                                        + ++i+  + +++ Kg++  i+af+ + +               + l+i+G             +e+ e+ ++ ++
  gene2496|gene2496|rna2496|rna2496 311 QSPYIIQTSSFDRLKGQKECIDAFRIIYDMistrindesdALYGLYLLIVGhgniddpegtaVFNELVEYLNEQHN 386
                                        56899999******************9888999999988888899***********99888744555556666699 PP

                                        HCTTCGGGEEECCH.SSSHHHHHHCESEEEEEESSBSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT CS
                    Glycos_transf_1  69 lelsdnviflgevs.redleellknadifvlpsisEgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpn 143
                                        + ++d+v +++  + ++ l  l++na ++++ s+ +gf + +++ +  ++p+++ n+gg++ +v +++tG++v+ +
  gene2496|gene2496|rna2496|rna2496 387 CAVRDRVLIVKIPPiEQILNVLIENARVALQLSQCDGFETRVTNCILKNVPAVVNNVGGLRLQVLENKTGYIVDRG 462
                                        9999999999999977778889999*************************************************** PP

                                        -HHHHHHHHHHHHHSHHHHHHHHHH CS
                    Glycos_transf_1 144 naealaeairklledeelrerlgen 168
                                        + +  a ++  ll+++  r+ ++e+
  gene2496|gene2496|rna2496|rna2496 463 DLQGVAHKVLYLLDNDSFRNGMIEY 487
                                        ********************99998 PP

>> Glyco_trans_1_4  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   0.0   7.4e-10   4.4e-06       4     134 .]     315     477 ..     312     477 .. 0.73

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 7.4e-10
                                        EEEES---GG.GTHHHHHHHHHHHH.........H.H....EEEEEES---..............HHHHHHHT.T- CS
                    Glyco_trans_1_4   4 ilfvGrleenvkgvdllleavpllr........kk.d....vrlvivGdgp.rp...........eeleelaa.gl 53 
                                        i+ ++++ ++ kg++  ++a+  +         ++ d    + l+ivG g+ ++           e l+e+++  +
  gene2496|gene2496|rna2496|rna2496 315 IIQTSSF-DRLKGQKECIDAFRIIYdmistrinDEsDalygLYLLIVGHGNiDDpegtavfnelvEYLNEQHNcAV 389
                                        5666666.45566666777766666555544433333677899*****9987444788888444344443443556 PP

                                        T.TEEEE---..TH.HHHHHHH-SEEEE--..---SHHHHHHHHTT-EEEE-TGGGTTT--..TTSSEE--TT-HH CS
                    Glyco_trans_1_4  54 eerveftGfv..ed.laellaaadvfvaPs..egfglkllEamaaglpvVatdvggiaevv..gengllvppgdpe 122
                                        ++rv ++     e+ l+ l+++a+v++  s   gf   +       +p V+ +vgg++  v  +++g++v+ gd +
  gene2496|gene2496|rna2496|rna2496 390 RDRVLIVKIPpiEQiLNVLIENARVALQLSqcDGFETRVTNCILKNVPAVVNNVGGLRLQVleNKTGYIVDRGDLQ 465
                                        67755555335555688889**********888***********************96666688************ PP

                                        HHHHHHHHHHH- CS
                    Glyco_trans_1_4 123 alaeailrLled 134
                                          a ++l Ll++
  gene2496|gene2496|rna2496|rna2496 466 GVAHKVLYLLDN 477
                                        *********987 PP

>> Glyco_trans_1_2  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   6.9e-07    0.0041       2      67 ..     415     482 ..     414     489 .. 0.94

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 6.9e-07
                    Glyco_trans_1_2   2 vLnpsrsespnlrlfEaaacGafaltddaegleelftpgkevilfe..dleelaekiryllanpeerr 67 
                                        +L +s+++++ +r+  +   +++a+++   gl+  + ++k++ +++  dl+ +a k+ yll+n+  r+
  gene2496|gene2496|rna2496|rna2496 415 ALQLSQCDGFETRVTNCILKNVPAVVNNVGGLRLQVLENKTGYIVDrgDLQGVAHKVLYLLDNDSFRN 482
                                        7889***********************************************************99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (542 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       426  (0.0237604); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.26s 00:00:00.82 Elapsed: 00:00:00.43
# Mc/sec: 3746.70
//
Query:       gene2497|gene2497|rna2497|rna2497  [L=1437]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.3e-11   42.7   0.1      3e-10   40.0   0.0    2.6  3  Bromodomain  Bromodomain


Domain annotation for each model (and alignments):
>> Bromodomain  Bromodomain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0      0.49   8.8e+03       7      25 ..     422     440 ..     418     455 .. 0.71
   2 ?   -3.2   0.1      0.51   9.1e+03      63      81 ..     606     624 ..     603     625 .. 0.82
   3 !   40.0   0.0   1.7e-14     3e-10      13      83 ..    1348    1415 ..    1336    1416 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 0.49
                                        HBHTTTCGGGGCSTT-GCC CS
                        Bromodomain   7 ellehklaepFlepvdpee 25 
                                        +l++++   +F  pv++ +
  gene2497|gene2497|rna2497|rna2497 422 DLKKNQVHVIFNGPVNTVV 440
                                        7899999999999995544 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 0.51
                                        HHHHHHHHHSHTTSHHHHH CS
                        Bromodomain  63 llfsNarkyngegsviyel 81 
                                          f N  +yn   s  y++
  gene2497|gene2497|rna2497|rna2497 606 AFFYNVLRYNDNSSNAYDD 624
                                        56889******99988875 PP

  == domain 3  score: 40.0 bits;  conditional E-value: 1.7e-14
                                         CGGGGCSTT-GCCSTTHHHH.SS---HHHHHHHHHTT--SSHHHHHHHHHHHHHHHHHHSHTTSHHHHHHH CS
                        Bromodomain   13 laepFlepvdpeefpdyyavikkPldLstIkkklesnkYksladfeadlkllfsNarkyngegsviyelae 83  
                                          ++ F   v + ++  y+av++ P+ L  I +k++++ Y+ + d++ d++l+  Na  +nge+sv++++ +
  gene2497|gene2497|rna2497|rna2497 1348 VCAEF---VGEVKVDGYDAVVRTPMYLDLIVEKIRDGVYGCVLDVQRDVELIAANAALFNGEDSVYAADSK 1415
                                         44555...47889999**************************************************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1437 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       890  (0.0496402); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 1.00u 0.32s 00:00:01.32 Elapsed: 00:00:00.51
# Mc/sec: 8400.72
//
Query:       gene2498|gene2498|rna2498|rna2498  [L=195]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    6.1e-54  182.1   0.6    7.2e-54  181.9   0.6    1.0  1  Rad52_Rad22  Rad52/22 family double-strand break repair prote
  ------ inclusion threshold ------
      0.081   13.5   0.0       0.14   12.7   0.0    1.4  1  FlgT_N       Flagellar assembly protein T, N-terminal domain


Domain annotation for each model (and alignments):
>> Rad52_Rad22  Rad52/22 family double-strand break repair protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  181.9   0.6     8e-58   7.2e-54       3     151 ..      14     160 ..      12     162 .. 0.97

  Alignments for each domain:
  == domain 1  score: 181.9 bits;  conditional E-value: 8e-58
                        Rad52_Rad22   3 etlqskLekklgpeyvsqregksgkkvaylegskviqlaNevFgfnGWsseiesievdeieeeqegqrysvkaeal 78 
                                        + ++++L+kklgpey+s r+  +++++ay+eg+++i+ aN++Fg+nGWss++++i++d+i+e ++  rysv+++a+
  gene2498|gene2498|rna2498|rna2498  14 SHISKELNKKLGPEYISYRQAFNNTHIAYIEGWTAINIANRIFGYNGWSSKLKQITIDYIDECNQ--RYSVGVSAV 87 
                                        6799********************************************************98877..9******** PP

                        Rad52_Rad22  79 vrvtlkdGtyrediGfgtatnvpskgeafekakKeAvtdAlKrAllqfgnvlGnclydleqekkvkklkkedg 151
                                        vrv l dG +red+Gfg+a+n + k +a+ekakKeAvtdAlKrAl+qfgn+lGnc+yd+e   +v ++k++d+
  gene2498|gene2498|rna2498|rna2498  88 VRVLLSDGAMREDVGFGSADNQRVKSQAIEKAKKEAVTDALKRALRQFGNALGNCCYDKEFLRHVRSVKRQDE 160
                                        ***************************************************************9999999886 PP

>> FlgT_N  Flagellar assembly protein T, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   1.6e-05      0.14      16      68 ..     117     169 ..     104     184 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.6e-05
                             FlgT_N  16 diAreqAredAlkqAllyagaqvgsisslqqllegsltetqfsngevrnvelv 68 
                                        + A+++A  dAlk Al++ g  +g+    ++ l   ++  ++  +  ++ el+
  gene2498|gene2498|rna2498|rna2498 117 EKAKKEAVTDALKRALRQFGNALGNCCYDKEFLRHVRSVKRQDEQVLNECELL 169
                                        78******************999988877777777777666665555556665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       925  (0.0515924); expected 358.6 (0.02)
Passed bias filter:                      654  (0.0364772); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.32s 00:00:00.83 Elapsed: 00:00:00.50
# Mc/sec: 1178.16
//
Query:       gene2499|gene2499|rna2499|rna2499  [L=55]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
        1.9    9.0  18.6        7.3    7.1  18.2    1.8  1  Somatomedin_B  Somatomedin B domain


Domain annotation for each model (and alignments):
>> Somatomedin_B  Somatomedin B domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1  18.2   0.00041       7.3       3      35 ..       6      35 ..       4      37 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.00041
                      Somatomedin_B  3 CkgrCgekferskkaCqCdedCveygdCCpDYe 35
                                       C + C e++   ++ C C +dC+e ++C +DY+
  gene2499|gene2499|rna2499|rna2499  6 CLDDCREDN--MND-CMCLDDCMEDNTCREDYR 35
                                       9999*6644..666.*****************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (55 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       439  (0.0244855); expected 358.6 (0.02)
Passed bias filter:                      154  (0.00858944); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 409.14
//
Query:       gene25|gene25|rna25|rna25  [L=143]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       400  (0.0223102); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1061.82
//
Query:       gene250|gene250|rna250|rna250  [L=106]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       531  (0.0296168); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 792.18
//
Query:       gene2500|gene2500|rna2500|rna2500  [L=847]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.8e-21   77.1   0.2      2e-18   67.1   0.2    2.4  2  PI3_PI4_kinase  Phosphatidylinositol 3- and 4-kinase


Domain annotation for each model (and alignments):
>> PI3_PI4_kinase  Phosphatidylinositol 3- and 4-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.0   0.00017         3       4      70 ..     594     656 ..     593     664 .. 0.94
   2 !   67.1   0.2   1.1e-22     2e-18     121     243 ..     668     788 ..     657     793 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.00017
                                        EEEECSSCHHHHHHHHHHHHHHHHHHHHTTTTCCCT-------EEESSSSEEEEE--TTEEEHHHHH CS
                     PI3_PI4_kinase   4 giykvgddlrqdelivqvfklmdeelskennpkrrklalktysviplgrkcgiielvassetaasll 70 
                                        +i k g+ l+ ++  +++++ m+++  +e+   +    l++y+++   +++g++e++ s+ +++++ 
  gene2500|gene2500|rna2500|rna2500 594 VIIKTGNELGPEMIALELLREMKQIIDEEGIRIW----LRPYQIYTVFHNAGFVEVISSASSIHEIK 656
                                        57899*****************************....**************************996 PP

  == domain 2  score: 67.1 bits;  conditional E-value: 1.1e-22
                                        HHHHSSSH...HHHHHHHHHHHHHHHHHHHHHHHHT-TT--TTTEEEETTTSEEEESSTTTCCTCSHCSSSS-.SS CS
                     PI3_PI4_kinase 121 Fvkkspsa...eewlearkqFvrslaklsvldyilgngDRhldNilvdktsgklihIDfGlilpdewkllpfpqek 193
                                        F +k+  +   +  ++a+++F +sl ++s ++y l + DRh++Nil+ + +g+++h+DfG+ l+  + ++ +  e+
  gene2500|gene2500|rna2500|rna2500 668 FLRKFYYEtygTGVDKAINNFLESLVGYSLVTYFLALKDRHNGNILI-DNEGHVVHVDFGFVLGLHPGFYCV--ET 740
                                        44444444222356677******************************.9**************999999997..69 PP

                                        SSSS-THHHHHHTSTTCCHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHH CS
                     PI3_PI4_kinase 194 vPfrltrelvlaidpskdeglfresceealealrrdqnlltrllkkavkd 243
                                         Pf+   e+++++     +  f+++ +e + a+r++++ l+++l++ + +
  gene2500|gene2500|rna2500|rna2500 741 APFKMSSEYIHLL--GNRMDEFKKLFVEGFMAIRKHSKRLLQILEICMNN 788
                                        *************..99999************************997655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (847 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       704  (0.039266); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.68u 0.30s 00:00:00.98 Elapsed: 00:00:00.45
# Mc/sec: 5669.81
//
Query:       gene2501|gene2501|rna2501|rna2501  [L=182]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      3e-18   65.9   0.6    4.3e-18   65.3   0.6    1.3  1  CBFD_NFYB_HMF  Histone-like transcription factor (CBF/NF-Y) a
    1.3e-09   38.5   0.4    1.7e-09   38.1   0.4    1.2  1  Histone        Core histone H2A/H2B/H3/H4
  ------ inclusion threshold ------
      0.053   13.8   0.6      0.098   13.0   0.5    1.5  1  CENP-X         CENP-S associating Centromere protein X


Domain annotation for each model (and alignments):
>> CBFD_NFYB_HMF  Histone-like transcription factor (CBF/NF-Y) and archaeal histone
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.3   0.6   7.3e-22   4.3e-18       2      65 .]      38     101 ..      37     101 .. 0.98

  Alignments for each domain:
  == domain 1  score: 65.3 bits;  conditional E-value: 7.3e-22
                                        XXXHHHHHHHHHCCTTXS-B-HHHHHHHHHHHHHHHHHHHHHHHHHHCCTTSSCE-HHHHHHHH CS
                      CBFD_NFYB_HMF   2 eLPiarvkkImksdpdarkiakdAkeliaecveefieelaseAaeickkekrKtikaehiklAv 65 
                                        +LP+ar+k++mk  ++++++a+++++l+++++e+fieel+ +A+  ++++kr+++++++++ Av
  gene2501|gene2501|rna2501|rna2501  38 QLPLARIKRLMKVEEEVKMVASEVPILFSKVAEMFIEELTLRAWINTEENKRRILQKNDLSAAV 101
                                        69************************************************************98 PP

>> Histone  Core histone H2A/H2B/H3/H4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.1   0.4   2.8e-13   1.7e-09      61     129 ..      35     102 ..       6     104 .. 0.91

  Alignments for each domain:
  == domain 1  score: 38.1 bits;  conditional E-value: 2.8e-13
                                        XSXHHHHHHHHHHHH.TTSSSXEEXHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTXSEEXHHHHHHHHH CS
                            Histone  61 liqklpfaRvvreivksekedlrisaeavlalqealEallvelfeeAnllakhaKRvTitpkDiqlArr 129
                                        +  +lp aR ++ ++k e+e +++ +e + ++ +++E +++el+ +A++ ++++KR+ +++ D+ +A+r
  gene2501|gene2501|rna2501|rna2501  35 KDLQLPLAR-IKRLMKVEEEVKMVASEVPILFSKVAEMFIEELTLRAWINTEENKRRILQKNDLSAAVR 102
                                        55689****.9999999***************************************************9 PP

>> CENP-X  CENP-S associating Centromere protein X
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.5   1.6e-05     0.098      14      61 ..      52      94 ..      40     109 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.6e-05
                                       STT-EE-CCCHHHHHHHHHHHHHHHHHHHHHHHHHTT-SE.....EEC CS
                             CENP-X 14 dektkItkdalelvaeylklFvrEavaRaaeeaeeegkeeseksklev 61
                                       +e   ++++   l+++  ++F++E  +Ra ++ ee++ +      l+ 
  gene2501|gene2501|rna2501|rna2501 52 EEVKMVASEVPILFSKVAEMFIEELTLRAWINTEENKRRI-----LQK 94
                                       44455677777899*****************888877766.....444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       521  (0.0290591); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1418.17
//
Query:       gene2503|gene2503|rna2503|rna2503  [L=180]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-21   76.3  19.3    3.9e-21   75.6  19.3    1.4  1  Got1      Got1/Sft2-like family
  ------ inclusion threshold ------
        5.2    5.7  12.7        3.8    6.2   2.8    2.0  2  DUF2207   Predicted membrane protein (DUF2207)


Domain annotation for each model (and alignments):
>> Got1  Got1/Sft2-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.6  19.3   4.3e-25   3.9e-21       2     108 ..      63     169 ..      52     174 .. 0.92

  Alignments for each domain:
  == domain 1  score: 75.6 bits;  conditional E-value: 4.3e-25
                               Got1   2 vllfllsllglpllflkprkFallytlGnilflastafLiGpkkqlkkmfskerliativyllsllltLyaalvlk 77 
                                        +l f++sl++++  +++p+kFal y+++n+lf+++++fL+G++k++k+ fs++r+++t+++l++++lt+y+a+ +k
  gene2503|gene2503|rna2503|rna2503  63 FLSFVYSLFNILGAIVSPAKFALPYAFSNFLFFTMIGFLVGFRKYFKSTFSQNRWKYTTTFLVCTFLTIYSAMKIK 138
                                        4557777887887888************************************************************ PP

                               Got1  78 stlltllfvivqllallwyllsyiPggrsal 108
                                        s+++ + ++i+q+ +++++ ++y+P g++ l
  gene2503|gene2503|rna2503|rna2503 139 SYFFNFTMAIMQIGSFVVFAITYLPKGTERL 169
                                        *************************999876 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   2.5   0.00077       6.9     366     420 ..      20     101 ..       2     105 .. 0.54
   2 ?    6.2   2.8   0.00042       3.8     369     446 ..     105     170 ..     103     176 .. 0.73

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.00077
                            DUF2207 366 k.......kergyfdkkgkkklkklsalglgliilglilillallllvll....................lvflli 414
                                        +       k+++yf++  k  l ++++     + +++i++++a+l++v+                     ++fl++
  gene2503|gene2503|rna2503|rna2503  20 NgiplkhnKYNRYFRDSTKYDLDYFGLTFSQRLGCFFIFFVAAFLSFVYSlfnilgaivspakfalpyafSNFLFF 95 
                                        1455555677788888876666655555444444444433333333333245666667777776666665555555 PP

                            DUF2207 415 lllill 420
                                        +++++l
  gene2503|gene2503|rna2503|rna2503  96 TMIGFL 101
                                        555554 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.00042
                            DUF2207 369 rgyfdkkgkkklkklsalglgliilglilillallllvlllvfllilllillliaiivlllfsrllgrrteeGael 444
                                        r+yf+++ +++++k+ +  l++++l ++ ++ +       ++f+++++ i  + +++v+++       + ++G+e 
  gene2503|gene2503|rna2503|rna2503 105 RKYFKSTFSQNRWKYTTTFLVCTFLTIYSAMKI------KSYFFNFTMAIMQIGSFVVFAIT------YLPKGTER 168
                                        689999999999999999999988888876444......38888888888888888888886......44555555 PP

                            DUF2207 445 la 446
                                        l+
  gene2503|gene2503|rna2503|rna2503 169 LG 170
                                        55 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       911  (0.0508115); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 1159.45
//
Query:       gene2504|gene2504|rna2504|rna2504  [L=291]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
       0.11   12.1   0.0       0.15   11.6   0.0    1.3  1  CDtoxinA        Cytolethal distending toxin A/C domain
       0.11   13.1  25.8      0.075   13.6  13.3    2.4  2  KRTAP           Keratin-associated matrix


Domain annotation for each model (and alignments):
>> CDtoxinA  Cytolethal distending toxin A/C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   1.7e-05      0.15      81     128 ..      84     126 ..      40     138 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 1.7e-05
                                        T-GGG-EEEEEBTTS-EEEEETTT--EEEE-SS-SS.S-B-EEEE--.- CS
                           CDtoxinA  81 ddketvFsliptttgavqikslssgeCitanflsrlpiaktltlekC.d 128
                                         + ++ F +   t ++v iks+ +g+Cit+n+ ++      ++ ++C d
  gene2504|gene2504|rna2504|rna2504  84 GKVNQRFIIAKLTHSNVRIKSA-NGQCITHNEKEKF-----FERKECsD 126
                                        577899**************96.79******99986.....77777743 PP

>> KRTAP  Keratin-associated matrix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6  13.3   8.4e-06     0.075      10      48 ..     156     192 ..     143     203 .. 0.50
   2 ?    4.8   4.5    0.0045        40      40      55 ..     222     238 ..     214     246 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 8.4e-06
                              KRTAP  10 GlgYGsggyG.glgcgygcgygsirrlGyGsGggygyGsG 48 
                                        G  +Gs g+G g g+g+g+g+g     G+GsG+g+g GsG
  gene2504|gene2504|rna2504|rna2504 156 GNEWGS-GWGsGWGSGWGSGWG--DEWGMGSGSGWGAGSG 192
                                        222333.333344444444444..4444444455554444 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.0045
                              KRTAP  40 GggygyGsGYG.gyGyg 55 
                                        Gg yg G GYG gy  g
  gene2504|gene2504|rna2504|rna2504 222 GGMYGGGKGYGnGYSSG 238
                                        44455555555444333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       450  (0.025099); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1953.18
//
Query:       gene2505|gene2505|rna2505|rna2505  [L=44]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (44 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       235  (0.0131073); expected 358.6 (0.02)
Passed bias filter:                      186  (0.0103743); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.40
# Mc/sec: 331.13
//
Query:       gene2506|gene2506|rna2506|rna2506  [L=220]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.9e-20   72.0   0.0    7.5e-20   71.7   0.0    1.0  1  Abhydrolase_2  Phospholipase/Carboxylesterase
    9.8e-07   28.6   0.1    4.5e-06   26.5   0.1    1.8  1  FSH1           Serine hydrolase (FSH1)
    1.5e-06   28.1   0.0    1.8e-06   27.8   0.0    1.1  1  Esterase       Putative esterase
    0.00022   20.9   0.0    0.00046   19.9   0.0    1.6  2  Abhydrolase_1  alpha/beta hydrolase fold
    0.00049   19.6   0.1     0.0011   18.5   0.0    1.6  2  Peptidase_S9   Prolyl oligopeptidase family
     0.0012   18.4   0.0     0.0018   17.9   0.0    1.2  1  DUF2974        Protein of unknown function (DUF2974)
     0.0026   17.1   0.0     0.0056   16.0   0.0    1.6  2  Hydrolase_4    Serine aminopeptidase, S33
     0.0035   16.4   0.2     0.0048   16.0   0.2    1.1  1  DUF1057        Alpha/beta hydrolase of unknown function (DUF1
     0.0069   16.3   0.0     0.0099   15.7   0.0    1.4  1  Lipase_3       Lipase (class 3)
  ------ inclusion threshold ------
       0.01   15.3   0.0      0.015   14.8   0.0    1.2  1  Esterase_phd   Esterase PHB depolymerase
      0.012   14.3   0.0      0.018   13.7   0.0    1.3  1  AXE1           Acetyl xylan esterase (AXE1)
      0.019   14.7   0.0      0.031   14.1   0.0    1.3  1  Abhydrolase_5  Alpha/beta hydrolase family
      0.028   14.4   0.0       0.34   10.8   0.0    2.1  2  Cutinase       Cutinase
      0.066   13.1   0.0      0.072   12.9   0.0    1.3  1  Abhydrolase_3  alpha/beta hydrolase fold
      0.066   12.9   0.0      0.096   12.4   0.0    1.3  1  PGAP1          PGAP1-like protein
       0.08   12.5   0.0       0.12   11.9   0.0    1.2  1  DLH            Dienelactone hydrolase family


Domain annotation for each model (and alignments):
>> Abhydrolase_2  Phospholipase/Carboxylesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.7   0.0   6.7e-23   7.5e-20      14     212 ..      14     204 ..       7     208 .. 0.88

  Alignments for each domain:
  == domain 1  score: 71.7 bits;  conditional E-value: 6.7e-23
                                        -EEEEEE--TT--S.HHHHHHHH.TT--TTEEEEEE---EEE-GGGTT-EEE-SS-B--SSTTS.-B-HHHHHHHH CS
                      Abhydrolase_2  14 qavviflHGlGdsg.hawaeaakteaalpnikfifphgpelpvtlnggmrmpaWfdlvglspek.kedeagikksa 87 
                                        +  ++flHGl  +  + +a+  ++  +lp +++i +++p++ v +  + +  aW+   ++++    e+ + +++s 
  gene2506|gene2506|rna2506|rna2506  14 KSFILFLHGLNTKTkDIIANFEMMAKELPDTQIILLQAPKQDVVIYKPVQVTAWYRF-KVDETVvYEERESMDESR 88 
                                        5679******9988799999999999*****************************85.6777776666669***** PP

                                        HHHHHHHHHHHHTT--GGGEEEEEETHHHHHHHHHHHT-SS--SEEEEES---TTGGGTTTTS-GGGGG-EEEEEE CS
                      Abhydrolase_2  88 ekleelidaelkkgipssriiigGFSqGaalalylaltlpkklggivafsgalplsqklessatavtkklpilqiH 163
                                        +k+ elid+     ip++r ii GFSqG+a+aly+alt ++k   ++++ +++++s  + ++         ++ i 
  gene2506|gene2506|rna2506|rna2506  89 RKILELIDEL---KIPKERLIISGFSQGGAMALYTALTHSEKFMAVIGM-CTYLSSHLFYQEVYDQK----VIMIS 156
                                        *******964...6*********************************99.55666666666555555....89999 PP

                                        ETT-SSS-HHHHHHHHHHHHTTS-GEEEEEETT--SS--HHHHHHHHHH CS
                      Abhydrolase_2 164 geeDpvvplalgkaakevlkkllkkvelksyeglaHsideeemqdikef 212
                                         + D+v  l +   +  ++  +  +  +  +  + H +    ++di+++
  gene2506|gene2506|rna2506|rna2506 157 AKNDEVFSLEFIRFLVSFYNRFFGNIIFMEMD-GDHTMNTLILRDIYKH 204
                                        99*****************9999999999999.8999999999999887 PP

>> FSH1  Serine hydrolase (FSH1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   0.1     4e-09   4.5e-06       7     200 ..      17     191 ..      12     194 .. 0.78

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 4e-09
                               FSH1   7 iLcLhGytqsgeiFraktsalrkllkklnvelvyldaplelaekadlpkseseeeekseeeeesraWfrkkde... 79 
                                        iL+LhG  ++++   a ++ + k+l +   +++ l+ap +      +            +  +  aW+r k +   
  gene2506|gene2506|rna2506|rna2506  17 ILFLHGLNTKTKDIIANFEMMAKELPD--TQIILLQAPKQD-----VV---------IYKPVQVTAWYRFKVDetv 76 
                                        788888888888888888888888885..888888887554.....44.........45788999***99999788 PP

                               FSH1  80 .kneyegleesldavkdyikengp...fdGiiGFSqGaalaallaslleellkeashpslkfailvsGfkleepky 151
                                          +e e+++es +++ + i+e +       i GFSqG+a+a + a + +e+        +  +i ++ + + ++ y
  gene2506|gene2506|rna2506|rna2506  77 vYEERESMDESRRKILELIDELKIpkeRLIISGFSQGGAMALYTALTHSEK--------FMAVIGMCTYLSSHLFY 144
                                        88888889999999999988844324367788*********9988777764........56899999999999999 PP

                               FSH1 152 eeyyeedkiqtptLhvlGelDtvvdeerseaLaeafkns...skvlkHpggH 200
                                        +e y       +++++  ++D+v + e  + L+  +++      +++ +g+H
  gene2506|gene2506|rna2506|rna2506 145 QEVY-----DQKVIMISAKNDEVFSLEFIRFLVSFYNRFfgnIIFMEMDGDH 191
                                        9999.....3468999999999999998888887777656556667777777 PP

>> Esterase  Putative esterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.8   0.0   1.6e-09   1.8e-06      27     152 ..      17     140 ..       9     182 .. 0.79

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 1.6e-09
                                        EEEE--T.THHCCHHHHHCHHCCCCHCCT.EEEEEECCCSS-TTTTTSBTTSB..B.TTEEETTCCCCCCHCHHHH CS
                           Esterase  27 vylldGl.tgwdqnfrakelleslaregeiaeviivvvprggessfysdwdlg..arfyenategpgaeayetflt 99 
                                        +++l+Gl t + +    +e++ +   +    ++i+   p+ +++  y+  ++    rf+++ t  ++ ++  +  +
  gene2506|gene2506|rna2506|rna2506  17 ILFLHGLnTKTKDIIANFEMMAKELPD---TQIILLQAPKQDVV-IYKPVQVTawYRFKVDETVVYEERESMDESR 88 
                                        789999988888888888888544444...57777888888888.7999988844444555555555555559999 PP

                                        THHHHHHHHHCSEECCCEEEEEETHHHHHHHHHHHCSTTTCCEEEEES--S-C CS
                           Esterase 100 qeLlplldanfrtapdgravaGqSmGGlgALilalkhpdrFgsvssfSpivnp 152
                                         ++l l+d+ +  +++   + G+S+GG +AL++al+h ++F  v+ +  +++ 
  gene2506|gene2506|rna2506|rna2506  89 RKILELIDELKIPKER-LIISGFSQGGAMALYTALTHSEKFMAVIGMCTYLSS 140
                                        9******987766666.9**************************999877664 PP

>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       3.9   4.3e+03       3      27 ..      17      43 ..      17      61 .. 0.56
   2 !   19.9   0.0   4.1e-07   0.00046      62     112 ..      91     143 ..      73     173 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 3.9
                                       EEEE-STTT....CGGGGTTGHHHHHHHH CS
                      Abhydrolase_1  3 lvilhGlpg....ssdvwaerglapaLak 27
                                       +++lhGl         ++    +a+ L++
  gene2506|gene2506|rna2506|rna2506 17 ILFLHGLNTktkdIIANFEM--MAKELPD 43
                                       68888888753332233444..5555554 PP

  == domain 2  score: 19.9 bits;  conditional E-value: 4.1e-07
                                        HHHHH.HHHCTTSSEEEEEETHHHHHHHHHHHHHGGGEEEEEEESE.CSSCCH CS
                      Abhydrolase_1  62 dldri.ldalgddkltlvGhSmGGmialayaaeyperVkalvllga.idpaas 112
                                        +l+ i   + + ++l++ G+S+GG++al+ a+ + e+  a++ +++ ++++  
  gene2506|gene2506|rna2506|rna2506  91 ILELIdELKIPKERLIISGFSQGGAMALYTALTHSEKFMAVIGMCTyLSSHLF 143
                                        55566666788999********************************6444433 PP

>> Peptidase_S9  Prolyl oligopeptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       2.3   2.6e+03      96     117 ..      62      85 ..      45      93 .. 0.60
   2 !   18.5   0.0   9.9e-07    0.0011      55      99 ..      94     138 ..      89     164 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 2.3
                                        SE---CCCHHCSTTS.THH.HCCC CS
                       Peptidase_S9  96 vpvvdvlrydsdtdl.lte.eyme 117
                                        v v+ + r++ d+++ ++e e m+
  gene2506|gene2506|rna2506|rna2506  62 VQVTAWYRFKVDETVvYEErESMD 85 
                                        445666666666655666655544 PP

  == domain 2  score: 18.5 bits;  conditional E-value: 9.9e-07
                                        HHHTTS--GGGEEEEEETHHHHHHHHHHHH-GGG-SEEEEESE-- CS
                       Peptidase_S9  55 lakegyvdserlaitGgSyGGyltgaalnqrpdlFkaavaevpvv 99 
                                        l++e  + +erl+i G S GG +++ ++  ++++F a++  +  +
  gene2506|gene2506|rna2506|rna2506  94 LIDELKIPKERLIISGFSQGGAMALYTALTHSEKFMAVIGMCTYL 138
                                        677778899***************************999766554 PP

>> DUF2974  Protein of unknown function (DUF2974)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   1.6e-06    0.0018      83     131 ..     102     150 ..      70     163 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.6e-06
                            DUF2974  83 egkiylgGhSkGGnlAvyaamnaeddlqeriskiysfDgpGfskevves 131
                                        +++++++G+S+GG +A+y a++ +++  + i  +  + +  f +ev+++
  gene2506|gene2506|rna2506|rna2506 102 KERLIISGFSQGGAMALYTALTHSEKFMAVIGMCTYLSSHLFYQEVYDQ 150
                                        3469******************999999888888877777777777765 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       2.2   2.4e+03       9      71 ..      19      39 ..      13      49 .. 0.49
   2 !   16.0   0.0     5e-06    0.0056      69     115 ..      98     142 ..      80     179 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 2.2
                        Hydrolase_4  9 lvHGlaehsgryaelaeaLaaqGfavyalDhrGhGrsegkrghvpsfddyvdDlaafvekvke 71
                                       ++HGl+                                            ++D+ a +e++++
  gene2506|gene2506|rna2506|rna2506 19 FLHGLNT------------------------------------------KTKDIIANFEMMAK 39
                                       5555543..........................................33444444444444 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 5e-06
                        Hydrolase_4  69 vkeehpelplfllGhSmGGliallyllrypdkvaglilsaPalkika 115
                                        +k   p+++l++ G S GG++al  +l++++k+ ++i +++ l+ + 
  gene2506|gene2506|rna2506|rna2506  98 LK--IPKERLIISGFSQGGAMALYTALTHSEKFMAVIGMCTYLSSHL 142
                                        33..678899*****************************99998775 PP

>> DUF1057  Alpha/beta hydrolase of unknown function (DUF1057)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.2   4.3e-06    0.0048      86     205 ..      85     213 ..      68     218 .. 0.67

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 4.3e-06
                            DUF1057  86 naeRnsyskalleelelk.gklillghsRGcenaLqlavtl.eahGlvlinptGlrvhkgirplsrletielvykl 159
                                        ++ R+     l++el++  ++li+ g s G+  aL +a t  e   +v+   t l  h   ++++  + i +  k 
  gene2506|gene2506|rna2506|rna2506  85 DESRRKIL-ELIDELKIPkERLIISGFSQGGAMALYTALTHsEKFMAVIGMCTYLSSHLFYQEVYDQKVIMISAKN 159
                                        44444433.4899****77*******************99855566666667778888777776655544443333 PP

                            DUF1057 160 lkk...klvdaiiyflykavG...lkvsdGeeavaa..lrsvitvaleeqlesi 205
                                         +      +  +  f+++++G   +   dG+ ++++  lr + +  lee+++si
  gene2506|gene2506|rna2506|rna2506 160 DEVfslEFIRFLVSFYNRFFGniiFMEMDGDHTMNTliLRDIYKHCLEENKNSI 213
                                        333112455555778888888333444688888876325788888888888887 PP

>> Lipase_3  Lipase (class 3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   8.9e-06    0.0099       9      88 ..      26     126 ..      17     163 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 8.9e-06
                                        ------------EEE-HHHH-G............TT-EEEHHHHHHHH.................S-HHHHHHHHH CS
                           Lipase_3   9 sakdwltdldfslteakellek............eggkvhsgfleaye.................eslreqvlkel 55 
                                        + kd++++++++ +e++++               +           ++                 +   ++ ++++
  gene2506|gene2506|rna2506|rna2506  26 KTKDIIANFEMMAKELPDTQIIllqapkqdvviyK----------PVQvtawyrfkvdetvvyeeRESMDESRRKI 91 
                                        55666777777777766653336644443333331..........2223333344445555555544555666677 PP

                                        HHHHHHTT..-EEEEEEEETHHHHHHHHHHHHHHH CS
                           Lipase_3  56 krllekyp..eysivvtGHSLGgalAlLaaldlve 88 
                                         +l+++ +  + +++++G S Gga+Al +al   e
  gene2506|gene2506|rna2506|rna2506  92 LELIDELKipKERLIISGFSQGGAMALYTALTHSE 126
                                        777777766699**************999987655 PP

>> Esterase_phd  Esterase PHB depolymerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   1.3e-05     0.015      18     125 ..      16     131 ..       4     149 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.3e-05
                       Esterase_phd  18 lvvmlhGctqsveefaaGtrmnl..ladklGvvvlypeqslran.aq..kcwnwykdtdraGrGeaavvva...lv 85 
                                        ++++lhG + ++++  a   m +  l d + + +  p+q            w  +k  +     e + +      +
  gene2506|gene2506|rna2506|rna2506  16 FILFLHGLNTKTKDIIANFEMMAkeLPDTQIILLQAPKQDVVIYkPVqvTAWYRFKVDETVVYEERESMDEsrrKI 91 
                                        5667777777777766666554322445555555566666543212301344444433333344444443300134 PP

                       Esterase_phd  86 dalvdehrvdaarvyvaGlsaGaaladllalhypdvfaav 125
                                          l+de ++   r+ ++G+s G+a+a   al++ ++f av
  gene2506|gene2506|rna2506|rna2506  92 LELIDELKIPKERLIISGFSQGGAMALYTALTHSEKFMAV 131
                                        467999*******************************998 PP

>> AXE1  Acetyl xylan esterase (AXE1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   1.6e-05     0.018     171     211 ..     100     141 ..      81     161 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.6e-05
                                        EEEEEEEEEEETHHHHHHHHHH.HH-SS-SEEEEES-SSSSH CS
                               AXE1 171 vDeeRvavlGasqGGalalava.alekrikavvadyPfLsdf 211
                                        + +eR+ + G sqGGa+al +a + +++  av+    +Ls +
  gene2506|gene2506|rna2506|rna2506 100 IPKERLIISGFSQGGAMALYTAlTHSEKFMAVIGMCTYLSSH 141
                                        5689***************87724567888999999999864 PP

>> Abhydrolase_5  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   2.7e-05     0.031      54     117 ..     101     166 ..      87     174 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.7e-05
                      Abhydrolase_5  54 pklekfvvgGhslGGvvasrfaaee.ekiegvvflasYPekdelsel..skkvlsivgteDgvlnvk 117
                                        pk e+++++G s GG++a   a  + ek  +v+ + +Y +   + ++   +kv+ i +++D+v + +
  gene2506|gene2506|rna2506|rna2506 101 PK-ERLIISGFSQGGAMALYTALTHsEKFMAVIGMCTYLSSHLFYQEvyDQKVIMISAKNDEVFSLE 166
                                        44.789*************999988459999999999999776666522567**********98766 PP

>> Cutinase  Cutinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0      0.22   2.5e+02      62      83 ..      27      48 ..      18      50 .. 0.86
   2 ?   10.8   0.0   0.00031      0.34      46      94 ..      68     118 ..      47     142 .. 0.65

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.22
                                       HHHHHHHHHHHHHH-TT-EEEE CS
                           Cutinase 62 akeaaalvqslaskCPdtkivl 83
                                       +k++ a ++ +a++ Pdt+i+l
  gene2506|gene2506|rna2506|rna2506 27 TKDIIANFEMMAKELPDTQIIL 48
                                       788899999***********98 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00031
                                        ----CGGSTTSS-HHHHHHHHHHHHHHHH..H-TT-EEEEEEETHHHHHHH CS
                           Cutinase  46 YpAdleqlyegseeagakeaaalvqslas..kCPdtkivlgGYSqGaqvid 94 
                                        Y+ +++++    e++ ++e ++ + +l    k P  +++++G+SqG++++ 
  gene2506|gene2506|rna2506|rna2506  68 YRFKVDETVVYEERESMDESRRKILELIDelKIPKERLIISGFSQGGAMAL 118
                                        666666644444555555555544444332278*************98764 PP

>> Abhydrolase_3  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   6.4e-05     0.072      60      95 ..      92     127 ..      31     175 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6.4e-05
                                        HHTHHHHTETTCEEEEEEETHHHHHHHHHHHHHHHT CS
                      Abhydrolase_3  60 aeqawelgadpsrivlaGdSaGGnlaaavalrarde 95 
                                        +e   el++ ++r+++ G S GG +a+++al   ++
  gene2506|gene2506|rna2506|rna2506  92 LELIDELKIPKERLIISGFSQGGAMALYTALTHSEK 127
                                        33335899**********************988876 PP

>> PGAP1  PGAP1-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   8.6e-05     0.096       8     149 ..      18     161 ..      14     189 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 8.6e-05
                              PGAP1   8 lFvpGnagsykqv.rslAseaaeayqelrkllknqnkkeldfftvdfneelsa.ldGrtlldqaeylndaIkyIls 81 
                                        lF++G+    k++  ++   a+e   ++  ll+  +++ + +  v +   + + +d + + +  e +++  ++Il+
  gene2506|gene2506|rna2506|rna2506  18 LFLHGLNTKTKDIiANFEMMAKELPDTQIILLQAPKQDVVIYKPVQVTAWYRFkVDETVVYEERESMDESRRKILE 93 
                                        66666666666654444444444444444444444444455555555544443145566778888889999***** PP

                              PGAP1  82 lysssekeptsviliGHSmGGivaraaltlknyikqsvntiltlasPhalpplsfdkdilklyervne 149
                                        l ++ + +++++i+ G S GG +a  ++  ++ +  +v  + t  s h   +  +d++++ + ++ +e
  gene2506|gene2506|rna2506|rna2506  94 LIDELKIPKERLIISGFSQGGAMALYTALTHSEKFMAVIGMCTYLSSHLFYQEVYDQKVIMISAKNDE 161
                                        ************************87665555455555555555555555555567666666655555 PP

>> DLH  Dienelactone hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00011      0.12      90     159 ..      96     164 ..      68     172 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00011
                                DLH  90 ksvpevstkkvgvvGfCmGGalalllaaev.pevdaavafYGlspekeleeaakikapilalfgeeDefip 159
                                         +  +  ++++ + Gf  GGa+al+ a    +++ a+++     ++++l +++   + ++++ +++De++ 
  gene2506|gene2506|rna2506|rna2506  96 DEL-KIPKERLIISGFSQGGAMALYTALTHsEKFMAVIGMCT-YLSSHLFYQEVYDQKVIMISAKNDEVFS 164
                                        333.366799*****************888799999999988.9999999999999999999999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       620  (0.0345808); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 1520.86
//
Query:       gene2507|gene2507|rna2507|rna2507  [L=184]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       672  (0.0374812); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1321.77
//
Query:       gene2508|gene2508|rna2508|rna2508  [L=690]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.018   14.8   0.2      0.038   13.7   0.2    1.5  1  DUF2284   Predicted metal-binding protein (DUF2284)
      0.031   13.9   0.2         23    4.7   0.0    3.5  4  Kelch_1   Kelch motif


Domain annotation for each model (and alignments):
>> DUF2284  Predicted metal-binding protein (DUF2284)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.2   4.2e-06     0.038      51     150 ..     219     314 ..     182     328 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.2e-06
                            DUF2284  51 allvqtkaeledeedd......keemkevkeelekillelekeafeagypkalalsagsCt..lCetCayeegepC 118
                                        ++l                   k++  + +e++ k +le  +e++++g +++ + +++s +  +C++C y e+e C
  gene2508|gene2508|rna2508|rna2508 219 VIL------------TnirkllKNGQIDEIEKILKNILENSSEMINNGPYEVQVHTTNSVDepMCRQCFYVEDESC 282
                                        333............24444443444456778888889999999999999**99999999999************* PP

                            DUF2284 119 rhpekarpsmealGidvfktaekaglelevgk 150
                                        ++     +s + lGi+ +k  e++  ++++ +
  gene2508|gene2508|rna2508|rna2508 283 QKIILYDSSFKDLGIKASKHQENMSGDVNLAT 314
                                        *******************9999876666655 PP

>> Kelch_1  Kelch motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0      0.32   2.8e+03       9      17 ..     329     337 ..     327     337 .. 0.85
   2 ?    4.7   0.0    0.0025        23       4      22 ..     356     374 ..     355     385 .. 0.79
   3 ?    4.2   0.0    0.0037        33      10      34 ..     439     463 ..     430     471 .. 0.86
   4 ?   -0.4   0.0     0.098   8.8e+02      30      45 ..     505     520 ..     500     521 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.32
                                        EETTEEEEE CS
                            Kelch_1   9 vvggkiYvi 17 
                                        ++++k+Yv+
  gene2508|gene2508|rna2508|rna2508 329 TLRNKLYVV 337
                                        789*****7 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.0025
                                        SEEEEEETTEEEEEEEBCS CS
                            Kelch_1   4 gagavvvggkiYviGGsdg 22 
                                        ++  + ++ ki  +GGs++
  gene2508|gene2508|rna2508|rna2508 356 NHKIAFHDKKILLVGGSRN 374
                                        788999***********97 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.0037
                                        ETTEEEEEEEBCSSSBEEEEEEEET CS
                            Kelch_1  10 vggkiYviGGsdggnalssvevyDp 34 
                                         g+ + viGG  g ++l+ +e+y +
  gene2508|gene2508|rna2508|rna2508 439 YGDILIVIGGKYGKSRLNFIEYYHL 463
                                        68899*************9999976 PP

  == domain 4  score: -0.4 bits;  conditional E-value: 0.098
                                        EEEETTTTEEEEECCC CS
                            Kelch_1  30 evyDpetntWrelpsM 45 
                                        +++  et +W++++++
  gene2508|gene2508|rna2508|rna2508 505 YAFEIETFKWEYIANL 520
                                        67888999*****987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (690 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       809  (0.0451224); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.24s 00:00:00.85 Elapsed: 00:00:00.42
# Mc/sec: 4938.66
//
Query:       gene2509|gene2509|rna2509|rna2509  [L=58]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (58 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       232  (0.0129399); expected 358.6 (0.02)
Passed bias filter:                      185  (0.0103185); expected 358.6 (0.02)
Passed Vit filter:                         7  (0.000390429); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 445.14
//
Query:       gene251|gene251|rna251|rna251  [L=252]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.3e-08   33.2   0.2    1.2e-07   32.0   0.2    1.6  1  DHHA2     DHHA2 domain
    5.4e-07   29.8   0.6    1.1e-06   28.8   0.6    1.5  1  DHH       DHH family
  ------ inclusion threshold ------
      0.039   14.1   3.3       0.23   11.6   1.9    2.4  2  MetOD2    Metanogen output domain 2
       0.08   13.1   0.8       0.17   12.1   0.8    1.6  1  Augurin   Oesophageal cancer-related gene 4
      0.086   13.1   1.4       0.14   12.5   1.4    1.3  1  DUF3069   Protein of unknown function (DUF3069)


Domain annotation for each model (and alignments):
>> DHHA2  DHHA2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.0   0.2   3.4e-11   1.2e-07       1     140 [.     106     241 ..     106     244 .. 0.75

  Alignments for each domain:
  == domain 1  score: 32.0 bits;  conditional E-value: 3.4e-11
                                    HHHHHHHT-STTS-HHHHTTTTEEEEE.ETTEEEEEEEEEES-HHHHHT.THHH............HHHHHHHHH.HHT- CS
                          DHHA2   1 kelkkaksdlsglsledllrrDyKeftgeggvkvgiasvpvslsewleekrkge............llaalekfaeerkl 68 
                                    k+lkka+ + ++ ++e +l++D+K ++   g+++g ++v   ++ w+++  +++            l+ ++e+f+++ + 
  gene251|gene251|rna251|rna251 106 KKLKKARRNDEHQNTEMILQKDMKVYE-CMGYRFGNSTVKYDFERWIDR-EGSKvtgiqknklgmiLSMKMEEFRKDLGF 183
                                    589************************.88*******************.444479*********9999******9999* PP

                                    SEEEEEEE.....ETTTEEEEEE...STT...HHHHHT---BTEEET...............T---HHHHTHHHH CS
                          DHHA2  69 dllvlmttfeeegdirrelllaaldaaek...laealekaseeleLeewkegaewrrvykqgnvkasRKqvaPll 140
                                    d++++    +++ ++      +          + ++++ +  el+ +           y    v+ +RK+++Pl+
  gene251|gene251|rna251|rna251 184 DFYFVGCKMKKQRHFIS----IN---FPYirfFVKKYRFQ--ELNYK--------GFSYFKIPVEMTRKILMPLV 241
                                    **999998433333332....22...11122333333322..34444........44455557888888888886 PP

>> DHH  DHH family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.8   0.6     3e-10   1.1e-06      27      99 ..       3      66 ..       1      68 [. 0.81

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 3e-10
                                   S--TCGGCGCCHHCCCSEEEEEEE-S---SS---SS--EEEE-SSS-HHHHHHHHHHHTT----HHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DHH 27 DhneksqavegeakeeaedviiiDHHrlgeefetlapilflnepvgstaeivaelleekkeeiskeiaellll 99
                                   Dhn++ ++      +++++ +i+DHH+l+++++   + ++++ +vgs+ ++v ++    ++eisk+ia +l++
  gene251|gene251|rna251|rna251  3 DHNKPVEEL-----SHCDINMIVDHHKLEKNISSV-KRIYIDIDVGSATTLVSKY---MGTEISKRIAMMLII 66
                                   666665555.....679***********9666666.788999*************...589999999998876 PP

>> MetOD2  Metanogen output domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0      0.11   4.1e+02      19      39 ..      16      36 ..      12      63 .. 0.85
   2 ?   11.6   1.9   6.5e-05      0.23      21      63 ..      83     123 ..      79     132 .. 0.76

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.11
                         MetOD2 19 keiidEYarLaksvevnkrll 39
                                    ++i ++ +L k++ + kr++
  gene251|gene251|rna251|rna251 16 INMIVDHHKLEKNISSVKRIY 36
                                   57899999******9999976 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 6.5e-05
                         MetOD2  21 iidEYarLaksvevnkrllslLsqtydidddkaevseeieaal 63 
                                    +++EY +L k v+v+k++l+ +++  +     ++ +++ ++++
  gene251|gene251|rna251|rna251  83 DVEEYKKLKKIVDVKKKKLKAMKKKLKKA--RRNDEHQNTEMI 123
                                    589*******************9976665..345555555555 PP

>> Augurin  Oesophageal cancer-related gene 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.8   4.8e-05      0.17      14      88 ..      87     164 ..      72     184 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 4.8e-05
                        Augurin  14 sapskasvavkeskakeflaklkrtkrnlwdr.srpdvqqwiqqflylG..fdeakleddlsywmdkarskdqGrqhh 88 
                                     +  k  v vk++k k++ +klk+ +rn   + +   +q+ ++ +  +G  f ++ ++ d+  w+d++ sk +G q++
  gene251|gene251|rna251|rna251  87 YKKLKKIVDVKKKKLKAMKKKLKKARRNDEHQnTEMILQKDMKVYECMGyrFGNSTVKYDFERWIDREGSKVTGIQKN 164
                                    34568899*******************976550455567778888889833579999***********9999998875 PP

>> DUF3069  Protein of unknown function (DUF3069)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   1.4   3.8e-05      0.14      87     112 ..      93     118 ..      50     124 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.8e-05
                                    HHHHHHTHHHHHHHHHHHHTT-HHHH CS
                        DUF3069  87 ldrvlenslKelvkklKkaRrdrslk 112
                                    +  v ++ lK + kklKkaRr+   +
  gene251|gene251|rna251|rna251  93 IVDVKKKKLKAMKKKLKKARRNDEHQ 118
                                    45688999*************97655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2522  (0.140666); expected 358.6 (0.02)
Passed bias filter:                      860  (0.047967); expected 358.6 (0.02)
Passed Vit filter:                        98  (0.005466); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.43
# Mc/sec: 1746.87
//
Query:       gene2510|gene2510|rna2510|rna2510  [L=143]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.052   13.6   1.0       0.09   12.9   1.0    1.4  1  CBM64     Carbohydrate-binding module 64


Domain annotation for each model (and alignments):
>> CBM64  Carbohydrate-binding module 64
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   1.0     5e-06      0.09      20      62 ..       5      47 ..       1      57 [. 0.89

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5e-06
                                       ES--TTEEEEESEEEEEETTEE-TT--GGGS---TTS-EEEEE CS
                              CBM64 20 tdedisyvnsWnldlLeinGvdytnkwsnsipakidGkyyiky 62
                                        ++di++v+  n d  e+nG+   n+    + +k++  + ik 
  gene2510|gene2510|rna2510|rna2510  5 KNDDIEFVDMVNADIFELNGTGTVNEDLIRVKSKSNHVWDIKS 47
                                       478************************9***********9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       436  (0.0243181); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.48
# Mc/sec: 902.04
//
Query:       gene2511|gene2511|rna2511|rna2511  [L=186]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      0.003   18.2   0.1      0.016   15.9   0.0    2.2  2  RicinB_lectin_2  Ricin-type beta-trefoil lectin domain-like
  ------ inclusion threshold ------
      0.031   14.5   0.0      0.057   13.7   0.0    1.4  1  Ricin_B_lectin   Ricin-type beta-trefoil lectin domain


Domain annotation for each model (and alignments):
>> RicinB_lectin_2  Ricin-type beta-trefoil lectin domain-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   1.8e-06     0.016      13      68 ..      52     104 ..      11     115 .. 0.83
   2 ?   -1.1   0.0      0.36   3.2e+03      19      35 ..     124     140 ..     112     152 .. 0.62

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.8e-06
                                        TEEEEECTSSSEEEECGCCTBCTTEEEEEE-TT.T-GGCEEEEECCESSEEEEEETT CS
                    RicinB_lectin_2  13 gyytiknvasgkvLdvaggstanganvqqwtcs.gaanqqWrledtgdgtyrivnka 68 
                                          ++ +  +++kv d++g++t+    + +w++  g+ nq+++l + ++g+++ivn  
  gene2511|gene2511|rna2511|rna2511  52 QDFVMVRSKDNKVWDISGNATK----LIYWSDRhGKINQLFMLIERPGGHVKIVNDM 104
                                        3466777779***********9....66666555*********999999*****965 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.36
                                        CTSSSEEEECGCCTBCT CS
                    RicinB_lectin_2  19 nvasgkvLdvaggstan 35 
                                        n+++ + Ld  g +t+n
  gene2511|gene2511|rna2511|rna2511 124 NANKHQLLDFVGVGTEN 140
                                        44445555444444442 PP

>> Ricin_B_lectin  Ricin-type beta-trefoil lectin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   6.4e-06     0.057       3      90 ..      55     138 ..      52     161 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6.4e-06
                                        EEEEETTTGEEEEETTCTTSTEBEEEEE-TSCCGGGEEEEE..TTSEEEETT.TTEEEEESSSSTTSBEEEEETTT CS
                     Ricin_B_lectin   3 geirnvasgkCLdvegeskagapvglydChgskgkQlwtlt..kdgeirskaqselCldvsstaegakvvlakChk 76 
                                        +++r++ ++k  d+ g+++  + +   d hg+ + Ql++l     g+++++++ ++C++   +++ +  + a+C++
  gene2511|gene2511|rna2511|rna2511  55 VMVRSK-DNKVWDISGNAT--KLIYWSDRHGKIN-QLFMLIerPGGHVKIVNDMKQCITY--DESLNYFIRAPCNN 124
                                        566666.899999999885..7777788888866.****874555**************8..5666677777***9 PP

                                        TSGGGCEEEETTTT CS
                     Ricin_B_lectin  77 gkgnqrWefdkdgt 90 
                                        ++++q+ +f   gt
  gene2511|gene2511|rna2511|rna2511 125 ANKHQLLDFVGVGT 138
                                        99999988764444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       502  (0.0279993); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1294.86
//
Query:       gene2512|gene2512|rna2512|rna2512  [L=125]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.4e-17   62.9   0.0    4.1e-17   62.7   0.0    1.1  1  ADK              Adenylate kinase
    2.1e-06   28.2   0.0    3.3e-06   27.5   0.0    1.2  1  AAA_17           AAA domain
  ------ inclusion threshold ------
      0.029   14.0   0.0      0.032   13.9   0.0    1.1  1  Thymidylate_kin  Thymidylate kinase


Domain annotation for each model (and alignments):
>> ADK  Adenylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.7   0.0   6.8e-21   4.1e-17      49     149 ..       1      97 [.       1      99 [. 0.95

  Alignments for each domain:
  == domain 1  score: 62.7 bits;  conditional E-value: 6.8e-21
                                        HHTTSS--HHHHHHHHHHHHHCHGTTTEEEEESB-SSHHHHHHHHHHHHHHTSEESEEEEEE--HHHHHHHHHT.. CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
                                ADK  49 mdkgelvpdevvvklvkeelekedkkkgfllDGfPRtveqaealeelleeekvkldlvleldvpeevlveRltg.. 122
                                        m  g lvpd++++++++ +l+ +     ++lDG+PRt++qa+ ++e        +d+ l ++v+e+  v+R++g  
  gene2512|gene2512|rna2512|rna2512   1 MGSGCLVPDDLIIEMMHLKLSGS---GSYILDGYPRTMKQAQLMKE--------VDAALFISVDEDECVRRIVGrn 65 
                                        67899**************9976...99**************9998........9********************* PP

                                        .....GSHHHHHHHHHHHHHHHHHHHHHHHHT CS
                                        .....xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                                ADK 123 .....DneetvkkRletykkqtkplidyykkk 149
                                             Dn+et   R + y+k+t p+++y +++
  gene2512|gene2512|rna2512|rna2512  66 qgrsdDNKETAMMRYRIYQKETLPVVEYLRDR 97 
                                        ****************************8876 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.5   0.0   5.6e-10   3.3e-06      66     134 ..      18      75 ..       3      76 .. 0.76

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 5.6e-10
                                        HHHHHSSEEEEEE-SEEEETTEEEESSHHHHHHHH..SEEEEEE--HHHHHHHHHHHTTST-TS-SHHH CS
                             AAA_17  66 aeeakkkgvlvdghprikeqagfldglpkevleelkpdaiilleadpeeilerrlkdrtrgrdddnees 134
                                         + ++++ +++dg+pr+ +qa++     ke      +da +++++d++e+++r    r++gr+ddn e+
  gene2512|gene2512|rna2512|rna2512  18 LKLSGSGSYILDGYPRTMKQAQL----MKE------VDAALFISVDEDECVRRIVG-RNQGRSDDNKET 75 
                                        23358899********9888874....443......37789**********99988.69*******997 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   5.3e-06     0.032     117     181 ..      43     112 ..      24     116 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.3e-06
                                        E-SEEEEEESSHHHHHTSCCTTSS.....TTTSHHHHHHHHHHHHHHHHHHHHTTSTEEEEETTS-HHHH CS
                    Thymidylate_kin 117 kPdltflldvdpevalkRlakrde.....ldeeeeeqldflrkvrerylelakederiliidasksieev 181
                                        + d+ ++++vd++++++R+  r++     ++e+  +++++++k +    e +++++ +  id ++s+e++
  gene2512|gene2512|rna2512|rna2512  43 EVDAALFISVDEDECVRRIVGRNQgrsddNKETAMMRYRIYQKETLPVVEYLRDRKVLSEIDGNRSVEAI 112
                                        55999*******************8865444555666666666666677777777777788888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       451  (0.0251548); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 851.80
//
Query:       gene2513|gene2513|rna2513|rna2513  [L=56]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (56 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       336  (0.0187406); expected 358.6 (0.02)
Passed bias filter:                      238  (0.0132746); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.41
# Mc/sec: 406.86
//
Query:       gene2514|gene2514|rna2514|rna2514  [L=252]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-53  181.1   0.3      2e-53  181.1   0.3    1.8  2  DUF5094   Domain of unknown function (DUF5094)


Domain annotation for each model (and alignments):
>> DUF5094  Domain of unknown function (DUF5094)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.1     0.056     1e+03       1      22 [.       6      28 ..       2      56 .. 0.71
   2 !  181.1   0.3   1.1e-57     2e-53       1     178 []      78     251 ..      78     251 .. 0.93

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.056
                            DUF5094  1 rkrltlrtp.kkstkkvskkknk 22
                                       +k++ + tp kk+++  +++ +k
  gene2514|gene2514|rna2514|rna2514  6 KKKVAFYTPsKKKIRCIQQNDEK 28
                                       45888899988888877655444 PP

  == domain 2  score: 181.1 bits;  conditional E-value: 1.1e-57
                            DUF5094   1 rkrltlrtp.kkstkkvskkknklssknlkekenvkvkeaeekkeekvtstkenkenekqdkd....sllkeikdi 71 
                                        rk+  ++ + k+++kk++ + +  +  ++    +v+v+++ +++e+++tstken++n+k++k+     ++kei +i
  gene2514|gene2514|rna2514|rna2514  78 RKSDPVGGRkKEAVKKRGGARRGGKAAMK----DVHVDHDVDRDESSATSTKENSANTKNSKNvdtrPSHKEILYI 149
                                        56777788867777777766666666666....89********************************99******* PP

                            DUF5094  72 enelieaykeeNeyLrslknevlltskllGltike.tgdtfivkykvekkeiekslkFeLkeedenYiYklieskn 146
                                        enel++ay+eeN++L+  ++ +++ts+l+G+t++e ++d+fiv+y++++    ++++F+L+++++nY+Y+lie+++
  gene2514|gene2514|rna2514|rna2514 150 ENELLQAYREENAFLK--TSVSSATSRLTGFTVTEpANDHFIVSYSAYD----RHINFRLVKNGRNYEYELIEHRC 219
                                        ****************..8******************************....*********************** PP

                            DUF5094 147 vdlpeyLseeisFekeqlkkFfykvmqiviek 178
                                        v+lpe+L++e++F++eql+kFf++vmq++++k
  gene2514|gene2514|rna2514|rna2514 220 VELPEFLTDELVFGEEQLPKFFFNVMQVMVGK 251
                                        *****************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       890  (0.0496402); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 1914.97
//
Query:       gene2515|gene2515|rna2515|rna2515  [L=54]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.067   13.1   0.0      0.072   13.0   0.0    1.0  1  FliM      Flagellar motor switch protein FliM


Domain annotation for each model (and alignments):
>> FliM  Flagellar motor switch protein FliM
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0     4e-06     0.072      69     113 ..       4      48 ..       1      50 [. 0.91

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4e-06
                                        EETTTEEEEEEEE-HHHHHHHHHHHTTS-S---S.TT----HHHH CS
                               FliM  69 rlkplkgtallevdpslvfsivdrllGGdgraaakegrefteiEr 113
                                        +++++++  l++ +++l + +vd++l  d  ++++  re  ++E+
  gene2515|gene2515|rna2515|rna2515   4 SIQEIENGCLVNANSELHYFVVDQFLSPDHVTIQRIVREIKKLEK 48 
                                        6899*****************************999999999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (54 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       594  (0.0331307); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 409.55
//
Query:       gene2516|gene2516|rna2516|rna2516  [L=447]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.88    9.9  11.9        7.3    6.9   0.1    4.6  5  DUF1722   Protein of unknown function (DUF1722)


Domain annotation for each model (and alignments):
>> DUF1722  Protein of unknown function (DUF1722)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.3    0.0021        38       7      53 ..      13      59 ..      11      62 .. 0.92
   2 ?    0.5   0.0     0.039   7.1e+02      28      53 ..      68      93 ..      59      97 .. 0.83
   3 ?   -1.2   0.1      0.13   2.4e+03       8      23 ..     149     164 ..     143     214 .. 0.67
   4 ?    6.9   0.1   0.00041       7.3      36      81 ..     326     371 ..     301     396 .. 0.86
   5 ?    1.7   0.1     0.017     3e+02      77     105 ..     405     433 ..     399     440 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.0021
                            DUF1722  7 hsqkeyrelgrlvanakkepleelaeeYeellmealskpatrkkhin 53
                                       +s  +  +l r + n++++p +e +++  e l+++l+  a++k+ i+
  gene2516|gene2516|rna2516|rna2516 13 YSTPKQSKLSRHMTNQSEQPHNEQLQTTAESLYDILKCYAKPKNLIE 59
                                       78889999**********************************99875 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.039
                            DUF1722 28 eelaeeYeellmealskpatrkkhin 53
                                       ++l+ +Y e+l+++ls + +++++++
  gene2516|gene2516|rna2516|rna2516 68 AALCRNYIENLRHILSVERQYSNVYK 93
                                       568899**********9999988776 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 0.13
                            DUF1722   8 sqkeyrelgrlvanak 23 
                                        s++ey+el ++v+   
  gene2516|gene2516|rna2516|rna2516 149 SPNEYEELTKMVKVLL 164
                                        5666666666665433 PP

  == domain 4  score: 6.9 bits;  conditional E-value: 0.00041
                            DUF1722  36 ellmealskpatrkkhinvlqhilgyfkkklsaeekqelleliekY 81 
                                        +l+ +++ ++ + k+ i  ++h +  f++  +++ek+++l +i + 
  gene2516|gene2516|rna2516|rna2516 326 KLFPRLFGTEKKEKNDISSYMHFFLPFSNIHNESEKNKVLPIIFHL 371
                                        56788899999***************************99988665 PP

  == domain 5  score: 1.7 bits;  conditional E-value: 0.017
                            DUF1722  77 liekYregkvplsvpltlLkhyarkydne 105
                                        l ++Y+++ v l+  ++ L++y++  +n+
  gene2516|gene2516|rna2516|rna2516 405 LKNEYQKDCVRLNRFIESLRKYLKTGNNS 433
                                        6689******************9987776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (447 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1220  (0.0680462); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.24s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 3082.77
//
Query:       gene2517|gene2517|rna2517|rna2517  [L=64]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (64 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1875  (0.104579); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.29s 00:00:00.70 Elapsed: 00:00:00.46
# Mc/sec: 417.82
//
Query:       gene2518|gene2518|rna2518|rna2518  [L=56]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (56 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1118  (0.0623571); expected 358.6 (0.02)
Passed bias filter:                      490  (0.02733); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 416.96
//
Query:       gene2519|gene2519|rna2519|rna2519  [L=57]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
       0.15   12.3   0.0       0.18   12.0   0.0    1.3  1  YchF-GTPase_C  Protein of unknown function (DUF933)


Domain annotation for each model (and alignments):
>> YchF-GTPase_C  Protein of unknown function (DUF933)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   9.9e-06      0.18      24      56 ..       2      35 ..       1      54 [. 0.73

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 9.9e-06
                      YchF-GTPase_C 24 pqaAgviHsDfekgFiraevikyedlvelgs.ea 56
                                        ++ g iH D++ gF++a   + +++ +l+  e+
  gene2519|gene2519|rna2519|rna2519  2 HECQGPIHVDLRSGFVSAISKANSKMWRLNDyEE 35
                                       57889************98888877777766333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (57 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       258  (0.0143901); expected 358.6 (0.02)
Passed bias filter:                      235  (0.0131073); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.33u 0.25s 00:00:00.58 Elapsed: 00:00:00.38
# Mc/sec: 451.87
//
Query:       gene252|gene252|rna252|rna252  [L=543]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.7e-73  244.9   0.4    9.3e-73  244.4   0.4    1.2  1  Peptidase_M1    Peptidase family M1 domain
    8.9e-08   32.5   0.6    1.2e-07   32.1   0.6    1.2  1  Peptidase_M1_N  Peptidase M1 N-terminal domain


Domain annotation for each model (and alignments):
>> Peptidase_M1  Peptidase family M1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  244.4   0.4     1e-76   9.3e-73       1     218 []      76     311 ..      76     311 .. 0.98

  Alignments for each domain:
  == domain 1  score: 244.4 bits;  conditional E-value: 1e-76
                                    HHHHHHHHHHHHHHHHHTS--SSSEEEEEEESSTTSSEEEETTEEEEEGGGC-SSTTTS-HHHHHHHHHHHHHHHHHHHB CS
                   Peptidase_M1   1 yalevtkkllefleeyfkvpYplpkldlvalpdfsagAMEnwglityreelllvdpenssesdkrsvaeviaHElaHqWf 80 
                                    yal v+ ++l+f+eeyf+++Ypl+kld+va+p+f agAMEnwglityre+ ll+++e+ss+++++ +a ++aHE+aHqWf
  gene252|gene252|rna252|rna252  76 YALRVADQVLKFFEEYFGIEYPLDKLDMVAVPEFLAGAMENWGLITYRETGLLFNKEKSSMTQRKLIAGTVAHEIAHQWF 155
                                    7999**************************************************************************** PP

                                    TTTEEESSGGGGHHHHHHHHHHHHHHHHHHSCCCH...................CHHHHHHHCHHHHHHHHTSTTHHHSS CS
                   Peptidase_M1  81 GnlVtmkwWddlwLnEGfatyleylildklepewe...................vseqllleeveealsedaldeshpit 141
                                    GnlVt +wWddlwLnEGfat++++l+++++ ++ +                    + +++ +++++ +++d+ld+shpi+
  gene252|gene252|rna252|rna252 156 GNLVTPRWWDDLWLNEGFATWAAALGCNAIREKQKndpsivnpvnkneplidwePWVSFINDDLNKGMESDMLDSSHPIK 235
                                    ******************************99555589*************99999999********************* PP

                                    GG-GSHHHHHHTSSHHHHHHHHHHHHHHHHHCTHHHHHHHHHHHHHHCTTEEE-HHHHHHHHHHCCCSCHHTHHHHH CS
                   Peptidase_M1 142 qevekpseidevFdsiaYeKGasllrmlekllgeevFqkglksYlkefkyknaetedlwdaleealnkdisevmdtw 218
                                    + v+++++++++  +i Y+K+asl+rm+e++lg evF+k + +Yl++++y+na+++dl++ l++  n++i+++m+ w
  gene252|gene252|rna252|rna252 236 VPVHHHKDVTQISGAILYSKSASLIRMVENYLGAEVFRKKIGRYLRKYSYGNASSKDLFEFLSDD-NNNITKFMEIW 311
                                    ***************************************************************88.99*******99 PP

>> Peptidase_M1_N  Peptidase M1 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.1   0.6   1.4e-11   1.2e-07     139     186 .]       1      47 [.       1      47 [. 0.93

  Alignments for each domain:
  == domain 1  score: 32.1 bits;  conditional E-value: 1.4e-11
                                    SEBEEEEEEEEETTSEEEESSECCCEEEETTCEEEEEEEEEESBEGGG CS
                 Peptidase_M1_N 139 vKAtftisikapkeetalSnmpeeeseklengqkiteFeqtpkmstYL 186
                                    +KAtf+i i+a++++t+lSnm+ + +e+ ++g+k++ F+   k+stYL
  gene252|gene252|rna252|rna252   1 MKATFDIDITADEKFTILSNMSAK-NETVKDGRKTVIFNHMKKTSTYL 47 
                                    7**********************9.556668****************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (543 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       317  (0.0176809); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.69u 0.35s 00:00:01.04 Elapsed: 00:00:00.57
# Mc/sec: 2855.07
//
Query:       gene2520|gene2520|rna2520|rna2520  [L=67]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (67 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       209  (0.0116571); expected 358.6 (0.02)
Passed bias filter:                      200  (0.0111551); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.52
# Mc/sec: 388.71
//
Query:       gene2521|gene2521|rna2521|rna2521  [L=130]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.11   12.2   0.0       0.15   11.7   0.0    1.2  1  dUTPase   dUTPase


Domain annotation for each model (and alignments):
>> dUTPase  dUTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   8.3e-06      0.15      78     128 ..      56     106 ..      52     107 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 8.3e-06
                                        EEEEE-SSS-EEE-TT-EEEEEEEEEBECGEEEEESST.TTESSBTTXTTTT CS
                            dUTPase  78 vvlfnltkkdvkikkgdRiAqLifariltaeleevetl.katergeggfgss 128
                                        + ++n   +++   + dR+A L+fa++++  +++v+++ +++  g +g g+s
  gene2521|gene2521|rna2521|rna2521  56 FLVTNMRIDEIVDGEADRVAELLFADVKA-AVMQVRRMdSNLSYGLQGAGRS 106
                                        6788888888888899*********9999.9999999989999999999988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       289  (0.0161191); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.47
# Mc/sec: 830.49
//
Query:       gene2522|gene2522|rna2522|rna2522  [L=285]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (285 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       508  (0.028334); expected 358.6 (0.02)
Passed bias filter:                      479  (0.0267165); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1839.14
//
Query:       gene2523|gene2523|rna2523|rna2523  [L=258]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       948  (0.0528752); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 1867.07
//
Query:       gene2524|gene2524|rna2524|rna2524  [L=881]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (881 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       584  (0.0325729); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.65u 0.27s 00:00:00.92 Elapsed: 00:00:00.47
# Mc/sec: 5689.57
//
Query:       gene2525|gene2525|rna2525|rna2525  [L=346]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.67   10.4   0.0       0.67   10.4   0.0    3.1  2  SRP72     SRP72 RNA-binding domain


Domain annotation for each model (and alignments):
>> SRP72  SRP72 RNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   7.3      0.74   1.3e+04      20      37 ..      54      77 ..      10      82 .. 0.65
   2 ?   10.4   0.0   3.7e-05      0.67      21      51 ..     104     134 ..      86     138 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 0.74
                              SRP72 20 k......krkkkrkRkvklPKnyd 37
                                       k       ++ + k + ++ Knyd
  gene2525|gene2525|rna2525|rna2525 54 KildkerMSSVQSKLRRRRKKNYD 77
                                       133334444555566666667777 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 3.7e-05
                              SRP72  21 krkkkrkRkvklPKnydpgvtpDPERWLPrr 51 
                                        +r+k   R++k   +yd g   +P RW+P++
  gene2525|gene2525|rna2525|rna2525 104 VRNKANSRNGKKTTKYDIGHLHNPVRWMPLK 134
                                        6889999**********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (346 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1307  (0.0728987); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.38
# Mc/sec: 2695.75
//
Query:       gene2526|gene2526|rna2526|rna2526  [L=223]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.1e-12   46.8   6.0    3.3e-12   46.2   6.0    1.3  1  TB2_DP1_HVA22  TB2/DP1, HVA22 family
  ------ inclusion threshold ------
       0.56   10.2   3.7       0.39   10.7   1.9    1.7  2  DUF3290        Protein of unknown function (DUF3290)


Domain annotation for each model (and alignments):
>> TB2_DP1_HVA22  TB2/DP1, HVA22 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.2   6.0   3.7e-16   3.3e-12      17      76 ..      28      87 ..      15      88 .. 0.90

  Alignments for each domain:
  == domain 1  score: 46.2 bits;  conditional E-value: 3.7e-16
                      TB2_DP1_HVA22 17 etkwltYWvvfafltvvesladvllswiPfYylfKllfllwlvlpqtqgatyvYekflrp 76
                                       +++   Y++++++++v++sl+++l++++Pf++++K++f++wl lp ++g  ++Y+ ++++
  gene2526|gene2526|rna2526|rna2526 28 NKHYRYYFLILCLFLVFDSLFSYLTNLVPFFQIAKFAFIIWLSLPMFNGPVFIYNFYMKK 87
                                       445889*************************************************99875 PP

>> DUF3290  Protein of unknown function (DUF3290)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   1.9   4.3e-05      0.39      20      60 ..       5      45 ..       1      54 [. 0.82
   2 ?   -2.0   0.0      0.36   3.3e+03       6      30 ..      49      73 ..      47      92 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 4.3e-05
                            DUF3290 20 yililvlllllivvlilylrnrldtkyRdLsiillllllll 60
                                       +i+ +  +ll++  ++ y+++r +  yR   +il l+l++ 
  gene2526|gene2526|rna2526|rna2526  5 VIVNITTVLLVLNNCYGYFKDRKNKHYRYYFLILCLFLVFD 45
                                       55666667777778899*********************985 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.36
                            DUF3290  6 dYlqsqqslndllryililvlllll 30
                                       +Yl++   + ++++ ++i+ l l +
  gene2526|gene2526|rna2526|rna2526 49 SYLTNLVPFFQIAKFAFIIWLSLPM 73
                                       6888888888888888887766554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       832  (0.0464053); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1537.96
//
Query:       gene2527|gene2527|rna2527|rna2527  [L=353]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (353 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       586  (0.0326845); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 2394.67
//
Query:       gene2528|gene2528|rna2528|rna2528  [L=258]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      0.001   19.1   4.0      0.001   19.1   4.0    2.2  2  WW        WW domain
  ------ inclusion threshold ------
      0.034   14.3   0.1      0.076   13.2   0.1    1.6  1  FF        FF domain


Domain annotation for each model (and alignments):
>> WW  WW domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   4.0   1.1e-07     0.001       8      31 .]      21      43 ..      16      43 .. 0.82
   2 ?   -0.0   0.8      0.11   9.7e+02      17      22 ..     167     172 ..     167     180 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.1e-07
                                       EE-TTTT-EEEEETTT--EESS-- CS
                                 WW  8 qwdpdsGrvYYyNheTgetqWekP 31
                                       + + ++G+ +YyN++T+++ W  P
  gene2528|gene2528|rna2528|rna2528 21 YHT-NTGKLFYYNTNTNKSYWIVP 43
                                       444.55***************877 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.11
                                        EEEETT CS
                                 WW  17 YYyNhe 22 
                                        YY+N e
  gene2528|gene2528|rna2528|rna2528 167 YYWNAE 172
                                        999976 PP

>> FF  FF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   8.5e-06     0.076       1      35 [.      70     103 ..      70     116 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 8.5e-06
                                        CCHHHHHHHHHHCSSS-TTSSHHHHHHHCTTSCCC CS
                                 FF   1 kareaFkeLLkehkeitpkstWseikkilenDpRY 35 
                                        k ++ F+eLL+ ++  + + t++++ k+l+++  Y
  gene2528|gene2528|rna2528|rna2528  70 KDKKLFFELLEQCN-MEESATMEDFDKKLGENILY 103
                                        5799**********.**************987555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       770  (0.0429472); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1767.44
//
Query:       gene2529|gene2529|rna2529|rna2529  [L=189]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0081   14.9   0.1     0.0081   14.9   0.1    1.1  1  Hanta_G1  Hantavirus glycoprotein G1
  ------ inclusion threshold ------
       0.25   11.5   1.8       0.52   10.5   1.5    1.7  1  DUF1283   Protein of unknown function (DUF1283)


Domain annotation for each model (and alignments):
>> Hanta_G1  Hantavirus glycoprotein G1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.1     9e-07    0.0081      52     120 ..      16      92 ..       1     140 [. 0.73

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 9e-07
                           Hanta_G1  52 lnt.itkytqvswrgkadqsqssqnsfetvstevdlkgtcvlkhkmv......eesyrsrksvtcydls.cnstyc 119
                                        +n  i++  ++s +  a+q    qnsf t+s ev+ k   v+k k +      e +y s k v    l   n  y 
  gene2529|gene2529|rna2529|rna2529  16 MNVrISNGEDISEKRDAEQELEGQNSFHTLSNEVEKKKRKVIKDKWLcsissdEHAYLSTKEVLTELLGvSNEKYN 91 
                                        443266777899999****************************997533344466788888776655541355565 PP

                           Hanta_G1 120 k 120
                                        k
  gene2529|gene2529|rna2529|rna2529  92 K 92 
                                        5 PP

>> DUF1283  Protein of unknown function (DUF1283)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   1.5   5.8e-05      0.52       5      42 ..      20      57 ..      16      77 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 5.8e-05
                            DUF1283  5 ienGdsalskeaarqskeqWnetrsLRnkvnkrvekef 42
                                       i+nG++  +k  a q+ e  n+ ++L n v+k++ k +
  gene2529|gene2529|rna2529|rna2529 20 ISNGEDISEKRDAEQELEGQNSFHTLSNEVEKKKRKVI 57
                                       89******************************998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (189 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1033  (0.0576162); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1342.20
//
Query:       gene253|gene253|rna253|rna253  [L=257]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
       0.37   10.6   9.8       0.57    9.9   9.8    1.3  1  MAJIN            Membrane-anchored junction protein
        0.5   10.2   4.0        1.5    8.7   4.0    1.8  1  Motilin_ghrelin  Motilin/ghrelin
        2.6    6.9  14.9        3.2    6.6  14.9    1.2  1  XRN_M            Xrn1 helical domain
        4.2    7.2   7.1        7.1    6.5   7.1    1.4  1  CemA             CemA family
        7.4    5.0   7.5        9.2    4.7   7.5    1.1  1  FUSC             Fusaric acid resistance protein family


Domain annotation for each model (and alignments):
>> MAJIN  Membrane-anchored junction protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   9.8   0.00016      0.57     103     236 ..      80     219 ..      74     224 .. 0.59

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00016
                          MAJIN 103 lyvemkwfhenlspGkpindsPlglvla...ekkaaeavlkkrkkveepssPsragldrakletsseaask.kkplketr 178
                                    l v +k+++e l +G+ i+    ++      e++a e+   ++k+ e+ ++  r +++r++    +++ +    + +e +
  gene253|gene253|rna253|rna253  80 LNVFVKFLSELLDEGNVIEREIDQIRYNkqlEQEAMEEEAARQKQEEQAAAMLRRAQEREEAARQKQEEQAaAMLRREQE 159
                                    67888999999999999886655554440014444444455778888888888999999876665554444044555666 PP

                          MAJIN 179 rnreeksqqekqeteasdatdv.qeqdskledslaGklvpplqksnp.lppkepkelkta 236
                                     + e+ +++e+q+  ++++ d  + +++k+e      +++  q++++ + + e++e +++
  gene253|gene253|rna253|rna253 160 AEAEKAAKHECQRKVEANIDDEgKRRQAKYEGCKDEGMTRVEQEQEDeIVKGEKEERGKT 219
                                    667777788888887777765415556666655544444444444440444444444544 PP

>> Motilin_ghrelin  Motilin/ghrelin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   4.0   0.00041       1.5       9      22 ..     132     145 ..     132     147 .. 0.93

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00041
                Motilin_ghrelin   9 lQKmQERErNKgqk 22 
                                    l+++QERE++ +qk
  gene253|gene253|rna253|rna253 132 LRRAQEREEAARQK 145
                                    79***********9 PP

>> XRN_M  Xrn1 helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6  14.9   0.00089       3.2      42     167 ..      75     208 ..      65     248 .. 0.60

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.00089
                          XRN_M  42 vYkkelkklggyltd...ngevkldrveklvsl....vgkveekifrkrkeredrk.ekklakeeeaskedaaneeaav. 112
                                     Y++ l+ +  +l +   +g+v    ++++  +     +++ee+  r+++e+++++  ++++++eea+++++++++aa+ 
  gene253|gene253|rna253|rna253  75 AYQRSLNVFVKFLSElldEGNVIEREIDQIRYNkqleQEAMEEEAARQKQEEQAAAmLRRAQEREEAARQKQEEQAAAMl 154
                                    56655555555544433367666666666643323224567777777766666554045555555555444444444431 PP

                          XRN_M 113 aeeklseskvaksaeaeaeaeaeaeaeakaekekrekaekeleeseeeeeeeDkv 167
                                      e+++e+++a ++e + + ea+++ e k+ + k e ++ e     e+e+ eD++
  gene253|gene253|rna253|rna253 155 RREQEAEAEKAAKHECQRKVEANIDDEGKRRQAKYEGCKDEGMTRVEQEQ-EDEI 208
                                    34444555555566666666666666666666666666655555444444.4544 PP

>> CemA  CemA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   7.1     0.002       7.1      37     109 ..      95     168 ..      58     174 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.002
                           CemA  37 rflekeqaelflnkeleeealee.lkefeekleleeligeapelseeeieeelkekaeelakeyreesseaikn 109
                                    + +e+e +++ +nk+le+ea+ee  ++ +++ +  +++++a+e +e   +++ ++ a+ l++e+++e ++a k+
  gene253|gene253|rna253|rna253  95 NVIEREIDQIRYNKQLEQEAMEEeAARQKQEEQAAAMLRRAQEREEAARQKQEEQAAAMLRREQEAEAEKAAKH 168
                                    566789999**********9986266777888889999999999998889999999999999999999998876 PP

>> FUSC  Fusaric acid resistance protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   7.5    0.0026       9.2     244     302 ..     116     173 ..      84     219 .. 0.54

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.0026
                           FUSC 244 rlraeeaaavpelaallaelaaleaaaaaealeaalaalrarlralrraleadadtaal 302
                                    +  a++++++++ aa+l+++++  ++aa +++e+++aa+ +r ++++++ +a+ + ++ 
  gene253|gene253|rna253|rna253 116 EEEAARQKQEEQAAAMLRRAQER-EEAARQKQEEQAAAMLRREQEAEAEKAAKHECQRK 173
                                    12222222222255555555552.22333333333333333333333333333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3475  (0.19382); expected 358.6 (0.02)
Passed bias filter:                      818  (0.0456244); expected 358.6 (0.02)
Passed Vit filter:                       168  (0.00937029); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.69u 0.32s 00:00:01.01 Elapsed: 00:00:00.46
# Mc/sec: 1671.97
//
Query:       gene2530|gene2530|rna2530|rna2530  [L=41]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (41 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       326  (0.0181828); expected 358.6 (0.02)
Passed bias filter:                      244  (0.0136092); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.32u 0.26s 00:00:00.58 Elapsed: 00:00:00.40
# Mc/sec: 310.45
//
Query:       gene2531|gene2531|rna2531|rna2531  [L=236]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.8e-36  123.2   0.1    8.2e-36  122.7   0.1    1.3  1  Ribosomal_S6e  Ribosomal protein S6e


Domain annotation for each model (and alignments):
>> Ribosomal_S6e  Ribosomal protein S6e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.7   0.1   4.6e-40   8.2e-36       1     114 [.       1     114 [.       1     137 [. 0.97

  Alignments for each domain:
  == domain 1  score: 122.7 bits;  conditional E-value: 4.6e-40
                                        -EEEEEETTTTEEEEEE-CHHHCTTCTT-BSSEEEECCTTTSSSTS-EEEEEEEEETTC-BB-TTS-SSSEEEEEE CS
                      Ribosomal_S6e   1 mklnisdpatgkqklievdekklrtligkrigeevdgdalGeelkgyvlkitggsdkqGfpmkqgvltpgrvrlLl 76 
                                        mklnis p++g++ ++ev+++  r ++gk++g+ +dg+++ +e++g ++ +tggsdkqGfpm  ++ t +r+rlL 
  gene2531|gene2531|rna2531|rna2531   1 MKLNISSPQNGTNITLEVTGNAERIFHGKSLGDIIDGSMIKQEYAGWKMLLTGGSDKQGFPMDTQINTDKRQRLLR 76 
                                        9*************************************************************************** PP

                                        ETTSSSS-SSSSS-EEEEEEE-SB--SSEEEEEEEEEE CS
                      Ribosomal_S6e  77 skggvgyrprrkGerkrksvrGcivsadisqlnlvivk 114
                                        +kg++g++prrkGe +rksvrG i+s+++s+l +++v+
  gene2531|gene2531|rna2531|rna2531  77 RKGDIGFKPRRKGELRRKSVRGAIISEETSALCMKVVN 114
                                        ************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       872  (0.0486363); expected 358.6 (0.02)
Passed bias filter:                      496  (0.0276647); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1657.79
//
Query:       gene2532|gene2532|rna2532|rna2532  [L=276]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.7e-17   63.0   1.6      8e-17   61.5   0.5    1.9  2  RhoGAP    RhoGAP domain
  ------ inclusion threshold ------
      0.081   12.9   0.0        2.3    8.3   0.0    2.4  2  Slx4      Slx4 endonuclease


Domain annotation for each model (and alignments):
>> RhoGAP  RhoGAP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0     0.068   6.1e+02      94     118 ..      23      47 ..       3      49 .. 0.76
   2 !   61.5   0.5   8.9e-21     8e-17       1     146 [.      89     244 ..      89     249 .. 0.94

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.068
                                        HHHHHHHTTS-HHHHHHHHHHHHHH CS
                             RhoGAP  94 ealkellekLPkenrdtLryLlehL 118
                                        e +++ le++ +en ++Lr++++++
  gene2532|gene2532|rna2532|rna2532  23 EDVRAYLENFVEENLNVLRSVFSVI 47 
                                        6788899999999999999998765 PP

  == domain 2  score: 61.5 bits;  conditional E-value: 8.9e-21
                                        BHHHHHHHHHHHHHTTTSTTTTTS-S-HHHHHHHHHHHHHTGGGCT....TTTTSCHHHHHHHHHHHHHHSSSTTT CS
                             RhoGAP   1 PiivekcvefiekrgldtegiyRvsgskarvkelreafdkgkavds....dleeedvhavaslLKrfLrelpepLl 72 
                                        P+ +++++ef    +l++ gi++ s s   v++  + f+++ ++ s    +l  +d  ++ s++K+ ++ ++ pL+
  gene2532|gene2532|rna2532|rna2532  89 PSELNEIMEFFLTLDLTQRGIFKRSPSIVIVEAAIKDFEECMRTRSsiheKLARYDAITIPSVFKNVFNYYEMPLF 164
                                        77789999999999******************************999***************************** PP

                                        TGGHHHHHHHHHTSSSHHHHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHHHTHHH......H---HHHHHHHHHHH CS
                             RhoGAP  73 tkelyeelieaaksedeeerlealkellekLPkenrdtLryLlehLkrvaenske......nkMtaknLaivfaPt 142
                                        +ke+++ + ++ +    +++  alk ll  +P++nr+tL++++++++ v+e +++       +M+ +    v++P 
  gene2532|gene2532|rna2532|rna2532 165 PKEFVDYFCRIKRLPRIDDQHTALKFLLLCMPRTNRSTLEAVIRFIEIVHELASQkdeehqEHMDFSGFVSVMMPK 240
                                        **************************************************94444466777*************** PP

                                        HHT- CS
                             RhoGAP 143 Llrp 146
                                        L+ +
  gene2532|gene2532|rna2532|rna2532 241 LMLK 244
                                        9976 PP

>> Slx4  Slx4 endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0     0.027   2.4e+02      31      53 ..       8      30 ..       4      31 .. 0.78
   2 ?    8.3   0.0   0.00025       2.3       4      26 ..     126     148 ..     122     160 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.027
                                       HHHHHH-GGGGGS-HHHHHHHHH CS
                               Slx4 31 awLnteglglkevdpaelrewcd 53
                                       + L+++ l ++ +d++++r++++
  gene2532|gene2532|rna2532|rna2532  8 QRLTEKQLTVNDIDDEDVRAYLE 30
                                       5677885556699********99 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00025
                                        HHHHHHT-HHHHHHHHTT--EEH CS
                               Slx4   4 iteaiksdpslhekILlYePIvL 26 
                                        + e+++++ s+hek  +Y+ I++
  gene2532|gene2532|rna2532|rna2532 126 FEECMRTRSSIHEKLARYDAITI 148
                                        5688999**************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (276 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       559  (0.0311785); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 2015.53
//
Query:       gene2533|gene2533|rna2533|rna2533  [L=362]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-29  103.7   0.2      1e-29  103.7   0.2    1.5  2  PseudoU_synth_2  RNA pseudouridylate synthase
  ------ inclusion threshold ------
       0.16   11.8   0.0       0.38   10.6   0.0    1.6  1  RuvC             Crossover junction endodeoxyribonuclease Ruv


Domain annotation for each model (and alignments):
>> PseudoU_synth_2  RNA pseudouridylate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.7   0.2   1.1e-33     1e-29       1     159 [.      87     225 ..      87     226 .. 0.94
   2 ?   -3.4   0.1         1   9.3e+03      40      48 ..     275     283 ..     248     290 .. 0.52

  Alignments for each domain:
  == domain 1  score: 103.7 bits;  conditional E-value: 1.1e-33
                    PseudoU_synth_2   1 dlvvvnKPagvpvqpeakdgsekekettatssraeeekkelklvhRLDkatsGllllAksseaanklakafeerkv 76 
                                        d++vvnKP+g++++p+          +  +  r  e+  +l+ ++RLD+ tsG+l+lA+    a+k ++++ ++++
  gene2533|gene2533|rna2533|rna2533  87 DYLVVNKPSGIACHPTS-------GYNLFSVTRVLEKYGNLSCINRLDVLTSGVLILAF--RNAKKYHNEMINHRI 153
                                        69***************.......555556666679999********************..88999999999**** PP

                    PseudoU_synth_2  77 rKkYlalvfgapeeeegaikkkiskdtekqegarrkaeeldgkkavtylkvlksgsseksakvslveleletGrkh 152
                                        +K Yla v+ +   +e ++ ++++k      ++++++  ++gkka t++k l  +     +++slve++++tGr h
  gene2533|gene2533|rna2533|rna2533 154 KKIYLAKVK-GRFHDEITVSASLKK-----NRFNFTEVSEEGKKAKTIFKCLFFH-----NGYSLVECRPVTGRSH 218
                                        ********7.***************.....9************************.....**************** PP

                    PseudoU_synth_2 153 QiRvhla 159
                                        QiRvhl+
  gene2533|gene2533|rna2533|rna2533 219 QIRVHLK 225
                                        *****97 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 1
                    PseudoU_synth_2  40 elklvhRLD 48 
                                        e k  hRLD
  gene2533|gene2533|rna2533|rna2533 275 EKKQEHRLD 283
                                        222334444 PP

>> RuvC  Crossover junction endodeoxyribonuclease RuvC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   4.2e-05      0.38      25      66 ..      40      82 ..      29      97 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 4.2e-05
                                       EEEEEEEE---S.-HHHHHHHHHHHHHHHHHHH--SEEEEEE- CS
                               RuvC 25 lltsgvirtksd.plserlkavfdaveelldayepdalaieqv 66
                                       ++  g i ++++   + r++++ +++++l++ +epda+ ie +
  gene2533|gene2533|rna2533|rna2533 40 AIRIGNITVNNEkSDKCRILSLGQTIQHLVHYHEPDACEIELL 82
                                       67889999999945567***********************965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (362 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       555  (0.0309554); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 2523.19
//
Query:       gene2534|gene2534|rna2534|rna2534  [L=435]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00025   20.9   0.8     0.0033   17.3   0.2    2.6  3  POT1             Telomeric single stranded DNA binding POT1/C
  ------ inclusion threshold ------
      0.072   13.0   0.1        4.1    7.3   0.0    3.1  4  POT1PC           ssDNA-binding domain of telomere protection 
       0.14   12.2   0.2        4.3    7.4   0.0    3.1  3  tRNA_anti-codon  OB-fold nucleic acid binding domain


Domain annotation for each model (and alignments):
>> POT1  Telomeric single stranded DNA binding POT1/CDC13
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.2   5.5e-07    0.0033       1      91 [.      35     117 ..      35     124 .. 0.85
   2 ?   -0.4   0.0      0.15   9.1e+02      90     141 ..      94     152 ..      90     153 .. 0.81
   3 ?    1.0   0.0     0.056   3.3e+02       9      83 ..     171     250 ..     164     256 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 5.5e-07
                                        CCCHHHHTCTTEEEEEEEEEEEEEECCCSCCEEEEECCCCCTTTSCCHCTTTEEEEEEEECCCCCCCCGGCCCCEE CS
                               POT1   1 fvdldkaeaekkvvnviGvVidasfpkktggsdyvctfkivDpsknkgdendglrvvlFsknfedLpivkkvgdii 76 
                                        f++++++ + + + ++i +V+    p k++g+dyv+t+ ++D+        d l +++F k+ + +     + dii
  gene2534|gene2534|rna2534|rna2534  35 FKNIKDL-KINEYASIIVLVKGHLEPTKSKGTDYVTTVDVIDEL------GDALDIKIFTKTPR-FANFFHESDII 102
                                        6789888.9***********************************......99999999999977.56666889999 PP

                                        ECCCCEEEESTTSCE CS
                               POT1  77 rlhraklqsyngepq 91 
                                        r+  +kl     + +
  gene2534|gene2534|rna2534|rna2534 103 RIPSVKLIGKGKAVT 117
                                        988888766555555 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.15
                                        CECCSEEEEEEECCCTTSCEEEEE.......CCCCCSTSTTCCCCSHCCHHHHHHHHHH CS
                               POT1  90 pqglanigfssswalFngnlnail.......letppilsskffelskeekkylkdlrkw 141
                                        ++++ ++++++++  + g+ +a++       + ++ +  ++++ +++ ek+ +++lr++
  gene2534|gene2534|rna2534|rna2534  94 NFFHESDIIRIPSVKLIGKGKAVTghgsnmeVLAHLNEEGTRVFVTESEKAKINKLREY 152
                                        67777888888888888888877788888888888888888898999999999999975 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.056
                                        CTTEEEEEEEEEEEEEECCCSCCEEEEECCCCCTTT..........SCCHCTTTEEEEEEEECCCCC.CCCGGCCC CS
                               POT1   9 aekkvvnviGvVidasfpkktggsdyvctfkivDps..........knkgdendglrvvlFsknfed.Lpivkkvg 73 
                                        +e  +++++G++i+++      ++ + +++  vD +          +++  ++ +l++++  ++ e+ + +  ++g
  gene2534|gene2534|rna2534|rna2534 171 KEYCSFSLVGMLISIRE-----ETPSLTVLLMVDYTaspliknivkNARFCNDMTLYIKVWGNRQEKnFGEL-RIG 240
                                        66667788888888885.....44455555555655568888888878888888888888888777768888.999 PP

                                        CEEECCCCEE CS
                               POT1  74 diirlhrakl 83 
                                        +++r++ ++ 
  gene2534|gene2534|rna2534|rna2534 241 KVYRIRKIRT 250
                                        9999998775 PP

>> POT1PC  ssDNA-binding domain of telomere protection protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0      0.55   3.3e+03       2      24 ..      38      60 ..      37      69 .. 0.74
   2 ?   -1.3   0.0       0.3   1.8e+03      79     122 ..      81     128 ..      78     153 .. 0.63
   3 ?    7.3   0.0   0.00068       4.1       2      43 ..     167     208 ..     166     215 .. 0.90
   4 ?    1.4   0.0     0.043   2.6e+02      75     118 ..     217     258 ..     210     289 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.55
                                       GGG--SSSEEEEEEEEEEEE-.. CS
                             POT1PC  2 lkdvqegeffDligqvvkkasdd 24
                                       +kd++ +e++ +i+ v    + +
  gene2534|gene2534|rna2534|rna2534 38 IKDLKINEYASIIVLVKGHLEPT 60
                                       899999*******9987666544 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.3
                                        EEEEE-HHHHHHHTTT--TT-EEEEEEEEEEE-TTS.......-EEEEE- CS
                             POT1PC  79 lqitlydehaefarenlkpgdfvrLrNvhiklgrkgs......klegflh 122
                                        l+i ++ +   fa+    + d++r+ +v++ +g+ ++      ++e   h
  gene2534|gene2534|rna2534|rna2534  81 LDIKIFTKTPRFANF-FHESDIIRIPSVKL-IGKGKAvtghgsNMEVLAH 128
                                        577777788888888.89999999999999.4443323333336665555 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.00068
                                        GGG--SSSEEEEEEEEEEEE-..SS-EEEEEE-S---TTS-- CS
                             POT1PC   2 lkdvqegeffDligqvvkkasddsgkvvLyvwDgtenpnlfs 43 
                                        +kd++e + f l+g+++++ +++ + +vL   D+t +p  ++
  gene2534|gene2534|rna2534|rna2534 167 IKDIKEYCSFSLVGMLISIREETPSLTVLLMVDYTASPLIKN 208
                                        8999999999**************************998765 PP

  == domain 4  score: 1.4 bits;  conditional E-value: 0.043
                                        BS-EEEEEE-HHHHHHHTTT--TT-EEEEEEEEEEE-TTS.-EE CS
                             POT1PC  75 gkltlqitlydehaefarenlkpgdfvrLrNvhiklgrkgskle 118
                                        +++tl i ++++  e    +l+ g++ r+r +++  ++ g +le
  gene2534|gene2534|rna2534|rna2534 217 NDMTLYIKVWGNRQEKNFGELRIGKVYRIRKIRT--DKLGMTLE 258
                                        469**********9999888**********9999..44444555 PP

>> tRNA_anti-codon  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.34     2e+03      18      54 ..      68     104 ..      50     104 .. 0.60
   2 ?    0.4   0.0      0.11   6.5e+02      32      55 ..     223     246 ..     177     248 .. 0.79
   3 ?    7.4   0.0   0.00072       4.3      16      49 ..     376     412 ..     367     415 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.34
                                        EEEEEEEETT.EEEEEEEETHHHHHHHTTS-TTSEEEE CS
                    tRNA_anti-codon  18 vifidlrDgt.griqvvlfreeatklaenlkeGdvvrv 54 
                                        v ++d+ D+  + + + +f  +  ++a+ + e d++r+
  gene2534|gene2534|rna2534|rna2534  68 VTTVDVIDELgDALDIKIFT-KTPRFANFFHESDIIRI 104
                                        44555555554466666666.77777777777777776 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.11
                                        EEEETHHHHHHHTTS-TTSEEEEE CS
                    tRNA_anti-codon  32 vvlfreeatklaenlkeGdvvrvt 55 
                                        + ++ + ++k + +l++G+v+r++
  gene2534|gene2534|rna2534|rna2534 223 IKVWGNRQEKNFGELRIGKVYRIR 246
                                        567777888999999999999985 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.00072
                                        TTEEEEEEEETTEEEEEEEET...HHHHHHHTTS-TT CS
                    tRNA_anti-codon  16 gkvifidlrDgtgriqvvlfr...eeatklaenlkeG 49 
                                         k++ i+++D +g i +vl +   e++ +l enl+++
  gene2534|gene2534|rna2534|rna2534 376 EKILKIQVKDASGFICIVLKNklvEKFIQLEENLRKE 412
                                        6999*****************9999999999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (435 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       556  (0.0310112); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 2983.06
//
Query:       gene2535|gene2535|rna2535|rna2535  [L=500]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.019   15.2   0.6      0.066   13.5   0.1    2.2  2  DUF2811   Protein of unknown function (DUF2811)


Domain annotation for each model (and alignments):
>> DUF2811  Protein of unknown function (DUF2811)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.1      0.26   4.6e+03       9      21 ..     362     374 ..     360     375 .. 0.83
   2 ?   13.5   0.1   3.7e-06     0.066      13      56 ..     446     487 ..     433     488 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.26
                            DUF2811   9 eLheslkkfleth 21 
                                        +L++s++ +l ++
  gene2535|gene2535|rna2535|rna2535 362 HLFSSMRLYLSKN 374
                                        68999*9999875 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 3.7e-06
                            DUF2811  13 slkkflethpnWDqdrllqaALslFLlqngssdravarvYletL 56 
                                        slk+++ +h n+D   + qa + +FLl n+++++a +  Yl  +
  gene2535|gene2535|rna2535|rna2535 446 SLKNYISKHYNYDVGTVDQA-I-TFLLSNNDKKNAFSLKYLSVM 487
                                        8*************998776.4.7***********999999765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (500 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       878  (0.0489709); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.24s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 3583.74
//
Query:       gene2536|gene2536|rna2536|rna2536  [L=186]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.2e-27   96.2   0.0    2.6e-27   96.0   0.0    1.1  1  Ham1p_like  Ham1 family
  ------ inclusion threshold ------
      0.036   14.1   0.4        0.5   10.4   0.1    2.0  2  DUF1638     Protein of unknown function (DUF1638)
      0.084   13.1   0.2       0.18   12.1   0.2    1.5  2  ARTD15_N    ARTD15 N-terminal domain


Domain annotation for each model (and alignments):
>> Ham1p_like  Ham1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.0   0.0   4.3e-31   2.6e-27       2     184 ..       4     170 ..       3     173 .. 0.87

  Alignments for each domain:
  == domain 1  score: 96.0 bits;  conditional E-value: 4.3e-31
                                        EEC-S-HHHHHHHHHHTTTECCCE.EECCCCEE----BSSSHHHHHHHHHHHHHH.H.TS-EEEEEEEEEEGGGTT CS
                         Ham1p_like   2 vfaTgNkgKlrevkeilaeellevkslkelelpeveEtqgtfeenalkKaraaae.a.glpvladDsgLevdaLng 75 
                                        +++++N +K++e+ke+l    + v+    +++  + + q+t++e +lkK +++ + + ++++l+d ++Le+  L+g
  gene2536|gene2536|rna2536|rna2536   4 FYFSSNVNKYNEIKELLP---FPVH----FQKARFIKQQQTLDETVLKKLKQLQNlYyHQAMLVDSTSLEIAGLHG 72 
                                        6789************93...3333....2334556899************9887535677*************** PP

                                        TBGGGTTTTTHTTCHHHHHHHHHHHHCTHTTS--EEEEEEEEEEEETTTTEEEEEEEEEEEEE-SS.--SSSSTTG CS
                         Ham1p_like  76 lPGvysarfagegaedeenlaklleeleeeeedrsArfvcvlaladpeeeeellfeGeveGeiveeprgeggfGyD 151
                                        lPG+y+  f+++g +   n++++++++      r+A+++ vl+la    +e +lf G ++G+ive  rge   G+D
  gene2536|gene2536|rna2536|rna2536  73 LPGPYIDAFLSLGYD---NIEEIVKKVG-----RRAKVKNVLGLALF--DEFILFDGVCDGTIVE-TRGEYSSGFD 137
                                        *********999988...*********5.....89******999885..6679***********6.9********* PP

                                        GGEEETT-SS.BTTTS.CHHHHHHSHHHHHHHHH CS
                         Ham1p_like 152 piFvpeegek.tfaelskeeknaiShRgkAlekl 184
                                        +iF+++  +  t+ae   +e++ iS Rg+++  l
  gene2536|gene2536|rna2536|rna2536 138 KIFMLDR-DCyTLAEHVFKERKVISPRGHSVFYL 170
                                        *****65.677*****************987655 PP

>> DUF1638  Protein of unknown function (DUF1638)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0      0.03   1.8e+02     114     142 ..      24      52 ..       4      71 .. 0.76
   2 ?   10.4   0.1   8.4e-05       0.5      27      86 ..     104     172 ..      77     181 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.03
                            DUF1638 114 kgYkrlvyidtgltddpeleeraeefaar 142
                                         +++++ +i++++t d+ + ++++++ + 
  gene2536|gene2536|rna2536|rna2536  24 VHFQKARFIKQQQTLDETVLKKLKQLQNL 52 
                                        38999999999999999999999988665 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 8.4e-05
                            DUF1638  27 d......ydqIllgYGlCggalagl...rsdecpveilkgddCislllgseeayaeelkdekgtffltp 86 
                                        +      +d+ +l+ G C g +++     s+    +++ + dC++l+    ++++ +  + + +f+l +
  gene2536|gene2536|rna2536|rna2536 104 NvlglalFDEFILFDGVCDGTIVETrgeYSSGFDKIFMLDRDCYTLAEHVFKERKVISPRGHSVFYLLK 172
                                        13444449***************99777677788899999*******9999987888777777999975 PP

>> ARTD15_N  ARTD15 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.2     3e-05      0.18      13      62 ..       2      55 ..       1      71 [. 0.81
   2 ?   -2.8   0.0       1.4   8.1e+03      34      56 ..      74      97 ..      70     106 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3e-05
                           ARTD15_N 13 klsLFvaAlqsyrrdsvlrPfPpqfises.ekdidaLlsvve.nlpslkel..l 62
                                       kl  F + ++ y   + l PfP +f +    k+ + L ++v  +l++l+ l  +
  gene2536|gene2536|rna2536|rna2536  2 KLFYFSSNVNKYNEIKELLPFPVHFQKARfIKQQQTLDETVLkKLKQLQNLyyH 55
                                       66679999********************99999999*88775599999988541 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.4
                           ARTD15_N 34 Ppqfises.ekdidaLlsvvenlp 56
                                       P+ +i+   +  +d+++++v++++
  gene2536|gene2536|rna2536|rna2536 74 PGPYIDAFlSLGYDNIEEIVKKVG 97
                                       666665555556666666666654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       648  (0.0361426); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1319.98
//
Query:       gene2537|gene2537|rna2537|rna2537  [L=481]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.6e-23   83.1   0.3    1.4e-22   80.1   0.2    2.5  2  Helicase_C  Helicase conserved C-terminal domain
    3.9e-17   62.6   0.0    1.3e-16   60.9   0.0    1.9  1  DEAD        DEAD/DEAH box helicase
    1.1e-08   35.2   0.0      3e-08   33.8   0.0    1.9  1  DUF4217     Domain of unknown function (DUF4217)
     0.0019   18.3   3.3      0.022   14.7   2.9    2.4  1  ResIII      Type III restriction enzyme, res subunit
     0.0046   17.0   1.2      0.021   14.9   0.3    2.3  2  PPO1_KFDV   Protein of unknown function (DUF_B2219)


Domain annotation for each model (and alignments):
>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.49   1.8e+03       6      59 ..      82     136 ..      77     157 .. 0.63
   2 !   80.1   0.2   3.8e-26   1.4e-22       2     110 ..     254     360 ..     253     361 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.49
                                        HHHHHHHTTTTSEEEEEESSHHHHHH....HHHHHHHTTSTEEEESTTSTHHHHHHHH CS
                         Helicase_C   6 llellkleeeggkilifvntidrlek....vklllekkgikvavlhgelpqnereeil 59 
                                        ll l     ++++ li+v+t + + +    +k ++++ gi++  l  +l ++  + +l
  gene2537|gene2537|rna2537|rna2537  82 LLPL---IMSERRGLIIVPTYELATQtydiAKAFTSRIGINAGQLCIDLRADIVICTL 136
                                        3334...366677777788887333333457777777788887777777666666555 PP

  == domain 2  score: 80.1 bits;  conditional E-value: 3.8e-26
                                        HHHHHHHHHHHTTTTSEEEEEESSHHHHHH.HHHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSS.EEEESGG CS
                         Helicase_C   2 kleallellkleeeggkilifvntidrlek.vklllekkgikvavlhgelpqnereeileqfnkgesd.vLiatdv 75 
                                        kl +++e+l ++++ +k+++f nti+++    +ll ++ +++v+++ g+l+q++r+ei+e++ + ++  vL++td 
  gene2537|gene2537|rna2537|rna2537 254 KLFIFIEFL-RKNRSKKMIVFFNTINSVVFyYNLL-KRMNFSVIAIFGRLNQRKRKEIMEKY-E-TVGgVLLCTDL 325
                                        566789999.99**************885445555.5568**********************.4.4445******* PP

                                        GTSSSTSTTESEEEESSSSSSHHHHHHHHTTSSST CS
                         Helicase_C  76 aerGidipkvnlVinfdlprnvtsyiqriGRtgRa 110
                                        ++rG d+++v+lV++f++ +++ +y++r+GR+gR 
  gene2537|gene2537|rna2537|rna2537 326 MSRGFDFKSVDLVVHFEPSFTLNNYVHRKGRAGRN 360
                                        **********************************6 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.9   0.0   3.6e-20   1.3e-16       2     171 ..      52     182 ..      51     187 .. 0.86

  Alignments for each domain:
  == domain 1  score: 60.9 bits;  conditional E-value: 3.6e-20
                                        HHHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSE CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               DEAD   2 diQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlr 77 
                                        ++Q +a++ + +g +v+++ +TGsGKTla+l+p++         ++ + li++Pt eLa qt++ +k f++ i+++
  gene2537|gene2537|rna2537|rna2537  52 EVQYKAYDKVFNGFNVMIQSNTGSGKTLAYLLPLI--------MSERRGLIIVPTYELATQTYDIAKAFTSRIGIN 119
                                        68*********************************........456799**********************86622 PP

                                        EEEEETTSSHHHHHHHHHTTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHC CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               DEAD  78 vlliiggvaardqlskldngvdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsdfinrilnqlpqit 153
                                                 a +    +d ++div+ t g++ ++       +++  f  +DEadr+l++  + f+n +++q+    
  gene2537|gene2537|rna2537|rna2537 120 ---------AGQLC--IDLRADIVICTLGKCREMY------MDDRVFCCIDEADRILEN--EVFLNGCFEQF---- 172
                                        .........22333..3459************977......66778************9..99999998888.... PP

                                        TTSTTTSEEEEEESSBS.H CS
                                        xxxxxxxxxxxxxxxxx.x RF
                               DEAD 154 cdgklqrqvivlSATlp.k 171
                                                 +++SAT+  k
  gene2537|gene2537|rna2537|rna2537 173 ---------VLVSATMDsK 182
                                        .........8889999844 PP

>> DUF4217  Domain of unknown function (DUF4217)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.8   0.0   8.4e-12     3e-08       2      61 .]     420     478 ..     419     478 .. 0.90

  Alignments for each domain:
  == domain 1  score: 33.8 bits;  conditional E-value: 8.4e-12
                            DUF4217   2 qqkleslcakdrdlkelAqkAfvsyvraYsvhlakeiFrvkkLdlealAksfGLleaPki 61 
                                        ++k+ ++++ d  l+++A++A +s++r Y     +  F+v++Ldl+++ + fG++++P+i
  gene2537|gene2537|rna2537|rna2537 420 THKIYEMVKNDVILHKMAVDALKSFLRIYEGNTGE-YFNVNSLDLNDITRTFGMKKMPRI 478
                                        578999*********************77665544.9*********************97 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   2.9   6.3e-06     0.022       6      79 ..      52     114 ..      37     270 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 6.3e-06
                                        HHHHHHHHHHT......TTSEEEEEESTTSTHHHHH.HHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTG CS
                             ResIII   6 eyQeeaienlleklkskrdkrglikmaTGtGKTlva.aklierllkkgkeekflflvprkslleqtleefkkfls 79 
                                        e Q +a +++ + +      +++i+  TG+GKTl + + li  +++    ++ l++vp+ +l  qt++  k f+s
  gene2537|gene2537|rna2537|rna2537  52 EVQYKAYDKVFNGF------NVMIQSNTGSGKTLAYlLPLI--MSE----RRGLIIVPTYELATQTYDIAKAFTS 114
                                        45555555554444......79***********97733333..233....377**************55544443 PP

>> PPO1_KFDV  Protein of unknown function (DUF_B2219)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.3   5.7e-06     0.021      26      52 ..       8      34 ..       2      41 .. 0.91
   2 ?   -0.3   0.0      0.31   1.1e+03      27      52 ..      43      70 ..      38      79 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 5.7e-06
                          PPO1_KFDV 26 eeeeevLviegIeidknvkvkfdVfvn 52
                                       +e+e v vi+g +i++++++kfdVf+ 
  gene2537|gene2537|rna2537|rna2537  8 DETEHVAVIDGFDIQPTKEIKFDVFIR 34
                                       689**********************96 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.31
                          PPO1_KFDV 27 eeeevLviegIeid..knvkvkfdVfvn 52
                                       e++ +Lv+++++++  ++v+  f+V++ 
  gene2537|gene2537|rna2537|rna2537 43 EKDGMLVMKEVQYKayDKVFNGFNVMIQ 70
                                       57789******99832455688999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (481 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       866  (0.0483016); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.48
# Mc/sec: 2992.41
//
Query:       gene2538|gene2538|rna2538|rna2538  [L=116]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
       0.17   11.7   0.1       0.28   10.9   0.1    1.3  1  She9_MDM33  She9 / Mdm33 family
        4.4    7.2  12.0    1.1e+02    2.8  12.0    2.1  1  DUF3487     Protein of unknown function (DUF3487)


Domain annotation for each model (and alignments):
>> She9_MDM33  She9 / Mdm33 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   3.2e-05      0.28     150     179 ..      64      93 ..      61     107 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 3.2e-05
                         She9_MDM33 150 twgtlvlmgvNvllfvvlqllvEPwkRrrL 179
                                         w t++  g+ v+lfv +++  E  +Rrr 
  gene2538|gene2538|rna2538|rna2538  64 EWYTFIPTGMFVFLFVAMIVSGEALRRRRH 93 
                                        599**********************99984 PP

>> DUF3487  Protein of unknown function (DUF3487)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8  12.0     0.012   1.1e+02      26      75 ..      37      91 ..       1      97 [. 0.74

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.012
                            DUF3487 26 lvla.glglvvglvlglllall....vgslaliptialllvllvvlvggkllarl 75
                                       +v+a ++ +v++++l  +++++    v+++++ipt++++ +++ ++v g++l+r 
  gene2538|gene2538|rna2538|rna2538 37 GVIAfSILVVFYILLVAPFLMIyygvVEWYTFIPTGMFVFLFVAMIVSGEALRRR 91
                                       44442222233333333333322333999**********************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1149  (0.0640861); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.31s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 733.37
//
Query:       gene2539|gene2539|rna2539|rna2539  [L=185]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    5.1e-43  147.2   0.0    5.7e-43  147.0   0.0    1.0  1  Ham1p_like  Ham1 family


Domain annotation for each model (and alignments):
>> Ham1p_like  Ham1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  147.0   0.0   3.2e-47   5.7e-43       1     186 [.       3     173 ..       3     174 .. 0.90

  Alignments for each domain:
  == domain 1  score: 147.0 bits;  conditional E-value: 3.2e-47
                                        EEEC-S-HHHHHHHHHHTTTECCCE.EECCCCEE----BSSSHHHHHHHHHHHHHHH....TS-EEEEEEEEEEGG CS
                         Ham1p_like   1 ivfaTgNkgKlrevkeilaeellevkslkelelpeveEtqgtfeenalkKaraaaea....glpvladDsgLevda 72 
                                        i+f+T+   K++e++ +l    +++ +l    + +++E+qgt e+++  K + a ++    + ++l+dD++L++d 
  gene2539|gene2539|rna2539|rna2539   3 IYFVTSSLSKFEEMRTLL---PINIYHL----KLKIDEVQGTSEDIINYKINFAKRKggldEVALLVDDTCLALDG 71 
                                        89***************9...5666655....44778**************98887544444449*********** PP

                                        GTTTBGGGTTTTTHTTCHHHHHHHHHHHHCTHTTS--EEEEEEEEEEEETTTTEEEEEEEEEEEEE-SS.--SSSS CS
                         Ham1p_like  73 LnglPGvysarfagegaedeenlaklleeleeeeedrsArfvcvlaladpeeeeellfeGeveGeiveeprgeggf 148
                                        L+g+PGvy++ f++ g++   n++ +++++      r+A++ c lal+ +  +++++f+G+v+G+iv+  rg ++f
  gene2539|gene2539|rna2539|rna2539  72 LHGFPGVYVKDFLKIGTD---NIEDIVQKVG-----RNATASCHLALYCN--NKVKTFSGHVKGQIVP-HRGGRQF 136
                                        ************999988...*********5.....89********9984..6669***********7.8****** PP

                                        TTGGGEEETT-SSBTTTS.CHHHHHHSHHHHHHHHHHH CS
                         Ham1p_like 149 GyDpiFvpeegektfaelskeeknaiShRgkAleklle 186
                                        G+D+iF++ +g+ktf+e++++ekn++ShRg A ++++e
  gene2539|gene2539|rna2539|rna2539 137 GFDSIFQV-DGNKTFSEMTMDEKNQVSHRGMACKAMVE 173
                                        ********.7799***********************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       462  (0.0257683); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.48
# Mc/sec: 1149.33
//
Query:       gene254|gene254|rna254|rna254  [L=956]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (956 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       642  (0.0358079); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.72u 0.30s 00:00:01.02 Elapsed: 00:00:00.49
# Mc/sec: 5869.67
//
Query:       gene2540|gene2540|rna2540|rna2540  [L=159]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       845  (0.0471303); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.29s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1129.96
//
Query:       gene2541|gene2541|rna2541|rna2541  [L=518]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      5e-49  166.1   0.1    9.8e-46  155.5   0.0    2.8  2  AAA              ATPase family associated with various cellul
    2.7e-15   55.9   0.0    5.1e-07   29.4   0.0    2.6  2  AAA_lid_3        AAA+ lid domain
    2.8e-09   37.1   0.0    5.8e-06   26.4   0.0    2.7  2  AAA_14           AAA domain
    9.6e-08   32.6   0.1    0.00034   21.0   0.0    3.5  4  AAA_16           AAA ATPase domain
    2.3e-07   30.7   0.0    5.7e-06   26.2   0.0    2.8  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    1.4e-06   28.4   0.0    6.1e-05   23.0   0.0    3.1  2  AAA_5            AAA domain (dynein-related subfamily)
    4.1e-06   27.0   0.0    1.1e-05   25.6   0.0    1.7  1  AAA_2            AAA domain (Cdc48 subfamily)
    1.2e-05   25.6   1.1     0.0039   17.5   0.0    3.2  3  AAA_22           AAA domain
    2.5e-05   24.5   0.0    0.00027   21.1   0.0    2.2  2  AAA_33           AAA domain
    2.9e-05   24.6   0.3     0.0011   19.5   0.0    2.8  3  AAA_18           AAA domain
      9e-05   22.3   0.0    0.00043   20.1   0.0    2.0  2  AAA_24           AAA domain
     0.0002   21.7   0.0     0.0015   18.9   0.0    2.3  2  RNA_helicase     RNA helicase
    0.00029   20.8   0.1      0.011   15.7   0.0    2.7  2  NACHT            NACHT domain
    0.00039   19.9   0.9       0.94    8.8   0.0    4.1  4  TniB             Bacterial TniB protein
    0.00043   19.7   0.4     0.0013   18.1   0.1    2.0  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    0.00045   19.5   0.0      0.027   13.6   0.0    2.4  2  DUF815           Protein of unknown function (DUF815)
    0.00076   19.5   0.0     0.0055   16.7   0.0    2.1  2  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
     0.0011   19.0   0.5       0.06   13.2   0.0    2.9  3  ATPase_2         ATPase domain predominantly from Archaea
     0.0012   18.6   0.0     0.0041   16.9   0.0    2.0  1  IstB_IS21        IstB-like ATP binding protein
     0.0023   17.6   0.1      0.085   12.4   0.1    2.7  2  AAA_25           AAA domain
     0.0045   17.5   0.0       0.18   12.3   0.0    2.6  2  ABC_tran         ABC transporter
     0.0053   16.0   0.0      0.015   14.5   0.0    1.8  2  TIP49            TIP49 P-loop domain
     0.0062   16.8   0.0      0.012   15.8   0.0    1.5  1  AAA_28           AAA domain
     0.0065   16.2   0.0      0.016   14.9   0.0    1.7  1  Viral_helicase1  Viral (Superfamily 1) RNA helicase
     0.0073   15.2   0.6        2.1    7.1   0.1    2.6  3  PPV_E1_C         Papillomavirus helicase
     0.0082   15.3   0.0      0.032   13.3   0.0    1.9  2  Parvo_NS1        Parvovirus non-structural protein NS1
     0.0099   15.4   0.0       0.44   10.0   0.0    2.7  2  AAA_7            P-loop containing dynein motor region
  ------ inclusion threshold ------
      0.013   14.9   2.1       0.14   11.5   0.1    3.3  5  ATPase           KaiC
      0.017   15.0   0.0      0.081   12.7   0.0    2.0  2  Bac_DnaA         Bacterial dnaA  protein
      0.018   14.9   0.0      0.061   13.2   0.0    1.8  1  SNAD1            Secreted Novel AID/APOBEC-like Deaminase 1
      0.045   14.2   0.2       0.31   11.5   0.0    2.3  2  AAA_23           AAA domain
      0.052   13.7   0.0       0.15   12.2   0.0    1.8  1  Sigma54_activ_2  Sigma-54 interaction domain
      0.059   13.1   0.0       0.55    9.9   0.0    2.6  2  Sigma54_activat  Sigma-54 interaction domain
       0.12   12.8   0.1       0.86   10.0   0.0    2.4  2  AAA_17           AAA domain
       0.12   12.2   0.0       0.23   11.3   0.0    1.5  1  AAA_3            ATPase family associated with various cellul
       0.23   11.4   1.4       0.47   10.4   0.1    2.2  1  HU-CCDC81_bac_2  CCDC81-like prokaryotic HU domain 2


Domain annotation for each model (and alignments):
>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.0    0.0086       4.3       1      29 [.      91     119 ..      91     189 .. 0.77
   2 !  155.5   0.0     2e-48   9.8e-46       1     132 []     310     438 ..     310     438 .. 0.98

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0086
                                        EEEESSTTSSHHHHHHHHHHHHTHEEEEE CS
                                AAA   1 vllyGppGtGKTllakavakelgveflei 29 
                                        +ll+G + tGK  + k+v+ e +v+fle 
  gene2541|gene2541|rna2541|rna2541  91 LLLVGAKNTGKRFFLKSVCVEYNVNFLES 119
                                        69***********************9985 PP

  == domain 2  score: 155.5 bits;  conditional E-value: 2e-48
                                        EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTT CS
                                AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksrsg 76 
                                        +llyGppG+GKT+la+a+a++l  +f+++ g+el++kyvg++ek++re+f++a++++ p++lf+DEid+l+++r  
  gene2541|gene2541|rna2541|rna2541 310 ILLYGPPGCGKTMLARAIANTLFCNFISVRGPELVNKYVGDTEKEMREVFNRARNQE-PCVLFFDEIDSLCSRR-- 382
                                        69****************************************************998.****************.. PP

                                        CCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETTS CS
                                AAA  77 seseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieiel 132
                                        +++++++r+vnq+lt ldg ++k +kv+++gatnr++ ld+a+lr gRfd++ie++l
  gene2541|gene2541|rna2541|rna2541 383 TDNDFQTRIVNQMLTLLDGIDDK-GKVFIVGATNRMHALDSAILRpGRFDKIIEVPL 438
                                        99********************6.77****************************985 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.0   5.9e-08   2.9e-05       1      39 [.     219     258 ..     219     267 .. 0.91
   2 !   29.4   0.0     1e-09   5.1e-07      11      43 ..     467     503 ..     466     505 .. 0.79

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 5.9e-08
                          AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrrgik.eit 39 
                                        +vdl eLA++T+Gy   Dl +lc  Aa  A+ ++++ ei+
  gene2541|gene2541|rna2541|rna2541 219 NVDLGELAKLTPGYLPIDLHNLCVSAASSAIIDNRQvEIN 258
                                        7******************************998874465 PP

  == domain 2  score: 29.4 bits;  conditional E-value: 1e-09
                          AAA_lid_3  11 TeGySGADlaalcreAallAlrrg...ike.itmedf 43 
                                        ++G++GAD+a l+re+al Al+ +   +k  +++ df
  gene2541|gene2541|rna2541|rna2541 467 MDGFTGADIAGLVRESALFALKNDfmnEKLvVGKNDF 503
                                        69********************973324445777776 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.0    0.0064       3.2       2      66 ..      88     154 ..      87     196 .. 0.76
   2 !   26.4   0.0   1.2e-08   5.8e-06       5     129 ..     310     442 ..     307     443 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0064
                             AAA_14   2 rkilvitGaRrvGKTtllkqlikellvkkesilyinldderd.....kkladpekllelileklkeekkt 66 
                                        rk l+++Ga+ +GK ++lk +  e+     ++l+  +d+e+d     +k+ d e  l ++ ++l++ek++
  gene2541|gene2541|rna2541|rna2541  88 RKSLLLVGAKNTGKRFFLKSVCVEYN---VNFLESYVDNEKDvcnayRKALDMEPCLLYLANQLTNEKEK 154
                                        57899****************99988...89999999999996655422333334455555555553443 PP

  == domain 2  score: 26.4 bits;  conditional E-value: 1.2e-08
                             AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqev.... 76 
                                        +++ G+  +GKT+l++ ++++l+    +++ +   +  +k   d+ek ++++++++++++  +lf+DEi  +    
  gene2541|gene2541|rna2541|rna2541 310 ILLYGPPGCGKTMLARAIANTLF---CNFISVRGPELVNKYVGDTEKEMREVFNRARNQEPCVLFFDEIDSLcsrr 382
                                        6899***************9999...6666666665555666677767777777766678999********99*** PP

                             AAA_14  77 ..........pewekalkslvd..egknldvivtGSnskllskeiatslagrvaeielyplsfaE 129
                                                  +     +  l+d  + ++++v++ G  + +   + a    gr ++i   pl  +E
  gene2541|gene2541|rna2541|rna2541 383 tdndfqtrivN----QMLTLLDgiD-DKGKVFIVGATNRMHALDSAILRPGRFDKIIEVPLPTRE 442
                                        **988844433....4444444322.3569********999999999999999988877776665 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0       1.4   7.1e+02      25      51 ..      89     115 ..      79     274 .. 0.73
   2 !   21.0   0.0   6.9e-07   0.00034      16      48 ..     299     331 ..     294     345 .. 0.85
   3 ?    6.1   0.0     0.027        14     122     146 ..     354     384 ..     349     411 .. 0.71
   4 ?   -1.8   0.0       7.3   3.6e+03       2      17 ..     438     453 ..     437     457 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 1.4
                             AAA_16  25 elvllsGesGvGKsslvrellralekd 51 
                                         ++ll+G++ +GK   ++++  +++ +
  gene2541|gene2541|rna2541|rna2541  89 KSLLLVGAKNTGKRFFLKSVCVEYNVN 115
                                        689999999999998888877555444 PP

  == domain 2  score: 21.0 bits;  conditional E-value: 6.9e-07
                             AAA_16  16 lervrsgrpelvllsGesGvGKsslvrellral 48 
                                        ++r   +r++ +ll+G++G+GK+ l+r++++ l
  gene2541|gene2541|rna2541|rna2541 299 FKRMGISRTSGILLYGPPGCGKTMLARAIANTL 331
                                        667778899*******************99865 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.027
                             AAA_16 122 llkrllallsrderplvlvlDdlq.......w 146
                                        ++++ ++++++ ++p vl++D+++       +
  gene2541|gene2541|rna2541|rna2541 354 EMREVFNRARN-QEPCVLFFDEIDslcsrrtD 384
                                        57788899999.999********955555442 PP

  == domain 4  score: -1.8 bits;  conditional E-value: 7.3
                             AAA_16   2 lvGReeeleqLlsale 17 
                                        l+ Ree+++ L+ +++
  gene2541|gene2541|rna2541|rna2541 438 LPTREEQIDILRKCVR 453
                                        788********99987 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.1      0.96   4.8e+02      64     103 ..     245     285 ..     236     292 .. 0.80
   2 !   26.2   0.0   1.1e-08   5.7e-06      35      97 ..     309     379 ..     300     426 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.96
                             RuvB_N  64 tsgPvl.ekagdlaalltnleekdvlfideihrlsraveev 103
                                        +s+ ++ +++ ++  +l nl++++ + +d+i  l  + +e+
  gene2541|gene2541|rna2541|rna2541 245 ASSAIIdNRQVEINDFLRNLTNENKITLDNIGALYAVKKEI 285
                                        455555257899*******************9998877776 PP

  == domain 2  score: 26.2 bits;  conditional E-value: 1.1e-08
                             RuvB_N  35 hvllyGpPGlGkttlakiiakelgvklkitsgPvl......ekagdlaalltnleekd..vlfideihrls 97 
                                         +llyGpPG Gkt la+ ia+ l  ++ +  gP l      + ++++  ++++ ++++  vlf dei  l 
  gene2541|gene2541|rna2541|rna2541 309 GILLYGPPGCGKTMLARAIANTLFCNFISVRGPELvnkyvgDTEKEMREVFNRARNQEpcVLFFDEIDSLC 379
                                        59*******************************88332222335678888887776666699****98875 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0      0.67   3.3e+02       2      27 ..      91     116 ..      90     126 .. 0.84
   2 !   23.0   0.0   1.2e-07   6.1e-05       2      77 ..     310     378 ..     309     416 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.67
                                        EEEE--SSSSHHHHHHHGGGGBS--E CS
                              AAA_5   2 vlLvGppGtgKselaerlaaalnrev 27 
                                        +lLvG++ tgK+++ ++++  +n ++
  gene2541|gene2541|rna2541|rna2541  91 LLLVGAKNTGKRFFLKSVCVEYNVNF 116
                                        89************999988777665 PP

  == domain 2  score: 23.0 bits;  conditional E-value: 1.2e-07
                                        EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------..G-SEEEEESGG CS
                              AAA_5   2 vlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar..egeilvlDEve 75 
                                        +lL GppG+gK++la+ +a  l +++  v +++      l+ ++    g+t+ +  ++ + ar  e+++l++DE++
  gene2541|gene2541|rna2541|rna2541 310 ILLYGPPGCGKTMLARAIANTLFCNFISVRGPE------LVNKYV---GDTEKEMREVFNRARnqEPCVLFFDEID 376
                                        89********************99999999987......999998...78888888888888889999999***99 PP

                                        G- CS
                              AAA_5  76 ra 77 
                                         +
  gene2541|gene2541|rna2541|rna2541 377 SL 378
                                        65 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.0   2.3e-08   1.1e-05       4     105 ..     308     401 ..     305     407 .. 0.82

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 2.3e-08
                                        --EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETG CS
                              AAA_2   4 isilllgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEi 77 
                                        + ill gp g+Gkt+la+a+a++lf+    ++i +   el      + + + ++  ++  ++a ++   ++++DEi
  gene2541|gene2541|rna2541|rna2541 308 SGILLYGPPGCGKTMLARAIANTLFC----NFISVRGPELVN----KYVGDTEKEMREVFNRARNQEpcVLFFDEI 375
                                        6699*********************8....***********9....66666666666666555544456******* PP

                                        GG-------------HHHHHHHHHHHH- CS
                              AAA_2  78 dKihpkessgadvSregVqrdLLqileg 105
                                        d  ++  + + +  ++ +++ +L +l+g
  gene2541|gene2541|rna2541|rna2541 376 DSLCS--RRTDNDFQTRIVNQMLTLLDG 401
                                        *****..555555677899999999997 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0       2.5   1.3e+03       6      38 ..      89     136 ..      86     191 .. 0.51
   2 !   17.5   0.0   7.8e-06    0.0039       6      29 ..     308     331 ..     302     347 .. 0.87
   3 ?    5.1   0.1     0.053        26      74     131 ..     351     414 ..     332     420 .. 0.65

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 2.5
                             AAA_22   6 gilvvtGesGtGKTtllrrlleqldeeakaee................e 38 
                                        ++l+++G + tGK + l+ +  +++ +++ e                  
  gene2541|gene2541|rna2541|rna2541  89 KSLLLVGAKNTGKRFFLKSVCVEYN-VNFLESyvdnekdvcnayrkalD 136
                                        5677777777776555555544442.22222223323333333333332 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 7.8e-06
                             AAA_22   6 gilvvtGesGtGKTtllrrlleql 29 
                                        + ++++G++G+GKT+l+r ++++l
  gene2541|gene2541|rna2541|rna2541 308 SGILLYGPPGCGKTMLARAIANTL 331
                                        5589****************9987 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.053
                             AAA_22  74 sseellealeqalraravielliiDEaqhlr..s......eealeeLrsllnlsrkgvqliLvGtp 131
                                        +++e++e +++a ++     +l  DE++ l   +       +++++  +ll+  +++ ++++vG +
  gene2541|gene2541|rna2541|rna2541 351 TEKEMREVFNRARNQEP--CVLFFDEIDSLCsrRtdndfqTRIVNQMLTLLDGIDDKGKVFIVGAT 414
                                        55555555555555554..5*********9865144555555555555555555666666666665 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0      0.94   4.7e+02       3      33 ..      92     131 ..      91     188 .. 0.70
   2 !   21.1   0.0   5.5e-07   0.00027       2      84 ..     310     420 ..     310     444 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.94
                             AAA_33   3 llvGlpGsGKstlaerllkklgavllssdt.........l 33 
                                        llvG++ +GK +++++++ +  + +l+s +         +
  gene2541|gene2541|rna2541|rna2541  92 LLVGAKNTGKRFFLKSVCVEYNVNFLESYVdnekdvcnaY 131
                                        799**************99988888887665445544442 PP

  == domain 2  score: 21.1 bits;  conditional E-value: 5.5e-07
                             AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlfgtdqqskt..........................dyt 49 
                                        +ll G+pG+GK+ la+ +++ l   ++ ++ ++l ++++g+ ++  +                            +
  gene2541|gene2541|rna2541|rna2541 310 ILLYGPPGCGKTMLARAIANTLFcnFISVRGPELVNKYVGDTEKEMRevfnrarnqepcvlffdeidslcsrrTDN 385
                                        6789***************999988888999997777777433333345666666667999999999999876555 PP

                             AAA_33  50 rvldrlyqilnelarkalsagrnvildatnlsrre 84 
                                        ++ +r+ +++  l++    +g+ +i+ atn++++ 
  gene2541|gene2541|rna2541|rna2541 386 DFQTRIVNQMLTLLDGIDDKGKVFIVGATNRMHAL 420
                                        67778888888999999999999999999999865 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.1      0.75   3.7e+02      51     104 ..     147     202 ..      92     206 .. 0.59
   2 ?   -1.4   0.0       6.6   3.3e+03      59     110 ..     255     302 ..     235     305 .. 0.72
   3 !   19.5   0.0   2.2e-06    0.0011       1      79 [.     310     411 ..     310     426 .. 0.75

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.75
                             AAA_18  51 rldedkldklldaleenssaleegknlvidghlaeleseaakdikk...vvLtaspe 104
                                        +l  +k +k+l ++e+n ++ ++ k l i ++ ++ + ++++ +     v L++++e
  gene2541|gene2541|rna2541|rna2541 147 QLTNEK-EKVLHEIEKNMEKVRDKKILTIFSCQSKAFIAENVSKMVtgeVALKTPDE 202
                                        333333.33333334433446678999999999999988777666679999999987 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 6.6
                             AAA_18  59 klldaleenssaleegknlvidghlaeleseaakdikkvvLtaspeelleRl 110
                                        + ++ + +   +l++++ + +d + a +   + ++++ + L +   e ++R+
  gene2541|gene2541|rna2541|rna2541 255 VEINDFLR---NLTNENKITLDNIGALYAVKKEIEMN-ILLPLQFPEKFKRM 302
                                        33333333...46788888999999988888888888.88888888888776 PP

  == domain 3  score: 19.5 bits;  conditional E-value: 2.2e-06
                             AAA_18   1 IlltGtpGvGKttlakeLskrlgf.....................gvnlrdvakenglllevdpe.aldeskrlde 54 
                                        Ill G+pG+GKt la+++++ l +                      +++   a++ +++  +++e +   s+r d 
  gene2541|gene2541|rna2541|rna2541 310 ILLYGPPGCGKTMLARAIANTLFCnfisvrgpelvnkyvgdtekeMREVFNRARNQEPCVLFFDEiDSLCSRRTDN 385
                                        99****************9998225699999999999999999999999999999999999999995555555555 PP

                             AAA_18  55 dkldklldaleenss.aleegknlvi 79 
                                        d++ ++++++    +   ++gk+ ++
  gene2541|gene2541|rna2541|rna2541 386 DFQTRIVNQMLTLLDgIDDKGKVFIV 411
                                        55555555554444333346776665 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       2.5   1.3e+03       4      26 ..      90     114 ..      88     174 .. 0.80
   2 !   20.1   0.0   8.6e-07   0.00043       5      33 ..     310     353 ..     307     404 .. 0.66

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 2.5
                             AAA_24   4 kiliyGpsgiGKTtlakel..gpkp 26 
                                        ++l++G   +GK  ++k+   ++++
  gene2541|gene2541|rna2541|rna2541  90 SLLLVGAKNTGKRFFLKSVcvEYNV 114
                                        6889999999999998887664444 PP

  == domain 2  score: 20.1 bits;  conditional E-value: 8.6e-07
                             AAA_24   5 iliyGpsgiGKTtlakelgpkplfi................dtek 33 
                                        il+yGp+g GKT+la+ +  ++lf+                dtek
  gene2541|gene2541|rna2541|rna2541 310 ILLYGPPGCGKTMLARAI-ANTLFCnfisvrgpelvnkyvgDTEK 353
                                        89****************.******55555555555555554444 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0       3.5   1.8e+03       2      23 ..      92     113 ..      91     135 .. 0.72
   2 !   18.9   0.0   2.9e-06    0.0015       1      58 [.     310     374 ..     310     410 .. 0.63

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 3.5
                       RNA_helicase   2 wlyGpsgeGKStlakeLakall 23 
                                        +l+G++++GK  + k+++ +  
  gene2541|gene2541|rna2541|rna2541  92 LLVGAKNTGKRFFLKSVCVEYN 113
                                        689999****999999776655 PP

  == domain 2  score: 18.9 bits;  conditional E-value: 2.9e-06
                       RNA_helicase   1 iwlyGpsgeGKStlakeLakallkkl......klkkkdsvys...rnpeddfwdgYt.gqevvvidDf 58 
                                        i+lyGp+g+GK++la+ +a++l  ++      +     + y+    +   ++++  + ++++v+++D 
  gene2541|gene2541|rna2541|rna2541 310 ILLYGPPGCGKTMLARAIANTLFCNFisvrgpE---LVNKYVgdtEKEMREVFNRARnQEPCVLFFDE 374
                                        789******************997777775542...33333301133444455555546667766664 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   2.1e-05     0.011       3      24 ..     310     331 ..     308     336 .. 0.91
   2 ?    1.8   0.1      0.39     2e+02      66      99 ..     352     384 ..     341     410 .. 0.65

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.1e-05
                                        EEEEC-TTTCHHHHHHHHHHHH CS
                              NACHT   3 vilqGeaGsGKTtLlqklalaw 24 
                                        ++l G++G+GKT+L++ +a ++
  gene2541|gene2541|rna2541|rna2541 310 ILLYGPPGCGKTMLARAIANTL 331
                                        789***************9876 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.39
                                        -SSS-CCHHHHCCSCCCEEEEEE-STT-SS-TCH CS
                              NACHT  66 aapvsevwavllelperlLlilDglDelvtdlgq 99 
                                        +++ +e + ++++++e  +l +D +D l++    
  gene2541|gene2541|rna2541|rna2541 352 EKEMRE-VFNRARNQEPCVLFFDEIDSLCSRRTD 384
                                        555555.456778888888888888888765444 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0      0.13        66      36      60 ..      89     113 ..      76     199 .. 0.75
   2 ?    0.7   0.0      0.58   2.9e+02     137     165 ..     252     280 ..     235     285 .. 0.84
   3 !    8.8   0.0    0.0019      0.94      31      54 ..     303     326 ..     293     331 .. 0.84
   4 ?    2.2   0.0       0.2     1e+02     104     138 ..     351     385 ..     341     433 .. 0.75

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.13
                               TniB  36 pnlllvGdsnnGKtmivekFarlhp 60 
                                        ++lllvG  n+GK   +++ + +++
  gene2541|gene2541|rna2541|rna2541  89 KSLLLVGAKNTGKRFFLKSVCVEYN 113
                                        799**********988877666555 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.58
                               TniB 137 rkqreflnalksLgnelkipivlvGteea 165
                                        ++q e+  +l++L+ne ki++  +G   a
  gene2541|gene2541|rna2541|rna2541 252 NRQVEINDFLRNLTNENKITLDNIGALYA 280
                                        567888999**********9988887655 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.0019
                               TniB  31 krkrmpnlllvGdsnnGKtmivek 54 
                                          +r++ +ll+G++ +GKtm+++ 
  gene2541|gene2541|rna2541|rna2541 303 GISRTSGILLYGPPGCGKTMLARA 326
                                        56899****************986 PP

  == domain 4  score: 2.2 bits;  conditional E-value: 0.2
                               TniB 104 vskleqqvlrllrelkvrvLiiDEihnllagsark 138
                                        ++k  ++v +  r+ ++ vL +DEi++l + + ++
  gene2541|gene2541|rna2541|rna2541 351 TEKEMREVFNRARNQEPCVLFFDEIDSLCSRRTDN 385
                                        566677788888999999********998655443 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.1   2.6e-06    0.0013      25      45 ..     310     330 ..     301     340 .. 0.87
   2 ?   -3.1   0.0       8.5   4.3e+03     109     184 ..     369     390 ..     355     400 .. 0.56

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 2.6e-06
                       Mg_chelatase  25 lllvGppGsGKtmlakrlpsl 45 
                                        +ll+GppG+GKtmla+++++ 
  gene2541|gene2541|rna2541|rna2541 310 ILLYGPPGCGKTMLARAIANT 330
                                        89**************99765 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 8.5
                       Mg_chelatase 109 vLfLDElpefkrkvlevLRePledgevtisrakakvefparfqlvaamNpcpcgklkdkekectcsekeierYlsk 184
                                        vLf+DE+                                                         cs ++ ++++++
  gene2541|gene2541|rna2541|rna2541 369 VLFFDEID------------------------------------------------------SLCSRRTDNDFQTR 390
                                        44444443......................................................34555555555555 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0     0.091        45      53      82 ..      88     117 ..      77     133 .. 0.87
   2 !   13.6   0.0   5.4e-05     0.027      14     155 ..     259     420 ..     247     426 .. 0.65

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.091
                             DUF815  53 annvLLwGarGtGKSslvkallneyaeegL 82 
                                         + +LL+Ga+ tGK   +k++  ey+ + L
  gene2541|gene2541|rna2541|rna2541  88 RKSLLLVGAKNTGKRFFLKSVCVEYNVNFL 117
                                        5789******************99987765 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 5.4e-05
                             DUF815  14 galepveevdevklddLvgidkqkealvent...eqfleg......lpannvLLwGarGtGKSslvkallneyaee 80 
                                        + l+ +++ ++++ld++  + + k+++  n+    qf e+       +++ +LL+G  G+GK  l +a+ n++  +
  gene2541|gene2541|rna2541|rna2541 259 DFLRNLTNENKITLDNIGALYAVKKEIEMNIllpLQFPEKfkrmgiSRTSGILLYGPPGCGKTMLARAIANTLFCN 334
                                        557777778888888888888888888888733324444311111245788*********************9888 PP

                             DUF815  81 g..Lrlievekedlkelpklvellr...erperfilfvDD...LsFeeeeeey.....ksLksvLeGsleakpenv 143
                                           +r  e+ ++ + + +k ++++    +++e ++lf D    L+  ++++++      ++ ++L+G ++ k  +v
  gene2541|gene2541|rna2541|rna2541 335 FisVRGPELVNKYVGDTEKEMREVFnraRNQEPCVLFFDEidsLCSRRTDNDFqtrivNQMLTLLDG-IDDK-GKV 408
                                        7556667777777777666666554122334568888654222777777777755444566777777.4444.445 PP

                             DUF815 144 liyaTsNrRhLl 155
                                         i   +Nr h l
  gene2541|gene2541|rna2541|rna2541 409 FIVGATNRMHAL 420
                                        555555777755 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0       2.3   1.1e+03      19      46 ..      88     115 ..      75     122 .. 0.77
   2 !   16.7   0.0   1.1e-05    0.0055      19      61 ..     307     349 ..     286     359 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 2.3
                                        TEEEEEEESTTSSHHHHHHHHHHHTT-- CS
                               TsaE  19 gdvilLeGdLGaGKTtlvrglakalgve 46 
                                        ++ +lL G   +GK  + ++++ +++v+
  gene2541|gene2541|rna2541|rna2541  88 RKSLLLVGAKNTGKRFFLKSVCVEYNVN 115
                                        5669999************999888775 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 1.1e-05
                                        TEEEEEEESTTSSHHHHHHHHHHHTT--..----TTTTSEEEEEE CS
                               TsaE  19 gdvilLeGdLGaGKTtlvrglakalgve..evkSPTFtlveeYel 61 
                                        ++ ilL+G+ G+GKT+l+r++a++l ++  +v+ P   lv++Y  
  gene2541|gene2541|rna2541|rna2541 307 TSGILLYGPPGCGKTMLARAIANTLFCNfiSVRGP--ELVNKYVG 349
                                        4459*********************9987888888..68888865 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.2      0.47   2.3e+02      22     100 ..      90     181 ..      83     196 .. 0.61
   2 !   13.2   0.0   0.00012      0.06      23      44 ..     310     331 ..     302     338 .. 0.88
   3 ?   -0.3   0.0       1.7   8.4e+02     101     149 ..     350     399 ..     333     420 .. 0.59

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.47
                           ATPase_2  22 iyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefie..............eeeekkklekal. 82 
                                         +++ G ++ GK  +lk +  +  + ++   y+++ +++ +++ +  ++              e   k+k+   + 
  gene2541|gene2541|rna2541|rna2541  90 SLLLVGAKNTGKRFFLKSVCVEY-NVNFLESYVDNEKDVCNAYRKA-LDmepcllylanqltnE---KEKVLHEIe 160
                                        56778999999999998888887.7788999998876665555444.45568888887775331...222233332 PP

                           ATPase_2  83 ..giavpkaeleeilk.eksk 100
                                          +++v+ +++ +i++ + ++
  gene2541|gene2541|rna2541|rna2541 161 knMEKVRDKKILTIFScQSKA 181
                                        223555555555666554444 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 0.00012
                           ATPase_2  23 yfiYGpegsGKtaLlkeiienl 44 
                                        +++YGp g+GKt L + i++ l
  gene2541|gene2541|rna2541|rna2541 310 ILLYGPPGCGKTMLARAIANTL 331
                                        789**************99876 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 1.7
                           ATPase_2 101 lvfkaielllekikkkgkk..iiiiiDelqklidlgln..gaellvkeLlnli 149
                                        + +k + ++++  ++   +   ++++De+  l +   +   ++  v+++l+l+
  gene2541|gene2541|rna2541|rna2541 350 DTEKEMREVFNRARN---QepCVLFFDEIDSLCSRRTDndFQTRIVNQMLTLL 399
                                        444444444444433...24589999999988755554223455566666555 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   8.3e-06    0.0041      44      78 ..     304     338 ..     299     414 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 8.3e-06
                          IstB_IS21  44 iekkenivllGpsGvGKshlaialgveavraglsv 78 
                                        i++  +i+l Gp+G GK+ la a++     + +sv
  gene2541|gene2541|rna2541|rna2541 304 ISRTSGILLYGPPGCGKTMLARAIANTLFCNFISV 338
                                        678899******************99876665555 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0      0.31   1.5e+02      28      56 ..      84     111 ..      66     117 .. 0.80
   2 !   12.4   0.1   0.00017     0.085      33      54 ..     307     328 ..     301     418 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.31
                             AAA_25  28 gllpagelallaGapgtGKttlaldlala 56 
                                        +l+p  +  ll+Ga  tGK +++ +++++
  gene2541|gene2541|rna2541|rna2541  84 NLVP-RKSLLLVGAKNTGKRFFLKSVCVE 111
                                        5555.556799********9999888875 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00017
                             AAA_25  33 gelallaGapgtGKttlaldla 54 
                                         + +ll+G+pg+GKt+la  +a
  gene2541|gene2541|rna2541|rna2541 307 TSGILLYGPPGCGKTMLARAIA 328
                                        56689************97766 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0      0.39   1.9e+02       5      96 ..      82     170 ..      79     228 .. 0.66
   2 !   12.3   0.0   0.00037      0.18       7      34 ..     303     330 ..     300     399 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.39
                                        EEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEET.TCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ABC_tran   5 slklkegekvaivGenGaGKStLlkllagllkpteGeilld.gkdlkeqeleslrkeigvlpqepqlfpeltvren 79 
                                         ++l + + + +vG   +GK  +lk ++ +++ +  e  +d +k    +  + +rk + + p    l ++lt++++
  gene2541|gene2541|rna2541|rna2541  82 RFNLVPRKSLLLVGAKNTGKRFFLKSVCVEYNVNFLESYVDnEK----DVCNAYRKALDMEPCLLYLANQLTNEKE 153
                                        57777778888888888888888888888887633333223122....3445677777777777777777777666 PP

                                        HHHTCHHHHHHHSTTGG CS
                                        xxxxxxxxxxxxxxxxx RF
                           ABC_tran  80 esdeeiekalsklglke 96 
                                        +   eiek ++k+++k+
  gene2541|gene2541|rna2541|rna2541 154 KVLHEIEKNMEKVRDKK 170
                                        66666666666666665 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00037
                                        EEETTSEEEEEESTTSSHHHHHHHHTTS CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ABC_tran   7 klkegekvaivGenGaGKStLlkllagl 34 
                                         +++ + + + G+ G+GK+ L++++a+ 
  gene2541|gene2541|rna2541|rna2541 303 GISRTSGILLYGPPGCGKTMLARAIANT 330
                                        6777788999***************975 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       8.8   4.4e+03     255     273 ..     152     170 ..     126     202 .. 0.59
   2 !   14.5   0.0     3e-05     0.015      51     103 ..     308     359 ..     298     411 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 8.8
                                        XXXXXXXXXXXXXXXXXXX CS
                              TIP49 255 teklreeinkkvakyveeg 273
                                        +ek+ +ei+k ++k +++ 
  gene2541|gene2541|rna2541|rna2541 152 KEKVLHEIEKNMEKVRDKK 170
                                        3344444444444433333 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 3e-05
                                        XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXX CS
                              TIP49  51 ravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkktev.ltqal 103
                                         ++Ll Gp+g Gkt la ai++ l     f+++ g e+    v  te  + + +
  gene2541|gene2541|rna2541|rna2541 308 SGILLYGPPGCGKTMLARAIANTLF--CNFISVRGPELVNKYVGDTEKeMREVF 359
                                        479********************98..89********99999999985233444 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   2.5e-05     0.012       2      39 ..     310     352 ..     309     375 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2.5e-05
                             AAA_28   2 ivitGgestGKTtlleaLaar....gypvv.pEaareileekl 39 
                                        i + G++++GKT l++a+a++     ++v  pE + +++ +  
  gene2541|gene2541|rna2541|rna2541 310 ILLYGPPGCGKTMLARAIANTlfcnFISVRgPELVNKYVGDTE 352
                                        7899***************999884444558888888886654 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   3.3e-05     0.016       4      71 ..     313     375 ..     310     381 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.3e-05
                    Viral_helicase1   4 hGvpGcGKStlirkllrts.liltvnrptaelltegkpklpnlsvrtvdsflmalvkstkgkililDEy 71 
                                         G pGcGK+ l r +++t  +++ ++r   el+++ + +++++  + ++ + ++  +     +l++DE+
  gene2541|gene2541|rna2541|rna2541 313 YGPPGCGKTMLARAIANTLfCNFISVRG-PELVNKYVGDTEKEMREVFNRARNQEPC-----VLFFDEI 375
                                        588***************9988888888.99****9999999988888877766554.....8999998 PP

>> PPV_E1_C  Papillomavirus helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1   0.1    0.0043       2.1     205     283 ..      22     109 ..      15     126 .. 0.61
   2 ?   -2.3   0.0         3   1.5e+03      35      94 ..     124     180 ..     113     190 .. 0.74
   3 ?    5.8   0.0      0.01       5.1     247     291 ..     294     336 ..     251     340 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0043
                           PPV_E1_C 205 kraemkkmsmse.wikkrlkevedegdWkei...vkflry....qgvelisfltalkefLkg..vPkknclvllGp 270
                                        k+a +++  +se +ik++lke ++ ++ ++    +k+l y     +  +i  l    e+L+   vP+k +l+l+G+
  gene2541|gene2541|rna2541|rna2541  22 KKASVTRSKISElYIKEHLKEENKIDSVHPRfssLKYLSYlkpfVHGSIIGPLFRTAEYLRFnlVPRK-SLLLVGA 96 
                                        56666666666556666666665444443320112333331111344677777788888874226776.58899** PP

                           PPV_E1_C 271 pntGkslfamsli 283
                                         ntGk +f +s+ 
  gene2541|gene2541|rna2541|rna2541  97 KNTGKRFFLKSVC 109
                                        ********99975 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 3
                           PPV_E1_C  35 seellealktlLkqhceylfvesraaeaglvlllllrfkaaksretvkklltsllnveel 94 
                                        ++++++a ++ L  +   l++ ++ ++ +  +l  ++ +++k r+   k + ++++++++
  gene2541|gene2541|rna2541|rna2541 124 EKDVCNAYRKALDMEPCLLYLANQLTNEKEKVLHEIEKNMEKVRD---KKILTIFSCQSK 180
                                        678889999999988888888888888888899999988888887...444455555555 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.01
                           PPV_E1_C 247 sfltalkefLkgvPkknclvllGppntGkslfamslikfLkGkvl 291
                                        +f  ++k+   g+ + + ++l+Gpp  Gk+++a ++ + L  + +
  gene2541|gene2541|rna2541|rna2541 294 QFPEKFKR--MGISRTSGILLYGPPGCGKTMLARAIANTLFCNFI 336
                                        44444444..37889999***************999988866665 PP

>> Parvo_NS1  Parvovirus non-structural protein NS1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       5.2   2.6e+03     111     128 ..      85     102 ..      80     109 .. 0.85
   2 !   13.3   0.0   6.5e-05     0.032     117     138 ..     310     331 ..     298     334 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 5.2
                          Parvo_NS1 111 lgkrntvwfyGpantGkt 128
                                        l++r  ++++G+ ntGk 
  gene2541|gene2541|rna2541|rna2541  85 LVPRKSLLLVGAKNTGKR 102
                                        679999**********96 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 6.5e-05
                          Parvo_NS1 117 vwfyGpantGktnlaeaIakav 138
                                        +++yGp+ +Gkt+la+aIa+++
  gene2541|gene2541|rna2541|rna2541 310 ILLYGPPGCGKTMLARAIANTL 331
                                        89*****************975 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0      0.22   1.1e+02      29      57 ..      84     112 ..      75     123 .. 0.78
   2 !   10.0   0.0   0.00089      0.44      30      57 ..     304     331 ..     297     397 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.22
                              AAA_7  29 llknkkpvllvGptGtGKtviikdllkkl 57 
                                         l  +k++llvG + tGK   +k+++ ++
  gene2541|gene2541|rna2541|rna2541  84 NLVPRKSLLLVGAKNTGKRFFLKSVCVEY 112
                                        5566899***********99999876655 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00089
                              AAA_7  30 lknkkpvllvGptGtGKtviikdllkkl 57 
                                        +++   +ll+Gp G+GKt++++ + ++l
  gene2541|gene2541|rna2541|rna2541 304 ISRTSGILLYGPPGCGKTMLARAIANTL 331
                                        6677889*************99987765 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       6.9   3.4e+03      19      35 ..      88     104 ..      85     112 .. 0.83
   2 ?    0.1   0.1      0.86   4.3e+02     136     190 ..     151     200 ..     142     209 .. 0.74
   3 ?   -2.3   0.0       4.6   2.3e+03     110     138 ..     256     284 ..     244     294 .. 0.68
   4 ?   11.5   0.1   0.00027      0.14      13      37 ..     301     325 ..     293     330 .. 0.86
   5 ?   -1.6   0.0       2.8   1.4e+03     118     153 ..     365     401 ..     340     420 .. 0.61

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 6.9
                             ATPase  19 grvvlitGepGtGKtif 35 
                                        +++ l++G   tGK +f
  gene2541|gene2541|rna2541|rna2541  88 RKSLLLVGAKNTGKRFF 104
                                        5778999*******887 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.86
                             ATPase 136 keavaReilrqlvrvlkklgvTailvsekssseeaaggygveefivdgvivLdlk 190
                                        +++++ +++ + ++ ++++++ +i+ ++    ++a+   +v++ +v+g + L+  
  gene2541|gene2541|rna2541|rna2541 151 EKEKVLHEIEKNMEKVRDKKILTIFSCQ----SKAFIAENVSK-MVTGEVALKTP 200
                                        4455556667777777888888888888....68999999999.99999999864 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 4.6
                             ATPase 110 elaeaikeika.krvviDsitglayeekea 138
                                        e+++ ++++   +++ +D+i++l y  k++
  gene2541|gene2541|rna2541|rna2541 256 EINDFLRNLTNeNKITLDNIGAL-YAVKKE 284
                                        55666666544388999999999.666655 PP

  == domain 4  score: 11.5 bits;  conditional E-value: 0.00027
                             ATPase  13 kgGipegrvvlitGepGtGKtifal 37 
                                          Gi + + +l++G pG+GKt++a 
  gene2541|gene2541|rna2541|rna2541 301 RMGISRTSGILLYGPPGCGKTMLAR 325
                                        579*******************985 PP

  == domain 5  score: -1.6 bits;  conditional E-value: 2.8
                             ATPase 118 ikakrvviDsitgl.ayeekeavaReilrqlvrvlkk 153
                                         +   +  D i++l +++++++   +i+ q+++ l +
  gene2541|gene2541|rna2541|rna2541 365 QEPCVLFFDEIDSLcSRRTDNDFQTRIVNQMLTLLDG 401
                                        4445555677777766666666666666666666543 PP

>> Bac_DnaA  Bacterial dnaA  protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       2.8   1.4e+03      34      82 ..     137     189 ..     110     209 .. 0.57
   2 ?   12.7   0.0   0.00016     0.081      37     180 ..     310     453 ..     301     468 .. 0.66

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 2.8
                                        S--EEEE-SSSSS..HHHHHHHHHHHHHHHSSSS-EEEE...EHHHHHHHHHHH CS
                           Bac_DnaA  34 ynPlfiygevGlG..ktHLlkaignevlenapelrvvYl...taeeFlnelvka 82 
                                        + P+++y    l   k  +l+ i++++++  ++++++ +   +++ F++e v+ 
  gene2541|gene2541|rna2541|rna2541 137 MEPCLLYLANQLTneKEKVLHEIEKNMEK-VRDKKILTIfscQSKAFIAENVSK 189
                                        45555555444432255566666555433.333333322111445555555544 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00016
                                        EEEE-SSSSSHHHHHHHHHHHHHHHSSSS-EEEEEHHHHHHHHHHHHHTT-HHHHHHHHT.T-SEEEEE-GGGGTT CS
                           Bac_DnaA  37 lfiygevGlGktHLlkaignevlenapelrvvYltaeeFlnelvkalrdkkaeefkeklr.kvDvLliDDiqflag 111
                                        +++yg+ G Gkt L +ai+n++  n+ +       + e +n+ v   +++  e f +    +  vL  D+i  l +
  gene2541|gene2541|rna2541|rna2541 310 ILLYGPPGCGKTMLARAIANTLFCNFISV-----RGPELVNKYVGDTEKEMREVFNRARNqEPCVLFFDEIDSLCS 380
                                        79********************9998765.....588899999998888777777655442567999999999988 PP

                                        -HHHHHHHHHHHHHHH......TTT-EEEEEESS-TTT-SS--HHHHHHHHSSEEEE-----HHHHHHHHHHHHH CS
                           Bac_DnaA 112 kektqeelfhtfnall......eegkqvvlssDrsPkeleeledrlrsrfeaGlvvdieppdletrlailkkkie 180
                                        + + ++    ++n++l      +++ +v++    + ++++ l++ +    +   ++++  p +e +++il+k ++
  gene2541|gene2541|rna2541|rna2541 381 RRTDNDFQTRIVNQMLtlldgiDDKGKVFIVG--ATNRMHALDSAILRPGRFDKIIEVPLPTREEQIDILRKCVR 453
                                        76443333344444321111213344444433..23456666666554444444666666667777777776665 PP

>> SNAD1  Secreted Novel AID/APOBEC-like Deaminase 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   0.00012     0.061      99     159 ..     352     411 ..     342     433 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00012
                              SNAD1  99 pnplkalLaaakpnatsCvvffsln.SPClekClnpdgatnIlpalrevfngidnnlkaFvF 159
                                         ++++++ + a+++ + Cv+ff  + S C+++  n+  +t I++++ + + gid++ k+F+ 
  gene2541|gene2541|rna2541|rna2541 352 EKEMREVFNRARNQ-EPCVLFFDEIdSLCSRRTDNDF-QTRIVNQMLTLLDGIDDKGKVFIV 411
                                        35788888777655.89*****864388988876665.59********************85 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.1       1.7   8.7e+02     176     196 ..     147     167 ..      86     224 .. 0.74
   2 ?   11.5   0.0   0.00063      0.31      21      46 ..     310     334 ..     246     406 .. 0.76

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 1.7
                             AAA_23 176 eqekekekeleeleeeleeil 196
                                        +  +ekek l+e+e+++e++ 
  gene2541|gene2541|rna2541|rna2541 147 QLTNEKEKVLHEIEKNMEKVR 167
                                        223345555555555555543 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00063
                             AAA_23  21 ltlItGpNGaGKTTildAiklaLyge 46 
                                        + l++Gp G+GKT + +Ai   L+  
  gene2541|gene2541|rna2541|rna2541 310 I-LLYGPPGCGKTMLARAIANTLFCN 334
                                        4.9****************9999864 PP

>> Sigma54_activ_2  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00031      0.15      20      82 ..     306     379 ..     295     395 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00031
                                        -SS-EEEEEETT--HHHHHHCC--T........TS-EE--SSTTHHHH-HHHHHHHT...TTSEEEEEE-TT-- CS
                    Sigma54_activ_2  20 sklpvfltGekGsgkelvArlLhkn........sgpwleifvverlaklpldlleqa...kggtLylkdiadls 82 
                                        +++ ++l G++G+gk++ Ar++++         +gp l  + v +  k+  +++++a   ++ +L++ +i++l 
  gene2541|gene2541|rna2541|rna2541 306 RTSGILLYGPPGCGKTMLARAIANTlfcnfisvRGPELVNKYVGDTEKEMREVFNRArnqEPCVLFFDEIDSLC 379
                                        57789***************998752222221133333333334444577889999855577799999999985 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       4.8   2.4e+03      23      41 ..      89     107 ..      79     116 .. 0.83
   2 ?    9.9   0.0    0.0011      0.55      20      44 ..     305     329 ..     292     419 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 4.8
                                        S-EEEECSTTSSHHHHHHH CS
                    Sigma54_activat  23 lsvlitGesGtGKellara 41 
                                         s+l++G + tGK ++ ++
  gene2541|gene2541|rna2541|rna2541  89 KSLLLVGAKNTGKRFFLKS 107
                                        57899********998765 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0011
                                        TSSS-EEEECSTTSSHHHHHHHHHH CS
                    Sigma54_activat  20 ktdlsvlitGesGtGKellaraihe 44 
                                        + ++ +l+ G  G+GK++larai +
  gene2541|gene2541|rna2541|rna2541 305 SRTSGILLYGPPGCGKTMLARAIAN 329
                                        445789****************976 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.1         6     3e+03      83     115 ..     150     182 ..     144     195 .. 0.69
   2 ?   10.0   0.0    0.0017      0.86       1      26 [.     313     338 ..     313     370 .. 0.70

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 6
                                        EETTEEEESSHHHHHHHH..SEEEEEE--HHHH CS
                             AAA_17  83 keqagfldglpkevleelkpdaiilleadpeei 115
                                        +e+++ l +++k++++  + +++++++++ +  
  gene2541|gene2541|rna2541|rna2541 150 NEKEKVLHEIEKNMEKVRDKKILTIFSCQSKAF 182
                                        466677777777776666666666677766654 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0017
                                        EE-TTSSHHHHHHHHHHHHTEEEEEH CS
                             AAA_17   1 lGgPGsGKgtqceklvekygfthlsa 26 
                                        +G+PG+GK+ +++ ++  +   ++s 
  gene2541|gene2541|rna2541|rna2541 313 YGPPGCGKTMLARAIANTLFCNFISV 338
                                        7***************9996666663 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00046      0.23       2      30 ..     310     338 ..     309     415 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00046
                              AAA_3   2 vllegvPGlaktllvkalakaldlefkri 30 
                                        +ll g PG +kt+l++a+a++l ++f  +
  gene2541|gene2541|rna2541|rna2541 310 ILLYGPPGCGKTMLARAIANTLFCNFISV 338
                                        7999******************9999766 PP

>> HU-CCDC81_bac_2  CCDC81-like prokaryotic HU domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.1   0.00094      0.47      25      49 ..     256     280 ..     252     285 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00094
                    HU-CCDC81_bac_2  25 eveelkqeLeeegrveleniGeLsl 49 
                                        e++++ + L +e++++l+niG L+ 
  gene2541|gene2541|rna2541|rna2541 256 EINDFLRNLTNENKITLDNIGALYA 280
                                        7889999****************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (518 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1007  (0.056166); expected 358.6 (0.02)
Passed bias filter:                      736  (0.0410508); expected 358.6 (0.02)
Passed Vit filter:                       114  (0.00635841); expected 17.9 (0.001)
Passed Fwd filter:                        36  (0.00200792); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              36  [number of targets reported over threshold]
# CPU time: 0.76u 0.34s 00:00:01.10 Elapsed: 00:00:00.53
# Mc/sec: 2926.04
//
Query:       gene2542|gene2542|rna2542|rna2542  [L=340]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.4e-57  193.6   0.1    5.5e-57  193.3   0.1    1.1  1  tRNA-synt_1b  tRNA synthetases class I (W and Y)


Domain annotation for each model (and alignments):
>> tRNA-synt_1b  tRNA synthetases class I (W and Y)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  193.3   0.1   3.1e-61   5.5e-57       4     291 ..      33     319 ..      31     321 .. 0.92

  Alignments for each domain:
  == domain 1  score: 193.3 bits;  conditional E-value: 3.1e-61
                                        S--EEEEEEETSSS-BGGGHHHHHHHHHHHHTTSEEEEEEEHHHHHTTTTT-SSHHHHHHHHHHHHHHHHHHHHHT CS
                       tRNA-synt_1b   4 rplrvysGidPTgklHlGylvplkklvelqkaghevffliaDlhAiigdpskaeerklrkreevlenaikaqlakg 79 
                                        ++ +vy+G+++Tg++H++y++pl k+ ++ +ag+ev +l+aD hA++++ + a+  ++ +r+e++  +i + l+ +
  gene2542|gene2542|rna2542|rna2542  33 KDPSVYWGTATTGRPHIAYILPLLKIKDFIDAGCEVKILLADIHAFLDNLK-ANFDEIDSRTEYYRILITETLKML 107
                                        6789***********************************************.99*******************999 PP

                                        CHTTTEEEEETHHHHTTHHHHHHHHHHHTTCBHHHHHHHHH.CCHHCSSSC--BHHHHHHHHHHHHHHHHTCHSEE CS
                       tRNA-synt_1b  80 ldpekaevvlqsewlehlelaellrdlgklgslnrmlqfks.vkkrleegegislgeftYplLqaaDilllkadlv 154
                                           +  ++v +s+ +  ++++ +l ++ +l+s ++  ++ + v+k+l + +   ++ ++Yp +qa+D+++l++d++
  gene2542|gene2542|rna2542|rna2542 108 NVTKGFTLVKGSDFQTDKNYTLDLYKICSLTSERDARKAGAsVVKQLDN-P--LISSLIYPSMQALDEQYLDVDIQ 180
                                        88888********************************999977777777.4..9********************** PP

                                        EEEGGGHHHHHHHHHHHHHHHHHSTTSS-EEEEET-BBSTTSSSBTTCETTCGC-BTTCCHHHHHHHHHHCHCSTT CS
                       tRNA-synt_1b 155 pgGsDQkqnielgrdlarrfnkkevfkkpegltvplltgldGekKmSKSagnsaIfLddekesvkkkiqkavtdsd 230
                                        +gG DQ+++++ + ++++++++k    k+++l++ +++gl+G  KmS S+ ns+I+ +d+ ++++ ki+k++++ +
  gene2542|gene2542|rna2542|rna2542 181 FGGLDQRKIFTYAMKYLPKLGYK----KRVHLMNFMVPGLNGD-KMSASDINSKIDFLDDGKTIRNKIKKCFCEEG 251
                                        **********************9....****************.******************************** PP

                                        C.SHHHHHHHHHTHHHCHHHHHHHH.CCSEE......ESSHHHHHHHHHCCCCHHHHHHHHHHHHHHHH CS
                       tRNA-synt_1b 231 e.evekllklktelsnelierleav.sgkkp......kreaeellaeevtklvhggdlkkalaealnel 291
                                        + + + l+ +k+++++ ++e+l+   + k +         +e l++ +++k+vh++d+k al+e ln++
  gene2542|gene2542|rna2542|rna2542 252 NtDTGLLPLMKHVIFP-VFEILDRKvTIKREdgteleFGNYEMLEKMFAEKKVHPQDFKIALSEMLNTI 319
                                        ****************.5555543322222232444445799**********************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (340 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       455  (0.0253779); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 2243.37
//
Query:       gene2543|gene2543|rna2543|rna2543  [L=183]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.4e-22   79.5   1.5    2.4e-22   79.5   1.5    2.2  2  RIO1            RIO1 family
  ------ inclusion threshold ------
      0.056   13.4   0.3      0.098   12.6   0.3    1.4  1  APH             Phosphotransferase enzyme family
      0.096   12.2   0.4       0.14   11.7   0.4    1.2  1  DAPG_hydrolase  DAPG hydrolase PhiG domain


Domain annotation for each model (and alignments):
>> RIO1  RIO1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.5   1.5     4e-26   2.4e-22     121     185 ..       1      65 [.       1      68 [. 0.95
   2 ?    0.2   6.1     0.084     5e+02      21      66 ..     134     176 ..     112     181 .. 0.76

  Alignments for each domain:
  == domain 1  score: 79.5 bits;  conditional E-value: 4e-26
                                        HHHTSTEEESS-STTSEEEETTEEEE--GTTEEETTSTTHHHHHHHHHHHHHHHHHTTC-----H CS
                               RIO1 121 lykeaglvHaDLSeyNvlvdedkvviIDvsQaveldhpnalefLerDveniikfFrrkgvekvde 185
                                        +y++a+lvH+DLSeyN+l+++dkv++IDv+Q+v+++h  a  fL  D+ n++kfF+rkgv+  ++
  gene2543|gene2543|rna2543|rna2543   1 MYRDAKLVHCDLSEYNLLYYDDKVYVIDVGQSVDVTHVYADVFLVNDIANVNKFFERKGVMVESV 65 
                                        799********************************************************996655 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.084
                                        ---SS-HHHHCTTTSTTSTCG--GS-HHHHHHHHHHHHHHHHHHHH CS
                               RIO1  21 stteFkkrkkyvsgekrfkdrksktnprklvklwaekEfrnLkrle 66 
                                        + + F + +++ ++ ++fkd+    + +++++   +kE + +kr +
  gene2543|gene2543|rna2543|rna2543 134 TKNAFLTKEEKLERRRKFKDE---RKMKRMSREKKKKETKVIKRKK 176
                                        456677777888888888766...5888999999999999988855 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.3   1.6e-05     0.098     168     204 ..       7      41 ..       3      57 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.6e-05
                                        EE-SS-SGGGEEEC..TTEEEEE---.TT-EEEECCHH CS
                                APH 168 llHgDlhpgNllvdpddgrvtGviDf.edaglgpplyD 204
                                        l+H+Dl+  Nll    d++v +viD  + + + ++ +D
  gene2543|gene2543|rna2543|rna2543   7 LVHCDLSEYNLLYY--DDKV-YVIDVgQSVDVTHVYAD 41 
                                        89************..9999.9***8334455555555 PP

>> DAPG_hydrolase  DAPG hydrolase PhiG domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.4   2.3e-05      0.14      85     197 ..      55     167 ..      35     182 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.3e-05
                     DAPG_hydrolase  85 lsleerylgnthyvtEdvgeglekleirFvdpeelGldeeklkekkvaaavcaevglgeepelklalmvHlvrete 160
                                        ++ +  ++++++ v E v  ++++++i+  + ++lG+d+ +l e   +   ca  +l  ++  ++  +   v++ +
  gene2543|gene2543|rna2543|rna2543  55 FERKGVMVESVRSVYERVTGKKMHFDIKGCEINKLGFDTGRLLELCDDREQCADTRL-LYDMNRTENVHEDVKRRK 129
                                        5556668899*********************************99999999999998.444456777777899999 PP

                     DAPG_hydrolase 161 gGlelrSrfwlgerv.arvaglekaaklvkalsegeav 197
                                        +G  +   f + e+  +r  + +++ k+ +   e++++
  gene2543|gene2543|rna2543|rna2543 130 DGQFTKNAFLTKEEKlERRRKFKDERKMKRMSREKKKK 167
                                        99999999988888774444555444444433333222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1831  (0.102125); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1327.39
//
Query:       gene2544|gene2544|rna2544|rna2544  [L=201]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.4e-26   90.9   0.1    1.2e-25   90.2   0.1    1.3  1  RIO1      RIO1 family
  ------ inclusion threshold ------
      0.057   13.4   0.1        1.9    8.4   0.0    2.2  2  CpeT      CpeT/CpcT family (DUF1001)


Domain annotation for each model (and alignments):
>> RIO1  RIO1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.2   0.1   1.4e-29   1.2e-25      11     102 ..      99     189 ..      78     199 .. 0.90

  Alignments for each domain:
  == domain 1  score: 90.2 bits;  conditional E-value: 1.4e-29
                                        EEEEEEEE-S---SS-HHHHCTTTSTTSTCG--GS-HHHHHHHHHHHHHHHHHHHHHTT--S--EEEEETTEEEEE CS
                               RIO1  11 kevaiKiyktstteFkkrkkyvsgekrfkdrksktnprklvklwaekEfrnLkrleeagvpvPkpielkrhvlvme 86 
                                        ++v+iKi++ts++eFk+r+ y+++e rfk+    +nprkl+k+waekE+rnL+rl+++g+p P+p+ lkr++++m+
  gene2544|gene2544|rna2544|rna2544  99 EDVVIKIFRTSILEFKNRNVYITNEIRFKNF-RISNPRKLIKTWAEKEVRNLTRLNNSGIPSPQPLYLKRNIIIMR 173
                                        489**************************77.689***************************************** PP

                                        --EETTEEGGBHHHCG CS
                               RIO1  87 figedgvaapklkdve 102
                                        +ig+d   a+klkd++
  gene2544|gene2544|rna2544|rna2544 174 LIGDDVHVAAKLKDLQ 189
                                        **************98 PP

>> CpeT  CpeT/CpcT family (DUF1001)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0    0.0093        83      96     125 ..      53      82 ..       9      93 .. 0.79
   2 ?    8.4   0.0   0.00021       1.9      55      99 ..     104     151 ..      96     162 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.0093
                                        HHTT--GGGEEE-TT--EEEEE-.SSSEEE CS
                               CpeT  96 llrtltpeelellpgCevivkreegnkfkG 125
                                        +++++  +++  +p+C++i + +++++f+ 
  gene2544|gene2544|rna2544|rna2544  53 KEANIYRAKIRCMPKCKFIRRSDSTENFHD 82 
                                        566777788999999999999988888875 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00021
                                        S-SEEEEEEEEEETT.E...EEEEEEEETTGGGGTTGGG-HH..HHTT CS
                               CpeT  55 qpYRqrvlrlipsed.skkaielenYklkdeeafagagrdpe..llrt 99 
                                        +++R  +l++++ +   +++i+++n+++ ++ ++++ + ++e   l +
  gene2544|gene2544|rna2544|rna2544 104 KIFRTSILEFKNRNVyITNEIRFKNFRISNPRKLIKTWAEKEvrNLTR 151
                                        79*********96554789******************99997434444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (201 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       542  (0.0302304); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1441.03
//
Query:       gene2545|gene2545|rna2545|rna2545  [L=101]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.033   14.3   0.7      0.043   13.9   0.5    1.4  1  DUF2120   Uncharacterized protein conserved in archaea (DUF21


Domain annotation for each model (and alignments):
>> DUF2120  Uncharacterized protein conserved in archaea (DUF2120)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.5   2.4e-06     0.043      33      78 ..      39      84 ..      22      98 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.4e-06
                            DUF2120 33 rkkeeleeleskleellekldaeevdleseeakkliekldesirev 78
                                        k ++ +e+ +++++l+e+ld+ ++++e ee  +l++++ e   e 
  gene2545|gene2545|rna2545|rna2545 39 SKIMDRNEIVDVVNYLFERLDELDIEVEYEECGNLVSIMYEICEED 84
                                       4556799*******************************99876664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       955  (0.0532657); expected 358.6 (0.02)
Passed bias filter:                      587  (0.0327403); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.35s 00:00:00.93 Elapsed: 00:00:00.57
# Mc/sec: 537.24
//
Query:       gene2546|gene2546|rna2546|rna2546  [L=71]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      5e-10   38.9   0.5    6.1e-10   38.7   0.5    1.3  1  LSM       LSM domain


Domain annotation for each model (and alignments):
>> LSM  LSM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.7   0.5   3.4e-14   6.1e-10       2      37 ..      12      47 ..      11      69 .. 0.94

  Alignments for each domain:
  == domain 1  score: 38.7 bits;  conditional E-value: 3.4e-14
                                       HHHHTTTSEEEEEETTSEEEEEEEEEEETTSEEEEE CS
                                LSM  2 flkklinkkvtvelkngrelrGtLkgfDqfmNlvLe 37
                                       +l+++i+++++v+l +gre++G Lk++D++ NlvL+
  gene2546|gene2546|rna2546|rna2546 12 DLNEYIDRTIIVKLIGGREVKGLLKSYDNNFNLVLK 47
                                       79*********************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (71 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       327  (0.0182386); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.31s 00:00:00.67 Elapsed: 00:00:00.45
# Mc/sec: 477.50
//
Query:       gene2547|gene2547|rna2547|rna2547  [L=742]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.1e-06   26.7   6.9    1.3e-05   25.4   6.9    1.8  1  zf-RING_2     Ring finger domain
     0.0012   18.7   1.2      0.003   17.4   1.2    1.7  1  C1_1          Phorbol esters/diacylglycerol binding domain (C
     0.0045   17.2   3.2     0.0098   16.2   3.2    1.5  1  zf-rbx1       RING-H2 zinc finger domain
     0.0053   17.0   5.9      0.013   15.8   5.9    1.7  1  zf-RING-like  RING-like domain
     0.0096   15.9   0.9      0.017   15.2   0.9    1.4  1  zf-ANAPC11    Anaphase-promoting complex subunit 11 RING-H2 f
  ------ inclusion threshold ------
      0.014   15.7   1.3      0.037   14.3   1.3    1.7  1  C1_2          C1 domain
      0.034   14.3   0.5       0.07   13.3   0.5    1.4  1  zf-HC5HC2H_2  PHD-zinc-finger like domain
      0.035   14.0   0.2      0.077   12.9   0.2    1.6  1  SIR2          Sir2 family
      0.053   13.8   1.4       0.11   12.8   1.4    1.5  1  zf-HC5HC2H    PHD-like zinc-binding domain
      0.067   12.8   3.2       0.17   11.6   3.2    1.6  1  Zn_ribbon_17  Zinc-ribbon, C4HC2 type
      0.094   13.3   1.0        0.2   12.3   1.0    1.4  1  NEAT          Iron Transport-associated domain
       0.14   12.3   7.1       0.49   10.6   7.1    2.0  1  FANCL_C       FANCL C-terminal domain
       0.16   11.9   5.6       0.34   10.9   5.6    1.5  1  PHD           PHD-finger
       0.19   11.7   7.0       0.48   10.4   7.0    1.8  1  zf-RING_5     zinc-RING finger domain
        0.3   11.0   6.7        1.2    9.1   6.7    2.1  1  zf-C3HC4_2    Zinc finger, C3HC4 type (RING finger)
       0.46   10.6   2.4        1.3    9.1   2.4    1.8  1  Zf_RING       KIAA1045 RING finger
        2.4    8.3   6.3       0.65   10.1   1.6    2.2  2  PHD_4         PHD-finger
        2.7    7.9   6.7        6.8    6.6   6.7    1.7  1  zf-C3HC4_3    Zinc finger, C3HC4 type (RING finger)
        3.6    7.5  12.2       0.79    9.6   8.4    2.0  1  zf-C3HC4      Zinc finger, C3HC4 type (RING finger)


Domain annotation for each model (and alignments):
>> zf-RING_2  Ring finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   6.9   1.4e-08   1.3e-05       2      44 .]     691     738 ..     690     738 .. 0.80

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 1.4e-08
                          zf-RING_2   2 eCpICleelssadsvl...llpCgHvfhreClerwlrssst..CPlCr 44 
                                        eC IC+  ++ + +++   ++ C+ +fh +C++++ ++s++  CP+Cr
  gene2547|gene2547|rna2547|rna2547 691 ECLICYYIVDMKGRLPnyeCTTCKNIFHVNCIDKYRAQSNNplCPFCR 738
                                        9****97777777766553446999*********977777789****9 PP

>> C1_1  Phorbol esters/diacylglycerol binding domain (C1 domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   1.2   3.1e-06     0.003      11      46 ..     689     725 ..     678     731 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 3.1e-06
                                        --B-TTT-SB--S.SSS-EEEETTT--EE-CCCCTTS CS
                               C1_1  11 ptfCkhCgeflwg.kekqglkCswCkllvHkkChekv 46 
                                         + C  C  ++ + ++++ + C++Ck ++H +C+ k 
  gene2547|gene2547|rna2547|rna2547 689 RKECLICYYIVDMkGRLPNYECTTCKNIFHVNCIDKY 725
                                        678999*****8889******************9886 PP

>> zf-rbx1  RING-H2 zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   3.2     1e-05    0.0098      27      55 .]     708     738 ..     685     738 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1e-05
                            zf-rbx1  27 vvlGeCgHaFHlhCiskWlkt..rkvCPlcr 55 
                                          + +C+  FH++Ci+k+  +  +  CP cr
  gene2547|gene2547|rna2547|rna2547 708 YECTTCKNIFHVNCIDKYRAQsnNPLCPFCR 738
                                        45678*************99976778****8 PP

>> zf-RING-like  RING-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   5.9   1.4e-05     0.013      12      43 .]     708     737 ..     692     737 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.4e-05
                       zf-RING-like  12 vrCsnesCnvrlHvdCfqhyirthsskkCpkC 43 
                                        + C+  +C+ ++Hv+C+++y  +++++ Cp C
  gene2547|gene2547|rna2547|rna2547 708 YECT--TCKNIFHVNCIDKYRAQSNNPLCPFC 737
                                        4698..9**************99999****99 PP

>> zf-ANAPC11  Anaphase-promoting complex subunit 11 RING-H2 finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.9   1.8e-05     0.017      43      81 ..     708     741 ..     667     742 .] 0.75

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.8e-05
                                        TTS-EEEBTTS-EEEHHHHHHHHHHHSTSSB-TTTSSB- CS
                         zf-ANAPC11  43 ddcplvlGkckhnfhlhcilkwletetskglcpmcrqtf 81 
                                         +c     +ck +fh+ ci k+ + ++ + lcp+cr ++
  gene2547|gene2547|rna2547|rna2547 708 YEC----TTCKNIFHVNCIDKYRA-QSNNPLCPFCRSIM 741
                                        444....47************965.56789******987 PP

>> C1_2  C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   1.3   3.9e-05     0.037      17      47 .]     688     722 ..     674     722 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.9e-05
                               C1_2  17 esfnCsaCgrkidgff....YsCseCdfslhvrCa 47 
                                        ++++C +C   +d +     Y+C++C+ ++hv+C+
  gene2547|gene2547|rna2547|rna2547 688 GRKECLICYYIVDMKGrlpnYECTTCKNIFHVNCI 722
                                        6799****99954444559***************6 PP

>> zf-HC5HC2H_2  PHD-zinc-finger like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.5   7.5e-05      0.07      45      89 ..     679     726 ..     661     734 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 7.5e-05
                       zf-HC5HC2H_2  45 dvekikkerlkekCllCkkr...kGaciqCskkeCktafHvtCalaag 89 
                                        +++  +k   +++Cl+C      kG   +   ++Ck++fHv+C+ + +
  gene2547|gene2547|rna2547|rna2547 679 KINLDNKMMGRKECLICYYIvdmKGRLPNYECTTCKNIFHVNCIDKYR 726
                                        4444455556789999987766689866655566*********98765 PP

>> SIR2  Sir2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.2   8.1e-05     0.077      94     139 ..     697     742 .]     663     742 .] 0.91

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 8.1e-05
                                        SEEETTEEEEEEEETTTSBEEECCGGHCHHHCCTT.B-TTTCCBEE CS
                               SIR2  94 kvvelHGslakakcvkcekkldkeelqeeieaekvpecekcgkllk 139
                                         +v++ G l + +c++c+++++ + + +   +++ p c+ c +++k
  gene2547|gene2547|rna2547|rna2547 697 YIVDMKGRLPNYECTTCKNIFHVNCIDKYRAQSNNPLCPFCRSIMK 742
                                        6899****************************************98 PP

>> zf-HC5HC2H  PHD-like zinc-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   1.4   0.00011      0.11      19      73 ..     672     729 ..     658     739 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00011
                         zf-HC5HC2H  19 iemeeiedvekikkerkklkCylCk...kkvGaciqCskkkCkkafHvtCakeaglll 73 
                                        +e  ++ +++  +k   +++C +C    + +G   + + ++Ck+ fHv C  + +++ 
  gene2547|gene2547|rna2547|rna2547 672 VEVLSLWKINLDNKMMGRKECLICYyivDMKGRLPNYECTTCKNIFHVNCIDKYRAQS 729
                                        55566677788888889999****97764467655555556*********99877655 PP

>> Zn_ribbon_17  Zinc-ribbon, C4HC2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   3.2   0.00018      0.17       4      46 ..     689     735 ..     686     737 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00018
                       Zn_ribbon_17   4 lksCayCe..lavkgrv..vlcgvCeHvlHasCarewfenddlaeCp 46 
                                        +k+C +C   + +kgr+  + c+ C+ + H +C+++   + + + Cp
  gene2547|gene2547|rna2547|rna2547 689 RKECLICYyiVDMKGRLpnYECTTCKNIFHVNCIDKYRAQSNNPLCP 735
                                        689*99972245577764478***************98888779998 PP

>> NEAT  Iron Transport-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   1.0   0.00021       0.2      11     113 ..     401     501 ..     397     505 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00021
                                        EEEEEETTSSSB-GGGGGB-SSEEEEEETTEE.EEEEEEESGGGEEEEEEEETTTEEEEEEEE.EEETTTT.EEEE CS
                               NEAT  11 dfkvlkdnsdeaSmankyidkpaklevknGky.yvtltlknsdwiknfkvekvnGykvkttvv.sedagkd.trvv 83 
                                        +f+vl+d+++e    n++i+kp  +e +n k+  vtl++ +sd +  +++ k ++y ++ + v +   +   + +v
  gene2547|gene2547|rna2547|rna2547 401 KFTVLHDKKKEIYLLNNFIVKPHYIENENLKKlKVTLKFIQSDKLLRVRYFKREKY-YELERViERLSNDIfNTYV 475
                                        79**************************999989999999****999999775565.5555551555555589999 PP

                                        EEEESTTTSEEEEEEEEEECCCCEEEEEEE CS
                               NEAT  84 kfevedldkklkvkvhvfvpignydqkyrv 113
                                        +++      ++   ++v v  +  d++y+v
  gene2547|gene2547|rna2547|rna2547 476 RMKSRRFYRTM---MKV-VNYFDDDVWYYV 501
                                        99998888888...666.655566666665 PP

>> FANCL_C  FANCL C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   7.1   0.00052      0.49       3      40 ..     690     725 ..     688     741 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00052
                                        -S-SSS--SS-TT-----B--S-TT----B-SGGGHHH CS
                            FANCL_C   3 veCgiCyayrldsgevpdisCdnekCnkkfHsaCLkeW 40 
                                        +eC iCy   + +g++p++ C    C+++fH +C+  +
  gene2547|gene2547|rna2547|rna2547 690 KECLICYYIVDMKGRLPNYECT--TCKNIFHVNCIDKY 725
                                        79*******************5..8*********9765 PP

>> PHD  PHD-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   5.6   0.00036      0.34      17      50 ..     709     738 ..     691     739 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00036
                                        EETTTSCEEETTTSSSTHSHHSHHSSTBSSTTTH CS
                                PHD  17 qCdgCkrwfHqkClkppleseekpegewlCekCk 50 
                                         C +Ck+ fH++C++    ++++p    lC+ C+
  gene2547|gene2547|rna2547|rna2547 709 ECTTCKNIFHVNCIDKYRAQSNNP----LCPFCR 738
                                        7**************998877777....7**997 PP

>> zf-RING_5  zinc-RING finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   7.0   0.00051      0.48       2      43 ..     692     738 ..     689     739 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00051
                          zf-RING_5   2 CnkCfekl..skeek....fyltsCgHifCekClkkll..ekeavCpiCr 43 
                                        C +C+  +  +   +    +  t+C+ if+ +C++k+    ++  Cp+Cr
  gene2547|gene2547|rna2547|rna2547 692 CLICYYIVdmK---GrlpnYECTTCKNIFHVNCIDKYRaqSNNPLCPFCR 738
                                        77777777332...12446788****************999999*****9 PP

>> zf-C3HC4_2  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   6.7    0.0012       1.2       2      40 .]     692     737 ..     691     737 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0012
                         zf-C3HC4_2   2 CpiCldmlkd.....psvvtpCgHvfCqkCilr.sLeekn.eCPlC 40 
                                        C iC+    +         t C+  f+ +Ci++   +++n  CP C
  gene2547|gene2547|rna2547|rna2547 692 CLICYYIVDMkgrlpNYECTTCKNIFHVNCIDKyRAQSNNpLCPFC 737
                                        888876555411111135679************534455589***9 PP

>> Zf_RING  KIAA1045 RING finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   2.4    0.0014       1.3       8      40 ..     692     728 ..     686     736 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0014
                            Zf_RING   8 CeiC....evytaeelypCRvCtkvfHegClrklgyl 40 
                                        C iC    ++  +   y+C  C+ +fH +C+ k +  
  gene2547|gene2547|rna2547|rna2547 692 CLICyyivDMKGRLPNYECTTCKNIFHVNCIDKYRAQ 728
                                        66664333444455689**************997655 PP

>> PHD_4  PHD-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.2       1.4   1.4e+03      31      40 ..     690     699 ..     680     702 .. 0.80
   2 ?   10.1   1.6   0.00069      0.65      31      48 ..     708     725 ..     700     737 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 1.4
                              PHD_4  31 meCsvCyeiv 40 
                                         eC +Cy iv
  gene2547|gene2547|rna2547|rna2547 690 KECLICYYIV 699
                                        49****9887 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00069
                              PHD_4  31 meCsvCyeivHpeClkek 48 
                                         eC+ C +i H +C+++ 
  gene2547|gene2547|rna2547|rna2547 708 YECTTCKNIFHVNCIDKY 725
                                        69*************985 PP

>> zf-C3HC4_3  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   6.7    0.0072       6.8       3      45 ..     690     739 ..     688     742 .] 0.83

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0072
                                        SB-TTTSS......SBS-EEETTEEEEEE-HHHHHHHHH..TT-B-TTT-- CS
                         zf-C3HC4_3   3 eeCviCle......rprnvvllpCgHlvlCeeCaekllk..rkkkCpiCrr 45 
                                        +eC+iC+       r  n  +  C+ + +  +C +k+++  +++ Cp+Cr+
  gene2547|gene2547|rna2547|rna2547 690 KECLICYYivdmkgRLPNYECTTCKNI-FHVNCIDKYRAqsNNPLCPFCRS 739
                                        79****998888887888888888755.556******98999********7 PP

>> zf-C3HC4  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   8.4   0.00084      0.79       1      41 []     692     737 ..     692     737 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00084
                                        -TTT-S--SS-E......E-TTS--B-CHHHHHHHHCTSSB--TTT CS
                           zf-C3HC4   1 CpiCleeakepn.....elleCkHsfCskCirkilksrkkvkCPlC 41 
                                        C iC   +  +      e ++Ck  f+ +Ci+k++ ++++  CP C
  gene2547|gene2547|rna2547|rna2547 692 CLICYYIVDMKGrlpnyECTTCKNIFHVNCIDKYRAQSNNPLCPFC 737
                                        8888888888778889999*****************888888**** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (742 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       626  (0.0349155); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.67u 0.25s 00:00:00.92 Elapsed: 00:00:00.48
# Mc/sec: 4604.58
//
Query:       gene2548|gene2548|rna2548|rna2548  [L=145]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1658  (0.0924759); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1002.47
//
Query:       gene2549|gene2549|rna2549|rna2549  [L=227]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.9e-09   37.2   0.0    2.7e-09   36.7   0.0    1.2  1  Kdo          Lipopolysaccharide kinase (Kdo/WaaP) family
    2.4e-07   30.5   0.4    5.7e-05   22.8   0.1    2.1  2  RIO1         RIO1 family
    3.1e-07   30.0   0.4    3.7e-07   29.8   0.4    1.1  1  Pkinase      Protein kinase domain
    1.3e-06   28.5   0.0    4.1e-05   23.6   0.0    2.0  1  APH          Phosphotransferase enzyme family
    0.00087   19.0   0.1     0.0012   18.6   0.1    1.2  1  WaaY         Lipopolysaccharide core biosynthesis protein (Wa
  ------ inclusion threshold ------
      0.038   13.3   0.0      0.045   13.0   0.0    1.3  1  Pkinase_Tyr  Protein tyrosine kinase


Domain annotation for each model (and alignments):
>> Kdo  Lipopolysaccharide kinase (Kdo/WaaP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.7   0.0     9e-13   2.7e-09      53     194 ..      50     191 ..      36     203 .. 0.83

  Alignments for each domain:
  == domain 1  score: 36.7 bits;  conditional E-value: 9e-13
                                Kdo  53 lgrtravrEfrllkrLeeagvavpkpvaagavkvgleyrAlllterlega..qdLedllakwae..laeelk...r 121
                                        + r r + E+++l+rL + +v +pk +   +  +++  +  + + ++ g+  +d+  +l++ +e  + ++      
  gene2549|gene2549|rna2549|rna2549  50 IRRKRTRTEMKVLERLAANQVSAPKLLKIDECSEQFDKQTTIYMTNVPGMnlKDVILCLEH-SEgqPIHRIAfsiP 124
                                        6788999****************************************87622677777775.44465555541114 PP

                                Kdo 122 allkavgrliaklhragvnHadlyaknillqqeeeeeaeiwliDldkarlrlradrwrekdLarLkrsflkie 194
                                         +++++g+l++k h+ gv H+dl   n+ l  +      i++iD+  ++  + ++ ++  dL  L++ + +i+
  gene2549|gene2549|rna2549|rna2549 125 VIFNKLGKLVRKVHACGVVHGDLTTANFILADDL-----IYVIDFGLSYFST-KEEDKAVDLYLLEKAVRTIH 191
                                        579***************************9997.....**********999.9999999**99999866554 PP

>> RIO1  RIO1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.3   0.0    0.0022       6.5      50      78 ..      50      78 ..      28      84 .. 0.84
   2 !   22.8   0.1   1.9e-08   5.7e-05     117     153 ..     132     168 ..      87     197 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0022
                                       HHHHHHHHHHHHHHHHHHTT--S--EEEE CS
                               RIO1 50 lvklwaekEfrnLkrleeagvpvPkpiel 78
                                       + +  ++ E++ L+rl++ +v++Pk +++
  gene2549|gene2549|rna2549|rna2549 50 IRRKRTRTEMKVLERLAANQVSAPKLLKI 78
                                       55677899****************98765 PP

  == domain 2  score: 22.8 bits;  conditional E-value: 1.9e-08
                                        HHHHHHHTSTEEESS-STTSEEEETTEEEE--GTTEE CS
                               RIO1 117 emrklykeaglvHaDLSeyNvlvdedkvviIDvsQav 153
                                        ++ + ++ +g+vH+DL   N ++ +d +++ID++ + 
  gene2549|gene2549|rna2549|rna2549 132 KLVRKVHACGVVHGDLTTANFILADDLIYVIDFGLSY 168
                                        4566778*************************98654 PP

>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8   0.4   1.2e-10   3.7e-07      42     153 ..      51     175 ..      18     196 .. 0.79

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 1.2e-10
                                        H.HHHHHHHHHHHHHS.....CTTB--EEEEEEE.SSEEEEEEE--TTEBHHHHHH.....HHSS--HH..HHHHH CS
                            Pkinase  42 e.kkvlrEikilkklk.....hpnivrlyevfee.kdelylvleyveggeladlle.....rkgslsee..eakki 103
                                        + k++++E+k+l++l       p+++++ e+ e+ +++ ++ +  v+g +l+d++      + + +      +  i
  gene2549|gene2549|rna2549|rna2549  51 RrKRTRTEMKVLERLAanqvsAPKLLKIDECSEQfDKQTTIYMTNVPGMNLKDVILclehsEGQPIHRIafSIPVI 126
                                        247888999999887754555788899999888877778899************9877553222233334577799 PP

                                        HHHHHHHHHHHHHTTEE-SS-SGGGEEEETTTEEEE-SGTTSEESSSSCS CS
                            Pkinase 104 akqilegleylHskgiiHrDlKpeNiLidekgelKitDFGlakelesssk 153
                                        ++++ + ++ +H+ g++H Dl ++N+++  ++ + ++DFGl+   +++++
  gene2549|gene2549|rna2549|rna2549 127 FNKLGKLVRKVHACGVVHGDLTTANFILA-DDLIYVIDFGLSYFSTKEED 175
                                        ****************************9.999*********98877665 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.0   1.4e-08   4.1e-05     125     229 ..      61     204 ..      54     218 .. 0.70

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 1.4e-08
                                        HHHHHHCHHHCCCGCCTCCHHHHHHHH.........................................HHHHHHHH CS
                                APH 125 llrqlesatarllaselldlleeleeq.........................................vlaalaal 159
                                        +l+ l++   +  a++ll+ + e+ eq                                         + ++l +l
  gene2549|gene2549|rna2549|rna2549  61 VLERLAAN--QVSAPKLLK-IDECSEQfdkqttiymtnvpgmnlkdvilclehsegqpihriafsipvIFNKLGKL 133
                                        55555555..677777777.66666667777888888888888888888888888888888888899988888888 PP

                                        --SSS-EEEE-SS-SGGGEEEC..TTEEEEE---TT-EEEECCHHHHCCH....HHCSCHCCCHCHHHHHHHHC CS
                                APH 160 lpgelptvllHgDlhpgNllvdpddgrvtGviDfedaglgpplyDlavll....rswtseldpeflaallraye 229
                                        +++  + +++HgDl + N+++   d+ + +viDf+++  +    D av l     +++    +e+ +++ ++y+
  gene2549|gene2549|rna2549|rna2549 134 VRKVHACGVVHGDLTTANFILA--DDLI-YVIDFGLSYFSTKEEDKAVDLylleKAVRTIHKDEYMDDFYDGYG 204
                                        88888999**************..8888.******998887777776555444433455555556666655555 PP

>> WaaY  Lipopolysaccharide core biosynthesis protein (WaaY)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.1   3.9e-07    0.0012     139     199 ..     125     187 ..      97     221 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 3.9e-07
                               WaaY 139 evkakikqsieklhqlgmvsgdphrgnfivkkdevriid..lsgkrasaerkakdridlerhy 199
                                         + +k+ + ++k+h+ g+v gd    nfi+ +d + +id  ls  ++  e ka d   le+ +
  gene2549|gene2549|rna2549|rna2549 125 VIFNKLGKLVRKVHACGVVHGDLTTANFILADDLIYVIDfgLSYFSTKEEDKAVDLYLLEKAV 187
                                        5668888999****************************9556778888899999998888765 PP

>> Pkinase_Tyr  Protein tyrosine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   1.5e-05     0.045     120     158 ..     138     175 ..      48     188 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.5e-05
                                        HHTTEEEST-SGGGEEEEETTEEEE-STTTHEETTTSSE CS
                        Pkinase_Tyr 120 eskklvHrdlaarNvLlsenkvvkisDfGLardiekdde 158
                                        ++  +vH dl++ N +l+ ++++ + DfGL+   +k+++
  gene2549|gene2549|rna2549|rna2549 138 HACGVVHGDLTTANFILA-DDLIYVIDFGLSYFSTKEED 175
                                        66789***********99.7889999****987755544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (227 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       523  (0.0291706); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.50u 0.22s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1605.67
//
Query:       gene255|gene255|rna255|rna255  [L=63]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.063   13.6   0.0      0.073   13.4   0.0    1.1  1  YfcL      YfcL protein


Domain annotation for each model (and alignments):
>> YfcL  YfcL protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   4.1e-06     0.073      42      71 ..      18      47 ..       7      52 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.1e-06
                           YfcL 42 eegetslealkekveeslekAikkgELspa 71
                                   ee+e++l+ l+++++e ++ Aik+gEL +a
  gene255|gene255|rna255|rna255 18 EETESTLRLLNSTLKEEISDAIKRGELMNA 47
                                   678899*********************876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (63 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       540  (0.0301188); expected 358.6 (0.02)
Passed bias filter:                      499  (0.027832); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 463.91
//
Query:       gene2550|gene2550|rna2550|rna2550  [L=186]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.4e-09   37.3   1.9    3.4e-09   37.3   1.9    2.3  2  CDP-OH_P_transf  CDP-alcohol phosphatidyltransferase


Domain annotation for each model (and alignments):
>> CDP-OH_P_transf  CDP-alcohol phosphatidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.3   1.9   1.9e-13   3.4e-09       1      66 []       8      68 ..       8      68 .. 0.82
   2 ?    0.2   0.7     0.072   1.3e+03       3      18 ..     128     142 ..      85     180 .. 0.57

  Alignments for each domain:
  == domain 1  score: 37.3 bits;  conditional E-value: 1.9e-13
                                       S-HHHHHHHHHHHHHHHHHGGGS-H..HHHHHHHHHHHHHTTHHHHHHHHTT---HHHHHHHHHHH CS
                    CDP-OH_P_transf  1 nlPnaiTllrlllsvlailllltyyplvlailllliasltDalDGklARrlnqvstlGkllDslaD 66
                                       n+Pn ++++r++l +++i+ l   +   l +l + +++ +D++DG +AR ++q++++G+ lD   D
  gene2550|gene2550|rna2550|rna2550  8 NIPNRVSYARIILLLTSIF-L--DD--DLFVLTFSVSTSLDLIDGTIARYYRQTTRMGACLDMYTD 68
                                       79***********777774.3..23..3555666699999*************888******9877 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.072
                                        HHHHHHHHHHHHHHHH CS
                    CDP-OH_P_transf   3 PnaiTllrlllsvlai 18 
                                        + ++Tl+     ++ i
  gene2550|gene2550|rna2550|rna2550 128 AVLVTLCAGTG-IYHI 142
                                        33344433332.2222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       569  (0.0317363); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1435.99
//
Query:       gene2551|gene2551|rna2551|rna2551  [L=364]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    6.1e-23   80.6   0.5    1.1e-22   79.8   0.5    1.4  1  CAP_GLY     CAP-Gly domain
  ------ inclusion threshold ------
      0.024   14.7   0.6      0.024   14.7   0.6    1.9  2  Myc-LZ      Myc leucine zipper domain
       0.29   10.6   1.2         18    4.9   0.1    2.3  2  p47_phox_C  NADPH oxidase subunit p47Phox, C terminal domain


Domain annotation for each model (and alignments):
>> CAP_GLY  CAP-Gly domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.8   0.5   1.8e-26   1.1e-22       9      64 ..      16      71 ..       8      72 .. 0.91

  Alignments for each domain:
  == domain 1  score: 79.8 bits;  conditional E-value: 1.8e-26
                            CAP_GLY  9 egrrGvvryvGpvpfakgewvGveldepnGkndGsvkgkrYFeckpnrGvFvrpek 64
                                       +   G++ry+G+v++++ge+vG+eld p+GkndGs++g++YF+ck+n+G+Fv+ +k
  gene2551|gene2551|rna2551|rna2551 16 KWGMGTIRYIGTVKGDEGEYVGIELDIPKGKNDGSIDGTKYFTCKNNHGLFVPIDK 71
                                       5568*************************************************988 PP

>> Myc-LZ  Myc leucine zipper domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.2       1.2   7.2e+03       6      17 ..     235     246 ..     235     247 .. 0.77
   2 ?   14.7   0.6     4e-06     0.024       2      21 ..     250     269 ..     249     277 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.2
                             Myc-LZ   6 LlSekEqLRkrr 17 
                                        L+S +  L+kr+
  gene2551|gene2551|rna2551|rna2551 235 LKSQIAELKKRC 246
                                        677777899997 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 4e-06
                             Myc-LZ   2 eEqrLlSekEqLRkrrEqLK 21 
                                        +  +L+Se + LRk+ + LK
  gene2551|gene2551|rna2551|rna2551 250 DNNKLISEVDRLRKENLKLK 269
                                        667**********9877777 PP

>> p47_phox_C  NADPH oxidase subunit p47Phox, C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.1     0.003        18      19      32 ..     244     257 ..     243     258 .. 0.87
   2 ?    4.3   0.1    0.0045        27      17      23 ..     306     312 ..     305     319 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.003
                         p47_phox_C  19 eRCsesTkrKlssa 32 
                                        +RCse+   Kl s+
  gene2551|gene2551|rna2551|rna2551 244 KRCSENDNNKLISE 257
                                        5*******999886 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.0045
                         p47_phox_C  17 ILeRCse 23 
                                        IL+RCs 
  gene2551|gene2551|rna2551|rna2551 306 ILNRCSQ 312
                                        9****96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (364 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1366  (0.0761894); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 2658.05
//
Query:       gene2552|gene2552|rna2552|rna2552  [L=560]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (560 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       551  (0.0307323); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.56u 0.25s 00:00:00.81 Elapsed: 00:00:00.42
# Mc/sec: 3994.48
//
Query:       gene2553|gene2553|rna2553|rna2553  [L=163]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.045   13.1   0.1      0.063   12.6   0.1    1.2  1  Foamy_BEL  Foamy virus BEL 1/2 protein


Domain annotation for each model (and alignments):
>> Foamy_BEL  Foamy virus BEL 1/2 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   3.5e-06     0.063      67     126 ..     100     158 ..      91     162 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3.5e-06
                          Foamy_BEL  67 nqdvgtilsfdksilkslillgrndgekdreilkkvlpvvvsweqsedhyaptlfglldr 126
                                        n  + +++  +  i+k+ i++ rn++  d +i+ + lp++vs ++  d+ a   +g++ +
  gene2553|gene2553|rna2553|rna2553 100 NVFIKSVFVQKNVICKNTIVMNRNNPVTDLNIVFN-LPLTVSMNMIVDKVANYKIGVITK 158
                                        4555667777889*********************9.*************99999998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       564  (0.0314574); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 1171.73
//
Query:       gene2554|gene2554|rna2554|rna2554  [L=123]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.3e-05   22.3   0.0    8.2e-05   22.2   0.0    1.1  1  Porin_3   Eukaryotic porin


Domain annotation for each model (and alignments):
>> Porin_3  Eukaryotic porin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0   4.6e-09   8.2e-05     184     260 ..      34     107 ..       4     115 .. 0.88

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 4.6e-09
                                        TTEEEEEEEEECCTTEEEEEEEEEETTEEEEEEEEEEEEEECTCEEEEEEEECTTEEEEEEEEEECTTEEEEEEEE CS
                            Porin_3 184 ggaltasyyqkvsekvevgaeltlnassqestttlGakydldksttvkakidsngkvgllleqkLrpgvtltlsae 259
                                         ++l++++y++++e v+v+ e+    ss  ++  +   +++ +    +  ++s ++v l++e+kL + + ++ +ae
  gene2554|gene2554|rna2554|rna2554  34 YDVLNLTFYRRLTEFVSVAGEMVAGNSSIGARLGVLLSTHFTDI---RVEVNSMMNVILMVEKKLLDCFVFSCCAE 106
                                        6899**********************999887777777777777...****************************9 PP

                                        E CS
                            Porin_3 260 l 260
                                        +
  gene2554|gene2554|rna2554|rna2554 107 V 107
                                        8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (123 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 942.03
//
Query:       gene2555|gene2555|rna2555|rna2555  [L=162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-07   31.2   0.0    3.2e-07   30.2   0.0    1.5  2  TRAPP     Transport protein particle (TRAPP) component


Domain annotation for each model (and alignments):
>> TRAPP  Transport protein particle (TRAPP) component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0     0.042   7.5e+02     103     122 ..      18      38 ..       5      53 .. 0.69
   2 !   30.2   0.0   1.8e-11   3.2e-07      24     144 ..      41     155 ..      20     157 .. 0.76

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.042
                              TRAPP 103 s.ylaflcGiirGaLenlgfp 122
                                        + ++ f cG i   L++   +
  gene2555|gene2555|rna2555|rna2555  18 NfVQFFSCGFIHHLLAQGTTD 38 
                                        357789999999888876555 PP

  == domain 2  score: 30.2 bits;  conditional E-value: 1.8e-11
                              TRAPP  24 krLekmGyrvGlrllelllarerpretdilevlkfickdlWkllfgkqidnlktnhrgeyvltdnefpltrf.vel 98 
                                        +  + +G++   +lle++ +++    +d+ ++l  i k +   l+  + +   t+ r+ yv+t+ +++l+r  v  
  gene2555|gene2555|rna2555|rna2555  41 TSYRDIGHKLAPKLLEMYKIHQ---TNDLDKMLLNI-KSILANLYSSKRSISITSDREYYVITESDPLLSRSgV-- 110
                                        5555666666666677555544...45555555555.777788888888888899****************954.. PP

                              TRAPP  99 pkelsylaflcGiirGaLenlgfpakVtahelpsdelrgrttfeik 144
                                         k+l+ +++++G+i+G L++  f+++V +++ ++++ ++++ ++ik
  gene2555|gene2555|rna2555|rna2555 111 -KSLNSNNLIAGLIEGLLDANLFDCDVLVSDGSDESNPNQVYYLIK 155
                                        .458899**********************88777888889998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       516  (0.0287802); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1165.47
//
Query:       gene2556|gene2556|rna2556|rna2556  [L=881]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.7e-05   23.1   0.1    5.3e-05   22.1   0.1    1.4  1  Nucleoporin_N  Nup133 N terminal like
     0.0051   16.6   0.1      0.023   14.5   0.1    2.1  1  Sas6_CC        Sas6/XLF/XRCC4 coiled-coil domain


Domain annotation for each model (and alignments):
>> Nucleoporin_N  Nup133 N terminal like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.1   5.9e-09   5.3e-05      28     112 ..      71     147 ..      48     189 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 5.9e-09
                                        EEEEEECTTTEEEEEETTEEEEEETTSSSS...EEEEEE----S---EEEEEE---SSSS-SSSCEEEEECTTSEE CS
                      Nucleoporin_N  28 tkgglfpeigrawitvdnklflWnYnstasspstdtipydgeehtilavglLvkpkpgtfveevgllLvvattgei 103
                                           g+  ei+  ++++dn l+l ++ s+       ++p++   +++l v  ++kpk+++f++++  +++v t +++
  gene2556|gene2556|rna2556|rna2556  71 IRYGVLEEINTLYVIHDNTLYLYSFLSSY----KNVLPFS---ENVLFVR-CLKPKASIFQKKILTIILVVTQTKL 138
                                        56799***********************9....8999999...69*****.************************* PP

                                        EEECECCS- CS
                      Nucleoporin_N 104 vyweviysa 112
                                        +++ v  ++
  gene2556|gene2556|rna2556|rna2556 139 FFFCVKEGE 147
                                        *99887766 PP

>> Sas6_CC  Sas6/XLF/XRCC4 coiled-coil domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.1   2.5e-06     0.023       3      14 ..     859     870 ..     858     871 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.5e-06
                                        HHHHHHCCHHHH CS
                            Sas6_CC   3 eVKKYLAvCLks 14 
                                        +VKKYLA C+ s
  gene2556|gene2556|rna2556|rna2556 859 DVKKYLAKCIRS 870
                                        9********987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (881 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       722  (0.04027); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.63u 0.28s 00:00:00.91 Elapsed: 00:00:00.44
# Mc/sec: 6071.24
//
Query:       gene2557|gene2557|rna2557|rna2557  [L=243]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.2e-26   93.4   0.1    1.5e-26   93.1   0.1    1.1  1  Proteasome  Proteasome subunit


Domain annotation for each model (and alignments):
>> Proteasome  Proteasome subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.1   0.1   8.4e-31   1.5e-26       2     189 ..      37     227 ..      36     228 .. 0.87

  Alignments for each domain:
  == domain 1  score: 93.1 bits;  conditional E-value: 8.4e-31
                                        HHS-EEEEEEETTEEEEEEEEEEEETTEEEESSSSTSEEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHSS CS
                         Proteasome   2 kkGttvvGikgkdgvvlaadkratagskllskstveKifkiddhigvafaGlaaDartlvrraraeaqlyrlrygr 77 
                                        ++ +tv+++k +d+v++aad+r++++  + ++++++Kif+  d  +++ +G +aD + +  r+r+e+++y+ + ++
  gene2557|gene2557|rna2557|rna2557  37 NNSGTVLAFKQQDYVIIAADTRHSSEMGI-NSRKMTKIFEF-DGFIFSGTGFYADLNEVYFRLRYEVERYENEVEK 110
                                        6789********************77777.66669******.5566899*************************** PP

                                        GTCHHHHHHHHHHHHHHHHHHCTTT.TTSEEEEEEEEETTTEEEEEEEETTSEEEEESSEEEESTTHHHHHHHHHH CS
                         Proteasome  78 pipverlvarvaaklqaytqrsgrr.pfgvslliagvdeeggpeLyqidpsGsyieekdavaiGsgseaaktalek 152
                                        +i ++    ++a kl++ +++++ +  ++v  +++g de+g+p Ly++dp+Gsy +   + + Gs+s +++++l++
  gene2557|gene2557|rna2557|rna2557 111 RIGIS----ALAHKLLNILYSRRGGlIYYVFSVLVGKDETGEPVLYSFDPIGSYEQV-MCKCYGSASPMIQPLLDS 181
                                        *****....77777777776664441457888999**********************.5****************9 PP

                                        HH.........STTBSHHHHHHHHHHHHHHHHHHBTTSCSSEEEEE CS
                         Proteasome 153 ey.........kedltleeavelavkalkealerdklsgknievav 189
                                                    + l +ee vel +ka  +a+erd+ +g+ ++++v
  gene2557|gene2557|rna2557|rna2557 182 TImkynqenasYQSLCMEESVELTKKAFFAAAERDVNTGDYLQIVV 227
                                        98888866666666778999*******************9999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       527  (0.0293937); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1648.51
//
Query:       gene2558|gene2558|rna2558|rna2558  [L=526]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.5e-33  115.8   3.3    1.5e-33  115.8   3.3    1.9  2  TFIID_NTD2   WD40 associated region in TFIID subunit, NTD2 do
    5.4e-29   99.8   9.4    5.7e-10   39.6   0.0    6.0  6  WD40         WD domain, G-beta repeat
    5.4e-08   33.0   0.1     0.0071   16.6   0.0    4.3  4  ANAPC4_WD40  Anaphase-promoting complex subunit 4 WD40 domain
    3.4e-05   23.3   2.1       0.04   13.2   0.0    4.0  5  WD40_like    WD40-like domain


Domain annotation for each model (and alignments):
>> TFIID_NTD2  WD40 associated region in TFIID subunit, NTD2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.8   3.3   3.4e-37   1.5e-33       9     130 .]       5     123 ..       3     123 .. 0.96
   2 ?   -2.6   0.0       1.3   5.8e+03      66      89 ..     196     219 ..     181     222 .. 0.80

  Alignments for each domain:
  == domain 1  score: 115.8 bits;  conditional E-value: 3.4e-37
                                        HHHHHHHHHHHTS-HHHHHHHGGGHHHHHHHHHHHHHHTT-HHHHHHHHHHHGGGGGGGHH.HHHHHTT--SHHHH CS
                         TFIID_NTD2   9 kayelLkkwiessldiykpeLsrllyPvFvhlyLelvakgaeeeakkFfekfkedhealhkedlkkLasisspehl 84 
                                        + y++Lk wie+sld ++++L +llyP+F+h+yL+l+  + ++ ak+Ff++ k+   ++++++l+ L+si +p+hl
  gene2558|gene2558|rna2558|rna2558   5 QGYAKLKAWIEDSLDQFRNDLMNLLYPLFIHIYLDLLFANDIKGAKEFFNANKD---DFYNQELQILESICTPQHL 77 
                                        78**********************************************998887...568999************* PP

                                        HHSHHHHHHHHS-EEEEEEHHHHHHHHHHHHHTT-HHHHHHHHHHE CS
                         TFIID_NTD2  85 eenelakafrenkyriklskaafelLlrfLeekekavllkilnehl 130
                                        +en l++a+r+nky+i++ k+af+l+++fLe+++++ +l ++n++l
  gene2558|gene2558|rna2558|rna2558  78 NENTLVSAYRTNKYSISMGKYAFDLFINFLERNQMTQILVLVNQYL 123
                                        *******************************************986 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.3
                                        GGHH.HHHHHTT--SHHHHHHSHH CS
                         TFIID_NTD2  66 alhkedlkkLasisspehleenel 89 
                                        ++ k+++++L+ + +   l++n+l
  gene2558|gene2558|rna2558|rna2558 196 SFIKQEIENLKDLCKRVSLNKNNL 219
                                        566889999999999999988875 PP

>> WD40  WD domain, G-beta repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       1.1   5.1e+03      12      34 ..     231     255 ..     222     257 .. 0.68
   2 !    9.3   0.0   0.00048       2.1       7      32 ..     293     319 ..     288     320 .. 0.88
   3 !   14.1   0.1   1.5e-05     0.067       3      38 .]     330     366 ..     328     366 .. 0.89
   4 !   13.1   0.0   3.1e-05      0.14       6      36 ..     375     406 ..     370     408 .. 0.84
   5 !   39.6   0.0   1.3e-13   5.7e-10       2      38 .]     413     450 ..     412     450 .. 0.93
   6 !   24.6   0.4   7.4e-09   3.3e-05       2      38 .]     455     492 ..     454     492 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.1
                                        S..EEEEEEETTSSEEEEEETTSEE CS
                               WD40  12 s..vtslafspdgawlasGsdDgtv 34 
                                        +  v++   s+d ++la G  D  +
  gene2558|gene2558|rna2558|rna2558 231 FerVCCAEISKDLKLLALGYSDSVL 255
                                        2458888899999999767447665 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00048
                                        EESS.SSEEEEEEETTSSEEEEEETTS CS
                               WD40   7 ltGH.ssvtslafspdgawlasGsdDg 32 
                                        l GH ++v  ++f  ++++++s+++D+
  gene2558|gene2558|rna2558|rna2558 293 LIGHtTCVLNVKFFNSKKYVLSCDMDR 319
                                        78**888****************9997 PP

  == domain 3  score: 14.1 bits;  conditional E-value: 1.5e-05
                                        EEEEEESS.SSEEEEEEETTSSEEEEEETTSEEEEEE CS
                               WD40   3 clrtltGH.ssvtslafspdgawlasGsdDgtvriWd 38 
                                        ++ t+++  ++++sla s +  +++sG+ D+tv +++
  gene2558|gene2558|rna2558|rna2558 330 LVSTYKACaFPIWSLAISNNDLMFCSGGADRTVSLFN 366
                                        56788888788**********************9987 PP

  == domain 4  score: 13.1 bits;  conditional E-value: 3.1e-05
                                        EEESS.SSEEEEEEETTSSEEEEEETTSEEEE CS
                               WD40   6 tltGH.ssvtslafspdgawlasGsdDgtvri 36 
                                         +t   s+v+sl f+p++++++ Gs D+ +r+
  gene2558|gene2558|rna2558|rna2558 375 LFTSAlSDVSSLVFHPNSQYVIFGSCDHRIRM 406
                                        56667788************988988****96 PP

  == domain 5  score: 39.6 bits;  conditional E-value: 1.3e-13
                                        EEEEEEESS.SSEEEEEEETTSSEEEEEETTSEEEEEE CS
                               WD40   2 qclrtltGH.ssvtslafspdgawlasGsdDgtvriWd 38 
                                        +++r++ GH + vt+la+spdg++l+sGs+D+tv +Wd
  gene2558|gene2558|rna2558|rna2558 413 ELVRVFIGHtDTVTALAVSPDGKLLLSGSKDRTVILWD 450
                                        5799*****666*************************9 PP

  == domain 6  score: 24.6 bits;  conditional E-value: 7.4e-09
                                        EEEEEEESS.SSEEEEEEETTSSEEEEEETTSEEEEEE CS
                               WD40   2 qclrtltGH.ssvtslafspdgawlasGsdDgtvriWd 38 
                                        +++ +++GH + v+s++f+  g+ ++s++ D ++r+Wd
  gene2558|gene2558|rna2558|rna2558 455 KKVNVFKGHtKTVYSVSFCYFGNVFVSCGADLSLRVWD 492
                                        56889****999***************999*******9 PP

>> ANAPC4_WD40  Anaphase-promoting complex subunit 4 WD40 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0     0.077   3.5e+02      37      68 ..     230     261 ..     209     277 .. 0.74
   2 ?    0.1   0.0      0.23     1e+03      40      69 ..     340     369 ..     316     378 .. 0.86
   3 !   10.6   0.0   0.00012      0.53      39      85 ..     381     426 ..     370     428 .. 0.88
   4 !   16.6   0.0   1.6e-06    0.0071      37      89 ..     421     472 ..     416     475 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.077
                        ANAPC4_WD40  37 edsevrsLaWkpdgklLavaysdgevrlldae 68 
                                        + ++v + + ++d klLa +ysd+ ++++  e
  gene2558|gene2558|rna2558|rna2558 230 TFERVCCAEISKDLKLLALGYSDSVLEIHALE 261
                                        55566666777888999999999988887554 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.23
                        ANAPC4_WD40  40 evrsLaWkpdgklLavaysdgevrlldaes 69 
                                         + sLa ++++ +++ + +d +v+l+++ s
  gene2558|gene2558|rna2558|rna2558 340 PIWSLAISNNDLMFCSGGADRTVSLFNIDS 369
                                        5778999999*************9998865 PP

  == domain 3  score: 10.6 bits;  conditional E-value: 0.00012
                        ANAPC4_WD40  39 sevrsLaWkpdgklLavaysdgevrlldaesgkvvhslsvksekavt 85 
                                        s v+sL ++p+ +   ++  d ++r++++es+++v+ +  +++ +vt
  gene2558|gene2558|rna2558|rna2558 381 SDVSSLVFHPNSQYVIFGSCDHRIRMHEIESAELVRVFIGHTD-TVT 426
                                        679********************************99977776.466 PP

  == domain 4  score: 16.6 bits;  conditional E-value: 1.6e-06
                        ANAPC4_WD40  37 edsevrsLaWkpdgklLavaysdgevrlldaesgkvvhslsvksekavtclgW 89 
                                        +  +v++La +pdgklL  + +d +v l d+ + k v+ ++ +++ +v ++++
  gene2558|gene2558|rna2558|rna2558 421 HTDTVTALAVSPDGKLLLSGSKDRTVILWDIMTSKKVNVFKGHTK-TVYSVSF 472
                                        5678************************************99988.5877766 PP

>> WD40_like  WD40-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.2      0.79   3.5e+03     218     219 ..     116     117 ..      61     159 .. 0.56
   2 ?   -1.4   0.0      0.25   1.1e+03     109     140 ..     285     316 ..     280     328 .. 0.83
   3 ?    1.9   0.0     0.026   1.2e+02       2      32 ..     340     370 ..     339     380 .. 0.88
   4 !   13.2   0.0   8.9e-06      0.04       3      74 ..     383     455 ..     381     458 .. 0.81
   5 !    8.2   0.1    0.0003       1.4       5      66 ..     427     489 ..     423     505 .. 0.78

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 0.79
                          WD40_like 218 ll 219
                                        l+
  gene2558|gene2558|rna2558|rna2558 116 LV 117
                                        22 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.25
                          WD40_like 109 kdlqleevllgqsseIkeikiennkiysLses 140
                                        +d+   + l+g+++ ++++k  n+k y Ls +
  gene2558|gene2558|rna2558|rna2558 285 EDIGKSTRLIGHTTCVLNVKFFNSKKYVLSCD 316
                                        57777788899999999999999999999865 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.026
                          WD40_like   2 eiYsidiskkgslilyGgkddkctvlklesl 32 
                                        +i+s+ is++  ++  Gg d ++ +++++s 
  gene2558|gene2558|rna2558|rna2558 340 PIWSLAISNNDLMFCSGGADRTVSLFNIDSF 370
                                        6999**********************99986 PP

  == domain 4  score: 13.2 bits;  conditional E-value: 8.9e-06
                          WD40_like   3 iYsidiskkgslilyGgkddkctvlkleslesvsivesfedSvifvkllddd.lilvvtlDGtillsllenee 74 
                                        + s+ + ++++++++G+ d+++++ ++es e+v ++ + +d v    +  d  l+l ++ D t++l ++  ++
  gene2558|gene2558|rna2558|rna2558 383 VSSLVFHPNSQYVIFGSCDHRIRMHEIESAELVRVFIGHTDTVTALAVSPDGkLLLSGSKDRTVILWDIMTSK 455
                                        56777889***********************************877665443277778888888777766665 PP

  == domain 5  score: 8.2 bits;  conditional E-value: 0.0003
                          WD40_like   5 sidiskkgslilyGgkddkctvlkleslesvsivesfedSvifvklld.ddlilvvtlDGtil 66 
                                        ++ +s++g+l+l G+kd ++ + ++ + ++v ++++ +  v  v +   +++++ +  D  + 
  gene2558|gene2558|rna2558|rna2558 427 ALAVSPDGKLLLSGSKDRTVILWDIMTSKKVNVFKGHTKTVYSVSFCYfGNVFVSCGADLSLR 489
                                        67899******************************9998766655543266777777776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (526 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       926  (0.0516482); expected 358.6 (0.02)
Passed bias filter:                      466  (0.0259914); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.56u 0.26s 00:00:00.82 Elapsed: 00:00:00.44
# Mc/sec: 3618.40
//
Query:       gene2559|gene2559|rna2559|rna2559  [L=92]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       247  (0.0137766); expected 358.6 (0.02)
Passed bias filter:                      233  (0.0129957); expected 358.6 (0.02)
Passed Vit filter:                         5  (0.000278878); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.28s 00:00:00.66 Elapsed: 00:00:00.44
# Mc/sec: 634.43
//
Query:       gene256|gene256|rna256|rna256  [L=72]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.7e-30  104.0   1.1      4e-30  103.9   1.1    1.0  1  CKS       Cyclin-dependent kinase regulatory subunit


Domain annotation for each model (and alignments):
>> CKS  Cyclin-dependent kinase regulatory subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.9   1.1   2.2e-34     4e-30       2      68 .]       7      72 .]       6      72 .] 0.98

  Alignments for each domain:
  == domain 1  score: 103.9 bits;  conditional E-value: 2.2e-34
                            CKS  2 eYSdkyeddeyeYRhViLpkellkkipksrlLsekewraLgIqqskgWehyeihkpephiLlfrrpk 68
                                    YSd ye + y YRhVi+pk++++ +p+ +lL+e+ewraLg+++s+gWehy+ihkpe h+Llfr++k
  gene256|gene256|rna256|rna256  7 FYSDPYETNDYIYRHVIIPKSTVQSLPE-KLLNESEWRALGLEMSVGWEHYMIHKPERHVLLFRKKK 72
                                   7**************************9.***********************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (72 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       271  (0.0151152); expected 358.6 (0.02)
Passed bias filter:                      212  (0.0118244); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.33u 0.26s 00:00:00.59 Elapsed: 00:00:00.41
# Mc/sec: 532.31
//
Query:       gene2560|gene2560|rna2560|rna2560  [L=309]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00037   19.8   0.1     0.0037   16.5   0.0    1.9  2  RTC       RNA 3'-terminal phosphate cyclase


Domain annotation for each model (and alignments):
>> RTC  RNA 3'-terminal phosphate cyclase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.1     0.011     2e+02      88     115 ..       7      32 ..       6      38 .. 0.90
   2 !   16.5   0.0   2.1e-07    0.0037     130     202 ..     116     276 ..     103     289 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.011
                                        HHHHHHHHHHHHTTSSS-EEEEEEEBSB CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                                RTC  88 itlllqtllplllfakkpseltlkGgTn 115
                                        i+ ++++ll++l+f k  +++ l G Tn
  gene2560|gene2560|rna2560|rna2560   7 ISCYINALLVILPFLK--IKIVLIGATN 32 
                                        678999*********8..99******98 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 2.1e-07
                                        HHHHHHHT.-EEEEEEEE--BTTTB-EEEEEEEE-.-S---EB................................. CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................................. RF
                                RTC 130 lpllkrfgvlelelelkkrGfypkGgGevelevepskklkpie................................. 172
                                        l+++k fg +e++ ++ +rGf    +G++el  ++   l+ +e                                 
  gene2560|gene2560|rna2560|rna2560 116 LSVMKLFG-AEIQHKILRRGFNS-TKGKLELVNTQI--LERFEsieltennctrintfivsshlsdflpksirsii 187
                                        7899****.8**********985.788888766655..5555555599999************************* PP

                                        ...........................................................BSS-HHHHHHHHHHHHH CS
                                        ...........................................................xxxxxxxxxxxxxxxxx RF
                                RTC 173 ...........................................................acvDehlqdqlilfmaL 189
                                                                                                    ++D  l d++++ m L
  gene2560|gene2560|rna2560|rna2560 188 kknipdaridmdrnkdsgtvglqvlmhceyfycetyrisrveecceklmkyifecilseNVFDDKLIDLVFVCMSL 263
                                        **************************************************************************** PP

                                        HT.-EEEEESS-- CS
                                        xxxxxxxxxxxxx RF
                                RTC 190 akgksrirvaelt 202
                                        a g s++r++ l+
  gene2560|gene2560|rna2560|rna2560 264 ATGVSQVRIRGLE 276
                                        *******997665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (309 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       899  (0.0501422); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 2189.50
//
Query:       gene2561|gene2561|rna2561|rna2561  [L=981]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        3.3    7.8   8.3         26    5.0   0.1    3.5  3  LisH      LisH


Domain annotation for each model (and alignments):
>> LisH  LisH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.1    0.0014        26       2      14 ..     275     287 ..     275     287 .. 0.94
   2 ?    3.8   1.1    0.0033        60       8      16 ..     292     300 ..     292     301 .. 0.95
   3 ?    1.4   0.1      0.02   3.5e+02      10      18 ..     726     734 ..     725     735 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.0014
                                        HHHHHHHHHHHHC CS
                               LisH   2 eLNrLIydYLvke 14 
                                        +LN LI+ +L+k+
  gene2561|gene2561|rna2561|rna2561 275 NLNELILGFLIKN 287
                                        69*********98 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.0033
                                        HHHHHHCT- CS
                               LisH   8 ydYLvkeGy 16 
                                        y+YL+++Gy
  gene2561|gene2561|rna2561|rna2561 292 YNYLMNNGY 300
                                        9******** PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.02
                                        HHHHCT-HH CS
                               LisH  10 YLvkeGyee 18 
                                        YL+ +Gy+ 
  gene2561|gene2561|rna2561|rna2561 726 YLQVKGYNR 734
                                        *******85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (981 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       708  (0.0394891); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.74u 0.27s 00:00:01.01 Elapsed: 00:00:00.47
# Mc/sec: 6282.37
//
Query:       gene2562|gene2562|rna2562|rna2562  [L=940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (940 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       598  (0.0333538); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.70u 0.28s 00:00:00.98 Elapsed: 00:00:00.48
# Mc/sec: 5926.22
//
Query:       gene2563|gene2563|rna2563|rna2563  [L=195]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.13   12.3   0.1       0.22   11.6   0.1    1.4  2  FtsJ      FtsJ-like methyltransferase


Domain annotation for each model (and alignments):
>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0      0.55   9.9e+03     146     164 ..      63      81 ..      57      87 .. 0.62
   2 ?   11.6   0.1   1.2e-05      0.22     117     161 ..     144     189 ..      92     192 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 0.55
                                        HHHHCCEEEEEEEE-SS-- CS
                               FtsJ 146 kqlkkfFekvsvvkPkssr 164
                                        + + + F +   vkPks+ 
  gene2563|gene2563|rna2563|rna2563  63 QICYNIFGSEIAVKPKSES 81 
                                        3366777777777887643 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 1.2e-05
                                        HHCCHCCCCECCCEEEECCCHCCCHH.HHHHHHHCCEEEEEEEE-S CS
                               FtsJ 117 alelalkllkpggtfvlkifrgeete.allkqlkkfFekvsvvkPk 161
                                         l+++ +l+++++ +++ +f++   + +l+ +l++fF+k+sv+k +
  gene2563|gene2563|rna2563|rna2563 144 LLTMSPRLFDKEALIMFNVFKNLVNDrNLFLKLNQFFRKISVCKKR 189
                                        5788899**************99999677777***********965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       499  (0.027832); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1356.00
//
Query:       gene2564|gene2564|rna2564|rna2564  [L=997]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (997 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       618  (0.0344693); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.65u 0.31s 00:00:00.96 Elapsed: 00:00:00.45
# Mc/sec: 6722.28
//
Query:       gene2565|gene2565|rna2565|rna2565  [L=70]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (70 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       511  (0.0285013); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.32u 0.23s 00:00:00.55 Elapsed: 00:00:00.37
# Mc/sec: 572.37
//
Query:       gene2566|gene2566|rna2566|rna2566  [L=117]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.1e-13   49.9  10.7    3.9e-13   49.1  10.7    1.4  1  Ribosomal_L40e  Ribosomal L40e family


Domain annotation for each model (and alignments):
>> Ribosomal_L40e  Ribosomal L40e family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.1  10.7   2.2e-17   3.9e-13       8      50 .]      70     111 ..      68     111 .. 0.89

  Alignments for each domain:
  == domain 1  score: 49.1 bits;  conditional E-value: 2.2e-17
                     Ribosomal_L40e   8 LAqKyncdKmiCrkCYArlpprAtnCrkkkCghsnnlrpKKkl 50 
                                        LA K + + ++CrkCYArl+ rA +Crk+ Cg s +lr KKk+
  gene2566|gene2566|rna2566|rna2566  70 LAAK-RLNVQVCRKCYARLSARAEHCRKRACGFSRKLRAKKKI 111
                                        6665.56779*******************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       604  (0.0336884); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.28s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 866.59
//
Query:       gene2567|gene2567|rna2567|rna2567  [L=325]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   2.5e-110  368.4   2.8     3e-110  368.1   2.8    1.1  1  Ribonuc_red_sm  Ribonucleotide reductase, small chain
  ------ inclusion threshold ------
      0.092   13.1   0.6        1.3    9.4   0.1    2.9  3  APP_N           Amyloid A4 N-terminal heparin-binding
       0.23   11.5   1.3       0.77    9.8   0.1    2.1  2  DUF3969         Protein of unknown function (DUF3969)


Domain annotation for each model (and alignments):
>> Ribonuc_red_sm  Ribonucleotide reductase, small chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  368.1   2.8  5.1e-114    3e-110       3     279 .]      18     283 ..      16     283 .. 0.98

  Alignments for each domain:
  == domain 1  score: 368.1 bits;  conditional E-value: 5.1e-114
                                        -TTS-SSHHHHHHHHHHHCT---GGGS-GHHHHHHHHSTS-HHHHHHHHHHHHHHHHHHHHHHHCHHHCHHCCBSS CS
                     Ribonuc_red_sm   3 vlfpikypeiwelykkleanfWtpeevdlskDlkdwkekLsedekefikkvlaflalldtivnenlverllsevqi 78 
                                        +lfp++ +++w++yk++ ++fWt eevdlskD++dw+ +L+ de++fi+ vlaf+a++d+ivnenl+e++++evq 
  gene2567|gene2567|rna2567|rna2567  18 TLFPLTNQDVWQMYKQALSSFWTVEEVDLSKDIDDWN-RLNCDERHFISYVLAFFAASDGIVNENLLENFSREVQL 92 
                                        79**********************************9.7************************************* PP

                                        HHHHHHHHHHHHHHHHHHHHHHHHHHHHT.-HHHHHHHHCHHHH-HHHHHHHHHHHHHHCTTTSCHHHHHHHHHHH CS
                     Ribonuc_red_sm  79 pearafygfqaamEniHaesYsllletlvkdekekdelfnaieenpalqkkaewikkwyeskkdeekfaerlvafa 154
                                        +ear+fygfq+++En+H+e+Ysll++t++kd++ekd lfnai +++ +++kaew+ kw+++k++  +fa+r++afa
  gene2567|gene2567|rna2567|rna2567  93 KEARCFYGFQIMIENVHSEMYSLLIDTYIKDQEEKDFLFNAIANINTVKRKAEWCFKWINDKDS--DFATRVIAFA 166
                                        ************************************************************9984..5********* PP

                                        HHHHCCCHHHHHHHHHHHHTTSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCSHHHHHHHHHHHHHHHHHHHHH CS
                     Ribonuc_red_sm 155 llegilfysgFaailwlkkrgllpglaeiielilrDeglHtdfagllfkelkeenelenkeleeeveelikeavel 230
                                        ++eg++f+++Fa+i+wlkkrgl+pgl++++eli+rDeglH +fa+l+ ++l+++        +e++ e++k+ave+
  gene2567|gene2567|rna2567|rna2567 167 CVEGLFFSGSFASIFWLKKRGLMPGLTFSNELISRDEGLHYQFAVLMNNTLVNR------CPKEKILEIVKDAVEI 236
                                        ***************************************************777......9*************** PP

                                        HHHHHHHHTTT.BTTCHHHHHHHHHHHHHHHHHHCTT---SS-TT---C CS
                     Ribonuc_red_sm 231 EkefitdalpvellglnkedvkqYieyvadrllmnlgyeklYnveeenP 279
                                        E+ef+ d+lpv+l+g+n+++++qYie+vad +l++lg+ + Ynv  +nP
  gene2567|gene2567|rna2567|rna2567 237 EEEFVSDSLPVSLIGMNCKLMCQYIEFVADGILVDLGVGRRYNV--QNP 283
                                        ********************************************..898 PP

>> APP_N  Amyloid A4 N-terminal heparin-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.32   1.9e+03      46      79 ..      30      62 ..      22      83 .. 0.67
   2 ?    9.4   0.1   0.00022       1.3      54      94 ..     133     175 ..     115     178 .. 0.81
   3 ?   -1.4   0.0      0.51     3e+03      79      98 ..     228     247 ..     212     248 .. 0.70

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.32
                              APP_N 46 vypk..lditnvveaskavkienWckkekkkcklsk 79
                                       +y++   +   v+e +    i++W + +   c  ++
  gene2567|gene2567|rna2567|rna2567 30 MYKQalSSFWTVEEVDLSKDIDDWNRLN---CDERH 62
                                       5544334455677888888899998776...33333 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00022
                              APP_N  54 nvveaskavkienWckk..ekkkcklskivkpyrClegefvsd 94 
                                         + + ++  +  +Wc k  + k   +++ v+ + C+eg f s 
  gene2567|gene2567|rna2567|rna2567 133 AIANINTVKRKAEWCFKwiNDKDSDFATRVIAFACVEGLFFSG 175
                                        4555566666678999988888999999************996 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.51
                              APP_N  79 kivkpyrClegefvsdallv 98 
                                        +ivk    +e efvsd+l v
  gene2567|gene2567|rna2567|rna2567 228 EIVKDAVEIEEEFVSDSLPV 247
                                        45555556789999999876 PP

>> DUF3969  Protein of unknown function (DUF3969)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.2      0.18   1.1e+03      26      57 ..     103     134 ..      99     137 .. 0.83
   2 ?    9.8   0.1   0.00013      0.77      22      65 ..     195     238 ..     186     270 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.18
                            DUF3969  26 isleeaesllFslemlelieelelsdelveii 57 
                                        i +e+++s ++sl +   i++ e +d l ++i
  gene2567|gene2567|rna2567|rna2567 103 IMIENVHSEMYSLLIDTYIKDQEEKDFLFNAI 134
                                        77899999999999999999988888888877 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00013
                            DUF3969  22 klkvisleeaesllFslemlelieelelsdelveiihkgmeLED 65 
                                        +++ is +e  ++ F + m +++ ++  +++++ei+++++e+E 
  gene2567|gene2567|rna2567|rna2567 195 SNELISRDEGLHYQFAVLMNNTLVNRCPKEKILEIVKDAVEIEE 238
                                        67889999999*******************************94 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (325 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       645  (0.0359752); expected 358.6 (0.02)
Passed bias filter:                      459  (0.025601); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2304.00
//
Query:       gene2568|gene2568|rna2568|rna2568  [L=166]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.5e-09   36.5   0.0    8.9e-09   35.8   0.0    1.3  1  Sld5      GINS complex protein


Domain annotation for each model (and alignments):
>> Sld5  GINS complex protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.8   0.0   4.9e-13   8.9e-09       2     108 ..      43     146 ..      42     147 .. 0.83

  Alignments for each domain:
  == domain 1  score: 35.8 bits;  conditional E-value: 4.9e-13
                                        EEEHHHHHHHHHTTSCCCHHCHHHCHHHHHHCCCHHTTS.SSSTTTTTTHHHHHHHHHHHHT...HCHHHHHHHHH CS
                               Sld5   2 eLPlWlaelLkrqrrveieppewlspesleailedetks.sdlpslpphflelavkllelard..ldelkrllrdl 74 
                                         +P+  a+ L +++ ++i +p +ls ++l+a++++e+++  + + + p+ +e+   ll    d  ++e++ ++ ++
  gene2568|gene2568|rna2568|rna2568  43 KVPIHTALFLHNTNLCKIPLPFFLSLDYLRAVKQAEKQHvNEYSPIYPYIFEVYDDLLRCV-DgrVEEIRMVISEI 117
                                        689999*********************************4444444555555555544333.357*********** PP

                                        HHHHHHHHHHTHCHHHHHHHTS-TCCHCCS-HHH CS
                               Sld5  75 levRlakirkfaenledaagggggellsglseeE 108
                                         ++R++k r ++ ++++ a     ++l++l+  E
  gene2568|gene2568|rna2568|rna2568 118 KDIRMEKSRRGLVSIDGRA-----LNLNNLTVYE 146
                                        *******************.....9999998766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       517  (0.028836); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 1111.62
//
Query:       gene2569|gene2569|rna2569|rna2569  [L=294]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.5e-30  103.9   2.6    4.5e-30  103.9   2.6    2.0  2  eIF-5_eIF-2B  Domain found in IF2B/IF5


Domain annotation for each model (and alignments):
>> eIF-5_eIF-2B  Domain found in IF2B/IF5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.9   2.6   2.5e-34   4.5e-30       3     116 ..       8     123 ..       6     124 .. 0.95
   2 ?   -1.3   0.1      0.11   1.9e+03      63      85 ..     270     292 ..     247     293 .. 0.77

  Alignments for each domain:
  == domain 1  score: 103.9 bits;  conditional E-value: 2.5e-34
                                        CCCSSSS--SSTT--EEEETT....EEEETTHHHHHHHHTTSHHHHHHHHHHHHTSEEEESETTEEEESSSSSCCH CS
                       eIF-5_eIF-2B   3 ekedkkerykmpklqvkvegkk...ktvivNfeeiakaLnrdpehvlkyllkelgtqgsidengrlilngkfeakk 75 
                                        +++d ++rykmp+l +k++gk    ktv+vN+ +i++aL+r++  + +++l+el++++++ +++ ++l+g++ a++
  gene2569|gene2569|rna2569|rna2569   8 NTKDPFYRYKMPHLITKQQGKLkntKTVLVNIGQISNALKRKEALLQQFILYELSVNSTV-KDNMFMLKGDYAASE 82 
                                        56799***************98899***********************************.999************ PP

                                        HHHHHHHHHHHHTSTSSSTSTCEEECCSSSCEEEEESSSTC CS
                       eIF-5_eIF-2B  76 leklldkyieeyVlCkeCkspetelekeerllvlkCkaCga 116
                                        ++++++ +ie  VlCkeC++pete+ +e++ + l C aCg 
  gene2569|gene2569|rna2569|rna2569  83 IQNIIYGFIELLVLCKECTNPETEMGVEGNEVSLCCYACGC 123
                                        ***************************876666******97 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.11
                                        TEEEESSSSSCCHHHHHHHHHHH CS
                       eIF-5_eIF-2B  63 grlilngkfeakkleklldkyie 85 
                                        ++ ++  k ++ +++++l +yi+
  gene2569|gene2569|rna2569|rna2569 270 KKSVVVDKKDSVRIRNTLMNYIN 292
                                        45566667778888999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (294 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       837  (0.0466841); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.22s 00:00:00.63 Elapsed: 00:00:00.37
# Mc/sec: 2356.39
//
Query:       gene257|gene257|rna257|rna257  [L=147]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        5.1    7.7  12.7        1.4    9.6   5.0    2.3  2  Pox_A21   Poxvirus A21 Protein


Domain annotation for each model (and alignments):
>> Pox_A21  Poxvirus A21 Protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.4    0.0062   1.1e+02      14      36 ..      21      41 ..      13      65 .. 0.75
   2 ?    9.6   5.0   7.6e-05       1.4       2      40 ..      90     129 ..      89     144 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.0062
                        Pox_A21 14 ifniivpaileklrlekeafeky 36
                                   +f +i   ilek++++++a++++
  gene257|gene257|rna257|rna257 21 VFGLI--LILEKVQVNQDAYVEI 41
                                   34444..499**********986 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 7.6e-05
                        Pox_A21   2 ivLFlvlcyFi.lifniivpaileklrlekeafekykklk 40 
                                    i +Fl+l++++ l++niiv  ++ +l   + a+  y+ l+
  gene257|gene257|rna257|rna257  90 IFIFLILVWYVlLVINIIVNLVFFRLLFYEFAWSSYALLG 129
                                    778999886662689********99998888888888764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1174  (0.0654805); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1024.24
//
Query:       gene2570|gene2570|rna2570|rna2570  [L=390]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.8e-48  163.6   1.4    9.2e-48  162.7   1.4    1.5  1  DUF155    Uncharacterised ACR, YagE family COG1723


Domain annotation for each model (and alignments):
>> DUF155  Uncharacterised ACR, YagE family COG1723
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  162.7   1.4   5.1e-52   9.2e-48       1     176 []     169     339 ..     169     339 .. 0.91

  Alignments for each domain:
  == domain 1  score: 162.7 bits;  conditional E-value: 5.1e-52
                             DUF155   1 vfiFknGsvVfwgldeeeeknflnkllkflneeselpreeeqeteeleyvydeqsessrikgdvivlksksllekl 76 
                                        vf+F++G+ Vfwg++e+ e+++l+ ++k  + +  + + ++ e e+++y + +  ++s + +dvi+l++++  +k+
  gene2570|gene2570|rna2570|rna2570 169 VFFFDYGVTVFWGVSENVETKILK-IIKISEYN--SYDTSKIEVENFQYGIID--TQSMFCNDVIYLNTEDYFHKM 239
                                        8***************99999999.55443332..334444447888887776..7789********9999***** PP

                             DUF155  77 aiShalaqSvkLdvlEesldellestekipkelakkgklklsrkellkktgellslrinlnlkselldtPdffWee 152
                                        +iS+a+aqSvkLd++E+++d+++es++++p+e+++ g++  +rke+lk +g+l++lri+lnl+ ++ld+P+++W+ 
  gene2570|gene2570|rna2570|rna2570 240 IISNAIAQSVKLDYFENLTDKTIESVKDLPEEVENWGRVGRNRKEILKMVGRLHKLRIDLNLVTNILDEPEVLWHF 315
                                        *************************************99889********************************** PP

                             DUF155 153 peleslyeavseyleikeRikiLn 176
                                        p++ +lye++++ leik R +iLn
  gene2570|gene2570|rna2570|rna2570 316 PRYSELYESLRRCLEIKARADILN 339
                                        ***********************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (390 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       800  (0.0446204); expected 358.6 (0.02)
Passed bias filter:                      441  (0.024597); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.38
# Mc/sec: 3040.17
//
Query:       gene2571|gene2571|rna2571|rna2571  [L=300]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.3e-49  167.1  11.6    3.2e-49  165.8  11.6    1.7  1  SRP_TPR_like  Putative TPR-like repeat
    7.7e-08   32.5   4.4    1.1e-06   28.8   1.7    2.4  2  ANAPC3        Anaphase-promoting complex, cyclosome, subunit 
  ------ inclusion threshold ------
        1.5    9.2   6.1         25    5.4   0.2    3.1  2  TPR_8         Tetratricopeptide repeat
          2    8.8   6.5        5.7    7.3   0.5    3.5  4  TPR_2         Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> SRP_TPR_like  Putative TPR-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  165.8  11.6   7.2e-53   3.2e-49       1     117 []       9     146 ..       9     146 .. 0.99

  Alignments for each domain:
  == domain 1  score: 165.8 bits;  conditional E-value: 7.2e-53
                       SRP_TPR_like   1 eneeyekilrlegkelkkfkvvaliklekyeeaLkllkkgs.....................alsedvrfEkaYvl 55 
                                        en+ey++il+leg ++++fkv++li+le+y++aL+l+kk++                     ++s+d+r+EkaY+l
  gene2571|gene2571|rna2571|rna2571   9 ENKEYQQILELEGVQYDRFKVTCLIHLERYRDALILMKKMDaehtkqqnevgdkmqkmqikeKMSGDMRYEKAYAL 84 
                                        689************************************************************************* PP

                       SRP_TPR_like  56 YklkkykkalkilkkveaeekvkvlksqvlYrlgsyekAYklLskekkedelvvNllAvdsl 117
                                        Yklkkykk+l+ilk++ea+e+v+vl+sqv+Y+l+sy+kAY++Lsk+k+e+e++vNl+A+dsl
  gene2571|gene2571|rna2571|rna2571  85 YKLKKYKKSLSILKRMEASERVNVLLSQVYYFLRSYRKAYNTLSKCKYEKERDVNLCAMDSL 146
                                        ************************************************************96 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.1     0.013        57      64      81 ..      30      47 ..      13      48 .. 0.81
   2 !   28.8   1.7   2.4e-10   1.1e-06      18      82 .]      69     130 ..      51     130 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.013
                                       HHHHHTT-HHHHHHHH-S CS
                             ANAPC3 64 qcllkLkkyeeAiaaLek 81
                                        cl+ L++y +A+ +++k
  gene2571|gene2571|rna2571|rna2571 30 TCLIHLERYRDALILMKK 47
                                       6999********987765 PP

  == domain 2  score: 28.8 bits;  conditional E-value: 2.4e-10
                                        HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCTSHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-SS CS
                             ANAPC3  18 aetespedayllAlclylngqykrAyellrkaklnskslgcrylfAqcllkLkkyeeAiaaLekl 82 
                                        +e+ s + +y +A++ly++++yk+ + +l+++   + s+++ +l+ q+++ L +y +A+++L+k+
  gene2571|gene2571|rna2571|rna2571  69 KEKMSGDMRYEKAYALYKLKKYKKSLSILKRM---EASERVNVLLSQVYYFLRSYRKAYNTLSKC 130
                                        455666679***********************...9999***********************987 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   1.5    0.0086        39       3      25 ..      76      98 ..      74      99 .. 0.87
   2 ?    5.4   0.2    0.0055        25       2      28 ..     105     131 ..     104     137 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.0086
                                       HHHHHHHHHHHTT-HHHHHHHHH CS
                              TPR_8  3 ayynlgsiylklgdyeeAkeyye 25
                                       + y +++++ kl++y+++ + ++
  gene2571|gene2571|rna2571|rna2571 76 MRYEKAYALYKLKKYKKSLSILK 98
                                       6799*************998876 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0055
                                        CHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                              TPR_8   2 eayynlgsiylklgdyeeAkeyyekal 28 
                                        ++ ++l+++y  l  y +A  ++ k+ 
  gene2571|gene2571|rna2571|rna2571 105 RVNVLLSQVYYFLRSYRKAYNTLSKCK 131
                                        67889*****************99995 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.1       3.6   1.6e+04      23      30 ..      12      19 ..      11      20 .. 0.80
   2 ?    1.1   0.0      0.12   5.5e+02      10      26 ..      31      47 ..      30      48 .. 0.86
   3 ?    7.3   0.5    0.0013       5.7       5      22 ..      78      95 ..      77     100 .. 0.86
   4 ?    1.1   0.0      0.12   5.6e+02       5      24 ..     108     127 ..     105     131 .. 0.79

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 3.6
                              TPR_2 23 afekAlel 30
                                        +++ lel
  gene2571|gene2571|rna2571|rna2571 12 EYQQILEL 19
                                       69999998 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.12
                              TPR_2 10 ayyklgdyeeAleafek 26
                                       ++++l +y +Al +++k
  gene2571|gene2571|rna2571|rna2571 31 CLIHLERYRDALILMKK 47
                                       78999******988876 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.0013
                              TPR_2  5 ynlGlayyklgdyeeAle 22
                                       y+ ++a+ykl++y++ l 
  gene2571|gene2571|rna2571|rna2571 78 YEKAYALYKLKKYKKSLS 95
                                       789***********9986 PP

  == domain 4  score: 1.1 bits;  conditional E-value: 0.12
                              TPR_2   5 ynlGlayyklgdyeeAleaf 24 
                                          l ++yy l  y +A + +
  gene2571|gene2571|rna2571|rna2571 108 VLLSQVYYFLRSYRKAYNTL 127
                                        578999**999999997655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (300 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1293  (0.0721178); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2187.46
//
Query:       gene2572|gene2572|rna2572|rna2572  [L=546]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   5.1e-125  417.3   2.3   6.2e-125  417.0   2.3    1.1  1  tRNA-synt_1g    tRNA synthetases class I (M)
    5.8e-09   34.8   0.1     0.0033   15.8   0.0    3.2  3  tRNA-synt_1     tRNA synthetases class I (I, L, M and V)
  ------ inclusion threshold ------
      0.011   14.7   0.3          4    6.3   0.0    3.0  2  tRNA-synt_1f    tRNA synthetases class I (K)
      0.013   15.5   0.1      0.037   14.0   0.1    1.8  2  Anticodon_1     Anticodon-binding domain of tRNA
        0.1   12.8   4.0       0.41   10.8   4.0    2.1  1  Laminin_EGF     Laminin EGF domain
       0.13   12.4   0.7        7.2    6.7   0.0    2.7  3  Sedlin_N        Sedlin, N-terminal conserved region


Domain annotation for each model (and alignments):
>> tRNA-synt_1g  tRNA synthetases class I (M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  417.0   2.3  2.1e-128  6.2e-125       2     391 .]       8     394 ..       7     394 .. 0.96

  Alignments for each domain:
  == domain 1  score: 417.0 bits;  conditional E-value: 2.1e-128
                                        EEEE--B--SS---HHHHH.HHHHHHHHHHHHHHTT-EEEEEEEE---SHHHHHHHHHTTS-HHHHHHHHHHHHHH CS
                       tRNA-synt_1g   2 lvttalpYangklHlGhll.evisaDifaRykrlrgeevlfvcgtDehGtpielkAekegvtpeelvekvheeike 76 
                                        ++t+alpY+n+++HlG+++ +v+saD++aR++r+++e+v+fvcgtD +Gt++e++A+k ++t ee+v+++++++ +
  gene2572|gene2572|rna2572|rna2572   8 VITAALPYVNNSPHLGNIIgSVLSADVYARFCRKSNEKVIFVCGTDDYGTATEITARKDNTTCEEVVKHNRQIMID 83 
                                        79************************************************************************** PP

                                        HHHHTT---SEEEETTSHHHHHHHHHHHHHHHHTT-EEEEEEEEEEETTTTEEE-GGG-EE........-TTS-EE CS
                       tRNA-synt_1g  77 lfkklnisfdkygrttseehkelvqeifkklkekgliyekeieqlycpkderflpdryvegtCPkckseeargdqc 152
                                        +f++++i+fd +g+t++ eh+++vq+if+++ +   i+e  ++q+ c k+e+fl+dry++gtC kcks   +gdqc
  gene2572|gene2572|rna2572|rna2572  84 VFDWFSIEFDCFGQTSDPEHSKVVQDIFHRIID--RIEEDVMQQYHCSKCEMFLADRYLTGTCSKCKSYGLQGDQC 157
                                        *******************************97..8**************************************** PP

                                        -TTSSB-E................EEE.EEEEEE-GGGGHHHHHHHH.HH-TTSHHHHHHHH.HHHHT----EE-E CS
                       tRNA-synt_1g 153 eecgkkleptelinpksaisgskpevketehlffklskfekklkewieeeekeleenvkkivkewlkegLkdlais 228
                                        ++cg  l+ +e+i+p++ai+g++p+++et+hlf+kl++++++l+  +e++++++++n+ +i+++wl+++L++++i+
  gene2572|gene2572|rna2572|rna2572 158 DACGILLKIDEIIDPECAICGERPQIRETRHLFLKLNELADDLRLKYEKNSSRWSKNACEITLQWLEKDLHKRCIT 233
                                        ********************************************999999999*********************** PP

                                        SS-SSS-EETTECCEEE-HHHHHHHHHHHTTTTT-...TTSGGGG.G--S.........EEEEEGGGHHHHHTHHH CS
                       tRNA-synt_1g 229 rdldwGipvPgaekkvlYVWldAligYisatkelakkkgeeekwkeyWakdke...velvhfigkdiikFHtifwP 301
                                        rdl+wG+pvP + +kv+YVW+dA+igY s++k++++++ e++k+++  + +++   +e v+f+gkd+++FHti+ P
  gene2572|gene2572|rna2572|rna2572 234 RDLKWGVPVP-DMNKVFYVWFDAVIGYFSFFKMYVERS-ENRKFESLKQLEEDflsYEFVQFMGKDNVPFHTIIMP 307
                                        **********.679*********************666.78899999965555444899***************** PP

                                        HHHHHTT----S-EEEE--EEE--------------HHHHHHH..H-HHHHHHHHHHHS-TTS-EEE-HHHHHHHH CS
                       tRNA-synt_1g 302 aillgaelklpkkvvaheyltvegkKlSkSrgvvvkakealer..ldadllRYylaaeapekkDldfswedfverv 375
                                        ail      + +k++++eyl++e+kK+SkS++++++ ++++++   + dl+RYyl++ +pe+kD++fs +df + +
  gene2572|gene2572|rna2572|rna2572 308 AILDF----IANKLSVTEYLMFENKKFSKSKQIGIFGSDLIHNeyGTCDLWRYYLVKVRPETKDSNFSVTDFLNST 379
                                        **975....67899*************************998873569*************************986 PP

                                        HHHCCCHHHHHHHHH. CS
                       tRNA-synt_1g 376 NseLadklgnlvnRvl 391
                                         s+L +++gnl nRvl
  gene2572|gene2572|rna2572|rna2572 380 -SDLQNNFGNLCNRVL 394
                                        .8************85 PP

>> tRNA-synt_1  tRNA synthetases class I (I, L, M and V)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   1.1e-06    0.0033      26      83 ..       8      66 ..       2     100 .. 0.85
   2 !   12.6   0.1   9.7e-06     0.029     367     432 ..     176     243 ..     155     284 .. 0.77
   3 !    2.8   0.0    0.0089        27     560     602 .]     326     371 ..     246     371 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.1e-06
                        tRNA-synt_1 26 ilvdgPPyvtGslHiGhalaktlk.divirykrmkGkevlyvpGwDhaGlaieakvekk 83
                                       ++++  Pyv+ s+H+G+++ ++l  d+  r+ r + ++v +v G+D  G a+e +  k 
  gene2572|gene2572|rna2572|rna2572  8 VITAALPYVNNSPHLGNIIGSVLSaDVYARFCRKSNEKVIFVCGTDDYGTATEITARKD 66
                                       567778****************964999************************9887665 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 9.7e-06
                        tRNA-synt_1 367 rskkpiiyrateqWfvrvkeladaalkave..kvqfvpkskekryaswleniqdWciSRqrwWGhrip 432
                                          ++    r t   f +++elad++  + e  + +++ +  e + + + ++ +  ci R++ WG+++p
  gene2572|gene2572|rna2572|rna2572 176 ICGERPQIRETRHLFLKLNELADDLRLKYEknSSRWSKNACEITLQWLEKDLHKRCITRDLKWGVPVP 243
                                        55555567888999*********9866665456777777777666555579****************9 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.0089
                        tRNA-synt_1 560 eGrKmSKslgNvidpldvi.kkyga.dalRltli.lsdvgrdinls 602
                                        e +K SKs++  i  +d+i ++yg+ d  R++l+   + ++d n+s
  gene2572|gene2572|rna2572|rna2572 326 ENKKFSKSKQIGIFGSDLIhNEYGTcDLWRYYLVkVRPETKDSNFS 371
                                        569*******9998887762689976999*****888999998875 PP

>> tRNA-synt_1f  tRNA synthetases class I (K)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0    0.0013         4      36      89 ..      19      73 ..      16     149 .. 0.90
   2 ?    5.0   0.0    0.0033        10     255     322 ..     303     373 ..     291     392 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0013
                       tRNA-synt_1f 36 liHiGnlr.evltadlvaralrkrgeevrlilisDdmDglRkvpenlpeklleky 89
                                       ++H+Gn+   vl+ad+ ar  rk  e+v +++  Dd+     + +  ++ ++e+ 
  gene2572|gene2572|rna2572|rna2572 19 SPHLGNIIgSVLSADVYARFCRKSNEKVIFVCGTDDYGTATEITARKDNTTCEEV 73
                                       58****7549***************************888777777776655555 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0033
                       tRNA-synt_1f 255 skia.eilggeaPekvvYelillkggekmssSkGnvltledwl..evaepevlrflilrrkPkka.kkldld 322
                                        + i+  il++ a +  v e+++ +++ k s+Sk  ++  +d++  e+++ ++ r+++++ +P+++  ++++ 
  gene2572|gene2572|rna2572|rna2572 303 TIIMpAILDFIANKLSVTEYLMFENK-KFSKSKQIGIFGSDLIhnEYGTCDLWRYYLVKVRPETKdSNFSVT 373
                                        55667788888878888888888887.9*************97558****************8751445544 PP

>> Anticodon_1  Anticodon-binding domain of tRNA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       3.6   1.1e+04      37      51 ..     387     401 ..     374     404 .. 0.69
   2 ?   14.0   0.1   1.2e-05     0.037       2      92 ..     417     506 ..     416     531 .. 0.78

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 3.6
                        Anticodon_1  37 ndlcdwylelvkprl 51 
                                         +lc+  l+++k+++
  gene2572|gene2572|rna2572|rna2572 387 GNLCNRVLKFIKNKM 401
                                        458888888888776 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 1.2e-05
                        Anticodon_1   2 rwilselnklvkevteayeeyrfnkaasalyeffwndlcdwylelvkprlysesaedkra.aqevllevletllrl 76 
                                        ++++s++n+l++e+++ + + +++k ++ l e ++  +c+++l+ + ++     ++d+++   ++++ v+  l  l
  gene2572|gene2572|rna2572|rna2572 417 QEFVSKINDLLSEYKRVMCHIKMKKGLTVLSEMCM--VCNHFLQKTFEHS---VDQDAKNdSFALVFSVIALLADL 487
                                        57899**************************9865..5899988654333...22233455789************ PP

                        Anticodon_1  77 laPfmPfitEelwqr...e 92 
                                         +Pf+P i+ +l +    +
  gene2572|gene2572|rna2572|rna2572 488 YEPFIPNICADLHEMceiK 506
                                        **********999444443 PP

>> Laminin_EGF  Laminin EGF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   4.0   0.00014      0.41      11      34 ..     129     160 ..     120     167 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00014
                                        SSEET......TTECES.BTT.TEESTTS-EE CS
                        Laminin_EGF  11 ssCds......stgqCl.Cke.nveGrkCdrC 34 
                                        s+C+        tg+C+ Ck  + +G++Cd C
  gene2572|gene2572|rna2572|rna2572 129 SKCEMfladryLTGTCSkCKSyGLQGDQCDAC 160
                                        556669999999*******9648********* PP

>> Sedlin_N  Sedlin, N-terminal conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0         3   8.9e+03      62      81 ..      33      59 ..      19      78 .. 0.68
   2 ?    6.7   0.0    0.0024       7.2      10      50 ..      88     128 ..      85     148 .. 0.87
   3 ?    3.1   0.2     0.031        94      13      74 ..     266     330 ..     260     391 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 3
                           Sedlin_N 62 svsa.yvtnskikflllhes......s 81
                                        v+a ++ +s+ k++ ++++      +
  gene2572|gene2572|rna2572|rna2572 33 DVYArFCRKSNEKVIFVCGTddygtaT 59
                                       566557888899999988864444440 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0024
                           Sedlin_N  10 yelefssskekeekelkeLnqfilhasLDivedlqwktnnl 50 
                                        + +ef+  ++++++e++++ q i h  +D +e+ ++++ ++
  gene2572|gene2572|rna2572|rna2572  88 FSIEFDCFGQTSDPEHSKVVQDIFHRIIDRIEEDVMQQYHC 128
                                        789******************************99997655 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.031
                           Sedlin_N  13 efssskekeekelkeL.nqfilhasLDivedlqwktnnlylgkvdkf..eklsvsayvtnskikf 74 
                                         +++s++++ ++lk+L   f+++     + + +   + + + ++  f  +klsv+ y+ + + kf
  gene2572|gene2572|rna2572|rna2572 266 YVERSENRKFESLKQLeEDFLSYEFVQFMGKDNVPFHTIIMPAILDFiaNKLSVTEYLMFENKKF 330
                                        45555555556799999999999999999999999999*********9************99999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (546 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       777  (0.0433376); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.60u 0.28s 00:00:00.88 Elapsed: 00:00:00.45
# Mc/sec: 3678.91
//
Query:       gene2573|gene2573|rna2573|rna2573  [L=66]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-16   60.1   2.4    1.7e-16   60.0   2.4    1.0  1  Tfb5      Transcription factor TFIIH complex subunit Tfb5


Domain annotation for each model (and alignments):
>> Tfb5  Transcription factor TFIIH complex subunit Tfb5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.0   2.4   9.4e-21   1.7e-16       1      66 [.       1      63 [.       1      65 [. 0.96

  Alignments for each domain:
  == domain 1  score: 60.0 bits;  conditional E-value: 9.4e-21
                               Tfb5  1 MvkaikGvLveCDpaikqlilkldeqepsqkfiiedLDethlfvkeevveelkkeleellekntye 66
                                       Mv+a+kG+ ++++++ik++i+ ++e+    +++ie++ ++ +f++ ++ ++lk+++e +l+++  +
  gene2573|gene2573|rna2573|rna2573  1 MVRATKGTYIKTEMSIKEVIMFINETD---NIVIEEIKDNAVFIQLNKTDMLKRKIEHILNSTYKH 63
                                       9*************************8...*******************************98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (66 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       910  (0.0507558); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.33u 0.26s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 501.79
//
Query:       gene2574|gene2574|rna2574|rna2574  [L=452]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (452 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       658  (0.0367003); expected 358.6 (0.02)
Passed bias filter:                      254  (0.014167); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 3279.16
//
Query:       gene2575|gene2575|rna2575|rna2575  [L=91]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       490  (0.02733); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.30s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 608.90
//
Query:       gene2576|gene2576|rna2576|rna2576  [L=419]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (419 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       785  (0.0437838); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 2903.75
//
Query:       gene2577|gene2577|rna2577|rna2577  [L=135]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       511  (0.0285013); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 975.48
//
Query:       gene2578|gene2578|rna2578|rna2578  [L=591]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (591 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1031  (0.0575046); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.44
# Mc/sec: 4071.00
//
Query:       gene2579|gene2579|rna2579|rna2579  [L=335]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    5.8e-24   84.5   0.1      4e-23   81.8   0.0    2.3  2  XPG_N       XPG N-terminal domain
      8e-24   83.8   1.4      8e-24   83.8   1.4    2.5  3  XPG_I       XPG I-region
     0.0003   21.3   1.3    0.00071   20.1   0.0    2.3  2  5_3_exonuc  5'-3' exonuclease, C-terminal SAM fold
  ------ inclusion threshold ------
       0.11   12.6   0.3        0.3   11.3   0.1    1.8  2  VIGSSK      Helicase-associated putative binding domain, C-te


Domain annotation for each model (and alignments):
>> XPG_N  XPG N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.8   0.0   8.9e-27     4e-23       1     100 [.       1     103 [.       1     104 [. 0.92
   2 ?   -0.7   0.0      0.45     2e+03      16      31 ..     115     130 ..     109     135 .. 0.78

  Alignments for each domain:
  == domain 1  score: 81.8 bits;  conditional E-value: 8.9e-27
                                        X--TTHHHHHHHH-GEEEEEGGGGTTEEEEEEHHHHHHHHHHHSE.ETTEE-BS...-HHHHHHHHHHHHHHHTTE CS
                              XPG_N   1 MGikgLlkllkevaairsvsiealegkklaiDaslwlyrfliavreqlgnalen...tshlmglfsrllrlldfgi 73 
                                        MGi+ L k++k+     +  + ++  kk+a Dasl+ y+ l+a+r+  ++  +n   tsh+ g+f++++ l + gi
  gene2579|gene2579|rna2579|rna2579   1 MGIHNLTKVIKKYYRPAEHPLSFYRTKKMAFDASLLTYQYLVAIRSDGAQLAHNsssTSHISGFFYKIINLAEIGI 76 
                                        **************666777999**********************766666555888******************* PP

                                        EEEEEE--S--GGGHHHHHHHHHHHHH CS
                              XPG_N  74 kPifVFdgkapdlkkeelekrserrqe 100
                                        kP+fVFdgk+p++k+ee+++r+err++
  gene2579|gene2579|rna2579|rna2579  77 KPLFVFDGKPPQVKSEEIARRNERRKD 103
                                        *************************97 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.45
                                        EEEEEGGGGTTEEEEE CS
                              XPG_N  16 irsvsiealegkklai 31 
                                        + +v++e++ ++kl i
  gene2579|gene2579|rna2579|rna2579 115 MDKVKMEKYDKRKLKI 130
                                        5789999999999988 PP

>> XPG_I  XPG I-region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.2      0.47   2.1e+03      58      79 ..     108     130 ..      91     142 .. 0.53
   2 !   83.8   1.4   1.8e-27     8e-24       2      94 .]     144     225 ..     143     225 .. 0.96
   3 ?   -3.2   0.1       2.6   1.2e+04      59      75 ..     251     267 ..     238     277 .. 0.51

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.47
                                        ..EEECEEEEEEHHHHHHH.HT- CS
                              XPG_I  58 kekekkkvevidlekvlke.lgl 79 
                                         ++++++++++++ek  k+ l++
  gene2579|gene2579|rna2579|rna2579 108 YSEAEEQMDKVKMEKYDKRkLKI 130
                                        24445556666665544332444 PP

  == domain 2  score: 83.8 bits;  conditional E-value: 1.8e-27
                                        HHT--EEE-SS-HHHHHHHHHHTTSSSEEE-SSSHHHHTT-SEEEESTT.ECECTT..EEECEEEEEEHHHHHHHH CS
                              XPG_I   2 lmgipyvvApgEAEAqcayLqkkglvdaviseDsDlllFGapkvlrnlskkkskkkkekekkkvevidlekvlkel 77 
                                        +mg+ y ++  EAEA ca+L++kg+vd+v++eD+D+l+F ap++l+n+     k+       +v +++l+++l+ +
  gene2579|gene2579|rna2579|rna2579 144 AMGVAYTISENEAEAFCAALCRKGIVDYVCTEDMDALCFRAPVLLKNFV----KD-------SVAEYRLDEILRDM 208
                                        79**********************************************8....33.......4899********** PP

                                        T--HHHHHHHHHHHCET CS
                              XPG_I  78 gltreqlidlaillgcD 94 
                                        +l+ ++++dl+illgcD
  gene2579|gene2579|rna2579|rna2579 209 KLEFDEFVDLCILLGCD 225
                                        ****************9 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 2.6
                                        .EEECEEEEEEHHHHHH CS
                              XPG_I  59 ekekkkvevidlekvlk 75 
                                          ++ +v+ +++ek+++
  gene2579|gene2579|rna2579|rna2579 251 IVKELQVTDYEYEKARE 267
                                        33445555555544443 PP

>> 5_3_exonuc  5'-3' exonuclease, C-terminal SAM fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.2         2   8.8e+03      43      66 ..     113     134 ..     100     144 .. 0.49
   2 !   20.1   0.0   1.6e-07   0.00071       8      67 ..     217     276 ..     210     280 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 2
                         5_3_exonuc  43 eilenldelkekk.lkekLeenkee 66 
                                        e    +d++k +k  k+kL+ +ke+
  gene2579|gene2579|rna2579|rna2579 113 EQ---MDKVKMEKyDKRKLKIGKEH 134
                                        32...33333333123455555554 PP

  == domain 2  score: 20.1 bits;  conditional E-value: 1.6e-07
                         5_3_exonuc   8 dlkaLvGDssDnipGvpgiGektAakLlkeygsleeilenld..elkekklkekLeenkeea 67 
                                        dl  L G   D    ++giG+ +A +L++++ s+e+i+++l+  + + +k++e++ + k+++
  gene2579|gene2579|rna2579|rna2579 217 DLCILLG--CDYAGTIKGIGPMKAETLIRKHRSIENIVKELQvtDYEYEKARETFLNMKNNV 276
                                        5555555..4555679***********************99865556688999888877766 PP

>> VIGSSK  Helicase-associated putative binding domain, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0      0.96   4.3e+03      14      19 ..     101     106 ..      89     120 .. 0.44
   2 ?   11.3   0.1   6.6e-05       0.3      12      45 ..     120     154 ..     109     156 .. 0.70

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.96
                             VIGSSK  14 kkkeak 19 
                                        +k++a+
  gene2579|gene2579|rna2579|rna2579 101 RKDAAE 106
                                        222222 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 6.6e-05
                             VIGSSK  12 kekkkeakks.tkkksDaiqAILasaGVeYTHens 45 
                                         ek +++k +  k+ +D i++ L + GV+YT + +
  gene2579|gene2579|rna2579|rna2579 120 MEKYDKRKLKiGKEHTDDIKSLLDAMGVAYTISEN 154
                                        333334343468999****************6655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (335 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1725  (0.0962128); expected 358.6 (0.02)
Passed bias filter:                      702  (0.0391544); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.45
# Mc/sec: 2212.85
//
Query:       gene258|gene258|rna258|rna258  [L=132]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       814  (0.0454013); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 886.98
//
Query:       gene2580|gene2580|rna2580|rna2580  [L=90]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.068   13.8   3.2      0.088   13.4   3.2    1.1  1  BEX       Brain expressed X-linked like family
      0.077   11.7   0.4      0.077   11.7   0.4    1.1  1  DUF773    CDK5 regulatory subunit-associated protein 3


Domain annotation for each model (and alignments):
>> BEX  Brain expressed X-linked like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   3.2   9.8e-06     0.088      84     116 ..      50      82 ..      45      89 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 9.8e-06
                                BEX  84 sneemireaddmervqeElrkvrqKlrefqwkq 116
                                         +ee ++e+ d++ ++eE rk ++++re  +++
  gene2580|gene2580|rna2580|rna2580  50 GREEFMKEFLDLSLFVEEKRKEMERMRESELMN 82 
                                        579*************************99986 PP

>> DUF773  CDK5 regulatory subunit-associated protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.4   8.6e-06     0.077     342     384 ..      39      81 ..       8      89 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 8.6e-06
                             DUF773 342 eealsllddteyRnkllddLlELeaFLkqRlvElsnestsvls 384
                                         + +++l++ + R++++++ l+L  F++ +  E+++  +s l 
  gene2580|gene2580|rna2580|rna2580  39 RKRICVLKECAGREEFMKEFLDLSLFVEEKRKEMERMRESELM 81 
                                        344599****************************998876664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       577  (0.0321825); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 631.23
//
Query:       gene2581|gene2581|rna2581|rna2581  [L=459]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   6.8e-143  476.1   0.1   8.3e-143  475.8   0.1    1.1  1  SHMT      Serine hydroxymethyltransferase


Domain annotation for each model (and alignments):
>> SHMT  Serine hydroxymethyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  475.8   0.1  4.6e-147  8.3e-143       2     398 ..      10     403 ..       9     404 .. 0.96

  Alignments for each domain:
  == domain 1  score: 475.8 bits;  conditional E-value: 4.6e-147
                                        HHHTHHHHHHHHHHHHHHHHSEE-STT-----HHHHHHHTSGGGG----EETTEESSST-HHHHHHHHHHHHHHHH CS
                               SHMT   2 eesdpevaeiikkekerqkeeieliasenftskavlealGsvltnkyaeGyPGkryyGGcefvdeveelaqdrake 77 
                                        +++d e++++i +ek+rq+e+ieliase ++s  vl+a  s l+nky+eG  G+ryyGG++++d++e+l++dra++
  gene2581|gene2581|rna2581|rna2581  10 KDTDIELYNLIMDEKQRQEESIELIASESYVSVPVLQASISLLHNKYSEGMVGERYYGGTDVIDKIESLCKDRALR 85 
                                        789************************************************************************* PP

                                        HCT-STTTEEEE---SSHHHHHHHHHHHHT-TT-EEEEESCTTTSTGGGT-BTSS-B-SHHHHHSEEEEE-B-TTT CS
                               SHMT  78 lfkldpakwgvnvqplsGsqanlavytallepgdrilgldladGGhlthGakveskkisassklfesveykvdket 153
                                        +f+ld + wgvnvqp+sG+ an+++y+al+ pg+r++gldl  GGhl+hG+k+e++kis++sk+fes +yk++ ++
  gene2581|gene2581|rna2581|rna2581  86 VFGLDENVWGVNVQPYSGAIANFEIYNALIGPGGRLMGLDLFSGGHLSHGFKIENRKISVTSKYFESYPYKLK-ND 160
                                        ************************************************************************9.99 PP

                                        SSB-HHHHHHHHHHH--SEEEEE-SST-S---HHHHHHHHHHTT-EEEEE-GGGHHHHHTTSS--GCCTSSEEEEE CS
                               SHMT 154 glidydelekkakefkPklivaGtsaysrlidyarlreiadevgayllvdmahiaGlvaagvipsPfeyadvvttt 229
                                        g idy+++++   + k  ++++G+say+r +dy+r+r+iad  +ayl++d+ahi+Glva+g + +Pfey+dvv tt
  gene2581|gene2581|rna2581|rna2581 161 GSIDYEQMQRDFVHNKVNILIGGASAYPRDFDYKRMRKIADLNNAYLMADIAHISGLVACGKMNNPFEYCDVVMTT 236
                                        **************************************************************************** PP

                                        SSSTT-S-S-EEEEEC-SEEEEETTTEEEEHHHHHHHHHHHTTTT-SS--HHHHHHHHHHHHHCTSHHHHHHHHHH CS
                               SHMT 230 thktlrGprgglillrkgvksvdktgkevleelekkinsavfPglqGGPlnhviaakavalkealepefkvyqkqv 305
                                          k l+Gp++++i++rk     +k+g     ++++  n +vfPg qGGP+n +ia++a alk a ++e++++  qv
  gene2581|gene2581|rna2581|rna2581 237 VQKMLKGPKAAMIFYRK-----EKNGV----NIQNLTNRSVFPGCQGGPHNQTIAGIAAALKIAKSEEYRNFIDQV 303
                                        ****************2.....45554....588999*************************************** PP

                                        HHHHHHHHHHHHHTT-EEGGGS-SSSEEEEEGGGG.......TS-HHHHHHHHHHTTEE-EEE--TTSSTTTT-SE CS
                               SHMT 306 lknakalaealkekgyklvsgGtdnhlvlvdlrek.......gldGkraekvlekvnitankntvPgdksalvtsG 374
                                        l n +a+++++ e+g kl+++Gt nhl ++d+r+         ldG+  e v++ vni+ nkn++P d s l + G
  gene2581|gene2581|rna2581|rna2581 304 LLNMQAMTKVFLESGVKLLTNGTINHLAMLDMRNIcmdgrvfSLDGSLFEWVCNFVNISLNKNSLPDDTSCLHPNG 379
                                        *********************************982222222355667899************************* PP

                                        EEEESHHHHHTT--HHHHHHHHHH CS
                               SHMT 375 lrlGtpaltsrgfkeedlekvakf 398
                                        +r+Gt ++t+rgfke+  +++a++
  gene2581|gene2581|rna2581|rna2581 380 IRVGTVSVTTRGFKEDGCTRIAEM 403
                                        ********************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (459 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       565  (0.0315132); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.25s 00:00:00.82 Elapsed: 00:00:00.43
# Mc/sec: 3215.43
//
Query:       gene2582|gene2582|rna2582|rna2582  [L=321]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   2.3e-109  365.6  18.9   2.8e-109  365.3  18.9    1.0  1  Glyco_transf_15  Glycolipid 2-alpha-mannosyltransferase


Domain annotation for each model (and alignments):
>> Glyco_transf_15  Glycolipid 2-alpha-mannosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  365.3  18.9  1.6e-113  2.8e-109      54     324 ..      12     282 ..       8     283 .. 0.98

  Alignments for each domain:
  == domain 1  score: 365.3 bits;  conditional E-value: 1.6e-113
                    Glyco_transf_15  54 enenAtllalvrnselakilrsikkvekrFnkkfnYpyvfindepftekfkekieklveeadvefgeipkeewsyP 129
                                        ++enA++l+l+rn e  +i +++k++e+ Fn+ ++Ypy f+nde+ft++f +k++++++ ++  fg++ ++ew yP
  gene2582|gene2582|rna2582|rna2582  12 SKENAVILILCRNREADEISTTLKNFENVFNSTYKYPYLFLNDEDFTDEFMKKVKEVIS-TEAVFGKLESHEWGYP 86 
                                        578********************************************************.9*************** PP

                    Glyco_transf_15 130 efideekaakareelad..iaygdsesyrhmcRyysGlfykhellkkydyYwRvePdiklycdieyDvfkymkdek 203
                                        ++id+ekaa  r++l +  i+y+dsesyrhmcR++sG+fy+ +++kkydyYwR+eP++k++c ++yD f ++k+++
  gene2582|gene2582|rna2582|rna2582  87 NWIDKEKAAANRKKLEKmgIIYADSESYRHMCRFFSGFFYRNKYIKKYDYYWRIEPGVKFFCKMNYDPFEFLKKKN 162
                                        **************99999********************************************************* PP

                    Glyco_transf_15 204 kiygFtlslkeieetiktlWdstkkflkenkefieeknslsflsdddqdtynlCeFwsnfeigdldffrseayekf 279
                                          ygF +++ e  eti+tlWd t +f+ ++k+ i ++n+l+ + d++ ++yn C+Fwsnfei++l+ffr+e y+k+
  gene2582|gene2582|rna2582|rna2582 163 LEYGFIINIREFMETIPTLWDATIEFITRHKDIIPNQNVLKEILDNN-KNYNGCHFWSNFEIANLNFFRGELYQKY 237
                                        *****************************************996655.56************************** PP

                    Glyco_transf_15 280 FeylDskGgffYerWgdapvhsiavslllpkdkihffedigyshd 324
                                        F++lD+kGgf+YerWgdap+hs+a+s++l k kihffedigy+h 
  gene2582|gene2582|rna2582|rna2582 238 FDFLDQKGGFYYERWGDAPIHSLAASIFLGKRKIHFFEDIGYEHP 282
                                        ******************************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (321 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       779  (0.0434492); expected 358.6 (0.02)
Passed bias filter:                      495  (0.0276089); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.67u 0.34s 00:00:01.01 Elapsed: 00:00:00.57
# Mc/sec: 1690.27
//
Query:       gene2583|gene2583|rna2583|rna2583  [L=292]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.2e-12   45.1   0.0    1.8e-11   43.8   0.0    1.7  1  TP6A_N    Type IIB DNA topoisomerase
  ------ inclusion threshold ------
        0.1   12.5   0.0       0.14   12.0   0.0    1.4  1  DUF2399   Protein of unknown function C-terminus (DUF2399)


Domain annotation for each model (and alignments):
>> TP6A_N  Type IIB DNA topoisomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.8   0.0     2e-15   1.8e-11       7      62 .]      28      83 ..      23      83 .. 0.93

  Alignments for each domain:
  == domain 1  score: 43.8 bits;  conditional E-value: 2e-15
                                       HHHHHHHHHHHHTT--EEHHHHHHHGGGS-SSHHHHHHHHHHHHHHHTS-GGGGTE CS
                             TP6A_N  7 lkvlelihelleegkvvTkRdiYYrdvelFksQaesdrliddievllgvsReeLnv 62
                                       lk  e+ih +l+ + + TkR+i+Y  ++ Fk+Q++++++id+ +++ +v   ++nv
  gene2583|gene2583|rna2583|rna2583 28 LKFYEIIHGMLVDNVKKTKREIFYASPNIFKRQETVNKMIDKFAHVHKVRLIDFNV 83
                                       67899****************************************99998777776 PP

>> DUF2399  Protein of unknown function C-terminus (DUF2399)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   1.6e-05      0.14      42      92 ..     151     201 ..     114     263 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.6e-05
                            DUF2399  42 aaplvctsGqpsaaalelldklaaagarlrYhGDfDwpGlaianklaerfg 92 
                                        +  lv  +G p   +l +l++l +  ++++   D+D+ Gl i ++   +++
  gene2583|gene2583|rna2583|rna2583 151 DFLLVTGKGYPDYNTLAFLRRLEHMKCQIYGLFDLDPFGLSIFKNYKSKIN 201
                                        44588889**********************************988776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (292 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       700  (0.0390429); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 1822.31
//
Query:       gene2584|gene2584|rna2584|rna2584  [L=377]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.3e-16   60.7   9.7    2.7e-05   24.8   0.4    5.5  6  WD40         WD domain, G-beta repeat
    7.9e-16   58.1   2.4    2.2e-06   27.9   0.0    4.7  5  ANAPC4_WD40  Anaphase-promoting complex subunit 4 WD40 domain
      3e-06   27.3   1.6      0.082   12.8   0.0    3.1  3  eIF2A        Eukaryotic translation initiation factor eIF2A
     0.0009   18.3   0.4       0.11   11.4   0.1    3.0  3  Ge1_WD40     WD40 region of Ge1, enhancer of mRNA-decapping p
    0.00095   18.6   0.0       0.05   12.9   0.0    2.4  2  Nbas_N       Neuroblastoma-amplified sequence, N terminal
  ------ inclusion threshold ------
      0.076   12.9   0.0       0.15   12.0   0.0    1.5  1  DUF1314      Protein of unknown function (DUF1314)


Domain annotation for each model (and alignments):
>> WD40  WD domain, G-beta repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.45   1.3e+03      17      38 .]     126     147 ..     113     147 .. 0.73
   2 !    5.8   0.2    0.0093        28       8      30 ..     158     179 ..     150     184 .. 0.71
   3 !   23.7   0.0   2.1e-08   6.4e-05       3      37 ..     193     228 ..     191     229 .. 0.91
   4 !   24.8   0.4     9e-09   2.7e-05       3      38 .]     235     274 ..     233     274 .. 0.80
   5 ?   -2.9   0.0       5.2   1.6e+04      30      37 ..     309     316 ..     288     317 .. 0.52
   6 !    7.1   0.0    0.0037        11       3      37 ..     323     358 ..     321     359 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.45
                                        EEETTSSEEEEE.ETTSEEEEEE CS
                               WD40  17 afspdgawlasG.sdDgtvriWd 38 
                                        +  ++g+ la+G s +g + ++d
  gene2584|gene2584|rna2584|rna2584 126 SLKSNGNVLAAGiS-NGDIAFYD 147
                                        45789999**9999.99887776 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0093
                                        ESS.SSEEEEEEETTSSEEEEEET CS
                               WD40   8 tGH.ssvtslafspdgawlasGsd 30 
                                        + H + vtsl  + +g+ l+sGs+
  gene2584|gene2584|rna2584|rna2584 158 SSHqTRVTSL--DWNGNVLSSGSR 179
                                        679677****..447777989885 PP

  == domain 3  score: 23.7 bits;  conditional E-value: 2.1e-08
                                        EEEEEESS.SSEEEEEEETTSSEEEEEETTSEEEEE CS
                               WD40   3 clrtltGH.ssvtslafspdgawlasGsdDgtvriW 37 
                                         + +++ H + v++l++s ++++lasG  D+ + iW
  gene2584|gene2584|rna2584|rna2584 193 EISKFKFHtQEVCGLKWSNSKRYLASGANDNCINIW 228
                                        5778999*777****************99******* PP

  == domain 4  score: 24.8 bits;  conditional E-value: 9e-09
                                        EEEEEESS.SSEEEEEEETTSSE.......EEEE..ETTSEEEEEE CS
                               WD40   3 clrtltGH.ssvtslafspdgaw.......lasG..sdDgtvriWd 38 
                                        + ++ltGH s v +l      +w       lasG  s+D+tvr+Wd
  gene2584|gene2584|rna2584|rna2584 235 PRYSLTGHsSAVKAL------DWcpwrvsiLASGggSKDKTVRFWD 274
                                        6689****666****......77777777778875569*******9 PP

  == domain 5  score: -2.9 bits;  conditional E-value: 5.2
                                        TTSEEEEE CS
                               WD40  30 dDgtvriW 37 
                                          + + +W
  gene2584|gene2584|rna2584|rna2584 309 SENDICLW 316
                                        25666666 PP

  == domain 6  score: 7.1 bits;  conditional E-value: 0.0037
                                        EEEEEESS.SSE..EEEEEETTSSEEEEEETTSEEEEE CS
                               WD40   3 clrtltGH.ssv..tslafspdgawlasGsdDgtvriW 37 
                                        ++ ++  H + v  t+l  spd++ las   D ++++W
  gene2584|gene2584|rna2584|rna2584 323 KICSFGKHdNRVlyTAL--SPDQTILASLAADENLKFW 358
                                        56678889777878888..*******86356******* PP

>> ANAPC4_WD40  Anaphase-promoting complex subunit 4 WD40 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   0.0   7.3e-10   2.2e-06      18      90 ..     101     170 ..      86     172 .. 0.81
   2 !   10.1   0.0   0.00025      0.74      36      82 ..     159     203 ..     157     206 .. 0.90
   3 !   18.9   0.1   4.6e-07    0.0014      35      90 ..     198     252 ..     185     254 .. 0.90
   4 !    6.4   0.1    0.0037        11      37      89 ..     242     295 ..     238     298 .. 0.81
   5 ?    4.5   0.0     0.014        42      15      67 ..     309     360 ..     300     372 .. 0.79

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 7.3e-10
                        ANAPC4_WD40  18 ellvfRlngqrvwtleedkedsevrsLaWkpdgklLavaysdgevrlldaesgkvvhslsvksekavtclgWg 90 
                                        e++++ +  + v +l  ++ ++ v + + k +g++La ++s+g + ++d+e+ k++ ++s +++ +vt+l+W+
  gene2584|gene2584|rna2584|rna2584 101 EIYLYDVASKDVINL--ATFEGGVYASSLKSNGNVLAAGISNGDIAFYDVEKCKLIGKSSSHQT-RVTSLDWN 170
                                        666666666666666..34444555556689********************************9.6******8 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00025
                        ANAPC4_WD40  36 kedsevrsLaWkpdgklLavaysdgevrlldaesgkvvhslsvksek 82 
                                        +++ +v+sL W  +g++L  +   g ++ ld  + k +++++ ++++
  gene2584|gene2584|rna2584|rna2584 159 SHQTRVTSLDW--NGNVLSSGSRTGLISNLDLRDNKEISKFKFHTQE 203
                                        57899******..699**************************99875 PP

  == domain 3  score: 18.9 bits;  conditional E-value: 4.6e-07
                        ANAPC4_WD40  35 dkedsevrsLaWkpdgklLavaysdgevrlldaesgkvvhslsvksekavtclgWg 90 
                                        + + +ev +L+W+++ + La + +d+ +++ +  s     sl+ +s+ av+ l+W+
  gene2584|gene2584|rna2584|rna2584 198 KFHTQEVCGLKWSNSKRYLASGANDNCINIWQLGSNSPRYSLTGHSS-AVKALDWC 252
                                        56789*************************************99999.6******6 PP

  == domain 4  score: 6.4 bits;  conditional E-value: 0.0037
                        ANAPC4_WD40  37 edsevrsLaWkp.dgklLava..ysdgevrlldaesgkvvhslsvksekavtclgW 89 
                                        ++s v++L W p   ++La +   +d +vr+ d+e+g + +s++++s+  v+ +++
  gene2584|gene2584|rna2584|rna2584 242 HSSAVKALDWCPwRVSILASGggSKDKTVRFWDIETGMCENSVEMSSQ--VCGIHF 295
                                        678899999998345788886226899****************99988..777776 PP

  == domain 5  score: 4.5 bits;  conditional E-value: 0.014
                        ANAPC4_WD40  15 edgellvfRl.ngqrvwtleedkedsevrsLaWkpdgklLavaysdgevrllda 67 
                                        +++++ +  + n++++ ++   k+d++v   a +pd ++La   +d ++++  +
  gene2584|gene2584|rna2584|rna2584 309 SENDICLWKVsNFKKICSF--GKHDNRVLYTALSPDQTILASLAADENLKFWRI 360
                                        5566666665488999999..899999999999*********999999887655 PP

>> eIF2A  Eukaryotic translation initiation factor eIF2A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.0   2.7e-05     0.082      84     152 ..     101     170 ..      97     176 .. 0.67
   2 ?    4.4   0.1      0.01        31      48     134 ..     191     277 ..     183     297 .. 0.62
   3 !    7.9   0.1   0.00086       2.6      51     108 ..     281     336 ..     268     369 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.7e-05
                                        EEEEEECSCEEEEEEEEES--EEEE-..TTSSEEEEE-TTSSS-EEEEEETTTTEEEEEEE-TT-..-EEEE- CS
                              eIF2A  84 kvslfdlkvkviskleeqkrNtiffs..pkgklvllaGfgnlaGeleiwdvkkkkkiakaeaana..tlvews 152
                                        +++l+d+  k + +l + +      s  ++g+ vl aG+ n  G+++++dv+k+k i k  + ++  t+++w+
  gene2584|gene2584|rna2584|rna2584 101 EIYLYDVASKDVINLATFEGGVYASSlkSNGN-VLAAGISN--GDIAFYDVEKCKLIGKSSSHQTrvTSLDWN 170
                                        56777777666666665554444433103444.67788876..9*************9998877722556665 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.01
                                        T--EEECCEESSS.EEEEEE-TTSS-EEEEESSSSCEEEEEECS.CEEEEEE..EEES--EEEE-TTSSEEEEE-T CS
                              eIF2A  48 kkksevvelkkegpihdvaWspkskefaviyGkmpakvslfdlk.vkviskl..eeqkrNtiffspkgklvllaGf 120
                                        +k+++ ++ +++ ++  ++Ws++++   +  G  ++++++++l   ++ ++l  ++++  ++ ++p    +l +G 
  gene2584|gene2584|rna2584|rna2584 191 NKEISKFKFHTQ-EVCGLKWSNSKRY--LASGANDNCINIWQLGsNSPRYSLtgHSSAVKALDWCPWRVSILASGG 263
                                        455666666555.4777777765553..447777777777777423334444113445567777777777777777 PP

                                        TSSS-EEEEEETTT CS
                              eIF2A 121 gnlaGeleiwdvkk 134
                                        g+   ++ +wd ++
  gene2584|gene2584|rna2584|rna2584 264 GSKDKTVRFWDIET 277
                                        77777777777764 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.00086
                                        EEECCEESSS.EEEEEE-TTSS-EEEEESSSSCEEEEEEC.SCEEEEEEEEES--EEEE CS
                              eIF2A  51 sevvelkkegpihdvaWspkskefaviyGkmpakvslfdl.kvkviskleeqkrNtiff 108
                                        +++ve++ +  +  ++  ++ ke++  +G++++++ l+++ + k+i++++++ +  + +
  gene2584|gene2584|rna2584|rna2584 281 ENSVEMSSQ--VCGIHFLTRYKEMITAHGYSENDICLWKVsNFKKICSFGKHDNRVL-Y 336
                                        566777666..7888888999******************966********9865444.4 PP

>> Ge1_WD40  WD40 region of Ge1, enhancer of mRNA-decapping protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0     0.014        41     189     217 ..     121     149 ..      99     173 .. 0.82
   2 ?    0.8   0.2     0.065   1.9e+02     222     289 ..     220     290 ..     212     324 .. 0.70
   3 !   11.4   0.1   3.7e-05      0.11     185     217 ..     329     361 ..     239     370 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.014
                           Ge1_WD40 189 liveaafspdGtalatasedGevkffqvy 217
                                         +  +++ ++G +la+  ++G + f+ v 
  gene2584|gene2584|rna2584|rna2584 121 GVYASSLKSNGNVLAAGISNGDIAFYDVE 149
                                        57788999******************996 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.065
                           Ge1_WD40 222 eeprCLheWkPhdGkslssllfldnhkeesdeqfWrfait...gadnnselklWscelWtClqtikfapsi 289
                                         ++ C+  W+     +  sl       +  d   Wr  i    g ++++ ++ W  e+  C   +++++++
  gene2584|gene2584|rna2584|rna2584 220 ANDNCINIWQLGSNSPRYSLTGHSSAVKALDWCPWRVSILasgGGSKDKTVRFWDIETGMCENSVEMSSQV 290
                                        56666666666666666666666666666677778877751114567788888888888888888887764 PP

  == domain 3  score: 11.4 bits;  conditional E-value: 3.7e-05
                           Ge1_WD40 185 eehsliveaafspdGtalatasedGevkffqvy 217
                                        +++  +  +a+spd t la  ++d  +kf+++ 
  gene2584|gene2584|rna2584|rna2584 329 KHDNRVLYTALSPDQTILASLAADENLKFWRIL 361
                                        33458999**********************996 PP

>> Nbas_N  Neuroblastoma-amplified sequence, N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0     0.018        54     229     267 ..     119     157 ..      90     168 .. 0.86
   2 !   12.9   0.0   1.7e-05      0.05     197     258 ..     296     360 ..     236     367 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.018
                             Nbas_N 229 kdgvfkmslspdgtllavihfsgklsiwdipslkqrgew 267
                                        + gv+  sl  +g +la+    g ++ +d+   k+ g+ 
  gene2584|gene2584|rna2584|rna2584 119 EGGVYASSLKSNGNVLAAGISNGDIAFYDVEKCKLIGKS 157
                                        689****************9**********998887654 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 1.7e-05
                             Nbas_N 197 vtsyeddvgal...akkrgllkllslklysrkaeekdgvfkmslspdgtllavihfsgklsiwdi 258
                                        +t y++ ++a+    +  +l+k+ ++k     ++ ++ v+  +lspd t+la +    +l  w i
  gene2584|gene2584|rna2584|rna2584 296 LTRYKEMITAHgysENDICLWKVSNFKKICSFGKHDNRVLYTALSPDQTILASLAADENLKFWRI 360
                                        566777776641114567899******************************************98 PP

>> DUF1314  Protein of unknown function (DUF1314)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   4.9e-05      0.15      78     117 ..     290     334 ..     278     374 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 4.9e-05
                            DUF1314  78 asglhllaqslgeflrktGlsnrdlmltrG.ti.....ydyhdsrl 117
                                          g+h+l++  +e+++ +G s+ d++l++  ++     +  hd+r+
  gene2584|gene2584|rna2584|rna2584 290 VCGIHFLTR-YKEMITAHGYSENDICLWKVsNFkkicsFGKHDNRV 334
                                        468****86.699***************851556666644455554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (377 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       445  (0.0248201); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 2603.93
//
Query:       gene2585|gene2585|rna2585|rna2585  [L=218]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-08   34.1   2.1    2.3e-08   34.1   2.1    1.9  2  CAF1A     Chromatin assembly factor 1 subunit A
  ------ inclusion threshold ------
      0.067   13.2   1.3        5.5    7.0   0.4    2.2  2  FokI_C    Restriction endonuclease FokI, catalytic domain


Domain annotation for each model (and alignments):
>> CAF1A  Chromatin assembly factor 1 subunit A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.1   2.1   2.5e-12   2.3e-08       2      72 ..     110     174 ..     109     178 .. 0.77
   2 !    7.1   2.1   0.00069       6.2      36      63 ..     159     186 ..     158     193 .. 0.71

  Alignments for each domain:
  == domain 1  score: 34.1 bits;  conditional E-value: 2.5e-12
                              CAF1A   2 llqFyedvRPpYyGTwtkkskvvgarnPfskdekeldYdyDSdaEWeeeeeeegedleseedeeeeeeddd 72 
                                        + +F++ +RP +   +tk +     +n +++ +  l+Yd DSd  W++  +e ge+++   d+ee++ ++d
  gene2585|gene2585|rna2585|rna2585 110 YVKFHDTIRPSFHTICTKYK----TSNSVKRIPFVLNYDEDSDLLWND--DESGESINYATDSEEDMVEED 174
                                        789**********9999733....344444555589**********77..568*****8888777765554 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.00069
                              CAF1A  36 eldYdyDSdaEWeeeeeeegedleseed 63 
                                        +++Y  DS+++ +ee++ e+  +e+ e+
  gene2585|gene2585|rna2585|rna2585 159 SINYATDSEEDMVEEDSFECSWIEEGEE 186
                                        68************98655555555444 PP

>> FokI_C  Restriction endonuclease FokI, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.4   0.00061       5.5      51      85 ..      18      51 ..       3      78 .. 0.69
   2 ?    5.0   0.0    0.0026        23      10      40 ..      81     111 ..      75     116 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.00061
                             FokI_C 51 elliqglaeaeeekekkklksdtegssDkYvrmia 85
                                       +  +++  ++ + +++++l +d+eg +Dk v+ i 
  gene2585|gene2585|rna2585|rna2585 18 KKCMETA-SSVKIEDENNLTQDMEGIADKDVKRIK 51
                                       5444444.444558999************998875 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0026
                             FokI_C  10 lsYPpvvrvLslLaeeehLtkfelGkklGfv 40 
                                        + +Pp + ++++    + + k+++Gkkl +v
  gene2585|gene2585|rna2585|rna2585  81 IDFPPNTLIFQIGHTIKSVRKYQVGKKLTYV 111
                                        56899999999999999***********997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       713  (0.039768); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1551.69
//
Query:       gene2586|gene2586|rna2586|rna2586  [L=235]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.02   14.6   0.7       0.22   11.3   0.4    2.6  2  MalM      Maltose operon periplasmic protein precursor (MalM)
        3.7    7.5   8.9        3.9    7.4   0.0    2.8  3  RF-1      RF-1 domain


Domain annotation for each model (and alignments):
>> MalM  Maltose operon periplasmic protein precursor (MalM)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0       0.1   8.9e+02       4      16 ..      90     102 ..      87     117 .. 0.76
   2 ?   11.3   0.4   2.5e-05      0.22      14     109 ..     129     224 ..     126     231 .. 0.75

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.1
                               MalM   4 savaafalPanrg 16 
                                        sa+a+f lP+n+ 
  gene2586|gene2586|rna2586|rna2586  90 SAFASFVLPKNTC 102
                                        89*******9975 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 2.5e-05
                               MalM  14 nrgsleltlsSlv.kdksvfaPnvlvLDeqfkvvatyssskFkyqparllkgdrleaelkltpaegqkeiYllvyt 88 
                                        nr++ + +l S++ +d +v+ Pn+lv +eq   ++ +++++ k ++++ ++++    + + t+ +++ ++    +t
  gene2586|gene2586|rna2586|rna2586 129 NRENAKRRLLSQLeNDSQVLCPNILVNNEQRDGTEGIDKDVDKKRRNKNVTESICGLQTE-TKRDEELTTEDECFT 203
                                        5667777999***9999******************9999998888888888776555552.233333333344788 PP

                               MalM  89 teedlakstklehpakayaka 109
                                        ++++l+  ++ ++p+k + ++
  gene2586|gene2586|rna2586|rna2586 204 KQKYLKMDVTAKKPKKTRTNE 224
                                        888888888888888887665 PP

>> RF-1  RF-1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.0   0.00044       3.9      51      72 ..      49      70 ..      42      84 .. 0.80
   2 ?    4.2   0.9    0.0042        38      56     106 ..     128     178 ..     123     183 .. 0.61
   3 ?   -0.8   2.0      0.15   1.4e+03      52     106 ..     172     225 ..     169     232 .. 0.53

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.00044
                                       SSSHHHHHHHHHHHHHHHHHHH CS
                               RF-1 51 eRsqekNrekAlerLkaklkek 72
                                        ++ +kN+++A+++L++++ ++
  gene2586|gene2586|rna2586|rna2586 49 YKKNIKNKKTAIKKLEHRIDAY 70
                                       57889**************664 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.0042
                                        HHHHHHHHHHHHHHHHHHHHHCCCCCHTTTTT-..S.-S---S.--ECEEEEC CS
                               RF-1  56 kNrekAlerLkaklkekeleeekeeekkrrvkk.ekkkigtgs.sekiRtynk 106
                                         Nre+A +rL ++l++ ++    +   ++++++ ++  i  ++ ++k+R++n+
  gene2586|gene2586|rna2586|rna2586 128 VNRENAKRRLLSQLENDSQVLCPNILVNNEQRDgTEG-I-DKDvDKKRRNKNV 178
                                        5*************77444443333333332332444.3.3444788888876 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 0.15
                                        SSHHHHHHHHHHHHHHHHHH.HHHHHCCCCCHTTTTT-.S.-S---S--ECEEEEC CS
                               RF-1  52 RsqekNrekAlerLkaklke.keleeekeeekkrrvkkekkkigtgssekiRtynk 106
                                        + + kN  + +  L+++ k+ +el  e+e  +k++  k   +++ ++ +k Rt++ 
  gene2586|gene2586|rna2586|rna2586 172 KRRNKNVTESICGLQTETKRdEELTTEDECFTKQKYLK--MDVTAKKPKKTRTNEQ 225
                                        55667777777777777755444444444444444333..3344444566666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1164  (0.0649228); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.33s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 1460.28
//
Query:       gene2587|gene2587|rna2587|rna2587  [L=91]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.3e-14   51.2   1.0    9.5e-14   50.8   1.0    1.1  1  Ribosomal_S27e  Ribosomal protein S27
  ------ inclusion threshold ------
      0.021   15.2   1.5      0.033   14.6   1.5    1.3  1  zf-C5HC2        C5HC2 zinc finger
        2.6    8.0   8.5        3.8    7.4   0.6    2.7  3  zf-LSD1         LSD1 zinc finger


Domain annotation for each model (and alignments):
>> Ribosomal_S27e  Ribosomal protein S27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.8   1.0   1.6e-17   9.5e-14       1      51 [.      33      83 ..      33      86 .. 0.97

  Alignments for each domain:
  == domain 1  score: 50.8 bits;  conditional E-value: 1.6e-17
                                       -S--EEEEE-TTTS-EEEEESS-SS-EEESSSTCEEEEECSSSEEESSCEE CS
                     Ribosomal_S27e  1 prskFldvkCpdCenetvvFshaatvvkCisCgkvLvePtGGkaklkaqil 51
                                       p++ F++vkC  C ++tv +sh +   +C  C   +  PtGG +kl +q+ 
  gene2587|gene2587|rna2587|rna2587 33 PNGSFIRVKCASCDAQTVCYSHTQIKRLCGECNASIWYPTGGAGKLAEQCA 83
                                       799**********************************************96 PP

>> zf-C5HC2  C5HC2 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   1.5   5.5e-06     0.033      12      37 ..      39      66 ..      37      72 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 5.5e-06
                           zf-C5HC2 12 avvckkcpskvvCleH..akelckecpp 37
                                       +v+c  c  ++vC +H  +k lc ec+ 
  gene2587|gene2587|rna2587|rna2587 39 RVKCASCDAQTVCYSHtqIKRLCGECNA 66
                                       699**99999*******99****98876 PP

>> zf-LSD1  LSD1 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.2       1.1   6.4e+03       8      12 ..      12      16 ..      12      16 .. 0.84
   2 ?    7.4   0.6   0.00064       3.8      17      24 ..      40      47 ..      38      47 .. 0.90
   3 ?    5.5   0.1    0.0026        15       1      13 [.      61      73 ..      61      75 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.1
                            zf-LSD1  8 LmYPr 12
                                       L YP+
  gene2587|gene2587|rna2587|rna2587 12 LLYPT 16
                                       89*96 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.00064
                            zf-LSD1 17 VrCalCqt 24
                                       V+Ca+C++
  gene2587|gene2587|rna2587|rna2587 40 VKCASCDA 47
                                       9*****96 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.0026
                            zf-LSD1  1 CggCrtlLmYPrG 13
                                       Cg C +   YP+G
  gene2587|gene2587|rna2587|rna2587 61 CGECNASIWYPTG 73
                                       ***********99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       643  (0.0358637); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.29s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 603.68
//
Query:       gene2588|gene2588|rna2588|rna2588  [L=295]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0021   17.0   0.0        1.2    8.0   0.0    2.1  2  RNA_pol_I_A49    A49-like RNA polymerase I associated factor
  ------ inclusion threshold ------
       0.19   11.1   0.0       0.27   10.5   0.0    1.1  1  Cyt_bd_oxida_II  Cytochrome bd terminal oxidase subunit II


Domain annotation for each model (and alignments):
>> RNA_pol_I_A49  A49-like RNA polymerase I associated factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.0   0.00013       1.2     151     192 ..     109     150 ..      89     186 .. 0.77
   2 !    7.2   0.0   0.00022         2     294     353 ..     218     277 ..     190     293 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00013
                                        XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                      RNA_pol_I_A49 151 elqaavassrplPpanldAtepedVYplsdlissaelealev 192
                                        ++++ + +++++P +n +A++ +++Y+l+ +  ++ l  + +
  gene2588|gene2588|rna2588|rna2588 109 DMEKYAGNEQIIPIFNSNAQNTKNIYRLDIMFDKNLLREVGQ 150
                                        778888899*******************98888777765544 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.00022
                                        XXXX..XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                      RNA_pol_I_A49 294 kskr..lskshkdkLlayilalaLhldnfsvdltdLaedLklkpkklnelfkelGckisklt 353
                                        k+ +   +  ++ k++a  ++++L++ ++++    +  +++++  ++++++k lGc+ +k +
  gene2588|gene2588|rna2588|rna2588 218 KK-YrrYDRYERYKFIAMACVILLIIHGYEIGAGAIP-NFGVNDIEMRKIMKLLGCTWDKDK 277
                                        22.2468889999**********************97.7*****************998765 PP

>> Cyt_bd_oxida_II  Cytochrome bd terminal oxidase subunit II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0     3e-05      0.27       8      53 ..     231     275 ..     229     280 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 3e-05
                    Cyt_bd_oxida_II   8 ligvllagYvvldGfDlGvGillpllakkdeerrlllnsigpvWdg 53 
                                        +i+++ ++++++ G+ +G+G++  + + +d e r +++ +g +Wd 
  gene2588|gene2588|rna2588|rna2588 231 FIAMACVILLIIHGYEIGAGAIPNF-GVNDIEMRKIMKLLGCTWDK 275
                                        5889999***************888.88888*************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (295 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       517  (0.028836); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 2123.63
//
Query:       gene2589|gene2589|rna2589|rna2589  [L=156]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       758  (0.0422779); expected 358.6 (0.02)
Passed bias filter:                      487  (0.0271627); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1193.85
//
Query:       gene259|gene259|rna259|rna259  [L=79]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       377  (0.0210274); expected 358.6 (0.02)
Passed bias filter:                      245  (0.013665); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.26s 00:00:00.60 Elapsed: 00:00:00.41
# Mc/sec: 581.13
//
Query:       gene2590|gene2590|rna2590|rna2590  [L=616]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0036   17.2   1.1     0.0036   17.2   1.1    3.8  3  DUF2202   Uncharacterized protein domain (DUF2202)
  ------ inclusion threshold ------
      0.076   13.0   1.7       0.18   11.8   0.2    2.5  2  P4Ha_N    Prolyl 4-Hydroxylase alpha-subunit, N-terminal regi
      0.092   13.0   0.2         42    4.5   0.0    3.5  3  HEAT_UF   Repeat of uncharacterized protein PH0542
       0.11   12.9   0.0       0.34   11.3   0.0    1.8  1  HEAT_2    HEAT repeats
        1.2    9.7   5.8        1.6    9.4   0.1    3.0  3  DUF1053   Domain of Unknown Function (DUF1053)


Domain annotation for each model (and alignments):
>> DUF2202  Uncharacterized protein domain (DUF2202)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   1.1     1e-06    0.0036       3      78 ..     225     306 ..     223     331 .. 0.63
   2 ?    0.7   4.8      0.12   4.3e+02      99     146 ..     437     484 ..     324     498 .. 0.77
   3 ?   -1.9   0.0      0.74   2.6e+03      12      69 ..     542     603 ..     537     611 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1e-06
                            DUF2202   3 dsllymreeeklarDvYlelYdrwklqiflniakseqthtdavksllekYeled......pvkederGkfedeelq 72 
                                        ++++ +++e k   +vY  lY++ +++if+ni    +     + +++++ + ++        + ++  ++++++l+
  gene2590|gene2590|rna2590|rna2590 225 NVIMKIKKEKKDIYEVYHFLYNKSGMEIFRNIEIRKKGLDAYLDHVIDRISRSEqccrkgNCHLHVLSTYRHTNLE 300
                                        6899****************************76655444444445555443330000002333456677888888 PP

                            DUF2202  73 elYnkL 78 
                                        ++Y  L
  gene2590|gene2590|rna2590|rna2590 301 KIYTLL 306
                                        888643 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.12
                            DUF2202  99 ldiaDlekalketdnkdikevYenllkGsrnhlRsfvrkleergkeYe 146
                                          i Dl k ++ +d +d+k+ +e++   s  +l + + ++++ ++ Y 
  gene2590|gene2590|rna2590|rna2590 437 SKIDDLSKSTNAEDVQDMKDAFEFIYMQSITYLSTKIDQFKRDDNFYY 484
                                        4799**********************9999999999999988887774 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 0.74
                            DUF2202  12 eklarDvYlelYdrwklqiflnia..kseqthtdavksllekYeledpv..kederGkfede 69 
                                        ek+ +   l+l +   ++ifl +   + e   +d+   l++  +l++ +  ++  +G f+++
  gene2590|gene2590|rna2590|rna2590 542 EKMTKTFKLRLKNYPSTEIFLILRgfQNEGASMDNFIPLIDMLSLDECIilENTAVGRFKEK 603
                                        67777777777777777777766422688889999999999999999873346678999865 PP

>> P4Ha_N  Prolyl 4-Hydroxylase alpha-subunit, N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.0       3.7   1.3e+04      32      46 ..     222     236 ..     220     252 .. 0.65
   2 ?   11.8   0.2     5e-05      0.18      16      91 ..     302     386 ..     289     431 .. 0.79

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 3.7
                             P4Ha_N  32 klkrfleeleeehes 46 
                                        k+k+++ ++++e+++
  gene2590|gene2590|rna2590|rna2590 222 KIKNVIMKIKKEKKD 236
                                        667777777766633 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 5e-05
                             P4Ha_N  16 veeLesyieeeekkleklkrfleeleeehesakedkeeylsnP........lnaFklikRltsdW.eelekllees 82 
                                        + +L s +++ ++ +e + ++le++++    +++ + + l +         ln F+l+kRl +d+ + ++++++  
  gene2590|gene2590|rna2590|rna2590 302 IYTLLSIVKDSRADIEIILKVLERIKNDVYVNSTYTTQILDKLyeygqiyrLNYFSLLKRLETDYqPYVNEIVKRI 377
                                        5667788888888888888888888888844444444433333344456679*************9999****999 PP

                             P4Ha_N  83 eseelieql 91 
                                        e+e+li+ +
  gene2590|gene2590|rna2590|rna2590 378 EHEDLIKYF 386
                                        999988765 PP

>> HEAT_UF  Repeat of uncharacterized protein PH0542
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0     0.012        42       7      26 ..      18      37 ..      14      39 .. 0.92
   2 ?   -1.7   0.0         1   3.7e+03      16      29 ..     121     134 ..     118     149 .. 0.67
   3 ?    4.2   0.1     0.014        52      13      27 ..     225     239 ..     208     241 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.012
                                       HHHHHHHHHHHHHCC-GGGH CS
                            HEAT_UF  7 VqKNalriivviakekeeLy 26
                                       + KN+l  ++++ k+ ++Ly
  gene2590|gene2590|rna2590|rna2590 18 ILKNSLEYLSQVFKQHPDLY 37
                                       57*****************9 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1
                                        HHHHCC-GGGHHHH CS
                            HEAT_UF  16 vviakekeeLyepl 29 
                                        vv+++e+ + ye +
  gene2590|gene2590|rna2590|rna2590 121 VVVVREIFSFYEKF 134
                                        78899999999975 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.014
                                        HHHHHHHCC-GGGHH CS
                            HEAT_UF  13 riivviakekeeLye 27 
                                         +i+ i kek+++ye
  gene2590|gene2590|rna2590|rna2590 225 NVIMKIKKEKKDIYE 239
                                        59************9 PP

>> HEAT_2  HEAT repeats
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   9.3e-05      0.34       1      56 [.     139     199 ..     139     226 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 9.3e-05
                             HEAT_2   1 ldaLlqalendpdpevrraairaLgrignp.....ealpaLvellede.dpavRraaaeaLg 56 
                                        +d+Ll al +d+ +evr +++r+L r+ n+       ++++ +l++d  ++ +R +aa+ L 
  gene2590|gene2590|rna2590|rna2590 139 IDKLLLAL-HDSKDEVRVEVLRTLRRLYNKykmeiGFVDIIKRLASDGiSSSTRSEAADFLY 199
                                        57899999.89999***********887766664445********99637899999999875 PP

>> DUF1053  Domain of Unknown Function (DUF1053)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.1       3.5   1.3e+04      57      83 ..      37      63 ..      18      75 .. 0.61
   2 ?    9.4   0.1   0.00044       1.6      55      98 ..     262     306 ..     231     309 .. 0.87
   3 ?    2.1   0.3     0.078   2.8e+02      38      86 ..     440     489 ..     418     495 .. 0.77

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 3.5
                            DUF1053 57 derleqaIdglsskklwkrsedlkkft 83
                                         +  ++I +++ +  +++  +l  ++
  gene2590|gene2590|rna2590|rna2590 37 YFKCWNNIKQNNDQAKFEKLSNLALLS 63
                                       555566777776666655555555544 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00044
                            DUF1053  55 elderleqaIdglsskklwkrsedlkkftl.iFkekslEkkYrql 98 
                                         ld+ l+++Id +s  +++ r+ + +   l +++  +lEk Y +l
  gene2590|gene2590|rna2590|rna2590 262 GLDAYLDHVIDRISRSEQCCRKGNCHLHVLsTYRHTNLEKIYTLL 306
                                        58999**************88887776555389*********876 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.078
                            DUF1053  38 lqdkkersasekarleeelderleqaIdglsskklw.krsedlkkftliF 86 
                                           +k ++a++++ +++  +   +q+I  ls k    kr ++++  + +F
  gene2590|gene2590|rna2590|rna2590 440 DDLSKSTNAEDVQDMKDAFEFIYMQSITYLSTKIDQfKRDDNFYYNLTKF 489
                                        44578899999999999999999*******99855448888888666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (616 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1074  (0.059903); expected 358.6 (0.02)
Passed bias filter:                      492  (0.0274416); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.61u 0.30s 00:00:00.90 Elapsed: 00:00:00.43
# Mc/sec: 4299.41
//
Query:       gene2591|gene2591|rna2591|rna2591  [L=278]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.3e-42  143.6   2.3    5.2e-38  130.9   0.5    2.0  2  Cpn60_TCP1    TCP-1/cpn60 chaperonin family
  ------ inclusion threshold ------
       0.12   12.4   1.4        1.6    8.8   0.0    3.1  3  Sigma70_r1_1  Sigma-70 factor, region 1.1
       0.12   12.0   0.0       0.23   11.2   0.0    1.4  1  DUF3440       Domain of unknown function (DUF3440)


Domain annotation for each model (and alignments):
>> Cpn60_TCP1  TCP-1/cpn60 chaperonin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.9   0.5   8.6e-42   5.2e-38     182     411 ..       2     227 ..       1     230 [. 0.94
   2 !   12.7   0.0     6e-06     0.036     453     490 ..     233     270 ..     231     271 .. 0.89

  Alignments for each domain:
  == domain 1  score: 130.9 bits;  conditional E-value: 8.6e-42
                                        SEEEESS--SSTTSSCEEECEEEEEESS-BS--HHCCHHHCCCCSCCHHHHHHHHHHHHHHHHHHHHHHTTECEEE CS
                         Cpn60_TCP1 182 eGlvldkgvlspdmpkklenakvllldvsLeiektetkttvvlsdaeeleklekaeekqleellekiiksgvnvvv 257
                                        +G+ l+k + ++    k +  k++++++sL+ie+tetk+t+ +++ae++ +++k+eek ++ l+++i  ++vn v+
  gene2591|gene2591|rna2591|rna2591   2 HGMFLEKALQGT---IKKSGGKIVIFNTSLDIERTETKGTLLFENAEDMLNFSKDEEKRMLCLVDSIS-ENVNAVI 73 
                                        688888887776...678889*********************************************96.58***** PP

                                        ESS-B-HHHHHHHHHCT-EEE-S--HHHHHHHHHHHT--EBSCGGGGGCGC-EEEEEEEECCETTCCEEEEECESS CS
                         Cpn60_TCP1 258 cqkgiddlalhflakngilalrrvkkkdlerlakatGatavssledltpeelGtakkveeekigsekttiieevks 333
                                        c++ i++   +f++ n++++++  +k+d++r++++ ++++++++ ++ +ee G+++++++   + ++++ +e+ k+
  gene2591|gene2591|rna2591|rna2591  74 CNGNINEQYAEFFNNNNVMVIKVNSKFDIRRIMRMSKGSLLQTVRRPRREETGEIDSITTVYDEGKTYLRLEK-KD 148
                                        **********************************************************888878888888998.** PP

                                        SSXEEEEEEESTCCCHHHHHHHHHHHHHHHHHHHH.HHEEEETTTCHHHHHHHHHHCCCCTSXCCHHHHHHHHHHH CS
                         Cpn60_TCP1 334 gkiatillrgatdtvldeieraiedAlnvvknaie.dekvvpGGGatelelakklkeyaksvsgeeqlaieafakA 408
                                        ++i++i+l+ +    lde e+ +e ++++++++ + d ++v GGG++e +l+ +l+e+++++ +  +l++ a+ kA
  gene2591|gene2591|rna2591|rna2591 149 SNIVSIVLKDSLASNLDESELLLEKGIKIMESLRDeDLYFVNGGGVFEKQLSDRLAEKSTNIRDSSKLVYSAVVKA 224
                                        *********************************9746799************************************ PP

                                        HTH CS
                         Cpn60_TCP1 409 Lev 411
                                        L++
  gene2591|gene2591|rna2591|rna2591 225 LSY 227
                                        *86 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 6e-06
                                        ECCCCTXEEEHHHHHHHHHHHHHHHHHHHCEEEEEXXX CS
                         Cpn60_TCP1 453 dlveagvvDplkvkrqalksAteaastiLrideiikak 490
                                        d+ +++  D+++vk++al+ A+++a+ +L+i++ ++ak
  gene2591|gene2591|rna2591|rna2591 233 DVDTEQLKDIYSVKQRALEYAFDLACEVLMIEDYLVAK 270
                                        55667788************************999887 PP

>> Sigma70_r1_1  Sigma-70 factor, region 1.1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.1      0.13     8e+02      40      58 ..      80      98 ..      30     111 .. 0.67
   2 ?   -0.6   0.0      0.23   1.4e+03      46      61 ..     170     185 ..     162     190 .. 0.81
   3 ?    8.8   0.0   0.00027       1.6      19      44 ..     215     244 ..     208     247 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.13
                                       HHHHHHHHCCT-EEE-SS- CS
                       Sigma70_r1_1 40 ediiemLedmgIdvveeae 58
                                       e+  e+++++++ v+  + 
  gene2591|gene2591|rna2591|rna2591 80 EQYAEFFNNNNVMVIKVNS 98
                                       5666777777777777665 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.23
                                        HHCCT-EEE-SS-... CS
                       Sigma70_r1_1  46 LedmgIdvveeaeded 61 
                                        L + gI+++e+  ded
  gene2591|gene2591|rna2591|rna2591 170 LLEKGIKIMESLRDED 185
                                        6688999999988776 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.00027
                                        CEEHHHHHHHG....CCSS--HHHHHHHHH CS
                       Sigma70_r1_1  19 yLtyeEindaL....pddeldseqiediie 44 
                                         L y+ + +aL    p+d++d+eq+ di++
  gene2591|gene2591|rna2591|rna2591 215 KLVYSAVVKALsyfcPPDDVDTEQLKDIYS 244
                                        589************99***********97 PP

>> DUF3440  Domain of unknown function (DUF3440)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   3.8e-05      0.23      90     156 ..     181     247 ..     171     262 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 3.8e-05
                            DUF3440  90 lkvsikfWrekGgalseetikelkeaeikieveeksnyktekkvvrlkeylddidikefkeiPtykr 156
                                        l+    ++ + Gg+++++  ++l e++++i+ + k  y+   k + +   +dd+d ++ k+i + k+
  gene2591|gene2591|rna2591|rna2591 181 LRDEDLYFVNGGGVFEKQLSDRLAEKSTNIRDSSKLVYSAVVKALSYFCPPDDVDTEQLKDIYSVKQ 247
                                        55556688999999999999**************************999*************99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (278 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       613  (0.0341904); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1799.76
//
Query:       gene2592|gene2592|rna2592|rna2592  [L=152]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    9.4e-14   50.9   0.2    1.2e-13   50.5   0.2    1.2  1  Cpn60_TCP1  TCP-1/cpn60 chaperonin family
  ------ inclusion threshold ------
      0.014   15.2   0.1       0.03   14.1   0.1    1.6  1  DIM1        Mitosis protein DIM1


Domain annotation for each model (and alignments):
>> Cpn60_TCP1  TCP-1/cpn60 chaperonin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.5   0.2   1.4e-17   1.2e-13       3     109 ..      35     140 ..      33     150 .. 0.89

  Alignments for each domain:
  == domain 1  score: 50.5 bits;  conditional E-value: 1.4e-17
                                        HHHHCCSSTTXXEEEEEETTSEEEEEXSHHHHHHCSXXXSHHHHHHHHHHHHCCCCCTTCHHHHHHHHHHHHHHHH CS
                         Cpn60_TCP1   3 divkttlGPkGmdKmlvnkggkvvvTnDGatilkeleiehPaakllveaaesqdeevGDGTttvviLageLleeae 78 
                                        di+++t+      K++v++++++ +T+  ++il+++++ hP+  l  ++  ++  + GDG t++++++g+Ll+e+ 
  gene2592|gene2592|rna2592|rna2592  35 DIIASTFRADPYRKIVVDSYNNLLITSETTKILSSIKLVHPIQFLFKDVLLKMS-KLGDGNTFLILFVGKLLRECR 109
                                        5666666666678******************************99999999985.79******************* PP

                                        HHHHCTXXHHHHHHHHHHHHHHHHHHHHHHX CS
                         Cpn60_TCP1  79 kliaagvhpttiiegyekalekaleaLkeia 109
                                        +l+ +g++   i++ ++k +++++ +++  +
  gene2592|gene2592|rna2592|rna2592 110 DLLVKGMKAPMIVSSLKKIKKELFVIMDDLK 140
                                        **********************999987663 PP

>> DIM1  Mitosis protein DIM1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   3.3e-06      0.03      93     130 ..      17      54 ..       8      57 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.3e-06
                                        SS--SSB-S----HHHHHHHHHHHHHHHHHT-SEEE-S CS
                               DIM1  93 tgdnnKlnfvledkqelidiietiyrgakkgkglvvsp 130
                                        + +n Kl++++++ +elidii   +r+    k++v s 
  gene2592|gene2592|rna2592|rna2592  17 QHKNVKLIMTVSKAEELIDIIASTFRADPYRKIVVDSY 54 
                                        56799**********************99999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       690  (0.0384851); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1119.61
//
Query:       gene2593|gene2593|rna2593|rna2593  [L=385]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (385 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       386  (0.0215294); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 2650.61
//
Query:       gene2594|gene2594|rna2594|rna2594  [L=283]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (283 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       391  (0.0218082); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1938.83
//
Query:       gene2595|gene2595|rna2595|rna2595  [L=452]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.036   14.0   1.0      0.066   13.2   1.0    1.4  1  T2SSF     Type II secretion system (T2SS), protein F


Domain annotation for each model (and alignments):
>> T2SSF  Type II secretion system (T2SS), protein F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   1.0   3.7e-06     0.066      84     124 ..       5      45 ..       2      46 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.7e-06
                                        HHHHHHHHHHHHHHHHHHHHTTXXXXXXXXXXXXXXXXXXX CS
                              T2SSF  84 laeyleeerelrrkllaallepllllvvallvllillaill 124
                                        l++++ee ++ rr+ +++++  +++l+val+ ++++ ++l+
  gene2595|gene2595|rna2595|rna2595   5 LQQMMEESYNDRRRAKSRFIRSVVILLVALITPFLFSMMLM 45 
                                        6899****************************999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (452 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       718  (0.0400469); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.21s 00:00:00.76 Elapsed: 00:00:00.41
# Mc/sec: 3333.20
//
Query:       gene2596|gene2596|rna2596|rna2596  [L=340]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.7e-16   58.4   1.0    1.8e-15   56.5   0.1    2.4  3  SWIB           SWIB/MDM2 domain
  ------ inclusion threshold ------
      0.076   13.2   0.1        0.3   11.3   0.1    2.0  1  Lipoprotein_3  Lipoprotein


Domain annotation for each model (and alignments):
>> SWIB  SWIB/MDM2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.1      0.18   1.6e+03      32      53 ..      23      44 ..      22      52 .. 0.77
   2 ?   -3.5   0.0       1.1     1e+04      13      27 ..      68      82 ..      65      83 .. 0.67
   3 !   56.5   0.1     2e-19   1.8e-15       2      73 ..     153     223 ..     152     224 .. 0.95

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.18
                               SWIB 32 kennLqdpedkreilcDekLkk 53
                                       k++ L +++  + i+c ++L+ 
  gene2596|gene2596|rna2596|rna2596 23 KKKLLVEESHYKRIKCAKRLRL 44
                                       6677888899999999999985 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 1.1
                               SWIB 13 lgekelsrpevvkkl 27
                                        +++el +++v+k +
  gene2596|gene2596|rna2596|rna2596 68 TNTTELRMSDVLKNV 82
                                       566777788887765 PP

  == domain 3  score: 56.5 bits;  conditional E-value: 2e-19
                               SWIB   2 pvklspeLaellgekelsrpevvkklweYIkennLqdpedkreilcDekLkklfggkdrvkffempkllkkH 73 
                                        ++kl ++ ++l+++++ +++  +  +w+YI+ n L  ++d   ++cDekLk++fg+ d++k+ +mp+l+++ 
  gene2596|gene2596|rna2596|rna2596 153 RYKLISPVRQLFKKETETKTGLLIDIWKYIRLNRLVIEADDFTVVCDEKLKEIFGC-DQFKILDMPELVSPL 223
                                        7999999***********************************************77.7***********986 PP

>> Lipoprotein_3  Lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   3.3e-05       0.3      23      64 ..     150     191 ..     143     210 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 3.3e-05
                      Lipoprotein_3  23 elnKknlitiLkeayesdpkgtvkvLldgWkytLldqkiLek 64 
                                        + ++ +li+ +++ +++++++ + +L+d Wky  l+  ++e 
  gene2596|gene2596|rna2596|rna2596 150 TFDRYKLISPVRQLFKKETETKTGLLIDIWKYIRLNRLVIEA 191
                                        5678899*************************9999988887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (340 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       476  (0.0265492); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.22s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 2590.83
//
Query:       gene2597|gene2597|rna2597|rna2597  [L=862]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    6.4e-61  206.7  40.0    3.4e-60  204.4  40.0    1.9  1  Ufd2P_core  Ubiquitin elongating factor core
    6.2e-17   61.5   0.3    1.8e-16   60.0   0.3    1.9  1  U-box       U-box domain


Domain annotation for each model (and alignments):
>> Ufd2P_core  Ubiquitin elongating factor core
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  204.4  40.0   3.8e-64   3.4e-60      28     625 .]     240     776 ..     220     776 .. 0.85

  Alignments for each domain:
  == domain 1  score: 204.4 bits;  conditional E-value: 3.8e-64
                                        -TT--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHT-GGGGSSS--GGGS--HHHHHHH CS
                         Ufd2P_core  28 trsksdlkstysslrqelktiqenlveiiknllkassesRervlkwlakilnlNekrakiqvdpskvssdgfmlNl 103
                                        +++ s+l+++ +++ ++l+ + +n+++i+ +l+++ ++ ++++l++l  i+n N++rak+ +d ++v sdgf +N+
  gene2597|gene2597|rna2597|rna2597 240 NKDISELRNIGTMIIHKLEYLAQNVFDILLKLVRKCEKIKNNFLNYLILIVNNNKNRAKMVYDYTEVISDGFAINF 315
                                        344446777899999************************************************************* PP

                                        HHHHHHHHGGGGSTT-TTGGGS-TTTTSS..-SSS.--.TT--BSSB-HHHHHHHHHHCTTS.............. CS
                         Ufd2P_core 104 lavLlrLcepfldatfskidkidpnylll.pskrl.dl.kdetrlnadeeeveefyeqkeke.............. 162
                                          vL  +c  ++ ++  ++ +i++  ++  +s    ++ +d+ +   de++ +                       
  gene2597|gene2597|rna2597|rna2597 316 NNVLALFCGQIVRKQLFNLINIKVMKIFDlKSIKEsENrEDQNKTM-DEQNGTG-------Yqtgdvsesgksgsk 383
                                        ***********96555344444443333321111112222222222.2222222.......022222233344455 PP

                                        ..---HHHHHHHHHHHHHHHTHHHHHHHHHTHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Ufd2P_core 163 ..kpnFiteiFfltlkalhlglkpaisefkrllqelkrlqdeleeleaeaaqleeqlkklkkelekllseklalea 236
                                          + +F t + f  l + ++++ + ++++k l +e+ +++ +       ++  + ql+ l+kele   s+ +al++
  gene2597|gene2597|rna2597|rna2597 384 tqNLSFSTVVLFAKLIFANYSYIKFLEHIKLLDNEIYSMELMQS-----ERDSHSQLEYLRKELE---SKCFALRI 451
                                        5699***********************************98544.....4677889999999999...89999999 PP

                                        HHT-HHHHHHHHHHHHHHHHHHHHHHSTT--TTSS---S-SSHTS-TTGGGSBTHHHHHHHHHHHHHTTSTT-TTT CS
                         Ufd2P_core 237 vlldpellqellkFlrlvaawllrvadpknlkpkkklklPlpeespeqfkvlPeffledivdfllfllrlkpkvle 312
                                        +++ + + q+     ++++++  +                        f+ lP  ++e ++++  +l+r +++ l 
  gene2597|gene2597|rna2597|rna2597 452 IFSCEFFKQQEEPITSFLIEFTEH----------------------VDFCDLPHLYFEVVFQIQTLLIREHQEFL- 504
                                        999999999999999999888843......................47*******************99654443. PP

                                        T.-TTH..HHHHHHHHHHHH-TTS---HHHHHHHHHHHHHCCS--TT--TTHHHHHH-HHHHCCHHHHHHHHHHHC CS
                         Ufd2P_core 313 sllssldldeliefiivflrsseyiknphlraklvevlfkgslplsekgalkklleshelakkhLlkaLlkfYidv 388
                                                + l+ +i  +++s+  i+n h++ +++++l+  +               + l+ + L +aL+ fY d 
  gene2597|gene2597|rna2597|rna2597 505 -------SNRLLGLIEKIMCSK--IRNLHFKESVIKILELKT---------------SSLT-ERLFHALILFYSDL 555
                                        .......467999******965..9*************9776...............5666.9***********88 PP

                                        CCT-SSSSSTCHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Ufd2P_core 389 EktgqssqFydKfniRyniseilkslwknesyrnqltklakeneelFvrFinlllNDvtflldealskLkeikelq 464
                                         +    + Fy+Kf+iRy+i  +l + +     ++ ++++a + e+  +rF+n++++D+   l  al+++ eik+ +
  gene2597|gene2597|rna2597|rna2597 556 HHFD--EFFYEKFSIRYHIHNVLMNDL-----NEHIKSIAPSTEN--LRFVNFVIDDTESQLSSALNSIIEIKRCE 622
                                        8776..99*************998766.....6778889999988..***************************** PP

                                        HHHH---....-----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-GGGGCSHHHHHHHHHHHHHHHHHH CS
                         Ufd2P_core 465 eeledqeewsslseeerqekeesleqlerqaksylqlanetvkllklltkeipepfltpeivdrlaamLnynLdqL 540
                                        e l+++     +++eer++ ++++ +++++a+s+  +  +++k+ ++l +e++ +++++e++++ ++ Ln+nL+ +
  gene2597|gene2597|rna2597|rna2597 623 ERLKHT-----NDREERRSLKSNMLRAKKKATSSFVFVDSSLKMVSFLVEECS-ILTRNEVLKKFVTILNCNLKMI 692
                                        ***963.....46799***********************************95.6788****************** PP

                                        HSHHHHT---SSGGGGT--HHHHHHHHHHHHHHCTT-HHHHHHHHH-TTT--HHHHHHHHHHHTTSTSSTHHHHHH CS
                         Ufd2P_core 541 vGpkcknLkVknpekynFrPkelLssiveiYlnLskeeeFvkavakDgRsYkkelFekavrilkregllseeelek 616
                                        vGpkc++L +knp++ynFrPkelL++i+ +Yl++s++  ++ a+++D  +++ +lF++a  i++++ +l +++l  
  gene2597|gene2597|rna2597|rna2597 693 VGPKCNDLHIKNPDEYNFRPKELLRKIIMVYLKMSND-VYLNAIVQDHSYFNLSLFKRACFICETKFILGQNDLSL 767
                                        **********************************776.************************************** PP

                                        HHHHHHHHH CS
                         Ufd2P_core 617 fkelaqkve 625
                                        fk+l++k+e
  gene2597|gene2597|rna2597|rna2597 768 FKRLVSKLE 776
                                        ******985 PP

>> U-box  U-box domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.0   0.3     2e-20   1.8e-16       1      70 [.     789     858 ..     789     861 .. 0.96

  Alignments for each domain:
  == domain 1  score: 60.0 bits;  conditional E-value: 2e-20
                                        SSGGGB-TTT-SB-SSEEEETTT.EEEEHHHHHHHHTT.SSB-TTT-SB--GGGSEE-HHHHHHHHHHHHH CS
                              U-box   1 iPdefldpitlelmkdPvilpsg.vvvdrstiekhllsrdktdPftrepltqdqlipnlelKekIdeflee 70 
                                        +Pdef+dpit   ++dPvil  + v+vdrst ++ +l  d++dPf+re+l+++++ +n+e+K+k d + e+
  gene2597|gene2597|rna2597|rna2597 789 VPDEFIDPITCDPIRDPVILLTSnVTVDRSTFDAIMLG-DQVDPFNREVLDESKVRDNEEMKKKLDVYWES 858
                                        8******************98888**************.***************************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (862 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       730  (0.0407162); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.70u 0.30s 00:00:01.00 Elapsed: 00:00:00.50
# Mc/sec: 5194.09
//
Query:       gene2598|gene2598|rna2598|rna2598  [L=109]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       218  (0.0121591); expected 358.6 (0.02)
Passed bias filter:                      189  (0.0105416); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.29s 00:00:00.63 Elapsed: 00:00:00.42
# Mc/sec: 781.56
//
Query:       gene2599|gene2599|rna2599|rna2599  [L=929]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (929 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       527  (0.0293937); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.70u 0.28s 00:00:00.98 Elapsed: 00:00:00.48
# Mc/sec: 5809.94
//
Query:       gene26|gene26|rna26|rna26  [L=801]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (801 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       703  (0.0392102); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.59u 0.25s 00:00:00.84 Elapsed: 00:00:00.42
# Mc/sec: 5774.28
//
Query:       gene260|gene260|rna260|rna260  [L=59]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.059   13.5   0.1      0.059   13.5   0.1    1.0  1  XisH      XisH protein


Domain annotation for each model (and alignments):
>> XisH  XisH protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   3.3e-06     0.059      73     120 ..       6      53 ..       1      59 [] 0.87

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.3e-06
                           XisH  73 ealGqyllYrllLeeeeperelyLAvseeiyekffqeeliqlvieenq 120
                                    +al    +Yr+++ee +pe++   ++ ++iy+++ +++  +++i+ ++
  gene260|gene260|rna260|rna260   6 QALFNLKNYRAAMEEIQPEQNTIESILKSIYKEMVERRGKSMTIDGYR 53 
                                    6777889*****************************999888887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1165  (0.0649785); expected 358.6 (0.02)
Passed bias filter:                      756  (0.0421663); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 411.24
//
Query:       gene2600|gene2600|rna2600|rna2600  [L=328]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (328 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1069  (0.0596241); expected 358.6 (0.02)
Passed bias filter:                      639  (0.0356406); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 2469.82
//
Query:       gene2601|gene2601|rna2601|rna2601  [L=48]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.052   13.5   0.5      0.098   12.6   0.0    1.6  2  DUF3746   Protein of unknown function (DUF3746)


Domain annotation for each model (and alignments):
>> DUF3746  Protein of unknown function (DUF3746)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   5.5e-06     0.098       8      24 ..       6      22 ..       5      24 .. 0.93
   2 ?   -1.7   0.2      0.16   2.9e+03      31      35 ..      39      43 ..      38      44 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.5e-06
                            DUF3746  8 LkvttsskKktCkKhif 24
                                       Lk++ s++ ++C+K ++
  gene2601|gene2601|rna2601|rna2601  6 LKDVLSCGSSYCRKTAY 22
                                       9*************999 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.16
                            DUF3746 31 Trtgs 35
                                       Trt++
  gene2601|gene2601|rna2601|rna2601 39 TRTFL 43
                                       89985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (48 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       514  (0.0286686); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.32u 0.22s 00:00:00.54 Elapsed: 00:00:00.36
# Mc/sec: 398.08
//
Query:       gene2602|gene2602|rna2602|rna2602  [L=46]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (46 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       254  (0.014167); expected 358.6 (0.02)
Passed bias filter:                      168  (0.00937029); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.29u 0.22s 00:00:00.51 Elapsed: 00:00:00.35
# Mc/sec: 388.57
//
Query:       gene2603|gene2603|rna2603|rna2603  [L=720]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.3e-12   45.6   0.0    1.1e-05   26.0   0.0    3.5  3  TPR_16    Tetratricopeptide repeat
    6.4e-09   35.3  12.9     0.0051   16.6   0.0    5.4  4  TPR_1     Tetratricopeptide repeat
    2.2e-07   30.4   4.4    3.6e-06   26.6   0.0    4.1  4  TPR_11    TPR repeat
    7.6e-07   28.8  14.0     0.0017   18.3   0.0    5.4  5  TPR_2     Tetratricopeptide repeat
    8.1e-06   25.5   8.4        2.1    8.6   0.0    6.2  6  TPR_7     Tetratricopeptide repeat
      3e-05   23.9  18.0       0.11   12.8   0.1    6.2  5  TPR_8     Tetratricopeptide repeat
    0.00047   20.8   0.0       0.47   11.4   0.0    4.6  5  TPR_14    Tetratricopeptide repeat
    0.00056   20.2  10.7      0.081   13.2   0.1    5.1  5  TPR_12    Tetratricopeptide repeat
     0.0022   18.5   0.1        5.3    7.6   0.0    3.5  3  TPR_19    Tetratricopeptide repeat
     0.0084   16.0   0.5       0.39   10.7   0.0    3.5  3  TPR_10    Tetratricopeptide repeat
  ------ inclusion threshold ------
      0.034   14.3  11.6       0.35   11.1   1.5    4.7  5  ANAPC3    Anaphase-promoting complex, cyclosome, subunit 3
        0.1   13.3   3.5         40    5.2   0.1    4.7  4  TPR_6     Tetratricopeptide repeat
       0.29   10.9   4.4          9    6.0   0.1    2.7  3  ABA_GPCR  Abscisic acid G-protein coupled receptor


Domain annotation for each model (and alignments):
>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   0.0   8.1e-09   1.1e-05       3      57 ..      29      80 ..      27      83 .. 0.91
   2 ?    4.0   0.0     0.058        80      23      53 ..     319     349 ..     315     358 .. 0.90
   3 !   11.3   0.0    0.0003      0.41      19      54 ..     646     679 ..     645     684 .. 0.89

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 8.1e-09
                             TPR_16  3 laraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaaly 57
                                       +a++ + ++++++A++ l++a++ +   P +++A++llg+++ +++++ eA +l+
  gene2603|gene2603|rna2603|rna2603 29 EANECFVQNNFEKAIKKLKRAIRIA---PTCHQAYYLLGLMHEENSEFSEAYELF 80
                                       6777789******************...**********************97776 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.058
                             TPR_16  23 alkrdpssPdaaeAllllgdaalrqgrlaeA 53 
                                        +lk++  +Pd+ + ++l   ++ +qg+ +eA
  gene2603|gene2603|rna2603|rna2603 319 YLKYFDLDPDDNHVRMLIYSIYKEQGNNEEA 349
                                        79999999********************999 PP

  == domain 3  score: 11.3 bits;  conditional E-value: 0.0003
                             TPR_16  19 aleaalkrdpssPdaaeAllllgdaalrqgrlaeAa 54 
                                        +l++al+rd+s+ d    +++lg+a+ ++g + +A+
  gene2603|gene2603|rna2603|rna2603 646 LLKRALERDGSEKD--LIMYNLGRAYHHFGLHGLAE 679
                                        689******97766..****************9998 PP

>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   3.7e-06    0.0051       8      34 .]      30      56 ..      27      56 .. 0.94
   2 !    9.8   0.3   0.00052      0.72       2      25 ..      58      81 ..      57      83 .. 0.94
   3 ?    3.6   0.3     0.047        65      10      25 ..     339     354 ..     338     355 .. 0.90
   4 !    9.9   0.4   0.00048      0.66       4      27 ..     662     685 ..     660     687 .. 0.94

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 3.7e-06
                                       HHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                              TPR_1  8 GnayfklgkydeAleyyekALelnPnn 34
                                       +n +f ++++++A++  ++A+++ P++
  gene2603|gene2603|rna2603|rna2603 30 ANECFVQNNFEKAIKKLKRAIRIAPTC 56
                                       7999*********************86 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00052
                                       HHHHHHHHHHHHTT-HHHHHHHHH CS
                              TPR_1  2 kalynlGnayfklgkydeAleyye 25
                                       +a+y lG+++ ++ ++ eA e ++
  gene2603|gene2603|rna2603|rna2603 58 QAYYLLGLMHEENSEFSEAYELFK 81
                                       69*******************997 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.047
                                        HHHHTT-HHHHHHHHH CS
                              TPR_1  10 ayfklgkydeAleyye 25 
                                        +y ++g+ +eA +y e
  gene2603|gene2603|rna2603|rna2603 339 IYKEQGNNEEAYKYIE 354
                                        8***********9965 PP

  == domain 4  score: 9.9 bits;  conditional E-value: 0.00048
                                        HHHHHHHHHHTT-HHHHHHHHHHH CS
                              TPR_1   4 lynlGnayfklgkydeAleyyekA 27 
                                         ynlG ay++ g +  A+ +y+k+
  gene2603|gene2603|rna2603|rna2603 662 MYNLGRAYHHFGLHGLAETCYKKC 685
                                        59********************97 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.0   2.6e-09   3.6e-06       2      41 ..      31      70 ..      30      71 .. 0.93
   2 ?   -1.6   0.0       1.6   2.2e+03      19      36 ..     255     272 ..     254     274 .. 0.76
   3 ?    1.4   0.3      0.19   2.6e+02       3      13 ..     339     349 ..     338     351 .. 0.90
   4 ?    0.5   0.1      0.36     5e+02      30      39 ..     661     670 ..     655     673 .. 0.86

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 2.6e-09
                             TPR_11  2 dayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykq 41
                                       ++++ q+++e+Ai+++k+A+++ P+   ayy LGl + ++
  gene2603|gene2603|rna2603|rna2603 31 NECFVQNNFEKAIKKLKRAIRIAPTCHQAYYLLGLMHEEN 70
                                       88999*****************************988765 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.6
                             TPR_11  19 kAlkldPdnaeayynLGl 36 
                                        + l++d  + +++++LG+
  gene2603|gene2603|rna2603|rna2603 255 EVLEYDDRYRDLFFELGD 272
                                        678888888888888886 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.19
                             TPR_11   3 ayyeqGkyeeA 13 
                                        +y eqG++eeA
  gene2603|gene2603|rna2603|rna2603 339 IYKEQGNNEEA 349
                                        89********9 PP

  == domain 4  score: 0.5 bits;  conditional E-value: 0.36
                             TPR_11  30 ayynLGlayy 39 
                                        + ynLG ay+
  gene2603|gene2603|rna2603|rna2603 661 IMYNLGRAYH 670
                                        66*******8 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   1.2e-06    0.0017       7      33 ..      29      55 ..      26      56 .. 0.91
   2 !    7.7   0.5     0.003       4.2       2      25 ..      58      81 ..      57      90 .. 0.88
   3 ?   -2.7   0.1       6.6   9.1e+03      22      34 .]     317     329 ..     316     329 .. 0.83
   4 ?    2.8   0.2      0.12   1.6e+02      10      25 ..     339     354 ..     338     354 .. 0.89
   5 ?    6.1   0.1      0.01        14       3      28 ..     661     686 ..     660     688 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.2e-06
                              TPR_2  7 lGlayyklgdyeeAleafekAleldPn 33
                                        ++ ++ ++++e+A++ +++A++++P+
  gene2603|gene2603|rna2603|rna2603 29 EANECFVQNNFEKAIKKLKRAIRIAPT 55
                                       68999*********************8 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.003
                              TPR_2  2 ealynlGlayyklgdyeeAleafe 25
                                       +a+y lGl ++++ ++ eA e+f+
  gene2603|gene2603|rna2603|rna2603 58 QAYYLLGLMHEENSEFSEAYELFK 81
                                       69********************98 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 6.6
                              TPR_2  22 eafekAleldPnn 34 
                                         ++ k   ldP++
  gene2603|gene2603|rna2603|rna2603 317 FYYLKYFDLDPDD 329
                                        6899999999986 PP

  == domain 4  score: 2.8 bits;  conditional E-value: 0.12
                              TPR_2  10 ayyklgdyeeAleafe 25 
                                        +y ++g+ eeA ++ e
  gene2603|gene2603|rna2603|rna2603 339 IYKEQGNNEEAYKYIE 354
                                        799*********9975 PP

  == domain 5  score: 6.1 bits;  conditional E-value: 0.01
                              TPR_2   3 alynlGlayyklgdyeeAleafekAl 28 
                                        + ynlG+ay + g +  A+ +++k+ 
  gene2603|gene2603|rna2603|rna2603 661 IMYNLGRAYHHFGLHGLAETCYKKCM 686
                                        57*********************985 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0     0.024        33      12      29 ..      36      51 ..      32      56 .. 0.82
   2 !    6.7   0.1    0.0061       8.4       1      24 [.      59      82 ..      59      92 .. 0.88
   3 ?   -1.7   0.2       2.8   3.9e+03      20      29 ..     121     130 ..     120     138 .. 0.83
   4 ?    4.4   0.0     0.034        46       7      29 ..     338     358 ..     338     375 .. 0.87
   5 ?   -1.6   0.1       2.6   3.6e+03       1      11 [.     562     572 ..     562     574 .. 0.90
   6 !    8.6   0.0    0.0015       2.1       3      28 ..     663     688 ..     661     697 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.024
                              TPR_7 12 lGdyeeAielyeqsLalt 29
                                       ++++e+Ai+ +++  a++
  gene2603|gene2603|rna2603|rna2603 36 QNNFEKAIKKLKR--AIR 51
                                       79***********..554 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0061
                              TPR_7  1 aLlnLarlysrlGdyeeAielyeq 24
                                       a++ L+ ++++  +++eA el++ 
  gene2603|gene2603|rna2603|rna2603 59 AYYLLGLMHEENSEFSEAYELFKI 82
                                       799******************985 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 2.8
                              TPR_7  20 elyeqsLalt 29 
                                        elye++L l+
  gene2603|gene2603|rna2603|rna2603 121 ELYEEQLSLC 130
                                        79***99886 PP

  == domain 4  score: 4.4 bits;  conditional E-value: 0.034
                              TPR_7   7 rlysrlGdyeeAielyeqsLalt 29 
                                        ++y ++G+ eeA ++ e   ++t
  gene2603|gene2603|rna2603|rna2603 338 SIYKEQGNNEEAYKYIEM--RTT 358
                                        69*************998..655 PP

  == domain 5  score: -1.6 bits;  conditional E-value: 2.6
                              TPR_7   1 aLlnLarlysr 11 
                                        a++nL r++ r
  gene2603|gene2603|rna2603|rna2603 562 AYNNLRRIHLR 572
                                        79******976 PP

  == domain 6  score: 8.6 bits;  conditional E-value: 0.0015
                              TPR_7   3 lnLarlysrlGdyeeAielyeqsLal 28 
                                        +nL+r+y+  G +  A+++y++++a+
  gene2603|gene2603|rna2603|rna2603 663 YNLGRAYHHFGLHGLAETCYKKCMAT 688
                                        7*********************7765 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0      0.01        14      15      34 .]      37      56 ..      30      56 .. 0.92
   2 ?    6.1   0.8     0.011        15       2      33 ..      58      89 ..      57      90 .. 0.91
   3 ?    0.4   0.1      0.72   9.9e+02      23      34 .]     318     329 ..     316     329 .. 0.91
   4 ?    5.7   0.7     0.014        20       9      25 ..     338     354 ..     338     354 .. 0.93
   5 !   12.8   0.1   7.7e-05      0.11       4      28 ..     662     686 ..     661     691 .. 0.93

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.01
                                       T-HHHHHHHHHHHHHHHHH. CS
                              TPR_8 15 gdyeeAkeyyekaleldpdn 34
                                       +++e+A++ +++a++++p++
  gene2603|gene2603|rna2603|rna2603 37 NNFEKAIKKLKRAIRIAPTC 56
                                       89****************85 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.011
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                              TPR_8  2 eayynlgsiylklgdyeeAkeyyekaleldpd 33
                                       +ayy+lg+ +++  ++ eA e ++ +  ++++
  gene2603|gene2603|rna2603|rna2603 58 QAYYLLGLMHEENSEFSEAYELFKICYNIKKK 89
                                       89*********************999988887 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.72
                                        HHHHHHHHHHH. CS
                              TPR_8  23 yyekaleldpdn 34 
                                        yy k+ +ldpd+
  gene2603|gene2603|rna2603|rna2603 318 YYLKYFDLDPDD 329
                                        9*********96 PP

  == domain 4  score: 5.7 bits;  conditional E-value: 0.014
                                        HHHHHTT-HHHHHHHHH CS
                              TPR_8   9 siylklgdyeeAkeyye 25 
                                        siy+++g+ eeA +y+e
  gene2603|gene2603|rna2603|rna2603 338 SIYKEQGNNEEAYKYIE 354
                                        69************987 PP

  == domain 5  score: 12.8 bits;  conditional E-value: 7.7e-05
                                        HHHHHHHHHHTT-HHHHHHHHHHHH CS
                              TPR_8   4 yynlgsiylklgdyeeAkeyyekal 28 
                                        +ynlg++y+  g +  A+ +y+k+ 
  gene2603|gene2603|rna2603|rna2603 662 MYNLGRAYHHFGLHGLAETCYKKCM 686
                                        79**********************6 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.0   0.00034      0.47      14      42 ..      36      64 ..      26      66 .. 0.90
   2 ?    3.6   0.0      0.11   1.5e+02       2      25 ..      58      81 ..      57      84 .. 0.92
   3 ?    2.0   0.0      0.37   5.1e+02       8      26 ..     337     355 ..     331     360 .. 0.82
   4 ?   -1.0   0.0       3.2   4.4e+03      19      35 ..     642     658 ..     636     668 .. 0.72
   5 ?   -0.4   0.0       2.2     3e+03       7      27 ..     665     685 ..     659     700 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00034
                             TPR_14 14 lGdpdeAiallrralalaPddaeawllla 42
                                       + ++++Ai+ l+ra++ aP+  +a++ll+
  gene2603|gene2603|rna2603|rna2603 36 QNNFEKAIKKLKRAIRIAPTCHQAYYLLG 64
                                       789**********************9997 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.11
                             TPR_14  2 eallalaeallalGdpdeAiallr 25
                                       +a+++l+  ++++ ++ eA +l++
  gene2603|gene2603|rna2603|rna2603 58 QAYYLLGLMHEENSEFSEAYELFK 81
                                       699******************997 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.37
                             TPR_14   8 aeallalGdpdeAiallrr 26 
                                         +++ ++G+ +eA ++ + 
  gene2603|gene2603|rna2603|rna2603 337 YSIYKEQGNNEEAYKYIEM 355
                                        47899**********9886 PP

  == domain 4  score: -1.0 bits;  conditional E-value: 3.2
                             TPR_14  19 eAiallrralalaPdda 35 
                                        +   ll+ral+++ ++ 
  gene2603|gene2603|rna2603|rna2603 642 KGFSLLKRALERDGSEK 658
                                        56678999999987664 PP

  == domain 5  score: -0.4 bits;  conditional E-value: 2.2
                             TPR_14   7 laeallalGdpdeAiallrra 27 
                                        l++a+ + G +  A+++++++
  gene2603|gene2603|rna2603|rna2603 665 LGRAYHHFGLHGLAETCYKKC 685
                                        89**************99986 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.1    0.0015       2.1      16      76 ..      36      88 ..      30      89 .. 0.85
   2 ?   -2.3   0.2       4.2   5.9e+03      11      28 ..     131     148 ..     126     148 .. 0.75
   3 ?   -0.3   0.0         1   1.4e+03      12      26 ..     339     353 ..     335     355 .. 0.83
   4 ?    0.0   0.0      0.78   1.1e+03      17      35 ..     383     401 ..     377     408 .. 0.64
   5 !   13.2   0.1   5.8e-05     0.081      25      73 ..     646     687 ..     639     689 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0015
                             TPR_12 16 lgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76
                                       + ++++A++ l++a++ia     p+ +   ++++ Lg ++++  ++ eA el++ +++i++
  gene2603|gene2603|rna2603|rna2603 36 QNNFEKAIKKLKRAIRIA-----PTCH---QAYYLLGLMHEENSEFSEAYELFKICYNIKK 88
                                       78999*********9999.....5543...49*****************999998888776 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 4.2
                             TPR_12  11 avlrrlgrydeAlellek 28 
                                          l++ +r +eA+ ++e+
  gene2603|gene2603|rna2603|rna2603 131 RYLNQEERAHEAIINHEQ 148
                                        557888899999988875 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 1
                             TPR_12  12 vlrrlgrydeAlell 26 
                                        ++ ++g+ +eA ++ 
  gene2603|gene2603|rna2603|rna2603 339 IYKEQGNNEEAYKYI 353
                                        788999999999986 PP

  == domain 4  score: 0.0 bits;  conditional E-value: 0.78
                             TPR_12  17 grydeAlellekaleiarr 35 
                                        +++ e ++++++ l+++++
  gene2603|gene2603|rna2603|rna2603 383 KECNEIRRIYNETLQLRKK 401
                                        4555666666666666655 PP

  == domain 5  score: 13.2 bits;  conditional E-value: 5.8e-05
                             TPR_12  25 llekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleeala 73 
                                        ll++al       + d  +   +++nLgr+y+ +g +  A+  +++++a
  gene2603|gene2603|rna2603|rna2603 646 LLKRAL-------ERDGSEKDLIMYNLGRAYHHFGLHGLAETCYKKCMA 687
                                        444444.......444444556899999999999999999999999987 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.0    0.0039       5.3       4      48 ..      36      80 ..      34      82 .. 0.91
   2 ?    5.2   0.0     0.021        30      15      46 ..     321     351 ..     317     356 .. 0.87
   3 ?    0.6   0.0      0.62   8.5e+02      12      39 ..     645     673 ..     644     688 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0039
                             TPR_19  4 egdyaeAlalleqalqedpknaearllLAeallalgqldeAealL 48
                                       +++++ A++ l++a+  +p    a +lL   + ++ ++ eA +l 
  gene2603|gene2603|rna2603|rna2603 36 QNNFEKAIKKLKRAIRIAPTCHQAYYLLGLMHEENSEFSEAYELF 80
                                       68999************************9999999999998775 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.021
                             TPR_19  15 eqalqedpknaearllLAeallalgqldeAea 46 
                                        ++ ++ dp++  +r+l   ++ ++g+ +eA +
  gene2603|gene2603|rna2603|rna2603 321 KY-FDLDPDDNHVRMLIYSIYKEQGNNEEAYK 351
                                        45.789***********************965 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.62
                             TPR_19  12 alleqalqedpk.naearllLAeallalg 39 
                                        +ll++al+ d    + + ++L +a+   g
  gene2603|gene2603|rna2603|rna2603 645 SLLKRALERDGSeKDLIMYNLGRAYHHFG 673
                                        589****9998845556669999997666 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1       1.5   2.1e+03      11      21 ..     339     349 ..     338     354 .. 0.86
   2 ?    0.7   0.0      0.38   5.2e+02      16      35 ..     383     402 ..     379     406 .. 0.86
   3 !   10.7   0.0   0.00028      0.39       4      31 ..     661     688 ..     660     693 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1.5
                             TPR_10  11 alrqrgrydeA 21 
                                        ++ ++g+ +eA
  gene2603|gene2603|rna2603|rna2603 339 IYKEQGNNEEA 349
                                        699*******9 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.38
                             TPR_10  16 grydeAealleealairrrl 35 
                                        ++ +e ++++ e+l++r++l
  gene2603|gene2603|rna2603|rna2603 383 KECNEIRRIYNETLQLRKKL 402
                                        5678999***********97 PP

  == domain 3  score: 10.7 bits;  conditional E-value: 0.00028
                             TPR_10   4 slnNLanalrqrgrydeAealleealai 31 
                                        ++ NL++a+++ g +  Ae  +++++a+
  gene2603|gene2603|rna2603|rna2603 661 IMYNLGRAYHHFGLHGLAETCYKKCMAT 688
                                        589***********************98 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   1.5   0.00025      0.35      36      79 ..      36      80 ..      25      98 .. 0.61
   2 ?    5.7   0.1     0.013        18      31      72 ..     204     245 ..     182     247 .. 0.85
   3 ?   -0.5   0.1       1.1   1.5e+03      44      79 ..     318     353 ..     310     358 .. 0.65
   4 ?   -1.1   0.0       1.6   2.2e+03      33      51 ..     553     571 ..     551     579 .. 0.81
   5 ?   -1.8   0.0       2.8   3.9e+03      22      39 ..     613     630 ..     603     634 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00025
                                       TT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH CS
                             ANAPC3 36 ngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaL 79
                                       ++++++A++ l++a +++++ +++ yl++    + +++ eA+ ++
  gene2603|gene2603|rna2603|rna2603 36 QNNFEKAIKKLKRAiRIAPTCHQAYYLLGLMHEENSEFSEAYELF 80
                                       555555555555555555555555555555555555555555444 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.013
                                        HHHHHTT-HHHHHHHHHCTSHHHC-HHHHHHHHHHHHHTT-H CS
                             ANAPC3  31 lclylngqykrAyellrkaklnskslgcrylfAqcllkLkky 72 
                                         +ly+n+ y+  y++++k++    s +  ++fA + +k ++y
  gene2603|gene2603|rna2603|rna2603 204 DTLYKNSSYDAVYQIYEKCGGVFLSTKNKLIFAISRIKSNNY 245
                                        579****************88888889999999999998888 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 1.1
                                        HHHHCTSHHHC-HHHHHHHHHHHHHTT-HHHHHHHH CS
                             ANAPC3  44 ellrkaklnskslgcrylfAqcllkLkkyeeAiaaL 79 
                                        ++l+ ++l++ +  +r+l+   + ++++ eeA++ +
  gene2603|gene2603|rna2603|rna2603 318 YYLKYFDLDPDDNHVRMLIYSIYKEQGNNEEAYKYI 353
                                        455555666666666666666666777777776655 PP

  == domain 4  score: -1.1 bits;  conditional E-value: 1.6
                                        HHHTT-HHHHHHHHHCTSH CS
                             ANAPC3  33 lylngqykrAyellrkakl 51 
                                        +++++ + +Ay+ lr+  l
  gene2603|gene2603|rna2603|rna2603 553 YCNSKSFRTAYNNLRRIHL 571
                                        899999*****99998744 PP

  == domain 5  score: -1.8 bits;  conditional E-value: 2.8
                                        -HHHHHHHHHHHHHTT-H CS
                             ANAPC3  22 spedayllAlclylngqy 39 
                                        s+ ++ llA  +++n++ 
  gene2603|gene2603|rna2603|rna2603 613 SDTNTVLLAIIYFNNSKS 630
                                        6778999*******9986 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0       0.1   1.4e+02      10      31 ..      34      54 ..      30      55 .. 0.83
   2 ?    5.2   0.1     0.029        40       1      24 [.      58      81 ..      58      85 .. 0.91
   3 ?   -1.0   0.0       2.6   3.5e+03      10      23 ..     340     353 ..     338     355 .. 0.82
   4 ?    0.9   0.0      0.67   9.2e+02       3      24 ..     662     683 ..     661     687 .. 0.72

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.1
                                       HHHHHHHHHHHHHHHHHHHH-T CS
                              TPR_6 10 yrklgdtdkAlealerlikeYP 31
                                       +  +++ +kA++ l+r i+  P
  gene2603|gene2603|rna2603|rna2603 34 FV-QNNFEKAIKKLKRAIRIAP 54
                                       44.559************9888 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.029
                                       HHHHHHHHHHHHHHHHHHHHHHHH CS
                              TPR_6  1 dAlyklalsyrklgdtdkAleale 24
                                       +A+y+l+l +++  + ++A e+++
  gene2603|gene2603|rna2603|rna2603 58 QAYYLLGLMHEENSEFSEAYELFK 81
                                       69**********88*******997 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 2.6
                                        HHHHHHHHHHHHHH CS
                              TPR_6  10 yrklgdtdkAleal 23 
                                        y+++g+ ++A ++ 
  gene2603|gene2603|rna2603|rna2603 340 YKEQGNNEEAYKYI 353
                                        8889******9875 PP

  == domain 4  score: 0.9 bits;  conditional E-value: 0.67
                                        HHHHHHHHHHHHHHHHHHHHHH CS
                              TPR_6   3 lyklalsyrklgdtdkAleale 24 
                                        +y+l+++y   g +  A + ++
  gene2603|gene2603|rna2603|rna2603 662 MYNLGRAYHHFGLHGLAETCYK 683
                                        8*******88446666655555 PP

>> ABA_GPCR  Abscisic acid G-protein coupled receptor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.7    0.0073        10      63     103 ..     493     533 ..     476     543 .. 0.83
   2 ?    6.0   0.1    0.0065         9       9      58 ..     541     595 ..     534     634 .. 0.79
   3 ?   -3.8   0.0       6.8   9.4e+03      28      49 ..     687     713 ..     665     717 .. 0.54

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0073
                           ABA_GPCR  63 ldlealsrqiSllLsgvlllaslssvlttissllrllpssl 103
                                          ++++ ++ S+ + ++++l ++s+ l  i+ l+r++++  
  gene2603|gene2603|rna2603|rna2603 493 SLEASIFKNTSFYFNIIFILIKFSTLLGNIKFLTRAVKKFY 533
                                        557788999**************************998755 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0065
                           ABA_GPCR   9 kllkvlgvvfaiYCvyrilktllnllpriil.....sssssDplavtlaklllrh 58 
                                        +l+ +l  +f+ YC  + + t +n l+ri+l     + +++D ++ +l++l ++ 
  gene2603|gene2603|rna2603|rna2603 541 NLYHFLLNFFVDYCNSKSFRTAYNNLRRIHLrhvdkNIKQNDDFTFLLSNLPFFL 595
                                        566677778999****************999****98899*********998222 PP

  == domain 3  score: -3.8 bits;  conditional E-value: 6.8
                           ABA_GPCR  28 ktllnllpriil.....sssssDplav 49 
                                        +t +++l    l     ss+s+D l  
  gene2603|gene2603|rna2603|rna2603 687 ATKFKKLAAFNLiliyrSSQSKDLLRH 713
                                        333333322222444455666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (720 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       987  (0.0550505); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.75u 0.32s 00:00:01.07 Elapsed: 00:00:00.54
# Mc/sec: 4014.39
//
Query:       gene2604|gene2604|rna2604|rna2604  [L=325]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-34  119.1   0.0    2.3e-34  118.8   0.0    1.1  1  Ribosomal_L4     Ribosomal protein L4/L1 family
     0.0017   18.4   0.0     0.0073   16.3   0.0    2.1  3  Ribos_L4_asso_C  60S ribosomal protein L4 C-terminal domain


Domain annotation for each model (and alignments):
>> Ribosomal_L4  Ribosomal protein L4/L1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.8   0.0   2.6e-38   2.3e-34       2     190 ..      18     255 ..      17     257 .. 0.93

  Alignments for each domain:
  == domain 1  score: 118.8 bits;  conditional E-value: 2.6e-38
                                        EE-HHHHSS---HHHHHHHHHHHHHSS-EE-----.-TTTSS---S-SS-SSSSSS---S-TT............S CS
                       Ribosomal_L4   2 eLspkvFaapirrdlihravvaylanrrqgtastk.arsevsgsgrklwkQKGtGrARvgsir............s 64 
                                        +L p vF +p+r dli  ++++   n+rq++a ++ a++  s+  + +++  G++ ARv++i+            +
  gene2604|gene2604|rna2604|rna2604  18 DL-PPVFRTPVRSDLISFVHKNVALNKRQPYAVSPnAGKNYSA--EGWGT--GRAVARVPRIKgsgtrragqgafA 88 
                                        68.99******************************99**9999..69***..************************ PP

                                        TTSTT---SS---S.EEHHHHHHHHHHHHHHHHHHHHHHHTT-EEEES....---.-S.............S--HH CS
                       Ribosomal_L4  65 piargGgvahgpkperdystklnkKvrrlAlrsaLsakakqglllvvd....nleple.............esktk 123
                                        +++rgG++ah++++ r++++k +   rrl  ++ +sa a +  ++ ++        l+             ++ktk
  gene2604|gene2604|rna2604|rna2604  89 NFCRGGHMAHPTSVMRRWQRKTPLSIRRLVTAMGISASALAPIVESRGhrisG---LKsiplvidnemlqgIEKTK 161
                                        ************************************************75553...444557799999999***** PP

                                        HHHHHHHHTT-.........................TTSSEEEEESSSSCHHHHHHTT-TTEEEEESTT--CHHHH CS
                       Ribosomal_L4 124 elvellkklgl.........................ksksvLivvsekdenlvlaarnlpgvevieveslnvydll 174
                                        ++v++l++lgl                          +k++Liv++   e  ++a+rn++gv++++v+sl+v++l 
  gene2604|gene2604|rna2604|rna2604 162 DAVRFLNELGLseemdktkevfiksgkgkmrnrrykVKKGPLIVYDG--EICAKAFRNVQGVDMCQVDSLSVLELC 235
                                        ********9999999999999999999999999888899******86..9************************** PP

                                        HSSE....EEEEHHHHHHHH CS
                       Ribosomal_L4 175 kadk....vvitksavekle 190
                                        ++ +    v++ k+a+ kl 
  gene2604|gene2604|rna2604|rna2604 236 PGGQpgrlVIWMKDAFLKLH 255
                                        ****************9986 PP

>> Ribos_L4_asso_C  60S ribosomal protein L4 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.0       1.5   1.4e+04      36      47 ..     102     113 ..      98     118 .. 0.70
   2 ?   -3.3   0.0       1.1   9.5e+03      29      46 ..     185     203 ..     181     203 .. 0.66
   3 !   16.3   0.0   8.2e-07    0.0073       2      59 ..     270     321 ..     269     324 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 1.5
                    Ribos_L4_asso_C  36 kkkrvqkkNPLk 47 
                                        + +r q+k PL 
  gene2604|gene2604|rna2604|rna2604 102 VMRRWQRKTPLS 113
                                        457788998986 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 1.1
                    Ribos_L4_asso_C  29 rpakkekkkkr.vqkkNPL 46 
                                        +  k++ +++r  +kk PL
  gene2604|gene2604|rna2604|rna2604 185 KSGKGKMRNRRyKVKKGPL 203
                                        5556666666678888887 PP

  == domain 3  score: 16.3 bits;  conditional E-value: 8.2e-07
                    Ribos_L4_asso_C   2 gynLPrpkmtnaDlsRiinSdeiqsvlrpakkekkkkrvqkkNPLknkqvmlrLNPya 59 
                                        g+ L   + +n D+++i  S e+q+ + ++        v k    kn+q   +LNPy 
  gene2604|gene2604|rna2604|rna2604 270 GFLLTGGIASNDDVEKIFYSCEVQAFIDEPCL------VDKPKLVKNVQEIEKLNPYL 321
                                        6788888999********************76......6666779************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (325 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 2187.20
//
Query:       gene2605|gene2605|rna2605|rna2605  [L=131]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.3e-19   69.2   1.2    7.7e-19   68.4   1.2    1.5  1  SRP19           SRP19 protein
  ------ inclusion threshold ------
        0.4    9.9   3.6       0.63    9.3   3.6    1.2  1  Chordopox_A33R  Chordopoxvirus A33R protein


Domain annotation for each model (and alignments):
>> SRP19  SRP19 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.4   1.2   8.6e-23   7.7e-19       2      88 ..       6     108 ..       5     130 .. 0.84

  Alignments for each domain:
  == domain 1  score: 68.4 bits;  conditional E-value: 8.6e-23
                                        EECCCCBTTS-CCCT--S-CCCSBSS--HHHHHHHHHHCTSCEEEEEEECTTSSTTCCEEEEEC-........... CS
                              SRP19   2 iYPvYldskktrkeGRrvpkelavenPtaqeiaealkalglevvvepeksyPrdwanpGrVrvkl........... 66 
                                        +YP+++++  ++k+GR+ +k+l+ +nPt+qe+ +a++algl+++ve++k +P+  + pGr+r  +           
  gene2605|gene2605|rna2605|rna2605   6 VYPCHINAALSHKHGRKYNKTLCTSNPTIQEMEKAAAALGLQFTVEEKKIHPKTPLDPGRIRFSKeygrltvvrgl 81 
                                        8***************************************************************977877777777 PP

                                        ...............SS-CHHHHHHHH CS
                              SRP19  67 .....kedgkevnekiknkkellkkia 88 
                                             + +  +v+++i +k+++  ki 
  gene2605|gene2605|rna2605|rna2605  82 kqeieELRIVKVEKEIAKKENVKAKIG 108
                                        665541223344555666666655555 PP

>> Chordopox_A33R  Chordopoxvirus A33R protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   3.6     7e-05      0.63      11      39 ..      98     126 ..      89     129 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 7e-05
                     Chordopox_A33R  11 dskdeaasfvGstiyGnklkkktkkkksk 39 
                                          k++ ++ +G+t++ ++ kkk+++kksk
  gene2605|gene2605|rna2605|rna2605  98 AKKENVKAKIGTTVFMPRTKKKKNEKKSK 126
                                        4578999*********************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1570  (0.0875676); expected 358.6 (0.02)
Passed bias filter:                      527  (0.0293937); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.34s 00:00:00.86 Elapsed: 00:00:00.53
# Mc/sec: 742.05
//
Query:       gene2606|gene2606|rna2606|rna2606  [L=279]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.7e-67  225.9   0.3    5.5e-67  225.7   0.3    1.0  1  TIM             Triosephosphate isomerase
     0.0053   16.9   0.1      0.022   14.9   0.1    1.9  2  HGTP_anticodon  Anticodon binding domain


Domain annotation for each model (and alignments):
>> TIM  Triosephosphate isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  225.7   0.3   6.1e-71   5.5e-67       2     242 ..      42     272 ..      41     273 .. 0.95

  Alignments for each domain:
  == domain 1  score: 225.7 bits;  conditional E-value: 6.1e-71
                                        EEEEE-TBTS-HHHHHHHHHHHHHHCHGCTSEEEEE--GGGHHHHHHHHTTSSECEEES--BSSSSBS-TT--BHH CS
                                TIM   2 liagNwKmnktleeakellkklkaklkeekvevviappflylekvkklleesklklgaqnvsaeksGafTGevsae 77 
                                        l++gN K+  +++  + l + +++++++  vev+ a+pf yl+ +++++  s+++++aq++s+  +Ga+TGevsae
  gene2606|gene2606|rna2606|rna2606  42 LLGGNLKLCCSKDRLNYLSTLINEEYND--VEVFYAVPFPYLSFAREIFP-SHVRIAAQDCSEFINGAYTGEVSAE 114
                                        789**********999998889988865..*************9999996.9************************ PP

                                        HHHHTT-SEEEES-HHHHHHST--HHHHHHHHHHHHHTT-EEEEEE---HHHHHTT.HHHHHHHHHHHHTTTS-CC CS
                                TIM  78 mlkdlgvkyviiGHsErrqlfkEtdelvakKvkaalksglkpilCvGEtleereagkteevvkeqlkeilkkldee 153
                                        ml d+gvk viiGHsErr+l+ ++ + v kKv +a k+g++++lCvGE++ +r++++t +vv++qlk++l+ + e+
  gene2606|gene2606|rna2606|rna2606 115 MLVDIGVKSVIIGHSERRKLYDDE-KSVCKKVMNAFKTGMNVLLCVGEDEVQRRQNETISVVAKQLKSVLECMIEQ 189
                                        *******************99876.67889********************************************** PP

                                        CGGCEEEEE--GGGSSSS----HHHHHHHHHHHHHHHHHHSTHHHHTTSEEEEESS--TTTHHHHHTSTT--EEEE CS
                                TIM 154 alknvviAYePvWAiGtgktatpeqaqevhaairkelaekvskevaekirilYGGsvnkenakellkqkdidGlLv 229
                                        +++ + +AYePvW+iGtg++ ++++++ev+++ir+el++      + + r++YGGsv+++n+++l++ k  dG+Lv
  gene2606|gene2606|rna2606|rna2606 190 NISCIDVAYEPVWSIGTGNVPNNKEIEEVISFIRQELNNY-----NVNGRVIYGGSVSEKNVETLCNIKCLDGFLV 260
                                        ************************************9776.....6799*************************** PP

                                        SGGGCSHHHHHHH CS
                                TIM 230 GgaslkaesFlki 242
                                        G++s   ++F++i
  gene2606|gene2606|rna2606|rna2606 261 GKSSTT-DEFVHI 272
                                        ***998.779988 PP

>> HGTP_anticodon  Anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.1   2.5e-06     0.022      31      70 ..     131     171 ..     114     189 .. 0.83
   2 ?   -1.4   0.0      0.31   2.8e+03       7      29 ..     211     230 ..     208     238 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.5e-06
                                        EEEEESSSSTHHHHHHHHHHTT-SEEEEE-HHHHHH.TEEE CS
                     HGTP_anticodon  31 rvelddsnesigkkireadllgipfavvvGekelek.gtvt 70 
                                        r++l+d+++s+ kk+ +a + g ++ + vGe+e+++ +  t
  gene2606|gene2606|rna2606|rna2606 131 RRKLYDDEKSVCKKVMNAFKTGMNVLLCVGEDEVQRrQNET 171
                                        789*******************************8633333 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.31
                                        SSSSHHHHHHHHHHHHHHHHTTT CS
                     HGTP_anticodon   7 lnekaeeleeyakklaeeLraag 29 
                                         n+   e+ee+ + +++eL++ +
  gene2606|gene2606|rna2606|rna2606 211 NNK---EIEEVISFIRQELNNYN 230
                                        455...78888888888888755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (279 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       611  (0.0340789); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 1717.44
//
Query:       gene2607|gene2607|rna2607|rna2607  [L=149]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       360  (0.0200792); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1088.82
//
Query:       gene2608|gene2608|rna2608|rna2608  [L=105]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.9e-05   22.3   0.9    0.00014   21.7   0.9    1.3  1  PLDc_N    Phospholipase_D-nuclease N-terminal
     0.0049   16.8   0.2     0.0079   16.2   0.2    1.3  1  SNARE     SNARE domain
  ------ inclusion threshold ------
       0.13   11.9   0.0       0.13   11.8   0.0    1.1  1  SARAF     SOCE-associated regulatory factor of calcium homoeo


Domain annotation for each model (and alignments):
>> PLDc_N  Phospholipase_D-nuclease N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.9   2.4e-08   0.00014      13      37 ..      69      97 ..      65      97 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 2.4e-08
                             PLDc_N 13 d....rnpssklaWllvilflPvlGailY 37
                                       d    r++++k++Wll+++++ ++ ++lY
  gene2608|gene2608|rna2608|rna2608 69 DpeekRSSGGKWIWLLFLIVVAFIAFVLY 97
                                       4445466777******************9 PP

>> SNARE  SNARE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.2   1.3e-06    0.0079      30      53 .]      73      96 ..      71      96 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.3e-06
                                       HHCTXXXXXXXXXXXXXXXXXXXX CS
                              SNARE 30 yqksnRklkciillilviillvvl 53
                                       + +s +k+ ++++li+v ++ +vl
  gene2608|gene2608|rna2608|rna2608 73 KRSSGGKWIWLLFLIVVAFIAFVL 96
                                       6799****************9996 PP

>> SARAF  SOCE-associated regulatory factor of calcium homoeostasis
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   2.2e-05      0.13     150     182 ..      67     102 ..      40     105 .] 0.74

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.2e-05
                              SARAF 150 e...vkkksssssasllfvvlvllviayivykafla 182
                                            ++k+ss++++ +l++++v+++ia+++yk  ++
  gene2608|gene2608|rna2608|rna2608  67 FkdpEEKRSSGGKWIWLLFLIVVAFIAFVLYKKQVT 102
                                        044466788889999999*************98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       742  (0.0413855); expected 358.6 (0.02)
Passed bias filter:                      562  (0.0313459); expected 358.6 (0.02)
Passed Vit filter:                        84  (0.00468515); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 785.44
//
Query:       gene2609|gene2609|rna2609|rna2609  [L=215]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (215 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       337  (0.0187964); expected 358.6 (0.02)
Passed bias filter:                      224  (0.0124937); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 1464.73
//
Query:       gene261|gene261|rna261|rna261  [L=44]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (44 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       240  (0.0133861); expected 358.6 (0.02)
Passed bias filter:                      181  (0.0100954); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.33u 0.25s 00:00:00.58 Elapsed: 00:00:00.39
# Mc/sec: 335.27
//
Query:       gene2610|gene2610|rna2610|rna2610  [L=201]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.3e-50  170.4   0.1    5.1e-50  170.1   0.1    1.1  1  MutS_V    MutS domain V
    4.2e-05   24.2   0.1    4.5e-05   24.1   0.1    1.1  1  AAA_23    AAA domain
     0.0021   17.8   0.1     0.0055   16.4   0.1    1.7  1  AAA_29    P-loop containing region of AAA domain
     0.0022   17.5   0.5      0.032   13.7   0.1    2.4  3  SMC_N     RecF/RecN/SMC N terminal domain
     0.0025   17.7   0.4     0.0045   16.8   0.4    1.6  1  AAA_21    AAA domain, putative AbiEii toxin, Type IV TA syste
     0.0058   16.7   0.1      0.011   15.7   0.1    1.6  1  AAA_14    AAA domain
     0.0068   16.9   0.5      0.026   15.0   0.1    1.9  2  ABC_tran  ABC transporter
     0.0097   15.8   0.1       0.14   12.0   0.1    2.0  1  Rad17     Rad17 P-loop domain
  ------ inclusion threshold ------
      0.011   15.3   0.4      0.036   13.6   0.1    2.0  3  AAA_25    AAA domain
      0.018   14.6   0.0       0.03   13.9   0.0    1.3  1  AAA_27    AAA domain
      0.023   14.4   0.7      0.043   13.5   0.7    1.3  1  AAA_15    AAA ATPase domain
      0.026   14.4   2.1        3.1    7.7   1.2    2.4  2  NTPase_1  NTPase


Domain annotation for each model (and alignments):
>> MutS_V  MutS domain V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  170.1   0.1   3.4e-53   5.1e-50       2     185 ..      24     200 ..      23     201 .] 0.92

  Alignments for each domain:
  == domain 1  score: 170.1 bits;  conditional E-value: 3.4e-53
                                        EEE-STTSSHHHHHHHHHHHHHHHHHT--BSSSEEEEE--SEEEEEE--------SS-HHHHHHHHHHHHHTT--T CS
                             MutS_V   2 litGpnmaGkstylrqvalivllaqiGsfvpaekaeisivdkiftRvgasDdlakgkstFmvEmlEtasilknate 77 
                                        ++tGpn aGkst+l+ +al v+l q+Gs vp +++++++ d i+ R gasD+   g stFm Em+++a+i + +te
  gene2610|gene2610|rna2610|rna2610  24 ILTGPNTAGKSTFLKTIALTVILGQMGSLVPGREVKFELRDGIYIRSGASDK--YGISTFMREMKDIARITNMCTE 97 
                                        99*************************************************8..599******************* PP

                                        TSEEEEESTS-SS-HHHHHHHHHHHHHHHHHTT--EEEEEES-GGGGGHHHHSTTEEEEEEEEEEETTEEEEEEEE CS
                             MutS_V  78 kslvilDElGRGtstydGlaialavaeyllekikaktlfatHyheltklaekleevknlhlavkeeeedivflykv 153
                                        ksl+++DElGRGts  dG++++ a+ eyll+ +ka ++fatH++   k ++ + + + ++l ++e  +  v++yk+
  gene2610|gene2610|rna2610|rna2610  98 KSLILIDELGRGTSYIDGISLSVAIKEYLLK-KKALAVFATHFTG--KNEKMFLDGQDVDLLCSEVVDG-VITYKI 169
                                        ******************************8.79*********86..4555566777888888777665.579*** PP

                                        EES--SS--HHHHHHHTT--HHHHHHHHHHHH CS
                             MutS_V 154 kegaaeksyGikvaklaglPesvverArevlk 185
                                        k+g+a +s Gi+vak +g+P++v+++A++ l+
  gene2610|gene2610|rna2610|rna2610 170 KKGVA-NSLGIDVAKRVGFPKEVINAAEKYLN 200
                                        ***98.59*******************99876 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.1     3e-08   4.5e-05      18     130 ..      19     131 ..       6     200 .. 0.69

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 3e-08
                             AAA_23  18 skgltlItGpNGaGKTTildAiklaL.ygetprlsrksgrgfe.ksdveiesegkvkay.veltfenkdgrytrsi 90 
                                        + ++t++tGpN aGK+T+l  i l    g+ + l ++++ +fe ++ + i s+   ++y ++   +  +++   +i
  gene2610|gene2610|rna2610|rna2610  19 NVNFTILTGPNTAGKSTFLKTIALTViLGQMGSLVPGREVKFElRDGIYIRSG-ASDKYgISTFMREMKDI--ARI 91 
                                        5689****************999865479999999999888885555666665.44444465554444443..346 PP

                             AAA_23  91 ererelskkkgkttkkaklelleideleqfisellgskki 130
                                        ++++++++       +  ++ ++   l   i+e+l +kk+
  gene2610|gene2610|rna2610|rna2610  92 TNMCTEKSLILIDELGRGTSYIDGISLSVAIKEYLLKKKA 131
                                        6665555555545555555555555555555555555554 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.1   3.7e-06    0.0055      22      42 ..      21      40 ..      10      51 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 3.7e-06
                             AAA_29 22 kgatlltGpsGsGKSTllDAi 42
                                       + +t+ltGp+ +GKST+l  i
  gene2610|gene2610|rna2610|rna2610 21 N-FTILTGPNTAGKSTFLKTI 40
                                       3.79*************9655 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.1   2.1e-05     0.032      10      45 ..       6      41 ..       2      52 .. 0.81
   2 ?    0.5   0.0      0.23   3.4e+02     127     156 ..      96     125 ..      65     135 .. 0.74
   3 ?    0.6   0.0      0.21   3.2e+02      92     117 ..     127     152 ..      93     173 .. 0.58

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.1e-05
                                       ETTEECEEEEEETTSSEEEEEESTTSSHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              SMC_N 10 FksyagktvilpfsksftaivGpNGSGKsnlldAil 45
                                       F  + ++ ++ +++ +ft+++GpN +GKs +l  i 
  gene2610|gene2610|rna2610|rna2610  6 FHPLVNNCIKNDINVNFTILTGPNTAGKSTFLKTIA 41
                                       666667778899999****************99875 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.23
                                        HHCTT-STTCS-HHHHHHHHHHHHHHHHCC CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              SMC_N 127 lesagiskelLSgGektLvalaLlfAiqkv 156
                                         e++ i +++L +G   +  ++L +Ai+++
  gene2610|gene2610|rna2610|rna2610  96 TEKSLILIDELGRGTSYIDGISLSVAIKEY 125
                                        356789999999999999999999999886 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.21
                                        SSSSCEEEEEEEETTSEEEEEETTEE CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              SMC_N  92 iekeevsisrrvkrkgeseykingke 117
                                         +k+ + +  + +++++ +++++g++
  gene2610|gene2610|rna2610|rna2610 127 LKKKALAVFATHFTGKNEKMFLDGQD 152
                                        33444445555555555555555555 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.4     3e-06    0.0045       1      63 [.      22      63 ..      22     120 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 3e-06
                             AAA_21  1 lnvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfefeie 63
                                       +++l+GpN +GKS++L+++                      +++i +   +  p  +++fe++
  gene2610|gene2610|rna2610|rna2610 22 FTILTGPNTAGKSTFLKTI---------------------ALTVILGQMGSLVPGREVKFELR 63
                                       89*****************.....................44555555555555555555555 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.1   7.7e-06     0.011       4      93 ..      22     132 ..      19     151 .. 0.63

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 7.7e-06
                             AAA_14   4 ilvitGaRrvGKTtllkqlikell..............vkkesilyinldderdkkladpekllelileklke..e 63 
                                          ++tG+  +GK+t+lk+++ + +               + ++ +yi     +++ ++++ + ++ i +  ++   
  gene2610|gene2610|rna2610|rna2610  22 FTILTGPNTAGKSTFLKTIALTVIlgqmgslvpgrevkFELRDGIYIRSGASDKYGISTFMREMKDIARI-TNmcT 96 
                                        679****************988889999996444444433444444444444444444443233333332.22667 PP

                             AAA_14  64 kktylflDEiqev......pewekalkslvdegknl 93 
                                        +k+++++DE  +        +++ a+k+++ ++k l
  gene2610|gene2610|rna2610|rna2610  97 EKSLILIDELGRGtsyidgISLSVAIKEYLLKKKAL 132
                                        99*******877644444444555555555555555 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.1   1.8e-05     0.026      14      42 ..      23      52 ..      19      75 .. 0.79
   2 ?   -0.7   0.0       1.3   1.9e+03     113     134 ..      82     105 ..      59     108 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.8e-05
                                       EEEEESTTSSHHHHHHHHTTSS--.SEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx.xxxxx RF
                           ABC_tran 14 vaivGenGaGKStLlkllagllkp.teGei 42
                                       + ++G+n aGKSt+lk++a  +   ++G++
  gene2610|gene2610|rna2610|rna2610 23 TILTGPNTAGKSTFLKTIALTVILgQMGSL 52
                                       6799**************977665466655 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.3
                                        HHHHHHHHHH..HHHTSSEEEEES CS
                                        xxxxxxxxxx..xxxxxxxxxxxx RF
                           ABC_tran 113 qkqrvalara..llkkpkllllDE 134
                                        ++++  +ar+  ++++++l+l+DE
  gene2610|gene2610|rna2610|rna2610  82 MREMKDIARItnMCTEKSLILIDE 105
                                        555555666433789999999999 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.1   9.7e-05      0.14      48     168 ..      23     134 ..       9     144 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 9.7e-05
                              Rad17  48 LLisGPsGCgkstvvkvLskelgiklrewlnpvslkepdnqksdfkgltekesrflsqiesfkeleLkdakylklq 123
                                         +++GP   gkst +k ++          l p    e +++  d   + +      s     + + +++ k   + 
  gene2610|gene2610|rna2610|rna2610  23 TILTGPNTAGKSTFLKTIALTVILGQMGSLVPGR--EVKFELRDG--IYIRSG--ASDKYGISTF-MREMKD--IA 89 
                                        5789999999999999888666555555554443..666655443..333322..3333444445.455555..44 PP

                              Rad17 124 klGddlrtdkklilvedlP.nkfyrdsdalrevirkylrssealpl 168
                                         +  ++ t+k+lil+++l     y+d  +l   i++yl  ++al++
  gene2610|gene2610|rna2610|rna2610  90 -RITNMCTEKSLILIDELGrGTSYIDGISLSVAIKEYLLKKKALAV 134
                                        .566999***********9888999************999999764 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   2.4e-05     0.036      33      61 ..      20      48 ..       4      70 .. 0.79
   2 ?   -1.6   0.0       1.1   1.7e+03     126     153 ..      81     108 ..      61     112 .. 0.75
   3 ?   -2.4   0.0       1.9   2.9e+03      29      46 ..     125     142 ..     118     145 .. 0.55

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.4e-05
                             AAA_25 33 gelallaGapgtGKttlaldlalavatGk 61
                                         +++l+G+  +GK+t++  +al+v +G+
  gene2610|gene2610|rna2610|rna2610 20 VNFTILTGPNTAGKSTFLKTIALTVILGQ 48
                                       5799*********************9876 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.1
                             AAA_25 126 ltadvdaleaaieevegvrlvviDplsr 153
                                          ++++++++  + + +  l+ iD l r
  gene2610|gene2610|rna2610|rna2610  81 FMREMKDIARITNMCTEKSLILIDELGR 108
                                        4566777777777777789999998866 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 1.9
                             AAA_25  29 llpagelallaGapgtGK 46 
                                        +l +++  ++++ + tGK
  gene2610|gene2610|rna2610|rna2610 125 YLLKKKALAVFATHFTGK 142
                                        444555555555555555 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0     2e-05      0.03      26      46 ..      20      40 ..       8      45 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2e-05
                             AAA_27 26 adlhliyGpNEAGKstalrAi 46
                                        +++++ GpN AGKst l+ i
  gene2610|gene2610|rna2610|rna2610 20 VNFTILTGPNTAGKSTFLKTI 40
                                       5799**************987 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.7   2.9e-05     0.043      14      44 ..      14      41 ..      12      49 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.9e-05
                             AAA_15 14 lkdveidlseeltvliGkNnsGKSsileald 44
                                       +k+   d++ ++t+l G+N +GKS++l+ + 
  gene2610|gene2610|rna2610|rna2610 14 IKN---DINVNFTILTGPNTAGKSTFLKTIA 41
                                       555...77777****************9985 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   1.2    0.0021       3.1       4      22 ..      25      43 ..      22     138 .. 0.65
   2 ?   -3.9   0.0       7.4   1.1e+04      30      41 ..     161     172 ..     159     177 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0021
                                       EE--TTSSHHHHHHHHHHH CS
                           NTPase_1  4 iTGppGvGKtTlvkkvlel 22
                                       +TGp   GK+T++k ++ +
  gene2610|gene2610|rna2610|rna2610 25 LTGPNTAGKSTFLKTIALT 43
                                       6777777777777666543 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 7.4
                                        EEEEEEEEE--- CS
                           NTPase_1  30 vgGfyteevreg 41 
                                        v+G++t ++++g
  gene2610|gene2610|rna2610|rna2610 161 VDGVITYKIKKG 172
                                        789999988865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (201 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       507  (0.0282782); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.51u 0.32s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 1253.56
//
Query:       gene2611|gene2611|rna2611|rna2611  [L=395]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.6e-07   29.5   0.3    1.6e-06   28.5   0.3    1.6  1  MutS_III  MutS domain III
  ------ inclusion threshold ------
       0.13   12.3   1.0        1.4    8.9   0.0    2.4  2  DUF1137   Protein of unknown function (DUF1137)


Domain annotation for each model (and alignments):
>> MutS_III  MutS domain III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.5   0.3   1.8e-10   1.6e-06      28     124 ..     250     338 ..     226     392 .. 0.69

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 1.8e-10
                                        -SSHHHHHHHHHHHH--BS-HHHHHHHHHHHHHT..TT.HHHHHHHHTT.---HHHHHHHHHTT---HHHHHHHHH CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           MutS_III  28 TvTamGaRlLrewllqPltdleeInaRldaVeeleneelreelrellrr.lpDleRllsrislgkakardlkalle 102
                                         +T +G+R + +++ +P++d++eI +R+++  ++         r+++ r +pDl R+++++  +k +++++  l +
  gene2611|gene2611|rna2611|rna2611 250 FKTTQGKRYFYTNIRAPSRDVNEILRRQKILFFFR--------RNNIGReFPDLLRIVKKVEREKISVNEIIVLCQ 317
                                        59*****************************9982........333444499***********9999999888888 PP

                                        HHHHHHTTTTT---SSTHHHHH CS
                                        xxxxxxxxxxxxxxxxxxxxxx RF
                           MutS_III 103 alkaleelvallekeklaesee 124
                                         l++ + l +   ++  +++ e
  gene2611|gene2611|rna2611|rna2611 318 ILEKKDCLLNDVLNTA-KKCAE 338
                                        8886444333332222.22222 PP

>> DUF1137  Protein of unknown function (DUF1137)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.0   0.00016       1.4      21      50 ..      41      70 ..      33      86 .. 0.83
   2 ?    1.4   0.2     0.035   3.1e+02       4      49 ..     293     339 ..     290     377 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00016
                            DUF1137 21 pekqlfyctvdkscmelhlsdaslackell 50
                                       p  + +  + dk+c++l+l + ++ c ++ 
  gene2611|gene2611|rna2611|rna2611 41 PSEDSLSAKTDKTCIKLYLKNDTYRCTDVS 70
                                       6666678899****************9984 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.035
                            DUF1137   4 ppflkikklgvrkriispekqlfyctv..dkscmelhlsdaslackel 49 
                                        p +l+i k  v+++ is +  +  c++   k c+   + +++ +c e 
  gene2611|gene2611|rna2611|rna2611 293 PDLLRIVKK-VEREKISVNEIIVLCQIleKKDCLLNDVLNTAKKCAEC 339
                                        677888775.55666788888999998656899999999999999885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (395 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       736  (0.0410508); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 2560.87
//
Query:       gene2612|gene2612|rna2612|rna2612  [L=163]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1013  (0.0565006); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1148.18
//
Query:       gene2613|gene2613|rna2613|rna2613  [L=130]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       570  (0.0317921); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 907.52
//
Query:       gene2614|gene2614|rna2614|rna2614  [L=56]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (56 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       530  (0.029561); expected 358.6 (0.02)
Passed bias filter:                      253  (0.0141112); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.46
# Mc/sec: 368.77
//
Query:       gene2615|gene2615|rna2615|rna2615  [L=362]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.027   14.5  24.8      0.039   13.9  24.8    1.3  1  TFIIA        Transcription factor IIA, alpha/beta subunit
      0.036   13.4   9.0      0.052   12.9   9.0    1.4  1  BUD22        BUD22
      0.043   13.6  17.3      0.085   12.6  17.3    1.5  1  Cwf_Cwc_15   Cwf15/Cwc15 cell cycle control protein
      0.081   11.4  15.7      0.086   11.3  15.7    1.2  1  Mpp10        Mpp10 protein
       0.16   11.3  22.4       0.25   10.6  22.4    1.3  1  NOA36        NOA36 protein
        3.2    7.1  12.9        6.9    6.0  12.9    1.6  1  CobT         Cobalamin biosynthesis protein CobT
          5    6.6  22.6        9.5    5.7  22.5    1.6  1  PPP4R2       PPP4R2
        7.7    5.8  15.9        9.8    5.5  15.9    1.2  1  SDA1         SDA1


Domain annotation for each model (and alignments):
>> TFIIA  Transcription factor IIA, alpha/beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9  24.8   1.8e-05     0.039     102     372 ..      35     361 ..       2     362 .] 0.27

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.8e-05
                              TFIIA 102 qsltanssaataatfslpakleppvqipagvtlqtasgqlykvnv....qasgaqqiaaqplqqvvqq........ 165
                                        +s+t   s++++a++  p ++++p    a++  +    ++y++        +g +q    p++++  +        
  gene2615|gene2615|rna2615|rna2615  35 HSNTIPRSMNEEAAQYYPGGSQYPSDPQANQYYPGG--SQYSSDPlanqYYPGDSQYPPDPQANQYYSgdsqypsd 108
                                        222222222222222222222221111111111111..11111111111111111111111111111111100000 PP

                              TFIIA 166 ...........sqgsaaqssvaalqaqsqqaqalaepqqqlekq................qqqqqqqqqqqqqq.q 213
                                                   ++++  q+s   +  +                q                ++++ +q +   +q +
  gene2615|gene2615|rna2615|rna2615 109 qqanqyypgdsQYPPDPQASQYYPGDS----------------QkssdnrflsstehytwNTTMLSQVSCDVNQvT 168
                                        000000111112222222222211111................011222333333333332222222222111113 PP

                              TFIIA 214 vqqqqqe...........................esqqaqqasqe......qvag.sqvessqtdgaedaleeesp 255
                                        ++++ q                            ++q aqq+s +      qv + s+++ ++t    + l+e+ +
  gene2615|gene2615|rna2615|rna2615 169 SSTSDQTlsdnpnathssfvaplntdvyleraygPNQVAQQQSTTviipekQVCNvSSSNLPETMDVHSRLDEHMS 244
                                        3333322222222333333333344444444443111111111111122111111122222222222211111111 PP

                              TFIIA 256 v......legelsaeeeagaqkeelsreeidrireealkakelekeskkkkraeessla................. 308
                                        +      l+  + ++e+a ++ +  s+++                             +                 
  gene2615|gene2615|rna2615|rna2615 245 AecaatnLDTAITSSENALSSAKGFSSDDTP---------------------------Qvidqayeqrlikefedl 293
                                        1112223333333333333333333333332...........................023333333333332222 PP

                              TFIIA 309 .......dlseilqlDGagddsdeeeeeeesdedsdsessddedeq.veEDplNSdDDvddeddddlfdtdn 372
                                                +se + + G++ +s     ++++++d+  ++++d+d +  ++D+   dDD dd++++d +d+d+
  gene2615|gene2615|rna2615|rna2615 294 mnqidlnYESEAISYFGPNYKSYF---DQKENTDEAGDEDEDNDDEnDDDDDDGDDDDGDDDEEED-DDDDD 361
                                        233333355666666666666655...455555544444444333314444444456666666666.66665 PP

>> BUD22  BUD22
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   9.0   2.3e-05     0.052      78     205 ..     187     357 ..     132     362 .] 0.51

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.3e-05
                              BUD22  78 lpealks....ikdkkpksnpeek.neelektkalenv.tsrLlnsktvkevveeivesvkkllgiek.kkkkkee 146
                                        ++++l++    ++  +p+  ++++ ++++  +k++ nv  s+L  +  v+++++e +++ + + +++   + ++++
  gene2615|gene2615|rna2615|rna2615 187 FVAPLNTdvylERAYGPNQVAQQQsTTVIIPEKQVCNVsSSNLPETMDVHSRLDEHMSAECAATNLDTaITSSENA 262
                                        4444444565533334433333344445444444444414677788888888888888888888888742222222 PP

                              BUD22 147 ekkkkkkkkkkkkkkeeee.......................................eeesdkeeesedsedeek 183
                                         +++k+ +++++ +  +++                                       e+++++ +e+ed++d   
  gene2615|gene2615|rna2615|rna2615 263 LSSAKGFSSDDTPQVIDQAyeqrlikefedlmnqidlnyeseaisyfgpnyksyfdqkENTDEAGDEDEDNDD--- 335
                                        2222222222222222222555777777777666677777777777776665554332222222222222222... PP

                              BUD22 184 eeseddeeeeeededdedaeed 205
                                        e+++dd++ +++d dd+++e+d
  gene2615|gene2615|rna2615|rna2615 336 ENDDDDDDGDDDDGDDDEEEDD 357
                                        2222222222222222222221 PP

>> Cwf_Cwc_15  Cwf15/Cwc15 cell cycle control protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6  17.3   3.8e-05     0.085      24     141 ..     223     357 ..     206     362 .] 0.49

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3.8e-05
                                        X--STTS----------TTT--HHHHHHS-HHHHHHHHHHHHHHHHH-----------.................. CS
                         Cwf_Cwc_15  24 qyssrdlpahtkLKfRqegqgteeelekrdlraeLeeaeaeakakkrkkaeleaeeee.................. 81 
                                        ++ss +lp  + +  R +   + +e +  +l + +++ e++ ++ k  ++  +++  +                  
  gene2615|gene2615|rna2615|rna2615 223 NVSSSNLPETMDVHSRLDEHMS-AECAATNLDTAITSSENALSSAKGFSSDDTPQVIDqayeqrlikefedlmnqi 297
                                        5677888888888888776554.77888888888888888888887654444433332445444444443333222 PP

                                        --------------------------.......................--------------------------- CS
                         Cwf_Cwc_15  82 ekekkeeeeeeeeeeakrrkeellee.....................areidaddedseeeeeeeeeesdddsdsd 136
                                        +                +       e                     +++ d+d+++++e+++++++ +ddd d+d
  gene2615|gene2615|rna2615|rna2615 298 D---------------LNY------EseaisyfgpnyksyfdqkentDEAGDEDEDNDDENDDDDDDGDDDDGDDD 352
                                        1...............111......111222333333222222111112333333333333333333333333333 PP

                                        ----- CS
                         Cwf_Cwc_15 137 sdddd 141
                                        +++dd
  gene2615|gene2615|rna2615|rna2615 353 EEEDD 357
                                        33333 PP

>> Mpp10  Mpp10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3  15.7   3.9e-05     0.086     208     281 ..     284     359 ..     149     362 .] 0.64

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 3.9e-05
                              Mpp10 208 deeidyfedlss..ddedeeekksaedlkYeDFFdkpeekkkkkkkkkdeeeadeeeedeeeeeeeeeeeeeeeee 281
                                        +  i+ fedl +  d + e+e+ s    +Y+ +Fd++e++++  ++++d+++++++++d++++++ +++eee++++
  gene2615|gene2615|rna2615|rna2615 284 QRLIKEFEDLMNqiDLNYESEAISYFGPNYKSYFDQKENTDEAGDEDEDNDDENDDDDDDGDDDDGDDDEEEDDDD 359
                                        3334444444444433444555789999*********994333333333333233333332222222222222222 PP

>> NOA36  NOA36 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6  22.4   0.00011      0.25     255     305 ..     309     359 ..     238     361 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00011
                              NOA36 255 dydaylkalasgddeddegdedddddddeedddeeeddedeeeeeeeesee 305
                                           +y++ +  ++++d+ gded+d+dd+++ddd++ dd+d +++eee++++
  gene2615|gene2615|rna2615|rna2615 309 FGPNYKSYFDQKENTDEAGDEDEDNDDENDDDDDDGDDDDGDDDEEEDDDD 359
                                        333444445555666666777766666666666666666655555555444 PP

>> CobT  Cobalamin biosynthesis protein CobT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0  12.9    0.0031       6.9     205     246 ..     318     359 ..     277     362 .] 0.48

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0031
                               CobT 205 eesaeepeeedeeeeedeeeeeeeseeeeeegedddkeeqee 246
                                        +++++++e  de+e++d+e+++++++ ++++g+dd++e++++
  gene2615|gene2615|rna2615|rna2615 318 DQKENTDEAGDEDEDNDDENDDDDDDGDDDDGDDDEEEDDDD 359
                                        333333333333333333333333332222222222222222 PP

>> PPP4R2  PPP4R2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7  22.5    0.0042       9.5     165     286 ..     185     357 ..     127     361 .. 0.47

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0042
                             PPP4R2 165 e..............keedkansssqedsedvslvsipwvdekteselspfikeidsimsvnlgfedeeekeedd. 225
                                                          +++ + +q+++   +  ++  v +++  e   ++  +d+ ms++ + ++ +   ++  
  gene2615|gene2615|rna2615|rna2615 185 SsfvaplntdvylerAYGPNQVAQQQSTTVIIPEKQVCNVSSSNLPETMDVHSRLDEHMSAECAATNLDTAITSSe 260
                                        0344444444444443333344444444444444444444444444444444444444444444444333333222 PP

                             PPP4R2 226 ....neseesaseseeiteekdesvkvee................................kdddeeddeedtdyv 265
                                            + ++ s+ ++ + + ++ e++ ++e                                ++d+  d++ed+d +
  gene2615|gene2615|rna2615|rna2615 261 nalsSAKGFSSDDTPQVIDQAYEQRLIKEfedlmnqidlnyeseaisyfgpnyksyfdqkeNTDEAGDEDEDNDDE 336
                                        2332222333333333333333333333355555555666666669999999999999866444444444444444 PP

                             PPP4R2 266 eeeeddesedddeeeeeeeee 286
                                        ++++dd+  ddd +++eee++
  gene2615|gene2615|rna2615|rna2615 337 NDDDDDDGDDDDGDDDEEEDD 357
                                        433333333333333333333 PP

>> SDA1  SDA1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5  15.9    0.0044       9.8      94     144 ..     321     358 ..     238     362 .] 0.55

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0044
                               SDA1  94 dsddeddeedwevesdddseedseggwidvesdeeeieesdesedeeeeee 144
                                        ++ de  +ed++ ++++d+ +d++g+            ++d ++deee+++
  gene2615|gene2615|rna2615|rna2615 321 ENTDEAGDEDEDNDDENDD-DDDDGD------------DDDGDDDEEEDDD 358
                                        1111111111111111111.111111............1111111111111 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (362 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       943  (0.0525964); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); expected 17.9 (0.001)
Passed Fwd filter:                        24  (0.00133861); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.59u 0.36s 00:00:00.95 Elapsed: 00:00:00.46
# Mc/sec: 2347.40
//
Query:       gene2616|gene2616|rna2616|rna2616  [L=64]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (64 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       536  (0.0298957); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.42
# Mc/sec: 459.25
//
Query:       gene2617|gene2617|rna2617|rna2617  [L=347]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      8e-14   51.2   0.1      8e-14   51.2   0.1    2.0  2  BHD_1         Rad4 beta-hairpin domain 1
    8.2e-07   29.3   0.0    1.6e-06   28.4   0.0    1.4  1  BHD_3         Rad4 beta-hairpin domain 3
  ------ inclusion threshold ------
       0.16   12.3   0.5       0.57   10.5   0.5    1.9  1  Mastoparan_2  Mastoparan peptide


Domain annotation for each model (and alignments):
>> BHD_1  Rad4 beta-hairpin domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.2   0.1   1.3e-17     8e-14       4      51 .]     192     238 ..     190     238 .. 0.96
   2 ?   -2.9   0.3       1.1   6.5e+03      36      51 .]     258     273 ..     249     273 .. 0.57

  Alignments for each domain:
  == domain 1  score: 51.2 bits;  conditional E-value: 1.3e-17
                              BHD_1   4 mPenlqdfKnhplYvLerhLkrnEvlhpdakpvgvfkkkepVYrRsdV 51 
                                        +P++l+ +K+hplYv+e+  k+n+++ p++  +g+fk +ep++ R+++
  gene2617|gene2617|rna2617|rna2617 192 IPRSLKNMKYHPLYVIESIIKKNQIIFPKRPILGYFK-GEPIFCRKNI 238
                                        8***********************************7.*******986 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.1
                              BHD_1  36 vgvfkkkepVYrRsdV 51 
                                        + ++  + + Yr+ dV
  gene2617|gene2617|rna2617|rna2617 258 IYKLVDGVKLYRKYDV 273
                                        3333336677777776 PP

>> BHD_3  Rad4 beta-hairpin domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4   0.0   2.7e-10   1.6e-06      12      70 ..     289     341 ..     287     345 .. 0.93

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 2.7e-10
                                        SSGGGS-TTEEEEE-TTHHHHHHHCT---EEEEEEEEE-SS-EE..EEEEEEEEEGGGH CS
                              BHD_3  12 fkpsmlPegavhislkgaakaakklgidyapAvvGFefkgrrgkgiPvidGivVaeede 70 
                                        ++++ +P+++v+ +++    +a++l+i y +++vGF +k      +P+++Gi   +ed+
  gene2617|gene2617|rna2617|rna2617 289 YHDNHVPKNCVYSKNELSVLVARLLDIRYSECIVGFRYK------MPIFQGIFLLKEDA 341
                                        7899*********99999999*****************9......6******9999986 PP

>> Mastoparan_2  Mastoparan peptide
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.5   9.5e-05      0.57       3      11 ..     247     255 ..     246     257 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 9.5e-05
                       Mastoparan_2   3 WLKLGKkVi 11 
                                        W KLGKkV+
  gene2617|gene2617|rna2617|rna2617 247 WFKLGKKVV 255
                                        ********6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (347 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       420  (0.0234257); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 2253.99
//
Query:       gene2618|gene2618|rna2618|rna2618  [L=85]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-25   88.5   0.9    2.6e-25   88.3   0.9    1.0  1  SPC12     Microsomal signal peptidase 12 kDa subunit (SPC12)


Domain annotation for each model (and alignments):
>> SPC12  Microsomal signal peptidase 12 kDa subunit (SPC12)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.3   0.9   1.4e-29   2.6e-25       1      70 [.      13      82 ..      13      83 .. 0.98

  Alignments for each domain:
  == domain 1  score: 88.3 bits;  conditional E-value: 1.4e-29
                              SPC12  1 iDFeGQklaekllqvilvlsaviafivGyitqdlkltlyillagvvltllvvvPpWpfYnrnplkWlkpk 70
                                       iD+ GQ la+k ++ il+l++ +a+ivGy+++dl++t+++++++v+++++vvvPpWpfY+rnp k++k k
  gene2618|gene2618|rna2618|rna2618 13 IDYYGQDLAKKAAYNILLLGYSLAWIVGYFMSDLRYTFITGIVTVLIAFIVVVPPWPFYRRNPFKFKKLK 82
                                       9*****************************************************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (85 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       755  (0.0421105); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 553.95
//
Query:       gene2619|gene2619|rna2619|rna2619  [L=154]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.056   13.6   0.8      0.091   13.0   0.8    1.3  1  Tau95_N   Tau95 Triple barrel domain


Domain annotation for each model (and alignments):
>> Tau95_N  Tau95 Triple barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.8   5.1e-06     0.091      28      98 ..      83     146 ..      56     153 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 5.1e-06
                                        HHHHHHH-G--EE-S-TT-TT---EE-EEE----EEEEE.......ETTTT.................... CS
                            Tau95_N  28 alkasekkkslelrlrpedpfshpilgeraptnnlllkvtvpkrtgkkrkrgssesekekdssakelrsle 98 
                                        al++s+k+ + e+r    +p+++ i++ +a++ ++l+ +++++  ++  k+       ++ +++++lr ++
  gene2619|gene2619|rna2619|rna2619  83 ALHRSRKRLGKEMRYADMNPIERKIVSLTAKKWRILVSIKKRREAERATKD-------RRGKPRHRLRTHK 146
                                        3444445447788888889********************776544433333.......3444444444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       739  (0.0412181); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 1171.57
//
Query:       gene262|gene262|rna262|rna262  [L=1134]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.7e-16   59.4   0.0    1.1e-15   57.9   0.0    1.8  1  DEAD        DEAD/DEAH box helicase
    4.8e-10   39.7   0.8      3e-09   37.1   0.0    2.5  3  ResIII      Type III restriction enzyme, res subunit
    1.8e-07   31.5   0.3    7.1e-07   29.6   0.0    2.2  2  Helicase_C  Helicase conserved C-terminal domain
  ------ inclusion threshold ------
      0.017   14.9   0.0      0.035   13.8   0.0    1.5  1  AAA_30      AAA domain
      0.029   14.6   0.0      0.079   13.2   0.0    1.7  1  AAA_22      AAA domain
      0.038   13.9   0.0       0.11   12.4   0.0    1.8  1  RMMBL       Zn-dependent metallo-hydrolase RNA specificity do
      0.087   13.3   2.1       0.19   12.2   2.1    1.5  1  DUF3106     Protein of unknown function (DUF3106)


Domain annotation for each model (and alignments):
>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.9   0.0   4.2e-19   1.1e-15       3     170 ..     205     355 ..     203     359 .. 0.83

  Alignments for each domain:
  == domain 1  score: 57.9 bits;  conditional E-value: 4.2e-19
                                    HHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD   3 iQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvllii 82 
                                     Q+e ++++ +g +++++a+T sGKT + + ++ +++      +g++ ++ +Pt++L++q++ ++  ++     r++  +
  gene262|gene262|rna262|rna262 205 WQKELLDAVDNGTSCVISAPTSSGKTFICFYAIEKAI-----AEGTRLIFCVPTKALVNQVAADILIRFGD---RCK--Y 274
                                    59999999********************999999888.....5689****************998665553...443..7 PP

                                    TTSSHHHHHHHHHTTCSEEEEEHHHHHHHH......HCTSSHCTTE.EEEEEETHHHHHHTTTHHHHHHHHHHSHHHCTT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD  83 ggvaardqlskldngvdivvgtpgrlddll......stgklnlsqv.rflVlDEadrlldqgfsdfinrilnqlpqitcd 155
                                    g v  + q++   +++d++v+ p +l  ll        +k + ++   ++++DE++++ +++++  i+r ++++     +
  gene262|gene262|rna262|rna262 275 GIVMPDYQVN---ADCDVLVTVPMMLEALLenapctA-HK-RAKHAhATVIIDEIHKINSDEMGAYIERSVHKV-----K 344
                                    8777765554...55**************98777531.22.34444278*************************.....4 PP

                                    STTTSEEEEEESSBS CS
                                    xxxxxxxxxxxxxxx RF
                           DEAD 156 gklqrqvivlSATlp 170
                                    g+    ++vlSATl 
  gene262|gene262|rna262|rna262 345 GP----LVVLSATLG 355
                                    66....*******97 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.3      0.45   1.2e+03     100     126 ..      39      62 ..       3      95 .. 0.59
   2 !   37.1   0.0   1.2e-12     3e-09       9     168 ..     207     353 ..     186     356 .. 0.79
   3 ?   -3.2   0.0       2.9   7.5e+03     141     161 ..     729     749 ..     729     753 .. 0.76

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.45
                                    ....-SEEEEEHHHHHHTH........ CS
                         ResIII 100 dstnkkilvttiqsldadseeeeeese 126
                                    ++++ +i+  ++++l+++s   ee++ 
  gene262|gene262|rna262|rna262  39 SAKQQQIVKQNEERLKKIS---EEKDR 62 
                                    3344444444444444444...22222 PP

  == domain 2  score: 37.1 bits;  conditional E-value: 1.2e-12
                                    HHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG....GEEE CS
                         ResIII   9 eeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkflseaykeigkk 88 
                                    +e ++++      ++ +  +i ++T +GKT++++ +ie+   +g   + +f vp+k+l++q   ++   + +    + ++
  gene262|gene262|rna262|rna262 207 KELLDAV------DNGTSCVISAPTSSGKTFICFYAIEKAIAEGT--RLIFCVPTKALVNQVAADILIRFGDRC--KYGI 276
                                    3333333......4556788**********************988..9***************99987777765..5777 PP

                                    ESSS-B--.......-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.TTTHHHHHT---..SEEEEEE CS
                         ResIII  89 vsgdkkkakekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakkswreilekfke..avllglT 166
                                    v  d + +      ++++lvt   +l a +e++  + ++  ++++  +iiDE H++++++    i +++ +    l+ l+
  gene262|gene262|rna262|rna262 277 VMPDYQVN-----ADCDVLVTVPMMLEALLENAPCTAHKRAKHAHATVIIDEIHKINSDEMGAYIERSVHKvkGPLVVLS 351
                                    77777777.....8****************9999999999******************6533335333332113345556 PP

                                    SS CS
                         ResIII 167 AT 168
                                    AT
  gene262|gene262|rna262|rna262 352 AT 353
                                    66 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 2.9
                                    GGGTTS.TTTHHHHHT---SE CS
                         ResIII 141 aHrlgakkswreilekfkeav 161
                                    +H+ g +k++rei+e + +++
  gene262|gene262|rna262|rna262 729 VHHNGMNKKYREIVEILFRNK 749
                                    5999999*****988765555 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.1       3.7   9.6e+03      14      53 ..     572     613 ..     559     624 .. 0.63
   2 !   29.6   0.0   2.8e-10   7.1e-07      40     111 .]     724     796 ..     696     796 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 3.7
                                    TTTSEEEEEESSHH...HHHHHHHHHHHTTSTEEEESTTSTHH CS
                     Helicase_C  14 eeggkilifvntid...rlekvklllekkgikvavlhgelpqn 53 
                                    ++ + + if+  ++   ++  v+l+ +++ +++   h++ +q 
  gene262|gene262|rna262|rna262 572 VRAYCTSIFTFVKRhglMARAVELM-NNETVRAFSTHSDVSQL 613
                                    4555555666665555433325666.45568888888887774 PP

  == domain 2  score: 29.6 bits;  conditional E-value: 2.8e-10
                                    TSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSSTSTTESEEEESSSS.SSHHHHHHHHTTSSSTT CS
                     Helicase_C  40 gikvavlhgelpqnereeileqfnkgesdvLiatdvaerGidipkvnlVinfdlp.rnvtsyiqriGRtgRag 111
                                     + + v+h  ++++ re +   f++++  v+ +t  ++ Gi++p+ ++V+  d +  +  s++q++GR+gR g
  gene262|gene262|rna262|rna262 724 YYGIGVHHNGMNKKYREIVEILFRNKNLGVVFSTHTLSLGINMPCKTVVFAGDSDaLDRISVVQMSGRAGRRG 796
                                    5678889999***************9999*********************999997789************75 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   1.4e-05     0.035       6     111 ..     206     338 ..     201     352 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.4e-05
                         AAA_30   6 QaaavealltsgdrvavltGpAGtGKttalkalreaweaaggrviglAptgkaAkvLa...................... 63 
                                    Q+++++a+ +++   +v+ +p  +GKt++   + e + a+g r+i + pt++  +++a                      
  gene262|gene262|rna262|rna262 206 QKELLDAVDNGT--SCVISAPTSSGKTFICFYAIEKAIAEGTRLIFCVPTKALVNQVAadilirfgdrckygivmpdyqv 283
                                    888887665554..69**************999999999*****************994444444443333333322222 PP

                         AAA_30  64 .eelgieastiakllkrlk....................grarlepg.tllivDEagmvdtkqlaallka 111
                                     +    ++          +                    + +r +++   +i+DE+  ++++++ a +++
  gene262|gene262|rna262|rna262 284 nA----DC----------DvlvtvpmmleallenapctaH-KRAKHAhATVIIDEIHKINSDEMGAYIER 338
                                    11....22..........022222233334557778*964.45555559*************99987765 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   3.1e-05     0.079       4     114 ..     215     339 ..     212     354 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.1e-05
                         AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelka............. 70 
                                    + +++v+ +++ +GKT+ +    e++ +e      + +++f+ +++     +++ ++l  +g+++k+             
  gene262|gene262|rna262|rna262 215 NGTSCVISAPTSSGKTFICFYAIEKAIAE------GTRLIFCVPTKAL-VNQVAADILIRFGDRCKYgivmpdyqvnadc 287
                                    57899********************8543......7777777666666.***************************9999 PP

                         AAA_22  71 .....erlsseellealeqalrarav..ielliiDEaqhlrseealeeL.rs 114
                                          +  +e+lle     +++ra+  ++ +iiDE+++++s+e+  ++ rs
  gene262|gene262|rna262|rna262 288 dvlvtVPMMLEALLENAPCTAHKRAKhaHATVIIDEIHKINSDEMGAYIeRS 339
                                    87777333333333333333333333667789********888887777444 PP

>> RMMBL  Zn-dependent metallo-hydrolase RNA specificity domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   4.4e-05      0.11       7      33 ..     597     624 ..     595     631 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4.4e-05
                          RMMBL   7 rieeid.fSgHadknellelirklkprn 33 
                                      e++  fS H+d ++l+ li++lk+  
  gene262|gene262|rna262|rna262 597 NNETVRaFSTHSDVSQLNTLISTLKKNE 624
                                    5689999*****************9865 PP

>> DUF3106  Protein of unknown function (DUF3106)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   2.1   7.5e-05      0.19      32      83 ..      30      82 ..       2      99 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 7.5e-05
                        DUF3106 32 eiaerykkltpeeqkrlqermeewakLspe.qreqarenyqklkqLppeeree 83
                                   + +++ kkl++++q+ ++++ e+ +k+s+e +r+ +r+ ++k+k+++  +++ 
  gene262|gene262|rna262|rna262 30 KSSSTKKKLSAKQQQIVKQNEERLKKISEEkDRAFLRNFFAKFKSMTLMQKKM 82
                                   55555567777777777777777777776524666777777777777777643 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1043  (0.0581739); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.80u 0.28s 00:00:01.08 Elapsed: 00:00:00.46
# Mc/sec: 7377.86
//
Query:       gene2620|gene2620|rna2620|rna2620  [L=214]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.8e-19   69.8   7.4    3.6e-19   69.4   7.4    1.3  1  MAT1            CDK-activating kinase assembly factor MAT1
    4.6e-17   61.6   8.1    4.6e-17   61.6   8.1    1.7  1  zf-C3HC4_5      Zinc finger, C3HC4 type (RING finger)
    4.5e-05   23.3   8.8    9.9e-05   22.2   8.8    1.6  1  zf-RING_5       zinc-RING finger domain
    6.9e-05   22.6  10.7    0.00029   20.6  10.9    1.9  1  zf-C3HC4        Zinc finger, C3HC4 type (RING finger)
    0.00011   22.0   7.6    0.00023   21.0   7.6    1.6  1  zf-C3HC4_3      Zinc finger, C3HC4 type (RING finger)
    0.00016   21.4   7.2      0.001   18.8   3.0    2.3  2  zf-RING_4       RING/Ubox like zinc-binding domain
    0.00083   19.3   7.0     0.0015   18.5   7.0    1.4  1  DZR             Double zinc ribbon
     0.0014   18.9   7.9     0.0032   17.8   7.9    1.6  1  zf-RING_2       Ring finger domain
     0.0025   17.6  11.1      0.016   15.0  11.1    2.2  2  zf-C3HC4_2      Zinc finger, C3HC4 type (RING finger)
  ------ inclusion threshold ------
      0.013   15.8   0.6      0.019   15.3   0.6    1.2  1  Gp-FAR-1        Nematode fatty acid retinoid binding protein 
      0.018   14.9   8.9      0.056   13.3   8.9    1.8  2  Prok-RING_4     Prokaryotic RING finger family 4
      0.026   15.0   0.6      0.045   14.2   0.6    1.4  1  RED_C           RED-like protein C-terminal region
      0.028   13.8   6.0       0.96    9.0   2.0    2.5  2  zf-ribbon_3     zinc-ribbon domain
      0.031   13.8   4.7       0.78    9.3   0.9    2.7  2  TF_Zn_Ribbon    TFIIB zinc-binding
      0.032   14.2   6.4      0.065   13.3   6.4    1.5  1  zf-RING_UBOX    RING-type zinc-finger
      0.048   14.1   2.0       0.27   11.7   0.2    2.6  2  zf-IS66         zinc-finger binding domain of transposase IS6
      0.093   12.9   7.9        4.4    7.5   7.9    2.3  1  zf-UDP          Zinc-binding RING-finger
       0.12   11.4   0.9       0.16   11.1   0.9    1.1  1  TMEM192         TMEM192 family
        0.2   11.7   2.2        1.5    8.9   0.1    2.5  2  DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domai
       0.38   11.1   1.4        6.6    7.1   2.8    2.0  2  DUF349          Domain of Unknown Function (DUF349)
       0.39   10.6   6.5        2.1    8.3   6.3    2.1  2  zf-RING_6       zf-RING of BARD1-type protein
       0.51   10.5   3.6        1.6    9.0   1.9    2.2  2  Ribosomal_L37e  Ribosomal protein L37e
        1.2    8.9   8.7         13    5.7   3.1    2.9  2  zinc_ribbon_2   zinc-ribbon domain
        1.6    8.9  12.7        1.1    9.4   2.9    3.4  3  Zn-ribbon_8     Zinc ribbon domain
        1.9    8.7   8.1        3.1    8.0   1.8    2.5  2  NOB1_Zn_bind    Nin one binding (NOB1) Zn-ribbon like
        2.6    8.0   8.7         13    5.7   4.2    3.0  3  DUF3797         Domain of unknown function (DUF3797)
        3.7    7.8  11.8         14    6.0  11.7    2.0  1  zf-C3HC4_4      zinc finger of C3HC4-type, RING
        6.5    7.2   7.9         52    4.3   0.1    3.2  3  GFA             Glutathione-dependent formaldehyde-activating


Domain annotation for each model (and alignments):
>> MAT1  CDK-activating kinase assembly factor MAT1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.4   7.4   5.7e-22   3.6e-19       1      90 [.      56     148 ..      56     183 .. 0.87

  Alignments for each domain:
  == domain 1  score: 69.4 bits;  conditional E-value: 5.7e-22
                               MAT1   1 LRknkFrvQiFeDvevekEvdiRkrvlkifNkkeeDFesLkeYndYLeeveeivfnLtngidveeTekkleqYeke 76 
                                        LR+ +F  Q+FeD++ve+E+ iRk + ++fNk+e DF++ +eY+dYLe+ e+++  L++  +  +  k++e+ + +
  gene2620|gene2620|rna2620|rna2620  56 LRRINFISQTFEDIDVERECRIRKMLNRVFNKEEIDFDNEEEYDDYLEKYEDLILELMQLKNDMQISKRIESLKDD 131
                                        9*****************************************************9877655555555555555543 PP

                               MAT1  77 ...nkelIlknkeklkq 90 
                                           +k++I +++++ ++
  gene2620|gene2620|rna2620|rna2620 132 tgvHKNEIVAKRRRIQE 148
                                        33399999998888765 PP

>> zf-C3HC4_5  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.6   8.1   7.1e-20   4.6e-17       1      49 [.       6      53 ..       6      54 .. 0.95

  Alignments for each domain:
  == domain 1  score: 61.6 bits;  conditional E-value: 7.1e-20
                         zf-C3HC4_5  1 deiCPvCkssrYlnpdleflinpeCYhkmCesCvdRlFsdGPnqCPvag 49
                                       d+ CP Cks+ Ylnp++++ + p CYhkmCe+Cv R+Fs+G   CP  g
  gene2620|gene2620|rna2620|rna2620  6 DQFCPQCKSDSYLNPNIKIYVSP-CYHKMCENCVSRIFSQGESACPECG 53
                                       789****************9988.**********************865 PP

>> zf-RING_5  zinc-RING finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   8.8   1.5e-07   9.9e-05       2      43 ..       9      53 ..       8      54 .. 0.94

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 1.5e-07
                          zf-RING_5  2 CnkCfekl..skeekfyltsCgHifCekClkkll.ekeavCpiCr 43
                                       C++C +    +++ k+y+ +C+H +Ce+C+++ + + e  Cp C+
  gene2620|gene2620|rna2620|rna2620  9 CPQCKSDSylNPNIKIYVSPCYHKMCENCVSRIFsQGESACPECG 53
                                       999*998889************************99********7 PP

>> zf-C3HC4  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6  10.9   4.5e-07   0.00029       1      41 []       9      52 ..       9      52 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 4.5e-07
                                       -TTT-S.--SS-E....E-TTS--B-CHHHHHHHHCTSSB--TTT CS
                           zf-C3HC4  1 CpiCle.eakepn...elleCkHsfCskCirkilksrkkvkCPlC 41
                                       Cp C++  + +pn    +++C H++C++C+++i + +++  CP+C
  gene2620|gene2620|rna2620|rna2620  9 CPQCKSdSYLNPNikiYVSPCYHKMCENCVSRIFS-QGESACPEC 52
                                       7777652344444566899****************.99999**** PP

>> zf-C3HC4_3  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   7.6   3.6e-07   0.00023       2      46 ..       6      55 ..       5      59 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 3.6e-07
                                       GSB-TTTSSS.....BS-EEETTEEEEEE-HHHHHHHHH.TT-B-TTT--B CS
                         zf-C3HC4_3  2 deeCviCler.....prnvvllpCgHlvlCeeCaekllk.rkkkCpiCrrp 46
                                       d+ C+ C++      + ++ + pC H  +Ce+C++++ +  +  Cp C + 
  gene2620|gene2620|rna2620|rna2620  6 DQFCPQCKSDsylnpNIKIYVSPCYHK-MCENCVSRIFSqGESACPECGTL 55
                                       578999*995445447778999*****.**********9999******875 PP

>> zf-RING_4  RING/Ubox like zinc-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.1      0.06        38      37      45 ..       6      14 ..       2      17 .. 0.82
   2 !   18.8   3.0   1.6e-06     0.001      16      43 ..      25      52 ..      20      55 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.06
                          zf-RING_4 37 egrCPaCre 45
                                       ++ CP+C++
  gene2620|gene2620|rna2620|rna2620  6 DQFCPQCKS 14
                                       678****97 PP

  == domain 2  score: 18.8 bits;  conditional E-value: 1.6e-06
                          zf-RING_4 16 kpCeCgyqiClfCyhrileeeegrCPaC 43
                                       +  +C +++C  C +ri ++ e  CP+C
  gene2620|gene2620|rna2620|rna2620 25 YVSPCYHKMCENCVSRIFSQGESACPEC 52
                                       5668************************ PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   7.0   2.4e-06    0.0015       9      49 .]       3      53 ..       2      53 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 2.4e-06
                                DZR  9 ppdarfCseCgtk..lkavaa.......edrCpsCgek.vdpearfCpeCG 49
                                       p+ ++fC++C+++  l++  +       +++C +C +   +++++ CpeCG
  gene2620|gene2620|rna2620|rna2620  3 PSMDQFCPQCKSDsyLNPNIKiyvspcyHKMCENCVSRiFSQGESACPECG 53
                                       56789*******9666644449999**********99989**********9 PP

>> zf-RING_2  Ring finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   7.9     5e-06    0.0032       3      43 ..       9      52 ..       7      53 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 5e-06
                          zf-RING_2  3 CpIC.leelssads.vlllpCgHvfhreClerwlrssst.CPlC 43
                                       Cp C  +++ +++  + + pC H ++++C++r++ + ++ CP C
  gene2620|gene2620|rna2620|rna2620  9 CPQCkSDSYLNPNIkIYVSPCYHKMCENCVSRIFSQGESaCPEC 52
                                       9999556664444425577**************9998889**99 PP

>> zf-C3HC4_2  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.6       1.2   7.7e+02      22      40 .]       8      12 ..       4      22 .. 0.74
   2 !   15.0  11.1   2.5e-05     0.016      13      40 .]      24      52 ..       8      52 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 1.2
                         zf-C3HC4_2 22 fCqkCilrsLeekneCPlC 40
                                       f              CP+C
  gene2620|gene2620|rna2620|rna2620  8 F--------------CPQC 12
                                       4..............6666 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 2.5e-05
                         zf-C3HC4_2 13 svvtpCgHvfCqkCilrsLeekn.eCPlC 40
                                       ++v pC H+ C++C+ r  ++++  CP C
  gene2620|gene2620|rna2620|rna2620 24 IYVSPCYHKMCENCVSRIFSQGEsACPEC 52
                                       4677***************99999****9 PP

>> Gp-FAR-1  Nematode fatty acid retinoid binding protein (Gp-FAR-1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.6     3e-05     0.019      18      93 ..      69     150 ..      61     160 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 3e-05
                           Gp-FAR-1  18 ltdeekaqlkevvkn.ykg....yknedellaalKkkspaLyekaeklqaklk..ekvdkLspeakeFvkkliakg 86 
                                        +  e    ++++ +  +++    + ne+e+   l +k++ L  ++++l++ ++  +++++L++++    ++++ak 
  gene2620|gene2620|rna2620|rna2620  69 IDVERECRIRKMLNRvFNKeeidFDNEEEYDDYL-EKYEDLILELMQLKNDMQisKRIESLKDDTGVHKNEIVAKR 143
                                        55555555555555433334456*******9999.678888877777776544339******************** PP

                           Gp-FAR-1  87 rkleaqv 93 
                                        r +++ +
  gene2620|gene2620|rna2620|rna2620 144 RRIQEGM 150
                                        **99765 PP

>> Prok-RING_4  Prokaryotic RING finger family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.3       2.3   1.5e+03      33      38 ..       9      14 ..       5      20 .. 0.73
   2 ?   13.3   8.9   8.7e-05     0.056       4      39 ..      12      55 ..       9      62 .. 0.76

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 2.3
                        Prok-RING_4 33 CPlCqr 38
                                       CP C++
  gene2620|gene2620|rna2620|rna2620  9 CPQCKS 14
                                       777765 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 8.7e-05
                        Prok-RING_4  4 Cgeq.....ekkailepCgHlvCkeCfdskdls...sCPlCqrr 39
                                       C++      + k+ ++pC H +C++C +   ++   +CP C + 
  gene2620|gene2620|rna2620|rna2620 12 CKSDsylnpNIKIYVSPCYHKMCENCVSRIFSQgesACPECGTL 55
                                       55555555588999**************99555556*****875 PP

>> RED_C  RED-like protein C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.6     7e-05     0.045      32      68 ..      83     119 ..      59     155 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 7e-05
                              RED_C  32 kkgpvgrwdfdteeeyseymekkealPkaafqyGvkm 68 
                                        +    + +dfd+eeey++y ek e l     q    m
  gene2620|gene2620|rna2620|rna2620  83 RVFNKEEIDFDNEEEYDDYLEKYEDLILELMQLKNDM 119
                                        44456789***************99876666655444 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.1     0.012       7.8       3      10 ..       7      14 ..       5      17 .. 0.71
   2 ?    9.0   2.0    0.0015      0.96       5      26 .]      34      56 ..      31      56 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.012
                        zf-ribbon_3  3 vrCPnCGa 10
                                       ++CP+C++
  gene2620|gene2620|rna2620|rna2620  7 QFCPQCKS 14
                                       46888875 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0015
                        zf-ribbon_3  5 CPnCGa.plssddnvCpyCGtkl 26
                                       C nC + + s + ++Cp CGt l
  gene2620|gene2620|rna2620|rna2620 34 CENCVSrIFSQGESACPECGTLL 56
                                       777777778889999****9865 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.1     0.025        16       2      12 ..       8      18 ..       7      25 .. 0.81
   2 ?    9.3   0.9    0.0012      0.78       2      29 ..      33      56 ..      32      61 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.025
                                       EETTTTCEECH CS
                       TF_Zn_Ribbon  2 kCPnCgstnlv 12
                                        CP C+s++++
  gene2620|gene2620|rna2620|rna2620  8 FCPQCKSDSYL 18
                                       5******9854 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0012
                                       EETTTTCEECHEETSTTCEEESSSSBEE CS
                       TF_Zn_Ribbon  2 kCPnCgstnlveDpergelvCtdCGlVl 29
                                       +C nC s+     +++ge  C++CG++l
  gene2620|gene2620|rna2620|rna2620 33 MCENCVSRI----FSQGESACPECGTLL 56
                                       677888763....789*********986 PP

>> zf-RING_UBOX  RING-type zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   6.4    0.0001     0.065       1      39 []       9      50 ..       9      50 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.0001
                       zf-RING_UBOX  1 CpICl.elftdP..lv.l.pCGHtFCreClwelskslegafkCP 39
                                       Cp C+ +++ +P  ++ + pC H  C++C+  ++  ++g+  CP
  gene2620|gene2620|rna2620|rna2620  9 CPQCKsDSYLNPniKIyVsPCYHKMCENCV--SRIFSQGESACP 50
                                       *****88999***844677***********..677777777777 PP

>> zf-IS66  zinc-finger binding domain of transposase IS66
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.1      0.82   5.3e+02       2       9 ..       7      14 ..       6      21 .. 0.76
   2 ?   11.7   0.2   0.00043      0.27       1      16 [.      46      61 ..      46      76 .. 0.78

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.82
                            zf-IS66  2 rtCpcCGg 9 
                                       + Cp+C +
  gene2620|gene2620|rna2620|rna2620  7 QFCPQCKS 14
                                       67999976 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00043
                            zf-IS66  1 prtCpcCGgllkpige 16
                                       +++Cp+CG+ll++i  
  gene2620|gene2620|rna2620|rna2620 46 ESACPECGTLLRRINF 61
                                       689******9999965 PP

>> zf-UDP  Zinc-binding RING-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   7.9    0.0068       4.4       9      63 ..       7      59 ..       6      71 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0068
                             zf-UDP  9 qiCqiCgddvgltedgelFvacnecafpvcrpcyeyerkdgnqsCPqCktrykrl 63
                                       q C  C  d  l+ + +  + ++ c   +c +c +   ++g+ +CP+C t  +r 
  gene2620|gene2620|rna2620|rna2620  7 QFCPQCKSDSYLNPNIK--IYVSPCYHKMCENCVSRIFSQGESACPECGTLLRRI 59
                                       56666666666655555..456789*************************99996 PP

>> TMEM192  TMEM192 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.9   0.00025      0.16     179     234 ..      69     127 ..      55     128 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00025
                            TMEM192 179 pDvleeekllslsqs.ststevgfrdgssleellekQadlIryLkqhna..kLsrrila 234
                                         Dv +e +++++ +    ++e+ f ++++ ++ lek  dlI  L+q ++  + s+ri +
  gene2620|gene2620|rna2620|rna2620  69 IDVERECRIRKMLNRvFNKEEIDFDNEEEYDDYLEKYEDLILELMQLKNdmQISKRIES 127
                                        79999999999999888899*********************999985441267777765 PP

>> DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.3      0.35   2.2e+02       2       7 ..       9      14 ..       8      16 .. 0.88
   2 ?    8.9   0.1    0.0023       1.5       2      11 ..      49      58 ..      48      75 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.35
                     DNA_ligase_ZBD  2 CPvCGs 7 
                                       CP C s
  gene2620|gene2620|rna2620|rna2620  9 CPQCKS 14
                                       ****98 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0023
                     DNA_ligase_ZBD  2 CPvCGsavvR 11
                                       CP+CG+ + R
  gene2620|gene2620|rna2620|rna2620 49 CPECGTLLRR 58
                                       ******9988 PP

>> DUF349  Domain of Unknown Function (DUF349)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   2.8      0.01       6.6       7      60 ..      78     129 ..      75     148 .. 0.76
   2 ?    0.3   0.0       1.4   8.7e+02      34      63 ..     135     161 ..     131     172 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.01
                             DUF349   7 raacdafferrkahfeeqdaereenlekKealieeaealaksttdwksatkrlk 60 
                                        r+  +++f++ +  f++ ++e+++ lek e+li e+ +l++++ ++++ ++ lk
  gene2620|gene2620|rna2620|rna2620  78 RKMLNRVFNKEEIDFDN-EEEYDDYLEKYEDLILELMQLKNDM-QISKRIESLK 129
                                        55666777766666654.7799*****************9987.4444444443 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 1.4
                             DUF349  34 kKealieeaealaksttdwksatkrlkelq 63 
                                         K++++++ + +++ +   ++++  + +l+
  gene2620|gene2620|rna2620|rna2620 135 HKNEIVAKRRRIQEGM---DKSVGVVDNLR 161
                                        5999999999998887...66666555555 PP

>> zf-RING_6  zf-RING of BARD1-type protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.1         2   1.3e+03      30      39 ..       8      17 ..       5      20 .. 0.82
   2 ?    8.3   6.3    0.0033       2.1      23      48 ..      26      54 ..       9      59 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 2
                          zf-RING_6 30 fcsncisdcf 39
                                       fc +c sd +
  gene2620|gene2620|rna2620|rna2620  8 FCPQCKSDSY 17
                                       8999999976 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0033
                          zf-RING_6 23 lggcehifcsncisdcfgsg...cpvcyt 48
                                       +  c h +c nc+s  f  g   cp c t
  gene2620|gene2620|rna2620|rna2620 26 VSPCYHKMCENCVSRIFSQGesaCPECGT 54
                                       567**************755333888865 PP

>> Ribosomal_L37e  Ribosomal protein L37e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0       1.5   9.6e+02      18      27 ..       8      17 ..       4      22 .. 0.86
   2 ?    9.0   1.9    0.0024       1.6      15      38 ..      30      53 ..      27      61 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 1.5
                     Ribosomal_L37e 18 lCrrCgkrsy 27
                                       +C +C + sy
  gene2620|gene2620|rna2620|rna2620  8 FCPQCKSDSY 17
                                       7*******99 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0024
                     Ribosomal_L37e 15 tHilCrrCgkrsyhvqkktCascG 38
                                        H +C+ C +r +   ++ C +cG
  gene2620|gene2620|rna2620|rna2620 30 YHKMCENCVSRIFSQGESACPECG 53
                                       599********************9 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.3     0.025        16      14      19 ..       7      12 ..       6      15 .. 0.82
   2 ?    5.7   3.1      0.02        13       2      21 ..      34      54 ..      33      56 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.025
                      zinc_ribbon_2 14 kFCpyC 19
                                       +FCp+C
  gene2620|gene2620|rna2620|rna2620  7 QFCPQC 12
                                       799999 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.02
                      zinc_ribbon_2  2 CpnCGael.qdnakFCpyCGt 21
                                       C nC   + + ++  Cp+CGt
  gene2620|gene2620|rna2620|rna2620 34 CENCVSRIfSQGESACPECGT 54
                                       667777777788889999998 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.1     0.068        43      27      35 ..       6      15 ..       2      17 .. 0.76
   2 ?    9.4   2.9    0.0017       1.1       8      39 ..      34      59 ..      28      59 .. 0.64
   3 ?   -0.6   0.4       2.3   1.5e+03       4       9 ..     187     192 ..     187     198 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.068
                        Zn-ribbon_8 27 ta.CPeCgse 35
                                        + CP+C+s+
  gene2620|gene2620|rna2620|rna2620  6 DQfCPQCKSD 15
                                       566****984 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0017
                        Zn-ribbon_8  8 CeeCghefevlqsisdapltaCPeCgsevrrv 39
                                       Ce+C ++   +       + aCPeCg  +rr+
  gene2620|gene2620|rna2620|rna2620 34 CENCVSR---IF---SQGESACPECGTLLRRI 59
                                       6666522...22...233678*****999995 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 2.3
                        Zn-ribbon_8   4 YeYrCe 9  
                                        Y Y+C+
  gene2620|gene2620|rna2620|rna2620 187 YTYECT 192
                                        99***8 PP

>> NOB1_Zn_bind  Nin one binding (NOB1) Zn-ribbon like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.5     0.074        47      23      32 ..       6      15 ..       2      27 .. 0.82
   2 ?    8.0   1.8    0.0049       3.1       7      39 ..      30      61 ..      21      83 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.074
                       NOB1_Zn_bind 23 kkFCpkCGnk 32
                                        +FCp+C ++
  gene2620|gene2620|rna2620|rna2620  6 DQFCPQCKSD 15
                                       58*****886 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0049
                       NOB1_Zn_bind  7 wvlrChaCfkvtkdmtkkFCpkCGnktLkrvav 39
                                       +  +C  C++ +  +    Cp+CG   L+r++ 
  gene2620|gene2620|rna2620|rna2620 30 YHKMCENCVSRIFSQGESACPECGT-LLRRINF 61
                                       6678******9999**********5.5677665 PP

>> DUF3797  Domain of unknown function (DUF3797)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   4.2     0.021        13      16      43 ..       9      35 ..       7      41 .. 0.87
   2 ?    3.0   0.0      0.15        93      15      20 ..      48      53 ..      42      60 .. 0.87
   3 ?   -1.6   0.0       4.1   2.6e+03       3      15 ..     177     189 ..     176     195 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.021
                            DUF3797 16 CPeCgNnkvlNsegkviieddtfyreCk 43
                                       CP+C+ +  lN + k+ ++   + + C+
  gene2620|gene2620|rna2620|rna2620  9 CPQCKSDSYLNPNIKIYVSP-CYHKMCE 35
                                       ****************9985.8999996 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.15
                            DUF3797 15 qCPeCg 20
                                       +CPeCg
  gene2620|gene2620|rna2620|rna2620 48 ACPECG 53
                                       8****9 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 4.1
                            DUF3797   3 iiqivkLdekYvq 15 
                                        ++++++L e Y +
  gene2620|gene2620|rna2620|rna2620 177 LKKAIELPEGYTY 189
                                        6899999999976 PP

>> zf-C3HC4_4  zinc finger of C3HC4-type, RING
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0  11.7     0.022        14       1      42 []       9      52 ..       9      52 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.022
                         zf-C3HC4_4  1 CPiCl..dYLekPvsl...eCGhsfClsCisslqkepdgeqllCplC 42
                                       CP C   +YL+  + +   +C h +C +C+s++  + ++   +Cp+C
  gene2620|gene2620|rna2620|rna2620  9 CPQCKsdSYLNPNIKIyvsPCYHKMCENCVSRIFSQGES---ACPEC 52
                                       88886335887777664457*************999877...5**** PP

>> GFA  Glutathione-dependent formaldehyde-activating enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.1     0.081        52      49      63 ..       6      20 ..       3      27 .. 0.80
   2 ?    3.5   1.9      0.14        92      49      63 ..      31      45 ..      26      49 .. 0.81
   3 ?    1.8   0.1      0.47     3e+02      50      59 ..      47      56 ..      43      65 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.081
                                GFA 49 rsfCpeCgsplysee 63
                                        +fCp+C s  y ++
  gene2620|gene2620|rna2620|rna2620  6 DQFCPQCKSDSYLNP 20
                                       57*******998764 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.14
                                GFA 49 rsfCpeCgsplysee 63
                                       +++C++C s+++s+ 
  gene2620|gene2620|rna2620|rna2620 31 HKMCENCVSRIFSQG 45
                                       789*********874 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.47
                                GFA 50 sfCpeCgspl 59
                                       s CpeCg+ l
  gene2620|gene2620|rna2620|rna2620 47 SACPECGTLL 56
                                       78*****976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1072  (0.0597914); expected 358.6 (0.02)
Passed bias filter:                      545  (0.0303977); expected 358.6 (0.02)
Passed Vit filter:                       106  (0.00591221); expected 17.9 (0.001)
Passed Fwd filter:                        29  (0.00161749); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              28  [number of targets reported over threshold]
# CPU time: 0.49u 0.23s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1533.32
//
Query:       gene2621|gene2621|rna2621|rna2621  [L=65]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.6e-13   49.9   0.0      3e-13   49.7   0.0    1.0  1  Ribosomal_S21e  Ribosomal protein S21e


Domain annotation for each model (and alignments):
>> Ribosomal_S21e  Ribosomal protein S21e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.7   0.0   1.7e-17     3e-13      15      68 ..       6      59 ..       2      63 .. 0.94

  Alignments for each domain:
  == domain 1  score: 49.7 bits;  conditional E-value: 1.7e-17
                     Ribosomal_S21e 15 rkcsatnrlItakDhasvqinvaevdetGratgesttyalsgairrkGesddsl 68
                                       r c+ + + I++ D+asvq++++++de+Gr+t+e t++ ++ga+r++G++d  +
  gene2621|gene2621|rna2621|rna2621  6 RICDLSRKPISSVDKASVQLTFVNLDENGRMTDELTVLNVCGALRKQGKADGLI 59
                                       789************************************************766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (65 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       219  (0.0122148); expected 358.6 (0.02)
Passed bias filter:                      199  (0.0110993); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.30s 00:00:00.68 Elapsed: 00:00:00.46
# Mc/sec: 422.97
//
Query:       gene2622|gene2622|rna2622|rna2622  [L=60]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (60 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       325  (0.0181271); expected 358.6 (0.02)
Passed bias filter:                      252  (0.0140554); expected 358.6 (0.02)
Passed Vit filter:                         6  (0.000334653); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.26s 00:00:00.60 Elapsed: 00:00:00.41
# Mc/sec: 443.53
//
Query:       gene2623|gene2623|rna2623|rna2623  [L=356]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (356 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       734  (0.0409393); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 2215.34
//
Query:       gene2624|gene2624|rna2624|rna2624  [L=59]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       637  (0.035529); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 423.43
//
Query:       gene2625|gene2625|rna2625|rna2625  [L=428]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-24   87.1  48.2    3.9e-16   59.4  13.3    3.4  4  Na_Ca_ex  Sodium/calcium exchanger protein


Domain annotation for each model (and alignments):
>> Na_Ca_ex  Sodium/calcium exchanger protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.4  15.9   7.6e-15   1.4e-10       4     150 ..      22     161 ..      19     162 .. 0.80
   2 ?    0.3   0.5     0.034     6e+02     127     150 ..     205     228 ..     186     229 .. 0.76
   3 ?   -3.2   6.7       0.4   7.1e+03     104     145 ..     236     279 ..     204     280 .. 0.64
   4 !   59.4  13.3   2.2e-20   3.9e-16       6     148 ..     270     415 ..     264     418 .. 0.90

  Alignments for each domain:
  == domain 1  score: 41.4 bits;  conditional E-value: 7.6e-15
                                        HHHHHHHHHHHHHHHHHHHHHHHHHHHTTCTHHHHHHHHHHHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHH CS
                           Na_Ca_ex   4 vlfilslllisvladflvssaeeiakslgisgsvlGltllAlgnslpElissiiaaltgevdlaignvlGsnifnl 79 
                                        + +++ + +  +  ++l++ +++ +k +++  +++++++l +gn lpEli+ +  + ++    ai   +G+ +f++
  gene2625|gene2625|rna2625|rna2625  22 LNMFMLFSGYLLVDEYLMQYLDNAVKQTKLQSELVAIIFLNIGNGLPELITGF-LCGQKDLLCAIYCSIGGMLFII 96 
                                        5578888999999************************************9864.444455999************* PP

                                        HTHHHHHHHHHHBTTSSCECCHHH...HHHHHHHHHHHHHHHHTCHHHHHHTEEHHHHHHHHHHHHHHHHHHHH CS
                           Na_Ca_ex  80 llviGlialigslkvdseslkldl...gllllvallllllvlllllplfvpgrltvleglvllllYalylvlsl 150
                                        ++v+G+++l++s   +  ++k++l   ++++l++ ++ll+++l+       + ++++ +l ++++Ya++lv+s+
  gene2625|gene2625|rna2625|rna2625  97 TVVLGSAILFKS---KTVEIKNSLfykNIMFLFLSYSLLTCILIR------EAVNIFIALFMVGTYAVFLVHSV 161
                                        **********77...333334444101455555555555555544......********************986 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.034
                                        HTEEHHHHHHHHHHHHHHHHHHHH CS
                           Na_Ca_ex 127 pgrltvleglvllllYalylvlsl 150
                                        ++  +   +l l++++a ++v+s+
  gene2625|gene2625|rna2625|rna2625 205 QKATSTPLALYLCSVFANFIVFSY 228
                                        56778888999**********997 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 0.4
                                        HHHHHHHHHHHHHHHHTCHHHHH..HTEEHHHHHHHHHHHHHHH CS
                           Na_Ca_ex 104 gllllvallllllvlllllplfv..pgrltvleglvllllYaly 145
                                         ++++++ +llll ++l+++  +   + ++   ++  ++l++++
  gene2625|gene2625|rna2625|rna2625 236 KVFFIAVPVLLLLSAVLYFFDTItpNKMIMNCYSMFIAILWIFF 279
                                        56677666666666666644444655556666666666777776 PP

  == domain 4  score: 59.4 bits;  conditional E-value: 2.2e-20
                                        HHHHHHHHHHHHHHHHHHHHHHHHHTTCTHHHHHHHHHHHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHT CS
                           Na_Ca_ex   6 filslllisvladflvssaeeiakslgisgsvlGltllAlgnslpElissiiaaltgevdlaignvlGsnifnlll 81 
                                        +++++l+i +++d +v+ +e +++ +++s+++++l++lA+gns+ +l+++ iaa++g v  a+++ + s i n+l+
  gene2625|gene2625|rna2625|rna2625 270 MFIAILWIFFTSDTIVNQIEMVSERFNMSKELSSLVFLAFGNSFADLVTNSIAARKGLVKTAVSSSMTSPIHNILF 345
                                        6789************************************************************************ PP

                                        HHHHHHHHHHBTTSSCECCHHH.HHHHHHHHHHHHHHHHTCHHHHH....HTEEHHHHHHHHHHHHHHHHHH CS
                           Na_Ca_ex  82 viGlialigslkvdseslkldl.gllllvallllllvlllllplfv....pgrltvleglvllllYalylvl 148
                                          Gl + + +l++    +  ++ +++++v  ++++  ++l+++ f      ++l++  + +l+++Y+l+++l
  gene2625|gene2625|rna2625|rna2625 346 NFGLLLSYFTLSNGT-IVLHSVrNAMFTVFPIVFV-PIALFIISFNyeirNRKLEIELAYTLFVIYGLFICL 415
                                        *****9998855554.4467777998888888866.666677776689999******************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (428 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1239  (0.0691059); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.44
# Mc/sec: 2930.06
//
Query:       gene2626|gene2626|rna2626|rna2626  [L=368]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.7e-19   69.0   0.0    6.2e-19   68.3   0.0    1.4  1  Sad1_UNC     Sad1 / UNC-like C-terminal
     0.0071   16.3   2.2      0.013   15.4   2.2    1.4  1  Sigma70_ner  Sigma-70, non-essential region
  ------ inclusion threshold ------
      0.087   12.8   0.9       0.21   11.6   0.2    2.0  2  Holin_BhlA   BhlA holin family
       0.09   12.6   1.0        1.8    8.4   0.2    2.4  2  DivIC        Septum formation initiator
       0.33   11.8   2.0       0.83   10.5   0.1    2.5  2  YMF19        Plant ATP synthase F0


Domain annotation for each model (and alignments):
>> Sad1_UNC  Sad1 / UNC-like C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.3   0.0   1.7e-22   6.2e-19       6     131 ..     248     365 ..     243     366 .. 0.92

  Alignments for each domain:
  == domain 1  score: 68.3 bits;  conditional E-value: 1.7e-22
                                        B-GGGGGSS--STT-SEEEESS-EEEEEEEEEEEEEEEEEEE---GGGSG-TTSB-EEEEEEESSTT----EEEEE CS
                           Sad1_UNC   6 kapkvilqedyspgeCwsfkgsrgfvvieLseeiiveavtlehveksvapisSapKdfevsgskrypekkwvllge 81 
                                        ++++++++e++ pg C+ ++g+ g+++ ++ ++ ++  v + h  ++    +Sa++++++ g+++++    v+lge
  gene2626|gene2626|rna2626|rna2626 248 RHINSVMSESLEPGDCFIMDGTTGHFIFRFTRPFKIVRVGIFHPMSKK--KASAVRNIKITGMDESE---KVELGE 318
                                        6788999************************************99944..9*************999...57**** PP

                                        EE--TTS-SEEEEE--TT----EEEEEEEE--BSS-SSEEEESEEEEEEE CS
                           Sad1_UNC  82 fsydedgknaqtFeleeskdilvkyvkleilsnyGneeytclyrlrVyGt 131
                                        ++y ++    q Fel+++    ++ +++++lsn+G++++tc+y+++++++
  gene2626|gene2626|rna2626|rna2626 319 YEY-KEAGAYQEFELHNDR--SFSALDFNVLSNHGAKDHTCVYKIYIFAE 365
                                        **9.5556779******98..9**************************87 PP

>> Sigma70_ner  Sigma-70, non-essential region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   2.2   3.6e-06     0.013      20      90 ..      37     129 ..      35     157 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 3.6e-06
                        Sigma70_ner  20 irLrdiidGflD........eeeeeeeeeeeedeeeeeeeeddd..eeeseseaadeeelkeealekfeelreqye 85 
                                         +++dii G+ +        ++e+e ++ ++e+ee ++e+      ++++ ++  d     e+++e++e+ +e  +
  gene2626|gene2626|rna2626|rna2626  37 KKVSDIINGLHEkhgdgnykNDENERKMLNTENEEISDEK---TneSDNEPKLHTDDTYCTEDVRERVEHSSERND 109
                                        589*********9988865432333333333333333332...2345689999999*****************999 PP

                        Sigma70_ner  86 klrk...............a 90 
                                         + +                
  gene2626|gene2626|rna2626|rna2626 110 AMDNtaltgydtinyersiF 129
                                        99885555555544444444 PP

>> Holin_BhlA  BhlA holin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       1.6   5.9e+03      25      43 ..      92     110 ..      91     113 .. 0.80
   2 ?   11.6   0.2   5.9e-05      0.21       6      51 ..     151     207 ..     148     211 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1.6
                         Holin_BhlA  25 Yilkkqekreekqeerekk 43 
                                        Y +   ++r e   er ++
  gene2626|gene2626|rna2626|rna2626  92 YCTEDVRERVEHSSERNDA 110
                                        8888889999999999876 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 5.9e-05
                         Holin_BhlA   6 lklaitqGiwavLfvvllvYilkkqekreekqe...........erekkyqeiikkl 51 
                                        l+++++q  w++L  vl+vYi+   ++     e            + k +q++i+kl
  gene2626|gene2626|rna2626|rna2626 151 LTYFLKQHFWVLLISVLMVYIVAYLNRTHGTTEedykkdiqllrTQNKGLQDMISKL 207
                                        57899***************9976665555555455677888888888888888887 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.2    0.0005       1.8      14      65 ..      50     101 ..      42     108 .. 0.88
   2 ?    2.2   0.0     0.042   1.5e+02      29      50 ..     186     207 ..     161     216 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0005
                                        XXXXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-XXXXXXXXXXXXXXX CS
                              DivIC  14 kgllaykqlkqeiaalqaelaklkaeneeLeaevkdLksdedyieerARsel 65 
                                        +g  +yk  ++e++ l+ e++++++e+ +  ++  +L+ d+ y +e  R++ 
  gene2626|gene2626|rna2626|rna2626  50 HGDGNYKNDENERKMLNTENEEISDEKTNESDNEPKLHTDDTYCTEDVRERV 101
                                        566789999****************************99****999999875 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.042
                                        HHHHHHHHHHHHHHHHHHHCC- CS
                              DivIC  29 lqaelaklkaeneeLeaevkdL 50 
                                         +++++ l+ +n+ L++ +++L
  gene2626|gene2626|rna2626|rna2626 186 YKKDIQLLRTQNKGLQDMISKL 207
                                        4677788888888888888777 PP

>> YMF19  Plant ATP synthase F0
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.4      0.54   1.9e+03      58      58 ..      48      48 ..       4      95 .. 0.56
   2 ?   10.5   0.1   0.00023      0.83       5      44 ..     150     199 ..     149     230 .. 0.63

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.54
                              YMF19 58 e 58
                                       e
  gene2626|gene2626|rna2626|rna2626 48 E 48
                                       2 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00023
                              YMF19   5 kftyf.tQffWlclf.FitlYivll........knilpkiarilklrkkl 44 
                                        k+tyf  Q fW++l+  +++Yiv++        ++   k +++l+ ++k 
  gene2626|gene2626|rna2626|rna2626 150 KLTYFlKQHFWVLLIsVLMVYIVAYlnrthgttEEDYKKDIQLLRTQNKG 199
                                        5665438****999977788887775555554433344444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (368 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1121  (0.0625244); expected 358.6 (0.02)
Passed bias filter:                      544  (0.0303419); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 2377.28
//
Query:       gene2627|gene2627|rna2627|rna2627  [L=170]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.3e-34  116.7   2.2    7.8e-34  116.4   2.2    1.1  1  Ribosomal_L18A  Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A


Domain annotation for each model (and alignments):
>> Ribosomal_L18A  Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.4   2.2   4.3e-38   7.8e-34       2     121 .]       5     126 ..       4     126 .. 0.98

  Alignments for each domain:
  == domain 1  score: 116.4 bits;  conditional E-value: 4.3e-38
                                        EEEEEEEEEEET................................................................ CS
                     Ribosomal_L18A   2 keYeVvGrklpsekepepkvyrmrifapnevvak...wyflkklkkvkkanGeilavkkieekkptkvknygiwlr 74 
                                        keY+V G+klps ++p+p++y m++fa+nev+a+   + +l+k +kvk +nG il++  + e+  t+vk ygi   
  gene2627|gene2627|rna2627|rna2627   5 KEYKVYGSKLPSSQAPSPQIYVMQVFAKNEVTARstfFRVLRKQHKVKSTNGCILKMVPVVEQ-ITHVKPYGIRFT 79 
                                        89**********************************9*************************5.9*********** PP

                                        ....TEEEEEEEEEEESSHHHHHHHHHHHHHHHS---GGGEEEEEEE CS
                     Ribosomal_L18A  75 ydsrsgthnfykeyrdlteegaveqvYselgsrhrakrssIqIekve 121
                                        y+s++gthn+yke+r +++ ++v+ +Y+++++rh++ r+ I I +v+
  gene2627|gene2627|rna2627|rna2627  80 YKSKKGTHNMYKEFRGVSRVDVVNDMYNDMAGRHSVGRTAIDIVSVK 126
                                        *******************************************9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       372  (0.0207485); expected 358.6 (0.02)
Passed bias filter:                      266  (0.0148363); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 1191.94
//
Query:       gene2628|gene2628|rna2628|rna2628  [L=390]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
       0.38   11.0   0.1       0.38   11.0   0.1    2.6  3  Peptidase_Prp  Cysteine protease Prp
        2.7    8.5   0.0        2.7    8.5   0.0    3.8  5  HAGH_C         Hydroxyacylglutathione hydrolase C-terminus


Domain annotation for each model (and alignments):
>> Peptidase_Prp  Cysteine protease Prp
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.2      0.28   2.5e+03      37      60 ..      16      49 ..      13      68 .. 0.56
   2 ?   -2.5   0.2      0.71   6.4e+03      59      68 ..     218     237 ..     203     256 .. 0.52
   3 ?   11.0   0.1   4.2e-05      0.38      37      86 ..     337     387 ..     335     390 .] 0.88

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.28
                                       HHHHHHHHHHHHHHS----..............T CS
                      Peptidase_Prp 37 Salvittvnaleevlkekvelee..........s 60
                                       ++l+ t++n  +e+  e++++++          +
  gene2628|gene2628|rna2628|rna2628 16 TILLTTACNISSEASIEAASVKItdsntsttekN 49
                                       5666777777666555555555454555544452 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.71
                                        ...........TTTTSHHHH CS
                      Peptidase_Prp  59 e..........seeekekaq 68 
                                        +          ++e+++k  
  gene2628|gene2628|rna2628|rna2628 218 NttetnikheeAQESNDKHG 237
                                        33333333333444444444 PP

  == domain 3  score: 11.0 bits;  conditional E-value: 4.2e-05
                                        HHHHHHHHHHHHHHS----.....TTTTSHHHHHHHHHHHHHHHHHHHH-T CS
                      Peptidase_Prp  37 Salvittvnaleevlkekvelee.seeekekaqllletlvlgLeeieeeyp 86 
                                        S +v +++n+ ee+ k   +le+ +++  eka +ll+t++ gLee+e+e +
  gene2628|gene2628|rna2628|rna2628 337 SRIVLGIYNSSEEMKKFGQRLEKkDKQYTEKAMTLLNTFLRGLEELEDEAQ 387
                                        778999999999999999988888888999****************99866 PP

>> HAGH_C  Hydroxyacylglutathione hydrolase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.0   0.00031       2.7      25      56 ..      47      78 ..      30     110 .. 0.76
   2 ?   -2.1   0.1      0.67     6e+03      30      43 ..     146     159 ..     121     179 .. 0.55
   3 ?    1.2   2.4     0.058   5.2e+02      17      46 ..     199     228 ..     192     231 .. 0.85
   4 ?   -1.8   0.5      0.52   4.6e+03      18      43 ..     257     282 ..     250     289 .. 0.70
   5 ?   -2.0   0.0       0.6   5.4e+03      48      53 ..     372     377 ..     345     387 .. 0.55

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00031
                             HAGH_C 25 kevkelrakgeptvpstladEkktNpFLRlde 56
                                       ++ k +++++++tv s  +dE k+  F+ +d 
  gene2628|gene2628|rna2628|rna2628 47 EKNKGEQEENQTTVSSEAHDEDKCSGFMTCDG 78
                                       3445556789********************73 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.67
                             HAGH_C  30 lrakgeptvpstla 43 
                                        +++ +++ ++s+++
  gene2628|gene2628|rna2628|rna2628 146 KQDVEKHDLQSQVE 159
                                        22223333333333 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.058
                             HAGH_C  17 nealkkrlkevkelrakgeptvpstladEk 46 
                                        +e+ ++++++++e ++k++ t  +++++E 
  gene2628|gene2628|rna2628|rna2628 199 EEQPENVVEKAQESESKEKNTTETNIKHEE 228
                                        5667889999*****************997 PP

  == domain 4  score: -1.8 bits;  conditional E-value: 0.52
                             HAGH_C  18 ealkkrlkevkelrakgeptvpstla 43 
                                        +++k+  ++ ++++++++pt+ ++ a
  gene2628|gene2628|rna2628|rna2628 257 HDVKQTSEKETAADEEHKPTLEVNPA 282
                                        45667777777777888999877655 PP

  == domain 5  score: -2.0 bits;  conditional E-value: 0.6
                             HAGH_C  48 tNpFLR 53 
                                        +N FLR
  gene2628|gene2628|rna2628|rna2628 372 LNTFLR 377
                                        355555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (390 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2468  (0.137654); expected 358.6 (0.02)
Passed bias filter:                      485  (0.0270511); expected 358.6 (0.02)
Passed Vit filter:                        79  (0.00440627); expected 17.9 (0.001)
Passed Fwd filter:                        26  (0.00145016); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.83u 0.30s 00:00:01.12 Elapsed: 00:00:00.47
# Mc/sec: 2477.55
//
Query:       gene2629|gene2629|rna2629|rna2629  [L=682]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.051   14.3   0.6       0.24   12.1   0.0    2.4  3  RicinB_lectin_2  Ricin-type beta-trefoil lectin domain-like
        2.6    7.8  19.5        2.3    8.0   0.3    3.0  3  MIR              MIR domain


Domain annotation for each model (and alignments):
>> RicinB_lectin_2  Ricin-type beta-trefoil lectin domain-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.1      0.66   5.9e+03      23      37 ..     413     427 ..     391     450 .. 0.56
   2 ?   -0.6   0.0      0.25   2.3e+03      39      65 ..     493     519 ..     467     523 .. 0.61
   3 ?   12.1   0.0   2.7e-05      0.24       5      80 ..     506     584 ..     504     591 .. 0.69

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.66
                                        SEEEECGCCTBCTTE CS
                    RicinB_lectin_2  23 gkvLdvaggstanga 37 
                                         k++ v++ ++++++
  gene2629|gene2629|rna2629|rna2629 413 EKAVKVENKHNNEKQ 427
                                        334444444443333 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.25
                                        EEEE-TTT-GGCEEEEECCESSEEEEE CS
                    RicinB_lectin_2  39 vqqwtcsgaanqqWrledtgdgtyriv 65 
                                        ++ ++++++   +Wr+++t++++ +i+
  gene2629|gene2629|rna2629|rna2629 493 IEMRDSNDQGFSLWRISSTDKNNEYIR 519
                                        444555555566788877776655555 PP

  == domain 3  score: 12.1 bits;  conditional E-value: 2.7e-05
                                        EEE......CETTT.....TEEEEECTSSSEEEECGCCTBCTTEEEEEE-TTT-GGCEEEEECCESS.EEEEEETT CS
                    RicinB_lectin_2   5 Wtl......gsggd.....gyytiknvasgkvLdvaggstanganvqqwtcsgaanqqWrledtgdg.tyrivnka 68 
                                        W++      +   +       +++kn++++++L + ++++ n      ++ s+ + q++++++ ++  +y++v   
  gene2629|gene2629|rna2629|rna2629 506 WRIsstdknN---EyirarEFFRLKNANTNLMLGIRSDGMLN-----GSNESKITRQTFMITECTNHaYYKMVQD- 572
                                        7776533221...123322479******************96.....44445788********998866666654. PP

                                        TTEEEEECGCS- CS
                    RicinB_lectin_2  69 sgkvLdvaggst 80 
                                        s+ +L  a+ +t
  gene2629|gene2629|rna2629|rna2629 573 SENMLRMANEKT 584
                                        444777665555 PP

>> MIR  MIR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.3      0.12   1.1e+03      84     117 ..     342     381 ..     336     397 .. 0.66
   2 ?    7.6   9.2   0.00035       3.1      85     162 ..     408     489 ..     400     496 .. 0.76
   3 ?    8.0   0.3   0.00026       2.3      29     108 ..     487     558 ..     483     595 .. 0.62

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.12
                                MIR  84 aseeekksplseseddqkevsayglegfegd.......nDk 117
                                        +++ee+ +p    ++++ e+s+y+ +++++        nD+
  gene2629|gene2629|rna2629|rna2629 342 KVHEEDDEPAE-IKEEERETSNYKIDETNNTrsdneqnNDI 381
                                        67777555544.44788888888888876556554444444 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.00035
                                MIR  85 seeekksplseseddqkevsayglegfegdnDk....veifekksttgmksaklvprdsyvrlqHvvtgcwLhsts 156
                                        se++k++ +  +++ ++e+++ + +  +++++k     + ++ k++++ + +++  ++  +rl+H++t++ ++st+
  gene2629|gene2629|rna2629|rna2629 408 SENDKEKAVKVENKHNNEKQNTERQHNKDEEEKkrkiQKNDKGKQKHNNNPDSFIRQNELIRLKHIETSKFISSTT 483
                                        555656666666666666666666555555444555678888899999**************************** PP

                                MIR 157 vklkke 162
                                         k++++
  gene2629|gene2629|rna2629|rna2629 484 DKVDQK 489
                                        **9987 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.00026
                                MIR  29 qevflritlypsadaanssraLWeievvqkdawrgglikwgkvyRlkHlaTgryLaseeekksplseseddqkevs 104
                                        +++f +i +++s d+  s   LW+i +  k   + ++i+  + +Rlk  +T   L    +   +l+ s++ + + +
  gene2629|gene2629|rna2629|rna2629 487 DQKFYKIEMRDSNDQGFS---LWRISSTDK---NNEYIRAREFFRLKNANTNLMLGIRSDG--MLNGSNESKITRQ 554
                                        445666666666666666...******999...99*****************999998874..3333333333333 PP

                                MIR 105 aygl 108
                                        ++  
  gene2629|gene2629|rna2629|rna2629 555 TFMI 558
                                        3333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (682 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2432  (0.135646); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); expected 358.6 (0.02)
Passed Vit filter:                        77  (0.00429472); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.81u 0.30s 00:00:01.11 Elapsed: 00:00:00.49
# Mc/sec: 4196.90
//
Query:       gene263|gene263|rna263|rna263  [L=156]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.041   13.4   4.1       0.06   12.9   0.4    2.3  3  IL10       Interleukin 10
       0.08   12.5   3.3      0.097   12.2   3.3    1.1  1  Cas_DxTHG  CRISPR-associated (Cas) DxTHG family
        3.8    8.5   6.1         27    5.8   0.2    2.3  2  PdaC       Deacetylase PdaC


Domain annotation for each model (and alignments):
>> IL10  Interleukin 10
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.4     1e-05      0.06      99     145 ..       7      53 ..       2      70 .. 0.90
   2 ?    0.4   0.1     0.066   3.9e+02      89     132 ..      60     101 ..      55     133 .. 0.62
   3 ?    1.2   0.2     0.037   2.2e+02      37      60 ..     111     140 ..      82     152 .. 0.57

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1e-05
                                    GGGHHHHHHHHHHHHHHHHHHHTSTTS-GGG---HHHHHHHHHHHTT CS
                           IL10  99 peikehvnslgeklktlrlrlrrchrflpcenkskavekvksafnkl 145
                                      i ++ n l eklk+lr    +  r  p  +k      +k++f+k+
  gene263|gene263|rna263|rna263   7 LRITDYFNNLKEKLKALRETYSKRFRNEPKVQKQENTSFIKQEFDKI 53 
                                    56899***************************************997 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.066
                                    THHHHHHHHSGGGHHHHHHHHHHHHHHHHHHHTSTTS-GGG--- CS
                           IL10  89 evmpqaenhgpeikehvnslgeklktlrlrlrrchrflpcenks 132
                                    e mpq ++   e+   vn +     tl +  +  + +l c +k 
  gene263|gene263|rna263|rna263  60 ECMPQLNDMLDELSRNVNNFES--ITLMVLEQLLKNYLVCTDKP 101
                                    6677777777777777776533..23333334444566666653 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.037
                                    HHHHHHHHHTTH......HHHCCC-SSSS- CS
                           IL10  37 lrelraafskvk......tffqkkdqldnl 60 
                                    ++e+r+ +++ k      tff+ kd   +l
  gene263|gene263|rna263|rna263 111 IKEIREFYAECKkytwdnTFFNDKDVCSKL 140
                                    566666665554333444899999864433 PP

>> Cas_DxTHG  CRISPR-associated (Cas) DxTHG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   3.3   1.6e-05     0.097     215     327 ..      11     116 ..       4     147 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.6e-05
                      Cas_DxTHG 215 keleefskalelirp.lell.ekaeklekeivek...lkeeleeiesleeeesakplellldeikkklekf....lkkqi 285
                                    + ++++++ l+++r+ +     ++ k++k+  e+   +k+e  +i   + +e +++l+ +lde+++++++f    l    
  gene263|gene263|rna263|rna263  11 DYFNNLKEKLKALREtYSKRfRNEPKVQKQ--ENtsfIKQEFDKIPYDDGAECMPQLNDMLDELSRNVNNFesitL---- 84 
                                    457888888899985444443355555555..2245588999***88899999******************44330.... PP

                      Cas_DxTHG 286 kwclekgliqqaltllreliisl.lle...gedilnkkkrreeiee 327
                                                  +l++l+ ++ ++    ++++l+k +  +ei+e
  gene263|gene263|rna263|rna263  85 -------------MVLEQLLKNYlVCTdkpSSEVLKKINI-KEIRE 116
                                    .............334444444434445554444433333.44433 PP

>> PdaC  Deacetylase PdaC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   2.1    0.0089        53      23      64 ..      14      57 ..       2      88 .. 0.79
   2 ?    5.8   0.2    0.0045        27      13      50 ..      93     127 ..      62     140 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.0089
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHH...HHHHTT---S-EEE CS
                           PdaC 23 kevqdkinkkiekdadkflkeyekeake..eakkndfpkrpyel 64
                                   +++++k+++  e ++++f +e + +++e  +  k++f k py+ 
  gene263|gene263|rna263|rna263 14 NNLKEKLKALRETYSKRFRNEPKVQKQEntSFIKQEFDKIPYDD 57
                                   44556666666889999999998888888888888998888875 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0045
                                    EEEEE-S-S-HHHHHHHHHHHHHHHHHHHHHHHHHHH. CS
                           PdaC  13 kyPvisglknkevqdkinkkiekdadkflkeyekeake 50 
                                    +y v++++ ++ev +kin k   ++++f++e +k++ +
  gene263|gene263|rna263|rna263  93 NYLVCTDKPSSEVLKKINIK---EIREFYAECKKYTWD 127
                                    78999999999999999999...999999999998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1534  (0.0855597); expected 358.6 (0.02)
Passed bias filter:                      715  (0.0398795); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1126.09
//
Query:       gene2630|gene2630|rna2630|rna2630  [L=149]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.4e-06   27.0   0.0      0.014   15.7   0.0    1.5  2  HEAT_2    HEAT repeats
  ------ inclusion threshold ------
       0.12   12.5   0.0       0.15   12.2   0.0    1.2  1  DUF5636   Family of unknown function (DUF5636)


Domain annotation for each model (and alignments):
>> HEAT_2  HEAT repeats
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   1.7e-06     0.015      31      87 ..      57     118 ..      40     119 .. 0.59
   2 !   15.7   0.0   1.6e-06     0.014       3      60 ..      61     123 ..      59     143 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.7e-06
                             HEAT_2  31 ealpaLvellededpavRraaae...aLgaigd...pealpaLkellddddddvvReaAaeaL 87 
                                         al+ ++ ll+ +d  vR + ++    L  +g+   +e+++ L++ +dd+++++ R a + +L
  gene2630|gene2630|rna2630|rna2630  57 GALKHVIYLLSKDDNKVRVHLVHnmaVLTIFGEeyvHEVIANLLRNMDDKNWRY-RIALIDGL 118
                                        566667777777777777777763333346664444667777777776665555.55555544 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 1.6e-06
                             HEAT_2   3 aLlqalendpdpevrraairaLg...rignp...ealpaLvellededpavRraaaeaLgaigd 60 
                                        + + +l +  d +vr + +++++    +g++   e+++ L++ ++d++++ R a ++ L  ++d
  gene2630|gene2630|rna2630|rna2630  61 HVIYLL-SKDDNKVRVHLVHNMAvltIFGEEyvhEVIANLLRNMDDKNWRYRIALIDGLCMVDD 123
                                        566677.667779999999999988435776666889999999999999999999998866655 PP

>> DUF5636  Family of unknown function (DUF5636)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   1.7e-05      0.15      67     132 ..      16      85 ..       4     110 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.7e-05
                                        SS-EEECCG----HHHHHHHHHTT--B-H.....HHSS-SS-SSHHHHHHHHHHHHXHH-GGGGTT--GGG CS
                            DUF5636  67 kgtsktiskdflskedFqellknglllkD.....sgagssHGeftHalQwfllieaqkedslflhavtviq 132
                                        + + +t+ ++  sk dF+el+ +  l+kD     s++++ HG   H + + l    +k   + +h++ v  
  gene2630|gene2630|rna2630|rna2630  16 VNDHQTVINKEESKIDFKELTMDLSLIKDrairtSAGADVHGALKHVIYL-LSKDDNKVRVHLVHNMAVLT 85 
                                        567788999999*******999999999955554456788********76.66677888889999998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       681  (0.0379832); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 954.89
//
Query:       gene2631|gene2631|rna2631|rna2631  [L=187]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00018   21.3   0.0    0.00047   20.0   0.0    1.7  1  Exo_endo_phos_2  Endonuclease-reverse transcriptase


Domain annotation for each model (and alignments):
>> Exo_endo_phos_2  Endonuclease-reverse transcriptase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   2.6e-08   0.00047       1     118 [.      13     126 ..      13     127 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 2.6e-08
                    Exo_endo_phos_2   1 lliisvYippsd.elenlestlekllselksp....kiiilGDfN.akhplWgsedtdssargeeLiefleehsls 70 
                                        +l+++vYip +  +++n+++ l ++l + +++    +i+++GD+N ++ ++  + + ++ a +ee++ f+ +    
  gene2631|gene2631|rna2631|rna2631  13 ILMVCVYIPCQGvARRNALDRLCNFLHRERDRgrfsEIVVMGDWNgVPGQSHRHLHARQVATNEEFLGFTRATRFA 88 
                                        6899********988888888888888887777899*********557788888777779999********99999 PP

                    Exo_endo_phos_2  71 llnllksgptfkssngsstiDltltsdnlalskleleeedlgSDHrpi 118
                                            + +            iD +++ +n  ++k++  ++  +SDH p+
  gene2631|gene2631|rna2631|rna2631  89 --RAPARRG--------RCIDYFVSLNNAIVEKQRVLRDVDLSDHYPV 126
                                        ..6666444........56**9999999999999***999*****998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       322  (0.0179597); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1372.63
//
Query:       gene2632|gene2632|rna2632|rna2632  [L=675]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (675 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       714  (0.0398237); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.61u 0.26s 00:00:00.87 Elapsed: 00:00:00.44
# Mc/sec: 4613.84
//
Query:       gene2633|gene2633|rna2633|rna2633  [L=339]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-51  174.6   0.0      3e-51  173.9   0.0    1.3  1  AAA_12           AAA domain
    5.2e-27   95.3   0.0    7.2e-27   94.8   0.0    1.2  1  AAA_11           AAA domain
    1.2e-06   28.5   0.0      0.012   15.4   0.0    2.1  2  Viral_helicase1  Viral (Superfamily 1) RNA helicase
  ------ inclusion threshold ------
      0.022   14.6   0.0       0.13   12.1   0.0    2.3  2  UvrD_C_2         UvrD-like helicase C-terminal domain
      0.029   13.9   0.0      0.043   13.3   0.0    1.2  1  UvrD-helicase    UvrD/REP helicase N-terminal domain


Domain annotation for each model (and alignments):
>> AAA_12  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  173.9   0.0   8.3e-55     3e-51       2     198 ..     100     285 ..      99     286 .. 0.93

  Alignments for each domain:
  == domain 1  score: 173.9 bits;  conditional E-value: 8.3e-55
                             AAA_12   2 erSlferllkkekekvvlLdtqYRmhpeIsrfpsklfYkgkLkdaesvkkrele...aqealeepleplvfidvek 74 
                                        + Slferl++ +   + lL++qYRmhp +++++s++fY+g+L +a+ ++  +++    ++a+ +   p++f+   +
  gene2633|gene2633|rna2633|rna2633 100 HVSLFERLIRLG-VVPYLLTVQYRMHPVLCEWVSNTFYDGALVSAQYTHGAHVRysaGTTAWFNLPMPTFFYVSRG 174
                                        68**********.*********************************555555554445678888889999999999 PP

                             AAA_12  75 seeekekkeksyiNeeEaelvvklvekllkkgseeerkkigvitpYraqvellkkklkekeeeksekeievntvdg 150
                                        +ee   +  +sy N++Ea+ ++ ++++l  +g++e  +++g+itpY+ q  ll++  +           ev+ vd+
  gene2633|gene2633|rna2633|rna2633 175 KEELFVSG-TSYLNKAEAQQCLAIIRHLKMNGVRE--TDVGIITPYEGQRVLLSRLTA----------CEVANVDA 237
                                        99999976.**************************..9***************99988..........89****** PP

                             AAA_12 151 fQGrekdviilslVRsnekkeigflkderrlNValTRAkskliivGnk 198
                                        fQGrek +ii+slVRsn+ ++igf++d+rr++ValTRAk+ l+ivGn+
  gene2633|gene2633|rna2633|rna2633 238 FQGREKAFIIISLVRSNNINDIGFVSDRRRMCVALTRAKHGLFIVGNP 285
                                        **********************************************96 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.8   0.0     2e-30   7.2e-27     174     261 .]       7      92 ..       1      92 [. 0.91

  Alignments for each domain:
  == domain 1  score: 94.8 bits;  conditional E-value: 2e-30
                             AAA_11 174 rkelskeleeaeesleeevldeaeivltTlsgagsklleklakkfdvviIDEAaqavEpstliPlrlgakkvvLvG 249
                                        +++ ++  ++ ++ l+ +++++a+++ +T+++ag++l++++  kf +v+IDEA qa+Ep tl+Pl + ++k++LvG
  gene2633|gene2633|rna2633|rna2633   7 KNKKNTHKDRLRDYLRYSFVKDARVITCTCVTAGQELFKRF--KFPYVLIDEAVQATEPLTLVPLIYSCRKLILVG 80 
                                        45556777778888889************************..9******************************** PP

                             AAA_11 250 DpkQLpatvisk 261
                                        D+kQL +t+++k
  gene2633|gene2633|rna2633|rna2633  81 DHKQLGPTILNK 92 
                                        *********975 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   3.3e-06     0.012      46     120 ..      32     105 ..       3     112 .. 0.70
   2 !   11.1   0.0   6.5e-05      0.23     177     233 ..     224     282 ..     188     283 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 3.3e-06
                    Viral_helicase1  46 svrtvdsflmalvkstkgkililDEylllhaGyilllaalskaklvilfGDplQipfhsrnasfllahlpsslsh 120
                                         + t+ ++ + l k+ k+ ++++DE+ +++   + l+  +++++ +il+GD++Q +    n+ + +a l +sl +
  gene2633|gene2633|rna2633|rna2633  32 ITCTCVTAGQELFKRFKFPYVLIDEAVQATE-PLTLVPLIYSCRKLILVGDHKQLGPTILNKRAANAGLHVSLFE 105
                                        44455556666666668*********99984.34447899**************987666666666666666655 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 6.5e-05
                    Viral_helicase1 177 kealgvrevttvhevqGlt..fdkVtlvllketdlelisesrenllvAlTRhrkslvil 233
                                        +++l ++ev  v   qG +  f   +lv++++ ++  + ++r  + vAlTR++ +l i+
  gene2633|gene2633|rna2633|rna2633 224 LSRLTACEVANVDAFQGREkaFIIISLVRSNNINDIGFVSDRRRMCVALTRAKHGLFIV 282
                                        55555667777888888663366788999988887778899*************99886 PP

>> UvrD_C_2  UvrD-like helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0      0.65   2.3e+03      15      31 ..      49      65 ..      48      80 .. 0.69
   2 ?   12.1   0.0   3.7e-05      0.13       6      52 .]     234     282 ..     230     282 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.65
                           UvrD_C_2 15 fpaVivfdpdlaaarmg 31
                                       fp+V +++++ a+++  
  gene2633|gene2633|rna2633|rna2633 49 FPYVLIDEAVQATEPLT 65
                                       89999988888877644 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 3.7e-05
                           UvrD_C_2   6 tihkaQGsefpaVivfdpdlaaarmgel.....rrrlLYtavTRAreklilv 52 
                                        ++  +QG e  ++i+   +l  + + ++      rr   +a+TRA++ l++v
  gene2633|gene2633|rna2633|rna2633 234 NVDAFQGREKAFIII---SLVRSNNINDigfvsDRRRMCVALTRAKHGLFIV 282
                                        677888888888888...444444455567788999999**********997 PP

>> UvrD-helicase  UvrD/REP helicase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   1.2e-05     0.043     247     294 ..      41      84 ..       9      99 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.2e-05
                                        HHHHHHHHHHSSEEEESSG.GG-BHHHHHHHHHHHTTTTTEEEEE-GGG CS
                      UvrD-helicase 247 eelaealrerykeiliDEy.QDTnkiQyrilkllasgheelfmvGDpkQ 294
                                        +el++  r +++++liDE+ Q T++   +++ l++s + +l++vGD kQ
  gene2633|gene2633|rna2633|rna2633  41 QELFK--RFKFPYVLIDEAvQATEPL--TLVPLIYSCR-KLILVGDHKQ 84 
                                        55544..679********87999985..79999**998.8********* PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (339 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       541  (0.0301746); expected 358.6 (0.02)
Passed bias filter:                      511  (0.0285013); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 2337.29
//
Query:       gene2634|gene2634|rna2634|rna2634  [L=93]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.8e-11   42.8  10.2    6.5e-11   42.4  10.2    1.3  1  UPF1_Zn_bind     RNA helicase (UPF2 interacting domain)
  ------ inclusion threshold ------
      0.069   13.5   1.5      0.069   13.5   1.5    2.4  2  Lar_restr_allev  Restriction alleviation protein Lar
       0.63   10.0  14.1        2.2    8.2   3.6    2.4  2  PHD              PHD-finger
       0.71    9.8  13.7       0.96    9.4   0.0    3.4  3  zf-trcl          Probable zinc-ribbon domain
       0.98    9.9   8.0         15    6.1   0.0    2.9  3  zf-C2HE          C2HE / C2H2 / C2HC zinc-binding finger
        8.2    6.7  17.0        2.2    8.5   7.8    3.2  3  zf-AN1           AN1-like Zinc finger


Domain annotation for each model (and alignments):
>> UPF1_Zn_bind  RNA helicase (UPF2 interacting domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.4  10.2   2.2e-14   6.5e-11       3      77 ..       3      68 ..       1      80 [. 0.92

  Alignments for each domain:
  == domain 1  score: 42.4 bits;  conditional E-value: 2.2e-14
                       UPF1_Zn_bind  3 CaYCgisdpesvvkCaackkwFCngkgktsashivthlvrskhkevslhkesplgdtvleCyncgsknvflLgfi 77
                                       C+YC+ ++   ++ Ca c++ FCn+ + t+ shi+ hl ++ hk++++       d  + C  cg++nvf+L+ +
  gene2634|gene2634|rna2634|rna2634  3 CSYCEAHS--HLITCADCHQTFCNTFKGTTISHIIFHLKKNAHKRIMI-------DRPVVCELCGESNVFVLRRM 68
                                       ****9885..79**********************************99.......88999***********9865 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   2.8      0.15   4.4e+02      28      36 ..      12      20 ..       2      45 .. 0.63
   2 ?   13.5   1.5   2.3e-05     0.069       6      36 ..      54      79 ..      52      89 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.15
                    Lar_restr_allev 28 cvyCadCga 36
                                        ++CadC  
  gene2634|gene2634|rna2634|rna2634 12 LITCADCHQ 20
                                       577777765 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 2.3e-05
                    Lar_restr_allev  6 CPfCggravlersqrvvaeigqcvyCadCga 36
                                       C  Cg+ +v + + r +     +v+C  Cg+
  gene2634|gene2634|rna2634|rna2634 54 CELCGESNVFVLR-RMDG----MVCCGSCGM 79
                                       9***********9.5555....********* PP

>> PHD  PHD-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   3.6   0.00075       2.2       2      25 ..       3      22 ..       2      31 .. 0.90
   2 ?    7.3   2.8    0.0015       4.4       2      22 ..      54      78 ..      52      81 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00075
                                       BTTTTSTTSTTSCEEEETTTSCEE CS
                                PHD  2 CavCkkksdeeeelvqCdgCkrwf 25
                                       C+ C++    +++l+ C +C+++f
  gene2634|gene2634|rna2634|rna2634  3 CSYCEA----HSHLITCADCHQTF 22
                                       999999....9**********986 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0015
                                       BTTTTS....TTSTTSCEEEETTTS CS
                                PHD  2 CavCkk....ksdeeeelvqCdgCk 22
                                       C++C++         + +v+C +C+
  gene2634|gene2634|rna2634|rna2634 54 CELCGEsnvfVLRRMDGMVCCGSCG 78
                                       9*****87776677999*******8 PP

>> zf-trcl  Probable zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   2.8    0.0035        11       5      15 ..      13      23 ..       9      27 .. 0.85
   2 ?    9.4   0.0   0.00032      0.96       2      17 ..      49      64 ..      48      66 .. 0.92
   3 ?    0.6   0.3      0.18   5.5e+02       2      11 ..      69      78 ..      68      82 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0035
                            zf-trcl  5 ltCkdCgaefv 15
                                       +tC+dC+++f 
  gene2634|gene2634|rna2634|rna2634 13 ITCADCHQTFC 23
                                       79******996 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00032
                            zf-trcl  2 DktltCkdCgaefvFt 17
                                       D++++C+ Cg++ vF 
  gene2634|gene2634|rna2634|rna2634 49 DRPVVCELCGESNVFV 64
                                       999***********95 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.18
                            zf-trcl  2 DktltCkdCg 11
                                       D  ++C +Cg
  gene2634|gene2634|rna2634|rna2634 69 DGMVCCGSCG 78
                                       56689****9 PP

>> zf-C2HE  C2HE / C2H2 / C2HC zinc-binding finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.2      0.92   2.7e+03      40      45 ..       3       8 ..       1      11 [. 0.79
   2 ?    3.7   4.9     0.029        85      38      52 ..      13      27 ..       4      28 .. 0.87
   3 ?    6.1   0.0     0.005        15      23      45 ..      37      59 ..      31      65 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.92
                            zf-C2HE 40 CtrCga 45
                                       C +C+a
  gene2634|gene2634|rna2634|rna2634  3 CSYCEA 8 
                                       ****95 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.029
                            zf-C2HE 38 LkCtrCganfgnkfp 52
                                        +C  C+++f+n+f+
  gene2634|gene2634|rna2634|rna2634 13 ITCADCHQTFCNTFK 27
                                       58***********97 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.005
                            zf-C2HE 23 slseeqskelilktpLkCtrCga 45
                                       +l+++ +k+++ ++p  C  Cg+
  gene2634|gene2634|rna2634|rna2634 37 HLKKNAHKRIMIDRPVVCELCGE 59
                                       5789999**************94 PP

>> zf-AN1  AN1-like Zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   7.8   0.00074       2.2       1      25 [.       3      24 ..       3      27 .. 0.87
   2 ?    3.1   0.1     0.037   1.1e+02      11      21 ..      49      59 ..      39      61 .. 0.77
   3 ?   -0.9   0.3      0.66     2e+03      14      20 ..      72      78 ..      65      80 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00074
                             zf-AN1  1 CsfksCkkkdflpfkCryCgkvFCl 25
                                       Cs+  C  + +  ++C +C+++FC 
  gene2634|gene2634|rna2634|rna2634  3 CSY--CEAHSH-LITCADCHQTFCN 24
                                       885..998887.79**********7 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.037
                             zf-AN1 11 flpfkCryCgk 21
                                         p+ C+ Cg+
  gene2634|gene2634|rna2634|rna2634 49 DRPVVCELCGE 59
                                       4689*****97 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 0.66
                             zf-AN1 14 fkCryCg 20
                                       + C +Cg
  gene2634|gene2634|rna2634|rna2634 72 VCCGSCG 78
                                       6788897 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       939  (0.0523733); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.47u 0.32s 00:00:00.79 Elapsed: 00:00:00.51
# Mc/sec: 548.12
//
Query:       gene2635|gene2635|rna2635|rna2635  [L=154]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
        1.3    9.1   3.1        2.6    8.1   3.1    1.5  1  PRIMA1      Proline-rich membrane anchor 1


Domain annotation for each model (and alignments):
>> PRIMA1  Proline-rich membrane anchor 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   3.1   0.00014       2.6      63      91 ..      40      69 ..      13      72 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00014
                             PRIMA1 63 iiiavvcaslvfl.lvlviicykaikrkpl 91
                                       iii v+   lvf+     ++cyk+i rk +
  gene2635|gene2635|rna2635|rna2635 40 IIIPVSIPILVFFkYYHFLVCYKTINRKNV 69
                                       7888888888877256789********975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       861  (0.0480228); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 1046.82
//
Query:       gene2636|gene2636|rna2636|rna2636  [L=615]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.5e-77  259.9   1.3    2.9e-77  259.7   0.1    1.7  2  Dynamin_M  Dynamin central region
    3.6e-47  160.5   0.1    6.7e-47  159.7   0.1    1.5  1  Dynamin_N  Dynamin family
    7.2e-21   74.1   1.5    2.2e-20   72.6   1.5    1.9  1  GED        Dynamin GTPase effector domain
    0.00018   21.6   0.0    0.00059   19.9   0.0    1.9  1  MMR_HSR1   50S ribosome-binding GTPase
  ------ inclusion threshold ------
       0.02   15.2   0.0      0.044   14.0   0.0    1.6  1  AAA_28     AAA domain
       0.11   12.1   0.6         15    5.0   0.0    2.5  2  FeoB_N     Ferrous iron transport protein B


Domain annotation for each model (and alignments):
>> Dynamin_M  Dynamin central region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.1       0.7   2.1e+03     225     253 ..      87     115 ..      73     122 .. 0.76
   2 !  259.7   0.1   9.8e-81   2.9e-77       1     278 [.     216     487 ..     216     493 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.7
                          Dynamin_M 225 lekelkrFpnLreeikevvedllreqeep 253
                                         e++++++ ++r+ei   + +l++++ + 
  gene2636|gene2636|rna2636|rna2636  87 SERTFTEYEHVRQEILAETARLIKNKHDV 115
                                        35599999999999999999999988765 PP

  == domain 2  score: 259.7 bits;  conditional E-value: 9.8e-81
                          Dynamin_M   1 vvdilenkvipLklGYvgVvnRsqkdInkkksieealkkEkaFFeshpayrkladkaGtpyLakkLnqiLvehIrk 76 
                                        vvd+l+++v++LklG++ VvnR+q+d++++ksi +al +E++FFe+h ayr+   ++Gt+yL +kL++iL+ehIr+
  gene2636|gene2636|rna2636|rna2636 216 VVDVLAGRVLSLKLGFIPVVNRGQNDVKNNKSIGDALADEQRFFETHRAYRRNRAYCGTAYLRTKLTSILYEHIRH 291
                                        79************************************************************************** PP

                          Dynamin_M  77 slPelkkkineklqklekeleelgeskpsdeektklllqlitkfkedfkklieGesevstkelsggarireiFnet 152
                                        +lPel++++n++++++++el+elg +       ++ +l+ i++++++f +l+ G++e   +el+ggar+++  ++ 
  gene2636|gene2636|rna2636|rna2636 292 TLPELQERVNTLIARTQAELDELGAFDL---TPKEHVLRTINEITKKFGDLLAGTAE-RGEELCGGARLSYTMHQS 363
                                        ************************9755...5789999****************944.69**************** PP

                          Dynamin_M 153 lekslekidpleelsdeeirtairnsrGrelplfvpekaFealvkkqikkleepalkcvelVyeelekivekleke 228
                                        +++ ++++++l+++ ++ irt++ n++G++++lf++e+aFe+l+++ i+ +++++lk+v  +++e+ ++++++   
  gene2636|gene2636|rna2636|rna2636 364 FAAFINSLNALHNMRNDHIRTVMLNASGSSSTLFFSERAFEMLARQSIALFKPHVLKLVSVIFTEMVRMMHTV--V 437
                                        ************************************************************************5..4 PP

                          Dynamin_M 229 lkrFpnLreeikevvedllreqeeptkemienliemelayintnhpdfig 278
                                         +rF +L+e+i+ ++  l+++++e+t  +++ lie+++ayi t hpdf++
  gene2636|gene2636|rna2636|rna2636 438 NTRFARLNEKISGALIALFKKNSEHTSMLVSALIEWNTAYISTRHPDFVR 487
                                        469*********************************************86 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  159.7   0.1   2.2e-50   6.7e-47       1     168 []      35     207 ..      35     207 .. 0.98

  Alignments for each domain:
  == domain 1  score: 159.7 bits;  conditional E-value: 2.2e-50
                                        EEEEEBTTTTHHHHHHHHHTS--S---SSS---S-EEEEECCT---CCS...SSEEEET-EB--CHHHHHHHHHHH CS
                          Dynamin_N   1 iavvGsqSsGKSSvlnaLlgedilprgpnptTrrplelqlgeeeeaseravkeelkekekkledfsevreeieket 76 
                                        i+v+G qS GKSSvl++++g d+lprg +++Trrpl+lql  ++e     + ++++  e+ ++++++vr+ei +et
  gene2636|gene2636|rna2636|rna2636  35 IVVIGGQSCGKSSVLENIVGTDFLPRGVGIVTRRPLILQLIYSKE-----EYVRFNHSERTFTEYEHVRQEILAET 105
                                        89**************************************99999.....67999999****************** PP

                                        HHHHTSSSS--SS-EEEEEEETTS-SEEEEE---B-SSSGTTS.........HHHHHHH.STTEEEEEEEETTS-C CS
                          Dynamin_N  77 ekiagankgiskkvillkilsllvkgltlvDlPGldsvnkrdq.........elvkeyi.kkadiilavtsanhdl 142
                                        +++ +++ ++s+++i+lk++s++v +ltlvDlPGl +v+++dq         e++k+yi +k++ii+av++a +d+
  gene2636|gene2636|rna2636|rna2636 106 ARLIKNKHDVSHVPITLKMYSPHVMTLTLVDLPGLVKVPTNDQpknivarveEICKRYIvNKNAIIIAVSAATSDI 181
                                        **************************************************************************** PP

                                        CC-CHHHHHHHHSTTBTTEEEEEE-C CS
                          Dynamin_N 143 snsealflarevdpkgkrtivvltkl 168
                                        ++s+al+la+ vdp  +rt++vltk+
  gene2636|gene2636|rna2636|rna2636 182 ASSDALQLAKTVDPGYERTLGVLTKV 207
                                        ************************96 PP

>> GED  Dynamin GTPase effector domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.6   1.5   7.4e-24   2.2e-20       2      90 ..     525     613 ..     524     615 .] 0.96

  Alignments for each domain:
  == domain 1  score: 72.6 bits;  conditional E-value: 7.4e-24
                                        XXXXTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHCCCCCHHHCCTTSGGGHHHHT---SCHCCCCHHHHH CS
                                GED   2 eeseveeirslvksYfnivrktiadqiPkaimhllvneakeslqkellakLykkedldeLLkEdeeiaekRkelkk 77 
                                        e  e++ i+slv sYf++ rk + dq+Pkaim+ lv ++ +++q++l++++y+ e +++L +Ed +++e R++lk+
  gene2636|gene2636|rna2636|rna2636 525 ESAEINLIKSLVASYFDVNRKILLDQVPKAIMCNLVMRSAQQMQEHLFREVYEMEGVEQLCEEDGSVKELRERLKR 600
                                        567999********************************************************************** PP

                                        HHHHHHHHCCCCC CS
                                GED  78 rlealkkAreils 90 
                                        +l+a+++A + + 
  gene2636|gene2636|rna2636|rna2636 601 NLKAMRQAHDLMC 613
                                        ********98775 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0     2e-07   0.00059       1      86 [.      34     177 ..      34     206 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 2e-07
                                        EEEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEE............................. CS
                           MMR_HSR1   1 evaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgke............................. 47 
                                        +++++G    GKS+++  ++g+         +Tr +   ++ ++++e                             
  gene2636|gene2636|rna2636|rna2636  34 QIVVIGGQSCGKSSVLENIVGTDFLPRGVGIVTRRPLILQLIYSKEEyvrfnhsertfteyehvrqeilaetarli 109
                                        589*********************99**********8888876655578888888999999999999********* PP

                                        ......................EEEEECGGCSS..HHHHHHHHHHHHHH.....HHCTSEEEEEEETT CS
                           MMR_HSR1  48 ......................ielvDtpGlie..gaseekglgkafla.....leeadlillvvdas 86 
                                                              ++lvD+pGl++  ++++ k++  ++++     + + ++i++ v+a+
  gene2636|gene2636|rna2636|rna2636 110 knkhdvshvpitlkmysphvmtLTLVDLPGLVKvpTNDQPKNIVARVEEickryIVNKNAIIIAVSAA 177
                                        ******************************98655444444444444432223322235555555544 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   1.5e-05     0.044       2      61 ..      35     103 ..      34     116 .. 0.61

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.5e-05
                             AAA_28   2 ivitGgestGKTtlleaLaar.......gypvv.pEaareileeklakgedalpwv.edllafaervle 61 
                                        iv++Gg+s+GK+++le++  +       g+++  p +   i++++   ++++++ +  +  ++++++l+
  gene2636|gene2636|rna2636|rna2636  35 IVVIGGQSCGKSSVLENIVGTdflprgvGIVTRrPLILQLIYSKEEYVRFNHSERTfTEYEHVRQEILA 103
                                        9***************99844444553344333444455555555555555555554555555555555 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.0    0.0052        15       2      23 ..      34      55 ..      33      58 .. 0.91
   2 ?    4.8   0.1    0.0063        19      47      89 ..     130     178 ..     115     248 .. 0.71

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.0052
                                       EEEEEESTTSSHHHHHHHHHTT CS
                             FeoB_N  2 tvalvGnpnvGkttlfnaltga 23
                                       +++++G + +Gk+++++++ g+
  gene2636|gene2636|rna2636|rna2636 34 QIVVIGGQSCGKSSVLENIVGT 55
                                       6899**************9986 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.0063
                                        EEEEEEE----SSS.......SSSSHHHHHHHHHHHCTSSSEEEEEEEGG CS
                             FeoB_N  47 keveivDlPGiYsl.......sayseeekvardflleeepdvvvnvvdat 89 
                                         ++++vDlPG  ++       + +++ e++ ++++++++  +++ v  at
  gene2636|gene2636|rna2636|rna2636 130 MTLTLVDLPGLVKVptndqpkNIVARVEEICKRYIVNKN-AIIIAVSAAT 178
                                        57899*******998888776667888999999999766.5777776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (615 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       836  (0.0466284); expected 358.6 (0.02)
Passed bias filter:                      597  (0.033298); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.57u 0.32s 00:00:00.88 Elapsed: 00:00:00.49
# Mc/sec: 3798.55
//
Query:       gene2637|gene2637|rna2637|rna2637  [L=535]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.3e-74  250.2   2.8    4.3e-74  249.8   2.8    1.1  1  TIP49            TIP49 P-loop domain
    5.2e-09   36.6   0.3    1.6e-05   25.4   0.0    2.3  2  AAA              ATPase family associated with various cellul
    2.9e-07   30.4   0.2    5.3e-05   23.0   0.0    2.2  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
      2e-05   25.1   0.0     0.0016   18.9   0.0    2.2  2  AAA_16           AAA ATPase domain
     0.0084   16.0   0.1      0.024   14.5   0.0    1.7  2  CPT              Chloramphenicol phosphotransferase-like prot
  ------ inclusion threshold ------
      0.012   15.1   0.0      0.021   14.4   0.0    1.3  1  AAA_7            P-loop containing dynein motor region
      0.022   14.8   0.0        3.9    7.5   0.0    2.3  2  AAA_14           AAA domain
      0.052   13.3   0.0      0.091   12.5   0.0    1.3  1  IstB_IS21        IstB-like ATP binding protein
      0.055   13.2   0.7        2.2    7.9   0.1    2.5  3  Sigma54_activat  Sigma-54 interaction domain
      0.059   13.4   0.0       0.14   12.1   0.0    1.6  1  Flexi_CP_N       Carlavirus coat
      0.061   13.3   0.1       0.39   10.7   0.0    2.0  2  AAA_5            AAA domain (dynein-related subfamily)
       0.15   12.6   0.0       0.27   11.8   0.0    1.4  1  ABC_tran         ABC transporter
       0.16   12.1   0.4        3.8    7.7   0.0    2.2  2  DUF150_C         RimP C-terminal SH3 domain


Domain annotation for each model (and alignments):
>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  249.8   2.8   3.1e-77   4.3e-74       3     316 ..      56     346 ..      54     368 .. 0.92

  Alignments for each domain:
  == domain 1  score: 249.8 bits;  conditional E-value: 3.1e-77
                                        XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                              TIP49   3 slhshikgLGldedgeaekeeeglvGqkkareaagvivelikekklaGravLlaGpsgtGktalaiaiskelgedv 78 
                                        s hshi++LGl++ +e+ +++++++Gqk+ar+aag+i+++++++k++GravLl Gps+ Gktala+a+ske++   
  gene2637|gene2637|rna2637|rna2637  56 SPHSHISSLGLEN-LEPIDTKNAILGQKNARKAAGIIIHMLRTNKMSGRAVLLLGPSSCGKTALAMAMSKEIS--S 128
                                        57*********76.699999****************************************************9..5 PP

                                        XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX-S-EEEEEEEEEEE...-SSS-..TTS--EEEEEE-SS-EE CS
                              TIP49  79 pfvalsgsevyslevkktevltqalrksigvrikeekevleGevveleveeaenplskekkikevkitlktakeek 154
                                         fv+lsg e+        e l+  +r++i v+++e k+v+eGe+++++++    +        + +i lk+ k+++
  gene2637|gene2637|rna2637|rna2637 129 NFVHLSGCELS------VEDLMMHVRRAIRVKLRELKKVYEGEITSIRLT----N-------LQFEIDLKSCKGST 187
                                        7******9973......578999************************984....2.......346799******** PP

                                        EEEE-HHHHHHHHHHT--TT-EEEEETTT--EEE-SSS-SS------S--------S---S----XXXXXXXXXXX CS
                              TIP49 155 klklgskiaeellkekvkegDviviekesGkvkklGrsearakefDiekdefvelPkGevekkkevvqevtLhdlD 230
                                        ++k+g++++e++  e+++ gDv++ie  +G +kk+Grse+   e+Die+ + v+lPk +v + k v+q ++Lhd+D
  gene2637|gene2637|rna2637|rna2637 188 TVKMGKSMYESVRDEELSIGDVVYIEPMCGIIKKVGRSENAF-EYDIERGKKVPLPKKDVLRTKVVTQILSLHDID 262
                                        **************************************9876.5******************************** PP

                                        XXXXXXXXXXXXX....XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                              TIP49 231 vanarpqdllslllqllkskkteiteklreeinkkvakyveegkaeivpGvlfiDevhmlDiecfsylnralesel 306
                                        va+  +++l   + +++ +k++ +   + +++n++v+ yve+g+ ++ pG+lfiDe h+l   +   + +a+e ++
  gene2637|gene2637|rna2637|rna2637 263 VAEDTSDQLKNTV-RHVLGKNA-VSIGTMHDTNEIVNAYVENGMGDVQPGILFIDECHLLSTHVLFQIIKAIEGDV 336
                                        *987665555555.66667665.8888999********************************************** PP

                                        XXXXXXXXXX CS
                              TIP49 307 aPivilatnr 316
                                        +P+v+latn 
  gene2637|gene2637|rna2637|rna2637 337 CPLVLLATNS 346
                                        *********6 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.0   1.1e-08   1.6e-05       1      53 [.     105     158 ..     105     169 .. 0.84
   2 !    9.2   0.1    0.0011       1.5      43     116 ..     289     351 ..     252     366 .. 0.67

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 1.1e-08
                                        EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCS.SSSTTHHHHHHHHHHHHH CS
                                AAA   1 vllyGppGtGKTllakavakelgvefleisgsell.skyvgesekkirelfkea 53 
                                        vll Gp  +GKT+la a+ ke++++f+ +sg el  ++++ +  + ir  ++e+
  gene2637|gene2637|rna2637|rna2637 105 VLLLGPSSCGKTALAMAMSKEISSNFVHLSGCELSvEDLMMHVRRAIRVKLREL 158
                                        79********************************96666666666666655555 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0011
                                        HHHHHHHHHHHHHTS....TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGG CS
                                AAA  43 ekkirelfkeakeka....kpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvivigatnrpdk 114
                                        +++++e++++  e+     +p ilfiDE + l ++            + q++++++g        +v++atn+ + 
  gene2637|gene2637|rna2637|rna2637 289 MHDTNEIVNAYVENGmgdvQPGILFIDECHLLSTHV-----------LFQIIKAIEGDVC----PLVLLATNSRQF 349
                                        344444554443333456789**********97666...........7777777777766....377777777665 PP

                                        ST CS
                                AAA 115 ld 116
                                        l+
  gene2637|gene2637|rna2637|rna2637 350 LE 351
                                        55 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.0   3.8e-08   5.3e-05       9      71 ..      78     140 ..      70     171 .. 0.89
   2 ?    5.1   0.0     0.012        17      86     110 ..     310     334 ..     283     349 .. 0.84

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 3.8e-08
                             RuvB_N   9 yigqekvkeklkifieaakkreealdhvllyGpPGlGkttlakiiakelgvklkitsgPvlek 71 
                                         +gq++ ++   i+i+  ++ + +   vll Gp   Gkt+la+ ++ke+ +++ + sg  l+ 
  gene2637|gene2637|rna2637|rna2637  78 ILGQKNARKAAGIIIHMLRTNKMSGRAVLLLGPSSCGKTALAMAMSKEISSNFVHLSGCELSV 140
                                        68***************************************************9999988765 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.012
                             RuvB_N  86 dvlfideihrlsraveevlysamed 110
                                         +lfide h ls++v   + +a+e 
  gene2637|gene2637|rna2637|rna2637 310 GILFIDECHLLSTHVLFQIIKAIEG 334
                                        59***********998888888875 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   1.2e-06    0.0016      16      51 ..      95     129 ..      89     167 .. 0.76
   2 ?    4.0   0.0     0.042        58      76     151 ..     247     324 ..     227     351 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.2e-06
                             AAA_16  16 lervrsgrpelvllsGesGvGKsslvrellralekd 51 
                                        l++ +  ++++vll G+s +GK++l+ +  ++++ +
  gene2637|gene2637|rna2637|rna2637  95 LRTNK-MSGRAVLLLGPSSCGKTALAMAMSKEISSN 129
                                        54444.4459********************999988 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.042
                             AAA_16  76 lareellrqlldeaesaeleawrekleealaavpelagaea......srllellkrllallsrderplvlvlDdlq 145
                                        l r ++++q+l+ ++ + +e+ +++l+ +++   ++ g+ a      ++ +e +++ ++    d +p +l++D+ +
  gene2637|gene2637|rna2637|rna2637 247 L-RTKVVTQILSLHDIDVAEDTSDQLKNTVR---HVLGKNAvsigtmHDTNEIVNAYVENGMGDVQPGILFIDECH 318
                                        5.55888888888888888888888888666...6666666777789***********666666999********* PP

                             AAA_16 146 wadeas 151
                                         + ++ 
  gene2637|gene2637|rna2637|rna2637 319 LLSTHV 324
                                        988765 PP

>> CPT  Chloramphenicol phosphotransferase-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   1.7e-05     0.024       1      43 [.     102     145 ..     102     207 .. 0.70
   2 ?   -1.8   0.0       1.7   2.3e+03      97     137 ..     269     311 ..     258     324 .. 0.58

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.7e-05
                                        --EEEEEE-TTSSHHHHHHHHHHHSSS-EEEE.EHHHHHHHS-G CS
                                CPT   1 ariilLnGgsssGKsslaralqevldepwlhl.gvDafvealpp 43 
                                        +r +lL G ss GK++la a+ + +   ++hl g    ve l+ 
  gene2637|gene2637|rna2637|rna2637 102 GRAVLLLGPSSCGKTALAMAMSKEISSNFVHLsGCELSVEDLMM 145
                                        6789***************************9345555565433 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.7
                                        H.HHHHHHHHHTTS-EEEEEEE--HH..HHHHHHHHHTSSSTTH CS
                                CPT  97 w.lvdllrrllsgldvllVGvrcple..vlerRelergdRepGl 137
                                        + l +++r++l g + + +G + +++  v +  e + gd +pG+
  gene2637|gene2637|rna2637|rna2637 269 DqLKNTVRHVL-GKNAVSIGTMHDTNeiVNAYVENGMGDVQPGI 311
                                        33677777777.44444455554444244455566666666664 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   1.5e-05     0.021      25      90 ..      94     159 ..      89     168 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.5e-05
                              AAA_7  25 llelllknkkpvllvGptGtGKtviikdllkkldkekylsltinfsaqtsanqlqdiiesklekrr 90 
                                        +l++   +++ vll Gp+ +GKt++++ + k+++++ +    +++s     +++++ i  kl   +
  gene2637|gene2637|rna2637|rna2637  94 MLRTNKMSGRAVLLLGPSSCGKTALAMAMSKEISSNFVHLSGCELSVEDLMMHVRRAIRVKLRELK 159
                                        5666667899************************99999999999999999999999999887654 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.0    0.0028       3.9       2      37 ..     102     134 ..     101     176 .. 0.78
   2 ?    5.1   0.0     0.015        21      50     122 ..     293     367 ..     268     369 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0028
                             AAA_14   2 rkilvitGaRrvGKTtllkqlikellvkkesilyin 37 
                                        ++++++ G+  +GKT l+  + ke     ++++ ++
  gene2637|gene2637|rna2637|rna2637 102 GRAVLLLGPSSCGKTALAMAMSKEIS---SNFVHLS 134
                                        5799*************988876655...5555554 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.015
                             AAA_14  50 ekllelilek.lkeekktylflDEiqevpe..wekalkslvdegknldvivtGSnskllskeiatslagrvaeiel 122
                                        +++ +++ e+ + + +  +lf+DE + +++  +++++k +  +   l +++t S + l  ++ a++l  r  +i++
  gene2637|gene2637|rna2637|rna2637 293 NEIVNAYVENgMGDVQPGILFIDECHLLSThvLFQIIKAIEGDVCPLVLLATNSRQFLERQD-AQDLFNRLFVIKM 367
                                        3456666666455568899*******997644788899988888888888888888777555.6777777777766 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   6.6e-05     0.091      48      93 ..     103     150 ..      81     162 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 6.6e-05
                          IstB_IS21  48 enivllGpsGvGKshlaialgveavraglsv..lfvrvedLveelkra 93 
                                         +++llGps  GK+ la+a+++e   + ++     ++vedL+ +++ra
  gene2637|gene2637|rna2637|rna2637 103 RAVLLLGPSSCGKTALAMAMSKEISSNFVHLsgCELSVEDLMMHVRRA 150
                                        5799****************9987765444311345677777777665 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.1    0.0016       2.2      12      55 ..      92     132 ..      78     146 .. 0.71
   2 ?    2.9   0.0     0.055        76      93     118 ..     308     333 ..     301     340 .. 0.85
   3 ?   -2.0   0.0       1.8   2.5e+03     147     167 ..     347     367 ..     335     368 .. 0.68

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0016
                                        HHHHHHHCTSSS-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEE CS
                    Sigma54_activat  12 leqikkvaktdlsvlitGesGtGKellaraiheaskrkekpfva 55 
                                        ++++++   +   vl++G s +GK+ la a+ ++ +   ++fv+
  gene2637|gene2637|rna2637|rna2637  92 IHMLRTNKMSGRAVLLLGPSSCGKTALAMAMSKEIS---SNFVH 132
                                        4555555566689****************9976544...44555 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.055
                                        TTSEEEEETGGGS-HHHHHHHHHHHH CS
                    Sigma54_activat  93 dgGtlfLDeigelplelQekLlrvlq 118
                                        + G+lf+De + l++++  +++++++
  gene2637|gene2637|rna2637|rna2637 308 QPGILFIDECHLLSTHVLFQIIKAIE 333
                                        67*************99888888876 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 1.8
                                        HHHHTTSS-HHHHHHHTSEEE CS
                    Sigma54_activat 147 eaveegkfredLyyrlnviei 167
                                        +++ e++  +dL+ rl vi++
  gene2637|gene2637|rna2637|rna2637 347 RQFLERQDAQDLFNRLFVIKM 367
                                        34445555689*****99976 PP

>> Flexi_CP_N  Carlavirus coat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0    0.0001      0.14       2      35 ..     155     188 ..     154     194 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.0001
                         Flexi_CP_N   2 LekLkellrkertasevtNpgfEiGRPaLkptde 35 
                                        L++Lk+++  e t++++tN  fEi+ ++ k ++ 
  gene2637|gene2637|rna2637|rna2637 155 LRELKKVYEGEITSIRLTNLQFEIDLKSCKGSTT 188
                                        789**********************998876655 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00028      0.39       2      31 ..     105     134 ..     104     168 .. 0.79
   2 ?    0.0   0.0      0.56   7.7e+02      64      90 ..     300     333 ..     267     360 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00028
                                        EEEE--SSSSHHHHHHHGGGGBS--EEEEE CS
                              AAA_5   2 vlLvGppGtgKselaerlaaalnreveyvq 31 
                                        vlL+Gp+ +gK+ la+ +++ + ++++   
  gene2637|gene2637|rna2637|rna2637 105 VLLLGPSSCGKTALAMAMSKEISSNFVHLS 134
                                        8*******************9988776555 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.56
                                        -.......G-SEEEEESGGG--HHHHHHHHHHHH CS
                              AAA_5  64 r.......egeilvlDEveraesevlnsLlslle 90 
                                                ++ il++DE + ++++vl   ++ +e
  gene2637|gene2637|rna2637|rna2637 300 VengmgdvQPGILFIDECHLLSTHVLFQIIKAIE 333
                                        233335778899*****99999999887777776 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00019      0.27      10      36 ..     101     127 ..      94     208 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00019
                                        TTSEEEEEESTTSSHHHHHHHHTTSS- CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ABC_tran  10 egekvaivGenGaGKStLlkllagllk 36 
                                         g+ v ++G++ +GK+ L+++++++ +
  gene2637|gene2637|rna2637|rna2637 101 SGRAVLLLGPSSCGKTALAMAMSKEIS 127
                                        58899******************9976 PP

>> DUF150_C  RimP C-terminal SH3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.0    0.0027       3.8      10      59 ..     146     192 ..     139     194 .. 0.87
   2 ?    2.4   0.1      0.13   1.7e+02      31      69 ..     217     254 ..     215     255 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0027
                           DUF150_C  10 flGelVkvklklpvegrkkftGkivevdeetitlevdgkkrkkettipla 59 
                                        ++ + ++vkl+   e +k ++G+i ++  +++ +e+d k+ k  tt+++ 
  gene2637|gene2637|rna2637|rna2637 146 HVRRAIRVKLR---ELKKVYEGEITSIRLTNLQFEIDLKSCKGSTTVKMG 192
                                        666889*****...9************************99999998876 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.13
                           DUF150_C  31 GkivevdeetitlevdgkkrkkettipladidkArlvpe 69 
                                        G+i+ v   +  +e d + r+k++ +p +d+ + ++v++
  gene2637|gene2637|rna2637|rna2637 217 GIIKKVGRSENAFEYDIE-RGKKVPLPKKDVLRTKVVTQ 254
                                        788888888888999999.8889**********999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (535 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       549  (0.0306208); expected 358.6 (0.02)
Passed bias filter:                      476  (0.0265492); expected 358.6 (0.02)
Passed Vit filter:                        79  (0.00440627); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.78u 0.35s 00:00:01.12 Elapsed: 00:00:00.56
# Mc/sec: 2899.00
//
Query:       gene2638|gene2638|rna2638|rna2638  [L=264]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.3e-10   40.9   0.4    2.2e-10   40.2   0.4    1.4  1  ubiquitin    Ubiquitin family
    6.1e-06   26.1   8.7    0.00063   19.6   2.3    2.7  2  STI1         STI1 domain
     0.0042   17.6   0.2     0.0081   16.6   0.2    1.5  1  UN_NPL4      Nuclear pore localisation protein NPL4
  ------ inclusion threshold ------
      0.019   15.0   0.0      0.034   14.1   0.0    1.5  1  HOIP-UBA     HOIP UBA domain pair
      0.073   13.1   1.1        0.3   11.1   0.3    2.3  2  Ubiquitin_4  Ubiquitin-like domain


Domain annotation for each model (and alignments):
>> ubiquitin  Ubiquitin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.2   0.4     6e-14   2.2e-10       2      70 ..       4      74 ..       3      76 .. 0.92

  Alignments for each domain:
  == domain 1  score: 40.2 bits;  conditional E-value: 6e-14
                                       EEEE.TTSEEEEEEEETTSBHHHHHHHHHHHHTSSGGGEEEEETTEEE.-TTSBHGGHTTSTTEEEEEEES CS
                          ubiquitin  2 tvkt.ldgkkitleveesdtveelKekiaekegipaeqqrLiysGkvL.edertleeygiqdgstlhlvlr 70
                                       t+++ ++++ ++l ++  +t+++lKeki+++ + pa+ + ++y+ + L +d++t++e++i++++++ l  r
  gene2638|gene2638|rna2638|rna2638  4 TITVqFQNNRMPLLMDIHETLLSLKEKISKRINTPASDISVYYNNRYLtDDKKTIKELKIENNAVVYLKKR 74
                                       6666689999********************************************************98655 PP

>> STI1  STI1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.5   0.00023      0.84       3      26 ..      85     108 ..      83     112 .. 0.84
   2 !   19.6   2.3   1.8e-07   0.00063       2      46 ..     114     158 ..     114     168 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00023
                               STI1   3 elfaklaanPetrellsDPefvak 26 
                                        ++ +++ +nP ++++l++Pe+++ 
  gene2638|gene2638|rna2638|rna2638  85 DATEQMLKNPMVKNMLKNPEVMKG 108
                                        56788999***********99984 PP

  == domain 2  score: 19.6 bits;  conditional E-value: 1.8e-07
                               STI1   2 pelfaklaanPetrellsDPefvakleeiqsNPqalqqymsDpri 46 
                                        p l +++ +nPe+r ++++P     +e+++ NP  ++q++++ +i
  gene2638|gene2638|rna2638|rna2638 114 PGLKKQINKNPELRMIMNNPNAIEEFEKLADNPEYMSQQLKNVDI 158
                                        667899**********************************99766 PP

>> UN_NPL4  Nuclear pore localisation protein NPL4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.2   2.3e-06    0.0081      22      79 ..      20      73 ..       2      74 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 2.3e-06
                                       TTSBHHHHHHHHHHHSS-STTT-EEESSTTCGCCCSSSSSSCCCTCH--TT-EEEEEX CS
                            UN_NPL4 22 ekstlktllekvaeelkfsengfslylernkttelvssssksvkevglkhGdmlyLkk 79
                                        ++tl  l+ek+ ++++ +  + s+y +      l ++++k++ke++++   ++yLkk
  gene2638|gene2638|rna2638|rna2638 20 IHETLLSLKEKISKRINTPASDISVYYNNRY---L-TDDKKTIKELKIENNAVVYLKK 73
                                       589***********************87554...4.4889****************97 PP

>> HOIP-UBA  HOIP UBA domain pair
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   9.6e-06     0.034     100     138 ..     224     262 ..     174     264 .] 0.86

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 9.6e-06
                           HOIP-UBA 100 RrkKvkelaslgffdreevveaLrqsgGdvegAlveLqr 138
                                         r+ ++e++++gf + +++ +aL + gGd++gA+  L +
  gene2638|gene2638|rna2638|rna2638 224 YRREINEIRKYGFDNINDIANALGKCGGDIDGAIDVLFK 262
                                        45679*****************************98865 PP

>> Ubiquitin_4  Ubiquitin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.42   1.5e+03       7      35 ..       8      36 ..       1      43 [. 0.74
   2 ?   11.1   0.3   8.5e-05       0.3      58      88 ..      44      74 ..      40      75 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.42
                        Ubiquitin_4  7 kldgeslevvvkqnatvkdLkkaierkve 35
                                       +++++ +++ ++   t+  Lk+ i + ++
  gene2638|gene2638|rna2638|rna2638  8 QFQNNRMPLLMDIHETLLSLKEKISKRIN 36
                                       46777888888888899999999998876 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 8.5e-05
                        Ubiquitin_4 58 LsfegekLkddkaklkeygirnkselsFvkr 88
                                        +++++ L+ddk+++ke+ i+n++ ++  kr
  gene2638|gene2638|rna2638|rna2638 44 VYYNNRYLTDDKKTIKELKIENNAVVYLKKR 74
                                       6899********************9987775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (264 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1141  (0.0636399); expected 358.6 (0.02)
Passed bias filter:                      644  (0.0359195); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.67u 0.35s 00:00:01.02 Elapsed: 00:00:00.58
# Mc/sec: 1381.41
//
Query:       gene2639|gene2639|rna2639|rna2639  [L=275]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.7e-05   24.0   0.0    2.8e-05   23.3   0.0    1.3  1  Rad21_Rec8  Conserved region of Rad21 / Rec8 like protein


Domain annotation for each model (and alignments):
>> Rad21_Rec8  Conserved region of Rad21 / Rec8 like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.0   1.6e-09   2.8e-05       3      48 ..     222     267 ..     220     272 .. 0.90

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 1.6e-09
                                        HHHTT----------HHHHHHHHHHHHHHHHTSEEEEESSTT--EE CS
                         Rad21_Rec8   3 kekdslsllpagktRkeAArlFyelLvLatkgvIkvkQeaPYgdIl 48 
                                        k+ +++ ++ +gk+R+e A  Fy lLv   kg ++v+Q + Yg+I 
  gene2639|gene2639|rna2639|rna2639 222 KDEFVFGEVVQGKPREEQADIFYGLLVNIEKGNVSVEQHECYGEIR 267
                                        5566778899**********************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (275 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       322  (0.0179597); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.31s 00:00:00.92 Elapsed: 00:00:00.54
# Mc/sec: 1530.57
//
Query:       gene264|gene264|rna264|rna264  [L=83]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.03   14.4   0.1      0.048   13.7   0.1    1.5  1  DUF3791   Protein of unknown function (DUF3791)


Domain annotation for each model (and alignments):
>> DUF3791  Protein of unknown function (DUF3791)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   2.7e-06     0.048      10      40 ..      18      48 ..       5      56 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.7e-06
                        DUF3791 10 yarklglsgkevykllkksgvldylidcYev 40
                                   ++++++ s k++y +l+++g ++yli++ e+
  gene264|gene264|rna264|rna264 18 VKDAFKRSIKNMYTYLNNYGSVEYLINMSEI 48
                                   78999*********************98776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (83 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       670  (0.0373696); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 611.97
//
Query:       gene2640|gene2640|rna2640|rna2640  [L=115]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       877  (0.0489152); expected 358.6 (0.02)
Passed bias filter:                      552  (0.0307881); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.31s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 767.41
//
Query:       gene2641|gene2641|rna2641|rna2641  [L=146]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0055   16.7   2.4     0.0071   16.3   2.4    1.2  1  DUF3439         Domain of unknown function (DUF3439)
  ------ inclusion threshold ------
       0.13   11.0   0.1       0.21   10.3   0.0    1.3  1  Glyco_transf_6  Glycosyltransferase family 6


Domain annotation for each model (and alignments):
>> DUF3439  Domain of unknown function (DUF3439)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   2.4   7.9e-07    0.0071      38      89 ..      21      73 ..       6      93 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 7.9e-07
                            DUF3439 38 kpvrsiicpttttttttttttmpttttlptttkmsmvkv.plvppeafgrvmn 89
                                        p  ++++p+t tttt tt+t+p   tl    +   v+  plvp      +m 
  gene2641|gene2641|rna2641|rna2641 21 TPPATLLVPATKTTTTLTTATLPIYQTLFFLKNGHCVQYgPLVPSTVVNDLMA 73
                                       67778999********************9888877776449999888777764 PP

>> Glyco_transf_6  Glycosyltransferase family 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   2.4e-05      0.21     122     180 ..      68     129 ..      45     137 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 2.4e-05
                                        ES-GGGS--.----TT..EEEEEEEBS--SSHHHHHHHHHHHHHHHHHHHHHHHSSEEEEEE CS
                     Glyco_transf_6 122 tddpakvPr.velkeg..rslkvlevksekrWqdismrrmelisefiakriqkevdylvcvd 180
                                        ++d  + P+ v+l+++  +  +++ +  e+ W di   rm ++s+        e d lvc +
  gene2641|gene2641|rna2641|rna2641  68 VNDLMACPVlVNLNKLyrHIYQLVGIVGEEGWTDIFKIRMGMLSKLLFVENFCEDDLLVCDE 129
                                        45555666436787763234689999*********************999999******965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       347  (0.0193541); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1060.88
//
Query:       gene2642|gene2642|rna2642|rna2642  [L=126]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-06   29.4   8.2      1e-06   29.4   8.2    1.6  2  Ctr       Ctr copper transporter family
  ------ inclusion threshold ------
      0.059   12.7   1.0       0.08   12.3   1.0    1.2  1  DUF4191   Domain of unknown function (DUF4191)
       0.11   11.1   2.3       0.13   10.9   2.3    1.0  1  H_PPase   Inorganic H+ pyrophosphatase


Domain annotation for each model (and alignments):
>> Ctr  Ctr copper transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.1      0.21   1.3e+03      26      50 ..      43      67 ..      21      78 .. 0.53
   2 !   29.4   8.2   1.7e-10     1e-06     108     145 ..      74     111 ..      51     113 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.21
                                Ctr 26 gsciglfllaifyeflralrerler 50
                                       +sci+ ++   ++e + +  e+l++
  gene2642|gene2642|rna2642|rna2642 43 VSCINELVTDYINEKMAVHAEKLKH 67
                                       3444444444444444444444443 PP

  == domain 2  score: 29.4 bits;  conditional E-value: 1.7e-10
                                Ctr 108 rallyvvqvllaYilMLlvMtyNvglflavilGagvGe 145
                                          ++ +v+v++ +i+M++ Mt+Nv++++ vilG ++G+
  gene2642|gene2642|rna2642|rna2642  74 IMAVNFVTVFINFIMMMVCMTFNVWVVCGVILGKLIGR 111
                                        4567789999**************************97 PP

>> DUF4191  Domain of unknown function (DUF4191)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   1.0   1.3e-05      0.08      20      64 ..      66     109 ..      50     118 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.3e-05
                            DUF4191  20 kedkkllwlllaaflvvvvvfvvlglllgslilllilgillgllv 64 
                                        k+ ++ ++++++ f+ v++ f+++++++ +  ++++ g++lg l+
  gene2642|gene2642|rna2642|rna2642  66 KHRRWKVYIMAVNFVTVFINFIMMMVCM-TFNVWVVCGVILGKLI 109
                                        6677788899999998888888888775.89999999**999886 PP

>> H_PPase  Inorganic H+ pyrophosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   2.3   2.2e-05      0.13     235     326 ..      26     112 ..       2     116 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 2.2e-05
                                        SHHHHHHHHHHHHHHHHHHHHHHHHHH.......HHSS--HHHHHHHHHHHHHHHHHHHHHHHHH-S-TTTTSHHH CS
                            H_PPase 235 aavklvllpllvaavgilasiigillvktkedasskkkeellkaLkkgllvsavlsvvlvallslllkeaaalklf 310
                                        ++++ +++ +l+a+++++ +i  +++  ++e+++++      ++Lk+  +   +++v +v++++ +++ +  +++ 
  gene2642|gene2642|rna2642|rna2642  26 THIQGLCFFVLLASLCLVSCINELVTDYINEKMAVH-----AEKLKHRRWKVYIMAVNFVTVFINFIMMMVCMTFN 96 
                                        367778888888888888877777766555554433.....44555555555555444444444444445678899 PP

                                        HHHHHHHHHHHHHHHH CS
                            H_PPase 311 lavlvGlvagllivll 326
                                        + v++G+++g li+ +
  gene2642|gene2642|rna2642|rna2642  97 VWVVCGVILGKLIGRV 112
                                        9999******999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1530  (0.0853366); expected 358.6 (0.02)
Passed bias filter:                      562  (0.0313459); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 892.47
//
Query:       gene2643|gene2643|rna2643|rna2643  [L=40]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (40 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       288  (0.0160634); expected 358.6 (0.02)
Passed bias filter:                      236  (0.013163); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.28s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 280.36
//
Query:       gene2644|gene2644|rna2644|rna2644  [L=886]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.6e-15   57.0   0.1    1.4e-14   54.6   0.1    2.4  1  NFACT-R_1  NFACT protein RNA binding domain
    1.1e-06   28.4   1.0    0.00047   20.0   0.0    3.9  3  NFACT-C    NFACT protein C-terminal domain
  ------ inclusion threshold ------
       0.25   11.3   3.0        2.2    8.3   0.9    2.8  2  RST        RCD1-SRO-TAF4 (RST) plant domain


Domain annotation for each model (and alignments):
>> NFACT-R_1  NFACT protein RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.6   0.1   2.4e-18   1.4e-14       4     109 .]     629     766 ..     627     766 .. 0.87

  Alignments for each domain:
  == domain 1  score: 54.6 bits;  conditional E-value: 2.4e-18
                          NFACT-R_1   4 wFk......ssdgylvimGkDkqeneelikkyleesdvwfhvdkessahvylr....................... 50 
                                        wF+      +s+g+lv++Gk++++ne l k+ +     +fh+d+++++ v +                        
  gene2644|gene2644|rna2644|rna2644 629 WFEkfnftiTSNGFLVLGGKNASQNEVLNKRKFLL---FFHADIKGGSAVTIDgtrinilgrcakhesssetsikr 701
                                        555555656*********************99888...*************************9998777666655 PP

                          NFACT-R_1  51 ..lsegeleeipeelleeaaqlakanSia.gnklssvdvvyvpasnlsktap....ldtGsvgfkg 109
                                           s++++  ++ee + +a q+++ +S+  + ++   d +yv+ +++sk+ap    l++G +++kg
  gene2644|gene2644|rna2644|rna2644 702 ivASSDNAYGLKEEDITDASQMCMVYSNCwKDRI-VSDSYYVNEDQVSKSAPsgefLSKGGFMVKG 766
                                        543333355********************88888.****************************986 PP

>> NFACT-C  NFACT protein C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0     0.058   3.5e+02      42      90 ..     276     329 ..     274     339 .. 0.68
   2 ?    2.6   0.1      0.02   1.2e+02      49      93 ..     364     440 ..     362     449 .. 0.72
   3 !   20.0   0.0   7.9e-08   0.00047       5      45 ..     842     882 ..     838     885 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.058
                            NFACT-C  42 KlqPGsvKkGkavkeilekflk....kkkkvdekeedkeklwpre.kelikalk 90 
                                        K+  G +++G+ +++i +  ++    ++k+ ++ ++d+++l+++  ke +k++ 
  gene2644|gene2644|rna2644|rna2644 276 KVRIGMARRGRKLNNISKNCITdplvSDKTAKHLSSDEKTLQTTAfKEYMKQID 329
                                        778899***********9999977763334444444444444333477777765 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.02
                            NFACT-C  49 KkGkavkeilekflk................................kkkkvdekeed..keklwprekelikalk 90 
                                        KkGka++ i+  f k                                k  kv++k +   +ek+++++ + i+++ 
  gene2644|gene2644|rna2644|rna2644 364 KKGKATNYICLDFHKidltgeflacyplnlrtfgsfndcvnsfyassK--KVQKKVNLskREKVREQQLKYIQEID 437
                                        999999999999999999999999999999999999999888887432..44443333115666666677777776 PP

                            NFACT-C  91 eee 93 
                                        +ee
  gene2644|gene2644|rna2644|rna2644 438 NEE 440
                                        554 PP

  == domain 3  score: 20.0 bits;  conditional E-value: 7.9e-08
                            NFACT-C   5 lslldsLvgtplpeDeileaipvcAPyaaLqkykYkvKlqP 45 
                                        +++   ++++p++ D i +a p+ + + +L++yk+ +K+ P
  gene2644|gene2644|rna2644|rna2644 842 QDMQMVFTASPAETDGISFAFPIAGSWDTLKTYKFAIKIVP 882
                                        5566679********************************99 PP

>> RST  RCD1-SRO-TAF4 (RST) plant domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0     0.045   2.7e+02      20      47 ..     452     479 ..     446     480 .. 0.86
   2 ?    8.3   0.9   0.00037       2.2      28      52 ..     582     606 ..     575     609 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.045
                                RST  20 lpkskmdllqkhYedlkkkkIsreefvr 47 
                                        +++++++ + k  +  k++kIs e f +
  gene2644|gene2644|rna2644|rna2644 452 MARDDINKIFKVLNYVKNNKISWELFFK 479
                                        57899999**************999987 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00037
                                RST  28 lqkhYedlkkkkIsreefvrklRsi 52 
                                         + +Y++ k+kkI+re+    l si
  gene2644|gene2644|rna2644|rna2644 582 MNYYYNQMKNKKIKREKIRNNLESI 606
                                        6779************988877766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (886 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1300  (0.0725082); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.77u 0.32s 00:00:01.09 Elapsed: 00:00:00.54
# Mc/sec: 4961.83
//
Query:       gene2645|gene2645|rna2645|rna2645  [L=104]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.057   13.1   0.0      0.069   12.8   0.0    1.1  1  CCDC85    CCDC85 family


Domain annotation for each model (and alignments):
>> CCDC85  CCDC85 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   3.8e-06     0.069     109     146 ..      42      79 ..      36      94 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.8e-06
                             CCDC85 109 valylqklkeLearqeellrenleLkelvllLdeekaa 146
                                        +++y  k+ +Le++ + l++ n+ Lk++v    +++  
  gene2645|gene2645|rna2645|rna2645  42 ISKYESKVCDLETKNNRLMKSNKVLKDVVAHYMNNQKI 79 
                                        67899**********************99766555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1089  (0.0607396); expected 358.6 (0.02)
Passed bias filter:                      612  (0.0341346); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 758.06
//
Query:       gene2646|gene2646|rna2646|rna2646  [L=36]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (36 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       229  (0.0127726); expected 358.6 (0.02)
Passed bias filter:                      146  (0.00814323); expected 358.6 (0.02)
Passed Vit filter:                         3  (0.000167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.32u 0.25s 00:00:00.57 Elapsed: 00:00:00.39
# Mc/sec: 280.05
//
Query:       gene2647|gene2647|rna2647|rna2647  [L=50]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (50 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       391  (0.0218082); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 365.94
//
Query:       gene2648|gene2648|rna2648|rna2648  [L=36]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (36 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       160  (0.00892409); expected 358.6 (0.02)
Passed bias filter:                      135  (0.0075297); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.33u 0.26s 00:00:00.59 Elapsed: 00:00:00.41
# Mc/sec: 264.78
//
Query:       gene2649|gene2649|rna2649|rna2649  [L=60]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (60 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       485  (0.0270511); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.42
# Mc/sec: 431.27
//
Query:       gene265|gene265|rna265|rna265  [L=164]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1022  (0.0570026); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1220.33
//
Query:       gene2650|gene2650|rna2650|rna2650  [L=26]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (26 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       255  (0.0142228); expected 358.6 (0.02)
Passed bias filter:                      155  (0.00864521); expected 358.6 (0.02)
Passed Vit filter:                         3  (0.000167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.28u 0.21s 00:00:00.49 Elapsed: 00:00:00.34
# Mc/sec: 225.98
//
Query:       gene2651|gene2651|rna2651|rna2651  [L=121]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       636  (0.0354733); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 881.92
//
Query:       gene2652|gene2652|rna2652|rna2652  [L=216]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.048   13.7   0.2      0.094   12.8   0.2    1.5  1  AAA_14    AAA domain
       0.18   11.7   0.0       0.94    9.5   0.0    2.0  2  PuR_N     Bacterial purine repressor, N-terminal


Domain annotation for each model (and alignments):
>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.2     1e-05     0.094      27      88 ..     152     211 ..     140     215 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1e-05
                             AAA_14  27 lvkkesilyinldderdkkladpekllelileklkeekktylflDEiqevpewekalkslvd 88 
                                          +  ++++ nld+ ++ ++++   l+++++++ ++ ++  +f+D i +++e++  +++ + 
  gene2652|gene2652|rna2652|rna2652 152 N-HCMNVFFNNLDHAQQLSIKQAPMLIRVCRDENYP-GMVSIFFDDIWMINEFFLEVQYAYL 211
                                        3.5568899999999999888766899999999777.99****************9999886 PP

>> PuR_N  Bacterial purine repressor, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0    0.0001      0.94      12      42 ..      56      91 ..      47      95 .. 0.85
   2 ?   -1.4   0.0      0.26   2.3e+03      39      57 ..     194     212 ..     189     214 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0001
                              PuR_N 12 iLlenPnklisltyfaerfeaA.....KSsiSeDla 42
                                       +Ll+ P+++i+l  f  r+e+A     K +iS D+ 
  gene2652|gene2652|rna2652|rna2652 56 RLLKVPSTTITLYIFLARYECAyiahnKMTISHDII 91
                                       6999****************9888888999**9985 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.26
                              PuR_N  39 eDlaiikealekeglGkle 57 
                                        +D+ +i+e + + ++++l+
  gene2652|gene2652|rna2652|rna2652 194 DDIWMINEFFLEVQYAYLN 212
                                        8999***999988887775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (216 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       604  (0.0336884); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 1377.24
//
Query:       gene2653|gene2653|rna2653|rna2653  [L=671]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (671 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1084  (0.0604607); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.63u 0.29s 00:00:00.92 Elapsed: 00:00:00.50
# Mc/sec: 4049.14
//
Query:       gene2654|gene2654|rna2654|rna2654  [L=965]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.9e-11   42.2  17.5    2.8e-10   40.5   7.2    3.7  4  RasGAP_C  RasGAP C-terminus
    1.2e-07   31.8   0.2    4.5e-07   30.0   0.2    2.0  1  CH        Calponin homology (CH) domain


Domain annotation for each model (and alignments):
>> RasGAP_C  RasGAP C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.7   0.5   0.00081       7.3      44      98 ..     213     267 ..     193     286 .. 0.74
   2 ?   -1.9   0.1      0.39   3.5e+03      65      87 ..     331     353 ..     319     385 .. 0.73
   3 ?   -3.5   0.0       1.2     1e+04      19      36 ..     671     688 ..     665     695 .. 0.79
   4 !   40.5   7.2   3.1e-14   2.8e-10       2     135 ..     774     892 ..     773     894 .. 0.93

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.00081
                           RasGAP_C  44 lrekrkeElesleetlktLseknnylesqlesYkayienvleqlkkkkgk..lpfsk 98 
                                        +  +  + l + ++  +++++ ++ l++q+es+++ i  v+ ++ kkk k  +  s+
  gene2654|gene2654|rna2654|rna2654 213 RLSRLVNNLCRYRQYREKVNSTKSILKEQIESLNNTIPIVIVEFIKKKLKerI--SR 267
                                        555566777788899999**************************999844221..22 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.39
                           RasGAP_C  65 knnylesqlesYkayienvleql 87 
                                         n  le+q+++    ie+vl++ 
  gene2654|gene2654|rna2654|rna2654 331 ENYDLETQIDKIMCTIEKVLDNT 353
                                        45679999999999999999987 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 1.2
                           RasGAP_C  19 gvisrennyqellneIak 36 
                                         v + e+++  ++++Ia 
  gene2654|gene2654|rna2654|rna2654 671 VVKDDEDRFAGVVEDIAD 688
                                        445899**********95 PP

  == domain 4  score: 40.5 bits;  conditional E-value: 3.1e-14
                           RasGAP_C   2 velkkkalenlkeLeelgvisrennyqellneIakdirnkgrlrekrkeElesleetlktLseknnylesqlesYk 77 
                                         elk ++ ++++ Le+ gv++ +n+y el+++  + i + + l  +r+ E+++ ++tl++L+++n++l+ ++++  
  gene2654|gene2654|rna2654|rna2654 774 DELKVSVCKRIEVLEKNGVLT-ANKYDELVQKMCERIEEMRILMSQRRMEIKINNKTLSNLKKQNKFLRVRMDTVT 848
                                        689*****************8.69**************************************************** PP

                           RasGAP_C  78 ayienvleqlkkkkgklpfskqyfkkrelkksgklpkfgsykysakqLeekgVLleie 135
                                        +y ++ le    k g+++ sk             ++  g+yky  k+L++k++L+ + 
  gene2654|gene2654|rna2654|rna2654 849 EYFQSLLESYFVK-GSGNCSK-------------KSVYGTYKYKFKHLQKKNILMAVH 892
                                        *********9888.4555555.............7999****************9876 PP

>> CH  Calponin homology (CH) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.0   0.2     5e-11   4.5e-07       6     108 ..      53     154 ..      49     155 .. 0.93

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 5e-11
                                        HHHHHHHHHHTTSTTSSTTSCHHHHHTTSHHHHHHHHHHSTTTSSGGGSTTTHHHHHHHHHHHHHHHHHHTTCHTT CS
                                 CH   6 ellrWinshleeagpkvkvedfeedlrDGvlLckLlnklapglvdkkklnksefkkleNinlaldvaekklgvpkv 81 
                                        ++++Wi + ++ + +++   +f+e lr G +L +L+n +  +  +  ++nk  +++ +N n ++d+++ ++++++ 
  gene2654|gene2654|rna2654|rna2654  53 QARDWISKNIHLEMSNN--LEFKEELRKGEILVDLANVISGKDMKAYRMNKLVYRHTDNHNAFIDFLR-EVKLNPC 125
                                        6789****999987776..8***********************999999999****************.******9 PP

                                        SS.-HHHHHTTSHH.HHHHHHHHHHHHHH CS
                                 CH  82 li.eaedlvegknk.svltllaqLfrafq 108
                                           ++ d ++  n  sv+ +l++L+++ q
  gene2654|gene2654|rna2654|rna2654 126 YHyGVLDAYDDVNIpSVIFCLHALSNHLQ 154
                                        999*******88888***********987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (965 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1368  (0.076301); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.88u 0.39s 00:00:01.27 Elapsed: 00:00:00.57
# Mc/sec: 5070.47
//
Query:       gene2655|gene2655|rna2655|rna2655  [L=598]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-15   56.9   7.8    4.1e-15   55.3   5.1    2.1  2  Nic96           Nup93/Nic96
  ------ inclusion threshold ------
        0.1   12.8   0.2       0.61   10.3   0.1    2.3  2  Phenyl_P_gamma  Phenylphosphate carboxylase gamma subunit (Ph


Domain annotation for each model (and alignments):
>> Nic96  Nup93/Nic96
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.3   5.1   4.6e-19   4.1e-15      38     227 ..     165     322 ..     120     346 .. 0.85
   2 !    2.1   0.0    0.0056        50     415     462 ..     438     493 ..     422     535 .. 0.74

  Alignments for each domain:
  == domain 1  score: 55.3 bits;  conditional E-value: 4.6e-19
                                        .....HHHHHHHHHHHHHHHHHHHHHCC....CTTSSSS-HHHHHHHHHHCTTBESSSCBSSTT--EETTEEHHHH CS
                              Nic96  38 elrkrivegarryLEkqfleyveeliaknpreaqlggvpsvvnkvraFvrvrlakknlaedaglldevngeplWal 113
                                          rk++  +  ++LEk+++++v++++ +n+++          n v+ +v++++      ++    ++ +g++l a 
  gene2655|gene2655|rna2655|rna2655 165 YKRKEVFSKEINFLEKSYYDHVQKVLLENNKD----------NSVEDYVKIKYP-----KEEYFIESYDGRYLFAE 225
                                        457778888889****************8888..........9*********93.....3444566889******* PP

                                        HHHHHTTT-HHHHHHHHHHTGGGS-TTTTHHHHHHHHCTTTTSS---TCCCHHHHHHHHHHTTT.-TTS-HHHHHH CS
                              Nic96 114 iyylLRaGdldeAlevvnenkeafrkldrsfaaylkayassedrrlpseleerlkleYnqrirnasedsDpykkav 189
                                        +y  +R+G +++Ale++++++  f++++ s+ + + a+ +++         ++l+ e +++i+n     D++k ++
  gene2655|gene2655|rna2655|rna2655 226 VYTYVRCGFVQKALELIDTFSVFFEQMAPSLRESIVAFFNNN-------YVNKLEFEKARSIKN-----DRFKLML 289
                                        *****************9999999999999999999998744.......557777774445555.....******* PP

                                        HHHHHT--CCC-S-T.TC--SHHHHHHHHHHH---TTS CS
                              Nic96 190 YkiigrcdlsrknlhqevaktieDwlWlqLslireddr 227
                                        Y+++  c +  ++++ ++ ++ eD+lW+++ ++r +++
  gene2655|gene2655|rna2655|rna2655 290 YQLV--CNV--EEAE-NLLENFEDFLWFRMLQARSVND 322
                                        ****..766..5677.99****************9887 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.0056
                                        HHHHHHHHHHHHHCT-HHHHHHHHHHTT-HHHHHHHHHHHHHHHHHC........S CS
                              Nic96 415 kkiieqaAreaeekgrledAilLydlageydkvlellnrlLsqvlst........q 462
                                        k+++ ++A  ++++   +  ++Ly l ++  +++ +ln+ L + +          +
  gene2655|gene2655|rna2655|rna2655 438 KTVVDRVAAILSKRNDRTRLLQLYYLFNDDVNIVGILNEYLIDHILRgkkelfnyT 493
                                        78999************************************999884443333330 PP

>> Phenyl_P_gamma  Phenylphosphate carboxylase gamma subunit (Phenyl_P_gamma)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1   6.8e-05      0.61       8      55 ..      69     115 ..      66     137 .. 0.84
   2 ?   -1.3   0.0      0.27   2.4e+03      25      57 ..     280     314 ..     269     321 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 6.8e-05
                     Phenyl_P_gamma   8 mdlaelaegkelelsvrtlndglkkytyqrvkvelsskldkfpdrlqv 55 
                                        +dl e+ +g  +e +vr  nd l k   +r+k+ +s+ + k+ ++ ++
  gene2655|gene2655|rna2655|rna2655  69 IDLREIINGY-FEHTVRMKNDILLKDGVRRAKAHISNLVKKLKEEDKM 115
                                        5888888885.89************************99998766554 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.27
                     Phenyl_P_gamma  25 tlndglkkytyqrv.kv.elsskldkfpdrlqvrl 57 
                                          nd +k   yq v  v e  + l++f d l  r+
  gene2655|gene2655|rna2655|rna2655 280 IKNDRFKLMLYQLVcNVeEAENLLENFEDFLWFRM 314
                                        45778888888876334256788999999998886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (598 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       915  (0.0510346); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.74u 0.37s 00:00:01.10 Elapsed: 00:00:00.59
# Mc/sec: 3068.15
//
Query:       gene2656|gene2656|rna2656|rna2656  [L=565]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.8e-18   64.1   0.1    2.6e-17   62.8   0.1    1.8  1  HGTP_anticodon  Anticodon binding domain
    1.4e-10   41.5   0.0    2.7e-10   40.5   0.0    1.7  1  tRNA-synt_2b    tRNA synthetase class II core domain (G, H, P


Domain annotation for each model (and alignments):
>> HGTP_anticodon  Anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.8   0.1   2.9e-21   2.6e-17      17      92 ..     476     551 ..     457     553 .. 0.91

  Alignments for each domain:
  == domain 1  score: 62.8 bits;  conditional E-value: 2.9e-21
                                        HHHHHHHHHHTTTSEEEEESSSSTHHHHHHHHHHTT-SEEEEE-HHHHHHTEEEEEETTTCEEEEEETTHHHHHHH CS
                     HGTP_anticodon  17 yakklaeeLraagirvelddsnesigkkireadllgipfavvvGekelekgtvtvrdrdtreqervsldelveklk 92 
                                          + + e+Lr  +irv ++++n sig++++ ad++g+p+ v+ + +++ +g vt+r+rd+++q+rvs++++ve++ 
  gene2656|gene2656|rna2656|rna2656 476 RLNNVFEQLRLRNIRVFVNERNVSIGRRYASADEIGVPYFVTFDSESASDGMVTIRERDSMDQIRVSIEKVVEIID 551
                                        55678899*****************************************************************986 PP

>> tRNA-synt_2b  tRNA synthetase class II core domain (G, H, P, S and T)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.5   0.0     3e-14   2.7e-10      12      86 ..     161     236 ..     154     438 .. 0.88

  Alignments for each domain:
  == domain 1  score: 40.5 bits;  conditional E-value: 3e-14
                                        EE-SSSHHHHHHHHHHHEE.EBGGSSEEEEEEEEEEBTTTSTBC.TTTB-SEEEEEEEEEEES.GGGHHHHHHHHH CS
                                        xxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx RF
                       tRNA-synt_2b  12 iLkPtneetfvelirdevl.rskrLPlklyqiqtkyRdEksdsr.GLlRvreFhqkdgyvfha.easlddslrdli 84 
                                        +L+P+  ++    +++    ++++ P+  + ++ ++R+E s  r GLlRvreF+q + + f++ ++++ d++ ++ 
  gene2656|gene2656|rna2656|rna2656 161 YLRPETAQGQFLNFKKVYElNNEKFPFGTFSVGKVFRNEIS-PRgGLLRVREFEQAELEFFVHpDEKVHDKYDEV- 234
                                        799999999888888753249999****************9.777******************668888888775. PP

                                        HH CS
                                        xx RF
                       tRNA-synt_2b  85 ka 86 
                                        k+
  gene2656|gene2656|rna2656|rna2656 235 KD 236
                                        44 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (565 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       436  (0.0243181); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.25s 00:00:00.81 Elapsed: 00:00:00.43
# Mc/sec: 3977.06
//
Query:       gene2657|gene2657|rna2657|rna2657  [L=94]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.057   12.8   0.0       0.06   12.8   0.0    1.0  1  DUF2034       Protein of unknown function (DUF2034)
       0.09   12.6   0.1       0.11   12.3   0.1    1.1  1  Pertussis_S1  Pertussis toxin, subunit 1


Domain annotation for each model (and alignments):
>> DUF2034  Protein of unknown function (DUF2034)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   6.7e-06      0.06     110     179 ..      24      89 ..       7      94 .] 0.75

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6.7e-06
                            DUF2034 110 fsshkakkkrkstlmilvspkllTksalklldklnipliylkisllkladgllsldlwnggalelvyena 179
                                        f+ ++    +++ l  l s  +   s+ ++++++++ +i +kis  +     ++    n+g+l + +e++
  gene2657|gene2657|rna2657|rna2657  24 FNVSH----DENVLENLTSESEQSCSTSNEINNSTVSFILCKISKTENGSKNNNTTGLNNGDLYMSFEEK 89 
                                        44333....6788889999999999******************875544447777888888888877765 PP

>> Pertussis_S1  Pertussis toxin, subunit 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   1.2e-05      0.11       7      55 ..       6      57 ..       2      67 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.2e-05
                                       EEEESS-HHHH..HHH-EE-SSSB--HHHHHCTGCCC.CCCESCCCCCCCCG CS
                       Pertussis_S1  7 yrvdlrsPeev..fenGfsalGdvdnvlehllGrsyf.vsssesatvairss 55
                                        r d +  e+v  f +Gf  +   +nvle l+  s +  s+s+    ++ s+
  gene2657|gene2657|rna2657|rna2657  6 LRNDRKVVEDVkeFSDGFFNVSHDENVLENLTSESEQsCSTSNEINNSTVSF 57
                                       588999999998899*****************88876357787766666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       892  (0.0497518); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 650.18
//
Query:       gene2658|gene2658|rna2658|rna2658  [L=120]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       517  (0.028836); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 777.13
//
Query:       gene2659|gene2659|rna2659|rna2659  [L=767]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.6e-73  247.6   0.2    2.5e-73  246.9   0.2    1.3  1  Piwi           Piwi domain
    6.6e-12   45.4   0.1    1.1e-11   44.6   0.1    1.4  1  PAZ            PAZ domain
      1e-09   37.9   0.4    3.3e-09   36.3   0.4    1.9  1  ArgoL1         Argonaute linker 1 domain
    4.4e-08   33.8   0.0    1.3e-07   32.3   0.0    1.8  1  ArgoN          N-terminal domain of argonaute
    2.4e-06   27.7   0.2    1.3e-05   25.4   0.0    2.4  2  ArgoMid        Mid domain of argonaute
  ------ inclusion threshold ------
      0.096   13.2   1.2       0.27   11.7   0.4    2.1  2  Baculo_LEF-11  Baculovirus LEF-11 protein


Domain annotation for each model (and alignments):
>> Piwi  Piwi domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  246.9   0.2   8.5e-77   2.5e-73       1     301 [.     451     748 ..     451     749 .. 0.93

  Alignments for each domain:
  == domain 1  score: 246.9 bits;  conditional E-value: 8.5e-77
                                        EEEEEECSSGHHCHHHHHHHHHHTCCCCEEEEEHHHHCTCCHHHHHHHHHHHHHHHHTT-BS-EEESSSTTSSE.. CS
                               Piwi   1 lilvilpekkkdkyheikkyletdlgiisqcillktilkrqlkkqtltnvllkinvKlGgknvliveikleldvsp 76 
                                        l++vil++k++  y+e+k++ + ++ +++qc++ ++++k+    + + n++lkin KlGg n + v+i      ++
  gene2659|gene2659|rna2659|rna2659 451 LVMVILQDKSSFVYQEVKRIADLNCSVVTQCVRKQNVEKFRD-GSFCGNIALKINTKLGGVN-FTVDIAQ----DE 520
                                        58**************************************66.******************6.5566666....56 PP

                                        ..EEEEEEEEEECCCSCCCEEEEEEEEEETSSEEEEEEEEESSCCCCHHHHHHHHHHHHHHHHHHTTTT-TTSEEE CS
                               Piwi  77 tliiGidishgtagtvdnpsvaavvasldkensrylaevstqassqelleklkeiikellrefkksskkkkperii 152
                                         +++G+d++h+  g+ +  s+aavv sldk+ sry  + ++q ++q+++e+lk+i  + l+ f++ + k  p++ii
  gene2659|gene2659|rna2659|rna2659 521 LIVFGADVTHPGFGDLSCNSIAAVVSSLDKHFSRYHTSLRMQPKRQDIVEDLKNITVDHLKRFRTCTTK-VPRKII 595
                                        79*************************************************************999998.****** PP

                                        EEESS....S..S-HHHHHHHHHHHHHHHHHCTTTEEEEEEEECSCS--EEESESTC.........CCEETTTCEE CS
                               Piwi 153 vyRdGvseGqfkqvlnsEvkelkealkklkeqyqpkltvivvqkrhhtrfFasdkae.........ksqnippGtv 219
                                        ++RdG +++ +++v+  E+++++ea+  l e+y+pklt++vvqkrh+ rf   d ++            n+ pGt+
  gene2659|gene2659|rna2659|rna2659 596 FFRDGIGDSLMQNVYFREIEAIREACATLHEGYKPKLTFVVVQKRHSVRFKG-DGRDeivkdkrrgPTCNPMPGTL 670
                                        *************************************************755.555569***9999999******* PP

                                        ETTEEEEEEEECCEEECCCCEEEEEEEEEEEEEEES..S-CCHHHHHHHHHCTGGTTTTSS-SS-HHHHHHHHHHH CS
                               Piwi 220 vdkkitlpeekdfylcshaglqgtvkPtkytvlvdeaklsadelqsltyklchmyqrstrsvsiPapvyyAhklAk 295
                                        +d+++t  e++dfy++sh  lqgt  P+ky+vlvde++++   +   +y++ch++ r+t+svs+++p+yyAh++A+
  gene2659|gene2659|rna2659|rna2659 671 IDSVGT--EYNDFYMISHFALQGTPCPIKYHVLVDENNIPN--FPLYIYNMCHVFTRATKSVSVVPPIYYAHLAAA 742
                                        ***997..789*************************65554..4446***************************** PP

                                        HHHTCC CS
                               Piwi 296 rvrnnl 301
                                        r+++++
  gene2659|gene2659|rna2659|rna2659 743 RAKCYV 748
                                        *99876 PP

>> PAZ  PAZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.6   0.1   3.8e-15   1.1e-11      19     136 ..     212     313 ..     188     314 .. 0.87

  Alignments for each domain:
  == domain 1  score: 44.6 bits;  conditional E-value: 3.8e-15
                                        ---HHCCCCTTBEEEETTTTS-CEEEEEEEESS--TTSEECCTTCT..CECCHHHHCCT---ST-TT--EEEEEES CS
                                PAZ  19 drkkaaealkgliVmtwynnrnktyyvadittdlapsstFpdkdkeneitfaeYfkkkYnieikdqdqplldvdkk 94 
                                        +++   + lk ++ +t ++++n +++  d+t++ a ++ F d+  +  +++aeYf k+Y   +++  +p+++v+k 
  gene2659|gene2659|rna2659|rna2659 212 KFRALGKFLKSVRLTTVHRKNNPKFKCVDVTDKGACDTLFGDD--N--VSVAEYFAKQYR-PLQHPYLPCVVVKK- 281
                                        56777789999*******9989******************999..6..9**********9.9999**********. PP

                                        -SS----EEEEE-CCCCEEESSBCCCCCTCCCHHHHCCCH.. CS
                                PAZ  95 tesehssqkqiLvpElcdihpisasqrykkkllpsilqrlnl 136
                                             ++ ++++++E+++i    ++q+y+kkl  s++q++ +
  gene2659|gene2659|rna2659|rna2659 282 -----KDGNIFFPIEVVKI---LEGQKYTKKL--SDFQTADV 313
                                        .....899***********...**********..****9875 PP

>> ArgoL1  Argonaute linker 1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.3   0.4   1.1e-12   3.3e-09       4      52 .]     131     183 ..     129     183 .. 0.89

  Alignments for each domain:
  == domain 1  score: 36.3 bits;  conditional E-value: 1.1e-12
                             ArgoL1   4 rsFfspp.....skqrvdLggggleawrGfyqSvRptqggLllNvDvsntaFyk 52 
                                        r Ff ++      ++r+ +  gg+e+w G+ q v+  +g+L+lNvDv+ t+Fy+
  gene2659|gene2659|rna2659|rna2659 131 RTFFVDGrkcvsAGDRSHV-TGGIELWNGVTQRVKFFNGRLFLNVDVAFTPFYE 183
                                        8899999888886677788.55*******************************6 PP

>> ArgoN  N-terminal domain of argonaute
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.3   0.0   4.5e-11   1.3e-07       3     107 ..      19     105 ..      18     129 .. 0.71

  Alignments for each domain:
  == domain 1  score: 32.3 bits;  conditional E-value: 4.5e-11
                              ArgoN   3 iklraNyFkvtslpdktlyhYdveitkka.krvglrriiellleeykkselagkkpayDgrknlysakkLp...ke 74 
                                        + l+aN  +++ +p+ tl+hY v i++   +r++   +++++++  +++++   +  yDg++ l+++k+L+     
  gene2659|gene2659|rna2659|rna2659  19 VPLTANLLELK-VPSLTLHHYAVLIEPVIaRRLN-PIVVSAIIQR-HAQQFDQISYGYDGNTILVTSKQLQgdiV- 90 
                                        78*********.9*********999866668899.7777777753.34667777788*************33221. PP

                              ArgoN  75 fedlpaaeesakkepsekrrrksrtfkvtikfa 107
                                            +       +e+         +  vtikf 
  gene2659|gene2659|rna2659|rna2659  91 ----D-------VEKV-----G--STDVTIKFE 105
                                        ....2.......1111.....1..334444444 PP

>> ArgoMid  Mid domain of argonaute
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       2.2   6.5e+03      33      59 ..     325     351 ..     321     356 .. 0.71
   2 !   25.4   0.0   4.3e-09   1.3e-05       2      76 ..     376     444 ..     375     448 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 2.2
                            ArgoMid  33 rkvkenkledfikqlvkiskdvgisle 59 
                                         ++ en+++++  +   ++++++++++
  gene2659|gene2659|rna2659|rna2659 325 FNCLENRIRSMHVTSNDVLTNINVQVS 351
                                        467777788877777777777777775 PP

  == domain 2  score: 25.4 bits;  conditional E-value: 4.3e-09
                            ArgoMid   2 prnGsWdmrgkqFlepkakikkWAilcfasqrkvkenkledfikqlvkiskdvgisleekpeirkyadderevet 76 
                                        p+ GsW++r+++   + + +  WA+l+ a++   + + +++ i +lvki++d+g+++ +  e+rk + +  ++e+
  gene2659|gene2659|rna2659|rna2659 376 PSRGSWNLRNQKVVRG-VAVVRWAVLVLADE---SVSFVNRQIPNLVKICNDMGVRMANPLEVRKVTLE--NIEE 444
                                        99**************.**********9943...3345777788899*********9988887776554..5555 PP

>> Baculo_LEF-11  Baculovirus LEF-11 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       2.5   7.4e+03      25      56 ..     201     233 ..     189     261 .. 0.73
   2 ?   11.7   0.4   9.2e-05      0.27      12      71 ..     412     473 ..     402     490 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 2.5
                      Baculo_LEF-11  25 edvtahhldtdsFetirefire.hadvivrkns 56 
                                        e+v +  +d  +F ++ +f+++ + + + rkn 
  gene2659|gene2659|rna2659|rna2659 201 EHVDLRRVDAGKFRALGKFLKSvRLTTVHRKNN 233
                                        567777888888999999998867777766654 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 9.2e-05
                      Baculo_LEF-11  12 revintlkstndtedvtahhldtds..FetirefirehadvivrknskrkavadHlkRlarL 71 
                                        r++ n  k  nd+ + +a+ l++ +   e i e+i+ ++ v+v+ + k  +v +  kR+a L
  gene2659|gene2659|rna2659|rna2659 412 RQIPNLVKICNDMGVRMANPLEVRKvtLENIEEHIKGKELVMVILQDKSSFVYQEVKRIADL 473
                                        6677999***************998889*******************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (767 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       555  (0.0309554); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.71u 0.27s 00:00:00.98 Elapsed: 00:00:00.46
# Mc/sec: 4978.63
//
Query:       gene266|gene266|rna266|rna266  [L=197]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      1e-33  116.7   3.7    1.2e-33  116.5   3.7    1.1  1  Sec62      Translocation protein Sec62
  ------ inclusion threshold ------
      0.013   15.6   0.2      0.014   15.5   0.2    1.2  1  GWT1       GWT1
      0.014   14.2   0.7      0.016   14.0   0.7    1.1  1  DUF2207    Predicted membrane protein (DUF2207)
       0.13   12.0   2.2       0.18   11.6   2.2    1.2  1  Claudin_2  PMP-22/EMP/MP20/Claudin tight junction
       0.23   11.4   5.9       0.33   10.9   5.9    1.2  1  Claudin_3  Tight junction protein, Claudin-like
       0.48   10.3   3.0        9.7    6.1   0.2    2.3  2  ODV-E18    Occlusion-derived virus envelope protein ODV-E18


Domain annotation for each model (and alignments):
>> Sec62  Translocation protein Sec62
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.5   3.7     4e-37   1.2e-33      77     207 ..      68     195 ..      16     197 .] 0.87

  Alignments for each domain:
  == domain 1  score: 116.5 bits;  conditional E-value: 4e-37
                          Sec62  77 kkkkvkleieeeqefvddnevYvWiYepkqlktlligllvvvailavvlFPLWPaelrkgvyYLSiaalgllglilalai 156
                                    +k++  ++i+  ++f ++++ Y+W+ ep++ ++l++++++++ +l++v++ +WP+ +r    Y+   ++++++++ +la+
  gene266|gene266|rna266|rna266  68 SKNNKDVTISLTKKF-NKRDSYIWVVEPTNHMHLILSVVLIAFVLILVMYQVWPSRIRSKMTYVFYPIFAFFIFLGILAV 146
                                    466667788888899.99************************************************************** PP

                          Sec62 157 vRlilflivllvtkgklhlWlfPnlfeDvGfldSFrPlYeyeekdkkkkkk 207
                                    +Rli+f i+++  +++  +WlfPnlf+DvGf+dSF P+++y+ k++k kkk
  gene266|gene266|rna266|rna266 147 LRLIVFAITFFSHPPG--IWLFPNLFADVGFVDSFLPVWSYHGKETKPKKK 195
                                    ****************..************************544333333 PP

>> GWT1  GWT1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   0.2   4.7e-06     0.014      39     108 ..      80     151 ..      11     196 .. 0.66

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 4.7e-06
                           GWT1  39 kkkkkkkesketlkllikl.lllsilllllllllelyvefvSRrlaNlpYvlwvvalnltllllflliel.l 108
                                    kk +k+ ++  +++ + ++ l+ls++l++++l+l +y    SR+   ++Yv++ +   +++l ++ ++ l +
  gene266|gene266|rna266|rna266  80 KKFNKRDSYIWVVEPTNHMhLILSVVLIAFVLILVMYQVWPSRIRSKMTYVFYPIFAFFIFLGILAVLRLiV 151
                                    33334444444444444331566666666667777777779************6655555555555555433 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.7   5.3e-06     0.016     324     443 ..      28     189 ..       2     195 .. 0.63

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.3e-06
                        DUF2207 324 dlLfdkseegkslkeikkyakkskkkakkfkkalkkwksavkk................kergyfdkkgkkklkklsalg 387
                                    ++++         ++  +y+kk++ + k +++ ++ + +  ++                +  + f+k+  ++++ +   +
  gene266|gene266|rna266|rna266  28 NMFK--------GEDAYEYLKKKNLDEKVINDLFNTLIE--EEiivrglvsknnkdvtiSLTKKFNKR-DSYIWVVEPTN 96 
                                    4444........566777888888777777777777666..334356677777777776666677777.89999999999 PP

                        DUF2207 388 lgliilglilillallllvll...................lvfllilllillliaiivlllfsr................ 432
                                     + +il+++li ++l+l+ +                    +      +++l+++a++ l++f++                
  gene266|gene266|rna266|rna266  97 HMHLILSVVLIAFVLILVMYQvwpsrirskmtyvfypifaF------FIFLGILAVLRLIVFAItffshppgiwlfpnlf 170
                                    99999999998888777666589******999985554331......333333333333333333334456666666666 PP

                        DUF2207 433 ........llgrrteeGae 443
                                            +l+ ++ +G+e
  gene266|gene266|rna266|rna266 171 advgfvdsFLPVWSYHGKE 189
                                    6666666666666666666 PP

>> Claudin_2  PMP-22/EMP/MP20/Claudin tight junction
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   2.2   5.9e-05      0.18      93     145 ..      97     154 ..      66     159 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 5.9e-05
                      Claudin_2  93 qvlliLslvlivlavvlgllallkqsv.....lllkaagilfllagvlgllavvvfie 145
                                     + liLs+vli  +++l++  ++ ++      +++   +  f+  g+l +l ++vf++
  gene266|gene266|rna266|rna266  97 HMHLILSVVLIAFVLILVMYQVWPSRIrskmtYVFYPIFAFFIFLGILAVLRLIVFAI 154
                                    56799**************999999888999999**********************86 PP

>> Claudin_3  Tight junction protein, Claudin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   5.9   0.00011      0.33      64     119 ..     100     156 ..      86     160 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00011
                      Claudin_3  64 lalflvvi.liyivivrkvkkngysksvrklffliallslliviltviaviliavnv 119
                                    l+l++v+i +++i+++++v  +   +++ + f+ i  ++++  il v+ +i++a+ +
  gene266|gene266|rna266|rna266 100 LILSVVLIaFVLILVMYQVWPSRIRSKMTYVFYPIFAFFIFLGILAVLRLIVFAITF 156
                                    4556666658999999**************************************987 PP

>> ODV-E18  Occlusion-derived virus envelope protein ODV-E18
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.2    0.0032       9.7      18      44 ..      88     114 ..      75     122 .. 0.72
   2 ?    4.4   0.2     0.011        33      26      45 ..     139     158 ..     135     162 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0032
                        ODV-E18  18 rlarlePsllltilvvlviiillvllv 44 
                                    ++  +eP+  + ++  +v+i+++++lv
  gene266|gene266|rna266|rna266  88 YIWVVEPTNHMHLILSVVLIAFVLILV 114
                                    677788887777666666666666655 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.011
                        ODV-E18  26 llltilvvlviiillvllvq 45 
                                    ++l il+vl +i++ + ++ 
  gene266|gene266|rna266|rna266 139 IFLGILAVLRLIVFAITFFS 158
                                    799***********999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1510  (0.0842211); expected 358.6 (0.02)
Passed bias filter:                      659  (0.0367561); expected 358.6 (0.02)
Passed Vit filter:                        85  (0.00474092); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 1368.14
//
Query:       gene2660|gene2660|rna2660|rna2660  [L=69]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (69 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       352  (0.019633); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.31u 0.23s 00:00:00.54 Elapsed: 00:00:00.36
# Mc/sec: 578.02
//
Query:       gene2661|gene2661|rna2661|rna2661  [L=157]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       316  (0.0176251); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1194.42
//
Query:       gene2662|gene2662|rna2662|rna2662  [L=59]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       488  (0.0272185); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.31u 0.26s 00:00:00.57 Elapsed: 00:00:00.38
# Mc/sec: 465.17
//
Query:       gene2663|gene2663|rna2663|rna2663  [L=104]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       433  (0.0241508); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.46
# Mc/sec: 684.85
//
Query:       gene2664|gene2664|rna2664|rna2664  [L=143]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.6e-12   46.3   0.0    6.5e-12   45.8   0.0    1.2  1  RNA_pol_A_bac  RNA polymerase Rpb3/RpoA insert domain
  ------ inclusion threshold ------
      0.017   14.5   0.0       0.02   14.3   0.0    1.2  1  RNA_pol_L      RNA polymerase Rpb3/Rpb11 dimerisation domain


Domain annotation for each model (and alignments):
>> RNA_pol_A_bac  RNA polymerase Rpb3/RpoA insert domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.8   0.0   7.3e-16   6.5e-12      15     111 ..       2      92 ..       1      93 [. 0.90

  Alignments for each domain:
  == domain 1  score: 45.8 bits;  conditional E-value: 7.3e-16
                                        HHCHHHCSTCBSSCHHHHHHHHCTT-ETSSSSTTCSEEEEEEEEESSEC..EEGGGCBESSSSCEESSTTSEEEEE CS
                      RNA_pol_A_bac  15 vaHrlgliplvsedvleillnlkelveeeeegeeeksvelkLnvkgpge..vtagdlkledadveivnpdilIakL 88 
                                        + Hrl+lipl     +  l+  +e+  +++ +++ +sv+++Ln+  ++   v a++l +  ++v + + + lI+k+
  gene2664|gene2664|rna2664|rna2664   2 LVHRLSLIPLPI---TT-LKRKEEC--TCNVSCPACSVTFSLNAVSNEGmsVNASHLFS--DAVDTTRLKGLICKM 69 
                                        78********94...44.5568888..8***************88777679******97..89************* PP

                                        ETT-EEEEEEEEEEESSEECTTT CS
                      RNA_pol_A_bac  89 rkgqeleleakvkkGiGkehakf 111
                                         ++q+++++a +++G++kehakf
  gene2664|gene2664|rna2664|rna2664  70 GEKQSVKMSALARTGTAKEHAKF 92 
                                        **********************9 PP

>> RNA_pol_L  RNA polymerase Rpb3/Rpb11 dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   2.2e-06      0.02      30      68 ..      79     130 ..      20     131 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.2e-06
                                        x..............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          RNA_pol_L  30 a..............pvvkvntdkdklilevetdgslkPeealkeAlkiLkek 68 
                                        a               v+ v+  +dk+ +ev  d + kP ++l +Al++Lk+k
  gene2664|gene2664|rna2664|rna2664  79 AlartgtakehakfcVVTVVRIGEDKIEFEVL-DEVGKPVDVLVMALRVLKDK 130
                                        04444444444444423335578999******.9999**************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       694  (0.0387082); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.28s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1012.47
//
Query:       gene2665|gene2665|rna2665|rna2665  [L=477]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.042   13.9   0.3      0.096   12.7   0.3    1.6  1  Bcr-Abl_Oligo   Bcr-Abl oncoprotein oligomerisation domain
      0.056   13.5   0.2      0.096   12.7   0.2    1.3  1  Halogen_Hydrol  5-bromo-4-chloroindolyl phosphate hydrolysis 
       0.16   12.1   0.7       0.63   10.2   0.1    2.1  2  DUF2845         Protein of unknown function (DUF2845)


Domain annotation for each model (and alignments):
>> Bcr-Abl_Oligo  Bcr-Abl oncoprotein oligomerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.3   1.6e-05     0.096      13      68 ..     339     395 ..     329     398 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.6e-05
                      Bcr-Abl_Oligo  13 fPeeevPkmeLdsvedieqeLerCkaslrrLekelneekfkviyLqtll.akerksy 68 
                                         P+  v +++   +++ ++ L++ k +l+ L+ + + ek   +y q  l  + r+sy
  gene2665|gene2665|rna2665|rna2665 339 LPDITVHNLQAMEMPAFKRKLKKYKRHLQDLKDVFTGEKNIEVYKQIFLmLRTRRSY 395
                                        688888889999999*******************************8652799**99 PP

>> Halogen_Hydrol  5-bromo-4-chloroindolyl phosphate hydrolysis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.2   1.6e-05     0.096      55     117 ..     341     406 ..     315     415 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.6e-05
                     Halogen_Hydrol  55 k...sglsrkelkyiretlkeakekikrlekalkrvrslevikqvreilriarrifkalekePrrl 117
                                        +   ++l+  e+  +++ lk+ k++++ l++ ++  +++ev kq+  +lr+ r ++++++k+   +
  gene2665|gene2665|rna2665|rna2665 341 DitvHNLQAMEMPAFKRKLKKYKRHLQDLKDVFTGEKNIEVYKQIFLMLRTRRSYIEYIQKDSSAF 406
                                        26668888999999***********************************************97666 PP

>> DUF2845  Protein of unknown function (DUF2845)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.1    0.0001      0.63       3      24 ..      76      97 ..      74     101 .. 0.93
   2 ?   -0.9   0.0      0.31   1.9e+03      13      31 ..     173     206 ..     164     243 .. 0.60

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0001
                            DUF2845  3 slrCgnglvslGdskeeVlakC 24
                                       ++rC+++l+s G s + V++ C
  gene2665|gene2665|rna2665|rna2665 76 NYRCKKKLISDGVSVYRVVSNC 97
                                       78******************** PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.31
                            DUF2845  13 lGdskeeVlakCGePlsk...............r 31 
                                         G  ++eV+++C   + +                
  gene2665|gene2665|rna2665|rna2665 173 DGVYEYEVVKECDGGNGRnddrvnrgdgkitigG 206
                                        5667888888887666665555544444444440 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (477 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       725  (0.0404373); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 3007.70
//
Query:       gene2666|gene2666|rna2666|rna2666  [L=65]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (65 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       250  (0.0139439); expected 358.6 (0.02)
Passed bias filter:                      226  (0.0126053); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.33u 0.27s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 488.53
//
Query:       gene2667|gene2667|rna2667|rna2667  [L=502]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (502 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       896  (0.0499749); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.56u 0.26s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 3302.17
//
Query:       gene2668|gene2668|rna2668|rna2668  [L=230]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.095   13.0   0.9       0.32   11.3   0.0    2.2  2  Orf78     Orf78 (ac78)
        9.9    6.3   7.5        0.5   10.5   0.8    2.5  2  TssO      Type VI secretion system, TssO


Domain annotation for each model (and alignments):
>> Orf78  Orf78 (ac78)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.4      0.26   2.3e+03      43      55 ..      51      63 ..      20      98 .. 0.55
   2 ?   11.3   0.0   3.6e-05      0.32      16      83 ..     129     205 ..     121     217 .. 0.55

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.26
                              Orf78 43 aaeknditekesn 55
                                       +a +++++ ++ +
  gene2668|gene2668|rna2668|rna2668 51 IARYSSLDRSDLQ 63
                                       3333333333333 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 3.6e-05
                              Orf78  16 yIPLKLAlndldnddndkaenkkekksaaeknditekesn............aaekaqalnillisllavvcvlvl 79 
                                         IP KLA  d ++++++++++  +   a+ + d++e + +              +ka+  ++++ +++a ++ l+l
  gene2668|gene2668|rna2668|rna2668 129 GIPDKLADVDAKSTKSEQNDR--KLICAKGQDDVQEFRGQqeatrctkffslP-SKAECGENIIWGIMAAFMTLLL 201
                                        5999***99964433333322..222222222222222223355677889854.4555555555555555555555 PP

                              Orf78  80 lyvi 83 
                                        + vi
  gene2668|gene2668|rna2668|rna2668 202 MVVI 205
                                        5554 PP

>> TssO  Type VI secretion system, TssO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.8   5.6e-05       0.5       3      56 ..       8      60 ..       6     152 .. 0.84
   2 ?   -2.8   0.6      0.67     6e+03      11      23 ..     197     208 ..     191     220 .. 0.48

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 5.6e-05
                               TssO  3 kkErrsgflyflllFlvtvlllflivffffkssplqekeillkelerkkkfeek 56
                                       ++Er s f+  +++F+++++ +++i  + + + ++ +k+ l +e+ r+++++ +
  gene2668|gene2668|rna2668|rna2668  8 ERERGSMFITYIVHFIFCLTAVSCINNYENTDKDTGNKQLL-DEIARYSSLDRS 60
                                       689********************888888888887777777.999999988765 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 0.67
                               TssO  11 lyflllFlvtvll 23 
                                        + + ll +v+v+l
  gene2668|gene2668|rna2668|rna2668 197 MTL-LLMVVIVGL 208
                                        222.222333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       968  (0.0539907); expected 358.6 (0.02)
Passed bias filter:                      530  (0.029561); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1516.78
//
Query:       gene2669|gene2669|rna2669|rna2669  [L=241]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.52   10.3   0.1       0.52   10.3   0.1    2.0  2  PsbW      Photosystem II reaction centre W protein (PsbW)


Domain annotation for each model (and alignments):
>> PsbW  Photosystem II reaction centre W protein (PsbW)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.4      0.28   5.1e+03     100     114 ..      41      55 ..      38      61 .. 0.76
   2 ?   10.3   0.1   2.9e-05      0.52      60     122 ..     168     229 ..     161     233 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.28
                               PsbW 100 lgwiLlgvfgliwal 114
                                         ++iL+ +f li  +
  gene2669|gene2669|rna2669|rna2669  41 FALILFVLFQLIMLV 55 
                                        678999999999755 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 2.9e-05
                               PsbW  60 gasllaaaaaatvsspalAlvDeRlsteGtGLplGlsnnllgwiLlgvfgliwalyfvytstl 122
                                        +++++ a+++  + +  +  vD  l + G    +G   +++  +L+ vf  ++ +yf++t+++
  gene2669|gene2669|rna2669|rna2669 168 TKAVVCAFCLLIIIN-SVSPVDMLLYAHGIVYEVGKVSKTVIAVLFPVFVCVFFVYFMFTKEI 229
                                        566777777755544.56779999999999999999999999******************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1250  (0.0697194); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 1495.55
//
Query:       gene267|gene267|rna267|rna267  [L=342]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (342 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1055  (0.0588432); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.61u 0.31s 00:00:00.92 Elapsed: 00:00:00.51
# Mc/sec: 2010.00
//
Query:       gene2670|gene2670|rna2670|rna2670  [L=224]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1026  (0.0572257); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.45
# Mc/sec: 1498.19
//
Query:       gene2671|gene2671|rna2671|rna2671  [L=214]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       877  (0.0489152); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.49
# Mc/sec: 1325.16
//
Query:       gene2672|gene2672|rna2672|rna2672  [L=1138]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.14   12.3   0.5       0.86    9.7   0.1    2.5  2  DUF2541   Protein of unknown function (DUF2541)
        1.2   10.0   4.8         49    5.0   0.1    4.7  3  LRR_1     Leucine Rich Repeat


Domain annotation for each model (and alignments):
>> DUF2541  Protein of unknown function (DUF2541)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.25   2.2e+03      91     113 ..     444     466 ..     351     471 .. 0.57
   2 ?    9.7   0.1   9.6e-05      0.86      42      88 ..     703     749 ..     691     770 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.25
                            DUF2541  91 netGWininsdndnkrcvskiti 113
                                        + +  i i +dnd    +sk t+
  gene2672|gene2672|rna2672|rna2672 444 DIAMPIVIGGDNDVNISISKCTF 466
                                        33445778888888888888887 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 9.6e-05
                            DUF2541  42 lklavcrvvkriklsadrGdvdlsgatvvfkaargasdrlnvvkrlk 88 
                                         kl+  r+ kr+kl+++  ++dls+a+++ k++  +   l+v   l 
  gene2672|gene2672|rna2672|rna2672 703 TKLTLGRRCKRLKLESLAVNIDLSQAALLEKVTLKDMSDLDVKDFLT 749
                                        4788899**********************999999999998877665 PP

>> LRR_1  Leucine Rich Repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.1         2   1.8e+04       4      12 ..     205     213 ..     199     222 .. 0.66
   2 ?    3.5   0.1     0.018   1.6e+02       1      13 [.     840     853 ..     840     877 .. 0.72
   3 ?    5.0   0.1    0.0055        49       1      15 [.     944     957 ..     944     976 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 2
                              LRR_1   4 hLdLsnnpl 12 
                                        +L +sn ++
  gene2672|gene2672|rna2672|rna2672 205 ELSISNSIG 213
                                        566666554 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.018
                              LRR_1   1 nLrhLdLsnnpl.l 13 
                                        +Lr+Ld+ +n + +
  gene2672|gene2672|rna2672|rna2672 840 KLRELDIAYNLNnE 853
                                        7*****98887643 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.0055
                              LRR_1   1 nLrhLdLsnnpllgl 15 
                                        +L++L+L +++l+ +
  gene2672|gene2672|rna2672|rna2672 944 KLEYLNLVGCSLS-K 957
                                        7**********93.3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       472  (0.0263261); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.67u 0.27s 00:00:00.94 Elapsed: 00:00:00.42
# Mc/sec: 8112.84
//
Query:       gene2673|gene2673|rna2673|rna2673  [L=323]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.52   10.1   3.9          3    7.6   0.1    2.1  2  SNF5      SNF5 / SMARCB1 / INI1


Domain annotation for each model (and alignments):
>> SNF5  SNF5 / SMARCB1 / INI1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.7    0.0034        62      30      84 ..      48     106 ..      35     130 .. 0.77
   2 ?    7.6   0.1   0.00017         3      19      54 ..     150     188 ..     136     213 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.0034
                               SNF5  30 lhetlitpeqFaqtlveDldlpeea..avveeiskqireqleey..agvalhelasekk 84 
                                        ++e++++ e+ a+  ++D+d+++++   + ++++ + +  +++y  + v +hela++++
  gene2673|gene2673|rna2673|rna2673  48 FSEHILKDEAIANLEIRDYDIQNDSlrIFQQNVQPHTNYNISNYnmEVVDEHELAKRRN 106
                                        57889999999***********9999888999999999999999444566677744432 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.00017
                               SNF5  19 k...yrlrDtFlwNlhetlitpeqFaqtlveDldlpeea 54 
                                        +   y++ D++l  l+++l    +Faq+l++D +l ++ 
  gene2673|gene2673|rna2673|rna2673 150 DdelYKVIDCLLNLLNDELPFLRIFAQQLIADTKLCDRL 188
                                        044599***************************998554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (323 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       739  (0.0412181); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 2032.92
//
Query:       gene2674|gene2674|rna2674|rna2674  [L=335]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0056   16.8   0.9     0.0097   16.0   0.9    1.3  1  THUMP     THUMP domain
  ------ inclusion threshold ------
      0.018   15.2   1.7      0.042   14.0   1.7    1.7  1  CHCH      CHCH domain


Domain annotation for each model (and alignments):
>> THUMP  THUMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.9   1.1e-06    0.0097      38     100 ..     131     199 ..     120     206 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.1e-06
                                        HHHHHHHHTST...TECEEEEEEEEEESSHHHHHHHHHHHHHHHHHHCT-....EEEEEEEESSSTSSSH CS
                              THUMP  38 ellkealekar...giqrvipvcevceadledileaakeivkkkfeeeke....tFaVrvkrrgkhfeft 100
                                        e++++++e +r   ++ +v+     +++++e+++++ +++vk ++e ek      F Vr+++ +k+  f+
  gene2674|gene2674|rna2674|rna2674 131 EIVEDIVELIRlieTVRKVLLKYLSVNERMEKLIKFCEQAVKVRKELEKYekefWFYVRCEKARKT-CFD 199
                                        5566666666644478888888*************999998877766666667***********99.765 PP

>> CHCH  CHCH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   1.7   4.6e-06     0.042       7      33 ..      39      70 ..      39      72 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.6e-06
                                       HHHHHHHHCTS.....STTTTHHHHHHHHHHH CS
                               CHCH  7 eylkClkdnsd.....efskCrkefeafkeCv 33
                                       +y+ Clk++++     ++s C++ ++ +++Cv
  gene2674|gene2674|rna2674|rna2674 39 KYFVCLKEQEElieaqNSSSCQFSLMRLMKCV 70
                                       699**********8866**************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (335 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1320  (0.0736237); expected 358.6 (0.02)
Passed bias filter:                      634  (0.0353617); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.31s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 2163.10
//
Query:       gene2675|gene2675|rna2675|rna2675  [L=99]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       598  (0.0333538); expected 358.6 (0.02)
Passed bias filter:                      453  (0.0252663); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.29s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 681.81
//
Query:       gene2676|gene2676|rna2676|rna2676  [L=1152]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00012   22.7   1.2         13    6.8   0.0    4.5  4  WD40      WD domain, G-beta repeat
  ------ inclusion threshold ------
       0.13   12.2   0.7       0.35   10.7   0.7    1.8  1  HIRA_B    HIRA B motif


Domain annotation for each model (and alignments):
>> WD40  WD domain, G-beta repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.6   0.0    0.0076        68      15      37 ..      24      41 ..       4      42 .. 0.71
   2 ?    0.3   0.0      0.18   1.6e+03      10      37 ..      69      95 ..      61      96 .. 0.65
   3 !    6.8   0.0    0.0015        13       4      38 .]     147     180 ..     144     180 .. 0.73
   4 !    5.7   0.0    0.0034        30      22      37 ..     284     299 ..     269     300 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.0076
                                       EEEEETTSSEEEEEETTSEEEEE CS
                               WD40 15 slafspdgawlasGsdDgtvriW 37
                                       sl      +++++Gs++g v iW
  gene2676|gene2676|rna2676|rna2676 24 SL-----DTFVVTGSYNGEVIIW 41
                                       33.....67799*********** PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.18
                                       S.SSEEEEEEETTSSEEEEEETTSEEEEE CS
                               WD40 10 H.ssvtslafspdgawlasGsdDgtvriW 37
                                       H ssv       +g +l++ +dD+ + ++
  gene2676|gene2676|rna2676|rna2676 69 HkSSVLNA--RFYGEYLITTGDDNLCILY 95
                                       75557545..3489999988878877665 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.0015
                                        EEEEESS.SSEEEEEEETTSSEEEEEETTSEEEEEE CS
                               WD40   4 lrtltGH.ssvtslafspdgawlasGsdDgtvriWd 38 
                                        l+++  H  ++tsl   +d ++l++G  Dg ++++d
  gene2676|gene2676|rna2676|rna2676 147 LQVIAHHkADITSL-HIKDDSFLTAGL-DGLIYVYD 180
                                        5555556666****.667777777666.******98 PP

  == domain 4  score: 5.7 bits;  conditional E-value: 0.0034
                                        SSEEEEEETTSEEEEE CS
                               WD40  22 gawlasGsdDgtvriW 37 
                                        g+ l++G+ D++v +W
  gene2676|gene2676|rna2676|rna2676 284 GNILICGCQDKSVVLW 299
                                        67799*********** PP

>> HIRA_B  HIRA B motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.7   3.9e-05      0.35      11      22 ..     718     729 ..     718     730 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 3.9e-05
                             HIRA_B  11 KKRVaPtLiSss 22 
                                        K+R++P+Li+++
  gene2676|gene2676|rna2676|rna2676 718 KRRITPVLIPQL 729
                                        9********985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1247  (0.0695521); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.79u 0.27s 00:00:01.06 Elapsed: 00:00:00.45
# Mc/sec: 7724.65
//
Query:       gene2677|gene2677|rna2677|rna2677  [L=103]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.4e-11   43.1   0.6    4.5e-11   42.7   0.6    1.2  1  tRNA_int_endo  tRNA intron endonuclease, catalytic C-terminal


Domain annotation for each model (and alignments):
>> tRNA_int_endo  tRNA intron endonuclease, catalytic C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.7   0.6   2.5e-15   4.5e-11       9      83 ..      13      83 ..       5      85 .. 0.86

  Alignments for each domain:
  == domain 1  score: 42.7 bits;  conditional E-value: 2.5e-15
                                       HHHHHTT-EEEECGGGTSSEEEETSCTTTSSCSEEEEEEETTSEEEHHHHHHHHHHHHHTTSEEEEEEETTTSCE CS
                      tRNA_int_endo  9 rdLrekGyvvrsGlkFGadFrvYqrrpslehseylVvvvsedeeldwpdlsaavrlahsvkKklilaivdaegdv 83
                                        +L   Gy v +G+k+G+dF++Y+++ +++h++y   v     + ++ +++a  r++++v K li+  v ++g+v
  gene2677|gene2677|rna2677|rna2677 13 SHLLAAGYEVTDGIKYGTDFLIYTHDRNKVHAKYACIV---YNKQSFLSVIAVQRVVNGVGKVLIFGDV-RDGKV 83
                                       688899****************************9998...44556789****************9988.55555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       543  (0.0302861); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 708.90
//
Query:       gene2678|gene2678|rna2678|rna2678  [L=48]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.17   11.7   3.1       0.25   11.1   3.1    1.3  1  Zds_C     Activator of mitotic machinery Cdc14 phosphatase ac


Domain annotation for each model (and alignments):
>> Zds_C  Activator of mitotic machinery Cdc14 phosphatase activation C-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   3.1   1.4e-05      0.25      39      48 ..      32      41 ..      29      43 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 1.4e-05
                              Zds_C 39 LlSNfMYsYL 48
                                        lSNfM+sYL
  gene2678|gene2678|rna2678|rna2678 32 FLSNFMFSYL 41
                                       59*******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (48 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       348  (0.0194099); expected 358.6 (0.02)
Passed bias filter:                      242  (0.0134977); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.30u 0.24s 00:00:00.54 Elapsed: 00:00:00.36
# Mc/sec: 395.79
//
Query:       gene2679|gene2679|rna2679|rna2679  [L=72]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (72 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       331  (0.0184617); expected 358.6 (0.02)
Passed bias filter:                      227  (0.0126611); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 531.95
//
Query:       gene268|gene268|rna268|rna268  [L=252]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.2e-29  100.9  14.8    1.8e-27   96.6  14.8    2.1  1  MIP              Major intrinsic protein
  ------ inclusion threshold ------
        0.6    9.9   0.0        0.6    9.9   0.0    2.4  3  Phage_holin_2_3  Bacteriophage holin family HP1


Domain annotation for each model (and alignments):
>> MIP  Major intrinsic protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.6  14.8     2e-31   1.8e-27       6     226 ..       8     243 ..       4     244 .. 0.85

  Alignments for each domain:
  == domain 1  score: 96.6 bits;  conditional E-value: 2e-31
                                    HHHHHHHHHHHHHHHHHHHHHHHHHCCCSSCSSSSTTSSHHHHHHHHHHHHHHHHHHHHHHHCHT-S-SHHHHHHHHHTT CS
                            MIP   6 kflravlAEflatlllvfigvgsalnvkkkvsslaslvsvtleavalafglalavlvylaagiSGaHlNPavTlallvar 85 
                                    + +++++AE+  ++++ f +  + l   ++ ++   +v+ +   v l+ g++ +v ++l+ ++  aH+NPa+T+a++v+r
  gene268|gene268|rna268|rna268   8 SKIQSYVAECACSFIFGFTVYSAIL--TTTLKN---MVA-GPILVGLSIGFVSIVIIFLFVDVTLAHFNPAITFAAIVFR 81 
                                    568999*******999888777555..344434...333.5667888889999999************************ PP

                                    SSSHHHHHHHHHHHHHHHHHHHHHHHHHCHHH.HHHTTTTSSSSSTTSSHHHHHHHHHHHHHHHHHHHHHHCSTTSSSST CS
                            MIP  86 kisllrailYivaQllGaivaaallklltkgl.esraglfanslkpglsagqalvvEiiltfvLvlvvfaltddkrkvsl 164
                                    +i+++ + +Yi+aQ +G ++a++++++++ g  e   +  +    +  ++g+ + +E++lt +Lv+ vf++++++ k ++
  gene268|gene268|rna268|rna268  82 RIPIISGFFYIIAQGIGFMIASLVVQGCFPGKfEPLMNIIRPKRVNDSTTGEMICIEMFLTGILVFSVFVMAINPYKKQK 161
                                    *****************************9973334444444455667789******************99876544443 PP

                                    CH....................GHHHHHHHHHHHHHHHHHHHHST-SSHHHHHHHHHHHTHSTTTTHHHHHHHHHHHHHH CS
                            MIP 165 ge....................laplaigllvaliilvgipltGaamNpArslgpavvlnkfedhwvylvGPliGailga 224
                                     e                    +ap++igl++     +g+  +G a Np    +p +++ ++ d w y+vG ++G+ +ga
  gene268|gene268|rna268|rna268 162 DErdqrelhidpseskipdrsrFAPIVIGLTLGFLGYLGGSTSGGAFNPGIVWAPVLFSGHWGDSWKYWVGEFVGGCVGA 241
                                    3346678888899999999999********************************************************** PP

                                    HH CS
                            MIP 225 lv 226
                                    ++
  gene268|gene268|rna268|rna268 242 FI 243
                                    97 PP

>> Phage_holin_2_3  Bacteriophage holin family HP1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.8      0.33   2.9e+03      28      41 ..      44      57 ..      11      61 .. 0.66
   2 ?    9.9   0.0   6.7e-05       0.6      29      51 ..     141     164 ..     139     168 .. 0.84
   3 ?   -3.8   0.6       1.3   1.2e+04      28      37 ..     187     196 ..     187     199 .. 0.65

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.33
                Phage_holin_2_3 28 iviGIicgvvTfli 41
                                   i++G+ +g+v+++i
  gene268|gene268|rna268|rna268 44 ILVGLSIGFVSIVI 57
                                   57788788777766 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 6.7e-05
                Phage_holin_2_3  29 viGI.icgvvTfliNwyykrkelr 51 
                                    ++GI +++v+ ++iN y+k+k+ r
  gene268|gene268|rna268|rna268 141 LTGIlVFSVFVMAINPYKKQKDER 164
                                    7888469**************987 PP

  == domain 3  score: -3.8 bits;  conditional E-value: 1.3
                Phage_holin_2_3  28 iviGIicgvv 37 
                                    iviG+ +g++
  gene268|gene268|rna268|rna268 187 IVIGLTLGFL 196
                                    5777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       845  (0.0471303); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.67u 0.35s 00:00:01.02 Elapsed: 00:00:00.58
# Mc/sec: 1304.31
//
Query:       gene2680|gene2680|rna2680|rna2680  [L=65]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
       0.11   12.9   0.0       0.12   12.7   0.0    1.2  1  EF-hand_14  EF-hand domain


Domain annotation for each model (and alignments):
>> EF-hand_14  EF-hand domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   6.9e-06      0.12      65      86 ..      22      43 ..       2      47 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 6.9e-06
                         EF-hand_14 65 retFkkcveenivLiakaLknq 86
                                         +F +cv+++ vLi +++k++
  gene2680|gene2680|rna2680|rna2680 22 PGEFVWCVRKCEVLIRRTFKQK 43
                                       468*****************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (65 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       276  (0.0153941); expected 358.6 (0.02)
Passed bias filter:                      195  (0.0108762); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.34s 00:00:00.77 Elapsed: 00:00:00.51
# Mc/sec: 385.98
//
Query:       gene2681|gene2681|rna2681|rna2681  [L=52]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (52 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       230  (0.0128284); expected 358.6 (0.02)
Passed bias filter:                      135  (0.0075297); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.46
# Mc/sec: 341.55
//
Query:       gene2682|gene2682|rna2682|rna2682  [L=68]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (68 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       193  (0.0107647); expected 358.6 (0.02)
Passed bias filter:                      169  (0.00942607); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.28s 00:00:00.66 Elapsed: 00:00:00.44
# Mc/sec: 464.39
//
Query:       gene2683|gene2683|rna2683|rna2683  [L=211]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1141  (0.0636399); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1465.76
//
Query:       gene2684|gene2684|rna2684|rna2684  [L=68]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (68 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       184  (0.0102627); expected 358.6 (0.02)
Passed bias filter:                      160  (0.00892409); expected 358.6 (0.02)
Passed Vit filter:                         6  (0.000334653); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.32u 0.25s 00:00:00.57 Elapsed: 00:00:00.37
# Mc/sec: 543.79
//
Query:       gene2685|gene2685|rna2685|rna2685  [L=144]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.7e-18   66.6   2.8    3.3e-18   66.3   2.8    1.1  1  Histone        Core histone H2A/H2B/H3/H4
     0.0038   17.5   0.0     0.0064   16.7   0.0    1.4  1  CBFD_NFYB_HMF  Histone-like transcription factor (CBF/NF-Y) a


Domain annotation for each model (and alignments):
>> Histone  Core histone H2A/H2B/H3/H4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.3   2.8   3.6e-22   3.3e-18      11     131 .]      13     139 ..       1     139 [. 0.80

  Alignments for each domain:
  == domain 1  score: 66.3 bits;  conditional E-value: 3.6e-22
                                        XXXEEXXXXXXXXXXHT..TS-SSSSB--....TTT-XTTHHHHHHHHHHHHXXSXXSXHHHHHHHHHHHH.TTSS CS
                            Histone  11 esektapekkvsakker..kasskskkkk....krryrpgtvalkeirkyqkstdlliqklpfaRvvreivkseke 80 
                                        +s++++ +++v +k +r  + s k+ ++k    k+ ++ + + +kei+ y++s ++l +k++f R+++  v + ++
  gene2685|gene2685|rna2685|rna2685  13 QSPTKRTRQPVISKVARkkSLSIKTPTVKqlpiKKPTKLRYHVEKEIKYYRQSITHLVPKACFIRMLKGMVLKMDT 88 
                                        34555666677777777764444555544111156667777899************************99999*** PP

                                        SXEEXHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTXSEEXHHHHHHHHHHT CS
                            Histone  81 dlrisaeavlalqealEallvelfeeAnllakhaKRvTitpkDiqlArrlr 131
                                         +r++++a+++lq a E ++v  +e+++l++ haKRvT+ p Di l r+++
  gene2685|gene2685|rna2685|rna2685  89 PMRFTKDALDMLQDAYESYIVANMETSYLATVHAKRVTLKPIDINLIRKIK 139
                                        ***********************************************9985 PP

>> CBFD_NFYB_HMF  Histone-like transcription factor (CBF/NF-Y) and archaeal histone
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   7.2e-07    0.0064      14      62 ..      86     133 ..      69     135 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 7.2e-07
                                        CCTTXS-B-HHHHHHHHHHHHHHHHHHHHHHHHHHCCTTSSCE-HHHHH CS
                      CBFD_NFYB_HMF  14 sdpdarkiakdAkeliaecveefieelaseAaeickkekrKtikaehik 62 
                                         d    +++kdA ++++++ e +i    + ++  + ++kr t+k+ +i 
  gene2685|gene2685|rna2685|rna2685  86 MD-TPMRFTKDALDMLQDAYESYIVANMETSYLATVHAKRVTLKPIDIN 133
                                        23.22349**************************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       543  (0.0302861); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 1127.96
//
Query:       gene2686|gene2686|rna2686|rna2686  [L=299]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       454  (0.0253221); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 2064.94
//
Query:       gene2687|gene2687|rna2687|rna2687  [L=353]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.1e-05   23.3   0.4    0.00021   21.8   0.0    1.9  2  PCI       PCI domain


Domain annotation for each model (and alignments):
>> PCI  PCI domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.1       0.8   1.4e+04      43      58 ..      49      64 ..      35      68 .. 0.48
   2 !   21.8   0.0   1.2e-08   0.00021       3      75 ..     212     283 ..     211     300 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 0.8
                                       HHHHHHHHHHHHHHCE CS
                                PCI 43 ekkvrerllrqvskiy 58
                                       +++   +++++++k +
  gene2687|gene2687|rna2687|rna2687 49 QREEHAECIKKITKNQ 64
                                       3333334455555544 PP

  == domain 2  score: 21.8 bits;  conditional E-value: 1.2e-08
                                        HHHHHHHHHHTSHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHCESEEEHHHHHHHHTSSHH CS
                                PCI   3 ysdllkalrsgnlsgfseelkdleeelladdglaqllesLekkvrerllrqvskiyssislerlaklldlsvd 75 
                                        y++   a++ g+ ++  +  +++ +  + +d++  l+ +L++ + ++ +r++s+ y++isl++++++ ++ ++
  gene2687|gene2687|rna2687|rna2687 212 YKEACDAVKMGDRKKLGRVIEEY-KSAFWEDKTFFLVCRLHHLIVQEGIRKISLVYTRISLQDVQEKYGIAEE 283
                                        66777888899999999999999.788888999999******************************9998764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (353 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       625  (0.0348597); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2583.03
//
Query:       gene2688|gene2688|rna2688|rna2688  [L=492]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        3.4    7.9   9.0        8.7    6.6   0.2    3.3  4  WHEP-TRS  WHEP-TRS domain


Domain annotation for each model (and alignments):
>> WHEP-TRS  WHEP-TRS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.2   0.00048       8.7      15      44 ..      50      79 ..      33      83 .. 0.73
   2 ?    6.1   0.1   0.00067        12      14      38 ..      83     107 ..      78     112 .. 0.87
   3 ?   -2.9   0.1      0.43   7.8e+03       7      22 ..     404     419 ..     403     424 .. 0.72
   4 ?   -2.4   0.1      0.31   5.6e+03      16      35 ..     470     489 ..     469     489 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.00048
                           WHEP-TRS 15 LKaekapkdeidaaVkkLLaLKaqykaltG 44
                                       +K+ k + +ei+ aV  +++ K q ++ +G
  gene2688|gene2688|rna2688|rna2688 50 MKEFKEQDEEIAGAVTLMKEFKEQDEEIAG 79
                                       567777778888888888888877777766 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.00067
                           WHEP-TRS  14 kLKaekapkdeidaaVkkLLaLKaq 38 
                                          K+ k + +ei+ aV+  ++LK +
  gene2688|gene2688|rna2688|rna2688  83 HIKEFKEEDEEIAGAVAHIKELKEE 107
                                        6799999****************86 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 0.43
                           WHEP-TRS   7 aQGelVRkLKaekapk 22 
                                        +Q + V  LK+e   k
  gene2688|gene2688|rna2688|rna2688 404 EQDDNVALLKKECELK 419
                                        6788888888876665 PP

  == domain 4  score: -2.4 bits;  conditional E-value: 0.31
                           WHEP-TRS  16 KaekapkdeidaaVkkLLaL 35 
                                        K+e ++ de  +a+  L +L
  gene2688|gene2688|rna2688|rna2688 470 KEETKESDEYNQAIDALASL 489
                                        88899999999999998665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (492 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1237  (0.0689944); expected 358.6 (0.02)
Passed bias filter:                      484  (0.0269954); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.31s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 3186.64
//
Query:       gene2689|gene2689|rna2689|rna2689  [L=166]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00015   22.0   0.2    0.00063   20.0   0.1    1.8  2  AAA_28           AAA domain
    0.00056   19.6   0.0      0.024   14.3   0.0    2.0  2  ATP-synt_ab      ATP synthase alpha/beta family, nucleotide-b
     0.0011   18.5   0.0     0.0015   18.1   0.0    1.2  1  AAA_7            P-loop containing dynein motor region
     0.0016   18.5   0.5     0.0044   17.0   0.5    1.9  1  AAA_14           AAA domain
     0.0017   17.6   0.1      0.003   16.8   0.1    1.3  1  DAP3             Mitochondrial ribosomal death-associated pro
     0.0033   18.0   0.2     0.0052   17.3   0.2    1.5  1  AAA_18           AAA domain
     0.0041   17.3   0.0     0.0064   16.7   0.0    1.3  1  Roc              Ras of Complex, Roc, domain of DAPkinase
      0.005   15.9   0.1     0.0088   15.1   0.1    1.4  1  T2SSE            Type II/IV secretion system protein
     0.0091   16.3   0.3      0.013   15.8   0.3    1.5  1  AAA_22           AAA domain
  ------ inclusion threshold ------
      0.014   15.8   0.0      0.019   15.4   0.0    1.2  1  AAA_16           AAA ATPase domain
      0.019   15.4   0.0      0.028   14.8   0.0    1.3  1  AAA              ATPase family associated with various cellul
      0.019   13.9   0.1      0.028   13.3   0.1    1.2  1  TrwB_AAD_bind    Type IV secretion-system coupling protein DN
       0.02   14.9   0.1      0.022   14.7   0.1    1.2  1  ResIII           Type III restriction enzyme, res subunit
      0.044   13.4   0.0      0.066   12.8   0.0    1.3  1  Ras              Ras family
      0.069   13.1   0.3       0.38   10.6   0.2    1.9  2  NTPase_1         NTPase
      0.077   12.7   0.1       0.18   11.5   0.0    1.6  2  AAA_24           AAA domain
      0.077   12.9   0.0       0.11   12.4   0.0    1.3  1  RsgA_GTPase      RsgA GTPase
      0.084   12.3   0.1       0.12   11.8   0.1    1.4  1  SRPRB            Signal recognition particle receptor beta su
      0.089   13.2   0.0       0.15   12.5   0.0    1.4  1  RNA_helicase     RNA helicase
      0.098   12.7   0.1       0.15   12.1   0.1    1.3  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
       0.12   12.0   0.0       0.19   11.5   0.0    1.2  1  Sigma54_activat  Sigma-54 interaction domain
       0.13   12.4   0.3        0.3   11.2   0.2    1.7  2  MMR_HSR1         50S ribosome-binding GTPase
       0.13   11.4   0.0       0.23   10.6   0.0    1.4  1  NB-ARC           NB-ARC domain


Domain annotation for each model (and alignments):
>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.1   8.1e-07   0.00063       1      28 [.      42      69 ..      42      82 .. 0.89
   2 ?   -0.1   0.0       1.3   9.9e+02     103     120 ..      92     110 ..      70     115 .. 0.62

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 8.1e-07
                             AAA_28  1 kivitGgestGKTtlleaLaargypvvp 28
                                       +i itG+ + GKT l+++L +r +p+vp
  gene2689|gene2689|rna2689|rna2689 42 RILITGTKGVGKTVLTNQLMNRTFPTVP 69
                                       799*******************888886 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1.3
                             AAA_28 103 aarekrydl.vfllppape 120
                                           ++ ydl vf+++ + e
  gene2689|gene2689|rna2689|rna2689  92 VKLRNGYDLiVFVFRDEIE 110
                                        3337779999999887765 PP

>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0     3e-05     0.024       5      37 ..      31      63 ..      28      78 .. 0.89
   2 ?    3.7   0.0     0.055        43      43      76 ..     117     150 ..      97     166 .] 0.80

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3e-05
                                       HHHHS-EBTT-EEEEEESTTSSHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        ATP-synt_ab  5 lDalfpivqGqrtlipgafgvGktvisqslskq 37
                                       l +l+ + + +r+li g +gvGktv+ ++l++ 
  gene2689|gene2689|rna2689|rna2689 31 LALLIRCKKRKRILITGTKGVGKTVLTNQLMNR 63
                                       6689999**********************9987 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.055
                                        EEEEEEESEEHHHHHHHHHHCHHSSGGGGEEEEE CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        ATP-synt_ab  43 aiiyvgiGergnevaevleefpegtimkrtvlva 76 
                                         +iyv  G+ g+++a+++++  ++  +kr  +++
  gene2689|gene2689|rna2689|rna2689 117 NVIYVSLGKEGKSLADLVTDKDKKYFVKRGNVFY 150
                                        69****************9999988888876665 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   1.9e-06    0.0015      30      56 ..      37      63 ..      19      89 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.9e-06
                              AAA_7 30 lknkkpvllvGptGtGKtviikdllkk 56
                                       +k++k +l++G++G+GKtv++++l+++
  gene2689|gene2689|rna2689|rna2689 37 CKKRKRILITGTKGVGKTVLTNQLMNR 63
                                       6899*******************8875 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.5   5.7e-06    0.0044       2      28 ..      40      68 ..      39     163 .. 0.71

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 5.7e-06
                             AAA_14  2 rkilvitGaRrvGKTtllkqlikell..v 28
                                       rk ++itG + vGKT+l +ql+++ +  v
  gene2689|gene2689|rna2689|rna2689 40 RKRILITGTKGVGKTVLTNQLMNRTFptV 68
                                       67799*****************9888432 PP

>> DAP3  Mitochondrial ribosomal death-associated protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.1   3.8e-06     0.003      21      45 ..      38      62 ..      31      67 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 3.8e-06
                                       S---EEEEE-SSSSSTTTTHHHHHH CS
                               DAP3 21 kkvkrlvltGekgsGKSvlLlqala 45
                                       kk kr+++tG kg+GK+vl +q++ 
  gene2689|gene2689|rna2689|rna2689 38 KKRKRILITGTKGVGKTVLTNQLMN 62
                                       799*******************996 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.2   6.7e-06    0.0052       1      22 [.      43      64 ..      43     111 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 6.7e-06
                             AAA_18  1 IlltGtpGvGKttlakeLskrl 22
                                       Il+tGt GvGKt l++ L +r+
  gene2689|gene2689|rna2689|rna2689 43 ILITGTKGVGKTVLTNQLMNRT 64
                                       99****************9985 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   8.2e-06    0.0064       1      40 [.      42      80 ..      42      99 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 8.2e-06
                                       EEEEESSTTSSHHHHHHCHCT-CCC-EEETTTTEEEEEEE CS
                                Roc  1 KvvlvGdsgvGKtsllkrfvedkfsekekstigvdfltke 40
                                       ++++ G +gvGKt l +++++++f  +  s + ++++t e
  gene2689|gene2689|rna2689|rna2689 42 RILITGTKGVGKTVLTNQLMNRTFP-TVPSLCDYTVVTPE 80
                                       58999******************95.44555666665554 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.1   1.1e-05    0.0088     125     151 ..      37      62 ..      25      80 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.1e-05
                              T2SSE 125 avrerglilvsGgTgsGKttllyallk 151
                                          ++r+ il++G+ g GKt+l++ l++
  gene2689|gene2689|rna2689|rna2689  37 C-KKRKRILITGTKGVGKTVLTNQLMN 62 
                                        3.699******************9886 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.3   1.6e-05     0.013       4      29 ..      39      64 ..      35     144 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.6e-05
                             AAA_22  4 tagilvvtGesGtGKTtllrrlleql 29
                                       +++ +++tG +G+GKT+l ++l+++ 
  gene2689|gene2689|rna2689|rna2689 39 KRKRILITGTKGVGKTVLTNQLMNRT 64
                                       67789****************99974 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   0.0   2.4e-05     0.019      25      47 ..      41      63 ..      28      95 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.4e-05
                             AAA_16 25 elvllsGesGvGKsslvrellra 47
                                         +l++G +GvGK+ l ++l+++
  gene2689|gene2689|rna2689|rna2689 41 KRILITGTKGVGKTVLTNQLMNR 63
                                       5689***************9975 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   3.6e-05     0.028       1      74 [.      43     116 ..      43     140 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3.6e-05
                                        EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTS.EEEEEETGGGHHHHH CS
                                AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakp.silfiDEidalaksr 74 
                                        +l++G++G+GKT l +++++ +  ++ ++   +++    + + ++i++ +k   +  +  + +f DEi+ + + +
  gene2689|gene2689|rna2689|rna2689  43 ILITGTKGVGKTVLTNQLMNRTFPTVPSLCDYTVVTPEYELTDQRIKKGVKLR-NGYDLiVFVFRDEIETVLPGK 116
                                        699******************87777777777777666777888888888763.333344777889998887655 PP

>> TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   3.6e-05     0.028      13      37 ..      38      62 ..      28      65 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.6e-05
                      TrwB_AAD_bind 13 retqhilivGttGsGKtqalekllr 37
                                       + ++ ili+Gt G GKt+ +++l++
  gene2689|gene2689|rna2689|rna2689 38 KKRKRILITGTKGVGKTVLTNQLMN 62
                                       56789******************97 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.1   2.9e-05     0.022      22      71 ..      38      88 ..      16     144 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.9e-05
                                       .TTSEEEEEESTTSTHHHHHHHHHHHH-S......-EEEEESSHHHHHHHH CS
                             ResIII 22 krdkrglikmaTGtGKTlvaaklierllkkgkee.kflflvprkslleqtl 71
                                       k++kr+li  + G+GKT++  +l+ r +   +      ++ p+ +l++q +
  gene2689|gene2689|rna2689|rna2689 38 KKRKRILITGTKGVGKTVLTNQLMNRTFPTVPSLcDYTVVTPEYELTDQRI 88
                                       899***********************9987665467788888888888766 PP

>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   8.5e-05     0.066       2      27 ..      43      68 ..      42      95 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 8.5e-05
                                       EEEEESTTSSHHHHHHHHHHSSCSSS CS
                                Ras  2 lvlvGdsavGKtslllrfvkdkFkee 27
                                       +++ G ++vGKt l+++ ++ +F++ 
  gene2689|gene2689|rna2689|rna2689 43 ILITGTKGVGKTVLTNQLMNRTFPTV 68
                                       7899*******************875 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.2   0.00049      0.38       1      21 [.      42      62 ..      42      71 .. 0.90
   2 ?    0.1   0.0      0.86   6.7e+02     113     155 ..     104     143 ..      99     155 .. 0.57

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00049
                                       EEEEE--TTSSHHHHHHHHHH CS
                           NTPase_1  1 kvfiTGppGvGKtTlvkkvle 21
                                       +++iTG  GvGKt l +++++
  gene2689|gene2689|rna2689|rna2689 42 RILITGTKGVGKTVLTNQLMN 62
                                       699***********9998876 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.86
                                        HHHHHHHHHHTTTSEEEEE--SS--SHHHHHHHT-TT-EEEE- CS
                           NTPase_1 113 kfkeaveevLksekpvlavihrrkdlalveeirerkdvkvfev 155
                                        +f++++e+vL  ++ v+ v   ++ ++l + +   kd k+f v
  gene2689|gene2689|rna2689|rna2689 104 VFRDEIETVLPGKN-VIYVSLGKEGKSLADLVT-DKDKKYF-V 143
                                        79999999997444.444433332344444444.4455555.4 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00022      0.18       2      25 ..      40      63 ..      39      74 .. 0.85
   2 ?   -1.7   0.0       2.7   2.1e+03     161     176 ..      95     110 ..      78     141 .. 0.55

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00022
                             AAA_24  2 klkiliyGpsgiGKTtlakelgpk 25
                                        ++ili+G  g+GKT l ++l ++
  gene2689|gene2689|rna2689|rna2689 40 RKRILITGTKGVGKTVLTNQLMNR 63
                                       689**************9999444 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2.7
                             AAA_24 161 keevDlvlranlkred 176
                                        ++  Dl++++  ++ +
  gene2689|gene2689|rna2689|rna2689  95 RNGYDLIVFVFRDEIE 110
                                        3334444443333322 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00014      0.11      98     122 ..      38      63 ..      29      91 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00014
                                        TT.SEEEEECSTTSSHHHHHHHHCTT CS
                        RsgA_GTPase  98 kd.ktsvlvGqSGvGKStLinallpe 122
                                        k+ k +++ G  GvGK+ L n+l+++
  gene2689|gene2689|rna2689|rna2689  38 KKrKRILITGTKGVGKTVLTNQLMNR 63 
                                        444888999**************986 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   0.00015      0.12       2      35 ..      39      71 ..      38     121 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00015
                                       ---EEEEE-STTSSHHHHHHHHHHSS---B---S CS
                              SRPRB  2 skpavllvGlsdsGKTslftrLttdsvkktvtSq 35
                                       +++++l+ G +  GKT l ++L++ +  +tv S+
  gene2689|gene2689|rna2689|rna2689 39 KRKRILITGTKGVGKTVLTNQLMNRT-FPTVPSL 71
                                       7899******************8764.4566665 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00019      0.15       1      22 [.      43      64 ..      43      94 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00019
                       RNA_helicase  1 iwlyGpsgeGKStlakeLakal 22
                                       i+++G +g+GK++l+++L+++ 
  gene2689|gene2689|rna2689|rna2689 43 ILITGTKGVGKTVLTNQLMNRT 64
                                       689**************99875 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   0.00019      0.15      19      50 ..      40      70 ..      21      94 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00019
                                       TEEEEEEESTTSSHHHHHHHHHHHTT------ CS
                               TsaE 19 gdvilLeGdLGaGKTtlvrglakalgveevkS 50
                                       ++ il++G  G+GKT+l+ +l++   + +v S
  gene2689|gene2689|rna2689|rna2689 40 RKRILITGTKGVGKTVLTNQLMNRT-FPTVPS 70
                                       5669*****************9876.223333 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00024      0.19      20      44 ..      38      62 ..      29      74 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00024
                                       TSSS-EEEECSTTSSHHHHHHHHHH CS
                    Sigma54_activat 20 ktdlsvlitGesGtGKellaraihe 44
                                       k++ ++litG +G+GK++l +++ +
  gene2689|gene2689|rna2689|rna2689 38 KKRKRILITGTKGVGKTVLTNQLMN 62
                                       45689**************998876 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.2   0.00038       0.3       1      24 [.      42      65 ..      42     103 .. 0.78
   2 ?   -0.8   0.0         2   1.6e+03      73      85 ..      94     107 ..      71     143 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00038
                                       EEEEEESTTSSHHHHHHHHHTSTE CS
                           MMR_HSR1  1 evaivGrpNvGKStLinaltgeka 24
                                       +++i G   vGK+ L n+l++++ 
  gene2689|gene2689|rna2689|rna2689 42 RILITGTKGVGKTVLTNQLMNRTF 65
                                       689*****************9843 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 2
                                        HHC.TSEEEEEEET CS
                           MMR_HSR1  73 lee.adlillvvda 85 
                                        l++  dli++v++ 
  gene2689|gene2689|rna2689|rna2689  94 LRNgYDLIVFVFRD 107
                                        33346888888762 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0    0.0003      0.23      22      43 ..      42      63 ..      30      78 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0003
                                       EEEEEESTTSSHHHHHHHHCCS CS
                             NB-ARC 22 vvalvGmgGvGKttlakqilnk 43
                                        + + G  GvGKt+l +q +n 
  gene2689|gene2689|rna2689|rna2689 42 RILITGTKGVGKTVLTNQLMNR 63
                                       67899*************9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1186  (0.0661498); expected 358.6 (0.02)
Passed bias filter:                      850  (0.0474092); expected 358.6 (0.02)
Passed Vit filter:                       150  (0.00836633); expected 17.9 (0.001)
Passed Fwd filter:                        23  (0.00128284); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              23  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 1065.67
//
Query:       gene269|gene269|rna269|rna269  [L=385]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.6e-26   92.4   0.8    2.6e-25   88.4   0.7    2.7  3  CAF1C_H4-bd  Histone-binding protein RBBP4 or subunit C of CA
    2.3e-19   69.4   2.5      0.018   15.9   0.0    5.5  5  WD40         WD domain, G-beta repeat
     0.0031   16.5   0.5       0.36    9.7   0.0    3.3  3  Ge1_WD40     WD40 region of Ge1, enhancer of mRNA-decapping p


Domain annotation for each model (and alignments):
>> CAF1C_H4-bd  Histone-binding protein RBBP4 or subunit C of CAF1 complex
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.4   0.7   4.4e-29   2.6e-25       1      66 [.      17      86 ..      17      87 .. 0.93
   2 ?   -2.4   0.0         1     6e+03      21      48 ..     244     264 ..     241     276 .. 0.65
   3 ?    0.7   0.0      0.11   6.5e+02      50      64 ..     362     376 ..     292     378 .. 0.82

  Alignments for each domain:
  == domain 1  score: 88.4 bits;  conditional E-value: 4.4e-29
                                   HHHHHHHHHHHHHEEEEEEEE-SS--S-EEE-S-.B--...-.EEEEEEEE----TTSS-EEEEEEEEEEE CS
                    CAF1C_H4-bd  1 eeylewkknapfLYdmlhshslewPsLsfdwlPd.tvs...s.lskqrllvGtqtsgkeqnylyvakvslp 66
                                   eey+ wkknap+LYdml +hsl wPsLs++++P+ t     + +++qrll++t+ts++e++++++++v++p
  gene269|gene269|rna269|rna269 17 EEYKLWKKNAPYLYDMLVTHSLSWPSLSVQFFPEaT-RnekNnTTTQRLLISTHTSQNEDEFIKILSVTIP 86
                                   7********************************963.3577889************************998 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1
                                    E-SS--S-EEE-S-B---EEEEEEEE-- CS
                    CAF1C_H4-bd  21 slewPsLsfdwlPdtvsslskqrllvGt 48 
                                    + e   Ls+  l d v       ++ G+
  gene269|gene269|rna269|rna269 244 TAEIYALSCSMLEDNV-------ICTGS 264
                                    5555567888877766.......55454 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.11
                                    -TTSS-EEEEEEEEE CS
                    CAF1C_H4-bd  50 tsgkeqnylyvakvs 64 
                                    +s  e+n ++++++s
  gene269|gene269|rna269|rna269 362 ASVAEDNVIQIWQMS 376
                                    355899999999997 PP

>> WD40  WD domain, G-beta repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.0    0.0008       4.8       6      38 .]     154     188 ..     150     188 .. 0.77
   2 !   15.1   0.1   5.3e-06     0.031       7      38 .]     197     230 ..     191     230 .. 0.77
   3 !   13.5   0.0   1.7e-05       0.1      10      38 .]     243     273 ..     234     273 .. 0.67
   4 !   15.9   0.0     3e-06     0.018       3      38 .]     280     317 ..     278     317 .. 0.81
   5 !   11.7   0.0   6.3e-05      0.37       8      37 ..     342     373 ..     336     374 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0008
                                    EEESS..SSEEEEEEETTSSE.EEEEETTSEEEEEE CS
                           WD40   6 tltGH..ssvtslafspdgaw.lasGsdDgtvriWd 38 
                                    +l+GH  ++ ++l+++ +++  la++++Dg v ++d
  gene269|gene269|rna269|rna269 154 ILKGHekGG-YGLSWNYNNKNiLATSGEDGLVCVFD 188
                                    678888544.699988888883578899*****998 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 5.3e-06
                                    EESSSS.EEEEEEETTSSEEE.EEETTSEEEEEE CS
                           WD40   7 ltGHss.vtslafspdgawla.sGsdDgtvriWd 38 
                                    l GH++ v ++ fs  +  ++ s++dD+++ +Wd
  gene269|gene269|rna269|rna269 197 LAGHDGvVGDCNFSFFSENVLfSCGDDRNIIMWD 230
                                    679*6657888877777775348999*******9 PP

  == domain 3  score: 13.5 bits;  conditional E-value: 1.7e-05
                                    S.SSEEEEEEETTSSE.EEEEETTSEEEEEE CS
                           WD40  10 H.ssvtslafspdgaw.lasGsdDgtvriWd 38 
                                    H   +++l+ s   +  +++Gs+D +v++Wd
  gene269|gene269|rna269|rna269 243 HtAEIYALSCSMLEDNvICTGSKDTSVKVWD 273
                                    64446666432223332679**********9 PP

  == domain 4  score: 15.9 bits;  conditional E-value: 3e-06
                                    EEEEEESS.SSEEEEEEETTSSEEE.EEETTSEEEEEE CS
                           WD40   3 clrtltGH.ssvtslafspdgawla.sGsdDgtvriWd 38 
                                     l tl  H + v  ++fsp+ + ++ s++ D+ v +Wd
  gene269|gene269|rna269|rna269 280 ELFTLLSHkKEVLQVQFSPHFSNILaSSGTDRRVCVWD 317
                                    6778889*888*****99999996525567*******9 PP

  == domain 5  score: 11.7 bits;  conditional E-value: 6.3e-05
                                    ESS.SSEEEEEEETTSSE.EEEEETTSEEEEE CS
                           WD40   8 tGH.ssvtslafspdgaw.lasGsdDgtvriW 37 
                                     GH + v+++af+   +w +as  +D+ + iW
  gene269|gene269|rna269|rna269 342 GGHtNTVCDFAFNGLEPWeIASVAEDNVIQIW 373
                                    59*999************9888899******* PP

>> Ge1_WD40  WD40 region of Ge1, enhancer of mRNA-decapping protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.1     0.079   4.7e+02     129     166 ..      47      84 ..       9     137 .. 0.67
   2 !    9.7   0.0     6e-05      0.36      39     105 ..     175     242 ..     154     297 .. 0.81
   3 ?    1.8   0.0     0.016        93      64     101 ..     344     381 ..     338     384 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.079
                       Ge1_WD40 129 yipeedaeesdddeaskllvltrgdkaeiwsvdmiask 166
                                    + pe   +e+++  +++ll+ t++++ e   +++++  
  gene269|gene269|rna269|rna269  47 FFPEATRNEKNNTTTQRLLISTHTSQNEDEFIKILSVT 84 
                                    55666666667777777788777777664444444444 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 6e-05
                       Ge1_WD40  39 kvkntgeglvrvvnketeeraLlkglkgevldlafahvsskillavdekgslfvykveeve.skllvs 105
                                     +++  +glv v ++e ++   l g  g v d +f++ s+++l +  +  ++++++ ++++ +kl   
  gene269|gene269|rna269|rna269 175 LATSGEDGLVCVFDIEKNTAEKLAGHDGVVGDCNFSFFSENVLFSCGDDRNIIMWDTRTQKhEKLENA 242
                                    4455558*************************************999********9987763566554 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.016
                       Ge1_WD40  64 lkgevldlafahvsskillavdekgslfvykveevesk 101
                                     +++v d+af  ++   +++v e   ++++++++ +++
  gene269|gene269|rna269|rna269 344 HTNTVCDFAFNGLEPWEIASVAEDNVIQIWQMSRAQKE 381
                                    67899**************************9988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (385 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       671  (0.0374254); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 2556.85
//
Query:       gene2690|gene2690|rna2690|rna2690  [L=268]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        2.1    8.6   0.0        2.1    8.6   0.0    3.3  3  UPF0239   Uncharacterised protein family (UPF0239)


Domain annotation for each model (and alignments):
>> UPF0239  Uncharacterised protein family (UPF0239)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.0   0.00012       2.1      25      75 ..       2      46 ..       1      68 [. 0.54
   2 ?   -1.5   1.4      0.17     3e+03      66      66 ..     120     120 ..      86     163 .. 0.61
   3 ?   -2.6   3.0      0.36   6.4e+03      55      70 ..     209     224 ..     193     268 .] 0.60

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00012
                            UPF0239 25 LflGAifqlvCilAiillpsskseesveeeaesseeksseqvkkpkaaaaq 75
                                       LflGAi+   C+l ++  +s+++ ++  +e   + +k  + +k++ + ++ 
  gene2690|gene2690|rna2690|rna2690  2 LFLGAILH--CVLCVM--ASNRDADQSLKEPLIKSDK--DGNKSNTEIVKV 46
                                       9*****87..666544..4444444433332222221..333333333333 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.17
                            UPF0239  66 v 66 
                                         
  gene2690|gene2690|rna2690|rna2690 120 S 120
                                        1 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 0.36
                            UPF0239  55 aesseeksseqvkkpk 70 
                                        +es+ +k++++ ++p+
  gene2690|gene2690|rna2690|rna2690 209 SESTVNKETSTSRSPE 224
                                        3333333333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (268 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1277  (0.0712254); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.42
# Mc/sec: 1913.64
//
Query:       gene2691|gene2691|rna2691|rna2691  [L=246]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
      0.068   12.8   0.5       0.09   12.4   0.5    1.2  1  T3SS_HrpK1  Type III secretion system translocator protein, H


Domain annotation for each model (and alignments):
>> T3SS_HrpK1  Type III secretion system translocator protein, HrpF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.5     5e-06      0.09     127     234 ..     111     218 ..      72     221 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 5e-06
                         T3SS_HrpK1 127 sggglttkedladLqknaglsaalknaakawstdGlfdaldraGedkatekaDkllsaknlssfikddaPtndeqe 202
                                        + g  t+ ++ + L   + + +  kn +   s++G++++ld a + ++  ++ + +s+ n  + i  d+  +  ++
  gene2691|gene2691|rna2691|rna2691 111 QLGIRTSTKKSKSLGCISKIDPVCKNMCDNISSNGAMSSLDTASTSRSYMNEKNRYSQANPVNEICYDSDVDSIDT 186
                                        555556666667777777788899************************9999999999998888999999999999 PP

                         T3SS_HrpK1 203 aallkdaalknitantDiskLnkDvfakPknY 234
                                          ++++ ++ n  +  +i++  + +f++P+  
  gene2691|gene2691|rna2691|rna2691 187 SGVFSNDGATNEDGWDEIARKLDAIFSDPETL 218
                                        99999999999999999*99999999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       528  (0.0294495); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1636.44
//
Query:       gene2692|gene2692|rna2692|rna2692  [L=108]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       416  (0.0232026); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 834.07
//
Query:       gene2693|gene2693|rna2693|rna2693  [L=56]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (56 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       406  (0.0226449); expected 358.6 (0.02)
Passed bias filter:                      196  (0.010932); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.26s 00:00:00.61 Elapsed: 00:00:00.42
# Mc/sec: 402.44
//
Query:       gene2694|gene2694|rna2694|rna2694  [L=114]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0012   19.0   0.0     0.0019   18.3   0.0    1.3  1  MutS_V    MutS domain V


Domain annotation for each model (and alignments):
>> MutS_V  MutS domain V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   1.1e-07    0.0019      18      59 ..      69     109 ..      63     113 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.1e-07
                                        HHHHHHHHHHT--BSSSEEEEE--SEEEEEE--------SS- CS
                             MutS_V  18 valivllaqiGsfvpaekaeisivdkiftRvgasDdlakgks 59 
                                         + i+++ qiG ++p + ++++i+dk++++++++D+l++  s
  gene2694|gene2694|rna2694|rna2694  69 LGQIIVMHQIGGYLPPD-THLPIFDKLYSKITTNDSLKTLFS 109
                                        56799**********86.69****************988665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (114 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       543  (0.0302861); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 843.58
//
Query:       gene2695|gene2695|rna2695|rna2695  [L=79]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.13   12.5   0.1       0.15   12.3   0.1    1.1  1  MutS_III  MutS domain III


Domain annotation for each model (and alignments):
>> MutS_III  MutS domain III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   8.4e-06      0.15     152     191 .]      15      54 ..       3      54 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 8.4e-06
                                        HHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHHHHHHHHH CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           MutS_III 152 iealeqelfqelleeveealerlrrlaealaeLDvllSlA 191
                                        i +le e+++el    e+++++++ +++ ++ LDv+ SlA
  gene2695|gene2695|rna2695|rna2695  15 IIDLELEILDELKIYTEKYTSQIKIAVDYISKLDVFNSLA 54 
                                        6788889999999888889********************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       632  (0.0352502); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 530.53
//
Query:       gene2696|gene2696|rna2696|rna2696  [L=260]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00014   21.4   0.0    0.00022   20.8   0.0    1.4  1  Exo_endo_phos    Endonuclease/Exonuclease/phosphatase family
  ------ inclusion threshold ------
      0.052   13.4   0.1       0.14   12.0   0.0    1.8  2  Exo_endo_phos_2  Endonuclease-reverse transcriptase
       0.11   13.0   0.0         18    5.9   0.0    2.4  2  CbiG_C           Cobalamin synthesis G C-terminus


Domain annotation for each model (and alignments):
>> Exo_endo_phos  Endonuclease/Exonuclease/phosphatase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   3.7e-08   0.00022       2     167 ..      77     232 ..      76     260 .] 0.63

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 3.7e-08
                                        EEEESTGCHHHHTHHHHHHHHHHHHHHCTTSEEEEEEEBSCTCHHHHHHHHHTTCEEEEECCHECSSSTTSSEEEE CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Exo_endo_phos   2 twNvngqaspalgssrrsdrladlltaydaDvlgLQEvdddelsriplllalggflgasstsptgggggggnggav 77 
                                        t+N+ng+ +        s  + + l + ++D+l++QE+  +e+  +        + ++++t     + ++ +g ++
  gene2696|gene2696|rna2696|rna2696  77 TFNINGFRN-------KSEEVYAFLDRRRPDILAMQETLLSEERYR-------TYIPGYTTI-EAKMTDREGGRGL 137
                                        9*****844.......4667*****************776665332.......222222222.2344455555555 PP

                                        EECSTE.EEEEEEEEEETSSSSGCEEEEEEEEEEEEEEE....CCCHHGHHHHHHHHHHHHHHHHHHHHHTTSEEE CS
                                        xxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Exo_endo_phos  78 lsrfpl.tslfrrtfiefndlvaalrreplaakleqlni....ashrdhdlvrdlqllalllqvealnadrgapvi 148
                                        l + ++ + l    +  + ++ a ++   +  k+++         + d +  r+++++   l   +l++++ + +i
  gene2696|gene2696|rna2696|rna2696 138 LLSVRNnRGLRLSEYKSDPNYLAGIIEGLDMQKEKFSMLiinvYASCDSKTKRQTIQQVCRLVERELQRQKFKEII 213
                                        5554443666555555555555555555555555555558877677777777777777777777777777778899 PP

                                        EEEE-SSSTSGGGBSCGHH CS
                                        xxxxxxxxxxxxxxxxxxx RF
                      Exo_endo_phos 149 vaGDfNarpsdddsrvlrt 167
                                         +GD N +p     r++  
  gene2696|gene2696|rna2696|rna2696 214 MLGDWNDTPEKTYNRLTKQ 232
                                        9******887766666554 PP

>> Exo_endo_phos_2  Endonuclease-reverse transcriptase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0      0.88   5.3e+03      42      61 ..      20      38 ..       8      55 .. 0.56
   2 ?   12.0   0.0   2.4e-05      0.14       1      42 [.     175     221 ..     175     250 .. 0.69

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 0.88
                    Exo_endo_phos_2 42 khplWgsedtds.sargeeLi 61
                                       +h  W    +++ +++++ ++
  gene2696|gene2696|rna2696|rna2696 20 RHDIWIA--SNTyKENEKLIL 38
                                       5555544..222123333333 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 2.4e-05
                    Exo_endo_phos_2   1 lliisvYippsdelenlestlekllselksp.......kiiilGDfNak 42 
                                        +lii+vY + ++  ++  +t++++++ + ++       +ii+lGD+N +
  gene2696|gene2696|rna2696|rna2696 175 MLIINVYASCDS--KTKRQTIQQVCRLVERElqrqkfkEIIMLGDWNDT 221
                                        589*********..6666666666665554444445679********54 PP

>> CbiG_C  Cobalamin synthesis G C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0     0.003        18      18      66 ..       7      54 ..       4      75 .. 0.86
   2 ?    4.7   0.0    0.0073        44      25      61 ..     169     205 ..     159     222 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.003
                                       HHHHHHHHHCT--GGGEEEEEESSCCSHHHHHHHHHHHCTSTEEEE-HH CS
                             CbiG_C 18 eaieealeeaglseeavaalatidlKadepgllelaeklglplktfsae 66
                                       + ++++l++ g  ++++  +a+ + K++e+ +l++ e lg p ++++++
  gene2696|gene2696|rna2696|rna2696  7 TKVKKILQKDGRRRHDI-WIASNTYKENEKLILQTLEGLGYPKTFIKQK 54
                                       67889999999988888.79********************998777665 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.0073
                                        HHCT--GGGEEEEEESSCCSHHHHHHHHHHHCTSTEE CS
                             CbiG_C  25 eeaglseeavaalatidlKadepgllelaeklglplk 61 
                                        +++++s+  ++  a+ d K + + ++++++ ++ +l+
  gene2696|gene2696|rna2696|rna2696 169 QKEKFSMLIINVYASCDSKTKRQTIQQVCRLVERELQ 205
                                        677788889999*****************98876665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       960  (0.0535445); expected 358.6 (0.02)
Passed bias filter:                      661  (0.0368676); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 1882.70
//
Query:       gene2697|gene2697|rna2697|rna2697  [L=100]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       657  (0.0366445); expected 358.6 (0.02)
Passed bias filter:                      580  (0.0323498); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 699.43
//
Query:       gene2698|gene2698|rna2698|rna2698  [L=80]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.049   13.8   0.0      0.056   13.6   0.0    1.2  1  SpoVG     SpoVG


Domain annotation for each model (and alignments):
>> SpoVG  SpoVG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   3.1e-06     0.056      25      53 ..      22      58 ..       7      79 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.1e-06
                              SpoVG 25 lddsfvirdikiiegkkg.lfvamPsrkt.......k 53
                                       + +sf  ++ kiie++++   v  P+rk        k
  gene2698|gene2698|rna2698|rna2698 22 VSNSFEAHNKKIIEQDNKrARVETPKRKIeevvaptK 58
                                       6799**********88888*********955555441 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1678  (0.0935914); expected 358.6 (0.02)
Passed bias filter:                      513  (0.0286129); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 528.77
//
Query:       gene2699|gene2699|rna2699|rna2699  [L=71]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (71 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       333  (0.0185733); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.31s 00:00:00.72 Elapsed: 00:00:00.48
# Mc/sec: 444.07
//
Query:       gene27|gene27|rna27|rna27  [L=169]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      6e-07   29.2   4.8      1e-06   28.4   4.8    1.4  1  Sec66           Preprotein translocase subunit Sec66
  ------ inclusion threshold ------
        0.1   11.8   2.1        1.9    7.7   0.1    2.1  2  MFS_Mycoplasma  Mycoplasma MFS transporter
       0.18   12.2   4.3          5    7.5   0.0    3.1  3  TSC22           TSC-22/dip/bun family


Domain annotation for each model (and alignments):
>> Sec66  Preprotein translocase subunit Sec66
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4   4.8   1.7e-10     1e-06      12     172 ..       6     151 ..       1     159 [. 0.78

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 1.7e-10
                      Sec66  12 avligslatfsslyrkrkakklaelepwFpenlqrdiYlsllhlekkkeekvpekvlkA.ALLrravedirrilklreskpale 94 
                                +++++sl+++ s+ r++ + + +      +++++ d Y+ l++          ++vlk  ALL+ a+ ++++     ++k  ++
  gene27|gene27|rna27|rna27   6 IIIFSSLILVFSILRRKSVDTCK------SNSTNLDAYYGLKEN--------ANNVLKTkALLEAAIANLKQREDNYSKKYIIQ 75 
                                45555555544444444444444......457888999999987........346777559*********************** PP

                      Sec66  95 vllqkGsvgddlwqrfqraekeleeElkdvvqeaealkpgWgqtifqsaneilanealrrrleeiekrkeeekeewek 172
                                +++++  ++ ++w+++++ +k le E   + +eae +kpgW+  if  a+ +l +++ r++  + e+r++e +   +k
  gene27|gene27|rna27|rna27  76 QMYNQRLLSPKIWDNLRTLIKDLEYEQLVIEAEAELIKPGWN--IFGDASKMLPHQKKREEKMDKENRTRENSFLLKK 151
                                *****************************************7..9*********998877665555555544433333 PP

>> MFS_Mycoplasma  Mycoplasma MFS transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.1   0.00032       1.9      45      96 ..       3      53 ..       1      59 [. 0.82
   2 ?    4.0   0.3    0.0043        26      60     102 ..     118     160 ..     111     167 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00032
             MFS_Mycoplasma 45 tvlillilvilivyalfgkevdtvakkekqtkteqtlskkvsalsvlKrket 96
                                v+i++++ +++v+ ++ ++     k+ + t+ +  ++ k  a +vlK+k+ 
  gene27|gene27|rna27|rna27  3 PVIIIIFSSLILVFSILRRKSVDTCKS-NSTNLDAYYGLKENANNVLKTKAL 53
                               578899999999999998885555555.89999999************9975 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.0043
             MFS_Mycoplasma  60 lfgkevdtvakkekqtkteqtlskkvsals.vlKrketyklili 102
                                +fg    ++++++k+  ++++ +++    s +lK+ket +  l+
  gene27|gene27|rna27|rna27 118 IFGDA-SKMLPHQKKREEKMDKENRTRENSfLLKKKETLENQLM 160
                                67776.78889989999999999987766637899999876555 PP

>> TSC22  TSC-22/dip/bun family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0    0.0054        32      13      45 ..      21      53 ..      14      66 .. 0.86
   2 ?    7.5   0.0   0.00084         5      17      41 ..      89     113 ..      88     118 .. 0.92
   3 ?   -0.9   0.3      0.35   2.1e+03      35      40 ..     143     148 ..     131     165 .. 0.55

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.0054
                      TSC22 13 rEeVevLkekIkeLeernseleeENslLkalas 45
                               r  V++ k++ ++L +     e+ N++Lk+ a 
  gene27|gene27|rna27|rna27 21 RKSVDTCKSNSTNLDAYYGLKENANNVLKTKAL 53
                               77899************************8875 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.00084
                      TSC22  17 evLkekIkeLeernseleeENslLk 41 
                                ++L++ Ik+Le++   +e E +l k
  gene27|gene27|rna27|rna27  89 DNLRTLIKDLEYEQLVIEAEAELIK 113
                                79******************99988 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 0.35
                      TSC22  35 eENslL 40 
                                +ENs+L
  gene27|gene27|rna27|rna27 143 RENSFL 148
                                455554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (169 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1112  (0.0620224); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1242.19
//
Query:       gene270|gene270|rna270|rna270  [L=121]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      9e-08   32.0   0.7    3.3e-06   26.9   0.4    2.0  2  DIM1      Mitosis protein DIM1


Domain annotation for each model (and alignments):
>> DIM1  Mitosis protein DIM1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.5   0.0    0.0015        27       6      59 ..       6      56 ..       4      64 .. 0.71
   2 !   26.9   0.4   1.8e-10   3.3e-06      77     128 ..      62     112 ..      46     115 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.0015
                                   -SHHHHHHHHHH-SSSEEEEEEE-TT-HHHHHHHHHHHHHHHHTTTTEEEEEEE CS
                           DIM1  6 etkeevdqailseeerlvviRFGrdedaeClklDelLakiaeklknfaviylvd 59
                                   +tk ++++ il++e+++ v+  Gr+  a+      l ++   +++++a++ + +
  gene270|gene270|rna270|rna270  6 KTKADLNTQILQNENHIKVVSHGRKYFAH---YSSLFNELEYRVSKLAKFVIYE 56
                                   57889999***************987654...5555555555666666555555 PP

  == domain 2  score: 26.9 bits;  conditional E-value: 1.8e-10
                                    EEEEEETTEEEEEE-SSS--SSB-S----HHHHHHHHHHHHHHHHHT-SEEE CS
                           DIM1  77 tilffyrnkhmkvDfgtgdnnKlnfvledkqelidiietiyrgakkgkglvv 128
                                     + f+y n  +kvD+g g+ + + + l +++++++ii+++y +a  g+ +v 
  gene270|gene270|rna270|rna270  62 GLQFYYDNCLIKVDCGIGNTEIVDYEL-TRDQFVEIIKVVYMAAVNGRKVVF 112
                                    577**************9988777777.5788****************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       590  (0.0329076); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 955.14
//
Query:       gene2700|gene2700|rna2700|rna2700  [L=63]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (63 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       216  (0.0120475); expected 358.6 (0.02)
Passed bias filter:                      159  (0.00886831); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.29s 00:00:00.67 Elapsed: 00:00:00.45
# Mc/sec: 419.17
//
Query:       gene2701|gene2701|rna2701|rna2701  [L=73]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (73 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       175  (0.00976072); expected 358.6 (0.02)
Passed bias filter:                      145  (0.00808746); expected 358.6 (0.02)
Passed Vit filter:                         5  (0.000278878); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 514.85
//
Query:       gene2702|gene2702|rna2702|rna2702  [L=41]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (41 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                        80  (0.00446204); expected 358.6 (0.02)
Passed bias filter:                       74  (0.00412739); expected 358.6 (0.02)
Passed Vit filter:                         6  (0.000334653); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.47
# Mc/sec: 261.86
//
Query:       gene2703|gene2703|rna2703|rna2703  [L=59]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.046   13.8   0.2      0.061   13.4   0.2    1.2  1  DUF397     Domain of unknown function (DUF397)
      0.083   12.4   0.0      0.095   12.2   0.0    1.0  1  AbiJ_NTD3  AbiJ N-terminal domain 3


Domain annotation for each model (and alignments):
>> DUF397  Domain of unknown function (DUF397)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.2   6.9e-06     0.061       3      36 ..       2      33 ..       1      41 [. 0.77

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 6.9e-06
                             DUF397  3 WrKSsySggggg.nCVEvaalpd.avavRDSkdpdg 36
                                       W  S   g++ g  C E  +  +    vR+Sk+p++
  gene2703|gene2703|rna2703|rna2703  2 WTTSVNGGQNTGaPCTETVR--EpE--VRESKEPSH 33
                                       99999999999966****44..445..******944 PP

>> AbiJ_NTD3  AbiJ N-terminal domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   1.1e-05     0.095      89     119 ..      18      48 ..      17      56 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.1e-05
                          AbiJ_NTD3  89 eelvhPdvrpdeeeqrrlveaiNelLrkdGy 119
                                        e++  P+vr+++e   +lv+++  +L +dGy
  gene2703|gene2703|rna2703|rna2703  18 ETVREPEVRESKEPSHQLVSRVRAYLDEDGY 48 
                                        56778*************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       313  (0.0174578); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.33u 0.27s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 440.45
//
Query:       gene2704|gene2704|rna2704|rna2704  [L=41]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (41 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       306  (0.0170673); expected 358.6 (0.02)
Passed bias filter:                      250  (0.0139439); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.31u 0.25s 00:00:00.56 Elapsed: 00:00:00.39
# Mc/sec: 317.53
//
Query:       gene2705|gene2705|rna2705|rna2705  [L=60]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.067   13.5   1.3      0.083   13.2   1.3    1.1  1  Comm      Commissureless
      0.074   12.8   0.0      0.077   12.8   0.0    1.0  1  DUF2157   Predicted membrane protein (DUF2157)
        1.6    8.2  11.8       0.34   10.4   1.9    2.1  2  HOK_GEF   Hok/gef family


Domain annotation for each model (and alignments):
>> Comm  Commissureless
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   1.3   1.4e-05     0.083       4      41 ..      18      54 ..      15      58 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.4e-05
                               Comm  4 eriindvwigivltLlilsl.vFclcsCflyrkfrtWkk 41
                                       ++ i+++  + v++L++ s  +F++++ fl    ++W+k
  gene2705|gene2705|rna2705|rna2705 18 KTAISKLIFVCVTILMVGSAiIFVCIAVFL--VLKEWNK 54
                                       567899999********9862577778888..6778986 PP

>> DUF2157  Predicted membrane protein (DUF2157)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   1.3e-05     0.077      12      62 ..       4      50 ..       1      56 [. 0.61

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.3e-05
                            DUF2157 12 eqaqallaryeaeeresarrrsfleallvlGalllglGlilfvAanWqgls 62
                                       +++   ++ry++e++++     +  +++++ +l++g ++i+++ a++  l 
  gene2705|gene2705|rna2705|rna2705  4 QTRHPTAKRYKEETKTAI----SKLIFVCVTILMVGSAIIFVCIAVFLVLK 50
                                       555556778877754444....46777777777777777777766654444 PP

>> HOK_GEF  Hok/gef family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   1.9   5.6e-05      0.34       2      16 ..      20      34 ..      19      35 .. 0.85
   2 ?    3.4   2.7    0.0085        51       5      14 ..      37      46 ..      36      49 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 5.6e-05
                            HOK_GEF  2 alvaliviCiTvLlf 16
                                       a+  li +C+T+L+ 
  gene2705|gene2705|rna2705|rna2705 20 AISKLIFVCVTILMV 34
                                       67779********95 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.0085
                            HOK_GEF  5 aliviCiTvL 14
                                       a+i +Ci+v 
  gene2705|gene2705|rna2705|rna2705 37 AIIFVCIAVF 46
                                       79******96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (60 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1336  (0.0745161); expected 358.6 (0.02)
Passed bias filter:                      767  (0.0427799); expected 358.6 (0.02)
Passed Vit filter:                        80  (0.00446204); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.29s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 411.29
//
Query:       gene2706|gene2706|rna2706|rna2706  [L=69]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (69 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       174  (0.00970495); expected 358.6 (0.02)
Passed bias filter:                      155  (0.00864521); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.31s 00:00:00.70 Elapsed: 00:00:00.46
# Mc/sec: 447.14
//
Query:       gene2707|gene2707|rna2707|rna2707  [L=753]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.9e-06   27.1   0.0    8.5e-06   25.5   0.0    1.8  2  Sec23_helical   Sec23/Sec24 helical domain
    7.3e-06   25.9   3.2    1.5e-05   24.9   3.2    1.5  1  zf-Sec23_Sec24  Sec23/Sec24 zinc finger


Domain annotation for each model (and alignments):
>> Sec23_helical  Sec23/Sec24 helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.0   9.5e-10   8.5e-06       4      77 ..     532     602 ..     529     620 .. 0.85
   2 ?   -3.4   0.0         1   8.9e+03       4      41 ..     666     703 ..     665     707 .. 0.75

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 9.5e-10
                                        HHHHHHHHHHHHHTTTS-HHHHHHHHHHHHHHHHHHHHHH-------------GGGTTHHHHHHHHHTSTTTS- CS
                      Sec23_helical   4 avtvllakqaidkalesgladarealdtslvdllsayrkvgasgsspsqlqlpeslklLPlyilallKspafrg 77 
                                        ++ ++++k + +++    +++ ++++   lv+ l++yr  +++ s+ + l+lpes+k LP+++ al K++ f  
  gene2707|gene2707|rna2707|rna2707 532 TIFAYYVKVMASEIG--RMEENKKFVMGNLVRTLRTYRMSTQG-SQENHLVLPESIKNLPVLVSALFKNRDFST 602
                                        566666666666664..48899999****************88.88889*********************9975 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 1
                                        HHHHHHHHHHHHHTTTS-HHHHHHHHHHHHHHHHHHHH CS
                      Sec23_helical   4 avtvllakqaidkalesgladarealdtslvdllsayr 41 
                                        +v  +l k++ +k +e++l++++++++    +++ +++
  gene2707|gene2707|rna2707|rna2707 666 VVFFYLLKMVEQKGDERELEELIASFVSEEKEMIENLK 703
                                        67788899999999999999988888777666666655 PP

>> zf-Sec23_Sec24  Sec23/Sec24 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   3.2   1.7e-09   1.5e-05       2      36 ..      92     124 ..      91     126 .. 0.91

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 1.7e-09
                     zf-Sec23_Sec24   2 irCrrCraylNpfckidfggkrwiCnfCnhknevp 36 
                                        +rC++C +y++ ++k    g+++ Cn+C+ kn + 
  gene2707|gene2707|rna2707|rna2707  92 VRCSQCTSYVCEYTKT--EGSTFYCNICGAKNRTE 124
                                        8***************..679***********876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (753 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       866  (0.0483016); expected 358.6 (0.02)
Passed bias filter:                      512  (0.0285571); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.65u 0.28s 00:00:00.93 Elapsed: 00:00:00.44
# Mc/sec: 5087.76
//
Query:       gene2708|gene2708|rna2708|rna2708  [L=416]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.8e-06   26.3   0.1     0.0031   16.8   0.0    3.4  3  Pyr_redox_2      Pyridine nucleotide-disulphide oxidoreductas
    1.3e-05   25.3   0.0     0.0024   17.9   0.0    2.9  3  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
      2e-05   23.9   0.0       0.93    8.6   0.0    3.1  3  K_oxygenase      L-lysine 6-monooxygenase (NADPH-requiring)
    4.1e-05   23.6   0.0    0.00034   20.6   0.0    2.4  2  NAD_binding_9    FAD-NAD(P)-binding
  ------ inclusion threshold ------
      0.012   14.9   0.0       0.21   10.8   0.0    2.6  3  Pyr_redox_3      Pyridine nucleotide-disulphide oxidoreductas
      0.027   15.0   0.2       0.33   11.5   0.0    2.8  3  Pyr_redox        Pyridine nucleotide-disulphide oxidoreductas
      0.073   12.7   0.0       0.27   10.9   0.0    2.0  2  ApbA             Ketopantoate reductase PanE/ApbA
      0.086   13.1   0.0         35    4.6   0.0    3.1  3  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
       0.11   11.7   0.0       0.77    8.9   0.0    2.1  2  FAD_binding_3    FAD binding domain


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0     0.047        95       2      27 ..       2      29 ..       1      63 [. 0.77
   2 !   16.8   0.0   1.5e-06    0.0031     100     189 ..      73     230 ..      67     242 .. 0.65
   3 ?    2.5   0.0     0.034        68     201     241 ..     328     372 ..     320     377 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.047
                                       SEEEE--SHHHHHHHHHHHHH..TS-EE CS
                                       xxxxxxxxxxxxxxxxxxxxx..xxxxx RF
                        Pyr_redox_2  2 dvvviGgGpAGlaaaltlaqa..gakvt 27
                                       ++++iG+Gp  + +  ++ ++  +  ++
  gene2708|gene2708|rna2708|rna2708  2 KICIIGAGPSTYYLTNHIHTHapSTTIH 29
                                       899******9999988888852344444 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 1.5e-06
                                        ESEEEE---EEE-BCTCTTC.....................................................TTB CS
                                        xxxxxxxxxxxxxxxxxxxx....................................................xxxx RF
                        Pyr_redox_2 100 ydklvlAtGssprdlgipGv....................................................aenv 123
                                        yd +v+A G+++r+l  +G+                                                    +   
  gene2708|gene2708|rna2708|rna2708  73 YDGIVVAVGGRARRL--DGAlnkfavygedvvrkggglegrtgrsarllesvleskrmlgrgrrsaeamgleK--- 143
                                        788888888888888..55555567777788887777777777777777777544333333333333323222... PP

                                        EECCSECHHHHHHCCSS-T....................................SEEEEES-SHHHHHHHHHHHH CS
                                        xxxxxxxxxxxxxxxxxxx....................................xxxxxxxxxxxxxxxxxxxxx RF
                        Pyr_redox_2 124 gklvrtldsaealklkllp....................................krivvvGgGyiGvElAaalak 163
                                                         ++                                    +r+++vG+G++++++A +l +
  gene2708|gene2708|rna2708|rna2708 144 -----------------KNkitknknneenentrkdvnsremheslvhakpfsrlRRVAIVGAGNVSLDVANMLYE 202
                                        .................224466666666666666666788888888899999*********************99 PP

                                        HT-E.EEEEESSSSSS.TTS-.HHHHHHH CS
                                        xxxx.xxxxxxxxxxx.xxxx.xxxxxxx RF
                        Pyr_redox_2 164 lgke.vtlveardrll.rald.kelsaal 189
                                         g+  + ++ + ++l   a++  el++++
  gene2708|gene2708|rna2708|rna2708 203 QGVPqIFILSR-NELAkCAFGsYELRRCM 230
                                        99962555554.44443445423444444 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.034
                                        EESCEEEEEEETTE..EEEEEETTSCE..EEESEEEE-S-EEES- CS
                                        xxxxxxxxxxxxxx..xxxxxxxxxxx..xxxxxxxxxxxxxxxx RF
                        Pyr_redox_2 201 klgtsvkeidgnge..klevvledgee..idadlvvvavGvrpst 241
                                         l+t+ + i++n +  +l +++ +g++   ++dlvv ++G++ ++
  gene2708|gene2708|rna2708|rna2708 328 LLNTVLQSIKKNVSlfNLALKTREGTKmlNNVDLVVNCTGYTGRD 372
                                        6788888899888877677889999998899*********98765 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0     0.033        66      14      47 ..       2      36 ..       1      58 [. 0.78
   2 !   17.9   0.0   1.2e-06    0.0024      13      46 ..     182     215 ..     173     223 .. 0.90
   3 ?   -1.0   0.0      0.85   1.7e+03      66      84 ..     349     367 ..     334     371 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.033
                                       EEEEES-SHHHHHHHHHHHCC.T-CEEEEEESSHH CS
                       Shikimate_DH 14 kvlliGaGemaelvakhLlak.gvkkvvvaNRtle 47
                                       k+++iGaG     +++h++++   + + v+  + +
  gene2708|gene2708|rna2708|rna2708  2 KICIIGAGPSTYYLTNHIHTHaPSTTIHVFEKNSS 36
                                       89****************99833456777766655 PP

  == domain 2  score: 17.9 bits;  conditional E-value: 1.2e-06
                                        -EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSH CS
                       Shikimate_DH  13 kkvlliGaGemaelvakhLlakgvkkvvvaNRtl 46 
                                        ++v ++GaG+++  va++L+++gv +++++ R+ 
  gene2708|gene2708|rna2708|rna2708 182 RRVAIVGAGNVSLDVANMLYEQGVPQIFILSRNE 215
                                        79******************************85 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.85
                                        GCGHHHHHHT-SEEEE-SS CS
                       Shikimate_DH  66 leelkellaeadvvisata 84 
                                          e +++l+++d+v+ +t+
  gene2708|gene2708|rna2708|rna2708 349 TREGTKMLNNVDLVVNCTG 367
                                        55667899*******9997 PP

>> K_oxygenase  L-lysine 6-monooxygenase (NADPH-requiring)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.8   0.0    0.0064        13     193     227 ..       2      36 ..       1      49 [. 0.76
   2 !    6.9   0.0    0.0014       2.9     188     263 ..     178     252 ..     151     288 .. 0.74
   3 !    8.6   0.0   0.00047      0.93     290     341 ..     320     369 ..     310     370 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.0064
                        K_oxygenase 193 riaVvGsGqSaaeifedllrrqkkvelklvtrsea 227
                                        +i ++G+G S+  +++++++++++++++++ ++++
  gene2708|gene2708|rna2708|rna2708   2 KICIIGAGPSTYYLTNHIHTHAPSTTIHVFEKNSS 36 
                                        67888888888888888888888888877766554 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0014
                        K_oxygenase 188 llakkriaVvGsGqSaaeifedllrrqkkvelklvtrsealeplddspfvneifsPeyvdyfyslpeekreallke 263
                                          + +r+a+vG+G    ++++ l+++    ++ +++r+e  + +  s     +++ + v+ +     ++r+ ++  
  gene2708|gene2708|rna2708|rna2708 178 FSRLRRVAIVGAGNVSLDVANMLYEQGV-PQIFILSRNELAKCAFGSYELRRCMHDKNVRVWGGTVGNDRRGMIVG 252
                                        56779**************998887744.69999999998888888887788888888888777777777766654 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.00047
                        K_oxygenase 290 kgeerlrllpnrevesaeaegkgeveltlrneesgeeetlevdavvlATGYr 341
                                        + +++l ll n+ ++s++++ +  ++l l+   +g++   +vd vv +TGY+
  gene2708|gene2708|rna2708|rna2708 320 QPKQTLYLLLNTVLQSIKKNVS-LFNLALKT-REGTKMLNNVDLVVNCTGYT 369
                                        44667899************97.99999988.7799999************6 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   1.7e-07   0.00034       1      63 [.       4      63 ..       4      78 .. 0.78
   2 ?   -0.6   0.0       0.6   1.2e+03       1      19 [.     185     203 ..     185     219 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 1.7e-07
                      NAD_binding_9  1 aivGaGprGlavlerLlarakkkspleitlfdp.sepgagrvwrtdqseelllNvpasemslft 63
                                       +i+GaGp++ ++++++  +a    +++i++f++ s+p +      + ++++++N +  ++++++
  gene2708|gene2708|rna2708|rna2708  4 CIIGAGPSTYYLTNHIHTHA---PSTTIHVFEKnSSPLQSLKLFHT-KPTMRINNVLCNIKVHK 63
                                       59*****************5...99********6666655555555.36778887777777665 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.6
                      NAD_binding_9   1 aivGaGprGlavlerLlar 19 
                                        aivGaG   l v++ L ++
  gene2708|gene2708|rna2708|rna2708 185 AIVGAGNVSLDVANMLYEQ 203
                                        8******999999999877 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0      0.84   1.7e+03       2       8 ..       5      11 ..       4      96 .. 0.63
   2 ?   10.8   0.0   0.00011      0.21     151     189 ..     168     206 ..     150     238 .. 0.75
   3 ?    0.8   0.0      0.12   2.4e+02     225     269 ..     323     370 ..     309     375 .. 0.75

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.84
                        Pyr_redox_3  2 IiGaGPa 8 
                                       IiGaGP 
  gene2708|gene2708|rna2708|rna2708  5 IIGAGPS 11
                                       6677764 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00011
                        Pyr_redox_3 151 khyskvkefhkya.gqkvvViGgknSavDaAlelvrkgae 189
                                        +h s v++  +++  ++v+++G++n + D+A  l+++g  
  gene2708|gene2708|rna2708|rna2708 168 MHESLVHAK-PFSrLRRVAIVGAGNVSLDVANMLYEQGVP 206
                                        555555444.5553789********************974 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.12
                        Pyr_redox_3 225 ekikvlfnaevkeikekeeey..kvktedgkkvevkddvvla.tGykp 269
                                        +++ +l n+ +++ik++ + +   +kt++g+k+ ++ d v+  tGy+ 
  gene2708|gene2708|rna2708|rna2708 323 QTLYLLLNTVLQSIKKNVSLFnlALKTREGTKMLNNVDLVVNcTGYTG 370
                                        5567778888888988776552256799999999988877777***85 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       1.5     3e+03       3      33 ..       4      36 ..       2      90 .. 0.61
   2 ?   11.5   0.0   0.00017      0.33       1      32 [.     183     215 ..     183     246 .. 0.75
   3 ?   -1.2   0.0       1.5     3e+03      57      70 ..     327     340 ..     322     349 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1.5
                                       EEECSSHHHHHHHHHHHHTT..SEEEEEESSSS CS
                          Pyr_redox  3 vvvGgGyiglElAgalaelg..kkVtvversdk 33
                                        ++G+G +   l + ++ ++    ++v+e ++ 
  gene2708|gene2708|rna2708|rna2708  4 CIIGAGPSTYYLTNHIHTHApsTTIHVFEKNSS 36
                                       566666554444444433332223334444433 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00017
                                        EEEEECSSHHHHHHHHHHHHTTS.EEEEEESSS CS
                          Pyr_redox   1 kvvvvGgGyiglElAgalaelgk.kVtvversd 32 
                                        +v++vG+G++ l++A++l e g  ++ ++ r++
  gene2708|gene2708|rna2708|rna2708 183 RVAIVGAGNVSLDVANMLYEQGVpQIFILSRNE 215
                                        79****************998863666666554 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 1.5
                                        EECSEEEEEEEEET CS
                          Pyr_redox  57 vllntkveeiegse 70 
                                        +llnt++++i+++ 
  gene2708|gene2708|rna2708|rna2708 327 LLLNTVLQSIKKNV 340
                                        78999999999886 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       2.7   5.5e+03       1      17 [.       3      19 ..       3      38 .. 0.69
   2 ?   10.9   0.0   0.00013      0.27       1      45 [.     184     228 ..     184     241 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 2.7
                                       EEEES-SHHHHHHHHHH CS
                               ApbA  1 iailGaGaiGsllaakL 17
                                       i+i+GaG    +l  ++
  gene2708|gene2708|rna2708|rna2708  3 ICIIGAGPSTYYLTNHI 19
                                       78999996655555555 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00013
                                        EEEES-SHHHHHHHHHHHHHTHCEEEE-SCHHHHHHHHHCEEEEE CS
                               ApbA   1 iailGaGaiGsllaakLakagadvtlilrsrrlealkknGlrlts 45 
                                        +ai+GaG ++  +a +L+++g + ++il +++l++     ++l++
  gene2708|gene2708|rna2708|rna2708 184 VAIVGAGNVSLDVANMLYEQGVPQIFILSRNELAKCAFGSYELRR 228
                                        69*********************9999999977766655555555 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.45     9e+02       1      42 [.       3      43 ..       3      71 .. 0.83
   2 ?    3.9   0.0      0.03        59       1      34 [.     184     215 ..     184     227 .. 0.88
   3 ?    4.6   0.0     0.018        35      64      81 ..     353     370 ..     331     380 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.45
                                       EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHC CS
                    Sacchrp_dh_NADP  1 vliiGaGsvGqavaellarhfdvdaeitvadrskeklealaa 42
                                       + iiGaG     ++  ++ h + + +i+v +++ + l+ l+ 
  gene2708|gene2708|rna2708|rna2708  3 ICIIGAGPSTYYLTNHIHTHAPST-TIHVFEKNSSPLQSLKL 43
                                       6799**999999999999999874.99999999998887754 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.03
                                        EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESSH CS
                    Sacchrp_dh_NADP   1 vliiGaGsvGqavaellarhfdvdaeitvadrsk 34 
                                        v i+GaG+v+  va +l +++    +i + +r++
  gene2708|gene2708|rna2708|rna2708 184 VAIVGAGNVSLDVANMLYEQGVP--QIFILSRNE 215
                                        689***************99865..9*9999986 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.018
                                        HHHHTTSSEEEE-SSGGG CS
                    Sacchrp_dh_NADP  64 aallkegdlvvnlsppis 81 
                                        +++l+  dlvvn+++++ 
  gene2708|gene2708|rna2708|rna2708 353 TKMLNNVDLVVNCTGYTG 370
                                        789************984 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.24   4.8e+02       3      19 ..       2      18 ..       1      40 [. 0.78
   2 ?    8.9   0.0   0.00039      0.77       4      32 ..     184     212 ..     182     220 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.24
                                       EEEEE--SHHHHHHHHH CS
                      FAD_binding_3  3 dVlIVGaGpaGlmlall 19
                                       +++I+GaGp+   l++ 
  gene2708|gene2708|rna2708|rna2708  2 KICIIGAGPSTYYLTNH 18
                                       689******87766665 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00039
                                        EEEE--SHHHHHHHHHHHHTTHHEEEEES CS
                      FAD_binding_3   4 VlIVGaGpaGlmlallLseaGvrvvlvek 32 
                                        V+IVGaG + l  a++L e+Gv  + +  
  gene2708|gene2708|rna2708|rna2708 184 VAIVGAGNVSLDVANMLYEQGVPQIFILS 212
                                        99********************8776644 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (416 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1053  (0.0587317); expected 358.6 (0.02)
Passed bias filter:                      617  (0.0344135); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.64u 0.28s 00:00:00.92 Elapsed: 00:00:00.46
# Mc/sec: 2691.21
//
Query:       gene2709|gene2709|rna2709|rna2709  [L=59]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.032   13.9   0.1      0.033   13.9   0.1    1.1  1  UTP15_C      UTP15 C terminal
      0.032   14.1   0.0      0.033   14.1   0.0    1.0  1  ATP13        Mitochondrial ATPase expression
      0.059   13.7   0.0      0.066   13.6   0.0    1.1  1  Uteroglobin  Uteroglobin family


Domain annotation for each model (and alignments):
>> UTP15_C  UTP15 C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   5.5e-06     0.033      76     115 ..       6      45 ..       1      56 [. 0.78

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.5e-06
                            UTP15_C  76 epiLkfllkhitdpryvsllvdvanvlldlyseklgqsee 115
                                          iL+++l  ++  ++++ ++d++n ++d y+e+ g +e 
  gene2709|gene2709|rna2709|rna2709   6 AIILSIILSIVCMHSHAQECLDLMNEIIDCYNESEGVNES 45 
                                        568888888889999*****************98766554 PP

>> ATP13  Mitochondrial ATPase expression
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   5.5e-06     0.033      56     100 ..       8      55 ..       3      59 .] 0.84

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 5.5e-06
                              ATP13  56 lLkaivssfsynneiesAlklvdkfskkYpe...ielkkefWeellew 100
                                        +L  i+s+ + +++ ++ l+l+++++  Y+e   ++ +++++++ ++ 
  gene2709|gene2709|rna2709|rna2709   8 ILSIILSIVCMHSHAQECLDLMNEIIDCYNEsegVNESRQVYSKRIRV 55 
                                        6778999999999*****************988888888888776655 PP

>> Uteroglobin  Uteroglobin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   1.1e-05     0.066       2      39 ..       3      40 ..       2      54 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.1e-05
                                       XXXXXXXXXXXXXXXXXXXX---HHHHHHHHHHHHS-H CS
                        Uteroglobin  2 klavvllLvalaLccyagsaegCpaleevvekflegse 39
                                       k ++++l ++l ++c+ ++a+ C +l++++ +  ++se
  gene2709|gene2709|rna2709|rna2709  3 KRSAIILSIILSIVCMHSHAQECLDLMNEIIDCYNESE 40
                                       778899999*********************99986554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       791  (0.0441185); expected 358.6 (0.02)
Passed bias filter:                      530  (0.029561); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.29s 00:00:00.69 Elapsed: 00:00:00.45
# Mc/sec: 391.06
//
Query:       gene271|gene271|rna271|rna271  [L=355]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.5e-50  172.4   8.6    2.7e-49  168.2   8.6    2.7  1  RNA_pol_Rpb1_1  RNA polymerase Rpb1, domain 1
  ------ inclusion threshold ------
       0.45   10.0   0.1       0.45   10.0   0.1    2.7  3  zf-FLZ          zinc-finger of the FCS-type, C2-C2
        1.3    9.4   3.7       0.55   10.6   0.3    2.1  2  Rpr2            RNAse P Rpr2/Rpp21/SNM1 subunit domain


Domain annotation for each model (and alignments):
>> RNA_pol_Rpb1_1  RNA polymerase Rpb1, domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  168.2   8.6   4.6e-53   2.7e-49       2     312 .]      28     340 ..      27     340 .. 0.76

  Alignments for each domain:
  == domain 1  score: 168.2 bits;  conditional E-value: 4.6e-53
                                    E---EEEEEE--HHHHHHH-SBB--STTSTCSTSSSSBBSSSSSSSSS-SSSSSTSTTTSSTTTT-----EEEEEECEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 RNA_pol_Rpb1_1   2 kkikeiqfgiaspeeirkwSvvevtkaetieekslkPeegGllDerlgtidkdleCetCgkkkkeCeghfGhieLakPvf 81 
                                     ki++i+fgi++++  +++Sv +++k+e+++ +++kP  gG+lD++lg ++    CetC+k+ +eC ghfGhieL+ Pvf
  gene271|gene271|rna271|rna271  28 TKIESINFGILTEQRAKELSVLKISKREIYDINTEKPMVGGVLDPKLGLSSPGELCETCNKTLQECAGHFGHIELTLPVF 107
                                    58****************************************************************************** PP

                                    -HHHHHHHHHHCTTCETTTTEBSS-TTSH....HHHHHHCSSSCCCCHHHHHHHHCCS-BE-SSSSB-EEE......... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......... RF
                 RNA_pol_Rpb1_1  82 higffklilkilecvckecskllldeekkkllsklkkrekleelkkrlkaieelckkinlcekCgavqpkl......... 152
                                    h g+ k+ +kil+++ck+cs++ll e+k      + +r + +++ +  + +    kk ++c  C  +++ +         
  gene271|gene271|rna271|rna271 108 HPGYQKMLVKILQTICKKCSRILLPEKKI-----FLYRINNKNIFNDDT-LFGEAKKNQTCFYCSYTNGAVkkgigtkil 181
                                    ************************99876.....334444444443333.333345556777777755555555555556 PP

                                    .................EEETTEEEEEESSSSTSCEEEE-HHHHHHHHHCSTHHHHHHTTSBTTTB-GGGCCECCEEE-- CS
                                    .................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 RNA_pol_Rpb1_1 153 .................eeegeklkaalkkskeeekeklsaekvkkllkriededvevlgfkssgsrPewliltvlPVpP 215
                                                      e+   l+ + k ++e  ++ + + +v + +++ +        ++++ +  +++++++++VpP
  gene271|gene271|rna271|rna271 182 ysgydlnpvvvrsllsqIEDYDLLNFNKKGCNELYDNICDTGRVDHSFNDTS----LQPHLRNDFNLFTNIVVSTVLVPP 257
                                    6665333333333333211112222222223333344444444444444444....44556666666689********** PP

                                    GGGS-BEESSSSSEEBECCCCHHHHHHHHHHHHHHHHHSSSSSTCHHHHHHHHHHHHHHCC-TTSSSSSEEBSTTSSS-- CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 RNA_pol_Rpb1_1 216 peiRPsvqldggrrsedDlteklrdiikrNnrLkkaeeegapeliieeekelLQehvatlfdneisglkpatqkskrplk 295
                                    ++ RPsv++d+   +edDlt kl++ ++   ++ + +++     ++ +++elL       f++ isg          +l+
  gene271|gene271|rna271|rna271 258 ACSRPSVKTDEFGSNEDDLTIKLSEMVQLSGTIVNSLTTSSL-TLLLNDWELLNN----TFNSYISG---------NNLR 323
                                    *********************************999999885.566678999854....45555555.........78** PP

                                    THHHHHTSSSSCCCCCT CS
                                    xxxxxxxxxxxxxxxxx RF
                 RNA_pol_Rpb1_1 296 slsqrLkGKeGrfRgnL 312
                                    sl +rLkGK+GrfR+nL
  gene271|gene271|rna271|rna271 324 SLLTRLKGKQGRFRNNL 340
                                    ****************9 PP

>> zf-FLZ  zinc-finger of the FCS-type, C2-C2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.7     0.046   2.8e+02      15      25 ..      82      92 ..      81      97 .. 0.85
   2 ?   10.0   0.1   7.6e-05      0.45      15      33 ..     122     140 ..     116     143 .. 0.90
   3 ?   -2.9   0.4      0.84     5e+03      14      20 ..     160     166 ..     157     167 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.046
                         zf-FLZ 15 aCflCkkkLge 25
                                    C  C+k L+e
  gene271|gene271|rna271|rna271 82 LCETCNKTLQE 92
                                   6********86 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 7.6e-05
                         zf-FLZ  15 aCflCkkkLgegkDiymYr 33 
                                    +C  C++ L ++k i++Yr
  gene271|gene271|rna271|rna271 122 ICKKCSRILLPEKKIFLYR 140
                                    7*****************9 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 0.84
                         zf-FLZ  14 saCflCk 20 
                                    ++Cf+C+
  gene271|gene271|rna271|rna271 160 QTCFYCS 166
                                    5799996 PP

>> Rpr2  RNAse P Rpr2/Rpp21/SNM1 subunit domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.3      0.59   3.5e+03      46      55 ..      81      90 ..      74      94 .. 0.83
   2 ?   10.6   0.3   9.1e-05      0.55      41      61 ..     116     136 ..     110     166 .. 0.72

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.59
                                   TB-TTT--B- CS
                           Rpr2 46 tvCkkCgsvl 55
                                   ++C++C++ l
  gene271|gene271|rna271|rna271 81 ELCETCNKTL 90
                                   5899999877 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 9.1e-05
                                    STCCCTB-TTT--B--CTTTE CS
                           Rpr2  41 psvkrtvCkkCgsvlipgvtc 61 
                                     ++ +t+CkkC+ +l+p+ + 
  gene271|gene271|rna271|rna271 116 VKILQTICKKCSRILLPEKKI 136
                                    57889************9765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (355 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       553  (0.0308439); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 2375.52
//
Query:       gene2710|gene2710|rna2710|rna2710  [L=220]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.014   15.2   0.0      0.021   14.6   0.0    1.3  1  UBA_4     UBA-like domain
      0.022   15.3   0.1      0.066   13.8   0.0    1.8  2  SEP       SEP domain


Domain annotation for each model (and alignments):
>> UBA_4  UBA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   2.3e-06     0.021       2      34 ..       5      37 ..       4      39 .. 0.94

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.3e-06
                              UBA_4  2 eliaqFqaiTGadeekArqlLeannWdLerAis 34
                                       ++i  +++ ++++  +A qlL+ +n d++ Ai+
  gene2710|gene2710|rna2710|rna2710  5 DKIKKLMSACNISQHEAEQLLQLSNDDVDLAIT 37
                                       689999*************************96 PP

>> SEP  SEP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   7.4e-06     0.066       1      64 [.      63     124 ..      63     133 .. 0.87
   2 ?   -3.3   0.0       1.6   1.5e+04      40      52 ..     148     160 ..     142     162 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 7.4e-06
                                SEP   1 ltlwknGFsvdDGelrsyddpenaeflesikkGevPeelekvekgeevevnledrrneeykppk 64 
                                        ++ +knG  +d + + ++d  e +++ ++i+ Ge+   +   +++e  e+++e + + +y +++
  gene2710|gene2710|rna2710|rna2710  63 IKTYKNGVLLD-DRFIEMDAAELKKLRTMIEHGEFDARMVGGKDNEMAEFEVE-NYDVDYGNTE 124
                                        678****9995.79**************************999*********9.5588887755 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 1.6
                                SEP  40 ekvekgeevevnl 52 
                                           + +++v+vn+
  gene2710|gene2710|rna2710|rna2710 148 VMDKSDQSVSVNI 160
                                        4334778888886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       637  (0.035529); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 1448.00
//
Query:       gene2711|gene2711|rna2711|rna2711  [L=378]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (378 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       844  (0.0470746); expected 358.6 (0.02)
Passed bias filter:                      590  (0.0329076); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.42
# Mc/sec: 2671.06
//
Query:       gene2712|gene2712|rna2712|rna2712  [L=110]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       573  (0.0319594); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.29s 00:00:00.63 Elapsed: 00:00:00.42
# Mc/sec: 786.75
//
Query:       gene2713|gene2713|rna2713|rna2713  [L=557]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-52  172.4  19.1    9.1e-08   31.4   0.4    8.9  9  PUF       Pumilio-family RNA binding repeat
     0.0015   18.9   0.4       0.17   12.3   0.0    3.9  3  CPL       CPL (NUC119) domain


Domain annotation for each model (and alignments):
>> PUF  Pumilio-family RNA binding repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0      0.57   5.1e+03      15      23 ..     108     116 ..     108     117 .. 0.90
   2 !   10.6   0.0   3.9e-05      0.35       6      29 ..     260     283 ..     257     286 .. 0.84
   3 !   23.5   0.0   3.2e-09   2.9e-05       6      25 ..     294     313 ..     292     315 .. 0.90
   4 !   19.5   0.0   6.2e-08   0.00056       7      30 ..     329     352 ..     324     356 .. 0.84
   5 !   21.0   0.1     2e-08   0.00018       1      29 [.     362     391 ..     362     395 .. 0.85
   6 !   31.4   0.4     1e-11   9.1e-08       4      33 ..     396     426 ..     393     428 .. 0.85
   7 !   25.2   0.3   9.3e-10   8.3e-06       1      25 [.     426     450 ..     426     454 .. 0.90
   8 !   24.9   0.1   1.2e-09     1e-05       2      32 ..     462     492 ..     461     495 .. 0.92
   9 !   23.0   0.0   4.8e-09   4.3e-05       4      27 ..     502     525 ..     500     529 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.57
                                        HHHHHHHHH CS
                                PUF  15 GnyvvQkll 23 
                                        G++ vQ+++
  gene2713|gene2713|rna2713|rna2713 108 GSNSVQNIF 116
                                        99****997 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 3.9e-05
                                        HHHHHTSTTHHHHHHHHHHHSCHH CS
                                PUF   6 lvqLstdqyGnyvvQkllehatee 29 
                                        ++ +++dq G++++Qk le +tee
  gene2713|gene2713|rna2713|rna2713 260 CTNIVKDQEGSRFIQKRLELSTEE 283
                                        6789***************86665 PP

  == domain 3  score: 23.5 bits;  conditional E-value: 3.2e-09
                                        HHHHHTSTTHHHHHHHHHHH CS
                                PUF   6 lvqLstdqyGnyvvQklleh 25 
                                        + +L++d +Gnyv+Qkl+e 
  gene2713|gene2713|rna2713|rna2713 294 IKELCIDLFGNYVIQKLIEN 313
                                        789***************95 PP

  == domain 4  score: 19.5 bits;  conditional E-value: 6.2e-08
                                        HHHHTSTTHHHHHHHHHHHSCHHH CS
                                PUF   7 vqLstdqyGnyvvQkllehateeq 30 
                                         ++s++ +G++vvQ+ll+  + e+
  gene2713|gene2713|rna2713|rna2713 329 KEMSVNAFGCRVVQRLLDEDVNEE 352
                                        589***************866655 PP

  == domain 5  score: 21.0 bits;  conditional E-value: 2e-08
                                        HHGGGHHHHHTSTTHHHHHHHHHHH.SCHH CS
                                PUF   1 sikgnlvqLstdqyGnyvvQklleh.atee 29 
                                        ++k ++++L+ d +Gn+vvQk+ e+  + e
  gene2713|gene2713|rna2713|rna2713 362 ELKAHILDLVYDSNGNHVVQKIVERkIDFE 391
                                        5899*******************9866555 PP

  == domain 6  score: 31.4 bits;  conditional E-value: 1e-11
                                        GGHHHHHTSTTHHHHHHHHHHH.SCHHHHHH CS
                                PUF   4 gnlvqLstdqyGnyvvQklleh.ateeqkkl 33 
                                        + ++qLs+++yG++v+Qkl+e+  +++ + +
  gene2713|gene2713|rna2713|rna2713 396 NDCIQLSNHKYGCRVLQKLFEKnESSTIINK 426
                                        779******************9888777665 PP

  == domain 7  score: 25.2 bits;  conditional E-value: 9.3e-10
                                        HHGGGHHHHHTSTTHHHHHHHHHHH CS
                                PUF   1 sikgnlvqLstdqyGnyvvQklleh 25 
                                        ++++n+++L+ +qyGnyv+Q++++ 
  gene2713|gene2713|rna2713|rna2713 426 KLIDNCLDLAENQYGNYVLQHIITI 450
                                        689********************84 PP

  == domain 8  score: 24.9 bits;  conditional E-value: 1.2e-09
                                        HGGGHHHHHTSTTHHHHHHHHHHHSCHHHHH CS
                                PUF   2 ikgnlvqLstdqyGnyvvQkllehateeqkk 32 
                                        +++++ + s ++++++v++k++++++e+q  
  gene2713|gene2713|rna2713|rna2713 462 LSPYIFSFSLHKFASNVIEKIIKMCDEKQLN 492
                                        799*************************975 PP

  == domain 9  score: 23.0 bits;  conditional E-value: 4.8e-09
                                        GGHHHHHTSTTHHHHHHHHHHHSC CS
                                PUF   4 gnlvqLstdqyGnyvvQkllehat 27 
                                        +++v++s d+y+nyvvQ++le  +
  gene2713|gene2713|rna2713|rna2713 502 NSIVKMSMDKYANYVVQRILESKS 525
                                        789******************643 PP

>> CPL  CPL (NUC119) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0      0.42   3.8e+03      66      90 ..     259     283 ..     226     314 .. 0.72
   2 !   12.3   0.0   1.9e-05      0.17      59     120 ..     320     382 ..     313     423 .. 0.87
   3 ?    1.3   0.2     0.046   4.1e+02      65      87 ..     502     524 ..     403     547 .. 0.59

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.42
                                CPL  66 naeellsdnlgsqfvaevLlsaegd 90 
                                        +++++++d+ gs f+++ L+ ++++
  gene2713|gene2713|rna2713|rna2713 259 TCTNIVKDQEGSRFIQKRLELSTEE 283
                                        4556667777777776666655554 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 1.9e-05
                                CPL  59 llsaiaknaeellsdnlgsqfvaevLlsaegdkqeaieaiaklakgdlvaee.kdeelhliek 120
                                        + +++   ++e+  +++g+ +v+ +L  + ++++e +++ia  +k+ + +   +++ +h+++k
  gene2713|gene2713|rna2713|rna2713 320 ITQYLEGCYKEMSVNAFGCRVVQRLLDEDVNEESEYYRRIADELKAHILDLVyDSNGNHVVQK 382
                                        568888999*************************99999999999997766678888888876 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.046
                                CPL  65 knaeellsdnlgsqfvaevLlsa 87 
                                        +++ ++ +d+ +  +v+ +L+s+
  gene2713|gene2713|rna2713|rna2713 502 NSIVKMSMDKYANYVVQRILESK 524
                                        33445555555555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (557 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       867  (0.0483574); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.42
# Mc/sec: 3950.27
//
Query:       gene2714|gene2714|rna2714|rna2714  [L=71]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.016   15.4   0.1      0.019   15.3   0.1    1.1  1  GUCT      GUCT (NUC152) domain


Domain annotation for each model (and alignments):
>> GUCT  GUCT (NUC152) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.1     1e-06     0.019       6      55 ..      19      67 ..      15      70 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1e-06
                               GUCT  6 kkRSLlsseegfvTllltssseirtvgyvwsilkrelseeaaekvkrirl 55
                                       ++RSL+ss e++ T+ l+++++  +   + +il++ l+e +++k++ + l
  gene2714|gene2714|rna2714|rna2714 19 SERSLISSVENQKTIDLSMDNSEWEQNEFPKILRK-LEEAKEKKIQTLYL 67
                                       68********************8888888888887.99999999988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (71 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       920  (0.0513135); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.27s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 536.30
//
Query:       gene2715|gene2715|rna2715|rna2715  [L=155]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.8e-10   41.0   0.1    4.3e-10   39.8   0.0    1.7  2  SHS2_Rpb7-N  SHS2 domain found in N terminus of Rpb7p/Rpc25p/
    4.7e-07   30.1   0.2    8.1e-07   29.3   0.2    1.4  1  S1           S1 RNA binding domain


Domain annotation for each model (and alignments):
>> SHS2_Rpb7-N  SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.8   0.0   4.8e-14   4.3e-10       2      68 ..       9      74 ..       8      76 .. 0.93
   2 ?   -2.5   0.0      0.79   7.1e+03      28      39 ..     143     155 .]     142     155 .] 0.87

  Alignments for each domain:
  == domain 1  score: 39.8 bits;  conditional E-value: 4.8e-14
                                       EEEEE-GGGTTSTHHHHHHHHHHHHHTTBEETTTEEEEEEEEEEEECCEEE-TTTSSEEEEEEEEEE CS
                        SHS2_Rpb7-N  2 dtvrlePsylgstledallerllekyegkvvpslGvivavldiaeysegkvlggsGsvyvrVtfral 68
                                       +t+ l P y++ +l+ a++  lle +eg ++ + G+i+avl i +++e     + Gsv ++V+++a+
  gene2715|gene2715|rna2715|rna2715  9 HTIHLSPNYFDTNLQYAVRSHLLEEVEGACSSDHGFILAVLSIQNVGEAVL-NHMGSVLFKVKYTAI 74
                                       699********************************************9755.555**********98 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.79
                                        TTBEETTT.EEEE CS
                        SHS2_Rpb7-N  28 egkvvpsl.Gviv 39 
                                        +g++++++ Gvi+
  gene2715|gene2715|rna2715|rna2715 143 VGTINEEFlGVIL 155
                                        7999999999986 PP

>> S1  S1 RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.3   0.2     9e-11   8.1e-07       4      70 ..      80     140 ..      77     142 .. 0.94

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 9e-11
                                        TTCEEEEEEEEEETTEEEEEETTTEEEEEEGGGSSSSCEESCHHHCEETTEEEEEEEEEEETTTTEE CS
                                 S1   4 kgevveGeVtsvtkgGafVelgngvegfvpaselsrdarvedpdevlkvGdevkvkvlkvdkdrrri 70 
                                         +ev+e +V +v+ +G+f ++g + ++fv+  +++++       e +k++  v++k+++++ d+++i
  gene2715|gene2715|rna2715|rna2715  80 RNEVIEVKVDEVNTMGLFAHIG-PLSIFVSNYQIPSN-----LQESIKKDTLVRLKIIGTKIDKNEI 140
                                        689*******************.************99.....9*****************9999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 1097.13
//
Query:       gene2716|gene2716|rna2716|rna2716  [L=85]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (85 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       294  (0.016398); expected 358.6 (0.02)
Passed bias filter:                      250  (0.0139439); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.42
# Mc/sec: 610.60
//
Query:       gene2717|gene2717|rna2717|rna2717  [L=628]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.1e-42  145.2   6.4    1.6e-31  109.5   0.6    2.9  3  Kinesin      Kinesin motor domain
    3.1e-08   33.7   7.2    1.5e-06   28.3   0.0    3.6  4  Microtub_bd  Microtubule binding
     0.0016   18.5   0.1     0.0033   17.5   0.1    1.5  1  DUF3856      Domain of Unknown Function (DUF3856)
  ------ inclusion threshold ------
      0.033   14.4   0.0      0.087   13.1   0.0    1.7  1  HHH_3        Helix-hairpin-helix motif
      0.057   13.5   0.0       0.12   12.5   0.0    1.5  1  HHH_2        Helix-hairpin-helix motif
       0.13   12.6   0.3        1.1    9.5   0.3    2.5  1  AAA_22       AAA domain


Domain annotation for each model (and alignments):
>> Kinesin  Kinesin motor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.1   0.1   2.8e-13   8.3e-10      33     106 ..      26     114 ..      10     135 .. 0.77
   2 !  109.5   0.6   5.3e-35   1.6e-31     195     333 .]     153     289 ..     148     289 .. 0.92
   3 ?   -3.4   0.1       1.2   3.5e+03     137     186 ..     567     615 ..     537     619 .. 0.78

  Alignments for each domain:
  == domain 1  score: 38.1 bits;  conditional E-value: 2.8e-13
                                        EEECTTSCEEEEESEEEETTS-.................HHHHHHHHHHHHHHHHHTTSEEEEEEEESTTSSHHHH CS
                            Kinesin  33 kenkeeeekkfkFdkvfdeeat.................qeevyeetakplvesvleGynatifaYGqtgsGKTyT 91 
                                        +   e++  +++Fd+vf +e++                 ++    + + +l +s       ti++YG tgsGKT+T
  gene2717|gene2717|rna2717|rna2717  26 EVFVESNGVRYNFDRVFVKESNksiyeylrkgiscgndlERAKIGN-TDELADSTSLSNALTIMCYGSTGSGKTFT 100
                                        4555667778999999998888889999999999987753333344.4899999999999**************** PP

                                        HTBCTTTSBSHHHHH CS
                            Kinesin  92 megkeeeeeGiipra 106
                                        m g+ ++e+Gi + +
  gene2717|gene2717|rna2717|rna2717 101 MLGN-KHEKGIFQLI 114
                                        ***8.8889987654 PP

  == domain 2  score: 109.5 bits;  conditional E-value: 5.3e-35
                                        TTSSCTSHHCCSEEEEEEEEEEEETTTTTCEEEEEEEEEEEEEEECCCHHHHSS...TCHHHHHHHHHHHHHHHHH CS
                            Kinesin 195 aetklneeSSRSHavftitleqknlkeeteekvkisklnLvDLAGsErasktga...aegerlkEaaniNkSLlaL 267
                                        + t+lneeSSRSH+++++ ++q++  +e++ + +  k+ L+DLAGsE  +ktg+    + + +kE++ iNkSL++L
  gene2717|gene2717|rna2717|rna2717 153 KRTALNEESSRSHTIMEMVVKQNRAVHEKH-TDELFKIILIDLAGSEDNRKTGNtpqLNPSLMKESSTINKSLFVL 227
                                        579*******************99887766.56899*****************9665456779************* PP

                                        HHHHHHHHHTCCTSTSCGGGSHHHHHTGGGHSSSSEEEEEEEE-TBGGGHHHHHHHHHHHHHHCTT CS
                            Kinesin 268 grvisaLaekkkskhipYRdSkLTrlLqdsLgGnsktlmivtvspssenleetlstlkfaerakei 333
                                        ++vi+a+ +k  +k +p+R+S LT+ L++++ G  ++++++tv  + + + e +stl+fa++ k+i
  gene2717|gene2717|rna2717|rna2717 228 RNVITAIYKK--RKSVPFRESVLTKYLKEYFRG--RVVLLATVVDDCDMMGEGISTLNFASMSKRI 289
                                        **********..*******************99..6899***********************9987 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 1.2
                                        TEEEETTSTTTTSTSSEBEEEECTTSCCEEETTS--EEESSHHHHHHHHH CS
                            Kinesin 137 eeiyDLLeskkskkkkklkiredskkgevyvkgltevevksaeevlelle 186
                                         e+  LL++ +  + kk+k + d++    +++ l+ ++++++e++ ++++
  gene2717|gene2717|rna2717|rna2717 567 KELLKLLNKADFLSLKKIKNIGDKRAM-KIIEYLKFKRIDKTEDLCKIFS 615
                                        566677777776666677777777765.7888899999999999888875 PP

>> Microtub_bd  Microtubule binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.2    0.0011       3.3      21      64 ..       3      48 ..       1      60 [. 0.79
   2 !   28.3   0.0   4.9e-10   1.5e-06      73     115 ..      74     115 ..      62     143 .. 0.69
   3 ?   -3.6   0.0       3.3   9.7e+03      94     120 ..     161     189 ..     159     191 .. 0.74
   4 ?   -0.4   0.1      0.33     1e+03      64     116 ..     476     514 ..     413     556 .. 0.63

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0011
                                       B-EEEEEEECCCS-.T.EEEETTT....TTTEEEE-SEEEECTTHC CS
                        Microtub_bd 21 niRvfarvrpeles.ekakikfpe.eekkkkkefsFdrvfeseseq 64
                                       ni v +r r++++s   +ki+ +e   +++  +++Fdrvf +es++
  gene2717|gene2717|rna2717|rna2717  3 NIKVLVRFRRPENSlPFTKITKNEvFVESNGVRYNFDRVFVKESNK 48
                                       8999999999888843366666667567999*********999865 PP

  == domain 2  score: 28.3 bits;  conditional E-value: 4.9e-10
                                        HHHHHHHTT--EEEEEEES................ST-HCHHH CS
                        Microtub_bd  73 qlvqsaldgynvcifaygqTGsGKtyTmegeeeeagmiprave 115
                                         l++s       +i++yg+TGsGKt+Tm g+++e+g  + +++
  gene2717|gene2717|rna2717|rna2717  74 ELADSTSLSNALTIMCYGSTGSGKTFTMLGNKHEKGIFQ-LIR 115
                                        5666666677789*****************776666554.333 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 3.3
                                        ................ST-HCHHHHHHHH CS
                        Microtub_bd  94 sGKtyTmeg..eeeeagmipraveeifet 120
                                        s +++T+++   ++++ ++++ ++e+f++
  gene2717|gene2717|rna2717|rna2717 161 SSRSHTIMEmvVKQNRAVHEKHTDELFKI 189
                                        55788877767778888888888888876 PP

  == domain 4  score: -0.4 bits;  conditional E-value: 0.33
                                        CCCCCCCCHHHHHHHHTT--EEEEEEES................ST-HCHHHH CS
                        Microtub_bd  64 qeevfeeisqlvqsaldgynvcifaygqTGsGKtyTmegeeeeagmipravee 116
                                        + +  e++++l+++  +++n  + a              + +++g+i++++++
  gene2717|gene2717|rna2717|rna2717 476 KRKALENYQMLLEMTEENKNGAVAA--------------SGDNSGQINSVIKN 514
                                        3333344444444444444444444..............44445555555555 PP

>> DUF3856  Domain of Unknown Function (DUF3856)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.1   1.1e-06    0.0033      75     135 ..     434     495 ..     424     501 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.1e-06
                                        HHHHHHHHHHHHHH--TTST.HHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH--S CS
                            DUF3856  75 lesadkalryfnrrGeleqd.eGklWiaavfsravaleelGrkdealkafrmagemiaerkG 135
                                        ++s d  ++ f+ + e ++    k+   a+++ra  +ee G k +al++++m  em +e k 
  gene2717|gene2717|rna2717|rna2717 434 FSSNDMIIHSFDCKEEENDKlVSKKVFDAILKRALQFEERGYKRKALENYQMLLEMTEENKN 495
                                        5677777788877766554425688889******************************9874 PP

>> HHH_3  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   2.9e-05     0.087       8      46 ..     573     610 ..     572     614 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.9e-05
                              HHH_3   8 iNtAsaeeLqklpGlgpklAknIvayReknGpfksreeL 46 
                                        +N+A+   L+k++ +g+k A +I++y  k +++ + e+L
  gene2717|gene2717|rna2717|rna2717 573 LNKADFLSLKKIKNIGDKRAMKIIEYL-KFKRIDKTEDL 610
                                        7*************************8.55566666666 PP

>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   4.1e-05      0.12      27      58 ..     571     602 ..     565     607 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4.1e-05
                              HHH_2  27 daLkkasleeLlevddiGeeiAqsivefFene 58 
                                          L ka++  L ++++iG++ A +i+e+++ +
  gene2717|gene2717|rna2717|rna2717 571 KLLNKADFLSLKKIKNIGDKRAMKIIEYLKFK 602
                                        5699************************9865 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.3   0.00037       1.1       4      26 ..      83     105 ..      79     290 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00037
                             AAA_22   4 tagilvvtGesGtGKTtllrrll 26 
                                        +a  ++++G +G+GKT+++   +
  gene2717|gene2717|rna2717|rna2717  83 NALTIMCYGSTGSGKTFTMLGNK 105
                                        567799***********985444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (628 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1040  (0.0580066); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.63u 0.30s 00:00:00.93 Elapsed: 00:00:00.46
# Mc/sec: 4096.82
//
Query:       gene2718|gene2718|rna2718|rna2718  [L=54]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (54 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       236  (0.013163); expected 358.6 (0.02)
Passed bias filter:                      162  (0.00903564); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.22s 00:00:00.56 Elapsed: 00:00:00.37
# Mc/sec: 432.14
//
Query:       gene2719|gene2719|rna2719|rna2719  [L=275]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.6e-54  181.5   0.5    6.9e-54  180.9   0.5    1.3  1  STE           STE like transcription factor
  ------ inclusion threshold ------
      0.012   15.2   0.3      0.028   14.0   0.3    1.5  1  Ndc80_HEC     HEC/Ndc80p family
      0.077   12.9   0.0       0.21   11.5   0.0    1.7  1  Rho_RNA_bind  Rho termination factor, RNA-binding domain


Domain annotation for each model (and alignments):
>> STE  STE like transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  180.9   0.5   1.2e-57   6.9e-54       2     110 .]      45     152 ..      44     152 .. 0.99

  Alignments for each domain:
  == domain 1  score: 180.9 bits;  conditional E-value: 1.2e-57
                                STE   2 virrykleeeegfiscvlwknlfyitgtdivkilvykleafGrkitdkkkfeeGifsdlrnlkigvdavleepkse 77 
                                         i++++l++ + fi+cvlw+++fyitgtdivkilv+++++ Gr+i++ kkfeeG+fsdlrnlk+g+da+le p+s+
  gene2719|gene2719|rna2719|rna2719  45 KIKKFQLKNGD-FIHCVLWNMHFYITGTDIVKILVWRFQNAGRQIVSLKKFEEGVFSDLRNLKPGIDATLEGPRSD 119
                                        69********8.**************************************************************** PP

                                STE  78 fldllyknkclrtqkkqkvfywfsvphdklfld 110
                                        fl++lykn c+rtqkkqkvf+w+svphd lf+d
  gene2719|gene2719|rna2719|rna2719 120 FLEFLYKNGCIRTQKKQKVFFWYSVPHDALFCD 152
                                        *******************************98 PP

>> Ndc80_HEC  HEC/Ndc80p family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.3   4.8e-06     0.028      26     104 ..      10     106 ..       6     112 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.8e-06
                          Ndc80_HEC  26 erDprplrdksfqseliqellefLken..nfe..hsisaktlks..............PsqkdfssifkfLykrld 83 
                                        ++++r l + ++ ++  +el++fL++   +f+  ++i++  lk+               +  d+++i+ + +++  
  gene2719|gene2719|rna2719|rna2719  10 HKNKRALVNTEMNMQTDKELFDFLSNApkEFTenEKIKKFQLKNgdfihcvlwnmhfyITGTDIVKILVWRFQNAG 85 
                                        6889********************9961155555444444444499999999999999****************** PP

                          Ndc80_HEC  84 psyefqkkieeevvkilkelr 104
                                         +    kk+ee v++ l++l+
  gene2719|gene2719|rna2719|rna2719  86 RQIVSLKKFEEGVFSDLRNLK 106
                                        999999***********9997 PP

>> Rho_RNA_bind  Rho termination factor, RNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   3.6e-05      0.21      28      47 ..      40      59 ..      27      64 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 3.6e-05
                                       EE-CCCCCCTT--TT-EEEE CS
                       Rho_RNA_bind 28 YVsasqirkfgLrtGDaveG 47
                                       +  ++ i+kf+L++GD++++
  gene2719|gene2719|rna2719|rna2719 40 FTENEKIKKFQLKNGDFIHC 59
                                       667899***********986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (275 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       599  (0.0334096); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1759.91
//
Query:       gene272|gene272|rna272|rna272  [L=739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-49  169.0   0.0    2.6e-49  168.1   0.0    1.5  1  RNA_pol_Rpb1_5  RNA polymerase Rpb1, domain 5
    2.2e-44  151.6   0.0    5.1e-44  150.4   0.0    1.6  1  RNA_pol_Rpb1_2  RNA polymerase Rpb1, domain 2
    7.2e-23   80.6   0.6    2.1e-21   75.9   0.3    2.9  2  RNA_pol_Rpb1_4  RNA polymerase Rpb1, domain 4
    4.6e-13   49.4   0.1    3.6e-11   43.2   0.1    2.5  1  RNA_pol_Rpb1_3  RNA polymerase Rpb1, domain 3


Domain annotation for each model (and alignments):
>> RNA_pol_Rpb1_5  RNA polymerase Rpb1, domain 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  168.1   0.0   5.8e-53   2.6e-49       1     151 [.     458     629 ..     458     698 .. 0.75

  Alignments for each domain:
  == domain 1  score: 168.1 bits;  conditional E-value: 5.8e-53
                                    B--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTEEEETTSEEEETTS-EEESSGGGTS....B--TT-BHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxx RF
                 RNA_pol_Rpb1_5   1 GLkvkefffhtmggReGLiDtAvkTaesGYlqRrlvkaledvvvkyddtvrnsggeivqflygedg....lvepGeavGi 76 
                                    GL++ efffh+  gReGL+DtAvkTae+GY+qRrl+kaled+    d++vr ++  ++qf  ++ +      +pG+avG+
  gene272|gene272|rna272|rna272 458 GLNAFEFFFHAISGREGLVDTAVKTAETGYMQRRLIKALEDLKLCFDGSVRGTD-CVIQFPDSNSSyfrkGFQPGDAVGA 536
                                    99************************************************8776.57788777776666679******** PP

                                    HHHHHHHHHHHCCCSSTTSSTCSSTSSSSSSHHHHHHHHTT-SS-SS-EEEEEB-SSSSSCHHHCHHHHHHHSE...... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...... RF
                 RNA_pol_Rpb1_5  77 iaaQSiGePgTQltlnTFHfaGvasknvtlGvprlkeilnvskniksksltvllvdeeakelekakkvkkaiek...... 150
                                    iaaQSiGePgTQ+tl+TFHfaGv+s+n+tlGvprlkei+n+s+ ++++ + ++ ++++ +++++   + + +        
  gene272|gene272|rna272|rna272 537 IAAQSIGEPGTQMTLKTFHFAGVGSMNITLGVPRLKEIINASA-CSTPVIRISGRRKTLSDMRRLNDLIQPLRIenvidy 615
                                    **************************************99765.678888888887777777776633322222345566 PP

                                    .............C CS
                                    .............x RF
                 RNA_pol_Rpb1_5 151 .............g 151
                                                  
  gene272|gene272|rna272|rna272 616 vdiniseniyvdfR 629
                                    66655555555552 PP

>> RNA_pol_Rpb1_2  RNA polymerase Rpb1, domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  150.4   0.0   1.1e-47   5.1e-44      39     162 ..       1     119 [.       1     122 [. 0.95

  Alignments for each domain:
  == domain 1  score: 150.4 bits;  conditional E-value: 1.1e-47
                                    -STTTHHHHHHHHHHTTTSSSSEEEEESTTSSEEETTTT-SCHHCCTTTTSEEEEE--TTSEEEEE-SSTTSGGGEEEEE CS
                 RNA_pol_Rpb1_2  39 vtelnikklrklvengpevyPgasyvkredgsekklkakkrklakelekgdiverhvkdgdvvllNRqPsLhklsimahr 118
                                    vte+ni++lrk+v ngp+ yPga+ ++++++++ +  ++     k++ +gd+verh++d+d vl+NRqPsLh+lsi +h 
  gene272|gene272|rna272|rna272   1 VTEFNIQSLRKCVLNGPKRYPGANFIINKENKRISTWYN-----KRILIGDVVERHLIDNDRVLFNRQPSLHRLSILSHF 75 
                                    899***********************9999988877777.....7799******************************** PP

                                    EEEESSSSEEEEGGGHCCCT--SSS-EEEEE--SSHHHHHHHHH CS
                 RNA_pol_Rpb1_2 119 vkvlekktlrlnlsvttayNaDFDGDemnlhlpqseearaEaee 162
                                    +k++++kt+ +n+sv+++yNaDFDGDemn+h+pq+  araE + 
  gene272|gene272|rna272|rna272  76 AKIVPNKTFCFNVSVCAPYNADFDGDEMNVHVPQTLFARAECSL 119
                                    *****************************************865 PP

>> RNA_pol_Rpb1_4  RNA polymerase Rpb1, domain 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.9   0.3   4.6e-25   2.1e-21       4      96 ..     257     349 ..     254     358 .. 0.74
   2 ?    1.3   0.0      0.07   3.1e+02      67      94 ..     381     409 ..     376     450 .. 0.79

  Alignments for each domain:
  == domain 1  score: 75.9 bits;  conditional E-value: 4.6e-25
                                    HCTHTCCHHHTTHCHHHHHH...HHHHHHHHHHHHHHHHHHHHCST.T.TSHHHHHHHCTSSS-HHHHHHHHTB-EEEEB CS
                 RNA_pol_Rpb1_4   4 aerygkledlpgksleelfe...akinkilnkardkagkiasksla.a.sNsiliMvksGaKGsiinisqiagclGqqnv 78 
                                    +++++k++ + +   e ++e   ++i+++++ +rdk    +sk+++ + +Ns liM++sG+KGs+ini+q+++++Gqq +
  gene272|gene272|rna272|rna272 257 KNEENKMIGIKTLIREYVEEmdsDNIAELSS-VRDK----ISKTIKlIpDNSALIMAESGSKGSKINITQMVAMVGQQVI 331
                                    5556777766666666666611155555554.5666....5555553356****************************** PP

                                    TTBSS--SSTSCSSTTSS CS
                 RNA_pol_Rpb1_4  79 egkripkgfsgrtlphfk 96 
                                    +g+r+p  +sgr+lph+ 
  gene272|gene272|rna272|rna272 332 NGQRVPLSYSGRSLPHYF 349
                                    ***************986 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.07
                                    HHHHTB-EEEEBTTBSS--S.STSCSSTT CS
                 RNA_pol_Rpb1_4  67 sqiagclGqqnvegkripkg.fsgrtlph 94 
                                    +q+ag+ Gq + ++++     +++r   +
  gene272|gene272|rna272|rna272 381 VQMAGICGQTSDQKNENVGDtMNNRFISS 409
                                    7********99987655444466666654 PP

>> RNA_pol_Rpb1_3  RNA polymerase Rpb1, domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.2   0.1   8.1e-15   3.6e-11       1     157 []     125     254 ..     125     254 .. 0.87

  Alignments for each domain:
  == domain 1  score: 43.2 bits;  conditional E-value: 8.1e-15
                                    CSEETTTTEESSS--THHHHHHHHHSSTTEEEEHHHHHHHHHHSSSCCS...SSSSSSSSBESSSEBEEHHHHHHCCCHC CS
                 RNA_pol_Rpb1_3   1 nilspqsgkPvigivQDsllGvyllTkedvfidreeaqqllykgvgsds...ktvtlrpailkpkelwtgkqtfsrilpn 77 
                                    n+ sp++++ +i++ QD++++vyl+  e  ++d+  +  +l++++  ++      ++rp il+p++ +tg+q+++ i+ +
  gene272|gene272|rna272|rna272 125 NLRSPKDNQLIIMPNQDFITSVYLIGNE--YFDEMSFSTYLFEVCHASKdyeMARKIRPSILRPTRIYTGQQLLGTIFKK 202
                                    6779**********************99..99999999999999888756775579********99*************6 PP

                                    CCCEEEESSSSSTSEEECSSEEEES--SHHHHSSSSTTSHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHCEB-TGGGG CS
                 RNA_pol_Rpb1_3  78 einyerkneekdgkvlikngelikGvidkkvvgkksqgslihvlakeygiketvrfldslqrlgfkyllqsgftigigDt 157
                                    +   +          li +++l           k        +   e + +e+v   +s+ r+  +++  +gf+ig++D+
  gene272|gene272|rna272|rna272 203 HGPFKT---------LITKKML-----------K--------QYLSEMSNEEIVIAENSIARVSARFIGERGFSIGVDDL 254
                                    666665.........8888888...........3........3455666799999999********************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (739 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       658  (0.0367003); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.65u 0.32s 00:00:00.97 Elapsed: 00:00:00.46
# Mc/sec: 4835.59
//
Query:       gene2720|gene2720|rna2720|rna2720  [L=60]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (60 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       374  (0.0208601); expected 358.6 (0.02)
Passed bias filter:                      237  (0.0132188); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 435.81
//
Query:       gene2721|gene2721|rna2721|rna2721  [L=57]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (57 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       360  (0.0200792); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.23s 00:00:00.57 Elapsed: 00:00:00.40
# Mc/sec: 425.26
//
Query:       gene2722|gene2722|rna2722|rna2722  [L=148]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       789  (0.0440069); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.28s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1058.03
//
Query:       gene2723|gene2723|rna2723|rna2723  [L=498]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (498 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1710  (0.0953762); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.59u 0.25s 00:00:00.84 Elapsed: 00:00:00.44
# Mc/sec: 3374.35
//
Query:       gene2724|gene2724|rna2724|rna2724  [L=384]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
       0.17   10.8   0.0       0.27   10.1   0.0    1.2  1  Peptidase_M30  Peptidase M30


Domain annotation for each model (and alignments):
>> Peptidase_M30  Peptidase M30
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   1.5e-05      0.27     175     229 ..     273     332 ..     267     344 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 1.5e-05
                      Peptidase_M30 175 ammmedlassdidpsynai...rdvrfpdylrygayncsl..ttftsfgascesysvsGs 229
                                         + me+++ + i++sy++     d+ +pd++r    +c     +f +f+a c+ ++v+G 
  gene2724|gene2724|rna2724|rna2724 273 DIIMEEVLKNVIEASYENClfkNDLVIPDHIRVELIDCRSdnDQFIAFSAGCDDFTVNGG 332
                                        678*************98645579**************752269**************94 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (384 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       627  (0.0349713); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2812.24
//
Query:       gene2725|gene2725|rna2725|rna2725  [L=363]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.093   12.8   0.1         17    5.6   0.0    2.5  2  AsiA      Anti-Sigma Factor A
       0.13   12.4   0.0       0.26   11.4   0.0    1.5  1  BLUF      Sensors of blue-light using FAD


Domain annotation for each model (and alignments):
>> AsiA  Anti-Sigma Factor A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.1    0.0045        40      14      32 ..     151     169 ..     138     185 .. 0.85
   2 ?    5.6   0.0    0.0019        17      20      62 ..     272     312 ..     263     321 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.0045
                                        HHHHHHTTTHHHHTSHHHH CS
                               AsiA  14 aslLvklsrdeivenrklf 32 
                                         + L+kl +d iv n+++ 
  gene2725|gene2725|rna2725|rna2725 151 MTTLIKLEYDSIVVNENNS 169
                                        5679*********998774 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0019
                                        TTTHHHHTSHHHHHHHHHHHT-.ESSSSE--HHHHHHHHHTS- CS
                               AsiA  20 lsrdeivenrklfvellneiGvrtteGkkltqnsfrkivarLt 62 
                                        +++d  ++ +kl+ve + +      + k l+q  f ++v +L 
  gene2725|gene2725|rna2725|rna2725 272 YAYDGKIKLQKLYVECCYDYHQ--SDTKSLEQWVFNNMVGELV 312
                                        578899999********99766..899*************996 PP

>> BLUF  Sensors of blue-light using FAD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   2.9e-05      0.26      11      81 ..      89     162 ..      81     173 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 2.9e-05
                                        .TTS-HHHHHHHHHHHHHHHHHHTEEEEEEE...ETTEEEEEEEEEHHHHHHHHHHHHT-TTEEEEEEEEEEEE CS
                               BLUF  11 aeelseeeleeileesrenNkelgitGvLly...degvflQvLEGeeeaveelyerIkkDpRhkdvevleeeei 81 
                                        a++ls+  l ++ ++s  nN+++   ++L     + ++f+ + EG ++ ++ ++++I k+p  + +  le ++i
  gene2725|gene2725|rna2725|rna2725  89 ANKLSRMFLPNMKSDSALNNRRKTQLSLLAAytkQTNYFCSIYEGYNDVINLILKKILKEPVMTTLIKLEYDSI 162
                                        56677777888899999999999999999753445799*********************999888888877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (363 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       664  (0.037035); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 2534.51
//
Query:       gene2726|gene2726|rna2726|rna2726  [L=949]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.14   12.2   0.1       0.53   10.3   0.0    2.1  2  HTH_19    Helix-turn-helix domain
        8.3    6.8  10.1        4.5    7.7   0.2    4.1  3  bPH_3     Bacterial PH domain


Domain annotation for each model (and alignments):
>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   5.9e-05      0.53      21      64 ..     189     231 ..     168     232 .. 0.90
   2 ?   -3.7   0.0       1.4   1.3e+04      26      40 ..     397     410 ..     389     415 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 5.9e-05
                             HTH_19  21 rlgisrskisaiEngkkdvpsaelllkiaealgidleyllqged 64 
                                        +lgi+ s++s+  + + ++++ ++l k++e+l++++e +l++++
  gene2726|gene2726|rna2726|rna2726 189 DLGITESYYSKKLHANEYNFN-GVLVKFCEILKQNVEFYLMKDA 231
                                        89*************999997.***************9999876 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 1.4
                             HTH_19  26 rskisaiEngkkdvp 40 
                                        ++kis i  +++ v+
  gene2726|gene2726|rna2726|rna2726 397 INKISSIKLENI-VF 410
                                        789999998887.65 PP

>> bPH_3  Bacterial PH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.3     0.048   4.3e+02      51      84 ..     398     432 ..     389     443 .. 0.84
   2 ?    1.0   0.6     0.061   5.4e+02      52      81 ..     503     532 ..     497     535 .. 0.89
   3 ?    7.7   0.2    0.0005       4.5      49      88 ..     671     711 ..     638     713 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.048
                              bPH_3  51 ksIksvdlkkgllgakitletsgktitidni.dks 84 
                                        ++I+s++l++ ++ + + ++ + ++++i  +  k+
  gene2726|gene2726|rna2726|rna2726 398 NKISSIKLENIVFENDFVFTREFERVHIYQCeVKK 432
                                        69*************************97664444 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.061
                              bPH_3  52 sIksvdlkkgllgakitletsgktitidni 81 
                                        sI ++ l++  + ++it+++++k+ ti+++
  gene2726|gene2726|rna2726|rna2726 503 SIDQIFLSDVEIFNTITINFNNKQQTINIC 532
                                        79999999999*********9999998865 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.0005
                              bPH_3  49 pYksIksvdlkkgllgakitlet.sgktitidnidksevrk 88 
                                        ++k+Ik + +k+ l + k+ le  s +t+++  +++ ev +
  gene2726|gene2726|rna2726|rna2726 671 EFKEIKHIMFKQTLSKYKFVLEDySADTYQMSRLQETEVYE 711
                                        79******************************999998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (949 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       683  (0.0380947); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.68u 0.27s 00:00:00.95 Elapsed: 00:00:00.44
# Mc/sec: 6498.98
//
Query:       gene2727|gene2727|rna2727|rna2727  [L=209]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       528  (0.0294495); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 1342.69
//
Query:       gene2728|gene2728|rna2728|rna2728  [L=325]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-41  142.6   1.4      2e-41  142.0   1.4    1.3  1  Choline_kinase  Choline/ethanolamine kinase
    2.8e-08   34.0   0.0    4.5e-07   30.0   0.0    2.1  1  APH             Phosphotransferase enzyme family
  ------ inclusion threshold ------
      0.025   14.4   0.7       0.54   10.0   0.1    2.4  2  DUF5105         Domain of unknown function (DUF5105)


Domain annotation for each model (and alignments):
>> Choline_kinase  Choline/ethanolamine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  142.0   1.4   3.3e-45     2e-41       4     208 ..      44     244 ..      17     251 .. 0.94

  Alignments for each domain:
  == domain 1  score: 142.0 bits;  conditional E-value: 3.3e-45
                                        EEEEEEE-TTCTTCCHHHHHHHHHHHHHHTTSSS-EEEEETTEEEEE--TCEE--TTGGGCHHHHHHHHHHHHHHT CS
                     Choline_kinase   4 kvllRiygkkteelidretElvvfallserglgpklygifenGrieefiesrtlstedlrepeiskkiAkklaelH 79 
                                        kv+ +iygk+t+++i+re E  ++ +l+++gl+p++++  enG i  ++++++l+ ++l++   ++ iA+k++++H
  gene2728|gene2728|rna2728|rna2728  44 KVVAKIYGKNTSDFINREVEKSNISYLHTYGLAPRMMASYENGFIIDYVPGKELQEQELQT--HYEVIARKMRKWH 117
                                        8999*******************************************************99..99*********** PP

                                        TCHH.TTSSSS-HHHHHHHHHHHCCS.TT..ECHHGGCCHCCCTHHHHHHHHHTHHHHHHCHGG-EEEE-S--SGG CS
                     Choline_kinase  80 sleleseskespslwktmqkwllnkeaqtkakkekkkkqlklinledlekelekleklleelespvvfcHnDlqeg 155
                                        +++        p l+ktm +w       + + ++++k+ l++ n++d+  e+e+  k++     +v fcHnDl+ +
  gene2728|gene2728|rna2728|rna2728 118 TIKS----PGVPTLFKTMLDW-------YWKAHVHHKSLLDKYNVYDFIIETERRVKHC-----EVGFCHNDLLAS 177
                                        ***9....7899*********.......666778888999********99999988888.....8*********** PP

                                        GEEE.......................-CTTEEEE--GTT-EEEEHHHHHHHHHHHTTEEHHHCSTSHEE-GGGS CS
                     Choline_kinase 156 Nill......................nkeekklvlIDFEYagynyrgfDlanhfiEwagdyeeeeaffkldysky 208
                                        Ni++                      + e +++ +IDFEY+++ny+++D+anhf+E+ g        + ld+s++
  gene2728|gene2728|rna2728|rna2728 178 NIIMlnspvceqdlvissvtqesaqpAYEVDEVQFIDFEYSSPNYIAYDVANHFAEYVG--------YSLDKSRM 244
                                        *************************999*****************************99........44444444 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.0   0.0   7.6e-11   4.5e-07       2     209 ..      24     231 ..      23     245 .. 0.83

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 7.6e-11
                                        EEEE--.SSCEEEEEEETT--EEEEEE-TTS-HHHHHHHHHHH..HHHHHTT-B--B-CTTBS-EEETTEEEEEEE CS
                                APH   2 vrelsggasnrtylvttpagryvlrrnpparaaeeirrevall..rlLakagvpvPevlagdtddeeigllfalie 75 
                                        ++++++g  n t ++t ++ ++v +++ +  +  +i rev+     +L+  g+ +P++ a     +e+g   ++i 
  gene2728|gene2728|rna2728|rna2728  24 LTQFKSGKTNTTLFCTNDDYKVVAKIYGKN-TSDFINREVEKSniSYLHTYGL-APRMMA----SYENG---FIID 90 
                                        789****************9**********.*********9555599999999.******....67888...6*** PP

                                        ----EE-SSHHHHHHHHHHHHHHHHHHCCHHCH.-STTTB-SHHCHTCCHHHHHHCHHHCCCGCCTCCHHHHHHHH CS
                                APH  76 yvpgrsllrklsaaqlpellealgeflaalhqvdpaalpladflaqdlellrqlesatarllaselldlleeleeq 151
                                        yvpg+ l +    ++l+  +e +++  ++ h +  +  p  + +  d++  + ++        s+l++ +   +  
  gene2728|gene2728|rna2728|rna2728  91 YVPGKELQE----QELQTHYEVIARKMRKWHTIKSPGVPTLFKTMLDWYWKAHVHHK------SLLDK-YNVYDF- 154
                                        *********....9*******************666666666664433333333333......44444.677777. PP

                                        HHHHHHHH--SSS-EEEE-SS-SGGGEEEC.........................TTEEEEE---TT-EEEECCHH CS
                                APH 152 vlaalaallpgelptvllHgDlhpgNllvd.......................pddgrvtGviDfedaglgpplyD 204
                                        ++++ ++  +   + +++H+Dl   N+++                        + d     +iDfe++++  ++yD
  gene2728|gene2728|rna2728|rna2728 155 IIETERRVKH--CEVGFCHNDLLASNIIMLnspvceqdlvissvtqesaqpayEVDEVQ--FIDFEYSSPNYIAYD 226
                                        7777666666..*****************99***************9999886444444..*************** PP

                                        HHCCH CS
                                APH 205 lavll 209
                                        +a + 
  gene2728|gene2728|rna2728|rna2728 227 VANHF 231
                                        *9887 PP

>> DUF5105  Domain of unknown function (DUF5105)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.1     0.018   1.1e+02      25      60 ..      40      75 ..       6     115 .. 0.86
   2 ?   10.0   0.1     9e-05      0.54      47      75 ..     246     274 ..     230     278 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.018
                                       ----THHHHHHSS-HHHHHHHHHHHHHHHHHHHTT- CS
                            DUF5105 25 dKdndkfdkltgedksevveeveesfkksfkralgy 60
                                       + d + ++k++g++ s++++   e+ + s+ +++g+
  gene2728|gene2728|rna2728|rna2728 40 NDDYKVVAKIYGKNTSDFINREVEKSNISYLHTYGL 75
                                       456666889999**9999998888778777777775 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 9e-05
                                        HHHHHHHHHHHTT--GGGGGSHHHHHHHH CS
                            DUF5105  47 eesfkksfkralgyssssvtdkeldnlfk 75 
                                         esfkk+f+r++ ys+  v+dk +d+++ 
  gene2728|gene2728|rna2728|rna2728 246 SESFKKEFIRTYMYSGFTVNDKIIDDFLA 274
                                        589***********************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (325 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       754  (0.0420548); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 2179.38
//
Query:       gene2729|gene2729|rna2729|rna2729  [L=140]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       387  (0.0215851); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 1045.26
//
Query:       gene273|gene273|rna273|rna273  [L=131]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.2e-16   59.5   0.1    4.1e-16   59.2   0.1    1.1  1  RNA_pol_Rpb1_5  RNA polymerase Rpb1, domain 5
  ------ inclusion threshold ------
      0.026   14.0   0.1      0.031   13.7   0.1    1.1  1  DUF5578         Family of unknown function (DUF5578)


Domain annotation for each model (and alignments):
>> RNA_pol_Rpb1_5  RNA polymerase Rpb1, domain 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.2   0.1   4.6e-20   4.1e-16     195     265 ..       5      75 ..       2      77 .. 0.95

  Alignments for each domain:
  == domain 1  score: 59.2 bits;  conditional E-value: 4.6e-20
                                    TTEEESSHHHHHHHHCHHHHHHHHHHHHHHHHHHTTS---HHHHHHHHHHHTTTSS---SSTTCHCCSSSH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 RNA_pol_Rpb1_5 195 geilsndiaeileilgieaarkallkeiqevykvqgvsvndrHlelivdqmtkkgeivavnrsGinkaels 265
                                    ++ l+ndi ei ++lgieaa++ +++ei  ++k++g+++n  H++l++d+m++kg++  ++r Gi++ ++s
  gene273|gene273|rna273|rna273   5 ETALTNDILEIESVLGIEAAQRSIINEIVFTLKSHGIEINVEHITLLADLMCFKGKVNGITRFGIKNFKSS 75 
                                    6789*************************************************************987765 PP

>> DUF5578  Family of unknown function (DUF5578)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   3.5e-06     0.031     216     253 ..      21      58 ..       6      66 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.5e-06
                        DUF5578 216 vkeakpsivepllelLkslhlevqyeaielikelmste 253
                                    +++a++si++ ++ +Lks  +e++ e i l+ +lm+++
  gene273|gene273|rna273|rna273  21 IEAAQRSIINEIVFTLKSHGIEINVEHITLLADLMCFK 58 
                                    7899*******************************874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       414  (0.0230911); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.33u 0.26s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 1048.01
//
Query:       gene2730|gene2730|rna2730|rna2730  [L=183]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.017   15.4   0.1       0.11   12.8   0.0    1.8  2  Darcynin         Darcynin, domain of unknown function
      0.018   13.8   0.1      0.023   13.5   0.1    1.1  1  G_glu_transpept  Gamma-glutamyltranspeptidase
      0.042   14.4   1.0      0.082   13.5   0.2    1.8  2  B_lectin         D-mannose binding lectin


Domain annotation for each model (and alignments):
>> Darcynin  Darcynin, domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   1.8e-05      0.11      43     101 ..      16      73 ..       5      79 .. 0.79
   2 ?    0.3   0.0      0.13   7.7e+02       4      62 ..      84     142 ..      79     150 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.8e-05
                           Darcynin  43 qvlpilekraagvrlrfydvefyaarvtdlwvweaedhhayqllvedl.retafwdryfe 101
                                         ++ +++   ++ ++ f d efy + +  l ++  +      llve+l +++ +wdr  +
  gene2730|gene2730|rna2730|rna2730  16 LFMKVIR-LNSHGKVEFSDNEFYNT-IKHLIMFVDNSSFILHLLVEKLiKNSRLWDRLKK 73 
                                        4555555.468999*********98.7788899889999999****9846788***9765 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.13
                           Darcynin   4 eetvtipsfepaltvfmlvktspewlaltveervdlleeqvlpilekraagvrlrfydv 62 
                                        +++++   fe  l+  m+      +la+  +++  ++ ++      k    v+lr  d+
  gene2730|gene2730|rna2730|rna2730  84 TDAISYNQFEMNLSNAMMEINNTTYLAVMDNQKNVAFISENSSTRAKTPVYVNLRNLDA 142
                                        55667788999998888877777788876655555555444445455556667766665 PP

>> G_glu_transpept  Gamma-glutamyltranspeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   3.9e-06     0.023     286     345 ..      55     121 ..      35     127 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.9e-06
                                        HCHHHHHT-HHHHHHHHTT.BTTB..SG........GGCSCGGCSCG.TTEEEEEEEEETTS-EEEEE CS
                    G_glu_transpept 286 telveellskeyakeraklIkdkaatps........seyykaaeaaeesggTthlsvvDregnaVSlt 345
                                        + lve+l++++ + +r k+I++k++++s        +   + ++a  e ++Tt+l+v+D++ n V+++
  gene2730|gene2730|rna2730|rna2730  55 HLLVEKLIKNSRLWDRLKKIDKKNNNKSktdaisynQFEMNLSNAMMEINNTTYLAVMDNQKN-VAFI 121
                                        45899******************9999999998885444556677777************977.5555 PP

>> B_lectin  D-mannose binding lectin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       0.5     3e+03      54      73 ..      46      68 ..      18      85 .. 0.53
   2 ?   13.5   0.2   1.4e-05     0.082      14      62 ..      96     145 ..      83     155 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.5
                           B_lectin 54 LldsGnLvl...esssnseevlW 73
                                       + d+  ++l    ++  +++ lW
  gene2730|gene2730|rna2730|rna2730 46 FVDNSSFILhllVEKLIKNSRLW 68
                                       44444444433333333333333 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 1.4e-05
                           B_lectin  14 dssgvlkisedgnLvllnesksvvwstssssssakntv.aqLldsGnLvl 62 
                                         s+++++i++++ L++++++k+v + +++ss+ ak++v ++L +   L l
  gene2730|gene2730|rna2730|rna2730  96 LSNAMMEINNTTYLAVMDNQKNVAFISENSSTRAKTPVyVNLRNLDALFL 145
                                        57889**********************77777777776477777776666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1210  (0.0674884); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1345.88
//
Query:       gene2731|gene2731|rna2731|rna2731  [L=156]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.098   12.5   0.1       0.28   11.0   0.0    1.8  2  rve_3     Integrase core domain


Domain annotation for each model (and alignments):
>> rve_3  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   1.5e-05      0.28      13      55 ..      16      54 ..       5      56 .. 0.79
   2 ?   -2.6   0.0      0.28   5.1e+03      15      28 ..      78      91 ..      67      96 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 1.5e-05
                              rve_3 13 PqqNglvEsfngtlrdellneelfrslaearekleawredYNt 55
                                        + Ng vE++++t+r+ + ++     ++e  + +++  ++YN+
  gene2731|gene2731|rna2731|rna2731 16 HKNNGCVERVIRTVREAIEKM----GVNEMGKTIKEVEDRYNK 54
                                       578************887663....346888888888888886 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.28
                              rve_3 15 qNglvEsfngtlrd 28
                                       +N +  + n+ +++
  gene2731|gene2731|rna2731|rna2731 78 ENSKDRRYNKLFKK 91
                                       56666677777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1179  (0.0657594); expected 358.6 (0.02)
Passed bias filter:                      540  (0.0301188); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1115.43
//
Query:       gene2732|gene2732|rna2732|rna2732  [L=201]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (201 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       281  (0.0156729); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.29s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 1346.64
//
Query:       gene2733|gene2733|rna2733|rna2733  [L=41]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (41 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       153  (0.00853366); expected 358.6 (0.02)
Passed bias filter:                      148  (0.00825478); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.33u 0.24s 00:00:00.57 Elapsed: 00:00:00.39
# Mc/sec: 315.20
//
Query:       gene2734|gene2734|rna2734|rna2734  [L=106]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.4e-16   60.2   7.4    2.4e-16   60.2   7.4    2.1  2  zinc_ribbon_15  zinc-ribbon family
    0.00047   20.1   8.5      0.011   15.7   1.1    2.8  2  DZR             Double zinc ribbon
     0.0085   15.8   1.1     0.0085   15.8   1.1    3.1  4  zinc_ribbon_2   zinc-ribbon domain
  ------ inclusion threshold ------
      0.028   14.1   0.2      0.028   14.1   0.2    4.0  4  zf-NADH-PPase   NADH pyrophosphatase zinc ribbon domain
       0.25   11.0  11.0        0.5   10.0   2.4    2.2  2  TackOD1         Thaumarchaeal output domain 1
       0.53   10.6   0.2       0.53   10.6   0.2    2.9  3  zf-Di19         Drought induced 19 protein (Di19), zinc-bindi
        2.9    7.5   8.6       0.21   11.2   2.1    2.2  3  DpnI            Dam-replacing family
        3.2    8.6   6.6         17    6.3   0.0    3.3  3  zf-WRNIP1_ubi   Werner helicase-interacting protein 1 ubiquit
        4.2    7.5   7.0        5.8    7.1   0.9    2.4  2  PknG_rubred     Protein kinase G rubredoxin domain
        5.6    6.6  20.4        4.8    6.8   5.2    3.8  3  RecR            RecR protein


Domain annotation for each model (and alignments):
>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.7      0.18   3.2e+02       2      20 ..       6      24 ..       3      27 .. 0.77
   2 !   60.2   7.4   1.3e-19   2.4e-16       1      86 []      28     100 ..      28     100 .. 0.99

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.18
                     zinc_ribbon_15  2 lCpkCgklskaelvkkkkv 20
                                        C  Cg ++k++ +k++++
  gene2734|gene2734|rna2734|rna2734  6 QCLICGVMTKIKSKKNENA 24
                                       5888888888888888775 PP

  == domain 2  score: 60.2 bits;  conditional E-value: 1.3e-19
                     zinc_ribbon_15   1 ilCpkCgklskaelvkkkkvlklffipvfkwkkkkpylacskCkslleaskelgkeiekkessekkeCknCgkeve 76 
                                        ++Cp C+++++a  + +k+++++ffip+f+++++++y+ c+ Ck ++++ +             +++C++C++ + 
  gene2734|gene2734|rna2734|rna2734  28 VYCPFCSNNVDAADIIHKYYFTFFFIPLFPVGSSTKYVGCEVCKGKFSDGR-------------VRICHKCRNIIL 90 
                                        58************************************************9.............************ PP

                     zinc_ribbon_15  77 eefkyCpkCg 86 
                                        ++++yC +Cg
  gene2734|gene2734|rna2734|rna2734  91 NDYRYCGRCG 100
                                        *********9 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   9.0   4.8e-05     0.087       8      49 .]      23     100 ..       2     100 .. 0.83
   2 !   15.7   1.1   6.3e-06     0.011       1      22 [.      82     103 ..      82     105 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 4.8e-05
                                DZR   8 lppdarfCseCgtklkavaa.....................................edrCpsCgekvdpearfCp 46 
                                        +  ++ +C+ C ++++a+ +                                      + C +C   + ++ r+C+
  gene2734|gene2734|rna2734|rna2734  23 NAVEDVYCPFCSNNVDAA-DiihkyyftfffiplfpvgsstkyvgcevckgkfsdgrVRICHKCRNIILNDYRYCG 97 
                                        666777888888888743.258888888888888888888888888888888888889****************** PP

                                DZR  47 eCG 49 
                                         CG
  gene2734|gene2734|rna2734|rna2734  98 RCG 100
                                        **9 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 6.3e-06
                                DZR   1 CpqCgeelppdarfCseCgtkl 22 
                                        C +C++ + +d r+C++Cg ++
  gene2734|gene2734|rna2734|rna2734  82 CHKCRNIILNDYRYCGRCGDAV 103
                                        9******************876 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.5       4.8   8.6e+03      16      20 ..       7      11 ..       7      11 .. 0.46
   2 !    5.5   0.6     0.008        14       8      19 ..      22      33 ..      20      37 .. 0.80
   3 ?   -1.8   0.2       1.6   2.9e+03      16      19 ..      67      70 ..      60      73 .. 0.74
   4 !   15.8   1.1   4.7e-06    0.0085       2      20 ..      82     100 ..      81     103 .. 0.95

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 4.8
                      zinc_ribbon_2 16 CpyCG 20
                                       C  CG
  gene2734|gene2734|rna2734|rna2734  7 CLICG 11
                                       44455 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.008
                      zinc_ribbon_2  8 elqdnakFCpyC 19
                                       e+  ++++Cp C
  gene2734|gene2734|rna2734|rna2734 22 ENAVEDVYCPFC 33
                                       66668999**99 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 1.6
                      zinc_ribbon_2 16 CpyC 19
                                       C+ C
  gene2734|gene2734|rna2734|rna2734 67 CEVC 70
                                       8888 PP

  == domain 4  score: 15.8 bits;  conditional E-value: 4.7e-06
                      zinc_ribbon_2   2 CpnCGaelqdnakFCpyCG 20 
                                        C +C + + ++ ++C +CG
  gene2734|gene2734|rna2734|rna2734  82 CHKCRNIILNDYRYCGRCG 100
                                        ******************9 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   1.0      0.21   3.7e+02      20      29 ..       3      12 ..       3      15 .. 0.82
   2 ?   -0.9   0.6      0.76   1.4e+03       5       9 ..      29      33 ..      28      35 .. 0.64
   3 ?    8.0   0.1    0.0012       2.2      18      30 ..      76      88 ..      75      89 .. 0.89
   4 ?   14.1   0.2   1.5e-05     0.028       2      12 ..      92     102 ..      91     104 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.21
                      zf-NADH-PPase 20 warvCpaCgl 29
                                       ++++C  Cg 
  gene2734|gene2734|rna2734|rna2734  3 HMCQCLICGV 12
                                       679*****95 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.76
                      zf-NADH-PPase  5 FCgrC 9 
                                       +C+ C
  gene2734|gene2734|rna2734|rna2734 29 YCPFC 33
                                       56665 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.0012
                      zf-NADH-PPase 18 ggwarvCpaCgle 30
                                       +g+ r C+ C+++
  gene2734|gene2734|rna2734|rna2734 76 DGRVRICHKCRNI 88
                                       79********986 PP

  == domain 4  score: 14.1 bits;  conditional E-value: 1.5e-05
                      zf-NADH-PPase   2 thrFCgrCGap 12 
                                        ++r+CgrCG +
  gene2734|gene2734|rna2734|rna2734  92 DYRYCGRCGDA 102
                                        68*******86 PP

>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   1.5    0.0041       7.4     102     134 ..       3      38 ..       1      46 [. 0.73
   2 ?   10.0   2.4   0.00028       0.5      64      95 ..      69     101 ..      61     103 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0041
                            TackOD1 102 elihhftCgnvgpeeeflkeg...kleCpkCktkLr 134
                                        ++ ++  Cg + + ++ ++e+   ++ Cp C++++ 
  gene2734|gene2734|rna2734|rna2734   3 HMCQCLICGVMTKIKSKKNENaveDVYCPFCSNNVD 38 
                                        577899***988877775555111577****99876 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00028
                            TackOD1  64 lleeelvd.rirlCpsCksghlnvrevCpkCkS 95 
                                        +++ ++ d r+r+C++C+   ln   +C  C+ 
  gene2734|gene2734|rna2734|rna2734  69 VCKGKFSDgRVRICHKCRNIILNDYRYCGRCGD 101
                                        56744444499********************86 PP

>> zf-Di19  Drought induced 19 protein (Di19), zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.3       1.6   2.9e+03      32      38 ..       5      11 ..       2      26 .. 0.59
   2 ?   10.6   0.2   0.00029      0.53       3      18 ..      28      43 ..      26      48 .. 0.72
   3 ?    4.4   0.4     0.026        46      28      43 ..      61      76 ..      59      92 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 1.6
                            zf-Di19 32 vvCPvCa 38
                                       + C +C 
  gene2734|gene2734|rna2734|rna2734  5 CQCLICG 11
                                       5577775 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00029
                            zf-Di19  3 ftCPyCgkeltvkeLv 18
                                       + CP+C+++++++ ++
  gene2734|gene2734|rna2734|rna2734 28 VYCPFCSNNVDAADII 43
                                       5688888888877765 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.026
                            zf-Di19 28 eskevvCPvCaekvtk 43
                                       ++k+v C vC+ k ++
  gene2734|gene2734|rna2734|rna2734 61 STKYVGCEVCKGKFSD 76
                                       679999****998776 PP

>> DpnI  Dam-replacing family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   2.1   0.00012      0.21      32      62 ..       5      36 ..       1      41 [. 0.85
   2 ?    0.2   0.1      0.27   4.9e+02     108     145 ..      37      70 ..      34      91 .. 0.63
   3 ?   -0.9   0.4      0.62   1.1e+03      29      38 ..      91     100 ..      67     103 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00012
                                       ---TTT--.SS-EE--------EEE-TTT--E CS
                               DpnI 32 lyCpkCgs.kklsefennkpvaDfyCesckee 62
                                       + C +Cg  +k+++ +n++ v D yC  c+++
  gene2734|gene2734|rna2734|rna2734  5 CQCLICGVmTKIKSKKNENAVEDVYCPFCSNN 36
                                       57*****62679*****************976 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.27
                                        EEEEEEE-GGG--GGGEEEEEEE--------EEEEEEE CS
                               DpnI 108 venlllipklfftpeiiekRkpLsetarRagwigcnid 145
                                        v    +i+k++ft   i    pL +    + ++gc++ 
  gene2734|gene2734|rna2734|rna2734  37 VDAADIIHKYYFTFFFI----PLFPVGSSTKYVGCEVC 70 
                                        55566788888887666....55555555556666654 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 0.62
                                        HHH---TTT- CS
                               DpnI  29 aknlyCpkCg 38 
                                        ++  yC  Cg
  gene2734|gene2734|rna2734|rna2734  91 NDYRYCGRCG 100
                                        2334455554 PP

>> zf-WRNIP1_ubi  Werner helicase-interacting protein 1 ubiquitin-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   2.3      0.38   6.9e+02       1      11 [.       3      13 ..       3      16 .. 0.86
   2 ?    6.3   0.0    0.0094        17       3      17 ..      28      42 ..      26      44 .. 0.87
   3 ?    0.9   0.1      0.51   9.1e+02       3       9 ..      65      71 ..      63      73 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.38
                      zf-WRNIP1_ubi  1 HqvqCPvCqqm 11
                                       H  qC +C  m
  gene2734|gene2734|rna2734|rna2734  3 HMCQCLICGVM 13
                                       889*****877 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0094
                      zf-WRNIP1_ubi  3 vqCPvCqqmmPAAHi 17
                                       v CP C   + AA i
  gene2734|gene2734|rna2734|rna2734 28 VYCPFCSNNVDAADI 42
                                       89*****99999987 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.51
                      zf-WRNIP1_ubi  3 vqCPvCq 9 
                                       v C vC+
  gene2734|gene2734|rna2734|rna2734 65 VGCEVCK 71
                                       88****6 PP

>> PknG_rubred  Protein kinase G rubredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.2     0.032        57      95     123 ..       7      36 ..       3      43 .. 0.81
   2 ?    7.1   0.9    0.0033       5.8      90     103 ..      91     104 ..      85     105 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.032
                                        -TTT--B-S.---SS----SEEE-TTT--E CS
                        PknG_rubred  95 CwrCGrpvG.RsekerkgaseGtCpkCgsp 123
                                        C  CG     +s+k++++ ++ +Cp C+++
  gene2734|gene2734|rna2734|rna2734   7 CLICGVMTKiKSKKNENAVEDVYCPFCSNN 36 
                                        7778876542889999999********986 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0033
                                        GGG-B-TTT--B-S CS
                        PknG_rubred  90 EskRfCwrCGrpvG 103
                                        +  R+C rCG +vG
  gene2734|gene2734|rna2734|rna2734  91 NDYRYCGRCGDAVG 104
                                        567**********9 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   3.5    0.0049       8.8      13      36 ..       1      35 [.       1      37 [. 0.85
   2 ?   -0.2   0.1      0.41   7.4e+02      19      22 ..      67      70 ..      61      73 .. 0.70
   3 ?    6.8   5.2    0.0027       4.8      15      36 ..      78     101 ..      75     102 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0049
                                       HHH-EE-TTT--EESSS...........S-CCCCS CS
                               RecR 13 kekvrhCsrCgnlteed...........lCaICsd 36
                                       ++++ +C +Cg +t               C++Cs+
  gene2734|gene2734|rna2734|rna2734  1 MSHMCQCLICGVMTKIKskknenavedvYCPFCSN 35
                                       578999*******8887788889988878****98 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.41
                                       -TTT CS
                               RecR 19 CsrC 22
                                       C++C
  gene2734|gene2734|rna2734|rna2734 67 CEVC 70
                                       5555 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.0027
                                        H-EE-TTT--E..ESSSS-CCCCS CS
                               RecR  15 kvrhCsrCgnl..teedlCaICsd 36 
                                        +vr C +C+n+   +   C  C d
  gene2734|gene2734|rna2734|rna2734  78 RVRICHKCRNIilNDYRYCGRCGD 101
                                        699********6666668*99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       828  (0.0461822); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 682.70
//
Query:       gene2735|gene2735|rna2735|rna2735  [L=51]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (51 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       193  (0.0107647); expected 358.6 (0.02)
Passed bias filter:                      163  (0.00909142); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.31u 0.23s 00:00:00.54 Elapsed: 00:00:00.37
# Mc/sec: 410.42
//
Query:       gene2736|gene2736|rna2736|rna2736  [L=188]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.022   14.6   0.0      0.039   13.8   0.0    1.4  1  VbhA      Antitoxin VbhA


Domain annotation for each model (and alignments):
>> VbhA  Antitoxin VbhA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   2.2e-06     0.039      28      47 .]      79      98 ..      73      98 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.2e-06
                               VbhA 28 eayvrGeIdadElvrrvraR 47
                                       eay +Ge+d++E+v++++ R
  gene2736|gene2736|rna2736|rna2736 79 EAYFDGEMDIAEAVEETLTR 98
                                       89***************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       519  (0.0289475); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 1255.80
//
Query:       gene2737|gene2737|rna2737|rna2737  [L=52]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0043   16.8   0.5     0.0043   16.8   0.5    1.0  1  SHE3            SWI5-dependent HO expression protein 3
  ------ inclusion threshold ------
      0.017   14.5   1.3      0.018   14.4   1.3    1.0  1  GAS             Growth-arrest specific micro-tubule binding
      0.026   14.0   0.0      0.036   13.5   0.0    1.1  1  Ribosomal_S5_C  Ribosomal protein S5, C-terminal domain


Domain annotation for each model (and alignments):
>> SHE3  SWI5-dependent HO expression protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.5   7.2e-07    0.0043      48      93 ..       3      48 ..       1      52 [] 0.84

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 7.2e-07
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                               SHE3 48 aslkhENdnLsslLkRKerrlkdlekelselkesveelklekkqlk 93
                                        +lk+E d L ++L+ Ke+rlkd+  +++   +  e + +  ++l+
  gene2737|gene2737|rna2737|rna2737  3 QQLKKELDGLDTFLRQKEQRLKDVSVKVKRQYNVLEAADATVEALE 48
                                       579*********************9999888888888877777766 PP

>> GAS  Growth-arrest specific micro-tubule binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   1.3   2.9e-06     0.018      29      78 ..       3      52 .]       1      52 [] 0.96

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.9e-06
                                GAS 29 kslKeeieelkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlk 78
                                       ++lK+e+  l++  +++e++l+++s + kr    L++a++ ve L+ +lk
  gene2737|gene2737|rna2737|rna2737  3 QQLKKELDGLDTFLRQKEQRLKDVSVKVKRQYNVLEAADATVEALEGELK 52
                                       78*******************************************98886 PP

>> Ribosomal_S5_C  Ribosomal protein S5, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0     6e-06     0.036      36      60 ..      24      48 ..      23      51 .. 0.95

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 6e-06
                                       -SEE---BS-SSHHHHHHHHHHHHH CS
                     Ribosomal_S5_C 36 kDvlakslgsrnpinvvkAtfeALk 60
                                       kDv++k+++  n +  + At+eAL+
  gene2737|gene2737|rna2737|rna2737 24 KDVSVKVKRQYNVLEAADATVEALE 48
                                       9***********************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (52 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       948  (0.0528752); expected 358.6 (0.02)
Passed bias filter:                      519  (0.0289475); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 376.40
//
Query:       gene2738|gene2738|rna2738|rna2738  [L=229]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (229 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       301  (0.0167884); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1801.23
//
Query:       gene2739|gene2739|rna2739|rna2739  [L=61]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       230  (0.0128284); expected 358.6 (0.02)
Passed bias filter:                      211  (0.0117686); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.31u 0.25s 00:00:00.56 Elapsed: 00:00:00.38
# Mc/sec: 482.36
//
Query:       gene274|gene274|rna274|rna274  [L=94]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       373  (0.0208043); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 685.26
//
Query:       gene2740|gene2740|rna2740|rna2740  [L=99]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       718  (0.0400469); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.23s 00:00:00.57 Elapsed: 00:00:00.36
# Mc/sec: 827.56
//
Query:       gene2741|gene2741|rna2741|rna2741  [L=302]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-21   76.3   0.0    3.7e-21   75.7   0.0    1.3  1  UDG       Uracil DNA glycosylase superfamily


Domain annotation for each model (and alignments):
>> UDG  Uracil DNA glycosylase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.7   0.0   2.1e-25   3.7e-21       5     151 ..     139     291 ..     135     294 .. 0.90

  Alignments for each domain:
  == domain 1  score: 75.7 bits;  conditional E-value: 2.1e-25
                                        CTT-SEEEEESSTCHH.HHHHSSSS.-STT.--HHHHHHH.CCCCCCCHHG.........CTEEEEESSS....S. CS
                                UDG   5 ppdakvvivGeaPgae.edatglpFsgrag.nllrkllne.aglkrdlese.........qgvyitnvvkcrppg. 67 
                                         +d+kvvi+G++P+++ + atgl+Fs++++  ++++l n+ a++ r++++          qgv+++n  +    + 
  gene2741|gene2741|rna2741|rna2741 139 ITDTKVVIIGQDPYHNkGRATGLAFSVPPNvPMPPSLRNImAEVRRNYKDAtcnledwakQGVLLLNDTL----Tv 210
                                        579************************999466667777788999987777*******************....64 PP

                                        ECGCTTCCCCTCCHH.HHHHHHHHHH...SSE.EEEESHHHHHH..HHHHSCESCCCSCT..SEEEEES-SSTTTT CS
                                UDG  68 nrdtptsaeikacap.lleeeiellk...prl.ivllGktaakallgeklgklrgklleak.irvlplphPsplnr 137
                                        + ++p s++   ++  ++++ ++ ++   +++ ++l+G  a k+           +l++ k + vl++ hPsp+++
  gene2741|gene2741|rna2741|rna2741 211 SEAKPGSHS-TYGWSiFTDRILKFVNekcKNVvFMLWGSFAGKK----------SALIDGKkHLVLTSMHPSPFSA 275
                                        4479*****.9******************6666***********..........89****99************** PP

                                        T..TTTSHHHHHHHHH CS
                                UDG 138 n..ffksnpelkaeaw 151
                                           f ++n++ ka+++
  gene2741|gene2741|rna2741|rna2741 276 DrgFNGCNHFVKANEY 291
                                        **************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       676  (0.0377043); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.38
# Mc/sec: 2391.88
//
Query:       gene2742|gene2742|rna2742|rna2742  [L=106]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.2e-09   37.3   6.1    2.5e-09   37.1   6.1    1.0  1  Cation_ATPase_C  Cation transporting ATPase, C-terminus
  ------ inclusion threshold ------
      0.011   15.8   1.3      0.014   15.4   1.3    1.1  1  MreD             rod shape-determining protein MreD


Domain annotation for each model (and alignments):
>> Cation_ATPase_C  Cation transporting ATPase, C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.1   6.1   2.8e-13   2.5e-09     107     181 ..       7      79 ..       1      80 [. 0.94

  Alignments for each domain:
  == domain 1  score: 37.1 bits;  conditional E-value: 2.8e-13
                    Cation_ATPase_C 107 lnlrsrreslfkfsglfsnkllllaillslllqvlivyvpglnavfgtaplsleewlialllalvvllvdelvKl 181
                                        +n+rs++  + +f ++++n +++++ ++ l+ q+++++   +n vf+t+ l+++ew+++++la+++l+++ ++++
  gene2742|gene2742|rna2742|rna2742   7 INARSLSSRVSPFLNIKRNNYFIGVNVAVLVCQLFVMQK--FNLVFRTQALTINEWTVSIILAALLLVYMAVIRR 79 
                                        89999999*******************************..****************************999886 PP

>> MreD  rod shape-determining protein MreD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   1.3   1.6e-06     0.014      72     133 ..      29      94 ..      26      99 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.6e-06
                               MreD  72 lGvyalvlslilylvaklqkvlrlnr....rflpavlqvlllellvlvialliglaeldligfvvy 133
                                        +Gv++ vl+  l++++k++ v+r+++    + +  ++ + ll+++ +vi+ l   +e++ i  + +
  gene2742|gene2742|rna2742|rna2742  29 IGVNVAVLVCQLFVMQKFNLVFRTQAltinEWTVSIILAALLLVYMAVIRRLENYWEDQRIARWNS 94 
                                        9***********************998777667777777778889*****9999999877766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       795  (0.0443416); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.32u 0.25s 00:00:00.57 Elapsed: 00:00:00.36
# Mc/sec: 872.63
//
Query:       gene2743|gene2743|rna2743|rna2743  [L=936]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.8e-37  126.2   7.9    2.6e-36  124.8   0.3    3.4  4  E1-E2_ATPase     E1-E2 ATPase
    6.4e-17   62.5   0.1    5.7e-14   52.9   0.1    2.6  2  Hydrolase        haloacid dehalogenase-like hydrolase
    5.6e-16   58.8   3.9    7.4e-16   58.4   0.4    2.7  3  Cation_ATPase_C  Cation transporting ATPase, C-terminus
    4.7e-11   42.6   0.1    1.5e-06   28.2   0.0    2.7  2  Cation_ATPase    Cation transport ATPase (P-type)
    3.5e-05   23.7   0.1    0.00065   19.5   0.1    2.7  2  Hydrolase_3      haloacid dehalogenase-like hydrolase
    0.00031   20.4   0.0    0.00086   18.9   0.0    1.8  1  Cation_ATPase_N  Cation transporter/ATPase, N-terminus


Domain annotation for each model (and alignments):
>> E1-E2_ATPase  E1-E2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.2      0.01        31     111     156 ..      98     148 ..      74     154 .. 0.79
   2 !  124.8   0.3   8.8e-40   2.6e-36       6     180 ..     173     357 ..     168     358 .. 0.91
   3 ?   -2.5   0.1       1.1   3.2e+03     111     139 ..     829     853 ..     807     868 .. 0.55
   4 ?   -0.8   0.0      0.31   9.2e+02     114     140 ..     902     928 ..     882     933 .. 0.73

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.01
                                        HHHHHHHHHHHHHHHHHHHHHHHHHS-STTTSSTT.....HHHHHHHHHHH CS
                       E1-E2_ATPase 111 lqkkldklgkvlvpvvlliallvflialllgksla.....eallralallv 156
                                        l k+++  + +l +++ +++l+v +++ l+++++       ++l a++++v
  gene2743|gene2743|rna2743|rna2743  98 LRKNMRDRILILLFIASAVSLIVGIYNTLYENEPYsyiegLSILLAVVIIV 148
                                        6788888889999********************976665544444444444 PP

  == domain 2  score: 124.8 bits;  conditional E-value: 8.8e-40
                                        EEEEE-TTS-EEEEGGG--TTSEEEEETT-B--SEEEEEEE-S.EEE-TTTS---S-EE-G-TTEE.-TT-EEEE- CS
                       E1-E2_ATPase   6 takvirdgteeeidakelvpGDivllkagdrvpaDgrivegsa.evdesaLTGEslpvekekgdmv.fsGtvvvsg 79 
                                        ++k ++dg   + +++e+ +GD++ +++gd+ paD+++v+  +  vdes+LTGEs  +ek+ +  v  +G+ v +g
  gene2743|gene2743|rna2743|rna2743 173 SVKYVEDGVFNTKKISEILVGDMLYVEPGDILPADAVLVSNDTlFVDESMLTGESNTMEKNMHMPVlRAGSYVQEG 248
                                        577889******************************************************976655169******* PP

                                        EEEEEEEE-TTTSTTTTTSTTS--------HHHHHHHHHHHHHHHHHHHHHHHHHHS-ST....TTSSTT...... CS
                       E1-E2_ATPase  80 eakavVtatgedtelgkiarlveeakskktplqkkldklgkvlvpvvlliallvfliall....lgksla...... 145
                                         a++ V+a+g +++ gk+ r++ ++ ++kt l+kk ++l+++l++ +l++++l+f ++++    l           
  gene2743|gene2743|rna2743|rna2743 249 AARCLVIAVGYNSTKGKLLRSMVRP-ARKTALEKKSEQLANQLATRALIVCFLFFCLHIVkiyvL----Egpytlt 319
                                        ************************9.99****************999999999999988744432....2334688 PP

                                        ...HHHHHHHHHHHHHS-TTHHHHHHHHHHHHHHHHHH CS
                       E1-E2_ATPase 146 ...eallralallvaaiPcaLplavplalalgarrlak 180
                                           + +++++al+v++iP++Lp+a+++al++g++r+ k
  gene2743|gene2743|rna2743|rna2743 320 yvvRKVIETIALAVMIIPEGLPMATTMALSFGTKRMLK 357
                                        999*********************************87 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 1.1
                                        HHHHHHHHHHHHHHHHHHHHHHHHHS-ST CS
                       E1-E2_ATPase 111 lqkkldklgkvlvpvvlliallvfliall 139
                                        + k+l+    v v++v+l+a+      l+
  gene2743|gene2743|rna2743|rna2743 829 IRKFLQLQLTVTVCTVVLMAVS----SLF 853
                                        3333333333333333333333....333 PP

  == domain 4  score: -0.8 bits;  conditional E-value: 0.31
                                        HHHHHHHHHHHHHHHHHHHHHHS-STT CS
                       E1-E2_ATPase 114 kldklgkvlvpvvlliallvflialll 140
                                         +++++k++v++++l +l+v l+++++
  gene2743|gene2743|rna2743|rna2743 902 LITRYMKHFVFFSTLYILMVTLFMYYT 928
                                        567888888888888888888887665 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.0   0.0    0.0021       6.3       3      30 ..     376     402 ..     374     502 .. 0.69
   2 !   52.9   0.1   1.9e-17   5.7e-14     106     210 .]     667     786 ..     547     786 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0021
                                        EEEEESBTTTBCHHHHHHHHHHHHCHHH CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          Hydrolase   3 tvvfDkdGTLttgepsvedvivsaalal 30 
                                         ++ Dk+GTLt  + +++ ++v++ ++l
  gene2743|gene2743|rna2743|rna2743 376 YLCTDKTGTLTYNRLRLRNAYVKR-KSL 402
                                        6889***************99999.222 PP

  == domain 2  score: 52.9 bits;  conditional E-value: 1.9e-17
                                        HHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHHTT.............GGGESEEEEHHC CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.............xxxxxxxxxxxx RF
                          Hydrolase 106 ralavftiadplkvkpeaaeavasLkaagievvlltgdnpetaeraanqlG.............ddyfdaviasdi 168
                                          l+ f ++dp  +++++ + ++  k+ag+++v+ltgd  e a  +a+++G             +           
  gene2743|gene2743|rna2743|rna2743 667 VFLGCFSFEDP--LREGIDQKIEVMKDAGLNIVMLTGDGLESASYIAEEIGildgkyeaitgkcF----------- 729
                                        56899******..**************************************99666655554442........... PP

                                        ES...............STTTSHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHHHTT CS
                                        xx...............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          Hydrolase 169 et...............vakpspegkvaaireLqgkpeevamVGDgvnDaaalaaAg 210
                                        +                +a + p +k++ ++ Lq k+e va+ GDg+nD +al+ A+
  gene2743|gene2743|rna2743|rna2743 730 KSmsddelmnrienirvIARATPIDKQRFVDILQRKGETVAVTGDGANDGPALKLAD 786
                                        333434444445559999999*********************************997 PP

>> Cation_ATPase_C  Cation transporting ATPase, C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.22   6.5e+02     150     172 ..     125     147 ..      91     210 .. 0.56
   2 ?   -2.7   0.0       1.3     4e+03      58      69 ..     294     305 ..     270     339 .. 0.54
   3 !   58.4   0.4   2.5e-19   7.4e-16       4      74 ..     861     931 ..     859     935 .. 0.95

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.22
                    Cation_ATPase_C 150 avfgtaplsleewlialllalvv 172
                                        ++ + +p+s  e l +ll ++++
  gene2743|gene2743|rna2743|rna2743 125 TLYENEPYSYIEGLSILLAVVII 147
                                        33333333333332222222222 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.3
                    Cation_ATPase_C  58 gllqalvtllvf 69 
                                        +l++ ++ ++++
  gene2743|gene2743|rna2743|rna2743 294 ALIVCFLFFCLH 305
                                        222222222222 PP

  == domain 3  score: 58.4 bits;  conditional E-value: 2.5e-19
                    Cation_ATPase_C   4 lsaiqiLwinLvtDllpalaLaleppekdimkrpPrkkkepliskkmlrriliqgllqalvtllvffltll 74 
                                        ++++q+LwinL +D + a++L++++p +  ++r+P+++++pli++ m   +++  l++++vtl++++  + 
  gene2743|gene2743|rna2743|rna2743 861 FTPLQLLWINLYMDAFSAISLSTDKPTAVHLSRKPEHPDNPLITRYMKHFVFFSTLYILMVTLFMYYTSFG 931
                                        9*****************************************************************87766 PP

>> Cation_ATPase  Cation transport ATPase (P-type)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.2   0.0   4.9e-10   1.5e-06       1      67 [.     427     489 ..     425     504 .. 0.92
   2 !   11.4   0.0   8.8e-05      0.26      67      90 ..     590     613 ..     575     614 .. 0.84

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 4.9e-10
                      Cation_ATPase   1 ilcNsaafsensekdevkllGnktEsALlvlaeklgldteelreetkkvqeipFnssrKrmsvvlkl 67 
                                        i+ Ns+af    ++ e  ++G+  Es Ll l  k g d++ +r++ + ++ + F+s+rK+m+++++ 
  gene2743|gene2743|rna2743|rna2743 427 IVFNSSAF----KNREGVYVGSRLESTLLALLVKTGVDVSVMRKKSHVLRRLCFSSERKYMATIIED 489
                                        57788999....888889*********************************************9975 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 8.8e-05
                      Cation_ATPase  67 lepekkvrlyvKGApeiilkrCth 90 
                                        ++++ +++++ KGA e i+k C++
  gene2743|gene2743|rna2743|rna2743 590 EQKKRQYVALLKGATEQIVKYCQY 613
                                        338899****************87 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.13     4e+02      21      54 ..     683     716 ..     676     743 .. 0.81
   2 !   19.5   0.1   2.2e-07   0.00065     197     255 .]     760     819 ..     755     819 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.13
                                        HHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCC CS
                        Hydrolase_3  21 keaikklkekgikvviATGRslravlpvleelgl 54 
                                         + i+ +k++g ++v  TG  l+++++++ee+g+
  gene2743|gene2743|rna2743|rna2743 683 DQKIEVMKDAGLNIVMLTGDGLESASYIAEEIGI 716
                                        5779999************************995 PP

  == domain 2  score: 19.5 bits;  conditional E-value: 2.2e-07
                                        HHCT--GGGEEEEESSGGGHHHHHHSSEEEEETTS-HHH.HHHSSEEE--GGGTHHHHHH CS
                        Hydrolase_3 197 kelnisleeviafGDgeNDieMLeaaglgvAmgnaseev.kkaAdyvtksnnedGVakal 255
                                          l+ + e v++ GDg ND + L+ a++g+ mg +s  + k+a++ v+ + n +++ +a+
  gene2743|gene2743|rna2743|rna2743 760 DILQRKGETVAVTGDGANDGPALKLADVGFSMGMSSTDIaKEASSVVVLDENFESIIRAI 819
                                        567888999************************776555055556666666669988876 PP

>> Cation_ATPase_N  Cation transporter/ATPase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   2.9e-07   0.00086      26      69 .]      74     117 ..      70     117 .. 0.94

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 2.9e-07
                    Cation_ATPase_N  26 aaerlkkyGpNelkekkkkslwvkllkqftnplvilLlvaalvs 69 
                                        a+e  + yG Ne+    ++s+  +l k++++ ++ilL++a++vs
  gene2743|gene2743|rna2743|rna2743  74 AQESKRMYGVNEIVVDDPRSITCILRKNMRDRILILLFIASAVS 117
                                        7888899***********************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (936 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       922  (0.0514251); expected 358.6 (0.02)
Passed bias filter:                      506  (0.0282224); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.77u 0.32s 00:00:01.09 Elapsed: 00:00:00.49
# Mc/sec: 5724.65
//
Query:       gene2744|gene2744|rna2744|rna2744  [L=786]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      8e-24   83.9   7.7      8e-24   83.9   7.7    2.2  2  zf-HC5HC2H_2  PHD-zinc-finger like domain
    3.9e-16   59.1   4.7    3.9e-16   59.1   4.7    2.8  3  zf-HC5HC2H    PHD-like zinc-binding domain
    6.1e-11   41.7   6.5    6.1e-11   41.7   6.5    2.8  3  PHD_2         PHD-finger
    4.3e-10   39.5   0.1    2.4e-09   37.1   0.1    2.4  2  Bromodomain   Bromodomain
    1.9e-08   34.1  10.4    1.9e-08   34.1  10.4    3.4  3  PHD           PHD-finger
     0.0023   18.3   5.3      0.027   14.8   0.1    2.8  3  EPL1          Enhancer of polycomb-like
  ------ inclusion threshold ------
        5.6    7.4  26.4       0.49   10.7   3.3    3.6  4  C1_2          C1 domain


Domain annotation for each model (and alignments):
>> zf-HC5HC2H_2  PHD-zinc-finger like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   2.8       3.7   9.5e+03      57      84 ..     116     145 ..     101     148 .. 0.72
   2 !   83.9   7.7   3.1e-27     8e-24       3      97 ..     170     265 ..     168     272 .. 0.95

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 3.7
                       zf-HC5HC2H_2  57 kCllCkkr....kGaciqCskkeCktafHvtC 84 
                                         C +C+++        + C    C+ + H  C
  gene2744|gene2744|rna2744|rna2744 116 VCNVCSHSnvrvDNNLVYCDG--CNLCVHQEC 145
                                        588888776666555666666..888888887 PP

  == domain 2  score: 83.9 bits;  conditional E-value: 3.1e-27
                       zf-HC5HC2H_2   3 CvlCkkkgGalkktsderwvHvlCallvpevsfsnvaerepvd.vekikkerlkekCllCkkrkGaciqCskkeCk 77 
                                        C++C k+gGa k+ts+ +w Hv+C+l++  + f n+  +ep++  ++ +++rlk++C+lC ++kG+ i+C+++eC+
  gene2744|gene2744|rna2744|rna2744 170 CRFCVKTGGAYKMTSTMKWGHVVCVLWNADLYFGNEVFMEPIEdPNRTNAHRLKHSCSLCGSTKGMHIRCAYTECD 245
                                        *******************************************999****************************** PP

                       zf-HC5HC2H_2  78 tafHvtCalaaglvmeledl 97 
                                          +HvtCa++++l+m+++++
  gene2744|gene2744|rna2744|rna2744 246 VWYHVTCAIEHNLYMDQSNV 265
                                        ***************98874 PP

>> zf-HC5HC2H  PHD-like zinc-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   2.7       1.4   3.5e+03      37      65 ..     115     145 ..      95     148 .. 0.73
   2 ?   -4.0   0.1         7   1.8e+04      38      48 ..     169     179 ..     167     180 .. 0.78
   3 !   59.1   4.7   1.5e-19   3.9e-16       1      89 [.     190     272 ..     190     273 .. 0.96

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.4
                         zf-HC5HC2H  37 lkCylCkkk....vGaciqCskkkCkkafHvtC 65 
                                         +C +C+++        + C+   C+ + H  C
  gene2744|gene2744|rna2744|rna2744 115 GVCNVCSHSnvrvDNNLVYCDG--CNLCVHQEC 145
                                        5788898554444456677766..888888888 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 7
                         zf-HC5HC2H  38 kCylCkkkvGa 48 
                                         C +C k+ Ga
  gene2744|gene2744|rna2744|rna2744 169 YCRFCVKTGGA 179
                                        69999998776 PP

  == domain 3  score: 59.1 bits;  conditional E-value: 1.5e-19
                         zf-HC5HC2H   1 HvvCalwipevvfeeekeiemeeiedvekikkerkklkCylCkkkvGaciqCskkkCkkafHvtCakeagllleee 76 
                                        HvvC+lw  +++f +e    me+ied ++ +++r k++C+lC +++G+ i+C+ ++C   +HvtCa e++l+++++
  gene2744|gene2744|rna2744|rna2744 190 HVVCVLWNADLYFGNEV--FMEPIEDPNRTNAHRLKHSCSLCGSTKGMHIRCAYTECDVWYHVTCAIEHNLYMDQS 263
                                        9************9876..6*****************************************************997 PP

                         zf-HC5HC2H  77 eekeklksyCkkH 89 
                                            ++ +yC +H
  gene2744|gene2744|rna2744|rna2744 264 ----NVLTYCGAH 272
                                        ....899999999 PP

>> PHD_2  PHD-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.6   1.8         7   1.8e+04      10      15 ..     117     122 ..     116     124 .. 0.64
   2 !   41.7   6.5   2.4e-14   6.1e-11       2      35 ..     129     161 ..     128     162 .. 0.96
   3 ?   -4.8   2.6         7   1.8e+04       7      18 ..     239     252 ..     236     253 .. 0.76

  Alignments for each domain:
  == domain 1  score: -4.6 bits;  conditional E-value: 7
                              PHD_2  10 CsvaVH 15 
                                        C+v+ H
  gene2744|gene2744|rna2744|rna2744 117 CNVCSH 122
                                        777766 PP

  == domain 2  score: 41.7 bits;  conditional E-value: 2.4e-14
                              PHD_2   2 npllsCdkCsvaVHasCYGvskesdgeeWlCrrC 35 
                                        n l++Cd+C+++VH++CYGv+ +++g +W C+ C
  gene2744|gene2744|rna2744|rna2744 129 NNLVYCDGCNLCVHQECYGVPIIPQG-SWFCKPC 161
                                        789***********************.*****99 PP

  == domain 3  score: -4.8 bits;  conditional E-value: 7
                              PHD_2   7 Cd..kCsvaVHasC 18 
                                        C+  +C v  H  C
  gene2744|gene2744|rna2744|rna2744 239 CAytECDVWYHVTC 252
                                        66568999999988 PP

>> Bromodomain  Bromodomain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       4.7   1.2e+04      22      49 ..     589     618 ..     580     624 .. 0.59
   2 !   37.1   0.1   9.6e-13   2.4e-09       5      75 ..     678     745 ..     673     754 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 4.7
                                        -GCCSTTHHH..H.SS---HHHHHHHHHTT CS
                        Bromodomain  22 dpeefpdyya..vikkPldLstIkkklesn 49 
                                        d++ +p y+   ++k++  L+ +k+ + ++
  gene2744|gene2744|rna2744|rna2744 589 DTTPYPCYSNeeRVKYQEWLKDVKQGCSHK 618
                                        555555555544677777777777666555 PP

  == domain 2  score: 37.1 bits;  conditional E-value: 9.6e-13
                                        HHHBHTTTCGGGGCSTT-GCCSTTHHHH.SS---HHHHHHHHHTT--SSHHHHHHHHHHHHHHHHHHSHTT CS
                        Bromodomain   5 lsellehklaepFlepvdpeefpdyyavikkPldLstIkkklesnkYksladfeadlkllfsNarkyngeg 75 
                                        +s +l++ ++  F e v+++  p+y++vi++P+d++++ +k+e+  Y+ + +f +dl+l+ +N+++yn++ 
  gene2744|gene2744|rna2744|rna2744 678 MS-ILDRGEYVLFKERVTEDIAPNYFDVIREPMDFEKVYSKVER--YEGVPQFFDDLRLIGTNCVTYNQQV 745
                                        44.78888999999***************************985..99********************964 PP

>> PHD  PHD-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.1  10.4   7.5e-12   1.9e-08       1      50 [.     116     162 ..     116     164 .. 0.91
   2 ?   -2.6   1.0       2.1   5.4e+03      23      30 ..     187     194 ..     169     199 .. 0.56
   3 !    9.7   5.8   0.00029      0.75       2      30 ..     226     253 ..     225     269 .. 0.84

  Alignments for each domain:
  == domain 1  score: 34.1 bits;  conditional E-value: 7.5e-12
                                        SBTTTTS.TTSTTSCEEEETTTSCEEETTTSSSTHSHHSHHSSTBSSTTTH CS
                                PHD   1 rCavCkk.ksdeeeelvqCdgCkrwfHqkClkppleseekpegewlCekCk 50 
                                        +C+vC+  +   +++lv+CdgC+ ++Hq+C+++p      p+g+w+C+ C+
  gene2744|gene2744|rna2744|rna2744 116 VCNVCSHsNVRVDNNLVYCDGCNLCVHQECYGVPII----PQGSWFCKPCT 162
                                        5******88888**********************76....8889******8 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2.1
                                        CEEETTTS CS
                                PHD  23 rwfHqkCl 30 
                                        +w H+ C+
  gene2744|gene2744|rna2744|rna2744 187 KWGHVVCV 194
                                        56666665 PP

  == domain 3  score: 9.7 bits;  conditional E-value: 0.00029
                                        BTTTTSTTSTTSCEEEET..TTSCEEETTTS CS
                                PHD   2 CavCkkksdeeeelvqCd..gCkrwfHqkCl 30 
                                        C++C++   +++  + C   +C+ w+H++C 
  gene2744|gene2744|rna2744|rna2744 226 CSLCGS---TKGMHIRCAytECDVWYHVTCA 253
                                        ******...7999****6548*********6 PP

>> EPL1  Enhancer of polycomb-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       1.5   3.7e+03       3      21 ..      16      34 ..      15      51 .. 0.77
   2 !   14.8   0.1   1.1e-05     0.027     114     157 .]      59      94 ..      38      94 .. 0.89
   3 ?    4.7   0.8     0.014        35      34      77 ..     515     586 ..     502     701 .. 0.51

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.5
                               EPL1  3 prldikkkLkviseeevdg 21
                                       p+ld++++L vi+e  +++
  gene2744|gene2744|rna2744|rna2744 16 PDLDVNTNLLVINELPLTD 34
                                       89*********99875544 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 1.1e-05
                               EPL1 114 eveYdMDEeDekWLeelnekrkkegvekisediFEivmdrlEke 157
                                        +v Y+ D+ D ++L+e+  +        +   +FE+++drlEke
  gene2744|gene2744|rna2744|rna2744  59 NVDYNADSYDLAFLKEYALT--------MPVSLFELIIDRLEKE 94 
                                        89******************........9999***********8 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.014
                               EPL1  34 knsnkens...........qqavetgvdkkeen..............ekhqviaaakkkesssasske........ 76 
                                        kn++k+++           + +v + +++k                 e+h     +++++++++++++        
  gene2744|gene2744|rna2744|rna2744 515 KNEEKVKNvideqilkhsdSRNV-QAQKHK--RrklpadyeldtchaEHH-----ERRAHNDTTQNTDrslitcts 582
                                        11111111333333322211111.111122..122445454444443333.....333333333333344444444 PP

                               EPL1  77 ...s 77 
                                            
  gene2744|gene2744|rna2744|rna2744 583 vfrR 586
                                        3330 PP

>> C1_2  C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   5.7   0.00049       1.3      15      46 ..     111     145 ..      97     146 .. 0.82
   2 ?   -3.9   2.1         7   1.8e+04      20      42 ..     157     165 ..     152     174 .. 0.58
   3 ?   -3.9   0.9         7   1.8e+04      20      27 ..     169     176 ..     161     180 .. 0.75
   4 ?   10.7   3.3   0.00019      0.49      18      47 .]     223     253 ..     213     253 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00049
                               C1_2  15 ssesfnCsaCgrk...idgffYsCseCdfslhvrC 46 
                                        +s+ + C++C ++   +d++  +C+ C+  +h++C
  gene2744|gene2744|rna2744|rna2744 111 ESNVGVCNVCSHSnvrVDNNLVYCDGCNLCVHQEC 145
                                        556689*******9887777799************ PP

  == domain 2  score: -3.9 bits;  conditional E-value: 7
                               C1_2  20 nCsaCgrkidgffYsCseCdfsl 42 
                                                       C+ C ++l
  gene2744|gene2744|rna2744|rna2744 157 F--------------CKPCTYQL 165
                                        4..............55555554 PP

  == domain 3  score: -3.9 bits;  conditional E-value: 7
                               C1_2  20 nCsaCgrk 27 
                                         C+ C ++
  gene2744|gene2744|rna2744|rna2744 169 YCRFCVKT 176
                                        69999887 PP

  == domain 4  score: 10.7 bits;  conditional E-value: 0.00019
                               C1_2  18 sfnCsaCgrkidgffYsCse..CdfslhvrCa 47 
                                        +++Cs+Cg + +g++ +C    Cd+  hv+Ca
  gene2744|gene2744|rna2744|rna2744 223 KHSCSLCGST-KGMHIRCAYteCDVWYHVTCA 253
                                        689******9.6999***7677*********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (786 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       982  (0.0547716); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.72u 0.29s 00:00:01.01 Elapsed: 00:00:00.50
# Mc/sec: 4759.77
//
Query:       gene2745|gene2745|rna2745|rna2745  [L=60]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.5e-08   32.8   0.1    4.5e-08   32.8   0.1    2.2  3  DUF1242   Protein of unknown function (DUF1242)


Domain annotation for each model (and alignments):
>> DUF1242  Protein of unknown function (DUF1242)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.8   0.1   2.5e-12   4.5e-08       7      35 .]       2      30 ..       1      30 [. 0.97
   2 ?   -2.4   0.1      0.24   4.4e+03       4       9 ..      43      48 ..      42      49 .. 0.75
   3 ?   -0.3   0.7     0.052   9.3e+02      28      35 .]      53      60 .]      48      60 .] 0.86

  Alignments for each domain:
  == domain 1  score: 32.8 bits;  conditional E-value: 2.5e-12
                            DUF1242  7 LlICTCTYvravfPslldrnksgfrGvfW 35
                                       L ICT TY++++fPsl+ r  +g+ +vf+
  gene2745|gene2745|rna2745|rna2745  2 LSICTTTYIKRQFPSLIGRSNKGMSSVFY 30
                                       89**************************8 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.24
                            DUF1242  4 VlLLlI 9 
                                       V LL+I
  gene2745|gene2745|rna2745|rna2745 43 VSLLCI 48
                                       778887 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.052
                            DUF1242 28 sgfrGvfW 35
                                       + f+++fW
  gene2745|gene2745|rna2745|rna2745 53 EMFLSFFW 60
                                       57999**9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (60 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       379  (0.0211389); expected 358.6 (0.02)
Passed bias filter:                      232  (0.0129399); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.28s 00:00:00.63 Elapsed: 00:00:00.43
# Mc/sec: 420.48
//
Query:       gene2746|gene2746|rna2746|rna2746  [L=194]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    8.2e-20   71.2   0.1      9e-20   71.1   0.1    1.0  1  MS_channel  Mechanosensitive ion channel
  ------ inclusion threshold ------
      0.048   13.1   0.3       0.06   12.8   0.3    1.1  1  OAF         Transcriptional regulator, Out at first
      0.097   12.9   0.1       0.19   12.0   0.1    1.6  1  BRICHOS     BRICHOS domain


Domain annotation for each model (and alignments):
>> MS_channel  Mechanosensitive ion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.1   0.1   1.5e-23     9e-20      28     205 ..       7     185 ..       1     186 [. 0.88

  Alignments for each domain:
  == domain 1  score: 71.1 bits;  conditional E-value: 1.5e-23
                                        HHHHHHHHHHHHHHHCHHHHHHHHHHHH.HTT-SS-TT-EEESSSEEEEEEEE-SSEEEEEETTSEEEEEEHHHHH CS
                         MS_channel  28 lavlGalglalglalkdlisnlvaGiil.lfekpfkiGDlveigdieGtVediglrttkirtfdgrivtiPnsslv 102
                                        l+++G   +a +  ++d+i++l   +++ l+++p+++GD+v i d e  V+ i l+ t++++ ++r+ +iPn sl+
  gene2746|gene2746|rna2746|rna2746   7 LTSVGPFLFAFSWIFQDSIKDLYKCFVFhLISHPYDVGDRVIIDDQENVVVRIDLLYTTFTNNNNRLAYIPNTSLF 82 
                                        6889999999**************9865499********************************************* PP

                                        TS-EEESSS.SSEEEEEEEEEE-TTS-...HHHHHHHHHHHHHH-TTB-TTS-EEEEEEEE-SSSEEEEEEEEEET CS
                         MS_channel 103 tsnieNlsresgtrrikvsigvtyssdvkklekvleelkealkekpevlkdkellvvldefgdsslnfevrvfvkt 178
                                         ++i N++r s ++  ++++ v+ +   k+l+++  +l e +kek++v +     +++ e++ +  ++++   ++ 
  gene2746|gene2746|rna2746|rna2746  83 GKKIDNVRR-SRNQYEQLTVFVDQNVRYKALDDLKYKLEELCKEKETVFT---GHAYIREVSKTDDKLQLVLALEH 154
                                        *********.***************************************6...55666666666666666655555 PP

                                        .......TTHHHHHHHHHHHHHHHHHHHT-- CS
                         MS_channel 179 ....vvpeeylsvqseinlrikkileeegie 205
                                            ++++e+++ ++e ++ ++++l+e gi+
  gene2746|gene2746|rna2746|rna2746 155 nsnfQDINEKYRRRKESIDVVERALNETGIR 185
                                        44668888888888888888*********97 PP

>> OAF  Transcriptional regulator, Out at first
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.3     1e-05      0.06      90     170 ..      80     160 ..      47     180 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1e-05
                                OAF  90 klrqknpktvRsaeekkgteeltldvavnvsksallskhiknlCaeakdavytreeDvkkwleregsalellek.a 164
                                         l+ k  + vR + ++ ++ ++ +d+ v  ++   l  ++++lC+e  ++v+t ++ +++  +++++ + +l   +
  gene2746|gene2746|rna2746|rna2746  80 SLFGKKIDNVRRSRNQYEQLTVFVDQNVRYKALDDLKYKLEELCKEK-ETVFTGHAYIREVSKTDDKLQLVLALeH 154
                                        578899999************************************97.9***********9999777666655403 PP

                                OAF 165 veklts 170
                                        ++++++
  gene2746|gene2746|rna2746|rna2746 155 NSNFQD 160
                                        445554 PP

>> BRICHOS  BRICHOS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   3.2e-05      0.19      37      89 ..      77     128 ..      52     130 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3.2e-05
                            BRICHOS  37 psleellrlleekkeeeeets.eslgvyvvkeepvkdlsqlgkkiqelCkglpt 89 
                                        p+   + +++++    +++++ e+l v+v++++++k l+ l  k +elCk+ +t
  gene2746|gene2746|rna2746|rna2746  77 PNTSLFGKKIDN--VRRSRNQyEQLTVFVDQNVRYKALDDLKYKLEELCKEKET 128
                                        555555666666..333444469999************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       996  (0.0555525); expected 358.6 (0.02)
Passed bias filter:                      483  (0.0269396); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1386.32
//
Query:       gene2747|gene2747|rna2747|rna2747  [L=529]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
       0.22   12.1   3.3        0.3   11.7   1.1    2.2  2  DUF4296    Domain of unknown function (DUF4296)
       0.79    9.6   4.7        0.2   11.5   0.5    2.0  2  Pox_LP_H2  Viral late protein H2


Domain annotation for each model (and alignments):
>> DUF4296  Domain of unknown function (DUF4296)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.29   2.6e+03      28      48 ..     403     418 ..     385     421 .. 0.55
   2 ?   11.7   1.1   3.4e-05       0.3      33      78 ..     449     503 ..     430     510 .. 0.71

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.29
                            DUF4296  28 eksldsdssk..keayyeavlkk 48 
                                        ++       +    +y+++v+kk
  gene2747|gene2747|rna2747|rna2747 403 RN-------RiwDANYKTYVFKK 418
                                        22.......13356799999998 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 3.4e-05
                            DUF4296  33 s.........dsskkeayyeavlkkygitsaefdsSlvyYsrnpeelekiyekve 78 
                                                  +++k e++ e+++   ++++ e+++  +y++++pee+++ + +++
  gene2747|gene2747|rna2747|rna2747 449 FlrhndlditTEEKAENIAESIFAYLDVDTLEYEQMSTYFQNRPEEVMQYLGNTN 503
                                        244433333244459******************************9988776665 PP

>> Pox_LP_H2  Viral late protein H2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.5   2.2e-05       0.2      12      61 ..     220     269 ..     207     302 .. 0.86
   2 ?   -0.9   0.3      0.14   1.3e+03      27      61 ..     365     399 ..     347     430 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 2.2e-05
                          Pox_LP_H2  12 eleyvrekeaksiraakvstliffvlilaisvlllllqvsdnsvlselak 61 
                                         l+y   k  +++r+     ++ f+++l  s+l ++++ sd+s++++l++
  gene2747|gene2747|rna2747|rna2747 220 YLHYKYRKVDRNLRMLVEVLIVCFLFMLFPSILYIWYRPSDYSIFKTLNH 269
                                        3889889999999999999999999*********************9975 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.14
                          Pox_LP_H2  27 akvstliffvlilaisvlllllqvsdnsvlselak 61 
                                        + +  + f++ +  +s++l++ ++  n + se++k
  gene2747|gene2747|rna2747|rna2747 365 TTYLCVTFIFWFSCLSAVLFFEKLLVNILTSEMKK 399
                                        34445556666667788888777776666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (529 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1415  (0.0789224); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.62u 0.27s 00:00:00.89 Elapsed: 00:00:00.44
# Mc/sec: 3584.98
//
Query:       gene2748|gene2748|rna2748|rna2748  [L=656]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.5e-21   76.6   0.0    4.2e-21   75.9   0.0    1.4  1  ABC_tran      ABC transporter
    1.1e-07   31.5   0.3     0.0075   15.7   0.0    3.1  3  SMC_N         RecF/RecN/SMC N terminal domain
    3.1e-05   23.9   0.3     0.0052   16.6   0.4    2.3  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
      7e-05   22.6   5.8    0.00015   21.5   5.8    1.6  1  ABC_membrane  ABC transporter transmembrane region
     0.0031   18.0   0.2     0.0081   16.7   0.2    1.7  1  AAA_23        AAA domain
  ------ inclusion threshold ------
      0.026   14.9   0.0      0.086   13.3   0.0    1.9  2  AAA           ATPase family associated with various cellular 
      0.032   14.0   0.0      0.067   12.9   0.0    1.5  1  AAA_29        P-loop containing region of AAA domain
      0.038   13.3   1.3      0.067   12.5   1.3    1.3  1  NicO          High-affinity nickel-transport protein
        0.5    9.5   1.5       0.78    8.9   1.5    1.3  1  Herpes_LMP1   Herpesvirus latent membrane protein 1 (LMP1)
        2.5    8.4  16.9      0.082   13.2   3.4    2.9  3  DUF996        Protein of unknown function (DUF996)


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.9   0.0   2.3e-24   4.2e-21       2     137 .]     467     613 ..     466     613 .. 0.89

  Alignments for each domain:
  == domain 1  score: 75.9 bits;  conditional E-value: 2.3e-24
                                        EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHH CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvr 77 
                                        k ++l++ ++ k+ i G+nG GKS++++++ g+ +   G+++++g +l+++++++l + ++++pq p +f+++ +r
  gene2748|gene2748|rna2748|rna2748 467 KPLNLSICKNDKILIKGPNGIGKSSIIRAIFGMID-YIGDVTIKGVPLQNINTSKLCAMMAICPQSPLVFKNT-IR 540
                                        6799*****************************98.79**********************************9.99 PP

                                        HH.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                        xx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ABC_tran  78 en.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                         n             ++ ++++ + + +++++  d+ + s+++++SgG+k+r+++ara lk+ +++ +DEpta
  gene2748|gene2748|rna2748|rna2748 541 FNlgygncatdegmtKMCKHMNLFDKLVEMEDGLDSLILSGGENFSGGEKKRLCVARAALKRCEIYWFDEPTA 613
                                        999****96655555555556666666666668999999999*****************************97 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.44     8e+02      51     119 ..     370     437 ..     359     448 .. 0.66
   2 !   11.7   0.3   7.1e-05      0.13      27      46 ..     479     497 ..     461     517 .. 0.87
   3 !   15.7   0.0   4.2e-06    0.0075     135     198 ..     583     640 ..     504     654 .. 0.75

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.44
                                        .TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEEEEEETTSEEEEEETTEEE- CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              SMC_N  51 rsakklrseklsdlihkskekasvkkaeveitfdnedkklkiekeevsisrrvkrkgeseykingkevt 119
                                        +s+k+l++++ sdli +   ++s + ++ + + d ++++ ++ + + +++++v    +  y+ ++++vt
  gene2748|gene2748|rna2748|rna2748 370 SSSKNLKASHDSDLIIA-GIGQSRDTCTDHGLSDSHSDEGEQPAAKRYLETTVTLPSKEIYYDENENVT 437
                                        47899**********99.566666666655555544444455556666666666655555555555555 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 7.1e-05
                                        EEEEESTTSSHHHHHHHHHH CS
                                        xxxxxxxxxxxxxxxxxxxx RF
                              SMC_N  27 taivGpNGSGKsnlldAilF 46 
                                          i GpNG GKs+++ Ai F
  gene2748|gene2748|rna2748|rna2748 479 ILIKGPNGIGKSSIIRAI-F 497
                                        5799**************.5 PP

  == domain 3  score: 15.7 bits;  conditional E-value: 4.2e-06
                                        TCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SS CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              SMC_N 135 elLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivislr 198
                                        e++SgGek+     L +A  + k+  +y +De  a LD +n+++v++++ + +    +i i ++
  gene2748|gene2748|rna2748|rna2748 583 ENFSGGEKK----RLCVARAALKRCEIYWFDEPTAGLDSTNMHAVVDFITRMK--GTVIAIMHT 640
                                        389999999....6777788889999***********************9887..555555555 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.4   2.9e-06    0.0052       3      36 ..     480     510 ..     479     520 .. 0.74
   2 ?    4.6   0.0     0.013        23     237     284 ..     585     629 ..     560     639 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 2.9e-06
                             AAA_21   3 vliGpNgsGKSnLLdaldllarldrdvegltdel 36 
                                        ++ GpNg GKS++++a+ ++   ++++ + t++ 
  gene2748|gene2748|rna2748|rna2748 480 LIKGPNGIGKSSIIRAIFGM---IDYIGDVTIKG 510
                                        688**************888...55555555544 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.013
                             AAA_21 237 lSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellke 284
                                        +S G k+ l+++ a l ++    ++ +DEp +gL+   ++ +++++ +
  gene2748|gene2748|rna2748|rna2748 585 FSGGEKKRLCVARAALKRC---EIYWFDEPTAGLDSTNMHAVVDFITR 629
                                        5778888888888888888...99********************9955 PP

>> ABC_membrane  ABC transporter transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   5.8   8.5e-08   0.00015     139     246 ..     212     318 ..     135     336 .. 0.89

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 8.5e-08
                                        HSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHTTTHHHHHHHHHHHHHHHH CS
                       ABC_membrane 139 lgwkltlvllailpliilvsaviakilkklkkkeqkavakassvaeEslsgirtVkafgreeyflekfekaleeak 214
                                        lg  + l++++++++ +l +++i  il  ++++++  +a++ +++ E ls++  V +  +e  ++++++ ++++++
  gene2748|gene2748|rna2748|rna2748 212 LGTTILLAIIFMIVITLLTNIIIIYILIYYRRRYNFLRAQLDNHVSECLSNHLLVTYCHKEMDEYQRYKMKVKNYR 287
                                        677889********************************************************************** PP

                                        HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       ABC_membrane 215 kagikkaianglligitqllgllsyalalwfG 246
                                        +a ++   ++ +l + ++l++++  +++++  
  gene2748|gene2748|rna2748|rna2748 288 TAVVMLESVEHVLEILLYLITNITKFVVYY-V 318
                                        ****************************66.3 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.2   4.5e-06    0.0081      17      40 ..     466     497 ..     450     502 .. 0.64

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 4.5e-06
                             AAA_23  17 F........skgltlItGpNGaGKTTildAik 40 
                                        F        ++   lI GpNG GK++i++Ai 
  gene2748|gene2748|rna2748|rna2748 466 FkplnlsicKNDKILIKGPNGIGKSSIIRAIF 497
                                        23333344444456****************96 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   4.8e-05     0.086       1      36 [.     479     523 ..     479     565 .. 0.86
   2 ?   -2.9   0.0       4.8   8.6e+03      89     114 ..     623     645 ..     597     655 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.8e-05
                                        EEEESSTTSSHHHHHHHHHHHH.........THEEEEEETTTCSS CS
                                AAA   1 vllyGppGtGKTllakavakel.........gvefleisgsells 36 
                                        +l+ Gp G+GK+++++a+   +         gv++ +i+ s+l+ 
  gene2748|gene2748|rna2748|rna2748 479 ILIKGPNGIGKSSIIRAIFGMIdyigdvtikGVPLQNINTSKLCA 523
                                        6899*****************866665556569999999999884 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 4.8
                                        HHHHHHHTTTSSSTEEEEEEESSGGG CS
                                AAA  89 Llteldgvkkkeskvivigatnrpdk 114
                                         + ++ ++k    +vi i+ t ++d+
  gene2748|gene2748|rna2748|rna2748 623 VVDFITRMKG---TVIAIMHTDEYDR 645
                                        3333333333...5777777766665 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   3.8e-05     0.067      19      42 ..     473     496 ..     461     500 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.8e-05
                             AAA_29  19 idlkgatlltGpsGsGKSTllDAi 42 
                                        i  ++ +l+ Gp+G GKS+++ Ai
  gene2748|gene2748|rna2748|rna2748 473 ICKNDKILIKGPNGIGKSSIIRAI 496
                                        5556689**************887 PP

>> NicO  High-affinity nickel-transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   1.3   3.7e-05     0.067      39     134 ..     169     272 ..     164     299 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.7e-05
                               NicO  39 rGillslgsslvvvlvavllvvaavlvlr........ltslsetgaaigteiasFllvilllnllllrklrklfrk 106
                                         Gi+ s+++  v++++ ++  +++ l+ r         ++  + g++i + i++ ++++ll n+++ + l+  +r+
  gene2748|gene2748|rna2748|rna2748 169 NGIFQSFVHRGVKGMTNLIRQLVLSLLARifsyffvmKETNDQLGTTILLAIIFMIVITLLTNIIIIYILIYYRRR 244
                                        5777777777776666554444433333332222221555566667777777777777788888888888888888 PP

                               NicO 107 lerlgrapaaeleaalakrgllsrilgk 134
                                        ++ l+++ ++++++ l+++ l++  +++
  gene2748|gene2748|rna2748|rna2748 245 YNFLRAQLDNHVSECLSNHLLVTYCHKE 272
                                        8889999999999999997444333333 PP

>> Herpes_LMP1  Herpesvirus latent membrane protein 1 (LMP1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   1.5   0.00044      0.78      23     146 ..     184     319 ..     175     411 .. 0.56

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00044
                                        XXXXXXXXXXXXXXXXXXXXXXX...XXXXXXXXXXXXXXXXX.....XXXXXXXXXXXXX...XXXXXXXXXXXX CS
                        Herpes_LMP1  23 sslglallllllallfwlyivms...dwtggallvlysfalll.....iiiiliififrrd...llcplgalclll 87 
                                        ++l   l+l lla +f  + vm    d  g ++l+   f +++     iiii i++ +rr    l + l   +   
  gene2748|gene2748|rna2748|rna2748 184 TNLIRQLVLSLLARIFSYFFVMKetnDQLGTTILLAIIFMIVItlltnIIIIYILIYYRRRynfLRAQLDNHVSEC 259
                                        55666799999*****999999622256677766554444332112223444444444553111222333332222 PP

                                        XXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                        Herpes_LMP1  88 lmitllli.alwnlhgqalylgivlfifgcllvlglwiyllellwrlgatiwqllaffla 146
                                        l   ll+  +  ++     y   v     ++++l    ++le+l  l + i +++ +++ 
  gene2748|gene2748|rna2748|rna2748 260 LSNHLLVTyCHKEMDEYQRYKMKVKNYRTAVVMLESVEHVLEILLYLITNITKFVVYYVI 319
                                        222222220222344444444444444555555555555666666665555555555554 PP

>> DUF996  Protein of unknown function (DUF996)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.8     0.032        58      72     123 ..      60     111 ..      36     127 .. 0.82
   2 ?   13.2   3.4   4.6e-05     0.082      16     103 ..     162     253 ..     159     262 .. 0.80
   3 ?   -1.6   0.3       1.7     3e+03      30      43 ..     306     319 ..     280     352 .. 0.57

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.032
                             DUF996  72 llllvliiayvlliisavflkksyellgkrtgvklFetagllyfiGaiLtiv 123
                                          ++++ i+++++i + +++k  +e+l + ++ k ++t   ++f  +i  i+
  gene2748|gene2748|rna2748|rna2748  60 PCFVIFTIVAIIFITELLLYKIRIENLRSLSSCKNYSTLRSFLFYTTICGII 111
                                        5567777888999999999999999999999999999999998888887766 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 4.6e-05
                             DUF996  16 iskavndekifsnaliafilsiialvva.ilalllvlgalatalelpgleeaas...lilllllvliiayvlliis 87 
                                        + + v d+ if++++   + ++ +l+   +l ll+ +++++ +++ ++ + ++    +i +++++ +++ +++i  
  gene2748|gene2748|rna2748|rna2748 162 LVESVTDNGIFQSFVHRGVKGMTNLIRQlVLSLLARIFSYFFVMKETNDQLGTTillAIIFMIVITLLTNIIIIYI 237
                                        567899*************999988876689999999999999999988887775545555555556666888888 PP

                             DUF996  88 avflkksyellgkrtg 103
                                         +++++ y+ l +++ 
  gene2748|gene2748|rna2748|rna2748 238 LIYYRRRYNFLRAQLD 253
                                        9999999998887765 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 1.7
                             DUF996  30 liafilsiialvva 43 
                                        li  i++++ ++v+
  gene2748|gene2748|rna2748|rna2748 306 LITNITKFVVYYVI 319
                                        22333333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (656 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1403  (0.0782531); expected 358.6 (0.02)
Passed bias filter:                      611  (0.0340789); expected 358.6 (0.02)
Passed Vit filter:                        96  (0.00535445); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.69u 0.32s 00:00:01.01 Elapsed: 00:00:00.44
# Mc/sec: 4466.39
//
Query:       gene2749|gene2749|rna2749|rna2749  [L=71]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.5e-06   24.0   0.1    8.8e-06   23.9   0.1    1.0  1  Herpes_Helicase  Helicase
      0.001   18.8   0.9     0.0029   17.4   0.3    2.1  2  UvrD_C_2         UvrD-like helicase C-terminal domain
     0.0058   16.4   0.0     0.0069   16.2   0.0    1.1  1  Viral_helicase1  Viral (Superfamily 1) RNA helicase


Domain annotation for each model (and alignments):
>> Herpes_Helicase  Helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.1   1.5e-09   8.8e-06     734     790 ..       1      58 [.       1      69 [. 0.76

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 1.5e-09
                    Herpes_Helicase 734 mtiaksqGlslekvAicFgnhknlklssvYvalsRatdseflvm..dvnPLrereekda 790
                                        mti ksqG s++kv +   n       ++Y+alsR+++++ l++    n  ++r  ++ 
  gene2749|gene2749|rna2749|rna2749   1 MTIHKSQGQSFDKVGVYLHNP-IFVHGQLYMALSRVRHADGLKVyiANNGDQNRADNNM 58 
                                        9****************9999.667899**********998865114455555555554 PP

>> UvrD_C_2  UvrD-like helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.3   4.8e-07    0.0029       5      44 ..       1      34 [.       1      38 [. 0.68
   2 ?   -1.8   0.0      0.48   2.8e+03      33      40 ..      54      61 ..      43      62 .. 0.55

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 4.8e-07
                           UvrD_C_2  5 ltihkaQGsefpaV..ivfdpdlaaarmgelrrrlLYtavTR 44
                                       +tihk+QG+ f+ V  ++ +p +   +        LY a++R
  gene2749|gene2749|rna2749|rna2749  1 MTIHKSQGQSFDKVgvYLHNPIFVHGQ--------LYMALSR 34
                                       7***********751166666666555........6666666 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.48
                           UvrD_C_2 33 lrrrlLYt 40
                                          +++Yt
  gene2749|gene2749|rna2749|rna2749 54 ADNNMVYT 61
                                       24566776 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   1.2e-06    0.0069     186     227 ..       1      36 [.       1      45 [. 0.77

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.2e-06
                    Viral_helicase1 186 ttvhevqGltfdkVtlvllketdlelisesrenllvAlTRhr 227
                                        +t h  qG++fdkV ++l+++    ++ +   +l+ Al+R r
  gene2749|gene2749|rna2749|rna2749   1 MTIHKSQGQSFDKVGVYLHNP----IFVH--GQLYMALSRVR 36 
                                        699****************66....6654..67999999733 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (71 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       318  (0.0177366); expected 358.6 (0.02)
Passed bias filter:                      235  (0.0131073); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.38u 0.28s 00:00:00.66 Elapsed: 00:00:00.44
# Mc/sec: 482.29
//
Query:       gene275|gene275|rna275|rna275  [L=164]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.02   15.0   0.0      0.051   13.7   0.0    1.6  1  VirE1     Single-strand DNA-binding protein


Domain annotation for each model (and alignments):
>> VirE1  Single-strand DNA-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   2.8e-06     0.051      17      38 ..      59      80 ..      56      84 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.8e-06
                                   XXXXXXXXXXXXXX-TTTTTS- CS
                          VirE1 17 veePqeihkeelsdnhqsnGft 38
                                   +e+ ++i  e++sd+ q nGft
  gene275|gene275|rna275|rna275 59 PEDIKKITLEKFSDHVQLNGFT 80
                                   78999****************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       629  (0.0350828); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1177.26
//
Query:       gene2750|gene2750|rna2750|rna2750  [L=791]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-91  306.0   0.0    1.7e-91  305.3   0.0    1.3  1  MCM              MCM P-loop domain
    4.5e-37  126.7   0.0    1.1e-36  125.4   0.0    1.7  1  MCM_OB           MCM OB domain
    6.9e-25   87.3   0.8    1.6e-24   86.1   0.8    1.7  1  MCM_lid          MCM AAA-lid domain
    4.5e-12   45.8   0.4    1.5e-08   34.2   0.1    2.7  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    1.2e-10   41.9   0.1    1.2e-10   41.9   0.1    2.8  2  MCM_N            MCM N-terminal domain
      4e-06   26.7   0.0    8.8e-06   25.6   0.0    1.6  1  AAA_3            ATPase family associated with various cellul
    1.6e-05   24.9   0.0    4.1e-05   23.6   0.0    1.8  1  AAA_5            AAA domain (dynein-related subfamily)
    0.00015   21.5   0.0       0.34   10.6   0.0    3.1  3  Sigma54_activat  Sigma-54 interaction domain
     0.0039   17.6   0.2      0.048   14.0   0.0    2.3  2  AAA_16           AAA ATPase domain
  ------ inclusion threshold ------
      0.014   15.3   0.2       0.92    9.5   0.1    2.6  2  SwrA             Swarming motility protein
      0.059   13.1   0.2       0.12   12.1   0.2    1.4  1  AAA_30           AAA domain
      0.073   13.5   0.1       0.32   11.4   0.1    2.2  1  AAA              ATPase family associated with various cellul
       0.11   12.6   0.1       0.33   11.1   0.0    1.9  2  AAA_2            AAA domain (Cdc48 subfamily)


Domain annotation for each model (and alignments):
>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  305.3   0.0   1.2e-94   1.7e-91       1     222 [.     336     563 ..     336     565 .. 0.94

  Alignments for each domain:
  == domain 1  score: 305.3 bits;  conditional E-value: 1.2e-94
                                        HHHHHHHHHTSSTHHHHHHHHSSTTSSS-HHHHHHHHHHHH---EBBBSS.......SSBBCSS-EEEEEESSTST CS
                                MCM   1 eveeikelakekdiieklvksiapsiyghedvkkaillqlfggvkkkled.......ktklrgdinvllvgdpgta 69 
                                        +++eik+la++++i+e+l++++ap+++gh +vk+a+ll+lfgg+ k +e+        +++rgdinvl++gdpgta
  gene2750|gene2750|rna2750|rna2750 336 DEKEIKRLARNPRIVEILSDALAPEVCGHPNVKRACLLALFGGQPKGREKendkasaAHRIRGDINVLIMGDPGTA 411
                                        5799***************************************98844431122222467**************** PP

                                        HHHHHHHHHHHSSSEEEEESSSSSSSHSSSEEEEESSSSSEEEEETHHHHTTTSEEEEESGGGSTCHHHHHHHHHH CS
                                MCM  70 KsqlLkyveklapravytsgkgssaagLtaavvrdeetgefvleaGalvladkGvcciDefdkmkeedrsalhEam 145
                                        KsqlL+++e++aprav ++g+g s++gLta+v++d+ ++e++le+Galvlad+G+++iDefdkm+e+drsa+hEam
  gene2750|gene2750|rna2750|rna2750 412 KSQLLRSLERVAPRAVLATGHGVSSVGLTASVRKDS-NNEWMLEGGALVLADNGIVLIDEFDKMQENDRSAIHEAM 486
                                        *******************************99987.578************************************ PP

                                        HHSEEEEESSSCEEEEE--EEEEEEE--SSSSCCTTS-HHHHSSSSHHHHHHSSEEEEE-SSTTHHHHHHHHHHHH CS
                                MCM 146 EqqtisiaKaGivatLnartsvlaAanpkagrydkkksvaeninlsaalLsrFDlifvllDkvdeekDeelaehiv 221
                                        Eqq+is++KaGiva+Lnar++v+aAanp++gry++  s++ n+nls+++LsrFD+++v++D +d+ +De++a++i+
  gene2750|gene2750|rna2750|rna2750 487 EQQSISVSKAGIVASLNARCAVVAAANPRKGRYNNALSLNANVNLSEPILSRFDILCVVRDVTDQVEDERIASFIL 562
                                        **************************************************************************98 PP

                                        H CS
                                MCM 222 s 222
                                        +
  gene2750|gene2750|rna2750|rna2750 563 K 563
                                        6 PP

>> MCM_OB  MCM OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  125.4   0.0   8.1e-40   1.1e-36       2     124 ..     180     306 ..     179     308 .. 0.94

  Alignments for each domain:
  == domain 1  score: 125.4 bits;  conditional E-value: 8.1e-40
                                        XGG--GGGTTSEEEEEEEEEEE---EEEEEEEEEEETTT-.-EE.ES---.....-SB-..TTT-HHH-EEE-GGG CS
                             MCM_OB   2 lRdlrsehigklvkveGivtrasevkpklkkavfeckkcgktve.velee.....PrkCeekeCeskdpfkletek 71 
                                        lR+lr+e++g lv+++Givtr+s v+p+l  a+f c+kc++t + + le+     P++C   eC+s++pf ++ e+
  gene2750|gene2750|rna2750|rna2750 180 LRELRNENLGCLVRIRGIVTRRSGVFPRLFLAKFICTKCRCTFGpFLLENdasfrPQSC--LECQSRGPFLVNEEE 253
                                        8****************************************99966444456667****..89************* PP

                                        SEEEEEEEEEEE-------------EEEEEEEGGGTT---TT-EEEEEEEEEE CS
                             MCM_OB  72 skfvdfqklklQEspeevpaGelPrslevileddlvdkvkPGdrvevtGiyra 124
                                        ++++dfqk+++QE p++vpaG+lPrs++v++ +dl+d +kPGd++e+tGiy++
  gene2750|gene2750|rna2750|rna2750 254 TVYRDFQKMTVQEIPGTVPAGTLPRSKDVLVFHDLIDLAKPGDEIELTGIYKS 306
                                        ***************************************************86 PP

>> MCM_lid  MCM AAA-lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.1   0.8   1.2e-27   1.6e-24       2      86 ..     615     694 ..     614     695 .. 0.95

  Alignments for each domain:
  == domain 1  score: 86.1 bits;  conditional E-value: 1.2e-27
                                        HHHHHHHHHHHTT--BETCHHHHHHHHHHHHHHHHHTSSTSSSST--HHHHHHHHHHHHHHHHHHTSSSE-HHHHH CS
                            MCM_lid   2 llrkYiayarekikPklseeakeklseaYvelRkeeedskrksipitvRqLesliRLseAlAklrlsevvteedve 77 
                                        l++kY+ ya+ +i+P+++e +k+k+s+ Y+elRke+     +s+pit+R++es++R+seAlA+++l+e+v +ed++
  gene2750|gene2750|rna2750|rna2750 615 LFKKYLIYAK-RIHPQIKEIDKDKISKLYAELRKESD----NSMPITARHIESIVRISEALARIKLNEYVCKEDID 685
                                        79********.***********************873....48********************************* PP

                                        HHHHHHHHH CS
                            MCM_lid  78 eairllkes 86 
                                         ai+++ +s
  gene2750|gene2750|rna2750|rna2750 686 TAIKITLDS 694
                                        *****9887 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.0   0.00055      0.76      19      59 ..     396     436 ..     381     453 .. 0.75
   2 !   34.2   0.1   1.1e-11   1.5e-08      98     203 ..     454     549 ..     432     553 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00055
                       Mg_chelatase  19 aaGgHnlllvGppGsGKtmlakrlpsllpplseeealevak 59 
                                        + G  n+l++G pG+ K+ l + l+ + p+   +  + v++
  gene2750|gene2750|rna2750|rna2750 396 IRGDINVLIMGDPGTAKSQLLRSLERVAPRAVLATGHGVSS 436
                                        57999*********************999876665555554 PP

  == domain 2  score: 34.2 bits;  conditional E-value: 1.1e-11
                       Mg_chelatase  98 kpGeislahnGvLfLDElpefkrkvlevLRePledgevtisrakakvefparfqlvaamNpcpcgklkdkekectc 173
                                        + G++ la nG++++DE+ +++++   ++ e +e++++++s+a   ++  ar+ +vaa+Np + g+++++      
  gene2750|gene2750|rna2750|rna2750 454 EGGALVLADNGIVLIDEFDKMQENDRSAIHEAMEQQSISVSKAGIVASLNARCAVVAAANPRK-GRYNNAL----- 523
                                        67999********************************************************76.4454222..... PP

                       Mg_chelatase 174 sekeierYlsklsgplldRidlqvevkkle 203
                                              +   +ls+p+l R+d+   v+ ++
  gene2750|gene2750|rna2750|rna2750 524 ----SLNANVNLSEPILSRFDILCVVRDVT 549
                                        ....22334679999999999999887765 PP

>> MCM_N  MCM N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.9   0.1   8.4e-14   1.2e-10       2      86 ..      87     163 ..      86     187 .. 0.92
   2 ?    0.8   0.8      0.54   7.5e+02       2      39 ..     709     739 ..     695     740 .. 0.85

  Alignments for each domain:
  == domain 1  score: 41.9 bits;  conditional E-value: 8.4e-14
                              MCM_N   2 ekFedFLeefkddsededgekkYrdqlqemaerekttLevdlddLaafdeeLaeailenpkeylplleealkevvk 77 
                                        + F +FL+++        g +kY++ +++m+ ++ ++L v+++d+++fd+ L++ ++   +  ++++++al+ vv 
  gene2750|gene2750|rna2750|rna2750  87 NLFAKFLSNY--------GGRKYIKLIKTMCAENGESLLVSYTDMESFDDLLVRVLVVCAEPAIEVFDDALRLVVL 154
                                        689*******........79******************************************************** PP

                              MCM_N  78 klepsykdd 86 
                                        +l+p+y   
  gene2750|gene2750|rna2750|rna2750 155 SLFPNYFMI 163
                                        ****99765 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.54
                              MCM_N   2 ekFedFLeefkddsededgekkYrdqlqemaerekttL 39 
                                        +kF ++L+e        d+ ++Y+  l+em + +++++
  gene2750|gene2750|rna2750|rna2750 709 KKFAKYLNEN-------DDFFVYLFILNEMFNDKIKSF 739
                                        6788888876.......567***********9998775 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.0   6.4e-09   8.8e-06       2     113 ..     402     515 ..     401     527 .. 0.85

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 6.4e-09
                              AAA_3   2 vllegvPGlaktllvkalakaldlefkriqftpdllPsdilGtevfeekekefefkkGpvf...anllladeinra 74 
                                        vl+ g PG+ak +l ++l ++     + +  t   + s  l ++v +++++e+ ++ G+++   + ++l de ++ 
  gene2750|gene2750|rna2750|rna2750 402 VLIMGDPGTAKSQLLRSLERVA---PRAVLATGHGVSSVGLTASVRKDSNNEWMLEGGALVladNGIVLIDEFDKM 474
                                        899*************999865...4667889998988888999999999********97633335********** PP

                              AAA_3  75 ppktqsalleameerqvtvege..thklpepflvlatqnPi 113
                                        +   +sa+ eame++ ++v+++    +l+    v+a+ nP 
  gene2750|gene2750|rna2750|rna2750 475 QENDRSAIHEAMEQQSISVSKAgiVASLNARCAVVAAANPR 515
                                        ***************998876511689*************5 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.0     3e-08   4.1e-05       1     128 [.     401     520 ..     401     539 .. 0.82

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 3e-08
                                        EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--..........--------G-SEEEEESGG CS
                              AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreik.ngttslvdsplvraaregeilvlDEve 75 
                                        +vl+ G+pGt+Ks+l ++l ++  r v+  +   + ++  l+ +++ + n +  l+ ++lv       i+++DE++
  gene2750|gene2750|rna2750|rna2750 401 NVLIMGDPGTAKSQLLRSLERVAPRAVL--ATGHGVSSVGLTASVRKDsNNEWMLEGGALV--LADNGIVLIDEFD 472
                                        69*******************9876655..56778999********764445555667777..77888******** PP

                                        G--HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--..-TT CS
                              AAA_5  76 raesevlnsLlslleerrllleeggelvkaknddllerfrviatanpld.rsln 128
                                        +++ +  ++ +  +e++ +++ + g + + ++        v+a+anp++ r  n
  gene2750|gene2750|rna2750|rna2750 473 KMQENDRSAIHEAMEQQSISVSKAGIVASLNAR-----CAVVAAANPRKgR-YN 520
                                        ********************9999999988885.....9*********952.33 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0       0.3   4.2e+02      35      68 ..      86     119 ..      85     121 .. 0.94
   2 !    5.9   0.0    0.0068       9.4      15      47 ..     392     424 ..     380     430 .. 0.79
   3 !   10.6   0.0   0.00025      0.34      87     142 ..     456     513 ..     450     526 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.3
                                        HHHHHHHHHHHSTTTTS-EEEEETTTS-TTCHHH CS
                    Sigma54_activat  35 Kellaraiheaskrkekpfvavncaaipeelles 68 
                                        K+l+a+ + +   rk  ++++  ca+  e+ll s
  gene2750|gene2750|rna2750|rna2750  86 KNLFAKFLSNYGGRKYIKLIKTMCAENGESLLVS 119
                                        899***************************9976 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0068
                                        HHHHCTSSS-EEEECSTTSSHHHHHHHHHHHST CS
                    Sigma54_activat  15 ikkvaktdlsvlitGesGtGKellaraiheask 47 
                                        +++ ++ d++vli+G+ Gt K+ l r++ +  +
  gene2750|gene2750|rna2750|rna2750 392 AAHRIRGDINVLIMGDPGTAKSQLLRSLERVAP 424
                                        45556788**************99988877655 PP

  == domain 3  score: 10.6 bits;  conditional E-value: 0.00025
                                        HHHHHTTTSEEEEETGGGS-HHHHHHHHHHHHHSEE..ESBTSSSEEE--EEEEEEES CS
                    Sigma54_activat  87 GlfekadgGtlfLDeigelplelQekLlrvlqegev..ervGsskeikvdvriiaatn 142
                                        G++  ad+G++++De  +++ +  + + ++++++++  ++ G  ++ ++ + ++aa+n
  gene2750|gene2750|rna2750|rna2750 456 GALVLADNGIVLIDEFDKMQENDRSAIHEAMEQQSIsvSKAGIVASLNARCAVVAAAN 513
                                        8999***************************9997522799999***********998 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.0   3.5e-05     0.048       4      62 ..     382     435 ..     379     447 .. 0.71
   2 ?    0.0   0.0      0.71   9.8e+02     138     162 ..     465     489 ..     455     500 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.5e-05
                             AAA_16   4 GReeeleqLlsalervrsgrpelvllsGesGvGKsslvrellralekdggiflrgkcdq 62 
                                        GRe+e ++  +a +r+ +g+  +vl+ G++G+ Ks l+r+l r + +  +++++g+ ++
  gene2750|gene2750|rna2750|rna2750 382 GREKENDKASAA-HRI-RGD-INVLIMGDPGTAKSQLLRSLERVAPR--AVLATGHGVS 435
                                        777776554444.444.455.59*******************75554..4667766655 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.71
                             AAA_16 138 vlvlDdlqwadeaslqllaaLlrll 162
                                        ++++D++++ +e +++++ + ++ +
  gene2750|gene2750|rna2750|rna2750 465 IVLIDEFDKMQENDRSAIHEAMEQQ 489
                                        789**********999988777765 PP

>> SwrA  Swarming motility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.1   0.00067      0.92      24      69 ..      73     118 ..      62     130 .. 0.85
   2 ?    2.8   0.0     0.078   1.1e+02      31     101 ..     607     679 ..     585     687 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00067
                               SwrA  24 tevtssaskavkllrlfsrylvnytsvkevedidkdcveeyfsyli 69 
                                        +ev    s+++k+  lf+++l ny   k ++ i+  c+e+  s l+
  gene2750|gene2750|rna2750|rna2750  73 KEVMENESYKLKIKNLFAKFLSNYGGRKYIKLIKTMCAENGESLLV 118
                                        5777888899999*************************98666655 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.078
                               SwrA  31 skavkllrlfsrylvnytsvk.evedidkdcveeyfsyl.idnhkrlslsltdikksmqliedlldvevdssl 101
                                        + av    lf +yl+    ++ ++++idkd + + ++ l  +    + ++   i   +++ e l  +++++++
  gene2750|gene2750|rna2750|rna2750 607 ARAVIDDDLFKKYLIYAKRIHpQIKEIDKDKISKLYAELrKESDNSMPITARHIESIVRISEALARIKLNEYV 679
                                        444444469******99999758******98766555551566677888888888888888888888888775 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.2   8.4e-05      0.12      17     120 ..     398     494 ..     385     499 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 8.4e-05
                             AAA_30  17 gdrvavltGpAGtGKttalkalreaweaaggrviglAptgkaAkvLaeelgieastiakllkrlkgrarlepgtll 92 
                                        gd  +++ G +Gt K+ +l++l++++ +a    ++++  g  +  L++++    ++ ++++   +g+  l+++ ++
  gene2750|gene2750|rna2750|rna2750 398 GDINVLIMGDPGTAKSQLLRSLERVAPRA----VLATGHGVSSVGLTASVR--KDSNNEWML-EGGALVLADNGIV 466
                                        4445899******************9976....344445555555776644..444455552.2355778889*** PP

                             AAA_30  93 ivDEagmvdtkqlaallkaaekagakvi 120
                                        ++DE   +  ++  a+ +a+e+++++v 
  gene2750|gene2750|rna2750|rna2750 467 LIDEFDKMQENDRSAIHEAMEQQSISVS 494
                                        ********************99888875 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   0.00023      0.32       1     111 [.     402     514 ..     402     532 .. 0.56

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00023
                                        EEEESSTTSSHHHHHHHHHHHHTHEEEEE.ETTTCSSSSTTHHHHHHHHHHHHHHHTS....TSEEEEEETGGGHH CS
                                AAA   1 vllyGppGtGKTllakavakelgveflei.sgsellskyvgesekkirelfkeakeka....kpsilfiDEidala 71 
                                        vl++G pGt K+ l +++ + + + +l +  g + +  + + ++++ +e + e    a    +  i++iDE+d++ 
  gene2750|gene2750|rna2750|rna2750 402 VLIMGDPGTAKSQLLRSLERVAPRAVLATgHGVSSVGLTASVRKDSNNEWMLEG--GAlvlaDNGIVLIDEFDKMQ 475
                                        689999999999999999888754443221222222222333333333333222..22335466***********8 PP

                                        HHHTTCCCHHHHHHHHHHHHHHHHTTTS......SSTEEEEEEESS CS
                                AAA  72 ksrsgseseeeervvnqLlteldgvkkk......eskvivigatnr 111
                                        +++       ++ + +++ ++   v+k       ++++ v++a+n 
  gene2750|gene2750|rna2750|rna2750 476 END-------RSAIHEAMEQQSISVSKAgivaslNARCAVVAAANP 514
                                        887.......222222222222222222455555777888888875 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00024      0.33      66      84 ..     460     480 ..     400     502 .. 0.78
   2 ?   -3.7   0.0       8.1   1.1e+04      17      53 ..     654     688 ..     644     693 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00024
                                        HHTTSEEEEETGGG----..- CS
                              AAA_2  66 aeegGivllDEidKihpk..e 84 
                                         +++Givl+DE dK +++  +
  gene2750|gene2750|rna2750|rna2750 460 LADNGIVLIDEFDKMQENdrS 480
                                        57899**********997641 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 8.1
                                        HHHHHHHHHHTT-....-EEEEEGGG-------THHH CS
                              AAA_2  17 telakalaellfvkkekkliradaselleeeevehlv 53 
                                        +++a+ ++++ ++  +++l+r+  +e+  +e++++ +
  gene2750|gene2750|rna2750|rna2750 654 PITARHIESIVRI--SEALARIKLNEYVCKEDIDTAI 688
                                        4566666666665..8899999999999999988877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (791 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       825  (0.0460148); expected 358.6 (0.02)
Passed bias filter:                      569  (0.0317363); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.68u 0.29s 00:00:00.97 Elapsed: 00:00:00.42
# Mc/sec: 5609.16
//
Query:       gene2751|gene2751|rna2751|rna2751  [L=577]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-36  125.0  11.4    9.7e-36  122.7   6.4    3.1  3  Rep_fac-A_C      Replication factor-A C terminal domain
    1.4e-17   63.4   4.3    2.2e-17   62.8   0.1    3.0  3  REPA_OB_2        Replication protein A OB domain
    2.3e-13   49.9   3.9    1.1e-09   38.1   0.2    3.7  4  tRNA_anti-codon  OB-fold nucleic acid binding domain
    2.6e-11   43.5   0.0    9.5e-11   41.6   0.0    2.1  1  Rep-A_N          Replication factor-A protein 1, N-terminal d
    3.6e-06   26.9   0.9       0.24   11.4   0.0    3.5  3  DUF4539          Domain of unknown function (DUF4539)


Domain annotation for each model (and alignments):
>> Rep_fac-A_C  Replication factor-A C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.1     0.015        55      56      83 ..     212     239 ..     201     269 .. 0.79
   2 ?   -2.5   0.0       1.1   3.9e+03      60      77 ..     336     353 ..     333     357 .. 0.85
   3 !  122.7   6.4   2.7e-39   9.7e-36       1     145 [.     428     570 ..     428     571 .. 0.97

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.015
                                        EEEEEE-SS-EEEEEEEHHHHHHHHSS- CS
                        Rep_fac-A_C  56 lsikvsDstgqlwvtlFneaaekllgls 83 
                                         s+++ D+tg++   +Fn+ a  + g+ 
  gene2751|gene2751|rna2751|rna2751 212 FSFELLDKTGNIKCVAFNDGADLFYGMI 239
                                        578999***************9999874 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.1
                                        EE-SS-EEEEEEEHHHHH CS
                        Rep_fac-A_C  60 vsDstgqlwvtlFneaae 77 
                                        ++D+tg++++tl+ +++e
  gene2751|gene2751|rna2751|rna2751 336 LADETGTVRATLWGDKSE 353
                                        78**********999876 PP

  == domain 3  score: 122.7 bits;  conditional E-value: 2.7e-39
                                        EEEEEEEEEEEETTTTEEEB--STT---B-EEETTTEEEETTTTEEESS--EEEEEEEEEE-SS-EEEEEEEHHHH CS
                        Rep_fac-A_C   1 yfsvkatvsfikkdnlvYkACpsedCnkKvveeedgewrCekCdkeveepkyryilsikvsDstgqlwvtlFneaa 76 
                                        y +++atv fi++dnl+Y+AC+ ++CnkKv  +++g ++Ce+C+++ e ++ ry+ +++v+D+t+q+w+++F++  
  gene2751|gene2751|rna2751|rna2751 428 YGTCSATVLFIREDNLFYNACA-NNCNKKVSLTDEG-YYCERCNQTREICNIRYLTTLHVADFTQQVWLNVFDDFC 501
                                        66899*****************.99*****999777.88************************************* PP

                                        HHHHSS-HHHHHHHCCC-HHHHHHHHHHTTT-EEEEEEEEE----------EEEEEEEEE--HHHHHHH CS
                        Rep_fac-A_C  77 ekllglsaeelkklkeedeeefekiiekvklkeflfrlrvkeesyndesrvrytvvkvepvdykkeskr 145
                                        ++++g++a elkk+ ee+ +++++ ++ + ++e++++++  ee yn+e+rvr   +++++++y +es r
  gene2751|gene2751|rna2751|rna2751 502 TEFFGMTAVELKKMGEENATQLQNYLKTLLYREYVIKMKRSEEVYNGEMRVRWRGLSIKKINYLDESVR 570
                                        ***************************************************************999865 PP

>> REPA_OB_2  Replication protein A OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.2      0.53   1.9e+03      23      53 ..     129     159 ..     117     183 .. 0.64
   2 ?    0.3   0.0      0.19   6.8e+02      27      74 ..     194     247 ..     190     269 .. 0.64
   3 !   62.8   0.1     6e-21   2.2e-17       2      97 ..     294     388 ..     293     389 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.53
                          REPA_OB_2  23 eevseitskstekelkkreltlvDesgasve 53 
                                        +++++ t+k    e + + +++ D+ g++ +
  gene2751|gene2751|rna2751|rna2751 129 KQSEKNTAKRAPDENNNKRVQVGDNNGKTAK 159
                                        4555555565555666666666666666544 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.19
                          REPA_OB_2  27 eitskstekelkkre.....ltlvDesgasvevtlWgkeaekfe..sseepvval 74 
                                        ++++ks+++e+kk++     ++l D++g ++++  +++ a+ f     e +vv +
  gene2751|gene2751|rna2751|rna2751 194 TVQKKSEMREFKKKDgkffsFELLDKTG-NIKCVAFNDGADLFYgmIVEGSVVEI 247
                                        4556666666666643333378889887.47777777777776644455555555 PP

  == domain 3  score: 62.8 bits;  conditional E-value: 6e-21
                          REPA_OB_2   2 selenvekdsivDvigvvksveevseitskstekelkkreltlvDesgasvevtlWgkeaekfesseepvvalkgv 77 
                                        s+l    +++ +Dvig+v+++ +vs + +k++++e+kkr+l l De+g +v+ tlWg+++ ++e +++pv+ lk v
  gene2751|gene2751|rna2751|rna2751 294 SNLAGRVNKANCDVIGIVHEAFPVSVVLAKASQREIKKRDLVLADETG-TVRATLWGDKS-EIELDDHPVLLLKDV 367
                                        56666778899************************************9.59*******65.56999********** PP

                          REPA_OB_2  78 kvsdFgg.rslsllssstlkv 97 
                                        +v++F+    ls+   s +kv
  gene2751|gene2751|rna2751|rna2751 368 RVGEFNNaVVLSTAFGSAVKV 388
                                        *****9857788888887776 PP

>> tRNA_anti-codon  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.14     5e+02      21      55 ..      45      78 ..      34      97 .. 0.86
   2 !   38.1   0.2   3.1e-13   1.1e-09       2      72 ..     190     272 ..     189     276 .. 0.93
   3 !    9.5   0.0   0.00026      0.93      17      39 ..     330     351 ..     296     371 .. 0.80
   4 ?   -2.5   0.0       1.5   5.3e+03      20      40 ..     482     521 ..     477     537 .. 0.67

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.14
                                       EEEEETTEEEEEEEETHHHHHHHTTS-TTSEEEEE CS
                    tRNA_anti-codon 21 idlrDgtgriqvvlfreeatklaenlkeGdvvrvt 55
                                       i++ Dg   ++ ++ + +++k   ++k++++++++
  gene2751|gene2751|rna2751|rna2751 45 ITISDGKLYMKGIFSS-QVSKEVGDIKVNTIIKIS 78
                                       6788888888888888.9**************997 PP

  == domain 2  score: 38.1 bits;  conditional E-value: 3.1e-13
                                        EEEEEEEEEE.....EEEETTEEEEEEEETTEEEEEEEETHHHHHHHTTS-TTSEEEEE.EEEEECTTS......S CS
                    tRNA_anti-codon   2 tvaGrvtsis.....drsggkvifidlrDgtgriqvvlfreeatklaenlkeGdvvrvt.Grvkrrpgg......e 65 
                                         v+G v+++s     +++ gk+++++l D+tg+i++v+f+++a+ ++  + eG+vv+++   vk  +++      +
  gene2751|gene2751|rna2751|rna2751 190 IVKGTVQKKSemrefKKKDGKFFSFELLDKTGNIKCVAFNDGADLFYGMIVEGSVVEISkAVVKMCNKKfantssD 265
                                        69*************************************************************9998888888999 PP

                                        EEEEEEE CS
                    tRNA_anti-codon  66 lelkvee 72 
                                        +e++ e+
  gene2751|gene2751|rna2751|rna2751 266 YEIHLEK 272
                                        9999887 PP

  == domain 3  score: 9.5 bits;  conditional E-value: 0.00026
                                        TEEEEEEEETTEEEEEEEETHHH CS
                    tRNA_anti-codon  17 kvifidlrDgtgriqvvlfreea 39 
                                        k  +++l D+tg+++++l+  ++
  gene2751|gene2751|rna2751|rna2751 330 KKRDLVLADETGTVRATLWG-DK 351
                                        666899*************9.33 PP

  == domain 4  score: -2.5 bits;  conditional E-value: 1.5
                                        EEEEEETTEEEEEEEET...................HHHH CS
                    tRNA_anti-codon  20 fidlrDgtgriqvvlfr...................eeat 40 
                                        ++ + D t ++ + +f+                   e+at
  gene2751|gene2751|rna2751|rna2751 482 TLHVADFTQQVWLNVFDdfcteffgmtavelkkmgeENAT 521
                                        6778899999999999866655555555555555555555 PP

>> Rep-A_N  Replication factor-A protein 1, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.6   0.0   2.7e-14   9.5e-11       3      97 ..       4      97 ..       2     101 .. 0.81

  Alignments for each domain:
  == domain 1  score: 41.6 bits;  conditional E-value: 2.7e-14
                                       TTHHHHHHH.TTSTS-..-TEEEEEEEEEE--..SSSS-EEEEEEESSSEEEEEEESGGGHHHHHTTSSSTT-EEEEE CS
                            Rep-A_N  3 egaiaaile.tgdasl..kpvlQvvelkkinskaeesseRyrlllsDgknkakamlatqLnslvksgklqklsivrlt 77
                                       +g+++a+ + t+d+ l  +pv+Q++ lkki+  +++++ Ry++ +sDgk ++k+++++q +++v  g ++ ++i++++
  gene2751|gene2751|rna2751|rna2751  4 PGTVEALYNnTKDSPLydTPVVQLLSLKKIEG-KSDKTVRYHITISDGKLYMKGIFSSQVSKEV--GDIKVNTIIKIS 78
                                       6777777775555555779************8.668899**********************998..88999******* PP

                                       EEEEEESTTSSEEEEEEEEE CS
                            Rep-A_N 78 eyvvneikegrkvlivlele 97
                                       ++v+ e + g+  + +  +e
  gene2751|gene2751|rna2751|rna2751 79 DFVILEKN-GNCFIYIKGCE 97
                                       ***96644.55555555555 PP

>> DUF4539  Domain of unknown function (DUF4539)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.1     0.018        66      11      65 ..      31      85 ..      24      94 .. 0.74
   2 !    8.1   0.0   0.00074       2.6      22      62 ..     212     252 ..     196     266 .. 0.83
   3 !   11.4   0.0   6.8e-05      0.24      21      65 ..     331     372 ..     315     379 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.018
                            DUF4539 11 ksintlnslgd..alvtlkDptGeidgtihrkvleeygkdlsvGavllLkqVsvfsp 65
                                       k+i+ ++++    +++t++D    ++g++  +v +e g d++v++++ + +  +++ 
  gene2751|gene2751|rna2751|rna2751 31 KKIEGKSDK-TvrYHITISDGKLYMKGIFSSQVSKEVG-DIKVNTIIKISDFVILEK 85
                                       555333333.24599*******************9985.669999998888777665 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.00074
                            DUF4539  22 alvtlkDptGeidgtihrkvleeygkdlsvGavllLkqVsv 62 
                                        ++  l D+tG+i+++  ++  + +  +++ G+v+ + +  v
  gene2751|gene2751|rna2751|rna2751 212 FSFELLDKTGNIKCVAFNDGADLFYGMIVEGSVVEISKAVV 252
                                        567789****************************9887665 PP

  == domain 3  score: 11.4 bits;  conditional E-value: 6.8e-05
                            DUF4539  21 dalvtlkDptGeidgtihrkvleeygkdlsvGavllLkqVsvfsp 65 
                                        +  ++l+D+tG++++t+  +  e    +l +  vllLk+V v + 
  gene2751|gene2751|rna2751|rna2751 331 KRDLVLADETGTVRATLWGDKSEI---ELDDHPVLLLKDVRVGEF 372
                                        46789************9998876...68999********99665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (577 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1246  (0.0694963); expected 358.6 (0.02)
Passed bias filter:                      526  (0.0293379); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.64u 0.27s 00:00:00.91 Elapsed: 00:00:00.45
# Mc/sec: 3835.62
//
Query:       gene2752|gene2752|rna2752|rna2752  [L=427]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      4e-30  104.4   1.2    3.2e-29  101.5   0.2    2.8  3  Helicase_C       Helicase conserved C-terminal domain
    7.4e-27   94.2   1.1      4e-26   91.9   0.6    2.4  2  DEAD             DEAD/DEAH box helicase
    5.4e-07   29.8   0.1    1.8e-06   28.0   0.1    2.0  1  ResIII           Type III restriction enzyme, res subunit
     0.0093   15.4   0.1      0.033   13.6   0.1    2.0  1  PhoH             PhoH-like protein
  ------ inclusion threshold ------
      0.038   14.4   0.8       0.18   12.2   0.8    2.4  1  AAA              ATPase family associated with various cellul
      0.099   13.0   1.4          3    8.2   0.0    3.0  3  B5               tRNA synthetase B5 domain
       0.18   12.1   4.9        7.1    6.9   0.2    2.9  2  PG_binding_4     Putative peptidoglycan binding domain
       0.25   11.0   2.7          1    9.0   0.1    2.7  2  Glyco_transf_7N  N-terminal region of glycosyl transferase gr
        4.5    7.3   7.3         24    5.0   0.2    3.7  4  Tfb5             Transcription factor TFIIH complex subunit T


Domain annotation for each model (and alignments):
>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.71   1.4e+03       6      44 ..      56      96 ..      52     106 .. 0.67
   2 ?   -2.1   0.0       2.4   4.7e+03      14      29 ..     203     218 ..     189     253 .. 0.61
   3 !  101.5   0.2   1.6e-32   3.2e-29       5     110 ..     256     358 ..     249     359 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.71
                                       HHHHHHHTTTTSEEEEEESSHHHHHH.HHHHHHHT...TSTEE CS
                         Helicase_C  6 llellkleeeggkilifvntidrlek.vklllekk...gikva 44
                                       l +ll ++++ + +l++v+t+d + + v+ll + +   g+k+a
  gene2752|gene2752|rna2752|rna2752 56 LHRLL-QHKKCNYVLVIVPTKDLVVQiVTLL-RMFsplGLKIA 96
                                       66677.778888899******9664433444.33345566655 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.4
                                        TTTSEEEEEESSHHHH CS
                         Helicase_C  14 eeggkilifvntidrl 29 
                                        +++ ++++f+ t d++
  gene2752|gene2752|rna2752|rna2752 203 KKTVQVMLFTATYDEA 218
                                        5666778888887744 PP

  == domain 3  score: 101.5 bits;  conditional E-value: 1.6e-32
                                        HHHHHHHHTTTTSEEEEEESSHHHHHHHHHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSS CS
                         Helicase_C   5 allellkleeeggkilifvntidrlekvklllekkgikvavlhgelpqnereeileqfnkgesdvLiatdvaerGi 80 
                                        +l+el     + +k++ifv +i   + ++ ll++ +++v+ ++g++pq+e+++i+++f+++e+ ++i+td+++rGi
  gene2752|gene2752|rna2752|rna2752 256 HLYEL---CTSISKCIIFVSRIFYTYLLSNLLKELNFNVCLINGRMPQKEKNAIIKSFKDNEYSIMITTDILSRGI 328
                                        44555...48999**********7766455555558**************************************** PP

                                        TSTTESEEEESSSSSSHHHHHHHHTTSSST CS
                         Helicase_C  81 dipkvnlVinfdlprnvtsyiqriGRtgRa 110
                                        dip v+++infdlp++ ++yi+r+GRt+R+
  gene2752|gene2752|rna2752|rna2752 329 DIPAVDNIINFDLPTSRKEYIHRVGRTARM 358
                                        *****************************7 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.9   0.6     2e-29     4e-26       1     170 [.      21     216 ..      21     222 .. 0.87
   2 ?   -2.2   0.0       1.5     3e+03      69     104 ..     282     321 ..     279     325 .. 0.64

  Alignments for each domain:
  == domain 1  score: 91.9 bits;  conditional E-value: 2e-29
                                        -HHHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTS CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               DEAD   1 tdiQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidl 76 
                                        t+iQa ++p +++++++++  +TG+GKTla+++p+l+++++  +k+ + +l+++Pt+ L+ q+++ l+ f   ++l
  gene2752|gene2752|rna2752|rna2752  21 TPIQALTVPYAIQKRNIIGISRTGTGKTLAYVLPALHRLLQ--HKKCNYVLVIVPTKDLVVQIVTLLRMFSP-LGL 93 
                                        89*************************************97..88888****************99876666.899 PP

                                        EEEEEETTSSHHHHHHHHHTTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHH CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               DEAD  77 rvlliiggvaardqlskldngvdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsdfinrilnqlpqi 152
                                        ++ ++i  ++       + n++++++gtpg l + ++  k  ++ v++lV+DE+d+l  +++++++++il++l  +
  gene2752|gene2752|rna2752|rna2752  94 KIASLIDRDE-------I-NDAHFIIGTPGALRKAVK--K--MKGVKVLVMDEVDKLFGKDYERDMRKILESLGLA 157
                                        9988877544.......4.788************885..5..99****************************9544 PP

                                        CTTSTTT.........................................SEEEEEESSBS CS
                                        xxxxxxx.........................................xxxxxxxxxxx RF
                               DEAD 153 tcdgklq.........................................rqvivlSATlp 170
                                          ++  +                                          qv++++AT  
  gene2752|gene2752|rna2752|rna2752 158 VVETGDNlketaddkqklmkrkkslksadhkdntrgikennvntlkktVQVMLFTATYD 216
                                        44333336688999999999999999999999999999999999998888999999986 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.5
                                        HHTTTSTSEEEEEETTSSHHHHHHHH....HTTCSEEEEE CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxx RF
                               DEAD  69 kfkkyidlrvlliiggvaardqlskl....dngvdivvgt 104
                                        +++k+++ +v+li g  +++++ + +    dn++ i+++t
  gene2752|gene2752|rna2752|rna2752 282 NLLKELNFNVCLINGRMPQKEKNAIIksfkDNEYSIMITT 321
                                        5677777888888775555444444444444778888887 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0   0.1   9.2e-10   1.8e-06      23     155 ..      33     152 ..       3     217 .. 0.78

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 9.2e-10
                                        TTSEEEEEESTTSTHHHHH.HHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG....GEEEESSS-B--. CS
                             ResIII  23 rdkrglikmaTGtGKTlva.aklierllkkgkeekflflvprkslleqtleefkkflseaykeigkkvsgdkkkak 97 
                                        ++++++    TGtGKTl + + +  rll+++k + +l++vp+k+l+ q  + ++ f++   k i   ++ d+ +  
  gene2752|gene2752|rna2752|rna2752  33 QKRNIIGISRTGTGKTLAYvLPALHRLLQHKKCNYVLVIVPTKDLVVQIVTLLRMFSPLGLK-IASLIDRDEIN-- 105
                                        4555666789*********999999999999999****************999999887653.55555555444.. PP

                                        ......-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.T...TTHHHHH CS
                             ResIII  98 ekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakk...swreile 155
                                             ++++++ t  +l ++          ++ +  +v+++DE+ +l +k+    +r+ile
  gene2752|gene2752|rna2752|rna2752 106 -----DAHFIIGTPGALRKAV---------KKMKGVKVLVMDEVDKLFGKDyerDMRKILE 152
                                        .....5899999999999988.........5566677888888877777423335555544 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.1   1.7e-05     0.033       2      56 ..      17      72 ..      16      84 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.7e-05
                                       ----SHHHHHHHHHHHH-SEEEEE--TTSSTTHHHHHHHHHHHHT.TS-SEEEEEE CS
                               PhoH  2 ikpktkeQkeylealkkndivfaiGpaGtGKtylavalavealkk.kkvkriiltr 56
                                       i++ t  Q+ ++    ++  +++i ++GtGKt+  v  a++ l + kk++ ++++ 
  gene2752|gene2752|rna2752|rna2752 17 ITALTPIQALTVPYAIQKRNIIGISRTGTGKTLAYVLPALHRLLQhKKCNYVLVIV 72
                                       8889999999998888888899******************9877636666666555 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.8   9.2e-05      0.18      37      85 ..     101     150 ..      40     225 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 9.2e-05
                                        S.......STTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTCCCHHHHHH CS
                                AAA  37 k.......yvgesekkirelfkeakekakpsilfiDEidalaksrsgseseeeerv 85 
                                                ++  ++  +r+ +k++k     ++l++DE+d+l++++    +++ +++
  gene2752|gene2752|rna2752|rna2752 101 RdeindahFIIGTPGALRKAVKKMKG---VKVLVMDEVDKLFGKD---YERDMRKI 150
                                        14555555777788888888877654...47************99...44444444 PP

>> B5  tRNA synthetase B5 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       2.6   5.2e+03      21      45 ..       8      73 ..       5      81 .. 0.44
   2 ?    8.2   0.0    0.0015         3       5      40 ..     132     165 ..     129     215 .. 0.85
   3 ?    2.3   0.1       0.1     2e+02       4      28 ..     375     411 ..     374     422 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 2.6
                                       HHHHHHHTT-E..........................................EESSTTCEEEE-- CS
                                       xxxxxxxxxxx.........................................xxxxxxxxxxxxxx RF
                                 B5 21 iikiLkrlgce.........................................riekdkdlllVtvP 45
                                       i++iL++ +++                                          + k+ + +lV vP
  gene2752|gene2752|rna2752|rna2752  8 ITEILNQNKITaltpiqaltvpyaiqkrniigisrtgtgktlayvlpalhrlLQHKKCNYVLVIVP 73
                                       555555555544444444444444444444444444444444444444443333334444555555 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0015
                                        HHHHHHHHTS---HHHHHHHHHHTT-E.EESSTTCE CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                                 B5   5 vekinkllGidlseeeiikiLkrlgceriekdkdll 40 
                                        ++++ kl G d+ e ++ kiL++lg+ +  +++d+l
  gene2752|gene2752|rna2752|rna2752 132 MDEVDKLFGKDY-ERDMRKILESLGLAV-VETGDNL 165
                                        68999****999.569**********96.4444444 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.1
                                        EHHHHHHHHT............S---HHHHHHHHHHT CS
                                        xxxxxxxxxx............xxxxxxxxxxxxxxx RF
                                 B5   4 rvekinkllG............idlseeeiikiLkrl 28 
                                        r+++i+k++G            +++++++++  L+++
  gene2752|gene2752|rna2752|rna2752 375 RLQRIEKMIGekmieykidenrMSINKDKVEAALEKV 411
                                        6899******999998888888888999999999876 PP

>> PG_binding_4  Putative peptidoglycan binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.2    0.0036       7.1      23      60 ..     191     225 ..     165     234 .. 0.74
   2 ?    5.7   0.7    0.0087        17      37      68 ..     386     417 ..     367     423 .. 0.70

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0036
                       PG_binding_4  23 tygrkgnelerlsetiaawkevdlrvsldeeklkeyld 60 
                                        t g+k n++++l++t++    + +  ++de+ +++y+d
  gene2752|gene2752|rna2752|rna2752 191 TRGIKENNVNTLKKTVQ---VMLFTATYDEALVRRYVD 225
                                        34556666666666666...467*************98 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0087
                       PG_binding_4  37 tiaawk...evd.lrvsldeeklkeyldeiakeidt 68 
                                                 ++d  r+s++++k+++ l+++ k+   
  gene2752|gene2752|rna2752|rna2752 386 K----MieyKIDeNRMSINKDKVEAALEKVYKKSKL 417
                                        3....243356689***************9998765 PP

>> Glyco_transf_7N  N-terminal region of glycosyl transferase group 7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.1   0.00052         1      51      87 ..      38      74 ..       5      78 .. 0.81
   2 ?    0.8   0.4      0.18   3.6e+02      50      73 ..     245     268 ..     233     323 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00052
                    Glyco_transf_7N 51 iiipyrnreehLkillkrLhpllqrQqldykiyvieq 87
                                       i i      + L ++l  Lh+llq+ +++y ++++  
  gene2752|gene2752|rna2752|rna2752 38 IGISRTGTGKTLAYVLPALHRLLQHKKCNYVLVIVPT 74
                                       44555556789*********************99965 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.18
                    Glyco_transf_7N  50 aiiipyrnreehLkillkrLhpll 73 
                                         +  py++r  hL  l + + + +
  gene2752|gene2752|rna2752|rna2752 245 YVFAPYKHRIYHLYELCTSISKCI 268
                                        577899999999999988887643 PP

>> Tfb5  Transcription factor TFIIH complex subunit Tfb5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.2      0.16   3.2e+02      50      65 ..       2      17 ..       1      20 [. 0.87
   2 ?    2.8   0.0     0.061   1.2e+02      44      67 ..     194     217 ..     189     218 .. 0.90
   3 ?   -3.5   0.0       5.5   1.1e+04      50      64 ..     300     314 ..     285     322 .. 0.52
   4 ?    5.0   0.2     0.012        24      29      57 ..     384     412 ..     375     420 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.16
                               Tfb5 50 eelkkeleelleknty 65
                                       ++lk+e++e+l++n+ 
  gene2752|gene2752|rna2752|rna2752  2 DQLKNEITEILNQNKI 17
                                       78***********986 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.061
                               Tfb5  44 vkeevveelkkeleellekntyep 67 
                                        +ke+ v++lkk ++ +l   ty++
  gene2752|gene2752|rna2752|rna2752 194 IKENNVNTLKKTVQVMLFTATYDE 217
                                        89**************99999875 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 5.5
                               Tfb5  50 eelkkeleelleknt 64 
                                        ++ k+++ +  ++n+
  gene2752|gene2752|rna2752|rna2752 300 QKEKNAIIKSFKDNE 314
                                        333444444444444 PP

  == domain 4  score: 5.0 bits;  conditional E-value: 0.012
                               Tfb5  29 sqkfiiedLDethlfvkeevveelkkele 57 
                                        ++k+i  ++De+++ +++++ve+  +++ 
  gene2752|gene2752|rna2752|rna2752 384 GEKMIEYKIDENRMSINKDKVEAALEKVY 412
                                        7799999*************998766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (427 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1486  (0.0828825); expected 358.6 (0.02)
Passed bias filter:                      582  (0.0324614); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.61u 0.32s 00:00:00.93 Elapsed: 00:00:00.46
# Mc/sec: 2769.33
//
Query:       gene2753|gene2753|rna2753|rna2753  [L=172]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.5e-27   94.2   4.0    7.6e-27   93.7   4.0    1.1  1  Med6      MED6 mediator sub complex component
  ------ inclusion threshold ------
      0.034   14.1   0.0      0.065   13.2   0.0    1.4  1  Swi3      Replication Fork Protection Component Swi3


Domain annotation for each model (and alignments):
>> Med6  MED6 mediator sub complex component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.7   4.0   8.4e-31   7.6e-27       3     132 ..       6     133 ..       5     134 .. 0.93

  Alignments for each domain:
  == domain 1  score: 93.7 bits;  conditional E-value: 8.4e-31
                               Med6   3 wkspewlqalgLtennvldYFaespFydktsnNevlkmqrqfnqaaeeal.LkkmkGleyvlahvqepdlfvirkq 77 
                                        + +++wl++++Lt ++vl+YF+ spFyd++s Ne+lkmq+qf++  + ++ L++++G++y +   q+ d+f i k 
  gene2753|gene2753|rna2753|rna2753   6 YTNQQWLETNPLTVETVLTYFSFSPFYDRSSLNEILKMQTQFTNFLDFSKkLTELNGVKYLIE--QKGDIFFIYKI 79 
                                        899***************************************998765545************..999******** PP

                               Med6  78 erksatevtvlaaYyiiggniYqapslysvvqsrllsalsslskalkelsslakf 132
                                        +++++ + ++l+ Yy++ g+iY+  +  s++++r+ + l+ l+++l ++ + ++f
  gene2753|gene2753|rna2753|rna2753  80 HKQKD-TEELLDFYYVFFGTIYKGATTNSIFRTRVFNFLFFLNESLPKYLRRRRF 133
                                        *8887.569*************************************999888777 PP

>> Swi3  Replication Fork Protection Component Swi3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   7.2e-06     0.065       5      55 ..      55     105 ..      51     111 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 7.2e-06
                               Swi3   5 erLlsekGlpaLrknfkklkfkgkgheaedlkkllqfyqlWahrLfPkakf 55 
                                        ++L++ +G+++L+++  ++ f  k h+ +d ++ll fy  +   ++  a+ 
  gene2753|gene2753|rna2753|rna2753  55 KKLTELNGVKYLIEQKGDIFFIYKIHKQKDTEELLDFYYVFFGTIYKGATT 105
                                        579999********************************9999888877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       551  (0.0307323); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 1176.44
//
Query:       gene2754|gene2754|rna2754|rna2754  [L=138]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.6e-54  182.3   0.1      4e-54  182.2   0.1    1.0  1  NifU_N    NifU-like N terminal domain


Domain annotation for each model (and alignments):
>> NifU_N  NifU-like N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  182.2   0.1   2.2e-58     4e-54       2     126 ..      15     136 ..      14     138 .] 0.98

  Alignments for each domain:
  == domain 1  score: 182.2 bits;  conditional E-value: 2.2e-58
                                        SCHHHHHHHHSSSSBSS-TTSSS--EEEEEEETTTTEEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHHHHH CS
                             NifU_N   2 ysdkvldhyknPrnvGvleeedakvgvgevgapacGDavrLqikvdeetdriedakFktfGCgsaiAssslltelv 77 
                                        y+  v+dh++nPrnvG+ +++ ++vg+g vgapacGD+++Lqikv++  d+i+dakF+tfGCgsaiAsssl+te++
  gene2754|gene2754|rna2754|rna2754  15 YHSSVIDHFENPRNVGSYDKSANDVGTGLVGAPACGDVMKLQIKVEN--DIIKDAKFRTFGCGSAIASSSLATEWI 88 
                                        99********************************************9..8************************** PP

                                        TTSBHHHHCCCCHHHHHHHHTCSCSSSCHCSCHHHHHHHHHHHHHHHHC CS
                             NifU_N  78 kgktleealkitnkeiaeelgglpkeklhcsvlaedalkaavkkYkakk 126
                                        kgk++ + lkitnk+ia++l+ lp++klhcs+laeda+kaa+++Y++k+
  gene2754|gene2754|rna2754|rna2754  89 KGKSISDSLKITNKDIAKKLS-LPPVKLHCSMLAEDAIKAAISDYQKKN 136
                                        *********************.*************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       365  (0.0203581); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 889.06
//
Query:       gene2755|gene2755|rna2755|rna2755  [L=82]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1324  (0.0738468); expected 358.6 (0.02)
Passed bias filter:                      532  (0.0296726); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 584.45
//
Query:       gene2756|gene2756|rna2756|rna2756  [L=274]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.8e-15   55.6   0.0      1e-14   55.0   0.0    1.2  1  TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
  ------ inclusion threshold ------
       0.09   13.4   0.0          1   10.0   0.0    2.3  2  VWA_2         von Willebrand factor type A domain


Domain annotation for each model (and alignments):
>> TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.0   0.0   1.1e-18     1e-14       1     205 [.       9     231 ..       9     238 .. 0.70

  Alignments for each domain:
  == domain 1  score: 55.0 bits;  conditional E-value: 1.1e-18
                       TP_methylase   1 klylVGvGpGdpellTvrAlralktadvvlgddsraleilldllaeeleleapmgkekepleeayeeiaealaeal 76 
                                        +l l+G+G+ d ++++++Al+++k+ad v+ +   +++i+   +++  e+ ++ +     ++++  e+ ++l+++ 
  gene2756|gene2756|rna2756|rna2756   9 MLRLIGLGLDDLNDISLKALQIVKNADKVYMEC--YTSIINSTVEQM-EHLYQRTIV--LADRHLLENTDTLVDEG 79 
                                        5779*************************9888..888887666542.344444444..45555677777776555 PP

                       TP_methylase  77 ragkdVvllvsGDPlvygtgselvealrareagieveviPGvsslqaaaarlgiplteggevlsvl......lpgl 146
                                        ++ +dVvllv+G Pl+++t+  l+ ++++  ++++++vi   s+ + +   +g+  + +g v+s+       +p+ 
  gene2756|gene2756|rna2756|rna2756  80 AQ-QDVVLLVPGTPLFATTHTDLLIRCTE--KNVKYQVINNTSIYNVIGH-IGLYSYSFGRVVSIPffsdgfRPQ- 150
                                        55.58*******************99999..99********887776665.555555566666666699966444. PP

                       TP_methylase 147 akeeereleallangdtlvll.......................kaprklaelaelLkealyddttpvavveragt 199
                                            +r le++++n +tl ll                       +a ++l e  +     +  + t+++v++r g+
  gene2756|gene2756|rna2756|rna2756 151 -SVFDRILENISNNLHTLCLLdikidksyydtngsstnrfmsanTAMHQLLEYERTVHSGVITERTKIFVICRFGC 225
                                        .4578999999999******97777777766655555444333322223333333333335666778888888888 PP

                       TP_methylase 200 edervv 205
                                         d+ ++
  gene2756|gene2756|rna2756|rna2756 226 HDQSLY 231
                                        888776 PP

>> VWA_2  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.11   9.9e+02      39      70 ..     126     161 ..     105     166 .. 0.75
   2 ?   10.0   0.0   0.00012         1       5      72 ..     174     241 ..     172     252 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.11
                              VWA_2  39 rvglvtfsdgpevlipltkd....kakilnalrnle 70 
                                        ++gl ++s g  v ip+ +d    ++ ++++l+n+ 
  gene2756|gene2756|rna2756|rna2756 126 HIGLYSYSFGRVVSIPFFSDgfrpQSVFDRILENIS 161
                                        799******999999995443555777777777765 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00012
                              VWA_2   5 lDtSgSmrngdygptrleaakdaveallkslpgdrvglvtfsdgpevliplt.kdkakilnalrnleak 72 
                                        +D S + +ng  +++r++ a  a+ +ll+  ++++ g++t +++  v++ +   d++   +++rnl  +
  gene2756|gene2756|rna2756|rna2756 174 IDKSYYDTNG-SSTNRFMSANTAMHQLLEYERTVHSGVITERTKIFVICRFGcHDQSLYYDEIRNLLST 241
                                        7888888887.5899**********************************99658899999999999864 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (274 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       452  (0.0252106); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 2062.11
//
Query:       gene2757|gene2757|rna2757|rna2757  [L=847]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.3e-40  136.9   0.1    6.7e-36  124.0   0.0    3.1  3  AAA_2            AAA domain (Cdc48 subfamily)
    7.5e-29   99.7   0.2    7.5e-29   99.7   0.2    2.9  2  AAA_lid_9        AAA lid domain
    6.8e-25   88.0   0.9      4e-12   46.7   0.0    3.9  3  AAA              ATPase family associated with various cellul
    3.6e-15   55.8   0.5    1.2e-14   54.1   0.5    2.0  1  ClpB_D2-small    C-terminal, D2-small domain, of ClpB protein
    6.6e-15   55.3   0.0    3.9e-10   39.9   0.0    3.4  2  AAA_5            AAA domain (dynein-related subfamily)
    1.3e-10   42.0   0.0      0.012   16.0   0.0    4.4  4  AAA_16           AAA ATPase domain
    1.6e-07   31.3   0.0      0.019   14.7   0.0    2.7  2  IstB_IS21        IstB-like ATP binding protein
    1.8e-07   31.0   0.0    0.00017   21.3   0.0    2.8  2  Sigma54_activat  Sigma-54 interaction domain
    1.9e-07   30.7   0.0    0.00019   20.9   0.0    3.2  2  TniB             Bacterial TniB protein
    3.7e-06   26.9   0.0     0.0083   16.1   0.0    2.5  2  NACHT            NACHT domain
    1.1e-05   25.1   0.0      0.016   14.8   0.0    2.6  2  AAA_7            P-loop containing dynein motor region
    1.2e-05   25.3   2.6      0.011   15.7   0.1    4.1  3  ATPase_2         ATPase domain predominantly from Archaea
      2e-05   24.6   0.1    0.00013   22.0   0.0    2.3  2  Clp_N            Clp amino terminal domain, pathogenicity isl
    2.2e-05   24.5   0.2      0.011   15.8   0.0    3.2  3  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
      7e-05   22.9   0.2       0.75    9.8   0.0    3.4  2  AAA_14           AAA domain
    0.00018   22.1   0.2       0.13   12.8   0.0    3.4  3  ABC_tran         ABC transporter
    0.00018   22.1   1.5       0.65   10.5   0.0    4.0  3  AAA_18           AAA domain
    0.00019   21.7   0.1        2.6    8.3   0.1    4.2  3  AAA_22           AAA domain
    0.00029   20.8   0.0       0.67    9.8   0.0    2.7  2  RsgA_GTPase      RsgA GTPase
    0.00031   20.4   0.1        4.9    7.0   0.0    3.6  3  AAA_29           P-loop containing region of AAA domain
    0.00031   20.1   1.6        1.1    8.4   0.2    3.3  3  TIP49            TIP49 P-loop domain
    0.00032   20.5   4.3       0.39   10.5   0.0    4.6  4  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    0.00046   19.6   0.1        1.3    8.3   0.0    3.3  3  Mg_chelatase     Magnesium chelatase, subunit ChlI
    0.00074   19.9   0.2        1.7    9.1   0.0    3.4  2  RNA_helicase     RNA helicase
     0.0012   18.5   0.0      0.053   13.1   0.0    2.6  2  AAA_25           AAA domain
     0.0013   18.5   0.0       0.13   11.9   0.0    2.5  2  AAA_30           AAA domain
     0.0031   17.4   0.0       0.75    9.6   0.0    2.7  2  Bac_DnaA         Bacterial dnaA  protein
      0.005   16.8   0.0        1.7    8.6   0.0    3.4  3  ResIII           Type III restriction enzyme, res subunit
     0.0058   16.4   0.1       0.58    9.8   0.0    3.0  2  AAA_24           AAA domain
     0.0061   16.8   0.0        3.4    7.9   0.0    2.8  2  Roc              Ras of Complex, Roc, domain of DAPkinase
     0.0066   16.1   0.1       0.69    9.5   0.0    2.8  2  SRP54            SRP54-type protein, GTPase domain
     0.0067   16.9  14.2       0.22   12.0   0.0    4.2  3  AAA_23           AAA domain
     0.0076   16.2   0.0        2.4    8.2   0.0    2.6  2  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
     0.0076   16.4   0.0        1.4    9.1   0.0    2.6  2  AAA_33           AAA domain
  ------ inclusion threshold ------
      0.013   15.0   0.2        4.2    6.8   0.0    2.5  2  PhoH             PhoH-like protein
      0.016   15.0   0.1       0.26   11.1   0.0    2.8  2  AAA_3            ATPase family associated with various cellul
      0.035   13.9   0.0       0.66    9.7   0.0    3.0  3  DNA_pol3_delta2  DNA polymerase III, delta subunit
      0.043   12.8   0.1        4.8    6.1   0.0    2.5  2  AAA_6            Hydrolytic ATP binding site of dynein motor 
      0.045   13.8   9.8       0.22   11.6   0.1    3.9  4  DUF87            Helicase HerA, central domain
       0.05   12.8   0.0        3.7    6.7   0.0    2.5  2  NB-ARC           NB-ARC domain
      0.064   12.4   2.1        5.9    6.0   0.0    3.3  3  ArsA_ATPase      Anion-transporting ATPase
      0.087   12.7   0.6         44    3.9   0.1    3.6  3  NTPase_1         NTPase
      0.089   13.0   0.0          3    8.1   0.0    2.8  2  AAA_28           AAA domain
       0.14   11.6   1.4        2.8    7.3   0.0    2.9  3  ParA             NUBPL iron-transfer P-loop NTPase
        1.2    9.6   4.5       0.81   10.2   1.1    2.4  2  DUF16            Protein of unknown function DUF16
        3.6    7.6   7.0        5.3    7.1   0.0    4.0  4  TcpS             Toxin-coregulated pilus protein S


Domain annotation for each model (and alignments):
>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.1       7.9   3.1e+03     147     169 ..      44      66 ..      16      68 .. 0.77
   2 !    9.4   0.0    0.0028       1.1       2      83 ..     170     256 ..     169     270 .. 0.67
   3 !  124.0   0.0   1.7e-38   6.7e-36       1     169 [.     577     733 ..     577     735 .. 0.97

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 7.9
                                        GGG--HHHHHHTT--HHHHTT-- CS
                              AAA_2 147 kkkeeveeelkkglipEllgRlp 169
                                          ++++++e k+ ++ El+ R++
  gene2757|gene2757|rna2757|rna2757  44 VLEKNLTREEKSRMKTELIRRID 66 
                                        56677888889999999999998 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0028
                                        ----EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS....... CS
                              AAA_2   2 piisilllgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG....... 70 
                                        ++++ +l+gp gvGkt +   la+l+   +e      + + +    +v ++v++  +  ++  ++ +         
  gene2757|gene2757|rna2757|rna2757 170 KKSNPMLVGPAGVGKTAIVCGLAQLIAK-DEA-PGLTNYRIYNV--DVGSMVANTGVRGEFEERVRKVVkeaeecp 241
                                        788999********************94.333.33334444444..556666665555555544444445555779 PP

                                        ..EEEEETGGG---- CS
                              AAA_2  71 ..ivllDEidKihpk 83 
                                          i+++DEi  + + 
  gene2757|gene2757|rna2757|rna2757 242 niILFIDEIHTVISA 256
                                        999999999887775 PP

  == domain 3  score: 124.0 bits;  conditional E-value: 1.7e-38
                                        -----EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS...... CS
                              AAA_2   1 rpiisilllgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG...... 70 
                                        rpi+ +l+lgp+gvGktelaka+a  lf ++ k ++++d+s+++     e ++++l+g + gyvg++egG      
  gene2757|gene2757|rna2757|rna2757 577 RPIGAFLFLGPSGVGKTELAKAIAFELF-DDAKGMVVLDMSDYAN----EISITKLLGVSAGYVGYAEGGaltepv 647
                                        6899************************.****************....*************************** PP

                                        ......EEEEETGGG-------------HHHHHHHHHHHH--EE-------EE-TT-EEEEEE--TTHHHHTTTS- CS
                              AAA_2  71 ......ivllDEidKihpkessgadvSregVqrdLLqileggtltdkqgrkvdtknilfImtgafgsskisdesrs 140
                                              +vl+DE+d +hp            V+++L+q+l++g++td + + +d++n++++mt+++g +ki +    
  gene2757|gene2757|rna2757|rna2757 648 kekpynVVLFDELDLAHP-----------KVVNVLYQLLDEGRVTDGKRNVIDFTNTVIVMTSNLGYEKILTGV-- 710
                                        ******************...........*******************************************44.. PP

                                        STTTTSGGG--HHHHHHTT--HHHHTT-- CS
                              AAA_2 141 keeeeekkkeeveeelkkglipEllgRlp 169
                                                 +e+e++l+  + p l++R++
  gene2757|gene2757|rna2757|rna2757 711 ------YDPSEIEKALNDRFGPALINRID 733
                                        ......468999****************9 PP

>> AAA_lid_9  AAA lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.7   0.2   1.9e-31   7.5e-29       1      93 [.     312     404 ..     312     416 .. 0.95
   2 ?   -0.9   0.9         4   1.6e+03      65      95 ..     456     486 ..     425     494 .. 0.75

  Alignments for each domain:
  == domain 1  score: 99.7 bits;  conditional E-value: 1.9e-31
                          AAA_lid_9   1 seeetieiLrglkekyekhHgvkisdealeaavklSkrYisdrflPdkAIDllDeaaarvrlkkeskpeeleklek 76 
                                        s+e++i++Lrgl++k+e hHg+ki+d+a++ +vk++k+Yi++r+lPd AIDl+D+a+a++ ++ es+p+e+ ++++
  gene2757|gene2757|rna2757|rna2757 312 SVEDSITMLRGLRNKMELHHGIKIEDSAIVFSVKMAKKYIPSRRLPDIAIDLVDTACASATIELESEPQEIMNMKN 387
                                        689************************************************************************* PP

                          AAA_lid_9  77 elaklekekealekeee 93 
                                        ++++le e++a+e++ +
  gene2757|gene2757|rna2757|rna2757 388 KIWSLELERAAIERDYK 404
                                        ***********999876 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 4
                          AAA_lid_9  65 eskpeeleklekelaklekekealekeeeke 95 
                                        +++ +e ++l+ +++++ ++ e++++++++ 
  gene2757|gene2757|rna2757|rna2757 456 RASVSEAKALKIKIDQIYNKIEEARRNNDTY 486
                                        3445667788888888888888888877754 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.7   0.0     1e-14     4e-12       2     111 ..     175     286 ..     174     308 .. 0.79
   2 ?    1.4   0.2       1.1   4.1e+02      38     101 ..     423     484 ..     382     519 .. 0.80
   3 !   35.7   0.0   2.6e-11     1e-08       2     112 ..     583     694 ..     582     725 .. 0.70

  Alignments for each domain:
  == domain 1  score: 46.7 bits;  conditional E-value: 1e-14
                                        EEESSTTSSHHHHHHHHHHHH.........THEEEEEETTTCSSS..STTHHHHHHHHHHHHHHHTSTSEEEEEET CS
                                AAA   2 llyGppGtGKTllakavakel.........gvefleisgsellsk..yvgesekkirelfkeakekakpsilfiDE 66 
                                        +l+Gp G+GKT+++  +a+ +         + +++++++ +++ +  + ge e+++r+++kea+e     ilfiDE
  gene2757|gene2757|rna2757|rna2757 175 MLVGPAGVGKTAIVCGLAQLIakdeapgltNYRIYNVDVGSMVANtgVRGEFEERVRKVVKEAEECP-NIILFIDE 249
                                        69**************99996555445444799**********444799**************9875.5******* PP

                                        GGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESS CS
                                AAA  67 idalaksrsgseseeeervvnqLlteldgvkkkeskvivigatnr 111
                                        i+ ++++    +++ + +  n L + l   k       +igat++
  gene2757|gene2757|rna2757|rna2757 250 IHTVISAG---STSGSLDFSNILKPSLAAGKI-----KIIGATTH 286
                                        *****999...666677777777777766655.....47777776 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 1.1
                                        STTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSS CS
                                AAA  38 yvgesekkirelfkeakekakpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkkes 101
                                        y +e++++++e+ +++ e +  + + ++E+++  +++  se +  +  ++q+++++++ +++++
  gene2757|gene2757|rna2757|rna2757 423 YGKETKERLNEVEAKIDEAR-RCLIPLEEAYEKERAS-VSEAKALKIKIDQIYNKIEEARRNND 484
                                        77899999999999998887.8999999999986666.56666677778899999998888754 PP

  == domain 3  score: 35.7 bits;  conditional E-value: 2.6e-11
                                        EEESSTTSSHHHHHHHHHHHH...THEEEEEETTTCSSS............STTHHHHHHHHHHHHHHHTSTS.EE CS
                                AAA   2 llyGppGtGKTllakavakel...gvefleisgsellsk............yvgesekkirelfkeakekakp.si 61 
                                        l+ Gp G+GKT laka+a el      ++ +++s+  ++            yvg +e    +l + +kek  p  +
  gene2757|gene2757|rna2757|rna2757 583 LFLGPSGVGKTELAKAIAFELfddAKGMVVLDMSDYANEisitkllgvsagYVGYAEGG--ALTEPVKEK--PyNV 654
                                        899*****************865413344444444444444444443455566655553..455556665..669* PP

                                        EEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSG CS
                                AAA  62 lfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvivigatnrp 112
                                        +++DE+d  +++            vn+L++ ld+ +  ++k  vi  tn++
  gene2757|gene2757|rna2757|rna2757 655 VLFDELDLAHPKV-----------VNVLYQLLDEGRVTDGKRNVIDFTNTV 694
                                        **********999...........************995555555555553 PP

>> ClpB_D2-small  C-terminal, D2-small domain, of ClpB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.1   0.5     3e-17   1.2e-14       1      72 [.     741     812 ..     741     823 .. 0.91

  Alignments for each domain:
  == domain 1  score: 54.1 bits;  conditional E-value: 3e-17
                                        SCHHHHHHHHHHHHHHHHHHSCTTTEEEEEHHHHHHHHHHHTSBTTTBTCCHHHHHHHHTHHHHHHHHHTTS CS
                      ClpB_D2-small   1 LtkeelkkIvdlalkklekrlkergvelevtdealdalaekgydpeyGARpLrriiqreiedplaeeilsge 72 
                                        L+  +l++I+d +l+ l+k l+e+++ l ++d++++ ++++ y+p+yGARpL+r+++ +  d++a  il++ 
  gene2757|gene2757|rna2757|rna2757 741 LSMVDLRNILDYKLEMLNKELNEKKIYLYLSDAVKQDVINRNYKPVYGARPLKRALRSTFMDAIAHIILTDS 812
                                        67789****************************************************************754 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.0   0.00053      0.21       3      76 ..     175     252 ..     173     263 .. 0.60
   2 !   39.9   0.0     1e-12   3.9e-10       2     138 .]     582     724 ..     581     724 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00053
                                        EEE--SSSSHHHHHHHGGGGB.S--EEEEE--TT--HH..HHH--B--.........--------.G-SEEEEESG CS
                              AAA_5   3 lLvGppGtgKselaerlaaal.nreveyvqltrdttee..dlkgrreikngttslvdsplvraar.egeilvlDEv 74 
                                        +LvGp G+gK+ ++  la+++ ++e     ++r ++ +   ++  + ++++ +++v +++++a +    il++DE+
  gene2757|gene2757|rna2757|rna2757 175 MLVGPAGVGKTAIVCGLAQLIaKDEAPGLTNYRIYNVDvgSMVANTGVRGEFEERVRKVVKEAEEcPNIILFIDEI 250
                                        7********************8444333333333322211333333332333345544444444455666777777 PP

                                        GG CS
                              AAA_5  75 er 76 
                                        ++
  gene2757|gene2757|rna2757|rna2757 251 HT 252
                                        75 PP

  == domain 2  score: 39.9 bits;  conditional E-value: 1e-12
                                        EEEE--SSSSHHHHHHHGGGGB...S--EEEEE--TT--HHHHH--B--..........--------..G-SEEEE CS
                              AAA_5   2 vlLvGppGtgKselaerlaaal...nreveyvqltrdtteedlkgrreik.ngttslvdsplvraar..egeilvl 71 
                                        +l +Gp+G+gK+ela+ +a  l    + +++  ++++ +e  ++  + ++ +     + ++l++ ++     ++++
  gene2757|gene2757|rna2757|rna2757 582 FLFLGPSGVGKTELAKAIAFELfddAKGMVVLDMSDYANEISITKLLGVSaGYVGYAEGGALTEPVKekPYNVVLF 657
                                        6899***************9999977778888899999999******9996667777888999999955558**** PP

                                        ESGGG--HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--........-TT-TTHHHHTT- CS
                              AAA_5  72 DEveraesevlnsLlslleerrllleeggelvkaknddllerfrviatanpld.......rslnelspalrsRf 138
                                        DE++ a+++v+n+L +ll+e r+  +  ++++++ n      + +++t+n  +       ++ +e+ +al +Rf
  gene2757|gene2757|rna2757|rna2757 658 DELDLAHPKVVNVLYQLLDEGRVT-DGKRNVIDFTN------TVIVMTSNLGYekiltgvYDPSEIEKALNDRF 724
                                        ***********************9.66677888888......89******999999999999**********99 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   3.6e-05     0.014       2      51 ..     152     198 ..     151     210 .. 0.80
   2 ?   -0.5   0.0       3.5   1.4e+03     121     146 ..     228     255 ..     206     270 .. 0.71
   3 !   16.0   0.0   3.1e-05     0.012       2      51 ..     551     606 ..     550     629 .. 0.79
   4 ?    3.4   0.0      0.23        88     135     163 ..     650     679 ..     642     688 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 3.6e-05
                             AAA_16   2 lvGReeeleqLlsalervrsgrpelvllsGesGvGKsslvrellralekd 51 
                                        ++GR +e++ + ++l + +++ p   +l+G++GvGK+++v  l++ + kd
  gene2757|gene2757|rna2757|rna2757 152 VIGRVKEIRSIIEILAKKKKSNP---MLVGPAGVGKTAIVCGLAQLIAKD 198
                                        67999999888888877766665...899***********8888777776 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 3.5
                             AAA_16 121 ellkrllallsrderplvlvlDdlq...w 146
                                        e +++ ++ +++  + ++l++D+++    
  gene2757|gene2757|rna2757|rna2757 228 ERVRKVVKEAEE-CPNIILFIDEIHtviS 255
                                        555555655555.555********95443 PP

  == domain 3  score: 16.0 bits;  conditional E-value: 3.1e-05
                             AAA_16   2 lvGReeeleqL.lsale.rvrsgrp....elvllsGesGvGKsslvrellralekd 51 
                                        ++G ++ ++++ + +l+ rv  ++p    ++ l+ G+sGvGK+ l+++++ +l +d
  gene2757|gene2757|rna2757|rna2757 551 VFGQDAAVDRVvQCILRnRVGLSEPdrpiGAFLFLGPSGVGKTELAKAIAFELFDD 606
                                        67888888888666666777777778889******************999887777 PP

  == domain 4  score: 3.4 bits;  conditional E-value: 0.23
                             AAA_16 135 rp.lvlvlDdlqwadeaslqllaaLlrlle 163
                                        +p  v+++D+l+ a +   ++l++Ll+++ 
  gene2757|gene2757|rna2757|rna2757 650 KPyNVVLFDELDLAHPKVVNVLYQLLDEGR 679
                                        555799********************9865 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.0   0.00011     0.042      44      75 ..     168     199 ..     124     263 .. 0.71
   2 !   14.7   0.0   4.8e-05     0.019      50      91 ..     582     623 ..     578     631 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 0.00011
                          IstB_IS21  44 iekkenivllGpsGvGKshlaialgveavrag 75 
                                         +kk n +l+Gp+GvGK+ + + l++  ++++
  gene2757|gene2757|rna2757|rna2757 168 KKKKSNPMLVGPAGVGKTAIVCGLAQLIAKDE 199
                                        46899*******************99766643 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 4.8e-05
                          IstB_IS21  50 ivllGpsGvGKshlaialgveavraglsvlfvrvedLveelk 91 
                                        +++lGpsGvGK+ la a++ e   + + ++ + ++d  +e++
  gene2757|gene2757|rna2757|rna2757 582 FLFLGPSGVGKTELAKAIAFELFDDAKGMVVLDMSDYANEIS 623
                                        789*****************9998877777777777666665 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.0     0.016       6.3       9     104 ..     157     252 ..     152     260 .. 0.66
   2 !   21.3   0.0   4.4e-07   0.00017      25     142 ..     582     699 ..     551     710 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.016
                                        HHHHHHHHHHCTSS.S-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETTTS-TTCHHHHHHEBSSSSSTTTSS CS
                    Sigma54_activat   9 kelleqikkvaktd.lsvlitGesGtGKellaraiheaskrkekpfvavncaaipeelleseLFGhekGaFtGAek 83 
                                        ke+++ i+ +ak++ ++ +++G  G+GK+ +   + +   ++e+p +  n   ++ ++ +      ++G F    +
  gene2757|gene2757|rna2757|rna2757 157 KEIRSIIEILAKKKkSNPMLVGPAGVGKTAIVCGLAQLIAKDEAPGL-TNYRIYNVDVGSMVANTGVRGEFEERVR 231
                                        44444445445443388999**********99888888877777644.3555555554444444556777777777 PP

                                        -BEHHHHHTTTSEEEEETGGG CS
                    Sigma54_activat  84 ekkGlfekadgGtlfLDeige 104
                                        +     e++ + +lf+Dei++
  gene2757|gene2757|rna2757|rna2757 232 KVVKEAEECPNIILFIDEIHT 252
                                        777777777777777777776 PP

  == domain 2  score: 21.3 bits;  conditional E-value: 4.4e-07
                                        EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETTTS-TTCHHHHHHEBSSSSSTTTSS-BE.HHHHHTTTSEEEE CS
                    Sigma54_activat  25 vlitGesGtGKellaraiheaskrkekpfvavncaaipeelleseLFGhekGaFtGAekekk.GlfekadgGtlfL 99 
                                         l +G sG+GK+ la+ai  +   ++k +v ++++++++e+  ++L G+++G    Ae       +++    ++++
  gene2757|gene2757|rna2757|rna2757 582 FLFLGPSGVGKTELAKAIAFELFDDAKGMVVLDMSDYANEISITKLLGVSAGYVGYAEGGALtEPVKEKPYNVVLF 657
                                        6899**************9999999999***********************9655565544445677777889999 PP

                                        ETGGGS-HHHHHHHHHHHHHSEEESBTSSSEEE--EEEEEEES CS
                    Sigma54_activat 100 DeigelplelQekLlrvlqegevervGsskeikvdvriiaatn 142
                                        De+    +++ + L ++l+eg+v+  G+++ i+++  +i+ t+
  gene2757|gene2757|rna2757|rna2757 658 DELDLAHPKVVNVLYQLLDEGRVTD-GKRNVIDFTNTVIVMTS 699
                                        *********************9987.88888887777777665 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   4.8e-07   0.00019      22     185 ..     158     309 ..     138     312 .. 0.80
   2 ?    0.3   0.0         1     4e+02      37      53 ..     581     597 ..     566     604 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 4.8e-07
                               TniB  22 rLeeLleypkrkrmpnlllvGdsnnGKtmivekFarlhppekdedaekvpvlvvqappkpdekrlyaaiLealgap 97 
                                        ++++++e   +k+ +n +lvG+  +GKt+iv   a+l  +++ +                ++ r+y+  + ++ a+
  gene2757|gene2757|rna2757|rna2757 158 EIRSIIEILAKKKKSNPMLVGPAGVGKTAIVCGLAQLIAKDEAPGL--------------TNYRIYNVDVGSMVAN 219
                                        5666777777777788888888888888888877777666664444..............4455666666677777 PP

                               TniB  98 lkararvskleqqvlrllrelkvrvLiiDEihnll.agsarkqreflnalksLgnelkipivlvGteeal.ralrt 171
                                        +  r + ++  ++v++  +e+   +L iDEih ++ ags +    f n+lk      ki i+++ t++ + + +++
  gene2757|gene2757|rna2757|rna2757 220 TGVRGEFEERVRKVVKEAEECPNIILFIDEIHTVIsAGSTSGSLDFSNILKPSLAAGKIKIIGATTHDEYrKYMEN 295
                                        888888888888999999**************9763799999**********************99876616899* PP

                               TniB 172 DpqlasRFepialp 185
                                        D+ + +RF +++++
  gene2757|gene2757|rna2757|rna2757 296 DAAFCRRFVKVTIN 309
                                        ********999876 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 1
                               TniB  37 nlllvGdsnnGKtmive 53 
                                          l++G+s +GKt +++
  gene2757|gene2757|rna2757|rna2757 581 AFLFLGPSGVGKTELAK 597
                                        57999********9987 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   2.1e-05    0.0083       5      32 ..     176     203 ..     174     213 .. 0.88
   2 !    8.0   0.0    0.0064       2.5       5      24 ..     584     603 ..     581     611 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 2.1e-05
                                        EEC-TTTCHHHHHHHHHHHHCTS-SCCC CS
                              NACHT   5 lqGeaGsGKTtLlqklalawaegklpqg 32 
                                        l G+aG+GKT+ +++la+++a+++ p+ 
  gene2757|gene2757|rna2757|rna2757 176 LVGPAGVGKTAIVCGLAQLIAKDEAPGL 203
                                        89********************999886 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0064
                                        EEC-TTTCHHHHHHHHHHHH CS
                              NACHT   5 lqGeaGsGKTtLlqklalaw 24 
                                          G++G+GKT L++ +a+++
  gene2757|gene2757|rna2757|rna2757 584 FLGPSGVGKTELAKAIAFEL 603
                                        68***************987 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0     4e-05     0.016      24     110 ..     161     251 ..     154     255 .. 0.64
   2 !    7.4   0.0    0.0073       2.9      36      74 ..     582     620 ..     579     630 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 4e-05
                              AAA_7  24 yllelllkn.kkpvllvGptGtGKtviikdllkkldkeky..lsltinfsaqtsanqlqdiiesklekrrkgvyg. 95 
                                         ++e l k+ k + +lvGp+G+GKt+i+  l + + k++   l++    +    ++   + +  ++e r ++v   
  gene2757|gene2757|rna2757|rna2757 161 SIIEILAKKkKSNPMLVGPAGVGKTAIVCGLAQLIAKDEApgLTNYRIYNVDVGSMVANTGVRGEFEERVRKVVKe 236
                                        56666666515678**************998877776554113344445555556666666666666665554431 PP

                              AAA_7  96 PpggkklvvFvDDln 110
                                        +    ++++F+D+++
  gene2757|gene2757|rna2757|rna2757 237 AEECPNIILFIDEIH 251
                                        445567777777775 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0073
                              AAA_7  36 vllvGptGtGKtviikdllkkldkekylsltinfsaqts 74 
                                        +l+ Gp+G+GKt ++k +  +l ++   ++++ +s + +
  gene2757|gene2757|rna2757|rna2757 582 FLFLGPSGVGKTELAKAIAFELFDDAKGMVVLDMSDYAN 620
                                        79**************97666666777777777777665 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.1   2.7e-05     0.011       4      68 ..     155     224 ..     153     269 .. 0.71
   2 ?   -1.3   0.8       4.3   1.7e+03      72     118 ..     438     481 ..     420     510 .. 0.57
   3 ?    5.2   0.0     0.044        17      26      49 ..     585     608 ..     573     628 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.7e-05
                           ATPase_2   4 RekelkeleeilerepneiyfiYGpegsGKtaLlkeiienledkdk.....yviyyialreesiskldef 68 
                                        R+ke++++ eil +++++  ++ Gp g+GKta++  +++   + +      y+iy  ++ +   ++  + 
  gene2757|gene2757|rna2757|rna2757 155 RVKEIRSIIEILAKKKKSNPMLVGPAGVGKTAIVCGLAQLIAKDEApgltnYRIYNVDVGSMVANTGVRG 224
                                        99***********9999999999*********98776666644333455668888887776655555444 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 4.3
                           ATPase_2  72 eeekkklekalgiavpkaeleeilk.eksklvfkaielllekikkkgk 118
                                         +e+++     +i++++a  +e  + ++ k ++ +i+++++ki++ ++
  gene2757|gene2757|rna2757|rna2757 438 IDEARRC----LIPLEEAYEKERASvSEAKALKIKIDQIYNKIEEARR 481
                                        2333333....3333333333333445566666777777777766554 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.044
                           ATPase_2  26 YGpegsGKtaLlkeiienledkdk 49 
                                         Gp g+GKt L k i+ +l d  k
  gene2757|gene2757|rna2757|rna2757 585 LGPSGVGKTELAKAIAFELFDDAK 608
                                        4*************9988855444 PP

>> Clp_N  Clp amino terminal domain, pathogenicity island component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.0   3.3e-07   0.00013       5      26 ..      20      41 ..      16      50 .. 0.89
   2 ?   -0.9   0.1       4.7   1.8e+03      35      52 ..     463     480 ..     453     486 .. 0.77

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 3.3e-07
                                       HHHTTCSSB-HHHHHHHHHHSC CS
                              Clp_N  5 AkslghqyistEHLLlALleed 26
                                       Ak++++ +i++EHLLlAL+e d
  gene2757|gene2757|rna2757|rna2757 20 AKKFKNYQIEPEHLLLALMESD 41
                                       9****************99976 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 4.7
                                        HHTTSSHHHHHHHHHHHH CS
                              Clp_N  35 kkaGvdldalrkaiekll 52 
                                        k++++ +d++ + ie+++
  gene2757|gene2757|rna2757|rna2757 463 KALKIKIDQIYNKIEEAR 480
                                        677788888888888776 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       6.2   2.4e+03      75     120 ..     116     164 ..      15     171 .. 0.57
   2 !   15.8   0.0   2.8e-05     0.011       9      96 ..     181     323 ..     177     356 .. 0.76
   3 ?    4.9   0.0     0.065        25       8      40 ..     588     620 ..     584     829 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 6.2
                                        .EEEEEEEEESS...-TTCHHHHHHHHHHC...TS-EEEEEE--CCHCC CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxx RF
                               CbiA  75 kiagvvlnrvdgeneetllkealeelkqry...gvpvlgviprdeavae 120
                                        k +  v+  v ++++ tl + a+e + ++     +pv+g +++  +++e
  gene2757|gene2757|rna2757|rna2757 116 KKLEAVVRTVSESKTPTLDSVAVEMVHEARttsMDPVIGRVKEIRSIIE 164
                                        3334444444444445555555554443224455555555555555555 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 2.8e-05
                                        TSSHHHHHHHHHHHHHHT......T--EEEEEEEESSCCCCHHTTEB-HHHH........................ CS
                                        xxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxx........................ RF
                               CbiA   9 GvGKTtlaanLaralarr......glrVllvDaDpqannlaileglendiep........................ 54 
                                        GvGKT ++++La+++a++      ++r+  vD++ +  n+ +    e    +                        
  gene2757|gene2757|rna2757|rna2757 181 GVGKTAIVCGLAQLIAKDeapgltNYRIYNVDVGSMVANTGVRGEFE----Ervrkvvkeaeecpniilfideiht 252
                                        9***************9644555579**********99998633333....3333477788888999999999999 PP

                                        ........................CCHCCCHHHHHHCHCHHHH.......EEEEEEEEESS...-TTCHHH CS
                                        ........................xxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxx RF
                               CbiA  55 ........................dlkrllellealgkkkall.....lkiagvvlnrvdgeneetllkea 96 
                                                                 +k ++ + ++ ++k+  +      +++ v +n +  e+++t+l+  
  gene2757|gene2757|rna2757|rna2757 253 visagstsgsldfsnilkpslaagKIKIIGATTHDEYRKYMENdaafcRRFVKVTINEPSVEDSITMLRGL 323
                                        99999999999999999999999888888888888888888888888888888888888888777766544 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.065
                                        TTSSHHHHHHHHHHHHHHTT--EEEEEEEESSC CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               CbiA   8 GGvGKTtlaanLaralarrglrVllvDaDpqan 40 
                                        +GvGKT la ++a+ l ++ +  +++D+   an
  gene2757|gene2757|rna2757|rna2757 588 SGVGKTELAKAIAFELFDDAKGMVVLDMSDYAN 620
                                        9*************9999999999988654444 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.0    0.0019      0.75       6      79 ..     175     256 ..     171     298 .. 0.65
   2 !    8.9   0.0    0.0037       1.5       6      90 ..     583     678 ..     580     700 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0019
                             AAA_14   6 vitGaRrvGKTtll...kqlikell...vkkesilyinldderd.kkla.dpe.kllelileklkeekktylflDE 72 
                                        +++G+  vGKT ++    qli +      ++ +i  +++ +    +  + ++e ++ ++++e  +e  + +lf+DE
  gene2757|gene2757|rna2757|rna2757 175 MLVGPAGVGKTAIVcglAQLIAKDEapgLTNYRIYNVDVGSMVAnTGVRgEFEeRVRKVVKEA-EECPNIILFIDE 249
                                        57899*******983334444444466655566666655554332222233432444555554.3335789***** PP

                             AAA_14  73 iqevpew 79 
                                        i+ v ++
  gene2757|gene2757|rna2757|rna2757 250 IHTVISA 256
                                        **99544 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0037
                             AAA_14   6 vitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpe.....kllelileklke.........ekkty 67 
                                        +  G+  vGKT l+k ++ el+ +++ ++ +++ d  ++  + ++       +  + e   +         +  ++
  gene2757|gene2757|rna2757|rna2757 583 LFLGPSGVGKTELAKAIAFELFDDAKGMVVLDMSDYANEI-SITKllgvsAGYVGYAE---GgaltepvkeKPYNV 654
                                        567999************9999888999999999988843.32222333311222222...133334663234455 PP

                             AAA_14  68 lflDEiqev.pewekalkslvdeg 90 
                                        +++DE   + p++ ++l +l+deg
  gene2757|gene2757|rna2757|rna2757 655 VLFDELDLAhPKVVNVLYQLLDEG 678
                                        99***9976588999999999877 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0       0.1        40      12      37 ..     172     197 ..     166     235 .. 0.86
   2 ?   -1.1   0.0       6.5   2.5e+03      27      52 ..     495     522 ..     493     562 .. 0.77
   3 !   12.8   0.0   0.00034      0.13      16      51 ..     584     620 ..     580     645 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.1
                                        SEEEEEESTTSSHHHHHHHHTTSS-- CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ABC_tran  12 ekvaivGenGaGKStLlkllagllkp 37 
                                        +   +vG+ G GK+ ++  la+l  +
  gene2757|gene2757|rna2757|rna2757 172 SNPMLVGPAGVGKTAIVCGLAQLIAK 197
                                        55679**********99888777655 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 6.5
                                        HHHHHTTSS--SEEEEEETTCEGGG..B CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxx..x RF
                           ABC_tran  27 LlkllagllkpteGeilldgkdlke..q 52 
                                        +l ++ ++lk  eG+il+ ++++ +   
  gene2757|gene2757|rna2757|rna2757 495 VLPVIERKLKEIEGSILITSAHIANviS 522
                                        577899999*******999998887441 PP

  == domain 3  score: 12.8 bits;  conditional E-value: 0.00034
                                        EEESTTSSHHHHHHHHT.TSS--SEEEEEETTCEGGG CS
                                        xxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxx RF
                           ABC_tran  16 ivGenGaGKStLlklla.gllkpteGeilldgkdlke 51 
                                        ++G++G GK+ L+k++a +l ++++G + ld+ d  +
  gene2757|gene2757|rna2757|rna2757 584 FLGPSGVGKTELAKAIAfELFDDAKGMVVLDMSDYAN 620
                                        79**************835567799999999888766 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0     0.027        11       2      44 ..     175     229 ..     175     251 .. 0.69
   2 ?    0.6   0.1         2   7.9e+02      62     108 ..     477     541 ..     414     552 .. 0.55
   3 !   10.5   0.0    0.0017      0.65       3      25 ..     584     612 ..     583     659 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.027
                             AAA_18   2 lltGtpGvGKttlakeLskrlgf............gvnlrdvakenglllevdpe 44 
                                        +l G++GvGKt +   L+++ +              v +++++++ g + e+++ 
  gene2757|gene2757|rna2757|rna2757 175 MLVGPAGVGKTAIVCGLAQLIAKdeapgltnyriyNVDVGSMVANTGVRGEFEER 229
                                        589*********9999977731134444455577777777777777777777666 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 2
                             AAA_18  62 daleenss...................aleegknlvidghlaeleseaakdikkvvLtaspeelle 108
                                        ++ ++n++                   ++ eg+ l+ + h+a+ +s +++di    Lt++++e+l 
  gene2757|gene2757|rna2757|rna2757 477 EEARRNNDtyqvldlqtevlpvierklKEIEGSILITSAHIANVIS-RWTDIPVKRLTLKENERLL 541
                                        2222222244444444444444445433334444444444444444.4555544677777777665 PP

  == domain 3  score: 10.5 bits;  conditional E-value: 0.0017
                             AAA_18   3 ltGtpGvGKttlakeLskrlgf.......g 25 
                                          G++GvGKt+lak+++ +l f       +
  gene2757|gene2757|rna2757|rna2757 584 FLGPSGVGKTELAKAIAFEL-FddakgmvV 612
                                        57*************97765.333443343 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.1    0.0068       2.6       4     102 ..     170     252 ..     167     293 .. 0.63
   2 ?    6.8   0.0     0.019       7.5       9      26 ..     583     600 ..     578     609 .. 0.85
   3 ?   -0.9   0.0       4.8   1.9e+03      84     120 ..     645     677 ..     640     688 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0068
                             AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelkaerlsseell 79 
                                        +++  +++G++G+GKT  +  l++               ++ ++p++t+ +    ++ + + + + +  ++ ee +
  gene2757|gene2757|rna2757|rna2757 170 KKSNPMLVGPAGVGKTAIVCGLAQLI-------------AKDEAPGLTNYRIYNVDVGSMVANTGVR--GEFEERV 230
                                        6677799*********9988888775.............2334555555555555555555555555..5555555 PP

                             AAA_22  80 ealeqalraravielliiDEaqh 102
                                        +++ + ++++    +l iDE++ 
  gene2757|gene2757|rna2757|rna2757 231 RKVVKEAEECPN-IILFIDEIHT 252
                                        666666666666.6666666666 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.019
                             AAA_22   9 vvtGesGtGKTtllrrll 26 
                                        +  G+sG+GKT l++ ++
  gene2757|gene2757|rna2757|rna2757 583 LFLGPSGVGKTELAKAIA 600
                                        667***********9875 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 4.8
                             AAA_22  84 qalraravielliiDEaqhlrseealeeLrsllnlsr 120
                                        + ++++    +++ DE +   ++++++ L +ll+  +
  gene2757|gene2757|rna2757|rna2757 645 EPVKEKPY-NVVLFDELDLA-HPKVVNVLYQLLD--E 677
                                        55566666.899*******9.9999999999998..4 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.0    0.0017      0.67      67     120 ..     139     192 ..     117     201 .. 0.81
   2 !    7.8   0.0    0.0071       2.8     103     120 ..     583     600 ..     578     623 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0017
                                        HHHHHHHHTTSEEEE--TTTHTTHHHHHHHCTTSEEEEECSTTSSHHHHHHHHC CS
                        RsgA_GTPase  67 elkeelealgyevllvsaktkegleelkellkdktsvlvGqSGvGKStLinall 120
                                        e+ +e +++ +++++ ++k+ +++ e+ ++ k++  +lvG+ GvGK++++  l+
  gene2757|gene2757|rna2757|rna2757 139 EMVHEARTTSMDPVIGRVKEIRSIIEILAKKKKSNPMLVGPAGVGKTAIVCGLA 192
                                        455667777788888889988999999999999999***********9987665 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0071
                                        EEECSTTSSHHHHHHHHC CS
                        RsgA_GTPase 103 vlvGqSGvGKStLinall 120
                                        +++G+SGvGK+ L +a++
  gene2757|gene2757|rna2757|rna2757 583 LFLGPSGVGKTELAKAIA 600
                                        79***********99886 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0     0.021       8.3      23      45 ..     172     194 ..     164     200 .. 0.78
   2 ?    7.0   0.0     0.012       4.9      23      43 ..     580     600 ..     573     607 .. 0.84
   3 ?    2.4   0.0      0.34   1.3e+02      36      50 ..     798     812 ..     797     816 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.021
                             AAA_29  23 gatlltGpsGsGKSTllDAiqal 45 
                                        ++ +l+Gp G+GK++++  ++ l
  gene2757|gene2757|rna2757|rna2757 172 SNPMLVGPAGVGKTAIVCGLAQL 194
                                        3789***********99766655 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.012
                             AAA_29  23 gatlltGpsGsGKSTllDAiq 43 
                                        ga+l+ GpsG+GK+ l  Ai+
  gene2757|gene2757|rna2757|rna2757 580 GAFLFLGPSGVGKTELAKAIA 600
                                        689**********99877775 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.34
                             AAA_29  36 STllDAiqalLvpak 50 
                                        ST++DAi+ +++ ++
  gene2757|gene2757|rna2757|rna2757 798 STFMDAIAHIILTDS 812
                                        9******99988766 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.2    0.0027       1.1      37      77 ..     161     198 ..     133     216 .. 0.72
   2 ?   -0.6   0.1       1.5   5.8e+02     258     289 ..     222     252 ..     212     254 .. 0.73
   3 !    8.4   0.0    0.0028       1.1      52      99 ..     581     628 ..     529     631 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0027
                                        XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                              TIP49  37 gvivelikekklaGravLlaGpsgtGktalaiaiskelged 77 
                                        ++i  l k+kk +    +l+Gp+g Gkta+  ++++ +++d
  gene2757|gene2757|rna2757|rna2757 161 SIIEILAKKKK-S--NPMLVGPAGVGKTAIVCGLAQLIAKD 198
                                        44444444444.4..46789****************99865 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.5
                                        XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                              TIP49 258 lreeinkkvakyveegkaeivpGvlfiDevhm 289
                                        +r e ++ v k v+e   e    +lfiDe+h 
  gene2757|gene2757|rna2757|rna2757 222 VRGEFEERVRKVVKEA-EECPNIILFIDEIHT 252
                                        6888888888887653.24444579*****96 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.0028
                                        XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                              TIP49  52 avLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkktevl 99 
                                        a L+ Gpsg Gkt la ai+ el +d + +++     y++e++ t +l
  gene2757|gene2757|rna2757|rna2757 581 AFLFLGPSGVGKTELAKAIAFELFDDAKGMVVLDMSDYANEISITKLL 628
                                        68999******************9988877766666799999887765 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0      0.58   2.3e+02      49      85 ..     132     169 ..     125     173 .. 0.82
   2 ?    3.7   2.3      0.12        47      36      57 ..     174     199 ..     144     258 .. 0.57
   3 !   10.5   0.0   0.00099      0.39      32      58 ..     578     604 ..     551     620 .. 0.86
   4 ?   -2.0   0.0       6.7   2.6e+03      84     111 ..     651     678 ..     643     683 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.58
                             RuvB_N  49 lakiiakelgvklkits.gPvlekagdlaalltnleek 85 
                                            +a e+  + ++ts  Pv+ + +++ +++  l +k
  gene2757|gene2757|rna2757|rna2757 132 TLDSVAVEMVHEARTTSmDPVIGRVKEIRSIIEILAKK 169
                                        5556899*******99956**********999888765 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.12
                             RuvB_N  36 vllyGpPGlGktt....lakiiakel 57 
                                         +l+Gp G+Gkt+    la++iak+ 
  gene2757|gene2757|rna2757|rna2757 174 PMLVGPAGVGKTAivcgLAQLIAKDE 199
                                        47899999999973333567777654 PP

  == domain 3  score: 10.5 bits;  conditional E-value: 0.00099
                             RuvB_N  32 aldhvllyGpPGlGkttlakiiakelg 58 
                                        ++   l+ Gp G+Gkt lak ia el 
  gene2757|gene2757|rna2757|rna2757 578 PIGAFLFLGPSGVGKTELAKAIAFELF 604
                                        556689*****************9985 PP

  == domain 4  score: -2.0 bits;  conditional E-value: 6.7
                             RuvB_N  84 ekdvlfideihrlsraveevlysamedf 111
                                        + +v++ de+   +++v +vly+ +++ 
  gene2757|gene2757|rna2757|rna2757 651 PYNVVLFDELDLAHPKVVNVLYQLLDEG 678
                                        5689999***************988765 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.0    0.0034       1.3      11      49 ..     159     198 ..     148     228 .. 0.75
   2 ?    6.0   0.0     0.018       7.1      25      43 ..     582     600 ..     580     624 .. 0.87
   3 ?    0.8   0.0       0.7   2.7e+02     109     157 ..     654     700 ..     641     734 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0034
                       Mg_chelatase  11 akraleiaaa.GgHnlllvGppGsGKtmlakrlpsllppl 49 
                                         +  +ei a   + n +lvGp+G GKt +   l++l+++ 
  gene2757|gene2757|rna2757|rna2757 159 IRSIIEILAKkKKSNPMLVGPAGVGKTAIVCGLAQLIAKD 198
                                        4556676554156789**************9999998764 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.018
                       Mg_chelatase  25 lllvGppGsGKtmlakrlp 43 
                                        +l++Gp+G GKt lak+++
  gene2757|gene2757|rna2757|rna2757 582 FLFLGPSGVGKTELAKAIA 600
                                        699*************986 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.7
                       Mg_chelatase 109 vLfLDElpefkrkvlevLRePledgevtisrakakvefparfqlvaamN 157
                                        v+++DEl   + kv++vL + l++g+vt  + ++ ++f  ++ +v++ N
  gene2757|gene2757|rna2757|rna2757 654 VVLFDELDLAHPKVVNVLYQLLDEGRVTDGK-RNVIDFT-NTVIVMTSN 700
                                        7788*********************998544.4556664.445555555 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0     0.025       9.8       3      25 ..     176     198 ..     175     219 .. 0.80
   2 !    9.1   0.0    0.0043       1.7       2      24 ..     583     605 ..     582     622 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.025
                       RNA_helicase   3 lyGpsgeGKStlakeLakallkk 25 
                                        l+Gp+g+GK+ ++  La+ ++k+
  gene2757|gene2757|rna2757|rna2757 176 LVGPAGVGKTAIVCGLAQLIAKD 198
                                        89*************99999854 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0043
                       RNA_helicase   2 wlyGpsgeGKStlakeLakallk 24 
                                        ++ Gpsg+GK+ lak +a +l +
  gene2757|gene2757|rna2757|rna2757 583 LFLGPSGVGKTELAKAIAFELFD 605
                                        589*************9988875 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.0   0.00014     0.053      36      97 ..     174     237 ..     140     262 .. 0.71
   2 ?    2.2   0.0      0.29   1.1e+02      37      56 ..     583     602 ..     575     615 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00014
                             AAA_25  36 allaGapgtGKttlaldlalavatGkpwlg..pvapeqgkV.lyvsaEdsedelrrRlravgeal 97 
                                         +l+G+ g+GKt++++ la  +a+++  +g  +++  ++ V  +v++ + + e+++R+r+v +++
  gene2757|gene2757|rna2757|rna2757 174 PMLVGPAGVGKTAIVCGLAQLIAKDE-APGltNYRIYNVDVgSMVANTGVRGEFEERVRKVVKEA 237
                                        48*********************766.67877554555555234555566779999999988776 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.29
                             AAA_25  37 llaGapgtGKttlaldlala 56 
                                        l+ G++g+GKt la  +a++
  gene2757|gene2757|rna2757|rna2757 583 LFLGPSGVGKTELAKAIAFE 602
                                        678**********9888876 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.0   0.00034      0.13      10      46 ..     163     199 ..     158     252 .. 0.81
   2 ?    3.8   0.0       0.1        40      23      50 ..     584     612 ..     580     680 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00034
                             AAA_30  10 vealltsgdrvavltGpAGtGKttalkalreaweaag 46 
                                        +e l+++++   +l+GpAG GKt ++ +l++++++++
  gene2757|gene2757|rna2757|rna2757 163 IEILAKKKKSNPMLVGPAGVGKTAIVCGLAQLIAKDE 199
                                        5566777777889*****************9998874 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.1
                             AAA_30  23 ltGpAGtGKttalkal.reaweaaggrvi 50 
                                          Gp G GKt + ka+  e++++a+g v+
  gene2757|gene2757|rna2757|rna2757 584 FLGPSGVGKTELAKAIaFELFDDAKGMVV 612
                                        579************96678877754444 PP

>> Bac_DnaA  Bacterial dnaA  protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0      0.06        23      31     111 ..     169     255 ..     156     351 .. 0.63
   2 !    9.6   0.0    0.0019      0.75      31      70 ..     576     615 ..     568     624 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.06
                                        TT.S--EEEE-SSSSSHHHHHHHHHHHHHHHSS....SS-EEEEEHHHHH.HHHHHHHHTT-HHHHHHHH..TT-S CS
                           Bac_DnaA  31 gkkynPlfiygevGlGktHLlkaignevlenap....elrvvYltaeeFl.nelvkalrdkkaeefkekl..rkvD 99 
                                        +kk nP+++ g+ G+Gkt ++  +++ + +++     + r+  +   + + n+ v+   ++++++  ++   + + 
  gene2757|gene2757|rna2757|rna2757 169 KKKSNPMLV-GPAGVGKTAIVCGLAQLIAKDEApgltNYRIYNVDVGSMVaNTGVRGEFEERVRKVVKEAeeCPNI 243
                                        457899876.*********999999888877641121455555544433313334333333333322222013445 PP

                                        EEEEE-GGGGTT CS
                           Bac_DnaA 100 vLliDDiqflag 111
                                        +L iD+i+ + +
  gene2757|gene2757|rna2757|rna2757 244 ILFIDEIHTVIS 255
                                        677777776654 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0019
                                        TT.S--EEEE-SSSSSHHHHHHHHHHHHHHHSSSS-EEEE CS
                           Bac_DnaA  31 gkkynPlfiygevGlGktHLlkaignevlenapelrvvYl 70 
                                        ++    +++ g++G+Gkt L kai+ e+ ++a+ + v+ +
  gene2757|gene2757|rna2757|rna2757 576 DRPIGAFLFLGPSGVGKTELAKAIAFELFDDAKGMVVLDM 615
                                        5555667899******************999999887655 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.0    0.0043       1.7      12      50 ..     159     197 ..     149     202 .. 0.86
   2 ?   -0.9   0.0       3.5   1.4e+03     133     147 ..     242     256 ..     217     307 .. 0.75
   3 ?    3.5   0.0      0.16        63      26      53 ..     581     608 ..     547     617 .. 0.70

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0043
                                        HHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S CS
                             ResIII  12 ienlleklkskrdkrglikmaTGtGKTlvaaklierllk 50 
                                        i++++e l +k++ + +++ + G+GKT + + l++ ++k
  gene2757|gene2757|rna2757|rna2757 159 IRSIIEILAKKKKSNPMLVGPAGVGKTAIVCGLAQLIAK 197
                                        7788888887899999**************999988776 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 3.5
                                        -SEEEEETGGGTTS. CS
                             ResIII 133 fdviiiDEaHrlgak 147
                                        + +++iDE H + ++
  gene2757|gene2757|rna2757|rna2757 242 NIILFIDEIHTVISA 256
                                        348999999988774 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.16
                                        EEEEEESTTSTHHHHHHHHHHHH-S... CS
                             ResIII  26 rglikmaTGtGKTlvaaklierllkkgk 53 
                                         +l+  + G+GKT +a +++ +l+  +k
  gene2757|gene2757|rna2757|rna2757 581 AFLFLGPSGVGKTELAKAIAFELFDDAK 608
                                        6788999***********9999998654 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0      0.17        65       6      21 ..     175     190 ..     170     256 .. 0.75
   2 !    9.8   0.0    0.0015      0.58       6      79 ..     583     665 ..     581     685 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.17
                             AAA_24   6 liyGpsgiGKTtlake 21 
                                        +++Gp+g+GKT ++  
  gene2757|gene2757|rna2757|rna2757 175 MLVGPAGVGKTAIVCG 190
                                        899********88755 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0015
                             AAA_24   6 liyGpsgiGKTtlakelgpkplfidtekGlksldadkfpdieswedfldevvel...........aaeladyktlv 70 
                                        l  Gpsg+GKT lak +   + ++d  kG+  ld  ++ +  s++++l   +             + ++++y+++ 
  gene2757|gene2757|rna2757|rna2757 583 LFLGPSGVGKTELAKAI--AFELFDDAKGMVVLDMSDYANEISITKLLGVSAGYvgyaeggaltePVKEKPYNVVL 656
                                        568**************..666667777888888888776667777777666667888999999888888899999 PP

                             AAA_24  71 iDtidelee 79 
                                        +D +d +  
  gene2757|gene2757|rna2757|rna2757 657 FDELDLAHP 665
                                        999987655 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0     0.048        19       3      20 ..     175     192 ..     174     217 .. 0.84
   2 !    7.9   0.0    0.0086       3.4       3      28 ..     583     608 ..     582     626 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.048
                                        EEESSTTSSHHHHHHCHC CS
                                Roc   3 vlvGdsgvGKtsllkrfv 20 
                                        +lvG +gvGKt ++  + 
  gene2757|gene2757|rna2757|rna2757 175 MLVGPAGVGKTAIVCGLA 192
                                        79**********997655 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0086
                                        EEESSTTSSHHHHHHCHCT-CCC-EE CS
                                Roc   3 vlvGdsgvGKtsllkrfvedkfseke 28 
                                        +++G sgvGKt l+k +  + f++ +
  gene2757|gene2757|rna2757|rna2757 583 LFLGPSGVGKTELAKAIAFELFDDAK 608
                                        689************99988887664 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.0    0.0018      0.69       5      28 ..     175     198 ..     171     205 .. 0.88
   2 ?    3.3   0.0      0.14        53       4      29 ..     582     607 ..     580     619 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0018
                                        EEEESTTSSHHHHHHHHHHHHHHT CS
                              SRP54   5 llvGlqGaGKTttlaKLaallkke 28 
                                        +lvG+ G+GKT  +  La+l+ k+
  gene2757|gene2757|rna2757|rna2757 175 MLVGPAGVGKTAIVCGLAQLIAKD 198
                                        9*****************999876 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.14
                                        EEEEESTTSSHHHHHHHHHHHHHHTT CS
                              SRP54   4 illvGlqGaGKTttlaKLaallkkeg 29 
                                        +l++G+ G+GKT  +  +a  l +++
  gene2757|gene2757|rna2757|rna2757 582 FLFLGPSGVGKTELAKAIAFELFDDA 607
                                        699*********99888887666654 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.1       8.5   3.3e+03     100     142 ..      51      93 ..       7     173 .. 0.51
   2 ?    5.1   5.8     0.073        29      25     200 .]     177     477 ..     174     477 .. 0.42
   3 !   12.0   0.0   0.00057      0.22      20      53 ..     580     613 ..     576     765 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 8.5
                             AAA_23 100 kgkttkkaklelleideleqfisellgskkiilnlilflgqer 142
                                         +++ +++++ + +id+l +  ++   +  +++++ l  +q++
  gene2757|gene2757|rna2757|rna2757  51 REEKSRMKTELIRRIDTLAKGNESTTPNPSSRFTNMLQDAQGN 93 
                                        3334444444444444444444444444444555555555554 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.073
                             AAA_23  25 tGpNGaGKTTildAiklaL.ygetprlsrks......grgfeksdveiesegkvkayveltfenkdgry....... 86 
                                        +Gp G GKT+i++ +       e+p+l + +      g+   +  v+ e+e+ v+++v+         +       
  gene2757|gene2757|rna2757|rna2757 177 VGPAGVGKTAIVCGLAQLIaKDEAPGLTNYRiynvdvGSMVANTGVRGEFEERVRKVVKEA-------Eecpniil 245
                                        6777777777777777555245556666655444444222222222222221111111111.......11222222 PP

                             AAA_23  87 ............................................................................ 86 
                                                                                                                    
  gene2757|gene2757|rna2757|rna2757 246 fideihtvisagstsgsldfsnilkpslaagkikiigatthdeyrkymendaafcrrfvkvtinepsvedsitmlr 321
                                        2222223333333333333333333345555555555555555555555555555555544444444444444444 PP

                             AAA_23  87 ...........................trsiererelskkkgkttkkaklelleideleqfisellgskki.il.n 133
                                                                   +++ +r+ + +  +           ++++    +i+ + + ++i ++ n
  gene2757|gene2757|rna2757|rna2757 322 glrnkmelhhgikiedsaivfsvkmakKYIPSRRLPDIAIDL----------VDTACASATIELESEPQEImNMkN 387
                                        444444444433333222222222222122222222111111..........111111111111111111111111 PP

                             AAA_23 134 lilflgqerfeefel......................kdkkerleelekeleeled.ekkllekleqekekekele 186
                                         i  l  er++ +++                      k++kerl+e+e +++e+    + l e+ e+e     e +
  gene2757|gene2757|rna2757|rna2757 388 KIWSLELERAAIERDykiksgadgkqgdaahpekgygKETKERLNEVEAKIDEARRcLIPLEEAYEKERASVSEAK 463
                                        111111111111111222222222222233333347777888***********99978888888899999999*** PP

                             AAA_23 187 eleeeleeilkele 200
                                        +l+ ++ +i +++e
  gene2757|gene2757|rna2757|rna2757 464 ALKIKIDQIYNKIE 477
                                        *********99997 PP

  == domain 3  score: 12.0 bits;  conditional E-value: 0.00057
                             AAA_23  20 gltlItGpNGaGKTTildAiklaLygetprlsrk 53 
                                        g +l+ Gp G GKT +  Ai + L+ +++++   
  gene2757|gene2757|rna2757|rna2757 580 GAFLFLGPSGVGKTELAKAIAFELFDDAKGMVVL 613
                                        679***********************99887665 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.0    0.0062       2.4       5      43 ..     157     195 ..     154     213 .. 0.81
   2 ?    5.1   0.0     0.054        21      22      42 ..     582     602 ..     552     610 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0062
                                        HHHHHHHHHHHHCHTEEEEEEESTTSSHHHHHHHHHHHT CS
                               TsaE   5 eetealgkklakalgdvilLeGdLGaGKTtlvrglakal 43 
                                        +e++++ + lak+ ++  +L G+ G+GKT++v gla+ +
  gene2757|gene2757|rna2757|rna2757 157 KEIRSIIEILAKKKKSNPMLVGPAGVGKTAIVCGLAQLI 195
                                        567777788888778889****************99876 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.054
                                        EEEEESTTSSHHHHHHHHHHH CS
                               TsaE  22 ilLeGdLGaGKTtlvrglaka 42 
                                        +l+ G+ G+GKT l++++a +
  gene2757|gene2757|rna2757|rna2757 582 FLFLGPSGVGKTELAKAIAFE 602
                                        7889*************9866 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0     0.082        32       3      20 ..     175     192 ..     174     236 .. 0.89
   2 !    9.1   0.0    0.0035       1.4       3      32 ..     583     617 ..     582     693 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.082
                             AAA_33   3 llvGlpGsGKstlaerll 20 
                                        +lvG++G+GK+  + +l+
  gene2757|gene2757|rna2757|rna2757 175 MLVGPAGVGKTAIVCGLA 192
                                        79*********9988877 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0035
                             AAA_33   3 llvGlpGsGKstlaerllkklg.....avllssdt 32 
                                        l+ G++G+GK+ la+ ++ +l      +v+l+  +
  gene2757|gene2757|rna2757|rna2757 583 LFLGPSGVGKTELAKAIAFELFddakgMVVLDMSD 617
                                        799************99877766667777777655 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0     0.026        10      12      40 ..     162     192 ..     152     205 .. 0.71
   2 ?    6.8   0.0     0.011       4.2      24      47 ..     584     607 ..     578     660 .. 0.91

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.026
                                        HHHHHH..H-SEEEEE--TTSSTTHHHHHHH CS
                               PhoH  12 ylealk..kndivfaiGpaGtGKtylavala 40 
                                        ++e+l   k++  + +GpaG GKt + + la
  gene2757|gene2757|rna2757|rna2757 162 IIEILAkkKKSNPMLVGPAGVGKTAIVCGLA 192
                                        5666664455577899********8755444 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.011
                                        EE--TTSSTTHHHHHHHHHHHHTT CS
                               PhoH  24 aiGpaGtGKtylavalavealkkk 47 
                                         +Gp+G GKt la a+a+e++ + 
  gene2757|gene2757|rna2757|rna2757 584 FLGPSGVGKTELAKAIAFELFDDA 607
                                        68****************998765 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0       2.1   8.2e+02       4      24 ..     176     196 ..     174     201 .. 0.85
   2 ?   11.1   0.0   0.00067      0.26      63     114 ..     652     704 ..     582     725 .. 0.65

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 2.1
                              AAA_3   4 legvPGlaktllvkalakald 24 
                                        l g  G++kt +v  la+ + 
  gene2757|gene2757|rna2757|rna2757 176 LVGPAGVGKTAIVCGLAQLIA 196
                                        66788************9986 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00067
                              AAA_3  63 anllladeinrappktqsalleameerqvtveget.hklpepflvlatqnPie 114
                                         n++l de++ a pk+   l + ++e +vt ++++  ++ ++ +v++ +   e
  gene2757|gene2757|rna2757|rna2757 652 YNVVLFDELDLAHPKVVNVLYQLLDEGRVTDGKRNvIDFTNTVIVMTSNLGYE 704
                                        489***************************87655145666666665544444 PP

>> DNA_pol3_delta2  DNA polymerase III, delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       6.5   2.5e+03      12      44 ..     165     196 ..     107     204 .. 0.74
   2 ?   -1.2   0.1         4   1.5e+03      81      97 ..     455     481 ..     369     485 .. 0.72
   3 ?    9.7   0.0    0.0017      0.66      16      48 ..     576     608 ..     566     623 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 6.5
                    DNA_pol3_delta2  12 alksgrlahayLfeGdegigkkelalnlakall 44 
                                        +l++++ ++  ++ G++g+gk ++   la+ + 
  gene2757|gene2757|rna2757|rna2757 165 ILAKKKKSNP-MLVGPAGVGKTAIVCGLAQLIA 196
                                        3444443333.4457788888877777777765 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 4
                    DNA_pol3_delta2  81 r..........sikldqirelieelsr 97 
                                        +          +ik+dqi + iee+ r
  gene2757|gene2757|rna2757|rna2757 455 ErasvseakalKIKIDQIYNKIEEARR 481
                                        033333333339999999998888765 PP

  == domain 3  score: 9.7 bits;  conditional E-value: 0.0017
                    DNA_pol3_delta2  16 grlahayLfeGdegigkkelalnlakallceek 48 
                                        +r   a+Lf G++g+gk ela+++a +l+ + k
  gene2757|gene2757|rna2757|rna2757 576 DRPIGAFLFLGPSGVGKTELAKAIAFELFDDAK 608
                                        566679*******************99998766 PP

>> AAA_6  Hydrolytic ATP binding site of dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0     0.056        22      34      58 ..     173     197 ..     151     200 .. 0.84
   2 ?    6.1   0.0     0.012       4.8      38      78 ..     585     628 ..     579     636 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.056
                              AAA_6  34 ggapaGpagtGKtEtvkdLakalak 58 
                                           + Gpag GKt  v  La+ +ak
  gene2757|gene2757|rna2757|rna2757 173 NPMLVGPAGVGKTAIVCGLAQLIAK 197
                                        45678**************999987 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.012
                              AAA_6  38 aGpagtGKtEtvkdLakal...akqvvvfncsdqldykslgkif 78 
                                         Gp+g GKtE  k +a +l   ak +vv++ sd  +  s++k++
  gene2757|gene2757|rna2757|rna2757 585 LGPSGVGKTELAKAIAFELfddAKGMVVLDMSDYANEISITKLL 628
                                        6***************9997778899999999998888888765 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.2     0.029        11     115     211 ..       7     105 ..       4     119 .. 0.86
   2 ?   -1.5   0.0       5.8   2.3e+03      29      51 ..     177     198 ..     176     204 .. 0.81
   3 ?   -1.8   0.3       7.1   2.8e+03     156     199 ..     453     482 ..     416     523 .. 0.53
   4 ?   11.6   0.1   0.00055      0.22      29      61 ..     585     616 ..     581     631 .. 0.91

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.029
                              DUF87 115 avqrsvleealdqaka.......keekeklssdepveklleelkkekeelrklknqaiarlldkledllrkggsf. 182
                                        ++ ++vle+ +++ak+       +e+   +  ++ ++ l+++l       r++k++ + +l+++++ l + ++s  
  gene2757|gene2757|rna2757|rna2757   7 STAQKVLERSFSTAKKfknyqiePEHLLLALMESDIPVLEKNLT------REEKSRMKTELIRRIDTLAKGNESTt 76 
                                        678899********999998888777777888888887888888......99999999999999999999999998 PP

                              DUF87 183 snsstdliallleklekegkitiidlsgv 211
                                         n s++++++l +  ++++ ++ idl g 
  gene2757|gene2757|rna2757|rna2757  77 PNPSSRFTNMLQDAQGNKEGVSEIDLLGA 105
                                        999999***********999999999875 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 5.8
                              DUF87  29 lgsTGsGKSntvavLleellekk 51 
                                        +g +G+GK+  v+ L + ++ k+
  gene2757|gene2757|rna2757|rna2757 177 VGPAGVGKTAIVCGLAQLIA-KD 198
                                        5789*********9999988.44 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 7.1
                              DUF87 156 elrklknqaiarlldkledllrkggsfsnsstdliallleklek 199
                                        e ++++ + +++l+ k++++ +k ++                 +
  gene2757|gene2757|rna2757|rna2757 453 EKERASVSEAKALKIKIDQIYNKIEEA--------------RRN 482
                                        333333333333333333333333333..............222 PP

  == domain 4  score: 11.6 bits;  conditional E-value: 0.00055
                              DUF87  29 lgsTGsGKSntvavLleellekkgatililDpH 61 
                                        lg +G+GK+ +++ +  el  ++   +++lD+ 
  gene2757|gene2757|rna2757|rna2757 585 LGPSGVGKTELAKAIAFELF-DDAKGMVVLDMS 616
                                        899*****************.9999******94 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0    0.0095       3.7       4      37 ..     158     188 ..     155     239 .. 0.85
   2 ?    3.4   0.0     0.093        36      24      41 ..     583     600 ..     558     625 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0095
                                        HHHHHHHHHHCTTTSCSEEEEEEESTTSSHHHHH CS
                             NB-ARC   4 svekviekLlekdelqslvvalvGmgGvGKttla 37 
                                        +++ +ie L +k++++     lvG +GvGKt ++
  gene2757|gene2757|rna2757|rna2757 158 EIRSIIEILAKKKKSN---PMLVGPAGVGKTAIV 188
                                        6788999999887777...6799********985 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.093
                                        EEEESTTSSHHHHHHHHC CS
                             NB-ARC  24 alvGmgGvGKttlakqil 41 
                                         + G  GvGKt lak i 
  gene2757|gene2757|rna2757|rna2757 583 LFLGPSGVGKTELAKAIA 600
                                        467***********9985 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0       0.1        40       6      28 ..     176     198 ..     174     203 .. 0.85
   2 ?   -0.2   0.4       1.1   4.3e+02     129     245 ..     363     476 ..     304     508 .. 0.60
   3 ?    6.0   0.0     0.015       5.9       4      36 ..     582     614 ..     580     624 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.1
                                        EEESTTSSHHHHHHHHHHHHHHT CS
                        ArsA_ATPase   6 vgGKGGVGKttvsaatavklsek 28 
                                        + G  GVGKt++ + +a  +++ 
  gene2757|gene2757|rna2757|rna2757 176 LVGPAGVGKTAIVCGLAQLIAKD 198
                                        56888************988876 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 1.1
                                        EEESBSCCHTCGGGGHHHHHHHHHHHHHHHHHHHHHHHHHHCCCSHCHHHHHH...HHHHHHHHHHHHHHHHHHHH CS
                        ArsA_ATPase 129 vlDtaPTGhtlrllslpevleklleklvklkeklsplakqlvkllglggvsie...ealeeleetkeeikkveeil 201
                                        ++Dta    t+ l s p+ + ++ +k+ +l+ +   + +  +  +g+ g++ +       + +etke++++ve+ +
  gene2757|gene2757|rna2757|rna2757 363 LVDTACASATIELESEPQEIMNMKNKIWSLELERAAIERDYKIKSGADGKQGDaahPEKGYGKETKERLNEVEAKI 438
                                        4789999999999999999888888888887755555555543333333333322123345577788888877777 PP

                                        TSTTTEEEEEEEESSHHHHHHHHHH.HHHHHHTT-EEEEEEEEEE CS
                        ArsA_ATPase 202 tdpertsfrlVvipEklslkEteRa.ikeLkkygikvdavivNkl 245
                                         +  r    + +  E+   +E eRa ++e k ++ik+d++  Nk+
  gene2757|gene2757|rna2757|rna2757 439 DEARR----CLIPLEEA--YEKERAsVSEAKALKIKIDQI-YNKI 476
                                        55555....44444443..566665256666677777764.4554 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.015
                                        EEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE CS
                        ArsA_ATPase   4 ilvgGKGGVGKttvsaatavklsekgkkvllis 36 
                                        +l+ G  GVGKt ++ a+a +l +  k ++++ 
  gene2757|gene2757|rna2757|rna2757 582 FLFLGPSGVGKTELAKAIAFELFDDAKGMVVLD 614
                                        5788999***************99999988874 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.1      0.11        44       4      26 ..     176     198 ..     173     204 .. 0.85
   2 ?    0.2   0.1       1.5     6e+02      79     104 ..     224     250 ..     207     253 .. 0.75
   3 ?    3.7   0.0      0.13        51       6      23 ..     586     603 ..     581     617 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.11
                                        EE--TTSSHHHHHHHHHHHH... CS
                           NTPase_1   4 iTGppGvGKtTlvkkvlellkss 26 
                                        + Gp GvGKt +v  +++l++++
  gene2757|gene2757|rna2757|rna2757 176 LVGPAGVGKTAIVCGLAQLIAKD 198
                                        78***********9999988765 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 1.5
                                        HHHHHHHHHHHHHHHHHH-.EEEE--- CS
                           NTPase_1  79 esfeelalealrkalsead.viviDEi 104
                                         +fee + +++++a + ++ ++ iDEi
  gene2757|gene2757|rna2757|rna2757 224 GEFEERVRKVVKEAEECPNiILFIDEI 250
                                        46999999999999888886678***9 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.13
                                        --TTSSHHHHHHHHHHHH CS
                           NTPase_1   6 GppGvGKtTlvkkvlell 23 
                                        Gp+GvGKt l k ++ +l
  gene2757|gene2757|rna2757|rna2757 586 GPSGVGKTELAKAIAFEL 603
                                        9***********998776 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0      0.86   3.4e+02       4      22 ..     176     194 ..     174     245 .. 0.71
   2 ?    8.1   0.0    0.0077         3       2      34 ..     582     622 ..     581     628 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.86
                             AAA_28   4 itGgestGKTtlleaLaar 22 
                                        ++G+ + GKT ++  La+ 
  gene2757|gene2757|rna2757|rna2757 176 LVGPAGVGKTAIVCGLAQL 194
                                        79**********9999953 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0077
                             AAA_28   2 ivitGgestGKTtlleaLa......argypvv..pEaarei 34 
                                        + ++G+++ GKT l++a+a      a+g++v+   ++a ei
  gene2757|gene2757|rna2757|rna2757 582 FLFLGPSGVGKTELAKAIAfelfddAKGMVVLdmSDYANEI 622
                                        5799***************8777655588887667777776 PP

>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0       1.7   6.8e+02      30     103 ..      90     166 ..      80     177 .. 0.63
   2 ?    1.0   0.1      0.62   2.4e+02      11      55 ..     178     221 ..     170     239 .. 0.76
   3 ?    7.3   0.0    0.0072       2.8      13      61 ..     588     638 ..     583     661 .. 0.75

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 1.7
                               ParA  30 kkglkvgllDaDiyGpsiprllgvee.ekpeqsekkliPveakgikvmSigflle...sedeavvwrGpmkskaik 101
                                        ++g k g+  +D+ G  i   +++e+ +k e+  +++   ++ ++  + ++++ e   ++ ++v+ r   + ++i+
  gene2757|gene2757|rna2757|rna2757  90 AQGNKEGVSEIDLLGAAIKC-VQIEGtKKLEAVVRTVSESKTPTLDSVAVEMVHEartTSMDPVIGRVKEIRSIIE 164
                                        789999999******99965.4455413344444445555556666666666665111345667777666666666 PP

                               ParA 102 ql 103
                                         l
  gene2757|gene2757|rna2757|rna2757 165 IL 166
                                        55 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.62
                               ParA  11 gKGGVGKStvavnlAlaLakkglkvgllDaDiyGpsiprllgvee 55 
                                        g  GVGK+ + + lA  +ak + + gl    iy  ++ +++  ++
  gene2757|gene2757|rna2757|rna2757 178 GPAGVGKTAIVCGLAQLIAK-DEAPGLTNYRIYNVDVGSMVANTG 221
                                        667************87765.556788888888888888776555 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.0072
                               ParA  13 GGVGKStvavnlAlaLakkglkvgllDaDiyG..psiprllgveeekpeqs 61 
                                         GVGK+ +a  +A++L +  + + +lD+  y    si +llgv+   +   
  gene2757|gene2757|rna2757|rna2757 588 SGVGKTELAKAIAFELFDDAKGMVVLDMSDYAneISITKLLGVSAGYVGYA 638
                                        5**************************966651258899999987655444 PP

>> DUF16  Protein of unknown function DUF16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.1       6.7   2.6e+03      17      65 ..      15      63 ..       4     130 .. 0.65
   2 ?   10.2   1.1    0.0021      0.81      28     104 .]     423     508 ..     412     508 .. 0.58

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 6.7
                                       TTB-BHHHHHHB-...BHHHHHHHHHHHH...HHHHHHHHHHHHHHHHHH CS
                              DUF16 17 teYVTrkqlnefkds.nkqrLkkieakvdklgeqinkleqkvekqgekik 65
                                         + T k++++++ +     L  +e  + +l++++ + e+k + ++e i+
  gene2757|gene2757|rna2757|rna2757 15 RSFSTAKKFKNYQIEpEHLLLALMESDIPVLEKNLTR-EEKSRMKTELIR 63
                                       5677778888777663223334455555555555443.333333344443 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0021
                                        B-..BHHHHHHHHHHHH...HHHHHHHHHHHHHHHHHHH...HHHHHHHHHH.............HHHHHHHHHHH CS
                              DUF16  28 fkdsnkqrLkkieakvdklgeqinkleqkvekqgekike...lkveqkaqgeeln......kvdetleliletLqk 94 
                                        + +++k+rL+++eak+d     +  le++ ek  + ++e   lk ++++  ++++         + l+l  e L  
  gene2757|gene2757|rna2757|rna2757 423 YGKETKERLNEVEAKIDEARRCLIPLEEAYEKERASVSEakaLKIKIDQIYNKIEearrnnDTYQVLDLQTEVLPV 498
                                        7889*************55555555555555555555331112223333333333444333444556666677777 PP

                                        HHHHHHHHC- CS
                              DUF16  95 inkRlDsieg 104
                                        i+ +l +ieg
  gene2757|gene2757|rna2757|rna2757 499 IERKLKEIEG 508
                                        7777777765 PP

>> TcpS  Toxin-coregulated pilus protein S
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.0     0.014       5.3      28      62 ..     376     410 ..     360     417 .. 0.84
   2 ?    0.9   0.4       1.1   4.3e+02      45      81 ..     426     465 ..     424     481 .. 0.66
   3 ?   -1.1   0.3       4.4   1.7e+03      22      63 ..     474     516 ..     459     538 .. 0.62
   4 ?   -1.7   0.1       6.8   2.6e+03      80     106 ..     653     677 ..     644     699 .. 0.67

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.014
                               TcpS  28 ennyksiesLknkleqLeLkkkileveieikeaed 62 
                                        e + ++i ++knk+  LeL++   e + +ik + d
  gene2757|gene2757|rna2757|rna2757 376 ESEPQEIMNMKNKIWSLELERAAIERDYKIKSGAD 410
                                        56678899**********************99876 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 1.1
                               TcpS  45 eLkkkileveieikeaedklqP...kvskaipvlskpkav 81 
                                        e k +++eve +i ea+  l P     +k  + +s++ka 
  gene2757|gene2757|rna2757|rna2757 426 ETKERLNEVEAKIDEARRCLIPleeAYEKERASVSEAKAL 465
                                        66889999******99999988322344555556656653 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 4.4
                               TcpS  22 delevyennyksiesLknkleqLe.Lkkkileveieikeaedk 63 
                                        +++e  + n  + + L  + e+L  +++k++e+e+ i+ ++  
  gene2757|gene2757|rna2757|rna2757 474 NKIEEARRNNDTYQVLDLQTEVLPvIERKLKEIEGSILITSAH 516
                                        4444444444455555555666642577888888887766644 PP

  == domain 4  score: -1.7 bits;  conditional E-value: 6.8
                               TcpS  80 avvkvellkeiesfdekLvkLly.Lvgn 106
                                         vv   l +e +   +k+v++ly L ++
  gene2757|gene2757|rna2757|rna2757 653 NVV---LFDELDLAHPKVVNVLYqLLDE 677
                                        444...7899999999999999933343 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (847 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1061  (0.0591779); expected 358.6 (0.02)
Passed bias filter:                      735  (0.040995); expected 358.6 (0.02)
Passed Vit filter:                       111  (0.00619109); expected 17.9 (0.001)
Passed Fwd filter:                        46  (0.00256568); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              46  [number of targets reported over threshold]
# CPU time: 0.90u 0.33s 00:00:01.23 Elapsed: 00:00:00.48
# Mc/sec: 5291.97
//
Query:       gene2758|gene2758|rna2758|rna2758  [L=479]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      6e-71  239.1   0.4    7.6e-71  238.8   0.4    1.1  1  tRNA-synt_2      tRNA synthetases class II (D, K and N)
    1.2e-06   28.4   0.2    3.5e-06   26.9   0.0    2.0  2  tRNA_anti-codon  OB-fold nucleic acid binding domain


Domain annotation for each model (and alignments):
>> tRNA-synt_2  tRNA synthetases class II (D, K and N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  238.8   0.4   8.5e-75   7.6e-71       3     312 ..     157     472 ..     155     474 .. 0.94

  Alignments for each domain:
  == domain 1  score: 238.8 bits;  conditional E-value: 8.5e-75
                                        CHHHHTHHHHCCSHHHHHHHHHHHHHHHHHHHHHHHTT-EE----SEESS--SSSS--EEEEETTT.TEEE....- CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....x RF
                        tRNA-synt_2   3 elrlknryldlrtekvskvlrlrstvtkavrkyleengfieietPiLsksdteegarlFkvksrekekeff....a 74 
                                        + rl++r+ldlr    ++++r+  +++  +r++l +++f+ei+tP L  s++e+ga+lF v       +ff    +
  gene2758|gene2758|rna2758|rna2758 157 NKRLDYRVLDLRGTMSQSIFRIIDQIMFTFRTFLRNEKFVEIKTPKLLGSASEGGANLFEV-------NFFkkkaY 225
                                        5799*********************************************************.......55555556 PP

                                        E-S-SHHHHHHHHHCTHSEEEEEEEEE--S--BTTB-S-CEEEEEEEEET-SCHHHHHHHHHHHHHHHHHHHHCSC CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        tRNA-synt_2  75 LtqspqlylellivagidrvfqiaraFRaEdsrtdrhlaEFtqieaemsfieeedimqvleelikslvkevlessa 150
                                        L+qspqly+++ i++ + rv++i++++RaE+s+ +r l+EF+ +++em+ +++ + ++++  +++ ++++v e+++
  gene2758|gene2758|rna2758|rna2758 226 LAQSPQLYKQMAIIGNLRRVYEIGHVYRAEESNINRYLSEFIGLDLEMESTDYLKTIRMIYSMLCAIIRDVYENNR 301
                                        ***************************************************************************9 PP

                                        CCCCHTTTTTS...EE-SSS-EEEEHHHHHHHHHTS-SS--HHH..HHHHHH........HS--SEEEEEEEBGGG CS
                                        xxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxx........xxxxxxxxxxxxxxxx RF
                        tRNA-synt_2 151 kdiefvirrns...kdlkkpfkrltykeaieklneigkdldkad..eralvk........keknepvfvtdfPael 213
                                        +d+e+  + n      ++++   l+++e +++l+e+g+d++ +d   r++ k        ++k +++ v d+P   
  gene2758|gene2758|rna2758|rna2758 302 QDVENLRKYNDfedLRFEDEPLILSHRECVDILKEHGEDIKYEDdfSRFMEKrlgtiiaeTKKIDFFVVKDYPTRN 377
                                        99999988875544444444559***************99988834588888999999999999************ PP

                                        STTCBBBSTTSTTBBSEEEEEETTEEEEEEEEB--SHHHHHHHHHHCCHHSSSGGGGHHHHHHHHCT--SEEEEEE CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        tRNA-synt_2 214 kpFyarkeeddkkltesyDllingvElvgGslRiedpeeleeklkskgldeeaeekfswylealeyGapphgGlgl 289
                                        +pFy+  + d +  ++syD++++g E+++G++Ri+++e+l+++  ++g+d   + +++ yl a++yGapph+G+g+
  gene2758|gene2758|rna2758|rna2758 378 RPFYTATCAD-PFYSKSYDFILRGEEILSGAQRINSYEQLRQSAINNGID---PVSIEGYLGAFKYGAPPHAGCGI 449
                                        **********.9**************************************...*********************** PP

                                        EHHHHHHHHCT-SSGGGCSSS-X CS
                                        xxxxxxxxxxxxxxxxxxxxxxx RF
                        tRNA-synt_2 290 GldRlvmlllgsesIrdviaFPk 312
                                        Gl+R+   l gs++Ir   +FP+
  gene2758|gene2758|rna2758|rna2758 450 GLERFAKALFGSSDIRCFNIFPR 472
                                        **********************8 PP

>> tRNA_anti-codon  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.9   0.0   3.9e-10   3.5e-06       2      76 .]      47     131 ..      46     131 .. 0.90
   2 ?   -3.0   0.0      0.82   7.3e+03      21      55 ..     162     199 ..     155     200 .. 0.69

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 3.9e-10
                                        EEEEEEEEEEEEEETTEEEEEEEETTEEEEEEEET.....HHHHHHHTTS-TTSEEEEEEEEEECTTS.......S CS
                    tRNA_anti-codon   2 tvaGrvtsisdrsggkvifidlrDgtgriqvvlfr.....eeatklaenlkeGdvvrvtGrvkrrpgg.......e 65 
                                         v+G v s+  ++  k+ f++lr g  r+q+v++      ee + +   +  +++vr+tG +k+  +        +
  gene2758|gene2758|rna2758|rna2758  47 EVHGFVESM--KNFPKFGFLTLRAGVCRLQCVFNLggkvdEEHFTQICGVSLESYVRITGVLKKAHKPikscsvsK 120
                                        58999****..************************9987777777777788**************77777889999 PP

                                        EEEEEEEEEEE CS
                    tRNA_anti-codon  66 lelkveeiell 76 
                                        +el v+e+e+l
  gene2758|gene2758|rna2758|rna2758 121 YELEVSELEVL 131
                                        *******9986 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 0.82
                                        EEEEETTEEEEEEEET...HHHHHHHTTS-TTSEEEEE CS
                    tRNA_anti-codon  21 idlrDgtgriqvvlfr...eeatklaenlkeGdvvrvt 55 
                                        + + D  g++  ++fr   + ++ +   l+++++v+++
  gene2758|gene2758|rna2758|rna2758 162 YRVLDLRGTMSQSIFRiidQIMFTFRTFLRNEKFVEIK 199
                                        55666667777777777766677777788888888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (479 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       474  (0.0264376); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 3309.94
//
Query:       gene2759|gene2759|rna2759|rna2759  [L=108]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.6e-10   40.7   1.8    3.3e-10   40.3   1.8    1.2  1  RNA_pol_Rpb4  RNA polymerase Rpb4


Domain annotation for each model (and alignments):
>> RNA_pol_Rpb4  RNA polymerase Rpb4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.3   1.8   1.9e-14   3.3e-10      54     120 ..      18     101 ..       5     104 .. 0.79

  Alignments for each domain:
  == domain 1  score: 40.3 bits;  conditional E-value: 1.9e-14
                                        CTHHTTSSHHH..................HHHHHHHHTTSTSTHHHHHHHHHCSTSSHHHHHHHSTTGTTTSTSHH CS
                       RNA_pol_Rpb4  54 nkfsrlkneek..................fnelvellksfeLtkaEklqlvnlkPesavelktlieeleerfedeq 111
                                        n    l++eek                  + + + +lk+++L + E++ql++  P+++ +l+ +ie++eerf+ ++
  gene2759|gene2759|rna2759|rna2759  18 N-ETMLTEEEKtmafavkelckncmptdvIYKTRLKLKKMNLYPLEICQLLDMWPKNLLDLQMVIEDMEERFSVHE 92 
                                        4.44444444455555555555566556789999999*************************************** PP

                                        HHHHHHHHH CS
                       RNA_pol_Rpb4 112 leeiLdelk 120
                                        le iLd+ +
  gene2759|gene2759|rna2759|rna2759  93 LEGILDIFR 101
                                        ******976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       626  (0.0349155); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.29s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 748.94
//
Query:       gene276|gene276|rna276|rna276  [L=822]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.2e-05   24.4   0.6      0.027   14.5   0.1    3.1  2  Cullin_Nedd8  Cullin protein neddylation domain
  ------ inclusion threshold ------
      0.058   13.0   0.2       0.12   12.0   0.2    1.5  1  RE_EcoO109I   Type II restriction endonuclease EcoO109I


Domain annotation for each model (and alignments):
>> Cullin_Nedd8  Cullin protein neddylation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.6   0.0   0.00086       7.7       4      37 ..      11      44 ..       9      50 .. 0.82
   2 !   14.5   0.1     3e-06     0.027       6      32 ..     771     797 ..     768     815 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.00086
                   Cullin_Nedd8  4 laiqaaIVRiMKsrktlshneLvsevieqlskrf 37
                                     iqaa+VR +Ks+  ++  + v++   q  + f
  gene276|gene276|rna276|rna276 11 TTIQAALVRRLKSHEYIKSYNTVFKYCTQRTNTF 44
                                   68************99998888877777766666 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 3e-06
                   Cullin_Nedd8   6 iqaaIVRiMKsrktlshneLvsevieq 32 
                                    +++ I RiMK+ k++++ +L + v + 
  gene276|gene276|rna276|rna276 771 LKCKIARIMKRSKRMNVADLQALVNDN 797
                                    7899****************9988665 PP

>> RE_EcoO109I  Type II restriction endonuclease EcoO109I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.2   1.3e-05      0.12     111     197 ..     405     493 ..     389     495 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.3e-05
                    RE_EcoO109I 111 Gpnwgnkdqvkklkenfkkakkllrtn.nikleie.avvGvcYGkdkekdkgkdkeyikliGqefWefisgdeelyveli 188
                                    G n+ ++ q k + ++  + +kl+  +   ++e++  ++G +Y ++ + +  k++ y+k+  ++f ++i  + ++y  ++
  gene276|gene276|rna276|rna276 405 GGNTAQEVQNKGMINDRLRCEKLVLDEeGYQKEYVtLINGFIYCSELNDTYFKSEDYQKMLREAFLARIKDKRKVYDAIV 484
                                    5566666677777666666666555442666666659***********9998889************************* PP

                    RE_EcoO109I 189 eplgekake 197
                                    + +++++k 
  gene276|gene276|rna276|rna276 485 QLMDRHVKH 493
                                    ****99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (822 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       880  (0.0490825); expected 358.6 (0.02)
Passed bias filter:                      484  (0.0269954); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.74u 0.27s 00:00:01.01 Elapsed: 00:00:00.48
# Mc/sec: 5107.00
//
Query:       gene2760|gene2760|rna2760|rna2760  [L=292]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      0.004   17.3   8.6       0.12   12.6   0.1    3.8  3  DUF2644        Protein of unknown function (DUF2644)
  ------ inclusion threshold ------
       0.77    9.6  28.7       0.56   10.1  14.2    3.0  3  DUF4271        Domain of unknown function (DUF4271)
        1.5    8.9  15.6        1.5    8.9   3.7    2.7  3  GWT1           GWT1
        2.6    6.8  18.4      0.036   12.9   8.1    2.1  2  EcsB           Bacterial ABC transporter protein EcsB
        7.1    6.5  11.4          3    7.8   7.4    2.1  2  DUF418         Protein of unknown function (DUF418)


Domain annotation for each model (and alignments):
>> DUF2644  Protein of unknown function (DUF2644)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.2      0.26   9.2e+02      15      33 ..     143     161 ..     141     177 .. 0.77
   2 !    6.5   0.9    0.0027       9.5      10      38 ..     185     213 ..     183     216 .. 0.91
   3 !   12.6   0.1   3.3e-05      0.12       1      52 [.     217     270 ..     217     272 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.26
                            DUF2644  15 fiQFfgalllagiLvyavy 33 
                                        fi F+ all+  +Lv+  +
  gene2760|gene2760|rna2760|rna2760 143 FIFFVLALLVDLVLVHYSM 161
                                        7889999999999987544 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0027
                            DUF2644  10 lSTTafiQFfgalllagiLvyavyldrpy 38 
                                        +ST ++i F  ++l+ +iL+ +++++  y
  gene2760|gene2760|rna2760|rna2760 185 ISTFSSIGFSPMVLIVAILAKTAIIESTY 213
                                        69******************999988877 PP

  == domain 3  score: 12.6 bits;  conditional E-value: 3.3e-05
                            DUF2644   1 eLltnkdGrlSTTafiQFfgalllagiLvyavyld..rpyveelfmtfaifcvG 52 
                                        +L t++dGr      + F+ +l++ +iL y+v+ +    y++++  + a ++ G
  gene2760|gene2760|rna2760|rna2760 217 QLRTTEDGRKKNVRILNFLIVLAVYSILFYCVFQNdiNEYINSVNDNLANYLYG 270
                                        5889****************************9873346777777777766665 PP

>> DUF4271  Domain of unknown function (DUF4271)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1  14.2   0.00015      0.56      50     169 ..      31     156 ..      14     173 .. 0.64
   2 ?   -2.8   6.8       1.4     5e+03      44      72 ..     163     191 ..     141     220 .. 0.49
   3 ?    7.8   1.0   0.00076       2.7      38      93 ..     217     272 ..     206     277 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00015
                            DUF4271  50 fqlflllltclllglllylllsefgslfgsyla..ssllllliiflilllylllKlllykllgwlFfdkkkirqwi 123
                                         ++ l +l+c++++++ ++   + + +++ +++  + +++l++i++i+l+++l+  ++y+ + ++ +     +  +
  gene2760|gene2760|rna2760|rna2760  31 SMISLAVLVCMSIAIVNLISCAQSNDIKNVQFTcnQCFMVLGVITAITLCVMLVAPVIYQSMIYICEGVPDKKMKM 106
                                        5677888888888865555555545555555558899***********************9999998766665555 PP

                            DUF4271 124 fsylsylsllglllfplvlllvyfplssq.....illililiillliklll 169
                                        +  ++ +  lgl+l+ +v+l++++p  ++       +++++++ ll+ l+l
  gene2760|gene2760|rna2760|rna2760 107 KRSVNQI-ALGLFLLTAVFLMILVPAMFHnnfakGPVFIFFVLALLVDLVL 156
                                        5555533.3455555555555555555441111144444444444444444 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.4
                            DUF4271  44 tksesrfqlflllltclllglllylllse 72 
                                        + ++s f++f+++ ++  +++l+  ++s 
  gene2760|gene2760|rna2760|rna2760 163 SEKNSPFRVFITISSVTGIAFLISTFSSI 191
                                        23344444444444444444444444433 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.00076
                            DUF4271  38 slfkeetksesrfqlflllltclllglllylllsefgslfgsylassllllliifl 93 
                                        +l+ +e+++   ++++ +l+++ ++++l+y+++++  +++ ++ +++l ++l+ fl
  gene2760|gene2760|rna2760|rna2760 217 QLRTTEDGRKKNVRILNFLIVLAVYSILFYCVFQNDINEYINSVNDNLANYLYGFL 272
                                        55556688888899999999999999999999999444444444499999988876 PP

>> GWT1  GWT1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   3.7   0.00042       1.5      52     142 ..      33     122 ..       7     127 .. 0.62
   2 ?   -0.9   0.1      0.45   1.6e+03      81     100 ..     163     182 ..     137     197 .. 0.44
   3 ?    7.7   1.2     0.001       3.7       7      89 ..     188     271 ..     186     278 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00042
                               GWT1  52 kllikllllsilllllllllelyvefvSRrlaNlpYvlwvvalnltllllflliel.lfvekeeekerkekatstv 126
                                          l  l+++si+++ l+ +++++   ++  ++N  ++++ v + +tl+++++     ++++     e   ++++++
  gene2760|gene2760|rna2760|rna2760  33 ISLAVLVCMSIAIVNLISCAQSNDIKNVQFTCNQCFMVLGVITAITLCVMLV--APvIYQSMIYICEGVPDKKMKM 106
                                        2233344444444444333333333367777777776665555555444444..22223355577888999999** PP

                               GWT1 127 leainrngLlvFLlaN 142
                                         +++n+  L +FLl  
  gene2760|gene2760|rna2760|rna2760 107 KRSVNQIALGLFLLTA 122
                                        *************975 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.45
                               GWT1  81 rlaNlpYvlwvvalnltlll 100
                                           N p+ ++++  ++t ++
  gene2760|gene2760|rna2760|rna2760 163 SEKNSPFRVFITISSVTGIA 182
                                        22344444443333333333 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.001
                               GWT1   7 fsliGylaiyllgvslgkyvlkrekeaeeeekkkkkkkkesketlkllikllllsilllllll.llelyvefvSRr 81 
                                        fs iG+  + l+   l k  + +++++ ++ ++++  +k++ ++l+ li l+++sil+++++   ++ y++ v   
  gene2760|gene2760|rna2760|rna2760 188 FSSIGFSPMVLIVAILAKTAIIESTYFVKQLRTTEDGRKKNVRILNFLIVLAVYSILFYCVFQnDINEYINSVNDN 263
                                        677888888887777777777677777777788888999999**************99998321345555558888 PP

                               GWT1  82 laNlpYvl 89 
                                        laN  Y +
  gene2760|gene2760|rna2760|rna2760 264 LANYLYGF 271
                                        88888865 PP

>> EcsB  Bacterial ABC transporter protein EcsB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   2.5      0.12   4.4e+02     129     187 ..      32      89 ..      21     100 .. 0.45
   2 ?   12.9   8.1     1e-05     0.036     104     232 ..     115     235 ..     101     243 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.12
                               EcsB 129 iaelllllllllllkllnlllkweelrlqgkkkrridr.lirlllnalllylllalapll 187
                                        +++  l +l+++++ ++nl +  ++  +++ + + ++  ++  +++a++l+++l + ++ 
  gene2760|gene2760|rna2760|rna2760  32 MIS--LAVLVCMSIAIVNLISCAQSNDIKNVQFTCNQCfMVLGVITAITLCVMLVAPVIY 89 
                                        223..3333333444456655555555555444444332333333444444444443333 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 1e-05
                               EcsB 104 llqllllllvllillPlllettglsiaelllllllllllkllnlllkweelrlqgkkkrridrlirlllnalllyl 179
                                        l  +ll++++l+il+P ++ ++++  + ++++++l+ll+ l+ +  ++ + +++        r++  + ++  +++
  gene2760|gene2760|rna2760|rna2760 115 LGLFLLTAVFLMILVPAMF-HNNFAKGPVFIFFVLALLVDLVLVHYSMVSEKNSP------FRVFITISSVTGIAF 183
                                        4457888999999999988.*******************9999888888888776......346777888888899 PP

                               EcsB 180 llalapllalllilllllvlllllkrkkkkklldWeklieeEqkrrmrfyrfl 232
                                        l+++++ +++   ++l++++l+    ++ ++ ++  +  e+ +k+ +r+++fl
  gene2760|gene2760|rna2760|rna2760 184 LISTFSSIGFSP-MVLIVAILAKTAIIESTYFVKQLRTTEDGRKKNVRILNFL 235
                                        999999999988.7777777777777777777777788888888888888887 PP

>> DUF418  Protein of unknown function (DUF418)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   7.4   0.00082         3      21     142 ..      31     162 ..      20     169 .. 0.78
   2 ?   -0.4   0.0      0.26   9.4e+02      26      78 ..     199     252 ..     188     267 .. 0.67

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.00082
                             DUF418  21 lligllvglplnllla......vlaeaaeesallelllsvlrylaglllalgyva.....lillllakekrrrllr 85 
                                         +i+l+v + ++++++      ++ ++ + ++++   ++vl  +++++l++++va     +++++++  + ++ ++
  gene2760|gene2760|rna2760|rna2760  31 SMISLAVLVCMSIAIVnliscaQSNDIKNVQFTCNQCFMVLGVITAITLCVMLVApviyqSMIYICEGVPDKK-MK 105
                                        4444444444444444333333668888889999999999999999999888887333335677899999988.9* PP

                             DUF418  86 alaavGRmALTnYllqslictllfygyglglfgslgraallllallifllqllfSkl 142
                                        + ++v + AL  +ll  +++++l   +  + f++ +++  ++lall+ l+ +  S +
  gene2760|gene2760|rna2760|rna2760 106 MKRSVNQIALGLFLLTAVFLMILVPAMFHNNFAKGPVFIFFVLALLVDLVLVHYSMV 162
                                        ***********************************************9999998876 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.26
                             DUF418  26 lvglplnllla.vlaeaaeesallelllsvlrylaglllalgyvalillllake 78 
                                        +v+++++ +++  ++ + +  ++     + +r l  l++ ++y  l++++++++
  gene2760|gene2760|rna2760|rna2760 199 IVAILAKTAIIeSTYFVKQLRTTEDGRKKNVRILNFLIVLAVYSILFYCVFQND 252
                                        444444444444555666666666666777777777777777777777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (292 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1430  (0.079759); expected 358.6 (0.02)
Passed bias filter:                      487  (0.0271627); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.67u 0.32s 00:00:00.99 Elapsed: 00:00:00.48
# Mc/sec: 1838.92
//
Query:       gene2761|gene2761|rna2761|rna2761  [L=197]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.5e-11   44.4   6.3    9.4e-11   41.8   6.3    2.1  1  Sybindin    Sybindin-like family
     0.0025   17.1   2.8     0.0028   16.9   2.8    1.1  1  Zip         ZIP Zinc transporter
     0.0064   16.2   5.9     0.0077   15.9   5.9    1.2  1  MecA        Negative regulator of genetic competence (MecA)
  ------ inclusion threshold ------
       0.33    9.7   7.3       0.42    9.4   7.3    1.1  1  NPR3        Nitrogen Permease regulator of amino acid transpo


Domain annotation for each model (and alignments):
>> Sybindin  Sybindin-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.8   6.3   2.1e-14   9.4e-11       2     132 ..       4     191 ..       3     195 .. 0.92

  Alignments for each domain:
  == domain 1  score: 41.8 bits;  conditional E-value: 2.1e-14
                           Sybindin   2 fslyiinkaGgliyqkeaneekkea................................................... 26 
                                         s +i+nk+Gg+iy+   +ee  ++                                                   
  gene2761|gene2761|rna2761|rna2761   4 SSFFIVNKSGGMIYKFLKQEEGITKdnstnrndksnenitdeskhlkvtssennidktitnkteqnkdelkrtnkk 79 
                                        689************9999998888999************************************************ PP

                           Sybindin  27 ..................rpklstneklllasmlhslkaiasklspvkakeelqgssgievletdtfkLhclqtlt 84 
                                                            +++ n+ l+l s+lh+++ +as +          +s+ + ++  +  +L +++t+t
  gene2761|gene2761|rna2761|rna2761  80 ananshtqrasnqnagvqLCTTNLNNLLVLNSTLHTIHQMASTIYG--------QSQKFYIYF-TGLTLTMFKTMT 146
                                        ****************998899999*****************9998........233455554.5689******** PP

                           Sybindin  85 GiKfvlitdtktnaeadsllrkiyelYsdyvlknPfyslempircelF 132
                                        G  f+ + d+k+    d l   +y+ +  yvl+nP y  +mpi    F
  gene2761|gene2761|rna2761|rna2761 147 GYTFIFVGDEKA---SDKLVYDVYKEFNLYVLRNPAYMDDMPINLCTF 191
                                        *********999...89999999999999**************87666 PP

>> Zip  ZIP Zinc transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   2.8   6.2e-07    0.0028      84     189 ..       1     108 [.       1     143 [. 0.84

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 6.2e-07
                                Zip  84 lGflllllveklltmivek..ksshkektpkkasssssesaakksvsndkveeseekedhvaeadtdadskeelrn 157
                                        +++  +++v+k   mi++   +++  +k +++ ++++s+++  ++ +  kv++se++ d+    +t+++++e +r 
  gene2761|gene2761|rna2761|rna2761   1 MSISSFFIVNKSGGMIYKFlkQEEGITKDNSTNRNDKSNENITDESKHLKVTSSENNIDKTITNKTEQNKDELKRT 76 
                                        5778899999999999999766666677777778888899999999999**************************9 PP

                                Zip 158 gkqeksesekeqaseeedkeklaslkvraiil 189
                                        +k+    s++++as++  + +l++ ++  +++
  gene2761|gene2761|rna2761|rna2761  77 NKKANANSHTQRASNQNAGVQLCTTNLNNLLV 108
                                        99999999999999888888888877765544 PP

>> MecA  Negative regulator of genetic competence (MecA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   5.9   1.7e-06    0.0077      77     178 ..      26     135 ..      10     171 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.7e-06
                                        XXXXXX......................XXXXXXXX....................XXXXXXXXXXXXX--SEEEE CS
                               MecA  77 itkvedpeeldtrfskftk.........ledlleklleel.ekeeeekkdkakeakekekekeeeeekeqsltrif 142
                                        itk+++ + +d+  +++t+              +++ +++ +k+e++k++ + ++k++++++ +++ ++q++   +
  gene2761|gene2761|rna2761|rna2761  26 ITKDNSTNRNDKSNENITDeskhlkvtsS---ENNIDKTItNKTEQNKDELKRTNKKANANSHTQRASNQNAGVQL 98 
                                        67776566666655555555555553332...33333333323344455555556666666666666667777788 PP

                                        EESSHHHHHHHHT.E......EEEEEEE.TTEEEEEE. CS
                               MecA 143 sfdsledvirlakalk..kiyessLYkdeegrYyLlle 178
                                        +  +l++++ l  +l+  + ++s+ Y + ++++y++++
  gene2761|gene2761|rna2761|rna2761  99 CTTNLNNLLVLNSTLHtiHQMASTIYGQ-SQKFYIYFT 135
                                        999999999999999854444*******.*****9985 PP

>> NPR3  Nitrogen Permease regulator of amino acid transport activity 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   7.3   9.3e-05      0.42      55     153 ..      27     124 ..       8     127 .. 0.48

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 9.3e-05
                               NPR3  55 krkrssrskekkskesskksesssksesseekksskeseeseekesneeeeeeededdeesekeeeekedkkknl. 129
                                         + +s+++++k++++ +++s++ + ++s++   + +++ +++++++++e ++ +++ +++s+++++++++   +l 
  gene2761|gene2761|rna2761|rna2761  27 TKDNSTNRNDKSNENITDESKHLKVTSSEN---NIDKTITNKTEQNKDELKRTNKKANANSHTQRASNQNAGVQLc 99 
                                        344444333333333333333333333222...2222223333333333333333333333334444444444442 PP

                               NPR3 130 .tmFhlvfvlnPplseynsrvdemY 153
                                         t  +  +vln  l+ +++  +++Y
  gene2761|gene2761|rna2761|rna2761 100 tTNLNNLLVLNSTLHTIHQMASTIY 124
                                        26778899***99999999999999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2884  (0.160857); expected 358.6 (0.02)
Passed bias filter:                      754  (0.0420548); expected 358.6 (0.02)
Passed Vit filter:                        90  (0.0050198); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.54u 0.35s 00:00:00.89 Elapsed: 00:00:00.50
# Mc/sec: 1193.92
//
Query:       gene2762|gene2762|rna2762|rna2762  [L=441]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.6e-19   70.2   0.0    2.5e-19   69.6   0.0    1.3  1  XPG_N       XPG N-terminal domain
    1.4e-15   57.4   0.0    2.6e-15   56.5   0.0    1.5  1  XPG_I       XPG I-region
    0.00042   19.9   0.0    0.00072   19.1   0.0    1.3  1  XPG_I_2     XPG domain containing
  ------ inclusion threshold ------
      0.026   15.1   0.0       0.05   14.2   0.0    1.4  1  5_3_exonuc  5'-3' exonuclease, C-terminal SAM fold
      0.026   14.2   0.1       0.88    9.3   0.0    2.3  2  DUF2292     Uncharacterized small protein (DUF2292)
       0.13   12.7   0.0       0.27   11.6   0.0    1.4  1  Rrf2        Transcriptional regulator


Domain annotation for each model (and alignments):
>> XPG_N  XPG N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.6   0.0   8.3e-23   2.5e-19       1     101 []       1      99 [.       1      99 [. 0.98

  Alignments for each domain:
  == domain 1  score: 69.6 bits;  conditional E-value: 8.3e-23
                                        X--TTHHHHHHHH-GEEEEEGGGGTTEEEEEEHHHHHHHHHHHSE.ETTEE-BS-HHHHHHHHHHHHHHHTTEEEE CS
                              XPG_N   1 MGikgLlkllkevaairsvsiealegkklaiDaslwlyrfliavreqlgnalentshlmglfsrllrlldfgikPi 76 
                                        MGikgLl+++++    ++ +i ++++++++iD+  wl+ +l +++ ql n++++t h  ++++r+  ++++g  P+
  gene2762|gene2762|rna2762|rna2762   1 MGIKGLLPIVSPCL--KKRHISSFKNHRIGIDGHSWLHSILPSIALQLYNNVQTTLHHEIFLKRVRVIQKYGAVPV 74 
                                        *************9..************************************************************ PP

                                        EEE--S--GGGHHHHHHHHHHHHHH CS
                              XPG_N  77 fVFdgkapdlkkeelekrserrqea 101
                                        +VFdg+ ++ k+   e+r+ +r+ea
  gene2762|gene2762|rna2762|rna2762  75 VVFDGESLPSKHVVNERRRMKREEA 99 
                                        *******************999875 PP

>> XPG_I  XPG I-region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.5   0.0   8.8e-19   2.6e-15       3      94 .]     140     220 ..     138     220 .. 0.90

  Alignments for each domain:
  == domain 1  score: 56.5 bits;  conditional E-value: 8.8e-19
                                        HT--EEE-SS-HHHHHHHHHHTTSSSEEE-SSSHHHHTT-SEEEESTT.ECECTT..EEECEEEEEEHHHHHHHHT CS
                              XPG_I   3 mgipyvvApgEAEAqcayLqkkglvdaviseDsDlllFGapkvlrnlskkkskkkkekekkkvevidlekvlkelg 78 
                                         g++++v+p+E +Aq+ayLq+ ++v+ +i+eDsDl+++ ++ vl ++     +         v +++    ++  +
  gene2762|gene2762|rna2762|rna2762 140 NGVEVIVSPYESDAQLAYLQRINYVHSIITEDSDLIVYKCNNVLYKYG----NGY-------VMHYERGAFRTANE 204
                                        79********************************************95....444.......77788877778888 PP

                                        --HHHHHHHHHHHCET CS
                              XPG_I  79 ltreqlidlaillgcD 94 
                                        +  ++l+d++il+gcD
  gene2762|gene2762|rna2762|rna2762 205 FVCDNLLDVSILSGCD 220
                                        9999***********9 PP

>> XPG_I_2  XPG domain containing
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   2.4e-07   0.00072       3      57 ..     127     179 ..     125     197 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 2.4e-07
                            XPG_I_2   3 pfmvpavieaLknrwkakditevvpgEADkfcAvlA.rklgcaVLTsDSDLlvhdl 57 
                                        p mv  ++  L+     ++ ++v p E D++ A+l   ++   + T+DSDL+v+  
  gene2762|gene2762|rna2762|rna2762 127 PHMVAQIAQFLR---DNGVEVIVSPYESDAQLAYLQrINYVHSIITEDSDLIVYKC 179
                                        779999999999...689******************7799**************75 PP

>> 5_3_exonuc  5'-3' exonuclease, C-terminal SAM fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   1.7e-05      0.05      11      50 ..     215     252 ..     207     272 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.7e-05
                         5_3_exonuc  11 aLvGDssDnipGvpgiGektAakLlkeygsleeilenlde 50 
                                         L G   D ++ v+g+G   A+k++++ygs+e +++++ +
  gene2762|gene2762|rna2762|rna2762 215 ILSG--CDYLENVRGVGISSAVKMMRRYGSVELVINEMRR 252
                                        5555..688999**********************998864 PP

>> DUF2292  Uncharacterized small protein (DUF2292)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0     0.044   1.3e+02      13      24 ..      68      79 ..      58      80 .. 0.77
   2 ?    9.3   0.0    0.0003      0.88       5      21 ..     230     247 ..     229     251 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.044
                            DUF2292 13 kyGsvtivvqdG 24
                                       kyG v +vv dG
  gene2762|gene2762|rna2762|rna2762 68 KYGAVPVVVFDG 79
                                       4********999 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0003
                            DUF2292   5 Ilealeelk.yGsvtivv 21 
                                        I +a++ ++ yGsv++v+
  gene2762|gene2762|rna2762|rna2762 230 ISSAVKMMRrYGSVELVI 247
                                        7889999999*******9 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0     9e-05      0.27      12      54 ..     100     142 ..      96     146 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 9e-05
                                        HHHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTS CS
                               Rrf2  12 hallyLakeeeeepvsseeiaerqnispsylekilakLrkagl 54 
                                        +++++L++ +++   +++ ia + +isp+++++i + Lr +g+
  gene2762|gene2762|rna2762|rna2762 100 RTMAELQMSKGNVREAMRYIACSISISPHMVAQIAQFLRDNGV 142
                                        78999******9999************************9995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (441 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       438  (0.0244297); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 3168.31
//
Query:       gene2763|gene2763|rna2763|rna2763  [L=361]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.023   14.7   0.0       0.26   11.4   0.0    2.4  2  SH3_10       SH3 domain
        2.2    6.8  48.9        1.8    7.0  24.8    2.1  2  TFIIF_alpha  Transcription initiation factor IIF, alpha subun


Domain annotation for each model (and alignments):
>> SH3_10  SH3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   2.9e-05      0.26      25      53 ..      14      42 ..       8      45 .. 0.85
   2 ?   -0.0   0.0      0.11   9.5e+02      33      51 ..     118     136 ..     103     141 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 2.9e-05
                             SH3_10 25 evsiekgeevtLldnsdrekWkVqtssGa 53
                                       +  i+k +++ L+d+++r++W+V   +G 
  gene2763|gene2763|rna2763|rna2763 14 HYVINKVNDCLLMDSNERKRWEVDGCRGG 42
                                       56789999***************988875 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.11
                             SH3_10  33 evtLldnsdrekWkVqtss 51 
                                         + L+d   +e+W V++ +
  gene2763|gene2763|rna2763|rna2763 118 LFYLVDDVLPEEWGVKEEE 136
                                        478999999******9876 PP

>> TFIIF_alpha  Transcription initiation factor IIF, alpha subunit (TFIIF-alpha)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8  16.1   0.00047       4.2     255     320 ..      27      91 ..      11     111 .. 0.67
   2 ?    7.0  24.8    0.0002       1.8     316     476 ..     133     304 ..     122     337 .. 0.52

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.00047
                                        ...XXXXXXXXXXXXX.XXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                        TFIIF_alpha 255 dddkkkkrgsdddadeydsddGddeg.rEldyisDdsasendpeeredkkseEeeekkeieqdedee 320
                                        d +++k+ ++d      d + G+d+g  E dy +D+++ +n+++ +e+k +eE++e+k+ e +++e+
  gene2763|gene2763|rna2763|rna2763  27 DSNERKRWEVDGCRGG-DYEGGNDQGdNEKDYEEDNDQGDNEED-KEQKVKEEDKEQKDYEGNNEED 91 
                                        3445555566655555.999998887369999999988886655.5555666666665555544443 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0002
                                        XXXXXXXXXXXXXXXXXXXXXXXX...XXXXXXXXXXX..XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                        TFIIF_alpha 316 dedeeekeeekkeeegklskkkkk...akklkkkkkekdkkdSddeedsddsDideedsvslvkakKkkekkkeek 388
                                        +e+ ee+eee+++ee+  ++  k    + k  +k++ ++   S ++   d+  i+e ++ ++vk++  ke++++e+
  gene2763|gene2763|rna2763|rna2763 133 KEE-EEREEESRKEEESRTRTVKVmegLDKCEEKENVQKSMMS-KNGLKDEMGIEEGKNEGVVKEEEGKEENDKEE 206
                                        333.333333333333333333320012333333333333333.44556666677777777777766555444433 PP

                                        X..XXXXXXX.XXXXXXXXXXXXXXXXXXXXX...........XXXXXX...XXXXXXXXXXXXXXXXXXXXXXXX CS
                        TFIIF_alpha 389 v.dsnessag.nsrparpspeqkdskskrkaa.........seeskspvsvpaKklktenapkssskkslpqtvsk 453
                                          ++  ++++ +s + r +p ++ sk+k ++a          +++++ vs   K +k+ +  + s   ++  t   
  gene2763|gene2763|rna2763|rna2763 207 EsNKIRGKKNvKSNKRRSTPRSSTSKEKEQQAvgqindrskIKNAQKGVSKRMKCIKLVKRVRPS--PNTSYTLFA 280
                                        30333344331455666666666666666666777755444345666666666666665554333..222223233 PP

                                        .XXXXXXX-SS--HHHHHHHHH.H CS
                        TFIIF_alpha 454 sksssnkadggvtEeavrryLm.r 476
                                        +++++n +++   E+ +  +L+  
  gene2763|gene2763|rna2763|rna2763 281 TENTENGDEEATRENFINTVLTnE 304
                                        378999999999999999999843 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (361 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1961  (0.109376); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        85  (0.00474092); expected 17.9 (0.001)
Passed Fwd filter:                        31  (0.00172904); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.86u 0.31s 00:00:01.17 Elapsed: 00:00:00.49
# Mc/sec: 2227.77
//
Query:       gene2764|gene2764|rna2764|rna2764  [L=686]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.6e-14   52.7   0.6    1.3e-13   50.9   0.6    2.0  1  TPP1      Shelterin complex subunit, TPP1/ACD
     0.0048   16.8   1.4      0.015   15.2   1.4    1.8  1  Sec34     Sec34-like family


Domain annotation for each model (and alignments):
>> TPP1  Shelterin complex subunit, TPP1/ACD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.9   0.6   1.5e-17   1.3e-13       2      99 ..       9      98 ..       8     104 .. 0.92

  Alignments for each domain:
  == domain 1  score: 50.9 bits;  conditional E-value: 1.5e-17
                                       -HHHHHHHT--TTTS--HHHHT-..GGGEEEEEEEEE.EETTEEEEEEE-SS-EEEEEE-HHHHHHHHHHHSS-TTSS CS
                               TPP1  2 WIeklvleaiklssdlspslntnkskaqllkvlkfaqdtsnsaitavlsDsthkIlaiftreavenfereekeritse 79
                                       WI +++  +++  ++     +t +++aqll +l    ++ +++i++vlsD++ +I a++t++av ++++  ++ + ++
  gene2764|gene2764|rna2764|rna2764  9 WIFNSLFSQLTTGKK----RQTIHNHAQLLVILY---NKPHKDIEVVLSDKHNTIIAELTQNAVTTYHQSFDHAF-TD 78
                                       999999999999999....688999*********...799****************************8888655.89 PP

                                       -TTSEEEEES-EEEEEEHHH CS
                               TPP1 80 tkgclllikdaslvfqerse 99
                                       +kgc+++ik++  vf+++++
  gene2764|gene2764|rna2764|rna2764 79 IKGCFVRIKRYAFVFCTSRK 98
                                       ****************9987 PP

>> Sec34  Sec34-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   1.4   1.6e-06     0.015       9      87 ..     203     282 ..     196     296 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.6e-06
                              Sec34   9 eeecdelleqtdealeqLeeleekfksvsektsslheaceqlleeqk.rleelaeeieekLkyFeeldpitrkLns 83 
                                        +++ ++l++++d ++++++ ++++ ++ ++++++l+++ ++l+++++ ++++    i++k +  ++ld+it+++++
  gene2764|gene2764|rna2764|rna2764 203 NNQGNDLISDVDGINNDVDGINNQGNDLNNQSNNLNRQRNDLINNKNvSISQGDVLINNKNNLIKALDQITSQIKN 278
                                        677789*************************************99882456666689****************988 PP

                              Sec34  84 pgss 87 
                                         + +
  gene2764|gene2764|rna2764|rna2764 279 DSKT 282
                                        7765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (686 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1055  (0.0588432); expected 358.6 (0.02)
Passed bias filter:                      233  (0.0129957); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.42
# Mc/sec: 4852.76
//
Query:       gene2765|gene2765|rna2765|rna2765  [L=129]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       595  (0.0331865); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 907.17
//
Query:       gene2766|gene2766|rna2766|rna2766  [L=80]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1689  (0.0942049); expected 358.6 (0.02)
Passed bias filter:                      558  (0.0311228); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 519.10
//
Query:       gene2767|gene2767|rna2767|rna2767  [L=133]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.6e-25   87.2   0.8    5.7e-25   86.6   0.8    1.3  1  Fip1      Fip1 motif


Domain annotation for each model (and alignments):
>> Fip1  Fip1 motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.6   0.8   3.2e-29   5.7e-25       1      42 [.      49      90 ..      49      91 .. 0.95

  Alignments for each domain:
  == domain 1  score: 86.6 bits;  conditional E-value: 3.2e-29
                               Fip1  1 didldqleekpWrkpGaDisDYFNYGfdEetWkeYcekqekl 42
                                       ++++d++e+kpWr+pGaDi+DYFNYGfdE+tWk Yc+kq++l
  gene2767|gene2767|rna2767|rna2767 49 EFEIDTIEDKPWRRPGADITDYFNYGFDEHTWKLYCAKQRSL 90
                                       579************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       425  (0.0237046); expected 358.6 (0.02)
Passed bias filter:                      219  (0.0122148); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 1046.61
//
Query:       gene2768|gene2768|rna2768|rna2768  [L=112]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.5e-10   39.6   5.5    3.5e-10   39.6   5.5    2.7  3  RNA_POL_M_15KD   RNA polymerases M/15 Kd subunit
     0.0011   19.4   6.9      0.084   13.4   3.2    2.2  2  Zn_ribbon_recom  Recombinase zinc beta ribbon domain
      0.007   16.2  12.2      0.013   15.4   3.2    3.5  3  TFIIS_C          Transcription factor S-II (TFIIS)
  ------ inclusion threshold ------
      0.014   15.6   0.5      0.014   15.6   0.5    2.0  2  FYVE_2           FYVE-type zinc finger
       0.13   12.4   9.9        2.6    8.2   1.9    2.8  2  Elf1             Transcription elongation factor Elf1 like
       0.42   10.6  14.5        1.7    8.6   0.2    3.9  3  zinc_ribbon_4    zinc-ribbon domain
       0.49   10.5  10.2       0.11   12.5   1.0    2.6  2  DZR              Double zinc ribbon
       0.51   10.1   8.3        2.7    7.8   0.7    2.8  3  zinc_ribbon_5    zinc-ribbon domain
        1.5    8.8  10.3       0.61   10.0   0.6    2.7  2  PHD              PHD-finger
        1.7    8.6   9.6       0.47   10.4   0.4    3.1  2  Nudix_N_2        Nudix N-terminal
        2.5    8.5   8.6        3.1    8.2   0.2    2.7  3  GFA              Glutathione-dependent formaldehyde-activatin
        5.9    6.8  11.0        4.8    7.1   0.9    3.2  3  zinc_ribbon_12   Probable zinc-ribbon domain
        6.2    6.8  11.0       0.65   10.0   3.3    2.7  3  Zn_ribbon_SprT   SprT-like zinc ribbon domain
        8.8    6.6  12.6        1.1    9.4   4.3    2.4  2  DUF2387          Probable metal-binding protein (DUF2387)


Domain annotation for each model (and alignments):
>> RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.6   5.5   2.8e-13   3.5e-10       2      33 ..       4      37 ..       4      40 .. 0.94
   2 ?   -1.6   0.2         2   2.5e+03      22      28 ..      74      80 ..      72      83 .. 0.70
   3 ?   -0.3   0.5      0.77   9.9e+02       4       7 ..     104     107 ..      95     110 .. 0.67

  Alignments for each domain:
  == domain 1  score: 39.6 bits;  conditional E-value: 2.8e-13
                                       EBESTTTSBEEEEECSCCCE..EEESSSS-EEES CS
                     RNA_POL_M_15KD  2 kFCpkCgNlLlpkedkegkn..feCrqCgYeepa 33
                                       +FCp+C N+L+pkedk  k   ++Cr+C  +e+a
  gene2768|gene2768|rna2768|rna2768  4 EFCPECSNMLYPKEDKIEKQlyMACRNCEHVEEA 37
                                       6***************9999999*********98 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2
                                       EEESSSS CS
                     RNA_POL_M_15KD 22 feCrqCg 28
                                       + C  Cg
  gene2768|gene2768|rna2768|rna2768 74 VKCGRCG 80
                                       5677776 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.77
                                        ESTT CS
                     RNA_POL_M_15KD   4 CpkC 7  
                                        C kC
  gene2768|gene2768|rna2768|rna2768 104 CKKC 107
                                        5555 PP

>> Zn_ribbon_recom  Recombinase zinc beta ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.1    0.0036       4.6       7      33 ..       5      32 ..       2      55 .. 0.82
   2 !   13.4   3.2   6.5e-05     0.084       6      32 ..      74     107 ..      69     109 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0036
                    Zn_ribbon_recom  7 rCgeCGspmtrrkrk.gkrhyYrCstyr 33
                                       +C eC + ++ +  k  k+ y  C+++ 
  gene2768|gene2768|rna2768|rna2768  5 FCPECSNMLYPKEDKiEKQLYMACRNCE 32
                                       8************999999*****9985 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 6.5e-05
                    Zn_ribbon_recom   6 lrCgeCGspmtr....rkrkgkr....hyYrCsty 32 
                                        ++Cg+CG+ + +    +++ + +    ++Y+C+++
  gene2768|gene2768|rna2768|rna2768  74 VKCGRCGHGYAVyfepKGN-NPDlelkICYICKKC 107
                                        79********997643333.3336777*****986 PP

>> TFIIS_C  Transcription factor S-II (TFIIS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.1      0.18   2.3e+02       3       8 ..       6      11 ..       4      13 .. 0.83
   2 ?    3.5   0.1     0.051        65      27      37 ..      24      34 ..      21      36 .. 0.78
   3 !   15.4   3.2     1e-05     0.013       2      38 ..      75     111 ..      74     112 .] 0.97

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.18
                            TFIIS_C  3 CpkCgs 8 
                                       Cp+C++
  gene2768|gene2768|rna2768|rna2768  6 CPECSN 11
                                       999987 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.051
                            TFIIS_C 27 vfykCtkCghr 37
                                       +++ C +C+h 
  gene2768|gene2768|rna2768|rna2768 24 LYMACRNCEHV 34
                                       57789999985 PP

  == domain 3  score: 15.4 bits;  conditional E-value: 1e-05
                            TFIIS_C   2 kCpkCgsreayffqlQtRsaDEpmtvfykCtkCghrW 38 
                                        kC +Cg+  a++f+      D +  + y C+kC + W
  gene2768|gene2768|rna2768|rna2768  75 KCGRCGHGYAVYFEPKGNNPDLELKICYICKKCYNIW 111
                                        8*********************************999 PP

>> FYVE_2  FYVE-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   1.6      0.38   4.9e+02      81     102 ..       5      33 ..       1      44 [. 0.48
   2 ?   15.6   0.5   1.1e-05     0.014      16      87 ..      35     106 ..      31     111 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.38
                             FYVE_2  81 vCkkCsve......nkkekvwl.CkiCse 102
                                         C +Cs+       + +++ ++ C++C++
  gene2768|gene2768|rna2768|rna2768   5 FCPECSNMlypkedKIEKQLYMaCRNCEH 33 
                                        45555555444443222333322555554 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 1.1e-05
                             FYVE_2  16 qrdeklrkkeeeRlgelkeklekekskrellgnqaklgethCilCleefkllvnskrqCldCklnvCkkCsv 87 
                                        + +++ +  e+    e+ e++++e++k   +  +  +++ +C +C + + +  + k +  d +l++C  C +
  gene2768|gene2768|rna2768|rna2768  35 EEAMNNKVVENVFHREFTEEIDQETAKDMTMDPTLFIANVKCGRCGHGYAVYFEPKGNNPDLELKICYICKK 106
                                        556666777777778999***************9**********************9999999988877754 PP

>> Elf1  Transcription elongation factor Elf1 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   1.9     0.002       2.6      24      66 ..       6      46 ..       1      57 [. 0.81
   2 ?    7.9   1.4    0.0025       3.1      35      58 ..      63      86 ..      53     112 .] 0.76

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.002
                               Elf1 24 CpfCnheksvevkldkkekiaevsCkvCgesfetkvnalsepv 66
                                       Cp C++   +  k dk ek  ++ C++C+   e   n++ e+v
  gene2768|gene2768|rna2768|rna2768  6 CPECSNM--LYPKEDKIEKQLYMACRNCEHVEEAMNNKVVENV 46
                                       9999998..999*****************98777766666654 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0025
                               Elf1 35 vkldkkekiaevsCkvCgesfetk 58
                                       +++d +  ia+v+C+ Cg  + + 
  gene2768|gene2768|rna2768|rna2768 63 MTMDPTLFIANVKCGRCGHGYAVY 86
                                       556666669999999999887754 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   3.6      0.16   2.1e+02       5      34 ..       6      34 ..       5      34 .. 0.65
   2 ?    8.6   0.2    0.0013       1.7      24      33 ..      72      81 ..      71      83 .. 0.89
   3 ?    5.1   0.3     0.017        22      28      35 ..     104     111 ..     103     112 .] 0.92

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.16
                      zinc_ribbon_4  5 CpsCkakyeiddeklpakgvkvrCskCghv 34
                                       Cp+C+      ++k+ ++   + C +C hv
  gene2768|gene2768|rna2768|rna2768  6 CPECSNMLYPKEDKIEKQ-LYMACRNCEHV 34
                                       555555544556666655.67789999997 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0013
                      zinc_ribbon_4 24 vkvrCskCgh 33
                                       ++v+C +Cgh
  gene2768|gene2768|rna2768|rna2768 72 ANVKCGRCGH 81
                                       68*******9 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.017
                      zinc_ribbon_4  28 CskCghvF 35 
                                        C+kC +++
  gene2768|gene2768|rna2768|rna2768 104 CKKCYNIW 111
                                        *******9 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   1.0   8.5e-05      0.11      12      37 ..       3      34 ..       1      42 [. 0.83
   2 ?    1.8   2.5       0.2   2.5e+02      15      33 ..      76     106 ..      71     110 .. 0.57

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 8.5e-05
                                DZR 12 arfCseCgtklkavaa......edrCpsCgek 37
                                       ++fC+eC + l + ++        +C +C++ 
  gene2768|gene2768|rna2768|rna2768  3 KEFCPECSNMLYPKEDkiekqlYMACRNCEHV 34
                                       579*******986666999999999****986 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.2
                                DZR  15 CseCgtklkavaa............edrCps 33 
                                        C++Cg+    + +             + C +
  gene2768|gene2768|rna2768|rna2768  76 CGRCGHGYAVYFEpkgnnpdlelkiCYICKK 106
                                        7777777554444556666666333333333 PP

>> zinc_ribbon_5  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.1    0.0054       6.9       5      34 ..       6      34 ..       5      37 .. 0.90
   2 ?    7.8   0.7    0.0021       2.7      26      33 ..      74      81 ..      72      85 .. 0.85
   3 ?   -1.7   0.1         2   2.5e+03      28      34 ..     104     110 ..     103     111 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0054
                      zinc_ribbon_5  5 CpdCdtkFklvdsklKksgkkVrCakCaev 34
                                       Cp+C  +    ++k+ + +    C  C +v
  gene2768|gene2768|rna2768|rna2768  6 CPECSNMLYPKEDKI-EKQLYMACRNCEHV 34
                                       **************6.77999999999998 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0021
                      zinc_ribbon_5 26 VrCakCae 33
                                       V+C++C++
  gene2768|gene2768|rna2768|rna2768 74 VKCGRCGH 81
                                       9******9 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 2
                      zinc_ribbon_5  28 CakCaev 34 
                                        C kC ++
  gene2768|gene2768|rna2768|rna2768 104 CKKCYNI 110
                                        8888766 PP

>> PHD  PHD-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   3.5      0.15   1.9e+02       1      23 [.       5      33 ..       5      35 .. 0.65
   2 ?   10.0   0.6   0.00047      0.61      20      50 ..      75     108 ..      60     109 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.15
                                       SBTTTTS....TTST..TSCEEEETTTSC CS
                                PHD  1 rCavCkk....ksde..eeelvqCdgCkr 23
                                       +C  C++    k+d+  ++  + C +C++
  gene2768|gene2768|rna2768|rna2768  5 FCPECSNmlypKEDKieKQLYMACRNCEH 33
                                       57777777776333333777788999976 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00047
                                        TTSCEEETTTSSSTHSHHSHHSS...TBSSTTTH CS
                                PHD  20 gCkrwfHqkClkppleseekpeg...ewlCekCk 50 
                                        +C+r+ H + + ++ + ++ + +    ++C+kC 
  gene2768|gene2768|rna2768|rna2768  75 KCGRCGHGYAVYFEPKGNNPDLElkiCYICKKCY 108
                                        799999999999888766666667899******6 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.4   0.00036      0.47       2      31 ..       5      34 ..       4      35 .. 0.95
   2 ?   -0.1   3.5      0.71     9e+02       3      11 ..      76      84 ..      76     111 .. 0.48

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00036
                                       B-TTT--B-EEE--TT-SS-EEEETTTTEE CS
                          Nudix_N_2  2 FCsqCGtpvelripdgDnreRlvCpaCgti 31
                                       FC++C + +  +  + +++    C +C+++
  gene2768|gene2768|rna2768|rna2768  5 FCPECSNMLYPKEDKIEKQLYMACRNCEHV 34
                                       9**********99999************99 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.71
                                       -TTT--B-E CS
                          Nudix_N_2  3 CsqCGtpve 11
                                       C  CG+  +
  gene2768|gene2768|rna2768|rna2768 76 CGRCGHGYA 84
                                       666666643 PP

>> GFA  Glutathione-dependent formaldehyde-activating enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.2    0.0024       3.1      47      69 ..       1      23 [.       1      28 [. 0.76
   2 ?    4.9   1.1     0.027        34       5      60 ..      28      84 ..      26     101 .. 0.59
   3 ?   -0.9   0.3       1.6   2.1e+03      50      55 ..     102     107 ..      84     110 .. 0.66

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0024
                                GFA 47 vtrsfCpeCgsplyseesaapev 69
                                       ++++fCpeC   ly +e++ +++
  gene2768|gene2768|rna2768|rna2768  1 MNKEFCPECSNMLYPKEDKIEKQ 23
                                       5789**********886665554 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.027
                                GFA  5 CsdCrkasgsaftanavvkae.alelleg....elkeykktadsgnkvtrsfCpeCgsply 60
                                       C++C + + ++ +   vv++  + e++e+    ++k  ++t d +  + +  C +Cg    
  gene2768|gene2768|rna2768|rna2768 28 CRNCEHVEEAMNN--KVVENVfHREFTEEidqeTAK--DMTMDPTLFIANVKCGRCGHGYA 84
                                       9999888864432..222222133333334222333..3447899999999*****97554 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 1.6
                                GFA  50 sfCpeC 55 
                                        ++C++C
  gene2768|gene2768|rna2768|rna2768 102 YICKKC 107
                                        455555 PP

>> zinc_ribbon_12  Probable zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.9    0.0037       4.8       9      40 ..       6      34 ..       5      37 .. 0.82
   2 ?    4.4   0.0     0.026        34      30      38 ..      72      80 ..      67      85 .. 0.85
   3 ?    0.2   1.2      0.51   6.6e+02       8      14 ..     103     109 ..     100     111 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0037
                     zinc_ribbon_12  9 CsnCfelLqlPkkflllkkkqqklrCGaCsev 40
                                       C +C+++L+  ++ +    kq  + C  C++v
  gene2768|gene2768|rna2768|rna2768  6 CPECSNMLYPKEDKIE---KQLYMACRNCEHV 34
                                       99******85566665...6789******998 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.026
                     zinc_ribbon_12 30 qklrCGaCs 38
                                       ++++CG+C 
  gene2768|gene2768|rna2768|rna2768 72 ANVKCGRCG 80
                                       579*****7 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.51
                     zinc_ribbon_12   8 vCsnCfe 14 
                                        +C++C++
  gene2768|gene2768|rna2768|rna2768 103 ICKKCYN 109
                                        6999986 PP

>> Zn_ribbon_SprT  SprT-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.59   7.6e+02       7      32 ..       6      11 ..       5      17 .. 0.58
   2 ?   -0.3   0.1      0.81     1e+03      26      30 ..      27      31 ..      18      34 .. 0.77
   3 ?   10.0   3.3   0.00051      0.65       6      30 ..      75     107 ..      75     109 .. 0.97

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.59
                     Zn_ribbon_SprT  7 CtgCgreythhlsirrhnYrCrrCkg 32
                                       C+ C                     +
  gene2768|gene2768|rna2768|rna2768  6 CPECS--------------------N 11
                                       56664....................4 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.81
                     Zn_ribbon_SprT 26 rCrrC 30
                                        Cr C
  gene2768|gene2768|rna2768|rna2768 27 ACRNC 31
                                       69999 PP

  == domain 3  score: 10.0 bits;  conditional E-value: 0.00051
                     Zn_ribbon_SprT   6 rCtgCgreythhlsirrhn........YrCrrC 30 
                                        +C++Cg  y + +  +  n        Y+C++C
  gene2768|gene2768|rna2768|rna2768  75 KCGRCGHGYAVYFEPKGNNpdlelkicYICKKC 107
                                        6******************************** PP

>> DUF2387  Probable metal-binding protein (DUF2387)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   4.3   0.00089       1.1      11      58 ..       6      56 ..       4      69 .. 0.69
   2 ?    3.0   0.6     0.086   1.1e+02       5      16 ..      70      81 ..      66     105 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00089
                            DUF2387 11 CPrCsemDkirmweedeveyrECvsCgftdelsek...gqsvakelktrvn 58
                                       CP Cs+m   +  + +++ y+ C +C++++e  ++   ++ + +e ++ + 
  gene2768|gene2768|rna2768|rna2768  6 CPECSNMLYPKEDKIEKQLYMACRNCEHVEEAMNNkvvENVFHREFTEEID 56
                                       ******9888888888899**********9876651112233344444444 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.086
                            DUF2387  5 FiAGavCPrCse 16
                                       FiA + C rC +
  gene2768|gene2768|rna2768|rna2768 70 FIANVKCGRCGH 81
                                       9*********75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1078  (0.0601261); expected 358.6 (0.02)
Passed bias filter:                      510  (0.0284455); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 772.29
//
Query:       gene2769|gene2769|rna2769|rna2769  [L=331]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (331 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1193  (0.0665402); expected 358.6 (0.02)
Passed bias filter:                      477  (0.0266049); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 2173.70
//
Query:       gene277|gene277|rna277|rna277  [L=565]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.8e-09   36.0   0.0    2.2e-08   34.1   0.0    2.0  2  DnaJ      DnaJ domain
    3.1e-08   33.1   0.2    2.3e-05   23.7   0.1    2.2  2  Sec63     Sec63 Brl domain
  ------ inclusion threshold ------
      0.036   13.9   0.5      0.092   12.6   0.5    1.6  1  DUF4896   Domain of unknown function (DUF4896)
      0.065   13.1   0.0       0.13   12.0   0.0    1.5  1  PqiA      Paraquat-inducible protein A
       0.12   12.1   1.5          4    7.2   0.0    2.7  2  NCE101    Non-classical export protein 1
       0.13   12.3   0.0        0.2   11.8   0.0    1.2  1  DDHD      DDHD domain


Domain annotation for each model (and alignments):
>> DnaJ  DnaJ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.1   0.0   7.2e-12   2.2e-08       1      55 [.      89     145 ..      89     148 .. 0.90
   2 ?   -2.5   0.0         2   5.9e+03      44      56 ..     267     279 ..     264     283 .. 0.82

  Alignments for each domain:
  == domain 1  score: 34.1 bits;  conditional E-value: 7.2e-12
                                    HHHHHHTSSTTG-HHHHHHHHHHHHHHHSTT..TSCCHHHHHHHHHHHHHHHHHHTS CS
                           DnaJ   1 dyYeiLgvskdasedeIkkaYrklalkyHPD..knpkdpeaeekFkeineAyevLsd 55 
                                    ++Ye+Lg+++ as  +I++++++l++ + PD  + p++  +e+  kei++Ay++L+ 
  gene277|gene277|rna277|rna277  89 NPYEVLGLEEGASRRDIQRSFKRLSRLHDPDyfEGPNKHANEQLLKEISRAYNMLKS 145
                                    68*****************************75556666889999**********85 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2
                                    HHHHHHHHHHTSH CS
                           DnaJ  44 keineAyevLsdp 56 
                                    k+i++ y+vL d 
  gene277|gene277|rna277|rna277 267 KKITNGYNVLIDH 279
                                    7899999999986 PP

>> Sec63  Sec63 Brl domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.1   7.6e-09   2.3e-05      13     170 ..     204     366 ..     201     414 .. 0.72
   2 !    7.4   0.0   0.00075       2.2     217     256 ..     524     560 ..     496     561 .. 0.72

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 7.6e-09
                                    --HHHHHHHHHHS-TT--.....HHHHHHHHHTSGGGGGS--.-TTHHHHHHHHHHTSSS--SSSTTSHHHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          Sec63  13 isyetiklfneslkpntt.....lkdlLeilssasEFeeipv.ReeEkkelkkLlekvpikvkediespeaKvniLlqay 86 
                                    + yet++++ +++++++t     ++ l+++++ ++E +e +  R+ + k   + +  vp++ +++i++ +   n+L+   
  gene277|gene277|rna277|rna277 204 LYYETMEMIYRRMHGECTntfigMRALINVIADSKELQEHRYkRQIDMKAFIENNYAVPLRESKKITNGY---NVLIDHL 280
                                    679***********99873333357899**********98762555666666666668888777777777...9998766 PP

                                    HTT---SSHHHHHHHHHHHHHHHHHHHHHHHHHHHTTBHHHHHHHHHHHHHHHHTS-.TT.....S--EEEEEEECEBTT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xx.....xxxxxxxxxxxxxxx RF
                          Sec63  87 isrlklegsdlvsDlkyilqnairilralveillskgwlslalslleLskmveqrlw.ds.....lPkleieaevqpitr 160
                                    +      g++  +Dl+y+ ++a  il+ +  ++   ++ +++ ++++L +mv+q++  +s     +P ++ +     + +
  gene277|gene277|rna277|rna277 281 FRT----GFAHPKDLEYVQKKALAILEGVKMVAFLTNNRAVLDNAFDLERMVVQAVPdPSfaamqFPYITYNQVFLNKGK 356
                                    643....47789********************************************954489999887777433333444 PP

                                    SEEEEEEEEE CS
                                    xxxxxxxxxx RF
                          Sec63 161 sklrvevtie 170
                                    s+ ++ + i 
  gene277|gene277|rna277|rna277 357 SVKELAMMID 366
                                    4444555555 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.00075
                                    TTEEEEEEEEEEE-.SSCCEEEEEEEEESSSSS-EEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          Sec63 217 astqevkleftvplsepgpkqltvrlisdswlgldqevti 256
                                     +t+e  + + +p++e ++ +l + l++d++ g+d + ++
  gene277|gene277|rna277|rna277 524 VGTKE--VILDIPVKE-RSATLEIVLVCDRYFGCDVKRKV 560
                                    44444..556665555.599***************88765 PP

>> DUF4896  Domain of unknown function (DUF4896)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.5   3.1e-05     0.092      16      39 ..     166     189 ..     163     190 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3.1e-05
                        DUF4896  16 LiqngyYeLgivlaiLlvLIDffI 39 
                                    Li+ngyY L++ ++++ vL  ff+
  gene277|gene277|rna277|rna277 166 LISNGYYSLAVYVLVFGVLFPFFA 189
                                    9******************99985 PP

>> PqiA  Paraquat-inducible protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   4.5e-05      0.13      26      69 ..     148     191 ..     139     217 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 4.5e-05
                           PqiA  26 lsllgstseatllsgvlalweegswlvAllvflasilvPllkll 69 
                                    l ++ +++++ ++ +   l+++g++ +A+ v+++ +l+P++  l
  gene277|gene277|rna277|rna277 148 LVINKNEKHHEVIAIPSWLISNGYYSLAVYVLVFGVLFPFFAYL 191
                                    56778899999****************************99765 PP

>> NCE101  Non-classical export protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.0    0.0013         4       5      24 ..      56      75 ..      55      86 .. 0.79
   2 ?    2.6   0.9     0.037   1.1e+02      10      43 ..     180     216 ..     179     218 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0013
                         NCE101  5 rflDPlLaifiGvaaYylyE 24
                                   r++ ++L + +Gv+aY++y 
  gene277|gene277|rna277|rna277 56 RTFPLILCMLVGVMAYLTYN 75
                                   66667999***********7 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.037
                         NCE101  10 lLaifiGvaaYylyEk...rterpeghrLneLlkkky 43 
                                    ++++ + ++aY+ + +   r++++   +++e++ +++
  gene277|gene277|rna277|rna277 180 VFGVLFPFFAYLHWKRytyRNKLGLYYETMEMIYRRM 216
                                    68999999*******9999999999999999999997 PP

>> DDHD  DDHD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   6.6e-05       0.2     115     219 ..     405     504 ..     321     508 .. 0.53

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 6.6e-05
                           DDHD 115 llnrslelaeeesaslaessksherasesskasqeskaaesstasssaksskaeekvelekvralnwwgRiDYaLqegal 194
                                    l+  +++  ++ + +++++   + +++e++++++++++++++++++++++s++    +l++ +  +++g  DY+L +++ 
  gene277|gene277|rna277|rna277 405 LVDDVQNGVDKGNGLNNAERGGSLNNAERRTDNKNNGQNDNNNETTNEDNSQS--INDLRTGVLVKQEGEFDYELLNAVG 482
                                    33333332222222333333333344555555555566655555555543333..34555556889999*******9987 PP

                           DDHD 195 eaeylsavasHasYWeseDvalFll 219
                                    +      v +Ha Y+ s+ ++   l
  gene277|gene277|rna277|rna277 483 TY---RHVPVHAPYFFSRAIVEWTL 504
                                    77...89999****99988876655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (565 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       904  (0.0504211); expected 358.6 (0.02)
Passed bias filter:                      509  (0.0283898); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.62u 0.27s 00:00:00.89 Elapsed: 00:00:00.46
# Mc/sec: 3715.96
//
Query:       gene2770|gene2770|rna2770|rna2770  [L=144]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.042   14.0   3.7      0.048   13.8   3.7    1.2  1  RRT14     Regular of rDNA transcription protein 14


Domain annotation for each model (and alignments):
>> RRT14  Regular of rDNA transcription protein 14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   3.7   2.7e-06     0.048      85     148 ..      56     121 ..      17     139 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.7e-06
                              RRT14  85 lkklakyeiikkkkeeeelteeekkyLnklvkk..ninalkklskiddleikeeleelkkeiLekt 148
                                        l+ + k+++++++k+e     ++ k  +k +kk  n n l++l++  +++ ++e++ +k+e+L   
  gene2770|gene2770|rna2770|rna2770  56 LNCITKLKNFENHKTERLIFPHNLKNFEKQIKKkeNNNFLSSLENRTQYQFEKEFSTIKQELLMFA 121
                                        567889*************************98445667***********************9755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1187  (0.0662056); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 966.86
//
Query:       gene2771|gene2771|rna2771|rna2771  [L=79]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       586  (0.0326845); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.32u 0.24s 00:00:00.56 Elapsed: 00:00:00.37
# Mc/sec: 647.52
//
Query:       gene2772|gene2772|rna2772|rna2772  [L=103]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-27   95.0   5.1      4e-27   94.5   5.1    1.2  1  Sod_Fe_N  Iron/manganese superoxide dismutases, alpha-hairpin


Domain annotation for each model (and alignments):
>> Sod_Fe_N  Iron/manganese superoxide dismutases, alpha-hairpin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.5   5.1   2.2e-31     4e-27       2      82 .]       2      91 ..       1      91 [. 0.89

  Alignments for each domain:
  == domain 1  score: 94.5 bits;  conditional E-value: 2.2e-31
                                       ------SS-TTTTTTTS-HHHHHHHHHTHHHHHHHHHHHHHHCHHHHCHCCHHHHHH.........HHHHHHHHHHHH CS
                           Sod_Fe_N  2 yeLpeLpYaydaLePhisketlelHhdkHhktYvnnlNkalekleeakkkleelvlk.........klekalrnnagg 70
                                       yeLpeLpY+ydaLeP+i+++t+ +Hh+kHh+ Y++nlN+al++++  ++++  l            +l++ l +nag 
  gene2772|gene2772|rna2772|rna2772  2 YELPELPYEYDALEPQIDENTMIIHHTKHHQKYIDNLNNALKDTKYPETTVGLLLNLikktddlndDLRNVLYFNAGS 79
                                       9*******************************************988887665543345578888799999******* PP

                                       HHHHHHHHHTB- CS
                           Sod_Fe_N 71 hvnHslfwknls 82
                                       h nH+++w+++s
  gene2772|gene2772|rna2772|rna2772 80 HYNHTMYWHCMS 91
                                       **********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       994  (0.0554409); expected 358.6 (0.02)
Passed bias filter:                      601  (0.0335211); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.30s 00:00:00.76 Elapsed: 00:00:00.48
# Mc/sec: 640.12
//
Query:       gene2773|gene2773|rna2773|rna2773  [L=553]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.9e-51  172.7   0.1    2.2e-50  171.2   0.1    1.8  1  FtsJ             FtsJ-like methyltransferase
      2e-13   50.5  13.0      2e-13   50.5  13.0    3.7  2  DUF3381          Domain of unknown function (DUF3381)
      5e-07   29.6  44.6    3.7e-05   23.4   9.2    3.4  3  Spb1_C           Spb1 C-terminal domain
     0.0011   18.9   0.0     0.0048   16.7   0.0    2.2  2  Methyltransf_23  Methyltransferase domain
  ------ inclusion threshold ------
      0.087   13.4   0.1       0.69   10.5   0.0    2.5  2  Rhodanese        Rhodanese-like domain


Domain annotation for each model (and alignments):
>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  171.2   0.1   6.2e-54   2.2e-50       1     177 []      24     196 ..      24     196 .. 0.98

  Alignments for each domain:
  == domain 1  score: 171.2 bits;  conditional E-value: 6.2e-54
                                        CCCCHHHHHHHHHHHHT-S-TT-EEEECT-TTSHHHHHHCCT.T.-SEEEEEESSSSHHHTTEEEECS-CCCSSHH CS
                               FtsJ   1 yrsRsayKLleidekfklfkpgktvvDlgaaPGgwsqvllqrlgakgkvvavDlqpmaplpgvttiqgditdpeti 76 
                                        yr+RsayKL+++++kf++++    vvDl++aPGgw qv++q+    + +++vDl p++++++v++i gdit   t 
  gene2773|gene2773|rna2773|rna2773  24 YRARSAYKLIQLNKKFNFLQSCSSVVDLCCAPGGWLQVAVQHN-I-PDIIGVDLYPIKKINNVKSIVGDITLSGTV 97 
                                        9****************99***********************5.4.9***************************** PP

                                        HHHCHCHHHSSEEEEEE--S-SS-CHHHHHHHHHCCCCHHHHCCHCCCCECCCEEEECCCHCCCHHHHHHHHHCCE CS
                               FtsJ  77 ekikealserkvdlvvsDgapdvsgvhdldeylqsqLllaalelalkllkpggtfvlkifrgeeteallkqlkkfF 152
                                        ++i++  +e   d+v++Dgap+v   +++d++ q +L+l a+++++k+lk++g+f++k+fr+++  ++l  l+++F
  gene2773|gene2773|rna2773|rna2773  98 KEILNIAGE--TDCVLHDGAPNVGVCWEQDAFEQNELVLHAIKISTKILKKDGIFLTKVFRSKDYFSILWVLNQLF 171
                                        ****98866..***************************************************************** PP

                                        EEEEEEE-SS--CCG-EEEEEEEEC CS
                               FtsJ 153 ekvsvvkPkssrsesseeflvcrgf 177
                                        e+v  +kP ssr++s+e+f+ crg+
  gene2773|gene2773|rna2773|rna2773 172 ESVVSTKPISSREQSAEIFVFCRGY 196
                                        ***********************96 PP

>> DUF3381  Domain of unknown function (DUF3381)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.5  13.0   5.5e-17     2e-13      16     155 ..     220     344 ..     215     355 .. 0.83
   2 ?  -20.8  26.0         5   1.8e+04     124     147 ..     459     482 ..     362     551 .. 0.58

  Alignments for each domain:
  == domain 1  score: 50.5 bits;  conditional E-value: 5.5e-17
                                        XXX--EEEHHHHHT-----HHHHH-SEEE--SHHHHH.HHSSSSS-SSHHHHHH-SSS--HHHHHHHHHHHHHHHH CS
                            DUF3381  16 ytlykelsvseFiksedpielLgkaneitfdkeelkekilkhpktteEikelckDLkVLGkkdlkkLLkWrkklrk 91 
                                         + yk++++seF++sedp ++L +++++ +d   +k   l  +   +  k++++DLk +Gk+d+kk+Lk r+kl k
  gene2773|gene2773|rna2773|rna2773 220 ENCYKVIKFSEFFNSEDPKSVLETYSKMLID---VKG-ELFDKVFDQNYKTMLDDLKQIGKHDMKKILKKREKLIK 291
                                        5689***************************...344.4566899******************************* PP

                                        H-XXXX.................XXXXX..XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                            DUF3381  92 elgleekkekeekeeeeeedeeeeeeeeeeaeeeeldeeeeiekeleelkeeekkkkKrekkka 155
                                        ++++ e          e  d      +e++++ +el ee ++++   e+k++++ +kKre   +
  gene2773|gene2773|rna2773|rna2773 292 YIQNGEY--------IEGLDV---PVKETVVSLDELPEESKLDQIKREMKKKQRDEKKREAHSK 344
                                        **76655........222222...3356788899999999999999999999999999987654 PP

  == domain 2  score: -20.8 bits;  conditional E-value: 5
                                        XXXXXXXXXXXXXXXXXXXXXXXX CS
                            DUF3381 124 eeeldeeeeiekeleelkeeekkk 147
                                        + ++++ ++++k+ +e+ ++  ++
  gene2773|gene2773|rna2773|rna2773 459 TIDDKNYKKVNKKQQEVMNRRIRR 482
                                        111111222222222222222222 PP

>> Spb1_C  Spb1 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   7.7     0.057   2.1e+02     136     169 ..     308     341 ..     258     358 .. 0.65
   2 !   16.6  11.8   1.3e-06    0.0048      17     114 ..     377     484 ..     363     492 .. 0.69
   3 !   23.4   9.2     1e-08   3.7e-05     155     209 ..     503     551 ..     491     552 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.057
                             Spb1_C 136 eliaededlsekeKakqieklmkkaakkkkkkkv 169
                                        e+++  ++l e++K +qi++ mkk ++ +kk++ 
  gene2773|gene2773|rna2773|rna2773 308 ETVVSLDELPEESKLDQIKREMKKKQRDEKKREA 341
                                        67889999*****************777544432 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 1.3e-06
                             Spb1_C  17 eekdsddeeeeede.........kidiltaealala...qqlatgkktke.dlidegfnryafndkdgLPeWFldD 79 
                                        +++d++++++             ++   ++e l l    ++l+ + k+ +      + n+ya+nd+++LP+ ++d+
  gene2773|gene2773|rna2773|rna2773 377 KNDDENKSKT---VkkaanidgiDEMSSDEESLELNsddKRLIVEMKNDReAFELRTVNKYALNDTSDLPKFYMDE 449
                                        2211111111...02234566665566666666665222455555555551555589******************* PP

                             Spb1_C  80 EkkhskpekpitkeavaaikeklralnarpiKKVa 114
                                         k+ ++ +  i  +  +++ +k++++  r i++ +
  gene2773|gene2773|rna2773|rna2773 450 QKNFNQLKSTIDDKNYKKVNKKQQEVMNRRIRRAM 484
                                        *****************************999876 PP

  == domain 3  score: 23.4 bits;  conditional E-value: 1e-08
                             Spb1_C 155 klmkkaakkkkkkkvkvvvakkankglsgrpkgvkgkykmVDkrmKkdlRalkri 209
                                        +l k   kk +kkk kvvv +k++       + +kg++k VD+rmKkdlR++kr+
  gene2773|gene2773|rna2773|rna2773 503 RLFKSCLKK-SKKKPKVVVCSKGKPA-----RTMKGRVKYVDRRMKKDLRKQKRV 551
                                        677777766.6777788888777554.....5689******************96 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   1.3e-06    0.0048      20      62 ..      42     118 ..      18     295 .. 0.64
   2 ?   -1.5   0.0      0.56     2e+03      61      89 ..     489     522 ..     388     524 .. 0.63

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.3e-06
                    Methyltransf_23  20 lraggrvLdiGcGtGillevlrengf.svtgvDlspeaveiae................................. 61 
                                        l++ ++v+d+ c+ G +l+v+ ++   +++gvDl+p++   +                                  
  gene2773|gene2773|rna2773|rna2773  42 LQSCSSVVDLCCAPGGWLQVAVQHNIpDIIGVDLYPIKK--INnvksivgditlsgtvkeilniagetdcvlhdga 115
                                        555669***************555555********9733..22345666666666666666666665555555555 PP

                    Methyltransf_23  62 ..k 62 
                                           
  gene2773|gene2773|rna2773|rna2773 116 pnV 118
                                        551 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.56
                    Methyltransf_23  61 e.....kakkaqkdqfdeqeaaepqgkfdlIvlr 89 
                                        e     ++ + ++   + ++ +++++k++++v++
  gene2773|gene2773|rna2773|rna2773 489 EimeeiSDENDRPRRLFKSCLKKSKKKPKVVVCS 522
                                        0333333444444444455666677777777775 PP

>> Rhodanese  Rhodanese-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.75   2.7e+03      27      68 ..     383     413 ..     368     444 .. 0.57
   2 ?   10.5   0.0   0.00019      0.69      26      82 ..     476     530 ..     417     546 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.75
                          Rhodanese  27 k.ghIpgAvnvskdtlsrakkseapllelpeellelgidnkkt 68 
                                        k   ++ A n+          +  +     ee lel  + +++
  gene2773|gene2773|rna2773|rna2773 383 KsKTVKKAANI----------DGIDEMSSDEESLEL--NSDDK 413
                                        43567777777..........333333333333333..22222 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00019
                          Rhodanese  26 ekghIpgAvnvskdtlsrakkseapllelpeellelgidnkktvvvycdgggraaaa 82 
                                           +I+ A  + k++  + + ++++   l+++ l++  ++kk+ vv+c++g+ a+  
  gene2773|gene2773|rna2773|rna2773 476 MNRRIRRAMKFKKEIMEEISDENDRPRRLFKSCLKK--SKKKPKVVVCSKGKPARTM 530
                                        445999999**9999999999999999999*****9..***********99985544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (553 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2085  (0.116292); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.80u 0.37s 00:00:01.17 Elapsed: 00:00:00.58
# Mc/sec: 2895.73
//
Query:       gene2774|gene2774|rna2774|rna2774  [L=393]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (393 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       884  (0.0493056); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.57u 0.33s 00:00:00.89 Elapsed: 00:00:00.52
# Mc/sec: 2286.75
//
Query:       gene2776|gene2776|rna2776|rna2776  [L=266]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.6e-57  193.5   0.5    4.9e-57  193.0   0.5    1.0  1  RrnaAD           Ribosomal RNA adenine dimethylase
    3.2e-08   34.1   0.0    6.6e-08   33.2   0.0    1.5  1  Methyltransf_25  Methyltransferase domain
    1.2e-06   28.1   0.0    1.9e-06   27.5   0.0    1.3  1  MTS              Methyltransferase small domain
    0.00061   19.6   0.0      0.001   18.9   0.0    1.4  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
    0.00066   20.3   0.0     0.0016   19.0   0.0    1.6  1  Methyltransf_11  Methyltransferase domain
     0.0014   19.3   0.0     0.0026   18.5   0.0    1.4  1  Methyltransf_12  Methyltransferase domain
     0.0049   16.4   0.0      0.013   15.1   0.0    1.7  2  DOT1             Histone methylation protein DOT1
     0.0075   15.9   0.0      0.012   15.2   0.0    1.3  1  Cons_hypoth95    Conserved hypothetical protein 95
  ------ inclusion threshold ------
      0.024   14.0   0.0      0.039   13.3   0.0    1.3  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
       0.03   13.9   0.0      0.058   13.0   0.0    1.6  2  Methyltransf_15  RNA cap guanine-N2 methyltransferase
      0.037   14.0   0.0       0.06   13.3   0.0    1.3  1  Methyltransf_32  Methyltransferase domain
      0.041   13.4   0.0      0.076   12.5   0.0    1.4  1  Methyltransf_4   Putative methyltransferase
      0.041   13.8   0.0      0.066   13.1   0.0    1.3  1  Methyltransf_18  Methyltransferase domain
       0.05   13.0   0.0      0.076   12.4   0.0    1.2  1  PrmA             Ribosomal protein L11 methyltransferase (Prm


Domain annotation for each model (and alignments):
>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  193.0   0.5   3.8e-60   4.9e-57       4     261 ..       5     256 ..       3     259 .. 0.90

  Alignments for each domain:
  == domain 1  score: 193.0 bits;  conditional E-value: 3.8e-60
                                        CXXGCG--EE--HHHHHHHHHHH-GGTTSEEEEES-TTTCCHHHHHCC-SEEEEE-S-HHHHHHHHCHTT...TCC CS
                             RrnaAD   4 lrksygqnflknkkvineIldklnleekltvleigpGkGilTeeLakrakqvvvlElderLakllqkkls...kde 76 
                                         +k++gq++lkn+ +i++I++ +n+ e++tvleig+G+G+lT++L+  ak+v  +E+der+a++l k+++    ++
  gene2776|gene2776|rna2776|rna2776   5 YKKDLGQHILKNPGIIDRIIERANILETDTVLEIGSGTGNLTVKLLAKAKKVICYEKDERMAAELVKRVKslnMYH 80 
                                        6899****************************************************************999999** PP

                                        CEEEE-S-CCGHHHHHHHCTTTCCCCEEEEEEE--TTTHHHHHHHHHHGGGGCEEEEEEEEEHHHHHHHH--TTST CS
                             RrnaAD  77 klkvvhqDflkfetpeevtekdsihqeflvvanlPyeistqlvkqlleesrfglvkmllwlqkefarrllarpgsk 152
                                        k+k+   D +k ++p +           l+v+n+Py+is+ l+++l++ + f  + + l+lq efa rl+arpgs 
  gene2776|gene2776|rna2776|rna2776  81 KMKLFVGDCMKSDFPHFD----------LCVSNIPYQISSVLIFKLFS-YNF--RAAFLMLQHEFAMRLVARPGSP 143
                                        ****************77..........9******************6.888..9********************* PP

                                        T-SHHHHHHHHHEEEEEEEEC-GGCECS--SSSEEEEEEEE-SS-S--S-HHHHHHHHHHHHCTTTSBCCCHCCCT CS
                             RrnaAD 153 krsrlsvlreaftdvklvakveksifsPppkvdsalvelerkdedlpqkdlkkyesvvrkllnrkrktlstslksl 228
                                        ++srlsv +++f  v+   kv +++f P pkv+sa+v+++++ e+ p+ +++++  ++r+++ rk+ktl  ++  +
  gene2776|gene2776|rna2776|rna2776 144 DYSRLSVSTQLFSKVEYMFKVSRKNFNPMPKVESAVVKIRKRLEQ-PDINVEEFANFLRICFKRKNKTLGGVFGDK 218
                                        ********************************************9.8**********************8777666 PP

                                        STCHHHHHCTT...T--...TTTCCCCSGHHHHHHHHH CS
                             RrnaAD 229 lpggelqalsst..gin...dnalvkklsaeqtldifk 261
                                           + + + + +  +i      ++++kl++e++l++f 
  gene2776|gene2776|rna2776|rna2776 219 SVVKTVGKEKREigEILstyGVKRANKLQVEDFLQVFL 256
                                        55555555444444444111456777888888888775 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.2   0.0   5.2e-11   6.6e-08       1      71 [.      35     103 ..      35     118 .. 0.92

  Alignments for each domain:
  == domain 1  score: 33.2 bits;  conditional E-value: 5.2e-11
                                        EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT..TEEEEESBCCGBSSSTTTEEEEEEE CS
                    Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl..nvefvqgdaedlpfedgsfDlvvss 71 
                                        vL++G GtG+lt +l+++   +kv++ + +e+m ++  +r+++ ++  ++++ +gd+ + +f++  fDl+vs+
  gene2776|gene2776|rna2776|rna2776  35 VLEIGSGTGNLTVKLLAKA--KKVICYEKDERMAAELVKRVKSLNMyhKMKLFVGDCMKSDFPH--FDLCVSN 103
                                        9***************996..9********************988889**************96..*****95 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.5   0.0   1.5e-09   1.9e-06      31     157 ..      31     159 ..      19     168 .. 0.82

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 1.5e-09
                                        TCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESB.HHHHHHHHHHHHHTTGC.EEEEE-STTTTSTTS-EEEEEE- CS
                                MTS  31 lsgkvlDlGcGaGvlgaalakespeaevtlvdvd.arAlesakenleankle.vevvasdvleeveekkfdlivsN 104
                                        ++++vl +G+G+G l+++l+++ ++  v ++++d  +A e+ k+  + n  + ++++  d+++     +fdl vsN
  gene2776|gene2776|rna2776|rna2776  31 ETDTVLEIGSGTGNLTVKLLAKAKK--VICYEKDeRMAAELVKRVKSLNMYHkMKLFVGDCMKSDF-PHFDLCVSN 103
                                        4578*****************9998..66666652679999999999999989********99888.8******** PP

                                        --STTTCHCHHHHHHHHHHHHHHHEEEEEEEEEEEETTSCHHHH...HHHHHS--E CS
                                MTS 105 PPfhagkatelavaeeliaeAkeaLkegGeLliVanrklgyesl...leelfgnve 157
                                         P++ ++    ++    +++A  +L+++  +++Va+   +  s     ++lf++ve
  gene2776|gene2776|rna2776|rna2776 104 IPYQISSVLIFKLFSYNFRAAFLMLQHEFAMRLVARPGSPDYSRlsvSTQLFSKVE 159
                                        ****************************9999999987765544132345555555 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   7.8e-07     0.001      58     134 ..      16      90 ..       1     106 [. 0.83

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 7.8e-07
                                        -HHHHHHHHHHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTC.SEEEEES- CS
                               PCMT  58 aphmvalalellelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldle.nvivvvgD 132
                                        +p ++ +++e  ++ + + vLe+GsG+G lt+   +l+ +  +v+  e+ +++++e  +++k l++  ++++ vgD
  gene2776|gene2776|rna2776|rna2776  16 NPGIIDRIIERANILETDTVLEIGSGTGNLTV---KLLAKAKKVICYEKDERMAAELVKRVKSLNMYhKMKLFVGD 88 
                                        56667777888889999************997...566777789*******************9875599999999 PP

                                        GG CS
                               PCMT 133 Gr 134
                                          
  gene2776|gene2776|rna2776|rna2776  89 CM 90 
                                        75 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   1.3e-06    0.0016       1      68 [.      36     103 ..      36     109 .. 0.92

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.3e-06
                                        EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-..EEEETTEECCCTSS-TT-EEEEEEE CS
                    Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseegl..kvefvvadaeklpfednsfDlvvss 68 
                                        L++G+GtG l+ +l  ++++v++ + +++m +   ++++  ++  k+++ v+d+ k  f+   fDl+vs+
  gene2776|gene2776|rna2776|rna2776  36 LEIGSGTGNLTVKLLAKAKKVICYEKDERMAAELVKRVKSLNMyhKMKLFVGDCMKSDFPH--FDLCVSN 103
                                        89*************999*************8887777777778999************99..***9997 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0     2e-06    0.0026       1      72 [.      36     102 ..      36     124 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 2e-06
                    Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvva 72 
                                        LeiG+GtG+l+  ll+k   +++++++ ++++ +   ++ ++ +    ++++l++ d  ++d + +fDl v+
  gene2776|gene2776|rna2776|rna2776  36 LEIGSGTGNLTVKLLAK--AKKVICYEKDERMAAELVKRVKSLN--MYHKMKLFVGDCMKSDFP-HFDLCVS 102
                                        8****************..**************66666666555..566999999999999998.9999775 PP

>> DOT1  Histone methylation protein DOT1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   9.9e-06     0.013      28     112 ..      17     101 ..      14     124 .. 0.74
   2 ?   -2.7   0.0       2.8   3.6e+03      83     109 ..     225     250 ..     209     254 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 9.9e-06
                                        HHHHHHHHHHTT--TT-EEEEES-TTSHHHHHHHHHH--SEEEEEE--HH.HHHHHHHHHHH.HHHHHHHTTB--- CS
                               DOT1  28 peflsevldkvnlkkedvFvDLGSGvGnvvlqaalevgcklsvGvEimdn.aselaekqkee.lkkrlklfGkkla 101
                                        p ++ +++++ n+ + d+ +++GSG Gn++++  ++   k+ +  E+ +  a+el ++ k+  + + +klf  + +
  gene2776|gene2776|rna2776|rna2776  17 PGIIDRIIERANILETDTVLEIGSGTGNLTVKLLAK--AKKVICYEKDERmAAELVKRVKSLnMYHKMKLFVGDCM 90 
                                        677899***********************9986555..55667778876426778777666414567888877777 PP

                                        -EEEESS-STT CS
                               DOT1 102 kiefirksFve 112
                                        k +f + +   
  gene2776|gene2776|rna2776|rna2776  91 KSDFPHFDLCV 101
                                        77776666555 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2.8
                                        HHHHHHHHHHHHHTTB----EEEESS- CS
                               DOT1  83 ekqkeelkkrlklfGkklakiefirks 109
                                         k+k+e+ + l+ +G+k a+ +++ ++
  gene2776|gene2776|rna2776|rna2776 225 GKEKREIGEILSTYGVKRAN-KLQVED 250
                                        56677788888888888654.444455 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   9.7e-06     0.012      40     102 ..      30      91 ..      21     119 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 9.7e-06
                                        HCC-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HH CS
                      Cons_hypoth95  40 iegarvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelkleeetaelkedale 102
                                        +e  +vL++ +G+G l +  l   akk+++ ekd+++++ l + +++l++ ++++ ++ d ++
  gene2776|gene2776|rna2776|rna2776  30 LETDTVLEIGSGTGNLTVKLLAK-AKKVICYEKDERMAAELVKRVKSLNMYHKMKLFVGDCMK 91 
                                        78899**************9986.7**************************999999988654 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0     3e-05     0.039      38     114 ..      22      96 ..       8     111 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3e-05
                                        HHHHH--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSS.TEEEEE--TTT-TT CS
                    Ubie_methyltran  38 fveklvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegki.nieflqanaeeLpf 112
                                         ++++ + ++  +vl++ +Gtg+l++kl+ +++   kv+  + +e m  +  k++k   ++ ++++ +++ ++ +f
  gene2776|gene2776|rna2776|rna2776  22 RIIERANILETDTVLEIGSGTGNLTVKLLAKAK---KVICYEKDERMAAELVKRVKSLNMYhKMKLFVGDCMKSDF 94 
                                        566778889999***************998765...799999**************98877799999999999888 PP

                                        S- CS
                    Ubie_methyltran 113 ed 114
                                          
  gene2776|gene2776|rna2776|rna2776  95 PH 96 
                                        75 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   4.6e-05     0.058       3      61 ..      34     100 ..      32     161 .. 0.84
   2 ?   -3.3   0.0       4.5   5.8e+03      44      70 ..     237     263 ..     235     265 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4.6e-05
                    Methyltransf_15   3 vilDlfsGaGGnviqfalvfekviaieinleklacaqhNaevYgvsdkitlvlgdvfe........l 61 
                                        ++l + sG+G  ++++  + +kvi+ e++++  a   +  ++ ++ +k++l +gd+++         
  gene2776|gene2776|rna2776|rna2776  34 TVLEIGSGTGNLTVKLLAKAKKVICYEKDERMAAELVKRVKSLNMYHKMKLFVGDCMKsdfphfdlC 100
                                        689999**********999*************************************98555555541 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 4.5
                    Methyltransf_15  44 vYgvsdkitlvlgdvfellaklkleki 70 
                                         Ygv+   +l + d+++++ ++kl+ki
  gene2776|gene2776|rna2776|rna2776 237 TYGVKRANKLQVEDFLQVFLNFKLRKI 263
                                        577777777777777777777777665 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   4.7e-05      0.06      12      83 ..      19      83 ..      12     104 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.7e-05
                    Methyltransf_32 12 lvakllkelakesgaltvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekraeklgkkfnkrls 83
                                       ++++++++ a+  +  tv+++G+G g L+  l      +  kv++ +  e+++++  kr + l+ ++ ++++
  gene2776|gene2776|rna2776|rna2776 19 IIDRIIER-ANILETDTVLEIGSGTGNLTVKLLA----KAKKVICYEKDERMAAELVKRVKSLN-MY-HKMK 83
                                       67777777.4667789*****************9....4789************9999999999.44.5555 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   5.9e-05     0.076       4      62 ..      34      91 ..      31      98 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.9e-05
                                       EEEEET-TTSHHHHHHHHHSTTSEEEEEES-HHHHHHHHHHHHHC.TTSSEEEEES-CCC CS
                     Methyltransf_4  4 vvleiGcGkGeflvalAkknPdknflGiEirvkvvakvlkkieal.elkNlrilrgdalk 62
                                       +vleiG+G G+++v+l  k   k+++  E+ +++ a+++k+++ l  ++ ++++ gd +k
  gene2776|gene2776|rna2776|rna2776 34 TVLEIGSGTGNLTVKLLAK--AKKVICYEKDERMAAELVKRVKSLnMYHKMKLFVGDCMK 91
                                       79*************8665..478999****************99556778888777765 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   5.1e-05     0.066      10      76 ..      28      91 ..      20     101 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 5.1e-05
                    Methyltransf_18 10 slvekgsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagledkievrlsdGle 76
                                       +++ ++++v+ iG+  g l+++l+   kakkvi  +  e   ++  + +++ ++ +k+++ ++d ++
  gene2776|gene2776|rna2776|rna2776 28 NIL-ETDTVLEIGSGTGNLTVKLL--AKAKKVICYEKDERMAAELVKRVKSLNMYHKMKLFVGDCMK 91
                                       444.4889****************..68899********************************9887 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   5.9e-05     0.076     159     234 ..      29     104 ..      20     119 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 5.9e-05
                               PrmA 159 vkegeevlDvGtGSGiLaiaaakLgakkvvavDiDe.vAvkvakeNaelNkvea.klevalseellk..eekadvi 230
                                        + e+++vl +G G+G L++  ++  akkv+ +  De +A +  k+  +lN  ++ kl v   ++ +k    ++d+ 
  gene2776|gene2776|rna2776|rna2776  29 ILETDTVLEIGSGTGNLTVK-LLAKAKKVICYEKDErMAAELVKRVKSLNMYHKmKLFV---GDCMKsdFPHFDLC 100
                                        56788************985.66789********976899**********999866655...44444223459*** PP

                               PrmA 231 vaNI 234
                                        v+NI
  gene2776|gene2776|rna2776|rna2776 101 VSNI 104
                                        ***9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (266 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       765  (0.0426683); expected 358.6 (0.02)
Passed bias filter:                      578  (0.0322383); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 1780.15
//
Query:       gene2777|gene2777|rna2777|rna2777  [L=76]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 515.86
//
Query:       gene2778|gene2778|rna2778|rna2778  [L=128]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.9e-28   98.5   0.8    3.3e-28   98.3   0.8    1.0  1  Ribosomal_L18   Ribosomal protein 60S L18 and 50S L18e
    0.00029   21.5   0.2    0.00052   20.7   0.2    1.5  1  Ribosomal_L27A  Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27


Domain annotation for each model (and alignments):
>> Ribosomal_L18  Ribosomal protein 60S L18 and 50S L18e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.3   0.8   3.7e-32   3.3e-28      52     175 ..       1     117 [.       1     126 [. 0.94

  Alignments for each domain:
  == domain 1  score: 98.3 bits;  conditional E-value: 3.7e-32
                      Ribosomal_L18  52 msrinrpplslsrlvkkvkkkeeekkiavvvgtvtdDvrllevPklsvaALrftetararilkaGGeiltlDqLal 127
                                        msr+nr+p+ +++l+++       +k++vvvg+v+d +r++++Pkl+++AL  +++ar+++ k GGei tlD+L  
  gene2778|gene2778|rna2778|rna2778   1 MSRSNRQPIKVAKLAEHA------GKVIVVVGKVLDSERVFTLPKLTIVALSASREARRKVKKFGGEIYTLDKLFK 70 
                                        8**********9998765......589************************************************* PP

                      Ribosomal_L18 128 raPtGkntvLlrGkkkareavkhfgaapgvphshkkpyvrskgrkfek 175
                                         + + kn+vL+ G++++r+a+k+fg a+g+ +s++ p++++k ++ ek
  gene2778|gene2778|rna2778|rna2778  71 VTSDLKNVVLVCGDRTKRKAYKYFG-AAGEKNSQTYPRTTNKRNSGEK 117
                                        *************************.699*********9999887775 PP

>> Ribosomal_L27A  Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.2   5.8e-08   0.00052      72     127 ..       6      63 ..       1      64 [. 0.75

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 5.8e-08
                                        --EEEGGGTTTTSSS....SE.EEE--S--.-..--EEEESEE-HHHHHHHHHTT-EEE CS
                     Ribosomal_L27A  72 aeeidleelaeaglikkkdgv.Kvlgkgel.tk.klkvkaskfSkkAkekIeaaGGkve 127
                                        +++i++++l +++  k    v Kvl ++++ t  kl++ a ++S++A+ k++++GG++ 
  gene2778|gene2778|rna2778|rna2778   6 RQPIKVAKL-AEHAGKVIVVVgKVLDSERVfTLpKLTIVALSASREARRKVKKFGGEIY 63 
                                        566777777.333333356778*****97735545*********************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       680  (0.0379274); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 883.00
//
Query:       gene2779|gene2779|rna2779|rna2779  [L=426]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.27   11.1   5.6        1.8    8.4   1.6    2.7  2  BP28CT    BP28CT (NUC211) domain


Domain annotation for each model (and alignments):
>> BP28CT  BP28CT (NUC211) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   1.6   9.9e-05       1.8      82     120 ..     218     256 ..     204     261 .. 0.87
   2 ?    3.5   0.1    0.0033        58      80     108 ..     328     356 ..     306     362 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 9.9e-05
                                        HHHHHHHHHHHH--------TTHHHHHHHHHHHHH---- CS
                             BP28CT  82 litfykllnklaekLkslftsYasyllenavelLkalne 120
                                         i fy++ + l+ ++ ++f+s++  +l  +++ Lk++++
  gene2779|gene2779|rna2779|rna2779 218 YINFYRFRDVLFYCFLNIFISFFDVILFFTIAELKEASN 256
                                        689*******************************98864 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.0033
                                        -HHHHHHHHHHHHH--------TTHHHHH CS
                             BP28CT  80 eRlitfykllnklaekLkslftsYasyll 108
                                        +  + fy+++ +++ +L s+++s + y+l
  gene2779|gene2779|rna2779|rna2779 328 KTGLLFYQVIRSIFCNLSSIIVSCVFYFL 356
                                        55678*****************9777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (426 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1322  (0.0737353); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.44
# Mc/sec: 2916.93
//
Query:       gene278|gene278|rna278|rna278  [L=57]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (57 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       575  (0.0320709); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.25s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 436.63
//
Query:       gene2780|gene2780|rna2780|rna2780  [L=204]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.5e-08   34.9   2.8    6.1e-08   33.0   0.7    2.3  2  Fcf1         Fcf1
  ------ inclusion threshold ------
      0.011   14.0   1.2      0.015   13.6   1.2    1.1  1  MCM3AP_GANP  MCM3AP domain of GANP
       0.31   11.5   8.9       0.13   12.7   6.3    1.6  2  DUF1690      Protein of Unknown function (DUF1690)


Domain annotation for each model (and alignments):
>> Fcf1  Fcf1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.1     0.053   3.2e+02       8      30 ..      56      78 ..      53     112 .. 0.72
   2 !   33.0   0.7     1e-11   6.1e-08      23      93 ..     116     184 ..      94     190 .. 0.78

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.053
                                       EEEEEHHHHHHHHHCT..-HHHH CS
                               Fcf1  8 kpliTqCviaeleklgkklkeal 30
                                       k+++++C +++++  g+k ++ +
  gene2780|gene2780|rna2780|rna2780 56 KLFTSRCLYKKCYGKGEKSDNSV 78
                                       789999****9999997744433 PP

  == domain 2  score: 33.0 bits;  conditional E-value: 1e-11
                                        T...-HHHHHHHTTSEEE----SS---HHHHHHHHH-BTB-TT-EEEE-S-HHHHHHHHTSTT--EEEEE-- CS
                               Fcf1  23 g.kklkealkiaktferlkCnhkkptsaddClvsvvkkkknkkryivAtqDkdlrrrlrkipgvPilyikrs 93 
                                        g ++ k+a+k+ak++e ++C hk+++++++C+ + vkk +n ++y++ +  +   ++ +  + vP++ ++r+
  gene2780|gene2780|rna2780|rna2780 116 GnQTSKTAMKFAKHIEIRNCLHKNEVTPAECIRKFVKK-SNANHYFLGCILN--NNKYKGLKNVPLVIFRRN 184
                                        2344689******************************5.5******998544..355667777888877776 PP

>> MCM3AP_GANP  MCM3AP domain of GANP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   1.2   2.5e-06     0.015     614     715 ..      17     116 ..       4     118 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.5e-06
                        MCM3AP_GANP 614 eeskrfeeqLqqwleedsealldslslPlylpqslvslpqaieiptlseseveseqskrseeqlressekteasls 689
                                        e s  f++ +q +l++   a ld++++P+ + + + + p+  +  ++  +++   + ++s+++ +e+ +++++s++
  gene2780|gene2780|rna2780|rna2780  17 ERSFAFRKPFQLLLDDMLLAYLDKVNFPITVINNTFNYPKLFT--SRCLYKKCYGKGEKSDNSVKENDKHESESVK 90 
                                        5677899999999999999**********************99..455555566666677777788999******* PP

                        MCM3AP_GANP 690 erLkeLerlikasreeelacelkLsa 715
                                        ++L e+ + +k + +e +  ++kL++
  gene2780|gene2780|rna2780|rna2780  91 SKLPEITEALKEEENEHKTQSVKLQG 116
                                        *******************9999985 PP

>> DUF1690  Protein of Unknown function (DUF1690)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       1.2   7.3e+03      38      46 ..       8      16 ..       3      25 .. 0.48
   2 ?   12.7   6.3   2.1e-05      0.13      63     131 ..      73     149 ..      61     153 .. 0.74

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1.2
                            DUF1690 38 rVaeeLkkL 46
                                       ++ + L+kL
  gene2780|gene2780|rna2780|rna2780  8 KIRKALQKL 16
                                       223333333 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 2.1e-05
                            DUF1690  63 kellkdeadakdelsskalnekieeLrkkleefkkkeeekl.........peevee.....areevveClrenkgk 124
                                        k  ++++ +++d++ s+++++k+ e+++ l+e ++++++++         +    +     +  e+ +Cl +n+ +
  gene2780|gene2780|rna2780|rna2780  73 K--SDNSVKENDKHESESVKSKLPEITEALKEEENEHKTQSvklqgnqtsK----TamkfaKHIEIRNCLHKNEVT 142
                                        3..33334589999****************997777665558888765442....1234446679*********** PP

                            DUF1690 125 pLdCwee 131
                                        p +C ++
  gene2780|gene2780|rna2780|rna2780 143 PAECIRK 149
                                        ****876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2223  (0.123989); expected 358.6 (0.02)
Passed bias filter:                      759  (0.0423336); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 1459.54
//
Query:       gene2781|gene2781|rna2781|rna2781  [L=631]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.5e-77  259.0  11.9    2.5e-77  259.0  11.9    1.9  2  zf-C2H2_aberr  Aberrant zinc-finger
  ------ inclusion threshold ------
       0.46   10.8   5.0        4.3    7.7   1.6    3.3  3  zf-C2H2_jaz    Zinc-finger double-stranded RNA-binding


Domain annotation for each model (and alignments):
>> zf-C2H2_aberr  Aberrant zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  259.0  11.9   2.8e-81   2.5e-77       1     176 []      17     188 ..      17     188 .. 1.00
   2 ?   -3.7   0.3       1.2   1.1e+04     100     143 ..     541     584 ..     528     585 .. 0.60

  Alignments for each domain:
  == domain 1  score: 259.0 bits;  conditional E-value: 2.8e-81
                      zf-C2H2_aberr   1 ykClykaCdlkyssvlglrrhlveykhslytnsefslkCpvrkCsesivelentelleehlekehaakllellkel 76 
                                        ykCl+++Cdl+y+svlglrrh+++y+h+ly+n ++slkCpvrkCs+siv+l+n+e+l++h+ekeha++l+++l+++
  gene2781|gene2781|rna2781|rna2781  17 YKCLHNSCDLFYDSVLGLRRHISHYDHNLYYNPGYSLKCPVRKCSVSIVKLDNVEFLYDHFEKEHAQRLAAQLRDI 92 
                                        9*************************************************************************** PP

                      zf-C2H2_aberr  77 eieikkteetekvnykgkivelkkedsvvnlsdvitendvlkdilltifvngvikiiDidkkdliyCripGCgkrf 152
                                         ++ikkt+et+k+ny     e++ +d++vnls+v++end+lkd+l++++++gviki+Didk+dli+C+ipGCgk+f
  gene2781|gene2781|rna2781|rna2781  93 LVRIKKTYETTKINYL----EHNVSDNCVNLSAVMRENDLLKDVLCSVYPSGVIKINDIDKPDLIFCGIPGCGKHF 164
                                        ****************....******************************************************** PP

                      zf-C2H2_aberr 153 kslmaYkYhckkflhslkelideY 176
                                        ks+maYkYhc+++lhs+++l+d+Y
  gene2781|gene2781|rna2781|rna2781 165 KSVMAYKYHCQTYLHSFATLFDSY 188
                                        ***********************9 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 1.2
                      zf-C2H2_aberr 100 kedsvvnlsdvitendvlkdilltifvngvikiiDidkkdliyC 143
                                        + d+vv  +++ +++ +  + +  i+ +   ++i +++ +l  C
  gene2781|gene2781|rna2781|rna2781 541 TYDGVVTTNSITKKKKICSEKIFEIIRRKEYYVICSEEYELSIC 584
                                        44666666667777777666666666666666666666555555 PP

>> zf-C2H2_jaz  Zinc-finger double-stranded RNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   1.6   0.00048       4.3       7      23 ..     160     176 ..     160     179 .. 0.91
   2 ?   -3.4   0.0       1.5   1.4e+04       9      17 ..     387     395 ..     387     395 .. 0.73
   3 ?    2.5   0.0     0.022     2e+02       6      20 ..     468     482 ..     467     482 .. 0.91

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00048
                                        TTBBBSSHHHHHCCTTS CS
                        zf-C2H2_jaz   7 CdKyFksenaldnHlkS 23 
                                        C K+Fks  a++ H+ +
  gene2781|gene2781|rna2781|rna2781 160 CGKHFKSVMAYKYHCQT 176
                                        9*************976 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 1.5
                                        BBBSSHHHH CS
                        zf-C2H2_jaz   9 KyFksenal 17 
                                        +y+k++++l
  gene2781|gene2781|rna2781|rna2781 387 RYCKNDQVL 395
                                        688888875 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.022
                                        TTTBBBSSHHHHHCC CS
                        zf-C2H2_jaz   6 lCdKyFksenaldnH 20 
                                        +Cd  F +e+   +H
  gene2781|gene2781|rna2781|rna2781 468 YCDIDFRDEQEILTH 482
                                        8*********98888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (631 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       804  (0.0448435); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.64u 0.28s 00:00:00.92 Elapsed: 00:00:00.48
# Mc/sec: 3968.83
//
Query:       gene2782|gene2782|rna2782|rna2782  [L=156]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       721  (0.0402142); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1125.62
//
Query:       gene2783|gene2783|rna2783|rna2783  [L=303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (303 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       885  (0.0493614); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 2186.50
//
Query:       gene2784|gene2784|rna2784|rna2784  [L=21]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (21 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                        85  (0.00474092); expected 358.6 (0.02)
Passed bias filter:                       75  (0.00418317); expected 358.6 (0.02)
Passed Vit filter:                         5  (0.000278878); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.29u 0.25s 00:00:00.54 Elapsed: 00:00:00.38
# Mc/sec: 164.60
//
Query:       gene2785|gene2785|rna2785|rna2785  [L=311]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-27   96.1   0.6    2.7e-27   95.7   0.6    1.1  1  RVT_1     Reverse transcriptase (RNA-dependent DNA polymerase


Domain annotation for each model (and alignments):
>> RVT_1  Reverse transcriptase (RNA-dependent DNA polymerase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.7   0.6   1.5e-31   2.7e-27       5     218 ..      52     291 ..      47     295 .. 0.91

  Alignments for each domain:
  == domain 1  score: 95.7 bits;  conditional E-value: 1.5e-31
                                        T....S-EEE......-THHHHCTB--...........-------HHHH................HCCHTS--EEE CS
                              RVT_1   5 g...pgsyRpisllsvdykalnkliakrLkdvl..ekllsenqpgfrpgrstldav...edllkalkkkkkaklll 72 
                                        +    ++ R is +++++k++ k++++ ++ ++  + +   +q gfr+ + ++ +    +++ k    +k +++++
  gene2785|gene2785|rna2785|rna2785  52 DlhsIDNHRGISSVNTLCKVVMKMVIDKITRICdaNRIHRCEQDGFRKLEKCVAQAtcfYEIIKRKILEKHKTIAI 127
                                        46667899*************************98888889***********99999**7777776788899**** PP

                                        EEEBCCGCCCSBB-GGGGGGG-EEET.........................TEEEEESB--ST-TTHHHHHHHHHH CS
                              RVT_1  73 klDlkkaFdsvpleellrkltafkvptklinliksflstrsfsvrvngeeskgryekkglpqGsvlSPllfnlfmn 148
                                        +l l+ka+d+  +e l+ kl+++ +  kl+n ik++   +  sv++  +++  + +++g++ G + SP+lf+l++n
  gene2785|gene2785|rna2785|rna2785 128 FLGLSKAYDRMLHEGLFAKLQSYDFGGKLLNFIKAIHIRPMSSVKMGDKRPNLFDYNTGVKRGYPASPILFTLYIN 203
                                        **********************************************99999************************* PP

                                        HHHTT-T..........TEEECTTEEEEEESSHHHHHHHHHHHHHHHHHTT--BEGGG-EEE.............. CS
                              RVT_1 149 ellrelrkra....kgvtllrYaDDililskskeelqelleaveewlkesglkinpeKtklvlft........... 209
                                        +l++ + ++     ++v  l++aDD ++++++ +e+++++  +++ +++ +++ n   +++++f+           
  gene2785|gene2785|rna2785|rna2785 204 DLFEGFIRKKigpnTSVPNLLFADDAVLFTEDCDEAKSCIPRIKQGCAKRKIEHNIMTCSVMTFNtettaiikykn 279
                                        ****9888778**99***********************************************99988887777766 PP

                                        .....ESSEEET CS
                              RVT_1 210 .v..kseevkyL 218
                                         +  + ++++yL
  gene2785|gene2785|rna2785|rna2785 280 mNilQVSSYRYL 291
                                        523566666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       591  (0.0329634); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 2011.91
//
Query:       gene2786|gene2786|rna2786|rna2786  [L=54]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (54 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       189  (0.0105416); expected 358.6 (0.02)
Passed bias filter:                      160  (0.00892409); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.27s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 392.90
//
Query:       gene2787|gene2787|rna2787|rna2787  [L=203]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.019   14.9   0.6      0.019   14.9   0.6    2.3  2  GnsAB_toxin  GnsA/GnsB toxin of bacterial toxin-antitoxin sys
      0.033   13.0   5.0      0.025   13.4   2.1    1.8  2  TssC         Type VI secretion system, TssC, VipB
      0.059   13.5   3.9        2.7    8.2   0.4    2.7  3  PRE_C2HC     Associated with zinc fingers
      0.075   13.7   2.1        3.1    8.5   0.1    2.5  2  Zn_ribbon_2  Putative zinc ribbon domain
       0.16   12.6   2.8        0.7   10.6   0.1    2.7  3  Edc3_linker  Linker region of enhancer of mRNA-decapping prot


Domain annotation for each model (and alignments):
>> GnsAB_toxin  GnsA/GnsB toxin of bacterial toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.4      0.17     6e+02       3      45 ..      30      53 ..      28      65 .. 0.52
   2 ?   14.9   0.6   5.2e-06     0.019      14      37 ..      68      91 ..      57      95 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.17
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHSSEEEEEEEEEEEETT CS
                        GnsAB_toxin  3 iEeLkkkAEeeiaeliakKiaELkKkTGkEVseieFtaREkmt 45
                                       i ++                   +Kk  kE s+  +t+ E ++
  gene2787|gene2787|rna2787|rna2787 30 ISNI-------------------QKKQIKEDSKAIYTTQESLK 53
                                       4444...................44444444444444444433 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 5.2e-06
                                       HHHHHHHHHHHHHHHHSSEEEEEE CS
                        GnsAB_toxin 14 iaeliakKiaELkKkTGkEVseie 37
                                       +a +i+kKi+ L K+  + Vsei+
  gene2787|gene2787|rna2787|rna2787 68 LAVYITKKIIKLLKQSNNQVSEIK 91
                                       588********************7 PP

>> TssC  Type VI secretion system, TssC, VipB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   2.1     7e-06     0.025      22      91 ..      28      99 ..      21     105 .. 0.86
   2 ?   -0.0   0.0     0.084     3e+02     151     165 ..     146     160 ..     132     171 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 7e-06
                               TssC 22 dgvqnlnpe..rkarkkiflteeekkeereelkkklelwiellessesveelvekskekaeeaeellkknlk 91
                                       ++++n++ +  +   k+i+ t+e+ k+e ++++++l +w  ++  ++++ +l+++s+++++e ++ ++kn +
  gene2787|gene2787|rna2787|rna2787 28 ENISNIQKKqiKEDSKAIYTTQESLKKETSQILTRLGVWRLAVYITKKIIKLLKQSNNQVSEIKSIIQKNGR 99
                                       56667665511456799**************************************************99965 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.084
                               TssC 151 nydrldlrenysllv 165
                                        n +r+dl++ny l++
  gene2787|gene2787|rna2787|rna2787 146 NIERIDLKNNYILIA 160
                                        679********8875 PP

>> PRE_C2HC  Associated with zinc fingers
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       1.3   4.7e+03      15      26 ..      27      38 ..      23      47 .. 0.70
   2 ?    5.7   0.1    0.0043        16       2      33 ..      74     105 ..      73     108 .. 0.91
   3 ?    8.2   0.4   0.00075       2.7       2      58 ..     116     173 ..     115     175 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.3
                           PRE_C2HC 15 vknihnmrkrnt 26
                                         ni+n++k++ 
  gene2787|gene2787|rna2787|rna2787 27 QENISNIQKKQI 38
                                       567777777744 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0043
                           PRE_C2HC   2 aqIeeaLkkhgfevknihnmrkrntktPqnmf 33 
                                        ++I++ Lk+ + +v +i  + ++n+++   m 
  gene2787|gene2787|rna2787|rna2787  74 KKIIKLLKQSNNQVSEIKSIIQKNGRSKSDMC 105
                                        78999*********************998886 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.00075
                           PRE_C2HC   2 aqIeeaLkkhgfevknihnmrkr.ntktPqnmfeveLkpaadkkeilkikqLgrqrVt 58 
                                         qI+++ + hg   k+ +  +++ + +tP+n+  + Lk++      l+i ++++ rV+
  gene2787|gene2787|rna2787|rna2787 116 TQIKANIERHGMYMKDFRYRKNNlSLQTPVNIERIDLKNNYILIATLNICSVLKKRVD 173
                                        69*************99888777799**************998889999999999885 PP

>> Zn_ribbon_2  Putative zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.2     0.018        63      43      82 .]      26      67 ..      20      67 .. 0.77
   2 ?    8.5   0.1   0.00086       3.1      29      59 ..     103     133 ..      94     147 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.018
                        Zn_ribbon_2 43 tmeemiekcvkklaeenke..lteeearkllkkllpkLkrWk 82
                                       + e++ ++  k+++e+ k+  +t+e+++k ++++l +L  W+
  gene2787|gene2787|rna2787|rna2787 26 EQENISNIQKKQIKEDSKAiyTTQESLKKETSQILTRLGVWR 67
                                       45566666667788887777788999************9996 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00086
                        Zn_ribbon_2  29 kyCykdGeftepdltmeemiekcvkklaeen 59 
                                         +C+ +G+ft+p+++++  ie+    +++ +
  gene2787|gene2787|rna2787|rna2787 103 DMCFGEGTFTKPKTQIKANIERHGMYMKDFR 133
                                        58******************99988888765 PP

>> Edc3_linker  Linker region of enhancer of mRNA-decapping protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.2      0.17     6e+02      24      48 ..      11      35 ..       2      59 .. 0.75
   2 ?   10.6   0.1    0.0002       0.7      66      93 ..      84     110 ..      80     111 .. 0.76
   3 ?   -1.5   0.0       1.1   4.1e+03       5      24 ..     136     154 ..     113     171 .. 0.70

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.17
                        Edc3_linker 24 sqevvtsPqqssksyvdrhldalkq 48
                                        + vv +P  +  sy++ ++ ++++
  gene2787|gene2787|rna2787|rna2787 11 DNRVVSQPIIYTRSYEQENISNIQK 35
                                       3456788899999999888887765 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.0002
                        Edc3_linker  66 anqstpkksgvkngqmrskdDECFGdgi 93 
                                         nq+ + ks ++    rsk D CFG+g+
  gene2787|gene2787|rna2787|rna2787  84 NNQVSEIKSIIQKNG-RSKSDMCFGEGT 110
                                        567777777775433.6*********97 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 1.1
                        Edc3_linker   5 kssksssapqailrradvks 24 
                                        k + s ++p++i r  d+k+
  gene2787|gene2787|rna2787|rna2787 136 KNNLSLQTPVNIER-IDLKN 154
                                        44556666666665.66655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1769  (0.098667); expected 358.6 (0.02)
Passed bias filter:                      596  (0.0332422); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 1478.19
//
Query:       gene2788|gene2788|rna2788|rna2788  [L=40]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (40 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       226  (0.0126053); expected 358.6 (0.02)
Passed bias filter:                      169  (0.00942607); expected 358.6 (0.02)
Passed Vit filter:                         7  (0.000390429); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.25s 00:00:00.59 Elapsed: 00:00:00.41
# Mc/sec: 293.45
//
Query:       gene2789|gene2789|rna2789|rna2789  [L=77]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       279  (0.0155614); expected 358.6 (0.02)
Passed bias filter:                      218  (0.0121591); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.28s 00:00:00.66 Elapsed: 00:00:00.44
# Mc/sec: 527.45
//
Query:       gene279|gene279|rna279|rna279  [L=310]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.5e-11   42.2   0.0    2.1e-10   41.0   0.0    1.6  1  RNA_pol_A_bac  RNA polymerase Rpb3/RpoA insert domain
    1.7e-08   33.7   0.0    2.5e-08   33.2   0.0    1.3  1  RNA_pol_L      RNA polymerase Rpb3/Rpb11 dimerisation domain


Domain annotation for each model (and alignments):
>> RNA_pol_A_bac  RNA polymerase Rpb3/RpoA insert domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.0   0.0   2.3e-14   2.1e-10       9     112 .]      57     191 ..      51     191 .. 0.84

  Alignments for each domain:
  == domain 1  score: 41.0 bits;  conditional E-value: 2.3e-14
                                    SS.HHHHHCHHHCSTCBSSCHHHHHHHHCTT-ETSSSSTTCSEEEEEEEEESSEC...EEGGGCBES............. CS
                  RNA_pol_A_bac   9 vlqDEvvaHrlgliplvsedvleillnlkelveeeeegeeeksvelkLnvkgpge...vtagdlkle............. 72 
                                    ++ +Ev+aHrlgl+p++ +  l     +          ++++ v ++++++g +    v + d++++             
  gene279|gene279|rna279|rna279  57 IVPEEVLAHRLGLVPIFCDALLL----VDSA-V---PTRNSC-VRMRIRKRGADGgvwVRSDDIEVVhfdsgrrmcswsr 127
                                    5789*************666555....2222.2...556666.99*******9999**********99999999999999 PP

                                    ........................SSSCEESSTTSEEEEEETT-EEEEEEEEEEESSEECTTT- CS
                  RNA_pol_A_bac  73 ........................dadveivnpdilIakLrkgqeleleakvkkGiGkehakfs 112
                                                            +a+  +++p++lI kL ++q l+ e+++ +G++kehak+s
  gene279|gene279|rna279|rna279 128 aveeddgleevdgdgianaldhtyNANLPMIKPGVLITKLGPNQCLDAEMYATRGTAKEHAKYS 191
                                    9999888888777777777777777777777*******************************97 PP

>> RNA_pol_L  RNA polymerase Rpb3/Rpb11 dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.2   0.0   2.8e-12   2.5e-08       3      67 ..      21     288 ..      19     290 .. 0.78

  Alignments for each domain:
  == domain 1  score: 33.2 bits;  conditional E-value: 2.8e-12
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxx.................................................... RF
                      RNA_pol_L   3 llrgvdhtlgNaLRrillsevpgvaiea.................................................... 30 
                                    ++++  + + NaLRr++l e+p vai +                                                    
  gene279|gene279|rna279|rna279  21 TISNAPLPFLNALRRTILEEIPAVAISKiifhkyvgivpeevlahrlglvpifcdalllvdsavptrnscvrmrirkrga 100
                                    57888899******************************************999999999999998888888888888888 PP

                                    ................................................................................ RF
                      RNA_pol_L  31 ................................................................................ 30 
                                                                                                                    
  gene279|gene279|rna279|rna279 101 dggvwvrsddievvhfdsgrrmcswsraveeddgleevdgdgianaldhtynanlpmikpgvlitklgpnqcldaemyat 180
                                    88888888888888888888888888888888888888888777777777777777777777777777666666666666 PP

                                    .....................xx...................................................xxxxxx RF
                      RNA_pol_L  31 .....................pv...................................................vkvntd 38 
                                                         p+                                                   v+v+ d
  gene279|gene279|rna279|rna279 181 rgtakehakyssvnicyyrmhPIltlnrsfknedahllkkrfkdgvigirrkgkdeeayvmddkevidvediegVSVRMD 260
                                    66666666666665555555511666666666666666666666666667777777777777777777777777888899 PP

                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      RNA_pol_L  39 kdklilevetdgslkPeealkeAlkiLke 67 
                                    +    + ve +  ++P e++k++l +L+e
  gene279|gene279|rna279|rna279 261 EHCVLFYVE-TEFIDPWEVVKRGLYVLVE 288
                                    999******.8899**********99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (310 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       380  (0.0211947); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 2032.52
//
Query:       gene2790|gene2790|rna2790|rna2790  [L=266]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0032   16.1   1.5     0.0056   15.2   1.5    1.4  1  Peptidase_S64  Peptidase family S64
  ------ inclusion threshold ------
      0.051   14.1   0.3        1.5    9.4   0.0    2.4  2  SLED           SLED domain


Domain annotation for each model (and alignments):
>> Peptidase_S64  Peptidase family S64
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   1.5   6.3e-07    0.0056     168     233 ..      19      85 ..       3      95 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 6.3e-07
                      Peptidase_S64 168 esvekeLkqLeedlaelmddinqsvinlskavieaieffkeFle.seekeklefevttennsslrki 233
                                         ++ keLk+L++ l++   ++ +s+ ++s+ v e  + fk+F++ +++++++e+++  +nn++lr  
  gene2790|gene2790|rna2790|rna2790  19 MAIMKELKSLKNVLVNENYQMTKSMSEVSNKVNEKANTFKNFNAfNKRTQEIEIKIRETNNKRLRAT 85 
                                        5799**************************************76144467889999999*****975 PP

>> SLED  SLED domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.3      0.03   2.7e+02      27      71 ..      17      59 ..       8      89 .. 0.52
   2 ?    9.4   0.0   0.00017       1.5      25      96 ..     113     185 ..     104     197 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.03
                               SLED 27 qvGpgpvslvlkevlqalvnaaykpkqvlklLkkgeggeveiita 71
                                       q  p  + + lk + + lvn +y+  + +++++++ + + ++++ 
  gene2790|gene2790|rna2790|rna2790 17 Q--PMAIMKELKSLKNVLVNENYQMTKSMSEVSNKVNEKANTFKN 59
                                       3..444444455555555555555555555555554333333332 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00017
                               SLED  25 PsqvGpgpvslvlkevlqalvnaayk.pkqvlklLkkgeggeveiitakiegkshtvklpvvesakevadfle 96 
                                        P+ +  gp+++v k  l+++  +  + p+++ +lL+ g   + +i+ + ++++++ + l  v++ +++++fl 
  gene2790|gene2790|rna2790|rna2790 113 PRILNGGPIQEVSKVQLKHFCGLGRNrPSNIRRLLRDGGIRSGSIVHVGFDKENRLEILAYVNTIEQIRKFLL 185
                                        7888899************9998765278889999999966677***************************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (266 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2360  (0.13163); expected 358.6 (0.02)
Passed bias filter:                      844  (0.0470746); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.43
# Mc/sec: 1841.02
//
Query:       gene2791|gene2791|rna2791|rna2791  [L=46]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (46 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       948  (0.0528752); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.32u 0.21s 00:00:00.53 Elapsed: 00:00:00.36
# Mc/sec: 387.37
//
Query:       gene2792|gene2792|rna2792|rna2792  [L=115]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
       0.15   10.4   3.8       0.16   10.4   3.8    1.1  1  Vitellogenin_N  Lipoprotein amino terminal region
       0.24   11.6   9.3       0.62   10.3   5.2    2.5  2  ProRS-C_1       Prolyl-tRNA synthetase, C-terminal


Domain annotation for each model (and alignments):
>> Vitellogenin_N  Lipoprotein amino terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   3.8   1.7e-05      0.16     151     231 ..      35     112 ..       2     114 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 1.7e-05
                                        EEEEEE...........E-SSSSEEEEEEEEEEEEEEEE--EEES-T.T-EE-HHHHHH--SEEEEEEEEEEEEEE CS
                     Vitellogenin_N 151 tlYdvsplpeellqeepeekegelievtKtknfdnCeqrvsyriGla.yaewcagtnkmgkflsrssvsryilkgk 225
                                        t  + +   + +  + ++  e   ++  +t+nf++C+++ ++ +  + ya +c  ++k++ + s s+++ ++  gk
  gene2792|gene2792|rna2792|rna2792  35 TVMKLK---KLITTNYQLTDEWRTFIKLRTRNFSSCTRLAKLGYIDNkYATECICCHKKNRKQS-STSCGCVRCGK 106
                                        333333...3333333366777777788**************998888*****99999999987.55555566666 PP

                                        TTEEEE CS
                     Vitellogenin_N 226 aknfti 231
                                        +++ ti
  gene2792|gene2792|rna2792|rna2792 107 TSERTI 112
                                        666665 PP

>> ProRS-C_1  Prolyl-tRNA synthetase, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.1       0.5   4.5e+03      24      31 ..       8      15 ..       3      28 .. 0.63
   2 ?   10.3   5.2   6.9e-05      0.62       6      62 ..      35     111 ..      30     113 .. 0.68

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.5
                                       HHHHHHHH CS
                          ProRS-C_1 24 cEekIkee 31
                                        E+k+ke+
  gene2792|gene2792|rna2792|rna2792  8 VEQKLKER 15
                                       46666665 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 6.9e-05
                                        HHHHTT-EEEEEESSGHHHHHHHHHHH...................S-EEEEEESSB.-SSCCCSB-TTT-SB-SE CS
                          ProRS-C_1   6 ealekkgfvlapWcgeeecEekIkeet...................gakslcipfdq.epseegtkCivcgkpakk 61 
                                        + ++ k+++ + ++ ++e+   Ik +t                   + +  c+  ++ ++s +++ C+ cgk +++
  gene2792|gene2792|rna2792|rna2792  35 TVMKLKKLITTNYQLTDEWRTFIKLRTrnfssctrlaklgyidnkyATECICCHKKNrKQSSTSCGCVRCGKTSER 110
                                        5667788999999999999999999997666666666666666644444444433335666777777777777776 PP

                                        E CS
                          ProRS-C_1  62 w 62 
                                        +
  gene2792|gene2792|rna2792|rna2792 111 T 111
                                        5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1187  (0.0662056); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 829.51
//
Query:       gene2793|gene2793|rna2793|rna2793  [L=223]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.1e-06   26.1   0.0    0.00044   20.1   0.0    2.3  1  Exo_endo_phos_2  Endonuclease-reverse transcriptase


Domain annotation for each model (and alignments):
>> Exo_endo_phos_2  Endonuclease-reverse transcriptase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   2.5e-08   0.00044       2     118 ..      28     137 ..      27     138 .. 0.73

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 2.5e-08
                    Exo_endo_phos_2   2 liisvYippsd.elenlestlekllselksp....kiiilGDfNakhplWgsedtdssargeeLiefleehslsll 72 
                                        li++vYip +  e++ +++ l  ++ ++ks+    +ii++GD+Na  +   s     ++rg +L +   +++ s  
  gene2793|gene2793|rna2793|rna2793  28 LIVNVYIPGKGtERRSALDRLAAFILTTKSTkrfsEIIMTGDWNALPKTTLSAL---QNRGLSLPNEALTFNQS-- 98 
                                        699*****999988888888888877777767789*********9765544422...23444444333333322.. PP

                    Exo_endo_phos_2  73 nllksgptfkssngsstiDltltsdnlalskleleeedlgSDHrpi 118
                                              ++ ++++g   iD  ++++++++++ +  ++  +SDH pi
  gene2793|gene2793|rna2793|rna2793  99 ------TRLSNRQG-RCIDYPVATNSTSIKTIKVLRKYDMSDHFPI 137
                                        ......55655555.9**************999999999*****98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       465  (0.0259356); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 1466.28
//
Query:       gene2794|gene2794|rna2794|rna2794  [L=48]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (48 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       254  (0.014167); expected 358.6 (0.02)
Passed bias filter:                      208  (0.0116013); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.25s 00:00:00.59 Elapsed: 00:00:00.40
# Mc/sec: 360.66
//
Query:       gene2795|gene2795|rna2795|rna2795  [L=101]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.7e-12   47.2  13.6    2.7e-12   47.2  13.6    1.7  2  zinc_ribbon_15   zinc-ribbon family
    0.00021   21.3  14.6    0.00097   19.1   6.6    2.6  2  DZR              Double zinc ribbon
     0.0054   16.4   0.5     0.0054   16.4   0.5    3.6  4  zf-NADH-PPase    NADH pyrophosphatase zinc ribbon domain
     0.0071   16.0   9.5      0.042   13.6   1.0    4.3  5  zinc_ribbon_2    zinc-ribbon domain
  ------ inclusion threshold ------
      0.039   13.9   2.4      0.039   13.9   2.4    2.3  2  zinc-ribbons_6   zinc-ribbons
      0.045   13.6   0.4      0.045   13.6   0.4    2.2  3  NinF             NinF protein
       0.13   11.8  14.8       0.15   11.6   0.7    4.0  4  TF_Zn_Ribbon     TFIIB zinc-binding
       0.34   10.8  12.9        1.5    8.7   1.7    3.1  3  zf-C3HC4_3       Zinc finger, C3HC4 type (RING finger)


Domain annotation for each model (and alignments):
>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.1       2.4   5.3e+03       6      15 ..       7      16 ..       2      23 .. 0.46
   2 !   47.2  13.6   1.2e-15   2.7e-12       1      86 []      24      96 ..      24      96 .. 0.99

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 2.4
                     zinc_ribbon_15  6 Cgklskaelv 15
                                       Cg++ k++ +
  gene2795|gene2795|rna2795|rna2795  7 CGTKRKTKRT 16
                                       4433333333 PP

  == domain 2  score: 47.2 bits;  conditional E-value: 1.2e-15
                     zinc_ribbon_15  1 ilCpkCgklskaelvkkkkvlklffipvfkwkkkkpylacskCkslleaskelgkeiekkessekkeCknCgkeveee 78
                                       i Cp+C  ++k+++  ++ +++++f+p++++ +++ y+ c++C ++l++++             +k+C++C++++ + 
  gene2795|gene2795|rna2795|rna2795 24 IFCPYCACSTKSVWLIDTMYFTFCFLPLYTIYNSSEYIGCKNCYKKLGDRS-------------VKTCERCTNVIIAG 88
                                       68************************************************9.............************** PP

                     zinc_ribbon_15 79 fkyCpkCg 86
                                       ++yC +Cg
  gene2795|gene2795|rna2795|rna2795 89 YRYCGRCG 96
                                       *******9 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   3.0      0.01        23       8      19 ..      19      30 ..       4      48 .. 0.62
   2 !   19.1   6.6   4.3e-07   0.00097       8      49 .]      56      96 ..      31      96 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.01
                                DZR  8 lppdarfCseCg 19
                                        + +++fC++C 
  gene2795|gene2795|rna2795|rna2795 19 QDTNDIFCPYCA 30
                                       334444555554 PP

  == domain 2  score: 19.1 bits;  conditional E-value: 4.3e-07
                                DZR  8 lppdarfCseCgtklkavaaedrCpsCgekvdpearfCpeCG 49
                                       ++++ + C++C +kl    + ++C +C+  + ++ r+C+ CG
  gene2795|gene2795|rna2795|rna2795 56 NSSEYIGCKNCYKKLG-DRSVKTCERCTNVIIAGYRYCGRCG 96
                                       6677888********5.6779********************9 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.1      0.17   3.8e+02       4       8 ..       5       9 ..       4      10 .. 0.84
   2 ?    1.6   1.8     0.099   2.2e+02       5      11 ..      25      31 ..      25      36 .. 0.78
   3 ?   -3.6   0.3       4.3   9.7e+03      24      27 ..      78      81 ..      76      83 .. 0.69
   4 !   16.4   0.5   2.4e-06    0.0054       3      15 ..      89     101 .]      87     101 .] 0.90

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.17
                      zf-NADH-PPase 4 rFCgr 8
                                      rFCg+
  gene2795|gene2795|rna2795|rna2795 5 RFCGT 9
                                      89995 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.099
                      zf-NADH-PPase  5 FCgrCGa 11
                                       FC+ C+ 
  gene2795|gene2795|rna2795|rna2795 25 FCPYCAC 31
                                       9****85 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 4.3
                      zf-NADH-PPase 24 CpaC 27
                                       C+ C
  gene2795|gene2795|rna2795|rna2795 78 CERC 81
                                       6666 PP

  == domain 4  score: 16.4 bits;  conditional E-value: 2.4e-06
                      zf-NADH-PPase   3 hrFCgrCGaptep 15 
                                        +r+CgrCG+++ep
  gene2795|gene2795|rna2795|rna2795  89 YRYCGRCGQAVEP 101
                                        69*******9886 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.1      0.39   8.7e+02      19      21 ..       7       9 ..       5      12 .. 0.65
   2 !   12.9   1.9   3.1e-05      0.07       7      19 ..      16      29 ..      15      31 .. 0.91
   3 ?   -3.7   1.2       5.1   1.1e+04      14      16 ..      45      47 ..      44      48 .. 0.74
   4 !   13.6   1.0   1.9e-05     0.042       2      19 ..      63      81 ..      63      85 .. 0.92
   5 !    6.6   5.5    0.0028       6.3       2      21 ..      78      97 ..      77      99 .. 0.93

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.39
                      zinc_ribbon_2 19 CGt 21
                                       CGt
  gene2795|gene2795|rna2795|rna2795  7 CGT 9 
                                       665 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 3.1e-05
                      zinc_ribbon_2  7 aelqd.nakFCpyC 19
                                       +e+qd n+ FCpyC
  gene2795|gene2795|rna2795|rna2795 16 TENQDtNDIFCPYC 29
                                       699988******** PP

  == domain 3  score: -3.7 bits;  conditional E-value: 5.1
                      zinc_ribbon_2 14 kFC 16
                                       +FC
  gene2795|gene2795|rna2795|rna2795 45 TFC 47
                                       689 PP

  == domain 4  score: 13.6 bits;  conditional E-value: 1.9e-05
                      zinc_ribbon_2  2 CpnCGaelqd.nakFCpyC 19
                                       C+nC ++l d  +k C++C
  gene2795|gene2795|rna2795|rna2795 63 CKNCYKKLGDrSVKTCERC 81
                                       ********9978888**** PP

  == domain 5  score: 6.6 bits;  conditional E-value: 0.0028
                      zinc_ribbon_2  2 CpnCGaelqdnakFCpyCGt 21
                                       C +C + +  + ++C +CG 
  gene2795|gene2795|rna2795|rna2795 78 CERCTNVIIAGYRYCGRCGQ 97
                                       *******************6 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.4     0.054   1.2e+02      12      24 ..      19      31 ..       3      41 .. 0.64
   2 ?   13.9   2.4   1.7e-05     0.039       3      40 ..      63     100 ..      61     101 .] 0.87

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.054
                                       E-SSEEE-TTT-- CS
                     zinc-ribbons_6 12 krgeqyhCeaCqe 24
                                       ++++ ++C  C  
  gene2795|gene2795|rna2795|rna2795 19 QDTNDIFCPYCAC 31
                                       3346666776654 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 1.7e-05
                                        -SSS-S--EE-SSEEE-TTT--.EEEEEEE-SSS-S--- CS
                     zinc-ribbons_6   3 CpeCqqelekrgeqyhCeaCqe.dlkkealCpeCeqele 40 
                                        C++C ++l  r+   +Ce C++  +    +C +C+q +e
  gene2795|gene2795|rna2795|rna2795  63 CKNCYKKLGDRS-VKTCERCTNvIIAGYRYCGRCGQAVE 100
                                        ********9988.679****995667789*******987 PP

>> NinF  NinF protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.1       2.9   6.5e+03      20      21 ..      29      30 ..      14      37 .. 0.61
   2 ?   13.6   0.4     2e-05     0.045      20      43 ..      63      86 ..      55      91 .. 0.85
   3 ?   -0.3   0.1      0.46     1e+03      20      29 ..      92     101 .]      86     101 .] 0.83

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 2.9
                               NinF 20 Ca 21
                                       Ca
  gene2795|gene2795|rna2795|rna2795 29 CA 30
                                       32 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 2e-05
                               NinF 20 CanCskkLevdevhvCeeCvaeli 43
                                       C nC kkL    v  Ce C   +i
  gene2795|gene2795|rna2795|rna2795 63 CKNCYKKLGDRSVKTCERCTNVII 86
                                       *******************87655 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.46
                               NinF  20 CanCskkLev 29 
                                        C  C++ +e+
  gene2795|gene2795|rna2795|rna2795  92 CGRCGQAVEP 101
                                        999**98876 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.7   6.8e-05      0.15       5      26 ..       6      30 ..       5      42 .. 0.88
   2 ?    1.3   0.2      0.11   2.5e+02      22      29 ..      63      70 ..      52      77 .. 0.63
   3 ?    1.5   3.4     0.094   2.1e+02      21      29 ..      77      85 ..      61      86 .. 0.70
   4 ?    4.0   0.1     0.016        36      19      30 ..      89     100 ..      87     101 .] 0.77

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 6.8e-05
                                       TTTCEE.C..HEETSTTCEEESSSS CS
                       TF_Zn_Ribbon  5 nCgstn.l..veDpergelvCtdCG 26
                                        Cg+++ +  +e+ ++++++C+ C 
  gene2795|gene2795|rna2795|rna2795  6 FCGTKRkTkrTENQDTNDIFCPYCA 30
                                       5888766777**************6 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.11
                                       ESSSSBEE CS
                       TF_Zn_Ribbon 22 CtdCGlVl 29
                                       C++C   l
  gene2795|gene2795|rna2795|rna2795 63 CKNCYKKL 70
                                       66665555 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.094
                                       EESSSSBEE CS
                       TF_Zn_Ribbon 21 vCtdCGlVl 29
                                       +C++C++V+
  gene2795|gene2795|rna2795|rna2795 77 TCERCTNVI 85
                                       899999997 PP

  == domain 4  score: 4.0 bits;  conditional E-value: 0.016
                                        CEEESSSSBEEE CS
                       TF_Zn_Ribbon  19 elvCtdCGlVle 30 
                                          +C++CG  +e
  gene2795|gene2795|rna2795|rna2795  89 YRYCGRCGQAVE 100
                                        568*****7766 PP

>> zf-C3HC4_3  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.6    0.0013       2.9       4      27 ..      25      48 ..      22      57 .. 0.91
   2 ?    8.7   1.7   0.00068       1.5      25      47 ..      62      85 ..      52      88 .. 0.84
   3 ?    5.5   2.0     0.007        16      25      48 ..      77     100 ..      73     101 .] 0.89

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0013
                                       B-TTTSSSBS-EEETTEEEEEE-H CS
                         zf-C3HC4_3  4 eCviClerprnvvllpCgHlvlCe 27
                                        C+ C  + ++v l++++++ +C 
  gene2795|gene2795|rna2795|rna2795 25 FCPYCACSTKSVWLIDTMYFTFCF 48
                                       6*********************96 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00068
                                       E-HHHHHHHHH.TT-B-TTT--B- CS
                         zf-C3HC4_3 25 lCeeCaekllk.rkkkCpiCrrpi 47
                                        C++C +kl + + k+C  C   i
  gene2795|gene2795|rna2795|rna2795 62 GCKNCYKKLGDrSVKTCERCTNVI 85
                                       7********98899***9998776 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.007
                                        E-HHHHHHHHHTT-B-TTT--B-- CS
                         zf-C3HC4_3  25 lCeeCaekllkrkkkCpiCrrpie 48 
                                        +Ce+C + + +  + C  C + +e
  gene2795|gene2795|rna2795|rna2795  77 TCERCTNVIIAGYRYCGRCGQAVE 100
                                        8******************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1025  (0.0571699); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 693.28
//
Query:       gene2796|gene2796|rna2796|rna2796  [L=76]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.055   14.2   1.1       0.51   11.1   0.1    2.0  2  ATPase-cat_bd  Putative metal-binding domain of cation transp


Domain annotation for each model (and alignments):
>> ATPase-cat_bd  Putative metal-binding domain of cation transport ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   2.8e-05      0.51      30      58 ..       8      37 ..       6      47 .. 0.77
   2 ?    2.3   0.1     0.016   2.8e+02      20      36 ..      50      66 ..      43      74 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 2.8e-05
                      ATPase-cat_bd 30 GCq.avaqliveaglesyYklrtekakkae 58
                                       GC  a  +++v++ +++yY++rt++++++e
  gene2796|gene2796|rna2796|rna2796  8 GCDlATLNAVVRDKFSTYYRYRTNESNEQE 37
                                       886366899**************8887554 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.016
                      ATPase-cat_bd 20 egeerefCCkGCqavaq 36
                                       +g+e+++C k C+ +++
  gene2796|gene2796|rna2796|rna2796 50 SGSEEHLCGKMCKMIIE 66
                                       68899999999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       551  (0.0307323); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.27s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 551.31
//
Query:       gene2797|gene2797|rna2797|rna2797  [L=232]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       533  (0.0297284); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 1649.97
//
Query:       gene2798|gene2798|rna2798|rna2798  [L=103]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      5e-14   52.8  15.7      5e-14   52.8  15.7    2.0  2  zinc_ribbon_15  zinc-ribbon family
    0.00048   19.7   0.7      0.022   14.4   0.1    4.1  5  zf-NADH-PPase   NADH pyrophosphatase zinc ribbon domain
     0.0006   19.8  13.5    0.00071   19.5   4.0    2.5  2  DZR             Double zinc ribbon
  ------ inclusion threshold ------
      0.033   13.9   0.7      0.033   13.9   0.7    3.5  4  zinc_ribbon_2   zinc-ribbon domain
        0.9    9.2   6.0       0.34   10.5   0.7    2.5  3  DpnI            Dam-replacing family
        1.2    8.7  14.7      0.076   12.7   4.6    2.1  2  TackOD1         Thaumarchaeal output domain 1


Domain annotation for each model (and alignments):
>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.5      0.31   9.3e+02       2      18 ..       3      19 ..       2      23 .. 0.73
   2 !   52.8  15.7   1.7e-17     5e-14       1      86 []      25      97 ..      25      97 .. 0.99

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.31
                     zinc_ribbon_15  2 lCpkCgklskaelvkkk 18
                                        C  Cg +s+  +++++
  gene2798|gene2798|rna2798|rna2798  3 NCMICGLTSRKITKRNE 19
                                       69999988777766665 PP

  == domain 2  score: 52.8 bits;  conditional E-value: 1.7e-17
                     zinc_ribbon_15  1 ilCpkCgklskaelvkkkkvlklffipvfkwkkkkpylacskCkslleaskelgkeiekkessekkeCknCgkeveee 78
                                       ++Cp+C++++++ ++ +k+++++ffip++++k+kk+y+ c  Ck ++++ +             +++C++C+++v ++
  gene2798|gene2798|rna2798|rna2798 25 VYCPHCSNTVTSCTIYEKYYFSFFFIPLCPVKTKKKYAGCGVCKIKFSDGR-------------VRVCSKCRSVVLNS 89
                                       58************************************************9.............************** PP

                     zinc_ribbon_15 79 fkyCpkCg 86
                                       ++yC +Cg
  gene2798|gene2798|rna2798|rna2798 90 YRYCGRCG 97
                                       *******9 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.2         2     6e+03      24      29 ..       4       9 ..       3      10 .. 0.66
   2 ?    2.3   0.3     0.047   1.4e+02      24      28 ..      27      31 ..      25      34 .. 0.66
   3 ?   -3.2   1.2       2.4   7.3e+03       6       9 ..      64      67 ..      64      67 .. 0.84
   4 !    9.7   0.0   0.00021      0.64      18      30 ..      73      85 ..      71      87 .. 0.88
   5 !   14.4   0.1   7.4e-06     0.022       2      12 ..      89      99 ..      88     101 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 2
                      zf-NADH-PPase 24 CpaCgl 29
                                       C  Cgl
  gene2798|gene2798|rna2798|rna2798  4 CMICGL 9 
                                       556775 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.047
                      zf-NADH-PPase 24 CpaCg 28
                                       Cp+C 
  gene2798|gene2798|rna2798|rna2798 27 CPHCS 31
                                       77776 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 2.4
                      zf-NADH-PPase  6 CgrC 9 
                                       Cg C
  gene2798|gene2798|rna2798|rna2798 64 CGVC 67
                                       8988 PP

  == domain 4  score: 9.7 bits;  conditional E-value: 0.00021
                      zf-NADH-PPase 18 ggwarvCpaCgle 30
                                       +g+ rvC+ C+  
  gene2798|gene2798|rna2798|rna2798 73 DGRVRVCSKCRSV 85
                                       79********976 PP

  == domain 5  score: 14.4 bits;  conditional E-value: 7.4e-06
                      zf-NADH-PPase  2 thrFCgrCGap 12
                                       ++r+CgrCG +
  gene2798|gene2798|rna2798|rna2798 89 SYRYCGRCGDE 99
                                       79*******75 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.5   2.0    0.0058        17      15      39 ..       4      35 ..       1      40 [. 0.69
   2 !   19.5   4.0   2.4e-07   0.00071       3      49 .]      52      97 ..      50     101 .. 0.92

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0058
                                DZR 15 CseCgtklkavaa.......edrCpsCgekvd 39
                                       C  Cg + ++ ++          Cp+C+  v+
  gene2798|gene2798|rna2798|rna2798  4 CMICGLTSRKITKrnengviDVYCPHCSNTVT 35
                                       77777776666666777777777888877665 PP

  == domain 2  score: 19.5 bits;  conditional E-value: 2.4e-07
                                DZR  3 qCgeelppdarfCseCgtklkavaaedrCpsCgekvdpearfCpeCG 49
                                        C  +++++   C+ C+ k +   + ++C++C + v +  r+C+ CG
  gene2798|gene2798|rna2798|rna2798 52 LCPVKTKKKYAGCGVCKIKFS-DGRVRVCSKCRSVVLNSYRYCGRCG 97
                                       588999999999*******97.6789********************9 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.5       1.1   3.4e+03      16      20 ..       4       8 ..       4       8 .. 0.65
   2 ?    7.1   0.5    0.0015       4.5       1       6 [.      26      31 ..      18      38 .. 0.73
   3 ?   -4.1   0.9       5.1   1.5e+04      16      17 ..      64      65 ..      62      67 .. 0.58
   4 ?   13.9   0.7   1.1e-05     0.033       2      21 ..      79      98 ..      78     100 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1.1
                      zinc_ribbon_2 16 CpyCG 20
                                       C  CG
  gene2798|gene2798|rna2798|rna2798  4 CMICG 8 
                                       66676 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0015
                      zinc_ribbon_2  1 fCpnCG 6 
                                       +Cp+C 
  gene2798|gene2798|rna2798|rna2798 26 YCPHCS 31
                                       566665 PP

  == domain 3  score: -4.1 bits;  conditional E-value: 5.1
                      zinc_ribbon_2 16 Cp 17
                                       C 
  gene2798|gene2798|rna2798|rna2798 64 CG 65
                                       33 PP

  == domain 4  score: 13.9 bits;  conditional E-value: 1.1e-05
                      zinc_ribbon_2  2 CpnCGaelqdnakFCpyCGt 21
                                       C++C   + +  ++C +CG 
  gene2798|gene2798|rna2798|rna2798 79 CSKCRSVVLNSYRYCGRCGD 98
                                       *******************6 PP

>> DpnI  Dam-replacing family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.7   0.00011      0.34      33      61 ..       3      32 ..       1      45 [. 0.76
   2 ?    1.2   0.1     0.083   2.5e+02     109     147 ..      35      72 ..      31      86 .. 0.72
   3 ?   -0.4   0.3      0.26   7.9e+02      30      38 ..      89      97 ..      75     102 .. 0.52

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00011
                                       --TTT--SS-EE.--------EEE-TTT-- CS
                               DpnI 33 yCpkCgskklse.fennkpvaDfyCescke 61
                                        C +Cg ++ +   +n++ v D yC +c++
  gene2798|gene2798|rna2798|rna2798  3 NCMICGLTSRKItKRNENGVIDVYCPHCSN 32
                                       6999996654430467778*********86 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.083
                                        EEEEEE-GGG--GGGEEEEEEE--------EEEEEEEGG CS
                               DpnI 109 enlllipklfftpeiiekRkpLsetarRagwigcnidls 147
                                        +  ++  k++f+    ++  p++++++ ag   c+i++s
  gene2798|gene2798|rna2798|rna2798  35 TSCTIYEKYYFSF-FFIPLCPVKTKKKYAGCGVCKIKFS 72 
                                        5555566666654.4456778888999999999999876 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.26
                                       HH---TTT- CS
                               DpnI 30 knlyCpkCg 38
                                       +  yC  Cg
  gene2798|gene2798|rna2798|rna2798 89 SYRYCGRCG 97
                                       233555555 PP

>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   2.5     0.048   1.4e+02     105     133 ..       3      34 ..       1      46 [. 0.70
   2 ?   12.7   4.6   2.5e-05     0.076      63      95 ..      65      98 ..      53     101 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.048
                            TackOD1 105 hhftCgnvgpeeeflkeg...kleCpkCktkL 133
                                        +++ Cg ++ + + ++e+   ++ Cp+C++++
  gene2798|gene2798|rna2798|rna2798   3 NCMICGLTSRKITKRNENgviDVYCPHCSNTV 34 
                                        68888888877766665523345699998776 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 2.5e-05
                            TackOD1 63 glle.eelvdrirlCpsCksghlnvrevCpkCkS 95
                                       g+++ +    r+r+C++C+s  ln   +C  C+ 
  gene2798|gene2798|rna2798|rna2798 65 GVCKiKFSDGRVRVCSKCRSVVLNSYRYCGRCGD 98
                                       77884555569*********************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1043  (0.0581739); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 739.57
//
Query:       gene2799|gene2799|rna2799|rna2799  [L=657]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (657 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       758  (0.0422779); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.60u 0.28s 00:00:00.88 Elapsed: 00:00:00.44
# Mc/sec: 4471.45
//
Query:       gene28|gene28|rna28|rna28  [L=71]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
     0.0033   17.7   0.4     0.0036   17.6   0.4    1.1  1  DUF5082     Domain of unknown function (DUF5082)
  ------ inclusion threshold ------
      0.023   14.6   1.9      0.027   14.4   1.9    1.3  1  Holin_BhlA  BhlA holin family
      0.036   14.0   1.5      0.036   14.0   1.5    1.7  2  Prefoldin   Prefoldin subunit
      0.056   12.0   2.0      0.058   11.9   2.0    1.1  1  Macoilin    Macoilin family
       0.06   13.6   1.6      0.067   13.4   1.6    1.0  1  PHM7_cyt    Cytosolic domain of 10TM putative phosphate trans
       0.12   12.7   0.7        1.2    9.6   0.7    1.9  1  UPF0184     Uncharacterised protein family (UPF0184)


Domain annotation for each model (and alignments):
>> DUF5082  Domain of unknown function (DUF5082)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.4   1.2e-06    0.0036      76     111 ..      33      68 ..       1      70 [. 0.67

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.2e-06
                    DUF5082  76 essyqtyvdkldelidaieeEIerLenqiseaqgvl 111
                                   ++t v++ld++id++ ++Ie Le++i+++  +l
  gene28|gene28|rna28|rna28  33 VNLCKTRVEELDSIIDKLTSKIEILEKKIEKMNLKL 68 
                                44588999**********************998766 PP

>> Holin_BhlA  BhlA holin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   1.9   9.2e-06     0.027      37      60 ..      36      59 ..       2      67 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 9.2e-06
                 Holin_BhlA 37 qeerekkyqeiikkltekfeivee 60
                                + r +++ +ii+klt k ei+e+
  gene28|gene28|rna28|rna28 36 CKTRVEELDSIIDKLTSKIEILEK 59
                               3499******************64 PP

>> Prefoldin  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.1      0.34     1e+03      85      99 ..       4      18 ..       1      31 [. 0.63
   2 ?   14.0   1.5   1.2e-05     0.036      80     111 ..      34      65 ..      24      68 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.34
                               HHHHHHHHHHHHHHH CS
                  Prefoldin 85 kleelekqlekleee 99
                               k +++e +lek  e+
  gene28|gene28|rna28|rna28  4 KNNDMELSLEKALEK 18
                               555555555555544 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 1.2e-05
                                HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                  Prefoldin  80 ellkkkleelekqlekleeeleklkdqittle 111
                                 l+k ++eel++ ++kl+ ++e l ++i++++
  gene28|gene28|rna28|rna28  34 NLCKTRVEELDSIIDKLTSKIEILEKKIEKMN 65 
                                68**************************9986 PP

>> Macoilin  Macoilin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   2.0   1.9e-05     0.058     508     552 ..      23      67 ..       1      69 [. 0.78

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.9e-05
                   Macoilin 508 alaaasrsecteslkskkreleaeikkLekelklkeeqirelelk 552
                                +l  + r+   + +k++ +el++ i+kL+ ++ + e++i++++lk
  gene28|gene28|rna28|rna28  23 SLYFSLRTADVNLCKTRVEELDSIIDKLTSKIEILEKKIEKMNLK 67 
                                4455668888999****************************9976 PP

>> PHM7_cyt  Cytosolic domain of 10TM putative phosphate transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   1.6   2.2e-05     0.067      48     114 ..       2      65 ..       1      70 [. 0.76

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.2e-05
                   PHM7_cyt  48 veerekavrkleaalskykkngkklpkkrpthklgflglkligkkvda.idyyrekleeldeeieeer 114
                                 ++ ++++ +le+al+k+ k      +   t  + +++++   ++ d+ id +++k+e l+++ie+ +
  gene28|gene28|rna28|rna28   2 EKKNNDMELSLEKALEKRSKSSLYF-SL-RTADVNLCKTR--VEELDSiIDKLTSKIEILEKKIEKMN 65 
                                5777888999999999888876555.23.46666666644..58889889**************9976 PP

>> UPF0184  Uncharacterised protein family (UPF0184)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.7   0.00039       1.2      15      56 ..      27      68 ..       1      69 [. 0.75

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00039
                    UPF0184 15 gaeteedefgeeEyeainsmLDqinsaLDalEernDdlnskL 56
                               ++ t + +  +  +e+++s +D++ s ++ lE++ +++n kL
  gene28|gene28|rna28|rna28 27 SLRTADVNLCKTRVEELDSIIDKLTSKIEILEKKIEKMNLKL 68
                               455556666677889999999999999999999999988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (71 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1311  (0.0731218); expected 358.6 (0.02)
Passed bias filter:                      625  (0.0348597); expected 358.6 (0.02)
Passed Vit filter:                        91  (0.00507558); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 537.50
//
Query:       gene280|gene280|rna280|rna280  [L=360]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    0.00033   20.2   0.0    0.00054   19.5   0.0    1.3  1  Lactamase_B_2  Beta-lactamase superfamily domain
     0.0094   16.0   0.1       0.04   13.9   0.0    1.9  2  Lactamase_B    Metallo-beta-lactamase superfamily


Domain annotation for each model (and alignments):
>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0     6e-08   0.00054      30     145 ..      46     139 ..      40     186 .. 0.74

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 6e-08
                                    SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHHHCCTTCGHHHCHTTTTEEEEEE-TTSEEEECSTTEEEEEEE CS
                  Lactamase_B_2  30 pidaVllthaHyDHlaglltlrelrpkklplyapkgvlavleanfvylaleeepavnvheldwgesfelgdggleitatp 109
                                    +++  +lth H DH+ gl       +   +++++  ++  ++ n++ +++       ++e++ ++  +++  +++i +++
  gene280|gene280|rna280|rna280  46 DVENTFLTHFHSDHYYGLKRSFN--K---NIFCSTTTANLVKLNIKVDVK------YINEMEMNTVYRVD--NVDIMCFE 112
                                    566679*********98654433..3...69***9999999999655444......566**********9..577***** PP

                                    E-EE--CTCCE-TTTSEEEEEECTTEEEEEESS-S- CS
                  Lactamase_B_2 110 arhksgrrldrnagdtlGlriegggkrvyyigDtgy 145
                                    a+h  g          +G+++  ++   +++gD  +
  gene280|gene280|rna280|rna280 113 ANHCPGA---------VGFIFCVQNVYYLHTGDFRF 139
                                    ***9998.........99999988888888899873 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.0   4.5e-06      0.04      44      63 ..      46      65 ..      42      81 .. 0.84
   2 ?   -1.2   0.0      0.19   1.7e+03     130     156 ..     116     142 ..     112     146 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.5e-06
                                   GEEEEE-SBSSHHHHTTGGG CS
                    Lactamase_B 44 dvdavilTHlHlDHiGglgg 63
                                   dv+  +lTH+H+DH+ gl+ 
  gene280|gene280|rna280|rna280 46 DVENTFLTHFHSDHYYGLKR 65
                                   677779***********985 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.19
                                    STSCCEEEEEETTCCEEEECTTTSSHH CS
                    Lactamase_B 130 ghghghgvveygggkvlftGDallage 156
                                     +g+++++++ ++  +l tGD+ ++ e
  gene280|gene280|rna280|rna280 116 CPGAVGFIFCVQNVYYLHTGDFRFNVE 142
                                    5889999999999999*****998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (360 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       587  (0.0327403); expected 358.6 (0.02)
Passed bias filter:                      247  (0.0137766); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 2561.14
//
Query:       gene2800|gene2800|rna2800|rna2800  [L=223]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.2e-15   55.3   0.0    1.1e-14   54.3   0.0    1.5  1  SBDS      Shwachman-Bodian-Diamond syndrome (SBDS) protein
  ------ inclusion threshold ------
      0.063   13.6   0.1        7.2    7.0   0.0    2.4  2  DUF5638   Family of unknown function (DUF5638)


Domain annotation for each model (and alignments):
>> SBDS  Shwachman-Bodian-Diamond syndrome (SBDS) protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.3   0.0   1.2e-18   1.1e-14       1      87 [.      12      96 ..      12      97 .. 0.92

  Alignments for each domain:
  == domain 1  score: 54.3 bits;  conditional E-value: 1.2e-18
                                       T-EEEEEEETTEEEEEEE-HHHHHHHHCTT---HHHHBSSSS-EEETTTTEE--HHHHHHHHS---HHHHHHHHHHHS CS
                               SBDS  1 nvsivrykkgkkrFeiavyknklleyregkeidLsevlqsekiFtnaskGetaskselekafgteskdeiikeILkkG 78
                                       nv+++ ++k++  +e+ +y+n+l+ y+++  i+Ls v+++++i++++skG   +k+ l+ + g++  d+ i+ IL++G
  gene2800|gene2800|rna2800|rna2800 12 NVTTITFRKNNVAYEVPIYPNTLKPYQNN-LIPLSSVVHTHSIYKSVSKGLLHNKEALKAIPGEN-MDQKIEYILRNG 87
                                       79999****999***************99.7*********************9999999887765.58999******* PP

                                       EEE--HHHH CS
                               SBDS 79 eiqvsaeer 87
                                       + ++++++r
  gene2800|gene2800|rna2800|rna2800 88 HDKQESMTR 96
                                       **9998876 PP

>> DUF5638  Family of unknown function (DUF5638)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0    0.0054        48      66      99 ..      53      86 ..      37      88 .. 0.89
   2 ?    7.0   0.0    0.0008       7.2      73     102 ..     120     149 ..      95     150 .. 0.92

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.0054
                                       HHHHHHTTSS-HHHHHHHHTTT---HHHHHHHHH CS
                            DUF5638 66 llsqvkngeisadeAleaiekktesrkidviihn 99
                                       + + v++g +  +eAl+ai  ++  +ki+ i++n
  gene2800|gene2800|rna2800|rna2800 53 IYKSVSKGLLHNKEALKAIPGENMDQKIEYILRN 86
                                       56789*******************9999999877 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0008
                                        TSS-HHHHHHHHTTT---HHHHHHHHHHHH CS
                            DUF5638  73 geisadeAleaiekktesrkidviihnllk 102
                                          is+deA+e ++k   s+ ++v+ +n++k
  gene2800|gene2800|rna2800|rna2800 120 RRISLDEAMEIVKKYDLSKDVKVVGNNIVK 149
                                        579************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       712  (0.0397122); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 1504.92
//
Query:       gene2801|gene2801|rna2801|rna2801  [L=154]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-32  113.0   2.8    1.4e-32  112.8   2.8    1.0  1  Ribosomal_S13  Ribosomal protein S13/S18
  ------ inclusion threshold ------
      0.056   12.2   0.0       0.07   11.9   0.0    1.1  1  FbpA           Fibronectin-binding protein A N-terminus (FbpA


Domain annotation for each model (and alignments):
>> Ribosomal_S13  Ribosomal protein S13/S18
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.8   2.8   1.5e-36   1.4e-32       1     127 [.      17     143 ..      17     144 .. 0.99

  Alignments for each domain:
  == domain 1  score: 112.8 bits;  conditional E-value: 1.5e-36
                      Ribosomal_S13   1 RilgtdidgkkkveialtaikGiGrrkakiilkkadvdedkrigelteeeiekieeivenkaqykipnwi.nrqkd 75 
                                        R+ +t+idg+k++  alt+ikGiG r a+++l+++++ +  r+gelt ee +++++ ++ +++  ip w+ n +k+
  gene2801|gene2801|rna2801|rna2801  17 RMCNTNIDGRKQILKALTTIKGIGMRFAQTLLTRTQIRN-CRAGELTAEEQQRLVDAIQDPKSVGIPIWMyNYRKE 91 
                                        899**********************************87.9*********************************** PP

                      Ribosomal_S13  76 ikdGkdshvvendlrrklredieRlkkirsyrGlRHkrGlkvRGQrTkttgR 127
                                        +++G+d+h+v n+++   r ++eR kki++ r  R  rG+kvRGQrTk++gR
  gene2801|gene2801|rna2801|rna2801  92 YTTGEDKHLVGNQIDAAFRFSLERGKKIKAVRECRLARGMKVRGQRTKSNGR 143
                                        ***************************************************9 PP

>> FbpA  Fibronectin-binding protein A N-terminus (FbpA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   7.9e-06      0.07     168     237 ..       8      75 ..       3      91 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 7.9e-06
                                        XTTSXXH.HHHHHHHHHS.XXXHHHHHHHBTTXXHHHHHHHHTTXSSSH...............HHHHHH CS
                               FbpA 168 nPleaeeleefkellskkekdlvkaLvkafqGlspllaeelleragldketsakelseedlerlyealqe 237
                                        +P++++ + ++++   +  k++ kaL +  +G++  +a+ ll+r+++++  +a el++e+ +rl +a+q+
  gene2801|gene2801|rna2801|rna2801   8 SPQTIQHMIRMCNTNIDGRKQILKALTTI-KGIGMRFAQTLLTRTQIRN-CRAGELTAEEQQRLVDAIQD 75 
                                        67777776666666445668888888776.7***************665.69***************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       600  (0.0334653); expected 358.6 (0.02)
Passed bias filter:                      509  (0.0283898); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.37s 00:00:00.95 Elapsed: 00:00:00.56
# Mc/sec: 826.61
//
Query:       gene2802|gene2802|rna2802|rna2802  [L=42]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (42 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                        85  (0.00474092); expected 358.6 (0.02)
Passed bias filter:                       76  (0.00423894); expected 358.6 (0.02)
Passed Vit filter:                         5  (0.000278878); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.45
# Mc/sec: 281.03
//
Query:       gene2803|gene2803|rna2803|rna2803  [L=58]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.082   12.6   0.0      0.097   12.4   0.0    1.1  1  Thymosin  Thymosin beta-4 family


Domain annotation for each model (and alignments):
>> Thymosin  Thymosin beta-4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   5.4e-06     0.097       5      26 ..      25      46 ..      21      46 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 5.4e-06
                           Thymosin  5 vsevesFdkskLKkveTqEKnv 26
                                       v  ++ F +sk+K+++ + Kn+
  gene2803|gene2803|rna2803|rna2803 25 VDHIDLFPRSKMKRADVETKNI 46
                                       667999**************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (58 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       273  (0.0152267); expected 358.6 (0.02)
Passed bias filter:                      238  (0.0132746); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.46
# Mc/sec: 379.94
//
Query:       gene2804|gene2804|rna2804|rna2804  [L=253]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.029   15.1   0.0       0.68   10.7   0.0    2.8  3  RicinB_lectin_2  Ricin-type beta-trefoil lectin domain-like
      0.067   13.5   0.0      0.094   13.0   0.0    1.2  1  Ricin_B_lectin   Ricin-type beta-trefoil lectin domain


Domain annotation for each model (and alignments):
>> RicinB_lectin_2  Ricin-type beta-trefoil lectin domain-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0     0.097   8.7e+02      14      31 ..      18      35 ..       5      51 .. 0.80
   2 ?   10.7   0.0   7.6e-05      0.68       9      66 ..      53     107 ..      43     122 .. 0.80
   3 ?   -1.1   0.0      0.37   3.3e+03      38      64 ..     120     145 ..     109     155 .. 0.67

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.097
                                       EEEEECTSSSEEEECGCC CS
                    RicinB_lectin_2 14 yytiknvasgkvLdvagg 31
                                        y+ikn + ++++  +g+
  gene2804|gene2804|rna2804|rna2804 18 PYKIKNSRANTYIGLEGD 35
                                       499999999999887776 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 7.6e-05
                                        ETTTTEEEEECT.SSSEEEECGCCTBCTTEEEEEE-TTT-GGCEEEEECCESSEEEEEE CS
                    RicinB_lectin_2   9 sggdgyytiknv.asgkvLdvaggstanganvqqwtcsgaanqqWrledtgdgtyrivn 66 
                                        s+++g + i++v  sgkv d++g+ ++    +     +g+anq++ +++ ++g  ri +
  gene2804|gene2804|rna2804|rna2804  53 SETEGRVLIEVVeISGKVWDIEGSVKN----LIFFHEHGGANQRFLVKRSDNGITRILS 107
                                        455678888555489********9998....5555568*************99999976 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 0.37
                                        EEEEE-TT.T-GGCEEEEECCESSEEEE CS
                    RicinB_lectin_2  38 nvqqwtcs.gaanqqWrledtgdgtyri 64 
                                        + + ++c+ g+  q++ + d +   +++
  gene2804|gene2804|rna2804|rna2804 120 RFEKQPCVdGTVDQEFLIADEN--GVTV 145
                                        4566666657889999985544..3443 PP

>> Ricin_B_lectin  Ricin-type beta-trefoil lectin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0     1e-05     0.094      10      96 ..      67     149 ..      59     173 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1e-05
                                        TGEEEEETTCTTSTEBEEEEE-TSCCGGGEEEEE.TTSEEEETT.TTEEEEESSSSTTSBEEEEETTTTSGGGCEE CS
                     Ricin_B_lectin  10 sgkCLdvegeskagapvglydChgskgkQlwtlt.kdgeirskaqselCldvsstaegakvvlakChkgkgnqrWe 84 
                                        sgk  d+eg+ k   +++ ++ hg+++ Q++ ++ +d+ i    ++++C++    +++++   ++C +g+ +q++ 
  gene2804|gene2804|rna2804|rna2804  67 SGKVWDIEGSVK---NLIFFHEHGGAN-QRFLVKrSDNGITRILSGDRCITF--VKSNNRFEKQPCVDGTVDQEFL 136
                                        677788888776...9999999***88.***99976666655457******9..599999999****999999999 PP

                                        .EETTTTEEEETT CS
                     Ricin_B_lectin  85 .fdkdgtqirhkk 96 
                                          d++g ++r ++
  gene2804|gene2804|rna2804|rna2804 137 iADENGVTVRTPD 149
                                        6677777677666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (253 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       411  (0.0229238); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1820.61
//
Query:       gene2805|gene2805|rna2805|rna2805  [L=68]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (68 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       205  (0.011434); expected 358.6 (0.02)
Passed bias filter:                      183  (0.0102069); expected 358.6 (0.02)
Passed Vit filter:                         7  (0.000390429); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.23s 00:00:00.57 Elapsed: 00:00:00.40
# Mc/sec: 509.62
//
Query:       gene2806|gene2806|rna2806|rna2806  [L=56]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (56 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       175  (0.00976072); expected 358.6 (0.02)
Passed bias filter:                      126  (0.00702772); expected 358.6 (0.02)
Passed Vit filter:                         6  (0.000334653); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.42
# Mc/sec: 403.47
//
Query:       gene2807|gene2807|rna2807|rna2807  [L=153]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.7e-05   25.0   0.1    2.9e-05   24.3   0.1    1.4  1  Ricin_B_lectin  Ricin-type beta-trefoil lectin domain
  ------ inclusion threshold ------
      0.011   15.3   0.5      0.015   14.9   0.5    1.2  1  CDtoxinA        Cytolethal distending toxin A/C domain


Domain annotation for each model (and alignments):
>> Ricin_B_lectin  Ricin-type beta-trefoil lectin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.1   3.3e-09   2.9e-05      19      93 ..      76     145 ..      59     149 .. 0.78

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 3.3e-09
                                        CTTSTEBEEEEE-TSCCGGGEEEEE..TTSEEEETT.TTEEEEESSSSTTSBEEEEETTTTSGGGCEE.EETTTTE CS
                     Ricin_B_lectin  19 eskagapvglydChgskgkQlwtlt..kdgeirskaqselCldvsstaegakvvlakChkgkgnqrWe.fdkdgtq 91 
                                        +   +++++ ++ hg ++ Q ++++  k+g i++ + +++Cl+    +++++  l+kC++gk +q +   d++g+ 
  gene2807|gene2807|rna2807|rna2807  76 N---KKRLIYFPEHGRSN-QIFEIQrsKHGWIKITN-NDKCLTY--IKNKKRFELRKCDDGKMTQVFLmADEEGK- 143
                                        2...56899999999977.99999877889999987.9999998..79999999999999999999983444443. PP

                                        EE CS
                     Ricin_B_lectin  92 ir 93 
                                        ++
  gene2807|gene2807|rna2807|rna2807 144 VM 145
                                        55 PP

>> CDtoxinA  Cytolethal distending toxin A/C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.5   1.6e-06     0.015      18      88 ..      64     136 ..      53     145 .. 0.64

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.6e-06
                                        -STT-BE...EEEEGGG-G.....GGGGGG-EEEE-SSTT-EEEEETTT--EEEEETTEE.EEE-.--TT-GGG-E CS
                           CDtoxinA  18 lasrnwlktnWelteidsk.....efgklrdklldkknaglvqfknvdegtClaayenGv.ialkkCdeddketvF 87 
                                         + rn +   W++ + +       e g+ ++++++ +++++  +k  ++++Cl+  +n + ++l kCd+ +  +vF
  gene2807|gene2807|rna2807|rna2807  64 TDLRNKV---WNIEKNKKRliyfpEHGR-SNQIFEIQRSKHGWIKITNNDKCLTYIKNKKrFELRKCDDGKMTQVF 135
                                        4445555...777665543111104444.3468887777777777777889***988876255666********99 PP

                                        E CS
                           CDtoxinA  88 s 88 
                                         
  gene2807|gene2807|rna2807|rna2807 136 L 136
                                        5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       729  (0.0406604); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 970.04
//
Query:       gene2808|gene2808|rna2808|rna2808  [L=202]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       333  (0.0185733); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 1455.55
//
Query:       gene2809|gene2809|rna2809|rna2809  [L=305]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.5e-36  122.2   1.0    3.4e-20   71.9   0.3    2.3  2  TFIIB           Transcription factor TFIIB repeat
    9.8e-12   44.2   3.8    1.7e-11   43.4   3.8    1.4  1  TF_Zn_Ribbon    TFIIB zinc-binding
    0.00031   20.5   0.0    0.00065   19.4   0.0    1.6  1  Cyclin_N        Cyclin, N-terminal domain
     0.0082   16.2   0.3      0.035   14.2   0.0    2.0  2  RB_B            Retinoblastoma-associated protein B domain
  ------ inclusion threshold ------
      0.029   14.2   0.0      0.073   12.9   0.0    1.6  2  DUF4370         Domain of unknown function (DUF4370)
      0.057   13.5   0.0       0.16   12.0   0.0    1.7  2  TFIIB_C_1       Transcription factor IIB C-terminal module 1
       0.15   12.2   0.0       0.54   10.3   0.0    1.9  2  Cyclin_C        Cyclin, C-terminal domain
       0.17   11.8   0.3         18    5.2   0.1    2.2  2  YqhR            Conserved membrane protein YqhR
        4.2    7.3   6.4       0.58   10.1   1.7    2.0  2  RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit


Domain annotation for each model (and alignments):
>> TFIIB  Transcription factor TFIIB repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.9   0.3   1.7e-23   3.4e-20       1      71 []     114     184 ..     114     184 .. 0.97
   2 !   49.1   0.0   2.2e-16   4.4e-13       1      71 []     207     278 ..     207     278 .. 0.95

  Alignments for each domain:
  == domain 1  score: 71.9 bits;  conditional E-value: 1.7e-23
                                        HHHHHHHTT--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHHHHSS--SHHH CS
                              TFIIB   1 ikrfadaleLpekVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkeissvlqVsekti 71 
                                        i++ +d+ ++++++ d+Ak ++k++ e+k+lkG+  +g++AAc+yiAcr+e+  rt+ke+s ++ V +k+i
  gene2809|gene2809|rna2809|rna2809 114 ISAYCDRSNISKTISDRAKLIFKRVDEKKILKGKNLEGVVAACIYIACRQEQSPRTFKEVSVLTAVPKKEI 184
                                        6788**************************************************************99997 PP

  == domain 2  score: 49.1 bits;  conditional E-value: 2.2e-16
                                        HHHHHHHTT--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTT.TSS--HHHHHHHSS--SHHH CS
                              TFIIB   1 ikrfadaleLpekVadaAkelaklaleekvlkGrspagiaAAclyiAcrke.evkrtqkeissvlqVsekti 71 
                                        + rf++ l+L   V++ A+++ k++ e++ ++G+sp+++aAA++y+ +  + ++k  qk+i+ v++V+++ti
  gene2809|gene2809|rna2809|rna2809 207 VARFCSDLNLGIDVQKIAVQISKNVIEKGCMAGKSPDSVAAAVIYMITYIFpNLKGVQKDIQYVTNVTDVTI 278
                                        579*******************************************99875499****************98 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.4   3.8   8.5e-15   1.7e-11       3      43 .]      12      53 ..      10      53 .. 0.96

  Alignments for each domain:
  == domain 1  score: 43.4 bits;  conditional E-value: 8.5e-15
                                       ETTTTCEE.CHEETSTTCEEESSSSBEEEECCCCCCCHHHHH CS
                       TF_Zn_Ribbon  3 CPnCgstn.lveDpergelvCtdCGlVlednsidegpewref 43
                                       C +C s++ ++ D+++g ++Ct+CG+++e+  ide+ ewr+f
  gene2809|gene2809|rna2809|rna2809 12 CRDCQSDQyITDDTKTGAVLCTNCGCIIENTLIDEKTEWRTF 53
                                       ******998999*****************************8 PP

>> Cyclin_N  Cyclin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   3.3e-07   0.00065      35     103 ..     111     178 ..      80     208 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 3.3e-07
                                        HHHHHHHHHHTT--TTHHHHHHHHHHHHHHHS---CCCHHHHHHHHHHHHHHHHSSS---HHHHHHHTT CS
                           Cyclin_N  35 idwlvevaekfkltpetlflavnyldRflskksvpkdklqlvgatcLllAaKveeisppkledlvyitd 103
                                         + +   + + ++++ +   a  ++ R+ +kk+++ ++l+ v+a+c+++A++ e+  p + +++ ++t 
  gene2809|gene2809|rna2809|rna2809 111 FNLISAYCDRSNISKTISDRAKLIFKRVDEKKILKGKNLEGVVAACIYIACRQEQS-PRTFKEVSVLTA 178
                                        34588899999999999999999*****************************9666.999999998873 PP

>> RB_B  Retinoblastoma-associated protein B domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   1.7e-05     0.035      21      78 ..     118     173 ..     110     182 .. 0.84
   2 ?   -0.4   0.1      0.54   1.1e+03      20      69 ..     210     257 ..     187     302 .. 0.54

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.7e-05
                               RB_B  21 cerLklsselrekiwtlfehvlveetellkdRhlDqillcavYvvakvtkeelsFkei 78 
                                        c+r ++s+++++++  +f++  v+e+++lk ++l+ ++ +++Y+ ++ +++ ++Fke+
  gene2809|gene2809|rna2809|rna2809 118 CDRSNISKTISDRAKLIFKR--VDEKKILKGKNLEGVVAACIYIACRQEQSPRTFKEV 173
                                        66667777777777777776..58999*****************************97 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.54
                               RB_B  20 LcerLklsselrekiwtlfehvlveetellkdRhlDqillcavYvvakvt 69 
                                         c+ L+l  ++++ + ++ ++v+   +  +  +  D +  + +Y+++ + 
  gene2809|gene2809|rna2809|rna2809 210 FCSDLNLGIDVQKIAVQISKNVIE--KGCMAGKSPDSVAAAVIYMITYIF 257
                                        455556665666655555555553..345666666666666666666554 PP

>> DUF4370  Domain of unknown function (DUF4370)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       1.3   2.6e+03      15      89 ..     118     189 ..     108     193 .. 0.52
   2 ?   12.9   0.0   3.7e-05     0.073      46     108 ..     240     302 ..     205     304 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1.3
                            DUF4370  15 aaassrlsaaaaasaalekhlssrslfavlsasskavlsdlrsplalslGsvrsfsedvshlPeikdsevkkafk 89 
                                        + +s   ++ + +++ + k++ +++++     + + v++ + +  + +  s r+f  +vs l ++  +e+ ++fk
  gene2809|gene2809|rna2809|rna2809 118 CDRSNISKTISDRAKLIFKRVDEKKIL--KGKNLEGVVAACIYIACRQEQSPRTFK-EVSVLTAVPKKEIGRSFK 189
                                        555554444444455555555555544..233344444444444444444555554.466666666666666666 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 3.7e-05
                            DUF4370  46 asskavlsdlrsplalslGsvrsfsedvshlPeikdsevkkafkdllaaswdelPdavvedak 108
                                         s+ +v + + + ++  + + +   +d++ + ++ d  +k+++k+l+  + d lP+ ++++a+
  gene2809|gene2809|rna2809|rna2809 240 KSPDSVAAAVIYMITYIFPNLKGVQKDIQYVTNVTDVTIKNTYKELMQYKEDILPKEILSKAR 302
                                        56667777777788888888889999********************************99885 PP

>> TFIIB_C_1  Transcription factor IIB C-terminal module 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   8.1e-05      0.16       8      75 ..     113     177 ..     109     186 .. 0.79
   2 ?   -2.9   0.0       3.6   7.2e+03      20      41 ..     218     235 ..     204     252 .. 0.52

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 8.1e-05
                          TFIIB_C_1   8 alevllklsrrdeavleealelakrfvGkrrergervekqeevaaaclmlaaerlrqPvPLaelrvld 75 
                                         + +++++s+   ++ ++a  + kr   k+  +g+   ++e v+aac+ +a+ + + P  ++e+ vl 
  gene2809|gene2809|rna2809|rna2809 113 LISAYCDRSNISKTISDRAKLIFKRVDEKKILKGK---NLEGVVAACIYIACRQEQSPRTFKEVSVLT 177
                                        56777888888888888888777776555555555...55689********************99986 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 3.6
                          TFIIB_C_1  20 eavleealelakrfvGkrrerg 41 
                                         +v++ a+++ k+ +    e+g
  gene2809|gene2809|rna2809|rna2809 218 IDVQKIAVQISKNVI----EKG 235
                                        555555666655544....333 PP

>> Cyclin_C  Cyclin, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       1.4   2.8e+03      49      71 ..     154     176 ..     152     199 .. 0.57
   2 ?   10.3   0.0   0.00027      0.54      39      89 ..     237     288 ..     209     296 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.4
                                        HHHHHHCCHHHHS--S-HHHHHH CS
                           Cyclin_C  49 aaalllarstlnspewtetlehy 71 
                                        aa++++a+++ +sp   +++  +
  gene2809|gene2809|rna2809|rna2809 154 AACIYIACRQEQSPRTFKEVSVL 176
                                        55555555553444433333333 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00027
                                        HCCS-HHHHHHHHHHHCCHHH.HS--S-HHHHHHC---HHHHHHHHHHHHHH CS
                           Cyclin_C  39 flsyppSliAaaalllarstl.nspewtetlehytgyskedlkpcvelilel 89 
                                        +++ +p  +Aaa++++ +++  n +  ++ ++++t ++   +k+ ++ + ++
  gene2809|gene2809|rna2809|rna2809 237 MAGKSPDSVAAAVIYMITYIFpNLKGVQKDIQYVTNVTDVTIKNTYKELMQY 288
                                        55678999************999999*******************9999875 PP

>> YqhR  Conserved membrane protein YqhR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0     0.014        28     114     144 ..     188     218 ..     150     235 .. 0.87
   2 ?    5.2   0.1    0.0091        18     108     142 ..     247     282 ..     243     292 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.014
                               YqhR 114 lnPlfPdvkavaelekntiittlclyilyGv 144
                                        ++ +fP++++++ ++++ i++ +c  +  G+
  gene2809|gene2809|rna2809|rna2809 188 FKLIFPHIEKLQCVTTDDIVARFCSDLNLGI 218
                                        788*********************7776665 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0091
                               YqhR 108 llvfyvlnPlfPdvkava.elekntiittlclyily 142
                                        + v+y++  +fP++k v+ +++  t +t + +   y
  gene2809|gene2809|rna2809|rna2809 247 AAVIYMITYIFPNLKGVQkDIQYVTNVTDVTIKNTY 282
                                        56899**********996479999999998876555 PP

>> RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   1.7   0.00029      0.58       2      30 ..      10      38 ..       9      42 .. 0.89
   2 ?   -3.4   0.2       4.8   9.5e+03       2       6 ..     209     213 ..     209     213 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00029
                                       EBESTTTSBEEEEECSCCCEEEESSSS-E CS
                     RNA_POL_M_15KD  2 kFCpkCgNlLlpkedkegknfeCrqCgYe 30
                                        FC++C +  ++++d ++  + C +Cg +
  gene2809|gene2809|rna2809|rna2809 10 PFCRDCQSDQYITDDTKTGAVLCTNCGCI 38
                                       6*****************89******965 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 4.8
                                        EBEST CS
                     RNA_POL_M_15KD   2 kFCpk 6  
                                        +FC++
  gene2809|gene2809|rna2809|rna2809 209 RFCSD 213
                                        7**86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (305 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       756  (0.0421663); expected 358.6 (0.02)
Passed bias filter:                      520  (0.0290033); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.51u 0.22s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2198.42
//
Query:       gene281|gene281|rna281|rna281  [L=130]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       297  (0.0165653); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.30s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 860.80
//
Query:       gene2810|gene2810|rna2810|rna2810  [L=120]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       965  (0.0538234); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 932.55
//
Query:       gene2811|gene2811|rna2811|rna2811  [L=49]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (49 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       394  (0.0219756); expected 358.6 (0.02)
Passed bias filter:                      253  (0.0141112); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.27s 00:00:00.62 Elapsed: 00:00:00.42
# Mc/sec: 351.59
//
Query:       gene2812|gene2812|rna2812|rna2812  [L=47]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (47 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       489  (0.0272742); expected 358.6 (0.02)
Passed bias filter:                      252  (0.0140554); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.30s 00:00:00.69 Elapsed: 00:00:00.46
# Mc/sec: 308.03
//
Query:       gene2813|gene2813|rna2813|rna2813  [L=409]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.072   13.0   0.5         15    5.6   0.0    2.7  2  RuvB_C    RuvB C-terminal winged helix domain


Domain annotation for each model (and alignments):
>> RuvB_C  RuvB C-terminal winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.1    0.0016        29       6      42 ..      38      76 ..      37      79 .. 0.86
   2 ?    5.6   0.0   0.00082        15       5      33 ..     136     164 ..     135     175 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.0016
                                       HHHHHHHHHHH..HT.TT--B-HHHHHHHTT--HHHHHH CS
                             RuvB_C  6 eldikyLkllk..ekfkggpvglktlaailgeeketied 42
                                       e+dikyL  ++  + f + +  l++l++ +ge++++i+d
  gene2813|gene2813|rna2813|rna2813 38 EEDIKYLFKINslKVFGEVKGTLQMLVESAGEDEKQIID 76
                                       7899**9888633479********************997 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.00082
                                        -HHHHHHHHHHHHT.TT--B-HHHHHHHT CS
                             RuvB_C   5 deldikyLkllkekfkggpvglktlaail 33 
                                        ++ d++y+++l++k ++ p+++  +aa l
  gene2813|gene2813|rna2813|rna2813 136 NNVDKRYISILNKKIRQLPLRMAFIAAYL 164
                                        678**********************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (409 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1212  (0.0676); expected 358.6 (0.02)
Passed bias filter:                      495  (0.0276089); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 2898.46
//
Query:       gene2814|gene2814|rna2814|rna2814  [L=439]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.6e-09   38.0   0.0    1.6e-09   38.0   0.0    2.6  3  POPLD        POPLD (NUC188) domain
      4e-07   30.2  10.4    1.3e-06   28.6   4.3    2.5  3  POP1         Ribonucleases P/MRP protein subunit POP1
  ------ inclusion threshold ------
      0.065   13.5   0.3       0.27   11.5   0.0    2.1  2  Tox-REase-9  Restriction endonuclease fold toxin 9


Domain annotation for each model (and alignments):
>> POPLD  POPLD (NUC188) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       1.8   1.1e+04      59      79 ..      12      32 ..       7      41 .. 0.67
   2 ?   -2.2   0.5      0.89   5.3e+03      62      79 ..      43      60 ..      38      68 .. 0.76
   3 !   38.0   0.0   2.7e-13   1.6e-09      19      84 ..     260     326 ..     242     357 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 1.8
                              POPLD 59 eeeeeaeekwerkPpskRvny 79
                                       e+++e +e  ++ Pp k+ n 
  gene2814|gene2814|rna2814|rna2814 12 ERSNEIQELEKSLPPRKKKNM 32
                                       455566666777888887764 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.89
                              POPLD 62 eeaeekwerkPpskRvny 79
                                       +++++++ ++  +k+ ny
  gene2814|gene2814|rna2814|rna2814 43 RRSSSHHRKRKRNKKGNY 60
                                       556667888999999998 PP

  == domain 3  score: 38.0 bits;  conditional E-value: 2.7e-13
                              POPLD  19 vrvgvrvgGlrerrqlalesgkpyfPddypdtkagekeekeeeeeaeekwerkPpskRvnysklg..i 84 
                                        +r+  rv+Gl+e  +l+l+ g + fP+d + ++ ++++e e    +++k++r+P++kR +ys+l+  i
  gene2814|gene2814|rna2814|rna2814 260 IRI-WRVIGLEEYLRLSLNYGFLVFPFDDVNSDWYKQYEREVFYTENQKYFRTPKGKRYDYSALEenI 326
                                        433.79*******************************************************9998553 PP

>> POP1  Ribonucleases P/MRP protein subunit POP1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6   4.3   2.1e-10   1.3e-06       1      46 [.       9      52 ..       9      59 .. 0.90
   2 !    5.0   0.0    0.0036        22     153     182 ..      60      89 ..      58     108 .. 0.84
   3 ?   -3.8   0.1       1.8   1.1e+04      72      96 ..     143     167 ..     125     171 .. 0.48

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 2.1e-10
                               POP1  1 FvksrefEIkaleealkkskkasstraFQslPrklRRRtaSHnvkR 46
                                       Fv+ r++EI++le++l   kk  ++  FQ+lP  lRRR+ SH+ kR
  gene2814|gene2814|rna2814|rna2814  9 FVNERSNEIQELEKSLPPRKK--KNMLFQKLPFYLRRRSSSHHRKR 52
                                       99**************99965..5679****************998 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0036
                               POP1 153 whaKRakmikrwgfaiplsptqKcyrlthR 182
                                        ++ KR+ mi   g +i++++ +K+  l h+
  gene2814|gene2814|rna2814|rna2814  60 YYGKRFSMICVNGHKIAYQRFEKTSSLLHK 89 
                                        789*************************99 PP

  == domain 3  score: -3.8 bits;  conditional E-value: 1.8
                               POP1  72 rkkkslskrkrlrlrtakkllrlaa 96 
                                        +  ++++++ rl+lr+ +k ++l++
  gene2814|gene2814|rna2814|rna2814 143 TYTSNIDANFRLYLRNGSKFQMLKT 167
                                        2223344455555555555555544 PP

>> Tox-REase-9  Restriction endonuclease fold toxin 9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0      0.72   4.3e+03      10      32 ..     132     154 ..     124     169 .. 0.75
   2 ?   11.5   0.0   4.6e-05      0.27      14      60 ..     294     339 ..     289     345 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.72
                        Tox-REase-9  10 rqmHkdykaekvlgvgrekEfkl 32 
                                        +++ ++y+ ++++  +    f+l
  gene2814|gene2814|rna2814|rna2814 132 QDIYQNYSQKNTYTSNIDANFRL 154
                                        67888888888888888777776 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 4.6e-05
                        Tox-REase-9  14 kdykaekvlgvgrekEfklpsgkRiDfvdfetkiiyELKPnnpraik 60 
                                        k+y+  +v  + + k f+ p+gkR D+  +e+ i    +P n ++i 
  gene2814|gene2814|rna2814|rna2814 294 KQYE-REVFYTENQKYFRTPKGKRYDYSALEENIGNRSRPSNTNQIM 339
                                        7788.777788899******************************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (439 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       775  (0.0432261); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 3002.06
//
Query:       gene2815|gene2815|rna2815|rna2815  [L=54]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (54 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       329  (0.0183502); expected 358.6 (0.02)
Passed bias filter:                      221  (0.0123264); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.42
# Mc/sec: 385.58
//
Query:       gene2816|gene2816|rna2816|rna2816  [L=564]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.4e-55  189.0  27.9    2.9e-55  187.9  27.9    1.4  1  TLC         TLC ATP/ADP transporter
  ------ inclusion threshold ------
      0.024   14.9   1.0      0.024   14.9   1.0    3.1  5  DMT_YdcZ    Putative inner membrane exporter, YdcZ


Domain annotation for each model (and alignments):
>> TLC  TLC ATP/ADP transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  187.9  27.9   3.2e-59   2.9e-55      14     491 .]      31     531 ..      18     531 .. 0.83

  Alignments for each domain:
  == domain 1  score: 187.9 bits;  conditional E-value: 3.2e-59
                                TLC  14 alwpverlelkkllplllllflilfnysilrdlKDslvvtasesgAEvipFlKvwgvlPsAilftliyaklsnkls 89 
                                         ++ v ++e +k+ ++  ++f+i ++ys++r+lKDs ++  +      i+FlK+  v P+ i ++ +  k     s
  gene2816|gene2816|rna2816|rna2816  31 GIYRVSKVEDSKFWLMGGMFFCIAYIYSVIRELKDSFIIKRQ--LPASISFLKLIYVPPVSIAASALVQKCLIFSS 104
                                        58899999*******************************999..55679***********************999* PP

                                TLC  90 kekvFyiivsfflvffllFafvlyPlrellhleaeadkl....esilppglkg...lialvrnWsyalfYvlaELW 158
                                        ++++  ++v+ f v+fl++++v+ Pl++ +  ++  +++     ++ ++gl+    ++  ++ W+ +l +v +E+W
  gene2816|gene2816|rna2816|rna2816 105 NKRILSYVVACFGVYFLVYGVVVLPLQDTIESSNFNATDdfsdSKMAYKGLESvsaIVLTLNCWTSTLHFVASEVW 180
                                        ******************************998765543111134445554441115666799************* PP

                                TLC 159 gsvvlsllfWgfaneitkveeakrFYsllglvanlalivaGevlillsnirkklasavdsweeslkvlvlivvilg 234
                                        g++vlsllf  f n++   ++  rF +l+ +++n+al+  G+ +++l+  + +   + ++++ +l++  +i++i++
  gene2816|gene2816|rna2816|rna2816 181 GTMVLSLLFMSFSNDVCPFRQFIRFMPLFYVLSNVALM--GSSITMLGYQHYNKLVDYSTKQMMLRIAFVIIAIFC 254
                                        ***********************************986..77777777767777778889999************* PP

                                TLC 235 liilllyrllnkkvltderlylaekkkkkkkkkklslkesfklllrskyllliavlviayglsinlvEvvWKaqik 310
                                        l+il+   +l++k+l    + ++ +++k++kk kls++e ++l+++sk +l i  +v+ay++ +n++E  +K+ +k
  gene2816|gene2816|rna2816|rna2816 255 LAILAFQIILERKILGRVLYTIEGEEQKRTKKVKLSFTEGIRLMFKSKLVLAICGIVLAYNIGTNMIESCYKSSLK 330
                                        ***************99888899999************************************************99 PP

                                TLC 311 ely.ptpne...ynafmgk.ltsltGvvtilim.llssnilrkfgWtvaAlitPlillvtgvlFFslilfeke... 377
                                         +  +t+++   +  + ++ ++++tG+v+il+     s  +   gW +  +i+Pli     v  F+l lf+     
  gene2816|gene2816|rna2816|rna2816 331 IVSmATKQDtgnHVLLKSSiIQFITGLVVILLLiSPFSRFIESRGWKIVGIIPPLIATAGFVGVFTLALFNTGrdg 406
                                        7641444441114444444156788988887774456899*****************9999999999998754111 PP

                                TLC 378 .laeliasll........gtsplllavvvGaiqnilsksaKyslfDatkemayipldeeskvkgkaaidvvgarlG 444
                                             i+++l          + l+   +v  +     k +Ky+ fD +ke   + +d+  + + k   d+v+ +lG
  gene2816|gene2816|rna2816|rna2816 407 eNIPPINMMLksevsddtRRKFLQFEETVCLLAVACFKICKYAAFDIAKETLSMKIDKRYRARFKGIYDGVCGKLG 482
                                        1222233333111111103345777888999999999*************************************** PP

                                TLC 445 KSggsli..qqllliifatlasispllavvlllvilvwiiavkklekqf 491
                                        K+gg+l+   +  li  + +  +s +  ++ l+++ +w + ++ l  ++
  gene2816|gene2816|rna2816|rna2816 483 KAGGALLllVSNQLINTTDIRRSSFFYLMISLVIVSIWFYLINYLAGKY 531
                                        *****862144566677778888888888999**********9999887 PP

>> DMT_YdcZ  Putative inner membrane exporter, YdcZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       1.3   1.2e+04      61      83 ..      38      60 ..      33      61 .. 0.62
   2 ?   -2.3   0.1      0.54   4.8e+03     105     138 ..      92     126 ..      88     129 .. 0.63
   3 ?   -2.0   0.3      0.45     4e+03      39      55 ..     179     195 ..     159     228 .. 0.61
   4 ?   -4.9   1.0         2   1.8e+04      36      51 ..     245     260 ..     242     263 .. 0.62
   5 ?   14.9   1.0   2.6e-06     0.024      30      81 ..     345     399 ..     334     403 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 1.3
                           DMT_YdcZ 61 lksvpwwallGGllGavfvtlni 83
                                       +++ + w++ G ++ +++++++i
  gene2816|gene2816|rna2816|rna2816 38 VEDSKFWLMGGMFFCIAYIYSVI 60
                                       55555666555566777777765 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.54
                           DMT_YdcZ 105 aslliDhfGlfgvekrplsl.trllGlllllaGvv 138
                                        as+l+  + +f ++kr ls     +G+ +l+ Gvv
  gene2816|gene2816|rna2816|rna2816  92 ASALVQKCLIFSSNKRILSYvVACFGVYFLVYGVV 126
                                        56666666666666666664145667777777776 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 0.45
                           DMT_YdcZ  39 lvGlivllllllllrks 55 
                                        + G++vl ll++ +++ 
  gene2816|gene2816|rna2816|rna2816 179 VWGTMVLSLLFMSFSND 195
                                        45666665555555443 PP

  == domain 4  score: -4.9 bits;  conditional E-value: 2
                           DMT_YdcZ  36 vsflvGlivlllllll 51 
                                        ++f++ +i++l++l +
  gene2816|gene2816|rna2816|rna2816 245 IAFVIIAIFCLAILAF 260
                                        4566666666666554 PP

  == domain 5  score: 14.9 bits;  conditional E-value: 2.6e-06
                           DMT_YdcZ  30 plaAalvsflvGlivllllllllrks...aalaalksvpwwallGGllGavfvtl 81 
                                         l+++++ f++Gl+v+lll+  +++      ++ +  +p ++ ++G++G+++++l
  gene2816|gene2816|rna2816|rna2816 345 LLKSSIIQFITGLVVILLLISPFSRFiesRGWKIVGIIPPLIATAGFVGVFTLAL 399
                                        5899************999998887766778888999**************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (564 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       903  (0.0503653); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.43
# Mc/sec: 3981.51
//
Query:       gene2817|gene2817|rna2817|rna2817  [L=33]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0066   16.6   0.1     0.0069   16.5   0.1    1.1  1  DNA_gyraseB_C  DNA gyrase B subunit, carboxyl terminus


Domain annotation for each model (and alignments):
>> DNA_gyraseB_C  DNA gyrase B subunit, carboxyl terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.1   3.9e-07    0.0069       5      25 ..      10      30 ..       7      33 .] 0.85

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 3.9e-07
                      DNA_gyraseB_C  5 eiqRfKGLGEmnpeqLweTTm 25
                                       +i+R+KG GE  ++ + +  m
  gene2817|gene2817|rna2817|rna2817 10 NITRYKGIGEILKKAMVDENM 30
                                       8*********99999888777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (33 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       245  (0.013665); expected 358.6 (0.02)
Passed bias filter:                      168  (0.00937029); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.44
# Mc/sec: 225.59
//
Query:       gene2818|gene2818|rna2818|rna2818  [L=227]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (227 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       690  (0.0384851); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1643.44
//
Query:       gene2819|gene2819|rna2819|rna2819  [L=912]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.6e-28   98.7   2.0    2.7e-15   56.9   0.0    3.3  3  Ribonuclease_3   Ribonuclease III domain
    3.4e-20   72.5   0.0    7.2e-10   39.1   0.0    3.2  2  Ribonucleas_3_3  Ribonuclease-III-like
    4.7e-08   33.1   0.1    1.6e-07   31.3   0.1    1.9  1  Dicer_dimer      Dicer dimerisation domain
  ------ inclusion threshold ------
      0.012   15.5   1.2        0.2   11.5   0.2    2.5  2  PAZ              PAZ domain
      0.031   14.7   0.2       0.16   12.5   0.2    2.3  1  DUF1493          Protein of unknown function (DUF1493)
       0.15   11.9   0.0          2    8.4   0.0    2.4  2  zf-CCCH_6        Chromatin remodeling factor Mit1 C-terminal 


Domain annotation for each model (and alignments):
>> Ribonuclease_3  Ribonuclease III domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.1       3.1   9.1e+03      18      45 ..      38      64 ..      36      90 .. 0.62
   2 !   56.9   0.0   8.9e-19   2.7e-15       1     105 []     532     648 ..     532     648 .. 0.87
   3 !   40.0   0.1   1.6e-13   4.9e-10       1     104 [.     791     882 ..     791     883 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 3.1
                                       HHHHHCTTSSHHHHHHHHHHHTSHHHHH CS
                     Ribonuclease_3 18 ylfetypdahegrlsklrsklvsnenla 45
                                       +lf+ y +++e+++++ + +++ + +  
  gene2819|gene2819|rna2819|rna2819 38 RLFR-YLKKSEEKITTKKGAYLEKSVAH 64
                                       5677.77788888888877776555444 PP

  == domain 2  score: 56.9 bits;  conditional E-value: 8.9e-19
                                        HHHHHHHHHHHHHHHHHHHHHHCTTSSHHHHHHHHHHHTSHHHHHHHHHCTTCHCCHCHH................ CS
                     Ribonuclease_3   1 erLeflGDavlklaittylfetypdahegrlsklrsklvsnenlarlakklglpkflrasefdpprnwlppgy... 73 
                                        erLeflGD +lk+++t++++  ++  + g + + + +++ n nl  +++kl+l+++  +  f+pp+   + ++   
  gene2819|gene2819|rna2819|rna2819 532 ERLEFLGDCILKYLVTKFFMLCFE-YDTGLIVDSKCRIIENSNLTLIGRKLKLESYFSNLVFQPPSLSENICKqlq 606
                                        8******************98676.89********************************************99777 PP

                                        ...........HHCCSTTCHCTSHHHHHHHHHHHHHHHHHCT CS
                     Ribonuclease_3  74 ..........klsddekedddadkvladvvEAliGaiyldsg 105
                                                  + ++  +++ +++k++ad+vEA+iGa+y+++g
  gene2819|gene2819|rna2819|rna2819 607 qyfnfkntafNSQTTICSQISSEKTYADIVEAIIGACYVENG 648
                                        777665554444444444555******************987 PP

  == domain 3  score: 40.0 bits;  conditional E-value: 1.6e-13
                                        HHHHHHHHHHHHHHHHHHHHHHCTTSSHHHHHHHHHHHTSHHHHHHHHHCTTCHCCHCHH..............HH CS
                     Ribonuclease_3   1 erLeflGDavlklaittylfetypdahegrlsklrsklvsnenlarlakklglpkflrasefdpprnwlppgykls 76 
                                        e+Le++GD++l++++t+ +f++y+   +  l+++r++lv+n+   +++ + +l +++ +  fd             
  gene2819|gene2819|rna2819|rna2819 791 EKLELIGDSILDVFVTKSIFNEYS--CPFALHEARKNLVNNQIYGNVLYTSKLFHYIET-CFDKD---------EL 854
                                        79*******************886..7******************************93.44433.........45 PP

                                        CCSTTCHCTSHHHHHHHHHHHHHHHHHC CS
                     Ribonuclease_3  77 ddekedddadkvladvvEAliGaiylds 104
                                        +d+   ++ +k ++d++EA+ Gai+ld 
  gene2819|gene2819|rna2819|rna2819 855 RDSYLVNNYKKLYGDIFEAINGAILLDL 882
                                        5555677799****************95 PP

>> Ribonucleas_3_3  Ribonuclease-III-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.1   0.0   2.4e-13   7.2e-10      16     122 ..     525     658 ..     519     662 .. 0.88
   2 !   28.4   0.0     5e-10   1.5e-06       4     112 ..     769     883 ..     766     897 .. 0.82

  Alignments for each domain:
  == domain 1  score: 39.1 bits;  conditional E-value: 2.4e-13
                    Ribonucleas_3_3  16 ngrkghNerLefLGdavLklsvseyllekaekdegeltklraslvseeslaeiAkelg.................. 73 
                                        n++ + +erLefLGd +Lk +v+++ +  +e d+g  +  +  ++++ +l  i+++l+                  
  gene2819|gene2819|rna2819|rna2819 525 NDKYPDYERLEFLGDCILKYLVTKFFMLCFEYDTGLIVDSKCRIIENSNLTLIGRKLKlesyfsnlvfqppslsen 600
                                        566689**************************99999999999***************999***********9999 PP

                    Ribonucleas_3_3  74 ....Lgkvlrl.....rkgeeetegsgrekvladaleAliGAiyldkgaevaqefvee 122
                                            L+++  +     + +++   + + ek  ad++eA+iGA y+++g + +++++ +
  gene2819|gene2819|rna2819|rna2819 601 ickqLQQYFNFkntafNSQTTICSQISSEKTYADIVEAIIGACYVENGLNSTEKMIFR 658
                                        99999999999766653434445666778899*********************99865 PP

  == domain 2  score: 28.4 bits;  conditional E-value: 5e-10
                    Ribonucleas_3_3   4 lleqaltHkSfan...grkghNerLefLGdavLklsvseyllekaekdegeltklraslvseeslaeiAkelgLgk 76 
                                         +e+a+ H S      g++++ e+Le +Gd++L++ v++ ++++++ +  +l + r++lv+++   ++  + +L +
  gene2819|gene2819|rna2819|rna2819 769 FIEKAMIHPSTRDkmfGTRSYFEKLELIGDSILDVFVTKSIFNEYSCP-FALHEARKNLVNNQIYGNVLYTSKLFH 843
                                        6789******9552336689***********************99886.456777889****************** PP

                    Ribonucleas_3_3  77 vlrl..rkgeee..tegsgrekvladaleAliGAiyldkg 112
                                        ++    +k+e +     ++ +k+ +d++eA+ GAi ld +
  gene2819|gene2819|rna2819|rna2819 844 YIETcfDKDELRdsYLVNNYKKLYGDIFEAINGAILLDLD 883
                                        **99774444331255677888**************9965 PP

>> Dicer_dimer  Dicer dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.3   0.1   5.5e-11   1.6e-07      32      85 ..      96     153 ..      44     158 .. 0.85

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 5.5e-11
                        Dicer_dimer  32 kergkfqaevtLPsnsp....lrkiegepmstkklAkrsaAfeackeLhkaglLddhL 85 
                                        + ++ f+++++LP  s+     ++  +++ ++k++A ++aAf+ +k L+++g Ld++L
  gene2819|gene2819|rna2819|rna2819  96 STSKGFVCHLKLPYVSNepvfTESHISQVERSKRAALQDAAFKSIKGLMACGCLDENL 153
                                        36889*********9999985599999******************************9 PP

>> PAZ  PAZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0     0.061   1.8e+02      69      93 ..     242     266 ..     227     317 .. 0.80
   2 ?   11.5   0.2   6.7e-05       0.2      61     119 ..     417     480 ..     406     496 .. 0.64

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.061
                                        CCHHHHCCT---ST-TT--EEEEEE CS
                                PAZ  69 faeYfkkkYnieikdqdqplldvdk 93 
                                        +++ fk+kY +++k+ ++p ++++ 
  gene2819|gene2819|rna2819|rna2819 242 VKNVFKQKYMVTLKKANLPKIKSRA 266
                                        5667*********999***999987 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 6.7e-05
                                        TTCT..CECCHHHHCCT---S...T-TT--EEEEEE..S-SS.----EEEEE-CCCCEEESSBCC CS
                                PAZ  61 kdkeneitfaeYfkkkYniei...kdqdqplldvdk..ktes.ehssqkqiLvpElcdihpisas 119
                                        +d++++i++ +Yf +kY+ ++    d+d  l+  +   + ++ +      +L  E ++++p +++
  gene2819|gene2819|rna2819|rna2819 417 NDNGEFISYLKYFEQKYGTHLkytDDNDKRLMFNGYiyS-HRgKGTATTSLLSSEIMRVTPCTKD 480
                                        33448****************886444454444444221.2222224455566666666665555 PP

>> DUF1493  Protein of unknown function (DUF1493)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.2   5.3e-05      0.16       3      83 ..     666     738 ..     664     753 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.3e-05
                            DUF1493   3 siekevlelireelgtklfkgkeveltldtdldedlkldeddaedllekffkrfnVdrgnfkiktYfvp.dtpllv 77 
                                        + ++ ++  ++e  ++k  ++k+++++ d+ l++ ++ld+d     +++f k+     + f++++Y++  +++ ++
  gene2819|gene2819|rna2819|rna2819 666 KYSDSIIGVFEEADSVK-NEWKKQKINTDKFLRDIFELDGDA---SMDTFAKT-----KTFDFSCYLENcNNGTFF 732
                                        56788999999999999.66************9999998875...68888875.....679999999777888888 PP

                            DUF1493  78 ileylk 83 
                                        + + + 
  gene2819|gene2819|rna2819|rna2819 733 RCNRFL 738
                                        888775 PP

>> zf-CCCH_6  Chromatin remodeling factor Mit1 C-terminal Zn finger 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.0   0.00066         2      15      46 ..      25      56 ..      21      60 .. 0.91
   2 ?    0.2   0.0      0.24   7.3e+02      10      32 ..     616     638 ..     613     640 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00066
                                       S--GGGSSHHHHHHHHHHHHT--S-HHHHHHH CS
                          zf-CCCH_6 15 rtCPhlksetqvrrmleaLkeStEprelveeA 46
                                       +tC  ++ +  v r+ + Lk+S+E+ ++++ A
  gene2819|gene2819|rna2819|rna2819 25 ETCKNIRADDGVHRLFRYLKKSEEKITTKKGA 56
                                       69**********************99998876 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.24
                                        --SSSS--GGGSSHHHHHHHHHH CS
                          zf-CCCH_6  10 HfGekrtCPhlksetqvrrmlea 32 
                                          ++  +C +++se++ + ++ea
  gene2819|gene2819|rna2819|rna2819 616 FNSQTTICSQISSEKTYADIVEA 638
                                        5578899*******998877766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (912 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       620  (0.0345808); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.68u 0.30s 00:00:00.98 Elapsed: 00:00:00.48
# Mc/sec: 5766.03
//
Query:       gene282|gene282|rna282|rna282  [L=286]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.4e-64  215.1   2.1    5.4e-64  215.1   2.1    1.7  2  Ribosomal_L5e    Ribosomal large subunit proteins 60S L5, and
    1.8e-24   86.5   9.5    1.8e-24   86.5   9.5    1.8  2  Ribosomal_L18_c  Ribosomal L18 C-terminal region
     0.0022   18.3   0.3     0.0022   18.3   0.3    1.9  2  Ribosomal_L18p   Ribosomal L18 of archaea, bacteria, mitoch. 


Domain annotation for each model (and alignments):
>> Ribosomal_L5e  Ribosomal large subunit proteins 60S L5, and 50S L18
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  215.1   2.1     9e-68   5.4e-64       2     163 .]      13     173 ..      12     173 .. 0.98
   2 ?   -2.4   0.9      0.69   4.1e+03      25      37 ..     251     264 ..     242     283 .. 0.53

  Alignments for each domain:
  == domain 1  score: 215.1 bits;  conditional E-value: 9e-68
                  Ribosomal_L5e   2 rfqvkfrrrregktdYyarkrliiqdknkyntpkyRlvVrvtnkdiicqiayakiegdkvlaaayskelpkygvkvgltn 81 
                                    rfq+k rrrre ktdY++r+++++ + ++y + k+RlvVr tn++iicqi++a  +gd+v++ a+s el++yg+ vgltn
  gene282|gene282|rna282|rna282  13 RFQTKKRRRRENKTDYTHRRNMLRPNLKNYGALKSRLVVRRTNRKIICQIVKAYADGDRVVVEATSDELRQYGLCVGLTN 92 
                                    9******************************************************************************* PP

                  Ribosomal_L5e  82 yaaaYatglllarrllkklgldkiyegqeevtgeeynveeideekrafkaiLdvGLartttgakvfgalkgavdgglsip 161
                                    y+aaYatgll+ar++l +++l  +y   ++v+g+  ++e++d+e+ra++++Ld+GL r+t+g++ f+a+kga+dggl+ip
  gene282|gene282|rna282|rna282  93 YSAAYATGLLVARKALVRMELGGVYG-AKQVDGKIEEQEDVDDERRAYQVFLDIGLGRSTRGSRYFAAMKGASDGGLKIP 171
                                    *************************6.6689************************************************* PP

                  Ribosomal_L5e 162 hs 163
                                    hs
  gene282|gene282|rna282|rna282 172 HS 173
                                    *7 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.69
                  Ribosomal_L5e  25 iqdknkyntp.kyR 37 
                                    +++++ y+++ kyR
  gene282|gene282|rna282|rna282 251 VKERKDYSANkKYR 264
                                    44444443320232 PP

>> Ribosomal_L18_c  Ribosomal L18 C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.4       1.8   1.1e+04      74      89 ..      17      32 ..       8      36 .. 0.60
   2 !   86.5   9.5     3e-28   1.8e-24       1      95 []     188     280 ..     188     280 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.8
                Ribosomal_L18_c 74 eskkykkkkltleqrk 89
                                   ++++ +++k ++  r+
  gene282|gene282|rna282|rna282 17 KKRRRRENKTDYTHRR 32
                                   3445566666666665 PP

  == domain 2  score: 86.5 bits;  conditional E-value: 3e-28
                Ribosomal_L18_c   1 AevlrkrIfgkhvaeYmeeLkeedeekykkqFskyikkgieaddleelykkahaaIredpvkkekkekkevkkeskkykk 80 
                                    A+vlr+rI+gk v++Ym +L+e+d+eky++ Fs+yik+gi ++dle +y+k+++++r+  +    ke+k++++ +kky+k
  gene282|gene282|rna282|rna282 188 AQVLRDRIYGKAVKDYMIMLRENDNEKYQRMFSEYIKNGIAPEDLEGMYEKVFENVRAVKEI-VVKERKDYSA-NKKYRK 265
                                    89*********************************************************997.5599999999.69**** PP

                Ribosomal_L18_c  81 kkltleqrkarvkqK 95 
                                    +k++ e++k+r  +K
  gene282|gene282|rna282|rna282 266 EKMSGEEKKKRALEK 280
                                    **********98776 PP

>> Ribosomal_L18p  Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.3   3.7e-07    0.0022       6      82 ..      27     108 ..      17     126 .. 0.75
   2 ?   -3.3   0.3       1.9   1.1e+04      15      24 ..     265     274 ..     243     284 .. 0.55

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 3.7e-07
                                    HHCHHHHHHTTT--.TTSSS-EEEEEE-SS-EEEEEE-TTT-..-EEEEECS-SCCCT....S-SSSCHHHHHHHHHHHH CS
                 Ribosomal_L18p   6 arkrRhkRirkkls.gtaerprlvvfrsnrhiyaQviddvkg..ktlasastlekelk....lkstknkeaakkvgeliA 78 
                                      ++R+  +r +l+   a + rlvv r+nr i  Q++   ++  +++++a + e   +         n +aa + g l+A
  gene282|gene282|rna282|rna282  27 DYTHRRNMLRPNLKnYGALKSRLVVRRTNRKIICQIVKAYADgdRVVVEATSDEL--RqyglCVGLTNYSAAYATGLLVA 104
                                    3455666789999954577******************986541145555554443..33466667788999999999999 PP

                                    HHHC CS
                 Ribosomal_L18p  79 erak 82 
                                    ++a+
  gene282|gene282|rna282|rna282 105 RKAL 108
                                    9986 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 1.9
                                    TTT--TTSSS CS
                 Ribosomal_L18p  15 rkklsgtaer 24 
                                    ++k+sg +++
  gene282|gene282|rna282|rna282 265 KEKMSGEEKK 274
                                    2333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1165  (0.0649785); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 1897.67
//
Query:       gene2820|gene2820|rna2820|rna2820  [L=239]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      2e-28   99.2   0.0    2.4e-28   98.9   0.0    1.1  1  Proteasome  Proteasome subunit
  ------ inclusion threshold ------
      0.015   15.2   1.1      0.077   12.8   0.3    2.0  2  DUF4897     Domain of unknown function (DUF4897)


Domain annotation for each model (and alignments):
>> Proteasome  Proteasome subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.9   0.0   2.7e-32   2.4e-28       3     189 ..      33     213 ..      31     214 .. 0.93

  Alignments for each domain:
  == domain 1  score: 98.9 bits;  conditional E-value: 2.7e-32
                                        HS-EEEEEEETTEEEEEEEEEEEETTEEEESSSSTSEEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHSSG CS
                         Proteasome   3 kGttvvGikgkdgvvlaadkratagskllskstveKifkiddhigvafaGlaaDartlvrraraeaqlyrlrygrp 78 
                                        +G   + +++kd + +aa k++  +s    +++   i ++++++ +a++G  aD++++v+ ++  a+++ ++ g +
  gene2820|gene2820|rna2820|rna2820  33 TGIPLIVLRTKDAIYCAAKKQTF-ESLE-IPKN-FNIVQVSEKVHLAISGFPADIDQIVNSVKDMAAKKTYELGFD 105
                                        66778999**********76666.5555.4553.79**************************************** PP

                                        TCHHHHHHHHHHHHHHHHHHCTTTTTSEEEEEEEEETTTEEEEEEEETTSEEEEESSEEEESTTHHHHHHHHHHHH CS
                         Proteasome  79 ipverlvarvaaklqaytqrsgrrpfgvslliagvdeeggpeLyqidpsGsyieekdavaiGsgseaaktalekey 154
                                        ++ ++l++++a+  q+ +qrsg rp    +++ g+de+  p Ly++d s+ ++++ +a  +G++s  +  +lek y
  gene2820|gene2820|rna2820|rna2820 106 VTADILARNLADERQELIQRSGERPMAFTAIFFGFDENT-PLLYHTDTSAVFYSY-YALGVGENSMKMNKYLEKGY 179
                                        ************************************777.***************.8******************* PP

                                        STTBSHHHHHHHHHHHHHHHHHHBTTSCSSEEEEE CS
                         Proteasome 155 kedltleeavelavkalkealerdklsgknievav 189
                                        + d++  +a+ ++vk l+e++ ++ +s++ni+v++
  gene2820|gene2820|rna2820|rna2820 180 HMDMDHAKALFTVVKGLSESIGNE-FSPGNISVCY 213
                                        **********************55.******9985 PP

>> DUF4897  Domain of unknown function (DUF4897)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0      0.04   3.6e+02      74     105 ..      61      93 ..      49     107 .. 0.70
   2 ?   12.8   0.3   8.6e-06     0.077      11      92 ..     147     235 ..     141     239 .] 0.77

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.04
                            DUF4897  74 teregileveEkav..lkglvkvengvvetslgd 105
                                         ++ +i++v Ek+   ++g+ ++ +++v+ s++d
  gene2820|gene2820|rna2820|rna2820  61 PKNFNIVQVSEKVHlaISGFPADIDQIVN-SVKD 93 
                                        45778999999886225678777777665.4454 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 8.6e-06
                            DUF4897  11 eydysgsavlttkaelkf.kdekkeeeyieqYqkasee...tfekylsqlseevgreikvvslessatereg...i 79 
                                         y  ++sav+ +   l   ++  k+++y+e+  + + +   ++   ++ lse++g e+   ++ +  t++++    
  gene2820|gene2820|rna2820|rna2820 147 LYHTDTSAVFYSYYALGVgENSMKMNKYLEKGYHMDMDhakALFTVVKGLSESIGNEFSPGNISVCYTKDNNelkY 222
                                        6778999999999999872456699****98555555535677788899********************6663556 PP

                            DUF4897  80 leveEkavlkglv 92 
                                        l+v+E+ ++   +
  gene2820|gene2820|rna2820|rna2820 223 LNVKEIDTILQKI 235
                                        7899988776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (239 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       596  (0.0332422); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 1572.20
//
Query:       gene2821|gene2821|rna2821|rna2821  [L=326]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (326 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1045  (0.0582855); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2303.30
//
Query:       gene2822|gene2822|rna2822|rna2822  [L=256]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0026   17.9   0.2      0.033   14.4   0.0    2.3  2  ANAPC3          Anaphase-promoting complex, cyclosome, subuni
     0.0095   16.4   0.0      0.018   15.6   0.0    1.4  1  TPR_19          Tetratricopeptide repeat
  ------ inclusion threshold ------
        0.1   12.8   0.6       0.22   11.6   0.2    1.8  2  Cyt_c_ox_IV     Cytochrome c oxidase subunit IV
       0.12   11.3   0.4       0.76    8.6   0.4    2.0  1  Glyco_hydro_47  Glycosyl hydrolase family 47


Domain annotation for each model (and alignments):
>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   7.3e-06     0.033      35      76 ..      28      70 ..      27      73 .. 0.93
   2 ?    0.6   0.0      0.15   6.6e+02      31      65 ..     112     146 ..      96     153 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 7.3e-06
                                       HTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHH CS
                             ANAPC3 35 lngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAi 76
                                       +n++y + ++ +++a k+  +++++ +++A +l++Lk++ eA 
  gene2822|gene2822|rna2822|rna2822 28 QNKDYVQVIDRISQArKKGASDPRIEIIYAYSLIQLKRFTEAQ 70
                                       799************99999*********************96 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.15
                                        HHHHHTT-HHHHHHHHHCTSHHHC-HHHHHHHHHH CS
                             ANAPC3  31 lclylngqykrAyellrkaklnskslgcrylfAqc 65 
                                        ++ +ln +y+ ++ l ++ k n+++  +  ++Aq 
  gene2822|gene2822|rna2822|rna2822 112 EVALLNYEYENCIMLGKEIKRNKNHFLVFPIIAQI 146
                                        56788999999999999999999998777777776 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0     4e-06     0.018       2      47 ..      27      72 ..      26      75 .. 0.96

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 4e-06
                             TPR_19  2 laegdyaeAlalleqalqedpknaearllLAeallalgqldeAeal 47
                                       l+++dy + +++ +qa ++ + ++++ + +A  l++l++++eA+++
  gene2822|gene2822|rna2822|rna2822 27 LQNKDYVQVIDRISQARKKGASDPRIEIIYAYSLIQLKRFTEAQKV 72
                                       899****************************************986 PP

>> Cyt_c_ox_IV  Cytochrome c oxidase subunit IV
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0      0.82   3.7e+03      12      30 ..     138     156 ..     135     161 .. 0.81
   2 ?   11.6   0.2     5e-05      0.22       6      65 ..     198     255 ..     193     256 .] 0.86

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.82
                        Cyt_c_ox_IV  12 avffllvavvYgvltkiee 30 
                                         vf ++++++Y   t+++e
  gene2822|gene2822|rna2822|rna2822 138 LVFPIIAQIIYETRTRHME 156
                                        5899999999*99998776 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 5e-05
                        Cyt_c_ox_IV   6 klflllavffllvavvYgvltkieelvGttalvltgglallvgtylafvarridarpedr 65 
                                          fl+l+ f+l+v+v    + +   +  +  l++   + +++g+++ +++rr+   p+d+
  gene2822|gene2822|rna2822|rna2822 198 CYFLILKEFLLMVGVYHSQWIE--TMQAMKKLLIFCLIIWMTGMFMSTLSRRTLVFPKDQ 255
                                        56999999*9999998888887..6778899999999***************99999986 PP

>> Glyco_hydro_47  Glycosyl hydrolase family 47
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.4   0.00017      0.76     162     231 ..      26      95 ..      15     248 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00017
                                        HHT-CHHHHHHHCCHHHHHCHCC.HHHTTB-BSEEETTT--EE.STEE-SSTTTHHHHHHHHHHHHHCTS- CS
                     Glyco_hydro_47 162 lTgdkkYedlaervtkaleelqektklpglvpikidastgkfv.aekislgargDSyYEYllKqylllgge 231
                                          ++k Y ++++r+ +a ++  +      ++  +  ++ ++f+ a+k+++    DS Y Y++K   +  ++
  gene2822|gene2822|rna2822|rna2822  26 DLQNKDYVQVIDRISQARKKGAS-DPRIEIIYAYSLIQLKRFTeAQKVTIPKIFDSNYTYIVKCIFVGLNQ 95 
                                        557899********999999664.4567788888888888888899*****************87665444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       947  (0.0528195); expected 358.6 (0.02)
Passed bias filter:                      526  (0.0293379); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 1769.50
//
Query:       gene2823|gene2823|rna2823|rna2823  [L=726]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (726 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       841  (0.0469072); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.41
# Mc/sec: 5291.33
//
Query:       gene2824|gene2824|rna2824|rna2824  [L=834]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      6e-82  275.6   3.0    9.7e-81  271.6   3.0    2.2  1  RNB       RNB domain
    8.9e-18   64.1   0.0    1.8e-17   63.1   0.0    1.6  1  OB_Dis3   Dis3-like cold-shock domain 2 (CSD2)
    0.00057   19.8   0.3     0.0016   18.4   0.3    1.8  1  Rrp44_S1  S1 domain
  ------ inclusion threshold ------
       0.11   12.7   0.1       0.47   10.6   0.1    2.2  1  CSD2      Cold shock domain


Domain annotation for each model (and alignments):
>> RNB  RNB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  271.6   3.0   2.2e-84   9.7e-81       1     324 [.     411     723 ..     411     725 .. 0.89

  Alignments for each domain:
  == domain 1  score: 271.6 bits;  conditional E-value: 2.2e-84
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                                RNB   1 RkdlrdllvitIdpedakdlDdAisieklpngnyelgVhIADvshyvkegspldkearkratsvyLpekvvpMLPq 76 
                                        R dlr+  v++Idp++++d+DdA++++ + +  +e+gVhIADvs+yv++++++d+ea++r+t+vyL ++ + MLP+
  gene2824|gene2824|rna2824|rna2824 411 RLDLRNEDVFSIDPPGCTDIDDALHCK-IGT-TTEIGVHIADVSSYVPRNTAVDEEAKRRGTTVYLNDRRIDMLPE 484
                                        78************************6.444.59****************************************** PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                                RNB  77 elsedlcSLnpgedrlalsvlidvdekgevlsveiylsvIkskarltydevqdlleqkdekeekktaedLellyel 152
                                         ls+dlcSL+ + drlalsv++++d++ ++   ++ ++++ks++ +tyd++q++l+  +   ++   + L++ly +
  gene2824|gene2824|rna2824|rna2824 485 VLSSDLCSLKSNVDRLALSVIFQFDADFNIIGSKVCETIVKSREAFTYDQAQNILDCDK---DHVLYAPLRRLYDV 557
                                        *******************************************************5444...34589********* PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...................xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                                RNB 153 akalrkkRlkkgalefdspeikllldedkg...................nrielkveeetkahslveelmllANel 209
                                        +++lrk+R+++gal ++s+ei ++ +  +g                     ++++++ e +  s++ee+m+lAN +
  gene2824|gene2824|rna2824|rna2824 558 SRKLRKSRIDNGALILNSKEIFVRRNR-NGkeikgrctqeneihrangdVNLSIDDKSEVETCSVIEEFMILANVT 632
                                        ****************77777777766.445888888888888888866666799999999*************** PP

                                        xxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                                RNB 210 vArflsel.eipailriheepsnekledliklakklglklednsskknlqeslekleeeeaeqllselllrllkea 284
                                        vA+f++e+ +   +lr+h+e + +++e+ i++ +                               s+l +r++++a
  gene2824|gene2824|rna2824|rna2824 633 VAKFMYEHiKNCSLLRRHPEVEMKEIESEIESVR-------------------------------SMLKRRSMAQA 677
                                        *****666266679********999998888888...............................44556677777 PP

                                        xxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                                RNB 285 kyssep......vgHfgLaleeYthfTSPirRYpDlvvhrllkall 324
                                         y+s+       ++HfgLa ++YthfTSPirRY+Dlvvhrl+k +l
  gene2824|gene2824|rna2824|rna2824 678 TYFSSGtvafadFKHFGLAEPIYTHFTSPIRRYADLVVHRLVKSVL 723
                                        777666777777*******************************998 PP

>> OB_Dis3  Dis3-like cold-shock domain 2 (CSD2)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.1   0.0   4.1e-21   1.8e-17       2      76 ..     304     370 ..     303     371 .. 0.97

  Alignments for each domain:
  == domain 1  score: 63.1 bits;  conditional E-value: 4.1e-21
                                        EEE--SSTTS--EEEETTSSTTTHHHHTTTTTT--EEEEE----TT-SS-EEEEEEE-HHHHHHHHHHHHHHHHT CS
                            OB_Dis3   2 vlfkPldkrlPriliptkelpeeflenpeelegklfvvkidsWsetsryPlGeivksLGeagdieaeteaiLlen 76 
                                        vl+kP+dk++P ++i+t+++        e+++++++ + i +W+ets+yP++ ++ +LG++gd+++e++ iL+ n
  gene2824|gene2824|rna2824|rna2824 304 VLVKPIDKKYPPCRIQTSNV--------ERYKNMRLKIVISEWKETSKYPNAVYIGMLGPVGDVQTEINSILILN 370
                                        89******************........********************************************977 PP

>> Rrp44_S1  S1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.3   3.5e-07    0.0016       3      52 ..     772     821 ..     770     833 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 3.5e-07
                                        EEEEEEEEESSEEEEEETTTTEEEEEEHHHCBS-GGG..-EEETTTTEEE CS
                           Rrp44_S1   3 eegyvikvfsNGvvvlvprfGiEglirledlaeeeeskeaefdeeeykle 52 
                                        +++yvik + NG  v+vp + ++g i+    ++ee +     d+e++ ++
  gene2824|gene2824|rna2824|rna2824 772 TQAYVIKSLANGSIVYVPEYDLDGFIKSVRTVNEEVKVRIVRDDENFFIN 821
                                        68************************988887777776777777777766 PP

>> CSD2  Cold shock domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   0.00011      0.47      27      70 ..     329     373 ..     306     375 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00011
                               CSD2  27 dkVvveiteypdk.knpeGevievLGkkgdpgveilsilakhglp 70 
                                           ++ i e+++  k p +  i  LG  gd ++ei+sil  ++++
  gene2824|gene2824|rna2824|rna2824 329 MRLKIVISEWKETsKYPNAVYIGMLGPVGDVQTEINSILILNEIS 373
                                        4456678999855256**********************9777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (834 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       791  (0.0441185); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.66u 0.29s 00:00:00.95 Elapsed: 00:00:00.44
# Mc/sec: 5689.63
//
Query:       gene2825|gene2825|rna2825|rna2825  [L=46]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (46 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       507  (0.0282782); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.28s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 323.66
//
Query:       gene2826|gene2826|rna2826|rna2826  [L=168]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.12   12.6   1.2       0.44   10.8   0.2    2.1  2  KLRAQ     Predicted coiled-coil domain-containing protein


Domain annotation for each model (and alignments):
>> KLRAQ  Predicted coiled-coil domain-containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.04   7.2e+02      55      76 ..      30      51 ..      15      74 .. 0.74
   2 ?   10.8   0.2   2.5e-05      0.44      16      77 ..      98     164 ..      88     168 .] 0.67

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.04
                              KLRAQ 55 rNkqLekrvellqeeleveekk 76
                                       rN q+ +  ++l e+++ e+k+
  gene2826|gene2826|rna2826|rna2826 30 RNIQIDRYTHQLCEDITCENKE 51
                                       8889999999999999888877 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 2.5e-05
                              KLRAQ  16 vLkkavleEqskeaslkeelk.......ekeqslrkseqEvdsLtFrNkqLekrvellqeeleveekkv 77 
                                        v + +v++    +  +ke++k        +   +rk++qE ds   r  qL+ r+ +l +e++++ k++
  gene2826|gene2826|rna2826|rna2826  98 VYRDGVVKGALPNFTVKEHVKiakinfyVQSLLIRKIRQEGDSELVR--QLKERIPVLSDEVDNAIKRM 164
                                        5555555555555555555551111111234569*********8876..9*************998873 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1006  (0.0561102); expected 358.6 (0.02)
Passed bias filter:                      540  (0.0301188); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1163.19
//
Query:       gene2827|gene2827|rna2827|rna2827  [L=100]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.032   14.0   1.1      0.034   13.9   1.1    1.2  1  DUF713    Protein of unknown function (DUF713)


Domain annotation for each model (and alignments):
>> DUF713  Protein of unknown function (DUF713)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   1.1   1.9e-06     0.034      80     136 ..       8      65 ..       1      91 [. 0.85

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.9e-06
                             DUF713  80 lsnLakkvlsaynkLeeafeklkel.sekfedkiFlkvLqksisdvatklleilevld 136
                                        +++++ ++ + +++L + f+ l++  ++++++   +  +q++i++v++ +l+i++ + 
  gene2827|gene2827|rna2827|rna2827   8 IRKINTSIEKIFDTLIDIFTMLSTTnTQDYKELRDIICIQRKIVQVSDTVLQIYNYTV 65 
                                        678999****************987267899999*******************88665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1010  (0.0563333); expected 358.6 (0.02)
Passed bias filter:                      494  (0.0275531); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 723.73
//
Query:       gene2828|gene2828|rna2828|rna2828  [L=226]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
     0.0013   18.7   0.6     0.0027   17.8   0.6    1.5  1  DASH_Dad3  DASH complex subunit Dad3
  ------ inclusion threshold ------
       0.52   11.0   2.6       0.32   11.6   0.5    1.8  2  DUF883     Bacterial protein of unknown function (DUF883)


Domain annotation for each model (and alignments):
>> DASH_Dad3  DASH complex subunit Dad3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.6     3e-07    0.0027       4      46 ..       6      48 ..       4      53 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 3e-07
                          DASH_Dad3  4 leqevLdeYerLaenlktLaselkeLasnsteeildgLReLEr 46
                                       l +++L+ Y++L  + ++L +e++++ sn++++i +++Re+ +
  gene2828|gene2828|rna2828|rna2828  6 LLSSILSAYKKLRLEFHKLRNEIRRMYSNTKKSIKQEIREVRM 48
                                       5579***********************************9866 PP

>> DUF883  Bacterial protein of unknown function (DUF883)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.5   3.6e-05      0.32       2      45 ..      16      59 ..      15      89 .. 0.89
   2 ?   -2.2   0.1      0.71   6.4e+03      33      46 ..     163     176 ..     144     192 .. 0.49

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 3.6e-05
                             DUF883  2 eleaeleslladleellkeaadeageeaeelRerleerlerare 45
                                       +l+ e+++l+++++ + ++++++ ++e++e+R +++ + +++r 
  gene2828|gene2828|rna2828|rna2828 16 KLRLEFHKLRNEIRRMYSNTKKSIKQEIREVRMNIRGTTRKSRR 59
                                       577799******************************99988874 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.71
                             DUF883  33 Rerleerlerarer 46 
                                         + ++e ler ++ 
  gene2828|gene2828|rna2828|rna2828 163 GNSVNEGLERKKQV 176
                                        23333333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1246  (0.0694963); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1514.91
//
Query:       gene2829|gene2829|rna2829|rna2829  [L=39]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (39 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       381  (0.0212505); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.41
# Mc/sec: 286.36
//
Query:       gene283|gene283|rna283|rna283  [L=590]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    0.00041   20.6   2.0    0.00055   20.2   0.1    2.2  2  Yop-YscD_cpl  Inner membrane component of T3SS, cytoplasmic d
    0.00055   20.2   0.0     0.0012   19.1   0.0    1.6  1  FHA           FHA domain


Domain annotation for each model (and alignments):
>> Yop-YscD_cpl  Inner membrane component of T3SS, cytoplasmic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.1   6.1e-08   0.00055      16      89 ..      24      94 ..      15      97 .. 0.84
   2 ?   -2.4   0.3      0.67     6e+03      60      70 ..     383     393 ..     369     423 .. 0.52

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 6.1e-08
                                   TEEEEEES-TT-SEE---TTS-TT-EEEEEETTEEEEEE-CESS--EETTEE-SECC.--TTSEEEETTEEEEEE CS
                   Yop-YscD_cpl 16 egevviGsdedcDivLsDkevsrkhlkLeveeesvrledlgsrngllvngerveele.lrpgdvlelGttelalv 89
                                   ++++++G++ +cD+ ++ ++v++khl++++++++++++    +++++vng  v+  +   +gdv+ +  t+++++
  gene283|gene283|rna283|rna283 24 HTKFTVGRSLKCDLRVQLPSVEDKHLVIYLDDRKYVVS----GDDVMVNGAVVSGEGvFVYGDVFDVRGTRFVVM 94
                                   67899*******************************99....889999999988555588888888877777665 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.67
                                    --EETTEE-SE CS
                   Yop-YscD_cpl  60 gllvngervee 70 
                                    ++++++ + +e
  gene283|gene283|rna283|rna283 383 ESTIDQVENQE 393
                                    44444433331 PP

>> FHA  FHA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   1.4e-07    0.0012       2      46 ..      28      71 ..      27      87 .. 0.74

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.4e-07
                                   EEESSTTSSEETTSTTSTTTEEEEEEETTCEEEEEEEESSSSSEE CS
                            FHA  2 tiGRssdcdivlddpsiSrkHalikfdkgsgkvyleDlgSknGtf 46
                                   t+GRs +cd++++ ps+  kH++i+ d+ ++ v   D+   nG  
  gene283|gene283|rna283|rna283 28 TVGRSLKCDLRVQLPSVEDKHLVIYLDDRKYVVSGDDV-MVNGAV 71
                                   89*************************99333333343.233333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (590 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2064  (0.115121); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.87u 0.33s 00:00:01.20 Elapsed: 00:00:00.47
# Mc/sec: 3805.68
//
Query:       gene2830|gene2830|rna2830|rna2830  [L=54]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (54 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       356  (0.0198561); expected 358.6 (0.02)
Passed bias filter:                      232  (0.0129399); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.31u 0.25s 00:00:00.56 Elapsed: 00:00:00.38
# Mc/sec: 426.09
//
Query:       gene2831|gene2831|rna2831|rna2831  [L=63]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (63 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       425  (0.0237046); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.45
# Mc/sec: 421.52
//
Query:       gene2832|gene2832|rna2832|rna2832  [L=178]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.9e-05   22.3   0.6    0.00019   21.0   0.6    1.7  1  S4            S4 domain
  ------ inclusion threshold ------
      0.011   16.6   2.7      0.018   15.9   2.7    1.5  1  Ribosomal_S4  Ribosomal protein S4/S9 N-terminal domain


Domain annotation for each model (and alignments):
>> S4  S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.6   2.2e-08   0.00019       1      46 [.     104     149 ..     104     151 .. 0.92

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 2.2e-08
                                        EEHHHHHHHTTSSSSHHHHHHHHHTTTEEETTEEE--TT-EE-TTC CS
                                 S4   1 rRLdkvlarlglassrreArqlIehGrVlVNGkvvkdpsyrVkpgD 46 
                                        rR  ++l+r ++ +    A +++e+G+V+V + +v++ s  V+ g+
  gene2832|gene2832|rna2832|rna2832 104 RRVPVLLKRNRMIENLGDAVKFVEQGHVRVGNTRVNNCSVLVSRGM 149
                                        7999999999999***********************9999999775 PP

>> Ribosomal_S4  Ribosomal protein S4/S9 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.9   2.7     2e-06     0.018       2      79 ..       4      61 ..       3     103 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2e-06
                                       T-S-CHHHHCHCTS-STSSSS-S-SSTTTTS-----CHCH.HHHHHHHHHHHHT-S.HHHHHHHHHHHHHCCSHHHHH CS
                       Ribosomal_S4  2 ykgpkckllRrvgfklflkgreyppGqhgkrrkklseYgk.qlrekqklkrrYgll.ekqfrryfkearrirGktgen 77
                                       +k ++++llR+ +f                      e++   +++++  + rY ++ ++++  y k++r ir  ++e 
  gene2832|gene2832|rna2832|rna2832  4 LKYHEQRLLRKTNFL---------------------EWRDtDTKNEHYYISRYYITrREDYYTYKKLVRIIR-TLSES 59
                                       689***********9.....................*********************************999.88887 PP

                                       HH CS
                       Ribosomal_S4 78 Ll 79
                                       + 
  gene2832|gene2832|rna2832|rna2832 60 IA 61
                                       76 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       683  (0.0380947); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 1257.12
//
Query:       gene2833|gene2833|rna2833|rna2833  [L=37]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (37 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       261  (0.0145574); expected 358.6 (0.02)
Passed bias filter:                      165  (0.00920297); expected 358.6 (0.02)
Passed Vit filter:                         7  (0.000390429); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.33u 0.24s 00:00:00.57 Elapsed: 00:00:00.40
# Mc/sec: 276.10
//
Query:       gene2834|gene2834|rna2834|rna2834  [L=374]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.016   14.6   0.2      0.016   14.6   0.2    2.7  3  UPF0014        Uncharacterised protein family (UPF0014)
        8.5    6.0   8.0        2.5    7.8   0.9    3.1  3  Baculo_11_kDa  Baculovirus 11 kDa family


Domain annotation for each model (and alignments):
>> UPF0014  Uncharacterised protein family (UPF0014)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.3     0.035   3.1e+02      65     117 ..      55     105 ..      47     125 .. 0.52
   2 ?   14.6   0.2   1.8e-06     0.016      36      81 ..     129     172 ..     123     181 .. 0.83
   3 ?   -1.3   0.1      0.12   1.1e+03      57     105 ..     244     291 ..     230     302 .. 0.73

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.035
                            UPF0014  65 vmllvAai.eaakrvkkklkklllivllsllvstlltlllllllviqpepwyep 117
                                        +++ + ++ ++++r + ++ + + i+++ l v +l+t ++ll+++ + +++   
  gene2834|gene2834|rna2834|rna2834  55 LLCSFCIYrIIMNR-NGSFLRKTGISFFVLSVCSLCTYMFLLIFL-S-TQMAVS 105
                                        55555555345555.444444455555555555555444444432.2.233333 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 1.8e-06
                            UPF0014  36 mvvQLllvGyvLklifalnslllvllillvmllvAaieaakrvkkk 81 
                                         +vQL+ v+y L+ if++   +l +li l m +v+a++ ++r+k k
  gene2834|gene2834|rna2834|rna2834 129 NIVQLVNVSYSLQHIFRT--SALYMLIGLWMPCVSAYALKRRTKLK 172
                                        58***************6..677789999*********99996544 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 0.12
                            UPF0014  57 llvllillvmllvAaieaakrvkkklkklllivllsllvstlltlllll 105
                                         + +l++l + ++++ e     +++ ++ l i++++llv t+l  +l +
  gene2834|gene2834|rna2834|rna2834 244 CAFFLLILQIKFFSTTEFDGE-DSRSTENLNILVFALLVNTFLKYTLHI 291
                                        455666777778888888887.777777788888899988888666555 PP

>> Baculo_11_kDa  Baculovirus 11 kDa family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.9   0.00027       2.5      25      60 ..      65     105 ..      61     113 .. 0.81
   2 ?   -0.5   0.1      0.11   9.6e+02      40      53 ..     243     256 ..     233     262 .. 0.74
   3 ?    0.2   0.1     0.063   5.6e+02      34      56 ..     302     325 ..     300     337 .. 0.65

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.00027
                      Baculo_11_kDa  25 lvsrNrsflrd.....FvLvicglvvfvvivlfilLlvvil 60 
                                        +++rN sflr      FvL +c+l  ++ +++f+   + ++
  gene2834|gene2834|rna2834|rna2834  65 IMNRNGSFLRKtgisfFVLSVCSLCTYMFLLIFLSTQMAVS 105
                                        679*****997777779********9999999987655555 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.11
                      Baculo_11_kDa  40 icglvvfvvivlfi 53 
                                        +c+++++++ + f+
  gene2834|gene2834|rna2834|rna2834 243 VCAFFLLILQIKFF 256
                                        67777777777766 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.063
                      Baculo_11_kDa  34 rdFvLvicglvvfvvivl.filLl 56 
                                         d+vL  c  + +v++ l + +Ll
  gene2834|gene2834|rna2834|rna2834 302 SDYVLQKCECISLVIVYLvMSTLL 325
                                        689999886666555544044555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (374 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       757  (0.0422221); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 2536.54
//
Query:       gene2835|gene2835|rna2835|rna2835  [L=54]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (54 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       253  (0.0141112); expected 358.6 (0.02)
Passed bias filter:                      174  (0.00970495); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.33u 0.29s 00:00:00.62 Elapsed: 00:00:00.42
# Mc/sec: 388.34
//
Query:       gene2836|gene2836|rna2836|rna2836  [L=195]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       803  (0.0447878); expected 358.6 (0.02)
Passed bias filter:                      518  (0.0288917); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1507.64
//
Query:       gene2837|gene2837|rna2837|rna2837  [L=417]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      4e-21   75.9   0.2    1.3e-07   31.7   0.0    3.2  3  IPPT             IPP transferase
    4.9e-07   29.4   0.0    7.7e-07   28.7   0.0    1.3  1  IPT              Isopentenyl transferase
     0.0005   20.5   0.0    0.00096   19.6   0.0    1.5  1  AAA              ATPase family associated with various cellul
    0.00053   20.5   0.5     0.0038   17.8   0.1    2.3  2  AAA_18           AAA domain
     0.0026   17.8   0.3      0.007   16.4   0.0    1.9  2  ResIII           Type III restriction enzyme, res subunit
     0.0037   16.8   0.1     0.0089   15.6   0.1    1.5  1  AAA_25           AAA domain
      0.004   16.4   0.0     0.0067   15.7   0.0    1.3  1  TIP49            TIP49 P-loop domain
     0.0095   16.2   0.2      0.047   14.0   0.1    1.8  2  AAA_22           AAA domain
  ------ inclusion threshold ------
       0.01   15.3   0.0      0.016   14.6   0.0    1.3  1  PhoH             PhoH-like protein
       0.01   15.7   0.0      0.018   15.0   0.0    1.4  1  NACHT            NACHT domain
      0.011   15.8   0.0      0.023   14.7   0.0    1.5  1  AAA_5            AAA domain (dynein-related subfamily)
      0.015   15.4   0.3      0.052   13.7   0.0    2.0  2  Cytidylate_kin2  Cytidylate kinase-like family
      0.018   14.4   0.0      0.026   13.8   0.0    1.2  1  DnaB_C           DnaB-like helicase C terminal domain
      0.024   14.2   0.0      0.036   13.7   0.0    1.3  1  SRP54            SRP54-type protein, GTPase domain
      0.029   14.4   0.0      0.059   13.4   0.0    1.5  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
      0.036   14.5   0.0       0.12   12.8   0.0    2.0  1  RNA_helicase     RNA helicase
      0.038   13.2   0.0      0.056   12.7   0.0    1.3  1  DUF2075          Uncharacterized conserved protein (DUF2075)
      0.043   14.1   0.0       0.12   12.7   0.0    1.8  2  AAA_28           AAA domain
      0.046   13.8   0.5        0.7   10.0   0.1    2.9  1  Torsin           Torsin
      0.048   13.8   0.0       0.11   12.6   0.0    1.6  1  AAA_2            AAA domain (Cdc48 subfamily)
      0.053   13.9   0.0      0.098   13.0   0.0    1.3  1  AAA_16           AAA ATPase domain
      0.054   13.2   0.0        0.1   12.3   0.0    1.4  1  IstB_IS21        IstB-like ATP binding protein
      0.057   12.9   0.0       0.11   12.0   0.0    1.4  1  AAA_7            P-loop containing dynein motor region
       0.12   12.4   0.8         15    5.7   0.1    2.9  2  SKI              Shikimate kinase
       0.13   12.5   0.3        0.3   11.3   0.0    1.7  2  Hydin_ADK        Hydin Adenylate kinase-like domain
       0.16   12.1   0.0       0.43   10.7   0.0    1.7  1  AAA_33           AAA domain
       0.19   11.4   0.0       0.36   10.6   0.0    1.4  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
       0.21   10.6   0.0       0.35    9.9   0.0    1.3  1  T2SSE            Type II/IV secretion system protein
       0.55   10.3   2.3       0.53   10.3   0.7    1.8  1  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai


Domain annotation for each model (and alignments):
>> IPPT  IPP transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.7   0.0   2.1e-10   1.3e-07       1      72 [.      78     151 ..      78     159 .. 0.84
   2 !   16.8   0.1   7.6e-06    0.0047     142     176 ..     158     192 ..     149     213 .. 0.84
   3 !   24.4   0.0   3.6e-08   2.2e-05     183     225 ..     304     350 ..     277     353 .. 0.82

  Alignments for each domain:
  == domain 1  score: 31.7 bits;  conditional E-value: 2.1e-10
                                        TTBTT-HTTTT---HHHHTTS-EESSS-B-TTS---HHHHHHHHHHHHHHHHH.......TT-E.EEEEES-HHHH CS
                               IPPT   1 qvYrgmdIgTakptaeeragvphhlidildpdeeysvadFqkdalkaieeila.......rgki.pilvGGTglYi 68 
                                        q++r+++Ig++k      +  +h ++d+ +  e+y+v ++++d l++i+++ +        g + +++vGG+glY+
  gene2837|gene2837|rna2837|rna2837  78 QIFRELNIGSNKER----E--NHLMVDVKHYGEKYDVEKYVNDSLNVIKNMEDcnrlvdcDGSVrVLVVGGCGLYM 147
                                        9***********43....3..6**************************987766667777555416779******* PP

                                        HHHH CS
                               IPPT  69 kall 72 
                                        + l 
  gene2837|gene2837|rna2837|rna2837 148 ERLS 151
                                        9875 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 7.6e-06
                                        EEEEEECSHHHHHHHHHHHHHHHHHTTHHHHHHHH CS
                               IPPT 142 lviglesdreelyeridkRvdemleaGlleEvekl 176
                                        + ++l ++r +ly+ +d+R++em+ +GlleE+ ++
  gene2837|gene2837|rna2837|rna2837 158 VKVFLFKNRRVLYRDLDRRCEEMVLNGLLEETLRV 192
                                        5667769************************9775 PP

  == domain 3  score: 24.4 bits;  conditional E-value: 3.6e-08
                                        STTSHHHHHHHT.TSS-HHH...HHHHHHHHHHHHHHHHHHHHHTTC CS
                               IPPT 183 aigykelleyle.gelslee...aieklkaatrqyaKrQltWfrkkk 225
                                         igyke +++l  g++s+++   +++ +k++tr+y++rQ t+f++k+
  gene2837|gene2837|rna2837|rna2837 304 PIGYKESYNFLIaGDYSYNAfisFLNTFKKNTRNYVRRQETFFKRKN 350
                                        69*******99647888775222779*****************9875 PP

>> IPT  Isopentenyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7   0.0   1.3e-09   7.7e-07       3      54 ..      45      96 ..      43     122 .. 0.90

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 1.3e-09
                                IPT  3 vylifGatttGKtaeaiklaketgapvivlDRvqcyselavgsGrpleeele 54
                                       +  + Gat+tGKta a kla++    +++ D vq + el +gs +  e+ l 
  gene2837|gene2837|rna2837|rna2837 45 IICLAGATGTGKTALALKLAHNLNTKILSCDSVQIFRELNIGSNKERENHLM 96
                                       56789**************************************999888875 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   1.5e-06   0.00096       1      46 [.      46      92 ..      46     121 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1.5e-06
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSS.STTHHHHHH CS
                                AAA  1 vllyGppGtGKTllakavakelgvefleisgsellsk.yvgesekki 46
                                       ++l G  GtGKT+la  +a++l++++l+ +  +++ +  +g ++++ 
  gene2837|gene2837|rna2837|rna2837 46 ICLAGATGTGKTALALKLAHNLNTKILSCDSVQIFRElNIGSNKERE 92
                                       689**************************999999443555555444 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.1   6.2e-06    0.0038       1      79 [.      46     140 ..      46     187 .. 0.73
   2 ?    0.4   0.1       1.5   9.2e+02      92     112 ..     347     367 ..     331     379 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 6.2e-06
                             AAA_18   1 IlltGtpGvGKttlakeLskrlgf............gvnlrdva.kenglllevdpe..aldeskrldedkldkll 61 
                                        I+l+G+ G+GKt la  L+  l+               n++++  +en+l  +v ++  ++d +k +++    +++
  gene2837|gene2837|rna2837|rna2837  46 ICLAGATGTGKTALALKLAHNLNTkilscdsvqifrELNIGSNKeRENHLMVDVKHYgeKYDVEKYVNDSL--NVI 119
                                        9*****************99887788977776666644444443144444455555576666666666666..777 PP

                             AAA_18  62 daleenss...aleegknlvi 79 
                                        +++e +++     ++  +lv+
  gene2837|gene2837|rna2837|rna2837 120 KNMEDCNRlvdCDGSVRVLVV 140
                                        777777765554444444455 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 1.5
                             AAA_18  92 kdikkvvLtaspeelleRlek 112
                                        k++++v++ a+ + l+eR++ 
  gene2837|gene2837|rna2837|rna2837 347 KRKNYVFINAERDDLMERIAG 367
                                        233339************986 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   1.1e-05     0.007      26      51 ..      45      70 ..      32     123 .. 0.87
   2 ?   -2.1   0.2       5.4   3.4e+03      87      96 ..     344     353 ..     324     404 .. 0.49

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.1e-05
                                       EEEEEESTTSTHHHHHHHHHHHH-S. CS
                             ResIII 26 rglikmaTGtGKTlvaaklierllkk 51
                                        ++++ aTGtGKT +a+kl+ +l +k
  gene2837|gene2837|rna2837|rna2837 45 IICLAGATGTGKTALALKLAHNLNTK 70
                                       689******************99886 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 5.4
                                        EEESSS-B-- CS
                             ResIII  87 kkvsgdkkka 96 
                                        ++++ +++ +
  gene2837|gene2837|rna2837|rna2837 344 TFFKRKNYVF 353
                                        3333333322 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1   1.4e-05    0.0089      31      56 ..      41      66 ..      36      73 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.4e-05
                             AAA_25 31 pagelallaGapgtGKttlaldlala 56
                                       p+  ++ laGa+gtGKt+lal la+ 
  gene2837|gene2837|rna2837|rna2837 41 PMSQIICLAGATGTGKTALALKLAHN 66
                                       7788999****************986 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   1.1e-05    0.0067      51      80 ..      44      73 ..      30      89 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.1e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                              TIP49 51 ravLlaGpsgtGktalaiaiskelgedvpf 80
                                       + + laG +gtGktala+ ++++l++++  
  gene2837|gene2837|rna2837|rna2837 44 QIICLAGATGTGKTALALKLAHNLNTKILS 73
                                       7899*********************98854 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.1   7.5e-05     0.047       6      31 ..      44      69 ..      42      77 .. 0.88
   2 ?   -1.8   0.0       5.5   3.4e+03      69     129 ..      88     141 ..      75     145 .. 0.52

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 7.5e-05
                             AAA_22  6 gilvvtGesGtGKTtllrrlleqlde 31
                                       +i+++ G +GtGKT l+ +l+++l+ 
  gene2837|gene2837|rna2837|rna2837 44 QIICLAGATGTGKTALALKLAHNLNT 69
                                       699******************99964 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 5.5
                             AAA_22  69 kaerlsseellealeqalraravielliiDEaqhlrseealeeLrsllnlsrkgvqliLvG 129
                                        ++   ++ +l+  + ++ ++++v e  + D    +   +++e++ +l++  + +v++++vG
  gene2837|gene2837|rna2837|rna2837  88 NK--ERENHLMVDVKHYGEKYDV-EKYVNDSLNVI---KNMEDCNRLVD-CDGSVRVLVVG 141
                                        44..5555555555555555555.44443333333...45555555555.55566666655 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   2.7e-05     0.016      18      46 ..      42      70 ..      35     139 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.7e-05
                                       H-SEEEEE--TTSSTTHHHHHHHHHHHHT CS
                               PhoH 18 kndivfaiGpaGtGKtylavalavealkk 46
                                        ++i++ +G +GtGKt la+ la ++ +k
  gene2837|gene2837|rna2837|rna2837 42 MSQIICLAGATGTGKTALALKLAHNLNTK 70
                                       568999****************9887655 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.0   2.9e-05     0.018       2      39 ..      45      80 ..      44      99 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.9e-05
                                       CEEEEC-TTTCHHHHHHHHHHHHCTS-SCCCC-SEEEE CS
                              NACHT  2 lvilqGeaGsGKTtLlqklalawaegklpqgafklvFf 39
                                       +++l G+ G GKT+L+ kla+ + ++ l ++   + +f
  gene2837|gene2837|rna2837|rna2837 45 IICLAGATGTGKTALALKLAHNLNTKILSCDS--VQIF 80
                                       689********************999888864..4444 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   3.8e-05     0.023       2      27 ..      46      71 ..      45      79 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.8e-05
                                       EEEE--SSSSHHHHHHHGGGGBS--E CS
                              AAA_5  2 vlLvGppGtgKselaerlaaalnrev 27
                                       ++L G++GtgK+ la +la+ ln+++
  gene2837|gene2837|rna2837|rna2837 46 ICLAGATGTGKTALALKLAHNLNTKI 71
                                       79*******************99876 PP

>> Cytidylate_kin2  Cytidylate kinase-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   8.4e-05     0.052       1      73 [.      45     116 ..      45     182 .. 0.74
   2 ?   -1.4   0.1       3.6   2.2e+03     118     145 ..     352     382 ..     347     407 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 8.4e-05
                    Cytidylate_kin2   1 iITIsreyGsgGetigeaLAekLglpfydreiieevakelglseeeveevdersrlssflskllaarvagdtl 73 
                                        iI++++  G+g+++++ +LA++L+ ++++ + + ++++el++  ++ +e +    +++  +k+  +++ +d l
  gene2837|gene2837|rna2837|rna2837  45 IICLAGATGTGKTALALKLAHNLNTKILSCDSV-QIFRELNIGSNKERENHLMVDVKHYGEKYDVEKYVNDSL 116
                                        8**************************999877.577777777777766666667777777777776655444 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 3.6
                    Cytidylate_kin2 118 vfltapledrvkr...vaereglseeearek 145
                                        vf+ a+++d ++r   v e e++s+e a ++
  gene2837|gene2837|rna2837|rna2837 352 VFINAERDDLMERiagVIEGERVSDEYAFKY 382
                                        7888888876666222445555565555544 PP

>> DnaB_C  DnaB-like helicase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   4.2e-05     0.026      19      46 ..      43      70 ..      36     116 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.2e-05
                                       TXEEEEEEXTTSSHHHHHHHHHHHHHHC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             DnaB_C 19 gdliiiAarpsmGktalalniaenaavk 46
                                       +++i +A+  ++Gktalal++a+n  +k
  gene2837|gene2837|rna2837|rna2837 43 SQIICLAGATGTGKTALALKLAHNLNTK 70
                                       78999******************98754 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   5.8e-05     0.036       2      31 ..      44      73 ..      43     136 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.8e-05
                                       EEEEEEESTTSSHHHHHHHHHHHHHHTTS- CS
                              SRP54  2 nvillvGlqGaGKTttlaKLaallkkegkk 31
                                       ++i l+G +G+GKT  + KLa+ l+++  +
  gene2837|gene2837|rna2837|rna2837 44 QIICLAGATGTGKTALALKLAHNLNTKILS 73
                                       6899******************99876443 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   9.6e-05     0.059      19      46 ..      43      70 ..      31     112 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 9.6e-05
                                       TEEEEEEESTTSSHHHHHHHHHHHTT-- CS
                               TsaE 19 gdvilLeGdLGaGKTtlvrglakalgve 46
                                       +++i+L G  G+GKT+l+ +la++l+ +
  gene2837|gene2837|rna2837|rna2837 43 SQIICLAGATGTGKTALALKLAHNLNTK 70
                                       678*********************9876 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   0.00019      0.12       1      31 [.      46      76 ..      46     127 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00019
                       RNA_helicase  1 iwlyGpsgeGKStlakeLakallkklklkkk 31
                                       i+l G++g+GK+ la +La++l +k+ +  +
  gene2837|gene2837|rna2837|rna2837 46 ICLAGATGTGKTALALKLAHNLNTKILSCDS 76
                                       7899*******************99944433 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   9.1e-05     0.056       2      73 ..      44     121 ..      43     140 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 9.1e-05
                            DUF2075   2 avvlVtGvaGtGKtvvllnllael......eddeeertavylsvNhplvlvlrealakkeekkkkkeafeklssfi 71 
                                        +++   G++GtGKt ++l+l+++l       d+ +  ++  +  N++  ++l  +++   ek++ ++ ++++ ++i
  gene2837|gene2837|rna2837|rna2837  44 QIICLAGATGTGKTALALKLAHNLntkilsCDSVQIFRELNIGSNKERENHLMVDVKHYGEKYDVEKYVNDSLNVI 119
                                        678889******************6666532222222222233344444455555554445555555555555555 PP

                            DUF2075  72 nn 73 
                                        +n
  gene2837|gene2837|rna2837|rna2837 120 KN 121
                                        55 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00019      0.12       2      27 ..      46      72 ..      45     136 .. 0.83
   2 ?   -2.3   0.0       7.6   4.7e+03      18      59 ..     364     409 ..     360     416 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00019
                             AAA_28  2 ivitGgestGKTtlleaLaar.gypvv 27
                                       i++ G+ +tGKT l+ +La + +++++
  gene2837|gene2837|rna2837|rna2837 46 ICLAGATGTGKTALALKLAHNlNTKIL 72
                                       89*****************77677655 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 7.6
                             AAA_28  18 aLaar..gypvvpEaareileekl.akgedalpwv.edllafaerv 59 
                                        ++a    g +v  E+a ++++ +   k+e++  ++ ed   f++r+
  gene2837|gene2837|rna2837|rna2837 364 RIAGVieGERVSDEYAFKYFKTLKqYKTENTYFKTeEDYEMFRKRC 409
                                        5554344778889999999988775556666666666666666665 PP

>> Torsin  Torsin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.1    0.0011       0.7      55      92 ..      45      82 ..      35     129 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0011
                                       EEEEEE-TTSSHHHHHHHHHHHHSTTGGGSTTEEEEEH CS
                             Torsin 55 vlsfhGwtGtGknfvaeiiaenlyrdGlrsdyvkkfva 92
                                       ++ + G tGtGk  +a  +a+nl  + l  d v+ f  
  gene2837|gene2837|rna2837|rna2837 45 IICLAGATGTGKTALALKLAHNLNTKILSCDSVQIFRE 82
                                       68899****************************99865 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00018      0.11       6      56 ..      46     115 ..      40     123 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00018
                                        EEEE--TTSSHHHHHHHHHHHTT-.......................-EEEEEGGG-------THHHHHH CS
                              AAA_2   6 illlgptgvGktelakalaellfv...................kkekkliradaselleeeevehlvsrl 56 
                                        i l+g tg+Gkt la +la  l+                    k++++  ++d + + e+ +ve++v+  
  gene2837|gene2837|rna2837|rna2837  46 ICLAGATGTGKTALALKLAHNLNTkilscdsvqifrelnigsnKERENHLMVDVKHYGEKYDVEKYVNDS 115
                                        5689*******************99*****************9999999****************99865 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   0.00016     0.098      24      51 ..      43      70 ..      36      95 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00016
                             AAA_16 24 pelvllsGesGvGKsslvrellralekd 51
                                       ++++ l G+ G+GK++l+ +l++ l+++
  gene2837|gene2837|rna2837|rna2837 43 SQIICLAGATGTGKTALALKLAHNLNTK 70
                                       47899*****************999987 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00016       0.1      48      77 ..      44      70 ..      38     101 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00016
                          IstB_IS21 48 enivllGpsGvGKshlaialgveavragls 77
                                       + i+l G +G+GK+ la  l+++  +   +
  gene2837|gene2837|rna2837|rna2837 44 QIICLAGATGTGKTALALKLAHNLNT---K 70
                                       679*****************997643...3 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00017      0.11      29      63 ..      39      73 ..      23      83 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00017
                              AAA_7 29 llknkkpvllvGptGtGKtviikdllkkldkekyl 63
                                       +   ++ ++l G tGtGKt+++ +l ++l+++ ++
  gene2837|gene2837|rna2837|rna2837 39 MHPMSQIICLAGATGTGKTALALKLAHNLNTKILS 73
                                       5556677899*******************966555 PP

>> SKI  Shikimate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.1     0.024        15       2      26 ..      53      77 ..      52     192 .. 0.87
   2 ?    4.2   0.0     0.071        44      77     107 ..     334     370 ..     329     406 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.024
                                       TSSHHHHHHHHHHHHTSEEEEHHHH CS
                                SKI  2 GaGKstvGkllAkklglefiDlDel 26
                                       G+GK+ ++ +lA+ l+ + + +D++
  gene2837|gene2837|rna2837|rna2837 53 GTGKTALALKLAHNLNTKILSCDSV 77
                                       99****************9999985 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.071
                                        HHHHHHH......HHSEEEEEE--HHHHHHHHHHTTS CS
                                SKI  77 enrellk......ekgiviyLdvsleellerlkadke 107
                                        ++r++++      +++  +++++++++l+er++   e
  gene2837|gene2837|rna2837|rna2837 334 NTRNYVRrqetffKRKNYVFINAERDDLMERIAGVIE 370
                                        56666666666668999**************986555 PP

>> Hydin_ADK  Hydin Adenylate kinase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00049       0.3       2      33 ..      46      77 ..      45      89 .. 0.93
   2 ?   -2.6   0.1       8.8   5.4e+03      50      74 ..     248     273 ..     234     297 .. 0.56

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00049
                          Hydin_ADK  2 iivhGaPlsGKtatavtLakkYeaAlltiDsv 33
                                       i + Ga  +GKta a +La++ ++ +l+ Dsv
  gene2837|gene2837|rna2837|rna2837 46 ICLAGATGTGKTALALKLAHNLNTKILSCDSV 77
                                       667899************************98 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 8.8
                          Hydin_ADK  50 relCaeaaieqaekekeea.aeeaek 74 
                                        r+ C+e a e + ++k  + ++  e+
  gene2837|gene2837|rna2837|rna2837 248 RKCCVENAEEDKVNDKVGNsGNGNEE 273
                                        55566666665554443220222222 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0    0.0007      0.43       2      32 ..      46      76 ..      45     128 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0007
                             AAA_33  2 vllvGlpGsGKstlaerllkklgavllssdt 32
                                       + l G+ G+GK+ la +l+ +l + +ls d+
  gene2837|gene2837|rna2837|rna2837 46 ICLAGATGTGKTALALKLAHNLNTKILSCDS 76
                                       6789*******************99999998 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00058      0.36      36      75 ..      46      85 ..      35     130 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00058
                             RuvB_N 36 vllyGpPGlGkttlakiiakelgvklkitsgPvlekagdl 75
                                       + l+G+ G Gkt+la  +a++l++k+ +  +  + ++ ++
  gene2837|gene2837|rna2837|rna2837 46 ICLAGATGTGKTALALKLAHNLNTKILSCDSVQIFRELNI 85
                                       6799******************999987777666666554 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00056      0.35     130     156 ..      44      70 ..      37      90 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00056
                              T2SSE 130 glilvsGgTgsGKttllyallkeinks 156
                                        ++i ++G+Tg+GKt l+  l + +n++
  gene2837|gene2837|rna2837|rna2837  44 QIICLAGATGTGKTALALKLAHNLNTK 70 
                                        6899************99999999886 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.7   0.00086      0.53       2      32 ..      46      73 ..      45     190 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00086
                                       EEEESSTTSSHHHHHHHHHHHHHHTT--EEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               CbiA  2 aiastkGGvGKTtlaanLaralarrglrVll 32
                                       +  ++  G+GKT la++La  l+    ++l 
  gene2837|gene2837|rna2837|rna2837 46 ICLAGATGTGKTALALKLAHNLNT---KILS 73
                                       5678999*************9987...5555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (417 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1105  (0.061632); expected 358.6 (0.02)
Passed bias filter:                      581  (0.0324056); expected 358.6 (0.02)
Passed Vit filter:                        99  (0.00552178); expected 17.9 (0.001)
Passed Fwd filter:                        29  (0.00161749); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              29  [number of targets reported over threshold]
# CPU time: 0.59u 0.30s 00:00:00.88 Elapsed: 00:00:00.45
# Mc/sec: 2790.59
//
Query:       gene2838|gene2838|rna2838|rna2838  [L=199]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1009  (0.0562775); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1454.75
//
Query:       gene2839|gene2839|rna2839|rna2839  [L=642]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00013   20.8   0.2       0.36    9.4   0.0    2.2  2  Cnd2      Condensin complex subunit 2


Domain annotation for each model (and alignments):
>> Cnd2  Condensin complex subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.0     2e-05      0.36     424     475 ..     171     219 ..     118     248 .. 0.66
   2 !    9.2   0.1   2.3e-05      0.41     661     686 ..     341     366 ..     335     377 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 2e-05
                               Cnd2 424 elrdilsyfdqalq...knWagPehWrirrikdvnkseeaakkkrkekepfeidF 475
                                        +++ + + fd++     k+WagP+ Wri  ++ +       +  ++ k++f  +F
  gene2839|gene2839|rna2839|rna2839 171 DECVLVDRFDATPFayhKAWAGPQNWRILTRRTA------GTAVKRAKKDFLEQF 219
                                        44566667777543344***********888652......222333344444444 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 2.3e-05
                               Cnd2 661 qYArvAKkvDvrrLKeelWklieeel 686
                                         YArv K+vD++rL +++  +++++ 
  gene2839|gene2839|rna2839|rna2839 341 RYARVPKRVDIKRLEQHISTVMKQKG 366
                                        5*******************999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (642 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       373  (0.0208043); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.64u 0.28s 00:00:00.92 Elapsed: 00:00:00.48
# Mc/sec: 4011.27
//
Query:       gene284|gene284|rna284|rna284  [L=138]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0016   17.9   0.2     0.0017   17.8   0.2    1.1  1  DUF604    Protein of unknown function, DUF604


Domain annotation for each model (and alignments):
>> DUF604  Protein of unknown function, DUF604
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.2   9.7e-08    0.0017     145     215 ..      20      88 ..       9     129 .. 0.71

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 9.7e-08
                         DUF604 145 qvyekivlarelekplrtfkewkrkaeeeefafntrevskdpCkrpvvfflksvekekekeeivseYkrke 215
                                    qvy+++++ + le+++r +++ +   ++++ ++ +++ ++++C+r++++ l++v++e   +     +k+ +
  gene284|gene284|rna284|rna284  20 QVYHNTYNINPLENVERRYSQLYVIDSDNATDLRSKNPANEKCDRAILYNLDRVMREV--NPYAEAFKNLA 88 
                                    89****************************************************9983..33333333222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       506  (0.0282224); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.37s 00:00:00.94 Elapsed: 00:00:00.56
# Mc/sec: 737.16
//
Query:       gene2840|gene2840|rna2840|rna2840  [L=197]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        0.9    8.6  15.3       0.97    8.4  15.3    1.1  1  LAP1C     Lamina-associated polypeptide 1C (LAP1C)


Domain annotation for each model (and alignments):
>> LAP1C  Lamina-associated polypeptide 1C (LAP1C)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4  15.3   5.4e-05      0.97      16     188 ..      13     189 ..       2     197 .] 0.63

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 5.4e-05
                                        XXX...XXXXXXXXXXXXXXXXX................XXXXXXXXXXXXXX..XXXXXXXXXXXX......... CS
                              LAP1C  16 ttvtasseeeaqtrkplsslkkdhqevetigsesadtedkseseqevnlseepkdetEeedsessqsgeeghklss 91 
                                          v  s + ++q+++ ++++k+d    e++ ++++ +  + ++++ ++++++ +d+ E+  + ++q+ge g  ++ 
  gene2840|gene2840|rna2840|rna2840  13 SIVE-SRNTSQQANDGTHESKND--LTESVQHSEMRKPSEMNTTDFTSVKDTRSDKLENSTQMTMQNGEPGRPTQQ 85 
                                        3333.233334455555555555..44555555666666666666677777888999******************* PP

                                        .XXXXXXXXXXXXXXXXXXXXXXXXXXX.....XXXXXXXXXX.XXXXXXXXXXX......XXXXXXXXXXXXXXX CS
                              LAP1C  92 eslgeekldsedsvsssdktgradaqle.....essaalseeasdrtaasqepsaadsqeaqssghskaeqeeqdt 162
                                        +++ + ++++e++ s++d++ +++a+ +     +  + ++ ++++  + sq+  ++++qe   s++  +++ +++ 
  gene2840|gene2840|rna2840|rna2840  86 DDTMKPPIRAESTESPKDQKRKSKAKEDtpkplSTLSLVPYSETNLRSFSQNIGTNEKQEKALSETLDRSNFSKSD 161
                                        *******************999998754111112333445667777778887777766665555555555555666 PP

                                        XXXXXX....XXXX..XXXXXXXXXXXX CS
                              LAP1C 163 lrrtrllv..peaeshqqetelleeske 188
                                        l++  l++      + +q+t  +++ k+
  gene2840|gene2840|rna2840|rna2840 162 LIKETLPTlyYPPTCLTQKTTIVDRIKS 189
                                        6665555533334445666666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1510  (0.0842211); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 1210.64
//
Query:       gene2841|gene2841|rna2841|rna2841  [L=167]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.1e-26   90.1   0.4    1.2e-25   89.8   0.4    1.1  1  Ribosomal_L22  Ribosomal protein L22p/L17e
  ------ inclusion threshold ------
      0.042   13.9   0.0      0.071   13.2   0.0    1.4  1  Med9           RNA polymerase II transcription mediator compl


Domain annotation for each model (and alignments):
>> Ribosomal_L22  Ribosomal protein L22p/L17e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.8   0.4   1.3e-29   1.2e-25       3     101 ..      19     155 ..      17     157 .. 0.96

  Alignments for each domain:
  == domain 1  score: 89.8 bits;  conditional E-value: 1.3e-29
                                        EEEESS-HHHHHHHHHHHTTSBHHHHHHHHHT..-SST....................................TH CS
                      Ribosomal_L22   3 gsnlrvsfkklrevarlIrgmkveeAlkyLkf..skkk....................................aa 40 
                                        +++lr++fk++rev   +++ ++++A+++Lk+  ++k                                      +
  gene2841|gene2841|rna2841|rna2841  19 AKSLRIKFKNAREVSVHLKRLTLTRATAFLKNviNRKDcikvtryakkcgrtaqakkyergssradsrgkwpvkPC 94 
                                        789*****************************955555************************************** PP

                                        HHHHHHHHHHHHHHH..HT-GGGEEEEEEEEEEEEEEEEEEEESTTEEEEEEEEEEEEEEE CS
                      Ribosomal_L22  41 kfvlklLknaeanaelkgldvdslvIeeiqvnkgpklkrrtyrArGrinpirkspchievv 101
                                        + ++ l+ n + +ae+kg ++d+lvI+++qvnk+p++ +r  rA Gr+np++ +pch+e++
  gene2841|gene2841|rna2841|rna2841  95 QAFIGLISNLVTEAEKKGIEPDDLVIVHCQVNKAPQIYGRIQRAYGRVNPYNTKPCHVEMI 155
                                        ************************************************************9 PP

>> Med9  RNA polymerase II transcription mediator complex subunit 9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0     8e-06     0.071      21      46 ..      12      37 ..       5      57 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 8e-06
                               Med9 21 skdletktgelrhkLkkarelirelp 46
                                       ++ ++t++ +lr k+k+are+   l+
  gene2841|gene2841|rna2841|rna2841 12 ANTVHTNAKSLRIKFKNAREVSVHLK 37
                                       799*****************976665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       698  (0.0389313); expected 358.6 (0.02)
Passed bias filter:                      553  (0.0308439); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1128.71
//
Query:       gene2842|gene2842|rna2842|rna2842  [L=156]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.9e-06   25.7   2.3    7.9e-06   25.7   2.3    1.8  2  TB2_DP1_HVA22  TB2/DP1, HVA22 family
  ------ inclusion threshold ------
       0.02   14.8   1.0       0.02   14.8   1.0    2.2  2  DUF5345        Family of unknown function (DUF5345)
      0.078   13.2   0.3       0.14   12.3   0.3    1.4  1  DUF3213        Protein of unknown function (DUF3213)
       0.22   11.4   0.0       0.22   11.4   0.0    2.3  2  DUF4321        Domain of unknown function (DUF4321)
       0.28   10.5   1.2       0.53    9.6   1.2    1.4  1  TraE           TraE protein


Domain annotation for each model (and alignments):
>> TB2_DP1_HVA22  TB2/DP1, HVA22 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.1      0.24   8.7e+02      29      53 ..      32      56 ..       6      58 .. 0.67
   2 !   25.7   2.3   2.2e-09   7.9e-06      18      60 ..      63     105 ..      48     114 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.24
                      TB2_DP1_HVA22 29 fltvvesla.dvllswiPfYylfKll 53
                                       fl  + sl+ +vl+ +iPf  +++l+
  gene2842|gene2842|rna2842|rna2842 32 FLP-IASLVsNVLCVVIPFQRTVRLV 56
                                       333.3344436666678887777765 PP

  == domain 2  score: 25.7 bits;  conditional E-value: 2.2e-09
                      TB2_DP1_HVA22  18 t.kwltYWvvfafltvvesladvllswiPfYylfKllfllwlvl 60 
                                        t  ++ +W++f++l+vv+  + v+++++PfYy+fK++++  +vl
  gene2842|gene2842|rna2842|rna2842  63 TlDLIVFWMTFGLLCVVDCSL-VVTRVVPFYYIFKMVAMNAIVL 105
                                        43699**************99.8888***********9987776 PP

>> DUF5345  Family of unknown function (DUF5345)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   1.0   5.7e-06      0.02      27      61 ..       3      37 ..       1      47 [. 0.87
   2 ?   -0.6   1.7      0.36   1.3e+03      40      74 ..      65     100 ..      63     103 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 5.7e-06
                            DUF5345 27 aeekerkrkrlrrElllFlliAllilsllllalvq 61
                                       ++ ++++  +l++E +l+++iAl ++++++l +++
  gene2842|gene2842|rna2842|rna2842  3 RKLQQKTNNKLKQEHILLIIIALSLITIIFLPIAS 37
                                       56789999*********************997766 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.36
                            DUF5345  40 ElllFlli.AllilsllllalvqapalfiviQvial 74 
                                        +l+ F+++  ll++    l++++ +  ++++  +a+
  gene2842|gene2842|rna2842|rna2842  65 DLIVFWMTfGLLCVVDCSLVVTRVVPFYYIFKMVAM 100
                                        789999875777777777777777777777777665 PP

>> DUF3213  Protein of unknown function (DUF3213)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.3     4e-05      0.14      21      65 ..     105     153 ..      97     155 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 4e-05
                                        TTTTB------TTSS--EEE--B....-S-SHHHHHHHT...TT-SS-- CS
                            DUF3213  21 kdervyrvflngyakvaevvide....ekvnieelkkkleelkgevvee 65 
                                         derv r  + gy + +++v ++     k  +e lk+k ++lkge+ e 
  gene2842|gene2842|rna2842|rna2842 105 LDERVCRFVVSGYKRMGFLVEEDigkrAKEAVEVLKEKSKHLKGELDEM 153
                                        589****************98774333466778899999999*998665 PP

>> DUF4321  Domain of unknown function (DUF4321)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   6.2       2.8   9.9e+03      31      46 ..      23      38 ..      18      39 .. 0.82
   2 ?   11.4   0.0   6.2e-05      0.22      14      29 ..      60      75 ..      51      77 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 2.8
                            DUF4321 31 fkinlasiiGiilAil 46
                                       + ++l++ii + +A l
  gene2842|gene2842|rna2842|rna2842 23 IALSLITIIFLPIASL 38
                                       7899999999999865 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 6.2e-05
                            DUF4321 14 sPltlDLgvlkltFgl 29
                                       +P tlDL v+  tFgl
  gene2842|gene2842|rna2842|rna2842 60 KPPTLDLIVFWMTFGL 75
                                       588************8 PP

>> TraE  TraE protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   1.2   0.00015      0.53       5      60 ..       4      57 ..       2      62 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00015
                               TraE  5 vsesrlknllaqnnllalllavllaanlllgslilratrkqrvvlvPpeikkpftv 60
                                       + +++++n l+q  +l +++a++l++ ++l ++   ++++   v++P+  + ++++
  gene2842|gene2842|rna2842|rna2842  4 KLQQKTNNKLKQEHILLIIIALSLITIIFLPIAS--LVSNVLCVVIPFQRTVRLVI 57
                                       6789***************************999..***********998866666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1346  (0.0750739); expected 358.6 (0.02)
Passed bias filter:                      652  (0.0363657); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1168.38
//
Query:       gene2843|gene2843|rna2843|rna2843  [L=52]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (52 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       334  (0.018629); expected 358.6 (0.02)
Passed bias filter:                      214  (0.011936); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.30s 00:00:00.70 Elapsed: 00:00:00.48
# Mc/sec: 328.06
//
Query:       gene2844|gene2844|rna2844|rna2844  [L=1090]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.2e-20   71.5   4.5    8.2e-14   50.8   0.0    3.9  4  Myosin_head  Myosin head (motor domain)
  ------ inclusion threshold ------
       0.13   12.5   0.8       0.82   10.0   0.8    2.2  1  DIL          DIL domain


Domain annotation for each model (and alignments):
>> Myosin_head  Myosin head (motor domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.8   0.0   9.1e-18   8.2e-14     367     476 ..      10     120 ..       5     135 .. 0.74
   2 !   12.7   0.3   2.9e-06     0.026     426     513 ..     168     244 ..     165     255 .. 0.78
   3 !    7.3   0.1   0.00013       1.1     562     592 ..     243     271 ..     239     291 .. 0.76
   4 ?   -0.3   0.0     0.025   2.3e+02     587     616 ..     372     401 ..     321     411 .. 0.85

  Alignments for each domain:
  == domain 1  score: 50.8 bits;  conditional E-value: 9.1e-18
                                        EEEEEE-B---SSB-HHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHTTS.....SGCGS-GGGCCHHHHHHHHSSS CS
                        Myosin_head 367 GvLDiaGFEifeknsFEqlcinyvnEkLqqlFnelvlklEqeeYvrEgi.....ewkfidfgldnqaiidLiekkp 437
                                         v+Di+GFE  e n++Eq+ iny+nEk+q+ + ++++++   eY rEgi     e++ +  ++d ++++  i++  
  gene2844|gene2844|rna2844|rna2844  10 SVIDIFGFECVERNGYEQFLINYANEKMQRCYLRELVVEREREYLREGIidcrgEMRGMVGSVDREEMVGSIDR-- 83 
                                        599***********************************999*******95444444445556788888888888.. PP

                                        TSHHHHHHHHHTSTTS-HHHHHHHHHHHHTTST.TEEETT CS
                        Myosin_head 438 lGilslLdeecllpkatdetfleklvkafskha.kfeksr 476
                                         G++  +d e ++ + +    ++k +++++kh+ +++ ++
  gene2844|gene2844|rna2844|rna2844  84 EGVVGSVDREGMVGSVDR---YDKHNDRYDKHNdRYSTPT 120
                                        488888888887765543...4555666655553555554 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 2.9e-06
                                        CHHHHHHHHSSSTSHHHHHHHHHTSTTS-HHHHHHHHHHHHTTSTTEEETTSTTTTTEEEEEETTCEEEEE-TTHH CS
                        Myosin_head 426 nqaiidLiekkplGilslLdeecllpkatdetfleklvkafskhakfeksrlkkgeakFiikHyAgkveYevegfl 501
                                        n++i+ Lie+k +Gi++++ +e++l     + +++k+  +f+++a       k ++++ +++H  g+v+Y+v +f+
  gene2844|gene2844|rna2844|rna2844 168 NNNILHLIENK-TGIINIIKDESKLK----TDLITKIR-SFNNTAII-----KAHNDRLTLMHSIGEVTYDVGEFV 232
                                        567999****6.9*********9985....34667764.56666655.....3457899***************** PP

                                        HHHH----HHHH CS
                        Myosin_head 502 eKnkDtlnedlv 513
                                         +n+  l ++  
  gene2844|gene2844|rna2844|rna2844 233 RRNNYDLVDSYR 244
                                        ***988777655 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.00013
                                        HHHHHHHHHHHHCTSEEEEEEEE-SSSS--T CS
                        Myosin_head 562 fkeslaeLmktlestnphfvRCikpnekkka 592
                                        +++++ ++++++   np fvRCikpn ++++
  gene2844|gene2844|rna2844|rna2844 243 YRREVDRMVDEI--VNPMFVRCIKPNRSNRS 271
                                        666666666665..58**********98765 PP

  == domain 4  score: -0.3 bits;  conditional E-value: 0.025
                                        SSS--TT---HHHHHHHHHHTTHHHHHHHH CS
                        Myosin_head 587 nekkkakkldeslvleqlrclGvlegirir 616
                                        n ++++ k+d++ v++ql ++G+l+ ++++
  gene2844|gene2844|rna2844|rna2844 372 NTNHTTVKYDKKYVKAQLLISGILNILQMS 401
                                        77888999****************988765 PP

>> DIL  DIL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.8   9.1e-05      0.82       2      28 ..     987    1013 ..     986    1072 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 9.1e-05
                                         HHHHHHHHHHHHHHHHHHHHS-SB-HH CS
                                DIL    2 lfsqlfyfinaelfNrlllrkklcsrs 28  
                                         ++++l+++in+e+fN+ll++ + ++r 
  gene2844|gene2844|rna2844|rna2844  987 IMNHLLQYINTEIFNKLLTNVREYERV 1013
                                         6899**************875544433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1090 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       794  (0.0442858); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.78u 0.29s 00:00:01.07 Elapsed: 00:00:00.46
# Mc/sec: 7087.68
//
Query:       gene2845|gene2845|rna2845|rna2845  [L=159]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
       0.34    9.2   0.8       0.32    9.3   0.8    1.1  1  Mem_trans    Membrane transport protein
       0.47    8.6   4.9       0.46    8.6   4.9    1.0  1  Nop14        Nop14-like family
        0.8    8.0   3.6       0.88    7.9   3.6    1.2  1  Menin        Menin


Domain annotation for each model (and alignments):
>> Mem_trans  Membrane transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.8   5.3e-05      0.32     165     225 ..      15      73 ..       4     143 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 5.3e-05
                          Mem_trans 165 sivsikvdsdvvsldgrkpleteaeikedgklhvtvrksnasrsdivs.sstprpsnltnae 225
                                        +++ + +d+d   ++ ++   ++++i++d+++  t+ ++ +s +d  s +st+++   tna 
  gene2845|gene2845|rna2845|rna2845  15 NDDGNDDDDDDNNNNNNDDNINDDNINDDNSINSTINSIDNSTNDNDSdNSTNPA---TNAN 73 
                                        55667778888888888899************************99997555555...3333 PP

>> Nop14  Nop14-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   4.9   7.7e-05      0.46     360     409 ..      17      65 ..       3     137 .. 0.45

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 7.7e-05
                              Nop14 360 dlveseseeeeeeeeedeeeeedeeeeeeeeededdlsdleseeeeeede 409
                                        d ++++++ +++++++d++ ++d+ +++++ +++ ++ d++++++++++ 
  gene2845|gene2845|rna2845|rna2845  17 DGNDDDDD-DNNNNNNDDNINDDNINDDNSINSTINSIDNSTNDNDSDNS 65 
                                        11111111.11111111111111111111111111111111111111111 PP

>> Menin  Menin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   3.6   0.00015      0.88     531     583 ..      17      70 ..       4     142 .. 0.52

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00015
                              Menin 531 ageeserreannnnnsksnsekeadkk....asttsnggeasstpsseseaavesps 583
                                         g++ ++ ++nnnnn ++ ++++ + +    +  t n+   +st++++s+++ +  +
  gene2845|gene2845|rna2845|rna2845  17 DGNDDDDDDNNNNNNDDNINDDNINDDnsinS--TINSI-DNSTNDNDSDNSTNPAT 70 
                                        33334444444444444444444433322221..22221.12222222222222111 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1281  (0.0714485); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 1125.04
//
Query:       gene2846|gene2846|rna2846|rna2846  [L=39]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (39 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       161  (0.00897987); expected 358.6 (0.02)
Passed bias filter:                      158  (0.00881254); expected 358.6 (0.02)
Passed Vit filter:                         5  (0.000278878); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.29u 0.21s 00:00:00.50 Elapsed: 00:00:00.34
# Mc/sec: 340.11
//
Query:       gene2847|gene2847|rna2847|rna2847  [L=111]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.027   14.3   1.0       0.17   11.8   0.1    2.5  2  UvrD_C_2       UvrD-like helicase C-terminal domain
      0.029   14.2   0.0      0.062   13.1   0.0    1.5  1  TTc_toxin_rep  Tripartite Tc toxins repeat


Domain annotation for each model (and alignments):
>> UvrD_C_2  UvrD-like helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   1.9e-05      0.17       2      44 ..      40      76 ..      39      80 .. 0.74
   2 ?    0.3   0.1     0.069   6.2e+02      21      39 ..      89     108 ..      84     111 .] 0.65

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1.9e-05
                           UvrD_C_2  2 ayaltihkaQGsefpaVivfdpdlaaarmgelrrrlLYtavTR 44
                                        +a+tihk+Q + f+ + v    +  ++ +   +r LY+a+ R
  gene2847|gene2847|rna2847|rna2847 40 SFAMTIHKSQAQLFDEIGV----YLHSPVF--VHRQLYVALPR 76
                                       58************99877....3343445..37889999877 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.069
                           UvrD_C_2  21 fdpdlaaarmgel.rrrlLY 39 
                                        ++ + + a+++++ +r+ +Y
  gene2847|gene2847|rna2847|rna2847  89 DNGYQDKADNNMVyTRNVVY 108
                                        44556777777777777777 PP

>> TTc_toxin_rep  Tripartite Tc toxins repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0     7e-06     0.062       8      21 ..       3      16 ..       2      24 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 7e-06
                      TTc_toxin_rep  8 iTVSnrSNRAVlss 21
                                       +TVS++SNRA++ +
  gene2847|gene2847|rna2847|rna2847  3 VTVSKKSNRAIILK 16
                                       6*********9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (111 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       323  (0.0180155); expected 358.6 (0.02)
Passed bias filter:                      220  (0.0122706); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 847.24
//
Query:       gene2848|gene2848|rna2848|rna2848  [L=209]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.9e-54  184.5   2.4    2.1e-54  184.3   2.4    1.0  1  ATP-synt_D  ATP synthase subunit D
  ------ inclusion threshold ------
      0.088   13.0   0.7        1.3    9.3   0.1    2.3  2  DUF5446     Family of unknown function (DUF5446)


Domain annotation for each model (and alignments):
>> ATP-synt_D  ATP synthase subunit D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  184.3   2.4   2.4e-58   2.1e-54       1     196 []      15     204 ..      15     204 .. 0.95

  Alignments for each domain:
  == domain 1  score: 184.3 bits;  conditional E-value: 2.4e-58
                                        HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSTSTTSTSHHHHHHHSSS.SS- CS
                         ATP-synt_D   1 eLirlkkrlklaqrghslLkkKrdaLilefreilkelkelreeleeelkeayfslaeafaaggeediesavlesvk 76 
                                        +L+  k+rlk a++g+slLk+K++aL+ + r+i ++l++ + +l++++ +ay  la+a  +g  ++i+ ++ e  +
  gene2848|gene2848|rna2848|rna2848  15 NLTLTKNRLKSAEKGYSLLKRKSEALQVKHRQIQHKLEKEQHNLKTAITNAYYLLAKAEFLG--SNIKMFLYECSR 88 
                                        68899*****************************************************6666..488988998888 PP

                                        ..TSS-SEEEEEEBTTSEEEEEEE-..S.SSTSSSSSSSSTCHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         ATP-synt_D  77 lakvvkvelktenvaGVkvpvfeleeeksdstelygllrtgaqldeavealrellellvelasletslelLdeeik 152
                                          + v++e++ e+v GV +pv++l+++    ++l+ l ++g+ + +a++a+r ++  l+elasl++s+++Lde++k
  gene2848|gene2848|rna2848|rna2848  89 --SPVSIESSIEQVSGVFLPVYTLKQDV--GNPLLFLDKSGSAYLSARNAFRTVIGRLIELASLKNSFVILDEVLK 160
                                        ..78********************8864..5699****************************************** PP

                                        HHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         ATP-synt_D 153 ktnrRvNaLekvvIPrleetikyIkseLdEqereeffrlkkvkk 196
                                         tnrRvNaL+ ++IPr+++ti yI+ eLdEq+reeffrlkk++k
  gene2848|gene2848|rna2848|rna2848 161 NTNRRVNALDFMLIPRINNTIDYINAELDEQDREEFFRLKKIQK 204
                                        ******************************************96 PP

>> DUF5446  Family of unknown function (DUF5446)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0     0.038   3.4e+02      21      62 ..      23      63 ..      16      69 .. 0.69
   2 ?    9.3   0.1   0.00014       1.3      21      56 ..     155     190 ..     153     192 .. 0.95

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.038
                            DUF5446 21 ltevEkelseavneteaekeekeeerldllekElkdLvlCig 62
                                       l+++Ek  s+ +++     ++k  ++  +lekE ++L+  i 
  gene2848|gene2848|rna2848|rna2848 23 LKSAEKGYSL-LKRKSEALQVKHRQIQHKLEKEQHNLKTAIT 63
                                       5666665554.3444445678888999999999999887765 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00014
                            DUF5446  21 ltevEkelseavneteaekeekeeerldllekElkd 56 
                                        l+ev k+ + +vn++    +  +++ +d ++ El++
  gene2848|gene2848|rna2848|rna2848 155 LDEVLKNTNRRVNALDFMLIPRINNTIDYINAELDE 190
                                        688999****************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1398  (0.0779742); expected 358.6 (0.02)
Passed bias filter:                      601  (0.0335211); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 1337.07
//
Query:       gene285|gene285|rna285|rna285  [L=44]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (44 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       345  (0.0192426); expected 358.6 (0.02)
Passed bias filter:                      187  (0.01043); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.29s 00:00:00.64 Elapsed: 00:00:00.44
# Mc/sec: 302.58
//
Query:       gene2850|gene2850|rna2850|rna2850  [L=405]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.3e-49  166.7   0.0    8.4e-49  166.3   0.0    1.2  1  Pkinase         Protein kinase domain
    3.4e-21   75.7   0.0    5.2e-21   75.1   0.0    1.1  1  Pkinase_Tyr     Protein tyrosine kinase
    3.3e-11   43.0   0.0      6e-11   42.2   0.0    1.4  1  Kinase-like     Kinase-like
     0.0023   17.3   0.0     0.0037   16.6   0.0    1.3  1  Kdo             Lipopolysaccharide kinase (Kdo/WaaP) family
     0.0073   16.3   0.0      0.014   15.3   0.0    1.4  1  APH             Phosphotransferase enzyme family
  ------ inclusion threshold ------
      0.011   15.5   0.0      0.039   13.7   0.0    2.0  1  KA1             Kinase associated domain 1
       0.12   11.2   0.1       0.37    9.5   0.0    1.7  2  Pkinase_fungal  Fungal protein kinase
       0.17   11.6   2.2        2.7    7.7   0.1    2.7  2  Fungal_KA1      Fungal kinase associated-1 domain


Domain annotation for each model (and alignments):
>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  166.3   0.0   3.8e-52   8.4e-49       2     264 .]       5     255 ..       4     255 .. 0.91

  Alignments for each domain:
  == domain 1  score: 166.3 bits;  conditional E-value: 3.8e-52
                                        EEEEEEEEESSEEEEEEEETTTTEEEEEEEEECHCHCHHHHHHHHHHHHHHHHHSCTTB--EEEEEEESSEEEEEE CS
                            Pkinase   2 ekleklGeGsfGkVykaveketgkivAvKkikkekakkkkekkvlrEikilkklkhpnivrlyevfeekdelylvl 77 
                                        +  + + +G++ +V +av+   g+++A+K++ ++ +k    k++ +E+ i+++l+h+niv+++e +  +d+ ++v+
  gene2850|gene2850|rna2850|rna2850   5 TLGNIIAQGTTCVVREAVD-ILGNKYAIKIVCRSARKY---KDIKKEMMIHQHLQHSNIVKFKELLIATDY-FIVM 75 
                                        6677899***********5.78999******9998876...4489*********************97665.679* PP

                                        E--TTEBHHHHHHHHSS--HHHHHHHHHHHHHHHHHHHHTTEE-SS-SGGGEEEETTTEEEE-SGTTSEESSSSCS CS
                            Pkinase  78 eyveggeladllerkgslseeeakkiakqilegleylHskgiiHrDlKpeNiLidekgelKitDFGlakelesssk 153
                                        e v   el+ ++e k+ ++   +  ++ q+++++ey+H+kgi+HrD+KpeNiL++  g+l +tDFG a+ ++ + +
  gene2850|gene2850|rna2850|rna2850  76 ERVAY-ELFVYIEPKVGMPRMLVHLFFVQLISAIEYMHDKGICHRDIKPENILLSAAGNLFVTDFGSATLFRYKGR 150
                                        ***95.5******************************************************************999 PP

                                        ...BCTTTSCGGGS-HHHHTTSCBSHHHHHHHHHHHHHHHHHSS-STTTSSHHHHHHHHHHTHHHHHHHCTSHH.. CS
                            Pkinase 154 ...ltsfvgtseYlAPEvlkeneyskkvDvWslGvilyelltgkppfsgekgkekvekeldqlekilkilgetkek 226
                                           l++++g+  Y+APEv k+   ++ +D+Ws+G++l+ + tg  p+s  ++++   +++++          +  +
  gene2850|gene2850|rna2850|rna2850 151 iriLNTICGSLPYIAPEVHKGAYNGAIADIWSCGIVLFVMATGILPWSRGDQTDIDLANYTK---------LKYHN 217
                                        9******************99999************************66666655555555.........24578 PP

                                        .HHHTTS-HHHHHHHHHHT-SSGCCSTTHHHHHTSGGG CS
                            Pkinase 227 lpeaseiseeakdllkkllkkdpkkRltaeellqhpyl 264
                                        ++  s +++++k++ + +++++  +R+t+  ++q++++
  gene2850|gene2850|rna2850|rna2850 218 YEPFSRLPRDVKHVFDGMCRVKVLERFTFGAIKQSSFF 255
                                        999*******************************9998 PP

>> Pkinase_Tyr  Protein tyrosine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.1   0.0   2.3e-24   5.2e-21      28     256 ..      26     250 ..       5     252 .. 0.84

  Alignments for each domain:
  == domain 1  score: 75.1 bits;  conditional E-value: 2.3e-24
                                        EEEEEEEEESTTSSHHHHHHHHHHHHHHHTS-BTTB--EEEEEESSSSEEEEEE--TTEBHHHHHHHTCTTTSBHH CS
                        Pkinase_Tyr  28 evkVavKtlkeeateeekeelleeakimkklkhpnivkllgvctkeepllivteyvkgGdLlkfLrkkekekltlk 103
                                          k a+K++ ++a++   +++ +e+ i ++l+h nivk+  + +    ++iv+e v++ +L  +++ k    +   
  gene2850|gene2850|rna2850|rna2850  26 GNKYAIKIVCRSARKY--KDIKKEMMIHQHLQHSNIVKFKELLIA-TDYFIVMERVAY-ELFVYIEPK--VGMPRM 95 
                                        5678999996666665..9*************************5.667*******99.788899887..555566 PP

                                        HHHHHHHHHHHHHHHHHHTTEEEST-SGGGEEEEETTEEEE-STTTHEETTTSSEEEETTSSTSGGGGS-HHHHHH CS
                        Pkinase_Tyr 104 dllsfalqvAkGmeyLeskklvHrdlaarNvLlsenkvvkisDfGLardiekddeyvkkeeaklpvkWmapEslke 179
                                         +  f +q+ +++ey+++k + Hrd+   N+Lls      ++DfG a     + + +  ++   ++ ++apE+ k 
  gene2850|gene2850|rna2850|rna2850  96 LVHLFFVQLISAIEYMHDKGICHRDIKPENILLSAAGNLFVTDFGSATLFRYKGRIRILNTICGSLPYIAPEVHKG 171
                                        6677999*******************************************99999999999999************ PP

                                        SEEEHHHHHHHHHHHHHHHHTTSSGTTTTS..HHHHHHHHHHTTEES-BB.TTSBHHHHHHHHHHT-SSGGGS--H CS
                        Pkinase_Tyr 180 kkftsksDvWsfGvllwEiftlgespypgl..kneevleklkegkrlekp.ekcpeelyelmkkcweedpeeRptf 252
                                              +D+Ws G++l+ ++t g  p+++   ++ +++++ k +++  +p +  p++++++     + +  eR tf
  gene2850|gene2850|rna2850|rna2850 172 AYNGAIADIWSCGIVLFVMAT-GILPWSRGdqTDIDLANYTKLKYHNYEPfSRLPRDVKHVFDGMCRVKVLERFTF 246
                                        *****************8887.999998772255567888888877666636789999999999999999999999 PP

                                        HHHH CS
                        Pkinase_Tyr 253 selv 256
                                         ++ 
  gene2850|gene2850|rna2850|rna2850 247 GAIK 250
                                        8876 PP

>> Kinase-like  Kinase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.2   0.0   2.7e-14     6e-11      93     283 ..      44     238 ..      31     243 .. 0.77

  Alignments for each domain:
  == domain 1  score: 42.2 bits;  conditional E-value: 2.7e-14
                        Kinase-like  93 qkkkpfiqlkskesiywvvnallllpaasvdleilnkvlqkrsethkkletiarlllTlqlirlaanLqakglvhg 168
                                         kk  +i+++ ++s       ll++ +  + +e++  +l    e +     +  +l  +qli  + ++++kg+ h 
  gene2850|gene2850|rna2850|rna2850  44 IKKEMMIHQHLQHSNIVKFKELLIATDYFIVMERVAYELFVYIEPKVGMPRMLVHLFFVQLISAIEYMHDKGICHR 119
                                        5677777777666666678899999999999999999999988889999888889999****************** PP

                        Kinase-like 169 kftvdnllldekgglmlggfta..Lvragtkvvl.seve..kgfaPpEllgsrggytrknktkmthkldaWqlGlv 239
                                        +++++n+ll   g l++++f++  L+r++ + ++ ++++    +  pE+      y+           d W  G+v
  gene2850|gene2850|rna2850|rna2850 120 DIKPENILLSAAGNLFVTDFGSatLFRYKGRIRIlNTICgsLPYIAPEVHKG--AYN-------GAIADIWSCGIV 186
                                        ********************7545*********9899995556777888644..443.......3567******** PP

                        Kinase-like 240 iyriwclklPltlateeakeew.........kfklckkipekvkaLlkkfLql 283
                                         + ++   lP     +   ++          ++++  + p  vk    ++ ++
  gene2850|gene2850|rna2850|rna2850 187 LFVMATGILPWSRGDQT-DIDLanytklkyhNYEPFSRLPRDVKHVFDGMCRV 238
                                        **********8653322.11212235565566666666666666666666665 PP

>> Kdo  Lipopolysaccharide kinase (Kdo/WaaP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   1.7e-06    0.0037     129     166 ..     106     139 ..      72     149 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.7e-06
                                Kdo 129 rliaklhragvnHadlyaknillqqeeeeeaeiwliDl 166
                                         +i+ +h+ g++H+d+ + nill +++    ++ + D+
  gene2850|gene2850|rna2850|rna2850 106 SAIEYMHDKGICHRDIKPENILLSAAG----NLFVTDF 139
                                        67999******************9998....6666666 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   6.5e-06     0.014     165     197 ..     113     143 ..     103     145 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 6.5e-06
                                        -EEEE-SS-SGGGEEEC..TTEEEEE---TT-E CS
                                APH 165 ptvllHgDlhpgNllvdpddgrvtGviDfedag 197
                                        +++++H+D++p N+l+ ++++ +  v Df+ a+
  gene2850|gene2850|rna2850|rna2850 113 DKGICHRDIKPENILLSAAGNLF--VTDFGSAT 143
                                        579**************999999..9***9997 PP

>> KA1  Kinase associated domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   1.8e-05     0.039      16      44 ..     373     401 ..     367     401 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.8e-05
                                KA1  16 slygvrfkRlsGdtwqYkrlasqilseLk 44 
                                        ++ ++ + R++G+t+ +k+++  il  Lk
  gene2850|gene2850|rna2850|rna2850 373 NMCVISINRVKGSTLEFKEFCNVILGHLK 401
                                        58899999****************99987 PP

>> Pkinase_fungal  Fungal protein kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.31     7e+02     152     184 ..       8      40 ..       6      63 .. 0.80
   2 ?    9.5   0.0   0.00016      0.37     314     341 ..     103     129 ..      89     187 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.31
                     Pkinase_fungal 152 aivgRgTtcwrarkegergkeyvvKdsWrdaer 184
                                        +i+ +gTtc   +  +  g++y +K++ r+a++
  gene2850|gene2850|rna2850|rna2850   8 NIIAQGTTCVVREAVDILGNKYAIKIVCRSARK 40 
                                        688999999888887777999999999887765 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00016
                     Pkinase_fungal 314 DaIkghrsLflkagiLHrDiSenNilit 341
                                        + I + + ++ ++gi HrDi  +Nil+ 
  gene2850|gene2850|rna2850|rna2850 103 QLISAIEYMH-DKGICHRDIKPENILLS 129
                                        5677888889.***************98 PP

>> Fungal_KA1  Fungal kinase associated-1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.1     0.047   1.1e+02      49      75 ..      43      69 ..      31      83 .. 0.84
   2 ?    7.7   0.1    0.0012       2.7      79     114 ..     368     403 ..     355     405 .] 0.84

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.047
                         Fungal_KA1 49 sdkesntitgkvsseNilslksvkFei 75
                                       + k++++i+ +++++Ni+++k++ ++ 
  gene2850|gene2850|rna2850|rna2850 43 DIKKEMMIHQHLQHSNIVKFKELLIAT 69
                                       557899***************987765 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0012
                         Fungal_KA1  79 svsehklSlvrftkekGsassfrklvkeiekvlrke 114
                                         +  ++++++ ++++kGs+  f+++++ i   l+++
  gene2850|gene2850|rna2850|rna2850 368 VKRINNMCVISINRVKGSTLEFKEFCNVILGHLKSK 403
                                        333359**********************99999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (405 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       602  (0.0335769); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 2905.94
//
Query:       gene2851|gene2851|rna2851|rna2851  [L=538]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.044   13.5   0.1        0.1   12.3   0.1    1.6  1  HipN      Hsp70-interacting protein N N-terminal domain


Domain annotation for each model (and alignments):
>> HipN  Hsp70-interacting protein N N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   5.8e-06       0.1      14      37 ..     408     431 ..     406     432 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5.8e-06
                               HipN  14 lckanPeiLhePeLaFFKeflesl 37 
                                        ++  +++ L++ ++ FFK+ les 
  gene2851|gene2851|rna2851|rna2851 408 FINRKTSFLNDADFIFFKDHLESA 431
                                        677899****************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (538 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1370  (0.0764125); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.43
# Mc/sec: 3722.86
//
Query:       gene2852|gene2852|rna2852|rna2852  [L=562]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.052   13.6   2.2        5.5    7.1   0.1    3.9  3  DUF2752   Protein of unknown function (DUF2752)


Domain annotation for each model (and alignments):
>> DUF2752  Protein of unknown function (DUF2752)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0     0.017   3.1e+02      17      35 ..     238     256 ..     237     258 .. 0.91
   2 ?    7.1   0.1   0.00031       5.5      18      42 ..     317     341 ..     316     347 .. 0.87
   3 ?    1.2   0.3     0.022     4e+02      27      49 .]     525     547 ..     520     548 .. 0.56

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.017
                            DUF2752  17 tRavhallhgdfaaAfryn 35 
                                        t ++++l+h ++ a+++y+
  gene2852|gene2852|rna2852|rna2852 238 TSSILSLMHQQIIASVEYY 256
                                        889*************996 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.00031
                            DUF2752  18 RavhallhgdfaaAfrynplgvlll 42 
                                        R++++ll+++f +A++ n+  +++l
  gene2852|gene2852|rna2852|rna2852 317 RSLLSLLRLKFVRAISINVITLFIL 341
                                        99****************9988776 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.022
                            DUF2752  27 dfaaAfrynplgvlllpllllll 49 
                                        +f++A ++ ++++++++++++++
  gene2852|gene2852|rna2852|rna2852 525 NFSDARSFSIVVLVFALVVFYFW 547
                                        45555555555555555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (562 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1018  (0.0567795); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 3921.24
//
Query:       gene2853|gene2853|rna2853|rna2853  [L=163]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.2e-20   72.2   1.3    4.5e-20   71.7   1.3    1.3  1  CBFD_NFYB_HMF  Histone-like transcription factor (CBF/NF-Y) a
    1.3e-05   25.6   0.7    1.8e-05   25.1   0.7    1.2  1  Histone        Core histone H2A/H2B/H3/H4
  ------ inclusion threshold ------
      0.021   14.8   0.1      0.048   13.7   0.1    1.6  1  Bromo_TP       Bromodomain associated
      0.071   13.2   0.1       0.11   12.6   0.1    1.3  1  CENP-T_C       Centromere kinetochore component CENP-T histon
       0.77    9.3   3.7        1.9    8.1   0.8    2.2  2  LepB_N         LepB N-terminal domain


Domain annotation for each model (and alignments):
>> CBFD_NFYB_HMF  Histone-like transcription factor (CBF/NF-Y) and archaeal histone
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.7   1.3   1.3e-23   4.5e-20       2      62 ..      48     109 ..      47     112 .. 0.96

  Alignments for each domain:
  == domain 1  score: 71.7 bits;  conditional E-value: 1.3e-23
                                        XXXHHHHHHHHHCC.TTXS-B-HHHHHHHHHHHHHHHHHHHHHHHHHHCCTTSSCE-HHHHH CS
                      CBFD_NFYB_HMF   2 eLPiarvkkImksd.pdarkiakdAkeliaecveefieelaseAaeickkekrKtikaehik 62 
                                         LPia++ kImk   p  +kiakdAkel++++++efi  ++ +A eic+ e+rKti+++++ 
  gene2853|gene2853|rna2853|rna2853  48 LLPIANISKIMKGPiPRSAKIAKDAKELMQKSASEFIAIVTCMAKEICESENRKTITGDDLI 109
                                        59**********************************************************97 PP

>> Histone  Core histone H2A/H2B/H3/H4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.7   5.1e-09   1.8e-05      28     124 ..      15     108 ..       2     114 .. 0.89

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 5.1e-09
                                        TS-SSSSB--TTT-XTTHHHHHHHHHHHHXXSXXSXHHHHHHHHH.HHH.TTSSSXEEXHHHHHHHHHHHHHHHHH CS
                            Histone  28 kasskskkkkkrryrpgtvalkeirkyqkstdlliqklpfaRvvr.eivksekedlrisaeavlalqealEallve 102
                                        ++  +++k k+ ++r ++   k+ +   kstd+l + + ++++++  i      + +i ++a +++q+ +  +++ 
  gene2853|gene2853|rna2853|rna2853  15 QDTTRPSKYKRLQFRSDMDIDKNSYGPLKSTDRLLPIANISKIMKgPIPR----SAKIAKDAKELMQKSASEFIAI 86 
                                        667788899999******************************99966666....********************** PP

                                        HHHHHHHHHHHTTXSEEXHHHH CS
                            Histone 103 lfeeAnllakhaKRvTitpkDi 124
                                        ++ +A  +++  +R+Tit  D+
  gene2853|gene2853|rna2853|rna2853  87 VTCMAKEICESENRKTITGDDL 108
                                        ******************9997 PP

>> Bromo_TP  Bromodomain associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   1.3e-05     0.048      29      73 ..      73     117 ..      67     120 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.3e-05
                                        HHHHHHHHHHHHHHHHHHHHHHHTTSS-SS--HHHHHHHHHHTT- CS
                           Bromo_TP  29 LEtLteiaqkYirelgeqaksfaehagRseptlkDvvltLqelgi 73 
                                         E++++ a ++i+ ++  ak+ +e ++R + t  D+++++++lg+
  gene2853|gene2853|rna2853|rna2853  73 KELMQKSASEFIAIVTCMAKEICESENRKTITGDDLIRSMKQLGM 117
                                        5899999***********************************996 PP

>> CENP-T_C  Centromere kinetochore component CENP-T histone fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1     3e-05      0.11       7      76 ..      48     114 ..      43     132 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3e-05
                           CENP-T_C   7 slPaavvkklakrfakasgskaklekealkalekasdkffeqvgeDLeayakHagRKtidesDvilLmkr 76 
                                         lP a ++k+ k       ++ak+ k+a + ++k+  +f+  v+   +   +   RKti  +D+i  mk+
  gene2853|gene2853|rna2853|rna2853  48 LLPIANISKIMKGPIP---RSAKIAKDAKELMQKSASEFIAIVTCMAKEICESENRKTITGDDLIRSMKQ 114
                                        4788888888777644...589********************************************9997 PP

>> LepB_N  LepB N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.1     0.039   1.4e+02      98     132 ..      60      96 ..      51     105 .. 0.66
   2 ?    8.1   0.8   0.00052       1.9      68      97 ..     106     135 ..      98     151 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.039
                             LepB_N  98 glfpaiaekakklkeklde..kllkdivskalkkipa 132
                                        g +p  a+ ak+ ke +++  +++  iv+++ k+i +
  gene2853|gene2853|rna2853|rna2853  60 GPIPRSAKIAKDAKELMQKsaSEFIAIVTCMAKEICE 96 
                                        5555555555555555554448999999999888865 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.00052
                             LepB_N  68 edilspleyqGlfnlkkftkgYilnykkik 97 
                                        +d++  ++  G+  ++++tk Y++ yk   
  gene2853|gene2853|rna2853|rna2853 106 DDLIRSMKQLGMYYYAEITKKYFMRYKDGG 135
                                        6888999999****************9755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       710  (0.0396006); expected 358.6 (0.02)
Passed bias filter:                      440  (0.0245412); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1169.25
//
Query:       gene2854|gene2854|rna2854|rna2854  [L=42]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (42 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       157  (0.00875676); expected 358.6 (0.02)
Passed bias filter:                      131  (0.0073066); expected 358.6 (0.02)
Passed Vit filter:                         6  (0.000334653); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.32u 0.27s 00:00:00.59 Elapsed: 00:00:00.40
# Mc/sec: 314.38
//
Query:       gene2855|gene2855|rna2855|rna2855  [L=275]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        3.1    8.3   7.7        3.4    8.2   0.3    3.2  3  PhoU      PhoU domain


Domain annotation for each model (and alignments):
>> PhoU  PhoU domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.5     0.011   2.1e+02      25      53 ..      31      59 ..       8      69 .. 0.69
   2 ?    0.1   0.0     0.064   1.2e+03       3      38 ..      93     126 ..      91     154 .. 0.74
   3 ?    8.2   0.3   0.00019       3.4      23      58 ..     174     207 ..     170     231 .. 0.74

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.011
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                               PhoU 25 elarevierddeidrlekeierslleala 53
                                       e +re + ++ ei++ +++i+ +l+++++
  gene2855|gene2855|rna2855|rna2855 31 EKIREQMYKEMEIEKVQNNIYQKLYNKMK 59
                                       55566666677777777777777777773 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.064
                                        HHHHHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHH CS
                               PhoU   3 rmaeiveemlddalealeekdtelarevierddeid 38 
                                         m++   em+d++ +  +++ + ++  ++  + eid
  gene2855|gene2855|rna2855|rna2855  93 NMGNDGIEMVDKVKQDAYTGSEGIVGTIV--ESEID 126
                                        69999999999998888888777777776..33333 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.00019
                                        -HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGG- CS
                               PhoU  23 dtelarevierddeidrlekeiersllealakrqpl 58 
                                        + ++a+++ ++dd i rlek+  r+  +++ k +pl
  gene2855|gene2855|rna2855|rna2855 174 NFDYAKDIKRQDDIIKRLEKRYLRK--KKVEKLEPL 207
                                        4489****************99776..444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (275 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1577  (0.0879581); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2040.37
//
Query:       gene2856|gene2856|rna2856|rna2856  [L=276]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (276 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       948  (0.0528752); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1888.89
//
Query:       gene2857|gene2857|rna2857|rna2857  [L=195]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-21   75.4   1.8      5e-21   74.4   1.8    1.5  1  SCA7      SCA7, zinc-binding domain


Domain annotation for each model (and alignments):
>> SCA7  SCA7, zinc-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.4   1.8   2.8e-25     5e-21       2      67 ..      33      97 ..      32      98 .. 0.95

  Alignments for each domain:
  == domain 1  score: 74.4 bits;  conditional E-value: 2.8e-25
                               SCA7  2 kkkkkkkkkkkkevdvdkqCGVilp.ngkpCtRsLtCksHslgakraVegRskpfdvLlaeykkkkq 67
                                       ++++kk +k kk ++vd++C+V  p ng pC++sLtC++Hsl+++++V+gR +p+++L++ +k++k+
  gene2857|gene2857|rna2857|rna2857 33 DNETKKLHKIKKAFSVDRHCAV--PeNGVPCRNSLTCRVHSLDQRNEVKGRIYPVEDLIRILKREKN 97
                                       578999****************..76**************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1027  (0.0572815); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1463.97
//
Query:       gene2858|gene2858|rna2858|rna2858  [L=125]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0001   20.4   0.0     0.0001   20.4   0.0    1.1  1  Herpes_Helicase  Helicase
    0.00032   20.4   0.2     0.0023   17.7   0.0    2.2  2  UvrD_C_2         UvrD-like helicase C-terminal domain
  ------ inclusion threshold ------
      0.016   15.2   0.0      0.027   14.6   0.0    1.3  1  CNOT1_HEAT       CCR4-NOT transcription complex subunit 1 HEA
      0.068   12.9   0.0      0.071   12.8   0.0    1.1  1  Viral_helicase1  Viral (Superfamily 1) RNA helicase


Domain annotation for each model (and alignments):
>> Herpes_Helicase  Helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   2.3e-08    0.0001     732     778 ..      53      98 ..      29     120 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 2.3e-08
                    Herpes_Helicase 732 lamtiaksqGlslekvAicFgnhknlklssvYvalsRatdseflvmd 778
                                         am i ksqG s++kv +   +       ++Yval R+++++ l++ 
  gene2858|gene2858|rna2858|rna2858  53 FAMAIHKSQGQSFDKVGVYLHSP-VFVHRQLYVALPRVRHADDLKVY 98 
                                        69*****************9999.5556789**********998764 PP

>> UvrD_C_2  UvrD-like helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   5.2e-07    0.0023       3      46 ..      53      90 ..      52      92 .. 0.80
   2 ?   -0.0   0.0      0.18   7.9e+02      21      39 ..     101     120 ..      97     121 .. 0.70

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 5.2e-07
                           UvrD_C_2  3 yaltihkaQGsefpaVivfdpdlaaarmgelrrrlLYtavTRAr 46
                                       +a+ ihk+QG+ f+ V v    +  ++ +   +r LY+a+ R r
  gene2858|gene2858|rna2858|rna2858 53 FAMAIHKSQGQSFDKVGV----YLHSPVF--VHRQLYVALPRVR 90
                                       6999************99....4444445..4999***997755 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.18
                           UvrD_C_2  21 fdpdlaaarmgel.rrrlLY 39 
                                        ++ d + a+++++ +r+ +Y
  gene2858|gene2858|rna2858|rna2858 101 DNGDQDKADNNMVyTRNVVY 120
                                        56678888888887777777 PP

>> CNOT1_HEAT  CCR4-NOT transcription complex subunit 1 HEAT repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0     6e-06     0.027      27      90 ..       4      67 ..       1      73 [. 0.94

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 6e-06
                                       HHHHHHHHHS-S-........-SHHHHHHHHTT-HHHHHHHS-TTCHHHCHHHHHHHT---HHH CS
                         CNOT1_HEAT 27 eidrqlllkalvdayakdplelsrIldvaqelkilsellnklpfnfaldLaalasrreyldlek 90
                                       + +++++++ +v  y+k +  +   +d+aq+   l  +l++++f+  l  a+++++ ++  ++k
  gene2858|gene2858|rna2858|rna2858  4 KLNNNFIIAMIVTGYTKGNRAIILKVDMAQSETQLPFILKQKQFPVLLPFAMAIHKSQGQSFDK 67
                                       67899**************999999*******************************99999988 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   1.6e-05     0.071     184     226 ..      53      89 ..      12      99 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.6e-05
                    Viral_helicase1 184 evttvhevqGltfdkVtlvllketdlelisesrenllvAlTRh 226
                                         ++  h  qG++fdkV ++l+++    ++   + +l+vAl R 
  gene2858|gene2858|rna2858|rna2858  53 FAMAIHKSQGQSFDKVGVYLHSP----VFV--HRQLYVALPRV 89 
                                        46889****************55....555..4789***9863 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       430  (0.0239835); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.43
# Mc/sec: 879.35
//
Query:       gene2859|gene2859|rna2859|rna2859  [L=825]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (825 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2227  (0.124212); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.72u 0.25s 00:00:00.97 Elapsed: 00:00:00.43
# Mc/sec: 5756.92
//
Query:       gene286|gene286|rna286|rna286  [L=208]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       425  (0.0237046); expected 358.6 (0.02)
Passed bias filter:                      163  (0.00909142); expected 358.6 (0.02)
Passed Vit filter:                         7  (0.000390429); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1524.13
//
Query:       gene2860|gene2860|rna2860|rna2860  [L=157]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1071  (0.0597356); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1096.39
//
Query:       gene2861|gene2861|rna2861|rna2861  [L=62]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (62 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       642  (0.0358079); expected 358.6 (0.02)
Passed bias filter:                      242  (0.0134977); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 440.49
//
Query:       gene2862|gene2862|rna2862|rna2862  [L=607]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-07   31.8   0.0    2.2e-07   31.0   0.0    1.3  1  NUDIX     NUDIX domain


Domain annotation for each model (and alignments):
>> NUDIX  NUDIX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.0   0.0   1.2e-11   2.2e-07       6      60 ..     492     542 ..     488     589 .. 0.68

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 1.2e-11
                                        EEEE.EEETTSEEEEEEESSSSTTT.EESSEEECBTTSHHHHHHHHHHHHHHSEEEE CS
                              NUDIX   6 vgvv.llnekgevLlvrrskkpfpg.WelPgGkvepgEtpeeAArREleEEtGleae 60 
                                        +gv+ ++ ek  ++lv  s    +g   lP+G+++ gE  +++A+RE++EE+G++ +
  gene2862|gene2862|rna2862|rna2862 492 AGVLgVIGEK--IVLVYNS----KGkMVLPKGTIKHGEGMKQCAAREAWEEAGIQGP 542
                                        6777778888..7777666....45468*************************9662 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (607 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1707  (0.0952089); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.73u 0.32s 00:00:01.05 Elapsed: 00:00:00.50
# Mc/sec: 3668.83
//
Query:       gene2863|gene2863|rna2863|rna2863  [L=68]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (68 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       388  (0.0216409); expected 358.6 (0.02)
Passed bias filter:                      231  (0.0128842); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.28s 00:00:00.66 Elapsed: 00:00:00.45
# Mc/sec: 457.24
//
Query:       gene2864|gene2864|rna2864|rna2864  [L=184]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.05   13.3   0.1      0.076   12.7   0.1    1.2  1  TerB_N    TerB N-terminal domain


Domain annotation for each model (and alignments):
>> TerB_N  TerB N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   4.2e-06     0.076      93     120 ..     113     140 ..     111     152 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.2e-06
                             TerB_N  93 YfygLerrvgvdnpqegyeklielpeiy 120
                                        ++++Lerr++vd+ + +y +l++ +e+y
  gene2864|gene2864|rna2864|rna2864 113 FVNELERRIVVDGDDRNYNTLVRVNEDY 140
                                        89**********************9999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       438  (0.0244297); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1323.28
//
Query:       gene2865|gene2865|rna2865|rna2865  [L=195]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.3e-06   28.1   0.5    3.3e-06   26.8   0.0    1.9  2  RRM_1        RNA recognition motif. (a.k.a. RRM, RBD, or RNP 
     0.0054   17.4   1.6     0.0079   16.9   1.6    1.3  1  Torus        Torus domain
     0.0059   16.6   0.1      0.015   15.3   0.1    1.7  1  Nup35_RRM_2  Nup53/35/40-type RNA recognition motif


Domain annotation for each model (and alignments):
>> RRM_1  RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8   0.0   5.6e-10   3.3e-06      16      70 .]      49     103 ..      31     103 .. 0.86
   2 ?   -1.6   0.1       0.4   2.4e+03      14      33 ..     170     189 ..     167     192 .. 0.76

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 5.6e-10
                                        HHHHHTTSCEEEEEEEEETTTSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE CS
                              RRM_1  16 kelFskfGpiksiklvrdetgkskgfafVeFeskedAekAlealngkklggrelk 70 
                                         e+F++fG ik++ + + +       a++++e++++A +++ ++++  l+gr lk
  gene2865|gene2865|rna2865|rna2865  49 NEFFGQFGNIKKLVIKNRSMTDQSVSAYITYEKESSAVRCITEVDESLLEGRALK 103
                                        489***********99998888899***************************986 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.4
                                        HHHHHHHTTSCEEEEEEEEE CS
                              RRM_1  14 eLkelFskfGpiksiklvrd 33 
                                        eL e + k+ ++k+++++ +
  gene2865|gene2865|rna2865|rna2865 170 ELNETLFKYKEVKNFRVPEK 189
                                        67777778888999998875 PP

>> Torus  Torus domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   1.6   1.3e-06    0.0079      44     107 ..      79     146 ..      51     148 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.3e-06
                                        S-----S----HHHH----HHH....HSTT--B-HHHHHT--SSGGG-SSB-S---SS----TTB-TT CS
                              Torus  44 kskekaktrcnikkdsGytkad....kekesyfClfFarGlCakGkkCeylHrlPteedlkekkvDiF 107
                                         +ke++++rc ++ d+   +++    +  ++ +C fF + l ++  +C ylH++ +++ + +k+  + 
  gene2865|gene2865|rna2865|rna2865  79 YEKESSAVRCITEVDESLLEGRalkcTFGTTKYCSFFLKNLICQNCECMYLHEIGEKDCALTKEEMCM 146
                                        46678888998888887776662221445669**********************98877555555565 PP

>> Nup35_RRM_2  Nup53/35/40-type RNA recognition motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.1   2.5e-06     0.015       4      49 ..      31      85 ..      28      88 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.5e-06
                        Nup35_RRM_2  4 vaVsGydteli.elVle...hFasfGeIvkhyvp.....kevsvmyvkfesekda 49
                                       v + G++   + e Vl    +F +fG+I k  +      +++ ++y+++e+e +a
  gene2865|gene2865|rna2865|rna2865 31 VYIIGIPVKYAdENVLKsneFFGQFGNIKKLVIKnrsmtDQSVSAYITYEKESSA 85
                                       55666666666566777777**********5555556779999*********998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       751  (0.0418874); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1473.82
//
Query:       gene2866|gene2866|rna2866|rna2866  [L=230]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    7.1e-24   84.3   0.0    8.2e-24   84.1   0.0    1.1  1  Proteasome   Proteasome subunit
  ------ inclusion threshold ------
      0.049   13.5   0.0       0.11   12.3   0.0    1.5  1  Homeodomain  Homeodomain


Domain annotation for each model (and alignments):
>> Proteasome  Proteasome subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.1   0.0   9.1e-28   8.2e-24       2     186 ..      30     210 ..      29     214 .. 0.92

  Alignments for each domain:
  == domain 1  score: 84.1 bits;  conditional E-value: 9.1e-28
                                        HHS-EEEEEEETTEEEEEEEEEEEETTEEEESSSSTSEEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHSS CS
                         Proteasome   2 kkGttvvGikgkdgvvlaadkratagskllskstveKifkiddhigvafaGlaaDartlvrraraeaqlyrlrygr 77 
                                        + G+t+++i+     +l +   +t  skl  ++ ++K+f + ++++++f+G ++D+  l+r++  e++++++  ++
  gene2866|gene2866|rna2866|rna2866  30 SLGSTALCITNHKQSILLCHHHST--SKL--QHAMRKVF-VRKNLFFTFSGITNDGLELIRYILDEMSTQNVWKNT 100
                                        67**********************..***..66689**9.68********************************** PP

                                        GTCHHHHHHHHHHHHHHHHHHCTTTTTSEEEEEEEEETTTEEEEEEEETTSEEEEESSEEEESTTHHHHHHHHHHH CS
                         Proteasome  78 pipverlvarvaaklqaytqrsgrrpfgvslliagvdeeggpeLyqidpsGsyieekdavaiGsgseaaktaleke 153
                                         i + r+ ++++  ++a t+ s+ r +g++ +  gv  +g+ ++ +  p+G++ + k avaiG+++++++t+lek 
  gene2866|gene2866|rna2866|rna2866 101 AIDPMRAFNEISVSASARTLISSDRLYGCGGI-LGVEYRGKIKVVEWMPTGTIRSAK-AVAIGNRAQSCRTVLEKY 174
                                        ******************************99.67888999***************8.****************** PP

                                        H..STTBSHHHHHHHHHHHHHHHHHHB.TTSCSSEE CS
                         Proteasome 154 y..kedltleeavelavkalkealerd.klsgknie 186
                                        +  + + + e++++la +a+++a+ +d +++ +n+e
  gene2866|gene2866|rna2866|rna2866 175 FeeNRNVSNEDMLDLAMSAMRNAHGQDgEMKRENLE 210
                                        *88888*****************9544157777776 PP

>> Homeodomain  Homeodomain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   1.3e-05      0.11      13      36 ..     169     192 ..     163     195 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.3e-05
                                        HHHHHHHHHSSS-SHHHHHHHHHH CS
                        Homeodomain  13 eeLeklFeenrypsaeereeLAkk 36 
                                        ++Lek+Feenr++s e++ +LA++
  gene2866|gene2866|rna2866|rna2866 169 TVLEKYFEENRNVSNEDMLDLAMS 192
                                        79*******************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       550  (0.0306766); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1658.21
//
Query:       gene2867|gene2867|rna2867|rna2867  [L=125]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
     0.0012   18.4   0.5     0.0014   18.2   0.5    1.1  1  Terminase_3  Phage terminase large subunit
  ------ inclusion threshold ------
      0.024   14.7   1.2      0.047   13.8   1.2    1.8  1  Bromodomain  Bromodomain
      0.054   13.8   0.3      0.073   13.4   0.3    1.2  1  Mrpl_C       54S ribosomal protein L8 C-terminal domain


Domain annotation for each model (and alignments):
>> Terminase_3  Phage terminase large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.5   2.3e-07    0.0014      45     116 ..      11      91 ..       1     101 [. 0.92

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 2.3e-07
                        Terminase_3  45 kdSvfaeikellselgltklfkilkskiei.elengskflFkglddpaklkSik........nlsdlwlEEasevs 111
                                        k  +f+ ++e  s+ +lt + k l+ + +i  len+   +Fk + + ++  Si         nl   ++EEa+e++
  gene2867|gene2867|rna2867|rna2867  11 KHDTFNLFTEYPSTNNLTTITKKLSHYTNIkALENDILAIFKTVMNAHNYNSIYvaesdrlsNLTRRVFEEAKELK 86 
                                        6779**************************999*******************99999**99999999********* PP

                        Terminase_3 112 eedid 116
                                        +e+++
  gene2867|gene2867|rna2867|rna2867  87 KEEFK 91 
                                        **997 PP

>> Bromodomain  Bromodomain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   1.2   7.9e-06     0.047      38      78 ..      26      64 ..       4      92 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 7.9e-06
                                       -HHHHHHHHHTT--SSHHHHHHHHHHHHHHHHHHSHTTSHH CS
                        Bromodomain 38 dLstIkkklesnkYksladfeadlkllfsNarkyngegsvi 78
                                       +L+tI kkl  ++Y++++++e+d+  +f+  +  ++ +s +
  gene2867|gene2867|rna2867|rna2867 26 NLTTITKKL--SHYTNIKALENDILAIFKTVMNAHNYNSIY 64
                                       689999998..68**************99777777766665 PP

>> Mrpl_C  54S ribosomal protein L8 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.3   1.2e-05     0.073      43     104 ..      32      94 ..      16      97 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.2e-05
                             Mrpl_C  43 kKmlkfkskeqllkeilavrkflkeeqelewdeeeekeavkalldqvakktlpkkkkke.sgY 104
                                        kK++++ + ++l+++ila+ k +++ ++ +     e++++++l+++v++++++ kk++   +Y
  gene2867|gene2867|rna2867|rna2867  32 KKLSHYTNIKALENDILAIFKTVMNAHNYNSIYVAESDRLSNLTRRVFEEAKELKKEEFkVDY 94 
                                        799999999***************99999888899************8877766665532555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1142  (0.0636957); expected 358.6 (0.02)
Passed bias filter:                      541  (0.0301746); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 885.80
//
Query:       gene2868|gene2868|rna2868|rna2868  [L=927]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.6e-31  105.7   3.7    2.1e-15   56.6   1.4    3.4  3  Myb_DNA-binding  Myb-like DNA-binding domain
    2.1e-21   75.9   2.5    1.2e-14   54.3   0.3    2.9  2  Myb_DNA-bind_6   Myb-like DNA-binding domain
  ------ inclusion threshold ------
       0.02   14.9   0.0         11    6.1   0.0    2.6  2  SLIDE            SLIDE


Domain annotation for each model (and alignments):
>> Myb_DNA-binding  Myb-like DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.14   8.4e+02      21      35 ..     259     273 ..     253     274 .. 0.89
   2 !   56.6   1.4   3.5e-19   2.1e-15       1      46 []     517     563 ..     517     563 .. 0.98
   3 !   46.5   0.0   5.2e-16   3.1e-12       3      43 ..     571     611 ..     569     613 .. 0.96

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.14
                                        TCHHHHHHHHTSS-H CS
                    Myb_DNA-binding  21 nrWkkIaerlggRte 35 
                                        +r+++I+e l gRt 
  gene2868|gene2868|rna2868|rna2868 259 VRPDRISEVLSGRTS 273
                                        5899*********97 PP

  == domain 2  score: 56.6 bits;  conditional E-value: 3.5e-19
                                        CSSSBHHHHHHHHHHHHHHT.TCHHHHHHHHTSS-HHHHHHHHHHHT CS
                    Myb_DNA-binding   1 rgkWteeEdelLleavkkhG.nrWkkIaerlggRtekqcrsrwrnyl 46 
                                        +g+W++eEd +L+ +v+ h  ++W++Ia+ + +R +kqcr+rw+n+l
  gene2868|gene2868|rna2868|rna2868 517 KGPWSKEEDRRLISLVNIHKpKNWSLIAKLMKTRIGKQCRERWHNHL 563
                                        79*******************************************97 PP

  == domain 3  score: 46.5 bits;  conditional E-value: 5.2e-16
                                        SSBHHHHHHHHHHHHHHTTCHHHHHHHHTSS-HHHHHHHHH CS
                    Myb_DNA-binding   3 kWteeEdelLleavkkhGnrWkkIaerlggRtekqcrsrwr 43 
                                        +++++Ed l+  +++++GnrW++Ia++l+gRt+++++++w+
  gene2868|gene2868|rna2868|rna2868 571 PFSTDEDRLICSLHARFGNRWSEIAKYLPGRTDNAIKNYWN 611
                                        89**************************************8 PP

>> Myb_DNA-bind_6  Myb-like DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.3   0.3     2e-18   1.2e-14       1      58 [.     520     578 ..     520     580 .. 0.96
   2 !   26.3   0.2   1.1e-09   6.4e-06       1      45 [.     572     616 ..     572     625 .. 0.88

  Alignments for each domain:
  == domain 1  score: 54.3 bits;  conditional E-value: 2e-18
                     Myb_DNA-bind_6   1 WteeEdeiLlklvekyg.ndWknIaealnrRtpkqcfdrwknkLrpkisrkkwskeedi 58 
                                        W++eEd++L++lv  +  ++W++Ia+ ++ R  kqc++rw+n+L+p i+++++s  ed+
  gene2868|gene2868|rna2868|rna2868 520 WSKEEDRRLISLVNIHKpKNWSLIAKLMKTRIGKQCRERWHNHLHPAINKAPFSTDEDR 578
                                        ****************8569********99*************************9996 PP

  == domain 2  score: 26.3 bits;  conditional E-value: 1.1e-09
                     Myb_DNA-bind_6   1 WteeEdeiLlklvekygndWknIaealnrRtpkqcfdrwknkLrp 45 
                                        ++ +Ed+++ +l+ ++gn W++Ia+ l+ Rt ++++++w++k+  
  gene2868|gene2868|rna2868|rna2868 572 FSTDEDRLICSLHARFGNRWSEIAKYLPGRTDNAIKNYWNSKVQK 616
                                        5779***********************55***********97654 PP

>> SLIDE  SLIDE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0    0.0018        11      49      80 ..     517     548 ..     497     554 .. 0.80
   2 ?    6.0   0.0     0.002        12      48     101 ..     568     616 ..     549     628 .. 0.66

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0018
                              SLIDE  49 kkeyteeeDrfllvllakyGygnyekikkeir 80 
                                        k  +++eeDr l+ l++ +  +n+  i k ++
  gene2868|gene2868|rna2868|rna2868 517 KGPWSKEEDRRLISLVNIHKPKNWSLIAKLMK 548
                                        5679*******************999987665 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.002
                              SLIDE  48 gkkeyteeeDrfllvllakyGygnyekikkeiresplFrfDwflksrtpqelqk 101
                                        +k  ++++eDr +  l a++G + + +i k +  +     D  +k +  +++qk
  gene2868|gene2868|rna2868|rna2868 568 NKAPFSTDEDRLICSLHARFGNR-WSEIAKYLPGRT----DNAIKNYWNSKVQK 616
                                        4556***********99999976.999988765443....33333333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (927 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       762  (0.042501); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.67u 0.31s 00:00:00.98 Elapsed: 00:00:00.47
# Mc/sec: 5969.12
//
Query:       gene2869|gene2869|rna2869|rna2869  [L=273]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.015   15.0   2.1      0.017   14.8   1.0    1.7  1  EMC3_TMCO1       Integral membrane protein EMC3/TMCO1-like
       0.45   10.2   3.9       0.71    9.6   3.9    1.4  1  Connexin         Connexin
       0.67   10.6   4.2        6.9    7.4   4.2    2.6  1  Renin_r          Renin receptor-like protein
          1    8.0   9.2        1.6    7.4   9.2    1.3  1  NPR3             Nitrogen Permease regulator of amino acid tr
        1.3    7.7   4.3          2    7.0   4.3    1.3  1  Ureide_permease  Ureide permease
        1.6    8.8  10.2        2.9    7.9  10.2    1.6  1  Peptidase_S49_N  Peptidase family S49 N-terminal
        5.7    7.0  12.1        5.4    7.1  10.5    1.8  2  UPF0242          Uncharacterised protein family (UPF0242) N-t


Domain annotation for each model (and alignments):
>> EMC3_TMCO1  Integral membrane protein EMC3/TMCO1-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   1.0   6.8e-06     0.017      45     109 ..     184     269 ..     164     273 .] 0.77

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 6.8e-06
                         EMC3_TMCO1  45 ekeqkrekelqkrarelqkngdklklkklekrqeelmedqsem.....................mmdqmkpmivtm 99 
                                        ++ ++r ++ +++ +++++n+  + ++k ++++    +++sem                      ++ mk+ ++++
  gene2869|gene2869|rna2869|rna2869 184 KRKEERRQKGEEKKKNVEENDTMKEKEKKAEERGNCEKKKSEMddsgsgklkseeitsktvnsaYSNAMKSVFFFG 259
                                        2223333344445555555888888999999999999999999********************************* PP

                         EMC3_TMCO1 100 ipqiliffwl 109
                                        i++i++   +
  gene2869|gene2869|rna2869|rna2869 260 ICMIVTLVAI 269
                                        ****998766 PP

>> Connexin  Connexin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   3.9   0.00028      0.71     101     148 ..     182     234 ..     145     270 .. 0.44

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00028
                           Connexin 101 eekekekeeeekeeeekeeekkk.kkekkkkkkkeeekekkkeegkr....ri 148
                                        eek+ke+++++ ee++k+ e+++  kek+kk++++ + ekkk+e ++    ++
  gene2869|gene2869|rna2869|rna2869 182 EEKRKEERRQKGEEKKKNVEENDtMKEKEKKAEERGNCEKKKSEMDDsgsgKL 234
                                        22222211111111111111111111111111111111111111111223333 PP

>> Renin_r  Renin receptor-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   4.2    0.0027       6.9      19      73 ..     210     270 ..     128     273 .] 0.76

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0027
                            Renin_r  19 ikkrkkrsileakeakdkkek.......klnlakkyssdYpaiFniiLwlvvvlvlaliaiv 73 
                                         kk ++r   e+k+++  + +       +   +k+++s Y+     ++++ ++++++l+ai 
  gene2869|gene2869|rna2869|rna2869 210 EKKAEERGNCEKKKSEMDD-SgsgklksEEITSKTVNSAYSNAMKSVFFFGICMIVTLVAIK 270
                                        2222223233333322222.1334344344457899***********************996 PP

>> NPR3  Nitrogen Permease regulator of amino acid transport activity 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   9.2   0.00063       1.6      46     137 ..     176     263 ..     136     268 .. 0.55

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.00063
                               NPR3  46 kskkkk...kkskrkrssrskekkskesskksesssksesseekksskeseeseekesneeeeeeededdeeseke 118
                                        +    +    ++krk+++r+k++++k++ +++++ +++e+++e++ + e+++se ++s + + ++e+ +++   + 
  gene2869|gene2869|rna2869|rna2869 176 N----NkesLEEKRKEERRQKGEEKKKNVEENDTMKEKEKKAEERGNCEKKKSEMDDSGSGKLKSEEITSK---TV 244
                                        2....122234444444444444444444444444444444444444333333333333333333332222...24 PP

                               NPR3 119 eeekedkkknltmFhlvfv 137
                                        ++  ++  k++  F ++++
  gene2869|gene2869|rna2869|rna2869 245 NSAYSNAMKSVFFFGICMI 263
                                        4555667777777777777 PP

>> Ureide_permease  Ureide permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   4.3    0.0008         2     118     210 ..     167     262 ..     162     270 .. 0.59

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0008
                    Ureide_permease 118 savhssnaadnkeklskskseekeetkeeekkeeesekkkeekdleege.....kaaekakagtaeflieleekra 188
                                        +++ + n ++nke l++ ++ee++++ ee+kk++e++ +++ek+ +++e     k++++++ + +  l + e + +
  gene2869|gene2869|rna2869|rna2869 167 TVIWNENYENNKESLEEKRKEERRQKGEEKKKNVEENDTMKEKEKKAEErgnceKKKSEMDDSGSGKL-KSE-EIT 240
                                        56788899999999999998888777766666555544444433322222234333333333333333.233.334 PP

                    Ureide_permease 189 ikvlgkstllGlaivlfaGvcf 210
                                         k +++     +  v+f G+c+
  gene2869|gene2869|rna2869|rna2869 241 SKTVNSAYSNAMKSVFFFGICM 262
                                        4667777777778888888887 PP

>> Peptidase_S49_N  Peptidase family S49 N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9  10.2    0.0011       2.9      46      94 ..     170     222 ..     136     246 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0011
                    Peptidase_S49_N  46 Lneeykelkeeleealldeeelkaaekkekkeekeekkaekkkake....eee 94 
                                         ne+y+++ke+lee+  +e+++k +ekk++ ee ++ k++ kka+e    e++
  gene2869|gene2869|rna2869|rna2869 170 WNENYENNKESLEEKRKEERRQKGEEKKKNVEENDTMKEKEKKAEErgncEKK 222
                                        599*********************99999999888888875555554555333 PP

>> UPF0242  Uncharacterised protein family (UPF0242) N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0         2   5.2e+03     127     143 ..      76      92 ..      63     104 .. 0.67
   2 ?    7.1  10.5    0.0021       5.4      57     140 ..     145     226 ..     121     247 .. 0.61

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 2
                            UPF0242 127 eaiaedfeelkleleeq 143
                                        e++++d++e+ + ++++
  gene2869|gene2869|rna2869|rna2869  76 EETVNDNSEVMQSMDDE 92 
                                        45555666665555554 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0021
                            UPF0242  57 wekalkekl.ekskleekeaklteld.eglktkeealeelqeeeeeLkeeldakeeelerlkeenqqLqekleaia 130
                                        ++++  + l e+s++  ++++ t    e++++++e+lee ++ee++ k       ee ++  een  ++ek +++ 
  gene2869|gene2869|rna2869|rna2869 145 FQTKQSTMLdENSTITDDKNVCTVIWnENYENNKESLEEKRKEERRQKG------EEKKKNVEENDTMKEKEKKAE 214
                                        3333333334455555555444443269999999999998888877555......455555556666665555555 PP

                            UPF0242 131 e..dfeelklel 140
                                        e  + e+ k e+
  gene2869|gene2869|rna2869|rna2869 215 ErgNCEKKKSEM 226
                                        433344444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (273 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2640  (0.147247); expected 358.6 (0.02)
Passed bias filter:                      588  (0.032796); expected 358.6 (0.02)
Passed Vit filter:                       111  (0.00619109); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.60u 0.26s 00:00:00.86 Elapsed: 00:00:00.42
# Mc/sec: 1948.38
//
Query:       gene287|gene287|rna287|rna287  [L=153]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       339  (0.0189079); expected 358.6 (0.02)
Passed bias filter:                      244  (0.0136092); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.21s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 1184.77
//
Query:       gene2870|gene2870|rna2870|rna2870  [L=330]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.4e-41  142.5   7.9    2.2e-41  141.9   7.9    1.2  1  RabGAP-TBC  Rab-GTPase-TBC domain


Domain annotation for each model (and alignments):
>> RabGAP-TBC  Rab-GTPase-TBC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  141.9   7.9   1.2e-45   2.2e-41       5     210 ..      82     275 ..      79     279 .. 0.92

  Alignments for each domain:
  == domain 1  score: 141.9 bits;  conditional E-value: 1.2e-45
                         RabGAP-TBC   5 gevWklllgyepevkrlkksekkqeksekeksklekseeskelsqIkkDvprtfpes..esfknkqgqnqLeriLk 78 
                                         +vW ++l+++         +k qe+s++e++ l++++ s  + qI+ D++rtf+++  +++  ++gq +L+r+L 
  gene2870|gene2870|rna2870|rna2870  82 NRVWTYMLRSR---------KKYQEVSWEEYTRLRDEY-SGFEYQIHVDIQRTFRNHalFYDAFGEGQCKLFRVLV 147
                                        78******995.........478899999999999988.5568************6669999999*********** PP

                         RabGAP-TBC  79 aysiynpevgYcqGmndivaplllvsldeeeaFwcfvsLlekyklrdlytsslpglkrklkvleellkkkdpklyk 154
                                        ay++ynp++gYcqGm    +++l ++ de eaF+++ ++l   +l+ l+  +l+ l + + v +e++  + p++y 
  gene2870|gene2870|rna2870|rna2870 148 AYANYNPHIGYCQGMASFTSLIL-MYFDELEAFNVLINIL--STLNALFDAQLSLLPTLMSVQKEVFILVIPEVYY 220
                                        ***********************.8889999*********..********************************** PP

                         RabGAP-TBC 155 hlkeegldlelfaikwfltlflrefpletvlrlwD.lllegekfvllrvalailkll 210
                                        +lk+e++dl lf+++w+ltlf + f+++++lr+wD +++ g+  +ll v++ail+++
  gene2870|gene2870|rna2870|rna2870 221 LLKNENVDLCLFVYSWYLTLF-SRFDIKLSLRIWDiFIFYGT-ASLLAVSCAILSFY 275
                                        *********************.77***********7777777.66********9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (330 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       697  (0.0388756); expected 358.6 (0.02)
Passed bias filter:                      453  (0.0252663); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 2158.83
//
Query:       gene2871|gene2871|rna2871|rna2871  [L=226]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.5e-06   25.6   8.8    2.7e-05   24.0   9.4    1.6  1  Tetraspanin     Tetraspanin family
      0.009   15.2   0.2     0.0096   15.1   0.2    1.1  1  CitMHS          Citrate transporter


Domain annotation for each model (and alignments):
>> Tetraspanin  Tetraspanin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   9.4     3e-09   2.7e-05       3     155 ..      13     143 ..      11     192 .. 0.76

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 3e-09
                                        XXXXXXXXXXXXXXXXXXXXXXXXXXXXX.....................XXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        Tetraspanin   3 yllfffnllfwligivllavGvwlrlkhaeaalacllsesaedpailaillivvGvllfllgflGcigalkenkcl 78 
                                        +l++++  lf++++i+l+++ + l      +++ + + + +++p  +    + +++l +ll ++G++ +++ +++ 
  gene2871|gene2871|rna2871|rna2871  13 ILFIVVQSLFLVFSILLIVLLITL------YSKLRSYLMLSVKPLLI---SLSISSLYVLLPVIGILIIVRHRITY 79 
                                        5788999999****9999996555......44455566778888888...999999*****************999 PP

                                        XXXXXXXXXXXXXXXXXXXXXXX--HHH........HHHHHHHHHHHHHHHHHHTHHHHHHHHHHT---SSHH..H CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        Tetraspanin  79 lltfsllllvlfllelaagilgfvfsdkargkvseiinnaievkyrddldlkkcqnlldslqkklsCCGvnsykDw 154
                                         +++++++l+l+ + + ++ + + + +            +     ++++d  + ++  + +q+kl+CCG+ + +D 
  gene2871|gene2871|rna2871|rna2871  80 TFLYIVMVLLLMNFDILLVSMEYNMVKN--------TPGYT----DKAWDKLS-NEQREHVQTKLGCCGFRDRNDR 142
                                        9999999999888888777766666666........44444....34444422.56789**********8877776 PP

                                        H CS
                                        x RF
                        Tetraspanin 155 s 155
                                        s
  gene2871|gene2871|rna2871|rna2871 143 S 143
                                        4 PP

>> CitMHS  Citrate transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.2   1.1e-06    0.0096      77     182 ..      11     131 ..       1     210 [. 0.61

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.1e-06
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             CitMHS  77 llvlltallsafvsndgvvlimipivlslakr...lkklppl.lliplalaaniggaltpiGtpttraaarpglsl 148
                                        l++l+ ++ s f+ +    +++i ++++l+ +     +l++  lli l+++    ++l+p+ ++++++  r+  ++
  gene2871|gene2871|rna2871|rna2871  11 LMILFIVVQSLFLVFS---ILLIVLLITLYSKlrsYLMLSVKpLLISLSIS--SLYVLLPVIGILIIVRHRITYTF 81 
                                        3666666667777443...44455555555540004555555765555555..55578999999777777777777 PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..................x RF
                             CitMHS 149 pnllllalllvgllplvllfmfgvalalpvnap..................k 182
                                        ++++++ ll++  + ++l+ m  ++++ ++ +                    
  gene2871|gene2871|rna2871|rna2871  82 LYIVMVLLLMN--FDILLVSMEYNMVKNTPGYTdkawdklsneqrehvqtkL 131
                                        77777877777..888888888888877777766666655555555555550 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1390  (0.077528); expected 358.6 (0.02)
Passed bias filter:                      495  (0.0276089); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.41
# Mc/sec: 1662.06
//
Query:       gene2872|gene2872|rna2872|rna2872  [L=387]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
       0.13   12.8   0.0       0.13   12.8   0.0    6.4  6  NPV_P10       Nucleopolyhedrovirus P10 protein
        1.6    9.0  64.7       0.16   12.2   1.4    4.5  4  Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain


Domain annotation for each model (and alignments):
>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   1.4e-05      0.13      26      60 ..      11      45 ..       3      50 .. 0.89
   2 ?    7.8   1.6    0.0005       4.5      11      36 ..      20      56 ..      19      92 .. 0.54
   3 ?   -0.3   2.5      0.17   1.5e+03      48      63 ..     108     123 ..      58     131 .. 0.70
   4 ?   -0.7   4.5      0.23   2.1e+03      19      42 ..     110     133 ..      96     212 .. 0.62
   5 ?   -0.5   1.7      0.19   1.7e+03      13      44 ..     210     242 ..     203     270 .. 0.64
   6 ?    0.9   2.2      0.07   6.3e+02      28      28 ..     336     336 ..     277     378 .. 0.53

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.4e-05
                            NPV_P10 26 qvddvqenlpdvtelnekLdaqsaqLaeletkven 60
                                       +v  ++e l+ + e+n++++a++a+++e ++k+ +
  gene2872|gene2872|rna2872|rna2872 11 RVPGISEHLKAIREINDRINAITASVKECKDKIAQ 45
                                       688899**********************9999865 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0005
                            NPV_P10 11 adikavddkVdalqqqv...........ddvqenlpd 36
                                       ++i++++d+++a+ ++v           ++ ++n+p+
  gene2872|gene2872|rna2872|rna2872 20 KAIREINDRINAITASVkeckdkiaqliKEEKSNSPK 56
                                       4555555555555555533333333333333444444 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.17
                            NPV_P10  48 saqLaeletkvenIqd 63 
                                         +++ el++k+++I+d
  gene2872|gene2872|rna2872|rna2872 108 KENVLELDNKIKEIND 123
                                        3344455555555554 PP

  == domain 4  score: -0.7 bits;  conditional E-value: 0.23
                            NPV_P10  19 kVdalqqqvddvqenlpdvtelne 42 
                                         V  l+++++++++n+ + t  ++
  gene2872|gene2872|rna2872|rna2872 110 NVLELDNKIKEINDNIMKCTLTTQ 133
                                        444444444444444444333333 PP

  == domain 5  score: -0.5 bits;  conditional E-value: 0.19
                            NPV_P10  13 ikavddkVdalqqqvddvqenlpdvt.elnekL 44 
                                        i++ d k++ l+++ d++ e+ ++v+ +++ek 
  gene2872|gene2872|rna2872|rna2872 210 IEENDAKISNLKKEKDELLEKRRKVQlQIQEKE 242
                                        677788888888888888888777662344433 PP

  == domain 6  score: 0.9 bits;  conditional E-value: 0.07
                            NPV_P10  28 d 28 
                                        +
  gene2872|gene2872|rna2872|rna2872 336 K 336
                                        2 PP

>> Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   8.4   7.4e-05      0.67      27     100 ..      11      87 ..       2      90 .. 0.76
   2 ?   -1.8   9.3      0.41   3.7e+03      15     104 ..      95     190 ..      89     194 .. 0.62
   3 ?    5.8  23.6    0.0018        16      12     105 ..     191     284 ..     183     287 .. 0.91
   4 ?   12.2   1.4   1.8e-05      0.16      52     100 ..     328     374 ..     292     377 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 7.4e-05
                                        HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTT...S-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH CS
                       Seryl_tRNA_N  27 dvdelleldekrrelqveleelqaerNelskeIgkakkkk...edaeeliaevkelkeelkaleaelkeleaelek 99 
                                         v  + e  ++ re++ +++++ a  +e+  +I++++k++     + +lia+ ++l+++l+a+ +e ++l +e ++
  gene2872|gene2872|rna2872|rna2872  11 RVPGISEHLKAIREINDRINAITASVKECKDKIAQLIKEEksnSPKVQLIAQKQQLNDDLSAVMEERDKLMEEKKA 86 
                                        455566666777888888888888888888888888877766666778*******************999998776 PP

                                        H CS
                       Seryl_tRNA_N 100 l 100
                                        l
  gene2872|gene2872|rna2872|rna2872  87 L 87 
                                        6 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.41
                                        HHHHCCCTCCCHHHHHHHHHHHHHHHHHHHHHHH...HHHHHHHHHHCCCCCCTT...S-TCCCCCCCHHHHHHHH CS
                       Seryl_tRNA_N  15 keklkkRgedkadvdelleldekrrelqveleel...qaerNelskeIgkakkkk...edaeeliaevkelkeelk 84 
                                        ke l++ ++  ++ + +leld+k +e++  + ++    ++ +e ++    +kkkk   +  +    ++k++++el 
  gene2872|gene2872|rna2872|rna2872  95 KEDLAAEKRKINLKENVLELDNKIKEINDNIMKCtltTQQEKEYANRLMDLKKKKtfcATLKGKELRIKTMGDELH 170
                                        5666666666777777888888887776655443222344444444444444444477667777777888888888 PP

                                        HHHHHHHHHHHHHHHHHCTS CS
                       Seryl_tRNA_N  85 aleaelkeleaeleklllai 104
                                         ++++l+   ++ +k+ l+i
  gene2872|gene2872|rna2872|rna2872 171 VIKDKLAHNANAAHKIKLSI 190
                                        88888887777777777766 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.0018
                                        HHHHHHHCCCTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHH CS
                       Seryl_tRNA_N  12 eavkeklkkRgedkadvdelleldekrrelqveleelqaerNelskeIgkakkkkedaeeliaevkelkeelkale 87 
                                          v++ l++ +e k +  ++ e d+k  +l++e +el ++r +++ +I+++ k++e   + +++ +e+ ++ k++ 
  gene2872|gene2872|rna2872|rna2872 191 NDVRNELNRLRETKIKNPRIEENDAKISNLKKEKDELLEKRRKVQLQIQEKEKEHERLMQEMEKQQEIENQKKEIV 266
                                        5678888777788899999********************************************************* PP

                                        HHHHHHHHHHHHHHCTS- CS
                       Seryl_tRNA_N  88 aelkeleaeleklllaiP 105
                                        +e++e e + + ll +i 
  gene2872|gene2872|rna2872|rna2872 267 KEMREKEGRKNLLLKEIV 284
                                        ******999998888876 PP

  == domain 4  score: 12.2 bits;  conditional E-value: 1.8e-05
                                        HHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Seryl_tRNA_N  52 rNelskeIgkakkkkedaeeliaevkelkeelkaleaelkeleaelekl 100
                                         N+l ++I+  kk  e  ++++ +v+++++++k+++ el + ++el k+
  gene2872|gene2872|rna2872|rna2872 328 INALLNTIKDRKK--EYESSIVGKVEDINKKIKDIDVELVKCKEELSKM 374
                                        5777777777776..56899*************************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (387 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3857  (0.215126); expected 358.6 (0.02)
Passed bias filter:                      634  (0.0353617); expected 358.6 (0.02)
Passed Vit filter:                       110  (0.00613531); expected 17.9 (0.001)
Passed Fwd filter:                        45  (0.0025099); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 1.18u 0.35s 00:00:01.52 Elapsed: 00:00:00.54
# Mc/sec: 2168.01
//
Query:       gene2873|gene2873|rna2873|rna2873  [L=48]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (48 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       268  (0.0149478); expected 358.6 (0.02)
Passed bias filter:                      238  (0.0132746); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.33u 0.28s 00:00:00.61 Elapsed: 00:00:00.42
# Mc/sec: 346.55
//
Query:       gene2874|gene2874|rna2874|rna2874  [L=157]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       368  (0.0205254); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.29s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 1071.96
//
Query:       gene2875|gene2875|rna2875|rna2875  [L=210]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       674  (0.0375927); expected 358.6 (0.02)
Passed bias filter:                      478  (0.0266607); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.29s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 1439.32
//
Query:       gene2876|gene2876|rna2876|rna2876  [L=412]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (412 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1382  (0.0770818); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 2798.71
//
Query:       gene2877|gene2877|rna2877|rna2877  [L=110]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       337  (0.0187964); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 805.17
//
Query:       gene2878|gene2878|rna2878|rna2878  [L=343]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    6.2e-26   91.6   2.9    5.7e-18   65.6   1.5    2.1  2  ATP_bind_1  Conserved hypothetical ATP binding protein
     0.0017   18.6   0.1      0.003   17.7   0.1    1.3  1  AAA_33      AAA domain
  ------ inclusion threshold ------
      0.018   15.6   0.3      0.055   14.0   0.3    1.9  1  AAA_18      AAA domain
      0.028   13.7   0.0       0.08   12.2   0.0    1.7  1  Zeta_toxin  Zeta toxin
       0.14   12.2   3.5        0.2   11.7   0.1    2.6  3  AAA_14      AAA domain
        0.2   12.1   1.9       0.37   11.2   0.8    2.2  2  AAA_17      AAA domain


Domain annotation for each model (and alignments):
>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.0   3.3e-09   9.8e-06       1      36 [.       7      40 ..       7      68 .. 0.87
   2 !   65.6   1.5   1.9e-21   5.7e-18      35     183 ..     116     257 ..     109     308 .. 0.79

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 3.3e-09
                         ATP_bind_1  1 vvGpaGsGKttfvgalseilelrgrsvavvNLDPAa 36
                                       +vG +GsGKtt+ +   ++l   gr+v++vNLDP+ 
  gene2878|gene2878|rna2878|rna2878  7 IVGLPGSGKTTYLKYKKNYLA--GRNVYTVNLDPGR 40
                                       79************9999998..77*********85 PP

  == domain 2  score: 65.6 bits;  conditional E-value: 1.9e-21
                         ATP_bind_1  35 AaeelpYeaavdirelitledvmedlglgpngalvvaleflresldwldeelekeeddyllfDtPGQielfthses 110
                                         ++  ++ ++ di +  ++++ m++ ++gpn a+   +e  + + +++++    +e+ y+l+DtPGQie     + 
  gene2878|gene2878|rna2878|rna2878 116 SVN--NFTFDYDITNKYDTRKYMKQREIGPNLAVKKIMEEYVANYEEIRNIF-CNEECYYLIDTPGQIESILNFDR 188
                                        555..667789**********************************9999988.66889************999999 PP

                         ATP_bind_1 111 lakiveeLes.efalvvvyLvDsqrltdptkfisgllsalsamlrlelPhvvvlnkfDllkeklekeleffedv 183
                                        l     +L++  ++lv+v+L D + +t+  ++  + ++++++m++l+  +++v++k+Dll++   + ++ ++++
  gene2878|gene2878|rna2878|rna2878 189 LL---LRLQRdGIRLVTVFLSDINSMTSIESLSYTYFMTMQTMVTLNHSQINVFTKLDLLDK--IRLIDKLSNL 257
                                        88...789988*****************9999999************************993..2223333322 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.1     1e-06     0.003       4      84 ..       7      86 ..       6      98 .. 0.69

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1e-06
                             AAA_33  4 lvGlpGsGKstlae...rllkklgavllssdt...lrrrlfgtdqqsktdytrvldrlyqilnelarkalsagrnvil 75
                                       +vGlpGsGK+t+++   ++l+ + +++++ d    +++r++++   ++t+ ++v d+++    +l r+++s g+nv+ 
  gene2878|gene2878|rna2878|rna2878  7 IVGLPGSGKTTYLKykkNYLAGRNVYTVNLDPgrwEKERHVNN---KDTYNNNVMDKTT----NLEREKQSDGNNVMD 77
                                       79*********99722245555558888888744333444443...4455455555444....677999999999998 PP

                             AAA_33 76 datnlsrre 84
                                          nl+r++
  gene2878|gene2878|rna2878|rna2878 78 KTANLEREK 86
                                       888888765 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.3   1.9e-05     0.055       2      83 ..       6      80 ..       6      94 .. 0.63

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.9e-05
                             AAA_18  2 lltGtpGvGKttlakeLskrlgfgvnlrdvakenglllevdpe.aldeskrldedkldklldaleenssaleegknlv 78
                                       l+ G pG+GKtt  k+ ++        r v + n     +++e  +++++  + +++dk  ++ +e  s   +g+n v
  gene2878|gene2878|rna2878|rna2878  6 LIVGLPGSGKTTYLKYKKN----YLAGRNVYTVNLDPGRWEKErHVNNKDTYNNNVMDKTTNLEREKQS---DGNN-V 75
                                       699*********9999533....3344444444444444444455577777777777776666666543...4444.7 PP

                             AAA_18 79 idghl 83
                                       +d   
  gene2878|gene2878|rna2878|rna2878 76 MDKTA 80
                                       77654 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   2.7e-05      0.08      20      55 ..       6      40 ..       5      81 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.7e-05
                         Zeta_toxin 20 llgGqpGAGKselaellkdelerqgnvvrldpDdlR 55
                                       l++G pG+GK++ +++ k++l+ ++nv +++ D  R
  gene2878|gene2878|rna2878|rna2878  6 LIVGLPGSGKTTYLKYKKNYLA-GRNVYTVNLDPGR 40
                                       789******************5.8888888777544 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   6.8e-05       0.2       6      59 ..       6      60 ..       5      79 .. 0.72
   2 ?    0.3   0.1      0.22   6.6e+02      51      90 ..     156     197 ..     110     222 .. 0.60
   3 ?    0.2   0.2      0.24   7.1e+02      55      90 ..     160     197 ..     138     293 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 6.8e-05
                             AAA_14  6 vitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpe...kllelilek 59
                                       +i+G+  +GKTt+lk + k++l   +++  +nld  r +k+++ +   ++++ +++k
  gene2878|gene2878|rna2878|rna2878  6 LIVGLPGSGKTTYLK-YKKNYL-AGRNVYTVNLDPGRWEKERHVNnkdTYNNNVMDK 60
                                       689999*******85.445666.89**********9998877442112444444444 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.22
                             AAA_14  51 kllelileklkeekktylflD...Eiqevpewekalkslvdeg 90 
                                         ++e+i++ +  +++ y ++D    i  + ++ + l +l ++g
  gene2878|gene2878|rna2878|rna2878 156 ANYEEIRNIFC-NEECYYLIDtpgQIESILNFDRLLLRLQRDG 197
                                        22333444333.5888888883333555555555555555555 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.24
                             AAA_14  55 lileklkeekktylflD...Eiqevpewekalkslvdeg 90 
                                        +i++ + + ++ y ++D    i  + ++ + l +l ++g
  gene2878|gene2878|rna2878|rna2878 160 EIRNIFCN-EECYYLIDtpgQIESILNFDRLLLRLQRDG 197
                                        34443333.666666663333444444444444444444 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.8   0.00012      0.37       1      19 [.       8      25 ..       8      97 .. 0.90
   2 ?   -3.7   0.0         5   1.5e+04      44      65 ..     134     155 ..     130     166 .. 0.57

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00012
                                       EE-TTSSHHHHHHHHHHHH CS
                             AAA_17  1 lGgPGsGKgtqceklveky 19
                                       +G+PGsGK+t++ k +++y
  gene2878|gene2878|rna2878|rna2878  8 VGLPGSGKTTYL-KYKKNY 25
                                       7***********.777776 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 5
                                        HHHCTSHHHHHHHHHHHHHHHH CS
                             AAA_17  44 demrklpleekkelqkeaaeki 65 
                                        ++m++ ++ ++ ++ k+++e +
  gene2878|gene2878|rna2878|rna2878 134 KYMKQREIGPNLAVKKIMEEYV 155
                                        5555555555555555555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (343 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1217  (0.0678789); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 2415.03
//
Query:       gene2879|gene2879|rna2879|rna2879  [L=63]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    0.00083   19.2   4.2    0.00083   19.2   4.2    1.6  1  Mid2         Mid2 like cell wall stress sensor
     0.0019   17.6   2.1     0.0019   17.6   2.1    1.8  2  SKG6         Transmembrane alpha-helix domain
  ------ inclusion threshold ------
      0.034   14.1   1.2       0.05   13.5   1.2    1.3  1  Syndecan     Syndecan domain
      0.073   14.0   0.0      0.081   13.8   0.0    1.1  1  EphA2_TM     Ephrin type-A receptor 2 transmembrane domain
       0.11   12.6   0.9       0.11   12.6   0.9    1.8  2  ETRAMP       Malarial early transcribed membrane protein (ETR
       0.31   11.1   3.3       0.42   10.7   3.3    1.2  1  Insulin_TMD  Insulin receptor trans-membrane segment
        1.3    9.0   4.2        4.4    7.2   4.2    1.8  1  ODV-E18      Occlusion-derived virus envelope protein ODV-E18


Domain annotation for each model (and alignments):
>> Mid2  Mid2 like cell wall stress sensor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   4.2   3.2e-07   0.00083      42      71 ..       2      30 ..       1      35 [. 0.76

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 3.2e-07
                               Mid2 42 skknrniviGcvvGigvPlllvillllyif 71
                                       ++k + i+iGcvvG+ v ++ +i+l +y+f
  gene2879|gene2879|rna2879|rna2879  2 ADKKKTIIIGCVVGVLVLII-LIALGFYFF 30
                                       789***********998555.455555555 PP

>> SKG6  Transmembrane alpha-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   2.1   7.2e-07    0.0019       9      33 ..       5      29 ..       2      30 .. 0.82
   2 ?   -2.5   1.7       1.4   3.6e+03       2      11 ..      50      59 ..      49      59 .. 0.64

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 7.2e-07
                               SKG6  9 tvaIavaVaVPVaViiivLlailif 33
                                       + +I ++ +V+V V ii+++ +++f
  gene2879|gene2879|rna2879|rna2879  5 KKTIIIGCVVGVLVLIILIALGFYF 29
                                       5688899999999999999999997 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.4
                               SKG6  2 sdssnsntva 11
                                       s+s+ +n+++
  gene2879|gene2879|rna2879|rna2879 50 SSSDDKNKTT 59
                                       6667777765 PP

>> Syndecan  Syndecan domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   1.2     2e-05      0.05      11      32 ..       7      28 ..       5      37 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2e-05
                           Syndecan 11 aviggvvvgllfaillvlflvY 32
                                        +i g+vvg+l++i+l+++  Y
  gene2879|gene2879|rna2879|rna2879  7 TIIIGCVVGVLVLIILIALGFY 28
                                       59***************99776 PP

>> EphA2_TM  Ephrin type-A receptor 2 transmembrane domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   3.2e-05     0.081       1      37 [.       8      49 ..       8      63 .] 0.64

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.2e-05
                           EphA2_TM  1 iiaaavaglvllvilvilvlvlvrrrsknrkqksdl.....k 37
                                       ii++ v+g+++l+il++l ++++ ++   +k ++ +     +
  gene2879|gene2879|rna2879|rna2879  8 IIIGCVVGVLVLIILIALGFYFFGSSGDGSKGSRWSsmfgtS 49
                                       78999****************997776666655433333321 PP

>> ETRAMP  Malarial early transcribed membrane protein (ETRAMP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.9   4.1e-05      0.11      51      76 ..       3      28 ..       1      33 [. 0.88
   2 ?    0.1   0.1      0.34   8.6e+02      28      53 ..      55      61 ..      44      63 .] 0.46

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.1e-05
                             ETRAMP 51 kkkKliiistiatalallvasalGlg 76
                                        kkK iii  ++ +l+l + +alG+ 
  gene2879|gene2879|rna2879|rna2879  3 DKKKTIIIGCVVGVLVLIILIALGFY 28
                                       589*********************63 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.34
                             ETRAMP 28 vnkkkekakkaikkiddkiekkkkkk 53
                                        nk                   ++kk
  gene2879|gene2879|rna2879|rna2879 55 KNK-------------------TTKK 61
                                       222...................2222 PP

>> Insulin_TMD  Insulin receptor trans-membrane segment
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   3.3   0.00017      0.42      16      39 ..       7      30 ..       1      31 [. 0.77

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00017
                        Insulin_TMD 16 kIvigPviciillllvigavfvvv 39
                                        I+ig v+ +++l+++i+  f+++
  gene2879|gene2879|rna2879|rna2879  7 TIIIGCVVGVLVLIILIALGFYFF 30
                                       59******8877777777778876 PP

>> ODV-E18  Occlusion-derived virus envelope protein ODV-E18
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   4.2    0.0017       4.4      31      54 ..      14      40 ..       5      61 .. 0.65

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0017
                            ODV-E18 31 lvvlviiillvl...lvqssstGsdss 54
                                       + vlv+iil+ l   ++ ss  Gs+ s
  gene2879|gene2879|rna2879|rna2879 14 VGVLVLIILIALgfyFFGSSGDGSKGS 40
                                       445555555554321666666665544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (63 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1214  (0.0677115); expected 358.6 (0.02)
Passed bias filter:                      821  (0.0457917); expected 358.6 (0.02)
Passed Vit filter:                       119  (0.00663729); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 471.01
//
Query:       gene288|gene288|rna288|rna288  [L=243]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       476  (0.0265492); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1609.38
//
Query:       gene2880|gene2880|rna2880|rna2880  [L=495]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-11   44.3   9.6       0.01   16.5   0.1    4.9  4  Sel1      Sel1 repeat


Domain annotation for each model (and alignments):
>> Sel1  Sel1 repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.1   5.7e-07      0.01       1      38 []     170     205 ..     170     205 .. 0.92
   2 !   10.8   0.0   3.4e-05      0.61      21      38 .]     222     239 ..     206     239 .. 0.73
   3 !    8.8   0.1   0.00015       2.6       7      32 ..     381     404 ..     378     405 .. 0.85
   4 !   11.2   0.5   2.7e-05      0.49       5      34 ..     415     442 ..     411     443 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 5.7e-07
                               Sel1   1 aeAmyrLGmfylylnGlgvpkDpekAiewyekAAeqGd 38 
                                        a Am  LG   lyl+G gv+k ++ A++++++ A++Gd
  gene2880|gene2880|rna2880|rna2880 170 AKAMTVLG--NLYLEGYGVEKCVSTAMHYFRQGAANGD 205
                                        6799****..677********9999***********97 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 3.4e-05
                               Sel1  21 kDpekAiewyekAAeqGd 38 
                                        kD ++A +++e AA++G+
  gene2880|gene2880|rna2880|rna2880 222 KDLSLAKKYFEEAASRGS 239
                                        59*************996 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.00015
                               Sel1   7 LGmfylylnGlgvpkDpekAiewyek 32 
                                        L+    y++G+g+++ + kA+ +y  
  gene2880|gene2880|rna2880|rna2880 381 LA--DTYFYGKGTEQSYTKAFSFYYA 404
                                        78..566**************99965 PP

  == domain 4  score: 11.2 bits;  conditional E-value: 2.7e-05
                               Sel1   5 yrLGmfylylnGlgvpkDpekAiewyekAA 34 
                                        y+L   y+y+nGlg  k ++ A+  + kA 
  gene2880|gene2880|rna2880|rna2880 415 YALS--YMYENGLGCTKSISDAMSMLYKAY 442
                                        9999..999*****9999999999888885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (495 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       546  (0.0304535); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 3238.33
//
Query:       gene2881|gene2881|rna2881|rna2881  [L=232]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.9e-47  161.2  17.9    2.9e-47  161.2  17.9    1.7  3  ER_lumen_recept  ER lumen protein retaining receptor
     0.0013   18.4  14.3      0.072   12.9   1.8    3.8  4  PQ-loop          PQ loop repeat


Domain annotation for each model (and alignments):
>> ER_lumen_recept  ER lumen protein retaining receptor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.1         2   1.8e+04      49      57 ..      18      26 ..       6      33 .. 0.43
   2 !  161.2  17.9   3.2e-51   2.9e-47       1     147 []      35     185 ..      35     185 .. 0.97
   3 ?   -3.4   0.1       1.7   1.5e+04      23      56 ..     209     215 ..     193     223 .. 0.47

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 2
                    ER_lumen_recept 49 yiiylilvk 57
                                       + +y +l+ 
  gene2881|gene2881|rna2881|rna2881 18 VHLYTMLIL 26
                                       223333333 PP

  == domain 2  score: 161.2 bits;  conditional E-value: 3.2e-51
                    ER_lumen_recept   1 svaGlSlktqilyalvfltryldlf.lylreeislyntlmkialillsiyiiylilvkfketyekekDtfklelli 75 
                                        sv+GlSlktq+ly++vf+ ryldlf + + + +++yn++mki++i+l++++iy+i++k+ ++y+   Dtf++  l+
  gene2881|gene2881|rna2881|rna2881  35 SVSGLSLKTQFLYLVVFVARYLDLFyFWFGSFLDVYNFIMKIIYISLQSVLIYMIRYKYFYSYDVFLDTFNVYNLV 110
                                        79**********************7566666********************************************* PP

                    ER_lumen_recept  76 vpslllallfhpg...ssktllevlwtfsiiLesvAilPQlillqktgevesltshyvfalglyRalyllnWivr 147
                                        vp+++la+++++g     ++++e+l tfs+ LesvAilPQl++lq++ge+e+lts+++f+lglyR++y++nWiv+
  gene2881|gene2881|rna2881|rna2881 111 VPCAVLAVFLKSGtygLVDYFVEFLYTFSVLLESVAILPQLVQLQESGEAETLTSQFIFFLGLYRLFYVVNWIVK 185
                                        ********99999999999******************************************************85 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 1.7
                    ER_lumen_recept  23 dlflylreeislyntlmkialillsiyiiylilv 56 
                                        d+f                           +i++
  gene2881|gene2881|rna2881|rna2881 209 DFF---------------------------VIYY 215
                                        222...........................2222 PP

>> PQ-loop  PQ loop repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.1     0.066   5.9e+02      37      55 ..       8      26 ..       5      31 .. 0.80
   2 !   12.1   0.3   1.4e-05      0.12      23      51 ..      29      57 ..      27      66 .. 0.87
   3 ?   -0.7   0.1      0.14   1.2e+03      39      57 ..      66      84 ..      63      88 .. 0.77
   4 !   12.9   1.8   8.1e-06     0.072       2      57 ..     132     187 ..     131     190 .. 0.94

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.066
                            PQ-loop 37 flllwllGdilsllyliln 55
                                       + ++ ++Gdi  l ++++ 
  gene2881|gene2881|rna2881|rna2881  8 YSIFRFTGDIVHLYTMLIL 26
                                       557889*****99999875 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 1.4e-05
                            PQ-loop 23 kNykrkSteGlSilflllwllGdilslly 51
                                       k+  +kS++GlS+ + +l l+ ++++ l 
  gene2881|gene2881|rna2881|rna2881 29 KIRETKSVSGLSLKTQFLYLVVFVARYLD 57
                                       67889****************99998765 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.14
                            PQ-loop 39 llwllGdilsllylilngf 57
                                       +l++  +i++++y+ l++ 
  gene2881|gene2881|rna2881|rna2881 66 FLDVYNFIMKIIYISLQSV 84
                                       6788888999999988875 PP

  == domain 4  score: 12.9 bits;  conditional E-value: 8.1e-06
                            PQ-loop   2 seilgyislvlwlvsyiPQiikNykrkSteGlSilflllwllGdilsllylilngf 57 
                                        +e+l ++s++l++v+ +PQ+++   +  +e l   f+++  l  +++++++i++ f
  gene2881|gene2881|rna2881|rna2881 132 VEFLYTFSVLLESVAILPQLVQLQESGEAETLTSQFIFFLGLYRLFYVVNWIVKLF 187
                                        578999*********************************************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       611  (0.0340789); expected 358.6 (0.02)
Passed bias filter:                      165  (0.00920297); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 1548.71
//
Query:       gene2882|gene2882|rna2882|rna2882  [L=223]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.7e-12   46.1   2.6    2.1e-11   44.0   0.7    2.7  2  Bromo_TP_like  Histone-fold protein
    8.9e-06   25.6   0.1    2.7e-05   24.1   0.1    1.8  1  Bromo_TP       Bromodomain associated
  ------ inclusion threshold ------
      0.079   11.8   0.1      0.095   11.5   0.1    1.2  1  DUF2791        P-loop Domain of unknown function (DUF2791)
        1.8    8.4   7.6        5.5    6.8   7.5    1.7  1  EssA           WXG100 protein secretion system (Wss), protein


Domain annotation for each model (and alignments):
>> Bromo_TP_like  Histone-fold protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.0   0.7   4.8e-15   2.1e-11       2     112 ..       9     104 ..       8     113 .. 0.73
   2 ?   -1.2   0.0      0.47   2.1e+03      28      51 ..     127     150 ..     123     171 .. 0.60

  Alignments for each domain:
  == domain 1  score: 44.0 bits;  conditional E-value: 4.8e-15
                      Bromo_TP_like   2 ilklvivEillQvGferiseqslniltdllkyyiekillkikkevdkdlleeilikllleeslgedsYkrnELlsF 77 
                                        ilkl+i+Eil+Q+Gfer++  +l +lt ll++yi  ++++  +         + +k l  +       +r ELls+
  gene2882|gene2882|rna2882|rna2882   9 ILKLCIAEILIQSGFERTTSMALTTLTHLLTFYIAYLTKRPFN------RPFLTTKHLFSNLCHR---ERTELLSY 75 
                                        9**********************************99987555......3344555555554444...48899999 PP

                      Bromo_TP_like  78 LkyqlnlkkqlktkeaveedeslleiLkvlpknhl 112
                                        L+ q +  ++ +    +     +le L+++p +++
  gene2882|gene2882|rna2882|rna2882  76 LQAQRKTCDRNQ----AAL--NILEQLRIMPDEKD 104
                                        998865544333....223..36777777776655 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.47
                      Bromo_TP_like  28 tdllkyyiekillkikkevdkdll 51 
                                        +d+l+ +i +   +i++e  k++ 
  gene2882|gene2882|rna2882|rna2882 127 SDVLHNFIVECKRRIEEEKSKEQH 150
                                        577777777777777774443333 PP

>> Bromo_TP  Bromodomain associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.1   6.1e-09   2.7e-05       3      45 ..       5      47 ..       3      50 .. 0.94

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 6.1e-09
                                       HHHHHHHHHHHHHHHHHT-SEE-HHHHHHHHHHHHHHHHHHHH CS
                           Bromo_TP  3 larsllkvvvsqileeaGfdsaeesaLEtLteiaqkYirelge 45
                                       + ++ lk  ++ il ++Gf+++++ aL tLt +++ Yi+ l++
  gene2882|gene2882|rna2882|rna2882  5 FHTQILKLCIAEILIQSGFERTTSMALTTLTHLLTFYIAYLTK 47
                                       67899**********************************9998 PP

>> DUF2791  P-loop Domain of unknown function (DUF2791)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   2.1e-05     0.095      98     170 ..     104     174 ..      72     206 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 2.1e-05
                            DUF2791  98 lealYrelvenlstktkpeggALrsildrwiseveeevaaegkeeddealeaavekkieerlaelselvegfd 170
                                         e++ + + en + kt  ++g  +++l ++i e+++++++e++  ++++ ++++++++ +++++ +++++ + 
  gene2882|gene2882|rna2882|rna2882 104 DETVEECVEENKEFKTMRDSGGVSDVLHNFIVECKRRIEEEKS--KEQHSDEETKDTLFDTVEQHRSMKNIPP 174
                                        444444455677889999*********************9998..6666777777777777777776666555 PP

>> EssA  WXG100 protein secretion system (Wss), protein EssA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   7.5    0.0012       5.5      32      86 ..     118     171 ..     100     175 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0012
                               EssA  32 kelkEtELdkaaieLFteeveeeinkkkkaEkkeieelkdsLFeeekesneavkd 86 
                                        k +++        + F  e +++i+++k +E++  ee kd LF   +e+  ++k+
  gene2882|gene2882|rna2882|rna2882 118 KTMRDSGGVSDVLHNFIVECKRRIEEEKSKEQHSDEETKDTLFDT-VEQHRSMKN 171
                                        5555555555666778999************************75.455557776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1124  (0.0626917); expected 358.6 (0.02)
Passed bias filter:                      517  (0.028836); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.60u 0.36s 00:00:00.96 Elapsed: 00:00:00.53
# Mc/sec: 1259.44
//
Query:       gene2883|gene2883|rna2883|rna2883  [L=85]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (85 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       234  (0.0130515); expected 358.6 (0.02)
Passed bias filter:                      206  (0.0114898); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.53u 0.33s 00:00:00.86 Elapsed: 00:00:00.53
# Mc/sec: 479.61
//
Query:       gene2884|gene2884|rna2884|rna2884  [L=752]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
     0.0048   16.5   2.4        1.2    8.9   0.1    2.9  2  zf_C2H2_ZHX  Zinc-fingers and homeoboxes C2H2 finger domain
  ------ inclusion threshold ------
      0.013   15.9   2.5      0.013   15.9   2.5    5.0  4  zf-C2H2      Zinc finger, C2H2 type


Domain annotation for each model (and alignments):
>> zf_C2H2_ZHX  Zinc-fingers and homeoboxes C2H2 finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.3   0.2    0.0008       7.2       4      23 ..     612     631 ..     611     635 .. 0.92
   2 !    8.9   0.1   0.00013       1.2       5      29 ..     642     666 ..     639     680 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0008
                        zf_C2H2_ZHX   4 sFvCveCsfsakkfegLalH 23 
                                         F Cv C+f  k+  +L+ H
  gene2884|gene2884|rna2884|rna2884 612 AFQCVRCKFYFKRLSTLKIH 631
                                        599**************999 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00013
                        zf_C2H2_ZHX   5 FvCveCsfsakkfegLalHNarsHp 29 
                                        F C+ C+   k++  L++H  + H 
  gene2884|gene2884|rna2884|rna2884 642 FGCTRCDSAYKTYSLLKKHGLKEHK 666
                                        89*******************9996 PP

>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.1      0.35   3.2e+03      14      21 ..       6      13 ..       3      14 .. 0.75
   2 ?   15.9   2.5   1.5e-06     0.013       1      23 []     613     635 ..     613     635 .. 0.98
   3 ?    9.9   0.7   0.00012       1.1       3      23 .]     644     665 ..     642     665 .. 0.94
   4 ?   -0.5   1.3      0.24   2.1e+03       6      19 ..     699     712 ..     697     712 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.35
                                       HHHHHHHH CS
                            zf-C2H2 14 snLkrHir 21
                                        +L++H++
  gene2884|gene2884|rna2884|rna2884  6 NHLNKHQS 13
                                       58899987 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 1.5e-06
                                        EEETTTTEEESSHHHHHHHHHCC CS
                            zf-C2H2   1 ykCpdCgksFkrksnLkrHirtH 23 
                                        ++C  C+  Fkr s Lk H+ +H
  gene2884|gene2884|rna2884|rna2884 613 FQCVRCKFYFKRLSTLKIHMISH 635
                                        89*******************99 PP

  == domain 3  score: 9.9 bits;  conditional E-value: 0.00012
                                        ETTTTEEESSHHHHHHHHHC.C CS
                            zf-C2H2   3 CpdCgksFkrksnLkrHirt.H 23 
                                        C+ C+  +k+ s+Lk+H  + H
  gene2884|gene2884|rna2884|rna2884 644 CTRCDSAYKTYSLLKKHGLKeH 665
                                        9****************98877 PP

  == domain 4  score: -0.5 bits;  conditional E-value: 0.24
                                        TTEEESSHHHHHHH CS
                            zf-C2H2   6 CgksFkrksnLkrH 19 
                                        C  +F+ + +Lk H
  gene2884|gene2884|rna2884|rna2884 699 CFNCFTYPKSLKLH 712
                                        8889********99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (752 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       887  (0.0494729); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.76u 0.37s 00:00:01.12 Elapsed: 00:00:00.55
# Mc/sec: 4080.03
//
Query:       gene2885|gene2885|rna2885|rna2885  [L=74]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (74 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       319  (0.0177924); expected 358.6 (0.02)
Passed bias filter:                      183  (0.0102069); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.55u 0.37s 00:00:00.92 Elapsed: 00:00:00.58
# Mc/sec: 382.70
//
Query:       gene2886|gene2886|rna2886|rna2886  [L=654]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00015   20.7   1.3    0.00015   20.7   1.3    2.7  3  ALMT      Aluminium activated malate transporter
  ------ inclusion threshold ------
        1.3    9.7   6.6        5.6    7.6   2.4    3.1  3  Pex14_N   Peroxisomal membrane anchor protein (Pex14p) conser
        4.5    5.5  24.5        1.7    6.8   0.0    3.4  4  CDC45     CDC45-like protein


Domain annotation for each model (and alignments):
>> ALMT  Aluminium activated malate transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   1.8     0.037   2.2e+02     362     408 ..      16      62 ..       2     103 .. 0.43
   2 !   20.7   1.3   2.5e-08   0.00015     323     457 ..     219     354 ..     187     365 .. 0.78
   3 ?   -1.7   0.2      0.16   9.6e+02     344     376 ..     488     510 ..     456     567 .. 0.45

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.037
                               ALMT 362 kkekaeeveekkeeekeseskkeeaeaveeaeseseksllkeskrsl 408
                                        +k++++++++ ++++ ++++ +++ ++ +++++++++ ++++++ + 
  gene2886|gene2886|rna2886|rna2886  16 QKRTNDHHRHINNQNANKTAANDQYDELKTTKTVNKHVKHEYKRMQR 62 
                                        22222222222222222222222222222222222222222222111 PP

  == domain 2  score: 20.7 bits;  conditional E-value: 2.5e-08
                               ALMT 323 lskveellkevkvaaeeLqskldskskLlvnsekweaakkkekaeeveekkeeekeseskkeeaeaveeaesesek 398
                                         s+  ++++ev+ + e+L+++l+++s+   n +  ++ak+k+k +++++++++++++++k +++e+++++ +++++
  gene2886|gene2886|rna2886|rna2886 219 TSE-RNISDEVNASNESLNENLNERSTANENPNGRNTAKEKNKVKHTKQYANQKRKTNQKCKTNEERKNNPHRNTT 293
                                        444.6899******************98888888889999999999999999999999988888888888888888 PP

                               ALMT 399 sllkeskrslklskkesapaeeslee..kqlskeeelkelelaealslatfaslLielvar 457
                                         +++++  +++++k +++ ++++     ++l  + +   ++ +  l+l  f+ +L+ ++ +
  gene2886|gene2886|rna2886|rna2886 294 LHKMQRFMQSMNKKMHKIITRQNNRTfyTALICNLKDDVIDALRFLHLPYFTGRLVLFILS 354
                                        8888777777777777776666444422555555566677888888888888888877655 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 0.16
                               ALMT 344 ldskskLlvnsekweaakkkekaeeveekkeee 376
                                        +++++          +++  e++++ +++++ +
  gene2886|gene2886|rna2886|rna2886 488 IKERI----------HTTCDEQQSTGTDNESVS 510
                                        11111..........111111111111111111 PP

>> Pex14_N  Peroxisomal membrane anchor protein (Pex14p) conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.16   9.3e+02      66      82 ..      25      42 ..       2     107 .. 0.49
   2 ?    7.6   2.4   0.00094       5.6      56     134 ..     243     322 ..     208     328 .. 0.39
   3 ?    1.3   0.0     0.084     5e+02      71     115 ..     507     560 ..     465     607 .. 0.47

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.16
                            Pex14_N 66 a.qeesasssatpqpqaa 82
                                       + ++++a+++a + +  +
  gene2886|gene2886|rna2886|rna2886 25 HiNNQNANKTAANDQYDE 42
                                       111111111111111111 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.00094
                            Pex14_N  56 a.vaassaseqaqeesasssatpqpqaasqtsqsspsps...ppaqqqqqqy..rpPivtypefltkppk.ppppP 124
                                        + ++++++     +++a+++++ ++++++ +++ +++++   ++  +++  +     ++ +++f+++++k  ++  
  gene2886|gene2886|rna2886|rna2886 243 StANENPNG----RNTAKEKNKVKHTKQYANQKRKTNQKcktNEERKNN--PhrNTTLHKMQRFMQSMNKkMHKII 312
                                        111222222....222222222222222222111111112111111122..1335667788888888555033334 PP

                            Pex14_N 125 lrtwrdllit 134
                                         r+ ++ ++t
  gene2886|gene2886|rna2886|rna2886 313 TRQNNRTFYT 322
                                        4455555555 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.084
                            Pex14_N  71 asssatpqpqaasqtsqsspsps..ppaqqqqqqy...............rpPivtypeflt 115
                                        +s s +++ q ++++s ++  ++  +                         pP++ y  +++
  gene2886|gene2886|rna2886|rna2886 507 ESVSDRSNDQYEQKSSIDNFLTAidT--------LkgnytidsikdnnadAPPQQPYSTIYA 560
                                        11122222222212111111111110........0111123334444455555555544444 PP

>> CDC45  CDC45-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.4    0.0029        17     151     239 ..      14     101 ..       2     104 .. 0.49
   2 ?   -0.2  14.9     0.038   2.3e+02     114     212 ..     200     308 ..     189     328 .. 0.45
   3 ?    1.5   0.1     0.012        71     484     567 ..     293     381 ..     286     401 .. 0.82
   4 ?    6.8   0.0   0.00029       1.7     415     480 ..     481     541 ..     424     548 .. 0.74

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.0029
                              CDC45 151 eeeeedeedeeedeeeskkkrksksdeeee.sddddersrkrrrsepsakklrrqlkkerrkyeavlekyysqgts 225
                                        +e++++++++ + +++ + ++ + +d+ +e ++++  +++ +++ + ++++ +   k++  ++++v ++  +   +
  gene2886|gene2886|rna2886|rna2886  14 DEQKRTNDHHRHINNQ-NANKTAANDQYDElKTTKTVNKHVKHEYK-RMQRINALHKNAAMRCNSVFMHGNAVLRF 87 
                                        1211111111122212.22222233333332333333333333322.44455555888888888899999999999 PP

                              CDC45 226 ygesvsslmYsLas 239
                                         ++s+ +++Y+L+ 
  gene2886|gene2886|rna2886|rna2886  88 TARSAVLVVYHLLV 101
                                        99999999999975 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.038
                              CDC45 114 eeleeereayealeeeeesdeedeeeeeeddddeeeeeeeeedeedeeedeeeskkkrksksdeeeesddddersr 189
                                        + lee+ + y +  ++ e+++e++ ++e + ++e+ +e+ +e++  +e+ + +++ k+k+k +++++ ++++++++
  gene2886|gene2886|rna2886|rna2886 200 DGLEEKSDLYRKGVFNGEATSERNISDEVNASNESLNENLNERSTANENPNGRNTAKEKNKVKHTKQYANQKRKTN 275
                                        5678888888888888888866664444444444434333344444444444444444433333333222222233 PP

                              CDC45 190 krrrse..........psakklrrqlkkerrky 212
                                        ++ +++          ++ +k++r  +++++k+
  gene2886|gene2886|rna2886|rna2886 276 QKCKTNeerknnphrnTTLHKMQRFMQSMNKKM 308
                                        332222111111111111111111133333333 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.012
                              CDC45 484 glelaqslqraivrtgtsliekkqirtlrafrlavlkdg.pdlelFth.paaLtkLalwllealresekekk.k.. 554
                                         l+  q++ +++ ++   +i++++ rt  +  ++ lkd+  d+  F h p +  +L l++l   ++++  ++ +  
  gene2886|gene2886|rna2886|rna2886 293 TLHKMQRFMQSMNKKMHKIITRQNNRTFYTALICNLKDDvIDALRFLHlPYFTGRLVLFILSYPKMMNIIRRiNif 368
                                        57778888999999999*********************9889999999899999******9987777766654466 PP

                              CDC45 555 kkkkllPlVlasl 567
                                           ++ Pl++ +l
  gene2886|gene2886|rna2886|rna2886 369 DGIERAPLIMHVL 381
                                        5556677776555 PP

  == domain 4  score: 6.8 bits;  conditional E-value: 0.00029
                              CDC45 415 ltAlLevgkgveaksekeaeesekeseeeeeeeeeeeaeeeekeeeewvknFweAydaLdkk.nidl 480
                                        + Al+ + k+        +++ ++++++ +++e+ +++++++ e+++ ++nF +A d+L+ +  id 
  gene2886|gene2886|rna2886|rna2886 481 VYALMRSIKER------IHTTCDEQQSTGTDNESVSDRSNDQYEQKSSIDNFLTAIDTLKGNyTIDS 541
                                        44455444422......11122222223444555566667789999*************86655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (654 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3259  (0.181773); expected 358.6 (0.02)
Passed bias filter:                      623  (0.0347482); expected 358.6 (0.02)
Passed Vit filter:                        77  (0.00429472); expected 17.9 (0.001)
Passed Fwd filter:                        24  (0.00133861); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.95u 0.34s 00:00:01.29 Elapsed: 00:00:00.53
# Mc/sec: 3697.59
//
Query:       gene2887|gene2887|rna2887|rna2887  [L=142]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.7e-37  127.5   0.0      3e-37  127.4   0.0    1.0  1  Ribosomal_S19e  Ribosomal protein S19e


Domain annotation for each model (and alignments):
>> Ribosomal_S19e  Ribosomal protein S19e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  127.4   0.0   1.7e-41     3e-37       2     135 ..       5     141 ..       4     142 .] 0.95

  Alignments for each domain:
  == domain 1  score: 127.4 bits;  conditional E-value: 1.7e-41
                                        SSSHHHHHHHHHS--S---S-SSS-SSSS-SS-S-SS-SSTTTHHHHHHHHHHHTS--TTS....GGGGS----SS CS
                     Ribosomal_S19e   2 vkdVpaeelikalaeeLkksgklevPewadlvKtgsakelapededWfyvRaAsilRkvyl....rgpvGverlrk 73 
                                        +++V+++++i++l+++Lk+++ l++P ++d+vK++s+k++ap ++dW+yvRaAs++R++ +    +++++++rl++
  gene2887|gene2887|rna2887|rna2887   5 IYQVEPSSFITTLSSHLKNNNLLTLPPNIDIVKSCSGKQNAPLNPDWLYVRAASVYRHFLTaqikNERITITRLAS 80 
                                        79*********************************************************99777778********* PP

                                        -SSS-------THHHHHHHHHTTSSS--SSS---SS-HHHHHTHHHHH--SS--S--XXXXX CS
                     Ribosomal_S19e  74 vYGgkkrrgvrpshfvkasgsvirkilqqLeklglvkkekkkgrrltkkGqrlldriaeeva 135
                                        vYG+kk+rg+rp ++v+a ++++r+il+++ +lg++ ++ ++g++++++G rl ++++e+++
  gene2887|gene2887|rna2887|rna2887  81 VYGCKKDRGSRPGKKVRAGRTHLRSILRDFGRLGWIVED-ERGKTVSEDGVRLSEQLIEKIL 141
                                        ************************************666.45***************99985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       305  (0.0170115); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 1054.05
//
Query:       gene2888|gene2888|rna2888|rna2888  [L=454]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.2e-47  161.7  28.8      3e-47  161.2  28.8    1.1  1  Na_H_Exchanger  Sodium/hydrogen exchanger family
  ------ inclusion threshold ------
        5.6    5.0   8.8        9.5    4.2   8.8    1.6  1  UPF0182         Uncharacterised protein family (UPF0182)


Domain annotation for each model (and alignments):
>> Na_H_Exchanger  Sodium/hydrogen exchanger family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  161.2  28.8   3.4e-51     3e-47       5     378 ..      40     417 ..      36     419 .. 0.88

  Alignments for each domain:
  == domain 1  score: 161.2 bits;  conditional E-value: 3.4e-51
                                        HHHHHHHHH..H.HHHTTSXHHHHHHHHHHHHTTTTTS.......HHHCHCCHHHHCHHCCHHHHCTCGCCTGCCT CS
                     Na_H_Exchanger   5 illallvgl..l.arrlklpeivgliiaGlllGpsglglieps..eedlevlselglilllFlaGleldlrelrkn 75 
                                        i++++++++  l  +rl+++e+v++ ++G+++Gp g++++e     + l +ls+ ++ l++ ++G  ++ r++ + 
  gene2888|gene2888|rna2888|rna2888  40 IFTLIFGLVslLiKERLYISETVIATLFGIVIGPKGFNILEFEdyPTMLFYLSRMVISLQVVAVGTIVPKRYVVRQ 115
                                        5555555556655*************************887777788888999*********************** PP

                                        HHHHHHHHHHHHHHHHHHHHHHHH.HHTXTTCHHHHHHHHHHHTSSXHHHHHHHC....CCCTSTCCCCCCHHHHH CS
                     Na_H_Exchanger  76 lksilllallgvlitvvliGlllylllilgiplleallfgailsatdpvvvlailk...eegrvperlgtlllges 148
                                        + s ++l+++++l+t ++++ l+ +    ++ l +++++ga++++tdpv+++++lk    ++ +p++l++ll+ es
  gene2888|gene2888|rna2888|rna2888 116 FQSLFILLVPLLLLTYAISTCLTFW--MTDLGLWASMIVGACVTPTDPVLASSVLKgkfANRYIPTHLRHLLILES 189
                                        ******************5555554..47999************************99988899************ PP

                                        HHHHHHCCCCCHHHHHHTXXXXXTSSSTSXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS....CTHHHHHHHHHH CS
                     Na_H_Exchanger 149 vlnDavavvllavllalakeeaggetslllllliflvvavgglllglvigwllrlitrft....dddrelevllvl 220
                                        +lnD+++++ll++ + ++       +   +l+++ l++++++++lgl+ig+++++++  +      d+e  ++  l
  gene2888|gene2888|rna2888|rna2888 190 GLNDGLGFPLLTLPIFAM-RLPFKKAFNKWLIHTWLYEIFLAVILGLAIGFVAKKLLVIShrknFIDKENILAYLL 264
                                        *************88777.3444445555778888888888888888888777777766666778*********** PP

                                        HHHHHHHHHHHTSXXXHHHHHHHHHHHHH.HHHHHTTHHHH.HHHHHHHHHHHHHHHHHHHHSXHHHHHXXHHHHH CS
                     Na_H_Exchanger 221 llallaallaellgvsgilgaflaGlvls.eyefsnklsek.lesfreglfnplfFvlvGlsldlkvlnnhlsvli 294
                                        +la+++ +++ ll+ ++il++f++G++++ ++e+  ++  + l  + +  +n  fF+l+G+s+         s+++
  gene2888|gene2888|rna2888|rna2888 265 ALAFVVTGITGLLKSDDILASFFCGMIFAwDGEYQDEIKDSsLYEVLDLMINASFFILFGASFT--------SHIR 332
                                        *****************************988889989999999999999*************9........8*** PP

                                        HHHHHHHHHHTHHHHHHHHHTTTX..SSXHHHHHHCC.CCSS.BHHHHHHHHHHHHHHXHHHHTTSSTTTCSTSXH CS
                     Na_H_Exchanger 295 lvllilvaillgrilavflllrll..glslrealiig.fgglqrgavalalaalgpalgllarelyallivvvlft 367
                                        ++ l+l++i+l+r++ + +  +++   +++rea+++g +g++++ga+ +++ a    +  l+ el+ ++ ++v+++
  gene2888|gene2888|rna2888|rna2888 333 YLPLALLIIFLRRLPLIIAGRPFIpqLFNMREAFFAGwYGPIGVGALFFITHANDCIK--LDDELVKIVNMMVMCS 406
                                        ************************855**********667777777777777777666..9*************** PP

                                        HHHHHHHHHHH CS
                     Na_H_Exchanger 368 vlvqGlslkpl 378
                                        v+++G++ +++
  gene2888|gene2888|rna2888|rna2888 407 VILHGTTAPII 417
                                        ******98875 PP

>> UPF0182  Uncharacterised protein family (UPF0182)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   8.8    0.0011       9.5     135     270 ..     205     345 ..      31     363 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.0011
                            UPF0182 135 YvFklPflelllslllalvllaliavllvyllsgeslgirl....kfaelskaarrhlsvllallllllalsywLd 206
                                        ++ +lPf +   ++l+ ++l+ +++++++ l  g +++ +l    +  +     ++ l+ llal +++ ++  +L+
  gene2888|gene2888|rna2888|rna2888 205 FAMRLPFKKAFNKWLIHTWLYEIFLAVILGLAIGFVAK-KLlvisH-RKNFIDKENILAYLLALAFVVTGITGLLK 278
                                        77899****************99999999999996662.2245642.344445567799999************** PP

                            UPF0182 207 ryellys...krgvvtGagYtdvnavlpaktilavialvvavlllvaivlkklklplialallvlla 270
                                          ++l s      ++   +Y d      ++ +l ++  +  ++l+ a ++++++++ +al++++l  
  gene2888|gene2888|rna2888|rna2888 279 SDDILASffcGMIFAWDGEYQDEIKDSSLYEVLDLMINASFFILFGASFTSHIRYLPLALLIIFLRR 345
                                        *******864333455678999999999999999998888888888889999988888887777654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (454 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       743  (0.0414412); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 2915.48
//
Query:       gene2889|gene2889|rna2889|rna2889  [L=46]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (46 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       609  (0.0339673); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.26s 00:00:00.61 Elapsed: 00:00:00.42
# Mc/sec: 331.58
//
Query:       gene289|gene289|rna289|rna289  [L=188]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       515  (0.0287244); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.22s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1444.28
//
Query:       gene2890|gene2890|rna2890|rna2890  [L=331]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (331 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1451  (0.0809303); expected 358.6 (0.02)
Passed bias filter:                      757  (0.0422221); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.45
# Mc/sec: 2211.39
//
Query:       gene2891|gene2891|rna2891|rna2891  [L=91]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.2e-17   61.4   1.8    1.2e-16   61.0   1.8    1.1  1  SUI1      Translation initiation factor SUI1
  ------ inclusion threshold ------
       0.06   13.7   0.1      0.088   13.1   0.1    1.5  1  PWI       PWI domain


Domain annotation for each model (and alignments):
>> SUI1  Translation initiation factor SUI1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.0   1.8   1.3e-20   1.2e-16       2      73 ..      11      79 ..      10      82 .. 0.92

  Alignments for each domain:
  == domain 1  score: 61.0 bits;  conditional E-value: 1.3e-20
                               SUI1  2 kpkihirleqrggrKkvTtvsgleafgidlkklakelkkkfacsgsvvkdggeeiqvQGdqrkkvaelLtek 73
                                       +++ih+r++q  g+K+vTt++g+e     + k+ kel++k++c+g  +kd+ +++q+QGd++  ++++L ++
  gene2891|gene2891|rna2891|rna2891 11 EKQIHVRIQQIYGKKRVTTITGIED--EIIVKIFKELRRKLSCGGHLSKDK-KVVQLQGDYSSSICDVLGKM 79
                                       689********************54..47899***************9999.89***************887 PP

>> PWI  PWI domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   9.8e-06     0.088       8      29 ..      24      45 ..      19      78 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 9.8e-06
                                PWI  8 akkitellgfeDdvvieyvlnl 29
                                       +k++t + g+eD+++++++ +l
  gene2891|gene2891|rna2891|rna2891 24 KKRVTTITGIEDEIIVKIFKEL 45
                                       59**************976554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       555  (0.0309554); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 656.68
//
Query:       gene2892|gene2892|rna2892|rna2892  [L=214]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       443  (0.0247086); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 1398.17
//
Query:       gene2893|gene2893|rna2893|rna2893  [L=233]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.4e-45  153.5   0.1    4.6e-45  153.1   0.1    1.1  1  Pho88     Phosphate transport (Pho88)


Domain annotation for each model (and alignments):
>> Pho88  Phosphate transport (Pho88)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  153.1   0.1   2.6e-49   4.6e-45       4     169 ..      10     180 ..       8     192 .. 0.87

  Alignments for each domain:
  == domain 1  score: 153.1 bits;  conditional E-value: 2.6e-49
                              Pho88   4 qvtnlviilvlmqvskkidfedpevllyvRilYvvsqliillvylyikskikkknDlttlky.vepasplske..e 76 
                                        q  n+v +lv+mq++k++++++p +l+++R+lYv+sql+++l++++ik++i ++nD++++k+ +e + +   e  e
  gene2893|gene2893|rna2893|rna2893  10 QALNIVASLVCMQATKYVELSHPLYLWTLRVLYVISQLMLFLCVHLIKKSIMRQNDRRVVKVpRELKWNEVPEtnE 85 
                                        789***********************************************************87755554444569 PP

                              Pho88  77 eklvttTvkdYDlaelkkllksilmgvammafmhlymkytnPLllQsimplknllesnlvkihllgkpaegdLkRP 152
                                        e+++++T+++YD++e+ +l+ks+l+++ +++f+hl++++++PL+lQ+i+ +k+++ ++l+  hl++k+    + RP
  gene2893|gene2893|rna2893|rna2893  86 EEFEEITYSEYDMREAGRLIKSALFQIPIVLFLHLKFGLPQPLALQAISIVKSFFLNPLFIAHLRHKS----VLRP 157
                                        9******************************************************************9....89** PP

                              Pho88 153 Fkaaagllgaa.......eaktdk 169
                                        F+ ++ l+g+a        +++d+
  gene2893|gene2893|rna2893|rna2893 158 FD-KNMLFGKAkedgeerRKREDE 180
                                        **.677787554444333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (233 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       753  (0.041999); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1570.75
//
Query:       gene2894|gene2894|rna2894|rna2894  [L=44]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (44 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       557  (0.031067); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.27s 00:00:00.63 Elapsed: 00:00:00.42
# Mc/sec: 315.34
//
Query:       gene2895|gene2895|rna2895|rna2895  [L=460]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0061   15.9   1.0      0.012   14.9   0.8    1.5  1  ATPase    KaiC


Domain annotation for each model (and alignments):
>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.8   6.9e-07     0.012     120     189 ..     315     383 ..     283     422 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 6.9e-07
                             ATPase 120 akrvviDsitglayeekeavaReilrqlvrvlkklgvTailvsekssseeaaggygveefivdgvivLdl 189
                                        +k+ + D+i+ +    + +v R+  ++l++v + l++T+ilvs +++++++++  ++ e+++++v++ ++
  gene2895|gene2895|rna2895|rna2895 315 IKQPINDNIQYI-LLFHLEVCRALRKNLMKVQRRLRITSILVSSRETKKKQKEVTNLDEYSISNVVIKHQ 383
                                        466677889988.8888899999999***********************************999987544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (460 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1147  (0.0639746); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.23s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 3325.75
//
Query:       gene2896|gene2896|rna2896|rna2896  [L=32]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (32 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       232  (0.0129399); expected 358.6 (0.02)
Passed bias filter:                      122  (0.00680462); expected 358.6 (0.02)
Passed Vit filter:                         5  (0.000278878); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.31u 0.24s 00:00:00.55 Elapsed: 00:00:00.38
# Mc/sec: 253.66
//
Query:       gene2897|gene2897|rna2897|rna2897  [L=329]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0027   16.3   9.5     0.0041   15.7   9.5    1.2  1  Peptidase_S64  Peptidase family S64
  ------ inclusion threshold ------
       0.15   12.7   7.2       0.41   11.2   3.6    2.5  2  DUF2408        Protein of unknown function (DUF2408)
       0.64    9.2   6.6          1    8.5   6.6    1.3  1  TMPIT          TMPIT-like protein
          5    6.6   7.6        1.8    8.0   1.2    2.2  3  Allexi_40kDa   Allexivirus 40kDa protein


Domain annotation for each model (and alignments):
>> Peptidase_S64  Peptidase family S64
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   9.5   9.2e-07    0.0041     114     232 ..      44     165 ..      10     168 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 9.2e-07
                      Peptidase_S64 114 kaedvgkplrv.letekltslntvleeeeeskekseeses.ssseekessvkeleeesvekeLkqLeedlaelmdd 187
                                        + +++g +  + +++ k +++++v e+++ + ++++e+++ +s+     ++ e++  ++ +eLk+L++ l++   +
  gene2897|gene2897|rna2897|rna2897  44 ESTKFGGADEItINNIKNKNKKNVNESDTYDGTENKENMTsHSDCGARIASLEQQLMAIMNELKSLKNVLVNGNYQ 119
                                        4444444444313434445566777777776665555444044445566667788889****************** PP

                      Peptidase_S64 188 inqsvinlskavieaieffkeF.leseekeklefevttennsslrk 232
                                          +s+ ++s  v e  ++fk+F + +++++++e+++  +nn++lr 
  gene2897|gene2897|rna2897|rna2897 120 TSKSMSEVSDKVNEKANVFKNFeAFNKQTQEIETKIRETNNKRLRA 165
                                        **********************53455578999***********97 PP

>> DUF2408  Protein of unknown function (DUF2408)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   3.6     9e-05      0.41       2      61 ..      93     160 ..      92     198 .. 0.74
   2 ?    2.2   0.1     0.056   2.5e+02      62     116 ..     262     319 ..     245     327 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 9e-05
                            DUF2408   2 eelspelepiyekLvsirrsLlslaakskaeeakesee......vkeelkelkeeLkkieskrde..e 61 
                                        ++l+++l++i+++L s++  L++ + ++++++++ s++      v +++++++++ ++ie+k  e  +
  gene2897|gene2897|rna2897|rna2897  93 ASLEQQLMAIMNELKSLKNVLVNGNYQTSKSMSEVSDKvnekanVFKNFEAFNKQTQEIETKIREtnN 160
                                        67999******************999999998888888888888666666666777777766555321 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.056
                            DUF2408  62 gkFkseegkevvekgqavlngLlddcfdlvedlkaqdgeekkv...asslqpiYdrLl 116
                                         kF  + +  ++e++ +v+ gL d++++ ++   ++ +e+k++    +++++i++r l
  gene2897|gene2897|rna2897|rna2897 262 RKFLLSFDGVCQENSRTVVGGLDDENLERLRTRMESATEQKDTtppVKRFNNIFKRFL 319
                                        5777777778999999999999999998766544444344444011456677777765 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   6.6   0.00023         1      10      91 ..      63     147 ..      54     164 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00023
                              TMPIT  10 efkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvk...eeeeeeveelkeelkerkkvl 82 
                                        + k+++e+ +   ++ +e  ++ s+c  +i++ +++l ++ ++lk+lk+ +     ++++ ++e++++++e+ +v+
  gene2897|gene2897|rna2897|rna2897  63 NKKNVNESDTYDGTENKENMTSHSDCGARIASLEQQLMAIMNELKSLKNVLVngnYQTSKSMSEVSDKVNEKANVF 138
                                        344555555444456667788899**********************998844344888999*************** PP

                              TMPIT  83 kevesllpk 91 
                                        k+ e++  +
  gene2897|gene2897|rna2897|rna2897 139 KNFEAFNKQ 147
                                        *99998544 PP

>> Allexi_40kDa  Allexivirus 40kDa protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   1.2   0.00039       1.8     100     171 ..      72     143 ..      34     148 .. 0.76
   2 ?    7.2   3.7   0.00069       3.1      75     158 ..      94     178 ..      80     194 .. 0.64
   3 ?   -2.3   0.0      0.54   2.4e+03      95     120 ..     286     311 ..     244     324 .. 0.56

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00039
                       Allexi_40kDa 100 vekklelsaetasdskllkklesietsleelhakldelsssetsesegPsssptkassaeaaasedLpiyqa 171
                                        + + +e++++ +s+s+   +++s+e++l ++ ++l+ l +   + + + s+s+++ s + ++ ++ ++ ++a
  gene2897|gene2897|rna2897|rna2897  72 TYDGTENKENMTSHSDCGARIASLEQQLMAIMNELKSLKNVLVNGNYQTSKSMSEVSDKVNEKANVFKNFEA 143
                                        344577888999999999*******************99999998888888887776655554444555554 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.00069
                       Allexi_40kDa  75 sqttlLselrdalrtltklldklk..svekklelsaetasdskllkklesietsleelhakldelsssetsesegP 148
                                        s +++L  + ++l+ l+++l + +  + ++ +e s + +++ ++ k++e+ +++ +e+ +k++e  ++  ++ + P
  gene2897|gene2897|rna2897|rna2897  94 SLEQQLMAIMNELKSLKNVLVNGNyqTSKSMSEVSDKVNEKANVFKNFEAFNKQTQEIETKIRETNNKRLRA-TWP 168
                                        5567788888888888887654430033444455666667778899****************8876654433.334 PP

                       Allexi_40kDa 149 sssptkassa 158
                                        +s ++++++a
  gene2897|gene2897|rna2897|rna2897 169 KSPEENEKNA 178
                                        3333333322 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 0.54
                       Allexi_40kDa  95 dklksvekklelsaetasdskllkkl 120
                                        ++l+++ +++e  +e+++ + ++k++
  gene2897|gene2897|rna2897|rna2897 286 ENLERLRTRMESATEQKDTTPPVKRF 311
                                        23444444444455555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (329 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2579  (0.143845); expected 358.6 (0.02)
Passed bias filter:                      677  (0.0377601); expected 358.6 (0.02)
Passed Vit filter:                        77  (0.00429472); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.42
# Mc/sec: 2332.60
//
Query:       gene2898|gene2898|rna2898|rna2898  [L=508]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.7e-05   22.5   0.1      0.036   13.9   0.0    3.5  2  Exo_endo_phos_2  Endonuclease-reverse transcriptase
  ------ inclusion threshold ------
      0.015   15.0   3.2      0.068   12.9   1.0    2.6  2  DUF956           Domain of unknown function (DUF956)


Domain annotation for each model (and alignments):
>> Exo_endo_phos_2  Endonuclease-reverse transcriptase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0     0.015   1.3e+02      74     102 ..      56      84 ..      44      96 .. 0.75
   2 !   13.9   0.0     4e-06     0.036       1     118 [.     235     348 ..     235     349 .. 0.67

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.015
                    Exo_endo_phos_2  74 llksgptfkssngsstiDltltsdnlals 102
                                        +++  ++ k++ng++ iDl++ +++l++ 
  gene2898|gene2898|rna2898|rna2898  56 EPTPIKRIKQRNGKDRIDLYIKNESLRKV 84 
                                        4444478888888***********99987 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 4e-06
                    Exo_endo_phos_2   1 lliisvYippsd.elenlestlekllselksp....kiiilGDfNakhplWgsedtdssargeeLiefleehslsl 71 
                                        +l++svYip  + + + +++ l ++l++ k++    +iii GD+N +  +         a    L++ +e++    
  gene2898|gene2898|rna2898|rna2898 235 ILFVSVYIPIPSeQKKAALNRLASFLRREKQEnkftEIIISGDWNDTPSDVLR------ALRMRLLSPCEDFIAF- 303
                                        689*****9666577777777777777777766778*******9865544433......3444555555555555. PP

                    Exo_endo_phos_2  72 lnllksgptfkssngsstiDltltsdnlalskleleeedlgSDHrpi 118
                                         +  ++ ++ ++++g   iD+ ++ +n+ + k++  ++  +SDH p+
  gene2898|gene2898|rna2898|rna2898 304 -KARTRWTRNINREG-RCIDFGISLNNTIITKQKVLRDVDLSDHYPV 348
                                        .44343455555554.8888888888888888888888888888876 PP

>> DUF956  Domain of unknown function (DUF956)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0     0.036   3.2e+02      31      55 ..     113     135 ..      79     160 .. 0.77
   2 ?   12.9   1.0   7.6e-06     0.068      52     108 ..     418     475 ..     413     483 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.036
                             DUF956  31 dkafefyndknvedyiqipWeevds 55 
                                        ++a+ fy++ n ++    +W++++ 
  gene2898|gene2898|rna2898|rna2898 113 NQAIKFYKEDNNKNT--ATWSNLKL 135
                                        8999***99998875..46776665 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 7.6e-06
                             DUF956  52 evdsvvasvlfkg.klirrfaivtkkngkfsFsskdskkvLkavrkyvgkekvvrsls 108
                                        + ++v asv+ k+ + i+r +i+++k+++ +Fs ++  ++ ka++k v++++  r+++
  gene2898|gene2898|rna2898|rna2898 418 KCETVSASVSSKTrRAIKRRKIYFRKHKNSNFSWQEYDRLRKAAKKCVEQDRKRRHKN 475
                                        6789*****98762689**********************************9888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (508 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1239  (0.0691059); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.26s 00:00:00.85 Elapsed: 00:00:00.45
# Mc/sec: 3386.31
//
Query:       gene2899|gene2899|rna2899|rna2899  [L=35]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (35 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       396  (0.0220871); expected 358.6 (0.02)
Passed bias filter:                      266  (0.0148363); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.26s 00:00:00.61 Elapsed: 00:00:00.43
# Mc/sec: 246.11
//
Query:       gene29|gene29|rna29|rna29  [L=259]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       825  (0.0460148); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.50u 0.31s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 1579.99
//
Query:       gene290|gene290|rna290|rna290  [L=530]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   2.6e-157  524.4   2.0   3.4e-157  524.0   2.0    1.2  1  PGI              Phosphoglucose isomerase
  ------ inclusion threshold ------
      0.075   13.2   0.0        2.9    8.1   0.0    2.5  2  Acetyltransf_CG  GCN5-related N-acetyl-transferase


Domain annotation for each model (and alignments):
>> PGI  Phosphoglucose isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  524.0   2.0  3.8e-161  3.4e-157       1     486 []      47     522 ..      47     522 .. 0.92

  Alignments for each domain:
  == domain 1  score: 524.0 bits;  conditional E-value: 3.8e-161
                                    E-TTSS--HHHHHHHHHHHHHTTHHHHHHHHHTT---BTTTTB---HHHHT-TT.----EETTE.ESHHH....HHHHHH CS
                            PGI   1 dysknkvddeilealvklaeeaklkaarealfaGekinstenravlhvalrnrs.nkpilvdGk.dvvpe....vkevld 74 
                                    dysk ++d   l++l    +    +++r+ +f+ e++n+te+r vlh+alr+++  ++i  +G+ d + e    v + l+
  gene290|gene290|rna290|rna290  47 DYSKTHIDTMLLHEL---NRGFRSTETRKGMFKKEELNFTEHRKVLHIALRDKNvLEAIEKNGSgDKLGEeeqlVFHELK 123
                                    9******98776655...5566667899***********************98735789888863555551222555689 PP

                                    HHHHHHHHHHTT-SB-TTS-B--EEEEE--GGGTHHHHHHHHHTGGG-TT.-EEEEE--SSHHHHHHHHTT--GGGEEEE CS
                            PGI  75 kmkefsekvrsGewkGatgkaitdvvniGiGGsdlGPvlvtealkkeser.lkvafvsnvdgthiaevlkkldpettlfi 153
                                    km++f  k++ Ge  G tgk+++ vvniGiGGsdlGP +vteal+ +++  +kv++++n+d+t+ ++v+ k+d e+tlfi
  gene290|gene290|rna290|rna290 124 KMRQFERKFEEGELLGVTGKKLRTVVNIGIGGSDLGPRMVTEALEFYKKDnVKVFYIANIDSTETERVFSKIDAEETLFI 203
                                    *********************************************9998779**************************** PP

                                    EE-SSS--HHHHHHHHHHHHHHHHHH--..GGGGGGTEEEESS-HHHHHHHT--GGGEEE--TTS-GGG-TTSGGGHHHH CS
                            PGI 154 vasktfttaetllnaesakewllkalke..dsavakhfvalstnaekveefGideknmfefwdwvGGryslwsaiGlsva 231
                                    v+sktftt etl na+ a + ++++l+    +  +khfva+s+n+e+v +fGi  +n f++wd+vGGr+slwsa+Gls+ 
  gene290|gene290|rna290|rna290 204 VVSKTFTTLETLANARLALKLMKERLNVdeREITEKHFVAVSANKEEVVNFGI--NNCFDMWDFVGGRFSLWSAVGLSII 281
                                    **********************9987653355678******************..589********************** PP

                                    HHH-HHHHHHHHHHHHHHHHHHHHS-GGG-HHHHHHHHHHHHHHTS---EEEEEES-GGGTTHHHHHHHHHHHHH---BB CS
                            PGI 232 lsiGfenfeelleGaaaidkhfleaplekniPvllalvgvwyvnflgaeteailpydqylerlaaylqqldmesnGksvt 311
                                    l+iGf nf  ll+Ga  +d+hf++  +ekn+P+l a+++v+y+nf+ +e++ +++yd+yl+ l  ylqql+mesnGk  t
  gene290|gene290|rna290|rna290 282 LYIGFTNFLSLLKGASIMDEHFKNEITEKNVPILQAYIEVYYTNFRKYESRCVVAYDEYLKNLYLYLQQLEMESNGKMAT 361
                                    *******************************************************************************9 PP

                                    TTS-B-SS--S-EEE---TTTGGGTSHHHHHHSSS---EEEEEEEE-...S-GGGGHHHHHHHHHHHHHHHHHHH-B-HH CS
                            PGI 312 kdgvlvdvetgeiifGeagtngqhafyqlihqGtkliPcdfiaavks...qnieiadhhkillsnffaqtealmvGksee 388
                                     +g+ v+ +tg +++G++gt +qh+f+ql+hqGt+ + ++fi +++    +++   +h ++l++n +aq++almvG +++
  gene290|gene290|rna290|rna290 362 FSGS-VSWNTGMVLWGGVGTSAQHSFFQLLHQGTRRVLVEFILPLQPlgdHKVMDHSHFEMLFANCVAQSQALMVGTETS 440
                                    9985.89*************************************9962214477788899****************9843 PP

                                    HHHHHHHHTHHHHHGGGG-B-----EEEEEEEE--HHHHHHHHHHHHHHHHHHHHHHTB-TT--GGGHHHHHHHHHHHHH CS
                            PGI 389 evkkelakakveklvphktfeGnrPsnsillekltpaelGalialyehkilvqGviwginsfdqwGvelGkelakkilke 468
                                    +                k f GnrPs +i  +kltpa lGalia+yehk++vqG+ w insfdq+GvelGk+lakk+l+ 
  gene290|gene290|rna290|rna290 441 N--------------NNKYFGGNRPSITICYTKLTPAVLGALIAFYEHKVFVQGLYWRINSFDQFGVELGKSLAKKVLEY 506
                                    3..............3579************************************************************* PP

                                    HSSS----SS-HHHHHHH CS
                            PGI 469 leasekvsdfdsstngli 486
                                    ++++   +d d st+ li
  gene290|gene290|rna290|rna290 507 IDDE--PKDVDNSTKNLI 522
                                    9988..67999***9997 PP

>> Acetyltransf_CG  GCN5-related N-acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.0   0.00032       2.9      29      60 ..     146     177 ..     141     181 .. 0.94
   2 ?    2.1   0.0     0.024   2.1e+02      39      60 ..     493     514 ..     490     517 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00032
                Acetyltransf_CG  29 hTeVpeelrGkGiAkkLvkaalddareeglkv 60 
                                     T+V+  ++G  ++ ++v++al++ ++ + kv
  gene290|gene290|rna290|rna290 146 RTVVNIGIGGSDLGPRMVTEALEFYKKDNVKV 177
                                    699***************************99 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.024
                Acetyltransf_CG  39 kGiAkkLvkaalddareeglkv 60 
                                      ++k L+k++l+++ +e + v
  gene290|gene290|rna290|rna290 493 VELGKSLAKKVLEYIDDEPKDV 514
                                    5689***********9887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (530 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       822  (0.0458475); expected 358.6 (0.02)
Passed bias filter:                      527  (0.0293937); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.46
# Mc/sec: 3490.06
//
Query:       gene2900|gene2900|rna2900|rna2900  [L=742]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.9e-47  160.0   0.0    1.6e-45  155.3   0.0    2.2  2  RVT_1     Reverse transcriptase (RNA-dependent DNA polymerase
  ------ inclusion threshold ------
       0.55   11.0   8.0        2.1    9.1   7.8    2.1  1  zf-RVT    zinc-binding in reverse transcriptase


Domain annotation for each model (and alignments):
>> RVT_1  Reverse transcriptase (RNA-dependent DNA polymerase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  155.3   0.0   1.8e-49   1.6e-45       1     221 [.      82     330 ..      82     331 .. 0.95
   2 ?    2.3   0.2     0.011     1e+02     178     207 ..     485     514 ..     478     541 .. 0.83

  Alignments for each domain:
  == domain 1  score: 155.3 bits;  conditional E-value: 1.8e-49
                                        EE-TT.....S-EEE......-THHHHCTB--...........-------HHHH................HCCHTS CS
                              RVT_1   1 ipKkg....pgsyRpisllsvdykalnkliakrLkdvl..ekllsenqpgfrpgrstldav...edllkalkkkkk 67 
                                        ipKkg    +++yR isl+++ +k+  k++a+r++ ++  +++l ++q gfr+ + ++ +     ++lk  + +++
  gene2900|gene2900|rna2900|rna2900  82 IPKKGdmsrTDNYRGISLINTVCKIATKIVAERISRICeaNNILINEQAGFRRLEECVAQAtslVEILKRRELEGQ 157
                                        89*******************************************************9999777666666677889 PP

                                        --EEEEEEBCCGCCCSBB-GGGGGGG-EEET.........................TEEEEESB--ST-TTHHHHH CS
                              RVT_1  68 aklllklDlkkaFdsvpleellrkltafkvptklinliksflstrsfsvrvngeeskgryekkglpqGsvlSPllf 143
                                         ++++++D+ ka+d+vp+ +ll+k++ ++++ kl+   +++++++++svrv + +s+ + ++ g++qG++ SP+lf
  gene2900|gene2900|rna2900|rna2900 158 TTYVVFIDFTKAYDRVPHGALLHKMKMLGLNGKLLGFTEALYRSPRASVRVGEDTSECFEYQIGVKQGCPASPILF 233
                                        9**************************************************8888899999*************** PP

                                        HHHHHHHHTT-T...........TEEECTTEEEEEESSHHHHHHHHHHHHHHHHHTT--BEGGG-EEE........ CS
                              RVT_1 144 nlfmnellrelrkra.....kgvtllrYaDDililskskeelqelleaveewlkesglkinpeKtklvlft..... 209
                                        n+++n+l++ l+        k +  l++aDD +il++s  +l++ ++++eew++++++++n +K+ ++ f+     
  gene2900|gene2900|rna2900|rna2900 234 NIYINDLFEGLSGIElepgaKPIPGLLFADDAVILAESLAALESDVRKLEEWCNKWKMRVNIDKCGFMIFGdetva 309
                                        ************9669*99999****************************************************** PP

                                        ...........ESSEEETTEE CS
                              RVT_1 210 ........v.kseevkyLGvt 221
                                                  +++e++yLG++
  gene2900|gene2900|rna2900|rna2900 310 tiswmgteIpRANEYRYLGLP 330
                                        **99987548*********87 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.011
                                        HHHHHHHHHHHHHHHHTT--BEGGG-EEE. CS
                              RVT_1 178 eelqelleaveewlkesglkinpeKtklvl 207
                                        e+++  +++ve++lke  ++  ++K+kl+ 
  gene2900|gene2900|rna2900|rna2900 485 ENIECTINMVEQKLKERHIRNDKSKCKLIR 514
                                        4488899********************994 PP

>> zf-RVT  zinc-binding in reverse transcriptase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   7.8   0.00023       2.1      11      81 ..     504     591 ..     500     593 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00023
                             zf-RVT  11 rekkekvklakliWkskappkvkfflW.............lllknrlptadnllkrgiesss...rCqlCgqe.eE 69 
                                        r++k k+kl +  Wk     k+k ++              +l ++      +l+k g+  ++   +C +C+++ +E
  gene2900|gene2900|rna2900|rna2900 504 RNDKSKCKLIRETWKVGTVMKFKKLITanyqltngwrtfvKLRTGNFSSCTRLAKLGYIDNKyatECICCHKKeQE 579
                                        556666666666676666666664444455555555555555667777888888888875433337*****999** PP

                             zf-RVT  70 tieHlfleCpfa 81 
                                        ti+Hl+  Cp+ 
  gene2900|gene2900|rna2900|rna2900 580 TIFHLLWMCPMW 591
                                        *********975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (742 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       481  (0.026828); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.69u 0.27s 00:00:00.96 Elapsed: 00:00:00.49
# Mc/sec: 4516.86
//
Query:       gene2901|gene2901|rna2901|rna2901  [L=50]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (50 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       392  (0.021864); expected 358.6 (0.02)
Passed bias filter:                      224  (0.0124937); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.27s 00:00:00.62 Elapsed: 00:00:00.42
# Mc/sec: 357.35
//
Query:       gene2902|gene2902|rna2902|rna2902  [L=127]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.046   14.1   0.6      0.072   13.5   0.1    1.5  2  L31       Mitochondrial ribosomal protein L31


Domain annotation for each model (and alignments):
>> L31  Mitochondrial ribosomal protein L31
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0      0.45   8.2e+03      20      20 ..      25      25 ..       5      40 .. 0.59
   2 ?   13.5   0.1     4e-06     0.072      33      73 ..      79     119 ..      68     124 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.45
                                L31 20 k 20
                                       k
  gene2902|gene2902|rna2902|rna2902 25 K 25
                                       1 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 4e-06
                                L31  33 vieavkeslkkkgvslkalekakaelpkesemspkdKYtvF 73 
                                         i++v+e+lkk+++++k+++k+++++ + ++ s+ d+Yt+ 
  gene2902|gene2902|rna2902|rna2902  79 SISTVAEALKKQSINYKNMDKTHNHFLTRKNTSSYDQYTLM 119
                                        599***********************************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       826  (0.0460706); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 973.95
//
Query:       gene2903|gene2903|rna2903|rna2903  [L=187]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       352  (0.019633); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 1285.11
//
Query:       gene2904|gene2904|rna2904|rna2904  [L=805]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (805 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       733  (0.0408835); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.63u 0.29s 00:00:00.92 Elapsed: 00:00:00.45
# Mc/sec: 5420.91
//
Query:       gene2905|gene2905|rna2905|rna2905  [L=128]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
       0.35    9.2   1.1       0.38    9.1   1.1    1.0  1  SID-1_RNA_chan  dsRNA-gated channel SID-1


Domain annotation for each model (and alignments):
>> SID-1_RNA_chan  dsRNA-gated channel SID-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   1.1   2.1e-05      0.38     133     213 ..       2      78 ..       1     106 [. 0.56

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 2.1e-05
                     SID-1_RNA_chan 133 fllltllvvivekvresseekrvkessssesaseslesvssavrsesessveeesdydtleeiesdknvirtkkvl 208
                                        +++++++++++++v ++ ++++ ++ +s +s+++ l++ s+++r ++ + +++++  ++ +e++++k+    k++l
  gene2905|gene2905|rna2905|rna2905   2 LYFVIIIYICWKSVFTTDNDRN-SRLRSLRSYNRMLRNHSNEMRDDKSETSQRQRTVSSRRELRENKKS---KTSL 73 
                                        4667777777765554443333.5567777777777777777777777777777777777666655432...2222 PP

                     SID-1_RNA_chan 209 vvsdl 213
                                          s+l
  gene2905|gene2905|rna2905|rna2905  74 QKSQL 78 
                                        22222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2113  (0.117854); expected 358.6 (0.02)
Passed bias filter:                      715  (0.0398795); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.31s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 835.15
//
Query:       gene2906|gene2906|rna2906|rna2906  [L=161]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.1e-39  132.5   5.9    6.4e-39  131.9   5.9    1.3  1  Ribosomal_L21e  Ribosomal protein L21e


Domain annotation for each model (and alignments):
>> Ribosomal_L21e  Ribosomal protein L21e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  131.9   5.9   3.6e-43   6.4e-39       1     101 []       1     101 [.       1     101 [. 0.99

  Alignments for each domain:
  == domain 1  score: 131.9 bits;  conditional E-value: 3.6e-43
                                        X--S-STTTT-TTTTS--GGG-SS--SHHHH----TT-EEEE---TT--SS---GGGTT-EEEE..EEEETTEEEE CS
                     Ribosomal_L21e   1 mknskglrrgtrklfskkfrkkgvpplstylreykkGdkVdikidpsvqkgmphkryhGktgrvynvtkravgviv 76 
                                        m++skg+rr+trk fs++frk+g+p++styl++yk+Gd+Vdik++p+v+kgmphk+yhG tg+v  v+k++  v +
  gene2906|gene2906|rna2906|rna2906   1 MTSSKGYRRQTRKRFSQPFRKHGMPSISTYLTTYKRGDYVDIKVNPAVHKGMPHKYYHGLTGKVAVVHKNSLTVRC 76 
                                        89************************************************************************** PP

                                        EEEETTE..EEEEEE-GGGEEE--. CS
                     Ribosomal_L21e  77 nkkvggkileKriivriehlkksks 101
                                        ++++g+k +++ i++r+ehl+ksk+
  gene2906|gene2906|rna2906|rna2906  77 TRRFGNKRIHRMIVCRVEHLRKSKC 101
                                        ***********************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1036  (0.0577835); expected 358.6 (0.02)
Passed bias filter:                      600  (0.0334653); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1160.48
//
Query:       gene2907|gene2907|rna2907|rna2907  [L=184]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.9e-10   38.7   0.1    1.2e-09   37.7   0.1    1.5  1  S4            S4 domain
      0.003   18.4   0.0     0.0045   17.9   0.0    1.4  1  Ribosomal_S4  Ribosomal protein S4/S9 N-terminal domain


Domain annotation for each model (and alignments):
>> S4  S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.7   0.1   1.3e-13   1.2e-09       1      47 [.     113     159 ..     113     159 .. 0.97

  Alignments for each domain:
  == domain 1  score: 37.7 bits;  conditional E-value: 1.3e-13
                                        EEHHHHHHHTTSSSSHHHHHHHHHTTTEEETTEEE--TT-EE-TTCE CS
                                 S4   1 rRLdkvlarlglassrreArqlIehGrVlVNGkvvkdpsyrVkpgDv 47 
                                        rRL+  +++lg+a s  +Ar lI ++r+ +N ++v++p+y V++ D+
  gene2907|gene2907|rna2907|rna2907 113 RRLQHRVFELGMANSVHHARNLIYQRRIMINDRIVNKPGYVVTGDDE 159
                                        79*****************************************9996 PP

>> Ribosomal_S4  Ribosomal protein S4/S9 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0     5e-07    0.0045      33      80 ..      11      59 ..       2     112 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 5e-07
                                       -----CHCH.HHHHHHHHHHHHT-S.HHHHHHHHHHHHHCCSHHHHHHHH CS
                       Ribosomal_S4 33 rkklseYgk.qlrekqklkrrYgll.ekqfrryfkearrirGktgenLlq 80
                                       ++ l ++++ +l  ++kl+++Ygl+ +k+++ + ++ +  + k ++ Ll 
  gene2907|gene2907|rna2907|rna2907 11 STPLRPFESdRLIAEMKLIGEYGLRnKKELWIFKNITNTTK-KRARDLLI 59
                                       5667799999**************************99999.99999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       464  (0.0258799); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.34s 00:00:00.93 Elapsed: 00:00:00.57
# Mc/sec: 976.23
//
Query:       gene2908|gene2908|rna2908|rna2908  [L=166]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1507  (0.0840538); expected 358.6 (0.02)
Passed bias filter:                      494  (0.0275531); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.34s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1051.99
//
Query:       gene2909|gene2909|rna2909|rna2909  [L=274]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        1.6    8.5  10.0         12    5.7   0.2    3.3  3  DivIC     Septum formation initiator


Domain annotation for each model (and alignments):
>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.1    0.0036        65      48      76 ..     116     144 ..     110     148 .. 0.86
   2 ?    5.7   0.2   0.00068        12      28      58 ..     155     186 ..     151     188 .. 0.89
   3 ?    3.4   1.7    0.0036        65      28      61 ..     194     227 ..     189     234 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.0036
                                        CC-XXXXXXXXXXXXXXXXXXXXXXXXXX CS
                              DivIC  48 kdLksdedyieerARselglvkpgEtvyr 76 
                                        +d  s+e++i ++ R  l++  + E  ++
  gene2909|gene2909|rna2909|rna2909 116 NDNDSEENRINQIIRMSLDYLSEQESSFK 144
                                        5666799*****************99887 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.00068
                                        HHHHHHHHHHHHHHHHHHHHCC-XX.XXXXXX CS
                              DivIC  28 alqaelaklkaeneeLeaevkdLks.dedyie 58 
                                        + q+++ ++  e+e+ ++e+++++  +++y++
  gene2909|gene2909|rna2909|rna2909 155 RAQDKIREVECEIERCKSEIEKWEEiGQEYVA 186
                                        67999******************769999986 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.0036
                                        HHHHHHHHHHHHHHHHHHHHCC-XXXXXXXXXXX CS
                              DivIC  28 alqaelaklkaeneeLeaevkdLksdedyieerA 61 
                                        +l++++ +lk e+++ +++  + ++++++i++ A
  gene2909|gene2909|rna2909|rna2909 194 RLKEKNTTLKHEENDKNDNAVLVEQNKERIAKLA 227
                                        7899999999999999999999999999999988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (274 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1145  (0.063863); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1796.18
//
Query:       gene291|gene291|rna291|rna291  [L=79]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.6e-06   27.7   0.0    3.1e-06   27.4   0.0    1.1  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    2.8e-05   24.0   0.0    3.4e-05   23.8   0.0    1.1  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    0.00017   22.0   0.1    0.00022   21.6   0.1    1.2  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
     0.0082   16.3   0.1       0.01   16.0   0.1    1.0  1  Acetyltransf_4   Acetyltransferase (GNAT) domain
  ------ inclusion threshold ------
      0.017   15.1   0.0      0.019   14.9   0.0    1.2  1  FR47             FR47-like protein


Domain annotation for each model (and alignments):
>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   0.0   8.7e-10   3.1e-06      66     114 ..       3      51 ..       1      54 [. 0.93

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 8.7e-10
                                    EEESGGGTTSSHHHHHHHHHHHHHHHTTESEEEEEEETTEHHHHHHHHH CS
                 Acetyltransf_1  66 laVspeyrgkGlGsaLlealeerareegikkivlaveedndaairlYek 114
                                    l V   y+ +G Gs++l  +e  ar+e i+ i+l+v+  n+ a r+Y k
  gene291|gene291|rna291|rna291   3 LGVIHGYQSQGFGSQMLSFVENMARSERIEWIYLHVQLRNVVASRFYLK 51 
                                    678889*****************************************76 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.0   9.4e-09   3.4e-05      59     110 ..       5      58 ..       2      67 .. 0.90

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 9.4e-09
                Acetyltransf_10  59 VdpeyrgqGigkaLleaveeeaekdgikl.eltvnasp.yavpfYeklGFkavg 110
                                    V + y++qG g+++l +ve+ a+ ++i+   l+v+  +  a +fY k  +++v+
  gene291|gene291|rna291|rna291   5 VIHGYQSQGFGSQMLSFVENMARSERIEWiYLHVQLRNvVASRFYLKWNYRVVK 58 
                                    5578************************9******9999************995 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.1   6.3e-08   0.00022      31      75 ..       4      55 ..       1      56 [. 0.70

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 6.3e-08
                                   EE-GGGTTSSHHHHHHHHTT.....SEEE.EE.EEEETHHHHHHHHHHTTEE CS
                 Acetyltransf_7 31 aVdpeyrgkGiGraLleaae.....kgii.le.qlelnaekaikfYeklGFe 75
                                    V   y+ +G G+++l ++e     + i+ ++ +++l++  a +fY k  ++
  gene291|gene291|rna291|rna291  4 GVIHGYQSQGFGSQMLSFVEnmarsERIEwIYlHVQLRNVVASRFYLKWNYR 55
                                   57778************833344433333444567776668999***99886 PP

>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.1   2.8e-06      0.01      90     146 ..      10      66 ..       5      70 .. 0.94

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2.8e-06
                 Acetyltransf_4  90 nkeglgrelidaleqvlkeqnienllaeiaspnensiqfhkalGFelvgifkkcikk 146
                                    +++g g++++ ++e++++   ie ++  +   n  +  f+ +  +++v+i+k+++kk
  gene291|gene291|rna291|rna291  10 QSQGFGSQMLSFVENMARSERIEWIYLHVQLRNVVASRFYLKWNYRVVKIEKDYYKK 66 
                                    78999*************************************************998 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   5.3e-06     0.019      32      80 ..       8      57 ..       1      71 [. 0.84

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 5.3e-06
                                   GG-SSSHHHHHHHHHHHHHHH.S-S-EEEEEETT-HHHHHHHHHHT-EEE CS
                           FR47 32 ehrrrGlgsrlvkalakeiae.rgktvllvvvasNtpsirlyeklGfeki 80
                                     + +G+gs++ + + +  +  r + + l+v+  N  ++r+y k ++++ 
  gene291|gene291|rna291|rna291  8 GYQSQGFGSQMLSFVENMARSeRIEWIYLHVQLRNVVASRFYLKWNYRVV 57
                                   57899*****988887777765778899*******************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       528  (0.0294495); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 534.02
//
Query:       gene2910|gene2910|rna2910|rna2910  [L=288]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-08   35.4  10.6    1.1e-08   35.4  10.6    3.2  3  CPBP      CPBP intramembrane metalloprotease
  ------ inclusion threshold ------
      0.045   13.8   2.2        0.1   12.6   0.5    2.4  2  DUF1655   Protein of unknown function (DUF1655)


Domain annotation for each model (and alignments):
>> CPBP  CPBP intramembrane metalloprotease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.1      0.19   1.7e+03      48      74 ..       3      28 ..       1      41 [. 0.66
   2 ?   -1.2   0.5      0.31   2.7e+03      56      56 ..      87      87 ..      27     115 .. 0.59
   3 !   35.4  10.6   1.2e-12   1.1e-08       7      91 ..     118     278 ..     112     279 .. 0.70

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.19
                                       HHHCSGGGHHHHHHHHHHHHHHHHHHH CS
                               CPBP 48 FglaHlpngpsvllaalaGlvlgylyl 74
                                       F l H +    ++l ++aGl+l   y+
  gene2910|gene2910|rna2910|rna2910  3 FKLSHCMS-ARIALSTVAGLALITTYY 28
                                       77888877.456667777776655544 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.31
                                       H CS
                               CPBP 56 g 56
                                       +
  gene2910|gene2910|rna2910|rna2910 87 K 87
                                       1 PP

  == domain 3  score: 35.4 bits;  conditional E-value: 1.2e-12
                                        HHHHHHHHHHHHHHHHHTTCHHHH.................................................... CS
                               CPBP   7 vfllalllapllEEllfRglllql.................................................... 30 
                                        ++++ +++ p++EE++fR +l+q                                                     
  gene2910|gene2910|rna2910|rna2910 118 FIIRDVIFYPFFEEFFFRHVLFQNlkygmvgieriwimnnepgdlkadtssvthtddrsdvtlstrvagttiknni 193
                                        68899****************5555555555555555555555555555555555555555555555555555555 PP

                                        ...............HHHH.S-..........HHHHHHHHHHHHHCSGGG...HHH.HHHHHHHHHHHHHHHHHTT CS
                               CPBP  31 ...............lqergss..........tlailissilFglaHlpn...gps.vllaalaGlvlgylylktg 77 
                                                       l     +          ++  +issilF+ aH  +    +  +++ ++ G+++++    t 
  gene2910|gene2910|rna2910|rna2910 194 vhrklivkdlntytvL-----EtaditfllviIYFAVISSILFATAHHFYdviLINdYIYRVISGIFYTIFVDLTH 264
                                        5555544443333333.....033455677779999***********99866644457****************** PP

                                        -HHHHHHHHHHHHH CS
                               CPBP  78 sllaaillHallnl 91 
                                        +ll+++++H+++nl
  gene2910|gene2910|rna2910|rna2910 265 NLLVSLICHSVHNL 278
                                        *************8 PP

>> DUF1655  Protein of unknown function (DUF1655)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1      0.24   2.1e+03      42      48 ..     187     193 ..     181     214 .. 0.66
   2 ?   12.6   0.5   1.1e-05       0.1      14      53 ..     229     271 ..     220     272 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.24
                            DUF1655  42 ttlendi 48 
                                        tt+ n+i
  gene2910|gene2910|rna2910|rna2910 187 TTIKNNI 193
                                        6666666 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 1.1e-05
                            DUF1655  14 llkakarhf...iklneyvyrlfdGqsvvtfttlendiqvemv 53 
                                        +l a a hf   i +n+y+yr+  G     f  l  ++ v ++
  gene2910|gene2910|rna2910|rna2910 229 ILFATAHHFydvILINDYIYRVISGIFYTIFVDLTHNLLVSLI 271
                                        78899***9666779**********999999999999988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (288 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       778  (0.0433934); expected 358.6 (0.02)
Passed bias filter:                      224  (0.0124937); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1890.42
//
Query:       gene2911|gene2911|rna2911|rna2911  [L=42]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.034   13.8   0.1      0.039   13.6   0.1    1.1  1  zf-Tim10_DDP  Tim10/DDP family zinc finger
       0.35   10.9   0.3       0.35   10.9   0.3    2.1  3  VEK-30        Plasminogen (Pg) ligand in fibrinolytic pathway


Domain annotation for each model (and alignments):
>> zf-Tim10_DDP  Tim10/DDP family zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   4.3e-06     0.039      14      38 ..      11      36 ..       7      39 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.3e-06
                       zf-Tim10_DDP 14 elvnkltekCfkkCigk.ypgssLds 38
                                        ++n++  +C  kCi++ + ++sL++
  gene2911|gene2911|rna2911|rna2911 11 RIINHFITSCILKCIHDkKVDKSLNN 36
                                       5799***********66246777665 PP

>> VEK-30  Plasminogen (Pg) ligand in fibrinolytic pathway
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.6      0.39   3.5e+03      10      12 ..       5       7 ..       5       7 .. 0.91
   2 ?   -2.5   0.2      0.64   5.8e+03      15      17 .]      26      28 ..      26      28 .. 0.73
   3 ?   10.9   0.3   3.9e-05      0.35       8      13 ..      34      39 ..      32      40 .. 0.95

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.39
                             VEK-30 10 NER 12
                                       NER
  gene2911|gene2911|rna2911|rna2911  5 NER 7 
                                       999 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.64
                             VEK-30 15 HDe 17
                                       HD+
  gene2911|gene2911|rna2911|rna2911 26 HDK 28
                                       886 PP

  == domain 3  score: 10.9 bits;  conditional E-value: 3.9e-05
                             VEK-30  8 LKNERH 13
                                       L+NERH
  gene2911|gene2911|rna2911|rna2911 34 LNNERH 39
                                       9***** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (42 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       296  (0.0165096); expected 358.6 (0.02)
Passed bias filter:                      188  (0.0104858); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.31u 0.25s 00:00:00.56 Elapsed: 00:00:00.38
# Mc/sec: 328.15
//
Query:       gene2912|gene2912|rna2912|rna2912  [L=302]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       449  (0.0250432); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2190.52
//
Query:       gene2913|gene2913|rna2913|rna2913  [L=287]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.7e-33  114.3   0.2    1.4e-31  109.7   0.2    2.4  1  DUF1749          Protein of unknown function (DUF1749)
     0.0016   17.8   0.0     0.0038   16.5   0.0    1.6  2  Hydrolase_4      Serine aminopeptidase, S33
     0.0023   17.5   0.1      0.023   14.2   0.0    2.0  2  LIDHydrolase     Lipid-droplet associated hydrolase
     0.0055   15.7   0.0     0.0097   14.8   0.0    1.5  1  Chlorophyllase2  Chlorophyllase enzyme
     0.0096   15.8   0.0      0.017   15.0   0.0    1.4  1  Ser_hydrolase    Serine hydrolase
  ------ inclusion threshold ------
       0.14   12.8   0.0       0.15   12.6   0.0    1.3  1  Abhydrolase_6    Alpha/beta hydrolase family
       0.14   11.7   0.0       0.33   10.5   0.0    1.6  1  DUF4964          Domain of unknown function (DUF4964)
       0.15   11.7   0.0       0.18   11.5   0.0    1.4  1  Abhydrolase_1    alpha/beta hydrolase fold


Domain annotation for each model (and alignments):
>> DUF1749  Protein of unknown function (DUF1749)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.7   0.2   6.3e-35   1.4e-31       8     254 ..      12     256 ..       5     277 .. 0.80

  Alignments for each domain:
  == domain 1  score: 109.7 bits;  conditional E-value: 6.3e-35
                            DUF1749   8 gllheyaerlvafeyetsgelkska.llFigGLgdGlltvpyvkelanaldeagwsvvelqlsssyggwGtgsLkr 82 
                                        + l  y e +    ++t++++++++ +l+igG+  Gl+   +v e+a+ +d a+++  ++ l  s+  +G  sL  
  gene2913|gene2913|rna2913|rna2913  12 VNLSVYDESNHLLILSTTQTVNTEViILYIGGMLSGLMHPKFVFEMADKMDFAQFA--QPML-RSHPFFGLWSLSD 84 
                                        6677888888888899999996666488*******************999988886..4444.457789999**** PP

                            DUF1749  83 DaeeieklveYlkktk................sG.eekkekvvlmGHstGsqdvlyYltssnerdrekvdgailqa 141
                                        Da++iek++ Y+ +                     + kk k++l+GHstG+q +l+Yl  +++   +k+  +il +
  gene2913|gene2913|rna2913|rna2913  85 DAKDIEKAITYICTSFqdkcnrsttaeaendiNIeRDKKPKIILLGHSTGCQSILHYLNTHKS--FTKITCSILLG 158
                                        ************87655567777666654443222456789********************88..9********** PP

                            DUF1749 142 pvsDReailkvleerkklkelvalakklvdkgkaeeilprelaekvgletpvsarRflsLasvdgdDDfFssDlsd 217
                                        pvsDRe   +++ +   l++ ++la ++            +++  ++ + pv a+R++sL s  gdDD+FssDlsd
  gene2913|gene2913|rna2913|rna2913 159 PVSDREYEEHTNPN---LQHNLELAMEN------------SKTTFLHSNCPVNAQRYISLFSKYGDDDLFSSDLSD 219
                                        ******98886655...66666666555............5566667799*************************9 PP

                            DUF1749 218 eklektfGkvkepllillsekDefvpesv.dkedller 254
                                        e ++ t  k  +pl +ll   De+v +s  d+ ++++ 
  gene2913|gene2913|rna2913|rna2913 220 EFFK-TINKSGTPLHFLLLKDDEYVINSNaDVLKMVNN 256
                                        9765.566777899999999999987765488888875 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       1.1   2.5e+03     168     209 ..      49      91 ..      44     112 .. 0.69
   2 !   16.5   0.0   1.7e-06    0.0038      71     169 ..     119     218 ..     110     233 .. 0.70

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.1
                        Hydrolase_4 168 itvrlllelldamkrleeraakit.lPllllhGeaDkvvdpea 209
                                        +  +++ e+ d m++++  ++ ++  P++ l + +D   d e+
  gene2913|gene2913|rna2913|rna2913  49 MHPKFVFEMADKMDFAQFAQPMLRsHPFFGLWSLSDDAKDIEK 91 
                                        5667777888888888877777776777777776666555555 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 1.7e-06
                        Hydrolase_4  71 eehpelplfllGhSmGGliallyllrypd..kvaglilsaPalkikaklk.appllklllkllgkllpklqvsnnl 143
                                        e+ ++ +++llGhS+G    l+yl ++++  k++  il +P+ + + + + ++p l+  l+l+ +  ++  + ++ 
  gene2913|gene2913|rna2913|rna2913 119 ERDKKPKIILLGHSTGCQSILHYLNTHKSftKITCSILLGPVSDREYE-EhTNPNLQHNLELAMENSKTTFL-HSN 192
                                        6778889*****************8888877999*******9765543.44666666655555544444444.445 PP

                        Hydrolase_4 144 kadslsrdpevvaayeadplvhgkit 169
                                         +   +r+ +   +y +d l + +++
  gene2913|gene2913|rna2913|rna2913 193 CPVNAQRYISLFSKYGDDDLFSSDLS 218
                                        56666666666666666666665555 PP

>> LIDHydrolase  Lipid-droplet associated hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0     1e-05     0.023      79     121 ..     118     161 ..      87     207 .. 0.80
   2 ?    1.2   0.0       0.1   2.3e+02     215     247 ..     219     253 ..     210     267 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1e-05
                       LIDHydrolase  79 aksekdvklilvGHSvGaYialevlkrlsers.ikkvvlLfPti 121
                                         +++k+ k+il+GHS G+  +l+ l+ +++ + i   +lL P+ 
  gene2913|gene2913|rna2913|rna2913 118 IERDKKPKIILLGHSTGCQSILHYLNTHKSFTkITCSILLGPVS 161
                                        6789**************99999999776644488888888865 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.1
                       LIDHydrolase 215 dvllkknkeka..lvfyfgkkDhWvpeetrdelke 247
                                        d ++k+ ++    l+f+  k+D++v ++ +d lk 
  gene2913|gene2913|rna2913|rna2913 219 DEFFKTINKSGtpLHFLLLKDDEYVINSNADVLKM 253
                                        3455554444457*************999998864 PP

>> Chlorophyllase2  Chlorophyllase enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   4.3e-06    0.0097      90     140 ..     124     173 ..      18     182 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 4.3e-06
                    Chlorophyllase2  90 sklalsgHSrGgktafalalgkaktslkfsaligvdPvagaskskqtepki 140
                                         k+ l gHS G++ +++  l+++k+ +k+   i + Pv+  + +++t+p++
  gene2913|gene2913|rna2913|rna2913 124 PKIILLGHSTGCQSILHY-LNTHKSFTKITCSILLGPVSDREYEEHTNPNL 173
                                        4899**********9986.56666689************999999999875 PP

>> Ser_hydrolase  Serine hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   7.4e-06     0.017      53      95 ..     122     165 ..     103     195 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 7.4e-06
                                        -STTEEEEEETCHHHHHHHHHH.HTTSSSEEEEEEET--SGGS. CS
                      Ser_hydrolase  53 aeekvvlvAHSlgclavlhaae.lqlakkvagalLVapadveee 95 
                                         + k++l+ HS gc  +lh+++  ++  k+   +L  p + +e 
  gene2913|gene2913|rna2913|rna2913 122 KKPKIILLGHSTGCQSILHYLNtHKSFTKITCSILLGPVSDREY 165
                                        45679****************98899999999999999875422 PP

>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   6.9e-05      0.15      62     101 ..     113     163 ..      51     268 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 6.9e-05
                                        ..........TTSEEEEEETCHHHHHHHHHHCC.........EE.EEES-..---- CS
                      Abhydrolase_6  62 a........gggpvvlvGHSlGGalalaaapla.......lvvg.vlldppptalp 101
                                        +          ++++l+GHS G+   l+   ++        + + +ll p  ++++
  gene2913|gene2913|rna2913|rna2913 113 EndinierdKKPKIILLGHSTGCQSILH---YLnthksftKITCsILLGP--VSDR 163
                                        04455565445667**************...6666699887677999999..2222 PP

>> DUF4964  Domain of unknown function (DUF4964)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00015      0.33      16      49 ..      55      88 ..      45      99 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00015
                            DUF4964 16 fkeekkseLRaPayPLvtidpylsiWsftdeLnd 49
                                       f+ + k ++   a P++ ++p++ +Ws +d+ +d
  gene2913|gene2913|rna2913|rna2913 55 FEMADKMDFAQFAQPMLRSHPFFGLWSLSDDAKD 88
                                       55666777778899***************98665 PP

>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   7.8e-05      0.18      71     108 ..     122     161 ..      79     247 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 7.8e-05
                                        TTSSEEEEEETHHHHHHHHHHHHH..GGGEEEEEEESECS CS
                      Abhydrolase_1  71 gddkltlvGhSmGGmialayaaey..perVkalvllgaid 108
                                        +  k++l+GhS G++  l+y+  +    ++ + +llg+++
  gene2913|gene2913|rna2913|rna2913 122 KKPKIILLGHSTGCQSILHYLNTHksFTKITCSILLGPVS 161
                                        5679********************7777899999999933 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       549  (0.0306208); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 2013.12
//
Query:       gene2915|gene2915|rna2915|rna2915  [L=132]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.9e-11   41.6   0.9    1.2e-10   41.3   0.9    1.1  1  PX        PX domain
     0.0021   18.4   0.1     0.0032   17.8   0.1    1.3  1  DUF1041   Domain of Unknown Function (DUF1041)


Domain annotation for each model (and alignments):
>> PX  PX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.3   0.9   1.4e-14   1.2e-10       5      97 ..      18     104 ..      14     126 .. 0.77

  Alignments for each domain:
  == domain 1  score: 41.3 bits;  conditional E-value: 1.4e-14
                                        EEEEEEEEEETTSSEEEEEEEEEETTS.....SSEEEEEEEHHHHHHHHHHHHHHHTTSTSTSSSTSGSSSSSCTT CS
                                 PX   5 qvsvleretsgskkhsyylyevelktg.....akewtvkRrYsdFeeLhskLlrkfprvkiPplPkkvlfgsvrkk 75 
                                        ++s+ +    ++k +++++ye+ + t+     + ++ v RrY++F +L++ L  k +    P++Pkk+ f      
  gene2915|gene2915|rna2915|rna2915  18 EISIPT----HKKLNNIIHYEILCITNlqeyrKCYSRVFRRYKQFRHLYKILSGKIV---QPEFPKKRFFNY---- 82 
                                        555555....6788888888888888888889999*****************99988...9*******9974.... PP

                                        SHHHHHHHHHHHHHHHHHHHTS CS
                                 PX  76 deefiekrrkgLeeyLqrllnh 97 
                                        +ee+i++r ++L ++L+ +++ 
  gene2915|gene2915|rna2915|rna2915  83 KEEVIKERMAMLGVWLRYVAKL 104
                                        8***************998864 PP

>> DUF1041  Domain of Unknown Function (DUF1041)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.1   3.6e-07    0.0032      40      85 ..      19      64 ..       1      71 [. 0.78

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 3.6e-07
                            DUF1041 40 eegtskkkleeltkLaeLvievlqqdkehyaevleafaweldlmve 85
                                        + +++kkl+++++   L+i+ lq+ +++y+ v+  + ++  l ++
  gene2915|gene2915|rna2915|rna2915 19 ISIPTHKKLNNIIHYEILCITNLQEYRKCYSRVFRRYKQFRHLYKI 64
                                       445899****************************888888887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       790  (0.0440627); expected 358.6 (0.02)
Passed bias filter:                      520  (0.0290033); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.29s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 915.73
//
Query:       gene2916|gene2916|rna2916|rna2916  [L=548]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (548 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1125  (0.0627475); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.44
# Mc/sec: 3744.00
//
Query:       gene2917|gene2917|rna2917|rna2917  [L=348]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (348 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1161  (0.0647554); expected 358.6 (0.02)
Passed bias filter:                      502  (0.0279993); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 2411.53
//
Query:       gene2918|gene2918|rna2918|rna2918  [L=533]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-14   53.8  18.8    2.9e-10   39.5   6.8    2.2  2  Sulfate_transp  Sulfate permease family


Domain annotation for each model (and alignments):
>> Sulfate_transp  Sulfate permease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   4.1   1.2e-08   0.00021       8     125 ..      16     154 ..      10     159 .. 0.84
   2 !   39.5   6.8   1.6e-14   2.9e-10     155     378 ..     166     393 ..     159     395 .. 0.76

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 1.2e-08
                     Sulfate_transp   8 GitvallaiPqalayal.lagl.ppiygL...........yssvvpqlvyalfGtsrqlavGpvavlsl.ivgeii 69 
                                        ++++ ++++ + l+y+  +++  +p+ ++           ys++ +ql++  f      ++ +v v+sl  + e +
  gene2918|gene2918|rna2918|rna2918  16 SLMAIIFQLMDMLSYGRaMFKSdDPEQNIivqnigmlcyiYSTIWSQLLFNYFSKIDAAIISSVIVESLpFMEENV 91 
                                        6778889999999999877777889999888999999999***********************9999884455566 PP

                     Sulfate_transp  70 akvaeee.......pekgieiattltllaGviqvllGllRLgflveflseavlsGfiaGaaiv 125
                                         k+++++         + i+i+++ ++  G++++ll   R g l++++++av+ G++++++++
  gene2918|gene2918|rna2918|rna2918  92 GKIINKHtsglngyITNFIAILLICSVGFGIVSLLLKYGRAGHLISLIPKAVVNGCLGAIGLT 154
                                        6663333345555589999*****************************************986 PP

  == domain 2  score: 39.5 bits;  conditional E-value: 1.6e-14
                     Sulfate_transp 155 tnlekvnlakvvlgllllvvLlvtkellkklkkllvipapaelvavivatlvsaif......elkreagvkivgei 224
                                        + +ek  ++ + +++ + v+L++ +  l      ++ip  + +++ +++ ++ +++      +++r +++  ++e 
  gene2918|gene2918|rna2918|rna2918 166 KGYEKKYWLLCTIAIAVAVILFILQFKL--AGADFLIPLYTLIIITLFYGIAFIFVgasdrmQYLRDNNWLPIKEA 239
                                        5666655555556666666666666533..3456899999888888888888888899999999999999999999 PP

                     Sulfate_transp 225 psglpelslpkvdwsll..sallpdalaialvglleaiavsksldk...kkgykvdsnkELvAlGfsNilsslfgg 295
                                        +  +p+  l ++d s+l  ++ + + + i  v +++++ ++  l +    +g + d   EL  +GfsN++      
  gene2918|gene2918|rna2918|rna2918 240 KILYPNYVLSRIDLSTLnwRSFVYNFFNILTVIFFNSVHIAVNLPAykiSTGVNFDFSDELGTQGFSNLF----TF 311
                                        9999999999666666422577777777777777776666666544223679999*************65....55 PP

                     Sulfate_transp 296 lpatgafsrsavnikaGaktqlsglvsalvvllvllvltplleyiPkavLaaiiivagkglLvelkelkklwklsk 371
                                        +p + +   s  ++kaG+  ++ g vsal+ +l+ +++  +  y+P+ vL+ + +v+g g L + +    +  +s 
  gene2918|gene2918|rna2918|rna2918 312 IPCYFVACYSIAFYKAGGTLKIYGYVSALAMILIAVFGLTIKGYVPNFVLSMLPFVMGAGFLYS-SFYEPIFTTSI 386
                                        666677789***************************************************9987.44444455677 PP

                     Sulfate_transp 372 ldflill 378
                                        +++ i +
  gene2918|gene2918|rna2918|rna2918 387 YEYSISV 393
                                        7776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (533 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1054  (0.0587874); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.62u 0.27s 00:00:00.89 Elapsed: 00:00:00.43
# Mc/sec: 3756.11
//
Query:       gene2919|gene2919|rna2919|rna2919  [L=278]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.2e-48  163.2   0.4    6.5e-23   81.5   0.1    2.0  2  ParA             NUBPL iron-transfer P-loop NTPase
    8.9e-09   35.5   0.4    2.2e-08   34.2   0.4    1.8  1  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
    4.5e-07   29.4   2.1    2.8e-06   26.7   0.5    2.4  2  ArsA_ATPase      Anion-transporting ATPase
    1.5e-06   28.3   4.7    2.1e-05   24.5   4.7    2.5  1  AAA_31           AAA domain
  ------ inclusion threshold ------
      0.013   15.7   1.0      0.028   14.5   0.3    1.8  2  DUF87            Helicase HerA, central domain
      0.029   13.6   0.3      0.057   12.6   0.1    1.6  2  NB-ARC           NB-ARC domain
      0.042   14.4   0.4      0.098   13.2   0.4    1.7  1  ABC_tran         ABC transporter
      0.048   14.0   0.0      0.075   13.4   0.0    1.3  1  AAA_16           AAA ATPase domain
      0.049   13.3   0.2        1.7    8.3   0.0    2.2  2  Thymidylate_kin  Thymidylate kinase
      0.061   13.1   0.9        1.2    8.9   0.0    2.2  2  AAA_26           AAA domain
      0.078   12.3   0.1       0.37   10.1   0.0    1.9  2  MipZ             ATPase MipZ
        0.1   13.1   0.5       0.37   11.3   0.5    2.0  1  AAA_18           AAA domain
       0.13   11.7   0.2        6.8    6.1   0.1    2.2  2  CBP_BcsQ         Cellulose biosynthesis protein BcsQ
       0.19   11.3   0.2       0.36   10.4   0.1    1.5  2  AAA_25           AAA domain
       0.19   11.0   0.0       0.41    9.9   0.0    1.4  1  Zeta_toxin       Zeta toxin


Domain annotation for each model (and alignments):
>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.5   0.1   5.4e-26   6.5e-23       5     106 ..       4     104 ..       2     110 .. 0.89
   2 !   80.2   0.0   1.3e-25   1.6e-22     114     242 ..     151     272 ..     141     276 .. 0.85

  Alignments for each domain:
  == domain 1  score: 81.5 bits;  conditional E-value: 5.4e-26
                               ParA   5 viavlSgKGGVGKStvavnlAlaLakkglkvgllDaDiyGpsiprllgveeekpeqsekkliPvea..kgikvmSi 78 
                                        +i v+SgKGGVGKSt+a+ +A++L+k+ + + llD Di+Gpsi +++ ++++ + +++++l P+++  +++ ++S+
  gene2919|gene2919|rna2919|rna2919   4 FISVVSGKGGVGKSTIAALIAAKLSKQ-APTLLLDFDICGPSIGNIFPASGK-VVKTRTGLKPLQVnnSSLYILSM 77 
                                        589*********************876.5677*******************7.5666669***9987688****** PP

                               ParA  79 gfllesedeavvwrGpmkskaikqllkd 106
                                          l++ +d++v+wr+p k ++ + ++++
  gene2919|gene2919|rna2919|rna2919  78 SSLIK-NDSSVIWRAPRKLQLYEMFYNS 104
                                        ****9.************9999988765 PP

  == domain 2  score: 80.2 bits;  conditional E-value: 1.3e-25
                               ParA 114 yLiiDlPPGtgDeqltvaqklplagaviVttpqevaladvkkaiemfkkvkvkvlGvveNmsgfvcpkcgekteif 189
                                        y++iD+PPG + ++  + +k   +++++Vtt q+va++d   +i++f k    + G++eNmsg++cp+c++ t+i+
  gene2919|gene2919|rna2919|rna2919 151 YVVIDTPPGITIVHSFIKEK--NTKILLVTTSQNVAISDSINTINFFGK----ISGIIENMSGLKCPNCKKITNIY 220
                                        99*******87777555554..589**********************97....67********************* PP

                               ParA 190 gkgggeklaeelgvpllgeipldpeireasdegkplvlkepeseaakaleeia 242
                                        +++gg++laee+++p+ g++ +d++i++ +++g+ l+++ ++   +++l++++
  gene2919|gene2919|rna2919|rna2919 221 SRNGGSQLAEEFNIPFYGTLEIDQNISQFIENGT-LYENINSLGCNNVLDTVV 272
                                        *********************************9.344444444555555555 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.2   0.4   1.8e-11   2.2e-08       1      55 [.       5     172 ..       5     256 .. 0.64

  Alignments for each domain:
  == domain 1  score: 34.2 bits;  conditional E-value: 1.8e-11
                                        EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH...................... CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...................... RF
                               CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep...................... 54 
                                        i+++s+kGGvGK+t+aa +a+ l++ +  +ll+D+D  +++   ++  ++++ +                      
  gene2919|gene2919|rna2919|rna2919   5 ISVVSGKGGVGKSTIAALIAAKLSK-QAPTLLLDFDICGPSIGNIFPASGKVVKtrtglkplqvnnsslyilsmss 79 
                                        789**********************.**********9998866544444444444446666666666666666666 PP

                                        ............................................................................ CS
                                        ............................................................................ RF
                               CbiA  55 ............................................................................ 54 
                                                                                                                    
  gene2919|gene2919|rna2919|rna2919  80 likndssviwraprklqlyemfynsayenilqnttesdpdsydildkhnnignktaqknvtvdescqlgykyvvid 155
                                        6666666666666666666666666666666666666666666666666666665555555555555555555555 PP

                                        ................C CS
                                        ................x RF
                               CbiA  55 ................d 55 
                                                        +
  gene2919|gene2919|rna2919|rna2919 156 tppgitivhsfikeknT 172
                                        55555555555555550 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.7   0.5   2.4e-09   2.8e-06       5      59 ..       7      63 ..       3     163 .. 0.53
   2 ?    1.2   0.0      0.14   1.7e+02      27      62 ..     169     205 ..     163     231 .. 0.79

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 2.4e-09
                                       EEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-S.TTTHHHHHHTS..--BSS-EEET CS
                        ArsA_ATPase  5 lvgGKGGVGKttvsaatavklsekgkkvllistD.PAhslsDsfdq..klgkeptkvk 59
                                       +v+GKGGVGK+t++a +a+kls++   +ll+  D   +s+  +f    k+ k+ t +k
  gene2919|gene2919|rna2919|rna2919  7 VVSGKGGVGKSTIAALIAAKLSKQA-PTLLLDFDiCGPSIGNIFPAsgKVVKTRTGLK 63
                                       69********************986.56777777345788888866443334333333 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.14
                                        HTTS-EEEEE-STTTHHHHHHTS.--BSS-EEETSSE CS
                        ArsA_ATPase  27 ekgkkvllistDPAhslsDsfdq.klgkeptkvkeNL 62 
                                        ek+ k+ll++t     +sDs ++ ++  +   + eN+
  gene2919|gene2919|rna2919|rna2919 169 EKNTKILLVTTSQNVAISDSINTiNFFGKISGIIENM 205
                                        7899999999999999999999755555555555555 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   4.7   1.7e-08   2.1e-05       3     155 ..       4     186 ..       2     205 .. 0.59

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 1.7e-08
                             AAA_31   3 vIaianqKGGvGKTTtsvnlaaalaklgkkvLlvDlDpQanatt...........................glgie 51 
                                         I+++  KGGvGK+T +  +aa l+k+   +Ll D+D  + +                                  
  gene2919|gene2919|rna2919|rna2919   4 FISVVSGKGGVGKSTIAALIAAKLSKQA-PTLLLDFDICGPSIGnifpasgkvvktrtglkplqvnnsslyI---- 74 
                                        69**********************9875.68999***98876555666666666654433332222222220.... PP

                             AAA_31  52 kneiektlyev..............li.eeknikeaiiktkvenl.....dlipssidLaeaeielvelekkeeil 107
                                                  +               + ++ ++ e+ +++ +en+     +  p s d+ + ++++ +++ ++++ 
  gene2919|gene2919|rna2919|rna2919  75 ----------LsmsslikndssviwRApRKLQLYEMFYNSAYENIlqnttESDPDSYDILDKHNNIGNKTAQKNV- 139
                                        ..........23233333344333212244444444444444444331113335555566666666555555555. PP

                             AAA_31 108 kellekvkdeYDyiiiDcpPsLglltenaLvasdsviipvqaeayale 155
                                         ++ e+ +  Y y++iD+pP + ++   +     +++ ++ +++ a++
  gene2919|gene2919|rna2919|rna2919 140 -TVDESCQLGYKYVVIDTPPGITIVHSFIKEKNTKILLVTTSQNVAIS 186
                                        .344677888***********999877666666666666666666655 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.3   2.4e-05     0.028      28      60 ..       8      38 ..       6      39 .. 0.92
   2 ?   -1.6   0.0         2   2.3e+03     173     193 ..     107     127 ..      61     155 .. 0.57

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.4e-05
                              DUF87 28 ilgsTGsGKSntvavLleellekkgatililDp 60
                                       + g+ G+GKS+ +a++ ++l   k+a++l+lD 
  gene2919|gene2919|rna2919|rna2919  8 VSGKGGVGKSTIAALIAAKLS--KQAPTLLLDF 38
                                       66999****************..99******96 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2
                              DUF87 173 edllrkggsfsnsstdliall 193
                                        e++l+++ + + +s+d++++ 
  gene2919|gene2919|rna2919|rna2919 107 ENILQNTTESDPDSYDILDKH 127
                                        222222222223333333333 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   4.8e-05     0.057      21      45 ..       4      28 ..       1      37 [. 0.84
   2 ?   -3.3   0.0       3.3     4e+03     129     144 ..     169     184 ..     162     194 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.8e-05
                                       EEEEEEESTTSSHHHHHHHHCCSHC CS
                             NB-ARC 21 lvvalvGmgGvGKttlakqilnksd 45
                                       ++  ++G+gGvGK+t+a+ i  k++
  gene2919|gene2919|rna2919|rna2919  4 FISVVSGKGGVGKSTIAALIAAKLS 28
                                       556689************9988855 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 3.3
                                        HTTSEEEEEESBCCCC CS
                             NB-ARC 129 enrlrvllTTRdeeva 144
                                        e+  ++ll T +++va
  gene2919|gene2919|rna2919|rna2919 169 EKNTKILLVTTSQNVA 184
                                        5556666666666665 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.4   8.2e-05     0.098      16      45 ..       8      37 ..       5     149 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 8.2e-05
                                       EEESTTSSHHHHHHHHTTSS--SEEEEEET CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ABC_tran 16 ivGenGaGKStLlkllagllkpteGeilld 45
                                       + G+ G GKSt+++l+a +l++++ ++lld
  gene2919|gene2919|rna2919|rna2919  8 VSGKGGVGKSTIAALIAAKLSKQAPTLLLD 37
                                       679******************999998665 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   6.3e-05     0.075      28      63 ..       7      41 ..       5      73 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 6.3e-05
                             AAA_16 28 llsGesGvGKsslvrellralekdggiflrgkcdql 63
                                       ++sG  GvGKs+++  ++  l+k+ + +l  ++d +
  gene2919|gene2919|rna2919|rna2919  7 VVSGKGGVGKSTIAALIAAKLSKQ-APTLLLDFDIC 41
                                       79********************99.44455555544 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.0    0.0014       1.7       3      32 ..      10      39 ..       8      63 .. 0.81
   2 ?    2.9   0.0     0.064        76       9      44 ..     133     169 ..     130     186 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0014
                                       ESTTSSHHHHHHHHHHHHHHTTE.EEEESS CS
                    Thymidylate_kin  3 GlDGaGKttqaellkerlkeegikvvltre 32
                                       G  G+GK+t+a+l++++l++++   +l + 
  gene2919|gene2919|rna2919|rna2919 10 GKGGVGKSTIAALIAAKLSKQAPTLLLDFD 39
                                       6679***************99866666665 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.064
                                        HHHHHHHHHHHHHHTTE..EEEESSSTTSHHHHHHHH CS
                    Thymidylate_kin   9 Kttqaellkerlkeegik.vvltrepggteiGekire 44 
                                        Kt q +  ++  ++ g+k vv+  +pg t + + i+e
  gene2919|gene2919|rna2919|rna2919 133 KTAQKNVTVDESCQLGYKyVVIDTPPGITIVHSFIKE 169
                                        999************************9998877776 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.3     0.068        81       5      28 ..       7      30 ..       4      34 .. 0.83
   2 ?    8.9   0.0     0.001       1.2     121     190 ..     164     242 ..     106     248 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.068
                             AAA_26  5 vtgtdtgvGKTvvslgLvralkrk 28
                                       v++   gvGK++++++++++l+++
  gene2919|gene2919|rna2919|rna2919  7 VVSGKGGVGKSTIAALIAAKLSKQ 30
                                       6777789***********999765 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.001
                             AAA_26 121 adiaknlgapvilVargglgtinqllltiealrqknvrvlGvilNk....vrnpe.........nvetlekksgip 183
                                          ++k+ + +++lV+++++ +i + + ti+++ +    + G+i N     ++n +            +l + ++ip
  gene2919|gene2919|rna2919|rna2919 164 HSFIKEKNTKILLVTTSQNVAISDSINTINFFGK----ISGIIENMsglkCPNCKkitniysrnGGSQLAEEFNIP 235
                                        5689999*************************99....99999886333334443222333333444455555577 PP

                             AAA_26 184 vlGvvPy 190
                                         +G+++ 
  gene2919|gene2919|rna2919|rna2919 236 FYGTLEI 242
                                        7777665 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00031      0.37       3      30 ..       5      32 ..       3      85 .. 0.81
   2 ?    0.1   0.0      0.34   4.1e+02      92     112 ..     141     161 ..     109     199 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00031
                                       EEE--SSTTSSHHHHHHHHHHHHHTTT- CS
                               MipZ  3 ivlgnekGGsGksttavhvavaLlkkGa 30
                                       i +   kGG Gkst+a  +a  L+k+  
  gene2919|gene2919|rna2919|rna2919  5 ISVVSGKGGVGKSTIAALIAAKLSKQAP 32
                                       667778***********99999988754 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.34
                                        HHHHHHHH-SEEEEE--SS-- CS
                               MipZ  92 lvadleaeldfividtPGsds 112
                                        + ++ +  + ++vidtP   +
  gene2919|gene2919|rna2919|rna2919 141 VDESCQLGYKYVVIDTPPGIT 161
                                        33445667899****996544 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.5   0.00031      0.37       3      25 ..       8      67 ..       7     163 .. 0.57

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00031
                             AAA_18  3 ltGtpGvGKttlakeLskrl.gf....................................g 25
                                       ++G+ GvGK+t+a  ++ +l +                                     +
  gene2919|gene2919|rna2919|rna2919  8 VSGKGGVGKSTIAALIAAKLsKQaptllldfdicgpsignifpasgkvvktrtglkplqV 67
                                       89**************99973225555555555555555555555555555555555551 PP

>> CBP_BcsQ  Cellulose biosynthesis protein BcsQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.1    0.0057       6.8       4      37 ..       5      37 ..       2      48 .. 0.76
   2 ?    3.4   0.0     0.039        46     113     150 ..     146     182 ..     123     189 .. 0.70

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0057
                           CBP_BcsQ  4 lalqGvRGGvGttsllaaLawalhelgesvlviD 37
                                       + +   +GGvG+++++a +a  l ++    l++D
  gene2919|gene2919|rna2919|rna2919  5 ISVVSGKGGVGKSTIAALIAAKLSKQAPT-LLLD 37
                                       5555558***************9887654.4444 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.039
                           CBP_BcsQ 113 keqyrwillDlpagasaltrellaladlvllvvepdan 150
                                        +  y+++++D p g + +++ + +  ++++l+v++ +n
  gene2919|gene2919|rna2919|rna2919 146 QLGYKYVVIDTPPGITIVHSFIKE-KNTKILLVTTSQN 182
                                        45799*********9877766666.5566655555555 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.1    0.0003      0.36      35      63 ..       5      33 ..       1      55 [. 0.86
   2 ?   -3.1   0.0         4   4.8e+03     139     150 ..     143     156 ..     116     156 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0003
                             AAA_25 35 lallaGapgtGKttlaldlalavatGkpw 63
                                       ++++ G +g+GK+t+a  +a+++++  p 
  gene2919|gene2919|rna2919|rna2919  5 ISVVSGKGGVGKSTIAALIAAKLSKQAPT 33
                                       67899***************999876665 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 4
                             AAA_25 139 eveg..vrlvviDp 150
                                        e ++  ++ vviD+
  gene2919|gene2919|rna2919|rna2919 143 ESCQlgYKYVVIDT 156
                                        33333389999997 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00034      0.41      20      52 ..       7      39 ..       4      41 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00034
                         Zeta_toxin 20 llgGqpGAGKselaellkdelerqgnvvrldpD 52
                                       +++G  G GKs++a+l++++l +q   + ld D
  gene2919|gene2919|rna2919|rna2919  7 VVSGKGGVGKSTIAALIAAKLSKQAPTLLLDFD 39
                                       799******************999998888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (278 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       687  (0.0383178); expected 358.6 (0.02)
Passed bias filter:                      511  (0.0285013); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 1791.81
//
Query:       gene292|gene292|rna292|rna292  [L=44]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.067   12.3   0.1      0.071   12.2   0.1    1.0  1  B277      Domain of unknown function


Domain annotation for each model (and alignments):
>> B277  Domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1     4e-06     0.071      94     133 ..       3      41 ..       1      43 [. 0.91

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 4e-06
                           B277  94 fsaehyvallqenqdglsilflrraklienqgylmlevkk 133
                                    +  ehy  ll  n+d  s lf+   k i +  y +  +kk
  gene292|gene292|rna292|rna292   3 YKNEHYQDLLT-NKDKHSFLFIYNGKYIGEASYNLCRIKK 41 
                                    5689**99985.89*********************99998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (44 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       352  (0.019633); expected 358.6 (0.02)
Passed bias filter:                      229  (0.0127726); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.29s 00:00:00.68 Elapsed: 00:00:00.45
# Mc/sec: 293.15
//
Query:       gene2920|gene2920|rna2920|rna2920  [L=543]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-10   40.9  20.2    5.2e-09   35.3  19.2    2.4  1  Sulfate_transp  Sulfate permease family
     0.0015   18.1   1.6      0.013   15.1   0.2    2.3  2  DUF998          Protein of unknown function (DUF998)
  ------ inclusion threshold ------
      0.042   14.2   0.6        5.6    7.4   0.0    2.7  2  DUF2484         Protein of unknown function (DUF2484)
        6.1    6.7   9.9         21    5.0   1.4    3.8  3  LapA_dom        Lipopolysaccharide assembly protein A domain


Domain annotation for each model (and alignments):
>> Sulfate_transp  Sulfate permease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.3  19.2   1.2e-12   5.2e-09       7     379 ..      33     408 ..      27     410 .. 0.70

  Alignments for each domain:
  == domain 1  score: 35.3 bits;  conditional E-value: 1.2e-12
                     Sulfate_transp   7 aGitvallaiPqalayal..laglppiygL.........yssvvpqlvyalfGtsrqlavGpvavlsl.ivgeiia 70 
                                         +i+v ++ + + l+y+   + + +  + +         y ++ + ++y +f t +  +v +  v+     +++ +
  gene2920|gene2920|rna2920|rna2920  33 CVIMVCIFELMDMLSYSGaiMENYNSSKDIdavcmilyiYPTISSMIFYNIFTTIPAGIVSSAIVENFrFFHKMSK 108
                                        56677777777777775531333344444455555577799*******************9999995523334444 PP

                     Sulfate_transp  71 kv..aeeepekgieiattltllaGviqvl....lGllRLgflveflseavlsGfiaGaaivillsqikvllglerv 140
                                        +v   ++++e  +  ++ l +++G+++++    +  lRLg+l+  +++av+ G  a ++i+ +   +++l+     
  gene2920|gene2920|rna2920|rna2920 109 NVrkNVDSEEALVTNSIFLFFVTGLLFAFssiiMMKLRLGRLILQIPKAVVYGIFATIGIIQIPVGLQELM----- 179
                                        4444447789999999999999999986522227789*******************999875555555554..... PP

                     Sulfate_transp 141 skkeslvsvlsslftnlekvnlakvvlgllllvvLlvtkellkklkkllvipapaelvavivatlvsaif...... 210
                                                     ++ +++ +l   +++  ++++++v +++  ++  +  +p  + + + +++ ++ + f      
  gene2920|gene2920|rna2920|rna2920 180 -------------PNGYNHEHLSMYIIAFAVVLIVFVLQKRYPNI--MYIMPLSMVVCMCLFYSFFIFQFkndliy 240
                                        .............33444445555666666666666666654433..12223333333333333333333333332 PP

                     Sulfate_transp 211 elkreagvki.....vgeipsglpelslpkvdwsllsallpdalaialvglleaiavsksldkkkgykvdsnkELv 281
                                        e +  +g+ +     v + ++ ++ ++l+ +++  l + l ++l++ ++ ll+ +    s+ +  + + d   EL 
  gene2920|gene2920|rna2920|rna2920 241 E-LILHGWLHerdnrVINPSMLFNMIELETLQFGFLLKNLRTVLVCVFFSLLHVTYNLPSYKMDLNIEFDYSAELG 315
                                        1.11122221333223255566******************************9777666666667*********** PP

                     Sulfate_transp 282 AlGfsNilsslfgglpatgafsrsavnikaGaktqlsglvsalvvllvllvltplleyiPkavLaaiiivagkglL 357
                                         +G++N++ ++++++ ++     s  ++++G+  ++ g++s+l++++v l++ ++  y+Pk  L    +++g+ ++
  gene2920|gene2920|rna2920|rna2920 316 TQGYTNLF-TFIPCYFISC---YSGPFYRSGGTKRIYGIISGLFLVFVALFGCSIRGYVPKFLLCMPPLLIGSTMI 387
                                        ******86.6888887765...57789*************************************998899999988 PP

                     Sulfate_transp 358 velkelkklwk.lskldflilla 379
                                         +  +l  +++ ++ ++ l++++
  gene2920|gene2920|rna2920|rna2920 388 YD--TLLTVISeTKVFEQLVVFV 408
                                        77..5555554477777777665 PP

>> DUF998  Protein of unknown function (DUF998)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.2   2.9e-06     0.013      44     152 ..     126     231 ..     117     241 .. 0.82
   2 ?    1.5   0.1     0.043   1.9e+02      77      98 ..     350     371 ..     309     390 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.9e-06
                             DUF998  44 aglvllgllvlalavgllraargragragrlllavaglglvlagvfptdpgggspslsglvHglasavaflalava 119
                                        + + ++gll+++ ++++++ + gr+    + +++ + +++++++  p +  + +p   ++ H    ++af+ +++ 
  gene2920|gene2920|rna2920|rna2920 126 FLFFVTGLLFAFSSIIMMKLRLGRLILQIPKAVVYGIFATIGIIQIPVGLQELMPNGYNHEHLSMYIIAFAVVLIV 201
                                        5689***************9**************99999****************555555555555555555555 PP

                             DUF998 120 vlllasaarrrawallrlvggvallllvaalvw 152
                                        ++l     r++   ++ +++ v+  +l+ +++ 
  gene2920|gene2920|rna2920|rna2920 202 FVLQK---RYPNIMYIMPLSMVVCMCLFYSFFI 231
                                        55555...9999999999999999888887765 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.043
                             DUF998  77 avaglglvlagvfptdpgggsp 98 
                                        +++gl+lv++++f ++++g  p
  gene2920|gene2920|rna2920|rna2920 350 IISGLFLVFVALFGCSIRGYVP 371
                                        5789999999999988887655 PP

>> DUF2484  Protein of unknown function (DUF2484)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.2     0.013        59      22      50 ..     180     209 ..     175     227 .. 0.76
   2 ?    7.4   0.0    0.0012       5.6      32      69 ..     403     442 ..     397     448 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.013
                            DUF2484  22 plR.whwsaaivLialgipllgyvtyehGP 50 
                                        p   +h    + +ia++++l+ +v  +  P
  gene2920|gene2920|rna2920|rna2920 180 PNGyNHEHLSMYIIAFAVVLIVFVLQKRYP 209
                                        5554677778899**********9876655 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0012
                            DUF2484  32 vLialgipllgyvt..yehGPwwgllvllaglSvlrwPli 69 
                                         L+++ i l+ y+t  y  G + g+l+ la+  +l++  i
  gene2920|gene2920|rna2920|rna2920 403 QLVVFVISLISYLTedYFLGVVTGILIHLAFYFMLKRRAI 442
                                        699***********55558*************99998766 PP

>> LapA_dom  Lipopolysaccharide assembly protein A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   1.4    0.0048        21      23      48 ..     125     150 ..     119     160 .. 0.78
   2 ?   -0.9   1.0      0.33   1.5e+03      17      32 ..     215     230 ..     196     233 .. 0.82
   3 ?    4.7   0.0    0.0061        27      28      56 ..     420     448 ..     406     454 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.0048
                           LapA_dom  23 llvafgiGallgwllslwsylrlrre 48 
                                        ++++f+ G+l+++   ++++lrl r 
  gene2920|gene2920|rna2920|rna2920 125 IFLFFVTGLLFAFSSIIMMKLRLGRL 150
                                        67788888888888888888887665 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.33
                           LapA_dom  17 lpLsllllvafgiGal 32 
                                        +pLs+++ ++++  ++
  gene2920|gene2920|rna2920|rna2920 215 MPLSMVVCMCLFYSFF 230
                                        8999999999987665 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.0061
                           LapA_dom  28 giGallgwllslwsylrlrrelrrlkkki 56 
                                        ++G++ g+l+ l +y+ l+r++ + ++++
  gene2920|gene2920|rna2920|rna2920 420 FLGVVTGILIHLAFYFMLKRRAISNEQRV 448
                                        79**********99998777776666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (543 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       876  (0.0488594); expected 358.6 (0.02)
Passed bias filter:                      256  (0.0142785); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.41
# Mc/sec: 3963.97
//
Query:       gene2921|gene2921|rna2921|rna2921  [L=96]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.014   14.9   0.1      0.021   14.3   0.1    1.3  1  RVT_1     Reverse transcriptase (RNA-dependent DNA polymerase


Domain annotation for each model (and alignments):
>> RVT_1  Reverse transcriptase (RNA-dependent DNA polymerase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1   1.2e-06     0.021       3      89 ..      36      95 ..      33      96 .] 0.68

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.2e-06
                                       -TT.S-EEE......-THHHHCTB--.........-------HHHH.............HCCHTS--EEEEEEBCCGC CS
                              RVT_1  3 KkgpgsyRpisllsvdykalnkliakrLkdvlekllsenqpgfrpgrstldavedllkalkkkkkaklllklDlkkaF 80
                                       Kk+ g++R++     +  +ln++++k         + ++  ++++                + +++k+++k+Dl +++
  gene2921|gene2921|rna2921|rna2921 36 KKN-GDVRLV----NNHIDLNNITKK---------DGHPCANMQDL-------------KLDLRGCKYFSKIDLNNGY 86
                                       555.555555....444455555555.........55555555555.............4478*************** PP

                                       CCSBB-GGG CS
                              RVT_1 81 dsvpleell 89
                                        +++ ++ +
  gene2921|gene2921|rna2921|rna2921 87 YQIEIAKKD 95
                                       ***998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       478  (0.0266607); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 716.97
//
Query:       gene2922|gene2922|rna2922|rna2922  [L=55]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      9e-09   35.2   0.2      9e-09   35.2   0.2    1.0  1  RVT_1     Reverse transcriptase (RNA-dependent DNA polymerase


Domain annotation for each model (and alignments):
>> RVT_1  Reverse transcriptase (RNA-dependent DNA polymerase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.2   0.2     5e-13     9e-09     161     206 ..      10      55 .]       1      55 [] 0.92

  Alignments for each domain:
  == domain 1  score: 35.2 bits;  conditional E-value: 5e-13
                                        .TEEECTTEEEEEESSHHHHHHHHHHHHHHHHHTT--BEGGG-EEE CS
                              RVT_1 161 vtllrYaDDililskskeelqelleaveewlkesglkinpeKtklv 206
                                        +++++Y DDi+i++ + ee++++le+v +++k+ +++in +K +++
  gene2922|gene2922|rna2922|rna2922  10 INVAAYLDDIIIFTLDAEEHKTVLEKVLQRFKQLNITINFDKLTFF 55 
                                        7899**************************************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (55 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       865  (0.0482459); expected 358.6 (0.02)
Passed bias filter:                      558  (0.0311228); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.31s 00:00:00.73 Elapsed: 00:00:00.48
# Mc/sec: 347.18
//
Query:       gene2923|gene2923|rna2923|rna2923  [L=47]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (47 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       725  (0.0404373); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.33u 0.28s 00:00:00.61 Elapsed: 00:00:00.41
# Mc/sec: 342.64
//
Query:       gene2924|gene2924|rna2924|rna2924  [L=53]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (53 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       192  (0.0107089); expected 358.6 (0.02)
Passed bias filter:                      166  (0.00925874); expected 358.6 (0.02)
Passed Vit filter:                         6  (0.000334653); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.42
# Mc/sec: 380.50
//
Query:       gene2925|gene2925|rna2925|rna2925  [L=326]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.17   11.5   7.4        1.7    8.3   0.2    2.6  2  CAP_C     Adenylate cyclase associated (CAP) C terminal


Domain annotation for each model (and alignments):
>> CAP_C  Adenylate cyclase associated (CAP) C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.2   9.4e-05       1.7      35      54 ..      87     106 ..      72     165 .. 0.78
   2 ?    5.2   2.7   0.00083        15      28      81 ..     210     264 ..     189     309 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 9.4e-05
                              CAP_C  35 yifkCknstiqikgKvnait 54 
                                        ++ +C++sti++k+K+ +i 
  gene2925|gene2925|rna2925|rna2925  87 LVLHCNDSTIEVKNKLPSIL 106
                                        6889***********98885 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.00083
                              CAP_C  28 telkqsvyifkCknstiqikgKvnaitldnck.kvsvvvdsvvSsvevincksvk 81 
                                        +++ q  ++   +nsti+i+     +++ nck  vs+   + + ++e+ nck++ 
  gene2925|gene2925|rna2925|rna2925 210 IKKLQLENVTCASNSTITISRDSLCLSILNCKcGVSLAESKFIEKLELANCKKIV 264
                                        5555666788899******************8558888899***********984 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (326 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       693  (0.0386525); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 2268.08
//
Query:       gene2926|gene2926|rna2926|rna2926  [L=249]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.014   14.2   0.3       0.02   13.7   0.3    1.2  1  p450       Cytochrome P450
      0.025   15.1   2.2      0.055   14.0   2.2    1.6  1  zf-CCCH_2  RNA-binding, Nab2-type zinc finger
       0.08   13.2   0.4          1    9.7   0.0    2.6  3  DUF3979    Protein of unknown function (DUF3979)
       0.69   10.0   4.7       0.81    9.8   1.0    2.4  2  zf_CCCH_4  Zinc finger domain


Domain annotation for each model (and alignments):
>> p450  Cytochrome P450
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.3   4.5e-06      0.02      23     135 ..     145     248 ..     134     249 .] 0.78

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.5e-06
                                        HHHHHHHHHHH-SEEEEEETTEEEEEEESHHHHHHHHCTSTTTTCEESSHHHHHHHHHTTTTSSSTTCGHHHHHHH CS
                               p450  23 hevlrklqkkygpifrlklgskpvvvlsgpeavkevlikkgeefsgrpdeallatsrkpfkgkgvlfangekwkkl 98 
                                        h  l+k++k+yg++f++k+ +++ +++  +++v+++l+  + + +        +  +k+f+ + v +++    +++
  gene2926|gene2926|rna2926|rna2926 145 HV-LEKYAKEYGNVFSIKMLNQQKFLVK-YDSVQSALQCIN-DQAP---VLGNKEIKKFFNRRRVDVKD--LFREH 212
                                        55.99*****************998887.********9885.3333...33333335588888888887..88888 PP

                                        HHHHHHHHTSHSTTTHHHHHHHHHHHHHHHHHCCCCH CS
                               p450  99 Rrfltptltsfgklsleelveeeaedlveklrkkage 135
                                          +l++ + ++  +++  +++ ++++  e+l+ ++++
  gene2926|gene2926|rna2926|rna2926 213 DELLIALFAKG-EKKFAMRLKNVSNRIKEALENSRKQ 248
                                        88888888888.5578888899888888888877765 PP

>> zf-CCCH_2  RNA-binding, Nab2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   2.2   1.2e-05     0.055       2      17 ..     110     126 ..     110     126 .. 0.97

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.2e-05
                          zf-CCCH_2   2 CrffpnCtnp.kCpFaH 17 
                                        Cr+++ C n  +C F+H
  gene2926|gene2926|rna2926|rna2926 110 CRDGNRCQNLkNCIFIH 126
                                        *******9999****** PP

>> DUF3979  Protein of unknown function (DUF3979)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.21   9.5e+02      16      49 ..      50      87 ..      33      99 .. 0.72
   2 ?   -1.0   0.0      0.44     2e+03      52      81 ..     148     180 ..     111     192 .. 0.60
   3 ?    9.7   0.0   0.00022         1      28      69 ..     194     235 ..     181     247 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.21
                            DUF3979 16 kyiiqerngkys....ivdelatekmsvelyfneydel 49
                                        +i++e   +y+    +++ l t+++  +ly   ++el
  gene2926|gene2926|rna2926|rna2926 50 NFIMEETGKHYEkvlpVIERLCTDHVGTDLYERLNNEL 87
                                       46666666667633335688889999999987777776 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.44
                            DUF3979  52 tly.keeepivtvqriaiskvel..eedeesiq 81 
                                        + y ke  ++++++ ++ +k  +  +  ++++q
  gene2926|gene2926|rna2926|rna2926 148 EKYaKEYGNVFSIKMLNQQKFLVkyDSVQSALQ 180
                                        344134456777777777776553344444555 PP

  == domain 3  score: 9.7 bits;  conditional E-value: 0.00022
                            DUF3979  28 ivdelatekmsvelyfneydelritlykeeepivtvqriais 69 
                                        i + +++ ++ v+  f e+del i l+ ++e++++++  ++s
  gene2926|gene2926|rna2926|rna2926 194 IKKFFNRRRVDVKDLFREHDELLIALFAKGEKKFAMRLKNVS 235
                                        555666777889999*******************99876665 PP

>> zf_CCCH_4  Zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   1.0   0.00018      0.81       3      17 ..     104     118 ..     103     119 .. 0.91
   2 ?    1.2   0.1     0.091   4.1e+02      14      19 .]     121     126 ..     120     126 .. 0.93

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00018
                          zf_CCCH_4   3 fflqGtCkkGdkCrF 17 
                                        f+++ +C+ G++C+ 
  gene2926|gene2926|rna2926|rna2926 104 FYKKRSCRDGNRCQN 118
                                        8999*********85 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.091
                          zf_CCCH_4  14 kCrFaH 19 
                                        +C F+H
  gene2926|gene2926|rna2926|rna2926 121 NCIFIH 126
                                        8****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       878  (0.0489709); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 1856.74
//
Query:       gene2927|gene2927|rna2927|rna2927  [L=81]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0046   17.0   7.5     0.0099   15.9   7.5    1.6  1  VPR              VPR/VPX protein
     0.0091   15.1   1.8     0.0099   15.0   1.8    1.1  1  WASH-7_mid       WASH complex subunit 7
  ------ inclusion threshold ------
      0.013   15.3   4.9      0.013   15.3   4.9    1.0  1  DUF445           Protein of unknown function (DUF445)
      0.022   15.0   0.6      0.026   14.8   0.6    1.0  1  D5_N             D5 N terminal like
       0.11   12.9  13.4       0.91   10.0   6.9    2.1  2  CelTOS           Cell-traversal protein for ookinetes and spo
       0.13   11.6   5.3       0.14   11.5   5.3    1.0  1  CorA             CorA-like Mg2+ transporter protein
       0.13   12.6   2.3        0.3   11.5   2.2    1.6  1  DUF3510          Domain of unknown function (DUF3510)
       0.25   11.9   6.0       0.78   10.3   6.0    1.8  1  YtxH             YtxH-like protein
       0.27   12.3   2.8        4.3    8.4   2.8    2.1  1  HK97-gp10_like   Bacteriophage HK97-gp10, putative tail-compo
       0.35   11.5   3.9       0.74   10.5   3.9    1.6  1  QIL1             MICOS complex subunit MIC13, QIL1
        0.6   10.0   4.9        3.8    7.4   4.8    2.0  1  DrrA_P4M         DrrA phosphatidylinositol 4-phosphate bindin
       0.62    9.3   2.5       0.69    9.1   2.5    1.1  1  Hydantoinase_A   Hydantoinase/oxoprolinase
        0.8    9.8  12.7         20    5.3  12.7    2.0  1  pP_pnuc_2        Predicted pPIWI-associating nuclease
          1    9.3   2.7        2.2    8.2   2.7    1.7  1  RNA_pol_Rpb1_4   RNA polymerase Rpb1, domain 4
          1    9.1   8.9    2.3e+02    1.4   8.9    2.2  1  GARS_A           Phosphoribosylglycinamide synthetase, ATP-gr
        1.1    9.6   4.7        2.5    8.5   4.7    1.8  1  Dynein_light     Dynein light chain type 1
        1.1    9.5   4.5        2.6    8.3   4.5    1.8  1  Tctex-1          Tctex-1 family
        1.3    8.5   6.6        1.5    8.3   6.6    1.2  1  DUF2587          Protein of unknown function (DUF2587)
        1.4    9.2   4.0    1.5e+02    2.7   4.0    3.1  1  Mpv17_PMP22      Mpv17 / PMP22 family
        1.7    8.9  10.3         90    3.4  10.3    2.2  1  Bac_DNA_binding  Bacterial DNA-binding protein
        1.8    8.6  11.6        2.8    8.0  11.6    1.4  1  YpjP             YpjP-like protein
        2.1    8.8  13.5         15    6.0  12.4    2.4  1  EnY2             Transcription factor e(y)2
        3.9    8.0   9.7      1e+02    3.5   9.7    2.2  1  TFIID_20kDa      Transcription initiation factor TFIID subuni
        5.3    6.5  12.7         12    5.4  12.7    1.6  1  DUF1002          Protein of unknown function (DUF1002)


Domain annotation for each model (and alignments):
>> VPR  VPR/VPX protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   7.5   1.3e-05    0.0099       8      61 ..       2      55 ..       1      74 [. 0.85

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.3e-05
                                VPR  8 nsieepqrEpfdeWleetleeikeeAvkHfprelliavwnyiyeetgdeqeasi 61
                                       ns++e ++E  +e +ee++eeikee v+    e++ ++ + i+ee ++e    i
  gene2927|gene2927|rna2927|rna2927  2 NSGKESIEEIVEEIVEEIVEEIKEEIVEEIKEEIVEEIKEEIVEEIKEEIVEEI 55
                                       6889999**************************************988765533 PP

>> WASH-7_mid  WASH complex subunit 7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   1.8   1.3e-05    0.0099      24      90 ..       6      72 ..       1      80 [. 0.76

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.3e-05
                         WASH-7_mid 24 srleyllsalsdcvsllkkakhlesaekkllesyekeiekalkeelleplckeiEtdLRlqvhshlk 90
                                       +++e +++++ + +    k + +e+++++++e++++ei +++kee++e++ +ei ++ Rl  ++ l 
  gene2927|gene2927|rna2927|rna2927  6 ESIEEIVEEIVEEIVEEIKEEIVEEIKEEIVEEIKEEIVEEIKEEIVEEIVEEIVESPRLVLYQDLL 72
                                       56666666655444444455578888888************************99999998887754 PP

>> DUF445  Protein of unknown function (DUF445)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   4.9   1.8e-05     0.013      82     320 ..       5      58 ..       1      78 [. 0.50

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.8e-05
                             DUF445  82 keslaaiveellkeiledlddesikellkknlkkkleevipepllgkllellleeerhkkllddlldriknllkde 157
                                        kes+++ivee+++ei+e+ ++e+i e++k+ + + ++e i e+++++++e+++e                      
  gene2927|gene2927|rna2927|rna2927   5 KESIEEIVEEIVEEIVEE-IKEEIVEEIKEEIVEEIKEEIVEEIKEEIVEEIVE---------------------- 57 
                                        445555555555555555.23333333444444444444444444444444443...................... PP

                             DUF445 158 evkekikelidelieeesgklvlesivsmflreltsilekvksdpdhllreeedkkvreliadllndpelaakvek 233
                                                                                                                    
  gene2927|gene2927|rna2927|rna2927   - ----------------------------------------------------------------------------   -
                                        ............................................................................ PP

                             DUF445 234 lkkkklsdlevqeyeealwealkdlllkdlneeesllrerisklleklgeklaedpklreklnkflenaaakvlek 309
                                                                                                                    
  gene2927|gene2927|rna2927|rna2927   - ----------------------------------------------------------------------------   -
                                        ............................................................................ PP

                             DUF445 310 yrldiskivee 320
                                                  e
  gene2927|gene2927|rna2927|rna2927  58 ----------E 58 
                                        ..........3 PP

>> D5_N  D5 N terminal like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.6   3.5e-05     0.026      33      96 ..      10      73 ..       3      78 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3.5e-05
                               D5_N 33 e..keaireladkvaeaiaeeaeeaksalkalkkfakssrskkkvdnvlreaaelprldleideld 96
                                       e  +e++ e++++++e i+ee    +++ +++k +  ++ +   v+++++e+ e prl+l  d l+
  gene2927|gene2927|rna2927|rna2927 10 EivEEIVEEIVEEIKEEIVEEI--KEEIVEEIKEEIVEEIKEEIVEEIVEEIVESPRLVLYQDLLE 73
                                       1335566666666666666666..99999***********************99999988777666 PP

>> CelTOS  Cell-traversal protein for ookinetes and sporozoites
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   6.9    0.0012      0.91      11      46 ..       6      41 ..       2      44 .. 0.72
   2 ?    7.9   5.6    0.0053       3.9       7      41 ..      29      60 ..      25      80 .. 0.50

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0012
                             CelTOS 11 kslssklseiiradldskgdelvdliandlekelqk 46
                                       +s+++ ++ei+ + ++++ +e+v+ i +++++e+++
  gene2927|gene2927|rna2927|rna2927  6 ESIEEIVEEIVEEIVEEIKEEIVEEIKEEIVEEIKE 41
                                       566667777777888888888888888888887765 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0053
                             CelTOS  7 erlqkslssklseiiradldskgdelvdliandle 41
                                       e ++++++++++e   + ++++ +e+v+ i+++++
  gene2927|gene2927|rna2927|rna2927 29 EEIKEEIVEEIKE---EIVEEIKEEIVEEIVEEIV 60
                                       3334444444443...3334444444444444443 PP

>> CorA  CorA-like Mg2+ transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   5.3   0.00019      0.14     103     155 ..       3      57 ..       1      74 [. 0.80

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00019
                               CorA 103 gkpkspgellyrlldeivdrlf.ellekleeel.deledeledstkkeilrelaq 155
                                        ++++s +e+++++++eiv+++  e++e+++ee+ +e+ +e+ +++k+ei++e+++
  gene2927|gene2927|rna2927|rna2927   3 SGKESIEEIVEEIVEEIVEEIKeEIVEEIKEEIvEEIKEEIVEEIKEEIVEEIVE 57 
                                        578899**************9615679999986589*****99999999999887 PP

>> DUF3510  Domain of unknown function (DUF3510)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   2.2    0.0004       0.3      36      79 ..      16      56 ..       2      69 .. 0.54

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.0004
                            DUF3510 36 vseilkplktfkkesekklseevleewlaevleevtsrYletis 79
                                       v+ei++ +k+   e  ++++ee++ee+ +e++ee+ ++ +e+i 
  gene2927|gene2927|rna2927|rna2927 16 VEEIVEEIKE---EIVEEIKEEIVEEIKEEIVEEIKEEIVEEIV 56
                                       4444444444...3344455555555555555555554444433 PP

>> YtxH  YtxH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   6.0    0.0011      0.78      22      68 ..       3      53 ..       1      62 [. 0.48

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0011
                               YtxH 22 sGketRkdlkek.....addlkekakelleeakeka.kekaedlkekvkek.ad 68
                                       sGke  ++++e+     ++++ke +   +ee+ke   +e  e+++e++ke+ ++
  gene2927|gene2927|rna2927|rna2927  3 SGKESIEEIVEEiveeiVEEIKEEI---VEEIKEEIvEEIKEEIVEEIKEEiVE 53
                                       6777777777766444444444444...44444444433334444444444433 PP

>> HK97-gp10_like  Bacteriophage HK97-gp10, putative tail-component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   2.8    0.0058       4.3       7      31 ..      20      44 ..       1      64 [. 0.55

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0058
                     HK97-gp10_like  7 leklserevekaikkalkkaAkevl 31
                                       +e+++e++ve+++++++++  +e++
  gene2927|gene2927|rna2927|rna2927 20 VEEIKEEIVEEIKEEIVEEIKEEIV 44
                                       2333333333333444444444444 PP

>> QIL1  MICOS complex subunit MIC13, QIL1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   3.9   0.00099      0.74      14      53 ..      13      52 ..       2      66 .. 0.44

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00099
                               QIL1 14 eelykkakeyipPyvd.evkkklclevpklpsveevkfslv 53
                                       ee+ +++ e+i++ +  e+k++++ e +k++ vee+k+++v
  gene2927|gene2927|rna2927|rna2927 13 EEIVEEIVEEIKEEIVeEIKEEIVEE-IKEEIVEEIKEEIV 52
                                       33333333333322221244444222.44444444444443 PP

>> DrrA_P4M  DrrA phosphatidylinositol 4-phosphate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   4.8    0.0051       3.8      20      63 ..      21      64 ..       3      71 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0051
                                       GGGTT--HHHHHHHHHHHHHHHHTT--SHHHHHHHHHHHHTSHH CS
                           DrrA_P4M 20 ekyqklkGDaLKtkILkdfKdkleeistkeeLeklvkefkksee 63
                                       e+ ++   +  K++I ++ K+++ e  ++e +e++v+e+ +s+ 
  gene2927|gene2927|rna2927|rna2927 21 EEIKEEIVEEIKEEIVEEIKEEIVEEIKEEIVEEIVEEIVESPR 64
                                       55555555678889999999998888888888888888888875 PP

>> Hydantoinase_A  Hydantoinase/oxoprolinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   2.5   0.00092      0.69     192     235 ..       9      53 ..       2      68 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00092
                     Hydantoinase_A 192 velarrafeelakelnlk.veevAegilsvavenmanavrklsve 235
                                        +e++++ +ee+ +e++++ vee+ e+i++  +e++++++++ +ve
  gene2927|gene2927|rna2927|rna2927   9 EEIVEEIVEEIVEEIKEEiVEEIKEEIVEEIKEEIVEEIKEEIVE 53 
                                        566666677777777666777777777777777777777765544 PP

>> pP_pnuc_2  Predicted pPIWI-associating nuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3  12.7     0.027        20       3      41 ..      18      56 ..       2      66 .. 0.52

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.027
                          pP_pnuc_2  3 dvreeliealeekiedevidelieetveeldeLathtvv 41
                                       ++ ee++e++ e+i++e+++e+ ee+vee++e   + +v
  gene2927|gene2927|rna2927|rna2927 18 EIVEEIKEEIVEEIKEEIVEEIKEEIVEEIKEEIVEEIV 56
                                       333444444444444444444444444444443333333 PP

>> RNA_pol_Rpb1_4  RNA polymerase Rpb1, domain 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   2.7     0.003       2.2      18      44 ..      20      46 ..       2      71 .. 0.54

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.003
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                     RNA_pol_Rpb1_4 18 leelfeakinkilnkardkagkiasks 44
                                       +ee++e+++++i++++ +++++ + ++
  gene2927|gene2927|rna2927|rna2927 20 VEEIKEEIVEEIKEEIVEEIKEEIVEE 46
                                       333333333333333333333322222 PP

>> GARS_A  Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   8.9      0.31   2.3e+02     138     156 ..      39      57 ..       2      75 .. 0.62

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.31
                                        S-HHHHHHHHHHTHHHHHH CS
                             GARS_A 138 vteellekikeeileptve 156
                                        + ee++e+ikeei+e++ve
  gene2927|gene2927|rna2927|rna2927  39 IKEEIVEEIKEEIVEEIVE 57 
                                        3444455555555555555 PP

>> Dynein_light  Dynein light chain type 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   4.7    0.0034       2.5       9      43 ..      19      50 ..       4      73 .. 0.61

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0034
                                       E-HHHHHHHHHHHHHHHHH-SSHH..HHHHHHHHH CS
                       Dynein_light  9 mseemqeeaielakealekfkkekekdiaayikke 43
                                       + ee++ee++e +ke++ + + +  ++i+++ik+e
  gene2927|gene2927|rna2927|rna2927 19 IVEEIKEEIVEEIKEEIVE-EIK--EEIVEEIKEE 50
                                       3344444444444444432.122..3555555555 PP

>> Tctex-1  Tctex-1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   4.5    0.0035       2.6       2      46 ..       8      49 ..       5      76 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0035
                                       HHHHHHHHHHHHHCTSSS--CCCHHHHHHHHHHHHHHHHHHHTS. CS
                            Tctex-1  2 lkqiakealesalesaesYdhekveqwnstiinsilkalkseste 46
                                       +++i++e++e+ +e+ +   +e ve++ ++i+++i++++ +e +e
  gene2927|gene2927|rna2927|rna2927  8 IEEIVEEIVEEIVEEIK---EEIVEEIKEEIVEEIKEEIVEEIKE 49
                                       56777777777776654...7777777777777777777766543 PP

>> DUF2587  Protein of unknown function (DUF2587)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   6.6     0.002       1.5      29      75 ..      13      59 ..       5      71 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.002
                            DUF2587 29 gtmikqlleevraapldeasrerlkeihersikeleeglaPelveel 75
                                         ++ +++ee+++  ++e   e ++ei+e+ ++e++e +  e+vee+
  gene2927|gene2927|rna2927|rna2927 13 EEIVEEIVEEIKEEIVEEIKEEIVEEIKEEIVEEIKEEIVEEIVEEI 59
                                       5678899999***99****9999****************99999997 PP

>> Mpv17_PMP22  Mpv17 / PMP22 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   4.0       0.2   1.5e+02      16      16 ..      32      32 ..       3      62 .. 0.67

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.2
                        Mpv17_PMP22 16 k 16
                                       k
  gene2927|gene2927|rna2927|rna2927 32 K 32
                                       2 PP

>> Bac_DNA_binding  Bacterial DNA-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4  10.3      0.12        90      16      39 ..      23      46 ..       2      76 .. 0.55

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.12
                                       --HHHHHHHHHHHHHHHHHHHHTT CS
                    Bac_DNA_binding 16 ltkkdakrvveafldtikeaLkkg 39
                                       ++++ ++++ e+++++ike++ ++
  gene2927|gene2927|rna2927|rna2927 23 IKEEIVEEIKEEIVEEIKEEIVEE 46
                                       333333333333333333333222 PP

>> YpjP  YpjP-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0  11.6    0.0038       2.8       5      51 ..      10      57 ..       2      74 .. 0.49

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0038
                               YpjP  5 kllellleeaeeqsllKlGkkiaekiedefeeeilpkieeviee.lle 51
                                       +++e+++ee +e+  + + ++i+e i +e++eei+ +i+e+i e ++e
  gene2927|gene2927|rna2927|rna2927 10 EIVEEIVEEIVEEIKEEIVEEIKEEIVEEIKEEIVEEIKEEIVEeIVE 57
                                       333344444444444444444444444444444444444333221333 PP

>> EnY2  Transcription factor e(y)2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0  12.4      0.02        15      53      82 ..      12      41 ..       1      62 [. 0.52

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.02
                                       HHHHHHHHHHHHHHHS-HHHHHHHHHHHHH CS
                               EnY2 53 veelveeitpkaralVPdevkkellqrIre 82
                                       vee+veei ++ ++ + +e+k+e++++I+e
  gene2927|gene2927|rna2927|rna2927 12 VEEIVEEIVEEIKEEIVEEIKEEIVEEIKE 41
                                       444444444444444444444444444443 PP

>> TFIID_20kDa  Transcription initiation factor TFIID subunit A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   9.7      0.14     1e+02       2      46 ..       5      48 ..       3      66 .. 0.61

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.14
                                       HHHHHHHHHCC-SS----HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        TFIID_20kDa  2 KrklqdLvqqvdsetkldedvedlLleiaddFvesvtkfacklak 46
                                       K++++++v+++ +e+ ++e  e+++ ei ++ ve++ + +++ +k
  gene2927|gene2927|rna2927|rna2927  5 KESIEEIVEEI-VEEIVEEIKEEIVEEIKEEIVEEIKEEIVEEIK 48
                                       66666666666.344555555555555555555555555554444 PP

>> DUF1002  Protein of unknown function (DUF1002)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4  12.7     0.016        12     139     183 ..      19      61 ..       1      74 [. 0.54

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.016
                            DUF1002 139 ttselaekigsekaaelvaevkeevakeklkteeeikkiveevan 183
                                         ++e++e+i +e  +e+v+e+kee+++e   +ee +++ivee+++
  gene2927|gene2927|rna2927|rna2927  19 IVEEIKEEIVEEIKEEIVEEIKEEIVEE--IKEEIVEEIVEEIVE 61 
                                        2344455555555555555555555555..455555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (81 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2483  (0.138491); expected 358.6 (0.02)
Passed bias filter:                      977  (0.0544927); expected 358.6 (0.02)
Passed Vit filter:                       182  (0.0101512); expected 17.9 (0.001)
Passed Fwd filter:                        42  (0.00234257); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              24  [number of targets reported over threshold]
# CPU time: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.45
# Mc/sec: 543.36
//
Query:       gene2928|gene2928|rna2928|rna2928  [L=883]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (883 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       872  (0.0486363); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.67u 0.32s 00:00:00.99 Elapsed: 00:00:00.50
# Mc/sec: 5328.40
//
Query:       gene2929|gene2929|rna2929|rna2929  [L=369]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.4e-09   36.9   0.0     0.0017   17.8   0.0    3.1  3  adh_short        short chain dehydrogenase
     0.0016   18.1   0.0        1.7    8.1   0.0    2.2  2  adh_short_C2     Enoyl-(Acyl carrier protein) reductase
  ------ inclusion threshold ------
      0.022   14.5   0.1      0.058   13.2   0.1    1.7  2  Eno-Rase_NADH_b  NAD(P)H binding domain of trans-2-enoyl-CoA 


Domain annotation for each model (and alignments):
>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.0   0.00013      0.77       1      32 [.      33      63 ..      33      71 .. 0.79
   2 !    6.3   0.0   0.00098       5.8      76     120 ..      88     132 ..      78     140 .. 0.88
   3 !   17.8   0.0   2.9e-07    0.0017     130     185 ..     227     282 ..     205     291 .. 0.92

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00013
                                       SEEEEESTTSHHHHHHHHHHHHTT-EEEEEES CS
                          adh_short  1 kvvlvtGassGIGraiakelakeGakvvvvdr 32
                                       k +l++G++sG+G+ +a +l + + +v v++r
  gene2929|gene2929|rna2929|rna2929 33 KNILIIGGTSGLGLSLALKLSNHN-NVSVTGR 63
                                       789****************98774.4555444 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.00098
                                        SSESEEEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHH CS
                          adh_short  76 gkldvLvnNAGitgsgpfselseeewervievNltgvflltravl 120
                                         + d++  +AG +  + f +l+ ee+ + ++vN++g++ + r+++
  gene2929|gene2929|rna2929|rna2929  88 AEYDAVFYCAGYAVAKYFVDLEWEEIVNDFSVNYFGAVRVLRMLA 132
                                        56699999*****************99************999875 PP

  == domain 3  score: 17.8 bits;  conditional E-value: 2.9e-07
                                        EEEEEEEGGGTSB-TTBHHHHHHHHHHHHHHHHHHHHHGGGTEEEEEEEESSBSSH CS
                          adh_short 130 rIvnvsSvagkvpvagvaaYsAsKaavagltrslakelaptgirvnavaPGlvdTd 185
                                        +Iv ++   ++ +v+g+aaYs sK a+  l+ +++ el++ +i         ++T+
  gene2929|gene2929|rna2929|rna2929 227 DIVLIGTPLAFFAVPGYAAYSPSKSALYNLFLTIQPELRKLNIYLYFYIMSTTKTP 282
                                        5999***************************************9998888888886 PP

>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.0   0.00028       1.7      69     115 ..      89     133 ..      85     144 .. 0.89
   2 !    7.7   0.0   0.00039       2.3      90     164 ..     196     269 ..     177     303 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00028
                                        SEEEEEE-----EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHH CS
                       adh_short_C2  69 klDilvnnagiapklkgpfletsreefdraldvnlyslfllakaalp 115
                                        + D ++ +ag+a +  + f+++++ee+ + ++vn  +++++++ ++ 
  gene2929|gene2929|rna2929|rna2929  89 EYDAVFYCAGYAVA--KYFVDLEWEEIVNDFSVNYFGAVRVLRMLAG 133
                                        57999*********..*************************998765 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.00039
                                        H-HHHHHHHHHHHTHHHHHHHHHHHHHCTSCCEEEEEEEGGGTSBSTTTTHHHHHHHHHHHHHHHHHHHHGGGTE CS
                       adh_short_C2  90 tsreefdraldvnlyslfllakaalplmkeggsivnlssvgaervvpnynaygaaKaalealtrylAvelgpkgi 164
                                        +s + f+ al v  ++ + + ++ ++ +k++  iv +    a  +vp+y+ay+ +K al +l  ++  el + +i
  gene2929|gene2929|rna2929|rna2929 196 LSTSPFRAALRVMHRGSAITNNRSQRTIKPR-DIVLIGTPLAFFAVPGYAAYSPSKSALYNLFLTIQPELRKLNI 269
                                        5666677777777777766666666666554.678888888999***************9988777666666555 PP

>> Eno-Rase_NADH_b  NAD(P)H binding domain of trans-2-enoyl-CoA reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   9.8e-06     0.058      34      60 ..      28      52 ..      18      62 .. 0.75
   2 ?   -3.3   0.0       1.4   8.1e+03      31      47 ..     218     232 ..     204     234 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 9.8e-06
                                       -----.-SEEEEESTSSHHHHHHHHHH CS
                    Eno-Rase_NADH_b 34 kkiekgpkkvLviGaStGYGLAsriaa 60
                                       +k+  + k++L+iG+ +G GL+  + +
  gene2929|gene2929|rna2929|rna2929 28 RKY--QNKNILIIGGTSGLGLSLALKL 52
                                       333..46**************976655 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 1.4
                                        HHS-----.-SEEEEES CS
                    Eno-Rase_NADH_b  31 ksqkkiekgpkkvLviG 47 
                                        +sq++i  +p+ +  iG
  gene2929|gene2929|rna2929|rna2929 218 RSQRTI--KPRDIVLIG 232
                                        333333..488888888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (369 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       569  (0.0317363); expected 358.6 (0.02)
Passed bias filter:                      468  (0.026103); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:01.91
# Mc/sec: 585.16
//
Query:       gene293|gene293|rna293|rna293  [L=364]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (364 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       602  (0.0335769); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 2394.29
//
Query:       gene2930|gene2930|rna2930|rna2930  [L=433]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-32  112.7  12.9    2.3e-32  112.3  12.9    1.1  1  PTR2             POT family
     0.0013   17.7  25.4     0.0025   16.8  25.2    1.4  1  MFS_1            Major Facilitator Superfamily
  ------ inclusion threshold ------
       0.62   10.0   8.8       0.85    9.5   0.2    2.3  2  DUF3487          Protein of unknown function (DUF3487)


Domain annotation for each model (and alignments):
>> PTR2  POT family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.3  12.9   3.9e-36   2.3e-32       1     145 [.      71     200 ..      71     216 .. 0.91

  Alignments for each domain:
  == domain 1  score: 112.3 bits;  conditional E-value: 3.9e-36
                                        CHHHHHHHHHHHHHHHHCCCCT.TTTSS--S--TCHHHHHHHHHHHHHHHHHHHHHHHHHHHCTTT-SSSSCHHHH CS
                               PTR2   1 fktIllgsiiyaiGhvvlalsa.ipslksaesagvrvallfigLalIalGtGgiKpnvSafgadqfeekdprersr 75 
                                        ++tI+++si+y++G ++l lsa ++s          ++ +++gL+l+a+GtGgiKp++S fg+dq  ++     s 
  gene2930|gene2930|rna2930|rna2930  71 YTTIVALSIVYVLGTAMLVLSAyTSS----------ILCFVSGLVLVAMGTGGIKPCISVFGGDQAAKN-----SN 131
                                        68********************6555..........5789************************98765.....67 PP

                                        HHHHHHHHHHHHHHHHHHHHHHHHCTT-HHHHHHHHHHHHHHHHHHHHCTTTS-EE------SHHHHCCC CS
                               PTR2  76 fFsiFyfsiNvGSLlsliitpylqenvgyplgFgipavlmiiallvFllGsrlykkkppkgnvltkvfkv 145
                                        fFs+FyfsiN+G+++s++ +p+++ n +y ++F++p+vl+  a++ F+ G+r+y+ + p+++  ++  + 
  gene2930|gene2930|rna2930|rna2930 132 FFSLFYFSINCGAMVSILTLPIIA-NTNYTVAFSVPFVLISTAVVLFVSGTRMYTMRAPDPKTYRELKAF 200
                                        **********************97.679*******************************99988776655 PP

>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8  25.2   4.2e-07    0.0025      11     172 ..      23     178 ..       9     205 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 4.2e-07
                              MFS_1  11 arsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrr.vlllglllfalglllllfa... 82 
                                         r++l   +p +l ++l +++s++  l+ +++++++++++++G++sd f r   ++++  ++++lg+++l+++   
  gene2930|gene2930|rna2930|rna2930  23 LRALL---FP-FLHNNLSYTVSAAKGLAHAFFFLSFFFAVIFGFVSDVFIRHYtTIVALSIVYVLGTAMLVLSayt 94 
                                        33333...33.6678888999998888888999999999********97666669999999999995555553464 PP

                              MFS_1  83 sslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyila 158
                                        ss+  ++ + vl ++g+g++ p + ++  d ++k   +  ++l++ ++++Ga++  l  +++a + +++++f +  
  gene2930|gene2930|rna2930|rna2930  95 SSILCFVSGLVLVAMGTGGIKPCISVFGGDQAAK--NSNFFSLFYFSINCGAMVSILTLPIIA-NTNYTVAFSVPF 167
                                        66668999999999999*******9999999998..66777899999*******999999999.888888888888 PP

                              MFS_1 159 ivsllafvlfllll 172
                                        ++   a+vl   ++
  gene2930|gene2930|rna2930|rna2930 168 VLISTAVVL---FV 178
                                        888887664...32 PP

>> DUF3487  Protein of unknown function (DUF3487)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   2.3    0.0061        36       4      67 ..      29      92 ..      27     100 .. 0.81
   2 ?    9.5   0.2   0.00014      0.85      24      84 ..     131     195 ..     119     208 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.0061
                            DUF3487  4 eflpdrLnrePvVfrGltadEllvlaglglvvglvlglllallvgslaliptialllvllvvlv 67
                                       +fl ++L  +    +Gl++  +++ + +++++g+v  +++   +  +al +  +l +++lv+  
  gene2930|gene2930|rna2930|rna2930 29 PFLHNNLSYTVSAAKGLAHAFFFLSFFFAVIFGFVSDVFIRHYTTIVALSIVYVLGTAMLVLSA 92
                                       688889999999999***999999***********99999999997777777777777766654 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00014
                            DUF3487  24 Ellvlaglglvvglvlglllallvgs....laliptialllvllvvlvggkllarlKRgkPdtyl 84 
                                         ++ l+ +++ +g+++++l ++++ +    +a+ + ++l++ ++v++v g+ + +++   P+ty 
  gene2930|gene2930|rna2930|rna2930 131 NFFSLFYFSINCGAMVSILTLPIIANtnytVAFSVPFVLISTAVVLFVSGTRMYTMRAPDPKTYR 195
                                        567778888899999999888876651111455666679999999************99999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (433 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       674  (0.0375927); expected 358.6 (0.02)
Passed bias filter:                      231  (0.0128842); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.47
# Mc/sec: 2782.48
//
Query:       gene2931|gene2931|rna2931|rna2931  [L=46]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (46 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       472  (0.0263261); expected 358.6 (0.02)
Passed bias filter:                      254  (0.014167); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.33u 0.27s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 348.92
//
Query:       gene2932|gene2932|rna2932|rna2932  [L=41]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (41 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       348  (0.0194099); expected 358.6 (0.02)
Passed bias filter:                      222  (0.0123822); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.27s 00:00:00.63 Elapsed: 00:00:00.42
# Mc/sec: 294.97
//
Query:       gene2933|gene2933|rna2933|rna2933  [L=798]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (798 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       526  (0.0293379); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.62u 0.24s 00:00:00.86 Elapsed: 00:00:00.42
# Mc/sec: 5731.95
//
Query:       gene2934|gene2934|rna2934|rna2934  [L=108]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-12   48.1   0.0    1.2e-12   47.9   0.0    1.0  1  RVT_1     Reverse transcriptase (RNA-dependent DNA polymerase


Domain annotation for each model (and alignments):
>> RVT_1  Reverse transcriptase (RNA-dependent DNA polymerase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.9   0.0   6.6e-17   1.2e-12       5      85 ..      13     102 ..      10     106 .. 0.90

  Alignments for each domain:
  == domain 1  score: 47.9 bits;  conditional E-value: 6.6e-17
                                        T.....S-EEE......-THHHHCTB--...........-------HHHH................HCCHTS--EE CS
                              RVT_1   5 g....pgsyRpisllsvdykalnkliakrLkdvl..ekllsenqpgfrpgrstldav...edllkalkkkkkakll 71 
                                        g    +++yR isl+s+++k++ k++a+rL+++   ek+l ++q gfr+ + ++      +++ ++ + k++a+++
  gene2934|gene2934|rna2934|rna2934  13 GgldfLDNYRGISLISTLCKIVTKICANRLSNFSerEKILIHKQAGFRKLEECIAHAtslYEIGRQRSLKGRATYA 88 
                                        45556789**************************99**************99988888988888887888899*** PP

                                        EEEEBCCGCCCSBB CS
                              RVT_1  72 lklDlkkaFdsvpl 85 
                                        ++lD++k +d+vp 
  gene2934|gene2934|rna2934|rna2934  89 AFLDFSKVYDRVPT 102
                                        ************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       339  (0.0189079); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 758.04
//
Query:       gene2935|gene2935|rna2935|rna2935  [L=49]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (49 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       295  (0.0164538); expected 358.6 (0.02)
Passed bias filter:                      236  (0.013163); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.42
# Mc/sec: 349.38
//
Query:       gene2936|gene2936|rna2936|rna2936  [L=440]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      5e-68  229.2   0.0    9.2e-68  228.3   0.0    1.4  1  Tubulin          Tubulin/FtsZ family, GTPase domain
    9.5e-44  148.6   0.1    1.5e-43  148.0   0.1    1.3  1  Tubulin_C        Tubulin C-terminal domain
    1.7e-07   31.6   0.0    3.7e-07   30.5   0.0    1.6  1  Misat_Tub_SegII  Misato Segment II tubulin-like domain
     0.0053   16.0   0.1       0.03   13.5   0.0    2.0  2  Tubulin_2        Tubulin like


Domain annotation for each model (and alignments):
>> Tubulin  Tubulin/FtsZ family, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  228.3   0.0   2.1e-71   9.2e-68       1     196 [.       3     211 ..       3     212 .. 0.99

  Alignments for each domain:
  == domain 1  score: 228.3 bits;  conditional E-value: 2.1e-71
                                        EEEEEEEHHHHHHHHHHHHH...HHHCH..............HHHT.....TTEEEEE....EEESBHHHHHTS-G CS
                            Tubulin   1 eiivigvGqcGnqignelwellakehgiqsdg..........dslesfFsesgkveyiprsvaidtdpqvlneika 66 
                                        eii+++ GqcGnqig+++we++ +ehgi++ g          d+++++++es++++y+pr+v++d++p +++ +++
  gene2936|gene2936|rna2936|rna2936   3 EIIHLQSGQCGNQIGTKFWEVISEEHGINNLGqytgtkdnqlDRISVYYNESSTKQYVPRAVLVDLEPGTMDTLRS 78 
                                        79**************************97779******************************************* PP

                                        S........EEEE--CCCCTTC--TT-HHHHHHHHHHTHHHHHHHHTT-SE.SEEEEEEETTSSHHHHHHHHHHHH CS
                            Tubulin  67 gs..elfnpnklllgkegagnngaggypevgkeaaeeileeirkevekcdslqgffitaslgGGTGSGlgpvilev 140
                                        g+  +lf+p++ ++g++gagnn+a+g+++ g+e++e +++++r+e+ek+++lqgf+it+slgGGTG G+g++++++
  gene2936|gene2936|rna2936|rna2936  79 GPlgSLFRPDNYVFGQSGAGNNWAKGHYTEGAELIENVMDCVRREAEKSNCLQGFQITHSLGGGTGAGMGTLLISK 154
                                        **************************************************************************** PP

                                        HHHTSTTSEEEEEEEE--.GG.G-HHHHHHHHHHHHHHHHT-SEEEEEEHHHHHCCS CS
                            Tubulin 141 lkeeypkalvvtvvvlPs.efsevvvepynailalkelieesdavividNdaLlkil 196
                                        ++ee+p+++++t++v+Ps + s+ vvepyna l++++l+e++d +++idN+aL++i+
  gene2936|gene2936|rna2936|rna2936 155 IREEFPDRMMCTFSVVPSpKVSDTVVEPYNATLSIHQLVENADETFCIDNEALYNIC 211
                                        ********************************************************8 PP

>> Tubulin_C  Tubulin C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  148.0   0.1   3.3e-47   1.5e-43       1     125 [.     261     382 ..     261     383 .. 0.99

  Alignments for each domain:
  == domain 1  score: 148.0 bits;  conditional E-value: 3.3e-47
                                        TTC-EEEEEEESSSCTTTTTCS-HHHHHHHHHTCSGGGBSSSTSTTTSSEEEEEEEEEESSSHHHHHHHHHHHHHT CS
                          Tubulin_C   1 PrlhFlltsyaPlvsaekaavektsvqdvtrallepknimvkvdprkgkylaiallirGdvepkevnkavqrikek 76 
                                        PrlhF+++++aPl+++  a++++ sv+++t++++++kn+m+++dp++g+yl++a ++rG++++k+v++++++i+++
  gene2936|gene2936|rna2936|rna2936 261 PRLHFFMIGFAPLIAEGMASYRSYSVSELTQQMFDSKNMMAASDPKHGRYLTVATIFRGNISMKDVDEQLHNIQSR 336
                                        9*************************************************************************** PP

                                        TTS-BSTTSTTTEEEEEEECECT-TTTSSCEEEEEEEEGGGHHHHHHHH CS
                          Tubulin_C  77 kkaqfveWiptgikvalnkkspyvkkqskvsvlmlaNttsiaelfkrll 125
                                        + ++fveWip+++k+a+++ +p + ++s   +++++Ntt+i+elfkr+ 
  gene2936|gene2936|rna2936|rna2936 337 NASNFVEWIPNNVKTAVCDIPPSTLDMS---ATFIGNTTAIQELFKRIA 382
                                        *************************999...***************985 PP

>> Misat_Tub_SegII  Misato Segment II tubulin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.5   0.0   8.1e-11   3.7e-07       1      73 [.       2      76 ..       2     109 .. 0.78

  Alignments for each domain:
  == domain 1  score: 30.5 bits;  conditional E-value: 8.1e-11
                    Misat_Tub_SegII  1 rEivtlqlGnyaNyvgtHfWNtQesyf......tydeeeeesevdhdvlfregetkqgqvtytPRllivDlkgslgsl 72
                                       rEi+ lq G+  N +gt fW +  +        +y+ +++ +++d+   + +   ++ + +y+PR+++vDl+ ++  +
  gene2936|gene2936|rna2936|rna2936  2 REIIHLQSGQCGNQIGTKFWEVISEEHginnlgQYTGTKD-NQLDRISVYYN---ESSTKQYVPRAVLVDLEPGTMDT 75
                                       8*******************98655443354567777777.88887766665...456789*********98655444 PP

                    Misat_Tub_SegII 73 r 73
                                        
  gene2936|gene2936|rna2936|rna2936 76 L 76
                                       3 PP

>> Tubulin_2  Tubulin like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.0   6.7e-06      0.03     139     203 ..     113     176 ..      98     191 .. 0.76
   2 ?   -0.4   0.1      0.11   5.1e+02      56     104 ..     305     348 ..     283     354 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 6.7e-06
                          Tubulin_2 139 lrdaikrlrgsage.eeglnvfVvgSLaGGTGSGiflDvayllrkilkeekqkvkiiglvllPdvf 203
                                        ++++++ +r++a++ + +  + +  SL GGTG+G+   ++  +r+++++      ++ +v++P+v 
  gene2936|gene2936|rna2936|rna2936 113 IENVMDCVRREAEKsNCLQGFQITHSLGGGTGAGMGTLLISKIREEFPDRMM--CTFSVVPSPKVS 176
                                        5555555565444433345677999***********************9997..588888888885 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.11
                          Tubulin_2  56 aekageslksrekealsissaevdrilrnllreetasaypsieeWlppe 104
                                        + k g++l+ +  +  +is ++vd+ l n ++++ +    +  eW+p++
  gene2936|gene2936|rna2936|rna2936 305 P-KHGRYLTVATIFRGNISMKDVDEQLHNIQSRNAS----NFVEWIPNN 348
                                        2.3456666666666699999999999999766544....778999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (440 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       533  (0.0297284); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 3076.79
//
Query:       gene2938|gene2938|rna2938|rna2938  [L=322]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.053   13.8   3.3      0.082   13.2   3.3    1.2  1  MMR1      Mitochondrial Myo2 receptor-related protein


Domain annotation for each model (and alignments):
>> MMR1  Mitochondrial Myo2 receptor-related protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   3.3   4.6e-06     0.082     133     228 ..     110     203 ..      95     210 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.6e-06
                               MMR1 133 qesekveeleksksereisetssaiSestlleledletteaetlnpnnsveekkpavektkspskrivStssvass 208
                                        ++++++++  +++ ++ + ++ + +Ses+++e++   +t ae  + ++s+ +   +v+ + + ++   S+ss+ ++
  gene2938|gene2938|rna2938|rna2938 110 EHNKIENSIDEKECQKGAGSSFQYLSESSVTEQQCPAQTSAEDRKIKDSDVDS--NVNDNITFEDTPLSNSSLNNE 183
                                        68899999999999**999999***********95555555555555555555..89999999************* PP

                               MMR1 209 leevelnelpkdleldalpt 228
                                          ++e+ +++ ++ + +l t
  gene2938|gene2938|rna2938|rna2938 184 EDDIEMRQIERNVSVRNLLT 203
                                        *************9988755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (322 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       992  (0.0553294); expected 358.6 (0.02)
Passed bias filter:                      496  (0.0276647); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.23s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 2403.48
//
Query:       gene2939|gene2939|rna2939|rna2939  [L=62]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (62 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       410  (0.022868); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 460.87
//
Query:       gene294|gene294|rna294|rna294  [L=476]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.5e-22   78.4   0.0    1.5e-21   77.0   0.0    1.6  2  Pkinase      Protein kinase domain
    1.3e-13   50.8   0.0    2.1e-13   50.2   0.0    1.2  1  Pkinase_Tyr  Protein tyrosine kinase
  ------ inclusion threshold ------
      0.017   15.3   0.3      0.017   15.3   0.3    1.7  2  OSR1_C       Oxidative-stress-responsive kinase 1 C-terminal 


Domain annotation for each model (and alignments):
>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.0   0.0   2.4e-25   1.5e-21     108     264 .]      12     158 ..       6     158 .. 0.85
   2 ?   -2.4   0.0       0.4   2.4e+03     167     185 ..     233     251 ..     224     264 .. 0.87

  Alignments for each domain:
  == domain 1  score: 77.0 bits;  conditional E-value: 2.4e-25
                                    HHHHHHHHHTTEE-SS-SGGGEEEE.TTTE..EEE-SGTTSEESSSSCSBCTTTSCGGGS-HHHHTTSCBSHHHHHHHHH CS
                        Pkinase 108 legleylHskgiiHrDlKpeNiLid.ekge..lKitDFGlakelessskltsfvgtseYlAPEvlkeneyskkvDvWslG 184
                                    l+ l+ +H ++iiH+ lK +N++++ ++g+  +K++DFG+++   ++   + +vgt+e+l+ E+ ++++y++ vDv+slG
  gene294|gene294|rna294|rna294  12 LRVLKCMHGMHIIHKNLKCSNVFLSvRDGKdvVKLGDFGISEAKFKNR--MPIVGTPEFLPREIYEGSRYTEGVDVYSLG 89 
                                    7889*********************9888889*********9877755..99**************************** PP

                                    HHHHHHHHSS-STTTSSHHHHHHHHHHTHHHHHHHCTSHH...HHHTTS-HHHHHHHHHHT-SSGCCSTTHHHHHTSGGG CS
                        Pkinase 185 vilyelltgkppfsgekgkekvekeldqlekilkilgetkeklpeaseiseeakdllkkllkkdpkkRltaeellqhpyl 264
                                     +l+el tg+ p+++ k+      e+d    + k+l   ++ ++ ++  ++ +k+l+ ++++    +R+t++ell+h+++
  gene294|gene294|rna294|rna294  90 FLLIELCTGTWPYAECKD------EFD---LLKKVLL-GQLPSAVHKIRDPCLKHLIFRCITS-TYDRITVDELLEHHVF 158
                                    **************2222......222...2334543.35667777777889999*****986.689**********987 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.4
                                    HHHTTSCBSHHHHHHHHHH CS
                        Pkinase 167 EvlkeneyskkvDvWslGv 185
                                    E++++n+y + +D++  G+
  gene294|gene294|rna294|rna294 233 EIIRTNMYAELCDLFKTGI 251
                                    8999999999999999987 PP

>> Pkinase_Tyr  Protein tyrosine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.2   0.0   3.5e-17   2.1e-13     117     256 ..      16     153 ..       4     155 .. 0.83

  Alignments for each domain:
  == domain 1  score: 50.2 bits;  conditional E-value: 3.5e-17
                                    HHHHHTTEEEST-SGGGEEEEE...TTEEEE-STTTHEETTTSSEEEETTSSTSGGGGS-HHHHHHSEEEHHHHHHHHHH CS
                    Pkinase_Tyr 117 eyLeskklvHrdlaarNvLlse...nkvvkisDfGLardiekddeyvkkeeaklpvkWmapEslkekkftsksDvWsfGv 193
                                    + ++ ++++H++l + Nv+ls    ++vvk++DfG++++       +++       ++++ E+ + +++t+  Dv+s G 
  gene294|gene294|rna294|rna294  16 KCMHGMHIIHKNLKCSNVFLSVrdgKDVVKLGDFGISEAK-----FKNRMPIVGTPEFLPREIYEGSRYTEGVDVYSLGF 90 
                                    5678999*************9766688**********998.....66777777888999********************* PP

                                    HHHHHHTTSSGTTTTS.HHHHHHHHHHTTEES-BBTTSB.HHHHHHHHHHT-SSGGGS--HHHHH CS
                    Pkinase_Tyr 194 llwEiftlgespypgl.kneevleklkegkrlekpekcp.eelyelmkkcweedpeeRptfselv 256
                                    ll+E++t g  py+++ ++ ++l+k+  g+  ++ +k+  + l++l+ +c +++  +R t  el+
  gene294|gene294|rna294|rna294  91 LLIELCT-GTWPYAECkDEFDLLKKVLLGQLPSAVHKIRdPCLKHLIFRCITST-YDRITVDELL 153
                                    *******.********77889999998887766666655156888999998765.4677766665 PP

>> OSR1_C  Oxidative-stress-responsive kinase 1 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.3   2.9e-06     0.017      23      47 ..     211     235 ..     206     240 .. 0.91
   2 ?   -2.5   0.1       1.1   6.5e+03       5      24 ..     450     469 ..     448     469 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.9e-06
                         OSR1_C  23 IqFeFdlgkDtaeevaqelvkaglv 47 
                                    I+F+F+ +kDt ++v +e+ + +++
  gene294|gene294|rna294|rna294 211 IRFKFHNDKDTIDSVMSEMLEEEII 235
                                    9*******************99987 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.1
                         OSR1_C   5 LrvrdakkrkekqkeneaIq 24 
                                    +r r+ k + +++ke   Iq
  gene294|gene294|rna294|rna294 450 MRTREEKALTQAKKERVSIQ 469
                                    68899999999999987776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (476 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       504  (0.0281109); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 3253.24
//
Query:       gene2940|gene2940|rna2940|rna2940  [L=239]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
       0.04   14.2   5.8        1.6    9.0   0.4    2.5  2  Med15_fungi  Mediator complex subunit 15
      0.043   14.1   0.4       0.13   12.6   0.1    1.9  2  DUF948       Bacterial protein of unknown function (DUF948)
        0.6   10.6   3.0       0.49   10.9   0.3    2.1  2  Knl1_RWD_C   Knl1 RWD C-terminal domain
        5.2    7.2   6.8         15    5.8   0.7    2.3  2  BRE1         BRE1 E3 ubiquitin ligase


Domain annotation for each model (and alignments):
>> Med15_fungi  Mediator complex subunit 15
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.4   0.00035       1.6      33      72 ..      47      86 ..      30      89 .. 0.89
   2 ?    7.4   0.7    0.0012       5.3      52     110 ..     115     177 ..      92     179 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00035
                        Med15_fungi 33 aaikqqlqeiqqmlarvdaliplfykltkneeavkrLlqm 72
                                       ++ +qq+  ++  +++++++ + f++++kne   k+L+++
  gene2940|gene2940|rna2940|rna2940 47 QMLNQQIDLVTGSMSSMKQIRSNFVAMSKNECVSKNLFAF 86
                                       566899999****************************986 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0012
                        Med15_fungi  52 liplfykltkneeavkrLlqmrimlkeqleklpq.....dqftikpeyLeklksqiqkyfeyvk 110
                                        +i ++ + + +++++k+++ +++m k + + ++      d+ ++++e+L+   +++  + e ++
  gene2940|gene2940|rna2940|rna2940 115 MINTVTITSIDKQNTKKVIDLKAMKKHIKD-SEFfknytDEIYLNVEKLKGFETRLYECLEEIR 177
                                        456666778899999999999999998876.344566778888999999999999888887776 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   2.9e-05      0.13      10      50 ..      21      61 ..      19      70 .. 0.91
   2 ?   -1.5   0.0       0.7   3.1e+03      34      34 ..     161     161 ..     117     192 .. 0.57

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.9e-05
                             DUF948 10 FvvLviflivvllklkktldeaaatieelekqvdpilkeve 50
                                       F++L+ + +++ ++++++lde+ + i+ l++q+d ++  + 
  gene2940|gene2940|rna2940|rna2940 21 FSILMSVGAITEKEVNRVLDEVVQKIQMLNQQIDLVTGSMS 61
                                       8999******************************9988765 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.7
                             DUF948  34 t 34 
                                         
  gene2940|gene2940|rna2940|rna2940 161 K 161
                                        1 PP

>> Knl1_RWD_C  Knl1 RWD C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.3   0.00011      0.49      52      91 ..      16      55 ..       2      61 .. 0.82
   2 ?   -0.7   0.1      0.47   2.1e+03      37      75 ..      88     133 ..      73     158 .. 0.54

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00011
                         Knl1_RWD_C 52 svplpftvqnkiGnigedeiaavlssvplgknylkkvvkk 91
                                       s+   f++   +G i+e+e++ vl +v  + ++l++ +  
  gene2940|gene2940|rna2940|rna2940 16 SAMYIFSILMSVGAITEKEVNRVLDEVVQKIQMLNQQIDL 55
                                       3455799*********************999999988866 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.47
                         Knl1_RWD_C  37 fakfeltlslsasypsvp......lpftvqn.kiGnigedeiaavl 75 
                                        f kf  t s  ++y  +       lp+ +++ +i +i +++ ++v+
  gene2940|gene2940|rna2940|rna2940  88 FDKFAATRSNLSEYFLAYenflcfLPYMINTvTITSIDKQNTKKVI 133
                                        5566666555555544430000013333333134444444444444 PP

>> BRE1  BRE1 E3 ubiquitin ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.7    0.0033        15      48      91 ..      33      76 ..      31      78 .. 0.92
   2 ?    4.3   0.7    0.0093        42      14      54 ..     123     163 ..     118     164 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0033
                               BRE1 48 faamrskdalenelkkLnkllsKsselieqLkelekefvrklke 91
                                       ++++r  d + +++++Ln++++  + +++ +k++ ++fv+  k+
  gene2940|gene2940|rna2940|rna2940 33 KEVNRVLDEVVQKIQMLNQQIDLVTGSMSSMKQIRSNFVAMSKN 76
                                       68899999******************************998887 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.0093
                               BRE1  14 elseqlskkvkeltileekklrleaekakadqkyfaamrsk 54 
                                          ++q+ kkv +l+++++ ++  e  k+  d+ y ++++ k
  gene2940|gene2940|rna2940|rna2940 123 SIDKQNTKKVIDLKAMKKHIKDSEFFKNYTDEIYLNVEKLK 163
                                        5789*******************999999999999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (239 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1654  (0.0922528); expected 358.6 (0.02)
Passed bias filter:                      666  (0.0371465); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 1629.32
//
Query:       gene2941|gene2941|rna2941|rna2941  [L=191]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.031   14.6   0.3      0.041   14.3   0.3    1.2  1  Cyclin    Cyclin
       0.22   11.6   2.0       0.38   10.9   1.1    1.9  2  DUF4760   Domain of unknown function (DUF4760)


Domain annotation for each model (and alignments):
>> Cyclin  Cyclin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.3   4.5e-06     0.041      48     104 ..      67     126 ..      29     154 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.5e-06
                                        ........T--SS-.-SS-HHHHHHHHH..HHTT--HHHHHHHHHHHHHHHH..H-TT-- CS
                             Cyclin  48 aqtpkessFatkav.paisigsylsrlq..kfgesaplvllgtliYldrivkrcvsealv 104
                                        ++ ++++ F+ + +  ++ i+s ++r++  +f e++ + +++++ Y+ +ivkr v e+  
  gene2941|gene2941|rna2941|rna2941  67 QRRAEKLYFSNRRKsINLYIKSVFARIEafEFKECTLDTYISLYEYVKKIVKRSVGEYKD 126
                                        4444444444433313556889999**988999*******************99877643 PP

>> DUF4760  Domain of unknown function (DUF4760)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.23   2.1e+03      92     123 ..      13      43 ..       8      60 .. 0.71
   2 ?   10.9   1.1   4.3e-05      0.38      52     130 ..     109     189 ..      63     190 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.23
                            DUF4760  92 dmikelsvttvikawdlleplikelredsnnd 123
                                         m +e+  + ++++   ++  i+++r + + d
  gene2941|gene2941|rna2941|rna2941  13 AMAYEYV-VLFMNHTYPMDDKINKIRSKLKPD 43 
                                        5777777.788888888888888888877665 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 4.3e-05
                            DUF4760  52 lleekksekgeeeserekiltvlNflEfvavgiesg..ildEdmikelsvttvikawdlleplikelredsnndki 125
                                        l+e  k+     + e + il+v+    +++v +++   +ldE ++++     +ik ++l+e     ++ +  ++ i
  gene2941|gene2941|rna2941|rna2941 109 LYEYVKKIVKRSVGEYKDILNVIEYSVYYCVIVKQArkCLDEGIVYDDLGIDLIKLDNLVEDQAVLVKLECLAKYI 184
                                        34444555555666677777777777789****98444*********99999********9887777777777777 PP

                            DUF4760 126 yqeFe 130
                                        +++Fe
  gene2941|gene2941|rna2941|rna2941 185 FENFE 189
                                        77776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (191 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       624  (0.0348039); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1429.86
//
Query:       gene2942|gene2942|rna2942|rna2942  [L=359]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (359 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       839  (0.0467957); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 2602.58
//
Query:       gene2943|gene2943|rna2943|rna2943  [L=759]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
        6.8    6.8   7.1        4.8    7.3   0.0    4.0  5  Tetrabrachion  Tetrabrachion


Domain annotation for each model (and alignments):
>> Tetrabrachion  Tetrabrachion
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.1     0.098   1.8e+03      14      40 ..      77     101 ..      74     117 .. 0.74
   2 ?   -3.8   0.1      0.79   1.4e+04      12      20 ..     162     170 ..     161     172 .. 0.78
   3 ?   -2.6   0.0      0.31   5.6e+03      24      36 ..     405     417 ..     403     424 .. 0.80
   4 ?    0.1   0.0     0.046   8.2e+02      23      38 ..     470     485 ..     464     494 .. 0.78
   5 ?    7.3   0.0   0.00027       4.8       5      38 ..     608     641 ..     606     646 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.098
                                        HHHHHHHHHHHHHHHHHHHHHHHHTTH CS
                      Tetrabrachion  14 tviiDDRYesLknLitLRaDRLemiin 40 
                                         v+i D  + Lkn   L  D++  i+n
  gene2943|gene2943|rna2943|rna2943  77 HVVIHD--DDLKNFDKLSPDKMLSILN 101
                                        566665..5799999999999888887 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 0.79
                                        HHHHHHHHH CS
                      Tetrabrachion  12 RLtviiDDR 20 
                                        RL  +iDD 
  gene2943|gene2943|rna2943|rna2943 162 RLISVIDDT 170
                                        888899996 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 0.31
                                        HHHHHHHHHHHHH CS
                      Tetrabrachion  24 LknLitLRaDRLe 36 
                                        Lkn i +R   L 
  gene2943|gene2943|rna2943|rna2943 405 LKNFIEVRVQDLK 417
                                        9****99987775 PP

  == domain 4  score: 0.1 bits;  conditional E-value: 0.046
                                        HHHHHHHHHHHHHHHT CS
                      Tetrabrachion  23 sLknLitLRaDRLemi 38 
                                        s k L+tL  +R e++
  gene2943|gene2943|rna2943|rna2943 470 SFKELLTLAEERDEIV 485
                                        99******99998876 PP

  == domain 5  score: 7.3 bits;  conditional E-value: 0.00027
                                        HHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT CS
                      Tetrabrachion   5 taDDivYRLtviiDDRYesLknLitLRaDRLemi 38 
                                        ta++i Y L v   +RY+  k +     DRLe i
  gene2943|gene2943|rna2943|rna2943 608 TANEILYELCVFNCERYDREKGVKNGTKDRLEGI 641
                                        9*******************99999999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (759 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1115  (0.0621897); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.62u 0.22s 00:00:00.84 Elapsed: 00:00:00.38
# Mc/sec: 5922.76
//
Query:       gene2944|gene2944|rna2944|rna2944  [L=262]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (262 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1290  (0.0719505); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 1851.74
//
Query:       gene2945|gene2945|rna2945|rna2945  [L=394]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-33  114.1   4.5    2.4e-17   62.5   0.2    2.6  2  RRM_1            RNA recognition motif. (a.k.a. RRM, RBD, or 
    6.7e-06   26.1   0.1      0.096   12.8   0.0    2.6  2  RRM_7            RNA recognition motif
    1.6e-05   24.8   0.1    4.3e-05   23.4   0.0    1.7  2  Nup35_RRM        Nup53/35/40-type RNA recognition motif
     0.0023   17.9   0.0     0.0046   16.9   0.0    1.5  1  Nup35_RRM_2      Nup53/35/40-type RNA recognition motif
     0.0052   15.4  21.7     0.0067   15.1  21.7    1.2  1  Macoilin         Macoilin family
  ------ inclusion threshold ------
      0.085   12.5   1.6        6.2    6.5   0.3    3.1  2  SET_assoc        Histone lysine methyltransferase SET associa
       0.42   10.8   2.8        2.1    8.6   2.8    2.2  1  CytadhesinP1     Trypsin-sensitive surface-exposed protein
       0.72    8.9  26.2        1.2    8.1  26.2    1.4  1  LAP1C            Lamina-associated polypeptide 1C (LAP1C)
        8.5    5.1  20.8         12    4.6  20.8    1.1  1  DUF4551          Protein of unknown function (DUF4551)


Domain annotation for each model (and alignments):
>> RRM_1  RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.5   0.2   1.2e-20   2.4e-17       1      69 [.     173     241 ..     173     242 .. 0.98
   2 !   52.7   0.6   1.4e-17   2.8e-14       1      66 [.     254     317 ..     254     320 .. 0.91

  Alignments for each domain:
  == domain 1  score: 62.5 bits;  conditional E-value: 1.2e-20
                                        EEEESETTTSSHHHHHHHHHTTSCEEEEEEEEE.TTTSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEE CS
                              RRM_1   1 lfVgnLppdvteeeLkelFskfGpiksiklvrd.etgkskgfafVeFeskedAekAlealngkklggrel 69 
                                        +fV+++ +dvte +++e F+k+G+++++++++d  t  +kgf++VeF +  +A+kAl  +ngk+l ++++
  gene2945|gene2945|rna2945|rna2945 173 IFVKGFDKDVTELMVEEEFGKIGKVVNVRMPKDrDTSENKGFCYVEFSNAQSAKKALT-YNGKTLLDCQI 241
                                        8*********************************************************.******99887 PP

  == domain 2  score: 52.7 bits;  conditional E-value: 1.4e-17
                                        EEEESETTTSSHHHHHHHHHTTSCEEEEEEEEE.TTTSEEEEEEEEESSHHHHHHHHHHHTTEEETT CS
                              RRM_1   1 lfVgnLppdvteeeLkelFskfGpiksiklvrd.etgkskgfafVeFeskedAekAlealngkklgg 66 
                                        lfV+nLp+++t +++k++F k++  k+++l++d   ++++gf+f+eF+++ d++k l+  n+ +++ 
  gene2945|gene2945|rna2945|rna2945 254 LFVKNLPYTATVDDIKKVFAKYNV-KNVRLPTDeDEERNRGFCFIEFNTEQDMRKVLN--NKFNMDE 317
                                        8*********************85.5*******************************9..6555555 PP

>> RRM_7  RNA recognition motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.0   4.8e-05     0.096       3      67 ..     172     229 ..     170     247 .. 0.79
   2 !   10.6   0.0   0.00023      0.47       4      78 ..     254     321 ..     252     331 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4.8e-05
                              RRM_7   3 kvFvGGlPiDiteeelkatfkefgkvl.vdwPkkaeskkkaaenskaakgyvflvfedeksvkaLl 67 
                                         +Fv G   D+te  +++ f++ gkv+ v  Pk   +++        +kg+ ++ f++ +s k+ l
  gene2945|gene2945|rna2945|rna2945 172 TIFVKGFDKDVTELMVEEEFGKIGKVVnVRMPKDRDTSE--------NKGFCYVEFSNAQSAKKAL 229
                                        59**********************975377776544322........3689999998888877655 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00023
                              RRM_7   4 vFvGGlPiDiteeelkatfkefgkvlvdwPkkaeskkkaaenskaakgyvflvfedeksvkaLleacteee.eely 78 
                                        +Fv  lP   t +++k+ f ++    v  P  + ++++        +g+ f+ f++e+ ++++l++  + + ++l+
  gene2945|gene2945|rna2945|rna2945 254 LFVKNLPYTATVDDIKKVFAKYNVKNVRLPTDEDEERN--------RGFCFIEFNTEQDMRKVLNNKFNMDeRKLF 321
                                        5999999999**************99*99987665433........59**************99987665424444 PP

>> Nup35_RRM  Nup53/35/40-type RNA recognition motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.0   2.1e-08   4.3e-05       3      82 ..     166     239 ..     158     249 .. 0.79
   2 ?   -3.5   0.0       5.1     1e+04      52      74 ..     289     311 ..     269     321 .. 0.71

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 2.1e-08
                                        XXXXXX-EEEE-S-GGGHHHHHH.HHHTTS-BSS--CCC------------EETTEEEEEBS-HHHHHHHHTTTTE CS
                          Nup35_RRM   3 ketsdtsvivFGfpesianevle.hFskfGeiledvqvlklgkglnpkpiptgenwvkltYksessaskAlqengt 77 
                                        ++ +d  + v Gf +  +  ++e +F k G++++           + + +++++++ ++++++  sa+kAl +ng+
  gene2945|gene2945|rna2945|rna2945 166 SQSDDATIFVKGFDKDVTELMVEeEFGKIGKVVNVR-------MPKDRDTSENKGFCYVEFSNAQSAKKALTYNGK 234
                                        45556669999*******988862699999988873.......334568999***********************8 PP

                                        EETTE CS
                          Nup35_RRM  78 ilngs 82 
                                         l + 
  gene2945|gene2945|rna2945|rna2945 235 TLLDC 239
                                        76554 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 5.1
                                        -EETTEEEEEBS-HHHHHHHHTT CS
                          Nup35_RRM  52 ptgenwvkltYksessaskAlqe 74 
                                         ++ ++  +++++e + +k l++
  gene2945|gene2945|rna2945|rna2945 289 ERNRGFCFIEFNTEQDMRKVLNN 311
                                        56677777888888888877765 PP

>> Nup35_RRM_2  Nup53/35/40-type RNA recognition motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   2.3e-06    0.0046       3      53 .]     172     229 ..     170     229 .. 0.95

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2.3e-06
                        Nup35_RRM_2   3 wvaVsGydtelielVle.hFasfGeIvkhyvp......kevsvmyvkfesekdaekAL 53 
                                        ++ V G+d +  el+ e  F  +G++v+  +p       ++ + yv+f +  +a+kAL
  gene2945|gene2945|rna2945|rna2945 172 TIFVKGFDKDVTELMVEeEFGKIGKVVNVRMPkdrdtsENKGFCYVEFSNAQSAKKAL 229
                                        899*************9999********9999999999889****************8 PP

>> Macoilin  Macoilin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1  21.7   3.3e-06    0.0067     235     369 ..      39     188 ..      14     319 .. 0.61

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.3e-06
                           Macoilin 235 sknnhslnkkdsslklpeleyrekkksakssrsdskkkhehnesvdsklqekeymenkskskrlsksessgsesel 310
                                        ++ ++s    ++s   +e++ +e++ +ak+ +++++k+ +++e+v s+ ++++  ++  + k+ +k+++s++ ++ 
  gene2945|gene2945|rna2945|rna2945  39 TESEQSV---TESSASTEISDSEESANAKEASASDEKQ-SDSEEVSSEEESED--ASAESIKKGNKQQTSEKVEKA 108
                                        1111111...1122222333333222222222222222.22233333333333..333333455555566677777 PP

                           Macoilin 311 lveesvkskssssssssnknskkasagsagssnssskkhsessksvtsssssknskkq.................. 368
                                          +es +s+++ss ++++  ++k+++g+ +  + s +k s++s+s ++s+s+k+s+k                   
  gene2945|gene2945|rna2945|rna2945 109 ALDESEDSSCASSLNDASDAKEKMESGAEQEESGSDAKSSAESSSAQESNSNKQSDKSqsddatifvkgfdkdvte 184
                                        7788888888887777777778888888888888889999999999999999888887444444444444444444 PP

                           Macoilin 369 ...k 369
                                           +
  gene2945|gene2945|rna2945|rna2945 185 lmvE 188
                                        4440 PP

>> SET_assoc  Histone lysine methyltransferase SET associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.1     0.026        51      34      63 ..     212     241 ..     208     244 .. 0.75
   2 ?    6.5   0.3    0.0031       6.2      12      31 ..     263     282 ..     255     322 .. 0.74

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.026
                          SET_assoc  34 tGy.YivFndskeAerCfraedgtklftyrm 63 
                                        +G+ Y+ F++ + A+++    +g++l+++++
  gene2945|gene2945|rna2945|rna2945 212 KGFcYVEFSNAQSAKKALT-YNGKTLLDCQI 241
                                        6666*************75.56666666665 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0031
                          SET_assoc  12 vtvedlkkrLkkyewerile 31 
                                         tv d+kk + ky++++++ 
  gene2945|gene2945|rna2945|rna2945 263 ATVDDIKKVFAKYNVKNVRL 282
                                        689***************94 PP

>> CytadhesinP1  Trypsin-sensitive surface-exposed protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   2.8    0.0011       2.1       7      39 ..     349     381 ..     345     389 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0011
                       CytadhesinP1   7 fnqrrhpswntftgFglsgtdnkkdgfqkenes 39 
                                        ++ +r+  +n  +gF++++  n kd  +k +  
  gene2945|gene2945|rna2945|rna2945 349 RGNNRERRFNDRGGFNKNDRRNAKDRGNKRYKE 381
                                        7889*********************76665432 PP

>> LAP1C  Lamina-associated polypeptide 1C (LAP1C)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1  26.2   0.00062       1.2      21     158 ..      31     168 ..      15     242 .. 0.51

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00062
                                        .XXXXXXXXXXXXXXXXX.................XXXXXXXXXXXXXX..XXXXXXXXXXXX..........XXX CS
                              LAP1C  21 sseeeaqtrkplsslkkdhqeveti.gsesadtedkseseqevnlseepkdetEeedsessqsgeeghklsseslg 95 
                                        ++++e+ ++++ +s  +   + e+  ++esa+++++s+s+++ + see + e+E+ed ++ + ++ +++++se++ 
  gene2945|gene2945|rna2945|rna2945  31 QKKDESSVTESEQSVTESSASTEISdSEESANAKEASASDEKQSDSEEVSSEEESEDASAESIKKGNKQQTSEKVE 106
                                        3333433333333333333333333033455555556666656666665555555555544444444555556666 PP

                                        XXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXX..XXXXXXXXXXX......XXXXXXXXXXX CS
                              LAP1C  96 eekldsedsvsssdk.tgradaqleessaalseea.sdrtaasqepsaadsqeaqssghskaeqe 158
                                        + +ld+++++s   +    +da+ + +s a +ee+ sd ++  + +sa   qe++s+++s ++q 
  gene2945|gene2945|rna2945|rna2945 107 KAALDESEDSSCASSlNDASDAKEKMESGAEQEESgSDAKSSAESSSA---QESNSNKQSDKSQS 168
                                        666654444333332022333333322222222220222222222222...33333332222222 PP

>> DUF4551  Protein of unknown function (DUF4551)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6  20.8    0.0061        12     102     238 ..      21     166 ..      10     201 .. 0.49

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.0061
                            DUF4551 102 talkselllskdkkself.kvspskasekksrressgaakkssslnessl.dakekeektvskk.sqlslslselr 174
                                        +++k++l+++++k ++++ + ++s + +++s++ s++  ++s + +e+s  d+k+++++ vs++  + ++s+ +++
  gene2945|gene2945|rna2945|rna2945  21 PMAKKQLKKQQKKDESSVtESEQSVTESSASTEISDS--EESANAKEASAsDEKQSDSEEVSSEeESEDASAESIK 94 
                                        5666665555444444330333333444444444443..4455666666655555555544444044445557777 PP

                            DUF4551 175 klseeekeelesekalkslrsasrplPesllsrapkpp..........sspkeppssslskderdskseessqv 238
                                        k ++++  e+ +++al +++ +s+    +  s a ++           s+ k++ +ss+ ++++++k++  +++
  gene2945|gene2945|rna2945|rna2945  95 KGNKQQTSEKVEKAALDESEDSSCASSLNDASDAKEKMesgaeqeesgSDAKSSAESSSAQESNSNKQS--DKS 166
                                        777777777777777777666666655333222222112232333333222222222222222222221..122 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (394 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2745  (0.153104); expected 358.6 (0.02)
Passed bias filter:                      601  (0.0335211); expected 358.6 (0.02)
Passed Vit filter:                       219  (0.0122148); expected 17.9 (0.001)
Passed Fwd filter:                        85  (0.00474092); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 1.32u 0.38s 00:00:01.70 Elapsed: 00:00:00.60
# Mc/sec: 1988.59
//
Query:       gene2946|gene2946|rna2946|rna2946  [L=55]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (55 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       356  (0.0198561); expected 358.6 (0.02)
Passed bias filter:                      175  (0.00976072); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.31s 00:00:00.69 Elapsed: 00:00:00.46
# Mc/sec: 359.88
//
Query:       gene2947|gene2947|rna2947|rna2947  [L=141]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.035   14.3   0.0      0.054   13.6   0.0    1.3  1  CBM_26    C-terminal carbohydrate-binding module


Domain annotation for each model (and alignments):
>> CBM_26  C-terminal carbohydrate-binding module
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0     3e-06     0.054      13      71 ..      23      80 ..      13      89 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3e-06
                                       EE--SSEEEEEE-..TT----BGGGEEEEEEESSTT--EEEEEEEETTS-EEEEEEE-- CS
                             CBM_26 13 tklkpGknevlvngksalldlrnssyqvdvrfsdpsvkelkatiWylnGrredlklekp 71
                                       t l+  +ne+l n k ++    + +y   ++  d  v e++  +  ++G re++ le+ 
  gene2947|gene2947|rna2947|rna2947 23 TSLNLHRNELLAN-KIKTEYFSDVRYGKMIKMMDECVVEMEKVVCDMKGMREKFALERG 80
                                       5577789*****9.77788899999999****************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       593  (0.0330749); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1023.96
//
Query:       gene2948|gene2948|rna2948|rna2948  [L=233]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (233 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       485  (0.0270511); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1639.90
//
Query:       gene2949|gene2949|rna2949|rna2949  [L=108]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.8e-37  126.5   6.4    4.3e-37  126.3   6.4    1.0  1  Ribosomal_L34e  Ribosomal protein L34e
  ------ inclusion threshold ------
      0.026   14.5   0.3      0.033   14.2   0.3    1.4  1  Cytochrome_C7   Cytochrome c7 and related cytochrome c


Domain annotation for each model (and alignments):
>> Ribosomal_L34e  Ribosomal protein L34e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.3   6.4   4.8e-41   4.3e-37       1      94 []       1      94 [.       1      94 [. 0.99

  Alignments for each domain:
  == domain 1  score: 126.3 bits;  conditional E-value: 4.8e-41
                     Ribosomal_L34e  1 MvqrltyrrrlsYntrsnkvrvvktpggklvyqykkkkgkapkCgdckkkLqGipalrpkelsrlsktkktvsRaYGg 78
                                       Mvqr t+r++++Y+trsn++++v+tpg++lv+++ kk+gk pkCg c+kkL Gi+ +rp+++sr++k+++tv+R YGg
  gene2949|gene2949|rna2949|rna2949  1 MVQRQTVRSHHTYRTRSNRMVKVRTPGKNLVLHNAKKRGKLPKCGTCHKKLLGIKMARPADFSRMKKHNRTVNRVYGG 78
                                       9***************************************************************************** PP

                     Ribosomal_L34e 79 slcakcvkerivrafl 94
                                       +lc+ cv+++i+ af+
  gene2949|gene2949|rna2949|rna2949 79 VLCSGCVRDKIIGAFM 94
                                       **************96 PP

>> Cytochrome_C7  Cytochrome c7 and related cytochrome c
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.3   3.6e-06     0.033      13      53 ..      41      84 ..       7      97 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.6e-06
                      Cytochrome_C7 13 gykCtdCHsklfeska.kkk.maemekgkskkaeves.ltCgaC 53
                                         kC +CH+kl   k+ + +  + m+k++ + ++v   + C  C
  gene2949|gene2949|rna2949|rna2949 41 LPKCGTCHKKLLGIKMaRPAdFSRMKKHNRTVNRVYGgVLCSGC 84
                                       45899999999755553322366666677766777777779888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       491  (0.0273858); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 790.86
//
Query:       gene295|gene295|rna295|rna295  [L=346]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-11   43.2  13.7       0.45   10.7   0.3    8.1  8  LRR_6     Leucine Rich repeat
    1.8e-08   34.0   7.4      0.012   15.4   0.0    5.7  5  LRR_8     Leucine rich repeat
    1.1e-06   28.9   5.7       0.32   11.5   0.0    5.6  6  LRR_4     Leucine Rich repeats (2 copies)
    8.2e-06   25.7   0.9         67    4.6   0.0    7.0  6  LRR_1     Leucine Rich Repeat


Domain annotation for each model (and alignments):
>> LRR_6  Leucine Rich repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.19   8.7e+02       6      15 ..      30      39 ..      29      47 .. 0.82
   2 !    6.7   0.0    0.0019       8.3       4      17 ..      89     102 ..      87     103 .. 0.88
   3 !    9.6   0.1   0.00022         1       4      24 .]     117     137 ..     117     137 .. 0.94
   4 !    4.7   0.0    0.0086        39       3      16 ..     147     160 ..     145     162 .. 0.89
   5 ?   -0.6   0.0      0.42   1.9e+03       3      15 ..     174     186 ..     174     188 .. 0.88
   6 !   10.7   0.3    0.0001      0.45       6      23 ..     204     221 ..     204     222 .. 0.92
   7 !    5.6   0.0    0.0043        19      10      23 ..     235     248 ..     231     248 .. 0.86
   8 !    5.8   0.2    0.0039        17       7      20 ..     269     282 ..     266     285 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.19
                          LRR_6  6 teLdLsgNdI 15
                                   ++++L+gN +
  gene295|gene295|rna295|rna295 30 KTVNLTGNVF 39
                                   89******76 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0019
                          LRR_6   4 hLteLdLsgNdIgD 17 
                                    +L eLdLs N I+ 
  gene295|gene295|rna295|rna295  89 NLVELDLSENAIST 102
                                    799********985 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.00022
                          LRR_6   4 hLteLdLsgNdIgDeGaeaLa 24 
                                    +L+ L +s++++g  G++ La
  gene295|gene295|rna295|rna295 117 KLKVLRMSDCGLGAIGGKNLA 137
                                    69****************997 PP

  == domain 4  score: 4.7 bits;  conditional E-value: 0.0086
                          LRR_6   3 thLteLdLsgNdIg 16 
                                    ++L++ d+s N+++
  gene295|gene295|rna295|rna295 147 SSLEYIDISKNKLD 160
                                    89*********986 PP

  == domain 5  score: -0.6 bits;  conditional E-value: 0.42
                          LRR_6   3 thLteLdLsgNdI 15 
                                    ++L++  +++N I
  gene295|gene295|rna295|rna295 174 PNLKTIKIQYNSI 186
                                    589********88 PP

  == domain 6  score: 10.7 bits;  conditional E-value: 0.0001
                          LRR_6   6 teLdLsgNdIgDeGaeaL 23 
                                    t+LdL++N I+ eG++ L
  gene295|gene295|rna295|rna295 204 TSLDLRDNLISVEGCKNL 221
                                    89************9987 PP

  == domain 7  score: 5.6 bits;  conditional E-value: 0.0043
                          LRR_6  10 LsgNdIgDeGaeaL 23 
                                    L ++ +g+eG+ea+
  gene295|gene295|rna295|rna295 235 LGDCLVGNEGLEAF 248
                                    899*********96 PP

  == domain 8  score: 5.8 bits;  conditional E-value: 0.0039
                          LRR_6   7 eLdLsgNdIgDeGa 20 
                                     Ld s+N+I+ +G+
  gene295|gene295|rna295|rna295 269 VLDFSYNNISQQGV 282
                                    59*******99997 PP

>> LRR_8  Leucine rich repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0      0.62   2.8e+03      19      24 ..      46      51 ..      28      58 .. 0.45
   2 !   15.4   0.0   2.6e-06     0.012      21      47 ..      84     110 ..      82     128 .. 0.88
   3 !    5.7   0.0    0.0028        12      21      38 ..     143     160 ..     116     162 .. 0.87
   4 !    9.7   0.1   0.00016      0.72      20      48 ..     169     197 ..     166     213 .. 0.77
   5 ?    2.1   0.2     0.037   1.7e+02      25      38 ..     265     278 ..     254     286 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.62
                                   TSSTT- CS
                          LRR_8 19 eaFkgl 24
                                   e Fk l
  gene295|gene295|rna295|rna295 46 ELFKEL 51
                                   333333 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 2.6e-06
                                    STT-TT--EEE--SS---GGGGGGGTT CS
                          LRR_8  21 FkglsnLkvLdLsnNllttlspgafsg 47 
                                    F +  nL +LdLs+N ++t+ p++f+ 
  gene295|gene295|rna295|rna295  84 FVDPANLVELDLSENAISTVLPETFVE 110
                                    77789********************85 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.0028
                                    STT-TT--EEE--SS--- CS
                          LRR_8  21 FkglsnLkvLdLsnNllt 38 
                                     k+ s+L+++d+s N+l+
  gene295|gene295|rna295|rna295 143 IKDKSSLEYIDISKNKLD 160
                                    566689999****99985 PP

  == domain 4  score: 9.7 bits;  conditional E-value: 0.00016
                                    SSTT-TT--EEE--SS---GGGGGGGTT- CS
                          LRR_8  20 aFkglsnLkvLdLsnNllttlspgafsgL 48 
                                    + + ++nLk++++ +N++++ s + f   
  gene295|gene295|rna295|rna295 169 TLSAFPNLKTIKIQYNSIKRASMDDFIKS 197
                                    667789**************999999765 PP

  == domain 5  score: 2.1 bits;  conditional E-value: 0.037
                                    TT--EEE--SS--- CS
                          LRR_8  25 snLkvLdLsnNllt 38 
                                    +n  vLd s+N+++
  gene295|gene295|rna295|rna295 265 TNNLVLDFSYNNIS 278
                                    55579*******98 PP

>> LRR_4  Leucine Rich repeats (2 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.1      0.45     2e+03      28      28 ..      47      47 ..      22      69 .. 0.57
   2 !   11.5   0.0   7.1e-05      0.32       2      37 ..      89     129 ..      88     137 .. 0.76
   3 !    8.1   0.0   0.00084       3.7       2      36 ..     117     159 ..     116     163 .. 0.76
   4 !   10.7   0.0   0.00012      0.55       2      36 ..     148     186 ..     147     196 .. 0.79
   5 ?    2.9   0.1     0.037   1.7e+02       4      25 ..     204     221 ..     204     223 .. 0.75
   6 ?    1.1   0.1      0.14   6.1e+02       5      15 ..     269     279 ..     268     306 .. 0.75

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.45
                                   E CS
                          LRR_4 28 L 28
                                   L
  gene295|gene295|rna295|rna295 47 L 47
                                   1 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 7.1e-05
                                    S--EEE--SS---.E-S-.HHH.-TT...--EEE-.-S---- CS
                          LRR_4   2 nLevLdLsnNqlt.dipl.lek.lpn...LkeLdLsgNnlit 37 
                                    nL +LdLs N ++  +p  +   l+    Lk+L +s++  ++
  gene295|gene295|rna295|rna295  89 NLVELDLSENAIStVLPEtFVEfLTRadkLKVLRMSDC-GLG 129
                                    899**********8888895533444444******998.555 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.00084
                                    S--EEE--SS---E-S-..HH......H.-TT--EEE-.-S--- CS
                          LRR_4   2 nLevLdLsnNqltdipl..le......k.lpnLkeLdLsgNnli 36 
                                    +L+vL  s++ l  i++  l+      k   +L+++d+s N ++
  gene295|gene295|rna295|rna295 117 KLKVLRMSDCGLGAIGGknLAmaleqiKdKSSLEYIDISKN-KL 159
                                    7999*****99999999873355555533566******999.44 PP

  == domain 4  score: 10.7 bits;  conditional E-value: 0.00012
                                    S--EEE--SS---.E-S-....HHH-TT--EEE-.-S--- CS
                          LRR_4   2 nLevLdLsnNqlt.dipl....leklpnLkeLdLsgNnli 36 
                                    +Le++d+s N+l          l+ +pnLk++ +  N  i
  gene295|gene295|rna295|rna295 148 SLEYIDISKNKLDyGATEmgktLSAFPNLKTIKIQYN-SI 186
                                    79***********554448777667*********777.33 PP

  == domain 5  score: 2.9 bits;  conditional E-value: 0.037
                                    -EEE--SS---E-S-HHH-TT- CS
                          LRR_4   4 evLdLsnNqltdiplleklpnL 25 
                                    ++LdL++N ++ +++   ++nL
  gene295|gene295|rna295|rna295 204 TSLDLRDNLIS-VEG---CKNL 221
                                    68999998888.566...6665 PP

  == domain 6  score: 1.1 bits;  conditional E-value: 0.14
                                    EEE--SS---E CS
                          LRR_4   5 vLdLsnNqltd 15 
                                    vLd+s N+++ 
  gene295|gene295|rna295|rna295 269 VLDFSYNNISQ 279
                                    69999999984 PP

>> LRR_1  Leucine Rich Repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.94   4.2e+03       3      12 ..      30      39 ..      29      53 .. 0.75
   2 ?    4.3   0.0      0.02        89       1      21 [.      89     109 ..      89     111 .. 0.87
   3 ?    3.1   0.0     0.048   2.1e+02       1      12 [.     117     128 ..     117     141 .. 0.85
   4 ?    4.6   0.0     0.015        67       1      13 [.     148     166 ..     148     199 .. 0.74
   5 ?    0.8   0.0      0.28   1.3e+03       4      12 ..     205     213 ..     204     227 .. 0.73
   6 ?    1.6   0.1      0.15   6.6e+02       4      21 ..     269     286 ..     269     288 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.94
                          LRR_1  3 rhLdLsnnpl 12
                                   ++ +L++n +
  gene295|gene295|rna295|rna295 30 KTVNLTGNVF 39
                                   7889999976 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.02
                          LRR_1   1 nLrhLdLsnnpllglppnsfq 21 
                                    nL +LdLs n ++  +p++f 
  gene295|gene295|rna295|rna295  89 NLVELDLSENAISTVLPETFV 109
                                    899*******99999998885 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.048
                          LRR_1   1 nLrhLdLsnnpl 12 
                                    +L++L +s++ l
  gene295|gene295|rna295|rna295 117 KLKVLRMSDCGL 128
                                    7*********98 PP

  == domain 4  score: 4.6 bits;  conditional E-value: 0.015
                          LRR_1   1 nLrhLdLsnnpl......l 13 
                                    +L+++d+s n l       
  gene295|gene295|rna295|rna295 148 SLEYIDISKNKLdygateM 166
                                    5899999999885555553 PP

  == domain 5  score: 0.8 bits;  conditional E-value: 0.28
                          LRR_1   4 hLdLsnnpl 12 
                                    +LdL++n +
  gene295|gene295|rna295|rna295 205 SLDLRDNLI 213
                                    799999876 PP

  == domain 6  score: 1.6 bits;  conditional E-value: 0.15
                          LRR_1   4 hLdLsnnpllglppnsfq 21 
                                    +Ld s+n++++ + n ++
  gene295|gene295|rna295|rna295 269 VLDFSYNNISQQGVNLLE 286
                                    59*******998888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (346 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       555  (0.0309554); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 2275.76
//
Query:       gene2950|gene2950|rna2950|rna2950  [L=261]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.3e-24   85.7   4.2    3.3e-12   46.5   0.0    3.0  3  HORMA         HORMA domain
  ------ inclusion threshold ------
       0.63   10.5   7.7       0.13   12.8   4.1    1.7  2  TAA-Trp-ring  Tryptophan-ring motif of head of Trimeric autot


Domain annotation for each model (and alignments):
>> HORMA  HORMA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.5   0.0   3.7e-16   3.3e-12      50      97 ..      35      82 ..      12      94 .. 0.86
   2 !   39.9   0.1   3.7e-14   3.3e-10     147     189 ..      92     134 ..      89     154 .. 0.86
   3 ?   -1.2   0.5      0.14   1.3e+03     113     126 ..     216     218 ..     156     254 .. 0.62

  Alignments for each domain:
  == domain 1  score: 46.5 bits;  conditional E-value: 3.7e-16
                              HORMA 50 drlldwLekGvfdaLekkyLealiltIykdkdepenvlEsYtFsfkyt 97
                                       +r+l wL++G+ daL+k+yL+++iltIy++k++p+ +lEsYt++++ +
  gene2950|gene2950|rna2950|rna2950 35 NRFLCWLNNGIRDALSKNYLHQIILTIYTEKNRPDAILESYTITVTGK 82
                                       56999**************************************99865 PP

  == domain 2  score: 39.9 bits;  conditional E-value: 3.7e-14
                              HORMA 147 litltqsLpplpekryltmkLlytddtPedyePpgFkaaaeee 189
                                        +  + + L plp++ryl+m+L+y++++P++yeP gFk+a+ e 
  gene2950|gene2950|rna2950|rna2950  92 IADVLKMLAPLPRTRYLSMRLVYNETCPDEYEPVGFKRADYEY 134
                                        56677889*******************************9987 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 0.14
                              HORMA 113 kkknleslsldeke 126
                                        ++           +
  gene2950|gene2950|rna2950|rna2950 216 EQ-----------K 218
                                        11...........1 PP

>> TAA-Trp-ring  Tryptophan-ring motif of head of Trimeric autotransporter adhesin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.1       1.6   1.4e+04      20      28 ..     140     148 ..     135     149 .. 0.58
   2 ?   12.8   4.1   1.4e-05      0.13       5      58 ..     167     225 ..     164     239 .. 0.74

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 1.6
                       TAA-Trp-ring  20 kyyseedik 28 
                                        ++  ++dik
  gene2950|gene2950|rna2950|rna2950 140 EVLVKDDIK 148
                                        366677776 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 1.4e-05
                       TAA-Trp-ring   5 kkdNGketelVKvgdkyyseediklatGkp...........dvstngsntattdtdegsglvtan 58 
                                         ++NG + e V v+dk+++e +     G++           +++  g +++  +t +++  +t+ 
  gene2950|gene2950|rna2950|rna2950 167 NDTNGARNERVVVDDKIIKERG----RGNEdmaerhgcchpTNN--GDSNEERKTEQKNSSATTT 225
                                        689*******************....*************86433..4444444444444444432 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1042  (0.0581181); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 1893.09
//
Query:       gene2951|gene2951|rna2951|rna2951  [L=149]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-07   31.5  11.4    1.9e-07   30.9  11.4    1.3  1  PHD            PHD-finger
     0.0076   16.4   1.5      0.011   15.9   0.0    1.8  2  Ribosomal_S25  S25 ribosomal protein
  ------ inclusion threshold ------
       0.02   14.4   0.1       0.04   13.5   0.1    1.5  1  HTH_24         Winged helix-turn-helix DNA-binding
       0.02   14.7   0.0       0.03   14.2   0.0    1.3  1  MarR_2         MarR family
      0.024   14.5   0.0       0.04   13.8   0.0    1.3  1  TrmB           Sugar-specific transcriptional regulator TrmB
      0.036   14.0   0.0       0.07   13.1   0.0    1.5  1  MarR           MarR family
      0.056   13.2   1.1      0.093   12.5   1.1    1.3  1  Hormone_1      Somatotropin hormone family


Domain annotation for each model (and alignments):
>> PHD  PHD-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.9  11.4   7.3e-11   1.9e-07       2      50 ..       4      50 ..       3      52 .. 0.94

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 7.3e-11
                                       BTTTTSTTSTTSCEEEETTTSCEEETTTSSSTHSHHSHHSSTBSSTTTH CS
                                PHD  2 CavCkkksdeeeelvqCdgCkrwfHqkClkppleseekpegewlCekCk 50
                                       C +C+  ++ + +++qCd+C+ w H+ C+++  +++++  + ++C+ C 
  gene2951|gene2951|rna2951|rna2951  4 C-ICRI-NHSDLDMLQCDKCNAWSHTVCCGFFSNNDKRIPQFYTCNICL 50
                                       8.****.99**********************9999999999*******6 PP

>> Ribosomal_S25  S25 ribosomal protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   4.4e-06     0.011      59      98 ..      75     114 ..      57     117 .. 0.86
   2 ?   -0.7   0.7      0.66   1.7e+03      17      30 ..     122     136 ..     113     146 .. 0.55

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 4.4e-06
                      Ribosomal_S25  59 psvvserlkingslArraLreleekgliklvskhraqviY 98 
                                        +  + +rl ++  +Arr+ ++l+++g+i+ ++ + +q+ Y
  gene2951|gene2951|rna2951|rna2951  75 VGWLGKRLGVKEGVARRIVKKLLNDGFIEIIALNTRQRKY 114
                                        556889*************************999999877 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.66
                      Ribosomal_S25  17 gkak.kKKwskgkvk 30 
                                         k+k kK    gkvk
  gene2951|gene2951|rna2951|rna2951 122 VKKKvKKYFYIGKVK 136
                                        233335544445554 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   1.5e-05      0.04      23      48 .]      78     103 ..      78     103 .. 0.94

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.5e-05
                             HTH_24  23 LAerlglSpstvnrrlkrLeeeGlIk 48 
                                        L +rlg+  +  +r +k+L ++G+I+
  gene2951|gene2951|rna2951|rna2951  78 LGKRLGVKEGVARRIVKKLLNDGFIE 103
                                        679*********************97 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   1.2e-05      0.03      24      53 ..      75     104 ..      58     113 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.2e-05
                                        HHHHHHHHTSSHHHHHHHHHHHHHTTSEEE CS
                             MarR_2  24 vgelarrlglsksavsrilkrLvaaGLver 53 
                                        vg l +rlg++ + + ri+k+L   G++e 
  gene2951|gene2951|rna2951|rna2951  75 VGWLGKRLGVKEGVARRIVKKLLNDGFIEI 104
                                        899*************************85 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   1.6e-05      0.04      29      66 ..      79     118 ..      70     120 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.6e-05
                                        CCCTTSSCHCHHHHHHHHHHCTSEEEESST..TTEEEE-- CS
                               TrmB  29 aeelgvprskvYevLrsLedkGlVerekgr..pklYravd 66 
                                         ++lgv +  + +++++L++ G++e++  +   ++Y+av+
  gene2951|gene2951|rna2951|rna2951  79 GKRLGVKEGVARRIVKKLLNDGFIEIIALNtrQRKYVAVK 118
                                        68999**********************9776678999996 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   2.7e-05      0.07      18      48 ..      73     103 ..      62     107 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.7e-05
                                        EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                               MarR  18 lsvseLakklgvskstvtrvldrLekkGlie 48 
                                        l v  L+k+lgv+ + + r++++L  +G+ie
  gene2951|gene2951|rna2951|rna2951  73 LGVGWLGKRLGVKEGVARRIVKKLLNDGFIE 103
                                        667779************************7 PP

>> Hormone_1  Somatotropin hormone family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   1.1   3.6e-05     0.093     174     205 ..      33      64 ..      15      69 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.6e-05
                                        ------HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Hormone_1 174 ssdedrrllafynLfsCLrkDsrkvdtylklL 205
                                         s++d+r+ +fy    CL++D++++  y + L
  gene2951|gene2951|rna2951|rna2951  33 FSNNDKRIPQFYTCNICLDNDISRLALYRRAL 64 
                                        59***********************9998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1099  (0.0612973); expected 358.6 (0.02)
Passed bias filter:                      581  (0.0324056); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1066.29
//
Query:       gene2952|gene2952|rna2952|rna2952  [L=172]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.021   13.8   0.3      0.025   13.5   0.3    1.0  1  Phage_min_cap2  Phage minor capsid protein 2
       0.37   10.2   1.4       0.45    9.9   1.4    1.1  1  RNA_pol_Rpb1_5  RNA polymerase Rpb1, domain 5


Domain annotation for each model (and alignments):
>> Phage_min_cap2  Phage minor capsid protein 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.3   2.8e-06     0.025      35     158 ..      22     149 ..      14     160 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.8e-06
                     Phage_min_cap2  35 tgeltntaewqieklaelgll.....nreilkliskltgksekelrkllkeagdkaiksddkelaiykeaglepkp 105
                                        + ++t+  +   ekl++l+       ++e + li++ t   ++e +k+  + g++ + + + ++ ++ ++ +++ +
  gene2952|gene2952|rna2952|rna2952  22 NLRITDYFNNLKEKLKALQETyskhfRNESKVLIKENTSFIKQEFDKIPYDDGTECMPQLN-DILEELNRSANDSK 96 
                                        45677778888888888887777888999******************************99.666677788899** PP

                     Phage_min_cap2 106 lekseelqqlveaylkqtegelkNltnttaltslekaYerildeavakvvsGa 158
                                        l +  +l  l++ yl  t++  + +++ + ++++++ Y ++ + ++ +++ G 
  gene2952|gene2952|rna2952|rna2952  97 LVNVMALSRLLKTYLICTNKPSSEVLKKINIKEIREFYAECKKYTTHNTFCGC 149
                                        **********************************************9998885 PP

>> RNA_pol_Rpb1_5  RNA polymerase Rpb1, domain 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   1.4     5e-05      0.45     116     217 ..      11     133 ..       4     144 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 5e-05
                                        TT-SS-SS-EEEEEB-SSSSSCHHHCHHHHHHHSECBTTEEEEEEEEEEEEEEET....................E CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....................x RF
                     RNA_pol_Rpb1_5 116 nvskniksksltvllvdeeakelekakkvkkaiekgikkikrilvkeaekgkeee....................k 171
                                        +++++  +   +++++d   + +ek k+++++ +k++ + +++l+ke+++  ++e                    +
  gene2952|gene2952|rna2952|rna2952  11 EINNAEMNDRKNLRITDYFNNLKEKLKALQETYSKHFRNESKVLIKENTSFIKQEfdkipyddgtecmpqlndilE 86 
                                        445555566667788888888999999*******************9996555556999************99999 PP

                                        EEEEEECS--HHHHTTSTTTBETTTEEES.SHHHHHHHHCHHHHHHH CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxx RF
                     RNA_pol_Rpb1_5 172 elvletegvnlsevlkveevvdageilsn.diaeileilgieaarka 217
                                        el  + ++ +l +v+  ++ +++  i++n    e+l+ + i++ r++
  gene2952|gene2952|rna2952|rna2952  87 ELNRSANDSKLVNVMALSRLLKTYLICTNkPSSEVLKKINIKEIREF 133
                                        99999999*********************55579*****99999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1349  (0.0752412); expected 358.6 (0.02)
Passed bias filter:                      515  (0.0287244); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1150.72
//
Query:       gene2953|gene2953|rna2953|rna2953  [L=504]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (504 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       492  (0.0274416); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 3293.72
//
Query:       gene2954|gene2954|rna2954|rna2954  [L=126]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.055   13.9   0.0      0.069   13.6   0.0    1.2  1  DUF2569   Protein of unknown function (DUF2569)
      0.082   13.3   0.3       0.13   12.7   0.3    1.4  1  Curto_V3  Curtovirus V3 protein


Domain annotation for each model (and alignments):
>> DUF2569  Protein of unknown function (DUF2569)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   7.7e-06     0.069      47      87 ..      38      84 ..       8      89 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 7.7e-06
                            DUF2569 47 s......lltlllileiitnialvafsilllvlffkrrksfPklyii 87
                                       +      +  l + +++++ +++va++++l++ f++ r+  ++++i+
  gene2954|gene2954|rna2954|rna2954 38 QvqkeelIELLHVSFDLLFLLFVVAVTMYLGIKFYRDRRLQRRHIIN 84
                                       1334443444567899***************************9996 PP

>> Curto_V3  Curtovirus V3 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.3   1.4e-05      0.13       6      40 ..      53      92 ..      49     125 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.4e-05
                           Curto_V3  6 dwlfllfvfsillqsginfygt..fqserisa...klssl 40
                                       d lfllfv ++ +  gi fy    +q  +i +   +lss 
  gene2954|gene2954|rna2954|rna2954 53 DLLFLLFVVAVTMYLGIKFYRDrrLQRRHIINsplRLSSR 92
                                       89******************74225666554412244444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       938  (0.0523175); expected 358.6 (0.02)
Passed bias filter:                      636  (0.0354733); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.35s 00:00:00.94 Elapsed: 00:00:00.56
# Mc/sec: 677.64
//
Query:       gene2955|gene2955|rna2955|rna2955  [L=277]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
     0.0022   18.0   6.5     0.0022   18.0   6.5    2.7  3  zf-BED     BED zinc finger
  ------ inclusion threshold ------
       0.41   11.1   3.7       0.31   11.5   1.3    2.0  2  Evr1_Alr   Erv1 / Alr family


Domain annotation for each model (and alignments):
>> zf-BED  BED zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.8       1.2   1.1e+04      27      38 ..      30      43 ..      25      43 .. 0.55
   2 ?   -1.4   0.0      0.27   2.5e+03      21      29 ..     109     117 ..     108     124 .. 0.81
   3 !   18.0   6.5   2.4e-07    0.0022       3      43 ..     235     273 ..     233     274 .. 0.94

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 1.2
                                       ---..SSTHHHHHH CS
                             zf-BED 27 srg..ggttnLkrH 38
                                        +g  +gt+  ++H
  gene2955|gene2955|rna2955|rna2955 30 QNGtnTGTHTVRAH 43
                                       33444467666666 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.27
                                        TTTEE---- CS
                             zf-BED  21 yCgkilsrg 29 
                                        +Cg+++++g
  gene2955|gene2955|rna2955|rna2955 109 FCGNEIDGG 117
                                        7*****998 PP

  == domain 3  score: 18.0 bits;  conditional E-value: 2.4e-07
                                        TTSSS----.GGSS--EETTTTEE----SSTHHHHHHHHHS- CS
                             zf-BED   3 vWkyftpvs.lkeqkavCryCgkilsrgggttnLkrHLrrkH 43 
                                         +kyf++++ +++++ vC yC +++ ++   ++L +H +++H
  gene2955|gene2955|rna2955|rna2955 235 MKKYFHKITsIRKKVFVCEYCRCKFVYK---KCLVNHVEKNH 273
                                        679****99999****************...**********9 PP

>> Evr1_Alr  Erv1 / Alr family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0      0.61   5.5e+03      60      78 ..      27      45 ..      14      58 .. 0.68
   2 ?   11.5   1.3   3.5e-05      0.31      17      51 ..     225     261 ..     216     274 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.61
                                       CCGSSHHHHHHHHHHHHHH CS
                           Evr1_Alr 60 kevesrdelvlWlweaHNe 78
                                       k+ ++ +++ + +++aHN 
  gene2955|gene2955|rna2955|rna2955 27 KNGQNGTNTGTHTVRAHNY 45
                                       3446666777777888885 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 3.5e-05
                                        S..HHH.HHHH-.CHHHHHHHHHHHSSCHHHHHHHHH CS
                           Evr1_Alr  17 kpteeq.qkela.vlkaflkliakfypCeeCaehfek 51 
                                        k ++++ ++e++  ++++ ++ +k++ Ce+C+ +f  
  gene2955|gene2955|rna2955|rna2955 225 KAENQNlNEEMKkYFHKITSIRKKVFVCEYCRCKFVY 261
                                        3333336999999*******************99976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (277 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1502  (0.0837749); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.63u 0.38s 00:00:01.01 Elapsed: 00:00:00.58
# Mc/sec: 1427.17
//
Query:       gene2956|gene2956|rna2956|rna2956  [L=25]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (25 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       130  (0.00725082); expected 358.6 (0.02)
Passed bias filter:                      120  (0.00669307); expected 358.6 (0.02)
Passed Vit filter:                         4  (0.000223102); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.34s 00:00:00.81 Elapsed: 00:00:00.51
# Mc/sec: 146.86
//
Query:       gene2957|gene2957|rna2957|rna2957  [L=233]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.048   13.7   0.1      0.082   13.0   0.1    1.4  1  DUF1398   Protein of unknown function (DUF1398)


Domain annotation for each model (and alignments):
>> DUF1398  Protein of unknown function (DUF1398)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   4.5e-06     0.082       8      53 ..     135     183 ..     132     206 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4.5e-06
                                        HHH---HHHHHHHHHH-SSEEEEE...TTTSEEEEE-SSS-EEEEE-ST CS
                            DUF1398   8 ksdadfpafiqelkrlgvskYeyf...vadgnvkyvgendevvevkakr 53 
                                        ++ ++f++f  +lk+l+vs+++y+    +++n+++v+++ + +  ++++
  gene2957|gene2957|rna2957|rna2957 135 RQTQNFQSFPPNLKHLKVSYFDYYescYESNNIRFVLNKLTLLMYNNEE 183
                                        7889***************999984335678888886655555444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (233 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       462  (0.0257683); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.63u 0.32s 00:00:00.95 Elapsed: 00:00:00.55
# Mc/sec: 1270.97
//
Query:       gene2958|gene2958|rna2958|rna2958  [L=447]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
   2.2e-114  382.8   6.0   2.4e-114  382.7   6.0    1.0  1  Cpn60_TCP1    TCP-1/cpn60 chaperonin family
  ------ inclusion threshold ------
       0.02   14.5   0.0      0.041   13.5   0.0    1.6  1  Peripla_BP_4  Periplasmic binding protein domain


Domain annotation for each model (and alignments):
>> Cpn60_TCP1  TCP-1/cpn60 chaperonin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  382.7   6.0  2.7e-118  2.4e-114      40     482 ..       4     447 .]       1     447 [] 0.96

  Alignments for each domain:
  == domain 1  score: 382.7 bits;  conditional E-value: 2.7e-118
                                        XXSHHHHHHHHHHHHCCCCCTTCHHHHHHHHHHHHHHHHHHHHCTXXHHHHHHHHHHHHHHHHHHHHHHXEEBXSC CS
                         Cpn60_TCP1  40 iehPaakllveaaesqdeevGDGTttvviLageLleeaekliaagvhpttiiegyekalekaleaLkeiaveisse 115
                                         e+P+ +ll++++++qdee+GDGTt+vv+ a++Ll +aekli++g+hp+++ egy+ a++ a+e+L++i++ei+ +
  gene2958|gene2958|rna2958|rna2958   4 TENPISRLLQRLSSAQDEEIGDGTTSVVLVASALLAKAEKLIEKGIHPIKVSEGYDVACKLAIEHLESIKEEIRPS 79 
                                        589******************************************************************9999987 PP

                                        STT.HHHHHHHHHHCTTSSXXSTHHHHHHHHHHHH.HCHCCCSEECSCCCEECCCCEECECTTSEEESEEEESS-- CS
                         Cpn60_TCP1 116 ekdreeLlkvartslsskltskeaeelsklvvdAv.klieenekeldlgrikvvkieggsledselveGlvldkgv 190
                                           +e+++++a tsl+sk+++k ++ +++ +v+A+ k+++++++++d++ ik+vk+ g + +  elv+G++ldk++
  gene2958|gene2958|rna2958|rna2958  80 -SLKENMKNAALTSLNSKIVRKAKDAVAEVCVNAIlKVCDKDRRDVDFELIKIVKKIGPDFKCIELVNGVLLDKSF 154
                                        .7999******************************99999999********************************* PP

                                        SSTTSSCEEECEEEEEESS-BS--HHCCHHHCCCCSCCHHHHHHHHHHHHHHHHHHHHHHTTECEEEESS-B-HHH CS
                         Cpn60_TCP1 191 lspdmpkklenakvllldvsLeiektetkttvvlsdaeeleklekaeekqleellekiiksgvnvvvcqkgiddla 266
                                        ++++m+k +e+ +++ll++++e++k +tk ++++s++e++++le+ e++++ e+++ i+++g+nv++cq+g+dd+a
  gene2958|gene2958|rna2958|rna2958 155 SHSQMSKAVEDGRIALLTCPFEPPKLKTKNELRISSVEDYKNLENYEKEKFVEMIRCIKNAGANVILCQWGFDDEA 230
                                        **************************************************************************** PP

                                        HHHHHHCT-EEE-S--HHHHHHHHHHHT--EBSCGGGGGCGC-EEEEEEEECCETT..CCEEEEECESSSSXEEEE CS
                         Cpn60_TCP1 267 lhflakngilalrrvkkkdlerlakatGatavssledltpeelGtakkveeekigs..ekttiieevksgkiatil 340
                                        +++l+++g+ a+r+v  +dle  a  tG++++s++edl +e+lG  ++++e ++g+  ek++ +e+ ++g+++til
  gene2958|gene2958|rna2958|rna2958 231 NSLLMEHGLPAVRWVGGQDLELAAVYTGGSIISRFEDLREEDLGR-GSLKEITMGTqsEKMIKLEN-NDGNTVTIL 304
                                        *******************************************98.45566676653388888888.9******** PP

                                        EEESTCCCHHHHHHHHHHHHHHHHHHHHHHEEEETTTCHHHHHHHHHHCCCCT.SXCCHHHHHHHHHHHHTHHHHH CS
                         Cpn60_TCP1 341 lrgatdtvldeieraiedAlnvvknaiedekvvpGGGatelelakklkeyaks.vsgeeqlaieafakALevipkt 415
                                        +r+++d  l+e+er + dAl++++n+++ + vv+GGG++e++++ kl+e  ++ ++gee+ + eaf+ ALe+ip +
  gene2958|gene2958|rna2958|rna2958 305 VRASSDLALAEAERCVTDALSAARNVLTCPFVVYGGGSSEIACSLKLQERLNKvDDGEERECLEAFCAALEEIPLI 380
                                        *************************************************99997889******************* PP

                                        HHHHCTSXHHHHHHHHHHHHHTTX.TTEEEETTTTCEEECCCCTXEEEHHHHHHHHHHHHHHHHHHHC CS
                         Cpn60_TCP1 416 LaeNaGldpievlaklraahnkge.kelgidvesgeiidlveagvvDplkvkrqalksAteaastiLr 482
                                        La+N+Gld+ ++l  l+a++ k +   lg+d+ +g+  d+++++v+D+l  k++ + +At++++++L+
  gene2958|gene2958|rna2958|rna2958 381 LARNSGLDSLQTLDALKAEQLKTKfYFLGVDC-TGNGNDMKKNKVFDSLVSKKKQMMMATQLVNMVLK 447
                                        ******************9866654899***9.78889****************************96 PP

>> Peripla_BP_4  Periplasmic binding protein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   4.5e-06     0.041     169     249 ..     361     444 ..     279     447 .] 0.69

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4.5e-06
                                        HHHHHHHHHHHH..TTTECEEEESSCCHHH.CHHHHHHHTTTTSTEEEEEES-HHHHHHHHHTTSSEEEEE--HHH CS
                       Peripla_BP_4 169 ekaqqaleallt..anpldgilaandgmae.galealeaaglagkvvvtgqDatpealeaikdGtidatvaqdpye 241
                                         + +++lea+ +  ++ +  ila n+g    + l+al+a++l++k+ + g+D+t    ++ k+  +d++v+++ ++
  gene2958|gene2958|rna2958|rna2958 361 GEERECLEAFCAalEE-IPLILARNSGLDSlQTLDALKAEQLKTKFYFLGVDCTGNGNDMKKNKVFDSLVSKKKQM 435
                                        4445556666663222.667777776665569****************************************9996 PP

                                        H.HHHHHHH CS
                       Peripla_BP_4 242 l.gyaavel 249
                                        + + + v +
  gene2958|gene2958|rna2958|rna2958 436 MmATQLVNM 444
                                        625555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (447 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       603  (0.0336327); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.65u 0.35s 00:00:01.00 Elapsed: 00:00:00.55
# Mc/sec: 2441.44
//
Query:       gene2959|gene2959|rna2959|rna2959  [L=126]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.018   14.8   1.3      0.033   13.9   1.3    1.4  1  Adeno_E3_CR2  Adenovirus E3 region protein CR2
       0.03   14.2   0.0      0.035   14.0   0.0    1.3  1  TMEM154       TMEM154 protein family
      0.051   13.5   0.4      0.079   12.9   0.2    1.5  1  Orthoreo_P10  Orthoreovirus membrane fusion protein p10
      0.094   13.6   0.1       0.21   12.5   0.1    1.5  2  EphA2_TM      Ephrin type-A receptor 2 transmembrane domain


Domain annotation for each model (and alignments):
>> Adeno_E3_CR2  Adenovirus E3 region protein CR2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   1.3   7.5e-06     0.033      10      35 ..      74      99 ..      73     102 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 7.5e-06
                       Adeno_E3_CR2 10 vaVvvGlaiIiicmlyYaCcYrkhra 35
                                       v V+++++i i  +++Y Cc r+ + 
  gene2959|gene2959|rna2959|rna2959 74 VSVLMVILIAIGIFFLYRCCKRRTQS 99
                                       56778888888899*********985 PP

>> TMEM154  TMEM154 protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   7.9e-06     0.035      66      97 ..      75     106 ..      18     124 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 7.9e-06
                            TMEM154  66 lvllillllvviiliqkkkrkrsKddekseae 97 
                                        +vl+++l+ ++i++  +++++r+  d++ ++ 
  gene2959|gene2959|rna2959|rna2959  75 SVLMVILIAIGIFFLYRCCKRRTQSDHTLQVT 106
                                        79*********************999887775 PP

>> Orthoreo_P10  Orthoreovirus membrane fusion protein p10
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.2   1.8e-05     0.079      46      83 ..      75     112 ..      33     121 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.8e-05
                       Orthoreo_P10  46 aagggliviilllallycckakvkadavrsvfrrelva 83 
                                        ++   +++ i ++ l+ cck + ++d + +v +r  v 
  gene2959|gene2959|rna2959|rna2959  75 SVLMVILIAIGIFFLYRCCKRRTQSDHTLQVTYRSPVR 112
                                        33334556666788889***********9999997665 PP

>> EphA2_TM  Ephrin type-A receptor 2 transmembrane domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       1.7   7.5e+03      31      31 ..      26      26 ..       3      57 .. 0.53
   2 ?   12.5   0.1   4.7e-05      0.21       8      36 ..      74     102 ..      69     122 .. 0.62

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.7
                           EphA2_TM 31 k 31
                                       +
  gene2959|gene2959|rna2959|rna2959 26 C 26
                                       2 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 4.7e-05
                           EphA2_TM   8 glvllvilvilvlvlvrrrsknrkqksdl 36 
                                        + vl+vil+++ ++++ r++k+r+q++++
  gene2959|gene2959|rna2959|rna2959  74 VSVLMVILIAIGIFFLYRCCKRRTQSDHT 102
                                        45667777777777777888887777654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1037  (0.0578393); expected 358.6 (0.02)
Passed bias filter:                      690  (0.0384851); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.42u 0.31s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 877.13
//
Query:       gene296|gene296|rna296|rna296  [L=223]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       576  (0.0321267); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1627.08
//
Query:       gene2960|gene2960|rna2960|rna2960  [L=786]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.022   15.1   0.0        1.2    9.5   0.0    3.0  3  TetR_C_22  Tetracyclin repressor-like, C-terminal domain


Domain annotation for each model (and alignments):
>> TetR_C_22  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.14   2.5e+03      26      79 ..     128     180 ..     118     186 .. 0.62
   2 ?    1.2   0.0     0.025   4.5e+02      29      70 ..     353     394 ..     348     405 .. 0.77
   3 ?    9.5   0.0   6.6e-05       1.2      63     102 ..     546     585 ..     536     590 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.14
                          TetR_C_22  26 alwlgdqadkalrdedadenralaarladalaplapdedaeelsrtaavlvela 79 
                                         +++g +++ + r+e +++  + a+r++  l +   +++  e+ r++  ++e +
  gene2960|gene2960|rna2960|rna2960 128 HVRHGNEISEKRRKELKEALNVCAERFSPFLVRAN-ARSEPEIARMCIAVFEHL 180
                                        56777777777777777777777777776666554.335555555555555555 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.025
                          TetR_C_22  29 lgdqadkalrdedadenralaarladalaplapdedaeelsr 70 
                                        + +++d ++   +  ++++  +r++++l+ +a++ d ++  +
  gene2960|gene2960|rna2960|rna2960 353 ITGPIDDRTNRNTTNRKTKKMQRICKILENIAQRYDSADNYT 394
                                        456777788888888889999***********9987766555 PP

  == domain 3  score: 9.5 bits;  conditional E-value: 6.6e-05
                          TetR_C_22  63 edaeelsrtaavlveladallrlaiakdeeedealideaK 102
                                        + ++++++ +++l+++ +al+r  +++de +d+++i+  +
  gene2960|gene2960|rna2960|rna2960 546 MRTDDFKFCFSILMRMRKALMRMNTRNDEPIDQKIIERCY 585
                                        5679999*****************************9665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (786 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       759  (0.0423336); expected 358.6 (0.02)
Passed bias filter:                      563  (0.0314016); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.66u 0.30s 00:00:00.96 Elapsed: 00:00:00.43
# Mc/sec: 5429.66
//
Query:       gene2961|gene2961|rna2961|rna2961  [L=330]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.7e-12   45.9   0.0    4.7e-08   32.8   0.0    2.7  2  DUF2415      Uncharacterised protein domain (DUF2415)
    0.00038   21.2   2.1          7    7.7   0.0    4.7  4  WD40         WD domain, G-beta repeat
    0.00062   19.2   7.1      0.065   12.5   3.0    2.9  2  WD40_like    WD40-like domain
    0.00091   19.5   0.1        5.3    7.4   0.0    3.5  3  ANAPC4_WD40  Anaphase-promoting complex subunit 4 WD40 domain
  ------ inclusion threshold ------
      0.068   13.5   0.4         21    5.6   0.0    3.7  4  Kelch_6      Kelch motif
        0.1   12.6   0.1        5.6    7.1   0.0    2.9  2  ID           Intracellular delivery domain
       0.22   12.3   1.1          1   10.1   0.8    2.4  2  WAK_assoc    Wall-associated receptor kinase C-terminal


Domain annotation for each model (and alignments):
>> DUF2415  Uncharacterised protein domain (DUF2415)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.0   0.00022      0.56      20      42 ..     211     232 ..     206     233 .. 0.89
   2 !   32.8   0.0   1.8e-11   4.7e-08       1      40 [.     242     279 ..     242     282 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00022
                            DUF2415  20 isEhvgrvHlvDlRtgldehqVi 42 
                                        is   g+v++ D+R +l++  Vi
  gene2961|gene2961|rna2961|rna2961 211 ISTQDGYVCIYDTR-NLSNNMVI 232
                                        67788*********.****9998 PP

  == domain 2  score: 32.8 bits;  conditional E-value: 1.8e-11
                            DUF2415   1 GAfRvckFSpesglnDLLvisEhvgrvHlvDlRtgldehq 40 
                                        GA R + FS ++ + DLL+++Ehv++  l+D+R +++++q
  gene2961|gene2961|rna2961|rna2961 242 GACRNVEFS-KKRSLDLLIFTEHVSYFTLLDAR-NYESKQ 279
                                        9********.55558******************.*99999 PP

>> WD40  WD domain, G-beta repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0      0.22   5.6e+02       9      24 ..      58      75 ..      48      89 .. 0.65
   2 !    7.7   0.0    0.0027         7       9      35 ..     106     134 ..      98     137 .. 0.74
   3 ?    3.5   0.0     0.057   1.4e+02       9      31 ..     148     170 ..     141     175 .. 0.81
   4 ?    3.7   0.1     0.049   1.3e+02      16      38 .]     200     222 ..     189     222 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.22
                                       SS.SS.EEEEEEETTSSE CS
                               WD40  9 GH.ss.vtslafspdgaw 24
                                       G  ++ +t+l+f p +  
  gene2961|gene2961|rna2961|rna2961 58 GAlDDiITDLSFFPTSIS 75
                                       6766657***98877655 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0027
                                        SS..SS.EEEEEEETTSSEEEEEETTSEEE CS
                               WD40   9 GH..ss.vtslafspdgawlasGsdDgtvr 35 
                                        GH  ++ v  +af+ d ++l+ +  D+t+r
  gene2961|gene2961|rna2961|rna2961 106 GHaiNNaVKICAFNNDTNFLF-CNNDNTIR 134
                                        995533354445*********.777****9 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.057
                                        SS.SSEEEEEEETTSSEEEEEETT CS
                               WD40   9 GH.ssvtslafspdgawlasGsdD 31 
                                        +H  +v+ + +s dg+ l+s + D
  gene2961|gene2961|rna2961|rna2961 148 THpWPVNNCEVSVDGKHLVSVG-D 170
                                        68556*************9878.6 PP

  == domain 4  score: 3.7 bits;  conditional E-value: 0.049
                                        EEEETTSSEEEEEETTSEEEEEE CS
                               WD40  16 lafspdgawlasGsdDgtvriWd 38 
                                        ++++  ++ +a ++ Dg v i+d
  gene2961|gene2961|rna2961|rna2961 200 VSWNATSTCFAISTQDGYVCIYD 222
                                        678888888999999******98 PP

>> WD40_like  WD40-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   3.0   2.5e-05     0.065       8     112 ..      74     181 ..      69     241 .. 0.77
   2 !    6.3   0.1    0.0021       5.3      22      73 ..     265     319 ..     243     324 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.5e-05
                          WD40_like   8 iskkgslilyGgkddkctvlkleslesv..sivesfedSvifvklldddlilvvtlDGtillsllen.ee.evene 79 
                                        is   +l+++Gg++ + +v +le++  v  ++ + +++ v  + + +d  +l + +D ti  +     +e ev ++
  gene2961|gene2961|rna2961|rna2961  74 ISATDTLVVVGGQKGQYAVKNLENERFVlgTVGHAINNAVKICAFNNDTNFLFCNNDNTIRRYSYDSlDElEVITH 149
                                        788999*******************9885578899*************************8877654144555566 PP

                          WD40_like  80 kieedistvkviddklliGtnkGsiyvfskdlq 112
                                            +   v+v++++l+  +++ +i++f+ + +
  gene2961|gene2961|rna2961|rna2961 150 PWPVNNCEVSVDGKHLVSVGDTNQIFYFNVE-S 181
                                        5555567778888888888889999999987.3 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0021
                          WD40_like  22 dkctvlkl...eslesvsivesfedSvifvklldddlilvvtlDGtillsllene 73 
                                           t+l+    es++s+ ++++++  +  + +l+d+  +  ++D +i++++len 
  gene2961|gene2961|rna2961|rna2961 265 SYFTLLDArnyESKQSIKVFDDMDKQISGSAFLEDEEKVFISMDDKIVQYKLENR 319
                                        55566655111566677777777889**************************996 PP

>> ANAPC4_WD40  Anaphase-promoting complex subunit 4 WD40 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0     0.071   1.8e+02       7      68 ..      78     139 ..      72     149 .. 0.72
   2 ?    5.1   0.0     0.011        27      45      80 ..     157     192 ..     148     195 .. 0.86
   3 !    7.4   0.0    0.0021       5.3      43      71 ..     199     227 ..     195     248 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.071
                        ANAPC4_WD40   7 mDLiAlatedgellvfRlngqr.vwtleedkedsevrsLaWkpdgklLavaysdgevrlldae 68 
                                          L+ ++ ++g+ +v+ l+ +r v ++  ++ ++ v+  a+++d ++L    +d+++r ++  
  gene2961|gene2961|rna2961|rna2961  78 DTLVVVGGQKGQYAVKNLENERfVLGTVGHAINNAVKICAFNNDTNFLFC-NNDNTIRRYSYD 139
                                        55778888888888888865552566677788888999999999998865.567777777655 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.011
                        ANAPC4_WD40  45 aWkpdgklLavaysdgevrlldaesgkvvhslsvks 80 
                                        + + dgk L+ + + +++  +++es++ v+s + ks
  gene2961|gene2961|rna2961|rna2961 157 EVSVDGKHLVSVGDTNQIFYFNVESARFVKSRTLKS 192
                                        56789************************9988776 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.0021
                        ANAPC4_WD40  43 sLaWkpdgklLavaysdgevrlldaesgk 71 
                                        +++W+   + +a++++dg v ++d  +  
  gene2961|gene2961|rna2961|rna2961 199 KVSWNATSTCFAISTQDGYVCIYDTRNLS 227
                                        579*********************98754 PP

>> Kelch_6  Kelch motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0     0.094   2.4e+02      28      38 ..      48      58 ..      44      63 .. 0.86
   2 ?    5.6   0.0    0.0083        21       4      23 ..      70      89 ..      67     102 .. 0.82
   3 ?    0.7   0.0      0.27     7e+02      27      40 ..     171     184 ..     151     193 .. 0.77
   4 ?   -3.1   0.0       4.3   1.1e+04      10      33 ..     214     221 ..     206     227 .. 0.56

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.094
                            Kelch_6 28 nkvwvydpetk 38
                                       nkv++++++t+
  gene2961|gene2961|rna2961|rna2961 48 NKVCRFNVRTG 58
                                       9********97 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0083
                            Kelch_6  4 ghslvsvggkiYifGGytds 23
                                       +++++s+ ++++++GG++++
  gene2961|gene2961|rna2961|rna2961 70 FPTSISATDTLVVVGGQKGQ 89
                                       67889************975 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.27
                            Kelch_6  27 lnkvwvydpetksW 40 
                                        +n+++ +++e+ ++
  gene2961|gene2961|rna2961|rna2961 171 TNQIFYFNVESARF 184
                                        48999999999886 PP

  == domain 4  score: -3.1 bits;  conditional E-value: 4.3
                            Kelch_6  10 vggkiYifGGytdsspylnkvwvy 33 
                                         +g+++i                y
  gene2961|gene2961|rna2961|rna2961 214 QDGYVCI----------------Y 221
                                        4455544................4 PP

>> ID  Intracellular delivery domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.0    0.0022       5.6      15      39 ..     203     228 ..     200     234 .. 0.83
   2 ?    2.0   0.0      0.08   2.1e+02       7      30 ..     289     312 ..     287     318 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0022
                                 ID  15 gagdesfaIntkddlVi.ckkeelep 39 
                                        +a++ +faI+t+d +V    +++l+ 
  gene2961|gene2961|rna2961|rna2961 203 NATSTCFAISTQDGYVCiYDTRNLSN 228
                                        67889***********7688888775 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.08
                                 ID   7 ktyeGifagagdesfaIntkddlV 30 
                                        k ++G      +e ++I+++d++V
  gene2961|gene2961|rna2961|rna2961 289 KQISGSAFLEDEEKVFISMDDKIV 312
                                        66777777788999*******998 PP

>> WAK_assoc  Wall-associated receptor kinase C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       2.9   7.5e+03      32      50 ..      15      34 ..       4      43 .. 0.65
   2 ?   10.1   0.8    0.0004         1      53      92 ..     180     223 ..     116     232 .. 0.69

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 2.9
                          WAK_assoc 32 eeC.eksvkvpvsesalkel 50
                                       +eC e+s+ vpv++ +l+++
  gene2961|gene2961|rna2961|rna2961 15 SECiEHSIAVPVQHWQLRDM 34
                                       45745678899976666554 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0004
                          WAK_assoc  53 e....eskegleevLkkgFelewkeksseCseCeksgGr.Cgynq 92 
                                        e     ++++l+++ + gF+++w+  +s+C + + ++G  C y++
  gene2961|gene2961|rna2961|rna2961 180 EsarfVKSRTLKSMNDGGFKVSWN-ATSTCFAISTQDGYvCIYDT 223
                                        14455678889999999******9.779******99998899974 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (330 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       717  (0.0399911); expected 358.6 (0.02)
Passed bias filter:                      495  (0.0276089); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 2243.21
//
Query:       gene2962|gene2962|rna2962|rna2962  [L=129]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.012   15.7   0.2      0.043   14.0   0.0    1.8  2  CCSMST1    CCSMST1 family
      0.014   16.0   0.0       0.05   14.2   0.0    1.8  2  OAD_gamma  Oxaloacetate decarboxylase, gamma chain
       0.13   12.3   0.0        8.6    6.5   0.0    2.0  2  TssO       Type VI secretion system, TssO


Domain annotation for each model (and alignments):
>> CCSMST1  CCSMST1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   7.2e-06     0.043      18      62 ..       2      46 ..       1      58 [. 0.84
   2 ?   -0.7   0.1      0.28   1.7e+03      55      74 ..      69      87 ..      65      88 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 7.2e-06
                            CCSMST1 18 eslggkqkeerpwykvlvislslaaflvYFcilReendlDeaLek 62
                                       +++++++k+ ++w  vl ++++l+a ++YF ++ + ++ D+++ +
  gene2962|gene2962|rna2962|rna2962  2 QTMKPEHKKYILWGIVLLAIICLSATVIYFGFFYNKSEDDTEISS 46
                                       577888887888888999*****************9999999843 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.28
                            CCSMST1 55 dlDeaLekslyerlpelekk 74
                                       + D++ + +l er++el+++
  gene2962|gene2962|rna2962|rna2962 69 EDDDWVVYTL-ERVKELKDQ 87
                                       4577777666.999999986 PP

>> OAD_gamma  Oxaloacetate decarboxylase, gamma chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   8.3e-06      0.05      12      58 ..      15      67 ..      14      77 .. 0.77
   2 ?   -1.0   0.0      0.45   2.7e+03      21      35 ..      91     105 ..      90     111 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 8.3e-06
                          OAD_gamma 12 gvVFvvLilLslvislfskiikkkakkkkkkakaaaaaaaaaaaaa......e 58
                                       g+V++++i+Ls  + +f+++ +k +   +  +++  + +++a+ ++       
  gene2962|gene2962|rna2962|rna2962 15 GIVLLAIICLSATVIYFGFFYNKSEDDTEISSPKRRPSETKASGNVpnnnsdT 67
                                       89**********************88888888888877777665556654432 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.45
                          OAD_gamma  21 Lslvislfskiikkk 35 
                                        L l+++l++ ii+  
  gene2962|gene2962|rna2962|rna2962  91 LLLLVKLIKEIINEL 105
                                        678899999999865 PP

>> TssO  Type VI secretion system, TssO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0    0.0078        47      15      40 ..      16      40 ..       5      55 .. 0.57
   2 ?    6.5   0.0    0.0014       8.6      32      87 ..      62     118 ..      60     120 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.0078
                               TssO 15 llFlvtvlllflivffffkssplqek 40
                                       +++l++++l+ ++++f f+ +  +e+
  gene2962|gene2962|rna2962|rna2962 16 IVLLAIICLSATVIYFGFF-YNKSED 40
                                       4455555555555555444.333333 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0014
                               TssO  32 fkssplqekeil.lkelerkkkfeekqkelkkkvdsiykkIdsLkpevnavfleneI 87 
                                        +++s+++e+++  +  ler k+++ +++ l   v+ i++ I+ L ++ ++ f   +I
  gene2962|gene2962|rna2962|rna2962  62 NNNSDTTEDDDWvVYTLERVKELKDQKDGLLLLVKLIKEIINELGAGAKDFFGLGNI 118
                                        56689999999999*******************************999999865555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1012  (0.0564449); expected 358.6 (0.02)
Passed bias filter:                      869  (0.048469); expected 358.6 (0.02)
Passed Vit filter:                        84  (0.00468515); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 945.08
//
Query:       gene2963|gene2963|rna2963|rna2963  [L=415]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.2e-34  117.2   0.1    1.1e-33  116.3   0.1    1.4  1  eRF1_2          eRF1 domain 2
    8.9e-25   87.4   0.2    2.4e-24   86.0   0.2    1.8  1  eRF1_3          eRF1 domain 3
    3.4e-12   46.5   0.0      7e-12   45.5   0.0    1.5  1  eRF1_1          eRF1 domain 1
    6.3e-07   29.7   0.0    1.4e-06   28.6   0.0    1.6  2  acVLRF1         Actinobacteria/chloroflexi VLRF1 release fact
    1.2e-05   25.6   0.0    2.1e-05   24.8   0.0    1.3  1  baeRF_family10  Bacterial archaeo-eukaryotic release factor f
     0.0045   16.7   0.0     0.0093   15.7   0.0    1.5  1  DUF4525         Domain of unknown function (DUF4525)
  ------ inclusion threshold ------
      0.053   14.2   0.1       0.54   10.9   0.0    2.4  2  VWA_2           von Willebrand factor type A domain


Domain annotation for each model (and alignments):
>> eRF1_2  eRF1 domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.3   0.1   4.4e-37   1.1e-33       2     131 ..     175     299 ..     174     301 .. 0.97

  Alignments for each domain:
  == domain 1  score: 116.3 bits;  conditional E-value: 4.4e-37
                                        EEEEEEETTEEEEEEEESSCEEEEEEEE------BSTTBSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCHTTTE CS
                             eRF1_2   2 vglivldegeAtigllkgsrtevlkkievsvPkKhkrGgqsarrfeRlreekleeflkkvaeaankafllvdkdkl 77 
                                        +g+iv+d++e+ +++l+++++++l++++vs+PkKh+rGgqs+ rf+Rlr ek+++++kkvae an+ f      + 
  gene2963|gene2963|rna2963|rna2963 175 FGFIVMDGSETVFATLNSNVKKILHTLSVSLPKKHGRGGQSSVRFARLRIEKRNHYVKKVAEIANSLFT-----NE 245
                                        8******************************************************************55.....66 PP

                                        SEEEEEESSTHHHHHHHHHHHHHHHHTCCEEEEE-S-TSCHHHHHHHHCCHHHH CS
                             eRF1_2  78 kgiilagpgfvkeefldkdlldaelkkkviklvdvsyggesglnevlekaaevl 131
                                        +g ilag +++k++++++ +l ++ k++vi +vd++ygge+gln+++e a+++l
  gene2963|gene2963|rna2963|rna2963 246 EGYILAGTADFKNQLFESAILLKNIKDRVIRVVDTNYGGENGLNQAIELAQDSL 299
                                        9*************************************************9988 PP

>> eRF1_3  eRF1 domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.0   0.2   9.2e-28   2.4e-24       2     112 ..     305     399 ..     304     400 .. 0.94

  Alignments for each domain:
  == domain 1  score: 86.0 bits;  conditional E-value: 9.2e-28
                                        HHHHHHHHHHHHHHHCTCSSEEESHHHHHHHHHTT-EEEEEEEHCHHTSSSHHHHHS-HHH-HHHHHHHHHHHHHH CS
                             eRF1_3   2 iqekklleefleelakdtgkavYGveevlkalemgAvetLLvseelersrdtlkekvketgeelelvelieelven 77 
                                         +e+k+l+ef+++l++d  ++vYG++++l+ l  +A+ +L+v+e++e s d++  +            +i++l+en
  gene2963|gene2963|rna2963|rna2963 305 LKERKVLQEFFKSLEND--MVVYGQKNTLRLLDEQAITKLIVYEDVEGSVDDQ--P------------IIDWLLEN 364
                                        68*************99..*****************************96432..2............79****** PP

                                        HHHTT-EEEEE-TTSHHHHHHHHHTTTEEEEESS- CS
                             eRF1_3  78 veesgakveiisseseeGeqlvkafgGiaaiLRyk 112
                                        ++ ++a++ i+s++s+eGeq++++fgGi++iL+yk
  gene2963|gene2963|rna2963|rna2963 365 YKRYNAELSIVSDKSTEGEQFKEGFGGIGGILKYK 399
                                        **********************************8 PP

>> eRF1_1  eRF1 domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.5   0.0   2.7e-15     7e-12       6     127 ..      55     167 ..      49     169 .. 0.95

  Alignments for each domain:
  == domain 1  score: 45.5 bits;  conditional E-value: 2.7e-15
                                        ECTBTTSCCEEEEEE-SCHHHHHHHHHCHTTHEEEEEEEECHHH.......--CEEEEEEEEEEEEEEECTT...S CS
                             eRF1_1   6 rdlekdgsgsvtLipeddedlwhlynliapgdsvrastvrkvqresstgsreservklkLtikvekvdfdkd...a 78 
                                        rd +++g++++tLi ++ +++ ++ +++ ++++++++++++v+r          +v++++t+ + k++  k+   +
  gene2963|gene2963|rna2963|rna2963  55 RDSRGNGTSMITLILPPRDQIPKALKMLVDEYGTASNIKSRVNR---------LSVLSAITSAQHKLRTFKNvppN 121
                                        6899**************************************99.........9**************9999999* PP

                                        SEEEEEEEEEEGGGG--TTSEEEEEE-TTSEEEEEECE.ESHHHHHHHHH CS
                             eRF1_1  79 gvlrisGkvieenehvklgafhtldlelkrpftiikee.wdsfalerLke 127
                                        g+  + G+v+++n+    ++++++ +e+ +p++++ +  +++f++e L e
  gene2963|gene2963|rna2963|rna2963 122 GLAIFVGTVMDNNK----EKKISVAMEPLKPINTSVYMcDSRFHTESLVE 167
                                        *************9....9*****************9999******9976 PP

>> acVLRF1  Actinobacteria/chloroflexi VLRF1 release factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6   0.0   5.4e-10   1.4e-06      32     123 ..     204     294 ..     173     300 .. 0.78
   2 ?   -3.5   0.0       4.5   1.2e+04      68      92 ..     313     337 ..     307     349 .. 0.65

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 5.4e-10
                            acVLRF1  32 dvqgrtaaGGwSqqRfaRrrenqadalleavaeaaarllaeesaevvlgGdrslvaevledar.laplatlareel 106
                                           +++ +GG+S  RfaR r ++ ++ +++vae a+ l+  +++  +l+G     +++ e+a  l+++++++ + +
  gene2963|gene2963|rna2963|rna2963 204 SLPKKHGRGGQSSVRFARLRIEKRNHYVKKVAEIANSLF-TNEEGYILAGTADFKNQLFESAIlLKNIKDRVIR-V 277
                                        56789**********************************.7777789999999999998885524444444444.7 PP

                            acVLRF1 107 ldvpdprravLedavrr 123
                                        +d+    ++ L++a++ 
  gene2963|gene2963|rna2963|rna2963 278 VDTNYGGENGLNQAIEL 294
                                        77777777777777765 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 4.5
                            acVLRF1  68 rllaeesaevvlgGdrslvaevled 92 
                                        + +++ ++++v+ G++++++ + e+
  gene2963|gene2963|rna2963|rna2963 313 EFFKSLENDMVVYGQKNTLRLLDEQ 337
                                        4444445557888888887777665 PP

>> baeRF_family10  Bacterial archaeo-eukaryotic release factor family 10
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.0     8e-09   2.1e-05       3     119 ..     162     277 ..     161     297 .. 0.82

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 8e-09
                     baeRF_family10   3 lapLlealdeyerygvvlvdreraRlfevylgeleeveevegevpgrtktggwksqdrfqrreeeqaerhlkevAe 78 
                                        ++ L+e  +e+e +g +++d ++  +++      +  ++++   p+++ +gg+ s  rf+r + e++ +++k+vAe
  gene2963|gene2963|rna2963|rna2963 162 TESLVEQFKENETFGFIVMDGSETVFATLNSNVKKILHTLSVSLPKKHGRGGQ-SSVRFARLRIEKRNHYVKKVAE 236
                                        678*******************997777766666668899999999999***9.********************** PP

                     baeRF_family10  79 llaklleergverlvlgGdeeetaalldr.lpkalrarvvgt 119
                                        ++++l+++++   ++ g  +   ++++++ l k++++rv+  
  gene2963|gene2963|rna2963|rna2963 237 IANSLFTNEE-GYILAGTADFKNQLFESAiLLKNIKDRVIRV 277
                                        *******999.6666666677777777654678888888765 PP

>> DUF4525  Domain of unknown function (DUF4525)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   3.6e-06    0.0093      38      98 ..     214     277 ..     197     290 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 3.6e-06
                            DUF4525  38 essaelreqildlskryvkalaeenknvmdgengaslagyadlkrti...avllddilqrlvkl 98 
                                        +ss+++    ++  + yvk +ae  +++   e+g  lag ad+k  +   a+ll +i  r+ ++
  gene2963|gene2963|rna2963|rna2963 214 QSSVRFARLRIEKRNHYVKKVAEIANSLFTNEEGYILAGTADFKNQLfesAILLKNIKDRVIRV 277
                                        5666665555566677*****************************987779*******999876 PP

>> VWA_2  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00021      0.54      29      98 ..     163     232 ..     157     240 .. 0.86
   2 ?   -0.3   0.0      0.64   1.6e+03      72      90 ..     280     300 ..     262     324 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00021
                              VWA_2  29 eallkslp.gdrvglvtfsdgpevlipltkdkakilnalrnleakgggtnlaaaLqlarkalkkrrkgekr 98 
                                        e+l+++++ + ++g ++++++ +v+++l+++ +kil  l    +k+ g   ++ +++ar  ++kr+ ++ +
  gene2963|gene2963|rna2963|rna2963 163 ESLVEQFKeNETFGFIVMDGSETVFATLNSNVKKILHTLSVSLPKKHGRGGQSSVRFARLRIEKRN-HYVK 232
                                        78999998466********************************99999999999999999999887.4444 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.64
                              VWA_2  72 k..gggtnlaaaLqlarkalk 90 
                                        +  gg+  l++a++la++ l 
  gene2963|gene2963|rna2963|rna2963 280 TnyGGENGLNQAIELAQDSLT 300
                                        235777888888888888664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (415 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       687  (0.0383178); expected 358.6 (0.02)
Passed bias filter:                      507  (0.0282782); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.58u 0.25s 00:00:00.83 Elapsed: 00:00:00.44
# Mc/sec: 2834.38
//
Query:       gene2964|gene2964|rna2964|rna2964  [L=145]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.1e-33  115.3   0.1    3.5e-33  115.1   0.1    1.0  1  Tyr_Deacylase  D-Tyr-tRNA(Tyr) deacylase


Domain annotation for each model (and alignments):
>> Tyr_Deacylase  D-Tyr-tRNA(Tyr) deacylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.1   0.1     2e-37   3.5e-33       2     144 .]       3     136 ..       2     136 .. 0.95

  Alignments for each domain:
  == domain 1  score: 115.1 bits;  conditional E-value: 2e-37
                                        EEEEEEEEEEEEETTEEEEEESSEEEEEEE-BTT--HHHHHHHHHHHHH-EEEEETTSSEEEETTTTT-EEEEEE- CS
                      Tyr_Deacylase   2 aviqrvksAsvtvegevvgsigkGllvlvgvekedteedleklakkilnlrifedeegkmnlsvkdvggevLvVsq 77 
                                        ++iq+vk+A+vtv+++  +si++Gll++vg++++dt++ ++++++ki +lr+f+d      + ++d + +++++s+
  gene2964|gene2964|rna2964|rna2964   3 LIIQKVKRAQVTVNNTPLSSISEGLLIYVGFHRTDTPAMIHQAVQKIKSLRLFND------TPLAD-HHHIMLISN 71 
                                        69***********9999*************************************9......67777.568****** PP

                                        GGGGSBTSSSSS-BGTTB--HHHHHHHHHHHHHHHHHCTCTTEEE--TTS-EEEEEEEEEEEEEEEE CS
                      Tyr_Deacylase  78 ftLyadtrkGrrpsfhkaakpeeaeelyekfveklrerlgekvetGeFgadmkvslvndGPvtilld 144
                                        +tLya++ kG++ ++h  ++ ++a++++e +v ++r+ +g  vetG+Fg +  v++  dGP+ +l +
  gene2964|gene2964|rna2964|rna2964  72 VTLYARM-KGNKLDYHMMMEYADAKRMFECMVGEMRKVHG-VVETGQFGSKSVVECAVDGPFNFLYE 136
                                        ******5.****************************9755.9********************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       423  (0.0235931); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1099.20
//
Query:       gene2965|gene2965|rna2965|rna2965  [L=1621]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.087   13.0   2.1       0.26   11.5   2.1    1.7  1  rve_2     Integrase core domain
       0.14   12.1   0.3        0.6   10.1   0.1    2.1  2  DUF1726   Domain of unknown function (DUF1726)


Domain annotation for each model (and alignments):
>> rve_2  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   2.1   2.8e-05      0.26       5      41 ..    1281    1319 ..    1278    1327 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 2.8e-05
                              rve_2    5 gsLKtElvyge.tfktleeleaaiedYIewYNn.kRlkg 41  
                                         ++LK++ +yg+ +  t++ l  +++ YI  YN   R+ +
  gene2965|gene2965|rna2965|rna2965 1281 HVLKNKSYYGQkHVTTMNILMNKVFYYIFNYNMrIRITY 1319
                                         79*****************************95145555 PP

>> DUF1726  Domain of unknown function (DUF1726)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0      0.44     4e+03      31      85 ..     116     171 ..     114     175 .. 0.70
   2 ?   10.1   0.1   6.7e-05       0.6      45      87 ..     288     331 ..     287     337 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.44
                            DUF1726  31 lvetVrGGGliilllp.pleelkqlytdfhkklvveplteevkkrfnkrfirklke 85 
                                        ++e+ +  G  + l++ +++e  q+++ f ++ v   ++ + + r+ ++++++++e
  gene2965|gene2965|rna2965|rna2965 116 IIEMMKNDGHNVWLTDsEIDEFAQYISLFVNEKVPILHQIDYQTRYDEKLMDRIEE 171
                                        56777777777777762578888888866666554444458999999999988876 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 6.7e-05
                            DUF1726  45 lppleelkqlytdfhkklvveplt.eevkkrfnkrfirklkehe 87 
                                         ++ +++k++y +++k+ vve++t e +k+ f+kr+i +l++ e
  gene2965|gene2965|rna2965|rna2965 288 CNKQRNWKDMYFNIKKEQVVEAITsEFLKSSFIKRLIIRLRNVE 331
                                        678899******************9***************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1621 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       655  (0.036533); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.88u 0.30s 00:00:01.18 Elapsed: 00:00:00.51
# Mc/sec: 9559.32
//
Query:       gene2966|gene2966|rna2966|rna2966  [L=232]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.7e-05   24.3   0.1    5.6e-05   23.7   0.1    1.3  1  YabA      Initiation control protein YabA
     0.0016   18.3  13.6     0.0016   18.3   1.3    2.7  2  Bap31     Bap31/Bap29 transmembrane region
     0.0064   15.7   1.1     0.0087   15.2   1.1    1.1  1  DUF4686   Domain of unknown function (DUF4686)
  ------ inclusion threshold ------
      0.048   12.8   3.4      0.069   12.3   3.4    1.1  1  Taxilin   Myosin-like coiled-coil protein
      0.051   13.0   1.0      0.079   12.4   1.0    1.2  1  DUF4618   Domain of unknown function (DUF4618)
      0.052   13.5   1.9      0.078   12.9   1.9    1.3  1  Wtap      WTAP/Mum2p family


Domain annotation for each model (and alignments):
>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.1   1.9e-08   5.6e-05       7      53 ..      87     141 ..      82     191 .. 0.79

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 1.9e-08
                                        HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH........X CS
                               YabA   7 fdkleeleeqleelleeleelkeelaelleenaeLeleneklrerl........e 53 
                                        + +l++ e +++ + +++e+ k+ + e++een++L+ en+ lr+r+        +
  gene2966|gene2966|rna2966|rna2966  87 VGRLKREEMEVSVMRRQIENHKKFVMEMVEENKKLKEENDGLRNRVvlgkdvgvR 141
                                        5677777889999*******************************99665554440 PP

>> Bap31  Bap31/Bap29 transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   5.7     0.012        36       1      30 [.       1      30 [.       1      65 [. 0.75
   2 !   18.3   1.3   5.5e-07    0.0016      99     130 ..      64      95 ..      55     100 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.012
                              Bap31  1 msLqytlvaalLvaeivvvllLvlPlpsav 30
                                       msL   ++  +L+ e++++++L+lP+  ++
  gene2966|gene2966|rna2966|rna2966  1 MSLTLLITQSFLLSELLFLTVLLLPFSPQK 30
                                       99***********************96543 PP

  == domain 2  score: 18.3 bits;  conditional E-value: 5.5e-07
                              Bap31  99 QRNlYlsGftLfLslvlrrlvtliselaklea 130
                                        Q  +Yl G+tLfL+l+l+r+++++ +l + e 
  gene2966|gene2966|rna2966|rna2966  64 QQYFYLNGITLFLFLILKRMLNVVGRLKREEM 95 
                                        6679******************9988877665 PP

>> DUF4686  Domain of unknown function (DUF4686)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   1.1   2.9e-06    0.0087     303     347 ..      89     133 ..      81     143 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.9e-06
                            DUF4686 303 rikqLeneiailksqsekekefqkqviaeNekLllekrkLleqls 347
                                        r k+ e+e+ ++++q+e++k+f  ++++eN kL +e+  L +++ 
  gene2966|gene2966|rna2966|rna2966  89 RLKREEMEVSVMRRQIENHKKFVMEMVEENKKLKEENDGLRNRVV 133
                                        567779**********************************99986 PP

>> Taxilin  Myosin-like coiled-coil protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   3.4   2.3e-05     0.069     249     293 ..      86     130 ..      81     133 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.3e-05
                            Taxilin 249 mtkktkklEketnlwkskfektnkallemaeertekkkeieklkk 293
                                        +   +k+ E e + ++++ e+ +k ++em+ee+++ k+e + l++
  gene2966|gene2966|rna2966|rna2966  86 VVGRLKREEMEVSVMRRQIENHKKFVMEMVEENKKLKEENDGLRN 130
                                        55678999*******************************998876 PP

>> DUF4618  Domain of unknown function (DUF4618)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   1.0   2.6e-05     0.079     179     222 ..      88     131 ..      75     137 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.6e-05
                            DUF4618 179 eaLlqktlenqvlkkeiekfrefieeleeeipeLkaeveqLqaq 222
                                          L+++ +e +v++++ie++++f+ e+ ee ++Lk+e + L+++
  gene2966|gene2966|rna2966|rna2966  88 GRLKREEMEVSVMRRQIENHKKFVMEMVEENKKLKEENDGLRNR 131
                                        5688899999**************************98888875 PP

>> Wtap  WTAP/Mum2p family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   1.9   2.6e-05     0.078     110     155 ..      86     131 ..      80     132 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.6e-05
                               Wtap 110 eegrvakLeselalqkkfveelkkaleeleelleeleeevevlqst 155
                                          gr+++ e+e+++ ++++e  kk   e+ e +++l+ee+++l + 
  gene2966|gene2966|rna2966|rna2966  86 VVGRLKREEMEVSVMRRQIENHKKFVMEMVEENKKLKEENDGLRNR 131
                                        479***************************************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1186  (0.0661498); expected 358.6 (0.02)
Passed bias filter:                      683  (0.0380947); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 1746.15
//
Query:       gene2967|gene2967|rna2967|rna2967  [L=42]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (42 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       332  (0.0185175); expected 358.6 (0.02)
Passed bias filter:                      232  (0.0129399); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.21s 00:00:00.55 Elapsed: 00:00:00.38
# Mc/sec: 329.45
//
Query:       gene2968|gene2968|rna2968|rna2968  [L=387]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.4e-40  137.8   0.1    5.1e-40  137.2   0.1    1.3  1  SRP54      SRP54-type protein, GTPase domain
    5.8e-05   22.9   0.0     0.0003   20.6   0.0    2.4  2  AAA_24     AAA domain
    0.00015   20.8   0.0    0.00045   19.3   0.0    1.8  1  MeaB       Methylmalonyl Co-A mutase-associated GTPase MeaB
    0.00065   19.3   1.6      0.029   13.9   1.6    2.3  1  cobW       CobW/HypB/UreG, nucleotide-binding domain
    0.00094   19.2   0.3     0.0068   16.5   0.1    2.4  2  CbiA       CobQ/CobB/MinD/ParA nucleotide binding domain
     0.0011   19.1   0.3     0.0054   16.8   0.3    2.2  1  MMR_HSR1   50S ribosome-binding GTPase
      0.004   16.9   0.1      0.011   15.4   0.0    1.7  2  AAA_30     AAA domain
     0.0052   17.3   0.0      0.032   14.8   0.0    2.2  2  ABC_tran   ABC transporter
     0.0078   16.5   0.0      0.017   15.4   0.0    1.5  1  AAA_19     AAA domain
  ------ inclusion threshold ------
      0.012   15.6   0.2       0.32   10.9   0.1    2.7  2  AAA_31     AAA domain
      0.018   15.3   0.9       0.03   14.6   0.0    1.8  1  AAA_28     AAA domain
       0.02   15.4   0.0       0.05   14.1   0.0    1.7  1  AAA_18     AAA domain
      0.034   13.6   0.0      0.073   12.5   0.0    1.6  1  Pox_A32    Poxvirus A32 protein
      0.038   13.2   0.0       0.11   11.8   0.0    1.7  2  Herpes_TK  Thymidine kinase from herpesvirus
      0.043   14.2   0.1       0.12   12.7   0.1    1.7  2  AAA_16     AAA ATPase domain
       0.05   13.1   0.0        2.1    7.9   0.0    2.5  2  AAA_7      P-loop containing dynein motor region
      0.053   13.4   0.0       0.15   12.0   0.0    1.7  2  NACHT      NACHT domain
       0.06   13.3   0.4       0.24   11.3   0.4    2.1  1  NTPase_1   NTPase
      0.075   12.6   2.0      0.093   12.3   0.2    2.1  2  AAA_25     AAA domain
       0.11   12.6   0.0       0.26   11.3   0.0    1.7  1  AAA_14     AAA domain
       0.11   12.9   0.1        1.1    9.7   0.0    2.3  2  AAA_17     AAA domain


Domain annotation for each model (and alignments):
>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  137.2   0.1   5.9e-43   5.1e-40       3     195 ..     197     385 ..     195     386 .. 0.91

  Alignments for each domain:
  == domain 1  score: 137.2 bits;  conditional E-value: 5.9e-43
                                        EEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTSSTTHHHHHHHHHHHTTEEEEE....SSTTSCHHHHHHH CS
                              SRP54   3 villvGlqGaGKTttlaKLaallkkegkkvllvaaDtfRaaAveQLktlaeklgvpvik....kkeeadpaavake 74 
                                         ++lvG++G+GKTttl+KL  ++  + k v ++a+DtfRa+A+eQL+t+ ++l+++       +  ++++ +va+ 
  gene2968|gene2968|rna2968|rna2968 197 RVALVGTNGVGKTTTLSKLCYHFAVRDKGVYVAACDTFRAGAIEQLQTYVNRLKINHRVeihqQGYNKEEWKVARS 272
                                        578*************************************************887542233337888899****** PP

                                        HHHHHHHTTSSEEEEEE--SSTTHHHHHHHHHHHHHHHSSSEEEEEEETTBHTHHHHHHHHHHHHSSCSEEEEEST CS
                              SRP54  75 avekakeekidvvlvDTaGrlqndkelmeelkkikkvvkpdevllvldattgqeavkqakaFkeavgitgviltkl 150
                                        a++  k+  +dv+lvDTaGr + +k l++ l+k+ +    d+v++v +a+ g+e  k + aF+ +   t++i+tk+
  gene2968|gene2968|rna2968|rna2968 273 ALQYGKA--YDVILVDTAGRVN-KKPLIDSLRKLTNLG-FDDVVYVSEALKGYE--KDVLAFDMV---TAIIVTKI 339
                                        *****99..***********86.678*********998.78999********98..578889875...59****** PP

                                        TS.SSSTTHHHHHHHHHTS-EEEEE-SSSTTGEEE--HHHHHHHHH CS
                              SRP54 151 Dg.dakgGaalsiaaelklPikfigvGekiedleefdperlvsrll 195
                                        D+ d + G++l++ + +k+P++f+g G++  dlee+d e++++ ll
  gene2968|gene2968|rna2968|rna2968 340 DTvDDRIGSILNLCYFSKKPVVFLGHGQSNVDLEEVDVEKVIETLL 385
                                        *85889*************************************998 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       5.4   4.6e+03     158     177 ..      23      44 ..      16      59 .. 0.64
   2 !   20.6   0.0   3.5e-07    0.0003       2      77 ..     195     291 ..     194     379 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 5.4
                             AAA_24 158 nelkeevDlvlranlkred..k 177
                                          ++++ D+v+r n+k  +   
  gene2968|gene2968|rna2968|rna2968  23 SYINNIIDTVVRKNIKHGEltV 44 
                                        5588899999998887555552 PP

  == domain 2  score: 20.6 bits;  conditional E-value: 3.5e-07
                             AAA_24   2 klkiliyGpsgiGKTtlakelgpkplfidtekGlksldadkfpdieswedfldevvel.................. 59 
                                        +++++++G +g+GKTt++++l +++++ d    +++ d  +   ie++++ ++ ++ +                  
  gene2968|gene2968|rna2968|rna2968 195 PYRVALVGTNGVGKTTTLSKLCYHFAVRDKGVYVAACDTFRAGAIEQLQTYVNRLKINhrveihqqgynkeewkva 270
                                        689******************8888876555555555555555566666666666666999999999999999999 PP

                             AAA_24  60 ...aaeladyktlviDtidel 77 
                                            +  + y+++ +Dt++ +
  gene2968|gene2968|rna2968|rna2968 271 rsaLQYGKAYDVILVDTAGRV 291
                                        998788889999999999876 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   5.3e-07   0.00045      21     131 ..     187     289 ..     165     294 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 5.3e-07
                                        HHGGG-S-SEEEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE------------------HCCCTSTTEEEEE CS
                               MeaB  21 rllakaGraqvvGltGvPGaGkstlvealglelrrrGkrvavlavDPsspftGGsilGDklRleelavdegvfiRs 96 
                                        rl ++a    +v l G+ G+Gk t++++l  +++ r k v v a D   +f  G+i   ++ +++l+ ++ v i  
  gene2968|gene2968|rna2968|rna2968 187 RLGQDACAPYRVALVGTNGVGKTTTLSKLCYHFAVRDKGVYVAACD---TFRAGAIEQLQTYVNRLKINHRVEIHQ 259
                                        56677888899*********************************99...689999999999999999999998877 PP

                                        E-----HHHHHHHHHHHHHHHHHTT-SEEEEEEES CS
                               MeaB  97 lpsrGalGGlaaktrevvllleaaGfDvvlietvG 131
                                           + +   +a+ +++      +  +Dv+l++t G
  gene2968|gene2968|rna2968|rna2968 260 QGYNKEEWKVARSALQ-----YGKAYDVILVDTAG 289
                                        7666666666665543.....46678888888877 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   1.6   3.5e-05     0.029       5     156 ..     200     345 ..     197     352 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.5e-05
                                        EEESTTCCHHHHHHHHHCT--SS-EEEEESS-SSCHCCCCCCHCCCT.EEEETTTTECCH..CTT-HHHHHHHHHH CS
                               cobW   5 ltGflGsGKTtLlnhllenraglklavivNefgevsiDaellretgveivelenGciCct..lredllkelealee 78 
                                        l+G  G GKTt l++l+ + a ++  v v    ++   a    +t v+ ++++     ++   +++  k++++ ++
  gene2968|gene2968|rna2968|rna2968 200 LVGTNGVGKTTTLSKLCYHFAVRDKGVYVAACDTFRAGAIEQLQTYVNRLKINHRVEIHQqgYNKEEWKVARSALQ 275
                                        6677777777777777733333333333333332222222222222333333333333332333333334444444 PP

                                        HHTT-SEEEEEECTTTTHHHHHTTSHHHHHCCCECEEEEEEETTTH.CCHCCHHHHHHHHHHTSSEEEEE-HHHHC CS
                               cobW  79 reerldviliEttGlaePapvafteeelksdltldavvavvDaknleaeeekieekaedqlaaadllvlnKtDlld 154
                                          + +dvil+ t G ++ +p+ + + +  ++l  d vv+v +a     ++ ++  +a d+++    ++++K+D++d
  gene2968|gene2968|rna2968|rna2968 276 YGKAYDVILVDTAGRVNKKPL-IDSLRKLTNLGFDDVVYVSEA----LKGYEKDVLAFDMVT---AIIVTKIDTVD 343
                                        4479*****************.44444456899**********....678888888888887...59********9 PP

                                        HC CS
                               cobW 155 ee 156
                                        ++
  gene2968|gene2968|rna2968|rna2968 344 DR 345
                                        86 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0         2   1.7e+03      54      94 ..      85     150 ..      14     181 .. 0.59
   2 !   16.5   0.1     8e-06    0.0068       6      85 ..     202     340 ..     198     353 .. 0.71

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 2
                                        H..........................CCHCCCHHHHHHCHCHHHH....EEEEEEEEESS...-TTCH CS
                                        x..........................xxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxx RF
                               CbiA  54 p..........................dlkrllellealgkkkall..lkiagvvlnrvdgeneetllk 94 
                                        +                          d ++ +++++ +  +k+ +  ++i++ v+  +d e   +ll 
  gene2968|gene2968|rna2968|rna2968  85 EhgvydrraavtkqekrrrwggtekelDYSSTSRTVSYVPDTKSAFnlFNIKRRVFKTFDRE---ALLA 150
                                        14444444555555555555555555555555555555555555555566666666666654...3333 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 8e-06
                                        SSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH........................... CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........................... RF
                               CbiA   6 tkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep........................... 54 
                                        ++ GvGKTt++ +L+  +a r + V +  +D+ +  +  +e+l+ ++++                           
  gene2968|gene2968|rna2968|rna2968 202 GTNGVGKTTTLSKLCYHFAVRDKGVYVAACDTFRAGA--IEQLQTYVNRlkinhrveihqqgynkeewkvarsalq 275
                                        5679**********************99999874332..4555555555667777777777777777777777777 PP

                                        ...............................CCHCCCHHHHHHCHCHHHH.....EEEEEEEEES CS
                                        ...............................xxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxx RF
                               CbiA  55 ...............................dlkrllellealgkkkall...lkiagvvlnrvd 85 
                                                                       + + ++ + eal++  ++     ++  ++++++d
  gene2968|gene2968|rna2968|rna2968 276 ygkaydvilvdtagrvnkkplidslrkltnlGFDDVVYVSEALKGYEKDVlafDMVTAIIVTKID 340
                                        77777777777777777777777777777776666666666666554444666666667777666 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.3   6.3e-06    0.0054       1      91 [.     197     322 ..     197     363 .. 0.57

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 6.3e-06
                                        EEEEEESTTSSHHHHHHHHH........T......STEEESSSTTSSSSEEEEEEEETTEE............... CS
                           MMR_HSR1   1 evaivGrpNvGKStLinalt........g......ekaivsdkpgtTrdinegrvklkgke............... 47 
                                        +va+vG   vGK+t +++l+        g      ++ +++++ +  + +n+ +++    +               
  gene2968|gene2968|rna2968|rna2968 197 RVALVGTNGVGKTTTLSKLCyhfavrdkGvyvaacDTFRAGAIEQLQTYVNRLKIN----Hrveihqqgynkeewk 268
                                        69******************555444430333332122222222222222222222....0223333345556666 PP

                                        .............EEEEECGGCSSHHHHHHHHHHHHHHHHC..TSEEEEEEETTTTCSH CS
                           MMR_HSR1  48 .............ielvDtpGliegaseekglgkaflalee..adlillvvdaseeklk 91 
                                                     ++lvDt+G ++    +k l +++++l +   d +++v +a  ++++
  gene2968|gene2968|rna2968|rna2968 269 varsalqygkaydVILVDTAGRVN----KKPLIDSLRKLTNlgFDDVVYVSEAL-KGYE 322
                                        6666677777777********655....55566666665554457777777644.3343 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.1       2.8   2.4e+03     160     190 ..      69      98 ..      59     100 .. 0.79
   2 !   15.4   0.0   1.3e-05     0.011      21     114 ..     198     305 ..     186     315 .. 0.73

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 2.8
                             AAA_30 160 seeraaalalregdaeealealadrgriheg 190
                                        + er aa+ l++g ++     +++r +++ +
  gene2968|gene2968|rna2968|rna2968  69 QIERMAAEYLEDGAVR-EHGVYDRRAAVTKQ 98 
                                        5678899999999998.55889998888766 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 1.3e-05
                             AAA_30  21 avltGpAGtGKttalkalreaweaaggrviglAptgkaAkvLae.elgieastiakllkrlk............gr 83 
                                        ++l+G  G GKtt+l++l  +++ + + v ++A     A ++++ ++ ++   i++ ++ ++            ++
  gene2968|gene2968|rna2968|rna2968 198 VALVGTNGVGKTTTLSKLCYHFAVRDKGVYVAACDTFRAGAIEQlQTYVNRLKINHRVEIHQqgynkeewkvarSA 273
                                        5799**************9999999889999999888888887432233333333333333355556677777866 PP

                             AAA_30  84 arlepg.tllivDEagmvdtkqlaallkaaek 114
                                         ++ ++ ++++vD ag v+ k l + l+++++
  gene2968|gene2968|rna2968|rna2968 274 LQYGKAyDVILVDTAGRVNKKPLIDSLRKLTN 305
                                        7888888*********9998887777776665 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0       1.5   1.3e+03      38      71 ..      38      69 ..      21     181 .. 0.61
   2 !   14.8   0.0   3.7e-05     0.032      13      35 ..     197     219 ..     192     306 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 1.5
                                       SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ABC_tran 38 teGeilldgkdlkeqeleslrkeigvlpqepqlf 71
                                       + Ge++++g+++ +  +++ +k i ++  ++  +
  gene2968|gene2968|rna2968|rna2968 38 KHGELTVQGRNVAY--RTVGKKVIMCVGDDADEQ 69
                                       45666666666666..555555555555552222 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 3.7e-05
                                        EEEEEESTTSSHHHHHHHHTTSS CS
                                        xxxxxxxxxxxxxxxxxxxxxxx RF
                           ABC_tran  13 kvaivGenGaGKStLlkllagll 35 
                                        +va+vG nG GK+t l+ l+ + 
  gene2968|gene2968|rna2968|rna2968 197 RVALVGTNGVGKTTTLSKLCYHF 219
                                        79***********9998877554 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0     2e-05     0.017      12     136 ..     197     364 ..     187     368 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2e-05
                             AAA_19  12 vllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerlaalgae................... 68 
                                         +++++  G GKT++l + + ++  + +  +   ++ +f   A ++l++ ++ l+ +                   
  gene2968|gene2968|rna2968|rna2968 197 RVALVGTNGVGKTTTLSKLCYHFAVRDKG-VYVAACDTFRAGAIEQLQTYVNRLKINhrveihqqgynkeewkvar 271
                                        57899***************999887754.4667777888888999999887766666555555555555555555 PP

                             AAA_19  69 .........................atTiHrlalldfddlltealelle.eaeeekklqeee.llivDEfqdvdel 117
                                                                 ++ + +l++l+fdd +    e+l+ ++++   + +   ++iv  +  vd+ 
  gene2968|gene2968|rna2968|rna2968 272 salqygkaydvilvdtagrvnkkplIDSLRKLTNLGFDDVV-YVSEALKgYEKDVLAF-DMVtAIIVTKIDTVDDR 345
                                        55555555555555555555555555555555558888888.6666777443333333.44458888888888888 PP

                             AAA_19 118 qyrLlkallgekkklllvG 136
                                        + ++l+ ++ +kk ++++G
  gene2968|gene2968|rna2968|rna2968 346 IGSILNLCYFSKKPVVFLG 364
                                        8888887777776677766 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   0.00037      0.32      12      40 ..     205     233 ..     200     266 .. 0.84
   2 ?    1.3   0.0      0.32   2.7e+02     104     126 ..     266     288 ..     251     296 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00037
                             AAA_31  12 GvGKTTtsvnlaaalaklgkkvLlvDlDp 40 
                                        GvGKTTt  +l++ +a ++k v +  +D+
  gene2968|gene2968|rna2968|rna2968 205 GVGKTTTLSKLCYHFAVRDKGVYVAACDT 233
                                        9*******************999988886 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.32
                             AAA_31 104 eeilkellekvkdeYDyiiiDcp 126
                                        e  + +   +  + YD+i++D+ 
  gene2968|gene2968|rna2968|rna2968 266 EWKVARSALQYGKAYDVILVDTA 288
                                        44455555567799*******97 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   3.5e-05      0.03       1      80 [.     197     287 ..     197     292 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.5e-05
                             AAA_28   1 kivitGgestGKTtlleaLaar......gypvv.pEaareileeklakgedalpwvedllafaervleeqleeeaa 69 
                                        +++++G+ + GKTt+l++L  +      g+ v   +++r    e+l++  + l+  +++   +++  +e+ + +++
  gene2968|gene2968|rna2968|rna2968 197 RVALVGTNGVGKTTTLSKLCYHfavrdkGVYVAaCDTFRAGAIEQLQTYVNRLKINHRVEIHQQGYNKEEWKVARS 272
                                        799****************955555566666555788887777777777776766544444445555555555555 PP

                             AAA_28  70 a....aankvlfcDr 80 
                                        a    +a +v+++D+
  gene2968|gene2968|rna2968|rna2968 273 AlqygKAYDVILVDT 287
                                        565777778888877 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   5.9e-05      0.05       1      80 [.     198     286 ..     198     304 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 5.9e-05
                             AAA_18   1 IlltGtpGvGKttlakeLskrlgf.....gvnlrdvakenglllevdpe.aldeskrldedkldklldaleenss. 69 
                                        ++l Gt GvGKtt    L  + ++      v   d+++ + ++  ++    l+ ++r++++++ ++ ++++ ++s 
  gene2968|gene2968|rna2968|rna2968 198 VALVGTNGVGKTTTLSKLCYHFAVrdkgvYVAACDTFRAGAIEQLQTYVnRLKINHRVEIHQQGYNKEEWKVARSa 273
                                        6899**********99995544335665566666666666666666666888889999999999999999999886 PP

                             AAA_18  70 ..aleegknlvid 80 
                                               +++++d
  gene2968|gene2968|rna2968|rna2968 274 lqYGKAYDVILVD 286
                                        6433334444554 PP

>> Pox_A32  Poxvirus A32 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   8.6e-05     0.073      12      87 ..     194     269 ..     186     318 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 8.6e-05
                            Pox_A32  12 kpFrlalvGgsGsGktvyLlsLlrtlvkkykhifLltp..vknseYdkyvwPdhinkvtseeeleYsLsatkekie 85 
                                        +p+r+alvG  G Gkt+ L  L   +  + k +++     +   + ++     ++n+++ ++++e   + + ++  
  gene2968|gene2968|rna2968|rna2968 194 APYRVALVGTNGVGKTTTLSKLCYHFAVRDKGVYVAACdtFRAGAIEQ--LQTYVNRLKINHRVEIHQQGYNKEEW 267
                                        69********************99999998888876653333333333..34455555555555555555555544 PP

                            Pox_A32  86 kl 87 
                                        k+
  gene2968|gene2968|rna2968|rna2968 268 KV 269
                                        54 PP

>> Herpes_TK  Thymidine kinase from herpesvirus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00012      0.11       1      28 [.     202     229 ..     202     250 .. 0.92
   2 ?   -2.7   0.0       3.1   2.7e+03      22      49 ..     309     337 ..     292     341 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00012
                                        SSTTSSHHHHH.HHHHHHSTTTTEEEE- CS
                          Herpes_TK   1 GafGiGkttvleellkalairdrilyve 28 
                                        G+ G+Gktt+l++l  ++a+rd+ +yv 
  gene2968|gene2968|rna2968|rna2968 202 GTNGVGKTTTLSKLCYHFAVRDKGVYVA 229
                                        789**********************996 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 3.1
                                        TTEEEE---HHHH.HTTSSSSHHHHHHHH CS
                          Herpes_TK  22 drilyveEPlkyW.rvlfaedaiteiytt 49 
                                        d+++yv E lk + +   a d++t i  t
  gene2968|gene2968|rna2968|rna2968 309 DDVVYVSEALKGYeKDVLAFDMVTAIIVT 337
                                        78999999998551445555888877665 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       5.5   4.7e+03      72      89 ..     139     156 ..      91     189 .. 0.68
   2 ?   12.7   0.1   0.00014      0.12      26      63 ..     197     236 ..     173     279 .. 0.68

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 5.5
                             AAA_16  72 laqalareellrqlldea 89 
                                        + ++++re ll+ ll++ 
  gene2968|gene2968|rna2968|rna2968 139 VFKTFDREALLAHLLNKN 156
                                        456666666666666663 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00014
                             AAA_16  26 lvllsGesGvGKsslvrell.ralekd.ggiflrgkcdql 63 
                                         v l+G  GvGK++ + +l  + + +d g++++++++ + 
  gene2968|gene2968|rna2968|rna2968 197 RVALVGTNGVGKTTTLSKLCyHFAVRDkGVYVAACDTFRA 236
                                        5889************555515555552577776666655 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.0    0.0024       2.1      35      57 ..     197     219 ..     188     245 .. 0.85
   2 ?    2.5   0.0      0.11        91       9      41 ..     331     365 ..     327     368 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0024
                              AAA_7  35 pvllvGptGtGKtviikdllkkl 57 
                                         v lvG+ G+GKt+++++l+ ++
  gene2968|gene2968|rna2968|rna2968 197 RVALVGTNGVGKTTTLSKLCYHF 219
                                        689*************9976655 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.11
                              AAA_7   9 fseilVptvdtv..rysyllelllknkkpvllvGp 41 
                                        ++ i+V  +dtv  r+  +l+l+  +kkpv++ G+
  gene2968|gene2968|rna2968|rna2968 331 VTAIIVTKIDTVddRIGSILNLCYFSKKPVVFLGH 365
                                        6789*******9778999**************996 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       4.7     4e+03     106     121 ..     146     161 ..     140     166 .. 0.85
   2 ?   12.0   0.0   0.00017      0.15       3      28 ..     198     223 ..     196     250 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 4.7
                                        ...HHHHHCTTTTT-- CS
                              NACHT 106 rtlLselirkkllpea 121
                                        + lL++l++k++ pe+
  gene2968|gene2968|rna2968|rna2968 146 EALLAHLLNKNVAPEV 161
                                        57999*****999986 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00017
                                        EEEEC-TTTCHHHHHHHHHHHHCTS- CS
                              NACHT   3 vilqGeaGsGKTtLlqklalawaegk 28 
                                        v+l G +G+GKTt l kl+   a ++
  gene2968|gene2968|rna2968|rna2968 198 VALVGTNGVGKTTTLSKLCYHFAVRD 223
                                        899****************9988776 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.4   0.00029      0.24       1      38 [.     197     231 ..     197     304 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00029
                                        EEEEE--TTSSHHHHHHHHHHHH...GGGEEEEEEEEE CS
                           NTPase_1   1 kvfiTGppGvGKtTlvkkvlellkssgvkvgGfyteev 38 
                                        +v++ G  GvGKtT ++k++       v+ +G+y+   
  gene2968|gene2968|rna2968|rna2968 197 RVALVGTNGVGKTTTLSKLCYHF---AVRDKGVYVAAC 231
                                        58899**************9988...566666666554 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.1       1.7   1.5e+03      67      96 ..      51      80 ..      42     107 .. 0.70
   2 ?   12.3   0.2   0.00011     0.093      35      82 ..     197     233 ..     170     335 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.7
                             AAA_25 67 vapeqgkVlyvsaEdsedelrrRlravgea 96
                                       +++   kV++ +++d+ ++++r +++ +e+
  gene2968|gene2968|rna2968|rna2968 51 YRTVGKKVIMCVGDDADEQIERMAAEYLED 80
                                       456778999999999998888887777765 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00011
                             AAA_25  35 lallaGapgtGKttlaldlalava.tGkpwlgpvapeqgkVlyvsaEds 82 
                                         ++l+G  g+GKtt ++ l+++ a ++            k +yv+a+d+
  gene2968|gene2968|rna2968|rna2968 197 RVALVGTNGVGKTTTLSKLCYHFAvRD------------KGVYVAACDT 233
                                        689********************9533............3445555554 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00031      0.26       5      56 ..     198     246 ..     196     305 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00031
                             AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpeklleli 56 
                                        ++++G   vGKTt l +l ++  v+++ +   ++d+ r  ++++     +++
  gene2968|gene2968|rna2968|rna2968 198 VALVGTNGVGKTTTLSKLCYHFAVRDKGVYVAACDTFRAGAIEQL---QTYV 246
                                        5799***************88888777777778888777555543...3333 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.89   7.6e+02      77     121 ..      30      75 ..      20     110 .. 0.59
   2 ?    9.7   0.0    0.0013       1.1       1     108 [.     201     314 ..     201     319 .. 0.57

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.89
                                        EE-SEEEETTEEEESSHHHHHHHH...SEEEEEE--HHHHHHHHHH CS
                             AAA_17  77 dghprikeqagfldglpkevleelkp.daiilleadpeeilerrlk 121
                                        d+  r + ++g+l    ++v       ++i ++ +d++e +er++ 
  gene2968|gene2968|rna2968|rna2968  30 DTVVRKNIKHGELTVQGRNVAYRTVGkKVIMCVGDDADEQIERMAA 75 
                                        5555555555555444444433322214444455555555555443 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0013
                                        EE-TTSSHHHHHHHHHHHH....TEEEEEHHHHHHHHHHTT..T....SHSSHHHHCTSHHHHHHHHHHHHHHHHH CS
                             AAA_17   1 lGgPGsGKgtqceklveky....gfthlsaGdllreeakrg..g....lakardemrklpleekkelqkeaaekia 66 
                                        +G  G+GK+t ++kl  ++    +  ++ a d +r+ a ++       l k +++++  ++  +ke  k a  +++
  gene2968|gene2968|rna2968|rna2968 201 VGTNGVGKTTTLSKLCYHFavrdKGVYVAACDTFRAGAIEQlqTyvnrL-KINHRVEIHQQGYNKEEWKVARSALQ 275
                                        6999***********9888777677889999999987765533111111.12222222222222222333333333 PP

                                        HHHHSSEEEEEE-SEEEETTEEEESSHHHHHHHH..SEEEEE CS
                             AAA_17  67 eeakkkgvlvdghprikeqagfldglpkevleelkpdaiill 108
                                          ++ + +lvd+  r+ +++ ++d l k  l++l  d ++++
  gene2968|gene2968|rna2968|rna2968 276 YGKAYDVILVDTAGRV-NKKPLIDSLRK--LTNLGFDDVVYV 314
                                        3334566777777776.44555555555..566666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (387 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       761  (0.0424452); expected 358.6 (0.02)
Passed bias filter:                      578  (0.0322383); expected 358.6 (0.02)
Passed Vit filter:                        91  (0.00507558); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.61u 0.32s 00:00:00.93 Elapsed: 00:00:00.47
# Mc/sec: 2463.61
//
Query:       gene2969|gene2969|rna2969|rna2969  [L=718]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (718 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2644  (0.147471); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.83u 0.31s 00:00:01.13 Elapsed: 00:00:00.47
# Mc/sec: 4545.04
//
Query:       gene297|gene297|rna297|rna297  [L=290]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      1e-07   32.0  10.1    0.00032   21.0   2.3    2.5  2  zf-C2H2    Zinc finger, C2H2 type
    5.3e-05   23.5   2.7    5.3e-05   23.5   2.7    2.8  3  zf-H2C2_2  Zinc-finger double domain
    6.8e-05   23.4   7.5       0.11   13.4   1.0    2.6  2  zf-C2H2_4  C2H2-type zinc finger
     0.0012   19.1   1.9       0.17   12.2   0.2    2.4  2  zf-C2H2_8  C2H2-type zinc ribbon
  ------ inclusion threshold ------
       0.11   12.7   6.7        1.3    9.3   3.9    2.4  2  IBR        IBR domain, a half RING-finger domain


Domain annotation for each model (and alignments):
>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   1.1   5.4e-06     0.019       1      23 []     222     246 ..     222     246 .. 0.97
   2 !   21.0   2.3   8.8e-08   0.00032       1      23 []     252     276 ..     252     276 .. 0.97

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 5.4e-06
                                    EEET..TTTEEESSHHHHHHHHHCC CS
                        zf-C2H2   1 ykCp..dCgksFkrksnLkrHirtH 23 
                                    y+Cp   Cgk F++ s  krH+ +H
  gene297|gene297|rna297|rna297 222 YYCPkkNCGKNFPSLSRVKRHYIVH 246
                                    89********************998 PP

  == domain 2  score: 21.0 bits;  conditional E-value: 8.8e-08
                                    EEET..TTTEEESSHHHHHHHHHCC CS
                        zf-C2H2   1 ykCp..dCgksFkrksnLkrHirtH 23 
                                    ykC   dC+ksF+rk+n+ +H+r H
  gene297|gene297|rna297|rna297 252 YKCLnpDCKKSFSRKDNMLQHYRNH 276
                                    899999*****************99 PP

>> zf-H2C2_2  Zinc-finger double domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   1.0     0.016        56      13      24 ..     220     233 ..     216     235 .. 0.85
   2 !   23.5   2.7   1.5e-08   5.3e-05       3      25 ..     240     264 ..     238     265 .. 0.93
   3 ?   -3.9   0.4         5   1.8e+04       5       9 ..     272     276 ..     270     276 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.016
                      zf-H2C2_2  13 kpyeCp..lCdkaF 24 
                                    k y Cp   C+k F
  gene297|gene297|rna297|rna297 220 KMYYCPkkNCGKNF 233
                                    56****999***99 PP

  == domain 2  score: 23.5 bits;  conditional E-value: 1.5e-08
                      zf-H2C2_2   3 rrHirkHtgekpyeCp..lCdkaFk 25 
                                    +rH  +Htg+kpy+C    C+k+F+
  gene297|gene297|rna297|rna297 240 KRHYIVHTGKKPYKCLnpDCKKSFS 264
                                    7**************9989*****8 PP

  == domain 3  score: -3.9 bits;  conditional E-value: 5
                      zf-H2C2_2   5 HirkH 9  
                                    H r+H
  gene297|gene297|rna297|rna297 272 HYRNH 276
                                    99998 PP

>> zf-C2H2_4  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.7   3.5e-05      0.12       1      23 [.     222     246 ..     222     247 .. 0.94
   2 !   13.4   1.0   3.1e-05      0.11       4      23 ..     257     276 ..     252     276 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.5e-05
                      zf-C2H2_4   1 fkCpi..CgksFsskkaLlrHlkth 23 
                                    ++Cp   Cgk+F+s ++++rH   h
  gene297|gene297|rna297|rna297 222 YYCPKknCGKNFPSLSRVKRHYIVH 246
                                    8999999**************9888 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 3.1e-05
                      zf-C2H2_4   4 piCgksFsskkaLlrHlkth 23 
                                    p C+ksFs+k+++l+H ++h
  gene297|gene297|rna297|rna297 257 PDCKKSFSRKDNMLQHYRNH 276
                                    56****************99 PP

>> zf-C2H2_8  C2H2-type zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.2   4.7e-05      0.17      29      70 ..     215     255 ..     205     257 .. 0.82
   2 !    7.0   0.2     0.002       7.1       2      29 ..     254     281 ..     253     289 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 4.7e-05
                      zf-C2H2_8  29 qslegklfrcstascaetfpsmqelvahtklhykpnryfkce 70 
                                    +  + k+++c  + c + fps+  +  h  +h    + +kc 
  gene297|gene297|rna297|rna297 215 YENDNKMYYCPKKNCGKNFPSLSRVKRHYIVHTGK-KPYKCL 255
                                    67789*******************99999998643.445665 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.002
                      zf-C2H2_8   2 cssygcrlafpnvrelaqhlrvhlsptq 29 
                                    c  + c+ +f    +++qh+r h++ ++
  gene297|gene297|rna297|rna297 254 CLNPDCKKSFSRKDNMLQHYRNHCTMSR 281
                                    78899*******************8765 PP

>> IBR  IBR domain, a half RING-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   3.9   0.00037       1.3       8      48 ..     211     263 ..     208     263 .. 0.65
   2 ?    5.6   0.9    0.0053        19      15      42 ..     248     278 ..     236     283 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00037
                            IBR   8 lkkslesdpnlkwCprpdCeaii.......eksegcks.........vtCsk..Cgfef 48 
                                    +k ++e+d+++ +Cp+++C++ +       +      +          +C +  C+++f
  gene297|gene297|rna297|rna297 211 FKVEYENDNKMYYCPKKNCGKNFpslsrvkR------HyivhtgkkpYKCLNpdCKKSF 263
                                    5667899999**********98855543330......2333344444677655577776 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0053
                            IBR  15 dpnlkwCprpdCeaiiekseg..cks..vtCs 42 
                                     ++  +C +pdC++ ++ +++  + +   +C+
  gene297|gene297|rna297|rna297 248 GKKPYKCLNPDCKKSFSRKDNmlQ-HyrNHCT 278
                                    555679*******98877777652.3223365 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (290 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1541  (0.0859501); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 2130.31
//
Query:       gene2970|gene2970|rna2970|rna2970  [L=35]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (35 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       418  (0.0233142); expected 358.6 (0.02)
Passed bias filter:                      197  (0.0109878); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.31u 0.24s 00:00:00.55 Elapsed: 00:00:00.38
# Mc/sec: 278.47
//
Query:       gene2971|gene2971|rna2971|rna2971  [L=44]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.088   13.2   0.2       0.12   12.8   0.2    1.3  1  NTS_2     N-terminal segments of P. falciparum erythrocyte me


Domain annotation for each model (and alignments):
>> NTS_2  N-terminal segments of P. falciparum erythrocyte membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.2   6.6e-06      0.12       3      19 ..       6      22 ..       4      29 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6.6e-06
                              NTS_2  3 ststigdkiEaYLekks 19
                                       +tst+ +k E++Lekk 
  gene2971|gene2971|rna2971|rna2971  6 KTSTMDEKYETWLEKKD 22
                                       89*************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (44 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       576  (0.0321267); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 320.32
//
Query:       gene2972|gene2972|rna2972|rna2972  [L=40]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (40 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1545  (0.0861732); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.27s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 296.85
//
Query:       gene2973|gene2973|rna2973|rna2973  [L=76]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       279  (0.0155614); expected 358.6 (0.02)
Passed bias filter:                      227  (0.0126611); expected 358.6 (0.02)
Passed Vit filter:                         5  (0.000278878); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.43
# Mc/sec: 534.10
//
Query:       gene2974|gene2974|rna2974|rna2974  [L=159]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       553  (0.0308439); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1164.63
//
Query:       gene2975|gene2975|rna2975|rna2975  [L=195]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.14   12.4   0.0       0.31   11.3   0.0    1.6  1  Megourin  Aphid Megourins


Domain annotation for each model (and alignments):
>> Megourin  Aphid Megourins
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   1.7e-05      0.31      16      39 ..     108     131 ..      98     149 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 1.7e-05
                           Megourin  16 eGavfnGrktcqiGcraacqqpGc 39 
                                        +   fnG +t  i    +cqqpG 
  gene2975|gene2975|rna2975|rna2975 108 QAITFNGIRTNYIIVEMICQQPGV 131
                                        5567******************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       433  (0.0241508); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.30s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 1245.48
//
Query:       gene2976|gene2976|rna2976|rna2976  [L=50]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.029   14.6   0.0      0.032   14.4   0.0    1.0  1  Ectoine_synth  Ectoine synthase


Domain annotation for each model (and alignments):
>> Ectoine_synth  Ectoine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   1.8e-06     0.032      72     110 ..       2      41 ..       1      43 [. 0.93

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.8e-06
                                        TT--EEEE-TTEEEEETTT-EEEEEESS.-EEEEEEEES- CS
                      Ectoine_synth  72 edgevyeikpgtlYlldkhdkHllrakk.elrlvcvFnPp 110
                                        e+ge  +i +g+lYl+ k d+ +lr ++ +l+   v nP+
  gene2976|gene2976|rna2976|rna2976   2 EKGELTAICKGDLYLIRKSDRKILRKRHyDLKAYGVRNPS 41 
                                        689999********************999*******9995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (50 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       309  (0.0172346); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.31s 00:00:00.69 Elapsed: 00:00:00.47
# Mc/sec: 316.75
//
Query:       gene2977|gene2977|rna2977|rna2977  [L=133]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.2e-09   37.0   0.0    4.9e-09   36.4   0.0    1.2  1  rve           Integrase core domain
  ------ inclusion threshold ------
      0.028   14.2   0.1      0.053   13.3   0.1    1.5  1  rve_3         Integrase core domain
      0.075   13.5   1.5       0.15   12.6   1.5    1.7  1  GlutR_dimer   Glutamyl-tRNAGlu reductase, dimerisation domain
       0.12   12.7   1.1       0.46   10.8   0.5    1.9  2  MADF_DNA_bdg  Alcohol dehydrogenase transcription factor Myb/


Domain annotation for each model (and alignments):
>> rve  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.4   0.0   1.1e-12   4.9e-09      63     117 ..       8      61 ..       2      63 .. 0.92

  Alignments for each domain:
  == domain 1  score: 36.4 bits;  conditional E-value: 1.1e-12
                                rve  63 ggvepervlsDngseytskafrefladlgirvsftrpgrpqdnGkvErfhrtlkd 117
                                        +gv pe++++Dn++e+++ +++++  + +i ++ t + + ++nG+vEr +rt+++
  gene2977|gene2977|rna2977|rna2977   8 WGV-PEMIITDNAKEFVAIETKTWMTEARIIHEKTSVESHKSNGRVERVIRTIRE 61 
                                        455.*************************************************97 PP

>> rve_3  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   1.2e-05     0.053       6      55 ..      39      84 ..      34      90 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.2e-05
                              rve_3  6 syiapgkPqqNglvEsfngtlrdellneelfrslaearekleawredYNt 55
                                       + + + + + Ng vE++++t+r+ + + e      e  +++++  ++YN+
  gene2977|gene2977|rna2977|rna2977 39 EKTSVESHKSNGRVERVIRTIREAIEKIEVN----EMGKAIKEVEDRYNK 84
                                       5566777889************998776555....889999999999996 PP

>> GlutR_dimer  Glutamyl-tRNAGlu reductase, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   1.5   3.2e-05      0.15       6      51 ..      36      80 ..      12     103 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3.2e-05
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-S..- CS
                        GlutR_dimer  6 IeeeveefeawlkslevvptIkalrekaeeireeeleralkklald 51
                                       I +e  + e+   + +v+ +I+ +re +e+i  +e+ +a+k+++ d
  gene2977|gene2977|rna2977|rna2977 36 IIHEKTSVESHKSNGRVERVIRTIREAIEKIEVNEMGKAIKEVE-D 80
                                       4455566677777779*************************997.3 PP

>> MADF_DNA_bdg  Alcohol dehydrogenase transcription factor Myb/SANT-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.5    0.0001      0.46      13      62 ..      39      88 ..      30     100 .. 0.81
   2 ?    1.9   0.1     0.064   2.9e+02      21      46 ..      90     111 ..      84     131 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0001
                       MADF_DNA_bdg 13 drsh.pdyrnkekrekaweeiaeelnekvdveeckkkwknLRdryrrelrk 62
                                       ++++ ++++++ + e++ ++i e ++ k++v+e+ k +k+  dry++ +  
  gene2977|gene2977|rna2977|rna2977 39 EKTSvESHKSNGRVERVIRTIREAIE-KIEVNEMGKAIKEVEDRYNKTYHA 88
                                       55554778899999***********7.8*******************9844 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.064
                       MADF_DNA_bdg  21 nkekrekaweeiaeelnekvdveeck 46 
                                         k++ ekaw+ i       v++  ++
  gene2977|gene2977|rna2977|rna2977  90 MKCTPEKAWKDITGIAA--VEK--VR 111
                                        56778999*99998875..332..22 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1033  (0.0576162); expected 358.6 (0.02)
Passed bias filter:                      488  (0.0272185); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 872.98
//
Query:       gene2978|gene2978|rna2978|rna2978  [L=109]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    8.7e-05   22.8   0.1     0.0016   18.7   0.0    2.2  2  RT_RNaseH  RNase H-like domain found in reverse transcriptase


Domain annotation for each model (and alignments):
>> RT_RNaseH  RNase H-like domain found in reverse transcriptase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   8.8e-08    0.0016      75     105 .]       4      35 ..       2      35 .. 0.89
   2 ?    2.1   0.0     0.013   2.4e+02      41      58 ..      68      85 ..      52      89 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 8.8e-08
                                        EE-SS--TTTTT----..---HHHHHHHC-XX CS
                          RT_RNaseH  75 vitDhknlkyllskks.lngrlarWaleLsey 105
                                        +itDhk+l+ + +k +  n+r +rW++ +++y
  gene2978|gene2978|rna2978|rna2978   4 LITDHKALEVIRNKPEfDNNRPNRWCEAIQQY 35 
                                        89**********7777478***********99 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.013
                                       -HHHHTS-HHHHHHHHHH CS
                          RT_RNaseH 41 sgaernystiekellAiv 58
                                       +++e++y+ti+ + l+ v
  gene2978|gene2978|rna2978|rna2978 68 KKTEKRYETINEKHLCTV 85
                                       789******999888766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       759  (0.0423336); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 808.58
//
Query:       gene2979|gene2979|rna2979|rna2979  [L=147]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-08   33.8   0.1    3.1e-08   33.4   0.1    1.2  1  RVT_1     Reverse transcriptase (RNA-dependent DNA polymerase


Domain annotation for each model (and alignments):
>> RVT_1  Reverse transcriptase (RNA-dependent DNA polymerase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.4   0.1   1.7e-12   3.1e-08     134     222 .]       3      79 ..       1      79 [. 0.95

  Alignments for each domain:
  == domain 1  score: 33.4 bits;  conditional E-value: 1.7e-12
                                        ST-TTHHHHHHHHHHHHHTT-T......TEEECTTEEEEEESSHHHHHHHHHHHHHHHHHTT--BEGGG-EEE... CS
                              RVT_1 134 qGsvlSPllfnlfmnellrelrkrakgvtllrYaDDililskskeelqelleaveewlkesglkinpeKtklvlft 209
                                         G++++P++f++++n++l +l      + + +Y+  i+i++k+   +++l+++v ++l+ ++l++n +K++ +   
  gene2979|gene2979|rna2979|rna2979   3 IGFKNAPMIFQRVINQVLDRLIG----NGVEVYMNGIIIHFKK---CDALVREVIKRLSMNKLNVNIKKVQYT--- 68 
                                        7*********************8....79************98...88999**********************... PP

                                        ..ESSEEETTEEE CS
                              RVT_1 210 vkseevkyLGvtl 222
                                          ++evk LGvt+
  gene2979|gene2979|rna2979|rna2979  69 --RQEVKLLGVTI 79 
                                        ..9********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       754  (0.0420548); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1017.03
//
Query:       gene298|gene298|rna298|rna298  [L=86]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       258  (0.0143901); expected 358.6 (0.02)
Passed bias filter:                      189  (0.0105416); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 634.96
//
Query:       gene2980|gene2980|rna2980|rna2980  [L=62]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.012   15.1   0.0      0.012   15.1   0.0    1.0  1  RVT_1     Reverse transcriptase (RNA-dependent DNA polymerase


Domain annotation for each model (and alignments):
>> RVT_1  Reverse transcriptase (RNA-dependent DNA polymerase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0   6.7e-07     0.012      46     100 ..      15      59 ..       2      62 .] 0.80

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 6.7e-07
                                        HHH.............HCCHTS--EEEEEEBCCGCCCSBB-GGGGGGG-EEET.. CS
                              RVT_1  46 rpgrstldavedllkalkkkkkaklllklDlkkaFdsvpleellrkltafkvptk 100
                                        ++++ +          ++ +++++ l+ lDlk  + +++ +e+++ +taf ++ +
  gene2980|gene2980|rna2980|rna2980  15 PDMKRI----------IETTTRSNNLTVLDLKEDYYQIEIDEVYKHKTAFEFENN 59 
                                        444333..........667899999**************************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (62 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       722  (0.04027); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.33s 00:00:00.89 Elapsed: 00:00:00.56
# Mc/sec: 335.84
//
Query:       gene2981|gene2981|rna2981|rna2981  [L=47]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (47 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       372  (0.0207485); expected 358.6 (0.02)
Passed bias filter:                      254  (0.014167); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.32s 00:00:00.78 Elapsed: 00:00:00.50
# Mc/sec: 281.37
//
Query:       gene2982|gene2982|rna2982|rna2982  [L=66]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (66 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       732  (0.0408277); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 501.96
//
Query:       gene2983|gene2983|rna2983|rna2983  [L=60]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (60 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       345  (0.0192426); expected 358.6 (0.02)
Passed bias filter:                      228  (0.0127168); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.29s 00:00:00.63 Elapsed: 00:00:00.43
# Mc/sec: 420.66
//
Query:       gene2984|gene2984|rna2984|rna2984  [L=626]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
   1.2e-113  379.5   1.4   1.2e-113  379.5   1.4    1.6  2  tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
    6.7e-07   28.4   4.2    8.7e-05   21.4   0.2    2.5  2  tRNA-synt_1g  tRNA synthetases class I (M)
      1e-06   27.3   0.0    4.7e-06   25.1   0.0    1.9  2  tRNA-synt_1   tRNA synthetases class I (I, L, M and V)
     0.0032   16.4   0.2      0.014   14.3   0.0    2.2  2  tRNA-synt_1c  tRNA synthetases class I (E and Q), catalytic d
  ------ inclusion threshold ------
      0.024   14.6   0.4        0.1   12.6   0.3    2.1  2  DUF3212       Protein of unknown function (DUF3212)
        0.2   12.2   1.3       0.99    9.9   0.0    2.7  3  Pox_D5        Poxvirus D5 protein-like


Domain annotation for each model (and alignments):
>> tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  379.5   1.4  3.9e-117  1.2e-113       3     300 ..      26     349 ..      24     350 .. 0.95
   2 ?   -3.0   0.2       1.2   3.5e+03      58     114 ..     493     553 ..     490     557 .. 0.39

  Alignments for each domain:
  == domain 1  score: 379.5 bits;  conditional E-value: 3.9e-117
                                        --SBTTEEEEEEEEEBTTS--BHHHHHHHHHHHHHHHHHHH.TT-EEEEEEEBB--SHHHHHHHHHTTS-...... CS
                       tRNA-synt_1e   3 kpleekkvtlYvCGptvydashlGhaRslvafDilrrilqa.lgYdvqfvqnvtDidDkiikrareeeks...... 71 
                                        +p++  ++++Y+CGptvyd +hlGhaR++++fD++rril+  + Ydv+fv n+t+idDki+k+a++  ++      
  gene2984|gene2984|rna2984|rna2984  26 TPITPSQIKMYICGPTVYDSAHLGHARTYICFDVIRRILEEhFHYDVTFVMNITNIDDKIVKKAEAIFSEflksnv 101
                                        678899*********************************999**********************998777899*** PP

                                        ....................HHHHHHHHHHHHHHHHHHTT----SB--BGGGGHHHHHHHHHHHHHTTSEEE-TTS CS
                       tRNA-synt_1e  72 ....................vkelaekfieefkkdleaLnvlkptleprvsekvdeiielvekliekgyaYavsdg 127
                                                            v+ ++ k++eef++d++ Lnv+ p++ ++v++++ ei+++ve+l+e+g aY+v+ g
  gene2984|gene2984|rna2984|rna2984 102 kyvnvdrlgqeqrrdafvecVEFVTRKYEEEFFEDMRRLNVRAPSFVTKVTDYMGEIVRFVERLVERGRAYVVN-G 176
                                        *******************9899999***********************************************9.* PP

                                        -EEE-GGG-TTTTTTTT--HHHHHHT----S--S-SSTT-EEEEEE--TTS.--B--TTSSEEE-SSHHHHHHHHH CS
                       tRNA-synt_1e 128 dvyfdvskkeeYgklskqnleelelgaegevseekkdkkDfaLWkaskege.pswdsPwgkGRPGWhieCsvmask 202
                                         vyfd+ k+ e g   + + ++    +e e  +ekk+++DfaLWk  keg+   ++sPw++GRPGWhieCs+m ++
  gene2984|gene2984|rna2984|rna2984 177 SVYFDMVKFMEEGGQRHFRGDDAVI-NEAEEGSEKKHRTDFALWKRCKEGDlYYFESPWSNGRPGWHIECSAMGMD 251
                                        *******999999877666666555.5555557999***************6689********************* PP

                                        HH-SSEEEEEEEGGGTTTHHHHHHHHHHHHSSS--EEEEEEE--EEETTBE--TTTT---BHHHHHTTS-HHHHHH CS
                       tRNA-synt_1e 203 llgseidihsGGiDLafPhhenelaqseaafdkqlvkyflhnghlkiegekmsksLknfitikdvlkkfdprqlRl 278
                                        +lg+++dih+GGiDL fPhhene+ qs+a++d+++v+yf+h+ghl+ieg kmsksLknfiti+d lkkf++rq+R+
  gene2984|gene2984|rna2984|rna2984 252 VLGHTMDIHAGGIDLQFPHHENEMIQSRALTDQPYVNYFMHTGHLHIEGLKMSKSLKNFITIQDCLKKFTARQIRV 327
                                        **************************************************************************** PP

                                        HHHSS-TTS-EEE-HHHHHHHH CS
                       tRNA-synt_1e 279 lllsahyrsqldfkeelleeak 300
                                        ++l++ y s++ ++ e++e+a+
  gene2984|gene2984|rna2984|rna2984 328 MFLNNCYDSTVTYRYEAMEYAE 349
                                        *****************99886 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.2
                                        SHHHHHHHHHTTS..-HHHHHHHHHHHHHHHHHHTT...----SB--BGGGGHHHHHHHHHH CS
                       tRNA-synt_1e  58 dDkiikrareeek..svkelaekfieefkkdleaLn...vlkptleprvsekvdeiielvek 114
                                        +Dk+++r  e  k    ++++++f + +k+  + Ln   + + ++     + ++ + +++++
  gene2984|gene2984|rna2984|rna2984 493 NDKMVLRMLEMAKkeVHESFCDNF-NTYKTLTAILNlitIMHQKMYNCSGQVIQLVLDYIKR 553
                                        677777765543200233333333.3344444444400033333333333334444444444 PP

>> tRNA-synt_1g  tRNA synthetases class I (M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.6    0.0004       1.2      12      56 ..      44      89 ..      35     137 .. 0.85
   2 !   21.4   0.2   2.9e-08   8.7e-05     312     381 ..     287     357 ..     269     362 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0004
                                       S---HHHHHHHHHHHHHHHHHHHT.T-EEEEEEEE---SHHHHHHH CS
                       tRNA-synt_1g 12 gklHlGhllevisaDifaRykrlr.geevlfvcgtDehGtpielkA 56
                                       ++ HlGh++++i  D++ R    +  ++v+fv    +   +i  kA
  gene2984|gene2984|rna2984|rna2984 44 DSAHLGHARTYICFDVIRRILEEHfHYDVTFVMNITNIDDKIVKKA 89
                                       679****************987665999*99977666555555555 PP

  == domain 2  score: 21.4 bits;  conditional E-value: 2.9e-08
                                        -S-EEEE--EEE--------------HHHHHHHH-HHHHHHHHHH.HS-TTS-EEE-HHHHHHHHHHHCCC CS
                       tRNA-synt_1g 312 pkkvvaheyltvegkKlSkSrgvvvkakealerldadllRYylaa.eapekkDldfswedfvervNseLad 381
                                        ++  + +++l +eg K+SkS +++++++++l++++a ++R +++    + +    ++  +  e++ ++L +
  gene2984|gene2984|rna2984|rna2984 287 VNYFMHTGHLHIEGLKMSKSLKNFITIQDCLKKFTARQIRVMFLNnCYDSTVTYRYEAMEYAEKIEKKLFN 357
                                        5667889*********************************8887734556666777777777777777765 PP

>> tRNA-synt_1  tRNA synthetases class I (I, L, M and V)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.12   3.7e+02      28      57 ..      36      65 ..      30     182 .. 0.66
   2 !   25.1   0.0   1.6e-09   4.7e-06     515     594 ..     255     333 ..     229     340 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.12
                        tRNA-synt_1 28 vdgPPyvtGslHiGhalaktlkdivirykr 57
                                       ++  P v  s H+Gha + +  d++ r+ +
  gene2984|gene2984|rna2984|rna2984 36 YICGPTVYDSAHLGHARTYICFDVIRRILE 65
                                       556677778888888888888888877643 PP

  == domain 2  score: 25.1 bits;  conditional E-value: 1.6e-09
                        tRNA-synt_1 515 fpadmlleGlDiirgWvarlillslaltgsePfkevlvhglvrdeeGrKmSKslgNvidpldvikkygadalRltl 590
                                        + +d+ + G+D  +   ++ +++s alt ++P+ + ++h   +  eG KmSKsl+N i  +d +kk  a  +R + 
  gene2984|gene2984|rna2984|rna2984 255 HTMDIHAGGIDLQFPHHENEMIQSRALT-DQPYVNYFMHTGHLHIEGLKMSKSLKNFITIQDCLKKFTARQIRVMF 329
                                        7789999999999999999999998887.57******************************************998 PP

                        tRNA-synt_1 591 ilsd 594
                                        +++ 
  gene2984|gene2984|rna2984|rna2984 330 LNNC 333
                                        8765 PP

>> tRNA-synt_1c  tRNA synthetases class I (E and Q), catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   4.8e-06     0.014      50      97 ..     127     174 ..     123     214 .. 0.94
   2 ?   -3.3   0.1       1.1   3.2e+03      93     120 ..     453     477 ..     451     513 .. 0.57

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.8e-06
                                        HHHHHHHHHHHHHTT---SSEEEEGGGGHHHHHHHHHHHHHTTSEEEE CS
                       tRNA-synt_1c  50 eeaeesiledlkwlgikwdekptyqsdrfdelkkyaeeLikkGkAYvc 97 
                                         ++ee+  ed+  l++ +   +t+ +d++ e+ +++e+L+++G AYv 
  gene2984|gene2984|rna2984|rna2984 127 RKYEEEFFEDMRRLNVRAPSFVTKVTDYMGEIVRFVERLVERGRAYVV 174
                                        6899*************9999*************************96 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 1.1
                                        SEEEE-STHHHHHHHHCCSSHSS-TTTT CS
                       tRNA-synt_1c  93 kAYvcectkeeleeereeqeklgskerd 120
                                        +AY++e t+e  +e  ++ ++   +++d
  gene2984|gene2984|rna2984|rna2984 453 MAYKDESTEEDPNERTGQLNN---TAKD 477
                                        588888888877666555222...2233 PP

>> DUF3212  Protein of unknown function (DUF3212)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.3   3.4e-05       0.1      40      91 ..      64     111 ..      54     138 .. 0.81
   2 ?   -2.7   0.0         2   5.8e+03      42      63 ..     562     583 ..     547     592 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3.4e-05
                                        HHHTT---HHHHHHHHH--S--SS-SSSHHHHHHHHHHHHHGGG--HHHHHH CS
                            DUF3212  40 aeerfrididyvfsiilniGdieraledeiedllssylssllpfvtkdmlka 91 
                                         ee+f+ d+ +v    +ni +i+ ++ +++e  +s +l+s + +v  d l +
  gene2984|gene2984|rna2984|rna2984  64 LEEHFHYDVTFV----MNITNIDDKIVKKAEAIFSEFLKSNVKYVNVDRLGQ 111
                                        588999888775....8999999999*******************9998754 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2
                                        HTT---HHHHHHHHH--S--SS CS
                            DUF3212  42 erfrididyvfsiilniGdier 63 
                                         + +i+ d + sii n     r
  gene2984|gene2984|rna2984|rna2984 562 AKQEIEEDMLPSIICNFRSEVR 583
                                        5567888999999998765445 PP

>> Pox_D5  Poxvirus D5 protein-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.1      0.79   2.3e+03      43      72 ..      75     107 ..      65     138 .. 0.67
   2 ?    9.9   0.0   0.00033      0.99       5      42 ..     157     193 ..     154     203 .. 0.91
   3 ?   -2.3   0.0       2.2   6.5e+03      48      75 ..     302     334 ..     285     348 .. 0.62

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.79
                             Pox_D5  43 vlskrtFqkrlkkilee...gfekkkkkkgqqp 72 
                                        v++ ++   ++ k  e    +f k + k+ ++ 
  gene2984|gene2984|rna2984|rna2984  75 VMNITNIDDKIVKKAEAifsEFLKSNVKYVNVD 107
                                        666666667777776666656999999954443 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00033
                             Pox_D5   5 pvldFveelfeeekstrvpsdvlYeaYkafcekngykp 42 
                                         ++ Fve+l+e  +  +v + ++Y  + +f+e+ g ++
  gene2984|gene2984|rna2984|rna2984 157 EIVRFVERLVE-RGRAYVVNGSVYFDMVKFMEEGGQRH 193
                                        6899*****99.9**********************987 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 2.2
                             Pox_D5  48 tFqkrlkkilee.....gfekkkkkkgqqpney 75 
                                        ++ k+lk+ +       +f++++ +  + +n y
  gene2984|gene2984|rna2984|rna2984 302 KMSKSLKNFITIqdclkKFTARQIRVMFLNNCY 334
                                        556666665555434433888888866666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (626 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       972  (0.0542138); expected 358.6 (0.02)
Passed bias filter:                      471  (0.0262703); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.69u 0.29s 00:00:00.98 Elapsed: 00:00:00.49
# Mc/sec: 3847.60
//
Query:       gene2985|gene2985|rna2985|rna2985  [L=838]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.2e-66  225.0   0.6    2.9e-66  223.7   0.6    1.6  1  Kinesin      Kinesin motor domain
    3.2e-14   53.1   0.0    7.1e-14   52.0   0.0    1.6  1  Microtub_bd  Microtubule binding
  ------ inclusion threshold ------
      0.096   13.6  16.3         16    6.6   0.1    6.6  6  WD40         WD domain, G-beta repeat
       0.11   12.8   0.1       0.36   11.1   0.0    1.9  2  AAA_22       AAA domain
       0.16   12.4   0.0       0.29   11.5   0.0    1.4  1  AAA_16       AAA ATPase domain
          8    5.0  10.3         15    4.1  10.3    1.4  1  MAP65_ASE1   Microtubule associated protein (MAP65/ASE1 famil


Domain annotation for each model (and alignments):
>> Kinesin  Kinesin motor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  223.7   0.6   9.6e-70   2.9e-66      39     330 ..      30     284 ..       5     286 .. 0.88

  Alignments for each domain:
  == domain 1  score: 223.7 bits;  conditional E-value: 9.6e-70
                                        SCEEEEESEEEETTS-HHHHHHHHHHHHHHHHHTTSEEEEEEEESTTSSHHHHHTBC...TTTSBSHHHHHHHHHH CS
                            Kinesin  39 eekkfkFdkvfdeeatqeevyeetakplvesvleGynatifaYGqtgsGKTyTmegk...eeeeeGiipraleelF 111
                                        + ++f+F ++    +tq ++ ++  +p ++s+l G n++i++YGqtgsGKTyTm  +    e+ +Gi+p +++ l 
  gene2985|gene2985|rna2985|rna2985  30 NAHTFTFTHI----HTQPDISSH-LQPTIQSFLAGNNTSIICYGQTGSGKTYTMGLTashIETCTGIVPASMRMLI 100
                                        5566666666....456777766.5999**************************9887775667999999999998 PP

                                        HHHHHCTTTHEEEEEEEEEEEEEETTEEEETTSTTTTSTSSEBEEEECTTSCCEEETTS--EEESSHHHHHHHHHH CS
                            Kinesin 112 esikkekeekekefsvkvsylEiYneeiyDLLeskkskkkkklkiredskkgevyvkgltevevksaeevlellek 187
                                        e++           sv + ++EiYnee+yDLL+ +      ++ +r+        v + +e+e+ ++e++ e++  
  gene2985|gene2985|rna2985|rna2985 101 ERV-----------SVYLAVFEIYNEEVYDLLDGR-----ARIVLRNCGA---ELVINAHEREICTYEQFGEVVVG 157
                                        877...........58899**************87.....3344555444...4799******************* PP

                                        HHHHHTSTTSSCTSHHCCSEEEEEEEEEEEETTTTTCEEEEEEEEEEEEEEECCCHHHHSSTCHHHHHHHHHHHHH CS
                            Kinesin 188 geknrkvaetklneeSSRSHavftitleqknlkeeteekvkisklnLvDLAGsErasktgaaegerlkEaaniNkS 263
                                        + ++r +++t++n+ SSRSHav++++                ++l ++DLAGsEr+++tg  ++++++Ea +iN+ 
  gene2985|gene2985|rna2985|rna2985 158 AIARRVTKSTRMNAGSSRSHAVIRVRT-------------ACATLVFIDLAGSERTKRTGV-SNDTMREAISINTG 219
                                        **********************88753.............35689***************7.6888********** PP

                                        HHHHHHHHHHHHHTCCTSTSCGGGSHHHHHTGGGHSSSSEEEEEEEE-TBGGGHHHHHHHHHHHHHH CS
                            Kinesin 264 LlaLgrvisaLaekkkskhipYRdSkLTrlLqdsLgGnsktlmivtvspssenleetlstlkfaera 330
                                        LlaLg+vi+aL ++  ++++pYRdSkLTr+L+  L+Gn+ + mi++vs + ++++et++tl++a+ra
  gene2985|gene2985|rna2985|rna2985 220 LLALGNVINALYNR--KRFVPYRDSKLTRILKPILDGNTVVRMIACVSDRYQDANETMNTLEYANRA 284
                                        **************..*************************************************98 PP

>> Microtub_bd  Microtubule binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.0   0.0   2.4e-17   7.1e-14      49     149 .]      31     121 ..       3     121 .. 0.77

  Alignments for each domain:
  == domain 1  score: 52.0 bits;  conditional E-value: 2.4e-17
                                        TEEEE-SEEEECTTHCCCCCCCCHHHHHHHHTT--EEEEEEES................ST-HCHHHHHHHHHHCC CS
                        Microtub_bd  49 kkefsFdrvfeseseqeevfeeisqlvqsaldgynvcifaygqTGsGKtyTmegeeeeagmipraveeifetisel 124
                                        +++f+F++      +q ++ + ++  +qs l g n++i++ygqTGsGKtyTm  + ++   i ++ + i+  + + 
  gene2985|gene2985|rna2985|rna2985  31 AHTFTFTH----IHTQPDISSHLQPTIQSFLAGNNTSIICYGQTGSGKTYTMGLTASH---I-ETCTGIVPASMRM 98 
                                        55555554....56899***********************************994333...3.4444555444444 PP

                                        TSCCCCEEEEEEEEEEESS-EEETT CS
                        Microtub_bd 125 kekgwkyeielqfveiynekvqDlL 149
                                             +++++l + eiyne+v+DlL
  gene2985|gene2985|rna2985|rna2985  99 --LIERVSVYLAVFEIYNEEVYDLL 121
                                        ..466799****************8 PP

>> WD40  WD domain, G-beta repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.1     0.086   2.6e+02       2      35 ..     570     602 ..     563     603 .. 0.65
   2 ?    6.6   0.1    0.0054        16      13      36 ..     652     673 ..     627     675 .. 0.70
   3 ?    1.8   0.1      0.17   5.1e+02      10      34 ..     687     710 ..     680     712 .. 0.69
   4 ?    4.8   0.0      0.02        59       9      38 .]     730     758 ..     720     758 .. 0.64
   5 ?    2.0   0.0      0.15   4.5e+02      25      38 .]     784     797 ..     773     797 .. 0.84
   6 ?    1.1   0.2      0.29   8.8e+02      13      35 ..     812     832 ..     805     833 .. 0.67

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.086
                                        EEEEEEESSSS....EEEEEEETTSSEEEEEETTSEEE CS
                               WD40   2 qclrtltGHss....vtslafspdgawlasGsdDgtvr 35 
                                        +++++l  Hss    + +l    +ga  +++s D+t+r
  gene2985|gene2985|rna2985|rna2985 570 KHVHSLAVHSStilsIMHL----NGAVYTTSS-DNTLR 602
                                        4577777783344444444....555546677.99998 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0054
                                        EEEEEEETTSSEEEEEETTSEEEE CS
                               WD40  13 vtslafspdgawlasGsdDgtvri 36 
                                        +t++  +   +++++G+ Dg vr+
  gene2985|gene2985|rna2985|rna2985 652 ITGV--HYKDTLVVTGHVDGRVRV 673
                                        5555..66677799*********8 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.17
                                        S.SSEEEEEEETTSSE...EEEEETTSEE CS
                               WD40  10 H.ssvtslafspdgaw...lasGsdDgtv 34 
                                        H ++v+++     g +   l +G+ Dgtv
  gene2985|gene2985|rna2985|rna2985 687 HrGCVNAV-----GVYdgvLYTGCVDGTV 710
                                        66667766.....33455489*******9 PP

  == domain 4  score: 4.8 bits;  conditional E-value: 0.02
                                        SS.SSEEEEEEETTSSEEEEEETTSEEEEEE CS
                               WD40   9 GH.ssvtslafspdgawlasGsdDgtvriWd 38 
                                        +H ++v  l f +   +++sGs+ gt+r W+
  gene2985|gene2985|rna2985|rna2985 730 AHnNCV-NLIFMHK-GYVFSGSKEGTIRKWK 758
                                        553334.3323333.33679********995 PP

  == domain 5  score: 2.0 bits;  conditional E-value: 0.15
                                        EEEEETTSEEEEEE CS
                               WD40  25 lasGsdDgtvriWd 38 
                                        + +G++Dg v+ W+
  gene2985|gene2985|rna2985|rna2985 784 FYTGCKDGVVKRWN 797
                                        579********998 PP

  == domain 6  score: 1.1 bits;  conditional E-value: 0.29
                                        EEEEEEETTSSEEEEEETTSEEE CS
                               WD40  13 vtslafspdgawlasGsdDgtvr 35 
                                        v +++   dg     G+ Dg+v+
  gene2985|gene2985|rna2985|rna2985 812 VVCMDGTGDGVV--VGGSDGNVY 832
                                        667755555555..4655**996 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00012      0.36       5      22 ..      61      78 ..      58     119 .. 0.90
   2 ?   -4.1   0.0         6   1.8e+04      39      67 ..     399     427 ..     391     437 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00012
                             AAA_22  5 agilvvtGesGtGKTtll 22
                                        ++++++G++G+GKT+++
  gene2985|gene2985|rna2985|rna2985 61 NTSIICYGQTGSGKTYTM 78
                                       689************997 PP

  == domain 2  score: -4.1 bits;  conditional E-value: 6
                             AAA_22  39 rpevvfvtlpsstsskdllrellralgle 67 
                                        ++++v+ t +++++ + +++++ + +  +
  gene2985|gene2985|rna2985|rna2985 399 PVSTVTTTNTNPSTNTPIRNKVINTVPTP 427
                                        67888888899999999999998877665 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   9.7e-05      0.29      11      55 ..      48      92 ..      44     198 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 9.7e-05
                             AAA_16 11 qLlsalervrsgrpelvllsGesGvGKsslvrellralekdggif 55
                                       +L+ ++++  +g   +++++G+ G+GK+  +   + ++e+  gi+
  gene2985|gene2985|rna2985|rna2985 48 HLQPTIQSFLAGNNTSIICYGQTGSGKTYTMGLTASHIETCTGIV 92
                                       677778888899999****************99999998775555 PP

>> MAP65_ASE1  Microtubule associated protein (MAP65/ASE1 family)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1  10.3    0.0052        15     499     584 ..     480     567 ..     391     578 .. 0.62

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.0052
                                        XXXXXXXXXXXXXXX.XXX...XXXXXX.................XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                         MAP65_ASE1 499 nerkrklpsanvisk.nsaagrakrsllarlnskkasasanq...nsskllrsPlrpvslfpnslnklsekerdsv 570
                                        n +++  +  n +s+ ns++ +a   ++a+  s   ++ a+    ++++++++P++p + +  ++nk s+k+++s+
  gene2985|gene2985|rna2985|rna2985 480 NDKEAETL--NTTSAiNSTKTNALNTINATTTSRATTTRATTnitTNKSRIEQPIQPLEQKTGIVNKPSRKNKNSP 553
                                        33333333..333554555445555555555555544444435789*************************99999 PP

                                        XXXXXXXXXXXXXX CS
                         MAP65_ASE1 571 ssqikklsskkelk 584
                                        +++ +  ++++ l+
  gene2985|gene2985|rna2985|rna2985 554 QETTTPSKRMRTLN 567
                                        55555555455554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (838 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1148  (0.0640303); expected 358.6 (0.02)
Passed bias filter:                      676  (0.0377043); expected 358.6 (0.02)
Passed Vit filter:                        90  (0.0050198); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.74u 0.30s 00:00:01.04 Elapsed: 00:00:00.42
# Mc/sec: 5940.13
//
Query:       gene2986|gene2986|rna2986|rna2986  [L=66]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (66 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       214  (0.011936); expected 358.6 (0.02)
Passed bias filter:                      127  (0.0070835); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.33u 0.27s 00:00:00.60 Elapsed: 00:00:00.41
# Mc/sec: 485.23
//
Query:       gene2987|gene2987|rna2987|rna2987  [L=1197]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.8e-18   65.6   0.1    1.6e-17   64.4   0.1    1.7  1  Patatin   Patatin-like phospholipase


Domain annotation for each model (and alignments):
>> Patatin  Patatin-like phospholipase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.4   0.1     9e-22   1.6e-17       1     202 [.     907    1069 ..     907    1071 .. 0.98

  Alignments for each domain:
  == domain 1  score: 64.4 bits;  conditional E-value: 9e-22
                            Patatin    1 LvlsGGGsrgafslgalkaLkkelgerfdiisGtSaGAiialllalgrdpaalvddlrnlllnkifdrdllire 74  
                                         Lvl+GGG+rg++++g+++aL  e +  +d+++GtS GA+++ l++  +d +   + +  ++++ + ++      
  gene2987|gene2987|rna2987|rna2987  907 LVLGGGGARGVAHVGIIEAL-LEYNVPIDMVGGTSMGAFVGGLYSISMDNFIVCSRVAYFCKRISSRWR----- 974 
                                         8******************9.9***********************************************..... PP

                            Patatin   75 laanlaarlsgllgkgglfdaealrellrkvladktlkrlsarlgklpllkslftanqavpaittataatasta 148 
                                                + + ++   ++f+++++ + l +++++  ++++ ++++++                           
  gene2987|gene2987|rna2987|rna2987  975 ------LLMDLTIPLCSFFTGHSFNRVLYTIFKKRRIEDTWIQFFCI--------------------------- 1015
                                         ......8999999999*******************************........................... PP

                            Patatin  149 nranglytedddddvdladavraSsafPglfppvsldgelyvDGGilsNvPila 202 
                                         +++ ++y e +   + +++ +raS+++  ++pp   ++ l++DGG  +NvP++ 
  gene2987|gene2987|rna2987|rna2987 1016 TTNLCTYGEIKHVSGLMWRYIRASMSIATILPPLCDKDALLLDGGYTNNVPVDR 1069
                                         9**********************************9999************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1966  (0.109655); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                       172  (0.0095934); expected 17.9 (0.001)
Passed Fwd filter:                        59  (0.00329076); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 1.65u 0.38s 00:00:02.02 Elapsed: 00:00:00.59
# Mc/sec: 6133.44
//
Query:       gene2988|gene2988|rna2988|rna2988  [L=73]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (73 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       879  (0.0490267); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.42
# Mc/sec: 525.04
//
Query:       gene2989|gene2989|rna2989|rna2989  [L=70]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.7e-06   27.1   0.0    4.1e-06   27.0   0.0    1.1  1  rve       Integrase core domain
    0.00042   20.0   0.1    0.00068   19.4   0.1    1.3  1  rve_3     Integrase core domain
  ------ inclusion threshold ------
       0.13   11.8   0.5       0.14   11.6   0.5    1.0  1  DUF4607   Domain of unknown function (DUF4607)


Domain annotation for each model (and alignments):
>> rve  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   0.0   6.8e-10   4.1e-06      75     118 ..       6      49 ..       1      50 [. 0.94

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 6.8e-10
                                rve  75 gseytskafrefladlgirvsftrpgrpqdnGkvErfhrtlkde 118
                                        g+e++s+ ++ f +++gi++ +t   +++ nG+vEr + t+++ 
  gene2989|gene2989|rna2989|rna2989   6 GKEFKSRLVTSFSEENGIEHHVTSTEHSEANGRVERLNCTIREY 49 
                                        99**************************************9975 PP

>> rve_3  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.1   1.1e-07   0.00068       1      42 [.      21      61 ..      21      67 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 1.1e-07
                              rve_3  1 lgielsyiapgkPqqNglvEsfngtlrdellneelfrslaea 42
                                       +gie++++   +   Ng vE++n t+r+ + +++   +++e 
  gene2989|gene2989|rna2989|rna2989 21 NGIEHHVTSTEHSEANGRVERLNCTIREYIRKKSNS-KIREK 61
                                       69*************************988887765.55555 PP

>> DUF4607  Domain of unknown function (DUF4607)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.5   2.4e-05      0.14      22      60 ..      15      55 ..      10      65 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2.4e-05
                            DUF4607 22 asfeeesygearpsptsssetde..apliftvreeikkrar 60
                                       +sf ee+ +e+  ++t  se +   + l  t+re i+k++ 
  gene2989|gene2989|rna2989|rna2989 15 TSFSEENGIEHHVTSTEHSEANGrvERLNCTIREYIRKKSN 55
                                       79******************986225799*******99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (70 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       670  (0.0373696); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.35s 00:00:00.90 Elapsed: 00:00:00.56
# Mc/sec: 376.24
//
Query:       gene299|gene299|rna299|rna299  [L=451]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.2e-07   30.6   0.3      0.036   14.9   0.0    4.1  4  WD40      WD domain, G-beta repeat


Domain annotation for each model (and alignments):
>> WD40  WD domain, G-beta repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0     2e-06     0.036       4      36 ..      12      46 ..       9      48 .. 0.84
   2 !    8.9   0.2   0.00017         3       6      37 ..      60      92 ..      56      93 .. 0.87
   3 ?    1.5   0.0     0.037   6.6e+02      13      34 ..     270     294 ..     264     297 .. 0.68
   4 ?   -3.3   0.0         1   1.8e+04      13      37 ..     392     416 ..     389     417 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2e-06
                                   EEEEESS.SSEEEEE.EETTSSEEEEEETTSEEEE CS
                           WD40  4 lrtltGH.ssvtsla.fspdgawlasGsdDgtvri 36
                                   ++ ltGH ++v++la     g++la+GsdD+ + +
  gene299|gene299|rna299|rna299 12 VQALTGHtGCVNALAiSRNIGRYLATGSDDKRIIL 46
                                   6789***777****988888999********9976 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00017
                                   EEESS.SSEEEEEEETTSSEEEEEETTSEEEEE CS
                           WD40  6 tltGH.ssvtslafspdgawlasGsdDgtvriW 37
                                   +l GH ++v s++f +  + + s++ Dg   ++
  gene299|gene299|rna299|rna299 60 VLHGHeNNVFSIKFGKQDNHVYSCGLDGFSFVY 92
                                   688**999****************999966555 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.037
                                    EEEEE.EETTSSE...EEEEETTSEE CS
                           WD40  13 vtsla.fspdgaw...lasGsdDgtv 34 
                                    v+ ++ f+  g++   +++Gs D+++
  gene299|gene299|rna299|rna299 270 VWTMKnFNFGGPYdkmILAGS-DKKL 294
                                    6666665555555555889**.8875 PP

  == domain 4  score: -3.3 bits;  conditional E-value: 1
                                    EEEEEEETTSSEEEEEETTSEEEEE CS
                           WD40  13 vtslafspdgawlasGsdDgtvriW 37 
                                    ++s+  ++  +++++++  + v+++
  gene299|gene299|rna299|rna299 392 INSVVMHSKMPLIFTAGVENIVHVY 416
                                    5666556666777777778888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (451 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       350  (0.0195214); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 3147.72
//
Query:       gene2990|gene2990|rna2990|rna2990  [L=289]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.024   14.8   1.4       0.05   13.8   0.6    1.9  2  Suppressor_P21  RNA silencing suppressor P21 C-terminal domai
       0.07   13.1   0.0       0.14   12.1   0.0    1.6  1  UBA             UBA/TS-N domain
        2.9    8.4  14.9        4.3    7.8  14.9    1.3  1  AAA_23          AAA domain
        7.1    6.0   9.2         16    4.8   9.2    1.6  1  DUF2220         Uncharacterized protein conserved in bacteria


Domain annotation for each model (and alignments):
>> Suppressor_P21  RNA silencing suppressor P21 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.6   1.1e-05      0.05      14      61 ..       9      59 ..       7      71 .. 0.83
   2 ?   -2.9   0.0       1.8   7.9e+03      26      46 ..     229     247 ..     223     253 .. 0.58

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.1e-05
                     Suppressor_P21 14 ffvreyinitpttfee.alsesmrkvvktv.LqhlSse.lklevsentFkq 61
                                       +f+  +i+i + tf+   ++  m+k+++ + L+   +    l++s+n+F +
  gene2990|gene2990|rna2990|rna2990  9 IFLLTFISIAHVTFDAwYMRVTMKKLKNHSfLFSQPRIcTLLDISINMFFC 59
                                       69999**********8469********987356555541458*******76 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.8
                     Suppressor_P21  26 tfeealsesmrkvvktvLqhl 46 
                                        +f+ +++ +  + v+t L+++
  gene2990|gene2990|rna2990|rna2990 229 SFDVIMKKN--ECVSTLLREI 247
                                        555555554..4566666655 PP

>> UBA  UBA/TS-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   3.1e-05      0.14       8      31 ..     100     124 ..      95     130 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.1e-05
                                        HHHHTTS-HHHHHHHHHHTTT.SHH CS
                                UBA   8 rLveMGFdreevveALratgn.NeE 31 
                                        +L+e GF+ e ++eAL +t   N+E
  gene2990|gene2990|rna2990|rna2990 100 QLLEQGFTNELIEEALKNTSStNLE 124
                                        89*****************988887 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8  14.9   0.00097       4.3     117     189 ..     107     203 ..      60     208 .. 0.64

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.00097
                             AAA_23 117 leqfisellgskki.ilnlilflgqer............feefelkdkkerleelekeleeledekkllekl.... 175
                                        ++++i+e l+++ + +l+++l + +er             e +e+ ++k++leel+k++e   +e+  l+kl    
  gene2990|gene2990|rna2990|rna2990 107 TNELIEEALKNTSStNLEILLDYIEERlskmescdersvLETKEDRERKKKLEELKKQKELRRQERLHLKKLrdqi 182
                                        3334444444333322233333334443333333333456666778889999999999999999999999998888 PP

                             AAA_23 176 .......eqekekekeleele 189
                                               eqek+ke e e++e
  gene2990|gene2990|rna2990|rna2990 183 kadrielEQEKKKEREQENVE 203
                                        777765544444444444444 PP

>> DUF2220  Uncharacterized protein conserved in bacteria C-term(DUF2220)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   9.2    0.0035        16     108     170 ..     133     193 ..     123     202 .. 0.69

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.0035
                            DUF2220 108 klpavksllMdretlekh.rkgvadeesaeiarelprLteaeaklyedlledelkerlRLEQEr 170
                                        +l++++s   d+  +++  +++ +++ + e+ +++++L  +e+   ++l+++  ++r+ LEQE+
  gene2990|gene2990|rna2990|rna2990 133 RLSKMESC--DERSVLETkEDRERKK-KLEELKKQKELRRQERLHLKKLRDQIKADRIELEQEK 193
                                        55555554..4444444314444444.4455556677**************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (289 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2361  (0.131686); expected 358.6 (0.02)
Passed bias filter:                      645  (0.0359752); expected 358.6 (0.02)
Passed Vit filter:                        86  (0.0047967); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.48
# Mc/sec: 1818.08
//
Query:       gene2991|gene2991|rna2991|rna2991  [L=833]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.3e-22   78.1   1.9    7.2e-21   74.3   0.0    2.7  3  Adaptin_N        Adaptin N terminal region
    1.3e-17   64.0   0.7    4.1e-17   62.4   0.7    1.8  1  Coatomer_b_Cpla  Coatomer beta subunit appendage platform
    1.1e-12   48.1   0.2    2.2e-12   47.1   0.2    1.5  1  Coatamer_beta_C  Coatomer beta C-terminal region
    3.5e-06   27.2   1.9    0.00017   21.7   0.0    3.2  3  Cnd1             non-SMC mitotic condensation complex subunit


Domain annotation for each model (and alignments):
>> Adaptin_N  Adaptin N terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.3   0.0   1.6e-24   7.2e-21      11     169 ..      16     181 ..      11     215 .. 0.88
   2 ?   -0.2   0.2     0.061   2.7e+02     249     298 ..     245     290 ..     238     305 .. 0.72
   3 ?    1.4   0.3     0.021        94     317     361 ..     285     328 ..     261     336 .. 0.71

  Alignments for each domain:
  == domain 1  score: 74.3 bits;  conditional E-value: 1.6e-24
                                        HHCCSSS.-SCHHHHHHHHHHHHHHHCT---GHHHHHHHC.CCCSS-CHHHHHHHHHHHHHCTTSCC.....HHCC CS
                          Adaptin_N  11 eilnsnk.dddekkkeavkkliylialGedvsflffevvk.lvaskdfelKrlvYlylellaeesed.....lalL 79 
                                        +il++   ++ +kk++a++  i l+ +  d+s++  + ++ + +++d++lK++ Yl+le +++ + +     ++lL
  gene2991|gene2991|rna2991|rna2991  16 KILSHLTsPKTSKKADALRAMITLLSQNADLSEYTTTAIReVCQCDDTQLKKIFYLFLEMIPKCDREgnmlaEILL 91 
                                        56666666799*********************999888861566***********************999999999 PP

                                        CCHHHHHHCCSSSHHHHHHHHHHHCCC--CCCHHHHHHHHHHHHT-SSHHHHHHHHHHHHHCCCCCHHCCCCCHHH CS
                          Adaptin_N  80 vtnslqkDlkdpnqlirglALrvLssirvpelaedlapaikkllkdrspyvrkkAalailklykkdpdllrkqlve 155
                                        + n+++kDl++pn+++rg  L++++++   ++ e ++  i   l++ + yvr++A+l+++k+y+     +++   +
  gene2991|gene2991|rna2991|rna2991  92 IANQVRKDLEHPNEYVRGKVLHFVCTLMYGDVIELMFGPIVHNLEHLHYYVRRNALLCVTKIYEHFGANFPD-IPD 166
                                        ****************************************************************98777777.377 PP

                                        HHHHCT.T-SSHHHH CS
                          Adaptin_N 156 eikell.sdkdpgvv 169
                                        +i   + ++++p ++
  gene2991|gene2991|rna2991|rna2991 167 RIRRCMaKETNPYCL 181
                                        777777666666665 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.061
                                        HHHHHHCCHCCCCSTHHHCCHHCHHHHHHSSCCTCHHHHHCHHHHHHHHX CS
                          Adaptin_N 249 letvnlivelapknelivlavnaLvrllsskdenlryvaLrtllkivkke 298
                                        + ++ l+++   + +   +av++  ++++ ++  l+ + L+++  +  ++
  gene2991|gene2991|rna2991|rna2991 245 FQCALLLMQHRHSED---RAVRIILEMIRAEPS-LKEIGLQCIKDVYYTR 290
                                        677777777444444...688888888888888.8888888888887777 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.021
                                        XHHHHHHHHHHHCCCXXTTTHHHHHHHHHHHTTSSXXHHHHHHHH CS
                          Adaptin_N 317 dvsirlkaldlllklvdesNvkeivkeLkkyvkevadedfksklv 361
                                        dv+  +  ++ ll+l+d sNv+ iv eL + v+e+ad+ + s+ v
  gene2991|gene2991|rna2991|rna2991 285 DVYYTRIQVNELLTLLD-SNVMHIVFELVYRVAEIADYPIISEFV 328
                                        55555555555666664.79************9*99998555554 PP

>> Coatomer_b_Cpla  Coatomer beta subunit appendage platform
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.4   0.7   9.2e-21   4.1e-17       4     124 ..     704     820 ..     702     823 .. 0.94

  Alignments for each domain:
  == domain 1  score: 62.4 bits;  conditional E-value: 9.2e-21
                    Coatomer_b_Cpla   4 vvilndikidimdyikpakiseeeFremWaefeWEnkiavktkltd.lkeyleelvkktnmklltpeeeleeeaef 78 
                                        v++++ +++ + ++++   +++eeF+++W  +eWEn+++ + ++t  + ++++ + ++++  +++    ++++ +f
  gene2991|gene2991|rna2991|rna2991 704 VLNMSTLSFRVNEFLQSRVLENEEFKTQWLGLEWENTYTSRFRCTRpVVHIFRAIAESVKAYVVD---VKTDDNTF 776
                                        78899999***********************************998799***************9...667899** PP

                    Coatomer_b_Cpla  79 lsanlyaksvfgedalanvsiekeeegkisgvvRiRsktqgialsl 124
                                        l+anl+ ++ +ged+l+n+ i ++e   i+  +R+Rs ++ +++sl
  gene2991|gene2991|rna2991|rna2991 777 LVANLVCTTFLGEDVLINLKIRRDE--MIHLDCRMRSTEEALVKSL 820
                                        *********************9998..9***************998 PP

>> Coatamer_beta_C  Coatomer beta C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.1   0.2   4.9e-16   2.2e-12      42     139 ..     600     697 ..     547     698 .. 0.83

  Alignments for each domain:
  == domain 1  score: 47.1 bits;  conditional E-value: 4.9e-16
                    Coatamer_beta_C  42 fasklkkvvqLtGfsDpvYaEayvkvnqfDivLdvlivNqtketLqnltvelatlgdlklvekpqsvtlaphdfak 117
                                         a + ++  q+tG+sD +Y+Ea  +v++  + +d+l+vNqt++ +qn+  +++t  ++       ++ l++++  +
  gene2991|gene2991|rna2991|rna2991 600 NADREENSCQMTGYSDHLYVEAAFRVSRLSVNIDLLVVNQTNKVIQNILFDFTTSCNIAHNFTCLPLSLGARSIIR 675
                                        347788999************************************************99999999999******** PP

                    Coatamer_beta_C 118 ikatvkvsstetGvifGnivYd 139
                                        +  +  ++   +G i G + Y 
  gene2991|gene2991|rna2991|rna2991 676 MPFSFTIKEVFNGFITGCVSYT 697
                                        99999999999******99995 PP

>> Cnd1  non-SMC mitotic condensation complex subunit 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.2     0.018        80      44     115 ..      17      83 ..      16     103 .. 0.73
   2 !   21.7   0.0   3.8e-08   0.00017       2      83 ..     107     189 ..     106     222 .. 0.88
   3 ?   -2.2   0.1      0.86   3.9e+03      71     106 ..     543     577 ..     540     606 .. 0.66

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.018
                               Cnd1  44 vvakLilndmvkekgflselaklleDenprVvanalaalteiseksenaiynllpdiisklsdalnecsewg 115
                                        ++++L ++++ k+ + l  + +ll+ +n+  ++ + +a+ e+ + +++    +l++i++ +++ + +c+++g
  gene2991|gene2991|rna2991|rna2991  17 ILSHLTSPKTSKKADALRAMITLLS-QNADLSEYTTTAIREVCQCDDT----QLKKIFYLFLEMIPKCDREG 83 
                                        5789999999999999999999987.6888999999999999999753....33444444444444555555 PP

  == domain 2  score: 21.7 bits;  conditional E-value: 3.8e-08
                               Cnd1   2 iRalairtlgcirvpnlveylvepLrkrLkDedpyVRktaaivvakLilndmvkekgflselakll.eDenprVva 76 
                                        +R+ ++   +++ + +++e +  p+ + L+  + yVR++a+++v+k++++      ++ +++++++ +++np    
  gene2991|gene2991|rna2991|rna2991 107 VRGKVLHFVCTLMYGDVIELMFGPIVHNLEHLHYYVRRNALLCVTKIYEHFGANFPDIPDRIRRCMaKETNPYCLR 182
                                        889999999****************************************999999999999999998888887777 PP

                               Cnd1  77 nalaalt 83 
                                         + a+l 
  gene2991|gene2991|rna2991|rna2991 183 QCYASLR 189
                                        7777765 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 0.86
                               Cnd1  71 nprVvanalaalteiseksenaiynllpdiisklsd 106
                                        n+ V +na++  +   + + n + n ++d++  ls 
  gene2991|gene2991|rna2991|rna2991 543 NTGVNENAVHHVMTTERTQ-NVVKNTNRDVLDALSL 577
                                        5666777777766655555.7777777777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (833 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       754  (0.0420548); expected 358.6 (0.02)
Passed bias filter:                      493  (0.0274974); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.67u 0.30s 00:00:00.97 Elapsed: 00:00:00.47
# Mc/sec: 5301.80
//
Query:       gene2992|gene2992|rna2992|rna2992  [L=941]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (941 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       590  (0.0329076); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.68u 0.30s 00:00:00.98 Elapsed: 00:00:00.47
# Mc/sec: 5981.82
//
Query:       gene2993|gene2993|rna2993|rna2993  [L=770]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-12   47.6   0.2      2e-12   47.6   0.2    2.7  3  ERCC4     ERCC4 domain


Domain annotation for each model (and alignments):
>> ERCC4  ERCC4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0      0.33     6e+03      98     118 ..     229     249 ..     206     289 .. 0.58
   2 ?   -1.0   1.1       0.1   1.8e+03      56     110 ..     421     498 ..     377     533 .. 0.54
   3 !   47.6   0.2   1.1e-16     2e-12       1     153 [.     571     694 ..     571     697 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.33
                                        -GGGTT............... CS
                              ERCC4  98 ldqykrknknsrnkqykakvr 118
                                        +d y ++ + s+  + k+kv+
  gene2993|gene2993|rna2993|rna2993 229 NDYYTHREEHSIDSDNKKKVE 249
                                        344444444444444444444 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.1
                                        ............EEEEEEEHHHHHHHH....CC....SHHHHHHHHH..HH..H-.SEEEEEEES-GGGTT..... CS
                              ERCC4  56 k...........vlverksaddlvasi....kd....grleeqvsrl..kr.ngy.kkpillvegldqykrknkns 108
                                        k           +lve+ + d l+ s     kd    ++  + ++ +  k+ +++ +++++l++ +   +rk++++
  gene2993|gene2993|rna2993|rna2993 421 KfknqklvelkkILVEHDDEDVLIVSKyehnKDvvlaQDMKSRIEFVkhKNlSEIkQNIVILLDFNLGTFRKIERM 496
                                        2333333444444444444443322221222112222233333333311111122133555556655555556555 PP

                                        .. CS
                              ERCC4 109 rn 110
                                        + 
  gene2993|gene2993|rna2993|rna2993 497 QK 498
                                        54 PP

  == domain 3  score: 47.6 bits;  conditional E-value: 1.1e-16
                                        EEGGGCTSHHHH..HHTTTSEEEEE--SSSSE.EE...CTT...............EEEEEEEHHHHHHHHCCSHH CS
                              ERCC4   1 iDsrelksgieeylleelgvevvietlpigdyilwrrkvkaeynleldieepceekvlverksaddlvasikdgrl 76 
                                        +D rel+ +++ + l++ + + ++ +l+ gdy l+    ++               ++verk++ dl+ s+++grl
  gene2993|gene2993|rna2993|rna2993 571 VDFRELRASLPFF-LYKAKNNLRVVCLEEGDY-LF----DN---------------FIVERKTVYDLIMSLNNGRL 625
                                        799*********9.999999************.77....88...............******************** PP

                                        HHHHHHHHH.H-SEEEEEEES-GGGTT................THHH.HHHHHHHHHHHH.S-EEEEESSHHHHHH CS
                              ERCC4  77 eeqvsrlkrngykkpillvegldqykrknknsrnkqykakvrqinrktiesaLvqlqldf.gvsilttesanetae 151
                                         +q+ rl + + ++++ll+e++++++    ++rn           r+ + s+ v l+++f +++ ++t++   +a+
  gene2993|gene2993|rna2993|rna2993 626 LSQMTRLFS-NHSNYYLLIEYENKLSLGAYSNRNET--------FRNGLISKFVLLAIKFpRLKFIYTNNDLLSAR 692
                                        *********.9**********777776655555553........34459999999999999999999999888887 PP

                                        HH CS
                              ERCC4 152 wl 153
                                        +l
  gene2993|gene2993|rna2993|rna2993 693 LL 694
                                        77 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (770 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1242  (0.0692732); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.78u 0.31s 00:00:01.09 Elapsed: 00:00:00.54
# Mc/sec: 4263.19
//
Query:       gene2994|gene2994|rna2994|rna2994  [L=395]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0004   19.8   0.1    0.00065   19.1   0.1    1.3  1  Lectin_leg-like  Legume-like lectin family
  ------ inclusion threshold ------
      0.069   12.9   0.2       0.12   12.1   0.2    1.4  1  PMP1_2           ATPase proteolipid family


Domain annotation for each model (and alignments):
>> Lectin_leg-like  Legume-like lectin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.1   7.3e-08   0.00065      32     107 ..      40     113 ..      33     139 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 7.3e-08
                                        EESSEEEEE-SSTTEEEEEEESS-BEE.SSEEEEEEEEEESS--SS-S-EEEEEEESSSSSCCSBTTB-SS-EEEE CS
                    Lectin_leg-like  32 ldsnqirltsdeqskkGslwtkspval.eswevevsFrvtgseselegdglaiwytsergkegpvFgskdkfdGla 106
                                        ++++ i +  +  +++Gsl   +++++ ++w  e++F+     +  e  g+ +wyt ++ + g   g ++kf+Gl 
  gene2994|gene2994|rna2994|rna2994  40 AKNEGIQMRVS--AERGSLVDFKNINTkDEWSFEFTFKNLHL-NYPEFAGIYLWYTDQKIHSGDFNGVNNKFSGLM 112
                                        55555555544..899****9999999899********9888.668889*************************97 PP

                                        E CS
                    Lectin_leg-like 107 i 107
                                         
  gene2994|gene2994|rna2994|rna2994 113 T 113
                                        6 PP

>> PMP1_2  ATPase proteolipid family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.2   1.4e-05      0.12       3      26 ..     358     381 ..     356     388 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.4e-05
                             PMP1_2   3 mstLPGGviLvFvLvGLACvAivl 26 
                                        ms +   +iLvFv+v L  +A+++
  gene2994|gene2994|rna2994|rna2994 358 MSRMNNNIILVFVIVALISIAVLM 381
                                        78888899*************864 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (395 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1025  (0.0571699); expected 358.6 (0.02)
Passed bias filter:                      743  (0.0414412); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.44
# Mc/sec: 2719.39
//
Query:       gene2995|gene2995|rna2995|rna2995  [L=130]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.041   12.7   0.1      0.047   12.5   0.1    1.1  1  DCD       2'-deoxycytidine 5'-triphosphate deaminase (DCD)


Domain annotation for each model (and alignments):
>> DCD  2'-deoxycytidine 5'-triphosphate deaminase (DCD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   2.6e-06     0.047     187     231 ..      69     113 ..      28     126 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.6e-06
                                DCD 187 eklvieeGvalsvdLsgeeedelvgyrakkhtgviDldkigalev 231
                                        ++ + ++G +++vdL++++e++ v  +++  ++viD+++++++++
  gene2995|gene2995|rna2995|rna2995  69 STPNDTSGNSFNVDLKESKETDAVNGKSRSVSNVIDVKNTSSNKA 113
                                        23334789******************************9988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       870  (0.0485247); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.28s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 933.63
//
Query:       gene2996|gene2996|rna2996|rna2996  [L=922]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (922 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2223  (0.123989); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.81u 0.31s 00:00:01.12 Elapsed: 00:00:00.48
# Mc/sec: 5751.69
//
Query:       gene2997|gene2997|rna2997|rna2997  [L=515]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (515 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2580  (0.143901); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); expected 358.6 (0.02)
Passed Vit filter:                        79  (0.00440627); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.83u 0.34s 00:00:01.17 Elapsed: 00:00:00.49
# Mc/sec: 3182.75
//
Query:       gene2998|gene2998|rna2998|rna2998  [L=274]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
       0.94    9.6  12.7       0.23   11.6   2.5    2.4  2  CPSF100_C    Cleavage and polyadenylation factor 2 C-terminal
          4    6.8   7.3       0.25   10.7   0.7    2.0  2  DUF3530      Protein of unknown function (DUF3530)
        6.7    5.7   6.3       0.44    9.5   0.2    1.8  2  CLN3         CLN3 protein
        7.6    7.0  16.8          2    8.9   6.6    2.4  2  Afi1         Docking domain of Afi1 for Arf3 in vesicle traff


Domain annotation for each model (and alignments):
>> CPSF100_C  Cleavage and polyadenylation factor 2 C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   2.7     0.014        62      44      89 ..       6      57 ..       1      89 [. 0.48
   2 ?   11.6   2.5   5.1e-05      0.23      21      81 ..     122     206 ..     107     258 .. 0.47

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.014
                          CPSF100_C 44 eeeeeeeeeeeeeeaskkqkl........aeksekeaseeeseekkeslptldv 89
                                       ++++++e+e+  +e++ + k+        + +++keas+++s++++++++t++ 
  gene2998|gene2998|rna2998|rna2998  6 KKKAKKEDEG--KEKKGRDKAsitkptpvTISRDKEASTSTSKDSERATKTISL 57
                                       1111111111..111112222345555664444444444444444444444433 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 5.1e-05
                          CPSF100_C  21 vatvtgeleieee..............a.................eeaeeeekeeeeeeeeeeeeeeeaskkqkl. 64 
                                        +a+++ +l    +              +                 +         ++e++++   ++e++k++k  
  gene2998|gene2998|rna2998|rna2998 122 IAKISSKLSS-CSigtvsvipvvpkppKyvlsldlptkknkkdikM---------KKENKDS---SDEKNKESKGk 184
                                        5555555552.22345444444443330334444443322211111.........1111111...11111111110 PP

                          CPSF100_C  65 .......aeksekeaseeeseekk 81 
                                               +  +++++++++ ++++
  gene2998|gene2998|rna2998|rna2998 185 akdededK--NKHSTKKSKLTTNE 206
                                        01111111..11111111111111 PP

>> DUF3530  Protein of unknown function (DUF3530)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   1.0      0.15   6.6e+02     144     167 ..      30      53 ..       4     108 .. 0.56
   2 ?   10.7   0.7   5.6e-05      0.25     120     170 ..     150     201 ..     149     248 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.15
                            DUF3530 144 settaaveataadkankasekkap 167
                                        + +t + +++a+++++k se +++
  gene2998|gene2998|rna2998|rna2998  30 TPVTISRDKEASTSTSKDSERATK 53 
                                        222222222333333222222222 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 5.6e-05
                            DUF3530 120 tLsitlpdpqeeaap.srpeysakasettaaveataadkankasekkaptda 170
                                        +Ls+ lp+++++++  ++ e +++++e++++ + +a+d+++++++  +++  
  gene2998|gene2998|rna2998|rna2998 150 VLSLDLPTKKNKKDIkMKKENKDSSDEKNKESKGKAKDEDEDKNKHSTKKSK 201
                                        69*******9999988888888888888888888888877766654444332 PP

>> CLN3  CLN3 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   1.6      0.28   1.2e+03     211     228 ..      35      52 ..       2      98 .. 0.41
   2 ?    9.5   0.2   9.7e-05      0.44     146     219 ..     132     205 ..     113     224 .. 0.49

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.28
                               CLN3 211 aaeeeeeeesselkkslk 228
                                        ++++e+++++s+ +++ +
  gene2998|gene2998|rna2998|rna2998  35 SRDKEASTSTSKDSERAT 52 
                                        111111111111111111 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 9.7e-05
                               CLN3 146 atllvslvlPlllllsyflllekkkskkeakaeeeeeeyekleeeeeeeeeeseeeelleseaasaaeeeeeee 219
                                         ++ +++v+P++     ++l    ++kk++k  ++++e+++ ++e+++e++ ++++e ++++++s+++++ +++
  gene2998|gene2998|rna2998|rna2998 132 CSIGTVSVIPVVPKPPKYVLSLDLPTKKNKKDIKMKKENKDSSDEKNKESKGKAKDEDEDKNKHSTKKSKLTTN 205
                                        46888999999877665555544444444444444444444444444443322333333332222222222222 PP

>> Afi1  Docking domain of Afi1 for Arf3 in vesicle trafficking
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   2.5     0.021        95      66     122 ..       5      61 ..       1      68 [. 0.59
   2 ?    8.9   6.6   0.00045         2      70     127 ..     159     220 ..     145     226 .. 0.44

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.021
                               Afi1  66 eeekknklekrkkkksededdvdeedeeeeddnedlde.lskdeeekagegepllyvl 122
                                        e++k++k ++ k+kk +d+ ++ + + + ++ +++ +  +skd+ e+a+++  l+y +
  gene2998|gene2998|rna2998|rna2998   5 EKKKAKKEDEGKEKKGRDKASITKPTPVTISRDKEASTsTSKDS-ERATKTISLIYTI 61 
                                        34445555555556666666677777777666666665344544.3477777777765 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00045
                               Afi1  70 knklekrkkkksededdvdeedeeeeddnedlde......lskdeeekagegepllyvlnvvnt 127
                                        knk++ + kk+++d++d+++++++ + ++ed+d+      +sk ++  ++e++ +l v n++++
  gene2998|gene2998|rna2998|rna2998 159 KNKKDIKMKKENKDSSDEKNKESKGKAKDEDEDKnkhstkKSKLTT--NEEEHGMLDVFNFLKK 220
                                        2222333333333222222222222222222222222111233333..5667778888888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (274 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2155  (0.120196); expected 358.6 (0.02)
Passed bias filter:                      500  (0.0278878); expected 358.6 (0.02)
Passed Vit filter:                        81  (0.00451782); expected 17.9 (0.001)
Passed Fwd filter:                        29  (0.00161749); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.67u 0.31s 00:00:00.98 Elapsed: 00:00:00.47
# Mc/sec: 1737.14
//
Query:       gene2999|gene2999|rna2999|rna2999  [L=389]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        5.3    6.8  12.3         34    4.1  11.8    2.2  1  RR_TM4-6  Ryanodine Receptor TM 4-6


Domain annotation for each model (and alignments):
>> RR_TM4-6  Ryanodine Receptor TM 4-6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1  11.8    0.0019        34      65     136 ..     180     249 ..      72     252 .. 0.70

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.0019
                                        XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXX......... CS
                           RR_TM4-6  65 kseagLgDlseteaeesptpelkkklaeeeeaeeekeeeeepeaeaeekadaengekeekekekeeeekese 136
                                        k+ +++gDl++ ++ ++ t++ +k +  +ee+e++  ++++++a +  k+  e++   ++ k+kee++k ++
  gene2999|gene2999|rna2999|rna2999 180 KTIGSFGDLFNLSSIKASTSTISKSVDWKEETEKKSTKKKDEKAGK--KKYDEKEAIGDEGKTKEEKKKTKK 249
                                        5557888888888888877666666553233322222222222222..223333333443333333333222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (389 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1506  (0.083998); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.45
# Mc/sec: 2622.77
//
Query:       gene3|gene3|rna3|rna3  [L=190]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.2e-18   66.7   0.1    2.4e-18   66.5   0.1    1.2  1  RNA_pol_Rpb1_5  RNA polymerase Rpb1, domain 5


Domain annotation for each model (and alignments):
>> RNA_pol_Rpb1_5  RNA polymerase Rpb1, domain 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.5   0.1   1.4e-22   2.4e-18     187     260 ..      57     130 ..       7     163 .. 0.85

  Alignments for each domain:
  == domain 1  score: 66.5 bits;  conditional E-value: 1.4e-22
                            TSTTTBETTTEEESSHHHHHHHHCHHHHHHHHHHHHHHHHHHTTS---HHHHHHHHHHHTTTSS---SSTTCHC CS
                            xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
         RNA_pol_Rpb1_5 187 kveevvdageilsndiaeileilgieaarkallkeiqevykvqgvsvndrHlelivdqmtkkgeivavnrsGin 260
                              ++++++ +++sndi ++ e+lgiea r+++++e++ v++++g++++ rHl+li+d mt +ge+va+nr+ + 
  gene3|gene3|rna3|rna3  57 YLNDYINFYTCISNDIYNTWEVLGIEACRAVIIREVRAVFQAYGIEIDIRHLMLIADKMTVTGEYVAFNRHKMS 130
                            44568*****************************************************************9554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (190 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       472  (0.0263261); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1427.82
//
Query:       gene30|gene30|rna30|rna30  [L=305]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
       0.11   12.5   0.1       0.23   11.5   0.1    1.5  1  PAPS_reduct  Phosphoadenosine phosphosulfate reductase family
       0.58   10.0   2.7         11    5.8   0.1    3.0  3  TyrRSs_C     Tyrosyl-tRNA synthetase C-terminal domain


Domain annotation for each model (and alignments):
>> PAPS_reduct  Phosphoadenosine phosphosulfate reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   2.6e-05      0.23       4      56 ..     231     283 ..     228     303 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 2.6e-05
                                EE--SSCTCHHHHHHHHHHCTTHEEEEEE-STB-HHHHHHHHHHHHHT.T-EEE CS
                PAPS_reduct   4 vsvsgGkdslVllhLalkafkpvpvvfvdtghefpetiefvdeleery.glrlk 56 
                                + +  Gkd +V ++L  + + +++ + +d + +f+e+ +f++e+++r+ + +++
  gene30|gene30|rna30|rna30 231 IEYHLGKD-TVRVILEGSSQSKFKYFELDNEIKFSEMDTFREEVRTRLiENKIE 283
                                66777887.688899999999999***********************9433333 PP

>> TyrRSs_C  Tyrosyl-tRNA synthetase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.1    0.0013        11      78     106 ..      75     103 ..      67     104 .. 0.92
   2 ?   -1.4   0.0      0.21   1.9e+03      80      97 ..     186     203 ..     179     212 .. 0.79
   3 ?    2.8   0.1     0.011        98      74     100 ..     217     243 ..     209     258 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0013
                                HHHHTT-SS-EEEEESSS-EEEEE---HH CS
                   TyrRSs_C  78 tkkflidgklLiLrkGkwkvriieivsDe 106
                                t+ fli ++ L+L k   +++i++ v+D+
  gene30|gene30|rna30|rna30  75 TTIFLIANDHLVLMKNETNFQIVKRVPDN 103
                                5679*********************9995 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.21
                                HHTT-SS-EEEEESSS-E CS
                   TyrRSs_C  80 kflidgklLiLrkGkwkv 97 
                                 fl d+++ iL +G  k+
  gene30|gene30|rna30|rna30 186 AFLTDDTIYILDIGNRKI 203
                                69999******9998764 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.011
                                SHHHHHHHTT-SS-EEEEESSS-EEEE CS
                   TyrRSs_C  74 kpeetkkflidgklLiLrkGkwkvrii 100
                                ++++ + f+i +k++   +Gk  vr+i
  gene30|gene30|rna30|rna30 217 FKNKRELFIIGEKVIEYHLGKDTVRVI 243
                                5678899******************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (305 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       786  (0.0438396); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 2233.34
//
Query:       gene300|gene300|rna300|rna300  [L=40]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (40 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       323  (0.0180155); expected 358.6 (0.02)
Passed bias filter:                      233  (0.0129957); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.25s 00:00:00.59 Elapsed: 00:00:00.41
# Mc/sec: 295.65
//
Query:       gene3000|gene3000|rna3000|rna3000  [L=535]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (535 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3235  (0.180434); expected 358.6 (0.02)
Passed bias filter:                      545  (0.0303977); expected 358.6 (0.02)
Passed Vit filter:                       240  (0.0133861); expected 17.9 (0.001)
Passed Fwd filter:                        91  (0.00507558); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 2.36u 0.42s 00:00:02.78 Elapsed: 00:00:00.70
# Mc/sec: 2299.70
//
Query:       gene3001|gene3001|rna3001|rna3001  [L=48]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (48 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       572  (0.0319036); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.44
# Mc/sec: 327.59
//
Query:       gene3002|gene3002|rna3002|rna3002  [L=118]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       354  (0.0197445); expected 358.6 (0.02)
Passed bias filter:                      239  (0.0133304); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.23s 00:00:00.57 Elapsed: 00:00:00.37
# Mc/sec: 954.76
//
Query:       gene3003|gene3003|rna3003|rna3003  [L=212]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.3e-13   49.8   4.3    3.3e-13   49.8   4.3    1.5  2  CPBP      CPBP intramembrane metalloprotease


Domain annotation for each model (and alignments):
>> CPBP  CPBP intramembrane metalloprotease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.1      0.36   6.5e+03      60      69 ..      54      63 ..      24      80 .. 0.51
   2 !   49.8   4.3   1.8e-17   3.3e-13       5      91 ..      95     202 ..      91     203 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.36
                                       HHHHHHHHHH CS
                               CPBP 60 llaalaGlvl 69
                                        +++++ +vl
  gene3003|gene3003|rna3003|rna3003 54 CAIICFDIVL 63
                                       3334444444 PP

  == domain 2  score: 49.8 bits;  conditional E-value: 1.8e-17
                                        HHHHHHHHHHHHHHHHHHHTTCHHHH..........HHHH.S-........HHHHHHHHHHHHHCSGGG.....HH CS
                               CPBP   5 llvfllalllapllEEllfRglllql..........lqergss........tlailissilFglaHlpn.....gp 57 
                                        l+ ++ +++++p+lEE++fR +l+ql          +++   s        ++ i i s lF+l+H+       +p
  gene3003|gene3003|rna3003|rna3003  95 LARIFTLVIFGPFLEEIIFRRFLYQLvkgdrrltkaIRN---SewrnifclVILITINSTLFALLHYDEhyvhfFP 167
                                        6778999******************96666663333222...145599*999999************999999844 PP

                                        H.HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                               CPBP  58 s.vllaalaGlvlgylylktgsllaaillHallnl 91 
                                          +l+ a+ G+ l+++ +   ++++a+++H+++n+
  gene3003|gene3003|rna3003|rna3003 168 WpFLYFACGGVNLCLACELCDNIVSAVFMHIFFNF 202
                                        459*******************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (212 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       805  (0.0448993); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.50
# Mc/sec: 1279.89
//
Query:       gene3004|gene3004|rna3004|rna3004  [L=522]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.4e-07   30.2  10.2    1.2e-05   24.6   0.2    3.4  3  Coatomer_WDAD  Coatomer WD associated region
    2.6e-05   24.9   2.2      0.041   14.8   0.1    3.4  3  WD40           WD domain, G-beta repeat
  ------ inclusion threshold ------
      0.066   13.4   1.0        4.2    7.7   0.0    3.3  3  TPR_2          Tetratricopeptide repeat
      0.074   11.7   0.7       0.16   10.6   0.7    1.5  2  Nup160         Nucleoporin Nup120/160
       0.11   12.5   0.8       0.23   11.4   0.8    1.5  1  FadR_C         FadR C-terminal domain
       0.15   12.2   1.6        1.6    8.8   0.1    3.2  4  bPH_1          Bacterial PH domain
       0.43   10.5   7.1          2    8.4   0.0    3.8  4  TPR_1          Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> Coatomer_WDAD  Coatomer WD associated region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0      0.56   1.4e+03      48      88 ..      89     134 ..      77     150 .. 0.67
   2 !    6.3   3.4    0.0017       4.2      19     234 ..     161     355 ..     155     367 .. 0.73
   3 !   24.6   0.2   4.6e-09   1.2e-05     270     389 ..     369     480 ..     361     487 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.56
                                        XX..XXXXXXXXXX...XXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                      Coatomer_WDAD  48 lV..cgdgeyiiyt...alalrnkaygkgldfvwvssnrfavless 88 
                                        +V   +dg y+iy+   ++   +   g+ +   wv++ +f v ++s
  gene3004|gene3004|rna3004|rna3004  89 IVtgAEDGYYKIYKrqgEQLEHSVFVGSRVWDSWVEEDAFYVATDS 134
                                        4456789999999966655556667777777777777776555544 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0017
                                        XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX. CS
                      Coatomer_WDAD  19 ellslqlkelgsieiypqslshnpngrfvlVcgdgeyiiytalalrnkaygkgldfvwvssnrfavlessksvkif 94 
                                        +++ l+ ke+g+i++ ++ +s+n  +++++  +++ + + + l++r+k +++g   v ++  + +v ++ + + i+
  gene3004|gene3004|rna3004|rna3004 161 DSVFLNDKEIGKINFEVERVSYN--NKIMCMQKKDGFVVFSYLGFREKMRDSGKALVLNE--KLVVSRD-NVMIIY 231
                                        67788999999999999999996..68999999999999999999999999998888766..5555554.455566 PP

                                        XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                      Coatomer_WDAD  95 knfkekktksikleyqvdkifgGalLgvksegsvsfYDweqgklvrridvkkvknVvwsddgelvalvskdtvyil 170
                                         ++++++  ++k+ y   k++   +   +s g  ++Y    +++v+  + + +++++   +   v +  ++ + i+
  gene3004|gene3004|rna3004|rna3004 232 DDLEKET--QFKILYGDFKLYDRFIVNYSSAG-FVIYSYSGETVVK-GTAD-IRDIFIIGN--KVVIS-NECTGII 299
                                        9999999..99999999999998888888888.7778877555554.3344.678888744..55555.3344444 PP

                                        XXXXX.............XXXXXXX.XXXXXXXXXXXXXXXXXXXX.XXXX.XXXXXXXXXXXXX CS
                      Coatomer_WDAD 171 synleaveeedeeegvedafevlhelsesiksgaWvgdvfiYttsnnrlky.lvngevgiikhld 234
                                        + +       ++ +g    +++ + ++  ++ g  + dv++++++n +l+y l ng   +i++++
  gene3004|gene3004|rna3004|rna3004 300 DIDGV-----KKSTG---RLSLHKVMDMPVEYGHVHHDVLYFMSNN-KLYYlLANGFFSMISYVN 355
                                        44444.....12222...3444444467999999999999999999.999999999998888765 PP

  == domain 3  score: 24.6 bits;  conditional E-value: 4.6e-09
                                        XXXXXXXXXXXXXXXXXXXXXXX.......XXXXXXXXXXXXXXXX-GGGSS-HHHHHHHHHHTT-HHHHHHHHHH CS
                      Coatomer_WDAD 270 fktavlrkdleevlkiiaasnllpeipkeegqkiirfLekkgypelAlqlvqDpetkFdLAlelgnLelAlelake 345
                                        f ++++ k ++e++     ++  +++ +   ++  ++L k+   elAl l   ++ kF++ l++++Le A+++a++
  gene3004|gene3004|rna3004|rna3004 369 FDKKLITKPIDEIIAWQCDEKKDKAL-EGREKECLSYLLKQKEYELALRL---FDCKFEIYLQMNKLENAFKVART 440
                                        66777777777755554333333333.55566778899999999*****9...69*******************87 PP

                                        H--HHHHHHHHHHHHHTT-HHHHHHHHHHTT-HHHHHHHHHHHT CS
                      Coatomer_WDAD 346 lddeekWkkLgdaAlsqgniklaeeayqkakdfdkLllLylstg 389
                                         +    +k Lg + ++qg+++ a ea+   +d + +l+L   +g
  gene3004|gene3004|rna3004|rna3004 441 PT---EYKMLGGLFMRQGKFSKATEAFRLGGDDE-MLFLCDFLG 480
                                        55...9*********************9999955.555555555 PP

>> WD40  WD domain, G-beta repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.2    0.0023       5.9      22      38 .]       8      24 ..       2      24 .. 0.79
   2 !   14.8   0.1   1.6e-05     0.041       3      37 ..      30      63 ..      28      64 .. 0.85
   3 ?   -1.4   0.0       2.1   5.3e+03      24      37 ..      88     101 ..      80     102 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0023
                                       SSEEEEEETTSEEEEEE CS
                               WD40 22 gawlasGsdDgtvriWd 38
                                        + l+s+s D t+++W+
  gene3004|gene3004|rna3004|rna3004  8 DDRLLSCSLDMTLKLWN 24
                                       445668999*******8 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 1.6e-05
                                       EEEEEESS.SSEEEEEEETTSSEEEEEETTSEEEEE CS
                               WD40  3 clrtltGH.ssvtslafspdgawlasGsdDgtvriW 37
                                       +l t++GH  +v+++  s +++ + s +dD+  riW
  gene3004|gene3004|rna3004|rna3004 30 LLMTFKGHtRGVNAI--SVYKNTFYSVGDDHCMRIW 63
                                       6889****766**99..778888888888******* PP

  == domain 3  score: -1.4 bits;  conditional E-value: 2.1
                                        EEEEEETTSEEEEE CS
                               WD40  24 wlasGsdDgtvriW 37 
                                        ++++G +Dg  +i+
  gene3004|gene3004|rna3004|rna3004  88 LIVTGAEDGYYKIY 101
                                        5899*99*987776 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.2     0.081   2.1e+02      11      24 ..     405     418 ..     403     419 .. 0.88
   2 ?   -2.1   0.0       2.4   6.1e+03      10      22 ..     424     436 ..     423     439 .. 0.83
   3 ?    7.7   0.0    0.0016       4.2       4      25 ..     444     465 ..     441     466 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.081
                              TPR_2  11 yyklgdyeeAleaf 24 
                                        ++k+++ye Al++f
  gene3004|gene3004|rna3004|rna3004 405 LLKQKEYELALRLF 418
                                        789********999 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.4
                              TPR_2  10 ayyklgdyeeAle 22 
                                        +y++++++e A +
  gene3004|gene3004|rna3004|rna3004 424 IYLQMNKLENAFK 436
                                        899*****99976 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.0016
                              TPR_2   4 lynlGlayyklgdyeeAleafe 25 
                                        + +lG + +++g++ +A eaf+
  gene3004|gene3004|rna3004|rna3004 444 YKMLGGLFMRQGKFSKATEAFR 465
                                        78999***************97 PP

>> Nup160  Nucleoporin Nup120/160
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.7   6.1e-05      0.16     225     257 ..       5      35 ..       1      86 [. 0.87
   2 ?   -2.3   0.0      0.51   1.3e+03     229     255 ..      47      72 ..      39     103 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 6.1e-05
                                        ....TTTEEEEEETT-EEEEEETTTTEEEEEEE CS
                             Nup160 225 vveigqtylfalsrdgkLrvWnlltgkclatid 257
                                        vv  +++ l++ s+d +L++Wn++t+ +l+t+ 
  gene3004|gene3004|rna3004|rna3004   5 VV--DDDRLLSCSLDMTLKLWNYKTNVLLMTFK 35 
                                        44..78999********************9954 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.51
                                        TTTEEEEEETT-EEEEEETTTTEEEEE CS
                             Nup160 229 gqtylfalsrdgkLrvWnlltgkclat 255
                                         +++ +++  d+ +r+W  ++++++  
  gene3004|gene3004|rna3004|rna3004  47 YKNTFYSVGDDHCMRIW-CNNACRVKE 72 
                                        5788899999*******.888877766 PP

>> FadR_C  FadR C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.8   8.9e-05      0.23      76     109 ..     326     359 ..     312     368 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 8.9e-05
                             FadR_C  76 klfrelafasgnkiYvLilNglkklYsrvgslyF 109
                                          +  l f+s+nk+Y L+ Ng+ ++ s v +++ 
  gene3004|gene3004|rna3004|rna3004 326 VHHDVLYFMSNNKLYYLLANGFFSMISYVNNIFL 359
                                        4456689******************999999886 PP

>> bPH_1  Bacterial PH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.87   2.2e+03      43      62 ..     129     148 ..     125     153 .. 0.83
   2 ?    8.8   0.1   0.00062       1.6      25      79 ..     265     322 ..     255     330 .. 0.83
   3 ?   -0.5   0.1      0.48   1.2e+03      39      52 ..     362     375 ..     354     385 .. 0.83
   4 ?   -3.5   0.0         4     1e+04      84      99 ..     418     433 ..     403     440 .. 0.65

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.87
                                        EEEESSEEEEEE---SSS-- CS
                              bPH_1  43 vvFTnkrlilvdkqgvtgkK 62 
                                        +v T+  +++ d+q + +++
  gene3004|gene3004|rna3004|rna3004 129 YVATDSGILIYDRQDAKVNR 148
                                        799***********987765 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00062
                                        GCGCT--EEEEEE-TSEEEEEESSEEEEEE---SS...S--EEEEEEETTTEEEEEEE CS
                              bPH_1  25 llidgEkilfafklirDevvFTnkrlilvdkqgvt...gkKkeyksipyssIsevsiE 79 
                                        +  +gE+++++   irD +++ nk +i  + +g++   g Kk+  +++ +++ ++ +E
  gene3004|gene3004|rna3004|rna3004 265 YSYSGETVVKGTADIRDIFIIGNKVVISNECTGIIdidGVKKSTGRLSLHKVMDMPVE 322
                                        67799*************************9998644488888888888888777666 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.48
                                        TSEEEEEESSEEEE CS
                              bPH_1  39 irDevvFTnkrlil 52 
                                         +D ++F +k+li 
  gene3004|gene3004|rna3004|rna3004 362 QNDCFCFFDKKLIT 375
                                        579*********96 PP

  == domain 4  score: -3.5 bits;  conditional E-value: 4
                                        TSSEEEEEEEETTTCC CS
                              bPH_1  84 fDldaeLkiwisgeee 99 
                                        fD  +e+ + ++  e+
  gene3004|gene3004|rna3004|rna3004 418 FDCKFEIYLQMNKLEN 433
                                        5778888777765554 PP

>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.2       3.5   8.9e+03       3      13 ..     339     349 ..     338     350 .. 0.77
   2 ?    3.0   0.4     0.039        99      11      25 ..     405     419 ..     404     420 .. 0.87
   3 ?    0.4   0.1      0.26   6.7e+02      10      20 ..     424     434 ..     423     436 .. 0.89
   4 ?    8.4   0.0   0.00079         2       4      25 ..     444     465 ..     441     466 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 3.5
                                        HHHHHHHHHHH CS
                              TPR_1   3 alynlGnayfk 13 
                                         +y l+n +f+
  gene3004|gene3004|rna3004|rna3004 339 LYYLLANGFFS 349
                                        79999997776 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.039
                                        HHHTT-HHHHHHHHH CS
                              TPR_1  11 yfklgkydeAleyye 25 
                                        ++k+++y+ Al  ++
  gene3004|gene3004|rna3004|rna3004 405 LLKQKEYELALRLFD 419
                                        689********9885 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.26
                                        HHHHTT-HHHH CS
                              TPR_1  10 ayfklgkydeA 20 
                                        +y++++k++ A
  gene3004|gene3004|rna3004|rna3004 424 IYLQMNKLENA 434
                                        8********99 PP

  == domain 4  score: 8.4 bits;  conditional E-value: 0.00079
                                        HHHHHHHHHHTT-HHHHHHHHH CS
                              TPR_1   4 lynlGnayfklgkydeAleyye 25 
                                        ++ lG +++++gk+ +A e+++
  gene3004|gene3004|rna3004|rna3004 444 YKMLGGLFMRQGKFSKATEAFR 465
                                        8899***************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (522 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       644  (0.0359195); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.60u 0.26s 00:00:00.86 Elapsed: 00:00:00.45
# Mc/sec: 3481.04
//
Query:       gene3005|gene3005|rna3005|rna3005  [L=116]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    6.9e-05   22.3   0.2    8.5e-05   22.0   0.2    1.1  1  WD40_like   WD40-like domain
    0.00018   22.2   0.1       0.49   11.4   0.0    3.2  3  WD40        WD domain, G-beta repeat
  ------ inclusion threshold ------
      0.043   13.1   0.1       0.66    9.2   0.0    1.9  2  RAB3GAP2_N  Rab3 GTPase-activating protein regulatory subunit


Domain annotation for each model (and alignments):
>> WD40_like  WD40-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.2   1.4e-08   8.5e-05      54     143 ..      22     109 ..      11     114 .. 0.76

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 1.4e-08
                          WD40_like  54 dlilvvtlDGtillslleneeeven..ekieedistvkviddklliGtnkGsiyvfskdlqleevllgqsseIkei 127
                                        + i+++   Gt+   l++ +++v++  +  + +i     +  +ll+Gt+ G+i v++  l   + +  ++  I++i
  gene3005|gene3005|rna3005|rna3005  22 NYIVCGLFTGTL---LFTADNTVKKqiKICNSAIRALAST-TNLLVGTDDGEIVVLDPSLRRIKSIKAHNDFIRKI 93 
                                        445555667888...6666665543104456666666555.5689******************************* PP

                          WD40_like 128 kiennkiysLsesafi 143
                                         +++++i++ s++  i
  gene3005|gene3005|rna3005|rna3005  94 RTSKEYIFTCSDDFTI 109
                                        ***********98665 PP

>> WD40  WD domain, G-beta repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0     0.013        78      13      35 ..      14      42 ..       9      47 .. 0.62
   2 ?    3.0   0.0     0.036   2.1e+02      15      36 ..      54      72 ..      43      74 .. 0.68
   3 !   11.4   0.0   8.1e-05      0.49       4      35 ..      80     110 ..      77     110 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.013
                                       EEEEEEETTSSEEEEE...ET.....TSEEE CS
                               WD40 13 vtslafspdgawlasG...sd.....Dgtvr 35
                                       v ++  +++++++++G   +      D+tv+
  gene3005|gene3005|rna3005|rna3005 14 VKCI--HKYSNYIVCGlftGTllftaDNTVK 42
                                       6666..8888887765432112333477776 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.036
                                       EEEEETTSSEEEEEETTSEEEE CS
                               WD40 15 slafspdgawlasGsdDgtvri 36
                                       +l   +  ++l+ G+dDg + +
  gene3005|gene3005|rna3005|rna3005 54 AL--ASTTNLLV-GTDDGEIVV 72
                                       55..34445565.*99**9875 PP

  == domain 3  score: 11.4 bits;  conditional E-value: 8.1e-05
                                        EEEEESS.SSEEEEEEETTSSEEEEEETTSEEE CS
                               WD40   4 lrtltGH.ssvtslafspdgawlasGsdDgtvr 35 
                                        ++++++H ++++ +++s++  +  ++sdD t++
  gene3005|gene3005|rna3005|rna3005  80 IKSIKAHnDFIRKIRTSKEYIF--TCSDDFTIK 110
                                        67899**555****66666666..9******97 PP

>> RAB3GAP2_N  Rab3 GTPase-activating protein regulatory subunit N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.1     0.014        82      57      93 ..       3      38 ..       1      43 [. 0.79
   2 ?    9.2   0.0   0.00011      0.66      73     131 ..      55     113 ..      41     116 .] 0.79

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.014
                         RAB3GAP2_N 57 ItailclplsskssqgspdwtviavGlssGylrfyte 93
                                       I++i ++p +   +  +  +++i++Gl +G l+f  +
  gene3005|gene3005|rna3005|rna3005  3 ISQIKVIPSDR-VKCIHKYSNYIVCGLFTGTLLFTAD 38
                                       77888888777.555588899***********99665 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00011
                         RAB3GAP2_N  73 spdwtviavGlssGylrfytengelLlsqllheepvlkikcvssqekeeseelsilypk 131
                                            t ++vG+++G + +++ +   + s   h++ + ki+ +++   ++s++++i  +k
  gene3005|gene3005|rna3005|rna3005  55 LASTTNLLVGTDDGEIVVLDPSLRRIKSIKAHNDFIRKIRTSKEYIFTCSDDFTIKRSK 113
                                        55678899********************************5455556677777775555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       580  (0.0323498); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.39u 0.30s 00:00:00.69 Elapsed: 00:00:00.45
# Mc/sec: 782.80
//
Query:       gene3006|gene3006|rna3006|rna3006  [L=338]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-26   92.3   0.4      2e-26   92.3   0.4    1.7  2  ArfGap    Putative GTPase activating protein for Arf


Domain annotation for each model (and alignments):
>> ArfGap  Putative GTPase activating protein for Arf
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.3   0.4   1.1e-30     2e-26       3      85 ..     105     187 ..     103     214 .. 0.88
   2 ?   -3.6   0.1      0.63   1.1e+04      92     109 ..     315     332 ..     296     335 .. 0.48

  Alignments for each domain:
  == domain 1  score: 92.3 bits;  conditional E-value: 1.1e-30
                                        HHHHHCCSCCCCB-TTT-SBS--EEETTTTEEE-HHHHHHHCCS.TTT--EEETTTS---HHHHHHHHHTCHHHHH CS
                             ArfGap   3 alkellkepenkvCaDCgakeptWaslnlgvflCieCsgvHrslgvhiskvrsltldkwedeelellkalgNkkan 78 
                                        ++kel    en +C++C++++ +Wasl++g+flCieC++vHrs+gv++s vrs+++dkw++e    +k +gN+k++
  gene3006|gene3006|rna3006|rna3006 105 KVKELSLLGENVHCIECNTRNTQWASLSYGIFLCIECASVHRSFGVRVSVVRSVNMDKWNEEGYLRMKMGGNEKFK 180
                                        5778888899****************************************************************** PP

                                        HHHTTTC CS
                             ArfGap  79 eileakl 85 
                                        +++  + 
  gene3006|gene3006|rna3006|rna3006 181 DFMRIQG 187
                                        9987665 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 0.63
                                        -TTCGHHHHHHHHHHHHT CS
                             ArfGap  92 skssskekreefirakYe 109
                                        +k+++  + +e ++ kY+
  gene3006|gene3006|rna3006|rna3006 315 NKKTEFGQTRENMQVKYK 332
                                        233334444455555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (338 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       864  (0.0481901); expected 358.6 (0.02)
Passed bias filter:                      495  (0.0276089); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 2280.81
//
Query:       gene3007|gene3007|rna3007|rna3007  [L=392]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.051   13.2   0.9        2.4    7.8   0.0    2.9  3  IL11      Interleukin 11


Domain annotation for each model (and alignments):
>> IL11  Interleukin 11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.0   0.00013       2.4     116     154 ..     128     167 ..     111     171 .. 0.77
   2 ?    2.8   0.0    0.0045        81     102     132 ..     243     273 ..     204     291 .. 0.78
   3 ?   -2.1   0.0      0.15   2.7e+03      18      32 ..     335     349 ..     328     362 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.00013
                               IL11 116 mskleaprvpv.vspslppssatawevlqsshelleklkl 154
                                        + ++ a++++v + p++  + ++++e +q+  e+++ ++l
  gene3007|gene3007|rna3007|rna3007 128 ILQHIAKKMTVpSLPTPNCTLKKHFEFIQFKLEIVDFFNL 167
                                        4444555555536677777889*************99998 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.0045
                               IL11 102 isklkrLlkslqllmskleaprvpvvspslp 132
                                        ++ l++L++ + ++++ +++p++++v + l 
  gene3007|gene3007|rna3007|rna3007 243 QELLSNLINTVREQINTINMPVNTFVDADLV 273
                                        4456788999999999999999999988874 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 0.15
                               IL11  18 trsLlkltkellkdh 32 
                                         +++l+lt+el++  
  gene3007|gene3007|rna3007|rna3007 335 FKQMLNLTQELYNSV 349
                                        577888888888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (392 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       965  (0.0538234); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 2742.88
//
Query:       gene3008|gene3008|rna3008|rna3008  [L=37]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (37 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       396  (0.0220871); expected 358.6 (0.02)
Passed bias filter:                      229  (0.0127726); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.42
# Mc/sec: 263.27
//
Query:       gene3009|gene3009|rna3009|rna3009  [L=543]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   1.9e-167  558.1   9.5   2.3e-167  557.8   9.5    1.0  1  HSP70     Hsp70 protein
    9.8e-08   31.2   1.1    3.6e-06   26.0   0.0    2.8  3  MreB_Mbl  MreB/Mbl protein
    6.4e-06   26.0   0.0    1.3e-05   25.1   0.0    1.4  1  FGGY_C    FGGY family of carbohydrate kinases, C-terminal dom
     0.0002   21.8   0.2        0.3   11.5   0.0    2.6  2  FtsA      Cell division protein FtsA
  ------ inclusion threshold ------
      0.042   12.8   3.6       0.16   10.9   0.1    2.6  3  DDR       Diol dehydratase reactivase ATPase-like domain


Domain annotation for each model (and alignments):
>> HSP70  Hsp70 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  557.8   9.5  6.3e-171  2.3e-167       1     538 [.       6     523 ..       6     542 .. 0.93

  Alignments for each domain:
  == domain 1  score: 557.8 bits;  conditional E-value: 6.3e-171
                                        EEEEEEXSSEEEEEEEETTEEEEEXXTTSXSSEESEEEEXTTSEEETHHHHHCTTTTGGGEEEXGGGTTTXBTTSH CS
                              HSP70   1 viGiDLGttnsvvavmeggkievianeegnrttPsvvaFtkkerlvGeaAkrqavtnpkntvfsvKrliGrkfsdp 76 
                                        ++GiDLGttns++++m+++ +++i+n+eg+rttPsv+  + ++ +vG++A+r+  t+p+ t+f+vKrliGrk++d 
  gene3009|gene3009|rna3009|rna3009   6 IVGIDLGTTNSCISIMQDNVATIIENQEGQRTTPSVINISGENVIVGKPAQRKLLTDPEHTIFNVKRLIGRKYAD- 80 
                                        69************************************************************************9. PP

                                        HHHHHHTTXSSEEEEETTSBEEEEEEETTEEEEHHHHHHHHHHHHHHHHHHHHTSBEEEEEEEEXTTXXHHHHHHH CS
                              HSP70  77 evqkeikelpykvvkkengkavveveaagekftpeqisamvLkklketaeaylgkkvtdavitvPaYfndaqRqat 152
                                         v++ +k lp++v  + ng+ +++v+  +++++p ++s++vL+kl++ ae++l+++v+ avitvPaYfn +qR+ t
  gene3009|gene3009|rna3009|rna3009  81 -VKEYTKRLPFSVIDD-NGELKIKVD--DKRYEPAKLSSFVLSKLRSAAESFLSRPVKFAVITVPAYFNHTQREET 152
                                        .************998.999999999..99********************************************** PP

                                        HHHHHHTTXEEEEEEEHHHHHHHHHHTCCSSSCEEEEEEEEXSSXEEEEEEEEETTEEEEEEEEEETTXSHHHHHH CS
                              HSP70 153 kdAgkiAGLnvlRivNepTAaalaYGldkkdkernvlvyDlGggtfdvSilelekGvfevkaTagDthlGGedfDe 228
                                        k Ag++AGL+vlR++NepT aal   +       +++vyDlGggtfd+Sile ++ +fevkaTagD+ lGG+d D+
  gene3009|gene3009|rna3009|rna3009 153 KKAGELAGLKVLRVLNEPTSAALNHAIT-----GHIAVYDLGGGTFDISILEKSDNIFEVKATAGDSFLGGDDIDN 223
                                        ***********************99885.....469**************************************** PP

                                        HHHHHHHHHHHHHHSXXGGGSHHHHHHHHHHHHHHHHHTTTSSCSEEEEEEEEEETTTEEEEEEEEHHHHHHHHHH CS
                              HSP70 229 alvehlveefkkkegidlskdkkalqrlkeaaekaKkeLSsskqteinleietvdedgkdlseklsRakfeelved 304
                                        +l+++l+e++k+ +++   +  k+  r+k+aae aKkeLS+  q++++++i  + + +++++ +l+Ra+fe++v++
  gene3009|gene3009|rna3009|rna3009 224 TLTDFLMERLKNGREMSDIDLAKIRPRIKKAAESAKKELST--QETVTIDIPYAYK-DTHFTYELKRAEFEDVVAP 296
                                        ************99886666678999***************..7888888888888.89***************** PP

                                        HHHHTHHHHHHHHHHCTEEGGGCSEEEEESGGGGSHHHHHHHHHHTTCHHBSSSHTTTHHHHHHHHHHHHHCTCGC CS
                              HSP70 305 llertlepvekalkdaklkkeeidevvlvGGstRiPkvqelvkelfgkepsktvnpDeavaiGAAvqagvlsgeee 380
                                        l++rt++p+ kalkda++  +++d++vlvGG+tR+P v++l +e+f+++p  t  pDe va GAA+qa++lsg  +
  gene3009|gene3009|rna3009|rna3009 297 LIKRTVKPCLKALKDANI--DQVDHLVLVGGMTRMPLVRKLSEEIFNRKPLFTASPDESVAQGAAIQAAILSG--D 368
                                        ****************97..58***************************************************..8 PP

                                        SHCCEEEEBESS-EEEEETTTEEEEEESTTCBSSEEEEEEEEESSTTSSSEEEEEEESSSSBGGGSEEEEEEEEEC CS
                              HSP70 381 vkdllllDvtpLslgietlggvmtkliernttiptkksqvfstaadnqtaveievlqgerelvkdnkllgsfeldg 456
                                        v++l llDvt+Lslgiet gg+m ++ +rn t+p kks vf+t +dnq++v ++++qge e vkdn  lg+  l++
  gene3009|gene3009|rna3009|rna3009 369 VNKL-LLDVTSLSLGIETVGGLMSTIVKRNSTLPLKKSSVFTTSEDNQEEVIVNIYQGESENVKDNCFLGKIILKD 443
                                        8875.78********************************************************************* PP

                                        ESSCSTTCSEEEEEEEEETTSCEEEEEEETTTCCEEEEEEECCSSSBHHHHHHHHHHHHHCHHHHHHHHHHHHHHH CS
                              HSP70 457 ippaprGvpqieVtfdidanGiltvsakdketgkeeeitieaseglseeeiekmvkdaeesaeedkkkkeaieakn 532
                                        i+ ap+Gvp+ieV f+ d+nGi +v+akd  tg+e++ +++  ++ +++  ekm+ + +e +e     k+ +++ n
  gene3009|gene3009|rna3009|rna3009 444 IKKAPKGVPRIEVGFEADVNGIYRVTAKDLLTGREQSAEVTGIQTKEKDVAEKMQDKVDEKDEM--VDKNDANKSN 517
                                        ************************************************9999999876655433..2222223333 PP

                                        HHHHHH CS
                              HSP70 533 eaeelv 538
                                        +  +l+
  gene3009|gene3009|rna3009|rna3009 518 RFFDLI 523
                                        333333 PP

>> MreB_Mbl  MreB/Mbl protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0     0.015        54       4      20 ..       7      23 ..       4      75 .. 0.67
   2 !   26.0   0.0     1e-09   3.6e-06      94     317 ..     134     360 ..     111     367 .. 0.78
   3 ?   -1.2   0.3       0.2   7.1e+02     215     271 ..     481     537 ..     467     541 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.015
                                       EEEEE-SSEEEEEETTT CS
                           MreB_Mbl  4 lgiDLGtantlvyvkgk 20
                                       +giDLGt+n  + + + 
  gene3009|gene3009|rna3009|rna3009  7 VGIDLGTTNSCISIMQD 23
                                       79*******99855433 PP

  == domain 2  score: 26.0 bits;  conditional E-value: 1e-09
                                        -EEEEEE-SS--HHHHHHHHHHHHHTT-SEEEEEEHHHHHHHHTT--TTSSS-EE.EEEE-SS-EEEEEEETTEEE CS
                           MreB_Mbl  94 prvvicvPsgiteverrAvkeaakkaGarevllieeplaAAiGaglpveepsgnm.vvdiGggttevavislggiv 168
                                        +  vi+vP   ++ +r+  k+a + aG +   +++ep  AA+   +     +g++ v d+Gggt +++++  ++ +
  gene3009|gene3009|rna3009|rna3009 134 KFAVITVPAYFNHTQREETKKAGELAGLKVLRVLNEPTSAALNHAI-----TGHIaVYDLGGGTFDISILEKSDNI 204
                                        4579*************************************97554.....5665378************987755 PP

                                        .EEEEES....-SHHHHHHHHHHHHHHHHS..EE--HHHHHHHHHHH-BSS--HHHH.....EEEEEEEETTTTCE CS
                           MreB_Mbl 169 .tsksvr....vaGdeldeaiikyirkkyn..lliGertaekikieigsavkeeeee.....kmeikGrdlvtglp 232
                                         + k+      ++Gd++d+++++++ ++ +    + +    ki+ +i +a++++++e     +++i      +   
  gene3009|gene3009|rna3009|rna3009 205 fEVKATAgdsfLGGDDIDNTLTDFLMERLKngREMSDIDLAKIRPRIKKAAESAKKElstqeTVTIDIPYAYKDTH 280
                                        1444432333389***********9765541156666666777777777766665555433466777777788888 PP

                                        EEEEEEHHHHHHHHHHHHHHHHHHHHHHHHTS-HHHHHHHHHH-EEEESGGGGSBTHHHHHHHHHSS-EEE-SSTT CS
                           MreB_Mbl 233 kevevsseevrealkepvsaiveavkevLektppeLaadivdrgivltGGgallkgldkllseetglpvkvaedpl 308
                                         + e++ +e +++++  +++ v+   ++L+++      d vd+ +vl+GG + +  ++kl +e ++ +   + +p 
  gene3009|gene3009|rna3009|rna3009 281 FTYELKRAEFEDVVAPLIKRTVKPCLKALKDANI----DQVDH-LVLVGGMTRMPLVRKLSEEIFNRKPLFTASPD 351
                                        8999999999999999999999999999988765....45554.6788*******999999999************ PP

                                        THHHHHHHH CS
                           MreB_Mbl 309 tcvakGtgk 317
                                        ++va+G+++
  gene3009|gene3009|rna3009|rna3009 352 ESVAQGAAI 360
                                        ******986 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 0.2
                                        HHHHEEEEEEEETTTTCEEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHTS-HHHHHH CS
                           MreB_Mbl 215 eeeekmeikGrdlvtglpkevevsseevrealkepvsaiveavkevLektppeLaad 271
                                        +e + ++ k +d+++ +  +v  ++e+v +  +++ ++  + +++ L k + e ++d
  gene3009|gene3009|rna3009|rna3009 481 AEVTGIQTKEKDVAEKMQDKVDEKDEMVDKNDANKSNRFFDLIQSLLSKNSQEVVGD 537
                                        444466777789999999999999999999999999999999999999999999888 PP

>> FGGY_C  FGGY family of carbohydrate kinases, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.0   3.5e-09   1.3e-05     136     196 ..     303     364 ..     301     365 .. 0.94

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 3.5e-09
                             FGGY_C 136 railealekdsgkpldrlavdGGgskndllmqllAdilg.vpVerpktaeatalGaAilAav 196
                                        + +l+al++    ++d l+++GG+++ +l+++l  +i++ +p+ ++ ++e++a GaAi Aa+
  gene3009|gene3009|rna3009|rna3009 303 KPCLKALKDANIDQVDHLVLVGGMTRMPLVRKLSEEIFNrKPLFTASPDESVAQGAAIQAAI 364
                                        56899**9998888**********************************************96 PP

>> FtsA  Cell division protein FtsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.0    0.0014       4.9       1      20 [.       7      26 ..       7      84 .. 0.76
   2 !   11.5   0.0   8.2e-05       0.3       2      87 ..     185     343 ..     184     364 .. 0.66

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0014
                                       EEEEE-SSSEEEEEEETTEE CS
                                       xxxxxxxxxxxxxxxxxxxx RF
                               FtsA  1 alvDiGagktdvavaedgal 20
                                       +++D+G++ +++++++d+  
  gene3009|gene3009|rna3009|rna3009  7 VGIDLGTTNSCISIMQDNVA 26
                                       68***************642 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 8.2e-05
                                        EEEE-SSSEEEEEEETTEEEE.EEEES-......-HHHHHHHHHHHHT--HHHHHHHHHHH--S--.......... CS
                                        xxxxxxxxxxxxxxxxxxxxx.xxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......... RF
                               FtsA   2 lvDiGagktdvavaedgalvh.lrvigv......ggngitkdiakalrtaveeAerikikyGsala.......... 60 
                                        + D+G+g+ d++++e++  ++ +    +      gg+ i++ +   l + +++  +++  +               
  gene3009|gene3009|rna3009|rna3009 185 VYDLGGGTFDISILEKSDNIFeV--KATagdsflGGDDIDNTLTDFLMERLKNGREMSD-I----Dlakirprikk 253
                                        66**************7654442..222445679********77777777777777771.1....01122334433 PP

                                        .....EEEEEHHHHH............................................................. CS
                                        .....xxxxxxxxxx............................................................. RF
                               FtsA  61 .....ekeigrkels............................................................. 70 
                                             +ke+     s                                                             
  gene3009|gene3009|rna3009|rna3009 254 aaesaKKEL-----Stqetvtidipyaykdthftyelkraefedvvaplikrtvkpclkalkdanidqvdhlvlvg 324
                                        333332222.....13444456677777777777777788888888888888888999999888888999999999 PP

                                        GGGGSTTHHHHHHHHH..T CS
                                        xxxxxxxxxxxxxxxx..x RF
                               FtsA  71 ggsalpnleelaeral..s 87 
                                        g + +p +++l e+++  +
  gene3009|gene3009|rna3009|rna3009 325 GMTRMPLVRKLSEEIFnrK 343
                                        9999999999999997442 PP

>> DDR  Diol dehydratase reactivase ATPase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   4.4e-05      0.16     134     166 ..     182     213 ..     169     217 .. 0.87
   2 ?    2.0   0.0     0.023        82     262     284 ..     305     326 ..     282     339 .. 0.77
   3 ?   -3.0   0.4      0.77   2.8e+03      14      67 ..     477     532 ..     468     541 .. 0.59

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 4.4e-05
                                DDR 134 plailDlGaGstDaalieeegevkavhlAGAGe 166
                                         +a+ DlG+G+ D +++e+++++  v  A AG+
  gene3009|gene3009|rna3009|rna3009 182 HIAVYDLGGGTFDISILEKSDNIFEVK-ATAGD 213
                                        689********************9964.77887 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.023
                                DDR 262 alkkvsptgnirdidfvvlvGgs 284
                                        +lk++   +ni ++d++vlvGg 
  gene3009|gene3009|rna3009|rna3009 305 CLKAL-KDANIDQVDHLVLVGGM 326
                                        44444.4578***********96 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 0.77
                                DDR  14 veevekiedirgeagtnvggmlerv..revmaeltekkvedikikDllavdtlvpq 67 
                                         e+ ++++ i+ +++  +++m ++v  ++ m + ++ ++++ ++  + ++ +   q
  gene3009|gene3009|rna3009|rna3009 477 REQSAEVTGIQTKEKDVAEKMQDKVdeKDEMVDKNDANKSNRFFDLIQSLLSKNSQ 532
                                        56677777788888888888888883334455555555555554444455555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (543 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       775  (0.0432261); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.45
# Mc/sec: 3649.35
//
Query:       gene301|gene301|rna301|rna301  [L=108]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.1e-14   52.1   0.0    4.8e-14   51.9   0.0    1.0  1  Ribosomal_L7Ae  Ribosomal protein L7Ae/L30e/S12e/Gadd45 famil


Domain annotation for each model (and alignments):
>> Ribosomal_L7Ae  Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.9   0.0   2.7e-18   4.8e-14       3      92 ..      11     101 ..       9     103 .. 0.93

  Alignments for each domain:
  == domain 1  score: 51.9 bits;  conditional E-value: 2.7e-18
                                    HHHHHHHHHHHTEEEESHHHHHHHHHTTTESEEEEETTSSSGGHHHHHHHHHH.HTTEEEEEES.CHHHHHHHTTSSSEC CS
                 Ribosomal_L7Ae   3 ieevlkkakkagklvlGlkevtkalergeaklvilAedvepeekkkllealck.ekevpyvkvk.skkeLGelvgkkrpv 80 
                                     e++l++a ++g +  G ke++k+l +++ k+v+++++ +p + +  le+++  +++vp+++ +  +++L++ ++k  + 
  gene301|gene301|rna301|rna301  11 FEDKLPLAIQTGDVLFGFKECIKSLMNQRCKMVVVSANLPPLKRRM-LEYYAYlNNNVPLYFFNgTNNDLARSCDKFYRI 89 
                                    6899******************************************.************987774459************ PP

                                    SEEEEEESTTTH CS
                 Ribosomal_L7Ae  81 salaikdegdsk 92 
                                     +l+i+d g+++
  gene301|gene301|rna301|rna301  90 GVLSIIDDGEAD 101
                                    ********9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       311  (0.0173462); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.30s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 731.48
//
Query:       gene3011|gene3011|rna3011|rna3011  [L=55]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.11   12.2   0.1       0.11   12.2   0.1    1.0  1  NAT       NAT, N-acetyltransferase, of N-acetylglutamate synt


Domain annotation for each model (and alignments):
>> NAT  NAT, N-acetyltransferase, of N-acetylglutamate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1     6e-06      0.11      20      68 ..       5      48 ..       1      53 [. 0.82

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 6e-06
                                       -XEEEESSCCCSSXCCHHHHHHTTSTTTSSXHHHHHHHHHTSXEEEEEE CS
                                NAT 20 lkvitvkslkelidlekLksliedsfkrkldvkdYldrlkgkiakiyia 68
                                        k++ + s +++  +++L++li++++    ++++Yldr+++ ++ i i+
  gene3011|gene3011|rna3011|rna3011  5 NKIELKASYDDF--MKNLSELIDSNN---PKADEYLDRIENAVFDILIE 48
                                       566677777777..899999999887...8899***********99885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (55 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       810  (0.0451782); expected 358.6 (0.02)
Passed bias filter:                      498  (0.0277762); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.31u 0.27s 00:00:00.58 Elapsed: 00:00:00.39
# Mc/sec: 420.09
//
Query:       gene3012|gene3012|rna3012|rna3012  [L=38]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (38 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       399  (0.0222544); expected 358.6 (0.02)
Passed bias filter:                      247  (0.0137766); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.32u 0.25s 00:00:00.57 Elapsed: 00:00:00.39
# Mc/sec: 295.67
//
Query:       gene3013|gene3013|rna3013|rna3013  [L=206]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      2e-45  153.9   0.0    2.5e-45  153.6   0.0    1.1  1  UQ_con     Ubiquitin-conjugating enzyme
  ------ inclusion threshold ------
      0.032   14.0   0.0      0.045   13.5   0.0    1.3  1  Prok-E2_B  Prokaryotic E2 family B


Domain annotation for each model (and alignments):
>> UQ_con  Ubiquitin-conjugating enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  153.6   0.0   2.8e-49   2.5e-45       1     139 [.      52     188 ..      52     189 .. 0.97

  Alignments for each domain:
  == domain 1  score: 153.6 bits;  conditional E-value: 2.8e-49
                                        HHHHHHHHHHHSTTTTEEEEEEETTEECEEEEEEEB.TTSTTTTEEEEEEEE--TTTTTS--EEEESST-SCTTBE CS
                             UQ_con   1 rlqkelkelakkkpsgisaklvddenlfewkvlikgpedtpYeggvFklelefpedYPlkpPkvkfvtkifHPnvd 76 
                                        rl+k+lk+l+++k++ + a++ +d ++ +w +li+gp+dtp+e+++F ++++f+e+YP +pP++kf++k++HPn++
  gene3013|gene3013|rna3013|rna3013  52 RLMKDLKDLENTKNRTVFAAPLQD-DILTWCALIIGPKDTPFEDATFSMTMSFDESYPCTPPTCKFISKVYHPNIY 126
                                        89**************99999997.*************************************************** PP

                                        TTSBB-CGGGSTTT--TTSHHHHHHHHHHHHHHS--TTS-SSHHHHHHHHHTHHHHHHHHHHH CS
                             UQ_con  77 ksGevcldiLkeekWspaltlesvllsiqsLlaepnpesplnkeaakllkkdreeykkkvkey 139
                                        ++G++cldiL  ++Wsp+ ++ +vl+s+qs+l++pn +sp+n eaa+l+ +dr+ y ++v+++
  gene3013|gene3013|rna3013|rna3013 127 ANGDLCLDILT-NRWSPTFNVMTVLMSVQSMLNDPNVQSPANLEAANLFDNDRKCYVRRVRDC 188
                                        ***********.55**********************************************987 PP

>> Prok-E2_B  Prokaryotic E2 family B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0     5e-06     0.045      34     113 ..      93     166 ..      49     179 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5e-06
                          Prok-E2_B  34 sggtvdlrlvypdsfpllppavflqdpeqlkllpHintfggaLClleeeldldewdpngsvadvleqlqqvLn.eg 108
                                        + +t+ +++ +++s+p  pp             p i+  +g+LCl      ++ w p  +v  vl ++q +Ln  +
  gene3013|gene3013|rna3013|rna3013  93 EDATFSMTMSFDESYPCTPPTCKFISKV---YHPNIYA-NGDLCL---DILTNRWSPTFNVMTVLMSVQSMLNdPN 161
                                        67899999999********998887666...5677888.8*****...9************************888 PP

                          Prok-E2_B 109 isgde 113
                                        +++  
  gene3013|gene3013|rna3013|rna3013 162 VQSPA 166
                                        87765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       614  (0.0342462); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1532.89
//
Query:       gene3014|gene3014|rna3014|rna3014  [L=201]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.063   12.8   0.3       0.25   10.8   0.0    1.9  2  DUF4992   Domain of unknown function


Domain annotation for each model (and alignments):
>> DUF4992  Domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   1.4e-05      0.25       9      45 ..       7      42 ..       1      45 [. 0.84
   2 ?   -0.5   0.1     0.043   7.8e+02     105     123 ..     175     193 ..     150     195 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 1.4e-05
                            DUF4992  9 rrkavallllaavvlllssCadgydddesfssgVknv 45
                                       + +a++ l +a +++l++ C++ ++++ +f s Vkn 
  gene3014|gene3014|rna3014|rna3014  7 K-RAIEVLFIAFLAFLIVCCTESLKENRRFLSFVKNN 42
                                       3.4568999999**********************995 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.043
                            DUF4992 105 svavakieDtnYklsiktl 123
                                         +  + +eD++Y ++i +l
  gene3014|gene3014|rna3014|rna3014 175 HFVYKCKEDASYDITIFVL 193
                                        4667889999999999776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (201 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       725  (0.0404373); expected 358.6 (0.02)
Passed bias filter:                      454  (0.0253221); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 1304.30
//
Query:       gene3015|gene3015|rna3015|rna3015  [L=120]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      7e-11   42.2   0.1    9.7e-11   41.8   0.1    1.1  1  Ribosomal_S10  Ribosomal protein S10p/S20e


Domain annotation for each model (and alignments):
>> Ribosomal_S10  Ribosomal protein S10p/S20e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.8   0.1   5.4e-15   9.7e-11       3      94 ..      25     113 ..      23     117 .. 0.92

  Alignments for each domain:
  == domain 1  score: 41.8 bits;  conditional E-value: 5.4e-15
                                        EEEESSHHHHHHHHHHHHHHTTSSS-EE---EEEEEEEEEEEEE--SS--.S--EEEEEEEEEEEEEEEE.E-HHH CS
                      Ribosomal_S10   3 rlkSydsklLekavkkivraakelgikvkgpvplPtkrkrvtvlksphvd.kksreqfeirthkRlidisdatket 77 
                                         l S++++ L+ ++++++  a +++ ++  +++l+t + +vt++ksp+++ + +++++++ ++ R +++   t + 
  gene3015|gene3015|rna3015|rna3015  25 LLLSTKKNILDIVCRDFYAYAMQHQENIPPVKHLKTIKGQVTTRKSPCGQgTATWSRYKLFVYGRKFEF-RTTHDF 99 
                                        57899****************************************************************.599999 PP

                                        HHHHS-...S---SS-E CS
                      Ribosomal_S10  78 idtllkllqlnlpegVs 94 
                                        +++++ +lq n    V+
  gene3015|gene3015|rna3015|rna3015 100 LEKVATFLQNN---DVE 113
                                        99999999988...555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       464  (0.0258799); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 865.74
//
Query:       gene3016|gene3016|rna3016|rna3016  [L=114]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (114 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       510  (0.0284455); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 878.57
//
Query:       gene3017|gene3017|rna3017|rna3017  [L=1393]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.36   11.5   2.6         56    4.5   0.0    4.2  3  DUF960    Staphylococcal protein of unknown function (DUF960)
        2.5    8.9   9.1      1e+02    3.8   0.0    6.2  7  LRR_2     Leucine Rich Repeat


Domain annotation for each model (and alignments):
>> DUF960  Staphylococcal protein of unknown function (DUF960)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0     0.037   3.4e+02      24      68 ..     659     705 ..     655     719 .. 0.82
   2 ?    4.5   0.0    0.0062        56      19      54 ..     817     851 ..     809     867 .. 0.89
   3 ?    1.1   0.3     0.069   6.2e+02      15      78 ..    1303    1366 ..    1297    1377 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.037
                                        HHHHTTTTS---SEEEEEE..EEETTEEEEEEEETT---EEEEEEEE CS
                             DUF960  24 idellkgvvpldylqiFeL..kenkgkltiehsqeepeyekeydlpl 68 
                                        id++++g + +d    F++   +++ +l i+++q e ++e++ +  +
  gene3017|gene3017|rna3017|rna3017 659 IDNDIEGLKIKDCTGKFKIpfISHEHELMINFTQSEYSLEITKTSVN 705
                                        8999999999999999**98899************998888765544 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.0062
                                        HHHHHHHHHTTTTS---SEEEEEEEEETTEEEEEEE CS
                             DUF960  19 llWeiidellkgvvpldylqiFeLkenkgkltiehs 54 
                                        ++++ +++ l+g +pl++l +F L++n+ ++++ h 
  gene3017|gene3017|rna3017|rna3017 817 SIYSSMENILRG-IPLNNLKNFLLNHNRTSINLIHV 851
                                        688899999999.***************99999996 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.069
                                         HHHHHHHHHHHHHTTTTS---SEEEEEEEEETTEEEEEEEETT---EEEEEEEEE--TTS-SEE CS
                             DUF960   15 elqlllWeiidellkgvvpldylqiFeLkenkgkltiehsqeepeyekeydlplkydnelpkkv 78  
                                         ++  l+ e+i   +++  +  +l  F++++++g++   +++ +  +   y +  ++ ++lp+++
  gene3017|gene3017|rna3017|rna3017 1303 KMNALFNELITFEIRNRLQHLNLVGFSISKKNGEQLKLFQNLKTLIVDYYFIDENFFSFLPSTL 1366
                                         5566666777777788888889999999999999999999888888777777777777777665 PP

>> LRR_2  Leucine Rich Repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.1     0.058   5.2e+02       3      12 ..     464     473 ..     463     479 .. 0.86
   2 ?   -0.7   0.0       0.3   2.7e+03       2      18 ..     641     657 ..     640     659 .. 0.88
   3 ?   -2.7   0.1       1.3   1.2e+04       4      17 ..     770     783 ..     768     784 .. 0.83
   4 ?   -3.0   0.0       1.6   1.5e+04      10      20 ..     868     878 ..     867     878 .. 0.86
   5 ?    3.8   0.0     0.012     1e+02       3      17 ..     900     914 ..     899     916 .. 0.83
   6 ?    3.2   0.0     0.018   1.6e+02       2      18 ..     981     997 ..     981     999 .. 0.92
   7 ?   -3.0   0.0       1.7   1.5e+04       1       8 [.    1343    1350 ..    1343    1351 .. 0.78

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.058
                              LRR_2   3 KtLhLdsVrf 12 
                                        KtL L  V+f
  gene3017|gene3017|rna3017|rna3017 464 KTLILKEVKF 473
                                        *********9 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.3
                              LRR_2   2 LKtLhLdsVrfsdedsl 18 
                                         K L L +++++  +sl
  gene3017|gene3017|rna3017|rna3017 641 IKRLKLKNIVIAENCSL 657
                                        699*********99998 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 1.3
                              LRR_2   4 tLhLdsVrfsdeds 17 
                                        tL+L+++ f+  +s
  gene3017|gene3017|rna3017|rna3017 770 TLVLHNMDFTENAS 783
                                        9******9987655 PP

  == domain 4  score: -3.0 bits;  conditional E-value: 1.6
                              LRR_2  10 Vrfsdedslek 20 
                                        V+ ++ed+le+
  gene3017|gene3017|rna3017|rna3017 868 VKLFNEDGLEN 878
                                        8889****996 PP

  == domain 5  score: 3.8 bits;  conditional E-value: 0.012
                              LRR_2   3 KtLhLdsVrfsdeds 17 
                                        K+LhL++Vr +++ +
  gene3017|gene3017|rna3017|rna3017 900 KILHLSHVRSANGST 914
                                        9********888765 PP

  == domain 6  score: 3.2 bits;  conditional E-value: 0.018
                              LRR_2   2 LKtLhLdsVrfsdedsl 18 
                                        L tL L++V+++  +++
  gene3017|gene3017|rna3017|rna3017 981 LQTLKLHNVVIKRSCMF 997
                                        89**********99998 PP

  == domain 7  score: -3.0 bits;  conditional E-value: 1.7
                              LRR_2    1 sLKtLhLd 8   
                                         +LKtL  d
  gene3017|gene3017|rna3017|rna3017 1343 NLKTLIVD 1350
                                         69***766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1393 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       558  (0.0311228); expected 358.6 (0.02)
Passed bias filter:                      238  (0.0132746); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.93u 0.36s 00:00:01.29 Elapsed: 00:00:00.58
# Mc/sec: 7218.14
//
Query:       gene3018|gene3018|rna3018|rna3018  [L=142]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.015   15.1   1.2      0.018   14.9   1.2    1.3  1  Rep_3     Initiator Replication protein


Domain annotation for each model (and alignments):
>> Rep_3  Initiator Replication protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   1.2     1e-06     0.018     116     180 ..      24      87 ..       2     125 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1e-06
                                        TTGGGSS--GGGEEEEEHHHHHH---HHHHHHHHHHHHTSS-EEEEEEHHHHHHHH.T-EESS-S CS
                              Rep_3 116 tlkpyllelkknftkyelaefskLrskyskrLyellkqfkstgkdeisleelkellglpkskykr 180
                                        ++    +el   f++y+l ++++++sk+s+   +++   +  + ++i  + + +++++ k++yk+
  gene3018|gene3018|rna3018|rna3018  24 DMSENYYELLF-FMSYNLFNTIRFSSKHSIYCWDIITTLECLNDKTIATKIFIHRFDCIKKYYKE 87 
                                        55666778888.************************99999******************888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       732  (0.0408277); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.34s 00:00:00.92 Elapsed: 00:00:00.55
# Mc/sec: 781.45
//
Query:       gene3019|gene3019|rna3019|rna3019  [L=118]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       773  (0.0431145); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.57u 0.35s 00:00:00.92 Elapsed: 00:00:00.54
# Mc/sec: 655.75
//
Query:       gene302|gene302|rna302|rna302  [L=322]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.017   16.0   6.3      0.033   15.1   0.1    3.6  3  WD40      WD domain, G-beta repeat
      0.088   13.3   2.4       0.22   12.0   0.1    2.7  3  PQQ_3     PQQ-like domain


Domain annotation for each model (and alignments):
>> WD40  WD domain, G-beta repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.2     0.045     4e+02      13      38 .]      75      99 ..      65      99 .. 0.72
   2 ?   15.1   0.1   3.7e-06     0.033       8      38 .]     109     138 ..     102     138 .. 0.77
   3 ?   -1.7   0.1      0.75   6.7e+03      23      33 ..     258     268 ..     245     287 .. 0.55

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.045
                                   EEEEEEETTSSE.EEEEETTSEEEEEE CS
                           WD40 13 vtslafspdgaw.lasGsdDgtvriWd 38
                                   + ++++  ++   +a ++ D +v+++d
  gene302|gene302|rna302|rna302 75 IFDVCWLTNSLIgIA-SG-DSNVYLFD 99
                                   788866666666555.57.99999987 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 3.7e-06
                                    ESS.SSEEEEEEETTSSE....EEEEETTSEEEEEE CS
                           WD40   8 tGH.ssvtslafspdgaw....lasGsdDgtvriWd 38 
                                    +GH +sv+++      +     + +G+ Dg+v  Wd
  gene302|gene302|rna302|rna302 109 RGHtKSVRCV------KHaagrVYTGGSDGKVFCWD 138
                                    6**999****......664444558877*******9 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 0.75
                                    SEEEEEETTSE CS
                           WD40  23 awlasGsdDgt 33 
                                    +++++G  ++ 
  gene302|gene302|rna302|rna302 258 DLVLAGFANKV 268
                                    33444442322 PP

>> PQQ_3  PQQ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.1      0.26   2.3e+03      26      37 ..      88      99 ..      88     100 .. 0.88
   2 ?   12.0   0.1   2.5e-05      0.22      22      40 .]     123     141 ..     120     141 .. 0.91
   3 ?   -2.4   0.1      0.85   7.6e+03      24      38 ..     260     273 ..     253     274 .. 0.72

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.26
                          PQQ_3 26 vgtgdGtlyAlD 37
                                   +++gd ++y +D
  gene302|gene302|rna302|rna302 88 IASGDSNVYLFD 99
                                   6899*****999 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 2.5e-05
                          PQQ_3  22 glvyvgtgdGtlyAlDaet 40 
                                    g+vy+g++dG++++ D ++
  gene302|gene302|rna302|rna302 123 GRVYTGGSDGKVFCWDVRS 141
                                    99**************986 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 0.85
                          PQQ_3  24 vyvgtgdGtlyAlDa 38 
                                    v +g   ++++ +Da
  gene302|gene302|rna302|rna302 260 VLAGF-ANKVVVFDA 273
                                    44444.489999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (322 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       412  (0.0229795); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.62u 0.34s 00:00:00.96 Elapsed: 00:00:00.55
# Mc/sec: 1764.16
//
Query:       gene3020|gene3020|rna3020|rna3020  [L=1506]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1506 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       642  (0.0358079); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.91u 0.30s 00:00:01.21 Elapsed: 00:00:00.51
# Mc/sec: 8809.46
//
Query:       gene3021|gene3021|rna3021|rna3021  [L=42]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (42 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       183  (0.0102069); expected 358.6 (0.02)
Passed bias filter:                      146  (0.00814323); expected 358.6 (0.02)
Passed Vit filter:                         7  (0.000390429); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.44
# Mc/sec: 286.81
//
Query:       gene3022|gene3022|rna3022|rna3022  [L=593]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.5e-39  133.2   1.0    3.2e-19   69.8   0.3    3.8  2  ABC_tran         ABC transporter
    4.3e-18   65.1   2.3    8.8e-18   64.1   2.3    1.5  1  ABC_tran_Xtn     ABC transporter
    2.6e-17   63.6   2.1     0.0014   18.5   0.1    4.3  4  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
    6.3e-11   42.1   0.6      0.035   13.5   0.1    4.2  4  SMC_N            RecF/RecN/SMC N terminal domain
    2.5e-10   40.7   0.3    1.2e-05   25.6   0.0    2.8  2  AAA_22           AAA domain
    9.7e-08   31.6   0.7     0.0013   18.5   0.0    2.4  2  AAA_29           P-loop containing region of AAA domain
    1.1e-07   32.4   0.2    0.00091   19.6   0.0    2.5  2  AAA_16           AAA ATPase domain
    2.8e-07   30.6   0.1      0.018   15.0   0.0    2.4  2  RsgA_GTPase      RsgA GTPase
    2.9e-07   30.6   0.1      0.002   18.1   0.0    2.4  2  NACHT            NACHT domain
    8.9e-07   28.8   0.0     0.0073   16.0   0.0    2.7  2  AAA_30           AAA domain
    2.3e-06   27.6   0.1      0.062   13.4   0.1    2.9  2  MMR_HSR1         50S ribosome-binding GTPase
    2.9e-06   27.8   0.1       0.18   12.4   0.0    3.1  3  AAA_18           AAA domain
    6.5e-06   26.1   0.0       0.11   12.2   0.0    2.5  2  AAA_15           AAA ATPase domain
    7.4e-06   25.6   0.1    0.00065   19.3   0.0    2.4  2  AAA_7            P-loop containing dynein motor region
    1.5e-05   25.2   0.0      0.054   13.7   0.0    2.4  2  Roc              Ras of Complex, Roc, domain of DAPkinase
    1.7e-05   25.4   2.3      0.041   14.4   0.3    2.7  2  AAA_23           AAA domain
    2.7e-05   24.4   1.0       0.36   11.0   0.0    3.0  3  AAA_28           AAA domain
    2.9e-05   24.2   0.5      0.062   13.5   0.0    2.7  2  AAA_33           AAA domain
    0.00022   21.3   0.1      0.089   12.8   0.0    3.3  3  AAA_14           AAA domain
    0.00027   20.7   0.1       0.12   12.0   0.0    2.4  2  AAA_24           AAA domain
    0.00062   19.1   0.0      0.031   13.6   0.0    2.3  2  Septin           Septin
    0.00071   18.7   0.0       0.17   10.9   0.0    2.3  2  MCM              MCM P-loop domain
    0.00076   19.9   0.1       0.38   11.2   0.0    2.8  2  AAA              ATPase family associated with various cellul
    0.00092   18.8   1.0       0.22   11.0   0.0    3.4  3  AAA_25           AAA domain
     0.0011   19.0   0.7        1.5    8.8   0.0    3.1  3  AAA_5            AAA domain (dynein-related subfamily)
     0.0013   18.2   0.1      0.021   14.2   0.0    2.3  2  Arf              ADP-ribosylation factor family
     0.0014   18.3   0.1        1.8    8.1   0.0    2.5  2  SRP54            SRP54-type protein, GTPase domain
     0.0014   18.1   1.0      0.011   15.1   0.1    2.3  2  FtsK_SpoIIIE     FtsK/SpoIIIE family
     0.0015   18.9   0.0       0.86   10.0   0.0    2.6  2  RNA_helicase     RNA helicase
     0.0018   17.5   0.0       0.77    8.9   0.0    2.4  2  NB-ARC           NB-ARC domain
     0.0019   17.8   1.5       0.16   11.5   0.1    2.8  2  cobW             CobW/HypB/UreG, nucleotide-binding domain
     0.0044   16.8   0.4         15    5.3   0.0    3.3  3  VirE             Virulence-associated protein E
     0.0046   16.6   0.0       0.13   11.9   0.0    2.3  2  AAA_27           AAA domain
     0.0048   16.1   0.5       0.35   10.0   0.0    2.6  2  DUF815           Protein of unknown function (DUF815)
     0.0055   16.8   0.1       0.15   12.1   0.0    2.8  2  Dynamin_N        Dynamin family
     0.0083   15.9   0.4        2.6    7.8   0.0    3.2  3  ATP_bind_1       Conserved hypothetical ATP binding protein
  ------ inclusion threshold ------
      0.012   15.6   0.1       0.72    9.7   0.0    2.8  2  ATPase_2         ATPase domain predominantly from Archaea
      0.014   15.0   0.0          4    7.0   0.0    2.5  2  Ras              Ras family
      0.015   15.1   1.4       0.76    9.5   0.1    2.4  2  CLP1_P           mRNA cleavage and polyadenylation factor CLP
      0.018   15.0   0.5        6.7    6.6   0.1    3.3  3  NTPase_1         NTPase
      0.024   14.1   0.0        2.1    7.8   0.0    2.4  2  SRPRB            Signal recognition particle receptor beta su
      0.033   13.3   0.0       0.74    8.9   0.0    2.2  2  G-alpha          G-protein alpha subunit
      0.035   13.8   0.0       0.17   11.6   0.0    1.9  2  Sigma54_activat  Sigma-54 interaction domain
       0.04   13.2   0.0        1.9    7.7   0.0    2.3  2  Zeta_toxin       Zeta toxin
      0.045   12.5   0.0       0.47    9.2   0.0    2.2  2  Adeno_IVa2       Adenovirus IVa2 protein
      0.047   13.7   0.0        1.7    8.7   0.0    2.4  2  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
       0.05   13.5   0.0        6.6    6.5   0.0    2.4  2  dNK              Deoxynucleoside kinase
      0.051   13.5   0.0        5.2    6.9   0.0    2.3  2  Ploopntkinase3   P-loop Nucleotide Kinase3
      0.057   13.2   0.0          1    9.0   0.0    2.4  2  Viral_helicase1  Viral (Superfamily 1) RNA helicase
      0.066   12.3   1.9      0.062   12.3   0.3    1.8  1  T2SSE            Type II/IV secretion system protein
      0.066   12.0   0.6        5.2    5.8   0.1    2.6  2  ABC_ATPase       Predicted ATPase of the ABC class
      0.069   12.9   0.0        3.5    7.3   0.0    2.3  2  PduV-EutP        Ethanolamine utilisation - propanediol utili
      0.086   12.2   0.1       0.59    9.5   0.0    2.3  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
       0.09   12.0   0.7         21    4.2   0.0    2.9  3  KAP_NTPase       KAP family P-loop domain
      0.091   11.7   0.1        2.2    7.2   0.0    2.2  2  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
      0.094   12.6   0.1        2.2    8.2   0.0    2.9  3  Rad17            Rad17 P-loop domain
       0.11   12.9   0.1         11    6.4   0.0    2.8  2  AAA_19           AAA domain
       0.11   12.4   0.6        4.9    7.1   0.0    3.0  2  MobB             Molybdopterin guanine dinucleotide synthesis
       0.12   12.1   0.1       0.44   10.2   0.0    1.9  1  Guanylate_kin    Guanylate kinase
       0.15   12.4   0.2         16    6.0   0.0    3.1  3  AAA_17           AAA domain
       0.22   10.6   4.1         16    4.6   0.0    3.5  3  DAP3             Mitochondrial ribosomal death-associated pro
        2.5    8.1   5.0        6.5    6.8   0.2    2.8  3  DUF87            Helicase HerA, central domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.6   0.0   3.2e-18   9.1e-16       1     137 []     116     245 ..     116     245 .. 0.81
   2 !   69.8   0.3   1.1e-21   3.2e-19       2     137 .]     408     530 ..     407     530 .. 0.78

  Alignments for each domain:
  == domain 1  score: 58.6 bits;  conditional E-value: 3.2e-18
                                        EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBH CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltv 76 
                                        lk+ sl l++g ++++vG nG GKStLl+ l +    t+  +  ++  +++        + + +        ++tv
  gene3022|gene3022|rna3022|rna3022 116 LKDGSLCLRRGLVYGLVGTNGVGKSTLLRWLKNRAF-TSTYLVRQESAWTSAAPACDGTRCAAVDNA----ARITV 186
                                        67889**************************99976.555554556666664555555555555555....55556 PP

                                        HHH...HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                        xxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ABC_tran  77 ren...esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                        +e    +++ e++k+l ++g kel++ v      +LSgG+++++al +all+  +llllDEpt+
  gene3022|gene3022|rna3022|rna3022 187 KEYlkeYDECEATKMLVQFGFKELTKYV-----CELSGGWQKKLALLKALLSPTNLLLLDEPTN 245
                                        66666699999************66666.....6*****************************8 PP

  == domain 2  score: 69.8 bits;  conditional E-value: 1.1e-21
                                        EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS..--S-TTSB CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxx RF
                           ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe..pqlfpelt 75 
                                        kn+++ +k ++k+ +vG+nGaGKStLlk+l++ ++     +            ++ + +i++++q+  +++ p+ +
  gene3022|gene3022|rna3022|rna3022 408 KNLNMIIKGDSKILVVGPNGAGKSTLLKTLLHSTS-----V-----------SRHPSLKISYFSQHhaHNFAPTER 467
                                        89*****************************9987.....4...........345666666666664333333333 PP

                                        HHHH......HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                        xxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ABC_tran  76 vren......esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                        v         + ++ + ++l++l+lk+ + + v    ssLSgGqk r++la++ l +p+llllDEpt+
  gene3022|gene3022|rna3022|rna3022 468 VLPYlltstrQPESAVRAVLASLNLKK-DYQFV----SSLSGGQKTRLMLAKLSLDNPDLLLLDEPTN 530
                                        333366433466667999999999999.77777....******************************8 PP

>> ABC_tran_Xtn  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.1   2.3     3e-20   8.8e-18       8      79 ..     290     361 ..     286     368 .. 0.92

  Alignments for each domain:
  == domain 1  score: 64.1 bits;  conditional E-value: 3e-20
                       ABC_tran_Xtn   8 lteYkGnYseyleekeerleqqqkayekqqkeikkleefIerfrakakkakqaqsrekaLeklekiekpeek 79 
                                        l+ YkGnY+ey +  + ++++++++yek+++ +++++ f++rfr +ak+a ++qsr k + ++++++ ++++
  gene3022|gene3022|rna3022|rna3022 290 LRVYKGNYDEYERLAALERANAEREYEKNEDTRRRMQLFVDRFRCNAKRAGMVQSRLKTMARMDTVQLENAD 361
                                        899**************************************************************9988544 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.0    0.0002     0.059       2      40 ..     129     161 ..     128     173 .. 0.75
   2 !   13.1   0.0   0.00022     0.063     236     302 ..     216     276 ..     213     277 .. 0.82
   3 !   18.5   0.1   4.8e-06    0.0014       3      21 ..     421     439 ..     420     458 .. 0.81
   4 !   14.8   0.0   6.7e-05     0.019     236     298 ..     501     557 ..     494     562 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.0002
                             AAA_21   2 nvliGpNgsGKSnLLdaldllarldrdvegltdelsggg 40 
                                         +l+G Ng+GKS+LL+ l       + ++ +t+  +  +
  gene3022|gene3022|rna3022|rna3022 129 YGLVGTNGVGKSTLLRWL------KNRAFTSTYLVRQES 161
                                        589*************99......666666666665555 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 0.00022
                             AAA_21 236 elSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHSplll 302
                                        elS G ++ lall all+      lll+DEp n L+   +  l + l +++     v++++H+  +l
  gene3022|gene3022|rna3022|rna3022 216 ELSGGWQKKLALLKALLSPT---NLLLLDEPTNMLDLPSIDFLERALAKTN---KTVLVVSHDIAFL 276
                                        6899999999*******966...89************66666666665555...5*******98776 PP

  == domain 3  score: 18.5 bits;  conditional E-value: 4.8e-06
                             AAA_21   3 vliGpNgsGKSnLLdaldl 21 
                                        +++GpNg+GKS+LL++l +
  gene3022|gene3022|rna3022|rna3022 421 LVVGPNGAGKSTLLKTLLH 439
                                        68***************54 PP

  == domain 4  score: 14.8 bits;  conditional E-value: 6.7e-05
                             AAA_21 236 elSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHS 298
                                        +lS G+k    +l+ l  +++  +lll+DEp n+L+   +  l   ++e +     v++++H+
  gene3022|gene3022|rna3022|rna3022 501 SLSGGQKTR-LMLAKLSLDNP--DLLLLDEPTNHLDIGSIVALRNAIREYKG---AVVCVSHD 557
                                        567777777.66666666666..9*************999999999977755...89999998 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0      0.14        41      28      41 ..     130     143 ..     123     162 .. 0.89
   2 !    8.0   0.0    0.0062       1.8     126     205 ..     206     279 ..     167     290 .. 0.75
   3 !   13.5   0.1   0.00012     0.035      26      57 ..     419     450 ..     406     460 .. 0.74
   4 !   12.1   0.0   0.00034     0.098     111     197 ..     471     556 ..     463     568 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.14
                                        EEEESTTSSHHHHH CS
                                        xxxxxxxxxxxxxx RF
                              SMC_N  28 aivGpNGSGKsnll 41 
                                         +vG NG GKs ll
  gene3022|gene3022|rna3022|rna3022 130 GLVGTNGVGKSTLL 143
                                        589********987 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0062
                                        HHHCTT-STTCS-HH.HHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHH CS
                                        xxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              SMC_N 126 llesagiskelLSgG.ektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivislree 200
                                         +++   +  +LSgG +k+L   aLl A+   +p+ l llDe    LD   +  + + l +++    ++v+s++  
  gene3022|gene3022|rna3022|rna3022 206 GFKELTKYVCELSGGwQKKL---ALLKAL--LSPTNLLLLDEPTNMLDLPSIDFLERALAKTN--KTVLVVSHDIA 274
                                        44444444558999955665...555554..57**************************9988..66999999988 PP

                                        HCCC- CS
                                        xxxxx RF
                              SMC_N 201 mleka 205
                                        +l+  
  gene3022|gene3022|rna3022|rna3022 275 FLNST 279
                                        87765 PP

  == domain 3  score: 13.5 bits;  conditional E-value: 0.00012
                                        EEEEEESTTSSHHHHHHHHHHHCTT.TTTTTT CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              SMC_N  26 ftaivGpNGSGKsnlldAilFvLGersakklr 57 
                                           +vGpNG+GKs ll  +l+  + +   +l+
  gene3022|gene3022|rna3022|rna3022 419 KILVVGPNGAGKSTLLKTLLHSTSVSRHPSLK 450
                                        4689**************99987776665665 PP

  == domain 4  score: 12.1 bits;  conditional E-value: 0.00034
                                        EEETTEEE-HHHHHHHHHCTT-STT.....CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHH CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              SMC_N 111 ykingkevtkkevsellesagiske.....lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvae 181
                                        y +  ++  ++ v+ +l+s +++k+     +LSgG+kt     L++A  + +   l llDe   +LD   + ++ +
  gene3022|gene3022|rna3022|rna3022 471 YLLTSTRQPESAVRAVLASLNLKKDyqfvsSLSGGQKTR----LMLAKLSLDNPDLLLLDEPTNHLDIGSIVALRN 542
                                        5566666677888888888888887777779******95....556666899999********************* PP

                                        HHHHHCTTSEEEEE-S CS
                                        xxxxxxxxxxxxxxxx RF
                              SMC_N 182 llkeksknaQfivisl 197
                                         ++e +    ++++s+
  gene3022|gene3022|rna3022|rna3022 543 AIREYK--GAVVCVSH 556
                                        **9988..56666666 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.1   0.00064      0.18      10      29 ..     131     150 ..     124     273 .. 0.65
   2 !   25.6   0.0     4e-08   1.2e-05       5     102 ..     417     530 ..     413     553 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00064
                             AAA_22  10 vtGesGtGKTtllrrlleql 29 
                                        ++G  G+GK+tllr+l++++
  gene3022|gene3022|rna3022|rna3022 131 LVGTNGVGKSTLLRWLKNRA 150
                                        89***************997 PP

  == domain 2  score: 25.6 bits;  conditional E-value: 4e-08
                             AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaee..............erpevvfvtlpsstsskdllrellralgl 66 
                                        ++ ++v+G+ G+GK+tll++ll++     ++                +  +v+ + l+s   +++  r++l  l+l
  gene3022|gene3022|rna3022|rna3022 417 DSKILVVGPNGAGKSTLLKTLLHSTSVSRHPSLkisyfsqhhahnfaPTERVLPYLLTSTRQPESAVRAVLASLNL 492
                                        56689*******************865555555********999998888888*********************** PP

                             AAA_22  67 elkaerlsseell.ealeqalrarav...ielliiDEaqh 102
                                        ++++  +  + l   + ++ + a+     + ll++DE  +
  gene3022|gene3022|rna3022|rna3022 493 KKDY--QFVSSLSgGQKTRLMLAKLSldnPDLLLLDEPTN 530
                                        9999..5555555566666666666666678999999555 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.1    0.0009      0.26      23      39 ..     126     143 ..     116     144 .. 0.84
   2 !   18.5   0.0   4.3e-06    0.0013      11      43 ..     406     435 ..     401     445 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0009
                             AAA_29  23 g.atlltGpsGsGKSTll 39 
                                        g ++ l+G++G+GKSTll
  gene3022|gene3022|rna3022|rna3022 126 GlVYGLVGTNGVGKSTLL 143
                                        556779**********98 PP

  == domain 2  score: 18.5 bits;  conditional E-value: 4.3e-06
                             AAA_29  11 tfdghtieidlkgatlltGpsGsGKSTllDAiq 43 
                                         f++  + i+ ++ +l++Gp+G+GKSTll   +
  gene3022|gene3022|rna3022|rna3022 406 IFKNLNMIIKGDSKILVVGPNGAGKSTLL---K 435
                                        566666666645599*************9...4 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.1    0.0019      0.54      29      57 ..     131     158 ..     119     337 .. 0.83
   2 !   19.6   0.0   3.2e-06   0.00091      16      84 ..     410     485 ..     406     526 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0019
                             AAA_16  29 lsGesGvGKsslvrellralekdggiflr 57 
                                        l+G  GvGKs+l+r l++++ ++  +++r
  gene3022|gene3022|rna3022|rna3022 131 LVGTNGVGKSTLLRWLKNRAFTS-TYLVR 158
                                        89*************99988877.33333 PP

  == domain 2  score: 19.6 bits;  conditional E-value: 3.2e-06
                             AAA_16  16 lervrsgrpelvllsGesGvGKsslvrellralekd.....g.giflrgkcdql...esaipysa.laqalareel 81 
                                        l+++ +g+ + +l++G+ G GKs+l+++ll++ + +     +  +f + +++ +   e+ +py+   +++   e+ 
  gene3022|gene3022|rna3022|rna3022 410 LNMIIKGD-SKILVVGPNGAGKSTLLKTLLHSTSVSrhpslKiSYFSQHHAHNFaptERVLPYLLtSTRQP--ESA 482
                                        55666777.5789*****************85444445888546676666666665566677744233333..244 PP

                             AAA_16  82 lrq 84 
                                        +r+
  gene3022|gene3022|rna3022|rna3022 483 VRA 485
                                        444 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.0   0.00024      0.07     101     133 ..     128     160 ..      84     163 .. 0.84
   2 !   15.0   0.0   6.2e-05     0.018      87     123 ..     404     441 ..     390     459 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00024
                                        EEEEECSTTSSHHHHHHHHCTT-----S----- CS
                        RsgA_GTPase 101 tsvlvGqSGvGKStLinallpelelktgevsek 133
                                        +  lvG  GvGKStL+  l++++ ++t  v+++
  gene3022|gene3022|rna3022|rna3022 128 VYGLVGTNGVGKSTLLRWLKNRAFTSTYLVRQE 160
                                        5669***************99988877777665 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 6.2e-05
                                        HTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT- CS
                        RsgA_GTPase  87 kegleelkellkd.ktsvlvGqSGvGKStLinallpel 123
                                           +++l+  +k+ + +++vG+ G+GKStL+++ll ++
  gene3022|gene3022|rna3022|rna3022 404 PYIFKNLNMIIKGdSKILVVGPNGAGKSTLLKTLLHST 441
                                        55677888888885667789*************99875 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.0     0.002      0.58       5      22 ..     131     148 ..     128     158 .. 0.86
   2 !   18.1   0.0     7e-06     0.002       3      72 ..     420     486 ..     418     525 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.002
                                        EEC-TTTCHHHHHHHHHH CS
                              NACHT   5 lqGeaGsGKTtLlqklal 22 
                                        l G +G+GK+tLl++l  
  gene3022|gene3022|rna3022|rna3022 131 LVGTNGVGKSTLLRWLKN 148
                                        78*************976 PP

  == domain 2  score: 18.1 bits;  conditional E-value: 7e-06
                                        EEEEC-TTTCHHHHHHHHHHHHCTS-SCCCC-SEEEEEETTTTTTS-...-HCHHHCCCCTS--SSS-CC CS
                              NACHT   3 vilqGeaGsGKTtLlqklalawaegklpqgafklvFflslrelsrsgnarsladllfsqlpepaapvsev 72 
                                        +++ G++G GK+tLl+ l +    ++ p+   k ++f + ++ +   ++r l +ll+s   +p+++v+ v
  gene3022|gene3022|rna3022|rna3022 420 ILVVGPNGAGKSTLLKTLLHSTSVSRHPSL--KISYFSQHHAHNFAPTERVLPYLLTST-RQPESAVRAV 486
                                        799**************************6..455554444444444446676666665.5666666664 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.0    0.0024      0.68      18     122 ..     126     269 ..     120     272 .. 0.68
   2 !   16.0   0.0   2.5e-05    0.0073      17     122 ..     416     554 ..     410     557 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0024
                             AAA_30  18 drvavltGpAGtGKttalkalreaweaaggrviglAptgkaAkvLaeelgi.....eastiakllkrlk....... 81 
                                         +v  l+G  G GK+t+l+ l++ + ++ + v   +    aA +      +     +  t++++lk+++       
  gene3022|gene3022|rna3022|rna3022 126 GLVYGLVGTNGVGKSTLLRWLKNRAFTSTYLVRQESAWTSAAPACDGTRCAavdnaARITVKEYLKEYDeceatkm 201
                                        568889***************7776667666664444444444443221110121122355555555557777777 PP

                             AAA_30  82 ..........................grarlepgtllivDE.agmvdtkqlaallkaaekagakvilv 122
                                                                   +a l+p +ll+ DE + m+d  +++ l +a++k++ +v++v
  gene3022|gene3022|rna3022|rna3022 202 lvqfgfkeltkyvcelsggwqkklalLKALLSPTNLLLLDEpTNMLDLPSIDFLERALAKTNKTVLVV 269
                                        77777888889999999999999988446788889999999556889999888888888877777766 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 2.5e-05
                             AAA_30  17 gdrvavltGpAGtGKttalkalreaweaag...........grviglAptgkaAkvLaeelgieastiakllkrlk 81 
                                        gd   +++Gp G+GK+t+lk+l +    +            ++ + +Apt+++   L +++  + s +  +l +l+
  gene3022|gene3022|rna3022|rna3022 416 GDSKILVVGPNGAGKSTLLKTLLHSTSVSRhpslkisyfsqHHAHNFAPTERVLPYLLTSTRQPESAVRAVLASLN 491
                                        5556789***************666665534799*****999999************99*9999999999999999 PP

                             AAA_30  82 .....................grarlepgtllivDEag.mvdtkqlaallkaaekagakvilv 122
                                                             ++ +l++ +ll+ DE    +d+ ++ al +a+++++  v++v
  gene3022|gene3022|rna3022|rna3022 492 lkkdyqfvsslsggqktrlmlAKLSLDNPDLLLLDEPTnHLDIGSIVALRNAIREYKGAVVCV 554
                                        999****************9977899999*******651679999999999999987777766 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   0.0     0.001       0.3       3      23 ..     130     150 ..     128     205 .. 0.87
   2 !   13.4   0.1   0.00022     0.062       1      24 [.     419     442 ..     419     454 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.001
                                        EEEESTTSSHHHHHHHHHTST CS
                           MMR_HSR1   3 aivGrpNvGKStLinaltgek 23 
                                        ++vG   vGKStL++ l +++
  gene3022|gene3022|rna3022|rna3022 130 GLVGTNGVGKSTLLRWLKNRA 150
                                        79*************998752 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 0.00022
                                        EEEEEESTTSSHHHHHHHHHTSTE CS
                           MMR_HSR1   1 evaivGrpNvGKStLinaltgeka 24 
                                        ++++vG   +GKStL+++l+ +++
  gene3022|gene3022|rna3022|rna3022 419 KILVVGPNGAGKSTLLKTLLHSTS 442
                                        589****************99744 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.0   0.00061      0.18       3      40 ..     131     165 ..     130     213 .. 0.64
   2 ?   -0.7   0.1       6.8     2e+03      40      94 ..     293     344 ..     259     376 .. 0.69
   3 !   11.7   0.0     0.001       0.3       1      22 [.     420     441 ..     420     527 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00061
                             AAA_18   3 ltGtpGvGKttlakeLskrlgfgvnlrdvakengllle 40 
                                        l Gt GvGK+tl + L++r    + ++ +++++   ++
  gene3022|gene3022|rna3022|rna3022 131 LVGTNGVGKSTLLRWLKNRA---FTSTYLVRQESAWTS 165
                                        89**************9993...444444444444333 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 6.8
                             AAA_18  40 evdpealdeskrldedkldklldaleenssaleegknlvidghlaeleseaakdi 94 
                                        +  ++  de++rl    ++++ ++ e+n +  +    l +d ++++   + +++ 
  gene3022|gene3022|rna3022|rna3022 293 YKGNY--DEYERLAALERANAEREYEKNED-TRRRMQLFVDRFRCNAKRAGMVQS 344
                                        44444..67777777777777777777765.566667788888877766666554 PP

  == domain 3  score: 11.7 bits;  conditional E-value: 0.001
                             AAA_18   1 IlltGtpGvGKttlakeLskrl 22 
                                        Il+ G+ G+GK+tl k L  ++
  gene3022|gene3022|rna3022|rna3022 420 ILVVGPNGAGKSTLLKTLLHST 441
                                        99**************993332 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.0   0.00063      0.18      28      83 ..     131     188 ..     115     331 .. 0.71
   2 !   12.2   0.0   0.00037      0.11      22      43 ..     417     437 ..     407     484 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00063
                             AAA_15  28 liGkNnsGKSsilealdlFlnnkekkn........kkvikiekedleifeniseskdikIdvef 83 
                                        l+G+N++GKS++l+ l   +n+    +        +++ + ++  ++ +++ + ++  +I+v++
  gene3022|gene3022|rna3022|rna3022 131 LVGTNGVGKSTLLRWL---KNRA---FtstylvrqESAWTSAAPACDGTRCAAVDNAARITVKE 188
                                        9***********9999...4433...22455666655556666666666666666666666666 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00037
                             AAA_15  22 seeltvliGkNnsGKSsileal 43 
                                        ++   +++G+N++GKS++l+ l
  gene3022|gene3022|rna3022|rna3022 417 DS-KILVVGPNGAGKSTLLKTL 437
                                        44.899**************99 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0      0.14        40      34      62 ..     127     155 ..     110     166 .. 0.77
   2 !   19.3   0.0   2.3e-06   0.00065      26      78 ..     410     462 ..     403     465 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.14
                              AAA_7  34 kpvllvGptGtGKtviikdllkkldkeky 62 
                                            lvG+ G+GK+++++ l ++  +++y
  gene3022|gene3022|rna3022|rna3022 127 LVYGLVGTNGVGKSTLLRWLKNRAFTSTY 155
                                        55569**********99886665554555 PP

  == domain 2  score: 19.3 bits;  conditional E-value: 2.3e-06
                              AAA_7  26 lelllknkkpvllvGptGtGKtviikdllkkldkekylsltinfsaqtsanql 78 
                                        l++++k + ++l+vGp G GK++++k+ll++ + +++ sl+i+  +q +a+++
  gene3022|gene3022|rna3022|rna3022 410 LNMIIKGDSKILVVGPNGAGKSTLLKTLLHSTSVSRHPSLKISYFSQHHAHNF 462
                                        688999***************************99999999999999888765 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.0    0.0056       1.6       4      28 ..     131     155 ..     129     174 .. 0.88
   2 !   13.7   0.0   0.00019     0.054       1      38 [.     419     455 ..     419     468 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0056
                                        EESSTTSSHHHHHHCHCT-CCC-EE CS
                                Roc   4 lvGdsgvGKtsllkrfvedkfseke 28 
                                        lvG +gvGK++ll+ + ++ f++++
  gene3022|gene3022|rna3022|rna3022 131 LVGTNGVGKSTLLRWLKNRAFTSTY 155
                                        89*************9999998776 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 0.00019
                                        EEEEESSTTSSHHHHHHCHCT-CCC-EEETTTTEEEEE CS
                                Roc   1 KvvlvGdsgvGKtsllkrfvedkfsekekstigvdflt 38 
                                        K+++vG +g+GK++llk +++++  +++ + + +++++
  gene3022|gene3022|rna3022|rna3022 419 KILVVGPNGAGKSTLLKTLLHSTSVSRH-PSLKISYFS 455
                                        9*******************88875554.444455444 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.0    0.0035         1      11      39 ..     117     146 ..     100     159 .. 0.73
   2 !   14.4   0.3   0.00014     0.041      22      37 ..     420     435 ..     406     441 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0035
                             AAA_23  11 rdqeidFskg.ltlItGpNGaGKTTildAi 39 
                                        +d ++ + +g ++ ++G NG GK+T+l+ +
  gene3022|gene3022|rna3022|rna3022 117 KDGSLCLRRGlVYGLVGTNGVGKSTLLRWL 146
                                        555555555524589***********9866 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 0.00014
                             AAA_23  22 tlItGpNGaGKTTild 37 
                                         l++GpNGaGK+T+l 
  gene3022|gene3022|rna3022|rna3022 420 ILVVGPNGAGKSTLLK 435
                                        589***********96 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.0    0.0017      0.49       4      31 ..     131     162 ..     129     203 .. 0.75
   2 ?   -1.3   0.1       8.1   2.3e+03      49      80 ..     300     331 ..     286     359 .. 0.75
   3 !   11.0   0.0    0.0013      0.36       1      43 [.     419     462 ..     419     488 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0017
                             AAA_28   4 itGgestGKTtlleaLaar....gypvv.pEaa 31 
                                        ++G+ + GK+tll+ L++r     y  v +E+a
  gene3022|gene3022|rna3022|rna3022 131 LVGTNGVGKSTLLRWLKNRaftsTY-LVrQESA 162
                                        78***************99765333.3347776 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 8.1
                             AAA_28  49 vedllafaervleeqleeeaaaaankvlfcDr 80 
                                        +e+l a++++  e ++e+ ++++ +  lf+Dr
  gene3022|gene3022|rna3022|rna3022 300 YERLAALERANAEREYEKNEDTRRRMQLFVDR 331
                                        45667777776666667777777777777777 PP

  == domain 3  score: 11.0 bits;  conditional E-value: 0.0013
                             AAA_28   1 kivitGgestGKTtlleaLaar.gypvvpEaareileeklakge 43 
                                        ki ++G+ ++GK+tll+ L     ++ +p     ++++++a ++
  gene3022|gene3022|rna3022|rna3022 419 KILVVGPNGAGKSTLLKTLLHStSVSRHPSLKISYFSQHHAHNF 462
                                        699*************9987432666777777777777766665 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.0    0.0092       2.7       4      33 ..     131     162 ..     128     205 .. 0.77
   2 !   13.5   0.0   0.00021     0.062       2      22 ..     420     440 ..     420     468 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0092
                             AAA_33   4 lvGlpGsGKstlaerllkklg...avllssdtl 33 
                                        lvG +G+GKstl++ l k+++   ++l+++ ++
  gene3022|gene3022|rna3022|rna3022 131 LVGTNGVGKSTLLRWL-KNRAftsTYLVRQESA 162
                                        79***********955.4544477777877765 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 0.00021
                             AAA_33   2 vllvGlpGsGKstlaerllkk 22 
                                        +l+vG++G+GKstl++ ll  
  gene3022|gene3022|rna3022|rna3022 420 ILVVGPNGAGKSTLLKTLLHS 440
                                        689**************9854 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.1      0.11        33       4      24 ..     128     148 ..     125     195 .. 0.84
   2 ?   -1.3   0.0       7.2   2.1e+03      60      89 ..     232     261 ..     184     300 .. 0.67
   3 !   12.8   0.0   0.00031     0.089       5      57 ..     420     473 ..     417     552 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.11
                             AAA_14   4 ilvitGaRrvGKTtllkqlik 24 
                                        ++ ++G   vGK+tll+ l +
  gene3022|gene3022|rna3022|rna3022 128 VYGLVGTNGVGKSTLLRWLKN 148
                                        67899**********986644 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 7.2
                             AAA_14  60 lkeekktylflDEiqevpew..ekalkslvde 89 
                                        l+   +++l+lDE  ++ ++   ++l + + +
  gene3022|gene3022|rna3022|rna3022 232 LS--PTNLLLLDEPTNMLDLpsIDFLERALAK 261
                                        32..4678999998887554113445555544 PP

  == domain 3  score: 12.8 bits;  conditional E-value: 0.00031
                             AAA_14   5 lvitGaRrvGKTtllkqlikell...vkkesilyinldderdkkladpekllelil 57 
                                        ++++G+  +GK+tllk+l+++      ++ +i y++  + ++   a +e++l ++l
  gene3022|gene3022|rna3022|rna3022 420 ILVVGPNGAGKSTLLKTLLHSTSvsrHPSLKISYFSQHHAHNF--APTERVLPYLL 473
                                        6899***************998855555555555554444442..22233444444 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0     0.026       7.5       3      28 ..     127     151 ..     125     224 .. 0.85
   2 !   12.0   0.0   0.00043      0.12       4      22 ..     419     437 ..     417     447 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.026
                             AAA_24   3 lkiliyGpsgiGKTtlakelgpkplf 28 
                                        l + ++G +g+GK+tl++ l ++ +f
  gene3022|gene3022|rna3022|rna3022 127 LVYGLVGTNGVGKSTLLRWL-KNRAF 151
                                        567899***********999.55444 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00043
                             AAA_24   4 kiliyGpsgiGKTtlakel 22 
                                        kil++Gp+g+GK+tl+k+l
  gene3022|gene3022|rna3022|rna3022 419 KILVVGPNGAGKSTLLKTL 437
                                        89***************99 PP

>> Septin  Septin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0      0.16        47       9      32 ..     131     154 ..     127     186 .. 0.81
   2 !   13.6   0.0   0.00011     0.031       6      32 ..     419     445 ..     415     469 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.16
                                        EEEBTTSSCCCCCCTTSSSS---- CS
                             Septin   9 vvGesglGkttlintlfetdliee 32 
                                        +vG++g+Gk+tl++ l ++  +++
  gene3022|gene3022|rna3022|rna3022 131 LVGTNGVGKSTLLRWLKNRAFTST 154
                                        69***********99887776665 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 0.00011
                                        EEEEEEBTTSSCCCCCCTTSSSS---- CS
                             Septin   6 tlmvvGesglGkttlintlfetdliee 32 
                                         ++vvG +g Gk+tl++tl++++ +++
  gene3022|gene3022|rna3022|rna3022 419 KILVVGPNGAGKSTLLKTLLHSTSVSR 445
                                        69*****************98876655 PP

>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0     0.034       9.7      62      92 ..     131     161 ..     110     169 .. 0.86
   2 !   10.9   0.0   0.00059      0.17      52      83 ..     412     443 ..     398     454 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.034
                                        EEESSTSTHHHHHHHHHHHSSSEEEEESSSS CS
                                MCM  62 lvgdpgtaKsqlLkyveklapravytsgkgs 92 
                                        lvg  g++Ks+lL+ +++ a +++y   + s
  gene3022|gene3022|rna3022|rna3022 131 LVGTNGVGKSTLLRWLKNRAFTSTYLVRQES 161
                                        89****************9999999877765 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00059
                                        SBBCSS-EEEEEESSTSTHHHHHHHHHHHSSS CS
                                MCM  52 tklrgdinvllvgdpgtaKsqlLkyveklapr 83 
                                        + ++gd ++l+vg  g +Ks+lLk++ + ++ 
  gene3022|gene3022|rna3022|rna3022 412 MIIKGDSKILVVGPNGAGKSTLLKTLLHSTSV 443
                                        5699********************98766555 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0     0.053        15       3      22 ..     131     150 ..     129     247 .. 0.75
   2 !   11.2   0.0    0.0013      0.38       1      25 [.     420     444 ..     420     528 .. 0.64

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.053
                                        EESSTTSSHHHHHHHHHHHH CS
                                AAA   3 lyGppGtGKTllakavakel 22 
                                        l+G+ G+GK++l + + + +
  gene3022|gene3022|rna3022|rna3022 131 LVGTNGVGKSTLLRWLKNRA 150
                                        89************998886 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.0013
                                        EEEESSTTSSHHHHHHHHHHHHTHE CS
                                AAA   1 vllyGppGtGKTllakavakelgve 25 
                                        +l++Gp G GK++l k + ++++v+
  gene3022|gene3022|rna3022|rna3022 420 ILVVGPNGAGKSTLLKTLLHSTSVS 444
                                        699****************998633 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.1       0.1        30      29      50 ..     122     143 ..     112     148 .. 0.83
   2 ?   -2.2   0.0       8.9   2.6e+03     172     188 ..     255     271 ..     221     271 .. 0.75
   3 !   11.0   0.0   0.00078      0.22      29      66 ..     413     461 ..     399     554 .. 0.71

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.1
                             AAA_25  29 llpagelallaGapgtGKttla 50 
                                        +l++g +  l+G  g+GK+tl+
  gene3022|gene3022|rna3022|rna3022 122 CLRRGLVYGLVGTNGVGKSTLL 143
                                        5677888889**********97 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 8.9
                             AAA_25 172 leriarrtgaavllvhH 188
                                        ler  ++t+ +vl+v H
  gene3022|gene3022|rna3022|rna3022 255 LERALAKTNKTVLVVSH 271
                                        45555677777777777 PP

  == domain 3  score: 11.0 bits;  conditional E-value: 0.00078
                             AAA_25  29 llpagelallaGapgtGKttlaldlalava.tGkpwlg..........p 66 
                                        ++  ++ +l++G+ g+GK+tl+  l ++++ + +p l+          +
  gene3022|gene3022|rna3022|rna3022 413 IIKGDSKILVVGPNGAGKSTLLKTLLHSTSvSRHPSLKisyfsqhhahN 461
                                        456678899*************999999887667666655555544443 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.0     0.022       6.3       4      34 ..     131     162 ..     130     183 .. 0.82
   2 ?   -1.1   0.1         6   1.7e+03      43      75 ..     330     383 ..     301     384 .. 0.59
   3 !    8.8   0.0    0.0052       1.5       2      23 ..     420     441 ..     419     454 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.022
                                        EE--SSSSHHHHHHHGGGGB.S--EEEEE--T CS
                              AAA_5   4 LvGppGtgKselaerlaaal.nreveyvqltr 34 
                                        LvG  G+gKs+l + l+ +  ++++++ q ++
  gene3022|gene3022|rna3022|rna3022 131 LVGTNGVGKSTLLRWLKNRAfTSTYLVRQESA 162
                                        89************999887566666666555 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 6
                                        --B--.........--------.....................G-SEEEEESGG CS
                              AAA_5  43 grreikngttslvdsplvraar.....................egeilvlDEve 75 
                                         r + + +++ +v+s l++ ar                     +gei++ ++v+
  gene3022|gene3022|rna3022|rna3022 330 DRFRCNAKRAGMVQSRLKTMARmdtvqlenadrqivvriaggmKGEIVRAEGVD 383
                                        444555666666666666666666666666666666666667777777777775 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.0052
                                        EEEE--SSSSHHHHHHHGGGGB CS
                              AAA_5   2 vlLvGppGtgKselaerlaaal 23 
                                        +l+vGp G gKs+l + l++ +
  gene3022|gene3022|rna3022|rna3022 420 ILVVGPNGAGKSTLLKTLLHST 441
                                        799***************9977 PP

>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0      0.84   2.4e+02      19      40 ..     131     152 ..     124     156 .. 0.84
   2 !   14.2   0.0   7.4e-05     0.021      12      46 ..     415     449 ..     405     458 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.84
                                        EEESTTSSHHHHHHHHHHSSCE CS
                                Arf  19 llGLDnaGKtTilkklkleelv 40 
                                        l+G  + GK+T+l  lk+  ++
  gene3022|gene3022|rna3022|rna3022 131 LVGTNGVGKSTLLRWLKNRAFT 152
                                        5788999*********998776 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 7.4e-05
                                        TTEEEEEEEESTTSSHHHHHHHHHHSSCEECSSSS CS
                                Arf  12 kkelrilllGLDnaGKtTilkklkleelvttvPTi 46 
                                        k + +il++G  +aGK+T+lk l +   v+  P +
  gene3022|gene3022|rna3022|rna3022 415 KGDSKILVVGPNGAGKSTLLKTLLHSTSVSRHPSL 449
                                        5689*********************9999999976 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.0    0.0091       2.6       4      47 ..     129     180 ..     127     216 .. 0.69
   2 !    8.1   0.0    0.0064       1.8       3      24 ..     419     440 ..     417     451 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0091
                                        EEEEESTTSSHHHHHHHHHH......HHHHT..TS-EEEEEESTSSTTHHHH CS
                              SRP54   4 illvGlqGaGKTttlaKLaa......llkke..gkkvllvaaDtfRaaAveQ 47 
                                        + lvG++G+GK t l  L +      +l ++  + + +  a+D  R aAv+ 
  gene3022|gene3022|rna3022|rna3022 129 YGLVGTNGVGKSTLLRWLKNraftstYLVRQesAWTSAAPACDGTRCAAVDN 180
                                        559***********98886511111144444345566777899999999985 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0064
                                        EEEEEESTTSSHHHHHHHHHHH CS
                              SRP54   3 villvGlqGaGKTttlaKLaal 24 
                                         il+vG++GaGK t l  L + 
  gene3022|gene3022|rna3022|rna3022 419 KILVVGPNGAGKSTLLKTLLHS 440
                                        69************99988775 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.1      0.79   2.3e+02      45      58 ..     132     145 ..     129     148 .. 0.89
   2 !   15.1   0.1   3.9e-05     0.011      39      69 ..     413     447 ..     398     449 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.79
                                        E--TTSSHHHHHHH CS
                       FtsK_SpoIIIE  45 aGatgsGKStalnt 58 
                                        +G+ g GKSt l+ 
  gene3022|gene3022|rna3022|rna3022 132 VGTNGVGKSTLLRW 145
                                        8**********985 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 3.9e-05
                                        -.....SEEEE--TTSSHHHHHHHHHHHHHTT--T CS
                       FtsK_SpoIIIE  39 a....shllvaGatgsGKStalntLilSlatthtP 69 
                                             s +lv+G  g GKSt l+tL+ S  +  +P
  gene3022|gene3022|rna3022|rna3022 413 IikgdSKILVVGPNGAGKSTLLKTLLHSTSVSRHP 447
                                        34444789*******************98777777 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0     0.043        13       3      36 ..     131     156 ..     129     208 .. 0.63
   2 !   10.0   0.0     0.003      0.86       1      22 [.     420     441 ..     420     463 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.043
                       RNA_helicase   3 lyGpsgeGKStlakeLakallkklklkkkdsvys 36 
                                        l+G +g+GKStl + L ++  ++         y 
  gene3022|gene3022|rna3022|rna3022 131 LVGTNGVGKSTLLRWLKNRAFTST--------YL 156
                                        689**********99766655333........22 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.003
                       RNA_helicase   1 iwlyGpsgeGKStlakeLakal 22 
                                        i+++Gp+g GKStl k+L ++ 
  gene3022|gene3022|rna3022|rna3022 420 ILVVGPNGAGKSTLLKTLLHST 441
                                        6899*************87665 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0     0.018       5.1      21      40 ..     127     146 ..     116     163 .. 0.85
   2 !    8.9   0.0    0.0027      0.77      17      49 ..     417     445 ..     406     527 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.018
                                        EEEEEEESTTSSHHHHHHHH CS
                             NB-ARC  21 lvvalvGmgGvGKttlakqi 40 
                                        lv +lvG  GvGK+tl++  
  gene3022|gene3022|rna3022|rna3022 127 LVYGLVGTNGVGKSTLLRWL 146
                                        5779************9755 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0027
                                        TSCSEEEEEEESTTSSHHHHHHHHCCSHCCCCC CS
                             NB-ARC  17 elqslvvalvGmgGvGKttlakqilnksdeveg 49 
                                        +++   + +vG  G GK+tl+k  l++  +v +
  gene3022|gene3022|rna3022|rna3022 417 DSK---ILVVGPNGAGKSTLLKTLLHS-TSVSR 445
                                        444...789***************999.55554 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.1     0.078        23       2      20 ..     128     146 ..     127     160 .. 0.84
   2 !   11.5   0.1   0.00056      0.16       3      24 ..     420     441 ..     418     451 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.078
                                        EEEEEESTTCCHHHHHHHH CS
                               cobW   2 vtvltGflGsGKTtLlnhl 20 
                                        v++l+G  G GK+tLl+ l
  gene3022|gene3022|rna3022|rna3022 128 VYGLVGTNGVGKSTLLRWL 146
                                        7899************865 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00056
                                        EEEEESTTCCHHHHHHHHHCT- CS
                               cobW   3 tvltGflGsGKTtLlnhllenr 24 
                                        ++++G+ G+GK+tLl++ll+ +
  gene3022|gene3022|rna3022|rna3022 420 ILVVGPNGAGKSTLLKTLLHST 441
                                        6799**************9554 PP

>> VirE  Virulence-associated protein E
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0     0.051        15      54      81 ..     128     155 ..     123     206 .. 0.85
   2 ?    2.7   0.3      0.31        90     115     162 ..     279     325 ..     256     349 .. 0.87
   3 ?    4.8   0.0     0.071        21      45      72 ..     410     437 ..     387     444 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.051
                               VirE  54 vlvLvGkqgsgKstfleklgeewftdsl 81 
                                        v  LvG  g+gKst+l+ l +  ft + 
  gene3022|gene3022|rna3022|rna3022 128 VYGLVGTNGVGKSTLLRWLKNRAFTSTY 155
                                        6779***************888887665 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.31
                               VirE 115 iKafitrkkdkfrapygrkvedfpresvlvgttNedeflkDktGeRRf 162
                                          +fi r kd +r+ y+ + +++ r + l +   e+e+ k +   RR 
  gene3022|gene3022|rna3022|rna3022 279 TCKFIIRMKDGLRV-YKGNYDEYERLAALERANAEREYEKNEDTRRRM 325
                                        568999*9999986.9999*********************99988885 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.071
                               VirE  45 lePgiKfDfvlvLvGkqgsgKstflekl 72 
                                        l+  iK D  + +vG+ g gKst+l++l
  gene3022|gene3022|rna3022|rna3022 410 LNMIIKGDSKILVVGPNGAGKSTLLKTL 437
                                        55678999999**************998 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0      0.44   1.3e+02      31      48 ..     131     148 ..     102     158 .. 0.83
   2 !   11.9   0.0   0.00043      0.13      29      46 ..     420     437 ..     407     441 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.44
                             AAA_27  31 iyGpNEAGKstalrAisd 48 
                                        ++G+N  GKst+lr +++
  gene3022|gene3022|rna3022|rna3022 131 LVGTNGVGKSTLLRWLKN 148
                                        689*********997765 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00043
                             AAA_27  29 hliyGpNEAGKstalrAi 46 
                                         l++GpN AGKst+l+ +
  gene3022|gene3022|rna3022|rna3022 420 ILVVGPNGAGKSTLLKTL 437
                                        59************9987 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.1      0.13        38      58      77 ..     131     150 ..     128     158 .. 0.86
   2 !   10.0   0.0    0.0012      0.35      43      78 ..     409     442 ..     402     463 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.13
                             DUF815  58 LwGarGtGKSslvkallney 77 
                                        L+G+ G+GKS+l++ l n++
  gene3022|gene3022|rna3022|rna3022 131 LVGTNGVGKSTLLRWLKNRA 150
                                        89***********9998865 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0012
                             DUF815  43 nteqfleglpannvLLwGarGtGKSslvkallneya 78 
                                        n +  ++g   +++L++G  G+GKS+l+k+ll++++
  gene3022|gene3022|rna3022|rna3022 409 NLNMIIKGD--SKILVVGPNGAGKSTLLKTLLHSTS 442
                                        555555554..589*****************99865 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0      0.84   2.4e+02       3      23 ..     131     151 ..     130     292 .. 0.82
   2 !   12.1   0.0   0.00051      0.15       1      28 [.     420     447 ..     420     529 .. 0.67

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.84
                                        EEEBTTTTHHHHHHHHHTS-- CS
                          Dynamin_N   3 vvGsqSsGKSSvlnaLlgedi 23 
                                        +vG+   GKS++l  L  +++
  gene3022|gene3022|rna3022|rna3022 131 LVGTNGVGKSTLLRWLKNRAF 151
                                        689999999999987776665 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00051
                                        EEEEEBTTTTHHHHHHHHHTS--S---S CS
                          Dynamin_N   1 iavvGsqSsGKSSvlnaLlgedilprgp 28 
                                        i+vvG   +GKS++l  Ll++    r+p
  gene3022|gene3022|rna3022|rna3022 420 ILVVGPNGAGKSTLLKTLLHSTSVSRHP 447
                                        89*****************998655555 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0      0.21        61       2      20 ..     132     150 ..     131     166 .. 0.84
   2 ?    1.1   0.0      0.95   2.8e+02     116     144 ..     257     285 ..     173     354 .. 0.71
   3 !    7.8   0.0     0.009       2.6       1      22 [.     422     443 ..     422     451 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.21
                         ATP_bind_1   2 vGpaGsGKttfvgalseil 20 
                                        vG+ G+GK+t+ + l + +
  gene3022|gene3022|rna3022|rna3022 132 VGTNGVGKSTLLRWLKNRA 150
                                        8**********98887655 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.95
                         ATP_bind_1 116 eeLesefalvvvyLvDsqrltdptkfisg 144
                                        ++L+++ ++v v+  D  +l+++ kfi +
  gene3022|gene3022|rna3022|rna3022 257 RALAKTNKTVLVVSHDIAFLNSTCKFIIR 285
                                        45555555666666666666666666544 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.009
                         ATP_bind_1   1 vvGpaGsGKttfvgalseilel 22 
                                        vvGp G+GK+t+ ++l   ++ 
  gene3022|gene3022|rna3022|rna3022 422 VVGPNGAGKSTLLKTLLHSTSV 443
                                        89************99876665 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0       0.4   1.2e+02      22      43 ..     128     149 ..     121     162 .. 0.78
   2 ?    9.7   0.0    0.0025      0.72      21      62 ..     418     462 ..     407     515 .. 0.71

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.4
                           ATPase_2  22 iyfiYGpegsGKtaLlkeiien 43 
                                        +y + G  g+GK++Ll+ + ++
  gene3022|gene3022|rna3022|rna3022 128 VYGLVGTNGVGKSTLLRWLKNR 149
                                        55667899********976555 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0025
                           ATPase_2  21 eiyfiYGpegsGKtaLlkeiienledkdk...yviyyialreesi 62 
                                        + +++ Gp g GK++Llk ++   + +     ++ y+++ + ++ 
  gene3022|gene3022|rna3022|rna3022 418 SKILVVGPNGAGKSTLLKTLLHSTSVSRHpslKISYFSQHHAHNF 462
                                        446777************998776444442335555555555554 PP

>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.0     0.014         4       4      29 ..     131     156 ..     129     177 .. 0.86
   2 ?    5.4   0.0     0.042        12       1      22 [.     419     440 ..     419     463 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.014
                                        EEESTTSSHHHHHHHHHHSSCSSSCT CS
                                Ras   4 lvGdsavGKtslllrfvkdkFkeeye 29 
                                        lvG ++vGK++ll    +  F+++y 
  gene3022|gene3022|rna3022|rna3022 131 LVGTNGVGKSTLLRWLKNRAFTSTYL 156
                                        79***********9999999999885 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.042
                                        EEEEEESTTSSHHHHHHHHHHS CS
                                Ras   1 KlvlvGdsavGKtslllrfvkd 22 
                                        K+++vG ++ GK++ll    ++
  gene3022|gene3022|rna3022|rna3022 419 KILVVGPNGAGKSTLLKTLLHS 440
                                        89*************9887665 PP

>> CLP1_P  mRNA cleavage and polyadenylation factor CLP1 P-loop
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.1    0.0026      0.76       1      22 [.     133     154 ..     133     157 .. 0.88
   2 ?    4.1   0.1      0.12        34       1      17 [.     424     440 ..     424     449 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0026
                             CLP1_P   1 GpkdsGKSTlarlLlNyalrkg 22 
                                        G + +GKSTl r+L N+a+ ++
  gene3022|gene3022|rna3022|rna3022 133 GTNGVGKSTLLRWLKNRAFTST 154
                                        7789*************98765 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.12
                             CLP1_P   1 GpkdsGKSTlarlLlNy 17 
                                        Gp+ +GKSTl ++Ll  
  gene3022|gene3022|rna3022|rna3022 424 GPNGAGKSTLLKTLLHS 440
                                        899***********965 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0      0.24        70       4      19 ..     131     146 ..     128     158 .. 0.82
   2 ?    1.1   0.0       1.1   3.2e+02      69     136 ..     208     274 ..     172     304 .. 0.77
   3 ?    6.6   0.1     0.023       6.7       1      21 [.     419     439 ..     419     446 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.24
                                        EE--TTSSHHHHHHHH CS
                           NTPase_1   4 iTGppGvGKtTlvkkv 19 
                                        + G  GvGK+Tl++ +
  gene3022|gene3022|rna3022|rna3022 131 LVGTNGVGKSTLLRWL 146
                                        6799********9765 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 1.1
                                        SEETTEEE-HHHHHHHHHHHHHHHHHHH-EEEE---STTGGG-HHHHHHHHHHHT.TTSEEEEE--SS- CS
                           NTPase_1  69 prvgkyvvdvesfeelalealrkalseadviviDEiGkmElkskkfkeaveevLk.sekpvlavihrrk 136
                                         ++ kyv ++   ++  l+ l+  ls ++++++DE  +m l  ++ ++ +e++L+ ++k vl+v h   
  gene3022|gene3022|rna3022|rna3022 208 KELTKYVCELSGGWQKKLALLKALLSPTNLLLLDEPTNM-LDLPS-IDFLERALAkTNKTVLVVSHDIA 274
                                        567799999999999999999999999999999998777.44443.45667777757777777777654 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.023
                                        EEEEE--TTSSHHHHHHHHHH CS
                           NTPase_1   1 kvfiTGppGvGKtTlvkkvle 21 
                                        k+++ Gp G GK+Tl+k +l+
  gene3022|gene3022|rna3022|rna3022 419 KILVVGPNGAGKSTLLKTLLH 439
                                        58999***********98876 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0      0.13        37       8      56 ..     131     180 ..     127     203 .. 0.79
   2 ?    7.8   0.0    0.0071       2.1       4      35 ..     418     449 ..     415     465 .. 0.74

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.13
                                        EE-STTSSHHHHHHHHHHSS---B---S.S-EEETTG...GGTT-SEEEE CS
                              SRPRB   8 lvGlsdsGKTslftrLttdsvkktvtSq.essaalkvksekgskltliDf 56 
                                        lvG    GK +l+  L + ++++t+    es  +    + +g++++ +D 
  gene3022|gene3022|rna3022|rna3022 131 LVGTNGVGKSTLLRWLKNRAFTSTYLVRqESAWTSAAPACDGTRCAAVDN 180
                                        7999********************98765877777777777777777775 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0071
                                        -EEEEE-STTSSHHHHHHHHHHSS---B---S CS
                              SRPRB   4 pavllvGlsdsGKTslftrLttdsvkktvtSq 35 
                                         ++l+vG+  +GK +l++ L+  +  +   S+
  gene3022|gene3022|rna3022|rna3022 418 SKILVVGPNGAGKSTLLKTLLHSTSVSRHPSL 449
                                        579****************9988665555554 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0      0.34     1e+02      28      54 ..     131     158 ..     124     175 .. 0.79
   2 ?    8.9   0.0    0.0026      0.74      21      47 ..     415     439 ..     403     492 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.34
                                        EEESTTSSHHHHHHHHH.HHCS----HH CS
                            G-alpha  28 llGqseSGKsTilkqlk.llykkgfsee 54 
                                        l+G+++ GKsT+l+ lk + ++ ++  +
  gene3022|gene3022|rna3022|rna3022 131 LVGTNGVGKSTLLRWLKnRAFTSTYLVR 158
                                        79************99976666664443 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0026
                                        ..EEEEEEEESTTSSHHHHHHHHHHHC CS
                            G-alpha  21 krevkllllGqseSGKsTilkqlklly 47 
                                        k + k+l++G ++ GKsT+lk l   +
  gene3022|gene3022|rna3022|rna3022 415 KGDSKILVVGPNGAGKSTLLKTLL--H 439
                                        4578*****************864..4 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       4.9   1.4e+03      27      44 ..     131     148 ..     123     162 .. 0.80
   2 ?   11.6   0.0   0.00058      0.17      12      50 ..     407     445 ..     400     457 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 4.9
                                        EECSTTSSHHHHHHHHHH CS
                    Sigma54_activat  27 itGesGtGKellaraihe 44 
                                        ++G +G+GK++l r + +
  gene3022|gene3022|rna3022|rna3022 131 LVGTNGVGKSTLLRWLKN 148
                                        679999999998776655 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00058
                                        HHHHHHHCTSSS-EEEECSTTSSHHHHHHHHHHHSTTTT CS
                    Sigma54_activat  12 leqikkvaktdlsvlitGesGtGKellaraiheaskrke 50 
                                        ++++++++k d+++l++G +G+GK++l +++ ++++ ++
  gene3022|gene3022|rna3022|rna3022 407 FKNLNMIIKGDSKILVVGPNGAGKSTLLKTLLHSTSVSR 445
                                        6788999*****************988776644444344 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0      0.19        56      18      41 ..     128     151 ..     120     188 .. 0.85
   2 ?    7.7   0.0    0.0065       1.9      19      40 ..     420     441 ..     406     452 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.19
                         Zeta_toxin  18 lillgGqpGAGKselaellkdele 41 
                                        ++ l+G  G GKs+l++ lk++  
  gene3022|gene3022|rna3022|rna3022 128 VYGLVGTNGVGKSTLLRWLKNRAF 151
                                        56699************9998865 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0065
                         Zeta_toxin  19 illgGqpGAGKselaellkdel 40 
                                        il++G  GAGKs+l++ l  ++
  gene3022|gene3022|rna3022|rna3022 420 ILVVGPNGAGKSTLLKTLLHST 441
                                        899************9998876 PP

>> Adeno_IVa2  Adenovirus IVa2 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.65   1.9e+02      86     107 ..     126     146 ..      66     154 .. 0.76
   2 ?    9.2   0.0    0.0016      0.47      91     118 ..     421     448 ..     406     469 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.65
                         Adeno_IVa2  86 qPviGviyGPtGsGksqllrnl 107
                                          v G+  G  G Gks llr l
  gene3022|gene3022|rna3022|rna3022 126 GLVYGL-VGTNGVGKSTLLRWL 146
                                        444454.478899*******87 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0016
                         Adeno_IVa2  91 viyGPtGsGksqllrnlissklisPiPe 118
                                        ++ GP G+Gks ll++l+ s  +s  P 
  gene3022|gene3022|rna3022|rna3022 421 LVVGPNGAGKSTLLKTLLHSTSVSRHPS 448
                                        478****************999998886 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0      0.59   1.7e+02      20      41 ..     127     148 ..     112     196 .. 0.81
   2 ?    8.7   0.0    0.0057       1.7      19      46 ..     417     444 ..     403     462 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.59
                                        EEEEEEESTTSSHHHHHHHHHH CS
                               TsaE  20 dvilLeGdLGaGKTtlvrglak 41 
                                         v  L G  G+GK+tl r l +
  gene3022|gene3022|rna3022|rna3022 127 LVYGLVGTNGVGKSTLLRWLKN 148
                                        567799**********998765 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0057
                                        TEEEEEEESTTSSHHHHHHHHHHHTT-- CS
                               TsaE  19 gdvilLeGdLGaGKTtlvrglakalgve 46 
                                         + il  G+ GaGK+tl + l+++  v+
  gene3022|gene3022|rna3022|rna3022 417 DSKILVVGPNGAGKSTLLKTLLHSTSVS 444
                                        345999****************998876 PP

>> dNK  Deoxynucleoside kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0       0.1        30       5      22 ..     133     150 ..     130     168 .. 0.82
   2 ?    6.5   0.0     0.023       6.6       1      24 [.     420     443 ..     420     471 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.1
                                        ESTTSSHHHHHHHHHCCS CS
                                dNK   5 GnIgaGKstlvklLskkl 22 
                                        G+ g+GKstl+  L++++
  gene3022|gene3022|rna3022|rna3022 133 GTNGVGKSTLLRWLKNRA 150
                                        7779***********987 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.023
                                        EEEEESTTSSHHHHHHHHHCCSTC CS
                                dNK   1 ivveGnIgaGKstlvklLskklgv 24 
                                        i v G+ gaGKstl+k+L + + v
  gene3022|gene3022|rna3022|rna3022 420 ILVVGPNGAGKSTLLKTLLHSTSV 443
                                        6688999*********99777654 PP

>> Ploopntkinase3  P-loop Nucleotide Kinase3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0      0.13        38       5      25 ..     127     148 ..     123     182 .. 0.72
   2 ?    6.9   0.0     0.018       5.2       6      30 ..     420     444 ..     417     494 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.13
                     Ploopntkinase3   5 liy.lvGqPGaGkstlmaeltk 25 
                                        l+y lvG+ G Gkstl+  l +
  gene3022|gene3022|rna3022|rna3022 127 LVYgLVGTNGVGKSTLLRWLKN 148
                                        66669***********988864 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.018
                     Ploopntkinase3   6 iylvGqPGaGkstlmaeltkgfdrs 30 
                                        i +vG  GaGkstl+ +l ++ + s
  gene3022|gene3022|rna3022|rna3022 420 ILVVGPNGAGKSTLLKTLLHSTSVS 444
                                        789************9998765544 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0      0.79   2.3e+02       7      30 ..     135     153 ..     132     197 .. 0.63
   2 ?    9.0   0.0    0.0036         1       2      26 ..     421     444 ..     420     486 .. 0.76

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.79
                    Viral_helicase1   7 pGcGKStlirkllrtsliltvnrp 30 
                                         G GKStl+r l +      + ++
  gene3022|gene3022|rna3022|rna3022 135 NGVGKSTLLRWLKNR-----AFTS 153
                                        699****88877666.....3333 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0036
                    Viral_helicase1   2 vvhGvpGcGKStlirkllrtslilt 26 
                                        +v G  G+GKStl+++ll++  +++
  gene3022|gene3022|rna3022|rna3022 421 LVVGPNGAGKSTLLKTLLHST-SVS 444
                                        677888************992.222 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.3   0.00021     0.062     121     152 ..     409     440 ..     339     447 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00021
                              T2SSE 121 vlrkavrerglilvsGgTgsGKttllyallke 152
                                         l+  ++    ilv G+ g GK+tll +ll+ 
  gene3022|gene3022|rna3022|rna3022 409 NLNMIIKGDSKILVVGPNGAGKSTLLKTLLHS 440
                                        46666777899******************986 PP

>> ABC_ATPase  Predicted ATPase of the ABC class
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0     0.078        23     241     265 ..     122     147 ..     118     152 .. 0.86
   2 ?    5.8   0.1     0.018       5.2     247     266 ..     420     439 ..     411     446 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.078
                                        EE-SS.EEEEEE-TTSSHHHHHHHHH CS
                         ABC_ATPase 241 gipkG.vtlIvGggfhGKsTLLeAle 265
                                         +++G v  +vG++  GKsTLL+ l+
  gene3022|gene3022|rna3022|rna3022 122 CLRRGlVYGLVGTNGVGKSTLLRWLK 147
                                        688998889*************9776 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.018
                                        EEEEE-TTSSHHHHHHHHHH CS
                         ABC_ATPase 247 tlIvGggfhGKsTLLeAlek 266
                                        +l+vG++  GKsTLL+ l +
  gene3022|gene3022|rna3022|rna3022 420 ILVVGPNGAGKSTLLKTLLH 439
                                        689*************9865 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0      0.28        81       6      26 ..     131     151 ..     129     168 .. 0.85
   2 ?    7.3   0.0     0.012       3.5       2      22 ..     418     438 ..     417     454 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.28
                          PduV-EutP   6 liGkvgsGKttLtqalkgeel 26 
                                        l+G+ g+GK tL + lk++++
  gene3022|gene3022|rna3022|rna3022 131 LVGTNGVGKSTLLRWLKNRAF 151
                                        79**************99765 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.012
                          PduV-EutP   2 kkilliGkvgsGKttLtqalk 22 
                                        +kil++G+ g+GK tL ++l 
  gene3022|gene3022|rna3022|rna3022 418 SKILVVGPNGAGKSTLLKTLL 438
                                        69**************99875 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0         5   1.4e+03      27      42 ..     131     146 ..     129     151 .. 0.87
   2 ?    9.5   0.0     0.002      0.59      15      42 ..     410     437 ..     405     455 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 5
                       Mg_chelatase  27 lvGppGsGKtmlakrl 42 
                                        lvG+ G GK+ l + l
  gene3022|gene3022|rna3022|rna3022 131 LVGTNGVGKSTLLRWL 146
                                        79********998766 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.002
                       Mg_chelatase  15 leiaaaGgHnlllvGppGsGKtmlakrl 42 
                                        l++ + G  ++l+vGp G+GK+ l k l
  gene3022|gene3022|rna3022|rna3022 410 LNMIIKGDSKILVVGPNGAGKSTLLKTL 437
                                        67778999***************98877 PP

>> KAP_NTPase  KAP family P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       2.9   8.3e+02     235     285 ..      17      63 ..       9      89 .. 0.69
   2 ?    4.1   0.1     0.081        23      18      43 ..     124     149 ..     114     242 .. 0.85
   3 ?    4.2   0.0     0.071        21      23      62 ..     420     455 ..     405     481 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 2.9
                         KAP_NTPase 235 hdYlekiiqlpvyLppsglrevkkvlmeaveaseettesesrdetlgnsas 285
                                        ++Yl+++  +p++    +++ev+ +l++ ++++     ++++   l+  +s
  gene3022|gene3022|rna3022|rna3022  17 KEYLKNLLNYPFT----DNEEVQHALSAYFSHINIPLLEKDEPLPLDTPVS 63 
                                        6899999999996....7777777777777777777766666655555555 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.081
                         KAP_NTPase  18 atpivvgLygkWGsGKssllnklede 43 
                                        ++++v gL g  G+GKs+ll  l++ 
  gene3022|gene3022|rna3022|rna3022 124 RRGLVYGLVGTNGVGKSTLLRWLKNR 149
                                        789999**************988875 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.071
                         KAP_NTPase  23 vgLygkWGsGKssllnkledelkefakpvrflfaefnaws 62 
                                        + + g+ G+GKs+ll+ l ++ +      r+   +++++s
  gene3022|gene3022|rna3022|rna3022 420 ILVVGPNGAGKSTLLKTLLHSTSVS----RHPSLKISYFS 455
                                        45556779**********9998887....44444444444 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.0    0.0075       2.2      26      49 ..     123     146 ..     107     156 .. 0.79
   2 ?    1.9   0.0       0.3        88      32      50 ..     420     438 ..     402     445 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0075
                                        -S-SEEEEEEE-TTSSHHHHHHHH CS
                               MeaB  26 aGraqvvGltGvPGaGkstlveal 49 
                                          r  v Gl G+ G+Gkstl+  l
  gene3022|gene3022|rna3022|rna3022 123 LRRGLVYGLVGTNGVGKSTLLRWL 146
                                        5578899*************9766 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.3
                                        EEEEE-TTSSHHHHHHHHH CS
                               MeaB  32 vGltGvPGaGkstlvealg 50 
                                        + + G  GaGkstl++ l 
  gene3022|gene3022|rna3022|rna3022 420 ILVVGPNGAGKSTLLKTLL 438
                                        5578999*******99885 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0       2.3   6.7e+02      47      66 ..     128     147 ..     102     167 .. 0.77
   2 ?   -1.7   0.0       7.8   2.3e+03       6      49 ..     325     366 ..     321     372 .. 0.69
   3 ?    8.2   0.0    0.0076       2.2      48      67 ..     420     439 ..     410     454 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 2.3
                              Rad17  47 iLLisGPsGCgkstvvkvLs 66 
                                        +  + G  G gkst ++ L 
  gene3022|gene3022|rna3022|rna3022 128 VYGLVGTNGVGKSTLLRWLK 147
                                        566899*********99885 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 7.8
                              Rad17   6 nelWfekykPekaeelavhkkkieevkewlkadvLesrkkriLL 49 
                                         +l++++++ + ++   + +++++ +   +++  Le++ ++i++
  gene3022|gene3022|rna3022|rna3022 325 MQLFVDRFRCNAKRAG-MVQSRLKTMA-RMDTVQLENADRQIVV 366
                                        6777788877766544.4456777664.6999999*99999754 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.0076
                              Rad17  48 LLisGPsGCgkstvvkvLsk 67 
                                        +L+ GP G gkst +k L  
  gene3022|gene3022|rna3022|rna3022 420 ILVVGPNGAGKSTLLKTLLH 439
                                        5899************9965 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.1      0.28        81      15     135 ..     131     269 ..     124     333 .. 0.64
   2 ?    6.4   0.0     0.037        11      11      39 ..     418     446 ..     411     544 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.28
                             AAA_19  15 vtaGpGtGKTrvlkhivallvelggvkp.............eeillvaftgrAakelrerlaalgaeatTiHrlal 77 
                                        +++  G GK+++l+   + +   + + +             +   ++a+ + A   ++e l+++++   T   l  
  gene3022|gene3022|rna3022|rna3022 131 LVGTNGVGKSTLLRWLKNRAFTSTYL-VrqesawtsaapacDGTRCAAVDNAARITVKEYLKEYDECEATKM-LVQ 204
                                        66677777777776544333332222.112333445555555555666666666666666655444333322.323 PP

                             AAA_19  78 ldfddlltealelle.....eaeeekklqeee.llivDE.fqdvd.elqyrLlkallgekkklllv 135
                                         +f++l++   el       + +  k l + + ll+ DE + ++d + +  L +al++++k++l+v
  gene3022|gene3022|rna3022|rna3022 205 FGFKELTKYVCEL-SggwqkKLALLKALLSPTnLLLLDEpTNMLDlPSIDFLERALAKTNKTVLVV 269
                                        3444444222222.3455442233334445555999999667888666666666676666666665 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.037
                             AAA_19  11 kvllvtaGpGtGKTrvlkhivallvelgg 39 
                                        + +lv+++ G GK+++lk+ ++     ++
  gene3022|gene3022|rna3022|rna3022 418 SKILVVGPNGAGKSTLLKTLLHSTSVSRH 446
                                        56899**************9988776664 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0      0.66   1.9e+02       2      19 ..     129     146 ..     128     159 .. 0.84
   2 ?    7.1   0.0     0.017       4.9       2      40 ..     420     462 ..     419     467 .. 0.73

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.66
                               MobB   2 lgivgksgsGKTtLlekl 19 
                                         g+vg++g GK tLl  l
  gene3022|gene3022|rna3022|rna3022 129 YGLVGTNGVGKSTLLRWL 146
                                        589***********9755 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.017
                               MobB   2 lgivgksgsGKTtLleklipel...karglrvgti.Khahhgf 40 
                                        + +vg +g+GK tLl+ l++     ++  l++++   h++h+f
  gene3022|gene3022|rna3022|rna3022 420 ILVVGPNGAGKSTLLKTLLHSTsvsRHPSLKISYFsQHHAHNF 462
                                        5689**************9765111455788887635666776 PP

>> Guanylate_kin  Guanylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0    0.0015      0.44       5      27 ..     420     442 ..     417     456 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0015
                                        EEEESTTTSSHHHHHHHHHHHST CS
                      Guanylate_kin   5 vvlvgpsgaGksslkkaLlselp 27 
                                        + +vgp+gaGks+l k+Ll++ +
  gene3022|gene3022|rna3022|rna3022 420 ILVVGPNGAGKSTLLKTLLHSTS 442
                                        789****************9875 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0      0.65   1.9e+02       1      16 [.     132     147 ..     132     168 .. 0.85
   2 ?   -1.1   0.0       8.4   2.4e+03      70      96 ..     323     349 ..     292     372 .. 0.59
   3 ?    6.0   0.0     0.054        16       1      17 [.     423     439 ..     423     453 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.65
                                        EE-TTSSHHHHHHHHH CS
                             AAA_17   1 lGgPGsGKgtqceklv 16 
                                        +G  G+GK+t+++ l+
  gene3022|gene3022|rna3022|rna3022 132 VGTNGVGKSTLLRWLK 147
                                        6999*******97665 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 8.4
                                        HSSEEEEEE-SEEEETTEEEESSHHHH CS
                             AAA_17  70 kkkgvlvdghprikeqagfldglpkev 96 
                                        +++++ vd + ++ ++ag+++   k +
  gene3022|gene3022|rna3022|rna3022 323 RRMQLFVDRFRCNAKRAGMVQSRLKTM 349
                                        555677777777777666655444433 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.054
                                        EE-TTSSHHHHHHHHHH CS
                             AAA_17   1 lGgPGsGKgtqceklve 17 
                                        +G+ G+GK+t++++l +
  gene3022|gene3022|rna3022|rna3022 423 VGPNGAGKSTLLKTLLH 439
                                        79**********99875 PP

>> DAP3  Mitochondrial ribosomal death-associated protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0     0.055        16      28      54 ..     131     157 ..     126     162 .. 0.90
   2 ?    3.9   0.1     0.085        25      24      45 ..     418     439 ..     412     451 .. 0.88
   3 ?    0.8   0.0      0.74   2.2e+02      99     134 ..     485     519 ..     471     524 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.055
                                        EE-SSSSSTTTTHHHHHHHGGGS--EE CS
                               DAP3  28 ltGekgsGKSvlLlqalayAlekgwvv 54 
                                        l G +g+GKS+lL  +   A+++ ++v
  gene3022|gene3022|rna3022|rna3022 131 LVGTNGVGKSTLLRWLKNRAFTSTYLV 157
                                        779**********99999999998877 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.085
                                        -EEEEE-SSSSSTTTTHHHHHH CS
                               DAP3  24 krlvltGekgsGKSvlLlqala 45 
                                         ++++ G +g GKS+lL  +l+
  gene3022|gene3022|rna3022|rna3022 418 SKILVVGPNGAGKSTLLKTLLH 439
                                        68999***********988777 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.74
                                        HHHTT-EE-S-EE-SSS-EE-SSEEHHHHHHHHHH- CS
                               DAP3  99 evLkklklskeyellkresvkagstLleLvklgikd 134
                                        +vL++l+l+k+y+++  ++  +++t l L+kl  ++
  gene3022|gene3022|rna3022|rna3022 485 AVLASLNLKKDYQFV-SSLSGGQKTRLMLAKLSLDN 519
                                        79************9.77777777777777777665 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.1      0.56   1.6e+02      27      47 ..     130     150 ..     128     157 .. 0.85
   2 ?   -1.3   0.0       6.7   1.9e+03     120     172 ..     254     329 ..     211     363 .. 0.68
   3 ?    6.8   0.2     0.023       6.5      26      48 ..     420     442 ..     416     451 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.56
                              DUF87  27 AilgsTGsGKSntvavLleel 47 
                                        + +g+ G+GKS++ + L +++
  gene3022|gene3022|rna3022|rna3022 130 GLVGTNGVGKSTLLRWLKNRA 150
                                        578999*******99997776 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 6.7
                              DUF87 120 vleealdqakakeekeklssdepveklleelk...........................kekeelrklknqaiarl 168
                                        +le+al+    k++k+ l + + +++l++ +k                             +e + ++++++++r+
  gene3022|gene3022|rna3022|rna3022 254 FLERALA----KTNKTVLVVSHDIAFLNSTCKfiirmkdglrvykgnydeyerlaalerANAEREYEKNEDTRRRM 325
                                        4444444....47777777888888888888877777777777777776666666655433334444444455555 PP

                              DUF87 169 ldkl 172
                                        +  +
  gene3022|gene3022|rna3022|rna3022 326 QLFV 329
                                        4444 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.023
                              DUF87  26 lAilgsTGsGKSntvavLleell 48 
                                        ++++g  G+GKS++ + Ll++  
  gene3022|gene3022|rna3022|rna3022 420 ILVVGPNGAGKSTLLKTLLHSTS 442
                                        6899999************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (593 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       675  (0.0376485); expected 358.6 (0.02)
Passed bias filter:                      574  (0.0320152); expected 358.6 (0.02)
Passed Vit filter:                       123  (0.00686039); expected 17.9 (0.001)
Passed Fwd filter:                        62  (0.00345808); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              62  [number of targets reported over threshold]
# CPU time: 0.81u 0.31s 00:00:01.12 Elapsed: 00:00:00.47
# Mc/sec: 3758.43
//
Query:       gene3023|gene3023|rna3023|rna3023  [L=77]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.1e-21   76.3   0.8    1.2e-21   76.2   0.8    1.0  1  ubiquitin    Ubiquitin family
    1.7e-07   30.9   1.0    1.9e-07   30.8   1.0    1.0  1  Rad60-SLD    Ubiquitin-2 like Rad60 SUMO-like
    2.6e-06   27.8   0.4    6.2e-06   26.6   0.4    1.6  1  Ubiquitin_2  Ubiquitin-like domain
    0.00049   20.1   1.4       0.54   10.3   0.0    2.0  2  Ubiquitin_4  Ubiquitin-like domain
    0.00059   20.4   0.0    0.00065   20.2   0.0    1.1  1  DUF2407      DUF2407 ubiquitin-like domain
     0.0032   17.6   0.1      0.018   15.1   0.1    1.9  1  Rad60-SLD_2  Ubiquitin-2 like Rad60 SUMO-like
  ------ inclusion threshold ------
      0.014   15.8   0.2       0.02   15.4   0.2    1.3  1  UN_NPL4      Nuclear pore localisation protein NPL4
       0.09   12.7   0.1       0.11   12.4   0.1    1.1  1  TBK1_ULD     TANK binding kinase 1 ubiquitin-like domain


Domain annotation for each model (and alignments):
>> ubiquitin  Ubiquitin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.2   0.8   5.4e-25   1.2e-21       1      72 []       3      75 ..       3      75 .. 0.97

  Alignments for each domain:
  == domain 1  score: 76.2 bits;  conditional E-value: 5.4e-25
                                       EEEEETTSEEEEEEEETTSBHHHHHHHHHHHHTSSGGGEEEEETTEEE.-TTSBHGGHTTSTTEEEEEEESSC CS
                          ubiquitin  1 itvktldgkkitleveesdtveelKekiaekegipaeqqrLiysGkvL.edertleeygiqdgstlhlvlrlr 72
                                       i++k+l g +  +e+ee+ tv++lK++i++ e ip+eqqrLiysGk+L +d + l++y++ dg+++++vl lr
  gene3023|gene3023|rna3023|rna3023  3 IKIKSLIGVEKQIEIEEKATVLSLKQQIEMLETIPPEQQRLIYSGKILtDDGKILSDYNVNDGCVVQMVLALR 75
                                       78999999999*************************************99*******************9876 PP

>> Rad60-SLD  Ubiquitin-2 like Rad60 SUMO-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.8   1.0   8.7e-11   1.9e-07       1      72 []       1      72 [.       1      72 [. 0.93

  Alignments for each domain:
  == domain 1  score: 30.8 bits;  conditional E-value: 8.7e-11
                                       EEEEEEESSS--EEEEEETTSBHHHHHHHHHHHHT----TT-EEEETTEE--TT.SBGGGSS--TTEEEEEEX CS
                          Rad60-SLD  1 ikiilkgkdgkevkikVkptttvskLieayrkkkgipeeqkvrLiFDGeeLdpn.stvedldiedgdtidvvi 72
                                       + i++k+  g e +i+++++ tv  L+++ +  + ip+ +++rLi+ G+ L ++ + + d+ ++dg ++++v+
  gene3023|gene3023|rna3023|rna3023  1 MHIKIKSLIGVEKQIEIEEKATVLSLKQQIEMLETIPP-EQQRLIYSGKILTDDgKILSDYNVNDGCVVQMVL 72
                                       68999*********************************.************77626679**********9986 PP

>> Ubiquitin_2  Ubiquitin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.4   2.8e-09   6.2e-06      15      79 ..      12      69 ..       2      71 .. 0.88

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 2.8e-09
                                       EEEEEEETTSBHHHHHHHHHHHH---TTCEEEEEE.-SSSSEEECSSGCCSBCCCCT--TTEEEE CS
                        Ubiquitin_2 15 sserrfsksltieelKekLelitGtspasmrLqlyddkkdnevsklddddalLgsYgvkdgmrih 79
                                        +++ ++++ t+ +lK+++e++  ++p+++rL +           l+dd + L++Y+v+dg+ ++
  gene3023|gene3023|rna3023|rna3023 12 EKQIEIEEKATVLSLKQQIEMLETIPPEQQRLIYS-------GKILTDDGKILSDYNVNDGCVVQ 69
                                       566889999***********************998.......45679***************987 PP

>> Ubiquitin_4  Ubiquitin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.5   0.00047         1       1      32 [.       1      32 [.       1      42 [. 0.86
   2 !   10.3   0.0   0.00024      0.54      57      85 ..      42      70 ..      39      74 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00047
                        Ubiquitin_4  1 lkvtvkkldgeslevvvkqnatvkdLkkaier 32
                                       +++++k l g   ++++++ atv  Lk+ ie 
  gene3023|gene3023|rna3023|rna3023  1 MHIKIKSLIGVEKQIEIEEKATVLSLKQQIEM 32
                                       67888888888889***************986 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00024
                        Ubiquitin_4 57 cLsfegekLkddkaklkeygirnkselsF 85
                                        L++ g+ L+dd + l++y +++++ ++ 
  gene3023|gene3023|rna3023|rna3023 42 RLIYSGKILTDDGKILSDYNVNDGCVVQM 70
                                       599**********************9975 PP

>> DUF2407  DUF2407 ubiquitin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   2.9e-07   0.00065      17      67 ..      14      62 ..       3      73 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 2.9e-07
                            DUF2407 17 dipdpntttvagLkqliRerlpaelasrrLrLIyaGrlLedttslasslkl 67
                                       +i+  +++tv +Lkq+i   l +++  ++ rLIy+G++L+d  ++ s+ ++
  gene3023|gene3023|rna3023|rna3023 14 QIEIEEKATVLSLKQQIE-ML-ETIPPEQQRLIYSGKILTDDGKILSDYNV 62
                                       4555589**********5.44.78999999**********99888777665 PP

>> Rad60-SLD_2  Ubiquitin-2 like Rad60 SUMO-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.1   8.1e-06     0.018       5      76 ..       3      67 ..       1      74 [. 0.71

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 8.1e-06
                                       EEEEETTS-EEEEEEEETT-BHHHHHHHHHHHS-TT-SSS--SCCCEEEEETTEEE-.TTSBCCCCS-TTTTT CS
                        Rad60-SLD_2  5 lkfrlvdGsDigpvkfsdaatvaelkekviaqWPkdkeekpksvndlklilaGkiLe.nnktlkelrlplgev 76
                                       +k++   G   + ++ +++atv +lk+++        e     +++ +li++GkiL  + k l+++++  g v
  gene3023|gene3023|rna3023|rna3023  3 IKIKSLIGV-EKQIEIEEKATVLSLKQQIEM-----LE--TIPPEQQRLIYSGKILTdDGKILSDYNVNDGCV 67
                                       566666666.677788889999999998832.....22..23345669********97899999998876665 PP

>> UN_NPL4  Nuclear pore localisation protein NPL4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   0.2   8.7e-06      0.02       7      72 ..       3      65 ..       1      73 [. 0.77

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 8.7e-06
                                       EEEEETTEE.EEEEE-TTSBHHHHHHHHHHHSS-STTT-EEESSTTCGCCCSSSSSSCCCTCH--TT CS
                            UN_NPL4  7 iRvqSadGi.kRieisekstlktllekvaeelkfsengfslylernkttelvssssksvkevglkhG 72
                                       i ++S +G+ k+iei+ek t+  l+++++    ++ +++ l      ++++ +++ k +++ +++ G
  gene3023|gene3023|rna3023|rna3023  3 IKIKSLIGVeKQIEIEEKATVLSLKQQIEMLETIPPEQQRLIY----SGKILTDDGKILSDYNVNDG 65
                                       89******9567*****************99999999888753....34555566666666666666 PP

>> TBK1_ULD  TANK binding kinase 1 ubiquitin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1     5e-05      0.11      17      53 ..      15      51 ..       8      60 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 5e-05
                           TBK1_ULD 17 iYihpyntvaifqeevakqTkiaaekQellfeghrll 53
                                       i i+++ tv  + +++     i++e+Q l++ g+ l 
  gene3023|gene3023|rna3023|rna3023 15 IEIEEKATVLSLKQQIEMLETIPPEQQRLIYSGKILT 51
                                       668899999999*********************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       597  (0.033298); expected 358.6 (0.02)
Passed bias filter:                      459  (0.025601); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.40u 0.31s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 512.17
//
Query:       gene3025|gene3025|rna3025|rna3025  [L=216]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (216 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       704  (0.039266); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1547.57
//
Query:       gene3026|gene3026|rna3026|rna3026  [L=45]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (45 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       326  (0.0181828); expected 358.6 (0.02)
Passed bias filter:                      209  (0.0116571); expected 358.6 (0.02)
Passed Vit filter:                         6  (0.000334653); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.28s 00:00:00.67 Elapsed: 00:00:00.45
# Mc/sec: 299.17
//
Query:       gene3027|gene3027|rna3027|rna3027  [L=776]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.027   14.7   0.1      0.073   13.3   0.1    1.7  1  Forkhead  Forkhead domain


Domain annotation for each model (and alignments):
>> Forkhead  Forkhead domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   4.1e-06     0.073      18      66 ..     178     233 ..     167     251 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.1e-06
                                        -TTT-B-HHHHHHHHHCC-HHHHCC.-CCHHHHHHHHHHHH........C--EEETT CS
                           Forkhead  18 spekkltLseIyefieenfpyyrtaakkgWqnSirhnLsln........kcFekvpr 66 
                                         ++ + +++eIye+i+  f  + ++  +  q S+ + L  n        ++F+   r
  gene3027|gene3027|rna3027|rna3027 178 HSDVQFSVNEIYEIIMGSFVLFMDN-GQMIQRSVCQQLFGNeniydqlnRIFVSKTR 233
                                        5677999*****************6.9***********8885444444455555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (776 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       694  (0.0387082); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.63u 0.26s 00:00:00.89 Elapsed: 00:00:00.43
# Mc/sec: 5469.49
//
Query:       gene3028|gene3028|rna3028|rna3028  [L=108]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-11   44.3   0.0    1.8e-11   44.0   0.0    1.0  1  RVT_1     Reverse transcriptase (RNA-dependent DNA polymerase


Domain annotation for each model (and alignments):
>> RVT_1  Reverse transcriptase (RNA-dependent DNA polymerase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.0   0.0   9.9e-16   1.8e-11       3      85 ..      11     102 ..      10     105 .. 0.91

  Alignments for each domain:
  == domain 1  score: 44.0 bits;  conditional E-value: 9.9e-16
                                        -TT.....S-EEE......-THHHHCTB--...........-------HHHH................HCCHTS-- CS
                              RVT_1   3 Kkg....pgsyRpisllsvdykalnkliakrLkdvl..ekllsenqpgfrpgrstldav...edllkalkkkkkak 69 
                                        Kkg    ++ yR is +s+++k++ k++a+rL+++   ek+l ++q gfr+ + ++      +++ ++ + k++a+
  gene3028|gene3028|rna3028|rna3028  11 KKGgldfLDHYRGISPTSTLCKIVTKICANRLSNFSerEKILIHKQAGFRKLEECIAHAtslYEIGRQRSLKGRAT 86 
                                        5555888899**************************99**************99988888988888887888899* PP

                                        EEEEEEBCCGCCCSBB CS
                              RVT_1  70 lllklDlkkaFdsvpl 85 
                                        ++++lD++k +d+vp 
  gene3028|gene3028|rna3028|rna3028  87 YAAFLDFSKVYDRVPT 102
                                        **************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       335  (0.0186848); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 711.29
//
Query:       gene3029|gene3029|rna3029|rna3029  [L=91]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-14   54.0   0.0    1.7e-14   53.9   0.0    1.0  1  RVT_1     Reverse transcriptase (RNA-dependent DNA polymerase


Domain annotation for each model (and alignments):
>> RVT_1  Reverse transcriptase (RNA-dependent DNA polymerase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.9   0.0   9.3e-19   1.7e-14     109     192 ..       2      90 ..       1      91 [] 0.93

  Alignments for each domain:
  == domain 1  score: 53.9 bits;  conditional E-value: 9.3e-19
                                        ...............TEEEEESB--ST-TTHHHHHHHHHHHHHTT-T...........TEEECTTEEEEEESSHHH CS
                              RVT_1 109 lstrsfsvrvngeeskgryekkglpqGsvlSPllfnlfmnellrelrkra.....kgvtllrYaDDililskskee 179
                                        ++ +++s+r  +++s  + +  g++qG++ SP+lfnl++n+l+  l++ a     +++  l+++DD +il++  +e
  gene3029|gene3029|rna3029|rna3029   2 YRRPHTSLRTGNTRSASFMYDIGVRQGCPASPILFNLYINDLFDGLSRIAmqpgmQSIPSLLFVDDAVILAEPAYE 77 
                                        6667778888888999*******************************988************************** PP

                                        HHHHHHHHHHHHH CS
                              RVT_1 180 lqelleaveewlk 192
                                        l++ l+++ +w++
  gene3029|gene3029|rna3029|rna3029  78 LKRSLKKINDWCR 90 
                                        ***********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       190  (0.0105974); expected 358.6 (0.02)
Passed bias filter:                      188  (0.0104858); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.33u 0.23s 00:00:00.56 Elapsed: 00:00:00.37
# Mc/sec: 729.83
//
Query:       gene303|gene303|rna303|rna303  [L=161]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00086   19.6   0.7       0.11   12.8   0.0    2.3  2  RWD       RWD domain


Domain annotation for each model (and alignments):
>> RWD  RWD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.4   0.1    0.0012        22       3      24 ..       5      26 ..       3      35 .. 0.83
   2 !   12.8   0.0   6.1e-06      0.11      57     109 ..      36      85 ..      31      92 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0012
                                   HHHHHHHHHHHSTTTCCCCHT- CS
                                   xxxxxxxxxxxxxxxxxxxxxx RF
                            RWD  3 qeqEleaLesIypdefeviene 24
                                    e+E+ +L+ I+  +++v++n+
  gene303|gene303|rna303|rna303  5 KEEEIAILQNIFRTDLSVEKNT 26
                                   689*************998854 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 6.1e-06
                                    EEEEE-SSTTSS--EEEEEECCSS-HHHHHHHHHHHHHHHHHTTTS--CHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            RWD  57 leiklpeeYPeeaPiislsstenlpkeqvksleekleelaeenlgepvifali 109
                                    l++ l ++YP++ Pi+ +  ++   k+  +++ + l e    ++g p+++ l+
  gene303|gene303|rna303|rna303  36 LNFVLDSSYPDTSPILDVYYEN---KKSAEQVVNYLTERSRMHQGRPMLYPLV 85 
                                    889999****************...8888889999999999899******875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       711  (0.0396564); expected 358.6 (0.02)
Passed bias filter:                      532  (0.0296726); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1121.59
//
Query:       gene3030|gene3030|rna3030|rna3030  [L=825]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.9e-20   72.6   1.6    3.9e-20   72.6   1.6    3.6  3  SPT16            FACT complex subunit (SPT16/CDC68)
    1.5e-14   54.1   0.3    1.5e-14   54.1   0.3    3.0  2  FACT-Spt16_Nlob  FACT complex subunit SPT16 N-terminal lobe d
    5.1e-13   49.3   2.7    4.2e-12   46.3   0.3    2.7  2  Rtt106           Histone chaperone Rttp106-like
     0.0054   16.7   0.4      0.022   14.7   0.3    2.0  2  Peptidase_S49    Peptidase family S49
  ------ inclusion threshold ------
       0.45   11.3   3.8       0.95   10.2   0.8    2.4  2  LTXXQ            LTXXQ motif family protein


Domain annotation for each model (and alignments):
>> SPT16  FACT complex subunit (SPT16/CDC68)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.3      0.82   2.9e+03      78      95 ..     340     357 ..     281     383 .. 0.58
   2 !   72.6   1.6   1.1e-23   3.9e-20       1     151 []     399     522 ..     399     522 .. 0.91
   3 ?   -1.1   0.2      0.53   1.9e+03      85     105 ..     575     595 ..     538     639 .. 0.56

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.82
                              SPT16  78 kklqevfreikelkkkvk 95 
                                        +k  e   ei+e +k+++
  gene3030|gene3030|rna3030|rna3030 340 QKALEKEIEINEHQKELM 357
                                        112222223333333333 PP

  == domain 2  score: 72.6 bits;  conditional E-value: 1.1e-23
                              SPT16   1 iyvdkkketillPifGiavPFhistiknvskseegdytylrinFnvpgsavgkkeealfknpeaifikeltfrskd 76 
                                        ++vd+++  +l+Pi+G++vPFhi+ +kn+s + ++    lrinF                      ik++t+rsk+
  gene3030|gene3030|rna3030|rna3030 399 LVVDRRNFGVLIPINGYMVPFHIEYVKNCSLNGND----LRINFREG-----------------EIIKSITYRSKA 453
                                        58****************************99885....*****987.................469*******99 PP

                              SPT16  77 ekklqevfreikelkkkvkkreaekkekedlveqekLilskskrkprLkdlyirpnie.g.kklaGtleaheNGlR 150
                                            +++++ei + ++++     e++e +++ eq +L + k+ r+  L d++i+++++ + k  aG+le+heNG++
  gene3030|gene3030|rna3030|rna3030 454 ---ANSLYNEIGDTRREYV----ERRETSNVGEQGTLCEIKG-RRHILGDVKIKTEVRtQkKSKAGNLELHENGFK 521
                                        ...5699*******99985....5588999**********99.5669**********95468899**********9 PP

                              SPT16 151 y 151
                                        +
  gene3030|gene3030|rna3030|rna3030 522 F 522
                                        8 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 0.53
                              SPT16  85 reikelkkkvkkreaekkeke 105
                                         +i +l+   k+r +e++ek 
  gene3030|gene3030|rna3030|rna3030 575 IDIMKLHPSQKERLEEEQEKI 595
                                        333333333333322222211 PP

>> FACT-Spt16_Nlob  FACT complex subunit SPT16 N-terminal lobe domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.1   0.3   4.2e-18   1.5e-14       2     152 ..       7     137 ..       6     146 .. 0.86
   2 ?    0.3   0.7      0.15   5.3e+02      63      96 ..     543     576 ..     496     625 .. 0.61

  Alignments for each domain:
  == domain 1  score: 54.1 bits;  conditional E-value: 4.2e-18
                                        -HHHHHHHHHHHHHHHHSHHHHHSTT-SEEEEEE-S--TT----HHHHHHHHHHSS--SSEEEEEESSEEEEEEEH CS
                    FACT-Spt16_Nlob   2 dkkafkkRlkklysawkeeeedkfssvdallvvlGksdeenpykKstalqtWLlGyefpdtlilltkkkiviltsk 77 
                                        + ++f +Rl k++++ +            ll+vlGk+ e + +  ++al ++Ll yefp+tl+l+tk++++ +ts 
  gene3030|gene3030|rna3030|rna3030   7 NLSQFVRRLTKIQESIS----------MPLLIVLGKKLEVEDFGPNSALFIYLLNYEFPETLLLITKDTCYAVTST 72 
                                        66677777777777777..........469********************************************** PP

                                        HHHHTTGGGCTSTT-.SSEEEEEEE-S-HHHHHHHHHHHHHHHHTTTSEEEE-TT----SHHHHHHHHHHCCCGG CS
                    FACT-Spt16_Nlob  78 kKaklLeplkekkeeekvevellvreKdadenkknfeklieaikeagkkvGvlaKdkseGkfveewkkalkeakk 152
                                        kK ++Le+++ +k      +++  r Kd   ++ + ++l+++  +    v +  +++ +G+f++++ +++k +++
  gene3030|gene3030|rna3030|rna3030  73 KKKEILESMRCTK------LKVYERMKDGSRDDFLKKELLKITDS----VLMSDRNNLQGHFCSTFINIFKVSDF 137
                                        ********99887......99******998888777777776654....56889999999999999999987776 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.15
                                        EEEEESSEEEEEEEHHHHHTTGGGCTSTT-.SSE CS
                    FACT-Spt16_Nlob  63 lilltkkkiviltskkKaklLeplkekkeeekve 96 
                                         il +k ++ i+   kKa  ++ +ke  e+ +++
  gene3030|gene3030|rna3030|rna3030 543 YILHFKLTVPIIFNGKKAYNVQFYKEVVENMSID 576
                                        3344444555555556666666666655554444 PP

>> Rtt106  Histone chaperone Rttp106-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.1     0.072   2.6e+02       3      59 ..     502     584 ..     500     620 .. 0.64
   2 !   46.3   0.3   1.2e-15   4.2e-12       6      86 ..     634     712 ..     629     714 .. 0.92

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.072
                             Rtt106   3 VkasrkakeGlLyflekgllfgfkkPllfiplediesvsfeRvsvtsrtfdlvvel.................... 58 
                                        V+ ++k+k G L + e+g+ f  +   ++i +++ie+  +++  +    f l+v +                    
  gene3030|gene3030|rna3030|rna3030 502 VRTQKKSKAGNLELHENGFKF--HD--TVILFNNIEHLFYQQGDAYILHFKLTVPIifngkkaynvqfykevvenm 573
                                        778899999999999999999..33..5788888998888855555555555555466666666665555555555 PP

                             Rtt106  59 ..........k 59 
                                                  +
  gene3030|gene3030|rna3030|rna3030 574 sidimklhpsQ 584
                                        55555555550 PP

  == domain 2  score: 46.3 bits;  conditional E-value: 1.2e-15
                             Rtt106   6 srkakeGlLyflekgllfgfkkPllfiplediesvsfeRvsvtsrtfdlvvelkk.eeveFsmidqeelegidefv 80 
                                        +   +++++ + +++l+++++ P+l++++e+ e ++feRv+  sr+fdl++ +k+ + +++++id ++++ + ef+
  gene3030|gene3030|rna3030|rna3030 634 R---QNVQIRPSSTCLVYLLEPPFLVVDFEKMEVANFERVNYVSRSFDLTFIFKDkTFMTITSIDSRSMDYLREFI 706
                                        5...7889999******************************************885666***************** PP

                             Rtt106  81 kskgik 86 
                                        +s++i 
  gene3030|gene3030|rna3030|rna3030 707 DSRNIC 712
                                        ***995 PP

>> Peptidase_S49  Peptidase family S49
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0      0.75   2.7e+03      29      48 ..     207     226 ..     204     230 .. 0.85
   2 !   14.7   0.3   6.2e-06     0.022      76     116 ..     584     624 ..     573     627 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.75
                                        SEEEE-TT-EEE---EEEEE CS
                      Peptidase_S49  29 dkivanpstivgsiGvitql 48 
                                         +iv ++ +i+ siGv  q 
  gene3030|gene3030|rna3030|rna3030 207 PRIVRDQDAITISIGVRHQS 226
                                        58999***********9875 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 6.2e-06
                                        TTSS--HHHHHHHHHHHHHHHHHHHHHHHHHHTS-HHHHHC CS
                      Peptidase_S49  76 lrrelteeereilqrlldetyqqFvqtVaknRnlsveqvdk 116
                                         ++ l+ee+ +i q+++ + y++F++ V +n nl +++v k
  gene3030|gene3030|rna3030|rna3030 584 QKERLEEEQEKIRQEMIKAEYDNFIKNVENNSNLRIDRVSK 624
                                        56788999999*************************99976 PP

>> LTXXQ  LTXXQ motif family protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.8   0.00027      0.95       5      54 ..     339     387 ..     337     400 .. 0.77
   2 ?    0.7   0.1      0.25   8.8e+02      14      34 ..     579     599 ..     572     608 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00027
                                        XXXSTTTT----HHHHHHHHHHHHHHHHHS---..-HHHHHHHHHHHTSS CS
                              LTXXQ   5 riaklkaeLkLtdaQkaalkalaeaaraeakplkakkeemramrkkvlaa 54 
                                        r++ l++e++++++Qk+ +++l +++ +  + ++ +++  ++++kk++a 
  gene3030|gene3030|rna3030|rna3030 339 RQKALEKEIEINEHQKELMDKLNDEMVRYYSDMETTEP-AETADKKFIAY 387
                                        7899***********************99999944444.44456656554 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.25
                                        ---HHHHHHHHHHHHHHHHHS CS
                              LTXXQ  14 kLtdaQkaalkalaeaaraea 34 
                                        kL ++Qk+ l++ +e+ r+e+
  gene3030|gene3030|rna3030|rna3030 579 KLHPSQKERLEEEQEKIRQEM 599
                                        778888888888888888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (825 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1637  (0.0913046); expected 358.6 (0.02)
Passed bias filter:                      588  (0.032796); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.78u 0.27s 00:00:01.05 Elapsed: 00:00:00.45
# Mc/sec: 5566.92
//
Query:       gene3031|gene3031|rna3031|rna3031  [L=287]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-11   44.8   0.1      1e-10   41.7   0.0    2.2  2  PRK              Phosphoribulokinase / Uridine kinase family
    0.00042   20.5   0.0    0.00076   19.7   0.0    1.4  1  AAA_33           AAA domain
     0.0074   16.3   0.0      0.014   15.4   0.0    1.4  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
  ------ inclusion threshold ------
      0.011   16.3   0.0      0.018   15.6   0.0    1.5  1  AAA_18           AAA domain
      0.016   15.6   0.0      0.026   14.9   0.0    1.3  1  AAA_16           AAA ATPase domain
      0.019   14.8   0.0       0.03   14.2   0.0    1.3  1  CPT              Chloramphenicol phosphotransferase-like prot
      0.024   13.8   0.0      0.058   12.6   0.0    1.6  2  NB-ARC           NB-ARC domain
      0.027   14.8   0.0      0.062   13.7   0.0    1.6  1  RNA_helicase     RNA helicase
      0.035   13.8   0.1       0.05   13.3   0.1    1.5  1  AAA_24           AAA domain
      0.042   14.1   0.0      0.076   13.3   0.0    1.5  1  AAA_22           AAA domain
      0.043   13.9   0.0       0.09   12.8   0.0    1.5  1  AAA_14           AAA domain
      0.067   12.9   0.0       0.12   12.1   0.0    1.3  1  Sigma54_activat  Sigma-54 interaction domain
      0.069   13.4   0.0       0.61   10.3   0.0    2.1  2  AAA_28           AAA domain
      0.071   12.4   0.0       0.11   11.9   0.0    1.3  1  FtsK_SpoIIIE     FtsK/SpoIIIE family
      0.074   12.9   0.0        9.6    6.0   0.0    2.3  2  dNK              Deoxynucleoside kinase
      0.091   11.8   0.0       0.14   11.2   0.0    1.2  1  T2SSE            Type II/IV secretion system protein
       0.13   11.7   0.1       0.19   11.1   0.1    1.2  1  Gamma_PGA_hydro  Poly-gamma-glutamate hydrolase


Domain annotation for each model (and alignments):
>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.7   0.0   9.9e-14     1e-10       1     121 [.      26     135 ..      26     149 .. 0.80
   2 ?    0.8   0.0      0.32   3.4e+02     132     178 ..     171     218 ..     155     246 .. 0.70

  Alignments for each domain:
  == domain 1  score: 41.7 bits;  conditional E-value: 9.9e-14
                                PRK   1 vIgvagsSGaGkttvarklekifgrekvkaaeiegdsflrldraekdleleerkrakekevsflspeandfdllye 76 
                                        vI++ g+S +Gktt+a++l  +++ e+++      + +l +d+ +k+ +     ++   +++f++p   d+d++  
  gene3031|gene3031|rna3031|rna3031  26 VIAIHGASTSGKTTFANNLYASLK-EHMP------TFLLHMDSYYKSFT-----DTDVTKYDFDNPSSVDWDKIHG 89 
                                        8**********************9.6667......67778888887765.....556678**************** PP

                                PRK  77 vlkelkegkkv.dkpiYsheteeaapdkeeliegadvlviEGlhal 121
                                        vl++ ++g +   +  Ys+++ ++  +     ++++vl+iEG++al
  gene3031|gene3031|rna3031|rna3031  90 VLRSIHDGDEFiPTYQYSFVSRKSTGPIMVRNNSPEVLIIEGIYAL 135
                                        ********9851444555555555554444456789********97 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.32
                                PRK 132 lkiyvdisidlelarklqRDiaeRGrs.leavldsilrrkpdyvnyik 178
                                        lki + i ++     ++ RD+ eR r  le+ l+  + + p+ +++++
  gene3031|gene3031|rna3031|rna3031 171 LKIRLNICKNRMEHTRVCRDVLERDRGyLESTLQFSTQVWPATTRWVH 218
                                        566777777777778999**9988765145555555577777776665 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   7.2e-07   0.00076       1      45 [.      26      74 ..      26      97 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 7.2e-07
                             AAA_33  1 lvllvGlpGsGKstlaerllkklg....avllssdtlrrrlfgtdqqsk 45
                                       ++ ++G++ sGK+t+a +l++ l+    ++ll  d++++  + td+++ 
  gene3031|gene3031|rna3031|rna3031 26 VIAIHGASTSGKTTFANNLYASLKehmpTFLLHMDSYYKSFTDTDVTKY 74
                                       7889***************9999889999*********99999887654 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   1.3e-05     0.014       5      59 ..       7      62 ..       3      88 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.3e-05
                                       HHHHHHHHHHHHCH...TEEEEEEESTTSSHHHHHHHHHHHTT------TTTTSE.EEE CS
                               TsaE  5 eetealgkklakal...gdvilLeGdLGaGKTtlvrglakalgveevkSPTFtlv.eeY 59
                                       ++t+++ + +++ l    +vi+++G   +GKTt++ +l ++l+    + PTF l   +Y
  gene3031|gene3031|rna3031|rna3031  7 AATNEVIAMVKRRLnnrIKVIAIHGASTSGKTTFANNLYASLKE---HMPTFLLHmDSY 62
                                       56666666776666654578*********************954...789998851445 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.6   0.0   1.7e-05     0.018       1      91 [.      27     141 ..      27     186 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.7e-05
                             AAA_18   1 IlltGtpGvGKttlakeLskrl.gf...gvnlrdvakenglllevdpealdeskrldedkldklldaleenss... 69 
                                        I++ G++ +GKtt+a++L  +l +       ++d  +++ + ++v+++++d+   +d dk + +l+ ++  ++   
  gene3031|gene3031|rna3031|rna3031  27 IAIHGASTSGKTTFANNLYASLkEHmptFLLHMDSYYKSFTDTDVTKYDFDNPSSVDWDKIHGVLRSIHDGDEfip 102
                                        8999**************6666333477666777777777777777777777777777777777777776666788 PP

                             AAA_18  70 .................aleegknlvidghlaeleseaa 91 
                                                         ++ ++++l+i+g+ a +++ + 
  gene3031|gene3031|rna3031|rna3031 103 tyqysfvsrkstgpimvRNNSPEVLIIEGIYALNLFNRI 141
                                        888888888888888888888889999998887777665 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   2.5e-05     0.026      14      55 ..      14      55 ..       7     101 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.5e-05
                             AAA_16 14 salervrsgrpelvllsGesGvGKsslvrellralekdggif 55
                                       ++++r   +r  ++ ++G+s +GK++ ++ l+ +l+++   f
  gene3031|gene3031|rna3031|rna3031 14 AMVKRRLNNRIKVIAIHGASTSGKTTFANNLYASLKEHMPTF 55
                                       677888889999********************9999995444 PP

>> CPT  Chloramphenicol phosphotransferase-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   2.8e-05      0.03       2      45 ..      25      70 ..      24      98 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.8e-05
                                       -EEEEEE-TTSSHHHHHHHHHHHSSS..-EEEEEHHHHHHHS-GGG CS
                                CPT  2 riilLnGgsssGKsslaralqevlde..pwlhlgvDafvealppkr 45
                                       ++i ++G+s sGK++ a+ l + l+e  p + l +D++ +   +  
  gene3031|gene3031|rna3031|rna3031 25 KVIAIHGASTSGKTTFANNLYASLKEhmPTFLLHMDSYYKSFTDTD 70
                                       6999****************999876447788999*9998776654 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   5.5e-05     0.058       8      48 ..      16      52 ..       6      71 .. 0.78
   2 ?   -2.8   0.0       2.8   2.9e+03     117     175 ..      83     145 ..      80     150 .. 0.52

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.5e-05
                                       HHHHHHCTTTSCSEEEEEEESTTSSHHHHHHHHCCSHCCCC CS
                             NB-ARC  8 viekLlekdelqslvvalvGmgGvGKttlakqilnksdeve 48
                                       v+ +L   + ++  v+a++G   +GKtt a++ + +++e  
  gene3031|gene3031|rna3031|rna3031 16 VKRRLN--NRIK--VIAIHGASTSGKTTFANNLYASLKEHM 52
                                       333333..5556..******************999977765 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 2.8
                                        HH.....HHHHCHTTSEEEEEESBCCCCCCS-S-....EEEEEESS--HHHHHHHHHHCCTS- CS
                             NB-ARC 117 dwdkigvvlparenrlrvllTTRdeevanavsat....sekievelLekdeawellenkvfek 175
                                        dwdki  vl + + + + + T     v+ +  ++    ++ +ev ++e   a++l++ +vf+ 
  gene3031|gene3031|rna3031|rna3031  83 DWDKIHGVLRSIHDGDEFIPTYQYSFVSRKSTGPimvrNNSPEVLIIEGIYALNLFNRIVFDT 145
                                        566666666666655555555554444444333221013444455555555666777777765 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   5.9e-05     0.062       1      27 [.      27      56 ..      27      95 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.9e-05
                       RNA_helicase  1 iwlyGpsgeGKStlakeLakallkkl...k 27
                                       i ++G+s  GK+t+a++L ++l +++    
  gene3031|gene3031|rna3031|rna3031 27 IAIHGASTSGKTTFANNLYASLKEHMptfL 56
                                       579********************9996431 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   4.8e-05      0.05       4      23 ..      26      51 ..      23     171 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.8e-05
                             AAA_24  4 kiliyGpsgiGKTtlakel......g 23
                                        i+i G s +GKTt+a++l       
  gene3031|gene3031|rna3031|rna3031 26 VIAIHGASTSGKTTFANNLyaslkeH 51
                                       799***************98887642 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   7.2e-05     0.076       6      50 ..      25      79 ..      21     135 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 7.2e-05
                             AAA_22  6 gilvvtGesGtGKTtllrrlleqldeeakaee.............erpevvfvtlpss 50
                                       ++++++G s +GKTt +++l  +l+e+                   + +v +++  ++
  gene3031|gene3031|rna3031|rna3031 25 KVIAIHGASTSGKTTFANNLYASLKEHM---PtfllhmdsyyksfTDTDVTKYDFDNP 79
                                       579********************96542...134566666666664444444444444 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   8.5e-05      0.09       3      46 ..      25      65 ..      23      94 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 8.5e-05
                             AAA_14  3 kilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkl 46
                                       k+++i Ga  +GKTt++++l+ +l    e++  + l  ++++k+
  gene3031|gene3031|rna3031|rna3031 25 KVIAIHGASTSGKTTFANNLYASLK---EHMPTFLLHMDSYYKS 65
                                       799*****************98888...5555555554444443 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00011      0.12       4      52 ..       5      54 ..       3      65 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00011
                                       -SHHHHHHHHHHHHHCTSSS-EE.EECSTTSSHHHHHHHHHHHSTTTTS- CS
                    Sigma54_activat  4 esealkelleqikkvaktdlsvl.itGesGtGKellaraiheaskrkekp 52
                                       +++a++e+++++k+  +++++v+ i+G s +GK+++a+ ++++ k++   
  gene3031|gene3031|rna3031|rna3031  5 KNAATNEVIAMVKRRLNNRIKVIaIHGASTSGKTTFANNLYASLKEHMPT 54
                                       57788999******99999887659****************987766555 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00058      0.61       2      22 ..      27      47 ..      26      75 .. 0.84
   2 ?    0.6   0.0      0.55   5.8e+02      36      95 ..     155     211 ..     142     229 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00058
                             AAA_28  2 ivitGgestGKTtlleaLaar 22
                                       i+i G++ +GKTt +++L a 
  gene3031|gene3031|rna3031|rna3031 27 IAIHGASTSGKTTFANNLYAS 47
                                       89***************9864 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.55
                             AAA_28  36 eeklakgedalpwvedllafaervleeqleeeaaaaankvlfcDrglldtlaYaraygge 95 
                                        +e+++++e++ p+ + +l+++  + ++++e  + +  ++vl  Drg+l+++    +  ++
  gene3031|gene3031|rna3031|rna3031 155 KEGYKENENEYPD-FGVLKIRLNICKNRMEHTRVC--RDVLERDRGYLESTLQFSTQVWP 211
                                        6778888888888.799999999999999876665..88888999988877655555555 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0    0.0001      0.11      42      63 ..      27      48 ..       5      54 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.0001
                                       EEEE--TTSSHHHHHHHHHHHH CS
                       FtsK_SpoIIIE 42 llvaGatgsGKStalntLilSl 63
                                       + ++Ga+ sGK+t+ n+L +Sl
  gene3031|gene3031|rna3031|rna3031 27 IAIHGASTSGKTTFANNLYASL 48
                                       68****************9998 PP

>> dNK  Deoxynucleoside kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0    0.0091       9.6       1      23 [.      27      49 ..      27      81 .. 0.80
   2 ?    4.8   0.0     0.021        22      90     173 ..     132     217 ..     109     249 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0091
                                       EEEEESTTSSHHHHHHHHHCCST CS
                                dNK  1 ivveGnIgaGKstlvklLskklg 23
                                       i++ G   +GK+t+++ L   l+
  gene3031|gene3031|rna3031|rna3031 27 IAIHGASTSGKTTFANNLYASLK 49
                                       7999************9987775 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.021
                                        THHHHHHHTTSS-HHHHHHHHHHHHHHH.HHCCH-SEEEEEE--HHHHHHHHHHCTTCCCT.TS-HHHHH.HHHHH CS
                                dNK  90 iFakalaekgtlseeelkiykelldnll.eelakpdlliYLkasletclerikkRgreeek.kieldYle.kLhek 162
                                        i+a +l+++ +++ ++++ y++  + +  +e ++pd+ + Lk+ l+ c++r+++     +  + ++ Yle +L+ +
  gene3031|gene3031|rna3031|rna3031 132 IYALNLFNRIVFDTNAFDSYDSSKEGYKeNENEYPDFGV-LKIRLNICKNRMEHTRVCRDVlERDRGYLEsTLQFS 206
                                        88999999999****************966666688888.9***********975544444488888888346666 PP

                                        HHHHHTSGGCS CS
                                dNK 163 yeewlkklnev 173
                                         + w +++ +v
  gene3031|gene3031|rna3031|rna3031 207 TQVWPATTRWV 217
                                        67777776666 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00013      0.14     118     156 ..      12      51 ..       2      65 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00013
                              T2SSE 118 iaevlrkavrer.glilvsGgTgsGKttllyallkeinks 156
                                        + +++++ +++r ++i + G+  sGKtt+++ l + ++++
  gene3031|gene3031|rna3031|rna3031  12 VIAMVKRRLNNRiKVIAIHGASTSGKTTFANNLYASLKEH 51 
                                        444444444544156779*************999999887 PP

>> Gamma_PGA_hydro  Poly-gamma-glutamate hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   0.00018      0.19      17      97 ..      12      95 ..       1     101 [. 0.77

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00018
                    Gamma_PGA_hydro 17 yrieeeekkksrllvlaiHGGgiEpgtseiaeaiae.adysvYlfeglkk..sgnkelHitStrFdeplalklakeae 91
                                           ++++ ++r+ v+aiHG +  + t+   +  a+ +++    + ++++  +  ++  +t   Fd+p +++  k + 
  gene3031|gene3031|rna3031|rna3031 12 VIAMVKRRLNNRIKVIAIHGASTSGKTTFANNLYASlKEHMPTFLLHMDSyyKSFTDTDVTKYDFDNPSSVDWDKIHG 89
                                       3445677889**************99999998888875555445556666335558999*************999999 PP

                    Gamma_PGA_hydro 92 vvvslH 97
                                       v  s+H
  gene3031|gene3031|rna3031|rna3031 90 VLRSIH 95
                                       999999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       643  (0.0358637); expected 358.6 (0.02)
Passed bias filter:                      522  (0.0291148); expected 358.6 (0.02)
Passed Vit filter:                        97  (0.00541023); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 1995.97
//
Query:       gene3032|gene3032|rna3032|rna3032  [L=1280]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1197  (0.0667633); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.81u 0.27s 00:00:01.08 Elapsed: 00:00:00.46
# Mc/sec: 8376.93
//
Query:       gene3033|gene3033|rna3033|rna3033  [L=765]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.081   12.8   0.0       0.18   11.7   0.0    1.6  1  DUF2507   Protein of unknown function (DUF2507)
       0.22   11.9   1.6        9.2    6.6   0.5    3.1  3  TINF2_N   TERF1-interacting nuclear factor 2 N-terminus
       0.61   10.4   2.4        1.8    8.9   2.4    1.8  1  Mto2_bdg  Micro-tubular organiser Mto1 C-term Mto2-binding re


Domain annotation for each model (and alignments):
>> DUF2507  Protein of unknown function (DUF2507)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0     3e-05      0.18      36      69 ..     643     676 ..     638     691 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3e-05
                            DUF2507  36 plesledlieffekagwGtLellkekkkelefeL 69 
                                        +l++ +++  ff+k++ G+L+++ ++kke+++  
  gene3033|gene3033|rna3033|rna3033 643 NLRNPSEIFIFFKKLNLGDLQMIYTNKKEMHYLF 676
                                        5778899***********************9964 PP

>> TINF2_N  TERF1-interacting nuclear factor 2 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0     0.032   1.9e+02      88     120 ..      31      63 ..       3      67 .. 0.79
   2 ?    2.6   0.2     0.027   1.6e+02      52     106 ..     192     250 ..     181     253 .. 0.70
   3 ?    6.6   0.5    0.0015       9.2      56     107 ..     232     283 ..     218     288 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.032
                            TINF2_N  88 qenflklvqsLledpeerekflqeefpeeYGek 120
                                        +++   l+q+L++  ++ + ++ ++f ++YG++
  gene3033|gene3033|rna3033|rna3033  31 NMSAELLIQNLSNVIKRYKFMFTDDFVVNYGTN 63 
                                        45556799***********************75 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.027
                            TINF2_N  52 rkek...aadlkaiqshlerlrasaa.kstkkkdekveeaqenflklvqsLledpeere 106
                                        r+++   +++l  i++++  +  s   ++++k++++ ++  +nf +l ++L +++ee +
  gene3033|gene3033|rna3033|rna3033 192 RDSTgvrKKELCDIKEFIGAMDRSEPmSKKMKENQSRNTQPDNFPELLEELKNQNEEFD 250
                                        5544444677778888888888776646666666666677799********99988765 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.0015
                            TINF2_N  56 aadlkaiqshlerlrasaakstkkkdekveeaqenflklvqsLledpeerek 107
                                        + +  ++ + l++ +    ++++++ + +++a+ +f +lv+ Ll+d + r++
  gene3033|gene3033|rna3033|rna3033 232 PDNFPELLEELKNQNEEFDRKKMTRRDIIKQAEGSFSHLVDMLLTDSSLRQE 283
                                        44444555566666665569999999********************988875 PP

>> Mto2_bdg  Micro-tubular organiser Mto1 C-term Mto2-binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   2.4   0.00031       1.8       4      41 ..     213     249 ..     212     256 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00031
                           Mto2_bdg   4 eRLreLerqLkaereaRlldrsgarerLeelkaeNrlL 41 
                                        +R + + +++k ++  R++ +    e Leelk++N++ 
  gene3033|gene3033|rna3033|rna3033 213 DRSEPMSKKMKENQ-SRNTQPDNFPELLEELKNQNEEF 249
                                        5667899*******.********************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (765 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       844  (0.0470746); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.69u 0.26s 00:00:00.95 Elapsed: 00:00:00.45
# Mc/sec: 5094.32
//
Query:       gene3034|gene3034|rna3034|rna3034  [L=41]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (41 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       217  (0.0121033); expected 358.6 (0.02)
Passed bias filter:                      178  (0.00992805); expected 358.6 (0.02)
Passed Vit filter:                         5  (0.000278878); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.43
# Mc/sec: 285.76
//
Query:       gene3035|gene3035|rna3035|rna3035  [L=245]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0011   18.4  19.1     0.0011   18.4  19.1    2.1  2  ABC2_membrane  ABC-2 type transporter


Domain annotation for each model (and alignments):
>> ABC2_membrane  ABC-2 type transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4  19.1   6.1e-08    0.0011      57     171 ..       7     118 ..       3     147 .. 0.88
   2 ?   -0.1   2.5     0.029   5.2e+02     124     152 ..     203     231 ..     197     238 .. 0.53

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 6.1e-08
                      ABC2_membrane  57 ffsvlflafsaltsvapvferergvlerelvsplyslsayvlakvlvelpvsllqalifllivyflvgldlsrffl 132
                                        + +  +++f+ +++  + f +e+++++re + ++ys  +y+++ +l+e ++ l + +if++ + +++g  ++  ++
  gene3035|gene3035|rna3035|rna3035   7 YSISATISFIPIITG-MAFNSEHKMVKREIAVNTYSITSYYFSVLLFEYLRCLPFMIIFMIGSKIIIGQMVD--LM 79 
                                        555566676777777.89*****************************************************9..** PP

                      ABC2_membrane 133 flllllltalaasslgllisalapsfedasqlaslvllp 171
                                        ++++ +l++ +++   l+ +++++  + ++++ +l++++
  gene3035|gene3035|rna3035|rna3035  80 IMFIYFLMFTTLIVAYLFYGSVLRGTKKVILVYGLFIIF 118
                                        ************************999999999888865 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.029
                      ABC2_membrane 124 gldlsrfflflllllltalaasslgllis 152
                                        g+++  +f +l  ++l++++++   l++s
  gene3035|gene3035|rna3035|rna3035 203 GYEIPIVFNYLTCVVLIIVYMLLCILMLS 231
                                        55554224444444455555544444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1239  (0.0691059); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 1810.77
//
Query:       gene3036|gene3036|rna3036|rna3036  [L=52]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (52 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       253  (0.0141112); expected 358.6 (0.02)
Passed bias filter:                      202  (0.0112667); expected 358.6 (0.02)
Passed Vit filter:                         6  (0.000334653); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.31u 0.25s 00:00:00.56 Elapsed: 00:00:00.39
# Mc/sec: 401.92
//
Query:       gene3037|gene3037|rna3037|rna3037  [L=50]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.094   13.0   0.0      0.095   12.9   0.0    1.0  1  DUF3102   Protein of unknown function (DUF3102)


Domain annotation for each model (and alignments):
>> DUF3102  Protein of unknown function (DUF3102)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   5.3e-06     0.095      69     108 ..       7      45 ..       1      49 [. 0.85

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5.3e-06
                            DUF3102  69 yGskllasadeassnsealsnltytqaliLlgvpeeeRee 108
                                         G+++ ++  e++++ +++++l+ +qal L++v e +R+e
  gene3037|gene3037|rna3037|rna3037   7 SGHQQPEEV-EEDPEEDQVRDLAPVQALALVQVLEHQRAE 45 
                                        577777776.99999***********************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (50 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       406  (0.0226449); expected 358.6 (0.02)
Passed bias filter:                      250  (0.0139439); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.26s 00:00:00.61 Elapsed: 00:00:00.41
# Mc/sec: 364.83
//
Query:       gene3038|gene3038|rna3038|rna3038  [L=41]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (41 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       670  (0.0373696); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.29s 00:00:00.63 Elapsed: 00:00:00.43
# Mc/sec: 283.75
//
Query:       gene3039|gene3039|rna3039|rna3039  [L=58]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (58 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       265  (0.0147805); expected 358.6 (0.02)
Passed bias filter:                      223  (0.0124379); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.26s 00:00:00.60 Elapsed: 00:00:00.42
# Mc/sec: 417.37
//
Query:       gene304|gene304|rna304|rna304  [L=76]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       238  (0.0132746); expected 358.6 (0.02)
Passed bias filter:                      218  (0.0121591); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.25s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 577.62
//
Query:       gene3040|gene3040|rna3040|rna3040  [L=700]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-16   60.8   0.0    3.2e-16   59.6   0.0    1.6  1  HA2              Helicase associated domain (HA2)
    1.5e-14   54.3   0.8    4.2e-14   52.8   0.8    1.8  1  Helicase_C       Helicase conserved C-terminal domain
    2.5e-10   40.6   0.0    6.8e-10   39.2   0.0    1.7  1  OB_NTP_bind      Oligonucleotide/oligosaccharide-binding (OB)
    3.6e-05   24.1   0.0    7.1e-05   23.2   0.0    1.5  1  AAA_19           AAA domain
    0.00046   20.2   0.2      0.025   14.6   0.2    2.8  1  ResIII           Type III restriction enzyme, res subunit
     0.0021   18.1   0.3     0.0098   15.9   0.1    2.3  2  AAA_14           AAA domain
     0.0021   17.8   0.2      0.013   15.3   0.2    2.2  1  DEAD             DEAD/DEAH box helicase
     0.0025   17.7   0.0     0.0059   16.5   0.0    1.6  1  Helicase_RecD    Helicase
      0.009   15.1   0.0      0.017   14.2   0.0    1.5  1  T2SSE            Type II/IV secretion system protein
  ------ inclusion threshold ------
      0.014   15.7   0.0      0.049   13.9   0.0    1.9  2  AAA_22           AAA domain
      0.016   15.0   0.0      0.029   14.1   0.0    1.3  1  AAA_30           AAA domain
      0.024   14.4   0.0       0.05   13.3   0.0    1.5  1  Viral_helicase1  Viral (Superfamily 1) RNA helicase
      0.025   14.2   0.0      0.048   13.3   0.0    1.5  1  SRP54            SRP54-type protein, GTPase domain
      0.041   13.3   0.0       0.17   11.3   0.0    2.0  2  PhoH             PhoH-like protein
      0.077   12.8   0.2       0.92    9.2   0.0    2.4  2  AAA_11           AAA domain
      0.079   12.2   0.0       0.14   11.4   0.0    1.4  1  DUF2075          Uncharacterized conserved protein (DUF2075)
       0.19   12.3   0.1       0.67   10.5   0.0    1.9  2  ABC_tran         ABC transporter
       0.19   12.6   1.0        2.1    9.2   0.1    2.8  2  RTTN_N           Rotatin, an armadillo repeat protein, centri


Domain annotation for each model (and alignments):
>> HA2  Helicase associated domain (HA2)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.6   0.0   3.2e-19   3.2e-16       1      78 [.     477     572 ..     477     598 .. 0.78

  Alignments for each domain:
  == domain 1  score: 59.6 bits;  conditional E-value: 3.2e-19
                                HA2   1 AlelLvalgALdeegnlTelGrkmaelPlsprlakmLlaaaeleegcldevitivAalsveeifleeneeekeeee 76 
                                        Ale+L++l+ALd+ g+lT+lG k+a+lPl+p l+  Ll +  ++ g++ ev ti+A+lsv++if   n ee ee +
  gene3040|gene3040|rna3040|rna3040 477 ALERLYRLKALDDGGSLTALGLKIARLPLEPELSIALLKS--FQLGVFTEVSTICALLSVQNIFNYTNIEEYEEIK 550
                                        89**************************************..666*******************888877766666 PP

                                HA2  77 e....................e 78 
                                        +                    +
  gene3040|gene3040|rna3040|rna3040 551 KkygdctgdlfflmnvyhaviK 572
                                        5666666655555544443331 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.8   0.8   4.2e-17   4.2e-14       3     110 ..     291     415 ..     289     416 .. 0.90

  Alignments for each domain:
  == domain 1  score: 52.8 bits;  conditional E-value: 4.2e-17
                                        HHHHHHHHHHTTTTSEEEEEESSHHHHHH.HHHHHHHT..TSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGG CS
                         Helicase_C   3 leallellkleeeggkilifvntidrlek.vklllekk..gikvavlhgelpqnereeileqfnkgesdvLiatdv 75 
                                        +++l++ll++ + + ++l+f+   +++++ ++l++ +   +  v +lh++l+ +++++i++++n+  s+++++t++
  gene3040|gene3040|rna3040|rna3040 291 IDQLKALLSNAQANLNTLVFLSGMQDIDRcFNLIKGQGfeKTVVFKLHSSLSFKDQQRIFRKYNE--SKIILSTNI 364
                                        678899999999*************9998788886666888999*******************65..78******* PP

                                        GTSSSTSTTESEEEESSSSSSH................HHHHHHHTTSSST CS
                         Helicase_C  76 aerGidipkvnlVinfdlprnv................tsyiqriGRtgRa 110
                                        ae++i+i ++++Vi+ ++ ++                 +++ qr+GR+gR 
  gene3040|gene3040|rna3040|rna3040 365 AETSITIGDLDVVIDSGFVKQKrmeggierlemiriskEQADQRSGRVGRT 415
                                        *******************7755688999999999999************6 PP

>> OB_NTP_bind  Oligonucleotide/oligosaccharide-binding (OB)-fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.2   0.0   6.8e-13   6.8e-10       3      78 ..     623     692 ..     621     695 .. 0.90

  Alignments for each domain:
  == domain 1  score: 39.2 bits;  conditional E-value: 6.8e-13
                                        HHHHHHHTTCEEEEEETTCCEEETTTCEEEEE-TTSTTTTT...TSSSEEEEEEEEESSSEEEEEEEEE-HHHHHH CS
                        OB_NTP_bind   3 aillaGlypqiarkdpskkdyktartktrvfihpsSvlaknekekepewvvytelvettklylrdltaidpawLll 78 
                                        ++ +aG++ + ar++  +  +k + ++ ++ +hpsS+l+     +++e+++yt+ v t+k+y++++++i  + Ll+
  gene3040|gene3040|rna3040|rna3040 623 KSFCAGYFLNTARRAGAS--FKMLLNDDEIRVHPSSMLNA----SNSEFILYTNVVFTDKTYAKNCVKIGREDLLE 692
                                        889*********886655..888889*************8....*************************9998886 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.0   7.1e-08   7.1e-05       1     125 [.     116     236 ..     116     247 .. 0.67

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 7.1e-08
                             AAA_19   1 qreave.alkekvllvtaGpGtGKTrvl.khivallvelggvkpeeillvaftgrAakelrerlaalgaeatTiHr 74 
                                        q+ ++e   +++v+l+ +G G+GK++ + k  +++++++   +p++i++v +++r   e+ erl       +T+ +
  gene3040|gene3040|rna3040|rna3040 116 QKMIIEaLEQNEVVLIEGGTGCGKSTQIpKFLLNYFEKIVVSQPRRIAAVNLAKRVSLEIDERL------GHTVGY 185
                                        56677756788999**********8877256789999999999*********************......566665 PP

                             AAA_19  75 lalldfddll..tealelle.....eaeeekklqeee.llivDEfqdvdelqyrLlkal 125
                                           + f ++    + l+++      +     + +e++ l+i+DE+ + +     ++ a+
  gene3040|gene3040|rna3040|rna3040 186 K--VRFGEKSsdRTRLKFVTdgillQ-----E-REKYdLVIIDEVHERKLNTDVFFAAM 236
                                        5..33333330022344433333222.....2.344459*****988765555555555 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.2   2.5e-05     0.025       5     170 ..     113     252 ..     109     253 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.5e-05
                                        -HHHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG CS
                             ResIII   5 reyQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkflse 80 
                                        + yQ+ +ie+l      ++++ +li+  TG+GK+  + k+  ++++     k+++  pr++    + ++++  ++e
  gene3040|gene3040|rna3040|rna3040 113 YAYQKMIIEAL------EQNEVVLIEGGTGCGKSTQIPKFLLNYFE-----KIVVSQPRRIAAVNLAKRVSLEIDE 177
                                        56777777766......47888999999999999999999999998.....6888888887777777777776666 PP

                                        ....GEEEESSS-B--.......-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.T.TTHHHHH CS
                             ResIII  81 aykeigkkvsgdkkkakekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakk.swreile 155
                                              + + g k ++ ek+s+ +++ ++t   l +++            +++d++iiDE+H  + ++  + ++++
  gene3040|gene3040|rna3040|rna3040 178 RL----GHTVGYKVRFGEKSSDRTRLKFVTDGILLQER------------EKYDLVIIDEVHERKLNTdVFFAAMN 237
                                        53....22223333333445688999999988888888............99**********98776345556677 PP

                                        T---SEEEEEESS-S CS
                             ResIII 156 kfkeavllglTATpe 170
                                         ++ + l+ ++AT +
  gene3040|gene3040|rna3040|rna3040 238 TYRYNRLILMSATVN 252
                                        7899*********86 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1   9.8e-06    0.0098       2      86 ..     126     235 ..     125     257 .. 0.69
   2 ?   -3.1   0.0       7.5   7.5e+03      54      84 ..     295     325 ..     269     349 .. 0.65

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 9.8e-06
                             AAA_14   2 rkilvitGaRrvGKTtllkqlikell.....vkkesilyinldderd..................kkladpeklle 54 
                                        +++++i+G   +GK+t + +++ +++      ++++i  +nl +                     +k++d  + l+
  gene3040|gene3040|rna3040|rna3040 126 NEVVLIEGGTGCGKSTQIPKFLLNYFekivvSQPRRIAAVNLAKRVSleiderlghtvgykvrfgEKSSDR-TRLK 200
                                        789*****************999999999998999******999777666666777777655554222222.2223 PP

                             AAA_14  55 lileklke.......ekktylflDEiqevpewekalksl 86 
                                        ++     +       ek  ++++DE++e +   ++    
  gene3040|gene3040|rna3040|rna3040 201 FVT----DgillqerEKYDLVIIDEVHERKLNTDVFFAA 235
                                        333....1233333356677*******976555555555 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 7.5
                             AAA_14  54 elileklkeekktylflDEiqevpewekalk 84 
                                        +++l++++++ +t++fl  +q +++ ++ +k
  gene3040|gene3040|rna3040|rna3040 295 KALLSNAQANLNTLVFLSGMQDIDRCFNLIK 325
                                        3333333334566777777777766666666 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.2   1.3e-05     0.013       2     170 ..     114     252 ..     113     257 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.3e-05
                                        HHHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSE CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               DEAD   2 diQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlr 77 
                                        ++Q+ +i+++ +++ vl+++ TG GK++     +l+ +         k+++  P r  a + +++++  +++   r
  gene3040|gene3040|rna3040|rna3040 114 AYQKMIIEALEQNEVVLIEGGTGCGKSTQIPKFLLNYF--------EKIVVSQPRRIAAVNLAKRVSLEIDE---R 178
                                        68*************************99887788666........5899999**99999999999766664...3 PP

                                        EEEEETTSSHHHHHHHHHTTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHC CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               DEAD  78 vlliiggvaardqlskldngvdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsdfinrilnqlpqit 153
                                        +  ++g + +    +    ++++ + t g l++  +      ++  ++++DE+++   +   d   + +n+ +   
  gene3040|gene3040|rna3040|rna3040 179 LGHTVGYKVR-FGEKSS-DRTRLKFVTDGILLQ--E-----REKYDLVIIDEVHERKLN--TDVFFAAMNTYR--- 240
                                        3333442222.222222.446777889999998..4.....3579999******98877..444444466662... PP

                                        TTSTTTSEEEEEESSBS CS
                                        xxxxxxxxxxxxxxxxx RF
                               DEAD 154 cdgklqrqvivlSATlp 170
                                              +++i++SAT++
  gene3040|gene3040|rna3040|rna3040 241 -----YNRLILMSATVN 252
                                        .....235999999987 PP

>> Helicase_RecD  Helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   5.9e-06    0.0059       2     126 ..     131     254 ..     130     256 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 5.9e-06
                      Helicase_RecD   2 ltAdRGRGKSaalGlalaaliaegksnilvtapskenvktlfeflakglea.lglkeeekkkkaekaelrvrkqri 76 
                                        + ++ G GKS+ + ++l +  ++    i+v+ p++ ++ +l +++  ++++ lg +      k +  e +++++r+
  gene3040|gene3040|rna3040|rna3040 131 IEGGTGCGKSTQIPKFLLNYFEK----IVVSQPRRIAAVNLAKRVSLEIDErLGHTVGY---KVRFGEKSSDRTRL 199
                                        778899*******9999988887....******************77776513333222...2222335567**** PP

                      Helicase_RecD  77 eyiapdellklkeqadllvvDEAAa..iplpllkkl...lekfkrvvlatTvhGY 126
                                        ++++   ll+++e+ dl+++DE     +++++  +     ++++ ++++ Tv++Y
  gene3040|gene3040|rna3040|rna3040 200 KFVTDGILLQEREKYDLVIIDEVHErkLNTDVFFAAmntYRYNRLILMSATVNSY 254
                                        **********************975225555555552324455678889999999 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   1.7e-05     0.017     116     154 ..     113     152 ..      51     180 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.7e-05
                              T2SSE 116 ekiaevlrkavrerglilvsGgTgsGKttll.yallkein 154
                                         ++++++ +a++++ ++l+ GgTg GK+t +   ll++++
  gene3040|gene3040|rna3040|rna3040 113 YAYQKMIIEALEQNEVVLIEGGTGCGKSTQIpKFLLNYFE 152
                                        56788999999******************87444444444 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0     5e-05     0.049       5     102 ..     126     224 ..     122     250 .. 0.76
   2 ?   -2.8   0.0         7   6.9e+03     111     136 ..     293     320 ..     277     321 .. 0.56

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5e-05
                             AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaee....erpevvfvtlpsstsskdllrellralglelkaerlsse 76 
                                          ++++ G +G+GK+t + ++l ++      e+    ++++++ v+l++   s ++ ++l + +g +    ++ss+
  gene3040|gene3040|rna3040|rna3040 126 NEVVLIEGGTGCGKSTQIPKFLLNYF-----EKivvsQPRRIAAVNLAKRV-SLEIDERLGHTVGYKVRFGEKSSD 195
                                        5678999*****************93.....33466567777799999999.889999999999988888555555 PP

                             AAA_22  77 ell.ealeqalrarav..ielliiDEaqh 102
                                        + + + +++ +  + +    l+iiDE++ 
  gene3040|gene3040|rna3040|rna3040 196 RTRlKFVTDGILLQERekYDLVIIDEVHE 224
                                        55556666666666666677*******97 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 7
                             AAA_22 111 eLrsllnl..srkgvqliLvGtpelrkl 136
                                        +L+ ll +  +  ++ ++L G+++++++
  gene3040|gene3040|rna3040|rna3040 293 QLKALLSNaqANLNTLVFLSGMQDIDRC 320
                                        3333333324444555667777777665 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   2.9e-05     0.029       6      97 ..     116     222 ..     112     232 .. 0.57

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.9e-05
                             AAA_30   6 QaaavealltsgdrvavltGpAGtGKttalkal.....reaweaaggrviglAptgkaAkvLaeelgi....east 72 
                                        Q+ ++eal +++  v++++G+ G GK+t + +      ++++ ++ +r++++   ++++ ++ e lg     + + 
  gene3040|gene3040|rna3040|rna3040 116 QKMIIEALEQNE--VVLIEGGTGCGKSTQIPKFllnyfEKIVVSQPRRIAAVNLAKRVSLEIDERLGHtvgyKVRF 189
                                        666666554444..*************9765552000033444444555555555555554445444322223333 PP

                             AAA_30  73 iakllkrlk..............grarlepgtllivDEa 97 
                                         +k                    +  + e+ +l+i+DE+
  gene3040|gene3040|rna3040|rna3040 190 GEKS----SdrtrlkfvtdgillQ--EREKYDLVIIDEV 222
                                        3333....1444577777787542..344559*****96 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0     5e-05      0.05       2      40 ..     130     177 ..     129     231 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5e-05
                    Viral_helicase1   2 vvhGvpGcGKStlirkllrts..liltvnrptaelltegk.......p 40 
                                        ++ G  GcGKSt i k+l +    i+++ ++++++++ +k       +
  gene3040|gene3040|rna3040|rna3040 130 LIEGGTGCGKSTQIPKFLLNYfeKIVVSQPRRIAAVNLAKrvsleidE 177
                                        799***************998987777777778888877755555551 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   4.8e-05     0.048       2      91 ..     127     221 ..     126     251 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.8e-05
                                        EEEEEEESTTSSHHHHHHHHHHHHHHT...TS-EEEEEESTSSTTHHHHHHHHHHHTTEEEEE..SSTTSCHHHHH CS
                              SRP54   2 nvillvGlqGaGKTttlaKLaallkke...gkkvllvaaDtfRaaAveQLktlaeklgvpvik..kkeeadpaava 72 
                                        +v+l+ G +G GK t + K    + ++    +   ++a+   +   +e  + l++++g +v    k++++   +++
  gene3040|gene3040|rna3040|rna3040 127 EVVLIEGGTGCGKSTQIPKFLLNYFEKivvSQPRRIAAVNLAKRVSLEIDERLGHTVGYKVRFgeKSSDRTRLKFV 202
                                        58999**************7655555558888899*******99999999999999875553322677778999** PP

                                        HHHHHHHHHTTSSEEEEEE CS
                              SRP54  73 keavekakeekidvvlvDT 91 
                                         +++  +++ek+d+v++D 
  gene3040|gene3040|rna3040|rna3040 203 TDGILLQEREKYDLVIIDE 221
                                        ******************5 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00017      0.17       8      34 ..     115     141 ..     111     185 .. 0.82
   2 ?   -3.5   0.0         6     6e+03      79      96 ..     286     303 ..     276     330 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00017
                                        HHHHHHHHHHH-SEEEEE--TTSSTTH CS
                               PhoH   8 eQkeylealkkndivfaiGpaGtGKty 34 
                                         Qk ++eal++n++v + G +G+GK+ 
  gene3040|gene3040|rna3040|rna3040 115 YQKMIIEALEQNEVVLIEGGTGCGKST 141
                                        69***********************84 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 6
                                        TTHHHHHHHTTTS-TTCH CS
                               PhoH  79 ylrplydaLkdllgaekv 96 
                                        y+r ++d+Lk ll++++ 
  gene3040|gene3040|rna3040|rna3040 286 YVRKIIDQLKALLSNAQA 303
                                        778888888888876654 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.0   0.00092      0.92       9      41 ..     118     150 ..     114     177 .. 0.81
   2 ?    0.2   0.1      0.52   5.2e+02     211     225 ..     208     221 ..     192     223 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00092
                             AAA_11   9 aiksalseseitliqGPPGtgKTktivellsql 41 
                                         i +al+++e++li+G  G+gK++ i ++l + 
  gene3040|gene3040|rna3040|rna3040 118 MIIEALEQNEVVLIEGGTGCGKSTQIPKFLLNY 150
                                        56789******************9999988765 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.52
                             AAA_11 211 leklakkfdvviIDE 225
                                        l++  +k+d+viIDE
  gene3040|gene3040|rna3040|rna3040 208 LQER-EKYDLVIIDE 221
                                        4444.59******** PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00014      0.14       2      99 ..     127     224 ..     126     251 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00014
                            DUF2075   2 avvlVtGvaGtGKtvvllnllael.eddeeertavylsvNhplvl..vlrealakkeekkkkkeafeklssfinnl 74 
                                        +vvl++G++G GK+    ++l ++ e+    + + ++ vN + +    + e+l  +     +k +f + ss  ++l
  gene3040|gene3040|rna3040|rna3040 127 EVVLIEGGTGCGKSTQIPKFLLNYfEKIVVSQPRRIAAVNLAKRVslEIDERLGHTV---GYKVRFGEKSSDRTRL 199
                                        69************9887777776566677777777888866654114445555544...4555555555555555 PP

                            DUF2075  75 sef.kkaeekkeepkedvvivDEAhr 99 
                                        + f  + +  +e++k d+vi+DE h 
  gene3040|gene3040|rna3040|rna3040 200 K-FvTDGILLQEREKYDLVIIDEVHE 224
                                        5.4578999**************994 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00067      0.67       8      28 ..     123     143 ..     118     157 .. 0.88
   2 ?   -2.4   0.0       6.3   6.2e+03      86     117 ..     318     349 ..     287     409 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00067
                                        EETTSEEEEEESTTSSHHHHH CS
                                        xxxxxxxxxxxxxxxxxxxxx RF
                           ABC_tran   8 lkegekvaivGenGaGKStLl 28 
                                        l+++e+v i G +G+GKSt +
  gene3040|gene3040|rna3040|rna3040 123 LEQNEVVLIEGGTGCGKSTQI 143
                                        7899***************65 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 6.3
                                        HHHHHHSTTGGTTCBGESTTSGGS-HHHHHHH CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ABC_tran  86 ekalsklglkelkdtvvksspssLSgGqkqrv 117
                                        ++  + ++ +++++tvv +  ssLS   +qr+
  gene3040|gene3040|rna3040|rna3040 318 DRCFNLIKGQGFEKTVVFKLHSSLSFKDQQRI 349
                                        44455555555666666565666665555554 PP

>> RTTN_N  Rotatin, an armadillo repeat protein, centriole functioning
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.1    0.0021       2.1      21      83 ..      18      79 ..       5      90 .. 0.81
   2 ?    0.3   0.0       1.3   1.3e+03      15      41 ..     579     605 ..     571     611 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0021
                             RTTN_N 21 eedlvkekellkkLlewFnfepvpeeeevLaLllkllkspsaaellkkigavefLsklrknve 83
                                       ++++++   +l+k  ++F +ep+ +++  ++L+  l   ++ ++++ k +  +fL+kl+++ e
  gene3040|gene3040|rna3040|rna3040 18 DQEVIEYILFLIKQKRLFEIEPLLQRADFVKLIDILCDDSKHKDIYIKRDEPHFLRKLKNI-E 79
                                       4555566666666678******************************************954.3 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 1.3
                             RTTN_N  15 ehgllseedlvkekellkkLlewFnfe 41 
                                        +++ +s++++++ k ++ +L  +F+++
  gene3040|gene3040|rna3040|rna3040 579 QRNKISFKAIIEAKLIIEQLHSLFGMH 605
                                        6778999*****************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (700 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       605  (0.0337442); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.71u 0.32s 00:00:01.03 Elapsed: 00:00:00.49
# Mc/sec: 4260.47
//
Query:       gene3041|gene3041|rna3041|rna3041  [L=118]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       628  (0.0350271); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 845.71
//
Query:       gene3042|gene3042|rna3042|rna3042  [L=207]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-09   37.5   2.5    5.3e-09   36.0   2.5    1.8  1  E2F_TDP   E2F/DP family winged-helix DNA-binding domain
    1.3e-08   34.8   6.5    1.3e-08   34.8   6.5    1.9  2  DP        Transcription factor DP
  ------ inclusion threshold ------
       0.17   12.5   1.0        2.9    8.5   0.2    2.5  2  KI67R     KI67R (NUC007) repeat
       0.38   10.3   5.2       0.76    9.4   1.0    2.3  2  HTH_24    Winged helix-turn-helix DNA-binding


Domain annotation for each model (and alignments):
>> E2F_TDP  E2F/DP family winged-helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.0   2.5   1.2e-12   5.3e-09       3      67 ..      16      76 ..      14      80 .. 0.91

  Alignments for each domain:
  == domain 1  score: 36.0 bits;  conditional E-value: 1.2e-12
                            E2F_TDP  3 ksLgvltkkfvellkesakgtlslneaakeLvdkkdekvkkRRiYDilNVLealglieKesknei 67
                                        +L++++  + +ll +  ++ ++++++++ ++ ++++++ +RR+YD+l V+ +l+++ K  k  +
  gene3042|gene3042|rna3042|rna3042 16 DGLKQISVSIHNLLLN--NKDITYQKICSSIN-TSNTNTLRRRVYDVLSVMRSLNMVVKA-KRCY 76
                                       79************66..888***********.9*************************9.6655 PP

>> DP  Transcription factor DP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.29   1.3e+03      26      43 ..      67      84 ..      39      89 .. 0.66
   2 !   34.8   6.5     3e-12   1.3e-08      13     108 ..      87     178 ..      73     197 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.29
                                 DP 26 eLilqqvalknLvqrNre 43
                                       +++++     nLv+rN  
  gene3042|gene3042|rna3042|rna3042 67 NMVVKAKRCYNLVRRNLL 84
                                       455666677799999965 PP

  == domain 2  score: 34.8 bits;  conditional E-value: 3e-12
                                 DP  13 reerikkkkeqlqeLilqqvalknLvqrNreleekkgapsensviqLPFiivnTskktvidcsiseDkseylfnFd 88 
                                        ++  +++k++ql++L+  +  ++++v +N    +   + s +  + LPF+iv ++k++++ c+  e+++ + f  +
  gene3042|gene3042|rna3042|rna3042  87 KRMVVEEKRKQLEDLQHMKEVFEHIVLKNAFKTH---SLSLD-RFYLPFMIVVAEKDSNVHCETNEERTFFKFRSS 158
                                        455699***********************96554...33333.579****************************** PP

                                 DP  89 ktFeihdDievLkrmglalg 108
                                        k  ++ +D+++Lk++   ++
  gene3042|gene3042|rna3042|rna3042 159 KPIKLVEDLDILKELYKNNE 178
                                        *************9866555 PP

>> KI67R  KI67R (NUC007) repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.2   0.00065       2.9      93     110 ..      92     109 ..      79     110 .. 0.78
   2 ?    2.1   0.0     0.062   2.8e+02      97     110 ..     162     175 ..     144     176 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00065
                              KI67R  93 KekaqslEDlagfkELFq 110
                                         ek + lEDl+++kE+F+
  gene3042|gene3042|rna3042|rna3042  92 EEKRKQLEDLQHMKEVFE 109
                                        567778**********96 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.062
                              KI67R  97 qslEDlagfkELFq 110
                                        + +EDl+ +kEL++
  gene3042|gene3042|rna3042|rna3042 162 KLVEDLDILKELYK 175
                                        679*********86 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   1.0   0.00017      0.76       5      37 ..      22      54 ..      18      54 .. 0.90
   2 ?    2.7   0.2     0.021        94       5      15 ..     166     176 ..     166     178 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00017
                             HTH_24  5 drkILelLqknprisqreLAerlglSpstvnrr 37
                                          I +lL  n +i+++ ++  ++ S ++++rr
  gene3042|gene3042|rna3042|rna3042 22 SVSIHNLLLNNKDITYQKICSSINTSNTNTLRR 54
                                       56799***********************99998 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.021
                             HTH_24   5 drkILelLqkn 15 
                                        d++IL++L+kn
  gene3042|gene3042|rna3042|rna3042 166 DLDILKELYKN 176
                                        89********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1322  (0.0737353); expected 358.6 (0.02)
Passed bias filter:                      494  (0.0275531); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1393.91
//
Query:       gene3043|gene3043|rna3043|rna3043  [L=942]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.4e-20   71.8   0.2    4.3e-11   41.8   0.1    3.3  3  tRNA-synt_1   tRNA synthetases class I (I, L, M and V)
    4.9e-20   71.6   0.0      3e-09   36.1   0.0    2.7  2  tRNA-synt_1g  tRNA synthetases class I (M)
    2.3e-06   27.2   0.0    5.4e-06   26.0   0.0    1.6  1  tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
     0.0023   17.9   0.4     0.0066   16.4   0.0    1.9  2  Anticodon_1   Anticodon-binding domain of tRNA


Domain annotation for each model (and alignments):
>> tRNA-synt_1  tRNA synthetases class I (I, L, M and V)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.8   0.1   9.6e-15   4.3e-11      10     171 ..      17     183 ..      10     191 .. 0.84
   2 !    4.4   0.0    0.0021       9.2     367     437 ..     367     438 ..     360     452 .. 0.86
   3 !   21.5   0.0   1.4e-08   6.1e-05     510     601 ..     503     595 ..     495     596 .. 0.89

  Alignments for each domain:
  == domain 1  score: 41.8 bits;  conditional E-value: 9.6e-15
                        tRNA-synt_1  10 dvfkkelekeke.kkefilvdgPPyvtGslHiGhalaktlkdivirykrmkGkevlyvpGwDhaGlaieakvekkl 84 
                                        ++fk+++e+  e ++++ ++ + Py +G+lH+Gh +  +  +++ ryk +kG+++ + + +   G++i a+  kkl
  gene3043|gene3043|rna3043|rna3043  17 KIFKNTVEHGGEkRPKYFVTFPYPYMNGKLHLGHLYSFSKSEFMARYKCLKGFDAFFPFAFHGTGMPISAAA-KKL 91 
                                        6899999998887999****************************************************9876.566 PP

                        tRNA-synt_1  85 gakekkerk...klgreef..rekvrewkaeyaeeirkqvkrlGvsvDfdreylT..ldkeleeavkevfvrladk 153
                                         + ++ +++   ++g ++    +  r+w  ++    ++ ++++   v +++  +T  l++ +   vk+ f rl  k
  gene3043|gene3043|rna3043|rna3043  92 CEGDQGTVQllnSIGIKNTepFKDARHWLYYFPPLAKDVITKFQSYVNWNHSFITtdLNPYYDSFVKWQFHRL--K 165
                                        6666666652225565543115679*****************************94455779999*******9..5 PP

                        tRNA-synt_1 154 gliyrgkklvnwstklkt 171
                                          i  gkk   ++t+++ 
  gene3043|gene3043|rna3043|rna3043 166 NYISYGKKETIYCTATNQ 183
                                        688899999999988775 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.0021
                        tRNA-synt_1 367 rskkpiiyrateqWfvrvke..ladaalkavekvqfvpkskekryaswleniqdWciSRqrwWGhriplfvsk 437
                                        r++   ++ +++qWf   ++   +  + + +e+++  p++k ++  + l  i  W +SR    G+    +v +
  gene3043|gene3043|rna3043|rna3043 367 RTGSKCVVALVNQWFLDYDNadWKRRVAECIEDMNCLPETK-RMLLDALGWIDKWGFSRTFGLGTSFREYVID 438
                                        888899999*********997788999999********986.577889999********99999887777765 PP

  == domain 3  score: 21.5 bits;  conditional E-value: 1.4e-08
                        tRNA-synt_1 510 elkkffpadmlleGlDiirgWvarlillslaltgsePf.kevlvhglvrdeeGrKmSKslgNvidpldvikkygad 584
                                         +++++p d+ ++G D i+  +   i+  +a++ +  + ++++++g ++ +   KmSKs gN +  ++ i+  ga 
  gene3043|gene3043|rna3043|rna3043 503 AFSRYYPVDLRVSGKDLIKNHLLFYIFHHVAIFPKDCWpRRIYTNGHLLLN-SAKMSKSEGNFLTAEESIQMFGAS 577
                                        7999****************************9999774789999977755.579********************* PP

                        tRNA-synt_1 585 alRltli.lsdvgrdinl 601
                                        + R +l+   d  +d n+
  gene3043|gene3043|rna3043|rna3043 578 VTRIVLAdAGDFNEDANF 595
                                        *******87888888877 PP

>> tRNA-synt_1g  tRNA synthetases class I (M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.5   0.0   8.2e-12   3.7e-08       1      59 [.      33      91 ..      33     117 .. 0.90
   2 !   36.1   0.0   6.8e-13     3e-09     286     369 ..     513     598 ..     491     615 .. 0.90

  Alignments for each domain:
  == domain 1  score: 32.5 bits;  conditional E-value: 8.2e-12
                                       EEEEE--B--SS---HHHHHHHHHHHHHHHHHHHTT-EEEEEEEE---SHHHHHHHHHT CS
                       tRNA-synt_1g  1 vlvttalpYangklHlGhllevisaDifaRykrlrgeevlfvcgtDehGtpielkAeke 59
                                       ++vt + pY+ngklHlGhl++  ++  +aRyk l+g + +f  +    G+pi  +A+k 
  gene3043|gene3043|rna3043|rna3043 33 YFVTFPYPYMNGKLHLGHLYSFSKSEFMARYKCLKGFDAFFPFAFHGTGMPISAAAKKL 91
                                       589*****************************************999999999999874 PP

  == domain 2  score: 36.1 bits;  conditional E-value: 6.8e-13
                                        EEEEGGGHHHHHTHHHHHHHH..TT----S-EEEE--EEE--------------HHHHHHHH-HHHHHHHHHHHS- CS
                       tRNA-synt_1g 286 hfigkdiikFHtifwPaillg..aelklpkkvvaheyltvegkKlSkSrgvvvkakealerldadllRYylaaeap 359
                                         + gkd ik H +f+     +   +   p++++++++l ++ +K+SkS+g++ +a+e ++ + a + R +la +++
  gene3043|gene3043|rna3043|rna3043 513 RVSGKDLIKNHLLFYIFHHVAifPKDCWPRRIYTNGHLLLNSAKMSKSEGNFLTAEESIQMFGASVTRIVLADAGD 588
                                        567***********99999997766669************************************************ PP

                                        TTS-EEE-HH CS
                       tRNA-synt_1g 360 ekkDldfswe 369
                                        +++D++fs++
  gene3043|gene3043|rna3043|rna3043 589 FNEDANFSQA 598
                                        *******975 PP

>> tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   0.0   1.2e-09   5.4e-06     208     295 ..     510     599 ..     503     604 .. 0.90

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 1.2e-09
                                        EEEEEEEGGGTTTHHHHHHHHHHHHSS.S--EEEEEEE--EEETTBE--TTTT---BHHHHHTTS-HHHHHHHHHS CS
                       tRNA-synt_1e 208 idihsGGiDLafPhhenelaqseaafd.kqlvkyflhnghlkiegekmsksLknfitikdvlkkfdprqlRlllls 282
                                        +d+ + G+DL+  h    +  + a f    + +    nghl ++  kmsks +nf+t ++ ++ f +++ R++l+ 
  gene3043|gene3043|rna3043|rna3043 510 VDLRVSGKDLIKNHLLFYIFHHVAIFPkDCWPRRIYTNGHLLLNSAKMSKSEGNFLTAEESIQMFGASVTRIVLAD 585
                                        799999*******************995678999999************************************997 PP

                                        S.-TTS-EEE-HHH CS
                       tRNA-synt_1e 283 a.hyrsqldfkeel 295
                                        a ++++  +f++ l
  gene3043|gene3043|rna3043|rna3043 586 AgDFNEDANFSQAL 599
                                        53899999999865 PP

>> Anticodon_1  Anticodon-binding domain of tRNA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.1       2.1   9.4e+03      22      52 ..     593     623 ..     587     630 .. 0.64
   2 !   16.4   0.0   1.5e-06    0.0066      10     110 ..     738     817 ..     730     851 .. 0.76

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 2.1
                        Anticodon_1  22 yrfnkaasalyeffwndlcdwylelvkprly 52 
                                         +f++a+++ y + ++++ ++   ++++ ++
  gene3043|gene3043|rna3043|rna3043 593 ANFSQALADTYVLKLHTFINYVESFIQEMIQ 623
                                        6888888888888777775555555555554 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 1.5e-06
                        Anticodon_1  10 klvkevteayeeyrfnkaasalyeffwndlcdwylelvkprlysesaedkraaqevllevletllrllaPfmPfit 85 
                                         lv+++++aye + ++++++  ++    ++ ++ +el  +   +    +k    e++l+++++ l +++P++  ++
  gene3043|gene3043|rna3043|rna3043 738 YLVSRCDQAYEGMMYRDVVKYGFH----EF-KTLIELCVSLG-C----SK----EAVLYAIKNNLLVMHPVITAVC 799
                                        6899****************9888....57.88899985544.3....33....899******************* PP

                        Anticodon_1  86 Eelwqreeeelgkkesimlaewpe.k 110
                                        ++l     e++    +    +wpe +
  gene3043|gene3043|rna3043|rna3043 800 DYLL----EKY----FNKTLSWPElS 817
                                        ****....442....22223677633 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (942 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       742  (0.0413855); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.73u 0.26s 00:00:00.99 Elapsed: 00:00:00.45
# Mc/sec: 6316.17
//
Query:       gene3044|gene3044|rna3044|rna3044  [L=221]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.4e-21   76.0  14.6    3.2e-21   75.6  14.3    1.4  1  zf-CCCH_3  Zinc-finger containing family


Domain annotation for each model (and alignments):
>> zf-CCCH_3  Zinc-finger containing family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.6  14.3   1.8e-25   3.2e-21       6      96 ..       2      93 ..       1     109 [. 0.87

  Alignments for each domain:
  == domain 1  score: 75.6 bits;  conditional E-value: 1.8e-25
                          zf-CCCH_3  6 ddcyffyystctkGdscpfrheeaalGsetvctlWqegrclrevckfrhme..idkkrkeipcywenqpaGcqklhca 81
                                       ddcy++ ys ctk  +c++rh+ aa  + ++c+ W + r  r+ c +rh +  ++k rk+i cywe   +Gcqk  c 
  gene3044|gene3044|rna3044|rna3044  2 DDCYYYLYSVCTK-KNCTYRHSAAAKKNLIMCKTWANKRECRNECPLRHSDyhLRKDRKDIYCYWEDMEGGCQKEFCD 78
                                       8************.57*********************************7522799********************** PP

                          zf-CCCH_3 82 flhekpravdgllla 96
                                       f h++p++ + + ++
  gene3044|gene3044|rna3044|rna3044 79 FRHRNPEKDEWKKVK 93
                                       *****9987665554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       759  (0.0423336); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1537.86
//
Query:       gene3045|gene3045|rna3045|rna3045  [L=837]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.51   10.4   2.2        1.2    9.2   0.1    2.7  3  Ovate     Transcriptional repressor, ovate


Domain annotation for each model (and alignments):
>> Ovate  Transcriptional repressor, ovate
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0      0.22   3.9e+03      24      35 ..      65      76 ..      54      83 .. 0.63
   2 ?   -2.2   0.1      0.23   4.2e+03      11      31 ..     375     396 ..     374     397 .. 0.74
   3 ?    9.2   0.1   6.6e-05       1.2       7      31 ..     665     694 ..     663     705 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.22
                              Ovate 24 weeLeeLLacYL 35
                                        ++L eLLa  +
  gene3045|gene3045|rna3045|rna3045 65 SDDLSELLALLI 76
                                       456666666543 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.23
                              Ovate  11 SMeeMiae.kgikdweeLeeLL 31 
                                        SM+ M ++ k+ ++ +++ e+L
  gene3045|gene3045|rna3045|rna3045 375 SMVDMCCQyKEFENGQFIYEML 396
                                        9****96547777778877777 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 6.6e-05
                              Ovate   7 dFrkSMeeMiae.....kgikdweeLeeLL 31 
                                        d+ +SM eMi +     ++  ++e Le LL
  gene3045|gene3045|rna3045|rna3045 665 DINRSMTEMIINnilyfEKTCRKEVLEALL 694
                                        899*******76699998889999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (837 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       929  (0.0518155); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.69u 0.28s 00:00:00.97 Elapsed: 00:00:00.45
# Mc/sec: 5603.73
//
Query:       gene3046|gene3046|rna3046|rna3046  [L=221]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.7e-34  117.9   0.6    2.9e-34  117.2   0.6    1.4  1  Forkhead        Forkhead domain
  ------ inclusion threshold ------
      0.035   14.5   0.1      0.063   13.6   0.1    1.4  1  Linker_histone  linker histone H1 and H5 family


Domain annotation for each model (and alignments):
>> Forkhead  Forkhead domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.2   0.6   3.2e-38   2.9e-34       1      85 [.      81     165 ..      81     167 .. 0.95

  Alignments for each domain:
  == domain 1  score: 117.2 bits;  conditional E-value: 3.2e-38
                                        ------HHHHHHHHHHT-TTT-B-HHHHHHHHHCC-HHHHCC.-CCHHHHHHHHHHHHC--EEETT.-T.TSS--E CS
                           Forkhead   1 skPpysYaaLIaqAiksspekkltLseIyefieenfpyyrtaakkgWqnSirhnLslnkcFekvpreee.egkgsl 75 
                                        +kP ysY++LI+qA++s+ +kkltLs+Iy+fi+++++yyr+ a+  WqnSirhnLslnk F+kv+r+++ +gkg +
  gene3046|gene3046|rna3046|rna3046  81 NKPAYSYSQLITQALESNADKKLTLSQIYAFIKDKYAYYRH-ADPVWQNSIRHNLSLNKNFKKVQRPQNmPGKGGF 155
                                        69**************************************9.5***********************88768***** PP

                                        EE--TTHHHH CS
                           Forkhead  76 wtidpeseek 85 
                                        w +d+ s ++
  gene3046|gene3046|rna3046|rna3046 156 WILDKTSDSE 165
                                        ****988776 PP

>> Linker_histone  linker histone H1 and H5 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   7.1e-06     0.063       3      38 ..      86     121 ..      84     151 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 7.1e-06
                     Linker_histone   3 sykdMikeAIkalkerkGsSrqaIkkyikakykvv.d 38 
                                        sy+++i++A++++ + k  ++ +I  +ik+ky +  +
  gene3046|gene3046|rna3046|rna3046  86 SYSQLITQALESNAD-KKLTLSQIYAFIKDKYAYYrH 121
                                        8**********9766.7799************97552 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       664  (0.037035); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 1666.14
//
Query:       gene3047|gene3047|rna3047|rna3047  [L=193]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0006   20.0  10.1    0.00084   19.5   3.7    2.3  2  Maf1      Maf1 regulator
  ------ inclusion threshold ------
      0.012   15.5   0.6        3.5    7.5   0.2    2.2  2  BAH       BAH domain
      0.013   15.7   0.3      0.019   15.2   0.3    1.2  1  MecA_N    NTF2-like N-terminal transpeptidase domain


Domain annotation for each model (and alignments):
>> Maf1  Maf1 regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.3   1.3    0.0034        20       4      31 ..      61      90 ..      58     100 .. 0.73
   2 !   19.5   3.7   1.4e-07   0.00084      63     173 ..      80     184 ..      77     185 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0034
                               Maf1  4 rlelYsckaagsdk..klykkiekelesel 31
                                       +le+Ysck +++ +  ++yk++ ++l ++l
  gene3047|gene3047|rna3047|rna3047 61 NLEAYSCKYTKKQRkrQNYKNTMAHLINTL 90
                                       79******9998773356788877776654 PP

  == domain 2  score: 19.5 bits;  conditional E-value: 1.4e-07
                               Maf1  63 rktlayLiatLnasfpdYDFsslrsseFkkekslksvinnidstLsslveekyeelreklWklideeidlkdCdiY 138
                                        ++t+a+Li+tL+ +       +l++++Fk   ++++++n+i   L+     + e++ + l   i++ + +++  i+
  gene3047|gene3047|rna3047|rna3047  80 KNTMAHLINTLELANLK-GKCKLKKEDFKLK-QFSEIKNDIFLILMCNNRFDAEKMIRMLVICIQNTVGINNTLIF 153
                                        56788888888887744.34569*****995.***********99987888888899999**************** PP

                               Maf1 139 sYkpdedsdpfkeegalwsfnYFffnkklKrvlfl 173
                                        s ++      +++++    + Y+f+n+k Kr+l+l
  gene3047|gene3047|rna3047|rna3047 154 SLENRIA--LLSDDK--HFLCYLFYNRKAKRILLL 184
                                        *****97..777774..5678************98 PP

>> BAH  BAH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.2   0.00059       3.5      47     109 ..      69     123 ..      21     133 .. 0.65
   2 ?    6.4   0.0    0.0013       7.8      99     117 ..     162     180 ..     147     184 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.00059
                                        ECGGGSTTTTHCCCTTEEEEEEEEEEEEGGGEEEEEEEEEHHHHCTECCHCHHCSTTEEEEEE CS
                                BAH  47 lrpeetksalklrqkrElfltrqseilplaairgkcrVvllsdleeaqnylpkklddtFycsl 109
                                        ++ +++ + ++  ++    + +  ++l la+ +gkc++ +++d++  q  ++  ++d+F+  +
  gene3047|gene3047|rna3047|rna3047  69 YTKKQR-KRQNYKNT----MAHLINTLELANLKGKCKL-KKEDFKLKQFSEI--KNDIFLILM 123
                                        444444.22222222....677789************6.5677777777777..888886544 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0013
                                        HCSTTEEEEEEEEETTTTE CS
                                BAH  99 kklddtFycslvydptakt 117
                                         ++d+ F+c l+y+++ak+
  gene3047|gene3047|rna3047|rna3047 162 LSDDKHFLCYLFYNRKAKR 180
                                        4689************986 PP

>> MecA_N  NTF2-like N-terminal transpeptidase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.3   3.2e-06     0.019      37     101 ..      41     107 ..      22     111 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 3.2e-06
                                        HHHHHHHHHCCCTT-EEEEE..EEEEEEEEETTEEEEEEEEEEEETTEEEEEEEEEEEEEEETTEEE CS
                             MecA_N  37 eavekyqaiydglqvkklki..eakkvkkdkentaeipykvsmntpagkiktldskltltkeeeewk 101
                                        ++ +  +ai+++l++k+ +i  ea + k  k++ +  +yk +m    ++++ +++k + + ++e++k
  gene3047|gene3047|rna3047|rna3047  41 NLISEANAIFNQLEAKNFSInlEAYSCKYTKKQRKRQNYKNTMAHLINTLELANLKGKCKLKKEDFK 107
                                        5667889*************999999******************99998865555555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (193 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1138  (0.0634726); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1358.43
//
Query:       gene3048|gene3048|rna3048|rna3048  [L=555]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.6e-13   49.1   0.3    1.9e-12   48.1   0.3    1.5  1  Metallophos     Calcineurin-like phosphoesterase
    5.5e-11   42.9   0.0    3.7e-10   40.2   0.0    2.3  1  Metallophos_2   Calcineurin-like phosphoesterase superfamily 
    1.6e-09   38.3   2.3      7e-09   36.2   0.1    2.9  2  Mre11_DNA_bind  Mre11 DNA-binding presumed domain


Domain annotation for each model (and alignments):
>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.1   0.3   3.2e-16   1.9e-12       1     204 []       1     218 [.       1     218 [. 0.66

  Alignments for each domain:
  == domain 1  score: 48.1 bits;  conditional E-value: 3.2e-16
                                        EEEEEEESBTB.......TTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSSHHHHHHHHH.HHHHHHH..... CS
                        Metallophos   1 lrilvigDlHl.......algggqlddllkllddllreekpdlvllaGDlvdrgdlekellel.laalvky..... 63 
                                        ++il+++D Hl        l   ++++++++l+     +++dl+++aGDl++ + ++ ++++  ++ l k      
  gene3048|gene3048|rna3048|rna3048   1 MKILITSDNHLgyketdpLLSLDSFNAFEEVLQGG---KECDLMIIAGDLFHNNRPSRFTMYKtIQLLKKHvlgnk 73 
                                        89********9999988866667888888888665...789*************8888888886666666688888 PP

                                        ...................TSEEEEEC-TTS......CHHH.HHHHHHHHHHHHHHHHEHHHCEEETSEEEEEETT CS
                        Metallophos  64 ...................pipvylllGNHe......gfee.ellnkygylgifsepwrsdaevfnnlplaslgsg 113
                                                             pv+++ GNH+       ++  ++l++ g  ++ +++++++       pl++ +++
  gene3048|gene3048|rna3048|rna3048  74 eiritankrlnyekpniniSLPVVVINGNHDdpcgfgSLSAlDVLHQTGLVNYVGKINNYE--RIVVEPLIVKMEQ 147
                                        88888888888899999999999********777443222222333322222222222222..2223344444444 PP

                                        EEEEEEEESECEEETHHHHHHHHHHHSCHHHHCCHHHHHH...HHHHTTCSEEEEEESSESS.CSSSCSCCHHHHH CS
                        Metallophos 114 slkvlllhGgspellvsldklgslnleleapepgdewlkd...lekrekadwvivlgHsply.rgsgylfgdeale 185
                                        ++ +++l +            +   l        ++++++      +++ad+ i++ H +   r+  +  ++e + 
  gene3048|gene3048|rna3048|rna3048 148 TVALYCLSHV-----------RDSRL--------YKLFSQnkiEFLKSNADINILIVHQNRIeRSRNDFLPSEFIP 204
                                        3223333333...........22222........555555555555559999999999999955555555555555 PP

                                        HHHHHTTESEEEEESSSSE CS
                        Metallophos 186 dllkkygvdlvisGHtHvy 204
                                        d+       l+++GH+H +
  gene3048|gene3048|rna3048|rna3048 205 DF-----FNLIVFGHEHDP 218
                                        66.....99********75 PP

>> Metallophos_2  Calcineurin-like phosphoesterase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.2   0.0   6.2e-14   3.7e-10       1     149 [.       1     237 [.       1     255 [. 0.71

  Alignments for each domain:
  == domain 1  score: 40.2 bits;  conditional E-value: 6.2e-14
                      Metallophos_2   1 MklaiiSDlH............snldaleavlealkevgvdaiihaGD...............leeeep....... 42 
                                        Mk++i SD H            ++++a e+vl+  ke+  d++i aGD               +    +       
  gene3048|gene3048|rna3048|rna3048   1 MKILITSDNHlgyketdpllslDSFNAFEEVLQGGKEC--DLMIIAGDlfhnnrpsrftmyktI----Qllkkhvl 70 
                                        **************************************..********5555555555555540....04554444 PP

                      Metallophos_2  43 ...........evleellela...........pvlaVrGNnD.................................. 62 
                                                            +           pv+++ GN+D                                  
  gene3048|gene3048|rna3048|rna3048  71 gnkeiritankR--------LnyekpninislPVVVINGNHDdpcgfgslsaldvlhqtglvnyvgkinnyerivv 138
                                        444443322221........123345556678**********************************9999865555 PP

                      Metallophos_2  63 .......eevveedvlreaaelgtdl...........p.eeaelel....agekvlliHgdplgvkdalaellkea 115
                                               e           ++++ +              ++ ++e+    a+ ++l++H+   + + +  + l ++
  gene3048|gene3048|rna3048|rna3048 139 eplivkmE-----------QTVALYClshvrdsrlykLfSQNKIEFlksnADINILIVHQN--RIERSRNDFLPSE 201
                                        55544431...........333333344443333344235555554555566679****99..5555555555555 PP

                      Metallophos_2 116 eegsd..vvvcGHtHvpevekeggvlvvnPGsvgep 149
                                          +++  ++v+GH H p ++++++++++  Gs  + 
  gene3048|gene3048|rna3048|rna3048 202 FIPDFfnLIVFGHEHDPLLFERNEQTYLQCGSTVRT 237
                                        5566678************************97665 PP

>> Mre11_DNA_bind  Mre11 DNA-binding presumed domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.2   0.1   1.2e-12     7e-09       2     122 ..     259     363 ..     258     396 .. 0.78
   2 ?   -1.6   0.3      0.49   2.9e+03      98     124 ..     512     538 ..     484     550 .. 0.57

  Alignments for each domain:
  == domain 1  score: 36.2 bits;  conditional E-value: 1.2e-12
                                        EEEEEE-SSS--EEEEEEECCC-TTT-CCTS-CCCHHHHHHHHHHHHHHHHHHHHSSSTTS------EEEEEEE-T CS
                     Mre11_DNA_bind   2 klepipLktvRpfvlkeisLsdvaelkkkeknkekvtkflrekVeelieeaeeeweeeaeeeepplPLiRLrVdys 77 
                                        k+e+i+Lk+vRpf+++++s            +ke v+  l+e+   + +  ++e    +   +  +PL+RLr + +
  gene3048|gene3048|rna3048|rna3048 259 KIEKIELKSVRPFLFDTLST----------GTKEVVQSKLEEMLGGVSKCEKCEG---EAFCDACKPLVRLRLEDD 321
                                        689*************9886..........5567788888888888777777777...66778889*******999 PP

                                        TT-----HHHHHHCCCTTBS-SSSSEEEE-S-XXXXXXXXXXXXX CS
                     Mre11_DNA_bind  78 ggfevenpqrfgqrFvgkVANpndvlqfyrkkkarkkkkkekaaa 122
                                             +n  ++ + +++kVANp d+  + +k+k    ++++  +a
  gene3048|gene3048|rna3048|rna3048 322 ---VSFNKLHLQNVYADKVANPGDIFLLIKKRKPVVIRENKPVHA 363
                                        ...889999**********************99887766554433 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.49
                                        -SSSSEEEE-S-XXXXXXXXXXXXXXX CS
                     Mre11_DNA_bind  98 Npndvlqfyrkkkarkkkkkekaaake 124
                                        N  d++ ++r ++  k++ ++k+a+ +
  gene3048|gene3048|rna3048|rna3048 512 NNLDLVEYARDNNLIKHDFSKKTAQRD 538
                                        444555555555544444443333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (555 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       716  (0.0399353); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.60u 0.24s 00:00:00.84 Elapsed: 00:00:00.44
# Mc/sec: 3793.23
//
Query:       gene3049|gene3049|rna3049|rna3049  [L=186]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00075   18.7   3.3        0.1   11.8   1.4    2.3  1  NAP       Nucleosome assembly protein (NAP)


Domain annotation for each model (and alignments):
>> NAP  Nucleosome assembly protein (NAP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   1.4   5.6e-06       0.1      10     164 ..      15     134 ..       8     145 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 5.6e-06
                                        HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT--S.............................--SSSS CS
                                NAP  10 qkelskleaefqeevlelekkyaalykplyekrseIingesepteeeveakedekeeeeeeeekeeekeeekkeea 85 
                                        q+++++  +ef+++ ++++ +y + +kp++++r + i+     +   +                            
  gene3049|gene3049|rna3049|rna3049  15 QSKVDQEYKEFAKNDFNVKLEYFNSLKPILKERDDFIQDLP--N---C---------------------------- 57 
                                        55555555555555555555555555555555555555322..2...2............................ PP

                                        TTSTTHHHHHHHTSHHHHTT..--HHHHHHHTTEEEEEEEE-------EEEEEEEE-S-SSB--SEEEEEEEE--- CS
                                NAP  86 kgipeFWltvlknvellael..iqerDepiLkhLkdirveyllskekegFtleFeFdeNpyFtnevLtktyilkse 159
                                        ++  +FW ++ +n++ + +l    e+D    + ++ +r+ y +++      +e + + N+y +n+ L+k++ l ++
  gene3049|gene3049|rna3049|rna3049  58 DEGANFWEKAAQNCPSFRDLlpLDEEDFS-VSWIESLRCWY-EEN--YVCGVEITLSRNDYLNNRRLSKKFSLLDH 129
                                        11247888888888888888333333333.48888888887.333..44666777788888888888888888766 PP

                                        -.... CS
                                NAP 160 vdked 164
                                        ++++ 
  gene3049|gene3049|rna3049|rna3049 130 TSEGT 134
                                        65544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       738  (0.0411624); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 1415.42
//
Query:       gene305|gene305|rna305|rna305  [L=441]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.6e-89  298.4   0.0    7.8e-89  298.2   0.0    1.0  1  Aminotran_5      Aminotransferase class-V
    4.6e-07   29.3   0.0    1.9e-06   27.3   0.0    1.8  1  Aminotran_1_2    Aminotransferase class I and II
    5.6e-07   29.1   0.0    7.5e-07   28.7   0.0    1.2  1  Beta_elim_lyase  Beta-eliminating lyase
    4.2e-05   23.0   0.1    6.5e-05   22.4   0.1    1.2  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
     0.0016   17.3   0.0     0.0023   16.7   0.0    1.3  1  Pyridoxal_deC    Pyridoxal-dependent decarboxylase conserved 
  ------ inclusion threshold ------
      0.015   14.8   0.1      0.042   13.4   0.1    1.7  1  EF-hand_5        EF hand
      0.099   11.2   0.0       0.15   10.6   0.0    1.2  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme


Domain annotation for each model (and alignments):
>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  298.2   0.0     3e-92   7.8e-89       1     370 [.      39     407 ..      39     408 .. 0.92

  Alignments for each domain:
  == domain 1  score: 298.2 bits;  conditional E-value: 3e-92
                                    EEEBTTTS----HHHHHHHHHHHHCTCCSSSSSSSHHHHHHHHHHHHHHHHHHHHHT-STGGGEEEESSHHHHHHHHHHH CS
                    Aminotran_5   1 iyldsaAttqkpqeVldalqeyytdynanvhrsvhhlgkeatkaveearekvaelinaeseeeiiftsGtteainlvals 80 
                                    iy+d +Att++ ++Vlda+  y+t+ ++n+h+ +h++g+e  kave+ar++va+li+a + +eiiftsG+te++nl++++
  gene305|gene305|rna305|rna305  39 IYFDFQATTPVDPRVLDAMLPYFTKKYGNPHSRTHSFGWESEKAVETARKQVADLIGAHE-KEIIFTSGATESNNLAIKG 117
                                    8**********************************************************6.******************* PP

                                    CCCC.-TTTS..EEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH--TTEEEEEEESBETTTTEB-- CS
                    Aminotran_5  81 lars.lkpgd..eivvteaehhanlvpwqelakrtgakvkvipldeegeldldelekllnektklvaithvsnvtGtiqp 157
                                    + ++  ++g+  ++++t++eh++ l  ++ l+ ++ga+v++++++++g +dl+el+  ++++t lv+i+ v+n++Gt+qp
  gene305|gene305|rna305|rna305 118 AVDWkAQDGNpvHVITTQVEHKCVLDSMRFLE-EKGARVTYMKVNKDGVIDLEELKRSISDDTVLVSIMGVNNEIGTVQP 196
                                    *9988777755589***********9999998.77********************************************* PP

                                    HHHHHHHHHHTT-EEEEE-TTTTTTS---HHHHTESEEEEETTTTTSSTT-EEEEEEHHHHHTS..SS.STTSEEEEETT CS
                    Aminotran_5 158 veeigklakkkgalvlvDaaqavghipidvkklgvDflafsghKllgPtGiGvlyvrkellekleplllggemveevsle 237
                                    +eeigk++k++++l+++Daaq++g+ +idv+k+++D+l++sghK++gP+G+G+lyvr++  ++l pl  gg+       +
  gene305|gene305|rna305|rna305 197 LEEIGKICKERNVLFHCDAAQMFGKLKIDVNKMNIDLLSISGHKIYGPKGVGALYVRRRPRVRLVPLFSGGG-------Q 269
                                    ************************************************************************.......9 PP

                                    EEEEHCTTGGGS.SS--HHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHCT.STTEEEES....-B-CTCBSEEE CS
                    Aminotran_5 238 ettfaeapskfeaGTpnvagiiglgaaleyleeigleaiekhekelaeyllerlks.lpgvrlyg...pdkaerrasivs 313
                                    e++       +++GT +++ i+glg+a+  + + ++++  +  ++l+++l+  lk+ +p+v  +g   +++ +  +++++
  gene305|gene305|rna305|rna305 270 ERG-------LRSGTLPTPLIVGLGKAAAVC-QEEMQRDLSWIESLSKKLYTCLKEnIPNVIKNGslqTNPLRWFPGCLN 341
                                    999.......9********************.66777777777777777777776556665554411155666678**** PP

                                    EEETTCSHHHHHHHHHHTTEEEEEE-TTT....HHHHHHTT.S.......-EEEEE--TTS-HHHHHH CS
                    Aminotran_5 314 fnfkgvhaedvatlLdeegIavrsGhhca....qplmkrlale.......gtvRaSlyiynteeevdr 370
                                    ++f+ v+ e + ++L++  Ia++sG++c+    +p+++++al        +++R+++++ +t  e++ 
  gene305|gene305|rna305|rna305 342 LSFPHVEGEGLLMALKN--IALSSGSACTsaslEPSYVLRALGnddelahSSIRFGIGRFTTPCEIKE 407
                                    ********999888876..**********9999999999999999****************9988875 PP

>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   0.0   7.4e-10   1.9e-06      48     237 ..      85     254 ..      81     330 .. 0.69

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 7.4e-10
                                    HHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHH...HTTT-E..EEEEESS-THHHHHHH...HTTSEEEE CS
                  Aminotran_1_2  48 eleealakflgrseklklkreaavvvgsGagaliealifllk...lnpgde..ilvpdptyasyknilr...lsggevvr 119
                                    ++++++a+++g        +e++++++sGa++ ++++i  +    ++ g    ++  +  +  + +  r     g+ v +
  gene305|gene305|rna305|rna305  85 TARKQVADLIG-------AHEKEIIFTSGATESNNLAIKGAVdwkAQDGNPvhVITTQVEHKCVLDSMRfleEKGARVTY 157
                                    67999999999.......56667999999999888888776333344554444777888898888776511155666777 PP

                                    EEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSH CS
                  Aminotran_1_2 120 yplyseedfhldlealeealkeapegnkktkvilvesphNPtGtvatleeleklldlakkynlllfvDeaYagfvfgsld 199
                                    ++++  +d  +dle+l++ +++       t ++ + +++N  Gtv +lee+ k+   +k++n+l  +D a    +fg+l 
  gene305|gene305|rna305|rna305 158 MKVN--KDGVIDLEELKRSISD------DTVLVSIMGVNNEIGTVQPLEEIGKI---CKERNVLFHCDAA---QMFGKL- 222
                                    7766..****************......788***********************...***********76...455532. PP

                                    THHHHGGSTTSTTEEEEEESSSTTSSGGG-EEEEEEEH CS
                  Aminotran_1_2 200 avatranveeepnllivgslsKafGlaGeRvGyilgna 237
                                          +v++   +l+  s  K +G  G  vG++++  
  gene305|gene305|rna305|rna305 223 ----KIDVNKMNIDLLSISGHKIYGPKG--VGALYVRR 254
                                    ....456666544677777777777777..77777754 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7   0.0   2.9e-10   7.5e-07      31     173 ..      80     220 ..      74     298 .. 0.77

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 2.9e-10
                                    -HHHHHHHHHHHHHTT-S..EEEEES-HHHHHHHHH......HHH--TTEEEEEETT-HHHHSSTTHHHHCC--EEEEE- CS
                Beta_elim_lyase  31 dktvnrLedavaelfgke..aalfvpqGtaAnsill......killqrgeevivtepahihfdetgaiaelagvklrdlk 102
                                    +k v++  ++va+l+g+    ++f+   t +n++++      k+       vi t+  h +        e +g++++ +k
  gene305|gene305|rna305|rna305  80 EKAVETARKQVADLIGAHekEIIFTSGATESNNLAIkgavdwKAQDGNPVHVITTQVEHKCVLDSMRFLEEKGARVTYMK 159
                                    5678888999*****98533567888889*******55443322222223456666677777777666677899999999 PP

                                    EBTTTBE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEEETTHHH CS
                Beta_elim_lyase 103 nkeaGkmdlekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlDgARfan 173
                                     +++G +dle+l++ i +  +    + l+s+   nn   G+v +   l+e+ +i+k++++ +h+D+A ++ 
  gene305|gene305|rna305|rna305 160 VNKDGVIDLEELKRSISD--D----TVLVSIMGVNNE-IGTVQP---LEEIGKICKERNVLFHCDAAQMFG 220
                                    9999*************9..3....678887777774.366666...5678899*************9885 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.1   2.5e-08   6.5e-05      21     150 ..      79     220 ..      71     228 .. 0.82

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 2.5e-08
                                    SSHHHHHHHHHHHHHHT..-SEEEEESSHHHHHHHHHHH...TTTTTT-..EEEEESSS-TH...HHHHHHHTT-EEEEE CS
                DegT_DnrJ_EryC1  21 sgpeveeFEkafaaylg..vkhaiavssGtaAlhlaLra...lgvgpgd..eVIvpsltFva...tanavlelgakpvfv 90 
                                    s++ ve   k++a+ +g  +k  i +s +t+++ la++     ++++g+   VI++++       ++    e ga++ ++
  gene305|gene305|rna305|rna305  79 SEKAVETARKQVADLIGahEKEIIFTSGATESNNLAIKGavdWKAQDGNpvHVITTQVEHKCvldSMRFLEEKGARVTYM 158
                                    56666777788999999756788999999********9775544445544479****9987611255667789******* PP

                                    -B-TTTSSB-GGGCGGG--TTE..EEEEEB-G.GGB---HHHHHHHHHHCT-EEEEE-TT-TT CS
                DegT_DnrJ_EryC1  91 Dvdpdtynidpaaieaaitert..kaIlpVhl.yGqvadmdalkaiaakhglkvieDaAhAlG 150
                                     v+ ++  id +++++ i   t    I+ V+   G v  ++++ +i+++ ++ +  DaA+ +G
  gene305|gene305|rna305|rna305 159 KVN-KDGVIDLEELKRSISDDTvlVSIMGVNNeIGTVQPLEEIGKICKERNVLFHCDAAQMFG 220
                                    **9.889***************998999997538**************************998 PP

>> Pyridoxal_deC  Pyridoxal-dependent decarboxylase conserved domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   8.8e-07    0.0023     155     237 ..     138     217 ..     102     257 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 8.8e-07
                                    -HHHHHHHHHHT-E...EEEE--BTTTBB-HHHHHHHHHHHHCTT.EEEEEEEEBS-TTT-BB--HHHHHHHHHHCT-EE CS
                  Pyridoxal_deC 155 hssvekaalvlgvk...lrvipldengklrgaalekaieedkekGlipffvvatlGttvlgaFddlkelgdicekydlwl 231
                                    h +v    + l+ k   + +++++++g +  ++l++ i +d      ++ v+  +Gt        l+e+g+ic++ ++  
  gene305|gene305|rna305|rna305 138 HKCVLDSMRFLEEKgarVTYMKVNKDGVIDLEELKRSISDDTVL-VSIMGVNNEIGTV-----QPLEEIGKICKERNVLF 211
                                    66664444443333333999999***************999988.5555888888886.....58*************** PP

                                    EEE-TT CS
                  Pyridoxal_deC 232 HvDAAy 237
                                    H DAA 
  gene305|gene305|rna305|rna305 212 HCDAAQ 217
                                    ****95 PP

>> EF-hand_5  EF hand
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   1.6e-05     0.042      10      23 ..     160     173 ..     160     175 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.6e-05
                                    SS-SSCE-HHHHHH CS
                      EF-hand_5  10 lNgDGkIskeELkt 23 
                                    +N+DG I+ eELk+
  gene305|gene305|rna305|rna305 160 VNKDGVIDLEELKR 173
                                    5***********97 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   5.8e-05      0.15      58     192 ..      87     234 ..      63     244 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 5.8e-05
                                    HHHHHHHHT-.SEEEEESSHHH.....HHHHHHHTTS-TTE..EEEEESTSSHHHHHHHHHTHHH.TTCEEEEEST...T CS
                Cys_Met_Meta_PP  58 eeriaaLegg.eaalavssGma.....AiaaailallkaGd..eivvsddlYggtqrllkkvlkk.lgievkfvdt...s 125
                                     +++a+L g+ e+ ++++sG +     Ai+ a+   ++ G+  ++++++  +++  + ++ + +k   +++  v++    
  gene305|gene305|rna305|rna305  87 RKQVADLIGAhEKEIIFTSGATesnnlAIKGAVDWKAQDGNpvHVITTQVEHKCVLDSMRFLEEKgARVTYMKVNKdgvI 166
                                    56777777775667778888762222233333333445555335676666666665555554444333444444443336 PP

                                    SHHHHHHHCCTTEEEEEEESS-TTTT----HHHHHHHHHHTT-EEEEEGTTTHT.TTS-GGGGT-SEE CS
                Cys_Met_Meta_PP 126 dleelekaikentklvylEtptnpllkvvDiekiaklakkagvlvvvDntfasp.llqrplklgaDiv 192
                                    dleel++ i++ t lv +  + n    v  +e+i k++k+++vl   D++ + + l +   k+++D+ 
  gene305|gene305|rna305|rna305 167 DLEELKRSISDDTVLVSIMGVNNEIGTVQPLEEIGKICKERNVLFHCDAAQMFGkLKIDVNKMNIDLL 234
                                    89**********************************************99887734444445666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (441 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       390  (0.0217525); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.40
# Mc/sec: 3335.31
//
Query:       gene3050|gene3050|rna3050|rna3050  [L=222]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.1e-10   40.6   0.1    1.3e-06   29.0   0.0    2.2  2  Ribosomal_L6  Ribosomal protein L6


Domain annotation for each model (and alignments):
>> Ribosomal_L6  Ribosomal protein L6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.0   0.0     7e-11   1.3e-06       1      76 []      49     121 ..      49     121 .. 0.94
   2 !    9.8   0.0   7.1e-05       1.3      12      76 .]     146     211 ..     133     211 .. 0.83

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 7e-11
                                        CSTTEEEEEETTTEEEEEESSEEEEEE-CTTSEEEEEECSTEEEEEECSESCHHHHHHHHHHHHHHHHHHHHHHTC CS
                       Ribosomal_L6   1 iPvgvrvsikggqlvlvlGpkgeltreipegvtvevkvegnkvtvivvsgidkekvAligtvrslinnmikGVteg 76 
                                        iP+g++v+i++ +++++    + + r++++   ++++  +++++   ++  ++e++ ++ t+ s+i nmi GVt+g
  gene3050|gene3050|rna3050|rna3050  49 IPEGCNVTINE-KVLSIECNGKRVVRNFSHL-VLTMDIHEGNIRLRLWNARRQERS-KLITCASHITNMILGVTKG 121
                                        8*********7.******************9.55666779****************.*****************98 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 7.1e-05
                                        TTEEEEEESSEEEEEE-CTTSEEEEEECSTEEEEEECSESCHHHH....HHHHHHHHHHHHHHHHHHTC CS
                       Ribosomal_L6  12 gqlvlvlGpkgeltreipegvtvevkvegnkvtvivvsgidkekv....AligtvrslinnmikGVteg 76 
                                          + + lG+k ++ ++++ +  v+    g  ++ +v+sg+++e+v      ++  ++++n + +++++g
  gene3050|gene3050|rna3050|rna3050 146 LVVKNYLGEKTSRYFNMRGD-SVA--RLGTDKDTVVISGTSIEDVsqsaGSVQDNCRPKNFDNRKFMDG 211
                                        445688**************.888..78999**************998878888899999999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       443  (0.0247086); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 1514.01
//
Query:       gene3051|gene3051|rna3051|rna3051  [L=89]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.8e-19   68.6   0.5    3.9e-19   68.1   0.5    1.2  1  zf-CSL        CSL zinc finger
     0.0092   15.8   0.3      0.015   15.1   0.3    1.3  1  zf-RING_4     RING/Ubox like zinc-binding domain
  ------ inclusion threshold ------
       0.33   10.5   6.5       0.11   12.0   1.8    2.1  2  TF_Zn_Ribbon  TFIIB zinc-binding


Domain annotation for each model (and alignments):
>> zf-CSL  CSL zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.1   0.5   6.5e-23   3.9e-19       1      59 []      26      80 ..      26      80 .. 0.98

  Alignments for each domain:
  == domain 1  score: 68.1 bits;  conditional E-value: 6.5e-23
                                       EEEEGGGSEEETTTTEEEEEETTSSEEEEEHHHHHTT....--EEEETTSSEEEEEE-- CS
                             zf-CSL  1 develedfefdeeeesyyypCRCgdeFelteedleegaegaevvvqCssCSLwikVkfa 59
                                       de++l+df++dee + y+ypC+Cgd+F++t ++l  g    e+ + C+sCSL++kV ++
  gene3051|gene3051|rna3051|rna3051 26 DEIDLDDFTYDEERNAYVYPCPCGDKFVITVDELMIG----ETKATCPSCSLVLKVSYN 80
                                       89**********************************9....***************985 PP

>> zf-RING_4  RING/Ubox like zinc-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.3   2.5e-06     0.015      10      43 ..      38      71 ..      29      74 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.5e-06
                          zf-RING_4 10 etdkdlkpCeCgyqiClfCyhrileeeegrCPaC 43
                                       e++  ++pC+Cg ++     + ++ e+++ CP C
  gene3051|gene3051|rna3051|rna3051 38 ERNAYVYPCPCGDKFVITVDELMIGETKATCPSC 71
                                       677789******999999988888899******* PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.2     0.074   4.4e+02      10      21 ..      32      43 ..      30      43 .. 0.82
   2 ?   12.0   1.8   1.8e-05      0.11       3      39 ..      46      85 ..      44      86 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.074
                                       ECHEETSTTCEE CS
                       TF_Zn_Ribbon 10 nlveDpergelv 21
                                       ++++D+er+ +v
  gene3051|gene3051|rna3051|rna3051 32 DFTYDEERNAYV 43
                                       5899***99876 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 1.8e-05
                                       ETTTTCEE.CHEE...TSTTCEEESSSSBEEEECCCCCCCH CS
                       TF_Zn_Ribbon  3 CPnCgstn.lveD...pergelvCtdCGlVlednsidegpe 39
                                       CP Cg ++ +++D     ++  +C++C lVl   ++   +e
  gene3051|gene3051|rna3051|rna3051 46 CP-CGDKFvITVDelmIGETKATCPSCSLVLKVSYNFDDVE 85
                                       55.9****99999866667777*********9988877776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       564  (0.0314574); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.46
# Mc/sec: 586.56
//
Query:       gene3052|gene3052|rna3052|rna3052  [L=366]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
          4    8.6   5.6         13    7.0   5.6    2.0  1  SAE2      DNA repair protein endonuclease SAE2/CtIP C-terminu


Domain annotation for each model (and alignments):
>> SAE2  DNA repair protein endonuclease SAE2/CtIP C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   5.6   0.00071        13      12      79 ..     152     218 ..     143     326 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.00071
                               SAE2  12 rkclpgCtkpeCcgkkfravaelearkeep....taskeeedkklleeklgdeayklakmsseerqeleiea 79 
                                        r++l+gC++ +C ++   a a  e +++++     ++++++  ++ ++k g++++  + m+     +l ie+
  gene3052|gene3052|rna3052|rna3052 152 RNKLQGCDQVRCLTAVLDAQASKESQNTGQaetnDRKSAADTGTVPTHKTGEDRNVQDAMQ-----DLRIEE 218
                                        899*********8888877777777666664433111222222222233333322222222.....222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (366 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1034  (0.0576719); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 2580.30
//
Query:       gene3053|gene3053|rna3053|rna3053  [L=444]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-54  185.6  13.3    1.7e-54  184.9  13.3    1.3  1  NMD3      NMD3 family


Domain annotation for each model (and alignments):
>> NMD3  NMD3 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  184.9  13.3   9.4e-59   1.7e-54       1     243 []      18     240 ..      18     240 .. 0.95

  Alignments for each domain:
  == domain 1  score: 184.9 bits;  conditional E-value: 9.4e-59
                               NMD3   1 CcrCGkeieelinglCedCllkevditegiek.ievevCkeCgryl.pkgkWvkaeleseellaeclkklvekgLk 74 
                                        Cc+CG++i +   ++C +C  +e+dit+g +  ++ve Ck+C+ryl p +kW+   +++ +ll+ +l +   k+++
  gene3053|gene3053|rna3053|rna3053  18 CCKCGISILPNCLNMCGRCRSTEIDITQGVKLcYTVENCKKCNRYLlPPKKWLVL-ENETDLLSFLLLRY--KEIR 90 
                                        ********866667*********************************666**888.67778999999999..9999 PP

                               NMD3  75 vseeveevkvelvdaefiwtephskrikvkvtvqgevrgenetilqqevevevkvkrqqCprCsriagg.yyeaiv 149
                                                ++++v++ f +te+hs+ri +++++ ++        l+ +++v +k++++qC +C +++++ y+++iv
  gene3053|gene3053|rna3053|rna3053  91 --------NLNIVNSGFKKTEEHSRRIVLELEIAKDD-------LKCNIDVVFKIRNKQCLDCDKMEAKqYWTSIV 151
                                        ........999****************9999998887.......5578**************************** PP

                               NMD3 150 QvRqkrelteeehkrtfelleqlilkhdahafiskikevkeGlDfyfgsksaArklveflksevggkvkeseklvs 225
                                        Q+Rq+     ++ krtf++leq ilkh++ + +++ike+k+G+Dfy+ +k+ A ++v+fl+s++g+k+  s++l++
  gene3053|gene3053|rna3053|rna3053 152 QIRQR-----SKSKRTFLYLEQSILKHKMYKRCTNIKERKDGIDFYYLDKHSAYEMVNFLESTIGTKLLVSNRLMT 222
                                        *****.....****************************************************************** PP

                               NMD3 226 edkksgkevyrltysvrl 243
                                        ed++++k +y+++ysv++
  gene3053|gene3053|rna3053|rna3053 223 EDRNNNKMKYKFSYSVEI 240
                                        ****************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (444 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       819  (0.0456802); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 3191.81
//
Query:       gene3055|gene3055|rna3055|rna3055  [L=390]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (390 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       442  (0.0246528); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 2763.54
//
Query:       gene3056|gene3056|rna3056|rna3056  [L=377]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (377 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       428  (0.0238719); expected 358.6 (0.02)
Passed bias filter:                      263  (0.014669); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 2392.61
//
Query:       gene3057|gene3057|rna3057|rna3057  [L=179]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.51   11.0   4.1        1.7    9.3   0.2    2.5  2  WBP-1     WW domain-binding protein 1


Domain annotation for each model (and alignments):
>> WBP-1  WW domain-binding protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.2   9.7e-05       1.7      20      57 ..      43      80 ..      37     112 .. 0.66
   2 ?    2.6   0.6     0.012   2.1e+02      77     104 .]     145     177 ..     111     177 .. 0.56

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 9.7e-05
                              WBP-1 20 ElwwfwlvwtllillsCicalakrraklrleqqerqre 57
                                       E ++f  + ++++ l+C+ +++k+r + r+   +++ +
  gene3057|gene3057|rna3057|rna3057 43 EGFIFAAMIIVILGLLCLYIYNKCRMHNRCRFGSTNDS 80
                                       67889997777777*********999966655544442 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.012
                              WBP-1  77 rllaslklPsy.eevlkaar....petPpPpYs 104
                                         ll  + +P++ ++v+   +    + +P+P Ys
  gene3057|gene3057|rna3057|rna3057 145 LLLYMFEPPPFyDDVVILPSydstEASPLPEYS 177
                                        345556665544666433322334667888886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (179 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       643  (0.0358637); expected 358.6 (0.02)
Passed bias filter:                      519  (0.0289475); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1192.78
//
Query:       gene3058|gene3058|rna3058|rna3058  [L=92]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.2e-11   43.0   0.3    3.9e-11   42.7   0.3    1.1  1  PIF1      PIF1-like helicase


Domain annotation for each model (and alignments):
>> PIF1  PIF1-like helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.7   0.3   2.2e-15   3.9e-11     328     364 .]       1      37 [.       1      37 [. 0.96

  Alignments for each domain:
  == domain 1  score: 42.7 bits;  conditional E-value: 2.2e-15
                                        SS-SCEEE-TT-EEEE-S--CTT-SC-TCEEEEEEEE CS
                               PIF1 328 lpnhvLkLkvGvpvmllrNldqsaGLcNGtrlivtql 364
                                        +p+h+L Lk G+ +mllrNld+++GL NGtrliv +l
  gene3058|gene3058|rna3058|rna3058   1 MPPHKLVLKRGALIMLLRNLDPANGLLNGTRLIVDEL 37 
                                        79********************************886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       263  (0.014669); expected 358.6 (0.02)
Passed bias filter:                      232  (0.0129399); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 685.95
//
Query:       gene3059|gene3059|rna3059|rna3059  [L=462]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        0.8   10.2   6.2       0.28   11.7   2.5    2.2  2  Pep1_7    Elicitor peptide 1-7


Domain annotation for each model (and alignments):
>> Pep1_7  Elicitor peptide 1-7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.1      0.22   3.9e+03      36      45 ..      62      71 ..      36      98 .. 0.53
   2 ?   11.7   2.5   1.5e-05      0.28       7      80 ..     100     171 ..      93     173 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.22
                             Pep1_7 36 esssskspss 45
                                       +s+  +++ +
  gene3059|gene3059|rna3059|rna3059 62 DSERTHKKTD 71
                                       2222222222 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 1.5e-05
                             Pep1_7   7 redeksyylwipfsfihqilraflkclGLesssskspsssseeeeeetetvevtsrglvakvlkrrpkqkeSSG 80 
                                        + + k+++l+ +++f+++  +    +  +++   k + +s ++++e++ ++e+++++ +    k  p + eS+G
  gene3059|gene3059|rna3059|rna3059 100 EHTTKRFSLCKACNFLNKSSKKAKIIRVFNIFRRKHKKQSASSANEDVIEKETSDDFKITT--KPNPMKFESTG 171
                                        33356999**********6665554556666666666666777788999999999999887..88888888888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (462 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1281  (0.0714485); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 3162.88
//
Query:       gene306|gene306|rna306|rna306  [L=139]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.028   14.5   0.2      0.033   14.3   0.2    1.2  1  ApoLp-III  Apolipophorin-III precursor (apoLp-III)


Domain annotation for each model (and alignments):
>> ApoLp-III  Apolipophorin-III precursor (apoLp-III)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.2   1.9e-06     0.033      23      74 ..      38      89 ..      26     109 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.9e-06
                      ApoLp-III 23 vvetiKensenlvdqlkqvikslqeelkkksdeleealkevkkkieetadkl 74
                                   +++ + +  +++v+++k  i +l  elkk +d  e +l+ ++++++++ d +
  gene306|gene306|rna306|rna306 38 FNKYLLKHRQKMVKKIKRKIIQLFTELKKRNDDPETVLEHFNEDLKNVEDVV 89
                                   56667777899**********************************9988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1291  (0.0720062); expected 358.6 (0.02)
Passed bias filter:                      635  (0.0354175); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 908.80
//
Query:       gene3060|gene3060|rna3060|rna3060  [L=411]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.1e-19   69.1  15.9    4.1e-19   69.1  15.9    2.6  3  MBOAT     MBOAT, membrane-bound O-acyltransferase family


Domain annotation for each model (and alignments):
>> MBOAT  MBOAT, membrane-bound O-acyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   1.4     0.094   1.7e+03     299     343 ..      16      60 ..      13      65 .. 0.82
   2 ?   -0.1   0.3     0.025   4.5e+02     249     261 ..      80      92 ..      78     107 .. 0.88
   3 !   69.1  15.9   2.3e-23   4.1e-19      93     307 ..     125     339 ..     119     378 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.094
                              MBOAT 299 vllllveklimrlvalsnlkfdrrrailsnvifwlgaflgpslal 343
                                         l+++++ + +r v+++n++ +    ++  ++ +  ++++  l+ 
  gene3060|gene3060|rna3060|rna3060  16 ILFQIFFSYAFRGVQKYNFVLSSLILLIAFGVKSYAVCMAFLLFN 60 
                                        689999999999999999999988888888888888888876665 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.025
                              MBOAT 249 vhkWLlryvYkpl 261
                                        ++ ++l+yvY+ +
  gene3060|gene3060|rna3060|rna3060  80 LNLFVLQYVYHLF 92 
                                        688********87 PP

  == domain 3  score: 69.1 bits;  conditional E-value: 2.3e-23
                              MBOAT  93 eylgYvffyplllvGPilsyseymsfvesplsrllyta.......................krnfavalyalflgl 145
                                        ++ +Y+f +p+ lvGP +s+ +y++  ++  +r  +++                       ++ + +++y +  + 
  gene3060|gene3060|rna3060|rna3060 125 DVVAYLFSIPCILVGPAISFVDYKNLQKNAKQRVMKETeggkpprkhpndlihclknvlyeQNGVIQGVYLCLQAV 200
                                        5789******************************9999***********************999************ PP

                              MBOAT 146 tylilieyvlskicakdftifkmlssaqllmrsvimrilllllllfllifdflglwlvalgedilsGlgvngarld 221
                                        +yl+++  ++ ++++ d+  +k++     ++  +++++++ + ++f++ ++      v+ +   l G +       
  gene3060|gene3060|rna3060|rna3060 201 FYLWVYLLLSKHFVVYDVINKKAY-----WRVFYMYIAHFCFKSKFYFVWT------VSQLCNHLYGCT------- 258
                                        *******99999999876555555.....2334778888888888888884......444455558975....... PP

                              MBOAT 222 rvadrniygdwenavsfsefwraWNipvhkWLlryvYkplgskkfklnkslatlatFlfsAvwHglalgyliwfvl 297
                                         ++++   g +e a++f+e   +WNi v++WL+  +++pl+        ++a ++tFl+s++wHg++ +y+  f+ 
  gene3060|gene3060|rna3060|rna3060 259 NLKNISKTG-VELAQDFKELTDSWNIYVNRWLKVAIFRPLK--PY--GYFFACFMTFLYSSLWHGTSICYFTLFMS 329
                                        789******.******************************6..33..56**********************99999 PP

                              MBOAT 298 rvllllvekl 307
                                         +l+  + k 
  gene3060|gene3060|rna3060|rna3060 330 VPLIMKPMKS 339
                                        8888766555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (411 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       854  (0.0476323); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 2807.80
//
Query:       gene3061|gene3061|rna3061|rna3061  [L=394]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.1e-17   63.0   9.6    3.1e-17   63.0   9.6    2.3  2  MBOAT        MBOAT, membrane-bound O-acyltransferase family


Domain annotation for each model (and alignments):
>> MBOAT  MBOAT, membrane-bound O-acyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   5.8     0.015   2.7e+02     123     190 ..      22      86 ..      14     105 .. 0.69
   2 !   63.0   9.6   1.7e-21   3.1e-17      93     305 ..     123     305 ..     115     343 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.015
                              MBOAT 123 lsrllytakrnfavalyalflgltylilieyvl.skicakdftifkmlssaqllmrsvimrilllllll 190
                                        +++++y    +f +al+++++g++ ++l+ yv+   + +++f + +   +  +l  s+  + l  + ++
  gene3061|gene3061|rna3061|rna3061  22 HQKYNY----LFGIALLFVAYGFMAVCLYFYVFfFNLLVIYFLRNYKHKKHVVLVVSITSLLLCSYYYK 86 
                                        556666....699**************999765145677777777777666666555554444444444 PP

  == domain 2  score: 63.0 bits;  conditional E-value: 1.7e-21
                              MBOAT  93 eylgYvffyplllvGPilsyseymsfvesplsrllytakrnfavalyalflgltylilieyvlskicakdftifkm 168
                                        ++++Yvf++p++++GP  s     +f++++ + +++      ++al  l+ +l+yl l+      ++ +++++   
  gene3061|gene3061|rna3061|rna3061 123 DIFNYVFCIPGVIAGPACSLT---DFEKNKSKAINK------KMALKKLAESLLYLALHL-----LITRNISYAIL 184
                                        789****************88...6999**999998......599999988666666666.....77777777777 PP

                              MBOAT 169 lssaqllmrsvimrilllllllfllifdflglwlvalgedilsGlgvngarldrvadrniygdwenavsfsefwra 244
                                        l+++ ++ +++++++l ++  +   +f     w ++++  i +G+         +++++ ++  e + +++e  ++
  gene3061|gene3061|rna3061|rna3061 185 LDRDLIFPYKILYLVLIGFGFKCRYYF----IWNFTDACYIFNGFQ-------NMTNIKAID-SELSSDMKELAQS 248
                                        777777777777777777777777777....679**********98.......569*****9.79*********** PP

                              MBOAT 245 WNipvhkWLlryvYkplgskkfklnkslatlatFlfsAvwHglalgyliwfvlrvllllve 305
                                        WN  +++WL+  v+  l+s    ++ +la + tF +sA+wHg  +gy++ f+   +  +v 
  gene3061|gene3061|rna3061|rna3061 249 WNLYTNRWLKDAVFDQLKS----RSVFLAATCTFIVSALWHGPKMGYFFMFLGFLFGTTVI 305
                                        *****************76....889*********************99666554444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (394 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1235  (0.0688828); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.62u 0.30s 00:00:00.92 Elapsed: 00:00:00.50
# Mc/sec: 2380.24
//
Query:       gene3062|gene3062|rna3062|rna3062  [L=36]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (36 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       220  (0.0122706); expected 358.6 (0.02)
Passed bias filter:                      208  (0.0116013); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.32u 0.28s 00:00:00.60 Elapsed: 00:00:00.41
# Mc/sec: 263.43
//
Query:       gene3063|gene3063|rna3063|rna3063  [L=328]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.6e-33  114.0   0.0    9.5e-33  113.7   0.0    1.1  1  Peptidase_M24  Metallopeptidase family M24


Domain annotation for each model (and alignments):
>> Peptidase_M24  Metallopeptidase family M24
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.7   0.0   5.3e-37   9.5e-33       2     189 ..      37     235 ..      36     274 .. 0.86

  Alignments for each domain:
  == domain 1  score: 113.7 bits;  conditional E-value: 5.3e-37
                                        HHHHHHHHHHHHHHHHHHHHHTTCBHHHHHHHHHHHHH.HHTT..TCEESSSSEEEEGGGGGSTTT..BCSSSB.. CS
                      Peptidase_M24   2 lirkaariasaaleavleaikpgvterelaaeieattl.krhg..arglafppivasgenaavlhy..tpndrv.. 70 
                                        + r+aa+++++++ ++ + ++pg++  e+++++e+ t    +g   +gl+fp  ++++ n++++hy  +p+d++  
  gene3063|gene3063|rna3063|rna3063  37 NARRAAEAHRRVRYHLQNSLRPGMSLSEICDLVENSTTtLLKGelNDGLGFP--TGVSLNDCAAHYsvNPGDQDif 110
                                        679*************999***************553322233459999***..************7555666688 PP

                                        --TTEEEEEEEEEEETTEEEEEEEEEECSSGSHHHHHHHHHHHHHHHHHHHC-STTSBHHHHHHHHHHHHHHTTB. CS
                      Peptidase_M24  71 lkegdlvlidagaeydgyasDitrTvlvGkftpeqrelyeavleaqeaaikavkpGvtlseidaaarevlesagl. 145
                                        lke d++++d+g +++g + D+++Tv     +p++++l+ea +ea+e++ik +  +v +sei++ + ev+ s++l 
  gene3063|gene3063|rna3063|rna3063 111 LKETDVLKVDFGTHVNGVIMDSAFTVTW---DPRMDKLLEASKEATEKGIKTMGVDVCVSEIGREISEVISSYELt 183
                                        9**************************9...99***************************************9667 PP

                                        .......CCGBSSCSEEEESS.SSSEEEEE..ESSSTTCSSB--TTBEEEEEEE CS
                      Peptidase_M24 146 .......akffphglGHgvGl.evhdegps..vsresndgrkleeGmvftiEpg 189
                                                +++ ++ GH++   ++h+++++  v   +nd+++le+   +++E+ 
  gene3063|gene3063|rna3063|rna3063 184 ldgrrvpIRPVANLNGHSIKPyKIHGGVSIplVE--NNDSDRLEADGFYALETF 235
                                        77777786888*********88***984442144..789************992 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (328 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       502  (0.0279993); expected 358.6 (0.02)
Passed bias filter:                      486  (0.0271069); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 2293.69
//
Query:       gene3064|gene3064|rna3064|rna3064  [L=339]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.7e-06   27.1   0.1    4.1e-06   26.5   0.1    1.3  1  Exo_endo_phos  Endonuclease/Exonuclease/phosphatase family


Domain annotation for each model (and alignments):
>> Exo_endo_phos  Endonuclease/Exonuclease/phosphatase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   0.1   2.3e-10   4.1e-06       1     233 []       6     276 ..       6     276 .. 0.77

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 2.3e-10
                                        EEEEESTGCHHHHTHHHHHHHHHHHHHHCTTS..EEEEEEEBSCTCHHHHHHHHH...............TTCEEE CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxx...............xxxxxx RF
                      Exo_endo_phos   1 ltwNvngqaspalgssrrsdrladlltaydaD..vlgLQEvdddelsriplllal...............ggflga 59 
                                        ltwNv+ ++++         +l+ +l++ +aD   ++LQE++d     +p++                        
  gene3064|gene3064|rna3064|rna3064   6 LTWNVQKNKNY-------LVDLHYMLKEKKADtiYIALQEAHDF---TVPWAIQKffmklffkaykyreiE----- 66 
                                        7******9888.......5559999999988655999***4444...344444445777766665555531..... PP

                                        EECCHECSSSTTSSEEEEEECSTEEEEEEEEEEETSSSSGCEEEEEEEEEEEEEEE.................... CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.................... RF
                      Exo_endo_phos  60 sstsptgggggggnggavlsrfpltslfrrtfiefndlvaalrreplaakleqlni.................... 115
                                                 +  g    +ls++++t++                    ++ ++++n                     
  gene3064|gene3064|rna3064|rna3064  67 ---------RFCGLVTIILSKYRITAV--------------------NTFVPFPNLyynkgavvtnlginytnill 113
                                        .........233333357777777555....................22222333333444444455555555566 PP

                                        .CCCHHGHHHHHHHHHHHHHHHHHHHHHTTSEEEEEEE-SSSTSGGGBSCGHHHHHHCTTTHHSSCESCETTTTTT CS
                                        .xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Exo_endo_phos 116 .ashrdhdlvrdlqllalllqvealnadrgapvivaGDfNarpsdddsrvlrtrglalapapvglyllgggptpty 190
                                         + h  h +  ++++  +   v++   +r   ++v+GDfN+                                   
  gene3064|gene3064|rna3064|rna3064 114 vNLHLHHGVINEARRVNQMKMVLRSIEGRFSYIFVCGDFNT----------------------------------- 154
                                        67889999999999999999999999999999*********................................... PP

                                        TTTTTEB-B................................................................... CS
                                        xxxxxxxxx................................................................... RF
                      Exo_endo_phos 191 vtraggsrl................................................................... 199
                                               r+                                                                   
  gene3064|gene3064|rna3064|rna3064 155 -------RVdvkkiptcfdlnefvmlsdwcnrtcregplnadadrewacaynlhmdkfkkadqmnafksifcldef 223
                                        .......********************************************************************* PP

                                        ..........................EEEEEECHHHCCEEEEEEECCHHEECTSSCSSSB CS
                                        ..........................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Exo_endo_phos 200 ..........................DrilaspalalfrsgvlppplalvrrealtlSDH 233
                                                                  Dril+++        + ++ l +  ++ + +SDH
  gene3064|gene3064|rna3064|rna3064 224 dvkflpsykyhartdaynlkqtpswcDRILFKT-------VNEIECLFYGSNMLVNTSDH 276
                                        ********************************7.......55555555555588888888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (339 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       856  (0.0477439); expected 358.6 (0.02)
Passed bias filter:                      518  (0.0288917); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2442.79
//
Query:       gene3065|gene3065|rna3065|rna3065  [L=782]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-59  200.7   1.2    2.1e-42  145.1   0.0    2.9  3  GNAT_acetyltr_2  GNAT acetyltransferase 2
    1.3e-52  178.2   0.0    4.8e-52  176.4   0.0    1.9  2  Helicase_RecD    Helicase
    1.2e-25   90.6   1.3    1.2e-25   90.6   1.3    1.8  2  tRNA_bind_2      Possible tRNA binding domain
      6e-15   55.0   0.7    6.7e-14   51.6   0.3    2.7  2  DUF1726          Domain of unknown function (DUF1726)
    1.4e-05   25.3   0.0      6e-05   23.3   0.0    2.1  2  Acetyltransf_1   Acetyltransferase (GNAT) family
    7.3e-05   23.1   0.2      0.001   19.5   0.0    2.8  3  Acetyltransf_7   Acetyltransferase (GNAT) domain
    0.00089   19.5   0.0      0.028   14.7   0.0    2.6  2  AAA_22           AAA domain
  ------ inclusion threshold ------
      0.011   15.6   0.0       0.41   10.6   0.0    2.8  2  Acetyltransf_10  Acetyltransferase (GNAT) domain
      0.082   12.8   0.3       0.19   11.6   0.3    1.5  1  Arteri_env       Arterivirus envelope protein


Domain annotation for each model (and alignments):
>> GNAT_acetyltr_2  GNAT acetyltransferase 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.2       1.9   3.7e+03     153     166 ..      66      79 ..      58     107 .. 0.42
   2 !  145.1   0.0   1.1e-45   2.1e-42       1     126 [.     444     558 ..     444     567 .. 0.94
   3 !   53.7   0.0   9.2e-18   1.8e-14     163     226 ..     567     630 ..     560     631 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.9
                    GNAT_acetyltr_2 153 sleeeklkprkelp 166
                                        +++++k+k++k+ +
  gene3065|gene3065|rna3065|rna3065  66 EEKKKKMKKEKKSA 79 
                                        11111122222211 PP

  == domain 2  score: 145.1 bits;  conditional E-value: 1.1e-45
                    GNAT_acetyltr_2   1 klvallvssHYknsPnDLqllsDaPahklfvLlapkkekkklpevlcvvqvalEGkiskesvknslsrgkrasGdl 76 
                                        ++++++vssHYkn+P+DL++++D P+h++fvLlap+k +kklp+++c+ +valEGk++           +r++G+l
  gene3065|gene3065|rna3065|rna3065 444 QMMSIFVSSHYKNTPDDLKIIADEPDHHVFVLLAPEK-EKKLPRIICAAHVALEGKVTG----------ERKDGNL 508
                                        69********************************997.58****************975..........599**** PP

                    GNAT_acetyltr_2  77 ipwtlsqqfqdeefaslsGaRivRiAvhpelqkmGYGsralellekyyeg 126
                                        ipwtls+qf d++f +  G RivRiAvhp++q+m YG+r++ell + ++ 
  gene3065|gene3065|rna3065|rna3065 509 IPWTLSEQFLDKNFLERRGCRIVRIAVHPDYQNMKYGTRMIELLVDTFSR 558
                                        ********************************************998764 PP

  == domain 3  score: 53.7 bits;  conditional E-value: 9.2e-18
                    GNAT_acetyltr_2 163 kelpplllklseekpekldylgvsfGltseLlkFWkragfspvylrqtaneltGEhsaimlrsl 226
                                        k ++ lll+ +e +++++d++gvs Gl ++++kFW r+ f pvy++qt n  tG+++ i+lr++
  gene3065|gene3065|rna3065|rna3065 567 KVTEALLLPSTELSMPRIDWMGVSMGLNTRIFKFWGRNAFYPVYIKQTLNFNTGDYTSILLRNV 630
                                        55678999******************************************************87 PP

>> Helicase_RecD  Helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0         1     2e+03      61      96 ..      64     109 ..      10     128 .. 0.48
   2 !  176.4   0.0   2.4e-55   4.8e-52       2     177 .]     221     406 ..     220     406 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1
                      Helicase_RecD  61 kkkaekaelrvr............kqrieyiapdellklkeqadllvv 96 
                                        +++++k++++++             +++ y + d ++ ++   ++lv 
  gene3065|gene3065|rna3065|rna3065  64 SREEKKKKMKKEkksakccindddIKKVSYQEVDIVMGNT--YEMLVL 109
                                        2222222222221111111222244445555544444432..355555 PP

  == domain 2  score: 176.4 bits;  conditional E-value: 2.4e-55
                      Helicase_RecD   2 ltAdRGRGKSaalGlalaaliaegksnilvtapskenvktlfeflakglealglke..........eekkkkaeka 67 
                                        l A+RGRGKSaalGla+a +++ ++s ++++ap+ envk lfef+ +gl+  g+ke          + ++  ++ +
  gene3065|gene3065|rna3065|rna3065 221 LKASRGRGKSAALGLAVADAVELRYSIVYIVAPHIENVKMLFEFVLRGLRGKGYKEnadfditrifKGRSYVQKIV 296
                                        79******************************************************78777777643333333333 PP

                      Helicase_RecD  68 elrvr.kqrieyiapdellklkeqadllvvDEAAaiplpllkkllekfkrvvlatTvhGYEGtGrgfslkflkqlk 142
                                          + + +q iey+   + +++    dllvvDEAAaiplp+lk l+ + + v++a+T+ GYEGtGr++s++f+++lk
  gene3065|gene3065|rna3065|rna3065 297 VKK-NhRQIIEYHGFLDKMDRY--PDLLVVDEAAAIPLPILKDLI-RANIVLMASTMDGYEGTGRSLSMRFIEKLK 368
                                        333.369******999888876..5********************.999*************************** PP

                      Helicase_RecD 143 ke...kkrelreleleepiRyaegdplEkwlndlLlLd 177
                                        k+   ++  ++e+el+e+iRy+++dp+E+wlnd+L+L+
  gene3065|gene3065|rna3065|rna3065 369 KNdkdNPYVFKEIELNESIRYKRNDPVERWLNDVLILK 406
                                        997777778**************************995 PP

>> tRNA_bind_2  Possible tRNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.1       1.3   2.6e+03      44      61 ..      67      84 ..      42      96 .. 0.50
   2 !   90.6   1.3   5.8e-29   1.2e-25       4     147 ..     636     777 ..     634     781 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.3
                                       ------------------ CS
                        tRNA_bind_2 44 kseekkeltkeeldells 61
                                       ++++k + +k++ +  ++
  gene3065|gene3065|rna3065|rna3065 67 EKKKKMKKEKKSAKCCIN 84
                                       111222222222223333 PP

  == domain 2  score: 90.6 bits;  conditional E-value: 5.8e-29
                                        HHHHHHHHHHHHHHHHHSS------S-----------.---------------------HHHHHHHHHHHHS---H CS
                        tRNA_bind_2   4 afakdFrkRflsLLsyqFrkfeavlaLsilesknkge.klekseekkeltkeeldellspfDlkRLesYannllDY 78 
                                         f+  Fr Rfl+L+ + + +f+  l++ + + k++ e ++ek++ +++   ++ ++ + +f+l RLesY n   + 
  gene3065|gene3065|rna3065|rna3065 636 RFYFIFRERFLNLINFMWCEFPVELCMMLTKIKQRNEmDTEKENLSNKSIDTKYKANFGEFELARLESYVNGYSEL 711
                                        68888**********************998877754313344445556667788999******************* PP

                                        HHHHSSSSHHHHHHHH--SSTTTS-SSSSSSHHHHHHTT---HHHHHHHHT--SSHHHHHHHHHHHHHH CS
                        tRNA_bind_2  79 hvilDllptlaklyFsgrlkeevkLsavqsaiLlaiGLQrksvddlekeLnlpsnQvlalFvkiirkvs 147
                                        +v++Dl+p +a+ yF++  +    Ls +q++iLla+G Q k+++ +++eL++ ++Qv  l  k++ k+ 
  gene3065|gene3065|rna3065|rna3065 712 NVVYDLIPIIARDYFHNARN---FLSVAQESILLAVGGQMKTMNVISRELDITKEQVQILVKKVVAKFL 777
                                        ****************9988...9************************************999999975 PP

>> DUF1726  Domain of unknown function (DUF1726)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.6   0.3   3.4e-17   6.7e-14       1      50 [.      93     141 ..      93     159 .. 0.84
   2 ?   -3.8   0.0       6.6   1.3e+04      76      86 ..     360     370 ..     349     372 .. 0.78

  Alignments for each domain:
  == domain 1  score: 51.6 bits;  conditional E-value: 3.4e-17
                            DUF1726   1 ykesekvLGqtydllvldlfealtPnalgrlvetVrGGGliilllpplee 50 
                                        y+e + v+G+ty++lvl+ fe+++Pn+l+++vetV+GGG+i++l+++  +
  gene3065|gene3065|rna3065|rna3065  93 YQEVDIVMGNTYEMLVLENFEKISPNTLAKTVETVKGGGVIVVLMDND-K 141
                                        7888999**************************************983.4 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 6.6
                            DUF1726  76 nkrfirklkeh 86 
                                          rfi+klk+ 
  gene3065|gene3065|rna3065|rna3065 360 SMRFIEKLKKN 370
                                        57999999876 PP

>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       4.1   8.2e+03      58      73 ..     287     302 ..     282     303 .. 0.85
   2 !   23.3   0.0     3e-08     6e-05      53     105 ..     520     573 ..     442     580 .. 0.69

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 4.1
                                        TTEEEEEEEEESGGGT CS
                     Acetyltransf_1  58 ggvayieslaVspeyr 73 
                                        +g+ y+  ++V++++r
  gene3065|gene3065|rna3065|rna3065 287 KGRSYVQKIVVKKNHR 302
                                        4788999*******99 PP

  == domain 2  score: 23.3 bits;  conditional E-value: 3e-08
                                        EETTSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHTTESEEEEEEETT.E CS
                     Acetyltransf_1  53 ipdekggvayieslaVspeyrgkGlGsaLlealeerareegikkivlaveed.n 105
                                        +++++++ + i ++aV+p+y+++ +G++++e l++ + + +++  ++ v+e   
  gene3065|gene3065|rna3065|rna3065 520 KNFLERRGCRIVRIAVHPDYQNMKYGTRMIELLVDTFSRGEARTFEFKVTEAlL 573
                                        333667778888***********************7777788888988877645 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.1      0.67   1.3e+03      16      45 ..     207     233 ..     190     274 .. 0.60
   2 ?   -3.5   0.0       7.3   1.5e+04      26      37 ..     291     302 ..     279     303 .. 0.73
   3 !   19.5   0.0     5e-07     0.001      24      49 ..     523     554 ..     468     579 .. 0.70

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.67
                                        EEEEEEEESTCTEEEEE-GGGTTSSHHHHH CS
                     Acetyltransf_7  16 GfialslldaeitrlaVdpeyrgkGiGraL 45 
                                        G i + +   + +++a +++ rg+G   aL
  gene3065|gene3065|rna3065|rna3065 207 GHILMDR---NNKNIALLKASRGRGKSAAL 233
                                        4333333...24447777777777754444 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 7.3
                                        CTEEEEE-GGGT CS
                     Acetyltransf_7  26 eitrlaVdpeyr 37 
                                        +  +++V++++r
  gene3065|gene3065|rna3065|rna3065 291 YVQKIVVKKNHR 302
                                        455699*99999 PP

  == domain 3  score: 19.5 bits;  conditional E-value: 5e-07
                                        S....TCTEEEEE-GGGTTSSHHHHHHHH..T CS
                     Acetyltransf_7  24 d....aeitrlaVdpeyrgkGiGraLlea..a 49 
                                             + i r+aV+p+y++  +G++++e+   
  gene3065|gene3065|rna3065|rna3065 523 LerrgCRIVRIAVHPDYQNMKYGTRMIELlvD 554
                                        0444467888*****************96331 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   1.4e-05     0.028       4     113 ..     215     338 ..     212     351 .. 0.86
   2 ?    1.8   0.0      0.13   2.6e+02      12      33 ..     351     372 ..     345     395 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.4e-05
                             AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelka......... 70 
                                        +++i ++ +  G GK+  l   +  ++e       r ++v++ +p+ ++ k l++ +lr l  ++ +         
  gene3065|gene3065|rna3065|rna3065 215 NKNIALLKASRGRGKSAALGLAVADAVEL------RYSIVYIVAPHIENVKMLFEFVLRGLRGKGYKenadfditr 284
                                        7899999999*********9999999876......***************************99999********* PP

                             AAA_22  71 ..............erlsseellealeqalraravielliiDEaqhlrseealeeLr 113
                                                      +++++   ++ + + ++++ +  ll++DEa  + +  +l++L 
  gene3065|gene3065|rna3065|rna3065 285 ifkgrsyvqkivvkKNHRQIIEYHGFLDKMDRYPD--LLVVDEAAAI-PLPILKDLI 338
                                        ****9999999984444444444888999998888..**********.999999993 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.13
                             AAA_22  12 GesGtGKTtllrrlleqldeea 33 
                                        G  GtG+++++r + + +++++
  gene3065|gene3065|rna3065|rna3065 351 GYEGTGRSLSMRFIEKLKKNDK 372
                                        789**********999887654 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0      0.14   2.7e+02      30      79 ..     191     240 ..     170     253 .. 0.72
   2 ?   10.6   0.0   0.00021      0.41      49      92 ..     525     569 ..     522     572 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.14
                    Acetyltransf_10  30 ealllvaeeggkiv..Gviel.rdgshisllfVdpeyrgqGigkaLleaveee 79 
                                        + l++ +++++ ++  G+i + r+++ i+ll   ++ rg+G ++aL  av ++
  gene3065|gene3065|rna3065|rna3065 191 NELCVTVDQDNAVAqlGHILMdRNNKNIALL---KASRGRGKSAALGLAVADA 240
                                        4445555566565588*****9999888887...7778888777776666555 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00021
                    Acetyltransf_10  49 rdgshisllfVdpeyrgqGigkaLleaveeeaekdgikl.eltvn 92 
                                        r+g +i +++V+p+y+  ++g++++e + + +++ + ++ e++v 
  gene3065|gene3065|rna3065|rna3065 525 RRGCRIVRIAVHPDYQNMKYGTRMIELLVDTFSRGEARTfEFKVT 569
                                        56669***********************99998888877777775 PP

>> Arteri_env  Arterivirus envelope protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.3   9.3e-05      0.19      27     109 ..      32     115 ..      24     126 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 9.3e-05
                         Arteri_env  27 nssatlclwfplaeGktslelslnytlcklclvseaaaeilep.gkslfcrigddrceesdsdeldlsvpdgvdll 101
                                        ns+ ++ + + l   + s+  s+ +  ck  + +e+ +++++   ks  c i dd  ++ + +e+d+ + + +++l
  gene3065|gene3065|rna3065|rna3065  32 NSKNNVPILYNLLSERCSFLPSVLWCYCKKSKSREEKKKKMKKeKKSAKCCINDDDIKKVSYQEVDIVMGNTYEML 107
                                        6667777888888999999999***********999988876515677899************************* PP

                         Arteri_env 102 klegytsv 109
                                         le +  +
  gene3065|gene3065|rna3065|rna3065 108 VLENFEKI 115
                                        99998554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (782 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1197  (0.0667633); expected 358.6 (0.02)
Passed bias filter:                      590  (0.0329076); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.76u 0.28s 00:00:01.04 Elapsed: 00:00:00.44
# Mc/sec: 5284.37
//
Query:       gene3066|gene3066|rna3066|rna3066  [L=429]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.068   11.8   5.8       0.12   10.9   5.8    1.4  1  FapA             Flagellar Assembly Protein A
        0.1   13.1   0.6        0.3   11.6   0.6    1.9  1  Acetyltransf_11  Udp N-acetylglucosamine O-acyltransferase; D
        3.7    6.3   5.2        5.4    5.8   5.2    1.2  1  LMBR1            LMBR1-like membrane protein


Domain annotation for each model (and alignments):
>> FapA  Flagellar Assembly Protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   5.8     2e-05      0.12     328     411 ..     340     422 ..     294     428 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 2e-05
                               FapA 328 vgldepelkeklkeleeeleeleeeleklkkkikklpklkaekqlesekkeqlkklletkeklkeeleeleeelke 403
                                        vg +  ++k+k++el ++ +++ee+l++l+++i++  k+k+ +  +++ + ++++l++ ++  k++  e e +  +
  gene3066|gene3066|rna3066|rna3066 340 VGDKGRAVKQKYDELFKRRKDVEEKLKMLNERIIHRVKEKE-NVKNPQLERMINELRHRMKTRKSRDYEDELKTIK 414
                                        37777899************************999888454.5457777778888888887777777777777777 PP

                               FapA 404 lkeelesk 411
                                        l++++ +k
  gene3066|gene3066|rna3066|rna3066 415 LQNSIFKK 422
                                        77777666 PP

>> Acetyltransf_11  Udp N-acetylglucosamine O-acyltransferase; Domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.6     5e-05       0.3      14      76 ..     325     396 ..     315     404 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 5e-05
                                        EEEEE-HHHHHHTT--HHHHHHHHHHHHHHHSSSS-HHHHHHHH.........HHHTTTSCCHHHHHHHHHH CS
                    Acetyltransf_11  14 rlrglNlvgLkRrgfseeeikalkkayrllyrsglsleealeel.........eeeaeespevqelldFiea 76 
                                        +l +lN    +++++  ++ +a+k+ y  l+++ + +ee l+ l         e+e+ ++p+++++++ +++
  gene3066|gene3066|rna3066|rna3066 325 ELDSLNKSFVEKAKLVGDKGRAVKQKYDELFKRRKDVEEKLKMLneriihrvkEKENVKNPQLERMINELRH 396
                                        678999999999999999**************************9999999886677778889998887774 PP

>> LMBR1  LMBR1-like membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   5.2   0.00091       5.4     193     299 ..     310     411 ..     268     428 .. 0.69

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.00091
                              LMBR1 193 eiksdldeelkklyfeaaklntekeeaereledllkevkklrksisesdplrkyleeilkkvPeeiaeklks...n 265
                                        e+k+++ + +k++y+e+++ln++  e+ + + d+ ++vk+ ++++    ++rk +ee lk  +e i  ++k+    
  gene3066|gene3066|rna3066|rna3066 310 EYKTRIIDGIKSIYIELDSLNKSFVEKAKLVGDKGRAVKQKYDEL---FKRRKDVEEKLKMLNERIIHRVKEkenV 382
                                        78899999*************888887777777777776666655...337799**************99996653 PP

                              LMBR1 266 enkteeslakle.kqlikalqkrertekqwkrlle 299
                                        +n+++e+++++  +++++      r+++ ++  l+
  gene3066|gene3066|rna3066|rna3066 383 KNPQLERMINELrHRMKT------RKSRDYEDELK 411
                                        334555554443022222......22222333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (429 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1232  (0.0687155); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.45
# Mc/sec: 2851.10
//
Query:       gene3067|gene3067|rna3067|rna3067  [L=442]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.057   12.7   0.1       0.12   11.6   0.1    1.5  1  Amj       Alternate to MurJ


Domain annotation for each model (and alignments):
>> Amj  Alternate to MurJ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   6.9e-06      0.12      79     126 ..      35      80 ..      26      95 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 6.9e-06
                                Amj  79 vgtllgilliPtfvrifsraikkleeagSvpklllkllsvsklkklkk 126
                                        + t++gi  +P  v +f+r ik+++++ Sv k+l ++l+++  +++++
  gene3067|gene3067|rna3067|rna3067  35 FVTIVGI--LPWNVLLFARLIKQMKTDDSVVKILAQVLEKQINERVEE 80 
                                        5577776..6****************************8887776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (442 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       847  (0.0472419); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 3414.78
//
Query:       gene3068|gene3068|rna3068|rna3068  [L=508]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.1e-82  275.2   1.5    7.7e-82  274.9   1.5    1.1  1  tRNA-synt_2      tRNA synthetases class II (D, K and N)
    2.2e-11   43.6   0.0    4.3e-11   42.6   0.0    1.5  1  tRNA_anti-codon  OB-fold nucleic acid binding domain
    8.1e-10   38.6   0.6    2.6e-05   23.8   0.2    2.4  2  tRNA-synt_2d     tRNA synthetases class II core domain (F)


Domain annotation for each model (and alignments):
>> tRNA-synt_2  tRNA synthetases class II (D, K and N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  274.9   1.5   1.3e-85   7.7e-82       2     313 ..     155     504 ..     154     505 .. 0.92

  Alignments for each domain:
  == domain 1  score: 274.9 bits;  conditional E-value: 1.3e-85
                                        CCHHHHTHHHHC.CSHHHHHHHHHHHHHHHHHHHHHHHTT-EE----SEESS--SSSS--EEEEETTT.TEEE-E- CS
                                        xxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        tRNA-synt_2   2 eelrlknryldl.rtekvskvlrlrstvtkavrkyleengfieietPiLsksdteegarlFkvksrekekeffaLt 76 
                                         el ++nryldl  +e+ ++ + +r+++++ +r++l+e+ f+e+etP++    ++++a++F ++++e + +++ L+
  gene3068|gene3068|rna3068|rna3068 155 SELIYRNRYLDLlMNEESRNRFITRTRIIQFLRRFLDERQFLEVETPMMNLIPGGAAANPFITHHNELKMDLY-LR 229
                                        57889*******9*******************************************************99999.** PP

                                        S-SHHHHHHHHHCTHSEEEEEEEEE--S--BTTB-S-CEEEEEEEEET-SCHHHHHHHHHHHHHHHHHHHHCSCCC CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        tRNA-synt_2  77 qspqlylellivagidrvfqiaraFRaEdsrtdrhlaEFtqieaemsfieeedimqvleelikslvkevlessakd 152
                                        +sp+lyl+ l+v+g+drv++i+r+FR+E ++ ++++ EFt++e++m++++++d++ ++eel++++vk v++s+ k 
  gene3068|gene3068|rna3068|rna3068 230 ISPELYLKKLVVGGMDRVYEIGRVFRNEGIDLTHNP-EFTMCEFYMAYADYNDLITMTEELLHEMVKFVKKSV-KV 303
                                        ************************************.********************************5555.66 PP

                                        CCHTTTTTS......EE-SSS-EEEEHHHHHHHHHTS-SS--HHHHHHHHH......................... CS
                                        xxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......................... RF
                        tRNA-synt_2 153 iefvirrns......kdlkkpfkrltykeaieklneigkdldkaderalvk......................... 197
                                         ++ ++r+        d+++pf+r+++ e ++       +++ + e +++k                         
  gene3068|gene3068|rna3068|rna3068 304 EYHPMKRECrpekveIDFSRPFRRIDMLEELSAK----LGMELNGENLELKekelveicekngikideprtlsrvl 375
                                        6666666667999999***************993....44444444444444466667777777788888888899 PP

                                        .........HS--SEEEEEEEBGGGSTTCBBBSTTSTTBBSEEEEEETTEEEEEEEEB--SHHHHHHHHHHCCHH. CS
                                        .........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                        tRNA-synt_2 198 .........keknepvfvtdfPaelkpFyarkeeddkkltesyDllingvElvgGslRiedpeeleeklkskgld. 263
                                                  e  +p+f+t++P  ++p++++++++ + lte+++l+ing E+v+++++++dp  ++e+++++  + 
  gene3068|gene3068|rna3068|rna3068 376 dklvghfiePECINPTFITNHPIVMSPLAKKHRSK-PGLTERFELFINGKEIVNAYTELNDPFDQRERFQKQVEEh 450
                                        99******977889*********************.9**********************************99999 PP

                                        ....SSSGGGGHHHHHHHHCT--SEEEEEEEHHHHHHHHCT-SSGGGCSSS-XX CS
                                        ....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        tRNA-synt_2 264 ....eeaeekfswylealeyGapphgGlglGldRlvmlllgsesIrdviaFPkl 313
                                            +ea+  ++ ++ a+eyG+ p++G+g+GldRl+m+l+++ +I+dv++FP +
  gene3068|gene3068|rna3068|rna3068 451 dagdNEAMLMDESFCVAMEYGLAPTAGWGIGLDRLTMFLTNAANIKDVLFFPAM 504
                                        9999999*********************************************87 PP

>> tRNA_anti-codon  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.6   0.0   7.2e-15   4.3e-11       1      76 []      63     138 ..      63     138 .. 0.88

  Alignments for each domain:
  == domain 1  score: 42.6 bits;  conditional E-value: 7.2e-15
                                        EEEEEEEEEEEEEEETTEEEEE.EEETTEEEEEEEET..HHHHHHHTTS-TTSEEEEEEEEEECTTSSEEEEEEEE CS
                    tRNA_anti-codon   1 VtvaGrvtsisdrsggkvifid.lrDgtgriqvvlfr..eeatklaenlkeGdvvrvtGrvkrrpggelelkveei 73 
                                        V +aGr++si  r+ g++ f++ l Dg+ +iqv+      e++++++nlk+Gd+++++G v+++++gel++ + +i
  gene3068|gene3068|rna3068|rna3068  63 VHIAGRLMSI--RGQGRMNFLKmLSDGE-QIQVIYVAdsVEKKAFFSNLKRGDILGISGNVGCSNTGELSVFAHNI 135
                                        779*******..**********555555.5555555556************************************* PP

                                        EEE CS
                    tRNA_anti-codon  74 ell 76 
                                        e+l
  gene3068|gene3068|rna3068|rna3068 136 EVL 138
                                        986 PP

>> tRNA-synt_2d  tRNA synthetases class II core domain (F)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.2   4.4e-09   2.6e-05     103     167 ..     246     307 ..     243     332 .. 0.85
   2 !   12.5   0.0   1.2e-05     0.074     209     234 ..     473     498 ..     459     502 .. 0.86

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 4.4e-09
                                        EEEEEEEEEBSST-SSSB-SEEEEEEEEEEETT--HHHHHHHHHHHHHHHCTSTEEEEEEECEET CS
                       tRNA-synt_2d 103 kiisigrvfRrdavDathlaeFhqveglvvdenvsladlkgvleellkklfgaevkvrfrpsyfp 167
                                        ++  igrvfR++ +D th +eF+ +e+ ++  +   +dl+ + eell+++  +  k  ++ +y p
  gene3068|gene3068|rna3068|rna3068 246 RVYEIGRVFRNEGIDLTHNPEFTMCEFYMAYAD--YNDLITMTEELLHEMVKFV-KKSVKVEYHP 307
                                        56679**********************998765..57***********996654.5555555555 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 1.2e-05
                                        SEEEEEEEEHHHHHHHHHT-SSGHHH CS
                       tRNA-synt_2d 209 vsgfafGlGveRlamlkygieDiRel 234
                                         + +++G+G++Rl+m+ ++  +i+++
  gene3068|gene3068|rna3068|rna3068 473 APTAGWGIGLDRLTMFLTNAANIKDV 498
                                        56789******************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (508 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       667  (0.0372023); expected 358.6 (0.02)
Passed bias filter:                      552  (0.0307881); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.60u 0.25s 00:00:00.85 Elapsed: 00:00:00.44
# Mc/sec: 3497.58
//
Query:       gene3069|gene3069|rna3069|rna3069  [L=208]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.8e-49  167.4   0.0    2.1e-49  167.2   0.0    1.0  1  Ras        Ras family
    1.7e-24   86.3   0.0    3.7e-24   85.3   0.0    1.5  2  Roc        Ras of Complex, Roc, domain of DAPkinase
    6.6e-07   29.0   0.0    8.5e-07   28.6   0.0    1.3  1  Arf        ADP-ribosylation factor family
    0.00092   18.6   0.0     0.0013   18.1   0.0    1.4  1  Gtr1_RagA  Gtr1/RagA G protein conserved region


Domain annotation for each model (and alignments):
>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  167.2   0.0   4.8e-53   2.1e-49       1     160 [.      19     185 ..      19     187 .. 0.96

  Alignments for each domain:
  == domain 1  score: 167.2 bits;  conditional E-value: 4.8e-53
                                        EEEEEESTTSSHHHHHHHHHHSSCSSSCTTTSSEEEEEEEEEET.TEEEEEEEEEETTSGGGHHHHHHHHTTESEE CS
                                Ras   1 KlvlvGdsavGKtslllrfvkdkFkeeyesTigvdfytkeievd.gkevkleiwDTAGqeefkslrelyyrdaegi 75 
                                        K+v+vGd+a+GKt+ll  f ++kF++ey++T+ vd+++ke++++  + v+l++wDTAGqe+++s+r+l+y+d++ +
  gene3069|gene3069|rna3069|rna3069  19 KIVVVGDGACGKTCLLEVFKRNKFPDEYIPTV-VDNFVKEVKINeAECVNLTLWDTAGQEDYDSVRPLSYKDTDLV 93 
                                        9*******************************.**********9445689************************** PP

                                        EEEEETTBHHHHHTHH.HHHHHHHHHSTTTSEEEEEEETTTGGG......G-SS-HHHHHHHHHHHT.SEEEEEBT CS
                                Ras  76 llvyditsresfenvk.kwveeikrvaeenvpivLvGnKvDlee......kravsteegeelakelg.lkfletSA 143
                                        ll+y i++ + ++n+  kw+ eik++++ + ++ L+G K D+++      +  vs+eeg+++a+e+g  +f+e+SA
  gene3069|gene3069|rna3069|rna3069  94 LLCYTIENCQVLSNIPkKWLFEIKNYCP-SANFFLIGLKKDIRDeqrghvQGIVSFEEGQNMANEIGaQAFIECSA 168
                                        ***************99***********.5**************99999999***************889****** PP

                                        TTTCTHHHHHHHHHHHH CS
                                Ras 144 ktnenveeafeellrei 160
                                        k+ env+++f e ++ i
  gene3069|gene3069|rna3069|rna3069 169 KSGENVDKVFLESAKYI 185
                                        ***********998876 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.3   0.0   8.2e-28   3.7e-24       1     119 [.      19     133 ..      19     134 .. 0.88
   2 ?   -2.6   0.0       1.4   6.2e+03      74     100 ..     176     200 ..     168     202 .. 0.52

  Alignments for each domain:
  == domain 1  score: 85.3 bits;  conditional E-value: 8.2e-28
                                        EEEEESSTTSSHHHHHHCHCT-CCC-EEETTTTEEEEEEECGGSGGCTTBTTTTCEEEEEEEE-SGGCTTTT-HHH CS
                                Roc   1 KvvlvGdsgvGKtsllkrfvedkfsekekstigvdfltkevtkikgvendkkvkkvklniWDtaGqerfrslhply 76 
                                        K+v+vGd++ GKt+ll+ f ++kf +++ +t+  +f++ ev ki++       + v+l +WDtaGqe+++s++pl 
  gene3069|gene3069|rna3069|rna3069  19 KIVVVGDGACGKTCLLEVFKRNKFPDEYIPTVVDNFVK-EV-KINE------AECVNLTLWDTAGQEDYDSVRPLS 86 
                                        9*******************************999865.55.4544......35699******************* PP

                                        HCTSCEEEEEEEGHHH...HCH.HHHHHHHHHHCSSS-EEEEEE-TT CS
                                Roc  77 lreaalailvydsrss...enl.keWlkelkkvagkspvilvgnkiD 119
                                        +++ +l++l+y+ ++    +n+ k+Wl e+k+++++++++l+g k D
  gene3069|gene3069|rna3069|rna3069  87 YKDTDLVLLCYTIENCqvlSNIpKKWLFEIKNYCPSANFFLIGLKKD 133
                                        ***********96654123566589******************9998 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.4
                                        HHHHCTSCEEEEEEEGHHHHCHHHHHH CS
                                Roc  74 plylreaalailvydsrssenlkeWlk 100
                                        +++l++a+ +i+ +++r  ++  +W+k
  gene3069|gene3069|rna3069|rna3069 176 KVFLESAK-YIMAFKKRI-KEQPSWFK 200
                                        55555554.445554433.33345665 PP

>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6   0.0   1.9e-10   8.5e-07      12      91 ..      15      99 ..       5     182 .. 0.73

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 1.9e-10
                                       TTEEEEEEEESTTSSHHHHHHHHHHSSCEE.CSSSSSEE.EEEEEE...TTEEEEEEEE-SSGGGGGGGGGGCTTESE CS
                                Arf 12 kkelrilllGLDnaGKtTilkklkleelvt.tvPTigfn.veelei...knlkftvwDvGGqeklRplWknYfektda 84
                                       + + +i+++G  + GKt +l+ +k +++ +  +PT+  n v+e++i   + +++t+wD  Gqe   ++    +++td 
  gene3069|gene3069|rna3069|rna3069 15 SVSGKIVVVGDGACGKTCLLEVFKRNKFPDeYIPTVVDNfVKEVKIneaECVNLTLWDTAGQEDYDSVRPLSYKDTDL 92
                                       4678**********************996549***98775899*994434589*********9988888888888888 PP

                                       EEEEEET CS
                                Arf 85 vifvvDs 91
                                       v+ +   
  gene3069|gene3069|rna3069|rna3069 93 VLLCYTI 99
                                       7765544 PP

>> Gtr1_RagA  Gtr1/RagA G protein conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   2.9e-07    0.0013       1      63 [.      19      81 ..      19     167 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 2.9e-07
                          Gtr1_RagA  1 kvLLmGksgsGKtsmrsiiFdnylardtlrlgatidveksevrflgnltlnlwDcgGqeafve 63
                                       k++ +G +  GKt++ ++   n  + + +   +   v++ +++  + ++l lwD  Gqe++  
  gene3069|gene3069|rna3069|rna3069 19 KIVVVGDGACGKTCLLEVFKRNKFPDEYIPTVVDNFVKEVKINEAECVNLTLWDTAGQEDYDS 81
                                       78999***********************99999999999999999**************9855 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       711  (0.0396564); expected 358.6 (0.02)
Passed bias filter:                      555  (0.0309554); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 1569.28
//
Query:       gene307|gene307|rna307|rna307  [L=260]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.4e-28   99.2   0.6    2.4e-28   99.2   0.6    2.1  3  DUF3449      Domain of unknown function (DUF3449)
    1.9e-05   24.9  10.3    1.9e-05   24.9   0.6    2.9  3  zf-met       Zinc-finger of C2H2 type
      8e-05   22.8   2.0      8e-05   22.8   2.0    3.0  2  zf-C2H2_jaz  Zinc-finger double-stranded RNA-binding
     0.0056   16.4   7.6     0.0086   15.8   0.4    2.6  2  zf-U1        U1 zinc finger
  ------ inclusion threshold ------
       0.08   13.1   0.5       0.22   11.7   0.5    1.8  1  Jas          TPL-binding domain in jasmonate signalling
        0.1   12.7   0.3       0.64   10.1   0.1    2.1  2  DUF1335      Protein of unknown function (DUF1335)
       0.16   11.6   6.4      0.055   13.1   1.0    2.1  2  CCDC84       Coiled coil protein 84


Domain annotation for each model (and alignments):
>> DUF3449  Domain of unknown function (DUF3449)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.65   1.7e+03     159     177 ..      52      70 ..      18      77 .. 0.70
   2 ?   -1.4   0.0      0.69   1.8e+03     152     174 ..      93     115 ..      59     125 .. 0.58
   3 !   99.2   0.6   9.4e-32   2.4e-28      57     147 ..     169     260 .]     131     260 .] 0.88

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.65
                                    XXXXXXXXXXXXXXXXXXX CS
                        DUF3449 159 eeveveDeeGnvmskkvYe 177
                                    +  e e ++ nv+ +kvY 
  gene307|gene307|rna307|rna307  52 RCAESENKTWNVFDTKVYC 70 
                                    3567888888888888885 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.69
                                    XXXX.XXXXXXXXXXXXXXXXXX CS
                        DUF3449 152 kekakeeeeveveDeeGnvmskk 174
                                    k+++   +++e+ De+G+ + +k
  gene307|gene307|rna307|rna307  93 KARTAFLKNIELPDENGDYVRNK 115
                                    22222234677777777765554 PP

  == domain 3  score: 99.2 bits;  conditional E-value: 9.4e-32
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXX CS
                        DUF3449  57 eeekiynplnlplgwdgkPipyWLykLhgLgkeykCeiCgnavYkGrkaFekHFseerHaeglkcLgie.ntklfkeitk 135
                                    e+ek + ++++  +  g+Pip WLy  +gL++ey CeiC n++YkGrk+Fe+HF+  +H++ l  Lgi+ n  ++++i++
  gene307|gene307|rna307|rna307 169 EKEKKTYSMKIYRDEAGNPIPRWLYNQRGLNVEYICEICDNTMYKGRKVFESHFNSDKHKQCLMKLGITsNFDKYRGISQ 248
                                    3445556788889999*****************************************************999******** PP

                                    XXXXXXXXXXXX CS
                        DUF3449 136 iedaleLweklk 147
                                    i++a++L +kl+
  gene307|gene307|rna307|rna307 249 IRNAQKLQDKLQ 260
                                    *********996 PP

>> zf-met  Zinc-finger of C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.3         7   1.8e+04       2       7 ..      69      74 ..      69      76 .. 0.72
   2 !    6.4   0.2    0.0048        12      13      25 .]      79      91 ..      77      91 .. 0.90
   3 !   24.9   0.6   7.5e-09   1.9e-05       1      25 []     202     227 ..     202     227 .. 0.98

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 7
                         zf-met  2 yCelCn 7 
                                   yC  C 
  gene307|gene307|rna307|rna307 69 YCMFCE 74
                                   787785 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0048
                         zf-met 13 esqlksHlqGKkH 25
                                   +s+++ H +GKkH
  gene307|gene307|rna307|rna307 79 KSVFEYHAKGKKH 91
                                   689999******* PP

  == domain 3  score: 24.9 bits;  conditional E-value: 7.5e-09
                         zf-met   1 fyCelC.nvtfnsesqlksHlqGKkH 25 
                                    + Ce+C n++++++++++sH+++ kH
  gene307|gene307|rna307|rna307 202 YICEICdNTMYKGRKVFESHFNSDKH 227
                                    78***********************9 PP

>> zf-C2H2_jaz  Zinc-finger double-stranded RNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   5.1      0.25   6.5e+02      12      26 ..      77      91 ..      67      91 .. 0.79
   2 !   22.8   2.0   3.1e-08     8e-05       2      27 .]     202     228 ..     201     228 .. 0.97

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.25
                                   SSHHHHHCCTTSHHH CS
                    zf-C2H2_jaz 12 ksenaldnHlkSKkH 26
                                   ++ ++++ H k+KkH
  gene307|gene307|rna307|rna307 77 ITKSVFEYHAKGKKH 91
                                   57899********** PP

  == domain 2  score: 22.8 bits;  conditional E-value: 3.1e-08
                                    CBBTTTT.BBBSSHHHHHCCTTSHHHH CS
                    zf-C2H2_jaz   2 fYCvlCd.KyFksenaldnHlkSKkHK 27 
                                    + C++Cd  ++k  ++++ H++S kHK
  gene307|gene307|rna307|rna307 202 YICEICDnTMYKGRKVFESHFNSDKHK 228
                                    89************************9 PP

>> zf-U1  U1 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.4   3.4e-06    0.0086       2      37 ..      66      98 ..      65      99 .. 0.85
   2 ?    3.5   1.7     0.023        60       4      32 ..     202     229 ..     200     233 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 3.4e-06
                                   XSEEETTTTEEESS-SHHHHHHHHTSHHHHHHHHHH CS
                          zf-U1  2 pkYyCdYCdiyLthDspsvRksHngGrkHkenvkdy 37
                                   +k yC +C++ +t    sv + H +G+kH +++ ++
  gene307|gene307|rna307|rna307 66 TKVYCMFCEMDIT---KSVFEYHAKGKKHGKARTAF 98
                                   588*********5...567789*********99876 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.023
                                    EEETTTTEEESS-SHHHHHHHHTSHHHHH CS
                          zf-U1   4 YyCdYCdiyLthDspsvRksHngGrkHke 32 
                                    Y C+ Cd  + + +  v +sH +  kHk+
  gene307|gene307|rna307|rna307 202 YICEICDNTMYKGR-KVFESHFNSDKHKQ 229
                                    88*****9999999.677*********98 PP

>> Jas  TPL-binding domain in jasmonate signalling
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.5   8.6e-05      0.22      37      67 ..      59      89 ..      35     102 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 8.6e-05
                            Jas 37 legsikrdgIvCsCCgkvlspseFeaHAGgk 67
                                   ++ ++  ++++C  C++ ++ s Fe HA gk
  gene307|gene307|rna307|rna307 59 KTWNVFDTKVYCMFCEMDITKSVFEYHAKGK 89
                                   455677899*******************543 PP

>> DUF1335  Protein of unknown function (DUF1335)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.31     8e+02      33      65 ..      65      97 ..      41     134 .. 0.70
   2 ?   10.1   0.1   0.00025      0.64      68      96 ..     203     232 ..     193     237 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.31
                        DUF1335 33 dfliGlGfsaenvtkklksmesvlrkhGlkesm 65
                                   d  + + f ++++tk++       +khG   + 
  gene307|gene307|rna307|rna307 65 DTKVYCMFCEMDITKSVFEYHAKGKKHGKARTA 97
                                   556778888999999998888888888865543 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00025
                        DUF1335  68 laeichrlkykGesianPivks.ysshClv 96 
                                    + eic+ + ykG ++    ++s  +++Cl+
  gene307|gene307|rna307|rna307 203 ICEICDNTMYKGRKVFESHFNSdKHKQCLM 232
                                    689***************999946899996 PP

>> CCDC84  Coiled coil protein 84
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   1.0   2.2e-05     0.055      22      99 ..      28     101 ..      13     185 .. 0.76
   2 ?    1.7   0.4     0.064   1.6e+02       2      27 ..     204     233 ..     202     254 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.2e-05
                         CCDC84  22 kkslsavLsrflskv..advrkfLkkpsverpe.eesenrlWCvfCdadveelvssvacgnaleHlaseeHlkkvkkFlw 98 
                                    ++ l+ + ++ +  +  ++++++L++++ e+   +  + ++ C+fC+ d+++ v +       +H +++ H k+  +Fl+
  gene307|gene307|rna307|rna307  28 QHYLKDFVHKSRPEIhhKKIKRLLRCAESENKTwNVFDTKVYCMFCEMDITKSVFE-------YHAKGKKHGKARTAFLK 100
                                    45566666666665633689**********99988899***********9986643.......45666666666666665 PP

                         CCDC84  99 k 99 
                                    +
  gene307|gene307|rna307|rna307 101 N 101
                                    5 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.064
                         CCDC84   2 CevCrrnhdqgrr....HkysrkHkkslsa 27 
                                    Ce+C ++  +gr+    H  s kHk+ l +
  gene307|gene307|rna307|rna307 204 CEICDNTMYKGRKvfesHFNSDKHKQCLMK 233
                                    9*********98766668889999988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1009  (0.0562775); expected 358.6 (0.02)
Passed bias filter:                      491  (0.0273858); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1772.27
//
Query:       gene3070|gene3070|rna3070|rna3070  [L=93]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0071   16.6   0.1      0.011   16.0   0.1    1.4  1  CBFD_NFYB_HMF  Histone-like transcription factor (CBF/NF-Y) a


Domain annotation for each model (and alignments):
>> CBFD_NFYB_HMF  Histone-like transcription factor (CBF/NF-Y) and archaeal histone
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.1   6.1e-07     0.011       8      63 ..      12      67 ..       5      69 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 6.1e-07
                                       HHHHHHCCTTXS-B-HHHHHHHHHHHHHHHHHHHHHHHHHHCCTTSSCE-HHHHHH CS
                      CBFD_NFYB_HMF  8 vkkImksdpdarkiakdAkeliaecveefieelaseAaeickkekrKtikaehikl 63
                                       +k ++k+  + r+i+ d  +l+ae +   + +la+++ +  +++k+++i   +ik 
  gene3070|gene3070|rna3070|rna3070 12 IKILLKKLAKKRRISGDTVHLLAELAFYTAAFLATASKSFSEEDKSEFIRNGDIKR 67
                                       66678888999******************************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       622  (0.0346924); expected 358.6 (0.02)
Passed bias filter:                      456  (0.0254337); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.29s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 642.68
//
Query:       gene3071|gene3071|rna3071|rna3071  [L=288]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-50  171.0   1.2    2.2e-50  170.6   1.2    1.2  1  Pyrophosphatase  Inorganic pyrophosphatase
  ------ inclusion threshold ------
       0.11   11.4   5.4       0.17   10.8   0.5    2.3  2  Kre28            Spindle pole body component


Domain annotation for each model (and alignments):
>> Pyrophosphatase  Inorganic pyrophosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  170.6   1.2   2.4e-54   2.2e-50       1     160 []      54     236 ..      54     236 .. 0.95

  Alignments for each domain:
  == domain 1  score: 170.6 bits;  conditional E-value: 2.4e-54
                                        EEEEE-TTCSEEEEEETTT...........TEEEEEEE-SSSB-BSSEEEEETT--BT.......CCBEETSSSEE CS
                    Pyrophosphatase   1 vvvEiprgsnaKyeidkee...........gklrldrvlftskgypanYGfipqTled.......telkGDgDPlD 58 
                                        vv Eipr +naK+ei+ke+           gk+r+++++f+  gyp+nYG+ipqT+ed       t++ GD+DPlD
  gene3071|gene3071|rna3071|rna3071  54 VVNEIPRFENAKFEINKEKkmnpimqdvknGKPRYVANIFPCRGYPWNYGAIPQTWEDpsvkntnTNCFGDDDPLD 129
                                        799************************************************************************* PP

                                        EEEESSS---TTEEEEEEEEEEEEEEETTEEEEEEEEEETTSGGGTT-SSGGG....STHHHHHHHHHHHHHTTTT CS
                    Pyrophosphatase  59 vlvlgeeplspgevvevkvlGvlamiDegetDdKiiavpvkdprlkkindied....lpgllleeiehfFetykdl 130
                                        v+++g++  ++gev+ +k++G++ +iD+ge D+Kii+++++d++ k++nd++d    +pgl  + + ++F +yk +
  gene3071|gene3071|rna3071|rna3071 130 VIEVGNVTKEVGEVYVAKIIGCIGLIDSGECDWKIIVIDKRDENAKHVNDVNDlkstFPGLQ-NVTYNWFMNYKLA 204
                                        *****9999**********************************99********888777766.************* PP

                                        SCCT-SE..EEEEEEEHHHHHHHHHHHHHHHH CS
                    Pyrophosphatase 131 egkkknv..kveewkdkeeAekvieeaheryk 160
                                        ++k kn    + e+k+ke+A+++i+e+he++k
  gene3071|gene3071|rna3071|rna3071 205 DNKPKNSflDYGELKSKEFAKNIIKECHENWK 236
                                        *99775536777*******************7 PP

>> Kre28  Spindle pole body component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.3    0.0059        53     307     356 ..      24      78 ..      18      83 .. 0.66
   2 ?   10.8   0.5   1.9e-05      0.17     204     249 ..     221     264 ..     203     277 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.0059
                              Kre28 307 tqyviiisLdd.kkstikdielfekdak.sivedk....elrkkvnnkylgkseif 356
                                         qy + ++L+d   s ++di ++ ++++ ++v+++    +++ ++n++ ++ ++i+
  gene3071|gene3071|rna3071|rna3071  24 AQYQVYVTLEDkIISPFHDIPVYADQDHiNVVNEIprfeNAKFEINKE-KKMNPIM 78 
                                        4899999999945688*********99987777651111444444443.3334444 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 1.9e-05
                              Kre28 204 kdteddlveetYeeWkslqkslqekeelkeeldrLkkekkeleevk 249
                                        k+  ++++ e+ e+Wk l   + e+e++ ++ + L+ke  ++ee+ 
  gene3071|gene3071|rna3071|rna3071 221 KEFAKNIIKECHENWKRL--MKIELETSISRVNALQKEHRSVEEIV 264
                                        5557899***********..889999999999*********99974 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (288 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       628  (0.0350271); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1932.32
//
Query:       gene3072|gene3072|rna3072|rna3072  [L=157]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.026   14.5   0.0       0.04   13.9   0.0    1.4  1  tRNA_anti-codon  OB-fold nucleic acid binding domain


Domain annotation for each model (and alignments):
>> tRNA_anti-codon  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   2.3e-06      0.04      12      75 ..      77     133 ..      56     134 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.3e-06
                                        EEEETTEEEEEEEETTEEEEEEEETHHHHHHHTTS-TTSEEEEE.EEEEECTTSSEEEEEEEEEE CS
                    tRNA_anti-codon  12 drsggkvifidlrDgtgriqvvlfreeatklaenlkeGdvvrvt.Grvkrrpggelelkveeiel 75 
                                        +r++  v ++ + D+tg+i+ ++f+       ++l+ Gd++ +   + ++++++ l ++ +e+++
  gene3072|gene3072|rna3072|rna3072  77 TRDNDVVYSYLVADDTGSIEYSIFN-------QSLDLGDIIAINyAYATFFKTR-LRVYNSELTV 133
                                        577777888899*************.......**********************.9999888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       528  (0.0294495); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 1106.68
//
Query:       gene3073|gene3073|rna3073|rna3073  [L=231]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.92    9.6   0.0       0.92    9.6   0.0    2.5  3  NDUF_B6   NADH:ubiquinone oxidoreductase, NDUFB6/B17 subunit


Domain annotation for each model (and alignments):
>> NDUF_B6  NADH:ubiquinone oxidoreductase, NDUFB6/B17 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.4      0.13   2.4e+03      87     107 ..       9      29 ..       2      57 .. 0.61
   2 ?    9.6   0.0   5.2e-05      0.92      93     129 ..      63      99 ..      36     111 .. 0.84
   3 ?   -0.5   0.0     0.066   1.2e+03      95     124 ..     203     229 ..     192     231 .] 0.72

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.13
                            NDUF_B6  87 vsvfklllvlvpvyivaYYlK 107
                                        + +f + l++v ++i+  Y+ 
  gene3073|gene3073|rna3073|rna3073   9 SLIFVVFLIVVFIFILVSYVY 29 
                                        445555555555555544442 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 5.2e-05
                            NDUF_B6  93 llvlvpvyivaYYlKYevkdwtrkkgyevveskkkiv 129
                                           l  ++i+  YlKY+++d  +++ +   + k+++ 
  gene3073|gene3073|rna3073|rna3073  63 NNNLCDIFIITIYLKYDINDKQKSNDLDCYHTKHSCE 99 
                                        5668899******************999999998875 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.066
                            NDUF_B6  95 vlvpvyivaYYlKYevkdwtrkkgyevves 124
                                         +++ +i  + lKY ++   +kk +e++ +
  gene3073|gene3073|rna3073|rna3073 203 KFFVFFINGFNLKYRQN---KKKRHESIVN 229
                                        57788889999*****9...5555555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1472  (0.0821016); expected 358.6 (0.02)
Passed bias filter:                      496  (0.0276647); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1491.19
//
Query:       gene3074|gene3074|rna3074|rna3074  [L=156]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.3e-13   50.8   0.1    1.7e-13   50.4   0.1    1.2  1  Cofilin_ADF  Cofilin/tropomyosin-type actin-binding protein


Domain annotation for each model (and alignments):
>> Cofilin_ADF  Cofilin/tropomyosin-type actin-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.4   0.1   9.7e-18   1.7e-13       8     120 ..      19     148 ..      12     149 .. 0.72

  Alignments for each domain:
  == domain 1  score: 50.4 bits;  conditional E-value: 9.7e-18
                                        HCTTT.SSEEEEEEECTT.TEEEEEE..SS-.........HHHHHHHHHHTTT.......-EEEEEEEEEECCSEC CS
                        Cofilin_ADF   8 lksgkktkyilfkidddk.eeivvee..ege.........tyeelreelpese.......prYavydveyehddes 64 
                                        + ++ + +y++f++ +      ++ +    +         t++++r+ ++e +        +Y+vyd+ +++ ++ 
  gene3074|gene3074|rna3074|rna3074  19 VNRR-ESTYVIFHVPNVRdARFQLLAvgG-SinpdasrlpTVDDIRKRFEECReevikydSCYIVYDFYFNNANGA 92 
                                        4443.467777776654443344433430.2334445677666666666432222333338*************** PP

                                        CEEEEEEEEE--T.TS-HHHHHHHHHHHHHHHHHCTTSEEEEEE-CGGCCSHHHHHH CS
                        Cofilin_ADF  65 krsklvfIswvPd.sapikqkmlyasskdalkkelkgisveieatdldelteeelke 120
                                         r+ l++Is++ d ++p+ ++  y+s++ +l++ + + +++i +++++e+t+++++e
  gene3074|gene3074|rna3074|rna3074  93 SRNILILISFINDeTCPTNKRFFYSSHSLELVNDI-HAAKHISVNSPSEFTYDYFEE 148
                                        *************99********************.55555************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       487  (0.0271627); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 1055.45
//
Query:       gene3075|gene3075|rna3075|rna3075  [L=97]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0049   17.2   8.1     0.0057   17.0   8.1    1.3  1  DUF4602   Domain of unknown function (DUF4602)
  ------ inclusion threshold ------
      0.049   12.9   1.8        1.1    8.5   0.2    2.0  2  DUF2709   Protein of unknown function (DUF2709)


Domain annotation for each model (and alignments):
>> DUF4602  Domain of unknown function (DUF4602)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   8.1   6.4e-07    0.0057      65     130 ..      32      96 ..       3      97 .] 0.85

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 6.4e-07
                            DUF4602  65 kerkkaekerlikLGAKppknpyinykelkgekkkakareeeekaeareagvvtkkkkkkkkkkkr 130
                                         ++ k+ ++r+++LGA  +k+   + ke +    ++k++ ++e++++   g +tk k+++ kk+++
  gene3075|gene3075|rna3075|rna3075  32 MSKVKFMQDRIVELGA-HKKKTFLPFKEGIMKSVEEKEAIRRERQMRVNVGLLTKNKSTRRKKQNK 96 
                                        6799************.677888******9999999999999999999999999999988888877 PP

>> DUF2709  Protein of unknown function (DUF2709)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.1    0.0026        23     165     191 ..       9      36 ..       5      44 .. 0.81
   2 ?    8.5   0.2   0.00012       1.1      44      86 ..      49      91 ..      41      93 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.0026
                            DUF2709 165 klfnskeaviedfkkny.lkklslvevq 191
                                        klf++ +++i+++kkn   k++++ +v+
  gene3075|gene3075|rna3075|rna3075   9 KLFQTMPSLINEIKKNSaYKNITMSKVK 36 
                                        9************998526889998887 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00012
                            DUF2709 44 kekiiyqsaedaikkleeekklwreteikisfgkasvneetkk 86
                                       k+k+    +e ++k +ee++ + re ++++++g  + n+ t++
  gene3075|gene3075|rna3075|rna3075 49 KKKTFLPFKEGIMKSVEEKEAIRRERQMRVNVGLLTKNKSTRR 91
                                       778888899*****************************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (97 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1111  (0.0619666); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 739.01
//
Query:       gene3076|gene3076|rna3076|rna3076  [L=390]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.1e-55  186.9  10.9      1e-54  185.9  10.9    1.5  1  Pox_MCEL         mRNA capping enzyme
    1.6e-11   44.3   0.0    2.9e-11   43.5   0.0    1.6  1  Methyltransf_23  Methyltransferase domain
    1.4e-10   41.8   0.0    4.1e-10   40.2   0.0    1.8  1  Methyltransf_25  Methyltransferase domain
    1.5e-09   37.8   0.0    2.9e-09   36.9   0.0    1.5  1  Methyltransf_31  Methyltransferase domain
    1.9e-08   34.8   0.0    5.8e-08   33.3   0.0    1.9  2  Methyltransf_11  Methyltransferase domain
    5.1e-07   30.3   0.0    1.6e-06   28.8   0.0    1.9  1  Methyltransf_12  Methyltransferase domain
     0.0011   18.7   0.0     0.0021   17.7   0.0    1.4  1  MetW             Methionine biosynthesis protein MetW
     0.0052   16.3   0.0     0.0095   15.5   0.0    1.3  1  MTS              Methyltransferase small domain
  ------ inclusion threshold ------
      0.011   15.8   1.3      0.045   13.7   0.0    2.3  2  Methyltransf_32  Methyltransferase domain
      0.057   12.8   0.0       0.11   11.8   0.0    1.4  1  PrmA             Ribosomal protein L11 methyltransferase (Prm


Domain annotation for each model (and alignments):
>> Pox_MCEL  mRNA capping enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  185.9  10.9   5.8e-58     1e-54      12     293 ..      97     366 ..      86     387 .. 0.86

  Alignments for each domain:
  == domain 1  score: 185.9 bits;  conditional E-value: 5.8e-58
                           Pox_MCEL  12 dlvathynerpetgellkkRiastiiylrnlnNyiKslLiseyasktkldesnklkvLdldcgkGgDLeKyekgeI 87 
                                        + +a+hyn+ p ++  +++R +s ii +rn+nN+iKs+L + y++++         vLdl+cgkGgDL Ky+k +I
  gene3076|gene3076|rna3076|rna3076  97 NEIAEHYNKIPSKS--YAERRKSYIINIRNMNNFIKSVLFNRYVKRNGR-------VLDLGCGKGGDLLKYKKMGI 163
                                        6689********87..9****************************9998.......******************** PP

                           Pox_MCEL  88 sklvatDiaeesieeckeRYnklrsekkskyykFdaelirsdsfvssvrevfedyelkfdivslQFaiHYsFesee 163
                                        s++ + Dia++si eck RY    s++k     F+a +  +d++++ ++        +fd++s+QF++HYsFesee
  gene3076|gene3076|rna3076|rna3076 164 SYYYGLDIADKSISECKYRY----SRHKCP---FKADFNVCDTYHTILNL-----GKRFDVISIQFSFHYSFESEE 227
                                        ********************....666665...***********998874.....459****************** PP

                           Pox_MCEL 164 kartvlrNvaellasGGkvlgTtpdgdelskltvkklkviekdlps.............fgNsiyvvkfeeekiev 226
                                           +  +N+ e l++ G++l T+pd +++ ++ ++   +  kd+++             fgN+ y++kf+++++  
  gene3076|gene3076|rna3076|rna3076 228 SFTITKQNINEHLHENGYLLLTVPDRNVILRRYHRSRTE--KDAEKsisgdqhttsdvcFGNEYYTIKFKDSPSDR 301
                                        **9999**********************95544332222..1111111111122334448**********666666 PP

                           Pox_MCEL 227 plfGakYeynledvvkdvpEyivkfealvklaeeYgleLvdkkdfaeiieesikkelkklikrvskl 293
                                          fG+kY++nl ++v++++E++v  + l + +++ gl  v++ +f ++++ +  +e+ +l +++  +
  gene3076|gene3076|rna3076|rna3076 302 -IFGNKYYFNLREAVNECVEFLVDVNFLEQEMKKIGLLVVENANFITFYNVH-SNEFAELRRKMLPM 366
                                        .************************************************999.67799999998766 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.5   0.0   1.6e-14   2.9e-11      19     125 ..     137     289 ..     109     342 .. 0.65

  Alignments for each domain:
  == domain 1  score: 43.5 bits;  conditional E-value: 1.6e-14
                    Methyltransf_23  19 klraggrvLdiGcGtGillevlrengfsvt.gvDlspeaveiae..........kakkaqkdqfdeqeaaepqgkf 83 
                                        + +++grvLd+GcG+G  l  +++ g s++ g D+ ++ +++ +          ka++++ d +  + + +  ++f
  gene3076|gene3076|rna3076|rna3076 137 YVKRNGRVLDLGCGKGGDLLKYKKMGISYYyGLDIADKSISECKyrysrhkcpfKADFNVCDTY--HTILNLGKRF 210
                                        35899***********99999******7555****99988888777776666444444444444..66677999** PP

                    Methyltransf_23  84 dlIvlrev....lehvpdppellrqiatllkpgGylllseplasl............................... 124
                                        d+I+  ++    +e+ ++++ + ++i+++l ++Gylll++p+++                                
  gene3076|gene3076|rna3076|rna3076 211 DVISIQFSfhysFESEESFTITKQNINEHLHENGYLLLTVPDRNVilrryhrsrtekdaeksisgdqhttsdvcfg 286
                                        ***86554000045555799999*******************9998888666655555555555555555555555 PP

                    Methyltransf_23 125 ..k 125
                                          +
  gene3076|gene3076|rna3076|rna3076 287 neY 289
                                        552 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.2   0.0   2.3e-13   4.1e-10       1      96 [.     144     243 ..     144     244 .. 0.82

  Alignments for each domain:
  == domain 1  score: 40.2 bits;  conditional E-value: 2.3e-13
                                        EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT..TEEEEESBC.CGBSSSTTTEEEEEEEST CS
                    Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl..nvefvqgda.edlpfedgsfDlvvssga 73 
                                        vLdlGcG+G ++l+  k  g + ++g+Di+++ + +++ r++++++  +++f ++d  +++    ++fD++ ++++
  gene3076|gene3076|rna3076|rna3076 144 VLDLGCGKGGDLLKYKKM-GISYYYGLDIADKSISECKYRYSRHKCpfKADFNVCDTyHTILNLGKRFDVISIQFS 218
                                        9***************99.69*********************999999****99999444556777********** PP

                                        GGG.SSHHHH.HHHHHHHHHHEEEE CS
                    Methyltransf_25  74 lhh.lsdedl.ekalkeiarvLkpg 96 
                                        +h+ ++ e+    + ++i ++L ++
  gene3076|gene3076|rna3076|rna3076 219 FHYsFESEESfTITKQNINEHLHEN 243
                                        **97765553033445666666655 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.9   0.0   1.6e-12   2.9e-09       3     114 ..     140     265 ..     138     307 .. 0.78

  Alignments for each domain:
  == domain 1  score: 36.9 bits;  conditional E-value: 1.6e-12
                    Methyltransf_31   3 kglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgld.nveFeqgdiee.leklledekfD 76 
                                        ++ rvlDlGCG+G ++++   ++g  + ++G+Di  ++i+ ++ + ++++    + F ++d  + + + l  ++fD
  gene3076|gene3076|rna3076|rna3076 140 RNGRVLDLGCGKGGDLLKYK-KMGI-SYYYGLDIADKSISECKYRYSRHKCPfKADFNVCDTYHtILN-LG-KRFD 211
                                        6889**************99.7664.67*********************99999*******9998776.45.89** PP

                    Methyltransf_31  77 lilsnevlnaladpdkile....eiervlkpggilliedpr............l 114
                                        +i  +  +++  ++++ +     +i + l+++g+ll++ p+            +
  gene3076|gene3076|rna3076|rna3076 212 VISIQFSFHYSFESEESFTitkqNINEHLHENGYLLLTVPDrnvilrryhrsrT 265
                                        *9998788777777777666667***************9994443322222222 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.3   0.0   3.2e-11   5.8e-08       1      95 [.     145     247 ..     145     248 .. 0.86
   2 ?   -3.2   0.0       7.5   1.3e+04      57      74 ..     294     311 ..     280     337 .. 0.49

  Alignments for each domain:
  == domain 1  score: 33.3 bits;  conditional E-value: 3.2e-11
                                        EEET-TTSHHHHHHHHTT.SEEEEEES-HHHHHHHHHHCCHHT-..EEEETTEECCC..TSS-TT-EEEEEEES-C CS
                    Methyltransf_11   1 LdvGcGtGrlaealakrg.arvvgvDlskemlklakekaseegl..kvefvvadaek..lpfednsfDlvvssevl 71 
                                        Ld+GcG+G  + +++k g + ++g+D++++ +  +k ++s+ +   k +f v+d  +  l++ +  fD++ +++++
  gene3076|gene3076|rna3076|rna3076 145 LDLGCGKGGDLLKYKKMGiSYYYGLDIADKSISECKYRYSRHKCpfKADFNVCDTYHtiLNLGK-RFDVISIQFSF 219
                                        8**************************************9999899999999999984446655.*********** PP

                                        CC-....CCHHHHHHHHHHHEEEEEEEE CS
                    Methyltransf_11  72 hhv....edpekalkeiaRvLkpgGllv 95 
                                        h+     e    + ++i   L  +G+l+
  gene3076|gene3076|rna3076|rna3076 220 HYSfeseESFTITKQNINEHLHENGYLL 247
                                        **98665566666678888888888876 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 7.5
                                        S-TT-EEEEEEES-CCC- CS
                    Methyltransf_11  57 fednsfDlvvssevlhhv 74 
                                        f+d+  D ++ +   +++
  gene3076|gene3076|rna3076|rna3076 294 FKDSPSDRIFGNKYYFNL 311
                                        444444433333322222 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.8   0.0   8.9e-10   1.6e-06       1      99 []     145     246 ..     145     246 .. 0.81

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 8.9e-10
                    Methyltransf_12   1 LeiGcGtGsllralleklpdieyt.gvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnv 75 
                                        L++GcG G  l    +   +i+y+ g+Di  ++i   k + ++++  + + +++ ++    l  g+ fD++ + + 
  gene3076|gene3076|rna3076|rna3076 145 LDLGCGKGGDLLKYKKM--GISYYyGLDIADKSISECKYRYSRHKCPFKADFNVCDTYHTILNLGKRFDVISIQFS 218
                                        8*************999..888777*********99999988877655555555555445555668********** PP

                    Methyltransf_12  76 lhhl....kdirevldnirklLkpgGrl 99 
                                        +h+     +    + +ni ++L  +G+l
  gene3076|gene3076|rna3076|rna3076 219 FHYSfeseESFTITKQNINEHLHENGYL 246
                                        ****887655566667**********86 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   1.1e-06    0.0021       8      53 ..     135     180 ..     130     185 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.1e-06
                               MetW   8 aelikpgsrvldlGcGdG.ellellkeekqvd.grGleldeegvaecv 53 
                                         +++k + rvldlGcG+G +ll++  +  +++  +Gl++ ++++ ec 
  gene3076|gene3076|rna3076|rna3076 135 NRYVKRNGRVLDLGCGKGgDLLKYK-K-MGISyYYGLDIADKSISECK 180
                                        68999***********972566665.3.4665268***********96 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   5.3e-06    0.0095      29     137 ..     139     248 ..     128     259 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 5.3e-06
                                        CCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC..EEEEE-STTTTST..TS-EEE CS
                                MTS  29 kelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle..vevvasdvleeve..ekkfdl 100
                                        k ++g+vlDlGcG G   ++ +k+  +     +d+  +++  +k  ++++k+   +++  +d ++++    k+fd+
  gene3076|gene3076|rna3076|rna3076 139 K-RNGRVLDLGCGKGGDLLKYKKMGIS-YYYGLDIADKSISECKYRYSRHKCPfkADFNVCDTYHTILnlGKRFDV 212
                                        3.6899*********665666555544.4899******************9998899********98744599*** PP

                                        EEE---STTTCHCHHHHHHHHHHHHHHHEEEEEEEEE CS
                                MTS 101 ivsNPPfhagkatelavaeeliaeAkeaLkegGeLli 137
                                        i     fh + + e++ +    ++ +e+L+e+G Ll+
  gene3076|gene3076|rna3076|rna3076 213 ISIQFSFHYSFESEESFT-ITKQNINEHLHENGYLLL 248
                                        *99999999887544433.223445688999998875 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   1.1      0.57     1e+03      61     111 ..       4      55 ..       2     106 .. 0.60
   2 ?   13.7   0.0   2.5e-05     0.045       6      80 ..     122     192 ..     119     245 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.57
                    Methyltransf_32  61 eelvekaekraeklgkkfnkrlsfaelsieeats..sktltkkveaeeekeeq 111
                                        ++ +e+++k++++++ ++ +  + ++ ++ ++++  s ++ +k+ + +eke +
  gene3076|gene3076|rna3076|rna3076   4 DQKTENSRKVEDEIETEL-EGKRNITSNRGNKNNneSLRTGCKSYKDKEKEIR 55 
                                        566777777777777666.3333333333333330023333333333333333 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 2.5e-05
                    Methyltransf_32   6 verlaelvakllkelakesgaltvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekraeklgkkfnk 80 
                                        ++++ ++++++l + +  +++ +v+D+G+Gkg  +  l++k++    + +g+d+ ++ +++++ r ++ +  f++
  gene3076|gene3076|rna3076|rna3076 122 IRNMNNFIKSVLFN-RYVKRNGRVLDLGCGKG--GDLLKYKKMG-ISYYYGLDIADKSISECKYRYSRHKCPFKA 192
                                        78899999998887.5677789**********..9*****5555.78899************9999888765644 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   6.2e-05      0.11     155     208 ..     134     187 ..     131     214 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 6.2e-05
                               PrmA 155 leklvkegeevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNk 208
                                        ++++vk++ +vlD+G+G G   +  +k+g +  +++Di + +++  k   ++ k
  gene3076|gene3076|rna3076|rna3076 134 FNRYVKRNGRVLDLGCGKGGDLLKYKKMGISYYYGLDIADKSISECKYRYSRHK 187
                                        57899**************999*****************999988776666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (390 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1054  (0.0587874); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 2767.39
//
Query:       gene3077|gene3077|rna3077|rna3077  [L=94]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.9e-32  109.5   0.7    7.5e-32  109.3   0.7    1.0  1  Ribosom_S12_S23  Ribosomal protein S12/S23
  ------ inclusion threshold ------
       0.13   12.3   0.0       0.15   12.2   0.0    1.1  1  CTXphi_pIII-N1   N-terminal N1 domain of Vibrio phage CTXphi 


Domain annotation for each model (and alignments):
>> Ribosom_S12_S23  Ribosomal protein S12/S23
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.3   0.7   8.4e-36   7.5e-32      23     113 ..       2      92 ..       1      93 [. 0.97

  Alignments for each domain:
  == domain 1  score: 109.3 bits;  conditional E-value: 8.4e-36
                                        EEEEEEE---TT--S-EEEEEEEET.TSEEEEEEE-SSS..----TT-EEEEEE--.....BTTSTTEEEEBETS- CS
                    Ribosom_S12_S23  23 vlekvtveakkPnsAlRkvvrvrLikngkevtafipgegalnfldEhdevlvrGirrkgkavkDlpGvrykvvkva 98 
                                        +l  ++veak+PnsA+Rk+vr++L   gk++ af+p +g ln+++ +dev+v G ++kg++v+D+pG+rykv kv+
  gene3077|gene3077|rna3077|rna3077   2 ILTFSGVEAKQPNSAVRKAVRIQLCGTGKKIIAFVPYDGGLNYIEHNDEVTVMGCGKKGRSVGDIPGIRYKVCKVQ 77 
                                        567789********************************************************************** PP

                                        --TSSSTTTTT---- CS
                    Ribosom_S12_S23  99 gvslkalskykkekp 113
                                        gv  k+l+ +kk+kp
  gene3077|gene3077|rna3077|rna3077  78 GVAIKSLVTKKKQKP 92 
                                        *********999997 PP

>> CTXphi_pIII-N1  N-terminal N1 domain of Vibrio phage CTXphi pIII
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   1.7e-05      0.15      32      88 ..      22      80 ..       2      87 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.7e-05
                     CTXphi_pIII-N1 32 hqllfgfgspivqsvlfdgcmldiekddygfvwsclsn..engdyckglykprfsqgvs 88
                                       +  l g g  i+  v +dg +  ie++d   v  c  +    gd     yk    qgv+
  gene3077|gene3077|rna3077|rna3077 22 RIQLCGTGKKIIAFVPYDGGLNYIEHNDEVTVMGCGKKgrSVGDIPGIRYKVCKVQGVA 80
                                       334789*****************************765115688888889988888886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       327  (0.0182386); expected 358.6 (0.02)
Passed bias filter:                      266  (0.0148363); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 689.11
//
Query:       gene3078|gene3078|rna3078|rna3078  [L=305]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.023   13.4   0.0      0.037   12.8   0.0    1.2  1  DUF1688   Protein of unknown function (DUF1688)
      0.041   13.5   0.0      0.061   12.9   0.0    1.2  1  TPD52     Tumour protein D52 family


Domain annotation for each model (and alignments):
>> DUF1688  Protein of unknown function (DUF1688)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   4.1e-06     0.037       5      54 ..      60     109 ..      58     117 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4.1e-06
                            DUF1688   5 lkavRerckkvlelakegklehfdvdeskleevadfvvkvikrdygpdlk 54 
                                        lkav+e+c+++++++++ ++ehf+v++s + ++  ++++v+ r+++++ k
  gene3078|gene3078|rna3078|rna3078  60 LKAVKEKCENIYKVVSTCEVEHFRVNTSLILSLYGIITDVMARSWEDEAK 109
                                        89*******************************************76655 PP

>> TPD52  Tumour protein D52 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   6.8e-06     0.061      14      96 ..      38     122 ..      31     158 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6.8e-06
                              TPD52  14 aesvsaseptlteeereeLkseLakleeeivtLrqvLaakekhlaelkrklGltalneLrqnlskswhdvq...ts 86 
                                        +++ ++++ ++ e  +ee+k +L  ++e+  ++ +v+++ e ++  +   l l++   +   +++sw+d      +
  gene3078|gene3078|rna3078|rna3078  38 VSTDQYTSHSIRERVNEEIKPKLKAVKEKCENIYKVVSTCEVEHFRVNTSLILSLYGIITDVMARSWEDEAklvIH 113
                                        4555666669999******************************************************995433345 PP

                              TPD52  87 naYkktsetl 96 
                                        ++Y   +e+l
  gene3078|gene3078|rna3078|rna3078 114 FVYYV-QEIL 122
                                        55543.5555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (305 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       932  (0.0519828); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2188.73
//
Query:       gene3079|gene3079|rna3079|rna3079  [L=481]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.04   14.2   1.1         12    6.3   0.0    3.0  3  TPR_20    Tetratricopeptide repeat
       0.13   11.4   1.1       0.26   10.4   0.6    1.7  1  Fumble    Fumble
        2.1    8.1   7.2        1.4    8.7   0.1    3.6  3  TPR_11    TPR repeat


Domain annotation for each model (and alignments):
>> TPR_20  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0    0.0041        25      23      63 ..      43      83 ..      25      91 .. 0.82
   2 ?    6.3   0.0     0.002        12      24      44 ..     250     270 ..     235     286 .. 0.86
   3 ?   -3.1   0.0       1.7     1e+04      10      27 ..     406     423 ..     404     438 .. 0.63

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0041
                             TPR_20 23 darldlAlallaagryeeAleqLleilkrdrkweddaarkq 63
                                         + +lAl+++++++ e  le+L   +++++  ++d  +  
  gene3079|gene3079|rna3079|rna3079 43 SSQQKLALLYYENNEFENCLELLKFCVSQNLFSSNDLQKLN 83
                                       67899******************999999988888776655 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.002
                             TPR_20  24 arldlAlallaagryeeAleq 44 
                                          ++ A++l+ +++yeeAle 
  gene3079|gene3079|rna3079|rna3079 250 FLYQRARQLHLKEQYEEALEC 270
                                        6799***************96 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 1.7
                             TPR_20  10 eleaalaanpddldarld 27 
                                        +le+a+++ ++d d  l+
  gene3079|gene3079|rna3079|rna3079 406 DLEDAIENVKNDPDRSLA 423
                                        567777777777666555 PP

>> Fumble  Fumble
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.6   4.3e-05      0.26      39     151 ..      41     200 ..      28     203 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 4.3e-05
                             Fumble  39 seelggrLhfikfetekieevleflkelllkskekekkkk.......tikaTGGGaykyaelikeel.gve.veke 105
                                        +++++++L ++++e++++e++le+lk  ++++  ++++ +        + +  G   ky +++++ + ++e  + +
  gene3079|gene3079|rna3079|rna3079  41 TTSSQQKLALLYYENNEFENCLELLKFCVSQNLFSSNDLQklnltllAFYIEQGRGGKYLDECTKLFlQLEnTKYK 116
                                        4567789******************999988888877777677776655777888889999998877566515567 PP

                             Fumble 106 demeclikGlkfll.teipkevftys....................................ee.kpkkavek.ke 142
                                        de++  ikG  fl  ++ ++ +f  s                                    ee + k++ ++ ++
  gene3079|gene3079|rna3079|rna3079 117 DELN-FIKGYFFLYkEKYDTALFLLSndvlgrnlihlsmkcpekvessdpllqgykaylendEEtAVKYFKQEyQK 191
                                        7776.89******945567778888888888888888888888888888888888888876522344454444366 PP

                             Fumble 143 seeiyPylL 151
                                        ++++ PylL
  gene3079|gene3079|rna3079|rna3079 192 NKKVLPYLL 200
                                        777888887 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1      0.28   1.6e+03       3      12 ..      51      60 ..      47      66 .. 0.65
   2 ?    8.7   0.1   0.00024       1.4       4      19 ..     258     273 ..     255     275 .. 0.85
   3 ?    1.0   0.6      0.06   3.6e+02      26      36 ..     329     339 ..     329     342 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.28
                             TPR_11  3 ayyeqGkyee 12
                                       +yye +++e+
  gene3079|gene3079|rna3079|rna3079 51 LYYENNEFEN 60
                                       5777777765 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00024
                             TPR_11   4 yyeqGkyeeAieaYkk 19 
                                        ++ + +yeeA+e+Y +
  gene3079|gene3079|rna3079|rna3079 258 LHLKEQYEEALECYIQ 273
                                        77899*********76 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.06
                             TPR_11  26 dnaeayynLGl 36 
                                        d+a+ y+n+G+
  gene3079|gene3079|rna3079|rna3079 329 DDATYYCNRGY 339
                                        79********5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (481 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1055  (0.0588432); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.44
# Mc/sec: 3315.48
//
Query:       gene308|gene308|rna308|rna308  [L=1176]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2314  (0.129065); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 1.52u 0.40s 00:00:01.92 Elapsed: 00:00:00.57
# Mc/sec: 6169.16
//
Query:       gene3080|gene3080|rna3080|rna3080  [L=337]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (337 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       844  (0.0470746); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.65u 0.37s 00:00:01.02 Elapsed: 00:00:00.58
# Mc/sec: 1755.75
//
Query:       gene3081|gene3081|rna3081|rna3081  [L=725]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.9e-18   64.4   0.0    6.4e-17   61.8   0.0    2.2  2  RhoGAP    RhoGAP domain


Domain annotation for each model (and alignments):
>> RhoGAP  RhoGAP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0     0.073   1.3e+03      93     114 ..     474     495 ..     448     498 .. 0.78
   2 !   61.8   0.0   3.5e-21   6.4e-17       6     147 ..     521     660 ..     517     664 .. 0.94

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.073
                                        HHHHHHHHTTS-HHHHHHHHHH CS
                             RhoGAP  93 lealkellekLPkenrdtLryL 114
                                        +  ++++++ LP  +r++L+ L
  gene3081|gene3081|rna3081|rna3081 474 VYCVRKIVKILPAKKRRVLNNL 495
                                        667899************9877 PP

  == domain 2  score: 61.8 bits;  conditional E-value: 3.5e-21
                                        HHHHHHHHHTTTSTTTTTS-S-HHHHHHHHHHHHHTGGGCTTTTTSCHHHHHHHHHHHHHHSSSTTTTGGHHHHHH CS
                             RhoGAP   6 kcvefiekrgldtegiyRvsgskarvkelreafdkgkavdsdleeedvhavaslLKrfLrelpepLltkelyeeli 81 
                                        +++++ +++g++++g++R++g+ +  +++ + +++g++    l+++++ +vas +K ++re  + ++  +++e+++
  gene3081|gene3081|rna3081|rna3081 521 EVLAYFREHGVRVQGLFRLPGKLSIYNKMLQDLREGRRI--VLKDYNIRDVASFFKAYIREDLNGIIVPSIIETIY 594
                                        6788999*******************************9..5********************************** PP

                                        HHHTSSSHHHHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHHHTHHHH---HHHHHHHHHHHHHT-T CS
                             RhoGAP  82 eaaksedeeerlealkellekLPkenrdtLryLlehLkrvaenskenkMtaknLaivfaPtLlrpk 147
                                        e+  s++ + + e  + l   +    r++L  +l + k +a+n++ ++M++ nLai+ aP++++++
  gene3081|gene3081|rna3081|rna3081 595 ECFTSDSYKIKDEVSQYLPFVFLGDRRELLMQILGLYKLLAANKDTTNMNITNLAICSAPSFFPKQ 660
                                        *99998888888888888889999**************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (725 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1472  (0.0821016); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.85u 0.36s 00:00:01.21 Elapsed: 00:00:00.58
# Mc/sec: 3791.32
//
Query:       gene3082|gene3082|rna3082|rna3082  [L=266]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.2e-13   51.3   0.1     0.0028   18.5   0.1    5.4  5  WD40         WD domain, G-beta repeat
  ------ inclusion threshold ------
        0.1   12.7   0.1        4.9    7.2   0.0    2.8  3  BBS2_Mid     Ciliary BBSome complex subunit 2, middle region
       0.13   12.6   0.0         32    4.9   0.0    3.0  3  ANAPC4_WD40  Anaphase-promoting complex subunit 4 WD40 domain


Domain annotation for each model (and alignments):
>> WD40  WD domain, G-beta repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.0   0.00014      0.85       7      37 ..       3      32 ..       1      33 [. 0.90
   2 ?    3.8   0.0      0.02   1.2e+02       3      25 ..      41      64 ..      39      77 .. 0.63
   3 ?    4.3   0.0     0.014        84       4      35 ..      89     119 ..      86     122 .. 0.67
   4 !    7.4   0.0    0.0015         9      13      37 ..     140     162 ..     127     162 .. 0.83
   5 !   18.5   0.1   4.6e-07    0.0028       4      37 ..     168     206 ..     165     207 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00014
                                       EESSSSEEEEEEETTSSEEEEEETTSEEEEE CS
                               WD40  7 ltGHssvtslafspdgawlasGsdDgtvriW 37
                                        ++H +++s++ ++  ++ +++s+D+++r++
  gene3082|gene3082|rna3082|rna3082  3 VSTH-PINSISINSAEDLAVTSSMDKKLRVF 32
                                       5789.9************999*9******96 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.02
                                       EEEEEESS.SS.EEEEEEETTSSEE CS
                               WD40  3 clrtltGH.ss.vtslafspdgawl 25
                                       ++++l GH s  v ++ f   ++++
  gene3082|gene3082|rna3082|rna3082 41 LQYELAGHeSEvVKAI-FVGGSDMI 64
                                       678999**77755777.44444444 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.014
                                        EEEEESSSSEEEEEEETTSSE.....EEEEETTSEEE CS
                               WD40   4 lrtltGHssvtslafspdgaw.....lasGsdDgtvr 35 
                                        +++++G   +tsl      ++     +++G+ Dg++r
  gene3082|gene3082|rna3082|rna3082  89 IKVFEGA--ITSL----TARLgrdvtVFCGCADGKIR 119
                                        5677777..7777....333355555678999****9 PP

  == domain 4  score: 7.4 bits;  conditional E-value: 0.0015
                                        EEEEEEETTSSEEEEEETTSEEEEE CS
                               WD40  13 vtslafspdgawlasGsdDgtvriW 37 
                                        vt+l  s +   l+sG++D +v ++
  gene3082|gene3082|rna3082|rna3082 140 VTCL--SCNDEHLVSGGMDFKVNLY 162
                                        9***..88999999*****999875 PP

  == domain 5  score: 18.5 bits;  conditional E-value: 4.6e-07
                                        EEEEESS.SSEEEEEEETTSSE....EEEEETTSEEEEE CS
                               WD40   4 lrtltGH.ssvtslafspdgaw....lasGsdDgtvriW 37 
                                        + t+  H + v+++a++p++++    +as+sdD++v i+
  gene3082|gene3082|rna3082|rna3082 168 VETFADHeNRVNDVAVCPSNKFgvfcFASCSDDKSVIIY 206
                                        668889*999*************99999********997 PP

>> BBS2_Mid  Ciliary BBSome complex subunit 2, middle region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0     0.034     2e+02      16     105 ..      21     118 ..      10     121 .. 0.54
   2 ?    0.1   0.0      0.14   8.3e+02      14      32 ..     108     126 ..      95     135 .. 0.75
   3 ?    7.2   0.0   0.00081       4.9      11      44 ..     146     179 ..     140     211 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.034
                           BBS2_Mid  16 vvgsddfeirvfkee....elvaeit.etekvvslarlekerfayale.NGtvgvyekkerlWrvksknevvalaa 85 
                                        v +s d ++rvf  +    +l  e+   +++vv  + + +++++++ +  G + ++  +++++  k++ +v+  a 
  gene3082|gene3082|rna3082|rna3082  21 VTSSMDKKLRVFTLKdsnlRLQYELAgHESEVVKAIFVGGSDMIASADfAGNLFLWTLDNKKYALKQRIKVFEGAI 96 
                                        6678888899886541111233333323455666666666665554442577777777777777777766665555 PP

                           BBS2_Mid  86 ydingd..gtkelivgwsnGkl 105
                                          ++ +      + +g+ +Gk+
  gene3082|gene3082|rna3082|rna3082  97 TSLTARlgRDVTVFCGCADGKI 118
                                        4444331133445567777766 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.14
                           BBS2_Mid  14 eLvvgsddfeirvfkeeel 32 
                                         ++ g  d +ir +k  + 
  gene3082|gene3082|rna3082|rna3082 108 TVFCGCADGKIRAYKLTDT 126
                                        4667889999999986655 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.00081
                           BBS2_Mid  11 geneLvvgsddfeirvfkeeelvaeitetekvvs 44 
                                        ++++Lv g  df++ ++ + +lv ++  +e+ v+
  gene3082|gene3082|rna3082|rna3082 146 NDEHLVSGGMDFKVNLYADSRLVETFADHENRVN 179
                                        4589*********************999887554 PP

>> ANAPC4_WD40  Anaphase-promoting complex subunit 4 WD40 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0       0.2   1.2e+03       6      71 ..      16      82 ..      11     102 .. 0.61
   2 ?    4.0   0.0      0.01        63      39      88 ..      94     144 ..      60     148 .. 0.67
   3 ?    4.9   0.0    0.0054        32      36      63 ..     219     246 ..     179     259 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.2
                        ANAPC4_WD40  6 tmDLiAlatedgellvfRlngqrv.wtleedkedsevrsLaWkpdgklLavaysdgevrlldaesgk 71
                                         DL    + d++l+vf l+  ++  + e ++++sev +  +     ++a a   g++ l    ++k
  gene3082|gene3082|rna3082|rna3082 16 AEDLAVTSSMDKKLRVFTLKDSNLrLQYELAGHESEVVKAIFVGGSDMIASADFAGNLFLWTLDNKK 82
                                       5677777777777777777443331333445666666666666666666666666666555555555 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.01
                        ANAPC4_WD40  39 sevrsLaWkp.dgklLavaysdgevrlldaesgkvvhslsvksekavtclg 88 
                                        + ++sL  +   +     +++dg++r ++  +++   +  +++e  vtcl+
  gene3082|gene3082|rna3082|rna3082  94 GAITSLTARLgRDVTVFCGCADGKIRAYKLTDTEYGATEIASNEYGVTCLS 144
                                        5556665553133445679*********99999988777777777888886 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.0054
                        ANAPC4_WD40  36 kedsevrsLaWkpdgklLavaysdgevr 63 
                                        + ++e  +L++++ g +L v+y +++ +
  gene3082|gene3082|rna3082|rna3082 219 EIGEECYELCFSKTGFVLTVGYGKNSFK 246
                                        55778889***************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (266 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       626  (0.0349155); expected 358.6 (0.02)
Passed bias filter:                      501  (0.0279436); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.63u 0.36s 00:00:00.99 Elapsed: 00:00:00.54
# Mc/sec: 1470.65
//
Query:       gene3083|gene3083|rna3083|rna3083  [L=61]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.093   12.6   0.0       0.11   12.3   0.0    1.2  1  Csm1_B    Csm1 subunit domain B


Domain annotation for each model (and alignments):
>> Csm1_B  Csm1 subunit domain B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   6.1e-06      0.11      12      46 ..       8      42 ..       3      55 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 6.1e-06
                                       HHHHHHHHHHHHHHHHHHHHTT--CCCEEEEETTE CS
                             Csm1_B 12 gRSfylellleeivdelleklelsranllYagGGh 46
                                       +  fy+ + +e+  +++le++e+ ra ++++g G+
  gene3083|gene3083|rna3083|rna3083  8 SHVFYVLMTIEKNNKTFLENVEIRRARVVMVGVGK 42
                                       667*****************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       638  (0.0355848); expected 358.6 (0.02)
Passed bias filter:                      502  (0.0279993); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 404.29
//
Query:       gene3084|gene3084|rna3084|rna3084  [L=258]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    0.00088   19.2   2.5    0.00088   19.2   2.5    5.1  6  zf-CCHC    Zinc knuckle
  ------ inclusion threshold ------
       0.54   10.0  32.7       0.21   11.4   0.7    5.3  5  zf-CCHC_4  Zinc knuckle


Domain annotation for each model (and alignments):
>> zf-CCHC  Zinc knuckle
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   2.5   9.8e-08   0.00088       1      18 []     115     132 ..     115     132 .. 0.94
   2 ?    0.5   0.5     0.086   7.7e+02       6      18 .]     141     153 ..     137     153 .. 0.85
   3 !    6.7   4.1   0.00092       8.3       2      18 .]     155     171 ..     154     171 .. 0.92
   4 ?   -3.5   0.6       1.5   1.4e+04       3       6 ..     182     185 ..     181     185 .. 0.79
   5 ?   -1.3   0.1      0.31   2.7e+03      11      17 ..     189     195 ..     189     196 .. 0.81
   6 !    3.6   2.2    0.0087        78       3      17 ..     215     229 ..     213     230 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 9.8e-08
                                        SCTSSSSSSSSTTTTSTS CS
                            zf-CCHC   1 rkCynCGepGHiardCpk 18 
                                        r+Cy CGe+GH+ + Cpk
  gene3084|gene3084|rna3084|rna3084 115 RVCYGCGETGHVESKCPK 132
                                        58***************7 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.086
                                        SSSSSSTTTTSTS CS
                            zf-CCHC   6 CGepGHiardCpk 18 
                                        CG + H   +Cp+
  gene3084|gene3084|rna3084|rna3084 141 CGYTDHPRFNCPQ 153
                                        8989999999997 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.00092
                                        CTSSSSSSSSTTTTSTS CS
                            zf-CCHC   2 kCynCGepGHiardCpk 18 
                                        +C +CG  GH+ r+C++
  gene3084|gene3084|rna3084|rna3084 155 VCTKCGLCGHRYRECKE 171
                                        8**************85 PP

  == domain 4  score: -3.5 bits;  conditional E-value: 1.5
                                        TSSS CS
                            zf-CCHC   3 CynC 6  
                                        C +C
  gene3084|gene3084|rna3084|rna3084 182 CTKC 185
                                        8888 PP

  == domain 5  score: -1.3 bits;  conditional E-value: 0.31
                                        STTTTST CS
                            zf-CCHC  11 HiardCp 17 
                                        H   dCp
  gene3084|gene3084|rna3084|rna3084 189 HTVPDCP 195
                                        7778**9 PP

  == domain 6  score: 3.6 bits;  conditional E-value: 0.0087
                                        TSSSSSSSSTTTTST CS
                            zf-CCHC   3 CynCGepGHiardCp 17 
                                        C nC +  H+  dC+
  gene3084|gene3084|rna3084|rna3084 215 CCNCLRNDHFVDDCD 229
                                        889999********7 PP

>> zf-CCHC_4  Zinc knuckle
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0     0.075   6.7e+02      26      35 ..      79      88 ..      77      89 .. 0.85
   2 ?   11.4   0.7   2.3e-05      0.21      32      49 .]     115     132 ..     114     132 .. 0.93
   3 ?    5.5   0.7    0.0016        14      31      48 ..     135     152 ..     133     153 .. 0.89
   4 ?    8.1   4.4   0.00024       2.2      32      48 ..     154     170 ..     153     171 .. 0.92
   5 ?    1.5   2.9     0.028   2.5e+02      31      48 ..     212     229 ..     210     230 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.075
                          zf-CCHC_4 26 kYErLrsfCy 35
                                       kYE+L+ f+ 
  gene3084|gene3084|rna3084|rna3084 79 KYEFLSLFYH 88
                                       8****99985 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 2.3e-05
                          zf-CCHC_4  32 sfCyiCgvlGHsdkrCdk 49 
                                        ++Cy Cg  GH++++C+k
  gene3084|gene3084|rna3084|rna3084 115 RVCYGCGETGHVESKCPK 132
                                        79**************95 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.0016
                          zf-CCHC_4  31 rsfCyiCgvlGHsdkrCd 48 
                                        +++C  Cg+  H + +C+
  gene3084|gene3084|rna3084|rna3084 135 QQICILCGYTDHPRFNCP 152
                                        789*********999997 PP

  == domain 4  score: 8.1 bits;  conditional E-value: 0.00024
                          zf-CCHC_4  32 sfCyiCgvlGHsdkrCd 48 
                                        ++C+ Cg+ GH  ++C+
  gene3084|gene3084|rna3084|rna3084 154 IVCTKCGLCGHRYRECK 170
                                        79**************6 PP

  == domain 5  score: 1.5 bits;  conditional E-value: 0.028
                          zf-CCHC_4  31 rsfCyiCgvlGHsdkrCd 48 
                                        r  C +C +  H +++Cd
  gene3084|gene3084|rna3084|rna3084 212 RMSCCNCLRNDHFVDDCD 229
                                        567**************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1148  (0.0640303); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1779.28
//
Query:       gene3085|gene3085|rna3085|rna3085  [L=335]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-14   54.1   0.6    3.8e-14   52.9   0.6    1.6  1  DUF382    Domain of unknown function (DUF382)
    5.6e-11   42.1   0.1    1.3e-10   41.0   0.1    1.6  1  PSP       PSP


Domain annotation for each model (and alignments):
>> DUF382  Domain of unknown function (DUF382)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.9   0.6   4.2e-18   3.8e-14       2     122 ..     139     253 ..     138     257 .. 0.83

  Alignments for each domain:
  == domain 1  score: 52.9 bits;  conditional E-value: 4.2e-18
                             DUF382   2 kPevvevaDvdakdPvllvklKssknvvpvpshWsskreylsgkrglekkpfelPkfikeTgieelrealeekeee 77 
                                        +P  v+++Dv+a++Pvll+k K+++n+vpvpshW++ ++       ++++++e P f+++    ++re++ e+ ++
  gene3085|gene3085|rna3085|rna3085 139 NPATVDIEDVSAPNPVLLNKYKNTRNAVPVPSHWKAGKMTF-----YTRERYE-PPFVNDEA-LKMRETFYEHADK 207
                                        799*******************************8866544.....4577787.66887765.58*********** PP

                             DUF382  78 kslkekarekvqpklg.kldidykkLhdaFfklqtkPkllkfGdly 122
                                        ++ k++ rek  pk+  ++ i +++++++  +     +ll+ G ly
  gene3085|gene3085|rna3085|rna3085 208 STEKQREREKKYPKMTnEFLIPQETMKNMLRSAYVSSRLLRAGILY 253
                                        **************96267888888888777776666777666655 PP

>> PSP  PSP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.0   0.1   1.4e-14   1.3e-10       5      45 ..     271     310 ..     270     311 .. 0.88

  Alignments for each domain:
  == domain 1  score: 41.0 bits;  conditional E-value: 1.4e-14
                                PSP   5 iSaeLReALglqegqlPpWiykMqrlGlPPgYpklkipGln 45 
                                        +S eL++A g+++  +PpW+ +Mqr+G+PP     +ipG+n
  gene3085|gene3085|rna3085|rna3085 271 MSTELKKACGMKKCTPPPWLHNMQRIGPPPDT-AYQIPGVN 310
                                        9*****************************84.44777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (335 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       960  (0.0535445); expected 358.6 (0.02)
Passed bias filter:                      550  (0.0306766); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 2497.12
//
Query:       gene3086|gene3086|rna3086|rna3086  [L=55]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (55 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       543  (0.0302861); expected 358.6 (0.02)
Passed bias filter:                      247  (0.0137766); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.27s 00:00:00.63 Elapsed: 00:00:00.42
# Mc/sec: 394.18
//
Query:       gene3087|gene3087|rna3087|rna3087  [L=50]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (50 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       301  (0.0167884); expected 358.6 (0.02)
Passed bias filter:                      256  (0.0142785); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 367.19
//
Query:       gene3088|gene3088|rna3088|rna3088  [L=656]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.5e-91  306.6   0.7    3.8e-91  305.3   0.1    2.0  2  tRNA-synt_1c    tRNA synthetases class I (E and Q), catalytic
    1.3e-16   60.9   1.2    4.6e-16   59.2   0.2    2.2  2  tRNA-synt_1c_C  tRNA synthetases class I (E and Q), anti-codo
     0.0032   16.9   0.0     0.0079   15.6   0.0    1.7  1  tRNA-synt_1e    tRNA synthetases class I (C) catalytic domain


Domain annotation for each model (and alignments):
>> tRNA-synt_1c  tRNA synthetases class I (E and Q), catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0      0.21   1.2e+03      51      90 ..      93     131 ..      87     142 .. 0.80
   2 !  305.3   0.1   6.3e-95   3.8e-91       2     295 ..     196     474 ..     195     492 .. 0.95

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.21
                                        HHHHHHHHHHHHTT---SSEEEEGGGGHHHHHHHHHHHHH CS
                       tRNA-synt_1c  51 eaeesiledlkwlgikwdekptyqsdrfdelkkyaeeLik 90 
                                        e e +  +++k ++++   k+++ +++fd+lk++++ L k
  gene3088|gene3088|rna3088|rna3088  93 EEEGALTNYVKSISFDE-CKLRKVAEKFDNLKDVMNYLSK 131
                                        55667788899999998.899999*******999988755 PP

  == domain 2  score: 305.3 bits;  conditional E-value: 6.3e-95
                                        -EEEE---SSSS-BHHHHHHHHHHHHHHHHTT-EEEEEE--SSCCC--HHHHHHHHHHHHHTT---SSEEEEGGGG CS
                       tRNA-synt_1c   2 VrtRfaPePtGyLHiGhakaallnylfAknnnGkfilRieDTdperekeeaeesiledlkwlgikwdekptyqsdr 77 
                                        + tRf+PeP+GyLHiGhaka+ l++ f      ++ilR++DT+p+ e +e+ esiled+ w+g+++ +k+t++sd+
  gene3088|gene3088|rna3088|rna3088 196 IITRFPPEPNGYLHIGHAKAMYLDFNFGN----RCILRYDDTNPKNEMAEYYESILEDVRWMGYTP-WKITRASDY 266
                                        78***********************8855....7********************************.********* PP

                                        HHHHHHHHHHHHHTTSEEEE-STHHHHHHHHCCSSHSS-TTTTS-HHHHHHHHHHHHHTTHSTTTS-EEEESSBTT CS
                       tRNA-synt_1c  78 fdelkkyaeeLikkGkAYvcectkeeleeereeqeklgskerdrydeenlklfeeemkkgkaegekavvRlkidee 153
                                        fdel ++a +L+++GkAYvc+ ++ee++++        s++r+r+ e nl+lf eem +gk +++ a++Rlk+d+ 
  gene3088|gene3088|rna3088|rna3088 267 FDELIDFARRLVRDGKAYVCHLSTEEIKAQV------LSPYRNRSPEVNLALF-EEMISGKWKEGTAILRLKMDMD 335
                                        ***************************9865......4599************.99******************** PP

                                        SS.GGGSSTEEEEEEESGGGSBTTTBTSTSEEE-HHHHHHHHHHHTT-SEEEEEGGGGCCHHHHHHHHHHTT-S.- CS
                       tRNA-synt_1c 154 ss.vefrDlvrgriklepqeihdlvivksdiyPtYdfavvidDaleeithvlrteefldntpkyiwllealglevp 228
                                        s+ + ++Dl+++ri  +    h    +k+ +yP+Yd++++i D+le+ith+++  ef +++ +y+wll++l+++ +
  gene3088|gene3088|rna3088|rna3088 336 SKnMLMHDLIAYRIIDKD---HLKADKKYYVYPSYDYTHCINDSLEDITHSFCSREFFSRRVSYYWLLDNLRVY-K 407
                                        *99***********9999...99999************************************************.* PP

                                        EEEEEE--EEETTSB-SHHHHHHHHHTTSSSSTT-TTSCBHHHHHHCTB-HHHHHHHHHHHCCCSSS CS
                       tRNA-synt_1c 229 pfiheylrlnlekkklSKRklsllvdekqvkewddlreallnflrrlGwtpekerelftreeliksf 295
                                        p+++e++rln+++++lSKRkl+ l+++  v +wdd+r+++l++lrr+G++p++++ ++++ +++ + 
  gene3088|gene3088|rna3088|rna3088 408 PVQWEFSRLNISNTVLSKRKLNALIAKGIVMGWDDPRLFTLRGLRRRGVPPQAINAFVEKVGITFNE 474
                                        *************************************************************998665 PP

>> tRNA-synt_1c_C  tRNA synthetases class I (E and Q), anti-codon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.17     1e+03      49      95 ..     128     173 ..     119     187 .. 0.77
   2 !   59.2   0.2   7.8e-20   4.6e-16      42     174 .]     507     639 ..     494     639 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.17
                     tRNA-synt_1c_C  49 yiereD.akrlkpgeevrLkelynikveevekdesgevtelkleydge 95 
                                        y++++D +    p++ +   + +n+k +++e   +g   e kl+y ++
  gene3088|gene3088|rna3088|rna3088 128 YLSKDDeMAFYDPKRAISVLKSFNVKSKKIE--RKGILNEGKLRYLHK 173
                                        78888875556678899999999****9995..578888888888764 PP

  == domain 2  score: 59.2 bits;  conditional E-value: 7.8e-20
                     tRNA-synt_1c_C  42 vpfskeiyiereD........akrlkpgeevrLkelynikveevekdesgevtelkleydgesleearkkkgiihW 109
                                        ++ +++i+i+ +D        + rl+ ++ v L + y ++  ++    +++  +  ++         r  k  ihW
  gene3088|gene3088|rna3088|rna3088 507 IEDQESILIDGDDfrekntedFLRLTYDQPVGLVNKYAVELVSI----DDRLLK--VRKTA------RTFKSRIHW 570
                                        55567999999998888888899999999999999999999888....223333..22233......455779*** PP

                     tRNA-synt_1c_C 110 vsa.eeaveaevrlYdrLfkeee.de.dfl..lnpdslkvleeglaepalanlkkgdivQfeRiGyfrvd 174
                                        + + +++v++ vr+ ++Lf + + +e dfl  + pds ++  egl+ep ++++k+g++vQf R+G+++ d
  gene3088|gene3088|rna3088|rna3088 571 LTKdAQNVKIRVRELSHLFRSFNpEEkDFLedVDPDSMQI-VEGLCEPGITDVKVGEVVQFFRKGWYCRD 639
                                        **97788999********9966655538889*******97.6*************************977 PP

>> tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   1.3e-06    0.0079      54     140 ..      53     302 ..      16     325 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.3e-06
                                        BB--SHHHHHHHHHTTS-.......................................................... CS
                       tRNA-synt_1e  54 vtDidDkiikrareeeks.......................................................... 71 
                                        +tD++D  +k+ ++  ++                                                          
  gene3088|gene3088|rna3088|rna3088  53 ITDLEDVYVKEIVNLIEQkivindnmlnkcielgkgkkcgeeegaltnyvksisfdecklrkvaekfdnlkdvmny 128
                                        5555555555554444444455566666666666666666666666666666777777777777777777777777 PP

                                        ............................................................................ CS
                       tRNA-synt_1e  72 ............................................................................ 71 
                                                                                                                    
  gene3088|gene3088|rna3088|rna3088 129 lskddemafydpkraisvlksfnvkskkierkgilnegklrylhkagenpqiseeilqahlkrtdgeiitrfppep 204
                                        7777777777777777777777777777777777777777777777777777777777777777777777777777 PP

                                        ...............................HHHHHHHHHHHHHHHHHHTT----SB--BGGGGHHHHHHHHHHHH CS
                       tRNA-synt_1e  72 ...............................vkelaekfieefkkdleaLnvlkptleprvsekvdeiielvekli 116
                                                                        +e+ae++ e+  +d++ ++  +  + +r+s++ de+i++  +l+
  gene3088|gene3088|rna3088|rna3088 205 ngylhighakamyldfnfgnrcilryddtnpKNEMAEYY-ESILEDVRWMGYTP-WKITRASDYFDELIDFARRLV 278
                                        777777777777777777777777777766566666655.56778899888776.7889***************** PP

                                        HTTSEEE-TTS-EEE-GGG-TTTT CS
                       tRNA-synt_1e 117 ekgyaYavsdgdvyfdvskkeeYg 140
                                          g aY+ +  ++  + +  + Y 
  gene3088|gene3088|rna3088|rna3088 279 RDGKAYVCHLSTEEIKAQVLSPYR 302
                                        *******99888887777666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (656 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       889  (0.0495845); expected 358.6 (0.02)
Passed bias filter:                      553  (0.0308439); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.65u 0.27s 00:00:00.92 Elapsed: 00:00:00.44
# Mc/sec: 4486.26
//
Query:       gene3089|gene3089|rna3089|rna3089  [L=312]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-40  139.4  20.5    1.5e-40  139.1  20.5    1.1  1  Cation_efflux  Cation efflux family
  ------ inclusion threshold ------
      0.034   14.4   1.9      0.034   14.4   1.9    2.7  3  DUF996         Protein of unknown function (DUF996)
       0.15   12.2   0.0        0.3   11.2   0.0    1.5  1  ZT_dimer       Dimerisation domain of Zinc Transporter
       0.16   11.5   0.1       0.16   11.5   0.1    2.8  4  E1-E2_ATPase   E1-E2 ATPase


Domain annotation for each model (and alignments):
>> Cation_efflux  Cation efflux family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  139.1  20.5   3.3e-44   1.5e-40       3     199 .]      26     221 ..      24     221 .. 0.94

  Alignments for each domain:
  == domain 1  score: 139.1 bits;  conditional E-value: 3.3e-44
                      Cation_efflux   3 lsllanlilalvelivglltnSlalladafhslsdlvsllllllalklsrkppderfpfGygrlevlgalvsglll 78 
                                        +++ + ++++l el + + +nSl+llad++h l+d++++l++l+al +++k+++++++fGy+r+ev+gal+s+l++
  gene3089|gene3089|rna3089|rna3089  26 RVMTIITVFMLLELWGHWHSNSLSLLADSVHLLVDILGFLVSLIALSWTKKKTNNKMTFGYHRYEVIGALISILFI 101
                                        56777889******************************************************************** PP

                      Cation_efflux  79 lglavfllleaiqklikegereihaglalvvalvslvvnlalllilrragrkl...rsaalkaaalhvlgDaltsl 151
                                        +++ ++l+le+i++++   ++ i++   ++va v+++vnl++l+ lr++        + ++ka ++h++gD+++s 
  gene3089|gene3089|rna3089|rna3089 102 WVATAYLILESIKRFL--YPKKINEKSFVLVATVGFIVNLFCLHSLRHGHSDKhvsTNLNMKATYVHIIGDLIQSC 175
                                        ****************..67778888888899999*********9998766557999******************* PP

                      Cation_efflux 152 gvlvsalvillfnlksgplaDpvaslligliilysalkllkeslseLl 199
                                        gvl+++ ++++f+      +D ++++++++i+l+s+l ++ e+ls+L+
  gene3089|gene3089|rna3089|rna3089 176 GVLLASALTFFFPKI--VFFDIACTFIFAFIVLVSTLLVVSEALSILV 221
                                        ************665..5****************************96 PP

>> DUF996  Protein of unknown function (DUF996)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       1.2   5.4e+03      28      35 ..      27      34 ..      11      53 .. 0.60
   2 ?   14.4   1.9   7.6e-06     0.034       2      78 ..      60     137 ..      59     146 .. 0.82
   3 ?    1.7   5.6     0.067     3e+02       4      89 ..     133     216 ..     130     228 .. 0.70

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.2
                             DUF996 28 naliafil 35
                                        + i +++
  gene3089|gene3089|rna3089|rna3089 27 VMTIITVF 34
                                       22221111 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 7.6e-06
                             DUF996   2 sivGliLvlvalkeiskavndekifsnaliafilsiialvva.ilalllvlgalatalelpgleeaaslilllllv 76 
                                         i+G+ + l+al+   k++n++  f +  + +i ++i+++++ +++  l+l+++  +l  ++++e +++++ ++ +
  gene3089|gene3089|rna3089|rna3089  60 DILGFLVSLIALSWTKKKTNNKMTFGYHRYEVIGALISILFIwVATAYLILESIKRFLYPKKINEKSFVLVATVGF 135
                                        699**********************************777664888889999999999999999988744444333 PP

                             DUF996  77 li 78 
                                        ++
  gene3089|gene3089|rna3089|rna3089 136 IV 137
                                        33 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.067
                             DUF996   4 vGliLvlvalkeiskavndekifsna.liafilsiialvvailalllvlgalatalelpgleeaaslilllllvli 78 
                                        vG+i+ l  l+++     d+ + +n+ + a+ + ii+ ++      +vl a+a    +p++  +  + ++++++++
  gene3089|gene3089|rna3089|rna3089 133 VGFIVNLFCLHSLRHGHSDKHVSTNLnMKATYVHIIGDLIQ---SCGVLLASALTFFFPKIVFFDIACTFIFAFIV 205
                                        89999999999999999999999887244555666666665...44555555555566666655556777777777 PP

                             DUF996  79 iayvlliisav 89 
                                        ++  ll++s +
  gene3089|gene3089|rna3089|rna3089 206 LVSTLLVVSEA 216
                                        77777777754 PP

>> ZT_dimer  Dimerisation domain of Zinc Transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   6.8e-05       0.3      13      77 ..     237     300 ..     229     302 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 6.8e-05
                                        HTT-SS-EEEEEEEEE-S----EEEEEEEE-TTS-HHHHHHHHHHHHHHHHHH-TT--EEEEEEE CS
                           ZT_dimer  13 iksvpgvkgvhdlrtrksGskifvdlhievdgdlsvkeaHeiadevekrikeefpgvadvliHve 77 
                                        +++ ++v++v dl++  +G + ++ +++ + +++ + e   i +++++ + e++ + ++  + +e
  gene3089|gene3089|rna3089|rna3089 237 LLEFDKVLEVLDLKVWSVGVNKHACMTVLLCENILIFEYEMILTKIKDILNEKY-RFSYLAVQIE 300
                                        567899**********************************************99.4456666665 PP

>> E1-E2_ATPase  E1-E2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   3.6e-05      0.16     102     158 ..       8      68 ..       2      72 .. 0.84
   2 ?   -2.2   0.1      0.56   2.5e+03     119     136 ..      93     110 ..      83     140 .. 0.54
   3 ?   -1.9   0.0      0.46   2.1e+03     122     146 ..     127     157 ..     114     185 .. 0.53
   4 ?    2.0   3.4     0.029   1.3e+02     119     165 ..     184     230 ..     173     231 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 3.6e-05
                                        --------HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTTSSTT....HHHHHHHHHHHHH CS
                       E1-E2_ATPase 102 eeakskktplqkkldklgkvlvpvvlliallvflialllgksla....eallralallvaa 158
                                         ++ s+++++   ++k+++v++++ ++++l ++ ++ ++  sl     + l+ +l++lv+ 
  gene3089|gene3089|rna3089|rna3089   8 TNTDSENPSTDTDISKIFRVMTIITVFMLLELWGHWHSNSLSLLadsvHLLVDILGFLVSL 68 
                                        566799999***************************9999999887766666677777765 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.56
                                        HHHHHHHHHHHHHHHHHS CS
                       E1-E2_ATPase 119 gkvlvpvvlliallvfli 136
                                        g+ ++++ +++a + +++
  gene3089|gene3089|rna3089|rna3089  93 GALISILFIWVATAYLIL 110
                                        444444444444444433 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 0.46
                                        HHHHHHHHHHHHHHS-STTTSSTT......H CS
                       E1-E2_ATPase 122 lvpvvlliallvflialllgksla......e 146
                                        +v+v+++ +++ ++ + +l++++       +
  gene3089|gene3089|rna3089|rna3089 127 FVLVATVGFIVNLFCLHSLRHGHSdkhvstN 157
                                        4444444444444444444333333355440 PP

  == domain 4  score: 2.0 bits;  conditional E-value: 0.029
                                        HHHHHHHHHHHHHHHHHS-STTTSSTTHHHHHHHHHHHHHS-TTHHH CS
                       E1-E2_ATPase 119 gkvlvpvvlliallvflialllgkslaeallralallvaaiPcaLpl 165
                                        + ++ ++v++ ++ +f++a+++  s+   + +al++lv + P  +p+
  gene3089|gene3089|rna3089|rna3089 184 TFFFPKIVFFDIACTFIFAFIVLVSTLLVVSEALSILVESAPKKIPM 230
                                        44455666666777788888888888788888********9999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (312 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1000  (0.0557756); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 2090.00
//
Query:       gene309|gene309|rna309|rna309  [L=472]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
        2.7    8.2  12.0       0.17   12.1   3.3    2.5  2  RMP             Retinal Maintenance
        3.9    5.8  11.0      0.097   11.1   2.2    1.9  2  Cellulose_synt  Cellulose synthase


Domain annotation for each model (and alignments):
>> RMP  Retinal Maintenance
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   3.3   1.9e-05      0.17       2      87 ..      10      98 ..       9     102 .. 0.67
   2 ?    0.3   1.5     0.084   7.5e+02      39      61 ..     260     282 ..     234     326 .. 0.51

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.9e-05
                            RMP  2 ddlldelleedekdkkakkkkkeqkkekkk..kkssskksvekslkalskkcspvllggssasnglgtasskkra.CdqLrC 80
                                   ++l+++l e++ ++++ + k+ e++++++    ++++k+ v +  ++++     ++++++  +n+l+ ++ +  +  ++++C
  gene309|gene309|rna309|rna309 10 EELIQKLEEKNRRKEQDECKTPEANEANTRehDETKNKTGVDEPDQQARVDNDVLYINQELLNNRLNRENKQPDTlKNAIKC 91
                                   57778777777766666555555554444400444555555555566666666679999999****99999875515789** PP

                            RMP 81 tsCdfrv 87
                                   ++C f+v
  gene309|gene309|rna309|rna309 92 IQCQFEV 98
                                   *****99 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.084
                            RMP  39 svekslkalskkcspvllggssa 61 
                                    + +k+lk++ ++  +v ++++ +
  gene309|gene309|rna309|rna309 260 ALKKVLKRKAEEMNAVSMDQEDK 282
                                    22222222222222222222221 PP

>> Cellulose_synt  Cellulose synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   2.2   1.1e-05     0.097     313     407 ..       5      98 ..       1     107 [. 0.74
   2 ?   -0.4   1.7     0.033     3e+02     315     396 ..     252     332 ..     231     341 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 1.1e-05
                 Cellulose_synt 313 rkkkkkkkkekkkkaskkkeseaeileledidealegdeeekssllsqlklekkfGqssvlvasilleeggvprealdaa 392
                                    rkk  ++  +k ++++++ke+++  +  +++ ++ e+de+++++ +++ + + +  +  ++++  ll++  + re+++  
  gene309|gene309|rna309|rna309   5 RKKIMEELIQKLEEKNRRKEQDECKTPEANEANTREHDETKNKTGVDEPDQQARVDNDVLYINQELLNNR-LNRENKQPD 83 
                                    3333334444444555555555555555556666777888888899*****************9998876.899999999 PP

                 Cellulose_synt 393 lvkeaisviscgyed 407
                                    ++k+ai+ i c +e 
  gene309|gene309|rna309|rna309  84 TLKNAIKCIQCQFEV 98 
                                    9***********995 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.033
                 Cellulose_synt 315 kkkkkkkekkkkaskkkeseaeileledidealegdeeekssllsqlklekkfGqssv.lvasilleeggvprealdaal 393
                                    k+++++ +  kk+ k+k +e+++++++++d++++++ e+ +  l++++   + G+ ++ + + i + ++ +   ++d ++
  gene309|gene309|rna309|rna309 252 KQESSSDDALKKVLKRKAEEMNAVSMDQEDKSVQQTSEQ-ELPLEEEQTSSTKGKNKMnFYTPISISDTYLVA-QSDGTV 329
                                    233333344667778888888888888888776665444.444455555555555444266667776665543.344555 PP

                 Cellulose_synt 394 vke 396
                                    + e
  gene309|gene309|rna309|rna309 330 ISE 332
                                    555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (472 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1852  (0.103296); expected 358.6 (0.02)
Passed bias filter:                      543  (0.0302861); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.63u 0.32s 00:00:00.95 Elapsed: 00:00:00.50
# Mc/sec: 2818.92
//
Query:       gene3090|gene3090|rna3090|rna3090  [L=309]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.3e-55  186.4   0.4    8.4e-55  186.0   0.4    1.2  1  Pkinase         Protein kinase domain
    1.8e-39  135.6   0.1    2.2e-39  135.3   0.1    1.1  1  Pkinase_Tyr     Protein tyrosine kinase
    2.4e-09   36.5   0.0    3.6e-09   35.9   0.0    1.2  1  Pkinase_fungal  Fungal protein kinase
    3.2e-06   26.9   0.7      0.064   12.9   0.3    2.9  2  FTA2            Kinetochore Sim4 complex subunit FTA2
    1.4e-05   24.6   0.0    3.2e-05   23.4   0.0    1.7  1  Kinase-like     Kinase-like
     0.0021   17.6   0.6     0.0058   16.2   0.0    2.0  2  YrbL-PhoP_reg   PhoP regulatory network protein YrbL
  ------ inclusion threshold ------
      0.049   13.6   0.0      0.088   12.7   0.0    1.4  1  APH             Phosphotransferase enzyme family


Domain annotation for each model (and alignments):
>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  186.0   0.4   3.3e-58   8.4e-55       1     212 [.      14     234 ..      14     271 .. 0.81

  Alignments for each domain:
  == domain 1  score: 186.0 bits;  conditional E-value: 3.3e-58
                                        EEEEEEEEEESSEEEEEEEETTTT.EEEEEEEEECHCHCHHHHHHHHHHHHHHHHHSCTTB--EEEEEEESSEEEE CS
                            Pkinase   1 yekleklGeGsfGkVykaveketg.kivAvKkikkekakkkkekkvlrEikilkklkhpnivrlyevfeekdelyl 75 
                                        y+ leklG+G+ G+Vy   ++e++ k v+ K ++ ++ k      +l+Ei+i+k+l+ ++ivr+y+++++++ +y+
  gene3090|gene3090|rna3090|rna3090  14 YRFLEKLGNGTHGTVYLLESRESKpKLVVFKSVSSKNLK-----YALNEIEIIKSLSYKRIVRFYGSMSSNNGMYI 84 
                                        67899************9988877255666766655444.....4899**************************** PP

                                        EEE--TTEBHHHHHH....HHSS--HHHHHHHHHHHHHHHHHHHHTTEE-SS-SGGGEEEE.TTTE......EEE- CS
                            Pkinase  76 vleyveggeladlle....rkgslseeeakkiakqilegleylHskgiiHrDlKpeNiLid.ekge......lKit 140
                                        ++e+++ g+l++l      ++ +++++ +  i++q++ +l+ylH+++iiHrD+Kp NiL++  kg       +K++
  gene3090|gene3090|rna3090|rna3090  85 MMEHANYGDLERLNCfireKNLNIDKSIIWTIFSQLIDALAYLHRNRIIHRDIKPGNILLNrVKGRscnflqVKLC 160
                                        *********766654554566669999**********************************65665899999**** PP

                                        SGTTSEESSSSCS..BCTTTSCGGGS-HHHHTTSCBSHHHHHHHHHHHHHHHHHSS-STTTSSHHHHHHHHHHT CS
                            Pkinase 141 DFGlakelesssk..ltsfvgtseYlAPEvlkeneyskkvDvWslGvilyelltgkppfsgekgkekvekeldq 212
                                        DF l+k+l+ +sk     +vgt++Y+APE+++++ y+ +vDvWs+Gv++yel+++  pf++e++ke +++++ q
  gene3090|gene3090|rna3090|rna3090 161 DFSLSKRLDDESKsnDGMIVGTPYYMAPEIIQKKAYDYSVDVWSMGVVMYELVSKMRPFESESKKELKRQIVFQ 234
                                        **********999656679*****************************************88777766666666 PP

>> Pkinase_Tyr  Protein tyrosine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  135.3   0.1   8.6e-43   2.2e-39       3     250 ..      16     261 ..      14     269 .. 0.88

  Alignments for each domain:
  == domain 1  score: 135.3 bits;  conditional E-value: 8.6e-43
                                        EEEEEEEESSEEEEEEEEETTTTSSEEEEEEEEESTTSSHHHHHHHHHHHHHHHTS-BTTB--EEEEEESSSSEEE CS
                        Pkinase_Tyr   3 lgkklGeGafGkVvegtlkgekekkevkVavKtlkeeateeekeelleeakimkklkhpnivkllgvctkeeplli 78 
                                        + +klG+G+ G+V+  + +   e+k   V+ K++    ++++ +  l+e++i+k+l+ ++iv+++g +++++ ++i
  gene3090|gene3090|rna3090|rna3090  16 FLEKLGNGTHGTVYLLESR---ESKPKLVVFKSV----SSKNLKYALNEIEIIKSLSYKRIVRFYGSMSSNNGMYI 84 
                                        679***********99988...777888999999....44556779****************************** PP

                                        EEE--TTEBHHH...HHHHTCTTTSBHHHHHHHHHHHHHHHHHHHHTTEEEST-SGGGEEEEE.......TTEEEE CS
                        Pkinase_Tyr  79 vteyvkgGdLlk...fLrkkekekltlkdllsfalqvAkGmeyLeskklvHrdlaarNvLlse.......nkvvki 144
                                        ++e +++GdL+    f+r+k + +++ + +  +  q+ ++++yL++++++Hrd+   N+Ll++         +vk+
  gene3090|gene3090|rna3090|rna3090  85 MMEHANYGDLERlncFIREK-NLNIDKSIIWTIFSQLIDALAYLHRNRIIHRDIKPGNILLNRvkgrscnFLQVKL 159
                                        ********875433399998.99999999*********************************99999886779*** PP

                                        -STTTHEETTTSSEEEETTSSTSGGGGS-HHHHHHSEEEHHHHHHHHHHHHHHHHTTSSGTTTTSHHHHHHHHHHT CS
                        Pkinase_Tyr 145 sDfGLardiekddeyvkkeeaklpvkWmapEslkekkftsksDvWsfGvllwEiftlgespypglkneevleklke 220
                                        +Df L++++ +d++ ++++       +mapE++++k +  + DvWs Gv+++E+++   +p+++ +++e+ +++  
  gene3090|gene3090|rna3090|rna3090 160 CDFSLSKRL-DDESKSNDGMIVGTPYYMAPEIIQKKAYDYSVDVWSMGVVMYELVS-KMRPFESESKKELKRQIVF 233
                                        *********.66666677777778889*****************************.789*********9999977 PP

                                        TEES-BBTTSBHHHHHHHHHHT-SSGGGS- CS
                        Pkinase_Tyr 221 gkrlekpekcpeelyelmkkcweedpeeRp 250
                                        ++    p+     l++++ +c++++  +R 
  gene3090|gene3090|rna3090|rna3090 234 QEIRVLPNCRDFFLKKIVLECLRKE--DRI 261
                                        77777777777789999****9864..555 PP

>> Pkinase_fungal  Fungal protein kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.9   0.0   1.4e-12   3.6e-09     312     397 ..     117     202 ..     109     210 .. 0.84

  Alignments for each domain:
  == domain 1  score: 35.9 bits;  conditional E-value: 1.4e-12
                     Pkinase_fungal 312 lrDaIkghrsLflkagiLHrDiSenNilitdskke..gerkglLiDLDlakelsddssesgarertGTleFmaiev 385
                                        + + I ++  L+   +i+HrDi  +Nil++  k    +  +  L D+ l k l+d +s+s+++  +GT+++ma e+
  gene3090|gene3090|rna3090|rna3090 117 FSQLIDALAYLH-RNRIIHRDIKPGNILLNRVKGRscNFLQVKLCDFSLSKRLDD-ESKSNDGMIVGTPYYMAPEI 190
                                        6677999999**.9****************55444345556779**********7.888889************** PP

                     Pkinase_fungal 386 lkgeeHsyrhDL 397
                                        ++++   y  D+
  gene3090|gene3090|rna3090|rna3090 191 IQKKAYDYSVDV 202
                                        **8878887776 PP

>> FTA2  Kinetochore Sim4 complex subunit FTA2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.0   6.5e-05      0.17      22      75 ..      12      66 ..       4      79 .. 0.77
   2 !   12.9   0.3   2.5e-05     0.064     149     204 ..      89     143 ..      62     166 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 6.5e-05
                               FTA2 22 kdiefleyLgkglhsiVlkvkirgkeYALKlFrfleaeele.eaeedlkipreal 75
                                       +d++fle Lg+g+h+ V+  + r+++  L +F+ ++ ++l+   +e + i+  ++
  gene3090|gene3090|rna3090|rna3090 12 DDYRFLEKLGNGTHGTVYLLESRESKPKLVVFKSVSSKNLKyALNEIEIIKSLSY 66
                                       689********************************99888853333444444444 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 2.5e-05
                               FTA2 149 eedgkkrpiraIVKelellkeqeelevsqlpkllrdlkklhklgIvvrDlkeenyi 204
                                         ++g  + + ++++e + l+ +++++  ++++l++ l  lh+  I++rD+k+ n++
  gene3090|gene3090|rna3090|rna3090  89 ANYGDLERLNCFIRE-KNLNIDKSIIWTIFSQLIDALAYLHRNRIIHRDIKPGNIL 143
                                        445556677899999.8899*******************************98875 PP

>> Kinase-like  Kinase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.0   1.2e-08   3.2e-05     149     280 ..     116     250 ..      47     260 .. 0.75

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 1.2e-08
                        Kinase-like 149 lTlqlirlaanLqakglvhgkftvdnlllde.kgg......lmlggftaLvragtkvvlseve.....kgfaPpEl 212
                                        +  qli   a+L+ + ++h ++++ n+ll++ kg+      ++l +f+   r  ++ + s+         +  pE+
  gene3090|gene3090|rna3090|rna3090 116 IFSQLIDALAYLHRNRIIHRDIKPGNILLNRvKGRscnflqVKLCDFSLSKRLDDESK-SNDGmivgtPYYMAPEI 190
                                        33699************************98334355555599****99999888888.55442333334555666 PP

                        Kinase-like 213 lgsrggytrknktkmthkldaWqlGlviyriwclklPltl.ateeakeewkfklckkipekvkaLlkkf 280
                                        + +           + +++d+W +G+v+y + +   P++   ++e k +  f+ ++  p+   + lkk+
  gene3090|gene3090|rna3090|rna3090 191 IQK---------KAYDYSVDVWSMGVVMYELVSKMRPFESeSKKELKRQIVFQEIRVLPNCRDFFLKKI 250
                                        655.........567899********************8615678889999999998888877777765 PP

>> YrbL-PhoP_reg  PhoP regulatory network protein YrbL
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   2.3e-06    0.0058      64     160 ..      53     152 ..      32     161 .. 0.74
   2 ?   -1.8   0.2       0.7   1.8e+03     174     198 ..     277     301 ..     273     303 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2.3e-06
                      YrbL-PhoP_reg  64 eyvqlsklreeidnsplarilGlvqTdlGlGlvvekirdadGnvaktLedlvkkeelta......elkeaLdefle 133
                                        + +++    +    + + r++G+   + G+ +++e  +  d    ++L+ ++++++l+        + ++L + l+
  gene3090|gene3090|rna3090|rna3090  53 YALNEIEIIKSLSYKRIVRFYGSMSSNNGMYIMMEHANYGD---LERLNCFIREKNLNIdksiiwTIFSQLIDALA 125
                                        44444445566677889999999999999988888766555...5678888866655431122225689999999* PP

                      YrbL-PhoP_reg 134 elldnhivtndlsakNivvkknsegee 160
                                        +l  n+i+ +d+++ Ni++++ + +  
  gene3090|gene3090|rna3090|rna3090 126 YLHRNRIIHRDIKPGNILLNRVKGRSC 152
                                        ********************9998874 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.7
                      YrbL-PhoP_reg 174 iplyawsrtlnrkklerklarlikk 198
                                        i +   ++t++  +lerk++r+ k+
  gene3090|gene3090|rna3090|rna3090 277 IIAEHRLKTYRLERLERKIHRMSKE 301
                                        5566677888888999999998875 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   3.4e-05     0.088     162     181 ..     123     145 ..      87     152 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.4e-05
                                        S...SS-EEEE-SS-SGGGEEEC CS
                                APH 162 g...elptvllHgDlhpgNllvd 181
                                        +     + +++H+D++pgN+l++
  gene3090|gene3090|rna3090|rna3090 123 AlayLHRNRIIHRDIKPGNILLN 145
                                        33335579*************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (309 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       644  (0.0359195); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 2028.14
//
Query:       gene3091|gene3091|rna3091|rna3091  [L=127]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.5e-29  101.4   2.8    4.1e-29  101.1   2.8    1.1  1  Ribosomal_L22e  Ribosomal L22e protein family
  ------ inclusion threshold ------
      0.014   15.3   1.7       0.12   12.4   0.2    2.4  3  YebF            YebF-like protein


Domain annotation for each model (and alignments):
>> Ribosomal_L22e  Ribosomal L22e protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.1   2.8   4.6e-33   4.1e-29       7     108 ..      26     126 ..      20     127 .] 0.96

  Alignments for each domain:
  == domain 1  score: 101.1 bits;  conditional E-value: 4.6e-33
                     Ribosomal_L22e   7 tidcskpvedkildvaefekfLkerikvngktgnlgdkveieregkskvtvtsevkfskrylkyltkkyLkkkqlr 82 
                                         +dcs ++ ++++d+++++++L  +ikv+gk+g+lg++++++++ +++v v+ +  ++kry+kyl kk+L++k+l+
  gene3091|gene3091|rna3091|rna3091  26 RLDCSLCTAESLFDTKDLTNYLLANIKVKGKKGQLGKNIKVDCD-ADNVRVEYKRFMTKRYVKYLGKKFLRTKKLN 100
                                        69******************************************.567**************************** PP

                     Ribosomal_L22e  83 dwlrvvasskesYeLryfnieedeee 108
                                         w+r+v+ sk  Y+++y+n+++ +ee
  gene3091|gene3091|rna3091|rna3091 101 SWVRLVSVSKVGYRFSYYNVDKGNEE 126
                                        **********************9987 PP

>> YebF  YebF-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0      0.57   5.2e+03      73      83 ..      21      31 ..      14      37 .. 0.73
   2 ?   12.4   0.2   1.4e-05      0.12      54      87 ..      41      74 ..      33      78 .. 0.81
   3 ?    2.5   0.1     0.016   1.5e+02      24      61 ..      80     116 ..      72     127 .] 0.75

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.57
                               YebF 73 lsYkvtvdCkk 83
                                       ++  v +dC+ 
  gene3091|gene3091|rna3091|rna3091 21 VESVVRLDCSL 31
                                       56678899975 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 1.4e-05
                               YebF 54 tgkddkykvplkvrGkkkdlsYkvtvdCkkgeik 87
                                       ++  + + + +kv+Gkk +l  +++vdC++++++
  gene3091|gene3091|rna3091|rna3091 41 KDLTNYLLANIKVKGKKGQLGKNIKVDCDADNVR 74
                                       55556667789******************98764 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.016
                               YebF  24 ylqnRiprwedDkkalGtskpvawvnaedvtgkddkyk 61 
                                        ++  R++++   kk l t+k++ wv   +v++    ++
  gene3091|gene3091|rna3091|rna3091  80 FMTKRYVKYL-GKKFLRTKKLNSWVRLVSVSKVGYRFS 116
                                        7777887775.5889999*******9999988776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       705  (0.0393218); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 895.66
//
Query:       gene3092|gene3092|rna3092|rna3092  [L=269]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-37  128.3   0.0    1.1e-26   93.3   0.0    2.1  2  Methyltransf_4   Putative methyltransferase
    0.00033   20.2   0.0     0.0031   17.1   0.0    2.1  2  MTS              Methyltransferase small domain
    0.00034   20.4   0.0    0.00056   19.7   0.0    1.4  1  Methyltransf_31  Methyltransferase domain
    0.00046   20.8   0.0      0.001   19.7   0.0    1.7  1  Methyltransf_25  Methyltransferase domain
    0.00048   20.7   0.0     0.0011   19.6   0.0    1.6  1  Methyltransf_11  Methyltransferase domain
    0.00048   20.0   0.0     0.0016   18.3   0.0    1.9  1  Methyltransf_23  Methyltransferase domain
     0.0015   19.3   0.0     0.0031   18.2   0.0    1.6  1  Methyltransf_12  Methyltransferase domain
  ------ inclusion threshold ------
      0.027   14.5   0.0       0.04   13.9   0.0    1.3  1  Methyltransf_32  Methyltransferase domain
      0.039   13.2   0.5       0.12   11.7   0.0    1.9  2  CMAS             Mycolic acid cyclopropane synthetase
      0.091   13.1   0.0       0.19   12.1   0.0    1.5  1  AdoMet_MTase     Predicted AdoMet-dependent methyltransferase


Domain annotation for each model (and alignments):
>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.1   0.0   1.9e-11   3.4e-08       5      49 ..      39      83 ..      35      93 .. 0.92
   2 !   93.3   0.0   6.2e-30   1.1e-26      42     165 ..     129     254 ..     113     262 .. 0.90

  Alignments for each domain:
  == domain 1  score: 33.1 bits;  conditional E-value: 1.9e-11
                                       EEEET-TTSHHHHHHHHHSTTSEEEEEES-HHHHHHHHHHHHHCT CS
                     Methyltransf_4  5 vleiGcGkGeflvalAkknPdknflGiEirvkvvakvlkkieale 49
                                        +++GcG+G+fl++ Ak +Pdk + G+Eir+kv + v +ki++l+
  gene3092|gene3092|rna3092|rna3092 39 YVDVGCGYGRFLLHVAKTRPDKVVYGLEIRKKVYEFVRDKIAELR 83
                                       79**************************************99986 PP

  == domain 2  score: 93.3 bits;  conditional E-value: 6.2e-30
                                        HHHHHHC..TTSSEEEEES-CCCHHHHCS-TTSEEEEEEES-----SGGGGGGSTTSHHHHHHHHHHEEEEEEEEE CS
                     Methyltransf_4  42 lkkieal..elkNlrilrgdalkvllelledgslekifilFPDPwfKkrhhKrRllqpellkelarvLkkgGvlel 115
                                        +++ +++   ++N +++r++a+ ++l++++++slekif+l+PDP+fK++++K R+++ ++++ + + L + G +++
  gene3092|gene3092|rna3092|rna3092 129 IRENGKEcvTYENAHVIRTNAMLFFLHFFKKRSLEKIFVLYPDPHFKNKKRKARMVTLQTIQCFDYCLAEHGRVYI 204
                                        444444466899**************************************************************** PP

                                        EESHHHHHHHHHHHHHCSTTEEESSCCCSCCTCHCHHCCCSSTTCCCCCC CS
                     Methyltransf_4 116 aTDveeyaeemlkvleeeplferlskeeeleeeplsvlriatkyeqkvqs 165
                                         TDv+e++  m++ +++   f+rls++e  ++e  + ++i t + +++ +
  gene3092|gene3092|rna3092|rna3092 205 STDVKELFTAMIDSFSNCAYFKRLSDSECCSDEFYDAIQIGTDESKRAGA 254
                                        ***************************************99999988765 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   1.7e-06    0.0031      32      96 ..      36     100 ..       9     109 .. 0.81
   2 ?    1.0   0.0      0.15   2.7e+02     103     158 ..     170     224 ..     123     229 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.7e-06
                                        CSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTTTSTTS CS
                                MTS  32 sgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasdvleeveek 96 
                                        + + +D+GcG+G   +++ak  p+  v  +++ ++  e+ +  +++ + ++ v ++  ++ +e k
  gene3092|gene3092|rna3092|rna3092  36 AANYVDVGCGYGRFLLHVAKTRPDKVVYGLEIRKKVYEFVRDKIAELRKNGVVEKHRSVSGTESK 100
                                        4679********************99******999999999988887777666666555555555 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.15
                                        E---STTTCHCHHHHHHHHHHHHHHHEEEEEEEEEEEETTSCHHHHHHHHHS--EE CS
                                MTS 103 sNPPfhagkatelavaeeliaeAkeaLkegGeLliVanrklgyeslleelfgnvev 158
                                          P f+++k +   v+ + i+    +L+e+G+ +i +    +  +++ ++f+n++ 
  gene3092|gene3092|rna3092|rna3092 170 PDPHFKNKKRKARMVTLQTIQCFDYCLAEHGRVYIST-DVKELFTAMIDSFSNCAY 224
                                        4688999999999999999999999******998754.455666677778888765 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   3.1e-07   0.00056       5      46 ..      37      77 ..      34     141 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 3.1e-07
                    Methyltransf_31  5 lrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielAre 46
                                        +++D+GCG G++++  a + +p++ v+G++i +++ e+ r 
  gene3092|gene3092|rna3092|rna3092 37 ANYVDVGCGYGRFLLHVA-KTRPDKVVYGLEIRKKVYEFVRD 77
                                       6899**************.99***********9987766665 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   5.8e-07     0.001       2      45 ..      40      83 ..      40     131 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 5.8e-07
                                       EEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTT CS
                    Methyltransf_25  2 LdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeg 45
                                       +d+GcG Gr++l++ak  +++ v+g++i ++  e +r +++e +
  gene3092|gene3092|rna3092|rna3092 40 VDVGCGYGRFLLHVAKTRPDKVVYGLEIRKKVYEFVRDKIAELR 83
                                       69**************987999***************9997733 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   6.2e-07    0.0011       1      43 [.      40      84 ..      40     104 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 6.2e-07
                                       EEET-TTSHHHHHHHHTT..SEEEEEES-HHHHHHHHHHCCHHT- CS
                    Methyltransf_11  1 LdvGcGtGrlaealakrg..arvvgvDlskemlklakekaseegl 43
                                       +dvGcG Gr++ ++ak+   + v+g+++ k++ + +++k+ e + 
  gene3092|gene3092|rna3092|rna3092 40 VDVGCGYGRFLLHVAKTRpdKVVYGLEIRKKVYEFVRDKIAELRK 84
                                       59*************88889****************999988764 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   9.1e-07    0.0016      21      81 ..      34     134 ..      21     225 .. 0.70

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 9.1e-07
                    Methyltransf_23  21 raggrvLdiGcGtGillevlrengf..svtgvDlspeaveiae................................. 61 
                                         + ++++d+GcG+G++l + ++ +    v+g +++ +  e ++                                 
  gene3092|gene3092|rna3092|rna3092  34 LPAANYVDVGCGYGRFLLHVAKTRPdkVVYGLEIRKKVYEFVRdkiaelrkngvvekhrsvsgteskeiddtpant 109
                                        4678****************88877645779999877666666888888888888777777777777777777777 PP

                    Methyltransf_23  62 .....kakkaqkdqfdeqeaaepqg 81 
                                                +++ +   +q+++e+ +
  gene3092|gene3092|rna3092|rna3092 110 yegllVNGTQKEKVDEQQCIRENGK 134
                                        7777633333333333455555554 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   1.7e-06    0.0031       1      48 [.      40      87 ..      40     111 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.7e-06
                    Methyltransf_12  1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnn 48
                                       +++GcG G++l ++++  pd+ ++g++i +++ e  + k+a+ ++n +
  gene3092|gene3092|rna3092|rna3092 40 VDVGCGYGRFLLHVAKTRPDKVVYGLEIRKKVYEFVRDKIAELRKNGV 87
                                       69*******************************999999999887654 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   2.2e-05      0.04      25     104 ..      35     116 ..      20     155 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.2e-05
                    Methyltransf_32  25 galtvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekraeklgkkfnkrlsfaelsieeatssktltk 100
                                        +a + vDvG+G g   f l+  +++    v+g+++++++ e  ++  ++l+k   + + +++ s+++++s++  ++
  gene3092|gene3092|rna3092|rna3092  35 PAANYVDVGCGYG--RFLLHVAKTRPDKVVYGLEIRKKVYEFVRDKIAELRK---NGVVEKHRSVSGTESKEIDDT 105
                                        56789*****988..45555544567899************99999999994...344444444444443332222 PP

                    Methyltransf_32 101 kve.......a 104
                                          +       +
  gene3092|gene3092|rna3092|rna3092 106 PANtyegllvN 116
                                        22234455551 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   6.6e-05      0.12      65     110 ..      38      84 ..      31     105 .. 0.81
   2 ?   -1.3   0.3      0.59   1.1e+03      19      38 ..     210     227 ..     203     237 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 6.6e-05
                                        EEEEES-TTSHHHHHHHH.HH--EEEEEES-HHHHHHHHHHHHTS-S CS
                               CMAS  65 tlLdiGcGWGslvrrave.rydvkvvglTlSkeqaklakkrvdeldl 110
                                        + +d+GcG+G  + + ++ r d  v gl + k+ ++ ++++++el  
  gene3092|gene3092|rna3092|rna3092  38 NYVDVGCGYGRFLLHVAKtRPDKVVYGLEIRKKVYEFVRDKIAELRK 84 
                                        568*******9887766526788899***************998764 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.59
                                        HHHCTTS-TT---S----SS CS
                               CMAS  19 dffalfldptmtYsCAyfer 38 
                                        ++f++++d      CAyf+r
  gene3092|gene3092|rna3092|rna3092 210 ELFTAMIDSFS--NCAYFKR 227
                                        56777777665..5****98 PP

>> AdoMet_MTase  Predicted AdoMet-dependent methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00011      0.19      60      91 ..      37      70 ..      23      88 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00011
                       AdoMet_MTase 60 tsfvdvgcgng.llvyvlaaegyk.gygidlrkr 91
                                         +vdvgcg g +l++v ++   k  yg+++rk+
  gene3092|gene3092|rna3092|rna3092 37 ANYVDVGCGYGrFLLHVAKTRPDKvVYGLEIRKK 70
                                       579*******9568899888766537******96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (269 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       528  (0.0294495); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1906.82
//
Query:       gene3093|gene3093|rna3093|rna3093  [L=82]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.2e-05   24.0   5.7    4.3e-05   23.0   5.7    1.4  1  DUF3149          Protein of unknown function (DUF3149)
     0.0031   18.5   0.3     0.0038   18.2   0.3    1.2  1  DUF4834          Domain of unknown function (DUF4834)
     0.0045   17.1   0.5     0.0053   16.9   0.5    1.1  1  CRA              Circumsporozoite-related antigen (CRA)
  ------ inclusion threshold ------
      0.012   15.9   0.4      0.014   15.6   0.4    1.1  1  MAP17            Membrane-associated protein 117 kDa, PDZK1-i
      0.014   15.4   0.1      0.014   15.3   0.1    1.2  1  OppC_N           N-terminal TM domain of oligopeptide transpo
      0.015   15.8   0.7      0.018   15.5   0.7    1.1  1  DUF2500          Protein of unknown function (DUF2500)
      0.045   13.5   0.1       0.07   12.8   0.1    1.3  1  Cation_ATPase_C  Cation transporting ATPase, C-terminus
      0.066   12.9   0.2      0.077   12.7   0.2    1.1  1  Baculo_VP91_N    Viral capsid protein 91 N-terminal
      0.077   12.8   0.0      0.096   12.5   0.0    1.1  1  TMEM208_SND2     SRP-independent targeting protein 2/TMEM208
        0.1   12.2   4.0       0.16   11.5   0.1    2.0  2  Baculo_11_kDa    Baculovirus 11 kDa family
       0.17   11.8   0.2        0.2   11.5   0.2    1.3  1  Lig_chan         Ligand-gated ion channel
        0.6   11.0   3.1        1.3   10.0   3.1    1.5  1  EphA2_TM         Ephrin type-A receptor 2 transmembrane domai
        1.3    9.2   7.0       0.19   11.8   3.4    1.4  2  DUF3671          Protein of unknown function
        3.8    7.6   7.3        7.6    6.6   7.3    1.5  1  Peptidase_S49_N  Peptidase family S49 N-terminal


Domain annotation for each model (and alignments):
>> DUF3149  Protein of unknown function (DUF3149)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   5.7   3.3e-08   4.3e-05       1      29 [.       7      35 ..       7      39 .. 0.94

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 3.3e-08
                            DUF3149  1 wkdLFssdvGLlSliVIvftigmgaffir 29
                                       +kd F++ +G++S+i I+++i+m+++++ 
  gene3093|gene3093|rna3093|rna3093  7 LKDFFTNVYGWISIIFILIVILMIVYIVK 35
                                       699***********************986 PP

>> DUF4834  Domain of unknown function (DUF4834)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.3     3e-06    0.0038       7      69 ..      18      78 ..      10      82 .] 0.29

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 3e-06
                            DUF4834  7 ilifiiailvigl.silsvilrtvfglgsrkkss.ksaqkqfgnstnsnqqksqsrsetkeegei 69
                                       i i++i+i+++++  i+ +++       +r + s  ++   +++  n +q+ks+++++++ e+++
  gene3093|gene3093|rna3093|rna3093 18 ISIIFILIVILMIvYIVKALVDDS---DNRPRDSqGNVIVVNQQMANMQQEKSKREERER-EKKE 78
                                       433333333333303333333333...333333322222222222222222221111111.1111 PP

>> CRA  Circumsporozoite-related antigen (CRA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.5   4.1e-06    0.0053       6      64 ..      21      80 ..      17      82 .] 0.67

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 4.1e-06
                                CRA  6 slfviilllvvycdevkGkkknngkkdvwksrftkkk.gkykknekevekaeekedenee 64
                                       ++++i++l++vy+ ++  +  +n  +d  +  +++ +   ++++ek+  ++ e e++++e
  gene3093|gene3093|rna3093|rna3093 21 IFILIVILMIVYIVKALVDDSDNRPRDSQGNVIVVNQqMANMQQEKSKREEREREKKEKE 80
                                       34556678888*****************99999988644455555544444444444333 PP

>> MAP17  Membrane-associated protein 117 kDa, PDZK1-interacting protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.6   0.4   1.1e-05     0.014      41      97 ..      24      80 ..      14      82 .] 0.63

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.1e-05
                              MAP17 41 FLflvfvlllvnrvWcskaraedeeeetfrmeankeedvslskeekkeeekekkekk 97
                                        +++ +++++v+ +    + + ++++ ++ + +++  +++++k++++e+e+ekkek+
  gene3093|gene3093|rna3093|rna3093 24 LIVILMIVYIVKALVDDSDNRPRDSQGNVIVVNQQMANMQQEKSKREEREREKKEKE 80
                                       345667899999988877777777767777777777788776666665344444333 PP

>> OppC_N  N-terminal TM domain of oligopeptide transport permease C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.1   1.1e-05     0.014       5      32 ..       5      32 ..       2      63 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.1e-05
                             OppC_N  5 dawrrFkrNklAvvglvilllllliaif 32
                                       ++++ F+ N   +++ +++l+++l+ ++
  gene3093|gene3093|rna3093|rna3093  5 EVLKDFFTNVYGWISIIFILIVILMIVY 32
                                       78999*******************9887 PP

>> DUF2500  Protein of unknown function (DUF2500)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   0.7   1.4e-05     0.018       2      60 ..      20      79 ..      17      82 .] 0.51

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.4e-05
                            DUF2500  2 llfiivialiivlatrqivrqikqeakndaapvltvqaevvdKreevipnr.rqreeiea 60
                                       ++fi++++l+iv +++++v+   ++ ++ +  v  v+ ++ + ++e+++++ r+re++e+
  gene3093|gene3093|rna3093|rna3093 20 IIFILIVILMIVYIVKALVDDSDNRPRDSQGNVIVVNQQMANMQQEKSKREeREREKKEK 79
                                       455555544444445566655555555555555555555555555555533455555544 PP

>> Cation_ATPase_C  Cation transporting ATPase, C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   5.5e-05      0.07     120     149 ..       8      35 ..       3      47 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 5.5e-05
                    Cation_ATPase_C 120 sglfsnkllllaillslllqvlivyvpgln 149
                                        + +f+n + +++i+++l+++++ivy+  ++
  gene3093|gene3093|rna3093|rna3093   8 KDFFTNVYGWISIIFILIVILMIVYI--VK 35 
                                        4789*********************9..54 PP

>> Baculo_VP91_N  Viral capsid protein 91 N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.2     6e-05     0.077       3      48 ..      19      64 ..      17      71 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 6e-05
                      Baculo_VP91_N  3 lvvfllilvvllflaivfefdntafterlkqrrrlvleeylksvga 48
                                        ++f+li+++++ + ++  +d+ ++ +r  q + +v+++ + ++++
  gene3093|gene3093|rna3093|rna3093 19 SIIFILIVILMIVYIVKALVDDSDNRPRDSQGNVIVVNQQMANMQQ 64
                                       589****99999999***************9999999887755555 PP

>> TMEM208_SND2  SRP-independent targeting protein 2/TMEM208
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   7.5e-05     0.096     114     167 ..      15      77 ..       5      81 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 7.5e-05
                       TMEM208_SND2 114 kfWll...ylviPayalYklwglilgpaff.kgagsa.......eeaaeeeeaksKrqeKlekRa 167
                                        + W+    +l++ ++++Y +  l+       + +  +       ++ a+ +++ksKr e+ + ++
  gene3093|gene3093|rna3093|rna3093  15 YGWISiifILIVILMIVYIVKALVDDSDNRpRDS--QgnvivvnQQMANMQQEKSKREEREREKK 77 
                                        4554311277888888888888888555553333..23489998888888899999998877765 PP

>> Baculo_11_kDa  Baculovirus 11 kDa family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   0.00013      0.16      32      63 ..       6      37 ..       4      50 .. 0.81
   2 ?    2.1   0.8      0.11   1.5e+02      57      76 ..      53      72 ..      51      79 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00013
                      Baculo_11_kDa 32 flrdFvLvicglvvfvvivlfilLlvvilkna 63
                                        l+dF   + g + ++ i++ il++v+i+k  
  gene3093|gene3093|rna3093|rna3093  6 VLKDFFTNVYGWISIIFILIVILMIVYIVKAL 37
                                       68999999999999999999999999998865 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.11
                      Baculo_11_kDa 57 vvilknaeaeeaekekrekt 76
                                       +v+++++ + ++ek+kre++
  gene3093|gene3093|rna3093|rna3093 53 IVVNQQMANMQQEKSKREER 72
                                       56677777777777777654 PP

>> Lig_chan  Ligand-gated ion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.2   0.00016       0.2       5      43 ..      17      56 ..      13      80 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00016
                                       XXXXXTXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxx RF
                           Lig_chan  5 Wlsvlvalilvsivlflverfspyewrepeea.aetvene 43
                                       W+s++++li++ +++++v+ ++  + ++p+++  +  + +
  gene3093|gene3093|rna3093|rna3093 17 WISIIFILIVILMIVYIVKALVDDSDNRPRDSqGNVIVVN 56
                                       **********************999998876633333333 PP

>> EphA2_TM  Ephrin type-A receptor 2 transmembrane domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   3.1   0.00099       1.3       3      39 ..      18      68 ..      15      82 .] 0.52

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00099
                           EphA2_TM  3 aaavaglvllvilvilvlvlvrrrsknrkqksdl.......k........sk 39
                                       +++++ l++++++v +v  lv   s nr ++s+        +        sk
  gene3093|gene3093|rna3093|rna3093 18 ISIIFILIVILMIVYIVKALV-DDSDNRPRDSQGnvivvnqQmanmqqekSK 68
                                       467777777777777777777.444454444444466655414443333211 PP

>> DUF3671  Protein of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   3.4   0.00015      0.19      79     109 ..       5      35 ..       2      39 .. 0.87
   2 ?   -2.8   0.1         5   6.4e+03      31      31 ..      64      64 ..      52      78 .. 0.50

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00015
                            DUF3671  79 evlatsieklytiffiilvviillvliYili 109
                                        evl++ ++++y  ++ii++ i++l+++Yi+ 
  gene3093|gene3093|rna3093|rna3093   5 EVLKDFFTNVYGWISIIFILIVILMIVYIVK 35 
                                        47788899*********************86 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 5
                            DUF3671 31 n 31
                                       +
  gene3093|gene3093|rna3093|rna3093 64 Q 64
                                       1 PP

>> Peptidase_S49_N  Peptidase family S49 N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   7.3    0.0059       7.6      13      71 ..      20      80 ..       9      82 .] 0.52

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0059
                    Peptidase_S49_N 13 lvtlvvailvvvvlivalaakkk..kekgelevtkLneeykelkeeleealldeeelkaae 71
                                       ++ ++++il++v ++ al   ++   ++ + +v  +n++  ++++e +++  +e+e+k++e
  gene3093|gene3093|rna3093|rna3093 20 IIFILIVILMIVYIVKALVDDSDnrPRDSQGNVIVVNQQMANMQQEKSKREEREREKKEKE 80
                                       3334444444444444443333323566677788888888888877555544444444332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3404  (0.18986); expected 358.6 (0.02)
Passed bias filter:                     1358  (0.0757432); expected 358.6 (0.02)
Passed Vit filter:                       195  (0.0108762); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.57u 0.31s 00:00:00.87 Elapsed: 00:00:00.49
# Mc/sec: 505.71
//
Query:       gene3094|gene3094|rna3094|rna3094  [L=273]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (273 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       666  (0.0371465); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1825.00
//
Query:       gene3095|gene3095|rna3095|rna3095  [L=109]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.83    9.9   9.3       0.24   11.6   2.2    2.6  2  XhlA      Haemolysin XhlA
        4.2    7.9  18.6          2    8.9   7.5    2.6  3  ZapB      Cell division protein ZapB


Domain annotation for each model (and alignments):
>> XhlA  Haemolysin XhlA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.6      0.02   1.8e+02      18      35 ..       3      20 ..       1      53 [. 0.58
   2 ?   11.6   2.2   2.7e-05      0.24      11      39 ..      70      98 ..      60     100 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.02
                               XhlA 18 ervdkleekaaeaeekik 35
                                       er+d +e  a + +ek  
  gene3095|gene3095|rna3095|rna3095  3 ERIDLIEAYAKKNREKMR 20
                                       445555555444444433 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 2.7e-05
                               XhlA 11 tkldnleervdkleekaaeaeekiknlee 39
                                       t++ +l++r+++le+k++  ++kik+le+
  gene3095|gene3095|rna3095|rna3095 70 TRQYKLKQRIEELEMKKDVYKKKIKQLEN 98
                                       788899*******************9985 PP

>> ZapB  Cell division protein ZapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.1      0.54   4.9e+03      41      43 ..      15      17 ..       3      34 .. 0.55
   2 ?    6.6   2.4    0.0012        11      25      47 ..      49      71 ..      41      76 .. 0.61
   3 ?    8.9   7.5   0.00023         2      21      52 ..      73     106 ..      67     109 .] 0.77

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.54
                               ZapB 41 nre 43
                                       nre
  gene3095|gene3095|rna3095|rna3095 15 NRE 17
                                       222 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0012
                               ZapB 25 meieeLkeeneelkeenreleee 47
                                       +e+ +L+++n elk+e+ e+   
  gene3095|gene3095|rna3095|rna3095 49 EENVKLQAKNIELKREALEVLTR 71
                                       46666666666666666666544 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.00023
                               ZapB  21 tlLqmeieeLkeeneelkeenrele..eeneqlk 52 
                                         +L+++ieeL++++  +k+++++le  +e + ++
  gene3095|gene3095|rna3095|rna3095  73 YKLKQRIEELEMKKDVYKKKIKQLEnmREAQSEQ 106
                                        58**********************9654444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2151  (0.119973); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 778.06
//
Query:       gene3096|gene3096|rna3096|rna3096  [L=374]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (374 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       725  (0.0404373); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.50u 0.23s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2729.40
//
Query:       gene3097|gene3097|rna3097|rna3097  [L=409]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.2e-61  205.9   0.1    4.3e-61  204.9   0.1    1.5  1  S-AdoMet_synt_C  S-adenosylmethionine synthetase, C-terminal 
    1.7e-39  134.7   0.0    4.2e-39  133.5   0.0    1.7  2  S-AdoMet_synt_M  S-adenosylmethionine synthetase, central dom
    7.4e-33  113.2   0.7    7.4e-33  113.2   0.7    1.7  2  S-AdoMet_synt_N  S-adenosylmethionine synthetase, N-terminal 
  ------ inclusion threshold ------
      0.011   14.6   0.4      0.031   13.1   0.1    1.8  2  AdoMet_Synthase  S-adenosylmethionine synthetase (AdoMet synt
      0.017   14.1   0.0      0.053   12.4   0.0    1.7  2  Glyco_hydro_79n  Glycosyl hydrolase family 79, N-terminal dom
      0.047   13.7   0.0        1.6    8.8   0.0    2.8  3  Mei5_like        Putative double-strand recombination repair-
       0.14   12.1   0.3       0.33   10.9   0.1    1.7  2  PB1              PB1 domain
       0.16   12.1   0.7        4.8    7.4   0.0    3.1  3  SapB_2           Saposin-like type B, region 2


Domain annotation for each model (and alignments):
>> S-AdoMet_synt_C  S-adenosylmethionine synthetase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  204.9   0.1   1.9e-64   4.3e-61       1     137 [.     266     402 ..     266     403 .. 0.99

  Alignments for each domain:
  == domain 1  score: 204.9 bits;  conditional E-value: 1.9e-64
                                        S-TTTTS-EETTS-TTTTTTTTSS---S---TTB-TTSHHHHHHHHHHHHHHHHHHTTSBSEEEEEEEE-TT-SS- CS
                    S-AdoMet_synt_C   1 iGgpkgdaGltgrkiivdtYgglaahgggafsgKdptkvDrsaayaaryvaknlvaaglakkvevqlsYaigvaep 76 
                                        iGgpkgd+Gltgrk+ivdtYgg++ hggg+fsgKd tkvDrs+ayaar++ak+lv ++++k+ +vq+sYaig+ +p
  gene3097|gene3097|rna3097|rna3097 266 IGGPKGDSGLTGRKTIVDTYGGFGLHGGGSFSGKDWTKVDRSGAYAARWIAKSLVDSNICKRALVQISYAIGIVSP 341
                                        8*************************************************************************** PP

                                        SEEEEEE-S-BSS-HHHHHHHHHHH----HHHHHHHHTTTSS--TGGGSS-SSS--T-TTS CS
                    S-AdoMet_synt_C  77 vsisvetfgtekvseeeiaeivkevfdlrpaaiieeldLkkpiykktaayghfgreelpwe 137
                                        vs++v+t+gt+ +++++i +i++e+fdlrp+ai+  l L+kp+y +++ yghfgr+ ++we
  gene3097|gene3097|rna3097|rna3097 342 VSCYVDTYGTGVIDNDKIIKIINENFDLRPKAICAALGLDKPVYGRLSVYGHFGRKGYKWE 402
                                        ************************************************************9 PP

>> S-AdoMet_synt_M  S-adenosylmethionine synthetase, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0         4   8.9e+03      47      60 ..      34      47 ..      21      76 .. 0.63
   2 !  133.5   0.0   1.9e-42   4.2e-39       1     120 []     125     264 ..     125     264 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 4
                    S-AdoMet_synt_M 47 ylrpDaKsqvtveY 60
                                       yl++D+ ++v ve 
  gene3097|gene3097|rna3097|rna3097 34 YLSKDSLAKVAVEC 47
                                       45555555555554 PP

  == domain 2  score: 133.5 bits;  conditional E-value: 1.9e-42
                    S-AdoMet_synt_M   1 eigAgDqGimfGYAtdeteelmPlpillahklaerlaelrkegeleylrpDaKsqvtveYee...elkpvrvdtvv 73 
                                        +igAgDqGimfGYAt+et+e mPl+++la++++e++++lrk+  +e++++D+KsqvtveYe+   el p+r+d+vv
  gene3097|gene3097|rna3097|rna3097 125 KIGAGDQGIMFGYATNETPERMPLTLMLANRIVEEIENLRKT--YEFIKSDCKSQVTVEYENrdnELVPLRIDNVV 198
                                        58**************************************85..99**************7566799********* PP

                    S-AdoMet_synt_M  74 istqhdeevs......................qeklredlkekvikkvlkeelldekktkllinptGkF 120
                                        +s+qh+++++                       e +r++l++k+ + vl+eell++  tk++i p+GkF
  gene3097|gene3097|rna3097|rna3097 199 LSVQHAADLEkwtnvmnecvygtsdqpsslkpLELFRAFLRKKIRE-VLPEELLKS--TKYHILPSGKF 264
                                        *****997765566666666666666665555456********966.777998754..8*********9 PP

>> S-AdoMet_synt_N  S-adenosylmethionine synthetase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.2   0.7   3.3e-36   7.4e-33       1      98 [.       6     103 ..       6     104 .. 0.99
   2 ?   -3.0   0.0       5.4   1.2e+04      29      41 ..     169     181 ..     152     190 .. 0.55

  Alignments for each domain:
  == domain 1  score: 113.2 bits;  conditional E-value: 3.3e-36
                    S-AdoMet_synt_N   1 kylftsesVseGHPDkvadqisdaildailkedpkarvacetlvttglvvvageittkakvdiekivrevikeigY 76 
                                        k+l+tsesV +GHPDk++dqi+d+ilda+l++d+ a+va+e++vt+++ +v+ge++++akv+++++v +vi+e gY
  gene3097|gene3097|rna3097|rna3097   6 KFLYTSESVGKGHPDKLCDQIADRILDAYLSKDSLAKVAVECIVTQNMACVFGEVNSTAKVNTKACVVDVIREAGY 81 
                                        589************************************************************************* PP

                    S-AdoMet_synt_N  77 ekeelgfdaktcevlvaleeqs 98 
                                        +++++g+d++++ v+ ++++qs
  gene3097|gene3097|rna3097|rna3097  82 DDASTGMDYRSVLVIENISAQS 103
                                        *********************9 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 5.4
                    S-AdoMet_synt_N  29 ilkedpkarvace 41 
                                        ++k+d k++v++e
  gene3097|gene3097|rna3097|rna3097 169 FIKSDCKSQVTVE 181
                                        3444444444444 PP

>> AdoMet_Synthase  S-adenosylmethionine synthetase (AdoMet synthetase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   1.4e-05     0.031      22      51 ..      12      42 ..      10      67 .. 0.79
   2 ?   -1.2   0.0       0.3   6.7e+02     211     235 ..     148     172 ..      61     197 .. 0.52

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.4e-05
                                       EEE-TTSHHHHHHHHHHHHHHH.HHHHHHHH CS
                    AdoMet_Synthase 22 ErKGiGHPDsiaDgiaeavsra.lskeylek 51
                                       E  G GHPD+++D+ia+++  a lsk  l k
  gene3097|gene3097|rna3097|rna3097 12 ESVGKGHPDKLCDQIADRILDAyLSKDSLAK 42
                                       6679*************99765266666655 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.3
                                        EEEEEEGGG--SHHHHHHHHHHHHH CS
                    AdoMet_Synthase 211 vavalvdrlvkdleeYlevkeeike 235
                                        +++ l +r+v+++e+  ++ e ik+
  gene3097|gene3097|rna3097|rna3097 148 LTLMLANRIVEEIENLRKTYEFIKS 172
                                        2233333444444433333333333 PP

>> Glyco_hydro_79n  Glycosyl hydrolase family 79, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   2.4e-05     0.053     149     244 ..     164     259 ..     149     266 .. 0.88
   2 ?   -2.3   0.0      0.74   1.7e+03     185     214 ..     346     375 ..     336     385 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.4e-05
                    Glyco_hydro_79n 149 snaedlikytvskgykidswelGnelsgsgvgakveaeqyakdvielkkiveevykkseekPlvlaPggffdkeWf 224
                                        + + ++ik  ++++ +++  +  nel    +   v + q+a+d+ +  ++++e+   ++++P+ l P  +f +   
  gene3097|gene3097|rna3097|rna3097 164 RKTYEFIKSDCKSQVTVEYENRDNELVPLRIDNVVLSVQHAADLEKWTNVMNECVYGTSDQPSSLKPLELFRAFLR 239
                                        56788999999999999999999******************************9999999***********98887 PP

                    Glyco_hydro_79n 225 kelleksgekvvdvvthhiy 244
                                        k++ e+  e+ ++   +hi 
  gene3097|gene3097|rna3097|rna3097 240 KKIREVLPEELLKSTKYHIL 259
                                        77777777778888888885 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.74
                    Glyco_hydro_79n 185 aeqyakdvielkkiveevykkseekPlvla 214
                                         + y++ vi+  ki++ + ++ + +P+ ++
  gene3097|gene3097|rna3097|rna3097 346 VDTYGTGVIDNDKIIKIINENFDLRPKAIC 375
                                        578999999999999999999999998765 PP

>> Mei5_like  Putative double-strand recombination repair-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       1.4   3.1e+03      55      77 ..      90     112 ..      76     114 .. 0.86
   2 ?    8.8   0.0   0.00071       1.6      75     109 ..     207     242 ..     201     250 .. 0.85
   3 ?    1.0   0.0      0.18   4.1e+02      84     108 ..     358     382 ..     352     387 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.4
                          Mei5_like  55 yrKLkliekfkkknkdleeliek 77 
                                        yr   +ie  + +  d+ + +ek
  gene3097|gene3097|rna3097|rna3097  90 YRSVLVIENISAQSDDIRSAVEK 112
                                        88899999999999999999987 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00071
                          Mei5_like  75 iekwkevieeciiiLkke.felkakevfkafdLkky 109
                                         ekw +v++ec+   +++  +lk+ e+f+af  kk+
  gene3097|gene3097|rna3097|rna3097 207 LEKWTNVMNECVYGTSDQpSSLKPLELFRAFLRKKI 242
                                        69**********9888773689*********98887 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.18
                          Mei5_like  84 eciiiLkkefelkakevfkafdLkk 108
                                        + i i++++f+l++k +  a+ L+k
  gene3097|gene3097|rna3097|rna3097 358 KIIKIINENFDLRPKAICAALGLDK 382
                                        67999****************9998 PP

>> PB1  PB1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   0.00015      0.33      30      67 ..     165     202 ..     159     222 .. 0.78
   2 ?   -3.6   0.0       4.8   1.1e+04      27      42 ..     238     254 ..     238     257 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00015
                                        HHHHHHTST.CCSEEEEEEETTSSEEEESSHHHHHHHHH CS
                                PB1  30 kvekrfkls.dedvklkYpdedgdlVtitsDeDLeeale 67 
                                        k  + +k++ +++v++ Y+++d++lV++  D+ +   ++
  gene3097|gene3097|rna3097|rna3097 165 KTYEFIKSDcKSQVTVEYENRDNELVPLRIDN-VVLSVQ 202
                                        5566677777899***************9998.444444 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 4.8
                                        HHHHHHHHHTST.CCSE CS
                                PB1  27 Lrakvekrfkls.dedv 42 
                                        Lr+k++++++++  +++
  gene3097|gene3097|rna3097|rna3097 238 LRKKIREVLPEElLKST 254
                                        79999999998765555 PP

>> SapB_2  Saposin-like type B, region 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0      0.19   4.3e+02       4      11 ..     279     286 ..     279     287 .. 0.93
   2 ?   -1.3   0.1       1.1   2.6e+03       6      11 ..     345     350 ..     344     355 .. 0.89
   3 ?    7.4   0.0    0.0022       4.8      14      33 ..     359     380 ..     357     380 .. 0.77

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.19
                                        HHHHHHHH CS
                             SapB_2   4 kslVdqYg 11 
                                        k++Vd+Yg
  gene3097|gene3097|rna3097|rna3097 279 KTIVDTYG 286
                                        89*****8 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.1
                                        HHHHHH CS
                             SapB_2   6 lVdqYg 11 
                                        +Vd+Yg
  gene3097|gene3097|rna3097|rna3097 345 YVDTYG 350
                                        8****9 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.0022
                                        HHCCHCTT..--HHHHHHHTTS CS
                             SapB_2  14 iiqlLlse..ldPkevCtalgl 33 
                                        ii+ + ++  l Pk++C+algl
  gene3097|gene3097|rna3097|rna3097 359 IIKIINENfdLRPKAICAALGL 380
                                        666666666677*********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (409 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       646  (0.036031); expected 358.6 (0.02)
Passed bias filter:                      538  (0.0300073); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.44
# Mc/sec: 2807.08
//
Query:       gene3098|gene3098|rna3098|rna3098  [L=172]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       572  (0.0319036); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 1143.73
//
Query:       gene3099|gene3099|rna3099|rna3099  [L=859]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-13   50.0  10.2    2.8e-13   50.0  10.2    1.9  2  MIF4G     MIF4G domain
      0.003   16.9   0.1     0.0081   15.4   0.1    1.8  1  UvdE      UV-endonuclease UvdE
  ------ inclusion threshold ------
       0.13   12.1   0.2        2.2    8.2   0.0    2.8  3  DUF4939   Domain of unknown function (DUF4939)
        2.6    8.6   9.9       0.28   11.7   1.1    3.5  3  CDT1_C    DNA replication factor Cdt1 C-terminal domain


Domain annotation for each model (and alignments):
>> MIF4G  MIF4G domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.1      0.57   2.6e+03      13      49 ..     329     365 ..     324     395 .. 0.77
   2 !   50.0  10.2   6.2e-17   2.8e-13       8     207 ..     445     657 ..     440     659 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.57
                                        TTTHHHHHHHHHHHHHCSCHHHHHHHHHHHHHHHHHC CS
                              MIF4G  13 kenfevlikqllklamdddknelkevielifekavee 49 
                                        k+nf+v+  +l + a ++++n +ke++  ++++ ++e
  gene3099|gene3099|rna3099|rna3099 329 KTNFHVCFLDLHDEAVTLNENFRKEFYGKFMKILEDE 365
                                        4788888888888888888888888877777766655 PP

  == domain 2  score: 50.0 bits;  conditional E-value: 6.2e-17
                                        HHCHTTTTHHHHHHHHHHHHHCSCHHHHHHHHHHHHHHHHHCGGGHHHHHHHHHHHHHHSH...........HHHH CS
                              MIF4G   8 lnklskenfevlikqllklamdddknelkevielifekaveepsfsplyarlcgklnsrfq...........qnFr 72 
                                        ln+++ +n ++ i+ + +l+    ++e+k+  e++feka++e  f+ lya ++++l+++f+           + F 
  gene3099|gene3099|rna3099|rna3099 445 LNRIAWTNCNSTIERIKRLKVRR-DDEIKKMAEILFEKAISEEAFCKLYAFVVQNLYKTFRsdeerrrsdtkSVFF 519
                                        78888888899999999999998.79**********************************************9999 PP

                                        HHHHHHHHHHHHHHC....................-S-HHHHHHHHHHHHHHHHHHHHHHHHHHTTSSEHHHHHHH CS
                              MIF4G  73 ikllnklqeefekry....................eleneleenedgnrrrrlglvrflgelfklkmltskilldc 128
                                        + l+  +q  + +++                    e  + +++++++++ r+lg+v+f++ l+ + ++  k +  c
  gene3099|gene3099|rna3099|rna3099 520 TTLIKLCQNILHSKEkwskahdlstlsmeeritmeETLENENIEKEVKKGRMLGTVKFISLLYSYTIIGFKGISAC 595
                                        988888888888777889****************9888888999******************************** PP

                                        HHHHHHGGCCCCSCCHSCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCHCSSSSHHHHHHHHH CS
                              MIF4G 129 lkellssltketaddppqdleeieilltllttigktlennekakkeldqffkriqkiledatrqelssrirfmlkd 204
                                        + +ll+  ++           ++e l+ ll ++g+++     +++el + ++ +++ ++     + s rirfm++d
  gene3099|gene3099|rna3099|rna3099 596 ISSLLDLDDE----------QNVETLCALLSNCGEKMV-QSGKHAELINVMNMLRQ-KR-----QWSNRIRFMVCD 654
                                        *******999..........99****************.77777777776665544.33.....459********9 PP

                                        HHH CS
                              MIF4G 205 lie 207
                                        ++e
  gene3099|gene3099|rna3099|rna3099 655 ILE 657
                                        976 PP

>> UvdE  UV-endonuclease UvdE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1   1.8e-06    0.0081     159     236 ..     368     451 ..     363     489 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.8e-06
                               UvdE 159 keaalerfkenikrlpdsvker...lvLENDdksytvadlLpvceelniPlVlDyHHhnvldlreesldeslp... 228
                                        +++  e++ + ++++ +s+k++   +v    d+ ytv+++L + e+ ++P+ +D   +  +++re  +d       
  gene3099|gene3099|rna3099|rna3099 368 QKDVGEKYIKSLQDIRKSLKSKydnVVRKDVDVRYTVEEILAIKERAEVPINVDKTIFATVPRRERREDAISLfrl 443
                                        4567899999999999999987332566666*******************************99999887654211 PP

                               UvdE 229 lveriveT 236
                                         ++ri+ T
  gene3099|gene3099|rna3099|rna3099 444 ELNRIAWT 451
                                        23344444 PP

>> DUF4939  Domain of unknown function (DUF4939)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.28   1.3e+03      37      69 ..     489     521 ..     463     530 .. 0.69
   2 ?   -1.0   0.0      0.35   1.6e+03      16      28 ..     638     650 ..     627     689 .. 0.65
   3 ?    8.2   0.0    0.0005       2.2      79     103 ..     731     755 ..     727     760 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.28
                            DUF4939  37 drlpefivqtlsymlv.dektfssdalkvtflit 69 
                                         +l  f+vq l   +  de+   sd+  v f+ t
  gene3099|gene3099|rna3099|rna3099 489 CKLYAFVVQNLYKTFRsDEERRRSDTKSV-FFTT 521
                                        488899***99887761555556665555.4444 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.35
                            DUF4939  16 lrqkrrwrnpipf 28 
                                        lrqkr+w+n i f
  gene3099|gene3099|rna3099|rna3099 638 LRQKRQWSNRIRF 650
                                        4566666666655 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.0005
                            DUF4939  79 vlpyikkdspllndyraflaemkrv 103
                                        v+  i +d p +ndy+a+++emk+ 
  gene3099|gene3099|rna3099|rna3099 731 VMSRIIEDVPHVNDYTALVNEMKER 755
                                        68889999***************85 PP

>> CDT1_C  DNA replication factor Cdt1 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   1.1   6.2e-05      0.28      14      73 ..     109     175 ..      94     184 .. 0.83
   2 ?   -2.1   1.1       1.2   5.3e+03       9      30 ..     196     225 ..     194     252 .. 0.50
   3 ?   -0.0   0.0      0.27   1.2e+03       9      45 ..     697     740 ..     693     765 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 6.2e-05
                             CDT1_C  14 a.......laamtreeelerrsallgrlpdvarilrllfvaekksalpmeevvkklkdSlrtpvske 73 
                                                 ++ t+e++   +s l++rl++  ri     v e++  + +++++k++ ++++t + +e
  gene3099|gene3099|rna3099|rna3099 109 EgesteeaSEESTKEPSHDNESLLSERLASTLRIAGETRVNEERLKIAIQKATKQIDNASKTVMVAE 175
                                        3444443356699************************************************988665 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.2
                             CDT1_C   9 Kearqa........laa.mtreeelerrsal 30 
                                        Ke+r+a          +  ++  e+e+r+a 
  gene3099|gene3099|rna3099|rna3099 196 KEQRRAveqpgaalP-SqTVTATEQEQRRAV 225
                                        666666544443321.133444444444444 PP

  == domain 3  score: -0.0 bits;  conditional E-value: 0.27
                             CDT1_C   9 Kearqa.......laamtreeelerrsallgrlpdvarilrllf 45 
                                        Ke r a       +++++   +++r+s ll  +  + ri+  + 
  gene3099|gene3099|rna3099|rna3099 697 KESRPAvehgtvpAQQAPAGNSKQRESLLLDTIDVMSRIIEDVP 740
                                        56666666666666778888889999999999999999998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (859 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1746  (0.0973841); expected 358.6 (0.02)
Passed bias filter:                      573  (0.0319594); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.91u 0.35s 00:00:01.26 Elapsed: 00:00:00.56
# Mc/sec: 4640.69
//
Query:       gene31|gene31|rna31|rna31  [L=383]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.4e-25   87.2  13.7    4.6e-07   30.4   0.4    7.2  7  WD40         WD domain, G-beta repeat
    1.7e-13   50.6   0.2       0.01   16.1   0.4    4.5  4  ANAPC4_WD40  Anaphase-promoting complex subunit 4 WD40 domain
      1e-07   31.6   0.0     0.0021   17.4   0.0    3.9  3  WD40_like    WD40-like domain
    3.9e-06   26.9   0.8       0.14   12.0   0.0    3.3  3  eIF2A        Eukaryotic translation initiation factor eIF2A


Domain annotation for each model (and alignments):
>> WD40  WD domain, G-beta repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.2   0.0    0.0047        21      12      38 .]      59      94 ..      49      94 .. 0.62
   2 !   13.7   0.0     2e-05     0.089       5      37 ..     102     135 ..      98     136 .. 0.91
   3 !    8.3   0.0     0.001       4.6       6      36 ..     144     173 ..     139     175 .. 0.77
   4 !   20.4   0.1   1.5e-07   0.00067       6      38 .]     183     216 ..     179     216 .. 0.83
   5 !    8.9   0.1   0.00068         3       3      35 ..     222     254 ..     220     255 .. 0.84
   6 ?    2.5   0.0     0.071   3.2e+02      13      34 ..     273     316 ..     260     317 .. 0.68
   7 !   30.4   0.4     1e-10   4.6e-07       2      38 .]     324     361 ..     323     361 .. 0.93

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0047
                               S..EEEEE.......EETTSSEEEEEETTSEEEEEE CS
                       WD40 12 s..vtsla.......fspdgawlasGsdDgtvriWd 38
                               +  ++ ++       f pdg+ l+sG+  g   +W+
  gene31|gene31|rna31|rna31 59 HvsINKMRcpinivrFTPDGRRLISGTSTGEFTLWN 94
                               333333334455555***********6577777776 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 2e-05
                                EEEESS.SSEEEEEEETTSSEEEEEETTSEEEEE CS
                       WD40   5 rtltGH.ssvtslafspdgawlasGsdDgtvriW 37 
                                ++l +H s+v++l f + g++l+s++  gtv++W
  gene31|gene31|rna31|rna31 102 TILQAHeSPVRGLEFTRLGDLLLSADTTGTVKFW 135
                                5789**999****************88******* PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.001
                                EEESS.SSEEEEEEETTSSEEEEEETTSEEEE CS
                       WD40   6 tltGH.ssvtslafspdgawlasGsdDgtvri 36 
                                +   H   ++++  s   ++++++sdD tvr+
  gene31|gene31|rna31|rna31 144 IRQCHeEAIRDM--SVADNYFVTASDDSTVRV 173
                                556786668888..778889999********8 PP

  == domain 4  score: 20.4 bits;  conditional E-value: 1.5e-07
                                EEESSSS.EEEEEEETTSSEEEEEETTSEEEEEE CS
                       WD40   6 tltGHss.vtslafspdgawlasGsdDgtvriWd 38 
                                +l+GH++ v+  +++p ++++asG++D+ v++Wd
  gene31|gene31|rna31|rna31 183 VLRGHNWdVRVAQYNPVSSLVASGGKDNLVKLWD 216
                                689**667844448999999*************9 PP

  == domain 5  score: 8.9 bits;  conditional E-value: 0.00068
                                EEEEEESS.SSEEEEEEETTSSEEEEEETTSEEE CS
                       WD40   3 clrtltGH.ssvtslafspdgawlasGsdDgtvr 35 
                                c+ t   H + v + ++ +d ++l+ +++D+ ++
  gene31|gene31|rna31|rna31 222 CVATMHCHkNTVLCARWIDDMNLLT-AGKDQVIK 254
                                899999**888****8888889885.677*9998 PP

  == domain 6  score: 2.5 bits;  conditional E-value: 0.071
                                EEEEE..................EETTSSE....EEEEETTSEE CS
                       WD40  13 vtsla..................fspdgaw....lasGsdDgtv 34 
                                vt+l+                  fs ++++    +a+G+ Dg++
  gene31|gene31|rna31|rna31 273 VTALCvmngcmdsstissasttnFSCNSPLrsglFAAGMADGSI 316
                                66666666555566666666777777777777767889889997 PP

  == domain 7  score: 30.4 bits;  conditional E-value: 1e-10
                                EEEEEEESS.SSEEEEEEETTSSEEEEEETTSEEEEEE CS
                       WD40   2 qclrtltGH.ssvtslafspdgawlasGsdDgtvriWd 38 
                                q++ + +GH s v+s++++p g+++asGs+D++vr+W+
  gene31|gene31|rna31|rna31 324 QNMCVVSGHeSTVWSIDYHPIGHLMASGSMDQSVRFWS 361
                                6778899**888*************************5 PP

>> ANAPC4_WD40  Anaphase-promoting complex subunit 4 WD40 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.6   0.0    0.0044        20      36      67 ..      64      95 ..      49     100 .. 0.84
   2 !    8.3   0.0   0.00063       2.8      35      71 ..     105     141 ..      96     160 .. 0.81
   3 !   16.1   0.4   2.3e-06      0.01      13      90 ..     165     239 ..     160     241 .. 0.87
   4 !   14.7   0.0   6.2e-06     0.028       9      81 ..     306     376 ..     302     382 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0044
                ANAPC4_WD40 36 kedsevrsLaWkpdgklLavaysdgevrllda 67
                               k    ++ +++ pdg+ L  ++s ge  l ++
  gene31|gene31|rna31|rna31 64 KMRCPINIVRFTPDGRRLISGTSTGEFTLWNS 95
                               556788999*****************998876 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00063
                ANAPC4_WD40  35 dkedsevrsLaWkpdgklLavaysdgevrlldaesgk 71 
                                ++++s vr+L++   g lL  a   g+v++ + +  +
  gene31|gene31|rna31|rna31 105 QAHESPVRGLEFTRLGDLLLSADTTGTVKFWHLSMNN 141
                                45899************************99987655 PP

  == domain 3  score: 16.1 bits;  conditional E-value: 2.3e-06
                ANAPC4_WD40  13 atedgellvfRlngqrvwtleedkedsevrsLaWkpdgklLavaysdgevrlldaesgkvvhslsvksekavtclgWg 90 
                                a++d+ ++v+ ++ +  + l   +++  vr  +++p  +l a + +d+ v+l d  ++ +v +++++++ +v c  W 
  gene31|gene31|rna31|rna31 165 ASDDSTVRVHSFEKNACVVL--RGHNWDVRVAQYNPVSSLVASGGKDNLVKLWDTRTKGCVATMHCHKN-TVLCARWI 239
                                66777777877777777777..67888999999**********************************99.6******7 PP

  == domain 4  score: 14.7 bits;  conditional E-value: 6.2e-06
                ANAPC4_WD40   9 LiAlatedgellvfRlngqrvwtleedkedsevrsLaWkpdgklLavaysdgevrlldaesgkvvhslsvkse 81 
                                L+A +++dg+++   +  q++  +  ++++s+v s+ ++p g+l+a +  d +vr+ +  ++++ ++++ ++e
  gene31|gene31|rna31|rna31 306 LFAAGMADGSIAHLQTFNQNMCVV--SGHESTVWSIDYHPIGHLMASGSMDQSVRFWSWRKEEINEEIENNEE 376
                                778888888887666666666666..6899*********************************9999887765 PP

>> WD40_like  WD40-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.6   0.0    0.0019       8.7      73     130 ..      57     117 ..      33     190 .. 0.60
   2 !   17.4   0.0   4.7e-07    0.0021       7      93 ..     195     281 ..     189     288 .. 0.92
   3 ?    1.8   0.0     0.027   1.2e+02       2      40 ..     335     373 ..     307     378 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0019
                  WD40_like  73 eeevenekieedistvkvidd..klliGtnkGsiyvfsk.dlqleevllgqsseIkeikie 130
                                 e+v+++k+   i +v+ + d  +l+ Gt++G+  +++   +++e++l  ++s+++ ++ +
  gene31|gene31|rna31|rna31  57 AEHVSINKMRCPINIVRFTPDgrRLISGTSTGEFTLWNSfSFNFETILQAHESPVRGLEFT 117
                                4566666666666666655332266777777777775442566777777777777766654 PP

  == domain 2  score: 17.4 bits;  conditional E-value: 4.7e-07
                  WD40_like   7 diskkgslilyGgkddkctvlkleslesvsivesfedSvifvklldddlilvvtlDGtillslleneeevenekieedistvkv 90 
                                ++++ +sl++ Ggkd+ +++ +++++  v  ++  ++ v+ ++ +dd  +l +  D  i +s l+      + k + +++  +v
  gene31|gene31|rna31|rna31 195 QYNPVSSLVASGGKDNLVKLWDTRTKGCVATMHCHKNTVLCARWIDDMNLLTAGKDQVIKQSELRMLRDNFTYKCKKEVTALCV 278
                                578889*****************************************************9999998887788999999999999 PP

                  WD40_like  91 idd 93 
                                +++
  gene31|gene31|rna31|rna31 279 MNG 281
                                875 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.027
                  WD40_like   2 eiYsidiskkgslilyGgkddkctvlkleslesvsives 40 
                                 ++sid+ + g+l++ G+ d+ ++  + + +e+   +e+
  gene31|gene31|rna31|rna31 335 TVWSIDYHPIGHLMASGSMDQSVRFWSWRKEEINEEIEN 373
                                589999999999999999999999998888877666665 PP

>> eIF2A  Eukaryotic translation initiation factor eIF2A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.0   3.2e-05      0.14      50     169 ..      56     173 ..      49     178 .. 0.77
   2 !   11.6   0.1   4.1e-05      0.19      85     161 ..     173     247 ..     162     254 .. 0.83
   3 ?   -0.6   0.0      0.24   1.1e+03      63      96 ..     337     368 ..     310     377 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3.2e-05
                                -EEECCEES.SS.EEEEEE-TTSS-EEEEESSSSCEEEEEEC...SCEEEEEEEEES--EEEE-TTSSEEEEE-TTSSS-EEEE CS
                      eIF2A  50 ksevvelkk.egpihdvaWspkskefaviyGkmpakvslfdl...kvkviskleeqkrNtiffspkgklvllaGfgnlaGelei 129
                                + e v+++k   pi  v   p+++++  i G +  + +l+++   + + i + +e++   + f   g l+l a   ++ G++++
  gene31|gene31|rna31|rna31  56 HAEHVSINKmRCPINIVRFTPDGRRL--ISGTSTGEFTLWNSfsfNFETILQAHESPVRGLEFTRLGDLLLSA---DTTGTVKF 134
                                45556665523568888888888875..899999999998876668999999999999999999999999998...68899999 PP

                                EETTTTEEEEEEE-TT--EEEE-TTSSEEEEEE-TTT-SS CS
                      eIF2A 130 wdvkkkkkiakaeaanatlvewspdgryvlTattaprlrv 169
                                w  + ++++   ++ +    + s +++y++Ta+    +rv
  gene31|gene31|rna31|rna31 135 WHLS-MNNVGIRQCHEEAIRDMSVADNYFVTASDDSTVRV 173
                                9987.45555556666667899999999999998877777 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 4.1e-05
                                EEEEECSCEEEEEEEEES--EEEE-TTSSEEEEE-TTSSS-EEEEEETTTTEEEEEEE.-TT--EEEE-TTSSEEEEE CS
                      eIF2A  85 vslfdlkvkviskleeqkrNtiffspkgklvllaGfgnlaGeleiwdvkkkkkiakae.aanatlvewspdgryvlTa 161
                                v+ f++++ v+ + ++       ++p   lv+ +G  nl   +++wd+ +k ++a+++ ++n++l+    d++ +lTa
  gene31|gene31|rna31|rna31 173 VHSFEKNACVVLRGHNWDVRVAQYNPVSSLVASGGKDNL---VKLWDTRTKGCVATMHcHKNTVLCARWIDDMNLLTA 247
                                55577777777777777888899****************...**************9846789999877788888887 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.24
                                EEEEE-TTSS-EEEEESSSSCEEEEEECSCEEEE CS
                      eIF2A  63 hdvaWspkskefaviyGkmpakvslfdlkvkvis 96 
                                  + + p ++  ++  G m+++v +++ + + i 
  gene31|gene31|rna31|rna31 337 WSIDYHPIGH--LMASGSMDQSVRFWSWRKEEIN 368
                                3333333333..3457888888888877655554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (383 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       548  (0.030565); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.69u 0.37s 00:00:01.06 Elapsed: 00:00:00.59
# Mc/sec: 1952.45
//
Query:       gene310|gene310|rna310|rna310  [L=415]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.2e-08   32.7   1.1    8.2e-08   32.7   1.1    2.4  2  PCI       PCI domain
  ------ inclusion threshold ------
        1.1   10.3   9.9         12    6.9   3.0    3.5  4  RAC_head  Ribosome-associated complex head domain


Domain annotation for each model (and alignments):
>> PCI  PCI domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.7   1.1   9.1e-12   8.2e-08      32     105 .]     303     376 ..     256     376 .. 0.84
   2 ?   -2.8   0.1         1   9.3e+03      38      53 ..     391     406 ..     384     409 .. 0.74

  Alignments for each domain:
  == domain 1  score: 32.7 bits;  conditional E-value: 9.1e-12
                                    HTTHHHHHHHHHHHHHHHHHHHHHHCESEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSSSEEEETTTTEEEECS CS
                            PCI  32 ddglaqllesLekkvrerllrqvskiyssislerlaklldlsvdevEkilvklIrdgeirakidqesgivvfkk 105
                                    ++ ++ + ++  + +  ++lr +s++  si++++l+ ll  + +++ + +++ +++  +++kidq++g+v+f++
  gene310|gene310|rna310|rna310 303 RRINSSYEKEILEAINDHNLRIISRFCASITFADLSALLMSPLNKCVEKICDEVNNHDLQCKIDQNNGVVFFEN 376
                                    4445558889999999*******************************************************985 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1
                                    HHHHHHHHHHHHHHHH CS
                            PCI  38 llesLekkvrerllrq 53 
                                     +++ ++++r+++l++
  gene310|gene310|rna310|rna310 391 NVDKAVMNIRKETLKR 406
                                    4678888999988875 PP

>> RAC_head  Ribosome-associated complex head domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       1.4   1.3e+04      52      63 ..     167     178 ..     161     206 .. 0.61
   2 ?    6.9   3.0    0.0014        12       1      62 [.     260     318 ..     259     324 .. 0.74
   3 ?   -1.8   0.0      0.74   6.6e+03      46      59 ..     349     362 ..     344     370 .. 0.87
   4 ?    5.9   0.0    0.0029        26      27      61 ..     373     407 ..     364     415 .] 0.86

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.4
                                    H--HHHHHHHHH CS
                       RAC_head  52 klddeeLaelae 63 
                                    k++++ L++ + 
  gene310|gene310|rna310|rna310 167 KVKKKHLEAAND 178
                                    333333333333 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0014
                                    XXXXXXXX-HHHHHHHHHHHHHHHTGGGSSSS--.HHHHHHHHHHHHHHHHH--HHHHHHHH CS
                       RAC_head   1 KKaKeaaKkalKKekralrgavkdanYFadgeaekakvidkvLedvdllieklddeeLaela 62 
                                    +K+K +  ++l K+k ++ ++ k+ +YF   + e  ++ ++v+  + ++ ++ ++e L++++
  gene310|gene310|rna310|rna310 260 RKEKAEYLEKLHKNKYNVEEIRKQIDYF--RSIELIDK-ENVMLVLRRINSSYEKEILEAIN 318
                                    688888889999****************..44443333.56777777777777766666655 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 0.74
                                    HHHHHHH--HHHHH CS
                       RAC_head  46 vdllieklddeeLa 59 
                                    v+++++++++ +L+
  gene310|gene310|rna310|rna310 349 VEKICDEVNNHDLQ 362
                                    89999999999997 PP

  == domain 4  score: 5.9 bits;  conditional E-value: 0.0029
                                    GGSSSS--.HHHHHHHHHHHHHHHHH--HHHHHHH CS
                       RAC_head  27 YFadgeaekakvidkvLedvdllieklddeeLael 61 
                                    +F+++e++ + +i++vL +vd+ + ++ +e L+  
  gene310|gene310|rna310|rna310 373 FFENTEESYPGMINQVLLNVDKAVMNIRKETLKRQ 407
                                    899999999********************999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (415 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1552  (0.0865637); expected 358.6 (0.02)
Passed bias filter:                      532  (0.0296726); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.64u 0.35s 00:00:00.99 Elapsed: 00:00:00.53
# Mc/sec: 2345.10
//
Query:       gene3100|gene3100|rna3100|rna3100  [L=408]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.9e-38  130.5  38.7    7.2e-30  104.2  14.3    2.1  2  Sugar_tr  Sugar (and other) transporter
    6.7e-13   48.3  31.7    6.7e-13   48.3  31.7    1.8  2  MFS_1     Major Facilitator Superfamily


Domain annotation for each model (and alignments):
>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.2  16.8   5.9e-12   5.3e-08      61     191 ..      77     201 ..      31     204 .. 0.81
   2 !  104.2  14.3   8.1e-34   7.2e-30     238     443 ..     212     403 ..     200     405 .. 0.91

  Alignments for each domain:
  == domain 1  score: 32.2 bits;  conditional E-value: 5.9e-12
                                        HHHHHHHHHHHHTTHHHHHHH..HHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHHHHHHHHTTS-SC CS
                           Sugar_tr  61 iGslfagllgdrfGRkkslli..aavlfvigavlqaaakgknsvevlivgRvlvGigvGlasvlvPmyisEiApkk 134
                                        i+ l++++l + +  k  l i  + +l +i+a+  ++      + vl++ R ++G++vGl +++vP y+s + +k+
  gene3100|gene3100|rna3100|rna3100  77 ISPLISSMLYNHINMKLNLWIglVLLLHSISAIGLMMPY----ILVLYAFRCVAGVAVGLSTAVVPQYVSRL-KKH 147
                                        555666777777777777777334455567777777766....99*************************99.899 PP

                                        CHHHHHHHHHHHHHHHHHHHHHHHHHHHTSS-TTHHHHHHHCCHHHHHHHHHHGGGS CS
                           Sugar_tr 135 lRgalvslyqlaitfGilvaaifglglnktsnadgwrillglqlvpallllilllfl 191
                                         Rg+++ l+q++i +Gil+++i+ + ++++     +ri +++ +++ ++++ + +f+
  gene3100|gene3100|rna3100|rna3100 148 RRGFFTFLFQVSILTGILIGQILSYYTSTVFL---FRIIFAVFSFFNVMFAGMSFFI 201
                                        99******************************...************6666665665 PP

  == domain 2  score: 104.2 bits;  conditional E-value: 8.1e-34
                                        ....HTTHHHHSH...HHHHHHHHHHHHHHTTHHHHHHHTTTHHHHSS-THHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           Sugar_tr 238 ekaswkellssktvrqrlligvvlqifqqltGinaimyysptifenlglsksllvtiivgvvnfvatfvaiflvdr 313
                                        e+  + +ll  k + + +l+++ ++i+qq+tGin i+ ys t++e+   +++ + ti +g    v+t+v++ +vd 
  gene3100|gene3100|rna3100|rna3100 212 ESRGITSLLAHKRHIKSVLLALCIHIGQQMTGINGIIVYSNTLLEENPGNPQ-MRTIFIGLFSLVVTLVSAAFVDV 286
                                        3455777888878899*******************************99999.*********************** PP

                                        S-SHHHHHHHHHHHHHHHHHHH..HHHHTTSS...CHHHHHHHHHHHHHHHTTTTHHHHHHHHHHSHTTTHHHHHH CS
                           Sugar_tr 314 fGRRtllllGaagmaicfvilgivalllvakskaasivaivfialfialfalgwgpvpwvlvsElfpqsvRskala 389
                                        fGR+ lll+++++  + +++l+      ++        +++ ++ f + +++g+gp+ w+l  Elfp++  ++a +
  gene3100|gene3100|rna3100|rna3100 287 FGRKFLLLFSSTIVGASLILLT------TK------KYVLASVLAFQFGYSVGLGPITWLLTNELFPLNYLQAANS 350
                                        ***********99999998887......33......35778899999***************************** PP

                                        HHHHHHHHHHHHHHHHHHHHHCHHHT-HHHHHHHHHHHHHHHHHHHHS--STT- CS
                           Sugar_tr 390 iavavnwlanflisllfpiiteaigggyvflvfaglavlfiifvfffvpetkgr 443
                                        i+v++nwl+ fl+ + f +   ++g     +++++++++f+ + ff + etkg+
  gene3100|gene3100|rna3100|rna3100 351 ICVTTNWLCAFLVVIGFEYSYLRVG-NALLWFYVCCMAVFTAIFFFYYNETKGK 403
                                        *************************.9999**********************98 PP

>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.3  31.7   7.4e-17   6.7e-13      24     351 ..      59     362 ..      26     364 .. 0.72
   2 ?   -2.2   2.4      0.16   1.4e+03     204     228 ..     373     395 ..     357     403 .. 0.49

  Alignments for each domain:
  == domain 1  score: 48.3 bits;  conditional E-value: 7.4e-17
                              MFS_1  24 aedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllll.fasslwlllvlrvlqGlg 98 
                                        +++l+ +  e+  l++l ++  +++s+++ ++  ++   ++ l+ ll ++++  ++l + + + +l+++r+++G++
  gene3100|gene3100|rna3100|rna3100  59 GNALH-TLKEYYVLASLLFISPLISSMLYNHINMKL-NLWIGLVLLLHSISA--IGLmM-PYILVLYAFRCVAGVA 129
                                        44444.566666688888888888888888887777.444444444444444..55525.6667************ PP

                              MFS_1  99 agalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsllafvlfllllpe 174
                                         g++++++  +++++ ++ +rg+ + l+++++  G+++g +l+ + ++ + +r +f ++ ++ +++   ++ ++ +
  gene3100|gene3100|rna3100|rna3100 130 VGLSTAVVPQYVSRLKKH-RRGFFTFLFQVSILTGILIGQILSYYTSTVFLFRIIFAVFSFFNVMF--AGMSFFIQ 202
                                        **************9988.***********************************************..556***** PP

                              MFS_1 175 epperkrkspkeeekgtgpaplvpawkallkdpvlw....illialllfffgfsglltllplylqevlglsgllla 246
                                        +p e ++ ++ +              ++l +++++     +l i++   ++g++g+ +++ ++l e  g +   + 
  gene3100|gene3100|rna3100|rna3100 203 KPAETETRRESRG----IT-------SLLAHKRHIKsvllALCIHIGQQMTGINGIIVYSNTLLEENPGNP--QMR 265
                                        ********99999....44.......44444554431111344444444778888********99999999..666 PP

                              MFS_1 247 glllallalvgailallagrlsdrlgrrrrlllallllllaalglallavtssavllllvlvliGfglgfv.fpsl 321
                                        +++++l++lv+    l++++++d +gr    +l l++ +++ ++l+ll +  ++vl+   ++ + fg+++   p+ 
  gene3100|gene3100|rna3100|rna3100 266 TIFIGLFSLVV---TLVSAAFVDVFGR---KFLLLFSSTIVGASLILLTTK-KYVLAS--VLAFQFGYSVGlGPIT 332
                                        669*******9...99********997...334444444444444444444.333433..3334554444448999 PP

                              MFS_1 322 lalasdlappeeagtasglfntagslggal 351
                                        + l+++l+p ++  +a+++  t++ l ++l
  gene3100|gene3100|rna3100|rna3100 333 WLLTNELFPLNYLQAANSICVTTNWLCAFL 362
                                        999999999999999999999888887776 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.16
                              MFS_1 204 lkdpvlwillialllfffgfsgllt 228
                                        +  + l  l++ +++++++++++++
  gene3100|gene3100|rna3100|rna3100 373 RVGNAL--LWFYVCCMAVFTAIFFF 395
                                        333433..33333333322222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (408 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1054  (0.0587874); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.26s 00:00:00.84 Elapsed: 00:00:00.43
# Mc/sec: 2828.26
//
Query:       gene3101|gene3101|rna3101|rna3101  [L=132]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.5e-12   45.2  25.4      0.015   16.1   0.3    4.2  4  zf-C2H2_4       C2H2-type zinc finger
      1e-10   41.4  24.5     0.0024   18.2   1.7    4.2  4  zf-C2H2         Zinc finger, C2H2 type
    1.8e-05   24.9  20.8      0.011   16.0   1.8    4.0  4  zf-C2H2_jaz     Zinc-finger double-stranded RNA-binding
    0.00081   19.7   2.7    0.00081   19.7   2.7    4.7  5  zf-H2C2_2       Zinc-finger double domain
     0.0019   18.6  11.9       0.71   10.3   0.2    3.9  3  zf-met          Zinc-finger of C2H2 type
     0.0026   18.0   4.1     0.0026   18.0   4.1    2.1  2  zf-C2H2_8       C2H2-type zinc ribbon
     0.0079   16.4   5.9      0.096   12.9   2.1    2.5  2  C1_4            TFIIH C1-like domain
     0.0083   15.7   8.0        1.5    8.5   0.2    3.2  3  zf_C2H2_ZHX     Zinc-fingers and homeoboxes C2H2 finger domai
      0.009   15.7   3.7      0.009   15.7   3.7    2.0  2  zf-SNAP50_C     snRNA-activating protein of 50kDa MW C termin
  ------ inclusion threshold ------
      0.046   13.7   0.1      0.046   13.7   0.1    4.0  4  zf-C2H2_6       C2H2-type zinc finger
      0.046   13.5   0.2      0.046   13.5   0.2    4.5  4  zf-C2H2_11      zinc-finger C2H2-type
       0.26   11.2  17.4       0.41   10.6   3.1    3.1  2  Zn_ribbon_SprT  SprT-like zinc ribbon domain
        5.9    7.1  17.2        7.1    6.9   0.1    4.5  4  zf-AN1          AN1-like Zinc finger


Domain annotation for each model (and alignments):
>> zf-C2H2_4  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.3   1.1e-05     0.015       1      23 [.       8      30 ..       8      31 .. 0.94
   2 !   15.8   2.2   1.3e-05     0.018       1      22 [.      35      56 ..      35      58 .. 0.94
   3 !   14.1   0.5   4.7e-05     0.064       4      23 ..      63      82 ..      61      83 .. 0.91
   4 !   13.6   3.2   6.8e-05     0.093       1      24 []     105     128 ..     105     128 .. 0.98

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.1e-05
                          zf-C2H2_4  1 fkCpiCgksFsskkaLlrHlkth 23
                                       f C iC+++++s k+L+ H   h
  gene3101|gene3101|rna3101|rna3101  8 FACLICQRNYPSEKSLNYHKIIH 30
                                       89*****************9887 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 1.3e-05
                          zf-C2H2_4  1 fkCpiCgksFsskkaLlrHlkt 22
                                       ++C+ C ksF  +++L++Hl t
  gene3101|gene3101|rna3101|rna3101 35 YYCEKCEKSFFYSDKLKKHLIT 56
                                       89*****************986 PP

  == domain 3  score: 14.1 bits;  conditional E-value: 4.7e-05
                          zf-C2H2_4  4 piCgksFsskkaLlrHlkth 23
                                       + Cg++F +kk + rH++ h
  gene3101|gene3101|rna3101|rna3101 63 CSCGRVFVRKKWYDRHMEEH 82
                                       48****************99 PP

  == domain 4  score: 13.6 bits;  conditional E-value: 6.8e-05
                          zf-C2H2_4   1 fkCpiCgksFsskkaLlrHlkthH 24 
                                        fkC++C+k  + +k+L  H +t+H
  gene3101|gene3101|rna3101|rna3101 105 FKCRHCKKGMKKRKTLEVHEQTVH 128
                                        8*********************99 PP

>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.3   0.00023      0.32       1      23 []       8      30 ..       8      30 .. 0.95
   2 !   18.2   1.7   1.7e-06    0.0024       1      21 [.      35      55 ..      35      56 .. 0.94
   3 !   14.4   0.3   2.8e-05     0.038       5      23 .]      64      82 ..      55      82 .. 0.83
   4 !   11.7   3.4   0.00021      0.29       1      23 []     105     128 ..     105     128 .. 0.97

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00023
                                       EEETTTTEEESSHHHHHHHHHCC CS
                            zf-C2H2  1 ykCpdCgksFkrksnLkrHirtH 23
                                       + C +C + +++  +L+ H  +H
  gene3101|gene3101|rna3101|rna3101  8 FACLICQRNYPSEKSLNYHKIIH 30
                                       78*****************9988 PP

  == domain 2  score: 18.2 bits;  conditional E-value: 1.7e-06
                                       EEETTTTEEESSHHHHHHHHH CS
                            zf-C2H2  1 ykCpdCgksFkrksnLkrHir 21
                                       y+C++C ksF  ++ Lk+H+ 
  gene3101|gene3101|rna3101|rna3101 35 YYCEKCEKSFFYSDKLKKHLI 55
                                       99*****************86 PP

  == domain 3  score: 14.4 bits;  conditional E-value: 2.8e-05
                                       TTTEEESSHHHHHHHHHCC CS
                            zf-C2H2  5 dCgksFkrksnLkrHirtH 23
                                        Cg++F rk  + rH+  H
  gene3101|gene3101|rna3101|rna3101 64 SCGRVFVRKKWYDRHMEEH 82
                                       69**************998 PP

  == domain 4  score: 11.7 bits;  conditional E-value: 0.00021
                                        EEETTTTEEESSHHHHHHHHHC.C CS
                            zf-C2H2   1 ykCpdCgksFkrksnLkrHirt.H 23 
                                        +kC +C+k  k +  L++H +t H
  gene3101|gene3101|rna3101|rna3101 105 FKCRHCKKGMKKRKTLEVHEQTvH 128
                                        8*******************9999 PP

>> zf-C2H2_jaz  Zinc-finger double-stranded RNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.1   3.2e-05     0.044       2      21 ..       8      27 ..       7      28 .. 0.92
   2 ?    5.4   3.0     0.017        24       2      21 ..      35      54 ..      34      56 .. 0.86
   3 ?   -0.6   0.1       1.3   1.7e+03       7      21 ..      65      79 ..      64      82 .. 0.77
   4 !   16.0   1.8     8e-06     0.011       2      23 ..     105     126 ..     104     129 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.2e-05
                                       CBBTTTTBBBSSHHHHHCCT CS
                        zf-C2H2_jaz  2 fYCvlCdKyFksenaldnHl 21
                                       f C +C++ + se++l  H+
  gene3101|gene3101|rna3101|rna3101  8 FACLICQRNYPSEKSLNYHK 27
                                       88**************9995 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.017
                                       CBBTTTTBBBSSHHHHHCCT CS
                        zf-C2H2_jaz  2 fYCvlCdKyFksenaldnHl 21
                                       +YC+ C+K F  +  l++Hl
  gene3101|gene3101|rna3101|rna3101 35 YYCEKCEKSFFYSDKLKKHL 54
                                       9*********8888888886 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 1.3
                                       TTBBBSSHHHHHCCT CS
                        zf-C2H2_jaz  7 CdKyFksenaldnHl 21
                                       C + F   + +d H+
  gene3101|gene3101|rna3101|rna3101 65 CGRVFVRKKWYDRHM 79
                                       888888888888887 PP

  == domain 4  score: 16.0 bits;  conditional E-value: 8e-06
                                        CBBTTTTBBBSSHHHHHCCTTS CS
                        zf-C2H2_jaz   2 fYCvlCdKyFksenaldnHlkS 23 
                                        f C +C+K +k+ ++l+ H+ +
  gene3101|gene3101|rna3101|rna3101 105 FKCRHCKKGMKKRKTLEVHEQT 126
                                        99*****************987 PP

>> zf-H2C2_2  Zinc-finger double domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.1      0.13   1.7e+02       9      22 ..       2      15 ..       1      18 [. 0.81
   2 !   19.7   2.7   5.9e-07   0.00081       1      24 [.      22      44 ..      22      46 .. 0.94
   3 ?   -1.0   0.4       2.1   2.9e+03      19      24 ..      64      69 ..      49      71 .. 0.52
   4 ?    2.8   6.1      0.13   1.8e+02       3      23 ..      76     113 ..      75     116 .. 0.73
   5 ?   -2.8   0.1       7.6     1e+04       3      10 ..     121     129 ..     120     130 .. 0.56

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.13
                          zf-H2C2_2  9 HtgekpyeCplCdk 22
                                       H + +p+ C  C  
  gene3101|gene3101|rna3101|rna3101  2 HAQSFPFACLICQR 15
                                       77889****99976 PP

  == domain 2  score: 19.7 bits;  conditional E-value: 5.9e-07
                          zf-H2C2_2  1 nLrrHirkHtgekpyeCplCdkaF 24
                                       +L++H   Ht ++ y C++C k+F
  gene3101|gene3101|rna3101|rna3101 22 SLNYHKIIHTRPN-YYCEKCEKSF 44
                                       69********999.*********9 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 2.1
                          zf-H2C2_2 19 lCdkaF 24
                                       +C+ +F
  gene3101|gene3101|rna3101|rna3101 64 SCGRVF 69
                                       355555 PP

  == domain 4  score: 2.8 bits;  conditional E-value: 0.13
                          zf-H2C2_2   3 rrHirkHtgek.................pyeCplCdka 23 
                                         rH+ +H + k                 +++C  C+k 
  gene3101|gene3101|rna3101|rna3101  76 DRHMEEHDVSKylsekkiievkptalkyIFKCRHCKKG 113
                                        699999997775555577777766666567*****995 PP

  == domain 5  score: -2.8 bits;  conditional E-value: 7.6
                          zf-H2C2_2   3 rrHirk.Ht 10 
                                        + H  + H+
  gene3101|gene3101|rna3101|rna3101 121 EVHEQTvHK 129
                                        668775365 PP

>> zf-met  Zinc-finger of C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.2   0.00052      0.71       1      19 [.       8      26 ..       8      28 .. 0.92
   2 ?    3.5   1.2     0.071        99       1      12 [.      35      46 ..      35      54 .. 0.75
   3 !   10.1   0.3   0.00061      0.85       1      21 [.     105     125 ..     105     126 .. 0.95

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00052
                             zf-met  1 fyCelCnvtfnsesqlksH 19
                                       f C +C++ + se++l+ H
  gene3101|gene3101|rna3101|rna3101  8 FACLICQRNYPSEKSLNYH 26
                                       5699************999 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.071
                             zf-met  1 fyCelCnvtfns 12
                                       +yCe C ++f  
  gene3101|gene3101|rna3101|rna3101 35 YYCEKCEKSFFY 46
                                       8*****999965 PP

  == domain 3  score: 10.1 bits;  conditional E-value: 0.00061
                             zf-met   1 fyCelCnvtfnsesqlksHlq 21 
                                        f C  C++ ++ +++l+ H q
  gene3101|gene3101|rna3101|rna3101 105 FKCRHCKKGMKKRKTLEVHEQ 125
                                        78*****************87 PP

>> zf-C2H2_8  C2H2-type zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   4.1   1.9e-06    0.0026      35      91 ..       5      59 ..       1      66 [. 0.88
   2 ?    1.2   0.2      0.32   4.4e+02      65      85 ..     103     123 ..      79     129 .. 0.73

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.9e-06
                          zf-C2H2_8 35 lfrcstascaetfpsmqelvahtklhykpnryfkcencllrfrthrslfkhlhvcsd 91
                                        f  +++ c   +ps + l  h  +h +pn y  ce+c   f     l khl  c  
  gene3101|gene3101|rna3101|rna3101  5 SFPFACLICQRNYPSEKSLNYHKIIHTRPNYY--CEKCEKSFFYSDKLKKHLITCGI 59
                                       56777889**********************87..99***9************99975 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.32
                          zf-C2H2_8  65 ryfkcencllrfrthrslfkh 85 
                                          fkc  c   ++  ++l  h
  gene3101|gene3101|rna3101|rna3101 103 YIFKCRHCKKGMKKRKTLEVH 123
                                        349999998888877776555 PP

>> C1_4  TFIIH C1-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   2.1   6.9e-05     0.096       2      35 ..      10      44 ..       9      48 .. 0.83
   2 ?    4.6   0.1     0.027        37      21      33 ..     100     112 ..      81     116 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6.9e-05
                               C1_4  2 CygCqkkfpklakkkkdee.ltssryrCekCkndF 35
                                       C+ Cq+++p+ ++ + ++   t   y CekC++ F
  gene3101|gene3101|rna3101|rna3101 10 CLICQRNYPSEKSLNYHKIiHTRPNYYCEKCEKSF 44
                                       99*******98876554443899********9988 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.027
                               C1_4  21 ltssryrCekCkn 33 
                                        + + +++C++Ck+
  gene3101|gene3101|rna3101|rna3101 100 ALKYIFKCRHCKK 112
                                        67889******97 PP

>> zf_C2H2_ZHX  Zinc-fingers and homeoboxes C2H2 finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.1     0.079   1.1e+02       5      23 ..       8      26 ..       6      29 .. 0.90
   2 !    7.7   0.9     0.002       2.8       3      23 ..      33      53 ..      31      57 .. 0.93
   3 !    8.5   0.2    0.0011       1.5       5      28 ..     105     128 ..     102     130 .. 0.94

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.079
                        zf_C2H2_ZHX  5 FvCveCsfsakkfegLalH 23
                                       F C+ C+ +  + ++L+ H
  gene3101|gene3101|rna3101|rna3101  8 FACLICQRNYPSEKSLNYH 26
                                       99*****999999999988 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.002
                        zf_C2H2_ZHX  3 PsFvCveCsfsakkfegLalH 23
                                       P+++C +C+ s    ++L++H
  gene3101|gene3101|rna3101|rna3101 33 PNYYCEKCEKSFFYSDKLKKH 53
                                       9*****************999 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.0011
                        zf_C2H2_ZHX   5 FvCveCsfsakkfegLalHNarsH 28 
                                        F C  C+   kk ++L+ H   +H
  gene3101|gene3101|rna3101|rna3101 105 FKCRHCKKGMKKRKTLEVHEQTVH 128
                                        99******************9999 PP

>> zf-SNAP50_C  snRNA-activating protein of 50kDa MW C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   3.7   6.5e-06     0.009     148     190 ..       9      52 ..       1      58 [. 0.81
   2 ?   -0.4   0.3      0.55   7.5e+02     148     165 ..     106     124 ..      97     131 .. 0.59

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 6.5e-06
                        zf-SNAP50_C 148 kCkvCekfs.akwvvlndkllpedpsyfCdkCfrslhydkngek 190
                                        +C +C+++   ++ ++ +k++   p y+C+kC +s+ y+++ +k
  gene3101|gene3101|rna3101|rna3101   9 ACLICQRNYpSEKSLNYHKIIHTRPNYYCEKCEKSFFYSDKLKK 52 
                                        7****987625566666*********************877654 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.55
                        zf-SNAP50_C 148 kCkvCekfsakwvvln.dk 165
                                        kC+ C+k   k  +l+ ++
  gene3101|gene3101|rna3101|rna3101 106 KCRHCKKGMKKRKTLEvHE 124
                                        6777776666555554344 PP

>> zf-C2H2_6  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   3.3e-05     0.046       2      24 ..       8      30 ..       8      33 .. 0.90
   2 ?    3.2   3.5     0.066        90       3      22 ..      36      55 ..      35      57 .. 0.85
   3 ?   -0.6   0.1         1   1.4e+03       7      12 ..      65      70 ..      64      71 .. 0.84
   4 ?    0.9   0.6      0.35   4.9e+02       2       9 ..     105     112 ..     104     129 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.3e-05
                          zf-C2H2_6  2 heCsvCsksFpslqaLggHkksH 24
                                       + C +C + +ps ++L+ Hk+ H
  gene3101|gene3101|rna3101|rna3101  8 FACLICQRNYPSEKSLNYHKIIH 30
                                       6799****************866 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.066
                          zf-C2H2_6  3 eCsvCsksFpslqaLggHkk 22
                                        C  C ksF + + L +H++
  gene3101|gene3101|rna3101|rna3101 36 YCEKCEKSFFYSDKLKKHLI 55
                                       599******99999999985 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 1
                          zf-C2H2_6  7 CsksFp 12
                                       C+++F 
  gene3101|gene3101|rna3101|rna3101 65 CGRVFV 70
                                       *****5 PP

  == domain 4  score: 0.9 bits;  conditional E-value: 0.35
                          zf-C2H2_6   2 heCsvCsk 9  
                                        ++C  C+k
  gene3101|gene3101|rna3101|rna3101 105 FKCRHCKK 112
                                        99**9*98 PP

>> zf-C2H2_11  zinc-finger C2H2-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.2   3.4e-05     0.046       7      26 ..      10      29 ..       8      30 .. 0.92
   2 ?    0.8   0.4      0.31   4.3e+02       7      25 ..      37      55 ..      35      57 .. 0.78
   3 ?   -0.2   0.7      0.65     9e+02       8      14 ..      63      69 ..      55      80 .. 0.67
   4 ?    0.1   5.1      0.52   7.2e+02       6      12 ..     106     112 ..     105     129 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.4e-05
                         zf-C2H2_11  7 CleCGlcftSqlsLsRHlfI 26
                                       Cl C +++ S+ sL+ H +I
  gene3101|gene3101|rna3101|rna3101 10 CLICQRNYPSEKSLNYHKII 29
                                       *****************876 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.31
                         zf-C2H2_11  7 CleCGlcftSqlsLsRHlf 25
                                       C +C   f  +  L++Hl+
  gene3101|gene3101|rna3101|rna3101 37 CEKCEKSFFYSDKLKKHLI 55
                                       7788777777778999985 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.65
                         zf-C2H2_11  8 leCGlcf 14
                                       + CG+ f
  gene3101|gene3101|rna3101|rna3101 63 CSCGRVF 69
                                       4577766 PP

  == domain 4  score: 0.1 bits;  conditional E-value: 0.52
                         zf-C2H2_11   6 qCleCGl 12 
                                        +C++C+ 
  gene3101|gene3101|rna3101|rna3101 106 KCRHCKK 112
                                        8****96 PP

>> Zn_ribbon_SprT  SprT-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   3.1   0.00029      0.41       3      31 ..       6      41 ..       4      47 .. 0.88
   2 ?    4.6   6.4     0.022        30       4      32 ..      60     113 ..      59     116 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00029
                     Zn_ribbon_SprT  3 yvYrCtgCgreythhlsirrhn.......YrCrrCk 31
                                       +   C  C+r+y+ + s + h+       Y+C +C 
  gene3101|gene3101|rna3101|rna3101  6 FPFACLICQRNYPSEKSLNYHKiihtrpnYYCEKCE 41
                                       6667999****************************6 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.022
                     Zn_ribbon_SprT   4 vYrCtgCgreythhlsirrhn.........................YrCrrCk.g 32 
                                         ++C +Cgr + +    +rh                            Cr+Ck g
  gene3101|gene3101|rna3101|rna3101  60 QWTC-SCGRVFVRKKWYDRHMeehdvskylsekkiievkptalkyiFKCRHCKkG 113
                                        59**.***8777777779999999********************9999****955 PP

>> zf-AN1  AN1-like Zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.1     0.049        67      11      23 ..       5      17 ..       2      20 .. 0.86
   2 ?    4.4   0.3      0.03        42      13      23 ..      33      44 ..      26      44 .. 0.78
   3 ?    0.0   3.1      0.72   9.9e+02      14      23 ..      61      69 ..      49      85 .. 0.78
   4 ?    6.9   0.1    0.0052       7.1      12      21 ..     103     112 ..      92     114 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.049
                             zf-AN1 11 flpfkCryCgkvF 23
                                       + pf C  C++++
  gene3101|gene3101|rna3101|rna3101  5 SFPFACLICQRNY 17
                                       469********99 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.03
                             zf-AN1 13 p.fkCryCgkvF 23
                                       p + C++C+k+F
  gene3101|gene3101|rna3101|rna3101 33 PnYYCEKCEKSF 44
                                       5689******98 PP

  == domain 3  score: 0.0 bits;  conditional E-value: 0.72
                             zf-AN1 14 fkCryCgkvF 23
                                        +C+ Cg+vF
  gene3101|gene3101|rna3101|rna3101 61 WTCS-CGRVF 69
                                       6899.*9999 PP

  == domain 4  score: 6.9 bits;  conditional E-value: 0.0052
                             zf-AN1  12 lpfkCryCgk 21 
                                         +fkCr+C+k
  gene3101|gene3101|rna3101|rna3101 103 YIFKCRHCKK 112
                                        35******97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1154  (0.064365); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 841.52
//
Query:       gene3102|gene3102|rna3102|rna3102  [L=255]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       857  (0.0477997); expected 358.6 (0.02)
Passed bias filter:                      553  (0.0308439); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1756.37
//
Query:       gene3103|gene3103|rna3103|rna3103  [L=384]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.5e-45  155.0   0.0    4.2e-45  154.3   0.0    1.4  2  NTP_transferase  Nucleotidyl transferase
      2e-08   33.7   3.9    2.4e-06   27.0   1.7    3.5  3  Hexapep          Bacterial transferase hexapeptide (six repea
    2.5e-08   34.4   0.0    3.1e-08   34.1   0.0    1.2  1  NTP_transf_3     MobA-like NTP transferase domain
  ------ inclusion threshold ------
      0.023   14.5   0.1      0.053   13.3   0.1    1.6  1  DUF257           Pyrococcus protein of unknown function, DUF2
      0.036   13.8   0.6      0.036   13.8   0.6    2.4  3  Hexapep_2        Hexapeptide repeat of succinyl-transferase
      0.043   12.7   0.2      0.079   11.9   0.2    1.5  1  Fucokinase       L-fucokinase
       0.06   11.5   1.0      0.083   11.0   1.0    1.3  1  DUF4954          Domain of unknown function (DUF4954)


Domain annotation for each model (and alignments):
>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  154.3   0.0   1.6e-48   4.2e-45       2     243 ..      45     269 ..      44     274 .. 0.94
   2 ?   -3.9   0.0       3.2   8.3e+03      87     111 ..     307     331 ..     304     331 .. 0.85

  Alignments for each domain:
  == domain 1  score: 154.3 bits;  conditional E-value: 1.6e-48
                                        EEEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGTSEEEE CS
                    NTP_transferase   2 avILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlansgieeiivvltqehsflveeqlkegskfgvevli 77 
                                        a+IL+GG+GtRL+PLt t++k+l+p+++  ++i +++++l + g+++ii+  +++++ +v +  k ++++g+e+ +
  gene3103|gene3103|rna3103|rna3103  45 AIILVGGYGTRLRPLTLTRPKPLIPFVNI-PIISHQIKKLHEFGTRKIILAANYRTEDIVCQMTKLANDLGIEIIF 119
                                        8****************************.********************************************** PP

                                        EEESS--BGGHHHHHTHHHHTTSSE..EEEEETTEEEESTTHHHHHHHHHTHSSTTSEEEEEEESS-CTTSEEEEE CS
                    NTP_transferase  78 alepegkgtAdAvalaaelledeksdelvlvLggDhlikdayeeavkkaiekaakgtvtfgivpveeateyGviea 153
                                        ++e+e  gt +++ala+++l++      v+vL++D+++++ + e+++ + + ++  ++t++++ v+++++yGvi  
  gene3103|gene3103|rna3103|rna3103 120 SVEKEVLGTGGPLALARQYLDEPTP---VFVLNSDVICEYPFDELFAAHLACKR--KATILTTIVDDPSRYGVILK 190
                                        *********************9885...**************************..9*****************88 PP

                                        CTTSBEEEEECS-SSHSHCSEECCSEEEEETTHHHHHHHCCHHHTTSSCHHHHHHHHHHHTTEEEEEECSTTEE-E CS
                    NTP_transferase 154 deegrverfvEKPkeakaselassGiYvfnsevllflakdleelkrgedeitdilpkaleegkvalaflfkdaeyW 229
                                        ++ ++++rfvEKPk+    +++++GiYv n+evl  +     +lk+ + e + + + a++++   +af  k    W
  gene3103|gene3103|rna3103|rna3103 191 EG-NAITRFVEKPKNYV-GNTINAGIYVLNREVLNDI-----PLKEVSLENEVFAQMAVRNE--LAAFELKS--FW 255
                                        77.59***********9.9******************.....99999999998888888885..44566777..6* PP

                                        EEXSSHHHHHHHHH CS
                    NTP_transferase 230 sDvGtldslleane 243
                                        +D+G+++++l a++
  gene3103|gene3103|rna3103|rna3103 256 KDIGQHRDYLVAQN 269
                                        *********98876 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 3.2
                                        GHHHHHTHHHHTTSSE..EEEEETT CS
                    NTP_transferase  87 AdAvalaaelledeksdelvlvLgg 111
                                        A+A++++a+l++++   ++++vL++
  gene3103|gene3103|rna3103|rna3103 307 AGAYIKNATLMDNTVVSDYCVVLNS 331
                                        7899999999999988999999975 PP

>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   1.7   9.5e-10   2.4e-06       4      36 .]     281     313 ..     280     313 .. 0.89
   2 ?    3.6   0.0     0.022        58       2      23 ..     314     334 ..     313     347 .. 0.63
   3 ?    3.0   0.0     0.036        92       2      28 ..     331     357 ..     330     360 .. 0.66

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 9.5e-10
                                        EETTEEE-TTEEEETTEEE-TTEEEETTEEEES CS
                            Hexapep   4 IGsnvlIgpfaviggnVkIGdnvkIgagvvigg 36 
                                        I + +++++ a ig+nV+IG+nvkIgag++i++
  gene3103|gene3103|rna3103|rna3103 281 IDDTAVVRKEAFIGENVVIGKNVKIGAGAYIKN 313
                                        667789999999******************985 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.022
                                        EEEETTEEE-TTEEEETTEEE- CS
                            Hexapep   2 tvIGsnvlIgpfaviggnVkIG 23 
                                        +++ +n+++  ++v+++ + IG
  gene3103|gene3103|rna3103|rna3103 314 ATLMDNTVVSDYCVVLNSI-IG 334
                                        4566777777777777766.44 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.036
                                        EEEETTEEE-TTEEEETTEEE-TTEEE CS
                            Hexapep   2 tvIGsnvlIgpfaviggnVkIGdnvkI 28 
                                        ++IG  ++I +++ +   +++ d v I
  gene3103|gene3103|rna3103|rna3103 331 SIIGFSCKISKWCRLEKLCVLADEVEI 357
                                        688999999887666665555555555 PP

>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.1   0.0   1.2e-11   3.1e-08       1     108 [.      45     163 ..      45     251 .. 0.83

  Alignments for each domain:
  == domain 1  score: 34.1 bits;  conditional E-value: 1.2e-11
                                        EEEEEESS-TTTT.....TTHHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSHC......HHHHHHTTCTS-EEE- CS
                       NTP_transf_3   1 aviLAGGrSsRmg.....gdKallplggkpllervldalraagvdevvvvggde......evlaalarlgvrvved 65 
                                        a+iL GG ++R+      ++K+l+p+ + p++ +++++l++ g ++++++++++      + ++ +++lg++++  
  gene3103|gene3103|rna3103|rna3103  45 AIILVGGYGTRLRpltltRPKPLIPFVNIPIISHQIKKLHEFGTRKIILAANYRtedivcQMTKLANDLGIEIIFS 120
                                        79**********7554436**********************************6566666677788999***9999 PP

                                        TTSS.-SHHHHHHHHHHHH.SSSCEEEEETT-TT--HHHHHHHH CS
                       NTP_transf_3  66 edpg.kgplaslaaalraaadadavlvlacDmPlltpelverll 108
                                         +++  g+++ la a + + + ++v+vl  D+++ +  + e ++
  gene3103|gene3103|rna3103|rna3103 121 VEKEvLGTGGPLALARQYLDEPTPVFVLNSDVIC-EYPFDELFA 163
                                        66654999999*****9999***********987.333333333 PP

>> DUF257  Pyrococcus protein of unknown function, DUF257
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   2.1e-05     0.053     113     172 ..     176     234 ..     164     254 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.1e-05
                             DUF257 113 inlvlglerllllldnrrdlyklvksikkylgnknRkafylinrnllesikPellplLEe 172
                                        +++v  + r  ++l++  ++++ v++ k+y+gn   + +y++nr++l+ i P   + LE+
  gene3103|gene3103|rna3103|rna3103 176 TTIVDDPSRYGVILKEGNAITRFVEKPKNYVGNTINAGIYVLNREVLNDI-PLKEVSLEN 234
                                        67777888888999**********************************98.455566663 PP

>> Hexapep_2  Hexapeptide repeat of succinyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.1       3.1   7.9e+03      26      32 ..     210     216 ..     209     217 .. 0.80
   2 ?   13.8   0.6   1.4e-05     0.036       1      26 [.     296     322 ..     290     328 .. 0.74
   3 ?   -3.5   0.2       3.6   9.2e+03       7      14 ..     330     337 ..     330     339 .. 0.60

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 3.1
                                        E-TT-EE CS
                          Hexapep_2  26 vgaGvvi 32 
                                        + aG+++
  gene3103|gene3103|rna3103|rna3103 210 INAGIYV 216
                                        7899998 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 1.4e-05
                                        .EEE-TT-EE-TT-EE.SEEE-TT-EE CS
                          Hexapep_2   1 pviIGdnCliGanagi.GvslGdncvv 26 
                                        +v IG+n+ iGa a+i   +l dn vv
  gene3103|gene3103|rna3103|rna3103 296 NVVIGKNVKIGAGAYIkNATLMDNTVV 322
                                        477888888888888766666666665 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 3.6
                                        T-EE-TT- CS
                          Hexapep_2   7 nCliGana 14 
                                        n++iG ++
  gene3103|gene3103|rna3103|rna3103 330 NSIIGFSC 337
                                        56666555 PP

>> Fucokinase  L-fucokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.2   3.1e-05     0.079     256     330 ..     273     345 ..     217     379 .. 0.57

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.1e-05
                         Fucokinase 256 tstafsaiknkkekkkesavvi.nSvlessvsvgegsviehsslkgnvsigsnsivsglelesseeslelpddtil 330
                                        +s+  s++ +++   +++a++  n v+ ++v++g+g++i++ +l +n+ +   ++v +  +  s    ++ + + l
  gene3103|gene3103|rna3103|rna3103 273 SSKGLSNVIDDTAVVRKEAFIGeNVVIGKNVKIGAGAYIKNATLMDNTVVSDYCVVLNSIIGFSC---KISKWCRL 345
                                        34444444344444444444431455667777777777777777777777777777666555442...23322222 PP

>> DUF4954  Domain of unknown function (DUF4954)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   1.0   3.2e-05     0.083     175     274 ..     286     377 ..     206     384 .] 0.62

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 3.2e-05
                            DUF4954 175 eigekvkilnagli.kNvkigdyatiegasklengtinSskeapveiGegViledfiissGskikdgavisr.cfv 248
                                        ++ +++ i +  +i kNvkig+ a+i++a+ ++n+   S         +  ++ ++ii   +ki++   +++ c++
  gene3103|gene3103|rna3103|rna3103 286 VVRKEAFIGENVVIgKNVKIGAGAYIKNATLMDNTV-VS---------DYCVVLNSIIGFSCKISKWCRLEKlCVL 351
                                        222222222222221455555555555554444432.22.........2233445666666666666665543555 PP

                            DUF4954 249 GqavklkkqfsaedsllfaNcqgeng 274
                                           v++k+  s+ ++++  N +++++
  gene3103|gene3103|rna3103|rna3103 352 ADEVEIKECISLRNCIVLPNKRVSEC 377
                                        66666666666666666666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (384 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       400  (0.0223102); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 2493.96
//
Query:       gene3104|gene3104|rna3104|rna3104  [L=362]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-38  131.6   0.0    2.9e-19   69.7   0.0    2.1  2  CTP_transf_like  Cytidylyltransferase-like
      8e-06   25.8   0.3       0.11   12.4   0.0    2.8  3  FAD_syn          FAD synthetase
  ------ inclusion threshold ------
      0.057   13.0   0.0       0.09   12.4   0.0    1.3  1  DDE_Tnp_1        Transposase DDE domain
      0.071   12.3   0.1        1.1    8.4   0.0    2.1  2  Pantoate_ligase  Pantoate-beta-alanine ligase


Domain annotation for each model (and alignments):
>> CTP_transf_like  Cytidylyltransferase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.7   0.0   6.4e-23   2.9e-19       2     137 ..      27     146 ..      26     181 .. 0.89
   2 !   60.1   0.0   5.8e-20   2.6e-16       1     118 [.     222     336 ..     222     359 .. 0.82

  Alignments for each domain:
  == domain 1  score: 69.7 bits;  conditional E-value: 6.4e-23
                                        EEE--TT--HHHHHHHHHHHHHSSESEEEEEESSTHCSST-.SCSSTHHHHHHHHHHHTTCTTEEEEEEESEHHHH CS
                    CTP_transf_like   2 agGtFDpiHlGHlrlleqakklleedlivgvpsdeppkkkk.kplasaeeRlemlelakevdevisvdpweltrev 76 
                                        ++G+FD++H+GH ++l+qa++l+++ l+vgv+s e+ +++k  p+++ +eR+  +e +++vdev+ ++p+ +  ++
  gene3104|gene3104|rna3104|rna3104  27 TDGCFDLFHFGHSNVLRQARELGSY-LVVGVHSLEEINHNKgLPVMNDDERYFIVESCRWVDEVYFDAPFITSCDL 101
                                        79***********************.**********999966********************************** PP

                                        HHHTTTTEEEEEEEHHHHHHHHCHHHHHHHHHHHHHEEEEEEHTTCEEEEEEECCTTTCSH CS
                    CTP_transf_like  77 lkklkpdklylvigadvledfsewkeleeilgnvklvvvsrpekqanvllkaekrtngiSs 137
                                        + + ++d   +v+g d++e++    +  +++g+ k  ++          + +  rt  +S+
  gene3104|gene3104|rna3104|rna3104 102 VLSMGVD--LVVHGNDSIESA----DGVDCYGEAKARGI----------FRTVDRTLHVST 146
                                        *******..***********9....88888888887777..........444444444444 PP

  == domain 2  score: 60.1 bits;  conditional E-value: 5.8e-20
                                        EEEE--TT--HHHHHHHHHHHHHSSESEEEEEESSTHCSST-..SCSSTHHHHHHHHHHHTTCTTEEEEEEESEHH CS
                    CTP_transf_like   1 lagGtFDpiHlGHlrlleqakklleedlivgvpsdeppkkkk..kplasaeeRlemlelakevdevisvdpweltr 74 
                                        +++GtFD++H GH+ +l++ k+ + +  +vg+ ++ ++ k k   p++s+ eR   + ++++v+++i+ +p ++++
  gene3104|gene3104|rna3104|rna3104 222 YVDGTFDLFHAGHASILKKCKENGWY-TVVGLFNQSVSYKLKrmNPIMSSVERELCVSACRYVNKIIRNAPLVPDK 296
                                        689***********************.77777777777777669******************************** PP

                                        HHHHHTTTTEEEEEEEHHHHHHHHCHHHHHHHHHHHHHEEEEEE CS
                    CTP_transf_like  75 evlkklkpdklylvigadvledfsewkeleeilgnvklvvvsrp 118
                                        e++k++++d  ++v+ga   +++ e ++l + l ++k+v+ ++p
  gene3104|gene3104|rna3104|rna3104 297 EFIKQYGID--IIVCGAN-DTSL-ENYHLVRDLVELKIVGSDFP 336
                                        *********..*****94.4555.33344444444677777666 PP

>> FAD_syn  FAD synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.0   8.8e-05      0.39      11      33 ..      27      49 ..      19      59 .. 0.86
   2 !   12.4   0.0   2.4e-05      0.11       5      47 ..     217     255 ..     213     277 .. 0.76
   3 ?   -3.3   0.0       1.6   7.3e+03      71      83 ..     298     310 ..     295     318 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 8.8e-05
                            FAD_syn 11 tlGnFDGvHlGHqallkkaveaa 33
                                       t G FD +H GH ++l++a+e+ 
  gene3104|gene3104|rna3104|rna3104 27 TDGCFDLFHFGHSNVLRQARELG 49
                                       6699***************9975 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 2.4e-05
                            FAD_syn   5 degavvtlGnFDGvHlGHqallkkaveaakekglpsvvvtFep 47 
                                        + + v + G FD +H GH ++lkk +e     g  +vv +F++
  gene3104|gene3104|rna3104|rna3104 217 HGKVVYVDGTFDLFHAGHASILKKCKEN----GWYTVVGLFNQ 255
                                        45566667**************998765....56666666665 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 1.6
                            FAD_syn  71 lleelgvdavlvv 83 
                                         ++++g+d +++ 
  gene3104|gene3104|rna3104|rna3104 298 FIKQYGIDIIVCG 310
                                        4566666666553 PP

>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0     2e-05      0.09      61     116 ..     198     266 ..     183     322 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2e-05
                          DDE_Tnp_1  61 dskglkqlldelrpr....kgklvlaDaGYas.....aelldtleekgvdyiirlkkntklyrk....g 116
                                           +l+ lld + ++    +gk+v++D+ ++      a++l++++e+g++ ++ l ++++ y++    +
  gene3104|gene3104|rna3104|rna3104 198 RQAYLRGLLDKFSIPehkiHGKVVYVDGTFDLfhaghASILKKCKENGWYTVVGLFNQSVSYKLkrmnP 266
                                        4445555999988889999***********9789999******************88887776644440 PP

>> Pantoate_ligase  Pantoate-beta-alanine ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0      0.03   1.4e+02      32      54 ..      34      56 ..      10      59 .. 0.86
   2 ?    8.4   0.0   0.00025       1.1      27      56 ..     225     254 ..     202     262 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.03
                                       -GHHHHHHHHHHHHHSSEEEEEE CS
                    Pantoate_ligase 32 LHeGHlsLvkaakeendvvvvSi 54
                                       +H GH +++++a+e  +++vv +
  gene3104|gene3104|rna3104|rna3104 34 FHFGHSNVLRQARELGSYLVVGV 56
                                       7*************999999987 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00025
                                        EE-SS-GHHHHHHHHHHHHHSSEEEEEEEE CS
                    Pantoate_ligase  27 pTmGaLHeGHlsLvkaakeendvvvvSiFv 56 
                                         T   +H+GH+s++k++ke+  ++vv +F 
  gene3104|gene3104|rna3104|rna3104 225 GTFDLFHAGHASILKKCKENGWYTVVGLFN 254
                                        577789********************9995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (362 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       414  (0.0230911); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.23s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 2717.82
//
Query:       gene3105|gene3105|rna3105|rna3105  [L=712]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.4e-65  219.1  18.0    6.4e-65  219.1  18.0    1.9  2  PMT       Dolichyl-phosphate-mannose-protein mannosyltransfer
    8.1e-38  130.0  14.1    8.1e-38  130.0  14.1    2.6  2  PMT_4TMC  C-terminal four TMM region of protein-O-mannosyltra
    3.8e-17   62.7   2.2    7.3e-17   61.8   2.2    1.4  1  MIR       MIR domain


Domain annotation for each model (and alignments):
>> PMT  Dolichyl-phosphate-mannose-protein mannosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  219.1  18.0   1.1e-68   6.4e-65       3     244 ..      64     298 ..      62     299 .. 0.98
   2 ?   -1.1   0.1       0.2   1.2e+03      67     122 ..     569     623 ..     530     646 .. 0.80

  Alignments for each domain:
  == domain 1  score: 219.1 bits;  conditional E-value: 1.1e-68
                                PMT   3 ltllallirlwrlslpnsvvfdevhfgkfasdYlehsffmdvhpplgkmllalggyLagkdgnftfesigaeyype 78 
                                        ++l+++l+r +++   n v++de+hfgkfas+Yl++ f++dvhpplgkml al+gy++g d nf+f+s   + yp+
  gene3105|gene3105|rna3105|rna3105  64 IFLVSFLVRSYKIEKGNFVIWDEAHFGKFASKYLQRLFYFDVHPPLGKMLTALSGYMFGQDVNFKFDSG--TSYPA 137
                                        7899*****************************************************************..8**** PP

                                PMT  79 nvpyvslRlfsallgslivplvyltllelgfskltallaallvllenslitlsryilldspLlfftllsmyclvkf 154
                                        +++yv++R f+a+ +s++++++yltl+e+ f+   + ++a++ ++ensl+ +sr+illds Llfft + my l k+
  gene3105|gene3105|rna3105|rna3105 138 QMDYVGMRRFHAFISSFVPVFSYLTLREMSFDVHCCSVIAFMIIFENSLVCISRLILLDSHLLFFTSMVMYALAKY 213
                                        **************************************************************************** PP

                                PMT 155 erkapfsrswwlwllltgvalglavsvKwvglftvllvgllliwelwqllgdkslllksivkhllaralaliviPv 230
                                              +++ +  l+l+g alg++ svKw+g ft++lvg+ +i elw ll +k + + +    ++ ral+li++P+
  gene3105|gene3105|rna3105|rna3105 214 -----IRKRTIPNLVLLGTALGCVQSVKWIGCFTTFLVGIFIIAELWLLLIQKDVAITRFARLFTERALFLIILPI 284
                                        .....799*************************************************999**************** PP

                                PMT 231 tlylavftvhfwll 244
                                         +yla+f +hf ++
  gene3105|gene3105|rna3105|rna3105 285 IIYLAFFLIHFGIV 298
                                        ***********765 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.2
                                PMT  67 tfesigaeyypenvpyvslRlfsallgslivplvyltllelgfskltallaallvl 122
                                        + +++ ++y ++  p +++  + ++l + +v+l+  ++   +++++ a +  ++ l
  gene3105|gene3105|rna3105|rna3105 569 WSDENVKFYMFG-NPFSWYLSLACVLAAPTVLLCKTLTQIRNRQRIDARMLIFCCL 623
                                        556677778888.8888898999999999988888777777777766655555544 PP

>> PMT_4TMC  C-terminal four TMM region of protein-O-mannosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   3.4      0.31   1.9e+03      62     116 ..     238     293 ..     199     299 .. 0.60
   2 !  130.0  14.1   1.4e-41   8.1e-38       2     199 .]     522     704 ..     521     704 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.31
                           PMT_4TMC  62 lstiallvfvllllalllrrqrgvkdleeeetr.llnsglflllgwalhylPfflm 116
                                        +++++ +++ ++++a+l+    + +   ++ +r ++  +lfl++  ++ yl ffl+
  gene3105|gene3105|rna3105|rna3105 238 IGCFTTFLVGIFIIAELWLLLIQKDVAITRFARlFTERALFLIILPIIIYLAFFLI 293
                                        33333333333333333333333332222333347777777777777777777775 PP

  == domain 2  score: 130.0 bits;  conditional E-value: 1.4e-41
                           PMT_4TMC   2 lkkflelqkamltsnnaltes.....hpyaSepyeWplllrgisywtkneekkqiyllGNpvlwwlstiallvfvl 72 
                                        + +++e ++ m+ +n++++++      ++ S++yeWp+l+rg++++++++e+ ++y++GNp+ w+ls++++l+   
  gene3105|gene3105|rna3105|rna3105 522 FYNIVEHNALMYITNKSFVQDddlepIRIVSQAYEWPILRRGLRMCSWSDENVKFYMFGNPFSWYLSLACVLAAPT 597
                                        567899*************96588777789******************************************9999 PP

                           PMT_4TMC  73 lllalllrrqrgvkdleeeetrllnsglflllgwalhylPfflmgRvlflhhYlpAllfailllaalldfllkslk 148
                                        +ll++ l++ r+ + +   ++r+l+ +++++ gwa+h+lPff++gRvl++hhYlpA++f++ +l ++++       
  gene3105|gene3105|rna3105|rna3105 598 VLLCKTLTQIRNRQRI---DARMLIFCCLFCGGWAIHFLPFFFIGRVLYFHHYLPAMYFSMHTLLVFVRNH----- 665
                                        9999999999988887...677889999********************************99988877764..... PP

                           PMT_4TMC 149 kslkkkklvklivvvvllvlviavFiffspltyGlpgtseevkklkwlssW 199
                                                    ++ ++l++ i++F+++spltyG+  +++ +++lk+l++W
  gene3105|gene3105|rna3105|rna3105 666 -----------KLLYTILFIQIIAFVLYSPLTYGFY-DQNVMRWLKLLPTW 704
                                        ...........5789999****************96.5569********** PP

>> MIR  MIR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.8   2.2   1.2e-20   7.3e-17      12     179 ..     345     492 ..     341     501 .. 0.83

  Alignments for each domain:
  == domain 1  score: 61.8 bits;  conditional E-value: 1.2e-20
                                MIR  12 fHshqdeyltiseqqqkqevflritlypsadaanssraLWeievvqkdawrgglikwgkvyRlkHlaTgryLasee 87 
                                         Hsh+dey++ +   +      ++t+y ++d++n+    W  + v + +++++ +k+++ + + H++T ryL +++
  gene3105|gene3105|rna3105|rna3105 345 LHSHKDEYPENEG--C------QMTTYGHKDENNY----WAFQKVVDGDTKVEMVKNNDEVVIMHMNTFRYLNLVD 408
                                        4999999997543..3......58***********....************************************* PP

                                MIR  88 ekksplseseddqkevsayglegfegdnDkveifekksttgmksaklvprdsyvrlqHvvtgcwLhstsvklkkek 163
                                        +  + ++++ +     +  ++e f+ +  kve++   ++  +k++k+++ ++ +rl+ v  +c+++st+ + ++++
  gene3105|gene3105|rna3105|rna3105 409 K-DAYVTKEDR--LLSTSPNTELFRSNLFKVEVV---DDMITKEDKIKTLTTRFRLKSVDENCYVRSTNKRYPQWG 478
                                        9.666665433..333333333343332247777...588899********************************* PP

                                MIR 164 fekvqqkvicakeked 179
                                        f+  q +v+c+++k  
  gene3105|gene3105|rna3105|rna3105 479 FR--QGEVTCSRKKDS 492
                                        **..******998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (712 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       913  (0.0509231); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.64u 0.29s 00:00:00.93 Elapsed: 00:00:00.47
# Mc/sec: 4594.21
//
Query:       gene3106|gene3106|rna3106|rna3106  [L=587]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-65  221.4   0.0    1.6e-65  221.0   0.0    1.1  1  E1_dh           Dehydrogenase E1 component
     0.0046   16.7   0.1     0.0075   16.1   0.1    1.3  1  TPP_enzyme_C    Thiamine pyrophosphate enzyme, C-terminal TPP
  ------ inclusion threshold ------
      0.056   12.6   0.0      0.088   12.0   0.0    1.2  1  DXP_synthase_N  1-deoxy-D-xylulose-5-phosphate synthase


Domain annotation for each model (and alignments):
>> E1_dh  Dehydrogenase E1 component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  221.0   0.0   2.8e-69   1.6e-65       3     299 ..     278     577 ..     276     578 .. 0.95

  Alignments for each domain:
  == domain 1  score: 221.0 bits;  conditional E-value: 2.8e-69
                                        HHHHHHHHHHHHHHHHTTSS-S-----TT-HHHHHHHHHTS-TTSEEEESS--HHHHHHTT--HHHHHHHHTT-T. CS
                              E1_dh   3 lvllrrvedaldalykrkkrigfyhlsagqealkvgiaaalekeDliiteYReagvllarglsleeilaeltgkv. 77 
                                        +  +rr+e+  ++l+ ++k++gf+hl  gqe + ++ + a+ k+D   ++YR++g  ++ g s + ilae+ g++ 
  gene3106|gene3106|rna3106|rna3106 278 MLSIRRLEECSQQLFDANKIRGFCHLVSGQESIYTAYKYAVAKDDTATSSYRCHGLSYVTGDSAKVILAEMLGREe 353
                                        66789999999****************************************************************7 PP

                                        ...TTSSGTT-.-E..BTT..BEEE-SSTTTHHHHHHHHHHHHH...........HHTS---EEEEEEGGGTT-HH CS
                              E1_dh  78 ...kgkggsrhelmyaekesrilggngivgaqvplvaGialaak...........iegkkevailliGDgAanqGd 139
                                            gkggs+h l+  +k   ++gg+givgaqvp+  G+a+ +k              +k+v+++++GDgAanqG+
  gene3106|gene3106|rna3106|rna3106 354 gmcGGKGGSMH-LY--NKT--FYGGHGIVGAQVPISLGLAFRHKyvnlekgdrldKMVAKNVSFAFYGDGAANQGQ 424
                                        77778888888.77..555..*******************************988777899*************** PP

                                        HHHHHHHHHHTT--EEEEEEEESEETTEEHHHH-S---GGG..TTTTS-EEEEETTSHHHHHHHHHHHHHHHHTTT CS
                              E1_dh 140 vyealnlaalwklpvifvveNNkygisTeaekasaskeladrargvgipglrVdgnDplavyeAvkfAaeraregk 215
                                        v+e++n+a lwklp+ifv+eNN yg+ T++e  s+  ++++  rg++ipg+rV  + +l   ++ kf +e+a + +
  gene3106|gene3106|rna3106|rna3106 425 VFESYNMAMLWKLPIIFVCENNAYGMWTKVETVSSNINFYK--RGDNIPGVRVRHENVLDLIAVFKFSREYALK-N 497
                                        *****************************************..******************************9.9 PP

                                        --EEEEEEE--SS-SSTTSHSHSSSHHHHHHHHHHHH-HHHHHHHHHHHTTSS-HHHHHHHHHHHHHHHHHHHHHH CS
                              E1_dh 216 gpllielvtYRyggHsesDdpstyrtreeveevrkkkdpiqrlkelLvkkgvvseeelkeiekevrkeveeavkka 291
                                         pl++e++tYR+  Hs  D    +r+ +e+++ ++  d i+ ++ +L    +v e+e  +iek+v   ++ +   a
  gene3106|gene3106|rna3106|rna3106 498 SPLIVEILTYRLCTHSARD-QVDFRSEQELKDKKSA-DSIEHFRSFLAR--FVPENEIVNIEKSVCDTIDGESSLA 569
                                        9******************.8999*99999997777.**********76..8********************9999 PP

                                        HHS----G CS
                              E1_dh 292 eskkelep 299
                                        +++ke+++
  gene3106|gene3106|rna3106|rna3106 570 QAAKEPQA 577
                                        99999875 PP

>> TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.1   1.3e-06    0.0075      24      91 ..     371     455 ..     359     487 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.3e-06
                                        ETTTS-TTTHHHHHHHHHH........H.......STTSEEEEEEEHHHHHHT..GGGHHHHHHTT-SEEEEEEE- CS
                       TPP_enzyme_C  24 sgglgtmGyglpaAiGakl........a.......kpdrevvaivGDGgflmi..lqelatavrrnlpitvvvlnN 82 
                                         gg+g  G ++p+++G+++        +         ++  +a+ GDG+      ++ +  a+  +lpi++v+ nN
  gene3106|gene3106|rna3106|rna3106 371 YGGHGIVGAQVPISLGLAFrhkyvnleKgdrldkmVAKNVSFAFYGDGAANQGqvFESYNMAMLWKLPIIFVCENN 446
                                        57*****************88777655155454332356789*******766664566666666688999988887 PP

                                        SBCCCHHHH CS
                       TPP_enzyme_C  83 egygmtggq 91 
                                        ++ + t+ +
  gene3106|gene3106|rna3106|rna3106 447 AYGMWTKVE 455
                                        766656555 PP

>> DXP_synthase_N  1-deoxy-D-xylulose-5-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   1.5e-05     0.088     133     209 ..     408     484 ..     368     506 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.5e-05
                     DXP_synthase_N 133 kkkvvaviGDgaltgGmafealnnigelkkkllvilNdNemsisknvGalskylskllsskayeklkkevkkllkk 208
                                        k+   a  GDga   G  fe+ n +   k  ++ +  +N   + ++v ++s+ ++ ++  +++  ++ + +++l+ 
  gene3106|gene3106|rna3106|rna3106 408 KNVSFAFYGDGAANQGQVFESYNMAMLWKLPIIFVCENNAYGMWTKVETVSSNINFYKRGDNIPGVRVRHENVLDL 483
                                        45567889*********************************************99999999999988888888875 PP

                     DXP_synthase_N 209 i 209
                                        i
  gene3106|gene3106|rna3106|rna3106 484 I 484
                                        4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (587 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       416  (0.0232026); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.74u 0.32s 00:00:01.06 Elapsed: 00:00:00.57
# Mc/sec: 3086.74
//
Query:       gene3107|gene3107|rna3107|rna3107  [L=603]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    5.3e-52  176.6   1.4    9.8e-52  175.7   1.4    1.4  1  Nop         snoRNA binding domain, fibrillarin


Domain annotation for each model (and alignments):
>> Nop  snoRNA binding domain, fibrillarin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  175.7   1.4   5.5e-56   9.8e-52       1     229 [.     127     349 ..     127     350 .. 0.87

  Alignments for each domain:
  == domain 1  score: 175.7 bits;  conditional E-value: 5.5e-56
                                        HHHHHHHHHHHHHHHHHHHHTTTSTCHH......HHS-SHHHHHHH..HHHCCCCHCCT.HHTT.HHHHHHHHHHH CS
                                Nop   1 lldeidkeintlhkrvrewYswhFpELe......slvkdnleYakv..vkligneredlekkeedeelakevimaa 68 
                                        +l++i+++i+++ kr+ e+Y ++ pEL+      +  ++++eY ++  v++i+ +  +++++    e  +++++++
  gene3107|gene3107|rna3107|rna3107 127 MLKQIESDIERYDKRAAEIYFNYLPELKirkrrdESDDEKVEYKQLydVEVIK-KLWKIKEN----EDIDSKYLWT 197
                                        589************************95433322334459996652234444.33344222....2568889999 PP

                                        HCHHHH-SSS-S-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSHHHHHHCHHHHHHHHHHHHSSHHHHHC CS
                                Nop  69 kvtastsmgaelseedlknikelcdrvleleelrkelleYlesrmsaiAPNlsaLvGeevaarLishaGgLtnLak 144
                                        +     s g+ ls++d++n+++l+d v   +e+ ++ll+Yle++++++APNl+aL+G ++aa+Li+ +G+L nLak
  gene3107|gene3107|rna3107|rna3107 198 RD----SVGVALSPNDWANLQKLIDLVELKRENMEKLLKYLEQQVEIHAPNLNALIGFRLAAELITLCGSLINLAK 269
                                        99....********************************************************************** PP

                                        S-HHHHTTTT-HHHHCCCHH.T---SSSCHHHCSHHHHHTS-CCCHHHHHHHHHHHHHHHHHHHHTT---.-SHHH CS
                                Nop 145 mPastiqilGaekalfralk.kkntpkyGliyhselvqkatppklkkkiaRllaaKvalaaRiDafsekd.gslGk 218
                                        +++st+q+lGaekalfr+lk k+ tpkyG++ ++e+ + + p     +++R la+K++l+aRiD f++++ +++Gk
  gene3107|gene3107|rna3107|rna3107 270 CSSSTVQVLGAEKALFRSLKsKTPTPKYGILKNNEITK-S-P-----RLIRSLASKIVLCARIDVFRRTKtDAYGK 338
                                        ********************8889************99.7.4.....9****************9988888***** PP

                                        HHHHHHHHHHH CS
                                Nop 219 klreeiekklk 229
                                        +lr+ +e+k+k
  gene3107|gene3107|rna3107|rna3107 339 ALRAVLETKIK 349
                                        *********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (603 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1749  (0.0975515); expected 358.6 (0.02)
Passed bias filter:                      491  (0.0273858); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.71u 0.32s 00:00:01.03 Elapsed: 00:00:00.50
# Mc/sec: 3618.19
//
Query:       gene3108|gene3108|rna3108|rna3108  [L=624]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.042   14.2   4.0          6    7.3   0.1    3.5  4  YvfG      YvfG protein
       0.11   13.0   0.1         34    5.1   0.0    3.1  2  Ank       Ankyrin repeat


Domain annotation for each model (and alignments):
>> YvfG  YvfG protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.1   0.00067         6       5      35 ..     159     189 ..     155     204 .. 0.90
   2 ?   -3.2   0.0       1.3   1.1e+04       4      14 ..     259     269 ..     258     273 .. 0.86
   3 ?   -3.7   0.0       1.9   1.7e+04      38      55 ..     536     553 ..     529     554 .. 0.71
   4 ?    6.3   0.1    0.0014        12       8      30 ..     590     612 ..     584     615 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.00067
                                        HHHHHHHHHHHHHC-SS.S-CCHHHHHHHHH CS
                               YvfG   5 verlienlkeyieqneayedkiqalnaYYkv 35 
                                        v +l+e + e  ++   +e+ +qal +YY++
  gene3108|gene3108|rna3108|rna3108 159 VSFLMEQINELEKMHGDHEEIVQALLSYYRS 189
                                        5789999**9999*9999************8 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 1.3
                                        SHHHHHHHHHH CS
                               YvfG   4 sverlienlke 14 
                                        ++e++i+n+++
  gene3108|gene3108|rna3108|rna3108 259 TTEKIIQNIRD 269
                                        8999****996 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 1.9
                                        HHHHHHSSS-HHHHHHHH CS
                               YvfG  38 ssllaDrlaknavllkRi 55 
                                        + +l     kna+l  +i
  gene3108|gene3108|rna3108|rna3108 536 GCMLRVSTMKNAELFAKI 553
                                        666666778999998776 PP

  == domain 4  score: 6.3 bits;  conditional E-value: 0.0014
                                        HHHHHHHHHHC-SS.S-CCHHHH CS
                               YvfG   8 lienlkeyieqneayedkiqaln 30 
                                        +++ +k+++e+n+    ki+ +n
  gene3108|gene3108|rna3108|rna3108 590 FVNLMKDFVEMNDEKDLKIHFMN 612
                                        77789*********999*****9 PP

>> Ank  Ankyrin repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0    0.0084        75       5      27 ..     154     191 ..     151     194 .. 0.71
   2 ?    5.1   0.0    0.0038        34      10      22 ..     394     406 ..     384     413 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.0084
                                        HHHHHH.............HHTTHHHHHHHH..TTTST CS
                                Ank   5 PLHlAa.............tngkkriiklLL..hGAnl 27 
                                        +LH  +             ++++++i+++LL  +++nl
  gene3108|gene3108|rna3108|rna3108 154 VLHSIVsflmeqinelekmHGDHEEIVQALLsyYRSNL 191
                                        57753356666667777767889********7436776 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0038
                                        HHHTTHHHHHHHH CS
                                Ank  10 atngkkriiklLL 22 
                                        ++ng+++iiklLL
  gene3108|gene3108|rna3108|rna3108 394 SSNGNEDIIKLLL 406
                                        579*********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (624 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1060  (0.0591221); expected 358.6 (0.02)
Passed bias filter:                      513  (0.0286129); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.66u 0.28s 00:00:00.94 Elapsed: 00:00:00.47
# Mc/sec: 3986.24
//
Query:       gene3109|gene3109|rna3109|rna3109  [L=261]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.4e-29  102.1   2.1    9.2e-29  100.2   0.1    2.4  2  TAFII55_N        TAFII55 protein conserved region
     0.0032   18.0   8.8     0.0038   17.8   8.8    1.2  1  AAA_23           AAA domain
  ------ inclusion threshold ------
      0.016   15.2  10.8      0.029   14.4   9.3    2.2  2  MIP-T3_C         Microtubule-binding protein MIP-T3 C-termina
      0.027   14.6   2.0      0.039   14.1   2.0    1.3  1  MnmE_helical     MnmE helical domain
        1.4    8.8  10.4       0.34   10.8   6.1    1.9  2  Cauli_AT         Aphid transmission protein
        1.5    7.9  11.2        3.4    6.8  11.2    1.6  1  Phage_HK97_TLTM  Tail length tape measure protein
        1.9    8.3  13.1       0.32   10.8   4.4    2.3  2  Exo84_C          Exocyst component 84 C-terminal
        2.2    7.9  11.5       0.33   10.6   5.5    1.9  2  LUC7             LUC7 N_terminus
        4.6    6.2  12.3        6.9    5.6  12.3    1.2  1  Atg14            Vacuolar sorting 38 and autophagy-related su
        5.2    7.2  10.4        1.4    9.0   0.6    2.8  2  Nup54            Nucleoporin complex subunit 54
        5.8    7.4   8.0    4.7e+02    1.3   8.0    3.2  1  NPV_P10          Nucleopolyhedrovirus P10 protein
          8    5.6   7.6         17    4.5   7.6    1.6  1  TMPIT            TMPIT-like protein
        9.5    6.2   7.9       0.91    9.5   1.0    2.4  2  Intein_splicing  Intein splicing domain


Domain annotation for each model (and alignments):
>> TAFII55_N  TAFII55 protein conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.2   0.1   6.7e-32   9.2e-29       1     159 [.       9     151 ..       9     152 .. 0.88
   2 ?    1.0   0.3      0.22   3.1e+02     111     143 ..     211     243 ..     160     257 .. 0.62

  Alignments for each domain:
  == domain 1  score: 100.2 bits;  conditional E-value: 6.7e-32
                          TAFII55_N   1 lEeqfiLRlppeeaeklreaiesgdvnkdklsiklekderravvkidgklyaaklvDLPtiiEslKtiDkknlyKt 76 
                                        +Ee++iLR+p++  e+  + ie+    + + ++++ +d+++++++++g++y+a l+ LP+i+E++Kt+D +++yK+
  gene3109|gene3109|rna3109|rna3109   9 VEEHVILRIPDTLREQFDREIEELG--HPDCEFDF-TDSENITLRYKGTKYKASLIPLPCILEAQKTFDGNQFYKI 81 
                                        69*******************9987..89******.**************************************** PP

                          TAFII55_N  77 aDisqmllv..keeeeakkeeeleeekskkkkkekkkekkfqyphGitpPlknvrkrRFrkrlkk.keieavekev 149
                                         D++ ml+v  k+ +e+               ++ ++ +k+  + GitpPlk v+ rR+r+r+++ +++e+vek+v
  gene3109|gene3109|rna3109|rna3109  82 NDVANMLVVwpKNYTEV---------------EI-NHYTKIYAASGITPPLKFVKYRRWRERAQSlSAVEEVEKKV 141
                                        *********32222222...............22.3556788899***************88766378999***** PP

                          TAFII55_N 150 krLlraDaea 159
                                        k+Ll+ D+ a
  gene3109|gene3109|rna3109|rna3109 142 KELLERDKLA 151
                                        *******876 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.22
                          TAFII55_N 111 kekkfqyphGitpPlknvrkrRFrkrlkkkeie 143
                                        +ek  + ++ +  +++ + +rRF + +k+  +e
  gene3109|gene3109|rna3109|rna3109 211 QEKIKEKKEFLKSATNIIVQRRFEEAIKNLSTE 243
                                        333333344455566667777777777765444 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   8.8   2.7e-06    0.0038      72     196 ..      93     255 ..      27     259 .. 0.68

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.7e-06
                             AAA_23  72 kayveltfenkdgry........trsiererelskkkgktt....kkaklelleideleqfise.llgskkiilnl 134
                                        k+y e+++++ +++y         ++++++r++ + ++ +      k+ +elle d+l   ++   ++ ++++ ++
  gene3109|gene3109|rna3109|rna3109  93 KNYTEVEINHYTKIYaasgitppLKFVKYRRWRERAQSLSAveevEKKVKELLERDKLATSVRIqTINADNEEEDV 168
                                        6788899999999999999999988888888888877666611114444444444555555554344444444444 PP

                             AAA_23 135 ilflgqer..........feefelkdkke..............rleelekeleeledekkllekl.......eqek 179
                                        +++ ++ +          +      +++e              +++e++++++e++++ k   +        e +k
  gene3109|gene3109|rna3109|rna3109 169 SSLAAELEhnlldeylvdQ------KQFEevavesemvrelkrQIAEIQEKIKEKKEFLKSATNIivqrrfeEAIK 238
                                        4444443444443333331......333344444555554444888888888888887777666677777777777 PP

                             AAA_23 180 ekekeleeleeeleeil 196
                                        +   el+e++ +l++++
  gene3109|gene3109|rna3109|rna3109 239 NLSTELDEIRTKLNSQD 255
                                        78888888888888776 PP

>> MIP-T3_C  Microtubule-binding protein MIP-T3 C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   9.3   2.1e-05     0.029      77     143 ..     165     231 ..     124     244 .. 0.85
   2 ?   -0.1   0.1      0.57   7.8e+02     107     130 ..     232     255 ..     222     260 .. 0.64

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.1e-05
                           MIP-T3_C  77 qdDidsMqrELemWrseyrqqaeelaeerrateealeplkaqlaeleeaIkdqkekisnvrakilkN 143
                                        ++D+ s++ ELe     +    ++  ee ++  e++ +lk q+ae++e+Ik++ke ++ + + i++ 
  gene3109|gene3109|rna3109|rna3109 165 EEDVSSLAAELEHNLLDEYLVDQKQFEEVAVESEMVRELKRQIAEIQEKIKEKKEFLKSATNIIVQR 231
                                        79**********988877788889999999*************************999988888764 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.57
                           MIP-T3_C 107 ateealeplkaqlaeleeaIkdqk 130
                                          eea+++l  +l e+  +++ q 
  gene3109|gene3109|rna3109|rna3109 232 RFEEAIKNLSTELDEIRTKLNSQD 255
                                        445666666666666666666554 PP

>> MnmE_helical  MnmE helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   2.0   2.8e-05     0.039      66     168 ..     129     254 ..      70     259 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.8e-05
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxx......xxxxxxx.................xxxxxxxxxxxxxx RF
                       MnmE_helical  66 elaekleelkeelekllatakrgellr.eGik......Dllkeke.................ekeeeevlkiSakt 117
                                        +  + +ee+++++++ll++ k    +r + i+      D                       ++++ e  ++++++
  gene3109|gene3109|rna3109|rna3109 129 QSLSAVEEVEKKVKELLERDKLATSVRiQTINadneeeD-----VsslaaelehnlldeylvDQKQFE--EVAVES 197
                                        566778888888888888887777666444557555551.....133433444433444433233333..344444 PP

                                        xxxxxxxxxxxxxxx.x.xxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       MnmE_helical 118 gegieeLeeaikele.l.eeiee.....eplltnaRhkealekalealeeakealeag 168
                                         e + eL+++i+e++ + +e +e     +++++++R  ea+++  ++l+e++++l+++
  gene3109|gene3109|rna3109|rna3109 198 -EMVRELKRQIAEIQeKiKEKKEflksaTNIIVQRRFEEAIKNLSTELDEIRTKLNSQ 254
                                        .55888888887755334222223444599*******************999999876 PP

>> Cauli_AT  Aphid transmission protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   3.9     0.035        48     133     160 ..     189     216 ..     120     216 .. 0.62
   2 ?   10.8   6.1   0.00024      0.34      93     158 ..     187     251 ..     167     253 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.035
                           Cauli_AT 133 kivtekllkeevkdlderlseirdslka 160
                                        + +  +   e+v++l++++ ei++++k+
  gene3109|gene3109|rna3109|rna3109 189 QFEEVAVESEMVRELKRQIAEIQEKIKE 216
                                        23333444579***************95 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00024
                           Cauli_AT  93 kkifkeggedkekktklletLkeaqnrikkleeetkklaekivtekllkeevkdlderlseirdsl 158
                                        +k f+e+ +++e   +l   + e+q++ik+ +e  k+ + +i  ++  +e +k+l  +l eir +l
  gene3109|gene3109|rna3109|rna3109 187 QKQFEEVAVESEMVRELKRQIAEIQEKIKEKKEFLKSAT-NIIVQRRFEEAIKNLSTELDEIRTKL 251
                                        678999***********************9988888865.56667889***************987 PP

>> Phage_HK97_TLTM  Tail length tape measure protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8  11.2    0.0025       3.4      70     160 ..     142     225 ..     122     259 .. 0.68

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0025
                    Phage_HK97_TLTM  70 eevadekdklkeslkeqnklvkeaeqkveelkkeldkyqvsingylvnkldskeeaiklaeatdklsesqsaleav 145
                                        +e+  e+dkl  s++ q +++++ e++v +l  el+ +   ++ ylv++ + +e a+     ++   e + +  ++
  gene3109|gene3109|rna3109|rna3109 142 KEL-LERDKLATSVRIQTINADNEEEDVSSLAAELEHNL--LDEYLVDQKQFEEVAVE----SEMVRELKRQIAEI 210
                                        333.3689******************************9..*******9988887775....33333334444555 PP

                    Phage_HK97_TLTM 146 tkkskeiqsaLtsve 160
                                        ++k ke ++ L+s+ 
  gene3109|gene3109|rna3109|rna3109 211 QEKIKEKKEFLKSAT 225
                                        555555555555532 PP

>> Exo84_C  Exocyst component 84 C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   2.1       0.1   1.4e+02      21      73 ..     129     182 ..     123     189 .. 0.75
   2 ?   10.8   4.4   0.00023      0.32      15      74 ..     186     248 ..     181     260 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.1
                            Exo84_C  21 eAVdlleklesklkklskklkdeeavlqdlislkv.eqrreelasklsrellsk 73 
                                        ++ + +e++e+k+k+l ++ k   +v  + i++   e+ +++la++l ++ll++
  gene3109|gene3109|rna3109|rna3109 129 QSLSAVEEVEKKVKELLERDKLATSVRIQTINADNeEEDVSSLAAELEHNLLDE 182
                                        677788889999999998888666777777777651567899999999999866 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00023
                            Exo84_C  15 arrkFee.AVd..lleklesklkklskklkdeeavlqdlislkveqrreelasklsrellskn 74 
                                         +++Fee AV+  ++++l+ +++++++k+k+++++l++ +++ v++r ee +++ls+el +  
  gene3109|gene3109|rna3109|rna3109 186 DQKQFEEvAVEseMVRELKRQIAEIQEKIKEKKEFLKSATNIIVQRRFEEAIKNLSTELDEIR 248
                                        577887647853379******************************************995432 PP

>> LUC7  LUC7 N_terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.5      0.14   1.9e+02      92     138 ..     133     178 ..     120     182 .. 0.73
   2 ?   10.6   5.5   0.00024      0.33      64     139 ..     178     248 ..     174     259 .. 0.77

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.14
                                        XXXXXXXXXXXXXXXXXXXXXXXXXXXXX....XXXXXXXXXXXXXX CS
                               LUC7  92 lledvdrkiqkgkqrleltqeekeeeeeakakkqeqlkeleekiekl 138
                                         +e+v++k+++  +r +l ++ + ++ +a  +++e++++l +++e+ 
  gene3109|gene3109|rna3109|rna3109 133 AVEEVEKKVKELLERDKLATSVRIQTINA-DNEEEDVSSLAAELEHN 178
                                        58899999999888888666665544444.37889999999888765 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00024
                                        HHHHHHHHH-XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX....XXXXXXXXXXXXXXX CS
                               LUC7  64 elkeeYeearkskkklgyeeeflrfleklledvdrkiqkgkqrleltqeekeeeeeakakkqeqlkeleekiekll 139
                                        +l +eY  ++k+ +++  e e++r+l++ ++++++ki+++k+ l+  ++   + +      +e +k+l+ ++++  
  gene3109|gene3109|rna3109|rna3109 178 NLLDEYLVDQKQFEEVAVESEMVRELKRQIAEIQEKIKEKKEFLKSATNIIVQRRF-----EEAIKNLSTELDEIR 248
                                        667899999999999*****************************998877744333.....455666555555443 PP

>> Atg14  Vacuolar sorting 38 and autophagy-related subunit 14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6  12.3     0.005       6.9      32     147 ..     128     251 ..     121     258 .. 0.62

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.005
                              Atg14  32 aklksekeslkkkiekalegkeeaeqledkiknkkakleelksliadlrer.......lqelkdklsqlkkeieek 100
                                        a+ +s+ e+++kk++++le+ + a++ + +  n  +  e+  sl a+l+ +        q+  + +    + ++e 
  gene3109|gene3109|rna3109|rna3109 128 AQSLSAVEEVEKKVKELLERDKLATSVRIQTINADNEEEDVSSLAAELEHNlldeylvDQKQFEEVAVESEMVREL 203
                                        556788899*************555555555555555555555555555556666665444445555555666666 PP

                              Atg14 101 kkklaklsdklkkRrsdleslqneleerrkk.qiaklqdaikrieqkl 147
                                        k+++a+ ++k+k++++ l+s++n + +rr +  i++l++++ +i+ kl
  gene3109|gene3109|rna3109|rna3109 204 KRQIAEIQEKIKEKKEFLKSATNIIVQRRFEeAIKNLSTELDEIRTKL 251
                                        666666666666777777777777777775414555655555555554 PP

>> Nup54  Nucleoporin complex subunit 54
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.6     0.001       1.4      45      80 ..     127     162 ..     124     177 .. 0.90
   2 ?    1.0   3.5      0.29     4e+02      41      65 ..     189     213 ..     185     259 .. 0.55

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.001
                                        HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              Nup54  45 vaqhrerlkeisdrleeleqkhqletsvrlekakkr 80 
                                         aq  ++++e++++++el ++ +l tsvr++++   
  gene3109|gene3109|rna3109|rna3109 127 RAQSLSAVEEVEKKVKELLERDKLATSVRIQTINAD 162
                                        5788899************************99765 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.29
                                        HHHHHHHHHHHHHHHHHHHHHHHHH CS
                              Nup54  41 Qqkevaqhrerlkeisdrleeleqk 65 
                                        Q +eva+  e++ e++ ++ e+++k
  gene3109|gene3109|rna3109|rna3109 189 QFEEVAVESEMVRELKRQIAEIQEK 213
                                        5556666666666666666666622 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   8.0      0.34   4.7e+02      13      66 ..     200     252 ..     128     260 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.34
                            NPV_P10  13 ikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenIqdiLn 66 
                                        +++++ ++  +q+++++ +e l+  t++  +  +  +++++l+t++++I   Ln
  gene3109|gene3109|rna3109|rna3109 200 VRELKRQIAEIQEKIKEKKEFLKSATNIIVQ-RRFEEAIKNLSTELDEIRTKLN 252
                                        7888889999999998888888887777554.4566677777777777777776 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   7.6     0.012        17       3      95 ..     123     227 ..     121     259 .. 0.68

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.012
                              TMPIT   3 eweelekefkeleetakeykqkleelsklqskcskei..kkqkkrlkelksslkklkksvk...........eeee 65 
                                        +w+e ++++ ++ee +k++k+ le+ +   s   ++i  +++++++++l ++l++   + +           + e+
  gene3109|gene3109|rna3109|rna3109 123 RWRERAQSLSAVEEVEKKVKELLERDKLATSVRIQTInaDNEEEDVSSLAAELEHNLLD-EylvdqkqfeevAVES 197
                                        68888888888888888888877654333333333330034444555555555544333.1355566777777888 PP

                              TMPIT  66 eeveelkeelkerkkvlkevesllpkkngl 95 
                                        e v+elk++++e+++ +ke +++l +   +
  gene3109|gene3109|rna3109|rna3109 198 EMVRELKRQIAEIQEKIKEKKEFLKSATNI 227
                                        888889999999999998888888777554 PP

>> Intein_splicing  Intein splicing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   1.0   0.00066      0.91      75     128 ..     135     182 ..      68     187 .. 0.90
   2 ?    0.4   1.3      0.42   5.7e+02      15      47 ..     184     215 ..     180     254 .. 0.47

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00066
                                        EEEEEECCC--TT-EEEEEHSCEEEEEEEEEEEEECEEEEEEEEETTT-EEEEC CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Intein_splicing  75 givEkradeLkegdliavpdadvvwdkvksievedeeeyVYdltvednhNFvan 128
                                        + vEk+++eL e d +a      +  +++ i+ ++eee+V +l  e +hN + +
  gene3109|gene3109|rna3109|rna3109 135 EEVEKKVKELLERDKLA------TSVRIQTINADNEEEDVSSLAAELEHNLLDE 182
                                        44799999999999999......568************************8765 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.42
                                        HCCECTTEEEEEETTTTEEEEEEEEEEEEEEEE CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Intein_splicing  15 lvekegeevlslnledlklevksvkkliklklk 47 
                                        lv+++ +e+++++ e +++ + ++ ++ + k+k
  gene3109|gene3109|rna3109|rna3109 184 LVDQKQFEEVAVESEMVRELKRQIAEIQE-KIK 215
                                        55566666666655555555555333222.111 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2607  (0.145407); expected 358.6 (0.02)
Passed bias filter:                      788  (0.0439511); expected 358.6 (0.02)
Passed Vit filter:                        80  (0.00446204); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.65u 0.29s 00:00:00.94 Elapsed: 00:00:00.48
# Mc/sec: 1628.98
//
Query:       gene311|gene311|rna311|rna311  [L=982]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.8e-76  255.3   0.2    8.9e-52  175.9   0.0    2.9  2  ThiF             ThiF family
    7.4e-47  160.4  10.1    7.1e-31  108.0   0.4    2.9  3  UBA_e1_thiolCys  Ubiquitin-activating enzyme active site
    1.9e-07   31.7   1.7      1e-06   29.3   0.2    2.7  2  E1_UFD           Ubiquitin fold domain
     0.0026   17.8   0.1        1.2    9.1   0.0    2.5  2  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
  ------ inclusion threshold ------
      0.041   13.2   0.2       0.63    9.4   0.0    2.9  4  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas


Domain annotation for each model (and alignments):
>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.2   0.1   1.4e-24     5e-21       1     230 [.      15     384 ..      15     405 .. 0.71
   2 !  175.9   0.0   2.5e-55   8.9e-52       5     218 ..     426     844 ..     421     863 .. 0.96

  Alignments for each domain:
  == domain 1  score: 75.2 bits;  conditional E-value: 1.4e-24
                                    THHHHHHHHHHHHHHHHTSEEEEE--SHHHHHHHHHHHHHTTTEEEEEESSB--GGGGGTBTTS-GGGTTSBHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ThiF   1 ysrqlallgedgqekLrdskvllvGaGglGsellknLalsGvgkltlvDnDkielsNlnRqflfreediGkpKaevaaea 80 
                                    ysrql +lg++   k+ +skvl++G+ glG+e++knL+l+Gv+  ++ D+  + +s+ln  f+f++ ++G+ K e++ +a
  gene311|gene311|rna311|rna311  15 YSRQLLVLGPKAHVKMMQSKVLIIGMSGLGQEIAKNLILAGVRT-DIYDDSLVRKSDLNTGFYFQSRNVGQRKDESVLNA 93 
                                    89****************************************97.*********************************** PP

                                    HHHT-TTSEEEEEES-CCG.CCS-HHHHTT-SEEEEESSSHHHHHHHHHHHHHHT-EEEEEEEETTEEEEEEE.E..... CS
                                    xxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.x..... RF
                           ThiF  81 lqeinpdveveavteritd.etvleellesvDlVvdalDniearrlvnracvkkgiplieagtlgfegqvvvi.i..... 153
                                    l+e+n +v+v    ++i++ +++ ee+l+s+ l v+    +  +  vn+a ++  i +i     g+ g v+   i     
  gene311|gene311|rna311|rna311  94 LRELNTYVHVG--IGDIMEnREMKEEVLKSYTLLVLVNADLFEQERVNEATRRCNIGFIGCLQRGLLGCVFNDfIhfttr 171
                                    ******98876..566666455799*************9999999*****999997777777777777666553333333 PP

                                    .......E.CCS-ECTSS-....T....GGS.EECCCCEEHHH..................................... CS
                                    .......x.xxxxxxxxxx....x....xxxxxxxxxxxxxxx..................................... RF
                           ThiF 154 .......p.gktgcyeCld....p....sstedptekkvplct..................................... 180
                                           + g  + + C+     +    +             +                                     
  gene311|gene311|rna311|rna311 172 dvngespKlGIIANISCESrddeYtedhI-------------Ehhrrdkkkrtgehnvytlrtvdrhnfedrdrvkigda 238
                                    33333330222222333332222022220.............01222222333333444456677777777777777777 PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                           ThiF 181 ................................................................................ 180
                                                                                                                    
  gene311|gene311|rna311|rna311 239 ifsvtvfnpyelkictktvvegdtyeeikktkifefrsfaeckkeendevfrllhthalfrkehsrdpsprnesdrnkfl 318
                                    77777777777777777777777777777777777777777777777777777777777777777777777777777888 PP

                                    ................HHHCT....E-B-HHHHHHHHHHHHHHHHHHHTTBCGGGCCEEEECCTTTTEEE CS
                                    ................xxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ThiF 181 ................siagn....ipaiatttavvaglaalellkllsgkeklenslltqvdllesrfe 230
                                                    +          ++ ++++v++g +a+e+lkl+s++ +   +++ +++ ++  + 
  gene311|gene311|rna311|rna311 319 eiyeknyseaknelpgD---FaetcAASFMPIVSVLGGYVAQEALKLCSERFTPLLQFY-YFNSYDLLLP 384
                                    88888875444444441...033233459999****************99997666655.6776665444 PP

  == domain 2  score: 175.9 bits;  conditional E-value: 2.5e-55
                                    HHHHHHHHHHHHHTSEEEEE--SHHHHHHHHHHHHHTTTEEEEEESSB--GGGGGTBTTS-GGGTTSBHHHHHHHHHHHT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ThiF   5 lallgedgqekLrdskvllvGaGglGsellknLalsGvgkltlvDnDkielsNlnRqflfreediGkpKaevaaealqei 84 
                                    ++l+g++ ++++ +sk++lvGaG++G+e lknL    v+ +t++D+D+ie sNlnRqflfr+++i   K+ vaa+ ++++
  gene311|gene311|rna311|rna311 426 IVLFGRKKLDQIVNSKIFLVGAGAIGCEHLKNL----VSDVTVTDMDTIEESNLNRQFLFRKKNISDFKSVVAANVICQM 501
                                    667999***************************....68***************************************** PP

                                    -TTS...EEEEEES-CCGCC...S-HHHHTT-SEEEEESSSHHHHHHHHHHHHHHT-EEEEEEEETTEEEEEEEEECCS- CS
                                    xxxx...xxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ThiF  85 npdv...eveavteritdet...vleellesvDlVvdalDniearrlvnracvkkgiplieagtlgfegqvvviipgktg 158
                                      ++   +++++t  ++++t   +++++l ++Dl ++alDn ear +++ ++v  ++pl ++gtlg++g+++++ip    
  gene311|gene311|rna311|rna311 502 REETradKIVPYTLAVNSSTenvFSDSFLGKYDLFALALDNAEARQYMDGRAVVLKKPLFDSGTLGTKGNAQCVIP---- 577
                                    ****9999********99444889***************************************************8.... PP

                                    ECTSS-TGGS.EECCCCEEHHH.......................................................... CS
                                    xxxxxxxxxxxxxxxxxxxxxx.......................................................... RF
                           ThiF 159 cyeCldpsstedptekkvplct.......................................................... 180
                                     y  + +ss++dp+ek++plct                                                          
  gene311|gene311|rna311|rna311 578 -YLTESYSSSRDPPEKEIPLCTvrnfphliehciewaltqfqmlftevkqtnntdesrsvniageedaksdevklgenlf 656
                                    .5555567889********************************************************************* PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                           ThiF 181 ................................................................................ 180
                                                                                                                    
  gene311|gene311|rna311|rna311 657 ehiskspprskkecikyaidlfvsffktniqklkelfpedhiteeglrfweppkrvpreielseesdlhllfllscsnll 736
                                    ******************************************************************************** PP

                                    .....................................................................HHHCT.E-B-H CS
                                    .....................................................................xxxxx.xxxxx RF
                           ThiF 181 .....................................................................siagn.ipaia 190
                                                                                                         +iag+ ipaia
  gene311|gene311|rna311|rna311 737 stcyldgrkitkddfcedideepcdsvqkkkiifekdddtnwhvdfiyaaanlraqnykiknaerldvkRIAGKiIPAIA 816
                                    ******************************************************************************** PP

                                    HHHHHHHHHHHHHHHHHHTTBCGGGCCE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ThiF 191 tttavvaglaalellkllsgkeklensl 218
                                    tttavv+gl++ e++++l +k+kl+n+ 
  gene311|gene311|rna311|rna311 817 TTTAVVSGLICIEMYRYLLNKDKLSNQQ 844
                                    ******************8888887765 PP

>> UBA_e1_thiolCys  Ubiquitin-activating enzyme active site
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.1      0.91   3.3e+03     164     188 ..     388     412 ..     377     435 .. 0.57
   2 !  108.0   0.4     2e-34   7.1e-31       1     140 [.     603     740 ..     603     767 .. 0.84
   3 !   57.8   1.5   4.2e-19   1.5e-15     210     252 .]     763     805 ..     744     805 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.91
                UBA_e1_thiolCys 164 kpkekvkiavsdeeakeeeeeeede 188
                                    +++++++++++++e+ke+ ++ +d+
  gene311|gene311|rna311|rna311 388 DESSEKQKEEDKTEKKEKRDTCADN 412
                                    4444444444444444333332223 PP

  == domain 2  score: 108.0 bits;  conditional E-value: 2e-34
                UBA_e1_thiolCys   1 PneieHtieWArdkFeglFekkpeevnkflkdkekfleelekekeeekletlekvlkllvkerpktfedCvkwArekfek 80 
                                    P+ ieH+ieWA  +F+ lF++  ++ n+  + + +++ e ++  ++++++  e++ + + k+ p++ ++C+k+A++ f +
  gene311|gene311|rna311|rna311 603 PHLIEHCIEWALTQFQMLFTEVKQTNNTDESRSVNIAGEEDA--KSDEVKLGENLFEHISKSPPRSKKECIKYAIDLFVS 680
                                    99*****************98777666655544444443333..33335789999999999******************* PP

                UBA_e1_thiolCys  81 lFnnkikqLlynfPkdsktsdGapFWsgpKraPkplefdlenelhleFvvaaanLraqvy 140
                                     F+++i++L + fP+d+ t++G +FW+ pKr+P+++e+++e++lhl F+++++nL+ ++y
  gene311|gene311|rna311|rna311 681 FFKTNIQKLKELFPEDHITEEGLRFWEPPKRVPREIELSEESDLHLLFLLSCSNLLSTCY 740
                                    ********************************************************9998 PP

  == domain 3  score: 57.8 bits;  conditional E-value: 4.2e-19
                UBA_e1_thiolCys 210 lklkpieFeKDddtnfhidfitaasNlRArnYkIkeadrlkvK 252
                                    ++ k+i FeKDddtn h+dfi+aa+NlRA+nYkIk+a+rl+vK
  gene311|gene311|rna311|rna311 763 VQKKKIIFEKDDDTNWHVDFIYAAANLRAQNYKIKNAERLDVK 805
                                    677999**********************************998 PP

>> E1_UFD  Ubiquitin fold domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.1       0.4   1.4e+03      56      84 ..     456     504 ..     452     514 .. 0.66
   2 !   29.3   0.2   2.9e-10     1e-06       1      57 [.     901     953 ..     901     961 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.4
                         E1_UFD  56 selveevt...................kkkipphqkyldlevsved.ee 84 
                                    ++lv +vt                   kk+i++ + ++  +v+++  ee
  gene311|gene311|rna311|rna311 456 KNLVSDVTvtdmdtieesnlnrqflfrKKNISDFKSVVAANVICQMrEE 504
                                    4555555555666666666777777778999999999999999997332 PP

  == domain 2  score: 29.3 bits;  conditional E-value: 2.9e-10
                         E1_UFD   1 WDrlevegeitlkelldyfkekkklevsmislgvsllYasflpkkkdkerlklklse 57 
                                    WD+lev+ ++t++++++ f    +l+v mis++++llY+sf++ +k++  + +++  
  gene311|gene311|rna311|rna311 901 WDQLEVK-DCTIEQFMKLFG---DLKVEMISHNNKLLYCSFYDTEKNDRYYYKNIMS 953
                                    *******.************...9*******************66666555555554 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.0   0.0    0.0031        11       9      37 ..      29      57 ..      22      96 .. 0.86
   2 !    9.1   0.0   0.00035       1.2       4      41 ..     431     464 ..     429     499 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0031
                                   ..TT-EEEEES-SHHHHHHHHHHHCCT-C CS
                   Shikimate_DH  9 slkekkvlliGaGemaelvakhLlakgvk 37
                                   ++ ++kvl+iG   +++++ak+L+ +gv+
  gene311|gene311|rna311|rna311 29 KMMQSKVLIIGMSGLGQEIAKNLILAGVR 57
                                   57799******************999987 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00035
                                    HHHHS..TT-EEEEES-SHHHHHHHHHHHCCT-CEEEE CS
                   Shikimate_DH   4 kkkleslkekkvlliGaGemaelvakhLlakgvkkvvv 41 
                                    +kkl+++ ++k+ l+GaG ++ + +k+L++     v+v
  gene311|gene311|rna311|rna311 431 RKKLDQIVNSKIFLVGAGAIGCEHLKNLVSD----VTV 464
                                    68899999********************964....444 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.0   0.00018      0.63      33      80 ..      29      75 ..      12     139 .. 0.89
   2 ?   -0.6   0.0      0.21   7.4e+02      33      54 ..     436     457 ..     430     491 .. 0.80
   3 ?   -2.2   0.0      0.62   2.2e+03      91     115 ..     779     803 ..     758     807 .. 0.83
   4 ?   -3.6   0.0       1.7   6.1e+03      64     105 ..     934     972 ..     929     977 .. 0.61

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00018
                                   -GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHHHTC CS
                   2-Hacid_dh_C 33 elsgktvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeeeelgv 80
                                   ++ +++v iiG+  +Gq++ak l   g++  +yd s  +++ + ++g+
  gene311|gene311|rna311|rna311 29 KMMQSKVLIIGMSGLGQEIAKNLILAGVRTDIYDDSLVRKS-DLNTGF 75
                                   67889*************************99999987666.444455 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.21
                                    -GTTSEEEEES-SHHHHHHHHH CS
                   2-Hacid_dh_C  33 elsgktvGiiGlGrIGqavakr 54 
                                    ++ ++++ ++G+G+IG +  k 
  gene311|gene311|rna311|rna311 436 QIVNSKIFLVGAGAIGCEHLKN 457
                                    67789999********876554 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 0.62
                                    H-SEEEE-S--STTTTTSBSHHHHH CS
                   2-Hacid_dh_C  91 esDivslhlpltpetrhlinaeela 115
                                    + D++  +++l ++++++ nae+l+
  gene311|gene311|rna311|rna311 779 HVDFIYAAANLRAQNYKIKNAERLD 803
                                    689*****************99985 PP

  == domain 4  score: -3.6 bits;  conditional E-value: 1.7
                                    EESSSHHHHHCHHHHTCEECSHHHHHHH-SEEEE-S--STTT CS
                   2-Hacid_dh_C  64 aydrskkkeeeeeelgvelvsleellaesDivslhlpltpet 105
                                    + + + ++   +++  +++  + ++ +++D+v++ +   +e 
  gene311|gene311|rna311|rna311 934 YCSFYDTE---KNDRYYYKNIMSTVDENCDFVMVDVLFDAEC 972
                                    55555442...2233345567888889999999987666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (982 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       898  (0.0500865); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.77u 0.29s 00:00:01.06 Elapsed: 00:00:00.47
# Mc/sec: 6258.87
//
Query:       gene3110|gene3110|rna3110|rna3110  [L=224]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.9e-28   99.2   5.0    4.4e-28   98.6   5.0    1.2  1  Peptidase_C48  Ulp1 protease family, C-terminal catalytic dom
     0.0033   17.1   0.4      0.011   15.5   0.1    1.8  2  LupA           Legionella ubiquitin-specific protease A domai


Domain annotation for each model (and alignments):
>> Peptidase_C48  Ulp1 protease family, C-terminal catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.6   5.0   4.9e-32   4.4e-28       1     207 [.      43     208 ..      43     213 .. 0.87

  Alignments for each domain:
  == domain 1  score: 98.6 bits;  conditional E-value: 4.9e-32
                                        ---BHHHHHHHHHHHHHHHHH.CCCTCCCEEE--THHHHHHC..........SS.......TCHCHHHCTTCCCCC CS
                      Peptidase_C48   1 ewlndtvidfylkllaerles.seskaervhflntffvskLtkavkdfkknkskkkfkeskkkdlyngvrrwtrkv 75 
                                        +w+nd++i+fy +l++      ++  + +v++++t+f++ L+                    +++++ v++ t+  
  gene3110|gene3110|rna3110|rna3110  43 QWFNDKIINFYFNLIK----IyATIFEIKVYVFSTYFYTSLK--------------------TKGIKWVQKYTKD- 93 
                                        7**************6....33999999**************....................4445555444555. PP

                                        S..-GGG-SEEEEEEEC.TTEEEEEEEETCCCEEEEE-TTS-SSH.HHHHHHHHHHHHHHHHHCCCCCSTT-.GGG CS
                      Peptidase_C48  76 nkedlfdkdiiyiPinedgkHWvlliinlpdktililDSlislhtvkkenrpinnlkpyLleealkkkqkqldltp 151
                                          e +f +d+i+iP++  ++HWv + +++++  i+++DSl s ++      ++  ++ yL +e ++k+ k +    
  gene3110|gene3110|rna3110|rna3110  94 --ENIFLNDYIFIPVHR-NNHWVFVNVDVNNDEIEYYDSLFSEYR------IVSDIIDYLESERAAKNLKPV---- 156
                                        ..5**************.*************************99......************888886666.... PP

                                        EEEEE.EE-----SSCCCHHHHHHHHHHHHHCTHHCHHHHHSS.HHHHHHHHHHHTT CS
                      Peptidase_C48 152 feier.ltkvpqqknsgDCGiyvlkfiellaegapqessvtltekdvdsfrkklald 207
                                         ++++   + p+q n++DCG++ +++++  + g+  +    +++k++ ++r +la +
  gene3110|gene3110|rna3110|rna3110 157 -KYTMvERNYPKQHNGYDCGLFICMYARNRIFGTHMS----FKNKNMYEYRLRLAHE 208
                                        .3333033789***********************999....688********99955 PP

>> LupA  Legionella ubiquitin-specific protease A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.13   1.2e+03      88     108 ..       8      28 ..       3      35 .. 0.79
   2 !   15.5   0.1   1.2e-06     0.011      50     146 ..     100     191 ..      78     204 .. 0.69

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.13
                                        HHGGGHHHHHHHHHHCT--GG CS
                               LupA  88 gaaalddfilkllekcgidke 108
                                        + + l  +i+k +++c ++++
  gene3110|gene3110|rna3110|rna3110   8 NKTKLVAYIRKNINNCVVKDH 28 
                                        556788999999999988764 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 1.2e-06
                                        -EEEEEEE.SSS-EEEEEE--------EEEEEE-TT-HHHHGGGHHHHHHHHHHCT--GGGEEEEEE..--SS-.- CS
                               LupA  50 khilipvg.pghwrgvyltkpadltdefdlelfdpygpegaaalddfilkllekcgidkeklnirhk..gpvhp.q 121
                                         +i+ipv    hw  v +  ++d+ + +d  lf  y      ++ d i++ le+    k++  ++++     +p q
  gene3110|gene3110|rna3110|rna3110 100 DYIFIPVHrNNHWVFVNVDVNNDEIEYYD-SLFSEYR-----IVSD-IIDYLESERAAKNLKPVKYTmvERNYPkQ 168
                                        599***97357998887777666644444.6777763.....4444.55677777777777666666114556735 PP

                                        --GGGHHHHHHHHHHHHHHHTT--G CS
                               LupA 122 gdayscgdftcayshkkmkelgapk 146
                                         ++y cg f c y+  +  ++g+  
  gene3110|gene3110|rna3110|rna3110 169 HNGYDCGLFICMYARNR--IFGTHM 191
                                        789**********9765..577643 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       707  (0.0394333); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1508.02
//
Query:       gene3111|gene3111|rna3111|rna3111  [L=38]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (38 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       324  (0.0180713); expected 358.6 (0.02)
Passed bias filter:                      227  (0.0126611); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.31u 0.23s 00:00:00.54 Elapsed: 00:00:00.37
# Mc/sec: 304.72
//
Query:       gene3112|gene3112|rna3112|rna3112  [L=625]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.9e-24   84.6   0.0    1.7e-23   83.7   0.0    1.4  1  ABC_tran        ABC transporter
    1.1e-08   35.2   1.0    0.00054   19.9   0.3    2.5  2  AAA_21          AAA domain, putative AbiEii toxin, Type IV TA
    1.4e-08   34.4   0.4    5.9e-08   32.4   0.4    1.8  1  SMC_N           RecF/RecN/SMC N terminal domain
    1.8e-05   25.0   0.0    4.2e-05   23.8   0.0    1.6  1  AAA_22          AAA domain
    4.2e-05   24.1   0.6    8.9e-05   23.1   0.1    1.8  1  AAA_23          AAA domain
    7.5e-05   23.2   0.0    0.00012   22.5   0.0    1.3  1  AAA_16          AAA ATPase domain
    0.00015   21.8   0.0    0.00033   20.7   0.0    1.5  1  ATPase_2        ATPase domain predominantly from Archaea
    0.00016   21.8   0.1    0.00039   20.5   0.1    1.7  1  MMR_HSR1        50S ribosome-binding GTPase
    0.00017   21.3   0.1    0.00035   20.3   0.1    1.4  1  AAA_29          P-loop containing region of AAA domain
    0.00037   20.0   9.6    0.00037   20.0   9.6    1.9  1  ABC2_membrane   ABC-2 type transporter
    0.00083   19.1   0.0     0.0016   18.3   0.0    1.5  1  Cytidylate_kin  Cytidylate kinase
     0.0011   18.9   0.0     0.0021   18.0   0.0    1.3  1  RsgA_GTPase     RsgA GTPase
     0.0012   18.0   0.1     0.0023   17.1   0.1    1.4  1  IIGP            Interferon-inducible GTPase (IIGP)
     0.0018   18.0   0.2      0.018   14.7   0.1    2.2  2  AAA_24          AAA domain
     0.0026   17.9   0.2     0.0065   16.6   0.2    1.8  1  AAA_33          AAA domain
     0.0028   17.6   0.0     0.0097   15.8   0.0    1.9  1  Rad17           Rad17 P-loop domain
     0.0049   17.0   1.7       0.12   12.5   0.6    2.6  2  DUF87           Helicase HerA, central domain
     0.0077   16.0   0.2      0.063   13.0   0.0    2.2  2  IstB_IS21       IstB-like ATP binding protein
     0.0077   16.8   0.2      0.026   15.0   0.2    1.9  1  AAA_18          AAA domain
  ------ inclusion threshold ------
      0.011   15.9   0.0      0.089   13.0   0.0    2.3  1  SbcCD_C         Putative exonuclease SbcCD, C subunit
      0.016   15.5   0.1      0.029   14.6   0.1    1.4  1  AAA_28          AAA domain
      0.022   15.1   0.0       0.06   13.7   0.0    1.8  1  RNA_helicase    RNA helicase
      0.022   14.7   0.4       0.14   12.1   0.1    2.2  2  NTPase_1        NTPase
      0.031   14.2   0.3      0.073   13.0   0.3    1.7  1  NACHT           NACHT domain
      0.035   13.7   0.2      0.066   12.8   0.2    1.4  1  AAA_25          AAA domain
      0.036   13.8   0.1        0.2   11.3   0.1    2.0  2  AAA_15          AAA ATPase domain
      0.038   14.4   0.2       0.11   12.9   0.0    1.9  1  AAA             ATPase family associated with various cellula
      0.043   13.8   0.0      0.076   13.0   0.0    1.5  1  tRNA-synt_2b    tRNA synthetase class II core domain (G, H, P
      0.045   13.5   0.1      0.073   12.8   0.1    1.3  1  AAA_30          AAA domain
      0.067   12.2   0.1        0.1   11.5   0.1    1.2  1  MeaB            Methylmalonyl Co-A mutase-associated GTPase M
      0.074   12.1   0.0       0.15   11.1   0.0    1.4  1  T2SSE           Type II/IV secretion system protein
      0.098   12.4   0.0       0.19   11.5   0.0    1.4  1  ATP_bind_1      Conserved hypothetical ATP binding protein
        0.1   11.9   0.0       0.22   10.8   0.0    1.5  1  FtsK_SpoIIIE    FtsK/SpoIIIE family
       0.11   12.7   0.2        1.8    8.8   0.0    2.3  2  Roc             Ras of Complex, Roc, domain of DAPkinase
       0.12   12.4   0.0       0.33   11.0   0.0    1.7  1  AAA_5           AAA domain (dynein-related subfamily)
       0.12   11.8   0.0       0.23   11.0   0.0    1.3  1  AAA_7           P-loop containing dynein motor region
       0.18   11.8   0.0       0.34   11.0   0.0    1.5  1  Dynamin_N       Dynamin family


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.7   0.0   3.4e-26   1.7e-23      13     137 .]      38     172 ..      32     172 .. 0.92

  Alignments for each domain:
  == domain 1  score: 83.7 bits;  conditional E-value: 3.4e-26
                                        EEEEEESTTSSHHHHHHHHTTSS--...SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH...... CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...... RF
                           ABC_tran  13 kvaivGenGaGKStLlkllagllkp...teGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren...... 79 
                                        ++ai+G++G+GKStL+k+lag l +     G ++l+g +    +++ + + +g++ q++ + ++lt+re+      
  gene3112|gene3112|rna3112|rna3112  38 LLAIIGPSGSGKSTLIKALAGRLAKdaaSTGVVTLNGIER---DIKTWTSVVGFVDQDDVIYKRLTARETvkytak 110
                                        78*******************9998666778888886553...6699***************************** PP

                                        ........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                        ........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ABC_tran  80 ........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                                + d++i+k+ ++lg+ ++k+ ++    ++LSgG+++rv++a  l+++p+l++lDEpt+
  gene3112|gene3112|rna3112|rna3112 111 fklrdkniDVDKKIDKLFERLGIAHIKNCKM----TNLSGGERKRVMVAVELVSDPRLIFLDEPTS 172
                                        *999999888899***************999....*****************************96 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.3   1.1e-06   0.00054       2      51 ..      39      91 ..      38     133 .. 0.71
   2 !   13.4   0.0    0.0001     0.051     238     299 ..     145     203 ..     112     206 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 1.1e-06
                             AAA_21  2 nvliGpNgsGKSnLLdaldllarl.....drdvegltdelsggggirkipslldl 51
                                        ++iGp gsGKS+L++al +  rl      + v  l+ +++++++++++ ++ d 
  gene3112|gene3112|rna3112|rna3112 39 LAIIGPSGSGKSTLIKALAG--RLakdaaSTGVVTLNGIERDIKTWTSVVGFVDQ 91
                                       58****************43..444455555555555555555555555555444 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 0.0001
                             AAA_21 238 SdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHSp 299
                                        S G ++   +++ l +++   +l+++DEp +gL+     ++++llk+l+  g  +i+t H+p
  gene3112|gene3112|rna3112|rna3112 145 SGGERKRVMVAVELVSDP---RLIFLDEPTSGLDSNSALKIIKLLKDLAMAGRTIIFTIHQP 203
                                        555555544444555555...9***********************998888*******8887 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.4   0.4   1.2e-10   5.9e-08      20     199 ..      32     202 ..      17     221 .. 0.75

  Alignments for each domain:
  == domain 1  score: 32.4 bits;  conditional E-value: 1.2e-10
                                        EETTSSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--.BTTCSSTTEEEEEEEEEETTEESSSSS CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              SMC_N  20 lpfsksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihk.skekasvkkaeveitfdnedkklkiek 94 
                                        ++ ++++ ai+Gp GSGKs l+ A+   L +++         + +++    e++  +  +v  ++d++d       
  gene3112|gene3112|rna3112|rna3112  32 GHAEQGLLAIIGPSGSGKSTLIKALAGRLAKDA-------ASTGVVTLnGIERDIKTWTSVVGFVDQDDVI----Y 96 
                                        56778899*****************66666443.......3444554423444555556666666666665....3 PP

                                        SCEEEEEEEETTSEEEEEETTEEE-H.HHHHHHHHCTT-STT......CS-HHHHHHHHHHHHHHHHCCS--SEEE CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              SMC_N  95 eevsisrrvkrkgeseykingkevtk.kevsellesagiske......lLSgGektLvalaLlfAiqkvkpaplyl 163
                                        ++++ +     k + ++k+ +k++   k++ +l+e+ gi         +LSgGe++ v++a    ++ v+   l +
  gene3112|gene3112|rna3112|rna3112  97 KRLTAR--ETVKYTAKFKLRDKNIDVdKKIDKLFERLGIAHIknckmtNLSGGERKRVMVA----VELVSDPRLIF 166
                                        344444..4444555799999999887999999999999654455555********88776....55677778999 PP

                                        ECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSH CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              SMC_N 164 lDeidaaLDeknvkkvaellkeksknaQfivislre 199
                                        lDe  + LD +   k+ +llk        i+ ++++
  gene3112|gene3112|rna3112|rna3112 167 LDEPTSGLDSNSALKIIKLLKDLAMAGRTIIFTIHQ 202
                                        ***********************9999999999876 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.0   8.6e-08   4.2e-05       4      56 ..      35     108 ..      33     204 .. 0.62

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 8.6e-08
                             AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaee.....................erpevvfvtlpsstsskdl 56 
                                        ++g+l+++G+sG+GK+tl++ l+ +l ++a+ +                       +++v++  l++ ++ k  
  gene3112|gene3112|rna3112|rna3112  35 EQGLLAIIGPSGSGKSTLIKALAGRLAKDAASTGvvtlngierdiktwtsvvgfvDQDDVIYKRLTARETVKYT 108
                                        689***********************887777778888888888888888888886666665555555544443 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.1   1.8e-07   8.9e-05      15      90 ..      24     109 ..      10     190 .. 0.62

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 1.8e-07
                             AAA_23  15 idF........skgltlItGpNGaGKTTildAiklaLygetprlsrksgrgfeksdve....iesegkvkayvelt 78 
                                        i +        ++gl +I+Gp G+GK+T++ A+   L  +++ ++    +g+e++  +    +++ ++++ ++++ 
  gene3112|gene3112|rna3112|rna3112  24 IKLisdacghaEQGLLAIIGPSGSGKSTLIKALAGRLAKDAASTGVVTLNGIERDIKTwtsvVGFVDQDDVIYKRL 99 
                                        5555555665589********************9999888877776664444433222222233444444444443 PP

                             AAA_23  79 fenkdgrytrsi 90 
                                          +++ +  ++ 
  gene3112|gene3112|rna3112|rna3112 100 TARETVK--YTA 109
                                        3333332..222 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.0   2.5e-07   0.00012      22      73 ..      33      89 ..      21     200 .. 0.70

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 2.5e-07
                             AAA_16 22 grp.elvllsGesGvGKsslvrellralekd....ggiflrgkcdqlesaipysala 73
                                       + + +l+ ++G+sG+GKs+l+++l+ +l kd    g+++l+g  ++ ++ ++ + ++
  gene3112|gene3112|rna3112|rna3112 33 HAEqGLLAIIGPSGSGKSTLIKALAGRLAKDaastGVVTLNGIERDIKTWTSVVGFV 89
                                       3344899**********************9988765666766666664434443333 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   6.8e-07   0.00033       6     113 ..      22     131 ..      20     135 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 6.8e-07
                           ATPase_2   6 kelkeleeilerepneiyfiYGpegsGKtaLlkeiienl.edkdkyviyyialreesiskldefieeeeekkklek 80 
                                        k +k +   +   ++  + i Gp gsGK++L+k ++ +l +d     +   +  e++i++ ++ ++  ++++ + k
  gene3112|gene3112|rna3112|rna3112  22 KRIKLISDACGHAEQGLLAIIGPSGSGKSTLIKALAGRLaKDAASTGVVTLNGIERDIKTWTSVVGFVDQDDVIYK 97 
                                        5678888888888999999********************8888889999999999999999999995555555555 PP

                           ATPase_2  81 al.giavpkaeleeilkeksklvfkaiellleki 113
                                         l + ++ k +++  l +k+ +v+k+i++l+e +
  gene3112|gene3112|rna3112|rna3112  98 RLtARETVKYTAKFKLRDKNIDVDKKIDKLFERL 131
                                        4425556666665555599**********99876 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.1   7.9e-07   0.00039       3      52 ..      40      90 ..      38     132 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 7.9e-07
                                       EEEESTTSSHHHHHHHHHTS.TEEESSSTTSSSSEEEEEEEETTEEEEEEE CS
                           MMR_HSR1  3 aivGrpNvGKStLinaltge.kaivsdkpgtTrdinegrvklkgkeielvD 52
                                       ai+G + +GKStLi+al g+ +  ++++  +T++ +e+ +k+  + + +vD
  gene3112|gene3112|rna3112|rna3112 40 AIIGPSGSGKSTLIKALAGRlAKDAASTGVVTLNGIERDIKTWTSVVGFVD 90
                                       8*******************5457788889999999998883334444444 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.1   7.1e-07   0.00035      22      43 ..      36      57 ..      29      64 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 7.1e-07
                             AAA_29 22 kgatlltGpsGsGKSTllDAiq 43
                                       +g   ++GpsGsGKSTl+ A++
  gene3112|gene3112|rna3112|rna3112 36 QGLLAIIGPSGSGKSTLIKALA 57
                                       56889*************9975 PP

>> ABC2_membrane  ABC-2 type transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   9.6   7.6e-07   0.00037       3     165 ..     309     494 ..     307     534 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 7.6e-07
                      ABC2_membrane   3 ikallkreflqrwrdpslgllwrliqplllalvfgtvfgnlg...nsedglnr....................... 52 
                                        ik+ll+r  ++ ++++  + ++ +i +++l++ + ++ + ++   n+ed l+                        
  gene3112|gene3112|rna3112|rna3112 309 IKLLLRRRCKLELGTKKNT-IFTIILIFILSISLFLARYIAKniwNREDKLMKvwklstadsrytkvqqeyikhrv 383
                                        7788888888888888777.66666666666666555554444555555553358888888888889999999986 PP

                      ABC2_membrane  53 .pgllffsvlflafsaltsvapvferergvlerelvsplyslsayvlakvlvelpvsllqalifllivyflvgldl 127
                                         + + +fs   +a ++  ++++ f  e+ +++re +++ ysl++y+l+ +++e ++ l + +++++ + +++g  +
  gene3112|gene3112|rna3112|rna3112 384 mLIVSIFSGCSMA-LIPLEAGTAFGFEHVNVKREIAANNYSLASYYLSVLIFEYVRHLPFLIAYMIGMKIIFGEVM 458
                                        6666666666666.44456669999************************************************999 PP

                      ABC2_membrane 128 srfflflllllltalaasslgllisalapsfedasqla 165
                                        +  +  +l+ +l++ +++ + ll+++++++ +  ++++
  gene3112|gene3112|rna3112|rna3112 459 D--LRSILTSCLIYTVSVVFYLLNGSVSRDSKRSAMIV 494
                                        8..*************************9887666655 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   3.2e-06    0.0016       2      32 ..      40      70 ..      39     128 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 3.2e-06
                                       EEE-STTSSHHHHHHHHHHHHT-EEEEHHHH CS
                     Cytidylate_kin  2 aiDGPagsGKssvaralaeklglkyldtgal 32
                                       ai GP+gsGKs++ +ala +l     +tg +
  gene3112|gene3112|rna3112|rna3112 40 AIIGPSGSGKSTLIKALAGRLAKDAASTGVV 70
                                       899*********************9999965 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   4.3e-06    0.0021      97     124 ..      34      61 ..       2      75 .. 0.71

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 4.3e-06
                                        CTTSEEEEECSTTSSHHHHHHHHCTT-- CS
                        RsgA_GTPase  97 lkdktsvlvGqSGvGKStLinallpele 124
                                         ++ + +++G+SG GKStLi+al+++l 
  gene3112|gene3112|rna3112|rna3112  34 AEQGLLAIIGPSGSGKSTLIKALAGRLA 61 
                                        4557899****************99764 PP

>> IIGP  Interferon-inducible GTPase (IIGP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.1   4.7e-06    0.0023      18      72 ..      21      71 ..       6      78 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 4.7e-06
                                       HHHHHHHHHHHHHHHT--EEEEEEESTTSSHHHHHHHHTT--TTSTTS--SSCHS CS
                               IIGP 18 qkvvsiikeaikeiesaklkiavtGdsGnGkssFinaLRliGheeedsAptGvve 72
                                       qk ++ i++a  ++e+  l  a++G sG+Gks+ i aL   G  ++d+A tGvv 
  gene3112|gene3112|rna3112|rna3112 21 QKRIKLISDACGHAEQGLL--AIIGPSGSGKSTLIKAL--AGRLAKDAASTGVVT 71
                                       5667777777777777765..789*************9..599**********96 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.1   3.8e-05     0.018       6      60 ..      40     101 ..      38     127 .. 0.79
   2 ?    0.5   0.0      0.87   4.2e+02     110     134 ..     181     205 ..     176     222 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.8e-05
                             AAA_24   6 liyGpsgiGKTtlakelgpkplfidtek.Glksldadkfpdieswedfldevvel........a 60 
                                        +i+Gpsg+GK+tl+k l    l  d    G+  l++++  di++w+ ++ +v+++        a
  gene3112|gene3112|rna3112|rna3112  40 AIIGPSGSGKSTLIKAL-AGRLAKDAAStGVVTLNGIE-RDIKTWTSVVGFVDQDdviykrltA 101
                                        89***************.55555555555999999999.5699***999999998555554441 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.87
                             AAA_24 110 efrrllkklqelrknvifiahektr 134
                                        ++++llk+l  ++ ++if+ h+  +
  gene3112|gene3112|rna3112|rna3112 181 KIIKLLKDLAMAGRTIIFTIHQPDD 205
                                        56677777777777*******8665 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.2   1.3e-05    0.0065       2      25 ..      39      69 ..      38     179 .. 0.59

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.3e-05
                             AAA_33  2 vllvGlpGsGKstlaerllkklg.......a 25
                                       + ++G++GsGKstl++ l+ +l+       +
  gene3112|gene3112|rna3112|rna3112 39 LAIIGPSGSGKSTLIKALAGRLAkdaastgV 69
                                       6789**************9665544444322 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0     2e-05    0.0097      42      72 ..      33      63 ..      15     131 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2e-05
                              Rad17 42 srkkriLLisGPsGCgkstvvkvLskelgik 72
                                       ++++ +L i GPsG gkst +k L+  l+ +
  gene3112|gene3112|rna3112|rna3112 33 HAEQGLLAIIGPSGSGKSTLIKALAGRLAKD 63
                                       555669*****************99877655 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.6   0.00024      0.12      26      53 ..      39      65 ..      38      72 .. 0.82
   2 ?    2.6   0.0      0.26   1.2e+02     125     209 ..     105     201 ..      70     216 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00024
                              DUF87 26 lAilgsTGsGKSntvavLleellekkga 53
                                       lAi+g +GsGKS++++ L  +l++ + a
  gene3112|gene3112|rna3112|rna3112 39 LAIIGPSGSGKSTLIKALAGRLAK-DAA 65
                                       69********************95.333 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.26
                              DUF87 125 ldqaka....keekeklssdepveklleelk..........kekeelrklknqaiarlldkledllrkggsf..sn 184
                                        ++        k +++ +++d+ + kl+e l           + + ++rk  + a + ++d++  +l+++ s   sn
  gene3112|gene3112|rna3112|rna3112 105 VK---YtakfKLRDKNIDVDKKIDKLFERLGiahiknckmtNLSGGERKRVMVAVELVSDPRLIFLDEPTSGldSN 177
                                        22...14447899999999999999999999999999999766678888888889999999999999888887677 PP

                              DUF87 185 sstdliallleklekegkitiidls 209
                                        s  ++i+ll ++l   g+  i+ ++
  gene3112|gene3112|rna3112|rna3112 178 SALKIIKLL-KDLAMAGRTIIFTIH 201
                                        777777777.555556666665555 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.0   0.00013     0.063      28      83 ..      17      72 ..       6      84 .. 0.69
   2 ?   -0.0   0.1       1.3   6.4e+02      79     114 ..     351     386 ..     338     391 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00013
                          IstB_IS21 28 rsldkrkvkeLatlsfiekkenivllGpsGvGKshlaialgveavraglsvlfvrv 83
                                       + ++++++k +      +++  ++++GpsG GKs l  al+ + +++  s+  v++
  gene3112|gene3112|rna3112|rna3112 17 KRYNQKRIKLISDACGHAEQGLLAIIGPSGSGKSTLIKALAGRLAKDAASTGVVTL 72
                                       455555555444333344455678****************9998888777665555 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 1.3
                          IstB_IS21  79 lfvrvedLveelkrarrdgklaralkrllkvdllil 114
                                        ++ r ++L++  k+  +d ++++ +++++k +++++
  gene3112|gene3112|rna3112|rna3112 351 IWNREDKLMKVWKLSTADSRYTKVQQEYIKHRVMLI 386
                                        688899999999*****************9988765 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.2   5.5e-05     0.026       2      23 ..      40      61 ..      39     132 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 5.5e-05
                             AAA_18  2 lltGtpGvGKttlakeLskrlg 23
                                       ++ G++G+GK+tl k+L+ rl+
  gene3112|gene3112|rna3112|rna3112 40 AIIGPSGSGKSTLIKALAGRLA 61
                                       589**************88863 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   0.00018     0.089      62      89 ..     160     187 ..     137     188 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00018
                            SbcCD_C  62 palrlvfLDEAFsklDeesiatllelle 89 
                                        +++rl+fLDE  s+lD++s+ ++++ll+
  gene3112|gene3112|rna3112|rna3112 160 SDPRLIFLDEPTSGLDSNSALKIIKLLK 187
                                        469*********************9997 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.1   5.9e-05     0.029       3      22 ..      40      59 ..      38      80 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 5.9e-05
                             AAA_28  3 vitGgestGKTtlleaLaar 22
                                       +i+G++++GK+tl++aLa r
  gene3112|gene3112|rna3112|rna3112 40 AIIGPSGSGKSTLIKALAGR 59
                                       89****************54 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   0.00012      0.06       3      26 ..      41      64 ..      39     108 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 0.00012
                       RNA_helicase  3 lyGpsgeGKStlakeLakallkkl 26
                                       + Gpsg GKStl+k La +l+k+ 
  gene3112|gene3112|rna3112|rna3112 41 IIGPSGSGKSTLIKALAGRLAKDA 64
                                       89******************9766 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   0.00028      0.14       3      44 ..      40      80 ..      38     143 .. 0.78
   2 ?    0.0   0.0       1.4     7e+02     113     144 ..     181     211 ..     141     219 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00028
                                       EEE--TTSSHHHHHHHHHHHH...GGGEEEEEEEEE------ CS
                           NTPase_1  3 fiTGppGvGKtTlvkkvlellkssgvkvgGfyteevreggrr 44
                                       +i Gp+G+GK+Tl+k ++  l  ++   +G++t +  e++ +
  gene3112|gene3112|rna3112|rna3112 40 AIIGPSGSGKSTLIKALAGRL-AKDAASTGVVTLNGIERDIK 80
                                       688******************.56688889998766665555 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 1.4
                                        HHHHHHHHHHTTTSEEEEE--SS--SHHHHHH CS
                           NTPase_1 113 kfkeaveevLksekpvlavihrrkdlalveei 144
                                        k+++ ++++   ++ ++++ih++ d  l++e+
  gene3112|gene3112|rna3112|rna3112 181 KIIKLLKDLAMAGRTIIFTIHQP-DDILTDEF 211
                                        667777787789999*******9.55666665 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.3   0.00015     0.073       3      28 ..      39      64 ..      37      72 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00015
                                       EEEEC-TTTCHHHHHHHHHHHHCTS- CS
                              NACHT  3 vilqGeaGsGKTtLlqklalawaegk 28
                                       +++ G++GsGK+tL++ la  +a++ 
  gene3112|gene3112|rna3112|rna3112 39 LAIIGPSGSGKSTLIKALAGRLAKDA 64
                                       789****************9999875 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.2   0.00014     0.066      31      92 ..      34     101 ..      21     201 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00014
                             AAA_25  31 pagelallaGapgtGKttlaldlalavatGkpwlg.......pvapeqgkVlyvsaEdsedelrrRlra 92 
                                        ++++l +++G++g+GK+tl   la  +a++   +g       ++  + ++ ++  + d+ d + +Rl a
  gene3112|gene3112|rna3112|rna3112  34 AEQGLLAIIGPSGSGKSTLIKALAGRLAKDAASTGvvtlngiERDIKTWTSVVG-FVDQDDVIYKRLTA 101
                                        578999*********************966555554444455433344443333.33333366666664 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   0.00041       0.2      13      44 ..      18      57 ..       9     144 .. 0.70
   2 ?   -1.0   0.0       2.2   1.1e+03     323     366 ..     161     203 ..     157     206 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00041
                             AAA_15 13 slkdveidlsee........ltvliGkNnsGKSsileald 44
                                       ++ +  i+l ++        l  +iG+ +sGKS++++al 
  gene3112|gene3112|rna3112|rna3112 18 RYNQKRIKLISDacghaeqgLLAIIGPSGSGKSTLIKALA 57
                                       5666677777777777778899****************95 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 2.2
                             AAA_15 323 knvilliEEPEahLHpqaqkvlikllkelandnktQviitTHSp 366
                                        ++ +++++EP   L  +    +ikllk+la  ++  +i+t H p
  gene3112|gene3112|rna3112|rna3112 161 DPRLIFLDEPTSGLDSNSALKIIKLLKDLAMAGR-TIIFTIHQP 203
                                        67899*************************9998.777777765 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   0.00023      0.11       3      31 ..      41      74 ..      39     110 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00023
                                       EESSTTSSHHHHHHHHHHHH.....THEEEEEET CS
                                AAA  3 lyGppGtGKTllakavakel.....gvefleisg 31
                                       ++Gp G GK++l+ka+a  l     ++ +++++g
  gene3112|gene3112|rna3112|rna3112 41 IIGPSGSGKSTLIKALAGRLakdaaSTGVVTLNG 74
                                       79****************9733332344565555 PP

>> tRNA-synt_2b  tRNA synthetase class II core domain (G, H, P, S and T)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   0.00016     0.076      62     125 ..      99     219 ..      96     383 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00016
                                        EEEEEEEEEESGGGHHHHHHHHHHHHHHHHHHTT.SCEEEEEE.GTTSCBTTSEEEEEEEEETT............ CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxx............ RF
                       tRNA-synt_2b  62 Fhqkdgyvfhaeaslddslrdlikaisriferlglefraiiel.msaksadykdkkefeavses............ 124
                                        ++  + + + a+ +l+d+  d+ k+i+++ferlg+   +i+++ m   +++++++k +++ +e             
  gene3112|gene3112|rna3112|rna3112  99 LTARETVKYTAKFKLRDKNIDVDKKIDKLFERLGIA--HIKNCkMT--NLSGGERKRVMVAVELvsdprlifldep 170
                                        56778888999999********************88..78998555..699*********9998777777777777 PP

                                        ................................................T CS
                                        ................................................x RF
                       tRNA-synt_2b 125 ................................................l 125
                                                                                        +
  gene3112|gene3112|rna3112|rna3112 171 tsgldsnsalkiikllkdlamagrtiiftihqpddiltdefdeilllsQ 219
                                        7777777777777777777775555555555555555555555555441 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   0.00015     0.073      16      45 ..      34      63 ..      18      87 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00015
                             AAA_30 16 sgdrvavltGpAGtGKttalkalreaweaa 45
                                        ++ + ++ Gp G+GK+t++kal+  ++++
  gene3112|gene3112|rna3112|rna3112 34 AEQGLLAIIGPSGSGKSTLIKALAGRLAKD 63
                                       3456899***************97655544 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   0.00022       0.1      17      64 ..      22      71 ..      10      76 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00022
                                       HHHHHHGGG-S-SEE..EEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEE CS
                               MeaB 17 ellerllakaGraqv..vGltGvPGaGkstlvealglelrrrGkrvavla 64
                                       + ++ +++ +G+a++  + + G  G+Gkstl++al+ +l++     +v+ 
  gene3112|gene3112|rna3112|rna3112 22 KRIKLISDACGHAEQglLAIIGPSGSGKSTLIKALAGRLAKDAASTGVVT 71
                                       55677888999997544899*******************99998888876 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00031      0.15     116     156 ..      25      63 ..       7      79 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00031
                              T2SSE 116 ekiaevlrkavrerglilvsGgTgsGKttllyallkeinks 156
                                        + i+++  +a  e+gl+ + G+ gsGK+tl+ al   ++k+
  gene3112|gene3112|rna3112|rna3112  25 KLISDACGHA--EQGLLAIIGPSGSGKSTLIKALAGRLAKD 63 
                                        5555555666..89999*****************9999887 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00038      0.19       1      32 [.      41      72 ..      41      80 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00038
                         ATP_bind_1  1 vvGpaGsGKttfvgalseilelrgrsvavvNL 32
                                       ++Gp GsGK+t+++al+  l +   s  vv L
  gene3112|gene3112|rna3112|rna3112 41 IIGPSGSGKSTLIKALAGRLAKDAASTGVVTL 72
                                       79**************9988888777777766 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00046      0.22      27      60 ..      22      57 ..      12      70 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00046
                                       TS-EEEEEGGGS-...SEEEE--TTSSHHHHHHHHH CS
                       FtsK_SpoIIIE 27 sgnplvldlkkma..shllvaGatgsGKStalntLi 60
                                        +++l++d+ ++a  + l ++G +gsGKSt +++L 
  gene3112|gene3112|rna3112|rna3112 22 KRIKLISDACGHAeqGLLAIIGPSGSGKSTLIKALA 57
                                       5778899999999888899*************9985 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0    0.0037       1.8       3      27 ..      40      64 ..      39      94 .. 0.71
   2 ?    1.0   0.0      0.94   4.6e+02      51      86 ..     352     388 ..     337     396 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0037
                                       EEESSTTSSHHHHHHCHCT-CCC-E CS
                                Roc  3 vlvGdsgvGKtsllkrfvedkfsek 27
                                        ++G sg+GK++l+k +  +  ++ 
  gene3112|gene3112|rna3112|rna3112 40 AIIGPSGSGKSTLIKALAGRLAKDA 64
                                       69*************9985544333 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.94
                                        TTTTCEEEEEEEE-S.GGCTTTT-HHHHCTSCEEEEE CS
                                Roc  51 kkvkkvklniWDtaG.qerfrslhplylreaalailv 86 
                                        ++ ++  +++W ++    r+ ++++ y++++ ++i+ 
  gene3112|gene3112|rna3112|rna3112 352 WNREDKLMKVWKLSTaDSRYTKVQQEYIKHRVMLIVS 388
                                        4445567899999873578889******999988875 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00068      0.33       4      24 ..      41      64 ..      39      85 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00068
                                       EE--SSSSHHHHHHHGGGGB...S CS
                              AAA_5  4 LvGppGtgKselaerlaaal...n 24
                                       ++Gp+G+gKs+l++ la +l    
  gene3112|gene3112|rna3112|rna3112 41 IIGPSGSGKSTLIKALAGRLakdA 64
                                       79***************9996433 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00047      0.23      33      70 ..      35      73 ..      19      90 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00047
                              AAA_7 33 kkpvl.lvGptGtGKtviikdllkkldkekylsltinfs 70
                                       ++ +l ++Gp+G+GK+++ik l  +l k+  ++ +++++
  gene3112|gene3112|rna3112|rna3112 35 EQGLLaIIGPSGSGKSTLIKALAGRLAKDAASTGVVTLN 73
                                       44444279******************9999888877765 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0    0.0007      0.34       1      22 [.      39      60 ..      39     146 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0007
                                       EEEEEBTTTTHHHHHHHHHTS- CS
                          Dynamin_N  1 iavvGsqSsGKSSvlnaLlged 22
                                       +a++G   sGKS+++ aL g+ 
  gene3112|gene3112|rna3112|rna3112 39 LAIIGPSGSGKSTLIKALAGRL 60
                                       589****************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (625 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       904  (0.0504211); expected 358.6 (0.02)
Passed bias filter:                      596  (0.0332422); expected 358.6 (0.02)
Passed Vit filter:                       120  (0.00669307); expected 17.9 (0.001)
Passed Fwd filter:                        37  (0.0020637); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              37  [number of targets reported over threshold]
# CPU time: 0.80u 0.33s 00:00:01.13 Elapsed: 00:00:00.49
# Mc/sec: 3861.07
//
Query:       gene3113|gene3113|rna3113|rna3113  [L=129]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1015  (0.0566122); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.58u 0.37s 00:00:00.95 Elapsed: 00:00:00.57
# Mc/sec: 683.95
//
Query:       gene3114|gene3114|rna3114|rna3114  [L=114]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-18   67.4   1.3    1.6e-18   67.1   1.3    1.1  1  RRS1      Ribosome biogenesis regulatory protein (RRS1)


Domain annotation for each model (and alignments):
>> RRS1  Ribosome biogenesis regulatory protein (RRS1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.1   1.3   8.7e-23   1.6e-18      28     123 ..      14     105 ..       2     113 .. 0.86

  Alignments for each domain:
  == domain 1  score: 67.1 bits;  conditional E-value: 8.7e-23
                                        HHHHHHHHHHHHHHHHHHHS-EEEE.TEEEEE-----S----SS-S---XXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                               RRS1  28 elkelardnvqlLinqllslptesteegvlakLpepttkLPRekplPkpkplTkWekFAkkKGikkkkekrsklvy 103
                                        ++++ ++  +++L+ ++ +lp +++e+  la Lp+p   LP  k++  pk++ kW+ FA++KGi  +k +r + vy
  gene3114|gene3114|rna3114|rna3114  14 KYEQPSQAHINALLTRISQLPVKKHENTKLAILPAPVLVLPH-KKCEVPKQKSKWQLFAERKGI--RK-RRCREVY 85 
                                        5677788999*******************************6.5566777889***********..44.689**** PP

                                        XXXXXXXXXXXXXXXXXX.. CS
                               RRS1 104 DeetkeWvprwGykgankek 123
                                        De+++++ pr+G  ++ k k
  gene3114|gene3114|rna3114|rna3114  86 DEKNDTFLPRYGRFSVSKMK 105
                                        ************99988865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (114 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       461  (0.0257125); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.34s 00:00:00.88 Elapsed: 00:00:00.54
# Mc/sec: 635.79
//
Query:       gene3115|gene3115|rna3115|rna3115  [L=181]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-08   34.6  20.0    1.7e-08   34.6  20.0    2.5  2  DHHC      DHHC palmitoyltransferase


Domain annotation for each model (and alignments):
>> DHHC  DHHC palmitoyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   2.3     0.064   1.2e+03      65      80 ..      19      34 ..       4      62 .. 0.50
   2 !   34.6  20.0   9.5e-13   1.7e-08       6      67 ..      70     131 ..      65     151 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.064
                               DHHC 65 alvlllialvklveee 80
                                       +++++l+++++l+  +
  gene3115|gene3115|rna3115|rna3115 19 ITITALYYITNLYICM 34
                                       2222222222222222 PP

  == domain 2  score: 34.6 bits;  conditional E-value: 9.5e-13
                               DHHC   6 kfCstcniykpprskHcrvCnrcvlrfDHhCpwlnnciGerNykyFllfllylllllilalv 67 
                                         +C  c+  + + ++Hc  C+rc  +  HhC w+  c+   N + F++f+l+ +l  + +l 
  gene3115|gene3115|rna3115|rna3115  70 GVCMRCHHLRYASTHHCMLCDRCYDDRSHHCAWISGCVYGGNKNEFVFFVLFAVLHGVCNLN 131
                                        58************************************999999999888888875444333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       914  (0.0509789); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.37s 00:00:00.97 Elapsed: 00:00:00.58
# Mc/sec: 937.60
//
Query:       gene3116|gene3116|rna3116|rna3116  [L=76]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
       0.18   11.7   0.0       0.21   11.5   0.0    1.1  1  Hypoth_Ymh  Protein of unknown function (Hypoth_ymh)


Domain annotation for each model (and alignments):
>> Hypoth_Ymh  Protein of unknown function (Hypoth_ymh)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   1.2e-05      0.21      72     113 ..      10      54 ..       5      63 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 1.2e-05
                         Hypoth_Ymh  72 seqeGlknLlaGivsaiRNpkaHeekkd...elseeealeaLall 113
                                        s+ + ++++l G+  ++RN+  H+ k++   + +e+e+   +++l
  gene3116|gene3116|rna3116|rna3116  10 SITRCTAHFLYGAPFLVRNVVGHHGKEErivTATEDECELKMVIL 54 
                                        6778899****************9999999988999986555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       324  (0.0180713); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.29s 00:00:00.63 Elapsed: 00:00:00.44
# Mc/sec: 523.80
//
Query:       gene3117|gene3117|rna3117|rna3117  [L=364]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.9e-11   42.0   2.8    1.1e-10   41.0   2.8    1.6  1  GATA      GATA zinc finger


Domain annotation for each model (and alignments):
>> GATA  GATA zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.0   2.8   5.9e-15   1.1e-10       1      34 [.     305     336 ..     305     338 .. 0.96

  Alignments for each domain:
  == domain 1  score: 41.0 bits;  conditional E-value: 5.9e-15
                               GATA   1 CsnCgttkTplWRrgpdgnksLCnaCGlyykkkg 34 
                                        C++Cgt+ T+lWR+  +g++ +CnaCGlyyk +g
  gene3117|gene3117|rna3117|rna3117 305 CAHCGTRVTSLWRKL-HGET-VCNACGLYYKIHG 336
                                        **************9.9999.**********998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (364 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       702  (0.0391544); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 2369.89
//
Query:       gene3118|gene3118|rna3118|rna3118  [L=77]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       685  (0.0382063); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 491.65
//
Query:       gene3119|gene3119|rna3119|rna3119  [L=29]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (29 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       459  (0.025601); expected 358.6 (0.02)
Passed bias filter:                      226  (0.0126053); expected 358.6 (0.02)
Passed Vit filter:                         7  (0.000390429); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.30u 0.24s 00:00:00.54 Elapsed: 00:00:00.39
# Mc/sec: 224.35
//
Query:       gene312|gene312|rna312|rna312  [L=115]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       991  (0.0552736); expected 358.6 (0.02)
Passed bias filter:                      520  (0.0290033); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.28s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 854.39
//
Query:       gene3120|gene3120|rna3120|rna3120  [L=146]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.8e-26   92.4   0.1    2.2e-26   92.2   0.1    1.0  1  UQ_con     Ubiquitin-conjugating enzyme
    8.3e-06   25.7   0.0    1.1e-05   25.3   0.0    1.1  1  UEV        UEV domain
     0.0062   16.2   0.0     0.0076   16.0   0.0    1.2  1  Prok-E2_B  Prokaryotic E2 family B


Domain annotation for each model (and alignments):
>> UQ_con  Ubiquitin-conjugating enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.2   0.1   3.7e-30   2.2e-26       1     135 [.       9     141 ..       9     145 .. 0.88

  Alignments for each domain:
  == domain 1  score: 92.2 bits;  conditional E-value: 3.7e-30
                                        HHHHHHHHHHHSTTTTEEEEEEETTEECEEEEEEEB.TTSTTTTEEEEEEEE--TTTTTS--EEEESST-.SCTTB CS
                             UQ_con   1 rlqkelkelakkkpsgisaklvddenlfewkvlikgpedtpYeggvFklelefpedYPlkpPkvkfvtki.fHPnv 75 
                                        r+ kelk l+++ p+ ++         + + + + g+++t+Y+g++F+l+le++++YP++pP+  fv +i ++ +v
  gene3120|gene3120|rna3120|rna3120   9 RFLKELKGLKQNMPTHFRLVSH---TSTALVLDMYGAPGTIYAGETFTLRLEINDNYPIDPPTAVFVRNIpVNEHV 81 
                                        6789999988888888876544...56899999**********************************8773699** PP

                                        ETTSBB-CGGGSTTT--TTSHHHHHHHHHHHHHHS-.-TTS-SSHHHHHHHHHTHHHHHHH CS
                             UQ_con  76 dksGevcldiLkeekWspaltlesvllsiqsLlaep.npesplnkeaakllkkdreeykkk 135
                                        +++G++c+++L+++ Wspa+tle v+++i+s+l++   +++p ++  ++ +k++++  ++k
  gene3120|gene3120|rna3120|rna3120  82 YTNGHICISVLHDD-WSPAMTLEMVVVAILSMLSDAkRKSKPPDNYFYTVFKRNKSPRDTK 141
                                        ************66.******************99879999********999998765555 PP

>> UEV  UEV domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.0   1.8e-09   1.1e-05       7     114 ..       9     112 ..       4     123 .. 0.73

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 1.8e-09
                                        HHHHH-TTEEEEEEEEE-..TTS-EEEEEEEEEEEE-SSSTTS-EEEEEEE--TTTTTS--EEEE-GCC--TSGGG CS
                                UEV   7 kvlqkfknlkprtevytf..edgesklllnlkGtipvkykgatyniPiliwvlesyPveaPivyvkptksmvikkn 80 
                                        ++l++ k lk ++ ++    ++ +++l l ++G   + y g t+ +   + + ++yP+ +P+ +       +i +n
  gene3120|gene3120|rna3120|rna3120   9 RFLKELKGLKQNMPTHFRlvSHTSTALVLDMYGAPGTIYAGETFTL--RLEINDNYPIDPPTAVFV----RNIPVN 78 
                                        566777777777765544357888899999***99999**999775..66789********97654....3699** PP

                                        GGB-TTSBB--HHHHS.--TTT--HHHHHHHHHH- CS
                                UEV  81 envdaqGlvylpyLee.Wkreksnlvslvqelaqa 114
                                        e+v ++G +   +L++ W++ +++l ++v  + ++
  gene3120|gene3120|rna3120|rna3120  79 EHVYTNGHICISVLHDdWSP-AMTLEMVVVAILSM 112
                                        **************963666.77766665544432 PP

>> Prok-E2_B  Prokaryotic E2 family B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   1.3e-06    0.0076      34     101 ..      48     109 ..       9     125 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.3e-06
                          Prok-E2_B  34 sggtvdlrlvypdsfpllppavflqdpeqlkllpHintfggaLClleeeldldewdpngsvadvleql 101
                                         g t+ lrl ++d++p  pp  + +     ++  H++t +g +C        d w p++++  v+  +
  gene3120|gene3120|rna3120|rna3120  48 AGETFTLRLEINDNYPIDPPTAVFVRNI--PVNEHVYT-NGHICI---SVLHDDWSPAMTLEMVVVAI 109
                                        6999**************9987766544..699*****.******...57778888888777666444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       393  (0.0219198); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1066.42
//
Query:       gene3121|gene3121|rna3121|rna3121  [L=275]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0064   14.8   1.4     0.0074   14.6   1.4    1.1  1  CDC45     CDC45-like protein
  ------ inclusion threshold ------
      0.013   13.8  13.5      0.018   13.3  13.5    1.1  1  Nop14     Nop14-like family
      0.014   14.0   4.5      0.021   13.4   4.5    1.2  1  RRN3      RNA polymerase I specific transcription initiation 
       0.57    9.5  13.0       0.77    9.0  13.0    1.2  1  BUD22     BUD22
          6    6.2  18.1        9.3    5.6  18.1    1.3  1  SDA1      SDA1


Domain annotation for each model (and alignments):
>> CDC45  CDC45-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   1.4   2.1e-06    0.0074     121     203 ..      52     133 ..      33     220 .. 0.50

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.1e-06
                              CDC45 121 eayealeeeeesdeedeeeeeeddddeeeeeeeeedeedeeedeeeskkkrksksdeeee..sddddersrkrrrs 194
                                         ++e+ ++  + dee   ee  d+d+e+ +++++ +++d++++e   + ++ s+++  ++  +d+++e   +r+ +
  gene3121|gene3121|rna3121|rna3121  52 ADVEQRSSSIDRDEE---EEGMDSDEEGMDSNDDGSDDDRSDEEGVGSISNDSSNEGMDSisNDTNNEGMDSRSST 124
                                        122222222222222...2222222222222222222222222222222222222222225444444444555555 PP

                              CDC45 195 epsakklrr 203
                                        +p++++  +
  gene3121|gene3121|rna3121|rna3121 125 NPNHTNNVN 133
                                        522222221 PP

>> Nop14  Nop14-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3  13.5   4.9e-06     0.018     284     447 ..       6     163 ..       2     185 .. 0.43

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.9e-06
                              Nop14 284 eklEeeRlkRMrgeedeeeeeekkkkkkke....asaDdldddfvleeeeeeeefglgkglkataeeeeeededdf 355
                                        e+ Ee+R+kR +g +  +  ++ ++++       +     +dd v+e++ + e+          ++++ ++de+++
  gene3121|gene3121|rna3121|rna3121   6 ERKEERRVKRTNGSKGGAIGNGWEESNGIGagecI---GREDDTVRERNADVEQ----------RSSSIDRDEEEE 68 
                                        67899999999998333333333333333122221...2345555555444442..........112233333333 PP

                              Nop14 356 eedddlveseseeeeeeeeedeeeeedeeeee.ee...eededdlsdlese...eeeeedeleeelleeekkaaee 424
                                          d+d++  +s+++     +d++ +++e  ++ ++   +e  d+ s++ ++   ++ ++ + +++++++ + ++  
  gene3121|gene3121|rna3121|rna3121  69 GMDSDEEGMDSNDDG----SDDDRSDEEGVGSiSNdssNEGMDSISNDTNNegmDSRSSTNPNHTNNVNPTTNEVY 140
                                        333333333333333....333333333333222200022222222222221222222222222223333333333 PP

                              Nop14 425 kkekkkkkkkseekakeelpytf 447
                                        ++ + ++++ +++   +++p+ +
  gene3121|gene3121|rna3121|rna3121 141 QTVHATHNALTQAVYTKNVPFLI 163
                                        33333555556666666666655 PP

>> RRN3  RNA polymerase I specific transcription initiation factor RRN3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   4.5     6e-06     0.021     222     348 ..      44     173 ..      39     181 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 6e-06
                               RRN3 222 deedeeleeelee..deddedddeddeesdlddlssdeeaeedeekdeeeeslkkikelvekLDailtllfe.hle 294
                                        d++ +e + ++e+  ++ d d++e+  +sd + ++s+++ ++d+++dee     + +   e +D+i +   +  ++
  gene3121|gene3121|rna3121|rna3121  44 DDTVRERNADVEQrsSSIDRDEEEEGMDSDEEGMDSNDDGSDDDRSDEEGVGSISNDSSNEGMDSISNDTNNeGMD 119
                                        33333344444443333333333333445555555555555554444444334455667789****9887651567 PP

                               RRN3 295 kkfssestkeeeeeeeglelfntLlslFkstiLptyksrhvqFll.Fhfssldpe 348
                                        ++ s++++++++ + +++e+++t  +  ++ + ++ +++ v Fl+ F ++  +++
  gene3121|gene3121|rna3121|rna3121 120 SRSSTNPNHTNNVNPTTNEVYQTVHAT-HNALTQAVYTKNVPFLInFTYCDAQSK 173
                                        767777777777888889999997665.678899*********987999988876 PP

>> BUD22  BUD22
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0  13.0   0.00021      0.77     165     264 ..      20     129 ..       1     163 [. 0.39

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00021
                              BUD22 165 e.....................eeesdkeeesedsedeekeeseddeeeeeededdedaeedeedeeaeerelaqy 219
                                        +                     +e++   e ++d e+   ++s+ d++eeee++d+++++ d ++++ ++++ ++ 
  gene3121|gene3121|rna3121|rna3121  20 KggaigngweesngigagecigREDDTVRERNADVEQ---RSSSIDRDEEEEGMDSDEEGMD-SNDDGSDDDRSDE 91 
                                        1334555555544555544444333333333333332...3333333333333333333321.2222222222333 PP

                              BUD22 220 dgllasddeded.eyneetdeesseesdssdssesasesesessek 264
                                        +g+        +  +n++++e+ ++ s++ +++  +s+s+++++ +
  gene3121|gene3121|rna3121|rna3121  92 EGV--------GsISNDSSNEGMDSISNDTNNEGMDSRSSTNPNHT 129
                                        332........23233333334444444444444444444333333 PP

>> SDA1  SDA1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6  18.1    0.0026       9.3      89     212 ..      16     151 ..       2     158 .. 0.41

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0026
                               SDA1  89 e........................eeeedsddeddeedwevesddds.eedseggwidvesdeeeieesd.esed 138
                                                                  +e   dd   e++ +ve+ ++s + d+e++   ++sdee ++++d  s+d
  gene3121|gene3121|rna3121|rna3121  16 TngskggaigngweesngigageciGRE---DDTVRERNADVEQRSSSiDRDEEEE--GMDSDEEGMDSNDdGSDD 86 
                                        2555566666666666666666554222...3356677788888777764444444..466777743333302334 PP

                               SDA1 139 eeeeeeeeeekeekeeeeeeeeeeeeeeeeeeeeeekekkkkkakeaseeekkkekeeekiskaselattrILT 212
                                        + ++ee   +  +++++e  ++     +++ ++e   + ++ ++++ + +++ +  +++++ + +  at   LT
  gene3121|gene3121|rna3121|rna3121  87 DRSDEEGVGSISNDSSNEGMDS----ISNDTNNE---GMDSRSSTNPNHTNNVNP-TTNEVYQ-TVHATHNALT 151
                                        4333332222222222222222....22222222...222212222222222222.2222222.3344444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (275 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       948  (0.0528752); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 1837.88
//
Query:       gene3122|gene3122|rna3122|rna3122  [L=122]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0018   19.2   0.1     0.0044   18.0   0.0    1.6  2  DUF4834        Domain of unknown function (DUF4834)
     0.0034   17.1   0.0     0.0047   16.6   0.0    1.3  1  SARAF          SOCE-associated regulatory factor of calcium h
      0.004   17.2   0.0     0.0051   16.8   0.0    1.2  1  Protocadherin  Protocadherin
  ------ inclusion threshold ------
      0.033   13.6   0.5      0.042   13.2   0.0    1.4  2  DUF5305        Family of unknown function (DUF5305)
      0.066   13.4   0.0      0.092   12.9   0.0    1.2  1  Pox_A14        Poxvirus virion envelope protein A14
      0.068   13.2   2.0       0.26   11.3   0.0    2.0  2  DUF4366        Domain of unknown function (DUF4366)
       0.12   12.2   0.0       0.22   11.4   0.0    1.4  1  ATG27          Autophagy-related protein 27
       0.14   11.9   1.9        0.2   11.4   1.9    1.2  1  PMP1_2         ATPase proteolipid family
       0.36   11.2   1.3        2.8    8.3   0.0    2.0  2  Orf78          Orf78 (ac78)
       0.91    9.4   5.9        1.3    8.9   5.9    1.2  1  PsbJ           PsbJ


Domain annotation for each model (and alignments):
>> DUF4834  Domain of unknown function (DUF4834)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.1       2.7   4.8e+03      66      68 ..      13      15 ..       2      23 .. 0.36
   2 !   18.0   0.0   2.4e-06    0.0044       2      75 ..      23      96 ..      22     113 .. 0.55

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 2.7
                            DUF4834 66 ege 68
                                       e+e
  gene3122|gene3122|rna3122|rna3122 13 EEE 15
                                       111 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 2.4e-06
                            DUF4834  2 hfLlfi.lifiiailviglsilsv.ilrtvfglgsrkkssksaqkqfgnstnsnqqksqsrsetkeegeiieeers 75
                                        fL++i ++++i+  + ++ i++  i++++f+  ++   +    + +g + +sn + ++++++ +eeg+ ++++++
  gene3122|gene3122|rna3122|rna3122 23 SFLKVIlVLLFIVAGIAVVGIVGYvIYNAYFSEAKKGGTE--LRDAGGFKAESNFAPNDDKPKDEEEGSKKKKKDK 96
                                       5899998888888888888888753778887755444333..3333333333333333333333333333333332 PP

>> SARAF  SOCE-associated regulatory factor of calcium homoeostasis
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   2.6e-06    0.0047     138     229 ..       7      92 ..       1     115 [. 0.44

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 2.6e-06
                              SARAF 138 seeskkeeekkeevkkksssssasllf...vvlvllviayivykaflaaeee..reaeaeggrrgegggggggggg 208
                                          ++++eee+++++ ++  +  + llf    ++v+++++y++y+a+++++++  +      + r  gg + +++  
  gene3122|gene3122|rna3122|rna3122   7 ASKHDDEEEQQQSSGTSFLKVILVLLFivaGIAVVGIVGYVIYNAYFSEAKKggT------ELRDAGGFKAESNFA 76 
                                        3334433333333222222222333331125689999**********77765221......222222222222221 PP

                              SARAF 209 pgseeeqddpPppysltksqk 229
                                              +dd P   + ++++k
  gene3122|gene3122|rna3122|rna3122  77 ----P-NDDKPKDEEEGSKKK 92 
                                        ....1.123333332222222 PP

>> Protocadherin  Protocadherin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   2.8e-06    0.0051      36     108 ..      26     100 ..       4     118 .. 0.55

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 2.8e-06
                      Protocadherin  36 drlkiliavlaGvvtvilvilivvlvRycrqkaksgyk...agk.KeeedfvtPkqenkeekg...kkkkkkkkkk 104
                                        + + +l+ ++aG+++v +v  ++  + + ++k k g +   ag  K e+  ++P+ ++ ++++   kkkkk+k+++
  gene3122|gene3122|rna3122|rna3122  26 KVILVLLFIVAGIAVVGIVGYVIYNAYFSEAK-KGGTElrdAGGfKAES-NFAPNDDKPKDEEegsKKKKKDKSTS 99 
                                        3344667899**99988877766666654444.4443311255545555.56888555444441214444444433 PP

                      Protocadherin 105 kaks 108
                                           +
  gene3122|gene3122|rna3122|rna3122 100 ---L 100
                                        ...3 PP

>> DUF5305  Family of unknown function (DUF5305)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   2.3e-05     0.042      97     144 ..       8      58 ..       1      66 [. 0.66
   2 ?   -3.1   0.2       2.4   4.3e+03      99     107 ..      88      94 ..      78     104 .. 0.41

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.3e-05
                            DUF5305  97 engeitetvtvkespslae...gilliilgllaliglvvlirriiftsska 144
                                         +++ +e+++ +   s+++   ++l+i++g++ ++++ ++i++ +f+  k+
  gene3122|gene3122|rna3122|rna3122   8 SKHDDEEEQQQSSGTSFLKvilVLLFIVAGIAVVGIVGYVIYNAYFSEAKK 58 
                                        334444444444444444467799999999999999999999999987774 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 2.4
                            DUF5305  99 geitetvtv 107
                                        g   +++++
  gene3122|gene3122|rna3122|rna3122  88 G--SKKKKK 94 
                                        2..222222 PP

>> Pox_A14  Poxvirus virion envelope protein A14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   5.1e-05     0.092      38      74 ..      19      55 ..      13      71 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5.1e-05
                            Pox_A14 38 sttdkawralsivsFilgivillglllfsmygrkCka 74
                                       s+  + ++++ ++ Fi++ ++++g++ +  y+ +   
  gene3122|gene3122|rna3122|rna3122 19 SSGTSFLKVILVLLFIVAGIAVVGIVGYVIYNAYFSE 55
                                       3445689**********99999999888888777644 PP

>> DUF4366  Domain of unknown function (DUF4366)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00014      0.26      97     137 ..       5      46 ..       1      59 [. 0.53
   2 ?    1.5   0.9      0.15   2.7e+02      95     114 ..      78      97 ..      50     114 .. 0.55

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00014
                            DUF4366  97 pepekeaepeepeeepekksn..nglllvvlavaligg.gaayy 137
                                        p  e++++ +e+e++++++++  + +l+++++va+i++ g++ y
  gene3122|gene3122|rna3122|rna3122   5 P--EASKHDDEEEQQQSSGTSflKVILVLLFIVAGIAVvGIVGY 46 
                                        3..33333333444444444454555555566666666444443 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.15
                            DUF4366  95 eepepekeaepeepeeepek 114
                                        + ++p++e+e +++++++++
  gene3122|gene3122|rna3122|rna3122  78 NDDKPKDEEEGSKKKKKDKS 97 
                                        33344444443333332222 PP

>> ATG27  Autophagy-related protein 27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00012      0.22     181     241 ..       8      66 ..       3      73 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00012
                              ATG27 181 kdkkdsskkkeksgwGfFtwlfiilflataaYlifgswlNynryGargwDllphgdtirdl 241
                                        ++ +d+++++++sg++f+   +i+++l+++a +++  ++ y  y+a ++++ + g  +rd 
  gene3122|gene3122|rna3122|rna3122   8 SKHDDEEEQQQSSGTSFLK--VILVLLFIVAGIAVVGIVGYVIYNAYFSEAKKGGTELRDA 66 
                                        3444444455559***955..5666666777777777888888888887777777766665 PP

>> PMP1_2  ATPase proteolipid family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   1.9   0.00011       0.2      11      31 ..      30      50 ..      24      59 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00011
                             PMP1_2 11 iLvFvLvGLACvAivltilYR 31
                                       +L F++ G+A v iv  ++Y 
  gene3122|gene3122|rna3122|rna3122 30 VLLFIVAGIAVVGIVGYVIYN 50
                                       567*****************7 PP

>> Orf78  Orf78 (ac78)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.0    0.0016       2.8      46      84 ..       9      49 ..       1      58 [. 0.42
   2 ?    1.9   0.4      0.16   2.8e+02      30      52 ..      78     100 ..      69     119 .. 0.44

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0016
                              Orf78 46 knditekesnaaekaqalnil..lisllavvcvlvll.yviy 84
                                       k+d +e++++ ++ +++l+++  l+ ++a ++v+ ++ yviy
  gene3122|gene3122|rna3122|rna3122  9 KHDDEEEQQQ-SSGTSFLKVIlvLLFIVAGIAVVGIVgYVIY 49
                                       2222222222.2333333333003333344444433348877 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.16
                              Orf78  30 dndkaenkkekksaaeknditek 52 
                                        ++dk+++++e +++++k ++t+ 
  gene3122|gene3122|rna3122|rna3122  78 NDDKPKDEEEGSKKKKKDKSTSL 100
                                        33333333333223333333222 PP

>> PsbJ  PsbJ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   5.9   0.00074       1.3      14      32 ..      34      52 ..      26      54 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00074
                                       HHHHHHHHHHHHHHHHHTT CS
                               PsbJ 14 tvaGlgvitvvglFfYGsY 32
                                       +vaG++v+++vg  +Y +Y
  gene3122|gene3122|rna3122|rna3122 34 IVAGIAVVGIVGYVIYNAY 52
                                       79**************999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1364  (0.0760779); expected 358.6 (0.02)
Passed bias filter:                      785  (0.0437838); expected 358.6 (0.02)
Passed Vit filter:                       105  (0.00585643); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 809.00
//
Query:       gene3123|gene3123|rna3123|rna3123  [L=590]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-22   80.7   0.0    2.2e-22   80.0   0.0    1.2  1  ABC_tran        ABC transporter
    0.00011   22.7   0.0    0.00016   22.1   0.0    1.3  1  AAA_16          AAA ATPase domain
    0.00016   21.2   0.2    0.00038   20.0   0.2    1.5  1  SMC_N           RecF/RecN/SMC N terminal domain
    0.00019   20.9  17.7    0.00019   20.9  17.7    2.1  2  ABC2_membrane   ABC-2 type transporter
    0.00021   21.3   0.7     0.0014   18.6   0.0    2.4  2  Rad17           Rad17 P-loop domain
    0.00021   21.8   0.0    0.00033   21.2   0.0    1.3  1  AAA_23          AAA domain
    0.00026   21.0   0.1    0.00053   20.0   0.1    1.4  1  ATPase_2        ATPase domain predominantly from Archaea
    0.00031   21.0   0.0    0.00055   20.2   0.0    1.4  1  AAA_22          AAA domain
    0.00081   19.2   0.8      0.029   14.1   0.7    2.4  1  AAA_24          AAA domain
     0.0021   18.5   1.1     0.0087   16.5   1.1    2.0  1  AAA             ATPase family associated with various cellula
     0.0035   17.0   0.2     0.0076   16.0   0.2    1.5  1  AAA_29          P-loop containing region of AAA domain
     0.0037   17.2   0.1     0.0063   16.4   0.1    1.3  1  MobB            Molybdopterin guanine dinucleotide synthesis 
     0.0039   17.7   0.0      0.007   16.9   0.0    1.4  1  AAA_18          AAA domain
     0.0046   16.9   0.1     0.0082   16.1   0.1    1.3  1  RsgA_GTPase     RsgA GTPase
     0.0074   16.1   0.1      0.022   14.6   0.1    1.8  2  AAA_21          AAA domain, putative AbiEii toxin, Type IV TA
     0.0084   15.9   0.0      0.012   15.3   0.0    1.3  1  Cytidylate_kin  Cytidylate kinase
  ------ inclusion threshold ------
      0.014   15.7   0.0      0.021   15.1   0.0    1.3  1  AAA_28          AAA domain
      0.016   14.8   0.1      0.025   14.2   0.1    1.2  1  AAA_25          AAA domain
      0.016   15.1   0.6      0.027   14.4   0.6    1.3  1  NACHT           NACHT domain
      0.017   14.9   0.0      0.032   14.0   0.0    1.4  1  ATP_bind_1      Conserved hypothetical ATP binding protein
      0.019   15.1   0.1      0.034   14.2   0.1    1.5  1  MMR_HSR1        50S ribosome-binding GTPase
       0.02   15.0   0.0      0.034   14.3   0.0    1.4  1  AAA_33          AAA domain
      0.034   14.6   0.0      0.064   13.6   0.0    1.5  1  RNA_helicase    RNA helicase
      0.046   13.6   0.2       0.09   12.7   0.2    1.5  1  NTPase_1        NTPase
      0.052   13.6   0.0      0.083   12.9   0.0    1.5  1  CbiA            CobQ/CobB/MinD/ParA nucleotide binding domain
      0.073   12.1   0.0       0.11   11.6   0.0    1.2  1  T2SSE           Type II/IV secretion system protein
       0.11   12.5   0.4       0.29   11.2   0.2    1.7  1  AAA_5           AAA domain (dynein-related subfamily)
       0.12   12.1   0.0       0.17   11.5   0.0    1.2  1  AAA_30          AAA domain
       0.13   12.3   0.1       0.25   11.4   0.1    1.4  1  TsaE            Threonylcarbamoyl adenosine biosynthesis prot
        0.2   11.2   0.4       0.34   10.5   0.4    1.3  1  cobW            CobW/HypB/UreG, nucleotide-binding domain
       0.33   11.0   2.3       0.48   10.5   1.4    1.6  2  DUF87           Helicase HerA, central domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.0   0.0   3.8e-25   2.2e-22      13     137 .]      38     172 ..      33     172 .. 0.90

  Alignments for each domain:
  == domain 1  score: 80.0 bits;  conditional E-value: 3.8e-25
                                        EEEEEESTTSSHHHHHHHHTTSS--...SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH...... CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...... RF
                           ABC_tran  13 kvaivGenGaGKStLlkllagllkp...teGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren...... 79 
                                        ++ai+G++G+GK+tL+k+lag l++     G ++l+g +   ++le +   ig++ q++++ + lt+r++      
  gene3123|gene3123|rna3123|rna3123  38 LLAIMGPSGSGKTTLVKALAGRLSKgssSTGVVKLNGVE---RNLETWVDMIGYVDQDDTIYEILTARQTveyaak 110
                                        689********************9966667777666554...577*********************9999*99999 PP

                                        ........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                        ........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ABC_tran  80 ........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                                +  e++e + +kl ++++ d  +    ++LSgG+++rv++a  l+++pk+++lDEpt+
  gene3123|gene3123|rna3123|rna3123 111 frlkdsniNVGEKVESLFKKLAITHILDCEM----RNLSGGERKRVMIAVELVTDPKIIFLDEPTS 172
                                        9998888878888************998888....*****************************96 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   2.8e-07   0.00016       9      63 ..      24      79 ..      18     157 .. 0.67

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 2.8e-07
                             AAA_16  9 leqLlsalervrsgrpelvllsGesGvGKsslvrellralekd....ggif.lrgkcdql 63
                                       ++ + +a +r+ +   +l+ + G+sG+GK++lv++l+ +l+k     g ++ l+g  + l
  gene3123|gene3123|rna3123|rna3123 24 IKLVSDACGRAEE---GLLAIMGPSGSGKTTLVKALAGRLSKGssstG-VVkLNGVERNL 79
                                       5555555555543...699******************99998866532.22244443333 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.2   6.5e-07   0.00038      20     149 ..      32     156 ..      12     167 .. 0.74

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 6.5e-07
                                        EETTSSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEE.EETTEESSSSS CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxx RF
                              SMC_N  20 lpfsksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitf.dnedkklkiek 94 
                                        ++ ++++ ai+Gp GSGK+ l+ A+   L+       + ++ + +++  +  ++  +  v+++   ++d++     
  gene3123|gene3123|rna3123|rna3123  32 GRAEEGLLAIMGPSGSGKTTLVKALAGRLS-------KGSSSTGVVKL-NGVERNLETWVDMIGyVDQDDT----I 95 
                                        56788999*****************65555.......45667777776.7777777888887521222222....3 PP

                                        SCEEEEEEEETTSEEEEEETTEEE-H.HHHHHHHHCTT-STT......CS-HHHHHHHHHHH CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxx......xxxxxxxxxxxxxx RF
                              SMC_N  95 eevsisrrvkrkgeseykingkevtk.kevsellesagiske......lLSgGektLvalaL 149
                                         e+ + r+ ++    ++++++++++  ++v++l+++  i+        +LSgGe++ v++a+
  gene3123|gene3123|rna3123|rna3123  96 YEILTARQTVEYA-AKFRLKDSNINVgEKVESLFKKLAITHIldcemrNLSGGERKRVMIAV 156
                                        4555555555544.5999*99999998899999999999866666666********999997 PP

>> ABC2_membrane  ABC-2 type transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9  17.7   3.4e-07   0.00019      33     171 ..     322     463 ..     275     491 .. 0.81
   2 ?   -1.5   1.9       2.4   1.4e+03     131     152 ..     555     576 ..     543     583 .. 0.49

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 3.4e-07
                      ABC2_membrane  33 alvfgtvfgnlgnsedglnr................pgllffsvlflafsaltsvapvferergvlerelvsplys 92 
                                        + ++g  ++                            ++++ +  +++f+ +++  + f +e+++++re + ++ys
  gene3123|gene3123|rna3123|rna3123 322 IRIIGAFYS----------DtkhgaflkdlisldvsSYAFYSISATISFIPIITG-MAFNSEHKMVKREIAVNTYS 386
                                        334444444..........044444445567778888888888888888888888.9******************* PP

                      ABC2_membrane  93 lsayvlakvlvelpvsllqalifllivyflvgldlsrfflflllllltalaasslgllisalapsfedasqlaslv 168
                                          +y+++ +l+e ++ l + +if++ + +++g  ++  ++++++ +l++ +++   l+ +++++  + ++++ +l+
  gene3123|gene3123|rna3123|rna3123 387 ITSYYFSVLLFEYLRCLPFMIIFMIGSKIIIGQMVD--LMIMFIYFLMFTTLIVAYLFYGSVLRGTKKVILVYGLF 460
                                        ***********************************9..**************************999999999888 PP

                      ABC2_membrane 169 llp 171
                                        +++
  gene3123|gene3123|rna3123|rna3123 461 IIF 463
                                        865 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.4
                      ABC2_membrane 131 flflllllltalaasslgllis 152
                                        f +l  ++l++++++   l++s
  gene3123|gene3123|rna3123|rna3123 555 FNYLTCVVLIIVYMLLCILMLS 576
                                        3333333333333333333333 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   2.3e-06    0.0014      24      71 ..      15      62 ..       7     136 .. 0.68
   2 ?    0.1   0.2       1.2   6.7e+02     122     173 ..     440     488 ..     381     495 .. 0.73

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 2.3e-06
                              Rad17 24 hkkkieevkewlkadvLesrkkriLLisGPsGCgkstvvkvLskelgi 71
                                       h k+ +e +  l +d   ++++ +L i GPsG gk+t vk L+  l+ 
  gene3123|gene3123|rna3123|rna3123 15 HNKRYKEKRIKLVSDACGRAEEGLLAIMGPSGSGKTTLVKALAGRLSK 62
                                       88888888889999999999999*****************99866543 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 1.2
                              Rad17 122 lqklGddlrtdkklilvedlPnkfyrdsdalrevirkylrssealplilvit 173
                                            G  lr+ kk+ilv  l   f+    ++  vi   +r  e l+ i++i+
  gene3123|gene3123|rna3123|rna3123 440 YLFYGSVLRGTKKVILVYGLFIIFNN--AQFCPVIAS-MRKDENLSKIFMIS 488
                                        44578999999****99999877775..456666654.45555556666665 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0   5.8e-07   0.00033      10      86 ..      19     107 ..      12     153 .. 0.62

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 5.8e-07
                             AAA_23  10 frdqeidF........skgltlItGpNGaGKTTildAiklaLygetprlsrksgrgfeksdveiese.......gk 70 
                                        ++++ i +        + gl +I Gp G+GKTT++ A+   L   ++ ++  + +g e++   +e++       ++
  gene3123|gene3123|rna3123|rna3123  19 YKEKRIKLvsdacgraEEGLLAIMGPSGSGKTTLVKALAGRLSKGSSSTGVVKLNGVERN---LETWvdmigyvDQ 91 
                                        666677777777777789********************9888765544444432222222...2222444444477 PP

                             AAA_23  71 vkayveltfenkdgry 86 
                                        +++++e+   +++ +y
  gene3123|gene3123|rna3123|rna3123  92 DDTIYEILTARQTVEY 107
                                        7777777766666553 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.1   9.1e-07   0.00053       5     113 ..      21     131 ..      19     137 .. 0.75

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 9.1e-07
                           ATPase_2   5 ekelkeleeilerepneiyfiYGpegsGKtaLlkeiienl.edkdkyviyyialreesiskldefieeeeekkkle 79 
                                        ek +k +   + r ++  + i Gp gsGKt+L+k ++ +l + ++   +   +  e+++++  ++i+  ++++ + 
  gene3123|gene3123|rna3123|rna3123  21 EKRIKLVSDACGRAEEGLLAIMGPSGSGKTTLVKALAGRLsKGSSSTGVVKLNGVERNLETWVDMIGYVDQDDTIY 96 
                                        78899999999999999**********************9655555666666666777777778889888888887 PP

                           ATPase_2  80 kal.giavpkaeleeilkeksklvfkaiellleki 113
                                        + l + ++ + +++  lk+ + +v +++e+l++k+
  gene3123|gene3123|rna3123|rna3123  97 EILtARQTVEYAAKFRLKDSNINVGEKVESLFKKL 131
                                        77733333333333334477788888888888876 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   9.5e-07   0.00055       4      36 ..      35      67 ..      33     127 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 9.5e-07
                             AAA_22  4 tagilvvtGesGtGKTtllrrlleqldeeakae 36
                                       ++g+l+++G+sG+GKTtl++ l+ +l + ++ +
  gene3123|gene3123|rna3123|rna3123 35 EEGLLAIMGPSGSGKTTLVKALAGRLSKGSSST 67
                                       5899*******************9997665544 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.7     5e-05     0.029       5      62 ..      39      95 ..      38     105 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 5e-05
                             AAA_24  5 iliyGpsgiGKTtlakelgpkplfidtekGlksldadkfpdie....swedfldevvelaae 62
                                       ++i+Gpsg+GKTtl+k l        + kG+ s+ + k++ +e    +w d++ +v+++++ 
  gene3123|gene3123|rna3123|rna3123 39 LAIMGPSGSGKTTLVKALAG-----RLSKGSSSTGVVKLNGVErnleTWVDMIGYVDQDDTI 95
                                       589*************9944.....4556666666666666666566888888888887554 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   1.1   1.5e-05    0.0087       3      34 ..      41      77 ..      39     170 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.5e-05
                                       EESSTTSSHHHHHHHHHHHH.....THEEEEEETTTC CS
                                AAA  3 lyGppGtGKTllakavakel.....gvefleisgsel 34
                                       ++Gp G GKT+l+ka+a  l     ++ +++++g e 
  gene3123|gene3123|rna3123|rna3123 41 IMGPSGSGKTTLVKALAGRLskgssSTGVVKLNGVER 77
                                       78*****************844333255666666554 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.2   1.3e-05    0.0076      22      43 ..      36      57 ..      30      63 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.3e-05
                             AAA_29 22 kgatlltGpsGsGKSTllDAiq 43
                                       +g   ++GpsGsGK+Tl+ A++
  gene3123|gene3123|rna3123|rna3123 36 EGLLAIMGPSGSGKTTLVKALA 57
                                       56789*************9875 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.1   1.1e-05    0.0063       2      36 ..      39      73 ..      38      81 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.1e-05
                               MobB  2 lgivgksgsGKTtLleklipelkarglrvgtiKha 36
                                       l+i+g sgsGKTtL++ l   l++   + g++K +
  gene3123|gene3123|rna3123|rna3123 39 LAIMGPSGSGKTTLVKALAGRLSKGSSSTGVVKLN 73
                                       899*****************************965 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   1.2e-05     0.007       2      25 ..      40      74 ..      39     136 .. 0.68

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.2e-05
                             AAA_18  2 lltGtpGvGKttlakeLskrlgf...........g 25
                                       +++G++G+GKttl k+L+ rl             g
  gene3123|gene3123|rna3123|rna3123 40 AIMGPSGSGKTTLVKALAGRLSKgssstgvvklnG 74
                                       599**************888722244544344441 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.1   1.4e-05    0.0082      74     123 ..       7      60 ..       2      76 .. 0.69

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.4e-05
                                        HTTSEEEE--TTTHTTHHHHHHHC....TTSEEEEECSTTSSHHHHHHHHCTT- CS
                        RsgA_GTPase  74 algyevllvsaktkegleelkell....kdktsvlvGqSGvGKStLinallpel 123
                                        +++++vl  +++ ke+  +l +      ++ + +++G+SG GK+tL++al+++l
  gene3123|gene3123|rna3123|rna3123   7 NIDISVLNHNKRYKEKRIKLVSDAcgraEEGLLAIMGPSGSGKTTLVKALAGRL 60 
                                        5666666666665554444444321111457899****************9975 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.1   3.9e-05     0.022       3      92 ..      40     129 ..      38     138 .. 0.67
   2 ?   -1.6   0.0       3.2   1.9e+03     235     268 ..     142     172 ..     126     172 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.9e-05
                             AAA_21   3 vliGpNgsGKSnLLdaldllarl.drdvegltdelsggggirkipslldlydpeipfefeieeflsqgvryryglr 77 
                                        ++ Gp gsGK++L +al +   l  +++  +  +l g   + + +    +y +  ++ +ei  +  q v+y   +r
  gene3123|gene3123|rna3123|rna3123  40 AIMGPSGSGKTTLVKALAGR--LsKGSSSTGVVKLNGVERNLETWVDMIGYVDQDDTIYEIL-TARQTVEYAAKFR 112
                                        789**************554..3333333333333333344444455666777777777777.9999999999999 PP

                             AAA_21  78 lersqv..eeklssvet 92 
                                        l++s++  +ek+ s+ +
  gene3123|gene3123|rna3123|rna3123 113 LKDSNInvGEKVESLFK 129
                                        99999966666655554 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 3.2
                             AAA_21 235 relSdGtkrllalltallralkkgsllliDEpEn 268
                                        r+lS G ++   +++ l  ++   +++++DEp +
  gene3123|gene3123|rna3123|rna3123 142 RNLSGGERKRVMIAVELVTDP---KIIFLDEPTS 172
                                        556666666634444444444...8*******75 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   2.1e-05     0.012       2      32 ..      40      70 ..      39     134 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.1e-05
                                       EEE-STTSSHHHHHHHHHHHHT-EEEEHHHH CS
                     Cytidylate_kin  2 aiDGPagsGKssvaralaeklglkyldtgal 32
                                       ai GP+gsGK ++ +ala +l+    +tg +
  gene3123|gene3123|rna3123|rna3123 40 AIMGPSGSGKTTLVKALAGRLSKGSSSTGVV 70
                                       899******************9988888865 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0   3.6e-05     0.021       3      22 ..      40      59 ..      38     111 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.6e-05
                             AAA_28  3 vitGgestGKTtlleaLaar 22
                                       +i+G++++GKTtl++aLa r
  gene3123|gene3123|rna3123|rna3123 40 AIMGPSGSGKTTLVKALAGR 59
                                       79****************66 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   4.3e-05     0.025      31      65 ..      34      68 ..      20      85 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.3e-05
                             AAA_25 31 pagelallaGapgtGKttlaldlalavatGkpwlg 65
                                       ++++l +++G++g+GKttl+  la  +++G++ +g
  gene3123|gene3123|rna3123|rna3123 34 AEEGLLAIMGPSGSGKTTLVKALAGRLSKGSSSTG 68
                                       578999**********************9999888 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.6   4.6e-05     0.027       3      29 ..      39      65 ..      37      72 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4.6e-05
                                       EEEEC-TTTCHHHHHHHHHHHHCTS-S CS
                              NACHT  3 vilqGeaGsGKTtLlqklalawaegkl 29
                                       +++ G++GsGKTtL++ la  + +g  
  gene3123|gene3123|rna3123|rna3123 39 LAIMGPSGSGKTTLVKALAGRLSKGSS 65
                                       7899***************99998875 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   5.5e-05     0.032       1      35 [.      41      75 ..      41     134 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.5e-05
                         ATP_bind_1  1 vvGpaGsGKttfvgalseilelrgrsvavvNLDPA 35
                                       ++Gp GsGKtt+v+al+  l++   s  vv L   
  gene3123|gene3123|rna3123|rna3123 41 IMGPSGSGKTTLVKALAGRLSKGSSSTGVVKLNGV 75
                                       79***************999999899999988655 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   5.8e-05     0.034       3      58 ..      40      90 ..      38     156 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 5.8e-05
                                       EEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSE.EEEEEEETTEEEEEEECGGCSS CS
                           MMR_HSR1  3 aivGrpNvGKStLinaltgekaivsdkpgtTrdi.negrvklkgkeielvDtpGlie 58
                                       ai+G + +GK+tL++al g+ ++ s+  g+ +   +e++++      ++vD+ G ++
  gene3123|gene3123|rna3123|rna3123 40 AIMGPSGSGKTTLVKALAGRLSKGSSSTGVVKLNgVERNLE------TWVDMIGYVD 90
                                       8******************9877766666644442333333......7888888433 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   5.9e-05     0.034       2      23 ..      39      60 ..      38     110 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 5.9e-05
                             AAA_33  2 vllvGlpGsGKstlaerllkkl 23
                                       + + G++GsGK+tl++ l+ +l
  gene3123|gene3123|rna3123|rna3123 39 LAIMGPSGSGKTTLVKALAGRL 60
                                       6689*************99776 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   0.00011     0.064       3      30 ..      41      68 ..      39     136 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 0.00011
                       RNA_helicase  3 lyGpsgeGKStlakeLakallkklklkk 30
                                       + Gpsg GK+tl+k La +l+k + ++ 
  gene3123|gene3123|rna3123|rna3123 41 IMGPSGSGKTTLVKALAGRLSKGSSSTG 68
                                       89******************97763333 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.2   0.00016      0.09       3      34 ..      40      70 ..      38      81 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00016
                                       EEE--TTSSHHHHHHHHHHHH...GGGEEEEE CS
                           NTPase_1  3 fiTGppGvGKtTlvkkvlellkssgvkvgGfy 34
                                       +i Gp+G+GKtTlvk ++  l s+g + +G++
  gene3123|gene3123|rna3123|rna3123 40 AIMGPSGSGKTTLVKALAGRL-SKGSSSTGVV 70
                                       689******************.7888888875 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   0.00014     0.083       5      55 ..      42     116 ..      38     361 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00014
                                        ESSTTSSHHHHHHHHHHHHHHTT--EEEEE.EEESSCCCCHHTTEB-HHHH........................C CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxx........................x RF
                               CbiA   5 stkGGvGKTtlaanLaralarrglrVllvD.aDpqannlaileglendiep........................d 55 
                                         + +G+GKTtl+ +La  l+++   + +v+  ++++n+ +      +++++                        +
  gene3123|gene3123|rna3123|rna3123  42 MGPSGSGKTTLVKALAGRLSKGSSSTGVVKlNGVERNLETW-VDMIGYVDQddtiyeiltarqtveyaakfrlkdS 116
                                        5779*****************99999999955555555443.2222333333455666655555555555555550 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00019      0.11     124     156 ..      33      63 ..       5     110 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00019
                              T2SSE 124 kavrerglilvsGgTgsGKttllyallkeinks 156
                                        +a  e+gl+ + G+ gsGKttl+ al   + k 
  gene3123|gene3123|rna3123|rna3123  33 RA--EEGLLAIMGPSGSGKTTLVKALAGRLSKG 63 
                                        33..789999***************99888765 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.2   0.00049      0.29       4      24 ..      41      63 ..      39      79 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00049
                                       EE--SSSSHHHHHHHGGGGB..S CS
                              AAA_5  4 LvGppGtgKselaerlaaal..n 24
                                       + Gp+G+gK++l++ la +l  +
  gene3123|gene3123|rna3123|rna3123 41 IMGPSGSGKTTLVKALAGRLskG 63
                                       68***************999752 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0    0.0003      0.17      17      41 ..      35      59 ..      19     101 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.0003
                             AAA_30 17 gdrvavltGpAGtGKttalkalrea 41
                                       ++ + ++ Gp G+GKtt++kal+  
  gene3123|gene3123|rna3123|rna3123 35 EEGLLAIMGPSGSGKTTLVKALAGR 59
                                       4458899**************9765 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   0.00043      0.25      14      43 ..      31      60 ..      16      69 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00043
                                       HHHCHTEEEEEEESTTSSHHHHHHHHHHHT CS
                               TsaE 14 lakalgdvilLeGdLGaGKTtlvrglakal 43
                                       +++a + ++++ G+ G+GKTtlv++la  l
  gene3123|gene3123|rna3123|rna3123 31 CGRAEEGLLAIMGPSGSGKTTLVKALAGRL 60
                                       33333557999***************9877 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.4   0.00059      0.34       4      22 ..      40      60 ..      38      77 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00059
                                       EEEESTTCCHHHHHHHHH..C CS
                               cobW  4 vltGflGsGKTtLlnhll..e 22
                                        + G+ GsGKTtL+++l    
  gene3123|gene3123|rna3123|rna3123 40 AIMGPSGSGKTTLVKALAgrL 60
                                       689************998642 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   1.4   0.00084      0.48      26      49 ..      39      62 ..      38      72 .. 0.83
   2 ?   -2.3   0.0       6.7   3.9e+03     120     151 ..     100     132 ..      70     161 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00084
                              DUF87 26 lAilgsTGsGKSntvavLleelle 49
                                       lAi+g +GsGK+++v+ L  +l +
  gene3123|gene3123|rna3123|rna3123 39 LAIMGPSGSGKTTLVKALAGRLSK 62
                                       69*****************99996 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 6.7
                              DUF87 120 vleealdqaka.keekeklssdepveklleelk 151
                                          ++++++a + + ++  +++ e ve+l+++l 
  gene3123|gene3123|rna3123|rna3123 100 TARQTVEYAAKfRLKDSNINVGEKVESLFKKLA 132
                                        334455555556677788888888888888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (590 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       992  (0.0553294); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); expected 358.6 (0.02)
Passed Vit filter:                       108  (0.00602376); expected 17.9 (0.001)
Passed Fwd filter:                        32  (0.00178482); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              31  [number of targets reported over threshold]
# CPU time: 0.73u 0.35s 00:00:01.08 Elapsed: 00:00:00.51
# Mc/sec: 3454.65
//
Query:       gene3124|gene3124|rna3124|rna3124  [L=439]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.5e-10   39.8  32.1    2.5e-10   39.8  32.1    2.1  2  MFS_1_like       MFS_1 like family
  ------ inclusion threshold ------
      0.028   14.7   1.9      0.028   14.7   1.9    3.8  4  DUF4064          Protein of unknown function (DUF4064)
        2.8    7.8   5.9        3.8    7.4   0.1    3.5  4  DUF2976          Protein of unknown function (DUF2976)


Domain annotation for each model (and alignments):
>> MFS_1_like  MFS_1 like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.8  32.1   4.2e-14   2.5e-10      41     371 ..      45     375 ..       5     386 .. 0.76
   2 ?    0.1   0.8     0.046   2.8e+02      88     248 ..     380     420 ..     368     437 .. 0.44

  Alignments for each domain:
  == domain 1  score: 39.8 bits;  conditional E-value: 4.2e-14
                         MFS_1_like  41 lilpltsilsppiwgvlaDrfgkrkkvvilslllsavlflsllfippskerqeesklevsvaqdvdaektfwilfl 116
                                         il  +si s+ +w+ laDr++ ++ ++++++l+ +++ ++ +                   + ++        +l
  gene3124|gene3124|rna3124|rna3124  45 QILGCLSIPSAFVWSYLADRTKWHTRIIAINALFYVIASIINF-N---------------LRNMTNRYAVQCGCVL 104
                                        466778999****************************999444.1...............1222223333344444 PP

                         MFS_1_like 117 lvvlasfflaailvlldaatlkel...gedrkdyGrqrlfGsvGyaifafitG...ilidhysvnllpysallyvl 186
                                         ++l ++   +++ ++ a+ l+ +   ++ +++ G  ++fG +G   +++++G   +l+  ++     +  +++vl
  gene3124|gene3124|rna3124|rna3124 105 AILLRQISAGGTFSIFFALLLNYVkrtNSSNRNVGTAKMFGILGITFVMMMLGlsgYLFPSTNARN--VALVICVL 178
                                        445555555566666666666665443777778*********999888887761115665555543..43455555 PP

                         MFS_1_like 187 aallvisllvvlilnetekesklkvtksl.....qvllnilknpeviifllvalilgmswgiienFlflYLkelga 257
                                         + + ++l++++ ++  + e  l  +k+      +  +   +n  v++f+l+++++g    +++nF + +++ lg+
  gene3124|gene3124|rna3124|rna3124 179 FGTFSAVLAFFSLPEFVKPEAVLFKRKISlkdlfK-RVYQYMNLIVLAFFLTTVLIGLNRIALDNFSTSFYHLLGY 253
                                        55555566666666666665555444443442222.2233456778999*************************** PP

                         MFS_1_like 258 sntllGslvalgvvaeiplfffaeklleklGhvklliiallayilrfllyaii........enawlvlpievLhgi 325
                                            +  +  ++++ e   +f + +l +++G+ +l +++ ++++lr +++ ++        ++  lv ++e+++g+
  gene3124|gene3124|rna3124|rna3124 254 EMHHIRLFFCFRMIIEAFALFHSDRLCKFIGLYNLFLLSAVFTVLRTFILTMFdllraskyRKIFLVCVVEAFKGV 329
                                        ***************************************************99999999999999*********** PP

                         MFS_1_like 326 sfgllwaaaveyvskiapksleatgqgllsglyfglGralGsliGG 371
                                        s+ +++ + +   + +a   +++  qgl   +y g+ + l s+i+ 
  gene3124|gene3124|rna3124|rna3124 330 STSAYFYSSTLIFRSFAKYDTQTLAQGLNGCAYNGVPSVLFSIISV 375
                                        ***********************************99999888884 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.046
                         MFS_1_like  88 skerqeesklevsvaqdvdaektfwilfllvvlasfflaailvlldaatlkelgedrkdyGrqrlfGsvGyaifaf 163
                                         +  + ++ + v+ + ++d    f+ ++++++++ +++                                      
  gene3124|gene3124|rna3124|rna3124 380 PQSSKHSDVITVNEKMQYDYFLVFFQIVTVLSFFGIII-------------------------------------- 417
                                        33334444444444444444444444444444443333...................................... PP

                         MFS_1_like 164 itGilidhysvnllpysallyvlaallvisllvvlilnetekesklkvtkslqvllnilknpeviifllvalilgm 239
                                                                                                                    
  gene3124|gene3124|rna3124|rna3124   - ----------------------------------------------------------------------------   -
                                        ............................................................................ PP

                         MFS_1_like 240 swgiienFl 248
                                              + +
  gene3124|gene3124|rna3124|rna3124 418 ------TAV 420
                                        ......333 PP

>> DUF4064  Protein of unknown function (DUF4064)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   8.8      0.78   4.7e+03      44     101 ..     126     184 ..      70     190 .. 0.68
   2 ?   -3.2   0.2       1.7     1e+04      30      30 ..     233     233 ..     219     275 .. 0.60
   3 ?   -2.9   0.1       1.4   8.6e+03      11      18 ..     291     298 ..     281     316 .. 0.57
   4 ?   14.7   1.9   4.7e-06     0.028      14      86 ..     365     429 ..     361     430 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.78
                            DUF4064  44 alsgedasavleflstllivlgvialiaivlgivgalllkknkk.vsGilfiiaailsl 101
                                        ++    +s+   + +  ++ ++ i +++  lg+ g l+ ++n + v+ ++ ++++ +s+
  gene3124|gene3124|rna3124|rna3124 126 NYVKRTNSSNRNVGTAKMFGILGITFVMMMLGLSGYLFPSTNARnVALVICVLFGTFSA 184
                                        23344455555666777778888899999999999999999999977666666666555 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 1.7
                            DUF4064  30 l 30 
                                        +
  gene3124|gene3124|rna3124|rna3124 233 I 233
                                        1 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 1.4
                            DUF4064  11 IGgilgil 18 
                                        +++++ +l
  gene3124|gene3124|rna3124|rna3124 291 LSAVFTVL 298
                                        22222222 PP

  == domain 4  score: 14.7 bits;  conditional E-value: 4.7e-06
                            DUF4064  14 ilgillglllllflfllssgefsqelteeqalsgedasavleflstllivlgvialiaivlgivgalllkknk 86 
                                        + ++l++++ +++++ +ss+         + + + + ++ ++++ +++ + +v++++ i+++ vg++l+kknk
  gene3124|gene3124|rna3124|rna3124 365 VPSVLFSIISVFVTNPQSSKH--------SDVITVNEKMQYDYFLVFFQIVTVLSFFGIIITAVGIYLVKKNK 429
                                        556677777777744443333........33446778888899***************************997 PP

>> DUF2976  Protein of unknown function (DUF2976)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0      0.54   3.2e+03      20      48 ..      57      85 ..      54      93 .. 0.77
   2 ?    1.1   0.3     0.059   3.5e+02      23      82 ..      96     156 ..      85     161 .. 0.55
   3 ?   -1.3   0.0      0.33     2e+03      14      36 ..     209     229 ..     191     245 .. 0.48
   4 ?    7.4   0.1   0.00064       3.8       5      51 ..     378     423 ..     376     437 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.54
                            DUF2976 20 ikgylkdgvillgLvlaavaflaVakaal 48
                                       ++ yl+d       ++a  a++ V+ +++
  gene3124|gene3124|rna3124|rna3124 57 VWSYLADRTKWHTRIIAINALFYVIASII 85
                                       67788888888888888888888887766 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.059
                            DUF2976  23 ylkdgvillgLvl...aavaflaVakaalkkfnei.segkaewgkfgltlvvGvvllvvviwLl 82 
                                        y+ +   +l+++l   +a + + +  a+l ++    +++  + g  +++ + G   + +v+++l
  gene3124|gene3124|rna3124|rna3124  96 YAVQCGCVLAILLrqiSAGGTFSIFFALLLNYVKRtNSSNRNVGTAKMFGILG---ITFVMMML 156
                                        55555566666542224555667777777766544244444555555555555...55555555 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 0.33
                            DUF2976  14 gdllelikgylkdgvillgLvla 36 
                                        +dl++ + +y++ +v  l+  l 
  gene3124|gene3124|rna3124|rna3124 209 KDLFKRVYQYMNLIV--LAFFLT 229
                                        445554544444333..333332 PP

  == domain 4  score: 7.4 bits;  conditional E-value: 0.00064
                            DUF2976   5 eaPssgekggdllelikgylkdgvillgLvlaavaflaVakaalkkf 51 
                                        ++P+s++  +d++++ +   +d +++   ++ +++f+ ++ +a++ +
  gene3124|gene3124|rna3124|rna3124 378 TNPQSSK-HSDVITVNEKMQYDYFLVFFQIVTVLSFFGIIITAVGIY 423
                                        6899998.999**999***********99*********999999988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (439 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       901  (0.0502538); expected 358.6 (0.02)
Passed bias filter:                      243  (0.0135535); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.48
# Mc/sec: 2751.71
//
Query:       gene3125|gene3125|rna3125|rna3125  [L=658]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.6e-23   80.7  35.9    3.8e-13   49.1   8.4    3.0  3  MFS_1     Major Facilitator Superfamily


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.1   8.4   2.1e-17   3.8e-13       3     177 ..      13     187 ..      10     235 .. 0.82
   2 !   28.8   8.1     3e-11   5.4e-07     205     326 ..     466     584 ..     424     586 .. 0.78
   3 !   31.6  20.3   4.3e-12   7.6e-08       1     171 [.     473     641 ..     473     657 .. 0.80

  Alignments for each domain:
  == domain 1  score: 49.1 bits;  conditional E-value: 2.1e-17
                              MFS_1   3 laaflsalarsilgpalpl.alaedlgispseigllltlyalgaavaslplGrlsdrfGrrr.vlllglllfalg. 75 
                                        +++f s+++++i +++    +l  +  +s  ei +l+++yal  ++  l++ ++++   +   v+l  l+l + + 
  gene3125|gene3125|rna3125|rna3125  13 IILFSSYFSYDIPAALNKNiHL-GSTKFSSYEITMLYSAYALPNIFVPLIFTFVTEYSESTLnVFLSFLVLAGQCv 87 
                                        5667777777776666666344.444799999************************98777768888888888885 PP

                              MFS_1  76 lllllfasslw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgW 150
                                        ++l++f  +++ + +++r+l G+g  +lf +   li+  f+++e ++a++++++   lG+++  l+ ++la  ++ 
  gene3125|gene3125|rna3125|rna3125  88 FTLGIF-KGVFyVSVFGRLLFGIGNETLFVIQSKLITTTFKGRELAFALAVFTSLGRLGIVFNFLITPYLAKRYSA 162
                                        555558.99999***********************************************************99999 PP

                              MFS_1 151 ravfyilaivsllafvlfllllpeepp 177
                                        +++ +i  ++ l+++vl   ll  ++p
  gene3125|gene3125|rna3125|rna3125 163 SVPSLIGLVLILVGLVL--NLLAKRRP 187
                                        99999999999999776..44433333 PP

  == domain 2  score: 28.8 bits;  conditional E-value: 3e-11
                              MFS_1 205 kdpvlwillialllfffgfsglltllplylqevlglsglllaglllallalvgailallagrlsdrlgrrrrllla 280
                                         +p++ il+++++l +f+++ ++ l pl++q++++++    ++ ++++l +v ++  + +g lsd +g  + l++a
  gene3125|gene3125|rna3125|rna3125 466 ISPYFSILVLIAFLSAFVWAPFYNLGPLLFQKRYNYT-REASASMMGVLEMVQMVTIIAIGVLSDFTGI-KLLFVA 539
                                        334443566666677779999****************.6889999********************9996.888888 PP

                              MFS_1 281 llllllaalglallavtssavllllvlvliGfglgfvfpsllalas 326
                                        l++llla   +++  ++ + v++++ l ++G  +++++p++ +la+
  gene3125|gene3125|rna3125|rna3125 540 LGALLLAISHVCIYLNC-NVVAVICTLGIAGPLHSCYWPCVSNLAA 584
                                        88888888888888888.8999999999999999999999998876 PP

  == domain 3  score: 31.6 bits;  conditional E-value: 4.3e-12
                              MFS_1   1 lllaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrr.vlllglllfalg 75 
                                        l+l+aflsa+ ++ ++ + pl+ ++ ++++  +   ++++   +++v+++ +G+lsd  G +  ++ lg+ll+a++
  gene3125|gene3125|rna3125|rna3125 473 LVLIAFLSAFVWAPFYNLGPLLFQKRYNYTREASASMMGVLEMVQMVTIIAIGVLSDFTGIKLlFVALGALLLAIS 548
                                        57899***************9******************************************9************ PP

                              MFS_1  76 .lllllfasslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllgglla.sslg 149
                                         +++ l   +   ++++ +  G++ g l +     ++ ++++e+ ++a++++s++ +l++ + pl++++l+   ++
  gene3125|gene3125|rna3125|rna3125 549 hVCIYL-NCN---VVAVICTLGIA-GPLHSCYWPCVSNLAAQERLSFAFAVISSFLNLSFTVSPLVASYLLqIDGS 619
                                        444444.245...55555555555.455555555566666679****************************55555 PP

                              MFS_1 150 Wravfyilaivsllafvlflll 171
                                        +r++  +  +++++ fv++l+l
  gene3125|gene3125|rna3125|rna3125 620 FRLIEGLSVVFAVFTFVIVLVL 641
                                        8888777777777766654444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (658 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1976  (0.110213); expected 358.6 (0.02)
Passed bias filter:                      453  (0.0252663); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.73u 0.32s 00:00:01.05 Elapsed: 00:00:00.47
# Mc/sec: 4177.87
//
Query:       gene3126|gene3126|rna3126|rna3126  [L=1089]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.1e-93  313.7   0.0    1.2e-60  205.8   0.0    2.5  2  GCS         Glutamate-cysteine ligase


Domain annotation for each model (and alignments):
>> GCS  Glutamate-cysteine ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.2   0.1   2.6e-34   4.7e-30       2      81 ..     537     616 ..     536     641 .. 0.93
   2 !  205.8   0.0   6.9e-65   1.2e-60      86     365 .]     771    1075 ..     719    1075 .. 0.88

  Alignments for each domain:
  == domain 1  score: 105.2 bits;  conditional E-value: 2.6e-34
                                GCS   2 ymDamgfGmGsccLQvtfqaknieearllYdqlaplaPillalsaaspiykGlladvdvrwnvisasvDdrteeEr 77 
                                         +D+mg+GmG+ccLQvt+q  ++++ar+++dqla+++P+ll l+ a+p+  G l ++d+rw++i+ svD+rt+eEr
  gene3126|gene3126|rna3126|rna3126 537 LIDSMGQGMGCCCLQVTVQPGSMDDARFIHDQLAIISPLLLRLTRATPFAGGRLLNTDTRWDMITYSVDCRTDEER 612
                                        68************************************************************************** PP

                                GCS  78 geep 81 
                                        g e 
  gene3126|gene3126|rna3126|rna3126 613 GCEV 616
                                        9886 PP

  == domain 2  score: 205.8 bits;  conditional E-value: 6.9e-65
                                GCS   86 k.......kripksrydsvdlylseekrlreeyndlelpldeevlkklleagvdellakhiahlfirdplvife 152 
                                         +        ripksr+++vdl+l    +  ++y dl++pl+e+ l++l+++g+d+ l++hia+lfirdp+  +e
  gene3126|gene3126|rna3126|rna3126  771 TlrqskksARIPKSRFSAVDLFL---WEGGRKYCDLPVPLHEHSLRTLRAHGIDDMLSTHIASLFIRDPMLAYE 841 
                                         0444444489*************...6789*******************************************6 PP

                                GCS  153 ekieqddekstdhFeniqstnWqtlrfKpPppesekigWrvefRpmevqltdfenaafsvfivLltrvilsfkl 226 
                                         ++       + d Feniqs+nW+++rfK+P   +   gWrve+R+me+q + fen+a + f++L+++ +l++++
  gene3126|gene3126|rna3126|rna3126  842 HT----HAGACDDFENIQSSNWRSVRFKIPL--D--DGWRVELRTMEIQPSVFENSAIVGFVMLFVQYVLKTRI 907 
                                         65....66789*******************9..3..4************************************* PP

                                GCS  227 nfyipiskvdenmkrA....hkrdavleekfyfrkniakkeeaaekak.......................... 270 
                                         n+y+p+s v++n++rA    h   a ++e++   +++++ +++a +++                          
  gene3126|gene3126|rna3126|rna3126  908 NLYVPMSCVNDNFRRAglftHPAGAYKDEQYERMEQLFSCARDALARNvpfseyrrifegyavkvpkdtttfay 981 
                                         ***************95555667799999999999999999988888899************************ PP

                                GCS  271 ..........eieemtideiingkegefpglipliesylesvevdvetrkklekylkliskrasgelltaAkwi 334 
                                                    i+e t+dei+ng+ +e +g+++l+ ++  s           +  l++++++asg+l+++A++ 
  gene3126|gene3126|rna3126|rna3126  982 rtnifesgdaVIREGTLDEIFNGT-HEQKGIVDLLIEEYPS----------YKAMLTFVKMKASGTLVSVADYF 1044
                                         *****99999999**********9.7888999887665555..........5889******************* PP

                                GCS  335 RefvakhpdYkkdSvvsdeinydLlkkveki 365 
                                         R fv +h++Y +d ++s e+++dL++kv++i
  gene3126|gene3126|rna3126|rna3126 1045 RYFVVNHRAYGNDGRISREVCNDLIRKVDEI 1075
                                         ***************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1089 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1438  (0.0802053); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); expected 358.6 (0.02)
Passed Vit filter:                       100  (0.00557756); expected 17.9 (0.001)
Passed Fwd filter:                        43  (0.00239835); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 1.12u 0.35s 00:00:01.47 Elapsed: 00:00:00.56
# Mc/sec: 5888.34
//
Query:       gene3127|gene3127|rna3127|rna3127  [L=444]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (444 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1729  (0.0964359); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.72u 0.35s 00:00:01.06 Elapsed: 00:00:00.58
# Mc/sec: 2305.87
//
Query:       gene3128|gene3128|rna3128|rna3128  [L=329]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.015   15.5   0.2       0.41   10.9   0.0    2.9  3  Plasmid_RAQPRD  Plasmid protein of unknown function (Plasmid_
       0.04   13.8   7.2       0.11   12.4   1.3    2.8  2  TFIIE_alpha     TFIIE alpha subunit
      0.057   13.8   2.5        2.9    8.3   0.1    2.5  2  Prok-TraM       Prokaryotic Transcriptional repressor TraM
       0.14   12.7   4.6       0.86   10.1   0.8    3.2  3  BMFP            Membrane fusogenic activity
       0.17   11.6   2.0       0.41   10.4   0.6    2.4  2  XPC-binding     XPC-binding domain
       0.25   12.2   5.6         43    5.0   0.1    3.9  4  FliT            Flagellar protein FliT
       0.96    9.9  15.0        0.9   10.0   0.9    3.3  3  ParB            ParB family
        1.6    8.6   6.9       0.24   11.3   0.5    2.9  3  Chordopox_L2    Chordopoxvirus L2 protein
        2.8    8.5   6.7         10    6.7   0.4    3.3  3  FliG_N          FliG N-terminal domain
        5.1    7.2   8.5       0.69    9.9   2.2    2.3  2  FlaF            Flagellar protein FlaF


Domain annotation for each model (and alignments):
>> Plasmid_RAQPRD  Plasmid protein of unknown function (Plasmid_RAQPRD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.35   6.3e+02      18      52 ..      47      81 ..      37      85 .. 0.68
   2 ?   -1.5   0.0       1.7     3e+03      48      58 ..     127     137 ..     117     157 .. 0.66
   3 ?   10.9   0.0   0.00023      0.41       9      61 ..     169     221 ..     167     234 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.35
                     Plasmid_RAQPRD 18 qlqalveraeaqakqeekaRvhfdYdrlrrDleri 52
                                       ++ ++v    ++ ++e k+R+ ++ ++++++l+ i
  gene3128|gene3128|rna3128|rna3128 47 KVIKVVVSNTTAVDDELKKRIMVRLEQMNEELDKI 81
                                       55555555555555556889999999999998877 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.7
                     Plasmid_RAQPRD  48 DleriraGIqs 58 
                                        Dl+ +++GI+s
  gene3128|gene3128|rna3128|rna3128 127 DLNVLAEGIKS 137
                                        66666666654 PP

  == domain 3  score: 10.9 bits;  conditional E-value: 0.00023
                     Plasmid_RAQPRD   9 LakllkqLdqlqalveraeaqakqeekaRvhfdYdrlrrDler.iraGIqsYLe 61 
                                        L ++l+qLd+l+++v +   + +++  +R+ ++ d+l++D++  + a ++++++
  gene3128|gene3128|rna3128|rna3128 169 LKNVLEQLDSLESIVLHFHPTNEKD-IERIAINNDQLNEDITKaVNAIVNEFIT 221
                                        77899****************9999.89*************7514555555655 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   1.3   5.9e-05      0.11      15      68 ..      45      98 ..      40     127 .. 0.91
   2 ?    3.8   0.5     0.028        51      13      60 ..     263     310 ..     231     318 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 5.9e-05
                                       HHHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEEEEEETTTE CS
                        TFIIE_alpha 15 avlvldvLlekgevteedlakelkidlnelrklLnrLyearlvkykrrrdeeks 68
                                       + +v++v++++    +++l+k + + l+++ + L ++  + +vk++   + +++
  gene3128|gene3128|rna3128|rna3128 45 MEKVIKVVVSNTTAVDDELKKRIMVRLEQMNEELDKITTDEMVKIRSILEKNQN 98
                                       568******************************************998886655 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.028
                                        HHHHHHHHHHHCTTSEBHHH.HHHHHTS-HHHHHHHHHHHHHCTSEEEE CS
                        TFIIE_alpha  13 eeavlvldvLlekgevteed.lakelkidlnelrklLnrLyearlvkyk 60 
                                         e ++vl+v++ +g+++  + ++ ++++  n +++++ +L +++l ++k
  gene3128|gene3128|rna3128|rna3128 263 WENKEVLKVVA-EGNTSIRQlINDNMNMLTNLIKQIISNLSDEGLGNVK 310
                                        57889999999.5666555516778999**************9996665 PP

>> Prok-TraM  Prokaryotic Transcriptional repressor TraM
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.1    0.0016       2.9       6      53 ..      55     102 ..      49     113 .. 0.82
   2 ?    4.9   0.4     0.018        33      12      82 ..     177     245 ..     168     259 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0016
                                        SSXXX.XSSTHHHHHCTTS-HHHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                          Prok-TraM   6 ssetdadelkplesllsslskseleaLaisAIrehRrllaaaeavyee 53 
                                        ++++ +delk+++ +     ++el++++ +   + R+ l+++++++ +
  gene3128|gene3128|rna3128|rna3128  55 NTTAVDDELKKRIMVRLEQMNEELDKITTDEMVKIRSILEKNQNIFYD 102
                                        3334478999888887788889*********************99965 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.018
                                        XSSTHHHHHCTTS-HHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHSCHHHHTTSCHHSHHHHHHHHHHHHH CS
                          Prok-TraM  12 delkplesllsslskseleaLaisAIrehRrllaaaeavyeewvrasadekvseavleelqeeYveaqkes 82 
                                        d l+ ++ ++++ +++++e++ai+  +      +a +a+ +e+  ++++ + ++   ++  e+Y++  +e 
  gene3128|gene3128|rna3128|rna3128 177 DSLESIVLHFHPTNEKDIERIAINNDQLNEDITKAVNAIVNEF--ITENINNASRKNRKTVEAYIKHVIEL 245
                                        67788889999*************9999989889999999997..77888888888888888888887765 PP

>> BMFP  Membrane fusogenic activity
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.8   0.00048      0.86       9      60 ..      44      95 ..      40      98 .. 0.89
   2 ?    2.1   0.0      0.16   2.8e+02      20      41 ..     200     221 ..     191     243 .. 0.83
   3 ?   -0.9   0.0       1.3   2.3e+03       7      36 ..     283     313 ..     250     322 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00048
                               BMFP  9 dlakkvgdalpaaagvreeieknvravlqealsklDLVtREEFdvqrevlar 60
                                       d+ k+++  +++ ++v++e++k +  +l+++ ++lD +t +E   +r +l++
  gene3128|gene3128|rna3128|rna3128 44 DMEKVIKVVVSNTTAVDDELKKRIMVRLEQMNEELDKITTDEMVKIRSILEK 95
                                       789999999********************************98766666665 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.16
                               BMFP  20 aaagvreeieknvravlqeals 41 
                                        +  +++e+i k+v a+++e+++
  gene3128|gene3128|rna3128|rna3128 200 NNDQLNEDITKAVNAIVNEFIT 221
                                        5556889999999999999876 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 1.3
                               BMFP   7 lddlakkvgdalpaaag.vreeieknvravl 36 
                                        ++d  + +++ +++    + +e   nv++++
  gene3128|gene3128|rna3128|rna3128 283 INDNMNMLTNLIKQIISnLSDEGLGNVKEMI 313
                                        4444444455555544445555555555555 PP

>> XPC-binding  XPC-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       5.9   1.1e+04      24      32 ..     169     177 ..     168     178 .. 0.78
   2 ?   10.4   0.6   0.00023      0.41      12      31 ..     278     297 ..     277     301 .. 0.92

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 5.9
                        XPC-binding  24 LqplLqqla 32 
                                        L+ +L+ql 
  gene3128|gene3128|rna3128|rna3128 169 LKNVLEQLD 177
                                        889999985 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00023
                        XPC-binding  12 qlRqlvqqnPqlLqplLqql 31 
                                         +Rql++ n ++L  l++q+
  gene3128|gene3128|rna3128|rna3128 278 SIRQLINDNMNMLTNLIKQI 297
                                        69*****************9 PP

>> FliT  Flagellar protein FliT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.1     0.024        43      34      76 ..      40      82 ..      24      97 .. 0.77
   2 ?   -0.7   0.1       1.5   2.7e+03      44      68 ..     191     215 ..     170     238 .. 0.68
   3 ?    4.0   0.1     0.048        86      32      69 ..     224     261 ..     190     263 .. 0.80
   4 ?    3.5   0.1     0.071   1.3e+02      44      75 ..     266     297 ..     261     302 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.024
                                       T--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHTH CS
                               FliT 34 plspaereekrellrrilandaeirallqprldelqkllgalr 76
                                        l+p++++ +  + +   a d+e++++++ rl+++ ++l+++ 
  gene3128|gene3128|rna3128|rna3128 40 LLTPDMEKVIKVVVSNTTAVDDELKKRIMVRLEQMNEELDKIT 82
                                       5666666666666677788999999999999999999999876 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.5
                                        HHHHHHHHHHHHHHHHHHHHHHHHH CS
                               FliT  44 rellrrilandaeirallqprldel 68 
                                        ++ ++ri  n++++ + + +  +++
  gene3128|gene3128|rna3128|rna3128 191 EKDIERIAINNDQLNEDITKAVNAI 215
                                        5667777777777776665555544 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.048
                                        -ST--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                               FliT  32 aaplspaereekrellrrilandaeirallqprldelq 69 
                                          ++s   r+  ++ +++++++ + i + +  r +el+
  gene3128|gene3128|rna3128|rna3128 224 INNASRKNRKTVEAYIKHVIELKDYILNKMLSRITELS 261
                                        566779999999*********************99997 PP

  == domain 4  score: 3.5 bits;  conditional E-value: 0.071
                                        HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHT CS
                               FliT  44 rellrrilandaeirallqprldelqkllgal 75 
                                         e+l+ + + +  ir+l++  ++ l +l++++
  gene3128|gene3128|rna3128|rna3128 266 KEVLKVVAEGNTSIRQLINDNMNMLTNLIKQI 297
                                        678888999999****************9997 PP

>> ParB  ParB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.9    0.0005       0.9      31      85 ..      40      94 ..      28     102 .. 0.87
   2 ?    5.3   3.2     0.015        26      11      81 ..     165     240 ..     160     256 .. 0.76
   3 ?    1.6   0.3      0.21   3.8e+02      13      59 ..     252     298 ..     243     322 .. 0.53

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0005
                               ParB 31 eliekvkeeiekvqsdtelaedeqkseilklikkeskrlkkpkkkdkavvekLae 85
                                        l+ ++++ i+ v s+t + +de k++i+  +++ +++l k  + +++++ ++ e
  gene3128|gene3128|rna3128|rna3128 40 LLTPDMEKVIKVVVSNTTAVDDELKKRIMVRLEQMNEELDKITTDEMVKIRSILE 94
                                       567889999********************************99999998888776 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.015
                               ParB  11 DYklLlkvaeklekkdvelseliekvkeeiekvq.sdtelaedeqk..seilk.likkeskrlkkpkkkdka.vve 81 
                                         Y +L +v e+l++ ++ +  +    +++ie +  ++++l+ed++k  ++i++ +i+++ +++ +++ k++   ++
  gene3128|gene3128|rna3128|rna3128 165 AYVILKNVLEQLDSLESIVLHFHPTNEKDIERIAiNNDQLNEDITKavNAIVNeFITENINNASRKNRKTVEaYIK 240
                                        699****************************9963678899***99556788625566666666666565543444 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.21
                               ParB  13 klLlkvaeklekkdvelseliekvkeeiekvqsdtelaedeqkseil 59 
                                        k+L+ ++e    +++e+ +++++ +++i ++ +d+ +      ++i+
  gene3128|gene3128|rna3128|rna3128 252 KMLSRITELSTWENKEVLKVVAEGNTSIRQLINDNMNMLTNLIKQII 298
                                        55666666666666666666666666665543333222222222233 PP

>> Chordopox_L2  Chordopoxvirus L2 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       3.1   5.6e+03       6      40 ..      88      97 ..      73     106 .. 0.57
   2 ?   11.3   0.5   0.00013      0.24       8      40 ..     222     254 ..     203     260 .. 0.93
   3 ?   -1.4   0.2       1.2   2.2e+03      56      72 ..     278     294 ..     268     300 .. 0.65

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 3.1
                       Chordopox_L2  6 klrsieeenkanekfldaiitevesqqpailrpll 40
                                       k+rsi e+n                          
  gene3128|gene3128|rna3128|rna3128 88 KIRSILEKN-------------------------Q 97
                                       444444443.........................3 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00013
                       Chordopox_L2   8 rsieeenkanekfldaiitevesqqpailrpll 40 
                                        ++i++ ++ n+k ++a i++v++ + +il ++l
  gene3128|gene3128|rna3128|rna3128 222 ENINNASRKNRKTVEAYIKHVIELKDYILNKML 254
                                        589**************************9997 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 1.2
                       Chordopox_L2  56 llfrlvvRNykvllill 72 
                                        ++ +l+  N+++l+ l+
  gene3128|gene3128|rna3128|rna3128 278 SIRQLINDNMNMLTNLI 294
                                        55566666666666554 PP

>> FliG_N  FliG N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.4    0.0057        10      30      81 ..      44      95 ..      33      98 .. 0.85
   2 ?    2.6   0.3      0.11     2e+02      28      79 ..     190     243 ..     181     259 .. 0.74
   3 ?    1.0   0.1      0.34   6.1e+02      35      68 ..     253     283 ..     243     319 .. 0.58

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0057
                                       HHHHHHHHHHHCHTTXXHHHHHHHHHHHHHHHHCCCCHHCHHHHHHHHHHHH CS
                             FliG_N 30 eeiekltkeiaslksvskeeveaVleefleeleaqeylseggeeyarelLek 81
                                       +  + +   +++   v+ e +++++    ++ e+ ++++++ +  +r++Lek
  gene3128|gene3128|rna3128|rna3128 44 DMEKVIKVVVSNTTAVDDELKKRIMVRLEQMNEELDKITTDEMVKIRSILEK 95
                                       44444555679999************************************99 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.11
                                        XHHHHHHHHHHHHCHTTXXHHHHHHHHHHHHHHH..HCCCCHHCHHHHHHHHHH CS
                             FliG_N  28 deeeiekltkeiaslksvskeeveaVleefleel..eaqeylseggeeyarelL 79 
                                        +e++ie+++    +l++   + v+a+++ef +e   +a+ +  +  e+y+++++
  gene3128|gene3128|rna3128|rna3128 190 NEKDIERIAINNDQLNEDITKAVNAIVNEFITENinNASRKNRKTVEAYIKHVI 243
                                        57788888888888888888999*******966522444555555666666665 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.34
                                        HHHHHHCHTTXXHHHHHHHHHHHHHHHHCCCCHH CS
                             FliG_N  35 ltkeiaslksvskeeveaVleefleeleaqeyls 68 
                                        +  +i +l + +++ev +V++e ++ +    +l+
  gene3128|gene3128|rna3128|rna3128 253 MLSRITELSTWENKEVLKVVAEGNTSI---RQLI 283
                                        445555555555555555555544333...3333 PP

>> FlaF  Flagellar protein FlaF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.5       0.4   7.2e+02      63     109 ..      53      99 ..      47     102 .. 0.83
   2 ?    9.9   2.2   0.00039      0.69      31     111 ..     209     291 ..     185     293 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.4
                               FlaF  63 aspenplpeelRadlislglfvlketsevlaepsekleaLIdinrni 109
                                         s+  + ++el+++++   + +++e +++ +++  k++++ + n+ni
  gene3128|gene3128|rna3128|rna3128  53 VSNTTAVDDELKKRIMVRLEQMNEELDKITTDEMVKIRSILEKNQNI 99 
                                        56677889999999988888899999999999999999999999888 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00039
                               FlaF  31 kaaeeagkese..eelaeAlkfnrrlWtilaedlaspenplpeelRadlislglfvlketsevlaepsekleaLId 104
                                        ++a +a  +++  e++++A ++nr+   + ++ + + +  + +++  ++ +l+++ +ke+ +v+ae ++++++LI+
  gene3128|gene3128|rna3128|rna3128 209 TKAVNAIVNEFitENINNASRKNRKTVEAYIKHVIELKDYILNKMLSRITELSTWENKEVLKVVAEGNTSIRQLIN 284
                                        44444444444435677888888888888888888888888888999***************************** PP

                               FlaF 105 inrniaa 111
                                         n+n+  
  gene3128|gene3128|rna3128|rna3128 285 DNMNMLT 291
                                        9999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (329 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2132  (0.118913); expected 358.6 (0.02)
Passed bias filter:                      661  (0.0368676); expected 358.6 (0.02)
Passed Vit filter:                        81  (0.00451782); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.76u 0.33s 00:00:01.09 Elapsed: 00:00:00.55
# Mc/sec: 1803.42
//
Query:       gene3129|gene3129|rna3129|rna3129  [L=959]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.83    9.9  13.0        1.3    9.2   0.0    5.4  7  FNIP      FNIP Repeat


Domain annotation for each model (and alignments):
>> FNIP  FNIP Repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.15   2.7e+03      14      31 ..      14      30 ..      13      31 .. 0.78
   2 ?   -2.8   0.0      0.42   7.5e+03       4      17 ..     306     319 ..     283     322 .. 0.76
   3 ?    9.2   0.0   7.4e-05       1.3      10      41 ..     393     422 ..     388     424 .. 0.88
   4 ?   -1.5   0.1      0.16   2.9e+03      11      21 ..     460     508 ..     435     509 .. 0.57
   5 ?   -2.8   0.0      0.42   7.6e+03      29      41 ..     578     590 ..     550     592 .. 0.63
   6 ?   -2.1   0.0      0.26   4.6e+03      13      23 ..     674     684 ..     662     688 .. 0.79
   7 ?    5.2   0.2    0.0013        24       9      27 ..     796     818 ..     792     827 .. 0.73

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.15
                               FNIP 14 leiLilgrdFnqkiligs 31
                                       ++iLi+ + + qk  +++
  gene3129|gene3129|rna3129|rna3129 14 VTILIF-DGYSQKACKDF 30
                                       79****.88888876666 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 0.42
                               FNIP   4 iikigeLPsnleiL 17 
                                        ii  ge+ +n++iL
  gene3129|gene3129|rna3129|rna3129 306 IIVNGEIFDNIKIL 319
                                        45666777899988 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 7.4e-05
                               FNIP  10 LPsnleiLilgrdFnqkil.igsLPnSlkeLyF 41 
                                         Psn+  L++   ++ +++ + sLP++lk+ ++
  gene3129|gene3129|rna3129|rna3129 393 MPSNVIRLEF---YQCEFEtNISLPSHLKSVEL 422
                                        69********...777787789********987 PP

  == domain 4  score: -1.5 bits;  conditional E-value: 0.16
                               FNIP  11 P......................................snleiLilgr 21 
                                                                               +++ei++l++
  gene3129|gene3129|rna3129|rna3129 460 FnridgklniispieykkqdeilslrlycvyvygivyidPSIEIITLNS 508
                                        0555555555556666666666666666666666666668999999985 PP

  == domain 5  score: -2.8 bits;  conditional E-value: 0.42
                               FNIP  29 igsLPnSlkeLyF 41 
                                        + +LP  ++++ +
  gene3129|gene3129|rna3129|rna3129 578 NIVLPEDCTSIVL 590
                                        3356666666655 PP

  == domain 6  score: -2.1 bits;  conditional E-value: 0.26
                               FNIP  13 nleiLilgrdF 23 
                                         + +L++++++
  gene3129|gene3129|rna3129|rna3129 674 EIHHLQFNNYY 684
                                        57899998776 PP

  == domain 7  score: 5.2 bits;  conditional E-value: 0.0013
                               FNIP   9 eLPsnleiL....ilgrdFnqki 27 
                                         LP+nl+iL    ++ r  nq+i
  gene3129|gene3129|rna3129|rna3129 796 NLPPNLKILniagKFDRTVNQPI 818
                                        59*******33333566667776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (959 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       583  (0.0325172); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.69u 0.29s 00:00:00.98 Elapsed: 00:00:00.48
# Mc/sec: 5961.93
//
Query:       gene313|gene313|rna313|rna313  [L=305]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (305 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       745  (0.0415528); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 2199.91
//
Query:       gene3130|gene3130|rna3130|rna3130  [L=542]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   2.8e-102  342.4   0.4    1.5e-83  280.9   0.2    2.1  2  TGT       Queuine tRNA-ribosyltransferase
  ------ inclusion threshold ------
        3.1    7.1   7.6        4.3    6.7   7.6    1.1  1  SDA1      SDA1


Domain annotation for each model (and alignments):
>> TGT  Queuine tRNA-ribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.9   0.0   2.6e-20   2.4e-16       2     107 ..      13     106 ..       9     111 .. 0.87
   2 !  280.9   0.2   1.6e-87   1.5e-83      99     349 ..     252     525 ..     187     526 .. 0.88

  Alignments for each domain:
  == domain 1  score: 59.9 bits;  conditional E-value: 2.6e-20
                                        TEEEEEEEETTEEEEESEEEEBETTSSBTTB-HHHHH.HTTES-EEEEHHHHHHTTTHHHHHHTTHHHHHHT--S- CS
                                TGT   2 gaRlGklelphgtietPafmpvgtqgtvkgltpdelkeelgaqiilsntyhlelrpgeelvakagglhkflgwdkp 77 
                                        +aR+++l+l+h t + P+fmpv+t+g +k+  ++      + +iil+nt+hl+        +   +lh+f+g+++ 
  gene3130|gene3130|rna3130|rna3130  13 NARISTLTLNHYTASLPTFMPVATHGILKA--KHGY----EDEIILGNTFHLR--------NLNRDLHSFMGLKGG 74 
                                        59*************************996..5566....579*********9........334589********* PP

                                        EEEE-SHHHHHHH.EEEESSEEEEE-T.TTS- CS
                                TGT  78 iltdsggfqvfsl.kkiteegvsfqsr.idGs 107
                                        +ltdsggfq++sl +k++e+gv f    +dG+
  gene3130|gene3130|rna3130|rna3130  75 LLTDSGGFQIISLkNKVNEDGVVFLDYdCDGK 106
                                        *************55*******9987656666 PP

  == domain 2  score: 280.9 bits;  conditional E-value: 1.6e-87
                                        EEE-TTTS-EEEE-HHHHHHHHHHHT-SEEE-------SS--HHHHHHHHHHHHHHHHHHHHHH....SEEEEEE- CS
                                TGT  99 sfqsridGskvlltpeesieiqeklgsDiimalddvvpspaskkrveksverTlrwldrcleah....qalfgivq 170
                                        ++++++  +++lltpe+s++iq++l+sDi+m+lddv+ + + k+r+  +v+r++rwldrcl+++    q lf+i+q
  gene3130|gene3130|rna3130|rna3130 252 TISHHY--KNFLLTPEKSMAIQNTLNSDIAMQLDDVIRPCSPKNRHLLAVKRSIRWLDRCLAHTkndaQLLFPIIQ 325
                                        445555..559************************99999999******************777999899****** PP

                                        -TT-HHHHHHHHHHHHHH--SEEEE-SSSSSSHHHHHHHHHHHHGGGS..-TTS-EEETTB-SHHHHHHHHHTT-- CS
                                TGT 171 GglyedlreesaeelakrdfdgyaigGlsvgeekeellevveavtell..pedkprylmGvgtPedlleavalGvD 244
                                        Ggl++dlr+ s++e++ r+++g+aigGl++ge+k++++++v ++++++    ++p+y+mGvg+Ped+++++ lG D
  gene3130|gene3130|rna3130|rna3130 326 GGLFNDLRMLSVDEIVLRGVKGIAIGGLCGGEDKKMFCNIVFNTVNYIrsKIECPIYVMGVGYPEDIVVSIFLGSD 401
                                        *****************************************6666666222378********************** PP

                                        EEEESHHHHHHHTTEEEETTEEEET.......................TSGGGTT--SBSSSS--SHHHHH-BHHH CS
                                TGT 245 mfdcvyptrtarngraltsegelnl.......................knakyaedfspldegCsCytCknytray 297
                                        m dcvyptrtar+gr++t++g++n+                       +n+++++    ++++C C tC++++ +y
  gene3130|gene3130|rna3130|rna3130 402 MSDCVYPTRTARFGRMFTDYGDINVnsfadgndayrgrssrrndtqayTNTRIRDG--VVYNECACRTCTRFSINY 475
                                        *************************8888888888887777766555555555533..69*********99***** PP

                                        HHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHT CS
                                TGT 298 lhhllktkemlgaiLltiHNlhyylelfkriReaIkegtfeefveefarkye 349
                                        l+++ +t +  ++iL+t+HNl+y+++l++r+++ I+ gt++ fv+e+++k++
  gene3130|gene3130|rna3130|rna3130 476 LKMIRNTPN--FCILMTEHNLFYLRDLIDRVKRNIRGGTLDIFVKEWMMKRF 525
                                        *********..*************************************9985 PP

>> SDA1  SDA1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   7.6   0.00048       4.3      87     172 ..     118     200 ..      98     269 .. 0.52

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.00048
                               SDA1  87 kreeeeedsddeddeedwevesdddseedseggwidvesdee...eieesdesedeeeeeeeeeekeekeeeeeee 159
                                            +++d+ ++d++e+++ e+++ s++d+++g  + ++++    +i+e+d  ++ +e++  ++ +e++  ++ +e
  gene3130|gene3130|rna3130|rna3130 118 GG--NDDDNRSNDNNEGNDDENESISNDDNNEGISNDQNEGRgidNINENDGIDNINENDGIDNINENDGIDNINE 191
                                        22..333333444444444455455566666664444444336663333333222222222111111111111111 PP

                               SDA1 160 eeeeeeeeeeeee 172
                                            ++  ++ +e
  gene3130|gene3130|rna3130|rna3130 192 ----NDGIDNINE 200
                                        ....111111111 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (542 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       600  (0.0334653); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.30s 00:00:00.88 Elapsed: 00:00:00.47
# Mc/sec: 3487.03
//
Query:       gene3131|gene3131|rna3131|rna3131  [L=369]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0083   15.8   1.5      0.013   15.1   1.5    1.3  1  SseC            Secretion system effector C (SseC) like famil
  ------ inclusion threshold ------
      0.032   14.1   4.4      0.026   14.4   1.5    2.1  2  Apolipoprotein  Apolipoprotein A1/A4/E domain
       0.38   11.3  15.8         37    4.9  10.4    4.2  2  YtxH            YtxH-like protein
        1.5    8.9  18.2      0.025   14.7   8.3    2.8  3  ApoLp-III       Apolipophorin-III precursor (apoLp-III)
        2.6    8.4   8.6      0.094   13.1   1.2    2.4  3  Gp-FAR-1        Nematode fatty acid retinoid binding protein 
        2.6    8.7   6.9        1.5    9.5   0.3    3.5  4  DUF883          Bacterial protein of unknown function (DUF883


Domain annotation for each model (and alignments):
>> SseC  Secretion system effector C (SseC) like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   1.5   4.3e-06     0.013     149     248 ..      74     205 ..      45     212 .. 0.59

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 4.3e-06
                               SseC 149 vvavgsaakgaaaavksg...aaklaeavaeaigkaikkaaekagkevaeqvskqvlnelakkatkvakavkegvv 221
                                        v+++ +++ ++++ +k+     + + e ++e+++++ik ++ +a+k+v+e     v +   kk++++++++k +++
  gene3131|gene3131|rna3131|rna3131  74 VSVLENVGDKTGDFLKNVgskLKDAKESLEENVSSTIKSVIDDAAKKVSE-----VKDDYVKKTEELGEKAKDIID 144
                                        56666666666666666555688889999999***************995.....555555555555555555553 PP

                               SseC 222 asavakalikavvv...................................aeggngiaqGain 248
                                        +++++k+ +  + +                                   +e++ ++a G+++
  gene3131|gene3131|rna3131|rna3131 145 REVLTKMNEGEI-TrnleeketealggikglidradellngklkenvnvVEKTSTAADGEVT 205
                                        222222222222.2133333333333333333333333333333333336666666666555 PP

>> Apolipoprotein  Apolipoprotein A1/A4/E domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   1.5   8.7e-06     0.026      41     113 ..      72     144 ..      54     207 .. 0.62
   2 ?   -0.3   0.1      0.28   8.3e+02      67      85 ..     312     330 ..     271     342 .. 0.54

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 8.7e-06
                                        HHHHHHHHHHHHCCCCHHHHHHCCCHHHHHHHHHCCHHHHHHHHHHHHCHHCCHHCHCCHCHHHHHHHHHHHH CS
                     Apolipoprotein  41 rlraeleevrarlepyrdevqeqlgqnleelrqrlapyteelrerlaadaeelqeqlavyaeelrerlerhve 113
                                        ++ + le+v ++  + + +v  +l++  e l + +++ ++ + + +a+++ e+++   ++ eel e++++ ++
  gene3131|gene3131|rna3131|rna3131  72 EVVSVLENVGDKTGDFLKNVGSKLKDAKESLEENVSSTIKSVIDDAAKKVSEVKDDYVKKTEELGEKAKDIID 144
                                        3445556666666666666666666666666666666666666666666666666666666665555555433 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.28
                                        HHHHHHHHCCHHHHHHHHH CS
                     Apolipoprotein  67 nleelrqrlapyteelrer 85 
                                        +++ l  +l+ + ++ ++ 
  gene3131|gene3131|rna3131|rna3131 312 HTDTLLDKLQKLRDKFKKH 330
                                        3333333333333333333 PP

>> YtxH  YtxH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9  10.4     0.012        37      34      69 ..      88     127 ..      35     208 .. 0.78
   2 ?    3.8   0.2     0.029        85      42      68 ..     274     332 ..     253     339 .. 0.68

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.012
                               YtxH  34 addlkekakelleeakeka....kekaedlkekvkekade 69 
                                        ++++  k+k+++e+++e++    k+ ++d+++kv+e  d+
  gene3131|gene3131|rna3131|rna3131  88 LKNVGSKLKDAKESLEENVsstiKSVIDDAAKKVSEVKDD 127
                                        4444444444444444444333333333333333333333 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.029
                               YtxH  42 kelleeakeka................................kekaedlkekvkekad 68 
                                        ke++e+ ke+                                  +k ++l++k+k+ ad
  gene3131|gene3131|rna3131|rna3131 274 KETIEKKKETLpdgtktttevhkkeeppketttavngvhtdtlLDKLQKLRDKFKKHAD 332
                                        33333333333333333344445556666777777777877888888888888888876 PP

>> ApoLp-III  Apolipophorin-III precursor (apoLp-III)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   8.3   8.3e-06     0.025      17     133 ..      32     147 ..      19     163 .. 0.81
   2 ?   -1.3   1.1      0.71   2.1e+03      69      69 ..     226     226 ..     156     299 .. 0.62
   3 ?   -0.2   0.2      0.32   9.6e+02      63      84 ..     316     336 ..     269     366 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 8.3e-06
                          ApoLp-III  17 lpsqeevvetiKensenlvdqlkqviksl..qeelkkksdeleealkevkkkieetadklseenPevkkkaqelqe 90 
                                        l   +ev + +K+  +  ++ +k v +++  +e++  +++e+ ++l++v +k   t d l++  + +k + + l+e
  gene3131|gene3131|rna3131|rna3131  32 LNTMKEVENILKNDKDITASPVKVVKEKVaeTEAIDPTTGEVVSVLENVGDK---TGDFLKNVGSKLKDAKESLEE 104
                                        5566777777887777777777777777722457777999999999999987...55566666668999999999* PP

                          ApoLp-III  91 kvQsgvqslvkesqklaeslkensqeakeklakaikqayddav 133
                                        +v s ++s++ +++k ++++k++  + +e+l ++ k ++d  v
  gene3131|gene3131|rna3131|rna3131 105 NVSSTIKSVIDDAAKKVSEVKDDYVKKTEELGEKAKDIIDREV 147
                                        ***************************************9765 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.71
                          ApoLp-III  69 e 69 
                                         
  gene3131|gene3131|rna3131|rna3131 226 T 226
                                        2 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.32
                          ApoLp-III  63 vkkkieetadklseenPevkkk 84 
                                        + +k+++ +dk+++ ++++  +
  gene3131|gene3131|rna3131|rna3131 316 LLDKLQKLRDKFKK-HADLDVQ 336
                                        24566666666666.5555555 PP

>> Gp-FAR-1  Nematode fatty acid retinoid binding protein (Gp-FAR-1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.1       1.6   4.9e+03      37      63 ..      33      59 ..      27      66 .. 0.56
   2 ?   13.1   1.2   3.2e-05     0.094      10      80 ..      72     144 ..      68     185 .. 0.85
   3 ?   -1.2   0.2       0.8   2.4e+03      50      66 ..     313     329 ..     272     334 .. 0.65

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.6
                           Gp-FAR-1 37 knedellaalKkkspaLyekaeklqak 63
                                       ++++e+ ++lK+ ++  +++++ +++k
  gene3131|gene3131|rna3131|rna3131 33 NTMKEVENILKNDKDITASPVKVVKEK 59
                                       455555666665555555555544444 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 3.2e-05
                           Gp-FAR-1  10 evvealknltdeekaqlkevvknykg..yknedellaalKkkspaLyekaeklqaklkekvdkLspeakeFvk 80 
                                        evv++l+n+ d+    lk+v ++ k+     e+++ + +K+  +  ++k+++++  + +k ++L+++ak+ ++
  gene3131|gene3131|rna3131|rna3131  72 EVVSVLENVGDKTGDFLKNVGSKLKDakESLEENVSSTIKSVIDDAAKKVSEVKDDYVKKTEELGEKAKDIID 144
                                        89999******************77733334777899********************************8775 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 0.8
                           Gp-FAR-1  50 spaLyekaeklqaklke 66 
                                        +++L  k++kl+ k+k+
  gene3131|gene3131|rna3131|rna3131 313 TDTLLDKLQKLRDKFKK 329
                                        34455555555555554 PP

>> DUF883  Bacterial protein of unknown function (DUF883)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.33     1e+03      11      38 ..      35      62 ..      33      65 .. 0.89
   2 ?    9.5   0.3   0.00051       1.5      13      70 ..      83     144 ..      71     151 .. 0.54
   3 ?   -2.5   0.0       2.8   8.2e+03       8      26 ..     172     190 ..     160     210 .. 0.61
   4 ?   -1.4   0.0       1.3   3.8e+03      10      24 ..     316     330 ..     302     337 .. 0.59

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.33
                             DUF883 11 ladleellkeaadeageeaeelRerlee 38
                                       ++++e++lk+ +d +++ ++ ++e++ e
  gene3131|gene3131|rna3131|rna3131 35 MKEVENILKNDKDITASPVKVVKEKVAE 62
                                       6899*******************99976 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00051
                             DUF883  13 dleellkeaadeageeaeelRer....leerlerarerlrdaeeavaerakeaaeaaddyVr 70 
                                        ++ ++lk+ +++ ++  e+l e+    +++ +++a +++++++++++++++e  e+a+d++ 
  gene3131|gene3131|rna3131|rna3131  83 KTGDFLKNVGSKLKDAKESLEENvsstIKSVIDDAAKKVSEVKDDYVKKTEELGEKAKDIID 144
                                        44444444444444444433333000044445566666677777777777777777777665 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 2.8
                             DUF883   8 eslladleellkeaadeag 26 
                                        + l++ ++ell+ + +e  
  gene3131|gene3131|rna3131|rna3131 172 KGLIDRADELLNGKLKENV 190
                                        4555555666555444443 PP

  == domain 4  score: -1.4 bits;  conditional E-value: 1.3
                             DUF883  10 lladleellkeaade 24 
                                        ll++l++l ++ +++
  gene3131|gene3131|rna3131|rna3131 316 LLDKLQKLRDKFKKH 330
                                        444444444443333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (369 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1754  (0.0978303); expected 358.6 (0.02)
Passed bias filter:                      612  (0.0341346); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.67u 0.30s 00:00:00.97 Elapsed: 00:00:00.49
# Mc/sec: 2254.65
//
Query:       gene3132|gene3132|rna3132|rna3132  [L=182]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.7e-14   52.1   5.7    9.5e-14   50.7   5.7    1.6  1  MAD             Mitotic checkpoint protein
    3.9e-07   30.1   8.4    2.5e-05   24.4   0.9    2.3  2  Cnn_1N          Centrosomin N-terminal motif 1
     0.0066   15.2   0.9      0.017   13.9   0.0    1.8  2  GOLGA2L5        Putative golgin subfamily A member 2-like pro
     0.0089   16.0   2.1       0.48   10.4   0.1    2.2  2  Succ_DH_flav_C  Fumarate reductase flavoprotein C-term
  ------ inclusion threshold ------
      0.014   15.5   0.2      0.046   13.8   0.2    1.9  1  TT1725          Hypothetical protein TT1725
      0.017   14.4   0.3      0.039   13.2   0.1    1.5  2  DXP_synthase_N  1-deoxy-D-xylulose-5-phosphate synthase
      0.024   14.3   0.2        5.1    6.8   0.1    2.8  2  DUF2312         Uncharacterized protein conserved in bacteria
      0.031   13.9   0.9        0.1   12.2   0.9    1.8  1  BB_PF           Beta barrel Pore-forming domain
       0.26   11.4   4.3        1.7    8.7   3.9    2.2  1  DivIVA          DivIVA protein
        0.4   11.1   6.3       0.71   10.3   6.3    1.3  1  DUF4600         Domain of unknown function (DUF4600)


Domain annotation for each model (and alignments):
>> MAD  Mitotic checkpoint protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.7   5.7   5.3e-17   9.5e-14     508     661 .]      13     180 ..       4     180 .. 0.88

  Alignments for each domain:
  == domain 1  score: 50.7 bits;  conditional E-value: 5.3e-17
                                MAD 508 kLqaEierlkellkkle..............edkekkvaslpessltlafkevleLrke....lesaelkiqrlKe 565
                                        +L +E++ lk ++ +le              e+ke++ +++  + l+  +ke le  ++    +   +  +++l +
  gene3132|gene3132|rna3132|rna3132  13 NLLKENNDLKLRIAALEhslskigntdtaahEQKENESNAFLVERLEKLEKEKLEWCANsnctVYRHQEELRQLTD 88 
                                        688999999999999999999999999998866677777888887888888887776642333778888999**** PP

                                MAD 566 vFkakiqEFRevvYmLlGYkidittnsqyRltSmYaeekedallfklsesnesklkLletpfSrtleelidlhlae 641
                                         +k   +  R+ v  LlGYk+d+  + q+ l S+Y+ + +d++ f+ +e+     +++++ f++  ++ id ++ +
  gene3132|gene3132|rna3132|rna3132  89 HYKEILKDIRKNVTGLLGYKLDVI-DDQVHLHSLYSFDRDDVFTFNVKEDCY---EMVNNHFAEGYRKEIDTYVVK 160
                                        **********************86.679*****************8888877...99******************* PP

                                MAD 642 qksiPaflsalTLeLfsrqt 661
                                          s+Pa+l+ +TL+L+s++t
  gene3132|gene3132|rna3132|rna3132 161 GRSVPALLAHVTLDLVSKKT 180
                                        ******************97 PP

>> Cnn_1N  Centrosomin N-terminal motif 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.9   1.4e-08   2.5e-05       6      44 ..       8      45 ..       4      52 .. 0.77
   2 !   10.1   1.3    0.0004      0.71      24      71 ..      52      99 ..      50     101 .. 0.95

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 1.4e-08
                             Cnn_1N  6 eeqidkLkKENFdLKLriyfLeerleklseeqkeellke 44
                                        e+  +L KEN dLKLri+ Le+ l k+++ + ++++++
  gene3132|gene3132|rna3132|rna3132  8 YEKYVNLLKENNDLKLRIAALEHSLSKIGN-TDTAAHEQ 45
                                       56667899**********************.33344333 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0004
                             Cnn_1N 24 yfLeerleklseeqkeellkenielkveveslqkelkekkkllreaek 71
                                       +fL erlekl++e+ e + ++n  +  + e+l++  + +k+ l++  k
  gene3132|gene3132|rna3132|rna3132 52 AFLVERLEKLEKEKLEWCANSNCTVYRHQEELRQLTDHYKEILKDIRK 99
                                       69******************************************9877 PP

>> GOLGA2L5  Putative golgin subfamily A member 2-like protein 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.0   9.2e-06     0.017     420     457 ..       4      40 ..       2      44 .. 0.89
   2 ?    0.3   0.3      0.12   2.1e+02      83     132 ..      49      99 ..      34     106 .. 0.53

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 9.2e-06
                                        XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                           GOLGA2L5 420 mekLqsrFtelmqekvdLkerveeLehrCiqLsGetDt 457
                                        m+ L +++++l++e+ dLk r+  Leh   +  G+tDt
  gene3132|gene3132|rna3132|rna3132   4 MNELYEKYVNLLKENNDLKLRIAALEHSLSK-IGNTDT 40 
                                        999************************8555.499999 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.12
                                        XXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXX CS
                           GOLGA2L5  83 eeeqrlqeeleqLqkekealagqlqaqv.rDneqLsrlnqeqeerLleler 132
                                        e++  l e+le+L+kek +  ++ +  v r  e+L +l+   +e L+++ +
  gene3132|gene3132|rna3132|rna3132  49 ESNAFLVERLEKLEKEKLEWCANSNCTVyRHQEELRQLTDHYKEILKDIRK 99 
                                        333445555555655554444444444335555555555555555555555 PP

>> Succ_DH_flav_C  Fumarate reductase flavoprotein C-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.3     0.012        21       4      54 ..       4      54 ..       3      61 .. 0.84
   2 !   10.4   0.1   0.00027      0.48       2      37 ..      64     100 ..      63     103 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.012
                                       HHHHHHHHSSSSB-HHHHHHHHHHHHHHHHHHTTB--S---SSS-HHHHHH CS
                     Succ_DH_flav_C  4 LgkimqkkvgvfRteegLkealkelkelrerlknvkvtdkskvaNqelvea 54
                                       ++++ +k+v+  +++++Lk  ++ l++  +++ n  ++ +++  N++  + 
  gene3132|gene3132|rna3132|rna3132  4 MNELYEKYVNLLKENNDLKLRIAALEHSLSKIGNTDTAAHEQKENESNAFL 54
                                       778899********************9999999999888888777765554 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00027
                                        HHHHHHHHHHSSSSB-HHHHHHHHHHHHHHHHH.HTT CS
                     Succ_DH_flav_C   2 keLgkimqkkvgvfRteegLkealkelkelrer.lkn 37 
                                        ++L+ + +++++v+R++e+L++  ++ ke+ ++  kn
  gene3132|gene3132|rna3132|rna3132  64 EKLEWCANSNCTVYRHQEELRQLTDHYKEILKDiRKN 100
                                        67888999**********************9994555 PP

>> TT1725  Hypothetical protein TT1725
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.2   2.6e-05     0.046      13     106 ..      47     132 ..      38     136 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.6e-05
                                        --S-HHHHHHHHHHHHTTTEEEEEEEETTEEEES--S------SEEEEEEEE-SSS---HHHHHHHHHHH.HTTSE CS
                             TT1725  13 kekdpeelaekleklaeeelkLkmitnrGvkvyPegleetfctdhwrcRfvakegkkvskeeileLlerlaeagld 88 
                                        ++++   l e+lekl++e  kL+  +n   +vy ++ e   +tdh++   +        +++++ Ll    +   d
  gene3132|gene3132|rna3132|rna3132  47 ENESNAFLVERLEKLEKE--KLEWCANSNCTVYRHQEELRQLTDHYKEILKD------IRKNVTGLLGYKLDVIDD 114
                                        45566779999****999..9999**********************864433......356899999999999999 PP

                                        EEEEEEEEEETTEESB-- CS
                             TT1725  89 viktenLyefdgkrgysl 106
                                         +++++Ly+fd  + ++ 
  gene3132|gene3132|rna3132|rna3132 115 QVHLHSLYSFDRDDVFTF 132
                                        9**********9999975 PP

>> DXP_synthase_N  1-deoxy-D-xylulose-5-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.73   1.3e+03     178     203 ..      24      49 ..       7      75 .. 0.58
   2 ?   13.2   0.1   2.2e-05     0.039      14      73 ..      79     139 ..      72     143 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.73
                     DXP_synthase_N 178 nvGalskylskllsskayeklkkevk 203
                                         + al++ lsk+ ++++ ++ +ke +
  gene3132|gene3132|rna3132|rna3132  24 RIAALEHSLSKIGNTDTAAHEQKENE 49 
                                        46666666666655554443333332 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 2.2e-05
                     DXP_synthase_N  14 skeeleelaeelrefliesvsktggHlasnLgvveLtlalhyvfdtpkDkl.vwDvgHqaY 73 
                                        ++eel++l+++ +e l +  ++ +g l+  L v++ ++ lh +++ ++D +  + v   +Y
  gene3132|gene3132|rna3132|rna3132  79 HQEELRQLTDHYKEILKDIRKNVTGLLGYKLDVIDDQVHLHSLYSFDRDDVfTFNVKEDCY 139
                                        5789**********99999999***********************9988752688888888 PP

>> DUF2312  Uncharacterized protein conserved in bacteria (DUF2312)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.1    0.0028       5.1       8      19 ..      54      65 ..      51      71 .. 0.89
   2 ?    4.5   0.0     0.015        27      12      36 ..      76     100 ..      75     123 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0028
                            DUF2312  8 fieRiErleeEk 19
                                       ++eR+E+le+Ek
  gene3132|gene3132|rna3132|rna3132 54 LVERLEKLEKEK 65
                                       69*********9 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.015
                            DUF2312  12 iErleeEkkaiaedikdvyaeaKse 36 
                                        ++r +eE ++++++ k++ ++++++
  gene3132|gene3132|rna3132|rna3132  76 VYRHQEELRQLTDHYKEILKDIRKN 100
                                        68999*************9998875 PP

>> BB_PF  Beta barrel Pore-forming domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.9   5.6e-05       0.1     165     197 ..      99     145 ..      57     150 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 5.6e-05
                              BB_PF 165 n..............kgnedyffvsvyrddvfvkpyddalyepvten 197
                                        +              ++ +   + s+ rddvf+ ++++++ye+v+ +
  gene3132|gene3132|rna3132|rna3132  99 KnvtgllgykldvidDQVHLHSLYSFDRDDVFTFNVKEDCYEMVNNH 145
                                        055555555555555677788899*******************9875 PP

>> DivIVA  DivIVA protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   3.9   0.00097       1.7      28      61 ..       5      38 ..       3      96 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00097
                                       HHHHHHHHHHHHHHHHHHHHHHCCCCTXXXXXXX CS
                             DivIVA 28 dqvakdyeallkeneelkekvkeleeklkeykel 61
                                       +++ ++y +llken++lk ++++le++l++  + 
  gene3132|gene3132|rna3132|rna3132  5 NELYEKYVNLLKENNDLKLRIAALEHSLSKIGNT 38
                                       67899**********************9987665 PP

>> DUF4600  Domain of unknown function (DUF4600)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   6.3   0.00039      0.71       3      69 ..       5      68 ..       4     104 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00039
                            DUF4600  3 newktrYetqlelNdqLekqiailkeklekirgnpsdrlasirvleklteeelnqllkqLekekksl 69
                                       ne+  +Y  +l+ N+ L+ +ia l+++l+ki   ++d  a  +  e+ +++ l ++l++Lekek + 
  gene3132|gene3132|rna3132|rna3132  5 NELYEKYVNLLKENNDLKLRIAALEHSLSKIG--NTD-TAAHEQKENESNAFLVERLEKLEKEKLEW 68
                                       89999**************************9..334.4556778999***************9764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1391  (0.0775838); expected 358.6 (0.02)
Passed bias filter:                      621  (0.0346366); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.56u 0.32s 00:00:00.88 Elapsed: 00:00:00.49
# Mc/sec: 1116.47
//
Query:       gene3133|gene3133|rna3133|rna3133  [L=167]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       586  (0.0326845); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1155.12
//
Query:       gene3134|gene3134|rna3134|rna3134  [L=238]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
     0.0015   19.2   2.4       0.16   12.7   0.2    2.5  2  Chordopox_G3  Chordopoxvirus G3 protein
  ------ inclusion threshold ------
       0.15   12.7   0.3        0.3   11.7   0.3    1.4  1  OAD_gamma     Oxaloacetate decarboxylase, gamma chain


Domain annotation for each model (and alignments):
>> Chordopox_G3  Chordopoxvirus G3 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.2   1.8e-05      0.16       5      47 ..      16      56 ..      12     105 .. 0.80
   2 !    6.4   0.1    0.0016        14      70     100 ..     171     201 ..     124     206 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.8e-05
                       Chordopox_G3  5 liffilfllvlyfltyyptnklelavkdlesenaiikkrddel 47
                                       +++fil+l+++y +     nk+++ v++  +e a i+++  ++
  gene3134|gene3134|rna3134|rna3134 16 VLLFILLLCMSYSMLQAVDNKYKAMVDKKLKESAKIRNE--FM 56
                                       789***********************9955555555443..44 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0016
                       Chordopox_G3  70 sydadtatvtvavkskkyvfrlddeedvrkL 100
                                          d+++  v+v+++s++ v++l  ++  ++L
  gene3134|gene3134|rna3134|rna3134 171 PKDKRNVFVAVSMDSNRKVYQLHVDDKKKTL 201
                                        4567788899999999999999977766665 PP

>> OAD_gamma  Oxaloacetate decarboxylase, gamma chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.3   3.4e-05       0.3       5      49 ..       8      51 ..       7      69 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.4e-05
                          OAD_gamma  5 lltllGmgvVFvvLilLslvislfskiikkkakkkkkkakaaaaa 49
                                       ++t++G +vV+++++lL++ +s ++++ +k+++  +kk k++a+ 
  gene3134|gene3134|rna3134|rna3134  8 TITIIG-TVVLLFILLLCMSYSMLQAVDNKYKAMVDKKLKESAKI 51
                                       577777.699***********************999999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (238 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1231  (0.0686597); expected 358.6 (0.02)
Passed bias filter:                      725  (0.0404373); expected 358.6 (0.02)
Passed Vit filter:                        78  (0.00435049); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 1768.12
//
Query:       gene3135|gene3135|rna3135|rna3135  [L=318]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.01   14.0   0.1      0.014   13.6   0.1    1.1  1  MSP1b     Major surface protein 1B


Domain annotation for each model (and alignments):
>> MSP1b  Major surface protein 1B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   7.7e-07     0.014     319     414 ..      29     126 ..      15     135 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 7.7e-07
                              MSP1b 319 vsmcvaaytaaivgvaailpat...lllaamdneslaeavvkvaeylhsnveqatkdlmasefammtfggimtcak 391
                                          m ++ y   i+  +++lp +    ++ +++n++   +vvk+  +l s    a k  +asef+m  + g+ t+ +
  gene3135|gene3135|rna3135|rna3135  29 YKMNISIYFYLIAIYSSALPISrlkQPFKMIQNRTFGTTVVKINVHLDSTALVALKIALASEFSM-DLNGMNTVRN 103
                                        55666677666666677777652114678899999****************************96.7899****** PP

                              MSP1b 392 lmkgsfaavnqkfeeinatlare 414
                                        ++ g f  +n+ +++i   +  +
  gene3135|gene3135|rna3135|rna3135 104 FFGGIFDIINEDIQNIGIQIRGD 126
                                        ************99998766555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (318 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       429  (0.0239277); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.37
# Mc/sec: 2575.36
//
Query:       gene3136|gene3136|rna3136|rna3136  [L=188]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.2e-07   29.8   3.1    5.7e-07   29.4   0.5    2.2  2  Sec20     Sec20
  ------ inclusion threshold ------
       0.13   12.1   0.8       0.21   11.4   0.8    1.3  1  LemA      LemA family


Domain annotation for each model (and alignments):
>> Sec20  Sec20
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.2     0.039   3.5e+02       3      32 ..      12      43 ..      10      94 .. 0.54
   2 !   29.4   0.5   6.3e-11   5.7e-07       9      92 .]      87     170 ..      80     170 .. 0.96

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.039
                              Sec20  3 akqiTeslraisqllsqevqq..Seenleeld 32
                                       ++qiT+ l    + + ++v++  S +n  el+
  gene3136|gene3136|rna3136|rna3136 12 EEQITNLLSIQPKEMEAHVHHvhSLINQYELQ 43
                                       56777777777777777776511333333333 PP

  == domain 2  score: 29.4 bits;  conditional E-value: 6.3e-11
                              Sec20   9 slraisqllsqevqqSeenleeldastkslekleeeykqvedvlsrskklvkklerrdktdkllvflalglflacv 84 
                                        +l +   l++++v+  ++n+  l++s+ +l++l  + k +e+ l+++++++     +++++ ++v +++ ++l ++
  gene3136|gene3136|rna3136|rna3136  87 QLFDTLSLMVSQVDTADQNILLLSESSVKLKSLCYNSKALEKELHTARNVIARSRANEMKEIRRVWIGIFIYLGVC 162
                                        67788899******************************************************************** PP

                              Sec20  85 vyvvkkRi 92 
                                        vy++  Ri
  gene3136|gene3136|rna3136|rna3136 163 VYILLGRI 170
                                        ****9997 PP

>> LemA  LemA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.8   2.4e-05      0.21      14     103 ..      53     143 ..      51     151 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 2.4e-05
                               LemA  14 DlipnLvetvkgyakhEketleevteaRakaaeaesveekaeaenqlssalsrllavaEnYPdLkan.enfleLqe 88 
                                        Dli + +++ +      ++  e +++ R +a++++ ++  + + +q+++a +++l+++E+  +Lk+   n ++L +
  gene3136|gene3136|rna3136|rna3136  53 DLIAKWLRMLRESIIASTQKEEPIINRRDDAEDKQLFDTLSLMVSQVDTADQNILLLSESSVKLKSLcYNSKALEK 128
                                        5555555555555555566667899*****************************************637999**** PP

                               LemA  89 elegtEnriavaRrr 103
                                        el++  n ia +R +
  gene3136|gene3136|rna3136|rna3136 129 ELHTARNVIARSRAN 143
                                        ***********9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       982  (0.0547716); expected 358.6 (0.02)
Passed bias filter:                      519  (0.0289475); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.37
# Mc/sec: 1535.91
//
Query:       gene3137|gene3137|rna3137|rna3137  [L=502]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (502 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2746  (0.15316); expected 358.6 (0.02)
Passed bias filter:                      610  (0.0340231); expected 358.6 (0.02)
Passed Vit filter:                       180  (0.0100396); expected 17.9 (0.001)
Passed Fwd filter:                        52  (0.00290033); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 1.31u 0.35s 00:00:01.66 Elapsed: 00:00:00.55
# Mc/sec: 2770.10
//
Query:       gene3138|gene3138|rna3138|rna3138  [L=245]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       945  (0.0527079); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1726.43
//
Query:       gene3139|gene3139|rna3139|rna3139  [L=186]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0044   16.6   0.1     0.0056   16.3   0.1    1.2  1  CD34_antigen    CD34/Podocalyxin family
     0.0098   15.7   0.0      0.018   14.8   0.0    1.4  1  TMIE            TMIE protein
  ------ inclusion threshold ------
      0.011   16.6   0.7       0.64   10.9   0.0    2.3  2  EphA2_TM        Ephrin type-A receptor 2 transmembrane domain
      0.012   14.1   0.2      0.014   13.8   0.2    1.1  1  SID-1_RNA_chan  dsRNA-gated channel SID-1
      0.012   15.6   0.5      0.025   14.6   0.0    1.7  2  LRR19-TM        Leucine-rich repeat family 19 TM domain
      0.015   15.0   0.1      0.015   15.0   0.1    2.0  2  FAM176          FAM176 family
      0.017   15.4   0.0      0.029   14.7   0.0    1.4  1  MLANA           Protein melan-A
      0.018   16.0   0.6       0.19   12.7   0.0    2.2  2  DUF4834         Domain of unknown function (DUF4834)
      0.025   14.7   0.0      0.038   14.1   0.0    1.4  1  SRTM1           Serine-rich and transmembrane domain-containi
      0.029   14.3   0.0      0.049   13.6   0.0    1.3  1  TMEM52          Transmembrane 52
       0.03   13.1   0.0      0.034   12.9   0.0    1.1  1  DUF2207         Predicted membrane protein (DUF2207)
      0.031   12.7   0.0       0.04   12.4   0.0    1.2  1  Rhabdo_glycop   Rhabdovirus spike glycoprotein
      0.038   13.8   0.0      0.038   13.8   0.0    2.1  2  GAPT            GRB2-binding adapter (GAPT)
      0.044   14.1   0.1       0.13   12.7   0.0    1.8  2  Ly49            Ly49-like protein, N-terminal region
      0.051   13.5   1.6      0.051   13.5   1.6    2.1  2  Syndecan        Syndecan domain
      0.084   13.3   0.4      0.084   13.3   0.4    2.4  3  SCIMP           SCIMP protein
      0.089   12.8   0.2       0.37   10.8   0.0    2.0  3  Mucin           Mucin-like glycoprotein
       0.14   11.5   0.0       0.18   11.1   0.0    1.1  1  OST3_OST6       OST3 / OST6 family, transporter family


Domain annotation for each model (and alignments):
>> CD34_antigen  CD34/Podocalyxin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.1   5.7e-06    0.0056      77     165 ..      74     159 ..      45     175 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 5.7e-06
                       CD34_antigen  77 dLeklgIqnltsvkeaqeedirseqdyskkllialvtsglllaiLlvagyYgclhrRlskskagerLgEelqyvEn 152
                                         + + +I+++  ++ a++ + +s  d s  + i+l +  l+l +Ll+  +Y  ++ R+s + + +r +Ee     +
  gene3139|gene3139|rna3139|rna3139  74 YFSNENITDIIVTTTAKQPEDESSVDWSLFISISLAIL-LILLLLLLCCLY-RIKIRRSGKYKVKR-AEEKSASKK 146
                                        57888999987555544444466668888888888884.445556667777.68899999999999.*****9999 PP

                       CD34_antigen 153 gyhdnptlsvaed 165
                                        ++ d++  s  ++
  gene3139|gene3139|rna3139|rna3139 147 KSEDEGSTSPKNE 159
                                        9999995554443 PP

>> TMIE  TMIE protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   1.8e-05     0.018      15      59 ..     104     149 ..      97     169 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.8e-05
                               TMIE  15 iaivllvvla.ivillCCvirfRiPRTkqeIeadyarkklakkfre 59 
                                        i i l+++l+ +++llCC+ r++i R  +    ++  k + kk  e
  gene3139|gene3139|rna3139|rna3139 104 ISISLAILLIlLLLLLCCLYRIKIRRSGKYKVKRAEEKSASKKKSE 149
                                        4455555544145789**********87766666666666665544 PP

>> EphA2_TM  Ephrin type-A receptor 2 transmembrane domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.6      0.12   1.2e+02      42      61 ..      44      71 ..       7      73 .. 0.56
   2 ?   10.9   0.0   0.00064      0.64       5      45 ..     108     148 ..     102     169 .. 0.43

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.12
                           EphA2_TM 42 kkeeensgk......k.glktY.vDPht 61
                                         +een+++      k ++k+Y vDP+t
  gene3139|gene3139|rna3139|rna3139 44 PDHEENNRTdeiinnKeDHKSYeVDPTT 71
                                       222222222233344469********99 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00064
                           EphA2_TM   5 avaglvllvilvilvlvlvrrrsknrkqksdlkskeekkee 45 
                                        +++ l+ll++l+ +   +  rrs + k k+ ++++++kk++
  gene3139|gene3139|rna3139|rna3139 108 LAILLILLLLLLCCLYRIKIRRSGKYKVKRAEEKSASKKKS 148
                                        23333333333333333333444444444433222222222 PP

>> SID-1_RNA_chan  dsRNA-gated channel SID-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.2   1.4e-05     0.014      98     198 ..      76     179 ..      47     185 .. 0.53

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.4e-05
                     SID-1_RNA_chan  98 knsnrtkk.vtvevkklikksvyvvavllvllvllsfllltllvvivekvresse.ekrvkes.sssesasesles 170
                                        +n+n t   vt + k+ +++s + +++++ +++ ++++ll+ll++++++++++ + +++vk++ ++s+s+++s+++
  gene3139|gene3139|rna3139|rna3139  76 SNENITDIiVTTTAKQPEDESSVDWSLFISISLAILLILLLLLLCCLYRIKIRRSgKYKVKRAeEKSASKKKSEDE 151
                                        3333333313444455555666777778888888888888888888887776443033333330333333344444 PP

                     SID-1_RNA_chan 171 vssavrsesessveeesdydtleeiesd 198
                                         s+++++e+  + + + d + ++ + ++
  gene3139|gene3139|rna3139|rna3139 152 GSTSPKNERSLEEDGNADSSPIQRVPKN 179
                                        4444444444444444555555555444 PP

>> LRR19-TM  Leucine-rich repeat family 19 TM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.3       3.9   3.9e+03      54      62 ..      44      52 ..      27      70 .. 0.53
   2 ?   14.6   0.0   2.5e-05     0.025       3      86 ..      88     166 ..      86     179 .. 0.71

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 3.9
                           LRR19-TM 54 eeseaetye 62
                                       +++e +++ 
  gene3139|gene3139|rna3139|rna3139 44 PDHEENNRT 52
                                       222222222 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 2.5e-05
                           LRR19-TM   3 tkaaekeksgksWaylvgvvvlalvtsllillaikckllykfllsYrHrrLeeseaetyeegltenrnslseasdt 78 
                                        t + ++++s+  W +++++ + +l++ ll+ll    ++  +    Y+ +r ee++a +++   +e++ s s+ +++
  gene3139|gene3139|rna3139|rna3139  88 TAKQPEDESSVDWSLFISISLAILLILLLLLLCCLYRIKIRRSGKYKVKRAEEKSASKKK---SEDEGSTSPKNER 160
                                        566777888999******999999999999998888888888889********9955433...2333332333333 PP

                           LRR19-TM  79 nsedddDG 86 
                                        + e  +DG
  gene3139|gene3139|rna3139|rna3139 161 SLE--EDG 166
                                        333..344 PP

>> FAM176  FAM176 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   1.4      0.45   4.5e+02      72      90 ..      44      62 ..       5      93 .. 0.46
   2 ?   15.0   0.1   1.5e-05     0.015      28      97 ..     104     175 ..      85     185 .. 0.57

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.45
                             FAM176 72 edeeeeeeeedsseseaee 90
                                        d ee++ +++  ++++++
  gene3139|gene3139|rna3139|rna3139 44 PDHEENNRTDEIINNKEDH 62
                                       1112122222222222222 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 1.5e-05
                             FAM176  28 lgvcvGLlltLcllviriscrkdlerlkkkkkklkeeseka..sededeeeeeeeedsseseaeeelsefer 97 
                                        +++++ +ll L+ll++   +r +++r+ k k k++ee++ +  +++++  +  ++e s e++ + + s ++r
  gene3139|gene3139|rna3139|rna3139 104 ISISLAILLILLLLLLCCLYRIKIRRSGKYKVKRAEEKSASkkKSEDEGSTSPKNERSLEEDGNADSSPIQR 175
                                        567777777777777777777777755555544444433221122333333344555555555555555544 PP

>> MLANA  Protein melan-A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   2.9e-05     0.029      27      83 ..     105     159 ..      81     179 .. 0.61

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.9e-05
                              MLANA  27 GigllvvvLaillllgCwyyk...rrsGYkslrskslkvstlktlvgegeleelakadsk 83 
                                         i+l ++++ +llll C y +   rrsG  +++  + k  + k++  eg+++     +++
  gene3139|gene3139|rna3139|rna3139 105 SISLAILLILLLLLLCCLY-RikiRRSGKYKVKRAEEKSASKKKSEDEGSTSP----KNE 159
                                        5666666666666677776.334578886556555555555555555544443....333 PP

>> DUF4834  Domain of unknown function (DUF4834)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.4      0.78   7.8e+02      55      77 ..      41      63 ..      11      74 .. 0.69
   2 ?   12.7   0.0   0.00019      0.19       6      64 ..     103     164 ..     101     182 .. 0.35

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.78
                            DUF4834 55 qksqsrsetkeegeiieeersek 77
                                       +++ +++e+++++eii++++++k
  gene3139|gene3139|rna3139|rna3139 41 HSYPDHEENNRTDEIINNKEDHK 63
                                       23335566666667777776666 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00019
                            DUF4834   6 filifiiailviglsilsvilrtvfglgsrkkss....ksaqkqfgnstnsnqqksqsrsetk 64 
                                        fi i + ++l++ l +l  ++r  +  + + k +    ksa+k+ +++ +++++ +++rs ++
  gene3139|gene3139|rna3139|rna3139 103 FISISLAILLILLLLLLCCLYRIKIRRSGKYKVKraeeKSASKK-KSEDEGSTSPKNERSLEE 164
                                        44444444455555555555554433222222220111222222.222222222222222222 PP

>> SRTM1  Serine-rich and transmembrane domain-containing protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   3.8e-05     0.038      33      65 ..      95     127 ..      66     152 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.8e-05
                              SRTM1  33 grlsnvyvyvsiflsllaflllllvialqrlkn 65 
                                            +  +++si l++l +lllll+ +l r+k 
  gene3139|gene3139|rna3139|rna3139  95 ESSVDWSLFISISLAILLILLLLLLCCLYRIKI 127
                                        222334579999******************995 PP

>> TMEM52  Transmembrane 52
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   4.9e-05     0.049      11      60 ..      96     146 ..      88     154 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.9e-05
                             TMEM52  11 aqaewvsLwyvwL.ilvivlllLlCgltasCvrfCclrkqqkaeeesppar 60 
                                        ++ +w+    + L il+i lllLlC l  + +r     k ++aee+s +++
  gene3139|gene3139|rna3139|rna3139  96 SSVDWSLFISISLaILLILLLLLLCCLYRIKIRRSGKYKVKRAEEKSASKK 146
                                        46789999999995677888999*********9888888888888776644 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   3.4e-05     0.034     177     243 ..      43     134 ..       5     149 .. 0.56

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.4e-05
                            DUF2207 177 narktsgnkldeilkeeqk............................ntreraarlslallillilllilllllll 224
                                        ++ ++ +n+ dei++  ++                            +  +++ ++s+ + +++ ++l +ll+lll
  gene3139|gene3139|rna3139|rna3139  43 YPDHEENNRTDEIINNKEDhksyevdpttpnyfsnenitdiivtttaK--QPEDESSVDWSLFISISLAILLILLL 116
                                        556666666677666666666777778888888888888888887432..33333333333333322222222222 PP

                            DUF2207 225 llliklllwkkygrepkvk 243
                                        lll+  l+  k  r  k+k
  gene3139|gene3139|rna3139|rna3139 117 LLLCC-LYRIKIRRSGKYK 134
                                        22222.2233333333333 PP

>> Rhabdo_glycop  Rhabdovirus spike glycoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0     4e-05      0.04     452     495 ..      94     135 ..      62     144 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4e-05
                      Rhabdo_glycop 452 dlglshWsffvlisaligiflvLlvalavCikrvrrseklkvtk 495
                                        d  + +Ws f+ is+ i++ l+Ll  l  C+ r++ ++++k + 
  gene3139|gene3139|rna3139|rna3139  94 DESSVDWSLFISISLAILLILLLL--LLCCLYRIKIRRSGKYKV 135
                                        667889*****9999887665555..556666665555554433 PP

>> GAPT  GRB2-binding adapter (GAPT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   2.5       1.5   1.5e+03     107     151 ..      37      80 ..       5      84 .. 0.81
   2 ?   13.8   0.0   3.8e-05     0.038       6      58 ..      98     150 ..      94     178 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1.5
                               GAPT 107 etdkelYentrqsnleeHiYgnetsseYynfqkpstsevpqdedi 151
                                        +t+ + Y + ++ n  + i  n+++ + y++ +p+t+++ ++e+i
  gene3139|gene3139|rna3139|rna3139  37 DTNEHSYPDHEENNRTDEIINNKEDHKSYEV-DPTTPNYFSNENI 80 
                                        5666778888888888888899988888887.4777777777766 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 3.8e-05
                               GAPT   6 gntsvavaigvsLllllvlcgiGcvwhwkhrestrftLPkflqrrssrkkdvt 58 
                                         + s  ++i +++ll+l+l  + c++  k r s ++ + +  ++  s+kk   
  gene3139|gene3139|rna3139|rna3139  98 VDWSLFISISLAILLILLLLLLCCLYRIKIRRSGKYKVKRAEEKSASKKKSED 150
                                        566888999***************************99999888888887443 PP

>> Ly49  Ly49-like protein, N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.1       3.6   3.5e+03      35      66 ..      48      59 ..      33      78 .. 0.61
   2 ?   12.7   0.0   0.00013      0.13       1      48 [.      97     146 ..      97     165 .. 0.73

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 3.6
                                       XXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                               Ly49 35 ekheleetlnlsqnysimqndinlkeelLrnk 66
                                       e+++                     +e+++nk
  gene3139|gene3139|rna3139|rna3139 48 ENNR--------------------TDEIINNK 59
                                       3333....................33333333 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00013
                                        XXXXXX.XXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXX.XXXXXXXXX CS
                               Ly49   1 svpwkl.ivvalgILclllLvtv.avLvtkifqysqekheleetlnlsqn 48 
                                        sv w l i + l IL +llL+ +  +  +ki +  + k +  e  + s++
  gene3139|gene3139|rna3139|rna3139  97 SVDWSLfISISLAILLILLLLLLcCLYRIKIRRSGKYKVKRAEEKSASKK 146
                                        7999863789****987776665156679999999999888777655544 PP

>> Syndecan  Syndecan domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.1       4.2   4.2e+03      36      47 ..      59      70 ..      57      78 .. 0.73
   2 ?   13.5   1.6   5.1e-05     0.051      16      57 ..     107     147 ..     101     152 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 4.2
                           Syndecan 36 KKDEGSYaLdep 47
                                       K D  SY++d  
  gene3139|gene3139|rna3139|rna3139 59 KEDHKSYEVDPT 70
                                       778889988854 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 5.1e-05
                           Syndecan  16 vvvgllfaillvlflvYRmrKKDEGSYaLdepkksnaaYkka 57 
                                         +++ll++ ll+l ++YR++ +  G Y++   ++++a+  k+
  gene3139|gene3139|rna3139|rna3139 107 SLAILLILLLLLLCCLYRIKIRRSGKYKVKRAEEKSASK-KK 147
                                        56789999999999**************99888766554.44 PP

>> SCIMP  SCIMP protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.96   9.6e+02      91     114 ..       7      30 ..       3      45 .. 0.76
   2 ?   -1.3   0.1       2.7   2.7e+03      54      75 ..      52      73 ..      39     102 .. 0.58
   3 ?   13.3   0.4   8.4e-05     0.084      12      54 ..     104     146 ..      98     162 .. 0.72

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.96
                              SCIMP  91 qppatyslvnkvrnkktvsipsyi 114
                                        q p t+s+ + +r++++ +ipsy 
  gene3139|gene3139|rna3139|rna3139   7 QLPCTHSTKKTIRDNRRGDIPSYD 30 
                                        668899999999999999999983 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2.7
                              SCIMP 54 eekmyenvlnqspvqlPplPPr 75
                                        +++ +n  ++++ ++ p  P 
  gene3139|gene3139|rna3139|rna3139 52 TDEIINNKEDHKSYEVDPTTPN 73
                                       4445555555555555555553 PP

  == domain 3  score: 13.3 bits;  conditional E-value: 8.4e-05
                              SCIMP  12 lavaiivvsvvlglilycvcrrllrqGkkweiakslkqkerde 54 
                                        +++++ ++ + l l+l c++r ++r+  k+++ ++ +++   +
  gene3139|gene3139|rna3139|rna3139 104 ISISLAILLILLLLLLCCLYRIKIRRSGKYKVKRAEEKSASKK 146
                                        34445555567788999***************99876644332 PP

>> Mucin  Mucin-like glycoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.2       1.5   1.5e+03      65      74 ..      81      90 ..      47      99 .. 0.54
   2 ?   -0.5   0.2       1.1   1.1e+03      99     114 ..      81      96 ..      62     112 .. 0.56
   3 ?   10.8   0.0   0.00037      0.37       6      48 ..     110     150 ..     105     185 .. 0.67

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 1.5
                              Mucin 65 sttittkttk 74
                                       +  i t+t+k
  gene3139|gene3139|rna3139|rna3139 81 TDIIVTTTAK 90
                                       2222233333 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.1
                              Mucin  99 aeaPtttttrapsrlr 114
                                        ++   ttt+++p    
  gene3139|gene3139|rna3139|rna3139  81 TDIIVTTTAKQPEDES 96 
                                        3333344444444444 PP

  == domain 3  score: 10.8 bits;  conditional E-value: 0.00037
                              Mucin   6 lLcalLvlaLcCCasvCvtangeGqsdaavveaaegqsklttt 48 
                                        +L  lL+l LcC   + ++ +g  +++ + +e +++++k+   
  gene3139|gene3139|rna3139|rna3139 110 ILLILLLLLLCCLYRIKIRRSG--KYKVKRAEEKSASKKKSED 150
                                        5665999999887777777666..6666666655555443332 PP

>> OST3_OST6  OST3 / OST6 family, transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00018      0.18     112     176 ..      59     127 ..      42     133 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00018
                          OST3_OST6 112 k.kkdtydfsrg..gf.daealakfisertgvkirikrppnyskiiitallvlllvlllklrrklllki 176
                                        k ++++y+++ +  ++ + e++ + i  +t ++ + +  +++s +i++ l++ll++lll l   + +ki
  gene3139|gene3139|rna3139|rna3139  59 KeDHKSYEVDPTtpNYfSNENITDIIVTTTAKQPEDESSVDWSLFISISLAILLILLLLLLCCLYRIKI 127
                                        23566666655543335*************************************999999888777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1487  (0.0829383); expected 358.6 (0.02)
Passed bias filter:                      788  (0.0439511); expected 358.6 (0.02)
Passed Vit filter:                       111  (0.00619109); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.42
# Mc/sec: 1318.00
//
Query:       gene314|gene314|rna314|rna314  [L=415]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.1e-53  181.2  37.2    4.8e-34  118.0  14.1    2.1  2  Sugar_tr  Sugar (and other) transporter
    3.6e-14   52.5  50.4    1.4e-13   50.5  25.0    2.0  2  MFS_1     Major Facilitator Superfamily
  ------ inclusion threshold ------
      0.027   14.4   0.5      0.027   14.4   0.5    4.2  4  PsbI      Photosystem II reaction centre I protein (PSII 4.8 


Domain annotation for each model (and alignments):
>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.3  15.4   4.9e-23   2.9e-19       6     184 ..      38     205 ..      29     213 .. 0.76
   2 !  118.0  14.1     8e-38   4.8e-34     239     444 ..     221     411 ..     206     415 .] 0.91

  Alignments for each domain:
  == domain 1  score: 69.3 bits;  conditional E-value: 4.9e-23
                                    HHHHHHHHHHHHCGGGTHHHHHHHHTSTT--SHHHHHH...HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHH CS
                       Sugar_tr   6 alggllfgYdtgvigafltllkfaknfglsksksskeessvlsglivsiflvGaiiGslfagllgdrfGRkkslliaavl 85 
                                    +l+++ fg++t  +     l +       ++++++ e +++ ++ + s+ ++GaiiG +f+ +l   +  k ++ + +++
  gene314|gene314|rna314|rna314  38 CLSSFFFGFHTTSMEILKPLFS------GETATAPFEMTDKMWSSLSSVIFLGAIIGNIFTVFLN--INLKLCMFVNIFI 109
                                    4444555555544443333333......233333333366799999**************99875..678********** PP

                                    HHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHHHHHHHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTSS CS
                       Sugar_tr  86 fvigavlqaaakgknsvevlivgRvlvGigvGlasvlvPmyisEiApkklRgalvslyqlaitfGilvaaifglglnkts 165
                                    f+ig v  + +    ++++++ gR+++Gi++G+ +++vP y++ +Ap ++Rg+++s +ql+i++G l ++ + +++ +++
  gene314|gene314|rna314|rna314 110 FFIGHVFVMDTS---NYYIMACGRLIIGIACGTSCATVPSYLGYLAPRHMRGTVGSAHQLFIVIGVLTGQLVSYFIRDNQ 186
                                    *****9988777...8************************************************************7777 PP

                                    -.TTHHHHHHHCCHHHHHHH CS
                       Sugar_tr 166 n.adgwrillglqlvpalll 184
                                      +  +r ++ l +++al+l
  gene314|gene314|rna314|rna314 187 IiNIFYRGFIVL-YIIALVL 205
                                    633444444444.4444333 PP

  == domain 2  score: 118.0 bits;  conditional E-value: 8e-38
                                    ...HTTHHHHSH...HHHHHHHHHHHHHHTTHHHHHHHTTTHHHHSS-THHHHHHHHHHHHHHHHHHHHHHHHHHS-SHH CS
                       Sugar_tr 239 kaswkellssktvrqrlligvvlqifqqltGinaimyysptifenlglsksllvtiivgvvnfvatfvaiflvdrfGRRt 318
                                    k  w+ l+ + + r+ l + ++ +i+qq tGinai+ +s +i+++ g++++ l+ti +g+  +v+t+v++ +vd+fGR++
  gene314|gene314|rna314|rna314 221 KSVWDLLKCR-EARKSLKLDMAFHIGQQATGINAILLFSNEILKK-GMKDPQLGTISLGACSIVSTIVSMCIVDKFGRKP 298
                                    3445555555.67999999************************98.788888**************************** PP

                                    HHHHHHHHHHHHHHHHH..HHHHTTSS...CHHHHHHHHHHHHHHHTTTTHHHHHHHHHHSHTTTHHHHHHHHHHHHHHH CS
                       Sugar_tr 319 llllGaagmaicfvilgivalllvakskaasivaivfialfialfalgwgpvpwvlvsElfpqsvRskalaiavavnwla 398
                                    + l++++  +i++++l+        +    + ++++ +++ i+ +a+g+gp+ w+++ E+f  + +++a+a++++vnw++
  gene314|gene314|rna314|rna314 299 MILISTFLILIALLMLT--------T----GRLVLTSLYIHIIGYAIGIGPITWFIINEIFRDEYKKAASALSMTVNWIS 366
                                    *******9999999997........4....789999******************************************** PP

                                    HHHHHHHHHHHHCHHHT-HHHHHHHHHHHHHHHHHHHHS--STT-- CS
                       Sugar_tr 399 nflisllfpiiteaigggyvflvfaglavlfiifvfffvpetkgrt 444
                                     f  ++ f ++   +g   +flv+ +l+++f+++v++ + etkgr 
  gene314|gene314|rna314|rna314 367 AFTATFSFSFMIIYMG-NLCFLVYFVLMIVFLFIVLLSFAETKGRR 411
                                    ****************.9**************************96 PP

>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.5  25.0   2.4e-17   1.4e-13       7     352 ..      46     370 ..      33     371 .. 0.79
   2 !   15.8  17.5   8.5e-07    0.0051      42     176 ..     277     408 ..     247     414 .. 0.72

  Alignments for each domain:
  == domain 1  score: 50.5 bits;  conditional E-value: 2.4e-17
                          MFS_1   7 lsalarsilgpalpl.alaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfa.ss 84 
                                    ++++++ il p+++  + +  + ++    + l ++ +lga+++++++ +l   +  + ++++ +++f++g  ++++  s+
  gene314|gene314|rna314|rna314  46 FHTTSMEILKPLFSGeTATAPFEMTDKMWSSLSSVIFLGAIIGNIFTVFLN--INLKLCMFVNIFIFFIG-HVFVMDtSN 122
                                    4455555566666655666667788888888*******************5..55599************.555543388 PP

                          MFS_1  85 lwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivslla 164
                                    +++++ +r++ G+++g++ +++ +++  ++p+  rg + +  ++++ +G++ g l++ ++ ++      +  + +++++a
  gene314|gene314|rna314|rna314 123 YYIMACGRLIIGIACGTSCATVPSYLGYLAPRHMRGTVGSAHQLFIVIGVLTGQLVSYFIRDNQIINIFYRGFIVLYIIA 202
                                    88***********************************************************9988999999999999999 PP

                          MFS_1 165 fvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsglltllplylqevlglsgll 244
                                    +vl  +   +++++ +r++++ +       +++    + +k+  l  + +++   ++g++++l ++  +l++ ++ +   
  gene314|gene314|rna314|rna314 203 LVLLTAIKNVRRVTTGRSKSVWD-----LLKCR----EARKSLKL-DMAFHIGQQATGINAILLFSNEILKKGMKDP--Q 270
                                    88766666666666666666666.....33333....33333333.367777777789999*******999999999..7 PP

                          MFS_1 245 laglllallalvgailallagrlsdrlgrrrrlllallllllaalglallavtssavllllvlvliGfglgfvfpsllal 324
                                    l+++ l+++++v+    +++  ++d++gr++++l++ +l+l+a+l+l    +     l+ l + +iG + g+  p+ + +
  gene314|gene314|rna314|rna314 271 LGTISLGACSIVS---TIVSMCIVDKFGRKPMILISTFLILIALLMLTTGRLV----LTSLYIHIIGYAIGI-GPITWFI 342
                                    7787799999999...9999999*****9888888887777777777777777....222233335666664.7888899 PP

                          MFS_1 325 asdlappeeagtasglfntagslggalg 352
                                    +++ +  e+  +as+l +t++ ++++ +
  gene314|gene314|rna314|rna314 343 INEIFRDEYKKAASALSMTVNWISAFTA 370
                                    9999998889999999999999998865 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 8.5e-07
                          MFS_1  42 algaavaslplGrlsdrfGrrrvlllglllfalglllllfasslwlllvlrvlqGlga.galfpagaaliadwfpkeerg 120
                                    ++ ++v++++ + ++d+fGr++++l++ +l +++ll+l+  ++  l+l +  +  +g+  ++ p+   +i ++f + e  
  gene314|gene314|rna314|rna314 277 GACSIVSTIVSMCIVDKFGRKPMILISTFLILIALLMLT--TGR-LVLTSLYIHIIGYaIGIGPITWFIINEIFRD-EYK 352
                                    34569999999***********************55555..332.3333333333333123458888999999999.888 PP

                          MFS_1 121 raigllsagfslGailgpllggllasslgWravfyilaivsllafvlfllllpeep 176
                                    +a + ls++++  +++++ ++  ++  +   ++f++  +++++++ ++ll + e++
  gene314|gene314|rna314|rna314 353 KAASALSMTVNWISAFTATFSFSFMIIYMGNLCFLVYFVLMIVFLFIVLLSFAETK 408
                                    88888888888888888888887776777889999999999998555555555444 PP

>> PsbI  Photosystem II reaction centre I protein (PSII 4.8 kDa protein)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.5   4.6e-06     0.027       2      23 ..      25      46 ..      25      48 .. 0.94
   2 ?   -0.0   1.9      0.15   8.7e+02      14      21 ..     103     110 ..      96     117 .. 0.64
   3 ?   -1.1   0.2      0.32   1.9e+03      10      23 ..     363     376 ..     358     377 .. 0.83
   4 ?   -3.1   3.9       1.3   7.9e+03       7      16 ..     390     399 ..     381     404 .. 0.53

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4.6e-06
                           PsbI  2 ltLKivVyivViffvslFvFGf 23
                                   lt K++Vy +V++  s F+FGf
  gene314|gene314|rna314|rna314 25 LTTKMLVYSTVMSCLSSFFFGF 46
                                   577******************9 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.15
                           PsbI  14 ffvslFvF 21 
                                    +fv +F+F
  gene314|gene314|rna314|rna314 103 MFVNIFIF 110
                                    56666666 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 0.32
                           PsbI  10 ivViffvslFvFGf 23 
                                     ++ +f + F F f
  gene314|gene314|rna314|rna314 363 NWISAFTATFSFSF 376
                                    48999*****9987 PP

  == domain 4  score: -3.1 bits;  conditional E-value: 1.3
                           PsbI   7 vVyivViffv 16 
                                    +V ++V++f+
  gene314|gene314|rna314|rna314 390 FVLMIVFLFI 399
                                    3344455555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (415 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1280  (0.0713927); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.73u 0.30s 00:00:01.03 Elapsed: 00:00:00.51
# Mc/sec: 2461.59
//
Query:       gene3140|gene3140|rna3140|rna3140  [L=769]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.025   14.3   0.0      0.062   13.0   0.0    1.6  1  FGGY_C           FGGY family of carbohydrate kinases, C-termi


Domain annotation for each model (and alignments):
>> FGGY_C  FGGY family of carbohydrate kinases, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   3.5e-06     0.062     153     196 ..     343     386 ..     317     387 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.5e-06
                             FGGY_C 153 lavdGGgskndllmqllAdilgvpVerpkt.aeatalGaAilAav 196
                                        + v+GG s+n +++++l + l v+V+r  + +e++ +GaAi++a+
  gene3140|gene3140|rna3140|rna3140 343 VEVVGGNSNNSFVREML-EQLRVKVRRSSDsHESVGFGAAIAGAL 386
                                        669************99.7799********************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (769 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1837  (0.10246); expected 358.6 (0.02)
Passed bias filter:                      631  (0.0351944); expected 358.6 (0.02)
Passed Vit filter:                        84  (0.00468515); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.79u 0.30s 00:00:01.09 Elapsed: 00:00:00.46
# Mc/sec: 4971.21
//
Query:       gene3141|gene3141|rna3141|rna3141  [L=239]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        0.2   11.6   1.2        0.4   10.7   1.2    1.4  1  FixQ      Cbb3-type cytochrome oxidase component FixQ


Domain annotation for each model (and alignments):
>> FixQ  Cbb3-type cytochrome oxidase component FixQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   1.2   2.2e-05       0.4      11      38 ..      10      37 ..       8      45 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 2.2e-05
                               FixQ 11 dswgllflvllfygvviyafrpgnrkdf 38
                                       ++++l +++++ ++v++y+f  + +k+f
  gene3141|gene3141|rna3141|rna3141 10 YFLFLALFLVICAIVILYTFLNQENKKF 37
                                       899******************9998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (239 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1284  (0.0716158); expected 358.6 (0.02)
Passed bias filter:                      604  (0.0336884); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.65u 0.37s 00:00:01.02 Elapsed: 00:00:00.58
# Mc/sec: 1239.89
//
Query:       gene3142|gene3142|rna3142|rna3142  [L=115]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1625  (0.0906353); expected 358.6 (0.02)
Passed bias filter:                      625  (0.0348597); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.57u 0.35s 00:00:00.92 Elapsed: 00:00:00.54
# Mc/sec: 645.30
//
Query:       gene3143|gene3143|rna3143|rna3143  [L=333]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    9.8e-25   88.3   0.5    1.4e-24   87.7   0.5    1.3  1  Metallophos  Calcineurin-like phosphoesterase


Domain annotation for each model (and alignments):
>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.7   0.5     8e-29   1.4e-24       4     201 ..      93     271 ..      90     274 .. 0.85

  Alignments for each domain:
  == domain 1  score: 87.7 bits;  conditional E-value: 8e-29
                                        EEEESBTBTTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSSHHHHHHHHHHHHHHHHTSEEEEEC-TTS.... CS
                        Metallophos   4 lvigDlHlalgggqlddllkllddllreekpdlvllaGDlvdrgdlekellellaalvkypipvylllGNHe.... 75 
                                        +v+gD+H     gq+ dll +  d   + k  ++l  GD+vdrg  + e++ +l+ +  ++ +vyll+GNHe    
  gene3143|gene3143|rna3143|rna3143  93 TVVGDIH-----GQFVDLLLFATD---D-KKFVFL--GDYVDRGTSSVEVILFLCLKKILHGNVYLLKGNHEmanq 157
                                        69*****.....********9933...2.555555..****************99999999*************** PP

                                        ....CHHHHHHHHHHHHHHHHHHHEHHHCEEETSEEEEEETTEEEEEEEESE.CEEE..THHHHHHHHHHHSCHHH CS
                        Metallophos  76 ....gfeeellnkygylgifsepwrsdaevfnnlplaslgsgslkvlllhGg.spel..lvsldklgslnleleap 144
                                            gf+ e+l ky+        +r+ +evf+ + +a+ ++   +++l+hGg sp++  +  ++ l++ ++     
  gene3143|gene3143|rna3143|rna3143 158 netyGFKSECLLKYD-----ISFYRKVNEVFEVMSIAAVVDR--TYFLVHGGiSPHIgnIADIMYLDRTDFGSFL- 225
                                        999999999999999.....7779999***************..********99999553333333333333333. PP

                                        HCCHHHHHHHHHHTTCSEEEEEESSESSCSSSCSCCHHHHHHHHHHTTESEEEEESS CS
                        Metallophos 145 epgdewlkdlekrekadwvivlgHsplyrgsgylfgdealedllkkygvdlvisGHt 201
                                            ++++d        +    g++  +rg+gylfg+++l ++l+++++ +v+++H+
  gene3143|gene3143|rna3143|rna3143 226 ---PLLWSD--------PQEENGYKTSPRGAGYLFGPDVLNKFLDDNQLSYVVRSHQ 271
                                        ...89****........77777777777****************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (333 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       451  (0.0251548); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 2166.56
//
Query:       gene3144|gene3144|rna3144|rna3144  [L=68]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.017   14.7   0.5      0.021   14.4   0.5    1.2  1  Apo-CIII  Apolipoprotein CIII (Apo-CIII)


Domain annotation for each model (and alignments):
>> Apo-CIII  Apolipoprotein CIII (Apo-CIII)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.5   1.2e-06     0.021      40      59 ..      48      67 ..      39      68 .] 0.89

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.2e-06
                           Apo-CIII 40 gWvtdslssLkdYwstfkgk 59
                                        W t ++s LkdYw  ++++
  gene3144|gene3144|rna3144|rna3144 48 SWATTEMSQLKDYWKVWTQR 67
                                       6**************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (68 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       285  (0.015896); expected 358.6 (0.02)
Passed bias filter:                      202  (0.0112667); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.25s 00:00:00.60 Elapsed: 00:00:00.41
# Mc/sec: 501.30
//
Query:       gene3145|gene3145|rna3145|rna3145  [L=89]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       184  (0.0102627); expected 358.6 (0.02)
Passed bias filter:                      146  (0.00814323); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.42
# Mc/sec: 637.68
//
Query:       gene3146|gene3146|rna3146|rna3146  [L=71]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (71 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       294  (0.016398); expected 358.6 (0.02)
Passed bias filter:                      188  (0.0104858); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.28s 00:00:00.67 Elapsed: 00:00:00.45
# Mc/sec: 477.93
//
Query:       gene3147|gene3147|rna3147|rna3147  [L=390]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
     0.0081   16.0   0.1      0.015   15.1   0.1    1.4  1  OAM_alpha  D-ornithine 4,5-aminomutase alpha-subunit


Domain annotation for each model (and alignments):
>> OAM_alpha  D-ornithine 4,5-aminomutase alpha-subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.1   8.5e-07     0.015      14      63 ..      44      94 ..      36     106 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 8.5e-07
                                       TTS-HHHHHHHHHHHHHHHHHHHHHHHHHEE-HHHHHHHH.HHTT--HHHH CS
                          OAM_alpha 14 aelsdeeleerfWelaekivdPlielarkhtspsiersvL.LrmGlsslea 63
                                        +l+ eel++   ++ +  v P+++ a k+t++ +++sv+ L   +ssl +
  gene3147|gene3147|rna3147|rna3147 44 STLTKEELNNTLINFFNTSVSPIVDKAVKQTTENVDKSVIqLCNHISSLYT 94
                                       4699**********************************9745566666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (390 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       960  (0.0535445); expected 358.6 (0.02)
Passed bias filter:                      554  (0.0308997); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.45
# Mc/sec: 2628.04
//
Query:       gene3148|gene3148|rna3148|rna3148  [L=544]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00048   19.9   6.4    0.00074   19.3   5.5    1.7  2  Nsp1_C          Nsp1-like C-terminal region
  ------ inclusion threshold ------
      0.019   14.9   0.9       0.03   14.2   0.9    1.2  1  HEPN-like_int   HEPN-like integron domain
       0.02   15.3   2.8       0.02   15.3   2.8    1.6  2  TSNAXIP1_N      Translin-associated factor X-interacting N-te
       0.23   11.5   0.1       0.35   10.8   0.1    1.2  1  DUF489          Protein of unknown function (DUF489)
        0.7   10.4   4.3       0.95   10.0   3.6    1.6  1  DUF16           Protein of unknown function DUF16
        2.6    7.5   4.9        3.8    6.9   4.9    1.2  1  Nop             snoRNA binding domain, fibrillarin
        4.3    8.3 136.3      0.044   14.6  53.7    5.8  6  Nucleoporin_FG  Nucleoporin FG repeat region


Domain annotation for each model (and alignments):
>> Nsp1_C  Nsp1-like C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   5.5   2.9e-07   0.00074      13     111 ..     409     512 ..     399     518 .. 0.80
   2 ?   -0.1   0.1      0.29   7.5e+02      58      95 ..     497     534 ..     492     542 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 2.9e-07
                             Nsp1_C  13 aslknktldelinkWtteLeeqekeFeeqakkvneWDrvLvengekIskLysevleaeqeqnkidqeLeyi....e 84 
                                         + ++k+ +e++++ + eLe+  k F+++a++v + D+ +++  +   kL + + + e + n+++++ e++    e
  gene3148|gene3148|rna3148|rna3148 409 LNFRQKSFNEILTEISAELEKDVKFFKKKAEEVFAQDEKIIRARNTYVKLLDRLKAEEDKINELEENVEFLfkwlE 484
                                        33899************************************************99999999*****9999722222 PP

                             Nsp1_C  85 s.qqdeLeslLdnyEkeleellsklesq 111
                                        s + d+  ++L+++E+  +e++  + +q
  gene3148|gene3148|rna3148|rna3148 485 SmKIDDSVKYLNELEQCYDEFMDGVMQQ 512
                                        2134566678888888888887555444 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.29
                             Nsp1_C  58 kIskLysevleaeqeqnkidqeLeyiesqqdeLeslLd 95 
                                        ++++ y+e ++   +q++i++e+  i ++   L s++d
  gene3148|gene3148|rna3148|rna3148 497 ELEQCYDEFMDGVMQQKNIEDEIAGIINENMKLISIID 534
                                        55667778888888889999998888888888877776 PP

>> HEPN-like_int  HEPN-like integron domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.9   1.2e-05      0.03      75     128 ..     415     472 ..     400     486 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.2e-05
                      HEPN-like_int  75 kkdrlltslpiElakelkelkkk...ffled..ikeyRntyvaHvldkdkekflsqeEl 128
                                         ++ +lt++++El+k++k +kkk    f +d  i   Rntyv   ld+ k    + +El
  gene3148|gene3148|rna3148|rna3148 415 SFNEILTEISAELEKDVKFFKKKaeeVFAQDekIIRARNTYVK-LLDRLKAEEDKINEL 472
                                        4679*****************96444677772255678***85.566655543333333 PP

>> TSNAXIP1_N  Translin-associated factor X-interacting N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   2.8   7.7e-06      0.02      38     108 ..     414     484 ..     411     487 .. 0.92
   2 ?   -2.8   0.1       3.2   8.3e+03      44      62 ..     495     513 ..     492     533 .. 0.65

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 7.7e-06
                         TSNAXIP1_N  38 kaYkdlLseIKkEYelyiahllesqreaqylkaklktlsessdkraleleekreelralekeskalleeid 108
                                        k++ ++L+eI +E e+ ++ ++++ +e +++ +k+  + ++ +k  + l+ +++++++le++++ l + ++
  gene3148|gene3148|rna3148|rna3148 414 KSFNEILTEISAELEKDVKFFKKKAEEVFAQDEKIIRARNTYVKLLDRLKAEEDKINELEENVEFLFKWLE 484
                                        689**********************************************************9987666555 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 3.2
                         TSNAXIP1_N  44 LseIKkEYelyiahllesq 62 
                                        L+e  + Y+++++   +++
  gene3148|gene3148|rna3148|rna3148 495 LNELEQCYDEFMDGVMQQK 513
                                        5566666777766555443 PP

>> DUF489  Protein of unknown function (DUF489)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   0.00014      0.35      18     134 ..     389     506 ..     377     519 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00014
                                        HHHHHS---HHHHHHHHHHHH--S-SSHHHHTTS.GGGGHHHHHHHHHHHHT--SCHHHHHHHHHHHHHHHHHHHH CS
                             DUF489  18 qlArtGqadeealetllkslletdpestedvygg.lanlklGletlleqlekekkkkdaeltryalsllalerkLs 92 
                                           ++  +d +++  + +  l+++++s++++  + +a+l++ ++ +++  e+    +d +++r   + ++l  +L+
  gene3148|gene3148|rna3148|rna3148 389 ASTTSEAVDGNSYVDITSVPLNFRQKSFNEILTEiSAELEKDVKFFKKKAEEVFA-QDEKIIRARNTYVKLLDRLK 463
                                        545555556666665556669999**********999***********9999998.89****************** PP

                                        HSTTHHHHHHHHHHTTHHHHTTS-TTSH.HHHHHHHHHHHHHT CS
                             DUF489  93 knkealaklgerieqierqlehfdllhe.nvlanlasiYsdti 134
                                         +++ +++l+e++e + + le +++ ++ + l++l + Y + +
  gene3148|gene3148|rna3148|rna3148 464 AEEDKINELEENVEFLFKWLESMKIDDSvKYLNELEQCYDEFM 506
                                        ******************9999877654378889999998865 PP

>> DUF16  Protein of unknown function DUF16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   3.6   0.00037      0.95      30      96 ..     414     487 ..     399     500 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00037
                                        ..BHHHHHHHHHHHH...HHHHHHHHHHHHHHHHH.......HHHHHHHHHHHH.......HHHHHHHHHHHHH CS
                              DUF16  30 dsnkqrLkkieakvdklgeqinkleqkvekqgeki.......kelkveqkaqgeelnkvdetleliletLqkin 96 
                                        +s ++ L++i a+++k  + ++k +++v +q+eki        +l  + ka ++++n+++e +e++ + L++++
  gene3148|gene3148|rna3148|rna3148 414 KSFNEILTEISAELEKDVKFFKKKAEEVFAQDEKIirarntyVKLLDRLKAEEDKINELEENVEFLFKWLESMK 487
                                        445666788888888666666666677776666662222211367778999999999***********999985 PP

>> Nop  snoRNA binding domain, fibrillarin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   4.9    0.0015       3.8       2     116 ..     420     530 ..     419     531 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0015
                                        HHHHHHHHHHHHHHHHHHHTTTSTCHHHHS-SHHHHHHHHHHCCCCHCCT.HHTT.HHHHHHHHHHHHCHHHH-SS CS
                                Nop   2 ldeidkeintlhkrvrewYswhFpELeslvkdnleYakvvkligneredlekkeedeelakevimaakvtastsmg 77 
                                        l+ei  e+++ +k+ ++  ++ F   e++++   +Y+k+  +++ e++++++ ee+ e   + ++ +k       +
  gene3148|gene3148|rna3148|rna3148 420 LTEISAELEKDVKFFKKKAEEVFAQDEKIIRARNTYVKLLDRLKAEEDKINELEENVEFLFKWLESMK----IDDS 491
                                        67899999999999999999************************998888555433323333333333....3667 PP

                                        S-S-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                                Nop  78 aelseedlknikelcdrvleleelrkelleYlesrmsai 116
                                        ++  +e  +   e++d v++ ++  +e++  ++++m+ i
  gene3148|gene3148|rna3148|rna3148 492 VKYLNELEQCYDEFMDGVMQQKNIEDEIAGIINENMKLI 530
                                        777777777888899999999999999999999999876 PP

>> Nucleoporin_FG  Nucleoporin FG repeat region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?  -10.8  35.8         7   1.8e+04      13      90 ..      17      96 ..       2     104 .. 0.48
   2 ?    1.5  50.9      0.21   5.4e+02       2      91 .]      66     160 ..      44     160 .. 0.75
   3 ?   14.6  53.7   1.7e-05     0.044       1      90 [.     110     214 ..     110     232 .. 0.89
   4 ?   13.6  23.1   3.5e-05      0.09      13      91 .]     196     267 ..     194     279 .. 0.75
   5 ?    5.6  25.1     0.011        28      10      83 ..     222     290 ..     213     320 .. 0.44
   6 ?   -1.6  26.4       2.1   5.3e+03      11      83 ..     249     328 ..     248     395 .. 0.79

  Alignments for each domain:
  == domain 1  score: -10.8 bits;  conditional E-value: 7
                     Nucleoporin_FG 13 glFGststtatstgglFG..asstatatasggglfgatsqtaasgglFGstnattqttatgglFGstaataqq...tt 85
                                       +lF +++++  ++    G  +++++t   +++g+fg+ +q  +sgglFG+ +   ++t+tg  F +++    +    +
  gene3148|gene3148|rna3148|rna3148 17 NLFPNNQQQ--NQRFSLGtgNKDNNTGLFTNTGSFGG-AQGGTSGGLFGTGPGFGSQTNTGTGFMNNQGPMPStnvGQ 91
                                       445444444..33333332122222222222235555.6666666666666665555554444444433333335566 PP

                     Nucleoporin_FG 86 sgglF 90
                                       +gglF
  gene3148|gene3148|rna3148|rna3148 92 TGGLF 96
                                       66666 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.21
                     Nucleoporin_FG   2 lFGaaatstsgglFGststt....atstgglFGasstatatasgg.glfgatsqtaasgglFGstnattqttatgg 72 
                                        +FG ++t+t++g   ++         +tgglF a +t ++   gg g+fg ++++++sg+lFG+t + + +t tgg
  gene3148|gene3148|rna3148|rna3148  66 GFG-SQTNTGTGFMNNQGPMpstnVGQTGGLFTAPATGSSGI-GGpGSFGLSNAANTSGSLFGNTGTGAGQT-TGG 138
                                        366.55555555444443336667778999999444444444.445899999**************998776.*** PP

                     Nucleoporin_FG  73 lFGstaataqq...ttsgglFG 91 
                                        lFG++aa++ +   +t+gglFG
  gene3148|gene3148|rna3148|rna3148 139 LFGTQAANTGTgtgQTTGGLFG 160
                                        ***88888877999*******9 PP

  == domain 3  score: 14.6 bits;  conditional E-value: 1.7e-05
                     Nucleoporin_FG   1 glFG.aaatstsgglFGststt.atstgglFG...asstatatasggglfgat......sqtaasgglFGstnatt 65 
                                        g FG ++a++tsg+lFG+t t   ++tgglFG   a++ + + +++gglfg++       + +++gglFG+++a++
  gene3148|gene3148|rna3148|rna3148 110 GSFGlSNAANTSGSLFGNTGTGaGQTTGGLFGtqaANTGTGTGQTTGGLFGTQaanagtGTGQTTGGLFGTQTANQ 185
                                        579*999***************999*******8863333344444446****9999999999999*********** PP

                     Nucleoporin_FG  66 qtta....tgglFGstaataqqttsgglF 90 
                                        ++ +    ++g F  +++++qq+++ glF
  gene3148|gene3148|rna3148|rna3148 186 SAGTssglNTGPFSMPQTNTQQQSTAGLF 214
                                        999989999999********99******9 PP

  == domain 4  score: 13.6 bits;  conditional E-value: 3.5e-05
                     Nucleoporin_FG  13 glFGststt..atstgglFGasstatatasggglfgatsqtaasgglFGstnattqttatgglFGstaataqqtts 86 
                                        g+F  ++t+  ++st+glF    t++++ +g++lf + + +  +++lF +++++t +  +g+lFGst +++   ++
  gene3148|gene3148|rna3148|rna3148 196 GPFSMPQTNtqQQSTAGLFS---TPNQNDAGTTLFKT-QPSVGTTNLFSAQPQATVP--GGSLFGSTPQNT---AG 262
                                        56655555555999999999...55555555569998.8999999999999999988..899999888877...34 PP

                     Nucleoporin_FG  87 gglFG 91 
                                           FG
  gene3148|gene3148|rna3148|rna3148 263 AASFG 267
                                        44444 PP

  == domain 5  score: 5.6 bits;  conditional E-value: 0.011
                     Nucleoporin_FG  10 tsgglFGststtatstgglFGasstatatasggglfgatsqtaasgglFGstnattqttatgglFGstaataqq 83 
                                        +++ lF ++++    t++lF   ++++at  gg+lfg+t q++a+   FG+++  ++ + t+g+ G+t +  +q
  gene3148|gene3148|rna3148|rna3148 222 AGTTLFKTQPSV--GTTNLFS--AQPQATVPGGSLFGSTPQNTAGAASFGAQQGVAPYN-TQGIAGTTISGPAQ 290
                                        555555555555..5555555..333344444445555555555555555555555444.33333322222222 PP

  == domain 6  score: -1.6 bits;  conditional E-value: 2.1
                     Nucleoporin_FG  11 sgglFGststtatstgglFGasstatatasggglfgat.......sqtaasgglFGstnattqtta..tgglFGst 77 
                                        +g+lFGst+++ t+++  FGa++  +  +++g + g+t       +++++ +g  G+++  + +++  t+g FG +
  gene3148|gene3148|rna3148|rna3148 249 GGSLFGSTPQN-TAGAASFGAQQGVAPYNTQG-IAGTTisgpaqpATASSITGTMGGQTIGNVAQQpaTSGPFGVA 322
                                        6899*****99.999999**666666666666.8999898886553333335555555555555556799999988 PP

                     Nucleoporin_FG  78 aataqq 83 
                                        a++  +
  gene3148|gene3148|rna3148|rna3148 323 APQPIS 328
                                        777644 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (544 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       988  (0.0551063); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.62u 0.27s 00:00:00.89 Elapsed: 00:00:00.44
# Mc/sec: 3724.41
//
Query:       gene3149|gene3149|rna3149|rna3149  [L=513]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00083   19.5   0.6      0.058   13.6   0.0    3.1  3  Myb_DNA-binding  Myb-like DNA-binding domain
  ------ inclusion threshold ------
      0.037   14.3   1.4        0.4   11.0   0.1    3.2  3  Myb_DNA-bind_6   Myb-like DNA-binding domain
       0.07   13.7   0.5       0.36   11.4   0.1    2.4  3  PSD4             Protein of unknown function (DUF1592)


Domain annotation for each model (and alignments):
>> Myb_DNA-binding  Myb-like DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.2       1.9   1.1e+04      17      25 ..       3      11 ..       3      11 .. 0.82
   2 ?    2.6   0.0     0.027   1.6e+02       2      19 ..     158     175 ..     158     180 .. 0.90
   3 !   13.6   0.0   9.7e-06     0.058       3      33 ..     233     264 ..     231     268 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 1.9
                                       HHHTTCHHH CS
                    Myb_DNA-binding 17 kkhGnrWkk 25
                                       k++G +Wk+
  gene3149|gene3149|rna3149|rna3149  3 KEMGRKWKR 11
                                       68999**95 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.027
                                        SSSBHHHHHHHHHHHHHH CS
                    Myb_DNA-binding   2 gkWteeEdelLleavkkh 19 
                                        g++ +eE+++L   v+++
  gene3149|gene3149|rna3149|rna3149 158 GPFNAEEQKILKHKVNEY 175
                                        6899***********997 PP

  == domain 3  score: 13.6 bits;  conditional E-value: 9.7e-06
                                        SSBHHHHHHHHHHHHHHTTCHHHHHHHHT.SS CS
                    Myb_DNA-binding   3 kWteeEdelLleavkkhGnrWkkIaerlg.gR 33 
                                         +t ++d+ L ++ k  G  W+kI++++  +R
  gene3149|gene3149|rna3149|rna3149 233 VFTLQDDLELMQLYKIIGPHWEKISKEMLsTR 264
                                        69**********************98663355 PP

>> Myb_DNA-bind_6  Myb-like DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.25   1.5e+03       1      16 [.     160     175 ..     160     183 .. 0.79
   2 ?   11.0   0.1   6.7e-05       0.4       1      40 [.     234     272 ..     234     293 .. 0.84
   3 ?   -1.1   0.1      0.41   2.4e+03      16      35 ..     445     466 ..     441     468 .. 0.73

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.25
                     Myb_DNA-bind_6   1 WteeEdeiLlklveky 16 
                                        + +eE++iL   v +y
  gene3149|gene3149|rna3149|rna3149 160 FNAEEQKILKHKVNEY 175
                                        5789999998888887 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 6.7e-05
                     Myb_DNA-bind_6   1 WteeEdeiLlklvekygndWknIaeal.nrRtpkqcfdrwk 40 
                                        +t ++d +L +l++  g  W++I++++ +  t  ++ ++++
  gene3149|gene3149|rna3149|rna3149 234 FTLQDDLELMQLYKIIGPHWEKISKEMlS--TRFRVHRKFL 272
                                        68899*********************945..6666666665 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 0.41
                     Myb_DNA-bind_6  16 ygnd..WknIaealnrRtpkqc 35 
                                        ++nd  W ++ +++n ++++++
  gene3149|gene3149|rna3149|rna3149 445 HENDifWLSVRDEFNDKHSENI 466
                                        6675668888888888888776 PP

>> PSD4  Protein of unknown function (DUF1592)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       2.6   1.5e+04      94     113 ..      54      73 ..      32      83 .. 0.71
   2 ?   -2.4   0.0       1.1   6.5e+03     123     126 ..     117     120 ..      91     155 .. 0.61
   3 ?   11.4   0.1   6.1e-05      0.36      25      96 ..     254     322 ..     253     339 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 2.6
                               PSD4  94 elfveevleedksvkellta 113
                                        + + +++ ++d+++k+ll+ 
  gene3149|gene3149|rna3149|rna3149  54 NDTSTDITKDDEDIKDLLSR 73 
                                        44555577777777777765 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.1
                               PSD4 123 aahY 126
                                         a+Y
  gene3149|gene3149|rna3149|rna3149 117 KAYY 120
                                        3333 PP

  == domain 3  score: 11.4 bits;  conditional E-value: 6.1e-05
                               PSD4  25 aaAeegeLrtpeeleaqvermladpraralveeFarqwlelerletvekdkelfpefdealreamreetelf 96 
                                        +++ ++ L+t+  + ++   m + +r +++  +F +++l+++++e+v+k    +++    +r++++ee+ ++
  gene3149|gene3149|rna3149|rna3149 254 EKISKEMLSTRFRVHRKFLAMQNLKRLKSCEGDFYNEYLKTRNIEKVAKM---YNTKYGYVRKKITEEIARV 322
                                        56788999**********************************99888754...4433344777777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (513 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1485  (0.0828267); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.62u 0.31s 00:00:00.93 Elapsed: 00:00:00.49
# Mc/sec: 3127.74
//
Query:       gene315|gene315|rna315|rna315  [L=975]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (975 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       695  (0.038764); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.71u 0.29s 00:00:01.00 Elapsed: 00:00:00.48
# Mc/sec: 6153.44
//
Query:       gene3150|gene3150|rna3150|rna3150  [L=33]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (33 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       249  (0.0138881); expected 358.6 (0.02)
Passed bias filter:                      170  (0.00948185); expected 358.6 (0.02)
Passed Vit filter:                         3  (0.000167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.31u 0.26s 00:00:00.57 Elapsed: 00:00:00.41
# Mc/sec: 243.31
//
Query:       gene3151|gene3151|rna3151|rna3151  [L=82]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       374  (0.0208601); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.29s 00:00:00.67 Elapsed: 00:00:00.44
# Mc/sec: 564.70
//
Query:       gene3152|gene3152|rna3152|rna3152  [L=60]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (60 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       303  (0.0169); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 425.64
//
Query:       gene3153|gene3153|rna3153|rna3153  [L=335]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (335 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       629  (0.0350828); expected 358.6 (0.02)
Passed bias filter:                      563  (0.0314016); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 2324.36
//
Query:       gene3154|gene3154|rna3154|rna3154  [L=40]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (40 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       184  (0.0102627); expected 358.6 (0.02)
Passed bias filter:                      134  (0.00747392); expected 358.6 (0.02)
Passed Vit filter:                         6  (0.000334653); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.26s 00:00:00.61 Elapsed: 00:00:00.41
# Mc/sec: 292.45
//
Query:       gene3155|gene3155|rna3155|rna3155  [L=126]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       702  (0.0391544); expected 358.6 (0.02)
Passed bias filter:                      515  (0.0287244); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 857.72
//
Query:       gene3156|gene3156|rna3156|rna3156  [L=69]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (69 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       329  (0.0183502); expected 358.6 (0.02)
Passed bias filter:                      203  (0.0113224); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.27s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 506.94
//
Query:       gene3157|gene3157|rna3157|rna3157  [L=163]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       510  (0.0284455); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1129.52
//
Query:       gene3158|gene3158|rna3158|rna3158  [L=719]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0019   18.1   0.3      0.026   14.4   0.1    2.3  2  Inhibitor_I66  Peptidase inhibitor I66


Domain annotation for each model (and alignments):
>> Inhibitor_I66  Peptidase inhibitor I66
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.1   1.4e-06     0.026      44      99 ..      97     156 ..      88     165 .. 0.83
   2 ?    1.0   0.0     0.019   3.4e+02      35      61 ..     611     636 ..     595     657 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.4e-06
                      Inhibitor_I66  44 skWvvekkddgtYilkakgaptaeidgklfAille.....eakeekWiiekqpqqgedvyt 99 
                                          +vvekk dg+Y+l ++++++    + +f    +       + ++W +e+ ++ g+d+  
  gene3158|gene3158|rna3158|rna3158  97 RLYVVEKK-DGEYVLVIDDQDVCRSGKDVFVGWAGnrlvvVGQMVRWGLEEWEWTGDDITS 156
                                        45899996.778******************99998776644599*************9865 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.019
                      Inhibitor_I66  35 lvlPkgveaskWvvekkddgtYilkak 61 
                                        +v+P +++a +++++++++g++ l ++
  gene3158|gene3158|rna3158|rna3158 611 MVIPYSHRAGSFFIKNTNKGAF-LYSD 636
                                        68899999*9*******99955.4444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (719 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       665  (0.0370907); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.27s 00:00:00.86 Elapsed: 00:00:00.43
# Mc/sec: 5028.32
//
Query:       gene3159|gene3159|rna3159|rna3159  [L=261]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.24   11.9   2.2       0.74   10.4   0.2    2.3  2  AAA_18    AAA domain


Domain annotation for each model (and alignments):
>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.2   4.1e-05      0.74      30     109 ..      45     118 ..       7     121 .. 0.91
   2 ?    0.8   0.1     0.038   6.9e+02      63     103 ..     217     254 ..     178     257 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 4.1e-05
                             AAA_18  30 dvakenglllevdpealdeskrldedkldklldaleenssaleegknlvidghlaeleseaakdikkvvLtaspee 105
                                        +++k n+l+++++++   ++k++++++ ++l  ++++ +   +++  ++id h+  ++ +++ ++  +++ +++ +
  gene3159|gene3159|rna3159|rna3159  45 KYIKRNQLRETYTEQ---QEKKFNRKYSEYLKALVKKRA---DDCFGVLIDFHIKFYRIDRYNRNELIFVLLPDYQ 114
                                        577888899999998...9999*****999999999976...599999**************99999********9 PP

                             AAA_18 106 lleR 109
                                         +eR
  gene3159|gene3159|rna3159|rna3159 115 IYER 118
                                        9999 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.038
                             AAA_18  63 aleenssaleegknlvidghlaeleseaakdikk....vvLtasp 103
                                        a+e       +++  v+ g+ +++e+ +  d ++    + +++++
  gene3159|gene3159|rna3159|rna3159 217 AIEM------DEEK-VLKGCDGQHEYISVQDVNRkqddILVQCRD 254
                                        3333......2333.899999999988887777778889999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1043  (0.0581739); expected 358.6 (0.02)
Passed bias filter:                      464  (0.0258799); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.37
# Mc/sec: 2100.43
//
Query:       gene316|gene316|rna316|rna316  [L=155]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.049   13.5   0.1       0.21   11.4   0.0    2.1  3  DUF3283   Protein of unknown function (DUF3283)


Domain annotation for each model (and alignments):
>> DUF3283  Protein of unknown function (DUF3283)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       0.3   5.4e+03      16      27 ..      46      57 ..      44      68 .. 0.60
   2 ?   -2.4   0.0      0.25   4.5e+03       9      17 ..      90      98 ..      84     103 .. 0.66
   3 ?   11.4   0.0   1.2e-05      0.21      11      36 ..     118     142 ..     115     152 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.3
                        DUF3283 16 DkqAsFlvwklk 27
                                   Dk    ++wk+ 
  gene316|gene316|rna316|rna316 46 DKYFLVTIWKMI 57
                                   555445667764 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.25
                        DUF3283  9 eknkieLDk 17
                                   ek+   LDk
  gene316|gene316|rna316|rna316 90 EKYLARLDK 98
                                   666666666 PP

  == domain 3  score: 11.4 bits;  conditional E-value: 1.2e-05
                        DUF3283  11 nkieLDkqAsFlvwklkqakagpeai 36 
                                      +e+D + sFl  k+kqak g+  +
  gene316|gene316|rna316|rna316 118 ACVEIDHD-SFLYLKVKQAKDGRSRV 142
                                    56899986.9************9765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       445  (0.0248201); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.30s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 1006.37
//
Query:       gene3160|gene3160|rna3160|rna3160  [L=455]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.055   14.1   0.0        0.2   12.3   0.0    1.9  1  Fapy_DNA_glyco  Formamidopyrimidine-DNA glycosylase N-termina


Domain annotation for each model (and alignments):
>> Fapy_DNA_glyco  Formamidopyrimidine-DNA glycosylase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   1.1e-05       0.2      13      70 ..     148     214 ..     138     236 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.1e-05
                                        HHHHHHTT-EEEEEEE-SSHHHTSTHHHHHTT-.SEEEEEEEEETTEEEEEE............EEEE CS
                     Fapy_DNA_glyco  13 glrrhllgkkiakvevlkdktlrgspaafakalkgrkiasvgrrGKyllleldg..........gevl 70 
                                        +  r +l+++i+++++ ++    +++   ++  +g +i++++r +K +++++ +          +++ 
  gene3160|gene3160|rna3160|rna3160 148 TS-RFVLDENIKDLDIANECLSVYQKGRKQQICNGYVIKDWERTAKNFWCTVLDtmdeipsamlTGAH 214
                                        44.568889999999966666666666667788*****************996644444444443333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (455 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       754  (0.0420548); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.23s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 3286.97
//
Query:       gene3161|gene3161|rna3161|rna3161  [L=141]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      2e-08   34.3   4.7    7.1e-08   32.5   4.7    1.7  1  Clat_adaptor_s  Clathrin adaptor complex small chain


Domain annotation for each model (and alignments):
>> Clat_adaptor_s  Clathrin adaptor complex small chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.5   4.7     4e-12   7.1e-08       2     134 ..       5     127 ..       4     133 .. 0.75

  Alignments for each domain:
  == domain 1  score: 32.5 bits;  conditional E-value: 4e-12
                                        EEEEEEE-TTS-EEEEEESSSS-CHHHHHHHHHHHHHHHTT-SSS-SEEEETTEEEEEEEETTEEEEEEEETTS-H CS
                     Clat_adaptor_s   2 ikaililnkkgkvrlakfytavddkkkqklieevyelvsaRdsklsniveledlkviYkryasLYFvvivdeqene 77 
                                        i+ i++ n +g+ r+ + +t  +     +l     +  +       n+  +e+   + k y  +  +v v e+en 
  gene3161|gene3161|rna3161|rna3161   5 INTIFLCNSEGEYRIRRSFTLEK----IDLRSAFKTKLAL-----RNFFRFEGKLYVVKTYKLVK-IVFVVEHENP 70 
                                        55566666666666666554322....1222222222233.....59999999777888886555.55555789** PP

                                        HHHHHHHHHHHHHHHHHCTS-SHHHHHHCHHHHHHHHHCCEETTEES---HHHHHHC CS
                     Clat_adaptor_s  78 liilelihlfvesLdkyfgnVceldlvfnfekvylildEivsgGeiletskkevlkr 134
                                         ii+  i+ +++ L++yf+   + +l++n+e+ y +ld ++  G++++ +++ +lk+
  gene3161|gene3161|rna3161|rna3161  71 FIIFYYIDSLFQLLNAYFSGFSDSNLIYNYEEAYYMLDSMFLDGKLIQNDREVILKN 127
                                        ****************************************************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       368  (0.0205254); expected 358.6 (0.02)
Passed bias filter:                      242  (0.0134977); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1063.32
//
Query:       gene3162|gene3162|rna3162|rna3162  [L=99]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0065   15.0   0.3     0.0066   15.0   0.3    1.0  1  Pox_E6    Pox virus E6 protein
  ------ inclusion threshold ------
      0.014   15.3   0.0      0.024   14.6   0.0    1.3  1  DUF5330   Family of unknown function (DUF5330)


Domain annotation for each model (and alignments):
>> Pox_E6  Pox virus E6 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.3   7.4e-07    0.0066     386     453 ..      27      96 ..       5      99 .] 0.78

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 7.4e-07
                             Pox_E6 386 nlvyetkdidlealeekkkcqiyn..edteyfikeyntylylneedplvldkGalvklsdvpkekrlslf 453
                                        +  + t+d +  +l +++  +iy+  +  ++ ik+   y +l+++d  ++d+G+ +k+++ ++++ ++++
  gene3162|gene3162|rna3162|rna3162  27 RQTFTTNDETRIVLSKTEGSEIYAlcDTEDFDIKDLFEYKFLQDDDNNIVDEGRQTKVKKAKQSSLFNFM 96 
                                        45677888888889999999999643667889************************99998888877665 PP

>> DUF5330  Family of unknown function (DUF5330)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   2.7e-06     0.024      13      39 ..       6      32 ..       3      35 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.7e-06
                            DUF5330 13 saavsDvsgfCerkPdvCetGkealta 39
                                       +++v+D  +fC+ +P+ C +  +++t+
  gene3162|gene3162|rna3162|rna3162  6 RSTVRDFDKFCSQNPTFCPIYRQTFTT 32
                                       789***************999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       650  (0.0362541); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.34u 0.25s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 766.75
//
Query:       gene3163|gene3163|rna3163|rna3163  [L=426]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
       0.31   11.1   1.6       0.66   10.0   1.6    1.5  1  Hep_core_N  Hepatitis core protein, putative zinc finger


Domain annotation for each model (and alignments):
>> Hep_core_N  Hepatitis core protein, putative zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   1.6   3.7e-05      0.66       1      15 [.       1      15 [.       1      18 [. 0.92

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 3.7e-05
                         Hep_core_N  1 mqLFPLCLiisCsCP 15
                                       m LF L  +isC CP
  gene3163|gene3163|rna3163|rna3163  1 MFLFTLYCVISCNCP 15
                                       88************* PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (426 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1399  (0.07803); expected 358.6 (0.02)
Passed bias filter:                      508  (0.028334); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.30s 00:00:00.88 Elapsed: 00:00:00.51
# Mc/sec: 2525.44
//
Query:       gene3164|gene3164|rna3164|rna3164  [L=65]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0019   18.2   0.3      0.002   18.1   0.3    1.1  1  CagS      Cag pathogenicity island protein S of Helicobacter 
  ------ inclusion threshold ------
      0.089   13.1   0.1       0.13   12.5   0.1    1.3  1  ARTD15_N  ARTD15 N-terminal domain
       0.18   11.8   1.1       0.35   10.9   1.1    1.5  1  FlxA      FlxA-like protein


Domain annotation for each model (and alignments):
>> CagS  Cag pathogenicity island protein S of Helicobacter pylori
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.3   3.4e-07     0.002      17      55 ..      21      59 ..       6      64 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 3.4e-07
                                       XXXX--HHHHHT--B--HHHHHHHHHHHHHHHHHHHHHC CS
                               CagS 17 dkkeklieslqenellstdekkkiidqiktmhdffkqmh 55
                                        kk k ++sl+en +l  +e   +  qi+++ d+fk++ 
  gene3164|gene3164|rna3164|rna3164 21 VKKLKYLNSLKENSVLPEEEEVSLFAQIQALNDLFKNLS 59
                                       48999*******************************975 PP

>> ARTD15_N  ARTD15 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   2.1e-05      0.13      39      78 ..       8      47 ..       5      49 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.1e-05
                           ARTD15_N 39 sesekdidaLlsvvenlpslkellkslqeldeealeLlhw 78
                                       +es+++i+ L++ v++l+ l++l++++  ++ee ++L+  
  gene3164|gene3164|rna3164|rna3164  8 RESNRQINTLKEYVKKLKYLNSLKENSVLPEEEEVSLFAQ 47
                                       6789*******************************99975 PP

>> FlxA  FlxA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   1.1   5.8e-05      0.35      15      62 ..      10      59 ..       4      65 .] 0.60

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 5.8e-05
                               FlxA 15 sasqiasLqkQiknlqkqLkelsesdeltkeekk...kqqqliqaQIqqlq 62
                                       s+ qi++L++ +k+l k L++l+e++ l++ee     +q+q +    ++l 
  gene3164|gene3164|rna3164|rna3164 10 SNRQINTLKEYVKKL-KYLNSLKENSVLPEEEEVslfAQIQALNDLFKNLS 59
                                       566777777777776.45777777766666655445555555555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (65 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1062  (0.0592336); expected 358.6 (0.02)
Passed bias filter:                      497  (0.0277205); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.36u 0.29s 00:00:00.64 Elapsed: 00:00:00.43
# Mc/sec: 450.71
//
Query:       gene3165|gene3165|rna3165|rna3165  [L=199]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.7e-10   38.8   2.9    1.2e-09   38.1   2.9    1.2  1  Syntaxin       Syntaxin
    7.1e-05   22.7   1.7    0.00017   21.5   1.7    1.7  1  SNARE          SNARE domain
  ------ inclusion threshold ------
      0.026   14.3   0.4      0.043   13.6   0.4    1.3  1  MCPsignal      Methyl-accepting chemotaxis protein (MCP) sign
      0.054   13.2   0.1      0.096   12.4   0.1    1.4  1  FBA            F-box associated region
       0.19   11.5   1.8       0.24   11.2   0.7    1.7  2  DUF2976        Protein of unknown function (DUF2976)
       0.41   10.7   4.2       0.81    9.8   3.7    1.8  1  YolD           YolD-like protein
       0.55   10.1   5.2       0.59   10.0   0.3    2.0  2  PCRF           PCRF domain
        2.2    8.1   8.3        1.6    8.6   5.8    2.2  2  Synaptobrevin  Synaptobrevin


Domain annotation for each model (and alignments):
>> Syntaxin  Syntaxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.1   2.9   5.4e-13   1.2e-09      80     199 ..      10     129 ..       4     130 .. 0.94

  Alignments for each domain:
  == domain 1  score: 38.1 bits;  conditional E-value: 5.4e-13
                           Syntaxin  80 gegsavdRirksqtaaLrkklkevmteynelrekireeykerieRrlevtGkevseeeieelietgesevflqkll 155
                                        ++ s++    k q ++L+++l +v+++++ ++ +++++ ke ++ ++ ++  e+se+ei el++t++   +l++++
  gene3165|gene3165|rna3165|rna3165  10 EKDSSTYNAIKEQWTTLTHNLTQVVSDFRYVQVEHNNREKEMLREQYLIARPEASEKEISELMTTNNAADVLKNAF 85 
                                        677888888999********************************************************99999999 PP

                           Syntaxin 156 qeqrgarealseieeRhkevlelekslkeLhqlFldmavLVEeQ 199
                                         + +++    ++ ++R ++++ +   +++L ql  d+  +V  Q
  gene3165|gene3165|rna3165|rna3165  86 INDNTHDLEYRQAQKRLEDIKVIVDYIDQLCQLLRDIDQMVAGQ 129
                                        9999998999***************************9999887 PP

>> SNARE  SNARE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   1.7   7.5e-08   0.00017       3      53 .]     133     183 ..     131     183 .. 0.97

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 7.5e-08
                                        HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTXXXXXXXXXXXXXXXXXXXX CS
                              SNARE   3 vDrIdtnVenaqsnveraqkeLkkavkyqksnRklkciillilviillvvl 53 
                                        vDrI+ +V  +++n+++ + +L+k +k+ + +  +k i+lli+++ llv++
  gene3165|gene3165|rna3165|rna3165 133 VDRIEIDVSVSRENTRNMNVNLRKTLKSTRRWKLFKRILLLIVGVALLVLI 183
                                        9***********************************************985 PP

>> MCPsignal  Methyl-accepting chemotaxis protein (MCP) signalling domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.4   1.9e-05     0.043      82     165 ..      59     140 ..      54     147 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.9e-05
                                        HHHHHHHHHHHHHH..............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          MCPsignal  82 ersaqaakeiealiieiqkeindsvesleetrqrveegselveetgealkeiveavaevadlvqeiaaaseeqsas 157
                                        +r   + kei++l+   +++  d+++      +  +    ++++  e++k iv+ ++++ +l+++i + ++ q+  
  gene3165|gene3165|rna3165|rna3165  59 ARPEASEKEISELM--TTNNAADVLKNAFINDNTHDLEYRQAQKRLEDIKVIVDYIDQLCQLLRDIDQMVAGQADF 132
                                        56677889999999..45555555554444556667788999999******************************9 PP

                                        HHHHHHHH CS
                          MCPsignal 158 ieevnqav 165
                                        ++ +   v
  gene3165|gene3165|rna3165|rna3165 133 VDRIEIDV 140
                                        99887655 PP

>> FBA  F-box associated region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   4.3e-05     0.096     118     170 ..       7      59 ..       2      64 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4.3e-05
                                FBA 118 efdtkelvteqwadrqwkqvshvFsnygkGvRfvrFehggkdtqfwaghygak 170
                                        + d k+  t +  ++qw+  +h  ++  +  R+v+ eh  +++++++++y + 
  gene3165|gene3165|rna3165|rna3165   7 HCDEKDSSTYNAIKEQWTTLTHNLTQVVSDFRYVQVEHNNREKEMLREQYLIA 59 
                                        556666777788899*********************************99765 PP

>> DUF2976  Protein of unknown function (DUF2976)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       3.5   7.8e+03      51      65 ..      16      27 ..      13      33 .. 0.66
   2 ?   11.2   0.7   0.00011      0.24      61      84 ..     164     189 ..     155     192 .. 0.75

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 3.5
                            DUF2976 51 fneisegkaewgkfg 65
                                       +n i   k++w+ + 
  gene3165|gene3165|rna3165|rna3165 16 YNAI---KEQWTTLT 27
                                       5555...77787765 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00011
                            DUF2976  61 wgkf..gltlvvGvvllvvviwLltk 84 
                                        w  f  +l+l+vGv llv++iw  + 
  gene3165|gene3165|rna3165|rna3165 164 WKLFkrILLLIVGVALLVLIIWVFNS 189
                                        5544115789************9876 PP

>> YolD  YolD-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   3.7   0.00036      0.81       4      74 ..      43     120 ..      41     139 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00036
                               YolD   4 EhvealrelkeeqkkvekpeLDeqqleeinek......lqealeeeqpvtityye.dgeleevtgyiekidelnke 72 
                                        Eh  + +e+ +eq  + +pe +e++++e+ ++      l  a+ ++ +  ++y + +++le++++ +++id+l + 
  gene3165|gene3165|rna3165|rna3165  43 EHNNREKEMLREQYLIARPEASEKEISELMTTnnaadvLKNAFINDNTHDLEYRQaQKRLEDIKVIVDYIDQLCQL 118
                                        999999**********************97533333339**************8735789***********99876 PP

                               YolD  73 lk 74 
                                        l+
  gene3165|gene3165|rna3165|rna3165 119 LR 120
                                        65 PP

>> PCRF  PCRF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   1.3      0.03        67      27      91 ..      23      86 ..       4      93 .. 0.52
   2 ?   10.0   0.3   0.00026      0.59      21      91 ..      92     159 ..      74     173 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.03
                                       TTHHHHHTHHHHHHHHHHHHHTTTHHH...HT....-S-.....-GGGTHHHHHHHHHH..HHHHHT- CS
                               PCRF 27 lskelaeleeivealeeleealedleeakelleedeela...elaeeeleelekeleeleeelkklLl 91
                                        ++  ++l+++v++++ ++ ++++ e+  e+l +++ l    e  e+e++el ++ +++ + lk+ ++
  gene3165|gene3165|rna3165|rna3165 23 WTTLTHNLTQVVSDFRYVQVEHNNREK--EML-REQYLIarpEASEKEISELMTTNNAA-DVLKNAFI 86
                                       233345567777777766666666555..777.34333311122244666666665555.55666665 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00026
                                        GGGSSSTTHHHHHTHHHHHHHHHHHHHTTTHHH...HT....-S-..-GGGTHHHHHHHHHH..HHHHHT- CS
                               PCRF  21 qekakklskelaeleeivealeeleealedleeakelleedeelaelaeeeleelekeleeleeelkklLl 91 
                                          ++++ +k+l++++ iv+ +++l ++l+d+++   +++ ++++ +  e +++  +++ ++++ +l+k L 
  gene3165|gene3165|rna3165|rna3165  92 DLEYRQAQKRLEDIKVIVDYIDQLCQLLRDIDQ---MVAGQADFVDRIEIDVSVSRENTRNMNVNLRKTLK 159
                                        24789999************************9...88667788887788888888888888778777775 PP

>> Synaptobrevin  Synaptobrevin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       2.3   5.2e+03      13      22 ..      66      75 ..      58      84 .. 0.62
   2 ?    8.6   5.8   0.00071       1.6      55      86 ..     156     187 ..      92     189 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 2.3
                                       HCCCCHHCCH CS
                      Synaptobrevin 13 devkdimkeN 22
                                       +e+ ++m+ N
  gene3165|gene3165|rna3165|rna3165 66 KEISELMTTN 75
                                       5677777665 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00071
                                        HHHHHHHHHHTXXXXXXXXXXXXXXXXXXXXX CS
                      Synaptobrevin  55 rklkrkmwwknmkliiililvvlililiiiiv 86 
                                        ++lk +  wk +k i++li+ v++l+lii+++
  gene3165|gene3165|rna3165|rna3165 156 KTLKSTRRWKLFKRILLLIVGVALLVLIIWVF 187
                                        67999999*********************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1986  (0.11077); expected 358.6 (0.02)
Passed bias filter:                      884  (0.0493056); expected 358.6 (0.02)
Passed Vit filter:                       105  (0.00585643); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.51u 0.32s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 1276.51
//
Query:       gene3166|gene3166|rna3166|rna3166  [L=618]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.014   15.8   3.9      0.014   15.8   3.9    3.4  3  DUF4215       Domain of unknown function (DUF4215)
       0.15   12.6   0.1       0.15   12.6   0.1    3.1  4  Reprolysin_3  Metallo-peptidase family M12B Reprolysin-like


Domain annotation for each model (and alignments):
>> DUF4215  Domain of unknown function (DUF4215)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.8     0.011        98      28      42 ..     209     223 ..     197     229 .. 0.71
   2 ?   -3.7   0.2         2   1.8e+04      36      42 ..     408     414 ..     406     416 .. 0.75
   3 ?   15.8   3.9   1.5e-06     0.014      15      46 ..     579     614 ..     570     615 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.011
                            DUF4215  28 gnEqCddgnqvqndg 42 
                                        + ++Cdd n+ ++ +
  gene3166|gene3166|rna3166|rna3166 209 DGKECDDMNTTEEEN 223
                                        559*****9998765 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 2
                            DUF4215  36 nqvqndg 42 
                                        n++qndg
  gene3166|gene3166|rna3166|rna3166 408 NNNQNDG 414
                                        7888887 PP

  == domain 3  score: 15.8 bits;  conditional E-value: 1.5e-06
                            DUF4215  15 qtC...esiCGDgiiagnEqCddgnqvqndgCnn.C 46 
                                         +C    + CG+gi+   E+Cddg ++ +  C   C
  gene3166|gene3166|rna3166|rna3166 579 GKCfddGQRCGNGIVDEGEECDDGLMYGSERCTReC 614
                                        567777889*********************997768 PP

>> Reprolysin_3  Metallo-peptidase family M12B Reprolysin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.5      0.68   6.1e+03      85      85 ..     167     167 ..     113     211 .. 0.60
   2 ?   -2.8   0.1      0.96   8.6e+03      40      56 ..     219     236 ..     190     256 .. 0.57
   3 ?   -0.8   0.4      0.23   2.1e+03      27      53 ..     395     421 ..     371     437 .. 0.63
   4 ?   12.6   0.1   1.7e-05      0.15      38     123 ..     463     547 ..     441     548 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.68
                       Reprolysin_3  85 g 85 
                                         
  gene3166|gene3166|rna3166|rna3166 167 D 167
                                        1 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 0.96
                       Reprolysin_3  40 kkda.tealdelaevtae 56 
                                        ++++ + + d+++++t+e
  gene3166|gene3166|rna3166|rna3166 219 TEEEnSINNDNTTRITEE 236
                                        222213333333333332 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 0.23
                       Reprolysin_3  27 aiiitdkasdpytkkdatealdelaev 53 
                                        ++  ++k+++++ ++++++ l+++ + 
  gene3166|gene3166|rna3166|rna3166 395 GTTKNEKKKTSKINNNQNDGLKKMNRK 421
                                        555666667777777777777776544 PP

  == domain 4  score: 12.6 bits;  conditional E-value: 1.7e-05
                       Reprolysin_3  38 ytkkdatealdelaevtaeaergqagyDlvhlftarde.sgvgGlAyvgsvcnsskkagvnsgssvlgkvgadtva 112
                                        ++ ++  +++d+l+++++++  + ++++l +lf+ +    +v  l + +++c+ +++++v+ ++   +  + +++ 
  gene3166|gene3166|rna3166|rna3166 463 SFLSNFADKFDSLKNDVRNE--KLNNVNLFVLFSSDSIsTTVDALTFRSGACSLANNYSVVFNTAFARMNTPKVLS 536
                                        44556688888888888888..799*********97776666677777999999999999999987777788**** PP

                       Reprolysin_3 113 HEiGHnfganH 123
                                        HEi H+++a+H
  gene3166|gene3166|rna3166|rna3166 537 HEILHSLSADH 547
                                        *********** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (618 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1975  (0.110157); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.76u 0.33s 00:00:01.09 Elapsed: 00:00:00.51
# Mc/sec: 3627.83
//
Query:       gene3167|gene3167|rna3167|rna3167  [L=165]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-18   66.8   4.1    1.7e-18   66.6   4.1    1.0  1  PRA1      PRA1 family protein
  ------ inclusion threshold ------
      0.014   15.0   3.2      0.015   14.9   3.2    1.1  1  SUR7      SUR7/PalI family
       0.12   12.6   1.7       0.34   11.1   1.7    1.8  1  DUF1378   Protein of unknown function (DUF1378)
       0.28   11.3   4.2       0.65   10.1   0.5    2.1  2  DUF962    Protein of unknown function (DUF962)
        5.3    7.3  10.6       0.41   10.9   1.8    2.1  2  VirB3     Type IV secretory pathway, VirB3-like protein


Domain annotation for each model (and alignments):
>> PRA1  PRA1 family protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.6   4.1   4.8e-22   1.7e-18       9     134 ..      31     157 ..      25     164 .. 0.86

  Alignments for each domain:
  == domain 1  score: 66.6 bits;  conditional E-value: 4.8e-22
                               PRA1   9 wsefldlsrfslP.kslskatsRvkkNllyfrtNYlivvllvlllslltnplslivllllvlawlflyflrseplv 83 
                                        ++ f+d+s++ +P ++ + ++ Rv++N++ f+ NYli+ +++++++l+++  +l+vl +l ++++f  +++ +++ 
  gene3167|gene3167|rna3167|rna3167  31 VRTFVDISNMGMPpAGKEHIKRRVSCNFERFKGNYLIISFVFIAVFLIRQLSALFVL-ALWAGYFFAADCFGDKFA 105
                                        5789********9999*********************99999988888888777776.56788999999******* PP

                               PRA1  84 lfgrelsdrvvlivllvvsvlllfltg.avlvllwalliglllvllHAsfrk 134
                                        ++g+el++  v+ +++v++vl l++++  ++ l+++l + +++v++H  ++k
  gene3167|gene3167|rna3167|rna3167 106 VGGYELKNEYVMYFCIVLTVLYLIVFNtIIVSLMVTLSLFMVVVVAHMLCYK 157
                                        ******8887777777777777777774788899*************87765 PP

>> SUR7  SUR7/PalI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   3.2   4.2e-06     0.015     118     176 ..      65     147 ..      11     159 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 4.2e-06
                               SUR7 118 lhiialvlsfislvvgllaic........................vspdnsrllsflnlllsvlsflatllaalld 169
                                         +ii++v+ ++ l+ +l a++                          ++++ ++++++l++  l+++ t++ +l++
  gene3167|gene3167|rna3167|rna3167  65 YLIISFVFIAVFLIRQLSALFvlalwagyffaadcfgdkfavggyELKNEYVMYFCIVLTVLYLIVFNTIIVSLMV 140
                                        689*****************999*******99999999999999777777778*********************** PP

                               SUR7 170 tllfvfv 176
                                        tl   +v
  gene3167|gene3167|rna3167|rna3167 141 TLSLFMV 147
                                        9976655 PP

>> DUF1378  Protein of unknown function (DUF1378)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   1.7   9.5e-05      0.34       6      21 ..     114     129 ..     110     132 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 9.5e-05
                            DUF1378   6 lllLYFCtvvcvLYLv 21 
                                          ++YFC v +vLYL+
  gene3167|gene3167|rna3167|rna3167 114 EYVMYFCIVLTVLYLI 129
                                        5689***********8 PP

>> DUF962  Protein of unknown function (DUF962)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.2     0.044   1.6e+02      31      58 ..      69      96 ..      55     104 .. 0.65
   2 ?   10.1   0.5   0.00018      0.65      26      72 ..     116     162 ..     113     164 .. 0.92

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.044
                             DUF962 31 illtvlllllraklklllalfvvgyifa 58
                                        +++++++l+r+  +l ++++ +gy+fa
  gene3167|gene3167|rna3167|rna3167 69 SFVFIAVFLIRQLSALFVLALWAGYFFA 96
                                       3344445555555566666666777765 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00018
                             DUF962  26 igvplilltvlllllraklklllalfvvgyifafvGHfvfEkrkPAl 72 
                                        +    i+ltvl+l+++ ++ + l++ +  +++  v+H++  k +P+l
  gene3167|gene3167|rna3167|rna3167 116 VMYFCIVLTVLYLIVFNTIIVSLMVTLSLFMVVVVAHMLCYKDEPSL 162
                                        6667899********************************99999986 PP

>> VirB3  Type IV secretory pathway, VirB3-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   1.8      0.11     4e+02      24      55 ..      67      94 ..      61      98 .. 0.40
   2 ?   10.9   1.8   0.00011      0.41      21      60 ..     114     158 ..     108     163 .. 0.67

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.11
                              VirB3 24 llnllvsvilflvglslwillllvplhlvlrl 55
                                       ++++++++++ +  ++l +l  +v++++++++
  gene3167|gene3167|rna3167|rna3167 67 IISFVFIAVFLI--RQLSAL--FVLALWAGYF 94
                                       333333333333..222222..3344444444 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00011
                              VirB3  21 elvllnllvsvilfl.....vglslwillllvplhlvlrliakrD 60 
                                        e+v+  ++v ++l+l     + +sl++ l l+++++v+ +++ +D
  gene3167|gene3167|rna3167|rna3167 114 EYVMYFCIVLTVLYLivfntIIVSLMVTLSLFMVVVVAHMLCYKD 158
                                        567777777777777445666666666666666677777777666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1472  (0.0821016); expected 358.6 (0.02)
Passed bias filter:                      579  (0.032294); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.45u 0.30s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1105.76
//
Query:       gene3168|gene3168|rna3168|rna3168  [L=1456]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.9e-16   60.3   0.0    5.2e-07   29.6   0.0    2.7  2  DEAD        DEAD/DEAH box helicase
    5.1e-12   45.5   0.1    2.4e-09   36.8   0.0    2.4  2  Sec63       Sec63 Brl domain
    6.9e-11   42.5   0.7    5.4e-10   39.6   0.1    2.9  3  Helicase_C  Helicase conserved C-terminal domain
    2.9e-08   33.9   6.3    0.00018   21.6   0.0    3.8  4  ResIII      Type III restriction enzyme, res subunit
  ------ inclusion threshold ------
        0.1   12.3   0.0        1.6    8.4   0.0    2.4  2  IstB_IS21   IstB-like ATP binding protein


Domain annotation for each model (and alignments):
>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6   0.0   1.5e-10   5.2e-07       2      72 ..     301     362 ..     300     390 .. 0.86
   2 !   27.7   0.0   5.5e-10     2e-06      97     172 ..     519     584 ..     500     588 .. 0.83

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 1.5e-10
                                        HHHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTT CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               DEAD   2 diQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkk 72 
                                        +iQ+e   ++ +++++++aa+TG+GKT ++++ ++          ++++++v+P+r+La +++ +l++ ++
  gene3168|gene3168|rna3168|rna3168 301 SIQSELHTIARTNNNFVLAAPTGTGKTDVAMMCIM---------GATRVVYVVPLRALATEIVGKLRRTFS 362
                                        699999999999*******************9999.........5568*****************999887 PP

  == domain 2  score: 27.7 bits;  conditional E-value: 5.5e-10
                                        TCSEEEEEHHHHHHHHHCTSSHCTTE.EEEEEETHHHHHHTTTHHHHHHHHHHSHHHCTTSTTTSEEEEEESSBSH CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               DEAD  97 gvdivvgtpgrlddllstgklnlsqv.rflVlDEadrlldqgfsdfinrilnqlpqitcdgklqrqvivlSATlpk 171
                                        +++ivv+tp++ld   st+kl+++    +l++DE++ l ++ ++  i+++++++      g+   +++ lSAT+p 
  gene3168|gene3168|rna3168|rna3168 519 NTHIVVTTPEKLDA--STRKLSFNFPfDLLIIDEIHLLEEE-RGSVIEALVARF-----IGR--TRIVGLSATVP- 583
                                        689**********9..889999776449********99998.*********999.....233..45*******99. PP

                                        H CS
                                        x RF
                               DEAD 172 d 172
                                        +
  gene3168|gene3168|rna3168|rna3168 584 N 584
                                        3 PP

>> Sec63  Sec63 Brl domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.2   0.0    0.0014       4.9       4      23 ..     992    1011 ..     989    1018 .. 0.86
   2 !   36.8   0.0   6.6e-13   2.4e-09      33     145 ..    1151    1259 ..    1145    1423 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0014
                                         HHHHHHHHT--HHHHHHHHH CS
                                         xxxxxxxxxxxxxxxxxxxx RF
                              Sec63    4 lGriaShYyisyetiklfne 23  
                                          Gr+a++Yy+ ++t+ +f +
  gene3168|gene3168|rna3168|rna3168  992 EGRVAAYYYLDFSTLVVFVR 1011
                                         69*************99975 PP

  == domain 2  score: 36.8 bits;  conditional E-value: 6.6e-13
                                         HHHHHHHTSGGGGGS---TTHHHHHHHHH.HTSSS--SSSTTSHHHHHHHHHHHHHTT---SSHHHHHHHHHHH CS
                                         xxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              Sec63   33 dlLeilssasEFeeipvReeEkkelkkLl.ekvpikvkediespeaKvniLlqayisrlklegsdlvsDlkyil 105 
                                         ++L+ +   +EF +i vR++E++ + +    ++ ++v     +p +K   L   ++ +++   ++lvsDl+++l
  gene3168|gene3168|rna3168|rna3168 1151 QILSTIFGTKEFGDILVRQNEQQFVLTTVgMSAAVEV-----TPCEKLLFLTAMHLMQMSTAIFSLVSDLAFVL 1219
                                         789999999*************987666536666665.....899***************************** PP

                                         HHHHHHHHHHHHHHHHTTBHHHHHHHHHHHHHHHHTS-TT CS
                                         xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              Sec63  106 qnairilralveillskgwlslalslleLskmveqrlwds 145 
                                         +n++r++ al ++++    ++l+ ++++L   +e+r  ++
  gene3168|gene3168|rna3168|rna3168 1220 KNVGRVMGALEQLAMLAHSYALCERIMRLRMRIEHRGGNT 1259
                                         *********************************9996655 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       2.5   8.9e+03       9      32 ..     190     215 ..     184     233 .. 0.63
   2 ?   -1.6   0.0      0.92   3.3e+03      19      88 ..     520     588 ..     510     591 .. 0.79
   3 !   39.6   0.1   1.5e-13   5.4e-10      10     110 ..     751     878 ..     743     879 .. 0.74

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 2.5
                                        HHHHTTTTSEEEEEESSHHHHHH...H CS
                         Helicase_C   9 llkleeeggkilifvntidrlek...v 32 
                                        +l +ee ++++ i+ nti+++ +   +
  gene3168|gene3168|rna3168|rna3168 190 EL-QEEPDKNAEIMNNTIKKIAQdlkL 215
                                        45.688899999999999977544322 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.92
                                        EEEEESSHHHHHH.HHHHHHHTTSTEEEEST.TSTHHHHHHHHHHHHTTSSSEEEESGGGTSSSTSTTESEE CS
                         Helicase_C  19 ilifvntidrlek.vklllekkgikvavlhg.elpqnereeileqfnkgesdvLiatdvaerGidipkvnlV 88 
                                        + i+v+t ++l+  ++ l  ++ +  ++++   l  +er  ++e+      +++  t++++ + ++p+v +V
  gene3168|gene3168|rna3168|rna3168 520 THIVVTTPEKLDAsTRKLSFNFPFDLLIIDEiHLLEEERGSVIEAL---VARFIGRTRIVGLSATVPNVYNV 588
                                        5677777777777778887777888888888789999999999999...45799999999999999999877 PP

  == domain 3  score: 39.6 bits;  conditional E-value: 1.5e-13
                                        H..HHTTTTSEEEEEESSHHHHHH.....HHHH..HHHT............TSTEEEESTTSTHHHHHHHHHHHHT CS
                         Helicase_C  10 l..kleeeggkilifvntidrlek.....vkll..lekk............gikvavlhgelpqnereeileqfnk 64 
                                        l  kl   ++++lifvn++ ++ k     vk l  +  +            +  v v+++ lp ++r+++ e f++
  gene3168|gene3168|rna3168|rna3168 751 LieKLLLCNNQSLIFVNSRYECFKtatllVKRLirN--EtytrpasfayllNNGVGVHNAGLPRQQRLHVEELFRR 824
                                        4455567899**********8866644442222341..14455555566666677889999*************** PP

                                        TSSSEEEESGGGTSSSTSTTESEEEESSSS.......SS..HHHHHHHHTTSSST CS
                         Helicase_C  65 gesdvLiatdvaerGidipkvnlVinfdlp.......rn..vtsyiqriGRtgRa 110
                                        +e +++++t+ ++ G+++p  ++V++ +         rn  ++++ q iGR+gR+
  gene3168|gene3168|rna3168|rna3168 825 KELKYVVCTKTLAWGVNLPA-ENVFIRGTEyysdgrhRNvsISDVLQIIGRAGRI 878
                                        *******************5.555555555466677744336************7 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   1.1      0.52   1.9e+03      87     121 ..     174     216 ..     101     239 .. 0.57
   2 !   12.8   0.0   2.4e-05     0.086      21      80 ..     308     363 ..     281     439 .. 0.76
   3 !   21.6   0.0     5e-08   0.00018      87     170 ..     507     583 ..     478     584 .. 0.82
   4 ?   -2.4   0.8       1.1     4e+03      64     104 ..    1050    1100 ..    1046    1113 .. 0.49

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.52
                                        EEESSS-B--...............-SEEEEEHHHHHHTH... CS
                             ResIII  87 kkvsgdkkka........kekdstnkkilvttiqsldadseee 121
                                         +++g+k++a        +e+ ++n++i+  ti+++ +d++ +
  gene3168|gene3168|rna3168|rna3168 174 DSKNGRKRTAirttnaelQEEPDKNAEIMNNTIKKIAQDLKLD 216
                                        2222222222556666666667777777777777777777555 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 2.4e-05
                                        ....TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG CS
                             ResIII  21 s..krdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkflse 80 
                                           + +++++++++TGtGKT va+  i   +      +++ +vp ++l      ++++++s+
  gene3168|gene3168|rna3168|rna3168 308 TiaRTNNNFVLAAPTGTGKTDVAMMCIMGAT------RVVYVVPLRALATEIVGKLRRTFSC 363
                                        244788899**************99888777......4788888887777766666555554 PP

  == domain 3  score: 21.6 bits;  conditional E-value: 5e-08
                                        EEESSS-B--.......-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS...TTTHH.HHHT--- CS
                             ResIII  87 kkvsgdkkkakekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgak..kswre.ilekfke 159
                                         +++gd+ ++    s n++i+vtt ++lda+       ++   +  fd++iiDE H l ++  + +++ +++ + +
  gene3168|gene3168|rna3168|rna3168 507 MEYTGDTPNQ----SLNTHIVVTTPEKLDAST------RKLSFNFPFDLLIIDEIHLLEEErgSVIEAlVARFIGR 572
                                        4577777777....99****************......7788888999************7544777756899999 PP

                                        SEEEEEESS-S CS
                             ResIII 160 avllglTATpe 170
                                          ++gl+AT +
  gene3168|gene3168|rna3168|rna3168 573 TRIVGLSATVP 583
                                        *********75 PP

  == domain 4  score: -2.4 bits;  conditional E-value: 1.1
                                         HHHHHHHHHHGGGGTGG..........GEEEESSS-B--..............- CS
                             ResIII   64 kslleqtleefkkflseayke......igkkvsgdkkka.......kekdstnk 104 
                                           + ++  ++f++  +e++ +      +   +++ + ++       ++++++n 
  gene3168|gene3168|rna3168|rna3168 1050 DRVNDRINDRFEEERQEKVPNdtnnvkN---IKNTNAERqekvlndTNNHTNND 1100
                                         5566666677766666665543332221...22222222333444433334444 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.0   0.00045       1.6      45      77 ..     311     343 ..     291     377 .. 0.70
   2 ?    0.6   0.0      0.11     4e+02     100     136 ..     534     568 ..     523     585 .. 0.68

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00045
                          IstB_IS21  45 ekkenivllGpsGvGKshlaialgveavragls 77 
                                        ++++n+vl  p+G+GK+ +a+   + a r  + 
  gene3168|gene3168|rna3168|rna3168 311 RTNNNFVLAAPTGTGKTDVAMMCIMGATRVVYV 343
                                        67899************9998766666655444 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.11
                          IstB_IS21 100 aralkrllkvdllilDdlgllpldqaeaellfeviek 136
                                        +r+l+    +dlli+D++ ll+  ++  +++  ++++
  gene3168|gene3168|rna3168|rna3168 534 TRKLSFNFPFDLLIIDEIHLLE--EERGSVIEALVAR 568
                                        5667777789*******98764..4444444445544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1456 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1460  (0.0814323); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 1.04u 0.28s 00:00:01.32 Elapsed: 00:00:00.50
# Mc/sec: 8716.29
//
Query:       gene3169|gene3169|rna3169|rna3169  [L=583]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.1e-72  242.3   0.6    3.2e-55  187.4   0.2    2.1  2  GDI            GDP dissociation inhibitor
  ------ inclusion threshold ------
      0.096   12.9   0.0       0.23   11.7   0.0    1.6  1  NAD_binding_8  NAD(P)-binding Rossmann-like domain
        6.6    4.8  18.2        8.8    4.4  18.2    1.1  1  Nop14          Nop14-like family


Domain annotation for each model (and alignments):
>> GDI  GDP dissociation inhibitor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  187.4   0.2   5.3e-59   3.2e-55       3     261 ..       2     254 ..       1     266 [. 0.93
   2 !   53.3   0.0   2.7e-18   1.6e-14     275     429 ..     426     577 ..     410     582 .. 0.92

  Alignments for each domain:
  == domain 1  score: 187.4 bits;  conditional E-value: 5.3e-59
                                        XEECEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSSCGGG-EE-HHHHHHHH-TTHHHHHHH--GGG--EESS-- CS
                                GDI   3 eeydvivlGtGlkecilsGllsvdgkkvlhldrndyyGgesasltleqlyerfkleekpeeklGkdrdwnvdlipk 78 
                                        ++yd+++lGtGl ec+ls +ls++g  vlh+d  d yG+     +  +l  r+ +   p        ++++d  pk
  gene3169|gene3169|rna3169|rna3169   2 DHYDIVILGTGLSECVLSAVLSHSGYSVLHVDSSDRYGTSFQNYNYADLCTRYGKPCLP-ILAPLTNKFSIDYTPK 76 
                                        69***************************************************998666.55667889******** PP

                                        BEETTSHHHHHHHHTTGGGCS-EEE-SEEEEEETCEEEE--SSHHHHHC-TTS-HHHHHHHHHHHHHHHH-BTTBG CS
                                GDI  79 fllanGelvkiliktdvtrylefkaveGsyvykegkiakvpanelealaspllglfekrrakkfleyvseyeeddp 154
                                        +lla+G   ++lik d++  ++f  + G yvyk+ +++ vp++e+++l++ l+++++k r+ +f+  v++y    p
  gene3169|gene3169|rna3169|rna3169  77 LLLAGGLTQRVLIKYDLSSLVNFLLIPGCYVYKH-RLYEVPTSETKSLQTGLISFLQKPRLVRFFYNVRKYFRRVP 151
                                        ********************************86.79****************************99999866554 PP

                                        GGSTT--TTTSBHHHHHHHCT--HHHHHHHHHHTS--SSSGGGGSBCHHHHHHHHHHHHHHCCCSS..-SEEEETT CS
                                GDI 155 ktyedldlkkatmkevykkfdlsedtkdfiGhalalyrdddylkqpaletleriklyaeslarygk..spylyply 228
                                                  atm+e y++++++e++ + iGha+al +dd+yl++    t+e+i+ly+esl + g   sp++yply
  gene3169|gene3169|rna3169|rna3169 152 IR------LMATMREQYRHYGIDEHSAQVIGHAVALNLDDEYLDERPECTFEKIRLYIESLRENGDeiSPFVYPLY 221
                                        32......2579***************************************************99656******** PP

                                        -TTHHHHHHHHHHHHTT-EEETS--ECEEEE-T CS
                                GDI 229 GlGelpqgfarlsaiyGGtymlnkpvdevvlde 261
                                        G+ e+ q+f r +++ G  y l ++v+e+  + 
  gene3169|gene3169|rna3169|rna3169 222 GMSEVCQAFVRKASVAGAVYRLRTSVVEIKSNG 254
                                        ***************************997654 PP

  == domain 2  score: 53.3 bits;  conditional E-value: 2.7e-18
                                        EEECEEEE-GGG-CCCEEEEEEEEEEEEEESS--TTSTT-SSEEEEE-GGGCTSSS-EEEEEEEGGGTSS-TT-EE CS
                                GDI 275 akakkvicdpsylpekvrkvgkviraicilshpipntddadsvqiiipqkqlgrksdiyvalvssahnvaakgkyl 350
                                        +++k +i++ sy p+k  +  kvira  i++  +p  ++  s qi+   + l+rk+d++  ++ +   va+kg+ +
  gene3169|gene3169|rna3169|rna3169 426 IRCKALISEISYTPNKQPTNKKVIRATLIIDGVVPLLKHVPSAQILFLSSGLHRKTDVFALVLGHRECVAPKGYKV 501
                                        69************************************************************************** PP

                                        EEEEEE--SS-HHHHTHHHHHTT-SECEEEEEEEEEEEESSSSTTTSEEE-----S-SBSHHHHHHHHHHHHHHHS CS
                                GDI 351 aivsttvetenpevelepalellgpieekfvkisdlyepvedgskdnifisksydatshfettvedvkdiykrltG 426
                                         ++s + e en    l++ ++l+g + ++fv+ ++++  v++      ++  + d + h e  +++v ++ +++  
  gene3169|gene3169|rna3169|rna3169 502 VLISYVKEGEND-RTLDRIVHLFGKVVDRFVREEEMM--VNERVDRGWYVVGGCDESMHVENGMQEVVKVLEKMKR 574
                                        ****99999886.57***************9988876..67888999***********************999976 PP

                                        S-- CS
                                GDI 427 kkl 429
                                        + +
  gene3169|gene3169|rna3169|rna3169 575 DGF 577
                                        655 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   3.9e-05      0.23       1      40 [.       8      47 ..       8      62 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.9e-05
                                       EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG-EECE CS
                      NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraasyev 40
                                       I+G+Gls +v+ + L+  g++vl ++++dr G   + y++
  gene3169|gene3169|rna3169|rna3169  8 ILGTGLSECVLSAVLSHSGYSVLHVDSSDRYGTSFQNYNY 47
                                       89*****************************988777765 PP

>> Nop14  Nop14-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4  18.2    0.0015       8.8     348     448 ..     305     415 ..     255     444 .. 0.45

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.0015
                              Nop14 348 eeededdfeedddlveseseeee..eeeeedeeeeedeeeee.eeeededdlsdlese.eeeeedeleeel..... 414
                                        ++e +++   d++ ++ + +  +  +++ +de+++++++e + +e  +++++ d++ + e+++e e +e++     
  gene3169|gene3169|rna3169|rna3169 305 GDESSKKGCGDESSKKGRGDGGSkdKKDRKDENNNTENDERNnNEIIENENKTDEKYKiEDKQEGECKEKEridgs 380
                                        2222222222221111111111111111111111111111111111222222222222333333333333332221 PP

                              Nop14 415 leeekkaaeekkekk.....kkkkkseekakeelpytfp 448
                                         +++ k+ae+    k     ++k+++++k+     +t++
  gene3169|gene3169|rna3169|rna3169 381 AKQNVKNAED----KddeplHSKNAEKNKKGPHYNFTVK 415
                                        3333333332....2344465555555555555666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (583 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1356  (0.0756317); expected 358.6 (0.02)
Passed bias filter:                      527  (0.0293937); expected 358.6 (0.02)
Passed Vit filter:                        89  (0.00496402); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.73u 0.30s 00:00:01.03 Elapsed: 00:00:00.46
# Mc/sec: 3788.62
//
Query:       gene317|gene317|rna317|rna317  [L=355]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.4e-28   96.5   4.1    1.5e-27   95.7   2.7    2.1  2  MMR_HSR1_Xtn     C-terminal region of MMR_HSR1 domain
      5e-19   68.5   0.4    1.5e-18   67.0   0.3    1.9  2  MMR_HSR1         50S ribosome-binding GTPase
    1.6e-17   63.3   0.5    4.9e-17   61.7   0.1    2.0  2  TGS              TGS domain
      2e-12   46.9   1.2      4e-12   45.9   0.3    1.9  2  FeoB_N           Ferrous iron transport protein B
  ------ inclusion threshold ------
      0.025   13.8   0.2      0.067   12.4   0.2    1.7  1  NB-ARC           NB-ARC domain
      0.026   14.7   0.7      0.079   13.2   0.1    2.2  2  Roc              Ras of Complex, Roc, domain of DAPkinase
      0.066   13.5   1.0       0.14   12.4   0.8    1.6  1  DUF3979          Protein of unknown function (DUF3979)
      0.073   13.3   0.5       0.25   11.6   0.0    2.1  2  AAA_28           AAA domain
       0.11   12.4   2.7       0.27   11.2   0.5    2.3  2  NTPase_1         NTPase
       0.16   11.2   0.0       0.27   10.5   0.0    1.3  1  Peptidase_M16_M  Middle or third domain of peptidase_M16
        6.5    6.9   8.8         20    5.3   1.5    3.0  3  DUF1192          Protein of unknown function (DUF1192)
          7    6.7   7.5        2.5    8.2   0.1    2.8  4  Dynamin_N        Dynamin family


Domain annotation for each model (and alignments):
>> MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.7   2.7     1e-30   1.5e-27       2     106 .]     183     280 ..     182     280 .. 0.95
   2 ?   -1.4   0.0       1.6   2.4e+03      34      59 ..     298     325 ..     294     327 .. 0.74

  Alignments for each domain:
  == domain 1  score: 95.7 bits;  conditional E-value: 1e-30
                   MMR_HSR1_Xtn   2 gGikitstvkltkldeetvkkilkeykihnaevliredvtvDdlidviegnrvYipclyvlNKiDlisleeldelarepn 81 
                                    gGi+i+s  +    +ee+++ ilke+ki+n+ v+i++++t +d+id+i++  vY+ c++v+NK+D +slee+++++    
  gene317|gene317|rna317|rna317 183 GGININSLEE---NNEEMIRFILKEFKINNCLVTIQDRITDEDMIDAITKRAVYMDCVFVYNKVDNLSLEEIKKIDG--- 256
                                    9****98855...89*********************************************************99866... PP

                   MMR_HSR1_Xtn  82 svviSaekelnldeLkekiweeLnL 106
                                     v iS+ek++n+d+Lk+ iw++L+L
  gene317|gene317|rna317|rna317 257 -VAISSEKGWNFDTLKDVIWRTLSL 280
                                    .89*******************987 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.6
                   MMR_HSR1_Xtn  34 vliredvtvDdlidviegnr..vYipcl 59 
                                    v+ir+d +v dl   i ++   +++ cl
  gene317|gene317|rna317|rna317 298 VIIRKDGKVSDLCKKIHKDFikKFKSCL 325
                                    8999999999999999764323777776 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.0   0.3   9.8e-22   1.5e-18       1     102 [.      65     166 ..      65     180 .. 0.84
   2 ?   -3.4   0.0       6.9     1e+04      46      58 ..     289     301 ..     274     326 .. 0.54

  Alignments for each domain:
  == domain 1  score: 67.0 bits;  conditional E-value: 9.8e-22
                                    EEEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSSHHHHHHHHHHHHHHHHC.TSEE CS
                       MMR_HSR1   1 evaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgkeielvDtpGliegaseekglgkaflalee.adli 79 
                                    +va++G p vGKStL++++t+++++++++ +tT d++ g+++++++ i+l+D+pG+i ga ++kg gk++ ++ + ++li
  gene317|gene317|rna317|rna317  65 RVALIGFPSVGKSTLFSKITNTQSKIAEHEFTTVDVIAGQLRIEESVIQLLDLPGIITGAASNKGRGKQVISVARtCNLI 144
                                    69*****************************************9***********9999*************99978999 PP

                                    EEEEETTTTCSHHHHHHHHHHHH CS
                       MMR_HSR1  80 llvvdaseeklkpldeeleelle 102
                                    ++v+  +ee+ + l +el+e+  
  gene317|gene317|rna317|rna317 145 VMVLT-KEEEKELLVNELNEMGI 166
                                    99998.53433334566666543 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 6.9
                                    EEEEEEECGGCSS CS
                       MMR_HSR1  46 keielvDtpGlie 58 
                                     e+  +Dtp +i 
  gene317|gene317|rna317|rna317 289 GEFPDLDTPVIIR 301
                                    4555677777664 PP

>> TGS  TGS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       1.7   2.5e+03      39      57 ..     207     225 ..     206     228 .. 0.80
   2 !   61.7   0.1   3.3e-20   4.9e-17       2      59 ..     282     353 ..     281     354 .. 0.98

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.7
                                    ECSEEEETTSBB-SSEEEE CS
                            TGS  39 VnGqrvgldhvLedgdvve 57 
                                    +n  +v +  ++ d+d + 
  gene317|gene317|rna317|rna317 207 INNCLVTIQDRITDEDMID 225
                                    67778999999*****986 PP

  == domain 2  score: 61.7 bits;  conditional E-value: 3.3e-20
                                    EEEE.TTSSEEE......EETTB-HHHHHHHHSTTHHHHEEEEEECS.......EEEETTSBB-SSEEEEEE CS
                            TGS   2 rvyt.PdGkvpd......lprgatveDfAykIhrslakkfiyAlVnG.......qrvgldhvLedgdvveIv 59 
                                    r+yt ++G+ pd      +++   v D+++kIh++++kkf+  lV+G       qrvgl+h L d+dvv+I 
  gene317|gene317|rna317|rna317 282 RIYTkKKGEFPDldtpviIRKDGKVSDLCKKIHKDFIKKFKSCLVWGrsvkhlpQRVGLNHLLSDEDVVQIY 353
                                    8*********************************************************************96 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.9   0.3   2.7e-15     4e-12       2     107 ..      65     167 ..      64     193 .. 0.79
   2 ?   -0.8   0.1      0.65   9.8e+02     124     153 ..     242     271 ..     186     274 .. 0.67

  Alignments for each domain:
  == domain 1  score: 45.9 bits;  conditional E-value: 2.7e-15
                                    EEEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEEEETTEEEEEEE----SSSSSSSHHHHHHHHHHH.CTSSS CS
                         FeoB_N   2 tvalvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegklklkgkeveivDlPGiYslsayseeekvardfll.eeepd 80 
                                    +val+G p vGk+tlf ++t++++k++ +  +tv+   g+l+++++ ++++DlPGi   +  ++++   ++++   ++ +
  gene317|gene317|rna317|rna317  65 RVALIGFPSVGKSTLFSKITNTQSKIAEHEFTTVDVIAGQLRIEESVIQLLDLPGII--TGAASNKGRGKQVISvARTCN 142
                                    69*****************************************************95..444555555566665155556 PP

                                    EEEEEEEGGGHHHHHHHHHHHHHTTSS CS
                         FeoB_N  81 vvvnvvdatnlernLyLtlqllelgvp 107
                                    ++v v+ +++ e++L L+ +l e+g++
  gene317|gene317|rna317|rna317 143 LIVMVL-TKEEEKEL-LVNELNEMGIR 167
                                    666655.44555655.56777777765 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.65
                                    EE-HHHHHHHHTS-EEEEBTTTTBTHHHHH CS
                         FeoB_N 124 eidlkkLsekLgvpvvktsakkkegieell 153
                                    ++d+ +L+e+ +++ v++s++k+ ++++l+
  gene317|gene317|rna317|rna317 242 KVDNLSLEEIKKIDGVAISSEKGWNFDTLK 271
                                    455555666666666666666666666655 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.2   4.5e-05     0.067      23      54 ..      66      98 ..      57     162 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4.5e-05
                                   EEEEESTTSSHHHHHHHHCCSHCCCCC.CBTEE CS
                         NB-ARC 23 valvGmgGvGKttlakqilnksdeveg.rFdsv 54
                                   val G + vGK+tl+++i n  +++ + +F  v
  gene317|gene317|rna317|rna317 66 VALIGFPSVGKSTLFSKITNTQSKIAEhEFTTV 98
                                   89******************9777655356443 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   5.3e-05     0.079       1      41 [.      65     105 ..      65     164 .. 0.88
   2 ?   -1.4   0.1       1.7   2.6e+03      98     119 ..     223     244 ..     201     245 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 5.3e-05
                                    EEEEESSTTSSHHHHHHCHCT-CCC-EEETTTTEEEEEEEC CS
                            Roc   1 KvvlvGdsgvGKtsllkrfvedkfsekekstigvdfltkev 41 
                                    +v l+G  +vGK++l++++++ + +  e++ + vd++  ++
  gene317|gene317|rna317|rna317  65 RVALIGFPSVGKSTLFSKITNTQSKIAEHEFTTVDVIAGQL 105
                                    589******************99999999988899887665 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.7
                                    HHHHHHHHCSSS-EEEEEE-TT CS
                            Roc  98 WlkelkkvagkspvilvgnkiD 119
                                     ++ ++k+a    +++v nk+D
  gene317|gene317|rna317|rna317 223 MIDAITKRAVYMDCVFVYNKVD 244
                                    4677888888888999999999 PP

>> DUF3979  Protein of unknown function (DUF3979)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.8   9.3e-05      0.14      16      87 ..     132     205 ..     121     217 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 9.3e-05
                        DUF3979  16 kyiiqerngkysivdelatekmsvelyfneydelritlykeeepivtvqria..iskvel.eedeesiqfvlerm 87 
                                    k +i   +    iv  + t++   el  ne +e+ i + + +  i+  q +a  i+   l e++ee i+f+l+ +
  gene317|gene317|rna317|rna317 132 KQVISVARTCNLIVM-VLTKEEEKELLVNELNEMGIRINRRKPRISINQTMAggININSLeENNEEMIRFILKEF 205
                                    556655555555554.55667788************9977665555445554334444556788999*****865 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.1         2   2.9e+03      28      65 ..      12      47 ..       4      56 .. 0.69
   2 ?   11.6   0.0   0.00017      0.25       1      30 [.      65      95 ..      65     115 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 2
                         AAA_28 28 pEaareileeklakgedalpwvedllafaervleeqle 65
                                   +E+ar+  ++ ++++ ++l++  ++ +++  ++e++ +
  gene317|gene317|rna317|rna317 12 EEIARTQKNKATERHIGHLKA--RISRLKLSMEEKKGK 47
                                   788888888888888888886..677777777766544 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00017
                         AAA_28  1 kivitGgestGKTtlleaLaargypvv.pEa 30
                                   +++++G +s GK+tl +++++++ ++  +E+
  gene317|gene317|rna317|rna317 65 RVALIGFPSVGKSTLFSKITNTQSKIAeHEF 95
                                   799****************998777665554 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.5   0.00018      0.27       2      99 ..      66     157 ..      65     184 .. 0.79
   2 ?    0.8   0.1      0.27     4e+02     109     148 ..     192     231 ..     185     251 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00018
                                    EEEE--TTSSHHHHHHHHHHHH...GGGEEEEEEEEE-------EEEEEET.T--EEEEEETT---SSEETTEEE-HHHH CS
                       NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvkvgGfyteevreggrrigFkivdlasgeegiLarveakreprvgkyvvdvesf 81 
                                    v++ G p vGK+Tl++k++++   s +  + f t +v  g+ ri  ++++l  +  gi+      ++   gk v+ v + 
  gene317|gene317|rna317|rna317  66 VALIGFPSVGKSTLFSKITNTQ--SKIAEHEFTTVDVIAGQLRIEESVIQL-LDLPGIITGAA--SNKGRGKQVISVART 140
                                    78899**************987..668888899999999999999999999.55566665555..667778888888888 PP

                                    HHHHHHHHHHHHHHH-EE CS
                       NTPase_1  82 eelalealrkalseadvi 99 
                                     +l++ +l+k+ +e++++
  gene317|gene317|rna317|rna317 141 CNLIVMVLTKE-EEKELL 157
                                    88888888875.455544 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.27
                                    GG-HHHHHHHHHHHTTTSEEEEE--SS-.-SHHHHHHHT-T CS
                       NTPase_1 109 lkskkfkeaveevLksekpvlavihrrk.dlalveeirerk 148
                                     + +++++ + + +k  ++ l++i+ r  d+++++ i +r+
  gene317|gene317|rna317|rna317 192 ENNEEMIRFILKEFKI-NNCLVTIQDRItDEDMIDAITKRA 231
                                    4444444444444443.457888988888999****99984 PP

>> Peptidase_M16_M  Middle or third domain of peptidase_M16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00018      0.27      35     132 ..     190     305 ..     186     319 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00018
                Peptidase_M16_M  35 leeydpelikellssLtpenarivlvsk.e.td......ekekwygteYsvekiseelleewksae.....eneeLhLPe 101
                                    lee ++e i+ +l++++++n+++++ ++ + +d      +++ +++  + ++k+++  lee+k+++      ++  ++ +
  gene317|gene317|rna317|rna317 190 LEENNEEMIRFILKEFKINNCLVTIQDRiTdEDmidaitKRAVYMDCVFVYNKVDNLSLEEIKKIDgvaisSEKGWNFDT 269
                                    67889***********************6561234455589999999998888888888888866556677778999999 PP

                Peptidase_M16_M 102 pNpFiptdfslk....keses.epakaPelirdtel 132
                                      + i +++slk    k++ +  + + P++ir++ +
  gene317|gene317|rna317|rna317 270 LKDVIWRTLSLKriytKKKGEfPDLDTPVIIRKDGK 305
                                    999999999999777644455577778888887755 PP

>> DUF1192  Protein of unknown function (DUF1192)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   1.5     0.013        20      25      44 ..       3      22 ..       2      26 .. 0.84
   2 ?    5.1   0.4     0.015        23      27      53 ..      25      51 ..      23      53 .. 0.88
   3 ?   -1.6   0.0         2     3e+03      18      27 ..     244     253 ..     241     254 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.013
                        DUF1192 25 LeerIalLeaEIaRleaaia 44
                                   +++ I++ e+EIaR+++  a
  gene317|gene317|rna317|rna317  3 IQDKITEIEEEIARTQKNKA 22
                                   6899**********998765 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.015
                        DUF1192 27 erIalLeaEIaRleaaiakkkasraAA 53
                                     I +L+a I Rl+  +++kk +  AA
  gene317|gene317|rna317|rna317 25 RHIGHLKARISRLKLSMEEKKGKAVAA 51
                                   5699****************9888777 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 2
                        DUF1192  18 slLSveELee 27 
                                    ++LS+eE+++
  gene317|gene317|rna317|rna317 244 DNLSLEEIKK 253
                                    89*****986 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.1       5.4     8e+03      67      80 ..       9      22 ..       4      49 .. 0.51
   2 ?    3.7   0.2     0.039        58       1      36 [.      66     101 ..      66     111 .. 0.82
   3 ?    8.2   0.1    0.0016       2.5      91     137 ..     100     149 ..      81     178 .. 0.75
   4 ?   -2.3   0.1       2.7     4e+03     112     146 ..     188     222 ..     187     242 .. 0.72

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 5.4
                                   HHHHHHHHHHHHHH CS
                      Dynamin_N 67 evreeieketekia 80
                                   e++eei + ++++a
  gene317|gene317|rna317|rna317  9 EIEEEIARTQKNKA 22
                                   44444433333333 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.039
                                    EEEEEBTTTTHHHHHHHHHTS--S---SSS---S-E CS
                      Dynamin_N   1 iavvGsqSsGKSSvlnaLlgedilprgpnptTrrpl 36 
                                    +a++G  S GKS++  +++  +    + + tT  ++
  gene317|gene317|rna317|rna317  66 VALIGFPSVGKSTLFSKITNTQSKIAEHEFTTVDVI 101
                                    7999***********999999888888888887666 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.0016
                                    EEEEEEETTS-SEEEEE---B-SSSGTTS...HHHHHHHSTTEEEEEEEE CS
                      Dynamin_N  91 illkilsllvkgltlvDlPGldsvnkrdq...elvkeyikkadiilavts 137
                                    ++   l + ++ + l+DlPG++  ++ ++   + v + ++ +++i++v+ 
  gene317|gene317|rna317|rna317 100 VIAGQLRIEESVIQLLDLPGIITGAASNKgrgKQVISVARTCNLIVMVLT 149
                                    4556677888899**********999998788777788877777777764 PP

  == domain 4  score: -2.3 bits;  conditional E-value: 2.7
                                    -SSSGTTSHHHHHHHSTTEEEEEEEETTS-CCC-C CS
                      Dynamin_N 112 dsvnkrdqelvkeyikkadiilavtsanhdlsnse 146
                                    +s +++++e+++ ++k+ +i  +++  +  +++ +
  gene317|gene317|rna317|rna317 188 NSLEENNEEMIRFILKEFKINNCLVTIQDRITDED 222
                                    56677777888888888888888887777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (355 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       892  (0.0497518); expected 358.6 (0.02)
Passed bias filter:                      561  (0.0312901); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.59u 0.32s 00:00:00.90 Elapsed: 00:00:00.48
# Mc/sec: 2237.80
//
Query:       gene3170|gene3170|rna3170|rna3170  [L=555]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      1e-22   80.9   0.4    3.2e-22   79.3   0.6    1.7  2  RIBIOP_C       40S ribosome biogenesis protein Tsr1 and BMS1 
  ------ inclusion threshold ------
       0.14   12.5   0.0       0.32   11.4   0.0    1.6  1  Ribosomal_S13  Ribosomal protein S13/S18


Domain annotation for each model (and alignments):
>> RIBIOP_C  40S ribosome biogenesis protein Tsr1 and BMS1 C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0      0.27   2.5e+03      11      28 ..     266     283 ..     261     299 .. 0.82
   2 !   79.3   0.6   3.5e-26   3.2e-22     128     291 ..     401     553 ..     374     554 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.27
                           RIBIOP_C  11 erfakyrglkslrtsewd 28 
                                        e f+ yrg+k l+t+++ 
  gene3170|gene3170|rna3170|rna3170 266 ESFKGYRGIKDLKTCTIH 283
                                        7899*********99875 PP

  == domain 2  score: 79.3 bits;  conditional E-value: 3.5e-26
                           RIBIOP_C 128 lifsvGfRrfqakPifsqedtknnkhklerylkpghtcvatfygpitfpntpvlafkelsskeasfrlvatGsvle 203
                                        +++++G+   ++ P f+ ++ ++++ kl+      ++ v++f  p+t++ntpv +f +  +     +lv   ++ +
  gene3170|gene3170|rna3170|rna3170 401 YTLEYGMFLHKVTPYFTMNT-SSSVFKLQDES--LKSGVVSFKVPYTPTNTPVKLFHA--Q-----KLVLSSNTYD 466
                                        56677777788999999999.58888887554..46699******************8..3.....5888888887 PP

                           RIBIOP_C 204 vdpsriivkrivLtGhpfkihkktaviryMFfnpedvawFkpveLrTksGrrGhIkeslgthGyfkatFddklkqs 279
                                         + +r+iv+  v++G+p+k +   + i++MF  ++dv +F+ v+L  + G  G I+ s+g +G fka F+ ++kq 
  gene3170|gene3170|rna3170|rna3170 467 HK-ERVIVEERVISGKPYKAYGTWCKIKNMFVCRDDVLFFRHVKLIGRGGNVGWIRSSVGVKGVFKAEFERPVKQG 541
                                        65.899999999**************************************************************** PP

                           RIBIOP_C 280 DiVlmslYkrvf 291
                                        D V m lY  v+
  gene3170|gene3170|rna3170|rna3170 542 DEVRMCLYRLVE 553
                                        ********8775 PP

>> Ribosomal_S13  Ribosomal protein S13/S18
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   3.6e-05      0.32      92     120 ..      78     106 ..      59     111 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3.6e-05
                      Ribosomal_S13  92 klredieRlkkirsyrGlRHkrGlkvRGQ 120
                                        +++ d+    +i +y G RH r +kvRG 
  gene3170|gene3170|rna3170|rna3170  78 TVSFDMGVSADIMCYEGTRHARRQKVRGT 106
                                        56667777789*****************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (555 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       464  (0.0258799); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 3865.12
//
Query:       gene3171|gene3171|rna3171|rna3171  [L=58]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (58 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       719  (0.0401026); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.22s 00:00:00.57 Elapsed: 00:00:00.38
# Mc/sec: 458.41
//
Query:       gene3172|gene3172|rna3172|rna3172  [L=114]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0046   16.8   0.3         10    6.3   0.0    3.2  3  MORN      MORN repeat
  ------ inclusion threshold ------
       0.14   12.7   0.1       0.21   12.1   0.1    1.2  1  Di19_C    Stress-induced protein Di19, C-terminal


Domain annotation for each model (and alignments):
>> MORN  MORN repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0     0.022   1.9e+02       9      17 ..      31      39 ..      26      40 .. 0.79
   2 !    6.3   0.0    0.0011        10       7      17 ..      46      56 ..      45      56 .. 0.89
   3 !    4.8   0.0    0.0032        28       7      17 ..      63      73 ..      62      76 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.022
                               MORN  9 krhGkGvyt 17
                                         hG+G+ t
  gene3172|gene3172|rna3172|rna3172 31 EEHGNGTRT 39
                                       57****986 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0011
                               MORN  7 nGkrhGkGvyt 17
                                       n+ +hG+G+ t
  gene3172|gene3172|rna3172|rna3172 46 NDEKHGNGTRT 56
                                       899*****986 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.0032
                               MORN  7 nGkrhGkGvyt 17
                                       n+  hG+G+ t
  gene3172|gene3172|rna3172|rna3172 63 NDEEHGNGTRT 73
                                       7899*****98 PP

>> Di19_C  Stress-induced protein Di19, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   2.4e-05      0.21      41      94 ..      41      94 ..      39      96 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.4e-05
                             Di19_C 41 nlptsdeeesskpessveessvkksseekvlersvdsslseeereekarrseFV 94
                                       n+pt+++e++ + +  +++ + + +++ + ++ +  ++l ++er++k++r+  V
  gene3172|gene3172|rna3172|rna3172 41 NFPTINDEKHGNGTRTENSPTINDEEHGNGTRTDNSPTLNDKERNKKTKRAMHV 94
                                       89****999999444444444444444444444444**************9887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (114 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       447  (0.0249317); expected 358.6 (0.02)
Passed bias filter:                      233  (0.0129957); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 808.44
//
Query:       gene3173|gene3173|rna3173|rna3173  [L=1522]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
       0.11   12.4   0.5        8.5    6.3   0.4    2.8  2  Crust_neurohorm  Crustacean CHH/MIH/GIH neurohormone family


Domain annotation for each model (and alignments):
>> Crust_neurohorm  Crustacean CHH/MIH/GIH neurohormone family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.4   0.00047       8.5      31      56 ..     579     606 ..     568     615 .. 0.79
   2 ?    2.7   0.0    0.0061   1.1e+02       3      18 ..    1186    1201 ..    1184    1204 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.00047
                    Crust_neurohorm  31 qlhrlCkkeCFtteyFkk..Cleallle 56 
                                        +++++C ++CF t +F+   C + ++ e
  gene3173|gene3173|rna3173|rna3173 579 SIRNICLRNCFGTLFFQDwpCFSKIMFE 606
                                        799*************965577777765 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.0061
                    Crust_neurohorm    3 eCkGkfdksifarldr 18  
                                         +C+Gkfd s   rld 
  gene3173|gene3173|rna3173|rna3173 1186 RCTGKFDLSETTRLDT 1201
                                         7*************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1522 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       593  (0.0330749); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.85u 0.29s 00:00:01.13 Elapsed: 00:00:00.48
# Mc/sec: 9485.42
//
Query:       gene3174|gene3174|rna3174|rna3174  [L=472]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
          1    9.8   4.2        1.1    9.7   0.8    2.5  2  Linker_histone  linker histone H1 and H5 family


Domain annotation for each model (and alignments):
>> Linker_histone  linker histone H1 and H5 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.8     6e-05       1.1      21      60 ..     214     253 ..     211     258 .. 0.83
   2 ?   -0.4   0.1     0.088   1.6e+03      33      60 ..     400     427 ..     395     429 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 6e-05
                     Linker_histone  21 sSrqaIkkyikakykvvdvskfksllkkalkkgvekgelv 60 
                                         Sr a++k+ ka++k ++++  k+ +kk  +k  +k+ ++
  gene3174|gene3174|rna3174|rna3174 214 LSRSAVQKFTKANNKNNETKTCKYIVKKLTRKSSKKEGFI 253
                                        69*************9555555999999999988887765 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.088
                     Linker_histone  33 kykvvdvskfksllkkalkkgvekgelv 60 
                                        ++ + + +++ +llk+ +k +++++ l 
  gene3174|gene3174|rna3174|rna3174 400 NHTIDQLKNIYKLLKQKIKDLCCSKLLR 427
                                        455534466699999*9*9999988775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (472 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1206  (0.0672653); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.30s 00:00:00.88 Elapsed: 00:00:00.49
# Mc/sec: 2920.54
//
Query:       gene3175|gene3175|rna3175|rna3175  [L=673]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
   2.7e-130  435.6   0.2   3.8e-130  435.1   0.2    1.2  1  Trehalase  Trehalase
  ------ inclusion threshold ------
      0.023   14.5   0.1      0.064   13.1   0.1    1.7  1  DUF2185    Protein of unknown function (DUF2185)
       0.22   11.8   0.8        6.5    7.1   0.0    2.8  3  Vps39_1    Vacuolar sorting protein 39 domain 1


Domain annotation for each model (and alignments):
>> Trehalase  Trehalase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  435.1   0.2  6.4e-134  3.8e-130      21     511 ..     130     611 ..     117     612 .. 0.92

  Alignments for each domain:
  == domain 1  score: 435.1 bits;  conditional E-value: 6.4e-134
                                        HHHHHHCHHCCHHEE..TTTTHHHHHHHHCE-SGGGS.EEE-TT-HHHHHHHHHHHCTGGHH.EECCHHCCTTCCC CS
                          Trehalase  21 llrlikaslekaltrridkedlkkfvedtfeetgselerivpkdekeqpeyflkkaedeelrleaeelnklwkalv 96 
                                        l + + + +  + t   + + l+kf++++fe++gs+l++   +d++++p+ fl+ + +e++r ++ eln+ wk+l 
  gene3175|gene3175|rna3175|rna3175 130 LVAYVMKLRP-ESTDAAKVHALQKFIDENFEAPGSDLTEHPLEDFQSEPP-FLSSITNENMRDVTLELNRMWKELS 203
                                        4444444444.4689999*******************99999********.9999********************* PP

                                        CHTTTS-SCE-TTECEEE-TT-EE-SBTTB-S-BCCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHSS--SBSB CS
                          Trehalase  97 rkikkkvgllpeassllplpkpfvVPGgRFrElYyWDsYfvilGLleskkvdlakgmvenfiyliekYGkilNgnR 172
                                        r    +v ++ ++s+ll lp+pf+VPGgRFrE+YyWD+Yf+ +GL++sk+ ++a ++++nf+++i++ G+i+Ng+R
  gene3175|gene3175|rna3175|rna3175 204 R---VAVVKKGHESTLLNLPHPFIVPGGRFREFYYWDTYFILEGLVVSKMDKTASNIIKNFMHIIDTLGYIPNGTR 276
                                        *...899999****************************************************************** PP

                                        GGGTT---S--HHHHHHHHHHHC...HCCHHHHHHHHHHHHHHHCCTTTCCETTCCC-C.TC-EEE--SSSTTS-T CS
                          Trehalase 173 sYYlsRSQPPlltdmvlrvyekt...eddallravlaalkkeyefwmaeqrldevtkls.kryllnrygvpeetpr 244
                                         YY+ RSQPP++  m+l++++       d +l + l+   key+f+  ++r++ v++ + k ++ln + v ++ pr
  gene3175|gene3175|rna3175|rna3175 277 KYYMYRSQPPFFPLMLLKLLDLNdgeYNDLILGKGLEMALKEYDFFD-KYRSVLVKGRDgKLHKLNYFHVTTDFPR 351
                                        *******************998777667889999************9.89998888877799************** PP

                                        CCCHHHHHHHHHCTTHCCHHHHHCCCCHHHHHCCHHCHHHHCCCCTT-S.TCCCCTGGGEE-HHHHHHHHHHHHHH CS
                          Trehalase 245 pesyledketaeklkkerkkeevyrelkaaaesgwdlssRwlresghdtgellelrtaklvpvDLNallyklekdi 320
                                        pes +ed +t+ + + +  + evy++lk++aesgwd+ssRw+++    ++ ++++++ + +pvDLNa+l++ e++i
  gene3175|gene3175|rna3175|rna3175 352 PESLSEDMHTYLSQQ-KLSEREVYSNLKSGAESGWDFSSRWFKD----ESDISTINAYNQIPVDLNAILFRDEQII 422
                                        *********999988.8999************************....5779************************ PP

                                        HHCCCHCC-CCHHHHHHHHHHHHHHHHHHHCEETTTTEE--EETTTTE.E----BGGGGHHHHCT-S-HHHHHHHH CS
                          Trehalase 321 aefedklgdsetseefeekaekrkkaidkvLWneeagvylDYdlkkkk.qtnyesatnlvpLwaglaskeqaaklv 395
                                        +++ +++g++ ++++f   + +r +ai++vLWn + + ++DYd++++k  +++++++n++pL +g+  +      +
  gene3175|gene3175|rna3175|rna3175 423 STLLKRAGKHDEARKFGDLSLRRMEAINQVLWNKDVNSWNDYDTENNKfVARRFYFSNVFPLIMGVEPPTG---NI 495
                                        *********************************************99736899**************9999...46 PP

                                        HHCHHHHCCCCCEESCCCC-SBSSS..-SSTTSTTEEEHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHC CS
                          Trehalase 396 akvlekleesgllvaegglgtsllk..sgrQWDyPngWaPlqilaveglerygeeelaerlaerwlktvtkafsde 469
                                         +vl+  +  +l ++ gg++ s+    +g+QWD+Pn+WaP+q l+ve+l + ge+++a ++a+ + ++v+  f+++
  gene3175|gene3175|rna3175|rna3175 496 YNVLQAYQ-RELFSYIGGVPVSGPGkdTGQQWDFPNVWAPHQFLIVEFLYNKGEHKMALQIARAFYNSVSTGFKQK 570
                                        66666555.4566669****9986556************************************************* PP

                                        TSEBSCEETTSTSTTBTT-SSSSTTCSBHHHHHHHHHHHCCH CS
                          Trehalase 470 gklvEKYdvtreaeygGgggeyvlqeGFGWvNgvvlelLell 511
                                        g+ +EKY++++ + +g  ggey++q+GFGW+Ng +l++++++
  gene3175|gene3175|rna3175|rna3175 571 GVFYEKYNAEQLGFTG-EGGEYAAQTGFGWTNGTALSFISKF 611
                                        **********777666.*********************9876 PP

>> DUF2185  Protein of unknown function (DUF2185)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   1.1e-05     0.064      25      75 ..     380     433 ..     369     441 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.1e-05
                            DUF2185  25 enDSGWrffa...gdesdeyindkenfgivdlntilniDpsiielleapigsaf 75 
                                           SGW f +    desd  + ++ n   vdln+il  D++ii+ l +  g + 
  gene3175|gene3175|rna3175|rna3175 380 GAESGWDFSSrwfKDESDISTINAYNQIPVDLNAILFRDEQIISTLLKRAGKHD 433
                                        478*****99444599999999**********************9998888765 PP

>> Vps39_1  Vacuolar sorting protein 39 domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       2.4   1.4e+04      35      59 ..     192     216 ..     188     217 .. 0.81
   2 ?    7.1   0.0    0.0011       6.5      45      68 ..     539     562 ..     534     580 .. 0.79
   3 ?    2.0   0.1      0.04   2.4e+02      43      82 ..     613     653 ..     603     673 .] 0.65

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 2.4
                            Vps39_1  35 iLkkekkykeLidlYygkklheeAL 59 
                                        +L+ ++++keL      kk he+ L
  gene3175|gene3175|rna3175|rna3175 192 TLELNRMWKELSRVAVVKKGHESTL 216
                                        5778899999999888888888766 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0011
                            Vps39_1  45 LidlYygkklheeALeLlkelade 68 
                                        ++++ y+k++h++AL++ + + ++
  gene3175|gene3175|rna3175|rna3175 539 IVEFLYNKGEHKMALQIARAFYNS 562
                                        589*************99988874 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.04
                            Vps39_1  43 keLidlYygkklheeALeLlkelade.deedeedsslkgek 82 
                                         +L + Y ++k+ +e +eLl + +++ +   ++++++kgek
  gene3175|gene3175|rna3175|rna3175 613 DQLAEAYDHQKEFKEIVELLAKKVNNeNLGPANKTNVKGEK 653
                                        5799999999*********9998887533334443333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (673 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       750  (0.0418317); expected 358.6 (0.02)
Passed bias filter:                      588  (0.032796); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.68u 0.30s 00:00:00.98 Elapsed: 00:00:00.47
# Mc/sec: 4316.54
//
Query:       gene3176|gene3176|rna3176|rna3176  [L=154]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       504  (0.0281109); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.32s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 976.13
//
Query:       gene3177|gene3177|rna3177|rna3177  [L=710]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.5e-91  303.0   0.0    1.8e-90  301.9   0.0    1.5  1  MCM           MCM P-loop domain
    1.7e-24   86.1   2.6    5.1e-24   84.5   2.6    1.9  1  MCM_lid       MCM AAA-lid domain
    3.9e-22   78.4   3.1    8.7e-22   77.3   3.1    1.6  1  MCM_OB        MCM OB domain
    9.8e-08   31.6   0.1    6.4e-06   25.7   0.0    2.5  2  Mg_chelatase  Magnesium chelatase, subunit ChlI
    5.8e-06   26.3   0.0    1.7e-05   24.8   0.0    1.9  1  AAA_5         AAA domain (dynein-related subfamily)
    8.8e-05   23.0   0.0    0.00051   20.6   0.0    2.3  1  MCM_N         MCM N-terminal domain
    0.00024   21.0   0.0    0.00053   19.8   0.0    1.6  1  AAA_3         ATPase family associated with various cellular 
     0.0035   16.9   0.1      0.011   15.2   0.1    2.0  1  HTH_24        Winged helix-turn-helix DNA-binding
  ------ inclusion threshold ------
      0.041   13.6   0.2       0.27   11.0   0.1    2.4  2  RuvB_N        Holliday junction DNA helicase RuvB P-loop doma
      0.056   13.8   0.3        9.9    6.5   0.0    3.6  4  AAA_16        AAA ATPase domain
       0.29   11.5   0.0       0.29   11.5   0.0    3.4  5  AAA           ATPase family associated with various cellular 


Domain annotation for each model (and alignments):
>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  301.9   0.0   1.1e-93   1.8e-90      13     224 .]     324     533 ..     320     533 .. 0.97

  Alignments for each domain:
  == domain 1  score: 301.9 bits;  conditional E-value: 1.1e-93
                                        THHHHHHHHSSTTSSS-HHHHHHHHHHHH---EBBBSSSSBBCSS-EEEEEESSTSTHHHHHHHHHHHSSSEEEEE CS
                                MCM  13 diieklvksiapsiyghedvkkaillqlfggvkkkledktklrgdinvllvgdpgtaKsqlLkyveklapravyts 88 
                                        + +e+++++iaps+ygh+dvkk+ill+++ggv+k++ +  +lrg+in+ll gdpg+aKsqlL +v+  + +++yts
  gene3177|gene3177|rna3177|rna3177 324 RRYERMAEMIAPSVYGHHDVKKGILLMMVGGVRKNHFN-CTLRGSINILLAGDPGVAKSQLLTFVN-QHTKGIYTS 397
                                        5699*****************************98877.99************************9.6789***** PP

                                        SSSSSSSHSSSEEEEESSSSSEEEEETHHHHTTTSEEEEESGGGSTCHHHHHHHHHHHHSEEEEESSSCEEEEE-- CS
                                MCM  89 gkgssaagLtaavvrdeetgefvleaGalvladkGvcciDefdkmkeedrsalhEamEqqtisiaKaGivatLnar 164
                                        g+gssa+gL a+v+rd etg+fvle+Galvl+d+Gvc+iDefdkm+++ r +lhEamEqq+isiaKaGi+++Ln r
  gene3177|gene3177|rna3177|rna3177 398 GQGSSAVGLSASVTRDVETGQFVLESGALVLSDHGVCIIDEFDKMNNHSRGVLHEAMEQQSISIAKAGIITSLNCR 473
                                        **************************************************************************** PP

                                        EEEEEEE--SSSSCCTTS-HHHHSSSSHHHHHHSSEEEEE-SSTTHHHHHHHHHHHHHHH CS
                                MCM 165 tsvlaAanpkagrydkkksvaeninlsaalLsrFDlifvllDkvdeekDeelaehivslh 224
                                        +s+la++np+++ +d+kks++en+nl+a+lLsrFDlif+llD+ d+e+De+ a++i++++
  gene3177|gene3177|rna3177|rna3177 474 CSILASCNPVNSVWDTKKSIIENVNLPATLLSRFDLIFILLDRNDKEQDERTARFIIDVY 533
                                        ********************************************************9875 PP

>> MCM_lid  MCM AAA-lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.5   2.6   3.1e-27   5.1e-24       3      87 .]     544     624 ..     542     624 .. 0.94

  Alignments for each domain:
  == domain 1  score: 84.5 bits;  conditional E-value: 3.1e-27
                                        HHHHHHHHHHTT--BETCHHHHHHHHHHHHHHHHHTSSTSSSST--HHHHHHHHHHHHHHHHHHTSSSE-HHHHHH CS
                            MCM_lid   3 lrkYiayarekikPklseeakeklseaYvelRkeeedskrksipitvRqLesliRLseAlAklrlsevvteedvee 78 
                                        l + ia ++  i P++s ea++++++ YvelR+ ++    ++i++t+RqLe++iRLseA+A++rlsevv++edv e
  gene3177|gene3177|rna3177|rna3177 544 LMECIAQSK-AIIPVISREAEKEIEDRYVELRSLNN---GNTITATTRQLEAIIRLSEAHARVRLSEVVEKEDVAE 615
                                        677799999.9**********************885...469********************************** PP

                                        HHHHHHHHH CS
                            MCM_lid  79 airllkesl 87 
                                        a+rl+kes+
  gene3177|gene3177|rna3177|rna3177 616 AVRLIKESM 624
                                        ******996 PP

>> MCM_OB  MCM OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.3   3.1   5.3e-25   8.7e-22       2     125 ..     133     252 ..     132     253 .. 0.89

  Alignments for each domain:
  == domain 1  score: 77.3 bits;  conditional E-value: 5.3e-25
                                        XGG--GGGTTSEEEEEEEEEEE---EEEEEEEEEEETTT-.-EEE.....S----SB-..TTT-HHH-EEE-GGGS CS
                             MCM_OB   2 lRdlrsehigklvkveGivtrasevkpklkkavfeckkcgktvev.....eleePrkCeekeCeskdpfkleteks 72 
                                        lR+l  ++i+k+v+++Giv+r+s+v p+l k ++ c++cgk+v +      ++eP  C   +C+s  +++l+ e+s
  gene3177|gene3177|rna3177|rna3177 133 LRKLCPSRIDKVVRIKGIVMRVSTVIPELIKGCYVCSSCGKSVVIekiknVIQEPGAC---DCGSFFSYSLSYERS 205
                                        79**************************************98887656544666****...9**999********* PP

                                        EEEEEEEEEEE-------------EEEEEEEGGGTT---TT-EEEEEEEEEEE CS
                             MCM_OB  73 kfvdfqklklQEspeevpaGelPrslevileddlvdkvkPGdrvevtGiyral 125
                                        ++ d+q +k+QE+  e    + P  ++v+   +++d+v PGdrve+ Gi++a 
  gene3177|gene3177|rna3177|rna3177 206 EYLDKQVVKIQEMESE----QEPMCFNVV--SYVIDRVMPGDRVEICGILKAA 252
                                        ************9876....567777665..789***************9875 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0     0.032        53      16      39 ..     361     384 ..     352     395 .. 0.83
   2 !   25.7   0.0   3.9e-09   6.4e-06      93     162 ..     417     486 ..     403     518 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.032
                       Mg_chelatase  16 eiaaaGgHnlllvGppGsGKtmla 39 
                                        + +  G+ n+ll+G pG  K+ l 
  gene3177|gene3177|rna3177|rna3177 361 NCTLRGSINILLAGDPGVAKSQLL 384
                                        56678999************9886 PP

  == domain 2  score: 25.7 bits;  conditional E-value: 3.9e-09
                       Mg_chelatase  93 ggskpkpGeislahnGvLfLDElpefkrkvlevLRePledgevtisrakakvefparfqlvaamNpcpcg 162
                                        g+   + G++ l+ +Gv ++DE+ +++++   vL e +e+++++i++a   ++  +r+ ++a+ Np  + 
  gene3177|gene3177|rna3177|rna3177 417 GQFVLESGALVLSDHGVCIIDEFDKMNNHSRGVLHEAMEQQSISIAKAGIITSLNCRCSILASCNPVNSV 486
                                        4447789***********************************************************9875 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.0   1.1e-08   1.7e-05       1     124 [.     369     484 ..     369     507 .. 0.84

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 1.1e-08
                                        EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--.HHHHH--B--.........--------G-SEEEEESGG CS
                              AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtt.eedlkgrreikngttslvdsplvraaregeilvlDEve 75 
                                        ++lL G+pG++Ks+l   + + ++  ++  q+++    ++ ++  +e   g+ +l+ ++lv       ++++DE++
  gene3177|gene3177|rna3177|rna3177 369 NILLAGDPGVAKSQLLTFVNQHTKGIYTSGQGSSAVGlSASVTRDVE--TGQFVLESGALV--LSDHGVCIIDEFD 440
                                        689********************999999999988872444555555..69999*******..9999********* PP

                                        G--HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS-- CS
                              AAA_5  76 raesevlnsLlslleerrllleeggelvkaknddllerfrviatanpld 124
                                        +++ +  ++L+  +e++ +++++ g  ++ +        +++a++np++
  gene3177|gene3177|rna3177|rna3177 441 KMNNHSRGVLHEAMEQQSISIAKAGIITSLNCR-----CSILASCNPVN 484
                                        ********************9998888877764.....89999999987 PP

>> MCM_N  MCM N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   3.1e-07   0.00051      21      86 ..      61     120 ..      48     157 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 3.1e-07
                              MCM_N  21 ekkYrdqlqemaerekttLevdlddLaafdeeLaeailenpkeylplleealkevvkklepsykdd 86 
                                        +k Y +++++m+  ++++L +d  dL+    +L +  +++p e++p+l+++l+e++ + eps+ + 
  gene3177|gene3177|rna3177|rna3177  61 DKHYQSRIRTMISLDQNSLFID--DLY----DLNQMCVNYPSEIIPILRKGLNEYILEKEPSFRQT 120
                                        689*****************96..886....5667899***********************98776 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   3.3e-07   0.00053       2     115 ..     370     485 ..     369     504 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 3.3e-07
                              AAA_3   2 vllegvPGlaktllvkalakaldlefkriqftpdllPsdilGtevfeekekefefkkGpvf...anllladeinra 74 
                                        +ll g PG+ak +l   + ++ +  ++  q  + +    +  +   + ++ +f +++G+++   + + + de ++ 
  gene3177|gene3177|rna3177|rna3177 370 ILLAGDPGVAKSQLLTFVNQHTKGIYTSGQGSSAVG---LSASVTRDVETGQFVLESGALVlsdHGVCIIDEFDKM 442
                                        79999********99999999999998888877653...333334567889*******987333359********* PP

                              AAA_3  75 ppktqsalleameerqvtvege..thklpepflvlatqnPieq 115
                                        + +++  l eame++ ++++++   ++l+    +la  nP+++
  gene3177|gene3177|rna3177|rna3177 443 NNHSRGVLHEAMEQQSISIAKAgiITSLNCRCSILASCNPVNS 485
                                        ****************9998662267999***********986 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1   6.9e-06     0.011       2      47 ..     654     699 ..     653     700 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 6.9e-06
                             HTH_24   2 detdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlI 47 
                                         e++++I ++L+k  r+ ++eLA ++g S   v++ +++L++e+ +
  gene3177|gene3177|rna3177|rna3177 654 EELKKRIQNVLKKRKRCKMAELATETGESERSVKEAVDELCDEEMV 699
                                        577889999**********************************987 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       3.1     5e+03      85      99 ..      76      90 ..      68      96 .. 0.79
   2 ?   11.0   0.1   0.00016      0.27      36     115 ..     370     461 ..     339     473 .. 0.71

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 3.1
                             RuvB_N 85 kdvlfideihrlsra 99
                                       ++ lfid+++ l+++
  gene3177|gene3177|rna3177|rna3177 76 QNSLFIDDLYDLNQM 90
                                       5679*****999986 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00016
                             RuvB_N  36 vllyGpPGlGkttlakiiakelgvklki...tsgPvl..ekagdlaa...lltn....leekdvlfideihrlsra 99 
                                        +ll+G PG+ k+ l + + +  +    +   +s+  l  + ++d+ +   +l +    l+++ v  ide  +++++
  gene3177|gene3177|rna3177|rna3177 370 ILLAGDPGVAKSQLLTFVNQHTKGIYTSgqgSSAVGLsaSVTRDVETgqfVLESgalvLSDHGVCIIDEFDKMNNH 445
                                        788888888888888888776654433311022222211223333221112322233388999************* PP

                             RuvB_N 100 veevlysamedfrldi 115
                                           vl+ ame  ++ i
  gene3177|gene3177|rna3177|rna3177 446 SRGVLHEAMEQQSISI 461
                                        ***********99987 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0      0.17   2.7e+02      33      54 ..     169     189 ..     165     224 .. 0.70
   2 ?    6.5   0.0    0.0061       9.9      26      47 ..     369     390 ..     358     420 .. 0.77
   3 ?   -1.1   0.0       1.4   2.2e+03     138     161 ..     433     456 ..     423     462 .. 0.81
   4 ?   -1.2   0.1       1.4   2.3e+03      85     127 ..     604     660 ..     502     675 .. 0.55

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.17
                             AAA_16  33 sGvGKsslvrellralekdggi 54 
                                        s +GKs +++++++ +++  g 
  gene3177|gene3177|rna3177|rna3177 169 SSCGKSVVIEKIKNVIQEP-GA 189
                                        689**********988888.33 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0061
                             AAA_16  26 lvllsGesGvGKsslvrellra 47 
                                        ++ll G++Gv Ks l++ + ++
  gene3177|gene3177|rna3177|rna3177 369 NILLAGDPGVAKSQLLTFVNQH 390
                                        799*************888853 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 1.4
                             AAA_16 138 vlvlDdlqwadeaslqllaaLlrl 161
                                        v ++D++++   +s+ +l + ++ 
  gene3177|gene3177|rna3177|rna3177 433 VCIIDEFDKMNNHSRGVLHEAMEQ 456
                                        889*********999998777765 PP

  == domain 4  score: -1.2 bits;  conditional E-value: 1.4
                             AAA_16  85 lldeaesaeleawrekleeala..avpelagaea............srllellkrll 127
                                        l +  e+ +++++ + ++e++   a+++l+g++             + +le+lk+ +
  gene3177|gene3177|rna3177|rna3177 604 LSEVVEKEDVAEAVRLIKESMLmyAIDPLTGKLDidlvmagrsagqRKMLEELKKRI 660
                                        111112222222222233333356444444444444444444444455555555555 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.1         5   8.2e+03      45      71 ..      67      88 ..      47      91 .. 0.62
   2 ?   -1.2   0.0       1.6   2.6e+03       9      49 ..     171     218 ..     169     226 .. 0.74
   3 ?   11.5   0.0   0.00018      0.29       1      77 [.     370     449 ..     370     483 .. 0.74
   4 ?   -1.3   0.5       1.6   2.6e+03      60      99 ..     591     635 ..     541     672 .. 0.48
   5 ?   -1.9   0.1       2.5   4.1e+03      44      52 ..     658     666 ..     601     701 .. 0.65

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 5
                                       HHHHHHHHHHHTSTSEEEEEETGGGHH CS
                                AAA 45 kirelfkeakekakpsilfiDEidala 71
                                       +ir +++   +      lfiD+++ l+
  gene3177|gene3177|rna3177|rna3177 67 RIRTMISL-DQ----NSLFIDDLYDLN 88
                                       44444432.33....449999998775 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.6
                                        SSHHHHHHHHHHHHT.......HEEEEEETTTCSSSSTTHHHHHHHHH CS
                                AAA   9 tGKTllakavakelg.......vefleisgsellskyvgesekkirel 49 
                                        +GK+ +++ + + ++        +f++ s+s  +s+y+ ++  ki+e+
  gene3177|gene3177|rna3177|rna3177 171 CGKSVVIEKIKNVIQepgacdcGSFFSYSLSYERSEYLDKQVVKIQEM 218
                                        899999998888875333334455999999999999988888888776 PP

  == domain 3  score: 11.5 bits;  conditional E-value: 0.00018
                                        EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHH...HHTS....TSEEEEEETGGG CS
                                AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkea...keka....kpsilfiDEida 69 
                                        +ll G pG+ K+ l   v ++++  + + +gs+ +    g s++ +r++ +     ++ a    ++ + +iDE+d+
  gene3177|gene3177|rna3177|rna3177 370 ILLAGDPGVAKSQLLTFVNQHTKGIYTSGQGSSAV----GLSASVTRDVETGQfvlESGAlvlsDHGVCIIDEFDK 441
                                        69*******************99988888888888....444444444433321114444778778********** PP

                                        HHHHHTTC CS
                                AAA  70 laksrsgs 77 
                                        ++++++g 
  gene3177|gene3177|rna3177|rna3177 442 MNNHSRGV 449
                                        *9988333 PP

  == domain 4  score: -1.3 bits;  conditional E-value: 1.6
                                        EEEEEETGGGHHHHH.....TTCCCHHHHHHHHHHHHHHHHTTTS CS
                                AAA  60 silfiDEidalaksr.....sgseseeeervvnqLlteldgvkkk 99 
                                         i+ + E++a ++ +     ++ ++ ++    + L+ ++d ++ k
  gene3177|gene3177|rna3177|rna3177 591 AIIRLSEAHARVRLSevvekEDVAEAVRLIKESMLMYAIDPLTGK 635
                                        666666666666655333222222222222233444444444443 PP

  == domain 5  score: -1.9 bits;  conditional E-value: 2.5
                                        HHHHHHHHH CS
                                AAA  44 kkirelfke 52 
                                        k+i++++k+
  gene3177|gene3177|rna3177|rna3177 658 KRIQNVLKK 666
                                        333333332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (710 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       991  (0.0552736); expected 358.6 (0.02)
Passed bias filter:                      596  (0.0332422); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.72u 0.30s 00:00:01.02 Elapsed: 00:00:00.48
# Mc/sec: 4484.27
//
Query:       gene3178|gene3178|rna3178|rna3178  [L=189]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.21   12.0   2.5       0.81   10.1   0.2    2.2  2  Ycf70     Uncharacterized Ycf70-like


Domain annotation for each model (and alignments):
>> Ycf70  Uncharacterized Ycf70-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.2     0.021   3.8e+02      45      56 ..       2      13 ..       1      20 [. 0.81
   2 ?   10.1   0.2   4.5e-05      0.81      34      84 ..     108     157 ..      93     160 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.021
                              Ycf70 45 lvlfiffdsfkq 56
                                       +vlf+ff sf +
  gene3178|gene3178|rna3178|rna3178  2 VVLFLFFVSFAR 13
                                       799****99975 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 4.5e-05
                              Ycf70  34 vsglyalfcvflvlfiffdsfkqesnklelsgkeekkklngenrlsrdiqn 84 
                                         +g+y+++ v+l + i++  +      ++l  ke + k++ + ++sr i +
  gene3178|gene3178|rna3178|rna3178 108 CAGFYSILHVLLTINIYYYNYMTT-AAVKLVKKELREKMEHNFKISRHIFK 157
                                        689***************999765.578999****************9965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (189 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1085  (0.0605165); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.30s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1260.92
//
Query:       gene3179|gene3179|rna3179|rna3179  [L=940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (940 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       699  (0.0389871); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.69u 0.30s 00:00:00.99 Elapsed: 00:00:00.47
# Mc/sec: 6024.56
//
Query:       gene318|gene318|rna318|rna318  [L=694]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.8e-85  283.9   0.0    8.9e-85  283.3   0.0    1.3  1  MCM           MCM P-loop domain
    6.9e-21   74.4   4.0    1.2e-20   73.6   4.0    1.3  1  MCM_OB        MCM OB domain
    8.6e-18   64.6   0.3    1.8e-17   63.5   0.3    1.6  1  MCM_lid       MCM AAA-lid domain
    1.9e-06   27.4   0.1    0.00011   21.7   0.0    2.3  2  Mg_chelatase  Magnesium chelatase, subunit ChlI
    0.00017   21.6   0.3     0.0016   18.4   0.0    2.7  2  AAA_5         AAA domain (dynein-related subfamily)
      0.006   17.1   0.1       0.02   15.5   0.1    2.0  1  MCM_N         MCM N-terminal domain
  ------ inclusion threshold ------
       0.16   11.9   0.0       0.52   10.2   0.0    1.9  2  AAA_lid_2     AAA lid domain


Domain annotation for each model (and alignments):
>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  283.3   0.0   3.5e-88   8.9e-85       4     224 .]     309     529 ..     306     529 .. 0.98

  Alignments for each domain:
  == domain 1  score: 283.3 bits;  conditional E-value: 3.5e-88
                                    HHHHHHTSSTHHHHHHHHSSTTSSS-HHHHHHHHHHHH---EBBBSSSSBBCSS-EEEEEESSTSTHHHHHHHHHHHSSS CS
                            MCM   4 eikelakekdiieklvksiapsiyghedvkkaillqlfggvkkkledktklrgdinvllvgdpgtaKsqlLkyveklapr 83 
                                    +++e+ +++  +++l++s+ap+iyg+ dvkk +ll+l+g+ + ++ d++++rgd nv+l+gdpg+aKs+lLky+  la r
  gene318|gene318|rna318|rna318 309 DVTEIDRTNYSVQNLMASFAPHIYGMYDVKKILLLMLIGSPSITKADGMRIRGDLNVMLMGDPGIAKSELLKYCIGLARR 388
                                    67899999999********************************************************************* PP

                                    EEEEESSSSSSSHSSSEEEEESSSSSEEEEETHHHHTTTSEEEEESGGGSTCHHHHHHHHHHHHSEEEEESSSCEEEEE- CS
                            MCM  84 avytsgkgssaagLtaavvrdeetgefvleaGalvladkGvcciDefdkmkeedrsalhEamEqqtisiaKaGivatLna 163
                                    +vyt g+gss++gLta+v rd+ t+efvleaGalvl+d+G+cc+De+dkm+e+dr +lhE++Eqq+isi+KaGi++ Lna
  gene318|gene318|rna318|rna318 389 GVYTAGRGSSGVGLTASVLRDPFTKEFVLEAGALVLSDRGICCLDEMDKMDENDRLSLHEVLEQQSISINKAGINVRLNA 468
                                    ******************************************************************************** PP

                                    -EEEEEEE--SSSSCCTTS-HHHHSSSSHHHHHHSSEEEEE-SSTTHHHHHHHHHHHHHHH CS
                            MCM 164 rtsvlaAanpkagrydkkksvaeninlsaalLsrFDlifvllDkvdeekDeelaehivslh 224
                                    r+ vl Aan k+g yd+kks+++n  l+ +l+srFD+i +l+D++de++D+elae++ ++h
  gene318|gene318|rna318|rna318 469 RCCVLGAANFKKGFYDDKKSLEHNTGLPVSLISRFDVIAILRDEKDESRDRELAEYVARQH 529
                                    ********************************************************98876 PP

>> MCM_OB  MCM OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.6   4.0   4.8e-24   1.2e-20       2     124 ..     132     259 ..     131     261 .. 0.88

  Alignments for each domain:
  == domain 1  score: 73.6 bits;  conditional E-value: 4.8e-24
                                    XGG--GGGTTSEEEEEEEEEEE---EEEEEEEEEEETTT-.-EEES---.....-SB-..TTT-...HHH-EEE-GGGSE CS
                         MCM_OB   2 lRdlrsehigklvkveGivtrasevkpklkkavfeckkcgktvevelee.....PrkCeekeCe...skdpfkleteksk 73 
                                    +R lrs+++g++v+ +Givt++s+++p++k av+ c++cg+++  ++++        C++++C+    +++++l t+ sk
  gene318|gene318|rna318|rna318 132 IRMLRSDKVGHFVTTRGIVTKVSHTRPSIKVAVYVCDSCGSETYQQVNNqeftlLAVCQSEKCKtmkIRGTLSLITRVSK 211
                                    79**************************************97775555534444559*******5433459********* PP

                                    EEEEEEEEEE-------------EEEEEEEGGGTT---TT-EEEEEEEEEE CS
                         MCM_OB  74 fvdfqklklQEspeevpaGelPrslevileddlvdkvkPGdrvevtGiyra 124
                                    f  f ++ lQE++++ p+G +Pr +++ ++d    +v+PGd + v G++ a
  gene318|gene318|rna318|rna318 212 FEPFVSVCLQEMQGDTPEGCIPRVINIEMKDA---EVRPGDCIYVCGVLMA 259
                                    *****************************996...789**********976 PP

>> MCM_lid  MCM AAA-lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.5   0.3     7e-21   1.8e-17       2      86 ..     546     622 ..     545     623 .. 0.95

  Alignments for each domain:
  == domain 1  score: 63.5 bits;  conditional E-value: 7e-21
                                    HHHHHHHHHHHTT--BETCHHHHHHHHHHHHHHHHHTSSTSSSST--HHHHHHHHHHHHHHHHHHTSSSE-HHHHHHHHH CS
                        MCM_lid   2 llrkYiayarekikPklseeakeklseaYvelRkeeedskrksipitvRqLesliRLseAlAklrlsevvteedveeair 81 
                                     l+ +i+ a+ +++P++  + +e ++ aY   R++ e       + t+R L sliRLs A+A+lrlse+v+eedvee +r
  gene318|gene318|rna318|rna318 546 DLKTFIQKAK-TLNPRIPSHLNERIVGAYTAARDKYE-------RLTPRFLLSLIRLSMAHARLRLSEEVNEEDVEESVR 617
                                    599*******.***********************874.......69********************************** PP

                                    HHHHH CS
                        MCM_lid  82 llkes 86 
                                    ll+ s
  gene318|gene318|rna318|rna318 618 LLEVS 622
                                    *9976 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0     0.018        47      12      41 ..     352     381 ..     342     388 .. 0.77
   2 !   21.7   0.0   4.2e-08   0.00011      98     159 ..     418     479 ..     413     494 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.018
                   Mg_chelatase  12 kraleiaaaGgHnlllvGppGsGKtmlakr 41 
                                     +a  + + G  n++l+G pG  K+ l k 
  gene318|gene318|rna318|rna318 352 TKADGMRIRGDLNVMLMGDPGIAKSELLKY 381
                                    556666678999************988765 PP

  == domain 2  score: 21.7 bits;  conditional E-value: 4.2e-08
                   Mg_chelatase  98 kpGeislahnGvLfLDElpefkrkvlevLRePledgevtisrakakvefparfqlvaamNpc 159
                                    + G++ l+ +G+  LDE+ +++++   +L e le+++++i++a  +v+  ar+ ++ a+N  
  gene318|gene318|rna318|rna318 418 EAGALVLSDRGICCLDEMDKMDENDRLSLHEVLEQQSISINKAGINVRLNARCCVLGAANFK 479
                                    67999******************************************************975 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   6.4e-07    0.0016       1     121 [.     364     477 ..     364     493 .. 0.80
   2 ?   -0.9   0.0       0.6   1.5e+03      61      76 ..     643     661 ..     573     689 .. 0.65

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 6.4e-07
                                    EEEEE--SSSSHHHHHHHGGGGB.S--EEEEE--T..T--HHHHH--B--.........--------G-SEEEEESGGG- CS
                          AAA_5   1 dvlLvGppGtgKselaerlaaal.nreveyvqltr..dtteedlkgrreikngttslvdsplvraaregeilvlDEvera 77 
                                    +v+L G+pG++Ksel ++   +  +  ++   +++  ++t++ l+ +     ++ +l+ ++lv       i++lDE +++
  gene318|gene318|rna318|rna318 364 NVMLMGDPGIAKSELLKYCIGLArRGVYTAGRGSSgvGLTASVLRDPFT---KEFVLEAGALV--LSDRGICCLDEMDKM 438
                                    69****************9999954445555555522356777777776...78899999999..88999********** PP

                                    -HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEES CS
                          AAA_5  78 esevlnsLlslleerrllleeggelvkaknddllerfrviatan 121
                                    + +   sL+ +le++ +++++ g  v+ ++        v+++an
  gene318|gene318|rna318|rna318 439 DENDRLSLHEVLEQQSISINKAGINVRLNAR-----CCVLGAAN 477
                                    ******************9999888877664.....55555555 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.6
                                    ----...G-SEEEEESGGG CS
                          AAA_5  61 raar...egeilvlDEver 76 
                                    + ++   +g++l+l++v r
  gene318|gene318|rna318|rna318 643 QIMKmktSGRTLRLEDVVR 661
                                    2222445677777777665 PP

>> MCM_N  MCM N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.1   7.7e-06      0.02       5      99 ..      22     119 ..      18     124 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 7.7e-06
                          MCM_N   5 edFLeefkddsededgekkYrdqlqemaerekttLevdlddLaafdeeLaeailenpkeylplleealkevvkklep... 81 
                                     +F+  f    +d+++e+kY++++ +      + + +dl+d+a +d  L++++++n   yl +l e ++ v    +    
  gene318|gene318|rna318|rna318  22 SSFIHFF----TDNNNEPKYLNMISH------KKIALDLNDIAIHDHMLVNRLRSNFMTYLRMLYEIIDGVNTPSDVami 91 
                                    5688877....577899******998......99*********************************9988643333333 PP

                          MCM_N  82 sykdd............a.kefpaeltrrfq 99 
                                        +            a k+fp+ l+r++ 
  gene318|gene318|rna318|rna318  92 H---RlermkekypgvdAaKKFPPALMRDYV 119
                                    0...133334456555424777777777775 PP

>> AAA_lid_2  AAA lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       4.1     1e+04      39      63 ..     412     437 ..     408     444 .. 0.66
   2 ?   10.2   0.0    0.0002      0.52      20      49 ..     589     618 ..     583     631 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 4.1
                      AAA_lid_2  39 tpeDvkeaaplVLaHRlr.repeaeg 63 
                                    t+e v ea  lVL+ R +    e+++
  gene318|gene318|rna318|rna318 412 TKEFVLEAGALVLSDRGIcCLDEMDK 437
                                    66778889999999997764444444 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0002
                      AAA_lid_2  20 lallraArAlAalegrdyVtpeDvkeaapl 49 
                                    l l+r + A+A l+  ++V++eDv+e ++l
  gene318|gene318|rna318|rna318 589 LSLIRLSMAHARLRLSEEVNEEDVEESVRL 618
                                    789**********************97765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (694 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       644  (0.0359195); expected 358.6 (0.02)
Passed bias filter:                      476  (0.0265492); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.63u 0.26s 00:00:00.89 Elapsed: 00:00:00.43
# Mc/sec: 4800.99
//
Query:       gene3180|gene3180|rna3180|rna3180  [L=949]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (949 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       624  (0.0348039); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.71u 0.23s 00:00:00.94 Elapsed: 00:00:00.42
# Mc/sec: 6767.43
//
Query:       gene3181|gene3181|rna3181|rna3181  [L=174]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
       0.19   12.5   0.4       0.19   12.5   0.4    2.3  3  Occludin_ELL  Occludin homology domain
       0.29   11.6   4.2       0.81   10.2   1.8    2.0  2  DUF2115       Uncharacterized protein conserved in archaea (D


Domain annotation for each model (and alignments):
>> Occludin_ELL  Occludin homology domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.1      0.29   2.6e+03      84      94 ..      15      25 ..       5      39 .. 0.55
   2 ?   12.5   0.4   2.1e-05      0.19       4      43 ..      46      85 ..      43     104 .. 0.85
   3 ?   -1.5   0.0      0.47   4.2e+03      40      40 ..     135     135 ..      98     156 .. 0.54

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.29
                       Occludin_ELL 84 yLkekLshiKk 94
                                       +Lk+ L+ +K+
  gene3181|gene3181|rna3181|rna3181 15 HLKSSLEALKQ 25
                                       34444444443 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 2.1e-05
                       Occludin_ELL  4 IksaeqrerYkaeFnkeYkeYkelhaeleevskkfseLer 43
                                       I++++qr r  +eFn  Y++Yk+  ++ ++++  +++  +
  gene3181|gene3181|rna3181|rna3181 46 INTTKQRPRHVEEFNMLYNSYKSYVKSRNNINTMIERAAS 85
                                       899********************99999999888776654 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 0.47
                       Occludin_ELL  40 e 40 
                                        +
  gene3181|gene3181|rna3181|rna3181 135 R 135
                                        1 PP

>> DUF2115  Uncharacterized protein conserved in archaea (DUF2115)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   1.8   9.1e-05      0.81      15     106 ..       3      93 ..       1      97 [. 0.71
   2 ?    2.0   0.0      0.03   2.7e+02      72     114 ..     126     170 ..     101     171 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 9.1e-05
                            DUF2115  15 kisieDlmkisarlekeikklpekyrkelseslteylfeaykelknkrsgdkseykeevideeelkeflemleeqc 90 
                                        ++s + l+  +++l+ +++ l+++y  ++++++ + +   +  + + ++++ ++ +e ++  +++k++++  ++  
  gene3181|gene3181|rna3181|rna3181   3 RFSAQSLETYNTHLKSSLEALKQNYAPSYHQETKDLITACIDLINT-TKQRPRHVEEFNMLYNSYKSYVKSRNNIN 77 
                                        68999999***********************988866555555555.44444555556666677777776666655 PP

                            DUF2115  91 eeekeekeerlrklyy 106
                                        +  ++  ++r  k+y+
  gene3181|gene3181|rna3181|rna3181  78 TMIERAASNRNDKMYR 93 
                                        5555555666666665 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.03
                            DUF2115  72 evideeelkeflemleeqceeekeek..eerlrklyylvslYliF 114
                                          ++++++++  ++++ +++++ke+k  ++ +  +    +lY+iF
  gene3181|gene3181|rna3181|rna3181 126 MDMNRDTMRRSNDEMKVTMRRRKESKmwKQVFGIMLVFCVLYCIF 170
                                        446777788888888888887777666666666666667777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1378  (0.0768587); expected 358.6 (0.02)
Passed bias filter:                      657  (0.0366445); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 1370.95
//
Query:       gene3182|gene3182|rna3182|rna3182  [L=209]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1051  (0.0586201); expected 358.6 (0.02)
Passed bias filter:                      494  (0.0275531); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 1585.14
//
Query:       gene3183|gene3183|rna3183|rna3183  [L=712]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.7e-13   49.6   0.5    1.5e-11   44.4   0.5    2.8  1  Sec23_trunk     Sec23/Sec24 trunk domain
    4.2e-11   42.7   3.1      1e-10   41.5   2.0    2.2  2  zf-Sec23_Sec24  Sec23/Sec24 zinc finger
    2.8e-06   28.0   0.0    2.9e-05   24.7   0.0    2.3  1  Sec23_BS        Sec23/Sec24 beta-sandwich domain
     0.0016   18.3   0.0     0.0033   17.3   0.0    1.4  1  Gelsolin        Gelsolin repeat
  ------ inclusion threshold ------
      0.017   14.9   0.0      0.039   13.8   0.0    1.6  1  Sec23_helical   Sec23/Sec24 helical domain


Domain annotation for each model (and alignments):
>> Sec23_trunk  Sec23/Sec24 trunk domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.4   0.5   4.1e-15   1.5e-11       4     232 ..     130     325 ..     127     336 .. 0.87

  Alignments for each domain:
  == domain 1  score: 44.4 bits;  conditional E-value: 4.1e-15
                                        -EEEEEEE-SHHHHHHTHHHHHHHHHHHHCTTSSTSTT-EEEEEEESSSEEEEETSTTSSSSEEEEECHTTSCCSS CS
                        Sec23_trunk   4 pvflFviDvsleaikegelkalkeslkqsLdllPeepralvglitfdsvvhffelkselrqpkelvvsdlqdvflp 79 
                                          ++Fv+  +++a k g + +++++l+ ++  l    +a+vg++ + +++ +       +    lvvsd + + l 
  gene3183|gene3183|rna3183|rna3183 130 CSYVFVVECTADAYKRGVVSSVCNTLRANVHCLG---SARVGVVFYAKTLCIV------ARGGALVVSDFEHLPLF 196
                                        57*******************************9...9***********9764......455689*****988787 PP

                                        TSSSSSEETTTTHHHHHHHHHHHHHHSTT-TTC-----HHHHHHHHHHHHCHCTS-EEEEEEESS---SSTTTSS- CS
                        Sec23_trunk  80 ladrlLvplseseavledlLeelpemfavtagkrperalgpalkaavellkavetggkiivfvgslptvgaggklk 155
                                          d++L ++ +++ +le++ e l +  +v+        +g +l++ + +l+  ++gg +++f +s p+ g      
  gene3183|gene3183|rna3183|rna3183 197 NMDDILFDA-QCMPELESTAEFLGRDASVH------CDFGGVLRVVHAMLG--TSGGSVVAFLSSVPNTGK----- 258
                                        889999997.69999999999988755555......779************..889**************9..... PP

                                        SBTTSCCTSSTTCHHCHSCSSSCHHHHHHHHHHHCTEEEEEEEECSS--SHHHHTHHHHTTT-EEEEETTTCCHHH CS
                        Sec23_trunk 156 sredeslldidkekaklvkkadkfYkkLakecvkqgisvDlFlfsldyvdlaelkqlaeltgGqvvlydsFsaekd 231
                                             sl +    + + ++++++ Yk++a  ++k  is+  ++fs    dl +l+ l+++tgG + ++++F a+  
  gene3183|gene3183|rna3183|rna3183 259 ----ASLAG----QPASLRCKNEYYKTMAAAFSKCNISLSYYVFSCRNADLPSLSLLSRFTGGFLAYFPNFDAN-- 324
                                        ....44445....3344667777************************************************933.. PP

                                        H CS
                        Sec23_trunk 232 a 232
                                         
  gene3183|gene3183|rna3183|rna3183 325 D 325
                                        3 PP

>> zf-Sec23_Sec24  Sec23/Sec24 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.5   2.0   2.8e-14     1e-10       2      35 ..      46      79 ..      45      82 .. 0.95
   2 ?   -1.6   0.0      0.81   2.9e+03      14      30 ..     318     334 ..     313     339 .. 0.78

  Alignments for each domain:
  == domain 1  score: 41.5 bits;  conditional E-value: 2.8e-14
                     zf-Sec23_Sec24  2 irCrrCraylNpfckidfggkrwiCnfCnhknev 35
                                       irC++Cr y+ p+c++   g +w+C +C h n v
  gene3183|gene3183|rna3183|rna3183 46 IRCTKCRGYISPYCEVLSPGEQWRCALCRHLNVV 79
                                       9*******************************87 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.81
                     zf-Sec23_Sec24  14 fckidfggkrwiCnfCn 30 
                                        f ++d + +++ C + +
  gene3183|gene3183|rna3183|rna3183 318 FPNFDANDRTFSCRLDE 334
                                        56799999*****8755 PP

>> Sec23_BS  Sec23/Sec24 beta-sandwich domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.0   8.1e-09   2.9e-05       1      95 [.     345     481 ..     345     482 .. 0.94

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 8.1e-09
                                        EEEEEEEEEE-TTEEEEEEESSSEECSTBESSEESECSESEEEEEEEETT--EEEEEEE................. CS
                           Sec23_BS   1 gfnatlevrtSkelkvsgliGncvslsnvsekeiGeggtsewklcsldpdstlavyfdi................. 59 
                                        +++++l+vr S+ +++ +++Gn++ +          ++   ++lc+++  +++++ f++                 
  gene3183|gene3183|rna3183|rna3183 345 AYEGVLRVRGSN-VQIVDYFGNFHLRA---------SDV--LSLCAVNFGHSITFGFKMnegvaeqstrnsakddl 408
                                        699******996.7************9.........899..9********************************** PP

                                        .....................................SSBTCTTSEEEEEEEEEEEETTSEEEEEEEEEEEEE CS
                           Sec23_BS  60 .....................................deklksgkqayiQfatlYthssgerrlRVttvalpv 95 
                                                                             +  + +++ +++Q+a++Y+++ g+rrlR  ++ +pv
  gene3183|gene3183|rna3183|rna3183 409 savnkilneisendacglsctddeladdggdktafvnNFLVGADDWVVFQVALMYSDERGSRRLRTNNFVVPV 481
                                        ********************************99986333667799***********************9998 PP

>> Gelsolin  Gelsolin repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   9.1e-07    0.0033       7      39 ..     587     621 ..     583     629 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 9.1e-07
                                        EBSSSGGGEETTSEEEEEESSEEEEEEHTT..SHH CS
                           Gelsolin   7 vvklsssslesgdcyLLdngftiflWiGke..ssq 39 
                                          +ls +sle ++ y+Ld+g+++f+++G++   ++
  gene3183|gene3183|rna3183|rna3183 587 RKELSLDSLEIDGFYVLDAGYNLFFFVGAGvdTNP 621
                                        56899************************975444 PP

>> Sec23_helical  Sec23/Sec24 helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   1.1e-05     0.039      57     101 ..     527     571 ..     499     573 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.1e-05
                                        GGGTTHHHHHHHHHTSTTTS--TT--HHHHHHHHHHHHH--HHHH CS
                      Sec23_helical  57 eslklLPlyilallKspafrggnsvpaDervfalslllslpvdql 101
                                        ++l  + +++l++ Ks ++r++  +p D r+f+  l+l+ p++ +
  gene3183|gene3183|rna3183|rna3183 527 KCLGNMGRLMLSIKKSVVLRPVLYTPMDYRAFYVYLVLTSPLRLI 571
                                        457778899******************************999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (712 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       406  (0.0226449); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.58u 0.26s 00:00:00.84 Elapsed: 00:00:00.41
# Mc/sec: 5173.23
//
Query:       gene3184|gene3184|rna3184|rna3184  [L=888]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-37  129.5   0.0    2.7e-36  124.9   0.0    2.4  2  AAA              ATPase family associated with various cellul
    5.2e-07   29.7   0.0    0.00029   20.9   0.0    2.7  2  AAA_5            AAA domain (dynein-related subfamily)
    1.4e-05   24.9   0.0      0.026   14.3   0.0    2.4  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    0.00011   22.5   1.0        2.8    8.2   0.6    4.2  3  AAA_22           AAA domain
    0.00022   21.6   0.0      0.089   13.2   0.0    3.0  2  RNA_helicase     RNA helicase
    0.00067   19.4   0.0     0.0013   18.4   0.0    1.5  1  AAA_lid_3        AAA+ lid domain
     0.0015   18.6   1.0      0.013   15.6   0.0    3.0  3  AAA_14           AAA domain
     0.0069   16.1   0.0       0.16   11.7   0.0    2.3  2  IstB_IS21        IstB-like ATP binding protein
     0.0085   16.5   1.6          6    7.4   0.0    3.4  3  DUF2660          Protein of unknown function (DUF2660)
     0.0096   15.9   0.0        2.1    8.4   0.0    2.4  2  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
  ------ inclusion threshold ------
      0.022   15.3   0.1        3.3    8.3   0.0    3.2  2  AAA_18           AAA domain
      0.026   14.9   0.0       0.74   10.2   0.0    2.4  2  AAA_16           AAA ATPase domain
      0.058   13.5   0.0        4.2    7.5   0.0    2.9  3  Sigma54_activ_2  Sigma-54 interaction domain
      0.084   12.6   0.0        7.8    6.2   0.0    2.6  3  Sigma54_activat  Sigma-54 interaction domain
      0.085   12.4   0.0        2.4    7.7   0.0    2.5  2  AAA_7            P-loop containing dynein motor region
       0.19   11.1   0.2        1.5    8.1   0.0    2.3  2  Mg_chelatase     Magnesium chelatase, subunit ChlI


Domain annotation for each model (and alignments):
>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0      0.22   2.5e+02       1      52 [.     296     347 ..     296     360 .. 0.62
   2 !  124.9   0.0   2.5e-39   2.7e-36       1     131 [.     542     669 ..     542     670 .. 0.97

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.22
                                        EEEESSTTSSHHHHHHHHHHHH..THEEEEEETTTCSSSSTTHHHHHHHHHHHH CS
                                AAA   1 vllyGppGtGKTllakavakel..gvefleisgsellskyvgesekkirelfke 52 
                                        ++l+G  GtGK +++  v   l  ++++   + ++l+     e e++i +  +e
  gene3184|gene3184|rna3184|rna3184 296 IVLSGEVGTGKRTFCMIVNDFLcaNMKVEVYKRANLI--RADEDEDNILDSYRE 347
                                        5799*********999887765334444444555555..455666666555555 PP

  == domain 2  score: 124.9 bits;  conditional E-value: 2.5e-39
                                        EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTT CS
                                AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksrsg 76 
                                        +llyGppG+ KTl+a+++ ++++ +f+ +s+s++ sk+vgese+++r+ f+ea+ ++ ps lfiDEida+a++r +
  gene3184|gene3184|rna3184|rna3184 542 ILLYGPPGCSKTLFARSLSSTFNYNFVYFSASSIKSKWVGESERNLRDKFREAELMQ-PSLLFIDEIDAIATNR-D 615
                                        69***************************************************9998.****************.8 PP

                                        CCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
                                AAA  77 seseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieie 131
                                        +++++e ++vn+Ll+ +dg +k+  +++v g tnr + +d+allr gRfd++++i+
  gene3184|gene3184|rna3184|rna3184 616 TSHNHEVSLVNTLLSLMDGIDKR--QTVVFGSTNRRNGIDKALLRpGRFDKHVYIG 669
                                        9999******************6..68**************************997 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.1   0.0    0.0095        11       2      28 ..     296     324 ..     295     346 .. 0.82
   2 !   20.9   0.0   2.6e-07   0.00029       2      78 ..     542     611 ..     541     657 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0095
                                        EEEE--SSSSHHHHHHHGGGGB..S--EE CS
                              AAA_5   2 vlLvGppGtgKselaerlaaal..nreve 28 
                                        ++L G+ GtgK+++ + +  +l  n +ve
  gene3184|gene3184|rna3184|rna3184 296 IVLSGEVGTGKRTFCMIVNDFLcaNMKVE 324
                                        689****************9995544444 PP

  == domain 2  score: 20.9 bits;  conditional E-value: 2.6e-07
                                        EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------G-SEEEEESGGG- CS
                              AAA_5   2 vlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraaregeilvlDEvera 77 
                                        +lL GppG+ K+ +a++l++ +n +++y   ++   +++ +g+ e +n + ++++ +l+    ++++l++DE++ +
  gene3184|gene3184|rna3184|rna3184 542 ILLYGPPGCSKTLFARSLSSTFNYNFVYFSASS--IKSKWVGESE-RNLRDKFREAELM----QPSLLFIDEIDAI 610
                                        89*********************9999876655..5666666666.4889999999999....999999**99976 PP

                                        - CS
                              AAA_5  78 e 78 
                                         
  gene3184|gene3184|rna3184|rna3184 611 A 611
                                        5 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.0    0.0019       2.1      29      63 ..     289     323 ..     283     348 .. 0.85
   2 !   14.3   0.0   2.3e-05     0.026      35      98 ..     541     612 ..     506     619 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0019
                             RuvB_N  29 reealdhvllyGpPGlGkttlakiiakelgvklki 63 
                                        + +++d ++l+G  G Gk t+++i+ + l +++k+
  gene3184|gene3184|rna3184|rna3184 289 KIDPIDTIVLSGEVGTGKRTFCMIVNDFLCANMKV 323
                                        55789********************9988888876 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 2.3e-05
                             RuvB_N  35 hvllyGpPGlGkttlakiiakelgvklkitsgPvl......ekagdlaall..tnleekdvlfideihrlsr 98 
                                         +llyGpPG  kt +a+ +++ ++ ++   s+  +      e +++l   +  ++l +  +lfidei  +++
  gene3184|gene3184|rna3184|rna3184 541 GILLYGPPGCSKTLFARSLSSTFNYNFVYFSASSIkskwvgESERNLRDKFreAELMQPSLLFIDEIDAIAT 612
                                        59************************99999988822222234567766552246788899*****988765 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.83   9.3e+02      37      66 ..     239     271 ..     222     289 .. 0.75
   2 ?    3.6   0.0     0.067        75       8      51 ..     296     340 ..     294     358 .. 0.69
   3 !    8.2   0.6    0.0025       2.8      73     130 ..     582     645 ..     536     651 .. 0.53

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.83
                             AAA_22  37 e...erpevvfvtlpsstsskdllrellralgl 66 
                                        e    + ++vf+++ +++  k +++++  +l+ 
  gene3184|gene3184|rna3184|rna3184 239 EyfvVDEQTVFINVRNKCFTKRIYQDINPILKA 271
                                        1455577899********99******9988875 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.067
                             AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaee.erpevvfvtlpsst 51 
                                        +v+ Ge+GtGK t +  + + l++  k e  +r+ +++ +  +++
  gene3184|gene3184|rna3184|rna3184 296 IVLSGEVGTGKRTFCMIVNDFLCANMKVEVyKRANLIRADEDEDN 340
                                        799********9999999998876655555666666665555555 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.0025
                             AAA_22  73 lsseellealeqalraravielliiDEaqhlr.....s....eealeeLrsllnlsrkgvqliLvGt 130
                                         s++ l++++++a   +    ll iDE++ +      s      ++++L sl++ + ++ q +++G 
  gene3184|gene3184|rna3184|rna3184 582 ESERNLRDKFREAELMQPS--LLFIDEIDAIAtnrdtShnheVSLVNTLLSLMD-GIDKRQTVVFGS 645
                                        3455566666666666655..888888888766644315555667777777777.555555555555 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.0     0.028        32       1      48 [.     296     346 ..     296     353 .. 0.74
   2 !   13.2   0.0     8e-05     0.089       1      64 [.     542     613 ..     542     646 .. 0.72

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.028
                       RNA_helicase   1 iwlyGpsgeGKStlakeLakallkkl...klkkkdsvysrnpeddfwdgYt 48 
                                        i+l+G+ g+GK t++  + + l+ ++    +k+++ + + + ed+++d+Y+
  gene3184|gene3184|rna3184|rna3184 296 IVLSGEVGTGKRTFCMIVNDFLCANMkveVYKRANLIRADEDEDNILDSYR 346
                                        789*************97777777775533444444444777788888886 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 8e-05
                       RNA_helicase   1 iwlyGpsgeGKStlakeLakallkkl.....klkkkdsvys..rnpeddfw.dgYtgqevvvidDfgqvkde 64 
                                        i+lyGp+g+ K+++a++L++++  ++      ++k+++v    rn +d+f      ++  + id++ ++ ++
  gene3184|gene3184|rna3184|rna3184 542 ILLYGPPGCSKTLFARSLSSTFNYNFvyfsaSSIKSKWVGEseRNLRDKFReAELMQPSLLFIDEIDAIATN 613
                                        789*******************98877887766666777544677777777445557777778888777755 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   1.2e-06    0.0013       7      40 ..     835     870 ..     830     871 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.2e-06
                          AAA_lid_3   7 LAerTeGySGADlaalcreAallAlrrgik.e.itm 40 
                                        + + T+G+SGA+l+a ++e  +   rr ++ e i+m
  gene3184|gene3184|rna3184|rna3184 835 IIKHTDGMSGAELKAAVNEGKMIFARRHRTnEcIGM 870
                                        7899***************99987777665345665 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.1       1.5   1.7e+03      53      79 ..     226     252 ..     206     278 .. 0.67
   2 ?   -2.5   0.0       4.5     5e+03       9      67 ..     300     355 ..     295     359 .. 0.41
   3 !   15.6   0.0   1.1e-05     0.013       5     103 ..     542     648 ..     540     701 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.5
                             AAA_14  53 lelileklkeekktylflDEiqevpew 79 
                                        +++  ek ++++++y++ DE     ++
  gene3184|gene3184|rna3184|rna3184 226 NRIETEKNTNKNDEYFVVDEQTVFINV 252
                                        333344445568889999997665444 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 4.5
                             AAA_14   9 GaRrvGKTtllkqlikell...vkkesilyinldderdkkladpekllelileklkeekkty 67 
                                        G   +GK t++  ++++ l   +k e +   nl + ++++    +++l+ ++e +++  k++
  gene3184|gene3184|rna3184|rna3184 300 GEVGTGKRTFC-MIVNDFLcanMKVEVYKRANLIRADEDE----DNILDSYREFVEK-TKEV 355
                                        55556666665.3333444333233333334444433333....3355555555433.2333 PP

  == domain 3  score: 15.6 bits;  conditional E-value: 1.1e-05
                             AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpe.kllelilek.lkeekktylflDEiqev.. 76 
                                        +++ G+  + KT +++ l ++      +++y++  + + k   ++e +l + ++e  l   + ++lf+DEi  +  
  gene3184|gene3184|rna3184|rna3184 542 ILLYGPPGCSKTLFARSLSSTFN---YNFVYFSASSIKSKWVGESErNLRDKFREAeL-M-QPSLLFIDEIDAIat 612
                                        57899999*******99997777...9*********9998877655467789999743.3.689**********88 PP

                             AAA_14  77 .........pewekalkslvdegknldvivtGSnsk 103
                                                  ++ ++l sl+d  ++ + +v GS + 
  gene3184|gene3184|rna3184|rna3184 613 nrdtshnheVSLVNTLLSLMDGIDKRQTVVFGSTNR 648
                                        988888887778888888888555668888888765 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0      0.16   1.8e+02      44      86 ..     290     331 ..     272     360 .. 0.73
   2 !   11.7   0.0   0.00014      0.16      44     127 ..     536     617 ..     506     646 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.16
                          IstB_IS21  44 iekkenivllGpsGvGKshlaialgveavraglsvlfvrvedL 86 
                                        i+  + ivl G  G+GK  + + +    + a+++v  ++ ++L
  gene3184|gene3184|rna3184|rna3184 290 IDPIDTIVLSGEVGTGKRTFCMIVNDFLC-ANMKVEVYKRANL 331
                                        677789***********988766555555.4455554444444 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00014
                          IstB_IS21  44 iekkenivllGpsGvGKshlaialgveavraglsvlfvrvedLvee.lkrarrdgklaralkrllkvdllilDdlg 118
                                        i+   +i+l Gp+G  K+ +a +l+      +++ ++++++ + ++ +   +r+ + + + ++l++++ll +D++ 
  gene3184|gene3184|rna3184|rna3184 536 IDYPTGILLYGPPGCSKTLFARSLSST---FNYNFVYFSASSIKSKwVGESERNLRDKFREAELMQPSLLFIDEID 608
                                        6667889*****************875...578888888888876636777888888889999***********98 PP

                          IstB_IS21 119 llpldqaea 127
                                            +++ +
  gene3184|gene3184|rna3184|rna3184 609 AIATNRDTS 617
                                        877776655 PP

>> DUF2660  Protein of unknown function (DUF2660)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       2.7     3e+03      52      74 ..     368     390 ..     358     393 .. 0.83
   2 !    7.4   0.0    0.0054         6      14      43 ..     597     626 ..     588     632 .. 0.83
   3 ?    5.7   0.6     0.019        21       4      38 ..     772     805 ..     768     826 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 2.7
                            DUF2660  52 lydltkiilkkfskedvvevnki 74 
                                        +y l ++   kfs+ d   v++i
  gene3184|gene3184|rna3184|rna3184 368 FYQLGNVCDVKFSRPDRGAVQRI 390
                                        4899999999******9999876 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0054
                            DUF2660  14 lpatlnyiddsdavalkrkksevkklslke 43 
                                        +  +l +id+ da+a +r  s ++ +sl +
  gene3184|gene3184|rna3184|rna3184 597 MQPSLLFIDEIDAIATNRDTSHNHEVSLVN 626
                                        4456779*******************9965 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.019
                            DUF2660   4 kkkvkqkknmlpatlnyiddsdavalkrkksevkk 38 
                                         + vk++k  +   +n i+ +d++++++++ + k 
  gene3184|gene3184|rna3184|rna3184 772 ERNVKENKT-VNLNINDIQTGDTISKEERRNKKKE 805
                                        378888888.8899***********9966655544 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.0    0.0019       2.1      13      41 ..     284     315 ..     270     333 .. 0.74
   2 ?    4.8   0.0     0.024        27      13      46 ..     527     566 ..     514     575 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0019
                                        HHHHCH...TEEEEEEESTTSSHHHHHHHHHH CS
                               TsaE  13 klakal...gdvilLeGdLGaGKTtlvrglak 41 
                                        kl+++     d+i+L+G++G+GK t++  +  
  gene3184|gene3184|rna3184|rna3184 284 KLKNSKidpIDTIVLSGEVGTGKRTFCMIVND 315
                                        444433344567**************976655 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.024
                                        HHHHCH.TEE......EEEEESTTSSHHHHHHHHHHHTT-- CS
                               TsaE  13 klakal.gdv......ilLeGdLGaGKTtlvrglakalgve 46 
                                         l++   + +      ilL+G+ G+ KT ++r+l ++++++
  gene3184|gene3184|rna3184|rna3184 527 CLTRRYpK-LidyptgILLYGPPGCSKTLFARSLSSTFNYN 566
                                        44443331.1344555*****************99988765 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0     0.098   1.1e+02       1      22 [.     296     317 ..     296     357 .. 0.64
   2 ?    8.3   0.0    0.0029       3.3       1      41 [.     542     600 ..     542     637 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.098
                             AAA_18   1 IlltGtpGvGKttlakeLskrl 22 
                                        I+l+G  G+GK t++  +++ l
  gene3184|gene3184|rna3184|rna3184 296 IVLSGEVGTGKRTFCMIVNDFL 317
                                        899************9886655 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0029
                             AAA_18   1 IlltGtpGvGKttlakeLskrlgf..................gvnlrdvakenglllev 41 
                                        Ill G+pG+ Kt +a+ Ls+  ++                   +nlrd ++e +l  + 
  gene3184|gene3184|rna3184|rna3184 542 ILLYGPPGCSKTLFARSLSSTFNYnfvyfsassikskwvgesERNLRDKFREAELMQPS 600
                                        99******************988888988888777777777777777777777766555 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0      0.27     3e+02      26      51 ..     295     320 ..     285     354 .. 0.77
   2 ?   10.2   0.0   0.00066      0.74      24      59 ..     539     571 ..     533     643 .. 0.72

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.27
                             AAA_16  26 lvllsGesGvGKsslvrellralekd 51 
                                         ++lsGe G+GK +    + + l+++
  gene3184|gene3184|rna3184|rna3184 295 TIVLSGEVGTGKRTFCMIVNDFLCAN 320
                                        689*********99877666666655 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00066
                             AAA_16  24 pelvllsGesGvGKsslvrellralekdggiflrgk 59 
                                        p  +ll+G++G+ K+  +r+l   ++ + ++f    
  gene3184|gene3184|rna3184|rna3184 539 PTGILLYGPPGCSKTLFARSLSSTFNYNFVYF---S 571
                                        6789******************9999884444...2 PP

>> Sigma54_activ_2  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0      0.13   1.4e+02      24      75 ..     296     359 ..     273     363 .. 0.74
   2 ?   -2.6   0.0         5   5.6e+03      97     120 ..     451     474 ..     438     482 .. 0.77
   3 ?    7.5   0.0    0.0038       4.2      16      80 ..     534     609 ..     526     617 .. 0.60

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.13
                                        EEEEEETT--HHHHHHCC--TTS-EE--SSTTHHHH-H............HHHHHHTTTSEEEE CS
                    Sigma54_activ_2  24 vfltGekGsgkelvArlLhknsgpwleifvverlaklp............ldlleqakggtLyl 75 
                                        + l Ge G+gk ++  +  ++ + ++++ v++r   +              +++e+ k++ +++
  gene3184|gene3184|rna3184|rna3184 296 IVLSGEVGTGKRTFCMIVNDFLCANMKVEVYKRANLIRadedednildsyREFVEKTKEVFFFI 359
                                        5689**********************99999887754444455555555566666666666665 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 5
                                        TTTT-EEEEEEEE-TTT..----H CS
                    Sigma54_activ_2  97 eksslrlVstsskdleqlleagaf 120
                                        + +++r+Vs++s+  ++ ++ +a+
  gene3184|gene3184|rna3184|rna3184 451 QYNHARVVSSGSEYYDSCIDDKAI 474
                                        467899***999988887776655 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.0038
                                        HHHT-SS-EEEEEETT--HHHHHHCC--TTS-EE--SSTTHHHH-H.........HHHHHH......TTTSEEEEE CS
                    Sigma54_activ_2  16 qaaqsklpvfltGekGsgkelvArlLhknsgpwleifvverlaklp.........ldlleq......akggtLylk 76 
                                        ++    + ++l G++G+ k+l+Ar L++    +   f   +  +            d   +      +++ +L++ 
  gene3184|gene3184|rna3184|rna3184 534 KLIDYPTGILLYGPPGCSKTLFARSLSSTFNYNFVYFSASSIKS-KwvgesernlRD---KfreaelMQPSLLFID 605
                                        555667889*****************987666555544433222.122333323322...1222222467777777 PP

                                        E-TT CS
                    Sigma54_activ_2  77 diad 80 
                                        +i+ 
  gene3184|gene3184|rna3184|rna3184 606 EIDA 609
                                        7665 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0     0.059        66      24      42 ..     295     313 ..     280     331 .. 0.81
   2 ?    6.2   0.0     0.007       7.8      14      59 ..     531     573 ..     525     584 .. 0.76
   3 ?   -2.9   0.0       4.4   4.9e+03      93     106 ..     598     611 ..     588     614 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.059
                                        -EEEECSTTSSHHHHHHHH CS
                    Sigma54_activat  24 svlitGesGtGKellarai 42 
                                        ++++ Ge GtGK ++   +
  gene3184|gene3184|rna3184|rna3184 295 TIVLSGEVGTGKRTFCMIV 313
                                        6899********9997665 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.007
                                        HHHHHCTSSS-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETT CS
                    Sigma54_activat  14 qikkvaktdlsvlitGesGtGKellaraiheaskrkekpfvavnca 59 
                                        +  k++++++ +l+ G  G+ K+l+ar++ ++    + +fv +  +
  gene3184|gene3184|rna3184|rna3184 531 RYPKLIDYPTGILLYGPPGCSKTLFARSLSSTF---NYNFVYFSAS 573
                                        556789999******************986543...3455555555 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 4.4
                                        TTSEEEEETGGGS- CS
                    Sigma54_activat  93 dgGtlfLDeigelp 106
                                        + + lf+Dei  + 
  gene3184|gene3184|rna3184|rna3184 598 QPSLLFIDEIDAIA 611
                                        5678******9875 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0      0.15   1.6e+02      35      67 ..     295     331 ..     283     369 .. 0.66
   2 ?    7.7   0.0    0.0021       2.4      29      72 ..     535     573 ..     528     614 .. 0.77

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.15
                              AAA_7  35 pvllvGptGtGK...tviikd.llkkldkekylslti 67 
                                         ++l G++GtGK    +i++d l+ +++ e y+ +++
  gene3184|gene3184|rna3184|rna3184 295 TIVLSGEVGTGKrtfCMIVNDfLCANMKVEVYKRANL 331
                                        57899*******5333567786667777666655544 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0021
                              AAA_7  29 llknkkpvllvGptGtGKtviikdllkkldkekylsltinfsaq 72 
                                        l++    +ll+Gp G++Kt+ +++l ++++     ++++ fsa+
  gene3184|gene3184|rna3184|rna3184 535 LIDYPTGILLYGPPGCSKTLFARSLSSTFN-----YNFVYFSAS 573
                                        66667789**************99988877.....444444444 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.57   6.4e+02      25      59 ..     296     330 ..     293     353 .. 0.77
   2 ?    8.1   0.0    0.0014       1.5      25      44 ..     542     561 ..     539     569 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.57
                       Mg_chelatase  25 lllvGppGsGKtmlakrlpsllpplseeealevak 59 
                                        ++l G  G+GK      ++  l++  + e+ + a+
  gene3184|gene3184|rna3184|rna3184 296 IVLSGEVGTGKRTFCMIVNDFLCANMKVEVYKRAN 330
                                        7899********99999999999888877766554 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0014
                       Mg_chelatase  25 lllvGppGsGKtmlakrlps 44 
                                        +ll+GppG+ Kt+ a+ l+s
  gene3184|gene3184|rna3184|rna3184 542 ILLYGPPGCSKTLFARSLSS 561
                                        89**************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (888 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1018  (0.0567795); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.68u 0.31s 00:00:00.99 Elapsed: 00:00:00.47
# Mc/sec: 5737.97
//
Query:       gene3185|gene3185|rna3185|rna3185  [L=137]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    6.9e-06   26.5   6.7    9.8e-06   26.1   6.7    1.2  1  V-ATPase_G  Vacuolar (H+)-ATPase G subunit
  ------ inclusion threshold ------
       0.14   11.8   0.2       0.14   11.8   0.2    2.1  2  DUF4637     Domain of unknown function (DUF4637)
        1.2    9.5  10.7      0.089   13.1   5.1    1.9  3  Csm1_N      Csm1 N-terminal domain


Domain annotation for each model (and alignments):
>> V-ATPase_G  Vacuolar (H+)-ATPase G subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   6.7   1.6e-09   9.8e-06       3     101 ..      33     130 ..      31     134 .. 0.89

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 1.6e-09
                                        HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSHHHHHHHHHHHHSSHH CS
                         V-ATPase_G   3 sqgIqqLLqAEkeAaeivkeArkrkakrlkqAkeeAekEieeyrakkekefkekeaeklgseeelekkieketeek 78 
                                        s+ +++L + E++A+e+v  Ar+++a+ l   + +A   i++ r+++e+ +++++ ++  + e+l k++++  e+ 
  gene3185|gene3185|rna3185|rna3185  33 SENVKKLVECERKAKEMVGRARNERADLLALSRIDADIAIAKLREENEQILEKERVKENEEVEKLIKELKEVREND 108
                                        67899****************************************************9999********9999999 PP

                                        HHHHHHHHHHHHHHHHHHHHHHH CS
                         V-ATPase_G  79 ikelkesvkknkeavvkellklv 101
                                        ++e+ +++    e+ v++++++v
  gene3185|gene3185|rna3185|rna3185 109 LREFGTEIIG-CEKLVDDIVSMV 130
                                        9999888754.456666666666 PP

>> DUF4637  Domain of unknown function (DUF4637)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.2   2.4e-05      0.14     130     151 ..      13      34 ..       8      49 .. 0.80
   2 ?    0.2   1.3     0.094   5.6e+02      32      43 ..      84      95 ..      67     116 .. 0.40

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.4e-05
                            DUF4637 130 rceilfckkcktlhsdpayvah 151
                                          +ilfc k k+lh++p     
  gene3185|gene3185|rna3185|rna3185  13 VSNILFCSKTKNLHAHPIMASE 34 
                                        678*************987655 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.094
                            DUF4637 32 eedraeeesaae 43
                                       e++r +e+ + e
  gene3185|gene3185|rna3185|rna3185 84 EKERVKENEEVE 95
                                       111111111111 PP

>> Csm1_N  Csm1 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.1      0.71   4.2e+03      28      42 ..      34      48 ..      30      55 .. 0.60
   2 ?   -2.7   0.0       1.3   7.6e+03      13      21 ..      53      61 ..      46      62 .. 0.79
   3 ?   13.1   5.1   1.5e-05     0.089      17      56 ..      67     107 ..      63     112 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.71
                             Csm1_N 28 ENsvLsqkletkdqe 42
                                       EN+ +  + e k +e
  gene3185|gene3185|rna3185|rna3185 34 ENVKKLVECERKAKE 48
                                       455544445554444 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.3
                             Csm1_N 13 erldsAdll 21
                                        r + Adll
  gene3185|gene3185|rna3185|rna3185 53 ARNERADLL 61
                                       577899997 PP

  == domain 3  score: 13.1 bits;  conditional E-value: 1.5e-05
                             Csm1_N  17 sAdllvsklvhENsvLsqkle.tkdqeiesLkeqlaeleek 56 
                                        +Ad++++kl +EN    +k + + ++e+e+L ++l+e++e+
  gene3185|gene3185|rna3185|rna3185  67 DADIAIAKLREENEQILEKERvKENEEVEKLIKELKEVREN 107
                                        59***********86555555055689******99999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (137 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1729  (0.0964359); expected 358.6 (0.02)
Passed bias filter:                      606  (0.0338); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 926.00
//
Query:       gene3186|gene3186|rna3186|rna3186  [L=314]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-61  208.5   0.7    1.4e-61  208.2   0.7    1.1  1  Pkinase         Protein kinase domain
    1.6e-26   93.1   0.1      2e-26   92.8   0.1    1.2  1  Pkinase_Tyr     Protein tyrosine kinase
    3.3e-05   23.9   0.0    8.7e-05   22.5   0.0    1.6  2  APH             Phosphotransferase enzyme family
  ------ inclusion threshold ------
      0.018   14.6   0.2      0.046   13.3   0.2    1.5  1  RIO1            RIO1 family
      0.019   14.5   1.2       0.14   11.7   0.0    2.2  2  Choline_kinase  Choline/ethanolamine kinase
      0.039   13.6   0.3        1.2    8.7   0.0    2.2  2  FTA2            Kinetochore Sim4 complex subunit FTA2
      0.068   11.9   0.4       0.18   10.6   0.2    1.7  1  Pkinase_fungal  Fungal protein kinase
      0.082   12.6   0.1       0.22   11.2   0.1    1.7  1  4HPAD_g_N       4-Hydroxyphenylacetate decarboxylase subunit 


Domain annotation for each model (and alignments):
>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  208.2   0.7   6.1e-65   1.4e-61       1     264 []      37     312 ..      37     312 .. 0.90

  Alignments for each domain:
  == domain 1  score: 208.2 bits;  conditional E-value: 6.1e-65
                                        EEEEEEEEEESSEEEEEEEETTTTEEEEEEEEECHCHCHHHHHHHHHHHHHHHHHSCTTB--EEEEEEE.SSEEE. CS
                            Pkinase   1 yekleklGeGsfGkVykaveketgkivAvKkikkekakkkkekkvlrEikilkklkhpnivrlyevfee.kdely. 74 
                                        y+ +++lG+G++++V+k++ + t+  +A+K++k  ++kk     + rE+ +lk+l+hpnivr+++v+++ +++ y 
  gene3186|gene3186|rna3186|rna3186  37 YKIIKRLGRGKYSEVFKGICTLTKSFIAIKVLKPVRQKK-----INREVLVLKQLDHPNIVRMVDVVKDsDTHTYs 107
                                        78899*****************************99987.....568*********************95333445 PP

                                        EEEE--TTEBHHHHHHHHSS--HHHHHHHHHHHHHHHHHHHHTTEE-SS-SGGGEEEE.TTTEEEE-SGTTSEESS CS
                            Pkinase  75 lvleyveggeladllerkgslseeeakkiakqilegleylHskgiiHrDlKpeNiLid.ekgelKitDFGlakele 149
                                        +++ey+e+ e   l ++   ls +e  ++akq+l++l+y Hs+giiHrD+Kp+N++i  +++ lKi+D+Gla+ + 
  gene3186|gene3186|rna3186|rna3186 108 IIFEYLEHRETRVLFTE---LSRKEFAFYAKQVLSALDYAHSRGIIHRDIKPHNMIICkDSRTLKIIDWGLAEFYL 180
                                        ********998888875...9*********************************999945666************* PP

                                        SSCSBCTTTSCGGGS-HHHH.TTSCBSHHHHHHHHHHHHHHHHHSS-STTTSSHHHHHHHHHHTHHHHHHHCTSHH CS
                            Pkinase 150 ssskltsfvgtseYlAPEvl.keneyskkvDvWslGvilyelltgkppfsgekgkekvekeldqlekilkilgetk 224
                                         ++ ++  v+++ Y  PE+l ++n y+ + D+Ws G+i++e +t+k pf    gk     ++dql+ i+++lg  +
  gene3186|gene3186|rna3186|rna3186 181 PGTAYNVKVASRFYKGPELLvDYNYYDYSLDMWSFGCIVAEYFTKKSPFF--FGK----DNIDQLFVITEVLGRDD 250
                                        ********************999999************************..444....499***********555 PP

                                        ...HHHTTS......................-HHHHHHHHHHT-SSGCCSTTHHHHHTSGGG CS
                            Pkinase 225 eklpeasei......................seeakdllkkllkkdpkkRltaeellqhpyl 264
                                        +    ++                         e ++dll+kll +d+ +Rl+a+e+l+h+++
  gene3186|gene3186|rna3186|rna3186 251 FYAYVKKYQisleegivvskntkrkkfnvdiGECVIDLLDKLLVYDHCERLSAKECLEHNFF 312
                                        4444443334788888999999999999999*****************************98 PP

>> Pkinase_Tyr  Protein tyrosine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.8   0.1   8.9e-30     2e-26       2     205 ..      38     228 ..      37     308 .. 0.86

  Alignments for each domain:
  == domain 1  score: 92.8 bits;  conditional E-value: 8.9e-30
                                        EEEEEEEEESSEEEEEEEEETTTTSSEEEEEEEEESTTSSHHHHHHHHHHHHHHHTS-BTTB--EEEEEE..SSSS CS
                        Pkinase_Tyr   2 elgkklGeGafGkVvegtlkgekekkevkVavKtlkeeateeekeelleeakimkklkhpnivkllgvct..keep 75 
                                        ++ k+lG+G++++V++g ++     ++  +a+K+lk   ++    ++ +e+ ++k+l+hpniv+++ v+   ++++
  gene3186|gene3186|rna3186|rna3186  38 KIIKRLGRGKYSEVFKGICT----LTKSFIAIKVLKPVRQK----KINREVLVLKQLDHPNIVRMVDVVKdsDTHT 105
                                        57899***************....88999******775554....599**********************655566 PP

                                        EEEEEE--TTEBHHHHHHHTCTTTSBHHHHHHHHHHHHHHHHHHHHTTEEEST-SGGGEEEEE.TTEEEE-STTTH CS
                        Pkinase_Tyr  76 llivteyvkgGdLlkfLrkkekekltlkdllsfalqvAkGmeyLeskklvHrdlaarNvLlse.nkvvkisDfGLa 150
                                        + i++ey+++ + +   ++     l+ k+   +a qv ++++y +s+ ++Hrd+   N+++++ +++ ki D GLa
  gene3186|gene3186|rna3186|rna3186 106 YSIIFEYLEHRETRVLFTE-----LSRKEFAFYAKQVLSALDYAHSRGIIHRDIKPHNMIICKdSRTLKIIDWGLA 176
                                        99********997655544.....799999****************************999872569********* PP

                                        EETTTSSEEEETTSSTSGGGGS-HHHHHHSEEEHHH.HHHHHHHHHHHHHTTSSGT CS
                        Pkinase_Tyr 151 rdiekddeyvkkeeaklpvkWmapEslkekkftsks.DvWsfGvllwEiftlgesp 205
                                        +       y++k  ++    +  pE l + ++   s D+WsfG ++ E ft+ +sp
  gene3186|gene3186|rna3186|rna3186 177 EFYLPGTAYNVKVASR---FYKGPELLVDYNYYDYSlDMWSFGCIVAEYFTK-KSP 228
                                        *998888887666544...5789***99998666655*************94.444 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.56   1.3e+03      31      83 ..      71     119 ..      56     129 .. 0.67
   2 !   22.5   0.0   3.9e-08   8.7e-05     148     197 ..     125     177 ..     102     182 .. 0.71

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.56
                                        TS-HHHHHHHHHHHHHHHHTT-B--B-CTTB.S-EEETTEEEEEEE----EE-S CS
                                APH  31 araaeeirrevallrlLakagvpvPevlagd.tddeeigllfalieyvpgrsll 83 
                                           + +i rev +l++L   ++   ++++    +d++ +  + ++ey++ r  +
  gene3186|gene3186|rna3186|rna3186  71 V-RQKKINREVLVLKQLDHPNI--VRMVDVVkDSDTHTY--SIIFEYLEHRETR 119
                                        4.56788888888888887777..355554424555555..7777777776655 PP

  == domain 2  score: 22.5 bits;  conditional E-value: 3.9e-08
                                        HHHHHHHHHHHH--S....SS-EEEE-SS-SGGGEEEC..TTEEEEE---TT-E CS
                                APH 148 leeqvlaalaallpg....elptvllHgDlhpgNllvdpddgrvtGviDfedag 197
                                        l +   a  a+ +++    + +++++H+D++p+N+++   d r   +iD+++a 
  gene3186|gene3186|rna3186|rna3186 125 LSRKEFAFYAKQVLSaldyAHSRGIIHRDIKPHNMIIC-KDSRTLKIIDWGLAE 177
                                        4444444445555555555899****************.5555557*****985 PP

>> RIO1  RIO1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.2   2.1e-05     0.046      76     150 ..     101     174 ..      69     176 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.1e-05
                                        EEEETTEEEEE--EETTEEGGBHHHCG-HHHHHHHHHHHHHHHHHHHHTSTEEESS-STTSEEEETT..EEEE--G CS
                               RIO1  76 ielkrhvlvmefigedgvaapklkdveeeeeaeelyeevleemrklykeaglvHaDLSeyNvlvded..kvviIDv 149
                                         + +   ++ e+++++++++    +++ ++e + ++++vl+++  +    g++H D+   N+++ +d   + iID+
  gene3186|gene3186|rna3186|rna3186 101 SDTHTYSIIFEYLEHRETRVLF-TELS-RKEFAFYAKQVLSALDYAH-SRGIIHRDIKPHNMIICKDsrTLKIIDW 173
                                        4555566788888844444333.3333.5677777778888666665.99*************999977889***9 PP

                                        T CS
                               RIO1 150 s 150
                                        +
  gene3186|gene3186|rna3186|rna3186 174 G 174
                                        6 PP

>> Choline_kinase  Choline/ethanolamine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   6.4e-05      0.14     129     174 ..     128     176 ..      94     183 .. 0.76
   2 ?    1.2   0.3       0.1   2.3e+02     168     193 ..     200     225 ..     196     239 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 6.4e-05
                                        HHHHTHHHHH.HCHGG-..EEEE-S--SGGGEEE.-CTTEEEE--GTT- CS
                     Choline_kinase 129 keleklekll.eelesp..vvfcHnDlqegNillnkeekklvlIDFEYa 174
                                        ke++ + k + + l++       H D+ ++N++  k+ ++l +ID+  a
  gene3186|gene3186|rna3186|rna3186 128 KEFAFYAKQVlSALDYAhsRGIIHRDIKPHNMIICKDSRTLKIIDWGLA 176
                                        45555544443444433346677***********************655 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.1
                                        E--GTT-EEEEHHHHHHHHHHHTTEE CS
                     Choline_kinase 168 lIDFEYagynyrgfDlanhfiEwagd 193
                                        l+D+ Y  y+  ++ ++ +++E+  +
  gene3186|gene3186|rna3186|rna3186 200 LVDYNYYDYSLDMWSFGCIVAEYFTK 225
                                        89********************9873 PP

>> FTA2  Kinetochore Sim4 complex subunit FTA2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.1      0.04        89      22      62 ..      35      77 ..      27      99 .. 0.75
   2 ?    8.7   0.0   0.00054       1.2     177     204 ..     133     160 ..      85     163 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.04
                               FTA2 22 kdiefleyLgkglhsiVlk..vkirgkeYALKlFrfleaeele 62
                                       +++++++ Lg+g  s V+k      ++  A+K+ + +++++ +
  gene3186|gene3186|rna3186|rna3186 35 DNYKIIKRLGRGKYSEVFKgiCTLTKSFIAIKVLKPVRQKKIN 77
                                       5899***************533445556799998888777665 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00054
                               FTA2 177 qlpkllrdlkklhklgIvvrDlkeenyi 204
                                        +++++l+ l+ +h+ gI++rD+k++n+i
  gene3186|gene3186|rna3186|rna3186 133 YAKQVLSALDYAHSRGIIHRDIKPHNMI 160
                                        57899*******************9986 PP

>> Pkinase_fungal  Fungal protein kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.2   7.9e-05      0.18     323     359 ..     145     176 ..     119     186 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 7.9e-05
                     Pkinase_fungal 323 flkagiLHrDiSenNilitdskkegerkglLiDLDla 359
                                        +   gi+HrDi  +N++i+    +++r+  +iD  la
  gene3186|gene3186|rna3186|rna3186 145 H-SRGIIHRDIKPHNMIIC----KDSRTLKIIDWGLA 176
                                        5.789**************....45666667776555 PP

>> 4HPAD_g_N  4-Hydroxyphenylacetate decarboxylase subunit gamma N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   9.9e-05      0.22      16      28 ..      53      65 ..      51      66 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 9.9e-05
                          4HPAD_g_N 16 KGiCrltkeivpi 28
                                       KGiC ltk ++ i
  gene3186|gene3186|rna3186|rna3186 53 KGICTLTKSFIAI 65
                                       **********987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (314 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       566  (0.031569); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 2060.68
//
Query:       gene3187|gene3187|rna3187|rna3187  [L=43]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (43 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       179  (0.00998383); expected 358.6 (0.02)
Passed bias filter:                      156  (0.00870099); expected 358.6 (0.02)
Passed Vit filter:                         7  (0.000390429); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.26s 00:00:00.61 Elapsed: 00:00:00.41
# Mc/sec: 317.94
//
Query:       gene3188|gene3188|rna3188|rna3188  [L=691]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
      0.013   14.9   2.5        3.1    7.1   0.0    2.9  3  CorA        CorA-like Mg2+ transporter protein
       0.19   11.4   0.3        1.7    8.4   0.3    2.5  2  Vac_Fusion  Chordopoxvirus multifunctional envelope protein A
       0.22   11.6   6.8       0.96    9.5   2.6    3.1  3  TPR_MLP1_2  TPR/MLP1/MLP2-like protein
       0.28   11.6   5.4        1.1    9.6   5.4    2.0  1  DUF4200     Domain of unknown function (DUF4200)
       0.38   10.6   2.7         17    5.2   0.1    2.5  2  Sec34       Sec34-like family


Domain annotation for each model (and alignments):
>> CorA  CorA-like Mg2+ transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.6    0.0021       7.4     170     223 ..     198     249 ..     192     252 .. 0.86
   2 ?   -0.8   0.1      0.21   7.5e+02     196     225 ..     306     335 ..     285     361 .. 0.71
   3 ?    7.1   0.0   0.00085       3.1     103     225 ..     425     544 ..     417     548 .. 0.73

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0021
                               CorA 170 nrevlkrllakaddkllddedkeylrdlldelerllemlealrerleslqdtys 223
                                         re+l+++++   +++ ++++++ +++ll++ + + ++ eal e l++l+++++
  gene3188|gene3188|rna3188|rna3188 198 DREALQDVIR--KGEEREKQMSKDIDELLSQCNEAKKQKEALTEELRVLNESLA 249
                                        5888999999..6666777777789*************************9986 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.21
                               CorA 196 dlldelerllemlealrerleslqdtyssl 225
                                          +d+l ++le++++++e  + + d++ss 
  gene3188|gene3188|rna3188|rna3188 306 GAMDKLVKVLEETTSISEDFQGVIDSHSSE 335
                                        466777777777777777777777777765 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.00085
                               CorA 103 gkpkspgellyrlldeivdrlfellekleeeldeledeledstkkeilrelaqlrrrlvklrralapnrevlkrll 178
                                        ++p++ ++ ++ +   ++++l+el  +l+e ++  e+ l+ +t k  +r  a +   l ++ + + +++++  +++
  gene3188|gene3188|rna3188|rna3188 425 QGPSDFFSAFLDCYSGMTESLRELDNELDEAVRVHESLLKAKTPKLVVRGAALMTSALKRYNKTVQNQQAAR-KMI 499
                                        566666777777777777777777777777777777777555555555555555555888888888888888.999 PP

                               CorA 179 akaddkllddedkeylrdlldelerllemlealrerleslqdtyssl 225
                                        +   +k + +   + l  + + le  ++ l al ++l  l++ y+++
  gene3188|gene3188|rna3188|rna3188 500 D--SAKSVVPCSDPVLHSIAITLEDNEDILAALTQKLLHLNNVYAQV 544
                                        9..344444444478**************************999987 PP

>> Vac_Fusion  Chordopoxvirus multifunctional envelope protein A27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.3   0.00046       1.7       5      42 ..     314     351 ..     310     354 .. 0.89
   2 ?   -1.3   0.0      0.49   1.8e+03      16      38 ..     431     453 ..     428     457 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00046
                                        HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-XXXXXXX CS
                         Vac_Fusion   5 leerllvlekdfqlvikcckrvnealkRlEnHleTlRk 42 
                                        + e  +++ +dfq vi++ +  +++++ + + l+T+R 
  gene3188|gene3188|rna3188|rna3188 314 VLEETTSISEDFQGVIDSHSSESKVIRDVSRRLNTVRE 351
                                        55567899*****************************7 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.49
                                        HHHHHHHHHHHHHHHHHHH-XXX CS
                         Vac_Fusion  16 fqlvikcckrvnealkRlEnHle 38 
                                        f    +c++ + e+l+ l n l+
  gene3188|gene3188|rna3188|rna3188 431 FSAFLDCYSGMTESLRELDNELD 453
                                        6778899*******999999775 PP

>> TPR_MLP1_2  TPR/MLP1/MLP2-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   2.6   0.00027      0.96      73     126 ..     188     241 ..     182     244 .. 0.86
   2 ?    0.7   0.0      0.14   5.1e+02      17      73 ..     297     353 ..     286     361 .. 0.81
   3 ?    0.9   0.1      0.12   4.5e+02      35      64 ..     475     504 ..     442     530 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00027
                         TPR_MLP1_2  73 iaelkaeaesakaeleeseesweeqkeelekelselekriedlneqNklLhdQl 126
                                           + ae  + +++l+    + ee+++++ k+++el +++++ ++q + L + l
  gene3188|gene3188|rna3188|rna3188 188 FDAMMAEYSKDREALQDVIRKGEEREKQMSKDIDELLSQCNEAKKQKEALTEEL 241
                                        5566677778889999999999*************************9998876 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.14
                         TPR_MLP1_2  17 keeaeaklqklqedlekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaei 73 
                                        +e++ ++   ++++l k  e+++   ++++  +  h++++k ++++  +ln++++++
  gene3188|gene3188|rna3188|rna3188 297 SEDLLQERDGAMDKLVKVLEETTSISEDFQGVIDSHSSESKVIRDVSRRLNTVRERV 353
                                        566666667777888888888888888888899999999999999999999999887 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.12
                         TPR_MLP1_2  35 aeiakeaqqkYerelvkhaedvkelqalre 64 
                                        a++++ a ++Y + ++++ ++ k + ++++
  gene3188|gene3188|rna3188|rna3188 475 AALMTSALKRYNKTVQNQQAARKMIDSAKS 504
                                        677888999999999999999999988875 PP

>> DUF4200  Domain of unknown function (DUF4200)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   5.4   0.00031       1.1      48     104 ..     186     242 ..     182     246 .. 0.93

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00031
                            DUF4200  48 lkfdkflkendakraralkkaeeerklkkekeaeikklkaeietlkseiekleekle 104
                                        ++fd ++ e  + r+  +  + + +++ k++ ++i +l +++++ k+++e l e+l+
  gene3188|gene3188|rna3188|rna3188 186 ARFDAMMAEYSKDREALQDVIRKGEEREKQMSKDIDELLSQCNEAKKQKEALTEELR 242
                                        689*******9999999999**********************************986 PP

>> Sec34  Sec34-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.3    0.0071        25      27      70 ..     200     243 ..     184     256 .. 0.66
   2 ?    5.2   0.1    0.0049        17      12      69 ..     290     347 ..     284     360 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.0071
                              Sec34  27 eeleekfksvsektsslheaceqlleeqkrleelaeeieekLky 70 
                                        e l++  ++ +e+ ++++++ ++ll++ ++ ++ +e+++e+L++
  gene3188|gene3188|rna3188|rna3188 200 EALQDVIRKGEEREKQMSKDIDELLSQCNEAKKQKEALTEELRV 243
                                        44455555556666667777777777777777777777777765 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0049
                              Sec34  12 cdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaeeieekLk 69 
                                        +d l++  +++l++ +   +k  +v e+t+s++e+ + +++++++ +++ ++++ +L+
  gene3188|gene3188|rna3188|rna3188 290 IDCLIAVSEDLLQERDGAMDKLVKVLEETTSISEDFQGVIDSHSSESKVIRDVSRRLN 347
                                        6778888888899999999999999999999999999999999999999999999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (691 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1230  (0.0686039); expected 358.6 (0.02)
Passed bias filter:                      785  (0.0437838); expected 358.6 (0.02)
Passed Vit filter:                       108  (0.00602376); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.76u 0.29s 00:00:01.05 Elapsed: 00:00:00.45
# Mc/sec: 4597.63
//
Query:       gene3189|gene3189|rna3189|rna3189  [L=120]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       714  (0.0398237); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.21s 00:00:00.60 Elapsed: 00:00:00.37
# Mc/sec: 962.24
//
Query:       gene319|gene319|rna319|rna319  [L=540]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
   5.3e-119  398.0   9.7   6.6e-119  397.7   9.7    1.0  1  Cpn60_TCP1  TCP-1/cpn60 chaperonin family


Domain annotation for each model (and alignments):
>> Cpn60_TCP1  TCP-1/cpn60 chaperonin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  397.7   9.7  3.7e-123  6.6e-119       1     488 [.      43     526 ..      43     528 .. 0.96

  Alignments for each domain:
  == domain 1  score: 397.7 bits;  conditional E-value: 3.7e-123
                                    HHHHHHCCSSTTXXEEEEEETTSEEEEEXSHHHHHHCSXXXSHHHHHHHHHHHHCCCCCTTCHHHHHHHHHHHHHHHHHH CS
                     Cpn60_TCP1   1 ladivkttlGPkGmdKmlvnkggkvvvTnDGatilkeleiehPaakllveaaesqdeevGDGTttvviLageLleeaekl 80 
                                    l++++kt++G  G+dKm +   g+v +TnDGatil+++++++P+a+l++e++++qd e+GDGTt vv+La++L+e++ +l
  gene319|gene319|rna319|rna319  43 LTNAIKTSYGALGLDKMCIGTTGDVLITNDGATILTNMDVKDPIANLIIELSRQQDVEMGDGTTGVVLLASALIEKGNEL 122
                                    789***************************************************************************** PP

                                    HHCTXXHHHHHHHHHHHHHHHHHHHHHHXEEBXSCSTT.HHHHHHHHHHCTTSSXXSTHHHHHHHHHHHHHCHCCCS... CS
                     Cpn60_TCP1  81 iaagvhpttiiegyekalekaleaLkeiaveisseekdreeLlkvartslsskltskeaeelsklvvdAvklieene... 157
                                    i++g+hp+++++gy++a+ +  +++ke+   ++++   + ++ +v+ t+lssk++++  +++ +l+++Avk++e  +   
  gene319|gene319|rna319|rna319 123 IKRGLHPSVVVSGYKMAFRESQRFIKEK---LENK---NVNIDAVIDTTLSSKVIHS--KHFNELTLKAVKAVEHVDflg 194
                                    *************************988...3333...367************8877..59************9999*** PP

                                    .EECSCCCEECCCCEECECTTSEEESEEEESS--SSTTSSCEEECEEEEEESS-BS--HHCCHHHCCCCSCCHHHHHHHH CS
                     Cpn60_TCP1 158 .keldlgrikvvkieggsledselveGlvldkgvlspdmpkklenakvllldvsLeiektetkttvvlsdaeelekleka 236
                                     +++ +++i+++k+egg+++ds  veG++++  ++s++mp k++n++v+lld+ L   +   ++++v++d++ le+ +k+
  gene319|gene319|rna319|rna319 195 kRRYGIKNINILKKEGGQMSDSFAVEGYAINARPCSTEMPAKMKNVRVALLDFDLGKIRLPLNVNIVVNDPDMLESNRKK 274
                                    *9****************************************************************************** PP

                                    HHHHHHHHHHHHHHTTECEEEESS-B-HHHHHHHHHCT-EEE-S--HHHHHHHHHHHT--EBSCGGGGGCGC-EEEEEEE CS
                     Cpn60_TCP1 237 eekqleellekiiksgvnvvvcqkgiddlalhflakngilalrrvkkkdlerlakatGatavssledltpeelGtakkve 316
                                    e  + +++++ki +s ++v+++ + idd++ +   +++ ++++rv  kdl+ l+ka++  + s+ e+++     ++++++
  gene319|gene319|rna319|rna319 275 EISMALDRVKKILES-ADVILSSRNIDDVCVKPIIEAKKIGIKRVPMKDLKVLSKALNIAI-SKTEEIET---AQIDEIT 349
                                    *************86.89****************************************865.55567766...5789999 PP

                                    ECCETTCCEEEEECESSSSXEEEEEEESTCCCHHHHHHHHHHHHHHHHHHHHHHEEEETTTCHHHHHHHHHHCCCCTSXC CS
                     Cpn60_TCP1 317 eekigsekttiieevksgkiatillrgatdtvldeieraiedAlnvvknaiedekvvpGGGatelelakklkeyaksvsg 396
                                    +e++  e++ti++    +++++i+lrg +dt l+e+er+++d+l+++k+++e e v++GGGa+e++l+  l+eya s+++
  gene319|gene319|rna319|rna319 350 VEQLAHEDYTILKF--GKNLSSIVLRGGNDTLLEEMERSVNDGLCAIKRTLECESVLAGGGAFECALSIFLEEYAFSLPS 427
                                    9************8..899************************************************************* PP

                                    CHHHHHHHHHHHHTHHHHHHHHHCTSXHHHHHHHHHHHHHTTX.......TTEEEETTTTCEEECCCCTXEEEHHHHHHH CS
                     Cpn60_TCP1 397 eeqlaieafakALevipktLaeNaGldpievlaklraahnkge.......kelgidvesgeiidlveagvvDplkvkrqa 469
                                    +e+ ai  ++++L+vipktLa NaGld+++vl++lra +n+g+       + +g+d+++gei++ +e+g+v+p   k +a
  gene319|gene319|rna319|rna319 428 KEAAAIFTYSESLLVIPKTLAMNAGLDANQVLSELRAFQNNGNqegvsdcFDYGLDIRTGEIVNNIERGIVEPGVSKIRA 507
                                    ***************************************999999999999***************************** PP

                                    HHHHHHHHHHHHCEEEEEX CS
                     Cpn60_TCP1 470 lksAteaastiLrideiik 488
                                    l +Ate+a +iLride+ik
  gene319|gene319|rna319|rna319 508 LRAATEVAISILRIDEVIK 526
                                    ******************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (540 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       740  (0.0412739); expected 358.6 (0.02)
Passed bias filter:                      523  (0.0291706); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.31s 00:00:00.92 Elapsed: 00:00:00.47
# Mc/sec: 3451.03
//
Query:       gene3190|gene3190|rna3190|rna3190  [L=46]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (46 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       367  (0.0204696); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.23s 00:00:00.57 Elapsed: 00:00:00.39
# Mc/sec: 357.56
//
Query:       gene3191|gene3191|rna3191|rna3191  [L=150]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.5e-35  118.2   0.5    1.7e-34  117.4   0.5    1.4  1  ubiquitin      Ubiquitin family
    2.2e-16   59.5   0.6    3.9e-16   58.6   0.6    1.4  1  Rad60-SLD      Ubiquitin-2 like Rad60 SUMO-like
    6.7e-16   58.2   2.7    1.5e-15   57.0   2.7    1.6  1  Ribosomal_S27  Ribosomal protein S27a
    5.6e-06   26.7   0.3      7e-05   23.2   0.1    2.4  2  Ubiquitin_2    Ubiquitin-like domain
    0.00014   21.9   0.4    0.00036   20.6   0.4    1.6  1  Rad60-SLD_2    Ubiquitin-2 like Rad60 SUMO-like
      0.003   17.9   0.9     0.0085   16.4   0.1    1.9  2  Ubiquitin_5    Ubiquitin-like domain
     0.0057   17.2   0.7      0.008   16.7   0.7    1.2  1  DUF2407        DUF2407 ubiquitin-like domain
      0.006   16.5   0.0     0.0093   15.9   0.0    1.3  1  TBK1_ULD       TANK binding kinase 1 ubiquitin-like domain
  ------ inclusion threshold ------
      0.012   15.6   1.1        3.8    7.6   0.2    2.5  2  Ubiquitin_4    Ubiquitin-like domain
      0.012   15.4   0.0      0.018   14.9   0.0    1.2  1  Sde2_N_Ubi     Silencing defective 2 N-terminal ubiquitin dom


Domain annotation for each model (and alignments):
>> ubiquitin  Ubiquitin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.4   0.5   9.6e-38   1.7e-34       1      72 []       3      74 ..       3      74 .. 0.99

  Alignments for each domain:
  == domain 1  score: 117.4 bits;  conditional E-value: 9.6e-38
                                       EEEEETTSEEEEEEEETTSBHHHHHHHHHHHHTSSGGGEEEEETTEEE-TTSBHGGHTTSTTEEEEEEESSC CS
                          ubiquitin  1 itvktldgkkitleveesdtveelKekiaekegipaeqqrLiysGkvLedertleeygiqdgstlhlvlrlr 72
                                       i+vktl+gk+itleve+sdt+e++K+ki++kegip++qqrLi++Gk+Led rtl++y+iq++stlhlvlrlr
  gene3191|gene3191|rna3191|rna3191  3 IFVKTLTGKTITLEVESSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLR 74
                                       9********************************************************************986 PP

>> Rad60-SLD  Ubiquitin-2 like Rad60 SUMO-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.6   0.6   2.2e-19   3.9e-16       1      72 []       1      71 [.       1      71 [. 0.98

  Alignments for each domain:
  == domain 1  score: 58.6 bits;  conditional E-value: 2.2e-19
                                       EEEEEEESSS--EEEEEETTSBHHHHHHHHHHHHT----TT-EEEETTEE--TTSBGGGSS--TTEEEEEEX CS
                          Rad60-SLD  1 ikiilkgkdgkevkikVkptttvskLieayrkkkgipeeqkvrLiFDGeeLdpnstvedldiedgdtidvvi 72
                                       ++i++k+ +gk+++++V+++ t+++++ + ++k+gip+ +++rLiF G++L++  t+ d+ i++++t+++v+
  gene3191|gene3191|rna3191|rna3191  1 MQIFVKTLTGKTITLEVESSDTIENVKAKIQDKEGIPP-DQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVL 71
                                       89************************************.******************************986 PP

>> Ribosomal_S27  Ribosomal protein S27a
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.0   2.7   8.6e-19   1.5e-15       1      43 [.     101     142 ..     101     143 .. 0.98

  Alignments for each domain:
  == domain 1  score: 57.0 bits;  conditional E-value: 8.6e-19
                                        SSSSCCESSSSSEEESS-B-SS-S-TTSBEEECTTEEEESSTT CS
                      Ribosomal_S27   1 vlkyYkvddsgkverlrkeCpreCGaGvfMAehkdRkyCGkCg 43 
                                        vl+ ++vd+sg+v+ lrkeC + CG+G+f+++ k+++yCG+C+
  gene3191|gene3191|rna3191|rna3191 101 VLTQFSVDKSGNVSVLRKECVQ-CGPGYFLGHSKGKEYCGHCH 142
                                        799*******************.*******************9 PP

>> Ubiquitin_2  Ubiquitin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.1   3.9e-08     7e-05      16      80 ..      13      69 ..       2      70 .. 0.86
   2 ?   -0.0   0.0       0.7   1.3e+03      48      79 ..      83     114 ..      75     118 .. 0.79

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 3.9e-08
                                       EEEEEETTSBHHHHHHHHHHHH---TTCEEEEEE.-SSSSEEECSSGCCSBCCCCT--TTEEEEE CS
                        Ubiquitin_2 16 serrfsksltieelKekLelitGtspasmrLqlyddkkdnevsklddddalLgsYgvkdgmrihV 80
                                        +  +++s+tie++K+k++   G++p+++rL +          k  +d ++L++Y+++  +++h 
  gene3191|gene3191|rna3191|rna3191 13 ITLEVESSDTIENVKAKIQDKEGIPPDQQRLIFA--------GKQLEDGRTLSDYNIQKESTLHL 69
                                       55678899************************99........5667899*********9999995 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.7
                                        EE.-SSSSEEECSSGCCSBCCCCT--TTEEEE CS
                        Ubiquitin_2  48 lyddkkdnevsklddddalLgsYgvkdgmrih 79 
                                        +y+++k+++  ++d  d  L +++v+   ++ 
  gene3191|gene3191|rna3191|rna3191  83 VYTTPKKEKPKRIDTKDVVLTQFSVDKSGNVS 114
                                        56778889999999999999999988766655 PP

>> Rad60-SLD_2  Ubiquitin-2 like Rad60 SUMO-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.4     2e-07   0.00036      12     108 ..      10      92 ..       2      95 .. 0.74

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 2e-07
                                        S-EEEEEEEETT-BHHHHHHHHHHHS-TT-SSS--SCCCEEEEETTEEE-TTSBCCCCS-TTTTTTTS-EEEEEEE CS
                        Rad60-SLD_2  12 GsDigpvkfsdaatvaelkekviaqWPkdkeekpksvndlklilaGkiLennktlkelrlplgevkggvtvmHvvv 87 
                                        G+ +  ++ ++++t++++k+k+     +dke  p  +++ +li aGk Le+ +tl++++++        +++H+v+
  gene3191|gene3191|rna3191|rna3191  10 GK-TITLEVESSDTIENVKAKI-----QDKEGIP--PDQQRLIFAGKQLEDGRTLSDYNIQK--E----STLHLVL 71 
                                        55.5556677778888888887.....4556533..34559*****************5443..3....57***** PP

                                        ---SS----.XXXXXXXXXXX CS
                        Rad60-SLD_2  88 renlsekksekkakkakkkkc 108
                                        r    +kk++k  + +kk+k+
  gene3191|gene3191|rna3191|rna3191  72 RLRGGKKKKKKVYTTPKKEKP 92 
                                        *99999999998777766665 PP

>> Ubiquitin_5  Ubiquitin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.1   4.7e-06    0.0085      34      93 ..      13      73 ..       5      78 .. 0.83
   2 ?    0.9   0.2      0.34   6.1e+02      28      46 ..      87     105 ..      65     148 .. 0.62

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 4.7e-06
                        Ubiquitin_5 34 klletkLdvtgkelvskiaeefglkensiKlilngklleldktLeeQgvknnskv.mvLkl 93
                                        +le++ + t +++ +ki ++ g+  ++ +li  gk+le ++tL + +++++s + +vL+l
  gene3191|gene3191|rna3191|rna3191 13 ITLEVESSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLhLVLRL 73
                                       5566666667889999999999**99***********************999875477776 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.34
                        Ubiquitin_5  28 tkeekkklletkLdvtgke 46 
                                        +k+ek+k ++tk  v ++ 
  gene3191|gene3191|rna3191|rna3191  87 PKKEKPKRIDTKDVVLTQF 105
                                        2334455555555554444 PP

>> DUF2407  DUF2407 ubiquitin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.7   4.4e-06     0.008      14      72 ..      13      81 ..       6     109 .. 0.69

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 4.4e-06
                            DUF2407 14 leLdipdpntttvagLkqliRerlpaelasrrLrLIyaGrlLedttslasslklpees..............v 72
                                       ++L+++  ++ t++++k  i ++    +   + rLI+aG+ Led  +l++   ++e++              +
  gene3191|gene3191|rna3191|rna3191 13 ITLEVE--SSDTIENVKAKIQDKE--GIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTlhlvlrlrggkkkkK 81
                                       566666..7789999999999987..67777789**************9865555454566665555443221 PP

>> TBK1_ULD  TANK binding kinase 1 ubiquitin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   5.2e-06    0.0093      19      53 ..      17      51 ..       4      72 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 5.2e-06
                           TBK1_ULD 19 ihpyntvaifqeevakqTkiaaekQellfeghrll 53
                                       +++ +t++++  +++++  i++++Q l+f g++l 
  gene3191|gene3191|rna3191|rna3191 17 VESSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLE 51
                                       67899***************************973 PP

>> Ubiquitin_4  Ubiquitin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.2    0.0021       3.8       1      32 [.       1      32 [.       1      36 [. 0.94
   2 ?    6.5   0.0    0.0049       8.7      58      86 ..      43      70 ..      39      73 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0021
                        Ubiquitin_4  1 lkvtvkkldgeslevvvkqnatvkdLkkaier 32
                                       +++ vk l g+++ ++v+++ t++++k+ i+ 
  gene3191|gene3191|rna3191|rna3191  1 MQIFVKTLTGKTITLEVESSDTIENVKAKIQD 32
                                       7899*************************997 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0049
                        Ubiquitin_4 58 LsfegekLkddkaklkeygirnkselsFv 86
                                       L+f g++L+ d  +l++y i+++s+l+ v
  gene3191|gene3191|rna3191|rna3191 43 LIFAGKQLE-DGRTLSDYNIQKESTLHLV 70
                                       889999986.6789************976 PP

>> Sde2_N_Ubi  Silencing defective 2 N-terminal ubiquitin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0     1e-05     0.018       2      89 ..       2      77 ..       1      78 [. 0.85

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1e-05
                         Sde2_N_Ubi  2 nvlvssfdgltlpstlsltlpstatvsdlvdklserlpeslkesliLttvsnkqlllssdvslssllassadsellsl 79
                                       +++v+++ g+    t++l++ s+ t++++ +k++++      +   L  + + ql  ++  +ls++  ++++    +l
  gene3191|gene3191|rna3191|rna3191  2 QIFVKTLTGK----TITLEVESSDTIENVKAKIQDKEGIPPDQ-QRLIFAGK-QL--EDGRTLSDYNIQKES----TL 67
                                       8999*99996....999*****************998877555.45555554.66..99999****999999....9* PP

                         Sde2_N_Ubi 80 rllvrlrGGK 89
                                       +l++rlrGGK
  gene3191|gene3191|rna3191|rna3191 68 HLVLRLRGGK 77
                                       *********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       923  (0.0514808); expected 358.6 (0.02)
Passed bias filter:                      527  (0.0293937); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.42u 0.22s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1185.78
//
Query:       gene3192|gene3192|rna3192|rna3192  [L=42]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (42 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       245  (0.013665); expected 358.6 (0.02)
Passed bias filter:                      157  (0.00875676); expected 358.6 (0.02)
Passed Vit filter:                         5  (0.000278878); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.44
# Mc/sec: 287.61
//
Query:       gene3193|gene3193|rna3193|rna3193  [L=231]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.6e-25   87.9   0.0    7.9e-25   87.5   0.0    1.2  1  Proteasome      Proteasome subunit
    1.2e-10   40.9   0.0    2.2e-10   40.0   0.0    1.5  1  Proteasome_A_N  Proteasome subunit A N-terminal signature


Domain annotation for each model (and alignments):
>> Proteasome  Proteasome subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.5   0.0   8.8e-29   7.9e-25      42     158 ..      79     192 ..      54     205 .. 0.93

  Alignments for each domain:
  == domain 1  score: 87.5 bits;  conditional E-value: 8.8e-29
                                        EETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHSSGTCHHHHHHHHHHHHHHHHHHCTTTTTSEEEEEEEEETTT CS
                         Proteasome  42 iddhigvafaGlaaDartlvrraraeaqlyrlrygrpipverlvarvaaklqaytqrsgrrpfgvslliagvdeeg 117
                                         d++i++af+Gl +Da ++++ ar+ a++yr+ y  +i++++l++++a ++q+yt ++g+rpfgv++++ gv e  
  gene3193|gene3193|rna3193|rna3193  79 ADQNIWLAFSGLRPDALQIISEARYMARQYRYVYMVDISLRQLASELAMYMQRYTITRGFRPFGVRVILFGVEEC- 153
                                        489**********************************************************************55. PP

                                        EEEEEEEETTSEEEEESSEEEESTTHHHHHHHHHHHHSTTB CS
                         Proteasome 118 gpeLyqidpsGsyieekdavaiGsgseaaktalekeykedl 158
                                          + + + p+G+y+e+k a+a+G++++ a ++le+++k+d+
  gene3193|gene3193|rna3193|rna3193 154 -ARAFVVGPDGNYLEYK-ACAVGQKADKAVQFLENNLKDDC 192
                                        .489************8.*****99************9996 PP

>> Proteasome_A_N  Proteasome subunit A N-terminal signature
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.0   0.0   2.5e-14   2.2e-10       1      23 []      16      38 ..      16      38 .. 0.99

  Alignments for each domain:
  == domain 1  score: 40.0 bits;  conditional E-value: 2.5e-14
                     Proteasome_A_N  1 YDrslttFSPdGRLfQVEYAmkA 23
                                       YD +l +FSPdGRL QVE A+kA
  gene3193|gene3193|rna3193|rna3193 16 YDHALAVFSPDGRLIQVENAQKA 38
                                       **********************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       446  (0.0248759); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1793.69
//
Query:       gene3194|gene3194|rna3194|rna3194  [L=867]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.1e-44  150.7   0.4    3.1e-44  150.7   0.4    2.0  2  DEAD_2         DEAD_2
    1.9e-36  125.8   0.1    2.5e-32  112.4   0.1    2.6  2  Helicase_C_2   Helicase C-terminal domain
    1.4e-07   31.7   2.3      8e-07   29.2   0.0    3.1  2  ResIII         Type III restriction enzyme, res subunit
    0.00019   21.3   0.3     0.0068   16.2   0.3    2.7  1  DEAD           DEAD/DEAH box helicase
    0.00054   19.5   0.1       0.36   10.3   0.0    2.3  2  PhoH           PhoH-like protein
     0.0094   15.8   0.1     0.0094   15.8   0.1    3.3  3  AAA_11         AAA domain
  ------ inclusion threshold ------
      0.012   15.3   0.0      0.087   12.5   0.0    2.0  2  AAA_30         AAA domain
      0.019   14.8   1.7      0.036   13.9   0.0    2.3  3  Helicase_RecD  Helicase
      0.036   14.4   0.0      0.098   13.0   0.0    1.7  1  AAA_19         AAA domain
      0.085   12.5   3.0       0.11   12.2   0.1    2.6  3  SWI2_SNF2      SWI2/SNF2 ATPase
      0.093   12.4   0.1       0.22   11.2   0.1    1.6  1  HBB            Helical and beta-bridge domain


Domain annotation for each model (and alignments):
>> DEAD_2  DEAD_2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  150.7   0.4   1.9e-47   3.1e-44       1     175 [.      73     226 ..      73     227 .. 0.94
   2 ?   -4.3   1.0       7.1   1.2e+04      53      86 ..     768     802 ..     748     819 .. 0.59

  Alignments for each domain:
  == domain 1  score: 150.7 bits;  conditional E-value: 1.9e-47
                                        EEESSHHHHHHHHHHHHHHHHHCHHHS---EEEE--CCCC-SCHHCCCHHCCCCHHHHHHHHHCCHHCCHTTTTTT CS
                             DEAD_2   1 ycsRThsqleqvvkelkklesykkkkekvkvviLgSRknlCineevkkekkekavneaCkelkkkkaeekeekCsf 76 
                                        +csRTh+ql+q+v++l+ + +y       kv++L+SR+ lC+n++++k     +vn+ C++l+kk       +C++
  gene3194|gene3194|rna3194|rna3194  73 ICSRTHKQLDQLVAQLRAT-AYAP-----KVCVLASRRALCLNKQALK----GDVNASCRDLVKKG------ECRY 132
                                        6*****************9.6777.....8*************99999....789**********9......6*** PP

                                        -SCCCCHHHHHHHHHHC---CHHHHHHHHHCT--HHHHHHHHHCCTSEEEEEHHHHTSCCCHHHHHT..GCGCEEE CS
                             DEAD_2  77 fenleelkklkkllleevvdiedlvelgeklklCPYylsrelledadiiilpYqyLldekireslkgislknsivi 152
                                        f  +e+l k        v die+l ++ge+++ CPYy+sr l eda i ++pY+y++d+ +r+++  i+lk+s+vi
  gene3194|gene3194|rna3194|rna3194 133 FMGKERLAK----SIGDVHDIEELRQAGERCTGCPYYASRMLSEDAAITFMPYNYVVDPMVRRTMG-IELKDSVVI 203
                                        *99977766....57889***********************************************6.********* PP

                                        ECTCCCHHHHHHHCC-EEEECHH CS
                             DEAD_2 153 lDEAhNiedvceeaasveisees 175
                                        +DEAhNied c++a s+e+++++
  gene3194|gene3194|rna3194|rna3194 204 VDEAHNIEDACRSAGSIELTNDT 226
                                        *******************9986 PP

  == domain 2  score: -4.3 bits;  conditional E-value: 7.1
                                        CCHHHHHHHHHCCHHCCH.TTTTTT-SCCCCHHHH CS
                             DEAD_2  53 kavneaCkelkkkkaeek.eekCsffenleelkkl 86 
                                        ++ +e C+e+ k+  +e+ +e C+ + + ++l+++
  gene3194|gene3194|rna3194|rna3194 768 ENGKEDCRESGKEGCNENgKEGCRENGRGNNLENS 802
                                        44455566665555444445666655444444443 PP

>> Helicase_C_2  Helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.0   0.00032      0.51       8      35 ..     453     480 ..     446     515 .. 0.89
   2 !  112.4   0.1   1.5e-35   2.5e-32      38     169 ..     593     715 ..     566     717 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00032
                       Helicase_C_2   8 vpggvlvffpSyklleevverlkeeles 35 
                                          gg++vf pSy+ +++vv+r+++++++
  gene3194|gene3194|rna3194|rna3194 453 QGGGTVVFLPSYHAVNKVVSRMRSRGTN 480
                                        4599*******************99865 PP

  == domain 2  score: 112.4 bits;  conditional E-value: 1.5e-35
                       Helicase_C_2  38 i....eifveekeesrekvleeykekkkkgaillavcrGklsEGidfsddllraviivglPfpnpkdpeveakrey 109
                                        +    ++f e+++++++kv+++yk+  + + illav+rGk sEG df+d+l+ravi+vg+P pn+k+  ve+ r++
  gene3194|gene3194|rna3194|rna3194 593 NncidNVFIETNDKNFSKVFAQYKK--HPNPILLAVYRGKASEGTDFKDKLARAVILVGMPCPNIKEIGVELMRNH 666
                                        13455789999**************..*******************************************999875 PP

                       Helicase_C_2 110 ldekgkknsgkewylpealravnQaiGRliRhkdDygaivllDeRfakeeireklpkwlr 169
                                                    wy+++ ++avnQaiGR++Rh+ D+g ++l+D R+++++   +l  w+r
  gene3194|gene3194|rna3194|rna3194 667 ---------RPGWYENQIFKAVNQAIGRCVRHRMDWGGVFLVDVRYRRDK--DRLCGWCR 715
                                        .........246***********************************988..88989887 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.2   0.0   4.9e-10     8e-07       2     148 ..      18     217 ..      17     252 .. 0.63
   2 ?   -1.2   0.5       1.1   1.7e+03      56      85 ..     820     849 ..     796     866 .. 0.62

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 4.9e-10
                                        -EE-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHH..HHHHHHH-S.....-EEEEESSH.HHHHHHHHHG CS
                             ResIII   2 lelreyQeeaienlleklkskrdkrglikmaTGtGKTlva..aklierllkkgkeekflflvprk.slleqtleef 74 
                                        +++++ Q+  + ++++ lk  ++k g+i+ +TGtGK++ +  a l+++ ++  +    +f++ r+ + l+q+  ++
  gene3194|gene3194|rna3194|rna3194  18 FKPYPAQILTCSKIIDCLK--NKKTGIIESPTGTGKSIAIlcAVLAWHATN--RS-TRIFICSRThKQLDQLVAQL 88 
                                        678999************5..9***************98833455555555..44.44555555436667776666 PP

                                        ..................................................GGGTGG....GEEEESSS-B--.... CS
                             ResIII  75 ..................................................kkflseaykeigkkvsgdkkka.... 96 
                                                                                                               a    
  gene3194|gene3194|rna3194|rna3194  89 ratayapkvcvlasrralclnkqalkgdvnascrdlvkkgecryfmgkerL--------------------Aksig 144
                                        555568888888887777777655555555555555555544333332220....................12233 PP

                                        .............................-SEEEEEHHHHHHTH........HHHTTT-S.EEEEETGGGTTS... CS
                             ResIII  97 ......................kekdstnkkilvttiqsldadseeeeeeseellrdrfd.viiiDEaHrlgak.. 147
                                                              ++  s+++ i+++ ++ +  ++      + +++ + +d v+i+DEaH++ ++  
  gene3194|gene3194|rna3194|rna3194 145 dvhdieelrqagerctgcpyyaSRMLSEDAAITFMPYNYVVDPM-----VRRTMGIELKDsVVIVDEAHNIEDAcr 215
                                        33333344445555566666668889999999999999999999.....666666666666*********998654 PP

                                        .T CS
                             ResIII 148 .k 148
                                         +
  gene3194|gene3194|rna3194|rna3194 216 sA 217
                                        40 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.1
                                        -EEEEESSHHHHHHHHHHGGGGTGG....G CS
                             ResIII  56 kflflvprkslleqtleefkkflseaykei 85 
                                        +  ++  + ++ eqt+ +  +f++ +yk+ 
  gene3194|gene3194|rna3194|rna3194 820 NNTIITKNAAIKEQTYLKNDNFIEREYKNR 849
                                        555677777888888866666666666542 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.3   4.2e-06    0.0068       6      63 ..      30     110 ..      23     233 .. 0.57

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 4.2e-06
                                        HHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS........................-EEEEEESSH CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........................xxxxxxxxxx RF
                               DEAD   6 eaiplilgggdvlvaaeTGsGKTlaflipvlqivyetkgktg........................pkalivePtr 57 
                                        ++i+++ +++  +++ +TG+GK+ a l +vl++ ++ +++t+                        pk+ +++  r
  gene3194|gene3194|rna3194|rna3194  30 KIIDCLKNKKTGIIESPTGTGKSIAILCAVLAWHAT-NRSTRificsrthkqldqlvaqlratayaPKVCVLASRR 104
                                        567788889999*******************88754.222224444444445555555555555557777777777 PP

                                        HHHHHH CS
                                        xxxxxx RF
                               DEAD  58 eLaeqt 63 
                                        +L+ + 
  gene3194|gene3194|rna3194|rna3194 105 ALCLNK 110
                                        776543 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.0   0.00022      0.36      11      60 ..      30      80 ..      24      97 .. 0.74
   2 !    6.6   0.0    0.0028       4.6     115     133 ..     194     212 ..     166     218 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00022
                                       HHHHHHHH-SEEEEE--TTSSTTHHHHHHHHHHHHT.TS-SEE.EEEE-S-- CS
                               PhoH 11 eylealkkndivfaiGpaGtGKtylavalavealkk.kkvkri.iltrpave 60
                                       ++++ lk+++  ++  p+GtGK+ +a+ +av a+++ ++ +ri i +r + +
  gene3194|gene3194|rna3194|rna3194 30 KIIDCLKNKKTGIIESPTGTGKS-IAILCAVLAWHAtNRSTRIfICSRTHKQ 80
                                       6789999***************9.6777787777653555555155666555 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0028
                                        T--B-SEEEEE-SGGG--H CS
                               PhoH 115 GrTlndafvilDEAQnttk 133
                                        G  l+d++vi+DEA n++ 
  gene3194|gene3194|rna3194|rna3194 194 GIELKDSVVIVDEAHNIED 212
                                        7789************986 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.1   5.8e-06    0.0094      12      87 ..      33      94 ..      28     155 .. 0.83
   2 ?    2.2   1.1      0.08   1.3e+02     122     198 ..     513     589 ..     461     605 .. 0.57
   3 ?   -1.9   3.0       1.4   2.3e+03     125     173 ..     808     856 ..     742     867 .] 0.54

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 5.8e-06
                             AAA_11 12 salseseitliqGPPGtgKTktivellsqllsrrkseeeksakpriLvCapSNaAvDellerllrglldsegekyk 87
                                        +l++++  +i+ P GtgK+ +i+  + +        ++ +++ ri +C+ +++  D+l+++l           y 
  gene3194|gene3194|rna3194|rna3194 33 DCLKNKKTGIIESPTGTGKSIAILCAVLAW-------HATNRSTRIFICSRTHKQLDQLVAQLRA-------TAYA 94
                                       578899999**************9999999.......35899******************99877.......4444 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.08
                             AAA_11 122 kaqlakeiskeleklakelrafeeeeekeklkkskekskskleqerrklkkerkelskeleeaeesleeevldeae 197
                                        +++ +++i++++ ++ + +++++ ++ +++ +++ ++++s++ +++r+ +  +++++k+++ + ++l++ + +++e
  gene3194|gene3194|rna3194|rna3194 513 NINNVNNINNRNLNNLNNINDKNINNVNTRNLNNLNNRNSNNINDKRTNSIFSNKIQKNIKIQGNTLRTAFQNRSE 588
                                        2333333333333333333333333333555555555666666666666666667777777777777666666665 PP

                             AAA_11 198 i 198
                                        i
  gene3194|gene3194|rna3194|rna3194 589 I 589
                                        5 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 1.4
                             AAA_11 125 lakeiskeleklakelrafeeeeekeklkkskekskskleqerrklkke 173
                                         ++ +++++++ ++++  +++ +++++ +k++++ +++++++++++ +e
  gene3194|gene3194|rna3194|rna3194 808 ENNPVNNKENDGNNTIITKNAAIKEQTYLKNDNFIEREYKNRKNTCDEE 856
                                        1122222222222222223333333455555555555555555555554 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   5.4e-05     0.087      17      70 ..      37      92 ..      29     122 .. 0.86
   2 ?   -0.1   0.0      0.39   6.3e+02      81      98 ..     189     208 ..     149     216 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.4e-05
                             AAA_30 17 gdrvavltGpAGtGKttalkalreaweaag..grviglAptgkaAkvLaeelgiea 70
                                       ++++ +++ p GtGK+ a+  ++ aw+a +   r+++++ t+k+ ++L ++l ++a
  gene3194|gene3194|rna3194|rna3194 37 NKKTGIIESPTGTGKSIAILCAVLAWHATNrsTRIFICSRTHKQLDQLVAQLRATA 92
                                       345889*******************99996569999*******9999988877666 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.39
                             AAA_30  81 k.grarlepg.tllivDEag 98 
                                          +++ +e + +++ivDEa 
  gene3194|gene3194|rna3194|rna3194 189 VrRTMGIELKdSVVIVDEAH 208
                                        354456777779******96 PP

>> Helicase_RecD  Helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   2.2e-05     0.036       2      50 ..      43      92 ..      42     149 .. 0.77
   2 ?   -1.9   0.0       1.6   2.6e+03      90     102 ..     198     210 ..     176     213 .. 0.82
   3 ?   -3.4   0.1       4.6   7.5e+03      41      62 ..     546     565 ..     520     601 .. 0.44

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.2e-05
                      Helicase_RecD  2 ltAdRGRGKSaalGlalaaliaegk.snilvtapskenvktlfeflakgl 50
                                       + +  G+GKS a+  a+ a+ a+++ ++i++++ +++++++l+++l+++ 
  gene3194|gene3194|rna3194|rna3194 43 IESPTGTGKSIAILCAVLAWHATNRsTRIFICSRTHKQLDQLVAQLRATA 92
                                       77889*****9887777777766666****************99986654 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.6
                      Helicase_RecD  90 qadllvvDEAAai 102
                                        +  +++vDEA  i
  gene3194|gene3194|rna3194|rna3194 198 KDSVVIVDEAHNI 210
                                        3479******877 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 4.6
                      Helicase_RecD  41 tlfeflakglealglkeeekkk 62 
                                        +l ++  +++++ +++  + ++
  gene3194|gene3194|rna3194|rna3194 546 NLNNRNSNNINDKRTN--SIFS 565
                                        2222222222222222..2222 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0     6e-05     0.098       8     115 ..      36     211 ..      29     217 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 6e-05
                             AAA_19   8 lkekvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerlaalgae......atTiHrlal 77 
                                         ++k+ ++  + GtGK+  + ++v  + ++++    +i +++ t++  ++l  +l+a   +      a        
  gene3194|gene3194|rna3194|rna3194  36 KNKKTGIIESPTGTGKSIAILCAVLAWHATNRS--TRIFICSRTHKQLDQLVAQLRATAYApkvcvlA-------S 102
                                        567888999999*****9999999888888865..9****************9995544444444440.......3 PP

                             AAA_19  78 .........................................................................ldf 80 
                                                                                                                 ++f
  gene3194|gene3194|rna3194|rna3194 103 rralclnkqalkgdvnascrdlvkkgecryfmgkerlaksigdvhdieelrqagerctgcpyyasrmlsedaaITF 178
                                        4445555555577777777777788888888888888888888888888888888888888887776544444333 PP

                             AAA_19  81 ddlltealelle.......eaeeekklqeeellivDEfqdvd 115
                                         +         +       +++   +l +  ++ivDE+ +++
  gene3194|gene3194|rna3194|rna3194 179 MPY--------NyvvdpmvRRTMGIEL-KDSVVIVDEAHNIE 211
                                        333........1333443223333344.55589999988876 PP

>> SWI2_SNF2  SWI2/SNF2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   6.7e-05      0.11       2     130 ..      24     208 ..      23     217 .. 0.55
   2 ?   -3.7   0.0       4.8   7.8e+03       3      19 ..     464     480 ..     464     489 .. 0.74
   3 ?   -3.6   0.1       4.2   6.9e+03     183     191 ..     556     564 ..     513     590 .. 0.56

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 6.7e-05
                          SWI2_SNF2   2 QyravekavervkegdrkgGviWHtqGSGKsltmvflakklleeelknpkvvvvtDRk..dLdkQlsktfaka.ge 74 
                                        Q+ +++k+++ +k+  +k G+i   +G GKs+  ++++ + ++  +++ + +++  R+  +Ld Ql ++++++   
  gene3194|gene3194|rna3194|rna3194  24 QILTCSKIIDCLKN--KKTGIIESPTGTGKSIAILCAVLAWHA--TNRSTRIFICSRThkQLD-QLVAQLRATaYA 94 
                                        88889999999998..69**************99998888777..566666677777511444.555555554233 PP

                          SWI2_SNF2  75 ekpkqaesrkeL...kellekesekiifttiqKfe.....eeek................................ 110
                                         k+    sr+ L   k+ l+ + +  +  +++K e        k                                
  gene3194|gene3194|rna3194|rna3194  95 PKVCVLASRRALclnKQALKGDVNASCRDLVKKGEcryfmG--Kerlaksigdvhdieelrqagerctgcpyyasr 168
                                        33334444444411122233223333333444433333221..023444555566666666666666666666666 PP

                          SWI2_SNF2 111 .....................eklevlsereniivlvDEaH 130
                                                             +  ++  e ++ +v+vDEaH
  gene3194|gene3194|rna3194|rna3194 169 mlsedaaitfmpynyvvdpmvR-RTMGIELKDSVVIVDEAH 208
                                        6666666666666655555431.222233334566666666 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 4.8
                          SWI2_SNF2   3 yravekavervkegdrk 19 
                                        y+av+k+v+r++++ ++
  gene3194|gene3194|rna3194|rna3194 464 YHAVNKVVSRMRSRGTN 480
                                        89********9983333 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 4.2
                          SWI2_SNF2 183 eDgavvpil 191
                                        +D+ +  i+
  gene3194|gene3194|rna3194|rna3194 556 NDKRTNSIF 564
                                        222222222 PP

>> HBB  Helical and beta-bridge domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00013      0.22      93     157 ..     326     392 ..     299     399 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00013
                                        HHHHHHHHHHTS.TTTEEEEEE.STT..EECCCCS-TCCHH..HHHHHCHCCCCCCTS-SSHHHHHHH CS
                                HBB  93 rlaefllawlssdeedYvrlvskeeg.esLeavcldPskal..rflkerlssllmsgtltpleeysdi 157
                                        +l + l+  +s ++ +Y+ +v+   + +sL+ + ld ++++   +++ ++  ++ sgtltp+ + ++ 
  gene3194|gene3194|rna3194|rna3194 326 SLVSVLMLVFSGKARSYALIVKGAPSaPSLNFMLLD-ADVMfnAVVQHVHALVVLSGTLTPFSAVENE 392
                                        445567777788999*******99888*********.7776457899**************9887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (867 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1018  (0.0567795); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.70u 0.27s 00:00:00.97 Elapsed: 00:00:00.44
# Mc/sec: 5860.34
//
Query:       gene3195|gene3195|rna3195|rna3195  [L=760]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
     3e-122  409.2  43.0   2.8e-114  382.9  22.8    2.3  2  HSP90         Hsp90 protein
    2.4e-11   43.6   2.1    3.2e-11   43.2   0.0    2.3  2  HATPase_c_3   Histidine kinase-, DNA gyrase B-, and HSP90-lik
    8.5e-10   39.1   0.0    3.4e-09   37.2   0.0    2.0  1  HATPase_c     Histidine kinase-, DNA gyrase B-, and HSP90-lik
     0.0052   15.3  18.5      0.011   14.3  18.5    1.5  1  Borrelia_P83  Borrelia P83/100 protein
  ------ inclusion threshold ------
       0.43    9.9  25.3        1.2    8.5  25.3    1.7  1  SDA1          SDA1


Domain annotation for each model (and alignments):
>> HSP90  Hsp90 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.0  16.3   3.5e-11   1.3e-07       1      79 [.     224     307 ..     224     311 .. 0.63
   2 !  382.9  22.8  7.8e-118  2.8e-114      28     488 ..     304     748 ..     300     760 .] 0.88

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 3.5e-11
                                        GGGSHHHHHHHHHHCCTTSSS-EEEEEEEEXXXXXXXXXXXXXXXXXX....XXXXXXXX.XXXXXX..XXXXXXX CS
                              HSP90   1 eyleekklkelvkkySeFinfpiyllkekeeekeveeeeeeeeeeeee....eeeeakve.eeeeeeeekkktkkv 71 
                                        e+++++k+kel+kkyS Fi +pi l + +e+e++ +e++ e + e+ e    +e+e+kv+ +++ee+e+ +++k++
  gene3195|gene3195|rna3195|rna3195 224 EFVKKEKIKELIKKYSMFIGYPIVLRTLEEKEVDDDEDKVEVDPETGEkvkvNEDEEKVKvDVDEEKEKVDEEKTT 299
                                        799**********************887766665554443333333225667666666664455555554444544 PP

                                        XXXEEEEE CS
                              HSP90  72 ketvkewe 79 
                                        +e++++ e
  gene3195|gene3195|rna3195|rna3195 300 TEEKQQDE 307
                                        44444444 PP

  == domain 2  score: 382.9 bits;  conditional E-value: 7.8e-118
                                        EEEXXXXXXXXXXXXXXXXXX...XXXXXXXXXXXXXX..XXXXXXXXXXEEEEEEESXXSXGGGSXGGGSXHHHH CS
                              HSP90  28 ekeeekeveeeeeeeeeeeee...eeeeakveeeeeeeeekkktkkvketvkewellNkqkpiWlrkpkevteeeY 100
                                        ++ e++ev+ e  e+ + +e+   eee+ ++e+++e  e+  k kk   + ++ el+Nk+kp+W  +pk+vt+e Y
  gene3195|gene3195|rna3195|rna3195 304 QQDEKVEVDPETGEKINVNEKvtdEEEKIDIEKNTERTEKPAKAKKL-VKEWKDELINKEKPLWSMNPKDVTKEMY 378
                                        45566677766555555555554455555566666665544444444.445999********************** PP

                                        HHHHHHTTTTTSXXSEEEEEEEXSSSXEEEEEEEXSSXXTTTTTTTTTSXXTTEEEEETTEEEESXXTTSSXGGGT CS
                              HSP90 101 keFYkslskdsedplavkhfsaegevefkaiLfvPkrapsdlfekykkkkknnikLYvrrVfitdefedllPkyLs 176
                                        ++FYk++s+d++d lavkh + eg v+f  +Lf  kr ++++f+++  +kk+ i+LY+  V++t+++e  lP++Ls
  gene3195|gene3195|rna3195|rna3195 379 TSFYKTISNDWDDYLAVKHSHLEGSVSFDVLLFALKRPRFNMFSEKG-SKKHLIRLYCNSVLVTEDLE--LPDWLS 451
                                        ********************************************977.88888*************97..9***** PP

                                        TXEEEEEESSSXSSSTHHHHHTCHHHHHHHHHHHHHHHHHHHTSXHHH..HHTHHHHHHHHHHHHHHHXGGGHHHH CS
                              HSP90 177 FvkGvvdsddLPLNvsREtlqqnkilkvikkklvrKvlemlkklaeekeeykkfykefsknlklGiiedsanrkkl 252
                                         v Gv+ s dLP+NvsRE lq +++ ++ikk+l +K++emlk++++e+  y++fykefs  +kl++ +d  n ++l
  gene3195|gene3195|rna3195|rna3195 452 CVVGVISSKDLPMNVSREFLQGENVKRLIKKTLRKKTIEMLKEMNKET--YDQFYKEFSGAIKLAVRDD--NEQQL 523
                                        ********************************************9976..*****************99..5689* PP

                                        HTTXEEEETTEEEEEEEHHHHHHHSXTTXXEEEEEEXSSHHHHHTSGGGHHHHHTTXXEEEEXSTTHHHHHHTXSE CS
                              HSP90 253 akLlrfksskseeeltsLedYvermkekqksiYyiageskeevekspflerlkkkgyevlylvdpiDeyvvqqlke 328
                                         +Llrf++sk e+  + L+dYv+ mke+q++iY i+g++keev kspfle +  k+yev++++d++Dey++q+++ 
  gene3195|gene3195|rna3195|rna3195 524 ESLLRFNTSKREN--IGLDDYVKDMKEGQNKIYVITGTTKEEVVKSPFLEYF--KDYEVIFMIDSMDEYLLQRFRA 595
                                        *********9655..***********************************99..589******************* PP

                                        ETTEEEEETTBSTXXXXXXHHHHHHHHHHHHHHHHHHHHHHHTTTTTESEEEEXSSXSSXSEEEEBXTTSXXHHHH CS
                              HSP90 329 yegkklvnvakegleleeeeeekkkkeelkkkfeeltkllkevlkdkvekvkvserlvdsPcvlvtseygwsanme 404
                                        y+g+++v++++eg+++++ e     ++e++++ ++l + ++++l+d+ve+v++ + l d+ +++ + +y +s+ me
  gene3195|gene3195|rna3195|rna3195 596 YKGNDVVKINQEGVDIPNAEV----SKEMQDELKALKENIEKTLGDSVERVEFLN-LGDKHMLVRSPKYSISPAME 666
                                        ****************87665....5566777888999999************99.******************** PP

                                        HHHHHHHHHHHSSTSSS.SSXEEEEEXTTSHHHHHHHHHHHHTTTXHHHHHHHHHHHHHHHHHTTXXXSXHHHHHH CS
                              HSP90 405 rimkaqalrdkskssym.sskktleinprhpiikeLkkkveedkedeeakdlaellyetallesGfsledpasfak 479
                                        +i+ aq   dks++ +  ++kk+l +n +hp+  +L++ +++    +++ +l +ll++ a+l++G+ l+dp  fa+
  gene3195|gene3195|rna3195|rna3195 667 KILAAQVAIDKSNMFMFpKGKKILQVNVTHPLTLKLNSVMSDA---TVFAKLLNLLFKVACLQCGYALDDPVGFAD 739
                                        ******99988777665267****************9988765...899*************************** PP

                                        HHHHHHTTT CS
                              HSP90 480 rierllkls 488
                                         + ++l + 
  gene3195|gene3195|rna3195|rna3195 740 MVSDVLMSD 748
                                        **9987653 PP

>> HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.2   0.0   8.9e-15   3.2e-11       5     105 ..      70     193 ..      65     216 .. 0.74
   2 ?   -2.7   1.1       1.3   4.7e+03     120     122 ..     299     301 ..     272     343 .. 0.55

  Alignments for each domain:
  == domain 1  score: 43.2 bits;  conditional E-value: 8.9e-15
                        HATPase_c_3   5 kAlaelvdNsldAdaen.............vkievnknr.gktgeivieDdGkGmseeelknalr.latsskeakr 65 
                                        + l el+ N+ dA  +              v+ +++      +++i++ D+G Gm++++l ++l  +a+s +++ r
  gene3195|gene3195|rna3195|rna3195  70 YFLRELISNCSDACDKLnalrqdlrekgvnVDMQLKMSVtPTEDTITVSDNGIGMTKDDLVKFLGcVANSGTRKFR 145
                                        5688********966656999*******66333333322123489*****************99747777666555 PP

                        HATPase_c_3  66 ksts.........lGkkGiGlklAslslgkkltvitkkegesstltldv 105
                                        ++ +         +G++G+G + As+ +++k++v+tk+ +e  ++ ++ 
  gene3195|gene3195|rna3195|rna3195 146 EAVKnakgpvddlIGQFGLG-FYASFLVADKVQVVTKYPTEDKQYMWTS 193
                                        3222445667777*******.****************888877776665 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.3
                        HATPase_c_3 120 tve 122
                                        t+e
  gene3195|gene3195|rna3195|rna3195 299 TTE 301
                                        222 PP

>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.2   0.0   9.5e-13   3.4e-09       5     110 ..      71     220 ..      67     221 .. 0.74

  Alignments for each domain:
  == domain 1  score: 37.2 bits;  conditional E-value: 9.5e-13
                                        HHHHHHHHHHHHHHHH......HSTTT....EEEEEEEEEETEEEEEEEESSSSSTTHHHT.......GTCS.TTC CS
                          HATPase_c   5 rLrqiisnlvdNavkf......atkag....eieveikaseddlvisveDnGiGipkedlk.......klfe.kfs 62 
                                        +Lr++isn +d+ +k          ++    + +++++++  + +i+v+DnGiG++k+dl        ++++ kf 
  gene3195|gene3195|rna3195|rna3195  71 FLRELISNCSDACDKLnalrqdL-REKgvnvDMQLKMSVTPTEDTITVSDNGIGMTKDDLVkflgcvaNSGTrKFR 145
                                        89**************6665320.3331222223344434479******************9****9999999999 PP

                                        H.....HCSTCHT.....STSSSHHHHHH.................HH.HHHHTT.TEEEEEEET...TTEEEEEE CS
                          HATPase_c  63 q.....ddstkrg.....gggtGlGlsiv.................kk.lvelmg.Geiwvesep...grGttftf 106
                                        +     +     g      g++GlG++ +                 k+ +++  g G+ +ve+ p   ++Gt++++
  gene3195|gene3195|rna3195|rna3195 146 EavknaK-----GpvddlIGQFGLGFYASflvadkvqvvtkyptedKQyMWTSSGlGHYTVEEVPvdmEHGTRVVL 216
                                        9776642.....1223346888888888877788888888888888776777677889999888899999****** PP

                                        EEES CS
                          HATPase_c 107 tlpl 110
                                        ++++
  gene3195|gene3195|rna3195|rna3195 217 HIKE 220
                                        9986 PP

>> Borrelia_P83  Borrelia P83/100 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3  18.5     3e-06     0.011     203     311 ..     237     362 ..     197     397 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3e-06
                       Borrelia_P83 203 l..............keresqedakraqvlkeeldkkq..kdadkakkkadtaednadkqrkevreklqeaknlpe 262
                                                        e+e + d  + +v  e  +k +  +d +k k ++d  ++++d ++ +++ek+q++k   +
  gene3195|gene3195|rna3195|rna3195 237 KysmfigypivlrtlEEKEVDDDEDKVEVDPETGEKVKvnEDEEKVKVDVDEEKEKVDEEKTTTEEKQQDEKVEVD 312
                                        145555555555555777777777788876666666550055555566666777899******************* PP

                       Borrelia_P83 263 padvsskkedkkva.eekkreiekaqkeikkkdeeakkakdakaedlkke 311
                                        p   ++ ++++kv  ee+k +iek  + ++k ++  k  k+ k e ++ke
  gene3195|gene3195|rna3195|rna3195 313 PETGEKINVNEKVTdEEEKIDIEKNTERTEKPAKAKKLVKEWKDELINKE 362
                                        *************7588888999966666666655555566655555555 PP

>> SDA1  SDA1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5  25.3   0.00032       1.2     102     198 ..     252     350 ..     224     363 .. 0.64

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00032
                               SDA1 102 edwevesddds..eedseggwidvesdeeeieesdesedeeeeeeeeeekeekeeeeeeeeeeeeeeeeeeeeeek 175
                                        e++ev++d+d+   + + g+ ++v++dee+++++ ++e+e+ +ee+ +++e++++e+ e + e+ e+ +++e+  +
  gene3195|gene3195|rna3195|rna3195 252 EEKEVDDDEDKveVDPETGEKVKVNEDEEKVKVDVDEEKEKVDEEKTTTEEKQQDEKVEVDPETGEKINVNEKVTD 327
                                        4567777777774333446699999999988877766777766666666666666666554444455555555555 PP

                               SDA1 176 ekkkkkakeaseeekkkekeeek 198
                                        e++k + ++++e+++k +k+++ 
  gene3195|gene3195|rna3195|rna3195 328 EEEKIDIEKNTERTEKPAKAKKL 350
                                        55555444444444444444333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (760 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2528  (0.141001); expected 358.6 (0.02)
Passed bias filter:                      616  (0.0343577); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.82u 0.32s 00:00:01.13 Elapsed: 00:00:00.47
# Mc/sec: 4826.36
//
Query:       gene3196|gene3196|rna3196|rna3196  [L=394]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (394 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       488  (0.0272185); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.49
# Mc/sec: 2429.36
//
Query:       gene3197|gene3197|rna3197|rna3197  [L=349]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        1.8    9.1   5.0         20    5.7   0.1    3.7  3  LRR_4     Leucine Rich repeats (2 copies)


Domain annotation for each model (and alignments):
>> LRR_4  Leucine Rich repeats (2 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.1     0.032   5.8e+02       2      30 ..     202     232 ..     190     237 .. 0.56
   2 ?    5.7   0.1    0.0011        20      19      31 ..     290     302 ..     284     306 .. 0.77
   3 ?    1.3   0.2     0.029   5.3e+02      17      30 ..     310     324 ..     308     329 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.032
                                        S--EEE--SS---E-S-HHH-TT..--EEE- CS
                              LRR_4   2 nLevLdLsnNqltdiplleklpn..LkeLdL 30 
                                        nL++L   n q++  +l +  +n  L+ L L
  gene3197|gene3197|rna3197|rna3197 202 NLKILAMVNIQISVAQLEGMSKNvlLENLKL 232
                                        5555555565555444333222244666655 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0011
                                        HHH-TT--EEE-. CS
                              LRR_4  19 leklpnLkeLdLs 31 
                                        l+k++nL+ Ld++
  gene3197|gene3197|rna3197|rna3197 290 LSKCKNLRRLDVN 302
                                        678********93 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.029
                                        S-.HHH-TT--EEE- CS
                              LRR_4  17 pl.leklpnLkeLdL 30 
                                        ++ l++l  L+eL+L
  gene3197|gene3197|rna3197|rna3197 310 ESkLNNLRCLRELHL 324
                                        455889999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (349 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       541  (0.0301746); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 2352.81
//
Query:       gene3198|gene3198|rna3198|rna3198  [L=134]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       444  (0.0247643); expected 358.6 (0.02)
Passed bias filter:                      218  (0.0121591); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.43
# Mc/sec: 944.71
//
Query:       gene3199|gene3199|rna3199|rna3199  [L=1207]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    9.3e-09   35.3   0.3    9.3e-09   35.3   0.3    1.9  2  Phosphodiest  Type I phosphodiesterase / nucleotide pyrophosp
  ------ inclusion threshold ------
        0.2    9.9   9.7      0.018   13.3   3.6    2.0  2  Nop14         Nop14-like family


Domain annotation for each model (and alignments):
>> Phosphodiest  Type I phosphodiesterase / nucleotide pyrophosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.6      0.21   1.9e+03      37      61 ..     309     333 ..     299     358 .. 0.85
   2 !   35.3   0.3     1e-12   9.3e-09     166     238 ..     426     495 ..     342     600 .. 0.73

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.21
                                        EE-SSS-SHHHHHHHHHHSS-HHHH CS
                       Phosphodiest  37 lrpvfPtlTfpnhaslvTGlyPgeH 61 
                                         +++ ++  +++++++ T ly  +H
  gene3199|gene3199|rna3199|rna3199 309 FLSMHNPSRITSLYTITTTLYIHSH 333
                                        5678889999999999999999999 PP

  == domain 2  score: 35.3 bits;  conditional E-value: 1e-12
                                        HHHCT...SSESEEEEEECCCHHHHHHH-T.TSHHHHHHHHHHHHHHHHHHHHHHHTTGTTTEEEEEEES---EEE CS
                       Phosphodiest 166 lekel...ekpdlllvyleetDtvgHkfGp.dspevedalrrvDkaigdLlealderglsaetniilvSDHGmadv 237
                                        +e  +   e+  ll+++l  +D+ gHk+G  +  +v+d lr + +++++L+ +lde+     t ++++SDHG++ +
  gene3199|gene3199|rna3199|rna3199 426 IE--QcdmENVELLVGHLVYLDHYGHKYGTiHCAQVRDVLRVYNDFVQRLICGLDED-----TLLVVSSDHGVENT 494
                                        22..2457999******************769*************************.....***********988 PP

                                        H CS
                       Phosphodiest 238 s 238
                                         
  gene3199|gene3199|rna3199|rna3199 495 G 495
                                        5 PP

>> Nop14  Nop14-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   3.6     2e-06     0.018     348     461 ..     215     326 ..     180     337 .. 0.37
   2 ?   -0.9   0.4     0.039   3.5e+02     674     704 ..     625     655 ..     544     736 .. 0.55

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2e-06
                              Nop14 348 eeededdfeedddlveseseeeeeeeeedeeeeedeeeeeeeeededdlsdlese.eeeeedeleeel..leeekk 420
                                        + +d++  ++dd  ++++s+++     ++++ ++d+ ++++ ++d+ +++d +++ +++++ + ++ +   ++++ 
  gene3199|gene3199|rna3199|rna3199 215 KGRDNNYGSNDDGSNDDGSNDDG----SNDDGSNDDGSNDDGSNDDGSNDDGNDDdDDSNDTNHIHANhiHANHTT 286
                                        22222222222222222222222....1111111111111111111111111111011111111111122111111 PP

                              Nop14 421 aaeekkekk....kkkkkseekakeelpytfpcPesheellelle 461
                                         + +    +    ++  +++++ +++l   ++ P+ +  l ++++
  gene3199|gene3199|rna3199|rna3199 287 IP-T----HtttpNTIPTTNHTINANLFLSMHNPSRITSLYTITT 326
                                        11.1....0222344455555555666666666666666666655 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.039
                              Nop14 674 keleekskkekkqrklslsdllkeesskees 704
                                         ++++k++k++k++k ++++ ++++++++++
  gene3199|gene3199|rna3199|rna3199 625 TTKTAKKAKKTKTNKQRIKENVNASHQSSKK 655
                                        2222222222222333333333322222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1290  (0.0719505); expected 358.6 (0.02)
Passed bias filter:                      492  (0.0274416); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.90u 0.33s 00:00:01.23 Elapsed: 00:00:00.47
# Mc/sec: 7688.38
//
Query:       gene32|gene32|rna32|rna32  [L=57]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (57 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       422  (0.0235373); expected 358.6 (0.02)
Passed bias filter:                      193  (0.0107647); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.48
# Mc/sec: 353.60
//
Query:       gene320|gene320|rna320|rna320  [L=150]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    4.6e-05   23.8   1.7    4.6e-05   23.8   1.7    2.1  2  EF-hand_7  EF-hand domain pair
    0.00058   19.2   0.6    0.00058   19.2   0.6    2.1  2  EF-hand_1  EF hand
    0.00093   18.9   3.9    0.00096   18.9   0.4    2.7  3  EF-hand_6  EF-hand domain
  ------ inclusion threshold ------
      0.068   12.8   0.0       0.11   12.2   0.0    1.2  1  RE_TdeIII  Type II restriction endonuclease, TdeIII
       0.08   12.5   0.1       0.24   10.9   0.1    1.9  1  EF-hand_5  EF hand


Domain annotation for each model (and alignments):
>> EF-hand_7  EF-hand domain pair
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.1      0.23   8.2e+02      18      52 ..      19      43 ..      15      66 .. 0.58
   2 !   23.8   1.7   1.3e-08   4.6e-05       3      69 ..      71     133 ..      69     135 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.23
                      EF-hand_7 18 yldkeellrllrkifqgagegsklsdeelellfke 52
                                   +++k +llr+          ++++++    +l+++
  gene320|gene320|rna320|rna320 19 KIRKKDLLRIAS------IKENPITK----HLLRK 43
                                   678888887554......34444444....22222 PP

  == domain 2  score: 23.8 bits;  conditional E-value: 1.3e-08
                      EF-hand_7   3 klkeaFkelDtdgdgyldkeellrllrkifqgagegsklsdeelellfkef..DtdkdGvisfdEFlkl 69 
                                    k+k  F+++D+d+dg +++++l ++++        +++l d  ++ +++    D+ +  +i+f+ F+k+
  gene320|gene320|rna320|rna320  71 KIKLLFDLYDCDNDGVISRCDLFNVIKM-----FSDESLCDSNIQNVVDRCflDLEC-EEITFERFKKF 133
                                    89999****************888***9.....567777888888777663257777.47888877776 PP

>> EF-hand_1  EF hand
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.6   1.6e-07   0.00058       2      28 ..      72      98 ..      71      99 .. 0.90
   2 ?   -2.7   0.1       1.6   5.8e+03      17      26 ..     125     134 ..     124     136 .. 0.66

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.6e-07
                                   HHHHHHHHTTTSSSEEEHHHHHHHHHH CS
                      EF-hand_1  2 lkeiFrefDkDgdGkIdfeEfkellkk 28
                                   +k +F+++D D+dG I++ ++ +++k+
  gene320|gene320|rna320|rna320 72 IKLLFDLYDCDNDGVISRCDLFNVIKM 98
                                   7789****************9999886 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.6
                                    EEHHHHHHHH CS
                      EF-hand_1  17 IdfeEfkell 26 
                                    I+fe fk+++
  gene320|gene320|rna320|rna320 125 ITFERFKKFI 134
                                    7777677665 PP

>> EF-hand_6  EF-hand domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.1       1.8   6.4e+03      21      27 ..      54      60 ..      49      64 .. 0.56
   2 !   18.9   0.4   2.7e-07   0.00096       2      28 ..      72      98 ..      71     106 .. 0.88
   3 ?   -0.4   0.0       0.4   1.4e+03      16      27 ..     124     135 ..     123     138 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.8
                      EF-hand_6 21 Elrkalr 27
                                    l +alr
  gene320|gene320|rna320|rna320 54 KLLDALR 60
                                   3444554 PP

  == domain 2  score: 18.9 bits;  conditional E-value: 2.7e-07
                      EF-hand_6  2 lreaFklfDkdgdGkidaeElrkalrk 28
                                   ++ +F+l+D d+dG i++ +l +++++
  gene320|gene320|rna320|rna320 72 IKLLFDLYDCDNDGVISRCDLFNVIKM 98
                                   5679******************99995 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.4
                      EF-hand_6  16 kidaeElrkalr 27 
                                    +i++e ++k++ 
  gene320|gene320|rna320|rna320 124 EITFERFKKFIE 135
                                    599999999986 PP

>> RE_TdeIII  Type II restriction endonuclease, TdeIII
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0     3e-05      0.11      63     146 ..       4      88 ..       3      96 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 3e-05
                      RE_TdeIII  63 EkvAkiiAkeefkeaksqkevsgtiseeaqerIdeildeltkskkkpdleeeleaire.aqegeekkaksvkaDlylkse 141
                                    E++  +iA+ +  + k +k+   +i + +++ I + l ++ + ++  ++e+ l+a+re a ++  + +++  +Dly  ++
  gene320|gene320|rna320|rna320   4 EQITAAIAEITSTQTKIRKKDLLRIASIKENPITKHLLRKFTVNETFEFEKLLDALREfALDDRLSPKIKLLFDLYDCDN 83 
                                    9999*********************************999999***************999999999*********9999 PP

                      RE_TdeIII 142 dgeky 146
                                    dg + 
  gene320|gene320|rna320|rna320  84 DGVIS 88 
                                    98765 PP

>> EF-hand_5  EF hand
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   6.8e-05      0.24       2      20 ..      73      91 ..      72      97 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 6.8e-05
                                   HHHHHHH-SS-SSCE-HHH CS
                      EF-hand_5  2 kdtFqaiDlNgDGkIskeE 20
                                   k +F+  D ++DG Is+  
  gene320|gene320|rna320|rna320 73 KLLFDLYDCDNDGVISRCD 91
                                   458*************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       707  (0.0394333); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 1057.13
//
Query:       gene3200|gene3200|rna3200|rna3200  [L=597]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.6e-09   35.7   4.1    7.8e-05   22.3   0.1    3.6  3  PPTA           Protein prenyltransferase alpha subunit repeat


Domain annotation for each model (and alignments):
>> PPTA  Protein prenyltransferase alpha subunit repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.1   4.3e-09   7.8e-05       6      26 ..      63      83 ..      61      84 .. 0.92
   2 !    5.8   0.0   0.00065        12       4      19 ..     235     250 ..     234     251 .. 0.92
   3 !    7.0   0.1   0.00028         5       4      21 ..     262     279 ..     261     280 .. 0.89

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 4.3e-09
                                       HHHHHH-TT-CHHHHHHHHHH CS
                               PPTA  6 ekliekdpkNYsaWnyRrwll 26
                                       e +i ++ k+YsaW+yR w++
  gene3200|gene3200|rna3200|rna3200 63 ERMIGMNVKSYSAWYYREWVM 83
                                       789****************98 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.00065
                                        HHHHHHHH-TT-CHHH CS
                               PPTA   4 ltekliekdpkNYsaW 19 
                                        l+++l+  d +N+++W
  gene3200|gene3200|rna3200|rna3200 235 LIKQLLIHDSRNFHCW 250
                                        78999999******** PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.00028
                                        HHHHHHHH-TT-CHHHHH CS
                               PPTA   4 ltekliekdpkNYsaWny 21 
                                        + + +i++d  NYsa +y
  gene3200|gene3200|rna3200|rna3200 262 FATFCIKRDITNYSALHY 279
                                        77889************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (597 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2229  (0.124324); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.67u 0.29s 00:00:00.96 Elapsed: 00:00:00.46
# Mc/sec: 3866.27
//
Query:       gene3202|gene3202|rna3202|rna3202  [L=217]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.7e-23   82.5   2.8    1.8e-21   77.0   0.0    2.7  3  Gti1_Pac2     Gti1/Pac2 family
  ------ inclusion threshold ------
       0.03   14.0   0.4      0.063   12.9   0.3    1.4  1  Peptidase_C5  Adenovirus endoprotease
      0.056   13.7   1.7        0.1   12.8   1.7    1.5  1  Imm5          Immunity protein Imm5


Domain annotation for each model (and alignments):
>> Gti1_Pac2  Gti1/Pac2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.0   0.0     3e-25   1.8e-21       2      83 ..       7      87 ..       6      90 .. 0.96
   2 !    5.7   0.1    0.0024        14     157     180 ..      87     110 ..      84     111 .. 0.88
   3 ?   -0.3   0.1      0.16   9.6e+02     137     176 ..     149     190 ..     122     209 .. 0.60

  Alignments for each domain:
  == domain 1  score: 77.0 bits;  conditional E-value: 3e-25
                                       EES---SHHHHHHHHHHHHTTSS---SS---HHHHHHHSSTTEEEEEEHHHH--SS---S--B---EEETTEEEEEB- CS
                          Gti1_Pac2  2 fkgyiettkdalllieavlegilkrvtrRlkekErkeliksGsvFvfeeeesgikRWTDGvsWSpSrilgnfLvYrel 79
                                       + g++++    l l++ + +  +++ +rRl+++E++  +++Gs ++++e+esgi+RWTD +sW pSr +++  +Y+e+
  gene3202|gene3202|rna3202|rna3202  7 YFGCMHKLSHYLSLFQLAVNHEVPTLKRRLSDTEKN-AVRAGSTYIYSENESGIRRWTDHLSWTPSRASNECVFYQEI 83
                                       89**********************************.****************************************9 PP

                                       ---- CS
                          Gti1_Pac2 80 dkkr 83
                                        +++
  gene3202|gene3202|rna3202|rna3202 84 ANHN 87
                                       7776 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0024
                                        ----EEEEEEEEEETTTEEEEEEE CS
                          Gti1_Pac2 157 kdgLvKkTisvtlkgkelhlisYy 180
                                        ++ ++Kk +++t+++ ++h++ Y 
  gene3202|gene3202|rna3202|rna3202  87 NQPMLKKVVTATIDKCKWHIVNYS 110
                                        45699******************6 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.16
                                        -----------.------------.-EEEEEEEEEETTTEEE CS
                          Gti1_Pac2 137 lekdserslvg.sltdsykfkkdg.LvKkTisvtlkgkelhl 176
                                        l+k+ +r++v  +  + y+f ++  L+ + + v+l  ++ hl
  gene3202|gene3202|rna3202|rna3202 149 LRKSLSRNYVRnNAKKIYSFVDESnLYGRRMDVKLLANQNHL 190
                                        333344444442333335554433366666666655555554 PP

>> Peptidase_C5  Adenovirus endoprotease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.3   1.1e-05     0.063     116     174 ..     128     186 ..     117     191 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.1e-05
                                        TTS-SSSSTTGGGS--EEGGGTTSGGGHHHHHHHHHHHHHHHHHH-HHHHHTHHHHHHH CS
                       Peptidase_C5 116 kqkpldgnpvidlvdGvkpsklnspqekellhrnqeklyaflekksayfrknaeelien 174
                                         + p+ +n v+++ +  ++++l+ +  ++ +++n +k+y+f+++   y r+   +l  n
  gene3202|gene3202|rna3202|rna3202 128 YDVPITHNIVVKTKVRCSRNTLRKSLSRNYVRNNAKKIYSFVDESNLYGRRMDVKLLAN 186
                                        467999*****999999999999*************************99988877665 PP

>> Imm5  Immunity protein Imm5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   1.7   1.7e-05       0.1      27     105 ..     106     184 ..      83     214 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.7e-05
                               Imm5  27 aigsprviqklaiecvkkvlplweevfaedqsplrlLekaedylyektdkeeiekeadklsndlendsgeeaeetv 102
                                         ++ + v + +  +c+ k   +    + ++  + + ++++ ++l+++ +++++ ++a+k+++++++++   ++ +v
  gene3202|gene3202|rna3202|rna3202 106 IVNYSTVSDEITGTCCAKYQAVYDVPITHNIVVKTKVRCSRNTLRKSLSRNYVRNNAKKIYSFVDESNLYGRRMDV 181
                                        4566677788*****************9**9999*******************************97777777777 PP

                               Imm5 103 ala 105
                                         l 
  gene3202|gene3202|rna3202|rna3202 182 KLL 184
                                        766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       617  (0.0344135); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1601.03
//
Query:       gene3203|gene3203|rna3203|rna3203  [L=30]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (30 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       338  (0.0188521); expected 358.6 (0.02)
Passed bias filter:                      207  (0.0115455); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.31u 0.25s 00:00:00.56 Elapsed: 00:00:00.40
# Mc/sec: 227.20
//
Query:       gene3204|gene3204|rna3204|rna3204  [L=238]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.016   13.6   5.3      0.021   13.3   5.3    1.1  1  SID-1_RNA_chan  dsRNA-gated channel SID-1
       0.22   11.0   2.2       0.34   10.4   2.2    1.5  1  gpUL132         Glycoprotein UL132


Domain annotation for each model (and alignments):
>> SID-1_RNA_chan  dsRNA-gated channel SID-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   5.3   2.3e-06     0.021      96     227 ..      17     173 ..       4     187 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.3e-06
                     SID-1_RNA_chan  96 ltknsnrtkkvtvevkklikksvyvvavllvllvllsfllltllvvivekvre....................... 148
                                         t ++ +t + +v+++++ k++  ++ ++ +l ++ + +l t+++++ +k+++                       
  gene3204|gene3204|rna3204|rna3204  17 ITIKTAHTNTNRVSLQSIKKNE--MIKLMNILHLISTTTLFTFVLTFSNKKKNgkkepkdelvkkddvilqpsfgi 90 
                                        5555666667777777777666..45555555555555555555555554444889******************** PP

                     SID-1_RNA_chan 149 .....sseekrvkessssesaseslesvssavrsesessveeesdydtleeiesdknvirtkkvlvvsdlsrkdkr 219
                                             + ++++ ++  + +++ ++++++++  ++++ ++ +e++d d  +ei+++     + k  +v  l +k+k+
  gene3204|gene3204|rna3204|rna3204  91 fdnknD-KTNKNHKDDNIRDTFKDSDKIAPIFTKDKRDDKKESDDKDKEKEISNEIMTQSSYKPPMVTMLLNKNKK 165
                                        987531.2222233345555667778888889999999999************99999999999999999999999 PP

                     SID-1_RNA_chan 220 vlekkyki 227
                                        + e+k ++
  gene3204|gene3204|rna3204|rna3204 166 EDERKEQL 173
                                        99999875 PP

>> gpUL132  Glycoprotein UL132
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   2.2   3.8e-05      0.34      29      68 ..      21      59 ..       5     144 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 3.8e-05
                            gpUL132 29 inmttthessvhnvrnneimkvlailfyivtgtsifsfia 68
                                          t t   s++ +++ne++k++ il  i t t++f+f+ 
  gene3204|gene3204|rna3204|rna3204 21 TAHTNTNRVSLQSIKKNEMIKLMNILHLIST-TTLFTFVL 59
                                       4457788999***************998876.66899975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (238 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2063  (0.115065); expected 358.6 (0.02)
Passed bias filter:                      468  (0.026103); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1536.76
//
Query:       gene3205|gene3205|rna3205|rna3205  [L=360]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
       0.09   13.2   0.4       0.09   13.2   0.4    2.8  4  HEPN_Apea  Apea-like HEPN


Domain annotation for each model (and alignments):
>> HEPN_Apea  Apea-like HEPN
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0      0.28     5e+03      30      64 ..      10      40 ..       5      57 .. 0.54
   2 ?   -0.4   0.1     0.085   1.5e+03      64      84 ..     175     197 ..      96     199 .. 0.46
   3 ?   13.2   0.4     5e-06      0.09      15      82 ..     187     284 ..     178     287 .. 0.75
   4 ?   -0.9   0.2      0.13   2.3e+03      47      73 ..     324     350 ..     283     355 .. 0.45

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.28
                          HEPN_Apea 30 ildlvialEaldllldkkeeitekislrsnaylke 64
                                       +++++ + ++    +++ + ++ k+++++ + +  
  gene3205|gene3205|rna3205|rna3205 10 FINVLQCTNIV---EQRISTLKTKLCKTV-SNFHV 40
                                       45555555555...444344777777777.66622 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.085
                          HEPN_Apea  64 e..dkeerkelkkkikklYdlRS 84 
                                        +   + ++k ++k+++   d RS
  gene3205|gene3205|rna3205|rna3205 175 SmyIHRNDKRYFKSWNTGIDRRS 197
                                        12234555666666666666665 PP

  == domain 3  score: 13.2 bits;  conditional E-value: 5e-06
                          HEPN_Apea  15 ewfgeaireeddedaildlvialEaldll..........................ldkkeeitekislrsn....a 60 
                                        + ++  i++++ +  +++ + a++ l+                            +++++ +  +i + ++    +
  gene3205|gene3205|rna3205|rna3205 187 KSWNTGIDRRSRDRDVINMMVAINRLFISdkdidiavntylervyknvydptvklFNSSGLLHSRIINSVSeyiiK 262
                                        55666777666656699*********666999999999999999999*9999998444443555554444333335 PP

                          HEPN_Apea  61 ylkedkeerkelkkkikklYdl 82 
                                        y+ +++++r  ++k i +lYd+
  gene3205|gene3205|rna3205|rna3205 263 YFLTVNDKRTFIDKDITRLYDC 284
                                        55559***************95 PP

  == domain 4  score: -0.9 bits;  conditional E-value: 0.13
                          HEPN_Apea  47 keeitekislrsn...aylkedkeerkelk 73 
                                         e i +++ +r+n    +l+   ++r+ +k
  gene3205|gene3205|rna3205|rna3205 324 IE-INDYL-ERLNtllEELFL-RHKRQHIK 350
                                        12.55555.566433333333.45555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (360 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1468  (0.0818785); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 2524.03
//
Query:       gene3206|gene3206|rna3206|rna3206  [L=227]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.2e-10   40.8   9.4    2.6e-10   40.6   9.4    1.1  1  DER1             Der1-like family
  ------ inclusion threshold ------
       0.28   11.6   8.6        2.2    8.7   3.0    2.2  2  Caps_synth_CapC  Capsule biosynthesis CapC


Domain annotation for each model (and alignments):
>> DER1  Der1-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.6   9.4   2.9e-14   2.6e-10       1     176 [.       7     184 ..       7     212 .. 0.73

  Alignments for each domain:
  == domain 1  score: 40.6 bits;  conditional E-value: 2.9e-14
                               DER1   1 iPavTRllltatvvltllgrlelispaklvlsyelvvkkvQiwRlltsllyfsstgfsflinlyfiyqysskLEeg 76 
                                        +P+v  ++l+ + v++llg l     +++v++    +k++ iwRl+t +++ +++++s ++ lyfi ++ss + e 
  gene3206|gene3206|rna3206|rna3206   7 VPPVVLAILLCASVIPLLGLLSPQFTMYFVYDK-SYLKRFEIWRLFTGIFV-TGVSISLIMRLYFIHKFSSLILEY 80 
                                        577777777777777777766544444555543.579*************9.999**************9975443 PP

                               DER1  77 sfrgr....sadyvylllflavlitllglladlvvLgqalilaivYvwskknk.dvqvsFfgvlrvkakylPlvll 147
                                        + r      + + +++++ + v + +   l  +    + + +a++ + s+  + + +++Ffg + ++ak + +v l
  gene3206|gene3206|rna3206|rna3206  81 NCRIDhvptEIELAFFMFTMFVPLMIGNQLEGINTFSECIPIALIRYFSELVPdNFRLNFFGTI-MSAKTYSIVSL 155
                                        3333355554555554444444444433333467778887766665555554449*****9988.6899999**** PP

                               DER1 148 afsfllgesvvvsligilvghiyyfledk 176
                                        a+ ++l++   +   g+l + iy +l++k
  gene3206|gene3206|rna3206|rna3206 156 AIDYVLNGGRSKVYYGFLHALIYVYLRKK 184
                                        ********9999**************854 PP

>> Caps_synth_CapC  Capsule biosynthesis CapC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   3.0   0.00025       2.2      21     110 ..       7     110 ..       6     115 .. 0.85
   2 ?    6.1   0.3    0.0016        14      38      79 ..     141     182 ..     126     200 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00025
                    Caps_synth_CapC  21 vvpGylalvl.dqplsllvtllialltylivrl..lsrflilyGrrrfvavlllgvlvklllelllllllpaelve 93 
                                        v p +la++l ++++ ll +l   + +y+++    l+rf i    r f+ ++++gv ++l+++l + + +++ ++e
  gene3206|gene3206|rna3206|rna3206   7 VPPVVLAILLcASVIPLLGLLSPQFTMYFVYDKsyLKRFEI-W--RLFTGIFVTGVSISLIMRLYFIHKFSSLILE 79 
                                        56889999999999999999999999999999896666666.4..8********************9999999988 PP

                    Caps_synth_CapC  94 ..............eleviGlivpgLiAndf 110
                                                      ++ ++ + vp +i n++
  gene3206|gene3206|rna3206|rna3206  80 yncridhvpteielAFFMFTMFVPLMIGNQL 110
                                        8888888888888878888888888887776 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0016
                    Caps_synth_CapC  38 vtllialltylivrllsrflilyGrrrfvavlllgvlvklll 79 
                                        + +++++ ty iv l  ++++  Gr +++  +l +++  +l 
  gene3206|gene3206|rna3206|rna3206 141 FGTIMSAKTYSIVSLAIDYVLNGGRSKVYYGFLHALIYVYLR 182
                                        5678999**********************9999988876655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (227 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       442  (0.0246528); expected 358.6 (0.02)
Passed bias filter:                      244  (0.0136092); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1569.75
//
Query:       gene3207|gene3207|rna3207|rna3207  [L=184]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       435  (0.0242624); expected 358.6 (0.02)
Passed bias filter:                      255  (0.0142228); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1332.37
//
Query:       gene3208|gene3208|rna3208|rna3208  [L=152]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.2e-05   22.6   0.0    0.00014   21.9   0.0    1.4  1  AAA_5            AAA domain (dynein-related subfamily)
    0.00049   20.5   0.0    0.00082   19.8   0.0    1.6  1  AAA              ATPase family associated with various cellul
     0.0012   18.4   0.0      0.002   17.7   0.0    1.5  1  AAA_7            P-loop containing dynein motor region
     0.0013   19.0   0.0      0.002   18.4   0.0    1.6  1  AAA_22           AAA domain
     0.0022   18.0   0.0     0.0029   17.6   0.0    1.4  1  ATPase_2         ATPase domain predominantly from Archaea
     0.0073   16.7   0.0       0.01   16.2   0.0    1.3  1  AAA_16           AAA ATPase domain
  ------ inclusion threshold ------
      0.016   15.1   0.1      0.019   14.8   0.0    1.4  1  AAA_11           AAA domain
      0.017   15.7   0.0      0.022   15.3   0.0    1.2  1  ABC_tran         ABC transporter
       0.02   15.2   0.2      0.077   13.3   0.2    2.0  1  AAA_19           AAA domain
      0.026   14.9   0.0      0.049   14.0   0.0    1.6  1  RNA_helicase     RNA helicase
      0.037   14.1   0.1      0.098   12.7   0.1    1.8  1  AAA_14           AAA domain
      0.043   12.6   0.0      0.055   12.3   0.0    1.2  1  Adeno_IVa2       Adenovirus IVa2 protein
      0.051   13.3   0.0       0.12   12.0   0.0    1.6  2  Sigma54_activat  Sigma-54 interaction domain
      0.055   13.3   0.0      0.077   12.8   0.0    1.2  1  Bac_DnaA         Bacterial dnaA  protein
       0.06   13.1   0.2       0.17   11.6   0.2    1.8  1  AAA_24           AAA domain
      0.061   13.3   0.0      0.089   12.7   0.0    1.4  1  Rad17            Rad17 P-loop domain
      0.064   13.2   0.1       0.17   11.8   0.0    1.7  2  RsgA_GTPase      RsgA GTPase
      0.069   13.7   0.1      0.093   13.2   0.1    1.4  1  AAA_23           AAA domain
      0.083   12.6   0.0       0.15   11.8   0.0    1.5  2  AAA_30           AAA domain
      0.083   12.0   0.0       0.13   11.4   0.0    1.3  1  PIF1             PIF1-like helicase
      0.097   12.7   0.0       0.31   11.0   0.0    1.8  2  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
       0.11   13.0   0.0       0.22   12.0   0.0    1.7  1  AAA_18           AAA domain


Domain annotation for each model (and alignments):
>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.0   1.7e-07   0.00014       2      47 ..      33      78 ..      32      96 .. 0.88

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 1.7e-07
                                       EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B-- CS
                              AAA_5  2 vlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrrei 47
                                       +l+ Gp+GtgKs+ ++++aa+l  ++eyv+ +++ + ++l+ +  i
  gene3208|gene3208|rna3208|rna3208 33 LLIYGPTGTGKSFHIRSIAAMLDMQLEYVMEPDKFSGKTLFKKHVI 78
                                       899***************************9999999888877665 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0     1e-06   0.00082       1      35 [.      33      67 ..      33     139 .. 0.65

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 1e-06
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCS CS
                                AAA  1 vllyGppGtGKTllakavakelgvefleisgsell 35
                                       +l+yGp GtGK+  ++++a  l++++  +  ++ +
  gene3208|gene3208|rna3208|rna3208 33 LLIYGPTGTGKSFHIRSIAAMLDMQLEYVMEPDKF 67
                                       699******************97554333333322 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   2.4e-06     0.002      32      64 ..      29      62 ..       5      84 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 2.4e-06
                              AAA_7 32 nkkpvllvGptGtGKtviikdllkkld.kekyls 64
                                       ++ p+l++GptGtGK+  i+++   ld + +y++
  gene3208|gene3208|rna3208|rna3208 29 SNTPLLIYGPTGTGKSFHIRSIAAMLDmQLEYVM 62
                                       5789*****************9999984445555 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   2.4e-06     0.002       7      59 ..      32      75 ..      28     147 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 2.4e-06
                             AAA_22  7 ilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllre 59
                                        l+++G++GtGK++ +r ++  l         + ++ +v  p + s k+l+++
  gene3208|gene3208|rna3208|rna3208 32 PLLIYGPTGTGKSFHIRSIAAML---------DMQLEYVMEPDKFSGKTLFKK 75
                                       689*******************9.........555556666666655555544 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   3.5e-06    0.0029       8      57 ..      18      67 ..      15     143 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 3.5e-06
                           ATPase_2  8 lkeleeilerepneiyfiYGpegsGKtaLlkeiienledkdkyviyyial 57
                                       l++l    ++ +n++++iYGp g GK+  ++ i+  l+ + +yv+  +++
  gene3208|gene3208|rna3208|rna3208 18 LDQLIGAFKNISNTPLLIYGPTGTGKSFHIRSIAAMLDMQLEYVMEPDKF 67
                                       55666666777899********************9997766666544444 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   1.3e-05      0.01       8      48 ..      17      54 ..      14     105 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.3e-05
                             AAA_16  8 eleqLlsalervrsgrpelvllsGesGvGKsslvrellral 48
                                        l+qL  a+++++ +    +l++G+ G+GKs  +r+++  l
  gene3208|gene3208|rna3208|rna3208 17 KLDQLIGAFKNIS-N--TPLLIYGPTGTGKSFHIRSIAAML 54
                                       5677777777554.3..4699*************9998644 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   2.3e-05     0.019      15      44 ..      30      57 ..      16     147 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.3e-05
                             AAA_11 15 seseitliqGPPGtgKTktivellsqllsr 44
                                       +++   li GP GtgK+++i ++ ++l  +
  gene3208|gene3208|rna3208|rna3208 30 NTP--LLIYGPTGTGKSFHIRSIAAMLDMQ 57
                                       333..69****************9999522 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.0   2.6e-05     0.022      14      80 ..      33     120 ..      25     148 .. 0.64

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.6e-05
                                        EEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS.--S-TTSBHHHH......... CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx......... RF
                           ABC_tran  14 vaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe.pqlfpeltvren......... 79 
                                        + i G++G+GKS  ++ +a +l+ + + + ++ ++++   ++ ++k++ ++  +  +  +++  r+n         
  gene3208|gene3208|rna3208|rna3208  33 LLIYGPTGTGKSFHIRSIAAMLDMQLEYV-MEPDKFSG--KTLFKKHVIYIDTDdIRDLRNM-PRNNvviesrcis 104
                                        6799********************99999.44444444..7788888888877743333333.4555666566666 PP

                                        ...............H CS
                                        ...............x RF
                           ABC_tran  80 ...............e 80 
                                                        
  gene3208|gene3208|rna3208|rna3208 105 svgrernamlikfgkV 120
                                        5554444444444433 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.2   9.4e-05     0.077       6      37 ..      26      57 ..      20     150 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 9.4e-05
                             AAA_19  6 ealkekvllvtaGpGtGKTrvlkhivallvel 37
                                       +++++++ll+ ++ GtGK+  ++ i a+l  +
  gene3208|gene3208|rna3208|rna3208 26 KNISNTPLLIYGPTGTGKSFHIRSIAAMLDMQ 57
                                       578999******************99988655 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0     6e-05     0.049       2      27 ..      34      59 ..      33      99 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 6e-05
                       RNA_helicase  2 wlyGpsgeGKStlakeLakallkklk 27
                                       ++yGp+g+GKS  ++++a+ l  +l+
  gene3208|gene3208|rna3208|rna3208 34 LIYGPTGTGKSFHIRSIAAMLDMQLE 59
                                       79**************9988876663 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   0.00012     0.098       2      49 ..      30      92 ..      29     136 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00012
                             AAA_14  2 rkilvitGaRrvGKTtllkqlikell................vkkesilyinldderdkkladp 49
                                       + +l+i G+  +GK++ ++ ++  l                   k++++yi+ dd rd ++  p
  gene3208|gene3208|rna3208|rna3208 30 NTPLLIYGPTGTGKSFHIRSIAAMLDmqleyvmepdkfsgktLFKKHVIYIDTDDIRDLRNM-P 92
                                       67899****************9877788899999999999998899*********9997644.2 PP

>> Adeno_IVa2  Adenovirus IVa2 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   6.7e-05     0.055      91     108 ..      34      51 ..       4      63 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 6.7e-05
                         Adeno_IVa2  91 viyGPtGsGksqllrnli 108
                                        +iyGPtG+Gks  +r++ 
  gene3208|gene3208|rna3208|rna3208  34 LIYGPTGTGKSFHIRSIA 51 
                                        6*************9874 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00015      0.12       9      44 ..      19      52 ..      11      66 .. 0.73
   2 ?   -2.0   0.0       3.1   2.5e+03     116     130 ..      97     111 ..      78     140 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00015
                                       HHHHHHHHHHCTSSS-EEEECSTTSSHHHHHHHHHH CS
                    Sigma54_activat  9 kelleqikkvaktdlsvlitGesGtGKellaraihe 44
                                        +l+   k++  +++++li G +GtGK++  r+i +
  gene3208|gene3208|rna3208|rna3208 19 DQLIGAFKNI--SNTPLLIYGPTGTGKSFHIRSIAA 52
                                       4444455544..45789***********98887765 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 3.1
                                        HHHHSEEESBTSSSE CS
                    Sigma54_activat 116 vlqegevervGsske 130
                                        v++++ ++ vG +++
  gene3208|gene3208|rna3208|rna3208  97 VIESRCISSVGRERN 111
                                        677777777776654 PP

>> Bac_DnaA  Bacterial dnaA  protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   9.5e-05     0.077      32      96 ..      28      93 ..      16      99 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 9.5e-05
                                       T.S--EEEE-SSSSSHHHHHHHHHHHH.HHHSSSS-EEEEEHHHHHHHHHHHHHTT-HHHHHHHHT CS
                           Bac_DnaA 32 kkynPlfiygevGlGktHLlkaignev.lenapelrvvYltaeeFlnelvkalrdkkaeefkeklr 96
                                        +  Pl+iyg++G Gk   +++i+  + ++ +  +     ++++  ++ v  + +++++++++  r
  gene3208|gene3208|rna3208|rna3208 28 ISNTPLLIYGPTGTGKSFHIRSIAAMLdMQLEYVMEPDKFSGKTLFKKHVIYIDTDDIRDLRNMPR 93
                                       4667*************9999999876234444455555666666666666666677766666655 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.2   0.00021      0.17       5      33 ..      33      84 ..      29     137 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00021
                             AAA_24  5 iliyGpsgiGKTtlakel.......................gpkplfidtek 33
                                       +liyGp g+GK+  ++++                       ++++++idt++
  gene3208|gene3208|rna3208|rna3208 33 LLIYGPTGTGKSFHIRSIaamldmqleyvmepdkfsgktlfKKHVIYIDTDD 84
                                       79***********999995555555555555555555555555555555555 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00011     0.089      46      83 ..      31      68 ..       9     103 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00011
                              Rad17 46 riLLisGPsGCgkstvvkvLskelgiklrewlnpvslk 83
                                         LLi GP+G gks  ++ ++  l ++l+  + p ++ 
  gene3208|gene3208|rna3208|rna3208 31 TPLLIYGPTGTGKSFHIRSIAAMLDMQLEYVMEPDKFS 68
                                       469************************99988887765 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00021      0.17      77     135 ..       8      66 ..       2      87 .. 0.76
   2 ?   -0.7   0.0       1.4   1.2e+03      36      65 ..     100     129 ..      69     149 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00021
                                        SEEEE--TTTHTTHHHHHHHCTTSEEEEECSTTSSHHHHHHHHCTT-----S------- CS
                        RsgA_GTPase  77 yevllvsaktkegleelkellkdktsvlvGqSGvGKStLinallpelelktgevseklg 135
                                        y++ ++s+++ ++l    +++++   ++ G++G GKS  i +++  l+++ + v e ++
  gene3208|gene3208|rna3208|rna3208   8 YKISTLSKNKLDQLIGAFKNISNTPLLIYGPTGTGKSFHIRSIAAMLDMQLEYVMEPDK 66 
                                        55566666655666556677777888999***************999999988877655 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.4
                                        HHHHHHHHHTT-EEEEEEE-GGG--HHHHH CS
                        RsgA_GTPase  36 drfLvlaeekgiepvivlnKiDlleeeeel 65 
                                        +r++  + +++  ++i + K+  ++ ++ l
  gene3208|gene3208|rna3208|rna3208 100 SRCISSVGRERNAMLIKFGKVSAIKIRKVL 129
                                        555555555555566666666555555522 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   0.00011     0.093      23      68 ..      34      83 ..      22     150 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00011
                             AAA_23 23 lItGpNGaGKTTildAiklaLygetprlsrks....grgfeksdveiese 68
                                       lI+Gp+G+GK+  ++ i  +L  + +     +    ++ f+k+ + i ++
  gene3208|gene3208|rna3208|rna3208 34 LIYGPTGTGKSFHIRSIAAMLDMQLEYVMEPDkfsgKTLFKKHVIYIDTD 83
                                       9**********999999999865553322222233344566666555554 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00019      0.15      21      45 ..      33      57 ..      19      72 .. 0.83
   2 ?   -3.3   0.0       7.8   6.4e+03     152     157 ..     126     131 ..     112     146 .. 0.49

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00019
                             AAA_30 21 avltGpAGtGKttalkalreaweaa 45
                                        ++ Gp GtGK++ +++++++++ +
  gene3208|gene3208|rna3208|rna3208 33 LLIYGPTGTGKSFHIRSIAAMLDMQ 57
                                       6899**************9998765 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 7.8
                             AAA_30 152 tevvRq 157
                                        ++v R 
  gene3208|gene3208|rna3208|rna3208 126 RKVLRE 131
                                        222222 PP

>> PIF1  PIF1-like helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00016      0.13       7      53 ..      15      61 ..       9      64 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00016
                                       HHHHHHH......HCTS-EEEEESTTSSCHHHHHHHHHHCHCTCCCE CS
                               PIF1  7 kkvfdaiieavlnekgklfFvtGsgGtgKtflwkallkklrsegkiv 53
                                       k+ +d+ i a +n +   + ++G  GtgK+f  + + ++l  + + v
  gene3208|gene3208|rna3208|rna3208 15 KNKLDQLIGAFKNISNTPLLIYGPTGTGKSFHIRSIAAMLDMQLEYV 61
                                       666899999999999999*******************9998877666 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00039      0.31       6      48 ..      17      61 ..       7      66 .. 0.76
   2 ?   -1.7   0.0       3.3   2.7e+03      30      40 ..      68      78 ..      61      82 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00039
                                       HHHHHHHHHHHCHTEEEEEEESTTSSHHHHHHHHHHHTT--..-- CS
                               TsaE  6 etealgkklakalgdvilLeGdLGaGKTtlvrglakalgve..ev 48
                                       ++++l  ++++  ++ +l++G+ G+GK+  +r++a+ l+++   v
  gene3208|gene3208|rna3208|rna3208 17 KLDQLIGAFKNISNTPLLIYGPTGTGKSFHIRSIAAMLDMQleYV 61
                                       44555555555446669*******************999876445 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 3.3
                                       SSHHHHHHHHH CS
                               TsaE 30 aGKTtlvrgla 40
                                       +GKT + ++++
  gene3208|gene3208|rna3208|rna3208 68 SGKTLFKKHVI 78
                                       69**9999875 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00028      0.22       2      58 ..      34      97 ..      33     132 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00028
                             AAA_18  2 lltGtpGvGKttlakeLskrlgf.........gvnlrdvakenglllevdpealdeskrldedkld 58
                                       l+ G+ G+GK+   + ++ +l +          +  + ++k++ ++++ d+   ++ + + ++++ 
  gene3208|gene3208|rna3208|rna3208 34 LIYGPTGTGKSFHIRSIAAMLDMqleyvmepdKFSGKTLFKKHVIYIDTDDI--RDLRNMPRNNVV 97
                                       699*****************98889999999655555555666666666666..777777666654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       621  (0.0346366); expected 358.6 (0.02)
Passed bias filter:                      511  (0.0285013); expected 358.6 (0.02)
Passed Vit filter:                        87  (0.00485247); expected 17.9 (0.001)
Passed Fwd filter:                        22  (0.00122706); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              22  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 986.51
//
Query:       gene3209|gene3209|rna3209|rna3209  [L=40]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (40 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       203  (0.0113224); expected 358.6 (0.02)
Passed bias filter:                      154  (0.00858944); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.43
# Mc/sec: 280.94
//
Query:       gene321|gene321|rna321|rna321  [L=105]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    7.8e-05   22.7   0.0    8.8e-05   22.6   0.0    1.1  1  TFIID-31kDa  Transcription initiation factor IID, 31kD subuni
     0.0034   17.9   0.1     0.0049   17.3   0.1    1.3  1  TFIID_20kDa  Transcription initiation factor TFIID subunit A
  ------ inclusion threshold ------
      0.071   13.5   0.0      0.098   13.0   0.0    1.2  1  Histone      Core histone H2A/H2B/H3/H4


Domain annotation for each model (and alignments):
>> TFIID-31kDa  Transcription initiation factor IID, 31kD subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0   1.5e-08   8.8e-05      11      77 ..      14      80 ..       6     102 .. 0.87

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 1.5e-08
                    TFIID-31kDa 11 ihliLaslgvteyeerVvlqLldfayrytssvLedAkvlaehakkkevslddvrlAiqsrlekqfke 77
                                   ++++++++  + ++ +V++ +  f  +++ +vL+ + +l+eh++  +++ +++   ++++++  f +
  gene321|gene321|rna321|rna321 14 LQNLINDTTEQPFDREVINRMQQFSRKFINDVLTRSALLSEHKNIGAITSEEIFYVVEKEFDFCFGD 80
                                   678888999999******************************************9999999987765 PP

>> TFIID_20kDa  Transcription initiation factor TFIID subunit A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.1   8.2e-07    0.0049       4      67 ..      13      75 ..      10      76 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 8.2e-07
                                   HHHHHHHCC-SS----HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHHHHHS- CS
                    TFIID_20kDa  4 klqdLvqqvdsetkldedvedlLleiaddFvesvtkfacklakhRksdklevrDiqlhlernyn 67
                                   klq+L+++  +e+  d +v + + +    F+++v ++++ l  h+    + +  i + +e++++
  gene321|gene321|rna321|rna321 13 KLQNLINDT-TEQPFDREVINRMQQFSRKFINDVLTRSALLSEHKNIGAITSEEIFYVVEKEFD 75
                                   677777753.56679**********************************************996 PP

>> Histone  Core histone H2A/H2B/H3/H4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   1.6e-05     0.098      77     124 ..      19      66 ..       6      72 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.6e-05
                                    TTSSSXEEXHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTXSEEXHHHH CS
                        Histone  77 sekedlrisaeavlalqealEallvelfeeAnllakhaKRvTitpkDi 124
                                    ++ +++ +++e ++ +q+++  ++ +++++++ll++h +   it+++i
  gene321|gene321|rna321|rna321  19 NDTTEQPFDREVINRMQQFSRKFINDVLTRSALLSEHKNIGAITSEEI 66 
                                    46788999******************************9999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       507  (0.0282782); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.34u 0.25s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 804.62
//
Query:       gene3210|gene3210|rna3210|rna3210  [L=220]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       337  (0.0187964); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 1464.81
//
Query:       gene3211|gene3211|rna3211|rna3211  [L=335]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-08   33.0   0.9    0.00088   17.9   0.1    2.2  2  GDI       GDP dissociation inhibitor


Domain annotation for each model (and alignments):
>> GDI  GDP dissociation inhibitor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.1   4.9e-08   0.00088      22     143 ..      18     136 ..       7     163 .. 0.83
   2 !   13.8   0.1   8.7e-07     0.016     214     273 ..     173     232 ..     155     252 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 4.9e-08
                                        HHHHTT--EEEE-SSSSSCGGG-EE-HHHHHHHH-TTHHHHHHH--GGG--EESS--BEETTSHHHHHHHHTTGGG CS
                                GDI  22 llsvdgkkvlhldrndyyGgesasltleqlyerfkleekpeeklGkdrdwnvdlipkfllanGelvkiliktdvtr 97 
                                        l+ + +k  ++ d  d+yG+ s+ l+l    +++ ++  ++ k+ +  +  ++  p+++ +nG l   l + d+  
  gene3211|gene3211|rna3211|rna3211  18 LFDIRKKDTIVYDNSDFYGTTSTPLDLPT--SKYVKD-VQTIKMTEP-KCLIETEPQLFRTNGRLLSKLEELDLLL 89 
                                        6778899999**************99865..455554.444677655.5789************************ PP

                                        CS-EEE-.SEEEEEETCEEEE--SSHHHHHC-TTS-HHHHHHHHHHH CS
                                GDI  98 ylefkav.eGsyvykegkiakvpanelealaspllglfekrrakkfl 143
                                         ++f ++ +  y+ ++  i+kvp  + e  +s+ l   ek+    f+
  gene3211|gene3211|rna3211|rna3211  90 NIDFIEIyDHLYIDENLCIYKVPYFDYEIANSNWLEAQEKNAYFYFV 136
                                        ****99845679999999*****************999998755444 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 8.7e-07
                                        HHCCCSS-SEEEETT-TTHHHHHHHHHHHHTT-EEETS--ECEEEE-TTS-EEEEEETTE CS
                                GDI 214 slarygkspylyplyGlGelpqgfarlsaiyGGtymlnkpvdevvldedgkvvGvkseee 273
                                         l+ +g  p+ yp+yG  e+ + ++r+ +    ++ +nk+ +   ++++  + G+  +  
  gene3211|gene3211|rna3211|rna3211 173 YLSSFGTPPFSYPMYGEREISDQLSRVLSFRNISFYVNKSLKCTRVNDHYEINGIYGNAT 232
                                        46788999********************************99999999999999876554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (335 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       557  (0.031067); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 2241.43
//
Query:       gene3212|gene3212|rna3212|rna3212  [L=413]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.5e-59  198.5   0.1    1.3e-58  197.8   0.1    1.2  1  MCM              MCM P-loop domain
    2.8e-12   46.6   0.5    5.4e-12   45.6   0.5    1.4  1  MCM_OB           MCM OB domain
    3.7e-05   23.5   0.1      0.018   14.8   0.0    2.6  2  Sigma54_activat  Sigma-54 interaction domain
    4.8e-05   22.8   0.3       0.16   11.3   0.0    2.6  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
     0.0015   18.5   0.0      0.013   15.5   0.0    2.6  2  AAA_5            AAA domain (dynein-related subfamily)
     0.0058   17.0   0.6      0.012   16.1   0.1    2.0  1  AAA              ATPase family associated with various cellul
  ------ inclusion threshold ------
       0.01   16.1   0.1      0.022   15.1   0.1    1.5  1  AAA_22           AAA domain
      0.012   15.7   0.6       0.03   14.4   0.6    1.6  1  DUF2318          Predicted membrane protein (DUF2318)
      0.012   14.9   0.1      0.021   14.2   0.1    1.3  1  FtsK_SpoIIIE     FtsK/SpoIIIE family
      0.017   15.5   0.1      0.024   15.0   0.1    1.3  1  AAA_16           AAA ATPase domain
      0.022   14.3   0.1      0.044   13.3   0.1    1.4  1  AAA_7            P-loop containing dynein motor region
      0.024   14.8   0.9      0.053   13.6   0.9    1.6  1  Zn-ribbon_8      Zinc ribbon domain
      0.031   14.6   0.0       0.05   13.9   0.0    1.4  1  AAA_19           AAA domain
      0.032   13.9   0.0      0.072   12.8   0.0    1.7  1  IstB_IS21        IstB-like ATP binding protein
      0.032   14.0   0.0      0.071   12.8   0.0    1.8  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
      0.038   13.1   0.1      0.061   12.5   0.1    1.3  1  DUF815           Protein of unknown function (DUF815)
      0.041   13.6   0.2       0.07   12.8   0.2    1.3  1  AAA_30           AAA domain
      0.047   12.6   0.1      0.074   12.0   0.1    1.2  1  AAA_10           AAA-like domain
      0.073   13.1   0.1       0.15   12.1   0.1    1.5  1  HypA             Hydrogenase/urease nickel incorporation, met
      0.083   12.8   0.0       0.21   11.5   0.0    1.7  1  NACHT            NACHT domain
      0.087   13.0   0.3       0.17   12.1   0.3    1.4  1  AAA_33           AAA domain
       0.11   12.4   0.1        1.1    9.1   0.1    2.2  1  AAA_3            ATPase family associated with various cellul
       0.15   10.9   0.0       0.23   10.3   0.0    1.1  1  TrwB_AAD_bind    Type IV secretion-system coupling protein DN
       0.21   11.5   1.1       0.32   10.9   0.3    1.7  2  NTPase_1         NTPase


Domain annotation for each model (and alignments):
>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  197.8   0.1   1.7e-61   1.3e-58      16     205 ..     226     406 ..     219     411 .. 0.93

  Alignments for each domain:
  == domain 1  score: 197.8 bits;  conditional E-value: 1.7e-61
                                        HHHHHHSSTTSSS-HHHHHHHHHHHH---EBBBSSSSBBCSS-EEEEEESSTSTHHHHHHHHHHHSSSEEEEESSS CS
                                MCM  16 eklvksiapsiyghedvkkaillqlfggvkkkledktklrgdinvllvgdpgtaKsqlLkyveklapravytsgkg 91 
                                        + l+k+++ +i+g e+vk +ill+++g   k +    ++r + +vllvg pgt+Ks++Lk+v++la ++v ++g g
  gene3212|gene3212|rna3212|rna3212 226 RFLIKTFMNEIVGCENVKLGILLSVIGKRGKDK----ETRNNSHVLLVGTPGTGKSHFLKSVAHLA-HSVSINGVG 296
                                        56999*********************9988744....46************************665.6899***** PP

                                        SSSSHSSSEEEEESSSSSEEEEETHHHHTTTSEEEEESGGGSTCHHHHHHHHHHHHSEEEEESSSCEEEEE--EEE CS
                                MCM  92 ssaagLtaavvrdeetgefvleaGalvladkGvcciDefdkmkeedrsalhEamEqqtisiaKaGivatLnartsv 167
                                        +s+agLt+  v+  + +e+ leaGal+lad+G+cciD fd     d+  l+E+mEqqt+s+aKaG+v tLnar+sv
  gene3212|gene3212|rna3212|rna3212 297 TSEAGLTTCAVK--QGKEWLLEAGALILADNGLCCIDSFDALPLYDKRGLLEVMEQQTLSVAKAGLVSTLNARCSV 370
                                        ******888774..6789********************************************************** PP

                                        EEEE--SSSSCCTTS-HHHHSSSSHHHHHHSSEEEEE- CS
                                MCM 168 laAanpkagrydkkksvaeninlsaalLsrFDlifvll 205
                                        +aA n ++  yd++ks+ +n++++++l+srFDlif+l+
  gene3212|gene3212|rna3212|rna3212 371 IAAYNISY--YDTTKSICDNLKITSPLISRFDLIFFLM 406
                                        ****9766..*************************986 PP

>> MCM_OB  MCM OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.6   0.5   7.3e-15   5.4e-12       8     124 ..      62     177 ..      56     178 .. 0.89

  Alignments for each domain:
  == domain 1  score: 45.6 bits;  conditional E-value: 7.3e-15
                                        GGTTSEEEEEEEEEEE---EEEEEEEEEEETTT-.-EEE...S---..-SB-..TTT-HHH-EEE-GGGSEEEEEE CS
                             MCM_OB   8 ehigklvkveGivtrasevkpklkkavfeckkcgktvev...elee..PrkCeekeCeskdpfkletekskfvdfq 78 
                                        ++i++lv ++G++++++ +  k ++ +++c  c +++ v   ++++     C  ++C+ kd+f+++   +k ++ q
  gene3212|gene3212|rna3212|rna3212  62 DKINHLVLLRGTIIKVNPILLKDVEQSYRCLYCDHSEIVksaNYKKkkKIVC--ERCG-KDNFRIDEVFTKAKNCQ 134
                                        79********************************977665553333335599..89**.9**************** PP

                                        EEEEE-------------EEEEEEEGGGTT---TT-EEEEEEEEEE CS
                             MCM_OB  79 klklQEspeevpaGelPrslevileddlvdkvkPGdrvevtGiyra 124
                                         +++Q+  +   + +++ ++e++++++   k  PG+++ev Gi+r 
  gene3212|gene3212|rna3212|rna3212 135 AIRIQDIGN---PQTMSDTIEILITGEQAGKFLPGENIEVLGIVRL 177
                                        *****9875...6799***************************985 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       7.4   5.5e+03      19      31 ..     147     159 ..     138     169 .. 0.77
   2 !   14.8   0.0   2.4e-05     0.018      20     144 ..     261     377 ..     252     390 .. 0.74

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 7.4
                                        CTSSS-EEEECST CS
                    Sigma54_activat  19 aktdlsvlitGes 31 
                                        ++ ++++litGe+
  gene3212|gene3212|rna3212|rna3212 147 MSDTIEILITGEQ 159
                                        4556899999996 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 2.4e-05
                                        TSSS-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETTTS-TTCHHHHHHEBSSSSSTTTSS-BEHHHHHTTTS CS
                    Sigma54_activat  20 ktdlsvlitGesGtGKellaraiheaskrkekpfvavncaaipeelleseLFGhekGaFtGAekekkGlfekadgG 95 
                                        +++++vl++G  GtGK+ + +++ +  +      v++n   ++e  l++    +++G        ++G++  ad+G
  gene3212|gene3212|rna3212|rna3212 261 RNNSHVLLVGTPGTGKSHFLKSVAHLAH-----SVSINGVGTSEAGLTTC--AVKQGK---EWLLEAGALILADNG 326
                                        5678899999999999988877765544.....46777666665533331..233332...12245699******* PP

                                        EEEEETGGGS-HHHHHHHHHHHHHSE..EESBTSSSEEE--EEEEEEESS- CS
                    Sigma54_activat  96 tlfLDeigelplelQekLlrvlqege..vervGsskeikvdvriiaatned 144
                                           +D    lpl     Ll+v+++++  v + G  ++ ++ + +iaa n +
  gene3212|gene3212|rna3212|rna3212 327 LCCIDSFDALPLYDKRGLLEVMEQQTlsVAKAGLVSTLNARCSVIAAYNIS 377
                                        **********************9986236799999999999****998865 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.2    0.0011      0.79      23      46 ..     264     287 ..     233     312 .. 0.83
   2 !   11.3   0.0   0.00021      0.16      96     196 ..     314     402 ..     297     412 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0011
                       Mg_chelatase  23 HnlllvGppGsGKtmlakrlpsll 46 
                                         ++llvG+pG+GK+   k ++ l 
  gene3212|gene3212|rna3212|rna3212 264 SHVLLVGTPGTGKSHFLKSVAHLA 287
                                        589***********9999887775 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00021
                       Mg_chelatase  96 kpkpGeislahnGvLfLDElpefkrkvlevLRePledgevtisrakakvefparfqlvaamNpcpcgklkdkekec 171
                                          + G++ la nG+  +D +  +       L e +e++++++++a    +  ar+ ++aa N +    ++++++ c
  gene3212|gene3212|rna3212|rna3212 314 LLEAGALILADNGLCCIDSFDALPLYDKRGLLEVMEQQTLSVAKAGLVSTLNARCSVIAAYNISY---YDTTKSIC 386
                                        5678999**********99999999989999999****************************874...44333444 PP

                       Mg_chelatase 172 tcsekeierYlsklsgplldRidlq 196
                                                    k+  pl+ R+dl 
  gene3212|gene3212|rna3212|rna3212 387 D---------NLKITSPLISRFDLI 402
                                        3.........235556666666665 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       3.1   2.3e+03      53      77 ..     121     144 ..      92     167 .. 0.58
   2 !   15.5   0.0   1.7e-05     0.013       1      23 [.     265     287 ..     265     399 .. 0.73

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 3.1
                                        ....--------G-SEEEEESGGG- CS
                              AAA_5  53 slvdsplvraaregeilvlDEvera 77 
                                         + d +++ +a++ + +++ ++ + 
  gene3212|gene3212|rna3212|rna3212 121 FRIDEVFT-KAKNCQAIRIQDIGNP 144
                                        23333333.5556666666666544 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 1.7e-05
                                        EEEEE--SSSSHHHHHHHGGGGB CS
                              AAA_5   1 dvlLvGppGtgKselaerlaaal 23 
                                        +vlLvG pGtgKs + +++a++ 
  gene3212|gene3212|rna3212|rna3212 265 HVLLVGTPGTGKSHFLKSVAHLA 287
                                        79******************997 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.1   1.6e-05     0.012       1      31 [.     266     294 ..     266     405 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.6e-05
                                        EEEESSTTSSHHHHHHHHHHHHTHEEEEEET CS
                                AAA   1 vllyGppGtGKTllakavakelgvefleisg 31 
                                        vll+G+pGtGK+ + k+va+ +++  ++i+g
  gene3212|gene3212|rna3212|rna3212 266 VLLVGTPGTGKSHFLKSVAHLAHS--VSING 294
                                        79*****************99642..33333 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.1   2.9e-05     0.022       4      32 ..     262     290 ..     258     320 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.9e-05
                             AAA_22   4 tagilvvtGesGtGKTtllrrlleqldee 32 
                                        + ++++++G +GtGK++ l+ +++ ++ +
  gene3212|gene3212|rna3212|rna3212 262 NNSHVLLVGTPGTGKSHFLKSVAHLAHSV 290
                                        7799*******************998765 PP

>> DUF2318  Predicted membrane protein (DUF2318)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.6     4e-05      0.03      22      79 ..      81     143 ..      66     160 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4e-05
                            DUF2318  22 vvkksdgklr.valdaCevCekkgYvqegeelvCknCgv.rfaldsigekkGGCnpipl....e 79 
                                        ++k+ ++++r    d  e+ +++ Y ++++++vC++Cg+ +f++d++ +k+  C+ i +    +
  gene3212|gene3212|rna3212|rna3212  81 LLKDVEQSYRcLYCDHSEIVKSANY-KKKKKIVCERCGKdNFRIDEVFTKAKNCQAIRIqdigN 143
                                        5555555555334455555566666.56789******973799**************9955442 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   2.8e-05     0.021      38      58 ..     262     282 ..     239     287 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.8e-05
                                        S-.SEEEE--TTSSHHHHHHH CS
                       FtsK_SpoIIIE  38 mashllvaGatgsGKStalnt 58 
                                        + sh+l++G++g+GKS +l++
  gene3212|gene3212|rna3212|rna3212 262 NNSHVLLVGTPGTGKSHFLKS 282
                                        347***************986 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.1   3.3e-05     0.024      24      51 ..     260     289 ..     244     357 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3.3e-05
                             AAA_16  24 p...elvllsGesGvGKsslvrellralekd 51 
                                        +   + vll+G +G+GKs  ++++++ l  +
  gene3212|gene3212|rna3212|rna3212 260 TrnnSHVLLVGTPGTGKSHFLKSVAH-LAHS 289
                                        345689***************99994.4444 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   5.9e-05     0.044      30      54 ..     260     284 ..     256     298 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5.9e-05
                              AAA_7  30 lknkkpvllvGptGtGKtviikdll 54 
                                         +n+ +vllvG+ GtGK+  +k++ 
  gene3212|gene3212|rna3212|rna3212 260 TRNNSHVLLVGTPGTGKSHFLKSVA 284
                                        57999**************999865 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.9   7.1e-05     0.053       6      35 ..      89     120 ..      88     123 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 7.1e-05
                        Zn-ribbon_8   6 YrCeeCghefevlqsis.daplta.CPeCgs.e 35 
                                        YrC  C+   e++ s++ +++++  C +Cg+ +
  gene3212|gene3212|rna3212|rna3212  89 YRCLYCD-HSEIVKSANyKKKKKIvCERCGKdN 120
                                        *******.89999999997777777*****966 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   6.7e-05      0.05       8      36 ..     261     289 ..     256     369 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 6.7e-05
                             AAA_19   8 lkekvllvtaGpGtGKTrvlkhivallve 36 
                                         +++++l+++ pGtGK++ lk + +l+ +
  gene3212|gene3212|rna3212|rna3212 261 RNNSHVLLVGTPGTGKSHFLKSVAHLAHS 289
                                        67899***************986544333 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   9.6e-05     0.072      45      71 ..     261     287 ..     221     299 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 9.6e-05
                          IstB_IS21  45 ekkenivllGpsGvGKshlaialgvea 71 
                                        +++  ++l+G +G+GKsh+  ++++ a
  gene3212|gene3212|rna3212|rna3212 261 RNNSHVLLVGTPGTGKSHFLKSVAHLA 287
                                        677889*************99988765 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   9.5e-05     0.071       6      55 ..     233     285 ..     228     403 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 9.5e-05
                             RuvB_N   6 leeyigqekvkeklkifieaakkre...ealdhvllyGpPGlGkttlakiiak 55 
                                        ++e +g e+vk  + + +   + ++   ++  hvll+G PG Gk+ + k +a+
  gene3212|gene3212|rna3212|rna3212 233 MNEIVGCENVKLGILLSVIGKRGKDketRNNSHVLLVGTPGTGKSHFLKSVAH 285
                                        77889999998776665554443331014568************987666654 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   8.1e-05     0.061      51      78 ..     261     288 ..     229     304 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 8.1e-05
                             DUF815  51 lpannvLLwGarGtGKSslvkallneya 78 
                                        ++ ++vLL+G+ GtGKS  +k++ + ++
  gene3212|gene3212|rna3212|rna3212 261 RNNSHVLLVGTPGTGKSHFLKSVAHLAH 288
                                        45689****************9987655 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.2   9.4e-05      0.07      17      44 ..     262     289 ..     258     311 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 9.4e-05
                             AAA_30  17 gdrvavltGpAGtGKttalkalreawea 44 
                                        ++  ++l+G +GtGK++ lk++++++++
  gene3212|gene3212|rna3212|rna3212 262 NNSHVLLVGTPGTGKSHFLKSVAHLAHS 289
                                        455789****************998875 PP

>> AAA_10  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   9.9e-05     0.074      12      44 ..     254     286 ..     245     295 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 9.9e-05
                             AAA_10  12 qevkgsktnasasliiGdlGnGKSvlakllvly 44 
                                        ++ + +  n+s++l++G +G GKS + k + + 
  gene3212|gene3212|rna3212|rna3212 254 RGKDKETRNNSHVLLVGTPGTGKSHFLKSVAHL 286
                                        556677889******************998775 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1    0.0002      0.15      51     100 ..      69     124 ..      44     131 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.0002
                                        HHCC.TTTT-EEEEEEE--EEEETTTS-EEECHH....H..HHS-TTTSSS-EEEE CS
                               HypA  51 laegtvlegaeLeieevpvkvrCreCgkefelee....k..alrCpkCgsadveiv 100
                                        l +gt+++   + +++v+ ++rC  C+++  +++    k  ++ C++Cg+ +++i 
  gene3212|gene3212|rna3212|rna3212  69 LLRGTIIKVNPILLKDVEQSYRCLYCDHSEIVKSanykKkkKIVCERCGKDNFRID 124
                                        457788888888899***********97655444334313455*******999885 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00028      0.21       3      26 ..     266     289 ..     264     297 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00028
                                        EEEEC-TTTCHHHHHHHHHHHHCT CS
                              NACHT   3 vilqGeaGsGKTtLlqklalawae 26 
                                        v+l G +G GK+++l+++a+++ +
  gene3212|gene3212|rna3212|rna3212 266 VLLVGTPGTGKSHFLKSVAHLAHS 289
                                        89****************998765 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.3   0.00022      0.17       2      20 ..     266     284 ..     266     298 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00022
                             AAA_33   2 vllvGlpGsGKstlaerll 20 
                                        vllvG pG+GKs+++++++
  gene3212|gene3212|rna3212|rna3212 266 VLLVGTPGTGKSHFLKSVA 284
                                        799*************987 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.1    0.0015       1.1       1     111 [.     265     375 ..     265     388 .. 0.61

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0015
                              AAA_3   1 hvllegvPGlaktllvkalakaldl.efkriqftpdllPsdilGtevfeekekefefkkGpvf.an..llladein 72 
                                        hvll g+PG++k  + k++a+  +  +++ +        + ++      ++ ke+ +++G+++ a+  l   d  +
  gene3212|gene3212|rna3212|rna3212 265 HVLLVGTPGTGKSHFLKSVAHLAHSvSINGVGTSE----AGLTT--CAVKQGKEWLLEAGALIlADngLCCIDSFD 334
                                        9****************999875430333333221....22322..223444566666666442222256667777 PP

                              AAA_3  73 rappktqsalleameerqvtvege..thklpepflvlatqn 111
                                          p   +  lle+me+++++v+++    +l+    v+a+ n
  gene3212|gene3212|rna3212|rna3212 335 ALPLYDKRGLLEVMEQQTLSVAKAglVSTLNARCSVIAAYN 375
                                        77777777777777777766654411456666667766665 PP

>> TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00031      0.23      12      34 ..     260     282 ..     257     289 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00031
                      TrwB_AAD_bind  12 eretqhilivGttGsGKtqalek 34 
                                         r ++h+l+vGt G+GK+  l++
  gene3212|gene3212|rna3212|rna3212 260 TRNNSHVLLVGTPGTGKSHFLKS 282
                                        57889*************99876 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       6.9   5.1e+03      56      97 ..     108     149 ..     104     154 .. 0.67
   2 ?   10.9   0.3   0.00043      0.32       1      37 [.     265     299 ..     265     310 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 6.9
                                        -EEEEEETT---SSEETTEEE-HHHHHHHHHHHHHHHHHHH- CS
                           NTPase_1  56 eegiLarveakreprvgkyvvdvesfeelalealrkalsead 97 
                                        +++i +++++k + r+++   + ++ + + ++ + + ++ +d
  gene3212|gene3212|rna3212|rna3212 108 KKKIVCERCGKDNFRIDEVFTKAKNCQAIRIQDIGNPQTMSD 149
                                        566677777777777777777777777777777766655555 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00043
                                        EEEEE--TTSSHHHHHHHHHHHH...GGGEEEEEEEE CS
                           NTPase_1   1 kvfiTGppGvGKtTlvkkvlellkssgvkvgGfytee 37 
                                        +v++ G pG+GK+ ++k v++l   + v+++G+ t+e
  gene3212|gene3212|rna3212|rna3212 265 HVLLVGTPGTGKSHFLKSVAHLA--HSVSINGVGTSE 299
                                        7999***************9988..579999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (413 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       766  (0.0427241); expected 358.6 (0.02)
Passed bias filter:                      544  (0.0303419); expected 358.6 (0.02)
Passed Vit filter:                        97  (0.00541023); expected 17.9 (0.001)
Passed Fwd filter:                        24  (0.00133861); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              24  [number of targets reported over threshold]
# CPU time: 0.61u 0.28s 00:00:00.89 Elapsed: 00:00:00.45
# Mc/sec: 2757.93
//
Query:       gene3213|gene3213|rna3213|rna3213  [L=129]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-11   44.1   0.1    3.2e-11   43.5   0.1    1.3  1  MCM_lid   MCM AAA-lid domain
     0.0022   17.3   0.0     0.0028   17.0   0.0    1.1  1  DUF1329   Protein of unknown function (DUF1329)


Domain annotation for each model (and alignments):
>> MCM_lid  MCM AAA-lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.5   0.1   3.5e-15   3.2e-11       3      87 .]      19      96 ..      17      96 .. 0.82

  Alignments for each domain:
  == domain 1  score: 43.5 bits;  conditional E-value: 3.5e-15
                                       HHHHHHHHHHTT--BETCHHHHHHHHHHHHHHHHHTSSTSSSST--HHHHHHHHHHHHHHHHHHTSSSE-HHHHHHHH CS
                            MCM_lid  3 lrkYiayarekikPklseeakeklseaYvelRkeeedskrksipitvRqLesliRLseAlAklrlsevvteedveeai 80
                                       lr+Y+++ r + +   + ea   l ++Y + Rk ++     + + t R+Les++RLse++Akl  +++ +e+ v +ai
  gene3213|gene3213|rna3213|rna3213 19 LRDYLEMIR-NDEKDATIEAT-DLIDTYFKWRKAQK-----TEMFTIRNLESILRLSESHAKLLGKNILDEDSVLMAI 89
                                       777888888.54545555555.5778999****774.....4589********************************* PP

                                       HHHHHHH CS
                            MCM_lid 81 rllkesl 87
                                        l+++sl
  gene3213|gene3213|rna3213|rna3213 90 FLVESSL 96
                                       ***9885 PP

>> DUF1329  Protein of unknown function (DUF1329)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   3.2e-07    0.0028     212     290 ..      39     115 ..      26     118 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 3.2e-07
                            DUF1329 212 Gapdry.dwklvgkkemyvpynnykleskklkyedllkpghlnpdlvryelhrVwvveAtlkegkrhiyskrvfYl 286
                                        + +d+y +w+   k em+   n   +   +++ ++ll+++ l +d v   l  ++ ve+ l   kr  + k+++++
  gene3213|gene3213|rna3213|rna3213  39 DLIDTYfKWRKAQKTEMFTIRNLESILRLSESHAKLLGKNILDEDSV---LMAIFLVESSLWGSKRIEFDKKRIFI 111
                                        5679999*************************************976...89************************ PP

                            DUF1329 287 Deds 290
                                        De +
  gene3213|gene3213|rna3213|rna3213 112 DEEY 115
                                        **86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       891  (0.049696); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 785.02
//
Query:       gene3214|gene3214|rna3214|rna3214  [L=377]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (377 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1163  (0.064867); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.61u 0.30s 00:00:00.90 Elapsed: 00:00:00.53
# Mc/sec: 2131.07
//
Query:       gene3215|gene3215|rna3215|rna3215  [L=49]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (49 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       541  (0.0301746); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.24s 00:00:00.58 Elapsed: 00:00:00.41
# Mc/sec: 354.72
//
Query:       gene3216|gene3216|rna3216|rna3216  [L=294]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.8e-75  253.1   0.0    3.2e-75  252.9   0.0    1.0  1  Pkinase        Protein kinase domain
    1.6e-35  122.6   0.0      2e-35  122.3   0.0    1.1  1  Pkinase_Tyr    Protein tyrosine kinase
    2.3e-06   27.1   0.0    5.2e-06   26.0   0.0    1.5  1  Kdo            Lipopolysaccharide kinase (Kdo/WaaP) family
    5.4e-06   25.6   0.4     0.0014   17.6   0.0    2.1  2  Haspin_kinase  Haspin like kinase domain
    3.4e-05   23.3   0.0    0.00014   21.3   0.0    1.8  2  Kinase-like    Kinase-like
     0.0048   16.6   0.3       0.27   10.8   0.0    2.1  2  FTA2           Kinetochore Sim4 complex subunit FTA2
     0.0056   16.6   0.0      0.079   12.9   0.2    1.8  2  APH            Phosphotransferase enzyme family
  ------ inclusion threshold ------
      0.022   14.4   0.0      0.035   13.7   0.0    1.3  1  RIO1           RIO1 family
      0.028   13.5   0.5       0.07   12.2   0.1    1.7  1  Seadorna_VP7   Seadornavirus VP7


Domain annotation for each model (and alignments):
>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  252.9   0.0   1.6e-78   3.2e-75       1     264 []       7     289 ..       7     289 .. 0.94

  Alignments for each domain:
  == domain 1  score: 252.9 bits;  conditional E-value: 1.6e-78
                                        EEEEEEEEEESSEEEEEEEETTTTEEEEEEEEECHCHCHHHHHHHHHHHHHHHHHSCTTB--EEEEEEESSEEEEE CS
                            Pkinase   1 yekleklGeGsfGkVykaveketgkivAvKkikkekakkkkekkvlrEikilkklkhpnivrlyevfeekdelylv 76 
                                        y++lek+GeG++G Vyka++k+t+kivA+Kki+ e++++   ++++rEi+ilk+l+ ++i++l++v+++++++y+v
  gene3216|gene3216|rna3216|rna3216   7 YQRLEKIGEGTYGIVYKAKNKSTNKIVALKKIRPENEEEGISTTTIREISILKNLNNNRIIKLMDVMYSNSSIYIV 82 
                                        7899************************************************************************ PP

                                        EE--TTEB...HHHHHHHHSS--HHHHHHHHHHHHHHHHHHHHTTEE-SS-SGGGEEEETTTEEEE-SGTTSEESS CS
                            Pkinase  77 leyvegge...ladllerkgslseeeakkiakqilegleylHskgiiHrDlKpeNiLidekgelKitDFGlakele 149
                                         ey+e++    l+d +++ ++++++  +++a+q++eg+++lH++gi+HrDlKp+NiLid +g++K++DFGl + l+
  gene3216|gene3216|rna3216|rna3216  83 YEYLETDLrrfLDDCISQGTTIDKDVRREMARQMVEGVAFLHCNGILHRDLKPQNILIDGNGNIKLADFGLGRTLR 158
                                        *****9977888888889999******************************************************* PP

                                        SSCS.BCTTTSCGGGS-HHHH.TTSCBSHHHHHHHHHHHHHHHHHSS-STTTSSHHHHHHHHHHTHHHHHHHCT.S CS
                            Pkinase 150 sssk.ltsfvgtseYlAPEvl.keneyskkvDvWslGvilyelltgkppfsgekgkekvekeldqlekilkilg.e 222
                                           k lt+ v+t +Y++PE+l ++++y ++vDvWsl++il+el+t kp+f+   g++    e+dql ki++ilg +
  gene3216|gene3216|rna3216|rna3216 159 LPIKtLTHDVITLWYRPPEILlGSKHYASSVDVWSLACILAELFTLKPIFP---GDS----EIDQLYKIFMILGtP 227
                                        99888****************999***************************...666....99**********975 PP

                                        HH...HHHTTS....................-HHHHHHHHHHT-SSGCCSTTHHHHHTSGGG CS
                            Pkinase 223 tkeklpeasei....................seeakdllkkllkkdpkkRltaeellqhpyl 264
                                         + ++++ + +                    +  ++dl+k++l++dp +R++a +++++py+
  gene3216|gene3216|rna3216|rna3216 228 DNTNWKNVTYFpnyqesfpkwepidlkiilkDGLFTDLIKSMLRYDPLDRVSALHAIDSPYF 289
                                        555666666668888888888888******9999***************************8 PP

>> Pkinase_Tyr  Protein tyrosine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.3   0.0     1e-38     2e-35       4     201 ..      10     204 ..       7     220 .. 0.88

  Alignments for each domain:
  == domain 1  score: 122.3 bits;  conditional E-value: 1e-38
                                        EEEEEEESSEEEEEEEEETTTTSSEEEEEEEEESTTSSHHH.HHHHHHHHHHHHTS-BTTB--EEEEEESSSSEEE CS
                        Pkinase_Tyr   4 gkklGeGafGkVvegtlkgekekkevkVavKtlkeeateee.keelleeakimkklkhpnivkllgvctkeeplli 78 
                                         +k+GeG++G V++++ k    +++  Va+K+++ e++ee  ++  ++e++i+k+l++++i+kl+ v++++++++i
  gene3216|gene3216|rna3216|rna3216  10 LEKIGEGTYGIVYKAKNK----STNKIVALKKIRPENEEEGiSTTTIREISILKNLNNNRIIKLMDVMYSNSSIYI 81 
                                        689*************99....88999******98888877688999***************************** PP

                                        EEE--TTEBHHHHHHHTCTTTSBHHH..HHHHHHHHHHHHHHHHHTTEEEST-SGGGEEEEETTEEEE-STTTHEE CS
                        Pkinase_Tyr  79 vteyvkgGdLlkfLrkkekekltlkd..llsfalqvAkGmeyLeskklvHrdlaarNvLlsenkvvkisDfGLard 152
                                        v ey++  dL+ fL +  ++ +t+++    ++a q+ +G+++L+ + ++Hrdl  +N+L++ n  +k++DfGL r+
  gene3216|gene3216|rna3216|rna3216  82 VYEYLET-DLRRFLDDCISQGTTIDKdvRREMARQMVEGVAFLHCNGILHRDLKPQNILIDGNGNIKLADFGLGRT 156
                                        *****86.9******9966655555511678********************************************* PP

                                        TTTSSEEEETTSSTSGGGGS-HHHHHHSE.EEHHHHHHHHHHHHHHHHTT CS
                        Pkinase_Tyr 153 iekddeyvkkeeaklpvkWmapEslkekk.ftsksDvWsfGvllwEiftl 201
                                        +  +   ++ ++  + + + +pE+l  +k + s+ DvWs + +l E+ftl
  gene3216|gene3216|rna3216|rna3216 157 L--RLPIKTLTHDVITLWYRPPEILLGSKhYASSVDVWSLACILAELFTL 204
                                        *..44556666777777778***988766599999*************96 PP

>> Kdo  Lipopolysaccharide kinase (Kdo/WaaP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   0.0   2.6e-09   5.2e-06      56     171 ..      49     156 ..      44     174 .. 0.75

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 2.6e-09
                                Kdo  56 travrEfrllkrLeeagvavpkpvaagavkvgleyrAlllterleg..aqdLedllakwaelaeelkrallkavgr 129
                                        t+  rE+++lk+L++  +  +  v++    +       ++ e le    + L+d++ ++ ++++ ++r++ ++   
  gene3216|gene3216|rna3216|rna3216  49 TTTIREISILKNLNNNRIIKLMDVMYSNSSIY------IVYEYLETdlRRFLDDCISQGTTIDKDVRREMARQMVE 118
                                        56666666777776666666666666555544......444444431134599*****999*************** PP

                                Kdo 130 liaklhragvnHadlyaknillqqeeeeeaeiwliDldkarl 171
                                         +a lh  g+ H+dl ++nil++ ++    +i l D+  +r+
  gene3216|gene3216|rna3216|rna3216 119 GVAFLHCNGILHRDLKPQNILIDGNG----NIKLADFGLGRT 156
                                        ***********************999....788888876654 PP

>> Haspin_kinase  Haspin like kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.4   0.1    0.0018       3.6     104     171 ..       9      85 ..       1     105 [. 0.59
   2 !   17.6   0.0   7.2e-07    0.0014     230     257 ..     130     157 ..     127     186 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0018
                      Haspin_kinase 104 sllndseklssevyqtke..kdkevvlKvipl....evledvtiskelsl....kelkslklvkgtypglllllqd 169
                                         l + +e+ ++ vy++k+  ++k v+lK+i      e ++  ti  e+s+    ++ + +kl+   y++  + +  
  gene3216|gene3216|rna3216|rna3216   9 RLEKIGEGTYGIVYKAKNksTNKIVALKKIRPeneeEGISTTTIR-EISIlknlNNNRIIKLMDVMYSNSSIYIVY 83 
                                        3334499999*******9656667888888775554333333333.344342224444455555556555555555 PP

                      Haspin_kinase 170 kv 171
                                        ++
  gene3216|gene3216|rna3216|rna3216  84 EY 85 
                                        44 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 7.2e-07
                      Haspin_kinase 230 HRdLhldniLvdknlnvtlidlklsRle 257
                                        HRdL+ +niL+d n+n+ l d+ l+R  
  gene3216|gene3216|rna3216|rna3216 130 HRDLKPQNILIDGNGNIKLADFGLGRTL 157
                                        **************************86 PP

>> Kinase-like  Kinase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.43   8.5e+02      17      46 ..      10      39 ..       5      61 .. 0.81
   2 !   21.3   0.0   6.8e-08   0.00014     112     215 ..      78     181 ..      65     199 .. 0.67

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.43
                        Kinase-like 17 gellkkgdrsvvfevkdqetgeplavkvfl 46
                                        e +++g  ++v+++k++ t++ +a+k   
  gene3216|gene3216|rna3216|rna3216 10 LEKIGEGTYGIVYKAKNKSTNKIVALKKIR 39
                                       56788999999*********9999998765 PP

  == domain 2  score: 21.3 bits;  conditional E-value: 6.8e-08
                        Kinase-like 112 nallllpaasvdleilnkvlqkrset.hkkletiarlllTlqlirlaanLqakglvhgkftvdnllldekgglmlg 186
                                        + ++++   ++dl ++ +   ++ +t +k      r  +  q++  +a L+ +g++h +++++n+l d +g ++l 
  gene3216|gene3216|rna3216|rna3216  78 SIYIVYEYLETDLRRFLDDCISQGTTiDKD----VRREMARQMVEGVAFLHCNGILHRDLKPQNILIDGNGNIKLA 149
                                        556777778888877766555555553333....344444566788****************************** PP

                        Kinase-like 187 gftaLvrag..tkvvl.sevekgfaPpEllgs 215
                                        +f+  ++     k      +   + PpE+l  
  gene3216|gene3216|rna3216|rna3216 150 DFGLGRTLRlpIKTLThDVITLWYRPPEILLG 181
                                        **754433200222221455577888887644 PP

>> FTA2  Kinetochore Sim4 complex subunit FTA2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.1     0.022        43      22      52 ..       5      37 ..       1      63 [. 0.73
   2 !   10.8   0.0   0.00013      0.27     167     206 ..     102     142 ..      75     153 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.022
                               FTA2 22 kdiefleyLgkglhsiVlkvkirgk..eYALKl 52
                                       ++++ le +g+g+ +iV+k+k +    + ALK 
  gene3216|gene3216|rna3216|rna3216  5 DSYQRLEKIGEGTYGIVYKAKNKSTnkIVALKK 37
                                       578899**************9775433888883 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00013
                               FTA2 167 lkeqeelevsqlpkllrdlkklhklgIvvrDlkeenyi.dg 206
                                         + ++ ++ ++++++++ +  lh  gI++rDlk++n++ dg
  gene3216|gene3216|rna3216|rna3216 102 TTIDKDVRREMARQMVEGVAFLHCNGILHRDLKPQNILiDG 142
                                        56678899999*************************86433 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0      0.14   2.8e+02      23     106 ..      33     124 ..      10     127 .. 0.74
   2 !   12.9   0.2     4e-05     0.079     167     187 ..     127     146 ..     124     155 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.14
                                        EEEEEE-TTS-HHHHH....HHHHHHHHHHHTT-.B--B-CTTBS-EEETTEEEEEEE----EE-SS......HHH CS
                                APH  23 yvlrrnpparaaeeir....revallrlLakagv.pvPevlagdtddeeigllfalieyvpgrsllr......kls 87 
                                        ++l+ ++p+ ++e i+    re  +l++L+++ + +   v +   ++  i+++++ +e    r l++      + +
  gene3216|gene3216|rna3216|rna3216  33 VALKKIRPENEEEGIStttiREISILKNLNNNRIiKLMDVMY---SNSSIYIVYEYLETDLRRFLDDcisqgtTID 105
                                        457777777777777777778999999999998877777777...8899998888888854444444999999999 PP

                                        HHHHHHHHHHHHHHHCCHH CS
                                APH  88 aaqlpellealgeflaalh 106
                                         ++++e++++++e  a lh
  gene3216|gene3216|rna3216|rna3216 106 KDVRREMARQMVEGVAFLH 124
                                        9999999999999998888 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 4e-05
                                        EEE-SS-SGGGEEEC..TTEE CS
                                APH 167 vllHgDlhpgNllvdpddgrv 187
                                        ++lH+Dl+p+N+l+d ++g +
  gene3216|gene3216|rna3216|rna3216 127 GILHRDLKPQNILID-GNGNI 146
                                        699************.66654 PP

>> RIO1  RIO1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   1.8e-05     0.035      43     149 ..      39     151 ..      17     160 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.8e-05
                                        -GS-HHHHHHHHHHHHHHHHHHHHHTT.--S--EEEEETTE.EEEE--EETTEEGGB..HHHCG-..HHHHHHHHH CS
                               RIO1  43 sktnprklvklwaekEfrnLkrleeag.vpvPkpielkrhv.lvmefigedgvaapk..lkdvee..eeeaeelye 112
                                           n  + + +++ +E+++Lk l++   ++  +++  ++ + +v e++++d  +  +  +++ ++  ++  +e+++
  gene3216|gene3216|rna3216|rna3216  39 RPENEEEGISTTTIREISILKNLNNNRiIKLMDVMYSNSSIyIVYEYLETDLRRFLDdcISQGTTidKDVRREMAR 114
                                        4677888888999999999999998876788888777777658999999554443321133333244677788888 PP

                                        HHHHHHHHHHHTSTEEESS-STTSEEEETT.EEEE--G CS
                               RIO1 113 evleemrklykeaglvHaDLSeyNvlvded.kvviIDv 149
                                        +++e + ++++++g+ H DL   N+l+d + ++ + D+
  gene3216|gene3216|rna3216|rna3216 115 QMVEGV-AFLHCNGILHRDLKPQNILIDGNgNIKLADF 151
                                        888865.55669***************99878888887 PP

>> Seadorna_VP7  Seadornavirus VP7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   3.5e-05      0.07     162     186 ..     126     150 ..     112     154 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 3.5e-05
                       Seadorna_VP7 162 tnllhGDcnpenlmcDknGylklvD 186
                                        +++lh D +p+n++ D nG++kl D
  gene3216|gene3216|rna3216|rna3216 126 NGILHRDLKPQNILIDGNGNIKLAD 150
                                        679********************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (294 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       515  (0.0287244); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.60u 0.32s 00:00:00.92 Elapsed: 00:00:00.50
# Mc/sec: 1784.60
//
Query:       gene3217|gene3217|rna3217|rna3217  [L=142]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      7e-09   35.4   0.1    1.8e-07   30.9   0.0    2.7  2  CSD       'Cold-shock' DNA-binding domain


Domain annotation for each model (and alignments):
>> CSD  'Cold-shock' DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.9   0.0     1e-11   1.8e-07       2      65 ..      24      99 ..      23     100 .. 0.84
   2 ?   -0.7   0.0     0.072   1.3e+03      21      31 ..     108     118 ..     105     138 .. 0.74

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 1e-11
                                       EEEEEEEETTTTEEEEEETTSS-E..........EEEETTTS-STT...TS--STSEEEEEEEECSSCEEEEEEEE CS
                                CSD  2 tGtVkwfnakkgfGFItredgdkd..........vFvHvsaiqgdg..frsLqegqeVeFevvegkkgpeAanVtk 65
                                       +Gt+k f+ ++g+GF  + d + +          vF+H+s+i+++   +  L   q  eFe+v+g +g  A+nVt 
  gene3217|gene3217|rna3217|rna3217 24 KGTIKFFSYERGYGFLVPHDPEINedgkllflisVFFHFSSISTQPgmVVYLLPQQICEFELVKGPRGYLAKNVTS 99
                                       7**************9987755311245555555********999878999***********************85 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.072
                                        TSS-EEEEETT CS
                                CSD  21 dgdkdvFvHvs 31 
                                        ++ +d++ H+ 
  gene3217|gene3217|rna3217|rna3217 108 QKTNDIYYHYY 118
                                        56679999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       704  (0.039266); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1011.57
//
Query:       gene3218|gene3218|rna3218|rna3218  [L=115]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-05   24.7   1.3    3.8e-05   23.7   1.3    1.4  1  Tcp10_C   T-complex protein 10 C-terminus


Domain annotation for each model (and alignments):
>> Tcp10_C  T-complex protein 10 C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   1.3   2.1e-09   3.8e-05      12      96 ..      21     106 ..      11     114 .. 0.68

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 2.1e-09
                                        E-TTS-EEEE-TTSS-EEEE-TTS-EEEE-TTS-EEEEETTTTEEEEE-TTS-EE..EE-TTS-EEEE-TTS-EEE CS
                            Tcp10_C  12 tyanGtvkevsadgktvtvsffNgDvketledgrviYyyaeaqtthttypdglev..lefpngqiekhykdgskei 85 
                                        +  n   k+++ ++k+v+     g ++  l dg++ Y+  +++ ++  y  +  +  +ef ngq+e+++++g kei
  gene3218|gene3218|rna3218|rna3218  21 KELNQEYKRMINEKKVVHEEQSKGKTRYYLCDGST-YVVSADKKYRYLYDAKSRIitYEFDNGQVERTFPNGLKEI 95 
                                        44577778888888888888888888888888875.5555555555555544444115788999999999999999 PP

                                        E-TTS-EEEE- CS
                            Tcp10_C  86 vfpdgtvkslk 96 
                                         + dg++   +
  gene3218|gene3218|rna3218|rna3218  96 RYSDGSIAVRN 106
                                        99998876654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1486  (0.0828825); expected 358.6 (0.02)
Passed bias filter:                      676  (0.0377043); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 751.25
//
Query:       gene3219|gene3219|rna3219|rna3219  [L=223]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0028   17.7   0.2     0.0044   17.1   0.2    1.3  1  DUF4366   Domain of unknown function (DUF4366)
  ------ inclusion threshold ------
      0.027   14.4   0.1      0.038   13.9   0.1    1.3  1  TMEM154   TMEM154 protein family
      0.039   14.8   0.6      0.071   13.9   0.6    1.4  1  Rsc14     RSC complex, Rsc14/Ldb7 subunit
       0.09   12.2   0.3       0.16   11.4   0.1    1.4  1  ECH_2     Enoyl-CoA hydratase/isomerase
       0.43   10.8  12.1       0.58   10.4  12.1    1.2  1  AP3D1     AP-3 complex subunit delta-1
        1.2    8.9   4.6       0.24   11.2   0.9    1.6  2  Connexin  Connexin


Domain annotation for each model (and alignments):
>> DUF4366  Domain of unknown function (DUF4366)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.2   1.5e-06    0.0044      59     139 ..     100     183 ..      93     190 .. 0.55

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.5e-06
                            DUF4366  59 Llalleedeeaakee.eevcactekcaagkvntdcpveepepekeaepee..peeepekksn...nglllvvlava 128
                                        L +++e+   + +e+  ++ + + k+++++  +++ v++p++e++ e+ +  +++ + ++ +    +++ + ++++
  gene3219|gene3219|rna3219|rna3219 100 LKKMVEKRPVTDTENkAKETKSSGKQNKKRSAKKSTVKKPKKEEKLEKGKfdNKKYQLDH-EllkYIFISIAVIII 174
                                        5666665554444330344444566777777788889***99999998876433333333.243244444444445 PP

                            DUF4366 129 ligggaayyfk 139
                                        l+ggg +  + 
  gene3219|gene3219|rna3219|rna3219 175 LVGGGYL--LA 183
                                        5554433..32 PP

>> TMEM154  TMEM154 protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   1.3e-05     0.038      15      98 ..     116     200 ..      87     214 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.3e-05
                            TMEM154  15 atleeesadatsaasteseslkqeeakeslssaelsnesdqlel.vlmiiiPlvllillllvviiliqkkkrkrsK 89 
                                        a+ ++ s +     s++++++k+ +++e+l +++++n++ ql+  +l +i  ++++i++l+ +  l  ++ r+r  
  gene3219|gene3219|rna3219|rna3219 116 AKETKSSGKQNKKRSAKKSTVKKPKKEEKLEKGKFDNKKYQLDHeLLKYIFISIAVIIILVGGGYLLAMYIRHRVM 191
                                        22333344444555666666777778999************99867778888999999888888888788888887 PP

                            TMEM154  90 ddekseaes 98 
                                         +++ e + 
  gene3219|gene3219|rna3219|rna3219 192 GKTEMEYYR 200
                                        777666655 PP

>> Rsc14  RSC complex, Rsc14/Ldb7 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.6   2.4e-05     0.071      18      81 ..      92     162 ..      77     166 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.4e-05
                              Rsc14  18 vsl.skeeLkeLvkkekekrkkkdeeekkkk..kekk...krvavhgYl.ggkvdlkeaseaaYdlshtLL 81 
                                        +++ sk+eLk++v+k+  ++ +++ +e+k++  ++kk   k+ +v +    +k++  + ++ +Y+l+h LL
  gene3219|gene3219|rna3219|rna3219  92 ITVpSKNELKKMVEKRPVTDTENKAKETKSSgkQNKKrsaKKSTVKKPKkEEKLEKGKFDNKKYQLDHELL 162
                                        544378999999998644333333322222222222224578888775514599999999999*******9 PP

>> ECH_2  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   5.4e-05      0.16      62     117 ..     140     194 ..     129     197 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 5.4e-05
                                        HHCS-THHHHHHHHHHHHHHHHHC-SS-EEEEE-BEEETHHHHHHTTSSEEEE-TT CS
                              ECH_2  62 akegkkeeeeffreeYklnyliatypkpvvalmdGivmGgGvGlsvhgsfrvvter 117
                                        +ke+k e+ +f +++Y+l++ + +y    +a++  i +GgG  l++  ++rv+ ++
  gene3219|gene3219|rna3219|rna3219 140 KKEEKLEKGKFDNKKYQLDHELLKYIFISIAVII-ILVGGGYLLAMYIRHRVMGKT 194
                                        344444457899*******************997.999**************9765 PP

>> AP3D1  AP-3 complex subunit delta-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4  12.1    0.0002      0.58      46     115 ..      79     150 ..      51     160 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0002
                              AP3D1  46 eipvaeld.lsvplkvpglkrsdkyleeeesrkakkkakeekkkkkkkkkkkkkkkk.kkkkkkeeessese 115
                                         ip+++ + +s ++ vp+ +++ k +e+   +  ++kake k++ k++kk++ kk   kk kk+e+ ++ + 
  gene3219|gene3219|rna3219|rna3219  79 VIPEVKSKtISPAITVPSKNELKKMVEKRPVTDTENKAKETKSSGKQNKKRSAKKSTvKKPKKEEKLEKGKF 150
                                        46655554267777**************88888888888888888888888887777566666665555444 PP

>> Connexin  Connexin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.1      0.68     2e+03      26      45 ..       2      21 ..       1      26 [. 0.87
   2 ?   11.2   0.9   7.9e-05      0.24     106     175 ..     114     185 ..      86     201 .. 0.44

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.68
                           Connexin 26 vlfifRilvlavagesvysD 45
                                       +lf+f+ ++     ++ y+D
  gene3219|gene3219|rna3219|rna3219  2 FLFVFKYVIASYNFDDFYDD 21
                                       799******99999999988 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 7.9e-05
                           Connexin 106 ekeeeekeeeekeeekkkkkekkkkkkkeeekekkkeegkr.rirggllrtYvlql.llrillEvaflvgqy 175
                                        +k +e+k++ +++++++ kk++ kk kkee+ ek k ++k+ +++++ll+  ++++ ++ il+  + l+++y
  gene3219|gene3219|rna3219|rna3219 114 NKAKETKSSGKQNKKRSAKKSTVKKPKKEEKLEKGKFDNKKyQLDHELLKYIFISIaVIIILVGGGYLLAMY 185
                                        111111111111111111222222222222222222222222557777666444440444444555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2207  (0.123097); expected 358.6 (0.02)
Passed bias filter:                      834  (0.0465168); expected 358.6 (0.02)
Passed Vit filter:                       112  (0.00624686); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.55u 0.33s 00:00:00.88 Elapsed: 00:00:00.48
# Mc/sec: 1397.70
//
Query:       gene322|gene322|rna322|rna322  [L=109]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.033   14.1   0.1      0.053   13.4   0.1    1.3  1  AKAP7_NLS  AKAP7 2'5' RNA ligase-like domain


Domain annotation for each model (and alignments):
>> AKAP7_NLS  AKAP7 2'5' RNA ligase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1     3e-06     0.053      64     116 ..      52     106 ..      41     108 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3e-06
                                    HHHHHHHHHHHHHTTS--EEEEEEEEEE.....T.TTEEEEEE--SHH.HHHHHH CS
                      AKAP7_NLS  64 vLkevkeeikdaldnkplslrlkGletfnddpak.arVlYakveeesn.eekLqe 116
                                     +k ++  +k+++ n ++ +r++ +++ n+d+++ a+Vl++k++ +++ +++L++
  gene322|gene322|rna322|rna322  52 SIKICEYALKEIVINGNFFVRINDMHYVNGDMSEvAQVLHLKLNYIGRkVKELLR 106
                                    567899999****99*******************99*******998876777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       572  (0.0319036); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 730.27
//
Query:       gene3220|gene3220|rna3220|rna3220  [L=520]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
   1.1e-130  436.6   8.6   1.2e-130  436.4   8.6    1.0  1  Cpn60_TCP1  TCP-1/cpn60 chaperonin family


Domain annotation for each model (and alignments):
>> Cpn60_TCP1  TCP-1/cpn60 chaperonin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  436.4   8.6  6.8e-135  1.2e-130       1     490 [.      32     518 ..      32     519 .. 0.97

  Alignments for each domain:
  == domain 1  score: 436.4 bits;  conditional E-value: 6.8e-135
                                        HHHHHHCCSSTTXXEEEEEETTSEEEEEXSHHHHHHCSXXXSHHHHHHHHHHHHCCCCCTTCHHHHHHHHHHHHHH CS
                         Cpn60_TCP1   1 ladivkttlGPkGmdKmlvnkggkvvvTnDGatilkeleiehPaakllveaaesqdeevGDGTttvviLageLlee 76 
                                        +++i++t+lGP++m+Km+  ++g++++TnDG++il+el+i+hPaak +ve+a++qd+evGDGTttv++La++Llee
  gene3220|gene3220|rna3220|rna3220  32 ISSILTTCLGPRSMQKMILTRIGTIQITNDGNAILRELDITHPAAKQIVELARTQDNEVGDGTTTVILLAAKLLEE 107
                                        689************************************************************************* PP

                                        HHHHHHCTXXHHHHHHHHHHHHHHHHHHHHHHXEEBXSCSTT.HHHHHHHHHHCTTSSXXSTHHHHHHHHHHHHHC CS
                         Cpn60_TCP1  77 aekliaagvhpttiiegyekalekaleaLkeiaveisseekdreeLlkvartslsskltskeaeelsklvvdAvkl 152
                                        +  l+++++hp+ i++ +++al ++l++L+e++  ++ +   ++e + ++r s+ +kl+   +  l++l+ +A ++
  gene3220|gene3220|rna3220|rna3220 108 MGVLLRDKIHPVHICKILKEALGECLSYLEEVSYPFKGS---EDEKIGIVRHSVANKLCTMLKVDLASLAYKAANI 180
                                        ********************************6666655...67789***************************54 PP

                                        HCCCSEECSCCC.EECCCCEECECTTSEEESEEEESS--SSTTSSCEEECEEEEEESS-BS--HHCCHHHCCCCSC CS
                         Cpn60_TCP1 153 ieenekeldlgr.ikvvkieggsledselveGlvldkgvlspdmpkklenakvllldvsLeiektetkttvvlsda 227
                                             k++d++  +k++ki   + +   +++G++++k++++++m +++++++v++ld+++e++k e+kt+ +l++ 
  gene3220|gene3220|rna3220|rna3220 181 A----KNCDIKTfVKIEKISAADFSGCDVLDGVIVNKSLIHSEMRREIRDPRVIILDTPIEYKKGESKTSYELKNQ 252
                                        4....459****9*************************************************************** PP

                                        CHHHHHHHHHHHHHHHHHHHHHHTTECEEEESS-B-HHHHHHHHHCT-EEE-S--HHHHHHHHHHHT--EBSCGGG CS
                         Cpn60_TCP1 228 eeleklekaeekqleellekiiksgvnvvvcqkgiddlalhflakngilalrrvkkkdlerlakatGatavssled 303
                                        +e+++ ++ ee+q++e+++ i +++ ++v+++kgi d al++++k+++ alrr kk+d+ r+a++tGat+vs+ ed
  gene3220|gene3220|rna3220|rna3220 253 AEYTRALEIEEEQVQEVVDHILALNPDIVITEKGICDSALSMFQKKNVTALRRFKKTDTLRIAAVTGATIVSRAED 328
                                        **************************************************************************** PP

                                        GGCGC-EEEEEE.EECCETTCCEEEEECESSSSXEEEEEEESTCCCHHHHHHHHHHHHHHHHHHHHHHEEEETTTC CS
                         Cpn60_TCP1 304 ltpeelGtakkv.eeekigsekttiieevksgkiatillrgatdtvldeieraiedAlnvvknaiedekvvpGGGa 378
                                        l+++++G  +++ +++++g+e+++ + e+ ++k+++++lrg++ ++l+e er+ edA++v++n+  + ++++GGGa
  gene3220|gene3220|rna3220|rna3220 329 LEEKHVGRNCRLfKVTRLGNEDYVNFVECVDPKACSVVLRGPSRDILNEFERNFEDAIKVARNLRMSDRLCAGGGA 404
                                        ********99999*************************************************************** PP

                                        HHHHHHHHHHCCCCT.....SXCCHHHHHHHHHHHHTHHHHHHHHHCTS.XHHHHHHHHHHHHHTTXTTEEEETTT CS
                         Cpn60_TCP1 379 telelakklkeyaks.....vsgeeqlaieafakALevipktLaeNaGl.dpievlaklraahnkgekelgidves 448
                                        te+ l k l + +++      s+ ++ +++ +a+AL  ip tLa+N+G  dp  ++a+l++   ++++ +gid  +
  gene3220|gene3220|rna3220|rna3220 405 TEMNLCKFLLRSSETtentrNSTLRKRVYDGIANALRMIPLTLAKNSGCdDPLGLIAELES---TNDVYMGIDGVN 477
                                        *********99999999999999**************************889*******99...7777******** PP

                                        TCEEECCCCTXEEEHHHHHHHHHHHHHHHHHHHCEEEEEXXX CS
                         Cpn60_TCP1 449 geiidlveagvvDplkvkrqalksAteaastiLrideiikak 490
                                        g+++d+ +  v++p++vkrqalksA+ea++++Lr+d +i+ k
  gene3220|gene3220|rna3220|rna3220 478 GKVVDVRN-LVMEPIAVKRQALKSAFEAVALLLRVDGVIQSK 518
                                        ******76.5*****************************988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (520 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       746  (0.0416086); expected 358.6 (0.02)
Passed bias filter:                      586  (0.0326845); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.34s 00:00:00.92 Elapsed: 00:00:00.48
# Mc/sec: 3232.70
//
Query:       gene3221|gene3221|rna3221|rna3221  [L=146]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.49   10.2   4.9       0.19   11.5   0.7    2.3  3  Scm3      Centromere protein Scm3


Domain annotation for each model (and alignments):
>> Scm3  Centromere protein Scm3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.7   1.1e-05      0.19      12      37 ..      33      57 ..      27      68 .. 0.81
   2 ?   -0.4   0.2     0.056     1e+03      20      29 ..      96     105 ..      91     108 .. 0.82
   3 ?   -3.6   0.0      0.57     1e+04      11      22 ..     134     145 ..     133     145 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 1.1e-05
                                       HHHHHHHHHHHHHSG..GGSS--B-T CS
                               Scm3 12 lkkrwesifeKYeridfedqgDEIDl 37
                                       + k++++if+KY++  ++  ++ ID+
  gene3221|gene3221|rna3221|rna3221 33 FFKKLAHIFDKYKN-KDDTFDEGIDI 57
                                       57999*********.77776777887 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.056
                                        HHHHHSG..G CS
                               Scm3  20 feKYeridfe 29 
                                         ++Ye+i+f+
  gene3221|gene3221|rna3221|rna3221  96 AQDYEDIHFS 105
                                        678****996 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 0.57
                                        HHHHHHHHHHHH CS
                               Scm3  11 rlkkrwesifeK 22 
                                        ++ ++++s f K
  gene3221|gene3221|rna3221|rna3221 134 NFDDVFNSVFRK 145
                                        677888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       880  (0.0490825); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 973.17
//
Query:       gene3222|gene3222|rna3222|rna3222  [L=289]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-06   28.4   0.1    1.7e-06   27.7   0.1    1.2  1  Guanylate_cyc  Adenylate and Guanylate cyclase catalytic doma
  ------ inclusion threshold ------
       0.13   12.3   0.0       0.34   11.0   0.0    1.7  1  DUF1968        Domain of unknown function (DUF1968)


Domain annotation for each model (and alignments):
>> Guanylate_cyc  Adenylate and Guanylate cyclase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7   0.1   1.9e-10   1.7e-06      11     153 ..     126     257 ..     124     274 .. 0.88

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 1.9e-10
                      Guanylate_cyc  11 ilFadIvgftalssahspievvklLnelyarfdelldekkvykvktiGdaymvvsglpeekaahaaklaelaLdml 86 
                                        il +dIv++t ++  h +  + ++L++++ + ++ll++ ++y v + Gd+ ++++          +++++++ ++ 
  gene3222|gene3222|rna3222|rna3222 126 ILMTDIVKSTYYMR-HYGRGMKNALKKHFRQAERLLRQFRGYLVAVEGDSLVCLFTDF-------QDAVSFGNELE 193
                                        7899*****98877.55*************************************9887.......78888888888 PP

                      Guanylate_cyc  87 ealeevaveskeglkvrvGihtGpvvagviGakkprydvwGntvnlAsrmestgkagkiqvseetye 153
                                        +  +++ +  +e+l++r  ih+G+ ++ ++        + G+t+  A  +  ++k++ i vs+ +y+
  gene3222|gene3222|rna3222|rna3222 194 KFSQKNFITGNENLRLRCLIHQGRLDMVMM---PYGVSIVGRTIAEAYVLCDNAKSEVITVSDYVYN 257
                                        888666666679************998777...7788999999999999999999999999999986 PP

>> DUF1968  Domain of unknown function (DUF1968)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   3.8e-05      0.34      13      32 ..     173     192 ..     169     210 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 3.8e-05
                                        SSEEEEEESE-TTSBCS-SS CS
                            DUF1968  13 nlsvCLfTDFdsqvnvsqsk 32 
                                        ++ vCLfTDF+  v + ++ 
  gene3222|gene3222|rna3222|rna3222 173 DSLVCLFTDFQDAVSFGNEL 192
                                        5669******9988776544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (289 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       608  (0.0339115); expected 358.6 (0.02)
Passed bias filter:                      488  (0.0272185); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1919.68
//
Query:       gene3223|gene3223|rna3223|rna3223  [L=235]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.5e-27   96.9   5.6    5.1e-22   78.7   2.8    2.1  2  RNA_pol_Rpc34  RNA polymerase Rpc34 subunit
     0.0004   20.2   0.0      0.001   18.9   0.0    1.6  2  MarR_2         MarR family
     0.0007   19.9   0.2     0.0017   18.7   0.2    1.6  1  Rrf2           Transcriptional regulator
  ------ inclusion threshold ------
       0.02   14.7   0.0      0.055   13.3   0.0    1.8  1  DUF433         Protein of unknown function (DUF433)
      0.072   13.1   2.5        2.4    8.2   0.2    3.4  2  HTH_46         Winged helix-turn-helix DNA binding
      0.098   12.6   1.9       0.16   11.9   1.6    1.5  1  CENP-R         Kinetochore component, CENP-R
       0.14   12.0   0.0       0.32   10.9   0.0    1.5  1  TrmB           Sugar-specific transcriptional regulator TrmB
       0.87    9.9   4.0         18    5.7   0.7    2.7  2  Rol_Rep_N      Rolling Circle replication initiation protein 
          1    9.6   3.8        9.4    6.5   1.5    2.8  2  ESCRT-II       ESCRT-II complex subunit


Domain annotation for each model (and alignments):
>> RNA_pol_Rpc34  RNA polymerase Rpc34 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.7   2.8   2.6e-25   5.1e-22      24     188 ..      14     165 ..       2     168 .. 0.91
   2 !   19.2   0.0   3.1e-07   0.00062     219     277 ..     170     230 ..     166     235 .] 0.83

  Alignments for each domain:
  == domain 1  score: 78.7 bits;  conditional E-value: 2.6e-25
                                        SSSHCCHHHHHHHSTTSHHHHHHHHHHHHHHCTSEECCC.STTSCECEE--CCCHHHHHTSXHHHHHHHHHHHHHX CS
                      RNA_pol_Rpc34  24 eqklfsqqdLqddipslslklllsavqeLldkkllvllknsndeLvyravsreeAkkktslsedeslVysiIeesG 99 
                                        ++ +++++d+++ +p ls+ +ll  +++   +++++  k  +++++y+             + de+ V+++ ++s 
  gene3223|gene3223|rna3223|rna3223  14 QPDGVTEEDILKRFPDLSKDQLLTELTKWHLENRIKKDK--KNKIMYVRN----------TEDDEKSVLDVLKKSK 77 
                                        58899999999999****999999999999999999888..666688765..........7889999********* PP

                                        SSXEEHHHHHHTTGXXHHHHHHHHHHHHHTTXXEEEEXSSSSSXEEEESSSTXXXXXXXXXXXXXSTTSSSSTHHH CS
                      RNA_pol_Rpc34 100 neGIwsrtiksklnLhksvvkkcLksLeskkyiksvksvkaptkkiYllanLePseevTGGpwftdgelDveFiee 175
                                         +G   r+i+ +++L ++++ k+L+ +   k +k+vk  k+++  i++ ++  P++evTGG wf++g+ DveF ++
  gene3223|gene3223|rna3223|rna3223  78 GQGCTIRDIRLTTKLSQNLITKILRKMQDMKMVKAVKGQKNRQ-NIFMVFEETPDDEVTGGIWFNNGDVDVEFTNQ 152
                                        **************************************99985.7******************************* PP

                                        HHHHHHHHHHCHC CS
                      RNA_pol_Rpc34 176 leeiifklvkqks 188
                                        l ++i+ +v++k+
  gene3223|gene3223|rna3223|rna3223 153 LIKLIYTFVRNKT 165
                                        **********998 PP

  == domain 2  score: 19.2 bits;  conditional E-value: 3.1e-07
                                        SSTXXBXSCHHHHHHHCSTTTSSSXSHCCHHHHHHHHCHSSSCEEETTT...XXXEEEETT CS
                      RNA_pol_Rpc34 219 gyksyptveeiakfineagitkvrLseediqqlvevLvyDgklekvkvs..agyrvqratk 277
                                         y + pt e+i  fi+e+++ + ++s++d +++++v+vy   l  ++ +   +yr+ r  +
  gene3223|gene3223|rna3223|rna3223 170 SYDHNPTIEDIKSFITESNVLSINISMADLRKIIDVMVYGQILLELRDGdrIMYRALRSHE 230
                                        58999**********************************9987777666555666666555 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   5.1e-07     0.001       9      57 ..      68     116 ..      63     120 .. 0.91
   2 ?   -3.7   0.0       5.9   1.2e+04       9      18 ..     210     219 ..     209     220 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 5.1e-07
                                        HHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEESS CS
                             MarR_2   9 rvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpgp 57 
                                         vL +L  + g+ +t++++  +++ls+  +++il+++++  +v  ++g+
  gene3223|gene3223|rna3223|rna3223  68 SVLDVLKKSKGQGCTIRDIRLTTKLSQNLITKILRKMQDMKMVKAVKGQ 116
                                        69*********999*****************************988875 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 5.9
                                        HHHHHHHCTT CS
                             MarR_2   9 rvLaaLgrrp 18 
                                        ++L++L++++
  gene3223|gene3223|rna3223|rna3223 210 QILLELRDGD 219
                                        6899998877 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.2   8.3e-07    0.0017      16      62 ..      72     117 ..      65     119 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 8.3e-07
                                        HHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTT- CS
                               Rrf2  16 yLakeeeeepvsseeiaerqnispsylekilakLrkaglvksvrGkg 62 
                                        +L+k ++++ +++++i   +++s++ + kil+k++  ++vk+v+G++
  gene3223|gene3223|rna3223|rna3223  72 VLKKSKGQG-CTIRDIRLTTKLSQNLITKILRKMQDMKMVKAVKGQK 117
                                        566666766.***********************************86 PP

>> DUF433  Protein of unknown function (DUF433)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   2.8e-05     0.055      30      50 ..      16      36 ..       6      40 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.8e-05
                                       TT--HHHHHHHH.TS-HHHHH CS
                             DUF433 30 aGesieeiledyPdLtlediq 50
                                       +G+++e+il+ +PdL+++++ 
  gene3223|gene3223|rna3223|rna3223 16 DGVTEEDILKRFPDLSKDQLL 36
                                       79***************9986 PP

>> HTH_46  Winged helix-turn-helix DNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.2    0.0012       2.4      29      58 ..      86     115 ..      70     119 .. 0.90
   2 ?    3.0   0.1     0.053   1.1e+02      42      55 ..     210     223 ..     157     227 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0012
                             HTH_46  29 IqkrtnLSrSsimkvLseLkkggyIeierG 58 
                                        I+  t+LS+  i k+L ++++ + ++  +G
  gene3223|gene3223|rna3223|rna3223  86 IRLTTKLSQNLITKILRKMQDMKMVKAVKG 115
                                        7889***************99999998887 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.053
                             HTH_46  42 kvLseLkkggyIei 55 
                                        ++L eL++g++I +
  gene3223|gene3223|rna3223|rna3223 210 QILLELRDGDRIMY 223
                                        68999999999876 PP

>> CENP-R  Kinetochore component, CENP-R
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   1.6   8.3e-05      0.16      35     101 ..      63     126 ..      47     131 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 8.3e-05
                             CENP-R  35 psngkrkkdnelslsrrkqstteddellvLlskveksleeileirqnLsslqaLegsreLenliGvs 101
                                          + +++ ++ l+ s+ + +t +d +l + ls+  +   +il+ +q+++ ++a +g+++ +n+  v+
  gene3223|gene3223|rna3223|rna3223  63 EDD-EKSVLDVLKKSKGQGCTIRDIRLTTKLSQ--NLITKILRKMQDMKMVKAVKGQKNRQNIFMVF 126
                                        222.23555666777777788888776666664..6789***********************98776 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00016      0.32      22      59 ..      80     117 ..      63     126 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00016
                                        CCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTT CS
                               TrmB  22 patadeiaeelgvprskvYevLrsLedkGlVerekgrp 59 
                                          t+++i   ++++++ + ++Lr++ d+ +V+ +kg++
  gene3223|gene3223|rna3223|rna3223  80 GCTIRDIRLTTKLSQNLITKILRKMQDMKMVKAVKGQK 117
                                        56899*****************************9985 PP

>> Rol_Rep_N  Rolling Circle replication initiation protein N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.2     0.018        35       3      72 ..       7      82 ..       5     102 .. 0.70
   2 ?    5.7   0.7    0.0092        18      10      64 ..     139     194 ..      85     198 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.018
                          Rol_Rep_N  3 liDylritfktldveeviedllkiklelfteeekgikgYerllkfge.ikvlvs..kkke....rgvllelkGqGCr 72
                                       ++D+++ + +  + e++++ + +++++ + +e ++  + e+++k ++  k+++   ++++      vl + kGqGC 
  gene3223|gene3223|rna3223|rna3223  7 VFDFIQAQPDGVTEEDILKRFPDLSKDQLLTELTK-WHLENRIKKDKkNKIMYVrnTEDDeksvLDVLKKSKGQGCT 82
                                       68999999999999999999999999999999555.45555565555355555522223333345555566899995 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0092
                          Rol_Rep_N  10 tfktldve.eviedllkiklelfteeekgikgYerllkfgeikvlvskkkergvll 64 
                                         f++ dv+ e+ ++l+k+ +++  ++ + + +Y++  ++++ik +  + +   + +
  gene3223|gene3223|rna3223|rna3223 139 WFNNGDVDvEFTNQLIKLIYTFVRNKTRDLISYDHNPTIEDIKSFITESNVLSINI 194
                                        555544444899******************************99988777655555 PP

>> ESCRT-II  ESCRT-II complex subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   1.5    0.0047       9.4      57     100 ..      85     131 ..      12     135 .. 0.77
   2 ?    1.9   0.0      0.12   2.5e+02      24      78 ..     153     208 ..     139     231 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0047
                           ESCRT-II  57 nkkinRrlsledirevleelvkkgraewvdkek..skal.vywrtpe 100
                                        + ++  +ls++ i ++l+++++ + ++ v+++k  ++++ v+ +tp+
  gene3223|gene3223|rna3223|rna3223  85 DIRLTTKLSQNLITKILRKMQDMKMVKAVKGQKnrQNIFmVFEETPD 131
                                        5577889*****************99999555522444436666665 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.12
                           ESCRT-II  24 WsslilaycrhhrifklslseaeeeeeeselF..knkkinRrlsledirevleelvk 78 
                                          +li  ++r+++   +s +++ +  e+ + F  + + ++ ++s +d+r++++ +v 
  gene3223|gene3223|rna3223|rna3223 153 LIKLIYTFVRNKTRDLISYDHNPTI-EDIKSFitESNVLSINISMADLRKIIDVMVY 208
                                        4678888888888888887755443.3344442245557778999999999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1125  (0.0627475); expected 358.6 (0.02)
Passed bias filter:                      499  (0.027832); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 1588.39
//
Query:       gene3224|gene3224|rna3224|rna3224  [L=472]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-12   47.5   0.4    3.6e-12   46.1   0.2    1.8  2  Acyltransferase  Acyltransferase


Domain annotation for each model (and alignments):
>> Acyltransferase  Acyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.1   0.2     2e-16   3.6e-12      13     134 ..     115     226 ..     104     227 .. 0.83
   2 ?   -3.2   0.0      0.33   5.9e+03      74      98 ..     350     375 ..     307     376 .. 0.64

  Alignments for each domain:
  == domain 1  score: 46.1 bits;  conditional E-value: 2e-16
                    Acyltransferase  13 kgpailvaNHqsylDvlllwlllyksngprnvviiakkellsipllgflmr....llgfifidRksnaraagslen 84 
                                        + p ++vaNH+s lD+++l+        ++ ++  +++++    l+gf+++    + g  +++R ++ ++  + e+
  gene3224|gene3224|rna3224|rna3224 115 NVPHVYVANHTSFLDFIVLSS-------HKFCHASLAENHG--GLFGFFFKnlllRNGSLYFKRCEKNDKSIVKER 181
                                        4689*****************.......4567777777744..577777774444668899999999999****** PP

                    Acyltransferase  85 iselleegkl.vviFPEGtrsregellpfkkGlvrlaakakkgvpivPvai 134
                                        i++ +++ k  ++iFPEGt+ ++ ++++f+k+++++      + +i+Pvai
  gene3224|gene3224|rna3224|rna3224 182 IKQHIQSMKTpMLIFPEGTCVNNKYTVMFQKSVFEI------DATICPVAI 226
                                        ***99999999*************************......889999998 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 0.33
                    Acyltransferase  74 snaraagsleniselleegkl.vviF 98 
                                         + +++++  +i++ +++gk  v++F
  gene3224|gene3224|rna3224|rna3224 350 LDNVGEKTNGQIVKSTKNGKHnVIYF 375
                                        44556666667777777777766666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (472 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       766  (0.0427241); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.25s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 3003.78
//
Query:       gene3225|gene3225|rna3225|rna3225  [L=389]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.7e-15   55.1  35.0    1.7e-14   53.9  34.8    1.8  1  MBOAT     MBOAT, membrane-bound O-acyltransferase family
    4.9e-05   23.5   5.2    4.9e-05   23.5   5.2    2.1  2  MBOAT_2   Membrane bound O-acyl transferase family


Domain annotation for each model (and alignments):
>> MBOAT  MBOAT, membrane-bound O-acyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.9  34.8   1.9e-18   1.7e-14      67     346 ..     111     376 ..      29     378 .. 0.68

  Alignments for each domain:
  == domain 1  score: 53.9 bits;  conditional E-value: 1.9e-18
                              MBOAT  67 l.......................klhslslvfrklasaallsklpslleylgYvffyplllvGPilsyseymsfv 119
                                        l                       +  + ++v +  +  + ++ +++++e+  ++ f   l++ P+l++ +  +  
  gene3225|gene3225|rna3225|rna3225 111 LysyiaetrkndavtrneppikenNTNTCANVHQHERITEDRRNDVPAPEFTYFIRF---LFL-PTLCFLD-ATRY 181
                                        055555555555555555555554444444455555555556666677777666666...666.9999999.5555 PP

                              MBOAT 120 esplsrllytakrnfavalyalf.lgltylilieyvlskicakdftifkmlssaqllmrsvimrilllllllflli 194
                                        + + ++ l++    + +a + ++ + ++++ +i  +l+ +  +df +++   ++   +  vi+ +++l++ +++l 
  gene3225|gene3225|rna3225|rna3225 182 RKRSVSALFYN---LIMASLLFSlVNFLVAFYIIPLLECYTIRDFVTDLTVFVRISATSFVIWVAMFLFFFKYYLS 254
                                        55555555662...33332222202334444444455555555555555555555666778999999999999997 PP

                              MBOAT 195 fdflglwlvalgedilsGlgvngarldrvadrniygdwenavsfsefwraWNipvhkWLlryvYkplgskkfklnk 270
                                        f         l+e+ +               ++i gdw+na+ f++fwr WNip+h+WL+ryv+ p+   +   +k
  gene3225|gene3225|rna3225|rna3225 255 F---------LAECTNYE-------------NKIFGDWWNARYFRDFWRLWNIPTHEWLRRYVFFPCY--RVIESK 306
                                        7.........34444433.............678889******************************5..789*** PP

                              MBOAT 271 slatlatFlfsAvwHglalgyliwfvlrvllllveklimrlvalsnlkfdrrrailsnvifwlgaflgpslallly 346
                                        +  tl++F +s++ H++   +l ++++ v++++  + ++ ++ l +  f      ++n +fw++++++ + ++ll+
  gene3225|gene3225|rna3225|rna3225 307 WTCTLIVFVISSILHEIVY-ILTFKKVGVVVFMSILSQFVFIYLEQVLF-----SPGNLLFWFVFCFIGQPVFLLS 376
                                        ******************9.9999*********9999999888777774.....5789999999998887777766 PP

>> MBOAT_2  Membrane bound O-acyl transferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.1      0.32   2.9e+03      32      58 ..     185     211 ..     177     222 .. 0.73
   2 !   23.5   5.2   5.5e-09   4.9e-05       3      81 ..     265     337 ..     263     346 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.32
                            MBOAT_2  32 stakkilrlllgsklarylqllvaFll 58 
                                        s++  + +l++ s l ++++ lvaF +
  gene3225|gene3225|rna3225|rna3225 185 SVSALFYNLIMASLLFSLVNFLVAFYI 211
                                        455555566666778888999999976 PP

  == domain 2  score: 23.5 bits;  conditional E-value: 5.5e-09
                            MBOAT_2   3 plfgslleayslrrfWgrfWHqlfrrglkstakkilrlllgsklarylqllvaFllSGllHaagdytqlapestal 78 
                                        ++fg++++a   r+fW r W+  + ++l++++ +++ ++ +s   + + +l++F++S +lH+++ + +++  ++ +
  gene3225|gene3225|rna3225|rna3225 265 KIFGDWWNARYFRDFW-RLWNIPTHEWLRRYVFFPCYRVIES---KWTCTLIVFVISSILHEIVYILTFK--KVGV 334
                                        79**************.89***********************...8899******************999..6655 PP

                            MBOAT_2  79 lfF 81 
                                        ++F
  gene3225|gene3225|rna3225|rna3225 335 VVF 337
                                        555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (389 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       965  (0.0538234); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.71u 0.36s 00:00:01.06 Elapsed: 00:00:00.59
# Mc/sec: 2001.23
//
Query:       gene3226|gene3226|rna3226|rna3226  [L=632]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.2e-09   36.6   0.9    1.9e-05   23.7   0.0    2.3  2  Oxysterol_BP  Oxysterol-binding protein
  ------ inclusion threshold ------
      0.059   13.9   2.2       0.13   12.7   0.6    2.5  2  PH            PH domain


Domain annotation for each model (and alignments):
>> Oxysterol_BP  Oxysterol-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.0   2.2e-09   1.9e-05      17     150 ..     332     456 ..     321     515 .. 0.76
   2 !   10.9   0.2   1.6e-05      0.14     285     332 ..     530     579 ..     512     584 .. 0.75

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 2.2e-09
                                        S---GGGEEEEEHHHHHHHCCTTCHHHHHHHC.SSHHHHHHHHHHHHHHCCCGCTSTSSSEEE---TT-EEEEEET CS
                       Oxysterol_BP  17 islPvffneplSlLqrlaedleyselLdkaakeddsleRlayVaaFalSsyastikrrlkKPFNPlLGEtfelvre 92 
                                          lPv+++ep S+Lqr+ae     + + +  + + + + +++Va +++  ++ +  r  k  F  l GEtf   + 
  gene3226|gene3226|rna3226|rna3226 332 ALLPVSLLEPQSTLQRMAEGALLFKNIRRNDSLS-EQHAVVLVAVYIVGLMNLQLDR--KFAFESLAGETFFAEH- 403
                                        569****************998888888877755.5778899999999999999843..469***********99. PP

                                        TCEEEEEEEEEETTTTEEEEEEEECTEEEEEEEEEEEEE-SSEEEEEE-SEEEEEEEE CS
                       Oxysterol_BP  93 dkgfrfiaEQVsHhPpvsAfhaesegweldgeikvkskflgkslevkpeGtahlellk 150
                                         +++++ +E++      s +ha  + ++l++ i++    + k + v  + +++l++  
  gene3226|gene3226|rna3226|rna3226 404 -ENTKIYCEKTLR---ASIVHAVDDLFTLTAVIDLAYDKRNKKIVVYNKSKCTLKI-S 456
                                        .678889**9986...4666666777777777777777777777777777777777.3 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 1.6e-05
                                        -HHHHCCT---.TT..GGS-TTBGGG-HHHHHHHTT-HHHHHHHHHHHHH CS
                       Oxysterol_BP 285 tkfavtlNeieeke..kslaptDsRlRpDqraleegdideAeeeKkrlEe 332
                                        ++  +++ +ie+ e  +   p+DsR R D++al+eg+++  + +++++ +
  gene3226|gene3226|rna3226|rna3226 530 SSNDFKKMKIEDYEdvHEYMPSDSRGRADIQALQEGRVQDVNVHRQKMKD 579
                                        33334444444444458899*********************999998866 PP

>> PH  PH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.6   1.5e-05      0.13       2      57 ..     117     169 ..     116     205 .. 0.81
   2 ?   -3.5   0.0       1.7   1.5e+04      26      57 ..     215     246 ..     206     257 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.5e-05
                                        EEEEEEEEETSSSSCSEEEEEEEEETTEEEEESSTTCTTESSEEEEEESTTEEEEE CS
                                 PH   2 vkeGwLlkkgsgkkkswkkrwfvLkdsellyykndksekdkepkgsislsncevve 57 
                                        v+ G L+k+++    +++ r+++L d+ ++yyk +  e +k +++++sl++++  +
  gene3226|gene3226|rna3226|rna3226 117 VRAGLLQKYTNIIN-RYQTRYVTLYDDFFSYYKIR--EGKKFLRKKLSLNTIRGIK 169
                                        68899*******99.********************..8888889999999988664 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 1.7
                                        ETTE..EEEESSTTCTTESSEEEEEESTTEEEEE CS
                                 PH  26 kdse..llyykndksekdkepkgsislsncevve 57 
                                        ++ +  llyy  +  +++ + + +i+  ++ +++
  gene3226|gene3226|rna3226|rna3226 215 NNYVfkLLYYLCE--KEARKEMLKIDHLSLYIKD 246
                                        4444556666665..4666666667666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (632 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       911  (0.0508115); expected 358.6 (0.02)
Passed bias filter:                      498  (0.0277762); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 4295.77
//
Query:       gene3227|gene3227|rna3227|rna3227  [L=27]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (27 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       227  (0.0126611); expected 358.6 (0.02)
Passed bias filter:                      125  (0.00697194); expected 358.6 (0.02)
Passed Vit filter:                         7  (0.000390429); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.31s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 175.70
//
Query:       gene3228|gene3228|rna3228|rna3228  [L=71]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (71 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       509  (0.0283898); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.58u 0.35s 00:00:00.93 Elapsed: 00:00:00.58
# Mc/sec: 371.61
//
Query:       gene3229|gene3229|rna3229|rna3229  [L=110]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       263  (0.014669); expected 358.6 (0.02)
Passed bias filter:                      206  (0.0114898); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.56u 0.33s 00:00:00.89 Elapsed: 00:00:00.54
# Mc/sec: 608.11
//
Query:       gene323|gene323|rna323|rna323  [L=537]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (537 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       750  (0.0418317); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.64u 0.31s 00:00:00.95 Elapsed: 00:00:00.49
# Mc/sec: 3288.96
//
Query:       gene3230|gene3230|rna3230|rna3230  [L=99]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       827  (0.0461264); expected 358.6 (0.02)
Passed bias filter:                      492  (0.0274416); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 722.47
//
Query:       gene3231|gene3231|rna3231|rna3231  [L=110]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       358  (0.0199677); expected 358.6 (0.02)
Passed bias filter:                      223  (0.0124379); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 802.47
//
Query:       gene3232|gene3232|rna3232|rna3232  [L=922]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (922 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       592  (0.0330191); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.67u 0.27s 00:00:00.94 Elapsed: 00:00:00.45
# Mc/sec: 6178.69
//
Query:       gene3233|gene3233|rna3233|rna3233  [L=445]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (445 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2730  (0.152267); expected 358.6 (0.02)
Passed bias filter:                      529  (0.0295053); expected 358.6 (0.02)
Passed Vit filter:                       237  (0.0132188); expected 17.9 (0.001)
Passed Fwd filter:                        69  (0.00384851); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 1.61u 0.44s 00:00:02.05 Elapsed: 00:00:00.63
# Mc/sec: 2131.99
//
Query:       gene3234|gene3234|rna3234|rna3234  [L=169]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (169 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1306  (0.0728429); expected 358.6 (0.02)
Passed bias filter:                      214  (0.011936); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1206.23
//
Query:       gene3235|gene3235|rna3235|rna3235  [L=183]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.7e-19   69.3  15.4    1.6e-10   40.6   2.4    2.3  2  zf-CCCH    Zinc finger C-x8-C-x5-C-x3-H type (and similar)
    9.8e-10   38.2  14.7    3.9e-06   26.7   4.8    2.4  2  zf_CCCH_4  Zinc finger domain
    0.00038   20.2  13.1      0.069   13.0   3.9    2.5  2  zf-CCCH_4  CCCH-type zinc finger
     0.0021   18.7   8.0       0.14   12.9   1.7    2.2  2  Torus      Torus domain
     0.0044   17.0   2.8      0.032   14.3   0.6    2.4  2  DUF2639    Protein of unknown function (DUF2639)
     0.0066   16.9  11.9      0.032   14.7   1.7    2.7  2  zf-CCCH_2  RNA-binding, Nab2-type zinc finger
  ------ inclusion threshold ------
        0.2   11.1   1.7       0.27   10.7   1.7    1.2  1  TMEM215    TMEM215 family


Domain annotation for each model (and alignments):
>> zf-CCCH  Zinc finger C-x8-C-x5-C-x3-H type (and similar)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.6   2.4   6.3e-14   1.6e-10       1      26 [.      35      60 ..      35      61 .. 0.98
   2 !   34.3   5.4   6.1e-12   1.6e-08       1      25 [.      73      97 ..      73      99 .. 0.98

  Alignments for each domain:
  == domain 1  score: 40.6 bits;  conditional E-value: 6.3e-14
                                       -HCHCBCHHHHHS--TTGGG-SSBSC CS
                            zf-CCCH  1 yktelCrffmrtGyCkyGdrCkFaHg 26
                                       ykte+Cr + ++GyC+y ++C+FaH+
  gene3235|gene3235|rna3235|rna3235 35 YKTEICRSYEENGYCRYNEKCQFAHS 60
                                       9************************8 PP

  == domain 2  score: 34.3 bits;  conditional E-value: 6.1e-12
                                       -HCHCBCHHHHHS--TTGGG-SSBS CS
                            zf-CCCH  1 yktelCrffmrtGyCkyGdrCkFaH 25
                                       ykte+C+++ + G+C+yG rC+F+H
  gene3235|gene3235|rna3235|rna3235 73 YKTEICKTYWEEGTCPYGKRCCFIH 97
                                       9************************ PP

>> zf_CCCH_4  Zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.7   4.8   1.5e-09   3.9e-06       1      19 []      40      59 ..      40      59 .. 0.99
   2 !   16.8   2.3     2e-06    0.0052       3      19 .]      81      97 ..      80      97 .. 0.94

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 1.5e-09
                          zf_CCCH_4  1 Ckfflq.GtCkkGdkCrFaH 19
                                       C+ + + G+C++++kC+FaH
  gene3235|gene3235|rna3235|rna3235 40 CRSYEEnGYCRYNEKCQFAH 59
                                       ******************** PP

  == domain 2  score: 16.8 bits;  conditional E-value: 2e-06
                          zf_CCCH_4  3 fflqGtCkkGdkCrFaH 19
                                       ++ +GtC++G +C F+H
  gene3235|gene3235|rna3235|rna3235 81 YWEEGTCPYGKRCCFIH 97
                                       9************9988 PP

>> zf-CCCH_4  CCCH-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   1.8   4.6e-05      0.12       2      21 ..      39      59 ..      38      60 .. 0.91
   2 !   13.0   3.9   2.7e-05     0.069       3      21 ..      78      97 ..      76      98 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 4.6e-05
                          zf-CCCH_4  2 lCpyfa.kGsCrfGdnCrFsH 21
                                       +C+++  +G Cr+ ++C F+H
  gene3235|gene3235|rna3235|rna3235 39 ICRSYEeNGYCRYNEKCQFAH 59
                                       79***9677************ PP

  == domain 2  score: 13.0 bits;  conditional E-value: 2.7e-05
                          zf-CCCH_4  3 Cpyfa.kGsCrfGdnCrFsH 21
                                       C+ +  +G C +G +C F H
  gene3235|gene3235|rna3235|rna3235 78 CKTYWeEGTCPYGKRCCFIH 97
                                       77666488***********9 PP

>> Torus  Torus domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.6   0.00048       1.2      69      98 ..      36      66 ..      17      72 .. 0.77
   2 !   12.9   1.7   5.5e-05      0.14      68      92 ..      74      98 ..      66     112 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00048
                                       T--B-HHH.HHT--SSGGG-SSB-S---SS- CS
                              Torus 69 esyfClfF.arGlCakGkkCeylHrlPteed 98
                                       ++ +C  +   G+C + +kC++ H++ + ++
  gene3235|gene3235|rna3235|rna3235 36 KTEICRSYeENGYCRYNEKCQFAHSIDELRK 66
                                       55677666257**************987666 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 5.5e-05
                                       TT--B-HHHHHT--SSGGG-SSB-S CS
                              Torus 68 kesyfClfFarGlCakGkkCeylHr 92
                                       k++++  ++  G+C++Gk+C ++H+
  gene3235|gene3235|rna3235|rna3235 74 KTEICKTYWEEGTCPYGKRCCFIHK 98
                                       445555899***************7 PP

>> DUF2639  Protein of unknown function (DUF2639)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.6   1.2e-05     0.032      19      34 ..      26      41 ..      18      43 .. 0.87
   2 ?    2.1   0.1     0.077     2e+02      10      31 ..      62      81 ..      61      82 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.2e-05
                            DUF2639 19 khegrKlesYKtyiLr 34
                                       ++e++K+e+YKt i r
  gene3235|gene3235|rna3235|rna3235 26 YYERKKIELYKTEICR 41
                                       68**********9987 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.077
                            DUF2639 10 keLKkaGIrkhegrKlesYKty 31
                                        eL+k  I++h + K e  Kty
  gene3235|gene3235|rna3235|rna3235 62 DELRK--INRHPRYKTEICKTY 81
                                       57776..899999999999998 PP

>> zf-CCCH_2  RNA-binding, Nab2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   1.7   1.2e-05     0.032       1      17 [.      39      59 ..      39      59 .. 0.91
   2 !    6.8   2.9    0.0038       9.7       7      17 ..      86      97 ..      77      97 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.2e-05
                          zf-CCCH_2  1 pCrffpn...C.tnpkCpFaH 17
                                       +Cr +     C +n+kC FaH
  gene3235|gene3235|rna3235|rna3235 39 ICRSYEEngyCrYNEKCQFAH 59
                                       6888888899*********** PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0038
                          zf-CCCH_2  7 nC.tnpkCpFaH 17
                                       +C ++++C F+H
  gene3235|gene3235|rna3235|rna3235 86 TCpYGKRCCFIH 97
                                       3*********** PP

>> TMEM215  TMEM215 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   1.7   0.00011      0.27     159     222 ..      43     106 ..      14     109 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00011
                            TMEM215 159 gdvstysvldkkcsardrsayseaedkvllvPrdsiivy...sykdnspydryccyinptevrwdqe 222
                                         +++ y+  ++kc    +++      k+   Pr +  ++       ++py++ cc+i++ ++  dq+
  gene3235|gene3235|rna3235|rna3235  43 YEENGYCRYNEKCQFAHSID---ELRKINRHPRYKTEICktyWEEGTCPYGKRCCFIHKENIIKDQD 106
                                        56677888888888666554...4456777777644443100345578*************999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       658  (0.0367003); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 1221.61
//
Query:       gene3236|gene3236|rna3236|rna3236  [L=503]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        1.3    8.7  61.9      0.074   12.8  47.7    2.4  2  Drf_FH1   Formin Homology Region 1


Domain annotation for each model (and alignments):
>> Drf_FH1  Formin Homology Region 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8  47.7   4.1e-06     0.074       5     130 ..     162     286 ..     151     296 .. 0.52
   2 ?    1.3   6.3     0.014   2.5e+02      45      68 ..     447     470 ..     426     483 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4.1e-06
                            Drf_FH1   5 plpgdsssaskvvippppplpggagippppllpgsaaipsppplpgaaaippppplpgaasippppplpgstgipp 80 
                                         +p   + +++++ip  pp  +  +ip  p+  ++ +ip  pp     +ip  pp  + ++ip  pp + +  ip 
  gene3236|gene3236|rna3236|rna3236 162 SIPFYPQYNNESCIPICPPYNKEPCIPICPPYNKEPCIPICPPYNKEPCIPICPPYNKEPCIPICPPYNKEPCIPI 237
                                        3333334455556666666666666666666666666666666666666666666666666666666666666666 PP

                            Drf_FH1  81 ppplpgsagipppppplpggagipppppplpggpgippppplp.gapgipp 130
                                         pp+  ++ ip  pp  p    i p  pp+p  p  p pp  p   p ip 
  gene3236|gene3236|rna3236|rna3236 238 CPPYNQEPCIPICPPYQPYKPCI-PICPPYPYPP-YPFPPFTPdNIPNIPC 286
                                        66666666665555555555555.3333333333.2222222212244443 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.014
                            Drf_FH1  45 ppplpgaaaippppplpgaasipp 68 
                                        p  lp  aa ppppp p+ + i p
  gene3236|gene3236|rna3236|rna3236 447 PYKLPSFAADPPPPPPPKPTPIVP 470
                                        345666666666666666555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (503 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       439  (0.0244855); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.44
# Mc/sec: 3416.74
//
Query:       gene3237|gene3237|rna3237|rna3237  [L=183]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       820  (0.045736); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 1205.42
//
Query:       gene3238|gene3238|rna3238|rna3238  [L=196]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.9e-35  120.2   6.9    8.1e-35  119.7   6.9    1.2  1  Mad3_BUB1_I_2  Putative Mad3/BUB1 like region 1 protein
    1.2e-06   28.5   0.7    2.3e-06   27.6   0.7    1.5  1  Mad3_BUB1_I    Mad3/BUB1 homology region 1


Domain annotation for each model (and alignments):
>> Mad3_BUB1_I_2  Putative Mad3/BUB1 like region 1 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.7   6.9   9.1e-39   8.1e-35       1     127 [.      38     163 ..      38     164 .. 0.96

  Alignments for each domain:
  == domain 1  score: 119.7 bits;  conditional E-value: 9.1e-39
                      Mad3_BUB1_I_2   1 llrkidipyfrnnpsyiekwkelYkktkdlkilfLmklKkIskfyyfvYlelsryFlkkgkkeaalfiLqegiknk 76 
                                        ++++id p+f+nn+  i++++elYk+t+++++lfLm+ ++I++f+y +Y+++++yF+k+ +  aa++iL++gi+++
  gene3238|gene3238|rna3238|rna3238  38 IEKYIDHPFFKNNTRVIQRLNELYKSTENENVLFLMYNRSIAQFHYSYYANFADYFIKVCNYAAADYILRKGIRME 113
                                        679************************************************************************* PP

                      Mad3_BUB1_I_2  77 vydkeilkeelksikklekklseeeakkllkpkkirlfGkeWveievnyla 127
                                        +y+k++l ++l++++  +  +++e++ k++k+k+i+lf keWv++e  y+ 
  gene3238|gene3238|rna3238|rna3238 114 CYRKQVLVDMLEKLPLQQ-IVADENVRKVFKRKSIVLFNKEWVNQERSYVS 163
                                        ***********9987666.99999**********************99985 PP

>> Mad3_BUB1_I  Mad3/BUB1 homology region 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   0.7   2.6e-10   2.3e-06      51     124 .]      38     110 ..       8     110 .. 0.90

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 2.6e-10
                                        HHHTTTSGGGTT-HHHHHHHHHHHTTSS-HHHHHHHHHHHTTSTTBHHHHHHHHHHHHHTT-HHHHHHHHHHH. CS
                        Mad3_BUB1_I  51 lkkfkdderYknDpRylklwlkyadlveepreifkflaskkiGtklalfYeewAellekkgrfkeAeevyelGi 124
                                        ++k+ d++ +kn++R ++   ++ + +e++  +f  +++++i + +  +Y ++A ++ k  +++ A+ ++++Gi
  gene3238|gene3238|rna3238|rna3238  38 IEKYIDHPFFKNNTRVIQRLNELYKSTENENVLF-LMYNRSIAQFHYSYYANFADYFIKVCNYAAADYILRKGI 110
                                        6788999***************999988877766.8*************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       839  (0.0467957); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1466.39
//
Query:       gene3239|gene3239|rna3239|rna3239  [L=167]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.2e-15   57.8   1.3    1.4e-15   57.6   1.3    1.1  1  DUF866        Eukaryotic protein of unknown function (DUF866)
  ------ inclusion threshold ------
       0.03   14.6   2.8       0.57   10.5   0.1    2.3  2  zf-HC5HC2H    PHD-like zinc-binding domain
      0.046   13.9   1.8       0.36   11.1   1.8    2.0  2  Yippee-Mis18  Yippee zinc-binding/DNA-binding /Mis18, centrom
        0.2   11.5   2.3       0.27   11.1   0.4    2.2  2  DUF1953       Domain of unknown function (DUF1953)
        3.3    7.5   6.4         12    5.8   0.4    2.5  2  zf-C2H2_10    C2H2 zinc-finger


Domain annotation for each model (and alignments):
>> DUF866  Eukaryotic protein of unknown function (DUF866)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.6   1.3   3.8e-19   1.4e-15       2     145 ..       5     152 ..       4     162 .. 0.75

  Alignments for each domain:
  == domain 1  score: 57.6 bits;  conditional E-value: 3.8e-19
                                        EEEEEEEESEEEEE--T...T--EEEEEEETTSS.-EEEEEEE-TT-BEE-TTSS-EESEEE--SSSS--EEEEEE CS
                             DUF866   2 LqikaelenvtslepadeeedfeytfkvkctsCreehpkevsisreekveisgsrgeanfvvkcklckressisik 77 
                                        ++i+ +++nv+++ +     d++  +k+kc+ C++ehp++v++s+e  +   + ++++n+ + c++ck+++ isi 
  gene3239|gene3239|rna3239|rna3239   5 IYIDGDFTNVKNVFI-----DQTVRVKIKCSICDQEHPNRVVVSEESFNR-VDDKEKTNLKITCSGCKSSMGISIR 74 
                                        68999**********.....57999****************887766665.58899******************99 PP

                                        -..........-TTTT..EEEGGTS-E..EEEEEEEESEEEEEE---S-EEEEETTS-EEEEE--TS.-EEEEETT CS
                             DUF866  78 ke.........teksy..taedsgkfk..tilefdcrGlelvefkpeggwkvesasgtkfedvdLsegeWydYdek 140
                                        +           ++++  + ++ ++f+   +  ++++ +el+  +++ +++v s ++  +e +  ++g W+ +d+k
  gene3239|gene3239|rna3239|rna3239  75 SPkgdritiirDNQPVrlQLSE-KEFNsfYVSFLETKKCELIG-EVDVDCSVLSGQKVLYEHITVEDGSWMGVDQK 148
                                        9855555544422222223333.2233669999********97.4454566666444559***************8 PP

                                        TTEEE CS
                             DUF866 141 ageeV 145
                                         g   
  gene3239|gene3239|rna3239|rna3239 149 -GLDS 152
                                        .4444 PP

>> zf-HC5HC2H  PHD-like zinc-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.3     0.014        49      27      45 ..      17      35 ..       7      40 .. 0.76
   2 ?   10.5   0.1   0.00016      0.57      20      51 ..      43      74 ..      36      79 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.014
                         zf-HC5HC2H 27 vekikkerkklkCylCkkk 45
                                       v   ++ r k kC++C+++
  gene3239|gene3239|rna3239|rna3239 17 VFIDQTVRVKIKCSICDQE 35
                                       4455677899******987 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00016
                         zf-HC5HC2H 20 emeeiedvekikkerkklkCylCkkkvGaciq 51
                                       ++e++++v++ +k++ k +C+ Ck+++G++i+
  gene3239|gene3239|rna3239|rna3239 43 SEESFNRVDDKEKTNLKITCSGCKSSMGISIR 74
                                       4688999*********************9986 PP

>> Yippee-Mis18  Yippee zinc-binding/DNA-binding /Mis18, centromere assembly
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.3      0.13   4.6e+02      54      63 ..      25      34 ..      10      36 .. 0.72
   2 ?   11.1   1.8   9.9e-05      0.36      32      74 ..      35      78 ..      28      88 .. 0.76

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.13
                                       EEEEETTT-- CS
                       Yippee-Mis18 54 stlsCkgCns 63
                                        +++C++C++
  gene3239|gene3239|rna3239|rna3239 25 VKIKCSICDQ 34
                                       4699****97 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 9.9e-05
                                       --CCCEEEECEEEET.TSTTEEEEEEEETTT--EEEEEEEECSC CS
                       Yippee-Mis18 32 kvtrnvvvgkelvtd.eegkctystlsCkgCnsvlGwkYkstee 74
                                       +  ++vvv++e+    ++++ t  +++C+gC+s +G   +s + 
  gene3239|gene3239|rna3239|rna3239 35 EHPNRVVVSEESFNRvDDKEKTNLKITCSGCKSSMGISIRSPKG 78
                                       5567888888888883446699999***********99887665 PP

>> DUF1953  Domain of unknown function (DUF1953)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.4   7.5e-05      0.27      31      54 ..       3      29 ..       1      34 [. 0.82
   2 ?   -1.2   0.1      0.51   1.8e+03      12      23 ..     122     133 ..     119     164 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 7.5e-05
                                       EEEEEEEEEEET...TTTEEEEEEEEE CS
                            DUF1953 31 ydieidGeytdv...itdetvrGrvkv 54
                                       y i idG++t+v     d+tvr ++k 
  gene3239|gene3239|rna3239|rna3239  3 YKIYIDGDFTNVknvFIDQTVRVKIKC 29
                                       99********7533279*****99985 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.51
                                        EEEEETTTEEEE CS
                            DUF1953  12 cGfmrGdkvlvi 23 
                                        c  + G+kvl  
  gene3239|gene3239|rna3239|rna3239 122 CSVLSGQKVLYE 133
                                        777888888754 PP

>> zf-C2H2_10  C2H2 zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.4    0.0032        12       3      11 ..      26      34 ..      24      35 .. 0.86
   2 ?    4.3   1.0    0.0096        34       3      10 ..      59      66 ..      58      68 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0032
                         zf-C2H2_10  3 kitCSYChe 11
                                       ki+CS C +
  gene3239|gene3239|rna3239|rna3239 26 KIKCSICDQ 34
                                       9******76 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.0096
                         zf-C2H2_10  3 kitCSYCh 10
                                       kitCS C+
  gene3239|gene3239|rna3239|rna3239 59 KITCSGCK 66
                                       9****998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       863  (0.0481343); expected 358.6 (0.02)
Passed bias filter:                      565  (0.0315132); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1211.19
//
Query:       gene324|gene324|rna324|rna324  [L=118]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1344  (0.0749624); expected 358.6 (0.02)
Passed bias filter:                      484  (0.0269954); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.23s 00:00:00.57 Elapsed: 00:00:00.35
# Mc/sec: 998.83
//
Query:       gene3240|gene3240|rna3240|rna3240  [L=721]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   1.7e-135  452.3   0.1    7.9e-73  245.7   0.0    2.2  2  Glyco_transf_20  Glycosyltransferase family 20
    5.2e-05   23.1   0.3    9.7e-05   22.2   0.3    1.3  1  Glyco_transf_5   Starch synthase catalytic domain
  ------ inclusion threshold ------
       0.12   12.3   0.0       0.51   10.2   0.0    2.1  2  CBP4             CBP4
       0.83    9.2  10.2      0.029   13.9   2.1    2.7  2  TF_Zn_Ribbon     TFIIB zinc-binding
        3.3    7.8   6.6        5.1    7.2   0.3    2.7  2  zinc_ribbon_6    Zinc-ribbon
        3.9    7.5  10.3        1.2    9.2   0.4    3.3  3  OrfB_Zn_ribbon   Putative transposase DNA-binding domain


Domain annotation for each model (and alignments):
>> Glyco_transf_20  Glycosyltransferase family 20
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  204.6   0.0   7.9e-64   2.3e-60       2     232 ..       2     220 ..       1     234 [. 0.93
   2 !  245.7   0.0   2.6e-76   7.9e-73     207     472 ..     436     716 ..     411     718 .. 0.92

  Alignments for each domain:
  == domain 1  score: 204.6 bits;  conditional E-value: 7.9e-64
                                        -EEEEEEE-SECEEE-S.SCG..EEECCGSSHHHHHCCCHHCCC-EEEEEEECCES-CCC..HCCCCHHHCCCCCE CS
                    Glyco_transf_20   2 klvvvsnrlplklereseeekeeyelkkssgglvsalkglkeetevvwvgwlgvevdeseeakekvskeleekfsv 77 
                                        +l++vsnrlp++++re+  ++  + +k++sgglv+ l  ++++  ++w+g    + +++e  ++++  +l++++s+
  gene3240|gene3240|rna3240|rna3240   2 RLIIVSNRLPISIKREN--GE--FVYKRNSGGLVTGLVCVAKSIPFTWIGNIPGNFTQEE--QQEIRTNLNDNHSS 71 
                                        689***********996..66..99**************************999999999..99************ PP

                                        EEEEE-HHHHHHHCCCHHHHCHHHHHTT-GG....G----HHHHHHHHHHHHHHHHHHHCC--TT-EEEEESGGGT CS
                    Glyco_transf_20  78 vpvflsdekveeyyngfsksvLWpllHYklpdsseekefersawdaYvkvnklFAdkiveeikdgdliwvhDYhLm 153
                                        +p f+++   +  y+g+++++LWpl+H+ ++       +   +++ Y++ n++F+++++e++  +d++wvhDYhLm
  gene3240|gene3240|rna3240|rna3240  72 IPLFVPEALNKMSYDGYCNKILWPLFHFFTD------IVVYDNYEYYREYNEMFCKTVLENAGANDIVWVHDYHLM 141
                                        ***************************6666......445557899****************************** PP

                                        THHHHHHHCCTTSEEEEEE-S----HHHHTTSTTHHHHHHHHTTSSEEEESSHHHHHHHHHHHHHHSSEEEECTTE CS
                    Glyco_transf_20 154 llPellRkkledakigfflHiPFPsseifriLpvreeilegllgadliGFhtedyarhFlsccsrllgleveskrg 229
                                        llP ll+k  + +++gfflHiPFPs e fr Lp ++eil g+lgadli+Fht  y ++F +cc+ +lg   e++++
  gene3240|gene3240|rna3240|rna3240 142 LLPALLKKYKPSLRVGFFLHIPFPSFETFRLLPEHREILLGILGADLIAFHTLVYSHNFRQCCEAILGNLNEQEKQ 217
                                        *******************************************************************987777776 PP

                                        EEE CS
                    Glyco_transf_20 230 gve 232
                                        +++
  gene3240|gene3240|rna3240|rna3240 218 QLT 220
                                        554 PP

  == domain 2  score: 245.7 bits;  conditional E-value: 2.6e-76
                                        HHHHHHHHHHHHHSS....................EEEECTTEEEEETTEEEEEEE------HHHHHHHCCSCHHH CS
                    Glyco_transf_20 207 dyarhFlsccsrllg....................leveskrggveykgrkvsvkalpigidverlesalkkesvs 262
                                        +y++h +++c+ +                      + ve   + +++++r++ +k +pigid+++++s+l+k+++ 
  gene3240|gene3240|rna3240|rna3240 436 KYTEHQINMCKCVGAptsepddashrkrsknygrpVCVECAFDRIRIDDREIAIKRVPIGIDPNHFRSCLEKKETI 511
                                        56666666666666666666666666666666666444444447899***************************** PP

                                        HHHHHHHHHT.TTSEEEEEEEEC-GGG-HHHHHHHHHHHHHH-GGGTTTEEEEEEEEB-STTSHHHHHHHHHHHHH CS
                    Glyco_transf_20 263 ekvkelkerfenkkklilgvDrlDyikGvkqkllaferfLeeypelrgkvvlvqiavpsredveeyqelekeveel 338
                                          +k+ ke f+++  ++lg Dr+DyikG++++l  +e+fL+++pe  +k+v++q+ vpsr+ ++ey+ le+ +   
  gene3240|gene3240|rna3240|rna3240 512 AFIKKYKEMFQDR-FVLLGIDRVDYIKGIPNRLAGYEQFLRKNPE--KKTVFIQVGVPSRTTIKEYNYLESAILSK 584
                                        **********996.******************************9..689************************** PP

                                        HHHHHHHH-BTTB-SEEEEES---HHHHHHHHHH-SEEEE--SSBSS-CHHHHHHHCSTTT--EEEEETTBGGGGT CS
                    Glyco_transf_20 339 vgrINgefgtldytPvvylersldfeeliallaaadvllvtslRdGmnlvakeyvvcqqekkgvLiLSeFaGaaqs 414
                                        vgrIN+++g ++ + v+yl++s++fee++al+++ad++lv+s+RdGmnlva+e+v+c+q+ +g L LSeFaG+a+ 
  gene3240|gene3240|rna3240|rna3240 585 VGRINSKYGGVTDSLVYYLNSSVKFEEMCALYSIADMCLVSSVRDGMNLVALEFVACSQN-NGILGLSEFAGTAST 659
                                        **********************************************************98.9************** PP

                                        -TTTSEEE-TT-HHHHHHHHHHHHC--HHHHHHHHHHHHHHHHHT-HHHHHHHHHHHH CS
                    Glyco_transf_20 415 LkdaailvNPwdieevaeaikeaLkmseeerkkrekkllkqvskhdvqsWaesflsel 472
                                        L  ++i  NPwd+e +  ai+e++km+  er +r k  +++v+k ++++Wae+ ++ l
  gene3240|gene3240|rna3240|rna3240 660 LP-GSIFLNPWDTETIVRAIEEGIKMDSGERMRRYKVNFENVTKFTAEKWAETNINYL 716
                                        **.78***********************************************999876 PP

>> Glyco_transf_5  Starch synthase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.3   3.2e-08   9.7e-05      94     156 ..      99     153 ..      80     164 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 3.2e-08
                     Glyco_transf_5  94 ffdreg.lYgdkgedyednaerfalfsraalelleklgwkpdvihahDWhtalvpallkelyke 156
                                        ff+    +Y     +ye+  e   +f++ +le +       d++ +hD+h +l+pallk+++++
  gene3240|gene3240|rna3240|rna3240  99 FFTD-IvVY----DNYEYYREYNEMFCKTVLENAGA----NDIVWVHDYHLMLLPALLKKYKPS 153
                                        4432.2488....46999999999***********9....8*******************8754 PP

>> CBP4  CBP4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       1.4   4.3e+03      55      77 ..     113     135 ..     108     137 .. 0.82
   2 ?   10.2   0.0   0.00017      0.51      38     103 ..     310     375 ..     308     405 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.4
                               CBP4  55 qkeqqelvkivketsksddpiWk 77 
                                        +++ + + k v e +  +d +W+
  gene3240|gene3240|rna3240|rna3240 113 REYNEMFCKTVLENAGANDIVWV 135
                                        4566779999************7 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00017
                               CBP4  38 rlsPelrkkyeknrelRqkeqqelvkivketsksddpiWktgpikspfeknadeklkdkekfekae 103
                                        ++ Pe r +  +nr+ R++     ++ +k t +s   i+ + + ++  ++  +++++++++++   
  gene3240|gene3240|rna3240|rna3240 310 QYEPESRLQLDRNRNTRKEHKGGVLDDIKLTKHSIAAIYDALRSSTTCDTYLQREKQKSDQLKDIV 375
                                        799************************************999988888886666666666655443 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   2.1   9.8e-06     0.029       3      25 ..     231     253 ..     229     258 .. 0.95
   2 ?   -1.8   1.3      0.78   2.3e+03      16      25 ..     397     406 ..     383     417 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 9.8e-06
                                        ETTTTCEECHEETSTTCEEESSS CS
                       TF_Zn_Ribbon   3 CPnCgstnlveDpergelvCtdC 25 
                                        CP+C+s+++ ++++  ++vC++C
  gene3240|gene3240|rna3240|rna3240 231 CPECSSSEIDRNFKVLTVVCKRC 253
                                        *********************** PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.78
                                        STTCEEESSS CS
                       TF_Zn_Ribbon  16 ergelvCtdC 25 
                                           +l+C++C
  gene3240|gene3240|rna3240|rna3240 397 RISNLRCEEC 406
                                        4557788888 PP

>> zinc_ribbon_6  Zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.3    0.0017       5.1      27      53 ..     226     253 ..     206     255 .. 0.85
   2 ?    2.5   1.3     0.049   1.5e+02      31      54 ..     384     407 ..     379     410 .. 0.92

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0017
                      zinc_ribbon_6  27 kvkilCnDCekkse.vkfhvlglkCkeC 53 
                                          +++C  C+++    +f+vl + Ck+C
  gene3240|gene3240|rna3240|rna3240 226 DSNVSCPECSSSEIdRNFKVLTVVCKRC 253
                                        5789*****987656************* PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.049
                      zinc_ribbon_6  31 lCnDCekksevkfhvlglkCkeCg 54 
                                        +C  C+k  e   ++  l+C+eC+
  gene3240|gene3240|rna3240|rna3240 384 TCMECHKLNENLPRISNLRCEECR 407
                                        699********************7 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.4   0.00039       1.2      17      55 ..     217     256 ..     205     258 .. 0.86
   2 ?   -2.4   0.0       1.5   4.6e+03      26      40 ..     352     366 ..     346     381 .. 0.77
   3 ?    2.1   2.0     0.063   1.9e+02      30      54 ..     384     408 ..     376     411 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00039
                     OrfB_Zn_ribbon  17 ikveevnpayTSktCseCgsknke.alsgrtfkCpnCgfe 55 
                                         +++ v+p  +  +C+eC s   + + +  t++C++C  +
  gene3240|gene3240|rna3240|rna3240 217 QQLTFVKPDDSNVSCPECSSSEIDrNFKVLTVVCKRCVNK 256
                                        56789999***********9999989***********876 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.5
                     OrfB_Zn_ribbon  26 yTSktCseCgsknke 40 
                                         +S+tC    ++ k+
  gene3240|gene3240|rna3240|rna3240 352 RSSTTCDTYLQREKQ 366
                                        599999988888887 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.063
                     OrfB_Zn_ribbon  30 tCseCgsknkealsgrtfkCpnCgf 54 
                                        tC eC + n++ +   +++C++C  
  gene3240|gene3240|rna3240|rna3240 384 TCMECHKLNENLPRISNLRCEECRN 408
                                        8*********99999********86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (721 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       727  (0.0405488); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.72u 0.29s 00:00:01.01 Elapsed: 00:00:00.51
# Mc/sec: 4277.15
//
Query:       gene3241|gene3241|rna3241|rna3241  [L=219]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.034   14.1   0.0      0.042   13.8   0.0    1.2  1  EMP24_GP25L  emp24/gp25L/p24 family/GOLD
      0.075   12.6   0.0        0.1   12.2   0.0    1.2  1  pEK499_p136  HEPN pEK499 p136


Domain annotation for each model (and alignments):
>> EMP24_GP25L  emp24/gp25L/p24 family/GOLD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   4.6e-06     0.042     101     180 ..     131     210 ..      75     212 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.6e-06
                        EMP24_GP25L 101 asdykdsakkekletleselkkleekldsikreqkylrereerlrdtnestnsrvvwwsilqllvlvlvavlqvyy 176
                                        +++   s+++++l +le++++  +   ++i++ +++    e +   ++ st + ++   +++++v++++ v+    
  gene3241|gene3241|rna3241|rna3241 131 KNPNVISQTDSTLRELERQIRYAIGACQEIENVMRMDLMDEGEYDGIMASTARLILGSILFKIVVVMVTFVYFNKK 206
                                        44456678899****************************************9999999999999999999987666 PP

                        EMP24_GP25L 177 Lkrf 180
                                        Lk f
  gene3241|gene3241|rna3241|rna3241 207 LKQF 210
                                        6666 PP

>> pEK499_p136  HEPN pEK499 p136
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   1.2e-05       0.1      85     154 ..     138     213 ..      91     216 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.2e-05
                        pEK499_p136  85 epnislkellrriRNgi.AHfgie....epitedklikgIkied.veknreetleaelevdelrtfakaiaeelle 154
                                        +  ++l+el r+iR +i A+++ie    +++ ++++ +gI         +++ ++++  +  +++f k++ +++++
  gene3241|gene3241|rna3241|rna3241 138 QTDSTLRELERQIRYAIgACQEIEnvmrMDLMDEGEYDGIMASTaRLILGSILFKIVVVMVTFVYFNKKLKQFYVT 213
                                        3889*************88999**9988899999999999966535677999999999999999999999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       586  (0.0326845); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1561.34
//
Query:       gene3242|gene3242|rna3242|rna3242  [L=251]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.5e-22   80.0   3.0    6.9e-20   71.3   3.0    2.1  1  Ribul_P_3_epim  Ribulose-phosphate 3 epimerase family


Domain annotation for each model (and alignments):
>> Ribul_P_3_epim  Ribulose-phosphate 3 epimerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.3   3.0   3.8e-24   6.9e-20       1     198 []      67     233 ..      67     233 .. 0.91

  Alignments for each domain:
  == domain 1  score: 71.3 bits;  conditional E-value: 3.8e-24
                                        EEEEBGGGS-GGGHHHHHHHHHHTT.-SEEEEEEEBSSSSS-B-B-HHHHHHHGGGE-S-EEEEEESSSHHHCHHH CS
                     Ribul_P_3_epim   1 kiapSllsadfarlgeevkaveeag.adllHvDvmDghfvpNltigplvvealrkltelpldvHLmveevdrivpe 75 
                                        +ia S+l a   +l++e+  +++      +H+D+ D++f +N+++gp +++++ +l  +++d+H+m++++ +++ +
  gene3242|gene3242|rna3242|rna3242  67 EIAISILNAPILTLQKELDILSQSHpQPRIHLDIIDTSFTNNISFGPSIINQILQLH-FQFDLHFMIKSPLALLTK 141
                                        599****************9998762568**************************99.****************99 PP

                                        HHHCT-SEEEEE-ST-TTHHHHHHHHHHTTSEEEEEE-TT--GGGGTTTCCC-SEEEEESS-TT-SS----CCHHH CS
                     Ribul_P_3_epim  76 faeagasiisvHaEalehlkrtiqeikeaGakaglvlnpatplealeyllekldlvllmsvePgfgGQkFipevle 151
                                           ++ s+i +H +                   g+++np  p+ + ++       vl+m+v  g g Q+Fi+   +
  gene3242|gene3242|rna3242|rna3242 142 IDCTNVSNIYMHEDVQ---------------DYGIAINPDEPVVYKQK-------VLVMTVYAGEGNQAFISP-GD 194
                                        9999999999995433...............3589*******987654.......79**************76.69 PP

                                        HHHHHHHHHHHHT---EEEEESS--TTTCHHHHHHT--EEEESHHHH CS
                     Ribul_P_3_epim 152 kikkvrklidekeldlkievDGGvkldnieqiaeagadvlVagsavf 198
                                        ki ++++  +       + vDGGv+l+n+  +   +ad++V+gsa f
  gene3242|gene3242|rna3242|rna3242 195 KIAELKRQGCY------VCVDGGVNLENVGSVR--DADCFVIGSAYF 233
                                        *****998886......9**************9..99*******987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       630  (0.0351386); expected 358.6 (0.02)
Passed bias filter:                      471  (0.0262703); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 1806.14
//
Query:       gene3243|gene3243|rna3243|rna3243  [L=567]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.5e-06   26.4   9.5    6.5e-06   26.1   0.7    3.7  3  Vps51     Vps51/Vps67
    0.00027   20.8   6.7    0.00027   20.8   6.7    3.1  2  Sec5      Exocyst complex component Sec5
     0.0049   16.9   7.4      0.025   14.6   2.6    3.3  2  COG2      COG (conserved oligomeric Golgi) complex component,
  ------ inclusion threshold ------
       0.14   12.8   0.1        6.8    7.4   0.0    3.0  2  SlyX      SlyX


Domain annotation for each model (and alignments):
>> Vps51  Vps51/Vps67
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.7   1.5e-09   6.5e-06       3      86 ..      23     115 ..      21     116 .. 0.96
   2 ?    3.8   0.2     0.014        61      40      60 ..     127     147 ..     120     154 .. 0.82
   3 ?   -0.9   0.1      0.39   1.8e+03      50      75 ..     440     465 ..     424     479 .. 0.80

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 1.5e-09
                              Vps51   3 spdfdaeayvrellakstlkellkveasllseiraldselkalVydnYskLisasdtIrkmksem.........dk 69 
                                        +++fd+  ++++ ++++tl  l  +  s++ +i +++ + ++lV ++ sk+++  + I++++++          ++
  gene3243|gene3243|rna3243|rna3243  23 QEAFDPLVFINSTMNEKTLGSLNDTLVSIKESINRNKIKNQELVRRHFSKFVHCRESIEEIRRNDafsyvknvfEQ 98 
                                        689*************************************************************9*********** PP

                              Vps51  70 ldqklselkqaiskiae 86 
                                        ++++l +l+++i++i++
  gene3243|gene3243|rna3243|rna3243  99 IEHNLTTLRNRIREISS 115
                                        ************99876 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.014
                              Vps51  40 selkalVydnYskLisasdtI 60 
                                        + ++a++ ++Y+kLi+  + +
  gene3243|gene3243|rna3243|rna3243 127 NVKRAQIAQHYNKLINLEQRL 147
                                        567999*********977655 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 0.39
                              Vps51  50 YskLisasdtIrkmksemdkldqkls 75 
                                        Y+ +++ s++I + ++++ ++   l+
  gene3243|gene3243|rna3243|rna3243 440 YRYFLQYSSKIINARTKLCQINRLLN 465
                                        99999999999999999866555444 PP

>> Sec5  Exocyst complex component Sec5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   6.7     6e-08   0.00027       4     142 ..      62     199 ..      59     202 .. 0.73
   2 ?   -1.6   4.8      0.46   2.1e+03     136     175 ..     468     509 ..     348     525 .. 0.66

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 6e-08
                               Sec5   4 lkslvksnftkfvkvkdtldqiyke..fseskteaqedslveeLeeslneairkttllfkpvlenkekadklraal 77 
                                         ++lv+ +f+kfv + +++++i+++  fs  k+      + e++e++l+ + ++  ++      +++ +d+  +  
  gene3243|gene3243|rna3243|rna3243  62 NQELVRRHFSKFVHCRESIEEIRRNdaFSYVKN------VFEQIEHNLTTLRNRIREISSSYGISAHSSDENVKRA 131
                                        589*******************97511444444......4455555555555555555555555555566666667 PP

                               Sec5  78 eviernkflFnLPksLkesiakgdydklindYkkakslfestrqslv.....eedkkqvkvfkkvwseve 142
                                        ++ + ++ l+nL + L+  ++  dy+ +++ Y+ a++l ++++  ++     + d+ +++ ++  ++++e
  gene3243|gene3243|rna3243|rna3243 132 QIAQHYNKLINLEQRLRYDLKYLDYEGFVKHYNSALKLKNDSK--FLmeklkAADAVKNRFLDILMAQIE 199
                                        899************************************9994..4333555666666666666666666 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.46
                               Sec5 136 kvwsevekiieeyrkklwekLleld..esqeeflkliskLle 175
                                          ++ v+kii++  +++ +++++    +s+e +l ++ kL e
  gene3243|gene3243|rna3243|rna3243 468 MNFKRVDKIIKKCETETIREFVKNIpnKSTEHVLMTLMKLKE 509
                                        336778888888888888887765423444444444444444 PP

>> COG2  COG (conserved oligomeric Golgi) complex component, COG2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   2.6   5.7e-06     0.025       6      99 ..      19     113 ..      15     151 .. 0.70
   2 ?    2.9   0.2     0.024   1.1e+02      53     130 ..     439     519 ..     436     522 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 5.7e-06
                               COG2   6 heFgvpdFdpdqFvselrhgvpLeslrrdLeaylkllekell...elvnedyadFvslSghLvglq..eeleeves 76 
                                        + F+ ++Fdp  F++++ + ++L sl + L ++ ++++++ +   elv++ +  Fv+  ++   ++  ++ ++v+ 
  gene3243|gene3243|rna3243|rna3243  19 DVFLQEAFDPLVFINSTMNEKTLGSLNDTLVSIKESINRNKIknqELVRRHFSKFVHCRESIEEIRrnDAFSYVKN 94 
                                        68***********************************986553447999999999998888777651134444444 PP

                               COG2  77 plaaarkkvesvreklsereeev 99 
                                         ++++  +++ +r+ + e    +
  gene3243|gene3243|rna3243|rna3243  95 VFEQIEHNLTTLRNRIRE----I 113
                                        444444444444443333....3 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.024
                               COG2  53 dyadFvslSghLvglqeeleevesplaaar..kkvesvrekls.ereeeveskleeakeleekrellklllkldev 125
                                        dy+ F++ S++ +  +++l +++  l++++  k+v+++++k + e+++e  +++ +++       l+kl  ++   
  gene3243|gene3243|rna3243|rna3243 439 DYRYFLQYSSKIINARTKLCQINRLLNNTMnfKRVDKIIKKCEtETIREFVKNIPNKSTEHVLMTLMKLKEMYFLS 514
                                        9999*******************99999874478999988886345666666666666666666666666666666 PP

                               COG2 126 vekle 130
                                         e le
  gene3243|gene3243|rna3243|rna3243 515 KETLE 519
                                        66665 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.0    0.0015       6.8      13      46 ..      35      68 ..      32      87 .. 0.88
   2 ?    2.0   0.0     0.075   3.4e+02      29      56 ..      92     119 ..      71     128 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0015
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT CS
                               SlyX 13 afqedtieeLndvvaeqqqqidrlqrqlrllaer 46
                                       +  e+t+ +Lnd+++   + i r + + ++l++r
  gene3243|gene3243|rna3243|rna3243 35 TMNEKTLGSLNDTLVSIKESINRNKIKNQELVRR 68
                                       5679***********************9999987 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.075
                                        HHHHHHHHHHHHHHHHHT-XXXXXXXXX CS
                               SlyX  29 qqqqidrlqrqlrllaerlkeleessga 56 
                                             +++++ l  l++r++e+++s g 
  gene3243|gene3243|rna3243|rna3243  92 VKNVFEQIEHNLTTLRNRIREISSSYGI 119
                                        56678999*************9998764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (567 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1175  (0.0655363); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.60u 0.27s 00:00:00.87 Elapsed: 00:00:00.43
# Mc/sec: 4003.29
//
Query:       gene3244|gene3244|rna3244|rna3244  [L=358]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (358 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       884  (0.0493056); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 2375.79
//
Query:       gene3245|gene3245|rna3245|rna3245  [L=158]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       446  (0.0248759); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 1061.67
//
Query:       gene3246|gene3246|rna3246|rna3246  [L=316]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.8e-12   47.6   0.2    3.4e-12   46.7   0.2    1.5  1  Helicase_C     Helicase conserved C-terminal domain
    0.00017   20.9   0.7    0.00031   20.0   0.5    1.5  2  ERCC3_RAD25_C  ERCC3/RAD25/XPB C-terminal helicase
  ------ inclusion threshold ------
      0.036   12.8   0.0      0.055   12.2   0.0    1.2  1  SNF2_N         SNF2 family N-terminal domain


Domain annotation for each model (and alignments):
>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.7   0.2   5.7e-16   3.4e-12       8     111 .]     148     248 ..     137     248 .. 0.89

  Alignments for each domain:
  == domain 1  score: 46.7 bits;  conditional E-value: 5.7e-16
                                        HHHHHTTTTSEEEEEESSHHHHHHHHHHHHHTTSTEEEESTTSTHHHHHHHHHHHH.TTSSS.EEEESGGGTSSST CS
                         Helicase_C   8 ellkleeeggkilifvntidrlekvklllekkgikvavlhgelpqnereeileqfn.kgesd.vLiatdvaerGid 81 
                                        +  + + +++k +if++ + ++    ++ +  ++ +++++g+ +++ r++ +++f+ +++++  +++ + a +G++
  gene3246|gene3246|rna3246|rna3246 148 Q--HIKDKKNKLVIFCHHKCMIT--GII-NALDVGYIKIDGSVNSSIRQRLVNSFQlDDNIKvAMLSITSANTGLN 218
                                        3..3478999************5..777.3448***********************988999899*********** PP

                                        STTESEEEESSSSSSHHHHHHHHTTSSSTT CS
                         Helicase_C  82 ipkvnlVinfdlprnvtsyiqriGRtgRag 111
                                        ++ +++Vi+ +l +n+ ++ q+ +R++R+g
  gene3246|gene3246|rna3246|rna3246 219 LTAADTVIFSELYWNPGNLLQAEDRVHRIG 248
                                        ****************************97 PP

>> ERCC3_RAD25_C  ERCC3/RAD25/XPB C-terminal helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0      0.35   2.1e+03      91     115 ..      92     116 ..      87     143 .. 0.74
   2 !   20.0   0.5   5.3e-08   0.00031      50     130 ..     144     227 ..     125     257 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.35
                      ERCC3_RAD25_C  91 eaerlkilqkfkknpkvntiflskv 115
                                        ++ r+ ++++f+++++ nt  +  +
  gene3246|gene3246|rna3246|rna3246  92 NTGRMGLINNFNARDTANTPNITPL 116
                                        5679999999999999988665544 PP

  == domain 2  score: 20.0 bits;  conditional E-value: 5.3e-08
                      ERCC3_RAD25_C  50 efLikyhekrgDkiivfsDnvfaLkeyakklkkpyi..yGetseaerlkilqkfkknpkvntiflskv.gDtsiDl 122
                                        e++ +  + +++k+++f+ +   ++ + ++l   yi   G+++++ r++++++f+ ++++++ +ls   ++t ++l
  gene3246|gene3246|rna3246|rna3246 144 EYINQHIKDKKNKLVIFCHHKCMITGIINALDVGYIkiDGSVNSSIRQRLVNSFQLDDNIKVAMLSITsANTGLNL 219
                                        55555556899*********9999999998888885227***************************7626789*** PP

                      ERCC3_RAD25_C 123 Peanvliq 130
                                          a  +i 
  gene3246|gene3246|rna3246|rna3246 220 TAADTVIF 227
                                        *9999884 PP

>> SNF2_N  SNF2 family N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   9.1e-06     0.055     255     289 ..      32      66 ..      11      70 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 9.1e-06
                                        HHHHHHHTT-STTEE---GGGT--S---EEEEEEE CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SNF2_N 255 kgrsrLlqllqrlmlrrakkdveknlPpkteeiif 289
                                         +  +L  ++  +m+rr+k+dv+ +lP+k  + ++
  gene3246|gene3246|rna3246|rna3246  32 SNYDELSLVIGGMMVRRTKDDVMSDLPRKYRKHVL 66 
                                        667789999999*****************988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (316 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       738  (0.0411624); expected 358.6 (0.02)
Passed bias filter:                      575  (0.0320709); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.32s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 2038.43
//
Query:       gene3247|gene3247|rna3247|rna3247  [L=499]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.032   14.4   1.3      0.074   13.2   1.3    1.7  1  FYVE      FYVE zinc finger


Domain annotation for each model (and alignments):
>> FYVE  FYVE zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   1.3   4.1e-06     0.074       4      40 ..     371     408 ..     368     458 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.1e-06
                                        -...--SB-TTT--B-.-SSS--EE-TTT--EE-STTS CS
                               FYVE   4 kddsevkkCeiCakkF.sllrrrhhCrlCGkvvCekCs 40 
                                        k+d+e+++C++ ++     + rr  Cr C ++ C++  
  gene3247|gene3247|rna3247|rna3247 371 KPDDECSTCPEKSTGTsGPVPRRTRCRECVRITCSHIK 408
                                        677777777765554425579*************7654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (499 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1033  (0.0576162); expected 358.6 (0.02)
Passed bias filter:                      557  (0.031067); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.63u 0.31s 00:00:00.94 Elapsed: 00:00:00.49
# Mc/sec: 3039.65
//
Query:       gene3248|gene3248|rna3248|rna3248  [L=41]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (41 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       192  (0.0107089); expected 358.6 (0.02)
Passed bias filter:                      149  (0.00831056); expected 358.6 (0.02)
Passed Vit filter:                         5  (0.000278878); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.33u 0.31s 00:00:00.64 Elapsed: 00:00:00.44
# Mc/sec: 280.14
//
Query:       gene3249|gene3249|rna3249|rna3249  [L=323]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.7e-14   52.7  13.6    4.7e-14   52.7  13.6    3.5  3  Glycos_transf_4  Glycosyl transferase family 4


Domain annotation for each model (and alignments):
>> Glycos_transf_4  Glycosyl transferase family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.2      0.02   3.6e+02      30      51 ..      30      55 ..      10      87 .. 0.47
   2 !   52.7  13.6   2.6e-18   4.7e-14       9     153 ..      91     213 ..      88     218 .. 0.82
   3 ?   -0.6   0.4     0.066   1.2e+03      55      75 ..     279     304 ..     217     312 .. 0.50

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.02
                    Glycos_transf_4 30 ilqilaalililtld....lslttlg 51
                                       i +i+++++ +++++    ++lt ++
  gene3249|gene3249|rna3249|rna3249 30 IYTITSSILTLILIKvvslFNLTGMD 55
                                       22222222222222222234444444 PP

  == domain 2  score: 52.7 bits;  conditional E-value: 2.6e-18
                    Glycos_transf_4   9 llilllGflDDvlglkarlKlilqilaalililtldlslttlgllltqvlielglilavlltllvivgvtNavNli 84 
                                        ++ + + +lDD+ +++++ K+i+ il+a+      d+++++++++             ++ +++++++  N vN++
  gene3249|gene3249|rna3249|rna3249  91 VVTFYIAVLDDIMEMTWKEKIIFPILLACN-----DVQMEEMRVMYV-----------LYRIVMTVFSC-NCVNIL 149
                                        5678899*****************999886.....567777777666...........34445555555.999*** PP

                    Glycos_transf_4  85 DGldGlaagvsiiialalvvlaavdgrsellllalallgallGfllfNrypAkvFmGDsgslflGlvla 153
                                         G++G+++g++iii+l++++l  vd+++ +     ++l + + +l+ N+yp+kvF+G+++  f G+++ 
  gene3249|gene3249|rna3249|rna3249 150 SGINGIEIGQVIIILLSMMTLKNVDTSTVI-----LFLSSSVPLLYLNFYPSKVFIGNAYLFFTGYFII 213
                                        *********************954444333.....35578899**********************9986 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.066
                    Glycos_transf_4  55 t.....qvlielglilavlltllviv 75 
                                        t      v+ +l  +l+v+ + ++i+
  gene3249|gene3249|rna3249|rna3249 279 TgpineGVFCNLFFLLQVVYCTVIIF 304
                                        02222224444444444443333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (323 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       859  (0.0479112); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 2207.34
//
Query:       gene325|gene325|rna325|rna325  [L=150]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       663  (0.0369792); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1047.61
//
Query:       gene3250|gene3250|rna3250|rna3250  [L=334]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-07   32.3   0.1      0.023   15.2   0.1    2.7  2  PseudoU_synth_1  tRNA pseudouridine synthase


Domain annotation for each model (and alignments):
>> PseudoU_synth_1  tRNA pseudouridine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   1.8e-06     0.033       4     108 .]       8     101 ..       5     101 .. 0.87
   2 !   15.2   0.1   1.3e-06     0.023      44      71 ..     232     283 ..     140     289 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.8e-06
                    PseudoU_synth_1   4 elvGthdfgsfckqkqekkntvrtileaaieevsgeekellvvtvkgsgFldhqVRamvgvlfavgqgklspedvk 79 
                                        +++G+++ g +  ++q+++ntv + ++aa++++   +     +t+++sg++d++V a   v+       ++p + +
  gene3250|gene3250|rna3250|rna3250   8 AYDGRKYHG-L--IDQPSQNTVFSQIRAALQRMRIPH----SLTIECSGRTDKGVSAANMVI---SLPVEKPGNYD 73 
                                        799******.5..79****************999886....9**************988888...45677888888 PP

                    PseudoU_synth_1  80 ellnakkrkkiavetapavglvlfhvrYd 108
                                         + n  ++++i v+    vg  +f++r+d
  gene3250|gene3250|rna3250|rna3250  74 VMFNNVLPDDIRVKRYALVGD-DFSARFD 101
                                        888888888888888888888.8888887 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 1.3e-06
                    PseudoU_synth_1  44 l.......................vvtvkgsgFldhqVRamvgvl.favgqg 71 
                                        +                       ++++ +++Fl++q+R+m   +   vg++
  gene3250|gene3250|rna3250|rna3250 232 TlfdqnfynrdidymrfkklneiyYMEIASKSFLHNQIRRMFYFIrKNVGKK 283
                                        244444445555555555555555*****************98776666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (334 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1142  (0.0636957); expected 358.6 (0.02)
Passed bias filter:                      466  (0.0259914); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 2298.64
//
Query:       gene3251|gene3251|rna3251|rna3251  [L=93]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       448  (0.0249875); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 714.49
//
Query:       gene3252|gene3252|rna3252|rna3252  [L=157]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       436  (0.0243181); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1142.12
//
Query:       gene326|gene326|rna326|rna326  [L=182]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
       0.08   13.0   0.2       0.12   12.4   0.2    1.4  1  Transposase_24  Plant transposase (Ptta/En/Spm family)


Domain annotation for each model (and alignments):
>> Transposase_24  Plant transposase (Ptta/En/Spm family)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.2   6.9e-06      0.12      53      99 ..      81     127 ..      75     166 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 6.9e-06
                 Transposase_24  53 ekgktpdraevfieTHtkkDGtyvdekaeeiaekvkerlqeresese 99 
                                    +k+ t+ r evf+   +k D +yvd ++++++++ +e+ q+ + e+ 
  gene326|gene326|rna326|rna326  81 TKRNTVIRNEVFDLMLKKNDFRYVDHEIRNMIKRDREEYQNLLAEIG 127
                                    4689*****************************99999988887766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       753  (0.041999); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.36
# Mc/sec: 1518.22
//
Query:       gene327|gene327|rna327|rna327  [L=279]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.013   15.5   0.1       0.02   14.8   0.1    1.4  1  LodA_N       L-Lysine epsilon oxidase N-terminal
       0.42   11.0   4.5        1.5    9.2   1.1    2.4  2  HisK_sensor  Histidine kinase sensor domain


Domain annotation for each model (and alignments):
>> LodA_N  L-Lysine epsilon oxidase N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.1   2.2e-06      0.02     141     196 ..      78     141 ..      20     157 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.2e-06
                                    S--S..EE---EEEEEEE-TTS-EEEE-----EEE...SS-......TTSTT--TTEEES--EEE CS
                         LodA_N 141 gsfp..egkivsLGelrtdekgrLlvlgGsGksas.ldgkp......ltsfanndgWyDdtsDGp 196
                                    +++   ++k++ LG+ + d++g+L++l ++Gk +s l +++       t+++n + +   t DG 
  gene327|gene327|rna327|rna327  78 EQYSknKNKKNLLGNPIFDDNGNLIILNSNGKDKSsL-KDHdsenirKTTVTNDSAYVKRTPDGE 141
                                    23432133799*********************99942.332356776778888888988888885 PP

>> HisK_sensor  Histidine kinase sensor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.1      0.02   1.8e+02      53      85 ..      23      55 ..      13      71 .. 0.79
   2 ?    9.2   1.1   0.00017       1.5      18      87 ..      75     145 ..      70     168 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.02
                    HisK_sensor 53 wyspeseelkklpleeikedkelskvfeegktv 85
                                    +++e+++++k+ ++++ ++k ls   ++ kt 
  gene327|gene327|rna327|rna327 23 SSNEEKNDMSKQLINWFFKEKLLSMLGTGLKTA 55
                                   345577899************999877776665 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00017
                    HisK_sensor  18 sileehede.elaleiaeellddetkvvIvkdkeevwyspeseelkklpleeikedkelskvfeegktvkk 87 
                                    + +e++ ++ ++     + + dd+ +++I++++++  +s ++++++++  +++++d+ + k   +g+++ +
  gene327|gene327|rna327|rna327  75 EAVEQYSKNkNKKNLLGNPIFDDNGNLIILNSNGKDKSSLKDHDSENIRKTTVTNDSAYVKRTPDGENIVE 145
                                    5677776653666666778999**********************************999887777777655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (279 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       765  (0.0426683); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.35s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 1762.01
//
Query:       gene328|gene328|rna328|rna328  [L=317]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (317 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1227  (0.0684366); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 2157.35
//
Query:       gene329|gene329|rna329|rna329  [L=33]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (33 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       130  (0.00725082); expected 358.6 (0.02)
Passed bias filter:                      110  (0.00613531); expected 358.6 (0.02)
Passed Vit filter:                         4  (0.000223102); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.32u 0.28s 00:00:00.60 Elapsed: 00:00:00.41
# Mc/sec: 242.26
//
Query:       gene33|gene33|rna33|rna33  [L=768]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (768 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       639  (0.0356406); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.60u 0.28s 00:00:00.88 Elapsed: 00:00:00.42
# Mc/sec: 5428.85
//
Query:       gene330|gene330|rna330|rna330  [L=217]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
       0.12   12.9   4.9       0.23   12.1   4.9    1.5  1  Sec16       Vesicle coat trafficking protein Sec16 mid-region
       0.37   10.9  12.2       0.45   10.6  11.7    1.5  1  ORC_WH_C    Origin recognition complex winged helix C-termina
        3.5    6.3  11.9        4.5    6.0  11.9    1.1  1  ALMT        Aluminium activated malate transporter


Domain annotation for each model (and alignments):
>> Sec16  Vesicle coat trafficking protein Sec16 mid-region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   4.9   3.9e-05      0.23      34      97 ..     105     180 ..      82     204 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.9e-05
                          Sec16  34 spgevkirslkelvpssedaskfPGPl......vkgkskkkevlkwLserieeleaevay...........aegelesaa 96 
                                    + ++ + ++ k++ +++ ++++ + P+      v++++kk +vlkwL++  +e+e++ +            +     +++
  gene330|gene330|rna330|rna330 105 NATPGEYDNFKQMEKEEIRTMNENQPIagetnnVNKEKKKFNVLKWLENYDDEMEEDSEAelqkilederkK-----QEE 179
                                    344556677888888777777778888888886666777777*************99998777676433221.....222 PP

                          Sec16  97 a 97 
                                    +
  gene330|gene330|rna330|rna330 180 E 180
                                    2 PP

>> ORC_WH_C  Origin recognition complex winged helix C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6  11.7   7.6e-05      0.45      46     114 ..     142     208 ..      79     212 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 7.6e-05
                       ORC_WH_C  46 grliNvyDwyeaFkqvlekereedkeseaeeeekakeeeaekkkkkkekeedeedeeewekelqarFir 114
                                     +  Nv  w e + + +e+++e + ++  e+e+k++eeea+++kkk e++e+e+  ++++++  +rF++
  gene330|gene330|rna330|rna330 142 KKKFNVLKWLENYDDEMEEDSEAELQKILEDERKKQEEEAKEQKKKLETKEREN--AKEKENRRIRFLQ 208
                                    4567***************99987777777777665555555555555555554..5555555677776 PP

>> ALMT  Aluminium activated malate transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0  11.9   0.00076       4.5     247     387 ..      56     202 ..      45     216 .. 0.62

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.00076
                           ALMT 247 ehgrfkfrhpwkqyvkvggvlrqca.ytvealhgcilseiqapeelrkkfk.....eelqrvslesakvlrelaesvkkm 320
                                    ++++  ++++ + y  + +vlr+ + y     +g i++++ + e++++ +      ++++++ +e ++ ++e +    ++
  gene330|gene330|rna330|rna330  56 NKTDDMMNFDQRLYHNIEQVLRKRSlYNTYHNNGIIDYNNSVKEKVNRGNAtpgeyDNFKQMEKEEIRTMNENQPIAGET 135
                                    5788899***************9873455556788899999999888776523333789***********9965555555 PP

                           ALMT 321 kklskveellkevkvaaeeLqskl..dskskLlvnsekweaakkkekaeeveekkeeekeseskkeeae 387
                                    ++ +k e+   +v + +e+   ++  ds+ +L+ + e  e +k++e+a+e+++k e+++++++k++e++
  gene330|gene330|rna330|rna330 136 NNVNK-EKKKFNVLKWLENYDDEMeeDSEAELQKILED-ERKKQEEEAKEQKKKLETKERENAKEKENR 202
                                    55544.45555555555666555522344444433333.223333334444444444444444444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3307  (0.18445); expected 358.6 (0.02)
Passed bias filter:                      610  (0.0340231); expected 358.6 (0.02)
Passed Vit filter:                       108  (0.00602376); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.60u 0.29s 00:00:00.88 Elapsed: 00:00:00.45
# Mc/sec: 1444.01
//
Query:       gene331|gene331|rna331|rna331  [L=191]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.58   10.2   5.1        2.8    8.0   0.1    2.4  2  YcbB      YcbB domain


Domain annotation for each model (and alignments):
>> YcbB  YcbB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.1   0.00015       2.8      91     127 ..      75     111 ..      68     115 .. 0.83
   2 ?    3.7   1.3    0.0033        60      51     103 ..     132     188 ..     116     191 .] 0.57

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00015
                           YcbB  91 snpkfeeYasklFdfkevrkkmkelekksesskgkin 127
                                     +     Y+s++  f+ + ++m++++   +++++ +n
  gene331|gene331|rna331|rna331  75 FDAALSGYSSRFNKFRRINNRMNNIRLAIKQNECVVN 111
                                    5666778*******************99999988777 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.0033
                           YcbB  51 ekk...easeeeieke.vkaieqRiRRaikkalknlAslGledysnp.kfeeYasklF 103
                                    e+k   ++ ++e+e++ ++a e+R  R +  a ++l +  led +++  f ++a + +
  gene331|gene331|rna331|rna331 132 EEKkmdKDLQREVENNvMHAKEKR-DRLMIMAEEHLKNRRLEDREHKnRFLQWARHEY 188
                                    333333222333344314566666.455556788888888888877525777777655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (191 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1353  (0.0754643); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1299.12
//
Query:       gene332|gene332|rna332|rna332  [L=577]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.055   13.8   0.3       0.55   10.6   0.7    2.4  2  EnY2      Transcription factor e(y)2
      0.099   12.7   0.2       0.18   11.8   0.2    1.4  1  CC190     Coiled-coil domain-containing protein 190


Domain annotation for each model (and alignments):
>> EnY2  Transcription factor e(y)2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.7   6.2e-05      0.55      31      72 ..     311     352 ..     311     354 .. 0.95
   2 ?   -1.8   0.0      0.46   4.1e+03      13      39 ..     461     487 ..     456     501 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 6.2e-05
                                    HHHHHHHHHHHHHH..HTSS.CHHHHHHHHHHHHHHHS-HHH CS
                           EnY2  31 rdevkelckeiirekgleeevsveelveeitpkaralVPdev 72 
                                    r++v+e+c  ++++++++  v+v+e+ e++  ++ + +P ev
  gene332|gene332|rna332|rna332 311 REDVSEECDVMLEKNQENRRVTVTEITENVDTNMDENIPLEV 352
                                    689**********9999999*******************998 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.46
                                    HHHHHHHHHHHHHHHTTHHHHHHHHHH CS
                           EnY2  13 ererlkelLrerLeesGWrdevkelck 39 
                                    +r+  k++L+++ e+  ++d++  +c+
  gene332|gene332|rna332|rna332 461 KRDFFKSFLKNKTEHDVFYDHIDPICS 487
                                    677789999999999999999999987 PP

>> CC190  Coiled-coil domain-containing protein 190
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.2   2.1e-05      0.18      22     110 ..     258     350 ..     255     398 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.1e-05
                          CC190  22 slrLqrLeeicLyhvkll.arEqRqLqkeLqrLqqadiiKKklsSylgngiqkr...pedvltlspqegqkhrvaeankv 97 
                                    ++ L+r e+i + +v  l ++ ++ L   L+ L q d   K +  yl+n+i kr   +e+  ++ +++++ +rv+ ++  
  gene332|gene332|rna332|rna332 258 KQFLNRNEDIFIRNVYRLqSQPKKNLNFILESLNQIDTFEKTYRTYLANKILKRedvSEECDVMLEKNQENRRVTVTEIT 337
                                    6778888888887776552455677888899**********************955556666666666666666666668 PP

                          CC190  98 ralatnltqeikk 110
                                     ++ tn+ ++i  
  gene332|gene332|rna332|rna332 338 ENVDTNMDENIPL 350
                                    8899998877655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (577 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1098  (0.0612416); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.45
# Mc/sec: 3846.81
//
Query:       gene333|gene333|rna333|rna333  [L=201]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.8e-17   63.1   0.0    3.5e-17   62.8   0.0    1.1  1  HhH-GPD        HhH-GPD superfamily base excision DNA repair p
      0.003   17.8   1.4     0.0055   17.0   1.4    1.4  1  EndIII_4Fe-2S  Iron-sulfur binding domain of endonuclease III
  ------ inclusion threshold ------
      0.013   15.4   0.0      0.098   12.6   0.0    2.4  2  HHH            Helix-hairpin-helix motif


Domain annotation for each model (and alignments):
>> HhH-GPD  HhH-GPD superfamily base excision DNA repair protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.8   0.0   5.8e-21   3.5e-17       2     105 ..      20     156 ..      19     159 .. 0.93

  Alignments for each domain:
  == domain 1  score: 62.8 bits;  conditional E-value: 5.8e-21
                                    HHHHHTTS-HHHHHHHHHHHHHHHS.....HCSHHHHHHSHHHHHHHHHTTSTTHHHHHHHHHHHHHHHH.......... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......... RF
                        HhH-GPD   2 sailsqqtsderanriierlferfg.....fptpedladadeekLrelirelGfyrrKakyikelArilv.......... 66 
                                    + ilsqqt+d+++++ i +l e+       +++p ++  ++ ++L + i+ + +y +Kak+ik +A+ +v          
  gene333|gene333|rna333|rna333  20 MLILSQQTRDKTTYTTIHNLNELLVrkygeGISPYTISLLSLDELSSSIKNANYYIKKAKNIKMIAEYFVnrkmateyde 99 
                                    57*****************9887767777*************************************************** PP

                                    ....................S-SSS--TTSHHHHHHHHHHTTSSSSTTHHHHHHHHHHH CS
                                    ....................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        HhH-GPD  67 ....................gkpdvlivvDvhvrrilkrlrsikekktkkkvekkleel 105
                                                        +k +v+i vD+hv+ri++rl+ + + kt+++++ +le++
  gene333|gene333|rna333|rna333 100 lvklpgignkiaflylqiacNK-TVGIGVDTHVHRIFNRLGVVTT-KTPEETRIQLEQI 156
                                    ******************9765.59******************99.6*****9998654 PP

>> EndIII_4Fe-2S  Iron-sulfur binding domain of endonuclease III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   1.4   9.2e-07    0.0055       1      14 [.     177     190 ..     177     191 .. 0.95

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 9.2e-07
                  EndIII_4Fe-2S   1 CTARkPkCeaCPLa 14 
                                    C ++kPkC +C+++
  gene333|gene333|rna333|rna333 177 CLPKKPKCNECVVN 190
                                    99*********997 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.25   1.5e+03      17      23 ..      49      55 ..      49      58 .. 0.87
   2 ?   12.6   0.0   1.6e-05     0.098      10      24 ..      97     111 ..      89     111 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.25
                                   TT-SHHH CS
                            HHH 17 PGVGpkt 23
                                   +G+ p+t
  gene333|gene333|rna333|rna333 49 EGISPYT 55
                                   6*****9 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 1.6e-05
                                    HHHHHTSTT-SHHHH CS
                            HHH  10 reeLlalPGVGpktA 24 
                                    ++eL++lPG+G k A
  gene333|gene333|rna333|rna333  97 YDELVKLPGIGNKIA 111
                                    79*********8876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (201 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1007  (0.056166); expected 358.6 (0.02)
Passed bias filter:                      515  (0.0287244); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 1289.18
//
Query:       gene334|gene334|rna334|rna334  [L=47]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (47 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       733  (0.0408835); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.22s 00:00:00.56 Elapsed: 00:00:00.38
# Mc/sec: 369.28
//
Query:       gene335|gene335|rna335|rna335  [L=60]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (60 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       461  (0.0257125); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.31s 00:00:00.74 Elapsed: 00:00:00.48
# Mc/sec: 374.59
//
Query:       gene336|gene336|rna336|rna336  [L=26]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (26 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       161  (0.00897987); expected 358.6 (0.02)
Passed bias filter:                      109  (0.00607954); expected 358.6 (0.02)
Passed Vit filter:                         3  (0.000167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.32u 0.23s 00:00:00.55 Elapsed: 00:00:00.38
# Mc/sec: 203.39
//
Query:       gene337|gene337|rna337|rna337  [L=123]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-09   38.2  10.6    2.1e-09   37.6  10.6    1.2  1  TBCA            Tubulin binding cofactor A
     0.0032   16.4   6.8     0.0037   16.2   6.8    1.0  1  Spc7            Spc7 kinetochore protein
  ------ inclusion threshold ------
      0.013   16.0   7.9      0.016   15.7   7.9    1.1  1  APG6_N          Apg6 coiled-coil region
      0.013   16.1   5.4      0.023   15.3   5.3    1.5  1  HIP1_clath_bdg  Clathrin-binding domain of Huntingtin-interac
      0.038   14.6   0.2      0.053   14.1   0.2    1.3  1  DM13            Electron transfer DM13
        0.7   10.1   8.1        0.2   11.9   3.9    2.1  2  DUF5446         Family of unknown function (DUF5446)
        1.9    8.7   9.5        8.4    6.6   9.3    2.0  1  PHM7_cyt        Cytosolic domain of 10TM putative phosphate t


Domain annotation for each model (and alignments):
>> TBCA  Tubulin binding cofactor A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.6  10.6   8.1e-13   2.1e-09       3      83 ..      42     119 ..      41     122 .. 0.90

  Alignments for each domain:
  == domain 1  score: 37.6 bits;  conditional E-value: 8.1e-13
                           TBCA   3 IktgvvkRlvKEeasYekEleeqearleklkadgdedeydlkkqeevleetkamipdlkkrlekavekLeelleeeeele 82 
                                    I t+++ Rl KE+++Y kE e+  ++++k +    +dey+lk  +e+l e ++ i  +++ +++ v kLe+l +ee++ e
  gene337|gene337|rna337|rna337  42 IFTNALDRLKKEHSYYVKEKENVLEKIKKYNG---SDEYELKLLNEMLTEVEQTILSVESNIQEYVSKLEKLEKEEKHAE 118
                                    88*****************9888888877765...469**********************************99998775 PP

                           TBCA  83 e 83 
                                    +
  gene337|gene337|rna337|rna337 119 K 119
                                    4 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   6.8   1.4e-06    0.0037     158     242 ..      36     120 ..      20     122 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.4e-06
                           Spc7 158 LekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelaelqeqleeleekie 237
                                    + k+++ ++++l++l++e++   +e e+  e+ ++ + +d+ eL+ l e l+e++++i + + +++e  ++le+le++ +
  gene337|gene337|rna337|rna337  36 MIKKRQIFTNALDRLKKEHSYYVKEKENVLEKIKKYNGSDEYELKLLNEMLTEVEQTILSVESNIQEYVSKLEKLEKEEK 115
                                    66889999************999999999999*******************************************99988 PP

                           Spc7 238 elkeq 242
                                    +++++
  gene337|gene337|rna337|rna337 116 HAEKS 120
                                    87765 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.7   7.9   6.3e-06     0.016      22     106 ..      37     122 ..      24     123 .] 0.72

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 6.3e-06
                         APG6_N  22 ekerdaYeeflkklkkekkeeekqdeeleeleeelek....lekeeeelleeLkelekereeleaelaaleeelealeee 97 
                                     k+r+ +++ l++lkke++   k   e e+  e+++k     e e + l e L e+e++  ++e+ ++++ ++le+le+e
  gene337|gene337|rna337|rna337  37 IKKRQIFTNALDRLKKEHSYYVK---EKENVLEKIKKyngsDEYELKLLNEMLTEVEQTILSVESNIQEYVSKLEKLEKE 113
                                    67888899999999998766553...334444444442221444555556668999999999999999999999999999 PP

                         APG6_N  98 eerfwreyn 106
                                    e+   ++yn
  gene337|gene337|rna337|rna337 114 EKHAEKSYN 122
                                    998888777 PP

>> HIP1_clath_bdg  Clathrin-binding domain of Huntingtin-interacting protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   5.3   8.9e-06     0.023      27      91 ..      38     102 ..      24     117 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 8.9e-06
                 HIP1_clath_bdg  27 rekkeleeelerlkeeaerkleeqkeelekLkreleakraelarlkssLesseqsgeqlssqlaa 91 
                                    ++++  ++ l+rlk+e++  ++e++  lek+k+   + + el+ l++ L++ eq+   ++s++++
  gene337|gene337|rna337|rna337  38 KKRQIFTNALDRLKKEHSYYVKEKENVLEKIKKYNGSDEYELKLLNEMLTEVEQTILSVESNIQE 102
                                    567778999************************99999999999999999998875555544443 PP

>> DM13  Electron transfer DM13
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.2   2.1e-05     0.053       9      79 ..      13      84 ..       6      96 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.1e-05
                           DM13  9 tsGtvsivd.dktlelegfatdgkgpdlkvwlgkseapsskkgfkipdedgvtlgplkaykgeq.ytlelpag 79
                                   ts +++ +  +++l l++f t g+ ++ +++  + ++ +++  + +++++ v + ++k+y+g++ y+l+l ++
  gene337|gene337|rna337|rna337 13 TSQRIRFSGsQNVLTLKKFGTHGMIKKRQIFTNALDRLKKEHSYYVKEKENVLE-KIKKYNGSDeYELKLLNE 84
                                   6666666664599****************9999888877744457777777776.*************99765 PP

>> DUF5446  Family of unknown function (DUF5446)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.1      0.56   1.4e+03      41      50 ..      59      68 ..      38      71 .. 0.54
   2 ?   11.9   3.9   7.7e-05       0.2      12      43 ..      84     115 ..      80     120 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.56
                        DUF5446 41 ekeeerldll 50
                                   +++e++l+++
  gene337|gene337|rna337|rna337 59 KEKENVLEKI 68
                                   3445555555 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 7.7e-05
                        DUF5446  12 qlLeeiEeeltevEkelseavneteaekeeke 43 
                                     +L e+E+ + +vE +++e v ++e+  +e++
  gene337|gene337|rna337|rna337  84 EMLTEVEQTILSVESNIQEYVSKLEKLEKEEK 115
                                    59********************9998666554 PP

>> PHM7_cyt  Cytosolic domain of 10TM putative phosphate transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   9.3    0.0033       8.4      42     119 ..      45     116 ..      27     122 .. 0.68

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0033
                       PHM7_cyt  42 kkldklveerekavrkleaalskykkngkklpkkrpthklgflglkligkkvdaidyyrekleeldeeieeerekvkk 119
                                    + ld+l +e+  +v+++e +l+k kk++ +         l++l+ +l  +  ++i   +++++e   ++e++++++k 
  gene337|gene337|rna337|rna337  45 NALDRLKKEHSYYVKEKENVLEKIKKYNGSD-----EYELKLLNEML-TEVEQTILSVESNIQEYVSKLEKLEKEEKH 116
                                    579*********************9998654.....23444454333.344556666666666666666666555433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (123 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2349  (0.131017); expected 358.6 (0.02)
Passed bias filter:                      639  (0.0356406); expected 358.6 (0.02)
Passed Vit filter:                        73  (0.00407162); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 878.69
//
Query:       gene338|gene338|rna338|rna338  [L=827]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (827 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1177  (0.0656478); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.66u 0.28s 00:00:00.94 Elapsed: 00:00:00.44
# Mc/sec: 5592.89
//
Query:       gene339|gene339|rna339|rna339  [L=180]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       808  (0.0450667); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1215.41
//
Query:       gene34|gene34|rna34|rna34  [L=79]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.013   14.9   0.1      0.015   14.7   0.1    1.1  1  Phage_capsid  Phage capsid family


Domain annotation for each model (and alignments):
>> Phage_capsid  Phage capsid family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.1   8.1e-07     0.015      92     131 ..      31      67 ..      24      77 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 8.1e-07
               Phage_capsid  92 vdleayiadelaeafarkedeaflnGdGdgngqpkGilas 131
                                + + +++++++++ +   ed+ +++G +dg  q +G+ + 
  gene34|gene34|rna34|rna34  31 I-VGRWMMERIRNFMVSIEDDTMVSGKEDG--QVNGLASG 67 
                                4.679*********************9999..****9954 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       473  (0.0263818); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 600.30
//
Query:       gene340|gene340|rna340|rna340  [L=220]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.6e-41  140.9   0.3    3.1e-41  140.7   0.3    1.1  1  Ras           Ras family
    1.8e-30  105.6   0.2    2.6e-30  105.1   0.2    1.2  1  Roc           Ras of Complex, Roc, domain of DAPkinase
    1.9e-17   63.3   0.3    2.3e-17   63.0   0.3    1.1  1  Arf           ADP-ribosylation factor family
    3.5e-07   29.8   0.1    4.5e-07   29.5   0.1    1.1  1  Gtr1_RagA     Gtr1/RagA G protein conserved region
    9.7e-07   28.4   0.0    1.3e-06   28.0   0.0    1.1  1  SRPRB         Signal recognition particle receptor beta subun
     0.0015   18.1   1.3     0.0054   16.3   0.5    1.9  2  GTP_EFTU      Elongation factor Tu GTP binding domain
     0.0018   18.1   0.7       0.27   11.0   0.1    2.3  2  ATP_bind_1    Conserved hypothetical ATP binding protein
     0.0023   18.2   0.2     0.0089   16.3   0.2    1.9  1  AAA_22        AAA domain
     0.0037   17.2   0.1        1.1    9.2   0.0    2.2  2  RsgA_GTPase   RsgA GTPase
      0.006   16.7   0.1       0.01   15.9   0.1    1.4  1  MMR_HSR1      50S ribosome-binding GTPase
     0.0067   16.2   1.0      0.018   14.8   1.0    1.9  1  PduV-EutP     Ethanolamine utilisation - propanediol utilisat
  ------ inclusion threshold ------
      0.013   15.7   0.1      0.026   14.7   0.1    1.5  1  AAA_33        AAA domain
      0.014   14.6   2.1       0.11   11.7   0.1    2.6  2  G-alpha       G-protein alpha subunit
      0.041   14.3   0.0      0.085   13.2   0.0    1.5  1  AAA_16        AAA ATPase domain
      0.055   13.2   1.2       0.35   10.6   0.2    2.0  2  AAA_24        AAA domain
      0.058   12.9   0.0       0.16   11.5   0.0    1.7  1  AAA_7         P-loop containing dynein motor region
      0.058   13.4   0.1        0.1   12.6   0.1    1.5  1  MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
      0.068   13.1   0.1       0.16   11.8   0.0    1.6  2  NACHT         NACHT domain
      0.076   13.0   0.1       0.14   12.1   0.1    1.6  1  AAA_5         AAA domain (dynein-related subfamily)
       0.13   12.8   0.1       0.23   12.0   0.0    1.6  1  AAA_18        AAA domain


Domain annotation for each model (and alignments):
>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  140.7   0.3   3.5e-44   3.1e-41       1     160 [.       9     171 ..       9     173 .. 0.94

  Alignments for each domain:
  == domain 1  score: 140.7 bits;  conditional E-value: 3.5e-44
                                    EEEEEESTTSSHHHHHHHHHHSSCSSSCTTTSSEEEEEEEEEET.TEEEEEEEEEETTSGGGHHHHHHHHTTESEEEEEE CS
                            Ras   1 KlvlvGdsavGKtslllrfvkdkFkeeyesTigvdfytkeievd.gkevkleiwDTAGqeefkslrelyyrdaegillvy 79 
                                    Kl+l+Gd+++GKt+ l r  +++F++ey++Tigvd    +++++ ++++++++wDTAGqe + +l++ yy +a+++++++
  gene340|gene340|rna340|rna340   9 KLILIGDGGTGKTTYLQRIKEGSFRREYIATIGVDVRDVTFKTNyNTDISFQVWDTAGQEMYAQLNDVYYIGASAAIIMF 88 
                                    89***********************************99999998999******************************** PP

                                    ETTBHHHHHTHHHHHHHHHHHST...TTSEEEEEEETTTGGGG-SS-HHHHHHHHHHHTSEEEEEBTTTTCTHHHHHHHH CS
                            Ras  80 ditsresfenvkkwveeikrvae...envpivLvGnKvDleekravsteegeelakelglkfletSAktnenveeafeel 156
                                    d+tsr +f+nv++w+++++  ++    n+p++++GnK+Dl++ r+v+++  +e  ++  + ++++SAk+n+++e  f  +
  gene340|gene340|rna340|rna340  89 DVTSRITFRNVETWLRKLRLLTTqnnVNIPVIVCGNKIDLKD-RKVNQKYIREHLSRDITCYVDISAKSNHHFEVPFLVA 167
                                    *****************9866655557899***********7.99*999999999999999****************999 PP

                                    HHHH CS
                            Ras 157 lrei 160
                                    +r++
  gene340|gene340|rna340|rna340 168 ARKL 171
                                    9986 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.1   0.2   2.9e-33   2.6e-30       1     120 []       9     128 ..       9     128 .. 0.85

  Alignments for each domain:
  == domain 1  score: 105.1 bits;  conditional E-value: 2.9e-33
                                    EEEEESSTTSSHHHHHHCHCT-CCC-EEETTTTEEEEEEECGGSGGCTTBTTTTCEEEEEEEE-SGGCTTTT-HHHHCTS CS
                            Roc   1 KvvlvGdsgvGKtsllkrfvedkfsekekstigvdfltkevtkikgvendkkvkkvklniWDtaGqerfrslhplylrea 80 
                                    K++l+Gd+g+GKt+ l+r+ e++f++++ +tigvd+ + ++   k+       +++++++WDtaGqe + +l+++y+ +a
  gene340|gene340|rna340|rna340   9 KLILIGDGGTGKTTYLQRIKEGSFRREYIATIGVDVRDVTF---KTN----YNTDISFQVWDTAGQEMYAQLNDVYYIGA 81 
                                    99**********************************88765...332....225799*********************** PP

                                    CEEEEEEE..GH.HHHCHHHHHHHHHHHCS....SS-EEEEEE-TTT CS
                            Roc  81 alailvyd..sr.ssenlkeWlkelkkvag....kspvilvgnkiDl 120
                                    ++ai+++d  sr +++n+++Wl++l+  ++    ++pvi++gnkiDl
  gene340|gene340|rna340|rna340  82 SAAIIMFDvtSRiTFRNVETWLRKLRLLTTqnnvNIPVIVCGNKIDL 128
                                    ********65335789********98654411226699*******95 PP

>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.0   0.3   2.5e-20   2.3e-17      11     143 ..       4     145 ..       1     179 [. 0.85

  Alignments for each domain:
  == domain 1  score: 63.0 bits;  conditional E-value: 2.5e-20
                                    .TTEEEEEEEESTTSSHHHHHHHHHHSSCEE.CSSSSSEEEEEEEE.....TTEEEEEEEE-SSGGGGGGGGGGCTTESE CS
                            Arf  11 kkkelrilllGLDnaGKtTilkklkleelvt.tvPTigfnveelei.....knlkftvwDvGGqeklRplWknYfektda 84 
                                    + ++++++l+G  ++GKtT l+++k++++ +  + Tig +v+++++      +++f+vwD  Gqe   +l + Y+    a
  gene340|gene340|rna340|rna340   4 QFNQYKLILIGDGGTGKTTYLQRIKEGSFRReYIATIGVDVRDVTFktnynTDISFQVWDTAGQEMYAQLNDVYYIGASA 83 
                                    56789***********************986589**********9966666689************************** PP

                                    EEEEEETT-CTTHHHHHHHHHH..HCTSGCCTTSEEEEEEE-TTSTTS.S-HHHHHHHTTGG CS
                            Arf  85 vifvvDsadreRleeakeeLka..lleeeelkevallvlaNKqDlpea.lseeelrellgle 143
                                     i + D++ r  +++ ++ L++  ll+++++ +++++v +NK+Dl++  ++++ +re+l+ +
  gene340|gene340|rna340|rna340  84 AIIMFDVTSRITFRNVETWLRKlrLLTTQNNVNIPVIVCGNKIDLKDRkVNQKYIREHLSRD 145
                                    ***********99999999986336999999**************98516677788888654 PP

>> Gtr1_RagA  Gtr1/RagA G protein conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.5   0.1     5e-10   4.5e-07       1     137 [.       9     142 ..       9     167 .. 0.72

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 5e-10
                      Gtr1_RagA   1 kvLLmGksgsGKtsmrsiiFdnylardtl.rlgatidveksevrflgnltlnlwDcgGqeafveeylssqkeeifrnvgv 79 
                                    k++L+G +g GKt+  + i +    r+ + ++g+ ++    + + +  + +++wD  Gqe + + +   +  +i    ++
  gene340|gene340|rna340|rna340   9 KLILIGDGGTGKTTYLQRIKEGSFRREYIaTIGVDVRDVTFKTNYNTDISFQVWDTAGQEMYAQLN---DVYYIG--ASA 83 
                                    89*******************99999876134443333333344455679*********9988774...555555..566 PP

                      Gtr1_RagA  80 liyVfDvesreleedletl.keilealrqyspeakvfvlihKmDliqedereeifeerk 137
                                     i +fDv+sr   +++et+ +++    +q++ ++ v v  +K+Dl +++ +++ ++e+ 
  gene340|gene340|rna340|rna340  84 AIIMFDVTSRITFRNVETWlRKLRLLTTQNNVNIPVIVCGNKIDLKDRKVNQKYIREHL 142
                                    77789****965555555505555556789999************98777776666543 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0   0.0   1.4e-09   1.3e-06       3     150 ..       7     155 ..       5     170 .. 0.83

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 1.4e-09
                                    --EEEEE-STTSSHHHHHHHHHHSS---B---S....S-EEETTG...GGTT-SEEEETT-GCCSHHHHHHHHHHGGEEE CS
                          SRPRB   3 kpavllvGlsdsGKTslftrLttdsvkktvtSq....essaalkvksekgskltliDfPGheklrqklleklkaksslkg 78 
                                    + +++l+G   +GKT+ ++r+ ++s+++ +++        ++ k++ + + ++++ D  G+e    +l + +   +s+  
  gene340|gene340|rna340|rna340   7 QYKLILIGDGGTGKTTYLQRIKEGSFRREYIATigvdVRDVTFKTNYNTDISFQVWDTAGQEMY-AQLNDVYYIGASAAI 85 
                                    5679********************998888776221234455566889999*********9865.689999999999*** PP

                                    EEEEEETTS-HHHHHHHHHHHHHHHHHHHHHTT---EEEEEE-TTSTT---.HHHHHHHHHHHHHHHHHCHHH CS
                          SRPRB  79 lvfvvDStidpkevkevAEllyeilliteklkdavdiliACnKqelflaks.pklikdaLEkElnkiierrsk 150
                                    ++f v S i  ++v++   +l ++ l t++++ ++++++  nK +l   k  +k i++ L ++++  +   +k
  gene340|gene340|rna340|rna340  86 IMFDVTSRITFRNVET---WLRKLRLLTTQNNVNIPVIVCGNKIDLKDRKVnQKYIREHLSRDITCYVDISAK 155
                                    *********9999876...7888888888888999***********999962678*******99976665555 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.1       0.3   2.7e+02       6      24 ..      10      28 ..       6      35 .. 0.84
   2 !   16.3   0.5     6e-06    0.0054      54     171 ..      40     163 ..      18     210 .. 0.69

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.3
                                   EEEEESTTSSHHHHHHHHH CS
                       GTP_EFTU  6 igiighvDhGKtTLtdrLl 24
                                   +++ig+  +GKtT + r+ 
  gene340|gene340|rna340|rna340 10 LILIGDGGTGKTTYLQRIK 28
                                   6789999******999885 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 6e-06
                                    SCSSCEEEEEET.TCSSEEEEEEEESSSGGGHHHHHHHHHT-SEEEEEEETTTB.....STHHHHHHHHHHHHTTTE..E CS
                       GTP_EFTU  54 iTiksaaislek.etkkylinliDtPGHvdFskevirglrvlDgavlvvdaveG.....vepqteevlrlalkegvp..i 125
                                    i +++  +++++   ++  +++ Dt G + + +     +  +  a++++d+++      ve+  +++  l  +++v+  +
  gene340|gene340|rna340|rna340  40 IGVDVRDVTFKTnYNTDISFQVWDTAGQEMYAQLNDVYYIGASAAIIMFDVTSRitfrnVETWLRKLRLLTTQNNVNipV 119
                                    556666666764367789999************99999999***********6644444777777777777777766669 PP

                                    EEEEESCGSTHHHHHH..HHHHHHHHHHHHHHHHHHHHHTTTTTEEEE CS
                       GTP_EFTU 126 ivfiNKmDrlkaelke..iveevkqklsrkeeklekygekgekevpvv 171
                                    iv+ NK+D  + ++++  i e +++++    +   ++ +k+++ ++v 
  gene340|gene340|rna340|rna340 120 IVCGNKIDLKDRKVNQkyIREHLSRDI----TCYVDISAKSNHHFEVP 163
                                    *********966655400344444443....22222333333344443 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.1     0.012        11       2      22 ..      13      33 ..      12      58 .. 0.74
   2 !   11.0   0.1   0.00031      0.27      92     181 ..      58     139 ..      43     167 .. 0.67

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.012
                     ATP_bind_1  2 vGpaGsGKttfvgalseilel 22
                                   +G  G GKtt+ +++ e    
  gene340|gene340|rna340|rna340 13 IGDGGTGKTTYLQRIKEGSFR 33
                                   7999**********9986554 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00031
                     ATP_bind_1  92 dyllfDtPGQielfthseslakiveeLesefalvvvyLvDsq...rltdptkfisgllsalsamlrlelPhvvvlnkfDl 168
                                    ++ + Dt GQ    ++ ++           +a  ++ ++D++   + +++ +++ + l  l +  ++++P +v+ nk+Dl
  gene340|gene340|rna340|rna340  58 SFQVWDTAGQEMYAQLNDVYY--------IGASAAIIMFDVTsriTFRNVETWLRK-LRLLTTQNNVNIPVIVCGNKIDL 128
                                    555666666644444444444........556666666664411134559999999.99999****************** PP

                     ATP_bind_1 169 lkeklekeleffe 181
                                     ++k   + +++ 
  gene340|gene340|rna340|rna340 129 KDRK--VNQKYIR 139
                                    7744..3334433 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.2   9.9e-06    0.0089       5     133 ..       7     128 ..       3     131 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 9.9e-06
                         AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelkaerlsseellealeq 84 
                                    ++ l+++G  GtGKTt l+r++e   ++     e   ++ v++   t  ++  +++  ++ +         +e++++l++
  gene340|gene340|rna340|rna340   7 QYKLILIGDGGTGKTTYLQRIKEGSFRR-----EYIATIGVDVRDVTFKTNYNTDISFQVWDT------AGQEMYAQLND 75 
                                    66799******************98433.....345555888888888888888888888842......34688888888 PP

                         AAA_22  85 alraravielliiDEaqhlr.s..eealeeLrsllnlsrkgvqliLvGtp.el 133
                                         a  ++++ D   +++ +  e+ l++Lr l   +  ++++i++G   +l
  gene340|gene340|rna340|rna340  76 VYYIGASAAIIMFDVTSRITfRnvETWLRKLRLLTTQNNVNIPVIVCGNKiDL 128
                                    88887776777777777785424677777776665545888888888876555 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.3   0.0    0.0094       8.5      96     121 ..       4      29 ..       1      55 [. 0.84
   2 !    9.2   0.0    0.0012       1.1      37      74 ..     107     144 ..      82     171 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0094
                                    HCTTSEEEEECSTTSSHHHHHHHHCT CS
                    RsgA_GTPase  96 llkdktsvlvGqSGvGKStLinallp 121
                                    ++++   +l+G  G GK+t + ++++
  gene340|gene340|rna340|rna340   4 QFNQYKLILIGDGGTGKTTYLQRIKE 29 
                                    56666789************999876 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0012
                                    HHHHHHHHTT-EEEEEEE-GGG--HHHHHHHHHHHHHH CS
                    RsgA_GTPase  37 rfLvlaeekgiepvivlnKiDlleeeeeleelkeelea 74 
                                    r+L++ ++ +i+++++ nKiDl +++ + + ++e+l++
  gene340|gene340|rna340|rna340 107 RLLTTQNNVNIPVIVCGNKIDLKDRKVNQKYIREHLSR 144
                                    889999999**************999966666555544 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1   1.1e-05      0.01       2     114 .]      10     125 ..       9     125 .. 0.60

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.1e-05
                                    EEEEESTTSSHHHHHHHHHTS...TEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSSHHHHHHHHHHHHHHHHCTSE CS
                       MMR_HSR1   2 vaivGrpNvGKStLinaltge...kaivsdkpgtTrdinegrvklkgkeielvDtpGliegaseekglgkaflaleeadl 78 
                                     +++G   +GK+t ++++ +    +  ++ +    rd+++++    + +++++Dt+G  e      +l++ +   + a++
  gene340|gene340|rna340|rna340  10 LILIGDGGTGKTTYLQRIKEGsfrREYIATIGVDVRDVTFKTNYNTDISFQVWDTAG-QE---MYAQLNDVYY--IGASA 83 
                                    5799**************9863323344444444444444443344689********.44...2335555555..34677 PP

                                    EEEEEETTTTCSHHHHHHHHHHHHH.........TTSEEEEEEES CS
                       MMR_HSR1  79 illvvdaseeklkpldeeleellee.........akkplilvlnk 114
                                    +++++d++++ +    +++e +l++          ++p+i++ nk
  gene340|gene340|rna340|rna340  84 AIIMFDVTSR-I--TFRNVETWLRKlrllttqnnVNIPVIVCGNK 125
                                    7778886622.3..2245555555555555555567777777665 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   1.0   2.1e-05     0.018       3      46 ..       9      67 ..       7     162 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.1e-05
                      PduV-EutP  3 killiGkvgsGKttLtqalkg...............eelkYkktqaiefsdeviDtPGe 46
                                   k++liG  g+GKtt  q++k+               +++++k    +++s +v Dt G+
  gene340|gene340|rna340|rna340  9 KLILIGDGGTGKTTYLQRIKEgsfrreyiatigvdvRDVTFKTNYNTDISFQVWDTAGQ 67
                                   89******************977666666666666666666666666666666666666 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.1   2.9e-05     0.026       3     110 ..      11     128 ..      10     145 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.9e-05
                         AAA_33   3 llvGlpGsGKstlaerl...lkklg....avllssdt..lrrrlfgtdqqsktdytrvldrlyqilnelarkalsagrnv 73 
                                    +l+G  G+GK+t+++r+              ++  d+  + ++  ++ + s + + ++ +++y++ln++  + +sa+  +
  gene340|gene340|rna340|rna340  11 ILIGDGGTGKTTYLQRIkegS---FrreyIATIGVDVrdVTFKTNYNTDISFQVWDTAGQEMYAQLNDVYYIGASAA-II 86 
                                    78999***********84440...35555555655542255555556666777777788889999999886554444.24 PP

                         AAA_33  74 ildat....nlsrrerarflklar.rlgvpvrivvvetdeet 110
                                    ++d t    +++ +++ r+l+l+  + +v++ ++v+    ++
  gene340|gene340|rna340|rna340  87 MFDVTsritFRNVETWLRKLRLLTtQNNVNIPVIVCGNKIDL 128
                                    445554444999999987777765378888888887655555 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   0.00012      0.11      23      55 ..       7      36 ..       1      45 [. 0.80
   2 ?    2.8   0.3      0.06        53     187     214 ..      38      69 ..      32     160 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00012
                                   EEEEEEEESTTSSHHHHHHHHHHHCS----HHH CS
                        G-alpha 23 evkllllGqseSGKsTilkqlkllykkgfseee 55
                                   ++kl+l+G ++ GK+T+l+ +k   +++f++e 
  gene340|gene340|rna340|rna340  7 QYKLILIGDGGTGKTTYLQRIK---EGSFRREY 36
                                   58***************99998...77788774 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.06
                                    ---SEEEEEEEC....T-TEEEEEEEE-SSHH CS
                        G-alpha 187 ktvGisetkfev....dsklefrivdvgGqrs 214
                                     t+G+   ++ +    +++++f+++d++Gq  
  gene340|gene340|rna340|rna340  38 ATIGVDVRDVTFktnyNTDISFQVWDTAGQEM 69 
                                    56666555554444667789999999999975 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   9.5e-05     0.085      27      63 ..      10      47 ..       6     112 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 9.5e-05
                         AAA_16 27 vllsGesGvGKsslvrellr.alekdggiflrgkcdql 63
                                   ++l+G+ G+GK++ ++++++ +++++++ ++  + ++ 
  gene340|gene340|rna340|rna340 10 LILIGDGGTGKTTYLQRIKEgSFRREYIATIGVDVRDV 47
                                   689****************9666666444433333333 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.2   0.00039      0.35       2      22 ..       7      27 ..       6      32 .. 0.88
   2 ?    1.1   0.0      0.32   2.9e+02      89     142 ..      48     100 ..      34     113 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00039
                         AAA_24  2 klkiliyGpsgiGKTtlakel 22
                                   ++k++++G+ g+GKTt + ++
  gene340|gene340|rna340|rna340  7 QYKLILIGDGGTGKTTYLQRI 27
                                   699*************99887 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.32
                         AAA_24  89 nekaeskedkgdgkGygelaeefrrllkklqelrknvifiahektrkdedpege 142
                                    + k + ++d+++ + ++ +++e+   l++++  +    +i+   t ++++++ e
  gene340|gene340|rna340|rna340  48 TFKTNYNTDISF-QVWDTAGQEMYAQLNDVYYIGASAAIIMFDVTSRITFRNVE 100
                                    555555555444.88999999999999999998886666666656555555544 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00018      0.16      32      62 ..       6      36 ..       3      57 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00018
                          AAA_7 32 nkkpvllvGptGtGKtviikdllkkldkeky 62
                                   n+++++l+G+ GtGKt++++++ +   +++y
  gene340|gene340|rna340|rna340  6 NQYKLILIGDGGTGKTTYLQRIKEGSFRREY 36
                                   578899**************96554443444 PP

>> MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   0.00011       0.1      50      94 ..     111     161 ..      65     164 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00011
                   MMR_HSR1_Xtn  50 egnrvYipclyvlNKiDlisleeldelare......pnsvviSaekelnld 94 
                                    ++n+v ip++++ NKiDl + +  ++  re        +v iSa+++ +++
  gene340|gene340|rna340|rna340 111 TQNNVNIPVIVCGNKIDLKDRKVNQKYIREhlsrdiTCYVDISAKSNHHFE 161
                                    67999*************777766666664444333455559999887765 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00018      0.16       3      21 ..      10      28 ..       8      37 .. 0.90
   2 ?   -3.0   0.0       6.7     6e+03      31      49 ..     158     175 ..     153     183 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00018
                                   EEEEC-TTTCHHHHHHHHH CS
                          NACHT  3 vilqGeaGsGKTtLlqkla 21
                                   +il G+ G GKTt lq++ 
  gene340|gene340|rna340|rna340 10 LILIGDGGTGKTTYLQRIK 28
                                   699**************96 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 6.7
                                    CCC-SEEEEEETTTTTTS- CS
                          NACHT  31 qgafklvFflslrelsrsg 49 
                                    + +f+++F++  r+l+ ++
  gene340|gene340|rna340|rna340 158 H-HFEVPFLVAARKLTGIE 175
                                    3.38888888888887765 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   0.00016      0.14       2      24 ..      10      33 ..       9     105 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00016
                                   EEEE--SSSSHHHHHHHGGGGB.S CS
                          AAA_5  2 vlLvGppGtgKselaerlaaal.n 24
                                   ++L+G+ GtgK++  +r+++   +
  gene340|gene340|rna340|rna340 10 LILIGDGGTGKTTYLQRIKEGSfR 33
                                   89***************9986543 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00025      0.23       2      40 ..      11      56 ..      10     117 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00025
                         AAA_18  2 lltGtpGvGKttlakeLskrlgf........gvnlrdvakengllle 40
                                   +l G  G+GKtt  +++++   f        gv +rdv ++ ++ ++
  gene340|gene340|rna340|rna340 11 ILIGDGGTGKTTYLQRIKEG-SFrreyiatiGVDVRDVTFKTNYNTD 56
                                   78999************665.56788899999999999998877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       568  (0.0316805); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); expected 358.6 (0.02)
Passed Vit filter:                        80  (0.00446204); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.44
# Mc/sec: 1489.25
//
Query:       gene341|gene341|rna341|rna341  [L=352]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-38  131.9   0.0    3.1e-38  131.6   0.0    1.1  1  Dus       Dihydrouridine synthase (Dus)


Domain annotation for each model (and alignments):
>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  131.6   0.0   1.8e-42   3.1e-38       2     238 ..       5     245 ..       4     301 .. 0.83

  Alignments for each domain:
  == domain 1  score: 131.6 bits;  conditional E-value: 1.8e-42
                                    E---TTTS-HHHHHHHHHTT-SSEEEEEEEE-SSS---HHHHHHH-GGGGGTSCEEEEEE-S-HHHHHHHH.HHHHHTT- CS
                            Dus   2 laPmagvtdlpfRelvrefgataLvvtemvtakaivreekvrirmlseeeeetplavQlggsdpallaeaA.klvadlga 80 
                                    laPm  vt+ +fR l+r ++++  ++tem++a+ i+++++++ r    ++    +++Qlggsdp  +  a+ k+  +++ 
  gene341|gene341|rna341|rna341   5 LAPMLKVTTPQFRSLIRIISSDVHLFTEMLSAEYILNNDNYQTRIGAYDP---LTIIQLGGSDPVKISLAVlKIISQTEF 81 
                                    9************************************9887777665554...56*********98887772555569** PP

                                    SCEEEEESSTTEEETTEEEGGGGGGSHHHHHHHHHHHHCCSSS-EEEEEESESSTTTC.HH..HHHHHHHHCT.-SEEEE CS
                            Dus  81 deIdlNvGCPskkvtrggaGaaLlrkpdlvaqivkavvkaveiPvtvkirigiddeeenal..elakiveaaG.aqaltv 157
                                       +lNvGCPs+kvt+g++Ga+L+ k++lv +i+++v + +++ +++k rig+d++  +a+   +++ v  +  +  + +
  gene341|gene341|rna341|rna341  82 RRFNLNVGCPSPKVTKGQFGASLMLKAQLVIDIINEVYNVTNVTLSIKCRIGVDENDSFAFfhGFVEQVASNTkCRDFYI 161
                                    ******************************************************66555542267777655444****** PP

                                    ESS.......ECCCTT-C.G--CHHHHHHHHH-S.S-EEEESS--SHHHHHHHHHHH--SEEEESCHHCCSTTHHHHHHH CS
                            Dus 158 HgR.......traqnyeg.tadweaIkevkqavs.ipviaNGdIkdaedaqaileetGadgvmigrgalgnPwlfaesta 228
                                    H+R       ++++n++   +++e ++++k++++ + +  NG++k + d        G dg+m gr   +n + f+  +a
  gene341|gene341|rna341|rna341 162 HARkcwlkglSPKENRNVpMLNYEFVYALKRKMPfLNIHLNGGVKCLADG------DGLDGIMLGRTVMKNVFAFEDIKA 235
                                    ******************99************************998876......59*************999987444 PP

                                    HHHSC----- CS
                            Dus 229 vktgeaepap 238
                                     ++  +e+++
  gene341|gene341|rna341|rna341 236 RNKAAYENND 245
                                    4444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (352 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       467  (0.0260472); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 2586.19
//
Query:       gene342|gene342|rna342|rna342  [L=47]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (47 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       284  (0.0158403); expected 358.6 (0.02)
Passed bias filter:                      204  (0.0113782); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.29s 00:00:00.67 Elapsed: 00:00:00.46
# Mc/sec: 307.11
//
Query:       gene343|gene343|rna343|rna343  [L=49]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (49 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       334  (0.018629); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.44
# Mc/sec: 331.34
//
Query:       gene344|gene344|rna344|rna344  [L=233]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.7e-34  118.3   5.6    4.5e-34  118.0   5.6    1.1  1  RabGAP-TBC  Rab-GTPase-TBC domain


Domain annotation for each model (and alignments):
>> RabGAP-TBC  Rab-GTPase-TBC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.0   5.6   2.5e-38   4.5e-34      39     215 .]       7     187 ..       1     187 [. 0.86

  Alignments for each domain:
  == domain 1  score: 118.0 bits;  conditional E-value: 2.5e-38
                     RabGAP-TBC  39 ekseeskelsqIkkDvprtfpesesfknkqgqnqLeriLkaysiynpevgYcqGmndivaplllvsldeee....aFwcf 114
                                    + + ++k  +qI+ Dv r  +++   +n +++    +iLk++++++p++gY+qGm d++ pl+ v+ +e      ++ +f
  gene344|gene344|rna344|rna344   7 KIDVDRKVAKQIEIDVDRIPSQHLVYNNISLKFIYVNILKIVAKRRPAIGYVQGMADLLIPLIEVYKNEFFvestVYATF 86 
                                    566778889*********966444445556666667***************************555544334555***** PP

                     RabGAP-TBC 115 vsLlekyklrdlytsslpglkrklkvleellkkkdpklykhlkeegldlelfaikwfltlflrefpletvlrlwD.lll. 192
                                    ++Ll  ++++d+++++++g+ +++k l+++l+ +dp ly h++++gl+l +fa++wf++lf+ref++e+ l  +D +l+ 
  gene344|gene344|rna344|rna344  87 SKLL--DTFQDYFIDGQQGITKAIKKLRRVLQMVDPILYAHITNLGLELHMFAFRWFNCLFVREFKIEYYLLFLDsMLAt 164
                                    ****..*********************************************************************55555 PP

                     RabGAP-TBC 193 egekfvllrvalailklleeell 215
                                     +++ +++++a++++ +l++e+l
  gene344|gene344|rna344|rna344 165 SNYELFVIYFAVSLVVNLRKEIL 187
                                    55588899999999999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (233 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       573  (0.0319594); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1663.06
//
Query:       gene345|gene345|rna345|rna345  [L=118]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       484  (0.0269954); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 959.45
//
Query:       gene346|gene346|rna346|rna346  [L=758]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.029   13.7   0.1      0.057   12.8   0.1    1.4  1  Rtf2      Rtf2 RING-finger


Domain annotation for each model (and alignments):
>> Rtf2  Rtf2 RING-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   3.2e-06     0.057      98     155 ..     597     652 ..     586     673 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.2e-06
                           Rtf2  98 afeeskkdatkdtkeapfiCpltglemngktkfvalrkCGcVfsekalkevksevClv 155
                                    +++++++    + k   fiC +   ++  k k++ l+ CG  + e+ lk++k+ vCl+
  gene346|gene346|rna346|rna346 597 EHSNNESADLLNFKTNIFICEIFTFNIRNKLKYLNLVGCG--LNEENLKTLKKLVCLQ 652
                                    34444445677889999*****999888888888888777..79*********99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (758 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       550  (0.0306766); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.26s 00:00:00.86 Elapsed: 00:00:00.41
# Mc/sec: 5527.06
//
Query:       gene347|gene347|rna347|rna347  [L=423]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (423 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1159  (0.0646439); expected 358.6 (0.02)
Passed bias filter:                      556  (0.0310112); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.39
# Mc/sec: 3242.84
//
Query:       gene348|gene348|rna348|rna348  [L=61]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       345  (0.0192426); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.22s 00:00:00.56 Elapsed: 00:00:00.38
# Mc/sec: 480.44
//
Query:       gene349|gene349|rna349|rna349  [L=427]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (427 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1726  (0.0962686); expected 358.6 (0.02)
Passed bias filter:                      625  (0.0348597); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 2996.11
//
Query:       gene35|gene35|rna35|rna35  [L=183]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      3e-12   46.5   0.0      1e-05   25.6   0.0    2.3  2  Myb_DNA-binding  Myb-like DNA-binding domain
    5.5e-10   39.3   0.0    2.1e-06   27.9   0.0    2.5  2  Myb_DNA-bind_6   Myb-like DNA-binding domain
     0.0011   18.9   0.3      0.074   13.1   0.0    3.1  3  SLIDE            SLIDE


Domain annotation for each model (and alignments):
>> Myb_DNA-binding  Myb-like DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.0   1.7e-09     1e-05       2      43 ..       2      43 ..       1      46 [. 0.94
   2 !   18.9   0.0   2.1e-07    0.0013       1      40 [.      48      86 ..      48      90 .. 0.87

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 1.7e-09
                               SSSBHHHHHHHHHHHHHHT.TCHHHHHHHHTSS-HHHHHHHHH CS
            Myb_DNA-binding  2 gkWteeEdelLleavkkhG.nrWkkIaerlggRtekqcrsrwr 43
                                kWt  Ed++Ll a +k+G +   kI+  l +R++ +c  r++
  gene35|gene35|rna35|rna35  2 VKWTSSEDKILLLAAQKYGlSHLHKISTLL-SRSPSACCARYN 43
                               59****************************.8******99998 PP

  == domain 2  score: 18.9 bits;  conditional E-value: 2.1e-07
                               CSSSBHHHHHHHHHHHHHHTTCHHHHHHHHTSS-HHHHHH CS
            Myb_DNA-binding  1 rgkWteeEdelLleavkkhGnrWkkIaerlggRtekqcrs 40
                               +++Wt   d++L+++ +k+ n++++Ia+ +g  t+ ++++
  gene35|gene35|rna35|rna35 48 KKEWTRSSDLQLIKYARKMPNQFNSIASLMG-TTAAHVQE 86
                               689***************************7.56666655 PP

>> Myb_DNA-bind_6  Myb-like DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   0.0   3.6e-10   2.1e-06       1      60 []       4      59 ..       4      59 .. 0.91
   2 !   12.1   0.0     3e-05      0.18       1      38 [.      51      87 ..      51      90 .. 0.95

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 3.6e-10
             Myb_DNA-bind_6  1 WteeEdeiLlklvekyg.ndWknIaealnrRtpkqcfdrwknkLrpkisrkkwskeedirL 60
                               Wt  Ed+iLl   +kyg +  ++I++ l+ R+p++c  r++  L    ++k+w+++ d +L
  gene35|gene35|rna35|rna35  4 WTSSEDKILLLAAQKYGlSHLHKISTLLS-RSPSACCARYNH-L---TRKKEWTRSSDLQL 59
                               *****************669*********.***********9.8...56899999887665 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 3e-05
             Myb_DNA-bind_6  1 WteeEdeiLlklvekygndWknIaealnrRtpkqcfdr 38
                               Wt   d  L+k+ +k+ n++++Ia+ ++  t+ ++++r
  gene35|gene35|rna35|rna35 51 WTRSSDLQLIKYARKMPNQFNSIASLMG-TTAAHVQER 87
                               9999999********************9.999999998 PP

>> SLIDE  SLIDE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.0   1.2e-05     0.074      51      83 ..       3      35 ..       1      38 [. 0.91
   2 ?    1.5   0.0     0.048   2.9e+02      75     108 ..      60      93 ..      44      96 .. 0.63
   3 ?   -0.7   0.0      0.23   1.4e+03      68      86 ..      97     115 ..      87     126 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.2e-05
                      SLIDE 51 eyteeeDrfllvllakyGygnyekikkeiresp 83
                               ++t+ eD++ll + +kyG+++ +ki   + +sp
  gene35|gene35|rna35|rna35  3 KWTSSEDKILLLAAQKYGLSHLHKISTLLSRSP 35
                               599**********************99888877 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.048
                      SLIDE  75 ikkeiresplFrfDwflksrtpqelqkRcetLlk 108
                                ik + +  ++F+    l+  t++ +q+R++ L+k
  gene35|gene35|rna35|rna35  60 IKYARKMPNQFNSIASLMGTTAAHVQERLDLLVK 93 
                                4444444455555556677788888888888876 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.23
                      SLIDE  68 GygnyekikkeiresplFr 86 
                                   +y++++++i + ++++
  gene35|gene35|rna35|rna35  97 DAFRYDELRENIHDGEEYK 115
                                3345999999999888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       619  (0.0345251); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1299.40
//
Query:       gene350|gene350|rna350|rna350  [L=351]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.014   15.9   0.4      0.039   14.4   0.1    1.8  2  DUF1690   Protein of Unknown function (DUF1690)
      0.032   13.2   0.3        1.6    7.6   0.1    2.4  2  PORR      Plant organelle RNA recognition domain
      0.086   12.7   0.0       0.12   12.2   0.0    1.2  1  FdhE      Protein involved in formate dehydrogenase formation


Domain annotation for each model (and alignments):
>> DUF1690  Protein of Unknown function (DUF1690)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.1   6.5e-06     0.039      18      69 ..     113     164 ..     108     181 .. 0.76
   2 ?   -2.1   0.0      0.78   4.7e+03      43      43 ..     327     327 ..     270     345 .. 0.62

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 6.5e-06
                        DUF1690  18 essketdasraqalekliqerVaeeLkkLraeeeetlkkfeeklekellkde 69 
                                    ++  et+++r +++++li+e Va++L+kL a++++ l++++++  k+++++ 
  gene350|gene350|rna350|rna350 113 SDIIETSFERGKEVNELIKEMVADRLEKLPASNNSSLSQLSSASPKASNSSL 164
                                    5567999**********************99999999988877665555444 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.78
                        DUF1690  43 L 43 
                                    L
  gene350|gene350|rna350|rna350 327 L 327
                                    2 PP

>> PORR  Plant organelle RNA recognition domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0    0.0059        35     260     297 ..      20      58 ..       3      62 .. 0.73
   2 ?    7.6   0.1   0.00027       1.6     254     285 ..      66      97 ..      60     117 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.0059
                           PORR 260 hlrkelglpqklrklllrhpgiFYl.stkgkthtVfLrE 297
                                     lr+++ l++k  +l+ +   iF + s  g++ht +L+E
  gene350|gene350|rna350|rna350  20 VLRNDIDLTKKHADLIGKGVAIFNVhSGDGNQHTFVLTE 58 
                                    488899999999999999999999856678889988887 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.00027
                           PORR 254 eveklshlrkelglpqklrklllrhpgiFYls 285
                                     +++ ++lrk + l q+ +++ll+   iFY s
  gene350|gene350|rna350|rna350  66 YLDEWAELRKTFMLYQRSQDALLKSFDIFYES 97 
                                    5677789***********************66 PP

>> FdhE  Protein involved in formate dehydrogenase formation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0     2e-05      0.12      57     161 ..      99     205 ..      59     240 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2e-05
                                    --HHHHHHHHHTT--TT-HHHHHHH-TTHHHHHHHHHT--S-SSHHHHHHHHHHHH--HHHHHHHHHHHHTT-GGGS-GG CS
                           FdhE  57 ldaeaieraqehgmpplaakalerdeawqelLqallealkeelpealrealerlrkadaeelealadallageleavdaa 136
                                    ++ ++ + ++ h+m  + ++++er ++++el+++++++  e+lp++ ++ l++l++a++++ ++ +++   ++  +++  
  gene350|gene350|rna350|rna350  99 IHSNKKSFKTGHNMSDIIETSFERGKEVNELIKEMVADRLEKLPASNNSSLSQLSSASPKASNSSLNSSTPQKKPQKTIT 178
                                    44444556788999*********************************************999999888777766655443 PP

                                    G..HHHHHHHHHHHHHHHHHT--TTSS CS
                           FdhE 137 k..avfvaaAlqvvwtklaaaldakal 161
                                    +   +f    + v +++ a++ +++++
  gene350|gene350|rna350|rna350 179 TpgRPFTDSKIPVPCSHKAQKTPTTQR 205
                                    322677777777777777777766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (351 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       873  (0.0486921); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 2441.31
//
Query:       gene351|gene351|rna351|rna351  [L=697]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
     0.0003   20.8   0.0     0.0003   20.8   0.0    3.0  3  RIFIN       Rifin
     0.0041   17.4   3.0     0.0041   17.4   3.0    4.7  4  Orf78       Orf78 (ac78)
  ------ inclusion threshold ------
      0.027   14.4   0.9      0.027   14.4   0.9    3.5  4  LRRC37AB_C  LRRC37A/B like protein 1 C-terminal domain
      0.054   13.4   0.3      0.054   13.4   0.3    3.4  3  TMEM154     TMEM154 protein family
      0.055   13.5   0.2      0.055   13.5   0.2    3.3  3  DUF4366     Domain of unknown function (DUF4366)
       0.19   12.3   0.1       0.19   12.3   0.1    3.2  4  Renin_r     Renin receptor-like protein


Domain annotation for each model (and alignments):
>> RIFIN  Rifin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.2       1.1   3.2e+03     235     254 ..      76      95 ..      27     126 .. 0.39
   2 ?   -5.7  10.6         6   1.8e+04     181     256 ..     331     408 ..     257     432 .. 0.46
   3 !   20.8   0.0     1e-07    0.0003     217     301 ..     611     695 ..     575     696 .. 0.75

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.1
                          RIFIN 235 vekivekaekkaaaaaaeaa 254
                                    ++ + +k ++ a+++++e++
  gene351|gene351|rna351|rna351  76 IKGADAKNQSPANDNNQEES 95 
                                    11111122222211111111 PP

  == domain 2  score: -5.7 bits;  conditional E-value: 6
                          RIFIN 181 tatnyknvtslvkaikee..yeescllklkkskaaltsakekekkeasskekikkkvekivekaekkaaaaaaeaaae 256
                                    + +n++ + + + +++ +   +e+   + k+++a +++++ + k+++++++ i++++++  ++ +kk +++++++a++
  gene351|gene351|rna351|rna351 331 NLNNFEAHPTDIPIVSVTevSTEKNDEQPKEKNASQSISRPQDKNHHHDEQIIQNDTSESFDNDTKKIESTTDDNASS 408
                                    223333322222222211001111222333333333444444444445555555555555554444444444433322 PP

  == domain 3  score: 20.8 bits;  conditional E-value: 1e-07
                          RIFIN 217 akekekkeasskekikkkvekivekaekkaaaaaaeaaaeataeaekaetaaveattaslqtaiiasivaivvIvLimvI 296
                                     ++ ++++ +s++  + + +k+++k +kk+++++++++++ +++  + +t+a+++ +++ +++i    ++ v+  ++ vI
  gene351|gene351|rna351|rna351 611 FRNDQRSNDNSNHHHEARGHKTQHKNQKKNTTDKSSTTDQDKTSQSNGSTKATKSNSKKNYNTILFLTITTVICLVVGVI 690
                                    33344444455555555566666666677777777777778888888899999******************99999**** PP

                          RIFIN 297 IYLiL 301
                                    +YLi+
  gene351|gene351|rna351|rna351 691 VYLII 695
                                    ***95 PP

>> Orf78  Orf78 (ac78)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.4      0.26   7.8e+02      27      39 ..      84      96 ..      50     133 .. 0.58
   2 ?   -1.2   1.1      0.87   2.6e+03      32      60 ..     294     322 ..     283     335 .. 0.54
   3 ?   -5.0   6.2         6   1.8e+04      55      55 ..     380     380 ..     330     443 .. 0.64
   4 !   17.4   3.0   1.4e-06    0.0041      29      88 ..     638     695 ..     611     697 .] 0.47

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.26
                          Orf78 27 dnddndkaenkke 39
                                   ++++nd++++++ 
  gene351|gene351|rna351|rna351 84 QSPANDNNQEESI 96
                                   2222222222211 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.87
                          Orf78  32 dkaenkkekksaaeknditekesnaaeka 60 
                                    ++  ++k+k ++++++di++++s++ e++
  gene351|gene351|rna351|rna351 294 QNRGSAKQKVNMETSEDIRKESSKEDEQQ 322
                                    33334444455555555555555533332 PP

  == domain 3  score: -5.0 bits;  conditional E-value: 6
                          Orf78  55 n 55 
                                    +
  gene351|gene351|rna351|rna351 380 E 380
                                    1 PP

  == domain 4  score: 17.4 bits;  conditional E-value: 1.4e-06
                          Orf78  29 ddndkaenkkekksaaeknditekesn.......aaekaqalnillisllavvcvlvllyviyYfvi 88 
                                    ++n++++++++++++++++       n       +++k++  +il++++ +v+c++  + vi+Y +i
  gene351|gene351|rna351|rna351 638 KKNTTDKSSTTDQDKTSQS-------NgstkatkSNSKKNYNTILFLTITTVICLV--VGVIVYLII 695
                                    1111111222222222222.......022333323445554455555555555554..455566655 PP

>> LRRC37AB_C  LRRC37A/B like protein 1 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.1       1.8   5.4e+03      81     101 ..      88     107 ..      73     129 .. 0.50
   2 ?   -2.1   3.8       1.1   3.2e+03      57      98 ..     284     325 ..     278     353 .. 0.64
   3 ?   -1.7   1.7      0.84   2.5e+03      73      95 ..     371     393 ..     345     423 .. 0.55
   4 ?   14.4   0.9   9.2e-06     0.027      70     134 ..     629     692 ..     614     696 .. 0.59

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.8
                     LRRC37AB_C  81 tetyinesteaqseqkeqksk 101
                                    ++++ +es  a+s+ +e  ++
  gene351|gene351|rna351|rna351  88 NDNNQEESISASSAYQEV-AN 107
                                    223333333333333332.22 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.1
                     LRRC37AB_C  57 LmkLlseqqevkvskaewdtdqwktetyinesteaqseqkeq 98 
                                    Lm  l e ++ +  +a++  +   +e+  +es++++++q+  
  gene351|gene351|rna351|rna351 284 LMEKLHEFEKQNRGSAKQKVNMETSEDIRKESSKEDEQQQGI 325
                                    676777777777777777777777777766665544444432 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 0.84
                     LRRC37AB_C  73 ewdtdqwktetyinesteaqseq 95 
                                     +d ++ ++e+ i+++t ++ ++
  gene351|gene351|rna351|rna351 371 PQDKNHHHDEQIIQNDTSESFDN 393
                                    33444444444444433333333 PP

  == domain 4  score: 14.4 bits;  conditional E-value: 9.2e-06
                     LRRC37AB_C  70 skaewdtdqwktetyinesteaqseqkeqkskeltkevpeygynnklilaisvtvvvmiliiilc 134
                                     ++++  +q k+ t  +  t+++++ +++ s++ tk  ++ +yn  l l+i+ +  +++  +i+ 
  gene351|gene351|rna351|rna351 629 GHKTQHKNQKKNTTDKSSTTDQDKTSQSNGSTKATKSNSKKNYNTILFLTITTVICLVVG-VIVY 692
                                    33444444555544444445555555566899999*9******99888877644433333.3333 PP

>> TMEM154  TMEM154 protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.4      0.44   1.3e+03      23      58 ..     300     334 ..     289     350 .. 0.70
   2 ?   -2.6   5.4       1.5   4.6e+03       5      55 ..     361     409 ..     352     420 .. 0.67
   3 ?   13.4   0.3   1.8e-05     0.054       2      80 ..     618     695 ..     614     697 .] 0.69

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.44
                        TMEM154  23 datsaasteseslkqeeakeslssaelsnesdqlel 58 
                                    +  +   t se +++e +ke ++++ ++ +sd+l++
  gene351|gene351|rna351|rna351 300 KQKVNMET-SEDIRKESSKEDEQQQGIQHKSDNLNN 334
                                    44444444.666667778888888888888888776 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.5
                        TMEM154   5 eksgdtaletatleeesadatsaasteseslk.....qeeakeslssaelsnesdq 55 
                                    ek+++ +++  + +++  d  ++++ +ses++              s+  +n s++
  gene351|gene351|rna351|rna351 361 EKNASQSISRPQDKNHHHDEQIIQNDTSESFDndtkkI-------ESTTDDNASSD 409
                                    788888888888888889999999999****9333221.......23333333333 PP

  == domain 3  score: 13.4 bits;  conditional E-value: 1.8e-05
                        TMEM154   2 eeseksgdtaletatleeesadatsaasteseslkqeeakeslssaelsnesdqlelvlmiiiPlvllillllvviili 80 
                                    ++ ++  + a   +t +++  + t+ +s++++  k+++++ s++    sn + + + +l + i  v+ +++ ++v ++i
  gene351|gene351|rna351|rna351 618 NDNSNHHHEARGHKTQHKNQKKNTTDKSSTTDQDKTSQSNGSTKA-TKSNSKKNYNTILFLTITTVICLVVGVIVYLII 695
                                    566677777777777777777777777776666665555555544.446777778889999999988888888887776 PP

>> DUF4366  Domain of unknown function (DUF4366)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.5       2.6   7.9e+03      92     100 ..      85      93 ..      41     119 .. 0.52
   2 ?   -7.1  10.5         6   1.8e+04      52      95 ..     277     347 ..     266     440 .. 0.61
   3 ?   13.5   0.2   1.8e-05     0.055      73     140 ..     627     695 ..     614     697 .] 0.43

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 2.6
                        DUF4366  92 cpveepepe 100
                                    +p +  ++e
  gene351|gene351|rna351|rna351  85 SPANDNNQE 93 
                                    222111111 PP

  == domain 2  score: -7.1 bits;  conditional E-value: 6
                        DUF4366  52 nqVdeaDLlalleedeeaakeeeev.cactekcaagkvntdcpv.............................e 95 
                                    n+ de+ L++ l e e+++  + ++ ++++   + +++ ++++                              +
  gene351|gene351|rna351|rna351 277 NLCDEQPLMEKLHEFEKQNRGSAKQkVNME---TSEDIRKESSKedeqqqgiqhksdnlnnfeahptdipivsV 347
                                    666666666655333332222222202211...12222222222223334444444445555544444444430 PP

  == domain 3  score: 13.5 bits;  conditional E-value: 1.8e-05
                        DUF4366  73 eeevcactekcaagkvntdcpveepepekeaepee...peeepekksnnglllvvlavaligggaayyfkv 140
                                    +   +++  +++++k  td + +++++++++++ +   ++++++k+ n++l l ++ v+ + +g ++y+ +
  gene351|gene351|rna351|rna351 627 ARGHKTQ--HKNQKKNTTDKSSTTDQDKTSQSNGStkaTKSNSKKNYNTILFLTITTVICLVVGVIVYLII 695
                                    2222223..33333333333335555554444443433444445555555555555555555565555554 PP

>> Renin_r  Renin receptor-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       3.4     1e+04      28      79 ..      97     149 ..      77     153 .. 0.51
   2 ?   -1.8   0.1       1.7   5.1e+03      13      34 ..     305     326 ..     291     351 .. 0.50
   3 ?   -0.9   0.8      0.87   2.6e+03       8      39 ..     348     379 ..     342     423 .. 0.64
   4 ?   12.3   0.1   6.4e-05      0.19      13      72 ..     633     692 ..     617     696 .. 0.60

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 3.4
                        Renin_r  28 leakeakdkke.kklnlakkyssdYpaiFniiLwlvvvlvlaliaivvalasm 79 
                                     ++++ ++ ++ ++ ++ ++ s+ Y     i+L  + +l+l  +  v+ + ++
  gene351|gene351|rna351|rna351  97 SASSAYQEVANeHQAQIPDPQSEIYFFQRGILLTASRILLLDSLNEVFDIDNI 149
                                    22222222222136666666666666666666666666666655555555555 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.7
                        Renin_r  13 vkaeekikkrkkrsileakeak 34 
                                    ++++e i+k ++++  +++ ++
  gene351|gene351|rna351|rna351 305 METSEDIRKESSKEDEQQQGIQ 326
                                    2333323222222222222222 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 0.87
                        Renin_r   8 velltvkaeekikkrkkrsileakeakdkkek 39 
                                     e+ t+k++e+ k +++++++++ + k+++++
  gene351|gene351|rna351|rna351 348 TEVSTEKNDEQPKEKNASQSISRPQDKNHHHD 379
                                    45666666666665555555554444443332 PP

  == domain 4  score: 12.3 bits;  conditional E-value: 6.4e-05
                        Renin_r  13 vkaeekikkrkkrsileakeakdkkekklnlakkyssdYpaiFniiLwlvvvlvlaliai 72 
                                    +++++k ++ +k+s+++++++++++ ++   +++ +++Y  i  + +  v++lv+ +i+ 
  gene351|gene351|rna351|rna351 633 QHKNQKKNTTDKSSTTDQDKTSQSNGSTKATKSNSKKNYNTILFLTITTVICLVVGVIVY 692
                                    222233333333333333333333333555667788999999999999999999888764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (697 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2259  (0.125997); expected 358.6 (0.02)
Passed bias filter:                      558  (0.0311228); expected 358.6 (0.02)
Passed Vit filter:                       103  (0.00574488); expected 17.9 (0.001)
Passed Fwd filter:                        38  (0.00211947); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 1.11u 0.34s 00:00:01.45 Elapsed: 00:00:00.54
# Mc/sec: 3918.36
//
Query:       gene352|gene352|rna352|rna352  [L=773]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-35  122.5  17.7    1.8e-22   79.8   4.8    3.3  3  DEAD_2         DEAD_2
    9.5e-33  113.8   0.0      4e-32  111.7   0.0    2.2  1  Helicase_C_2   Helicase C-terminal domain
    7.1e-09   35.9   0.5     0.0035   17.4   0.0    2.9  3  ResIII         Type III restriction enzyme, res subunit
     0.0016   18.3   0.0      0.066   13.0   0.0    2.7  2  DEAD           DEAD/DEAH box helicase
     0.0025   17.3   0.3        1.8    7.9   0.0    2.8  3  PhoH           PhoH-like protein
  ------ inclusion threshold ------
      0.024   14.4   2.8      0.021   14.6   1.0    1.8  2  AAA_11         AAA domain
      0.025   14.5   0.1       0.15   12.0   0.0    2.3  2  Hydrophobin_2  Fungal hydrophobin
       0.13   11.3   0.0       0.26   10.3   0.0    1.4  1  T2SSE          Type II/IV secretion system protein


Domain annotation for each model (and alignments):
>> DEAD_2  DEAD_2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.0       4.1   9.3e+03      66      82 ..      14      30 ..       7      53 .. 0.49
   2 !   47.2   4.6     8e-16   1.8e-12       1      81 [.     110     179 ..     110     215 .. 0.82
   3 !   79.8   4.8   7.9e-26   1.8e-22      75     174 ..     271     366 ..     196     368 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 4.1
                                   HHCCHTTTTTT-SCCCC CS
                         DEAD_2 66 kaeekeekCsffenlee 82
                                   +++ ++++C f+ +  +
  gene352|gene352|rna352|rna352 14 EQRGTKSTCYFYPHPMR 30
                                   33445788998866522 PP

  == domain 2  score: 47.2 bits;  conditional E-value: 8e-16
                                    EEESSHHHHHHHHHHHHHHHHHCHHHS---EEEE--CCCC-SCHHCCCHHCCCCHHHHHHHHHCCHHCCHTTTTTT-SCC CS
                         DEAD_2   1 ycsRThsqleqvvkelkklesykkkkekvkvviLgSRknlCineevkkekkekavneaCkelkkkkaeekeekCsffenl 80 
                                    ycsRThsql+q+v+elk+l+ +       ++v+LgSR  +C +++v+   + + +ne+C+el++k       kC++f nl
  gene352|gene352|rna352|rna352 110 YCSRTHSQLNQAVNELKRLK-V-----ACNAVVLGSRMLYCKQPSVNALDNLEMMNERCRELREKD------KCEYFINL 177
                                    9*****************94.3.....468*********************************999......69998777 PP

                                    .C CS
                         DEAD_2  81 .e 81 
                                      
  gene352|gene352|rna352|rna352 178 nG 179
                                    42 PP

  == domain 3  score: 79.8 bits;  conditional E-value: 7.9e-26
                                    TT-SCCCCHHHHHHHHHHC---CHHHHHHHHHCT--HHHHHHHHHCCTSEEEEEHHHHTSCCCHHHHHT..GCGCEEEEC CS
                         DEAD_2  75 sffenleelkklkkllleevvdiedlvelgeklklCPYylsrelledadiiilpYqyLldekireslkgislknsivilD 154
                                    + ++++ ++ +++++ +++++diedl++  +++++CPYy s++l ++a i +lpYq+L+++ +r+s+k + ++nsi+i+D
  gene352|gene352|rna352|rna352 271 NLYKTV-TSLSTSSFKNDGIYDIEDLKN--SNCNFCPYYKSKQLSKSASITFLPYQMLFSKDARDSFK-LPISNSIIIID 346
                                    455455.34445789999********96..689**********************************9.9********** PP

                                    TCCCHHHHHHHCC-EEEECH CS
                         DEAD_2 155 EAhNiedvceeaasveisee 174
                                    EAhNi + +++++s++++ +
  gene352|gene352|rna352|rna352 347 EAHNIYESVIQMNSASVNYH 366
                                    ***************99865 PP

>> Helicase_C_2  Helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.7   0.0   1.8e-35     4e-32       6     170 ..     606     751 ..     601     752 .. 0.87

  Alignments for each domain:
  == domain 1  score: 111.7 bits;  conditional E-value: 1.8e-35
                   Helicase_C_2   6 evvpggvlvffpSyklleevverlkeeleskkieifveekeesrekvleeykekkkkgaillavcrGklsEGidfsddll 85 
                                    + ++gg+++f pS ++l+ v+er++++ +s+   if++      e++ +e +    k+ +l+av++G+lsEGi++sd+ +
  gene352|gene352|rna352|rna352 606 RNTHGGIVCFLPSKNFLKIVRERFDSKRNSDVSYIFDN-----LEQFTKECSV---KTTVLFAVMGGRLSEGINYSDHFC 677
                                    6789**********************988777777776.....5666666665...************************ PP

                   Helicase_C_2  86 raviivglPfpnpkdpeveakreyldekgkknsgkewylpealravnQaiGRliRhkdDygaivllDeRfakeeireklp 165
                                    r++iivg+Pfp+++  e++++ +          g+++ +  al++vnQa+GR++Rhk+D++ ivl+DeR+ k  +++ l+
  gene352|gene352|rna352|rna352 678 RLLIIVGIPFPSLN-VELRERIK--------FHGQDYTTVIALKTVNQALGRALRHKNDHSGIVLIDERYGK--LQHLLS 746
                                    ***********994.44444433........4588************************************9..669999 PP

                   Helicase_C_2 166 kwlre 170
                                     w+re
  gene352|gene352|rna352|rna352 747 PWIRE 751
                                    99987 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   1.6e-06    0.0035       3      50 ..      35      80 ..      33     102 .. 0.84
   2 !   15.7   0.1     5e-06     0.011      96     160 ..     299     375 ..     263     388 .. 0.70
   3 ?   -3.7   0.0       4.6     1e+04     112     140 ..     712     736 ..     696     737 .. 0.65

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.6e-06
                                   EE-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S CS
                         ResIII  3 elreyQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllk 50
                                   +l++ Q++ i++  +++  ++++ +++  +TGtGKTl ++  +  + +
  gene352|gene352|rna352|rna352 35 TLYDSQKDFIQKAQQTI--ENNQTAIFSSPTGTGKTLSLLLSVVPYIE 80
                                   68999*********999..59999************988655555544 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 5e-06
                                    -...............-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.....T....TTHHHHHT--- CS
                         ResIII  96 a........kekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgak....k....swreilekfke 159
                                    +        +++ s++++i++  +q+l ++       +  +l+ ++ +iiiDEaH+++++    +    ++  +++++k+
  gene352|gene352|rna352|rna352 299 NcnfcpyykSKQLSKSASITFLPYQMLFSKD----ARDSFKLPISNSIIIIDEAHNIYESviqmNsasvNYHLLKKYIKA 374
                                    13335666667788999************99....566666777778************655441555677777777776 PP

                                    S CS
                         ResIII 160 a 160
                                    +
  gene352|gene352|rna352|rna352 375 F 375
                                    3 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 4.6
                                    HHHHHTH........HHHTTT-SEEEEET CS
                         ResIII 112 qsldadseeeeeeseellrdrfdviiiDE 140
                                    +++++++        + ++d++ +++iDE
  gene352|gene352|rna352|rna352 712 KTVNQAL----GRALRHKNDHSGIVLIDE 736
                                    4444444....455666777777999998 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.0     3e-05     0.066       6      71 ..      46     129 ..      37     175 .. 0.69
   2 ?    2.2   0.0     0.058   1.3e+02     123     137 ..     341     355 ..     306     392 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3e-05
                                    HHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHS..................TTSTS-EEEEEESSHHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..................xxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD   6 eaiplilgggdvlvaaeTGsGKTlaflipvlqivyet..................kgktgpkalivePtreLaeqtlnnl 67 
                                    +a ++i +++  + + +TG+GKTl  l+ v+  + ++                   + +++ + + + t++  +q +n+l
  gene352|gene352|rna352|rna352  46 KAQQTIENNQTAIFSSPTGTGKTLSLLLSVVPYIEKNvvhdfsgvsaankalineLNFNNTPIYYCSRTHSQLNQAVNEL 125
                                    344566688999*****************998885446666665555555555443444455555555555666666666 PP

                                    HHHT CS
                                    xxxx RF
                           DEAD  68 kkfk 71 
                                    k++k
  gene352|gene352|rna352|rna352 126 KRLK 129
                                    6555 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.058
                                    EEEEEETHHHHHHTT CS
                                    xxxxxxxxxxxxxxx RF
                           DEAD 123 rflVlDEadrlldqg 137
                                    +++++DEa+++ ++ 
  gene352|gene352|rna352|rna352 341 SIIIIDEAHNIYESV 355
                                    589******998774 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.0   0.00082       1.8      11      45 ..      46      80 ..      36      95 .. 0.73
   2 ?   -2.4   0.0       1.2   2.8e+03     138     178 ..     123     165 ..     116     193 .. 0.60
   3 !    6.2   0.1    0.0027       6.1     118     138 ..     338     358 ..     336     362 .. 0.91

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00082
                                   HHHHHHHH-SEEEEE--TTSSTTHHHHHHHHHHHH CS
                           PhoH 11 eylealkkndivfaiGpaGtGKtylavalavealk 45
                                   ++ +++++n+  +   p+GtGKt+  +   v +++
  gene352|gene352|rna352|rna352 46 KAQQTIENNQTAIFSSPTGTGKTLSLLLSVVPYIE 80
                                   344677799999***********865555555554 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.2
                                    HHHTTB-TT-EEEEEE---.-----.------THHHHHHTTT- CS
                           PhoH 138 mfltRlGenskvvvtGdvt.qidlp.kgkksGlaealevlknv 178
                                      l Rl   + +vv+G+   ++++p ++  + l+ + e++++ 
  gene352|gene352|rna352|rna352 123 NELKRLKVACNAVVLGSRMlYCKQPsVNALDNLEMMNERCREL 165
                                    5578999999999999854155555555666666666655543 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.0027
                                    B-SEEEEE-SGGG--HHHHHH CS
                           PhoH 118 lndafvilDEAQnttkeqmkm 138
                                    ++++++i+DEA n+ ++ ++m
  gene352|gene352|rna352|rna352 338 ISNSIIIIDEAHNIYESVIQM 358
                                    689***********9999988 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   1.0   9.4e-06     0.021       3     184 ..      37     240 ..      35     287 .. 0.47
   2 ?   -2.9   0.0       2.1   4.8e+03     219     226 ..     341     348 ..     329     354 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 9.4e-06
                         AAA_11   3 ndsqreai...ksalseseitliqGPPGtgKT.ktivellsqll................srrkseeeksakpriLvCap 62 
                                     dsq++ i   ++++++++ ++++ P GtgKT + +++++ ++                      +e + ++  i +C+ 
  gene352|gene352|rna352|rna352  37 YDSQKDFIqkaQQTIENNQTAIFSSPTGTGKTlSLLLSVVPYIEknvvhdfsgvsaankaL---INELNFNNTPIYYCSR 113
                                    689999994445556666699***********97777777777644445555544443330...4445556666666666 PP

                         AAA_11  63 SNaAvDellerllrglldsegekykpkivRvgnee..............eriseavksvsleekvekrlekee....... 121
                                    ++   ++ +  l r        k   + v +g+                e ++e+ +++             +       
  gene352|gene352|rna352|rna352 114 THSQLNQAVNELKR-------LKVACNAVVLGSRMlyckqpsvnaldnlEMMNERCREL-------------Rekdkcey 173
                                    66666666666666.......33344444444444433211122211111222222222.............12223444 PP

                         AAA_11 122 ......................kaqlakeiskeleklakelrafeeeeekeklkkskekskskleqerrklkkerkelsk 179
                                                          +                  +++ ++ e++ +k+s   +k+ + ++r++ + +++++s+
  gene352|gene352|rna352|rna352 174 finlngefdiirsefddhvlshN------------------NERIAKVEDNHVKYSTFCKKEAEPRKREDDSTSKRSFSQ 235
                                    44333333222222222211111..................111111111111111111111122222222222222333 PP

                         AAA_11 180 eleea 184
                                    ++ e+
  gene352|gene352|rna352|rna352 236 NIAEH 240
                                    33222 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 2.1
                         AAA_11 219 dvviIDEA 226
                                     ++iIDEA
  gene352|gene352|rna352|rna352 341 SIIIIDEA 348
                                    689****9 PP

>> Hydrophobin_2  Fungal hydrophobin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   6.8e-05      0.15      10      50 ..     130     171 ..     123     179 .. 0.89
   2 ?   -2.0   0.0       1.6   3.6e+03      15      29 ..     414     428 ..     411     436 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 6.8e-05
                  Hydrophobin_2  10 qcCatdvlgvadldCatpsk.tptsaaefkaiCaasgqqakC 50 
                                      C++ vlg   l C++ps  + ++++ +++ C + +++ kC
  gene352|gene352|rna352|rna352 130 VACNAVVLGSRMLYCKQPSVnALDNLEMMNERCRELREKDKC 171
                                    67****************9747789999************99 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.6
                  Hydrophobin_2  15 dvlgvadldCatpsk 29 
                                    d+lg++d  C++ +k
  gene352|gene352|rna352|rna352 414 DILGLLDDFCENNKK 428
                                    89********99876 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00011      0.26     111     154 ..      40      77 ..      23      86 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00011
                          T2SSE 111 eealkekiaevlrkavrerglilvsGgTgsGKttllyallkein 154
                                    ++++ +k     ++ ++++++ ++s +Tg+GKt +l  ll+ ++
  gene352|gene352|rna352|rna352  40 QKDFIQKA----QQTIENNQTAIFSSPTGTGKTLSL--LLSVVP 77 
                                    33333333....3445667999***********987..333343 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (773 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       864  (0.0481901); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.70u 0.27s 00:00:00.97 Elapsed: 00:00:00.46
# Mc/sec: 5079.33
//
Query:       gene353|gene353|rna353|rna353  [L=1177]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1111  (0.0619666); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.76u 0.31s 00:00:01.07 Elapsed: 00:00:00.46
# Mc/sec: 7618.88
//
Query:       gene354|gene354|rna354|rna354  [L=296]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-60  205.1   0.5    1.4e-60  204.9   0.5    1.0  1  Pkinase         Protein kinase domain
    9.8e-33  113.5   0.1    1.4e-32  113.0   0.1    1.4  1  Pkinase_Tyr     Protein tyrosine kinase
    4.6e-05   22.9   0.2    7.8e-05   22.1   0.2    1.4  1  Kdo             Lipopolysaccharide kinase (Kdo/WaaP) family
    0.00028   20.9   0.0       0.59   10.0   0.0    2.2  2  APH             Phosphotransferase enzyme family
    0.00062   19.4   0.2      0.001   18.7   0.2    1.3  1  RIO1            RIO1 family
    0.00096   18.5   0.0     0.0015   18.0   0.0    1.4  1  Kinase-like     Kinase-like
  ------ inclusion threshold ------
      0.099   11.4   0.2         11    4.6   0.2    2.1  2  Pkinase_fungal  Fungal protein kinase
       0.11   12.1   0.4        1.2    8.7   0.1    2.2  2  FTA2            Kinetochore Sim4 complex subunit FTA2


Domain annotation for each model (and alignments):
>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  204.9   0.5   6.2e-64   1.4e-60       1     264 []      15     291 ..      15     291 .. 0.84

  Alignments for each domain:
  == domain 1  score: 204.9 bits;  conditional E-value: 6.2e-64
                                    EEEEEEEEEESSEEEEEEEETTTTEEEEEEEEECHCHCHHHH..HHHHHHHHHHHHHSCTTB--EEEE.EEESSEEEEEE CS
                        Pkinase   1 yekleklGeGsfGkVykaveketgkivAvKkikkekakkkke..kkvlrEikilkklkhpnivrlyev.feekdelylvl 77 
                                    y+ ++k+ +Gs+++Vy a+  +++k +A+Kk      ++ ++   +  +Ei+ilk+l+hpn+++l ++ +e+++++ylvl
  gene354|gene354|rna354|rna354  15 YVIQKKISSGSSATVYLAT--KDEKFYAIKKPYILTFSDPNNvrLSSENEISILKELRHPNVINLHDIvWENNSQVYLVL 92 
                                    67889**************..79*******9666555555554478899******************7267799****** PP

                                    E--TTEBHHHHHH..HHSS--HHHHHHHHHHHHHHHHHHHHTTEE-SS-SGGGEEEETTTEEEE-SGTTSEESSSSCSBC CS
                        Pkinase  78 eyveggeladlle..rkgslseeeakkiakqilegleylHskgiiHrDlKpeNiLidekgelKitDFGlakelesssklt 155
                                    eyv+ + la++++  ++ +l+++e k+++ qi+++l+y+H+kgiiHrDlK +NiL++ ++++Ki+DFG ++++  +  +t
  gene354|gene354|rna354|rna354  93 EYVPYD-LASVIRdkKNLKLTKTEHKNWLLQIASALSYMHAKGIIHRDLKASNILCS-NNVVKIADFGSSRHIAGQ--MT 168
                                    ****77.******65556699************************************.9**************995..7* PP

                                    TTTSCGGGS-HHHH.TTSCBSHHHHHHHHHHHHHHHHHSS-STTTSSHHHHHHHHHHTHHHHHHHCT............. CS
                        Pkinase 156 sfvgtseYlAPEvl.keneyskkvDvWslGvilyelltgkppfsgekgkekvekeldqlekilkilg............. 221
                                      v t +Y++PE+l ++++y++++D+WslG+i yel++g+ +f ++++     ++ld+   i+ ++g             
  gene354|gene354|rna354|rna354 169 GNVTTLWYRSPELLlGKTNYGEEIDIWSLGCIAYELICGELLFIENTEI----QMLDK---IFSTFGfpstviapnlcyl 241
                                    **************999***************************44443....45555...4444444223333444433 PP

                                    .SHH...HHHTTS................-HHHHHHHHHHT-SSGCCSTTHHHHHTSGGG CS
                        Pkinase 222 .etkeklpeasei................seeakdllkkllkkdpkkRltaeellqhpyl 264
                                     +          +                see  ++l++ + ++ +kR+ta+ +lq++yl
  gene354|gene354|rna354|rna354 242 rQ----------MnhhtyhfddilrdkccSEEQVQFLERFFVYEAEKRVTAKGVLQSEYL 291
                                    32..........14444555777999999****************************996 PP

>> Pkinase_Tyr  Protein tyrosine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.0   0.1   6.2e-36   1.4e-32       3     218 ..      17     223 ..      15     287 .. 0.84

  Alignments for each domain:
  == domain 1  score: 113.0 bits;  conditional E-value: 6.2e-36
                                    EEEEEEEESSEEEEEEEEETTTTSSEEEEEEEEE...STTSSHHHHHHHHHHHHHHHTS-BTTB--EEEEEE.SSSSEEE CS
                    Pkinase_Tyr   3 lgkklGeGafGkVvegtlkgekekkevkVavKtl...keeateeekeelleeakimkklkhpnivkllgvct.keeplli 78 
                                    ++kk+ +G+ ++V+ +t +      e   a+K+    + +  ++ + +  +e++i+k+l+hpn+++l+ ++  +++++++
  gene354|gene354|rna354|rna354  17 IQKKISSGSSATVYLATKD------EKFYAIKKPyilTFSDPNNVRLSSENEISILKELRHPNVINLHDIVWeNNSQVYL 90 
                                    6789999999999999988......34445554311122333333567778********************977788*** PP

                                    EEE--TTEBHHHHHHHTCTTTSBHHHHHHHHHHHHHHHHHHHHTTEEEST-SGGGEEEEETTEEEE-STTTHEETTTSSE CS
                    Pkinase_Tyr  79 vteyvkgGdLlkfLrkkekekltlkdllsfalqvAkGmeyLeskklvHrdlaarNvLlsenkvvkisDfGLardiekdde 158
                                    v+eyv++ dL + +r+k++ klt ++  ++ lq+A++++y+++k ++Hrdl a N+L s n+vvki+DfG +r+i     
  gene354|gene354|rna354|rna354  91 VLEYVPY-DLASVIRDKKNLKLTKTEHKNWLLQIASALSYMHAKGIIHRDLKASNILCS-NNVVKIADFGSSRHI----- 163
                                    ******9.9************************************************98.99*************..... PP

                                    EEETTSSTSGGGGS-HHHHHHSE.EEHHHHHHHHHHHHHHHHTTSSGTTTTSHHHHHHHHH CS
                    Pkinase_Tyr 159 yvkkeeaklpvkWmapEslkekk.ftsksDvWsfGvllwEiftlgespypglkneevlekl 218
                                      + +++ + + + +pE l  k+ + ++ D+Ws G + +E+++ ge  + + ++ ++l+k+
  gene354|gene354|rna354|rna354 164 AGQMTGNVTTLWYRSPELLLGKTnYGEEIDIWSLGCIAYELIC-GELLFIENTEIQMLDKI 223
                                    55556666666777***9876655*****************99.88776666666666655 PP

>> Kdo  Lipopolysaccharide kinase (Kdo/WaaP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.2   3.5e-08   7.8e-05     103     154 ..      97     150 ..      52     167 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 3.5e-08
                            Kdo 103 qdLedllakwae..laeelkrallkavgrliaklhragvnHadlyaknillqqe 154
                                     dL+ ++++ ++  l ++ +++ l +++ + + +h+ g+ H+dl a nil  ++
  gene354|gene354|rna354|rna354  97 YDLASVIRDKKNlkLTKTEHKNWLLQIASALSYMHAKGIIHRDLKASNILCSNN 150
                                    58999999988888999999******************************9876 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.0   0.00034      0.76       3     106 ..      19     131 ..      18     133 .. 0.77
   2 !   10.0   0.0   0.00026      0.59     165     195 ..     132     159 ..     117     164 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00034
                                    EEE--.SSCEEEEEEETT-......-EEEEEE-TTS-HHHHHHHHHHHHHHHHTT-.B--B-CTTBS-EEETTEEEEEEE CS
                            APH   3 relsggasnrtylvttpag......ryvlrrnpparaaeeirrevallrlLakagv.pvPevlagdtddeeigllfalie 75 
                                    + +s+g s  +yl t +++      +y+l+++ p     + ++e  +l+ L+  +v     +++     e +  +++++e
  gene354|gene354|rna354|rna354  19 KKISSGSSATVYLATKDEKfyaikkPYILTFSDPNNVRLSSENEISILKELRHPNViNLHDIVW-----ENNSQVYLVLE 93 
                                    5799*****9999999998899******************************888888889999.....55555666666 PP

                                    ----EE-SS.......HHHHHHHHHHHHHHHHHHCCHH CS
                            APH  76 yvpgrsllr.......klsaaqlpellealgeflaalh 106
                                    yvp   ++        kl+  + +++l +++++l  +h
  gene354|gene354|rna354|rna354  94 YVPYDLASVirdkknlKLTKTEHKNWLLQIASALSYMH 131
                                    66655555444476666666666666666666666665 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00026
                                    -EEEE-SS-SGGGEEEC..TTEEEEE---TT CS
                            APH 165 ptvllHgDlhpgNllvdpddgrvtGviDfed 195
                                    +++++H+Dl+  N+l    ++ v  + Df+ 
  gene354|gene354|rna354|rna354 132 AKGIIHRDLKASNILCS--NNVV-KIADFGS 159
                                    799**************..6666.5777765 PP

>> RIO1  RIO1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.2   4.5e-07     0.001      49     151 ..      53     159 ..      27     169 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 4.5e-07
                                    HHHHHHHHHHHHHHHHHHHTT--S--EEEEETT...EEEEE--EETTEEGGBH.HHCG.-HHHHHHHHHHHHHHHHHHHH CS
                           RIO1  49 klvklwaekEfrnLkrleeagvpvPkpielkrh...vlvmefigedgvaapkl.kdve.eeeeaeelyeevleemrklyk 123
                                    + v+l+ e+E+++Lk+l++ +v   + i ++++    lv+e++  d   + +  k+++ +++e ++ + ++ +++   ++
  gene354|gene354|rna354|rna354  53 NNVRLSSENEISILKELRHPNVINLHDIVWENNsqvYLVLEYVPYDLASVIRDkKNLKlTKTEHKNWLLQIASALSY-MH 131
                                    56889999*********9999877788888877444599****9555544443034443378888888888886555.55 PP

                                    TSTEEESS-STTSEEEETTEEEE--GTT CS
                           RIO1 124 eaglvHaDLSeyNvlvdedkvviIDvsQ 151
                                      g++H DL   N+l++++ v i D++ 
  gene354|gene354|rna354|rna354 132 AKGIIHRDLKASNILCSNNVVKIADFGS 159
                                    99******************99999975 PP

>> Kinase-like  Kinase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   6.5e-07    0.0015     148     255 ..     119     216 ..      64     233 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 6.5e-07
                    Kinase-like 148 llTlqlirlaanLqakglvhgkftvdnllldekgglmlggftaLvragtkvvlsevekgfaPpEllgsrggytrknktkm 227
                                     l lq+     +++akg++h ++++ n+l  +   +++ +f++ +    ++  + +   +  pEll          kt++
  gene354|gene354|rna354|rna354 119 WL-LQIASALSYMHAKGIIHRDLKASNILCSN-NVVKIADFGSSRHIAGQMTGNVTTLWYRSPELLLG--------KTNY 188
                                    34.677888899***************98776.57********999888888799999******9987........5677 PP

                    Kinase-like 228 thkldaWqlGlviyriwclklPltlate 255
                                      ++d W lG  +y + c +l + + te
  gene354|gene354|rna354|rna354 189 GEEIDIWSLGCIAYELICGELLFIENTE 216
                                    779***************9987766665 PP

>> Pkinase_fungal  Fungal protein kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0    0.0058        13     137     211 ..       6      86 ..       2     119 .. 0.79
   2 ?    4.6   0.2     0.005        11     322     341 ..     130     148 ..     120     161 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.0058
                 Pkinase_fungal 137 etekleleeplarqraivgRgTtcwrarkeger...gkeyvvKdsWrdaerk...sEaelLkkaeergvegvarlvahed 210
                                    ++e + + + +++++   g + t++ a+k+++    +k y++ +s  ++ r    +E  +Lk+ ++ +v ++  +v++++
  gene354|gene354|rna354|rna354   6 TSEIFKISQYVIQKKISSGSSATVYLATKDEKFyaiKKPYILTFSDPNNVRLsseNEISILKELRHPNVINLHDIVWENN 85 
                                    566788888888888888999********7665999999*****9998877542367789***************99987 PP

                 Pkinase_fungal 211 v 211
                                     
  gene354|gene354|rna354|rna354  86 S 86 
                                    4 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.005
                 Pkinase_fungal 322 LflkagiLHrDiSenNilit 341
                                    ++  +gi+HrD  + Nil  
  gene354|gene354|rna354|rna354 130 MH-AKGIIHRDLKASNILCS 148
                                    55.89************976 PP

>> FTA2  Kinetochore Sim4 complex subunit FTA2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.1     0.078   1.7e+02      28      60 ..      19      51 ..       5      71 .. 0.68
   2 ?    8.7   0.1   0.00055       1.2     176     213 ..     118     159 ..      55     161 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.078
                           FTA2 28 eyLgkglhsiVlkvkirgkeYALKlFrfleaee 60
                                   + + +g ++ V+ +  ++k YA+K  + l+ ++
  gene354|gene354|rna354|rna354 19 KKISSGSSATVYLATKDEKFYAIKKPYILTFSD 51
                                   455679999**************9544444444 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00055
                           FTA2 176 sqlpkllrdlkklhklgIvvrDlkeenyidg....kLvDlsa 213
                                    + l ++ + l  +h+ gI++rDlk++n++ +    k+ D+++
  gene354|gene354|rna354|rna354 118 NWLLQIASALSYMHAKGIIHRDLKASNILCSnnvvKIADFGS 159
                                    456689999******************986533335667665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (296 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       518  (0.0288917); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 1904.64
//
Query:       gene355|gene355|rna355|rna355  [L=247]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.4e-08   32.4   0.2    3.4e-07   30.2   0.1    1.8  2  zf-ZPR1   ZPR1 zinc-finger domain


Domain annotation for each model (and alignments):
>> zf-ZPR1  ZPR1 zinc-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.2   0.1   1.9e-11   3.4e-07       2     120 ..       8     123 ..       7     153 .. 0.78
   2 ?    0.0   0.0     0.038   6.7e+02     127     157 ..     187     217 ..     164     234 .. 0.63

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 1.9e-11
                        zf-ZPR1   2 lCpsCgkengetrlllt.kiPyfkeviimsfeCehCgyknnevks.ageieekGkritlkveseedlnrqvlkSetatve 79 
                                    +C +C+   g+ + +++ +   + +  ++s++C  C  ++  +k  +++ ++kG +i + ++s +dln+ v+  + + v+
  gene355|gene355|rna355|rna355   8 TCWKCS-T-GMDENYVVsN--LIDNTPLSSLSCVGCTANEFLIKErLNTGNNKGIEIRCDIRSINDLNNFVFLNSDSVVK 83 
                                    699995.4.4444444414..4789999********9999999862577889**************************** PP

                        zf-ZPR1  80 ipeleleippgtlegrlttvEGlLeqikeele.....keegdqaer 120
                                    i +  ++ + +++e  +tt   lL++i+++l+     +       +
  gene355|gene355|rna355|rna355  84 ITKNRFTYHYSKSETVYTTTGNLLKKIIRDLQyyldiE------IK 123
                                    *******************************7654331......22 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.038
                        zf-ZPR1 127 kieefl.ekleeliegeepftlildDpagnSf 157
                                    ++++f  ++l+ +i+ ++++ l + D  g S 
  gene355|gene355|rna355|rna355 187 EVAKFNhHNLDLVIK-DKSCDLLIVDLEGVSR 217
                                    333333133444444.5555666666655554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       779  (0.0434492); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1761.48
//
Query:       gene356|gene356|rna356|rna356  [L=213]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-32  112.3   0.0    2.6e-32  112.0   0.0    1.1  1  CoaE      Dephospho-CoA kinase
    3.5e-06   27.6   0.7    8.9e-06   26.3   0.6    1.8  1  AAA_18    AAA domain
     0.0052   16.9   0.0      0.075   13.2   0.0    2.2  2  AAA_33    AAA domain
  ------ inclusion threshold ------
      0.029   14.5   0.3        2.2    8.4   0.0    2.9  3  SKI       Shikimate kinase
      0.034   13.4   0.4      0.068   12.4   0.0    1.6  2  DUF2075   Uncharacterized conserved protein (DUF2075)
      0.044   14.0   0.0       0.12   12.6   0.0    1.7  2  AAA_28    AAA domain
      0.095   12.7   0.4       0.29   11.1   0.1    1.9  2  DUF2118   Uncharacterized protein conserved in archaea (DUF21


Domain annotation for each model (and alignments):
>> CoaE  Dephospho-CoA kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.0   0.0     1e-35   2.6e-32       1     176 [.       2     172 ..       2     174 .. 0.89

  Alignments for each domain:
  == domain 1  score: 112.0 bits;  conditional E-value: 1e-35
                                    EEEEEEESTTSSHHHHHHHHHHTT-EEEEHHHHHHHTTCCTHHHHHHHHHHHGGGCB.TTSSE-HHHHHHHHHTSHHHHH CS
                           CoaE   1 livgltGgiasGKstvanlfadlgvpivDaDlvArqvvepgsealkkiveeFgeeildedGeLdReaLrkkvFadpeekk 80 
                                    +ivg+tG+i++GKs+v +l+++ g+ +vDaD++ r+v e+++e l   +++F+e  ++   +  +++L++ +F+++++kk
  gene356|gene356|rna356|rna356   2 YIVGITGNIGTGKSLVGSLLRQKGYCVVDADKISREVLEHNKELL---RRNFPELFVN--NQFSKAKLKEIIFKKEKNKK 76 
                                    69**************************************99986...5679886654..5799**************** PP

                                    HHHHHHHHHHHHHHHHHH..HH--S..SEEEEE-TTTTTTTGGGGSSEEEEEE--HHHHHHHHHHCCTSTHHHHHHHHHH CS
                           CoaE  81 aLnallhPlirreikkel..akles..kyvlldvPLLvEkqlekliervlvvdvelelqveRlvardgvseeevkaiiaa 156
                                    a++ +lh  i+ ++   +  ++l +  ++v+l++PL +E +l++ ++ + vv +++++q eR+  rdg s   ++++++a
  gene356|gene356|rna356|rna356  77 AIERILHYKITVKMCYIVlmEAL-KfkRVVFLEIPLFFEYNLDRFFDSI-VVYCDKSTQAERITGRDGNSL--LNEKLKA 152
                                    **********9999865411344.35899***************99986.789***************886..7899*** PP

                                    S--HHHHHHH-SEEEE-.SS CS
                           CoaE 157 QlseeerlaladvvldNdss 176
                                    Q + ee++++ ++++dN +s
  gene356|gene356|rna356|rna356 153 QKTMEEKKKRGTFLIDNGGS 172
                                    *****************776 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.6   3.5e-09   8.9e-06       1     117 [.       4     144 ..       4     160 .. 0.63

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 3.5e-09
                         AAA_18   1 IlltGtpGvGKttlakeLskrlgf...........gvnlrdvakenglllevdpealdeskrldedkldklldaleenss 69 
                                    +++tG +G+GK+ ++  L++++ +           + ++++     +ll  ++pe l  ++++ + kl++++ + e+n +
  gene356|gene356|rna356|rna356   4 VGITGNIGTGKSLVGSLLRQKG-YcvvdadkisreVLEHNK-----ELLRRNFPE-LFVNNQFSKAKLKEIIFKKEKNKK 76 
                                    78****************9995.6699*7433333222222.....333333444.333333333333333333333333 PP

                         AAA_18  70 ....................aleegknlvidghlaeleseaakdikkvvLtaspeelleRlekRgyee 117
                                                           + k +v+  ++  +e+  +++   +v+++++++ +eR+  R+ ++
  gene356|gene356|rna356|rna356  77 aierilhykitvkmcyivlmEALKFKRVVFLEIPLFFEYNLDRFFDSIVVYCDKSTQAERITGRDGNS 144
                                    33366667787777777666444556667777777777666665555*****************9664 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.0   2.9e-05     0.075       5      43 ..       7      44 ..       3      87 .. 0.74
   2 ?    1.6   0.0      0.11   2.9e+02     102     123 ..     124     147 ..     114     173 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.9e-05
                         AAA_33  5 vGlpGsGKstlaerllkklgavllssdtlrrrlfgtdqq 43
                                    G  G+GKs +  +ll++ g+++++ d+++r + +  ++
  gene356|gene356|rna356|rna356  7 TGNIGTGKSLV-GSLLRQKGYCVVDADKISREVLEHNKE 44
                                   6889****965.66999***********99988764333 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.11
                         AAA_33 102 vvvetdeetlkeRlakRaang..d 123
                                    +vv +d +t +eR+  R  n+  +
  gene356|gene356|rna356|rna356 124 IVVYCDKSTQAERITGRDGNSllN 147
                                    566778888899999988875331 PP

>> SKI  Shikimate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.0   0.00087       2.2       2      31 ..      11      39 ..      10      58 .. 0.82
   2 ?    1.4   0.0      0.12   3.1e+02      88     128 ..     125     163 ..     115     169 .. 0.75
   3 ?    1.4   0.0      0.12     3e+02      61     103 ..     162     204 ..     153     207 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00087
                                   TSSHHHHHHHHHHHHTSEEEEHHHHHHHHH CS
                            SKI  2 GaGKstvGkllAkklglefiDlDeliekrt 31
                                   G+GKs vG ll  + g++++D+D++  ++ 
  gene356|gene356|rna356|rna356 11 GTGKSLVGSLLR-QKGYCVVDADKISREVL 39
                                   99*******995.569*******9876654 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.12
                                    EEEEE--HHHHHHHHHHTTSSGGGCSCHHHHHHHHHHHHHH CS
                            SKI  88 viyLdvsleellerlkadkeRPllqekskeeelleelaere 128
                                    v+   ++  +++er++ ++   ll+ek k+++ +ee ++r 
  gene356|gene356|rna356|rna356 125 VV--YCDKSTQAERITGRDGNSLLNEKLKAQKTMEEKKKRG 163
                                    33..4566788999999999899999999777777777775 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.12
                                    CSSEEEEE-TTGGGSHHHHHHHHHHSEEEEEE--HHHHHHHHH CS
                            SKI  61 eeglViatGGGavlseenrellkekgiviyLdvsleellerlk 103
                                    +    i  GG++  ++   + lk +g++iy   ++ +l  +l+
  gene356|gene356|rna356|rna356 162 RGTFLIDNGGSVEYTKMQINNLKFSGYTIYFYFTVAVLTCYLA 204
                                    4466677788888888899999*************99999986 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   2.7e-05     0.068       3      58 ..       3      75 ..       1      92 [. 0.62
   2 ?   -1.8   0.1      0.55   1.4e+03      15      52 ..     144     181 ..     139     188 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.7e-05
                        DUF2075  3 vvlVtGvaGtGKtvvllnllael.........edde........eertavylsvNhplvlvlrealakkeekk 58
                                   +v +tG+ GtGK++v++ l  +          +++         +++   +++ N+   ++l+e + kke++k
  gene356|gene356|rna356|rna356  3 IVGITGNIGTGKSLVGSLLRQKGycvvdadkiSREVlehnkellRRNFPELFVNNQFSKAKLKEIIFKKEKNK 75
                                   5669*************99998888888777733332222233344444555555555555555555555222 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.55
                        DUF2075  15 tvvllnllaeleddeeertavylsvNhplvlvlreala 52 
                                    +++  +l a+ +++e++++ ++l+ N+  v+  + +++
  gene356|gene356|rna356|rna356 144 SLLNEKLKAQKTMEEKKKRGTFLIDNGGSVEYTKMQIN 181
                                    55555666666778888888888888888877777765 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   4.9e-05      0.12       4      48 ..       6      52 ..       3      82 .. 0.80
   2 ?   -1.6   0.0       1.1   2.7e+03      60      81 ..     150     170 ..     125     178 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.9e-05
                         AAA_28  4 itGgestGKTtlleaLaargypvv..pEaareileeklakgedalpw 48
                                   itG  +tGK+ + + L ++gy vv    + re+le++ +  +++ p+
  gene356|gene356|rna356|rna356  6 ITGNIGTGKSLVGSLLRQKGYCVVdaDKISREVLEHNKELLRRNFPE 52
                                   99**********************9999******9999766665554 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.1
                         AAA_28  60 leeqleeeaaaaankvlfcDrg 81 
                                    l++q+ + ++ ++++++++D g
  gene356|gene356|rna356|rna356 150 LKAQK-TMEEKKKRGTFLIDNG 170
                                    22222.2233356677777665 PP

>> DUF2118  Uncharacterized protein conserved in archaea (DUF2118)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   0.00011      0.29       2      49 ..      49      96 ..      48     104 .. 0.91
   2 ?   -1.5   0.0      0.83   2.1e+03      18      43 ..     164     189 ..     140     196 .. 0.54

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00011
                        DUF2118  2 klPrlYvEgkeseeevevileeeeevekfadkveekklkgkvvYeell 49
                                   ++P+l+v ++ s+ ++++i+ ++e+ +k ++++  +k+  k  Y +l+
  gene356|gene356|rna356|rna356 49 NFPELFVNNQFSKAKLKEIIFKKEKNKKAIERILHYKITVKMCYIVLM 96
                                   69********************************99999999997744 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.83
                        DUF2118  18 evileeeeevekfadkveekklkgkv 43 
                                      ++ ++++ve+ + ++++ k+ g  
  gene356|gene356|rna356|rna356 164 TFLIDNGGSVEYTKMQINNLKFSGYT 189
                                    23344445555555555555555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       952  (0.0530983); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.46u 0.30s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 1447.52
//
Query:       gene357|gene357|rna357|rna357  [L=337]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (337 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       939  (0.0523733); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 2232.13
//
Query:       gene358|gene358|rna358|rna358  [L=164]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
      0.016   15.6   3.1        2.6    8.5   0.1    2.5  2  NAPRTase_N  Nicotinate phosphoribosyltransferase (NAPRTase) N


Domain annotation for each model (and alignments):
>> NAPRTase_N  Nicotinate phosphoribosyltransferase (NAPRTase) N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.1   0.00014       2.6      63     113 ..      16      62 ..       3      66 .. 0.71
   2 ?    7.6   0.1   0.00027       4.9      57      87 ..      83     113 ..      63     122 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00014
                     NAPRTase_N  63 yLkrklpyfkedfleyLrtfrfkpsevaveeeevvfpgepeirveGpwiea 113
                                    +Lk   +y k+dfl yL+ + f+    +ve  ++ f ++ ++++  +++++
  gene358|gene358|rna358|rna358  16 MLK---KYEKDDFLHYLKVISFNIVL-NVEFRTSYFGNNTHLEIIKKICQI 62 
                                    333...6799************9654.555555578888888887666665 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.00027
                     NAPRTase_N  57 teeeieyLkrklpyfkedfleyLrtfrfkps 87 
                                    ++ e + L  +++ f+++f++y+r++rf  s
  gene358|gene358|rna358|rna358  83 ESTETHDLDINTKPFHDKFVQYMRSLRFILS 113
                                    33344445556666*************9665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       871  (0.0485805); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1077.56
//
Query:       gene359|gene359|rna359|rna359  [L=586]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
      0.036   13.6   0.0       0.08   12.5   0.0    1.6  1  ArsA_HSP20  HSP20-like domain found in ArsA


Domain annotation for each model (and alignments):
>> ArsA_HSP20  HSP20-like domain found in ArsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   4.5e-06      0.08      21      63 .]     411     454 ..     408     454 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4.5e-06
                     ArsA_HSP20  21 srsgdeLtIkig.nfrRqitLPsvlarkevtsAkfedgvLeIrF 63 
                                     r+g+ L I+++     ++ LPs ++++ + + +++++vL+I++
  gene359|gene359|rna359|rna359 411 VRNGQLLKIQVEkGVENVVLLPSPVNNLYALGLEYNNKVLKIHL 454
                                    688999999999778889************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (586 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       896  (0.0499749); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.25s 00:00:00.82 Elapsed: 00:00:00.43
# Mc/sec: 4058.38
//
Query:       gene36|gene36|rna36|rna36  [L=73]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.38   10.3   4.1       0.39   10.2   4.1    1.0  1  DUF1700   Protein of unknown function (DUF1700)


Domain annotation for each model (and alignments):
>> DUF1700  Protein of unknown function (DUF1700)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   4.1   2.2e-05      0.39       1      62 [.       1      62 [.       1      72 [. 0.84

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 2.2e-05
                    DUF1700  1 mnkkefLkeLesaLeklpeeekkdilsdYeehFesgkeeGksEeeivkeLgdPkeIakelta 62
                               m k+ + k+L+ + +k+++e +++i +   e  +  + + + Ee+i+ +  d k+ +ke+ +
  gene36|gene36|rna36|rna36  1 MTKHIYNKRLDINTRKIENEKRDEIHKSNSELENGKNTNNRREENIIMKYLDDKKSSKEYYK 62
                               89999*************999999987777776666789999*9999998888999999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (73 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1623  (0.0905237); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.29s 00:00:00.65 Elapsed: 00:00:00.44
# Mc/sec: 494.55
//
Query:       gene360|gene360|rna360|rna360  [L=358]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (358 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       731  (0.0407719); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 2509.38
//
Query:       gene361|gene361|rna361|rna361  [L=307]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (307 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       958  (0.053433); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 2334.91
//
Query:       gene362|gene362|rna362|rna362  [L=396]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.9e-26   90.9   8.0    1.6e-22   80.2   8.0    2.9  1  TIP49         TIP49 P-loop domain
    1.3e-07   31.6   0.5    3.2e-07   30.4   0.1    1.9  1  TIP49_C       TIP49 AAA-lid domain
      6e-06   26.6   0.0      0.014   15.7   0.0    2.3  2  AAA_22        AAA domain
    7.5e-06   26.0   2.6     0.0015   18.6   0.0    2.5  2  AAA_14        AAA domain
    0.00013   22.4   0.0     0.0015   18.9   0.0    2.1  2  AAA_16        AAA ATPase domain
    0.00013   21.9   3.7    0.00014   21.9   1.6    2.0  1  ATPase_2      ATPase domain predominantly from Archaea
     0.0035   17.8   0.2       0.11   12.9   0.0    2.5  2  AAA           ATPase family associated with various cellular 
     0.0065   16.0   0.0      0.014   15.0   0.0    1.5  1  CobU          Cobinamide kinase / cobinamide phosphate guanyl
     0.0077   16.8   0.2        0.3   11.7   0.0    2.3  2  AAA_18        AAA domain
  ------ inclusion threshold ------
      0.014   15.3   0.0      0.023   14.5   0.0    1.3  1  CPT           Chloramphenicol phosphotransferase-like protein
      0.028   14.1   0.3       0.16   11.7   0.0    2.1  2  RuvB_N        Holliday junction DNA helicase RuvB P-loop doma
      0.031   13.7   0.0      0.051   13.0   0.0    1.3  1  Mg_chelatase  Magnesium chelatase, subunit ChlI
       0.11   12.3   0.1       0.31   10.9   0.1    1.8  1  Myosin_N      Myosin N-terminal SH3-like domain


Domain annotation for each model (and alignments):
>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.2   8.0   1.2e-25   1.6e-22       1     321 [.      48     305 ..      48     317 .. 0.83

  Alignments for each domain:
  == domain 1  score: 80.2 bits;  conditional E-value: 1.2e-25
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          TIP49   1 rislhshikgLGldedgeaekeeeglvGqkkareaagvivelikekklaGravLlaGpsgtGktalaiaiskelgedvpf 80 
                                    ri+lhshi++LG+ ++   ++e++glvGq+kar a +    l +e+    r vLl Gp+ +Gk+ala a+sk+       
  gene362|gene362|rna362|rna362  48 RIGLHSHIHSLGVVDN--RTHENSGLVGQEKARIALS----LSRERS---RIVLLHGPRNSGKSALATALSKDTE---NC 115
                                    799*********9998..456789*********8865....555554...99********************987...45 PP

                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX-S-EEEEEEEEEEE...-SSS-..TTS--EEEEEE-SS-EEEEEE-H CS
                          TIP49  81 valsgsevyslevkktevltqalrksigvrikeekevleGevveleveeaenplskekkikevkitlktakeekklklgs 160
                                    v +s+++v        e l + +     v + ee++v+eGe+v+++                  ++l+t+++e+++++ +
  gene362|gene362|rna362|rna362 116 VYISAAQVE-----NVEDLDKLILSVQVVVLMEETTVIEGEIVSISG---------------NSVILRTTDMESTFTVRE 175
                                    678887764.....44555554444445667899*********9955...............4699***********987 PP

                                    HHHHHHHHHT--TT-EEEEETTT--EEE-SSS-SS------S--------S---S----XXXXXXXXXXXXXXXXXXXXX CS
                          TIP49 161 kiaeellkekvkegDviviekesGkvkklGrsearakefDiekdefvelPkGevekkkevvqevtLhdlDvanarpqdll 240
                                     +         +egDv++i    G++k++G++++ ++  D  +  +v +PkG++ + k + ++ t  dl   n ++ d  
  gene362|gene362|rna362|rna362 176 VV-------GFTEGDVLQIV--NGTIKRMGTTRTSES-VD-PNVPIVGIPKGNLIQTKILKKRTTFADLIENNDKNADKY 244
                                    65.......5789****997..699*****9987765.55.67899************9999999999987777776655 PP

                                    XXX....XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          TIP49 241 slllqllkskkteiteklreeinkkvakyveegkaeivpGvlfiDevhmlDiecfsylnraleselaPivilatnrgiak 320
                                    ++                     +kv ++++e kaei +  l iDe+h+lD     yl +  e e +P ++l +   i +
  gene362|gene362|rna362|rna362 245 LIY--------------------EKVREWINENKAEIPKSTLIIDEAHLLDERLLNYLFKISELEYSPFILLVSKDDINE 304
                                    544....................567789*******************************************99877665 PP

                                    X CS
                          TIP49 321 i 321
                                     
  gene362|gene362|rna362|rna362 305 T 305
                                    5 PP

>> TIP49_C  TIP49 AAA-lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.4   0.1   2.3e-10   3.2e-07       1      66 []     323     387 ..     323     387 .. 0.97

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 2.3e-10
                        TIP49_C   1 IlkiRakeEgvkldeeAldlLakigtetSLRYaiqLltpasilakkrkkkevevedveeveeLFlD 66 
                                    I k+R  eE+v l++e ++ L +i  + ++RYai+ +t++  l++ ++++  +++d + v+eLFlD
  gene362|gene362|rna362|rna362 323 IFKLRGIEEEVTLNDELITNLLNIERNMGMRYAINVITLVGALSSFHQRD-PNLNDLKCVSELFLD 387
                                    7899****************************************999998.7*************9 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.0    0.0015       2.1       4      53 ..      87     126 ..      84     145 .. 0.75
   2 !   15.7   0.0     1e-05     0.014      72     124 ..     240     292 ..     206     305 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0015
                         AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstss 53 
                                    + +i++++G+  +GK+ l+  l +              +v++ +++ ++ 
  gene362|gene362|rna362|rna362  87 RSRIVLLHGPRNSGKSALATALSKDT----------ENCVYISAAQVENV 126
                                    6789***************9998874..........44555555555555 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 1e-05
                         AAA_22  72 rlsseellealeqalrarav...ielliiDEaqhlrseealeeLrsllnlsrkgvq 124
                                    ++++  ++e++++ +++ ++   ++ liiDEa+ l  e++l++L ++++      +
  gene362|gene362|rna362|rna362 240 NADKYLIYEKVREWINENKAeipKSTLIIDEAHLL-DERLLNYLFKISE--LEYSP 292
                                    345555568888888888888888***********.9*******88887..44444 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   1.1e-06    0.0015       2      49 ..      88     131 ..      87     161 .. 0.76
   2 !    6.1   1.2    0.0076        10      24      78 ..     220     276 ..     216     308 .. 0.67

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.1e-06
                         AAA_14   2 rkilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladp 49 
                                    ++i+++ G+R +GK+ l+  l k+     e+++yi+  + ++ +  d+
  gene362|gene362|rna362|rna362  88 SRIVLLHGPRNSGKSALATALSKDT----ENCVYISAAQVENVEDLDK 131
                                    689**************98887554....6******999887554432 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0076
                         AAA_14  24 kellvkkesilyinldderdkkladpekllelileklke....ekktylflDEiqevpe 78 
                                    ++++  k+++ + +l +++dk+++++  ++e ++e ++e      k+ l++DE++ ++e
  gene362|gene362|rna362|rna362 220 QTKI-LKKRTTFADLIENNDKNADKY-LIYEKVREWINEnkaeIPKSTLIIDEAHLLDE 276
                                    4554.577788888888888766644.344444444322234445777******99875 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   1.1e-06    0.0015      19      60 ..      83     122 ..      72     169 .. 0.79
   2 ?    1.3   0.0      0.29     4e+02     137     162 ..     264     286 ..     213     297 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.1e-06
                         AAA_16  19 vrsgrpelvllsGesGvGKsslvrellralekdggiflrgkc 60 
                                    +++ r+++vll+G++ +GKs+l+++l +  e  +++++++  
  gene362|gene362|rna362|rna362  83 LSRERSRIVLLHGPRNSGKSALATALSKDTE--NCVYISAAQ 122
                                    556677******************9997332..355555444 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.29
                         AAA_16 137 lvlvlDdlqwadeaslqllaaLlrll 162
                                      l++D+++ +de  l    +L++ +
  gene362|gene362|rna362|rna362 264 STLIIDEAHLLDERLL---NYLFKIS 286
                                    5699********9544...4444444 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   1.6   9.9e-08   0.00014      11     131 ..      79     275 ..      74     292 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 9.9e-08
                       ATPase_2  11 leeilerepneiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefieeeeekkklekal........ 82 
                                    +   l+re+++i+++ Gp++sGK+aL   + +      ++ +y++a + e+ + ld+ i   +++  +e+++        
  gene362|gene362|rna362|rna362  79 IALSLSRERSRIVLLHGPRNSGKSALATALSKDT----ENCVYISAAQVENVEDLDKLILSVQVVVLMEETTviegeivs 154
                                    6667899*******************88766555....569*****************9966666655555566666688 PP

                       ATPase_2  83 ...................................................................giavpkaeleeil 95 
                                                                                                       +i  +++++  ++
  gene362|gene362|rna362|rna362 155 isgnsvilrttdmestftvrevvgftegdvlqivngtikrmgttrtsesvdpnvpivgipkgnliqtKILKKRTTFADLI 234
                                    99999999999999999999999999999999999999999999999999999999999999999876777777788888 PP

                       ATPase_2  96 keksklvfkai..elllekikkkgkk...iiiiiDelqkli 131
                                    +++ k+++k++  e++ e i++++ +     +iiDe+  l 
  gene362|gene362|rna362|rna362 235 ENNDKNADKYLiyEKVREWINENKAEipkSTLIIDEAHLLD 275
                                    86666666654338899999999888766799999987665 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.0   8.3e-05      0.11       1      35 [.      91     124 ..      91     209 .. 0.76
   2 ?    2.6   0.1      0.12   1.7e+02      44      72 ..     248     276 ..     240     335 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 8.3e-05
                                    EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCS CS
                            AAA   1 vllyGppGtGKTllakavakelgvefleisgsell 35 
                                    vll+Gp   GK++la a+ k++  +++ is++++ 
  gene362|gene362|rna362|rna362  91 VLLHGPRNSGKSALATALSKDT-ENCVYISAAQVE 124
                                    79*******************6.446666666555 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.12
                                    HHHHHHHHHHHHTSTS.EEEEEETGGGHHH CS
                            AAA  44 kkirelfkeakekakp.silfiDEidalak 72 
                                    +k+re ++e k++  p s l+iDE++ l +
  gene362|gene362|rna362|rna362 248 EKVREWINENKAEI-PkSTLIIDEAHLLDE 276
                                    57788888877766.669*******98833 PP

>> CobU  Cobinamide kinase / cobinamide phosphate guanyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0     1e-05     0.014       1      37 [.      91     126 ..      91     134 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1e-05
                           CobU   1 ilvtGgarSGKSefAeklaeeskekvvYiATaealDe 37 
                                    +l+ G+  SGKS++A +l ++ +e++vYi +a++ + 
  gene362|gene362|rna362|rna362  91 VLLHGPRNSGKSALATALSKD-TENCVYISAAQVENV 126
                                    6899**************775.6999****9998754 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.0   0.00021       0.3       1      31 [.      91     129 ..      91     142 .. 0.84
   2 ?    2.8   0.1      0.12   1.6e+02      47     125 ..     236     322 ..     196     327 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00021
                         AAA_18   1 IlltGtpGvGKttlakeLskrl.gf.......gvnlrdv 31 
                                    +ll G+  +GK+ la +Lsk + ++       ++n+ d+
  gene362|gene362|rna362|rna362  91 VLLHGPRNSGKSALATALSKDTeNCvyisaaqVENVEDL 129
                                    6899*****************977798887776666665 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.12
                         AAA_18  47 deskrldedkldklldaleenssaleegknlvidghlaeleseaakdikk..........vvLtaspeelleRlekRgye 116
                                    ++ k +d+    + ++++ + ++a+   ++l+id   a+l++e++  + +          + L  ++++   Rl k +++
  gene362|gene362|rna362|rna362 236 NNDKNADKYLIYEKVREWINENKAEIPKSTLIIDE--AHLLDERLLNYLFkiseleyspfILLVSKDDINETRLLKIRTS 313
                                    34444444444444444444444556678888886..4555555555555566688899999988889998898888888 PP

                         AAA_18 117 eakikenee 125
                                    +   ke+e+
  gene362|gene362|rna362|rna362 314 NYTDKEKEK 322
                                    777666654 PP

>> CPT  Chloramphenicol phosphotransferase-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   1.7e-05     0.023       2      28 ..      89     115 ..      88     124 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.7e-05
                                    -EEEEEE-TTSSHHHHHHHHHHHSSS- CS
                            CPT   2 riilLnGgsssGKsslaralqevldep 28 
                                    ri+lL+G   sGKs+la al + ++++
  gene362|gene362|rna362|rna362  89 RIVLLHGPRNSGKSALATALSKDTENC 115
                                    8*******************9999887 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00012      0.16      21      83 ..      79     137 ..      64     155 .. 0.75
   2 ?   -0.1   0.0       0.5   6.9e+02      85     108 ..     263     286 ..     254     316 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00012
                         RuvB_N  21 ifieaakkreealdhvllyGpPGlGkttlakiiakelgvklkitsgPvlekagdlaalltnle 83 
                                    i+++ +++r++    vll+Gp   Gk++la+ ++k+ +  +   s+  +e+  dl  l+ +++
  gene362|gene362|rna362|rna362  79 IALSLSRERSR---IVLLHGPRNSGKSALATALSKDTENCV-YISAAQVENVEDLDKLILSVQ 137
                                    44444455544...59********************98666.557778999999999887765 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.5
                         RuvB_N  85 kdvlfideihrlsraveevlysam 108
                                    k  l ide h l++ + ++l++  
  gene362|gene362|rna362|rna362 263 KSTLIIDEAHLLDERLLNYLFKIS 286
                                    56799*******999998888654 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   3.7e-05     0.051       5      43 ..      71     109 ..      68     135 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.7e-05
                   Mg_chelatase   5 vkGqeeakraleiaaaGgHnlllvGppGsGKtmlakrlp 43 
                                    ++Gqe+a+ al ++   +  +ll Gp  sGK+ la++l+
  gene362|gene362|rna362|rna362  71 LVGQEKARIALSLSRERSRIVLLHGPRNSGKSALATALS 109
                                    68*********************************9986 PP

>> Myosin_N  Myosin N-terminal SH3-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   0.00023      0.31      14      35 ..     148     170 ..     148     175 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00023
                                    EEEEEEEEESSEEEEEE.TTSEE CS
                       Myosin_N  14 vkGeIkeeeGdkvtVet.edGkt 35 
                                    ++GeI++++G++v+ +t +  +t
  gene362|gene362|rna362|rna362 148 IEGEIVSISGNSVILRTtDMEST 170
                                    79***************444455 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (396 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       784  (0.043728); expected 358.6 (0.02)
Passed bias filter:                      504  (0.0281109); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.44
# Mc/sec: 2685.28
//
Query:       gene363|gene363|rna363|rna363  [L=126]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.6e-40  135.5   0.9      1e-39  135.3   0.9    1.1  1  DUF5099   Domain of unknown function (DUF5099)
     0.0076   16.9   0.0      0.022   15.4   0.0    1.8  2  PBECR1    phage-Barnase-EndoU-ColicinE5/D-RelE like nuclease1


Domain annotation for each model (and alignments):
>> DUF5099  Domain of unknown function (DUF5099)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  135.3   0.9   1.1e-43     1e-39       1     109 []      19     125 ..      19     125 .. 0.98

  Alignments for each domain:
  == domain 1  score: 135.3 bits;  conditional E-value: 1.1e-43
                        DUF5099   1 Kkpklvliinkysevskeeikklkkkygik.ivkligekkdkvlikeeidfenksvlpdlvilcndklvFklksplllyk 79 
                                    Kkp+l++iin+y+++s +ei++l++kygi+ iv l++++ d+++++e++d    ++lpdl+i+cn kl+Fkl++p++lyk
  gene363|gene363|rna363|rna363  19 KKPNLIFIINAYQNISLDEIQRLRDKYGIEkIVGLQRDDFDTFYTQEQLDR---NNLPDLIIYCNIKLEFKLRQPEILYK 95 
                                    99***************************97999****************9...99************************ PP

                        DUF5099  80 aEilfkrkdfsedvlvkaLehYseCeirnG 109
                                    aEi+f+r+ fse+++vkaL+h+s+C i+nG
  gene363|gene363|rna363|rna363  96 AEIVFSRFGFSEGLFVKALDHFSKCIINNG 125
                                    *****************************9 PP

>> PBECR1  phage-Barnase-EndoU-ColicinE5/D-RelE like nuclease1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.31   2.8e+03      87     103 ..      16      32 ..       7      35 .. 0.74
   2 !   15.4   0.0   2.5e-06     0.022      23      64 ..      42      83 ..      36     117 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.31
                         PBECR1  87 gfkgkgdnkwvitayek 103
                                    +f +k +  ++i ay++
  gene363|gene363|rna363|rna363  16 TFAKKPNLIFIINAYQN 32 
                                    56666677799999986 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 2.5e-06
                         PBECR1 23 kkgfGLahilekhledfkefkekaeklinkleeiiekgkvke 64
                                   ++++G+++i+  +++df +f+++++   n+l++ i   ++k 
  gene363|gene363|rna363|rna363 42 RDKYGIEKIVGLQRDDFDTFYTQEQLDRNNLPDLIIYCNIKL 83
                                   689******************************997766554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       521  (0.0290591); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 829.76
//
Query:       gene364|gene364|rna364|rna364  [L=175]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (175 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       376  (0.0209716); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 1221.64
//
Query:       gene365|gene365|rna365|rna365  [L=332]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0014   17.0   0.1     0.0021   16.5   0.1    1.3  1  CDC45     CDC45-like protein
  ------ inclusion threshold ------
       0.62   11.1   5.9       0.83   10.6   0.6    2.9  3  NlpE      NlpE N-terminal domain


Domain annotation for each model (and alignments):
>> CDC45  CDC45-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.1   2.3e-07    0.0021     245     380 ..       9     149 ..       1     163 [. 0.77

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 2.3e-07
                          CDC45 245 dndlLWlAIvGltslelserisae..ryerlrallrdeVrrlnpss..ktekietkarspddtsirlseelrllLlRhWs 320
                                     n+ LW   +  ++ ++ +r  ae    +++   l+ e ++ ++++  + + ++++++++ ++ + +++++ l  l   +
  gene365|gene365|rna365|rna365   9 GNETLWPILIYFSYYDVFYRNGAEcdVCNSILLELKYELEKNETNQvvSGTFEASNSETNVTNALLYKRDINLPYLFSTN 88 
                                    57778877777777777777666544677777777777777555434333444555667777789999999999999999 PP

                          CDC45 321 LydSmlhssYvaskLklWs.ekGrkrLhkLLAkmGvsLaqakqkYthmdlelkreLrekle 380
                                    Ly  + ++  +  + k+++  k + +L+++LAk G+s++ ak+++  +  ++k+ + + l 
  gene365|gene365|rna365|rna365  89 LYLTLNNNITFLVQKKIFTkIKSETKLNEFLAKSGISIQMAKESFINLCKKYKDLIYQTLP 149
                                    999999997777777888736999****************************998888775 PP

>> NlpE  NlpE N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.3     0.059   5.3e+02      28      55 ..      42      70 ..      36     104 .. 0.70
   2 ?   -0.3   0.0      0.25   2.2e+03      16      35 ..      90     109 ..      86     156 .. 0.69
   3 ?   10.6   0.6   9.3e-05      0.83      23      78 ..     223     281 ..     201     287 .. 0.72

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.059
                                   EEEE.ESTT-EEEEEEEEEEEETTTSEEE CS
                           NlpE 28 seey.lgksekefeekGkfswnekgsilt 55
                                   + +y l+k+e++ + +G+f+ +++++ +t
  gene365|gene365|rna365|rna365 42 ELKYeLEKNETNQVVSGTFEASNSETNVT 70
                                   55665677789999999999755444443 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.25
                                    EEEE-TTSEEEEEEEEESTT CS
                           NlpE  16 tLtLnadgtyelseeylgks 35 
                                     LtLn++ t+ ++++   k 
  gene365|gene365|rna365|rna365  90 YLTLNNNITFLVQKKIFTKI 109
                                    58999999998888765544 PP

  == domain 3  score: 10.6 bits;  conditional E-value: 9.3e-05
                                    SEEEEEEEEESTT.-EEEEEEEEEEEETTTSEEEECE..---TCEEEEECTCEEEEEEC CS
                           NlpE  23 gtyelseeylgks.ekefeekGkfswnekgsiltltp..eedektyykvgenklrmldr 78 
                                    +++e s+ y +k+ +k+ ++ G++s++ek+  + l +  +e+ k+  +v++ k+  l  
  gene365|gene365|rna365|rna365 223 RNFEQSQDYDEKNaSKSRTSAGSYSLKEKNVYFLLMHtfKENIKKIKQVNNVKILFLST 281
                                    38***********77**********9888888888775444434444445555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (332 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1203  (0.067098); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 2057.91
//
Query:       gene366|gene366|rna366|rna366  [L=124]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.8e-12   44.8   0.1    1.1e-11   44.5   0.1    1.1  1  Fer2      2Fe-2S iron-sulfur cluster binding domain
  ------ inclusion threshold ------
       0.33   10.6   0.2       0.33   10.6   0.2    1.8  2  MCR       Magnetochrome domain


Domain annotation for each model (and alignments):
>> Fer2  2Fe-2S iron-sulfur cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.5   0.1   1.2e-15   1.1e-11       4      77 ..      17      96 ..      14      97 .. 0.83

  Alignments for each domain:
  == domain 1  score: 44.5 bits;  conditional E-value: 1.2e-15
                                   TTEEEEEEEETTTHBHHHHHHHTTTTTSTTSSSSSS.SSTTEEEEEESCE..CTT.SSSSTHHHHHTTEE.....EEGGGSE CS
                           Fer2  4 dgkevevevadgettlldaaeenggidipysCgggg.CgtClvevlegev..qsd.etelegeeldegkl.....rlaCqti 76
                                   d ++ ev  ++g+t ll++a  n +id++ +C+g+  C+tC+v ++++ +    + +++ e + l+++++     rl Cq++
  gene366|gene366|rna366|rna366 17 DKTPKEVFSVPGKT-LLEVAHAN-KIDLEGACEGSLaCSTCHVILDKKLYnsL-EePSDREYDLLEQAFMpcntsRLGCQVR 95
                                   55666665667788.*****988.**********99*******8887777854.3589999999988888**********99 PP

                                   E CS
                           Fer2 77 v 77
                                   v
  gene366|gene366|rna366|rna366 96 V 96
                                   8 PP

>> MCR  Magnetochrome domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.2   3.7e-05      0.33      19      27 ..      51      59 ..      49      62 .. 0.85
   2 ?   -3.1   0.3      0.69   6.2e+03      18      21 ..      83      86 ..      83      87 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 3.7e-05
                                   -GGGT--BS CS
                            MCR 19 nCtkCHqIi 27
                                   +C++CH+I+
  gene366|gene366|rna366|rna366 51 ACSTCHVIL 59
                                   8*******8 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 0.69
                                   S-GG CS
                            MCR 18 mnCt 21
                                   m+C+
  gene366|gene366|rna366|rna366 83 MPCN 86
                                   99*8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       456  (0.0254337); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 864.02
//
Query:       gene367|gene367|rna367|rna367  [L=72]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.031   13.8   0.3      0.031   13.8   0.3    1.1  1  VirArc_Nuclease  Viral/Archaeal nuclease


Domain annotation for each model (and alignments):
>> VirArc_Nuclease  Viral/Archaeal nuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.3   1.7e-06     0.031      37      81 ..       5      47 ..       1      64 [. 0.84

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.7e-06
                VirArc_Nuclease 37 kwkekgllkfdvyirrtgvgtltsvinedyykdlldkydltlyvk 81
                                   ++k+  +++ ++y+r+   gtlt   +e+y+k +  k ++  ++ 
  gene367|gene367|rna367|rna367  5 RYKSDKVIEPNFYMRND--GTLTYFFDEEYFKSIVGKLKIVEFMM 47
                                   5788899*******876..69**************9998865554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (72 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       345  (0.0192426); expected 358.6 (0.02)
Passed bias filter:                      212  (0.0118244); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.42
# Mc/sec: 511.84
//
Query:       gene368|gene368|rna368|rna368  [L=179]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.7e-06   27.0   0.2    1.8e-05   25.4   0.0    1.8  2  Methyltransf_12  Methyltransferase domain
    5.3e-05   23.1   0.0    9.2e-05   22.3   0.0    1.3  1  Methyltransf_23  Methyltransferase domain
     0.0003   21.4   0.1     0.0016   19.1   0.0    2.2  2  Methyltransf_25  Methyltransferase domain
     0.0018   18.1   0.0       0.01   15.6   0.0    1.9  2  Methyltransf_31  Methyltransferase domain
  ------ inclusion threshold ------
       0.17   12.5   0.0        0.4   11.4   0.0    1.6  1  Methyltransf_11  Methyltransferase domain


Domain annotation for each model (and alignments):
>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.1      0.82     3e+03      33      33 ..      30      30 ..       4      67 .. 0.51
   2 !   25.4   0.0   5.1e-09   1.8e-05       1      41 [.      89     141 ..      89     147 .. 0.95

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.82
                Methyltransf_12 33 i 33
                                   +
  gene368|gene368|rna368|rna368 30 L 30
                                   2 PP

  == domain 2  score: 25.4 bits;  conditional E-value: 5.1e-09
                Methyltransf_12   1 LeiGcGtGsllrallekl............pdieytgvDispsaiedakekla 41 
                                    Le+GcG+Gs l+++l+ +            ++ +++g+D+sp+ai   ++k +
  gene368|gene368|rna368|rna368  89 LELGCGVGSSLHHFLKINeeensatsargeSRFDVHGCDFSPQAISIYQQKYK 141
                                    8********************************************99999876 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.0   2.6e-08   9.2e-05      21      74 ..      83     150 ..      59     169 .. 0.78

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 2.6e-08
                Methyltransf_23  21 raggrvLdiGcGtGillevlre..............ngfsvtgvDlspeaveiaekakkaqkdqfdeq 74 
                                      + r+L++GcG+G+ l ++ +               +f+v g D sp+a++i+++++k ++  +d +
  gene368|gene368|rna368|rna368  83 LNRRRILELGCGVGSSLHHFLKineeensatsargeSRFDVHGCDFSPQAISIYQQKYKGVFFVHDLI 150
                                    4577**********9988885545566777777666679**************998888887777655 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       1.1   4.1e+03      34      45 ..      30      41 ..       9      65 .. 0.57
   2 !   19.1   0.0   4.4e-07    0.0016       1      61 [.      88     156 ..      88     172 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.1
                                   HHHHHHHHHHTT CS
                Methyltransf_25 34 leaareraeeeg 45
                                   le+a +++++++
  gene368|gene368|rna368|rna368 30 LEKALKKVNDDN 41
                                   444444443333 PP

  == domain 2  score: 19.1 bits;  conditional E-value: 4.4e-07
                                    EEEET-TTSHHHHHHHCT.........S.T..SSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSS CS
                Methyltransf_25   1 vLdlGcGtGrltlalakr.........l.g..kakvtgvDiseemleaareraeeeglnvefvqgdaedlpfe 61 
                                    +L+lGcG G  + +++k            g  + +v+g+D+s++++ + +++++     v fv+  ++d p++
  gene368|gene368|rna368|rna368  88 ILELGCGVGSSLHHFLKIneeensatsArGesRFDVHGCDFSPQAISIYQQKYK----GVFFVHDLISDTPLP 156
                                    8***********99998877777776514345899******************4....566666666776655 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.15   5.3e+02      88     111 ..      24      47 ..       6      78 .. 0.66
   2 !   15.6   0.0   2.9e-06      0.01       6      47 ..      87     139 ..      82     156 .. 0.76

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.15
                Methyltransf_31  88 adpdkileeiervlkpggillied 111
                                      +d++le++ + ++++  +++++
  gene368|gene368|rna368|rna368  24 EIKDDVLEKALKKVNDDNLCISRN 47 
                                    456667777777777666666554 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 2.9e-06
                Methyltransf_31   6 rvlDlGCGtGeltfelae...elgpkae.........vvGiDiseeaielAren 47 
                                    r+l+lGCG G  ++ + +   e ++ a+         v+G D+s++ai+  +++
  gene368|gene368|rna368|rna368  87 RILELGCGVGSSLHHFLKineEENS-ATsargesrfdVHGCDFSPQAISIYQQK 139
                                    79********999999977764444.11344667888***********988774 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00011       0.4       1      58 [.      89     156 ..      89     168 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00011
                                    EEET-TTSHHHHHHH...........HTT...SEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS- CS
                Methyltransf_11   1 LdvGcGtGrlaeala...........krg...arvvgvDlskemlklakekaseeglkvefvvadaeklpfe 58 
                                    L++GcG G+ + ++             rg    +v g+D+s++++ + ++k+++      fv+  ++++p++
  gene368|gene368|rna368|rna368  89 LELGCGVGSSLHHFLkineeensatsARGesrFDVHGCDFSPQAISIYQQKYKGVF----FVHDLISDTPLP 156
                                    89**********999999998877764447889***************99999876....577777777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (179 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       697  (0.0388756); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1236.13
//
Query:       gene369|gene369|rna369|rna369  [L=209]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0075   16.5   2.0        0.7   10.2   0.0    2.6  3  Ribosomal_L13  Ribosomal protein L13
  ------ inclusion threshold ------
       0.11   12.1   0.1       0.17   11.5   0.1    1.2  1  NEMP           NEMP family
       0.12   12.2   0.0       0.22   11.3   0.0    1.3  1  DUF4158        Domain of unknown function (DUF4158)
       0.12   12.4   0.0       0.21   11.7   0.0    1.3  1  Gp138_N        Phage protein Gp138 N-terminal domain


Domain annotation for each model (and alignments):
>> Ribosomal_L13  Ribosomal protein L13
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.8   0.0    0.0035        16       4      23 ..      18      38 ..      16      41 .. 0.84
   2 !   10.2   0.0   0.00016       0.7      42     106 ..      44     108 ..      36     120 .. 0.63
   3 ?   -3.1   0.1         2   9.1e+03      51      58 ..     179     186 ..     165     204 .. 0.54

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0035
                                   EEEETTSBHHHHHHHHHH.HH CS
                  Ribosomal_L13  4 viDAegqvlgrlaskiak.vL 23
                                   vi+A+++v g+la+ +ak +L
  gene369|gene369|rna369|rna369 18 VINAKDHVAGKLATFVAKnIL 38
                                   89**************97245 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00016
                                    EEEEGGCBB-SSTHHTT-EEEEE-SSTTSEEEEEHHHHHCCSHHHHHHHHHHCCS-SSHHHHHHG CS
                  Ribosomal_L13  42 vvinaekvaltgkkleqkvyyrhtgypgglkevtakellekkpeeilekaVkgmLpknklgrrrl 106
                                     v+ +e++++tg   +    ++     ++l +     +++++p +++++ V++m pk+k + +  
  gene369|gene369|rna369|rna369  44 TVVHTENIVFTGPIERGVGRFKDFLNKRKLTNPLRGPFHHRSPAMLFTRIVRRMVPKKKYKGQCA 108
                                    5666666666665333322222222333333333345899*****************99876654 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 2
                                    -SSTHHTT CS
                  Ribosomal_L13  51 ltgkkleq 58 
                                     t +k+++
  gene369|gene369|rna369|rna369 179 ETKEKIAE 186
                                    22223222 PP

>> NEMP  NEMP family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   3.9e-05      0.17     137     220 ..     109     195 ..     107     205 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 3.9e-05
                           NEMP 137 valvlilqssldpelalaalilllllknl...pelvlsllkrklrkrklfplkkpkrrllteeEyreqgeketkkaleel 213
                                    ++l+ +  s+ d  +a+ ++++   + +    p++ ++++k ++ k  +++ ++ +r+    eE+r++++++++k  e++
  gene369|gene369|rna369|rna369 109 LSLLTVHDSCPDDLVATQCMVCPRAMLKYtadPIRRFYYMKDLCSKFGWKYFNEVERQNVIVEEIRRKAKETKEKIAEKV 188
                                    789999***************9653333336999*********9666666666888888889999999887666666665 PP

                           NEMP 214 reycrsp 220
                                     +  +s 
  gene369|gene369|rna369|rna369 189 NSIKESD 195
                                    5444444 PP

>> DUF4158  Domain of unknown function (DUF4158)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0     5e-05      0.22      74     134 ..     122     182 ..     113     185 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 5e-05
                        DUF4158  74 fiaeqlgledpsalakyasreqtrrehlaeIrellgyrpfteadl.releewlaqlAtetdr 134
                                     +a+q+ +  p+a+ ky +    r+ +++ +++++g++ f+e ++ + ++e++++ A+et++
  gene369|gene369|rna369|rna369 122 LVATQCMV-CPRAMLKYTADPIRRFYYMKDLCSKFGWKYFNEVERqNVIVEEIRRKAKETKE 182
                                    6999****.7*********************************9978889999999988876 PP

>> Gp138_N  Phage protein Gp138 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   4.6e-05      0.21      12      60 ..      12      62 ..       4      74 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 4.6e-05
                        Gp138_N 12 avtatvqpaikkklsdg..etvelpllvdvpvvfprgggvtltfpvkaGde 60
                                   ++  ++ ++ k + + +  + v+  +l+ vpv++ +++++++t p+++G  
  gene369|gene369|rna369|rna369 12 NQSREIVINAKDHVAGKlaTFVAKNILEGVPVTVVHTENIVFTGPIERGVG 62
                                   4444455555555555455889999***********************965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1926  (0.107424); expected 358.6 (0.02)
Passed bias filter:                      973  (0.0542696); expected 358.6 (0.02)
Passed Vit filter:                       110  (0.00613531); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 1442.56
//
Query:       gene37|gene37|rna37|rna37  [L=70]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.6e-06   27.2   0.0    4.1e-06   27.0   0.0    1.1  1  rve       Integrase core domain
     0.0008   19.1   0.1     0.0013   18.4   0.1    1.4  1  rve_3     Integrase core domain
  ------ inclusion threshold ------
      0.028   13.9   0.2      0.031   13.7   0.2    1.0  1  DUF4607   Domain of unknown function (DUF4607)


Domain annotation for each model (and alignments):
>> rve  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   0.0   6.8e-10   4.1e-06      75     118 ..       6      49 ..       1      50 [. 0.94

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 6.8e-10
                        rve  75 gseytskafrefladlgirvsftrpgrpqdnGkvErfhrtlkde 118
                                g+e++s+ ++ f +++gi++ +t   +++ nG+vEr + t+++ 
  gene37|gene37|rna37|rna37   6 GKEFKSRLVTSFSEENGIEHHVTSTEHSEANGRVERLNCTIREY 49 
                                99**************************************9975 PP

>> rve_3  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.1   2.2e-07    0.0013       1      35 [.      21      55 ..      21      67 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 2.2e-07
                      rve_3  1 lgielsyiapgkPqqNglvEsfngtlrdellneel 35
                               +gie++++   +   Ng vE++n t+r+ + +++ 
  gene37|gene37|rna37|rna37 21 NGIEHHVTSTEHSEANGRVERLNCTIREYIRKRSN 55
                               69************************987776554 PP

>> DUF4607  Domain of unknown function (DUF4607)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.2   5.2e-06     0.031      22      63 ..      15      58 ..      10      67 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.2e-06
                    DUF4607 22 asfeeesygearpsptsssetde..apliftvreeikkrarrap 63
                               +sf ee+ +e+  ++t  se +   + l  t+re i+kr+    
  gene37|gene37|rna37|rna37 15 TSFSEENGIEHHVTSTEHSEANGrvERLNCTIREYIRKRSNPKI 58
                               79******************986225799*********987554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (70 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       486  (0.0271069); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 480.27
//
Query:       gene370|gene370|rna370|rna370  [L=138]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.7e-41  141.0   1.1    2.1e-41  140.7   1.1    1.1  1  Ribosomal_L32e  Ribosomal protein L32


Domain annotation for each model (and alignments):
>> Ribosomal_L32e  Ribosomal protein L32
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  140.7   1.1   1.2e-45   2.1e-41       1     108 []      21     128 ..      21     128 .. 0.99

  Alignments for each domain:
  == domain 1  score: 140.7 bits;  conditional E-value: 1.2e-45
                                    ------TTTTT-TTS-SS------TT-TTTTT-TTS-----GGG---TTTTT--TTS-EEEEESSGGGGTT--TTTE..E CS
                 Ribosomal_L32e   1 tkkFirhqsdryvklkeswrkprGidnrvrrrfkgqilmpkiGYgspkktrgllpsGfkkvlVhnvkeLevllmenksya 80 
                                    +k F+r++sdr++++k swr+prGidnrvrr+f+g+i+mp+ G+++ + +++l+p+G++kv+V+nv+eLe+l+  n+ y+
  gene370|gene370|rna370|rna370  21 KKTFNRFKSDRFKRVKPSWRHPRGIDNRVRRKFRGTISMPNKGFKTASVIKNLTPDGYRKVMVSNVRELEALKSLNTYYC 100
                                    689***************************************************************************** PP

                                    EEE-TTS-HHHHHHHHHHHHHTT-EBSS CS
                 Ribosomal_L32e  81 aeiahsVsskkrkeiverAaelgikVtN 108
                                    aei h V++kkr+eiv++A+e +i VtN
  gene370|gene370|rna370|rna370 101 AEIRHGVGAKKRIEIVSKADEYNIVVTN 128
                                    ***************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       471  (0.0262703); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 1067.55
//
Query:       gene371|gene371|rna371|rna371  [L=82]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.016   15.4   0.9      0.026   14.8   0.9    1.3  1  DUF1761   Protein of unknown function (DUF1761)


Domain annotation for each model (and alignments):
>> DUF1761  Protein of unknown function (DUF1761)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.9   1.4e-06     0.026      44     102 ..       2      79 ..       1      81 [. 0.72

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.4e-06
                        DUF1761  44 alamglslvlslliay...........vlaallaalga........rtfkagallglllglgfiapaiisnalfekks 102
                                    +l++++++++sl+i+            +l+++   +++        ++++a++++ + ++lgf + +  +  l++kk+
  gene371|gene371|rna371|rna371   2 ILPFIFTFLGSLMITCglevlynfewnFLEVICSSYQCldanmnkeASMVAYLVTLFSFALGFGIQIPTILKLHKKKP 79 
                                    689*************77777777777555555555558888888888888888888887777776666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       677  (0.0377601); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 668.06
//
Query:       gene372|gene372|rna372|rna372  [L=110]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.2e-18   64.9   0.0    9.2e-18   64.1   0.0    1.4  1  Swi5      Swi5


Domain annotation for each model (and alignments):
>> Swi5  Swi5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.1   0.0   5.1e-22   9.2e-18      24      77 ..      55     108 ..      42     110 .] 0.90

  Alignments for each domain:
  == domain 1  score: 64.1 bits;  conditional E-value: 5.1e-22
                                    HHHHHHH.HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTSHCGGGHHHCT- CS
                           Swi5  24 eelkekkdpeetvkrhIklLheYNEiKDvgqgLigliAeargvrikevfeefGv 77 
                                    e ++ ++d e++vk+ I++L++YNE+KD + +L+g+iAe rgvrik+v eef++
  gene372|gene372|rna372|rna372  55 ESMNMPDDVEAVVKNFIRKLNTYNELKDCCESLVGKIAELRGVRIKDVREEFEL 108
                                    5567788*********************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       740  (0.0412739); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 768.03
//
Query:       gene373|gene373|rna373|rna373  [L=750]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.7e-31  107.4   8.9    1.1e-29  103.8   8.9    2.6  1  Syja_N    SacI homology domain


Domain annotation for each model (and alignments):
>> Syja_N  SacI homology domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.8   8.9   6.2e-34   1.1e-29       2     315 ..      44     347 ..      43     355 .. 0.77

  Alignments for each domain:
  == domain 1  score: 103.8 bits;  conditional E-value: 6.2e-34
                         Syja_N   2 gilGlirllsgsyllvitkreevgt.lkgkkeiykitevellplsseeeaekalkslkaktekkkeekeleekllkllek 80 
                                    gilG i +++++yll ++++      l  + +i +i+++e+ +++s    e+  k++  +t++        +k  +l+++
  gene373|gene373|rna373|rna373  44 GILGKIMVNDNMYLLYVKESFLALDnL--GYKIHRIKNIECANITSI---EEFCKRKILRTKD--------KKNFRLVKD 110
                                    9*******************8886634..469999999999999766...3333332222222........334445555 PP

                         Syja_N  81 lfessgsfYFsy.dlDltrslqrqlekssesskslplweraderFvWNrhllkplieaeldswllpviqGfveqsklkls 159
                                    +f +    + s    +l + l+++   + ++++ +      de+F+WN+ l +++++a+ +  ++ +  G+++ +++   
  gene373|gene373|rna373|rna373 111 EFLNAM-SHQSKdMENLVKFLNESPLYY-TRDEIE------DEKFLWNKVLRSNMNDAQNQTGIVYLYNGYFNVKAC--- 179
                                    554222.233541125555555554432.333444......999***********9999999**********55554... PP

                         Syja_N 160 ksqkekekkevtltlisRrsrkraGtRylrRGiddeGnvANfvEtEqilevessekeskilSfvqiRGSiPlfWsqeptl 239
                                             +++++l+s  s++r G Ry++RG+d eGnv+Nfv +  ++ +    + s i+  + +RGS+P++W+q+++l
  gene373|gene373|rna373|rna373 180 --------ANFDYVLLSFISSNRVGPRYFSRGVDVEGNVSNFVKSKYLVVK----NGSVIIDVIIYRGSVPVYWEQTGSL 247
                                    ........35****************************************5....3479*******************75 PP

                         Syja_N 240 kykpkirierseeenleafkkHfekllkrY.....................................gkvvvvnLlekkg 282
                                    +   +++   +e+++ +a+ kHf + +++                                      +++ v+nLl++k+
  gene373|gene373|rna373|rna373 248 R---ELQC--NEKDSFRACFKHFYNNFRDGepvvekqqddervsefsgvmennlqnrgaftqpichfNNILVINLLSNKK 322
                                    5...4555..46667788888887777777888999999999999999999999999999999999899*********** PP

                         Syja_N 283 rEkkLgeayekavkklnklekekkklkyveFDf 315
                                    +E+kL+  y++++k+ln        ++y  F+ 
  gene373|gene373|rna373|rna373 323 SEQKLSMIYKELLKNLN--------IQYLDFNL 347
                                    ****************8........56666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (750 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       881  (0.0491383); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.63u 0.23s 00:00:00.86 Elapsed: 00:00:00.41
# Mc/sec: 5495.68
//
Query:       gene374|gene374|rna374|rna374  [L=232]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.018   15.2   0.0      0.033   14.3   0.0    1.4  1  SSPI      Small, acid-soluble spore protein I
        0.5   10.3   9.8        1.1    9.2   9.8    1.6  1  DUF4083   Domain of unknown function (DUF4083)


Domain annotation for each model (and alignments):
>> SSPI  Small, acid-soluble spore protein I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   3.7e-06     0.033       4      41 ..     105     145 ..     103     157 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.7e-06
                           SSPI   4 RkaiiqnlkgsskeeleetIedaiqskeEk...tLpGLGVl 41 
                                       + ++l+++++++l ++I+da +++ E+   tLpG GV+
  gene374|gene374|rna374|rna374 105 GTKVYEKLRQDTHDQLSTMIKDAKSRNIEAlviTLPGSGVF 145
                                    56799**********************9974447******9 PP

>> DUF4083  Domain of unknown function (DUF4083)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   9.8   0.00013       1.1       5      29 ..     206     230 ..     204     232 .] 0.92

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00013
                        DUF4083   5 liyliivivLilllvfsftlfiRrv 29 
                                    +++ i+++v+++l v+s+ +f+Rr 
  gene374|gene374|rna374|rna374 206 ILISIAIVVILILTVVSIFFFLRRY 230
                                    5899*******************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1117  (0.0623013); expected 358.6 (0.02)
Passed bias filter:                      746  (0.0416086); expected 358.6 (0.02)
Passed Vit filter:                        92  (0.00513135); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.31s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 1508.30
//
Query:       gene375|gene375|rna375|rna375  [L=80]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       355  (0.0198003); expected 358.6 (0.02)
Passed bias filter:                      213  (0.0118802); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.42
# Mc/sec: 568.90
//
Query:       gene376|gene376|rna376|rna376  [L=207]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       736  (0.0410508); expected 358.6 (0.02)
Passed bias filter:                      535  (0.0298399); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 1437.35
//
Query:       gene377|gene377|rna377|rna377  [L=139]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       444  (0.0247643); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 985.60
//
Query:       gene378|gene378|rna378|rna378  [L=264]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      8e-16   58.5   1.4    9.1e-16   58.4   0.4    1.5  2  DcpS_C    Scavenger mRNA decapping enzyme C-term binding
     0.0011   19.7   1.4      0.017   15.9   0.9    2.6  2  DcpS      Scavenger mRNA decapping enzyme (DcpS) N-terminal


Domain annotation for each model (and alignments):
>> DcpS_C  Scavenger mRNA decapping enzyme C-term binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       1.3   1.1e+04      43      58 ..      52      68 ..      39      83 .. 0.68
   2 !   58.4   0.4     1e-19   9.1e-16       2     107 ..     125     229 ..     124     234 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 1.3
                                   S.---SGGG--TTTTTH CS
                         DcpS_C 43 r.dikslrdLtkehlpl 58
                                   + +++++++L++e++++
  gene378|gene378|rna378|rna378 52 EiELNEIEKLKTEKYEV 68
                                   25666777777777665 PP

  == domain 2  score: 58.4 bits;  conditional E-value: 1e-19
                                    -HHHHHHTTSS-B-EEEE-SSEEEEE-SS....-SSSEEEEEEESS.---SGGG--TTTTTHHHHHHHHHHHHHHHTT-T CS
                         DcpS_C   2 wvfnilakgkepervvyedekfvvlkDik....pkaklhllvipkr.dikslrdLtkehlpllkemrekakkvieekyne 76 
                                    w+ +i  k+ e e  ++ d++f+v++D+k    + ++l+ll i k+  + ++r+L+   l l+ + +++a +v++  y +
  gene378|gene378|rna378|rna378 125 WIQKI--KDGEYEIPIHVDSRFIVINDYKwdmsDVSQLYLLLIFKDqGLFTVRELN---LNLIVDAKKTALQVLNTIY-G 198
                                    55555..66677777999***********966666***********9********9...99*****************.7 PP

                                    -EEEEE--SCCCT--S-S--EEEEE...... CS
                         DcpS_C  77 vdaeelrvgvhyqPsvyhlHlHvisldfesp 107
                                    + ++++ +++hy+Ps+y lHlH+++l+ +++
  gene378|gene378|rna378|rna378 199 LSEQDVLMYFHYRPSYYTLHLHIVNLERKME 229
                                    79999********************988876 PP

>> DcpS  Scavenger mRNA decapping enzyme (DcpS) N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.9   1.9e-06     0.017      20     102 ..      32     100 ..      19     102 .. 0.64
   2 ?   -1.7   0.0      0.57   5.1e+03      69      95 ..     151     187 ..     132     198 .. 0.65

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.9e-06
                           DcpS  20 risllGtidsepAililektafeteeaaklaslkesleelknlgandiYtwllavlkqkeeelpdlkinliyPatekhik 99 
                                    ++++lGt++++ +i++++ +++e +e +k      + e+ + +     Y             +++  + +i P++e+hik
  gene378|gene378|rna378|rna378  32 NTVILGTLNDKLSIVLVQGKEIELNEIEK-----LKTEKYEVTLMITPYMR---------MVSAHYTLRVISPCSEHHIK 97 
                                    56666777777777777666666666322.....22222222333333443.........344678999*********** PP

                           DcpS 100 KYs 102
                                    KY 
  gene378|gene378|rna378|rna378  98 KYG 100
                                    **6 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.57
                           DcpS  69 twllavlk..........qkeeelpdlkinliyPate 95 
                                    +w ++ ++          q   ++++l +nli  a +
  gene378|gene378|rna378|rna378 151 KWDMSDVSqlylllifkdQGLFTVRELNLNLIVDAKK 187
                                    5555544444444444434446667777777776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (264 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       704  (0.039266); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 1874.22
//
Query:       gene379|gene379|rna379|rna379  [L=172]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.15   11.3   0.1       0.16   11.2   0.1    1.2  1  Macro_2   Macro-like domain


Domain annotation for each model (and alignments):
>> Macro_2  Macro-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   9.2e-06      0.16      78     106 ..      71      99 ..      22     120 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 9.2e-06
                        Macro_2  78 sfGylGGGfdlalfeyfGGkpfetwfrkk 106
                                     +  +G G d+ + +y+G k  ++w+r++
  gene379|gene379|rna379|rna379  71 EYDRIGCGSDREMNKYYGDKGGNSWYRND 99 
                                    57889**********************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       367  (0.0204696); expected 358.6 (0.02)
Passed bias filter:                      195  (0.0108762); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1316.71
//
Query:       gene38|gene38|rna38|rna38  [L=382]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (382 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       550  (0.0306766); expected 358.6 (0.02)
Passed bias filter:                      491  (0.0273858); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.21s 00:00:00.67 Elapsed: 00:00:00.36
# Mc/sec: 3143.21
//
Query:       gene380|gene380|rna380|rna380  [L=417]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.8e-05   22.8   6.3     0.0023   17.5   0.3    4.5  4  PUF       Pumilio-family RNA binding repeat


Domain annotation for each model (and alignments):
>> PUF  Pumilio-family RNA binding repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.1     0.013   2.4e+02       2      16 ..      30      44 ..      29      62 .. 0.73
   2 ?   -2.5   0.0       0.3   5.4e+03       6      20 ..      68      82 ..      66      83 .. 0.80
   3 !    3.5   0.1    0.0036        64      17      33 ..     192     208 ..     192     210 .. 0.89
   4 !   17.5   0.3   1.3e-07    0.0023       1      29 [.     230     259 ..     230     261 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.013
                                   HGGGHHHHHTSTTHH CS
                            PUF  2 ikgnlvqLstdqyGn 16
                                   ik++++ Lst +  +
  gene380|gene380|rna380|rna380 30 IKPYITGLSTSKTTS 44
                                   899******999877 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.3
                                   HHHHHTSTTHHHHHH CS
                            PUF  6 lvqLstdqyGnyvvQ 20
                                   ++ L+ +  G+ v++
  gene380|gene380|rna380|rna380 68 VENLVFHNLGSKVLE 82
                                   667777999999996 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.0036
                                    HHHHHHHHHSCHHHHHH CS
                            PUF  17 yvvQkllehateeqkkl 33 
                                    +v+Q+l+++ ++++ k+
  gene380|gene380|rna380|rna380 192 HVLQTLFTYEKLTEMKY 208
                                    9********99999887 PP

  == domain 4  score: 17.5 bits;  conditional E-value: 1.3e-07
                                    HHGGGHHHHHTSTTHHHHHHHHHHH.SCHH CS
                            PUF   1 sikgnlvqLstdqyGnyvvQklleh.atee 29 
                                    +ik++l+ L++++y ny +Q ++e+  ++ 
  gene380|gene380|rna380|rna380 230 KIKNKLQLLAVNKYSNYMIQSFIEKyEDTI 259
                                    699*********************955554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (417 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1593  (0.0888505); expected 358.6 (0.02)
Passed bias filter:                      456  (0.0254337); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 2771.98
//
Query:       gene381|gene381|rna381|rna381  [L=58]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.4e-16   58.5   6.3    7.8e-16   57.7   6.2    1.6  1  TFIIS_C        Transcription factor S-II (TFIIS)
     0.0028   17.3   4.3      0.011   15.4   0.1    2.2  2  Baculo_LEF5_C  Baculoviridae late expression factor 5 C-termi


Domain annotation for each model (and alignments):
>> TFIIS_C  Transcription factor S-II (TFIIS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.7   6.2   8.7e-20   7.8e-16       2      34 ..      26      58 .]      21      58 .] 0.97

  Alignments for each domain:
  == domain 1  score: 57.7 bits;  conditional E-value: 8.7e-20
                        TFIIS_C  2 kCpkCgsreayffqlQtRsaDEpmtvfykCtkC 34
                                    C+kCg + a+f+++QtRsaDEpmt+fy+C++C
  gene381|gene381|rna381|rna381 26 ICEKCGYNTASFYEMQTRSADEPMTIFYQCLQC 58
                                   59******************************* PP

>> Baculo_LEF5_C  Baculoviridae late expression factor 5 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    3.4   0.9    0.0068        61      30      41 ..      20      31 ..      14      32 .. 0.77
   2 !   15.4   0.1   1.2e-06     0.011      20      40 ..      38      58 .]      34      58 .] 0.93

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.0068
                  Baculo_LEF5_C 30 ivsfvryCskCg 41
                                   ++   + C kCg
  gene381|gene381|rna381|rna381 20 MAKCEKICEKCG 31
                                   5555679****9 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 1.2e-06
                  Baculo_LEF5_C 20 iEiQnRagDEivsfvryCskC 40
                                    E Q+R+ DE   +  +C +C
  gene381|gene381|rna381|rna381 38 YEMQTRSADEPMTIFYQCLQC 58
                                   69****************999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (58 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       911  (0.0508115); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 423.81
//
Query:       gene382|gene382|rna382|rna382  [L=706]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     5e-105  352.0   2.4   6.3e-105  351.6   2.4    1.0  1  HSP70     Hsp70 protein
    4.2e-10   39.0   0.1    4.6e-09   35.5   0.0    2.6  2  MreB_Mbl  MreB/Mbl protein


Domain annotation for each model (and alignments):
>> HSP70  Hsp70 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  351.6   2.4    7e-109  6.3e-105       1     595 [.      45     685 ..      45     688 .. 0.81

  Alignments for each domain:
  == domain 1  score: 351.6 bits;  conditional E-value: 7e-109
                                    EEEEEEXSSEEEEEEEE...TTEEEEEXXTTSXSSEESEEEE.......XTTSEEETHHHH.....HCTTTTGGGEEEXG CS
                          HSP70   1 viGiDLGttnsvvavme...ggkievianeegnrttPsvvaF.......tkkerlvGeaAk.....rqavtnpkntvfsv 65 
                                    +iGiDLGtt+s+v+v+    ++++e++   +g++t Psvv +       tkk++++ +++      +  +  p+  ++++
  gene382|gene382|rna382|rna382  45 AIGIDLGTTYSCVGVVGptgATSMEILDLGQGRQTLPSVVKYipyrdevTKKQQYMAKTGWevyneNMRTPSPNTYLYAF 124
                                    59*************9622256789****************9333333334455555554311111222333455589** PP

                                    GGTTTXB..TTSHHHHHHHTTXSSEEEEETTSB......EEEEEEETTE....EEEHHHHHHHHHHHHHHHHHHHHT.SB CS
                          HSP70  66 KrliGrk..fsdpevqkeikelpykvvkkengk......avveveaage....kftpeqisamvLkklketaeaylg.kk 132
                                    Kr++G +   +dp++    k+++y++++  n+k      +++ ++  ++    + ++ + sa +L++l + +++  g k+
  gene382|gene382|rna382|rna382 125 KRYMGLSslQDDPSLSGIQKKVTYTLEEVVNEKdpskksIYMLIKDVNDnvvkRVSAIDASAYILEHLMKVVNDRYGaKN 204
                                    *****8733478999999999999887765543111111222222222246668999999*******9888776655167 PP

                                    EEEEEEEEXTTXXHHHHHHHHHHHHHTTXEEEEEEEHHHHHHHHHHTCCSS...SCEEEEEEEEXSSXEEEEEEEEETTE CS
                          HSP70 133 vtdavitvPaYfndaqRqatkdAgkiAGLnvlRivNepTAaalaYGldkkd...kernvlvyDlGggtfdvSilelekGv 209
                                    +++++itvPaYf + q qat+ A++iAGL   R vNep Aaa aY + +kd        lv+DlGggt+dvSile e Gv
  gene382|gene382|rna382|rna382 205 IANVIITVPAYFSEMQVQATRTAATIAGLSLSRTVNEPVAAAYAYQVRNKDrsaALDSFLVFDLGGGTMDVSILEYEGGV 284
                                    ***************************************************65555678********************* PP

                                    EEEEEEEEETTXSHHHHHHHHHHHHHHHHHHHHSXXGGGSHHHHHHHHHHHHHHHHHTTTSSCS...EEEEEEEEEETTT CS
                          HSP70 210 fevkaTagDthlGGedfDealvehlveefkkkegidlskdkkalqrlkeaaekaKkeLSsskqt...einleietvdedg 286
                                    +ev+  +g + lGGe+  ++l +h+   ++k+   ++  ++    rl+  ae+ K++L +++ +   ++++e e +   +
  gene382|gene382|rna382|rna382 285 LEVQTYSGSNFLGGENINDCLFKHFYGLMEKS---NILLNDVEKLRLRGFAERFKISLCTRQLEeggDAEFEDEFIYLGD 361
                                    *************************9999887...4555666778**************976442225778878888877 PP

                                    EEEEEEEEHHHHHHHHHHHHHHTHHHHH....HHHHHCTEE....GGGCSEEEEESGGGGSHHHHHHHHHHTTCH.HBSS CS
                          HSP70 287 kdlseklsRakfeelvedllertlepve....kalkdaklk....keeidevvlvGGstRiPkvqelvkelfgke.pskt 357
                                    k ++ kl  ++f+++++++ +r+ + ++     +l   k k    k++i++v+lvGGstR+P v++++  +fgk+  s +
  gene382|gene382|rna382|rna382 362 KVFTFKLRTSEFNKVCDEVSKRIRHYLTgdvdGILYKYKQKldkdKDDIKKVLLVGGSTRVPFVRDILYGIFGKDkVSAE 441
                                    **********************9876541111556443322223489**************************8626889 PP

                                    SHTTTHHHHHHHHHHHHHCTCGCSHCCEEEEBESS-EEEEETTTEEEEEESTTCBSSEEEEEEEEESSTTSSSEEEEEEE CS
                          HSP70 358 vnpDeavaiGAAvqagvlsgeeevkdllllDvtpLslgietlggvmtkliernttiptkksqvfstaadnqtaveievlq 437
                                    +npD +va GAA  ++ +      + + l Dv+p+ +gi +  + ++ + +   +ip+ ++++f+t +dnq +v+i+v q
  gene382|gene382|rna382|rna382 442 LNPDTVVAEGAAYYSANMLNYLLDDSIHLIDVVPMNIGICVDSDTFESILDMESAIPATQTKTFTTGHDNQMKVNIRVAQ 521
                                    ************98776666699999****************************************************** PP

                                    SSSSBGGGSEEEEEEEEECESSCSTTCSEEEEEEEEETTSCEEEEEEETTTCCEEEEE.EECCSSSBHHHHHHHHHHHHH CS
                          HSP70 438 gerelvkdnkllgsfeldgippaprGvpqieVtfdidanGiltvsakdketgkeeeit.ieaseglseeeiekmvkdaee 516
                                    g r + ++n +lg+fel+  +p+prGvpqieVt++id++  ++v+a dk t+ke++i+ ++++ +ls++   +m kd e+
  gene382|gene382|rna382|rna382 522 GLRYQYHKNMHLGEFELTLEKPQPRGVPQIEVTISIDKQRDIHVTAVDKLTKKEAKIKfVKTDYELSDARRSEMLKDRES 601
                                    *********************************************************94566667*************** PP

                                    CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH..GGGSTHHHHHHHHHHHHHHHCHT...TSSCHHHHHHHHHHHHHHHH CS
                          HSP70 517 saeedkkkkeaieakneaeelvyslekkleee..aekvseaekekvesaieeLkeel...eeeekeeieakteelkkvve 591
                                    ++++d++ k + ++ +e+e++ + ++++ ++   a++v+ ++ +++++  + L+e+     + ++++++ + +e++++v+
  gene382|gene382|rna382|rna382 602 NKAADERMKVKDQRVKELENYKDVVNSAAQQPtvAQEVRVEAYKAINKLDDFLREAKnplGGVSADDVSLRHKEFEREVM 681
                                    ***********999999999988877776665566666666666666655555555311145558888888888888888 PP

                                    HHHH CS
                          HSP70 592 kiae 595
                                    ++++
  gene382|gene382|rna382|rna382 682 PLMS 685
                                    7765 PP

>> MreB_Mbl  MreB/Mbl protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.1     0.058   5.2e+02       3      17 ..      45      59 ..      43      64 .. 0.82
   2 !   35.5   0.0   5.1e-13   4.6e-09      68     321 ..     179     458 ..     160     463 .. 0.72

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.058
                                   EEEEEE-SSEEEEEE CS
                       MreB_Mbl  3 dlgiDLGtantlvyv 17
                                    +giDLGt+   v v
  gene382|gene382|rna382|rna382 45 AIGIDLGTTYSCVGV 59
                                   69*******998865 PP

  == domain 2  score: 35.5 bits;  conditional E-value: 5.1e-13
                                    ESSHHHHHHHHHHHHHHHHTSS-S.S--EEEEEE-SS--HHHHHHHHHHHHHTT-SEEEEEEHHHHHHHHTT--TTSSS- CS
                       MreB_Mbl  68 iadlevaeellkyfikkvkkkksl.skprvvicvPsgiteverrAvkeaakkaGarevllieeplaAAiGaglpveepsg 146
                                    ++ +++ + +l++++k v+++    + ++v+i+vP   +e++ +A + aa+ aG +    ++ep+aAA   ++  ++ s+
  gene382|gene382|rna382|rna382 179 VSAIDASAYILEHLMKVVNDRYGAkNIANVIITVPAYFSEMQVQATRTAATIAGLSLSRTVNEPVAAAYAYQVRNKDRSA 258
                                    34567778899****99999766526789*****************************************9998887776 PP

                                    E....EEEEE-SS-EEEEEEETTEEE.....EEEEES-SHHHHHHHHHHH...HHHHHSEE--HHH.......HHHHHHH CS
                       MreB_Mbl 147 n....mvvdiGggttevavislggiv.....tsksvrvaGdeldeaiiky...irkkynlliGert.......aekikie 207
                                         +v d+Gggt +v+++ + g v     +s s  ++G+++++ + k+   + +k n+l+ + +       ae+ ki+
  gene382|gene382|rna382|rna382 259 AldsfLVFDLGGGTMDVSILEYEGGVlevqtYSGSNFLGGENINDCLFKHfygLMEKSNILLNDVEklrlrgfAERFKIS 338
                                    533337**************9866542222235567799*******9998445568889998865433444448999999 PP

                                    H-BSS--HHHH.....EEEEEEEETTTTCEEEEEEEH..HHHHHHHHHHHHHHHHHHHHHHHTS-HHHHHHHHH.H-EEE CS
                       MreB_Mbl 208 igsavkeeeee.....kmeikGrdlvtglpkevevss..eevrealkepvsaiveavkevLektppeLaadivd.rgivl 279
                                    + +   ee  +     ++   G ++ t   ++ e ++  +ev++ ++   + ++  v  +L k +  L +d  d + ++l
  gene382|gene382|rna382|rna382 339 LCTRQLEEGGDaefedEFIYLGDKVFTFKLRTSEFNKvcDEVSKRIR---HYLTGDVDGILYKYKQKLDKDKDDiKKVLL 415
                                    98877665444434446667788888888888887642223333332...333445556666666666666554467999 PP

                                    ESGGGGSBTHHHHHHHHHSS.-EEE-SSTTTHHHHHHHHTTC- CS
                       MreB_Mbl 280 tGGgallkgldkllseetgl.pvkvaedpltcvakGtgkvlek 321
                                    +GG++ +  ++++l+  +g  +v+   +p t+va+G++ +  +
  gene382|gene382|rna382|rna382 416 VGGSTRVPFVRDILYGIFGKdKVSAELNPDTVVAEGAAYYSAN 458
                                    9999999999999999998625666669999999999887766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (706 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       895  (0.0499191); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.66u 0.31s 00:00:00.97 Elapsed: 00:00:00.47
# Mc/sec: 4556.14
//
Query:       gene383|gene383|rna383|rna383  [L=718]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      8e-39  133.1   0.1    1.4e-38  132.4   0.1    1.3  1  Trehalose_PPase  Trehalose-phosphatase
    3.8e-18   65.4   7.7    1.6e-17   63.4   7.7    1.9  1  Glyco_transf_20  Glycosyltransferase family 20
    2.6e-05   24.1   1.9    0.00036   20.3   0.0    3.0  3  Hydrolase_3      haloacid dehalogenase-like hydrolase
    0.00075   19.1   0.0       0.34   10.4   0.0    2.5  2  S6PP             Sucrose-6F-phosphate phosphohydrolase
  ------ inclusion threshold ------
       0.11   12.9   0.1       0.37   11.3   0.1    1.9  1  FDX-ACB          Ferredoxin-fold anticodon binding domain


Domain annotation for each model (and alignments):
>> Trehalose_PPase  Trehalose-phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  132.4   0.1   3.8e-42   1.4e-38       1     198 [.     498     683 ..     498     707 .. 0.92

  Alignments for each domain:
  == domain 1  score: 132.4 bits;  conditional E-value: 3.8e-42
                                    EEETBTTTB---SSGGG--B-TTHHHHHHHHHTTS-..EEEE-SS-HHHHHHHH---SSEEEEGGGTEEE-TT--EEE-H CS
                Trehalose_PPase   1 flDydGTlspivedpdaavpssellslLkkLasdpknvvaivSGrslkeeellvkvpelglaaeHGaeirspsgedwenq 80 
                                    +lDydGTl++iv+ p +a ps+e++slL++L+s  + +v+i +Grs++e+++ +  +++ l aeH a++r++++  w   
  gene383|gene383|rna383|rna383 498 ILDYDGTLTEIVPIPSDAAPSDEIISLLDHLTSLKNLTVVIATGRSKDEADKWFTSSKIQLYAEHSAYYRKKGQ--WIR- 574
                                    59***********************************************99999*****************999..998. PP

                                    HHHTTHHHHHHHHHHHHHHHTTSTT-EEEEETTEEEEE-TT--TT....THHHHHHHHHHHHHHH.--EEEE-SSEEEEE CS
                Trehalose_PPase  81 aevedlewlkevkeileektertpGsyiEekkfalsvHyrnadde..elqakelaehlesvltdkpdlevtqgkkvvevr 158
                                        dl+w+++++++ +e+++ tp++++Eek +al++Hyrnad++    qa+++ ++l ++l+     +v++gk++vev 
  gene383|gene383|rna383|rna383 575 -RDVDLSWMDTARRVINEYVACTPNTKLEEKNTALVFHYRNADESyrDEQAERCRKALVQALKGR--ANVKVGKCIVEVN 651
                                    .9*******************************************77777888888777777766..88999*******9 PP

                                    -S---HHHHHHHHHHTS--------EEEEEE-SSTTHHHH CS
                Trehalose_PPase 159 pqgvsKGkaverlleslgsadseddfvlciGDdrtDedmF 198
                                     +   K  +v+    ++++     df lc+GDd tDe+mF
  gene383|gene383|rna383|rna383 652 CKDIGKDYVVR----QYEN----CDFGLCAGDDTTDEKMF 683
                                    99888766654....5554....6999************9 PP

>> Glyco_transf_20  Glycosyltransferase family 20
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.4   7.7   4.5e-21   1.6e-17      70     452 ..     107     452 ..      67     461 .. 0.79

  Alignments for each domain:
  == domain 1  score: 63.4 bits;  conditional E-value: 4.5e-21
                                    HHCCCCCEEEEEE-HHHHHHHCCCHHHHCHHHHHTT-GG....G----HHHHHHHHHHHHHHHHHHHCC--TT-EEEEES CS
                Glyco_transf_20  70 eleekfsvvpvflsdekveeyyngfsksvLWpllHYklpdsseekefersawdaYvkvnklFAdkiveeikdgdliwvhD 149
                                     +  + +++pv+ + +k++    +f+ ++L  l   + +d   ++++e+  ++++v+  k + d + +++ ++d +++ D
  gene383|gene383|rna383|rna383 107 FFLRDKHCLPVLPDLNKYNYESCKFA-QYLKCLAFTREWDALFKDHNEKLMYEDFVNYTKSYYDVLKNVLGENDEVIIMD 185
                                    33334448888877666665555565.57777777777889999999********************************* PP

                                    GGGTTHHHHHHHCCTTSEEEEEE-S----HHHHTTSTTHHHHHHHHTTSSEEEESSHHHHHHHHHHHHHHSSEEEECTTE CS
                Glyco_transf_20 150 YhLmllPellRkkledakigfflHiPFPsseifriLpvreeilegllgadliGFhtedyarhFlsccsrllgleveskrg 229
                                     +L+llP++l    +++k++    iPF ++e f++  +  eil++ll+a li F+++d ++ Fl+ c   +         
  gene383|gene383|rna383|rna383 186 PELWLLPSYL----NNVKVSVAFQIPFFKVEFFKCVYNNMEILKSLLNAHLI-FQNKDEMNSFLELCAINI--------- 251
                                    *******998....56777777789**************************9.*************97433......... PP

                                    EEEETTEEEEEEE------HHHHHHHCCSCHHHHHHHHHHHHT.TTSEEEEEEEEC-GGG-HHHHHHHHHHHHHH-GGGT CS
                Glyco_transf_20 230 gveykgrkvsvkalpigidverlesalkkesvsekvkelkerfenkkklilgvDrlDyikGvkqkllaferfLeeypelr 309
                                      ++++r+vs ++lp gid++ ++ +lk + ++e+v+++k+++++k k+i+ v +   +   ++ l+af+++L e +   
  gene383|gene383|rna383|rna383 252 -PNFEERSVSAQVLPFGIDTNYVT-TLKGPRLNERVAQIKDDYKDK-KIIVTVLNTVNSELSENVLIAFNNLLDETE--- 325
                                    .45789*************99886.6788**************885.******999999999999********9875... PP

                                    TTEEEEEEEEB-STTSHHHHHHHHHHHHHHHHHHHHH-BTTB-SEEEEES---HHHHHHHHHH-SEEEE--SSBSS-CHH CS
                Glyco_transf_20 310 gkvvlvqiavpsredveeyqelekeveelvgrINgefgtldytPvvylersldfeeliallaaadvllvtslRdGmnlva 389
                                       vlvqi v+s        +++k +e ++++I    +t +   +  ++ + +  e++++laaad+ l        n  +
  gene383|gene383|rna383|rna383 326 --AVLVQIEVHSDL-----IDAQKRIE-MITAISFITTTRGNDCILTIT-PTNDLEYYSFLAAADLGLFLFDHSVTNKGC 396
                                    ..689999887643.....34566664.455665555555555555554.477788999999999988877777889999 PP

                                    HHHHHCSTTT--EEEEETTBGGGGT-TTTSEEE-TT-HHHHHHHHHHHHC--HHHHHHHHHHH CS
                Glyco_transf_20 390 keyvvcqqekkgvLiLSeFaGaaqsLkdaailvNPwdieevaeaikeaLkmseeerkkrekkl 452
                                     +++++++    + iLS  + + +  +  ++lvNP + +e+ e +ke+L++ e+  ++ + k+
  gene383|gene383|rna383|rna383 397 CDFIAVNNV---PFILS--VNSVNHFS--SLLVNPNNPNELLEKMKEGLSIGEDDMHSHNMKV 452
                                    999999877...99999..56778888..5899999999999999999999888776666555 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.2      0.35   1.3e+03      74     159 ..     147     245 ..     129     262 .. 0.65
   2 !   20.3   0.0     1e-07   0.00036       1      58 [.     497     560 ..     497     590 .. 0.88
   3 ?    2.2   0.0     0.036   1.3e+02      99     196 ..     557     665 ..     554     685 .. 0.57

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.35
                                    EEE--B-HHHHHHHHHHHHHTT..CEEEEEESSEEEESTT.............THHHHHHHHHCHCTCEEEESHHHHHCH CS
                    Hydrolase_3  74 lykstiskedvkeiikllkenn..veillytedkvyvlnk............eksekkkkeeektkkkkeeidseeeled 139
                                    l+k++ +k  +++++++ k++   ++ +l ++d+v++ ++            + s   +   +k++++k+ +++ e l++
  gene383|gene383|rna383|rna383 147 LFKDHNEKLMYEDFVNYTKSYYdvLKNVLGENDEVIIMDPelwllpsylnnvKVSVAFQIPFFKVEFFKCVYNNMEILKS 226
                                    44555555555666666666666655555555666555555666666677777777777777777777777777766666 PP

                                    CSESEEEEES-HHHHHHHHH CS
                    Hydrolase_3 140 eeiakililkdkekldelek 159
                                      ++  li+++k++++++ +
  gene383|gene383|rna383|rna383 227 -LLNAHLIFQNKDEMNSFLE 245
                                    .5555556666666666655 PP

  == domain 2  score: 20.3 bits;  conditional E-value: 1e-07
                                    EEEEIIIIIS-.....TTS---HHHHHHHHHHHH.TTSEEEEE-SS-HHHHHHHHHHCCCCSEE CS
                    Hydrolase_3   1 ialDlDGTLln.....sdkkisektkeaikklke.kgikvviATGRslravlpvleelgldlpv 58 
                                    i+lD DGTL       sd   s+++++ +  l + k+ +vviATGRs  ++ + + + +++l++
  gene383|gene383|rna383|rna383 497 IILDYDGTLTEivpipSDAAPSDEIISLLDHLTSlKNLTVVIATGRSKDEADKWFTSSKIQLYA 560
                                    799******9999999******************9********************999998553 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.036
                                    EEEESSEEEESTT.........THHHHHHHHHCHCTCEEEESHHHHHCHCSESEEE......EES-HHHHHHHHHHHHHH CS
                    Hydrolase_3  99 llytedkvyvlnk........eksekkkkeeektkkkkeeidseeeledeeiakil......ilkdkekldelekelksk 164
                                    +ly e+++y+ +k        +   +  + ++ + ++    + +++le+++ a ++       ++ +e+ ++++k+l + 
  gene383|gene383|rna383|rna383 557 QLYAEHSAYYRKKgqwirrdvD--LSWMDTARRVINEYVACTPNTKLEEKNTALVFhyrnadESYRDEQAERCRKALVQA 634
                                    5666666666666666655331..22222222222222222233333333333333453444566666677777777777 PP

                                    CTTTEEEEEESTTEEEEEETT-SHHHHHHHHH CS
                    Hydrolase_3 165 lnklltitssskgyleimpkgvsKgtalkkla 196
                                    l+   ++++ +k ++e++ k++ K   ++++ 
  gene383|gene383|rna383|rna383 635 LKGR-ANVKVGKCIVEVNCKDIGKDYVVRQYE 665
                                    6665.999****************99988876 PP

>> S6PP  Sucrose-6F-phosphate phosphohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.0   9.6e-05      0.34       2      54 ..     494     552 ..     493     557 .. 0.88
   2 !    6.0   0.0    0.0021       7.4     185     217 ..     671     703 ..     657     715 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 9.6e-05
                                    SEEEEE-TBTTTB......S-HHHHHHHHHHHH..GGGGGEEEEEE-SS-HHHHHHHHH CS
                           S6PP   2 klllvsdLDntlv.....dgdnealarlnelle.aeerkdvllvfaTGRsldsakellk 54 
                                    k++++ d D+tl+     ++d++  +++ +ll+  ++ k+ ++v+aTGRs d+a +  +
  gene383|gene383|rna383|rna383 494 KRVIILDYDGTLTeivpiPSDAAPSDEIISLLDhLTSLKNLTVVIATGRSKDEADKWFT 552
                                    689*********9999*9999999999999999677899************99988766 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0021
                                    EEEE-SGGGHHHH.TSSSEEEE-TT--HHHHHHH CS
                           S6PP 185 lvcGdsgnDeell.ignvlgVvVgnaqeellqwl 217
                                    l +Gd   De+++ ++ + g+vVg + ++  +++
  gene383|gene383|rna383|rna383 671 LCAGDDTTDEKMFgRECFVGIVVGKKISK-AEYY 703
                                    889**********99*********97665.4444 PP

>> FDX-ACB  Ferredoxin-fold anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1    0.0001      0.37      47      92 ..     597     642 ..     584     643 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0001
                                    TTS-SSEEEEEEEEEE--SSS---HHHHHHHHHHHHHHHHTT.T-B CS
                        FDX-ACB  47 kklaegkkSlalrltlqskertLtdeevnaaiekvvealekklgae 92 
                                    ++ + ++k+ al + +++++++  de+ +++ + +v+al+ +++++
  gene383|gene383|rna383|rna383 597 PNTKLEEKNTALVFHYRNADESYRDEQAERCRKALVQALKGRANVK 642
                                    4555689**********************************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (718 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       697  (0.0388756); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.75u 0.29s 00:00:01.04 Elapsed: 00:00:00.51
# Mc/sec: 4259.47
//
Query:       gene384|gene384|rna384|rna384  [L=360]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.1e-26   92.1   3.3    7.1e-26   91.0   3.3    1.6  1  RPN7      26S proteasome subunit RPN7
    1.2e-08   35.4   1.4    2.8e-08   34.2   0.1    2.2  2  PCI       PCI domain


Domain annotation for each model (and alignments):
>> RPN7  26S proteasome subunit RPN7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.0   3.3   7.9e-30   7.1e-26      20     173 ..      64     214 ..      60     215 .. 0.96

  Alignments for each domain:
  == domain 1  score: 91.0 bits;  conditional E-value: 7.9e-30
                                    HHHHHHHHHTT-HHHHHHHHHHHHHHHHHCT-HHHHHHHHHTCCCC--SHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                           RPN7  20 daelkdakenlgkeeirrakldlaehYlkigdleeAlkaysrireyctslkhkidmllnlirvaiffndwdlvskyleka 99 
                                    ++ l++  e++++ + +  k+++ e+ +kig+l++    +++ r+ + +++ k+d++l+ ir+++ f+d++l+   ++  
  gene384|gene384|rna384|rna384  64 EEMLQKISEQQTEDDGKSIKKERLEYLAKIGNLSS---FVEESRDAVLTTSTKMDIVLCQIRLGMIFKDYSLIHDKINAG 140
                                    5668888899999********************85...88999************************************* PP

                                    HCSSS---.HHHHHHHHHHHHHHHHHTT-HHHHHHHHCTS-GGGT.TTT--HHHHHHHHHHHHHHH--HHHHHH CS
                           RPN7 100 kellekggdwerknrlkvyeGlallairkfkeAaellldilstftskellsyedlavyavlcalatldRkdLka 173
                                     +l ek +dw+rkn++kvy + ++l   +++ Aa+l+ ++l+tf+++el sye  + y+++c+l++++R++L +
  gene384|gene384|rna384|rna384 141 LKLSEKDCDWDRKNKFKVYYAFYNLLKSDYELAADLFASSLATFQCNELFSYEMAVNYTIFCSLLSFSREQLHE 214
                                    ***********************************************************************975 PP

>> PCI  PCI domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1      0.32   2.9e+03      22      37 ..      67      82 ..      26     117 .. 0.62
   2 !   34.2   0.1   3.1e-12   2.8e-08       5     104 ..     234     333 ..     232     334 .. 0.97

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.32
                                   HHHHHHHHHHHTTHHH CS
                            PCI 22 lkdleeelladdglaq 37
                                   l++ +e++ +ddg + 
  gene384|gene384|rna384|rna384 67 LQKISEQQTEDDGKSI 82
                                   3333333333333333 PP

  == domain 2  score: 34.2 bits;  conditional E-value: 3.1e-12
                                    HHHHHHHHTSHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHCESEEEHHHHHHHHTSSHHHHHHHHHHH CS
                            PCI   5 dllkalrsgnlsgfseelkdleeelladdglaqllesLekkvrerllrqvskiyssislerlaklldlsvdevEkilvkl 84 
                                    dl +a++++ +++   +l  +++ +++d ++ + + ++ ++++ r++ q+ ++yssi le++a ++++s++ +E  l k+
  gene384|gene384|rna384|rna384 234 DLAQAIYNCYYDKIFPCLVAFSSYYMDDIFIGDKIHYFINETKIRSYNQLLESYSSIGLESMALTFGVSEEYLEADLGKF 313
                                    79999*************************************************************************** PP

                                    HHTTSSSEEEETTTTEEEEC CS
                            PCI  85 Irdgeirakidqesgivvfk 104
                                      ++++++ id  +++v +k
  gene384|gene384|rna384|rna384 314 LVNERMKCVIDKIDKMVLVK 333
                                    *****************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (360 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       843  (0.0470188); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 2341.94
//
Query:       gene385|gene385|rna385|rna385  [L=349]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-08   34.8   1.1     0.0013   18.5   0.1    3.7  3  RRM_1     RNA recognition motif. (a.k.a. RRM, RBD, or RNP dom
    0.00021   21.8   0.1       0.11   13.2   0.0    3.4  4  NID       Nmi/IFP 35 domain (NID)
  ------ inclusion threshold ------
      0.058   13.4   0.1       0.64   10.1   0.2    2.4  2  RRM_3     RNA binding motif
       0.85    9.4   3.3        1.6    8.5   0.2    2.5  2  Scm3      Centromere protein Scm3


Domain annotation for each model (and alignments):
>> RRM_1  RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.1   2.9e-07    0.0013       1      67 [.     100     161 ..     100     174 .. 0.94
   2 !   12.3   0.0   2.6e-05      0.12       1      59 [.     181     233 ..     181     246 .. 0.83
   3 ?    0.4   0.0      0.13     6e+02      45      60 ..     298     313 ..     271     322 .. 0.62

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 2.9e-07
                                    EEEESETTTSSHHHHHHHHHTTSCEEEEEEEEETTTSEEEEEEEEESSHHHHHHHHHHHTTEEETTE CS
                          RRM_1   1 lfVgnLppdvteeeLkelFskfGpiksiklvrdetgkskgfafVeFeskedAekAlealngkklggr 67 
                                    ++ +n+  d+++e  +++  k G+i++ k++++     k++  V+F + e+A +++e+l++   ++r
  gene385|gene385|rna385|rna385 100 IYFSNIDDDMDKEYFEDICTKHGEIENMKISKE-----KRHVQVRFYKFESAMSCMESLHKGSGKNR 161
                                    67789***************************8.....*********************99776666 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 2.6e-05
                                    EEEESETTTSSHHHHHHHHHTTSCEEEEEEEEETTTSEEEEEEEEESSHHHHHHHHHHH CS
                          RRM_1   1 lfVgnLppdvteeeLkelFskfGpiksiklvrdetgkskgfafVeFeskedAekAleal 59 
                                    l++gn+  ++t + +  + ++   + sik  r+     k++af +F ++ +Ae+ l ++
  gene385|gene385|rna385|rna385 181 LYLGNIQAEITASSVLNHCKGGAIF-SIKFLRE-----KKCAFLTFINPHAAEAFLYNC 233
                                    7999999999999999999886666.9999997.....****************99875 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.13
                                    EESSHHHHHHHHHHHT CS
                          RRM_1  45 eFeskedAekAlealn 60 
                                    +F s  +A+kA+e+l 
  gene385|gene385|rna385|rna385 298 NFLSLYAATKAMENLR 313
                                    3555556666666665 PP

>> NID  Nmi/IFP 35 domain (NID)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.75   3.3e+03      51      68 ..      10      25 ..       4      33 .. 0.70
   2 ?    4.2   0.0     0.015        69      46      74 ..      91     117 ..      69     125 .. 0.78
   3 ?   -3.7   0.0         4   1.8e+04      51      68 ..     177     192 ..     174     198 .. 0.66
   4 !   13.2   0.0   2.4e-05      0.11       1      71 [.     216     285 ..     216     289 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.75
                            NID 51 skrtvllsgipdvlelde 68
                                    +rt+ ++++pd l+   
  gene385|gene385|rna385|rna385 10 NTRTIRIENVPDALS--I 25
                                   678999999999654..3 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.015
                            NID  46 vklevskrtvllsgipdvleldeeeleDk 74 
                                     + +  +r++ +s+i+d  ++d+e  eD 
  gene385|gene385|rna385|rna385  91 AHQAGASRSIYFSNIDD--DMDKEYFEDI 117
                                    45556789*********..78***99996 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 4
                            NID  51 skrtvllsgipdvlelde 68 
                                    ++rt+ l +i++  e+  
  gene385|gene385|rna385|rna385 177 CNRTLYLGNIQA--EITA 192
                                    778888888877..4444 PP

  == domain 4  score: 13.2 bits;  conditional E-value: 2.4e-05
                            NID   1 AlitFeeeeVaqril.kkkkhkvelekkkvrvkvspvelkelkklqvklevskrtvllsgipdvleldeeel 71 
                                    A +tF +++ a+  l +++  +++++k++++v+     +  ++ +    + s+r++++++i+dvl  d ++l
  gene385|gene385|rna385|rna385 216 AFLTFINPHAAEAFLyNCSLNPITIKKHRIKVTHGNNSNIPINMMLALYHGSTRSIKVKNIDDVL--DMDQL 285
                                    789********99771556678*****99*****9999999**********************88..55555 PP

>> RRM_3  RNA binding motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.2   0.00014      0.64       6      58 ..     102     154 ..      99     164 .. 0.90
   2 ?   -0.4   0.0      0.26   1.2e+03      31      70 ..     207     246 ..     196     249 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00014
                                    EEE-SSS--HHHHHHHCHCCS-ECEEEE-TTSSEEEEEESSHHHHHHHHHHHH CS
                          RRM_3   6 lsGlnkelsredikellsklgevayvdyekgdkegevrFkedeeakkalekat 58 
                                    +s +++++ +e + ++  k+ge++ +  +k++   +vrF + e+a   +e++ 
  gene385|gene385|rna385|rna385 102 FSNIDDDMDKEYFEDICTKHGEIENMKISKEKRHVQVRFYKFESAMSCMESLH 154
                                    5667889999***********************************99999876 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.26
                                    EEE-TTSSEEEEEESSHHHHHHHHHHHHHC-B-CCTSSEE CS
                          RRM_3  31 vdyekgdkegevrFkedeeakkalekateaklkikdaevt 70 
                                    + + +++k + + F ++++a+++l +     ++ik++ ++
  gene385|gene385|rna385|rna385 207 IKFLREKKCAFLTFINPHAAEAFLYNCSLNPITIKKHRIK 246
                                    7788999999999****99*99999999999999998876 PP

>> Scm3  Centromere protein Scm3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.3       0.1   4.6e+02      13      52 ..     111     127 ..      99     132 .. 0.57
   2 ?    8.5   0.2   0.00036       1.6      27      48 ..     272     294 ..     269     296 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.1
                                    HHHHHHHHHHHHSG..GGSS--B-TTT-SB-XXXXXXXXX CS
                           Scm3  13 kkrwesifeKYeridfedqgDEIDlatgeivvDnGhlrel 52 
                                    k+ +e+i+ K ++i                       +++
  gene385|gene385|rna385|rna385 111 KEYFEDICTKHGEI-----------------------ENM 127
                                    44555555555555.......................444 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00036
                                    ..GGSS--B-TTT-S.B-XXXXX CS
                           Scm3  27 dfedqgDEIDlatge.ivvDnGh 48 
                                      ++++D++D+ + e +++DnG 
  gene385|gene385|rna385|rna385 272 KVKNIDDVLDMDQLEsVYKDNGA 294
                                    56789******88889******5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (349 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       519  (0.0289475); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 2612.44
//
Query:       gene386|gene386|rna386|rna386  [L=143]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1258  (0.0701657); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 936.44
//
Query:       gene387|gene387|rna387|rna387  [L=190]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.2e-13   50.2   0.9    4.6e-13   49.7   0.9    1.2  1  Brix      Brix domain
  ------ inclusion threshold ------
      0.017   14.9   2.3       0.24   11.1   0.1    2.6  3  CO_dh     CO dehydrogenase beta subunit/acetyl-CoA synthase e
       0.18   12.2   3.8        6.4    7.3   3.8    2.3  1  CLAMP     Flagellar C1a complex subunit C1a-32


Domain annotation for each model (and alignments):
>> Brix  Brix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.7   0.9   7.7e-17   4.6e-13       3     192 ..      17     179 ..      16     180 .. 0.77

  Alignments for each domain:
  == domain 1  score: 49.7 bits;  conditional E-value: 7.7e-17
                                    T--HHHHHHHHHHHHHCTTSEEEEEE.ECT-TTTHHHHHHH...-HHHHHHHH.HCTCSEEEEEE..SSTTEEEEEEEEE CS
                           Brix   3 ktssrlrqllkdlrslmkphtasflk.rnsnklkdlvelag...vthlellse.kndcslfvfelskkrPngptlefkve 77 
                                    k+s++++ ll+ ++++++p+t ++    n+  lk + +la+   +  +++l e k+ ++++++++     +  +++++v 
  gene387|gene387|rna387|rna387  17 KVSKKTKVLLTSIKRMFEPNTNTKFNeTNKFDLKLYKKLAEmypIDIFIVLKEsKSGVHIKICKA----NEQTSVYLQVI 92 
                                    567889*************988855534445555667777787577777777787778*******....999*******9 PP

                                    CECTGGGSTTTSTS-TT---EEEEES.HHHHHHHHHHHHHH..SEEEG..-B-GG-SEEEEEEES.CCTTTECEEEEEEE CS
                           Brix  78 nyslmkdlkkakktefgsrPllvfngkenfkllksllqdlFrvpkislkspklsglrrvvlftaaenqetdktisfRhYa 157
                                     +   +  ++    +++s  ll fn   +f      + +lF   k + k+   ++++rv+ ft +  ++ +  i++RhY+
  gene387|gene387|rna387|rna387  93 AFDAYSV-NG----NYKSDALLTFN---GFD-EDDAFRKLF--GKQHFKN--VDSVERVINFT-K--NN-E-LIYVRHYK 154
                                    9876654.44....48999******...885.356778888..6666644..367********.4..33.3.8******* PP

                                    EEEE..STTTTECT..T..EEEEEEESEEEEEEEE CS
                           Brix 158 iklkksgkklpnlekekkerveLeEiGPrfdLklr 192
                                    i +k++g+ +         ++ L+E+GP++++k +
  gene387|gene387|rna387|rna387 155 I-IKTEGRCV---------KIGLKEVGPKIQMKYV 179
                                    *.46666665.........5************976 PP

>> CO_dh  CO dehydrogenase beta subunit/acetyl-CoA synthase epsilon subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1     4e-05      0.24     132     168 .]      23      59 ..      16      59 .. 0.91
   2 ?    2.9   0.0     0.014        82     135     164 ..      96     123 ..      78     126 .. 0.82
   3 ?   -1.9   0.0      0.43   2.6e+03      59      90 ..     148     178 ..     135     188 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 4e-05
                                    T-EEEE-SSS--TTSSEEE---GGGHHHHHHHHHHHH CS
                          CO_dh 132 kittiaidkyyhpdAdvslanlskeeeeylemleell 168
                                    k+  ++i++++ p+++  +++ +k +++ +++l+e++
  gene387|gene387|rna387|rna387  23 KVLLTSIKRMFEPNTNTKFNETNKFDLKLYKKLAEMY 59 
                                    678899*****************************96 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.014
                                    EEE-SSS--TTSSEEE---GGGHHHHHHHH CS
                          CO_dh 135 tiaidkyyhpdAdvslanlskeeeeyleml 164
                                    + ++   y++dA +++++ ++++   +++l
  gene387|gene387|rna387|rna387  96 AYSVNGNYKSDALLTFNGFDEDD--AFRKL 123
                                    5567778*************999..66665 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 0.43
                                    HHTSSSEEEEET..HHHTT-G..GGSE-HHHHHH CS
                          CO_dh  59 ilekklkvvata..lkeaglkdyekknklveltk 90 
                                    i +++ k+++t     ++glk   ++ +++++++
  gene387|gene387|rna387|rna387 148 IYVRHYKIIKTEgrCVKIGLK---EVGPKIQMKY 178
                                    555666666666554445555...4444444444 PP

>> CLAMP  Flagellar C1a complex subunit C1a-32
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   3.8    0.0011       6.4      13      88 ..      19     157 ..       7     159 .. 0.59

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0011
                          CLAMP  13 veqtsafltilkkllenliekslenvek...................sfkyfkelllrhsverppesig........... 62 
                                    +++t ++lt +k+++e ++++++++ +k                   +            ++++ ++++           
  gene387|gene387|rna387|rna387  19 SKKTKVLLTSIKRMFEPNTNTKFNETNKfdlklykklaemypidifiV------------LKESKSGVHikickaneqts 86 
                                    566677777777777777777666666566665554433333333331............23333322233333333333 PP

                          CLAMP  63 ..........................................lFsvdqvkaiieYiltt...yfrhykLYk 88 
                                                                              + +vd+v+ +i++ +++   y+rhyk++k
  gene387|gene387|rna387|rna387  87 vylqviafdaysvngnyksdalltfngfdeddafrklfgkqhFKNVDSVERVINFTKNNeliYVRHYKIIK 157
                                    344444444444446666666666666666677777666664558999**********9999******987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (190 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       791  (0.0441185); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1320.86
//
Query:       gene388|gene388|rna388|rna388  [L=66]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.023   14.0   1.3      0.022   14.0   1.3    1.1  1  MIS13     Mis12-Mtw1 protein family


Domain annotation for each model (and alignments):
>> MIS13  Mis12-Mtw1 protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   1.3   1.3e-06     0.022     153     192 ..       6      45 ..       1      65 [. 0.79

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.3e-06
                                    ..XXSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCH CS
                          MIS13 153 klpnaknieneenlailkekikalknEikeWaklladskd 192
                                     l n++ni  e+ +++l + i+alk+E+ke +++  + k 
  gene388|gene388|rna388|rna388   6 DLVNERNIIAEKIISELLQSIDALKKERKEMKNSYFKIKT 45 
                                    488**************************98887766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (66 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1261  (0.070333); expected 358.6 (0.02)
Passed bias filter:                      479  (0.0267165); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.32s 00:00:00.69 Elapsed: 00:00:00.45
# Mc/sec: 442.81
//
Query:       gene389|gene389|rna389|rna389  [L=108]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    6.4e-29   99.9   0.0    7.2e-29   99.7   0.0    1.0  1  S10_plectin  Plectin/S10 domain


Domain annotation for each model (and alignments):
>> S10_plectin  Plectin/S10 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.7   0.0     4e-33   7.2e-29       3      91 ..       5      92 ..       3      94 .. 0.95

  Alignments for each domain:
  == domain 1  score: 99.7 bits;  conditional E-value: 4e-33
                                   HCHHHHHHHHCCCCSCEEEE--SS----SSS---HHHHHHHHHHCCCCTSEEEEEETTEEEEEE-HHHHHHHHHHHXXXXSX CS
                    S10_plectin  3 kknrkaiyeylfkegvlvakkdfelkkheelnvpnlqvikalqSLksrgyvkeqfaWrhyYytLtneGieylreylhlpeei 84
                                   ++++ +i +y+f+egv++++++ + + h+el++++ qv+k++ SL s+g+ ++qf+Wrh+Y+++t+eGi+ l++ l+l+++ 
  gene389|gene389|rna389|rna389  5 RDEMLTIKKYFFREGVCLVEEKSN-QPHPELEINDKQVMKFMTSLVSKGLARKQFNWRHAYFFITDEGIDALKKDLSLEDNE 85
                                   567889**************9999.89******************************************************* PP

                                   HHHHHXX CS
                    S10_plectin 85 vPatlkk 91
                                   +P t+ +
  gene389|gene389|rna389|rna389 86 MPLTHLE 92
                                   ****976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       403  (0.0224776); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 734.13
//
Query:       gene39|gene39|rna39|rna39  [L=261]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.09   13.0   1.8       0.96    9.7   0.1    3.3  2  FNIP      FNIP Repeat
      0.091   13.2   4.5        1.2    9.7   0.0    3.4  3  LRR_4     Leucine Rich repeats (2 copies)
        1.3    9.2   3.8         16    5.9   0.1    3.8  4  LRR_6     Leucine Rich repeat
          3    8.6  12.4        6.9    7.5   0.1    4.8  4  LRR_2     Leucine Rich Repeat


Domain annotation for each model (and alignments):
>> FNIP  FNIP Repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.2      0.21   9.4e+02      13      29 ..      82      95 ..      60     102 .. 0.68
   2 ?    9.7   0.1   0.00021      0.96      11      41 ..     138     176 ..     106     178 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.21
                       FNIP 13 nleiLilgrdFnqkili 29
                               n++ L++   Fn k li
  gene39|gene39|rna39|rna39 82 NVKMLKF---FNLKTLI 95
                               5566666...5555444 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00021
                       FNIP  11 P.......snleiLilgrdFnqkil.igsLPnSlkeLyF 41 
                                +       +nl++L l+++F +  + ++ LP +l+ L+F
  gene39|gene39|rna39|rna39 138 TmkgfrshQNLKSLVLNDRFLRVGSlFNNLPVHLELLEF 176
                                255555558***********9877669999999999998 PP

>> LRR_4  Leucine Rich repeats (2 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.1      0.31   1.4e+03      25      33 ..      68      76 ..      63      82 .. 0.70
   2 ?    9.7   0.0   0.00026       1.2       2      36 ..      90     123 ..      89     129 .. 0.77
   3 ?    2.3   0.6     0.053   2.4e+02       1      23 [.     146     168 ..     146     177 .. 0.69

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.31
                               --EEE-.-S CS
                      LRR_4 25 LkeLdLsgN 33
                               L++L+L ++
  gene39|gene39|rna39|rna39 68 LTYLNLEDF 76
                               777777554 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00026
                                S--EEE--SS---.E-S-HHH-TT.--EEE-.-S--- CS
                      LRR_4   2 nLevLdLsnNqlt.diplleklpn.LkeLdLsgNnli 36 
                                nL++L Ls++ ++ d  ++  lp  Lk+L L +  +i
  gene39|gene39|rna39|rna39  90 NLKTLILSGCSIKgD--FFLYLPVyLKTLKLRST-PI 123
                                9************55..64449999999999444.44 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.053
                                SS--EEE--SS---E-S-HHH-T CS
                      LRR_4   1 pnLevLdLsnNqltdiplleklp 23 
                                +nL++L L++  l+  +l+++lp
  gene39|gene39|rna39|rna39 146 QNLKSLVLNDRFLRVGSLFNNLP 168
                                69999999974455444466655 PP

>> LRR_6  Leucine Rich repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.36   1.6e+03       4      11 ..      67      74 ..      65      75 .. 0.81
   2 ?    5.9   0.1    0.0036        16       4      17 ..      90     103 ..      89     104 .. 0.89
   3 ?    1.4   0.0     0.096   4.3e+02       4      17 ..     112     126 ..     110     127 .. 0.84
   4 ?   -1.0   0.2      0.56   2.5e+03       2      11 ..     145     154 ..     144     155 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.36
                      LRR_6  4 hLteLdLs 11
                                Lt+L+L 
  gene39|gene39|rna39|rna39 67 RLTYLNLE 74
                               59****95 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0036
                      LRR_6   4 hLteLdLsgNdIgD 17 
                                +L++L Lsg+ I +
  gene39|gene39|rna39|rna39  90 NLKTLILSGCSIKG 103
                                7*********9986 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.096
                      LRR_6   4 hLteLdLsgNd.IgD 17 
                                +L++L L++   I+D
  gene39|gene39|rna39|rna39 112 YLKTLKLRSTPiIDD 126
                                69******9997766 PP

  == domain 4  score: -1.0 bits;  conditional E-value: 0.56
                      LRR_6   2 nthLteLdLs 11 
                                +++L++L L+
  gene39|gene39|rna39|rna39 145 HQNLKSLVLN 154
                                689****886 PP

>> LRR_2  Leucine Rich Repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.1    0.0015       6.9       1      16 [.      90     105 ..      90     108 .. 0.88
   2 ?   -0.1   0.6      0.39   1.7e+03       2       9 ..     113     120 ..     113     121 .. 0.90
   3 ?    5.6   0.2    0.0063        28       7      19 ..     124     136 ..     123     137 .. 0.90
   4 ?   -0.5   0.1      0.51   2.3e+03       1       7 [.     147     153 ..     147     155 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0015
                      LRR_2   1 sLKtLhLdsVrfsded 16 
                                +LKtL L+ + ++++ 
  gene39|gene39|rna39|rna39  90 NLKTLILSGCSIKGDF 105
                                6***********9994 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.39
                      LRR_2   2 LKtLhLds 9  
                                LKtL L+s
  gene39|gene39|rna39|rna39 113 LKTLKLRS 120
                                9***9987 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.0063
                      LRR_2   7 LdsVrfsdedsle 19 
                                +d+V+f d+ sl+
  gene39|gene39|rna39|rna39 124 IDDVWFRDDKSLC 136
                                79****9999997 PP

  == domain 4  score: -0.5 bits;  conditional E-value: 0.51
                      LRR_2   1 sLKtLhL 7  
                                +LK+L+L
  gene39|gene39|rna39|rna39 147 NLKSLVL 153
                                69***99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       438  (0.0244297); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1804.92
//
Query:       gene390|gene390|rna390|rna390  [L=328]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    9.8e-48  162.8   0.4    4.9e-37  127.7   0.1    2.0  2  Aldo_ket_red  Aldo/keto reductase family
  ------ inclusion threshold ------
        0.4   10.7   3.0        1.5    8.8   0.0    3.2  4  DASH_Dad4     DASH complex subunit Dad4


Domain annotation for each model (and alignments):
>> Aldo_ket_red  Aldo/keto reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  127.7   0.1   5.4e-41   4.9e-37       2     192 ..      45     240 ..      44     242 .. 0.94
   2 !   33.6   0.0   2.5e-12   2.3e-08     234     293 ..     256     311 ..     248     312 .. 0.95

  Alignments for each domain:
  == domain 1  score: 127.7 bits;  conditional E-value: 5.4e-41
                                    EEEE-SSS-ST.TS-HHHHHHHHHHHHHTT--EEE--TT-TTTHHHHHHHHHHHH....-TTTGGG-EEEEEE--SSSTT CS
                   Aldo_ket_red   2 lglGtwqlgskeeiskeealellrraleaGinffDtAevYgkgqseellGealkk....srkkreeviiatKvdlrdaei 77 
                                    +g+Gtwql +     k+    ++++a++ G+++fD+A vY   ++e+ +G +l++    + + r+e++i++K+       
  gene390|gene390|rna390|rna390  45 IGFGTWQLIG-----KDNIRTMIQAAIQKGYRHFDLAHVY---ENEKDIGDVLSEilekEVVTRDELFITSKI------- 109
                                    9*****9998.....588888899999*************...77777777777777669*************....... PP

                                    SSSS-HHHHHHHHHHHHHHHT-S-EEEEEE-S--TTS-....................HHHHHHHHHHHHHTTSEEEEEE CS
                   Aldo_ket_red  78 ksglskeniresleeslkrLgtdyvDllllHrpdpslp...................sieevldaleelvkeGkiraiGv 138
                                     ++  ++n++ ++e++lk+L++dy+Dl+l+H+p ++ p                   ++ ++++ +e lv+ Gk r+iGv
  gene390|gene390|rna390|rna390 110 -WNTYHDNVDLAIETTLKNLRLDYLDLYLVHWPVSAKPdanfneikdqnknvvlnefNLKKLWADMERLVETGKTRSIGV 188
                                    .666789************************************************************************* PP

                                    ES--HHHHHHHHHTTT--EEEEE-B-BTT-HHHHTTHHHHHHHTT-EEEEBSTT CS
                   Aldo_ket_red 139 Snfsveqlekakkkkkvkivavqveynllreleeegllelckkkgvpliayspl 192
                                    +nf  + ++++++  k+k+v++q+e++++  l++e+ll+lc ++ + + ays l
  gene390|gene390|rna390|rna390 189 CNFGLKNMKSLLSFCKIKPVCLQIEMHPF--LKQEELLKLCDANFIVITAYSSL 240
                                    *****************************..************888888***98 PP

  == domain 2  score: 33.6 bits;  conditional E-value: 2.5e-12
                                    HHHHHTT--HHHHHHHHHTTSTT-SEEEE--SSHHHHHHHHGGGG----HHHHHHHHHHH CS
                   Aldo_ket_red 234 elakehgvslaqlalryalsqpavgivipgasnieqlednldalelklseeevaeldell 293
                                    ++ak++g+s+a + ++y+l  +++++vi ++s++e+le+n++ +  klse++++ +de+ 
  gene390|gene390|rna390|rna390 256 DIAKKYGCSVASVIINYLL--SKNVVVINKTSRPERLEENMRKV--KLSESDINLIDEIK 311
                                    79*****************..9**********************..***********985 PP

>> DASH_Dad4  DASH complex subunit Dad4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0   0.00017       1.5      40      65 ..      99     124 ..      87     128 .. 0.79
   2 ?   -0.1   0.1      0.11   9.5e+02      33      46 ..     149     162 ..     146     179 .. 0.80
   3 ?   -2.4   0.0      0.52   4.7e+03      33      55 ..     242     262 ..     241     266 .. 0.65
   4 ?   -2.3   0.2      0.49   4.4e+03      29      46 ..     289     306 ..     275     313 .. 0.59

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00017
                      DASH_Dad4  40 kNknvelvsqlwenYqrnvqfnLeat 65 
                                       ++ ++s++w+ Y+ nv+  +e+t
  gene390|gene390|rna390|rna390  99 TRDELFITSKIWNTYHDNVDLAIETT 124
                                    5567899*************999987 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.11
                      DASH_Dad4  33 eleeinkkNknvel 46 
                                    +++ei+++Nknv l
  gene390|gene390|rna390|rna390 149 NFNEIKDQNKNVVL 162
                                    67899999999976 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 0.52
                      DASH_Dad4  33 eleeinkkNknvelvsqlwenYq 55 
                                    ++ +in++N +v    ++ ++Y 
  gene390|gene390|rna390|rna390 242 CIPDINDRNGKVI--IDIAKKYG 262
                                    6678888888764..46666665 PP

  == domain 4  score: -2.3 bits;  conditional E-value: 0.49
                      DASH_Dad4  29 elnkeleeinkkNknvel 46 
                                    +l++++++++ + ++++l
  gene390|gene390|rna390|rna390 289 RLEENMRKVKLSESDINL 306
                                    344444445444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (328 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       890  (0.0496402); expected 358.6 (0.02)
Passed bias filter:                      604  (0.0336884); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.41
# Mc/sec: 2379.37
//
Query:       gene391|gene391|rna391|rna391  [L=160]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    9.4e-05   22.4   0.0    0.00014   21.8   0.0    1.3  1  RNase_PH_C  3' exoribonuclease family, domain 2


Domain annotation for each model (and alignments):
>> RNase_PH_C  3' exoribonuclease family, domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.0   7.9e-09   0.00014       5      36 ..      97     128 ..      93     152 .. 0.79

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 7.9e-09
                                    EEEEEEETTEEEES--HHHHHHSSEEEEEEEE CS
                     RNase_PH_C   5 avtvgkvddqfvlDptkeEedlsegdltlava 36 
                                    a+t g++dd ++ Dp+  Ee+ s++ lt+ + 
  gene391|gene391|rna391|rna391  97 AITYGLIDDLCITDPSFVEEEASDATLTVLYR 128
                                    8************************9999773 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       523  (0.0291706); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 1120.26
//
Query:       gene392|gene392|rna392|rna392  [L=183]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
       0.04   13.9   1.6      0.081   12.9   0.3    1.9  2  DUF1043     Protein of unknown function (DUF1043)
      0.075   13.0   2.9       0.11   12.4   1.7    1.8  2  NOG1_N      NOG1 N-terminal helical domain
        0.1   12.5   1.0       0.18   11.7   1.0    1.5  1  DASH_Spc19  Spc19


Domain annotation for each model (and alignments):
>> DUF1043  Protein of unknown function (DUF1043)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.1     0.088   5.2e+02      54      72 ..      44      62 ..       4      73 .. 0.52
   2 ?   12.9   0.3   1.4e-05     0.081      19      86 ..      66     134 ..      61     145 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.088
                        DUF1043 54 saelLetlaedyqkLyqhl 72
                                    +elLe+l   ++k+ q++
  gene392|gene392|rna392|rna392 44 KKELLEQLIPFTHKVIQNI 62
                                   2334444444444444333 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 1.4e-05
                        DUF1043  19 tnsklkkqkklekelekakaeleeqkqeled.HfaqsaelLetlaedyqkLyqhlaksseeLlpeleeq 86 
                                     +++ k+ +++ek+ e++k   + +k  +ed  ++ + e   ++++d +kL++++++sse+++++ e+ 
  gene392|gene392|rna392|rna392  66 ITAQPKTYQDIEKKYERTKYMYDSYKSTVEDtDLNGNYEKAVSIKNDINKLNDYIKESSETITFNYENS 134
                                    5566688899*******************984699***************************9976665 PP

>> NOG1_N  NOG1 N-terminal helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   1.7   1.9e-05      0.11      46     140 ..       4      98 ..       1     118 [. 0.86
   2 ?   -0.5   0.0      0.18   1.1e+03      33      68 ..     111     142 ..     102     163 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.9e-05
                         NOG1_N  46 vrtasntlsdkLeeivkkfPnldelhpFyrelldvlvdkdelkksLaqv.kwarklirkigkeyvnklkkaddkkeakel 124
                                    + ta + l d++++++ k P++++++   + l+ +++   + k+ L+q+   + k i++i++  +++ k  +d+++  e 
  gene392|gene392|rna392|rna392   4 LSTAIKSL-DNMNALLAKVPKIEKIDAPSKTLMPTMLAEQRKKELLEQLiPFTHKVIQNIEEYITAQPKTYQDIEKKYER 82 
                                    56777778.9*************************************961567888999998888899999999998888 PP

                         NOG1_N 125 rreafgrvasvlkkvd 140
                                     + ++    s+++  d
  gene392|gene392|rna392|rna392  83 TKYMYDSYKSTVEDTD 98 
                                    8888888888887655 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.18
                         NOG1_N  33 neikrlrnlearkvrtasntlsdkLeeivkkfPnld 68 
                                    n i++l       +++ s+t+  ++e+ vk f  ++
  gene392|gene392|rna392|rna392 111 NDINKL----NDYIKESSETITFNYENSVKLFDTVE 142
                                    444444....33344566667777777777665555 PP

>> DASH_Spc19  Spc19
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   1.0     3e-05      0.18      44     121 ..      34     111 ..       1     129 [. 0.75

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3e-05
                                    ---TTTHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH......HHHHT-XXXXXXXXXX CS
                     DASH_Spc19  44 LipesdleaakaslaeeiePqieellekaekeleklerreetLkaklelqegrlsnaesskkeeeeseeskeeeeeee 121
                                    L p    e++k++l e++ P   + ++ +e++++ + +  + +++k+e  +  +++++s+ ++++ + + +++ + ++
  gene392|gene392|rna392|rna392  34 LMPTMLAEQRKKELLEQLIPFTHKVIQNIEEYITAQPKTYQDIEKKYERTKYMYDSYKSTVEDTDLNGNYEKAVSIKN 111
                                    5666666899**********************************************9888887777766666544433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1513  (0.0843884); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1282.88
//
Query:       gene393|gene393|rna393|rna393  [L=1073]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.8e-20   71.2   5.0    4.2e-19   69.1   5.0    2.1  1  CNOT1_HEAT       CCR4-NOT transcription complex subunit 1 HEA
    4.4e-16   59.0   6.2    4.4e-16   59.0   6.2    3.1  3  CNOT1_CAF1_bind  CCR4-NOT transcription complex subunit 1 CAF
    1.2e-08   34.3   3.5    3.8e-08   32.7   3.5    1.8  1  CNOT1_TTP_bind   CCR4-NOT transcription complex subunit 1 TTP
    1.4e-06   28.3   2.3    1.7e-06   28.0   0.0    2.3  3  DUF3819          Domain of unknown function (DUF3819)
  ------ inclusion threshold ------
       0.06   13.0   0.2       0.23   11.1   0.2    2.0  1  STAS             STAS domain


Domain annotation for each model (and alignments):
>> CNOT1_HEAT  CCR4-NOT transcription complex subunit 1 HEAT repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.1   5.0   1.2e-22   4.2e-19       3     150 .]     218     364 ..     215     364 .. 0.92

  Alignments for each domain:
  == domain 1  score: 69.1 bits;  conditional E-value: 1.2e-22
                                    HHHHHHHHHHHHS-GGGHHHHC--HHHHHHHHHS-S-.........-SHHHHHHHHTT-HHHHHHHS-TT.CHHHCHHHH CS
                     CNOT1_HEAT   3 lidelfplflsnhpnsalvlhklweidrqlllkalvdayakdp.lelsrIldvaqelkilsellnklpfn.faldLaala 80 
                                    ++delf +fl+  ++  l l+ + ++++ ll+k+l++  a+d+  +l+++ld++ elkil ++l++++ + f+ ++ +l 
  gene393|gene393|rna393|rna393 218 IFDELFLQFLK--KERILFLSVIFRNSPALLIKKLAE--ARDKgFSLNKLLDIILELKILPAILEIMNPSfFCYEILILS 293
                                    78899999996..44678999999*************..7888688*********************5566********* PP

                                    HHHT---HHHHHHHH--TT...THHHHHHHHHHHHH--T........TTSSSSTTTS--HHHHHHHHHHHH CS
                     CNOT1_HEAT  81 srreyldlekwledklkehgekfvqalldfLeekakqelerq.eekpsnepepkskslsvetvatlLevLq 150
                                    srr++l+l  w+++ +k +++ f+++l+ +++ek ++ ++   ++ + +e+ +  ksl++ t  + L++Lq
  gene393|gene393|rna393|rna393 294 SRRDHLNLSIWITNAFKLKKDVFANSLIGYITEKFSRAEQLLkSSIKLDEETTAEKSLYPLTFEITLNILQ 364
                                    *************************************9966698999999999****************98 PP

>> CNOT1_CAF1_bind  CCR4-NOT transcription complex subunit 1 CAF1-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.3      0.25   9.1e+02      37      96 ..     124     186 ..     115     203 .. 0.72
   2 ?   -2.6   0.1       0.8   2.9e+03      65     109 ..     470     508 ..     439     511 .. 0.67
   3 !   59.0   6.2   1.2e-19   4.4e-16       5     217 ..     636     849 ..     632     857 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.25
                                    -GGGHHHHHHHHHHHTTTT-GGGHHHHHHHH...HHHT-HHHHHHHHHHHHHHHHHHHHBS-G CS
                CNOT1_CAF1_bind  37 keeylkwfaqyLVekrvsiepnfhklYlkll...ekleskkLaeevlketlknikklLnsekt 96 
                                    + e+++ f +y++e+r +    +++++l+ +   e l+++kL++ +  e+  n+ ++++  k+
  gene393|gene393|rna393|rna393 124 NAETQENFLNYFIESREECLRVYNNVFLTRIitpEDLKRDKLKDDIHLESHFNCLEFFKILKE 186
                                    567778889999999999999999998765434467888888888888887777766665555 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.8
                                    HHHHHHT-HHHHHHHHHHHHHHHHHHHHBS-G..GGS-HHHHHHH CS
                CNOT1_CAF1_bind  65 kllekleskkLaeevlketlknikklLnsektlessserslLknL 109
                                    +l   +e++ + ++ +++ l+ i +lL++ +t   ++ r  L+ L
  gene393|gene393|rna393|rna393 470 RL---IEKRLFPKFYMQKALRIIANLLKNVTT---KEFRFALHTL 508
                                    33...456677778888888888888888777...5555555555 PP

  == domain 3  score: 59.0 bits;  conditional E-value: 1.2e-19
                                    --HHHHHHHHHHHHS--TTTHHHHHHHHHHH-...........-GGGHHHHHHHHHHHTTTT-GGGHHHHHHHHHHHT-H CS
                CNOT1_CAF1_bind   5 peeevqdkilfilnnlseenleeklkelkell...........keeylkwfaqyLVekrvsiepnfhklYlklleklesk 73 
                                     +e++++ki+f+ nn s+ +l+e+ + ++++            ++++l++f +y+ ek++  e+n+h l l+  e++ + 
  gene393|gene393|rna393|rna393 636 NDEHITKKINFFDNNSSTCTLDENPQCINQVYlcylkqvnfsmNNTNLQHFLRYFFEKKIF-ETNNHFLLLRYFEHFGD- 713
                                    578999999999999999999998877777644555655565588999***********96.***************98. PP

                                    HHHHHHHHHHHHHHHHHHHBS-G..GGS-HHHHHHHHHHHHHHTGGGT----TTTB-HHHHHHHHHHTT-HHHHHHHHHH CS
                CNOT1_CAF1_bind  74 kLaeevlketlknikklLnsektlessserslLknLgsWLGsiTlarnkpikhknlalkeLLleayekgrlevvipfvck 153
                                    ++++  ++ ++ ++ + Ln+ ++    +e    k Lg++ G++T++ n+    + +++ke ++  +e++r+ + + f+  
  gene393|gene393|rna393|rna393 714 DFYSLFCSLVF-EMFRYLNKYRI---DNEMRFAKSLGQFFGRFTIGMNRLYALDVFNMKEYVIGCVERKRIFFCVIFMVY 789
                                    56666555554.45566777777...6788899*********************************************** PP

                                    HHGGGGG-TTTSTT-HHHHHHHHHHHHHHHHT---HHHHHHHHHHHHHTT--TTSS---S---- CS
                CNOT1_CAF1_bind 154 vLesakkSkvFkppnpWlmailklLaelyeladlklnlkFeievLckeLkldlkdlepsellke 217
                                     +++ k   vFkp+np++m+++ lL e+ e +  k +lk eie L+ eLkl++  ++++++l +
  gene393|gene393|rna393|rna393 790 FIRQGKFGLVFKPKNPFIMNLIYLLNEICEYT--KDQLKEEIESLFAELKLTH--VKQTSMLVN 849
                                    ****************************8875..79************99865..555555555 PP

>> CNOT1_TTP_bind  CCR4-NOT transcription complex subunit 1 TTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.7   3.5   1.1e-11   3.8e-08      32     171 ..     401     538 ..     377     544 .. 0.89

  Alignments for each domain:
  == domain 1  score: 32.7 bits;  conditional E-value: 1.1e-11
                 CNOT1_TTP_bind  32 eveeeansyFqklYseeisveevietLkkfksskskrekevfacmiknLfdEyrffpqYPekeLkitaqLfGsiieeqLv 111
                                      e++ n +  ++ s++ +v++  e+++ + +  s +e+e+   +  +++d y  f++   +  k  a LfG +ie++L+
  gene393|gene393|rna393|rna393 401 SLEQQSNDFITSVVSGTRTVDQATEIIQSLVN-GSLNERELAMKIFSTMLDNYHNFHRISSS--KSLAFLFGRLIEKRLF 477
                                    5799999********************99865.67899***************999997655..57799*********** PP

                 CNOT1_TTP_bind 112 sykalgiaLrivLealrkppgskmfefgikaLeqf..ksrLkeypqycqhlasiphlkefpp 171
                                     +  ++ aLri+ + l++   +k f+f+++ L+ f  ++r  e+  + +++++i+++kef +
  gene393|gene393|rna393|rna393 478 PKFYMQKALRIIANLLKNV-TTKEFRFALHTLSMFcdSQRKGEFDAFFEEISKIDKVKEFLQ 538
                                    ***********99999885.7************995557999**************999866 PP

>> DUF3819  Domain of unknown function (DUF3819)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.1       2.4   8.5e+03      82     108 ..     391     414 ..     367     433 .. 0.50
   2 ?   -3.3   0.1       2.1   7.5e+03      72     111 ..     822     855 ..     817     859 .. 0.57
   3 !   28.0   0.0   4.8e-10   1.7e-06       5     133 ..     875     996 ..     872    1003 .. 0.93

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 2.4
                                    HHHH-----..-------.---HHHHH CS
                        DUF3819  82 nlrqllknaltkqlkeqeleqaiqilv 108
                                    +l+++ +++l  +l++q  ++ i+ +v
  gene393|gene393|rna393|rna393 391 ELKNITEKKL--SLEQQS-NDFITSVV 414
                                    4444444442..333333.33333333 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 2.1
                                    HHHHHHHHHHHHHH-----..-------.---HHHHHHHH CS
                        DUF3819  72 kepLresissnlrqllknaltkqlkeqeleqaiqilvndN 111
                                    k++L+e i+s + +l  +++    k q+   +++ ++ dN
  gene393|gene393|rna393|rna393 822 KDQLKEEIESLFAELKLTHV----K-QT-SMLVNHVSMDN 855
                                    56666666666666666652....2.22.45566666666 PP

  == domain 3  score: 28.0 bits;  conditional E-value: 4.8e-10
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTT---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        DUF3819   5 klvqlaierairEiiqpvversvtiAvitteelvkKDFalepdenkmrkaahlmvrnLagsLalvtckepLresissnlr 84 
                                    k++ + i+ +irE+  p++er+++i++ t + l ++    +++++ +    ++++ nL g+L++v + ep+ ++i  n+ 
  gene393|gene393|rna393|rna393 875 KVISMGIDFSIREVTFPLMERIMNISMKTMNFLFRR--RKDRKDEYVYDYKRNFMINLIGNLTVVCSLEPMCAAIIGNVP 952
                                    789999****************************98..688999999999****************************** PP

                                    H-----..-------.---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        DUF3819  85 qllknaltkqlkeqeleqaiqilvndNlelacaliekaaaekavreide 133
                                     +lk a   +l+  e ++ ++ ++++N+e + ++i++a++ k+++++++
  gene393|gene393|rna393|rna393 953 YFLKMA---GLE-VE-NERVHAVARNNIEKCNNIIRNAIVTKVLEDLER 996
                                    ****99...343.34.688**************************9985 PP

>> STAS  STAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.2   6.4e-05      0.23      17      91 ..     815     891 ..     806     911 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 6.4e-05
                                    EEESHHHHHHHHHHHHHHHHCCC..........-SEEEEEEEEEEEE-HHHHHHHHHHHHHHHHTT-EEEEES--HH CS
                           STAS  17 gpidfanaesfkeklkravgeeperve..kkeslkslildlsavsfiDssGvraLkeilkelkrigvevvlvnikpe 91 
                                    ++i+ ++++++ke++++  +e ++     ++  ++++ +d ++v f+Ds  ++ + +++ ++ + g+++ +  ++  
  gene393|gene393|rna393|rna393 815 NEICEYTKDQLKEEIESLFAELKLTHVkqTSMLVNHVSMDNTTVVFLDSYNLGHFDKVHSKVISMGIDFSIREVTFP 891
                                    689999**************99876666677789*********************************9988776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1073 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1394  (0.0777511); expected 358.6 (0.02)
Passed bias filter:                      568  (0.0316805); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.80u 0.32s 00:00:01.12 Elapsed: 00:00:00.47
# Mc/sec: 6835.43
//
Query:       gene394|gene394|rna394|rna394  [L=234]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.044   13.9   0.3       0.14   12.3   0.1    1.8  2  DUF4070   Domain of unknown function (DUF4070)


Domain annotation for each model (and alignments):
>> DUF4070  Domain of unknown function (DUF4070)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.1     0.043   7.6e+02      24      65 ..      85     129 ..      65     143 .. 0.65
   2 ?   12.3   0.1   7.7e-06      0.14      29      63 ..     137     171 ..     115     202 .. 0.71

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.043
                        DUF4070  24 tnfiPt.mpleelakeyvevleql..YspeayleRvdklllklkp 65 
                                    +nfi   ++  ++  e+++++e +   + e+y  R++++l+++ +
  gene394|gene394|rna394|rna394  85 LNFIVAlLNQLNMPYEFINTIEAVskLNEEKYESRIYNMLKEVSN 129
                                    666655566666666777776665223568899999998888764 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 7.7e-06
                        DUF4070  29 tmpleelakeyvevleqlYspeayleRvdklllkl 63 
                                     ++ ++l +eyv++++ ++spe+yl  ++++l++ 
  gene394|gene394|rna394|rna394 137 ELSGSNLFDEYVKIMKYSFSPEKYLGTFFNVLNEK 171
                                    377889*******************9998886543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       727  (0.0405488); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1753.72
//
Query:       gene395|gene395|rna395|rna395  [L=319]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (319 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       704  (0.039266); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2259.19
//
Query:       gene396|gene396|rna396|rna396  [L=559]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.5e-13   50.3   5.2    3.4e-12   47.1   2.5    2.9  2  SET        SET domain
    3.1e-06   27.0  10.0    3.1e-06   27.0  10.0    3.7  5  PHD        PHD-finger


Domain annotation for each model (and alignments):
>> SET  SET domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.21   1.8e+03      27      83 ..     163     184 ..      83     248 .. 0.58
   2 !   47.1   2.5   3.8e-16   3.4e-12       1     169 []     435     537 ..     435     537 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.21
                                    HHHHHHHHHH..HTEEEEEXGGXXGGSXHHHHHHHTTSSHHHHHHHHHHHHHHHHHHTH CS
                                    xxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            SET  27 kdeadksele..aylfslpeapknlaftkelakasastllqklakdqkqaekedtdaal 83 
                                    +++++k++                                          +++  ++++
  gene396|gene396|rna396|rna396 163 SNKKNKNGILktD-------------------------------------KYNSAQKNN 184
                                    2222222222221.....................................222222222 PP

  == domain 2  score: 47.1 bits;  conditional E-value: 3.8e-16
                                    SCEEEESSXBXTTXEEEEEE.ECCEECHHHHHHHHHH....HTEEEEEXGGXXGGSXHHHHHHHTTSSHHHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            SET   1 GrGvfAtedIpkgeficeyp.eeiiltkdeadksele....aylfslpeapknlaftkelakasastllqklakdqkqae 75 
                                    G+G+f+t+   k+e i+ey+ e  ++ + eadk+e+      y+f  +                                
  gene396|gene396|rna396|rna396 435 GYGLFSTRLYDKDEPIIEYVgE--LIDDYEADKREKIykdrIYMFRKN-------------------------------- 480
                                    8999999999999999999977..999999999998877775555533................................ PP

                                    HHHHHHTHHHHHHHXTTTSXXXHCCCCCHCCCHEEEETEEEEEECCCGTTGGGCEEXSSSSEEEEEEEETTSSEEEEEES CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            SET  76 kedtdaalkasskaesdlnaskpeagafsaiagysidaralksgngagplarflNHsCdpNcnltvqnvlrgprvavfAt 155
                                                                   ++ ++d  a+  gn a     ++NHsC+pNc++t +   +  ++++ A 
  gene396|gene396|rna396|rna396 481 -------------------------------SKIILD--ATVVGNLA----KYINHSCEPNCYATKVICGTASCIIICAK 523
                                    ...............................456688..66888888....***********7777777*********** PP

                                    SXBXTTEEEEEXTT CS
                                    xxxxxxxxxxxxxx RF
                            SET 156 rdIkkGeEltidYg 169
                                    r I k+eEl++dY+
  gene396|gene396|rna396|rna396 524 RIITKNEELSYDYN 537
                                    *************7 PP

>> PHD  PHD-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    3.4   0.4    0.0078        70      41      51 ..      89      99 ..      82     100 .. 0.76
   2 !   27.0  10.0   3.5e-10   3.1e-06       1      51 [.      93     148 ..      93     149 .. 0.92
   3 ?    0.2   5.1     0.079   7.1e+02       1      31 [.     235     262 ..     235     267 .. 0.80
   4 ?   -3.5   0.0       1.2     1e+04      10      19 ..     394     403 ..     391     404 .. 0.76
   5 ?   -1.8   0.0      0.33     3e+03      26      38 ..     420     432 ..     417     436 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.0078
                                   SSTBSSTTTHT CS
                            PHD 41 egewlCekCke 51
                                   +++++C+kC++
  gene396|gene396|rna396|rna396 89 MTSYYCPKCNQ 99
                                   358******87 PP

  == domain 2  score: 27.0 bits;  conditional E-value: 3.5e-10
                                    SBTTTTS...TTSTTSCEEEETTTSCEEETTTSSSTHSHHSHHSS..TBSSTTTHT CS
                            PHD   1 rCavCkk...ksdeeeelvqCdgCkrwfHqkClkppleseekpeg..ewlCekCke 51 
                                    +C  C++   + d+  ++v Cd+C rw H +C +++ +++ k  +  ++ C  C+e
  gene396|gene396|rna396|rna396  93 YCPKCNQkydNHDYTVKMVHCDECTRWLHIECENITWREYAKFGSlpRYECMLCRE 148
                                    7******99878889***********************99998889********85 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.079
                                    SBTTTTSTTSTTSCEEEETTTS.CEEETTTSS CS
                            PHD   1 rCavCkkksdeeeelvqCdgCk.rwfHqkClk 31 
                                    rCa Ck+     + ++ C  Ck r +H+ C k
  gene396|gene396|rna396|rna396 235 RCANCKR----IGATIKCLFCKdRYYHVPCAK 262
                                    6999999....888999999972578999976 PP

  == domain 4  score: -3.5 bits;  conditional E-value: 1.2
                                    STTSCEEEET CS
                            PHD  10 deeeelvqCd 19 
                                    +++++++qC 
  gene396|gene396|rna396|rna396 394 EYSHDTIQCS 403
                                    6788999996 PP

  == domain 5  score: -1.8 bits;  conditional E-value: 0.33
                                    ETTTSSSTHSHHS CS
                            PHD  26 HqkClkpplesee 38 
                                    H  C +p+l+++ 
  gene396|gene396|rna396|rna396 420 HLRCSRPKLSKSA 432
                                    99*****998665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (559 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       854  (0.0476323); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.44
# Mc/sec: 3795.72
//
Query:       gene397|gene397|rna397|rna397  [L=308]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.022   14.4   0.4      0.076   12.7   0.4    2.0  1  GGA_N-GAT  GGA N-GAT domain
       0.13   12.3   0.5       0.91    9.6   0.0    2.5  3  Sel_put    Selenoprotein, putative


Domain annotation for each model (and alignments):
>> GGA_N-GAT  GGA N-GAT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.4   8.4e-06     0.076       2      18 ..      44      60 ..      44      62 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 8.4e-06
                      GGA_N-GAT  2 edeeksklLarLLkSkn 18
                                   +deek+ +L++LL S++
  gene397|gene397|rna397|rna397 44 QDEEKEIHLKKLLESGK 60
                                   59*************87 PP

>> Sel_put  Selenoprotein, putative
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.1      0.35   3.1e+03      23      44 ..      85     105 ..      85     107 .. 0.80
   2 ?   -1.4   0.0      0.28   2.5e+03      14      24 ..     122     132 ..     119     132 .. 0.85
   3 ?    9.6   0.0    0.0001      0.91       8      36 ..     145     174 ..     140     181 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.35
                        Sel_put  23 erYvehmrrhHpdkppmsereF 44 
                                    e+Y++h r   p++ ++ e+++
  gene397|gene397|rna397|rna397  85 EKYIKHGRDV-PNEYVLQEEDY 105
                                    6899998877.88888888887 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.28
                        Sel_put  14 rllvGepdYer 24 
                                     +++G ++Ye+
  gene397|gene397|rna397|rna397 122 TKMIGTKEYEK 132
                                    689******96 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.0001
                        Sel_put   8 rvrqylrllvGepdYerYvehmrrhH.pdk 36 
                                    + ++ + +l+G +dY++Y+  ++r++ p++
  gene397|gene397|rna397|rna397 145 YYSKRMVKLIGNDDYDAYLCFRKRTNvPGR 174
                                    566667789**********98888876765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (308 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       960  (0.0535445); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1981.89
//
Query:       gene398|gene398|rna398|rna398  [L=113]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.9e-12   44.9   2.2    1.4e-11   44.0   2.2    1.5  1  YL1_C     YL1 nuclear protein C-terminal domain
     0.0058   16.5   0.2     0.0083   16.0   0.2    1.2  1  zf-HIT    HIT zinc finger


Domain annotation for each model (and alignments):
>> YL1_C  YL1 nuclear protein C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.0   2.2   1.5e-15   1.4e-11       1      26 [.      60      85 ..      60      87 .. 0.97

  Alignments for each domain:
  == domain 1  score: 44.0 bits;  conditional E-value: 1.5e-15
                          YL1_C  1 yCdITGlpAkYrDPkTgLpYanveay 26
                                   +CdITGlpA+Y++PkT+L+Y ++++y
  gene398|gene398|rna398|rna398 60 LCDITGLPANYTCPKTRLNYFDKDVY 85
                                   6************************9 PP

>> zf-HIT  HIT zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.2   9.3e-07    0.0083       2      23 ..      58      79 ..      57      79 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 9.3e-07
                                   --B-TTT-SB-SEE-TTT--EE CS
                         zf-HIT  2 rklCgvCgfpakYkCpkCntry 23
                                   +klC + g pa+Y+Cpk++  y
  gene398|gene398|rna398|rna398 58 MKLCDITGLPANYTCPKTRLNY 79
                                   589999999*********9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (113 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       642  (0.0358079); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 765.75
//
Query:       gene399|gene399|rna399|rna399  [L=296]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.3e-35  120.8   0.5    7.3e-35  120.8   0.5    1.5  2  DNA_ligase_A_N  DNA ligase N terminus
    1.9e-14   53.8   0.0    3.6e-14   52.9   0.0    1.4  1  DNA_ligase_A_M  ATP dependent DNA ligase domain
     0.0033   15.8   0.1      0.019   13.3   0.0    1.9  2  DRIM            Down-regulated in metastasis
  ------ inclusion threshold ------
      0.019   15.3   0.1       0.22   11.8   0.0    2.1  2  RNA_ligase      RNA ligase
       0.09   12.9   0.1       0.18   11.9   0.1    1.5  1  ColG_sub        Collagenase G catalytic helper subdomain


Domain annotation for each model (and alignments):
>> DNA_ligase_A_N  DNA ligase N terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.8   0.5     2e-38   7.3e-35       2     171 ..       5     174 ..       4     176 .. 0.95
   2 ?   -2.6   0.0       1.7   6.1e+03     129     147 ..     182     200 ..     180     202 .. 0.77

  Alignments for each domain:
  == domain 1  score: 120.8 bits;  conditional E-value: 2e-38
                                    CHHHHHHHHHHCC.---HHHHHHHHHHHHHTS-..SHHHHHHHHHH....SS-CCCS------HHHHHHHHHHHHT--HH CS
                 DNA_ligase_A_N   2 FaelaelfekieestkkrlekrailanffrkvesagpedlypalrL....llPdydgreygigesllakalaealglskk 77 
                                    F++l+++f++iee ++ rle+++il+n++++++   +e++ +a++L    ++P y+++e++ige +l+k++++++g + k
  gene399|gene399|rna399|rna399   5 FKDLCSVFKEIEE-KSGRLEIQQILSNYLSTLD---KENMIIAFYLctgtVYPTYENKELNIGEGILYKVIGDMTGKNIK 80 
                                    9************.999************7765...679***************************************99 PP

                                    HHHHHHHHHS-HHHHHHHHHCCHHHH------BHHHHHHHHHHHHH-.STTHHHHHHHHHHHHHHHS-HHHHHHHHHHHC CS
                 DNA_ligase_A_N  78 kikdalakvgDlgevaeevlskrstlakkspltieevnelLdklaaa.gkgsedekkkilkkllkraspeEakyliriil 156
                                     +k+++a++gDlg++a +++ ++   + +++  ++e+++ L+k+ +  gk+ + +kk+++ k+l+ +sp+E+ky++r+++
  gene399|gene399|rna399|rna399  81 VLKKEYAEYGDLGQIACKYKINKLI-KVEKSFELNEIYNGLKKIGEIeGKDAMFRKKNAILKMLSVMSPNEIKYFVRLLE 159
                                    9*****************9987765.999***************87799******************************* PP

                                    T---SS--HHHHHHH CS
                 DNA_ligase_A_N 157 kdlriglsektvlda 171
                                    ++l+igl+ +tvl  
  gene399|gene399|rna399|rna399 160 GKLKIGLAIQTVLIS 174
                                    ************976 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.7
                                    HHHHHHHHHHHHHHS-HHH CS
                 DNA_ligase_A_N 129 edekkkilkkllkraspeE 147
                                    +++  ++lkk ++r+ + E
  gene399|gene399|rna399|rna399 182 KEDSLDLLKKAYDRCASVE 200
                                    4567899999999998766 PP

>> DNA_ligase_A_M  ATP dependent DNA ligase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.9   0.0     1e-17   3.6e-14       3      65 ..     229     286 ..     224     291 .. 0.81

  Alignments for each domain:
  == domain 1  score: 52.9 bits;  conditional E-value: 1e-17
                                    EEEEESCHHHHHHHTTTSEEEEEEEESSEEEEEEEETTEEEEEETTS-B-GGGCHHHHHHHHH CS
                 DNA_ligase_A_M   3 LAeslksiekalkkleekafivEiKyDGeRaqvhkegdkvklfSRrlkditaakpelvkalke 65 
                                    L+++l+s+     ++  ++fi+E+KyDGeR+q+hk++d+vk++SR+++d t ++p+lv  +++
  gene399|gene399|rna399|rna399 229 LCNPLNSF---TVNF--SDFICEVKYDGERIQIHKKNDQVKFYSRNGEDSTFKYPDLVAVIRK 286
                                    44444433...3333..789*************************************998876 PP

>> DRIM  Down-regulated in metastasis
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0     0.049   1.8e+02     476     503 ..       4      31 ..       2      45 .. 0.82
   2 !   13.3   0.0   5.4e-06     0.019     118     159 ..     125     166 ..     120     204 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.049
                           DRIM 476 llktlsslfsrlkdreaRklLcevlkal 503
                                    l+k l+s+f+ +++++ R  + ++l+ +
  gene399|gene399|rna399|rna399   4 LFKDLCSVFKEIEEKSGRLEIQQILSNY 31 
                                    6899999999999999999999998765 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 5.4e-06
                           DRIM 118 sasgkagqqarRaavLrfLaglseeelssFldlalgplkkvl 159
                                      +gk+ +  +++a+L +L+ +s++e++ F++l+ g+lk+ l
  gene399|gene399|rna399|rna399 125 EIEGKDAMFRKKNAILKMLSVMSPNEIKYFVRLLEGKLKIGL 166
                                    5567888999**************************998654 PP

>> RNA_ligase  RNA ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0      0.12   4.3e+02     130     149 ..      37      74 ..       5      84 .. 0.61
   2 ?   11.8   0.0   6.1e-05      0.22       2      35 ..     242     277 ..     241     291 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.12
                                    C..................H.HHHTC--EEEEEESSSS CS
                     RNA_ligase 130 l.................ll.skgnkrEGlVikpesel 149
                                    +                 ++ ++ n++EG+  k   ++
  gene399|gene399|rna399|rna399  37 KenmiiafylctgtvyptYEnKELNIGEGILYKVIGDM 74 
                                    0333456666777776643347899*****99987776 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 6.1e-05
                                    EEEEEEE-SSEEEEEEEETT.EEEEETTCEB.CTTT CS
                     RNA_ligase   2 evvvtEKlDGtnfriylvke.vgvasRsqil.pfge 35 
                                     +++++K DG++++i++ ++ v++ sR+++  +f++
  gene399|gene399|rna399|rna399 242 DFICEVKYDGERIQIHKKNDqVKFYSRNGEDsTFKY 277
                                    5899*************9778*******98732444 PP

>> ColG_sub  Collagenase G catalytic helper subdomain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   5.2e-05      0.18      13      80 ..      76     146 ..      69     155 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 5.2e-05
                                    ---HHHHHHHHHHHHT--S-EEEEEE-SSE...EEEEEEEEEEESS---HHHHHHHHHHHHHHHHHHHHTS CS
                       ColG_sub  13 eksleeikseiedvaklkdvkikkeksqff...ktftlrgtytggkskGesedWkemnekvnevLkeLsek 80 
                                     k+++ +k+e ++  +l ++  k +  +     k+f+l+ +y g k+ Ge+e  ++m +k n +Lk Ls  
  gene399|gene399|rna399|rna399  76 GKNIKVLKKEYAEYGDLGQIACKYKINKLIkveKSFELNEIYNGLKKIGEIEGKDAMFRKKNAILKMLSVM 146
                                    56777777777777777777766655544322279********************************9965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (296 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       632  (0.0352502); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1966.48
//
Query:       gene4|gene4|rna4|rna4  [L=520]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.2e-20   74.0   7.8    3.4e-13   49.6   1.4    3.3  3  Pkinase      Protein kinase domain
    5.6e-08   32.4  14.8    1.1e-06   28.1   7.7    3.3  3  Pkinase_Tyr  Protein tyrosine kinase
  ------ inclusion threshold ------
       0.16   11.6   4.8       0.29   10.7   0.2    2.9  3  FTA2         Kinetochore Sim4 complex subunit FTA2
        0.7    9.8   5.5        5.4    7.0   0.0    4.4  4  Phage_NinH   Phage NinH protein


Domain annotation for each model (and alignments):
>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.4     1e-09   4.5e-06       2      69 ..      12      73 ..      11     161 .. 0.87
   2 !   49.6   1.4   7.6e-17   3.4e-13      90     152 ..     372     436 ..     355     450 .. 0.84
   3 ?   -0.2   0.0      0.11   5.1e+02     179     197 ..     441     459 ..     435     513 .. 0.82

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 1e-09
                           EEEEEEEEESSEEEEEEEETTTTEEEEEEEEECHCHCHHHHHHHHHHHHHHHHHSCTTB--EEEEEEE CS
                Pkinase  2 ekleklGeGsfGkVykaveketgkivAvKkikkekakkkkekkvlrEikilkklkhpnivrlyevfee 69
                           +  +klG+G+ ++Vyk+++ +tg+++A+K+i+   +++ ++     E+ + +++ h+ni+++ + f +
  gene4|gene4|rna4|rna4 12 KFTQKLGQGTHASVYKMMNVHTGQHFALKEINLCYQEDVHN-----EC-LPRHITHKNIMKYTKLFVS 73
                           6789*****************************98888665.....65.6789999***999998876 PP

  == domain 2  score: 49.6 bits;  conditional E-value: 7.6e-17
                            HHHSS--HHHHHHHHHHHHHHHHHHHHTTEE-SS-SGGGEEEETTTE..EEE-SGTTSEESSSSC CS
                Pkinase  90 erkgslseeeakkiakqilegleylHskgiiHrDlKpeNiLidekge..lKitDFGlakelesss 152
                            ++k++++ + +  ++k i++g+ ylH ++i+H+D+K++NiL++++ +   Ki+DFGl + ++ ++
  gene4|gene4|rna4|rna4 372 QNKRCINRHFIAMLFKDIVRGILYLHTNNIFHCDIKSNNILLKHETVlvPKISDFGLRRSVKCRK 436
                            357779999999*******************************7776789*******99887655 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.11
                            HHHHHHHHHHHHHHSS-ST CS
                Pkinase 179 DvWslGvilyelltgkppf 197
                            Dv+ +Gv+ +e+l+     
  gene4|gene4|rna4|rna4 441 DVYDCGVLYFEMLCPVKTV 459
                            99**********9865554 PP

>> Pkinase_Tyr  Protein tyrosine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.2   0.1    0.0025        11       2      75 ..      12      76 ..      11      85 .. 0.79
   2 !   28.1   7.7   2.6e-10   1.1e-06      95     154 ..     360     433 ..      96     440 .. 0.79
   3 ?    3.0   0.1     0.012        52     185     244 ..     439     496 ..     433     514 .. 0.69

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0025
                           EEEEEEEEESSEEEEEEEEETTTTSSEEEEEEEEESTTSSHHHHHHHHHHHHHHHTS-BTTB--EEEEEESSSS CS
            Pkinase_Tyr  2 elgkklGeGafGkVvegtlkgekekkevkVavKtlkeeateeekeelleeakimkklkhpnivkllgvctkeep 75
                           ++++klG+G+ ++V++        ++ ++ a+K ++  ++e+ ++    e  + +++ h+ni+k++ + ++e+p
  gene4|gene4|rna4|rna4 12 KFTQKLGQGTHASVYKMMNV----HTGQHFALKEINLCYQEDVHN----E-CLPRHITHKNIMKYTKLFVSERP 76
                           7899***********99888....788999*****8888887333....3.35578899999998887776555 PP

  == domain 2  score: 28.1 bits;  conditional E-value: 2.6e-10
                            T............CTTTSBHHHHHHHHHHHHHHHHHHHHTTEEEST-SGGGEEEEETT..EEEE-STTTHEETT CS
            Pkinase_Tyr  95 k............ekekltlkdllsfalqvAkGmeyLeskklvHrdlaarNvLlsenk..vvkisDfGLardie 154
                                         +k+ ++ + +  +  ++ +G+ yL+++++ H d+ + N+Ll++++  v kisDfGL r+++
  gene4|gene4|rna4|rna4 360 YfylynssiinyqNKRCINRHFIAMLFKDIVRGILYLHTNNIFHCDIKSNNILLKHETvlVPKISDFGLRRSVK 433
                            0555555555554667777777888899***************************9883345*********995 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.012
                            HHHHHHHHHHHHHHHTTSSGTTTTSHHHHHHH.HHHTTEES-B.BTTSBHHHHHHHHHHT-S CS
            Pkinase_Tyr 185 ksDvWsfGvllwEiftlgespypglkneevle.klkegkrlek.pekcpeelyelmkkcwee 244
                              Dv+  Gvl +E+++    p++++++++vl+ +lke  +l++   ++  e ++++++c++ 
  gene4|gene4|rna4|rna4 439 YKDVYDCGVLYFEMLC----PVKTVMEMDVLRtRLKETGELPEwFVSAYGEETDIIRRCMSG 496
                            56*************9....888887777765145655555541456667777788888765 PP

>> FTA2  Kinetochore Sim4 complex subunit FTA2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.2   6.4e-05      0.29      22      82 ..       9      68 ..       2      75 .. 0.69
   2 ?   -2.0   0.0      0.51   2.3e+03     162     198 ..      80     116 ..      79     120 .. 0.81
   3 ?    1.7   0.1     0.037   1.7e+02     173     203 ..     381     411 ..     313     419 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 6.4e-05
                   FTA2 22 kdiefleyLgkglhsiVlkvk..irgkeYALKlFrfleaeeleeaeedlkiprealkelasys 82
                           +d++f + Lg+g+h+ V+k+     g+ +ALK    +++e+++++  + +i+++++ ++   +
  gene4|gene4|rna4|rna4  9 RDFKFTQKLGQGTHASVYKMMnvHTGQHFALKEINLCYQEDVHNECLPRHITHKNIMKY---T 68
                           79*****************97446789*****766666666655555555544444443...3 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.51
                   FTA2 162 KelellkeqeelevsqlpkllrdlkklhklgIvvrDl 198
                            K++   +++e+  v +++kl++ ++ ++++ I+  ++
  gene4|gene4|rna4|rna4  80 KDVIASDNDEQDCVLDMQKLRNRVRAMNEHSIFSDGV 116
                            56555677777788899*************9998876 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.037
                   FTA2 173 levsqlpkllrdlkklhklgIvvrDlkeeny 203
                            ++   +++++r +  lh   I++ D+k++n+
  gene4|gene4|rna4|rna4 381 FIAMLFKDIVRGILYLHTNNIFHCDIKSNNI 411
                            5555688999*****************9987 PP

>> Phage_NinH  Phage NinH protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.31   1.4e+03      43      58 ..      20      35 ..       5      36 .. 0.73
   2 ?   -0.4   0.2      0.24   1.1e+03      28      50 ..     218     239 ..     214     240 .. 0.63
   3 ?    1.0   0.2     0.092   4.1e+02      37      50 ..     281     294 ..     254     296 .. 0.77
   4 ?    7.0   0.0    0.0012       5.4       8      30 ..     475     497 ..     470     501 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.31
             Phage_NinH 43 kqHAivngvLmvhrGq 58
                             HA v  ++ vh Gq
  gene4|gene4|rna4|rna4 20 GTHASVYKMMNVHTGQ 35
                           36999*99999**998 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.24
             Phage_NinH  28 csRatvRkYvrDkeakqHAivng 50 
                            +sR+ v    +D+    H ivn+
  gene4|gene4|rna4|rna4 218 TSRQSVLNDHDDRT-GHHSIVNN 239
                            55555555555554.47****96 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.092
             Phage_NinH  37 vrDkeakqHAivng 50 
                             +D +   H ivn+
  gene4|gene4|rna4|rna4 281 HDDIKPGHHSIVND 294
                            46778888888887 PP

  == domain 4  score: 7.0 bits;  conditional E-value: 0.0012
             Phage_NinH   8 iPdlLvetyGnqtEvARrlkcsR 30 
                            +P+  v +yG  t++ Rr  + R
  gene4|gene4|rna4|rna4 475 LPEWFVSAYGEETDIIRRCMSGR 497
                            79****************98877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (520 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       965  (0.0538234); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.47
# Mc/sec: 3294.92
//
Query:       gene40|gene40|rna40|rna40  [L=86]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       420  (0.0234257); expected 358.6 (0.02)
Passed bias filter:                      228  (0.0127168); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.55u 0.34s 00:00:00.89 Elapsed: 00:00:00.56
# Mc/sec: 463.83
//
Query:       gene400|gene400|rna400|rna400  [L=360]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.6e-28   99.9   0.0    2.1e-28   99.5   0.0    1.1  1  PfkB          pfkB family carbohydrate kinase
    1.7e-06   27.6   0.0    2.6e-06   27.0   0.0    1.2  1  Phos_pyr_kin  Phosphomethylpyrimidine kinase


Domain annotation for each model (and alignments):
>> PfkB  pfkB family carbohydrate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.5   0.0   2.4e-32   2.1e-28      28     292 ..      82     346 ..      65     352 .. 0.83

  Alignments for each domain:
  == domain 1  score: 99.5 bits;  conditional E-value: 2.4e-32
                                    ESEEEEEEESHHHHHHHHHHHTT.-EEEEEEEEESSHHHHHHHHHHHHTTEEETTEEEESSSEEEEEEEEETTTSEEEEE CS
                           PfkB  28 vktveksaGGagaNvAvalarlg.advafigavGdDnfGeflleelkkegvdtdyvkidedtrtglalivvdedgertiv 106
                                     +++  s GG+ +N+   ++ +  +d  f+ga+GdD+ Ge+l  ++ k+gvd  + ki ++  tg ++i +++  +r ++
  gene400|gene400|rna400|rna400  82 KQKIMTSLGGSSLNTFLKIKECTdIDLKFFGAIGDDKEGEDLCGLMTKSGVDFYFEKIAAR-GTGRCFIGLKRS-KRILC 159
                                    56778899*********************************************88886666.**********97.9**** PP

                                    EEEGGGGGHHHHHHHHHHHHHGCTSEEEEESEECTTSHHHHHHHHHHHHHHTTE.EEEEECESSSHH.HHHHHHHHHCTE CS
                           PfkB 107 fnrgaaadltkeeleededlleeadllyisgllsselpeavleelaeaaknggt.fdpnlldplgaq.fkeallellala 184
                                    +++ a++ +++   e++++++e+a + y+s+++ s ++  +++   +  + + t +++  +++l ++  +  ++ ll  a
  gene400|gene400|rna400|rna400 160 TWLDASELMEPFFIEKNKNIVEQARIAYLSTFIIS-FNINTVHSFLKYLNDSVTlVINLGSEKLYSDdNMMFIQMLLKNA 238
                                    ***********7777****************7777.666677777777777776577777888888896677999999** PP

                                    SEEEEEHHHHHHHHTSCT...HSHHHHHHHHHHHHHTTSSEEEEEEGGGEEEEEETTEEEEEEE..SSSS-SBGTTHHHH CS
                           PfkB 185 dllkpneeElealtgekl...edieealaalhklkakgaktvvvtlGkeGalvvekdgelkvpav.pkvkvvDttGAGDs 260
                                     ++++n +E+ al +++l   ++ e  +a     +++  ++++ t G e + ++ +++ ++v+     +   Dt GAGD+
  gene400|gene400|rna400|rna400 239 KVIIGNKSEANALIEKTLggsVSTERGMAE----ISRKGTLFICTNGPESVKYAFNGEIHEVEVSkGRQVFQDTCGAGDA 314
                                    *****************9654333333333....333458***********999655555554431234456******** PP

                                    HHHHHHHHHHTTHHHHHHHHHHHHHHHHHHTS CS
                           PfkB 261 fvggflaallegksleealrfanavAalvvqk 292
                                    f++g+l++l +++   e+++++++ A  +++k
  gene400|gene400|rna400|rna400 315 FAAGVLVGLYNNQATGECVKLGVEYALTTLEK 346
                                    *************************9988876 PP

>> Phos_pyr_kin  Phosphomethylpyrimidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   0.0   2.9e-10   2.6e-06      96     235 ..     214     347 ..     190     357 .. 0.76

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 2.9e-10
                                    SSCTSSSBSSHHHHHHHHHHTGGG-SEEE-BHHHHHHHHT---SSHHHHHHHHHHHHHTT-SEEEEEEGGS-SSSEEEEE CS
                   Phos_pyr_kin  96 vaksgselleeeavealkeeLlplatvitPNlpEaeaLlgekikteedmkeaakkllklgakaVlikGghlegeeavvtd 175
                                    v + gse l ++   ++ + Ll+ a+vi+ N  Ea+aL+++++    + ++ + ++++ g+  +   G +     +v ++
  gene400|gene400|rna400|rna400 214 VINLGSEKLYSDDNMMFIQMLLKNAKVIIGNKSEANALIEKTLGGSVSTERGMAEISRKGTLFICTNGPE-----SV-KY 287
                                    44555555555555566667********************999999999999999999887776655544.....34.45 PP

                                    EEETSSEEEEEEEE----S--BTHHHHHHHHHHHHHHCTSSHHHHHHHHHHHHHHHHHCG CS
                   Phos_pyr_kin 176 vlydgeeveeleaerietknthGtGCtlssaiaaelakgesleeAvkkAkeyvteaikea 235
                                     +  + +++e+++ r   ++t G+G+++++ +   l +++   e vk + ey  ++++++
  gene400|gene400|rna400|rna400 288 AFNGEIHEVEVSKGRQVFQDTCGAGDAFAAGVLVGLYNNQATGECVKLGVEYALTTLEKN 347
                                    5555555566666666669*********************************99999854 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (360 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       509  (0.0283898); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 2431.24
//
Query:       gene401|gene401|rna401|rna401  [L=53]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (53 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       304  (0.0169558); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.43
# Mc/sec: 372.89
//
Query:       gene402|gene402|rna402|rna402  [L=100]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       525  (0.0292822); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 739.23
//
Query:       gene403|gene403|rna403|rna403  [L=121]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.69    9.9   2.8        1.1    9.2   2.8    1.3  1  APAF1_C   APAF-1 helical domain


Domain annotation for each model (and alignments):
>> APAF1_C  APAF-1 helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   2.8   6.3e-05       1.1      14      41 ..       5      32 ..       2      37 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 6.3e-05
                        APAF1_C 14 kkykeeelskldkddlywysyleyHlak 41
                                    +yk+++l++ d +d y +++l yHl++
  gene403|gene403|rna403|rna403  5 DTYKKQFLIQYDLNDEYAFRFLYYHLHE 32
                                   6899**********************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       454  (0.0253221); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 884.58
//
Query:       gene404|gene404|rna404|rna404  [L=102]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       598  (0.0333538); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 728.33
//
Query:       gene405|gene405|rna405|rna405  [L=241]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.2e-15   56.4   1.7    5.4e-15   55.6   1.7    1.4  1  zf-ZPR1   ZPR1 zinc-finger domain
  ------ inclusion threshold ------
       0.12   12.3   0.4       0.12   12.3   0.4    2.7  3  zf-HIT    HIT zinc finger
        5.6    7.5   8.9        3.7    8.1   5.8    2.2  2  zf-CHY    CHY zinc finger


Domain annotation for each model (and alignments):
>> zf-ZPR1  ZPR1 zinc-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.6   1.7     9e-19   5.4e-15       2     158 ..      27     210 ..      26     211 .. 0.83

  Alignments for each domain:
  == domain 1  score: 55.6 bits;  conditional E-value: 9e-19
                        zf-ZPR1   2 lCpsCgkengetrllltkiPyfkeviimsfeCehCgyknnevksageieekG.kritlkveseedlnrqvlkSetatvei 80 
                                    +C++C+ +++  ++++++ P     i+++++C++C+ ++n + + + ++ +G  +it+k ++++dl+r v   + + +++
  gene405|gene405|rna405|rna405  27 QCTQCN-NPAFLKTMRVDTPGQCAQILSTYTCPTCNIQDNAILPYEDKNSRGgIKITCKFTNKDDLKRYVCVFQNTILQF 105
                                    7****5.99***********************************9999887669************************** PP

                        zf-ZPR1  81 peleleippgtlegrlttv.EGlLeqikeele.....ke....................egdqaer.......ed.eeke 126
                                    ++ ++  +  +++ ++ttv E +L+++++e+      k+                    +     +       e+ ++ +
  gene405|gene405|rna405|rna405 106 KKDDFIYEY-SSSMDVTTVaEIVLRNAIDEIAqmwniKKktfgsvfdlrqelsnssaslS-----HsgsvtslESiQDVD 179
                                    *****9999.77788999845689*******97776611567777877777655444331.....155555565566788 PP

                        zf-ZPR1 127 kieeflekleeliegeepftlildDpagnSfi 158
                                    +++  +e l+++++ ++ f + l Dp+g S +
  gene405|gene405|rna405|rna405 180 NAKYAIEMLQDMVS-NSGFVMELCDPSGFSRV 210
                                    88899999999998.889**********9987 PP

>> zf-HIT  HIT zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.6     0.088   5.2e+02      15      22 ..      27      34 ..      17      36 .. 0.69
   2 ?   12.3   0.4     2e-05      0.12       8      21 ..      48      62 ..      46      70 .. 0.89
   3 ?   -2.4   0.2      0.78   4.6e+03      11      16 ..      91      96 ..      80      97 .. 0.54

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.088
                                   E-TTT--E CS
                         zf-HIT 15 kCpkCntr 22
                                    C +Cn +
  gene405|gene405|rna405|rna405 27 QCTQCNNP 34
                                   47777654 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 2e-05
                                   T-S.B-SEE-TTT-- CS
                         zf-HIT  8 Cgf.pakYkCpkCnt 21
                                   C +  + Y+Cp+Cn+
  gene405|gene405|rna405|rna405 48 CAQiLSTYTCPTCNI 62
                                   888899*******97 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 0.78
                                   B-SEE- CS
                         zf-HIT 11 pakYkC 16
                                    ++Y C
  gene405|gene405|rna405|rna405 91 LKRYVC 96
                                   456666 PP

>> zf-CHY  CHY zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   5.8   0.00062       3.7      45      74 ..      16      62 ..       3      63 .. 0.77
   2 ?    4.4   1.7    0.0087        52      59      74 ..      47      62 ..      42     101 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00062
                         zf-CHY 45 llCeteqekavlCkkCkk.................efaeyfCpiCkl 74
                                    +C++ ++++++C++C++                  +++y+Cp+C+ 
  gene405|gene405|rna405|rna405 16 DTCNSPKQVEIQCTQCNNpaflktmrvdtpgqcaqILSTYTCPTCNI 62
                                   5788888888888888888888888777777766578899*****85 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.0087
                         zf-CHY 59 kCkkefaeyfCpiCkl 74
                                   +C + +++y+Cp+C+ 
  gene405|gene405|rna405|rna405 47 QCAQILSTYTCPTCNI 62
                                   5666677777777764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       920  (0.0513135); expected 358.6 (0.02)
Passed bias filter:                      510  (0.0284455); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.31s 00:00:00.86 Elapsed: 00:00:00.51
# Mc/sec: 1411.68
//
Query:       gene406|gene406|rna406|rna406  [L=88]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       232  (0.0129399); expected 358.6 (0.02)
Passed bias filter:                      220  (0.0122706); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.30s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 566.86
//
Query:       gene407|gene407|rna407|rna407  [L=324]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.5e-22   79.5   0.4    6.5e-22   77.5   0.1    2.1  2  tRNA_bind  Putative tRNA binding domain


Domain annotation for each model (and alignments):
>> tRNA_bind  Putative tRNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.5   0.1   3.6e-26   6.5e-22       1      92 [.     169     257 ..     169     260 .. 0.97
   2 ?   -0.9   0.0       0.1   1.8e+03      16      58 ..     272     312 ..     264     319 .. 0.72

  Alignments for each domain:
  == domain 1  score: 77.5 bits;  conditional E-value: 3.6e-26
                                    EEEEEEEEEEEETTSSTEEEEEEEESSSSEEEEEESCTTTSTHHHHTTEEEEEETTSESEEETTEEESSEE-EEECCESS CS
                      tRNA_bind   1 lrvGkvleaeehpnadkLlvlkvdvGeeeprqivsgaknvyepeelvakkvvvvanlkpkklrGveSeGMilsaeeldek 80 
                                    +r+G++++++eh nad+L+v+kv +G+ e +q+vsg++  +e e++ +k    ++n++  k+rG+ S+GMil+a+  d++
  gene407|gene407|rna407|rna407 169 IRIGRIVDIKEHTNADSLYVEKVYLGNDE-LQVVSGLRGKMEMEDMKGKSFLFIVNMQKSKFRGEVSNGMILCAK--DGD 245
                                    79***************************.*********************************************..8** PP

                                    CEEEEEESST-- CS
                      tRNA_bind  81 evgilelpadve 92 
                                    + ++l+ p d++
  gene407|gene407|rna407|rna407 246 NLEVLQAPVDIP 257
                                    *****9998865 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.1
                                    STEEEEEEEESSSSEEEEEESCTTTSTHHHHTTEEEEEETTSE CS
                      tRNA_bind  16 dkLlvlkvdvGeeeprqivsgaknvyepeelvakkvvvvanlk 58 
                                    ++  v k+   +e++ +++s +k  ++  +lv k+ +v++  k
  gene407|gene407|rna407|rna407 272 RNFNVPKISKSNEAFSEVMSELKIRNN--KLVFKDKIVLCAGK 312
                                    555666777777778888888877666..88888888888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (324 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       587  (0.0327403); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2337.64
//
Query:       gene408|gene408|rna408|rna408  [L=519]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.024   14.6   0.1      0.086   12.8   0.0    1.9  2  L27_2     L27_2


Domain annotation for each model (and alignments):
>> L27_2  L27_2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   4.8e-06     0.086       9      38 ..      44      76 ..      42      98 .. 0.68
   2 ?   -3.4   0.0      0.56     1e+04      28      38 ..     380     390 ..     361     392 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4.8e-06
                                   HHHHHHHHHHHT-TTTHHHHHHHH...HHHH-H CS
                          L27_2  9 veRLqakLkeRGevateekLsLLk...svLqsP 38
                                    eRLqak+k   ev ++e +s++k   s L  P
  gene408|gene408|rna408|rna408 44 LERLQAKIKKQPEVYQNEYISMIKtyqSLLNVP 76
                                   59********************98333556543 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 0.56
                                    HHHHHHHHH-H CS
                          L27_2  28 LsLLksvLqsP 38 
                                    +sL+ks  + P
  gene408|gene408|rna408|rna408 380 ISLIKSYFKVP 390
                                    47777766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (519 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1447  (0.0807072); expected 358.6 (0.02)
Passed bias filter:                      627  (0.0349713); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.63u 0.29s 00:00:00.92 Elapsed: 00:00:00.45
# Mc/sec: 3437.08
//
Query:       gene409|gene409|rna409|rna409  [L=618]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.1e-50  170.5  10.3    2.4e-33  115.8   3.3    2.3  2  SAC3_GANP      SAC3/GANP family
  ------ inclusion threshold ------
      0.036   14.1   0.0      0.081   12.9   0.0    1.6  1  Bap31_Bap29_C  Bap31/Bap29 cytoplasmic coiled-coil domain


Domain annotation for each model (and alignments):
>> SAC3_GANP  SAC3/GANP family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.7   0.6   6.4e-20   5.7e-16       1      76 [.      27      91 ..      27     105 .. 0.92
   2 !  115.8   3.3   2.7e-37   2.4e-33      81     276 ..     132     329 ..     117     337 .. 0.85

  Alignments for each domain:
  == domain 1  score: 58.7 bits;  conditional E-value: 6.4e-20
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX-----HHHHHHHHHHHHHHTG CS
                      SAC3_GANP  1 GtCedmCPekEraeRevqkdlsrfEkekkktkkvdpskaVKeysRsaagqeeplpsdlRppevLkkTldYLlkeil 76
                                   G+C+++CP +E++eR  ++d+srfEk          + ++K+y Rsaag ++ l +d+Rp +vL +  dYL+ ++l
  gene409|gene409|rna409|rna409 27 GSCQSFCPYFEMVERRLRNDVSRFEK----------DFMIKKYVRSAAGRNKALEEDVRPLPVLCSCFDYLM-DVL 91
                                   89***********************4..........79**********************************.555 PP

  == domain 2  score: 115.8 bits;  conditional E-value: 2.7e-37
                                    .GTTTCHHHHHHHHHHHHHHHHHTT--SHHHHHHHHHHHHHHHHHHHHHHHTTS.---CHHHHHHHHHHHHHHHHHHHHH CS
                      SAC3_GANP  81 eelaevydFiwDRtRaiRqDltiqnlskaeaveilerivrfhilslhrlceepessfdeqqnleqLqkclqsLlelYddl 160
                                     +l evy+F++DRtRaiR D+++q+ls+ ++v +l++i+ fhi+ + +l + +  +f+e++n +q++++l sL+e+Y+  
  gene409|gene409|rna409|rna409 132 PSLFEVYKFVEDRTRAIRLDISVQELSCGRTVVLLQQICNFHIVFNCLLYDDE--KFEEHLNADQIRRVLLSLMECYKLR 209
                                    57889**********************************************99..8*********************998 PP

                                    H...---TTHHHHHHHHHHHTTT-......HHHHHHHCTS..-HHHHTSHHHHHHHHHHHHH--TTHHHHHHHHTTS-HH CS
                      SAC3_GANP 161 rkkkeelpneaefrayylLlnlrd......pdilrevqel..pseilkspevqlalklvaalqennyvrffklvkevsyl 232
                                    r +      ++   +y+++l++++       ++ ++  ++  +s   + + ++ a++l +a+q++n +rffk +k++ +l
  gene409|gene409|rna409|rna409 210 R-SVPMTLDQQRYYSYNVMLRISSdtacygDELFSTDDKIvnNSTHSQYEVINDAFDLLSAVQRGNTSRFFKFMKHADFL 288
                                    8.3344557899**********66454443333333334422333345567999************************** PP

                                    HHHHHGGGHHHHHHHHHHHHHHHS-TT---EEHHHHHHHTT-SS CS
                      SAC3_GANP 233 qacllerhfnevRrkalkalsraykskskkvpleeLaelLlfdd 276
                                      cll +++  vR+ a++++++++    +k+ ++ ++++L++ d
  gene409|gene409|rna409|rna409 289 TRCLLTTQLRYVRQAAMDMFKMCF---YEKIDCSLVMSWLHITD 329
                                    ************************...56788888888888776 PP

>> Bap31_Bap29_C  Bap31/Bap29 cytoplasmic coiled-coil domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   9.1e-06     0.081      25      41 ..       2      18 ..       1      27 [. 0.87

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 9.1e-06
                  Bap31_Bap29_C 25 eglakEYDrLadehskl 41
                                   e l++EYDrL++e+sk 
  gene409|gene409|rna409|rna409  2 ETLKQEYDRLLNERSKK 18
                                   889***********997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (618 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       825  (0.0460148); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.25s 00:00:00.84 Elapsed: 00:00:00.44
# Mc/sec: 4255.86
//
Query:       gene41|gene41|rna41|rna41  [L=44]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (44 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       387  (0.0215851); expected 358.6 (0.02)
Passed bias filter:                      236  (0.013163); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.29s 00:00:00.63 Elapsed: 00:00:00.44
# Mc/sec: 299.61
//
Query:       gene410|gene410|rna410|rna410  [L=318]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (318 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1019  (0.0568353); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 2149.55
//
Query:       gene411|gene411|rna411|rna411  [L=37]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (37 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       227  (0.0126611); expected 358.6 (0.02)
Passed bias filter:                      158  (0.00881254); expected 358.6 (0.02)
Passed Vit filter:                         4  (0.000223102); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.31u 0.26s 00:00:00.57 Elapsed: 00:00:00.40
# Mc/sec: 275.05
//
Query:       gene412|gene412|rna412|rna412  [L=473]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    8.7e-40  136.3   0.0    1.1e-39  136.0   0.0    1.2  1  GTP_EFTU     Elongation factor Tu GTP binding domain
      1e-22   80.5   0.0      3e-22   79.0   0.0    1.8  1  GTP_EFTU_D3  Elongation factor Tu C-terminal domain
    1.9e-08   34.6   0.6    7.2e-08   32.7   0.5    2.1  2  GTP_EFTU_D2  Elongation factor Tu domain 2
     0.0076   16.3   0.1      0.034   14.2   0.1    2.1  1  MMR_HSR1     50S ribosome-binding GTPase
     0.0094   15.3   0.3      0.046   13.1   0.3    2.0  1  Gtr1_RagA    Gtr1/RagA G protein conserved region
  ------ inclusion threshold ------
       0.24   10.1   0.0       0.57    8.9   0.0    1.5  2  DUF4785      Domain of unknown function (DUF4785)


Domain annotation for each model (and alignments):
>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  136.0   0.0   3.7e-43   1.1e-39       1     182 [.       6     201 ..       6     315 .. 0.87

  Alignments for each domain:
  == domain 1  score: 136.0 bits;  conditional E-value: 3.7e-43
                                    TCEEEEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHH...HHHST............HCHSHHHHHHTSCSSCEEEEEET CS
                       GTP_EFTU   1 krirnigiighvDhGKtTLtdrLlyktgaiskkgeka...eeerv............lDtlkeErergiTiksaaislek 65 
                                    k+i+n+++ighvD+GK+T++++L +++gai+ +++++   e  +             +D  ++Er rgiTi+++ ++le 
  gene412|gene412|rna412|rna412   6 KPILNVCFIGHVDSGKSTTVGNLAFQLGAIDPRKMEKlkkE--AEergrgtfsfayvMDMSAAERDRGITITTSLMKLE- 82 
                                    5799*******************************997532..2256799*****************************. PP

                                    TCSSEEEEEEEESSSGGGHHHHHHHHHT-SEEEEEEETTTB......STHHHHHHHHHHHHTTTE.EEEEEESCGST.HH CS
                       GTP_EFTU  66 etkkylinliDtPGHvdFskevirglrvlDgavlvvdaveG......vepqteevlrlalkegvp.iivfiNKmDrl.ka 137
                                     t k+ +n+iD+PGH+dF+k++ +g++++D+ v++v ++             + ++ +   +g++ +iv++NK+D +  +
  gene412|gene412|rna412|rna412  83 -TPKHMLNVIDCPGHKDFIKNMVTGAAQADVGVVLVPCATNefesciSGGTLKDHIMISGVLGCRkLIVCVNKCDTVeAS 161
                                    .***********************************999888888866677899**********99***********955 PP

                                    HHHHHHHHHHHHHHHHHHHHHHHHHTTTTTEEEEEEBTTTTBTHH CS
                       GTP_EFTU 138 elkeiveevkqklsrkeeklekygekgekevpvvfgSalkgegvk 182
                                    ++k   +ev++++    + + k + ++  +  ++++S+++g ++ 
  gene412|gene412|rna412|rna412 162 KMKSRFDEVRKEM---LNIIAKCHPDK--DPIIIPISGYNGINIV 201
                                    5666666666555...33344444443..5789999999999875 PP

>> GTP_EFTU_D3  Elongation factor Tu C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.0   0.0     1e-25     3e-22       2     108 ..     336     439 ..     335     441 .. 0.89

  Alignments for each domain:
  == domain 1  score: 79.0 bits;  conditional E-value: 1e-25
                                    -EEECCEEEEEEESSS..SS-BSTT-EEEEESSS-EEEEEEEEEEECCSSTTSB-BS..S-SSCCSTT-CEEEEEEECCE CS
                    GTP_EFTU_D3   2 ikphtkfeAqvyilekerhtpitagYrpvlyirtadvtgkvveLlskldkktekvse..kkpefvkpGdnvivevelikp 79 
                                    ++ ++  +A+v+++e+  ++ i  gY+pv+++ t +v +++ ++ s   kk ++v++    p++v +G+nv++ ++++kp
  gene412|gene412|rna412|rna412 336 VTVYEAARAKVVVVEH--PKGIKPGYCPVMDLGTHHVPCQISKFFS---KKMQGVADeiIGPDVVSKGENVTCIIHPQKP 410
                                    66777889********..************************9954...555555552358******************* PP

                                    EEE--TTTHCCCCEEEEECTTCEEEEEEE CS
                    GTP_EFTU_D3  80 ialekgseypqlGrFaiReggrTvaaGvv 108
                                    +++e+ +e p l rFa+R+ggr v++G +
  gene412|gene412|rna412|rna412 411 VVMETIKEVPSLARFALRDGGRIVGIGAI 439
                                    ***************************98 PP

>> GTP_EFTU_D2  Elongation factor Tu domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       5.5   1.7e+04      23      38 ..      15      28 ..      12      31 .. 0.76
   2 !   32.7   0.5   2.4e-11   7.2e-08       1      62 [.     259     315 ..     259     328 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 5.5
                                   C.TCTTSEEEEEEEEEE CS
                    GTP_EFTU_D2 23 g.ndtskkeivtrissl 38
                                   g +d++k+   t+++ l
  gene412|gene412|rna412|rna412 15 GhVDSGKS---TTVGNL 28
                                   55889999...999876 PP

  == domain 2  score: 32.7 bits;  conditional E-value: 2.4e-11
                                    EEEEEEEEEESEEETTEEEEEECTCTTSEEEEEEEEEEEEETEEESEEETTSEEEEEEEESS CS
                    GTP_EFTU_D2   1 GtvalgrvysGtlkkGdevrilgndtskkeivtrissletfhededeavaganaGvivaikg 62 
                                    G v +grv +G++++G+ + +  ++t   + v +++ le ++ +  e++ g+n+Gv +++  
  gene412|gene412|rna412|rna412 259 GMVYTGRVSTGVIRPGMVISV--QPT---GVVAEVKTLEIHKTPRSEVISGENCGVALKAAT 315
                                    7899*****************..999...677*************************99865 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.1   1.1e-05     0.034       1      88 [.      10     122 ..      10     190 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.1e-05
                                    EEEEEESTTSSHHHHHHHHH...................T............STEEESSSTTSSSSEEEEEEEETTEEEE CS
                       MMR_HSR1   1 evaivGrpNvGKStLinalt...................g............ekaivsdkpgtTrdinegrvklkgkeie 49 
                                    +v+++G+  +GKSt +  l                    +            + + +++  g T+++   ++++ ++ ++
  gene412|gene412|rna412|rna412  10 NVCFIGHVDSGKSTTVGNLAfqlgaidprkmeklkkeaeErgrgtfsfayvmDMSAAERDRGITITTSLMKLETPKHMLN 89 
                                    599****************87777776666665555554044555555444345667777788888888888877788** PP

                                    EEECGGCSSHHHHHHHHHHHHHHHHCTSEEEEEEETTTT CS
                       MMR_HSR1  50 lvDtpGliegaseekglgkaflaleeadlillvvdasee 88 
                                    ++D+pG  +    +  +++ +    +ad+ +++v ++++
  gene412|gene412|rna412|rna412  90 VIDCPG-HK----D-FIKNMVTGAAQADVGVVLVPCATN 122
                                    ******.33....2.345555556668888888877633 PP

>> Gtr1_RagA  Gtr1/RagA G protein conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.3   1.5e-05     0.046      33     146 ..      72     180 ..      11     195 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.5e-05
                      Gtr1_RagA  33 atidveksevrflgnltlnlwDcgGqeafveeylssqkeeifrnvgvliyVfDvesreleedle..tlkeilealrqysp 110
                                    +ti ++  +++ + + +ln++Dc+G ++f++++++  +     +vgv++    + ++e+e+ ++  tlk+ +  ++ +  
  gene412|gene412|rna412|rna412  72 ITITTSLMKLE-TPKHMLNVIDCPGHKDFIKNMVTGAA---QADVGVVLV--PCATNEFESCISggTLKDHI-MISGVLG 144
                                    44444444443.34567***************866544...468888764..45545666666522555554.4566666 PP

                      Gtr1_RagA 111 eakvfvlihKmDliqedereeifeerkeeireeiek 146
                                      k+ v ++K+D ++ ++ ++ f+e ++e+ + i+k
  gene412|gene412|rna412|rna412 145 CRKLIVCVNKCDTVEASKMKSRFDEVRKEMLNIIAK 180
                                    678889999999999999999999999988887775 PP

>> DUF4785  Domain of unknown function (DUF4785)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       0.9   2.7e+03      44      64 ..      56      76 ..      50      78 .. 0.89
   2 ?    8.9   0.0   0.00019      0.57      31     100 ..     242     315 ..     239     318 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 0.9
                                   ESEEEEEEEHHHHHH-EEEE- CS
                        DUF4785 44 sysykkkvsleqlergvilsi 64
                                   s++y+  +s+++ +rg+++++
  gene412|gene412|rna412|rna412 56 SFAYVMDMSAAERDRGITITT 76
                                   899999***********9986 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00019
                                    ----------EEE....ESEEEEEEEHHHHHH-EEEE-SSSS-EEEEEESSSSB---EEEE-TT--EEEGGGGS CS
                        DUF4785  31 eeplkanisnvrk....sysykkkvsleqlergvilsilapgavvriipledkaipelelksaknqllslkeas 100
                                    ++pl+ +i  v+k       y  +vs   ++ g+++s++  g v  +  le +  p  e+ s +n  ++lk a+
  gene412|gene412|rna412|rna412 242 DKPLRMPIDSVHKipgiGMVYTGRVSTGVIRPGMVISVQPTGVVAEVKTLEIHKTPRSEVISGENCGVALKAAT 315
                                    6788888888888333335699*************************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (473 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       571  (0.0318478); expected 358.6 (0.02)
Passed bias filter:                      488  (0.0272185); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.42
# Mc/sec: 3343.77
//
Query:       gene413|gene413|rna413|rna413  [L=27]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (27 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                        94  (0.0052429); expected 358.6 (0.02)
Passed bias filter:                       89  (0.00496402); expected 358.6 (0.02)
Passed Vit filter:                         4  (0.000223102); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.42
# Mc/sec: 190.78
//
Query:       gene414|gene414|rna414|rna414  [L=954]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.055   13.5   0.5         22    5.2   0.0    3.3  3  DUF1830   Domain of unknown function (DUF1830)


Domain annotation for each model (and alignments):
>> DUF1830  Domain of unknown function (DUF1830)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.13   2.3e+03       6      28 ..     318     340 ..     315     344 .. 0.85
   2 ?    4.5   0.1    0.0019        34       5      39 ..     390     424 ..     386     449 .. 0.80
   3 ?    5.2   0.0    0.0012        22      34      63 ..     635     664 ..     620     667 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.13
                        DUF1830   6 atskiqilRitnipnwyfErvvf 28 
                                    +++ ++ lR+  +++ ++E +v 
  gene414|gene414|rna414|rna414 318 DSDFMKLLRCQFFEEEHIENIVI 340
                                    678899*************9996 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.0019
                        DUF1830   5 NatskiqilRitnipnwyfErvvfPgerllFeApp 39 
                                    N     qi ++ n  + ++E ++f  + ++ +A +
  gene414|gene414|rna414|rna414 390 NINTIQQITKVENLTHVELEDIIFSSDFVINKAWK 424
                                    6666679*****************99887776655 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.0012
                        DUF1830  34 lFeAppeaeLEIhtgelagailedripcse 63 
                                     F+  +  eLE+  ++++++++ + ipc+e
  gene414|gene414|rna414|rna414 635 EFNPKSRNELEVEGMSNINELVLENIPCDE 664
                                    57888899********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (954 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       761  (0.0424452); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.71u 0.31s 00:00:01.02 Elapsed: 00:00:00.49
# Mc/sec: 5846.14
//
Query:       gene415|gene415|rna415|rna415  [L=54]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (54 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       220  (0.0122706); expected 358.6 (0.02)
Passed bias filter:                      166  (0.00925874); expected 358.6 (0.02)
Passed Vit filter:                         6  (0.000334653); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.42
# Mc/sec: 389.79
//
Query:       gene416|gene416|rna416|rna416  [L=194]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       593  (0.0330749); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1442.21
//
Query:       gene417|gene417|rna417|rna417  [L=211]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       630  (0.0351386); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1527.76
//
Query:       gene418|gene418|rna418|rna418  [L=1542]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.17   10.4   0.0       0.32    9.5   0.0    1.3  1  Actin     Actin


Domain annotation for each model (and alignments):
>> Actin  Actin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0   1.8e-05      0.32     217     332 ..     367     516 ..     323     521 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 1.8e-05
                          Actin 217 lekltesyktleeeevleeiKesvcevsedpegdeekss...sspeksYeLPDgs.eiklgeeRfkvpEiLFdpsligse 292
                                      +++ s++t++++++   +Ke+v+  s +   + ++ s   s++ ++ +LPD   +++l++ R  v   L   +++++ 
  gene418|gene418|rna418|rna418 367 GVQIDLSFDTISNKQLHVYCKECVVSFSTHSSSNLKTLSiidSKICCDLVLPDTLeTFILEKTRIIVGYELRVTEICKHI 446
                                    567889*********************999997555555777999*********65777788888777777777777777 PP

                          Actin 293 saleee..............................kskllgiselivaainacdvdlrpeLlanivvtG 332
                                    s ++++                               +k++ i  ++++++  ++ ++++ +l+niv+ G
  gene418|gene418|rna418|rna418 447 SINQNHgkiripyfehtfsallpsdgtfellrsgdiIEKITLINVIFYDSVVTMPNNIQEIILKNIVLDG 516
                                    765555777788888888888888888899999**999999999***********************988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1542 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       598  (0.0333538); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.83u 0.29s 00:00:01.11 Elapsed: 00:00:00.46
# Mc/sec: 10068.06
//
Query:       gene419|gene419|rna419|rna419  [L=112]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       334  (0.018629); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 747.80
//
Query:       gene42|gene42|rna42|rna42  [L=76]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       712  (0.0397122); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.45
# Mc/sec: 505.15
//
Query:       gene420|gene420|rna420|rna420  [L=257]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.087   13.1   0.2       0.26   11.5   0.1    1.7  2  CobA_CobO_BtuR  ATP:corrinoid adenosyltransferase BtuR/CobO/C


Domain annotation for each model (and alignments):
>> CobA_CobO_BtuR  ATP:corrinoid adenosyltransferase BtuR/CobO/CobP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.13   2.4e+03      72     104 ..      76     106 ..      47     114 .. 0.47
   2 ?   11.5   0.1   1.5e-05      0.26      56     125 ..     172     241 ..     154     249 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.13
                 CobA_CobO_BtuR  72 eekeedaaaakealekakealaseeydlvvlDE 104
                                    e++ +++ a ++a++++   +  ++    ++DE
  gene420|gene420|rna420|rna420  76 EDQGTKEVAEQTAMKHIIMPA--SNPATDIMDE 106
                                    222222222222333333222..2344445666 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 1.5e-05
                 CobA_CobO_BtuR  56 ielerlgkegfv.kmeeeekeedaaaakealekakealaseeydlv.vlDEinyalklglldeeevlellkk 125
                                    ++++r g   f  +m +ee++  +++ + +l+++++ ++++e+ ++  +DE n++++l+l++ e++ +++++
  gene420|gene420|rna420|rna420 172 LDFIRGG--DFNdTMIDEEQDSIRKQLRVQLDRTNRIFNDKEHGILtCVDETNNTFDLNLIAAERFAAIVEN 241
                                    4455555..33344778899999*****************988865279****************9999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       697  (0.0388756); expected 358.6 (0.02)
Passed bias filter:                      490  (0.02733); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1773.35
//
Query:       gene421|gene421|rna421|rna421  [L=560]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.2e-07   29.7   0.0    1.1e-06   28.4   0.0    1.7  1  LisH         LisH
  ------ inclusion threshold ------
       0.13   11.5   0.0       0.23   10.7   0.0    1.3  1  GSDH         Glucose / Sorbosone dehydrogenase
       0.21   11.9   0.7          2    8.8   0.0    2.7  3  ANAPC4_WD40  Anaphase-promoting complex subunit 4 WD40 domain


Domain annotation for each model (and alignments):
>> LisH  LisH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4   0.0   1.8e-10   1.1e-06       2      27 .]      18      43 ..      17      43 .. 0.96

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 1.8e-10
                                   HHHHHHHHHHHHCT-HHHHHHHHHHT CS
                           LisH  2 eLNrLIydYLvkeGyeetAeaFekEa 27
                                   +LN LI++YL k+++ +tA +F++Ea
  gene421|gene421|rna421|rna421 18 LLNVLIHEYLTKNNFPQTAMTFKNEA 43
                                   79***********************8 PP

>> GSDH  Glucose / Sorbosone dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   3.9e-05      0.23     209     289 ..     217     298 ..     213     315 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 3.9e-05
                                    EEE-TT-B--TTT-S......S-.....-S-TTS---SEEETT---EEEEEEE.........TTEEEEEETTTTEEEEEE CS
                           GSDH 209 nlieaGknYGWplvsygeeYsgkkigesetreglekpvlvwtpsiapsglafytgda.fpewkgdllvggLksqsllrle 287
                                    n +++G+nYG++   + +  + ++ ++ ++ e++++ + v+++s+   +  f++ +   ++  ++ll+ +L+ ++++ ++
  gene421|gene421|rna421|rna421 217 NPPTPGNNYGYNSLINLNLETRRQSAPDSKFEDVKETKKVYQNSLKEINSFFFDQKIsCSASTNNLLFVALSDRTVQIIN 296
                                    56789*******999777777778888899**************988888888776538999************999998 PP

                                    EE CS
                           GSDH 288 ld 289
                                    l 
  gene421|gene421|rna421|rna421 297 LL 298
                                    75 PP

>> ANAPC4_WD40  Anaphase-promoting complex subunit 4 WD40 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0   0.00034         2      50      84 ..     280     313 ..     271     322 .. 0.87
   2 ?   -3.7   0.0       2.6   1.6e+04       9      25 ..     347     363 ..     344     368 .. 0.71
   3 ?   -0.2   0.1      0.21   1.2e+03       7      64 ..     463     532 ..     460     556 .. 0.60

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00034
                    ANAPC4_WD40  50 gklLavaysdgevrlldaesgkvvhslsvksekav 84 
                                    ++lL va sd +v++++  s k+v s++ +++  v
  gene421|gene421|rna421|rna421 280 NNLLFVALSDRTVQIINLLSMKIVGSFEPHAKP-V 313
                                    689*************************99885.4 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 2.6
                    ANAPC4_WD40   9 LiAlatedgellvfRln 25 
                                    L+   + ++e+ vfR +
  gene421|gene421|rna421|rna421 347 LLCTNSREKEIKVFRAS 363
                                    55556677788888865 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.21
                    ANAPC4_WD40   7 mDLiAlatedgell....vfRlngqrvwtl........eedkedsevrsLaWkpdgklLavaysdgevrl 64 
                                    +DL+Al   d+ ++    ++Rln   v++         e++   +  r++ W+  ++l+    + g++  
  gene421|gene421|rna421|rna421 463 NDLFALLHRDMVVIfgsdLKRLNAISVVNRmnslavldENNVFVGVYRQIYWHSFNSLITNEKHSGTITA 532
                                    5788888777777433336777776665555555544222222223356666666666666666665554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (560 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       529  (0.0295053); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.41
# Mc/sec: 4127.30
//
Query:       gene422|gene422|rna422|rna422  [L=234]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      2e-65  216.8   1.1    4.9e-32  109.7   0.0    2.1  2  TBP           Transcription factor TFIID (or TATA-binding pro
    3.3e-05   23.9   0.5       0.11   12.7   0.0    2.7  3  DUF3378       Domain of unknown function (DUF3378)
  ------ inclusion threshold ------
      0.012   15.5   0.1      0.058   13.2   0.0    2.1  2  DUF4295       Domain of unknown function (DUF4295)
        0.1   12.7   0.4        1.6    8.8   0.0    2.1  2  Alpha_kinase  Alpha-kinase family


Domain annotation for each model (and alignments):
>> TBP  Transcription factor TFIID (or TATA-binding protein, TBP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.1   0.2   1.5e-34   6.7e-31       2      84 ..      59     139 ..      58     140 .. 0.97
   2 !  109.7   0.0   1.1e-35   4.9e-32       1      85 []     148     231 ..     148     231 .. 0.97

  Alignments for each domain:
  == domain 1  score: 106.1 bits;  conditional E-value: 1.5e-34
                                    EEEEEEEEEEE-SSCE-HHHHHHHCCTTTEEE-TTTSSSEEEEETTTTEEEEE-TTSEEEEECESSHHHHHHHHHHHHHH CS
                            TBP   2 fkiqNvvasanlgleldLeklalkaekrnaeYeperfpglvyrlrepkvtaliFssGkvvitGakseeelreaakkiapi 81 
                                    ++ qNvva++nl+++l+L+ +al+a  rnaeY+p+rf ++++r+r+pk+taliF+sGk+vitGakse+ +r aakk+a+i
  gene422|gene422|rna422|rna422  59 PTLQNVVATVNLECRLELKVIALRA--RNAEYNPKRFAAVIMRIRDPKTTALIFASGKMVITGAKSEQASRIAAKKYARI 136
                                    578*******************998..***************************************************** PP

                                    HHH CS
                            TBP  82 lkk 84 
                                    + k
  gene422|gene422|rna422|rna422 137 IHK 139
                                    *98 PP

  == domain 2  score: 109.7 bits;  conditional E-value: 1.1e-35
                                    EEEEEEEEEEEE-SSCE-HHHHHHHCCTTTEEE-TTTSSSEEEEETTTTEEEEE-TTSEEEEECESSHHHHHHHHHHHHH CS
                            TBP   1 dfkiqNvvasanlgleldLeklalkaekrnaeYeperfpglvyrlrepkvtaliFssGkvvitGakseeelreaakkiap 80 
                                    dfkiqN+v s++ +++++Le+la+  ++++++Yepe fpgl+yr+ +pk+++liF+sGk+v+tGak ++e+++a+++i+p
  gene422|gene422|rna422|rna422 148 DFKIQNIVSSCDTKFNIRLEGLAYA-HSNFCSYEPELFPGLIYRMVNPKIVLLIFVSGKIVLTGAKVRDEIYQAFENIYP 226
                                    69********************988.79**************************************************** PP

                                    HHHHC CS
                            TBP  81 ilkkl 85 
                                    +l k+
  gene422|gene422|rna422|rna422 227 VLTKY 231
                                    **985 PP

>> DUF3378  Domain of unknown function (DUF3378)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.1       2.8   1.3e+04      14      22 ..      22      30 ..      18      33 .. 0.71
   2 !   12.7   0.0   2.4e-05      0.11      28      60 ..      94     126 ..      80     136 .. 0.85
   3 !    8.8   0.0    0.0004       1.8      25      56 ..     182     213 ..     173     225 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 2.8
                        DUF3378 14 mkeyykskl 22
                                   +k++yk+++
  gene422|gene422|rna422|rna422 22 LKQKYKKQR 30
                                   778887764 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 2.4e-05
                        DUF3378  28 pyavfaakkndttItaYtSgKVlFQGknaeaeA 60 
                                      +++++++++tt  ++ SgK ++ G++ e+ +
  gene422|gene422|rna422|rna422  94 AAVIMRIRDPKTTALIFASGKMVITGAKSEQAS 126
                                    56899**********************999865 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.0004
                        DUF3378  25 kkppyavfaakkndttItaYtSgKVlFQGkna 56 
                                    +  p+ +++  +++++  ++ SgK+++ G++ 
  gene422|gene422|rna422|rna422 182 ELFPGLIYRMVNPKIVLLIFVSGKIVLTGAKV 213
                                    5679***********************99875 PP

>> DUF4295  Domain of unknown function (DUF4295)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   1.3e-05     0.058       3      35 ..      77     111 ..      77     122 .. 0.87
   2 ?   -0.9   0.1      0.33   1.5e+03      13      21 ..     129     137 ..     114     139 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.3e-05
                        DUF4295   3 KvVAtlkkga..sgkkytKvIkmvKspKTGaYtFk 35 
                                    Kv+A ++ +a  + k+++ vI  +++pKT a +F 
  gene422|gene422|rna422|rna422  77 KVIALRARNAeyNPKRFAAVIMRIRDPKTTALIFA 111
                                    89998888877889******************996 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.33
                        DUF4295  13 sgkkytKvI 21 
                                      kky+++I
  gene422|gene422|rna422|rna422 129 AAKKYARII 137
                                    578999988 PP

>> Alpha_kinase  Alpha-kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.1     0.034   1.5e+02      36      79 ..      22      65 ..      12      94 .. 0.69
   2 ?    8.8   0.0   0.00035       1.6      15      80 ..     120     189 ..     104     221 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.034
                                   -HHHHHHHHHHHHHHHHHHHHHH......HT--SS--E.E---EE CS
                   Alpha_kinase 36 elelykeevkvqalakelakeFnakarakekkppkkie.flealv 79
                                    +++yk++    + a  l+ +Fn +++a+e++++++i+  l++ v
  gene422|gene422|rna422|rna422 22 LKQKYKKQRDTPMDAPNLSYDFN-ADSAQEQNKKTRITpTLQNVV 65
                                   4567999999999999*******.444555555555542444433 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00035
                                    HHT-TT-EEEEEEE-STCCTT-HHHHHHHHHHHHHHHHHHHHHH..........HT--SS--EE---EEE CS
                   Alpha_kinase  15 kgdekgnklVaKefkkkaeqkelelykeevkvqalakelakeFn....akarakekkppkkieflealvl 80 
                                     ++e+ +++ aK++ +++++  ++  ++++k+q++ +++ ++Fn      a a++++++ + e+++ l++
  gene422|gene422|rna422|rna422 120 AKSEQASRIAAKKYARIIHKLGFNTQFSDFKIQNIVSSCDTKFNirleGLAYAHSNFCSYEPELFPGLIY 189
                                    567889999*********99999999******************66554455555566666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       582  (0.0324614); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.22s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1767.53
//
Query:       gene423|gene423|rna423|rna423  [L=50]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (50 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1033  (0.0576162); expected 358.6 (0.02)
Passed bias filter:                      500  (0.0278878); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 344.42
//
Query:       gene424|gene424|rna424|rna424  [L=1027]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.4e-20   72.6   0.0    7.2e-20   71.5   0.0    1.6  1  DEAD        DEAD/DEAH box helicase
    8.4e-15   55.1   0.0    3.7e-14   53.0   0.0    2.2  1  Helicase_C  Helicase conserved C-terminal domain
      4e-09   36.7   0.0    2.3e-08   34.2   0.0    2.3  2  ResIII      Type III restriction enzyme, res subunit
    1.8e-05   25.1   0.0    6.1e-05   23.3   0.0    1.9  1  AAA_22      AAA domain
    0.00031   20.5   0.1      0.016   14.9   0.0    2.5  2  IstB_IS21   IstB-like ATP binding protein
  ------ inclusion threshold ------
      0.029   14.5   0.1        0.1   12.8   0.1    1.9  1  DUF3718     Protein of unknown function (DUF3718)
        0.1   12.0   0.0        0.3   10.5   0.0    1.7  2  PhoH        PhoH-like protein


Domain annotation for each model (and alignments):
>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.5   0.0   2.8e-23   7.2e-20       3     174 ..      95     275 ..      93     277 .. 0.84

  Alignments for each domain:
  == domain 1  score: 71.5 bits;  conditional E-value: 2.8e-23
                                    HHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHS.........................TTSTS-EEEEEESSH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.........................xxxxxxxxxxxxxxx RF
                           DEAD   3 iQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyet.........................kgktgpkalivePtr 57 
                                     Qa+a++ i  + +v+++ +TGsGKT ++l+ +l+++  +                         ++ +++++++++P++
  gene424|gene424|rna424|rna424  95 CQAAALEFINAECNVVICSPTGSGKTVMALFFILRALGYDiatedggnadeqphakqtdkpsnhtRTAEKTRIVYLSPLK 174
                                    699*******************************8885557777788888887777777777766666669********* PP

                                    HHHHHHHHHHHHHTTTSTSEEEEEETTSSHHHHHHHHHTTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD  58 eLaeqtlnnlkkfkkyidlrvlliiggvaardqlskldngvdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqg 137
                                    +L+ q+++ +   ++ + ++v+  i  ++ +  +s+l  + +++++tp+++d++l+ ++  +  v +l++DE++ l ++ 
  gene424|gene424|rna424|rna424 175 SLCSQIFSFFADKLSRL-INVS--IATSDDSLTRSQL-MESNLIISTPEKFDSILR-KY--VLPVDLLIIDEIHVLNSD- 246
                                    **********9999963.2344..4555666789999.999************994.66..899**************8. PP

                                    THHHHHHHHHHSHHHCTTSTTTSEEEEEESSBSHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD 138 fsdfinrilnqlpqitcdgklqrqvivlSATlpkdvk 174
                                    ++  ++++++++   t       +++ +SAT+p ++k
  gene424|gene424|rna424|rna424 247 RGAVLETMISRM-IGT------CRMLGMSATIP-NLK 275
                                    ************.233......449*******9.665 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.0   0.0   1.4e-17   3.7e-14       5     109 ..     320     422 ..     316     424 .. 0.89

  Alignments for each domain:
  == domain 1  score: 53.0 bits;  conditional E-value: 1.4e-17
                                    HHHHHHHHTTTTSEEEEEESSHHHHHH.HHHHHHHTTSTEEEESTTSTHHHHHHHHHHHH.TTSSSEEEESGGGTSSSTS CS
                     Helicase_C   5 allellkleeeggkilifvntidrlek.vklllekkgikvavlhgelpqnereeileqfn.kgesdvLiatdvaerGidi 82 
                                     l +ll  +e++g++++f++++ ++e+ + ++ +++ +k++++h+ l++++r  + ++f  +++++vL +t+ ++ G+++
  gene424|gene424|rna424|rna424 320 VLERLL--NEIEGNTIVFIRRRAEVEEcCAVFSKHSTYKCLYHHAGLSKSKRTSVESSFMlDDSRKVLFSTSTLAWGVNL 397
                                    445554..899**************99999998888***********************9777777************** PP

                                    TTESEEEESSSSSSHHHHHHHHTTSSS CS
                     Helicase_C  83 pkvnlVinfdlprnvtsyiqriGRtgR 109
                                    p +++Vi+fd  +++ +++q++GR+gR
  gene424|gene424|rna424|rna424 398 P-ADNVIIFDDFTDY-DIVQMMGRAGR 422
                                    9.9999999988886.689******** PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.2   0.0   8.9e-12   2.3e-08      22     170 ..     104     272 ..      75     273 .. 0.84
   2 ?   -3.9   0.0       4.8   1.2e+04      56      76 ..     310     330 ..     300     363 .. 0.70

  Alignments for each domain:
  == domain 1  score: 34.2 bits;  conditional E-value: 8.9e-12
                                    .TTSEEEEEESTTSTHHHHHHHHHHHH-S.................................-EEEEESSHHHHHHHHHH CS
                         ResIII  22 krdkrglikmaTGtGKTlvaaklierllkkgkee............................kflflvprkslleqtlee 73 
                                    + + +++i  +TG+GKT++a+ +i r l                                  +++ l p ksl++q  + 
  gene424|gene424|rna424|rna424 104 NAECNVVICSPTGSGKTVMALFFILRALGYDIATedggnadeqphakqtdkpsnhtrtaektRIVYLSPLKSLCSQIFSF 183
                                    6677899*****************99998655448999****************************************** PP

                                    GGGGTGG....GEEEESSS-B--.......-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS...TTTH CS
                         ResIII  74 fkkflseaykeigkkvsgdkkkakekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgak..kswr 151
                                    f++ ls   + ++  +s+d+ ++  ++  +++++++t +++d+++        ++     d++iiDE H l+++  +  +
  gene424|gene424|rna424|rna424 184 FADKLSRLIN-VSIATSDDSLTR--SQLMESNLIISTPEKFDSIL--------RKYVLPVDLLIIDEIHVLNSDrgAVLE 252
                                    *999998853.444555555555..9999****************........66777789************7443555 PP

                                    H.HHHT---SEEEEEESS-S CS
                         ResIII 152 e.ilekfkeavllglTATpe 170
                                      i +++  + +lg++AT++
  gene424|gene424|rna424|rna424 253 TmISRMIGTCRMLGMSATIP 272
                                    557888999*********86 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 4.8
                                    -EEEEESSHHHHHHHHHHGGG CS
                         ResIII  56 kflflvprkslleqtleefkk 76 
                                     +++  +++s+le++l+e++ 
  gene424|gene424|rna424|rna424 310 AVVLARNNLSVLERLLNEIEG 330
                                    333344556888888887754 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.0   2.4e-08   6.1e-05       8     116 ..     109     258 ..     105     269 .. 0.81

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 2.4e-08
                         AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaee..................erpevv.fvtlpsstsskdllrellralglel 68 
                                    +v++ ++G+GKT+ +  +  ++  +  a+e                  ++ +++ +  +  ++ +k+l++++++++ ++l
  gene424|gene424|rna424|rna424 109 VVICSPTGSGKTVMALFFILRALGYDIATEdggnadeqphakqtdkpsNHTRTAeKTRIVYLSPLKSLCSQIFSFFADKL 188
                                    699*******************99888888***********9998877555555677777777999************** PP

                         AAA_22  69 ka..........erlsseell.ealeqalrarav.........ielliiDEaqhlr..seealeeLrsll 116
                                    ++            l++++l+ + l     ++++         + lliiDE++ l+  + ++le+  s++
  gene424|gene424|rna424|rna424 189 SRlinvsiatsdDSLTRSQLMeSNLIISTPEKFDsilrkyvlpVDLLIIDEIHVLNsdRGAVLETMISRM 258
                                    ********9999555555555555555544554466667778*************976599999887665 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   6.3e-06     0.016      37      70 ..      96     129 ..      91     139 .. 0.83
   2 ?    2.6   0.0     0.037        95      97     124 ..     219     247 ..     203     264 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 6.3e-06
                      IstB_IS21  37 eLatlsfiekkenivllGpsGvGKshlaialgve 70 
                                    + a+l+fi+++ n+v++ p+G GK+ +a  +  +
  gene424|gene424|rna424|rna424  96 QAAALEFINAECNVVICSPTGSGKTVMALFFILR 129
                                    56899*********************99866554 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.037
                      IstB_IS21  97 gklaralkrllkv.dllilDdlgllpldq 124
                                    +k+ ++l++++ + dlli+D++ +l+ d+
  gene424|gene424|rna424|rna424 219 EKFDSILRKYVLPvDLLIIDEIHVLNSDR 247
                                    67888888877544*******98877665 PP

>> DUF3718  Protein of unknown function (DUF3718)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1     4e-05       0.1      13      45 ..      34      66 ..      29      85 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4e-05
                        DUF3718 13 LrkklkesrlkkrrvaegivCNGesllqfAysn 45
                                   L ++lk++ + +r+++ +++C + +l+q + ++
  gene424|gene424|rna424|rna424 34 LTQQLKDNYVAYRNIFAKLNCEETDLYQRVTLH 66
                                   889*************************99443 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00012       0.3       6      42 ..      93     129 ..      91     134 .. 0.86
   2 ?   -4.0   0.0       3.3   8.4e+03      17      33 ..     409     425 ..     404     444 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00012
                                    SHHHHHHHHHHHH-SEEEEE--TTSSTTHHHHHHHHH CS
                           PhoH   6 tkeQkeylealkkndivfaiGpaGtGKtylavalave 42 
                                    +  Q+++le ++++  v++  p+G+GKt +a+   ++
  gene424|gene424|rna424|rna424  93 NVCQAAALEFINAECNVVICSPTGSGKTVMALFFILR 129
                                    5679999*****999999*************976655 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 3.3
                                    HH-SEEEEE--TTSSTT CS
                           PhoH  17 kkndivfaiGpaGtGKt 33 
                                    +++div ++G+aG  K 
  gene424|gene424|rna424|rna424 409 TDYDIVQMMGRAGREKY 425
                                    67899999999997765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1027 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       860  (0.047967); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.75u 0.28s 00:00:01.03 Elapsed: 00:00:00.46
# Mc/sec: 6776.29
//
Query:       gene425|gene425|rna425|rna425  [L=440]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.3e-24   86.1   0.1    6.4e-24   84.7   0.0    1.8  2  DEAD        DEAD/DEAH box helicase
    9.8e-16   58.1   2.0    2.4e-14   53.6   0.4    2.9  2  Helicase_C  Helicase conserved C-terminal domain
    4.5e-08   33.3   1.6    9.8e-08   32.2   0.1    2.3  2  ResIII      Type III restriction enzyme, res subunit
  ------ inclusion threshold ------
      0.026   14.0   0.1      0.083   12.3   0.1    1.8  1  PhoH        PhoH-like protein


Domain annotation for each model (and alignments):
>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.7   0.0   1.4e-27   6.4e-24       1     171 [.      43     189 ..      43     194 .. 0.87
   2 ?   -2.7   0.0      0.93   4.2e+03     137     157 ..     256     276 ..     244     291 .. 0.67

  Alignments for each domain:
  == domain 1  score: 84.7 bits;  conditional E-value: 1.4e-27
                                    -HHHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD   1 tdiQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvll 80 
                                    t++Q+e+i++il+ ++ +   +TGsGK+  +++ +  i y++++ ++ +a+iv Pt+eL+eq+++ lk++  + ++r+++
  gene425|gene425|rna425|rna425  43 TKVQKEIINAILNRKSAIFLSNTGSGKSYGYSLGLA-IRYHREKGKKLRAVIVLPTKELVEQMYTILKQIVRK-TIRIVS 120
                                    789*******************************99.55566888899************************8.479999 PP

                                    EETTSSHHHHHHHHHTTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCTTSTTTS CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD  81 iiggvaardqlskldngvdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsdfinrilnqlpqitcdgklqr 160
                                    + +  +++++++kl+n++++vv+t gr+          +s++++l+lDE+d ll +gf  +  r  n             
  gene425|gene425|rna425|rna425 121 LSSAFPEEKDRKKLENDPEVVVTTAGRFKL--------VSNFNLLILDEVDLLLREGFAIDEIR--N------------Y 178
                                    9999************************97........899***************88633222..2............2 PP

                                    EEEEEESSBSH CS
                                    xxxxxxxxxxx RF
                           DEAD 161 qvivlSATlpk 171
                                    q+i  SAT+++
  gene425|gene425|rna425|rna425 179 QLIGTSATFNN 189
                                    36777777765 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 0.93
                                    TTHHHHHHHHHHSHHHCTTST CS
                                    xxxxxxxxxxxxxxxxxxxxx RF
                           DEAD 137 gfsdfinrilnqlpqitcdgk 157
                                    +f+d+i+ i+  l+++  +++
  gene425|gene425|rna425|rna425 256 KFKDQIDGIHGDLDSQFREQN 276
                                    678888888877765554443 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0     0.037   1.7e+02      13      60 ..      85     135 ..      74     156 .. 0.74
   2 !   53.6   0.4   5.4e-18   2.4e-14      15     111 .]     230     327 ..     219     327 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.037
                                    TTTTSEEEEEESSHHHHHH.HHHHHHHT....TSTEEEESTTSTHHHHHHHHH CS
                     Helicase_C  13 eeeggkilifvntidrlek.vklllekk....gikvavlhgelpqnereeile 60 
                                    + ++ +++i+++t++ +e+  ++l  k+     i+++ l +  p ++ ++ le
  gene425|gene425|rna425|rna425  85 KGKKLRAVIVLPTKELVEQmYTIL--KQivrkTIRIVSLSSAFPEEKDRKKLE 135
                                    45566789*******888764444..222444899999999999888777665 PP

  == domain 2  score: 53.6 bits;  conditional E-value: 5.4e-18
                                    TTSEEEEEESSHHHHHH.HHHH..HHHT..TSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSSTSTTESEEE CS
                     Helicase_C  15 eggkilifvntidrlek.vkll..lekk..gikvavlhgelpqnereeileqfnkgesdvLiatdvaerGidipkvnlVi 89 
                                    + + i++f+ ++ r+e+ v ++  +     + ++  +hg+l ++ re+   +f++ + ++L+ tdva+rG+++ ++++++
  gene425|gene425|rna425|rna425 230 RFESIIVFASSRVRVEEiVLYFkqH--DkfKDQIDGIHGDLDSQFREQNCLSFKRRQLRILVVTDVASRGLNM-NATCIV 306
                                    66899**********9876666433..345999****************************************.7***** PP

                                    ESSSSSSHHHHHHHHTTSSSTT CS
                     Helicase_C  90 nfdlprnvtsyiqriGRtgRag 111
                                    n+d+ ++ +s+i+r+GR+ R+g
  gene425|gene425|rna425|rna425 307 NYDIADE-ESLIHRKGRIVRGG 327
                                    ****955.9***********86 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.2   0.1   2.2e-11   9.8e-08       4     140 ..      42     161 ..      39     189 .. 0.74
   2 ?   -1.2   0.1      0.39   1.7e+03      15      15 ..     413     413 ..     350     436 .. 0.56

  Alignments for each domain:
  == domain 1  score: 32.2 bits;  conditional E-value: 2.2e-11
                                    E-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHH.HHHHHHH-S......-EEEEESSHHHHHHHHHHGGGGTGG. CS
                         ResIII   4 lreyQeeaienlleklkskrdkrglikmaTGtGKTlva.aklierllkkgkee.kflflvprkslleqtleefkkflsea 81 
                                    + + Q+e+i+++l      ++k +++   TG+GK++ + + l+ r++++++++ +++++ p+k+l+eq+++ +k++  ++
  gene425|gene425|rna425|rna425  42 PTKVQKEIINAIL------NRKSAIFLSNTGSGKSYGYsLGLAIRYHREKGKKlRAVIVLPTKELVEQMYTILKQIVRKT 115
                                    6778999999998......678999***********999999999999888888***********************999 PP

                                    .....GEEEESSS-B--.......-SEEEEEHHHHHHTH........HHHTTT-SEEEEET CS
                         ResIII  82 yke..igkkvsgdkkkakekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDE 140
                                          +  +  ++k+ ++k +++ +++vtt  +++  s             +f+++i DE
  gene425|gene425|rna425|rna425 116 IRIvsLSSAFP-EEKD-RKKLENDPEVVVTTAGRFKLVS-------------NFNLLILDE 161
                                    77654222222.2222.2467889999999987776655.............445555555 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.39
                                    H CS
                         ResIII  15 l 15 
                                    +
  gene425|gene425|rna425|rna425 413 T 413
                                    1 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   1.9e-05     0.083       6      61 ..      43     100 ..      39     121 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.9e-05
                                    SHHHHHHHHHHHH-SEEEEE--TTSSTTH.HHHHHHHHHHHT.TS-SEEEEEE-S--T CS
                           PhoH   6 tkeQkeylealkkndivfaiGpaGtGKty.lavalavealkk.kkvkriiltrpavea 61 
                                    tk Qke+++a+ + +  + + ++G+GK+y  ++ la+++ ++ +k  r +++ p+ e 
  gene425|gene425|rna425|rna425  43 TKVQKEIINAILNRKSAIFLSNTGSGKSYgYSLGLAIRYHREkGKKLRAVIVLPTKEL 100
                                    789**************************66888999988774444466666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (440 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       794  (0.0442858); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.50
# Mc/sec: 2658.37
//
Query:       gene426|gene426|rna426|rna426  [L=142]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.065   13.5   5.7       0.13   12.5   5.7    1.6  1  Mlp       Mlp lipoprotein family
       0.13   12.7   0.0        2.4    8.6   0.0    2.1  2  PorB      Alpha helical Porin B
        2.7    8.9   9.2         50    4.8   9.2    2.0  1  CDC37_N   Cdc37 N terminal kinase binding


Domain annotation for each model (and alignments):
>> Mlp  Mlp lipoprotein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   5.7   2.2e-05      0.13      14     113 ..      13     104 ..       3     137 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.2e-05
                            Mlp  14 qkElpqqeKiklksdEeklfesLsavfkytiekltneiqgcsddnkskcnnfldWLktdiqkqkelaqafkkvykFLesk 93 
                                    qk ++q+ Kik+ s E+ l ++L   f   +ek+++++   +++ k +         t i+k+ ++++ ++ ++  +   
  gene426|gene426|rna426|rna426  13 QKQASQRRKIKSISAEDELSKKLLPFFGGILEKISKDLIVKEKQGKRR------HTTTSIEKKTNIIT-VTSFKT-ITIT 84 
                                    78889*******************************998777666662......22344555444433.333333.3333 PP

                            Mlp  94 kekdksfdtyiKseldckkg 113
                                    k+ +k++d+  K+ +++  +
  gene426|gene426|rna426|rna426  85 KDAKKDADEGKKTVINTVYA 104
                                    55566666666666666555 PP

>> PorB  Alpha helical Porin B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.0    0.0004       2.4       7      64 ..      25      82 ..      17      99 .. 0.84
   2 ?    2.1   0.0     0.044   2.7e+02      16      39 ..     117     140 ..     112     142 .] 0.90

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0004
                                   XXXXXXS-GGGSHHHHHHHHHHHHHTT---TTEBHHHHHHHHHHHH-SHHHHH-HHHH CS
                           PorB  7 sssakelsdridwvdCgileaalkaaGlaeegstnseLaaaleekaanfaatgfeqig 64
                                    s+ +els+++  +  gile   k   + e + ++++   ++e+k++ +  t f+ i 
  gene426|gene426|rna426|rna426 25 ISAEDELSKKLLPFFGGILEKISKDLIVKEKQGKRRHTTTSIEKKTNIITVTSFKTIT 82
                                   57889***************99999999999999999********9999999998764 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.044
                                    GGSHHHHHHHHHHHHHTT---TTE CS
                           PorB  16 ridwvdCgileaalkaaGlaeegs 39 
                                     i++ +C i + ++ +  + +e++
  gene426|gene426|rna426|rna426 117 MINNANCLITQEGVIVKTVFKENK 140
                                    5899************99999996 PP

>> CDC37_N  Cdc37 N terminal kinase binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   9.2    0.0084        50      29      91 ..       1      70 [.       1     128 [. 0.62

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.0084
                        CDC37_N 29 firwKq..rdihekreqrkaeikklklereindkllkridkllealkekevee.....eevvfkalnesl 91
                                   +i++Kq  ++  +k++ ++++ik++ +e e+ +kll+ +  +le+++++   +     ++ +++++++++
  gene426|gene426|rna426|rna426  1 MIKQKQlqNQHLQKQASQRRKIKSISAEDELSKKLLPFFGGILEKISKDLIVKekqgkRRHTTTSIEKKT 70
                                   57777631455578888999*****************999999998877655544454222222332222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1349  (0.0752412); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 923.93
//
Query:       gene427|gene427|rna427|rna427  [L=59]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1335  (0.0744604); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.43
# Mc/sec: 411.13
//
Query:       gene428|gene428|rna428|rna428  [L=551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
          7    6.0   9.2       0.22   10.9   2.3    2.0  2  DUF604    Protein of unknown function, DUF604


Domain annotation for each model (and alignments):
>> DUF604  Protein of unknown function, DUF604
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   2.3   1.2e-05      0.22     179     250 ..     218     287 ..     139     292 .. 0.72
   2 ?   -2.3   0.7      0.13   2.3e+03     192     201 ..     488     497 ..     440     545 .. 0.49

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 1.2e-05
                         DUF604 179 trevskdpCkrpvvfflksveke.kekeeivseYkrkekkkkkeCksksessakkvekikvlskkeeeewkka 250
                                    tr+++k+  ++      ++ ek+ + +++ +seY   ++++k+eC+s+++++++++++++v+++k++++ +k+
  gene428|gene428|rna428|rna428 218 TRTITKEVTTTIGRTSTDECEKSsDGESNKTSEY---NSETKSECSSEKKTKENEIKTVTVTKDKNKTDEEKT 287
                                    4555544444444444455555412344566778...4577999*******************8888777665 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.13
                         DUF604 192 vfflksveke 201
                                     +  ++v+++
  gene428|gene428|rna428|rna428 488 RYKTTTVTSK 497
                                    1111111111 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (551 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2728  (0.152156); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                       103  (0.00574488); expected 17.9 (0.001)
Passed Fwd filter:                        40  (0.00223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 1.12u 0.36s 00:00:01.48 Elapsed: 00:00:00.51
# Mc/sec: 3223.45
//
Query:       gene429|gene429|rna429|rna429  [L=423]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.4e-46  156.3  36.6    1.2e-45  156.0  36.6    1.0  1  Na_H_Exchanger   Sodium/hydrogen exchanger family
  ------ inclusion threshold ------
       0.71   10.1   8.0       0.68   10.1   2.9    3.2  2  ATPase_gene1     Putative F0F1-ATPase subunit Ca2+/Mg2+ trans
        7.7    6.2  13.9        1.2    8.9   0.4    3.9  3  DUF3149          Protein of unknown function (DUF3149)
        9.3    5.8   8.8       0.47   10.0   2.3    2.2  2  Cytochrome-c551  Photosystem P840 reaction-centre cytochrome 


Domain annotation for each model (and alignments):
>> Na_H_Exchanger  Sodium/hydrogen exchanger family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  156.0  36.6   2.6e-49   1.2e-45       5     377 ..      13     393 ..       6     396 .. 0.88

  Alignments for each domain:
  == domain 1  score: 156.0 bits;  conditional E-value: 2.6e-49
                                    HHHHHHHHH...HHHHTTSXHHHHHHHHHHHHTTTTTS.........HHHCHCCHHHHCHHCCHHHHCTCGCCTGCCTHH CS
                 Na_H_Exchanger   5 illallvgl...larrlklpeivgliiaGlllGpsglglieps....eedlevlselglilllFlaGleldlrelrknlk 77 
                                    +++++++++   + ++l l+e+++ ii+G+l+Gp++l++++ s    +++  ++++++l++++  a+++l+  +++k  k
  gene429|gene429|rna429|rna429  13 LFILAFGLVsnfVKEKLFLSEPTVSIIFGILIGPYVLNVLNTSyiesKIVMYHFARVVLCIQVMTAAMSLPQGYILKQAK 92 
                                    233333333674599999********************5444456556******************************** PP

                                    HHHHHHHHHHHHHHHHHHHHHH.HHTXTTCHHHHHHHHHHHTSSXHHHHHHHC....CCCTSTCCCCCCHHHHHHHHHHH CS
                 Na_H_Exchanger  78 silllallgvlitvvliGlllylllilgiplleallfgailsatdpvvvlailk...eegrvperlgtlllgesvlnDav 154
                                    s ++l +++ ++  ++ ++++ +  +  ++ + +l+++a+l++tdp++ ++i+k       vperl+tll +es++nD+v
  gene429|gene429|rna429|rna429  93 SLFVLVIVVSIAKYFI-TFIIVY-SFSHYNAAVSLAIAACLTPTDPILSSSIVKskfADENVPERLRTLLSAESGINDGV 170
                                    ***************9.888886.5899**************************99977889****************** PP

                                    CCCCCHHHHHHTXXXXXTSSSTSXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS....CTHHHHHHHHHHHHHHHHHHHH CS
                 Na_H_Exchanger 155 avvllavllalakeeaggetslllllliflvvavgglllglvigwllrlitrft....dddrelevllvlllallaalla 230
                                    ++ ll++ l +  +e+  +     +l ++l+ + + ++lg++ig+++r++++++        e++++  l+l +++ +l+
  gene429|gene429|rna429|rna429 171 GLSLLFFPLHIFYSENMLVGLKNYFLNVILYQCMLPIVLGVFIGYFSRKMLKYCygndLVGIESFLIYGLALTFFCLGLM 250
                                    *****998888867777777778899999*************************986444457888889*********** PP

                                    HTSXXXHHHHHHHHHHHHH.HHHHHTTHHHH.HHHHHHHHHHHHHHHHHHHHSXHHHHHXXHHHHHHHHHHHHHHHTHHH CS
                 Na_H_Exchanger 231 ellgvsgilgaflaGlvls.eyefsnklsek.lesfreglfnplfFvlvGlsldlkvlnnhlsvlilvllilvaillgri 308
                                    e ++ s ++ +f+ G+++s + +f  +++e+ l  + ++lf + fFv++G  +d++ +     v ++++ ++++i l+r+
  gene429|gene429|rna429|rna429 251 ETIKSSELICIFFTGALFSwDEWFVLETRESrLQEVTDSLFSTSFFVFFGSRIDFTRI----TV-PVIVSSILIICLRRT 325
                                    *******************9999999999999**********************4444....45.555555555559*** PP

                                    HHHHHHTTTX..SSXHHHHHHCCCCSS.BHHHHHHHHHHHHHHXHHHHTTSSTTTCSTSXHHHHHHHHHHH CS
                 Na_H_Exchanger 309 lavflllrll..glslrealiigfgglqrgavalalaalgpalgllarelyallivvvlftvlvqGlslkp 377
                                     + +ll +++  + + real++g+ g  +g  al+ a+l+ +   l++ ++ ++ vvvlf+v+++Gl+++ 
  gene429|gene429|rna429|rna429 326 FPCLLLFKFIpqIRTKREALFVGWFGP-IGVAALYYALLIDRI--LDTLTIDFVSVVVLFSVIIHGLTVPL 393
                                    **********987899***********.9********999995..99888******************986 PP

>> ATPase_gene1  Putative F0F1-ATPase subunit Ca2+/Mg2+ transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.2      0.16   7.1e+02      15      41 ..      15      42 ..      10      56 .. 0.60
   2 ?   10.1   2.9   0.00015      0.68      10      50 ..     202     246 ..     197     248 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.16
                   ATPase_gene1 15 illggllGywLDkkfgt.spwfliigll 41
                                   il++gl+ ++  +k+    p + ii+ +
  gene429|gene429|rna429|rna429 15 ILAFGLVSNFVKEKLFLsEPTVSIIFGI 42
                                   5666666666655553335555554433 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00015
                   ATPase_gene1  10 elvapillggllGyw....LDkkfgtspwfliiglllGlaaGfyn 50 
                                    + ++pi+lg+++Gy+    L   +g++ ++   +l+ Gla+ f++
  gene429|gene429|rna429|rna429 202 QCMLPIVLGVFIGYFsrkmLKYCYGNDLVGIESFLIYGLALTFFC 246
                                    5578***********777777788***************999986 PP

>> DUF3149  Protein of unknown function (DUF3149)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.2       2.3     1e+04      24      32 ..       7      15 ..       6      16 .. 0.76
   2 ?    3.5   2.4     0.012        54      18      32 ..      94     108 ..      93     111 .. 0.90
   3 ?    8.9   0.4   0.00026       1.2      24      37 ..     209     222 ..     204     223 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 2.3
                        DUF3149 24 gaffiryFi 32
                                   ++ f+++Fi
  gene429|gene429|rna429|rna429  7 VVCFVSLFI 15
                                   677899886 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.012
                        DUF3149  18 vftigmgaffiryFi 32 
                                    +f++++++ ++ yFi
  gene429|gene429|rna429|rna429  94 LFVLVIVVSIAKYFI 108
                                    799***********8 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.00026
                        DUF3149  24 gaffiryFirKmke 37 
                                     ++fi+yF+rKm +
  gene429|gene429|rna429|rna429 209 LGVFIGYFSRKMLK 222
                                    579*********75 PP

>> Cytochrome-c551  Photosystem P840 reaction-centre cytochrome c-551
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   2.3    0.0001      0.47      53      89 ..       4      41 ..       1      95 [. 0.82
   2 ?   -1.7   0.3      0.39   1.8e+03      50      94 ..     346     386 ..     338     402 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0001
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXX CS
                Cytochrome-c551 53 wflliffasliilglGklsskisdkwflsfp.lsilvi 89
                                   +fl++ f sl il++G +s  + +k fls p +si+  
  gene429|gene429|rna429|rna429  4 FFLVVCFVSLFILAFGLVSNFVKEKLFLSEPtVSIIFG 41
                                   7999999**********************994454432 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.39
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                Cytochrome-c551  50 fmGwflliffasliilglGklsskisdkwflsfplsilvivavmf 94 
                                    f+Gwf  i +a+l       l  +i d   + f +s++v+ +v++
  gene429|gene429|rna429|rna429 346 FVGWFGPIGVAALYYAL---LIDRILDTLTIDF-VSVVVLFSVII 386
                                    78888888777775433...3456666666655.45555555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (423 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1008  (0.0562218); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 2765.07
//
Query:       gene43|gene43|rna43|rna43  [L=125]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.087   12.5   0.0        0.1   12.3   0.0    1.2  1  Glyco_transf_10  Glycosyltransferase family 10 (fucosyltransf


Domain annotation for each model (and alignments):
>> Glyco_transf_10  Glycosyltransferase family 10 (fucosyltransferase) C-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   5.6e-06       0.1      28      71 ..      64     107 ..      43     124 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5.6e-06
            Glyco_transf_10  28 h.levdvyGkcgklkveelsekeveelikkykFYLafEnsickDY 71 
                                  ++ d + +  ++k   ++++e+   +++ kFY+afE+  c  +
  gene43|gene43|rna43|rna43  64 LlIRCDGFDRVHRHK-IISKKNEMIGFMNELKFYIAFESLECIAF 107
                                447788888887777.6778889999************9988655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       411  (0.0229238); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 900.22
//
Query:       gene430|gene430|rna430|rna430  [L=389]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-17   63.6   0.1    3.5e-17   62.5   0.1    1.6  1  TAF6_C    TAF6 C-terminal HEAT repeat domain
      2e-17   63.1   0.1    4.8e-17   61.9   0.1    1.6  1  TAF       TATA box binding protein associated factor (TAF)
  ------ inclusion threshold ------
      0.076   13.4   0.1       0.15   12.4   0.1    1.5  1  Histone   Core histone H2A/H2B/H3/H4


Domain annotation for each model (and alignments):
>> TAF6_C  TAF6 C-terminal HEAT repeat domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.5   0.1   5.8e-21   3.5e-17       2      87 ..     278     356 ..     277     359 .. 0.97

  Alignments for each domain:
  == domain 1  score: 62.5 bits;  conditional E-value: 5.8e-21
                         TAF6_C   2 ltcllakklgakseledhwaLRdfAAslLakilkkysssyktLkprvtrtllkvlldpkkslgtlyGallglaalGeeav 81 
                                    ltc+++k++       +++++R++AA++++++++ky+ +y tL pr+++tl+kv+ld++ks +++y al++l+ l +++v
  gene430|gene430|rna430|rna430 278 LTCIIGKRV-------KNVDIRKLAAETIKYVYDKYAITYDTLGPRIIKTLTKVWLDKDKSEDAHYSALFTLSILSRNVV 350
                                    9********.......89************************************************************** PP

                         TAF6_C  82 rklvlp 87 
                                     +++l 
  gene430|gene430|rna430|rna430 351 SSVILK 356
                                    ***986 PP

>> TAF  TATA box binding protein associated factor (TAF)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.9   0.1     8e-21   4.8e-17       4      65 ..      27      87 ..      25      88 .. 0.95

  Alignments for each domain:
  == domain 1  score: 61.9 bits;  conditional E-value: 8e-21
                                   --HHHHHHHHHHTT---B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHH CS
                            TAF  4 lpkesvkviAeslGitnLsdeaaalLaedveyrlkeivqeaakfmrhskRqkLtvaDvdsAL 65
                                   ++k+s    A+  G+ +++dea  +La+dveyr+ke  qeaakfm  skR+kL+ +Dv++AL
  gene430|gene430|rna430|rna430 27 FNKDSFLAYAQAKGL-EIEDEAVSILAQDVEYRVKELCQEAAKFMLFSKRTKLSIDDVNNAL 87
                                   788899999******.9********************************************8 PP

>> Histone  Core histone H2A/H2B/H3/H4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   2.5e-05      0.15      79     127 ..      38      86 ..      31      90 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.5e-05
                                    SSSXEEXHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTXSEEXHHHHHHH CS
                        Histone  79 kedlrisaeavlalqealEallvelfeeAnllakhaKRvTitpkDiqlA 127
                                     ++l i  eav +l++ +E+   el +eA++ +  +KR  +   D+  A
  gene430|gene430|rna430|rna430  38 AKGLEIEDEAVSILAQDVEYRVKELCQEAAKFMLFSKRTKLSIDDVNNA 86 
                                    568999************************************9999877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (389 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       797  (0.0444531); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.24s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 2741.73
//
Query:       gene431|gene431|rna431|rna431  [L=146]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0013   18.3   0.2     0.0018   17.8   0.2    1.2  1  Utp21            Utp21 specific WD40 associated putative doma
     0.0041   17.4   0.0     0.0063   16.8   0.0    1.2  1  Utp12            Dip2/Utp12 Family
     0.0094   16.3   0.3      0.014   15.7   0.3    1.3  1  EbsA             EbsA-like protein
  ------ inclusion threshold ------
      0.098   12.6   0.5       0.25   11.3   0.0    1.9  3  INCENP_ARK-bind  Inner centromere protein, ARK binding region


Domain annotation for each model (and alignments):
>> Utp21  Utp21 specific WD40 associated putative domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.2     4e-07    0.0018     101     211 ..      22     131 ..       5     139 .. 0.68

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 4e-07
                                    -----.------HHHHHHHHHHSS--HHHHHHHHH-S-HHHHHT--------S-SHHHHHHHHHHHHHTTTS-HHHHHHH CS
                          Utp21 101 ilkldklgteseftklLeegsetgdysefleyLkslspsaidleirsLesaesleelvafvkaltarLksrrdfeLvqai 180
                                     l++++ +   +f++ Le+++e+ dy+++++ +k+l    i   i  L    + ++l   +    + Lk++ d++ v a+
  gene431|gene431|rna431|rna431  22 ELEIENPKVYDKFSRALERSKEDADYDALFNAIKELDMGDISSIISGL----DNNSLYVVL----QALKNNIDYNVVLAV 93 
                                    23333356899*************************************....555555544....456778888888875 PP

                                    HHHH...HHHTTTTTTT-SH.......HHHHHHHHHHHH CS
                          Utp21 181 lsvf...LkvHgdviaeeeee.....elkealeelkeeq 211
                                     +vf      H + +ae+++      e++  +e l++  
  gene431|gene431|rna431|rna431  94 -KVFfsiVEHHRYFVAENQSAyvvykEIRGRVELLRQLI 131
                                    .33302145677777777766777765555555555554 PP

>> Utp12  Dip2/Utp12 Family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   1.4e-06    0.0063       9     101 ..      53     137 ..      46     140 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.4e-06
                                    HHHSS-TTTHHHHHHCS-CTCHHHHHHHHHHHH.HTTTTHHHHHHHHHHHHHHHHHHHHHSH..HHHHHHHHHHHHHHHH CS
                          Utp12   9 vlekippsdirltvlrLpssyvlkLLeflaerlaeksphlelllrwlkallrvHgsylvasps.dlvpaLrslqkslrer 87 
                                     ++  +  di+++++ L+   ++ +L++l++   +  +++ l +++ ++++  H++y+va  + ++      ++k +r r
  gene431|gene431|rna431|rna431  53 AIKELDMGDISSIISGLDNNSLYVVLQALKN---NIDYNVVLAVKVFFSIV-EHHRYFVAENQsAY-----VVYKEIRGR 123
                                    566678889**********************...55899********9999.67778887665344.....79******* PP

                                    HHHHHHHHHHHHHH CS
                          Utp12  88 lktlskllglnlgr 101
                                    +++l++l+++n ++
  gene431|gene431|rna431|rna431 124 VELLRQLIKENEYK 137
                                    **********9876 PP

>> EbsA  EbsA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.3   3.2e-06     0.014      29      82 ..      73     126 ..      64     138 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 3.2e-06
                           EbsA  29 slilllEntriylksnlvlllflvlvilgfkryliieedkliikslrffkkkki 82 
                                    sl ++l   + ++  n+vl++ +++ i+  +ry++ e+++ ++++ ++  + ++
  gene431|gene431|rna431|rna431  73 SLYVVLQALKNNIDYNVVLAVKVFFSIVEHHRYFVAENQSAYVVYKEIRGRVEL 126
                                    788899999999****************************99999877666555 PP

>> INCENP_ARK-bind  Inner centromere protein, ARK binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       2.3   1.1e+04      24      32 ..      16      24 ..      14      28 .. 0.63
   2 ?   11.3   0.0   5.6e-05      0.25      28      54 ..      35      62 ..      32      62 .. 0.92
   3 ?   -2.9   0.0       1.5   6.6e+03      26      34 ..     125     133 ..     124     138 .. 0.69

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 2.3
                INCENP_ARK-bind 24 speLrqaLi 32
                                   s+eL+++L+
  gene431|gene431|rna431|rna431 16 SSELEKELE 24
                                   566666665 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 5.6e-05
                INCENP_ARK-bind 28 rqaLikq.epiDpdeiFGpikplnleei 54
                                    +aL++  e+ D d +F  ik+l++ +i
  gene431|gene431|rna431|rna431 35 SRALERSkEDADYDALFNAIKELDMGDI 62
                                   68999999*****************987 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 1.5
                INCENP_ARK-bind  26 eLrqaLikq 34 
                                    eL ++Lik 
  gene431|gene431|rna431|rna431 125 ELLRQLIKE 133
                                    577888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       861  (0.0480228); expected 358.6 (0.02)
Passed bias filter:                      563  (0.0314016); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1069.40
//
Query:       gene432|gene432|rna432|rna432  [L=153]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2257  (0.125885); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 1103.09
//
Query:       gene433|gene433|rna433|rna433  [L=279]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.5e-13   49.3  10.7      1e-12   48.1  10.7    1.7  1  zf-RING_2     Ring finger domain
    1.5e-09   37.5   9.3    3.1e-09   36.5   9.3    1.6  1  zf-C3HC4_2    Zinc finger, C3HC4 type (RING finger)
    1.6e-08   34.7   7.9    4.6e-08   33.2   7.9    1.8  1  zf-rbx1       RING-H2 zinc finger domain
    3.7e-08   33.0   6.4    7.7e-08   31.9   6.4    1.6  1  zf-RING_11    RING-like zinc finger
    1.6e-06   27.9  10.1    3.3e-06   26.9  10.1    1.6  1  zf-C3HC4      Zinc finger, C3HC4 type (RING finger)
    1.9e-06   27.8   4.5    9.1e-06   25.6   4.8    2.0  2  zf-RING_UBOX  RING-type zinc-finger
    5.1e-06   26.4   9.2    1.1e-05   25.3   9.2    1.6  1  zf-RING_5     zinc-RING finger domain
    8.8e-06   25.5   7.7    1.9e-05   24.4   7.7    1.5  1  zf-C3HC4_3    Zinc finger, C3HC4 type (RING finger)
    1.4e-05   25.0   2.9    3.7e-05   23.7   2.9    1.7  1  zf-ANAPC11    Anaphase-promoting complex subunit 11 RING-H2 f
    0.00029   21.0  10.7     0.0014   18.7   8.8    2.6  1  FANCL_C       FANCL C-terminal domain
     0.0018   18.5   8.5     0.0037   17.5   8.5    1.6  1  zf-RING-like  RING-like domain
  ------ inclusion threshold ------
      0.012   15.5   8.2      0.023   14.5   8.2    1.5  1  Prok-RING_4   Prokaryotic RING finger family 4
      0.016   15.3   8.9      0.044   13.9   8.9    1.8  1  RINGv         RING-variant domain
      0.017   14.7   6.6      0.039   13.6   6.6    1.6  1  Zn_ribbon_17  Zinc-ribbon, C4HC2 type
       0.31   10.7   6.2       0.67    9.6   6.2    1.5  1  DUF4750       Domain of unknown function (DUF4750)
       0.32   11.1   3.7       0.99    9.5   3.7    1.8  1  zf-C3H2C3     Zinc-finger
       0.38   11.0   6.9        1.3    9.4   6.9    1.9  1  zf-HC5HC2H    PHD-like zinc-binding domain
       0.53   10.1   8.2        1.6    8.5   8.2    1.9  1  zf-RING_4     RING/Ubox like zinc-binding domain
       0.61   10.0   8.4        1.3    9.0   8.4    1.6  1  PHD           PHD-finger
       0.75   10.0   6.7        3.9    7.7   7.2    2.0  1  zf-RING_10    zinc RING finger of MSL2
       0.86    9.8   6.7        3.5    7.9   6.7    2.1  1  zf-C3HC4_4    zinc finger of C3HC4-type, RING
          2    8.6   8.0        2.6    8.2   5.4    2.2  2  Zf_RING       KIAA1045 RING finger
        7.8    6.4   8.1        5.8    6.8   5.4    2.1  2  zf-Nse        Zinc-finger of the MIZ type in Nse subunit


Domain annotation for each model (and alignments):
>> zf-RING_2  Ring finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.1  10.7   1.3e-15     1e-12       2      44 .]     226     269 ..     225     269 .. 0.95

  Alignments for each domain:
  == domain 1  score: 48.1 bits;  conditional E-value: 1.3e-15
                      zf-RING_2   2 eCpICleelssadsvlllpCgHvfhreClerwlrssst.CPlCr 44 
                                    +C IC++e+++++ +++l C+H fh+eC++ wl+++s+ CP+Cr
  gene433|gene433|rna433|rna433 226 SCLICMDEFTNESVCRVLRCNHNFHKECVDPWLKTKSSrCPYCR 269
                                    8********999999999***************999999****9 PP

>> zf-C3HC4_2  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.5   9.3     4e-12   3.1e-09       2      40 .]     227     268 ..     226     268 .. 0.93

  Alignments for each domain:
  == domain 1  score: 36.5 bits;  conditional E-value: 4e-12
                     zf-C3HC4_2   2 CpiCldmlkdpsvvt..pCgHvfCqkCilrsLeekn.eCPlC 40 
                                    C iC+d++ + sv     C+H f+++C++++L+ k+ +CP C
  gene433|gene433|rna433|rna433 227 CLICMDEFTNESVCRvlRCNHNFHKECVDPWLKTKSsRCPYC 268
                                    **********9876677*****************999***** PP

>> zf-rbx1  RING-H2 zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.2   7.9   5.9e-11   4.6e-08      12      55 .]     225     269 ..     220     269 .. 0.75

  Alignments for each domain:
  == domain 1  score: 33.2 bits;  conditional E-value: 5.9e-11
                        zf-rbx1  12 eacieckapgdee..cpvvlGeCgHaFHlhCiskWlkt.rkvCPlcr 55 
                                    e c+ c  + ++e  c v   +C+H+FH++C++ Wlkt +++CP cr
  gene433|gene433|rna433|rna433 225 ESCLICMDEFTNEsvCRVL--RCNHNFHKECVDPWLKTkSSRCPYCR 269
                                    4566666666666456665..5****************6677****8 PP

>> zf-RING_11  RING-like zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.9   6.4   9.9e-11   7.7e-08       2      29 .]     227     254 ..     226     254 .. 0.98

  Alignments for each domain:
  == domain 1  score: 31.9 bits;  conditional E-value: 9.9e-11
                     zf-RING_11   2 CsICLeefkpgqalfilpCsHtFHfkCI 29 
                                    C IC++ef+++   ++l C+H FH +C+
  gene433|gene433|rna433|rna433 227 CLICMDEFTNESVCRVLRCNHNFHKECV 254
                                    ***************************7 PP

>> zf-C3HC4  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.9  10.1   4.2e-09   3.3e-06       1      41 []     227     268 ..     227     268 .. 0.97

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 4.2e-09
                                    -TTT-S--SS-E...E-TTS--B-CHHHHHHHHCTSSB--TTT CS
                       zf-C3HC4   1 CpiCleeakepn..elleCkHsfCskCirkilksrkkvkCPlC 41 
                                    C iC++e+++++  ++l C+H+f+++C++ +lk  k+  CP C
  gene433|gene433|rna433|rna433 227 CLICMDEFTNESvcRVLRCNHNFHKECVDPWLK-TKSSRCPYC 268
                                    99**********9********************.99999***9 PP

>> zf-RING_UBOX  RING-type zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   4.8   1.2e-08   9.1e-06       1      39 []     227     266 ..     227     268 .. 0.76
   2 ?   -0.7   0.2       1.9   1.5e+03       1       8 [.     265     272 ..     265     275 .. 0.84

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 1.2e-08
                   zf-RING_UBOX   1 CpIClelftdP...lvlpCGHtFCreCl..welskslegafkCP 39 
                                    C IC+++ft+     vl C H+F++eC+  w     + ++ +CP
  gene433|gene433|rna433|rna433 227 CLICMDEFTNEsvcRVLRCNHNFHKECVdpW----LKTKSSRCP 266
                                    99*******887653357**********554....555555665 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.9
                   zf-RING_UBOX   1 CpIClelf 8  
                                    Cp C+el 
  gene433|gene433|rna433|rna433 265 CPYCRELI 272
                                    9***9986 PP

>> zf-RING_5  zinc-RING finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   9.2   1.4e-08   1.1e-05       2      43 ..     227     269 ..     226     270 .. 0.96

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 1.4e-08
                      zf-RING_5   2 CnkCfeklskeekfyltsCgHifCekClkkll.ekeavCpiCr 43 
                                    C +C++++++e+ + +++C H f+++C++  l +k+ +Cp Cr
  gene433|gene433|rna433|rna433 227 CLICMDEFTNESVCRVLRCNHNFHKECVDPWLkTKSSRCPYCR 269
                                    ******************************999*********9 PP

>> zf-C3HC4_3  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   7.7   2.4e-08   1.9e-05       4      48 ..     226     273 ..     224     274 .. 0.86

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 2.4e-08
                                    B-TTTSSS...BS-EEETTEEEEEE-HHHHHHHHH.TT-B-TTT--B-- CS
                     zf-C3HC4_3   4 eCviCler...prnvvllpCgHlvlCeeCaekllk.rkkkCpiCrrpie 48 
                                     C+iC+++   ++ + +l+C+H  + +eC++ +lk ++ +Cp+Cr+ i+
  gene433|gene433|rna433|rna433 226 SCLICMDEftnESVCRVLRCNHN-FHKECVDPWLKtKSSRCPYCRELIK 273
                                    7******633366688889****.**********99*********9875 PP

>> zf-ANAPC11  Anaphase-promoting complex subunit 11 RING-H2 finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   2.9   4.7e-08   3.7e-05      50      84 ..     243     275 ..     222     276 .. 0.82

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 4.7e-08
                                    BTTS-EEEHHHHHHHHHHHSTSSB-TTTSSB--BE CS
                     zf-ANAPC11  50 Gkckhnfhlhcilkwletetskglcpmcrqtfklk 84 
                                     +c+hnfh+ c+  wl+t++s  +cp cr+ +k++
  gene433|gene433|rna433|rna433 243 LRCNHNFHKECVDPWLKTKSS--RCPYCRELIKVH 275
                                    47***************9998..5*****998876 PP

>> FANCL_C  FANCL C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   8.8   1.8e-06    0.0014       4      68 ..     226     275 ..     224     277 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.8e-06
                                    S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-SEEEGG CS
                        FANCL_C   4 eCgiCyayrldsgevpdisCdnekCnkkfHsaCLkeWlrslkesrqsfdvlfGeCPyCkkkisvk 68 
                                    +C iC+ ++       + +C   +Cn++fH++C+  Wl++ ++          +CPyC++ i+v+
  gene433|gene433|rna433|rna433 226 SCLICMDEFT-----NESVCRVLRCNHNFHKECVDPWLKTKSS----------RCPYCRELIKVH 275
                                    6999999988.....6789*******************99765..........599998888775 PP

>> zf-RING-like  RING-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   8.5   4.8e-06    0.0037       1      43 []     227     268 ..     227     268 .. 0.95

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 4.8e-06
                   zf-RING-like   1 CeaCkeivtqGvrCsnesCnvrlHvdCfqhyirthsskkCpkC 43 
                                    C +C +  t    C    Cn  +H++C++  ++t+ss +Cp C
  gene433|gene433|rna433|rna433 227 CLICMDEFTNESVCRVLRCNHNFHKECVDPWLKTKSS-RCPYC 268
                                    99******************************77766.***99 PP

>> Prok-RING_4  Prokaryotic RING finger family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   8.2     3e-05     0.023       1      41 [.     227     273 ..     227     277 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3e-05
                    Prok-RING_4   1 CvlCgeq...ekkailepCgHlvCkeCfdsk...dlssCPlCqrris 41 
                                    C++C  +   e++ ++  C+H + keC d +   ++s+CP C++ i+
  gene433|gene433|rna433|rna433 227 CLICMDEftnESVCRVLRCNHNFHKECVDPWlktKSSRCPYCRELIK 273
                                    99998776669999***************99887888******8775 PP

>> RINGv  RING-variant domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   8.9   5.6e-05     0.044       1      48 []     227     268 ..     227     268 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.6e-05
                                    ETTTTEE-SSSS--B-SS--STCCCSB-HHHHHHHHHHTCT-SB-TTT CS
                          RINGv   1 CriCleeeeeseplispCkCrGslklvHesClekWldekeantqCeiC 48 
                                    C iC++e ++++     C+  + ++ +H++C++ Wl++  ++++C  C
  gene433|gene433|rna433|rna433 227 CLICMDEFTNES----VCRVLRCNHNFHKECVDPWLKT--KSSRCPYC 268
                                    99*****88876....899999999************9..88999999 PP

>> Zn_ribbon_17  Zinc-ribbon, C4HC2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   6.6   4.9e-05     0.039       4      46 ..     224     266 ..     221     268 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.9e-05
                   Zn_ribbon_17   4 lksCayCelavkgrv.vlcgvCeHvlHasCarewfenddlaeCp 46 
                                     +sC +C  + +    +   +C+H  H++C++ w++++  + Cp
  gene433|gene433|rna433|rna433 224 FESCLICMDEFTNESvCRVLRCNHNFHKECVDPWLKTKS-SRCP 266
                                    578999998887655045679***************999.9998 PP

>> DUF4750  Domain of unknown function (DUF4750)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   6.2   0.00087      0.67       3      25 ..     165     187 ..     164     191 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00087
                        DUF4750   3 eevllfvlrlllalliVlllill 25 
                                    e v+++++++ll++liVl++i l
  gene433|gene433|rna433|rna433 165 ERVFIVAFYFLLTVLIVLCFITL 187
                                    689******************87 PP

>> zf-C3H2C3  Zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   3.7    0.0013      0.99      16      34 ..     244     268 ..     242     269 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0013
                      zf-C3H2C3  16 sCkHlvHakCade......evCPkC 34 
                                    +C+H +H++C+d+        CP C
  gene433|gene433|rna433|rna433 244 RCNHNFHKECVDPwlktksSRCPYC 268
                                    6**********98333333457777 PP

>> zf-HC5HC2H  PHD-like zinc-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   6.9    0.0016       1.3      37      66 ..     225     254 ..     208     270 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0016
                     zf-HC5HC2H  37 lkCylCkkkvGaciqCskkkCkkafHvtCa 66 
                                     +C +C+++      C+  +C+++fH  C 
  gene433|gene433|rna433|rna433 225 ESCLICMDEFTNESVCRVLRCNHNFHKECV 254
                                    68***************************6 PP

>> zf-RING_4  RING/Ubox like zinc-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   8.2    0.0021       1.6       1      45 [.     227     270 ..     225     273 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0021
                      zf-RING_4   1 cplCdeeldetdkdlkpCeCgyqiClfCyhrileeeegrCPaCre 45 
                                    c +C++e+  +++  +   C++++   C +  l++++ rCP Cre
  gene433|gene433|rna433|rna433 227 CLICMDEF-TNESVCRVLRCNHNFHKECVDPWLKTKSSRCPYCRE 270
                                    55666666.2333444558999999*******************8 PP

>> PHD  PHD-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   8.4    0.0017       1.3       2      51 ..     227     270 ..     226     271 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0017
                                    BTTTTSTTSTTSCEEEET..TTSCEEETTTSSSTHSHHSHHSSTBSSTTTHT CS
                            PHD   2 CavCkkksdeeeelvqCd..gCkrwfHqkClkppleseekpegewlCekCke 51 
                                    C +C +  +  +e v C   +C++ fH++C++p l++++       C+ C+e
  gene433|gene433|rna433|rna433 227 CLICMD--EFTNESV-CRvlRCNHNFHKECVDPWLKTKSS-----RCPYCRE 270
                                    888988..3444444.54348*************994444.....6999975 PP

>> zf-RING_10  zinc RING finger of MSL2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   7.2    0.0051       3.9       2      52 ..     226     277 ..     225     279 .] 0.85

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0051
                     zf-RING_10   2 sCvvCckLLvdPlepkekeCqHyvCrlCvgkkkklk.psCsqCkdyekyeen 52 
                                    sC++C    ++    +  +C+H+  + Cv    k k ++C+ C++  k +e+
  gene433|gene433|rna433|rna433 226 SCLICMDEFTNESVCRVLRCNHNFHKECVDPWLKTKsSRCPYCRELIKVHED 277
                                    8****************************9987776267****987665554 PP

>> zf-C3HC4_4  zinc finger of C3HC4-type, RING
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   6.7    0.0045       3.5       1      42 []     227     268 ..     227     268 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0045
                     zf-C3HC4_4   1 CPiCldYLekP.v..sleCGhsfClsCisslqkepdgeqllCplC 42 
                                    C iC+d +++  v   l C h+f  +C++ + k +++   +Cp C
  gene433|gene433|rna433|rna433 227 CLICMDEFTNEsVcrVLRCNHNFHKECVDPWLKTKSS---RCPYC 268
                                    778888776541322699***************9977...6**99 PP

>> Zf_RING  KIAA1045 RING finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0       1.4   1.1e+03      26      52 ..     105     131 ..     102     137 .. 0.74
   2 ?    8.2   5.4    0.0033       2.6       6      35 ..     225     255 ..     222     273 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 1.4
                        Zf_RING  26 tkvfHegClrklgylqdesalellkrA 52 
                                    +++++ +C + ++++ ++ ++ +l  A
  gene433|gene433|rna433|rna433 105 ERNYYLNCTEIMEKMMKRRNKAVLVLA 131
                                    689999999999888777766665544 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0033
                        Zf_RING   6 elCeiC.evytaeelypCRv..CtkvfHegClr 35 
                                    e C iC + +t e+   CRv  C+++fH++C+ 
  gene433|gene433|rna433|rna433 225 ESCLICmDEFTNESV--CRVlrCNHNFHKECVD 255
                                    6799**666666665..77777*********97 PP

>> zf-Nse  Zinc-finger of the MIZ type in Nse subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       2.1   1.7e+03      15      30 ..     194     209 ..     186     210 .. 0.80
   2 ?    6.8   5.4    0.0075       5.8      28      56 ..     241     268 ..     221     269 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 2.1
                                    TTTSSB-SSEEEESSS CS
                         zf-Nse  15 PltlqpfeePvtskkC 30 
                                      t++p+ +P+   +C
  gene433|gene433|rna433|rna433 194 QTTKNPLITPYELNRC 209
                                    5689999999998888 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0075
                                    S..SS--EEEHHHHHHHCTTTS-EE-SCCC- CS
                         zf-Nse  28 k..kCpHvFEreaIlelikrkktvkCPvagC 56 
                                    +  +C+H F +e +   + ++k+ +CP   C
  gene433|gene433|rna433|rna433 241 RvlRCNHNFHKECVDPWL-KTKSSRCPY--C 268
                                    3558**************.78899***8..6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (279 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1052  (0.0586759); expected 358.6 (0.02)
Passed bias filter:                      506  (0.0282224); expected 358.6 (0.02)
Passed Vit filter:                        73  (0.00407162); expected 17.9 (0.001)
Passed Fwd filter:                        23  (0.00128284); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              23  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 1724.59
//
Query:       gene434|gene434|rna434|rna434  [L=185]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.3e-08   32.4   0.3    1.7e-07   31.3   0.3    1.6  1  DnaJ      DnaJ domain


Domain annotation for each model (and alignments):
>> DnaJ  DnaJ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.3   0.3   9.3e-12   1.7e-07      13      51 ..      15      50 ..       8      61 .. 0.84

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 9.3e-12
                                   -HHHHHHHHHHHHHHHSTTTSCCHHHHHHHHHHHHHHHH CS
                           DnaJ 13 sedeIkkaYrklalkyHPDknpkdpeaeekFkeineAye 51
                                   +  ++kk+Y  l+lkyHPD++   + ++ekF +i eAy+
  gene434|gene434|rna434|rna434 15 TLHNLKKNYTALVLKYHPDRK---TGNREKFTQIFEAYK 50
                                   56789**************99...5667**********7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1140  (0.0635841); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1306.39
//
Query:       gene435|gene435|rna435|rna435  [L=495]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-36  125.8   1.2    9.3e-36  123.7   1.2    2.0  1  NPL4             NPL4 family
      2e-24   86.4   1.2      4e-22   78.9   1.2    2.5  1  zf-NPL4          NPL4 family, putative zinc binding region
     0.0007   18.9   2.3     0.0007   18.9   2.3    2.4  2  zf-RanBP         Zn-finger in Ran binding protein and others
  ------ inclusion threshold ------
          2    8.5   8.2        1.4    9.0   2.0    2.8  2  LRV_FeS          LRV protein FeS4 cluster


Domain annotation for each model (and alignments):
>> NPL4  NPL4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.7   1.2   2.1e-39   9.3e-36       1     217 [.     193     381 ..     193     490 .. 0.86

  Alignments for each domain:
  == domain 1  score: 123.7 bits;  conditional E-value: 2.1e-39
                           NPL4   1 RlgylyGryekydevPlGikavveaiyEPpqedeldgltlledeeekevdeiakklglekvGviftDlldagakdgtvlc 80 
                                    R+g+l G+ + y+ vPlG  avv aiy+P qe+  dg  ++e +e +++ ++   +gl  +G+i+tDl            
  gene435|gene435|rna435|rna435 193 RFGFLLGKIKDYERVPLGKTAVVSAIYDPLQENFPDGFVVHE-KECSKIRALLDYIGLDVIGMIYTDLN----------- 260
                                    9************************************98876.56789*******************95........... PP

                           NPL4  81 kRhkdsyflsslEvilaaklqlkhpnvtkysetgkfsskFvtvvvsgdeegeieiesyqvsneaealvradiiepstdPs 160
                                      hk  y ls+ E+   ak+q+++       +   f s+Fv vvv   ++  +e+e+y vs++ + l++++ii+p+td +
  gene435|gene435|rna435|rna435 261 --HKRDYLLSCTEIDAMAKFQNENM--FADDDGKVFNSRFVSVVVRN-NDAGVELEAYSVSEQGMVLIDENIIKPCTDKQ 335
                                    ..6778***************9865..45556778*******99975.5778*************************965 PP

                           NPL4 161 layvresseerYvpevfYkkkneyglevkenakPalPveyLlvslthgfpkepkplF 217
                                     ++v           + Y +kney l v++n+   +PveyL+v+++hgf +++   F
  gene435|gene435|rna435|rna435 336 -TFVST-------HPIIYLEKNEYDLVVEKNTMR-VPVEYLIVDIPHGFSEKSM--F 381
                                    .45555.......3699**************998.**************87654..4 PP

>> zf-NPL4  NPL4 family, putative zinc binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.9   1.2     9e-26     4e-22      18     145 .]      84     190 ..      70     190 .. 0.82

  Alignments for each domain:
  == domain 1  score: 78.9 bits;  conditional E-value: 9e-26
                        zf-NPL4  18 krkrdeklcrhgekgmceycsplepydeeylkekkikhlsfhaylrklnekknkkesssskiapLeelsykvkkecksgh 97 
                                    + ++d  +c+hg+++mc +c+p+ p+d + l+e+ ik+lsf a+  k  +              +e l+y  ++eck++ 
  gene435|gene435|rna435|rna435  84 TGNKD-IFCNHGDNAMCVNCAPVSPWDPKLLRERGIKYLSFGAFKEKN-Q-------------RIERLTY--RNECKHA- 145
                                    44566.79***********************************84432.2.............2333444..5678763. PP

                        zf-NPL4  98 apwPkgicskcqPsaitlqrqkfRmvDhvefesseivdkfldaWRktg 145
                                        +  c++c   +i+l++q++Rm+Dhve+++s+ vd+f+++WR tg
  gene435|gene435|rna435|rna435 146 ---QNVKCTRCMERTIALKQQNYRMIDHVEIDHSKTVDNFISFWRGTG 190
                                    ...3456**************************************998 PP

>> zf-RanBP  Zn-finger in Ran binding protein and others
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.7      0.36   1.6e+03      18      25 ..     147     154 ..     145     154 .. 0.78
   2 !   18.9   2.3   1.6e-07    0.0007       1      28 [.     465     492 ..     465     493 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.36
                                    SSB-TTT- CS
                       zf-RanBP  18 stkCvaCq 25 
                                    ++kC +C+
  gene435|gene435|rna435|rna435 147 NVKCTRCM 154
                                    67999995 PP

  == domain 2  score: 18.9 bits;  conditional E-value: 1.6e-07
                                    GSSSEE-SSS--EEESSSSB-TTT--BT CS
                       zf-RanBP   1 regdWdCskClvqNfawstkCvaCqapk 28 
                                    r++ WdC+ C+++N   + +C++C++ +
  gene435|gene435|rna435|rna435 465 RKEEWDCKICTYRNLDGTDRCEMCETQR 492
                                    7899*********************976 PP

>> LRV_FeS  LRV protein FeS4 cluster
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.5     0.047   2.1e+02      13      41 ..     141     169 ..     130     182 .. 0.77
   2 ?    9.0   2.0   0.00031       1.4       8      28 ..     468     488 ..     465     491 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.047
                        LRV_FeS  13 sCehrellaeGrCelgkaCvadryarrid 41 
                                    +C+h +  +  rC  ++  ++ +  r id
  gene435|gene435|rna435|rna435 141 ECKHAQNVKCTRCMERTIALKQQNYRMID 169
                                    57777777777777776666666666665 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00031
                        LRV_FeS   8 evdCasCehrellaeGrCelg 28 
                                    e dC+ C++r+l  + rCe+ 
  gene435|gene435|rna435|rna435 468 EWDCKICTYRNLDGTDRCEMC 488
                                    569***************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (495 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       763  (0.0425568); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.62u 0.31s 00:00:00.93 Elapsed: 00:00:00.52
# Mc/sec: 2840.87
//
Query:       gene436|gene436|rna436|rna436  [L=419]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.6e-26   92.8   0.0    5.8e-26   91.6   0.0    1.5  1  Hexokinase_1  Hexokinase
    2.5e-13   50.0   0.3    9.1e-09   35.1   0.2    2.3  2  Hexokinase_2  Hexokinase
  ------ inclusion threshold ------
       0.14   11.9   3.9       0.56    9.9   0.1    2.4  2  DUF2913       Protein of unknown function (DUF2913)


Domain annotation for each model (and alignments):
>> Hexokinase_1  Hexokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.6   0.0   9.8e-30   5.8e-26       8     197 ..      21     209 ..      17     210 .. 0.82

  Alignments for each domain:
  == domain 1  score: 91.6 bits;  conditional E-value: 9.8e-30
                                    HH---HHHHHHHHHHHHHHHHHHHS.S.STS--EE----S...---S--EEEEEEEEESSSEEEEEEEEEESSS.-EEEE CS
                   Hexokinase_1   8 qfelsdeklkelvdrfleemekgLakekeslkmlptyvtr...lPtGkekGtylAlDlGgtnlRvllveLlges.kveit 83 
                                     fe+s+ +l++++d++ + +++  + ++++  +l t+v+r   + + + + ++lA+D+Ggt l+  l +++ ++ k + +
  gene436|gene436|rna436|rna436  21 VFEYSQRDLEAIADDVAKWIKEAKS-SGSESMCLRTFVSRnsnILEATSHREMLAIDFGGTSLKLGLYKIEANQaKTTKE 99 
                                    699999**********777777766.44556799999999444455788899******************9766344444 PP

                                    EEEEE--GGGGGS...BHHHHHHHHHHHHHHHHHHH....ST..T-S-EEEEEEE-SSEE-SBTT--EE-S--TT---TT CS
                   Hexokinase_1  84 qekykipeelktg...taeeLFdfiakciaefleeegeekkeekeeeelplGftFSFPveqtsldegtlirwtKgfaikd 160
                                     +k++ip+  +++   ++ +++++i ++i+e l ++ + k           G+tFS+P++q+s+++g+++++ K+f  + 
  gene436|gene436|rna436|rna436 100 VKKIPIPKIETEEdrkNNGNMYEWIYNRIDEYLGDNYDVK---------LAGLTFSYPLRQESINSGKILSLHKNFPFEW 170
                                    44555554333333449999***************98774.........57*************************9966 PP

                                    -T..TSBHHHHHHHHHHHTT-SEEEEEEE-HHHHHHHHH CS
                   Hexokinase_1 161 ve..gkdvvqllqealerkglpvkvvalvNDTvgtllsl 197
                                     +    d v+ l++ +e+kg ++ + al+NDT++tl+sl
  gene436|gene436|rna436|rna436 171 LSsdATDPVASLNKIFEQKGRKIVIKALANDTTATLMSL 209
                                    444589*******************************95 PP

>> Hexokinase_2  Hexokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.1   0.2   1.5e-12   9.1e-09       2      79 ..     218     284 ..     217     302 .. 0.79
   2 !   12.9   0.0   9.4e-06     0.056     153     233 ..     324     407 ..     284     408 .. 0.69

  Alignments for each domain:
  == domain 1  score: 35.1 bits;  conditional E-value: 1.5e-12
                                    EEEEESSSEEEEEEEEGGG-GGGTTTS-TTSEEEEE--GGGTTTT-SS-..--HHHHHHHHHSSSTTS-..HHHHCCSHH CS
                   Hexokinase_2   2 iGlIlGtGtNacyleklsnieklegkkeksgemviNtEwgafgdegklpllrtkyDkeldeespnpgeq..lfEkmiSGm 79 
                                    iG++lGtGtN++y+   +    l+g        +iNtEw +f++ ++l+  +tkyD+ +++e +++++q   ++ m +G+
  gene436|gene436|rna436|rna436 218 IGIVLGTGTNGAYFTSNQ----LNGS------EAINTEWASFDS-KSLK--KTKYDELIQDELIKKKQQwkCLDCMLGGY 284
                                    8*************9763....3333......38********98.4455..8**********999999965677777776 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 9.4e-06
                                    HHHHHHHHHHHHHHHCHHHHHHHHH-.....SSEEEEEESHHHHHSTTH.HHHHHHHHHHH...HT--S.......-SEE CS
                   Hexokinase_2 153 revceavsrRaarlvAagiaallkklgkeekekvtvgvdGslyekypkf.rerlqealrel...lgeepe......kkvk 222
                                    ++v   v +Raa++++a + ++lk  + ++k++++   +G+++e+  +f r++l+e ++e+   +    +      ++++
  gene436|gene436|rna436|rna436 324 KHV-YQVKNRAAKIISALVFGILKSENVNAKNNISLILNGTILEQ--DFdRKLLKEQINEMkeyF----NdglykdTSFN 396
                                    444.4478****************97778899***********94..341566777777774432....12333447888 PP

                                    EEE---TTTHH CS
                   Hexokinase_2 223 lklaedGsgvG 233
                                    + + e++s+vG
  gene436|gene436|rna436|rna436 397 FYVPEEASLVG 407
                                    88888888877 PP

>> DUF2913  Protein of unknown function (DUF2913)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.1   9.4e-05      0.56      52     111 ..      30      94 ..      25     116 .. 0.70
   2 ?    2.4   1.1     0.018   1.1e+02      42      65 ..     251     274 ..     237     375 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 9.4e-05
                        DUF2913  52 klvakdLkrwqkqgrskGknaqLkalleriseqykevaeeekel.....dskleallaeleekew 111
                                      +a+d+ +w+k+++s G+++   +++   ++   e+  + + l     +++l+  l ++e+++ 
  gene436|gene436|rna436|rna436  30 EAIADDVAKWIKEAKSSGSESMCLRTFVSRNSNILEATSHREMLaidfgGTSLKLGLYKIEANQA 94 
                                    579*****************999998855555555554444444666666666666666666665 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.018
                        DUF2913  42 tkaLKskrfdklvakdLkrwqkqg 65 
                                    +k+LK+ ++d l++++L +  +q 
  gene436|gene436|rna436|rna436 251 SKSLKKTKYDELIQDELIKKKQQW 274
                                    689*************98776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (419 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1104  (0.0615762); expected 358.6 (0.02)
Passed bias filter:                      649  (0.0361983); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.47
# Mc/sec: 2675.98
//
Query:       gene437|gene437|rna437|rna437  [L=93]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       587  (0.0327403); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.47
# Mc/sec: 594.93
//
Query:       gene438|gene438|rna438|rna438  [L=56]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (56 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       557  (0.031067); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 397.64
//
Query:       gene439|gene439|rna439|rna439  [L=90]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       427  (0.0238162); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.27s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 661.04
//
Query:       gene44|gene44|rna44|rna44  [L=636]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      3e-79  266.4   0.0    5.5e-79  265.5   0.0    1.4  1  Transketolase_N  Transketolase, thiamine diphosphate binding 
    4.2e-35  121.0   0.0    1.2e-33  116.3   0.0    2.4  3  Transket_pyr     Transketolase, pyrimidine binding domain
    2.3e-07   30.7   0.0    7.5e-07   29.1   0.0    1.8  1  Transketolase_C  Transketolase, C-terminal domain
    1.2e-05   24.5   0.0      2e-05   23.7   0.0    1.3  1  E1_dh            Dehydrogenase E1 component
     0.0017   18.1   0.0     0.0034   17.2   0.0    1.4  1  TPP_enzyme_C     Thiamine pyrophosphate enzyme, C-terminal TP
  ------ inclusion threshold ------
      0.098   11.8   0.0       0.18   11.0   0.0    1.4  1  DXP_synthase_N   1-deoxy-D-xylulose-5-phosphate synthase


Domain annotation for each model (and alignments):
>> Transketolase_N  Transketolase, thiamine diphosphate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  265.5   0.0   1.8e-82   5.5e-79       2     304 ..       7     287 ..       6     312 .. 0.93

  Alignments for each domain:
  == domain 1  score: 265.5 bits;  conditional E-value: 1.8e-82
                                HHHHHHHHHHHHHHHHHHHT-S--HHHHHHHHHHHHHHHHT--B-TTBTT-TTS-EEEESSGGGHHHHHHHHHHTTSS--HHHH CS
            Transketolase_N   2 dkkavnaiRvLavDavekaksGhPGaplgladiaevlfkkllkhnPndpkwidRDRfvLsnGhaslllYsllhLtGydlsledl 85 
                                d+k+v+ +R L    v++a+sGhPG+pl+l +  +vl+ k+l+ + ++ ++ +RD f++snGha++++Y++l+L G  l++edl
  gene44|gene44|rna44|rna44   7 DEKIVQNVRYLCAQVVQRANSGHPGTPLALTPFMHVLYGKILRIHSKKLDHPNRDIFIMSNGHACVIQYVMLVLHGI-LKMEDL 89 
                                6899************************************************************************8.9***** PP

                                TTTTSTT-SS-SS--TTTSTT--S---STTHHHHHHHHHHHHHHHHHHHH-BTTB-S----EEEEEEHHHHHSHHHHHHHHHHH CS
            Transketolase_N  86 ksfrqlgsktpGhPelghtagvevttGPLGqGianavglalaektlaatynkpgfdivdhytyvilgDgclmeGvsseasslag 169
                                ++frqlgsktpGhPe+  t+gve+ttGPLGqG+anavg ++   ++ ++           ++yvi gDgc +eG+s+ea sla+
  gene44|gene44|rna44|rna44  90 ENFRQLGSKTPGHPEI-FTDGVEATTGPLGQGLANAVGYSISIMKIRSK----------AKVYVIFGDGCYQEGISHEAFSLAS 162
                                ***************6.588********************998777655..........469********************** PP

                                HTT-TTEEEEEEESSEETTEEGGGT--S-HHHHHHHTT-EEEEETTTT-HHHHHHHHHHHHH-TTS-EEEEEE--TTTTSTTTT CS
            Transketolase_N 170 tlkLgkLivlyDdnkisidGeteisftedvakrfeaygWhvievedgedveaikaaieeakaekdkPsliklrtviGygspaka 253
                                +l L ++  +yD+n+++idG+te s+++d   rf++y++++ e  +ged+ +i++ +   k e +kP li lrt i  g   + 
  gene44|gene44|rna44|rna44 163 HLVLKNITFIYDSNNVTIDGSTELSMSDDPVLRFRSYDFEIYE-VNGEDLFEIERVL---KIEPKKPKLIILRTRIAEGC-SRV 241
                                *****************************************99.6799******988...577889**************.99* PP

                                TSGGGTSS---HHHHHHHHHHTTS-TT-TS---HHHHHHHHHHHHHHHHHH CS
            Transketolase_N 254 gtedvhGapLgedevaalkkklGfdpeksfevpeevydaykekvaegakae 304
                                g  ++hGapLg++ v++lk+ +G      fe+ + v + y+e   +++++ 
  gene44|gene44|rna44|rna44 242 GDFKTHGAPLGQAVVDELKNGFG-----DFELDDSVLKFYDEARLKNQRLF 287
                                ******************99776.....58999999999998888777654 PP

>> Transket_pyr  Transketolase, pyrimidine binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0     0.054   1.6e+02      64     134 ..     124     195 ..     120     230 .. 0.85
   2 !  116.3   0.0     4e-37   1.2e-33       2     176 ..     325     495 ..     324     496 .. 0.91
   3 ?   -3.7   0.0       2.8   8.3e+03     100     137 ..     578     615 ..     556     615 .. 0.70

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.054
                                HHHHHHHCTTEEEEEEEEHHHHGGG.HHGGHHHHHCHHHHHT--EEEEESBSGGGSTTGTTTSBSSHHHHHH CS
               Transket_pyr  64 avGaalagpllviveaqFgdFangA.qiyadqairsgeakgklkvgvvtrlpigvgedGpehqsaeleaflr 134
                                avG++++  + +     ++ F +g+ q  ++   +s++++  lk + ++ ++  v  dG +  s+++  +lr
  gene44|gene44|rna44|rna44 124 AVGYSISIMKIRSKAKVYVIFGDGCyQEGISHEAFSLASHLVLKNITFIYDSNNVTIDGSTELSMSDDPVLR 195
                                6666666655555666899999999977777777779************************99999887776 PP

  == domain 2  score: 116.3 bits;  conditional E-value: 4e-37
                                EEEHHHHHHHHHHHHHCTTTTEEEEESSTHHHHTTCHCCHHEGGT...TEGEEE--S-HHHHHHHHHHHHHHCTTEEEEEEEEH CS
               Transket_pyr   2 kiawrkaeaealaellkedpevvligaDvaggtfsvrkgllhdqg...egrvidsgisEqavlgfavGaalagpllviveaqFg 82 
                                k+a+r+ + + l+e + e  ++++++ D++ +t++  +   ++ +   +g++i++gi+E+a+ ++ +G  ++g +++ ++ +F+
  gene44|gene44|rna44|rna44 325 KMATREHIPHILDEFG-EVFRIIGGSGDLTPSTLTRNETDIDFTKnnrNGTYIRFGIREHAMFAIQNGVTAHG-YYRAFGSTFL 406
                                5666666666666655.5689**********************99999*************************.8********* PP

                                HHHGGGHHGGHHHHHCHHHHHT--EE.EEESBSGGGSTTGTTTSBSSHHHHHHTSTTEEEE--SSHHHHHHHHHHHHHSSS.SE CS
               Transket_pyr  83 dFangAqiyadqairsgeakgklkvg.vvtrlpigvgedGpehqsaeleaflrlipglkvvrPsdpaetkhllrrairredrkP 165
                                +F++    y ++a+r ++a+++++ + ++t+++ig+gedGp+hq++e++ +lr++p+l+v+rP+d  e + ++  a++r+ + P
  gene44|gene44|rna44|rna44 407 NFIS----YGFPAVR-LAALSRIPNIyLMTHDSIGLGEDGPTHQPIEILPLLRATPNLYVFRPCDGLESRFAFWFAATRR-SSP 484
                                ****....*******.**************************************************99876666666654.57* PP

                                EEEEE-SSEEC CS
               Transket_pyr 166 vvlrlpksllr 176
                                +v+ +++++++
  gene44|gene44|rna44|rna44 485 TVISFTRQKVP 495
                                ********987 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 2.8
                                HHHHT--EEEEESBSGGGSTTGTTTSBSSHHHHHHTST CS
               Transket_pyr 100 eakgklkvgvvtrlpigvgedGpehqsaeleaflrlip 137
                                ea + +    + + +ig++e G + ++  l+ ++ l+p
  gene44|gene44|rna44|rna44 578 EAASTFGWSRYAHYSIGIDEFGHSAKAEDLYDHFGLVP 615
                                55555555556788888888888888888888877766 PP

>> Transketolase_C  Transketolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1   0.0   2.5e-10   7.5e-07       8     123 ..     516     617 ..     510     618 .. 0.85

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 2.5e-10
                                TTSSEEEEEETTHHHHHHHHHHHHHTTTTCEEEEE-SEEESHHHHHHHHHHHHHSEEEEEEEEESTTSHHHHHHHHHHHCCCTT CS
            Transketolase_C   8 egkdvtlvayGsmveealeAaeeLekegisaeVvdlrtvkplDketilesvkktgrlvvveeavkrgGigsevaaalaeeafdg 91 
                                +++++t++a Gs+v+ ale a  L +++i + Vv+  +++ + ++ ++       +  v++++++ ++++++ +         g
  gene44|gene44|rna44|rna44 516 DNSQITILASGSEVSIALETAVLLGSRNIPTAVVSFLSFELFEEQSLD------YKETVLHDGMR-VSLEAASTF--------G 584
                                5899*******************************************9......77778899888.666555444........4 PP

                                CSSEEEEEEE-SS.SSSSGHHHHHHHTT-SHHH CS
            Transketolase_C  92 ldapvkrvggpdv.iepgsaeelekafgldaek 123
                                + ++ +   g d+ + +++ae+l+++fgl ++k
  gene44|gene44|rna44|rna44 585 WSRYAHYSIGIDEfGHSAKAEDLYDHFGLVPCK 617
                                45588888888888999***********98876 PP

>> E1_dh  Dehydrogenase E1 component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.0   6.8e-09     2e-05      66     205 ..      80     219 ..      45     223 .. 0.67

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 6.8e-09
                                HHHHHHHHTT-TTTSSGTT-.-E..BTT..BEEE-SSTTTHHHHHHHHHHHHH.......HHTS---EEEEEEGGGTT-HHHHH CS
                      E1_dh  66 leeilaeltgkvkgkggsrhelmyaekesrilggngivgaqvplvaGialaak.......iegkkevailliGDgAanqGdvye 142
                                l+ il+  + +   ++gs+ +++  ++    ++     ++  pl++G+a a         i+ k +v  +++GDg   +G+ +e
  gene44|gene44|rna44|rna44  80 LHGILKMEDLENFRQLGSKTPGH--PEI---FTDGVE-ATTGPLGQGLANAVGysisimkIRSKAKV-YVIFGDGCYQEGISHE 156
                                44444444444445666666666..333...322222.33336777777766655665546666555.6799************ PP

                                HHHHHHHTT--EEEEE.EEESEETTEEHHHH-S---GGG..TTTTS-EEEEETTSHHHHHHHHH CS
                      E1_dh 143 alnlaalwklpvifvv.eNNkygisTeaekasaskeladrargvgipglrVdgnDplavyeAvk 205
                                a+ la+   l  i ++   N+  i  ++e +  s++++ r r +   + +V+g+D +++  + k
  gene44|gene44|rna44|rna44 157 AFSLASHLVLKNITFIyDSNNVTIDGSTELS-MSDDPVLRFRSYDFEIYEVNGEDLFEIERVLK 219
                                *****99988886555256666666655554.467778889****************9998877 PP

>> TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   1.1e-06    0.0034      24      64 ..     111     155 ..      93     188 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.1e-06
                                ETTTS-TTTHHHHHHHHHH....HSTTSEEEEEEEHHHHHHTGGG CS
               TPP_enzyme_C  24 sgglgtmGyglpaAiGakl....akpdrevvaivGDGgflmilqe 64 
                                ++++g +G gl+ A+G ++     + +++v++i GDG+++  +++
  gene44|gene44|rna44|rna44 111 EATTGPLGQGLANAVGYSIsimkIRSKAKVYVIFGDGCYQEGISH 155
                                6689***************765426689***********987432 PP

>> DXP_synthase_N  1-deoxy-D-xylulose-5-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0     6e-05      0.18     114     176 ..     118     181 ..      48     188 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 6e-05
             DXP_synthase_N 114 stsisaalGlavardlkgekkkvvaviGDgaltgGmafealnnigel.kkkllvilNdNemsis 176
                                +  ++ a+G +++  +  +k kv  + GDg    G+++ea+  +++l  k++  i+  N+ +i+
  gene44|gene44|rna44|rna44 118 GQGLANAVGYSISIMKIRSKAKVYVIFGDGCYQEGISHEAFSLASHLvLKNITFIYDSNNVTID 181
                                55677888888888888889999999******************99846889999999998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (636 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       449  (0.0250432); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.60u 0.26s 00:00:00.86 Elapsed: 00:00:00.43
# Mc/sec: 4422.95
//
Query:       gene440|gene440|rna440|rna440  [L=76]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.072   13.3   0.0      0.091   13.0   0.0    1.2  1  ASH       Abnormal spindle-like microcephaly-assoc'd, ASPM-SP


Domain annotation for each model (and alignments):
>> ASH  Abnormal spindle-like microcephaly-assoc'd, ASPM-SPD-2-Hydin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   5.1e-06     0.091      32      72 ..      28      66 ..      16      68 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 5.1e-06
                                   ESS-SS--EEEEEEEE--XXXXXXXXXXXXXXXXXXXXXXX CS
                            ASH 32 eNpseepaevkvskvpaaekgfsveetelevqpgesvtltv 72
                                   +Np+  ++e+ ++++   + +fsv+ ++ e+qp+ s+ l++
  gene440|gene440|rna440|rna440 28 DNPTMCNTEILYERIR--TLKFSVDYRNNELQPKRSIDLCL 66
                                   79999999******99..9******************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       428  (0.0238719); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.28s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 529.16
//
Query:       gene441|gene441|rna441|rna441  [L=41]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (41 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       123  (0.00686039); expected 358.6 (0.02)
Passed bias filter:                       98  (0.005466); expected 358.6 (0.02)
Passed Vit filter:                         5  (0.000278878); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.32u 0.23s 00:00:00.55 Elapsed: 00:00:00.39
# Mc/sec: 317.54
//
Query:       gene442|gene442|rna442|rna442  [L=68]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (68 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       265  (0.0147805); expected 358.6 (0.02)
Passed bias filter:                      234  (0.0130515); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.26s 00:00:00.61 Elapsed: 00:00:00.41
# Mc/sec: 499.24
//
Query:       gene443|gene443|rna443|rna443  [L=459]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-12   46.7  18.7    2.9e-12   46.3  18.7    1.1  1  B56       Protein phosphatase 2A regulatory B subunit (B56 fa


Domain annotation for each model (and alignments):
>> B56  Protein phosphatase 2A regulatory B subunit (B56 family)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.3  18.7   1.6e-16   2.9e-12     111     395 ..     126     409 ..      89     424 .. 0.93

  Alignments for each domain:
  == domain 1  score: 46.3 bits;  conditional E-value: 1.6e-16
                            B56 111 HlqlvYeillrfvespefdakvakkyidqsFvlkllelfdseDprERdylktilhriygkfldlrsfirkainniflrfi 190
                                     l++  ei+ r++ s++ +++v+k  ++++ + +++  +++   + R ++ ++++ +  k +++r  + + i+n ++ +i
  gene443|gene443|rna443|rna443 126 LLEYAIEIFRRYLGSQKCSITVLKSAFEEREIENFFAKIKTVTVKARIMIVRCVQILLLKAVEYRYLLKNCIYNELVYYI 205
                                    57778899************************************************************************ PP

                            B56 191 yeterhngiaelLeilgsiingfalplkeehkkflervllpLhkvkslslyhqqLaycvvqfiekdpklaeevikgllky 270
                                    ++ ++ ++i  lL+i+  ++ +      +e + fl + +lpL ++++   y ++ + +++ ++    + ++ v++   k+
  gene443|gene443|rna443|rna443 206 ENGKNLKCIDVLLDICAFYVLKDIYHDMHELRYFLINYVLPLFTNSNAFCYRDDVILLFTSICYCSDSFMDMVFTHFSKI 285
                                    ****************99998888888999999*********************************************** PP

                            B56 271 WPitnsqKevlFLneleeileviepeefqkilkplfkrlakcissphfqVaeralylwnnekivnlisenseeilpilfp 350
                                    +  tn++ + l ++   ++l+  ++ ++   +  + + +   ++ ++      +  l++ + +   +++n ++ lp++f+
  gene443|gene443|rna443|rna443 286 FFETNTPTKTLIMEITLKVLNE-KCRDMYPYIPMITEFINFALKEQNSALIVIMKLLFSLPVLFLSLKRNIAHFLPLIFT 364
                                    *******999998888888776.788888999************************************************ PP

                            B56 351 aleknskkHWnktvrglalnvlkllmeldpelfdecaakykeeke 395
                                    +l+k+sk+ Wn + r + +++++ +m +d++lfd c  +y++e+ 
  gene443|gene443|rna443|rna443 365 NLYKTSKNYWNVEERCVLYEIISNIMIIDKDLFDWCLMNYNKERY 409
                                    ****************************************99874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (459 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       786  (0.0438396); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 3140.05
//
Query:       gene444|gene444|rna444|rna444  [L=109]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.012   15.1   1.1       0.02   14.3   0.7    1.5  2  DUF1919   Domain of unknown function (DUF1919)


Domain annotation for each model (and alignments):
>> DUF1919  Domain of unknown function (DUF1919)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.7   1.1e-06      0.02      49      95 ..       6      53 ..       1      60 [. 0.88
   2 ?   -1.4   0.0     0.075   1.3e+03     140     165 ..      67      92 ..      54     104 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.1e-06
                                   SEE--HHHHHHHHHS.HHHHHCS--E.ECE--BGG-EEEESCEEEEES CS
                        DUF1919 49 nLyleskdyikflkn.ldyyleqelvfieeeeskYpvgklddieihfl 95
                                   nL l+++++i++l+n  + y++ ++  i+e +++Y   ++++ +i+f 
  gene444|gene444|rna444|rna444  6 NLNLTEHEFIEYLENeCKEYIRSQILRIDEDKHAYLDDSIHNERIFFH 53
                                   99***********975799**********************9999884 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.075
                                    SS-SSEEEE-SS--S.STTEE--HHH CS
                        DUF1919 140 LpyknKviftakeypelkSavyikgf 165
                                    L+ k+ v +  ++y+ ++  +yi g+
  gene444|gene444|rna444|rna444  67 LESKHGVTIEIRNYDRYTECMYITGR 92 
                                    55566666666677766666666654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       534  (0.0297841); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 775.69
//
Query:       gene445|gene445|rna445|rna445  [L=124]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.1e-06   27.4   4.5    6.6e-06   26.4   4.5    1.4  1  Ribosomal_L27e  Ribosomal L27e protein family
  ------ inclusion threshold ------
      0.015   15.6   0.1      0.027   14.8   0.1    1.4  1  DUF4160         Domain of unknown function (DUF4160)
      0.093   12.7   0.3       0.28   11.2   0.0    1.9  2  KOW             KOW motif


Domain annotation for each model (and alignments):
>> Ribosomal_L27e  Ribosomal L27e protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4   4.5   1.1e-09   6.6e-06       8      83 ..      47     121 ..      42     122 .. 0.83

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 1.1e-09
                 Ribosomal_L27e   8 kkkiakrskikpFvKvvnynhlmpTRYtvdvedlkelvkkealkdpakrkeakkevkkkfeeryksgknkwffkkL 83 
                                    ++k + +++  +F+K +n  h+++T +  +v dl+    +++++d++ ++++ k++++ +e+r + ++ +w+ k L
  gene445|gene445|rna445|rna445  47 RNKNRNNKSATMFIKRMNPMHVLATEHVANV-DLSVEDVEKVFADMKYKRDTLKTIEQLIEKRADDRNVQWMKKSL 121
                                    345556667889***************7777.4444444569*************************9****9877 PP

>> DUF4160  Domain of unknown function (DUF4160)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.1   4.5e-06     0.027      11      65 ..      61     116 ..      56     117 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 4.5e-06
                        DUF4160  11 kdheppHvHvkyggdeakiwl..edve.llegsglpkkelklieewveehqeellekW 65 
                                    k+ +p+Hv +   ++ a ++l  edve + +  ++++ +lk ie+++e++ ++   +W
  gene445|gene445|rna445|rna445  61 KRMNPMHVLA--TEHVANVDLsvEDVEkVFADMKYKRDTLKTIEQLIEKRADDRNVQW 116
                                    4589*****9..66678888888555415566689***************99877777 PP

>> KOW  KOW motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   4.7e-05      0.28       5      26 ..      14      35 ..      13      40 .. 0.88
   2 ?   -1.8   0.2      0.58   3.5e+03      22      32 .]      77      90 ..      74      90 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 4.7e-05
                                   EEESSSTTTTCEEEEEEEETTT CS
                            KOW  5 VkVvsGphkGktGkVvkvdqhk 26
                                   V+ ++G+ + ++++V++v ++ 
  gene445|gene445|rna445|rna445 14 VILTRGRQASRKAVVLEVLEDE 35
                                   899***************9886 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.58
                                   EETTT...TEEEEE CS
                            KOW 22 vdqhk...vrVfvd 32
                                   vd  +   ++Vf+d
  gene445|gene445|rna445|rna445 77 VDLSVedvEKVFAD 90
                                   55555554678876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1199  (0.0668749); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 875.73
//
Query:       gene446|gene446|rna446|rna446  [L=963]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (963 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       607  (0.0338558); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.83u 0.33s 00:00:01.15 Elapsed: 00:00:00.57
# Mc/sec: 5065.85
//
Query:       gene447|gene447|rna447|rna447  [L=42]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (42 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       288  (0.0160634); expected 358.6 (0.02)
Passed bias filter:                      190  (0.0105974); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.26s 00:00:00.60 Elapsed: 00:00:00.42
# Mc/sec: 302.26
//
Query:       gene448|gene448|rna448|rna448  [L=67]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (67 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       197  (0.0109878); expected 358.6 (0.02)
Passed bias filter:                      115  (0.00641419); expected 358.6 (0.02)
Passed Vit filter:                         7  (0.000390429); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.25s 00:00:00.59 Elapsed: 00:00:00.41
# Mc/sec: 493.79
//
Query:       gene449|gene449|rna449|rna449  [L=45]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (45 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       180  (0.0100396); expected 358.6 (0.02)
Passed bias filter:                      139  (0.0077528); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.32u 0.27s 00:00:00.59 Elapsed: 00:00:00.40
# Mc/sec: 335.51
//
Query:       gene45|gene45|rna45|rna45  [L=362]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
       0.84   10.0   3.8       0.84   10.0   1.8    1.9  2  Flagellin_C  Bacterial flagellin C-terminal helical region


Domain annotation for each model (and alignments):
>> Flagellin_C  Bacterial flagellin C-terminal helical region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   1.8   4.7e-05      0.84      22      54 ..     277     309 ..     272     320 .. 0.87
   2 ?   -0.5   0.1     0.091   1.6e+03      26      48 ..     315     337 ..     309     355 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 4.7e-05
                                HHHHHHHHHHHHHHHCHHHHHHCHHCCHHHHHH CS
                Flagellin_C  22 qnRlesaitnlkaqsenlkaaesrledvDpaee 54 
                                q++++sa+++++ +se  + + s+++d D+a+ 
  gene45|gene45|rna45|rna45 277 QEKFQSANSEMDSMSESNTVRLSDIQDMDTADI 309
                                99****************************974 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.091
                                HHHHHHHHHHHCHHHHHHCHHCC CS
                Flagellin_C  26 esaitnlkaqsenlkaaesrled 48 
                                e++++  k+ ++n+ka+++++ +
  gene45|gene45|rna45|rna45 315 EKTTKTPKTPKKNTKAKQKDITE 337
                                77888888899999999999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (362 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2046  (0.114117); expected 358.6 (0.02)
Passed bias filter:                      466  (0.0259914); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 2374.59
//
Query:       gene450|gene450|rna450|rna450  [L=60]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (60 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.47
# Mc/sec: 379.90
//
Query:       gene451|gene451|rna451|rna451  [L=81]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (81 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       756  (0.0421663); expected 358.6 (0.02)
Passed bias filter:                      241  (0.0134419); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 583.78
//
Query:       gene452|gene452|rna452|rna452  [L=161]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-46  158.5   2.0    1.3e-46  158.2   2.0    1.1  1  Ribosomal_S8e  Ribosomal protein S8e


Domain annotation for each model (and alignments):
>> Ribosomal_S8e  Ribosomal protein S8e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  158.2   2.0   7.1e-51   1.3e-46       1     137 []       1     143 [.       1     143 [. 0.96

  Alignments for each domain:
  == domain 1  score: 158.2 bits;  conditional E-value: 7.1e-51
                                    XXXBXXCCCSEESSTEEXXXSSXXXCCSBXXXXXXXEESSHEEEEEEETTCEEEEEEESESEEEEEETTTTEEEEEEEEE CS
                  Ribosomal_S8e   1 mgisrdskhkrkltGgkakllrkkrkielgrkekatklgaervkvvrvrgGkrkkralrlkkanvthpeekvtkklkIlg 80 
                                    mgisr++ hkrk+tGgk++ ++kkrk++ gr++++tk+g ++vk +rvrgG++k+ralrl+++++t +++++tk + I++
  gene452|gene452|rna452|rna452   1 MGISRSNAHKRKATGGKKRTHEKKRKHNSGRAPSNTKIGPTKVKAMRVRGGNIKRRALRLNSGSFTCKSHNITKPCAIVQ 80 
                                    99****************************************************************************** PP

                                    EECSSSTCHHHHTTC--TTEEEEEESHH......HHHHHHTTEEEEEEESEHHHHSSEEEEEE CS
                  Ribosomal_S8e  81 VkknpsnneyvrlgvltKgaiievdvse......LgevtqsgkvvAqvtsrPgqdGcvnavlL 137
                                    V+++p+nne++r+++lt++ai++vd +        +e +++g  +A++tsrPgqdG+++++lL
  gene452|gene452|rna452|rna452  81 VMYHPTNNELMRTNTLTRSAIVKVDGTGfkevlgGEEGFKEGAYYARITSRPGQDGVADGYLL 143
                                    **************************9966665556778999999*****************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       584  (0.0325729); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1232.41
//
Query:       gene454|gene454|rna454|rna454  [L=245]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    0.00078   19.4   1.8     0.0031   17.4   1.8    1.8  1  BPL_LplA_LipB  Biotin/lipoate A/B protein ligase family


Domain annotation for each model (and alignments):
>> BPL_LplA_LipB  Biotin/lipoate A/B protein ligase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   1.8   1.7e-07    0.0031       3     131 .]       7     121 ..       5     124 .. 0.64

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.7e-07
                                    EEES-HHHHHH..GCGGG--TT-EEEEE..EESS-B....-B--B-TTSEEEEEEEEESS...-CCGTHHHHHHHHHHHH CS
                  BPL_LplA_LipB   3 evikstntllkeslnsselesgglvvvr..rqtgGr....nvwhspkgeltyslllspeqktfqnrvlelyvsllvlavl 76 
                                    + i+st    k  +ns++++++++ v+    qt G      +w+s   +l++s ++ +   +++  v+ ++ ++lv +++
  gene454|gene454|rna454|rna454   7 KTISST---QKHLINSTSTYKDTYPVIAtmHQTRGVgrtnSTWQSLIHTLSFSYVTHAHVAYID--VIGRVRHVLVDQGV 81 
                                    566666...4445566666666655543125777777787888887777777777775554444..44444555555555 PP

                                    HHH......HHTT-TTEEEETTTEEEE....TTEEEEEEEEEEEETTS-EEEEEEEEEE CS
                  BPL_LplA_LipB  77 ealgyrdskpgiegipvfikwpnDlyv....ngrKlaGiavtstrgktlhhivigvgvn 131
                                    +al                kwpnD++v    ++ K+ G ++ ++ +    + v+gvgvn
  gene454|gene454|rna454|rna454  82 DAL---------------CKWPNDVLVrngeTYHKVCGALIDVIGE----YAVVGVGVN 121
                                    555...............55**********************9994....444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       609  (0.0339673); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.63u 0.33s 00:00:00.96 Elapsed: 00:00:00.57
# Mc/sec: 1293.25
//
Query:       gene455|gene455|rna455|rna455  [L=110]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0075   16.3   0.1      0.011   15.7   0.1    1.3  1  Ac76           Orf76 (Ac76)
     0.0089   16.0   0.1      0.011   15.6   0.1    1.2  1  Hum_adeno_E3A  Human adenovirus early E3A glycoprotein
  ------ inclusion threshold ------
       0.03   14.6   0.8       0.03   14.6   0.8    1.5  2  Orf78          Orf78 (ac78)
      0.034   13.1   0.1      0.039   12.9   0.1    1.0  1  Serinc         Serine incorporator (Serinc)
      0.036   13.7   0.6      0.048   13.3   0.6    1.3  1  UL45           UL45 protein, carbohydrate-binding C-type lect
        2.5    7.9  10.9       0.39   10.5   7.0    1.7  2  Adeno_E3_CR2   Adenovirus E3 region protein CR2


Domain annotation for each model (and alignments):
>> Ac76  Orf76 (Ac76)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.1   3.8e-06     0.011      24      63 ..      35      74 ..      29      89 .. 0.66

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 3.8e-06
                           Ac76 24 sellltllllfvlFiillnvyyikteStpadlytekakki 63
                                    ++++++ +l+ +Fii++ +yy+    t + +  +++  +
  gene455|gene455|rna455|rna455 35 MHMFIYMGVLLTVFIIIMCMYYACIRETQDAVIIQNVAYT 74
                                   579*******************855444444444333333 PP

>> Hum_adeno_E3A  Human adenovirus early E3A glycoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1   3.8e-06     0.011       9      64 ..       5      61 ..       2      86 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 3.8e-06
                  Hum_adeno_E3A  9 tvdtvnstatgltsaldlpqvsafvndwasldmwwfsialmfvcliimwli.cclkr 64
                                   t  t+n ta   t    +pq +  +    ++ m+ +   l+ v +iim +  +c++ 
  gene455|gene455|rna455|rna455  5 TRTTMNDTAHTTTNNTTIPQTRGNISFEVDMHMFIYMGVLLTVFIIIMCMYyACIRE 61
                                   5568899*******************99******99999999999998765134433 PP

>> Orf78  Orf78 (ac78)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.8     1e-05      0.03      40      97 ..      11      68 ..       3      74 .. 0.64
   2 ?   -2.9   0.0       2.8   8.4e+03      31      34 ..      92      95 ..      80     106 .. 0.51

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1e-05
                          Orf78 40 kksaaeknditekesnaaekaqalnillisllavvcvlvllyviyYfvilrerqkssv 97
                                   +++++++n++t  +++ + + ++   ++i++ ++++v+++++ +yY  i   ++  + 
  gene455|gene455|rna455|rna455 11 DTAHTTTNNTTIPQTRGNISFEVDMHMFIYMGVLLTVFIIIMCMYYACIRETQDAVII 68
                                   333444444444444445666677788999999999*****99999888666555544 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 2.8
                          Orf78 31 ndka 34
                                   +d++
  gene455|gene455|rna455|rna455 92 DDEQ 95
                                   2222 PP

>> Serinc  Serine incorporator (Serinc)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   1.3e-05     0.039     282     340 ..      19      97 ..       3     109 .. 0.50

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.3e-05
                         Serinc 282 tasv.....................vigliltflcvlYstlraasssqveklralkaaeeegalpesaleeeeeeeeeke 340
                                    ++++                     ++ ++++++c+ Y+++r+++ +   +  a +++++  +  +++ ee++++e+  +
  gene455|gene455|rna455|rna455  19 NTTIpqtrgnisfevdmhmfiymgvLLTVFIIIMCMYYACIRETQDAVIIQNVAYTRERRRPKRLDTVFEEQDDDEQ-PN 97 
                                    222244455555566777788777688889999999*******9994333322222222222222222222222222.22 PP

>> UL45  UL45 protein, carbohydrate-binding C-type lectin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.6   1.6e-05     0.048      44      75 ..      27      58 ..       1      65 [. 0.55

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.6e-05
                           UL45 44 spaaalllil.ggialGvlltvfvivatlvfav 75
                                    +   + + + ++i +Gvlltvf+i++ + +a 
  gene455|gene455|rna455|rna455 27 GNIS-FEVDMhMFIYMGVLLTVFIIIMCMYYAC 58
                                   2222.3444415678************998775 PP

>> Adeno_E3_CR2  Adenovirus E3 region protein CR2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   7.0   0.00013      0.39      10      30 ..      41      60 ..      37      63 .. 0.88
   2 ?   -2.5   0.1       1.6   4.7e+03      28      34 ..      75      81 ..      66      82 .. 0.58

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00013
                   Adeno_E3_CR2 10 vaVvvGlaiIiicmlyYaCcY 30
                                    +V++ + iIi+cm yYaC +
  gene455|gene455|rna455|rna455 41 MGVLLTVFIIIMCM-YYACIR 60
                                   599**********7.9***76 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.6
                   Adeno_E3_CR2 28 CcYrkhr 34
                                     +r+++
  gene455|gene455|rna455|rna455 75 RERRRPK 81
                                   4466665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1003  (0.0559429); expected 358.6 (0.02)
Passed bias filter:                      528  (0.0294495); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.58u 0.35s 00:00:00.93 Elapsed: 00:00:00.55
# Mc/sec: 605.82
//
Query:       gene456|gene456|rna456|rna456  [L=397]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.6e-38  132.2   0.7    2.7e-38  131.5   0.7    1.4  1  DEAD           DEAD/DEAH box helicase
    9.8e-23   80.6   0.7    2.5e-22   79.3   0.3    2.0  2  Helicase_C     Helicase conserved C-terminal domain
    8.4e-06   25.9   0.0    1.4e-05   25.2   0.0    1.4  1  ResIII         Type III restriction enzyme, res subunit
    3.3e-05   23.4   0.1    5.7e-05   22.6   0.1    1.4  1  CMS1           U3-containing 90S pre-ribosomal complex subuni
      0.004   17.4   0.0       0.01   16.1   0.0    1.7  1  AAA_22         AAA domain
  ------ inclusion threshold ------
      0.014   15.0   0.0      0.025   14.1   0.0    1.4  1  UvrD-helicase  UvrD/REP helicase N-terminal domain
      0.017   14.8   0.1       0.03   14.0   0.1    1.4  1  AAA_30         AAA domain
      0.073   12.4   2.2       0.37   10.0   2.2    2.0  1  SecA_DEAD      SecA DEAD-like domain
       0.08   13.4   0.5       0.87   10.0   0.4    2.8  1  AAA            ATPase family associated with various cellular
       0.19   12.0   1.4       0.67   10.3   1.4    2.3  1  AAA_19         AAA domain


Domain annotation for each model (and alignments):
>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  131.5   0.7   1.5e-41   2.7e-38       2     174 ..      50     217 ..      49     219 .. 0.94

  Alignments for each domain:
  == domain 1  score: 131.5 bits;  conditional E-value: 1.5e-41
                                    HHHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHS.TTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD   2 diQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyet.kgktgpkalivePtreLaeqtlnnlkkfkkyidlrvll 80 
                                    ++Q+++ip ++ g d++++a+ G+GKT +f++ +lq++  +  +  + +++ v+ t+e++ q++n++++f++y+dl+v++
  gene456|gene456|rna456|rna456  50 AVQQQVIPKAVLGADIICQAKSGTGKTVVFVLSALQRINAEdVSPARVQVMAVANTKEMVVQIANEFRRFMSYTDLKVEM 129
                                    69************************************877779999********************************* PP

                                    EETTSSHHHHHHHHHTTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHT.TTHHHHHHHHHHSHHHCTTSTTT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD  81 iiggvaardqlskldngvdivvgtpgrlddllstgklnlsqvrflVlDEadrlldq.gfsdfinrilnqlpqitcdgklq 159
                                    ++ggv+ + +++kl+++vd+vvgtpgrl+dl+++g l++s +r+l++DE+d +l++ + + +++ri+ ++       +  
  gene456|gene456|rna456|rna456 130 VFGGVDVNGDVEKLKARVDVVVGTPGRLFDLIQRGALDVSALRILIIDEVDSILSSlSSRWTVQRIIYRT-------PVA 202
                                    **************999***************************************88888899999999.......555 PP

                                    SEEEEEESSBSHHHH CS
                                    xxxxxxxxxxxxxxx RF
                           DEAD 160 rqvivlSATlpkdvk 174
                                    +q+++++ATl++++k
  gene456|gene456|rna456|rna456 203 KQTMLFTATLSNEMK 217
                                    67********97776 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       3.8   6.8e+03      16      25 ..      73      82 ..      64     126 .. 0.58
   2 !   79.3   0.3   1.4e-25   2.5e-22       2     110 ..     255     363 ..     254     364 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 3.8
                                   TSEEEEEESS CS
                     Helicase_C 16 ggkilifvnt 25
                                   +gk+++fv +
  gene456|gene456|rna456|rna456 73 TGKTVVFVLS 82
                                   5555555543 PP

  == domain 2  score: 79.3 bits;  conditional E-value: 1.4e-25
                                    HHHHHHHHHHHTTTTSEEEEEESSHHHHHH.HHHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSS CS
                     Helicase_C   2 kleallellkleeeggkilifvntidrlek.vklllekkgikvavlhgelpqnereeileqfnkgesdvLiatdvaerGi 80 
                                    k ++l+ l+++ ++ ++++if++ ++r+e  ++ l ++kg+ +++++++  +ner + + +f++ ++++L++t+ ++rGi
  gene456|gene456|rna456|rna456 255 KRDKLIGLIDSIRDISQCVIFCRDKRRVEVlCEHL-KTKGLPAVAITSDYDTNERMQRFMSFKNLNYRFLVTTNLMARGI 333
                                    5667777888889999************7666666.6779**************************************** PP

                                    TSTTESEEEESSSSSSHHHHHHHHTTSSST CS
                     Helicase_C  81 dipkvnlVinfdlprnvtsyiqriGRtgRa 110
                                    di ++nlV+n+d+ ++ ++y +r+GR+gR+
  gene456|gene456|rna456|rna456 334 DIAEINLVVNYDMAEDAQTYLHRVGRAGRF 363
                                    *****************************7 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.0   7.8e-09   1.4e-05      27     169 ..      65     212 ..      33     214 .. 0.78

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 7.8e-09
                                    EEEEESTTSTHHHHHHHHHHHH-S.........-EEEEESSHHHHHHHHHHGGGGTGG.........GEEEESSS-B--. CS
                         ResIII  27 glikmaTGtGKTlvaaklierllkkgkee....kflflvprkslleqtleefkkflseayke.....igkkvsgdkkkak 97 
                                    ++ ++  GtGKT+v +  + +  ++++ +    +++ ++++k+++ q  +ef++f+s ++ +      g +v+gd +k  
  gene456|gene456|rna456|rna456  65 IICQAKSGTGKTVVFVLSALQRINAEDVSparvQVMAVANTKEMVVQIANEFRRFMSYTDLKvemvfGGVDVNGDVEKL- 143
                                    6778899********777777777767668999************************9988876665455577777777. PP

                                    ......-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.T....TTHHHHHT-.--SEEEEEESS- CS
                         ResIII  98 ekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakk....swreilekf.keavllglTATp 169
                                       +   +++v t  +l   +     ++  l+ ++  ++iiDE+  + ++     ++++i+     ++  + +TAT+
  gene456|gene456|rna456|rna456 144 ---KARVDVVVGTPGRLFDLI-----QRGALDVSALRILIIDEVDSILSSLssrwTVQRIIYRTpVAKQTMLFTATL 212
                                    ...8999************99.....7778888888899****9888885245556677644431345566678886 PP

>> CMS1  U3-containing 90S pre-ribosomal complex subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.1   3.2e-08   5.7e-05     153     209 ..     124     178 ..      72     195 .. 0.77

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 3.2e-08
                           CMS1 153 dskvakLFakhikleesvtylkksrigiavGtpgRildLleeeslsvdeLkrivlDa 209
                                    d kv  +F+  + ++ +v  lk +r+ + vGtpgR+ dL++ ++l v+ L+ +++D 
  gene456|gene456|rna456|rna456 124 DLKVEMVFG-GVDVNGDVEKLK-ARVDVVVGTPGRLFDLIQRGALDVSALRILIIDE 178
                                    555666665.366777777776.69******************************95 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   5.8e-06      0.01       8     104 ..      65     184 ..      64     231 .. 0.67

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 5.8e-06
                         AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaee............erpevvfvtlpsst....sskdl.lrellralglelka 70 
                                    +++ + sGtGKT++    + q  ++++               e    + v+++++     s +dl  ++++  ++++++ 
  gene456|gene456|rna456|rna456  65 IICQAKSGTGKTVVFVLSALQRINAEDVSParvqvmavantkE----MVVQIANEFrrfmSYTDLkVEMVFGGVDVNGDV 140
                                    678899********98888887555444444455554432111....233333333334466666666666666655555 PP

                         AAA_22  71 .........erlsseellealeqalraravielliiDEaqh.lr 104
                                               ++  +l++++++ + + ++ ++liiDE++  l+
  gene456|gene456|rna456|rna456 141 eklkarvdvVVGTPGRLFDLIQRGALDVSALRILIIDEVDSiLS 184
                                    99999999988899999999999988888889*********553 PP

>> UvrD-helicase  UvrD/REP helicase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   1.4e-05     0.025       8      67 ..      57     114 ..      50     142 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.4e-05
                                    HHHS-SSEEEEEE-TTSSHHHHHHHHHHHHHHTSSSTGGGEEEEESSHHHHHHHHHHHHH CS
                  UvrD-helicase   8 aiaslggpilveAsAGsGKTfvlaerilrlikeeeiepdrilvvTFTnkAaeElkeRiee 67 
                                    + a lg +i+  A  G+GKT v +   l+ i++e ++p r+ v+   n  ++E+   i++
  gene456|gene456|rna456|rna456  57 PKAVLGADIICQAKSGTGKTVVFVLSALQRINAEDVSPARVQVMAVAN--TKEMVVQIAN 114
                                    33448999999*****************************76665444..5566555555 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   1.7e-05      0.03       4      97 ..      50     179 ..      47     207 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.7e-05
                         AAA_30   4 aeQaaavealltsgdrvavltGpAGtGKt..talkalreaweaag....grviglAptgkaAkvLaeelg.ieastiakl 76 
                                    a Q++++ +++ + d   + ++  GtGKt  ++l+al+++ +++      +v+++A t+++  ++a+e+  + ++t  k+
  gene456|gene456|rna456|rna456  50 AVQQQVIPKAVLGAD--IICQAKSGTGKTvvFVLSALQRINAEDVsparVQVMAVANTKEMVVQIANEFRrFMSYTDLKV 127
                                    568888888888887..899*********4446888888877773588899999******99999975543444444444 PP

                         AAA_30  77 lkrlk...............................grarlepgtllivDEa 97 
                                        +                               g+ ++++ ++li+DE+
  gene456|gene456|rna456|rna456 128 EMVFGgvdvngdveklkarvdvvvgtpgrlfdliqrGALDVSALRILIIDEV 179
                                    4333344555555555566667777777888888776677777788888886 PP

>> SecA_DEAD  SecA DEAD-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   2.2   0.00021      0.37      34     210 ..       2     183 ..       1     187 [. 0.67

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00021
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      SecA_DEAD  34 sdeeLrakteelkerlaegealdellpeaf...alvreaakrvlg.mrhydvQliGglvlhegkiaemkTGEGKtlvatl 109
                                    sdeeL + +e+++++ ++++ + + +pe +    l++ +    l+     + Q+i   vl    i + k G GKt+v +l
  gene456|gene456|rna456|rna456   2 SDEELIEYAETVQTEKTKNTDVISSFPELLlkdELIKAIRDANLEhPSAVQQQVIPKAVLGADIICQAKSGTGKTVVFVL 81 
                                    66777777777776666666655555554411123333333333223456789*************************99 PP

                                    xxx..xxx..xxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      SecA_DEAD 110 pay..lna..ltgkgvhvvtvnd..YLakrdaewmgpvyeflGlsvgviese..leseerreaYeaditYgtnnelgfdy 181
                                    +a+  +na  ++   v+v++v +   +  + a+++++++++  l+v+++     ++ +  + + + d++ gt   l fd 
  gene456|gene456|rna456|rna456  82 SALqrINAedVSPARVQVMAVANtkEMVVQIANEFRRFMSYTDLKVEMVFGGvdVNGDVEKLKARVDVVVGTPGRL-FDL 160
                                    9873334433666778887775412577778899999999999999999887224445555566779999998876.776 PP

                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      SecA_DEAD 182 LrDnlalskeelvqrglnfaivDEvDsvL 210
                                    ++      + +l    l + i+DEvDs+L
  gene456|gene456|rna456|rna456 161 IQ------RGALDVSALRILIIDEVDSIL 183
                                    53......223333568889999999998 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.4   0.00049      0.87      37      74 ..     120     186 ..      65     219 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00049
                                    S............................STTHHHHHHHHHHHHHHHTS....TSEEEEEETGGGHHHHH CS
                            AAA  37 k............................yvgesekkirelfkeakeka....kpsilfiDEidalaksr 74 
                                    +                            +v  ++ ++ +l+++    a    +  il+iDE+d++ +s 
  gene456|gene456|rna456|rna456 120 MsytdlkvemvfggvdvngdveklkarvdVVVGTPGRLFDLIQRG---AldvsALRILIIDEVDSILSSL 186
                                    044444455555555555555555555554555556666666662...22233579**********9887 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   1.4   0.00037      0.67       3      61 ..      54     115 ..      52     387 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00037
                         AAA_19   3 eave.alkekvllvtaGpGtGKTrvlkhivallvelggvkp..eeillvaftgrAakelrer 61 
                                    + +  a+    ++  a  GtGKT v +      +++++v+p   ++++va t+  + +++++
  gene456|gene456|rna456|rna456  54 QVIPkAVLGADIICQAKSGTGKTVVFVLSALQRINAEDVSParVQVMAVANTKEMVVQIANE 115
                                    55533666677888999********9999999999999999333455555555555444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (397 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       729  (0.0406604); expected 358.6 (0.02)
Passed bias filter:                      512  (0.0285571); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.72u 0.35s 00:00:01.06 Elapsed: 00:00:00.55
# Mc/sec: 2179.70
//
Query:       gene457|gene457|rna457|rna457  [L=1748]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   6.5e-104  347.6   0.0   1.2e-103  346.7   0.0    1.5  1  RNA_pol_Rpb1_1  RNA polymerase Rpb1, domain 1
    3.1e-85  285.9   0.4      6e-85  284.9   0.4    1.5  1  RNA_pol_Rpb1_5  RNA polymerase Rpb1, domain 5
    7.1e-71  237.8   0.1    1.3e-70  236.9   0.1    1.5  1  RNA_pol_Rpb1_2  RNA polymerase Rpb1, domain 2
    2.1e-65  219.5   2.3      3e-65  219.0   0.1    2.4  3  RNA_pol_Rpb1_3  RNA polymerase Rpb1, domain 3
    6.3e-34  116.2   6.4    8.6e-34  115.7   0.3    2.9  2  RNA_pol_Rpb1_4  RNA polymerase Rpb1, domain 4
    2.4e-24   85.9   0.9    5.6e-24   84.7   0.9    1.6  1  RNA_pol_Rpb1_7  RNA polymerase Rpb1, domain 7
     0.0049   17.2   9.9     0.0049   17.2   9.9    7.0  7  RNA_pol_Rpb1_R  RNA polymerase Rpb1 C-terminal repeat


Domain annotation for each model (and alignments):
>> RNA_pol_Rpb1_1  RNA polymerase Rpb1, domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  346.7   0.0  4.8e-107  1.2e-103       1     312 []      21     320 ..      21     320 .. 0.97

  Alignments for each domain:
  == domain 1  score: 346.7 bits;  conditional E-value: 4.8e-107
                                    BE---EEEEEE--HHHHHHH-SBB--STTSTCSTSSSSBBSSSSSSSSS-SSSSSTSTTTSSTTTT-----EEEEEECEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 RNA_pol_Rpb1_1   1 ekkikeiqfgiaspeeirkwSvvevtkaetieekslkPeegGllDerlgtidkdleCetCgkkkkeCeghfGhieLakPv 80 
                                    +k+ik+iqfg++sp+e+r+ Svv+++++et++++   P+egGl+D rlgt+++++ C+tCg+++  C ghfGhieL++Pv
  gene457|gene457|rna457|rna457  21 KKRIKSIQFGLFSPQELRASSVVRIDHPETLSNQ--APKEGGLIDLRLGTTERQYLCATCGQSNLTCVGHFGHIELTRPV 98 
                                    589******************************9..8******************************************* PP

                                    E-HHHHHHHHHHCTTCETTTTEBSS-TTSH....HHHHHHCSSSCCCCHHHHHHHHCCS-BE-SSSSB-EEEEEETTEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 RNA_pol_Rpb1_1  81 fhigffklilkilecvckecskllldeekkkllsklkkrekleelkkrlkaieelckkinlcekCgavqpkleeegeklk 160
                                    fh+g++++i+k+le+vc++cs++   + +k               +++l   + lck +++c +C+ +qp ++++g +l 
  gene457|gene457|rna457|rna457  99 FHVGYMNKIKKLLETVCFYCSRIKAYDVHK-----------EGVHRQGLSYFWGLCKGKTQCMHCQSKQPLIKRDGLSLI 167
                                    ***********************8766544...........3556789999***************************** PP

                                    EEESSSST.SCEEEE-HHHHHHHHHCSTHHHHHHTTSBTTTB-GGGCCECCEEE--GGGS-BEESSSSSEEBECCCCHHH CS
                                    xxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 RNA_pol_Rpb1_1 161 aalkkske.eekeklsaekvkkllkriededvevlgfkssgsrPewliltvlPVpPpeiRPsvqldggrrsedDlteklr 239
                                    a ++ +++ e k  l+ e+v++++kri++e++e lgf+++++rPew+i++vl VpPp +RPsv+l+g+ r+edDlt+kl+
  gene457|gene457|rna457|rna457 168 AFIRGEDNtEGKVILNGERVHTVFKRISTEECEALGFDEQYARPEWMIISVLNVPPPAVRPSVVLEGMLRGEDDLTHKLA 247
                                    ****9888577899****************************************************************** PP

                                    HHHHHHHHHHHHHHSSSSSTCHHHHHHHHHHHHHHCC-TTSSSSSEEBSTTSSS--THHHHHTSSSSCCCCCT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 RNA_pol_Rpb1_1 240 diikrNnrLkkaeeegapeliieeekelLQehvatlfdneisglkpatqkskrplkslsqrLkGKeGrfRgnL 312
                                    di+k+N +L k e+egap +ii++ ++lLQ+hvatl+dn+i+gl+++ qks+rplksls+rLkGKeGr+RgnL
  gene457|gene457|rna457|rna457 248 DIVKANANLAKYEREGAPGHIIRDYESLLQYHVATLMDNNIPGLPQSLQKSGRPLKSLSARLKGKEGRVRGNL 320
                                    ************************************************************************9 PP

>> RNA_pol_Rpb1_5  RNA polymerase Rpb1, domain 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  284.9   0.4   2.3e-88     6e-85       1     265 [.     869    1536 ..     869    1538 .. 0.96

  Alignments for each domain:
  == domain 1  score: 284.9 bits;  conditional E-value: 2.3e-88
                                     B--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTEEEETTSEEEETTS-EEESSGGGTS............ CS
                                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............ RF
                 RNA_pol_Rpb1_5    1 GLkvkefffhtmggReGLiDtAvkTaesGYlqRrlvkaledvvvkyddtvrnsggeivqflygedg............ 66  
                                     GL ++efffh+mggReGLiDtAvkTae+GY+qRrl+k++e++ +  d++vr+ + ++v+flyg+dg            
  gene457|gene457|rna457|rna457  869 GLRAHEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKSMENCQIAFDGSVRS-ERDVVSFLYGDDGfdggrverveic 945 
                                     99************************************************75.6799********************* PP

                                     .............................................................................. CS
                                     .............................................................................. RF
                 RNA_pol_Rpb1_5   67 .............................................................................. 66  
                                                                                                                   
  gene457|gene457|rna457|rna457  946 grdyylpfnfervyneftggvvdkgegkvsnidredrvsnidgedrvsnidgedrvsnidgedrvssidrvssidged 1023
                                     ****************************************************************************** PP

                                     .............................................................................. CS
                                     .............................................................................. RF
                 RNA_pol_Rpb1_5   67 .............................................................................. 66  
                                                                                                                   
  gene457|gene457|rna457|rna457 1024 rinirttlspnnpslttnhnpslttitnttipnttipnttipnttinkntvlkdlltfspnrvlsfylklkadklrll 1101
                                     ****************************************************************************** PP

                                     ...................B--TT-BHHHHHHHHHHHHHHCCCSSTTSSTCSSTSSSSSSHHHHHHHHTT-SS-SS-E CS
                                     ...................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 RNA_pol_Rpb1_5   67 ...................lvepGeavGiiaaQSiGePgTQltlnTFHfaGvasknvtlGvprlkeilnvskniksks 125 
                                                        lv pGe+vG++a+QSiGeP+TQ+tlnTFH+aG+as+ +t Gvprlke++nv+k ik++s
  gene457|gene457|rna457|rna457 1102 dlktlirmsnvirekyyraLVCPGEMVGTLASQSIGEPATQMTLNTFHYAGIAST-ITMGVPRLKELINVAKSIKTPS 1178
                                     ****************************************************986.59******************** PP

                                     EEEEB-SSSSSCHHHCHHHHHHHSE..................................................... CS
                                     xxxxxxxxxxxxxxxxxxxxxxxxx..................................................... RF
                 RNA_pol_Rpb1_5  126 ltvllvdeeakelekakkvkkaiek..................................................... 150 
                                     + + l +e+ ++l++a  vk++ie+                                                     
  gene457|gene457|rna457|rna457 1179 MLLTLKKEY-ADLKNANMVKNTIEYkelkhviesiavvydpnvtdtvipedrefvrahylfpdeeradmlspwvlrvk 1255
                                     ***999998.8888889999999999999************************************************* PP

                                     .............................................................................. CS
                                     .............................................................................. RF
                 RNA_pol_Rpb1_5  151 .............................................................................. 150 
                                                                                                                   
  gene457|gene457|rna457|rna457 1256 lsrnrmvrygvtlgmvkamvkqridvevvmtdenaaeyvvrmrmvgecddgrvrkvmdwvvgvriggvkgisrvylle 1333
                                     ****************************************************************************** PP

                                     .............................................................................. CS
                                     .............................................................................. RF
                 RNA_pol_Rpb1_5  151 .............................................................................. 150 
                                                                                                                   
  gene457|gene457|rna457|rna457 1334 degndglvdgaggvdskgsdglvggsdvdgrgidglvggndglvggngaggsdgsidkavdkaiykdkdnnlnhtidn 1411
                                     ****************************************************************************** PP

                                     ............CBTTEEEEEEEEEE.EEEEETEEEEEEECS--HHHHTTSTTTBETTTEEESSHHHHHHHHCHHHHH CS
                                     ............xxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 RNA_pol_Rpb1_5  151 ............gikkikrilvkeae.kgkeeekelvletegvnlsevlkveevvdageilsndiaeileilgieaar 215 
                                                  +++ ++  ++ ++ ++ +++++++l+t+g+nl e+l++e    +++++snd+ e++ +lgieaar
  gene457|gene457|rna457|rna457 1412 ttdntidntidhTTNNTTNNTTNPTTtTNPTTTNRWMLQTSGTNLLEILHNEY---ITDCYSNDLTEVCAVLGIEAAR 1486
                                     *999999966653333333333333323333349*************998888...89******************** PP

                                     HHHHHHHHHHHHHTTS---HHHHHHHHHHHTTTSS---SSTTCHCCSSSH CS
                                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 RNA_pol_Rpb1_5  216 kallkeiqevykvqgvsvndrHlelivdqmtkkgeivavnrsGinkaels 265 
                                     ++l+kei++v++++g++vn+rHl+l+ d+mt +g ++ ++r+G+nk+ +s
  gene457|gene457|rna457|rna457 1487 NVLIKEIKKVIESDGSYVNQRHLMLLGDIMTSTGVLLGITRHGFNKKGSS 1536
                                     *********************************************98765 PP

>> RNA_pol_Rpb1_2  RNA polymerase Rpb1, domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  236.9   0.1   5.2e-74   1.3e-70       1     165 [.     322     484 ..     322     485 .. 0.98

  Alignments for each domain:
  == domain 1  score: 236.9 bits;  conditional E-value: 5.2e-74
                                    SEEESSEEEEEEEEESSS-TTEEEEEHHHHTTSEEEEE-STTTHHHHHHHHHHTTTSSSSEEEEESTTSSEEETTTT-SC CS
                 RNA_pol_Rpb1_2   1 GkrvdysaRsvispdpnlkldevgvPisvakkltvpeivtelnikklrklvengpevyPgasyvkredgsekklkakkrk 80 
                                    Gkrvd+saRsvispd+n++l evgvP ++a+++t+pe vt++n+++l+ lv+ngp+++Pga+ v+redg++ +l+ +  +
  gene457|gene457|rna457|rna457 322 GKRVDFSARSVISPDSNISLCEVGVPEQIARIHTFPEHVTAFNKARLEALVRNGPNKWPGANFVTREDGQRIDLRFN--R 399
                                    9****************************************************************************..5 PP

                                    HHCCTTTTSEEEEE--TTSEEEEE-SSTTSGGGEEEEEEEEESSSSEEEEGGGHCCCT--SSS-EEEEE--SSHHHHHHH CS
                 RNA_pol_Rpb1_2  81 lakelekgdiverhvkdgdvvllNRqPsLhklsimahrvkvlekktlrlnlsvttayNaDFDGDemnlhlpqseearaEa 160
                                     +  l++g++verh++ gdvvl+NRqPsLhk+s+mahr++v+++kt+rlnlsvt++yNaDFDGDemnlh+pqs+++raE+
  gene457|gene457|rna457|rna457 400 NSILLTEGCVVERHMTAGDVVLFNRQPSLHKMSMMAHRARVMKGKTFRLNLSVTSPYNADFDGDEMNLHMPQSHNTRAEL 479
                                    68999*************************************************************************** PP

                                    HHCSB CS
                 RNA_pol_Rpb1_2 161 eelll 165
                                    e+++ 
  gene457|gene457|rna457|rna457 480 ENICG 484
                                    **997 PP

>> RNA_pol_Rpb1_3  RNA polymerase Rpb1, domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  219.0   0.1   1.2e-68     3e-65       1     157 []     488     732 ..     488     732 .. 0.97
   2 ?   -1.9   0.1       1.1   2.9e+03      52     101 ..    1031    1076 ..     992    1117 .. 0.69
   3 ?   -2.7   0.0         2     5e+03      69      74 ..    1419    1424 ..    1382    1490 .. 0.47

  Alignments for each domain:
  == domain 1  score: 219.0 bits;  conditional E-value: 1.2e-68
                                    CSEETTTTEESSS--THHHHHHHHHSSTTEEEEHHHHHHHHHHSSSCC................................ CS
                 RNA_pol_Rpb1_3   1 nilspqsgkPvigivQDsllGvyllTkedvfidreeaqqllykgvgsd................................ 48 
                                    n+ls+q++kPv+givQDsl+Gv+++T+++vfi+++e+q+llyk+vgsd                                
  gene457|gene457|rna457|rna457 488 NVLSCQGNKPVMGIVQDSLVGVRKMTDDGVFIEWYEGQHLLYKVVGSDdrgygnddrvygngndgwgrvdgysgddrgyg 567
                                    8******************************************************************************* PP

                                    ..............................................................S....SSSSSSSSBESSS CS
                 RNA_pol_Rpb1_3  49 ..............................................................s....ktvtlrpailkpk 62 
                                                                                                  +    +t+t+rpa+l+p+
  gene457|gene457|rna457|rna457 568 ygysgedninkgkdsngilinydtthstntytinsniintnpitntntntntintintnpitNanppPTNTVRPAVLRPR 647
                                    ***********************************************99999998887776615688999********** PP

                                    EBEEHHHHHHCCCHCCCCEEEESSSSSTSEEECSSEEEES--SHHHHSSSSTTSHHHHHHHHCHHHHHHHHHHHHHHHHH CS
                 RNA_pol_Rpb1_3  63 elwtgkqtfsrilpneinyerkneekdgkvlikngelikGvidkkvvgkksqgslihvlakeygiketvrfldslqrlgf 142
                                    +l+tgkq+fs++lp +inyer      g+vlik+g+likG+idkkvvg +sqgsl+hvla+e+  k++vrf+dslqr+++
  gene457|gene457|rna457|rna457 648 RLFTGKQMFSCTLP-CINYER------GDVLIKHGILIKGCIDKKVVG-TSQGSLVHVLALEN--KHIVRFFDSLQRVVN 717
                                    **************.******......9********************.**************..*************** PP

                                    HHHHHHCEB-TGGGG CS
                 RNA_pol_Rpb1_3 143 kyllqsgftigigDt 157
                                    +yllq+gft+g+gDt
  gene457|gene457|rna457|rna457 718 GYLLQAGFTMGVGDT 732
                                    **************7 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.1
                                     SSSSSSBESSSEBEEHHHHHHCCCHCCCCEEEESSSSSTSEEECSSEEEE CS
                 RNA_pol_Rpb1_3   52 vtlrpailkpkelwtgkqtfsrilpneinyerkneekdgkvlikngelik 101 
                                     ++++ + l ++ + ++ ++   ++pn+  ++ + +++   + i++++ +k
  gene457|gene457|rna457|rna457 1031 LSPNNPSLTTNHNPSLTTITNTTIPNTTIPNTT-IPN---TTINKNTVLK 1076
                                     555555555655566677777777776666663.332...3444444433 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 2
                                     HHHHCC CS
                 RNA_pol_Rpb1_3   69 qtfsri 74  
                                     +t+  +
  gene457|gene457|rna457|rna457 1419 NTIDHT 1424
                                     222222 PP

>> RNA_pol_Rpb1_4  RNA polymerase Rpb1, domain 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.7   0.3   3.4e-37   8.6e-34       5     108 .]     760     862 ..     757     862 .. 0.96
   2 ?    1.8   1.4     0.087   2.2e+02       3      58 ..    1399    1453 ..    1397    1454 .. 0.75

  Alignments for each domain:
  == domain 1  score: 115.7 bits;  conditional E-value: 3.4e-37
                                    CTHTCCHHHTTHCHHHHHHHHHHHHHHHHHHHHHHHHHHCSTTTSHHHHHHHCTSSS-HHHHHHHHTB-EEEEBTTBSS- CS
                 RNA_pol_Rpb1_4   5 erygkledlpgksleelfeakinkilnkardkagkiaskslaasNsiliMvksGaKGsiinisqiagclGqqnvegkrip 84 
                                     r+g l ++pg++l+e+fe++i+++ln+ard +g++a+  l + N++ +Mv +G+KGs inisq+++c+Gqqnveg+ri 
  gene457|gene457|rna457|rna457 760 ARSGTLRRMPGMNLRETFESRISQALNRARDVSGSSANAGLGTANNVRMMVMAGSKGSLINISQMTACVGQQNVEGHRIA 839
                                    455999************************************66************************************ PP

                                    -SSTSCSSTTSSSSESSTTTSSEE CS
                 RNA_pol_Rpb1_4  85 kgfsgrtlphfkkidespesrGFv 108
                                    +  ++rtlphf+k+d++p srGFv
  gene457|gene457|rna457|rna457 840 FS-NQRTLPHFHKDDDRPASRGFV 862
                                    *9.99******************8 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.087
                                     HHCTHTCCHHHTTHCHHHHHHHHHHHHHHHHHHHHHHHHHHCSTTTSHHHHHHHCT CS
                 RNA_pol_Rpb1_4    3 eaerygkledlpgksleelfeakinkilnkardkagkiaskslaasNsiliMvksG 58  
                                     ++++ ++l++++ ++++++ ++ i++  n+ ++++ +   +++++  +  ++  sG
  gene457|gene457|rna457|rna457 1399 KDKD-NNLNHTIDNTTDNTIDNTIDHTTNNTTNNTTNPTTTTNPTTTNRWMLQTSG 1453
                                     4555.899999999999999999999999888887777777766435566666665 PP

>> RNA_pol_Rpb1_7  RNA polymerase Rpb1, domain 7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.7   0.9   2.2e-27   5.6e-24       3     103 ..    1205    1302 ..    1203    1315 .. 0.92

  Alignments for each domain:
  == domain 1  score: 84.7 bits;  conditional E-value: 2.2e-27
                                     GGGTEEEEEEEB---TTS-SSGGGGHHHHTTS-------------SBEEEEEE-SHHHHHTT--HHHHHHHHHHHHTT CS
                 RNA_pol_Rpb1_7    3 LrkvtaateiyYDPdprntvieeDrefveeyyelpdedveksrlspWlLRieLdrkkmtdkkltmeevaekikeefkn 80  
                                     L++v+++++++YDP++++tvi eDrefv+++y +pde+  ++ lspW+LR++L+r++m+   +t+  v++ +k++   
  gene457|gene457|rna457|rna457 1205 LKHVIESIAVVYDPNVTDTVIPEDREFVRAHYLFPDEER-ADMLSPWVLRVKLSRNRMVRYGVTLGMVKAMVKQRI-- 1279
                                     99*********************************9988.79******************************9987.. PP

                                     TEEEEE--TTSSSEEEEEEE--- CS
                 RNA_pol_Rpb1_7   81 dlkvifsddnaeklvlririvke 103 
                                     d++v+++d+na + v+r+r+v e
  gene457|gene457|rna457|rna457 1280 DVEVVMTDENAAEYVVRMRMVGE 1302
                                     688*****************974 PP

>> RNA_pol_Rpb1_R  RNA polymerase Rpb1 C-terminal repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.1       3.8   9.7e+03       7      12 ..     450     455 ..     449     455 .. 0.82
   2 !    6.8   4.7    0.0037       9.5       4      14 .]    1627    1637 ..    1625    1637 .. 0.98
   3 !   17.2   9.9   1.9e-06    0.0049       1      14 []    1646    1659 ..    1646    1659 .. 0.99
   4 ?    4.9   4.7     0.015        39       7      14 .]    1673    1680 ..    1672    1680 .. 0.91
   5 !   11.6  11.3   0.00011      0.28       1      14 []    1674    1687 ..    1674    1687 .. 0.98
   6 !    8.1   4.5    0.0014       3.7       1      14 []    1681    1698 ..    1681    1698 .. 0.95
   7 ?   -4.7  15.0         7   1.8e+04       3      11 ..    1702    1710 ..    1702    1721 .. 0.71

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 3.8
                 RNA_pol_Rpb1_R   7 ySPtSP 12 
                                    +S tSP
  gene457|gene457|rna457|rna457 450 LSVTSP 455
                                    799999 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0037
                 RNA_pol_Rpb1_R    4 SPaySPtSPgY 14  
                                     SP y+P SP+Y
  gene457|gene457|rna457|rna457 1627 SPRYTPASPTY 1637
                                     9*********9 PP

  == domain 3  score: 17.2 bits;  conditional E-value: 1.9e-06
                 RNA_pol_Rpb1_R    1 SPTSPaySPtSPgY 14  
                                     SPTSPay+PtSP+Y
  gene457|gene457|rna457|rna457 1646 SPTSPAYTPTSPKY 1659
                                     9************9 PP

  == domain 4  score: 4.9 bits;  conditional E-value: 0.015
                 RNA_pol_Rpb1_R    7 ySPtSPgY 14  
                                     ySPtSP+Y
  gene457|gene457|rna457|rna457 1673 YSPTSPSY 1680
                                     9*****99 PP

  == domain 5  score: 11.6 bits;  conditional E-value: 0.00011
                 RNA_pol_Rpb1_R    1 SPTSPaySPtSPgY 14  
                                     SPTSP+ySP SP Y
  gene457|gene457|rna457|rna457 1674 SPTSPSYSPASPRY 1687
                                     9***********98 PP

  == domain 6  score: 8.1 bits;  conditional E-value: 0.0014
                 RNA_pol_Rpb1_R    1 SPTSPaySPt....SPgY 14  
                                     SP+SP y+P+    SP Y
  gene457|gene457|rna457|rna457 1681 SPASPRYNPGrsagSPQY 1698
                                     9**********9999998 PP

  == domain 7  score: -4.7 bits;  conditional E-value: 7
                 RNA_pol_Rpb1_R    3 TSPaySPtS 11  
                                     +SP+ySPtS
  gene457|gene457|rna457|rna457 1702 ASPSYSPTS 1710
                                     699999995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1748 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       643  (0.0358637); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 1.05u 0.32s 00:00:01.37 Elapsed: 00:00:00.55
# Mc/sec: 9495.92
//
Query:       gene458|gene458|rna458|rna458  [L=705]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (705 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       539  (0.030063); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.58u 0.25s 00:00:00.83 Elapsed: 00:00:00.41
# Mc/sec: 5135.56
//
Query:       gene459|gene459|rna459|rna459  [L=53]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (53 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       491  (0.0273858); expected 358.6 (0.02)
Passed bias filter:                      180  (0.0100396); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.28s 00:00:00.67 Elapsed: 00:00:00.45
# Mc/sec: 351.14
//
Query:       gene46|gene46|rna46|rna46  [L=479]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.5e-12   47.4   2.1    4.6e-12   45.9   1.2    2.4  2  DnaJ        DnaJ domain
    0.00053   20.2   0.8          1    9.7   0.0    3.4  3  ANAPC3      Anaphase-promoting complex, cyclosome, subunit 3
     0.0036   17.8   0.1      0.071   13.6   0.0    2.6  2  TPR_19      Tetratricopeptide repeat
  ------ inclusion threshold ------
      0.087   13.7   0.0        4.3    8.4   0.0    3.3  3  TPR_14      Tetratricopeptide repeat
       0.19    9.8  10.5       0.39    8.7  10.5    1.5  1  DUF2828     Domain of unknown function (DUF2828)
       0.52    9.6  11.7        1.6    7.9   8.2    2.2  2  CENP-N      Kinetochore protein CHL4 like
       0.55   10.7   2.0         24    5.6   0.1    3.8  4  TPR_17      Tetratricopeptide repeat
        0.8    9.8   4.8        1.3    9.1   4.8    1.4  1  DDHD        DDHD domain
        1.3    7.7  10.1        1.8    7.2  10.1    1.2  1  Presenilin  Presenilin
        2.8    7.8  36.6       0.17   11.8  29.5    2.2  2  ARGLU       Arginine and glutamate-rich 1
          6    5.9  27.1       0.13   11.3  20.2    1.7  2  PDCD7       Programmed cell death protein 7


Domain annotation for each model (and alignments):
>> DnaJ  DnaJ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0         4   6.5e+03      10      26 ..      43      59 ..      42      61 .. 0.77
   2 !   45.9   1.2   2.8e-15   4.6e-12       2      63 .]     355     422 ..     354     422 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 4
                               TTG-HHHHHHHHHHHHH CS
                       DnaJ 10 kdasedeIkkaYrklal 26
                               +d+s++ ++k+Y    +
  gene46|gene46|rna46|rna46 43 NDSSNALVRKKYASFLM 59
                               578889999*9987766 PP

  == domain 2  score: 45.9 bits;  conditional E-value: 2.8e-15
                                HHHHHTSSTTG-HHHHHHHHHHHHHHHSTTTSCCHH.HHHH.....HHHHHHHHHHHHTSHHHHHHHH CS
                       DnaJ   2 yYeiLgvskdasedeIkkaYrklalkyHPDknpkdp.eaee.....kFkeineAyevLsdpekRkqYD 63 
                                yY++Lgv+++a+ ++Ik++Y kl+lky  D+++ +p e+e+     k   in+A +vL +p+kRk YD
  gene46|gene46|rna46|rna46 355 YYKLLGVEPTATPKDIKARYNKLVLKYDVDRQKVKPtEQEKerltqKLAMINQARDVLLNPKKRKLYD 422
                                9*****************************884444322223444499*******************9 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.0   0.00061         1      32      80 ..      23      72 ..       7      73 .. 0.94
   2 ?    0.1   0.1      0.59   9.5e+02      24      44 ..     125     148 ..     110     168 .. 0.53
   3 !    6.1   0.0     0.008        13      11      49 ..     238     275 ..     231     288 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00061
                               HHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH- CS
                     ANAPC3 32 clylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLe 80
                               ++  ngq  +A ++++++ + +s++  +r  +A  l +L+ y++ +a+++
  gene46|gene46|rna46|rna46 23 SYVDNGQLRTARQVISNLfDNDSSNALVRKKYASFLMELGDYDKVLAVFK 72
                               6999*****************************************99986 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.59
                                HHHHHHHHHHHHTT-...HHHHHH CS
                     ANAPC3  24 edayllAlclylngq...ykrAye 44 
                                + ++ +A+ l+++ +   y rA++
  gene46|gene46|rna46|rna46 125 YTLLSKAEMLFKDDDkiiYLRALY 148
                                222223555555555444444443 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.008
                                HHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT CS
                     ANAPC3  11 laerllaaetespedayllAlclylngqykrAyellrka 49 
                                +ae+l+ +  + +++  ll ++l+  g+ k+ +e + k 
  gene46|gene46|rna46|rna46 238 YAELLC-KLEKKDDSYVLLIKALLAEGKVKESCEQIGKI 275
                                899***.778888888889***********999999887 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.0   4.3e-05     0.071       2      47 ..      25      70 ..      24      73 .. 0.92
   2 ?    0.9   0.0      0.42   6.9e+02      21      43 ..     245     267 ..     236     276 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.3e-05
                     TPR_19  2 laegdyaeAlalleqalqedpknaearllLAeallalgqldeAeal 47
                               +++g++  A +  +++++ d  na +r  +A  l++lg++d+  a+
  gene46|gene46|rna46|rna46 25 VDNGQLRTARQVISNLFDNDSSNALVRKKYASFLMELGDYDKVLAV 70
                               689**************************************97665 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.42
                     TPR_19  21 dpknaearllLAeallalgqlde 43 
                                  k ++   lL++alla g ++e
  gene46|gene46|rna46|rna46 245 LEKKDDSYVLLIKALLAEGKVKE 267
                                44555666677888888887776 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0      0.16   2.6e+02       5      42 ..      18      55 ..      15      55 .. 0.85
   2 ?    8.4   0.0    0.0026       4.3       4      26 ..      51      73 ..      48      73 .. 0.90
   3 ?   -2.0   0.0       5.9   9.6e+03       4      20 ..     252     268 ..     250     272 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.16
                     TPR_14  5 lalaeallalGdpdeAiallrralalaPddaeawllla 42
                               l+l   +  +G++++A+++   + + + ++a ++  +a
  gene46|gene46|rna46|rna46 18 LDLFFSYVDNGQLRTARQVISNLFDNDSSNALVRKKYA 55
                               567778999**********9999999988888887776 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0026
                     TPR_14  4 llalaeallalGdpdeAiallrr 26
                               ++++a++l++lGd+d+ +a++++
  gene46|gene46|rna46|rna46 51 RKKYASFLMELGDYDKVLAVFKD 73
                               679***************99985 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 5.9
                     TPR_14   4 llalaeallalGdpdeA 20 
                                + +l +alla G+ +e+
  gene46|gene46|rna46|rna46 252 YVLLIKALLAEGKVKES 268
                                56789999999998876 PP

>> DUF2828  Domain of unknown function (DUF2828)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7  10.5   0.00024      0.39     123     201 ..     277     355 ..     219     362 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00024
                    DUF2828 123 egelvlkdpkkvlnvkkekkkeekkkkkkkkkkekkkerkkeekekkeeekeeakekrkekeaeraeklleklesdkky 201
                                + +l +++++++  +kk+k +e+k++++++k+++k+k++++e+k++ ee+++++ke++++++a+++++   + ++ k y
  gene46|gene46|rna46|rna46 277 NASLRERTERTIEVMKKKKIEERKRAEEQRKSENKRKTNEEERKRRVEEQRRQEKERKEKQRASQHQRYAGTNTDSKGY 355
                                4555556666777777777777777777777777777777777777777777888888888888888876655544444 PP

>> CENP-N  Kinetochore protein CHL4 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.1     0.038        62     115     146 ..      69     100 ..      65     106 .. 0.87
   2 ?    7.9   8.2   0.00098       1.6     276     340 ..     287     353 ..     254     412 .. 0.69

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.038
                     CENP-N 115 klkksdgseviprldpstFlsnLqeelsplvk 146
                                 + k+d++ v + ++++t+l+nL+e +++++ 
  gene46|gene46|rna46|rna46  69 AVFKDDEKLVGEAVKMKTMLKNLKENVHKIYL 100
                                5667888999999****************986 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.00098
                     CENP-N 276 Pldprkkhpilsekeedegdkeekksargrkekerlteesks.tkerkkr.rklvaqerfgekdsla 340
                                  +  kk++i ++k+ +e+ k+e+k + +++e++r+ ee+++ +kerk++ r +  q+  g++++++
  gene46|gene46|rna46|rna46 287 TIEVMKKKKIEERKRAEEQRKSENKRKTNEEERKRRVEEQRRqEKERKEKqRASQHQRYAGTNTDSK 353
                                4444556666666666888888888888877777777777774444444444555556666665554 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0      0.29   4.7e+02      23      34 .]      24      35 ..      17      35 .. 0.85
   2 ?    5.6   0.1     0.015        24       8      31 ..      43      66 ..      39      69 .. 0.91
   3 ?   -2.6   0.0       6.3     1e+04      15      34 .]     141     160 ..     135     160 .. 0.68
   4 ?   -0.7   0.0       1.5   2.4e+03      18      30 ..     237     249 ..     236     263 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.29
                     TPR_17 23 llknGdlmtArq 34
                               +  nG+l+tArq
  gene46|gene46|rna46|rna46 24 YVDNGQLRTARQ 35
                               668*******98 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.015
                     TPR_17  8 ldPnnadaynnLAelllknGdlmt 31
                               +d +na +   +A +l ++Gd+++
  gene46|gene46|rna46|rna46 43 NDSSNALVRKKYASFLMELGDYDK 66
                               7999******************86 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 6.3
                     TPR_17  15 aynnLAelllknGdlmtArq 34 
                                  +++A +++ + + + A+q
  gene46|gene46|rna46|rna46 141 IIYLRALYHAFRSENQLAHQ 160
                                56777877777777777765 PP

  == domain 4  score: -0.7 bits;  conditional E-value: 1.5
                     TPR_17  18 nLAelllknGdlm 30 
                                ++Aell+k+ +++
  gene46|gene46|rna46|rna46 237 EYAELLCKLEKKD 249
                                6899999988776 PP

>> DDHD  DDHD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   4.8   0.00079       1.3      90     170 ..     265     367 ..     234     442 .. 0.62

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00079
                       DDHD  90 lkesltsigaalkqkvsglvsslsallnrslelaeeesaslaessksherasesskasqeskaaesstasssaksskaee.... 169
                                +kes+++ig+ ++ + ++ ++     + + ++++e+++a+++++s+++++++e++ +++++++++++++ +++++ ++++    
  gene46|gene46|rna46|rna46 265 VKESCEQIGKIKNASLRERTERT-IEVMKKKKIEERKRAEEQRKSENKRKTNEEERKRRVEEQRRQEKERKEKQRASQHQryag 347
                                45555555555444443333333.234445556666666666666555555555555555555555555555554444444555 PP

                       DDHD 170 ...................k 170
                                                    
  gene46|gene46|rna46|rna46 348 tntdskgyykllgveptatP 367
                                55555555555555554440 PP

>> Presenilin  Presenilin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2  10.1    0.0011       1.8     212     299 ..     257     344 ..     241     401 .. 0.49

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0011
                 Presenilin 212 paLiYsatvvvlaaeek...kaevaeseeeeeaekkkeeasesskeeeseeesseksaqsseseeeseeesseaessaeessee 292
                                +aL+ + +v+ + ++     +a+ +e++e++ +  kk++++e++++ee+++++++++++++e++++ ee+++++++++e++   
  gene46|gene46|rna46|rna46 257 KALLAEGKVKESCEQIGkikNASLRERTERTIEVMKKKKIEERKRAEEQRKSENKRKTNEEERKRRVEEQRRQEKERKEKQ--- 337
                                555555555554433332211122222222222222222222222222222222222222222222222222222222222... PP

                 Presenilin 293 keseess 299
                                ++s++++
  gene46|gene46|rna46|rna46 338 RASQHQR 344
                                1111111 PP

>> ARGLU  Arginine and glutamate-rich 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8  29.5    0.0001      0.17      52     129 ..     266     343 ..     229     350 .. 0.89
   2 ?   -0.5   0.6       0.6   9.8e+02     117     136 ..     383     402 ..     371     421 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0001
                      ARGLU  52 kqveeelerereaeleeekrkeeeerkkreelerileenkrkveeaqrklaEerlaeleekrrlkeerqrlkkeeekk 129
                                k+  e++ + ++a+l+e+ ++  e  kk++  er  +e++rk e++++  +Eer +++ee+rr+++er++ ++  +++
  gene46|gene46|rna46|rna46 266 KESCEQIGKIKNASLRERTERTIEVMKKKKIEERKRAEEQRKSENKRKTNEEERKRRVEEQRRQEKERKEKQRASQHQ 343
                                56678999************************************************************9999887765 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.6
                      ARGLU 117 eerqrlkkeeekkekeeqev 136
                                 +rq++k  e++ke+  q+ 
  gene46|gene46|rna46|rna46 383 VDRQKVKPTEQEKERLTQKL 402
                                45566665555555555553 PP

>> PDCD7  Programmed cell death protein 7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3  20.2   8.3e-05      0.13      47     128 ..     265     345 ..     218     350 .. 0.81
   2 ?   -3.4   0.5       2.5   4.1e+03     117     127 ..     393     403 ..     380     420 .. 0.41

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 8.3e-05
                      PDCD7  47 lkkelqeklalLedaerleelkrklerrkkkRarrkrrkeerkeekkekeerraereakidkWrrkqiqeveekkkeqelke 128
                                +k++ +e++ ++++a+++e+ +r +e++kkk+  +++r ee  + +++++ + +er++++++ rr++ ++ e+++ +q+++ 
  gene46|gene46|rna46|rna46 265 VKES-CEQIGKIKNASLRERTERTIEVMKKKKIEERKRAEEQRKSENKRKTNEEERKRRVEEQRRQEKERKEKQRASQHQRY 345
                                4444.669999**********************99988888888888888888****************9999999999875 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 2.5
                      PDCD7 117 veekkkeqelk 127
                                +e+++  q+l 
  gene46|gene46|rna46|rna46 393 QEKERLTQKLA 403
                                22222222221 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (479 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2945  (0.164259); expected 358.6 (0.02)
Passed bias filter:                      830  (0.0462937); expected 358.6 (0.02)
Passed Vit filter:                       195  (0.0108762); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.80u 0.30s 00:00:01.10 Elapsed: 00:00:00.45
# Mc/sec: 3199.14
//
Query:       gene460|gene460|rna460|rna460  [L=83]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    0.00037   20.7   0.5    0.00051   20.2   0.5    1.3  1  Pox_EPC_I2-L1  Poxvirus entry protein complex L1 and I2


Domain annotation for each model (and alignments):
>> Pox_EPC_I2-L1  Poxvirus entry protein complex L1 and I2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.5   2.9e-08   0.00051      17      50 ..      20      56 ..      14      68 .. 0.70

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 2.9e-08
                  Pox_EPC_I2-L1 17 ddDfnnFievVksVLtdekaskktas...sgtklwlt 50
                                   +d+ nnFi+vV+  L+d+++  ++++   s + +w  
  gene460|gene460|rna460|rna460 20 EDEKNNFIDVVRGWLSDSETKFEKKHhsnSYNVIWQA 56
                                   67789************99654444400033445544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (83 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       768  (0.0428356); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.45
# Mc/sec: 555.19
//
Query:       gene462|gene462|rna462|rna462  [L=166]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      0.004   16.9   2.3      0.004   16.9   2.3    1.2  1  8TM_micro  8TM Microsporidial transmembrane domain


Domain annotation for each model (and alignments):
>> 8TM_micro  8TM Microsporidial transmembrane domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   2.3   2.3e-07     0.004     131     194 ..      50     113 ..       9     159 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2.3e-07
                      8TM_micro 131 tkc..HaPslnifwflnlqmfeqYselfydiflivflfLlslvkkstklelilvFkdstyksylll 194
                                     +c   +Pslni  + +l++f+ Y + +  +++ +f++L  l ++++ l++++ F   +  +y+++
  gene462|gene462|rna462|rna462  50 PHCpwLYPSLNIHSYTLLNIFDPYYHPLVMLYISTFIYL--LLTSRHTLYVLISFVGYNELEYVMV 113
                                    5555458********************************..7778888888887766666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       626  (0.0349155); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1305.72
//
Query:       gene463|gene463|rna463|rna463  [L=157]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-16   60.6  16.1    1.9e-08   34.6   2.5    2.7  2  HMG_box         HMG (high mobility group) box
    7.1e-12   45.8  18.3    2.5e-08   34.4   7.3    2.4  2  HMG_box_2       HMG-box domain
      0.005   17.0   5.2       0.14   12.4   1.4    2.1  2  Protamine_like  Protamine and protamine like
     0.0056   17.3   2.1     0.0061   17.1   1.4    1.4  1  YABBY           YABBY protein
  ------ inclusion threshold ------
       0.03   14.7   1.6       0.03   14.7   1.6    2.6  3  DUF1104         Protein of unknown function (DUF1104)
        1.2    9.0   3.0         10    6.1   0.4    2.5  2  DUF1289         Protein of unknown function (DUF1289)
        3.4    7.6   8.8       0.19   11.7   0.4    2.5  3  DUF2489         Protein of unknown function (DUF2489)
        8.6    6.2   8.4        9.2    6.1   1.0    2.6  3  DUF501          Protein of unknown function (DUF501)


Domain annotation for each model (and alignments):
>> HMG_box  HMG (high mobility group) box
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.6   2.5   8.6e-12   1.9e-08       1      69 []      13      80 ..      13      80 .. 0.94
   2 !   31.0   5.8   1.2e-10   2.6e-07       2      63 ..      99     156 ..      98     157 .] 0.89

  Alignments for each domain:
  == domain 1  score: 34.6 bits;  conditional E-value: 8.6e-12
                                   --SS--HHHHHHHHHHHHHHHHSTTS-HHHHHHHHHHHHHHSHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        HMG_box  1 pkRplsafflfskeqraklkaenPelknaeiskklgekWkalseeeKkkYeekaekekaryekekpeyk 69
                                   pk+p s+++ f+++ r++  a   ++  ++  ++ + kW+ ls+ ++k Ye+++++  + y++e+++yk
  gene463|gene463|rna463|rna463 13 PKKPASSYLSFCSHLRKTDEALK-SMAPSDQRQHFATKWRTLSDTDRKGYEDDYQQRLQAYREEYKKYK 80
                                   8************9998877766.6888999*************************************8 PP

  == domain 2  score: 31.0 bits;  conditional E-value: 1.2e-10
                                    -SS--HHHHHHHHHHHHHHHHSTTS-HHHHHHHHHHHHHHSHHHHHHHHHHHHHHHHHHHHH CS
                        HMG_box   2 kRplsafflfskeqraklkaenPelknaeiskklgekWkalseeeKkkYeekaekekaryek 63 
                                    kRp sa+++f+ e+ +k+     + + ae+    +++Wk+++eeeK+ +++kae+++++ ++
  gene463|gene463|rna463|rna463  99 KRPKSAYNVFVAEEYKKVEGSSFGEHTAEL----SRRWKSMNEEEKMVFRRKAEELRKENME 156
                                    9*****************988777777776....579********************99877 PP

>> HMG_box_2  HMG-box domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   3.1   2.9e-06    0.0064       4      72 ..      13      79 ..      10      80 .. 0.87
   2 !   34.4   7.3   1.1e-11   2.5e-08       3      66 ..      97     155 ..      95     157 .] 0.88

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 2.9e-06
                                   .-SS--HHHHHHHTTHHHHHHHT---SSHHHHTGGGHHHHHHS-HHHHHHHHHHHHHHHHHHHH-SS-- CS
                      HMG_box_2  4 pkaarnAYalfvqemipelkrkGnpviglaevsklcsekWkalseeeKekYeekAkedkkrydrealty 72
                                   pk + ++Y+ f    +++  +   + +  ++  +    kW++ls+ +++ Ye+  ++  ++y++e ++y
  gene463|gene463|rna463|rna463 13 PKKPASSYLSFCSHLRKTDEAL--KSMAPSDQRQHFATKWRTLSDTDRKGYEDDYQQRLQAYREEYKKY 79
                                   8899999999998887765554..66778999999****************************999887 PP

  == domain 2  score: 34.4 bits;  conditional E-value: 1.1e-11
                                    -.-SS--HHHHHHHTTHHHHHHHT---SSHHHHTGGGHHHHHHS-HHHHHHHHHHHHHHHHHHH CS
                      HMG_box_2   3 kpkaarnAYalfvqemipelkrkGnpviglaevsklcsekWkalseeeKekYeekAkedkkryd 66 
                                    k k++++AY++fv e+ +++  +      ++e + ++s +Wk+++eeeK  + +kA e++k+  
  gene463|gene463|rna463|rna463  97 KKKRPKSAYNVFVAEEYKKVEGS-----SFGEHTAELSRRWKSMNEEEKMVFRRKAEELRKENM 155
                                    559**********9876665555.....9*******************************9865 PP

>> Protamine_like  Protamine and protamine like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.7   0.2    0.0034       7.7      82     125 ..      16      62 ..       1      78 [. 0.78
   2 !   12.4   1.4   6.2e-05      0.14      65     132 ..      85     151 ..      71     156 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0034
                 Protamine_like  82 tnnaylnfvrefkkkfynlk...Prelvakaakawarlsearkdayk 125
                                       +yl f  + +k    lk   P +  ++ a +w  ls ++++ y 
  gene463|gene463|rna463|rna463  16 PASSYLSFCSHLRKTDEALKsmaPSDQRQHFATKWRTLSDTDRKGYE 62 
                                    4578**********87766544499**999*********99887775 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 6.2e-05
                 Protamine_like  65 rkvkcaPrqkrskvarvtnnaylnfvrefkkkfynlkPrelvakaakawarlsearkdaykrvackvk 132
                                     k+ c  + k sk+ r    ay  fv e  kk  + +  e  a  +++w  + e++k  ++r a +++
  gene463|gene463|rna463|rna463  85 YKQDCEAIGKESKKKRP-KSAYNVFVAEEYKKVEGSSFGEHTAELSRRWKSMNEEEKMVFRRKAEELR 151
                                    5889********99885.789******99999******************************998765 PP

>> YABBY  YABBY protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   1.4   2.7e-06    0.0061      47     133 ..      33     117 ..      20     122 .. 0.56

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 2.7e-06
                          YABBY  47 ralllapaaaelqslkkqlelksellskelassskssekskksalasssseqeeeeeekvvnrppekrqRvPsaYnrFik 126
                                    +  ++ap++++ q+ +++ ++ s++++k ++++ ++  ++ + + +++ ++++  ++   ++    k++R  saYn F+ 
  gene463|gene463|rna463|rna463  33 ALKSMAPSDQR-QHFATKWRTLSDTDRKGYEDDYQQRLQAYR-EEYKKYKASDLYKQDCEAIGKESKKKRPKSAYNVFVA 110
                                    44444454333.444444444444444444433333333322.33444444455555667777788999*********** PP

                          YABBY 127 eeiqRik 133
                                    ee +++ 
  gene463|gene463|rna463|rna463 111 EEYKKVE 117
                                    **99875 PP

>> DUF1104  Protein of unknown function (DUF1104)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   2.2     0.056   1.3e+02      14      81 ..      12      83 ..       2      99 .. 0.54
   2 ?    2.9   1.1     0.062   1.4e+02      25      66 ..      61     102 ..      52     120 .. 0.68
   3 ?   14.7   1.6   1.3e-05      0.03      16      57 ..     115     156 ..     102     157 .] 0.93

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.056
                                   TTTS-GGGHHHHHHHHHHHHHHS-H....HHHHHHHHHHHHHHHHHHTTS-H.HHHHHHHHHHHHHHHH.T--- CS
                        DUF1104 14 aGkvapeevldykmevaKrlkslke....kekkkfkkklkeaaeknlekmtv.kefeklrkevrkalkk.kikk 81
                                   a k++++ +l + + ++K  ++lk     +++++f  k +      ++++    +++++ ++ r++ kk k  +
  gene463|gene463|rna463|rna463 12 APKKPASSYLSFCSHLRKTDEALKSmapsDQRQHFATKWRTLS--DTDRKGYeDDYQQRLQAYREEYKKyKASD 83
                                   6677777777777888876544444111355555555544433..33444330456666666666666644444 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.062
                                    HHHHHHHHHHHS-HHHHHHHHHHHHHHHHHHHTTS-HHHHHH CS
                        DUF1104  25 ykmevaKrlkslkekekkkfkkklkeaaeknlekmtvkefek 66 
                                    y+ + + rl++  e+ kk   ++l ++ ++++ k ++k + k
  gene463|gene463|rna463|rna463  61 YEDDYQQRLQAYREEYKKYKASDLYKQDCEAIGKESKKKRPK 102
                                    555566777777777777777778888887777777776655 PP

  == domain 3  score: 14.7 bits;  conditional E-value: 1.3e-05
                                    TS-GGGHHHHHHHHHHHHHHS-HHHHHHHHHHHHHHHHHHHT CS
                        DUF1104  16 kvapeevldykmevaKrlkslkekekkkfkkklkeaaeknle 57 
                                    kv+ + + + ++e+ +r ks++e+ek  f+ k +e +++n+e
  gene463|gene463|rna463|rna463 115 KVEGSSFGEHTAELSRRWKSMNEEEKMVFRRKAEELRKENME 156
                                    78889999********************************97 PP

>> DUF1289  Protein of unknown function (DUF1289)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.1     0.044        98      27      47 ..      48      68 ..      41      69 .. 0.88
   2 ?    6.1   0.4    0.0044        10      27      45 ..     130     148 ..     124     151 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.044
                        DUF1289 27 aaWssmsdeerravlarleqr 47
                                   ++W+++sd+ r+   ++ +qr
  gene463|gene463|rna463|rna463 48 TKWRTLSDTDRKGYEDDYQQR 68
                                   68*********9988888887 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0044
                        DUF1289  27 aaWssmsdeerravlarle 45 
                                    ++W+sm++ee+  + +++e
  gene463|gene463|rna463|rna463 130 RRWKSMNEEEKMVFRRKAE 148
                                    69*********98777665 PP

>> DUF2489  Protein of unknown function (DUF2489)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.4   8.3e-05      0.19      77     125 ..      23      71 ..       9      75 .. 0.87
   2 ?   -0.0   0.1      0.34   7.7e+02      95     119 ..      74      98 ..      71     104 .. 0.85
   3 ?   -0.1   1.6      0.38   8.4e+02      76     113 ..     103     141 ..      89     157 .] 0.48

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 8.3e-05
                        DUF2489  77 eypalyelyekvkdmpthearkalkkkermkldlereklEaeledeike 125
                                     +++l +  e+ k+m+  ++r++++ k r   d  r  +E ++++ +++
  gene463|gene463|rna463|rna463  23 FCSHLRKTDEALKSMAPSDQRQHFATKWRTLSDTDRKGYEDDYQQRLQA 71 
                                    56788899999********************************998775 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.34
                        DUF2489  95 earkalkkkermkldlereklEael 119
                                    e++k+ k+ +  k+d e   +E++ 
  gene463|gene463|rna463|rna463  74 EEYKKYKASDLYKQDCEAIGKESKK 98 
                                    7899999999999999999988875 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.38
                        DUF2489  76 seypaly.elyekvkdmpthearkalkkkermkldlere 113
                                    s y++++ e y+kv+    +e   +l+++ +   + e +
  gene463|gene463|rna463|rna463 103 SAYNVFVaEEYKKVEGSSFGEHTAELSRRWKSMNEEEKM 141
                                    555555324556665555555554444443333332222 PP

>> DUF501  Protein of unknown function (DUF501)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.4     0.019        42      60      98 ..      29      67 ..      18      75 .. 0.77
   2 ?    1.4   0.1      0.11   2.5e+02      63      99 ..      63      99 ..      60     116 .. 0.79
   3 ?    6.1   1.0    0.0041       9.2      72      99 ..     123     150 ..     109     156 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.019
                         DUF501 60 aedeelaqalekahaeyaakReellteeerseleksees 98
                                   ++de+l+    + ++++ a++++ l++ +r+  e   ++
  gene463|gene463|rna463|rna463 29 KTDEALKSMAPSDQRQHFATKWRTLSDTDRKGYEDDYQQ 67
                                   4566677777778999**************998765444 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.11
                         DUF501 63 eelaqalekahaeyaakReellteeerselekseess 99
                                   ++ +q+l++  +ey + + + l +++ + + k+++++
  gene463|gene463|rna463|rna463 63 DDYQQRLQAYREEYKKYKASDLYKQDCEAIGKESKKK 99
                                   6788999999999999999999888888876666554 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.0041
                         DUF501  72 ahaeyaakReellteeerselekseess 99 
                                     h + +++R+++++eee+ ++++++e+ 
  gene463|gene463|rna463|rna463 123 EHTAELSRRWKSMNEEEKMVFRRKAEEL 150
                                    69999****************9998873 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1433  (0.0799264); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1073.75
//
Query:       gene464|gene464|rna464|rna464  [L=85]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (85 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       597  (0.033298); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.26s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 632.37
//
Query:       gene465|gene465|rna465|rna465  [L=592]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-08   33.3   0.0    4.6e-08   32.6   0.0    1.4  1  SAP       SAP domain


Domain annotation for each model (and alignments):
>> SAP  SAP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.6   0.0   2.6e-12   4.6e-08       1      32 [.     530     561 ..     530     563 .. 0.95

  Alignments for each domain:
  == domain 1  score: 32.6 bits;  conditional E-value: 2.6e-12
                                    HTT--HHHHHHHHHHTT--TTS-HHHHHHHHH CS
                            SAP   1 lskltVaeLKeeLkkrGLptsGkKaeLieRLk 32 
                                    +++ tV++LK ++k++GL  +GkK +LieR+k
  gene465|gene465|rna465|rna465 530 YENVTVQQLKNIMKEFGLNHTGKKIDLIERVK 561
                                    7889**************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (592 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       687  (0.0383178); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.23s 00:00:00.75 Elapsed: 00:00:00.37
# Mc/sec: 4812.85
//
Query:       gene466|gene466|rna466|rna466  [L=308]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0042   17.2   0.2       0.01   15.9   0.2    1.7  1  DUF2973   Protein of unknown function (DUF2973)


Domain annotation for each model (and alignments):
>> DUF2973  Protein of unknown function (DUF2973)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.2   5.8e-07      0.01       1      32 [.       9      40 ..       9      69 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 5.8e-07
                        DUF2973  1 mLhllYilaftvlaflAvanLirslitlsads 32
                                   +++++ il+f ++ f A+a Li+s +++ ++ 
  gene466|gene466|rna466|rna466  9 LFQIIIILCFAIISFSAIACLIKSGLAFVFEI 40
                                   69**********************99887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (308 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       823  (0.0459033); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 2250.82
//
Query:       gene467|gene467|rna467|rna467  [L=68]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.035   14.0   0.0      0.039   13.9   0.0    1.1  1  Prefoldin      Prefoldin subunit
      0.047   13.2   0.0      0.058   12.9   0.0    1.2  1  AA_permease_N  Amino acid permease N-terminal


Domain annotation for each model (and alignments):
>> Prefoldin  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   4.3e-06     0.039      27      84 ..      13      67 ..       2      68 .] 0.82

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.3e-06
                                   HHHHHHTT.-TT-EEEEEEETTEEEEEE--STTEEEEEEETTEEEEEEHHHHHHHHHH CS
                      Prefoldin 27 etlktlkkedegkevlvplgaglyvkaevkdtdkvlvdlGagyyveksleeAiellkk 84
                                   e  ++lkk   +k ++v+l+++ly+   +++++++lv+    ++v+ ++ +A ++l+ 
  gene467|gene467|rna467|rna467 13 ELHRNLKK--LSKSATVKLSDELYCGF-IIPDNNILVEQADYIFVKIDAADAAKYLDS 67
                                   33344444..667999********866.9999************************96 PP

>> AA_permease_N  Amino acid permease N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   6.4e-06     0.058      37      56 ..       6      25 ..       1      34 [. 0.77

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6.4e-06
                  AA_permease_N 37 lsRPsLaeLHeelkknsala 56
                                     RPs +eLH +lkk s+ a
  gene467|gene467|rna467|rna467  6 YERPSAKELHRNLKKLSKSA 25
                                   57************987763 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (68 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       471  (0.0262703); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.34u 0.25s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 531.38
//
Query:       gene469|gene469|rna469|rna469  [L=187]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.6e-19   68.8   0.2    1.3e-18   67.1   0.0    2.0  2  Mnd1         Mnd1 HTH domain
    0.00029   20.9   0.0     0.0007   19.6   0.0    1.6  1  LZ3wCH       Leucine zipper with capping helix domain
     0.0015   18.2   1.7     0.0017   18.1   0.2    1.8  2  DivIC        Septum formation initiator
  ------ inclusion threshold ------
      0.012   15.5   1.2      0.019   14.8   1.2    1.4  1  TFIIE_alpha  TFIIE alpha subunit
      0.029   14.6   0.6      0.029   14.6   0.6    1.8  2  TMF_TATA_bd  TATA element modulatory factor 1 TATA binding
      0.072   13.0   1.3      0.097   12.6   0.1    1.8  2  DUF3198      Protein of unknown function (DUF3198)
       0.45   10.1   4.3        8.6    5.9   0.7    2.2  2  DDRGK        DDRGK domain


Domain annotation for each model (and alignments):
>> Mnd1  Mnd1 HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.1   0.0   4.9e-22   1.3e-18       4      58 ..      17      69 ..      13      71 .. 0.91
   2 ?   -1.5   0.0       1.3   3.2e+03      14      20 ..      87      93 ..      82     110 .. 0.68

  Alignments for each domain:
  == domain 1  score: 67.1 bits;  conditional E-value: 4.9e-22
                           Mnd1  4 ifqeskefytlKeleklapkekgivsqsVkdvlqsLvdDglveveKiGssnvyWs 58
                                   +f+   ++y+lKelekl +k  gi+s+ Vkd++++L++D+l+ ++KiG s++yW+
  gene469|gene469|rna469|rna469 17 LFN-PTTVYNLKELEKLSSK-LGIRSNLVKDLVTELTNDNLITSDKIGISTYYWR 69
                                   554.479*************.9********************************7 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.3
                           Mnd1 14 lKelekl 20
                                   +Kelek 
  gene469|gene469|rna469|rna469 87 VKELEKQ 93
                                   5666663 PP

>> LZ3wCH  Leucine zipper with capping helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   2.7e-07    0.0007      11      53 ..     142     184 ..     139     186 .. 0.94

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 2.7e-07
                         LZ3wCH  11 kkakeaanrWtdnifdikswikekfpkskkelneefgIetDeD 53 
                                    ++ ++ +nr t  +f ++ +++ ++++   +++++fg+ +D++
  gene469|gene469|rna469|rna469 142 DVMRDDVNRITEDVFVLRRFVCDTYGMLVGDFDRNFGVGDDFE 184
                                    68899************************************97 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.1       2.4   6.2e+03      29      51 ..      29      51 ..      25      56 .. 0.53
   2 !   18.1   0.2   6.5e-07    0.0017      15      61 ..      74     119 ..      70     129 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 2.4
                                   HHHHHHHHHHHHHHHHHHHCC-X CS
                          DivIC 29 lqaelaklkaeneeLeaevkdLk 51
                                   l++   kl  + +  ++ v +L+
  gene469|gene469|rna469|rna469 29 LEKLSSKLGIRSNLVKDLVTELT 51
                                   44444455555555556666664 PP

  == domain 2  score: 18.1 bits;  conditional E-value: 6.5e-07
                                    XXXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-XXXXXXXXXXX CS
                          DivIC  15 gllaykqlkqeiaalqaelaklkaeneeLeaevkdLksdedyieerA 61 
                                    +   yk+l ++++ ++ e ++l++++++L+ae  d  s  d+i+e+A
  gene469|gene469|rna469|rna469  74 NSTEYKRLTSQLHVKELEKQRLTQQEQQLKAERCDA-SRADMIDEYA 119
                                    556899******************************.8********9 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   1.2   7.4e-06     0.019      31      99 ..      30      93 ..       2     100 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 7.4e-06
                                   HHHHHHHTS-HHHHHHHHHHHHHCTSEEEEEEEETTTEEEEEEEEEECCCHCCCHHHHHHHHHHHHHHH CS
                    TFIIE_alpha 31 edlakelkidlnelrklLnrLyearlvkykrrrdeekswykyywrinyeklvdvvkrkleevvkkLeek 99
                                   e l+ +l+i  n ++ l+ +L ++ l+       +++++ +yywri +++ ++  +   +  vk+Le++
  gene469|gene469|rna469|rna469 30 EKLSSKLGIRSNLVKDLVTELTNDNLITS-----DKIGISTYYWRIPPNNSTEYKRLTSQLHVKELEKQ 93
                                   89*************************75.....789*********99999988777777778888875 PP

>> TMF_TATA_bd  TATA element modulatory factor 1 TATA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       1.3   3.4e+03      16      16 ..      31      31 ..       4      53 .. 0.58
   2 ?   14.6   0.6   1.1e-05     0.029      10      46 ..      74     110 ..      71     124 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.3
                    TMF_TATA_bd 16 r 16
                                   +
  gene469|gene469|rna469|rna469 31 K 31
                                   1 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 1.1e-05
                    TMF_TATA_bd  10 svqlverlsseirrlEgElaslkeelerleaerdear 46 
                                    +++  +rl s+++ +E E++ l ++ ++l+aer +a+
  gene469|gene469|rna469|rna469  74 NSTEYKRLTSQLHVKELEKQRLTQQEQQLKAERCDAS 110
                                    666779***************************8875 PP

>> DUF3198  Protein of unknown function (DUF3198)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   3.8e-05     0.097      19      33 ..      23      37 ..       9      40 .. 0.87
   2 ?   -2.6   0.2         2   5.2e+03      23      27 ..      88      92 ..      86     103 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3.8e-05
                                   HHHHHHHHHHHHHH- CS
                        DUF3198 19 vknlkeLekiarklG 33
                                   v nlkeLek++ klG
  gene469|gene469|rna469|rna469 23 VYNLKELEKLSSKLG 37
                                   88************9 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2
                                   HHHHH CS
                        DUF3198 23 keLek 27
                                   keLek
  gene469|gene469|rna469|rna469 88 KELEK 92
                                   56664 PP

>> DDRGK  DDRGK domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.7    0.0033       8.6      94     144 ..       7      57 ..       1      58 [. 0.77
   2 ?    5.6   0.1    0.0042        11      71      98 ..      74     101 ..      71     124 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0033
                                    XXXXXXHHHHHHHHHHH-SEE-HHHHHHHH-S-HHHHHHHHHHHHHHSSS- CS
                          DDRGK  94 aeeeeklleefinyikekKvvlleelavkfklktqevierikeLeeqgslt 144
                                    +e++++++ ++ n      + +le l++k++++++ v + + eL +++ +t
  gene469|gene469|rna469|rna469   7 KEQKKEIILSLFNPTTVYNLKELEKLSSKLGIRSNLVKDLVTELTNDNLIT 57 
                                    33333366677777777778899**********************999886 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0042
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          DDRGK  71 eqeeyeklksefvveeegtekesaeeee 98 
                                    ++ ey++l s++ v+e  +++ +++e++
  gene469|gene469|rna469|rna469  74 NSTEYKRLTSQLHVKELEKQRLTQQEQQ 101
                                    6789999999999999888777777744 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1069  (0.0596241); expected 358.6 (0.02)
Passed bias filter:                      629  (0.0350828); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1406.44
//
Query:       gene47|gene47|rna47|rna47  [L=257]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.6e-05   23.9   4.9    9.1e-05   22.6   4.9    1.7  1  zf-CCCH_3  Zinc-finger containing family
      8e-05   23.0  14.8     0.0016   18.9   1.6    2.7  2  zf-CCCH_2  RNA-binding, Nab2-type zinc finger
     0.0001   22.0   4.8    0.00051   19.8   1.0    2.6  2  zf-CCCH_4  CCCH-type zinc finger
    0.00026   20.8   1.4    0.00026   20.8   1.4    2.8  3  zf-CCCH    Zinc finger C-x8-C-x5-C-x3-H type (and similar)
    0.00047   20.1   3.3    0.00047   20.1   3.3    3.1  2  zf_CCCH_4  Zinc finger domain
     0.0011   19.6   3.8     0.0011   19.6   3.8    2.3  2  Torus      Torus domain
  ------ inclusion threshold ------
      0.017   15.7   0.4      0.033   14.8   0.4    1.4  1  Com_YlbF   Control of competence regulator ComK, YlbF/YmcA


Domain annotation for each model (and alignments):
>> zf-CCCH_3  Zinc-finger containing family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   4.9   3.5e-08   9.1e-05       5      59 ..     185     236 ..     181     253 .. 0.79

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 3.5e-08
                  zf-CCCH_3   5 gddcyffyystctkGdscpfrheeaalGsetvctlWqegrclrevckfrhmeidk 59 
                                ++ c ff    ctkGd c++ h    l +     +  + +c r+ c f h  i+ 
  gene47|gene47|rna47|rna47 185 SQICRFFLTHSCTKGDACSYSHDIKRLPCKA---FHMKKNCSRKNCMFSHEPISV 236
                                667********************99997654...456889**********87754 PP

>> zf-CCCH_2  RNA-binding, Nab2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   1.6   6.1e-07    0.0016       1      17 [.     187     206 ..     187     206 .. 0.98
   2 !    8.9   5.8   0.00085       2.2       7      17 ..     221     231 ..     212     231 .. 0.92

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 6.1e-07
                  zf-CCCH_2   1 pCrffpn..C.tnpkCpFaH 17 
                                +Crff +  C +++ C+++H
  gene47|gene47|rna47|rna47 187 ICRFFLThsCtKGDACSYSH 206
                                8******************* PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00085
                  zf-CCCH_2   7 nCtnpkCpFaH 17 
                                nC +++C+F+H
  gene47|gene47|rna47|rna47 221 NCSRKNCMFSH 231
                                8********** PP

>> zf-CCCH_4  CCCH-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   1.0     2e-07   0.00051       2      22 .]     187     207 ..     186     207 .. 0.97
   2 ?    3.1   0.1     0.033        85      16      22 .]     226     232 ..     225     232 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 2e-07
                  zf-CCCH_4   2 lCpyfakGsCrfGdnCrFsHd 22 
                                +C++f++ sC+ Gd C +sHd
  gene47|gene47|rna47|rna47 187 ICRFFLTHSCTKGDACSYSHD 207
                                7*******************9 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.033
                  zf-CCCH_4  16 nCrFsHd 22 
                                nC FsH+
  gene47|gene47|rna47|rna47 226 NCMFSHE 232
                                9*****7 PP

>> zf-CCCH  Zinc finger C-x8-C-x5-C-x3-H type (and similar)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       1.7   4.5e+03       3      12 ..      31      40 ..      31      42 .. 0.74
   2 !   20.8   1.4     1e-07   0.00026       1      26 [.     183     207 ..     183     208 .. 0.88
   3 !    6.1   3.6    0.0042        11       2      25 ..     209     231 ..     209     233 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.7
                               CHCBCHHHHH CS
                    zf-CCCH  3 telCrffmrt 12
                               t+lC+  +r 
  gene47|gene47|rna47|rna47 31 TKLCKALLRF 40
                               6899987775 PP

  == domain 2  score: 20.8 bits;  conditional E-value: 1e-07
                                -HCHCBCHHHHHS--TTGGG-SSBSC CS
                    zf-CCCH   1 yktelCrffmrtGyCkyGdrCkFaHg 26 
                                y+  +Crff+  ++C  Gd+C+++H+
  gene47|gene47|rna47|rna47 183 YRSQICRFFLT-HSCTKGDACSYSHD 207
                                56789**8888.*************6 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.0042
                                HCHCBCHHHHHS--TTGGG-SSBS CS
                    zf-CCCH   2 ktelCrffmrtGyCkyGdrCkFaH 25 
                                k+ +C+ f+    C++  +C F+H
  gene47|gene47|rna47|rna47 209 KRLPCKAFHMKKNCSR-KNCMFSH 231
                                6779************.******* PP

>> zf_CCCH_4  Zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   3.3   1.8e-07   0.00047       1      19 []     188     206 ..     188     206 .. 0.99
   2 ?    0.9   3.0      0.21   5.3e+02       1      19 []     213     231 ..     213     231 .. 0.67

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 1.8e-07
                  zf_CCCH_4   1 CkfflqGtCkkGdkCrFaH 19 
                                C+ffl+ +C+kGd+C ++H
  gene47|gene47|rna47|rna47 188 CRFFLTHSCTKGDACSYSH 206
                                ******************* PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.21
                  zf_CCCH_4   1 Ckfflq.GtCkkGdkCrFaH 19 
                                Ck f+   +C++  +C F+H
  gene47|gene47|rna47|rna47 213 CKAFHMkKNCSRK-NCMFSH 231
                                7777777888773.566666 PP

>> Torus  Torus domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.1      0.37   9.6e+02      47      68 ..      59      80 ..      44      97 .. 0.71
   2 !   19.6   3.8   4.5e-07    0.0011      47      94 ..     162     209 ..     110     230 .. 0.62

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.37
                               ---S----HHHH----HHHHST CS
                      Torus 47 ekaktrcnikkdsGytkadkek 68
                               e+ +  +n k+d G t++d+ +
  gene47|gene47|rna47|rna47 59 EAKNDTMNNKQDYGKTEEDELE 80
                               3344568999999999998654 PP

  == domain 2  score: 19.6 bits;  conditional E-value: 4.5e-07
                                ---S----HHHH----HHHHSTT--B-HHHHHT--SSGGG-SSB-S-- CS
                      Torus  47 ekaktrcnikkdsGytkadkekesyfClfFarGlCakGkkCeylHrlP 94 
                                +++++ +++ ++    + +++ +s +C fF    C+kG  C+y H++ 
  gene47|gene47|rna47|rna47 162 NVSRQPIQTPQRRTDSTKQSNYRSQICRFFLTHSCTKGDACSYSHDIK 209
                                3444444443333333334466789********************763 PP

>> Com_YlbF  Control of competence regulator ComK, YlbF/YmcA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.4   1.3e-05     0.033      11      90 ..      27     103 ..      22     109 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.3e-05
                                HHHHSHHHHHHHHHHHHHHCSHHHHHHHHHH.HHHHHHHHHHHHTT----HHHHHHHHHHHHHHHTSHHHHHHHHHHHHHH CS
                   Com_YlbF  11 aIkeseeykeykeaeealeedeelqklikef.kklqkelqekqmkgeelkeeekkelqelkeeldknplvkeyleaeqeln 90 
                                ++  ++ +k++ + + a+  d +l++ +k++ +++++++++kq +g   k ee+ el+e +  ++   +v+e ++ e++l+
  gene47|gene47|rna47|rna47  27 MLVPTKLCKALLRFRTAILTDSDLKDELKDVsEAKNDTMNNKQDYG---KTEED-ELEEGEVYIKRKRVVSESYQGEKRLK 103
                                5566778899999******************666666778888666...33444.89998888999888888888888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1229  (0.0685482); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1855.29
//
Query:       gene470|gene470|rna470|rna470  [L=238]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.8e-25   88.4   0.2      1e-24   87.4   0.0    1.6  2  CTP_transf_like  Cytidylyltransferase-like


Domain annotation for each model (and alignments):
>> CTP_transf_like  Cytidylyltransferase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.4   0.0   5.6e-29     1e-24       1     142 [.       4     131 ..       4     132 .. 0.97
   2 ?   -2.1   0.0      0.22     4e+03     101     113 ..     179     191 ..     150     225 .. 0.65

  Alignments for each domain:
  == domain 1  score: 87.4 bits;  conditional E-value: 5.6e-29
                                    EEEE--TT--HHHHHHHHHHHHHSSES.EEEEEESSTHCSST-.SCSSTHHHHHHHHHHHTTCTTEEEEEEESEHHHHHH CS
                CTP_transf_like   1 lagGtFDpiHlGHlrlleqakklleed.livgvpsdeppkkkk.kplasaeeRlemlelakevdevisvdpweltrevlk 78 
                                    +++G++D++H+GH+r l qak+l+ +  l+vgv++d ++ ++k   +++++eR+e ++++++vdevi ++pw +t  +++
  gene470|gene470|rna470|rna470   4 YCDGVYDLFHYGHMRSLMQAKHLFPNVyLLVGVTNDCTTLQNKgSLVFNEHERTESVRHCRYVDEVIQDAPWSITDAFIE 83 
                                    689**********************************9999966************************************ PP

                                    HTTTTEEEEEEEHHHHHHHHCHHHHHHHHHHHHHEEEEEEHTTCEEEEEEECCTTTCSHHHHHH CS
                CTP_transf_like  79 klkpdklylvigadvledfsewkeleeilgnvklvvvsrpekqanvllkaekrtngiSstkire 142
                                     +++d  y+ ++  +++ +    +  ++++++k++ +          ++++ rt giS+t i++
  gene470|gene470|rna470|rna470  84 AHRID--YVCHDNVPYSCA----HTADVYDSLKRANK----------FIPTRRTLGISTTNIIT 131
                                    *****..*****9999988....**************..........***************86 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.22
                                    HHHHHHHHHHHHE CS
                CTP_transf_like 101 keleeilgnvklv 113
                                    +e++ei ++++++
  gene470|gene470|rna470|rna470 179 NEIREIRDELRIA 191
                                    2555555555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (238 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       697  (0.0388756); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.30s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 1536.48
//
Query:       gene471|gene471|rna471|rna471  [L=531]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (531 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1181  (0.0658709); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.59u 0.26s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 3504.37
//
Query:       gene472|gene472|rna472|rna472  [L=43]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (43 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       327  (0.0182386); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.27s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 316.02
//
Query:       gene473|gene473|rna473|rna473  [L=145]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.9e-26   89.5   2.5    1.3e-25   89.1   2.5    1.2  1  CutA1     CutA1 divalent ion tolerance protein


Domain annotation for each model (and alignments):
>> CutA1  CutA1 divalent ion tolerance protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.1   2.5   7.4e-30   1.3e-25       1      98 [.      45     142 ..      45     143 .. 0.98

  Alignments for each domain:
  == domain 1  score: 89.1 bits;  conditional E-value: 7.4e-30
                                    EEEEEEESSHHHHHHHHHHHHHTTS-SEEEEEEEEEEEEEETTEEEEEEEEEEEEEEEGGGHHHHHHHHHHHSSSSS-EE CS
                          CutA1   1 vlvlvtapseeeakklaralveeklaACvnilpkieSvYrWkgkieedkEvllliktreekveelekrvkelhpyevpei 80 
                                    v++++ +++e+e + + ++l+++kl+AC++ ++++eS+Y+W+gkie+++E+++ + t +++v+++e+ ++++h+y+  ++
  gene473|gene473|rna473|rna473  45 VIIFTAFKDENETNLILESLLRKKLIACAQKIQRVESTYVWNGKIENEEEIQVKMTTFNRCVPSIENIITKMHSYSFYQF 124
                                    58999*************************************************************************** PP

                                    EEEEESEEEHHHHHHHHH CS
                          CutA1  81 ialpieagseaYlkWiee 98 
                                    ia+++e ++e+Y++W+++
  gene473|gene473|rna473|rna473 125 IAVRLEYVNEKYIEWMRQ 142
                                    ***************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       718  (0.0400469); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 1041.25
//
Query:       gene474|gene474|rna474|rna474  [L=255]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    6.4e-72  242.1   2.1    7.5e-72  241.9   2.1    1.0  1  IP_trans    Phosphatidylinositol transfer protein
  ------ inclusion threshold ------
       0.09   12.5   0.1       0.15   11.7   0.1    1.3  1  Cactin_mid  Conserved mid region of cactin


Domain annotation for each model (and alignments):
>> IP_trans  Phosphatidylinositol transfer protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  241.9   2.1   8.3e-76   7.5e-72       3     245 ..       5     242 ..       3     244 .. 0.97

  Alignments for each domain:
  == domain 1  score: 241.9 bits;  conditional E-value: 8.3e-76
                                    EEEEEEEESS-HHHHHHHHHHHHHHHHTT-SSTTTTEEEEEEEEEE-TTS-EEEEEEEEEE-GGGS-HHHHTTS-TTTTE CS
                       IP_trans   3 ikeYriilPltveeyqiaqlYmvakaskeetgggegvevlknepyedeeggkgqytekiyhlesklPswlrallpkkalt 82 
                                    ++eY+i+lP+t ++y++aqlY+va  s +e++g+  +++++n++++d+++gk++yteki+ l+sk+P+++ra++pkkal 
  gene474|gene474|rna474|rna474   5 YREYQIPLPFTTKDYRVAQLYTVAMISANEATGDTSIRIVENKDITDDKYGKCRYTEKIFFLNSKVPRAIRAVVPKKALI 84 
                                    68****************************************************************************** PP

                                    EEEEEEEETTEEEEEEEET.TTGGGEEEEEEEEEESSSS--SSTT---HHHHTT-EEEEE-TT-GGG-GGG--GGG-TTT CS
                       IP_trans  83 veekawnaypytkTvytnp.lmkekfsikietvhkedngtqeNvfnlskeelkkreveviDivndkisskdykeeedptl 161
                                    vee a+na+p ++T ytn+ + +++fs ++ ++h +++ t +N++n++   + k++v+ iD++++      ++++ dpt+
  gene474|gene474|rna474|rna474  85 VEERAYNAFPTCHTFYTNQaFSTDTFSASVMSTHVNNDLTLKNALNIDRAIYDKTKVKLIDVCSNI-----VNPQYDPTK 159
                                    *******************9********************************************66.....788889999 PP

                                    ---TTT------T.HHHTST---EEEEEEEEEEE--SS-HHHHHHHHHHHHHHHHHHHHHHHHHTHHHHTT--HHHHHHH CS
                       IP_trans 162 fksektgrgpLkegWrkksekpvmcaYKlvtvefkvwglqtkveefihkalrklflkfhrqafcwideWygltmedirel 241
                                       + ++  pL+ gW+++ + +vm++YK+vt +f+++gl++ v+e+  k++ k+f+++h+q++c +deWyg ++ed+re+
  gene474|gene474|rna474|rna474 160 TPLKINNDCPLSAGWYENPSYDVMMCYKFVTLKFNCFGLGWLVHEI-EKQIDKIFTSSHQQMVCIMDEWYGKSIEDVREI 238
                                    99999999*********9*************************995.5******************************** PP

                                    HHHH CS
                       IP_trans 242 Eeet 245
                                    E+ +
  gene474|gene474|rna474|rna474 239 EDSI 242
                                    *987 PP

>> Cactin_mid  Conserved mid region of cactin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   1.7e-05      0.15     137     172 ..     202     252 ..     197     255 .] 0.91

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 1.7e-05
                     Cactin_mid 137 hasveadikkilk..............gksleeLeelekqikekLesge.a 172
                                     +++e++i+ki++              gks+e+ +e+e++i+ekL+++e +
  gene474|gene474|rna474|rna474 202 VHEIEKQIDKIFTsshqqmvcimdewyGKSIEDVREIEDSIREKLNEKEgK 252
                                    57899*****************************************88744 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       747  (0.0416643); expected 358.6 (0.02)
Passed bias filter:                      483  (0.0269396); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 1804.61
//
Query:       gene475|gene475|rna475|rna475  [L=226]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       706  (0.0393775); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1609.94
//
Query:       gene476|gene476|rna476|rna476  [L=56]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0015   18.4   0.4     0.0016   18.4   0.4    1.0  1  DUF1635   Protein of unknown function (DUF1635)
     0.0026   18.3   0.2     0.0028   18.2   0.2    1.1  1  ING       Inhibitor of growth proteins N-terminal histone-bin


Domain annotation for each model (and alignments):
>> DUF1635  Protein of unknown function (DUF1635)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.4   1.7e-07    0.0016      17      56 ..      10      49 ..       2      55 .. 0.92

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.7e-07
                        DUF1635 17 LettklkaqeelrkrdeeviqLkdlLkktikErdeAqekl 56
                                   Le++k   +e++r   ++ +++++ Lk+ ++Erd+A+++l
  gene476|gene476|rna476|rna476 10 LEEIKNVQNEKMRVVGKQATHVQKNLKRFTRERDNANDRL 49
                                   9************************************986 PP

>> ING  Inhibitor of growth proteins N-terminal histone-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.2   3.1e-07    0.0028      61      96 ..       5      40 ..       1      45 [. 0.90

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 3.1e-07
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            ING 61 riqeelkeaqelldeKiqlaqqaldlvdkhlrrLdq 96
                                   +i++ l+e++++++eK+ ++ + +  v+k+l+r+ +
  gene476|gene476|rna476|rna476  5 DIEKYLEEIKNVQNEKMRVVGKQATHVQKNLKRFTR 40
                                   89******************************9866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (56 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1568  (0.0874561); expected 358.6 (0.02)
Passed bias filter:                      667  (0.0372023); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.29s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 374.99
//
Query:       gene477|gene477|rna477|rna477  [L=85]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.05   13.5   0.1       0.16   11.9   0.0    1.8  2  TPR_10    Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   8.6e-06      0.16       7      28 ..      33      54 ..      32      57 .. 0.94
   2 ?   -1.6   0.0      0.15   2.8e+03      15      24 ..      61      70 ..      59      80 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 8.6e-06
                         TPR_10  7 NLanalrqrgrydeAealleea 28
                                   NLa+ + ++g+++  +++++ea
  gene477|gene477|rna477|rna477 33 NLAMFYKRMGNGKNFVRFMKEA 54
                                   9*******************99 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.15
                         TPR_10 15 rgrydeAeal 24
                                   rg+yd+ e  
  gene477|gene477|rna477|rna477 61 RGNYDGIELC 70
                                   7888876655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (85 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       471  (0.0262703); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.29s 00:00:00.69 Elapsed: 00:00:00.45
# Mc/sec: 573.28
//
Query:       gene478|gene478|rna478|rna478  [L=644]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (644 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       917  (0.0511462); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.63u 0.27s 00:00:00.90 Elapsed: 00:00:00.45
# Mc/sec: 4307.17
//
Query:       gene479|gene479|rna479|rna479  [L=61]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       313  (0.0174578); expected 358.6 (0.02)
Passed bias filter:                      231  (0.0128842); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.24s 00:00:00.58 Elapsed: 00:00:00.41
# Mc/sec: 449.57
//
Query:       gene48|gene48|rna48|rna48  [L=267]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.014   15.7   0.9      0.014   15.7   0.9    2.1  3  DUF5625   Domain of unknown function (DUF5625)
       0.89    9.5   9.3        2.2    8.2   9.3    1.6  1  DUF327    Protein of unknown function (DUF327)


Domain annotation for each model (and alignments):
>> DUF5625  Domain of unknown function (DUF5625)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.1       1.3   1.2e+04      67      83 ..       6      22 ..       3      40 .. 0.65
   2 ?   -1.8   0.0       0.4   3.6e+03      18      43 ..      50      74 ..      45      93 .. 0.66
   3 ?   15.7   0.9   1.6e-06     0.014      60     124 ..     204     263 ..     164     265 .. 0.76

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 1.3
                               TTS-EEEEEEEEEEE-S CS
                    DUF5625 67 kkndkkvildkkinakg 83
                               +k+d++  ldk  n+++
  gene48|gene48|rna48|rna48  6 TKKDNNKTLDKNANTME 22
                               45566666777776655 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.4
                               EE-SSEEEEEEEEE----CCCCTTHH CS
                    DUF5625 18 eieekgsyqlaLlfavndqkeemerv 43
                               +i+e + +++ L++++ +   e +++
  gene48|gene48|rna48|rna48 50 KINEFYGTEVVLEIDEDEM-REANNE 74
                               6777777777777776655.344444 PP

  == domain 3  score: 15.7 bits;  conditional E-value: 1.6e-06
                                EEEEEE-TTS-EEEEEEEEEEE-S--SSTTE...EEEEEEEE-SEEEEEEEEE-S--GGGTT--E CS
                    DUF5625  60 klkivknkkndkkvildkkinakglgsgaateyereIktlsLkkGkYsirietledvpelnglkv 124
                                 +   kn kn++kv++d k ++ +++   +   e  +++l++ kG+ +  ie+ e + e+n+ k 
  gene48|gene48|rna48|rna48 204 NI---KNVKNNTKVVFDTKTKTFKYSDFLKP--EMSLDELKMFKGRVKQLIEYFEKLKEMNDHKC 263
                                33...3456899***********99888666..556*************************9886 PP

>> DUF327  Protein of unknown function (DUF327)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   9.3   0.00025       2.2      10      81 ..     173     254 ..     165     264 .. 0.68

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00025
                                XXXXXXXXXX.....XXXXX-HHHHHHHHHHH.....HHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHH CS
                     DUF327  10 lkkskktkkk.....ekkkksFsetlekeeee.....eseeelkelleeidkqgerLaesrtiedlkkYkklvkeflkevvk 81 
                                 k+ kktkkk     +++ ksF ++++ ++++     ++ + + + +++  k  + L+ ++++++lk +k  vk+++++  k
  gene48|gene48|rna48|rna48 173 PKNPKKTKKKndetlATTFKSFFSSFTPKKKNiknvkNNTKVVFDTKTKTFKYSDFLKPEMSLDELKMFKGRVKQLIEYFEK 254
                                222222222234345667788888885555555555545555778888889999**********************998654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1852  (0.103296); expected 358.6 (0.02)
Passed bias filter:                      544  (0.0303419); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 1868.23
//
Query:       gene480|gene480|rna480|rna480  [L=105]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       494  (0.0275531); expected 358.6 (0.02)
Passed bias filter:                      207  (0.0115455); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 799.03
//
Query:       gene481|gene481|rna481|rna481  [L=248]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.6e-26   92.0  18.3    3.8e-25   88.6   0.2    2.1  2  Utp14     Utp14 protein


Domain annotation for each model (and alignments):
>> Utp14  Utp14 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.9  14.8   0.00043       7.8     219     244 ..      22      47 ..       5      69 .. 0.79
   2 !   88.6   0.2   2.1e-29   3.8e-25     621     737 ..     109     221 ..      62     223 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.00043
                          Utp14 219 eakakRikKIKSKtYrRihrKekeke 244
                                     +k kRik IKS++Yr++++ +++ e
  gene481|gene481|rna481|rna481  22 DKKMKRIKQIKSRKYRKHLKIARRNE 47 
                                    689***************99887765 PP

  == domain 2  score: 88.6 bits;  conditional E-value: 2.1e-29
                          Utp14 621 DDVvaeFekEKkevveeedpkevdktLPGWGsWaGegvkkrkkkkrkflkkvegvkkkkRkDaklknVIInEkrdkkaak 700
                                    D+  + F+kEK + v+++ p+e    LPGWGsW+G+g++ ++ + + +   +eg+ +k RkD ++ +VIInE + k++ k
  gene481|gene481|rna481|rna481 109 DEHLEIFKKEKMDHVKQNMPEETTMVLPGWGSWGGQGLETKQTSLNTICSSKEGIVPKRRKDFRMGRVIINENALKNNIK 188
                                    555677**************99999**************9998888889999***6667*******************99 PP

                          Utp14 701 ylvsqLPfpFeskeqYErslrlPlGpeWntketfqkl 737
                                        +LP+ F +k +YE+ l++P+ +e nt + fqk 
  gene481|gene481|rna481|rna481 189 I---DLPYGF-NKLEYEALLNMPVSKESNTLKIFQKF 221
                                    6...9*****.5789********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (248 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1336  (0.0745161); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1589.28
//
Query:       gene482|gene482|rna482|rna482  [L=221]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       742  (0.0413855); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1411.12
//
Query:       gene483|gene483|rna483|rna483  [L=119]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-11   43.4   1.4    2.9e-11   42.9   1.4    1.3  1  LSM       LSM domain


Domain annotation for each model (and alignments):
>> LSM  LSM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.9   1.4   1.6e-15   2.9e-11       2      66 ..      17      82 ..      16      83 .. 0.90

  Alignments for each domain:
  == domain 1  score: 42.9 bits;  conditional E-value: 1.6e-15
                                   HHHHTTTSEEEEEETTSEEEEEEEEEEETTSEEEEEEEEEEETTET.EEEEEEEEEEEGGGEEEEE CS
                            LSM  2 flkklinkkvtvelkngrelrGtLkgfDqfmNlvLedveetlkdkk.ekrklglvliRGnnivlis 66
                                   f++k ink+++velkng +++G+L ++D f+N+ L dv++ + ++      ++++ +RG+ + ++ 
  gene483|gene483|rna483|rna483 17 FFQKNINKNIIVELKNGLVISGKLLSCDIFLNIKLCDVTVKDLENYrGLSGVSTLSVRGSCVKYVK 82
                                   7899***********************************999886555556699******999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       593  (0.0330749); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.48
# Mc/sec: 745.36
//
Query:       gene484|gene484|rna484|rna484  [L=578]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.7e-10   40.7   0.9    1.7e-10   40.7   0.9    2.8  3  SMC_N      RecF/RecN/SMC N terminal domain
    2.6e-10   41.1  28.5    2.6e-10   41.1  28.5    3.9  2  AAA_23     AAA domain
      1e-06   28.8  29.8      1e-06   28.8  29.8    2.5  2  AAA_15     AAA ATPase domain
    2.4e-05   24.6   0.0    7.2e-05   23.1   0.0    1.9  1  SMC_hinge  SMC proteins Flexible Hinge Domain
  ------ inclusion threshold ------
      0.012   15.4   0.2      0.043   13.6   0.1    2.0  2  AAA_29     P-loop containing region of AAA domain
      0.042   14.1   3.1       0.17   12.2   3.1    2.2  1  FCH        Fes/CIP4, and EFC/F-BAR homology domain
        0.1   12.4  12.3       0.31   10.8   2.6    2.4  2  AAA_21     AAA domain, putative AbiEii toxin, Type IV TA syst
        6.2    6.6  10.1        1.7    8.4   0.1    3.2  3  MukB       MukB N-terminal
        7.9    6.9  42.6       0.34   11.4  30.7    2.2  2  Fez1       Fez1


Domain annotation for each model (and alignments):
>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.7   0.9   8.6e-14   1.7e-10       2     117 ..       7     117 ..       6     134 .. 0.82
   2 ?   -2.6   0.1       1.5     3e+03      92     118 ..     197     224 ..     143     244 .. 0.52
   3 ?    0.9   3.0      0.13   2.7e+02      60     119 ..     270     332 ..     254     350 .. 0.65

  Alignments for each domain:
  == domain 1  score: 40.7 bits;  conditional E-value: 8.6e-14
                                    EEEEEEESETTEECEEEEEETTSSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N   2 lkrleienFksyagktvilpfsksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaevei 81 
                                    +k+++++nF     ++  lpf + +t+i G NGSGKs ++ Ai  vLG+r++   r +++++li++       ++a++++
  gene484|gene484|rna484|rna484   7 IKSITLSNFMCH--TNLRLPFISPITVIGGFNGSGKSAIMIAIGIVLGQRTNALDRGSSAKSLIQN-----GKSSAKIQL 79 
                                    899******999..79********************************999966699********9.....556777888 PP

                                    EEEETTEESSSS..SSCEEEEEEEETTSEEEEEETTEE CS
                                    xxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N  82 tfdnedkklkie..keevsisrrvkrkgeseykingke 117
                                     ++n +++++     +++ ++r +kr+   +++i++ +
  gene484|gene484|rna484|rna484  80 ELSNVQHRFNYGffGNSIILERVIKRDAAHSIRIKNDS 117
                                    88888888554311566777788888877777776655 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.5
                                    SSSSCEEEE.EEEETTSEEEEEETTEEE CS
                                    xxxxxxxxx.xxxxxxxxxxxxxxxxxx RF
                          SMC_N  92 iekeevsis.rrvkrkgeseykingkev 118
                                     ++e ++i  rr+k+k + ++ ++g+++
  gene484|gene484|rna484|rna484 197 LNEELLEIDaRRKKKKSDLDIVVDGSKI 224
                                    2222334431223333334555555554 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.13
                                    CCCCCC--BTTCSSTTEEEEEEEE...EETTEESSSSSSCEEEEEEEETTSEEEEEETTEEE- CS
                                    xxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N  60 klsdlihkskekasvkkaeveitf...dnedkklkiekeevsisrrvkrkgeseykingkevt 119
                                    + + +i++ k++++ k++ev+ +    ++ +k l++  ++++++ r ++++  e +in +e +
  gene484|gene484|rna484|rna484 270 QNHLMINEMKKEEQEKECEVKRIRaeiSERKKILEEAVKNYELEEREMKNDLEELTINYNEKK 332
                                    444577778899999999999876322444444666677788888888888878777654432 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.1  28.5   1.3e-13   2.6e-10       1     194 [.       9     298 ..       9     311 .. 0.50
   2 ?  -22.5  42.9         9   1.8e+04     102     196 ..     277     379 ..     241     488 .. 0.60

  Alignments for each domain:
  == domain 1  score: 41.1 bits;  conditional E-value: 1.3e-13
                         AAA_23   1 kLkienfrsfrdqeidFskgltlItGpNGaGKTTildAiklaLygetprlsrks.......................... 54 
                                    +++++nf+++ +  + F +++t+I G NG+GK++i+ Ai  +L+ +t+ l+r+s                          
  gene484|gene484|rna484|rna484   9 SITLSNFMCHTNLRLPFISPITVIGGFNGSGKSAIMIAIGIVLGQRTNALDRGSsaksliqngkssakiqlelsnvqhrf 88 
                                    699**********************************************9998755444444444333333333333333 PP

                         AAA_23  55 grgfeksdveiese..gkvkayveltfenkdgry.............................................t 87 
                                    + gf+ +++ +e    ++ + +++++  n++g+                                               
  gene484|gene484|rna484|rna484  89 NYGFFGNSIILERVikRDAAHSIRIK--NDSGKIfstkkedldyiidyfqlhidnplnfltqenskkflkitkaedlysL 166
                                    22333333333333322222223333..2222223444444466666666666555444333333333333333332220 PP

                         AAA_23  88 rsiererelskkkgkttkkaklelleideleqfisellgskkiilnlilflgqerfeefelkdkke.............. 153
                                                         l+++e d+  ++ +e  +++ +  +++ +l +e  e  ++ +kk+              
  gene484|gene484|rna484|rna484 167 --------------------FLRGTELDDVAELHDEANKKTTEMKTRLELLNEELLEIDARRKKKKsdldivvdgskide 226
                                    ....................333333333333333333333333333333333332222222222245555555555555 PP

                         AAA_23 154 .................................rleelekeleeledekkllekleqekekekeleeleeelee 194
                                                                     +++el ++++++  ++++++k+eqeke   e + ++ e+ e
  gene484|gene484|rna484|rna484 227 kiaqlkneiewsrlkeslleirarkeemdvlsrEVKELDNKINQNHLMINEMKKEEQEKE--CEVKRIRAEISE 298
                                    555555555555555555556666666666666777777777777777777776665544..233333333333 PP

  == domain 2  score: -22.5 bits;  conditional E-value: 9
                         AAA_23 102 kttkkaklelleideleqfisellgskkiilnlilflgqerfeefel........kdkkerleeleke..leeledekkl 171
                                    + +k+++++++e++  + +ise  ++ ++  +++     e+ e++++        ++kk+rl++l++   +++l ++k l
  gene484|gene484|rna484|rna484 277 EMKKEEQEKECEVKRIRAEISERKKILEEAVKNYE---LEEREMKNDleeltinyNEKKQRLQNLNRLggIDKLAEKKAL 353
                                    22333333444443333333333333322222111...111111111122333345555555555555445555555555 PP

                         AAA_23 172 lekle.qekekekeleeleeeleeil 196
                                    le+++  e+++ ++le+l +++ e +
  gene484|gene484|rna484|rna484 354 LEQKLgMEEKYSAQLETLSQKMAEEN 379
                                    55553233334444444444444332 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.8  29.8     5e-10     1e-06       3     288 ..       7     345 ..       6     359 .. 0.56
   2 ?   -4.4  14.2       6.2   1.2e+04      97     209 ..     349     485 ..     343     492 .. 0.82

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 5e-10
                         AAA_15   3 IkkikikNFRslkdveidlseeltvliGkNnsGKSsilealdlFlnnkekkn............................ 54 
                                    Ik+i++ NF ++ +  +++ + +tv+ G N+sGKS i+ a+ + l +    n                            
  gene484|gene484|rna484|rna484   7 IKSITLSNFMCHTNLRLPFISPITVIGGFNGSGKSAIMIAIGIVLGQR--TNaldrgssaksliqngkssakiqlelsnv 84 
                                    9*********************************************76..333466666666666666666666666666 PP

                         AAA_15  55 .......................kkvikiekedleifeniseskdikIdvefaekekakeyektlkskekkkadlllkkk 111
                                                              i i++++ +if  ++e+ d  Id+         +++ ++  ++++++++l + k
  gene484|gene484|rna484|rna484  85 qhrfnygffgnsiilervikrdaAHSIRIKNDSGKIFSTKKEDLDYIIDYFQ-----LHIDNPLNFLTQENSKKFLKITK 159
                                    6666665555555555555555544455555555555555555554444322.....22222222233333333344444 PP

                         AAA_15 112 esdlkktikdkklklkknelsdekisvekkkskkelpkekeeklekekeelkidkedlkklikkleeslkkee....... 184
                                     +dl++++   +  ++         +++++  +k+  ++k+  + +++e l+id   +kk ++ l   + +++       
  gene484|gene484|rna484|rna484 160 AEDLYSLFLRGTELDD-------VAELHDEA-NKKTTEMKTRLELLNEELLEIDARRKKKKSD-LDIVVDGSKidekiaq 230
                                    4444444444444422.......22222222.2233333344444444444444333333333.3333333335544443 PP

                         AAA_15 185 .........elknvlksaiiklllisakRnvsdedsekkssllgklkekileealqekl........eeelteklkeiqe 247
                                             +++++l+  ++k + +   R+v++ d++ +++                 l        e+e++++ k+i  
  gene484|gene484|rna484|rna484 231 lkneiewsrLKESLLEIRARKEEMDVLSREVKELDNKINQNH----------------LminemkkeEQEKECEVKRIRA 294
                                    323222222444444444444444444444444333332222................2222222338899999999999 PP

                         AAA_15 248 klkeidkklaeelk......kilkkkidkikkfnykgkkneeieik.....d 288
                                    +++e +k+l+e  k      +++k++++++  +ny++kk+ + +++     d
  gene484|gene484|rna484|rna484 295 EISERKKILEEAVKnyeleeREMKNDLEEL-TINYNEKKQRLQNLNrlggiD 345
                                    999999999999999999887788888885.999999999887776665551 PP

  == domain 2  score: -4.4 bits;  conditional E-value: 6.2
                         AAA_15  97 kskekkkadlllkkkesdlkktikdkklklkknelsdekisvekkkskkelpkekeeklekekeelkidkedlkklikkl 176
                                    ++k+  +++l +++k+s+  +t+ +k+ + ++   s++ + v++++ + ++ k  e+ ++ ek++l +   +++++++++
  gene484|gene484|rna484|rna484 349 EKKALLEQKLGMEEKYSAQLETLSQKMAEENERSSSNKAKLVQHRQTESNISKQIEFLKKIEKNKLLFFHTKINDILREI 428
                                    4555667778899999999************************************************************* PP

                         AAA_15 177 eeslkkee......................elknvlksaii..klllisakRnvsde 209
                                    ++++  ++                       lkn l+++i   k + i+ kR ++++
  gene484|gene484|rna484|rna484 429 RSCKFNDDvigpigsyitlkdfkwnkaisiILKNTLSNFIAfcKEDKIKLKRIFNKY 485
                                    *99999999999999999998888887777666666665542244555666666665 PP

>> SMC_hinge  SMC proteins Flexible Hinge Domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.0   3.6e-08   7.2e-05       3     109 ..     436     545 ..     434     553 .. 0.77

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 3.6e-08
                      SMC_hinge   3 gvlGrladlievd.egyekAveaalgnrlqalvvedeetakkiieflkkknagratflpldrikqknkadgandknsgav 81 
                                    +v+G++++ i+++  ++ kA++++l n l++++   +e+  k+ + + k +  + t+l+    +++++a+ +++k  g  
  gene484|gene484|rna484|rna484 436 DVIGPIGSYITLKdFKWNKAISIILKNTLSNFIAFCKEDKIKLKRIFNKYD-ANFTILVP---SSRSDAPINYEKRTGHN 511
                                    699**********99*******************99999999999999994.34555444...4444555555555599* PP

                      SMC_hinge  82 plidlvevddelrkalr......yllgdtlvvds 109
                                    ++id++ev+   ++++       + l ++++v++
  gene484|gene484|rna484|rna484 512 FAIDVIEVNHPRKNVILnqliimNSLENIILVED 545
                                    ***********88888445555566777777776 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   2.2e-05     0.043      12      47 ..      18      52 ..       7      63 .. 0.74
   2 ?   -2.4   0.0         2   4.1e+03      40      51 ..     486     497 ..     485     500 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.2e-05
                         AAA_29 12 fdghtieidlkg.atlltGpsGsGKSTllDAiqalLv 47
                                    ++ ++++   + +t++ G +GsGKS+++ Ai ++L 
  gene484|gene484|rna484|rna484 18 HTNLRLPFI--SpITVIGGFNGSGKSAIMIAIGIVLG 52
                                   555555554..33899*************99999985 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 2
                         AAA_29  40 DAiqalLvpakk 51 
                                    DA  ++Lvp+++
  gene484|gene484|rna484|rna484 486 DANFTILVPSSR 497
                                    9999*****984 PP

>> FCH  Fes/CIP4, and EFC/F-BAR homology domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   3.1   8.6e-05      0.17      12      70 ..     343     397 ..     316     410 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 8.6e-05
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCT----TT-.....HHHHHHHHHHHHHHHH CS
                            FCH  12 gialledlqeflkeRaeiEkeYakkLqkLakkylkrrkkkseestlvtawtvlleetek 70 
                                    gi+ l + +++l ++   E+ Y+++L+ L++k++++     e+s++++a  v+  +te+
  gene484|gene484|rna484|rna484 343 GIDKLAEKKALLEQKLGMEEKYSAQLETLSQKMAEEN----ERSSSNKAKLVQHRQTES 397
                                    67777778889999999******************65....457777776666666664 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   2.6   0.00016      0.31       1     106 [.      29     139 ..      29     156 .. 0.72
   2 ?    5.9   3.2     0.005        10      30     217 ..     149     314 ..     142     339 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00016
                         AAA_21   1 lnvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfefeieeflsqgvryryglrler 80 
                                    ++v+ G NgsGKS ++ a+ ++ + ++++ ++++++ +  +++k + ++ l   +   +f    f+ +++  +  ++ + 
  gene484|gene484|rna484|rna484  29 ITVIGGFNGSGKSAIMIAIGIVLGQRTNALDRGSSAKSLIQNGKSSAKIQLELSNVQHRFNYG-FFGNSIILERVIKRDA 107
                                    79*****************99987788888888888888888888888888888888888888.5555555555555555 PP

                         AAA_21  81 sqv......eeklssvetllesgllldkrsle 106
                                     +       + k++s ++  +++++++ +  +
  gene484|gene484|rna484|rna484 108 AHSirikndSGKIFSTKKEDLDYIIDYFQLHI 139
                                    55546666666666666666666666555554 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.005
                         AAA_21  30 egltdelsggggirkipslldlydpeipfefeieeflsqgvryryglrlersqveeklssvetllesgllldkrsleeed 109
                                    e+++ +l  ++ ++ ++ +l++++ +  +e+++e  +++ ++ + +l+l ++ +                   +++ +++
  gene484|gene484|rna484|rna484 149 ENSKKFLKITKAEDLYSLFLRGTELDDVAELHDE-ANKKTTEMKTRLELLNEEL------------------LEIDARRK 209
                                    5566666667777888888888888888888888.8888888888888888888..................99999999 PP

                         AAA_21 110 vfnpeargirggvsvfslkelsvsepndlqfgkaltditsrawsllllldglrkerigllnifadyfgfakekrllqrlv 189
                                    ++ ++ +   +g +  + ++ +++e ++   ++ l++i++r+++   l+++    + + + i ++++  ++ k+  q+ +
  gene484|gene484|rna484|rna484 210 KKKSDLDIVVDGSKIDEKIAQLKNEIEWSRLKESLLEIRARKEEMDVLSREV---KELDNKINQNHLMINEMKKEEQEKE 286
                                    999999**************************************99999999...************************* PP

                         AAA_21 190 rslklveielsdlgegeeliasvderlr 217
                                     ++k++++e+s  ++  e+  ++ e++ 
  gene484|gene484|rna484|rna484 287 CEVKRIRAEISERKKILEEAVKNYELEE 314
                                    **********999887776655555544 PP

>> MukB  MukB N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.1   0.00087       1.7       7      50 ..       8      51 ..       2      64 .. 0.83
   2 ?    1.3   1.1      0.12   2.4e+02     104     156 ..     257     296 ..     238     312 .. 0.52
   3 ?    0.5   1.1      0.23   4.5e+02     117     197 ..     307     385 ..     293     404 .. 0.65

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00087
                                   EEEEEEEETTEEEEEE-HHHHHHHHHS--SHHHHHHHHHHHHHH CS
                           MukB  7 ksltlinWnGffartfdldelvttlsGgnGaGksttmaafvtal 50
                                   ks+tl n+      +  + + +t + G nG+Gks++m+a+ ++l
  gene484|gene484|rna484|rna484  8 KSITLSNFMCHTNLRLPFISPITVIGGFNGSGKSAIMIAIGIVL 51
                                   6777777777777777777889*****************97766 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.12
                                    EEEE-SSTTT-EEEEEEEEES--TT--HHHHHEE--SSS--EE--HHHHHHHH CS
                           MukB 104 rleqvagrdkkvdikpfalqgleedvkltdvlleklddkkarvrelnelkekl 156
                                      ++v + d+k++ + +++++++++ + ++  ++              +++++
  gene484|gene484|rna484|rna484 257 LSREVKELDNKINQNHLMINEMKKEEQEKECEVK-------------RIRAEI 296
                                    2234455555555555555555555555544444.............444333 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.23
                                    EEEEEEES--TT--HHHHHEE--SSS--EE--HHHHH..HHHHTSTT-EEEE-S-HHHHHHHHHHTTSBSS---SHHHHH CS
                           MukB 117 ikpfalqgleedvkltdvlleklddkkarvrelnelk..ekleelegvrlkkfnsvtdyhallfdlGvipkrlrssedrs 194
                                    +k + l++ e++  l ++ + + ++kk+r+++ln l   +kl+e +++  +k    + y a+l     ++++++++++rs
  gene484|gene484|rna484|rna484 307 VKNYELEEREMKNDLEEL-TINYNEKKQRLQNLNRLGgiDKLAEKKALLEQKLGMEEKYSAQL---ETLSQKMAEENERS 382
                                    455666666666666554.55567779999999988533677776665555555555555544...34677777777777 PP

                                    HHH CS
                           MukB 195 kfy 197
                                      +
  gene484|gene484|rna484|rna484 383 SSN 385
                                    544 PP

>> Fez1  Fez1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   3.9       0.2   3.9e+02      39     103 ..     172     235 ..     157     239 .. 0.75
   2 ?   11.4  30.7   0.00017      0.34      18     164 ..     239     395 ..     237     420 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.2
                           Fez1  39 qlrelrakleekeeeikeleesleektlelevcenelqrkkseaellrekvekleeelkelreel 103
                                    +l ++ +  +e +++++e++++le  ++el +++++ ++kks+ +++ +  +k++e++++l++e+
  gene484|gene484|rna484|rna484 172 ELDDVAELHDEANKKTTEMKTRLELLNEELLEIDARRKKKKSDLDIVVD-GSKIDEKIAQLKNEI 235
                                    4445555556778888888888888888888888888888888888888.788888999988876 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00017
                           Fez1  18 QLkdsqaevtqklseivalkaqlrelrakleekeeeikeleesleektlelevcenelqrkkseaellrekvekleeelk 97 
                                     Lk+s  e+ ++ +e+  l  +++el +k++++   i+e++++ +ek+ e++++ +e++++k   ++l+e v+++e e +
  gene484|gene484|rna484|rna484 239 RLKESLLEIRARKEEMDVLSREVKELDNKINQNHLMINEMKKEEQEKECEVKRIRAEISERK---KILEEAVKNYELEER 315
                                    69********************************************************9986...78999999999999* PP

                           Fez1  98 elreelselsleeeeaa............lesdeakaq.rqeaeeleelkreverlraeLkeerqkkeeqassFeqERrt 164
                                    e++++l+el+ + +e++             +  e+ka  +q+    e+ ++++e l ++++ee++++ +++++  q R+t
  gene484|gene484|rna484|rna484 316 EMKNDLEELTINYNEKKqrlqnlnrlggiDKLAEKKALlEQKLGMEEKYSAQLETLSQKMAEENERSSSNKAKLVQHRQT 395
                                    ****9999887766655677788888776333333333133456677889999***********9999999999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (578 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2510  (0.139997); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); expected 358.6 (0.02)
Passed Vit filter:                        81  (0.00451782); expected 17.9 (0.001)
Passed Fwd filter:                        24  (0.00133861); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.94u 0.35s 00:00:01.29 Elapsed: 00:00:00.52
# Mc/sec: 3329.34
//
Query:       gene485|gene485|rna485|rna485  [L=290]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.3e-09   38.1   0.6    5.3e-09   36.0   0.6    1.9  1  NIF         NLI interacting factor-like phosphatase
  ------ inclusion threshold ------
       0.04   14.3   0.4       0.17   12.3   0.1    2.2  2  EntA_Immun  Enterocin A Immunity


Domain annotation for each model (and alignments):
>> NIF  NLI interacting factor-like phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.0   0.6     6e-13   5.3e-09      31     151 ..      95     202 ..      79     207 .. 0.91

  Alignments for each domain:
  == domain 1  score: 36.0 bits;  conditional E-value: 6e-13
                            NIF  31 vsvlkRpgldefLkelsklyevvifTasseeyaeavidildpekkllshrlyrescvkkkgeyvKdLsllgrdlsrvviv 110
                                      + +Rp+ d fL  l+++ye++ + + +++  + + ++ldp+++ +++r+   s              l+rd sr +++
  gene485|gene485|rna485|rna485  95 LKIVLRPYSDIFLFDLAQNYELISYGMFTPSESKFIYKHLDPYGC-INYRINTASID------------LNRDTSRLIVI 161
                                    57899***************************************8.99999888883............689******** PP

                            NIF 111 Ddspdsfelqpe.ngipiksffsdkkDneLlkllpllkelak 151
                                    + + +++ ++ + n+++i+s+   k+D+ L+ l ++l +l +
  gene485|gene485|rna485|rna485 162 ETENRQWDKKYDeNILRIESWN-GKDDERLFLLDQFLSNLLY 202
                                    *********9999********7.689999********98865 PP

>> EntA_Immun  Enterocin A Immunity
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   1.9e-05      0.17      39      68 ..      42      73 ..      27      74 .. 0.82
   2 ?   -2.3   0.0      0.69   6.2e+03      47      59 ..     193     205 ..     184     216 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.9e-05
                     EntA_Immun 39 nvsv..vasrLeqelrsyalknkikLppevsd 68
                                   + s+  + ++L + ++++++++k++Lpp++ +
  gene485|gene485|rna485|rna485 42 QISFlsIFAELRNRISPLSMTKKHQLPPQQQK 73
                                   44445599********************9976 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.69
                     EntA_Immun  47 Leqelrsyalknk 59 
                                    L+q l+++++++k
  gene485|gene485|rna485|rna485 193 LDQFLSNLLYTDK 205
                                    7788888888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (290 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       560  (0.0312343); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.50
# Mc/sec: 1740.28
//
Query:       gene486|gene486|rna486|rna486  [L=214]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.039   13.6   0.0      0.073   12.7   0.0    1.3  1  Fe_bilin_red  Ferredoxin-dependent bilin reductase
       0.37   10.7   3.2        1.2    9.1   0.3    2.6  3  SIKE          SIKE family


Domain annotation for each model (and alignments):
>> Fe_bilin_red  Ferredoxin-dependent bilin reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   8.2e-06     0.073     102     209 ..      98     211 ..      82     212 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 8.2e-06
                                    STTS---HHHHHHHHCT-.-..---SS...B----GGGG.GS-TT-EEE-...--SHHH....HHHHHHHHHHHHHHHHH CS
                   Fe_bilin_red 102 sqdkdykekyvekLkklkekyqealee...gkklpedatkyFSpavlfar...esseee....eerlleafkeylqaylq 171
                                    +++ dy +++v ++ +l+e  ++ +++   +kk  +  t   S++v  +r   e+s+++    e+ + ++ + +++ yl+
  gene486|gene486|rna486|rna486  98 ETRLDYMKAFVAQIHSLEEINNPPFRKvenSKKAENVTTIACSKYVTITRkevEGSKKVisefENGVENVCDMFITSYLK 177
                                    555689999999999999855544443110333333344446********998555555001145555566666666666 PP

                                    HHHH--B--HHHHHHHHHHHHHHHHHHHCCHHCHHHHH CS
                   Fe_bilin_red 172 lldeaepeaeaeeeaevleaqkaYdayqaekDpargll 209
                                    l+d+  +     +++e++ + ++  + q e+Dp +g+l
  gene486|gene486|rna486|rna486 178 LSDALLQI----RKKEIKFENDQVKQLQHENDPLNGML 211
                                    66665555....55666666666778999999999998 PP

>> SIKE  SIKE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.18   1.6e+03      23     150 ..      17      45 ..       5      62 .. 0.54
   2 ?    0.2   0.0      0.07   6.2e+02      28      57 ..      90     119 ..      87     142 .. 0.75
   3 ?    9.1   0.3   0.00013       1.2      67      89 ..     189     211 ..     182     212 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.18
                           SIKE  23 taAdsLleqaqalnkkiesmkqyqeevkelneiakekprseLiagiqqenrqireLqqENreLrasleehqsaLelImsK 102
                                    t++ds+ ++ ++++ +i + k                                                           
  gene486|gene486|rna486|rna486  17 TSTDSITSNLSSIKMRIAELK----------------------------------------------------------- 37 
                                    445555555555555555554........................................................... PP

                           SIKE 103 YReqvskllkakkeekkeavlkkklseevesqeekieeMaaVmrkave 150
                                                                            +  ++  +
  gene486|gene486|rna486|rna486  38 ----------------------------------------RTFESYLS 45 
                                    ........................................33333333 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.07
                           SIKE  28 Lleqaqalnkkiesmkqyqeevkelneiak 57 
                                    L+e  + ++++++ mk++  ++++l+ei +
  gene486|gene486|rna486|rna486  90 LVELLSYTETRLDYMKAFVAQIHSLEEINN 119
                                    566667788999999999999999998877 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.00013
                           SIKE  67 giqqenrqireLqqENreLrasl 89 
                                    +i+ en q+++Lq+EN+ L+ +l
  gene486|gene486|rna486|rna486 189 EIKFENDQVKQLQHENDPLNGML 211
                                    5788*************998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       895  (0.0499191); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 1351.34
//
Query:       gene487|gene487|rna487|rna487  [L=197]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       776  (0.0432818); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1426.17
//
Query:       gene488|gene488|rna488|rna488  [L=1566]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      3e-23   82.5  12.6    4.5e-19   68.9   2.6    3.0  3  VPS13_C   Vacuolar-sorting-associated 13 protein C-terminal
  ------ inclusion threshold ------
      0.084   13.2   0.0       0.17   12.3   0.0    1.5  1  ATG_C     Autophagy-related protein C terminal domain


Domain annotation for each model (and alignments):
>> VPS13_C  Vacuolar-sorting-associated 13 protein C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.1      0.64   5.7e+03      39      79 ..    1076    1118 ..    1064    1131 .. 0.74
   2 !   68.9   2.6     5e-23   4.5e-19       2     167 ..    1221    1368 ..    1220    1371 .. 0.90
   3 !   19.6   0.5   7.1e-08   0.00063     107     166 ..    1387    1446 ..    1385    1450 .. 0.95

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 0.64
                        VPS13_C   39 lllllnslgvtlt..niddapikLnalelenvflsleslieki 79  
                                     ++ l+nsl+v+l   n++ +++ ++ le  +++++l++l++  
  gene488|gene488|rna488|rna488 1076 FVVLINSLTVSLFenNCEFVNLYFRDLEAVKQIDTLKNLFTYA 1118
                                     4445999999995226777888889999999999999888765 PP

  == domain 2  score: 68.9 bits;  conditional E-value: 5e-23
                        VPS13_C    2 iYfeklhlqPiklhlsfslsekknkeeslekeqsllslllllnslgvtltniddapikLnalelenvflsleslieki 79  
                                     ++   lh++Pi+l+l +  s+kk+  +         +       +g+ ++n++++ + ++ l+ ++  ++     + i
  gene488|gene488|rna488|rna488 1221 LFCTLLHIHPINLRLNLLISKKKHFIH---------K------LIGFLVSNLSEVRLSFTTLIFSQFEYN----NDLI 1279
                                     578889999999999999998888733.........3......3588899************99888777....4557 PP

                        VPS13_C   80 kkhYsqqllkqlykilgsldvlGNPvglfnnissGvkdlfyePiqglvkg.peefgeglakGaksLvkktvfGvadsv 156 
                                     ++ Y+ q+l+q+++++g+ld+lGN   l++++s Gv+dlfyeP+ gl ++    f++g+ kG k +v+  + G++++v
  gene488|gene488|rna488|rna488 1280 INAYKMQMLSQIFNLIGGLDLLGNLSSLVEELSLGVHDLFYEPYVGLKHDdLFMFTKGILKGGKNFVTYCISGLTSTV 1357
                                     889**********************************************98999************************ PP

                        VPS13_C  157 skitgsvskgl 167 
                                      k+  s+s++ 
  gene488|gene488|rna488|rna488 1358 GKMGRSISRTS 1368
                                     *****999876 PP

  == domain 3  score: 19.6 bits;  conditional E-value: 7.1e-08
                        VPS13_C  107 lfnnissGvkdlfyePiqglvkgpeefgeglakGaksLvkktvfGvadsvskitgsvskg 166 
                                     l++n+  G++ ++ +P++g+ kg + f++g+ +G k  + k + G+++ +++i+++++++
  gene488|gene488|rna488|rna488 1387 LIENVVDGLSGIITKPVKGAKKGVKGFLKGVGSGLKGALMKPIAGISEFAANISDNIKTN 1446
                                     89*****************************************************99876 PP

>> ATG_C  Autophagy-related protein C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   1.9e-05      0.17      21      85 ..    1386    1449 ..    1382    1461 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.9e-05
                          ATG_C   21 slskglksaaqtilavpsevaeskgakgavkavvravPvavlrPligateavsktlqGvrnqldp 85  
                                      l +++    + i+++p + a+ kg+kg++k+v   +  a+++P+ g++e ++++   ++ +++ 
  gene488|gene488|rna488|rna488 1386 DLIENVVDGLSGIITKPVKGAK-KGVKGFLKGVGSGLKGALMKPIAGISEFAANISDNIKTNMNG 1449
                                     5778888999999999999765.9*******************************9999888754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1566 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       589  (0.0328518); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.79u 0.28s 00:00:01.07 Elapsed: 00:00:00.43
# Mc/sec: 10918.14
//
Query:       gene489|gene489|rna489|rna489  [L=211]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.2e-19   67.8   3.7    5.2e-19   67.8   3.7    1.7  2  Homeodomain  Homeodomain


Domain annotation for each model (and alignments):
>> Homeodomain  Homeodomain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.8   3.7   2.9e-23   5.2e-19       2      57 .]      29      84 ..      28      84 .. 0.98
   2 ?   -2.4   0.0      0.24   4.4e+03       7      27 ..     141     161 ..     134     166 .. 0.55

  Alignments for each domain:
  == domain 1  score: 67.8 bits;  conditional E-value: 2.9e-23
                                   T-SSSS-HHHHHHHHHHHHHSSS-SHHHHHHHHHHHTS-HHHHHHHHHHHHHHHHH CS
                    Homeodomain  2 rkRttftkeqleeLeklFeenrypsaeereeLAkklgLeerqVkvWFqNrRakekk 57
                                   ++R + +k+ql++Lek Fe n +p+a  r +L+++lg++ r V+vWFqNrRak+kk
  gene489|gene489|rna489|rna489 29 KHRKRTSKTQLKILEKTFETNIKPDAVLRNQLSEQLGMTPRSVQVWFQNRRAKQKK 84
                                   7899***************************************************8 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.24
                                    S-HHHHHHHHHHHHHSSS-SH CS
                    Homeodomain   7 ftkeqleeLeklFeenrypsa 27 
                                    +++   ++L+k+ ++++y ++
  gene489|gene489|rna489|rna489 141 ISPVHDKALKKMAQNDHYATR 161
                                    444444556666666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1413  (0.0788109); expected 358.6 (0.02)
Passed bias filter:                      637  (0.035529); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.22s 00:00:00.68 Elapsed: 00:00:00.38
# Mc/sec: 1668.76
//
Query:       gene49|gene49|rna49|rna49  [L=190]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        1.3    9.5   7.5        1.1    9.7   1.0    2.5  2  ICMT      Isoprenylcysteine carboxyl methyltransferase (ICMT)


Domain annotation for each model (and alignments):
>> ICMT  Isoprenylcysteine carboxyl methyltransferase (ICMT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.5     0.008   1.4e+02      50      88 ..       9      43 ..       5      48 .. 0.72
   2 ?    9.7   1.0   6.1e-05       1.1      31      75 ..     105     149 ..      87     159 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.008
                       ICMT 50 llfvilelatllLlcnakltalvllalvalllfvRikeE 88
                               +l  + +l +llL  n    ++ +++l+alllf  i++ 
  gene49|gene49|rna49|rna49  9 FL--LGSLHVLLLRYNT--PCTTVFSLYALLLFLYIYTT 43
                               44..6667777777776..78888888999999877765 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 6.1e-05
                       ICMT  31 pdhklvksglykylrHPnYllfvilelatllLlcnakltalvlla 75 
                                ++++   +gl++++rHP     +i  ++  + l ++  +a+++  
  gene49|gene49|rna49|rna49 105 SNTTTPFTGLFSVVRHPLHSSLFIFLVGSCVYLSSFVSLAVLVWY 149
                                55555668**********************999999888877655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (190 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       689  (0.0384294); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.22s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1488.36
//
Query:       gene490|gene490|rna490|rna490  [L=117]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.3e-06   25.4   1.7    8.3e-06   25.4   1.7    2.4  2  SAP       SAP domain
    0.00031   20.6   0.2    0.00059   19.7   0.2    1.4  1  Rho_N     Rho termination factor, N-terminal domain
     0.0011   18.6   0.3     0.0037   16.9   0.3    1.8  1  HeH       HeH/LEM domain
  ------ inclusion threshold ------
        0.1   11.9   0.0       0.19   11.0   0.0    1.4  1  LETM1     LETM1-like protein


Domain annotation for each model (and alignments):
>> SAP  SAP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   1.7   1.9e-09   8.3e-06       1      31 [.       3      34 ..       3      38 .. 0.81
   2 ?   -2.6   0.1       1.2   5.2e+03      26      30 ..     100     104 ..      99     104 .. 0.71

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 1.9e-09
                                   HTT--HHHHHHHHHHTT--TTS-.HHHHHHHH CS
                            SAP  1 lskltVaeLKeeLkkrGLptsGk.KaeLieRL 31
                                   ++kltVa+L+ee+kkr + t  + K+eLie L
  gene490|gene490|rna490|rna490  3 FKKLTVAQLREECKKRDINTVNLkKTELIEHL 34
                                   69****************98544488888755 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.2
                                    HHHHH CS
                            SAP  26 eLieR 30 
                                    eL+eR
  gene490|gene490|rna490|rna490 100 ELQER 104
                                    78887 PP

>> Rho_N  Rho termination factor, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.2   1.3e-07   0.00059       3      36 ..       4      36 ..       2      39 .. 0.94

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1.3e-07
                                   HHS-HHHHHHHHHHTT-TTGGGS-HHHHHHHHHH CS
                          Rho_N  3 kektlseLraiAkelgienysrlRKqdLIfaIlk 36
                                   k++t+++Lr+  k+ +i n+  l+K +LI+++l 
  gene490|gene490|rna490|rna490  4 KKLTVAQLREECKKRDI-NTVNLKKTELIEHLLR 36
                                   89***************.*************996 PP

>> HeH  HeH/LEM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.3   8.3e-07    0.0037       2      33 ..       4      34 ..       4      36 .. 0.94

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 8.3e-07
                            HeH  2 ksLtVaqLRriLvehgveyPsnaKKadLveLf 33
                                   k+LtVaqLR++  + ++   +n KK +L+e++
  gene490|gene490|rna490|rna490  4 KKLTVAQLREECKKRDINT-VNLKKTELIEHL 34
                                   79***************96.9*********97 PP

>> LETM1  LETM1-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   4.3e-05      0.19     218     248 ..       4      34 ..       2      37 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 4.3e-05
                          LETM1 218 dsLseeeLqeacrsRGlraaglseeelreqL 248
                                    ++L++ +L+e c++R +++++l+++el+e+L
  gene490|gene490|rna490|rna490   4 KKLTVAQLREECKKRDINTVNLKKTELIEHL 34 
                                    68*************************9988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       630  (0.0351386); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 884.97
//
Query:       gene491|gene491|rna491|rna491  [L=90]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.2e-15   55.6   2.1    3.7e-15   55.4   2.1    1.1  1  LSM        LSM domain
  ------ inclusion threshold ------
       0.13   12.2   0.1       0.86    9.5   0.0    1.8  2  Tail_tube  Phage tail tube protein


Domain annotation for each model (and alignments):
>> LSM  LSM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.4   2.1   4.1e-19   3.7e-15       2      66 ..       9      72 ..       8      73 .. 0.95

  Alignments for each domain:
  == domain 1  score: 55.4 bits;  conditional E-value: 4.1e-19
                                   HHHHTTTSEEEEEETTSEEEEEEEEEEETTSEEEEEEEEEEETTETEEEEEEEEEEEGGGEEEEE CS
                            LSM  2 flkklinkkvtvelkngrelrGtLkgfDqfmNlvLedveetlkdkkekrklglvliRGnnivlis 66
                                   +l ++ n ++tvel ng++  G+L+ +D+ mNl L+dv+ t  ++ ++++++++++RG+ i li+
  gene491|gene491|rna491|rna491  9 LLYECENFQLTVELDNGTKATGKLVQVDDLMNLTLDDVVLTEING-HNTRIERMMVRGSLIQLII 72
                                   6778999**************************************.***************9997 PP

>> Tail_tube  Phage tail tube protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0   9.6e-05      0.86      61      89 ..       3      31 ..       1      45 [. 0.82
   2 ?    2.2   0.1     0.018   1.6e+02      62      86 ..      32      56 ..      26      67 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 9.6e-05
                      Tail_tube 61 edldleelkaltnatvtfeldnGktyvls 89
                                   ++++l+ l++ +n  +t+eldnG + + +
  gene491|gene491|rna491|rna491  3 PSVPLKLLYECENFQLTVELDNGTKATGK 31
                                   67999******************987765 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.018
                      Tail_tube 62 dldleelkaltnatvtfeldnGkty 86
                                    +++++l++lt  +v++   nG+  
  gene491|gene491|rna491|rna491 32 LVQVDDLMNLTLDDVVLTEINGHNT 56
                                   57899**********9999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       332  (0.0185175); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.29s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 611.66
//
Query:       gene492|gene492|rna492|rna492  [L=207]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-39  135.8   2.5    3.2e-30  105.2   0.2    2.1  2  DUF5092          Domain of unknown function (DUF5092)
  ------ inclusion threshold ------
      0.014   15.5   6.2      0.014   15.5   6.2    1.5  2  DUF3671          Protein of unknown function
       0.21   11.5   2.9       0.44   10.4   1.5    1.9  2  Peptidase_M48_N  CAAX prenyl protease N-terminal, five membra


Domain annotation for each model (and alignments):
>> DUF5092  Domain of unknown function (DUF5092)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.2   0.2   5.3e-34   3.2e-30       1      91 [.      20     114 ..      20     116 .. 0.97
   2 !   31.9   0.1   1.8e-11   1.1e-07     126     163 .]     115     155 ..     113     155 .. 0.95

  Alignments for each domain:
  == domain 1  score: 105.2 bits;  conditional E-value: 5.3e-34
                        DUF5092   1 vEtftleefrklilesrkkkkdfilArVttk....dpedqsslynvyYdAeelnkvlFevvieserrllhrkkvkdPlnn 76 
                                    +E ft+++f +li+e++++++d++lArV++     d+  + s ++++YdA++l+k++Fe+vi +++r++++k++kdP+ +
  gene492|gene492|rna492|rna492  20 TEIFTQKRFIDLISEAHSQSQDYYLARVRCVgmrkDKGVNVSGIYFCYDARQLCKYVFEMVIGPKGRKIQIKNFKDPIYK 99 
                                    599***************************999889999999************************************** PP

                        DUF5092  77 mkIkqvyyYkltvee 91 
                                     +I+++++++l +++
  gene492|gene492|rna492|rna492 100 RTITELSFFRLCYDS 114
                                    ************997 PP

  == domain 2  score: 31.9 bits;  conditional E-value: 1.8e-11
                        DUF5092 126 klilkaeyfasdddFLeksevre..yfkenaldad.dnFlF 163
                                    +++lkaey++s +dFL ++++r+  ++ke++lda+ ++F F
  gene492|gene492|rna492|rna492 115 ETPLKAEYMGSYRDFLDSNCFRTkiFHKEDPLDALsVSFKF 155
                                    789********************************999998 PP

>> DUF3671  Protein of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       2.1   1.3e+04      32      45 ..      89     102 ..      82     110 .. 0.54
   2 ?   15.5   6.2   2.3e-06     0.014      13      68 ..     137     193 ..     129     207 .] 0.78

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 2.1
                        DUF3671  32 dkkkfkkkvlkkyg 45 
                                    + k+fk  ++k+  
  gene492|gene492|rna492|rna492  89 QIKNFKDPIYKRTI 102
                                    44555555555544 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 2.3e-06
                        DUF3671  13 KkiFdkidkidelakkkn.ndkkkfkkkvlkkyglllilpvllpliglivpilfeak 68 
                                     kiF k d +d l+  ++ n+kkk+  +  kk++ ++i+++l+  i++i+++++e+ 
  gene492|gene492|rna492|rna492 137 TKIFHKEDPLDALSVSFKfNKKKKMSVISRKKMFSIFITLILILCIVSILVVVVEKG 193
                                    59************9988356677888888999999999999999999999987654 PP

>> Peptidase_M48_N  CAAX prenyl protease N-terminal, five membrane helices
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.0      0.12   6.9e+02      21      37 ..      33      49 ..      24      77 .. 0.88
   2 ?   10.4   1.5   7.4e-05      0.44     109     153 ..     152     197 ..     148     199 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.12
                Peptidase_M48_N 21 kekfdksraYgldksrf 37
                                    e++++s++Y l+++r+
  gene492|gene492|rna492|rna492 33 SEAHSQSQDYYLARVRC 49
                                   57899*******99875 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 7.4e-05
                Peptidase_M48_N 109 khGfnkqtlklfikdk.lkslllalviglpllaallwiiewggeyf 153
                                     + fnk++ +  i+ k + s++++l+++l ++++l++++e+g  +f
  gene492|gene492|rna492|rna492 152 SFKFNKKKKMSVISRKkMFSIFITLILILCIVSILVVVVEKGHIKF 197
                                    699***99999888766***********************987665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1282  (0.0715043); expected 358.6 (0.02)
Passed bias filter:                      754  (0.0420548); expected 358.6 (0.02)
Passed Vit filter:                        77  (0.00429472); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.38
# Mc/sec: 1616.21
//
Query:       gene493|gene493|rna493|rna493  [L=652]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (652 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1866  (0.104077); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.65u 0.24s 00:00:00.89 Elapsed: 00:00:00.43
# Mc/sec: 4587.39
//
Query:       gene494|gene494|rna494|rna494  [L=62]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (62 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       434  (0.0242066); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.29s 00:00:00.65 Elapsed: 00:00:00.44
# Mc/sec: 419.32
//
Query:       gene495|gene495|rna495|rna495  [L=70]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (70 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       312  (0.017402); expected 358.6 (0.02)
Passed bias filter:                      204  (0.0113782); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.46
# Mc/sec: 459.19
//
Query:       gene496|gene496|rna496|rna496  [L=242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00071   19.5   4.2    0.00071   19.5   4.2    2.2  2  DUF5089   Domain of unknown function (DUF5089)
  ------ inclusion threshold ------
       0.17   11.7   2.1        2.1    8.2   0.2    2.8  3  STN       Secretin and TonB N terminus short domain
        2.2    8.6   6.9       0.73   10.1   2.1    2.3  2  DUF4634   Domain of unknown function (DUF4634)


Domain annotation for each model (and alignments):
>> DUF5089  Domain of unknown function (DUF5089)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   1.9      0.17     1e+03      93     128 ..      22      65 ..       1     100 [. 0.54
   2 !   19.5   4.2   1.2e-07   0.00071      15      66 ..     159     209 ..     142     221 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.17
                        DUF5089  93 kdkkaeeeveeiknkeeea.........keeeedkkeeeefiped 128
                                    k++k ee+v+++++ ++++         ++ + +  + ++  +++
  gene496|gene496|rna496|rna496  22 KNRK-EENVHAQQEGNQKNfydcvyqkiQDFNTNVATYTSLLKKE 65 
                                    2222.4455555544444444343333333333333333333333 PP

  == domain 2  score: 19.5 bits;  conditional E-value: 1.2e-07
                        DUF5089  15 yetakkarkkLesaartqkkTtkelrkQgekLekakqsaikvhknaekgeel 66 
                                    y+  k+ rk L+++ + q++ + +l+ Q+e+++++ ++++++++n++ g++ 
  gene496|gene496|rna496|rna496 159 YQ-MKQTRKSLQEIKHIQDQISLNLNVQNESIDQIFNKSKSINENVKGGNKY 209
                                    55.599*****************************************99875 PP

>> STN  Secretin and TonB N terminus short domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0      0.63   3.8e+03      34      46 ..      25      37 ..      25      37 .. 0.82
   2 ?    1.9   0.0     0.032   1.9e+02       7      23 ..     109     124 ..     105     127 .. 0.83
   3 ?    8.2   0.2   0.00036       2.1      15      31 ..     179     195 ..     175     195 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.63
                            STN 34 kgtgLqykitgnt 46
                                   k+ +++++++gn+
  gene496|gene496|rna496|rna496 25 KEENVHAQQEGNQ 37
                                   56799****9996 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.032
                            STN   7 selvrgnqtvslnignv 23 
                                    s++++++++ ++n +n 
  gene496|gene496|rna496|rna496 109 SADIQAKKRRFIN-KNI 124
                                    79***********.996 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.00036
                            STN  15 tvslnignvtideaLde 31 
                                    +++ln+ n++id+++++
  gene496|gene496|rna496|rna496 179 SLNLNVQNESIDQIFNK 195
                                    689************95 PP

>> DUF4634  Domain of unknown function (DUF4634)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   2.1   0.00012      0.73      26      76 ..      31      81 ..      21     115 .. 0.76
   2 ?    0.3   0.2      0.13   7.9e+02      64      96 ..     136     168 ..     118     192 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00012
                        DUF4634 26 eeddyyqvvyyytvtPnyddfsanftvdysifesedrlnrldkevteavet 76
                                    +++  q  +y  v  + +df++n     s+ + e+++n+l++e+++  + 
  gene496|gene496|rna496|rna496 31 AQQEGNQKNFYDCVYQKIQDFNTNVATYTSLLKKEQEFNKLQRETVDLFKV 81
                                   4566778889999999****************************9998664 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.13
                        DUF4634  64 nrldkevteavettisleteradhqkpvtvkpv 96 
                                    n  +++  e+++  i+ et+  d q   t k++
  gene496|gene496|rna496|rna496 136 NAHHDKNLEMENKMIMKETHSLDYQMKQTRKSL 168
                                    444555677777778888888888877777754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (242 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2214  (0.123487); expected 358.6 (0.02)
Passed bias filter:                      454  (0.0253221); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 1664.88
//
Query:       gene497|gene497|rna497|rna497  [L=271]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (271 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       579  (0.032294); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.50
# Mc/sec: 1637.46
//
Query:       gene498|gene498|rna498|rna498  [L=462]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.3e-21   76.6   0.0    6.2e-21   75.2   0.0    1.7  1  Fe_hyd_lg_C  Iron only hydrogenase large subunit, C-terminal 
  ------ inclusion threshold ------
       0.91    9.8   3.1          2    8.7   0.2    2.8  3  DUF1462      Protein of unknown function (DUF1462)


Domain annotation for each model (and alignments):
>> Fe_hyd_lg_C  Iron only hydrogenase large subunit, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.2   0.0   6.9e-25   6.2e-21      29     243 .]      93     409 ..      78     409 .. 0.83

  Alignments for each domain:
  == domain 1  score: 75.2 bits;  conditional E-value: 6.9e-25
                                    HHHHHHHH.TT-SEEEETHHHHHHHHHHHHHHHHHHHHHTS-SSEE----HHHHHHHHHH-GGGGGGB--B--HHHHHHH CS
                                    xxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Fe_hyd_lg_C  29 klvaalrk.lGfdkVfdtafgadltimeeasellerleeeeklpmitScCPgwvkyvekkypellpnlssvkSPqqilga 107
                                     l +alr+ + ++++++t   ++l+     +ell++        +i S CPg+v+yve++ p+l+p+ls+v S qq+++ 
  gene498|gene498|rna498|rna498  93 YLQNALRRkFSVKRIVNTYDYQQLSNYMIYNELLTKN------KLILSECPGVVAYVERRRPDLIPYLSEVPSLQQMCAY 166
                                    5667777778888888888777777766666665544......49*********************************99 PP

                                    HHHTHHHHHGGEEEEEEES-SSHHHHHTSTT-BBTBBSS-EEEEHHHHHHHHHHTT--GGGS-------TTSSSSSTSS- CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Fe_hyd_lg_C 108 liKkylaekekivvVsimPCtaKklEaareefksagrdvDavlTtrElaellkeagidlakleeeeldnplgessgagki 187
                                    l  +     e + +V +m C +K+lE     +      vD+vl+ +++ e+  + +i++ ++++++ d   +   g+   
  gene498|gene498|rna498|rna498 167 LCEE-----EGVLTVGVMQCHDKRLEGG---V-----RVDYVLSSKDIYEICSDVRINF-EVDNNDRDIYDDVGVGNEGK 232
                                    9833.....359**************86...3.....79********************.45444444443333332222 PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                    Fe_hyd_lg_C 188 ................................................................................ 187
                                                                                                                    
  gene498|gene498|rna498|rna498 233 gdnngrdihddvgvgnegkgdnngrdtyddvgvgnegkgdnngrdiyddvgvngkdnniyetcngvhtndkddnntnthn 312
                                    5669999********************************************************99999999999999999 PP

                                    ..........................................TTEEEEE..EEE-TSEEEEEEEESHHHHHHHHHHHHTT CS
                                    ..........................................xxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Fe_hyd_lg_C 188 ..........................................egvkeae..velegktlkvavvnGlknikklleklkag 223
                                                                              ++++++   +++++++l++a ++Glkn+ ++   l+++
  gene498|gene498|rna498|rna498 313 drlspeqhsknssehvltnekefltgitpylikmlnltieriQTINKSYrvLHFKNSSLTFAHITGLKNLLNF---LNDE 389
                                    999999999999999999999999999999999888888665444444365556778999******9998888...5599 PP

                                    SS--SEEEEESSTTSGGG-T CS
                                    xxxxxxxxxxxxxxxxxxxx RF
                    Fe_hyd_lg_C 224 eakydfiEvmaCpgGCigGg 243
                                    e+ y+f+++  C + C gG+
  gene498|gene498|rna498|rna498 390 EMRYNFVDIFLCDDRCFGGP 409
                                    *******************7 PP

>> DUF1462  Protein of unknown function (DUF1462)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.1       0.1     9e+02       8      27 ..      29      48 ..      26      84 .. 0.79
   2 ?    8.7   0.2   0.00023         2      14      44 ..      83     112 ..      73     130 .. 0.82
   3 ?   -1.8   0.0      0.44   3.9e+03      35      50 ..     388     403 ..     380     447 .. 0.60

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.1
                        DUF1462  8 iCasCvnlPssketyeWlea 27
                                    C+ Cv++  +k t+e l+ 
  gene498|gene498|rna498|rna498 29 ACSGCVSMEETKITAEDLQN 48
                                   6999****999999998886 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00023
                        DUF1462  14 nlPssketyeWleaalkrkypeqkleleyvD 44 
                                    ++ + ke y +l+ al+rk++ +++  +y D
  gene498|gene498|rna498|rna498  83 HAITVKEWYAYLQNALRRKFSVKRIVNTY-D 112
                                    6678899***************9998776.3 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 0.44
                        DUF1462  35 eqkleleyvDieeeke 50 
                                    ++++++++vDi    +
  gene498|gene498|rna498|rna498 388 DEEMRYNFVDIFLCDD 403
                                    4556666666654443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (462 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       832  (0.0464053); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.45
# Mc/sec: 3072.85
//
Query:       gene499|gene499|rna499|rna499  [L=66]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.11   12.3   1.5        7.6    6.3   0.1    2.3  3  DUF2859   Protein of unknown function (DUF2859)
       0.55   10.5   6.3         17    5.7   1.8    3.1  3  PRODH     Proline utilization A proline dehydrogenase N-termi
        4.7    6.9   7.6         55    3.5   0.1    3.5  4  PikAIV_N  Narbonolide/10-deoxymethynolide synthase PikA4 N-te


Domain annotation for each model (and alignments):
>> DUF2859  Protein of unknown function (DUF2859)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.2    0.0032        19      99     117 ..      12      30 ..       7      34 .. 0.88
   2 ?    4.9   0.2    0.0034        21      99     117 ..      28      46 ..      25      50 .. 0.88
   3 ?    6.3   0.1    0.0013       7.6      99     117 ..      44      62 ..      33      64 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.0032
                        DUF2859  99 vGlvvnvesaaalqelrel 117
                                     Glvv +++++a+++lr l
  gene499|gene499|rna499|rna499  12 RGLVVMADEEEAVTALRGL 30 
                                    69**************976 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.0034
                        DUF2859  99 vGlvvnvesaaalqelrel 117
                                     Glvv +++++a+++lr l
  gene499|gene499|rna499|rna499  28 RGLVVMADEEEAVTALRGL 46 
                                    69**************977 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.0013
                        DUF2859  99 vGlvvnvesaaalqelrel 117
                                     Glvv +++++a+++lr++
  gene499|gene499|rna499|rna499  44 RGLVVMIDEEEAVTALRRI 62 
                                    6****************87 PP

>> PRODH  Proline utilization A proline dehydrogenase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   1.8    0.0029        17      13      34 ..      18      39 ..      16      42 .. 0.83
   2 ?    4.5   1.4    0.0071        42      13      26 ..      34      47 ..      31      57 .. 0.75
   3 ?    3.8   0.1     0.012        70      13      22 ..      50      59 ..      47      61 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0029
                          PRODH 13 rpEaecVapLleaArlpeaera 34
                                   ++E+e+V +L     + ++e+a
  gene499|gene499|rna499|rna499 18 ADEEEAVTALRGLVVMADEEEA 39
                                   79********999888888766 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.0071
                          PRODH 13 rpEaecVapLleaA 26
                                   ++E+e+V +L    
  gene499|gene499|rna499|rna499 34 ADEEEAVTALRGLV 47
                                   79******997765 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.012
                          PRODH 13 rpEaecVapL 22
                                   ++E+e+V +L
  gene499|gene499|rna499|rna499 50 IDEEEAVTAL 59
                                   79*****999 PP

>> PikAIV_N  Narbonolide/10-deoxymethynolide synthase PikA4 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.26   1.5e+03       7      11 ..       8      12 ..       8      13 .. 0.86
   2 ?    3.5   0.1    0.0092        55       2      11 ..      19      28 ..      18      29 .. 0.88
   3 ?    3.5   0.1    0.0092        55       2      11 ..      35      44 ..      34      45 .. 0.88
   4 ?    2.8   0.3     0.015        90       3      11 ..      52      60 ..      51      61 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.26
                       PikAIV_N  7 VeALR 11
                                   V ALR
  gene499|gene499|rna499|rna499  8 VTALR 12
                                   78**9 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.0092
                       PikAIV_N  2 sdeklVeALR 11
                                   ++e+ V ALR
  gene499|gene499|rna499|rna499 19 DEEEAVTALR 28
                                   6899****** PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.0092
                       PikAIV_N  2 sdeklVeALR 11
                                   ++e+ V ALR
  gene499|gene499|rna499|rna499 35 DEEEAVTALR 44
                                   6899****** PP

  == domain 4  score: 2.8 bits;  conditional E-value: 0.015
                       PikAIV_N  3 deklVeALR 11
                                   +e+ V ALR
  gene499|gene499|rna499|rna499 52 EEEAVTALR 60
                                   7999***** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (66 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       270  (0.0150594); expected 358.6 (0.02)
Passed bias filter:                      203  (0.0113224); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.35u 0.25s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 508.86
//
Query:       gene5|gene5|rna5|rna5  [L=560]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        6.8    7.0   6.3        3.5    7.9   3.7    1.9  2  EGF_CA    Calcium-binding EGF domain


Domain annotation for each model (and alignments):
>> EGF_CA  Calcium-binding EGF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0      0.54   9.6e+03       2       9 ..     315     322 ..     315     323 .. 0.76
   2 ?    7.9   3.7    0.0002       3.5       2      30 ..     409     442 ..     409     446 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 0.54
                 EGF_CA   2 vdECasgt 9  
                            ++EC  g+
  gene5|gene5|rna5|rna5 315 LNECVIGN 322
                            69**9875 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0002
                 EGF_CA   2 vdECasgthnC..pentvCvNteG..sfeCv..Ce 30 
                            vdEC+  + +C  ++nt+ +N+ G  s +C   C+
  gene5|gene5|rna5|rna5 409 VDECEHMQ-HCmeHNNTKAINNTGmsSNTCLiqCK 442
                            8*****99.899*9*********966677777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (560 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       667  (0.0372023); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.23s 00:00:00.72 Elapsed: 00:00:00.37
# Mc/sec: 4550.08
//
Query:       gene50|gene50|rna50|rna50  [L=188]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.048   13.4   0.3      0.079   12.7   0.3    1.3  1  DUF1673   Protein of unknown function (DUF1673)


Domain annotation for each model (and alignments):
>> DUF1673  Protein of unknown function (DUF1673)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.3   4.4e-06     0.079     181     210 ..      31      60 ..       2      72 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.4e-06
                    DUF1673 181 lgevvssfisgllllllwliylqviywekk 210
                                +++ +++ ++gl+ ++++++++++i+w ++
  gene50|gene50|rna50|rna50  31 VDFYIYMEVGGLFGVIIFMFFFTIIFWLAR 60 
                                33478999*******************888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       778  (0.0433934); expected 358.6 (0.02)
Passed bias filter:                      546  (0.0304535); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1356.39
//
Query:       gene500|gene500|rna500|rna500  [L=919]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.8e-59  199.5   2.8    1.5e-58  198.5   2.8    1.4  1  Haspin_kinase  Haspin like kinase domain
     0.0033   16.8   0.2     0.0033   16.8   0.2    2.4  2  Pkinase        Protein kinase domain


Domain annotation for each model (and alignments):
>> Haspin_kinase  Haspin like kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  198.5   2.8   1.7e-62   1.5e-58      48     328 ..     571     899 ..     463     916 .. 0.83

  Alignments for each domain:
  == domain 1  score: 198.5 bits;  conditional E-value: 1.7e-62
                  Haspin_kinase  48 vkdqvsrdkikkklrnsesllslnsqeevkdfdevilsqilelckikkilnea.dlasllnd......seklssevyqtk 120
                                    +k    r+k +   ++ +s+ls n + + ++  + + +++l+  ++ +il ++ ++ s +n       +e+++s+vy+ k
  gene500|gene500|rna500|rna500 571 IKRD--RKKYQIEFKDDSSILSSNDKCPDENVPCRV-EKMLSEAELVNILAPKtRYFSAMNFkgvkkiAEASFSDVYRFK 647
                                    3333..788888999999999999888877766555.5566777777888887444444444889999************ PP

                  Haspin_kinase 121 ekdkevvlKvipl.......evledvtiskelsl....kelkslklvkgtypglllllqdkvlkek......pdfyseqq 183
                                    +     ++K+ip+       e l +v + ++l+     ++l+++ ++kg+y+++l+ ++d +++++      p++  ++ 
  gene500|gene500|rna500|rna500 648 D----KIYKIIPFteyytkeEFLREVYVLRTLQNekyvIKLRNFFVCKGAYNQHLHAAWDAYARDHksenkrPNSDGKNG 723
                                    9....8**************888888765444433344**************************99999*********** PP

                  Haspin_kinase 184 lflvlllkdkGtdLeevklkswkqalsifwqivkiLyvaEtkfeFEHRdLhldniLvdkn.................... 243
                                     +  l+++d+GtdLe+ ++k+++++l  +  i++ L+v E k++FEHRdLh++niL+++n                    
  gene500|gene500|rna500|rna500 724 EYGCLVMDDAGTDLENYQFKKMSDILLFLKIIIECLSVLEFKYQFEHRDLHWGNILIQHNnmrndslcafsenvrnsnls 803
                                    ******************************************************************************** PP

                  Haspin_kinase 244 ..........lnvtlidlklsRlessegkvlytrld.dpllFqGggDyqfeiYrlMrsllskswaefePrtNllwlhyLa 312
                                               +v +id+ lsR++  ++ v+y +l+ +++lFqG gD q+++Yr M++++ ++w++f+P+tN+lwl+yL+
  gene500|gene500|rna500|rna500 804 ghfvpedsapFKVSIIDFGLSRFS-TDHGVVYKDLSpEKELFQGTGDEQYDVYRQMKRICCNDWSKFNPITNVLWLKYLV 882
                                    ***********************8.8889*******99****************************************** PP

                  Haspin_kinase 313 vkLlkkkn.kklnseae 328
                                     kL +k   +k+  + +
  gene500|gene500|rna500|rna500 883 GKLRHKGLsEKMCNMVM 899
                                    ***99876455544444 PP

>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.4      0.22     2e+03     192     248 ..      20      80 ..      15      83 .. 0.56
   2 !   16.8   0.2   3.7e-07    0.0033      30     150 ..     652     829 ..     629     847 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.22
                                    HSS-STTTSSHHHHHHHHHHT.HHHHHHHCTSHH...HHHTTS.....-HHHHHHHHHHT-SS CS
                        Pkinase 192 tgkppfsgekgkekvekeldq.lekilkilgetkeklpeasei.....seeakdllkkllkkd 248
                                     + p f++ ++ e  ++++++    + ki +++++k +++s i     se +++ll ++++ +
  gene500|gene500|rna500|rna500  20 VKDPSFNKITKME--HNKIENtSCLFEKIRNDYQQKKKNKSYIqstlfSEGIQQLLMSIISDN 80 
                                    5556666444444..222222134455555555555555555566667888999988888766 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 3.7e-07
                                    EEEECHCHCHHHHHHHHHHHHHHHHHS.CTTB--EEEEEEE................................SSEEEEE CS
                        Pkinase  30 KkikkekakkkkekkvlrEikilkklk.hpnivrlyevfee................................kdelylv 76 
                                    K+i   +   k  +++lrE+ +l++l+  +++++l ++f                                   ++ +lv
  gene500|gene500|rna500|rna500 652 KIIPFTEYYTK--EEFLREVYVLRTLQnEKYVIKLRNFFVCkgaynqhlhaawdayardhksenkrpnsdgknGEYGCLV 729
                                    55555555544..469***********999********999899999999999999999999999999998877777888 PP

                                    EE--TTEBHHHHHHHHSS--HHHHHHHHHHHHHHHHHHH.HTTEE-SS-SGGGEEEET...................... CS
                        Pkinase  77 leyveggeladllerkgslseeeakkiakqilegleylH.skgiiHrDlKpeNiLide...................... 133
                                    ++ + ++ l+++       +++++  ++k i+e l+ l  + ++ HrDl   NiLi++                      
  gene500|gene500|rna500|rna500 730 MDDAGTD-LENYQ----FKKMSDILLFLKIIIECLSVLEfKYQFEHRDLHWGNILIQHnnmrndslcafsenvrnsnlsg 804
                                    8888755.55554....35778999999999999999965999**************75888888888888887777755 PP

                                    ....TTE.....EEE-SGTTSEESSS CS
                        Pkinase 134 ....kge.....lKitDFGlakeles 150
                                        + +     + i+DFGl++  + 
  gene500|gene500|rna500|rna500 805 hfvpE-DsapfkVSIIDFGLSRFSTD 829
                                    55541.15677799999999998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (919 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       850  (0.0474092); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.69u 0.27s 00:00:00.96 Elapsed: 00:00:00.43
# Mc/sec: 6475.51
//
Query:       gene501|gene501|rna501|rna501  [L=37]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.37   10.6   0.1       0.37   10.6   0.1    2.2  2  PglL_A    Protein glycosylation ligase


Domain annotation for each model (and alignments):
>> PglL_A  Protein glycosylation ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   4.6     0.041   7.3e+02      17      25 ..      16      24 ..      15      26 .. 0.78
   2 ?   10.6   0.1   2.1e-05      0.37       2      11 ..      27      36 ..      27      37 .] 0.87

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.041
                         PglL_A 17 lGlaaalyL 25
                                   +G+aa+  +
  gene501|gene501|rna501|rna501 16 WGWAATFAW 24
                                   9***99855 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 2.1e-05
                         PglL_A  2 yGNlrQpNhl 11
                                   +GNl+Qp  l
  gene501|gene501|rna501|rna501 27 VGNLQQPSLL 36
                                   6******876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (37 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       406  (0.0226449); expected 358.6 (0.02)
Passed bias filter:                      214  (0.011936); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.41
# Mc/sec: 270.31
//
Query:       gene502|gene502|rna502|rna502  [L=487]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.7e-53  182.1   5.4      4e-52  178.2   5.4    2.0  1  Sec1      Sec1 family
  ------ inclusion threshold ------
      0.091   13.2   0.2         13    6.2   0.1    2.7  2  DUF4258   Domain of unknown function (DUF4258)


Domain annotation for each model (and alignments):
>> Sec1  Sec1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  178.2   5.4   4.5e-56     4e-52       2     573 ..      21     479 ..      20     481 .. 0.79

  Alignments for each domain:
  == domain 1  score: 178.2 bits;  conditional E-value: 4.5e-56
                                    EEEE-HHHHHHHHTT--HHHHHTTTEEETT..T.--S-.....BTTSEEEEEE-S-HHHHHHHHHHHHSS-SBS-EEEEE CS
                           Sec1   2 vLvlDkelskilssvlkvsdlleegVtkieklk.krepskrealphlkaiyflrptkenidrlakdfisarrykeyhiff 80 
                                    vL+lD+ + +i++ ++++++l++ ++t i++l+ +re+       +  aiyf+  +  n+  +++d i ar+y++y+++f
  gene502|gene502|rna502|rna502  21 VLILDDTTFPIINALFRFTELRRLNITTIFRLEnTREN------VTASAIYFVHSK--NLHSIVSDVI-ARTYSSYNLNF 91 
                                    8*********************88******99655555......57889****998..9999997754.49********* PP

                                    SS---HHHHHHHHH...SG......GGGEEEEE----SEEEETTEEE-STTHHHHSTTG.....GG.......--HHHHH CS
                           Sec1  81 tprlseslleglakad.ee.....vvkkvklkelnldfvplesdlfslnpelplsfrdlyldndnsaleeeieslldria 154
                                    ++ +s++ le+la ++ +e      v++v   + +l+f++l++++f+                            + ++a
  gene502|gene502|rna502|rna502  92 IDCVSRDGLEMLA-GTlSErrlalKVESVW--DRHLNFLALDNNVFVVG-G-----------------------GVHEMA 144
                                    *************.5646457877777777..****************4.2.......................1334** PP

                                    HHHHHHHHHH-..--EEEE-TT-.........HHHHHHHH..........HHHHTTT--SS--EEEEE-GGG-SSTTTS- CS
                           Sec1 155 kgLlsvllslekkiPiirykgsa.........asmvakkladelkekidskknfesessrqrpvLiIlDRsvDlvtpllh 225
                                     gL+s++  l    P i+   ++          ++va+ l+++++ ++ +       +++ rp+Li++ R  D +tpl h
  gene502|gene502|rna502|rna502 145 AGLFSLFFNL-DNEPFIVSGDENvsgdknvsgDESVAELLYKKMRNNLVR-------KKDRRPLLILFRRENDVITPLEH 216
                                    **********.446766664444699999998776777888888877766.......7899******************* PP

                                    --BHHHHHHHHS--BTEEEEEE--SSSEEEEEE--TT..-TTHHHHTTSBHHHHHHHHHHHHHHHHHHHHTTT...-TTH CS
                           Sec1 226 qwTYqaliddllgglnnnnvvleeepkeekeaelvesssDeffaelrhlnfgevgeklkkeakeyqeenekkrngakesi 305
                                     wTY +li+d+l  l n n+v+++++ ++ + +++ +  D f+a ++++ f+ v e+++ke  +y++e   k+n    +i
  gene502|gene502|rna502|rna502 217 NWTYAGLINDVLS-L-NINTVKYTKDDRPCTYTITPD--DTFYATNKYEKFPVVTERIEKEHLNYKKEI-GKKN--Y-DI 288
                                    ************7.7.555555555466666666666..*****************************9.5554..2.34 PP

                                    HHHHHHHHH-GGGHHHHHHHHHHHHHHHHHHHHS-HHH.HHHHHHHHHHHHSS--.B--..-HHHHHHHH-TTS-H.HHH CS
                           Sec1 306 adlkkfvaklpelqeekkklskHtnlaeellkevkkrkldellelEqdlatgesdkkikekkvieeliaddeptseledk 385
                                    a          el+   + ++ H++++  l++e+++r +de++e+Eq  a++       ++  i +++++  +   +ed+
  gene502|gene502|rna502|rna502 289 A----------ELNRSNEMIDAHMSICLNLINEISDRGYDEYYEMEQRNASD-------DQ--IYKMVEK-GT---VEDV 345
                                    4..........45668999******************************833.......23..6689986.44...68** PP

                                    HHHHHHHHH...-B.-HT--GG......GGHHHHG.GGGG........---.BGGG-------.......---------S CS
                           Sec1 386 lRLlllyslvegglkekelkellr..elvqsalyg.leylktlrsleklgllkkrkgkksskkksslklikeeedeesny 462
                                     R ++ +    +g +++ ++++     + q    + +e++ +  ++e+++llk+ ++  s+                 n 
  gene502|gene502|rna502|rna502 346 KRFVCTLLR--KGARPEVIEYIMAkrGITQ----QfVEHVVQRIKIEENTLLKRATNILSKII---------------N- 403
                                    *****9866..5889997777733223333....13777777777888888866666443333...............2. PP

                                    ...TT-----HHHHHHHHHTTT-S-TTTS-BSS-GGGS--------------------------S-EEEEEEEEEE-HHH CS
                           Sec1 463 dlsgvsryaPllvrlvealikgkklssespslskkdpsqeesssslrsakktnsaskesaekkkkqrviVffvGGvTysE 542
                                        v   +Pl+v++ e + k  +  +    +                    + ++   +e      v Vf+vGG++y E
  gene502|gene502|rna502|rna502 404 ----VDTSTPLSVYVGEIVAK-ARKGELRV-M--------------------GGRKVYYEEV---AGVYVFVVGGGCYKE 454
                                    ....44579999999888888.44444443.3....................3344444444...77************* PP

                                    HHHHHHHT...TSSSEEEEEEEEE--HHHHH CS
                           Sec1 543 iralrllskqekknkeiiigttsilnpksfl 573
                                    i +lr +       ++i++g+ +il +++ l
  gene502|gene502|rna502|rna502 455 IDSLRRMD------RDIVYGCGEILDGRRAL 479
                                    ****9998......79**********99876 PP

>> DUF4258  Domain of unknown function (DUF4258)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.1    0.0015        13       8      33 ..     322     347 ..     321     365 .. 0.75
   2 ?    4.2   0.0    0.0065        58       9      27 ..     366     384 ..     365     425 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0015
                        DUF4258   8 rmaeRgIseedieevlenGeiieeys 33 
                                    +m++R+ s+++i + +e+G++   ++
  gene502|gene502|rna502|rna502 322 EMEQRNASDDQIYKMVEKGTVEDVKR 347
                                    7******************8666555 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.0065
                        DUF4258   9 maeRgIseedieevlenGe 27 
                                    ma+RgI+ + +e v+++ +
  gene502|gene502|rna502|rna502 366 MAKRGITQQFVEHVVQRIK 384
                                    9*************98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (487 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       776  (0.0432818); expected 358.6 (0.02)
Passed bias filter:                      478  (0.0266607); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.27s 00:00:00.86 Elapsed: 00:00:00.45
# Mc/sec: 3249.09
//
Query:       gene503|gene503|rna503|rna503  [L=75]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       182  (0.0101512); expected 358.6 (0.02)
Passed bias filter:                      168  (0.00937029); expected 358.6 (0.02)
Passed Vit filter:                         6  (0.000334653); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.42
# Mc/sec: 538.21
//
Query:       gene504|gene504|rna504|rna504  [L=330]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (330 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       590  (0.0329076); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 2288.11
//
Query:       gene505|gene505|rna505|rna505  [L=319]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      2e-25   89.7   0.3    2.6e-25   89.3   0.3    1.1  1  Pkinase         Protein kinase domain
    5.1e-11   42.3   0.1    6.3e-11   42.0   0.1    1.1  1  Pkinase_Tyr     Protein tyrosine kinase
    3.5e-08   32.7   0.1    4.5e-08   32.3   0.1    1.2  1  Pkinase_fungal  Fungal protein kinase
     0.0036   17.3   0.0       0.01   15.8   0.0    1.7  2  APH             Phosphotransferase enzyme family
     0.0057   16.0   0.1     0.0096   15.3   0.1    1.3  1  Kinase-like     Kinase-like
  ------ inclusion threshold ------
       0.11   11.8   0.0       0.23   10.8   0.0    1.5  1  Kdo             Lipopolysaccharide kinase (Kdo/WaaP) family
       0.12   12.5   0.0       0.28   11.3   0.0    1.6  1  AbrB-like       AbrB-like transcriptional regulator


Domain annotation for each model (and alignments):
>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.3   0.3     1e-28   2.6e-25       3     210 ..      32     251 ..      30     270 .. 0.82

  Alignments for each domain:
  == domain 1  score: 89.3 bits;  conditional E-value: 1e-28
                                    EEEEEEEESSEEEEEEEETTTTEEEEEEEEECHCHCHHHHHHHHHHHHHHHHHS...CTTB--EEEEEEE.....SSEEE CS
                        Pkinase   3 kleklGeGsfGkVykaveketgkivAvKkikkekakkkkekkvlrEikilkklk...hpnivrlyevfee.....kdely 74 
                                      +klG+G+fG Vy  ++ +t++++A+K+ kk+       + +++E ki  +l+    ++++r y ++ +     + +  
  gene505|gene505|rna505|rna505  32 ITHKLGTGTFGDVYAFLDCKTNRKMALKIEKKNC------NLLRNEYKIYVRLNrtmNDFVCRTY-FYGKvrlnnTLNNA 104
                                    6789************************866553......347889**99999987556666654.33334553344555 PP

                                    EEEE--TTEBHHHHHHHHSS--HHHHHHHHHHHHHHHHHHHHTTEE-SS-SGGGEEEE...TTTEEEE-SGTTSEESSSS CS
                        Pkinase  75 lvleyveggeladllerkgslseeeakkiakqilegleylHskgiiHrDlKpeNiLid...ekgelKitDFGlakeless 151
                                    +v++++     + ++++++ +se ++ ++   +++ +e+lH+++++HrD+Kp+N+ +    ++++l ++D+Glak+++ss
  gene505|gene505|rna505|rna505 105 MVMDLLGLSLQKLFIRQHKRFSEVTVLRLGIMMISCVEFLHARHFVHRDIKPDNFVFGlgaNSDKLYLIDLGLAKKYRSS 184
                                    9****997755556779999***********************************9875334555*************** PP

                                    CS........BCTTTSCGGGS-HHHHTTSCBSHHHHHHHHHHHHHHHHHSS-STTTSSHHHHHHHHH CS
                        Pkinase 152 sk........ltsfvgtseYlAPEvlkeneyskkvDvWslGvilyelltgkppfsgekgkekvekel 210
                                    ++         +  vgt +Y +  v +++e s+  D+ slG  l+ ++ gk p++g k ++k+ek++
  gene505|gene505|rna505|rna505 185 TTythiphknGKLLVGTARYASVNVHRGEEQSRRDDLESLGYCLIFFVKGKLPWQGLKASNKQEKHM 251
                                    99999998887889*****************************************877666544433 PP

>> Pkinase_Tyr  Protein tyrosine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.0   0.1   2.5e-14   6.3e-11       1     214 [.      30     246 ..      30     291 .. 0.77

  Alignments for each domain:
  == domain 1  score: 42.0 bits;  conditional E-value: 2.5e-14
                                    EEEEEEEEEESSEEEEEEEEETTTTSSEEEEEEEEESTTSS..HHHHHHHHHHHHHHHTS-BTTB--EEEEEE..SSSSE CS
                    Pkinase_Tyr   1 lelgkklGeGafGkVvegtlkgekekkevkVavKtlkeeat..eeekeelleeakimkklkhpnivkllgvct..keepl 76 
                                    +++++klG G+fG+V+         k++ k a+K+ k++++  ++e +  ++  ++m+++  +    ++g +   ++ + 
  gene505|gene505|rna505|rna505  30 IQITHKLGTGTFGDVYAFLDC----KTNRKMALKIEKKNCNllRNEYKIYVRLNRTMNDFVCR--TYFYGKVRlnNTLNN 103
                                    57899**********976555....78888999988766551133344444444555555444..357788875455669 PP

                                    EEEEE--TTEBHHHHHHHTCTTTSBHHHHHHHHHHHHHHHHHHHHTTEEEST-SGGGEEEE...ETTEEEE-STTTHEET CS
                    Pkinase_Tyr  77 livteyvkgGdLlkfLrkkekekltlkdllsfalqvAkGmeyLeskklvHrdlaarNvLls...enkvvkisDfGLardi 153
                                     +v++++     + f+r++  ++++  ++l++ + + + +e+L+++++vHrd+   N +     ++++  + D GLa++ 
  gene505|gene505|rna505|rna505 104 AMVMDLLGLSLQKLFIRQH--KRFSEVTVLRLGIMMISCVEFLHARHFVHRDIKPDNFVFGlgaNSDKLYLIDLGLAKKY 181
                                    *******998777888887..9999********************************9875222688999********** PP

                                    TTSSEE..EETTSSTS...GGGGS-HHHHHHSEEEHHHHHHHHHHHHHHHHTTSSGTTTTSHHHHH CS
                    Pkinase_Tyr 154 ekddey..vkkeeakl...pvkWmapEslkekkftsksDvWsfGvllwEiftlgespypglkneev 214
                                     ++ +y    ++++kl     ++ ++ + + ++ + + D  s G +l+  ++ g+ p++glk+++ 
  gene505|gene505|rna505|rna505 182 RSSTTYthIPHKNGKLlvgTARYASVNVHRGEEQSRRDDLESLGYCLIFFVK-GKLPWQGLKASNK 246
                                    888888663344444312267999999999999*************996555.****999966553 PP

>> Pkinase_fungal  Fungal protein kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.3   0.1   1.8e-11   4.5e-08     317     407 ..     139     231 ..     102     232 .. 0.85

  Alignments for each domain:
  == domain 1  score: 32.3 bits;  conditional E-value: 1.8e-11
                 Pkinase_fungal 317 kghrsLflkagiLHrDiSenNilitdskkegerkglLiDLDlakelsddssesga......rertGTleFmaievlkgee 390
                                       + L+    ++HrDi  +N ++      +++k  LiDL lak++   ++   +      +  +GT+ + +++v +gee
  gene505|gene505|rna505|rna505 139 SCVEFLH-ARHFVHRDIKPDNFVFG--LGANSDKLYLIDLGLAKKYRSSTTYT-HiphkngKLLVGTARYASVNVHRGEE 214
                                    5556688.8999************9..667899*************9633333.2344445889**************** PP

                 Pkinase_fungal 391 HsyrhDLESffyvllwi 407
                                     s r+DLES+ y l++ 
  gene505|gene505|rna505|rna505 215 QSRRDDLESLGYCLIFF 231
                                    **********9999875 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0     4e-06      0.01     164     197 ..     145     179 ..     112     181 .. 0.89
   2 ?   -1.9   0.0      0.97   2.5e+03      67      95 ..     222     252 ..     207     254 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 4e-06
                                    S-EEEE-SS-SGGGEEEC....TTEEEEE---TT-E CS
                            APH 164 lptvllHgDlhpgNllvd..pddgrvtGviDfedag 197
                                     ++ ++H+D++p+N+++   ++ +++ ++iD+++a+
  gene505|gene505|rna505|rna505 145 HARHFVHRDIKPDNFVFGlgANSDKL-YLIDLGLAK 179
                                    47889**************9999999.******985 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.97
                                    TTEEEEEEE----EE-SS..HHHHHHHHHHH CS
                            APH  67 igllfalieyvpgrsllr..klsaaqlpell 95 
                                    + l + li +v g+ +++  k s +q +++l
  gene505|gene505|rna505|rna505 222 ESLGYCLIFFVKGKLPWQglKASNKQEKHML 252
                                    3347899999999999998877777777765 PP

>> Kinase-like  Kinase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.1   3.8e-06    0.0096     116     177 ..     101     161 ..      92     193 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 3.8e-06
                    Kinase-like 116 llpaasvdl.eilnkvlqkrsethkkletiarlllTlqlirlaanLqakglvhgkftvdnlll 177
                                    l  a+++dl ++  + l +r+ ++++++t+ rl +   +i  +  L+a+  vh ++++dn+++
  gene505|gene505|rna505|rna505 101 LNNAMVMDLlGLSLQKLFIRQHKRFSEVTVLRLGIM--MISCVEFLHARHFVHRDIKPDNFVF 161
                                    567888888444457788888899999999998884..6**********************98 PP

>> Kdo  Lipopolysaccharide kinase (Kdo/WaaP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0     9e-05      0.23     131     167 ..     141     176 ..     112     187 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 9e-05
                            Kdo 131 iaklhragvnHadlyaknillqqeeeeeaeiwliDld 167
                                    ++ lh+++  H+d+ + n+ +  ++ +  +++liDl 
  gene505|gene505|rna505|rna505 141 VEFLHARHFVHRDIKPDNFVFGLGA-NSDKLYLIDLG 176
                                    6779********************7.99*******96 PP

>> AbrB-like  AbrB-like transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00011      0.28      29      58 ..     185     214 ..     177     217 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00011
                      AbrB-like  29 asYrvsVqknGnLliGsaYTkklgLkpGde 58 
                                     +Y+   +knG+Ll+G a  + ++++ G+e
  gene505|gene505|rna505|rna505 185 TTYTHIPHKNGKLLVGTARYASVNVHRGEE 214
                                    6788888***********999999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (319 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       613  (0.0341904); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 2218.19
//
Query:       gene506|gene506|rna506|rna506  [L=59]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       437  (0.0243739); expected 358.6 (0.02)
Passed bias filter:                      253  (0.0141112); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.44
# Mc/sec: 400.14
//
Query:       gene507|gene507|rna507|rna507  [L=291]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.12   12.4   0.0       0.27   11.3   0.0    1.6  1  CARD      Caspase recruitment domain


Domain annotation for each model (and alignments):
>> CARD  Caspase recruitment domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   1.5e-05      0.27      48      73 ..     263     288 ..     255     290 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 1.5e-05
                                    HHHHHHHHHHTSCHHHHHHHHHHHHH CS
                           CARD  48 kareLldlvqkkgekacqaflealke 73 
                                    ++  ++ ++++k +++cq+f++ l++
  gene507|gene507|rna507|rna507 263 QTMSFIQSLPNKAKNWCQSFYNMLRS 288
                                    67789******************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       882  (0.049194); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 2137.35
//
Query:       gene508|gene508|rna508|rna508  [L=231]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0005   20.4  13.7     0.0078   16.6   0.2    3.3  3  zf-C2H2        Zinc finger, C2H2 type
    0.00075   20.1  12.5       0.78   10.7   0.1    3.6  3  zf-C2H2_4      C2H2-type zinc finger
     0.0046   17.1  17.1       0.04   14.1   1.4    3.3  3  zf-C2H2_aberr  Aberrant zinc-finger
  ------ inclusion threshold ------
      0.037   14.7   8.8        1.5    9.5   0.4    3.7  4  FOXP-CC        FOXP coiled-coil domain
      0.038   13.7   4.3       0.52   10.1   0.1    2.4  2  zf_Hakai       C2H2 Hakai zinc finger domain
       0.65   10.1   8.6       0.37   10.9   3.1    2.4  2  zf-BED         BED zinc finger


Domain annotation for each model (and alignments):
>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.3      0.44   1.3e+03       6      23 .]      88     106 ..      88     106 .. 0.84
   2 !   16.6   0.2   2.6e-06    0.0078       1      23 []     169     194 ..     169     194 .. 0.96
   3 !    9.6   3.2   0.00044       1.3       2      23 .]     205     229 ..     204     229 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.44
                                    TTEEESSHHHHHHHHHC.C CS
                        zf-C2H2   6 CgksFkrksnLkrHirt.H 23 
                                    Cg  F +  ++ +H++  H
  gene508|gene508|rna508|rna508  88 CGNYFDTFNSFAQHRNFeH 106
                                    8888999999999998766 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 2.6e-06
                                    EEET..TTTEEESSHHHHHHHHHC.C CS
                        zf-C2H2   1 ykCp..dCgksFkrksnLkrHirt.H 23 
                                    y+C+  +C+k +++ + L+ Hi   H
  gene508|gene508|rna508|rna508 169 YRCDitGCKKAYTSAYGLRYHIENgH 194
                                    99********************9888 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.00044
                                    EET..TTTEEESSHHHHHHHHHC.C CS
                        zf-C2H2   2 kCp..dCgksFkrksnLkrHirt.H 23 
                                     C    Cgk++k++  Lk H+   H
  gene508|gene508|rna508|rna508 205 ICAfsNCGKRYKNSNGLKYHLEHfH 229
                                    577779**************98777 PP

>> zf-C2H2_4  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.5     0.024        71       5      24 .]      87     106 ..      86     106 .. 0.88
   2 !   10.7   0.1   0.00026      0.78       1      21 [.     169     191 ..     169     192 .. 0.93
   3 !    9.9   2.6   0.00048       1.4       2      24 .]     205     229 ..     204     229 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.024
                      zf-C2H2_4   5 iCgksFsskkaLlrHlkthH 24 
                                     Cg  F + +++ +H +  H
  gene508|gene508|rna508|rna508  87 CCGNYFDTFNSFAQHRNFEH 106
                                    59*************98776 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00026
                      zf-C2H2_4   1 fkCpi..CgksFsskkaLlrHlk 21 
                                    ++C+i  C+k ++s ++L+ H++
  gene508|gene508|rna508|rna508 169 YRCDItgCKKAYTSAYGLRYHIE 191
                                    89*******************86 PP

  == domain 3  score: 9.9 bits;  conditional E-value: 0.00048
                      zf-C2H2_4   2 kCpi..CgksFsskkaLlrHlkthH 24 
                                    +C +  Cgk+++++++L+ Hl+  H
  gene508|gene508|rna508|rna508 205 ICAFsnCGKRYKNSNGLKYHLEHFH 229
                                    566666**************99877 PP

>> zf-C2H2_aberr  Aberrant zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   1.2     0.044   1.3e+02     108     168 ..      40     107 ..       6     111 .. 0.62
   2 !   11.2   1.1    0.0001       0.3     139     164 ..     167     192 ..     153     195 .. 0.84
   3 !   14.1   1.4   1.3e-05      0.04     127     166 ..     192     229 ..     190     231 .] 0.86

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.044
                  zf-C2H2_aberr 108 sdvitendvlkdilltifvngvikiiDidkk........dliyCripGCgkrfkslmaYkYhckkflhs 168
                                     ++ +e+ vl+++ll i  +   k  D            + +  ++  Cg  f+ + ++  h ++f hs
  gene508|gene508|rna508|rna508  40 YKMNREQIVLENLLLNIEEDVLFKERDEVSMeevlesteKRFLNNLDCCGNYFDTFNSFAQH-RNFEHS 107
                                    44555555555555554444333333322222223333356888999999999999999999.688887 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.0001
                  zf-C2H2_aberr 139 dliyCripGCgkrfkslmaYkYhckk 164
                                    + + C i+GC k + s  + +Yh ++
  gene508|gene508|rna508|rna508 167 KPYRCDITGCKKAYTSAYGLRYHIEN 192
                                    5578*******************976 PP

  == domain 3  score: 14.1 bits;  conditional E-value: 1.3e-05
                  zf-C2H2_aberr 127 ngvikiiDidkkdliyCripGCgkrfkslmaYkYhckkfl 166
                                    ng ++  D++k+    C    Cgkr+k+  + kYh ++f+
  gene508|gene508|rna508|rna508 192 NGHVQKDDSNKP--HICAFSNCGKRYKNSNGLKYHLEHFH 229
                                    677777888888..67*******************99986 PP

>> FOXP-CC  FOXP coiled-coil domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.1       3.1   9.2e+03      38      59 ..      45      66 ..      32      70 .. 0.59
   2 ?    9.5   0.4   0.00051       1.5      12      37 ..      88     113 ..      86     118 .. 0.91
   3 ?    4.3   0.0     0.021        61       7      36 ..     171     200 ..     168     204 .. 0.90
   4 ?    4.6   0.2     0.017        50       6      31 ..     205     230 ..     202     231 .] 0.92

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 3.1
                        FOXP-CC 38 aqlrvqmqvvqqlekqlvkEke 59
                                   +q+ +   +++  e+ l kE++
  gene508|gene508|rna508|rna508 45 EQIVLENLLLNIEEDVLFKERD 66
                                   3444444445555556666665 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00051
                        FOXP-CC  12 CekvledveeflkhlnseHalddkst 37 
                                    C + ++++++f +h n eH+ +++s+
  gene508|gene508|rna508|rna508  88 CGNYFDTFNSFAQHRNFEHSNEEESA 113
                                    899*****************999986 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.021
                        FOXP-CC   7 CkWPgCekvledveeflkhlnseHalddks 36 
                                    C+  gC+k+ +++  +  h+++ H  +d s
  gene508|gene508|rna508|rna508 171 CDITGCKKAYTSAYGLRYHIENGHVQKDDS 200
                                    7778********************999887 PP

  == domain 4  score: 4.6 bits;  conditional E-value: 0.017
                        FOXP-CC   6 vCkWPgCekvledveeflkhlnseHa 31 
                                    +C+  +C k  ++++ +  hl++ H+
  gene508|gene508|rna508|rna508 205 ICAFSNCGKRYKNSNGLKYHLEHFHK 230
                                    79********************9997 PP

>> zf_Hakai  C2H2 Hakai zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.1   0.00017      0.52       4      31 ..     169     195 ..     168     196 .. 0.91
   2 ?    4.5   0.9    0.0098        29       5      31 ..     205     230 ..     204     231 .] 0.93

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00017
                       zf_Hakai   4 FmCtvvegCrRTYLSqRDLqAHIkhRHl 31 
                                    + C +  gC+  Y S   L  HI+  H+
  gene508|gene508|rna508|rna508 169 YRCDI-TGCKKAYTSAYGLRYHIENGHV 195
                                    67999.9*****************9996 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.0098
                       zf_Hakai   5 mCtvvegCrRTYLSqRDLqAHIkhRHl 31 
                                    +C + ++C   Y     L+ H +h H+
  gene508|gene508|rna508|rna508 205 ICAF-SNCGKRYKNSNGLKYHLEHFHK 230
                                    7999.9******************998 PP

>> zf-BED  BED zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.3     0.084   2.5e+02      22      43 ..     176     194 ..     165     195 .. 0.79
   2 ?   10.9   3.1   0.00012      0.37      22      44 .]     211     230 ..     204     230 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.084
                                    TTEE----SSTHHHHHHHHHS- CS
                         zf-BED  22 CgkilsrgggttnLkrHLrrkH 43 
                                    C+k +++     +L++H++ +H
  gene508|gene508|rna508|rna508 176 CKKAYTS---AYGLRYHIENGH 194
                                    5555555...489*****9999 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00012
                                    TTEE----SSTHHHHHHHHHS-H CS
                         zf-BED  22 CgkilsrgggttnLkrHLrrkHp 44 
                                    Cgk ++++   ++Lk+HL+++H+
  gene508|gene508|rna508|rna508 211 CGKRYKNS---NGLKYHLEHFHK 230
                                    88888876...***********6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       735  (0.040995); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 1448.06
//
Query:       gene509|gene509|rna509|rna509  [L=317]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.085   13.0   1.0       0.21   11.7   1.0    1.6  1  DUF749    Domain of unknown function (DUF749)


Domain annotation for each model (and alignments):
>> DUF749  Domain of unknown function (DUF749)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   1.0   1.2e-05      0.21      23      78 ..     209     268 ..     204     275 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 1.2e-05
                                    HHHHCTTT---SS--EEEEEE-TTTT-EEEEE-S--....-S-HHHHHHHHHHHHSSS-S CS
                         DUF749  23 klkaalekkelkdddeiaIlniegTtsyhvlFldsy....esieeikkeLkeadaklnhd 78 
                                    ++ka ++k  l +d+ei Il+ ++T  y+   ++++    ++  ++ + +k  ++k n++
  gene509|gene509|rna509|rna509 209 EAKAFIQKNTLYEDEEIRILDFQSTYTYQKQEIEEQpkktKEYAKVFELMKSENSKTNFK 268
                                    689*************************98888754211133344555555556666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (317 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1138  (0.0634726); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 2163.75
//
Query:       gene51|gene51|rna51|rna51  [L=236]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.9e-10   40.1   0.0      7e-10   39.3   0.0    1.4  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
    0.00049   20.0   0.0    0.00056   19.8   0.0    1.3  1  NAD_binding_10   NAD(P)H-binding
     0.0033   17.3   0.1     0.0051   16.7   0.1    1.2  1  NTNH_C           Nontoxic nonhaemagglutinin C-terminal


Domain annotation for each model (and alignments):
>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.3   0.0   1.2e-13     7e-10       1     130 []       6     121 ..       6     121 .. 0.87

  Alignments for each domain:
  == domain 1  score: 39.3 bits;  conditional E-value: 1.2e-13
                                EEEE--.SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHHHTTSSEEEE-SSGG..G CS
            Sacchrp_dh_NADP   1 vliiGa.GsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaialdaenyeavLaallkegdlvvnlsppi..s 81 
                                +++ Ga G++++ ++  l++  ++  +i++  r+ +k  +     + ++   i++d +n e     + +++ +++n+++p+  +
  gene51|gene51|rna51|rna51   6 IVVYGAsGFTARHIISHLQKY-PL--RIALSARTPSKISH-----NPKNYPVIQCDTNNLEI----ITSKAMVLLNCAGPYirC 77 
                                7999********999999986.45..9**********444.....55678888999988776....555779************ PP

                                HHHHHHHHHHHT-EEEE....SS-BCGCCSCHCCSHHHHHTHHHHHHCTSEEE CS
            Sacchrp_dh_NADP  82 sldvlkaCietgvhyvd....tsiskeertnyalreavlklkekakeagvtav 130
                                +++v++ Ci + +hyvd    t +         +++ + k++eka+e+gv+++
  gene51|gene51|rna51|rna51  78 GEAVVESCINNNCHYVDitgeTTF---------INNIIKKFDEKAREKGVYVL 121
                                *****************7666555.........9****************985 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   9.4e-08   0.00056       1      55 [.      10      61 ..      10     155 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 9.4e-08
                               TTTSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCTTTCEEEE--TT-CCHHH CS
             NAD_binding_10  1 GAtGkvGrllvkellargghevtalvRnpeklaeleaeeglevvegdvtdvedla 55
                               GA+G ++r+++++l +   +++ + +R+p+k+++    ++  v++ d ++ e ++
  gene51|gene51|rna51|rna51 10 GASGFTARHIISHLQKYP-LRIALSARTPSKISHN--PKNYPVIQCDTNNLEIIT 61
                               9****************5.**************64..589*******99987665 PP

>> NTNH_C  Nontoxic nonhaemagglutinin C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.1   8.5e-07    0.0051      40     110 ..      40     110 ..      25     132 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 8.5e-07
                     NTNH_C  40 vkennniylsik.dtndlnlqaakfkllsidtnkqyvqkldevvvsllddeekyvdissednrlqlvdskdt 110
                                + +n + y  i+ dtn+l++ ++k   + ++    y++  + vv s ++++ +yvdi+ e   ++ + +k +
  gene51|gene51|rna51|rna51  40 ISHNPKNYPVIQcDTNNLEIITSKAM-VLLNCAGPYIRCGEAVVESCINNNCHYVDITGETTFINNIIKKFD 110
                                56666667666549*********975.5589999****9999999*************99776665544433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       553  (0.0308439); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 1450.44
//
Query:       gene510|gene510|rna510|rna510  [L=255]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.1e-81  272.1   6.9    3.6e-81  271.9   6.9    1.0  1  14-3-3    14-3-3 protein
  ------ inclusion threshold ------
      0.083   13.0   0.1       0.23   11.6   0.0    1.8  2  DUF1818   Domain of unknown function (DUF1818)


Domain annotation for each model (and alignments):
>> 14-3-3  14-3-3 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  271.9   6.9     4e-85   3.6e-81       2     222 .]      14     240 ..      13     240 .. 0.96

  Alignments for each domain:
  == domain 1  score: 271.9 bits;  conditional E-value: 4e-85
                                    HHHHHHCCHHHHHHHHHCHHHHC....SS---HCHHHHHHHHHHHHHHHHHHHCHHHHHHHCCCCTCCHHHHHHHHHHHH CS
                         14-3-3   2 aklaeqaeryddmveymkkvvel....keeLskeernlLsvayKnvvgarRaswrvlssieqkeeskeekkvelikeyre 77 
                                    a l+e+aery+dm++ mk+v++l    k e++ + rn++s+a+Kn++g+rRa+wr+l+  ++k ++++ ++ ++i +y  
  gene510|gene510|rna510|rna510  14 ASLSERAERYEDMIKDMKRVIQLhwenKIEITPKVRNYFSMAFKNLTGTRRAAWRTLCIEKDKYKDTNLENYNVIVDYLV 93 
                                    789**********************99999****************************6577777777889********* PP

                                    HHHHHHHHHHHHHHHHHHHCCHCH....-SHHHHHHHHHHHHHHHHHHHCC--HHHHHHHHHHHHHHHHHHHHHHHTTTG CS
                         14-3-3  78 kiekeLkeiceevlelldktlipka...tseeskvfylkmkgDyyRYlaEfaegeekkeaaekakeaYeeAleiakkelq 154
                                    ++e+eL++ic++v+  +dk++++++    + es+vf+lkmkgDy+RY+aE+a g++   +++++k+aYe+A+eia +el+
  gene510|gene510|rna510|rna510  94 EVENELNTICDDVIGHIDKHILKENeiaLDVESQVFFLKMKGDYFRYKAEVAAGQDFLAFKTESKNAYEKASEIA-NELA 172
                                    **********************543356899********************************************.89** PP

                                    CC-HHHHHHHHHHHHHHHCTT--HHHHHHHHHHHHHCCHCCCCCS.TTTHHHHHHHHHHHHHHHHHHC CS
                         14-3-3 155 pthpirLglaLNySVflyeilnspekAcelakkafdeaiaeldelseesykdstlilqlLrdnltlWt 222
                                    p++ +rLgl+LNySVf+yei + p+kAc lak+afd+ai+++d lsee+ykdstli+qlLrdnl+lWt
  gene510|gene510|rna510|rna510 173 PVNSLRLGLCLNYSVFYYEIEKMPDKACMLAKQAFDDAIKDIDVLSEEHYKDSTLIMQLLRDNLSLWT 240
                                    *******************************************************************8 PP

>> DUF1818  Domain of unknown function (DUF1818)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0      0.54   4.8e+03      28      28 ..      42      42 ..      12      73 .. 0.61
   2 ?   11.6   0.0   2.5e-05      0.23      48      86 ..     106     144 ..      88     173 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.54
                                   E CS
                        DUF1818 28 i 28
                                   i
  gene510|gene510|rna510|rna510 42 I 42
                                   3 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 2.5e-05
                                    HHHCCHTTSSTTSEEEEEEEETTEEEEEEEETTEEEEEE CS
                        DUF1818  48 qlkalaeeLmdeEkialeaesdllwleveGdkeaysLrl 86 
                                     + ++ +++++e +ial++es+ + l+++Gd  +y+ ++
  gene510|gene510|rna510|rna510 106 VIGHIDKHILKENEIALDVESQVFFLKMKGDYFRYKAEV 144
                                    4568999************************99998766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       943  (0.0525964); expected 358.6 (0.02)
Passed bias filter:                      466  (0.0259914); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1671.55
//
Query:       gene511|gene511|rna511|rna511  [L=970]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      2e-09   38.4   0.0      2e-09   38.4   0.0    4.0  5  CAP         Cysteine-rich secretory protein family


Domain annotation for each model (and alignments):
>> CAP  Cysteine-rich secretory protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.4   0.0   1.1e-13     2e-09       3     123 ..      21     127 ..      19     130 .. 0.84
   2 ?   -3.6   0.1         1   1.8e+04      43      58 ..     202     217 ..     190     250 .. 0.52
   3 ?   -5.6   5.0         1   1.8e+04      38      38 ..     373     373 ..     304     424 .. 0.56
   4 ?   -1.9   0.8      0.32   5.7e+03      50      59 ..     495     515 ..     468     564 .. 0.49
   5 ?   -2.5   0.2      0.47   8.4e+03      43      61 ..     856     872 ..     817     916 .. 0.58

  Alignments for each domain:
  == domain 1  score: 38.4 bits;  conditional E-value: 1.1e-13
                                    HHHHHHHHTT----EE-HHHHHHHHHHHHHHHHH.T---S-GGG--HHHHHHTT-T..EEEEEES--CCCHHHHHHTSHH CS
                            CAP   3 ahNeyRaaaglppLkwdatLekaAqdhardcaashsdsssspeggdllkyaenagk..eniaaaseaaedavdsWysepg 80 
                                     +NeyRa++ l+pL++ ++L +aA ++a+++++++s  ++  +g+ +  +   a      +++ +++  ++++ W+++++
  gene511|gene511|rna511|rna511  21 ITNEYRAQNALAPLAVHPSLTRAASQQANTMCTRKSLVHNNLSGRLAAVDFVGARIgeNIARSVENDEHRVFEVWLKSEM 100
                                    68*****************************999977777777766666666666553366666777999********** PP

                                    .............HHHHHT-SS--EEEEEEEEBTTS-E..EEE CS
                            CAP  81 tynkgketegsighftnllwpkstkvGcavatcgngsftfivv 123
                                                 h+ n++  +++ vG +   +g+g+f  ++v
  gene511|gene511|rna511|rna511 101 -------------HRDNIV-GDYEFVGEGKCVDGDGYF--YYV 127
                                    .............******.***************988..665 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 1
                                    -GGG--HHHHHHTT-T CS
                            CAP  43 speggdllkyaenagk 58 
                                    +p+  ++ +y+ ++g+
  gene511|gene511|rna511|rna511 202 DPNTPNTIGYISSYGA 217
                                    3334444444444442 PP

  == domain 3  score: -5.6 bits;  conditional E-value: 1
                                    T CS
                            CAP  38 s 38 
                                     
  gene511|gene511|rna511|rna511 373 I 373
                                    1 PP

  == domain 4  score: -1.9 bits;  conditional E-value: 0.32
                                    HHHHHTT-T...........E CS
                            CAP  50 lkyaenagk...........e 59 
                                    +++ en g+           +
  gene511|gene511|rna511|rna511 495 NDKGENGGNntknstkskddQ 515
                                    222222221222222222221 PP

  == domain 5  score: -2.5 bits;  conditional E-value: 0.47
                                    -GGG--HHHHHHTT-TEEE CS
                            CAP  43 speggdllkyaenagkeni 61 
                                    + +g ++ ++ e ++  ++
  gene511|gene511|rna511|rna511 856 PDDGKKTKDGDETND--QN 872
                                    222222222222222..22 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (970 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2155  (0.120196); expected 358.6 (0.02)
Passed bias filter:                      490  (0.02733); expected 358.6 (0.02)
Passed Vit filter:                       185  (0.0103185); expected 17.9 (0.001)
Passed Fwd filter:                        67  (0.00373696); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 2.27u 0.42s 00:00:02.69 Elapsed: 00:00:00.72
# Mc/sec: 4071.75
//
Query:       gene512|gene512|rna512|rna512  [L=592]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.2e-67  225.3   0.1    1.6e-66  224.4   0.0    1.5  2  Pkinase         Protein kinase domain
    1.3e-33  116.4   0.0      2e-33  115.8   0.0    1.3  1  Pkinase_Tyr     Protein tyrosine kinase
    2.2e-07   30.2   0.1    3.5e-07   29.5   0.1    1.3  1  Haspin_kinase   Haspin like kinase domain
    5.4e-07   29.2   0.0    9.3e-07   28.4   0.0    1.3  1  Kinase-like     Kinase-like
    5.5e-06   25.9   0.0    1.2e-05   24.8   0.0    1.4  1  Kdo             Lipopolysaccharide kinase (Kdo/WaaP) family
    0.00028   20.9   0.1     0.0055   16.7   0.1    2.2  2  APH             Phosphotransferase enzyme family
     0.0033   17.1   0.5     0.0099   15.5   0.2    1.9  2  RIO1            RIO1 family
  ------ inclusion threshold ------
      0.054   12.3   0.2       0.18   10.5   0.0    1.9  2  Pkinase_fungal  Fungal protein kinase
       0.11   12.7   0.0       0.26   11.5   0.0    1.6  1  NitrOD2         Nitrososphaera output domain 2


Domain annotation for each model (and alignments):
>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  224.4   0.0   8.1e-70   1.6e-66       1     264 []      95     353 ..      95     353 .. 0.91
   2 ?   -3.4   0.0       2.4   4.9e+03     152     171 ..     365     384 ..     359     405 .. 0.64

  Alignments for each domain:
  == domain 1  score: 224.4 bits;  conditional E-value: 8.1e-70
                                    EEEEEEEEEESSEEEEEEEETTTTEEEEEEEEECHCHCHHHH........HHHHHHHHHHHHHSCTTB--EEEEEEESSE CS
                        Pkinase   1 yekleklGeGsfGkVykaveketgkivAvKkikkekakkkke........kkvlrEikilkklkhpnivrlyevfeekde 72 
                                    y+ l++lG+Gsf+kV  a  + +g++vA+K+i ++ + ++ +        +++ rE  i + + hp+i++l  +f+++ +
  gene512|gene512|rna512|rna512  95 YTLLRTLGKGSFSKVKLAA-SPDGQHVAIKIIPRNLRYNSINkesrckreERIYREAIITALVCHPHIIKLRAFFYNDLH 173
                                    67899*************9.7**********98765544433345677789***************************** PP

                                    EEEEEE--TTEBHHHHHHHHSS--HHHHHHHHHHHHHHHHHHHHTTEE-SS-SGGGEEEETTTEEEE-SGTTSEESSSSC CS
                        Pkinase  73 lylvleyveggeladllerkgslseeeakkiakqilegleylHskgiiHrDlKpeNiLidekgelKitDFGlakelesss 152
                                    +y+v eyv+g +l + ++++g+l+e+ a+k+++qi+ +++++Hs+ i+HrDlK eNiLid+ g++Ki+DFGl++ ++s++
  gene512|gene512|rna512|rna512 174 FYMVYEYVSGRSLLNCIRENGVLDEQLARKFFTQIVDAVNFMHSNAIVHRDLKIENILIDKGGNIKIIDFGLSNFYDSKQ 253
                                    ******************************************************************************** PP

                                    SBCTTTSCGGGS-HHHHTTSCB.SHHHHHHHHHHHHHHHHHSS-STTTSSHHHHHHHHHHTHHHHHHHCTSHH...HHHT CS
                        Pkinase 153 kltsfvgtseYlAPEvlkeney.skkvDvWslGvilyelltgkppfsgekgkekvekeldqlekilkilgetkeklpeas 231
                                     l +f+g+ ++ APE+l+++ y +++vD+WslGvily ++ g+ pf  +k+ +    +l+      k    +k  ++ ++
  gene512|gene512|rna512|rna512 254 FLGTFCGSLQFAAPELLRGRVYtGPEVDMWSLGVILYVMVVGTLPFD-DKDVS----ILHS-----K---IKKGRFAFRR 320
                                    *****************999999************************.33323....3333.....2...234689999* PP

                                    TS-HHHHHHHHHHT-SSGCCSTTHHHHHTSGGG CS
                        Pkinase 232 eiseeakdllkkllkkdpkkRltaeellqhpyl 264
                                    e+s +a++l+  l++ d kkR+ ++++l++++l
  gene512|gene512|rna512|rna512 321 EVSASARKLIGGLIESDAKKRYRMRDVLKSDWL 353
                                    *******************************97 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 2.4
                                    CSBCTTTSCGGGS-HHHHTT CS
                        Pkinase 152 skltsfvgtseYlAPEvlke 171
                                    ++ +++  t+ Y+ P v + 
  gene512|gene512|rna512|rna512 365 QNEQQYAHTHPYMNPTVTSM 384
                                    44667777777777777643 PP

>> Pkinase_Tyr  Protein tyrosine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.8   0.0   9.8e-37     2e-33       3     256 ..      97     348 ..      95     350 .. 0.86

  Alignments for each domain:
  == domain 1  score: 115.8 bits;  conditional E-value: 9.8e-37
                                    EEEEEEEESSEEEEEEEEETTTTSSEEEEEEEEEST.........TSSHHHHHHHHHHHHHHHTS-BTTB--EEEEEESS CS
                    Pkinase_Tyr   3 lgkklGeGafGkVvegtlkgekekkevkVavKtlke.........eateeekeelleeakimkklkhpnivkllgvctke 73 
                                    l ++lG+G+f+kV  +        + ++Va+K++ +         e++ +++e++++ea i   + hp+i+kl ++ +++
  gene512|gene512|rna512|rna512  97 LLRTLGKGSFSKVKLAASP-----DGQHVAIKIIPRnlrynsinkESRCKREERIYREAIITALVCHPHIIKLRAFFYND 171
                                    6799**********99988.....77889999874322222222144445578888898888888*************** PP

                                    SSEEEEEE--TTEBHHHHHHHTCTTTSBHHHHHHHHHHHHHHHHHHHHTTEEEST-SGGGEEEEETTEEEE-STTTHEET CS
                    Pkinase_Tyr  74 epllivteyvkgGdLlkfLrkkekekltlkdllsfalqvAkGmeyLeskklvHrdlaarNvLlsenkvvkisDfGLardi 153
                                     + ++v eyv+g +Ll+ +r++    l+ +   +f +q+ +++++++s+ +vHrdl   N+L++++  +ki DfGL++  
  gene512|gene512|rna512|rna512 172 LHFYMVYEYVSGRSLLNCIREN--GVLDEQLARKFFTQIVDAVNFMHSNAIVHRDLKIENILIDKGGNIKIIDFGLSNFY 249
                                    *********************9..9999999***********************************************99 PP

                                    TTSSEEEETTSSTSGGGGS-HHHHHHSEEEH.HHHHHHHHHHHHHHHTTSSGTTTTSHHHHHHHHHHTTEES-BBTTSBH CS
                    Pkinase_Tyr 154 ekddeyvkkeeaklpvkWmapEslkekkfts.ksDvWsfGvllwEiftlgespypglkneevleklkegkrlekpekcpe 232
                                       d+ +  ++   ++++ apE l+ +++t  + D+Ws Gv+l+ ++  g  p+ + + + + +k+k+g r +  +++++
  gene512|gene512|rna512|rna512 250 ---DSKQFLGTFCGSLQFAAPELLRGRVYTGpEVDMWSLGVILYVMVV-GTLPFDDKDVSILHSKIKKG-RFAFRREVSA 324
                                    ...4445566777899************995489**********7666.*******9999888888876.6777777999 PP

                                    HHHHHHHHHT-SSGGGS--HHHHH CS
                    Pkinase_Tyr 233 elyelmkkcweedpeeRptfselv 256
                                    +  +l+    e+d+++R ++++++
  gene512|gene512|rna512|rna512 325 SARKLIGGLIESDAKKRYRMRDVL 348
                                    *****************9999886 PP

>> Haspin_kinase  Haspin like kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.5   0.1   1.7e-10   3.5e-07      95     259 ..      85     251 ..       7     271 .. 0.78

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 1.7e-10
                  Haspin_kinase  95 kilneadlasllnd...seklssevyqtke.kdkevvlKviplevledvtiskelslkelkslklvkgtypglllllqdk 170
                                    ++lne ++++ +     +++++s+v  + + + ++v++K+ip   l    i+ke++ k  +  ++ + +    +l+++ +
  gene512|gene512|rna512|rna512  85 RMLNERRIKEYTLLrtlGKGSFSKVKLAASpDGQHVAIKIIPR-NLRYNSINKESRCKREE--RIYREA-IITALVCHPH 160
                                    4566664444332234599999***9999989999*******8.66666777888887655..567777.5567778888 PP

                  Haspin_kinase 171 vlkekpdfyseqqlflvlllkdkGtdLeev....klkswkqalsifwqivkiLyvaEtkfeFEHRdLhldniLvdknlnv 246
                                    ++k +  f+ ++ +f +++   +G +L ++     + + + a + f qiv  +    ++    HRdL+++niL+dk +n+
  gene512|gene512|rna512|rna512 161 IIKLR-AFFYNDLHFYMVYEYVSGRSLLNCirenGVLDEQLARKFFTQIVDAVNFMHSN-AIVHRDLKIENILIDKGGNI 238
                                    88888.6777777777777778999999997754456677899999*******999877.688***************** PP

                  Haspin_kinase 247 tlidlklsRless 259
                                     +id+ ls + +s
  gene512|gene512|rna512|rna512 239 KIIDFGLSNFYDS 251
                                    *******988744 PP

>> Kinase-like  Kinase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4   0.0   4.7e-10   9.3e-07     141     288 .]     197     341 ..     184     341 .. 0.83

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 4.7e-10
                    Kinase-like 141 letiarlllTlqlirlaanLqakglvhgkftvdnllldekgglmlggftaLvragtkvvlseve..kgfaPpEllgsrgg 218
                                     e++ar+  T q++  +  ++++ +vh +++ +n+l d+ g +++ +f+    +  k  l + +    fa pEll  r  
  gene512|gene512|rna512|rna512 197 DEQLARKFFT-QIVDAVNFMHSNAIVHRDLKIENILIDKGGNIKIIDFGLSNFYDSKQFLGTFCgsLQFAAPELLRGRV- 274
                                    5789999996.7************************************999999999999888877789****997743. PP

                    Kinase-like 219 ytrknktkmthkldaWqlGlviyriwclklPltlateea.keew...kfklckkipekvkaLlkkfLqlsqedR 288
                                    y          ++d W lG+  y +   +lP++ +   + +++     f   ++++   + L+ ++++ + ++R
  gene512|gene512|rna512|rna512 275 Y-------TGPEVDMWSLGVILYVMVVGTLPFDDKDVSIlHSKIkkgRFAFRREVSASARKLIGGLIESDAKKR 341
                                    3.......4579********************876544303333555677777899999999999999888887 PP

>> Kdo  Lipopolysaccharide kinase (Kdo/WaaP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.0   5.8e-09   1.2e-05     103     166 ..     184     243 ..     174     249 .. 0.91

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 5.8e-09
                            Kdo 103 qdLedllakwaelaeelkrallkavgrliaklhragvnHadlyaknillqqeeeeeaeiwliDl 166
                                    ++L +++++  +l+e+l r+ + ++  +++ +h+  + H+dl + nil+++++    +i +iD+
  gene512|gene512|rna512|rna512 184 RSLLNCIRENGVLDEQLARKFFTQIVDAVNFMHSNAIVHRDLKIENILIDKGG----NIKIIDF 243
                                    578889998777****************************************9....9999999 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0      0.06   1.2e+02      37     100 ..     140     210 ..     114     219 .. 0.67
   2 !   16.7   0.1   2.7e-06    0.0055     164     196 ..     216     246 ..     194     250 .. 0.75

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.06
                                    HHHHHHHHHHHH.HTT-B--B-CTTBS-EEETTEEEEEEE----EE-SS......HHHHHHHHHHHHHHHH CS
                            APH  37 irrevallrlLa.kagvpvPevlagdtddeeigllfalieyvpgrsllr......klsaaqlpellealge 100
                                    + re +++r     a v  P ++ ++   +  ++ + ++eyv grsll+       l+++ +++++ ++++
  gene512|gene512|rna512|rna512 140 CKREERIYREAIiTALVCHPHIIKLRAFFYNDLHFYMVYEYVSGRSLLNcirengVLDEQLARKFFTQIVD 210
                                    555555554433234343455555555667777899*************9966555555555555555555 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 2.7e-06
                                    S-EEEE-SS-SGGGEEEC..TTEEEEE---TT- CS
                            APH 164 lptvllHgDlhpgNllvdpddgrvtGviDfeda 196
                                     +  ++H+Dl+  N+l+d++++    +iDf+++
  gene512|gene512|rna512|rna512 216 HSNAIVHRDLKIENILIDKGGNIK--IIDFGLS 246
                                    56789*************555555..****986 PP

>> RIO1  RIO1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       2.5     5e+03       5      21 ..     112     128 ..     109     149 .. 0.66
   2 !   15.5   0.2     5e-06    0.0099     103     150 ..     197     244 ..     173     253 .. 0.75

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 2.5
                                    EEETTTEEEEEEEE-S- CS
                           RIO1   5 avsedgkevaiKiykts 21 
                                    a+s dg++vaiKi   +
  gene512|gene512|rna512|rna512 112 AASPDGQHVAIKIIPRN 128
                                    66789999999997544 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 5e-06
                                    -HHHHHHHHHHHHHHHHHHHHTSTEEESS-STTSEEEETT.EEEE--GT CS
                           RIO1 103 eeeeaeelyeevleemrklykeaglvHaDLSeyNvlvded.kvviIDvs 150
                                    +e+ a++ + +++++++ +++ + +vH DL   N+l+d++ ++ iID++
  gene512|gene512|rna512|rna512 197 DEQLARKFFTQIVDAVN-FMHSNAIVHRDLKIENILIDKGgNIKIIDFG 244
                                    26678888999999655.55699*****************9******96 PP

>> Pkinase_fungal  Fungal protein kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   9.3e-05      0.18     316     389 ..     212     273 ..     195     294 .. 0.72
   2 ?   -1.8   0.0       0.5     1e+03     281     322 ..     391     440 ..     318     444 .. 0.56

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 9.3e-05
                 Pkinase_fungal 316 IkghrsLflkagiLHrDiSenNilitdskkegerkglLiDLDlakelsddssesgarertGTleFmaievlkge 389
                                    +   + ++    i+HrD  ++Nili      ++ +  +iD+ l   ++    ++  ++  G l+F a e+l+g 
  gene512|gene512|rna512|rna512 212 V---NFMH-SNAIVHRDLKIENILID-----KGGNIKIIDFGLSNFYDS---KQFLGTFCGSLQFAAPELLRGR 273
                                    3...3445.778*************9.....7889999*****999994...4445789999999999999973 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.5
                 Pkinase_fungal 281 r.........lenrvhrrlvispvGkpiekaespkellealrDaIkghrsL 322
                                    +         +  r +   ++++ G  ++   +   +l+++r  Ik +r L
  gene512|gene512|rna512|rna512 391 PnsfnsafidV-LRKVGGKAFENTGTDMQACADDVSMLSCIRPTIKMYRLL 440
                                    13444444432.244445577888888888888889999999999998877 PP

>> NitrOD2  Nitrososphaera output domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00013      0.26      34      78 ..     375     419 ..     370     432 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00013
                        NitrOD2  34 dylggemdvrtailqrpdlferalvellGeiGekvlakvcedlqa 78 
                                     y+++ +   ta ++ p+ f+ a++++l ++G k + +   d+qa
  gene512|gene512|rna512|rna512 375 PYMNPTVTSMTAKMRAPNSFNSAFIDVLRKVGGKAFENTGTDMQA 419
                                    5889999999***********************999998888885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (592 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       582  (0.0324614); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.75u 0.33s 00:00:01.08 Elapsed: 00:00:00.55
# Mc/sec: 3233.70
//
Query:       gene513|gene513|rna513|rna513  [L=281]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.9e-19   67.8  12.5    1.1e-18   67.3  12.5    1.2  1  Far-17a_AIG1     FAR-17a/AIG1-like protein
  ------ inclusion threshold ------
      0.028   12.8   0.2      0.064   11.6   0.1    1.7  2  Mem_trans        Membrane transport protein
      0.059   13.1   0.5       0.18   11.6   0.2    2.0  2  Phage_holin_2_3  Bacteriophage holin family HP1
       0.14   11.3   1.8       0.23   10.7   1.8    1.3  1  Zip              ZIP Zinc transporter
       0.32   11.0   4.6       0.53   10.2   4.6    1.4  1  Glycos_transf_4  Glycosyl transferase family 4


Domain annotation for each model (and alignments):
>> Far-17a_AIG1  FAR-17a/AIG1-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.3  12.5   3.1e-22   1.1e-18      11     193 ..      12     188 ..       2     196 .. 0.81

  Alignments for each domain:
  == domain 1  score: 67.3 bits;  conditional E-value: 3.1e-22
                   Far-17a_AIG1  11 csyaalfypfhsekelanea..ayGgkfkyLtfiglvlqalfftlallaDeltlsallklrdnllavlafPvevlvsvlF 88 
                                      + ++  +++  kela++   + Gg+ ++Lt+ig+ l++l+ +l +l      +     ++n +  +a+  e+++s++F
  gene513|gene513|rna513|rna513  12 LLLLYSLSDASIPKELADHFntQKGGRNQFLTIIGVQLTILTLLLNVLKY----R----RAHNFIYPIALATEFTISITF 83 
                                    33333334444444444444679**********************99955....2....23444455566789******* PP

                   Far-17a_AIG1  89 WgLyliDrelvypkl..ldelipdWlnhsmHtvvlvailleifllkhkypsrlaalalsaafallYliwiervaqfngvw 166
                                    W +y+++++ ++++   +++l p +++++ H+++l+a+++e f+ + ++ s +++ ++  ++ ++Y iw  +  + ngvw
  gene513|gene513|rna513|rna513  84 WFFYFTNPANLMRPIpgVETLLPFYMDIVYHLLPLLALIVEAFVIDLSAISLSPCTFA--MVPIAYYIWAAYLSKSNGVW 161
                                    ********9988865337888******************************9999988..67789*************** PP

                   Far-17a_AIG1 167 vYPvlealslegrvlffalsavvmall 193
                                    +YP+l+ +s   r++ f   +++ +++
  gene513|gene513|rna513|rna513 162 PYPMLDNMSSTKRMIYFGYYTLIGIVS 188
                                    ******************999998876 PP

>> Mem_trans  Membrane transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.21   7.4e+02     135     153 ..      48      66 ..      13      75 .. 0.78
   2 ?   11.6   0.1   1.8e-05     0.064     108     220 ..     159     276 ..     111     281 .] 0.77

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.21
                      Mem_trans 135 ciiiytlllflfeyrgakl 153
                                    + +i+tlll++++yr+a +
  gene513|gene513|rna513|rna513  48 QLTILTLLLNVLKYRRAHN 66 
                                    4678999999999998876 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 1.8e-05
                      Mem_trans 108 lvlgipllkalyge....ygvslmvqvvvlqciiiytlllflfeyrgaklliseefpdtaasivsikvdsdvvsldgrkp 183
                                    +v ++p+l+ +  +    y + ++++  v  +i++ +   +     +ak++   ++  + + ++  +v++dv s d++  
  gene513|gene513|rna513|rna513 159 GVWPYPMLDNMSSTkrmiYFGYYTLIGIVSSQIFVSVARRISRHCFKAKNDEPRQNVPENEDEQPRQVEQDVSSEDEQPS 238
                                    567889999999987777555555555554555554444433334446666666666677889999*************9 PP

                      Mem_trans 184 leteaeikedgklhvtvrksnasrsdivs.sstprpsn 220
                                      ++  +++++ +hv+ ++s + +++ ++ +stp+ ++
  gene513|gene513|rna513|rna513 239 HVEDVSNEDEQPSHVEDVSSEDDQRSHTQeQSTPNTEQ 276
                                    99999999999*****9999999998888666766544 PP

>> Phage_holin_2_3  Bacteriophage holin family HP1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.2     5e-05      0.18      24      50 ..      39      65 ..      38      69 .. 0.88
   2 ?   -2.6   0.0       1.4   4.9e+03      28      37 ..     182     191 ..     178     209 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 5e-05
                Phage_holin_2_3 24 seWAiviGIicgvvTfliNwyykrkel 50
                                   ++  ++iG+ ++++T+l+N+ ++r+  
  gene513|gene513|rna513|rna513 39 NQFLTIIGVQLTILTLLLNVLKYRRAH 65
                                   67889****************999976 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.4
                Phage_holin_2_3  28 iviGIicgvv 37 
                                    ++iGI+ + +
  gene513|gene513|rna513|rna513 182 TLIGIVSSQI 191
                                    5788886655 PP

>> Zip  ZIP Zinc transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   1.8   6.3e-05      0.23      81     171 ..     185     269 ..     155     281 .] 0.37

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 6.3e-05
                            Zip  81 lvllGflllllveklltmivekksshkektpkkasssssesaakksvsndkveeseekedhvaeadtdadskeelrngkq 160
                                     ++ + +++ ++ ++ +++++      ++ ++ ++ +++e +  ++v++d ++e+e+  +hv+ +  +++++++  + ++
  gene513|gene513|rna513|rna513 185 GIVSSQIFVSVARRISRHCFKA-----KNDEPRQNVPENEDEQPRQVEQDVSSEDEQP-SHVEDVSNEDEQPSHVEDVSS 258
                                    3344445555555555555555.....2222222222222222222222222222222.122222222222222222222 PP

                            Zip 161 eksesekeqas 171
                                    e ++ +++q++
  gene513|gene513|rna513|rna513 259 EDDQRSHTQEQ 269
                                    22222222211 PP

>> Glycos_transf_4  Glycosyl transferase family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   4.6   0.00015      0.53      34     136 ..      45     155 ..       3     157 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00015
                Glycos_transf_4  34 laalililtldlslttlgllltqvlielglil.avlltllvivgvtNavNliDGldGlaagvsiiialalvvla...... 106
                                    + + + iltl l++ +++  +   ++ + l   + + + ++++ +tN  Nl+  + G+++ + + + +++ +l       
  gene513|gene513|rna513|rna513  45 IGVQLTILTLLLNVLKYRRAHN-FIYPIALATeFTISITFWFFYFTNPANLMRPIPGVETLLPFYMDIVYHLLPllaliv 123
                                    3333333333323333332222.22222222213466899*****************99998887766666655555766 PP

                Glycos_transf_4 107 ..avdgrsellllalallgallGfllfNrypA 136
                                      +v + s++ l  ++++++ ++++++ +y +
  gene513|gene513|rna513|rna513 124 eaFVIDLSAISLSPCTFAMVPIAYYIWAAYLS 155
                                    66777888888889999999999**9998866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1233  (0.0687713); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.60u 0.28s 00:00:00.88 Elapsed: 00:00:00.50
# Mc/sec: 1692.75
//
Query:       gene514|gene514|rna514|rna514  [L=59]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-15   57.2   5.6    1.8e-15   56.9   5.6    1.0  1  Ribosomal_S30  Ribosomal protein S30


Domain annotation for each model (and alignments):
>> Ribosomal_S30  Ribosomal protein S30
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.9   5.6   9.8e-20   1.8e-15       6      55 ..       7      57 ..       5      58 .. 0.85

  Alignments for each domain:
  == domain 1  score: 56.9 bits;  conditional E-value: 9.8e-20
                                   STTTTHHHHHS-------------THHHHHHHHHHHTTS.SS--SSSSS-S CS
                  Ribosomal_S30  6 LarAGKVrnqTPKveKqekkKkptGRakkRlqYnrRfvn.vvvggkkkkgp 55
                                   L+rAGKVrnqT Kv K+ek+ ++tGRa++R  Y+rR ++   ++g+ +++p
  gene514|gene514|rna514|rna514  7 LNRAGKVRNQTAKVPKKEKERAKTGRARRREMYSRRVEQgLFKNGTMRFNP 57
                                   9**************************************444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       695  (0.038764); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.43
# Mc/sec: 415.06
//
Query:       gene515|gene515|rna515|rna515  [L=548]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.7e-20   72.8   0.9    5.5e-20   71.8   0.1    1.9  2  MS_channel    Mechanosensitive ion channel
  ------ inclusion threshold ------
       0.03   14.2   1.7       0.22   11.5   0.2    2.9  3  EF-hand_6     EF-hand domain
      0.053   14.0   2.2       0.28   11.7   0.1    2.6  2  EF-hand_7     EF-hand domain pair
      0.058   13.2   0.0       0.28   11.0   0.0    2.1  2  DDDD          Putative mitochondrial precursor protein
        0.1   12.3   1.9       0.46   10.2   1.8    2.1  1  Tetraspanin   Tetraspanin family
       0.12   12.0   2.6       0.18   11.4   0.2    2.6  3  EF-hand_1     EF hand


Domain annotation for each model (and alignments):
>> MS_channel  Mechanosensitive ion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.1       1.2   3.6e+03      27      51 ..     116     140 ..     108     146 .. 0.70
   2 !   71.8   0.1   1.9e-23   5.5e-20       9     178 ..     339     507 ..     331     529 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1.2
                                    HHHHHHHHHHHHHHHHCHHHHHHHH CS
                     MS_channel  27 llavlGalglalglalkdlisnlva 51 
                                    l   l ++   ++l l ++++n+++
  gene515|gene515|rna515|rna515 116 LRITLSIGLYLVMLTLTTSLQNIFS 140
                                    5556666777788888888888887 PP

  == domain 2  score: 71.8 bits;  conditional E-value: 1.9e-23
                                    HHHHHHHHHHTTT--.SCCHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHTT.-SS-TT-EEESSSEEEEEEEE-SSEEEE CS
                     MS_channel   9 ivvgilivlsllgvn.vsallavlGalglalglalkdlisnlvaGiillfe.kpfkiGDlveigdieGtVediglrttki 86 
                                     +v + +++ l  ++ +++++ + Gal l+l++a+ +l s+ + ++i++f  +pf+iGD++eig+ ++ V d+gl+  ++
  gene515|gene515|rna515|rna515 339 PAVLFSTFIVLGAQSeFQNFFKSIGALLLSLSFAFSKLASDTFQSLIFVFFiRPFDIGDIIEIGGKTYVVSDLGLLYSTL 418
                                    3444444444444447999************************9988776527**********************98777 PP

                                    EETTSEEEEEEHHHHHTS-EEESSS.SSEEEEEEEEEE-TTS-...HHHHHHHHHHHHHH-TTB-TTS-EEEEEEEE-SS CS
                     MS_channel  87 rtfdgrivtiPnsslvtsnieNlsresgtrrikvsigvtyssdvkklekvleelkealkekpevlkdkellvvldefgds 166
                                       d r+ t Pn+ l +s+i+Nl++ s+++ +k++ +++y+   +kl+k+ e++  +l+e+p+  +++   ++++ +  +
  gene515|gene515|rna515|rna515 419 L-SDSRYETFPNELLRNSSIKNLRK-STHVTAKFEYCFKYDDY-SKLDKLKEMISSFLLENPTKYHEQFDINHFEILNEN 495
                                    5.577899*****************.***************99.99********************99999********* PP

                                    SEEEEEEEEEET CS
                     MS_channel 167 slnfevrvfvkt 178
                                     ++f++++++  
  gene515|gene515|rna515|rna515 496 KMKFTIQIVLSC 507
                                    ******998765 PP

>> EF-hand_6  EF-hand domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0      0.45   1.3e+03      16      27 ..     266     277 ..     257     281 .. 0.82
   2 ?   11.5   0.2   7.4e-05      0.22       4      24 ..     283     303 ..     282     308 .. 0.90
   3 ?   -2.5   0.0       2.3     7e+03      20      30 ..     353     362 ..     352     363 .. 0.68

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.45
                      EF-hand_6  16 kidaeElrkalr 27 
                                     ++ +++rk++ 
  gene515|gene515|rna515|rna515 266 VLTLDDFRKFFG 277
                                    689999999986 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 7.4e-05
                      EF-hand_6   4 eaFklfDkdgdGkidaeElrk 24 
                                    ++F lfD d +++++++E+ k
  gene515|gene515|rna515|rna515 283 KIFGLFDIDENNEVTRDEFTK 303
                                    68****************965 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 2.3
                      EF-hand_6  20 eElrkalrkal 30 
                                    +E++++++ + 
  gene515|gene515|rna515|rna515 353 SEFQNFFK-SI 362
                                    68888887.55 PP

>> EF-hand_7  EF-hand domain pair
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.2      0.19   5.6e+02      37      70 ..     241     276 ..     220     277 .. 0.62
   2 ?   11.7   0.1   9.4e-05      0.28      48      70 ..     283     305 ..     278     306 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.19
                      EF-hand_7  37 egsklsdeelellfke.fDtdkdG..visfdEFlkly 70 
                                    +g +l+++e  ++++  fD+ + G  v+++d+F+k++
  gene515|gene515|rna515|rna515 241 TGTELDEDE-TDWSNViFDSMCIGkeVLTLDDFRKFF 276
                                    455555555.34444423555544449*******997 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 9.4e-05
                      EF-hand_7  48 llfkefDtdkdGvisfdEFlkly 70 
                                    ++f  fD d + ++++dEF k y
  gene515|gene515|rna515|rna515 283 KIFGLFDIDENNEVTRDEFTKRY 305
                                    79*****************9977 PP

>> DDDD  Putative mitochondrial precursor protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   9.5e-05      0.28      18      57 ..      19      60 ..       3      67 .. 0.77
   2 ?   -2.2   0.0       1.2   3.6e+03      28      43 ..     186     201 ..     169     211 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 9.5e-05
                           DDDD 18 vttrsGaikp.kPkktpFgLlrvilvVipg.llvGtliSknv 57
                                      ++G i+  kP ++++ +l+vil+++ + + vG+ +Sk+v
  gene515|gene515|rna515|rna515 19 SERKTGKILSrKPVNIAWIVLSVILMIVSFaMAVGAYMSKKV 60
                                   456778877538**********99988887257*******97 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.2
                           DDDD  28 kPkktpFgLlrvilvV 43 
                                    k +++ F+Ll v+ + 
  gene515|gene515|rna515|rna515 186 KYENIVFALLIVFSTL 201
                                    6678889999998775 PP

>> Tetraspanin  Tetraspanin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   1.8   0.00015      0.46      49     107 ..      32     170 ..      12     242 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00015
                                    ....XXXXXXXXXXXXXXXXXXXXXXXX.......XXXXXXXXXXXXXXXXXXXXXXXXX--HHH............... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............... RF
                    Tetraspanin  49 laillivvGvllfllgflGcigalkenk.......cllltfsllllvlfllelaagilgfvfsdk............... 106
                                    + i+ iv++v+l++++f+  +ga+  +k       +  ++   +l+++f++++ a++l+++   +               
  gene515|gene515|rna515|rna515  32 VNIAWIVLSVILMIVSFAMAVGAYMSKKvldknadFYNVWWHACLVLFFFFMVNATLLMIARVVDptgkgesflaymldq 111
                                    55679*****************9999996777777556666678888888888777766665555455666666666666 PP

                                    ........................................................... CS
                                    ..........................................................x RF
                    Tetraspanin 107 ..........................................................a 107
                                                                                              +
  gene515|gene515|rna515|rna515 112 nmmllritlsiglylvmltlttslqnifspmpvitapnsepivvpkdpsdtagskpesK 170
                                    66666666666666666666666666666666666666666666666666666665551 PP

>> EF-hand_1  EF hand
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0         1     3e+03      16      26 ..     266     276 ..     263     278 .. 0.81
   2 ?   11.4   0.2     6e-05      0.18       4      24 ..     283     303 ..     282     308 .. 0.90
   3 ?   -2.9   0.0       2.2   6.7e+03      21      28 ..     354     361 ..     353     362 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1
                                    EEEHHHHHHHH CS
                      EF-hand_1  16 kIdfeEfkell 26 
                                     +++++f++++
  gene515|gene515|rna515|rna515 266 VLTLDDFRKFF 276
                                    6899***9987 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 6e-05
                                    HHHHHHTTTSSSEEEHHHHHH CS
                      EF-hand_1   4 eiFrefDkDgdGkIdfeEfke 24 
                                    +iF +fD D +  ++++Ef +
  gene515|gene515|rna515|rna515 283 KIFGLFDIDENNEVTRDEFTK 303
                                    79*****************76 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 2.2
                                    HHHHHHHH CS
                      EF-hand_1  21 Efkellkk 28 
                                    Ef++++k+
  gene515|gene515|rna515|rna515 354 EFQNFFKS 361
                                    89999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (548 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1064  (0.0593452); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.42
# Mc/sec: 3904.78
//
Query:       gene516|gene516|rna516|rna516  [L=234]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       624  (0.0348039); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 1533.73
//
Query:       gene517|gene517|rna517|rna517  [L=93]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.5e-15   55.1   0.1    9.4e-15   54.6   0.1    1.2  1  Glutaredoxin   Glutaredoxin
    9.4e-06   26.0   0.0    1.2e-05   25.6   0.0    1.1  1  GST_N_3        Glutathione S-transferase, N-terminal domain
     0.0052   16.8   0.1      0.008   16.2   0.1    1.3  1  Thioredoxin_3  Thioredoxin domain
  ------ inclusion threshold ------
      0.032   14.6   0.1      0.051   13.9   0.1    1.3  1  NusA_N         NusA N-terminal domain
      0.096   12.3   0.0       0.16   11.6   0.0    1.5  1  DUF953         Eukaryotic protein of unknown function (DUF953
       0.47   10.8   4.0        7.3    7.0   1.0    2.3  2  ATP-synt_E_2   ATP synthase epsilon subunit


Domain annotation for each model (and alignments):
>> Glutaredoxin  Glutaredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.6   0.1   3.2e-18   9.4e-15       4      60 .]      25      81 ..      22      81 .. 0.95

  Alignments for each domain:
  == domain 1  score: 54.6 bits;  conditional E-value: 3.2e-18
                                   EESTSSHHHHHHHHHHHHTTGGEEEEEGCCSHHHHHHHHHHHTSSSSSEEEETTEEE CS
                   Glutaredoxin  4 ftkptCpyCkkakrlLkelgvkfeeidvdkdeeireelkelsgvrtvPqvfidgkhv 60
                                    +++ CpyC++a ++L++++++f++i    +ee+ ee+k+  g +t P++fi+g++v
  gene517|gene517|rna517|rna517 25 IGFKECPYCVRAEEILNTKNIEFDYIYRAREEELEEEIKKCYGHETYPMIFINGEFV 81
                                   56789**************************************************97 PP

>> GST_N_3  Glutathione S-transferase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.0   4.1e-09   1.2e-05       1      57 [.      24      81 ..      24      88 .. 0.86

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 4.1e-09
                                   EES-TTSHHHHHHHHHHHHHT--EEEE--.-TTTTHHHHHHH-TT--SSEEETTS-EE CS
                        GST_N_3  1 LygfpaSpyarrvrlaLnekglpvevvev.tpgehdeellaknplgkvPvLeddgeal 57
                                   L+gf+ +py+ r+ ++Ln k++++ +     ++e  ee+++ +++ ++P++ ++ge +
  gene517|gene517|rna517|rna517 24 LIGFKECPYCVRAEEILNTKNIEFDYIYRaREEELEEEIKKCYGHETYPMIFINGEFV 81
                                   899********************99855504555599**************9999866 PP

>> Thioredoxin_3  Thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1   2.7e-06     0.008       8      60 ..      28      81 ..      20      89 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2.7e-06
                                   SSSTTCHHHHHHHHHHCHCCTCEC....EEECCTTHHHH.HHCT-SSSSEEECTTCEE CS
                  Thioredoxin_3  8 pgCakCpklekavkeaaaekgika....evekvtdfeei.ekygVmsvPalvidgkvv 60
                                   + C++C ++    +e++++k+i++       + +  eei + yg ++ P ++i+g++v
  gene517|gene517|rna517|rna517 28 KECPYCVRA----EEILNTKNIEFdyiyRAREEELEEEIkKCYGHETYPMIFINGEFV 81
                                   56****965....55666666666323355666777888889*************976 PP

>> NusA_N  NusA N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   1.7e-05     0.051       7      41 ..      37      71 ..      35      80 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.7e-05
                                   CCCCCCS---HHHHHHHHHHHHHHHHHCCT-SSS- CS
                         NusA_N  7 eelakekgiskevviealeeaLakaykknygeden 41
                                   ee+ + k+i+ + +++a ee+L+ ++kk yg+++ 
  gene517|gene517|rna517|rna517 37 EEILNTKNIEFDYIYRAREEELEEEIKKCYGHETY 71
                                   78999************************987644 PP

>> DUF953  Eukaryotic protein of unknown function (DUF953)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   5.3e-05      0.16      36      49 ..      28      41 ..       9      49 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 5.3e-05
                                   BSSHHHHHHHHHHH CS
                         DUF953 36 sWCPdCvkaepvie 49
                                     CP+Cv+ae++++
  gene517|gene517|rna517|rna517 28 KECPYCVRAEEILN 41
                                   56*********986 PP

>> ATP-synt_E_2  ATP synthase epsilon subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.1     0.012        37      42      54 ..      12      24 ..       3      28 .. 0.85
   2 ?    7.0   1.0    0.0024       7.3      25      48 ..      37      60 ..      34      66 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.012
                   ATP-synt_E_2 42 RLdeLeklKrkvL 54
                                   R++eL + Kr++L
  gene517|gene517|rna517|rna517 12 RINELKEKKRNIL 24
                                   8899999999998 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0024
                   ATP-synt_E_2 25 sElLkkiNmEYEKlLKqRLdeLek 48
                                   +E+L+  N+E++ + + R +eLe+
  gene517|gene517|rna517|rna517 37 EEILNTKNIEFDYIYRAREEELEE 60
                                   79********************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       795  (0.0443416); expected 358.6 (0.02)
Passed bias filter:                      529  (0.0295053); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 658.20
//
Query:       gene518|gene518|rna518|rna518  [L=575]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.9e-10   39.6   3.5    3.9e-10   39.6   3.5    1.8  2  MS_channel    Mechanosensitive ion channel
    0.00044   20.0   0.2     0.0016   18.2   0.2    2.0  1  EF-hand_6     EF-hand domain
     0.0023   17.7   0.3     0.0023   17.7   0.3    3.8  3  EMC3_TMCO1    Integral membrane protein EMC3/TMCO1-like
     0.0049   16.3   0.1      0.018   14.5   0.1    2.0  1  EF-hand_1     EF hand
  ------ inclusion threshold ------
      0.078   13.5   1.9       0.27   11.8   0.7    2.5  2  YbaJ          Biofilm formation regulator YbaJ
       0.67    9.4   3.6       0.62    9.6   0.2    2.5  3  E1-E2_ATPase  E1-E2 ATPase
        9.8    6.1   8.8         19    5.2   0.0    3.9  3  LapA_dom      Lipopolysaccharide assembly protein A domain


Domain annotation for each model (and alignments):
>> MS_channel  Mechanosensitive ion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.0   0.1       3.5   9.1e+03     180     199 ..     187     206 ..     180     208 .. 0.71
   2 !   39.6   3.5   1.5e-13   3.9e-10       8     200 ..     376     568 ..     369     573 .. 0.74

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 3.5
                                    ..TTHHHHHHHHHHHHHHHH CS
                     MS_channel 180 vpeeylsvqseinlrikkil 199
                                     ++++ + ++e+ ++i+ki 
  gene518|gene518|rna518|rna518 187 NYKNRVKHNREVLKHIQKIN 206
                                    37777888888888888876 PP

  == domain 2  score: 39.6 bits;  conditional E-value: 1.5e-13
                                    HHHHHHHHHHHTTT--SCCHHHHHHHHHHHH...HHHHCHHHHHHHHHHHHHTT.-SS-TT-EEESSSEEEEEEEE-SSE CS
                     MS_channel   8 iivvgilivlsllgvnvsallavlGalglal...glalkdlisnlvaGiillfe.kpfkiGDlveigdieGtVediglrt 83 
                                    ++v +i+ +l ++   + ++  ++ ++gl++   ++a+k+l++++++++i++f  kpf+ GD+  +++ +++V +ig++ 
  gene518|gene518|rna518|rna518 376 LFVPFIVFILLVFTGHLPSFQNSFTMAGLVIfpfTFAFKSLVEEIFSSVIFVFFiKPFDYGDIFFVEGKRYEVLSIGILY 455
                                    55556777777777777777777777777765559*************98776538************************ PP

                                    EEEEETTSEEEEEEHHHHHTS-EEESSS.SSEEEEEEEEEE-TTS-...HHHHHHHHHHHHHH-TTB-TTS-EEEEEEEE CS
                     MS_channel  84 tkirtfdgrivtiPnsslvtsnieNlsresgtrrikvsigvtyssdvkklekvleelkealkekpevlkdkellvvldef 163
                                    t++   d + +t  n+ +  ++i Nl++ s+  + +++++++y+s  ++ ++ +++l e  + +p      +  ++  e 
  gene518|gene518|rna518|rna518 456 TDFLLDD-KFITLKNNFFNAAQIFNLRK-SDFISTVYTFKFDYKSFKENEREFTKKLDEYFNDTPSNS--YKIGNYSVER 531
                                    **97655.5*******************.****************98888888888887777777444..3444455555 PP

                                    -SSSEEEEEEEEEET...TTHHHHHHHHHHHHHHHHH CS
                     MS_channel 164 gdsslnfevrvfvktvvpeeylsvqseinlrikkile 200
                                    ++ s+++ev+ +++ ++++  ++ ++e++l + + +e
  gene518|gene518|rna518|rna518 532 TTISVTLEVKNVIPYQEIDTLEERNDEFVLFVNNLIE 568
                                    5555555555555555555555555555555555555 PP

>> EF-hand_6  EF-hand domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.2   6.1e-07    0.0016       4      24 ..     323     343 ..     318     349 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 6.1e-07
                      EF-hand_6   4 eaFklfDkdgdGkidaeElrk 24 
                                    e+F lfD+d++++++++E++k
  gene518|gene518|rna518|rna518 323 EIFSLFDFDRNNQVTRHEFIK 343
                                    79*****************86 PP

>> EMC3_TMCO1  Integral membrane protein EMC3/TMCO1-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   3.9      0.34   8.8e+02     105     164 ..      34      93 ..      30      99 .. 0.76
   2 ?   -0.2   0.7      0.29   7.4e+02      98     118 ..     120     140 ..     104     172 .. 0.73
   3 !   17.7   0.3   9.1e-07    0.0023      68     152 ..     290     429 ..     153     438 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.34
                     EMC3_TMCO1 105 iffwlnsffsgfvvaklpfpltgrfksllqrglesldvrfvssiswYflcsfglsqiirk 164
                                    i  ++++ff+g v++ l + + + +   + + +  l++++   i w   + f  ++i+r+
  gene518|gene518|rna518|rna518  34 IGKVVFYFFAGLVLLGLSLVPYYSLPYYMNQQIIRLVLYVSFYICWCVASFFIAESIVRL 93 
                                    666899***********9999998888887777777776666666666666666666665 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.29
                     EMC3_TMCO1  98 tmipqiliffwlnsffsgfvv 118
                                     +i++++if+ ln+ f+ f+ 
  gene518|gene518|rna518|rna518 120 RVIFTFIIFSSLNFLFHRFMG 140
                                    468899999999999996654 PP

  == domain 3  score: 17.7 bits;  conditional E-value: 9.1e-07
                     EMC3_TMCO1  68 lklkklekrqeelmedqsem.....................................................mmdqmkp 94 
                                      ++k+e+r+++ ++++++                                                      + ++ k 
  gene518|gene518|rna518|rna518 290 PGKEKIERREAKKKKNNRNYlvredfdrlfnepeifslfdfdrnnqvtrhefikrylalfeererlkraleqnSNNMVKI 369
                                    4455555555555555555566666666777777777777777777777777777777777777777777777******* PP

                     EMC3_TMCO1  95 mivtmipqiliffwlnsffs........gfvvaklp.fpltgrfksllqrglesldvrfvssiswYf 152
                                    +i +  ++++ +  +  +f          f++a l+ fp+t+ fksl          +f s i+++f
  gene518|gene518|rna518|rna518 370 NILISSLFVPFIVFILLVFTghlpsfqnSFTMAGLViFPFTFAFKSLV-------EEIFSSVIFVFF 429
                                    *********9999999999999999999999999988********987.......334455555555 PP

>> EF-hand_1  EF hand
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.1   7.1e-06     0.018       4      24 ..     323     343 ..     323     345 .. 0.94

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 7.1e-06
                                    HHHHHHTTTSSSEEEHHHHHH CS
                      EF-hand_1   4 eiFrefDkDgdGkIdfeEfke 24 
                                    eiF++fD D++ ++++ Ef++
  gene518|gene518|rna518|rna518 323 EIFSLFDFDRNNQVTRHEFIK 343
                                    79*****************85 PP

>> YbaJ  Biofilm formation regulator YbaJ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.7   0.00011      0.27      43      99 ..     477     531 ..     444     543 .. 0.84
   2 ?   -0.7   0.0      0.81   2.1e+03      71      99 ..     547     574 ..     532     575 .] 0.65

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00011
                           YbaJ  43 avnlqlneliehiaafvlnfkikykeesdlseqideylddtyalfssygineadlrk 99 
                                      nl+  ++i  + +f + +k   ++e ++++++dey++dt     sy+i ++ +++
  gene518|gene518|rna518|rna518 477 IFNLRKSDFISTVYTFKFDYKSFKENEREFTKKLDEYFNDTPS--NSYKIGNYSVER 531
                                    569999**********************************964..566666655554 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.81
                           YbaJ  71 dlseqideylddtyalfssygineadlrk 99 
                                    + ++ ++e  +d ++lf ++ i+e ++++
  gene518|gene518|rna518|rna518 547 QEIDTLEER-NDEFVLFVNNLIEELNITQ 574
                                    445555554.4568999999998888765 PP

>> E1-E2_ATPase  E1-E2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1       0.5   1.3e+03      96     137 ..      11      52 ..       9      93 .. 0.66
   2 ?   -1.8   0.0      0.75   1.9e+03     105     131 ..     145     171 ..     140     181 .. 0.55
   3 ?    9.6   0.2   0.00024      0.62      89     153 ..     337     402 ..     334     413 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.5
                                    TTSTTS--------HHHHHHHHHHHHHHHHHHHHHHHHHHS- CS
                   E1-E2_ATPase  96 kiarlveeakskktplqkkldklgkvlvpvvlliallvflia 137
                                    +i +l+ e+  +k ++q+k++  ++ +v+  ++ ++l+ l +
  gene518|gene518|rna518|rna518  11 QIETLLDEQIFTKIEFQEKINDTIGKVVFYFFAGLVLLGLSL 52 
                                    566667777777888888888777776666666655555443 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.75
                                    -----HHHHHHHHHHHHHHHHHHHHHH CS
                   E1-E2_ATPase 105 kskktplqkkldklgkvlvpvvllial 131
                                    ++k +++ + l+k++ +l ++ +++++
  gene518|gene518|rna518|rna518 145 EEKYASFNHLLTKITVTLGLTLFCLFI 171
                                    444455555555555555555444444 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.00024
                                    TTTSTTTTTSTTS--------HHHHHHHHHHHH.HHHHHHHHHHHHHHS-STTTSSTTHHHHHHHH CS
                   E1-E2_ATPase  89 gedtelgkiarlveeakskktplqkkldklgkv.lvpvvlliallvflialllgkslaeallrala 153
                                     ++ ++++  +l ee ++ k  l+++ ++++k+ + + +l++ ++vf++++++g+ + +   +++a
  gene518|gene518|rna518|rna518 337 TRHEFIKRYLALFEERERLKRALEQNSNNMVKInILISSLFVPFIVFILLVFTGHLPSFQNSFTMA 402
                                    567899999************************777777888889999999999887633333333 PP

>> LapA_dom  Lipopolysaccharide assembly protein A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.1      0.78     2e+03      24      40 ..      38      54 ..      37      68 .. 0.75
   2 ?    5.2   0.0    0.0072        19       7      60 ..     150     203 ..     148     213 .. 0.79
   3 ?    0.7   4.0      0.19   4.8e+02       4      27 ..     365     388 ..     361     390 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.78
                       LapA_dom 24 lvafgiGallgwllslw 40
                                   ++ f++G++l +l  ++
  gene518|gene518|rna518|rna518 38 VFYFFAGLVLLGLSLVP 54
                                   56688999888887665 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0072
                       LapA_dom   7 tvnflfaqvelpLsllllvafgiGallgwllslwsylrlrrelrrlkkkikkle 60 
                                    ++n l++++++ L+l l+  f+ G ++ +l +++ ++ ++ +++  ++ +k+ +
  gene518|gene518|rna518|rna518 150 SFNHLLTKITVTLGLTLFCLFISGTIVDYLDFYSYQMNYKNRVKHNREVLKHIQ 203
                                    78999999*******************999999888866666666555555544 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.19
                       LapA_dom   4 qpVtvnflfaqvelpLsllllvaf 27 
                                     +V +n+l++++ +p ++ +l++f
  gene518|gene518|rna518|rna518 365 NMVKINILISSLFVPFIVFILLVF 388
                                    68*******************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (575 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2039  (0.113726); expected 358.6 (0.02)
Passed bias filter:                      544  (0.0303419); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.64u 0.25s 00:00:00.89 Elapsed: 00:00:00.40
# Mc/sec: 4286.13
//
Query:       gene519|gene519|rna519|rna519  [L=122]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      7e-13   49.4   2.5      7e-13   49.4   2.5    1.9  2  TFIIA     Transcription factor IIA, alpha/beta subunit


Domain annotation for each model (and alignments):
>> TFIIA  Transcription factor IIA, alpha/beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.7     0.019   3.3e+02       1      39 [.      10      45 ..      10      47 .. 0.82
   2 !   49.4   2.5   3.9e-17     7e-13     353     415 .]      60     122 .]      43     122 .] 0.82

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.019
                          TFIIA  1 vYrsvIedVIesvredFeeeGvdeqvLeeLkqlWesKll 39
                                   vYr ++e+V    r +  e+ vd + + +Lk +W + l+
  gene519|gene519|rna519|rna519 10 VYRDIVEEVG---RMLENESDVDLKKIHDLKVMWLNNLT 45
                                   7899999885...55557999*************88776 PP

  == domain 2  score: 49.4 bits;  conditional E-value: 3.9e-17
                          TFIIA 353 lNSd.DDvddeddddlfdtdnvivCqYDKvhRsKNKWKftLKDGvmtvnGkdYVFsKAiGeaEW 415
                                    + S     +++d++  ++t n ++C+YDKv++sK KW   +K G +++++ dY Fs ++G+  W
  gene519|gene519|rna519|rna519  60 VESAsCSDSEDDIKG-KNTQNFMMCLYDKVTKSKYKWRVNFKQGFLNIGNSDYAFSLGQGDLDW 122
                                    445443456668888.9********************************************999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       641  (0.0357521); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.29s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 857.20
//
Query:       gene52|gene52|rna52|rna52  [L=148]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       751  (0.0418874); expected 358.6 (0.02)
Passed bias filter:                      224  (0.0124937); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1027.90
//
Query:       gene520|gene520|rna520|rna520  [L=95]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    5.4e-07   29.8   4.0    5.4e-07   29.8   4.0    2.0  2  ATP-synt_C  ATP synthase subunit C


Domain annotation for each model (and alignments):
>> ATP-synt_C  ATP synthase subunit C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.9     0.021   3.8e+02      46      60 .]       2      16 ..       1      16 [. 0.80
   2 !   29.8   4.0     3e-11   5.4e-07       1      60 []      33      92 ..      33      92 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.021
                                   HHHHHHHHHHHHHHH CS
                     ATP-synt_C 46 aeaialygLivalil 60
                                     +i++y+Li + ++
  gene520|gene520|rna520|rna520  2 GSTIFVYALILCTLI 16
                                   67999****998775 PP

  == domain 2  score: 29.8 bits;  conditional E-value: 3e-11
                                   HHHHHHH.GGGHHHHHHHHHHHHHHHHHHHHSGHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     ATP-synt_C  1 lgaglavGlsalgsGigiGkagsagiravarnpklftksliilafaeaialygLivalil 60
                                   +gag++ G sa +sG++ G +++ +   + ++   ++ ++  l+ +e i l+g++++l+l
  gene520|gene520|rna520|rna520 33 FGAGVMFGCSAYFSGMAFGEVCKRSYLTLEKREGFYIIFICTLSAVELITLFGFLISLFL 92
                                   79*******************************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       614  (0.0342462); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 739.59
//
Query:       gene521|gene521|rna521|rna521  [L=87]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       348  (0.0194099); expected 358.6 (0.02)
Passed bias filter:                      233  (0.0129957); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.33u 0.23s 00:00:00.56 Elapsed: 00:00:00.35
# Mc/sec: 736.56
//
Query:       gene522|gene522|rna522|rna522  [L=297]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (297 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       779  (0.0434492); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2230.16
//
Query:       gene523|gene523|rna523|rna523  [L=148]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.013   14.8   0.2      0.016   14.5   0.2    1.1  1  MIG-14_Wnt-bd  Wnt-binding factor required for Wnt secretion
      0.019   15.7   0.0      0.031   15.0   0.0    1.4  1  Cadherin_C_2   Cadherin cytoplasmic C-terminal


Domain annotation for each model (and alignments):
>> MIG-14_Wnt-bd  Wnt-binding factor required for Wnt secretion
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.2   1.8e-06     0.016     185     235 ..      44      92 ..      24      97 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.8e-06
                  MIG-14_Wnt-bd 185 pfysiwssal....ilkilaiilavlyflyLlylifrsfseirskrvkegdi.Rfk 235
                                     +y           +++i++i + +l + yLly++++ + ++r+++  e ++ R++
  gene523|gene523|rna523|rna523  44 CYY------GsmniYIIIIIIGISLLSLAYLLYCMMKRCENCRTSKK-EKKFtRLR 92 
                                    333......133358999999***********************775.44444765 PP

>> Cadherin_C_2  Cadherin cytoplasmic C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.0   3.5e-06     0.031       2      54 ..      49     125 ..      48     146 .. 0.61

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3.5e-06
                   Cadherin_C_2   2 ltlYLviaLasvSflFLltvivlvavrlrkerksaalqk........................kkslvskpalkvpp 54 
                                    +++Y +i +  +S+l+L+  +  +++r+ + r s++ +k                        +++l+s  +l++++
  gene523|gene523|rna523|rna523  49 MNIYIIIIIIGISLLSLAYLLYCMMKRCENCRTSKKEKKftrlrnkdlirkkqndlydskydhSNNLMSSESLNAKT 125
                                    689*************************5555555555544455555555544444444443211233333344444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1475  (0.0822689); expected 358.6 (0.02)
Passed bias filter:                      629  (0.0350828); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 988.77
//
Query:       gene524|gene524|rna524|rna524  [L=71]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (71 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       342  (0.0190752); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 515.51
//
Query:       gene525|gene525|rna525|rna525  [L=570]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0081   16.5   0.2      0.045   14.1   0.0    2.2  2  TetR_C_26        Tetracyclin repressor-like, C-terminal domai
     0.0086   15.8   1.0     0.0086   15.8   1.0    2.7  3  ThylakoidFormat  Thylakoid formation protein


Domain annotation for each model (and alignments):
>> TetR_C_26  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.0     5e-06     0.045      36     104 ..     255     323 ..     230     327 .. 0.89
   2 ?   -1.5   0.0      0.35   3.1e+03      12      58 ..     400     450 ..     391     467 .. 0.56

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 5e-06
                                    HHHHHHHHHHHHHHHHHHHHTTSB-TT--HHHHHHHHHHHHHHHHHHHHT.S---SS-HHHHHHHHHHH CS
                      TetR_C_26  36 eeiYePlYewleelleeakkkeeireeieveataklligliEsaaEqlylydeeeeeeveekkkellkf 104
                                      +++Pl + l++ l++ +++++ r+e e e t  l+ g++ s a  + + de+++++++++  +l+ f
  gene525|gene525|rna525|rna525 255 LLVFTPLQRLLNSRLKQHNNSGSKRKEAEREITQSLISGALKSHASDMSVLDEQSKHHMKQHYIDLTAF 323
                                    5699******************************************99999**********99999887 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.35
                                    HHHHHHHHHHHHHHHHHTT-HHHHHH.HH...HHHHHHHHHHHHHHHHTTS CS
                      TetR_C_26  12 teeykdllalvysGlastesleeWee.iY...ePlYewleelleeakkkee 58 
                                    t++ k +  l+   +a++ +le + + +Y   + lY+ l+++l++ + +++
  gene525|gene525|rna525|rna525 400 TQHIKRISELINLLIAKNRKLECFINaLYlahDFLYTILKQILTKRQPNKN 450
                                    555555555555555666655555331331113456666666666665554 PP

>> ThylakoidFormat  Thylakoid formation protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   1.0   9.6e-07    0.0086      82     168 ..      48     135 ..      39     160 .. 0.75
   2 ?   -3.2   0.1      0.63   5.7e+03     144     173 ..     261     290 ..     231     314 .. 0.60
   3 ?    1.7   0.7      0.02   1.8e+02     157     210 ..     361     419 ..     353     421 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 9.6e-07
                                    -HHHHHHHHHGGGGGTT-.BHHHHHHHHHTS---TTGGG..........TS-BS--HHHHHHHHHHHHHSBTHTT.T... CS
                ThylakoidFormat  82 dpeqyredaeeleelakeksaeellsllkqeeeeeeaedlakslkaiaenskfkYSrlfaiGlftlLeeadaelv.kdee 160
                                     +++y+++a+++++l k+ks e l+++ ++    ++ + + ++ ++i+ n+  +  ++ +iG++ +L+ ++++   ++++
  gene525|gene525|rna525|rna525  48 VTQRYKNKASRVSTLLKSKSCEVLSATSSKPDGRKKMTWMRDQKDNIKLNHCKSKDKISSIGFYDVLQASENDEDlEKSS 127
                                    5799***************9988888888887777766699**********99***************988765414444 PP

                                    THHHHHHH CS
                ThylakoidFormat 161 kreealek 168
                                    +++ea+++
  gene525|gene525|rna525|rna525 128 TENEAFRR 135
                                    44555443 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 0.63
                                    HHHHHHHSBTHTTT...THHHHHHHHGGGS CS
                ThylakoidFormat 144 lftlLeeadaelvkdeekreealeklaeal 173
                                    l +lL++  ++  ++ +kr+ea ++++++l
  gene525|gene525|rna525|rna525 261 LQRLLNSRLKQHNNSGSKRKEAEREITQSL 290
                                    555555555555555555555544444443 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.02
                                    T...THHHHHHHHGGGS-S-HHHHHHH.....HHHHHHHHHHHHHHHHHHHHHHHHHHS CS
                ThylakoidFormat 157 kdeekreealeklaealglskekvekD.....ldlYrsnlekleqakelmeeileaerk 210
                                     d++k  + l++l++a+ l +  ++kD     l+ Y++  + ++++ el++ +++++rk
  gene525|gene525|rna525|rna525 361 LDKKKLLTRLHELSTAVLLIRPMISKDkksveLHSYEELTQHIKRISELINLLIAKNRK 419
                                    57788888888888887665555544433333899****************99999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (570 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1184  (0.0660383); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.25s 00:00:00.83 Elapsed: 00:00:00.44
# Mc/sec: 3901.74
//
Query:       gene526|gene526|rna526|rna526  [L=67]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (67 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       371  (0.0206927); expected 358.6 (0.02)
Passed bias filter:                      227  (0.0126611); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.45
# Mc/sec: 445.83
//
Query:       gene527|gene527|rna527|rna527  [L=70]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      9e-06   25.6   0.1    1.1e-05   25.4   0.1    1.2  1  Prefoldin_2  Prefoldin subunit
  ------ inclusion threshold ------
      0.031   14.6   0.0       0.04   14.3   0.0    1.1  1  PH_2         Plant pleckstrin homology-like region
       0.17   11.8   0.0       0.19   11.6   0.0    1.0  1  CHD5         CHD5-like protein


Domain annotation for each model (and alignments):
>> Prefoldin_2  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.1   1.8e-09   1.1e-05      27      80 ..      12      64 ..       4      67 .. 0.85

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 1.8e-09
                                   HHHHHHHHHHHHHHS-TT--EEEEETTEEEEE-HHHHHHHHHHHHHHHHHHHHH CS
                    Prefoldin_2 27 qlkelelvleelelldedtkvyklvGdvlvkqdkeevkeeLeerketlekeikt 80
                                   q++ ++  l+ ++  d +  vy + Gdv++ ++k+ ++++Le++k+++ +ei++
  gene527|gene527|rna527|rna527 12 QCEQIDYELDVISRYDGS-VVYTKDGDVFIPMPKNRAIDQLEKKKKNIVMEINN 64
                                   566666667777777777.9******************************9986 PP

>> PH_2  Plant pleckstrin homology-like region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   6.6e-06      0.04      17      52 ..      29      64 ..      27      69 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 6.6e-06
                           PH_2 17 svyinkksqVvlklkskhvggafskkkksvVldvsk 52
                                   sv+  k++ V++ + +++    ++kkkk++V+++ +
  gene527|gene527|rna527|rna527 29 SVVYTKDGDVFIPMPKNRAIDQLEKKKKNIVMEINN 64
                                   78899999************************9985 PP

>> CHD5  CHD5-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   3.1e-05      0.19      39      92 ..       4      66 ..       2      69 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 3.1e-05
                           CHD5 39 keqrklkkellklkeelnsisaqDefAkWaK.........lnRkldkleeeleklkkelsask 92
                                   k++r+l  +  ++  el  is  D    ++K          nR +d+le++ ++   e+++s+
  gene527|gene527|rna527|rna527  4 KKYRDLLLQCEQIDYELDVISRYDGSVVYTKdgdvfipmpKNRAIDQLEKKKKNIVMEINNSN 66
                                   7999***********************************************999988888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (70 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       656  (0.0365888); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.39u 0.28s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 487.62
//
Query:       gene528|gene528|rna528|rna528  [L=48]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00041   20.4   0.3    0.00049   20.1   0.3    1.1  1  Myb_DNA-bind_5  Myb/SANT-like DNA-binding domain
  ------ inclusion threshold ------
      0.011   16.1   0.7      0.012   16.0   0.7    1.1  1  ZapB            Cell division protein ZapB


Domain annotation for each model (and alignments):
>> Myb_DNA-bind_5  Myb/SANT-like DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.3   5.5e-08   0.00049      43      76 ..       2      35 ..       1      37 [. 0.93

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 5.5e-08
                 Myb_DNA-bind_5 43 eiaervnalgsveRtaeelkkkwedlkrraKkkl 76
                                   +i ++v ++g+ +R  +el++ +++lk++ + k+
  gene528|gene528|rna528|rna528  2 QIYDKVEKIGELQRKYNELRDEYKNLKCKYREKH 35
                                   79999*************************9986 PP

>> ZapB  Cell division protein ZapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   16.0   0.7   1.4e-06     0.012      17      44 ..       7      34 ..       2      47 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.4e-06
                           ZapB 17 idtitlLqmeieeLkeeneelkeenrel 44
                                   +++i +Lq ++ eL+ e ++lk + re 
  gene528|gene528|rna528|rna528  7 VEKIGELQRKYNELRDEYKNLKCKYREK 34
                                   8999999999999999999999988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (48 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1384  (0.0771934); expected 358.6 (0.02)
Passed bias filter:                      637  (0.035529); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.29s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 317.18
//
Query:       gene529|gene529|rna529|rna529  [L=131]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       676  (0.0377043); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 903.59
//
Query:       gene53|gene53|rna53|rna53  [L=147]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       570  (0.0317921); expected 358.6 (0.02)
Passed bias filter:                      234  (0.0130515); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1067.70
//
Query:       gene530|gene530|rna530|rna530  [L=542]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.7e-42  145.2   2.4      2e-40  139.1   2.4    2.2  1  Syja_N    SacI homology domain
  ------ inclusion threshold ------
      0.028   14.7   0.3      0.071   13.4   0.3    1.6  1  DUF2757   Protein of unknown function (DUF2757)


Domain annotation for each model (and alignments):
>> Syja_N  SacI homology domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  139.1   2.4   2.2e-44     2e-40       2     318 ..      64     321 ..      60     322 .. 0.82

  Alignments for each domain:
  == domain 1  score: 139.1 bits;  conditional E-value: 2.2e-44
                         Syja_N   2 gilGlirllsgsyllvitkreevgtlkgkkeiykitevellplsseeeaekalkslkaktekkkeekeleekllkllekl 81 
                                    g++G++ l ++sy++++tk+ +++++ +  ++y+i ev + +l  +        +        ++  + ++ llk  ++ 
  gene530|gene530|rna530|rna530  64 GVYGMLCLGENSYVIFVTKSAKIARIAS-YPVYEIREVLIKELLIK--------N--------TKGTN-DAFLLKRAQDF 125
                                    67788887789**************966.6**********887333........2........12222.45577777667 PP

                         Syja_N  82 fessgsfYFsydlDltrslqrqlekssesskslplweraderFvWNrhllkpliea...eldswllpviqGfveqsklkl 158
                                    f+ + ++ +s  + l +s          +++ +      +++F++N++l+  l ++    ++s+++  i+G ++ ++++ 
  gene530|gene530|rna530|rna530 126 FK-NPGIMYSK-FPLYSS----------NMDPE------NTDFIFNYNLIGMLKSHvrgSVSSYVIRAIYGSFQYIDFE- 186
                                    75.55566665.223222..........22333......456********99875556699************666653. PP

                         Syja_N 159 sksqkekekkevtltlisRrsrkraGtRylrRGiddeGnvANfvEtEqilevessekeskilSfvqiRGSiPlfWsqept 238
                                              +++++lisRrs+k+ G+R+ rRG++ e ++AN +EtEq +  +   +e+ + Sf+q+RGSiPl+W+q+ t
  gene530|gene530|rna530|rna530 187 ----------QFSIVLISRRSWKNVGARFIRRGLNREKEAANSIETEQYVILS--GDEEPTNSFLQLRGSIPLYWKQDLT 254
                                    ..........4*************************************99964..5566899****************** PP

                         Syja_N 239 lkykpkirierseeenleafkkHfekllkrYgkvvvvnLlekkgrEkkLgeayekavkklnklekekkklkyveFDfhke 318
                                    +ky+p i+i      +++ +k++  kl+k+Y++v ++nL+++ g E+ L++ y +    l      ++ lky +FDf +e
  gene530|gene530|rna530|rna530 255 YKYRPIIKIV-----KTNPLKEYDTKLCKKYKNVFYLNLIQNVGYESGLNKIYISR---LA-----DNCLKYLHFDFVRE 321
                                    *********6.....5678*********************************9877...54.....578********876 PP

>> DUF2757  Protein of unknown function (DUF2757)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.3   7.9e-06     0.071      35      63 ..       9      37 ..       7      42 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 7.9e-06
                                   HHHHHTSSS-TT-S-EEEE--HHHHHHHH CS
                        DUF2757 35 eerqdmieyeengdikvkviCedCqeale 63
                                   +e+q m+ ye+n ++ +k + ++C+e+l+
  gene530|gene530|rna530|rna530  9 MEKQHMLVYENNEKLVIKNVSDECEETLT 37
                                   79************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (542 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       452  (0.0252106); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.23s 00:00:00.77 Elapsed: 00:00:00.40
# Mc/sec: 4027.70
//
Query:       gene531|gene531|rna531|rna531  [L=119]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.089   12.4   0.0       0.12   12.0   0.0    1.2  1  DUF953    Eukaryotic protein of unknown function (DUF953)


Domain annotation for each model (and alignments):
>> DUF953  Eukaryotic protein of unknown function (DUF953)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   6.9e-06      0.12      40      81 ..       7      48 ..       5      60 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 6.9e-06
                                   HHHHHHHHHHHHHHH-SS-EEEEEEE---HHHHT-TTSHHHH CS
                         DUF953 40 dCvkaepvieealkeapedvklvrvdvGdrevWkdpanpfRk 81
                                   +Cv   + + + l +   ++k+++v+  dr++Wk +++ fRk
  gene531|gene531|rna531|rna531  7 NCVYIQKWLLQYLGQEERNAKFMNVHLLDRAYWKLKHKIFRK 48
                                   588888888888999999***********************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       536  (0.0298957); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 876.53
//
Query:       gene532|gene532|rna532|rna532  [L=120]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.039   14.1   0.1       0.07   13.3   0.1    1.3  1  GCN5L1    GCN5-like protein 1 (GCN5L1)


Domain annotation for each model (and alignments):
>> GCN5L1  GCN5-like protein 1 (GCN5L1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   3.9e-06      0.07      22      76 ..      54     108 ..      47     110 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.9e-06
                         GCN5L1  22 eaiesaaaltealvdklnsgvaeayanqkklekeakalqanvakfakqtdqWlal 76 
                                    + +++  ++++ +vd+ ns v +a  n+ +   ++++l  + ++ +++t+++ +l
  gene532|gene532|rna532|rna532  54 KYLKEYYSVANDVVDAFNSLVLRADLNEARFHIQLRKLLHQCKQHMNNTTNFKKL 108
                                    56678899*****************************************998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1028  (0.0573373); expected 358.6 (0.02)
Passed bias filter:                      562  (0.0313459); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.34s 00:00:00.94 Elapsed: 00:00:00.56
# Mc/sec: 645.45
//
Query:       gene533|gene533|rna533|rna533  [L=1286]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.9e-24   85.6   1.1    2.6e-15   56.4   0.1    3.9  5  E1-E2_ATPase   E1-E2 ATPase
    2.5e-12   47.5   3.2    0.00024   21.4   0.0    3.4  3  Hydrolase      haloacid dehalogenase-like hydrolase
    5.4e-07   29.8   0.2    1.8e-06   28.1   0.2    1.9  1  P5-ATPase      P5-type ATPase cation transporter
    0.00026   21.0   0.0    0.00068   19.7   0.0    1.6  1  Cation_ATPase  Cation transport ATPase (P-type)
      0.003   17.4   0.9       0.94    9.2   0.3    2.5  2  Hydrolase_3    haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
      0.041   13.5   5.9       0.11   12.1   5.9    1.8  1  DUF998         Protein of unknown function (DUF998)


Domain annotation for each model (and alignments):
>> E1-E2_ATPase  E1-E2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.7   1.5         5   1.5e+04     115     156 ..     151     187 ..     144     190 .. 0.51
   2 !   56.4   0.1   8.8e-19   2.6e-15       5      77 ..     215     286 ..     211     291 .. 0.95
   3 !   37.6   0.1   5.3e-13   1.6e-09      80     181 .]     430     531 ..     427     531 .. 0.97
   4 ?   -4.9   1.3       5.8   1.7e+04     120     136 ..    1078    1094 ..    1067    1117 .. 0.52
   5 ?    1.3   0.7     0.072   2.1e+02     104     145 ..    1195    1236 ..    1171    1259 .. 0.78

  Alignments for each domain:
  == domain 1  score: -4.7 bits;  conditional E-value: 5
                                    HHHHHHHHHHHHHHHHHHHHHS-STTTSSTTHHHHHHHHHHH CS
                   E1-E2_ATPase 115 ldklgkvlvpvvlliallvflialllgkslaeallralallv 156
                                    l+ ++++++   +l +l++++i+     s +++l+ ++ llv
  gene533|gene533|rna533|rna533 151 LQIVVNHFTSNLFLYTLVCVFIW-----SQIDYLIYSVILLV 187
                                    34445555555555555555555.....22255555555555 PP

  == domain 2  score: 56.4 bits;  conditional E-value: 8.8e-19
                                    -EEEEE-TTS-EEEEGGG--TTSEEEEETT-B--SEEEEEEE-SEEE-TTTS---S-EE-G-TTEE-TT-EEE CS
                   E1-E2_ATPase   5 ptakvirdgteeeidakelvpGDivllkagdrvpaDgrivegsaevdesaLTGEslpvekekgdmvfsGtvvv 77 
                                    ++ +v+rd++ +e d+k+l p Div + +g+ + aD++i++g+  vdes+LTGEs pv+k kg  v +Gtvv+
  gene533|gene533|rna533|rna533 215 KSMNVFRDNQFREQDTKNLFPSDIVAIAPGE-IEADVQILSGEVIVDESFLTGESIPVYKRKGGIVRAGTVVM 286
                                    6789**************************8.8**************************************98 PP

  == domain 3  score: 37.6 bits;  conditional E-value: 5.3e-13
                                    EEEEEEEE-TTTSTTTTTSTTS--------HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTTSSTTHHHHHHHHHHHHHS CS
                   E1-E2_ATPase  80 eakavVtatgedtelgkiarlveeakskktplqkkldklgkvlvpvvlliallvflialllgkslaeallralallvaai 159
                                    +++++V+ tg +t+ g+++r +  +++ + ++ ++ +kl  +++ ++++i+++ fl+ l+++ s+ +al+ +++l+v +i
  gene533|gene533|rna533|rna533 430 HVIGRVISTGFNTTKGTLIRNILLPTKPNLKFFNQSKKLLFIMFGIGTFISIFYFLFSLFHEISVKNALYYSFDLIVTII 509
                                    6789**************************************************************************** PP

                                    -TTHHHHHHHHHHHHHHHHHHT CS
                   E1-E2_ATPase 160 PcaLplavplalalgarrlakk 181
                                     +aLp+a+ + + l++++l++k
  gene533|gene533|rna533|rna533 510 TPALPAAIRIGMNLSVKSLKRK 531
                                    *****************99986 PP

  == domain 4  score: -4.9 bits;  conditional E-value: 5.8
                                     HHHHHHHHHHHHHHHHS CS
                   E1-E2_ATPase  120 kvlvpvvlliallvfli 136 
                                     +++v ++++++++vf+ 
  gene533|gene533|rna533|rna533 1078 NQFVSFIVMMLFFVFAS 1094
                                     33333333333333333 PP

  == domain 5  score: 1.3 bits;  conditional E-value: 0.072
                                     ------HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTTSSTT CS
                   E1-E2_ATPase  104 akskktplqkkldklgkvlvpvvlliallvflialllgksla 145 
                                     + +++ ++ k    ++ vl+ vvl+++l+++l++ ++ k+  
  gene533|gene533|rna533|rna533 1195 QPHREHKMRKRSFVFVVVLSYVVLVAVLVLMLLNSIVVKWYE 1236
                                     447778888889999999999999999999999888777665 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.9   0.00027      0.82       1      14 [.     547     560 ..     547     569 .. 0.88
   2 !   21.4   0.0   8.2e-08   0.00024     103     157 ..     852     917 ..     744     936 .. 0.78
   3 !   14.3   0.0   1.3e-05     0.038     162     207 ..     982    1022 ..     960    1024 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00027
                                    SSEEEEESBTTTBC CS
                                    xxxxxxxxxxxxxx RF
                      Hydrolase   1 iktvvfDkdGTLtt 14 
                                    i tvvfDk+GTLt+
  gene533|gene533|rna533|rna533 547 ISTVVFDKTGTLTE 560
                                    689**********6 PP

  == domain 2  score: 21.4 bits;  conditional E-value: 8.2e-08
                                    H...........TTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHHTT..G CS
                                    x...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..x RF
                      Hydrolase 103 l...........qaralavftiadplkvkpeaaeavasLkaagievvlltgdnpetaeraanqlG..d 157
                                    +           +   l+ + +a++  +k  +  +++ Lk+agi   ++tgdn  ta ++a+++G  +
  gene533|gene533|rna533|rna533 852 KgdqnygqqnehDLTFLGFIVFANK--LKGATIPVIHNLKQAGITCLMATGDNILTAISVAKECGmiE 917
                                    13333333333334889999***99..999999********************************442 PP

  == domain 3  score: 14.3 bits;  conditional E-value: 1.3e-05
                                     EEEEHHCES...STTTSHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHH CS
                                     xxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Hydrolase  162 aviasdiet...vakpspegkvaaireLqgkpeevamVGDgvnDaaala 207 
                                       i     +    a  +p++k+ +++++     e+++VGDg+nD+ al+
  gene533|gene533|rna533|rna533  982 DQIIE---KtvvYARMNPDQKKMLCNRM-----ECIFVGDGANDVGALQ 1022
                                     33333...33559999************.....5************997 PP

>> P5-ATPase  P5-type ATPase cation transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.2     6e-10   1.8e-06      18      85 ..      21      90 ..      12     115 .. 0.72

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 6e-10
                      P5-ATPase 18 alyilgciltlGlllLlfrWlPewrvkltgkpcpLkeadvvlie.defgelsvkkv.rkleyerplstvf 85
                                    ly+ +cil++G+l + +r +P +++k+t+++++L +++ vl+  +   e+  ++v + ++++++ ++v 
  gene533|gene533|rna533|rna533 21 YLYYTACILSFGILPITMRIFPLVKIKWTTRRSSLDRCSHVLVLsNTSIEFVEVDViNLKKFKKCRNSVY 90
                                   79*************************************9999864444443333302333445555554 PP

>> Cation_ATPase  Cation transport ATPase (P-type)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   2.3e-07   0.00068      19      84 ..     671     739 ..     620     742 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 2.3e-07
                  Cation_ATPase  19 llGnktEsALlvlaekl.gldteelree....tkkvqeipFnssrKrmsvvlklepekkvrlyvKGApeii 84 
                                    +lG++ ++ + ++ ++  + +t+ +  +     +++++ +F+ +r+rmsvv++ e  ++  ++vKG++e+i
  gene533|gene533|rna533|rna533 671 CLGDPLDVKMFKYSDASmQDNTITISGDvpyqCTILHINEFDPTRRRMSVVVQFE--QRRYVFVKGSAESI 739
                                    5666666666666666532222233332444388999****************86..9999********98 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.9   0.0     0.003       9.1      17      54 ..     878     915 ..     873     924 .. 0.84
   2 !    9.2   0.3   0.00032      0.94     199     230 ..    1001    1032 ..     994    1042 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.003
                                    -HHHHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCC CS
                    Hydrolase_3  17 sektkeaikklkekgikvviATGRslravlpvleelgl 54 
                                    +  t+ +i++lk++gi+   ATG ++ ++++v++e g+
  gene533|gene533|rna533|rna533 878 KGATIPVIHNLKQAGITCLMATGDNILTAISVAKECGM 915
                                    5578889***************************9884 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00032
                                     CT--GGGEEEEESSGGGHHHHHHSSEEEEETT CS
                    Hydrolase_3  199 lnisleeviafGDgeNDieMLeaaglgvAmgn 230 
                                     + +++ e+i +GDg ND+  L+ + +g A++ 
  gene533|gene533|rna533|rna533 1001 MLCNRMECIFVGDGANDVGALQSSTVGLALNK 1032
                                     5578889**********************975 PP

>> DUF998  Protein of unknown function (DUF998)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   5.9   3.7e-05      0.11      67     183 ..    1128    1259 ..    1104    1261 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.7e-05
                         DUF998   67 ragragrlllavaglglvlagvfptdpgggspslsglvHgl.....asavaflalavavl....lla...saarrraw 132 
                                     r + ++++++ ++++ l+ + vf + ++ g   +sg +H++      s+++f++ av ++    +l+       +r +
  gene533|gene533|rna533|rna533 1128 RCEILSVRFVFAFVMHLAIDCVFLLCCAFGR--HSGSAHQYeyktaMSTLVFFMTAVQAVnkgiILTdgqP---HREH 1200
                                     5566778888999999999999999999776..58888865444326777777777777777766665541...4444 PP

                         DUF998  133 allrlvggvallllvaalvwllaa........aldgslllGlaerllvlaitawllala 183 
                                     +++++  + +++l  ++lv++l+          +++  +l l er++++a++++ +al+
  gene533|gene533|rna533|rna533 1201 KMRKRSFVFVVVLSYVVLVAVLVLmllnsivvKWYEFEVLTLNERVFLVAGVLLNTALS 1259
                                     44444333333333333333333334459999*******************99888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1099  (0.0612973); expected 358.6 (0.02)
Passed bias filter:                      500  (0.0278878); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 1.06u 0.33s 00:00:01.39 Elapsed: 00:00:00.59
# Mc/sec: 6538.87
//
Query:       gene534|gene534|rna534|rna534  [L=146]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       958  (0.053433); expected 358.6 (0.02)
Passed bias filter:                      597  (0.033298); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 927.97
//
Query:       gene535|gene535|rna535|rna535  [L=322]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (322 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       831  (0.0463495); expected 358.6 (0.02)
Passed bias filter:                      509  (0.0283898); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2354.20
//
Query:       gene536|gene536|rna536|rna536  [L=57]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (57 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       436  (0.0243181); expected 358.6 (0.02)
Passed bias filter:                      231  (0.0128842); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.27s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 416.58
//
Query:       gene537|gene537|rna537|rna537  [L=176]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.2e-22   79.3   0.2    3.1e-22   78.8   0.2    1.2  1  CH           Calponin homology (CH) domain
     0.0011   19.2   0.1     0.0019   18.4   0.1    1.3  1  CDC24        CDC24 Calponin
     0.0019   18.3   0.0     0.0027   17.8   0.0    1.3  1  CH_2         CH-like domain in sperm protein
  ------ inclusion threshold ------
      0.046   13.6   0.0      0.071   12.9   0.0    1.4  1  CAMSAP_CH    CAMSAP CH domain
       0.05   12.9   0.0      0.066   12.5   0.0    1.1  1  Luteo_P1-P2  Luteovirus RNA polymerase P1-P2/replicase


Domain annotation for each model (and alignments):
>> CH  Calponin homology (CH) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.8   0.2   8.5e-26   3.1e-22       3     107 ..       4     104 ..       2     106 .. 0.90

  Alignments for each domain:
  == domain 1  score: 78.8 bits;  conditional E-value: 8.5e-26
                                    HHHHHHHHHHHHHTTSTTSSTTSCHHHHHTTSHHHHHHHHHHSTTTSSGGGSTTTHHHHHHHHHHHHHHHHHHTTCHTTS CS
                             CH   3 qkkellrWinshleeagpkvkvedfeedlrDGvlLckLlnklapglvdkkklnksefkkleNinlaldvaekklgvpkvl 82 
                                    q  el +Wi+  + e   +   +++ee+l+DG++LckL+nkl+pg++++++  ks+f ++eNi  ++ +a+ k+gv++++
  gene537|gene537|rna537|rna537   4 QNTELKEWIEHITLET-IG---DNLEESLKDGIILCKLMNKLQPGSCNYSEK-KSAFLQRENIFAFIRAAK-KIGVEEYE 77 
                                    778999****999553.33...79**************************99.56*************777.******** PP

                                    S.-HHHHHTTSHH.HHHHHHHHHHHHH CS
                             CH  83 i.eaedlvegknk.svltllaqLfraf 107
                                    i + +dl+eg n+ +v  +l++L r  
  gene537|gene537|rna537|rna537  78 IfDINDLYEGSNFnQVRICLYALCRCL 104
                                    **********************98875 PP

>> CDC24  CDC24 Calponin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.1   5.4e-07    0.0019       6      80 ..      24      94 ..      22      98 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 5.4e-07
                          CDC24  6 lwkllrqGspLlalfNalkpeeklevdevksddlkvcKksvydFllackkeLgfedeelftisdlfsedttdlvk 80
                                   l + l+ G  L+ l N l+p +    +  +++ +   ++ ++ F+ a k ++g+e+ e+f i dl++ +  + v+
  gene537|gene537|rna537|rna537 24 LEESLKDGIILCKLMNKLQPGSC---NYSEKKSAFLQRENIFAFIRAAK-KIGVEEYEIFDINDLYEGSNFNQVR 94
                                   6678999*************864...4578888889999*******986.69**************987665555 PP

>> CH_2  CH-like domain in sperm protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   7.7e-07    0.0027       2      69 ..       9      73 ..       8     100 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 7.7e-07
                           CH_2  2 lkWlqsldlsrsvknlkrdfsdGvlvAeilkkyypklvdlhnysngsslaaklnNWetLekvlkklgi 69
                                    +W+++++l+   +nl++ + dG+++ ++++k++p      nys+++s+  +++N   + +  kk+g+
  gene537|gene537|rna537|rna537  9 KEWIEHITLETIGDNLEESLKDGIILCKLMNKLQPG---SCNYSEKKSAFLQRENIFAFIRAAKKIGV 73
                                   58**********************************...889*****999999998888777777766 PP

>> CAMSAP_CH  CAMSAP CH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0     2e-05     0.071      14      65 ..      22      68 ..       9      87 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2e-05
                      CAMSAP_CH 14 edllrdlsdGvaLaalihfYcPqliklediclkesmsladslyNiqllqefc 65
                                   ++l ++l+dG+ L++l++ + P + +    +  e+ s ++  +Ni  +  ++
  gene537|gene537|rna537|rna537 22 DNLEESLKDGIILCKLMNKLQPGSCNY---S--EKKSAFLQRENIFAFIRAA 68
                                   7999*******************9965...4..7778888888886665444 PP

>> Luteo_P1-P2  Luteovirus RNA polymerase P1-P2/replicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   1.9e-05     0.066     183     259 ..      65     147 ..      57     157 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.9e-05
                    Luteo_P1-P2 183 araaakigaemfapvdvqdlysftevkkvetglmkev.vkekngeeek.hlepimeevrsikdt....aeardaastwit 256
                                     raa kig e +   d++dly  ++ ++v   l        k ge +   + p m e + i  t     ++r aas +++
  gene537|gene537|rna537|rna537  65 IRAAKKIGVEEYEIFDINDLYEGSNFNQVRICLYALCrCLRKTGEFKGpLIGPKMAEKQKIEFTpaqlNKSRTAASPYVS 144
                                    69********************9999999999976541456777765515689999999998763222467888888887 PP

                    Luteo_P1-P2 257 etv 259
                                    +  
  gene537|gene537|rna537|rna537 145 NKA 147
                                    665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       430  (0.0239835); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1236.10
//
Query:       gene538|gene538|rna538|rna538  [L=120]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0018   18.4   0.1      0.003   17.7   0.1    1.3  1  GCN5L1    GCN5-like protein 1 (GCN5L1)


Domain annotation for each model (and alignments):
>> GCN5L1  GCN5-like protein 1 (GCN5L1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.1   1.7e-07     0.003      21      76 ..      53     108 ..      44     110 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.7e-07
                         GCN5L1  21 keaiesaaaltealvdklnsgvaeayanqkklekeakalqanvakfakqtdqWlal 76 
                                    +e +++  ++++ +vd+ ns v +a  n+ + + ++k+l  + ++ +++t+++ +l
  gene538|gene538|rna538|rna538  53 EEYLKEYYSVANDVVDAFNSLVLRADLNEARFDIQLKKLLHQCKQHMNNTTNFKKL 108
                                    67889999******************************************998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1086  (0.0605723); expected 358.6 (0.02)
Passed bias filter:                      616  (0.0343577); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.32s 00:00:00.92 Elapsed: 00:00:00.56
# Mc/sec: 648.57
//
Query:       gene539|gene539|rna539|rna539  [L=154]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       630  (0.0351386); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.57u 0.31s 00:00:00.87 Elapsed: 00:00:00.52
# Mc/sec: 884.62
//
Query:       gene54|gene54|rna54|rna54  [L=146]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       371  (0.0206927); expected 358.6 (0.02)
Passed bias filter:                      199  (0.0110993); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.58u 0.33s 00:00:00.90 Elapsed: 00:00:00.55
# Mc/sec: 794.80
//
Query:       gene540|gene540|rna540|rna540  [L=843]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (843 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1712  (0.0954878); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.75u 0.29s 00:00:01.04 Elapsed: 00:00:00.50
# Mc/sec: 5096.85
//
Query:       gene541|gene541|rna541|rna541  [L=140]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       569  (0.0317363); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 951.50
//
Query:       gene542|gene542|rna542|rna542  [L=244]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.05   13.3   0.0        0.1   12.4   0.0    1.6  1  Ski_Sno   SKI/SNO/DAC family
      0.075   13.5   1.1       0.15   12.5   0.2    1.9  2  zf-C4pol  C4-type zinc-finger of DNA polymerase delta


Domain annotation for each model (and alignments):
>> Ski_Sno  SKI/SNO/DAC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   1.1e-05       0.1      41      74 ..     112     145 ..      83     175 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.1e-05
                        Ski_Sno  41 pqilnlvLkdfsleeintklkeLeitcvrCtpeQ 74 
                                    p  ++++L +++ +ei +++keL+  c++C+ + 
  gene542|gene542|rna542|rna542 112 PEKFTIMLSNMNNNEISNHFKELKKLCINCSMSE 145
                                    667899************************9765 PP

>> zf-C4pol  C4-type zinc-finger of DNA polymerase delta
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       0.8   7.2e+03      26      35 ..      56      65 ..      43      81 .. 0.51
   2 ?   12.5   0.2   1.7e-05      0.15      15      52 ..     106     144 ..      92     157 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.8
                       zf-C4pol 26 kllsrlkele 35
                                   ++ +++k+++
  gene542|gene542|rna542|rna542 56 TQANEVKNTH 65
                                   2223333333 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 1.7e-05
                       zf-C4pol  15 kCrsdkqes..llkllsrlkelekklneletvCqsCaqgs 52 
                                    +C +++ e+  ++  +++ +e+ ++++el+++C +C+ +s
  gene542|gene542|rna542|rna542 106 DCDQNRPEKftIMLSNMNNNEISNHFKELKKLCINCS-MS 144
                                    798777777445555666678889************4.33 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (244 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       928  (0.0517597); expected 358.6 (0.02)
Passed bias filter:                      515  (0.0287244); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.23s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 1732.33
//
Query:       gene543|gene543|rna543|rna543  [L=49]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.039   14.5   0.3      0.044   14.3   0.3    1.0  1  PLAT      PLAT/LH2 domain
      0.092   12.5   0.1       0.15   11.9   0.1    1.3  1  DUF348    G5-linked-Ubiquitin-like domain


Domain annotation for each model (and alignments):
>> PLAT  PLAT/LH2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.3   4.9e-06     0.044      28      65 ..       9      45 ..       2      48 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.9e-06
                                   EEEEEEEEEEE.TTSEEETTT-EEEEEEEESS-ECSEEE CS
                           PLAT 28 gesasleltld.tsgpdfergatdsFkvdtdvdlGallk 65
                                    ++  +++++  ++++d++ +++++   +t++d+G +lk
  gene543|gene543|rna543|rna543  9 NKE--YTQKITgPDNNDIHVNNEQKVHKTTKKDIGNVLK 45
                                   444..778888899*********************9987 PP

>> DUF348  G5-linked-Ubiquitin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   1.6e-05      0.15       3      26 ..      24      47 ..      23      48 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.6e-05
                                   EEETTEEEEE----SSHHHHHHHT CS
                         DUF348  3 ltvDGktvtvrTaadTVgdlLeea 26
                                   + v+ ++++ +T++ + g +L+++
  gene543|gene543|rna543|rna543 24 IHVNNEQKVHKTTKKDIGNVLKDN 47
                                   789*******************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (49 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       870  (0.0485247); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.33u 0.22s 00:00:00.55 Elapsed: 00:00:00.36
# Mc/sec: 405.49
//
Query:       gene544|gene544|rna544|rna544  [L=204]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.27   11.1   4.4        0.2   11.5   1.3    2.0  2  Tma16     Translation machinery-associated protein 16


Domain annotation for each model (and alignments):
>> Tma16  Translation machinery-associated protein 16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   1.3   1.1e-05       0.2      47     102 ..     102     163 ..      77     170 .. 0.65
   2 ?   -0.1   0.1     0.042   7.6e+02      67      81 ..     180     194 ..     169     196 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 1.1e-05
                          Tma16  47 qealdeekkplsleelkeliekylkRndeeleelkser.....rkgrpkskre...elleekke 102
                                     ++++e    ++ ee+++  ++ylkR+++e+++l se+       + p++k+    + l+ k e
  gene544|gene544|rna544|rna544 102 TNNVQE--PCVKTEEVRDSFKSYLKRHNDEMKKLFSEKiafnkVVNTPPKKQVrgvDQLKRKAE 163
                                    333444..57899*********************999988876334444444300144444444 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.042
                          Tma16  67 ekylkRndeeleelk 81 
                                    +kyl+++ ee+++lk
  gene544|gene544|rna544|rna544 180 NKYLEQYREEVQRLK 194
                                    59*********9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1004  (0.0559987); expected 358.6 (0.02)
Passed bias filter:                      573  (0.0319594); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1519.79
//
Query:       gene545|gene545|rna545|rna545  [L=445]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (445 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       766  (0.0427241); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 3262.36
//
Query:       gene546|gene546|rna546|rna546  [L=265]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-53  181.1   1.8    9.7e-40  136.6   0.2    2.0  2  DS        Deoxyhypusine synthase


Domain annotation for each model (and alignments):
>> DS  Deoxyhypusine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.0   0.2   1.1e-16     2e-12       2      97 ..       9     102 ..       8     108 .. 0.89
   2 !  136.6   0.2   5.4e-44   9.7e-40     114     285 ..      95     258 ..      87     261 .. 0.92

  Alignments for each domain:
  == domain 1  score: 47.0 bits;  conditional E-value: 1.1e-16
                             DS   2 llesyekigfqatslgeaidilnkmrkdekctiflgltsnlissGlreiiadlvkeklvdvivtTaggieeDlikal.gk 80 
                                    ll+ y+++ f++++++ a+++++km   +k ++f++lt+n+   G+ +++  l+++++v v+vtT+  +  D++++l gk
  gene546|gene546|rna546|rna546   9 LLRIYKNSLFEGRNVYLACKEIAKM---TKYKVFMALTANILNNGTYDLLFSLIEKNMVHVVVTTGDFVVYDILRTLiGK 85 
                                    8999*********************...7899******************************************987255 PP

                             DS  81 ktylgdfelddeeLrek 97 
                                    +   + f+++dee  ++
  gene546|gene546|rna546|rna546  86 DLNEKAFTAEDEETIKN 102
                                    55667889999887665 PP

  == domain 2  score: 136.6 bits;  conditional E-value: 5.4e-44
                             DS 114 kfedwvreildkleeeqk..vwspselikelGkeindeeSilywAykndipvfcpaltDgslGdqlllfhsvkekkklkl 191
                                    + e+++++++ ++  e+   ++ ps++ik +G+++   +Sil +A++n++  + p+++D+ +G+   +++      ++++
  gene546|gene546|rna546|rna546  95 EDEETIKNFIGQIALENCgaTIPPSKFIKIIGEKLG-FNSILGQAARNNVHFYAPTICDSLIGI---YCT------DIHV 164
                                    55888899998888765344669************5.89*************************...555......589* PP

                             DS 192 divkDirelndialkakktgaiilGGGvpKhhilnanlmrngadyavyittaqefdGslsgatldEavSwgkikaeaksv 271
                                    d++kD+ ++n  ++  kktgaiilG +v+Kh +lnanl++ng++ +v ++t +e dGs+sg  +dEa+Swgki+ +++sv
  gene546|gene546|rna546|rna546 165 DSLKDVYNINYECFFVKKTGAIILGTSVIKHTVLNANLFKNGLNSCVIVNTCNEVDGSDSGGDVDEAISWGKIRGNTTSV 244
                                    ******************************************************************************** PP

                             DS 272 kvyaDaTivlPLlv 285
                                    k+ aD ++++P++ 
  gene546|gene546|rna546|rna546 245 KIRADPSVIFPIIG 258
                                    ************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (265 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       608  (0.0339115); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 1661.53
//
Query:       gene547|gene547|rna547|rna547  [L=196]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      2e-25   88.8   0.1    4.4e-25   87.7   0.1    1.6  1  UPF0113    UPF0113 PUA domain
    9.3e-22   77.4   0.7      2e-21   76.4   0.7    1.6  1  UPF0113_N  UPF0113 Pre-PUA domain
    0.00023   21.0   0.0    0.00043   20.2   0.0    1.4  1  PUA        PUA domain


Domain annotation for each model (and alignments):
>> UPF0113  UPF0113 PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.7   0.1   7.3e-29   4.4e-25       1      76 []     112     191 ..     112     191 .. 0.98

  Alignments for each domain:
  == domain 1  score: 87.7 bits;  conditional E-value: 7.3e-29
                        UPF0113   1 kvvvkekaeklFLYGrdvlkesilkitesvkenqvvvVlnengeplGiGkirkdt...k.aspgkivvknlaDiGeYlRr 76 
                                    kv++k++ae++FLYG++vlk+++l+ te++k+++vv+++n ++ +lG+G++++++   + a+++++++ +++D+GeY+R+
  gene547|gene547|rna547|rna547 112 KVWIKWSAEMNFLYGNNVLKSHVLRTTEDLKDRDVVFLYNPRDVLLGFGITARNMdsfNrADHNSLFIIKQCDKGEYIRN 191
                                    89*******************************************************967*******************6 PP

>> UPF0113_N  UPF0113 Pre-PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.4   0.7   3.3e-25     2e-21       1      82 []      22      99 ..      22      99 .. 0.98

  Alignments for each domain:
  == domain 1  score: 76.4 bits;  conditional E-value: 3.3e-25
                      UPF0113_N  1 RklseeetrivfekLtkyigdnvkelldrkdgtycfrlkkkrVyyvseellklaetikpenlisaGtclGkftktkkFrlsi 82
                                   R+l++ee ++vf kL++++gd+ +ell+    +++++l++k+V+yvs+ l+k++++i+++n+ ++Gt++G+ft++++F+l++
  gene547|gene547|rna547|rna547 22 RRLTQEESDKVFAKLDQFVGDRKDELLK----DHNIYLHNKNVFYVSNLLYKKVSNIPKKNIAMIGTHIGRFTRSDRFFLKV 99
                                   89**************************....699********************************************985 PP

>> PUA  PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   7.2e-08   0.00043       1      53 [.     111     163 ..     111     176 .. 0.91

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 7.2e-08
                                    CEEEE-HHHHHHHHTT-EEEGGGEEEEETT--TTSEEEEEETTSCEEEEEEES CS
                            PUA   1 grvvvddgAvkallsgasLlapGvvevegdfeegdvVaivdedgelvavGlan 53 
                                    ++v+++ +A    l+g ++l   v+++ +d++  dvV ++++ + l++ G++ 
  gene547|gene547|rna547|rna547 111 KKVWIKWSAEMNFLYGNNVLKSHVLRTTEDLKDRDVVFLYNPRDVLLGFGITA 163
                                    589***********************************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       566  (0.031569); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.30s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1310.15
//
Query:       gene548|gene548|rna548|rna548  [L=363]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-13   51.3  23.4    1.2e-13   51.3  23.4    3.6  2  DHHC      DHHC palmitoyltransferase
    1.6e-08   35.0   2.3      3e-06   27.7   0.3    2.7  2  Ank_2     Ankyrin repeats (3 copies)
    3.5e-06   27.5   0.2    0.00067   20.2   0.0    2.8  2  Ank_4     Ankyrin repeats (many copies)
    6.5e-06   26.1   3.7      0.032   14.7   0.0    3.6  4  Ank_3     Ankyrin repeat
    0.00067   19.9   1.6       0.29   11.5   0.0    3.0  3  Ank_5     Ankyrin repeats (many copies)
  ------ inclusion threshold ------
      0.025   15.0   2.6       0.05   14.1   0.0    2.7  3  Ank       Ankyrin repeat
       0.48   10.5   2.3         26    5.0   0.1    2.6  2  PKHD_C    PKHD-type hydroxylase C-terminal domain
       0.96    9.4   6.3        1.2    9.1   1.0    3.4  3  Syndecan  Syndecan domain


Domain annotation for each model (and alignments):
>> DHHC  DHHC palmitoyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.4  11.8         8   1.8e+04      41      57 ..     180     196 ..     107     246 .. 0.55
   2 !   51.3  23.4   5.5e-17   1.2e-13       2      68 ..     258     324 ..     257     362 .. 0.94

  Alignments for each domain:
  == domain 1  score: -4.4 bits;  conditional E-value: 8
                           DHHC  41 nciGerNykyFllflly 57 
                                      + ++N  +++ f++y
  gene548|gene548|rna548|rna548 180 LFVSYHNLLIYIKFMFY 196
                                    11222222222222222 PP

  == domain 2  score: 51.3 bits;  conditional E-value: 5.5e-17
                           DHHC   2 ekelkfCstcniykpprskHcrvCnrcvlrfDHhCpwlnnciGerNykyFllfllylllllilalvl 68 
                                    ++e++fC  c +yk   +kHc+ Cn cv +fDHhCp+l+nc+ ++    F+++lly ++l+++ +vl
  gene548|gene548|rna548|rna548 258 FNEKEFCAICLRYKNTDTKHCNNCNVCVDGFDHHCPCLDNCVCAKMSALFYFYLLYSITLCFVRIVL 324
                                    789***********************************************************99886 PP

>> Ank_2  Ankyrin repeats (3 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7   0.3   1.3e-09     3e-06      22      81 ..      20      89 ..       5      91 .. 0.80
   2 !    6.2   0.1    0.0069        16      28      74 ..      95     148 ..      89     156 .. 0.70

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 1.3e-09
                          Ank_2 22 pn.k..ngktaLhyAakngnleivklLleh...ad....ndgrtpLhyAarsghleivklLlekgadinl 81
                                   +n +  ++k ++h+Aa ++n +++k  l+    +d    ++  tpL++A+ +++  ++ lLle+ga++n 
  gene548|gene548|rna548|rna548 20 INyTfnDNKHIIHFAALYNNMDLIKKCLSSgvgVDvkggKYQSTPLYFAVYNKNHSTMLLLLENGANPNY 89
                                   4441348899*********999998888766785565789999********9777************996 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0069
                          Ank_2  28 taLh.yAakngnleivklLleh.......ad.ndgrtpLhyAarsghleivklLle 74 
                                    + L+ +++ +g  +i+++Ll         ++ +++   L +A++  + ++v++L +
  gene548|gene548|rna548|rna548  95 NSLQkICICRG--DILSFLLLDiynvekhLRsRENDKSLKLAVKLRQAQFVNYLKK 148
                                    55664666688..9**9999533343444335778899*****99999*****974 PP

>> Ank_4  Ankyrin repeats (many copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0     3e-07   0.00067       4      54 ..      30      80 ..      27      81 .. 0.83
   2 !    7.4   0.1     0.003       6.8      14      37 ..      74      96 ..      72     112 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 3e-07
                          Ank_4  4 aLhyaaisgrlelvrlLlekgadinaqdnrsGetalhiAakrgnveilklL 54
                                   ++h aa +++++l++ +l++g+ ++    +++ t+l++A+++ n +   lL
  gene548|gene548|rna548|rna548 30 IIHFAALYNNMDLIKKCLSSGVGVDVKGGKYQSTPLYFAVYNKNHSTMLLL 80
                                   79******************9999999557788**********64444444 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.003
                          Ank_4 14 lelvrlLlekgadinaqdnrsGet 37
                                   + +  lLle+ga++n++ n s ++
  gene548|gene548|rna548|rna548 74 HSTMLLLLENGANPNYV-NLSKNS 96
                                   56677999*********.988876 PP

>> Ank_3  Ankyrin repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.0    0.0003      0.67       4      30 ..      29      54 ..      26      56 .. 0.82
   2 !   14.7   0.0   1.4e-05     0.032       2      30 ..      61      88 ..      60      88 .. 0.94
   3 ?   -3.5   0.1         8   1.8e+04      15      23 ..     105     113 ..     102     118 .. 0.68
   4 ?   -3.0   0.0         8   1.8e+04      10      23 ..     210     222 ..     201     227 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0003
                          Ank_3  4 tpLhlAarsgnleivkfLlenkgadvn 30
                                    ++h+Aa+++n +++k +l   g+ v+
  gene548|gene548|rna548|rna548 29 HIIHFAALYNNMDLIKKCLS-SGVGVD 54
                                   679***************99.566554 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 1.4e-05
                          Ank_3  2 GetpLhlAarsgnleivkfLlenkgadvn 30
                                   + tpL++A+ + n++ + +Lle +ga++n
  gene548|gene548|rna548|rna548 61 QSTPLYFAVYNKNHSTMLLLLE-NGANPN 88
                                   67************99******.8***98 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 8
                          Ank_3  15 leivkfLle 23 
                                     +i+ fLl 
  gene548|gene548|rna548|rna548 105 GDILSFLLL 113
                                    578888886 PP

  == domain 4  score: -3.0 bits;  conditional E-value: 8
                          Ank_3  10 arsgnleivkfLle 23 
                                    ++++  + v++L+ 
  gene548|gene548|rna548|rna548 210 VEYNLAC-VILLIP 222
                                    5666666.777776 PP

>> Ank_5  Ankyrin repeats (many copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.0   0.00013      0.29      15      56 .]      28      68 ..      15      68 .. 0.87
   2 !   10.6   0.1   0.00025      0.55      15      46 ..      60      91 ..      54      97 .. 0.78
   3 ?   -3.0   0.0       4.5     1e+04      19      25 ..     130     136 ..     108     146 .. 0.52

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00013
                          Ank_5 15 ggntpLhvAakygaadvvrlLlargadlnltdsrG.ltaldlA 56
                                   +  +++h+Aa y++ d+++++l  g+  +++ + + +t+l +A
  gene548|gene548|rna548|rna548 28 K--HIIHFAALYNNMDLIKKCLSSGVGVDVKGGKYqSTPLYFA 68
                                   2..99*****************999999999999999999887 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00025
                          Ank_5 15 ggntpLhvAak.ygaadvvrlLlargadlnltd 46
                                   +  tpL +A++ +++++++ lLl++ga++n  +
  gene548|gene548|rna548|rna548 60 YQSTPLYFAVYnKNHSTML-LLLENGANPNYVN 91
                                   556********77777766.5667999998765 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 4.5
                          Ank_5  19 pLhvAak 25 
                                     L +A+k
  gene548|gene548|rna548|rna548 130 SLKLAVK 136
                                    3344555 PP

>> Ank  Ankyrin repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       1.1   2.5e+03       7      22 ..      32      47 ..      28      55 .. 0.76
   2 ?   14.1   0.0   2.2e-05      0.05       4      31 ..      63      91 ..      60      92 .. 0.87
   3 ?   -2.4   0.1       3.7   8.2e+03      10      22 ..     103     112 ..     101     118 .. 0.72

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1.1
                                   HHHHHHTTHHHHHHHH CS
                            Ank  7 HlAatngkkriiklLL 22
                                   H Aa +++ + ik  L
  gene548|gene548|rna548|rna548 32 HFAALYNNMDLIKKCL 47
                                   9999999988887555 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 2.2e-05
                                   BHHHHHHHHTTHHHHHHHH.TTTSTTCBT CS
                            Ank  4 TPLHlAatngkkriiklLL.hGAnlnald 31
                                   TPL  A++n++++   lLL +GAn+n ++
  gene548|gene548|rna548|rna548 63 TPLYFAVYNKNHSTMLLLLeNGANPNYVN 91
                                   *******88888888888899*****887 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 3.7
                                    HHHTTHHHHHHHH CS
                            Ank  10 atngkkriiklLL 22 
                                    ++++   i+++LL
  gene548|gene548|rna548|rna548 103 CRGD---ILSFLL 112
                                    5666...999887 PP

>> PKHD_C  PKHD-type hydroxylase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.2     0.015        34      13      37 ..      16      40 ..      13      40 .. 0.94
   2 ?    5.0   0.1     0.011        26      26      38 ..     176     188 ..     170     188 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.015
                         PKHD_C 13 aIqrlraelgddpavvaLtgvYHNL 37
                                   +Iq+++ + +d++ ++++ ++Y N+
  gene548|gene548|rna548|rna548 16 EIQNINYTFNDNKHIIHFAALYNNM 40
                                   7***********************6 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.011
                         PKHD_C  26 avvaLtgvYHNLL 38 
                                     +v L   YHNLL
  gene548|gene548|rna548|rna548 176 IIVMLFVSYHNLL 188
                                    57889999****8 PP

>> Syndecan  Syndecan domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.55   1.2e+03      34      44 ..     146     156 ..     140     157 .. 0.84
   2 ?    0.3   0.1      0.29   6.6e+02      20      46 ..     214     242 ..     207     263 .. 0.68
   3 ?    9.1   1.0   0.00053       1.2      13      38 ..     336     362 ..     331     363 .] 0.84

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.55
                       Syndecan  34 mrKKDEGSYaL 44 
                                    ++K+ E SY+L
  gene548|gene548|rna548|rna548 146 LKKRNEISYKL 156
                                    89*******98 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.29
                       Syndecan  20 llfaillvlflv..YRmrKKDEGSYaLde 46 
                                    l ++ill+ + +  YR+ +   G+ + d+
  gene548|gene548|rna548|rna548 214 LACVILLIPYYIafYRLTRSKTGTKTGDK 242
                                    78999999765545888776666655555 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.00053
                       Syndecan  13 iggvvvgllfaill.vlflvYRmrKKD 38 
                                    ++  vv llf + + + flvYR rK+D
  gene548|gene548|rna548|rna548 336 VVFFVVVLLFRVYVnLRFLVYRERKRD 362
                                    66679999999998467*********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (363 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1399  (0.07803); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 2510.05
//
Query:       gene549|gene549|rna549|rna549  [L=889]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.7e-62  209.1   0.0    1.3e-61  207.9   0.0    1.6  1  MutS_V          MutS domain V
      1e-31  109.5   0.1    2.7e-31  108.1   0.1    1.8  1  MutS_I          MutS domain I
    1.1e-28  100.8   1.3    1.1e-28  100.8   1.3    2.0  2  MutS_III        MutS domain III
    8.4e-12   45.3   3.7    3.5e-11   43.3   3.7    2.2  1  MutS_IV         MutS family domain IV
     0.0031   18.0   0.4      0.013   16.0   0.0    2.2  2  ABC_tran        ABC transporter
     0.0067   16.9   0.0     0.0067   16.9   0.0    3.7  3  AAA_23          AAA domain
  ------ inclusion threshold ------
      0.011   15.5   0.0      0.028   14.1   0.0    1.6  1  AAA_29          P-loop containing region of AAA domain
      0.038   13.4   0.1       0.86    8.9   0.0    2.4  2  FtsK_SpoIIIE    FtsK/SpoIIIE family
      0.087   12.8   0.1       0.25   11.4   0.0    1.7  2  DUF1521         Domain of Unknown Function (DUF1521)
       0.11   12.1   0.0       0.38   10.3   0.0    1.9  2  AAA_27          AAA domain


Domain annotation for each model (and alignments):
>> MutS_V  MutS domain V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  207.9   0.0   7.4e-65   1.3e-61       2     186 ..     693     873 ..     692     875 .. 0.96

  Alignments for each domain:
  == domain 1  score: 207.9 bits;  conditional E-value: 7.4e-65
                                    EEE-STTSSHHHHHHHHHHHHHHHHHT--BSSSEEEEE--SEEEEEE--------SS-HHHHHHHHHHHHHTT--TTSEE CS
                         MutS_V   2 litGpnmaGkstylrqvalivllaqiGsfvpaekaeisivdkiftRvgasDdlakgkstFmvEmlEtasilknatekslv 81 
                                    l+tGpnmaGkst+lr ++l v+l+q+G  v a++++ +++d+iftR+gasD+l +g+stFmvEm+Et  il+++t +sl+
  gene549|gene549|rna549|rna549 693 LLTGPNMAGKSTFLRTICLNVILSQMGMKVTADRMDSRVFDRIFTRLGASDNLLRGESTFMVEMKETGVILNECTPDSLI 772
                                    89****************************************************************************** PP

                                    EEESTS-SS-HHHHHHHHHHHHHHHHHTT--EEEEEES-GGGGGHHHHSTTEEEEEEEEEEETTEEEEEEEEEES--SS- CS
                         MutS_V  82 ilDElGRGtstydGlaialavaeyllekikaktlfatHyheltklaekleevknlhlavkeeeedivflykvkegaaeks 161
                                    i+DElGRGtst dG +ia av+eyl +  + ++lf+tHyh + +   k+++v++  +++  +++di+fl k++eg++  s
  gene549|gene549|rna549|rna549 773 IIDELGRGTSTKDGESIARAVIEYLNR-RNIYSLFSTHYHRIVD---KVQNVRKGFMDAIVDDDDIIFLFKLREGVCYDS 848
                                    *************************98.6899********9865...6789***************************** PP

                                    -HHHHHHHTT--HHHHHHHHHHHHH CS
                         MutS_V 162 yGikvaklaglPesvverArevlke 186
                                     Gi va+lag+P+ + +rA ev ++
  gene549|gene549|rna549|rna549 849 QGIPVARLAGVPKFITDRAIEVRTK 873
                                    *******************998766 PP

>> MutS_I  MutS domain I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.1   0.1   1.5e-34   2.7e-31       1     111 [.     112     234 ..     112     236 .. 0.95

  Alignments for each domain:
  == domain 1  score: 108.1 bits;  conditional E-value: 1.5e-34
                                    HHHHHHHHCCCHH-TTCEEEEEETTEEEEECHHHHHHHHHCSSSSTT.ESSSSC.EEEEEEEHHHHHHHHHHHHHTT-EE CS
                         MutS_I   1 tplmkqylelkkkykdavlffrvGdfYelfgeDAviaareleitltkrkkssekeipmagvPehalekylrkLvekgykV 80 
                                    tp++kq++++kk+y+d++++f++G+fYel+++DA+i+a+++++++     ++ + ++mag+P + ++ ++ +++ekgykV
  gene549|gene549|rna549|rna549 112 TPFEKQFWSIKKNYFDTIVCFKKGKFYELYENDAEIGAKLFDMKIA----DRVN-MRMAGFPVSCFDMWAGRFLEKGYKV 186
                                    8*******************************************99....6677.************************* PP

                                    EEEEE-S-HHHH.................S.S--EEEEEEEBTTC-TT CS
                         MutS_I  81 avveqtetpaek.................kgvvkrevvrviTpGtltd 111
                                    a+++q e++  k                 +++++re+ +viT Gt+++
  gene549|gene549|rna549|rna549 187 ARIDQKENMIGKrirekeekenrvantkgREIIERELKEVITAGTVYN 234
                                    **********99************9997656**************975 PP

>> MutS_III  MutS domain III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.92   1.6e+03     151     152 ..      74     189 ..       4     289 .. 0.48
   2 !  100.8   1.3   5.9e-32   1.1e-28       2     191 .]     367     648 ..     366     648 .. 0.68

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.92
                                    T............................................................................... CS
                                    x............................................................................... RF
                       MutS_III 151 a............................................................................... 151
                                    +                                                                               
  gene549|gene549|rna549|rna549  74 Ekrygfladirdskgrrindegydkstlfiseqdmnmltpfekqfwsikknyfdtivcfkkgkfyelyendaeigaklfd 153
                                    13444444444444444444444444444444444444444444444444444444444444444444444444444444 PP

                                    ...................................H CS
                                    ...................................x RF
                       MutS_III 152 ...................................i 152
                                                                       i
  gene549|gene549|rna549|rna549 154 mkiadrvnmrmagfpvscfdmwagrflekgykvarI 189
                                    444444444444444444444444444444444440 PP

  == domain 2  score: 100.8 bits;  conditional E-value: 5.9e-32
                                    HHHHTTSSS-TTS.SSSS-HHHHH---SSHHHHHHHHHHHH--BS-HHHHHHHHHHHHHT..TT.HHHHHHHHTT---HH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       MutS_III   2 TlrnLeilenlrggskegsLlgvldrTvTamGaRlLrewllqPltdleeInaRldaVeeleneelreelrellrrlpDle 81 
                                    +l nL+i+        + sL++++++++T+ G+RlLr+wll Pl d+++I++R+++ +e+e+ e   ++ e+l  ++Dl+
  gene549|gene549|rna549|rna549 367 SLANLNIIDE------KTSLFNAINHCSTPYGQRLLRQWLLYPLADVTRIEERQEVTSEIEKLE-IGAIKEELAAIGDLD 439
                                    6899***543......45*****************************************98888.999************ PP

                                    HHHHHHHTT---HHHHHH........................HHHHHHHHHTTTTT---SSTHHHHH..........HHH CS
                                    xxxxxxxxxxxxxxxxxx........................xxxxxxxxxxxxxxxxxxxxxxxxx..........xxx RF
                       MutS_III  82 Rllsrislgkakardlka........................llealkaleelvallekeklaesee..........esl 127
                                    Rl  ++++++ ++rdl +                        l                                   +l
  gene549|gene549|rna549|rna549 440 RLTGKLNNRNYTVRDLFNlqanlllacafldkflartnnspiL-----------------------TakfrsygdvvCEL 496
                                    ********98999996442223222222222221112222221.......................12333333333122 PP

                                    HHHHHHHB-SS--SSGGGS--B-T........................................................ CS
                                    xxxxxxxxxxxxxxxxxxxxxxxx........................................................ RF
                       MutS_III 128 aelleeaideeplalekegedlra........................................................ 151
                                    ++ ++e   ++ + +e+e++++++                                                        
  gene549|gene549|rna549|rna549 497 KKNMKE-FSDKYTVSENEVKASEKqndeytvytkelsniecrlkeylekqksrlnckllsykdlgkeifqievpstisvp 575
                                    222222.2222222222222222233333455555555555566666666666667778888999999999999999999 PP

                                    .................................HHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHHHHHHHHH CS
                                    .................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       MutS_III 152 .................................iealeqelfqelleeveealerlrrlaealaeLDvllSlA 191
                                                                     i +++  ++ +  +++ e+ + +++++++l+e+D++lS+A
  gene549|gene549|rna549|rna549 576 tsyflvsstktakryytqdlkdlvnehnecserIFQAKGLILIRATQKFLESYSLFYKISDMLSEIDCFLSFA 648
                                    99999999999999999999998887666655533333334555688897778*******************9 PP

>> MutS_IV  MutS family domain IV
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.3   3.7   1.9e-14   3.5e-11       3      91 ..     521     607 ..     519     608 .. 0.95

  Alignments for each domain:
  == domain 1  score: 43.3 bits;  conditional E-value: 1.9e-14
                                    SHHHHHHHHHHHHHHHHHHHHHCCCCCCCT-TTBEECCCSSSEEEEEE-TCCCTTT--SEEEEEECTCEEEEECCCHHHH CS
                        MutS_IV   3 deeLdelrdrleelekeleeleekereklgikslkveynkvlGyylevtrseakkvpkefirlqtlknseryttaelkkl 82 
                                    ++e+  + + l+++e +l+e++ek++++l++k l++++ ++  +++ev+   + +vp+ + +++++k ++ry+t++lk+l
  gene549|gene549|rna549|rna549 521 NDEYTVYTKELSNIECRLKEYLEKQKSRLNCKLLSYKDLGKEIFQIEVP--STISVPTSYFLVSSTKTAKRYYTQDLKDL 598
                                    789999*******************************************..557************************** PP

                                    HHHHHHHHH CS
                        MutS_IV  83 eaelleaee 91 
                                     +e +e+ e
  gene549|gene549|rna549|rna549 599 VNEHNECSE 607
                                    ***999877 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.2       2.9   5.1e+03      51      51 ..     483     483 ..     377     548 .. 0.52
   2 !   16.0   0.0   7.2e-06     0.013       5      37 ..     683     715 ..     681     753 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 2.9
                                    G CS
                                    x RF
                       ABC_tran  51 e 51 
                                    +
  gene549|gene549|rna549|rna549 483 T 483
                                    0 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 7.2e-06
                                    EEEEETTSEEEEEESTTSSHHHHHHHHTTSS-- CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran   5 slklkegekvaivGenGaGKStLlkllagllkp 37 
                                    ++++k ++++ ++G+n aGKSt+l++++ ++  
  gene549|gene549|rna549|rna549 683 DFEFKDSKTLLLTGPNMAGKSTFLRTICLNVIL 715
                                    6899***********************987765 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   1.0      0.42   7.5e+02     118     194 ..     112     225 ..      16     230 .. 0.54
   2 ?   -1.8   7.2       2.1   3.8e+03      90     199 ..     410     545 ..     376     608 .. 0.55
   3 !   16.9   0.0   3.8e-06    0.0067      13      41 ..     682     711 ..     675     730 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.42
                         AAA_23 118 eqfisellgskkiilnlilflgqerfeefelkdkke......................................rleele 159
                                    + f ++  ++kk+ ++ i+++++++f +++ +++ e                                      +++ + 
  gene549|gene549|rna549|rna549 112 TPFEKQFWSIKKNYFDTIVCFKKGKF-YELYENDAEigaklfdmkiadrvnmrmagfpvscfdmwagrflekgyKVARID 190
                                    33333344445556777777777774.22222222244455556666677788888888888888887777777444444 PP

                         AAA_23 160 keleeledekkllekleqekekekeleeleeelee 194
                                    ++ + + +++++ e++e++  + k  e +e+el+e
  gene549|gene549|rna549|rna549 191 QKENMIGKRIREKEEKENRVANTKGREIIERELKE 225
                                    44444444444444444444455555555555555 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 2.1
                         AAA_23  90 iererelskkkgkttkkaklelleideleqfisellgskkiilnlilflgqer....................feefel. 148
                                    ie+++e++++ +k   +a++e+l      ++++ +l++++   + ++ l++                      +      
  gene549|gene549|rna549|rna549 410 IEERQEVTSEIEKLEIGAIKEELAAIGDLDRLTGKLNNRNYTVRDLFNLQANLllacafldkflartnnspilT----Ak 485
                                    55555555555555555544444442222222223333333222222222222233332223333333233331....02 PP

                         AAA_23 149 ........kdkkerleelekeleeledekkllekleqe.kekekeleeleeeleeilkel 199
                                             + k+ ++e+++++   e+e k  ek+++e   + kel+++e +l+e+l++ 
  gene549|gene549|rna549|rna549 486 frsygdvvCELKKNMKEFSDKYTVSENEVKASEKQNDEyTVYTKELSNIECRLKEYLEKQ 545
                                    222333333333355555444444444444444432220224446666665555555543 PP

  == domain 3  score: 16.9 bits;  conditional E-value: 3.8e-06
                         AAA_23  13 qeidF.skgltlItGpNGaGKTTildAikl 41 
                                     +++F +++  l+tGpN aGK+T+l+ i+l
  gene549|gene549|rna549|rna549 682 NDFEFkDSKTLLLTGPNMAGKSTFLRTICL 711
                                    56899888999*****************97 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   1.6e-05     0.028      14      39 ..     681     706 ..     678     714 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.6e-05
                         AAA_29  14 ghtieidlkgatlltGpsGsGKSTll 39 
                                    g+++e++ + + lltGp+ +GKST+l
  gene549|gene549|rna549|rna549 681 GNDFEFKDSKTLLLTGPNMAGKSTFL 706
                                    567888877799************98 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0     0.088   1.6e+02     146     181 ..     326     366 ..     275     385 .. 0.70
   2 ?    8.9   0.0   0.00048      0.86      10      66 ..     654     716 ..     648     723 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.088
                                    ---B-TT-...........................------ CS
                   FtsK_SpoIIIE 146 fgdvflvlDnyddlaaene.....ritsLsnqgpsygvhvl 181
                                    + + fl+lDny ++  + e      i  ++ ++ +++++ +
  gene549|gene549|rna549|rna549 326 EYVCFLYLDNYMQFLRRAEfkenvVIKRMADRRDYMVIDSI 366
                                    34689*********988888755455556666666666655 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00048
                                    HHHT---TTEEEEEEETTS-EEEEEGGGS-.......SEEEE--TTSSHHHHHHHHHHHHHTT CS
                   FtsK_SpoIIIE  10 kfrtessqlpvalgkeisgnplvldlkkma......shllvaGatgsGKStalntLilSlatt 66 
                                    +++t++ ++++ l +e  +np+  ++ ++         ll+ G    GKSt+l+t+ l++++ 
  gene549|gene549|rna549|rna549 654 NTNTAYTKFTGNLAFENLRNPIFPNYLGNDfefkdsKTLLLTGPNMAGKSTFLRTICLNVILS 716
                                    56778888888888888888888888888888888778999***************9998876 PP

>> DUF1521  Domain of Unknown Function (DUF1521)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.1       5.1   9.2e+03      13      27 ..     502     516 ..     495     529 .. 0.70
   2 ?   11.4   0.0   0.00014      0.25     110     164 ..     747     800 ..     710     804 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 5.1
                        DUF1521  13 dlGdkytitldekdg 27 
                                    ++ dkyt+  +e ++
  gene549|gene549|rna549|rna549 502 EFSDKYTVSENEVKA 516
                                    578999998887554 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00014
                        DUF1521 110 dGknnlkvtqsnaGatldeltsdGaqtieeatgqGwvdlsGevvrqasidaneng 164
                                     G   + v + ++G +l+e t+d   +i+e  g+G + + Ge + +a+i+  ++ 
  gene549|gene549|rna549|rna549 747 RGESTFMVEMKETGVILNECTPDSLIIIDE-LGRGTSTKDGESIARAVIEYLNRR 800
                                    5888999*********************99.9*****************986655 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       3.1   5.6e+03     136     163 ..     597     623 ..     595     628 .. 0.76
   2 ?   10.3   0.0   0.00021      0.38      18      46 ..     683     709 ..     669     720 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 3.1
                         AAA_27 136 alleaegelgqlLfeasaGlaslrevle 163
                                    +l+++++e ++ +f+a+ Gl  +r++++
  gene549|gene549|rna549|rna549 597 DLVNEHNECSERIFQAK-GLILIRATQK 623
                                    799999*********98.5666666655 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00021
                         AAA_27  18 sldfsaeeadlhliyGpNEAGKstalrAi 46 
                                     ++f+  +++  l+ GpN AGKst lr i
  gene549|gene549|rna549|rna549 683 DFEFK--DSKTLLLTGPNMAGKSTFLRTI 709
                                    44554..6777899************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (889 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1060  (0.0591221); expected 358.6 (0.02)
Passed bias filter:                      499  (0.027832); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.78u 0.34s 00:00:01.12 Elapsed: 00:00:00.48
# Mc/sec: 5619.30
//
Query:       gene55|gene55|rna55|rna55  [L=163]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.9e-12   46.2   0.1    9.7e-12   44.9   0.1    1.7  1  Gar1      Gar1/Naf1 RNA binding region


Domain annotation for each model (and alignments):
>> Gar1  Gar1/Naf1 RNA binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.9   0.1   5.4e-16   9.7e-12      17     125 ..      35     124 ..      21     152 .. 0.74

  Alignments for each domain:
  == domain 1  score: 44.9 bits;  conditional E-value: 5.4e-16
                                TS-EEEEEEEEEEETTEEEEEE---S--B--BTT-EEEETT--EEEE--EEES-SSS-EEEEE--GGHHHHHHHTTTTSEEEEE CS
                       Gar1  17 peevleiGtvssivenevviksttsgekkvldfnsilflenktqiGkVdEifGpvnepyysVklnsseeikaksfkvgdkvyia 100
                                +++ + +Gt+s+ v++ +v + tt+   +v++ n+ ++ e++  +G+VdEifG++ e+y+sV+            k g+++y+ 
  gene55|gene55|rna55|rna55  35 NAQKIILGTFSHRVNDLMVLRLTTK---DVPYPNTKVYAEKG--VGTVDEIFGKLDEMYCSVRGL----------KDGTRFYVE 103
                                4556779****************55...9***********98..******************977..........567778777 PP

                                -X..XXXXXXXXXXXXXXXXXXXXX CS
                       Gar1 101 pdlplerfllteelkkkkgpdasne 125
                                 +    rf+   +l+  +gp  +n+
  gene55|gene55|rna55|rna55 104 EN----RFIPRARLDGGNGPVVNNK 124
                                77....6665555555544443333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       588  (0.032796); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1189.95
//
Query:       gene550|gene550|rna550|rna550  [L=368]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (368 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       870  (0.0485247); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 2505.38
//
Query:       gene551|gene551|rna551|rna551  [L=113]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
      0.066   13.8   3.4       0.13   12.9   3.2    1.6  2  Sas10_Utp3  Sas10/Utp3/C1D family


Domain annotation for each model (and alignments):
>> Sas10_Utp3  Sas10/Utp3/C1D family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   3.2   7.5e-06      0.13      25      61 ..      19      55 ..       4      84 .. 0.68
   2 ?   -0.9   0.0      0.14   2.6e+03      11      25 ..      70      84 ..      61     108 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 7.5e-06
                     Sas10_Utp3 25 eekkslsd.eklsegisllslKnelllaYllnlllyll 61
                                   ++ k + d e++ +  ++ +lK +ll+aYl +l+ y +
  gene551|gene551|rna551|rna551 19 SK-KIEHDlENDYDNNEVAQLKIDLLTAYLKSLSTYNY 55
                                   22.22222444445556*****************9955 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.14
                     Sas10_Utp3 11 lqeslepllskakae 25
                                   ++++le++l+ ++++
  gene551|gene551|rna551|rna551 70 ISTLLEKFLQFENKK 84
                                   455666666643333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (113 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       928  (0.0517597); expected 358.6 (0.02)
Passed bias filter:                      231  (0.0128842); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.28s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 807.08
//
Query:       gene552|gene552|rna552|rna552  [L=476]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.1e-29  102.5   0.0    5.4e-29  101.2   0.0    1.7  2  DEAD            DEAD/DEAH box helicase
    1.8e-27   95.9   0.2    1.4e-26   93.0   0.1    2.4  2  Helicase_C      Helicase conserved C-terminal domain
    4.2e-08   33.4   0.2    2.8e-07   30.7   0.0    2.3  3  ResIII          Type III restriction enzyme, res subunit
     0.0042   17.3   0.0     0.0093   16.1   0.0    1.5  1  Helicase_C_2    Helicase C-terminal domain
  ------ inclusion threshold ------
      0.025   14.7   0.0       0.39   10.9   0.0    2.3  2  Malt_amylase_C  Maltogenic Amylase, C-terminal domain
      0.068   13.5   0.0       0.22   11.9   0.0    1.8  2  AAA_19          AAA domain
       0.13   12.6   0.2       0.59   10.4   0.2    2.2  1  AAA_22          AAA domain


Domain annotation for each model (and alignments):
>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.2   0.0   2.1e-32   5.4e-29       1     170 [.     116     272 ..     116     277 .. 0.88
   2 ?   -2.5   0.0       1.5   3.7e+03      47      73 ..     318     344 ..     298     395 .. 0.50

  Alignments for each domain:
  == domain 1  score: 101.2 bits;  conditional E-value: 2.1e-32
                                    -HHHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD   1 tdiQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvll 80 
                                    t+iQ ++ipl+lgg +v+++  TG+GKTl+f++p++   +e  + + + a+i++PtreL+ q+   l+ f +     v++
  gene552|gene552|rna552|rna552 116 TPIQMQMIPLVLGGYNVFGQSMTGTGKTLCFALPLIMMKLE-ANHSFNGAIILVPTRELCLQIKAFLEHFVS-----VKS 189
                                    89**********************************77777.6777778*********************99.....556 PP

                                    EETTSSHHHHHHHHHTT..CSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCTTSTT CS
                                    xxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD  81 iiggvaardqlskldng..vdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsdfinrilnqlpqitcdgkl 158
                                     +gg+  + ++++ + g   +i+v+tpg+l++ll++++   ++++ l+lDEad++ + +f + i++i+++++        
  gene552|gene552|rna552|rna552 190 AFGGTVHKTEKARCNVGmsGEIYVATPGKLLQLLEKNN-FARECSHLILDEADKMTSPEFVRNIKTIVEKMK-------- 260
                                    79999888888888755669**************7666.3899****************************2........ PP

                                    TSEEEEEESSBS CS
                                    xxxxxxxxxxxx RF
                           DEAD 159 qrqvivlSATlp 170
                                      q++vl AT  
  gene552|gene552|rna552|rna552 261 RPQFCVLAATCF 272
                                    235999999975 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.5
                                    S-EEEEEESSHHHHHHHHHHHHHHTTT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD  47 gpkalivePtreLaeqtlnnlkkfkky 73 
                                    g  +li + ++  a +   +l++f+k+
  gene552|gene552|rna552|rna552 318 GQNVLIFVNSKDRADELTLKLRNFFKT 344
                                    555666666666666666666666662 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.64   1.6e+03      11      43 ..     156     189 ..     147     202 .. 0.71
   2 !   93.0   0.1   5.4e-30   1.4e-26       4     110 ..     311     430 ..     303     431 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.64
                                    HHTTTTSEEEEEESSHHHHHHHHHHHHHT.TSTE CS
                     Helicase_C  11 kleeeggkilifvntidrlekvklllekk.gikv 43 
                                    + +++ + ++i v+t++ + ++k +le++ ++k+
  gene552|gene552|rna552|rna552 156 EANHSFNGAIILVPTRELCLQIKAFLEHFvSVKS 189
                                    5677788899*******77667888888854444 PP

  == domain 2  score: 93.0 bits;  conditional E-value: 5.4e-30
                                    HHHHHHHHHTTTTSEEEEEESSHHHHHH.....HHHH..HHHT...............TSTEEEESTTSTHHHHHHHHHH CS
                     Helicase_C   4 eallellkleeeggkilifvntidrlek.....vkll..lekk...............gikvavlhgelpqnereeileq 61 
                                    + l+e+     +g+++lifvn++dr+++        +  +  +               + kv  lh+  +q +r++i+eq
  gene552|gene552|rna552|rna552 311 AFLKEI-----VGQNVLIFVNSKDRADEltlklR-NFfkT--EcrtgsndtspyswkmSAKVESLHAGKEQIDRNKIIEQ 382
                                    444444.....69***********9987654532.22350..14455556667777779********************* PP

                                    HHTTSSSEEEESGGGTSSSTSTTESEEEESSSSSSHHHHHHHHTTSSST CS
                     Helicase_C  62 fnkgesdvLiatdvaerGidipkvnlVinfdlprnvtsyiqriGRtgRa 110
                                    fn+g++ +Li+t+ ++rGid+ kv++Vin+d+p ++++yi+riGRtgR+
  gene552|gene552|rna552|rna552 383 FNSGSIEILICTSLLSRGIDF-KVDCVINYDCPHTIDDYIHRIGRTGRM 430
                                    *********************.6*************************7 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.95   2.4e+03      70     112 ..      12      63 ..      10      94 .. 0.69
   2 !   30.7   0.0   1.1e-10   2.8e-07      31     169 ..     136     271 ..     117     273 .. 0.78
   3 ?   -1.1   0.1      0.66   1.7e+03      55      83 ..     319     347 ..     300     394 .. 0.59

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.95
                                    HHHHGGGGTGG.......GEEEESSS-B--.............-SEEEEEHH CS
                         ResIII  70 tleefkkflseayke...igkkvsgdkkka......kekdstnkkilvttiq 112
                                    +++ f  f++e   +   +g +v++dk++       + ++ +++k++v t++
  gene552|gene552|rna552|rna552  12 MKDSFDAFYDEVERRlreEGRIVTEDKHNVqvdntcNIQNMDHSKFFVRTYS 63 
                                    6667777776665556667777777777775665555555566666666655 PP

  == domain 2  score: 30.7 bits;  conditional E-value: 1.1e-10
                                    ESTTSTHHHHH..HHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG....GEEEESSS-B--.......-SEEE CS
                         ResIII  31 maTGtGKTlva..aklierllkkgkeekflflvprkslleqtleefkkflseaykeigkkvsgdkkkakekdstnkkilv 108
                                      TGtGKTl+     ++ +l  +++ + +++lvp+++l+ q +  +++f s + ++ g+ v++ +k +  +   + +i+v
  gene552|gene552|rna552|rna552 136 SMTGTGKTLCFalPLIMMKLEANHSFNGAIILVPTRELCLQIKAFLEHFVSVKSAF-GGTVHKTEKAR-CNVGMSGEIYV 213
                                    67********94235788888888888***********************999876.44444444444.466789***** PP

                                    EEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.TTTHHH...HHT---SEEEEEESS- CS
                         ResIII 109 ttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakkswrei...lekfkeavllglTATp 169
                                    +t  +l + +      ++ +   +   +i DEa ++++ +++r+i   +ek+k+     l AT+
  gene552|gene552|rna552|rna552 214 ATPGKLLQLL------EKNNFARECSHLILDEADKMTSPEFVRNIktiVEKMKRPQFCVLAATC 271
                                    **********......44555556667899********98666664447777765555556775 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 0.66
                                    .-EEEEESSHHHHHHHHHHGGGGTGG... CS
                         ResIII  55 ekflflvprkslleqtleefkkflseayk 83 
                                    +++l++v++k+  + +  ++++f++++  
  gene552|gene552|rna552|rna552 319 QNVLIFVNSKDRADELTLKLRNFFKTECR 347
                                    48999999997777766666666555433 PP

>> Helicase_C_2  Helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   3.6e-06    0.0093       6      84 ..     315     407 ..     311     416 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 3.6e-06
                   Helicase_C_2   6 evvpggvlvffpSyklleevverlke................el.eskkieifvee.keesrekvleeykekkkkgaill 67 
                                    e+v ++vl+f++S +  +e++ +l++                ++  s k+e ++   ++ +r+k++e++++  ++  il+
  gene552|gene552|rna552|rna552 315 EIVGQNVLIFVNSKDRADELTLKLRNffktecrtgsndtspySWkMSAKVESLHAGkEQIDRNKIIEQFNS--GSIEILI 392
                                    7899******************999988777776655544441134445555555434459**********..8888888 PP

                   Helicase_C_2  68 avcrGklsEGidfsddl 84 
                                    ++    ls Gidf+ d 
  gene552|gene552|rna552|rna552 393 CTS--LLSRGIDFKVDC 407
                                    887..********9664 PP

>> Malt_amylase_C  Maltogenic Amylase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0      0.19   4.9e+02      38      73 ..      97     132 ..      89     133 .. 0.84
   2 ?   10.9   0.0   0.00015      0.39      13      41 ..     309     337 ..     303     352 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.19
                                    E--GGGTT-EEEETTTTEE-----SSEEEEE-TT-E CS
                 Malt_amylase_C  38 ldlselagrvpvelfggeefpaigelytltLppygf 73 
                                    + ls    ++++e+  +++ p + +   l L+ y +
  gene552|gene552|rna552|rna552  97 VRLSLCIYNKLREMNINQPTPIQMQMIPLVLGGYNV 132
                                    556666678899************99******9976 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00015
                                    EEEEEEEETTEEEEEEEESS-EEEEE--G CS
                 Malt_amylase_C  13 vlaYlReyedetilvvaNrsaqaveldls 41 
                                     +a+l+e  ++++l+++N +++a el+l+
  gene552|gene552|rna552|rna552 309 KFAFLKEIVGQNVLIFVNSKDRADELTLK 337
                                    58****************99999999998 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   8.4e-05      0.22      19     128 ..     138     258 ..     132     268 .. 0.74
   2 ?   -2.3   0.0         2   5.1e+03      88     123 ..     441     475 ..     422     476 .] 0.79

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 8.4e-05
                         AAA_19  19 pGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerlaalgae....atTiHrlal............ldfdd 82 
                                     GtGKT +    + +++ + + + +  +++ +t+  + +++  l+ +         T+H+               +    
  gene552|gene552|rna552|rna552 138 TGTGKTLCFALPLIMMKLEANHSFNGAIILVPTRELCLQIKAFLEHFVSVksafGGTVHKTEKarcnvgmsgeiyV---- 213
                                    59*****999888888888888889***************998855444367777899988556777553333221.... PP

                         AAA_19  83 lltealelleeaeeekklqeeellivDEfqdvd.elqyrLlkallge 128
                                       ++ +ll+  e++++ +e+ +li DE+  ++ +  +r +k+++++
  gene552|gene552|rna552|rna552 214 --ATPGKLLQLLEKNNFARECSHLILDEADKMTsPEFVRNIKTIVEK 258
                                    ..33444555445667776777*******988889999999998844 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 2
                         AAA_19  88 lelleeaeeekklqeeellivDEfqdvdelqyrLlk 123
                                     +lle++++++ l   + +++D    +de + +Ll+
  gene552|gene552|rna552|rna552 441 YTLLEKTDKTNVL-CLYKFWIDSNVRLDENILNLLN 475
                                    5667777777777.6669999999999998888886 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.2   0.00023      0.59      70     117 ..     204     257 ..     132     274 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00023
                         AAA_22  70 a.......erlsseellealeqalraravielliiDEaqhlrseealeeLrslln 117
                                    +       + ++   ll++le++  ar   + li+DEa++++s+e +++++++++
  gene552|gene552|rna552|rna552 204 NvgmsgeiYVATPGKLLQLLEKNNFAREC-SHLILDEADKMTSPEFVRNIKTIVE 257
                                    25665555666677777777777777778.99********978********9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (476 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       588  (0.032796); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.59u 0.26s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 3131.75
//
Query:       gene553|gene553|rna553|rna553  [L=572]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.5e-10   38.9   1.4    1.5e-08   34.8   0.2    2.7  3  PI3_PI4_kinase  Phosphatidylinositol 3- and 4-kinase


Domain annotation for each model (and alignments):
>> PI3_PI4_kinase  Phosphatidylinositol 3- and 4-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0      0.13   2.4e+03     208     224 ..      84     100 ..      77     140 .. 0.78
   2 ?    1.7   0.0     0.011   1.9e+02       4      74 ..     339     399 ..     336     413 .. 0.75
   3 !   34.8   0.2   8.1e-13   1.5e-08     140     195 ..     415     468 ..     408     511 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.13
                                    TTCCHHHHHHHHHHHHH CS
                 PI3_PI4_kinase 208 pskdeglfresceeale 224
                                    ++kd++lfr++c ++l 
  gene553|gene553|rna553|rna553  84 DLKDTHLFRSCCKQFLY 100
                                    67888888888877764 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.011
                                    EEEECSSCHHHHHHHHHHHHHHHHHHHHTTTTCCCT-------EEESSSSEEEEE--TTEEEHHHHHHHHH CS
                 PI3_PI4_kinase   4 giykvgddlrqdelivqvfklmdeelskennpkrrklalktysviplgrkcgiielvassetaaslldekl 74 
                                    ++yk+ d l +d     +f l+  e  +  + ++    +  y+++ +++++g+ie+++ ++t+  ++++k 
  gene553|gene553|rna553|rna553 339 MLYKCDDNLSND-----FFMLCVSEYVSYLLRLK----IAKYKILLFTSHSGVIEMLD-ADTFSAVYRNKA 399
                                    567888888886.....67777777777777777....999**************998.567666666655 PP

  == domain 3  score: 34.8 bits;  conditional E-value: 8.1e-13
                                    HHHHHHHHHHHHHT-TT--TTTEEEETTTSEEEESSTTTCCTCSHCSSSS-.SSSS CS
                 PI3_PI4_kinase 140 rslaklsvldyilgngDRhldNilvdktsgklihIDfGlilpdewkllpfpqekvP 195
                                    + +a ++ + y++g+gDR++dN+lv + ++++  ID+ + l+d++k +++  + +P
  gene553|gene553|rna553|rna553 415 KTFAFCVLMAYLFGIGDRNDDNFLV-TPKKQVLQIDYSYLLGDDPKPFKNS-IVIP 468
                                    56788999*****************.**********************984.4444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (572 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       767  (0.0427799); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 3701.54
//
Query:       gene554|gene554|rna554|rna554  [L=376]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.1e-33  115.4   4.2    5.6e-33  113.1   1.7    2.4  2  MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
    2.4e-21   75.9   0.2    5.2e-21   74.8   0.2    1.6  1  MMR_HSR1      50S ribosome-binding GTPase
    5.9e-19   67.9   0.1    1.1e-18   67.0   0.1    1.4  1  TGS           TGS domain
    4.8e-12   45.7   0.4    1.5e-11   44.1   0.1    2.0  2  FeoB_N        Ferrous iron transport protein B
    0.00049   20.2   2.1       0.45   10.6   0.0    2.7  3  Dynamin_N     Dynamin family
  ------ inclusion threshold ------
      0.013   15.1   0.0          6    6.4   0.0    3.2  3  GTP_EFTU      Elongation factor Tu GTP binding domain
      0.016   14.6   0.2      0.035   13.6   0.2    1.5  1  SRPRB         Signal recognition particle receptor beta subun
      0.021   13.8   0.0       0.05   12.6   0.0    1.6  1  MeaB          Methylmalonyl Co-A mutase-associated GTPase Mea
      0.042   14.1   0.0      0.088   13.0   0.0    1.5  1  AAA_28        AAA domain
      0.078   13.3   0.0       0.24   11.7   0.0    1.8  2  AAA_22        AAA domain


Domain annotation for each model (and alignments):
>> MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.1   1.7   3.1e-36   5.6e-33       1     106 []     184     301 ..     184     301 .. 0.95
   2 ?    2.1   0.0      0.11   1.9e+02      34      53 ..     317     336 ..     312     343 .. 0.89

  Alignments for each domain:
  == domain 1  score: 113.1 bits;  conditional E-value: 3.1e-36
                   MMR_HSR1_Xtn   1 kgGikitstvkltkldeetvkkilkeykihnaevliredvt..........vDdlidviegnr.....vYipclyvlNKi 65 
                                    +gG++++s+vk   +de++vk++lkey+i+++e++i++d++          +Dd+id+ie +      vYipcly+lNK+
  gene554|gene554|rna554|rna554 184 RGGVNLISSVK---IDEAVVKDVLKEYRINSCEIIIEKDYShnandaeneiIDDIIDTIEMHInpssiVYIPCLYLLNKV 260
                                    69*******99...*********************************************664445777************ PP

                   MMR_HSR1_Xtn  66 DlisleeldelarepnsvviSaekelnldeLkekiweeLnL 106
                                    D+isl+el+ ++r +ns++iS+ +++++++Lk+kiw+eLnL
  gene554|gene554|rna554|rna554 261 DRISLAELEVMCRLRNSFPISSFHAWGIERLKDKIWKELNL 301
                                    ***************************************98 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.11
                   MMR_HSR1_Xtn  34 vliredvtvDdlidviegnr 53 
                                    v++r + tv d+ d+i +n 
  gene554|gene554|rna554|rna554 317 VVLRRNSTVADFCDAIHKNM 336
                                    8999************9986 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.8   0.2   2.9e-24   5.2e-21       1     103 [.      64     169 ..      64     182 .. 0.86

  Alignments for each domain:
  == domain 1  score: 74.8 bits;  conditional E-value: 2.9e-24
                                    EEEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSSHHHHHHHHHHHHHHHHC.TSEE CS
                       MMR_HSR1   1 evaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgkeielvDtpGliegaseekglgkaflalee.adli 79 
                                    +++++G p vGKStL+n+lt++k+ v+++ +tT++++ g +++++++++++D+pG+i+gas + g gk++l++ + ++l+
  gene554|gene554|rna554|rna554  64 RIGFIGFPSVGKSTLMNQLTNAKSVVAEYEFTTLKTVPGIMEMHQTKLQILDLPGIIKGASLGSGRGKQVLSVAKtCNLL 143
                                    699***************************************999***************************99978*** PP

                                    EEEEETT..TTCSHHHHHHHHHHHHH CS
                       MMR_HSR1  80 llvvdas..eeklkpldeeleellee 103
                                    ++v+d++   ++l+ ++ ele++  +
  gene554|gene554|rna554|rna554 144 VIVLDSTksLTGLTTIKDELEAVGIR 169
                                    *****775433566677777666544 PP

>> TGS  TGS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.0   0.1     6e-22   1.1e-18       1      60 []     302     373 ..     302     373 .. 0.98

  Alignments for each domain:
  == domain 1  score: 67.0 bits;  conditional E-value: 6e-22
                                    EEEEE.TTSSEEE....EETTB-HHHHHHHHSTTHHHHEEEEEECS.......EEEETTSBB-SSEEEEEEE CS
                            TGS   1 irvyt.PdGkvpd....lprgatveDfAykIhrslakkfiyAlVnG.......qrvgldhvLedgdvveIvt 60 
                                    ir++  P+ +++d    l+r++tv Df+ +Ih+ +++k++yA V+G       qrvg +hvL dgdv++Iv+
  gene554|gene554|rna554|rna554 302 IRIFPkPKNMEIDdpvvLRRNSTVADFCDAIHKNMKEKVTYAWVWGasvkhnpQRVGKEHVLYDGDVIQIVK 373
                                    799999999*************************************************************97 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.1   0.1   8.2e-15   1.5e-11       3      90 ..      65     151 ..      63     174 .. 0.85
   2 ?   -1.9   0.0       1.2   2.1e+03      57      80 ..     187     210 ..     178     219 .. 0.77

  Alignments for each domain:
  == domain 1  score: 44.1 bits;  conditional E-value: 8.2e-15
                                    EEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEEEETTEEEEEEE----SSSSSSSHHHHHHHHHHH.CTSSSE CS
                         FeoB_N   3 valvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegklklkgkeveivDlPGiYslsayseeekvardfll.eeepdv 81 
                                    + ++G p vGk+tl+n+lt+ak+ v+ +  +t +   g +++++++++i+DlPGi  ++  s      +++l   ++ ++
  gene554|gene554|rna554|rna554  65 IGFIGFPSVGKSTLMNQLTNAKSVVAEYEFTTLKTVPGIMEMHQTKLQILDLPGI--IKGASLGSGRGKQVLSvAKTCNL 142
                                    7899**************************************************9..56667777777777753667788 PP

                                    EEEEEEGGG CS
                         FeoB_N  82 vvnvvdatn 90 
                                    +v v+d+t+
  gene554|gene554|rna554|rna554 143 LVIVLDSTK 151
                                    888888876 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.2
                                    -SSSSSSSHHHHHHHHHHHCTSSS CS
                         FeoB_N  57 iYslsayseeekvardflleeepd 80 
                                    +  +s++ ++e v++d+l e +++
  gene554|gene554|rna554|rna554 187 VNLISSVKIDEAVVKDVLKEYRIN 210
                                    555788899999999999876654 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.1   0.00089       1.6       1      32 [.      65      96 ..      65     101 .. 0.83
   2 !   10.6   0.0   0.00025      0.45      96     143 ..     104     154 ..      98     169 .. 0.87
   3 ?   -3.2   0.1       4.3   7.7e+03     136     146 ..     218     228 ..     192     248 .. 0.52

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00089
                                   EEEEEBTTTTHHHHHHHHHTS--S---SSS-- CS
                      Dynamin_N  1 iavvGsqSsGKSSvlnaLlgedilprgpnptT 32
                                   i ++G  S GKS+++n+L+ ++  + + + tT
  gene554|gene554|rna554|rna554 65 IGFIGFPSVGKSTLMNQLTNAKSVVAEYEFTT 96
                                   6789999***********99987777766666 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00025
                                    EETTS-SEEEEE---B-SSSGTTS...HHHHHHHSTTEEEEEEEETTS-CC CS
                      Dynamin_N  96 lsllvkgltlvDlPGldsvnkrdq...elvkeyikkadiilavtsanhdls 143
                                     + ++ +l ++DlPG+++ +       + v + +k +++++ v+++ ++l+
  gene554|gene554|rna554|rna554 104 MEMHQTKLQILDLPGIIKGASLGSgrgKQVLSVAKTCNLLVIVLDSTKSLT 154
                                    67899*************998887888999999999999999999998876 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 4.3
                                    EETTS-CCC-C CS
                      Dynamin_N 136 tsanhdlsnse 146
                                     +++h + ++e
  gene554|gene554|rna554|rna554 218 KDYSHNANDAE 228
                                    33333333333 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0    0.0033         6       3      32 ..      62      91 ..      60     112 .. 0.84
   2 ?   -1.2   0.0      0.67   1.2e+03      66      81 ..     105     120 ..      87     159 .. 0.62
   3 ?    4.4   0.0     0.013        23     111     140 ..     239     269 ..     230     301 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0033
                                   EEEEEEEESTTSSHHHHHHHHHHHTTSSCH CS
                       GTP_EFTU  3 irnigiighvDhGKtTLtdrLlyktgaisk 32
                                   i  ig+ig    GK+TL+ +L+ +++ +++
  gene554|gene554|rna554|rna554 62 IARIGFIGFPSVGKSTLMNQLTNAKSVVAE 91
                                   5679999**************988777665 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.67
                                    TCSSEEEEEEEESSSG CS
                       GTP_EFTU  66 etkkylinliDtPGHv 81 
                                    e ++++++++D PG +
  gene554|gene554|rna554|rna554 105 EMHQTKLQILDLPGII 120
                                    4677777888888754 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.013
                                    HHHHHHHHHHTTTEEEEEEESCGST.HHHHH CS
                       GTP_EFTU 111 teevlrlalkegvpiivfiNKmDrl.kaelk 140
                                     e +++  + + +p   ++NK+Dr+  ael+
  gene554|gene554|rna554|rna554 239 IEMHINPSSIVYIPCLYLLNKVDRIsLAELE 269
                                    5677777888889999999****99544444 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.2   1.9e-05     0.035       7     100 ..      66     164 ..      62     180 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.9e-05
                                    EEE-STTSSHHHHHHHHHHSS---B---S.S-EEETTG...GGTT-SEEEETT-GC...CSHHHHHHHHHHGG.EEEEEE CS
                          SRPRB   7 llvGlsdsGKTslftrLttdsvkktvtSq.essaalkvksekgskltliDfPGhek...lrqklleklkakss.lkglvf 81 
                                     ++G    GK +l+++Lt+ +   +       +++  + + +++kl+++D+PG  k   l +   ++++  ++    lv 
  gene554|gene554|rna554|rna554  66 GFIGFPSVGKSTLMNQLTNAKSVVAEYEFtTLKTVPGIMEMHQTKLQILDLPGIIKgasLGSGRGKQVLSVAKtCNLLVI 145
                                    589***************985554444443556666668999***********765222555555555554444778889 PP

                                    EEETTS-HHHHHHHHHHHH CS
                          SRPRB  82 vvDStidpkevkevAElly 100
                                    v+DSt     ++++ + l 
  gene554|gene554|rna554|rna554 146 VLDSTKSLTGLTTIKDELE 164
                                    9999877666666655555 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   2.8e-05      0.05      30      51 ..      63      84 ..      56      89 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.8e-05
                                   EEEEEEE-TTSSHHHHHHHHHH CS
                           MeaB 30 qvvGltGvPGaGkstlvealgl 51
                                    ++G+ G+P +Gkstl+++l+ 
  gene554|gene554|rna554|rna554 63 ARIGFIGFPSVGKSTLMNQLTN 84
                                   58****************9985 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   4.9e-05     0.088       1      27 [.      64      90 ..      64     105 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4.9e-05
                         AAA_28  1 kivitGgestGKTtlleaLaargypvv 27
                                   +i ++G +s GK+tl+++L++ + +v 
  gene554|gene554|rna554|rna554 64 RIGFIGFPSVGKSTLMNQLTNAKSVVA 90
                                   5779****************9865544 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00014      0.24      11     116 ..      68     170 ..      64     183 .. 0.73
   2 ?   -3.1   0.0       4.8   8.5e+03      48      66 ..     320     338 ..     288     356 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00014
                         AAA_22  11 tGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst...sskdllrellralglelkaerlsseell.ealeqal 86 
                                    +G + +GK+tl+++l++ +          + v++++ + ++   +  ++ +  l++l+l++  +++s+   + +++   +
  gene554|gene554|rna554|rna554  68 IGFPSVGKSTLMNQLTNAK----------SVVAEYEFTTLKtvpGIMEMHQTKLQILDLPGIIKGASLGSGRgKQVLSVA 137
                                    8999*************95..........555566666666333666777777777777776699999999999999999 PP

                         AAA_22  87 raravielliiDEaqhlr..s..eealeeLrsll 116
                                    +++    ++++D    l+  +  ++ le + ++l
  gene554|gene554|rna554|rna554 138 KTCNL-LVIVLDSTKSLTglTtiKDELEAVGIRL 170
                                    99999.9999998877754414566666655555 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 4.8
                         AAA_22  48 psstsskdllrellralgl 66 
                                       ++ +d++ ++ +++++
  gene554|gene554|rna554|rna554 320 RRNSTVADFCDAIHKNMKE 338
                                    3344566666666666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (376 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       763  (0.0425568); expected 358.6 (0.02)
Passed bias filter:                      569  (0.0317363); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.78
# Mc/sec: 1458.40
//
Query:       gene555|gene555|rna555|rna555  [L=756]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
       0.12   12.3   0.3       0.66   10.0   0.0    2.5  2  INCENP_ARK-bind  Inner centromere protein, ARK binding region


Domain annotation for each model (and alignments):
>> INCENP_ARK-bind  Inner centromere protein, ARK binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.1      0.48   8.6e+03      28      52 ..     576     600 ..     569     601 .. 0.72
   2 ?   10.0   0.0   3.7e-05      0.66      17      48 ..     700     730 ..     690     737 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 0.48
                INCENP_ARK-bind  28 rqaLikqepiDpdeiFGpikplnle 52 
                                    rq++   ++   ++ F +ik l le
  gene555|gene555|rna555|rna555 576 RQQILTEKNKKLNQTFEKIKNLFLE 600
                                    4566666888888999999988776 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 3.7e-05
                INCENP_ARK-bind  17 kipsWAqspeLrqaLikqepiDpdeiFGpikp 48 
                                    + + WA+++ +++ + +q+++ +++ FG +  
  gene555|gene555|rna555|rna555 700 NKKPWAKEHSIAEIVSNQNHFEIEKYFGVP-A 730
                                    5678***********************964.3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (756 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3642  (0.203135); expected 358.6 (0.02)
Passed bias filter:                      491  (0.0273858); expected 358.6 (0.02)
Passed Vit filter:                       199  (0.0110993); expected 17.9 (0.001)
Passed Fwd filter:                        42  (0.00234257); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 1.67u 0.43s 00:00:02.10 Elapsed: 00:00:00.68
# Mc/sec: 3355.13
//
Query:       gene556|gene556|rna556|rna556  [L=923]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.3e-12   44.9   0.3    9.3e-12   44.9   0.3    2.6  3  CPSF_A    CPSF A subunit region
  ------ inclusion threshold ------
       0.12   12.4   1.1         13    5.8   0.1    2.8  2  Tfb5      Transcription factor TFIIH complex subunit Tfb5


Domain annotation for each model (and alignments):
>> CPSF_A  CPSF A subunit region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.1      0.06   5.4e+02      64     107 ..      34      74 ..       5     159 .. 0.67
   2 ?   -3.7   0.1      0.62   5.5e+03     125     145 ..     502     522 ..     497     530 .. 0.62
   3 !   44.9   0.3     1e-15   9.3e-12      24     319 ..     631     894 ..     621     897 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.06
                                    EEEEEEEEEE-SS--EEEEEEEEEEEES----EEEETTE..EEEE- CS
                         CPSF_A  64 GrilvfeiievpetnrkLklvhkeevkgavtalaefqGr..llvgv 107
                                     ++  ++i +      k++++ + ++   v a+ +++++  +l+++
  gene556|gene556|rna556|rna556  34 KYLNFYDIMDG-----KFHKIGELQLGSFVVAVIPIENKkfVLISL 74 
                                    34444444442.....555555555555555555553322244444 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 0.62
                                    EEEEE-SS-EEEEEEETTEEE CS
                         CPSF_A 125 kafldtqlyvvslkvlgnrii 145
                                    ++ l  ++yv++l +++ r++
  gene556|gene556|rna556|rna556 502 VCTLTSKIYVMDLATQQARLL 522
                                    555555556666666555544 PP

  == domain 3  score: 44.9 bits;  conditional E-value: 1e-15
                                    EEEEEEEE--B-SSTTT---B--EEEEEEE---SSS--E.EEEEEEEEEE-SS--EEEEEEEEEEEES----EEEETTEE CS
                         CPSF_A  24 EavlsvksvelessettkekkellvVGtafnlgedpaarsGrilvfeiievpetnrkLklvhkeevkgavtalaefqGrl 103
                                    E+v+++ +  + s +   + +++lvV+t +    d +   +r+ +++         k+ +v      ga  ++   ++++
  gene556|gene556|rna556|rna556 631 EHVMKIPNEVIRSAK---RINKYLVVATNYKDAHDNNY--SRLVLLKKMT------KIYEVC---KPGALFSIDVSKDYV 696
                                    666666666665443...46889****99999998833..6888876555......555555...57999999999**** PP

                                    EEE-SSEEEEEEE-TTS-EEEEEEEE-SS-EEEEEEETTEEEEEESSS-EEEEEE-SSS--EEEEEEESS---EEEEEEE CS
                         CPSF_A 104 lvgvgqkvrvydlgedktLlrkafldtqlyvvslkvlgnriivgDlmkSvtfveydeenyklilfardtqkrwvtaaefl 183
                                    + + g  ++vy + ++  L++ a++ +++++ ++      ++++D+++S+++ ++d e +++i+ +r ++k  +     +
  gene556|gene556|rna556|rna556 697 ATSHGVFLTVYSVLNQV-LVELAQIPCPIFPWKIRFNAYNLMICDVFRSFSVYQFDPETNTIIETSRCFEKFVADEGVPI 775
                                    *****************.******************999******************9999********99877666666 PP

                                    --SSSEEEEEETTSEEEEEE--TTSGGGTTTT.EEEEEEEEE-SS----E...EEEE..SSS--S-EEEEEE-TTS-EEE CS
                         CPSF_A 184 vdgedtvlvaDkfgnlfvlrydpeasessdgdprleeraefhlgeivtslrkgslvp.geaesssspqllyatldGsigl 262
                                     +  + +lv+D+ gnlf +  d     ++d +  + +r +f+ +e v ++ +gsl   +++++       ++t +Gsig 
  gene556|gene556|rna556|rna556 776 -E--NEYLVSDAIGNLFNCVSD-----DMDNE--IIKRGSFNYQEGVICIERGSLNVkKDRDT-----YYFSTSSGSIG- 839
                                    .3..58***********98887.....34544..999******************99555555.....9**********. PP

                                    EEE.--HHHHHHHHHHHHHHHHHS--SSS--HHHHS---...----.---EEHHHHHH CS
                         CPSF_A 263 lvPliseeeyrrlqaLqqqLrkelkhlgGldhrafRsyysp.kseevkgviDgdller 319
                                    ++   + e+ r l ++++ +     +l+  + +   +y+++   + + ++iD+d+l  
  gene556|gene556|rna556|rna556 840 VIK--KYEDNRILDQIKNVIEVIGANLV-FNYNDATAYETEdGTKGSTCFIDCDVLGG 894
                                    444..67788889888877765555554.77777777776633333888888887765 PP

>> Tfb5  Transcription factor TFIIH complex subunit Tfb5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.1    0.0015        13      29      49 ..      66      86 ..      59      89 .. 0.86
   2 ?    4.1   0.1    0.0051        46      25      47 ..     407     428 ..     393     433 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0015
                           Tfb5 29 sqkfiiedLDethlfvkeevv 49
                                   ++kf++  LD+++++v++++v
  gene556|gene556|rna556|rna556 66 NKKFVLISLDNQYVVVNDQKV 86
                                   679*************98876 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.0051
                           Tfb5  25 eqepsqkfiiedLDethlfvkee 47 
                                    ++e s+ +++ d+D+++++v ++
  gene556|gene556|rna556|rna556 407 AKE-SKSIVLSDIDDERVVVYTD 428
                                    444.789************9765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (923 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       577  (0.0321825); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.70u 0.29s 00:00:00.99 Elapsed: 00:00:00.47
# Mc/sec: 5884.77
//
Query:       gene557|gene557|rna557|rna557  [L=118]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.8e-15   56.2  17.4    5.7e-14   52.5  16.1    2.3  1  CIAPIN1   Cytokine-induced anti-apoptosis inhibitor 1, Fe-S b
  ------ inclusion threshold ------
      0.011   15.1   0.5      0.014   14.9   0.5    1.1  1  EURL      EURL protein
       0.99    9.2   7.0        2.9    7.7   3.4    2.6  3  S_100     S-100/ICaBP type calcium binding domain


Domain annotation for each model (and alignments):
>> CIAPIN1  Cytokine-induced anti-apoptosis inhibitor 1, Fe-S biogenesis
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.5  16.1   9.5e-18   5.7e-14      10      98 ..      43     115 ..      34     117 .. 0.79

  Alignments for each domain:
  == domain 1  score: 52.5 bits;  conditional E-value: 9.5e-18
                        CIAPIN1  10 kkakkrrkackdctCGlkeleeeeekkkraaadkalekkvkleeeelaevdftvegktssCgsCaLGDafrCsgCPylGl 89 
                                     + +k+++ac +c CG +e +++ +++       +l+   k+++ee++++      ++++Cg C +GDafrC  CP+ Gl
  gene557|gene557|rna557|rna557  43 RRVQKKKRACENCVCGRAEGKKKLSRE-------ELK---KMSREEVKKL------ANAGCGGCKMGDAFRCGDCPFYGL 106
                                    4678*************9987766633.......232...3344554444......578********************* PP

                        CIAPIN1  90 PafkpGekv 98 
                                    P+f+ G++v
  gene557|gene557|rna557|rna557 107 PSFEEGDEV 115
                                    *******98 PP

>> EURL  EURL protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.5   2.3e-06     0.014     173     227 ..      30      84 ..       8      87 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.3e-06
                           EURL 173 gllqdagalwssreraqkkektesdseasvqrrhphysreelnsmtleelkqlne 227
                                     l +da+   s+  r qkk+++  +  +     + + sreel++m+ ee+k+l++
  gene557|gene557|rna557|rna557  30 FLDEDASESVSNSRRVQKKKRACENCVCGRAEGKKKLSREELKKMSREEVKKLAN 84 
                                    34456666777889999999999999999999999****************9975 PP

>> S_100  S-100/ICaBP type calcium binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.1     0.028   1.7e+02      28      35 ..       6      13 ..       4      16 .. 0.86
   2 ?    7.7   3.4   0.00048       2.9      18      37 ..      59      78 ..      56      83 .. 0.81
   3 ?    1.6   0.1     0.039   2.3e+02      24      35 ..      73      84 ..      73      88 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.028
                                   HHHHHHHH CS
                          S_100 28 kELkeLle 35
                                   +++k+Lle
  gene557|gene557|rna557|rna557  6 DDFKKLLE 13
                                   79*****9 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.00048
                                   SSSSTTSEEHHHHHHHHHHH CS
                          S_100 18 keGdkdtLsKkELkeLlekE 37
                                   +   k +Ls++ELk++ ++E
  gene557|gene557|rna557|rna557 59 RAEGKKKLSREELKKMSREE 78
                                   555699*********98777 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.039
                                   SEEHHHHHHHHH CS
                          S_100 24 tLsKkELkeLle 35
                                   ++s++E k+L +
  gene557|gene557|rna557|rna557 73 KMSREEVKKLAN 84
                                   69*******966 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1535  (0.0856155); expected 358.6 (0.02)
Passed bias filter:                      630  (0.0351386); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 847.64
//
Query:       gene558|gene558|rna558|rna558  [L=514]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    0.00018   21.2   0.6     0.0011   18.6   0.6    2.5  1  IDEAL          IDEAL domain
     0.0042   17.6   1.6     0.0042   17.6   1.6    3.4  3  DUF3456        TLR4 regulator and MIR-interacting MSAP
     0.0076   16.3   4.1     0.0076   16.3   4.1    3.9  3  Vps51          Vps51/Vps67
  ------ inclusion threshold ------
      0.068   12.4   0.0       0.11   11.7   0.0    1.4  1  GlcNAc_2-epim  N-acylglucosamine 2-epimerase (GlcNAc 2-epimer
       0.17   11.6   0.1       0.17   11.6   0.1    2.3  3  MDD_C          Mevalonate 5-diphosphate decarboxylase C-termi
        1.2    9.3  11.3       0.46   10.6   2.1    3.1  2  TolA_bind_tri  TolA binding protein trimerisation
        3.2    7.7   5.6        5.7    6.9   1.8    3.2  2  Raptor_N       Raptor N-terminal CASPase like domain


Domain annotation for each model (and alignments):
>> IDEAL  IDEAL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.6   4.5e-07    0.0011      18      35 ..     434     451 ..     426     452 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 4.5e-07
                          IDEAL  18 IDeALdnrDkeaFleLte 35 
                                    ID+ALd+rD e+F++L +
  gene558|gene558|rna558|rna558 434 IDKALDERDFERFNQLIQ 451
                                    ****************75 PP

>> DUF3456  TLR4 regulator and MIR-interacting MSAP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   1.5      0.66   1.7e+03     101     138 ..      32      72 ..       4     133 .. 0.58
   2 ?    2.7   0.3     0.062   1.6e+02     114     151 ..     352     390 ..     337     394 .. 0.79
   3 !   17.6   1.6   1.6e-06    0.0042      53     126 ..     394     483 ..     390     488 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.66
                        DUF3456 101 lgipselkdep.aevkelkkaCeel..veeyEdeleelfke 138
                                     ++++el  +  ++ +++ ++C +l  v+e  d+l+el  +
  gene558|gene558|rna558|rna558  32 EKNDQELLSTItTSYSQIIDFCITLngVNESLDNLIELNNQ 72 
                                    23344444443466666666666665555555666666555 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.062
                        DUF3456 114 vkelkkaCeelveey.EdeleelfkeeeeedleekLCee 151
                                    +++  ++C++++e+y   ++  lf+++ ++ l e++C +
  gene558|gene558|rna558|rna558 352 IESYISKCKKIMENYsIKDIRMLFYKNVDDLLLEYFCLD 390
                                    5556689********55789999999669999*****75 PP

  == domain 3  score: 17.6 bits;  conditional E-value: 1.6e-06
                        DUF3456  53 tevleevCekmldYalhkekktskrvykkmse................dlkelkelkdkevkvdlgipselkdepaevke 116
                                    + vl+ +C ++ dY+ ++++k+s+++  +                   d++++++l ++e +  ++i+ + +++++ +++
  gene558|gene558|rna558|rna558 394 LVVLDRICGEFVDYKFRAQNKKSREITSNYNRikdyhlkvidkalderDFERFNQLIQNETSELNDIKLNSNEKKELIND 473
                                    579******************99988888777889999***********************98889999888888***** PP

                        DUF3456 117 lkkaCeelve 126
                                    +k +C + + 
  gene558|gene558|rna558|rna558 474 MKAYCMNKLQ 483
                                    *****87665 PP

>> Vps51  Vps51/Vps67
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   4.1     3e-06    0.0076      22      84 ..      18      80 ..       5      86 .. 0.86
   2 ?    0.6   0.5      0.23   5.9e+02      37      72 ..     294     329 ..     280     334 .. 0.71
   3 ?    0.3   0.3      0.29   7.5e+02      22      48 ..     447     473 ..     434     476 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 3e-06
                          Vps51 22 kellkveasllseiraldselkalVydnYskLisasdtIrkmksemdkldqklselkqaiski 84
                                   ++ +++ +++++ei+ +d+el +++ ++Ys+ i+ + t++  ++++d+l +  ++ ++ +++ 
  gene558|gene558|rna558|rna558 18 SDNQQLLSNMQKEIEKNDQELLSTITTSYSQIIDFCITLNGVNESLDNLIELNNQSNSYLQDT 80
                                   5678999***************************************99988877777777665 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.23
                          Vps51  37 aldselkalVydnYskLisasdtIrkmksemdkldq 72 
                                    ++ +++k+ +y++ ++L+   ++++ ++   +++++
  gene558|gene558|rna558|rna558 294 QNIKNKKSDIYEHKNDLLVLKEALVALNYRYKDVED 329
                                    444556777899999999999999988877776665 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.29
                          Vps51  22 kellkveasllseiraldselkalVyd 48 
                                     +l++ e s l +i+ + +e+k+l+ d
  gene558|gene558|rna558|rna558 447 NQLIQNETSELNDIKLNSNEKKELIND 473
                                    688899999999999999999999976 PP

>> GlcNAc_2-epim  N-acylglucosamine 2-epimerase (GlcNAc 2-epimerase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   4.5e-05      0.11      60     129 ..     284     352 ..     280     439 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 4.5e-05
                                    TTSSB-SEEETTEEEE--EEHHHHHHHHHHHHHHHTTT-TTHHHHHHHHHHHHHHHTEETTTTEE--EE- CS
                  GlcNAc_2-epim  60 ehggyfsalrdggvldaskdaYdhaFvllalasalaageeeakdlldetlavlekhlweekaglvkeesd 129
                                    ++g+ +++l ++   +++ d+Y+h   ll l +al a++ ++kd+ de+++++ + ++eeka+++  ++ 
  gene558|gene558|rna558|rna558 284 NYGNLVHRLLQNI-KNKKSDIYEHKNDLLVLKEALVALNYRYKDVEDELFKIIFTFFQEEKANITTFSDI 352
                                    6788887775544.68999******************************************999876654 PP

>> MDD_C  Mevalonate 5-diphosphate decarboxylase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.1      0.98   2.5e+03      72      72 ..      54      54 ..      17     107 .. 0.55
   2 ?   -3.1   0.1       2.2   5.5e+03     123     148 ..     328     353 ..     319     378 .. 0.57
   3 ?   11.6   0.1   6.6e-05      0.17      33      85 ..     423     475 ..     411     490 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.98
                          MDD_C 72 l 72
                                   +
  gene558|gene558|rna558|rna558 54 I 54
                                   1 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 2.2
                          MDD_C 123 veellsllkklfppesdaeefvkgak 148
                                     +el +++  +f++e++  +++++ +
  gene558|gene558|rna558|rna558 328 EDELFKIIFTFFQEEKANITTFSDIE 353
                                    45677888888887664433333333 PP

  == domain 3  score: 11.6 bits;  conditional E-value: 6.6e-05
                          MDD_C  33 akevvperieelekAikekdFetfaeitmkdSnqlhavcldtyPpifYlndtS 85 
                                    ++++ + +++ ++kA+ e+dFe+f +++ ++  +l  + l++      +nd+ 
  gene558|gene558|rna558|rna558 423 YNRIKDYHLKVIDKALDERDFERFNQLIQNETSELNDIKLNSNEKKELINDMK 475
                                    5666778999************************9999888777666666665 PP

>> TolA_bind_tri  TolA binding protein trimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   2.1   0.00018      0.46       5      34 ..       7      38 ..       4      41 .. 0.89
   2 ?    2.5   2.0     0.062   1.6e+02       8      39 ..      62      93 ..      59     122 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00018
                  TolA_bind_tri  5 rvarLErilears..qlllelqqqlealqqel 34
                                    ++++Er++++++  qll ++q+++e++ qel
  gene558|gene558|rna558|rna558  7 SLKKIERASKSSDnqQLLSNMQKEIEKNDQEL 38
                                   6899*****998788****************8 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.062
                  TolA_bind_tri  8 rLErilearsqlllelqqqlealqqelreLRG 39
                                   +L++++e ++q++  lq   ++ q  l eLR 
  gene558|gene558|rna558|rna558 62 SLDNLIELNNQSNSYLQDTAQKIQMNLEELRS 93
                                   67888888899******************994 PP

>> Raptor_N  Raptor N-terminal CASPase like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   1.8    0.0022       5.7      65     126 ..     162     220 ..       8     223 .. 0.83
   2 ?   -0.4   0.1      0.38   9.8e+02      40      89 ..     327     375 ..     286     378 .. 0.61

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0022
                       Raptor_N  65 dptvedvkklcqslrrnakdervlfHYnGhgvprptengeiwvfdksytqyiplslaelqew 126
                                    d+ +   k++ +++++ +++   lf + G ++ r  +n++ ++fd +y+ ++ ++++e+   
  gene558|gene558|rna558|rna558 162 DKIF---KRIKNNVKEWMRKVGELFNFLGSEFVRMMNNEHSMIFDFRYNLMKNVPIQEVYDF 220
                                    3333...4444455555666778***********************************9765 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.38
                       Raptor_N  40 l.eeiaknlqdqyeslqlrarykqlldptvedvkklcqslrrnakdervlf 89 
                                    + +e  k + +++++ ++++++ + ++ ++ + kk+++++   +kd r+lf
  gene558|gene558|rna558|rna558 327 VeDELFKIIFTFFQEEKANITTFSDIESYISKCKKIMENYS--IKDIRMLF 375
                                    24666677777888877777888888888888888877764..34666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (514 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2211  (0.12332); expected 358.6 (0.02)
Passed bias filter:                      542  (0.0302304); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.63u 0.28s 00:00:00.91 Elapsed: 00:00:00.44
# Mc/sec: 3470.91
//
Query:       gene559|gene559|rna559|rna559  [L=339]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
        2.4    8.2   6.4        2.5    8.1   0.4    3.1  3  Hydrophobin_2  Fungal hydrophobin


Domain annotation for each model (and alignments):
>> Hydrophobin_2  Fungal hydrophobin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.4   0.00014       2.5      11      51 ..      52      92 ..      45     100 .. 0.88
   2 ?    2.0   0.1     0.012   2.1e+02      30      53 ..     101     124 ..      96     130 .. 0.84
   3 ?   -1.2   0.1      0.11     2e+03      12      24 ..     183     195 ..     159     222 .. 0.69

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00014
                  Hydrophobin_2 11 cCatdvlgvadldCatpsktptsaaefkaiCaasgqqakCC 51
                                    C  ++ ++ +l  ++p+++ +++ +fk+ C  +g   +C 
  gene559|gene559|rna559|rna559 52 KCHSNLINLRCLPQSEPEQNSNTMITFKTKCYPNGLVNNCT 92
                                   5888888889999999*******************999996 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.012
                  Hydrophobin_2  30 tptsaaefkaiCaasgqqakCCvl 53 
                                    +++s++ f  +C+++  +a  C+ 
  gene559|gene559|rna559|rna559 101 NMKSITGFDMTCKTKTADALGCTG 124
                                    6789999*******9999999985 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 0.11
                  Hydrophobin_2  12 CatdvlgvadldC 24 
                                    C+ d+lg     C
  gene559|gene559|rna559|rna559 183 CQGDILGRSGTSC 195
                                    5555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (339 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       766  (0.0427241); expected 358.6 (0.02)
Passed bias filter:                      521  (0.0290591); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 2256.09
//
Query:       gene56|gene56|rna56|rna56  [L=1163]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.6e-42  143.2   0.0    9.6e-42  143.2   0.0    2.3  3  Pkinase        Protein kinase domain
      9e-16   57.9   2.8    8.3e-10   38.4   0.0    3.0  3  Pkinase_Tyr    Protein tyrosine kinase
    1.2e-06   28.0   0.5      0.001   18.4   0.0    3.5  3  Kinase-like    Kinase-like
    0.00021   21.1   7.6    0.00021   21.1   7.6    3.1  3  C1_1           Phorbol esters/diacylglycerol binding domain (
     0.0066   16.5   3.3     0.0066   16.5   3.3    3.9  4  HR1            Hr1 repeat
  ------ inclusion threshold ------
      0.017   15.0   0.0      0.087   12.8   0.0    2.2  1  Titin_Ig-rpts  Titin repeat
       0.02   14.4   7.1       0.12   12.0   7.1    2.4  1  PHD_2          PHD-finger
        0.7   10.2  10.9        6.2    7.1   2.6    3.9  3  KLRAQ          Predicted coiled-coil domain-containing protei


Domain annotation for each model (and alignments):
>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  143.2   0.0   4.3e-45   9.6e-42       4     264 .]      49     321 ..      46     321 .. 0.92
   2 ?   -3.5   0.1       2.3   5.2e+03     211     258 ..     449     492 ..     430     495 .. 0.56
   3 ?   -4.2   0.7       3.8   8.5e+03      32      63 ..     897     928 ..     884     963 .. 0.52

  Alignments for each domain:
  == domain 1  score: 143.2 bits;  conditional E-value: 4.3e-45
                                EEEEEEESSEEEEEEEETTTTEEEEEEEEECHCHCHHHH.HHHHHHHHHHHHHS.CTTB--EEEEEEESSEEEEEEE--TTEBH CS
                    Pkinase   4 leklGeGsfGkVykaveketgkivAvKkikkekakkkke.kkvlrEikilkklk.hpnivrlyevfeekdelylvleyveggel 85 
                                ++ + +G++G+Vy + ++++++ +A+K+ikk+   ++ +   + +E + lk+ +  +++v +  +f++++++++++++ +++ l
  gene56|gene56|rna56|rna56  49 IRGIAKGGYGSVYLVQSNQSQQYYALKVIKKQVVIDMPHlALFENEKAALKSARdAQYLVFMHCSFQNERSIFFLMDFYPCELL 132
                                566889******************************99989999*********99*************************9966 PP

                                HHHHHHHSS--HHHHHHHHHHHHHHHHHHHHTTEE-SS-SGGGEEEETTTEEEE-SGTTSEESSSSCS................ CS
                    Pkinase  86 adllerkgslseeeakkiakqilegleylHskgiiHrDlKpeNiLidekgelKitDFGlakelesssk................ 153
                                +++     + +e+e++++a+ +l ++e lH+ g +HrD+KpeNi++d+ g +K++DFG +++++  +                 
  gene56|gene56|rna56|rna56 133 ERVP----VHDEQELRFYAAGVLLAIEELHKLGYVHRDIKPENIFLDSAGYVKLADFGSCCRIKDAKGcineneamrstcsrkf 212
                                6666....58*******************************************************9999*************** PP

                                ................BCTTTSCGGGS-HHHHTTSCBSHHHHHHHHHHHHHHHHHSS-STTTSSHHHHHHHHHHTHHHHHHHCT CS
                    Pkinase 154 ................ltsfvgtseYlAPEvlkeneyskkvDvWslGvilyelltgkppfsgekgkekvekeldqlekilkilg 221
                                                 + +vgt++Y+APE   +ne + +vD+W++Gv+lyel   ++pf++ +  +++++++++         
  gene56|gene56|rna56|rna56 213 tggsarssgstgsatrSEIMVGTPDYIAPECF-TNEQGVEVDMWAYGVVLYELKKDETPFYAATL-TETQSNIRE--------- 285
                                **************988889***********9.7889************************4444.446666666......... PP

                                SHH...HHHTTS-HHHHHHHHHHT-SSGCCSTTHHHHHTSGGG CS
                    Pkinase 222 etkeklpeaseiseeakdllkkllkkdpkkRltaeellqhpyl 264
                                       + +++   + dl+++ll+++ ++R+ ++++++hp++
  gene56|gene56|rna56|rna56 286 ------IKYEKCAGVFGDLIDRLLQYK-HERINVQQCKEHPFF 321
                                ......245788999*********996.68***********98 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 2.3
                                HTHHHHHHHCT.SHH...HHHTTS-HHHHHHHHHHT-SSGCCSTTHHHH CS
                    Pkinase 211 dqlekilkilg.etkeklpeaseiseeakdllkkllkkdpkkRltaeel 258
                                +     +ki +  ++++ + +s   ++  + +++ ++  p+kRlt++++
  gene56|gene56|rna56|rna56 449 H-----RKINHeLYDKSKESHSAQANTTDSACNQNMHGMPTKRLTCTSC 492
                                2.....2444422333444444456666667777788888888888765 PP

  == domain 3  score: -4.2 bits;  conditional E-value: 3.8
                                EECHCHCHHHH.HHHHHHHHHHHHHSCTTB--E CS
                    Pkinase  32 ikkekakkkke.kkvlrEikilkklkhpnivrl 63 
                                +k ++++kk+     ++E++i kkl+ ++i+r+
  gene56|gene56|rna56|rna56 897 LKIREQEKKEVeLMNTTEVTIRKKLE-KEILRY 928
                                33333333222122334555555443.234444 PP

>> Pkinase_Tyr  Protein tyrosine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.4   0.0   3.7e-13   8.3e-10       3     157 ..      48     195 ..      46     208 .. 0.78
   2 !   18.6   0.0     4e-07    0.0009     166     220 ..     233     285 ..     215     317 .. 0.77
   3 ?   -2.1   0.5      0.82   1.8e+03      26      82 ..     887     947 ..     877     978 .. 0.67

  Alignments for each domain:
  == domain 1  score: 38.4 bits;  conditional E-value: 3.7e-13
                                EEEEEEEESSEEEEEEEEETTTTSSEEEEEEEEESTTS..SHHHHHHHHHHHHHHHTS.-BTTB--EEEEEESSSSEEEEEE-- CS
                Pkinase_Tyr   3 lgkklGeGafGkVvegtlkgekekkevkVavKtlkeea..teeekeelleeakimkkl.khpnivkllgvctkeepllivteyv 83 
                                l + +++G +G+V+  + +    ++++  a+K++k++   +  + + + +e + +k+  + + +v ++    +e+++++++++ 
  gene56|gene56|rna56|rna56  48 LIRGIAKGGYGSVYLVQSN----QSQQYYALKVIKKQVviDMPHLALFENEKAALKSArDAQYLVFMHCSFQNERSIFFLMDFY 127
                                567899*********9999....555566666666554114455788888********777777777777779999*******9 PP

                                TTEBHHHHHHHTCTTTSBHHHHHHHHHHHHHHHHHHHHTTEEEST-SGGGEEEEETTEEEE-STTTHEETTTSS CS
                Pkinase_Tyr  84 kgGdLlkfLrkkekekltlkdllsfalqvAkGmeyLeskklvHrdlaarNvLlsenkvvkisDfGLardiekdd 157
                                +   Ll+ +  +     + ++l  +a+ v  ++e L++  +vHrd+   N++l++   vk++DfG + +i++ +
  gene56|gene56|rna56|rna56 128 PCE-LLERVPVH-----DEQELRFYAAGVLLAIEELHKLGYVHRDIKPENIFLDSAGYVKLADFGSCCRIKDAK 195
                                985.55555555.....56677779999*************************************998885544 PP

  == domain 2  score: 18.6 bits;  conditional E-value: 4e-07
                                TSGGGGS-HHHHHHSEEEHHHHHHHHHHHHHHHHTTSSGTTTTSHHHHHHHHHHT CS
                Pkinase_Tyr 166 klpvkWmapEslkekkftsksDvWsfGvllwEiftlgespypglkneevleklke 220
                                     ++apE++++++  ++ D+W++Gv+l+E+ +  e+p+   + +e+ ++++e
  gene56|gene56|rna56|rna56 233 VGTPDYIAPECFTNEQ-GVEVDMWAYGVVLYELKK-DETPFYAATLTETQSNIRE 285
                                556689*****98766.6899***********988.7888888777776666654 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 0.82
                                SSEEEEEEEEESTTSSHHHHHHHHHHHHHHHTS.-BTTB--EEEEEE...SSSSEEEEEE- CS
                Pkinase_Tyr  26 kkevkVavKtlkeeateeekeelleeakimkkl.khpnivkllgvct...keepllivtey 82 
                                +++++   K+lk + +e+++ el++ +++  +    ++i+++ + +     ++++ iv++ 
  gene56|gene56|rna56|rna56 887 NRDIRTLSKMLKIREQEKKEVELMNTTEVTIRKkLEKEILRYKAEIKrlrAKGEINIVFKV 947
                                5667777899999999999999998555443332455677766666555455556666655 PP

>> Kinase-like  Kinase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   4.7e-07     0.001     158     204 ..     155     202 ..     131     220 .. 0.86
   2 ?    3.0   0.0     0.024        54     229     284 ..     250     306 ..     241     309 .. 0.67
   3 ?    1.3   1.0     0.078   1.7e+02     110     150 ..     876     916 ..     809     921 .. 0.65

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 4.7e-07
                Kinase-like 158 anLqakglvhgkftvdnllldekgglmlggftaLvragt.kvvlseve 204
                                 +L+++g vh +++++n++ld  g ++l +f++  r ++ k+ ++e+e
  gene56|gene56|rna56|rna56 155 EELHKLGYVHRDIKPENIFLDSAGYVKLADFGSCCRIKDaKGCINENE 202
                                68*********************************9986255557665 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.024
                Kinase-like 229 hkldaWqlGlviyriwclklPltlat....eeakeewkfklck.kipekvkaLlkkfLqls 284
                                 ++d W+ G+v y +   + P+  at    +  + e k+++c+   ++    L+ ++Lq++
  gene56|gene56|rna56|rna56 250 VEVDMWAYGVVLYELKKDETPFYAATltetQSNIREIKYEKCAgVFGD----LIDRLLQYK 306
                                679******************976551111233344577777744454....666666665 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.078
                Kinase-like 110 vvnallllpaasvdleilnkvlqkrsethkkletiarlllT 150
                                 ++   l+ +++ d+ +l k+l++r++++k+ e +    +T
  gene56|gene56|rna56|rna56 876 EIDIVSLYRRMNRDIRTLSKMLKIREQEKKEVELMNTTEVT 916
                                4567889******************9999888877666665 PP

>> C1_1  Phorbol esters/diacylglycerol binding domain (C1 domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.3      0.39   8.7e+02      16      35 ..     474     493 ..     463     496 .. 0.76
   2 ?   -3.2   1.1       3.7   8.3e+03      12      21 ..     646     655 ..     639     665 .. 0.65
   3 !   21.1   7.6   9.4e-08   0.00021       1      49 [.    1086    1130 ..    1086    1135 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.39
                                TT-SB--SSSS-EEEETTT- CS
                       C1_1  16 hCgeflwgkekqglkCswCk 35 
                                 C++ ++g  +  l+C+ C+
  gene56|gene56|rna56|rna56 474 ACNQNMHGMPTKRLTCTSCG 493
                                67777766788889999997 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 3.7
                                -B-TTT-SB- CS
                       C1_1  12 tfCkhCgefl 21 
                                + C+ C + +
  gene56|gene56|rna56|rna56 646 NSCECCSNGC 655
                                4555555555 PP

  == domain 3  score: 21.1 bits;  conditional E-value: 9.4e-08
                                 --EEEE--SS--B-TTT-SB--SSSS-EEEETTT--EE-CCCCTTS-SB CS
                       C1_1    1 HhwvhrnfkqptfCkhCgeflwgkekqglkCswCkllvHkkChekvpke 49  
                                 H +v+++   +++C+ C+e+     +  l+C++C+++vH +C++++ ++
  gene56|gene56|rna56|rna56 1086 HVFVRKK-GLSGYCNFCDEPH---YSISLSCEQCGITVHRQCYMLAMSC 1130
                                 9999999.99***********...*******************998665 PP

>> HR1  Hr1 repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.2      0.56   1.3e+03       6      23 ..     424     441 ..     424     470 .. 0.80
   2 ?   -1.1   0.2      0.93   2.1e+03      54      65 ..     817     828 ..     810     860 .. 0.64
   3 ?   -3.0   1.0       3.6   8.1e+03      35      52 ..     916     933 ..     891     938 .. 0.59
   4 !   16.5   3.3     3e-06    0.0066       2      63 ..    1012    1067 ..    1011    1072 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.56
                        HR1   6 ekklekElkireGAenll 23 
                                ++++++ ++i ++A n  
  gene56|gene56|rna56|rna56 424 NDEIDRNKRIENAASNHN 441
                                679********9999965 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.93
                        HR1  54 LreqLeelqasv 65 
                                L+++Le++q+ +
  gene56|gene56|rna56|rna56 817 LESELERMQRNN 828
                                445555554432 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 3.6
                        HR1  35 kvrqeaeselsesnskie 52 
                                 +r + e e+   + +i+
  gene56|gene56|rna56|rna56 916 TIRKKLEKEILRYKAEIK 933
                                355555555555555555 PP

  == domain 4  score: 16.5 bits;  conditional E-value: 3e-06
                        HR1    2 leelekklekElkireGAenllraleskktqnkkvrqeaeselsesnskielLreqLeelqa 63  
                                 +++l   l+kE+++ + +e+l        +   kv+++a ++l+ s +ki++L+ ++e   +
  gene56|gene56|rna56|rna56 1012 RSQLLEDLRKEKRLYASIEKLST------MHTGKVLEKARTQLEGSLRKIKYLEAEIENADD 1067
                                 6899999****************......68899***********************98766 PP

>> Titin_Ig-rpts  Titin repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   3.9e-05     0.087       5      19 ..    1046    1060 ..    1045    1061 .. 0.95

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.9e-05
              Titin_Ig-rpts    5 TQhPeGLeKIQqLED 19  
                                 TQ++++L KI++LE+
  gene56|gene56|rna56|rna56 1046 TQLEGSLRKIKYLEA 1060
                                 9*************7 PP

>> PHD_2  PHD-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   7.1   5.3e-05      0.12       3      20 ..    1108    1125 ..    1106    1134 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 5.3e-05
                      PHD_2    3 pllsCdkCsvaVHasCYG 20  
                                 + lsC +C + VH++CY 
  gene56|gene56|rna56|rna56 1108 ISLSCEQCGITVHRQCYM 1125
                                 569**************6 PP

>> KLRAQ  Predicted coiled-coil domain-containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.1    0.0057        13      33      72 ..     605     644 ..     597     675 .. 0.79
   2 ?    7.1   2.6    0.0028       6.2      27      76 ..     799     848 ..     770     876 .. 0.84
   3 ?   -2.0   0.2       1.9   4.2e+03      59      85 ..     886     915 ..     850     930 .. 0.59

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0057
                      KLRAQ  33 eelkekeqslrkseqEvdsLtFrNkqLekrvellqeelev 72 
                                ++l + +q l k ++E + L+ rN  L+  v+  q e ++
  gene56|gene56|rna56|rna56 605 KTLISTNQRLVKYKEECEDLKIRNGVLTNIVKREQLERMS 644
                                5677889**********************99988876554 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0028
                      KLRAQ  27 keaslkeelkekeqslrkseqEvdsLtFrNkqLekrvellqeeleveekk 76 
                                k+++lk+++  k + +   e E++ ++ +N+ L+ r++ + ++ +  +++
  gene56|gene56|rna56|rna56 799 KCSQLKDNVLIKTERMIELESELERMQRNNNELKGRIARMSDDKARYKRR 848
                                8899************************************9998765543 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 1.9
                      KLRAQ  59 Lekrvellqeelevee..kk.vksksknks 85 
                                +++ +++l + l+ +e  kk v+  ++ ++
  gene56|gene56|rna56|rna56 886 MNRDIRTLSKMLKIREqeKKeVELMNTTEV 915
                                444444444444443322222333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1762  (0.0982765); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.89u 0.33s 00:00:01.22 Elapsed: 00:00:00.51
# Mc/sec: 6821.14
//
Query:       gene560|gene560|rna560|rna560  [L=821]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0016   18.5   0.3     0.0016   18.5   0.3    4.2  5  Cnd1      non-SMC mitotic condensation complex subunit 1
  ------ inclusion threshold ------
      0.028   14.7   0.0         43    4.8   0.0    3.9  3  HEAT      HEAT repeat


Domain annotation for each model (and alignments):
>> Cnd1  non-SMC mitotic condensation complex subunit 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0     0.071   6.4e+02      53      84 ..      30      62 ..      27      78 .. 0.71
   2 ?   -0.5   0.0      0.12   1.1e+03      48     104 ..      89     146 ..      83     171 .. 0.78
   3 ?   -3.4   0.0      0.99   8.8e+03      83      99 ..     305     323 ..     297     331 .. 0.41
   4 !   18.5   0.3   1.7e-07    0.0016      13     149 ..     347     483 ..     338     497 .. 0.84
   5 ?    2.5   0.3     0.015   1.3e+02      73     136 ..     509     568 ..     488     596 .. 0.68

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.071
                           Cnd1 53 mvkekgflselak.lleDenprVvanalaalte 84
                                   +v +k+f+  l    ++D++p +++ + +++++
  gene560|gene560|rna560|rna560 30 LVSNKEFVYSLPGtYMKDSDPLIRQVSATFFKN 62
                                   566666666665414588888888888888865 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.12
                           Cnd1  48 Lilndmvkekgflselakll.eDenprVvanalaalteiseksenaiynllpdiiskl 104
                                    +i++ + k+k+ + ++++++  D+ ++  + al++l+ ++e++ +++ n   +++ + 
  gene560|gene560|rna560|rna560  89 IISQHVAKNKEYVVDFQNIIrGDTGKESFDTALLILNAYAERDRTKFSNAATSSLLQS 146
                                    5778888999999999999988999999999***********9888888766655444 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 0.99
                           Cnd1  83 teisek..senaiynllpd 99 
                                    t+i++   +++ai++ +++
  gene560|gene560|rna560|rna560 305 TDILKVsnKQDAILQYMKN 323
                                    4444442222333333332 PP

  == domain 4  score: 18.5 bits;  conditional E-value: 1.7e-07
                           Cnd1  13 irvpnlveylvepLrkrLkDedpyVRktaaivvakL.ilndmvkekgflselaklleDenprVvanalaalteisek..s 89 
                                    +r +nl  ++ve ++++L+D++  ++ +a++++  + i+n     + ++++++++l+  ++++++n+ ++l    +    
  gene560|gene560|rna560|rna560 347 LRGSNLYPEFVESVKACLEDPHNFIKSQAFYALQLMdIENIGEDRRRVFNMVLDALKSGDESIRTNSALCLPIFFDAadL 426
                                    677889999***********************988866666666666*******************99998777777433 PP

                           Cnd1  90 enaiynllpdiisklsdalnecsewgqitilefLlsyipkdkqeaeslveklcprlqhan 149
                                     n + ++lp i++ l+   n ++ ++  + le++++  + +   a +l++k+++ ++  n
  gene560|gene560|rna560|rna560 427 RNDVERNLPIILNTLV--YNPLNLEQISETLETVIDTFDISCY-AVDLCKKMIDSVKIDN 483
                                    399************9..6789999999999999998888888.8888888888777666 PP

  == domain 5  score: 2.5 bits;  conditional E-value: 0.015
                           Cnd1  73 rVvanalaalteiseksenaiynllpdiisklsdalnecsewgqitilefLlsyipkdkqeaes 136
                                    ++ ++al  l  ++++++  +y+ + diis+++     + + g ++ile++    ++d++e  +
  gene560|gene560|rna560|rna560 509 KIYELALPTLFYVLKNKKYDFYTETLDIISNVL----YVFKTGDQNILELVRMVLESDQKELIN 568
                                    466777777788888888899999999999999....577888888999988888888886433 PP

>> HEAT  HEAT repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0       0.1   9.2e+02       9      22 ..      45      58 ..      43      62 .. 0.84
   2 ?    3.8   0.0    0.0096        86       5      25 ..     360     380 ..     356     382 .. 0.85
   3 ?    4.8   0.0    0.0048        43       2      24 ..     395     417 ..     394     421 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.1
                                   HT-SSHHHHHHHHH CS
                           HEAT  9 lsDpspeVReaAak 22
                                   ++D++p +R+ +a 
  gene560|gene560|rna560|rna560 45 MKDSDPLIRQVSAT 58
                                   79********9986 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.0096
                                    HHHHHT-SSHHHHHHHHHHHH CS
                           HEAT   5 llkllsDpspeVReaAakaLg 25 
                                    +  +l+Dp+ ++ + A++aL 
  gene560|gene560|rna560|rna560 360 VKACLEDPHNFIKSQAFYALQ 380
                                    56789**************95 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.0048
                                    HHHHHHHHT-SSHHHHHHHHHHH CS
                           HEAT   2 lPlllkllsDpspeVReaAakaL 24 
                                    ++++l +l++ + ++R ++a++L
  gene560|gene560|rna560|rna560 395 FNMVLDALKSGDESIRTNSALCL 417
                                    678999****************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (821 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       864  (0.0481901); expected 358.6 (0.02)
Passed bias filter:                      477  (0.0266049); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.71u 0.31s 00:00:01.02 Elapsed: 00:00:00.48
# Mc/sec: 5131.42
//
Query:       gene561|gene561|rna561|rna561  [L=293]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    7.5e-13   48.7   1.2    3.1e-06   27.8   0.1    4.6  4  WD40         WD domain, G-beta repeat
    1.1e-06   28.2   8.0      0.013   14.8   3.8    2.6  3  WD40_like    WD40-like domain
    6.1e-06   26.4   1.9     0.0014   18.9   0.1    3.5  4  ANAPC4_WD40  Anaphase-promoting complex subunit 4 WD40 domain
     0.0088   16.1   0.6          6    7.0   0.0    3.3  4  BBS2_Mid     Ciliary BBSome complex subunit 2, middle region
  ------ inclusion threshold ------
      0.014   15.9   1.0        2.5    8.7   0.0    3.4  4  PQQ_3        PQQ-like domain
       0.45   10.5   3.0         85    3.3   0.1    4.2  4  PQQ          PQQ enzyme repeat


Domain annotation for each model (and alignments):
>> WD40  WD domain, G-beta repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1   0.1    0.0037        11       4      33 ..      44      72 ..      41      75 .. 0.75
   2 !    6.3   0.0    0.0067        20       6      37 ..     130     160 ..     126     161 .. 0.75
   3 ?    2.8   0.0     0.081   2.4e+02       3      37 ..     172     204 ..     170     205 .. 0.65
   4 !   27.8   0.1     1e-09   3.1e-06       8      37 ..     257     287 ..     249     288 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0037
                                   EEEEESS.SSEEEEEEETTSSEEEEEETTSE CS
                           WD40  4 lrtltGH.ssvtslafspdgawlasGsdDgt 33
                                   +++l  H +s++++   +dg  +++Gs+Dg+
  gene561|gene561|rna561|rna561 44 QKILCQHeKSIRCI-AAKDGV-IVCGSYDGN 72
                                   778889*999****.444444.568999996 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0067
                                    EEESS.SSEEEEEEETTSSEEEEEETTSEEEEE CS
                           WD40   6 tltGH.ssvtslafspdgawlasGsdDgtvriW 37 
                                    +l+ H ++v +++f  +  +  + ++D+tv+++
  gene561|gene561|rna561|rna561 130 ILEDHtQDVKGVKFFNNLLY--TYGYDNTVKVY 160
                                    57889888999977666555..5445*****98 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.081
                                    EEEEEESS.SSEEEEEEETTSSE...EEEEETTSEEEEE CS
                           WD40   3 clrtltGH.ssvtslafspdgaw...lasGsdDgtvriW 37 
                                    +l++l+++   v+++       +   l+ +s Dg ++++
  gene561|gene561|rna561|rna561 172 LLQSLEAQkETVWDV------EMltkLFVASNDGCIYVY 204
                                    567778884448888......66344334677****997 PP

  == domain 4  score: 27.8 bits;  conditional E-value: 1e-09
                                    ESS.SSEEEEEEETTSSEEEEEETTSEEEEE CS
                           WD40   8 tGH.ssvtslafspdgawlasGsdDgtvriW 37 
                                    ++H ++++++++s+d+++l+++sdDg ++++
  gene561|gene561|rna561|rna561 257 DAHqKDINCVKYSDDNNMLVTCSDDGCLKVY 287
                                    48*999***********************98 PP

>> WD40_like  WD40-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.1   5.7e-06     0.017      80     134 ..      10      64 ..       3      69 .. 0.91
   2 !    8.7   0.7   0.00032      0.95      52     142 ..      60     156 ..      53     169 .. 0.74
   3 !   14.8   3.8   4.4e-06     0.013       7     183 ..      99     286 ..      90     291 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 5.7e-06
                      WD40_like  80 kieedistvkviddklliGtnkGsiyvfskdlqleevllgqsseIkeikiennki 134
                                    + +e +    v++d +l G++k  ++++s dl+++++l  ++  I+ i  ++++i
  gene561|gene561|rna561|rna561  10 QFDEKLLSLAVTKDSVLTGGTKKILHKLSTDLHTQKILCQHEKSIRCIAAKDGVI 64 
                                    6778888899**************************************9998877 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00032
                      WD40_like  52 dddlilvvtlDGtillslleneeeve.nekieedistvkvi.....ddklliGtnkGsiyv..fskdlqleevllgqsse 123
                                    +d +i++++ DG+   ++l ++++ + +e  e +i  v+ +     d+ +++ t   +++v  ++  ++++ +l  ++ +
  gene561|gene561|rna561|rna561  60 KDGVIVCGSYDGNA--TVLYEDKILDlIEGPETEIKGVDLLngnrrDNYIALSTRGKTVWVckLNDKIEIDSILEDHTQD 137
                                    56799999999999..99999996662344566777776651111156788888888888877888999999999***** PP

                      WD40_like 124 IkeikiennkiysLsesaf 142
                                    +k +k  nn +y+   ++ 
  gene561|gene561|rna561|rna561 138 VKGVKFFNNLLYTYGYDNT 156
                                    ************9865554 PP

  == domain 3  score: 14.8 bits;  conditional E-value: 4.4e-06
                      WD40_like   7 diskkgslilyGgkddkctvlkleslesv.sivesfedSvifvklldddlilvvtlDGtills...lleneeevenekie 82 
                                    + +++ ++i+   + +++ v+kl+ ++++ si+e+ ++ v  vk+ ++ l+     D t+  +   ++  +  v  +++e
  gene561|gene561|rna561|rna561  99 NGNRRDNYIALSTRGKTVWVCKLNDKIEIdSILEDHTQDVKGVKFFNN-LLYTYGYDNTVKVYqrfTMYDDSWVLLQSLE 177
                                    4478899*****************999985788************966.5667788998865422268888866555554 PP

                      WD40_like  83 ...edistvkviddklliGtnkGsiyvfsk..dlqleevllgqsseIkeikiennki.ysLsesafivfdlfsq..niey 154
                                       e +  v+++  kl + +n G iyv+ k  d  ++  +     +I++++ +++++  +  ++ +++ d+  q    + 
  gene561|gene561|rna561|rna561 178 aqkETVWDVEML-TKLFVASNDGCIYVYRKekDWVFDYCCNISVYPILSLCRIRDFLaLAVDSKSLVIVDESLQvkCSLE 256
                                    111556666655.57899**********861155666667677789******9999824555566777776544113456 PP

                      WD40_like 155 kisvkdiktfeiienkdilligte.geili 183
                                    + + kdi++++  +++++l+ + + g++++
  gene561|gene561|rna561|rna561 257 DAHQKDINCVKYSDDNNMLVTCSDdGCLKV 286
                                    788999999999999998887765145555 PP

>> ANAPC4_WD40  Anaphase-promoting complex subunit 4 WD40 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0         1   3.1e+03      66      81 ..      27      42 ..      10      60 .. 0.51
   2 ?    4.6   0.0     0.014        40       9      65 ..     106     160 ..     101     184 .. 0.79
   3 ?   -1.2   0.0      0.87   2.6e+03      12      31 ..     194     213 ..     191     217 .. 0.78
   4 !   18.9   0.1   4.7e-07    0.0014       2      67 ..     225     289 ..     224     293 .] 0.94

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1
                    ANAPC4_WD40 66 daesgkvvhslsvkse 81
                                      ++k++h+ls++ +
  gene561|gene561|rna561|rna561 27 TGGTKKILHKLSTDLH 42
                                   3445566666555433 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.014
                    ANAPC4_WD40   9 LiAlatedgellvfRlngqrvwtleedkedsevrsLaWkpdgklLavaysdgevrll 65 
                                     iAl t  + ++v+ ln +   +   +++ + v+++++ +  +lL     d++v+++
  gene561|gene561|rna561|rna561 106 YIALSTRGKTVWVCKLNDKIEIDSILEDHTQDVKGVKFFN--NLLYTYGYDNTVKVY 160
                                    59**************998655555778888888888765..466666666666655 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 0.87
                    ANAPC4_WD40  12 latedgellvfRlngqrvwt 31 
                                    +a++dg ++v+R +   v++
  gene561|gene561|rna561|rna561 194 VASNDGCIYVYRKEKDWVFD 213
                                    57888999999988877775 PP

  == domain 4  score: 18.9 bits;  conditional E-value: 4.7e-07
                    ANAPC4_WD40   2 swcptmDLiAlatedgellvfRlngqrvwtleedkedsevrsLaWkpdgklLavaysdgevrllda 67 
                                    s c  +D +Ala ++++l++   + q   +l ed++++ +++++++ d+++L+   +dg ++++++
  gene561|gene561|rna561|rna561 225 SLCRIRDFLALAVDSKSLVIVDESLQVKCSL-EDAHQKDINCVKYSDDNNMLVTCSDDGCLKVYHV 289
                                    78999*********************99999.9*****************************9998 PP

>> BBS2_Mid  Ciliary BBSome complex subunit 2, middle region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0      0.88   2.6e+03      14      34 ..      63      83 ..      55      93 .. 0.79
   2 ?   -2.5   0.0       1.8   5.3e+03      54      67 ..     150     162 ..     129     167 .. 0.68
   3 !    7.0   0.0     0.002         6      13      32 ..     190     210 ..     182     248 .. 0.79
   4 !    5.6   0.0    0.0054        16      10      29 ..     270     289 ..     263     292 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.88
                       BBS2_Mid 14 eLvvgsddfeirvfkeeelva 34
                                    +v gs d + +v+ e++++ 
  gene561|gene561|rna561|rna561 63 VIVCGSYDGNATVLYEDKILD 83
                                   488999999999999998875 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.8
                       BBS2_Mid  54 ayaleNGtvgvyek 67 
                                     y+ +N tv+vy++
  gene561|gene561|rna561|rna561 150 TYGYDN-TVKVYQR 162
                                    455555.7777765 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.002
                       BBS2_Mid  13 neLvvgsddfeirvfkee.el 32 
                                    ++L+v+s+d +i v+++e + 
  gene561|gene561|rna561|rna561 190 TKLFVASNDGCIYVYRKEkDW 210
                                    789************998344 PP

  == domain 4  score: 5.6 bits;  conditional E-value: 0.0054
                       BBS2_Mid  10 dgeneLvvgsddfeirvfke 29 
                                    d++n Lv +sdd +++v++ 
  gene561|gene561|rna561|rna561 270 DDNNMLVTCSDDGCLKVYHV 289
                                    56899************975 PP

>> PQQ_3  PQQ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.0   0.00085       2.5      17      36 ..      57      76 ..      38      76 .. 0.84
   2 ?   -1.9   0.2       1.8   5.4e+03      22      33 ..     146     157 ..     143     160 .. 0.85
   3 ?    3.8   0.0      0.03        90      23      37 ..     191     205 ..     190     207 .. 0.87
   4 ?   -3.5   0.0       5.6   1.7e+04      21      32 ..     272     283 ..     268     287 .. 0.67

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00085
                          PQQ_3 17 pavdgglvyvgtgdGtlyAl 36
                                    a+ +g++++g++dG+ + l
  gene561|gene561|rna561|rna561 57 IAAKDGVIVCGSYDGNATVL 76
                                   4899************9876 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.8
                          PQQ_3  22 glvyvgtgdGtl 33 
                                    +l+y+ ++d+t+
  gene561|gene561|rna561|rna561 146 NLLYTYGYDNTV 157
                                    799*99999987 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.03
                          PQQ_3  23 lvyvgtgdGtlyAlD 37 
                                    +++v++ dG +y + 
  gene561|gene561|rna561|rna561 191 KLFVASNDGCIYVYR 205
                                    59**********985 PP

  == domain 4  score: -3.5 bits;  conditional E-value: 5.6
                          PQQ_3  21 gglvyvgtgdGt 32 
                                    ++ +++ ++dG 
  gene561|gene561|rna561|rna561 272 NNMLVTCSDDGC 283
                                    456777777875 PP

>> PQQ  PQQ enzyme repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.1     0.055   1.7e+02       1      11 [.      62      72 ..      61      76 .. 0.77
   2 ?    0.8   0.0      0.18   5.3e+02      18      33 ..     110     126 ..     109     131 .. 0.77
   3 ?    3.3   0.1     0.029        85       2      15 ..     191     204 ..     190     204 .. 0.88
   4 ?    0.1   0.0      0.29   8.7e+02       2      14 ..     273     286 ..     272     287 .. 0.75

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.055
                                   TEEEEEETTSE CS
                            PQQ  1 gvvylgsadGy 11
                                   gv+++gs+dG+
  gene561|gene561|rna561|rna561 62 GVIVCGSYDGN 72
                                   677888****8 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.18
                                    TT.CCEEEEEESSSCGS CS
                            PQQ  18 dT.GkvlWrfktggpvl 33 
                                    +T Gk +W+ k+++++ 
  gene561|gene561|rna561|rna561 110 STrGKTVWVCKLNDKIE 126
                                    577*****999988875 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.029
                                    EEEEEETTSEEEEE CS
                            PQQ   2 vvylgsadGylyAl 15 
                                    +++++s+dG++y +
  gene561|gene561|rna561|rna561 191 KLFVASNDGCIYVY 204
                                    689*********86 PP

  == domain 4  score: 0.1 bits;  conditional E-value: 0.29
                                    EEEEE.ETTSEEEE CS
                            PQQ   2 vvylg.sadGylyA 14 
                                    ++ ++ s+dG+l  
  gene561|gene561|rna561|rna561 273 NMLVTcSDDGCLKV 286
                                    666777*****986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (293 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       611  (0.0340789); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.53u 0.32s 00:00:00.85 Elapsed: 00:00:00.51
# Mc/sec: 1712.12
//
Query:       gene562|gene562|rna562|rna562  [L=78]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.082   12.9   2.0      0.094   12.7   2.0    1.1  1  Suf       Suppressor of forked protein (Suf)


Domain annotation for each model (and alignments):
>> Suf  Suppressor of forked protein (Suf)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   2.0   5.2e-06     0.094      64      98 ..      13      47 ..      10      58 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5.2e-06
                            Suf 64 KkFpedeefvlkYldyLislnddnnaRvlfekvvs 98
                                    k++  + f++k+  +L++ nd+++ R+lf++ + 
  gene562|gene562|rna562|rna562 13 NKYTATQFFLYKNFLFLMEKNDNKTKRALFQNGII 47
                                   68899999***********************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       577  (0.0321825); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.45
# Mc/sec: 519.53
//
Query:       gene563|gene563|rna563|rna563  [L=369]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    6.1e-31  107.7   0.1    8.4e-31  107.3   0.1    1.1  1  Pkinase      Protein kinase domain
    2.5e-15   56.5   0.0    3.7e-15   55.9   0.0    1.2  1  Pkinase_Tyr  Protein tyrosine kinase


Domain annotation for each model (and alignments):
>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.3   0.1   9.4e-35   8.4e-31      28     264 .]      77     303 ..      68     303 .. 0.89

  Alignments for each domain:
  == domain 1  score: 107.3 bits;  conditional E-value: 9.4e-35
                                    EEEEEECHCHCHHHH.HHHHHHHHHHHHHSCTTB--EEEEEEESSEEEEEEE--TTEBHHHHHHHHSS--HHHHHHHHHH CS
                        Pkinase  28 AvKkikkekakkkke.kkvlrEikilkklkhpnivrlyevfeekdelylvleyveggeladllerkgslseeeakkiakq 106
                                     v ++kk+k+ + ++ k + +E  + ++++h ++++++ +f++ +++y v+e++ gg ++ +l++++ ls++ea +++++
  gene563|gene563|rna563|rna563  77 MVRVMKKKKMVSYDKlKLLKQEFDVRRSVRHTFLINFICSFQDLKQVYYVTELALGGYFFYYLRDRKRLSSDEAAFYIAE 156
                                    56778888888877778899************************************************************ PP

                                    HHHHHHHHHHTTEE-SS-SGGGEEEETTTEEEE.-SGTTSEESSSSCSBCTTTSCGGGS-HHHHTTSCBSHHHHHHHHHH CS
                        Pkinase 107 ilegleylHskgiiHrDlKpeNiLidekgelKi.tDFGlakelessskltsfvgtseYlAPEvlkeneyskkvDvWslGv 185
                                    i+ +++ylH+k++++r l p+ i+++e+g++K+  DF      +++ +l++f    +Y++   +++ ++ + +D+W++Gv
  gene563|gene563|rna563|rna563 157 IIIAVQYLHRKKLLYRSLFPNTIMLSETGHIKLrLDF----LNKQGLELNDFENHIQYISIDYISGDSVRSDSDYWGIGV 232
                                    *********************************5588....3344445899***************************** PP

                                    HHHHHHHSS-STTTSSHHHHHHHHHHTHHHHHHHCTSHH...HHHTTS-HHHHHHHHHHT-SSGCCSTT.....HHHHHT CS
                        Pkinase 186 ilyelltgkppfsgekgkekvekeldqlekilkilgetkeklpeaseiseeakdllkkllkkdpkkRlt.....aeellq 260
                                    ilyelltg++pf    g++     +d+    ++il    + ++ +++++ +akdl+ +llk+++k+Rl+     a+ + +
  gene563|gene563|rna563|rna563 233 ILYELLTGCNPFL---GTN----FVDT---RYNIL---YKPIEFPDSFDLSAKDLILSLLKRNRKERLGympadAKLIRN 299
                                    *************...443....3333...22333...347999*************************88888888888 PP

                                    SGGG CS
                        Pkinase 261 hpyl 264
                                    hp++
  gene563|gene563|rna563|rna563 300 HPFF 303
                                    8887 PP

>> Pkinase_Tyr  Protein tyrosine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.9   0.0   4.1e-19   3.7e-15      32     214 ..      77     252 ..      58     290 .. 0.80

  Alignments for each domain:
  == domain 1  score: 55.9 bits;  conditional E-value: 4.1e-19
                                    EEEEESTTSS..HHHHHHHHHHHHHHHTS-BTTB--EEEEEESSSSEEEEEE--TTEBHHHHHHHTCTTTSBHHHHHHHH CS
                    Pkinase_Tyr  32 avKtlkeeat..eeekeelleeakimkklkhpnivkllgvctkeepllivteyvkgGdLlkfLrkkekekltlkdllsfa 109
                                    +v+++k++++   ++ + l +e ++ ++++h  +++++    + ++++ vte++ gG +  +Lr++  ++l+ ++   ++
  gene563|gene563|rna563|rna563  77 MVRVMKKKKMvsYDKLKLLKQEFDVRRSVRHTFLINFICSFQDLKQVYYVTELALGGYFFYYLRDR--KRLSSDEAAFYI 154
                                    566665544410344666777********************************************8..99********** PP

                                    HHHHHHHHHHHHTTEEEST-SGGGEEEEETTEEEE-.STTTHEETTTSSEEEETTSSTSGGGGS-HHHHHHSEEEHHHHH CS
                    Pkinase_Tyr 110 lqvAkGmeyLeskklvHrdlaarNvLlsenkvvkis.DfGLardiekddeyvkkeeaklpvkWmapEslkekkftsksDv 188
                                    +++  +++yL++kkl+ r l    ++lse+ ++k+  Df L ++        + ++ +  ++++++  ++  ++ s sD 
  gene563|gene563|rna563|rna563 155 AEIIIAVQYLHRKKLLYRSLFPNTIMLSETGHIKLRlDF-LNKQG------LELNDFENHIQYISIDYISGDSVRSDSDY 227
                                    **********************************96255.55555......567778889******************** PP

                                    HHHHHHHHHHHTTSSGTTTTSHHHHH CS
                    Pkinase_Tyr 189 WsfGvllwEiftlgespypglkneev 214
                                    W  Gv+l+E++t g +p+ g +  ++
  gene563|gene563|rna563|rna563 228 WGIGVILYELLT-GCNPFLGTNFVDT 252
                                    ************.8888877755544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (369 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       523  (0.0291706); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 2620.41
//
Query:       gene564|gene564|rna564|rna564  [L=225]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (225 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       545  (0.0303977); expected 358.6 (0.02)
Passed bias filter:                      249  (0.0138881); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1612.01
//
Query:       gene565|gene565|rna565|rna565  [L=745]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (745 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       879  (0.0490267); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.64u 0.32s 00:00:00.96 Elapsed: 00:00:00.48
# Mc/sec: 4633.62
//
Query:       gene566|gene566|rna566|rna566  [L=305]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0087   16.2   0.6      0.033   14.3   0.1    2.2  2  DUF3911   Protein of unknown function (DUF3911)


Domain annotation for each model (and alignments):
>> DUF3911  Protein of unknown function (DUF3911)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.1   1.9e-06     0.033      13      68 ..      62     120 ..      56     125 .. 0.88
   2 ?   -1.8   0.1      0.19   3.4e+03      28      41 ..     195     209 ..     188     235 .. 0.57

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.9e-06
                        DUF3911  13 vvemlqlfdlmdtkGfckfknyveve...anetkhnefvasidlqanessaqdtlndql 68 
                                      +ml   + +dt  fck  n  e++   a+++++++++ s d  ++e++a d++ d +
  gene566|gene566|rna566|rna566  62 RTQMLSRINDIDTCPFCKCGNRKEINdsdAEDHENEQLLGSGDKATKETEAMDKVRDDI 120
                                    56899999****************9865577888999*****************99975 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.19
                        DUF3911  28 fckfknyveve.ane 41 
                                     +kf+   e e a++
  gene566|gene566|rna566|rna566 195 SSKFNHVFEAElAQD 209
                                    567777666663333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (305 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       764  (0.0426125); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 2064.81
//
Query:       gene567|gene567|rna567|rna567  [L=1039]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
   8.3e-142  473.5   0.3      2e-96  323.7   0.0    2.4  2  tRNA-synt_2c  tRNA synthetases class II (A)
    5.7e-09   35.9   0.8    1.5e-08   34.5   0.8    1.8  1  tRNA_SAD      Threonyl and Alanyl tRNA synthetase second addi


Domain annotation for each model (and alignments):
>> tRNA-synt_2c  tRNA synthetases class II (A)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  323.7   0.0  2.2e-100     2e-96       2     254 ..      10     265 ..       9     281 .. 0.94
   2 !  147.2   0.3   6.4e-47   5.8e-43     263     533 ..     359     620 ..     328     627 .. 0.84

  Alignments for each domain:
  == domain 1  score: 323.7 bits;  conditional E-value: 2.2e-100
                                    HHHHHHHHHHCTT-EEE----SS-SSSTTCSS--SGGGGGHHHHTTSS.CGGSSSEEEEEEEEE-EETTEEGGGGTTTSS CS
                   tRNA-synt_2c   2 irekFldfFekkgHtvvksssvvpendptllfvnAgmaqfkpiflgke.akpklkravnsQkciRagGkhnDlenVGkta 80 
                                    +r +Fl++F+k+gHt+v+sssv+p+ndptllfvn+gm+qfk +fl++  + + lkra+++Q+ciRagGkhnDle+VG ++
  gene567|gene567|rna567|rna567  10 LRTAFLEYFQKNGHTIVESSSVLPHNDPTLLFVNSGMVQFKSMFLNQPcQFTGLKRAASIQRCIRAGGKHNDLEDVGFDT 89 
                                    799********************************************98999**************************** PP

                                    S--SEEEEEEEEESSSS-HHHHHHHHHHHHHTTTT--GGGEEEEEETTEH..........HHHHHHHHTTTTEGGGEEEE CS
                   tRNA-synt_2c  81 rHhTfFeMlGnfsfgdYfkeeaiefawelltkelgldkerlyvtvfeedd..........eaveiweklvgvpeerilrf 150
                                    +HhTfFeM+Gn+sfgdY ke ai +a+ +lt+el ld +r+yv+++  ++          e++ iw+k+  +pe+ril+f
  gene567|gene567|rna567|rna567  90 YHHTFFEMMGNWSFGDYGKEHAIDLAFRFLTEELRLDSSRMYVSYYVPENdgvaglhadqETRTIWRKY--LPETRILPF 167
                                    ********************************************99665557*****************..7******** PP

                                    -HHHHEEESSSSEEEEEEEEEEEECETTSHHCHCCCCTTCTCCHEEEEEEEEEEEEEESTTSHEEEEEEEEEEEEEEHHH CS
                   tRNA-synt_2c 151 gekdnfwemgdtgpcgpcseiyydrgeeigkrkaaseveadddrvleiwnlvfmqfnreedgtlkpLpkksidtGmgler 230
                                     +++nfwemgdtgpcgpc+ei+yd     g++ + ++v++dd+ ++eiwnlvfmqf r+e+g+l+pL + s+dtGmg+er
  gene567|gene567|rna567|rna567 168 -TAENFWEMGDTGPCGPCTEIHYDL---TGTHGP-EHVNTDDPACIEIWNLVFMQFYRDEQGVLSPLDALSVDTGMGMER 242
                                    .999*********************...444334.55566**************************************** PP

                                    HHHHHTTHSSGGGSCCTHHHHHHH CS
                   tRNA-synt_2c 231 lvavLqevrsnydtdlfvpvieai 254
                                    +  +L+  ++ny tdlf+p++e +
  gene567|gene567|rna567|rna567 243 VLGILNG-TTNYGTDLFMPLFEMT 265
                                    *****87.579**********976 PP

  == domain 2  score: 147.2 bits;  conditional E-value: 6.4e-47
                                    CSTCCHHHHHHHHHHHHHHHHHHHHTT--SSSSHHHHHHHHHHHHHHHHHHHTT-SSTHHHHHHHHHHHHHTTTGCCHHC CS
                   tRNA-synt_2c 263 edkdetdealrviaDHvralafaladGvvpsnegrgYvlRrllRravrhakkLglkekflaklvavvvevlgdvypelke 342
                                    +++ + ++a r+iaDH+r++a+ l  Gv +s eg+gYvlRr+ Rr +r ++  ++++     lv+  +++lg   + l++
  gene567|gene567|rna567|rna567 359 TNNFSDSVAQRIIADHARTIAVCLFYGVEFSSEGAGYVLRRITRRMIRVLHSKNVHDL--PALVHKAAQILG---TPLTD 433
                                    4566778999****************************************99998875..899999999999...45554 PP

                                    CHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHCCCCSEEXHHHHHHHHHCHXXXHHHHHHHHHCTTXEEXHHHHHHHHH CS
                   tRNA-synt_2c 343 keekveeiieeEeerFakTlerGlklleelikklkkkkelsgedafkLydtyGfPvdltkeiaeekglkvdiegfekame 422
                                    ++   +  + +E + F+kTl++G k++++         ++  +++f L dtyGfP dlt+++++ekg+ vd ++ +++ e
  gene567|gene567|rna567|rna567 434 QQ---MAQLAHEHALFKKTLAQGVKYFNQFG-------TITAKEMFILKDTYGFPFDLTAQMCREKGIVVDRDELRRLVE 503
                                    44...56899*****************9875.......58899************************************* PP

                                    HHHHHHCCHHSXSSXXXXXXXXTTSHCHHCCTSTTTXXXXXXTSXXXXXXSEEE..EEEEEEETTEEEESEEXXXXSSSS CS
                   tRNA-synt_2c 423 eqrerskkekkekklikkdvealkelkkteeflgyeeleaeakvlallkdkefv..eeveegeevgvvLdrTpfYaesGG 500
                                    +  +rsk+ k ++    ++     e+ +t efl+ ++++ e++ l  ++++ +v  +e+ e  + g+v drT+fY+e+GG
  gene567|gene567|rna567|rna567 504 QGVRRSKARKGARI--GVKRAWAVEHARTAEFLQRDYAHFESTALFAFDEDAIVplDELRERMKIGLVADRTCFYSEKGG 581
                                    ******77766655..566666667777888899888888888888888888764479999999**************** PP

                                    CSXXXEEEEESS......EEEEESEEEEETTEEEEEXSS CS
                   tRNA-synt_2c 501 qigDeGliekeg......aefrvkdvqkakgvvlhkgkl 533
                                    q gD+G+i+  +       ++ v+d+ k +++v+h g +
  gene567|gene567|rna567|rna567 582 QVGDTGVISFLDehgrvvRTMSVCDTYKSGEYVVHYGVI 620
                                    ******77644434477778999************9876 PP

>> tRNA_SAD  Threonyl and Alanyl tRNA synthetase second additional domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.5   0.8   1.7e-12   1.5e-08       1      43 [.     842     883 ..     842     884 .. 0.97

  Alignments for each domain:
  == domain 1  score: 34.5 bits;  conditional E-value: 1.7e-12
                                    EEEEEETT.EEEEESS---SBGGGC-SEEEECCECCCTCEEEE CS
                       tRNA_SAD   1 vrvvsiGdisvelCgGtHvpnTgeIgafkilseesiakglrRI 43 
                                    vr+v+ G    elCgG Hv+   +I+ fki+se +i+++ rRI
  gene567|gene567|rna567|rna567 842 VRIVDAGG-ARELCGGLHVRMLAHIRCFKIVSEGAISANTRRI 883
                                    89*****8.9********************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1039 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1149  (0.0640861); expected 358.6 (0.02)
Passed bias filter:                      619  (0.0345251); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.77u 0.34s 00:00:01.11 Elapsed: 00:00:00.51
# Mc/sec: 6087.58
//
Query:       gene568|gene568|rna568|rna568  [L=389]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (389 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       853  (0.0475766); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 2528.65
//
Query:       gene569|gene569|rna569|rna569  [L=119]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    9.7e-13   47.8   0.1    1.4e-12   47.3   0.1    1.3  1  RNA_pol_Rpb6  RNA polymerase Rpb6


Domain annotation for each model (and alignments):
>> RNA_pol_Rpb6  RNA polymerase Rpb6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.3   0.1   7.8e-17   1.4e-12       1      49 []      31      84 ..      31      84 .. 0.94

  Alignments for each domain:
  == domain 1  score: 47.3 bits;  conditional E-value: 7.8e-17
                                   HHTTSS--HHHHHHHHHHHHHHH....HT........S.S-SSSSTTCHHHHTT-S-- CS
                   RNA_pol_Rpb6  1 rltskvltrYelvriaakRArQieegesl........e.tqkpvviAlrEiaegkipi 49
                                   r ts+ +t+Ye++ri++ RA Q+    s+        e +++ + iA++E ++ kip+
  gene569|gene569|rna569|rna569 31 RVTSPLMTKYEKTRIIGMRAMQL----SMnapplveiEaETDALRIAEKEFYARKIPF 84
                                   5699*******************....99999999997779****************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       346  (0.0192983); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.42
# Mc/sec: 842.05
//
Query:       gene57|gene57|rna57|rna57  [L=57]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (57 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       367  (0.0204696); expected 358.6 (0.02)
Passed bias filter:                      221  (0.0123264); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 406.60
//
Query:       gene570|gene570|rna570|rna570  [L=58]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.13   12.1   0.0       0.16   11.8   0.0    1.2  1  Pox_E10   E10-like protein conserved region


Domain annotation for each model (and alignments):
>> Pox_E10  E10-like protein conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   9.1e-06      0.16      40      53 ..      40      53 ..      27      58 .] 0.79

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 9.1e-06
                        Pox_E10 40 lNyiyfFfislfNn 53
                                    N iyf fi++fN 
  gene570|gene570|rna570|rna570 40 GNLIYFVFITFFNT 53
                                   599**********7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (58 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       294  (0.016398); expected 358.6 (0.02)
Passed bias filter:                      217  (0.0121033); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.41
# Mc/sec: 427.07
//
Query:       gene571|gene571|rna571|rna571  [L=906]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   6.9e-146  487.4  63.4    6.3e-88  295.7  15.4    6.1  5  V_ATPase_I      V-type ATPase 116kDa subunit family


Domain annotation for each model (and alignments):
>> V_ATPase_I  V-type ATPase 116kDa subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   0.3   1.1e-10     2e-06       2      99 ..      26     124 ..      25     134 .. 0.82
   2 !   61.4   6.5   2.4e-21   4.3e-17     157     333 ..     130     312 ..     119     327 .. 0.90
   3 ?   -8.6  10.0         1   1.8e+04     653     681 ..     448     475 ..     418     499 .. 0.32
   4 !  295.7  15.4   3.5e-92   6.3e-88     320     640 ..     505     791 ..     500     793 .. 0.92
   5 !  136.1   1.9     6e-44   1.1e-39     693     813 .]     788     900 ..     786     900 .. 0.95

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 1.1e-10
                     V_ATPase_I   2 eLGelglvqfrDlnedvnafqrkfvkevrrcdemerklrfleeeieklekavikeeea..eesleapeekeldeleeele 79 
                                    eLG+l+l+qf+Dln+++++ +  + ke+ +++++  k++fl  eie +e   + ++e+  +e+  +++ ++l el++  +
  gene571|gene571|rna571|rna571  26 ELGKLKLIQFIDLNTHLKNEHLPYNKEILHYEKLRSKINFLMGEIEAYELD-VPCTEHvfDEDAVERHFNRLLELKAIRD 104
                                    8**********************************************6555.4555543555666666778888999999 PP

                     V_ATPase_I  80 kleeelkelnenleklkkel 99 
                                     ++e+l++lnenl  l++ +
  gene571|gene571|rna571|rna571 105 GAQEQLTNLNENLFILEEMK 124
                                    99999999999987776654 PP

  == domain 2  score: 61.4 bits;  conditional E-value: 2.4e-21
                     V_ATPase_I 157 elsfvaGvikrekveaferilwralrgnlflrqaeieepledpetgekveksvfiiffqgeqlkekikkicesfgaklye 236
                                    + s ++G+i+++kv  ++ril  +l+ nl+++ ++               ++vf+if++ge+  ekikkic sf+a+++ 
  gene571|gene571|rna571|rna571 130 ASSCLTGIIDNDKVLLLRRILESVLKNNLVVHVKTGR-------------RTVFVIFTHGEEAFEKIKKICVSFNARIFM 196
                                    35789*************************9886654.............59**************************** PP

                     V_ATPase_I 237 lpeseeereeklkeveeriedle......................kvleqteealkevleeiakeleewklkvkkekaiy 294
                                    +++++e+  e+ +  +er +d +                      +v  ++e++++++l++ia+++++w+ k +++  i 
  gene571|gene571|rna571|rna571 197 MKNEAERSVEEENAQDERAQDQKdepedenqtnilrvtaliqqyqHVYANNENSIRSELSTIAQHIYTWRYKTRQMLRIL 276
                                    ***99999999999999999999999******************99********************************** PP

                     V_ATPase_I 295 htLnlfnldvtkkvliaegWvpkeeleeiqkalkeatee 333
                                    +tLn +   ++++ +i+eg+vp+++    q+a++ + ++
  gene571|gene571|rna571|rna571 277 KTLNRL---RESTAFIGEGYVPESKFAVFQSAVNAICDA 312
                                    ******...56789**************99999887654 PP

  == domain 3  score: -8.6 bits;  conditional E-value: 1
                     V_ATPase_I 653 eeeeeeeeeeeeeeeeaeeeeeeeeeeee 681
                                    +ee+ ee++++++e+ ++ ++ e+++ ++
  gene571|gene571|rna571|rna571 448 KEESVEESTRRRKERPNKMKN-EDKKIKD 475
                                    111111111111111111111.1111111 PP

  == domain 4  score: 295.7 bits;  conditional E-value: 3.5e-92
                     V_ATPase_I 320 leeiqkalkeateessssvpsilneietketpPTyfrtnkfteafQeivdaYGiarYrEvNpalftiitFPFlFavMFGD 399
                                     ++++++++++ ++++++     ++++++e+pPT+f+tn ft+ fQe+ d YG+++YrE+Npa+fti+tFPFlF+ MFGD
  gene571|gene571|rna571|rna571 505 NSSLSNSMEDIRAAREQNED---HKMNEHEMPPTFFKTNIFTRPFQEMNDVYGVPSYREINPAPFTIVTFPFLFGAMFGD 581
                                    55566666666644433333...45666789************************************************* PP

                     V_ATPase_I 400 iGHGlllllfalllvlkekklkkkkkdeilemlfsgRYiillmGlfsiYtGliYNdifskslnlfgSswevkekaveeee 479
                                    +GHGl+l+l+a++++++    ++    e++em+++gRY++l  G+ s+Y Gl+Y ++f+++l lf+ +  +         
  gene571|gene571|rna571|rna571 582 VGHGLILVLIAVAFIMRPGLARA---HEMVEMVVNGRYMLLACGVASMYFGLLYSECFGVALPLFKFGGVT--------- 649
                                    ***************98876555...59************************************9855444......... PP

                     V_ATPase_I 480 lkkekkeekvYpfGlDpaWklaenellflnSlKmKlsvilGviqMlfgvllslvNalyfkkkldiilefiPqllfllsif 559
                                                fG+Dp W+ a+n ++ +nSlKmK+sv++G ++M +g+ l ++N+l   ++l ++++++P++l + ++ 
  gene571|gene571|rna571|rna571 650 -----------YFGVDPSWHEARNGMNLMNSLKMKMSVVIGTLHMGLGLGLAAFNTLLSGDTLLFYCKVLPRILSFACFA 718
                                    ...........4******************************************************************** PP

                     V_ATPase_I 560 gYlvlliiyKWlvdweaekekapsllntlinmflskgkvkeeelyegqetvqvvLlllalvcvpvlllvkPlilklkhkk 639
                                    gYl++li++KW+  +      +ps++nt++ m+  + k   e +y+gq++vq ++l l+ +c+p+++   Pl+l ++h++
  gene571|gene571|rna571|rna571 719 GYLSVLIVIKWIRPF------KPSIINTIVLMYTDPFKA--ELFYPGQQYVQLFMLALFAMCMPWMMASYPLMLFVRHRR 790
                                    **************9......6***************98..68**********************************998 PP

                     V_ATPase_I 640 k 640
                                    k
  gene571|gene571|rna571|rna571 791 K 791
                                    6 PP

  == domain 5  score: 136.1 bits;  conditional E-value: 6e-44
                     V_ATPase_I 693 eeefdfgevfihqvIhtIEfvLgciSnTASYLRLWALSLAHaqLseVlwemvlkkallksksvlgvillvilfavfavlt 772
                                    ++++++++v+ih  I++IEf +g iSn +SYLR+WA+SLAH+qL  ++++ ++ ++        +v+l +++  v++++t
  gene571|gene571|rna571|rna571 788 HRRKNLSDVIIHFGIEAIEFNIGLISNISSYLRIWAVSLAHSQLTGIIHKYTMGSS--------SVLLRIVTAPVWLAAT 859
                                    67889************************************************992........3677788999****** PP

                     V_ATPase_I 773 vavLllmeglsafLHaLRLhWVEfqsKFykgdGykFepfsf 813
                                    ++ ++ +egls+ LHa+RL+W+Ef+sKFy g+G +Fep++f
  gene571|gene571|rna571|rna571 860 MVLMVALEGLSSSLHAMRLNWIEFNSKFYDGQGNAFEPLNF 900
                                    ***************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (906 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1876  (0.104635); expected 358.6 (0.02)
Passed bias filter:                      525  (0.0292822); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.89u 0.28s 00:00:01.17 Elapsed: 00:00:00.51
# Mc/sec: 5343.95
//
Query:       gene572|gene572|rna572|rna572  [L=85]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.11   12.8   0.0       0.13   12.5   0.0    1.1  1  DUF5056   Domain of unknown function (DUF5056)


Domain annotation for each model (and alignments):
>> DUF5056  Domain of unknown function (DUF5056)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   7.4e-06      0.13      27      77 ..      24      74 ..      18      83 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 7.4e-06
                        DUF5056 27 rrlPerskrlariwtavcavlavvLFvvldGlelllevlrevftsaiqsla 77
                                   rr+P   +   r+    + v ++ +Fv  dG+   ++vlr+++ + +++  
  gene572|gene572|rna572|rna572 24 RRMPFSLEEYFRMHGESVRVTCCCMFVGGDGIVKEMSVLRNIIDEYFTEYH 74
                                   6788888888899999999************************99988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (85 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       326  (0.0181828); expected 358.6 (0.02)
Passed bias filter:                      250  (0.0139439); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.30s 00:00:00.71 Elapsed: 00:00:00.47
# Mc/sec: 542.68
//
Query:       gene573|gene573|rna573|rna573  [L=65]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (65 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       210  (0.0117129); expected 358.6 (0.02)
Passed bias filter:                      185  (0.0103185); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.42
# Mc/sec: 464.38
//
Query:       gene574|gene574|rna574|rna574  [L=426]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.5e-26   91.0  27.3    7.9e-07   29.7   0.2    6.4  6  WD40         WD domain, G-beta repeat
    5.9e-07   29.1   0.1    8.3e-05   22.1   0.0    2.4  2  WD40_like    WD40-like domain
      9e-06   25.9   1.1          6    7.2   0.0    4.5  4  ANAPC4_WD40  Anaphase-promoting complex subunit 4 WD40 domain
    0.00033   20.7   0.2        4.7    7.3   0.1    4.4  5  BBS2_Mid     Ciliary BBSome complex subunit 2, middle region
  ------ inclusion threshold ------
      0.041   13.8   0.4       0.81    9.7   0.0    2.7  2  DUF2415      Uncharacterised protein domain (DUF2415)
      0.049   12.6   0.2        5.5    5.8   0.0    2.9  3  PALB2_WD40   Partner and localizer of BRCA2 WD40 domain
      0.049   13.4   0.0        4.7    7.1   0.0    2.6  2  NifZ         NifZ domain
       0.25    9.9   3.4         16    4.0   0.1    3.5  4  Nup160       Nucleoporin Nup120/160


Domain annotation for each model (and alignments):
>> WD40  WD domain, G-beta repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   0.0   0.00025      0.56       7      38 .]     108     138 ..      98     138 .. 0.77
   2 !   21.8   1.8   1.1e-07   0.00024       2      38 .]     142     177 ..     141     177 .. 0.84
   3 !   29.7   0.2   3.5e-10   7.9e-07       1      38 []     181     217 ..     181     217 .. 0.93
   4 !   28.6   0.9   7.9e-10   1.8e-06       2      38 .]     221     256 ..     220     256 .. 0.90
   5 ?   -0.1   0.0      0.92   2.1e+03       7      35 ..     266     293 ..     260     294 .. 0.57
   6 !   14.5   0.5   2.2e-05     0.049       2      38 .]     300     342 ..     299     342 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00025
                                    EESSSS.EEEEEEETTSSEEEEEETTSEEEEEE CS
                           WD40   7 ltGHss.vtslafspdgawlasGsdDgtvriWd 38 
                                    +++ ++ +t++  + + ++++ +sdD++++i+d
  gene574|gene574|rna574|rna574 108 FSTNQPdITHV--QCNDRYIVVSSDDQSIKIFD 138
                                    55553359999..888999998999******98 PP

  == domain 2  score: 21.8 bits;  conditional E-value: 1.1e-07
                                    EEEEEEESS.SSEEEEEEETTSSE....EEEEETTSEEEEEE CS
                           WD40   2 qclrtltGH.ssvtslafspdgaw....lasGsdDgtvriWd 38 
                                    ++ r l GH ++v+ +      +w    ++sGs D+++r+Wd
  gene574|gene574|rna574|rna574 142 NLRRNLVGHfGGVWTF------QWhkdvIVSGSTDKSIRVWD 177
                                    5678899**888**99......77666578***********9 PP

  == domain 3  score: 29.7 bits;  conditional E-value: 3.5e-10
                                    TEEEEEEESS.SSEEEEEEETTSSEEEEEETTSEEEEEE CS
                           WD40   1 gqclrtltGH.ssvtslafspdgawlasGsdDgtvriWd 38 
                                    g++lr+l+GH s v++l    ++++++sG +D tv++W+
  gene574|gene574|rna574|rna574 181 GWPLRHLKGHrSTVRCL--RVYKDYIVSGARDSTVKVWN 217
                                    679*******999****..77999999***********8 PP

  == domain 4  score: 28.6 bits;  conditional E-value: 7.9e-10
                                    EEEEEEESS.SSEEEEEEETTSSEEEEEETTSEEEEEE CS
                           WD40   2 qclrtltGH.ssvtslafspdgawlasGsdDgtvriWd 38 
                                     +l+tl+GH  sv+++  +  +++l+sGs+Dgtv +Wd
  gene574|gene574|rna574|rna574 221 VLLHTLRGHgESVRCI--DVCHTMLVSGSYDGTVILWD 256
                                    579******888****..777888*************9 PP

  == domain 5  score: -0.1 bits;  conditional E-value: 0.92
                                    EESS.SSEEEEEEETTSSEEEEEETTSEEE CS
                           WD40   7 ltGH.ssvtslafspdgawlasGsdDgtvr 35 
                                    l+ H   v+++      + ++sG+ D  ++
  gene574|gene574|rna574|rna574 266 LKSHlLRVYAV--LIGRNHIISGGQDTFIH 293
                                    55565445555..22223367899998776 PP

  == domain 6  score: 14.5 bits;  conditional E-value: 2.2e-05
                                    EEEEEEESS.SS..........EEEEEEETTSSEEEEEETTSEEEEEE CS
                           WD40   2 qclrtltGH.ss..........vtslafspdgawlasGsdDgtvriWd 38 
                                    q ++tl +H s           v  +      ++l+s++ Dg++ iWd
  gene574|gene574|rna574|rna574 300 QFVTTLHAHrSIvawleltsdpVQRI-----DHLLVSAGADGHICIWD 342
                                    56777777854433344444444444.....222677777*******9 PP

>> WD40_like  WD40-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   3.7e-08   8.3e-05     110     298 ..     101     291 ..      96     294 .. 0.84
   2 !    4.6   0.0    0.0079        18      53     132 ..     326     405 ..     309     415 .. 0.73

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 3.7e-08
                      WD40_like 110 dlqleevllgqsseIkeikiennkiysLsesafi.vfdlfsq.nieykisvkdiktfeiienkdilligtegeililkkn 187
                                     +++++v++  + +I +++ ++ +i   s+++ i +fd++++ + +   ++ ++ tf+    kd+++ g  ++++ +  +
  gene574|gene574|rna574|rna574 101 HMESRTVFSTNQPDITHVQCNDRYIVVSSDDQSIkIFDVDGNlRRNLVGHFGGVWTFQWH--KDVIVSGSTDKSIRVW-D 177
                                    567889*******************999999888579**985245566788999999998..9999888777665433.3 PP

                      WD40_like 188 vi....lqkidv.egkPecillvddylivGgsfkyllliNiklnvntfklrlevegiskikkisefvvafsTlcgkvgig 262
                                    ++    l++++   ++  c+ + +dy+++G+  + +++ N++  v  ++lr + e ++ i   ++ +++   ++g+v + 
  gene574|gene574|rna574|rna574 178 FVtgwpLRHLKGhRSTVRCLRVYKDYIVSGARDSTVKVWNMD-GVLLHTLRGHGESVRCIDV-CHTMLVSGSYDGTVILW 255
                                    332333777764145679************************.99999**********9987.888888899******** PP

                      WD40_like 263 DiRdketfkllesgvGviydmkfenntiyvgGeaGl 298
                                    D  ++  ++ l+s++  +y + + +n i+ gG+  +
  gene574|gene574|rna574|rna574 256 DYPKGTMVRRLKSHLLRVYAVLIGRNHIISGGQDTF 291
                                    ********************************9877 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.0079
                      WD40_like  53 ddlilvvtlDGtillslleneeevenekiee.distvkviddklliGtn.kGsiyvfskdlqleevllgqsseIkeikie 130
                                    d+l++ +  DG i   +l+ +   +++ +e   i+t+   ++ l +G + + ++y +  d q++ +l+   s + ++  +
  gene574|gene574|rna574|rna574 326 DHLLVSAGADGHICIWDLRTGT-LRSKIVESmPITTIALKNECLFVGVHsRVKVYDLR-DAQFKRTLIDNLSSVYKVYCT 403
                                    4566667899999888888887.44444443269999999999999975134455444.558888888888888877766 PP

                      WD40_like 131 nn 132
                                    ++
  gene574|gene574|rna574|rna574 404 ES 405
                                    55 PP

>> ANAPC4_WD40  Anaphase-promoting complex subunit 4 WD40 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0      0.11   2.5e+02      47      68 ..     119     140 ..     106     161 .. 0.84
   2 ?    4.9   0.0     0.015        33      44      88 ..     157     198 ..     149     202 .. 0.86
   3 !    7.2   0.0    0.0027         6      23      79 ..     209     269 ..     199     281 .. 0.78
   4 !    7.1   0.0    0.0031       6.9      49      79 ..     325     355 ..     287     366 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.11
                    ANAPC4_WD40  47 kpdgklLavaysdgevrlldae 68 
                                    + +++ ++v+ +d +++++d+ 
  gene574|gene574|rna574|rna574 119 QCNDRYIVVSSDDQSIKIFDVD 140
                                    568999*************985 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.015
                    ANAPC4_WD40  44 LaWkpdgklLavaysdgevrlldaesgkvvhslsvksekavtclg 88 
                                    ++W++   +++ +  d ++r+ d  +g  +++l+ +++ +v cl 
  gene574|gene574|rna574|rna574 157 FQWHK--DVIVSGSTDKSIRVWDFVTGWPLRHLKGHRS-TVRCLR 198
                                    55655..599************************9999.599985 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.0027
                    ANAPC4_WD40  23 Rlngqrvwtl......eedkedsevrsLaWkpdgklLavaysdgevrlldaesgkvvhslsvk 79 
                                    R +  +vw++      +  +++++vr++      ++L+ +  dg+v l d  +g++v+ l+ +
  gene574|gene574|rna574|rna574 209 RDSTVKVWNMdgvllhTLRGHGESVRCID--VCHTMLVSGSYDGTVILWDYPKGTMVRRLKSH 269
                                    45555666666666666688899999886..5778**********************999876 PP

  == domain 4  score: 7.1 bits;  conditional E-value: 0.0031
                    ANAPC4_WD40  49 dgklLavaysdgevrlldaesgkvvhslsvk 79 
                                     ++lL+ a +dg++ + d  +g++ +++  +
  gene574|gene574|rna574|rna574 325 IDHLLVSAGADGHICIWDLRTGTLRSKIVES 355
                                    489*******************999887444 PP

>> BBS2_Mid  Ciliary BBSome complex subunit 2, middle region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.3   0.1    0.0021       4.7      11      30 ..     121     140 ..     114     147 .. 0.83
   2 ?    1.5   0.0      0.13     3e+02      12      28 ..     161     177 ..     154     182 .. 0.83
   3 ?    4.6   0.0     0.015        33      12      66 ..     201     256 ..     193     278 .. 0.85
   4 ?    0.4   0.0      0.28   6.4e+02      11      50 ..     279     319 ..     270     366 .. 0.78
   5 ?   -0.6   0.0      0.61   1.4e+03      17      68 ..     331     382 ..     321     413 .. 0.64

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0021
                       BBS2_Mid  11 geneLvvgsddfeirvfkee 30 
                                    +++++vv+sdd++i++f+ +
  gene574|gene574|rna574|rna574 121 NDRYIVVSSDDQSIKIFDVD 140
                                    4689*************876 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.13
                       BBS2_Mid  12 eneLvvgsddfeirvfk 28 
                                    ++ +v gs+d +irv++
  gene574|gene574|rna574|rna574 161 KDVIVSGSTDKSIRVWD 177
                                    567899********985 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.015
                       BBS2_Mid  12 eneLvvgsddfeirvfkee.elvaeitetekvvslarlekerfayaleNGtvgvye 66 
                                    ++++v g+ d +++v++ +  l+++++ + + v  +++ ++ ++ +   Gtv +++
  gene574|gene574|rna574|rna574 201 KDYIVSGARDSTVKVWNMDgVLLHTLRGHGESVRCIDVCHTMLVSGSYDGTVILWD 256
                                    5799*************994667899999999999**********99999998876 PP

  == domain 4  score: 0.4 bits;  conditional E-value: 0.28
                       BBS2_Mid  11 geneLvvgsddfeirvfkee.elvaeitetekvvslarlek 50 
                                    g+n+++ g +d  i v + + + v++++ +  +v+  +l++
  gene574|gene574|rna574|rna574 279 GRNHIISGGQDTFIHVSDMKgQFVTTLHAHRSIVAWLELTS 319
                                    67999999999999998755488888888888888777765 PP

  == domain 5  score: -0.6 bits;  conditional E-value: 0.61
                       BBS2_Mid  17 vgsddfeirvf..keeelvaeitetekvvslarlekerfayaleNGtvgvyekk 68 
                                     +  d +i ++  + ++l ++i e+  ++  ++l++e++ ++++   v+vy+ +
  gene574|gene574|rna574|rna574 331 SAGADGHICIWdlRTGTLRSKIVESMPIT-TIALKNECLFVGVHS-RVKVYDLR 382
                                    45566655554114556666666655444.456888888888864.67777755 PP

>> DUF2415  Uncharacterised protein domain (DUF2415)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0   0.00036      0.81      15      41 ..     326     352 ..     321     354 .. 0.81
   2 ?    0.9   0.1       0.2   4.5e+02      25      34 ..     374     383 ..     372     391 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00036
                        DUF2415  15 nDLLvisEhvgrvHlvDlRtgldehqV 41 
                                    + LLv +   g++++ DlRtg+ +  +
  gene574|gene574|rna574|rna574 326 DHLLVSAGADGHICIWDLRTGTLRSKI 352
                                    579999999***********9877655 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.2
                        DUF2415  25 grvHlvDlRt 34 
                                    +rv + DlR 
  gene574|gene574|rna574|rna574 374 SRVKVYDLRD 383
                                    8********5 PP

>> PALB2_WD40  Partner and localizer of BRCA2 WD40 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0     0.017        37     188     233 ..     159     202 ..     153     205 .. 0.81
   2 ?   -0.9   0.0      0.26   5.9e+02     190     222 ..     201     233 ..     197     247 .. 0.72
   3 ?    5.8   0.0    0.0024       5.5     186     216 ..     322     352 ..     293     368 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.017
                     PALB2_WD40 188 GekdallgttvlnniviWnlktGqllkkieigesyqasvclkaysd 233
                                      kd +++ +++++i +W+  tG  l++++   s  +  cl+ y d
  gene574|gene574|rna574|rna574 159 WHKDVIVSGSTDKSIRVWDFVTGWPLRHLKGHRS--TVRCLRVYKD 202
                                    57899*******************9998875444..5567777766 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.26
                     PALB2_WD40 190 kdallgttvlnniviWnlktGqllkkie.igesy 222
                                    kd +++ + ++ + +Wn+  G ll++++  ges+
  gene574|gene574|rna574|rna574 201 KDYIVSGARDSTVKVWNMD-GVLLHTLRgHGESV 233
                                    788999999999*****86.88888875234554 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.0024
                     PALB2_WD40 186 veGekdallgttvlnniviWnlktGqllkki 216
                                    v+ +   l+++ ++ +i iW+l+tG l +ki
  gene574|gene574|rna574|rna574 322 VQRIDHLLVSAGADGHICIWDLRTGTLRSKI 352
                                    77778889999***************98887 PP

>> NifZ  NifZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0     0.029        65      23      41 ..     321     339 ..     318     373 .. 0.88
   2 ?    7.1   0.0    0.0021       4.7      51      68 ..     396     413 ..     389     417 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.029
                           NifZ  23 pgkeigelLvkkGdvGvvv 41 
                                    p ++i++lLv +G  G+++
  gene574|gene574|rna574|rna574 321 PVQRIDHLLVSAGADGHIC 339
                                    67899***********996 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0021
                           NifZ  51 eiYlVeFleeglvVGcle 68 
                                     +Y+V   e+++vVGc++
  gene574|gene574|rna574|rna574 396 SVYKVYCTESRVVVGCKR 413
                                    79**************86 PP

>> Nup160  Nucleoporin Nup120/160
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0      0.45     1e+03     149     248 ..     112     140 ..      97     149 .. 0.51
   2 ?    2.4   0.1     0.022        49     229     254 ..     160     185 ..     153     190 .. 0.85
   3 ?    4.0   0.1     0.007        16     222     248 ..     193     219 ..     188     223 .. 0.89
   4 ?    1.8   0.0     0.032        72     226     348 ..     236     387 ..     232     398 .. 0.58

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.45
                                    -EEEE.EE-SSSEEEEEETTS-EEEEEEETTEEEEEEEEE-------B--TTTT.TSS--SS---TT-ECEEEEET.... CS
                         Nup160 149 kpgrl.aavssnellvsladggllklkrdedggawkesvfepksfllslsgllglladpsrrksgasvalsldvavavve 227
                                    +p    +  +   ++vs++d  + +++                                                     
  gene574|gene574|rna574|rna574 112 QPDIThVQCNDRYIVVSSDDQSIKIFDV---------------------------------------------------- 139
                                    3332223344445555555555555554.................................................... PP

                                    .TTTEEEEEETT-EEEEEETT CS
                         Nup160 228 igqtylfalsrdgkLrvWnll 248
                                                        +
  gene574|gene574|rna574|rna574 140 --------------------D 140
                                    ....................4 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.022
                                    TTTEEEEEETT-EEEEEETTTTEEEE CS
                         Nup160 229 gqtylfalsrdgkLrvWnlltgkcla 254
                                    +++++++ s d+ +rvW+  tg +l+
  gene574|gene574|rna574|rna574 160 HKDVIVSGSTDKSIRVWDFVTGWPLR 185
                                    7899999************9997766 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.007
                                    ET.....TTTEEEEEETT-EEEEEETT CS
                         Nup160 222 avavveigqtylfalsrdgkLrvWnll 248
                                    +v++ ++ ++y+++  rd +++vWn +
  gene574|gene574|rna574|rna574 193 TVRCLRVYKDYIVSGARDSTVKVWNMD 219
                                    678888899****************86 PP

  == domain 4  score: 1.8 bits;  conditional E-value: 0.032
                                    ...TTTEEEEEETT-EEEEEETTTTEEEEE.EE--..........-SSSTTS--SSEESEEESSSSEEEE.......... CS
                         Nup160 226 veigqtylfalsrdgkLrvWnlltgkclat.idll.........rdeeaqdessskstldpaesslirvs.......... 285
                                    +++  t+l++ s dg++ +W++  g+ ++  ++ l         r+ +    ++   ++++ + +++             
  gene574|gene574|rna574|rna574 236 IDVCHTMLVSGSYDGTVILWDYPKGTMVRRlKSHLlrvyavligRNHIISGGQDTFIHVSDMKGQFVTTLhahrsivawl 315
                                    55556778888888888888888887777754433444444444333333333333344444444444436666666677 PP

                                    ..............E--GGG-EEEEEEEEEEE-...SSSEEEEES-S--.----S-TT........--EEEEEEEE CS
                         Nup160 286 ....dggqsylvvtyspssggefkvwkvkkedtsvslglvdlfleqtiv.padpdssn........vweLrDfalt 348
                                        d  q+   ++ s+  +g +++w+ ++      +++v+ ++ +ti+  ++    +        v++LrD +++
  gene574|gene574|rna574|rna574 316 eltsDPVQRIDHLLVSAGADGHICIWDLRTGTL--RSKIVESMPITTIAlKNE-CL-FvgvhsrvkVYDLRDAQFK 387
                                    777655666666666777777777777666643..356777777777664443.22.2346666667777777666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (426 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       598  (0.0333538); expected 358.6 (0.02)
Passed bias filter:                      471  (0.0262703); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.59u 0.24s 00:00:00.83 Elapsed: 00:00:00.44
# Mc/sec: 2891.81
//
Query:       gene575|gene575|rna575|rna575  [L=162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    0.00028   20.9  11.6       0.12   12.4   7.2    2.1  2  Baculo_PEP_C   Baculovirus polyhedron envelope protein, PEP, 
     0.0052   15.7   2.8     0.0054   15.6   2.2    1.3  1  Nup188_C       Nuclear pore protein NUP188 C-terminal domain
  ------ inclusion threshold ------
      0.024   14.6   2.4       0.84    9.6   0.2    2.2  2  DUF2095        Uncharacterized protein conserved in archaea (
      0.033   14.2   1.4      0.087   12.9   0.2    2.1  2  DUF3929        Protein of unknown function (DUF3929)
      0.096   12.2  15.8       0.13   11.8  15.8    1.2  1  CENP-K         Centromere-associated protein K
      0.097   12.9   7.9       0.19   12.0   3.5    2.6  2  DUF948         Bacterial protein of unknown function (DUF948)
        0.1   13.2  10.1        2.7    8.7   0.1    3.2  3  SlyX           SlyX
       0.11   12.8   2.5       0.17   12.1   0.2    2.4  2  FliG_M         FliG middle domain
       0.13   10.9  20.3       0.15   10.6  20.3    1.0  1  AAA_13         AAA domain
       0.35   11.2  15.7       0.47   10.8   3.9    2.2  2  OmpH           Outer membrane protein (OmpH-like)
       0.38   10.3  10.5       0.49    9.9  10.5    1.2  1  Exonuc_VII_L   Exonuclease VII, large subunit
       0.73    9.9  10.6        4.9    7.2  10.5    2.2  1  ENTH           ENTH domain
       0.91    9.2  17.1      0.094   12.4   5.1    2.4  3  Syntaxin       Syntaxin
          1    8.0  11.3        1.2    7.7  11.3    1.0  1  Peptidase_S46  Peptidase S46
        2.7    8.3   8.4          3    8.1   2.1    2.7  3  MRP-L51        Mitochondrial ribosomal subunit
        3.3    8.4   7.1          5    7.8   1.0    2.6  2  DUF883         Bacterial protein of unknown function (DUF883)
        3.3    6.9   5.5        2.2    7.5   0.1    2.1  3  LCIB_C_CA      Limiting CO2-inducible proteins B/C beta carbo
        3.7    7.6  13.1        1.2    9.1   3.7    2.2  2  DUF1664        Protein of unknown function (DUF1664)
        3.8    7.3   9.7      0.089   12.6   1.7    2.1  2  DUF1635        Protein of unknown function (DUF1635)
        3.8    7.4  14.6       0.36   10.7   1.2    2.9  3  ACCA           Acetyl co-enzyme A carboxylase carboxyltransfe
        4.8    7.4  10.3       0.29   11.3   1.7    2.8  2  DUF1492        Protein of unknown function (DUF1492)
        6.2    6.6   8.6         40    3.9   6.3    2.7  2  Lectin_N       Hepatic lectin, N-terminal domain
        8.3    5.9  10.7        0.4   10.2   0.8    2.8  3  SseC           Secretion system effector C (SseC) like family
        9.4    6.9   9.3        4.6    7.9   0.8    3.0  3  MerR-DNA-bind  MerR, DNA binding


Domain annotation for each model (and alignments):
>> Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   7.2   0.00016      0.12      16      89 ..       7      82 ..       2      92 .. 0.81
   2 !   12.2   0.2   0.00019      0.14       4      75 ..      80     151 ..      78     161 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00016
                   Baculo_PEP_C 16 ldLtnvLnairlqnvqilaqlatlldaietqLnalsedlksllaeldtrldtlltnLtdalnalq.....dtlrneLtn 89
                                    +L n+ +ai+  n++  ++l + l+ i     + ++++k+ll+  ++rl+++ +++t+ ln ++      +l+++++ 
  gene575|gene575|rna575|rna575  7 KELINIREAIKRENSTFKTNLMNELNIITH---NKKKEIKALLQRKQKRLTNTKKEITALLNDFNakaiiADLNSKIEK 82
                                   5899999*******************9998...44789***************************74444444444444 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00019
                   Baculo_PEP_C   4 vqqLnggggnqfldLtnvLnairlqnvqilaqlatlldaietqLnalsedlksllaeldtrldtlltnLtda 75 
                                    +++ n+  +  + +L ++++ ir  +++  +++++ l++++++ n+   ++ +  ++++++l+ ++ + ++a
  gene575|gene575|rna575|rna575  80 IEKFNVVITKRQKELEKQIAKIRKIKSTCFTEIERYLEELKGVQNENIRAIDKQATHVQKNLERFTREKDNA 151
                                    56667777778889*******************************99999**********999998776655 PP

>> Nup188_C  Nuclear pore protein NUP188 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   2.2   7.2e-06    0.0054     233     329 ..      57     155 ..      44     161 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 7.2e-06
                                    HHHHHHHHCT-HHH..HHCCCCTT-----------------B-SHHHHHHHHHHHHHHHHHHHHTT-SS--------HHH CS
                       Nup188_C 233 ApEvaafLnqFpel..LkrsverleapeasrtssskeakkkitllaasEvhsLalltrilealrevnardipevewdaas 310
                                      E++a+Ln F+++  ++   +++e+ +   t+++ke +k+i+ +       ++ + r le+l+ v++++i +++ +a++
  gene575|gene575|rna575|rna575  57 KKEITALLNDFNAKaiIADLNSKIEKFNVVITKRQKELEKQIAKIRKIKSTCFTEIERYLEELKGVQNENIRAIDKQATH 136
                                    57*********87533455555666666666665667788898888888888999************************* PP

                                    HHHHHHHHHT-HHHHHHHB CS
                       Nup188_C 311 vkedvefwlssrklLrerl 329
                                    v+ ++e + +++ +  +rl
  gene575|gene575|rna575|rna575 137 VQKNLERFTREKDNASDRL 155
                                    ************9999987 PP

>> DUF2095  Uncharacterized protein conserved in archaea (DUF2095)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.2    0.0011      0.84      84     120 ..      24      60 ..       8      65 .. 0.87
   2 ?    5.2   0.2     0.027        20       9      51 ..      93     136 ..      85     155 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0011
                        DUF2095  84 iinwmeergeithemakelrvvlvkkgvrafgpkkew 120
                                      n m+e   ith+  ke++  l +k  r    kke 
  gene575|gene575|rna575|rna575  24 KTNLMNELNIITHNKKKEIKALLQRKQKRLTNTKKEI 60 
                                    5699***************************999996 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.027
                        DUF2095   9 elawqeydleefkrr.fpalareleeergleidairldeeevle 51 
                                    el  q   + ++k + f  + r lee +g++ ++ir  ++++  
  gene575|gene575|rna575|rna575  93 ELEKQIAKIRKIKSTcFTEIERYLEELKGVQNENIRAIDKQATH 136
                                    55666667777776548999****************98888754 PP

>> DUF3929  Protein of unknown function (DUF3929)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.1       1.4     1e+03      24      42 ..      44      63 ..      34      81 .. 0.71
   2 ?   12.9   0.2   0.00012     0.087      10      49 ..     100     137 ..      93     146 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 1.4
                        DUF3929 24 kvlervknrvtdn.revtai 42
                                    +l+r ++r+t+  +e+ta+
  gene575|gene575|rna575|rna575 44 ALLQRKQKRLTNTkKEITAL 63
                                   45677777777642567775 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 0.00012
                        DUF3929  10 tikdvkefyyrdqnkvlervknrvtdnrevtaidkqGtli 49 
                                     i+ +k  ++ + ++ le +k   + n+++ aidkq t +
  gene575|gene575|rna575|rna575 100 KIRKIKSTCFTEIERYLEELKG--VQNENIRAIDKQATHV 137
                                    5999**************9875..79**********9965 PP

>> CENP-K  Centromere-associated protein K
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8  15.8   0.00017      0.13      82     200 ..      14     140 ..       2     147 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00017
                         CENP-K  82 algkeelqklksqLelvlsii.qsknkklkedLkrEqewleeqqeilesLkektk......elkkqvvafsektrk.... 150
                                    +  k+e    k++L   l+ii + k+k++k+ L+r q+ l + ++ +++L +  +      +l+++ ++f+    +    
  gene575|gene575|rna575|rna575  14 EAIKRENSTFKTNLMNELNIItHNKKKEIKALLQRKQKRLTNTKKEITALLNDFNakaiiaDLNSKIEKFN----Vvitk 89 
                                    4556666677777766666652679999***********99999988888765441111114444444444....14444 PP

                         CENP-K 151 .saelkekirkikeykeeLltaLgefLdehfplpeeeeasvkkkkkqkqep 200
                                      +el+++i ki++ k+  +t ++ +L+e    ++e+  +++k+ +++q+ 
  gene575|gene575|rna575|rna575  90 rQKELEKQIAKIRKIKSTCFTEIERYLEELKGVQNENIRAIDKQATHVQKN 140
                                    699**********************************999**998887765 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   3.5   0.00025      0.19      29      78 ..      40      91 ..       9     103 .. 0.83
   2 ?    3.9   0.6     0.085        63      29      79 ..      92     139 ..      87     160 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00025
                         DUF948 29 deaaatieelekqvdpilkevedllakvne..lledvneklekvdplteava 78
                                   +e++a ++  +k+++++ ke+++ll+  n+  + +d+n+k+ek + ++++ +
  gene575|gene575|rna575|rna575 40 KEIKALLQRKQKRLTNTKKEITALLNDFNAkaIIADLNSKIEKFNVVITKRQ 91
                                   4667778888899*************888777*************9876543 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.085
                         DUF948  29 deaaatieelekqvdpilkevedllakvnelledvneklekvdplteavad 79 
                                    +e++++i++++k      +e+e+ l++ + ++   ne + ++d+  ++v++
  gene575|gene575|rna575|rna575  92 KELEKQIAKIRKIKSTCFTEIERYLEELKGVQ---NENIRAIDKQATHVQK 139
                                    56666677776666666666666666666622...3355555555555553 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.6      0.14     1e+02      13      50 ..      22      60 ..      19      71 .. 0.71
   2 ?    8.7   0.1    0.0037       2.7      13      44 ..      74     105 ..      70     113 .. 0.88
   3 ?    6.5   0.4     0.018        13      16      50 ..     113     147 ..     107     156 .. 0.61

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.14
                                   HHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHT-XXX CS
                           SlyX 13 afqedtieeLndvvaeqqqqidr.lqrqlrllaerlkel 50
                                   +f  ++++eLn +  +  ++i++ lqr+ ++l++  ke+
  gene575|gene575|rna575|rna575 22 TFKTNLMNELNIITHNKKKEIKAlLQRKQKRLTNTKKEI 60
                                   677788889999999999999752577777777665554 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0037
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           SlyX  13 afqedtieeLndvvaeqqqqidrlqrqlrlla 44 
                                    a +   ie+ n v+++ q++++++ +++r+++
  gene575|gene575|rna575|rna575  74 ADLNSKIEKFNVVITKRQKELEKQIAKIRKIK 105
                                    6677789*****************99999876 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.018
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXX CS
                           SlyX  16 edtieeLndvvaeqqqqidrlqrqlrllaerlkel 50 
                                    e+ +eeL  v  e  + id++ +++++  er+   
  gene575|gene575|rna575|rna575 113 ERYLEELKGVQNENIRAIDKQATHVQKNLERFTRE 147
                                    66667777777777777777777776666666322 PP

>> FliG_M  FliG middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.2       1.3   9.6e+02      54      74 ..      35      55 ..      25      57 .. 0.76
   2 ?   12.1   0.2   0.00023      0.17      38      67 ..      89     118 ..      60     133 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 1.3
                                   SHHHHHHHHHHHHHHCHHHHH CS
                         FliG_M 54 spevlkeveevLekklssvga 74
                                   + +  ke++ +L++k + +++
  gene575|gene575|rna575|rna575 35 THNKKKEIKALLQRKQKRLTN 55
                                   555668999999999988776 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00023
                                    HHHHHHHHHHHTCCTCSHHHHHHHHHHHHH CS
                         FliG_M  38 elraevirriatlekvspevlkeveevLek 67 
                                    ++++e+ ++ia+++k+++    e+e+ Le+
  gene575|gene575|rna575|rna575  89 KRQKELEKQIAKIRKIKSTCFTEIERYLEE 118
                                    899*************************97 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6  20.3   0.00021      0.15     308     441 ..      11     150 ..       1     155 [. 0.57

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00021
                         AAA_13 308 avsde.asensafeed.keelkaeaealeeqLkglqraleaKrkepfksvelesvkakiesikklvaeineliakhNekv 385
                                    ++ ++ ++ens f+ +  +el+  + + ++++k+l ++ +++ ++  k  e++ + ++ + +k ++a++n  i+k+N  +
  gene575|gene575|rna575|rna575  11 NIREAiKRENSTFKTNlMNELNIITHNKKKEIKALLQRKQKRLTNTKK--EITALLNDFN-AKAIIADLNSKIEKFNVVI 87 
                                    222222455555555556777777777777777776666666666555..5555555555.6678888888888888888 PP

                         AAA_13 386 anleeekeeakkklelhlveeleseldeyk........kkykklekaieklekelkeeeaelkk 441
                                    ++ ++e e+   k+++   + +  e+++y         +++++++k++++++k+l+  ++e+ +
  gene575|gene575|rna575|rna575  88 TKRQKELEKQIAKIRKI-KSTCFTEIERYLeelkgvqnENIRAIDKQATHVQKNLERFTREKDN 150
                                    88888777777777773.3333344444431111333466777777777777777666666554 PP

>> OmpH  Outer membrane protein (OmpH-like)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   4.3     0.011       8.3      40      92 ..       7      62 ..       2      72 .. 0.51
   2 ?   10.8   3.9   0.00062      0.47      17      74 ..      69     139 ..      63     161 .. 0.62

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.011
                                   HHHHHHHHHHHHHTTTS.-HHHHHH....HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           OmpH 40 kelqklqeelqkkakklekeekeqe....lqkkeqelqqkqqqkaqelqkkqqellk 92
                                   kel + +e++++++++  k++  +e      +k++e+++++q+k++ l + ++e+++
  gene575|gene575|rna575|rna575  7 KELINIREAIKRENSTF-KTNLMNElniiTHNKKKEIKALLQRKQKRLTNTKKEITA 62
                                   44445555555444442.455555555555566666666666666666666655444 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00062
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTS..............-HHHHHHHHHHHHHHHH CS
                           OmpH  17 gkaaqeqlekkfkklqaeleakekelqklqeelqkkakkl.e............keekeqelqkkeqelqq 74 
                                    +ka+ ++l++k++k++  +++++kel+k+++++ k +++  +            ++e  ++++k+ + +q+
  gene575|gene575|rna575|rna575  69 AKAIIADLNSKIEKFNVVITKRQKELEKQIAKIRKIKSTCfTeieryleelkgvQNENIRAIDKQATHVQK 139
                                    6899999**************************75444443354443333222222222223333333332 PP

>> Exonuc_VII_L  Exonuclease VII, large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9  10.5   0.00066      0.49     143     251 ..      25     143 ..       4     159 .. 0.59

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00066
                   Exonuc_VII_L 143 aeleeqleelerrlekaikrlleekkqrleklasrl.....k.speellerkrqrldeleerleralkkqlkkkrerlee 216
                                    ++l ++l+ ++++ +k+ik ll++k++rl+++++++       ++++++++ ++++++++  +++  +k+l+k+ +++++
  gene575|gene575|rna575|rna575  25 TNLMNELNIITHNKKKEIKALLQRKQKRLTNTKKEItallnDfNAKAIIADLNSKIEKFNVVITK-RQKELEKQIAKIRK 103
                                    44566777777788888888889999999999888866665335666777777777776666666.56666666666666 PP

                   Exonuc_VII_L 217 lkerlkekleekkerlkklkerle.....lleekkerlee 251
                                    +k+++ +++e+  e+lk ++++       ++++ +++le+
  gene575|gene575|rna575|rna575 104 IKSTCFTEIERYLEELKGVQNENIraidkQATHVQKNLER 143
                                    6655544455555555444222222222222222222222 PP

>> ENTH  ENTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2  10.5    0.0065       4.9       6      60 ..      10      64 ..       5     155 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0065
                                   HHHHHHTSSSSSS--HHHHHHHHHHTTSH.HHHHHHHHHHHHHHHH--GGGHHHHH CS
                           ENTH  6 skvreatnndpwGpsnkllteiarltysk.kelseiisvitkrLqnnkgkewrsvl 60
                                   +++rea + ++   +++l++e+   t++k ke++  ++  +krL  n++ke+  +l
  gene575|gene575|rna575|rna575 10 INIREAIKRENSTFKTNLMNELNIITHNKkKEIKALLQRKQKRL-TNTKKEITALL 64
                                   68**************************999*************.66666665554 PP

>> Syntaxin  Syntaxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   4.8      0.31   2.3e+02      13      35 ..      40      63 ..       2      82 .. 0.38
   2 ?    1.3   8.7      0.32   2.4e+02      13      77 ..      40     103 ..      28     107 .. 0.70
   3 ?   12.4   5.1   0.00013     0.094      11      75 ..      87     151 ..      81     155 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.31
                       Syntaxin 13 keie.kleeevkklkkqneeskts 35
                                   kei+  l+++ k+l+++++e+ + 
  gene575|gene575|rna575|rna575 40 KEIKaLLQRKQKRLTNTKKEITAL 63
                                   111101222222222222222222 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.32
                       Syntaxin  13 keie.kleeevkklkkqneesktstraksvk.lkkrmesdikeikkraesvkarLeaLdksnkenek 77 
                                    kei+  l+++ k+l+++++e+ +  + ++ k + ++++s   +i+k    + +r ++L+k++++ +k
  gene575|gene575|rna575|rna575  40 KEIKaLLQRKQKRLTNTKKEITALLNDFNAKaIIADLNS---KIEKFNVVITKRQKELEKQIAKIRK 103
                                    4554157889999***********999999666666555...5555555666666666666665554 PP

  == domain 3  score: 12.4 bits;  conditional E-value: 0.00013
                       Syntaxin  11 ikkeiekleeevkklkkqneesktstraksvklkkrmesdikeikkraesvkarLeaLdksnken 75 
                                    i k  ++le++++k++k +++  t  ++   +lk   +++i++i k+a +v+++Le++ ++ +++
  gene575|gene575|rna575|rna575  87 ITKRQKELEKQIAKIRKIKSTCFTEIERYLEELKGVQNENIRAIDKQATHVQKNLERFTREKDNA 151
                                    778899******************99998888*************************99987654 PP

>> Peptidase_S46  Peptidase S46
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7  11.3    0.0016       1.2     261     398 ..      11     149 ..       3     160 .. 0.67

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0016
                                    HHHHHHHTHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHH CS
                  Peptidase_S46 261 eleerrdvalparievleeriallkeemkkdpeirikyasklagleNylKnliGmlealkkkkvlekkqaeeaalrawlk 340
                                    ++ e++++++ + ++ l +++++++   +k++ei+   + k ++l+N+ K++++ l+ +++k+++++ +++ ++++  ++
  gene575|gene575|rna575|rna575  11 NIREAIKRENSTFKTNLMNELNIIT--HNKKKEIKALLQRKQKRLTNTKKEITALLNDFNAKAIIADLNSKIEKFNVVIT 88 
                                    5678888999999999999999995..5677888899999999************************************9 PP

                                    HCT-H.HHHTTHHHHHHHHHHHHHHHHHHHHHHHHHTTTT........SHHHHHHHHHHHHHHHHH CS
                  Peptidase_S46 341 kdpekkekygkalselealvkekrklaersalleeaessg........sellslarklvrlaeere 398
                                    k++++   ++k +++++++ ++    +e +++lee++  +        ++ +++ ++l+r+++e++
  gene575|gene575|rna575|rna575  89 KRQKE---LEKQIAKIRKIKST--CFTEIERYLEELKGVQneniraidKQATHVQKNLERFTREKD 149
                                    99975...55555555555433..233333444444433300000000333444444444444333 PP

>> MRP-L51  Mitochondrial ribosomal subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   2.1     0.004         3      50      91 ..      29      70 ..       7      72 .. 0.87
   2 ?   -1.0   0.1       2.7     2e+03      68      83 ..      85     100 ..      75     107 .. 0.63
   3 ?    3.3   0.1      0.13        98      41      75 ..     113     150 ..     102     161 .. 0.68

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.004
                        MRP-L51 50 nElqrllrkrklvaeklkeaepekwkelekrikyLykklNrk 91
                                   nEl+ +++++k   + l + +++++++ +k i+ L++ +N k
  gene575|gene575|rna575|rna575 29 NELNIITHNKKKEIKALLQRKQKRLTNTKKEITALLNDFNAK 70
                                   9*****999887777799999*******************87 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 2.7
                        MRP-L51  68 eaepekwkelekriky 83 
                                     + +++ kelek+i  
  gene575|gene575|rna575|rna575  85 VVITKRQKELEKQIAK 100
                                    4455666677776655 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.13
                        MRP-L51  41 Pkwlrgvkg..nElqrllrkr.klvaeklkeaepekwk 75 
                                     ++l  +kg  nE +r + k+ + v+++l++++ ek +
  gene575|gene575|rna575|rna575 113 ERYLEELKGvqNENIRAIDKQaTHVQKNLERFTREKDN 150
                                    55666666666999998888834556678888777654 PP

>> DUF883  Bacterial protein of unknown function (DUF883)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.7      0.11        85      21      57 ..      34      70 ..      14      75 .. 0.73
   2 ?    7.8   1.0    0.0067         5       4      67 ..      73     136 ..      70     156 .. 0.61

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.11
                         DUF883 21 aadeageeaeelRerleerlerarerlrdaeeavaer 57
                                      + ++e+++l +r ++rl++++++++++ ++  ++
  gene575|gene575|rna575|rna575 34 ITHNKKKEIKALLQRKQKRLTNTKKEITALLNDFNAK 70
                                   4556678888888999999999998888877766555 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0067
                         DUF883   4 eaeleslladleellkeaadeageeaeelRerleerlerarerlrdaeeavaerakeaaeaadd 67 
                                     a+l+s +++ + ++ + ++e +++++++R+  +  +++    l++++    e+++++ ++a +
  gene575|gene575|rna575|rna575  73 IADLNSKIEKFNVVITKRQKELEKQIAKIRKIKSTCFTEIERYLEELKGVQNENIRAIDKQATH 136
                                    5666666777777777777777777777776666666666666666666555555555555543 PP

>> LCIB_C_CA  Limiting CO2-inducible proteins B/C beta carbonyic anhydrases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   1.3      0.24   1.8e+02     135     179 ..      22      67 ..       3      94 .. 0.50
   2 ?    1.4   0.9      0.21   1.6e+02     123     170 ..      49      96 ..      34     119 .. 0.53
   3 ?    7.5   0.1     0.003       2.2     118     166 ..     108     156 ..     101     161 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.24
                                    ----TTTHHHHHHHHHHGGGHH.HHHH-SSHHHHHHHHHHHHHHHH CS
                      LCIB_C_CA 135 galdelDaeqsiikqrllkrle.eiekaeddlveltkvayeaikdd 179
                                       ++l  e++ii++  +k+++  +++++++l++  k +    +d 
  gene575|gene575|rna575|rna575  22 TFKTNLMNELNIITHNKKKEIKaLLQRKQKRLTNTKKEITALLNDF 67 
                                    4444555666666666666666323555555555544444444332 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.21
                                    H---------------TTTHHHHHHHHHHGGGHH....HHHH-SSHHHHHHH CS
                      LCIB_C_CA 123 kkeglekeskepgaldelDaeqsiikqrllkrle....eiekaeddlveltk 170
                                    k+++  +++k++ ++   D++ + i   l++++e          ++  el k
  gene575|gene575|rna575|rna575  49 KQKR-LTNTKKEITALLNDFNAKAIIADLNSKIEkfnvV---ITKRQKELEK 96 
                                    3333.3344444455577777777777777777743221...2222333333 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.003
                                    HHHHHH---------------TTTHHHHHHHHHHGGGHHHHHH-SSHHH CS
                      LCIB_C_CA 118 alkelkkeglekeskepgaldelDaeqsiikqrllkrleeiekaeddlv 166
                                    +++e+++   e +  +++++ ++D + + +++ l +  +e+++a+d+l+
  gene575|gene575|rna575|rna575 108 CFTEIERYLEELKGVQNENIRAIDKQATHVQKNLERFTREKDNASDRLF 156
                                    5677777778888899999*********************99*999986 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   3.6     0.043        32      57     120 ..      20      83 ..       3      86 .. 0.77
   2 ?    9.1   3.7    0.0017       1.2      44     112 ..      74     143 ..      69     155 .. 0.70

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.043
                        DUF1664  57 laatkrhLssridrvdk.kldeqkeiskeikeevtevredlseigedvesvkeavegleskleri 120
                                     ++ k +L+++++ + + k +e k++ +  ++ +t+ +++++++ +d+++ k+++ +l+sk+e+ 
  gene575|gene575|rna575|rna575  20 NSTFKTNLMNELNIITHnKKKEIKALLQRKQKRLTNTKKEITALLNDFNA-KAIIADLNSKIEKF 83 
                                    45668899999998865156778888999999999999999999999975.89999999999875 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0017
                        DUF1664  44 esvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevr.edlseigedvesvkeaveg 112
                                    +++ +++e++   +++ +++L+++i+++ k    +   ++   ee++ v+ e++++i+++ ++v++  e 
  gene575|gene575|rna575|rna575  74 ADLNSKIEKFNVVITKRQKELEKQIAKIRKIKSTCFTEIERYLEELKGVQnENIRAIDKQATHVQKNLER 143
                                    5666777777777777777788888777777777777777777777777524677777777777766554 PP

>> DUF1635  Protein of unknown function (DUF1635)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   1.8       1.8   1.3e+03      39      50 ..      43      54 ..       4     108 .. 0.55
   2 ?   12.6   1.7   0.00012     0.089      17      56 ..     116     155 ..      96     161 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.8
                        DUF1635 39 kdlLkktikErd 50
                                   k lL++ +k   
  gene575|gene575|rna575|rna575 43 KALLQRKQKRLT 54
                                   222222222222 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.00012
                        DUF1635  17 LettklkaqeelrkrdeeviqLkdlLkktikErdeAqekl 56 
                                    Le++k   +e++r  d++ +++++ L++ ++E+d+A ++l
  gene575|gene575|rna575|rna575 116 LEELKGVQNENIRAIDKQATHVQKNLERFTREKDNASDRL 155
                                    99**********************************9986 PP

>> ACCA  Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   2.4     0.068        51      15      53 ..      28      66 ..       2      72 .. 0.66
   2 ?   10.7   1.2   0.00048      0.36       5      58 ..      70     123 ..      64     124 .. 0.89
   3 ?    5.4   0.2     0.021        16       9      47 ..     110     148 ..     106     161 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.068
                           ACCA 15 ieelkklaeesevdlseeieklekkleklkkeiyknltp 53
                                   ++el+ ++++++ ++++ +++ +k+l+++kkei++ l++
  gene575|gene575|rna575|rna575 28 MNELNIITHNKKKEIKALLQRKQKRLTNTKKEITALLND 66
                                   456666667777777777777777777777777666554 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00048
                           ACCA   5 ekpiaeleekieelkklaeesevdlseeieklekkleklkkeiyknltpwqkvq 58 
                                    ++ ia+l++kie+++ + ++++ +l+++i+k++k  +++ +ei + l++++ vq
  gene575|gene575|rna575|rna575  70 KAIIADLNSKIEKFNVVITKRQKELEKQIAKIRKIKSTCFTEIERYLEELKGVQ 123
                                    45699*********************************9999999999887776 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.021
                           ACCA   9 aeleekieelkklaeesevdlseeieklekkleklkkei 47 
                                    +e+e+ +eelk +++e+   ++++ ++++k+le+ ++e 
  gene575|gene575|rna575|rna575 110 TEIERYLEELKGVQNENIRAIDKQATHVQKNLERFTREK 148
                                    578888899999988888888888888888888877765 PP

>> DUF1492  Protein of unknown function (DUF1492)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.7      0.85   6.4e+02      60      60 ..      42      42 ..       4      78 .. 0.53
   2 ?   11.3   1.7   0.00039      0.29      31      63 ..      77     109 ..      65     123 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.85
                        DUF1492 60 s 60
                                    
  gene575|gene575|rna575|rna575 42 I 42
                                   2 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00039
                        DUF1492  31 kediekktaeaikkklelqrlidklensdsrsv 63 
                                    + +iek+ + + k+++el+++i+k+++++s   
  gene575|gene575|rna575|rna575  77 NSKIEKFNVVITKRQKELEKQIAKIRKIKSTCF 109
                                    5689***********************999765 PP

>> Lectin_N  Hepatic lectin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   6.3     0.054        40      79     122 ..      46     120 ..       2     125 .. 0.58
   2 ?   -0.4   0.0       1.2   8.8e+02      45      71 ..     129     155 ..     122     161 .. 0.72

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.054
                       Lectin_N  79 ss...............................qggslsekvtsleaklekkqqdlkadhselllhvkqlvkdLr 122
                                                                     + ++ +  +t  + +lek+ +++++ +s+ +  + ++ ++L+
  gene575|gene575|rna575|rna575  46 LQrkqkrltntkkeitallndfnakaiiadlnsKIEKFNVVITKRQKELEKQIAKIRKIKSTCFTEIERYLEELK 120
                                    333333333333333333334444443333322666777777777777777777777777777777777776665 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.2
                       Lectin_N  45 VigsqnsqLqreLetLketfsnfssst 71 
                                     i +q +++q++Le +  + +n s + 
  gene575|gene575|rna575|rna575 129 AIDKQATHVQKNLERFTREKDNASDRL 155
                                    467788888888888877777777665 PP

>> SseC  Secretion system effector C (SseC) like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   1.0      0.75   5.6e+02      17     288 ..      38      62 ..      27      71 .. 0.49
   2 ?   10.2   0.8   0.00054       0.4      11      44 ..      70     103 ..      61     106 .. 0.88
   3 ?    0.7   0.1      0.43   3.2e+02     269     302 ..     120     153 ..     110     156 .. 0.76

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.75
                           SseC  17 leskqkllkelqekqeklrqeqveeireqikkaeekakkaGiigkIfGwilaivsvvagalkvgaslllaavgvAgglmd 96 
                                    ++ ++k+l + ++k+  ++++                                                           
  gene575|gene575|rna575|rna575  38 KKKEIKALLQRKQKRLTNTKK----------------------------------------------------------- 58 
                                    333333333333333333333........................................................... PP

                           SseC  97 aalgiadevvaaattkslideemqpimdvvdkaqlageivgavvaavavvaavvavgsaakgaaaavksgaaklaeavae 176
                                                                                                                    
  gene575|gene575|rna575|rna575   - --------------------------------------------------------------------------------   -
                                    ................................................................................ PP

                           SseC 177 aigkaikkaaekagkevaeqvskqvlnelakkatkvakavkegvvasavakalikavvvaeggngiaqGainiqrAklqk 256
                                                                                                                    
  gene575|gene575|rna575|rna575   - --------------------------------------------------------------------------------   -
                                    ................................................................................ PP

                           SseC 257 kaaqlqAdtkllravleqlqkvldeaaeeike 288
                                                                ei+ 
  gene575|gene575|rna575|rna575  59 ----------------------------EITA 62 
                                    ............................3333 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00054
                           SseC  11 kaaedsleskqkllkelqekqeklrqeqveeire 44 
                                    ka  + l+sk+++++   +k++k++++q+++ir+
  gene575|gene575|rna575|rna575  70 KAIIADLNSKIEKFNVVITKRQKELEKQIAKIRK 103
                                    6667889*************************97 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.43
                           SseC 269 ravleqlqkvldeaaeeikellesiqellksmsq 302
                                    + v  ++  ++d++a++ +++le +++  +++s+
  gene575|gene575|rna575|rna575 120 KGVQNENIRAIDKQATHVQKNLERFTREKDNASD 153
                                    5555666678889999999999998888888877 PP

>> MerR-DNA-bind  MerR, DNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.5     0.091        68      35      58 ..      40      63 ..      31      69 .. 0.69
   2 ?    7.9   0.8    0.0061       4.6      33      59 ..      79     105 ..      58     107 .. 0.75
   3 ?   -1.4   0.1       4.9   3.7e+03      38      50 ..     127     139 ..     110     148 .. 0.54

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.091
                                   HHHHHHHHHHHHHHHHHHHHHHHH CS
                  MerR-DNA-bind 35 qdvrallarklaeleeriaeLqal 58
                                    + +all+rk ++l    +e++al
  gene575|gene575|rna575|rna575 40 KEIKALLQRKQKRLTNTKKEITAL 63
                                   566677777777776666666666 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0061
                                    BHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                  MerR-DNA-bind  33 pcqdvrallarklaeleeriaeLqalr 59 
                                      ++ + ++ ++ +ele++ia++++++
  gene575|gene575|rna575|rna575  79 KIEKFNVVITKRQKELEKQIAKIRKIK 105
                                    5556678999*************9887 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 4.9
                                    HHHHHHHHHHHHH CS
                  MerR-DNA-bind  38 rallarklaelee 50 
                                     + +++++ ++++
  gene575|gene575|rna575|rna575 127 IRAIDKQATHVQK 139
                                    3445555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3328  (0.185621); expected 358.6 (0.02)
Passed bias filter:                      661  (0.0368676); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); expected 17.9 (0.001)
Passed Fwd filter:                        28  (0.00156172); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              24  [number of targets reported over threshold]
# CPU time: 0.66u 0.35s 00:00:01.01 Elapsed: 00:00:00.52
# Mc/sec: 941.70
//
Query:       gene576|gene576|rna576|rna576  [L=47]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (47 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       179  (0.00998383); expected 358.6 (0.02)
Passed bias filter:                      152  (0.00847788); expected 358.6 (0.02)
Passed Vit filter:                         4  (0.000223102); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.33u 0.24s 00:00:00.57 Elapsed: 00:00:00.40
# Mc/sec: 351.08
//
Query:       gene577|gene577|rna577|rna577  [L=145]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      3e-09   36.7   0.0    4.2e-09   36.3   0.0    1.2  1  RVT_1        Reverse transcriptase (RNA-dependent DNA polymer
  ------ inclusion threshold ------
      0.011   15.5   0.1      0.015   15.0   0.1    1.1  1  CAP_assoc_N  CAP-associated N-terminal


Domain annotation for each model (and alignments):
>> RVT_1  Reverse transcriptase (RNA-dependent DNA polymerase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.3   0.0   4.7e-13   4.2e-09      15     149 ..      46     139 ..      29     141 .. 0.85

  Alignments for each domain:
  == domain 1  score: 36.3 bits;  conditional E-value: 4.7e-13
                                    ...-THHHHCTB--.........-------HHHH.............HCCHTS--EEEEEEBCCGCCCSBB-GGGGGGG- CS
                          RVT_1  15 lsvdykalnkliakrLkdvlekllsenqpgfrpgrstldavedllkalkkkkkaklllklDlkkaFdsvpleellrklta 94 
                                    +   ++++++l+        + l +++++ +++++ +          +k+++++k l+ lDlk ++ +++ ee ++ +ta
  gene577|gene577|rna577|rna577  46 PDDGMRIVSNLMLL------NDLTEKDLYKIPDMKRI----------VKATTGSKNLTVLDLKEGYYQIEIEETDKHKTA 109
                                    55556666666666......77799999999999888..........7799***************************** PP

                                    EEET.........................TEEEEESB--ST-TTHHHHHHHHHHH CS
                          RVT_1  95 fkvptklinliksflstrsfsvrvngeeskgryekkglpqGsvlSPllfnlfmne 149
                                    f +                             ye+ g+ +G+++ P++f++++n+
  gene577|gene577|rna577|rna577 110 FEFG-------------------------NNVYEWYGMVMGFKNTPMIFQRVINR 139
                                    ****.........................789********************996 PP

>> CAP_assoc_N  CAP-associated N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.1   1.7e-06     0.015      46     111 ..      52     117 ..      47     129 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.7e-06
                    CAP_assoc_N  46 kVvtlytngeeiaikpfkigesleevekklgipeeveveikkgsyrfelseedlnerplvkv.dgty 111
                                     V  l+ +++ +++  +ki + +  v+ ++g ++   +++k+g y++e++e+d ++++ +++ +++y
  gene577|gene577|rna577|rna577  52 IVSNLMLLNDLTEKDLYKIPDMKRIVKATTGSKNLTVLDLKEGYYQIEIEETD-KHKTAFEFgNNVY 117
                                    57778888888889999999999999999998888889**************9.99999***99988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       612  (0.0341346); expected 358.6 (0.02)
Passed bias filter:                      441  (0.024597); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 985.40
//
Query:       gene578|gene578|rna578|rna578  [L=45]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      3e-06   27.5   0.0    3.1e-06   27.4   0.0    1.0  1  RT_RNaseH  RNase H-like domain found in reverse transcriptase


Domain annotation for each model (and alignments):
>> RT_RNaseH  RNase H-like domain found in reverse transcriptase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   0.0   1.7e-10   3.1e-06      55      97 ..       2      45 .]       1      45 [] 0.88

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 1.7e-10
                                   HHHHHHHHHHHHHHTS--EEEE-SS--TTTTT----..---HHH CS
                      RT_RNaseH 55 lAivaalkkfrhylqgrkftvitDhknlkyllskks.lngrlar 97
                                   +A+ + ++k+ + l+ rkf++itDhk l+++ +k +  n++l+r
  gene578|gene578|rna578|rna578  2 VALKWGIEKLSYELKARKFHLITDHKVLEFIRNKPEfDNNKLNR 45
                                   79******************************776645688876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (45 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       292  (0.0162865); expected 358.6 (0.02)
Passed bias filter:                      211  (0.0117686); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.26s 00:00:00.61 Elapsed: 00:00:00.42
# Mc/sec: 320.88
//
Query:       gene579|gene579|rna579|rna579  [L=86]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.8e-08   34.4   0.6      3e-08   33.7   0.6    1.4  1  Integrase_H2C2  Integrase zinc binding domain
  ------ inclusion threshold ------
      0.016   15.4   1.4      0.041   14.1   0.3    2.1  2  zf-H2C2         H2C2 zinc finger


Domain annotation for each model (and alignments):
>> Integrase_H2C2  Integrase zinc binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.7   0.6   3.3e-12     3e-08      26      57 ..       7      38 ..       3      39 .. 0.93

  Alignments for each domain:
  == domain 1  score: 33.7 bits;  conditional E-value: 3.3e-12
                 Integrase_H2C2 26 lerlrrryyWpgmrkdvkkyvksCetCqrrkp 57
                                   +  l++ryyW +m++++ +++k+ etCqr+++
  gene579|gene579|rna579|rna579  7 YYELKERYYWLSMKRHITEIIKRYETCQRNNR 38
                                   7789**************************97 PP

>> zf-H2C2  H2C2 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.3   4.6e-06     0.041      15      39 .]      10      34 ..       9      34 .. 0.92
   2 ?   -0.5   0.0      0.17   1.5e+03       4      13 ..      39      48 ..      37      51 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4.6e-06
                        zf-H2C2 15 larkYhwlgiketvseVissCkaCq 39
                                   l+++Y+wl  k+++ e+i++  +Cq
  gene579|gene579|rna579|rna579 10 LKERYYWLSMKRHITEIIKRYETCQ 34
                                   6899***************988887 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.17
                        zf-H2C2  4 tHlGinklta 13
                                    H G n + a
  gene579|gene579|rna579|rna579 39 KHTGGNEMVA 48
                                   699**99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       619  (0.0345251); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 645.73
//
Query:       gene58|gene58|rna58|rna58  [L=465]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.2e-17   63.8   0.0    3.5e-17   63.2   0.0    1.3  1  ABC_tran         ABC transporter
    1.1e-06   28.7   0.0     0.0081   16.0   0.0    2.2  2  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
    5.7e-06   25.9   0.1    2.9e-05   23.6   0.1    2.0  1  SMC_N            RecF/RecN/SMC N terminal domain
    5.5e-05   23.5   0.0    0.00011   22.5   0.0    1.6  1  AAA_22           AAA domain
    0.00045   20.7   0.0    0.00071   20.0   0.0    1.3  1  AAA_16           AAA ATPase domain
     0.0041   17.0   0.2      0.012   15.5   0.1    1.8  1  RsgA_GTPase      RsgA GTPase
     0.0042   17.0   3.6      0.034   14.0   0.4    2.7  2  ATPase_2         ATPase domain predominantly from Archaea
  ------ inclusion threshold ------
      0.011   15.9   0.0       0.02   15.0   0.0    1.4  1  AAA_33           AAA domain
      0.012   15.4   0.5      0.058   13.1   0.1    2.1  2  AAA_29           P-loop containing region of AAA domain
      0.012   15.8   0.2      0.031   14.4   0.1    1.7  1  NAF              NAF domain
      0.013   15.4   0.0      0.032   14.1   0.0    1.6  1  NACHT            NACHT domain
      0.019   15.4   0.1      0.054   13.9   0.0    1.9  2  AAA              ATPase family associated with various cellul
      0.028   14.1   0.0      0.054   13.2   0.0    1.4  1  Guanylate_kin    Guanylate kinase
      0.037   14.5   0.4      0.037   14.5   0.4    1.9  2  AAA_23           AAA domain
      0.041   13.1   0.1      0.092   11.9   0.1    1.6  1  NB-ARC           NB-ARC domain
      0.063   13.2   0.0       0.13   12.2   0.0    1.6  1  Rad17            Rad17 P-loop domain
      0.074   12.8   0.2       0.25   11.1   0.0    1.9  2  Viral_helicase1  Viral (Superfamily 1) RNA helicase
      0.081   12.7   0.5        2.4    8.0   0.1    2.4  2  zf-UBP_var       Variant UBP zinc finger
      0.085   13.2   0.3       0.67   10.4   0.0    2.5  2  RNA_helicase     RNA helicase
        0.1   13.1   0.1       0.21   12.0   0.1    1.5  1  AAA_17           AAA domain
        0.1   12.7   0.0       0.41   10.7   0.0    2.1  1  MMR_HSR1         50S ribosome-binding GTPase
       0.14   12.5   0.1        0.5   10.7   0.1    1.8  2  AAA_19           AAA domain
       0.16   11.6   0.0       0.32   10.7   0.0    1.6  1  Cytidylate_kin   Cytidylate kinase


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.2   0.0   4.5e-20   3.5e-17      13     136 ..      38     171 ..      27     172 .. 0.81

  Alignments for each domain:
  == domain 1  score: 63.2 bits;  conditional E-value: 4.5e-20
                                EEEEEESTTSSHHHHHHHHTTSS--...SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH.............. CS
                                xxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.............. RF
                   ABC_tran  13 kvaivGenGaGKStLlkllagllkp...teGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren.............. 79 
                                 +a++G++G+GK+tLl++++g++      +Gei + g++     l ++ +   +l q +++   lt++e               
  gene58|gene58|rna58|rna58  38 FTAVIGPSGCGKTTLLRTILGKVPSeyiSSGEISYCGRKR---VLDEWTRMTTYLDQCESVSAFLTAKEClyyaavfsskytks 118
                                4799******************98888899***8885543...34578888888888888888888888888888887775444 PP

                                HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   ABC_tran  80 esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                   e+ie++++kl+lk++ +  +     +LSgGq +rv++a  l+ + +++llDEpt
  gene58|gene58|rna58|rna58 119 VIYEKIEEIAKKLSLKNVLNCAM----VNLSGGQVKRVQIALELIIDMPIILLDEPT 171
                                44445888888888888888777....*****************************9 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0     1e-05    0.0081       1      20 [.      38      57 ..      38      73 .. 0.91
   2 !   10.6   0.0   0.00046      0.36     236     294 ..     143     197 ..     123     204 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1e-05
                     AAA_21  1 lnvliGpNgsGKSnLLdald 20
                               ++++iGp g+GK++LL+++ 
  gene58|gene58|rna58|rna58 38 FTAVIGPSGCGKTTLLRTIL 57
                               89***************994 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00046
                     AAA_21 236 elSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQvil 294
                                +lS G+ +   +++ l+ +    +++l+DEp +g +  l  r++e+lke +    ++++
  gene58|gene58|rna58|rna58 143 NLSGGQVKRVQIALELIIDM---PIILLDEPTTGVDNVLAYRIIEFLKEIAG-YNKIVV 197
                                56666655557778888877...9***********************99888.666655 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.1   3.7e-08   2.9e-05      18     199 ..      30     202 ..      25     215 .. 0.76

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 3.7e-08
                                EEEETTSSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEE.SSSSSSCEEEE CS
                                xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxx RF
                      SMC_N  18 vilpfsksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfdnedkk.lkiekeevsis 100
                                v +++  +fta++Gp G+GK+ ll  i   LG+  ++ + s ++s    k   +   +  +++ ++d+ ++  +  +++e+   
  gene58|gene58|rna58|rna58  30 VCGEIRAGFTAVIGPSGCGKTTLLRTI---LGKVPSEYISSGEISYCGRK---RVLDEWTRMTTYLDQCESVsAFLTAKECLYY 107
                                6678999********************...**999988888887765444...3333344555555444433356677777777 PP

                                EEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHH CS
                                xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      SMC_N 101 rrvkrkgeseykingkevtkkevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellk 184
                                  v++++ ++  i +k  + ++  +l +  +  + +LSgG+ + v +aL + i      p+ llDe     D+    ++ e+lk
  gene58|gene58|rna58|rna58 108 AAVFSSKYTKSVIYEKIEEIAKKLSLKNVLNCAMVNLSGGQVKRVQIALELIID----MPIILLDEPTTGVDNVLAYRIIEFLK 187
                                777777777777766655544444444445556668*******99999988775....6************************* PP

                                HHCTTSEEEEE-SSH CS
                                xxxxxxxxxxxxxxx RF
                      SMC_N 185 eksknaQfivislre 199
                                e      ++v s+++
  gene58|gene58|rna58|rna58 188 EIAGYNKIVVCSIHQ 202
                                *99888888888865 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.0   1.4e-07   0.00011       4      38 ..      35      74 ..      33     169 .. 0.73

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 1.4e-07
                     AAA_22  4 tagilvvtGesGtGKTtllrrlleqldeeakaee.....e 38
                               +ag+++v+G+sG+GKTtllr++l + + e+          
  gene58|gene58|rna58|rna58 35 RAGFTAVIGPSGCGKTTLLRTILGKVPSEYISSGeisycG 74
                               589*******************999876655544555541 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   9.1e-07   0.00071      25      82 ..      37      92 ..      23     186 .. 0.69

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 9.1e-07
                     AAA_16 25 elvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareell 82
                               + + ++G+sG+GK++l+r++l  +  +  +  +g+   +++++ ++ ++++ +  + +
  gene58|gene58|rna58|rna58 37 GFTAVIGPSGCGKTTLLRTILGKVPSE--YISSGEISYCGRKRVLDEWTRMTTYLDQC 92
                               5789*****************999988..45555555555554444444444333333 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.1   1.5e-05     0.012      92     123 ..      29      60 ..       4      76 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.5e-05
                                HHHHHCTTSEEEEECSTTSSHHHHHHHHCTT- CS
                RsgA_GTPase  92 elkellkdktsvlvGqSGvGKStLinallpel 123
                                ++  +++  +++++G+SG GK+tL+ ++l++ 
  gene58|gene58|rna58|rna58  29 NVCGEIRAGFTAVIGPSGCGKTTLLRTILGKV 60 
                                45556777899*****************9874 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.4   4.4e-05     0.034      19      45 ..      35      62 ..      25     198 .. 0.54
   2 ?    2.6   0.2      0.14   1.1e+02     143     177 ..     363     397 ..     354     418 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.4e-05
                   ATPase_2 19 pneiyfiYGpegsGKtaLlkeiienl.e 45
                               ++ +  + Gp g+GKt+Ll+ i+ +  +
  gene58|gene58|rna58|rna58 35 RAGFTAVIGPSGCGKTTLLRTILGKVpS 62
                               55667799**************988732 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.14
                   ATPase_2 143 keLlnliesltkekhlcvviclsSeglfiervyne 177
                                k++lnl ++lt++ +  +++cls   l i++  n+
  gene58|gene58|rna58|rna58 363 KQILNLEKELTNHIQSSLCFCLSNVALYINQYKNQ 397
                                678899999********************944443 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.0   2.6e-05      0.02       4      32 ..      41      69 ..      39     155 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.6e-05
                     AAA_33  4 lvGlpGsGKstlaerllkklgavllssdt 32
                               ++G++G+GK+tl++ +l k + + +ss +
  gene58|gene58|rna58|rna58 41 VIGPSGCGKTTLLRTILGKVPSEYISSGE 69
                               79****************99999988876 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   7.5e-05     0.058      20      39 ..      35      53 ..      24      58 .. 0.84
   2 ?   -0.6   0.1       1.5   1.1e+03       3      11 ..     213     221 ..     211     230 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 7.5e-05
                     AAA_29 20 dlkgatlltGpsGsGKSTll 39
                               + +g+t ++GpsG GK+Tll
  gene58|gene58|rna58|rna58 35 R-AGFTAVIGPSGCGKTTLL 53
                               3.689**************8 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.5
                     AAA_29   3 rlqlvNWgt 11 
                                r+ l+NWg 
  gene58|gene58|rna58|rna58 213 RVILMNWGR 221
                                7899***97 PP

>> NAF  NAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.1     4e-05     0.031      26      51 ..     109     134 ..      94     135 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4e-05
                        NAF  26 arFtskkpaeeiiskleevakklgfk 51 
                                a F sk + ++i +k+ee+akkl++k
  gene58|gene58|rna58|rna58 109 AVFSSKYTKSVIYEKIEEIAKKLSLK 134
                                78********************9986 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   4.1e-05     0.032       4      29 ..      40      65 ..      38      75 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4.1e-05
                               EEEC-TTTCHHHHHHHHHHHHCTS-S CS
                      NACHT  4 ilqGeaGsGKTtLlqklalawaegkl 29
                               ++ G++G+GKTtLl+ +  +  +++ 
  gene58|gene58|rna58|rna58 40 AVIGPSGCGKTTLLRTILGKVPSEYI 65
                               799*************9887766665 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0     7e-05     0.054       3      27 ..      41      65 ..      39     101 .. 0.84
   2 ?   -2.8   0.0       9.9   7.7e+03      40      66 ..     146     169 ..     117     178 .. 0.56

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 7e-05
                               EESSTTSSHHHHHHHHHHHHTHEEE CS
                        AAA  3 lyGppGtGKTllakavakelgvefl 27
                               ++Gp G+GKT+l + +  ++ +e++
  gene58|gene58|rna58|rna58 41 VIGPSGCGKTTLLRTILGKVPSEYI 65
                               79**************999766554 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 9.9
                                THHHHHHHHHHHHHHHTSTSEEEEEET CS
                        AAA  40 gesekkirelfkeakekakpsilfiDE 66 
                                g + k+++  ++ +       i+++DE
  gene58|gene58|rna58|rna58 146 GGQVKRVQIALELIID---MPIILLDE 169
                                4444444444444433...35777776 PP

>> Guanylate_kin  Guanylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0     7e-05     0.054       7      92 ..      41     130 ..      38     155 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 7e-05
                                EESTTTSSHHHHHHHHHHHSTTTE.E.E--EEESS---TTS-TTTSEEE--HHHHHHHHHTTTEEEEEEETTEEEEEEH..HHH CS
              Guanylate_kin   7 lvgpsgaGksslkkaLlselpekf.g.vsvshtTrdprkgevdGkdYyFvskeemekdiskneflEaaefsgnlygtsv..eai 86 
                                ++gpsg Gk +l  ++l + p+++ +   +s+  r++  +e      y    e++ +   ++e l +a + ++ y +sv  e+i
  gene58|gene58|rna58|rna58  41 VIGPSGCGKTTLLRTILGKVPSEYiSsGEISYCGRKRVLDEWTRMTTYLDQCESVSAFLTAKECLYYAAVFSSKYTKSViyEKI 124
                                79********************9964578**********99999999999*******************888888876434899 PP

                                HHHHHT CS
              Guanylate_kin  87 eevlek 92 
                                ee+++k
  gene58|gene58|rna58|rna58 125 EEIAKK 130
                                999886 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.4   4.8e-05     0.037      19      39 ..      36      56 ..      29      58 .. 0.90
   2 ?   -2.5   0.1         8   6.2e+03     172     186 ..     359     373 ..     348     397 .. 0.59

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4.8e-05
                     AAA_23 19 kgltlItGpNGaGKTTildAi 39
                                g+t+++Gp G+GKTT+l+ i
  gene58|gene58|rna58|rna58 36 AGFTAVIGPSGCGKTTLLRTI 56
                               699***************876 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 8
                     AAA_23 172 lekleqekekekele 186
                                l++++q+++ ekel+
  gene58|gene58|rna58|rna58 359 LNTEKQILNLEKELT 373
                                333333333333333 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   0.00012     0.092      17      43 ..      33      59 ..      18     135 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00012
                               TSCSEEEEEEESTTSSHHHHHHHHCCS CS
                     NB-ARC 17 elqslvvalvGmgGvGKttlakqilnk 43
                               e+   + a+ G  G+GKttl++ il k
  gene58|gene58|rna58|rna58 33 EIRAGFTAVIGPSGCGKTTLLRTILGK 59
                               55556889***************9987 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00016      0.13      46      67 ..      37      59 ..       8     137 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00016
                      Rad17 46 riLLisGPsGCgkstvvk.vLsk 67
                                   + GPsGCgk+t ++ +L k
  gene58|gene58|rna58|rna58 37 GFTAVIGPSGCGKTTLLRtILGK 59
                               556689*********99823444 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00032      0.25       3      23 ..      41      63 ..      39     108 .. 0.63
   2 ?   -1.5   0.1       2.2   1.7e+03     110     159 ..     364     412 ..     359     426 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00032
            Viral_helicase1  3 vhGvpGcGKStlirkllrts..l 23
                               v G  GcGK+tl+r++l +    
  gene58|gene58|rna58|rna58 41 VIGPSGCGKTTLLRTILGKVpsE 63
                               55778************984431 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.2
            Viral_helicase1 110 llahlpsslshrvgrrttyllpsdvaeilsakvgteveversgelkvete 159
                                ++ +l+++l+++ + + + +l +   +i++ k +++v +  ++ ++ +++
  gene58|gene58|rna58|rna58 364 QILNLEKELTNHIQSSLCFCLSNVALYINQYK-NQTVFLAVKEINRHAYT 412
                                78889999999999999999999999998888.66665555555544444 PP

>> zf-UBP_var  Variant UBP zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.1    0.0031       2.4      35      57 ..     280     302 ..     275     305 .. 0.89
   2 ?    2.5   0.1      0.16   1.3e+02      37      61 ..     381     406 ..     376     409 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0031
                 zf-UBP_var  35 Flgfckkhaekhaektghpvyln 57 
                                +l  c+kh +k++ek+++++yl+
  gene58|gene58|rna58|rna58 280 YLLTCRKHKRKYVEKKSNEFYLR 302
                                6678*****************98 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.16
                 zf-UBP_var  37 gfckkhaekhaekt.ghpvylnikrt 61 
                                 fc + + ++ +++ +++v+l +k+ 
  gene58|gene58|rna58|rna58 381 CFCLSNVALYINQYkNQTVFLAVKEI 406
                                68999999999999678999*99986 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00085      0.67       3      26 ..      41      64 ..      39     130 .. 0.81
   2 ?   -0.4   0.1       1.9   1.5e+03      26      53 ..     376     400 ..     363     416 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00085
               RNA_helicase  3 lyGpsgeGKStlakeLakallkkl 26
                               + Gpsg+GK+tl +++  ++ +++
  gene58|gene58|rna58|rna58 41 VIGPSGCGKTTLLRTILGKVPSEY 64
                               78************9877776555 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.9
               RNA_helicase  26 lklkkkdsvysrnpeddfwdgYtgqevv 53 
                                +   +++ +++ ++   + ++Y++q+v 
  gene58|gene58|rna58|rna58 376 I---QSSLCFCLSNVALYINQYKNQTVF 400
                                3...333344455566677888888775 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   0.00027      0.21       1      29 [.      42      70 ..      42      73 .. 0.95

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00027
                               EE-TTSSHHHHHHHHHHHHTEEEEEHHHH CS
                     AAA_17  1 lGgPGsGKgtqceklvekygfthlsaGdl 29
                               +G+ G+GK+t+++++  k+  +++s G++
  gene58|gene58|rna58|rna58 42 IGPSGCGKTTLLRTILGKVPSEYISSGEI 70
                               59************************986 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00053      0.41       3      23 ..      40      60 ..      38      90 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00053
                               EEEESTTSSHHHHHHHHHTST CS
                   MMR_HSR1  3 aivGrpNvGKStLinaltgek 23
                               a++G +  GK+tL+++++g++
  gene58|gene58|rna58|rna58 40 AVIGPSGCGKTTLLRTILGKV 60
                               89****************972 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   0.00064       0.5       7      32 ..      33      58 ..      28      74 .. 0.85
   2 ?   -1.8   0.0       4.5   3.5e+03      52      52 ..     202     202 ..     150     277 .. 0.53

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00064
                     AAA_19  7 alkekvllvtaGpGtGKTrvlkhiva 32
                               +++++  +v+++ G+GKT++l++i+ 
  gene58|gene58|rna58|rna58 33 EIRAGFTAVIGPSGCGKTTLLRTILG 58
                               57788999**************9976 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 4.5
                     AAA_19  52 g 52 
                                +
  gene58|gene58|rna58|rna58 202 Q 202
                                1 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00041      0.32       2      32 ..      40      70 ..      39     151 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00041
                               EEE-STTSSHHHHHHHHHHHHT-EEEEHHHH CS
             Cytidylate_kin  2 aiDGPagsGKssvaralaeklglkyldtgal 32
                               a+ GP+g GK ++ r++  k+  +y+++g++
  gene58|gene58|rna58|rna58 40 AVIGPSGCGKTTLLRTILGKVPSEYISSGEI 70
                               677**************************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (465 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       887  (0.0494729); expected 358.6 (0.02)
Passed bias filter:                      522  (0.0291148); expected 358.6 (0.02)
Passed Vit filter:                        84  (0.00468515); expected 17.9 (0.001)
Passed Fwd filter:                        23  (0.00128284); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              23  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.44
# Mc/sec: 3168.65
//
Query:       gene580|gene580|rna580|rna580  [L=346]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.8e-51  173.8   0.1      9e-51  172.1   0.1    1.8  2  MCM           MCM P-loop domain
    2.8e-22   78.9   3.5    5.8e-22   77.9   3.5    1.6  1  MCM_lid       MCM AAA-lid domain
    0.00019   20.9   0.1    0.00082   18.8   0.0    1.9  2  Mg_chelatase  Magnesium chelatase, subunit ChlI


Domain annotation for each model (and alignments):
>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  172.1   0.1   1.5e-54     9e-51      74     222 ..       2     146 ..       1     148 [. 0.96
   2 ?   -1.5   0.0      0.18   1.1e+03      21      38 ..     188     205 ..     179     237 .. 0.78

  Alignments for each domain:
  == domain 1  score: 172.1 bits;  conditional E-value: 1.5e-54
                                    HHHHHHHSSSEEEEESSSSSSSHSSSEEEEESSSSSEEEEETHHHHTTTSEEEEESGGGSTCHHHHHHHHHHHHSEEEEE CS
                            MCM  74 LkyveklapravytsgkgssaagLtaavvrdeetgefvleaGalvladkGvcciDefdkmkeedrsalhEamEqqtisia 153
                                    L  +++l+p++++++g+++++agLt++ ++d+ ++++v +aGalv++d+G+cciDefdk ++   ++l+E+mE+q++s+a
  gene580|gene580|rna580|rna580   2 LLNACSLLPKSTFVCGNSATTAGLTVSLTHDPVSNDYVADAGALVISDNGLCCIDEFDKLEN--PTSLLEVMEDQMVSVA 79 
                                    5567789*****************************************************99..99************** PP

                                    SSSCEEEEE--EEEEEEE--SSSSCCTTS-HHHHSSSSHHHHHHSSEEEEE-SSTTHHHHHHHHHHHHH CS
                            MCM 154 KaGivatLnartsvlaAanpkagrydkkksvaeninlsaalLsrFDlifvllDkvdeekDeelaehivs 222
                                    K+G+v++++art+++aAanpk+g+yd +k+++eni+++++++srFDl+++l+++v+  +D++++e i++
  gene580|gene580|rna580|rna580  80 KGGVVCKVPARTTIIAAANPKFGHYDASKKIKENIRFKQQVISRFDLVYLLRENVN--EDYNVSENIIK 146
                                    ****************************************************9887..68999999987 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.18
                                    HSSTTSSS-HHHHHHHHH CS
                            MCM  21 siapsiyghedvkkaill 38 
                                     +ap+iy++e  kk il 
  gene580|gene580|rna580|rna580 188 RVAPTIYEQELLKKYILY 205
                                    479999999999998875 PP

>> MCM_lid  MCM AAA-lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.9   3.5   9.7e-26   5.8e-22       1      86 [.     197     274 ..     197     275 .. 0.96

  Alignments for each domain:
  == domain 1  score: 77.9 bits;  conditional E-value: 9.7e-26
                                    HHHHHHHHHHHHTT--BETCHHHHHHHHHHHHHHHHHTSSTSSSST--HHHHHHHHHHHHHHHHHHTSSSE-HHHHHHHH CS
                        MCM_lid   1 ellrkYiayarekikPklseeakeklseaYvelRkeeedskrksipitvRqLesliRLseAlAklrlsevvteedveeai 80 
                                    ell+kYi yar+ ++P+l+ eak+kl+++Yv+lRk+e  +      it R Lesl+RL+eA Ak++l+++++++d+e  i
  gene580|gene580|rna580|rna580 197 ELLKKYILYARNVVNPVLTAEAKTKLQNYYVRLRKNE--N------ITIRDLESLMRLTEAKAKMELRNIASKKDAEIII 268
                                    68*********************************77..4......********************************** PP

                                    HHHHHH CS
                        MCM_lid  81 rllkes 86 
                                    +l++++
  gene580|gene580|rna580|rna580 269 QLYEKT 274
                                    **9876 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   1.4e-07   0.00082      97     167 ..      40     107 ..      33     131 .. 0.81
   2 ?   -1.0   0.0      0.16   9.6e+02      40      86 ..     238     284 ..     221     290 .. 0.62

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.4e-07
                   Mg_chelatase  97 pkpGeislahnGvLfLDElpefkrkvlevLRePledgevtisrakakvefparfqlvaamNpcpcgklkdk 167
                                    +  G++  + nG+  +DE+ ++++ +  +L e +ed+ v++++    ++ par++++aa+Np   g+++ +
  gene580|gene580|rna580|rna580  40 ADAGALVISDNGLCCIDEFDKLENPT--SLLEVMEDQMVSVAKGGVVCKVPARTTIIAAANPK-FGHYDAS 107
                                    56799999***********9998875..78899*****************************5.4555533 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.16
                   Mg_chelatase  40 krlpsllpplseeealevakiasvagkkeeekllkrrpfraphhsas 86 
                                    + l+sl+   + +  +e ++ias ++++   +l+++  f++  +++ 
  gene580|gene580|rna580|rna580 238 RDLESLMRLTEAKAKMELRNIASKKDAEIIIQLYEKTLFKEREQTIK 284
                                    44555666666666666666666666666666666666666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (346 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1057  (0.0589548); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 2344.01
//
Query:       gene581|gene581|rna581|rna581  [L=410]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.1e-39  133.7   0.1    1.5e-38  132.2   0.0    1.8  2  AAA           ATPase family associated with various cellular 
    7.6e-12   44.8   0.2    2.2e-10   40.1   0.2    2.5  1  AAA_lid_3     AAA+ lid domain
    1.4e-07   31.4   0.0    4.6e-07   29.7   0.0    2.0  1  Vps4_C        Vps4 C terminal oligomerisation domain
    7.3e-06   25.8   0.0    1.4e-05   24.9   0.0    1.5  1  RuvB_N        Holliday junction DNA helicase RuvB P-loop doma
      2e-05   24.8   0.1    9.3e-05   22.6   0.0    2.0  2  AAA_2         AAA domain (Cdc48 subfamily)
    4.4e-05   23.5   0.1    0.00033   20.7   0.1    2.3  1  AAA_5         AAA domain (dynein-related subfamily)
    7.1e-05   23.1   0.8      0.018   15.3   0.5    2.9  2  AAA_22        AAA domain
    9.7e-05   21.7   0.0    0.00014   21.2   0.0    1.3  1  TIP49         TIP49 P-loop domain
    0.00033   20.1   0.8       0.24   10.7   0.0    2.7  2  ATPase        KaiC
    0.00036   21.0   1.8      0.017   15.5   0.1    2.7  3  AAA_16        AAA ATPase domain
     0.0077   15.8   0.1        2.8    7.5   0.0    2.4  2  AAA_25        AAA domain
     0.0082   16.2   0.2      0.033   14.2   0.0    2.2  3  AAA_14        AAA domain
  ------ inclusion threshold ------
       0.01   16.3   0.0      0.036   14.6   0.0    2.0  2  AAA_18        AAA domain
      0.033   13.6   0.0      0.073   12.5   0.0    1.5  1  Mg_chelatase  Magnesium chelatase, subunit ChlI
      0.034   14.6   0.1       0.27   11.6   0.0    2.5  2  RNA_helicase  RNA helicase
      0.034   13.9   0.1       0.11   12.2   0.1    1.8  1  AAA_24        AAA domain
      0.036   13.8   0.0        0.3   10.8   0.0    2.1  2  AAA_11        AAA domain
       0.04   13.3   1.3        3.9    6.8   0.0    3.1  3  TniB          Bacterial TniB protein
      0.097   12.6   0.0        0.3   11.0   0.0    1.8  1  GRAB          GRIP-related Arf-binding domain
       0.16   11.5   0.1       0.48    9.9   0.1    1.8  1  AAA_7         P-loop containing dynein motor region


Domain annotation for each model (and alignments):
>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  132.2   0.0   1.6e-41   1.5e-38       1     132 []     176     306 ..     176     306 .. 0.96
   2 ?   -2.0   0.0       4.9   4.4e+03      65      96 ..     360     388 ..     315     395 .. 0.58

  Alignments for each domain:
  == domain 1  score: 132.2 bits;  conditional E-value: 1.6e-41
                                    EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTCCCH CS
                            AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksrsgsese 80 
                                    +ll+GppGtGKTl+ k +a++++++f++is+s+l sk+vge+ek +r+lf  ak+k+ ps++fiDEid+l ++r+++e+e
  gene581|gene581|rna581|rna581 176 ILLFGPPGTGKTLIGKCIASQIKATFFSISASSLASKWVGEGEKLVRALFHVAKQKE-PSVIFIDEIDSLLSQRTDNENE 254
                                    69******************************************************8.********************** PP

                                    HHHHHHHHHHHHHHHTTTS.SSTEEEEEEESSGGGSTHHHHSTTSSEEEETTS CS
                            AAA  81 eeervvnqLlteldgvkkk.eskvivigatnrpdkldpallrgRfdrkieiel 132
                                    +++++  ++l ++dg     ++++++igatnrp+++d+a + +R+ ++i+++l
  gene581|gene581|rna581|rna581 255 SARKIKTEFLVQFDGAGCTnKERILIIGATNRPHEIDEAAR-RRLVKRIYVPL 306
                                    **************987654678******************.7******9985 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 4.9
                                    ETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHT CS
                            AAA  65 DEidalaksrsgseseeeervvnqLlteldgv 96 
                                     Eid + k+    e + +e + + +l++l++ 
  gene581|gene581|rna581|rna581 360 REIDDISKAV---EGSTREILKSDFLKALKQI 388
                                    4666665555...4445555555566555555 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.1   0.2   2.5e-13   2.2e-10       1      36 [.     329     364 ..     329     399 .. 0.79

  Alignments for each domain:
  == domain 1  score: 40.1 bits;  conditional E-value: 2.5e-13
                      AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrrgik 36 
                                    d d++e+ ++TeGySG D+ +lcreAa++ lr+  +
  gene581|gene581|rna581|rna581 329 DDDYSEIGAATEGYSGSDMFNLCREAAMEPLREIDD 364
                                    6699*****************************533 PP

>> Vps4_C  Vps4 C terminal oligomerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.7   0.0   5.1e-10   4.6e-07      27      61 .]     374     408 ..     352     408 .. 0.91

  Alignments for each domain:
  == domain 1  score: 29.7 bits;  conditional E-value: 5.1e-10
                         Vps4_C  27 PpvtlkDflkalkkarptVskeDLekheeFTkefG 61 
                                    +++  +Dflkalk+ r++Vsk+DLe + ++ +++G
  gene581|gene581|rna581|rna581 374 REILKSDFLKALKQIRKSVSKDDLEAFMKWNDDYG 408
                                    578899*************************9998 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.0   1.6e-08   1.4e-05      36     101 ..     176     249 ..     170     301 .. 0.69

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 1.6e-08
                         RuvB_N  36 vllyGpPGlGkttlakiiakelgvklkitsgPvleka.....gdlaalltnl...eekdvlfideihrlsrave 101
                                    +ll+GpPG Gkt + k ia+++++++ + s+  l  +       l+  l ++   +e  v+fidei  l ++  
  gene581|gene581|rna581|rna581 176 ILLFGPPGTGKTLIGKCIASQIKATFFSISASSLASKwvgegEKLVRALFHVakqKEPSVIFIDEIDSLLSQRT 249
                                    8***********************99988888776532322245666555551114457*******98866544 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0     1e-07   9.3e-05       6     139 ..     176     296 ..     172     329 .. 0.75
   2 ?   -1.3   0.1       2.3     2e+03      74     102 ..     362     388 ..     358     393 .. 0.75

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 1e-07
                                    EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG---..----THHHHHHHHHTTT-HHHHTTSEEEEETGGG---- CS
                          AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselle..eeevehlvsrligappgyvgaeegGivllDEidKihpk 83 
                                    ill gp g+Gkt++ k +a+ +++    ++  + as+l+     e e    +l+ a     +++e  ++++DEid   ++
  gene581|gene581|rna581|rna581 176 ILLFGPPGTGKTLIGKCIASQIKA----TFFSISASSLASkwVGEGE----KLVRALFHVAKQKEPSVIFIDEIDSLLSQ 247
                                    7899*****************995....9*********993333334....4444445566778889************9 PP

                                    ---------HHHHHHHHHHHH--EE-------EE-TT-EEEEEE--TTHHHHTTTS CS
                          AAA_2  84 essgadvSregVqrdLLqileggtltdkqgrkvdtknilfImtgafgsskisdesr 139
                                    ++ +++ S   + + +L  ++g+  t+k+        il+I +++   +  + ++r
  gene581|gene581|rna581|rna581 248 RTDNENESARKIKTEFLVQFDGAGCTNKER-------ILIIGATNRPHEIDEAARR 296
                                    99999*****************99998887.......8888888776666555444 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2.3
                                    EETGGG-------------HHHHHHHHHH CS
                          AAA_2  74 lDEidKihpkessgadvSregVqrdLLqi 102
                                    +D+i K+ +   s++++ + + +++L qi
  gene581|gene581|rna581|rna581 362 IDDISKAVE--GSTREILKSDFLKALKQI 388
                                    455555555..999999998888888776 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.1   3.7e-07   0.00033       2     137 ..     176     297 ..     175     298 .. 0.71

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 3.7e-07
                                    EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------G-SEEEEESGGG--HHH CS
                          AAA_5   2 vlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraaregeilvlDEveraesev 81 
                                    +lL GppGtgK+ + + +a+ ++++++ +  ++      l  ++   +g++  +    v + +e++++++DE++ + s+ 
  gene581|gene581|rna581|rna581 176 ILLFGPPGTGKTLIGKCIASQIKATFFSISASS------LASKWVG-EGEKLVRALFHVAKQKEPSVIFIDEIDSLLSQR 248
                                    89*************************876655......8888883.3333334444444555***********888777 PP

                                    HHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--.-TT-TTHHHHTT CS
                          AAA_5  82 lnsLlslleerrllleeggelvkaknddllerfrviatanpldrslnelspalrsR 137
                                    ++  +    + +  +   +   ++ n+   er+ +i+++n+++    e+++a r+R
  gene581|gene581|rna581|rna581 249 TDNENESARKIKTEFLVQFDGAGCTNK---ERILIIGATNRPH----EIDEAARRR 297
                                    776666555555554444444444443...3499999999999....888888888 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.5     2e-05     0.018       8      64 ..     176     224 ..     170     288 .. 0.63
   2 ?   -1.7   0.0       3.7   3.3e+03      64      64 ..     327     327 ..     283     392 .. 0.52

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2e-05
                         AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst.sskdllrellral 64 
                                    ++++G++GtGKT+  + +++q          +++++++ ++s+  ++    ++l+ral
  gene581|gene581|rna581|rna581 176 ILLFGPPGTGKTLIGKCIASQI---------KATFFSISASSLAsKWVGEGEKLVRAL 224
                                    89*******************9.........555555555555533333333333333 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 3.7
                         AAA_22  64 l 64 
                                    l
  gene581|gene581|rna581|rna581 327 L 327
                                    2 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0   1.6e-07   0.00014      51     144 ..     174     263 ..     131     335 .. 0.86

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 1.6e-07
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX-S-EEEEEEEEEEE... CS
                          TIP49  51 ravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkktevltqalrksigvrikeekevleGevveleveea 130
                                    +++Ll Gp+gtGkt +   i+ ++     f ++s+s + s  v   e l++al +    + ke + ++  e+ +l  +++
  gene581|gene581|rna581|rna581 174 KGILLFGPPGTGKTLIGKCIASQIK--ATFFSISASSLASKWVGEGEKLVRALFHV--AKQKEPSVIFIDEIDSLLSQRT 249
                                    89*********************97..7899*******************999764..4789999999999999999888 PP

                                    -SSS-..TTS--EE CS
                          TIP49 131 enplskekkikevk 144
                                    +n+ ++++kik+  
  gene581|gene581|rna581|rna581 250 DNENESARKIKTEF 263
                                    88888666666554 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1   0.3    0.0035       3.1      22      37 ..     176     191 ..     164     198 .. 0.88
   2 !   10.7   0.0   0.00027      0.24     103     158 ..     216     274 ..     196     319 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0035
                         ATPase  22 vlitGepGtGKtifal 37 
                                    +l+ G pGtGKt++++
  gene581|gene581|rna581|rna581 176 ILLFGPPGTGKTLIGK 191
                                    899**********996 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00027
                         ATPase 103 dleelieelaeaikeikakrvviDsitgl.ayee..keavaReilrqlvrvlkklgvTa 158
                                    + e+l++ l ++ k+++ + + iD i++l ++++  +++ aR+i  +++ ++ + g+T+
  gene581|gene581|rna581|rna581 216 EGEKLVRALFHVAKQKEPSVIFIDEIDSLlSQRTdnENESARKIKTEFLVQFDGAGCTN 274
                                    568999***********************85544113455********99999999996 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.1   1.9e-05     0.017      21      51 ..     170     200 ..     160     218 .. 0.82
   2 ?    3.7   0.1     0.082        73     123     147 ..     220     244 ..     217     266 .. 0.78
   3 ?   -1.7   0.0       3.6   3.2e+03     106     126 ..     344     388 ..     288     397 .. 0.51

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.9e-05
                         AAA_16  21 sgrpelvllsGesGvGKsslvrellralekd 51 
                                    +g p  +ll G++G+GK+ + ++++ +++++
  gene581|gene581|rna581|rna581 170 RGPPKGILLFGPPGTGKTLIGKCIASQIKAT 200
                                    666799*******************999987 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.082
                         AAA_16 123 lkrll.allsrderplvlvlDdlqwa 147
                                    l r+l   +++ ++p v+++D+++ +
  gene581|gene581|rna581|rna581 220 LVRALfHVAKQ-KEPSVIFIDEIDSL 244
                                    45555477888.778********955 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 3.6
                         AAA_16 106 a....................avpelagaea....srllellkrl 126
                                    +                    ++++++g+ +    s++l +lk++
  gene581|gene581|rna581|rna581 344 GsdmfnlcreaameplreiddISKAVEGSTReilkSDFLKALKQI 388
                                    244444444444444444444444555555544445555555444 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.5   0.0    0.0031       2.8      27      50 ..     167     190 ..     159     200 .. 0.76
   2 !    5.9   0.0    0.0097       8.7     130     167 ..     221     258 ..     212     273 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0031
                         AAA_25  27 kgllpagelallaGapgtGKttla 50 
                                     gl+   + +ll+G+pgtGKt + 
  gene581|gene581|rna581|rna581 167 TGLRGPPKGILLFGPPGTGKTLIG 190
                                    55666666689**********976 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0097
                         AAA_25 130 vdaleaaieevegvrlvviDplsralgg.densnsdvga 167
                                    v+al  ++++ +++ ++ iD ++++l+    n+n+ +++
  gene581|gene581|rna581|rna581 221 VRALFHVAKQ-KEPSVIFIDEIDSLLSQrTDNENESARK 258
                                    6788999999.89***********999985555555443 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       7.9   7.1e+03      54      86 ..     124     155 ..     103     157 .. 0.52
   2 !   14.2   0.0   3.7e-05     0.033       5      76 ..     176     244 ..     173     301 .. 0.86
   3 ?   -2.4   0.0       5.2   4.7e+03      67      76 ..     359     368 ..     314     395 .. 0.51

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 7.9
                         AAA_14  54 elileklkeekktylflDEiqevpewekalksl 86 
                                    + i +++ +  +     D i  ++++++++k++
  gene581|gene581|rna581|rna581 124 SKIESEILT-TTLNTSWDDIAGLENAKRIIKEI 155
                                    333333222.22334456666667777776665 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 3.7e-05
                         AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqev 76 
                                    +++ G+  +GKT + k ++ +++  k  ++ i+  +   k   + ekl ++++  +k+++ +++f+DEi  +
  gene581|gene581|rna581|rna581 176 ILLFGPPGTGKTLIGKCIA-SQI--KATFFSISASSLASKWVGEGEKLVRALFHVAKQKEPSVIFIDEIDSL 244
                                    7899********9976666.556..599999999999999888888999999998777899********865 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 5.2
                         AAA_14  67 ylflDEiqev 76 
                                    +  +D i+++
  gene581|gene581|rna581|rna581 359 LREIDDISKA 368
                                    3334444444 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       5.3   4.8e+03      25      62 ..      65     104 ..      32     131 .. 0.65
   2 ?   14.6   0.0     4e-05     0.036       1     104 [.     176     309 ..     176     326 .. 0.58

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 5.3
                         AAA_18  25 gvnlrdvakenglllevdpe..aldeskrldedkldklld 62 
                                     ++++++++++++  +++++  a+++++r   +++ + ++
  gene581|gene581|rna581|rna581  65 IDKIGSLLTDKEIPGDFFDDtcATERTERKPCEFTTAKSQ 104
                                    5667777777777777777777666666666655555444 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 4e-05
                         AAA_18   1 IlltGtpGvGKttlakeLskrlgf.....................gvnlrdvakenglllevdpe....aldeskrlded 55 
                                    Ill G+pG+GKt ++k +++  +                      ++ l +vak+++++  + +e            ++d
  gene581|gene581|rna581|rna581 176 ILLFGPPGTGKTLIGKCIASQIKAtffsisasslaskwvgegeklVRALFHVAKQKEPSVIFIDEidslL-----SQRTD 250
                                    99****************9886335787788855555555555555555555555555555555532221.....22222 PP

                         AAA_18  56 kldklldaleenss..................aleegknlvidghlaeleseaakdikk...vvLtaspe 104
                                    +            +                     ++  l+i      +e ++a ++     +++ +++e
  gene581|gene581|rna581|rna581 251 NE-----------NesarkikteflvqfdgagCTNKERILIIGATNRPHEIDEAARRRLvkrIYVPLPEE 309
                                    22...........122222222233445556656666666666666666655554444445566655555 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   8.1e-05     0.073      25      44 ..     176     195 ..     173     216 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 8.1e-05
                   Mg_chelatase  25 lllvGppGsGKtmlakrlps 44 
                                    +ll+GppG+GKt++ k+++s
  gene581|gene581|rna581|rna581 176 ILLFGPPGTGKTLIGKCIAS 195
                                    89*************99976 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.1         2   1.8e+03      55     106 ..      82     136 ..      81     137 .. 0.77
   2 ?   11.6   0.0    0.0003      0.27       1      28 [.     176     208 ..     176     278 .. 0.71

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 2
                   RNA_helicase  55 idDfgqvkdee.nps.dlaelirlvsstpyplnmasleekg.tlftSkvvivtsN 106
                                    +dD ++++ +e +p    + + + ++  +  + + +le++    ++S+++ +t N
  gene581|gene581|rna581|rna581  82 FDDTCATERTErKPCeFTTAKSQPINKEKGSTSTSNLEDHLiSKIESEILTTTLN 136
                                    7888888888777777778888889999999999999988877788887776655 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.0003
                   RNA_helicase   1 iwlyGpsgeGKStlakeLakallkkl.....kl 28 
                                    i+l+Gp+g+GK+++ k +a+++  ++      +
  gene581|gene581|rna581|rna581 176 ILLFGPPGTGKTLIGKCIASQIKATFfsisaSS 208
                                    689******************998885555433 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   0.00012      0.11       5      82 ..     176     249 ..     173     266 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00012
                         AAA_24   5 iliyGpsgiGKTtlakel..gpkplfidtek.Glksldadkfpdieswedfldevvel..aaeladyktlviDtidelee 79 
                                    il++Gp+g+GKT + k +  + k+ f+ + + +l+s  + +++      +++ +   l   a++++ ++++iD id l +
  gene581|gene581|rna581|rna581 176 ILLFGPPGTGKTLIGKCIasQIKATFFSISAsSLASKWVGEGE------KLVRA---LfhVAKQKEPSVIFIDEIDSLLS 246
                                    89************99998877788888888455555555555......33333...23344555569999999999876 PP

                         AAA_24  80 lcl 82 
                                    + +
  gene581|gene581|rna581|rna581 247 QRT 249
                                    544 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.1      0.48   4.3e+02     166     206 ..      96     138 ..       7     152 .. 0.66
   2 ?   10.8   0.0   0.00033       0.3      21      73 ..     177     296 ..     167     399 .. 0.62

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.48
                         AAA_11 166 errklkkerkelskeleeaeesleeevld..eaeivltTlsga 206
                                     + +  k++  ++++  + +++le+++++  e+ei  tTl+++
  gene581|gene581|rna581|rna581  96 CEFTTAKSQPINKEKGSTSTSNLEDHLISkiESEILTTTLNTS 138
                                    3333344444455666677777778888733578999999887 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00033
                         AAA_11  21 liqGPPGtgKT...ktivellsqll.................................................sr.... 44 
                                    l+ GPPGtgKT   k i++ +++                                                   ++    
  gene581|gene581|rna581|rna581 177 LLFGPPGTGKTligKCIASQIKATFfsisasslaskwvgegeklvralfhvakqkepsvifideidsllsqrtdNEnesa 256
                                    788********666555555555547887877777777777777777777776666666666666555554444004444 PP

                         AAA_11  45 .........rkseeeksakpriLvCapSNa..AvDeller 73 
                                             +   +  ++k+riL+ + +N    +De + r
  gene581|gene581|rna581|rna581 257 rkikteflvQFDGAGCTNKERILIIGATNRphEIDEAARR 296
                                    4554445433366667777777777777743356666555 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0      0.08        72      36      53 ..     174     191 ..     169     208 .. 0.83
   2 ?    6.8   0.0    0.0043       3.9     106     147 ..     219     260 ..     212     262 .. 0.86
   3 ?    0.2   0.1      0.47   4.3e+02      65     149 ..     294     388 ..     275     393 .. 0.57

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.08
                           TniB  36 pnlllvGdsnnGKtmive 53 
                                    + +ll+G++ +GKt i +
  gene581|gene581|rna581|rna581 174 KGILLFGPPGTGKTLIGK 191
                                    679***********9866 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0043
                           TniB 106 kleqqvlrllrelkvrvLiiDEihnllagsarkqreflnalk 147
                                    kl ++  ++ ++ ++ v+ iDEi++ll+ + ++ +e    +k
  gene581|gene581|rna581|rna581 219 KLVRALFHVAKQKEPSVIFIDEIDSLLSQRTDNENESARKIK 260
                                    56677789999999*************999999998888777 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.47
                           TniB  65 edaekvpvlvvqappkpdekrlyaaiLealgaplkara.......rvskleqqvlrllrelkvrvLi.iDEihnllagsa 136
                                    ++++ v+ ++v +p++    ++ ++++++++ +l  ++       +     +++ +l+re  ++ L  iD i ++++gs 
  gene581|gene581|rna581|rna581 294 ARRRLVKRIYVPLPEEQARIQMIRSLMKEFKFNLTDDDyseigaaTEGYSGSDMFNLCREAAMEPLReIDDISKAVEGST 373
                                    44445566666666666666666666666666654443333332222233344555555555555533777888888877 PP

                           TniB 137 rk..qreflnalksL 149
                                    r+  +  fl alk++
  gene581|gene581|rna581|rna581 374 REilKSDFLKALKQI 388
                                    763345677777776 PP

>> GRAB  GRIP-related Arf-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00033       0.3       5      14 ..      48      57 ..      48      58 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00033
                           GRAB  5 nVDKrLISNL 14
                                   +VDK+LISN+
  gene581|gene581|rna581|rna581 48 KVDKELISNF 57
                                   59*******7 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.1   0.00053      0.48      35      63 ..     175     203 ..     172     247 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00053
                          AAA_7  35 pvllvGptGtGKtviikdllkkldkekyl 63 
                                     +ll Gp GtGKt+i k + ++++ + ++
  gene581|gene581|rna581|rna581 175 GILLFGPPGTGKTLIGKCIASQIKATFFS 203
                                    689************99999888844333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (410 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       828  (0.0461822); expected 358.6 (0.02)
Passed bias filter:                      677  (0.0377601); expected 358.6 (0.02)
Passed Vit filter:                        96  (0.00535445); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.64u 0.33s 00:00:00.97 Elapsed: 00:00:00.48
# Mc/sec: 2583.70
//
Query:       gene582|gene582|rna582|rna582  [L=78]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       926  (0.0516482); expected 358.6 (0.02)
Passed bias filter:                      539  (0.030063); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.55u 0.33s 00:00:00.88 Elapsed: 00:00:00.54
# Mc/sec: 432.93
//
Query:       gene583|gene583|rna583|rna583  [L=398]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-27   96.4   0.0    2.6e-27   95.8   0.0    1.3  1  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
     0.0062   15.7   0.0       0.02   14.0   0.0    1.7  2  Fibrillarin      Fibrillarin
  ------ inclusion threshold ------
      0.059   13.0   0.0        0.1   12.2   0.0    1.4  1  Cons_hypoth95    Conserved hypothetical protein 95
       0.12   12.5   0.0       0.31   11.1   0.0    1.6  1  DUF1163          Protein of unknown function (DUF1163)


Domain annotation for each model (and alignments):
>> Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.8   0.0   5.8e-31   2.6e-27       2     165 ..     201     353 ..     200     391 .. 0.80

  Alignments for each domain:
  == domain 1  score: 95.8 bits;  conditional E-value: 5.8e-31
                                    HHH---TT-EEEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CTCCHHHHCC..EE CS
                Methyltr_RsmB-F   2 llLapqeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDarkidkvlggelfD 81 
                                    ++L+p  + t++D ca+PG KT+h++++m+n+g ++Av+++ +R k +++nl+  +v+n++ ++ D  + +        +
  gene583|gene583|rna583|rna583 201 YILNPPFNSTVIDTCASPGNKTSHLSAIMNNTGLIYAVEKDFKRYKILKQNLELCNVKNVKTMNNDFLELNLNA-----E 275
                                    689****************************************************************9995444.....4 PP

                                    EEEEEE--CCGGGTTT-TCHHHH--HHHHHHHHHHHHHHHHHHCCCEEEEEEEEEEES--STTTTHHHHHHHHHH-TTEE CS
                Methyltr_RsmB-F  82 riLlDaPCsgtgvirrdpdvklrrkekdiaqlaklqkellsaaidllkkgGvlvYsTCsvlveEneevieeaLkkredve 161
                                     +L+D  Csg g+   +  v   ++ + ++ l++ qk++l  a+++      +vYsTCs + eEne v++++Lk+++ +e
  gene583|gene583|rna583|rna583 276 YLLVDPSCSGSGIH--NDYV---KNHNRVKLLSSFQKKILIHALNTSG-AKRVVYSTCSSHKEENEIVVDHVLKDEKLAE 349
                                    79**********95..3445...788999*********9976665443.3369*********************987665 PP

                                    EESS CS
                Methyltr_RsmB-F 162 lvet 165
                                    +  +
  gene583|gene583|rna583|rna583 350 MWRL 353
                                    5444 PP

>> Fibrillarin  Fibrillarin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0      0.41   1.9e+03     133     146 ..      55      68 ..      31      87 .. 0.64
   2 !   14.0   0.0   4.4e-06      0.02      73     105 ..     210     242 ..     199     262 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.41
                                    GGTTTS--EEEEEE CS
                    Fibrillarin 133 kYralvekvDvifa 146
                                    kY++++   Dv+++
  gene583|gene583|rna583|rna583  55 KYASMLMVQDVVYN 68 
                                    56666666666664 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 4.4e-06
                                    EEEEESTTTSHHHHHHHHHHTTTSEEEEEESSH CS
                    Fibrillarin  73 kvLYlGaasGttvsHvsDivgeegvvyavefsp 105
                                     v+   a+ G   sH+s i++++g++yave   
  gene583|gene583|rna583|rna583 210 TVIDTCASPGNKTSHLSAIMNNTGLIYAVEKDF 242
                                    666677999********************9754 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   2.3e-05       0.1      44     105 ..     210     272 ..     198     306 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.3e-05
                                    EEEETT-..TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHC CS
                  Cons_hypoth95  44 rvLDlfa..GsGalglEAlSRgakkavlvekdkeavkilkenleelkleeetaelkedaleall 105
                                    +v+D +a  G+ +  l A+  +   +++vekd + +kilk+nle +++++ ++++++d le  l
  gene583|gene583|rna583|rna583 210 TVIDTCAspGNKTSHLSAIMNNTGLIYAVEKDFKRYKILKQNLELCNVKN-VKTMNNDFLELNL 272
                                    577777744555677888888889999********************997.9999999877654 PP

>> DUF1163  Protein of unknown function (DUF1163)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   6.9e-05      0.31      30      54 ..     358     382 ..     341     385 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 6.9e-05
                        DUF1163  30 CRekttgvmsyaCdevtlrFepgse 54 
                                    C  +t+g   y C e  lrFe g++
  gene583|gene583|rna583|rna583 358 CPYGTKGIEGYLCSESVLRFERGEH 382
                                    88999****************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (398 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       758  (0.0422779); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 2669.36
//
Query:       gene584|gene584|rna584|rna584  [L=359]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.1e-13   51.0   1.7    2.8e-13   49.7   0.2    2.5  2  La          La domain


Domain annotation for each model (and alignments):
>> La  La domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.7   0.2   1.6e-17   2.8e-13       1      58 [.       4      59 ..       4      60 .. 0.91
   2 ?   -1.3   0.1      0.13   2.3e+03      16      33 ..     269     285 ..     268     304 .. 0.65

  Alignments for each domain:
  == domain 1  score: 49.7 bits;  conditional E-value: 1.6e-17
                                   HHHHHHHHHHTT-TTT-HHHHHHHTTSTTS---HHHHHTSSHHHHHHSSHHHHHHHHH CS
                             La  1 ilkQvEfYFSdeNLpkDkFLrkkmdkdpegwVplsliasfkrmkkltkdveliaealr 58
                                   ++kQ+EfYFS++N  kD++Lr++++++    + ++ i++fk+++  +   e++ +al 
  gene584|gene584|rna584|rna584  4 LKKQLEFYFSNQNYHKDTYLRTTCEEN--DGIAIEKILKFKKLQPCNYSEEDVRKALA 59
                                   58***********************94..46*************99888899999986 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.13
                                    T-HHHHHHHTTSTTS--- CS
                             La  16 kDkFLrkkmdkdpegwVp 33 
                                    +D++L k+ dk   ++V+
  gene584|gene584|rna584|rna584 269 RDEYLTKNKDKL-YKFVS 285
                                    789998887762.34554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (359 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2345  (0.130794); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.41
# Mc/sec: 2621.05
//
Query:       gene585|gene585|rna585|rna585  [L=247]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.046   14.0   0.2       0.09   13.0   0.2    1.5  1  Archease  Archease protein family (MTH1598/TM1083)


Domain annotation for each model (and alignments):
>> Archease  Archease protein family (MTH1598/TM1083)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.2     5e-06      0.09      38     120 ..     162     246 ..     157     247 .] 0.76

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 5e-06
                                    TT---S-EEEEEEEESSSHHHHHHHHHHHHHHHHHT--S----EEEE..E-SSSEEEEEEEE----..-TT-.---.--- CS
                       Archease  38 skvepkeekeieveaedledlLfdfLdellylfdteyfvfkevkvdee.eeeeeleleaeargekf.dkekh.evq.tev 113
                                    s+v+p   + i+++++++++lL++ ++  l l +  + ++k+++++++ e e+e+  e ea+ +++ +  k  e++ + v
  gene585|gene585|rna585|rna585 162 SRVQPL--RCIQIDGDERKELLVNRIKPTLTLEEYSERILKRMQENTTkEYEKEVMSELEAYDKEIeELVKMdEFKdEMV 239
                                    667776..689********************************7755235556666666777777742223347787889 PP

                                    -B--S-- CS
                       Archease 114 KAvTyhe 120
                                    K+ Ty +
  gene585|gene585|rna585|rna585 240 KGNTYRQ 246
                                    9999975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1415  (0.0789224); expected 358.6 (0.02)
Passed bias filter:                      598  (0.0333538); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 1705.29
//
Query:       gene586|gene586|rna586|rna586  [L=400]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.9e-64  216.1   1.0    1.1e-63  215.5   1.0    1.2  1  Hist_deacetyl  Histone deacetylase domain
  ------ inclusion threshold ------
       0.02   14.7   0.0      0.039   13.8   0.0    1.4  1  NIL            NIL domain


Domain annotation for each model (and alignments):
>> Hist_deacetyl  Histone deacetylase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  215.5   1.0   1.3e-67   1.1e-63      74     307 .]      57     345 ..      16     345 .. 0.89

  Alignments for each domain:
  == domain 1  score: 215.5 bits;  conditional E-value: 1.3e-67
                                    S........TSSSSSTHCTTTCCHHHHHHHHHHHHHHHHHHTTSSSEEEETT.SS--TT-BTTB-BTTBSS-HHHHHHHH CS
                                    x........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Hist_deacetyl  74 s........klldddtpvspktlkaallavgavleavdavlsgsvkaafvlv.rPpgHHakaseasGFClvNnvaiaiky 144
                                    +          ++dd+p++ +    +   + +++ a++a+l+     +++++  +++HHa+++ +sGFC++N++++ai++
  gene586|gene586|rna586|rna586  57 HpdgypfddMKTTDDCPLFYGRKAFCAEYTSSSICAANALLTY----DVAINwAGGMHHARKNSPSGFCYMNDIVMAIQR 132
                                    133333322246899**************************55....8888889************************** PP

                                    HHHCC-SS-EEEEE-SSS--HHHHHHCTT-TTEEEEEEEE-CCTSTTSS--TT---........................ CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........................ RF
                  Hist_deacetyl 145 lqakhelkrvailDvDvHhGnGteeafysdpdvltlSiHryegifyPgtgaledlg........................ 200
                                    l +  +++rv+++D+D+HhG+G+eeaf  +++vlt+S+H+y+++++Pgtg+l +                          
  gene586|gene586|rna586|rna586 133 LLS--SFERVMYIDIDIHHGDGVEEAFGLNERVLTCSFHKYGDGYFPGTGNLLSNHfscnkagtqqmpcgaddgvqkdvq 210
                                    *99..577********************************************888789********************** PP

                                    ...............................SGGGTTSEEEEEE-TT-BHHHHHHHHHHCHHHHHCCH--SEEEEEE-ST CS
                                    ...............................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Hist_deacetyl 201 ...............................egkgkgfnlnvpleegtgdeeylkvfeeilrpvleefkPdlilvsaGfD 249
                                                                   ++k+ ++ +nvpl++g++d +y +vfe ++ +++++f+Pd+i+v++G+D
  gene586|gene586|rna586|rna586 211 aggvsdectggsavhsecsgadplamhrpfqKDKKIKNVINVPLRTGIDDWSYKYVFEPVTSSIIRKFDPDVIVVQCGAD 290
                                    *****************************98777777******************************************* PP

                                    TBTTSTT-S-BB-HHHHHHHHHHHCCCHGS-G.EEEEE-S---HHHHHHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Hist_deacetyl 250 alkgdplgelnlsvegykeltkklaeladkvkkvvllleGGYnlealaravtavlsal 307
                                    +l +d+lg +nlsv+g++ ++++l+++ +   k++++++GGY+l+++ ra+t+ +s+l
  gene586|gene586|rna586|rna586 291 SLGEDRLGCFNLSVQGHGACVEYLKSFNK---KMLVVGGGGYTLKNVVRAWTYETSVL 345
                                    ****************************9...89*******************99875 PP

>> NIL  NIL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   4.3e-06     0.039      11      62 ..     265     316 ..     262     324 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.3e-06
                                    S-SS-HHHHHHHHHT-EEEEEEEEEEEETTEEEEEEEEEEES-HHHHHHHHH CS
                            NIL  11 savePllshlvrqlglevnIlqGsveriqgtpfGqlvielsgsqesiaaalq 62 
                                     + eP+ s+++r+++ +v ++q + + +++ ++G + ++++g  + ++ ++ 
  gene586|gene586|rna586|rna586 265 YVFEPVTSSIIRKFDPDVIVVQCGADSLGEDRLGCFNLSVQGHGACVEYLKS 316
                                    678*************************************996554444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (400 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       411  (0.0229238); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 2787.05
//
Query:       gene587|gene587|rna587|rna587  [L=54]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.6e-09   37.1   0.0    2.7e-09   37.0   0.0    1.0  1  Peptidase_C97  PPPDE putative peptidase domain


Domain annotation for each model (and alignments):
>> Peptidase_C97  PPPDE putative peptidase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.0   0.0   1.5e-13   2.7e-09     106     148 ..       2      44 ..       1      47 [. 0.92

  Alignments for each domain:
  == domain 1  score: 37.0 bits;  conditional E-value: 1.5e-13
                                    TTB-HHHHHHHHHHHHHS----HHHHTHHHHHHTSHHHHHHTT CS
                  Peptidase_C97 106 iskNCnhFtdelvdfLtgkkiPewinrlarivlstptvklllp 148
                                    + +NCnhF+de+v fL +k++P++i++  + vl tp  ++++ 
  gene587|gene587|rna587|rna587   2 LLNNCNHFSDEVVFFLLEKNLPRYIMDIHESVLRTPLAASFIG 44 
                                    679********************************99988875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (54 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       192  (0.0107089); expected 358.6 (0.02)
Passed bias filter:                      187  (0.01043); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.45
# Mc/sec: 358.74
//
Query:       gene588|gene588|rna588|rna588  [L=214]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.7e-17   62.6   4.5    6.9e-17   61.7   4.5    1.5  1  Ribosomal_S3_C  Ribosomal protein S3, C-terminal domain


Domain annotation for each model (and alignments):
>> Ribosomal_S3_C  Ribosomal protein S3, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.7   4.5   3.9e-21   6.9e-17       1      83 []     104     187 ..     104     187 .. 0.95

  Alignments for each domain:
  == domain 1  score: 61.7 bits;  conditional E-value: 3.9e-21
                                    HHHHHHTT--HHHHHHHHHHHHHHCC-SEEEEEEEC-SS.TTT--EEEEEEC----..TCHHHH-EEEEEEEEETTEEEE CS
                 Ribosomal_S3_C   1 iaeqlekrvsfRramkkairramkagakGikiqvsGrLggaeiarsekykeGrvpl..htlradidyavaeaktkyGiiG 78 
                                    i++++++++++Rra++ a+r++ +aga+G+ i+vsG+L+ +++ars+k++  + +   ++ +++++ +++++++k+G+iG
  gene588|gene588|rna588|rna588 104 IRKKMSEGLAYRRAVNGALRTIKEAGAQGCIIVVSGKLK-GQRARSQKMMWQTNIYsgSPKEEYMRGGKSTVHLKQGVIG 182
                                    7899***********************************.9*******9987766669********************** PP

                                    EEEEE CS
                 Ribosomal_S3_C  79 vkVwI 83 
                                    + V+I
  gene588|gene588|rna588|rna588 183 IIVKI 187
                                    ***98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       532  (0.0296726); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1423.13
//
Query:       gene589|gene589|rna589|rna589  [L=219]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.7e-31  107.9   0.8    6.8e-31  107.3   0.8    1.2  1  RIO1         RIO1 family
    0.00012   21.5   0.1      0.009   15.4   0.0    2.1  2  Kdo          Lipopolysaccharide kinase (Kdo/WaaP) family
     0.0014   18.6   0.0     0.0026   17.7   0.0    1.4  1  APH          Phosphotransferase enzyme family
     0.0067   15.8   0.5      0.011   15.1   0.5    1.5  1  Pkinase      Protein kinase domain
  ------ inclusion threshold ------
       0.01   16.0   0.7      0.029   14.6   0.7    1.7  1  Rio2_N       Rio2, N-terminal
      0.069   12.4   0.2       0.39    9.9   0.2    2.1  1  Pkinase_Tyr  Protein tyrosine kinase


Domain annotation for each model (and alignments):
>> RIO1  RIO1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.3   0.8   2.3e-34   6.8e-31       9     182 ..      49     204 ..      42     210 .. 0.86

  Alignments for each domain:
  == domain 1  score: 107.3 bits;  conditional E-value: 2.3e-34
                                    TTEEEEEEEE-S---SS-HHHHCTTTSTTSTCG--GS-HHHHHHHHHHHHHHHHHHHHHTT--S--EEEEETTEEEEE-- CS
                           RIO1   9 dgkevaiKiyktstteFkkrkkyvsgekrfkdrksktnprklvklwaekEfrnLkrleeagvpvPkpielkrhvlvmefi 88 
                                    +g  vaiK+y++++t++++ +++ + + +           k + +  ++E+++L+ l +++  +  p+ ++rhvl+ ++ 
  gene589|gene589|rna589|rna589  49 NGMLVAIKMYRIGRTSYRRTENRDNIKMD---------MYKRSMMYCQREYKILRSLTSEN--IAMPVGCNRHVLITRYY 117
                                    56679***********9988776555544.........455677889*************5..66679************ PP

                                    EETTEEGGBHHHCG-HHHHHHHHHHHHHHHHHHHHTSTEEESS-STTSEEEETTEEEE--GTTEEETTSTTHHHHHHHHH CS
                           RIO1  89 gedgvaapklkdveeeeeaeelyeevleemrklykeaglvHaDLSeyNvlvdedkvviIDvsQaveldhpnalefLerDv 168
                                    + + +  ++l+d++        y+++++ +  ly  +g+vH+D++eyNvl++++++v++D++Q v++++p+a e+L++Dv
  gene589|gene589|rna589|rna589 118 ECKPLVRTRLDDLD------YFYNKLMNLVVDLY-SMGYVHGDFNEYNVLINDKQIVLVDFPQCVPTTDPRAGEYLRKDV 190
                                    *6666666776666......89******9999**.********************************************* PP

                                    HHHHHHHHTTC--- CS
                           RIO1 169 eniikfFrrkgvek 182
                                    +++ ++F+rk+ ++
  gene589|gene589|rna589|rna589 191 QCVKEYFERKYRYI 204
                                    **********9873 PP

>> Kdo  Lipopolysaccharide kinase (Kdo/WaaP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.1   0.1    0.0088        26      19      76 ..      49     104 ..      41     111 .. 0.81
   2 !   15.4   0.0     3e-06     0.009     126     176 ..     136     181 ..     131     211 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.0088
                            Kdo  19 ttwfvvaekvnaalrkyyrggllgklskdlyrfklgrtravrEfrllkrLeeagvavp 76 
                                    +++ v+ + +      y+r +   ++  d y +++      rE+++l+ L ++ +a p
  gene589|gene589|rna589|rna589  49 NGMLVAIKMYRIGRTSYRRTENRDNIKMDMYKRSMM--YCQREYKILRSLTSENIAMP 104
                                    666777777778888999999999999997766655..5689***********99987 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 3e-06
                            Kdo 126 avgrliaklhragvnHadlyaknillqqeeeeeaeiwliDldkarlrlrad 176
                                    ++  l+ +l ++g  H+d++  n+l++ ++     i+l+D+ ++ + + ++
  gene589|gene589|rna589|rna589 136 KLMNLVVDLYSMGYVHGDFNEYNVLINDKQ-----IVLVDFPQCVPTTDPR 181
                                    55678999*******************997.....*********9988643 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   8.8e-07    0.0026     144     196 ..     126     174 ..     111     180 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 8.8e-07
                                    HHHHHHHHHHHHHHHH--SSS-EEEE-SS-SGGGEEEC..TTEEEEE---TT- CS
                            APH 144 lleeleeqvlaalaallpgelptvllHgDlhpgNllvdpddgrvtGviDfeda 196
                                    +l +l+  ++++l  l+    +++ +HgD++  N+l++ d++ v  ++Df  +
  gene589|gene589|rna589|rna589 126 RLDDLDY-FYNKLMNLVVDLYSMGYVHGDFNEYNVLIN-DKQIV--LVDFPQC 174
                                    4555666.7777888888889999**************.55666..9**9544 PP

>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.5   3.8e-06     0.011      43     143 ..      84     172 ..      30     198 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.8e-06
                                    HHHHHHHHHHHHHSCTTB--EEEEEEESSEEEEEEE--TTEBHHHHHHHHSS--HHHHHHHHHHHHHHHHHHHHTTEE-S CS
                        Pkinase  43 kkvlrEikilkklkhpnivrlyevfeekdelylvleyveggeladllerkgslseeeakkiakqilegleylHskgiiHr 122
                                       +rE kil++l ++ni   +++ +     +l++ y e++ l +          +++  + +++++ +  l+s+g +H 
  gene589|gene589|rna589|rna589  84 MYCQREYKILRSLTSENIAMPVGCNR----HVLITRYYECKPLVR-------TRLDDLDYFYNKLMNLVVDLYSMGYVHG 152
                                    56789999999999999988888765....678899999774443.......356899999999**************** PP

                                    S-SGGGEEEETTTEEEE-SGT CS
                        Pkinase 123 DlKpeNiLidekgelKitDFG 143
                                    D    N+Li+ ++++ ++DF 
  gene589|gene589|rna589|rna589 153 DFNEYNVLIN-DKQIVLVDFP 172
                                    **********.99*******5 PP

>> Rio2_N  Rio2, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.7   9.6e-06     0.029      64      82 .]       8      26 ..       2      26 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 9.6e-06
                         Rio2_N 64 YkLtyeGyDyLALktlvkr 82
                                   Y Lty+GyD LAL  ++k+
  gene589|gene589|rna589|rna589  8 YTLTYKGYDHLALAYFKKK 26
                                   9************999886 PP

>> Pkinase_Tyr  Protein tyrosine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.2   0.00013      0.39      44     145 ..      82     169 ..      30     174 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00013
                                    HHHHHHHHHHHHHTS-BTTB--EEEEEESSSSEEEEEE--TTEBHHHHHHHTCTTTSBHHHHHHHHHHHHHHHHHHHHTT CS
                    Pkinase_Tyr  44 ekeelleeakimkklkhpnivkllgvctkeepllivteyvkgGdLlkfLrkkekekltlkdllsfalqvAkGmeyLeskk 123
                                    ++    +e+ki+++l  +ni   +g+      ++++t y +   L            +l+dl  f  ++ + +  L s+ 
  gene589|gene589|rna589|rna589  82 SMMYCQREYKILRSLTSENIAMPVGCNR----HVLITRYYECKPLVRT---------RLDDLDYFYNKLMNLVVDLYSMG 148
                                    3444556888888888888877777655....6788888887766532.........23444444444444445589999 PP

                                    EEEST-SGGGEEEEETTEEEE- CS
                    Pkinase_Tyr 124 lvHrdlaarNvLlsenkvvkis 145
                                    +vH d    NvL++++++v   
  gene589|gene589|rna589|rna589 149 YVHGDFNEYNVLINDKQIVL-V 169
                                    **************877764.3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       455  (0.0253779); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1411.46
//
Query:       gene59|gene59|rna59|rna59  [L=70]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (70 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       593  (0.0330749); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.30s 00:00:00.73 Elapsed: 00:00:00.47
# Mc/sec: 444.48
//
Query:       gene590|gene590|rna590|rna590  [L=51]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.053   12.9   0.3      0.053   12.9   0.3    1.0  1  SAM_adeno_trans  S-adenosyl-l-methionine hydroxide adenosyltr


Domain annotation for each model (and alignments):
>> SAM_adeno_trans  S-adenosyl-l-methionine hydroxide adenosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.3     3e-06     0.053     144     174 ..      17      46 ..       2      51 .] 0.70

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3e-06
                                    GGS-SSSE.CSCEEEEEEEE-TTS-EEEEEE. CS
                SAM_adeno_trans 144 eelvrlee.derlegevlyvDrFGNvitnisk 174
                                    +e+v+  e +++++  vl +D+F N+it+ ++
  gene590|gene590|rna590|rna590  17 KEIVK--EyKDNVNEAVLNIDEFNNIITGQNH 46 
                                    33333..3478899**************9874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (51 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       902  (0.0503096); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 388.41
//
Query:       gene591|gene591|rna591|rna591  [L=134]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.1e-46  156.7   1.0    2.6e-46  156.4   1.0    1.1  1  DMAP1_like  Putative DMAP1-like
  ------ inclusion threshold ------
       0.11   11.5   0.0       0.15   11.2   0.0    1.3  1  HpaB        4-hydroxyphenylacetate 3-hydroxylase C terminal


Domain annotation for each model (and alignments):
>> DMAP1_like  Putative DMAP1-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  156.4   1.0   2.9e-50   2.6e-46       2     113 .]      15     125 ..      14     125 .. 0.98

  Alignments for each domain:
  == domain 1  score: 156.4 bits;  conditional E-value: 2.9e-50
                     DMAP1_like   2 eflkllknieelkkkRksilerhfgEllkyaideledkelkikeiinkkqsypnvfLaSslgfskstwnkkvekiLkkfg 81 
                                    +++++l +++++ ++R++il++hfgE+l +ai+++ed+e+ki++ii+k +++p+++LaS++gfsk+twn++vekiL++fg
  gene591|gene591|rna591|rna591  15 TYRDFLGSLPSTLDRRRKILQTHFGEIL-VAIPTEEDFESKINNIIGKLHPHPYIYLASTIGFSKMTWNRSVEKILDQFG 93 
                                    799*************************.9************************************************** PP

                     DMAP1_like  82 ldkklkyptlrnmlrfEkLKyLiikymekkkk 113
                                    l++klkyptl+n+lr+EkLKyL+i+y++k+k+
  gene591|gene591|rna591|rna591  94 LKMKLKYPTLKNYLRYEKLKYLLIRYFDKRKE 125
                                    *****************************985 PP

>> HpaB  4-hydroxyphenylacetate 3-hydroxylase C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   1.6e-05      0.15      96     134 ..      24      61 ..       8      82 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 1.6e-05
                                    HHHHHHHHHHHHHHHGGGGT----HHHHHST.THHHHHH CS
                           HpaB  96 trlypriveilqdiaGGglitlPseadfknpeigpllek 134
                                    ++++ r ++ilq   G +l+++P+e+df++  i  ++ k
  gene591|gene591|rna591|rna591  24 PSTLDRRRKILQTHFGEILVAIPTEEDFESK-INNIIGK 61 
                                    566778899*********************7.8888766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 968.98
//
Query:       gene592|gene592|rna592|rna592  [L=241]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0011   18.2   6.7       0.19   10.9   4.5    2.4  2  GLE1      GLE1-like protein


Domain annotation for each model (and alignments):
>> GLE1  GLE1-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   4.5     1e-05      0.19      10      54 ..      44      87 ..      36     126 .. 0.83
   2 !    7.4   0.0   0.00013       2.3     202     250 ..     170     215 ..     152     216 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 1e-05
                           GLE1 10 lleqvkedkelkkllgdlkrkInpkvgQltnsseqlkkitkelke 54
                                   +l+q ++ k + ++ ++lk  +n+++gQ+t++ ++++ it++lk+
  gene592|gene592|rna592|rna592 44 ILSQ-QKKKITTQSYTQLKLTVNKRIGQITTDIDHINLITQHLKQ 87
                                   3433.33566778889**************************997 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.00013
                           GLE1 202 WrwlarilnlpleplsnitatllaafLevagnrllkaYgkqfqKlleli 250
                                    + ++a +ln    p +  +++++ a L v+g+++  ++gk f+ ++++i
  gene592|gene592|rna592|rna592 170 YDFFAGVLNE--VP-ASHSFHVVEAYLLVLGQDMSMVFGKKFRGVINYI 215
                                    7799******..44.5569************************999988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       898  (0.0500865); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1751.72
//
Query:       gene593|gene593|rna593|rna593  [L=145]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1322  (0.0737353); expected 358.6 (0.02)
Passed bias filter:                      558  (0.0311228); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 961.82
//
Query:       gene594|gene594|rna594|rna594  [L=169]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (169 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       734  (0.0409393); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 1054.52
//
Query:       gene595|gene595|rna595|rna595  [L=139]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1019  (0.0568353); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.30s 00:00:00.76 Elapsed: 00:00:00.49
# Mc/sec: 857.98
//
Query:       gene596|gene596|rna596|rna596  [L=36]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (36 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       186  (0.0103743); expected 358.6 (0.02)
Passed bias filter:                      137  (0.00764125); expected 358.6 (0.02)
Passed Vit filter:                         3  (0.000167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.25s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 268.01
//
Query:       gene597|gene597|rna597|rna597  [L=865]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.4e-33  113.2   0.8    8.4e-33  113.2   0.8    2.1  2  Ribonuc_2-5A  Ribonuclease 2-5A
    1.2e-14   54.3   2.0    5.7e-11   42.3   0.0    3.4  3  Pkinase       Protein kinase domain
    0.00064   19.1   1.0      0.033   13.5   0.0    2.5  2  Pkinase_Tyr   Protein tyrosine kinase


Domain annotation for each model (and alignments):
>> Ribonuc_2-5A  Ribonuclease 2-5A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.1      0.48   2.9e+03       8      55 ..     463     513 ..     457     541 .. 0.62
   2 !  113.2   0.8   1.4e-36   8.4e-33       2     126 ..     742     864 ..     741     865 .] 0.95

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.48
                   Ribonuc_2-5A   8 vSdrfeiekrdpese..llkkLeseasev.vksdWtkkldkelvdslgkyr 55 
                                    +S+++++++ d +++  ++++L+ ++++v ++s   ++l+++++++ ++  
  gene597|gene597|rna597|rna597 463 ISNEVNVRSADFDENegSSDELNGTRKDVsMHSMNASELENTILSNKTNTH 513
                                    677777777655443348888887777776666777777777776654433 PP

  == domain 2  score: 113.2 bits;  conditional E-value: 1.4e-36
                   Ribonuc_2-5A   2 lefLrdvSdrfeiekrdpesellkkLeseasevvksdWtkkldkelvdslgkyrkYkgdsvrdLLRaiRNkkeHyeelpe 81 
                                    ++f   +Sd +e+++ + + +++++Le+++++v++++W ++ldk + d+++ +r Y+++s++ LLR+iRNk++Hy+el  
  gene597|gene597|rna597|rna597 742 YNFYATLSDILENKN-EMSYKIFCRLERNKNKVFSGNWANRLDKVMKDEISVHRIYNFNSLKGLLRVIRNKGRHYQELAG 820
                                    7999**********9.68889*********************************************************** PP

                   Ribonuc_2-5A  82 dvkeilgelpegflsYftkrFPkLlievyevvketlkeeevfkky 126
                                    ++++i++++p+gf++Yf+ rFP+Ll+++y+  k + ++ee ++++
  gene597|gene597|rna597|rna597 821 EIRQIFKSFPDGFVDYFRMRFPNLLMVCYYSGKVA-ASEELLENF 864
                                    ******************************99988.777777776 PP

>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    3.6   0.0    0.0059        35      36      81 ..     384     429 ..     356     455 .. 0.73
   2 !    5.8   0.3    0.0013       7.5     101     137 ..     523     558 ..     487     580 .. 0.71
   3 !   42.3   0.0   9.6e-15   5.7e-11     138     264 .]     613     735 ..     605     735 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.0059
                                    CHCHHHHHHHHHHHHHHHHHSCTTB--EEEEEEESSEEEEEEE--T CS
                        Pkinase  36 kakkkkekkvlrEikilkklkhpnivrlyevfeekdelylvleyve 81 
                                    k+  k++ ++l+E++il  l+ p  +++ +  e+k+e ++v++ + 
  gene597|gene597|rna597|rna597 384 KIYRKTDIRYLNELNILGMLDVPCFIKYTYREEKKQECFFVVDECG 429
                                    2233344789***************************999988775 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0013
                                    HHHHHHHHHHHHHHHHTTEE-SS-SGGGEEEETTTEE CS
                        Pkinase 101 kkiakqilegleylHskgiiHrDlKpeNiLidekgel 137
                                       + ++++ ++ lH+k+i H+ l   N++  +++ +
  gene597|gene597|rna597|rna597 523 LGTFLKLVRVVQILHDKHIAHCNLALVNVFTRNDE-V 558
                                    34577899**********************99544.4 PP

  == domain 3  score: 42.3 bits;  conditional E-value: 9.6e-15
                                    EE-S..GTTSEESSSSCSBCTTTSCGGGS-HHHH........TTSCBSHHHHHHHHHHHHHHHHHSS-STTTSSHHHHHH CS
                        Pkinase 138 KitD..FGlakelessskltsfvgtseYlAPEvl........keneyskkvDvWslGvilyelltgkppfsgekgkekve 207
                                    K++D  FG + +  +++kl+   gt++++APE++         + e  +k+Dv+sl+vi     +g++pf++++ k    
  gene597|gene597|rna597|rna597 613 KLSDrkFGDVLRHPEEHKLEFGLGTENFRAPEIIkynvfdeaLDIEKCQKADVFSLAVIWHVTAFGQHPFNKDNYKV-ED 691
                                    56664455555555666699999***********444443221233457899*******************333322.22 PP

                                    HHHHTHHHHHHHCTSHH...HHHTTS-HHHHHHHHHHT-SSGCCSTTHHHHHTSGGG CS
                        Pkinase 208 keldqlekilkilgetkeklpeaseiseeakdllkkllkkdpkkRltaeellqhpyl 264
                                    + +             + ++  +s+i+  ++dl++ +lk + k+Rl+++++ +hp++
  gene597|gene597|rna597|rna597 692 NVI-------------HDNYSLNSNIKGPLLDLMHHMLKNNYKERLSIHSVEKHPVF 735
                                    222.............3478999********************************97 PP

>> Pkinase_Tyr  Protein tyrosine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   1.6     0.015        87     100     140 ..     517     557 ..     364     564 .. 0.76
   2 !   13.5   0.0   5.5e-06     0.033     170     256 ..     639     730 ..     619     732 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.015
                                    SBHHHHHHHHHHHHHHHHHHHHTTEEEST-SGGGEEEEETT CS
                    Pkinase_Tyr 100 ltlkdllsfalqvAkGmeyLeskklvHrdlaarNvLlsenk 140
                                     ++++ l   l++ + ++ L++k++ H +la  Nv+ ++++
  gene597|gene597|rna597|rna597 517 DNVNEQLGTFLKLVRVVQILHDKHIAHCNLALVNVFTRNDE 557
                                    35677888889999999******************987654 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 5.5e-06
                                    GGS-HHHHHHSE........EEHHHHHHHHHHHHHHHHTTSSGTTTTSHHHHHHHHH.HTTEES-BBTTSBHHHHHHHHH CS
                    Pkinase_Tyr 170 kWmapEslkekk........ftsksDvWsfGvllwEiftlgespypglkneevlekl.kegkrlekpekcpeelyelmkk 240
                                    ++ apE++k+++          +k+Dv+s +v +w +  +g++p+++ +n +v +++ ++++ l+   +++  l +lm++
  gene597|gene597|rna597|rna597 639 NFRAPEIIKYNVfdealdieKCQKADVFSLAV-IWHVTAFGQHPFNK-DNYKVEDNViHDNYSLNS--NIKGPLLDLMHH 714
                                    578999999999666666555689******98.699*********76.666666666388887765..56889******* PP

                                    HT-SSGGGS--HHHHH CS
                    Pkinase_Tyr 241 cweedpeeRptfselv 256
                                     ++++ +eR +++++ 
  gene597|gene597|rna597|rna597 715 MLKNNYKERLSIHSVE 730
                                    *********9998775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (865 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       667  (0.0372023); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.66u 0.28s 00:00:00.94 Elapsed: 00:00:00.44
# Mc/sec: 5907.67
//
Query:       gene598|gene598|rna598|rna598  [L=122]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.8e-14   53.2   0.4    3.2e-14   53.0   0.4    1.0  1  RNase_P_Rpp14  Rpp14/Pop5 family


Domain annotation for each model (and alignments):
>> RNase_P_Rpp14  Rpp14/Pop5 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.0   0.4   1.8e-18   3.2e-14       1     101 [.       7     107 ..       7     109 .. 0.93

  Alignments for each domain:
  == domain 1  score: 53.0 bits;  conditional E-value: 1.8e-18
                                    EEEEEEEEESS........-HHHHHHHHHHHHHHHHHHHHHHH--..EEEEEETTTTEEEEEEEGGGHHHHHHHHHT--E CS
                  RNase_P_Rpp14   1 RYllveilypdeee..elteksllkairesvqelfGdyglgklgsslsvkyfspatstaiiRcsresyrlvwaaLtlitk 78 
                                    RY++++i + ++ +  +++e+sll++ r+++ e++G +g+ ++++ + +  f   +++++++++r   ++++ a++ +++
  gene598|gene598|rna598|rna598   7 RYVIFKIESGNN-TllKMSEESLLNIFRDQMYEMYGSFGMMHFQN-VYITLFLLYNQIIVLKVPRVVKNEICYAMQHCKN 84 
                                    9**********6.3345788*************************.6788888888************************ PP

                                    ETTEEEEEEEEEEESSHHHHHHH CS
                  RNase_P_Rpp14  79 iegrpvvfrvvrvsGTikkaeee 101
                                    i gr+v f++v    +ik+++++
  gene598|gene598|rna598|rna598  85 IAGRNVKFNPVMAKSSIKRVKKY 107
                                    ********************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1121  (0.0625244); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 971.44
//
Query:       gene599|gene599|rna599|rna599  [L=162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.6e-09   36.6  16.3    9.4e-08   32.2   1.4    4.2  4  zf-H2C2_2    Zinc-finger double domain
      8e-08   32.3  19.4    2.7e-06   27.5   1.4    3.9  4  zf-C2H2      Zinc finger, C2H2 type
    2.5e-05   24.2   1.0    2.5e-05   24.2   1.0    2.2  2  zf-C2H2_6    C2H2-type zinc finger
    0.00012   22.6  16.1    0.00017   22.1   0.7    3.9  3  zf-C2H2_4    C2H2-type zinc finger
    0.00057   20.1   1.1       0.01   16.0   0.1    2.3  2  COG5         Golgi transport complex subunit 5
     0.0035   17.3   2.1     0.0035   17.3   2.1    3.2  3  Zap1_zf2     Zap1 zinc finger 2
     0.0073   16.9  14.2      0.039   14.6   1.4    3.7  4  FOXP-CC      FOXP coiled-coil domain
  ------ inclusion threshold ------
      0.022   14.5   0.3        0.6    9.9   0.0    2.5  2  zf-C2H2_11   zinc-finger C2H2-type
      0.065   13.5   0.5      0.065   13.5   0.5    3.3  3  zf-C2H2_jaz  Zinc-finger double-stranded RNA-binding
      0.093   12.5  18.5       0.35   10.6   0.3    3.6  3  zf-H2C2_5    C2H2-type zinc-finger domain
       0.11   12.1   7.2        4.9    6.9   0.1    2.5  2  zf_C2H2_ZHX  Zinc-fingers and homeoboxes C2H2 finger domain
        4.1    7.9   9.0         14    6.1   1.1    2.8  3  OrsD         Orsellinic acid/F9775 biosynthesis cluster prote


Domain annotation for each model (and alignments):
>> zf-H2C2_2  Zinc-finger double domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.2       0.6     9e+02      15      25 ..       2      14 ..       1      15 [. 0.81
   2 !    6.7   0.3    0.0073        11       2      17 ..      19      33 ..      18      40 .. 0.84
   3 !   32.2   1.4   6.3e-11   9.4e-08       2      26 .]      50      74 ..      49      74 .. 0.95
   4 ?    6.0   0.1     0.012        17       1      11 [.      77      87 ..      77      92 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.6
                      zf-H2C2_2 15 yeCp..lCdkaFk 25
                                   +eC+  +C +++ 
  gene599|gene599|rna599|rna599  2 LECKwkECEYKTE 14
                                   5899989**9986 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0073
                      zf-H2C2_2  2 LrrHirkHtgekpyeC 17
                                   L++H+ +Ht+e+ ++C
  gene599|gene599|rna599|rna599 19 LVKHTNNHTNES-LTC 33
                                   99********98.666 PP

  == domain 3  score: 32.2 bits;  conditional E-value: 6.3e-11
                      zf-H2C2_2  2 LrrHirkHtgekpyeCplCdkaFkt 26
                                   L+ H+rkHtg++p++C +C k++++
  gene599|gene599|rna599|rna599 50 LQAHLRKHTGDRPFKCNECEKTYTR 74
                                   899*******************985 PP

  == domain 4  score: 6.0 bits;  conditional E-value: 0.012
                      zf-H2C2_2  1 nLrrHirkHtg 11
                                   +L++Hi+ H +
  gene599|gene599|rna599|rna599 77 ALNKHIKRHEK 87
                                   79*******76 PP

>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.7   0.00095       1.4       2      23 .]       3      26 ..       2      26 .. 0.94
   2 ?    5.8   2.0     0.014        22      11      23 .]      45      57 ..      44      57 .. 0.93
   3 !   27.5   1.4   1.8e-09   2.7e-06       1      23 []      63      85 ..      63      85 .. 0.99
   4 ?   -1.8   0.0       3.7   5.6e+03      13      21 ..      92     100 ..      90     101 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00095
                                   EET..TTTEEESSHHHHHHHHHCC CS
                        zf-C2H2  2 kCp..dCgksFkrksnLkrHirtH 23
                                   +C+  +C ++  + ++L++H + H
  gene599|gene599|rna599|rna599  3 ECKwkECEYKTENHEELVKHTNNH 26
                                   69999****************999 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.014
                                   SSHHHHHHHHHCC CS
                        zf-C2H2 11 krksnLkrHirtH 23
                                   ++k+ L++H+r+H
  gene599|gene599|rna599|rna599 45 STKYTLQAHLRKH 57
                                   689*********9 PP

  == domain 3  score: 27.5 bits;  conditional E-value: 1.8e-09
                                   EEETTTTEEESSHHHHHHHHHCC CS
                        zf-C2H2  1 ykCpdCgksFkrksnLkrHirtH 23
                                   +kC++C k+++r++ L++Hi++H
  gene599|gene599|rna599|rna599 63 FKCNECEKTYTRSDALNKHIKRH 85
                                   8*********************9 PP

  == domain 4  score: -1.8 bits;  conditional E-value: 3.7
                                    HHHHHHHHH CS
                        zf-C2H2  13 ksnLkrHir 21 
                                    + +L  Hi+
  gene599|gene599|rna599|rna599  92 NKELIYHIN 100
                                    678999*97 PP

>> zf-C2H2_6  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.2         2     3e+03      17      24 ..      50      57 ..      48      58 .. 0.72
   2 !   24.2   1.0   1.7e-08   2.5e-05       2      26 ..      63      87 ..      63      88 .. 0.97

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 2
                      zf-C2H2_6 17 LggHkksH 24
                                   L  H++ H
  gene599|gene599|rna599|rna599 50 LQAHLRKH 57
                                   55788877 PP

  == domain 2  score: 24.2 bits;  conditional E-value: 1.7e-08
                      zf-C2H2_6  2 heCsvCsksFpslqaLggHkksHrk 26
                                   ++C++C k++   +aL++H k+H+k
  gene599|gene599|rna599|rna599 63 FKCNECEKTYTRSDALNKHIKRHEK 87
                                   89*********************97 PP

>> zf-C2H2_4  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.7       0.1   1.5e+02       3      23 ..       4      26 ..       2      27 .. 0.78
   2 !    6.8   0.2    0.0093        14      11      23 ..      45      57 ..      36      58 .. 0.90
   3 !   22.1   0.7   1.2e-07   0.00017       1      23 [.      63      85 ..      63      86 .. 0.97

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.1
                      zf-C2H2_4  3 Cpi..CgksFsskka..LlrHlkth 23
                                   C++  C   +++ ++  L +H ++h
  gene599|gene599|rna599|rna599  4 CKWkeC--EYKTENHeeLVKHTNNH 26
                                   777779..788777778****9998 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0093
                      zf-C2H2_4 11 sskkaLlrHlkth 23
                                   s+k++L+ Hl++h
  gene599|gene599|rna599|rna599 45 STKYTLQAHLRKH 57
                                   7999********9 PP

  == domain 3  score: 22.1 bits;  conditional E-value: 1.2e-07
                      zf-C2H2_4  1 fkCpiCgksFsskkaLlrHlkth 23
                                   fkC  C k++++++aL++H+k+h
  gene599|gene599|rna599|rna599 63 FKCNECEKTYTRSDALNKHIKRH 85
                                   8*********************9 PP

>> COG5  Golgi transport complex subunit 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.1     0.084   1.3e+02      54      71 ..      13      30 ..       8      49 .. 0.86
   2 !   16.0   0.1     7e-06      0.01      53      99 ..      71     117 ..      68     142 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.084
                                   XXXXXXXXXXXXXXXXXX CS
                           COG5 54 tsnhleLlehlsksksls 71
                                   t+nh+eL +h+++++++s
  gene599|gene599|rna599|rna599 13 TENHEELVKHTNNHTNES 30
                                   789999***999998765 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 7e-06
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX-TTHHHH CS
                           COG5  53 itsnhleLlehlskskslssvlselksslesLsasyerlkskvlepy 99 
                                    + ++ + L +h++++++++s+++el  ++++L+  ++r k  +++  
  gene599|gene599|rna599|rna599  71 TYTRSDALNKHIKRHEKADSYNKELIYHINELNGVIDRFKAMIVQER 117
                                    567888999*********************************99865 PP

>> Zap1_zf2  Zap1 zinc finger 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   2.1   2.4e-06    0.0035       1      22 [.       4      25 ..       4      28 .. 0.95
   2 ?   -1.2   1.0       1.5   2.2e+03       1       6 [.      33      38 ..      33      39 .. 0.88
   3 ?    0.9   0.1      0.31   4.6e+02      16      22 ..      95     101 ..      94     102 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 2.4e-06
                       Zap1_zf2  1 CnWkDCdFegeDicSLiNHINd 22
                                   C+Wk+C++++e  + L+ H N 
  gene599|gene599|rna599|rna599  4 CKWKECEYKTENHEELVKHTNN 25
                                   *******************995 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.5
                       Zap1_zf2  1 CnWkDC 6 
                                   C W+ C
  gene599|gene599|rna599|rna599 33 CLWEGC 38
                                   99**99 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.31
                       Zap1_zf2  16 LiNHINd 22 
                                    Li HIN+
  gene599|gene599|rna599|rna599  95 LIYHINE 101
                                    899***5 PP

>> FOXP-CC  FOXP coiled-coil domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   1.4   2.6e-05     0.039       6      29 ..       3      26 ..       2      32 .. 0.88
   2 ?    4.9   0.6     0.028        42       6      28 ..      32      56 ..      28      66 .. 0.67
   3 ?    5.5   0.3     0.017        26      11      36 ..      67      92 ..      63     129 .. 0.74
   4 ?   -0.6   0.0       1.4   2.1e+03      39      47 ..     115     123 ..      91     153 .. 0.56

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.6e-05
                        FOXP-CC  6 vCkWPgCekvledveeflkhlnse 29
                                   +CkW +Ce  +e++ee++kh n++
  gene599|gene599|rna599|rna599  3 ECKWKECEYKTENHEELVKHTNNH 26
                                   6*******************9864 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.028
                        FOXP-CC  6 vCkWPgCekvledvee..flkhlns 28
                                   +C W gC+k+   +++  +++hl++
  gene599|gene599|rna599|rna599 32 TCLWEGCKKLDPHSTKytLQAHLRK 56
                                   7******998666665114555543 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.017
                        FOXP-CC 11 gCekvledveeflkhlnseHalddks 36
                                   +Cek  + ++++ kh++++ + d+ +
  gene599|gene599|rna599|rna599 67 ECEKTYTRSDALNKHIKRHEKADSYN 92
                                   6***************9877666554 PP

  == domain 4  score: -0.6 bits;  conditional E-value: 1.4
                        FOXP-CC  39 qlrvqmqvv 47 
                                    q r++ +++
  gene599|gene599|rna599|rna599 115 QERMRNDML 123
                                    444444333 PP

>> zf-C2H2_11  zinc-finger C2H2-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.2      0.13     2e+02      13      23 ..      47      57 ..      45      58 .. 0.91
   2 ?    9.9   0.0    0.0004       0.6       5      24 ..      63      82 ..      62      83 .. 0.94

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.13
                     zf-C2H2_11 13 cftSqlsLsRH 23
                                   ++t q  L++H
  gene599|gene599|rna599|rna599 47 KYTLQAHLRKH 57
                                   8********** PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0004
                     zf-C2H2_11  5 cqCleCGlcftSqlsLsRHl 24
                                   ++C eC   +t + +L++H 
  gene599|gene599|rna599|rna599 63 FKCNECEKTYTRSDALNKHI 82
                                   69*****************6 PP

>> zf-C2H2_jaz  Zinc-finger double-stranded RNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   1.8      0.46   6.8e+02       6      22 ..       8      24 ..       7      26 .. 0.85
   2 ?    0.7   0.1      0.47   7.1e+02      13      22 ..      46      55 ..      45      57 .. 0.81
   3 ?   13.5   0.5   4.3e-05     0.065       2      22 ..      63      83 ..      62      83 .. 0.96

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.46
                                   TTTBBBSSHHHHHCCTT CS
                    zf-C2H2_jaz  6 lCdKyFksenaldnHlk 22
                                   +C+   ++++ l +H +
  gene599|gene599|rna599|rna599  8 ECEYKTENHEELVKHTN 24
                                   69999999*******88 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.47
                                   SHHHHHCCTT CS
                    zf-C2H2_jaz 13 senaldnHlk 22
                                   + ++l++Hl+
  gene599|gene599|rna599|rna599 46 TKYTLQAHLR 55
                                   6789****97 PP

  == domain 3  score: 13.5 bits;  conditional E-value: 4.3e-05
                                   CBBTTTTBBBSSHHHHHCCTT CS
                    zf-C2H2_jaz  2 fYCvlCdKyFksenaldnHlk 22
                                   f C +C+K++  + al +H+k
  gene599|gene599|rna599|rna599 63 FKCNECEKTYTRSDALNKHIK 83
                                   99*****************98 PP

>> zf-H2C2_5  C2H2-type zinc-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   1.1     0.029        43       5      25 ..       8      27 ..       5      28 .. 0.87
   2 ?   10.6   0.3   0.00024      0.35      11      26 .]      45      59 ..      45      59 .. 0.93
   3 ?    6.3   4.7    0.0055       8.2       1      25 [.      63      86 ..      63      87 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.029
                      zf-H2C2_5  5 qCDYstawksnLkRHlrrkHt 25
                                   +C Y+t    +L +H    Ht
  gene599|gene599|rna599|rna599  8 ECEYKTENHEELVKHTN-NHT 27
                                   8**************77.776 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00024
                      zf-H2C2_5 11 awksnLkRHlrrkHtg 26
                                   ++k +L+ Hlr kHtg
  gene599|gene599|rna599|rna599 45 STKYTLQAHLR-KHTG 59
                                   6899*******.***8 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.0055
                      zf-H2C2_5  1 YKCsqCDYstawksnLkRHlrrkHt 25
                                   +KC++C  + ++++ L++H++  H+
  gene599|gene599|rna599|rna599 63 FKCNECEKTYTRSDALNKHIK-RHE 86
                                   9******9999999*******.786 PP

>> zf_C2H2_ZHX  Zinc-fingers and homeoboxes C2H2 finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   3.1    0.0033         5       9      29 ..       8      27 ..       6      46 .. 0.76
   2 ?    6.9   0.1    0.0033       4.9       5      23 ..      63      81 ..      59      93 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0033
                    zf_C2H2_ZHX  9 eCsfsakkfegLalHNarsHp 29
                                   eC++ ++++e+L +H  + H+
  gene599|gene599|rna599|rna599  8 ECEYKTENHEELVKHTNN-HT 27
                                   8**************544.44 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0033
                    zf_C2H2_ZHX  5 FvCveCsfsakkfegLalH 23
                                   F C eC+ + ++ ++L++H
  gene599|gene599|rna599|rna599 63 FKCNECEKTYTRSDALNKH 81
                                   99***************** PP

>> OrsD  Orsellinic acid/F9775 biosynthesis cluster protein D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   1.1    0.0095        14      88     112 ..       3      26 ..       2      28 .. 0.87
   2 ?    4.2   1.7     0.037        56      14      36 ..      65      87 ..      37     103 .. 0.69
   3 ?    6.0   0.2      0.01        15      14      49 ..      65      99 ..      61     122 .. 0.68

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0095
                           OrsD  88 rCrakakCkyltrslktlrkHlqkk 112
                                    +C + ++C+y t + ++l kH +++
  gene599|gene599|rna599|rna599   3 EC-KWKECEYKTENHEELVKHTNNH 26 
                                    68.679***************9976 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.037
                           OrsD 14 CreCkyavlp.selerHLrkrhrq 36
                                   C+eC+   +   +l++H++ rh++
  gene599|gene599|rna599|rna599 65 CNECEKTYTRsDALNKHIK-RHEK 87
                                   5555555555445555555.5554 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.01
                           OrsD 14 CreCkyavlp.selerHLrkrhrqlkrektqelletv 49
                                   C+eC+   +   +l++H++ rh++ ++   +el  ++
  gene599|gene599|rna599|rna599 65 CNECEKTYTRsDALNKHIK-RHEKADSY-NKELIYHI 99
                                   8888877777567788888.77776555.44555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1424  (0.0794244); expected 358.6 (0.02)
Passed bias filter:                      572  (0.0319036); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 1202.10
//
Query:       gene6|gene6|rna6|rna6  [L=220]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00026   20.4   7.8    0.00037   20.0   7.8    1.3  1  UPF0121   Uncharacterised protein family (UPF0121)


Domain annotation for each model (and alignments):
>> UPF0121  Uncharacterised protein family (UPF0121)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   7.8   2.1e-08   0.00037      92     203 ..      73     176 ..      44     194 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 2.1e-08
                UPF0121  92 ysliFlfsaPvtlallPvflfallHaasytktl..ldvlgsnslvvarllkvislvesqaeniLrliAlieivlmpllivllllgkas 177
                            ++l+F++ +P  l +lP+ + +++ ++s + t   l+ +g +s+         + ++++ e+i+ +  +ie+ ++pl+++  +lg +s
  gene6|gene6|rna6|rna6  73 FCLLFFLTNPPLLYMLPFYISSIVNISSVVITHpkLKRYGFASY--------CHGINKNRESIIMISYIIELCMIPLVVLFSVLGYSS 152
                            9*************************997665411334444444........47889******************************* PP

                UPF0121 178 lllpllYyqfLklRYsSrrnPytrea 203
                            ++ ++ Y   +++  +  +   +r+a
  gene6|gene6|rna6|rna6 153 FFNMVSYGLLIRMSLK--IDMMMRRA 176
                            *******988777555..66555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       634  (0.0353617); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1590.99
//
Query:       gene60|gene60|rna60|rna60  [L=87]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       266  (0.0148363); expected 358.6 (0.02)
Passed bias filter:                      231  (0.0128842); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.32u 0.24s 00:00:00.56 Elapsed: 00:00:00.38
# Mc/sec: 690.79
//
Query:       gene600|gene600|rna600|rna600  [L=81]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      9e-15   54.4   0.2    1.1e-14   54.1   0.2    1.1  1  Ribosomal_S28e  Ribosomal protein S28e


Domain annotation for each model (and alignments):
>> Ribosomal_S28e  Ribosomal protein S28e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.1   0.2   6.2e-19   1.1e-14       2      63 ..      20      78 ..      19      78 .. 0.96

  Alignments for each domain:
  == domain 1  score: 54.1 bits;  conditional E-value: 6.2e-19
                                   --EEEEEEEEEE---SSSSEEEEEEEE-S-SS-S-EEEEEEES---TT-EEEES--S--TT- CS
                 Ribosomal_S28e  2 eaklAeVikvlgrtGsrGevtqVrvellegkdkgriiiRnVkGPvreGDiLtLlEterEArr 63
                                   +++  +Vik ++r G  G +t ++ el e+   +r++ R ++GPv+eGD+++Ll++erE rr
  gene600|gene600|rna600|rna600 20 KVYIGKVIKKIERSGPGGPITLCQLELTEE---KRTLQRAIMGPVQEGDLIMLLDSEREHRR 78
                                   78899*************************...6*************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (81 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       339  (0.0189079); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.33u 0.21s 00:00:00.54 Elapsed: 00:00:00.34
# Mc/sec: 706.85
//
Query:       gene601|gene601|rna601|rna601  [L=175]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.025   14.4   0.1       0.25   11.1   0.1    2.0  1  DUF2451   Protein of unknown function C-terminus (DUF2451)
      0.031   14.2   0.0      0.061   13.2   0.0    1.5  1  DUF5049   Domain of unknown function (DUF5049)
      0.062   13.2   0.7      0.083   12.7   0.5    1.4  1  Xol-1_N   Switch protein XOL-1, N-terminal


Domain annotation for each model (and alignments):
>> DUF2451  Protein of unknown function C-terminus (DUF2451)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   4.1e-05      0.25     101     195 ..      17     126 ..       8     139 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 4.1e-05
                        DUF2451 101 vesfskklqelkerlklpeevkkalweaavevvtetLvegysk..vkkcseeGRalMql...Dvqqllakleklski... 172
                                    v+ f+k++++   + kl+ ++ k l + + + +++++++ +s+    +c   GRa M     D+ +l  +l +  +    
  gene601|gene601|rna601|rna601  17 VRIFHKNINK---HKKLEPKHFKRLSRIVRNNMVSQFLKLLSTftNNECIVIGRAIMKNkmdDFDELVDFLVSRKSKyhi 93 
                                    4444444444...4456666666666666666666666666663235677777777753222444444333222111333 PP

                        DUF2451 173 ..........ksvpnleyveeYIkayylpekel 195
                                              ++ +n++ v++YIk ++  e+ +
  gene601|gene601|rna601|rna601  94 iiltctlckgRKLKNVDSVRNYIKSFFGDENGI 126
                                    444444444499***************888765 PP

>> DUF5049  Domain of unknown function (DUF5049)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0     1e-05     0.061      32      55 ..      74      97 ..      56      99 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1e-05
                        DUF5049 32 ergfyeLvvyleehkkeYarFILT 55
                                     +f+eLv++l   k+ Y   ILT
  gene601|gene601|rna601|rna601 74 MDDFDELVDFLVSRKSKYHIIILT 97
                                   468********************9 PP

>> Xol-1_N  Switch protein XOL-1, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.5   1.4e-05     0.083      41      99 ..      58     115 ..      45     169 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.4e-05
                                    EEEEEEEEEEEEESS--SSGGGSEE------TTHHHHHHHHHHHHHHH--SSEEEEEEE CS
                        Xol-1_N  41 vnrqclvkGkkilareakdvnehliddlpdhkdddrtldilrefidqlklqnvyeikil 99 
                                     n  c+v G++i+ ++  d  + l+d l   k   + + +   + ++ kl+nv +++ +
  gene601|gene601|rna601|rna601  58 TNNECIVIGRAIMKNKM-DDFDELVDFLVSRKSKYHIIILTCTLCKGRKLKNVDSVRNY 115
                                    5899*******987665.556779**************9999***********998755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (175 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       801  (0.0446762); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 1227.48
//
Query:       gene602|gene602|rna602|rna602  [L=167]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1810  (0.100954); expected 358.6 (0.02)
Passed bias filter:                      561  (0.0312901); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.30s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 1113.03
//
Query:       gene603|gene603|rna603|rna603  [L=589]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.5e-21   74.8   1.9    3.3e-16   59.9   0.3    2.4  2  Glyco_hydro_19  Chitinase class I
  ------ inclusion threshold ------
      0.042   13.9   0.0      0.081   13.0   0.0    1.5  1  UPF0154         Uncharacterised protein family (UPF0154)
       0.11   12.7   0.2       0.24   11.6   0.2    1.5  1  Clavanin        Clavanin


Domain annotation for each model (and alignments):
>> Glyco_hydro_19  Chitinase class I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.9   0.3   5.5e-20   3.3e-16      51     165 ..     431     537 ..     415     539 .. 0.79
   2 !   14.0   0.1   5.7e-06     0.034     186     226 ..     540     580 ..     536     584 .. 0.91

  Alignments for each domain:
  == domain 1  score: 59.9 bits;  conditional E-value: 5.5e-20
                 Glyco_hydro_19  51 keiaaflaqtshettGgsataedgpyawGycfvkekgassdycessakwplaagkkyyGrGpiqlsynynygeaGq..ai 128
                                    +e a flaq  he+ G   + e+g      c +++ + + +y +     + ++gk y+GrG iqls+  ny++a +   +
  gene603|gene603|rna603|rna603 431 NEAAMFLAQIIHESGGLVQLIEKG------CEQDQAKCGKNYDDG----QGKPGKYYFGRGFIQLSWAANYKAASEgiGM 500
                                    577888888888877776555554......666665556666544....45789*******************9882255 PP

                 Glyco_hydro_19 129 Gqdllnnpdlvatdavvsfktalwfwmtaqspkpsch 165
                                    G++ll+npd+v +d+ ++++t++w+w t+  ++p ++
  gene603|gene603|rna603|rna603 501 GTKLLDNPDQVGKDPKIAMQTSVWYWQTKVANAPGVK 537
                                    789***************************9999765 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 5.7e-06
                 Glyco_hydro_19 186 GyGvitniingglecgkgedtrvedrigfyrrycdilgvdp 226
                                     +G  t  ing lec  ++ ++ ++r + y++  ++l++++
  gene603|gene603|rna603|rna603 540 KFGATTKAINGALECKGQNVDKSKKRYDIYKKVVKVLNIKN 580
                                    69*************99999*****************9975 PP

>> UPF0154  Uncharacterised protein family (UPF0154)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   1.4e-05     0.081      27      58 ..     393     424 ..     391     426 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.4e-05
                        UPF0154  27 nPpinekmirammkqmGrkPSekqikqvmrsm 58 
                                    n  i+e++i++  ++ G+kP  + +k v  ++
  gene603|gene603|rna603|rna603 393 NAKITESQIKQVTSELGYKPPDANVKAVADQI 424
                                    789************************99887 PP

>> Clavanin  Clavanin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.2     4e-05      0.24      31      76 ..     434     479 ..     418     482 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 4e-05
                       Clavanin  31 lrllgkvihgvgnlvygisvvlgddqqdngkfygyyaedngkhwyd 76 
                                      +l ++ih+ g lv  i +   +dq   gk y       gk+++ 
  gene603|gene603|rna603|rna603 434 AMFLAQIIHESGGLVQLIEKGCEQDQAKCGKNYDDGQGKPGKYYFG 479
                                    45899****************************9998889998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (589 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1837  (0.10246); expected 358.6 (0.02)
Passed bias filter:                      527  (0.0293937); expected 358.6 (0.02)
Passed Vit filter:                       115  (0.00641419); expected 17.9 (0.001)
Passed Fwd filter:                        47  (0.00262145); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 1.10u 0.39s 00:00:01.49 Elapsed: 00:00:00.55
# Mc/sec: 3229.52
//
Query:       gene604|gene604|rna604|rna604  [L=500]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.1e-63  211.7   3.7    1.4e-62  210.6   3.7    1.6  1  MOZ_SAS         MOZ/SAS family
    7.4e-10   38.3   1.0    2.3e-09   36.7   1.0    1.9  1  zf-MYST         MYST family zinc finger domain
    0.00024   21.0  25.1      0.002   18.0   9.4    3.6  3  PHD             PHD-finger
    0.00049   19.9  31.7     0.0015   18.4   8.3    4.0  4  C1_1            Phorbol esters/diacylglycerol binding domain 
     0.0011   18.5   2.9     0.0011   18.5   2.9    3.2  3  Zn_ribbon_17    Zinc-ribbon, C4HC2 type
     0.0016   18.8   0.0     0.0039   17.6   0.0    1.6  1  Acetyltransf_7  Acetyltransferase (GNAT) domain
     0.0039   17.3  18.4      0.089   12.9   7.8    2.7  2  Zf_RING         KIAA1045 RING finger
  ------ inclusion threshold ------
       0.95    9.4  21.4       0.22   11.5   4.7    2.9  2  Prok-RING_1     Prokaryotic RING finger family 1
        7.3    6.6  20.1       0.22   11.5   4.5    3.0  3  UPF1_Zn_bind    RNA helicase (UPF2 interacting domain)


Domain annotation for each model (and alignments):
>> MOZ_SAS  MOZ/SAS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  210.6   3.7   6.9e-66   1.4e-62       2     178 ..     297     468 ..     296     469 .. 0.95

  Alignments for each domain:
  == domain 1  score: 210.6 bits;  conditional E-value: 6.9e-66
                        MOZ_SAS   2 pGkeiYrkeklsvfevdGekeklycqnLcllaklFldhktlyydvepFlfYvlteadeegahivGyFskekesaeeynla 81 
                                    +G+ +Y + kl+++e+dGe ++++c+nLcl+ak+FldhktlyydvepFlfY+l+  d   ++++GyFs+ek s+ + nl+
  gene604|gene604|rna604|rna604 297 RGNLVYSHGKLKLYEIDGEIDTIFCRNLCLVAKCFLDHKTLYYDVEPFLFYTLYDDD---SNFIGYFSREKFST-KFNLS 372
                                    5999**************************************************655...67*********765.9**** PP

                        MOZ_SAS  82 CilvlPpyqrkgyGklliefsYeLskrekkigtPekPlsdlgllsyrsywkeeilellkekekkkisieeisektgikee 161
                                    Ci+vlP+yq kg+G +li+fsY L+++ k+ gtPekPlsd gl+ y++ywk++++++l++  k ++sie is++ +++++
  gene604|gene604|rna604|rna604 373 CIVVLPCYQGKGFGYFLIDFSYCLCRIYKRKGTPEKPLSDQGLAVYKKYWKYKVYNYLSRI-KGSLSIEAISDELAMTHS 451
                                    **********************************************************985.589*************** PP

                        MOZ_SAS 162 Diistleelkllkyakg 178
                                    D++ +le l++lk+a+g
  gene604|gene604|rna604|rna604 452 DVVYALELLEFLKKADG 468
                                    ***********998765 PP

>> zf-MYST  MYST family zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.7   1.0   1.1e-12   2.3e-09       4      55 .]     244     292 ..     243     292 .. 0.93

  Alignments for each domain:
  == domain 1  score: 36.7 bits;  conditional E-value: 1.1e-12
                        zf-MYST   4 iekieiGeyeiktWYfSpYPeelankekLyvCefClkYmksakelerHkkkC 55 
                                    ++k+ iG+ ++ + Y Sp+   ++ +  +yvCe C+ Y+k++ +lerH+ kC
  gene604|gene604|rna604|rna604 244 VNKLYIGNKKLSPRYLSPF---INVSHVMYVCEKCFFYFKDSVSLERHRLKC 292
                                    7899**************9...555679************************ PP

>> PHD  PHD-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   9.4   9.9e-07     0.002       2      51 ..     115     162 ..     114     163 .. 0.91
   2 !    7.7   9.8    0.0017       3.3       2      32 ..     160     191 ..     159     200 .. 0.90
   3 ?    0.3   0.1      0.34   6.8e+02      43      49 ..     269     275 ..     261     277 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 9.9e-07
                                    BTTTTSTTSTTSCEEEETTTSCEEETTTSSSTHSHHSHHSSTBSSTTTHT CS
                            PHD   2 CavCkkksdeeeelvqCdgCkrwfHqkClkppleseekpegewlCekCke 51 
                                    C++C+k     + +v C +C++ fH++C k   +  ek + +++C+ C+ 
  gene604|gene604|rna604|rna604 115 CNFCGK--ILRKIFVKCLKCEKKFHNSCSKKGSRIVEKYDISFICNDCNM 162
                                    ******..67999*******************998888888*******86 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0017
                                    BTTTTS.TTSTTSCEEEETTTSCEEETTTSSS CS
                            PHD   2 CavCkk.ksdeeeelvqCdgCkrwfHqkClkp 32 
                                    C++C +   +++e  v C  C r fH++C + 
  gene604|gene604|rna604|rna604 160 CNMCTEcGLNNGESAVRCLVCPRIFHKACTTA 191
                                    99999998899******************865 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.34
                                    TBSSTTT CS
                            PHD  43 ewlCekC 49 
                                     ++CekC
  gene604|gene604|rna604|rna604 269 MYVCEKC 275
                                    6999999 PP

>> C1_1  Phorbol esters/diacylglycerol binding domain (C1 domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   8.3   7.3e-07    0.0015       8      45 ..     109     143 ..      98     149 .. 0.90
   2 !   11.2   6.8   0.00013      0.27      14      44 ..     160     190 ..     149     193 .. 0.82
   3 ?    0.8   0.1      0.23   4.5e+02      11      23 ..     191     203 ..     189     211 .. 0.77
   4 ?   -0.0   0.1      0.42   8.3e+02      25      37 ..     266     278 ..     260     293 .. 0.73

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 7.3e-07
                                    -SS--B-TTT-SB--SSSS-EEEETTT--EE-CCCCTT CS
                           C1_1   8 fkqptfCkhCgeflwgkekqglkCswCkllvHkkChek 45 
                                     ++ ++C+ Cg++l   +k  +kC  C+ ++H++C +k
  gene604|gene604|rna604|rna604 109 NDSHKKCNFCGKIL---RKIFVKCLKCEKKFHNSCSKK 143
                                    47899*********...******************987 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00013
                                    -TTT-SB--SSSS-EEEETTT--EE-CCCCT CS
                           C1_1  14 CkhCgeflwgkekqglkCswCkllvHkkChe 44 
                                    C+ C e+    +  +++C +C +++Hk C +
  gene604|gene604|rna604|rna604 160 CNMCTECGLNNGESAVRCLVCPRIFHKACTT 190
                                    6666665566899****************75 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.23
                                    --B-TTT-SB--S CS
                           C1_1  11 ptfCkhCgeflwg 23 
                                     +fC  C+e l++
  gene604|gene604|rna604|rna604 191 AQFCRPCREKLYM 203
                                    589******9965 PP

  == domain 4  score: -0.0 bits;  conditional E-value: 0.42
                                    SS-EEEETTT--E CS
                           C1_1  25 ekqglkCswCkll 37 
                                    +++++ C+ C ++
  gene604|gene604|rna604|rna604 266 SHVMYVCEKCFFY 278
                                    6778888888655 PP

>> Zn_ribbon_17  Zinc-ribbon, C4HC2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   2.9   5.7e-07    0.0011       3      34 ..     111     142 ..     109     147 .. 0.93
   2 !    4.9  10.6      0.01        20       5      37 ..     161     193 ..     157     197 .. 0.91
   3 ?   -0.7   0.2      0.55   1.1e+03      12      24 ..     263     275 ..     262     278 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 5.7e-07
                   Zn_ribbon_17   3 llksCayCelavkgrvvlcgvCeHvlHasCar 34 
                                    + k+C++C   +++ +v c +Ce   H+sC +
  gene604|gene604|rna604|rna604 111 SHKKCNFCGKILRKIFVKCLKCEKKFHNSCSK 142
                                    679***************************87 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.01
                   Zn_ribbon_17   5 ksCayCelavkgrvvlcgvCeHvlHasCarewf 37 
                                    ++C+ C l+   + v c vC  + H++C  + f
  gene604|gene604|rna604|rna604 161 NMCTECGLNNGESAVRCLVCPRIFHKACTTAQF 193
                                    68**************************98776 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.55
                   Zn_ribbon_17  12 lavkgrvvlcgvC 24 
                                    ++v  ++++c++C
  gene604|gene604|rna604|rna604 263 INVSHVMYVCEKC 275
                                    5788999*****9 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0     2e-06    0.0039       6      49 ..     347     398 ..     334     421 .. 0.64

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 2e-06
                                    EEEEET.TEEEEEEEEEEES..TCTEEEEE-GGGTTSSHHHHHHHH.....T CS
                 Acetyltransf_7   6 fVaedd.gkivGfialslld..aeitrlaVdpeyrgkGiGraLlea.....a 49 
                                    + ++dd  +++G+ + +  +  +++ +++V+p y+gkG G  L+++     +
  gene604|gene604|rna604|rna604 347 YTLYDDdSNFIGYFSREKFStkFNLSCIVVLPCYQGKGFGYFLIDFsyclcR 398
                                    444444488889765444446666666******************8444331 PP

>> Zf_RING  KIAA1045 RING finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   2.9   0.00066       1.3       5      36 ..     112     143 ..     108     153 .. 0.88
   2 !   12.9   7.8   4.4e-05     0.089       6      36 ..     161     191 ..     156     210 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00066
                        Zf_RING   5 delCeiCevytaeelypCRvCtkvfHegClrk 36 
                                     + C+ C    ++  ++C  C+k fH++C +k
  gene604|gene604|rna604|rna604 112 HKKCNFCGKILRKIFVKCLKCEKKFHNSCSKK 143
                                    567**************************887 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 4.4e-05
                        Zf_RING   6 elCeiCevytaeelypCRvCtkvfHegClrk 36 
                                    ++C+ C   ++e+ + C vC ++fH+ C   
  gene604|gene604|rna604|rna604 161 NMCTECGLNNGESAVRCLVCPRIFHKACTTA 191
                                    79**************************865 PP

>> Prok-RING_1  Prokaryotic RING finger family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   4.7   0.00011      0.22       2      39 ..     110     145 ..     109     154 .. 0.87
   2 ?    2.8   8.8     0.055   1.1e+02       6      36 ..     159     190 ..     154     202 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00011
                    Prok-RING_1   2 ytgkkCpvCgkelkeedDiVvCpeCgtpyHraCyekag 39 
                                    +  kkC+ Cgk l++    V C +C   +H +C +k  
  gene604|gene604|rna604|rna604 110 DSHKKCNFCGKILRKI--FVKCLKCEKKFHNSCSKKGS 145
                                    5689***********9..9**************98755 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.055
                    Prok-RING_1   6 kCpvCgk.elkeedDiVvCpeCgtpyHraCye 36 
                                     C++C +  l++++ +V C +C   +H+aC  
  gene604|gene604|rna604|rna604 159 DCNMCTEcGLNNGESAVRCLVCPRIFHKACTT 190
                                    68899773599*******************65 PP

>> UPF1_Zn_bind  RNA helicase (UPF2 interacting domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   4.5   0.00011      0.22       2      38 ..     114     149 ..     113     154 .. 0.90
   2 ?    4.0   3.2     0.023        45       2      26 ..     162     186 ..     161     196 .. 0.86
   3 ?   -2.9   0.1       3.1   6.1e+03      83      96 ..     315     328 ..     266     336 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00011
                   UPF1_Zn_bind   2 aCaYCgisdpesvvkCaackkwFCngkgktsashivt 38 
                                    +C++Cg    +  vkC +c+k F n+  ++++s iv+
  gene604|gene604|rna604|rna604 114 KCNFCGKILRKIFVKCLKCEKKFHNSC-SKKGSRIVE 149
                                    7*************************5.778899986 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.023
                   UPF1_Zn_bind   2 aCaYCgisdpesvvkCaackkwFCn 26 
                                     C+ Cg+++ es v+C +c + F  
  gene604|gene604|rna604|rna604 162 MCTECGLNNGESAVRCLVCPRIFHK 186
                                    6999*****************9955 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 3.1
                   UPF1_Zn_bind  83 svvvllcrepcasa 96 
                                    +  ++ cr+ c+ a
  gene604|gene604|rna604|rna604 315 EIDTIFCRNLCLVA 328
                                    44567788877655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (500 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1449  (0.0808188); expected 358.6 (0.02)
Passed bias filter:                      486  (0.0271069); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.63u 0.34s 00:00:00.97 Elapsed: 00:00:00.51
# Mc/sec: 2938.11
//
Query:       gene605|gene605|rna605|rna605  [L=135]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.9e-10   39.8   0.4      6e-10   38.8   0.4    1.6  1  zf-Nse        Zinc-finger of the MIZ type in Nse subunit
     0.0054   17.0   0.9     0.0086   16.4   0.9    1.3  1  zf-RING_2     Ring finger domain
     0.0056   16.3   0.7     0.0081   15.8   0.7    1.2  1  Zn_ribbon_17  Zinc-ribbon, C4HC2 type


Domain annotation for each model (and alignments):
>> zf-Nse  Zinc-finger of the MIZ type in Nse subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.8   0.4     1e-13     6e-10       1      57 []      70     125 ..      70     125 .. 0.93

  Alignments for each domain:
  == domain 1  score: 38.8 bits;  conditional E-value: 1e-13
                                    SXXXXXSSBXXSB-TTTSSB-SSEEEESSS--EEEHHHHHHHCTTTS-EE-SCCC-S CS
                         zf-Nse   1 delaieeerislkCPltlqpfeePvtskkCpHvFEreaIlelikrkktvkCPvagCs 57 
                                    d + +++ +is  C lt+++++e   +  C H  Er+a+l+++k++k+++CPv+gC+
  gene605|gene605|rna605|rna605  70 DTILVQNIKISDICCLTQMKIRERW-EGVCGHAMERSAVLNYMKKNKSARCPVVGCN 125
                                    56889999**************965.569***************************7 PP

>> zf-RING_2  Ring finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.9   1.4e-06    0.0086       5      42 ..      83     121 ..      81     125 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.4e-06
                      zf-RING_2   5 ICleelssadsvlllpCgHvfhreClerwlrssst..CPl 42 
                                    +Cl +++ ++++  + CgH + r+ + ++++++++  CP+
  gene605|gene605|rna605|rna605  83 CCLTQMKIRERWEGV-CGHAMERSAVLNYMKKNKSarCPV 121
                                    469**********99.****************999****7 PP

>> Zn_ribbon_17  Zinc-ribbon, C4HC2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.7   1.4e-06    0.0081       7      55 ..      83     130 ..      75     133 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.4e-06
                   Zn_ribbon_17   7 CayCelavkgrvvlcgvCeHvlHasCarewfenddlaeCps.GCGckcle 55 
                                    C++ +++++      gvC+H +  s + +  +++++a Cp+ GC   + e
  gene605|gene605|rna605|rna605  83 CCLTQMKIRE--RWEGVCGHAMERSAVLNYMKKNKSARCPVvGCNMLLKE 130
                                    5444555554..5679************************9999766555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       777  (0.0433376); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 1019.81
//
Query:       gene606|gene606|rna606|rna606  [L=106]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.058   13.4   0.0      0.068   13.1   0.0    1.3  1  P-mevalo_kinase  Phosphomevalonate kinase


Domain annotation for each model (and alignments):
>> P-mevalo_kinase  Phosphomevalonate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   3.8e-06     0.068      76     110 ..      33      65 ..       5      80 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.8e-06
                P-mevalo_kinase  76 glFcraaiekieaakkdvliisDiRrktdleyfke 110
                                     +F ++ +e+  +++k+ + i DiR+k++l+yfk 
  gene606|gene606|rna606|rna606  33 MVFSKHLFEA--VSHKETVTIPDIRDKKPLRYFKP 65 
                                    4588888885..4778999**************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       802  (0.044732); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 774.24
//
Query:       gene607|gene607|rna607|rna607  [L=84]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.12   12.6   0.0       0.14   12.4   0.0    1.1  1  DUF3102   Protein of unknown function (DUF3102)


Domain annotation for each model (and alignments):
>> DUF3102  Protein of unknown function (DUF3102)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   7.6e-06      0.14      33      96 ..      14      78 ..       5      83 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 7.6e-06
                        DUF3102 33 kEakellpyGewlkwLeesvsysqrtAerl..mrlfeeyGskllasadeassnsealsnltytqal 96
                                   +   e +  G + kw++++++ys  + + +  ++l +++ s+ l+ +  +s  ++ l+++++++ +
  gene607|gene607|rna607|rna607 14 SRGSEQIIVGRFFKWIKSDIQYSPDNKSDVlyLKLRKDFSSNILKLS-VSSDIMKRLASIKFKREV 78
                                   556678889**************876665412788999999988876.666666777777776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (84 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       352  (0.019633); expected 358.6 (0.02)
Passed bias filter:                      244  (0.0136092); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.27s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 609.00
//
Query:       gene608|gene608|rna608|rna608  [L=109]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       345  (0.0192426); expected 358.6 (0.02)
Passed bias filter:                      218  (0.0121591); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 760.82
//
Query:       gene609|gene609|rna609|rna609  [L=239]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.2e-07   30.6   0.1      0.022   15.2   0.0    2.9  3  BRCT            BRCA1 C Terminus (BRCT) domain
    2.8e-06   27.1   0.0    3.6e-05   23.6   0.0    2.4  2  RTT107_BRCT_5   Regulator of Ty1 transposition protein 107 BR
    0.00034   20.5   0.1       0.17   11.8   0.0    2.7  2  PTCB-BRCT       twin BRCT domain
     0.0016   18.7   0.3      0.076   13.3   0.0    2.9  3  LIG3_BRCT       DNA ligase 3 BRCT domain
  ------ inclusion threshold ------
      0.053   13.9   0.3       0.18   12.3   0.1    2.0  2  BRCT_2          BRCT domain, a BRCA1 C-terminus domain
      0.095   12.7   0.0       0.25   11.4   0.0    1.7  1  Sulfolobus_pRN  Sulfolobus plasmid regulatory protein


Domain annotation for each model (and alignments):
>> BRCT  BRCA1 C Terminus (BRCT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.0   5.1e-05      0.15      32      79 .]       1      39 [.       1      39 [. 0.94
   2 !   15.2   0.0   7.2e-06     0.022      35      72 ..      91     128 ..      69     130 .. 0.84
   3 ?   -2.3   0.0         2     6e+03      68      74 ..     198     204 ..     186     220 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 5.1e-05
                                   TTCEEESSCSTTSSEEEESSSHSHHHHHHHHHHTTSEEEETHHHHHHH CS
                           BRCT 32 hGGkvttevskktthlvvgepesrslkylealklnipivheewlldci 79
                                   +GG+  + ++ ++th+v++++         +l++n ++v+ ew+  c+
  gene609|gene609|rna609|rna609  1 MGGRTKQKYDYTVTHIVTQHD---------SLRKNAKCVRVEWVDRCL 39
                                   5999999**************.........899*************97 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 7.2e-06
                                    EE.ESSCSTTSSEEEESSSHSHHHHHHHHHHTTSEEEET CS
                           BRCT  35 kv.ttevskktthlvvgepesrslkylealklnipivhe 72 
                                    k+  +e+++ +thlv g+  ++s+k+l a+ ++ipi+++
  gene609|gene609|rna609|rna609  91 KCaDSEHMQGVTHLVSGSL-ATSEKFLCAMVSGIPIIKP 128
                                    555678999**********.*****************98 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 2
                                    EEEETHH CS
                           BRCT  68 pivheew 74 
                                    +iv+e+w
  gene609|gene609|rna609|rna609 198 EIVDEKW 204
                                    4555554 PP

>> RTT107_BRCT_5  Regulator of Ty1 transposition protein 107 BRCT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.17   5.2e+02      70      89 ..      22      41 ..      18      51 .. 0.82
   2 !   23.6   0.0   1.2e-08   3.6e-05      13      81 ..      61     129 ..      51     143 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.17
                                   HCCCTTEEE-CHHHHHHHHH CS
                  RTT107_BRCT_5 70 sLskapkilspdfiedvLkk 89
                                   sL k+ k + +++++ +L  
  gene609|gene609|rna609|rna609 22 SLRKNAKCVRVEWVDRCLYA 41
                                   78888999*********975 PP

  == domain 2  score: 23.6 bits;  conditional E-value: 1.2e-08
                                    XXX--EEEEESSS.TT..SSHHHHHHHHHTTEEE-S..GCCT-SEEE-SS---SHHHHHHCCCTTEEE-CH CS
                  RTT107_BRCT_5  13 kpevkiravlTgceeevnkedsdkkkLrklGikivq..eakkcntliApkilRTeKFLksLskapkilspd 81 
                                    + +++  + +Tg+     ++++ k++L+ l+ik+ +  +++ +++l++ ++   eKFL+++  +  i++p+
  gene609|gene609|rna609|rna609  61 TYNTHTMVQFTGIPPA--LKHTLKEQLNALDIKCADseHMQGVTHLVSGSLATSEKFLCAMVSGIPIIKPN 129
                                    4455566678999888..89999************9755566*******************9988888875 PP

>> PTCB-BRCT  twin BRCT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.8   0.1    0.0043        13      23      47 ..       1      25 [.       1      34 [. 0.87
   2 !   11.8   0.0   5.8e-05      0.17       9      61 ..      74     128 ..      67     129 .. 0.73

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0043
                                   TT-EEESSEETT-SEEEECSS-CHH CS
                      PTCB-BRCT 23 mGaeyskdltksvTHLicksgeGek 47
                                   mG+  +++   +vTH + ++ + +k
  gene609|gene609|rna609|rna609  1 MGGRTKQKYDYTVTHIVTQHDSLRK 25
                                   899999************9998887 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 5.8e-05
                                    -TTCHHHHHHHHHHTT-EEESSE.ETT-SEEEE.CSS-CHHHHHHHHCT-EEE-C CS
                      PTCB-BRCT   9 sgddrkslqklieamGaeyskdl.tksvTHLic.ksgeGekyekAkkwgipvVsv 61 
                                     +  +++l+++++a+  ++ +   ++ vTHL++   +++ek+ +A   gip++++
  gene609|gene609|rna609|rna609  74 PPALKHTLKEQLNALDIKCADSEhMQGVTHLVSgSLATSEKFLCAMVSGIPIIKP 128
                                    555555666666666666655555788******55589**************987 PP

>> LIG3_BRCT  DNA ligase 3 BRCT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.0   2.6e-05     0.076      41      76 ..      11      39 ..       2      44 .. 0.83
   2 ?    2.0   0.0     0.088   2.6e+02      28      51 ..      86     109 ..      70     118 .. 0.78
   3 ?   -1.7   0.0       1.3   3.8e+03      24      50 ..     189     211 ..     171     223 .. 0.62

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.6e-05
                      LIG3_BRCT 41 keaTHvvvskkeeskkekeksknakaVtaewiwesI 76
                                    ++TH+v++++       +  knak V +ew++ + 
  gene609|gene609|rna609|rna609 11 YTVTHIVTQHD-------SLRKNAKCVRVEWVDRCL 39
                                   569******77.......899*************97 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.088
                      LIG3_BRCT  28 iAydGdlvkeekekeaTHvvvskk 51 
                                     A d +  ++e+++ +TH v+ + 
  gene609|gene609|rna609|rna609  86 NALDIKCADSEHMQGVTHLVSGSL 109
                                    5677788899999******98765 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 1.3
                      LIG3_BRCT  24 rRYfiAydGdlvkeekekeaTHvvvsk 50 
                                    +R ++  ++++v+    ++ TH  +sk
  gene609|gene609|rna609|rna609 189 QRVLVCGGAEIVD----EKWTHCFKSK 211
                                    5555555566665....4566766664 PP

>> BRCT_2  BRCT domain, a BRCA1 C-terminus domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   5.9e-05      0.18      32      80 ..       2      46 ..       1      49 [. 0.84
   2 ?   -2.2   0.0       1.9   5.7e+03      31      47 ..     195     208 ..     183     229 .. 0.48

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5.9e-05
                         BRCT_2 32 GGevvetitsavyiviaesneeelaekrkrrvvspkyIkdCikkgkllp 80
                                   GG+ +++ + +v+++++++     + +++++ v++++++ C+ + + ++
  gene609|gene609|rna609|rna609  2 GGRTKQKYDYTVTHIVTQHD----SLRKNAKCVRVEWVDRCLYAMRRCD 46
                                   88888888888999888887....569**************98877665 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.9
                         BRCT_2  31 nGGevvetitsavyivi 47 
                                     G e+v++     ++++
  gene609|gene609|rna609|rna609 195 GGAEIVDEKW---THCF 208
                                    4556666653...2222 PP

>> Sulfolobus_pRN  Sulfolobus plasmid regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   8.3e-05      0.25      37      68 ..     152     184 ..     125     186 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 8.3e-05
                 Sulfolobus_pRN  37 vyltrlykrGlisrkWr.kiaGkkvreyclkyr 68 
                                    +  + +y rG+i r  r  ++G +vr  c k r
  gene609|gene609|rna609|rna609 152 IVRAVMYWRGVIRRTHRlPFSGWRVRLLCTKAR 184
                                    45567*********999459**********988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (239 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       481  (0.026828); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.64u 0.37s 00:00:01.01 Elapsed: 00:00:00.59
# Mc/sec: 1225.24
//
Query:       gene61|gene61|rna61|rna61  [L=64]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (64 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       369  (0.0205812); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.54u 0.32s 00:00:00.86 Elapsed: 00:00:00.52
# Mc/sec: 370.41
//
Query:       gene610|gene610|rna610|rna610  [L=215]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
       0.73   10.1   6.8        4.9    7.5   3.2    2.5  2  zf-LITAF-like  LITAF-like zinc ribbon domain


Domain annotation for each model (and alignments):
>> zf-LITAF-like  LITAF-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.1    0.0044        79      28      57 ..      14      44 ..       5      45 .. 0.56
   2 ?    7.5   3.2   0.00027       4.9      20      52 ..     175     206 ..     167     213 .. 0.58

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.0044
                  zf-LITAF-like 28 wllalllclfgc.llccliPfcvdslkdveh 57
                                   +l++   clf + + +++i ++ ++ k+++h
  gene610|gene610|rna610|rna610 14 MLISYHTCLFPWlMSILCIVIYENQNKNKKH 44
                                   4555556666654333445556677777666 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.00027
                  zf-LITAF-like  20 eyksgkltwllalllclfgcllccliPfcvdsl 52 
                                    e +++ +t l+al+ c fg+ +c+ + +c+  +
  gene610|gene610|rna610|rna610 175 ELSHQFITLLAALIGCSFGM-CCFSLFLCIGAC 206
                                    44556666677677777775.333334555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (215 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       668  (0.0372581); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.34s 00:00:00.94 Elapsed: 00:00:00.55
# Mc/sec: 1186.37
//
Query:       gene611|gene611|rna611|rna611  [L=93]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.6e-19   69.2   5.6    3.1e-19   69.0   5.6    1.1  1  Ribosomal_L36e  Ribosomal protein L36e
     0.0055   16.8   2.2     0.0059   16.7   2.2    1.0  1  DUF3461         Protein of unknown function (DUF3461)
  ------ inclusion threshold ------
      0.023   14.5   0.0      0.026   14.4   0.0    1.1  1  RMI1_C          Recq-mediated genome instability protein 1, C


Domain annotation for each model (and alignments):
>> Ribosomal_L36e  Ribosomal protein L36e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.0   5.6   5.1e-23   3.1e-19      12      92 ..      12      92 ..       5      93 .] 0.87

  Alignments for each domain:
  == domain 1  score: 69.0 bits;  conditional E-value: 5.1e-23
                 Ribosomal_L36e 12 hkvtknvsklrpsrrkgrltkrtkfvrdiirevaGfapyerrvmellkvskdKralKfaKkrlgthirakrKreelsnvla 92
                                   hk+ k     ++++   ++++++ f rdi++e++G apye ++m++++ s+dK++ K+++krlg+++ ak+K++ l+n ++
  gene611|gene611|rna611|rna611 12 HKTVKTPFPRKSKKFDLSKSQKAFFARDIVKEIVGKAPYELCAMDMIRKSQDKKVKKYLRKRLGSLKCAKKKIDALTNEIH 92
                                   555555555555555668899999*****************************************************9876 PP

>> DUF3461  Protein of unknown function (DUF3461)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   2.2   9.8e-07    0.0059      35     123 ..       4      92 ..       1      93 [] 0.84

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 9.8e-07
                        DUF3461  35 kkekgellaksvkfkfprqrkkvlvdsgseeykevseisavlrkvleeLdklte.kkkeekdikekllkdlkhlekvvns 113
                                    +k+ + l +k vk  fpr++kk    + ++ +   + +++++ k+  eL  +   +k+++k++k+ l k l  l k  ++
  gene611|gene611|rna611|rna611   4 NKKARALHHKTVKTPFPRKSKKFDLSKSQKAFFARDIVKEIVGKAPYELCAMDMiRKSQDKKVKKYLRKRLGSL-KCAKK 82 
                                    5778899*******************999999888888888888999998886658889999999999999888.56788 PP

                        DUF3461 114 kikeierkle 123
                                    ki+ + ++++
  gene611|gene611|rna611|rna611  83 KIDALTNEIH 92 
                                    8888877775 PP

>> RMI1_C  Recq-mediated genome instability protein 1, C-terminal OB-fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   4.3e-06     0.026      53     100 ..      27      72 ..      14      89 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4.3e-06
                         RMI1_C  53 DGsaildvdlssevlteligfspaelkeslalkkdqkkrqklkealke 100
                                    D s+  ++ +++++++e++g  p el ++  ++  +++ +k+k++l++
  gene611|gene611|rna611|rna611  27 DLSKSQKAFFARDIVKEIVGKAPYELCAMDMIR--KSQDKKVKKYLRK 72 
                                    557788999***************997776666..3344455544443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       911  (0.0508115); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.49
# Mc/sec: 575.57
//
Query:       gene612|gene612|rna612|rna612  [L=45]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (45 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       171  (0.00953762); expected 358.6 (0.02)
Passed bias filter:                      157  (0.00875676); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.27s 00:00:00.63 Elapsed: 00:00:00.43
# Mc/sec: 314.64
//
Query:       gene613|gene613|rna613|rna613  [L=639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.9e-23   81.4   0.0      2e-22   79.9   0.0    1.7  2  Aminotran_1_2    Aminotransferase class I and II
    0.00081   18.0   0.0     0.0013   17.3   0.0    1.2  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme


Domain annotation for each model (and alignments):
>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.9   0.0   2.2e-26     2e-22      21     289 ..     102     343 ..      90     358 .. 0.87
   2 ?   -3.2   0.0      0.38   3.4e+03     341     358 ..     611     629 ..     576     632 .. 0.55

  Alignments for each domain:
  == domain 1  score: 79.9 bits;  conditional E-value: 2.2e-26
                                    HHHHHHHHH..HHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHHHTTT-EEEE CS
                  Aminotran_1_2  21 pevakaeke..galaggtlneygpidglpeleealakflgrseklklkreaavvvgsGagaliealifllklnpgdeilv 98 
                                    ++ +k++++  g++ +g+  +yg+ d++ ele+++a ++g         ++a+++++ ++ ++++++ +++  +gd i+ 
  gene613|gene613|rna613|rna613 102 KDEIKQTIRhyGVGTCGPPGFYGTLDLHLELEKKIANLVG--------LSSAILYCNSFTCVNSVITCFCR--RGDIIFY 171
                                    5556777778******************************........888*********99999888888..******* PP

                                    EESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B--HHHHHHHHHHHH CS
                  Aminotran_1_2  99 pdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvilvesphNPtGtvatleeleklldlak 178
                                    ++ + + + ++l + +++ +++           +  lee+l++   +++ + +i+ e+ + +tG++++l+++ ++   ++
  gene613|gene613|rna613|rna613 172 HRCSNEAILRGLYATKATTIEFD----------MCTLEEKLSRYVNRKQ-RNFIIAEGLFRNTGKILDLPKILEM---KR 237
                                    ************99999999998..........8888888888666666.99***********************...** PP

                                    HTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTT..EEEEEESSSTTSSGGG-EEEEEEEHHHHHHHHHHHHHHTSSHHH CS
                  Aminotran_1_2 179 kynlllfvDeaYagfvfgsldavatranveeepn..llivgslsKafGlaGeRvGyilgnaavvsqlrklsrpflsssll 256
                                    k  l+l+vDe  ++  +++++      +  +++n  ++i gs++  f + G   ++++gn +vv+++r l+ ++++s++l
  gene613|gene613|rna613|rna613 238 KFPLRLIVDESLSIPLLDKHGI---STFYGTDVNdiDIIIGSFAHTFCSNG---AFAAGNMHVVDYQRLLAPAYCFSASL 311
                                    ******************8754...344444444557**************...************************** PP

                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                  Aminotran_1_2 257 qaavaaalsdallkqseleemrqrlqkrrkelr 289
                                    +a++++ +  al+   ++ + ++r++++ +++r
  gene613|gene613|rna613|rna613 312 PAFLTKFVLLALEL-PFHLFDARRIHEEFRSIR 343
                                    ****9999888865.688888888888877765 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 0.38
                                    TTEEEEEC.TTS-HHHHHH CS
                  Aminotran_1_2 341 pgrlRitv.Aglteeelee 358
                                    +  +Ri+v   ++++ +e+
  gene613|gene613|rna613|rna613 611 EPGIRICVkNEMSTDVVEK 629
                                    2337777766666666665 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   1.5e-07    0.0013      56     182 ..     131     255 ..     127     268 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.5e-07
                                    HHHHHHHHHHT-SEEEEESSHHHHHHHHHHTTS-TTEEEEEESTSSHHHHHHHHHTHHHTTCEEEEESTTSHHHHHHHCC CS
                Cys_Met_Meta_PP  56 vleeriaaLeggeaalavssGmaAiaaailallkaGdeivvsddlYggtqrllkkvlkklgievkfvdtsdleelekaik 135
                                     le++ia+L g ++a+++    + ++++i+ +++ Gd i  +++     +++l+ ++     +++f  ++ +e+l + ++
  gene613|gene613|rna613|rna613 131 ELEKKIANLVGLSSAILYCNSFTCVNSVITCFCRRGDIIFYHRCS---NEAILRGLYATKATTIEFDMCTLEEKLSRYVN 207
                                    69*****************99****************88777664...44556666666666777777788999999999 PP

                                    T.TEEEEEEESS-TTTT----HHHHHHHHHHTT-EEEEEGTTTHTTTS CS
                Cys_Met_Meta_PP 136 e.ntklvylEtptnpllkvvDiekiaklakkagvlvvvDntfaspllq 182
                                      + + +  E +   + k++D++ki+++ +k  + ++vD +++ pll 
  gene613|gene613|rna613|rna613 208 RkQRNFIIAEGLFRNTGKILDLPKILEMKRKFPLRLIVDESLSIPLLD 255
                                    845678899*********************************999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (639 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1410  (0.0786435); expected 358.6 (0.02)
Passed bias filter:                      492  (0.0274416); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.63u 0.28s 00:00:00.91 Elapsed: 00:00:00.43
# Mc/sec: 4483.55
//
Query:       gene614|gene614|rna614|rna614  [L=41]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0002   20.9   1.3     0.0002   20.9   1.3    2.5  3  GATA           GATA zinc finger
    0.00074   19.6   2.6    0.00074   19.6   2.6    1.5  2  Spt4           Spt4/RpoE2 zinc finger
     0.0053   16.8   6.8      0.016   15.3   6.9    1.6  1  DZR            Double zinc ribbon
  ------ inclusion threshold ------
      0.016   14.6   5.7       0.19   11.2   0.3    2.9  3  zf-ribbon_3    zinc-ribbon domain
       0.03   14.3   6.4       0.25   11.3   2.0    2.1  2  zf-RING_5      zinc-RING finger domain
      0.077   12.7   2.1      0.077   12.7   2.1    2.3  2  Rubredoxin_2   Rubredoxin metal binding domain
      0.092   12.6  12.8        1.8    8.5   5.6    2.3  2  zf-HIT         HIT zinc finger
        0.1   13.1   6.3       0.15   12.6   6.3    1.3  1  zf-CHY         CHY zinc finger
       0.18   11.9   6.9        4.1    7.6   6.9    2.4  1  Zn-ribbon_8    Zinc ribbon domain
       0.18   11.4   7.7       0.59    9.8   1.4    1.9  1  TackOD1        Thaumarchaeal output domain 1
       0.22   11.5   8.0        1.4    8.9   8.0    1.9  1  HypA           Hydrogenase/urease nickel incorporation, metal
       0.26   11.2  10.4        0.2   11.6   3.7    2.0  2  zf-C3HC4_3     Zinc finger, C3HC4 type (RING finger)
       0.45   10.5   4.9      0.084   12.9   1.6    1.6  2  Anti-TRAP      Tryptophan RNA-binding attenuator protein inhi
       0.89    9.4   8.2        2.1    8.3   0.2    2.6  3  zf-C2H2_3      zinc-finger of acetyl-transferase ESCO
       0.91    9.2   6.0        4.9    6.8   0.2    2.9  3  zf_UBZ         Ubiquitin-Binding Zinc Finger
        1.2    9.4   6.1        2.6    8.4   2.2    2.6  3  zinc_ribbon_9  zinc-ribbon
        1.4    8.9   9.5         51    3.9   5.7    3.0  2  Nudix_N_2      Nudix N-terminal
        8.5    6.5  13.3        4.1    7.5   0.8    3.0  3  ADK_lid        Adenylate kinase, active site lid


Domain annotation for each model (and alignments):
>> GATA  GATA zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   1.3     2e-07    0.0002      22      35 ..       2      15 ..       1      16 [. 0.92
   2 ?   -0.3   0.3      0.83   8.2e+02       1       5 [.      17      21 ..      17      23 .. 0.77
   3 ?   -1.2   0.3       1.6   1.6e+03       1       6 [.      34      39 ..      34      40 .. 0.77

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 2e-07
                           GATA 22 LCnaCGlyykkkgl 35
                                   LCnaCGl+y k+++
  gene614|gene614|rna614|rna614  2 LCNACGLRYSKYRR 15
                                   9**********996 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.83
                           GATA  1 CsnCg 5 
                                   C +C+
  gene614|gene614|rna614|rna614 17 CMQCN 21
                                   88887 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 1.6
                           GATA  1 CsnCgt 6 
                                   C +C++
  gene614|gene614|rna614|rna614 34 CPKCKS 39
                                   889986 PP

>> Spt4  Spt4/RpoE2 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.1       3.7   3.7e+03      21      24 ..       3       6 ..       2      12 .. 0.58
   2 !   19.6   2.6   7.4e-07   0.00074       2      25 ..      15      39 ..      14      41 .] 0.91

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 3.7
                           Spt4 21 CpnC 24
                                   C+ C
  gene614|gene614|rna614|rna614  3 CNAC 6 
                                   5555 PP

  == domain 2  score: 19.6 bits;  conditional E-value: 7.4e-07
                           Spt4  2 rACllCklvktedqFeeegCpnC.e 25
                                   r C++C+ v  +++Fe+  Cp C +
  gene614|gene614|rna614|rna614 15 RVCMQCNKVGVKANFEKVSCPKCkS 39
                                   99*********************44 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   6.9   1.6e-05     0.016       1      36 [.       3      39 ..       3      41 .] 0.73

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.6e-05
                            DZR  1 CpqCgeelppdarfCseCgtk.lkavaaedrCpsCge 36
                                   C  Cg   ++  r+C +C++  +ka  ++  Cp+C++
  gene614|gene614|rna614|rna614  3 CNACGLRYSKYRRVCMQCNKVgVKANFEKVSCPKCKS 39
                                   7788888888888888888776666666888888876 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.1     0.037        37       5      23 ..       3       7 ..       1       9 [. 0.58
   2 ?    1.9   0.1      0.16   1.6e+02       4      11 ..      16      23 ..      14      29 .. 0.71
   3 ?   11.2   0.3   0.00019      0.19       2      10 ..      31      39 ..      30      41 .] 0.81

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.037
                    zf-ribbon_3  5 CPnCGaplssddnvCpyCG 23
                                   C++C              G
  gene614|gene614|rna614|rna614  3 CNAC--------------G 7 
                                   5555..............5 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.16
                    zf-ribbon_3  4 rCPnCGap 11
                                    C +C+++
  gene614|gene614|rna614|rna614 16 VCMQCNKV 23
                                   58899986 PP

  == domain 3  score: 11.2 bits;  conditional E-value: 0.00019
                    zf-ribbon_3  2 tvrCPnCGa 10
                                   +v+CP+C++
  gene614|gene614|rna614|rna614 31 KVSCPKCKS 39
                                   79*****98 PP

>> zf-RING_5  zinc-RING finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   2.0   0.00025      0.25      23      44 .]       1      22 [.       1      22 [. 0.92
   2 ?    5.7   0.1     0.014        14      35      43 ..      30      38 ..      24      39 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00025
                      zf-RING_5 23 ifCekClkkllekeavCpiCrk 44
                                   ++C++C  ++++ ++vC +C+k
  gene614|gene614|rna614|rna614  1 VLCNACGLRYSKYRRVCMQCNK 22
                                   68*********99*******86 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.014
                      zf-RING_5 35 keavCpiCr 43
                                   +++ Cp C+
  gene614|gene614|rna614|rna614 30 EKVSCPKCK 38
                                   6789****8 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   2.1   7.8e-05     0.077       3      21 ..       3      21 ..       2      24 .. 0.94
   2 ?    3.7   1.2     0.052        52      17      22 ..      34      39 ..      33      40 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 7.8e-05
                   Rubredoxin_2  3 CsqCGfesakwfGrCpsCg 21
                                   C++CG +++k+   C +C+
  gene614|gene614|rna614|rna614  3 CNACGLRYSKYRRVCMQCN 21
                                   ******************8 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.052
                   Rubredoxin_2 17 CpsCgs 22
                                   Cp C+s
  gene614|gene614|rna614|rna614 34 CPKCKS 39
                                   ****97 PP

>> zf-HIT  HIT zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   5.6    0.0018       1.8       4      20 ..       2      21 ..       1      24 [. 0.92
   2 ?    7.6   5.2    0.0034       3.4       2      21 ..      14      39 ..      14      41 .] 0.84

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0018
                                   B-TTT-S.B-SEE..-TTT- CS
                         zf-HIT  4 lCgvCgf.pakYk..CpkCn 20
                                   lC  Cg   +kY+  C +Cn
  gene614|gene614|rna614|rna614  2 LCNACGLrYSKYRrvCMQCN 21
                                   8***********988***99 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0034
                                   --B-TTT-S......B-SEE-TTT-- CS
                         zf-HIT  2 rklCgvCgf......pakYkCpkCnt 21
                                   r +C  C++      + k +CpkC+ 
  gene614|gene614|rna614|rna614 14 RRVCMQCNKvgvkanFEKVSCPKCKS 39
                                   56899999888888899*******85 PP

>> zf-CHY  CHY zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   6.3   0.00015      0.15      43      74 ..       2      39 ..       1      40 [. 0.84

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00015
                         zf-CHY 43 lcllCeteq.ekavlCkkCkk.....efaeyfCpiCkl 74
                                   lc  C  +  +   +C +C+k     +f++ +Cp+Ck+
  gene614|gene614|rna614|rna614  2 LCNACGLRYsKYRRVCMQCNKvgvkaNFEKVSCPKCKS 39
                                   799999876366788****999999999999*****96 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   6.9    0.0041       4.1       8      34 ..       3      39 ..       1      41 [] 0.56

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0041
                    Zn-ribbon_8  8 CeeCghefevlqsis.dap........lta.CPeCgs 34
                                   C++Cg ++ + +++  + +        +++ CP+C+s
  gene614|gene614|rna614|rna614  3 CNACGLRYSKYRRVCmQCNkvgvkanfEKVsCPKCKS 39
                                   6777777773333333333334444456667****98 PP

>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   1.4   0.00059      0.59      75      99 ..       2      26 ..       1      29 [. 0.84

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00059
                        TackOD1 75 lCpsCksghlnvrevCpkCkSidie 99
                                   lC+ C     ++r vC +C+ + ++
  gene614|gene614|rna614|rna614  2 LCNACGLRYSKYRRVCMQCNKVGVK 26
                                   7999999999999999999987665 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   8.0    0.0014       1.4      68      94 ..      12      39 ..       1      41 [] 0.70

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0014
                                   --EEEETTTS-EEECHHH.HHS-TTTSS CS
                           HypA 68 pvkvrCreCgkefeleek.alrCpkCgs 94
                                   + +  C +C+k + +++  +++CpkC+s
  gene614|gene614|rna614|rna614 12 KYRRVCMQCNKVGVKANFeKVSCPKCKS 39
                                   5566788888777766634779999987 PP

>> zf-C3HC4_3  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   3.7    0.0002       0.2      24      45 ..       1      22 [.       1      27 [. 0.93
   2 ?    4.7   0.5     0.028        28      36      45 ..      30      39 ..      24      41 .] 0.73

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0002
                                   EE-HHHHHHHHHTT-B-TTT-- CS
                     zf-C3HC4_3 24 vlCeeCaekllkrkkkCpiCrr 45
                                   vlC++C  ++ k ++ C+ C++
  gene614|gene614|rna614|rna614  1 VLCNACGLRYSKYRRVCMQCNK 22
                                   59********9*********97 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.028
                                   TT-B-TTT-- CS
                     zf-C3HC4_3 36 rkkkCpiCrr 45
                                   +k +Cp C++
  gene614|gene614|rna614|rna614 30 EKVSCPKCKS 39
                                   5568999987 PP

>> Anti-TRAP  Tryptophan RNA-binding attenuator protein inhibitory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.7     0.045        45      16      35 ..       3      22 ..       1      27 [. 0.61
   2 ?   12.9   1.6   8.4e-05     0.084      12      37 ..      16      38 ..       7      40 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.045
                                   TTTTSEETTE......E-TT CS
                      Anti-TRAP 16 CngsGkiepeeprasleCPk 35
                                   Cn  G   ++  r  ++C k
  gene614|gene614|rna614|rna614  3 CNACGLRYSKYRRVCMQCNK 22
                                   66666666666666666655 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 8.4e-05
                                   E-TTTTTTSEETTE......E-TTTT CS
                      Anti-TRAP 12 kCdaCngsGkiepeeprasleCPkCs 37
                                    C +Cn+ G  +       + CPkC+
  gene614|gene614|rna614|rna614 16 VCMQCNKVGVKANF---EKVSCPKCK 38
                                   6********98887...5789****8 PP

>> zf-C2H2_3  zinc-finger of acetyl-transferase ESCO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.2    0.0021       2.1      16      26 ..       3      13 ..       1      16 [. 0.89
   2 ?   -0.2   0.4       0.9     9e+02      15      20 ..      15      21 ..      11      22 .. 0.65
   3 ?    6.2   0.3     0.009       8.9       9      20 ..      27      38 ..      23      39 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0021
                      zf-C2H2_3 16 CkeCgMvYnpg 26
                                   C+ Cg+ Y+++
  gene614|gene614|rna614|rna614  3 CNACGLRYSKY 13
                                   ********986 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.9
                      zf-C2H2_3 15 q.CkeCg 20
                                   + C +C+
  gene614|gene614|rna614|rna614 15 RvCMQCN 21
                                   2499996 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.009
                      zf-C2H2_3  9 ksfgasqCkeCg 20
                                    +f ++ C++C+
  gene614|gene614|rna614|rna614 27 ANFEKVSCPKCK 38
                                   5788999****6 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.1      0.28   2.8e+02       4      11 ..       2       9 ..       1      13 [. 0.78
   2 ?    3.6   0.2     0.051        50       4      10 ..      16      22 ..      14      24 .. 0.87
   3 ?    6.8   0.2     0.005       4.9       2      11 ..      31      40 ..      30      41 .] 0.81

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.28
                         zf_UBZ  4 lCerCgke 11
                                   lC  Cg +
  gene614|gene614|rna614|rna614  2 LCNACGLR 9 
                                   7999*966 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.051
                         zf_UBZ  4 lCerCgk 10
                                   +C +C+k
  gene614|gene614|rna614|rna614 16 VCMQCNK 22
                                   8*****9 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.005
                         zf_UBZ  2 tylCerCgke 11
                                    + C++C+++
  gene614|gene614|rna614|rna614 31 KVSCPKCKSS 40
                                   679****986 PP

>> zinc_ribbon_9  zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.1      0.34   3.4e+02      23      28 ..       2       7 ..       1      10 [. 0.82
   2 ?    2.8   0.2      0.14   1.4e+02      22      28 ..      16      21 ..      11      24 .. 0.77
   3 ?    8.4   2.2    0.0026       2.6       5      29 ..      17      39 ..      16      40 .. 0.71

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.34
                  zinc_ribbon_9 23 lCPhCg 28
                                   lC+ Cg
  gene614|gene614|rna614|rna614  2 LCNACG 7 
                                   7****8 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.14
                  zinc_ribbon_9 22 vlCPhCg 28
                                   v C +C+
  gene614|gene614|rna614|rna614 16 V-CMQCN 21
                                   4.99998 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.0026
                  zinc_ribbon_9  5 ChqCdrfVsvspdedsdvlCPhCgg 29
                                   C qC+  V v ++ +  v+CP C++
  gene614|gene614|rna614|rna614 17 CMQCN-KVGVKANFEK-VSCPKCKS 39
                                   77888.7887665444.46****87 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   5.7     0.051        51      20      31 ..      12      23 ..       2      24 .. 0.84
   2 ?    2.7   0.1      0.12   1.2e+02      25      29 ..      34      38 ..      28      41 .] 0.69

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.051
                                   S-EEEETTTTEE CS
                      Nudix_N_2 20 reRlvCpaCgti 31
                                   + R vC +C+ +
  gene614|gene614|rna614|rna614 12 KYRRVCMQCNKV 23
                                   6799*****987 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.12
                                   ETTTT CS
                      Nudix_N_2 25 CpaCg 29
                                   Cp+C 
  gene614|gene614|rna614|rna614 34 CPKCK 38
                                   55553 PP

>> ADK_lid  Adenylate kinase, active site lid
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.3     0.065        65       3      12 ..       2      11 ..       1      13 [. 0.79
   2 ?    7.5   0.8    0.0041       4.1       1      10 [.      14      23 ..      14      23 .. 0.91
   3 ?    3.6   1.0     0.065        65       3      10 ..      33      40 ..      32      40 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.065
                                   E-TTT--EEE CS
                        ADK_lid  3 vCpkCGrsYh 12
                                    C +CG  Y+
  gene614|gene614|rna614|rna614  2 LCNACGLRYS 11
                                   6999998887 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0041
                                   EEE-TTT--E CS
                        ADK_lid  1 RrvCpkCGrs 10
                                   RrvC +C+++
  gene614|gene614|rna614|rna614 14 RRVCMQCNKV 23
                                   9******975 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.065
                                   E-TTT--E CS
                        ADK_lid  3 vCpkCGrs 10
                                    CpkC+ s
  gene614|gene614|rna614|rna614 33 SCPKCKSS 40
                                   6****976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (41 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       769  (0.0428914); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.43
# Mc/sec: 286.15
//
Query:       gene615|gene615|rna615|rna615  [L=79]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       503  (0.0280551); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 622.89
//
Query:       gene616|gene616|rna616|rna616  [L=491]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.3e-15   54.8   0.5    8.8e-10   38.5   0.1    3.2  3  Thioredoxin    Thioredoxin
      2e-10   40.9   2.4    3.2e-05   23.9   0.2    3.4  3  Thioredoxin_6  Thioredoxin-like domain
    6.4e-05   23.4   0.3      0.011   16.1   0.1    3.2  2  Thioredoxin_2  Thioredoxin-like domain
  ------ inclusion threshold ------
      0.038   13.8   0.7        1.1    9.1   0.0    2.6  3  TraF           F plasmid transfer operon protein
       0.15   12.5   0.1       0.36   11.3   0.1    1.6  1  DUF4713        Domain of unknown function (DUF4713)


Domain annotation for each model (and alignments):
>> Thioredoxin  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.5   0.1   2.4e-13   8.8e-10      19     102 ..      23     107 ..       9     108 .. 0.90
   2 !   11.5   0.0     6e-05      0.22      38     101 ..     157     219 ..     137     221 .. 0.83
   3 ?    1.0   0.1      0.12   4.1e+02       3      28 ..     228     254 ..     226     277 .. 0.84

  Alignments for each domain:
  == domain 1  score: 38.5 bits;  conditional E-value: 2.4e-13
                                    SEEEEEEE-TTSHHHHCHHHHHHHHHHHCTT...TSEEEEEETTTSHHHHHHTT-SSSSEEEEEETTEEEEEEESS-HHH CS
                    Thioredoxin  19 klvlveFyApwCghCkalaPeleklaeelkd...kvklakvdvdenedlakkyevegiPtlklfkngkevkkyegareke 95 
                                    +  l +Fy + C hC++++P+++++ + l      +k+ ++ +de+   ++ +++ ++Ptl+l k  +e++++ g ++ +
  gene616|gene616|rna616|rna616  23 SVYLTKFYKENCVHCQNMSPHINEIEDMLMRhdtGIKFKQISCDEC--DCDALDIVAVPTLILNKGKEEISRLRGYSDYN 100
                                    66799**********************99888889***********..588889*******9998888************ PP

                                    HHHHHHH CS
                    Thioredoxin  96 klaaflk 102
                                     +a+f++
  gene616|gene616|rna616|rna616 101 GIAKFIT 107
                                    ***9996 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 6e-05
                                    HHHHHHHHHCTTTSEEEEEETTTSHHHHHHTT-SSSSEEEEEETTEEEEEEESS-HHHHHHHHH CS
                    Thioredoxin  38 PeleklaeelkdkvklakvdvdenedlakkyevegiPtlklfkngkevkkyegarekeklaafl 101
                                      ++++a+++++++k+ ++  ++  +l ++++++ +P+++ + ng   + y+g+++ +++ +f+
  gene616|gene616|rna616|rna616 157 TIVADVAKKYSGQLKVGEISENNAVNLTHRFNIQTFPAVIAIYNGI-LAGYSGKHTPASVFEFV 219
                                    557899*********************************9998886.67778877767766666 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.12
                                    EESSHHHHHHHHTT.TSSEEEEEEE-T CS
                    Thioredoxin   3 lvltkenFeeevak.ekklvlveFyAp 28 
                                    ++++ e+Fe+ v+k +k++ +v Fy++
  gene616|gene616|rna616|rna616 228 KEINLEEFEQLVSKdAKSPKFVVFYSN 254
                                    5678899*****997888999999986 PP

>> Thioredoxin_6  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0     0.024        86      40      75 ..      76     110 ..      51     118 .. 0.81
   2 !   11.9   0.2   4.3e-05      0.15       6     103 ..     153     252 ..     148     286 .. 0.78
   3 !   23.9   0.2   8.8e-09   3.2e-05      45     168 ..     308     425 ..     262     436 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.024
                                    -S.SEEEEEETTTTEEEEEETHT--HHHHHHHHHHH- CS
                  Thioredoxin_6  40 ke.pavllfrkfdeekvkydgekitvddlkkfiekns 75 
                                       p+++l ++  ee+  + g   +++ ++kfi++n 
  gene616|gene616|rna616|rna616  76 VAvPTLILNKG-KEEISRLRGY-SDYNGIAKFITDNL 110
                                    44489998888.6778999998.7**********995 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 4.3e-05
                                    STHHHHHHHHTTT-T.TSEEEEE--HHHHHH...TT--S.SEEEEEETTTTEEEEEETHT--HHHHHHHHHHH---SEEE CS
                  Thioredoxin_6   6 keeseiFekvakelkgdvrfgvtkskevadk...lgvke.pavllfrkfdeekvkydgekitvddlkkfieknslplvre 81 
                                    ++ ++i   vak+++g + +g ++++++++    +++++ pav+ + +     + y+g+  t  ++ +f++  + p + e
  gene616|gene616|rna616|rna616 153 DPIRTIVADVAKKYSGQLKVGEISENNAVNLthrFNIQTfPAVIAIYNG--ILAGYSGK-HTPASVFEFVDRLMAPSFKE 229
                                    566667778*****************95555555*****9**9999983..33679997.8******************* PP

                                    -SHHHHHHHHTSS--.EEEEEEE CS
                  Thioredoxin_6  82 ltpenaeelfeeglp.pllllfl 103
                                    ++ e +e+l +++ + p +++f+
  gene616|gene616|rna616|rna616 230 INLEEFEQLVSKDAKsPKFVVFY 252
                                    ********988875414555555 PP

  == domain 3  score: 23.9 bits;  conditional E-value: 8.8e-09
                                    EEEETTTTEEEEEETHT--HHHHHHHHHHH---SEEE-SHHHHHHHHTSS--EEEEEEE-TTSTTHHHHHHHHHHHHHHT CS
                  Thioredoxin_6  45 llfrkfdeekvkydgekitvddlkkfieknslplvreltpenaeelfeeglppllllflkkddeeteklkkaiekvakef 124
                                    ++f+++  ++  ++++  + + +++++ +  +p+v+ +t +n+ ++f+  +p ++ll++ ++de  e l++a +++ + +
  gene616|gene616|rna616|rna616 308 TVFKDNVFHRCPIPLS--NPQGIAEWLFNSHFPNVTRITNDNFYTVFHGIKP-AVLLLT-QNDELVELLEDAANRINTGL 383
                                    4566655566677775..9*****************************9988.555555.45666666666666666555 PP

                                    ..TTT-EEEEEETTGGHHHHHHTT--GGG-SEEEEEESSSS-EEEE CS
                  Thioredoxin_6 125 ..kdkinfaladaksfkrpleylglsssdlPvivivdsashkykyp 168
                                      +d+   a++d+ +f  +l  l l   + Pv+vi+d   +++ ++
  gene616|gene616|rna616|rna616 384 pfNDQ-VMAVLDVNEFSMFLPAL-LPGLKSPVMVIFD--PQRQLFF 425
                                    32566.88899999999999988.5557899999999..3333333 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.1   3.2e-06     0.011       6     107 ..      23     104 ..      19     106 .. 0.87
   2 ?    3.6   0.0     0.025        88      67      96 ..     178     206 ..     139     217 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 3.2e-06
                  Thioredoxin_2   6 kpvlvvftdpdCpyCkklkkelkelddvtvrvllfplkpsfepkavaiwcakekkkafkdieenvelarkygvrgtPtiv 85 
                                       l+ f++++C  C+ +   + e++d   r        +  +k+ +i+c++                +++++ ++Pt++
  gene616|gene616|rna616|rna616  23 SVYLTKFYKENCVHCQNMSPHINEIEDMLMR-------HDTGIKFKQISCDECDC-------------DALDIVAVPTLI 82 
                                    567888*******************888555.......6678**********995.............89********** PP

                  Thioredoxin_2  86 fldgkeivarlpGyvpaeelea 107
                                    +  gke++ rl+Gy + + +++
  gene616|gene616|rna616|rna616  83 LNKGKEEISRLRGYSDYNGIAK 104
                                    **************98777665 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.025
                  Thioredoxin_2  67 eenvelarkygvrgtPtiv.fldgkeivarl 96 
                                    +  v l ++++++ +P+++ +++g   +a +
  gene616|gene616|rna616|rna616 178 NNAVNLTHRFNIQTFPAVIaIYNGI--LAGY 206
                                    455779999********77466664..4444 PP

>> TraF  F plasmid transfer operon protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.0    0.0003       1.1     133     169 ..      26      67 ..      19      90 .. 0.70
   2 ?    2.2   0.0     0.036   1.3e+02     150     200 ..     158     199 ..     143     202 .. 0.65
   3 ?   -2.9   0.1       1.4     5e+03      72     109 ..     259     297 ..     258     304 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0003
                           TraF 133 LlfFyrgkcpyceaqapilqafad.....kyglevraVsvdg 169
                                    L  Fy+++c  c+ ++p++++++d     ++g++ + +s+d+
  gene616|gene616|rna616|rna616  26 LTKFYKENCVHCQNMSPHINEIEDmlmrhDTGIKFKQISCDE 67 
                                    667****************98766111114577777777765 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.036
                           TraF 150 ilqafadky..glevraVsvdgrplpelpnarvdkgqaarlgvkrtPalvlvd 200
                                    i+ ++a+ky  +l+v  +s ++ ++  l +         r++++++Pa++++ 
  gene616|gene616|rna616|rna616 158 IVADVAKKYsgQLKVGEISENNAVN--LTH---------RFNIQTFPAVIAIY 199
                                    5555555553345555555555555..666.........**********9986 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 1.4
                           TraF  72 qrvaldkaskFaevwqrvllanPeLdytlr.rPvsnlar 109
                                    ++++++ a++++ ++q +  ++P L + +  +P ++   
  gene616|gene616|rna616|rna616 259 NSFYRKAAHEYKLRAQIFKSKDPALFQRASiYPKKADEE 297
                                    567788888888888888888888887777677665554 PP

>> DUF4713  Domain of unknown function (DUF4713)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1    0.0001      0.36      12      43 ..     450     480 ..     441     482 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0001
                        DUF4713  12 lkLqslqpfqspwdiaaFvvlllFigtVllLl 43 
                                    +kL+   p  s w    F +++lFi+ +l+ l
  gene616|gene616|rna616|rna616 450 GKLKPY-PYRSSWKKYMFGIIFLFILGFLVSL 480
                                    688888.*******************999755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (491 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       724  (0.0403815); expected 358.6 (0.02)
Passed bias filter:                      611  (0.0340789); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.47
# Mc/sec: 3110.33
//
Query:       gene617|gene617|rna617|rna617  [L=35]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.017   14.5   0.1      0.017   14.5   0.1    1.0  1  DUF3379   Protein of unknown function (DUF3379)


Domain annotation for each model (and alignments):
>> DUF3379  Protein of unknown function (DUF3379)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1   9.4e-07     0.017      40      66 ..       8      34 ..       2      35 .] 0.90

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 9.4e-07
                        DUF3379 40 aldkklkqalkvdvPedLaeklllkqs 66
                                   +++++l++ l+ +v e+L++++ll++s
  gene617|gene617|rna617|rna617  8 EVNEELNEELNEEVNEELNDRILLEKS 34
                                   68999*******************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (35 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1141  (0.0636399); expected 358.6 (0.02)
Passed bias filter:                      504  (0.0281109); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.30s 00:00:00.65 Elapsed: 00:00:00.44
# Mc/sec: 240.40
//
Query:       gene618|gene618|rna618|rna618  [L=386]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.035   14.5   1.5      0.088   13.2   1.5    1.6  1  SRP9-21   Signal recognition particle 9 kDa protein (SRP9)


Domain annotation for each model (and alignments):
>> SRP9-21  Signal recognition particle 9 kDa protein (SRP9)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   1.5   4.9e-06     0.088      26      80 ..      56     113 ..      48     116 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.9e-06
                        SRP9-21  26 tkYsikakkkkkkkkkkkaksekkaskas...pprgtltlKtydpvsGvclkYkTnka 80 
                                     kY+ + kk+k+k+kkk+++++k++s+++    p ++  ++++d +   c+kY+T+ +
  gene618|gene618|rna618|rna618  56 YKYRGSYKKRKEKRKKKSEDTKKQPSNRRivnLPASQPYIRIVDGEERLCFKYNTKIS 113
                                    67888866666666666666666665555888999999*****************865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (386 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1401  (0.0781416); expected 358.6 (0.02)
Passed bias filter:                      464  (0.0258799); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.44
# Mc/sec: 2629.83
//
Query:       gene619|gene619|rna619|rna619  [L=132]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      6e-08   32.7  10.9      6e-08   32.7  10.9    1.6  1  zf-AN1    AN1-like Zinc finger


Domain annotation for each model (and alignments):
>> zf-AN1  AN1-like Zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.7  10.9   3.4e-12     6e-08       1      38 [.      69     107 ..      69     109 .. 0.93

  Alignments for each domain:
  == domain 1  score: 32.7 bits;  conditional E-value: 3.4e-12
                         zf-AN1   1 CsfksCkkkdflp.fkCryCgkvFClkHrlpedHdCkkl 38 
                                    C+f +Ck k + +  +Cr+C+  FC kH +pe+H Ck+ 
  gene619|gene619|rna619|rna619  69 CDFVDCKLKRSKVcSDCRFCKYLFCGKHKMPEEHMCKEI 107
                                    99********8777**********************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1340  (0.0747392); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 857.82
//
Query:       gene62|gene62|rna62|rna62  [L=49]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (49 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       181  (0.0100954); expected 358.6 (0.02)
Passed bias filter:                      147  (0.00819901); expected 358.6 (0.02)
Passed Vit filter:                         7  (0.000390429); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.29s 00:00:00.64 Elapsed: 00:00:00.44
# Mc/sec: 332.12
//
Query:       gene620|gene620|rna620|rna620  [L=137]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.5e-34  118.5   2.1    1.8e-34  118.3   2.1    1.0  1  Ribosomal_S17e  Ribosomal S17


Domain annotation for each model (and alignments):
>> Ribosomal_S17e  Ribosomal S17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.3   2.1     1e-38   1.8e-34       2     112 ..       8     118 ..       7     126 .. 0.97

  Alignments for each domain:
  == domain 1  score: 118.3 bits;  conditional E-value: 1e-38
                                    X----HHHHHHHHHHHHS-TTT--S-HHHHHHHHHHHS----SHHHHHHHHHHHHHHHHTTSS--SS---HHHHHHHHHH CS
                 Ribosomal_S17e   2 grvrtktvKkaarviiekyyskltndFhtnkkvceevaiipskklrnkiaGyvthlmkriqkgpvrgislklqeeererr 81 
                                    g+++ k vKkaa++i+ekyy  l++dF +nkkv+++ + i++kk  nk++Gyvthl+k + kg+ +g  +k  ee+re++
  gene620|gene620|rna620|rna620   8 GQIKIKSVKKAAKQIVEKYYVYLNEDFYHNKKVVSDFTEIQTKKTLNKVTGYVTHLVKLVLKGTSKGLYIKKHEEDREKK 87 
                                    7899**************************************************************************** PP

                                    H-----------------HHHHHHHHHH-X. CS
                 Ribosomal_S17e  82 dnyvpevsaldqeaievdkdtkemlkslgfe 112
                                    + y p+vs ld++ +evd+ t+em+++ gfe
  gene620|gene620|rna620|rna620  88 EGYLPKVSFLDSNRVEVDSVTMEMVNAYGFE 118
                                    **************************99985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (137 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       975  (0.0543812); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 981.77
//
Query:       gene621|gene621|rna621|rna621  [L=79]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       368  (0.0205254); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 594.26
//
Query:       gene622|gene622|rna622|rna622  [L=337]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (337 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2401  (0.133917); expected 358.6 (0.02)
Passed bias filter:                      470  (0.0262145); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 2456.01
//
Query:       gene623|gene623|rna623|rna623  [L=500]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00026   21.1   1.3    0.00026   21.1   1.3    4.3  6  XhlA             Haemolysin XhlA
    0.00039   20.5  14.9      0.002   18.1   3.8    2.6  3  DUF1664          Protein of unknown function (DUF1664)
     0.0015   17.5  14.3     0.0015   17.5  14.3    2.9  3  Spc7             Spc7 kinetochore protein
     0.0067   16.5   2.5     0.0067   16.5   2.5    3.1  3  Baculo_PEP_C     Baculovirus polyhedron envelope protein, PEP
  ------ inclusion threshold ------
      0.028   14.6   4.2      0.061   13.5   4.2    1.6  1  Cob_adeno_trans  Cobalamin adenosyltransferase
      0.031   14.3  15.9       0.23   11.5   5.4    3.1  2  TolA_bind_tri    TolA binding protein trimerisation
       0.05   12.9   9.1       0.11   11.8   9.1    1.6  1  JMY              Junction-mediating and -regulatory protein
      0.093   12.4  11.4       0.02   14.6   2.9    3.3  3  DUF4988          Domain of unknown function
       0.21   11.5   8.0       0.25   11.3   0.1    3.7  4  Type2_restr_D3   Type-2 restriction enzyme D3 domain
       0.25   11.6   7.9        4.3    7.7   0.4    3.4  3  Rx_N             Rx N-terminal domain
       0.38   11.3   7.3        1.1    9.8   0.3    3.5  3  NPV_P10          Nucleopolyhedrovirus P10 protein
       0.66    9.3  31.8      0.071   12.5  22.6    2.8  2  Tropomyosin      Tropomyosin
       0.87    8.0   2.9        1.2    7.6   2.9    1.1  1  FUSC             Fusaric acid resistance protein family
        1.4    9.1   7.0        6.9    7.0   0.5    3.8  4  Plasmid_RAQPRD   Plasmid protein of unknown function (Plasmid
        2.9    8.4  12.5        2.3    8.7   0.3    4.4  4  FlaC_arch        Flagella accessory protein C (FlaC)
        4.7    6.7  34.5      0.095   12.2  26.3    2.1  2  MscS_porin       Mechanosensitive ion channel porin domain
        5.4    6.5  23.9      0.071   12.7  15.3    2.2  2  Exonuc_VII_L     Exonuclease VII, large subunit
        7.2    6.5  16.7       0.31   11.0   0.4    3.8  4  Prefoldin        Prefoldin subunit
        8.3    7.0  24.8        6.4    7.4   7.3    3.8  3  Syntaxin-6_N     Syntaxin 6, N-terminal


Domain annotation for each model (and alignments):
>> XhlA  Haemolysin XhlA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   1.0       1.5   1.4e+03      28      44 ..     153     169 ..     138     172 .. 0.71
   2 !   21.1   1.3   2.7e-07   0.00026       4      49 ..     331     376 ..     328     380 .. 0.97
   3 ?    1.0   0.3      0.52   4.9e+02      14      46 ..     376     408 ..     375     416 .. 0.82
   4 ?    1.0   0.7      0.54   5.1e+02       5      37 ..     402     431 ..     398     437 .. 0.71
   5 ?    0.4   0.4      0.79   7.4e+02      13      47 ..     431     465 ..     428     471 .. 0.74
   6 ?   -0.8   0.1         2   1.9e+03      10      20 ..     456     466 ..     450     494 .. 0.48

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 1.5
                           XhlA  28 aeaeekiknleedlkkl 44 
                                    +e +e ik++++ lk+l
  gene623|gene623|rna623|rna623 153 NELREDIKSINDLLKEL 169
                                    55666666666666665 PP

  == domain 2  score: 21.1 bits;  conditional E-value: 2.7e-07
                           XhlA   4 erlerietkldnleervdkleekaaeaeekiknleedlkklesnqk 49 
                                    erl++i++ + +l+++++ l+e+ +  +++++n+ +dl+ l+s++k
  gene623|gene623|rna623|rna623 331 ERLATIDRLQHTLQDKINGLKERLSSLQAQLENAKHDLSTLTSMIK 376
                                    9*******************************************98 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.52
                           XhlA  14 dnleervdkleekaaeaeekiknleedlkkles 46 
                                    + lee  + + +++++  ++i  l+++l+ + +
  gene623|gene623|rna623|rna623 376 KGLEESASSVSKRQERNNARIRLLNNELSAINK 408
                                    677888888889999999999999999998865 PP

  == domain 4  score: 1.0 bits;  conditional E-value: 0.54
                           XhlA   5 rlerietkldnleervdkleekaaeaeekiknl 37 
                                    +l  i+++ld+l+ +   + +k++e+e  + nl
  gene623|gene623|rna623|rna623 402 ELSAINKRLDSLNAE---IALKKDEHEIYAHNL 431
                                    577899999999995...667777776666665 PP

  == domain 5  score: 0.4 bits;  conditional E-value: 0.79
                           XhlA  13 ldnleervdkleekaaeaeekiknleedlkklesn 47 
                                    l nleer ++  +k++++      le d++ +++ 
  gene623|gene623|rna623|rna623 431 LRNLEERKEQMMDKKEKVNVMMYGLERDINTIKDR 465
                                    55777777777778888888888888888888875 PP

  == domain 6  score: -0.8 bits;  conditional E-value: 2
                           XhlA  10 etkldnleerv 20 
                                    e++++++++r+
  gene623|gene623|rna623|rna623 456 ERDINTIKDRI 466
                                    55555555554 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       6.7   6.3e+03      98     113 ..     154     169 ..     143     174 .. 0.61
   2 !   18.1   3.8   2.1e-06     0.002      56     124 .]     323     389 ..     303     389 .. 0.87
   3 !    9.1   1.5    0.0014       1.3      39     102 ..     399     465 ..     394     480 .. 0.66

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 6.7
                        DUF1664  98 eigedvesvkeavegl 113
                                    e++ed++s++++ ++l
  gene623|gene623|rna623|rna623 154 ELREDIKSINDLLKEL 169
                                    3455555555555544 PP

  == domain 2  score: 18.1 bits;  conditional E-value: 2.1e-06
                        DUF1664  56 slaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeaveglesklerieekQ 124
                                    +l   k++ s+r++++d+ +   ++ ++ +ke +++++ +l++ ++d++++ ++++gle++ ++++++Q
  gene623|gene623|rna623|rna623 323 QL--KKKQASERLATIDRLQHTLQDKINGLKERLSSLQAQLENAKHDLSTLTSMIKGLEESASSVSKRQ 389
                                    33..588899******************************************************99988 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.0014
                        DUF1664  39 lsdavesvskqleqvseslaatkrh...Lssridrvdkkldeqkeiskeikeevtevredlseiged 102
                                    l++ ++ + k+l+++ +++a  k++    ++++ +++++ +++++ +++++  +  +++d+++i++ 
  gene623|gene623|rna623|rna623 399 LNNELSAINKRLDSLNAEIALKKDEheiYAHNLRNLEERKEQMMDKKEKVNVMMYGLERDINTIKDR 465
                                    6677777788888888888777766232345666666666666666666666666666666666655 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   1.4       1.6   1.5e+03     230     252 ..     153     175 ..     124     188 .. 0.52
   2 !   13.5  10.9   2.6e-05     0.024     157     251 ..     302     397 ..     294     401 .. 0.84
   3 !   17.5  14.3   1.6e-06    0.0015     133     256 ..     332     458 ..     332     470 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.6
                           Spc7 230 eeleekieelkeqkseleeeiae 252
                                    +el+e+i+++++  +el ++ ++
  gene623|gene623|rna623|rna623 153 NELREDIKSINDLLKELLTKKEK 175
                                    33333333333333333333333 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 2.6e-05
                           Spc7 157 lLekqeeeldellpeleeekaeleeeleklqe.aaeelesidkeeLeelreelaelkaeieekkkelaelqeqleeleek 235
                                     L++ e+   +  ++ +++k++l+++ ++++    + l+   +++++ l+e+l++l+a++e+ k +l++l++ ++ lee+
  gene623|gene623|rna623|rna623 302 SLQSLESFSRRTFNQATQRKKQLKKKQASERLaTIDRLQHTLQDKINGLKERLSSLQAQLENAKHDLSTLTSMIKGLEES 381
                                    566666666777888899999999888887764677888888************************************** PP

                           Spc7 236 ieelkeqkseleeeia 251
                                     ++++++ ++ +++i+
  gene623|gene623|rna623|rna623 382 ASSVSKRQERNNARIR 397
                                    ***9988888887775 PP

  == domain 3  score: 17.5 bits;  conditional E-value: 1.6e-06
                           Spc7 133 RmqllegLkegleenlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeeles...idkeeLeelreela 209
                                    R+  ++ L+++l+++++gl+e  + L++q e+++  l  l++  + lee + +  +++e  ++   + ++eL ++ ++l+
  gene623|gene623|rna623|rna623 332 RLATIDRLQHTLQDKINGLKERLSSLQAQLENAKHDLSTLTSMIKGLEESASSVSKRQERNNArirLLNNELSAINKRLD 411
                                    5667899********************************************999997766555654669999999***** PP

                           Spc7 210 elkaeieekkkelaelqeqleeleekieelkeqkseleeeiaeaerv 256
                                    +l+aei+ kk+e++    +l +lee+ e++ ++k++++  +   er 
  gene623|gene623|rna623|rna623 412 SLNAEIALKKDEHEIYAHNLRNLEERKEQMMDKKEKVNVMMYGLERD 458
                                    *******9999999999999999999999999999998776666665 PP

>> Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.3      0.97   9.2e+02      79      99 ..     151     171 ..     134     174 .. 0.74
   2 !   16.5   2.5   7.2e-06    0.0067      68     125 ..     328     385 ..     296     396 .. 0.65
   3 ?    4.7   0.8      0.03        28      36     100 ..     399     465 ..     389     471 .. 0.46

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.97
                   Baculo_PEP_C  79 lqdtlrneLtnlnsiltnLls 99 
                                    l+++lr++++++n  l +Ll+
  gene623|gene623|rna623|rna623 151 LNNELREDIKSINDLLKELLT 171
                                    567788888888887777764 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 7.2e-06
                   Baculo_PEP_C  68 lltnLtdalnalqdtlrneLtnlnsiltnLlssvtNinstLnnllqalnnldlgalsq 125
                                    ++++  +++ +lq tl+ ++++l+  l++L++++ N +  L+ l + +++l++ a s 
  gene623|gene623|rna623|rna623 328 QASERLATIDRLQHTLQDKINGLKERLSSLQAQLENAKHDLSTLTSMIKGLEESASSV 385
                                    2333445688888888888888888888888888888888888888888887665554 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.03
                   Baculo_PEP_C  36 latlldaietqLnalsedlksllaeldtrldtlltnLtdalnalq...dtlrneLtnlnsiltnLlss 100
                                    l++ l ai+++L++l++++    ++ ++  +++l nL++   ++    ++++  + +l+ +++++   
  gene623|gene623|rna623|rna623 399 LNNELSAINKRLDSLNAEIAL-KKDEHEIYAHNLRNLEERKEQMMdkkEKVNVMMYGLERDINTIKDR 465
                                    333333333333333333332.2222223444455555544444444455555555555555555444 PP

>> Cob_adeno_trans  Cobalamin adenosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   4.2   6.4e-05     0.061      18     134 ..     322     442 ..     314     489 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 6.4e-05
                                    XXXTTHHHHHHHHHHHHHHHHHHHHHHHCTTTTHHHHHHHHHHHHHHHHHHHHHHT.....-BTCCG-S--HHHHHHHHH CS
                Cob_adeno_trans  18 rvsKddprveayGtvDelnsaiglarallaeeeeelkeaLeeiqneLfdlgaelatp....ekkkekkkiteeeveelek 93 
                                    +  K+++  e ++t+D l+ ++   ++ l+e  ++l+++Le+ +++L +l + +       ++ +++++ ++++++ l++
  gene623|gene623|rna623|rna623 322 KQLKKKQASERLATIDRLQHTLQDKINGLKERLSSLQAQLENAKHDLSTLTSMIKGLeesaSSVSKRQERNNARIRLLNN 401
                                    45577888899999****99999999999888999999999999999999999853366653334444455667999*** PP

                                    HHHHHHHHS--EESEEES-SSHHHHHHHHHHHHHHHHHHHH CS
                Cob_adeno_trans  94 eideleaelpplksfilpggspaaaalhvaRtvcRraERav 134
                                    e+ +++++l+ l+  i  ++++    +h +R +  r E  +
  gene623|gene623|rna623|rna623 402 ELSAINKRLDSLNAEIALKKDEHEIYAHNLRNLEERKEQMM 442
                                    ****************9999999999999998887777665 PP

>> TolA_bind_tri  TolA binding protein trimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   5.4   0.00025      0.23      10      52 ..     331     372 ..     318     394 .. 0.86
   2 ?    8.0   1.5    0.0032         3      19      59 ..     402     442 ..     392     450 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00025
                  TolA_bind_tri  10 ErilearsqlllelqqqlealqqelreLRGqiEelqyqleqle 52 
                                    Er++   ++l++ lq +++ l++ l++L+ q+E  +++l++l 
  gene623|gene623|rna623|rna623 331 ERLATI-DRLQHTLQDKINGLKERLSSLQAQLENAKHDLSTLT 372
                                    444444.699*****************************9986 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0032
                  TolA_bind_tri  19 lllelqqqlealqqelreLRGqiEelqyqleqleerQrdlY 59 
                                     l  + ++l++l++e++  + + E  +++l++leer  ++ 
  gene623|gene623|rna623|rna623 402 ELSAINKRLDSLNAEIALKKDEHEIYAHNLRNLEERKEQMM 442
                                    5677899*****************************98876 PP

>> JMY  Junction-mediating and -regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   9.1   0.00012      0.11     236     345 ..     307     427 ..     295     456 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00012
                            JMY 236 krfgkaawaaaaprlekLklllaketLqllrakelclkqkraeikeemesleekeka.vae.......vdeLeiqyyel. 306
                                    + f++ ++++a++r ++Lk  +a e L  +   + +l+ k + +ke++ sl+++ ++  +        +  Le ++  + 
  gene623|gene623|rna623|rna623 307 ESFSRRTFNQATQRKKQLKKKQASERLATIDRLQHTLQDKINGLKERLSSLQAQLENaKHDlstltsmIKGLEESASSVs 386
                                    579*************************9999999999999999999999887754413341111111444554443331 PP

                            JMY 307 .qLelyevqleiLkeeellltaqLdslrrqikekqdev.vy 345
                                     + e  ++++ +L++e + + ++Ldsl+++i  k+de  +y
  gene623|gene623|rna623|rna623 387 kRQERNNARIRLLNNELSAINKRLDSLNAEIALKKDEHeIY 427
                                    14577899************************999985255 PP

>> DUF4988  Domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.2       1.1     1e+03      20      48 ..     153     179 ..     150     196 .. 0.83
   2 ?   14.6   2.9   2.1e-05      0.02       1      59 [.     343     403 ..     343     451 .. 0.73
   3 ?    1.2   0.1      0.26   2.5e+02       1      24 [.     455     478 ..     455     488 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1.1
                        DUF4988  20 kelndniealkklleegkviteveensdg 48 
                                    +el ++i++++ ll  ++++t+ e+++dg
  gene623|gene623|rna623|rna623 153 NELREDIKSINDLL--KELLTKKEKKNDG 179
                                    57888999999999..7788888888888 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 2.1e-05
                        DUF4988   1 leddvndlkdrvaaleeqvkelndniealkkll....eegkviteveensdg.syvltlsdgkt 59 
                                    l+d++n lk+r ++l++q+++ ++++++l  ++    e     ++v+++++  +  + l +++ 
  gene623|gene623|rna623|rna623 343 LQDKINGLKERLSSLQAQLENAKHDLSTLTSMIkgleE---SASSVSKRQERnNARIRLLNNEL 403
                                    89***************************999954423...34444443332257888888764 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.26
                        DUF4988   1 leddvndlkdrvaaleeqvkelnd 24 
                                    le d+n +kdr+ a+  +  +l++
  gene623|gene623|rna623|rna623 455 LERDINTIKDRICAMVGKKGALDK 478
                                    7899**********9877777665 PP

>> Type2_restr_D3  Type-2 restriction enzyme D3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.2      0.89   8.4e+02      32      54 ..     144     166 ..     135     171 .. 0.76
   2 ?    1.9   0.1      0.23   2.1e+02      32      50 ..     318     336 ..     303     353 .. 0.63
   3 ?   -2.1   0.0       4.1   3.8e+03      16      51 ..     372     407 ..     369     417 .. 0.70
   4 ?   11.3   0.1   0.00026      0.25      18      57 ..     430     469 ..     427     472 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.89
                 Type2_restr_D3  32 eeikayLklagleEdveTIkDDi 54 
                                    +  k+ L    l+Ed++ I D +
  gene623|gene623|rna623|rna623 144 KTEKNSLLNNELREDIKSINDLL 166
                                    55578888899********9965 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.23
                 Type2_restr_D3  32 eeikayLklagleEdveTI 50 
                                    ++ k++Lk +   E ++TI
  gene623|gene623|rna623|rna623 318 TQRKKQLKKKQASERLATI 336
                                    4557788888888888777 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 4.1
                 Type2_restr_D3  16 tiilkylleskkrrsleeikayLklagleEdveTIk 51 
                                    t ++k l+es + +s  + ++  ++  l+ ++  I 
  gene623|gene623|rna623|rna623 372 TSMIKGLEESASSVSKRQERNNARIRLLNNELSAIN 407
                                    567888888888888877777666666666666665 PP

  == domain 4  score: 11.3 bits;  conditional E-value: 0.00026
                 Type2_restr_D3  18 ilkylleskkrrsleeikayLklagleEdveTIkDDiqgl 57 
                                     l+ l+e k+++  ++ k    + gle d++TIkD i+++
  gene623|gene623|rna623|rna623 430 NLRNLEERKEQMMDKKEKVNVMMYGLERDINTIKDRICAM 469
                                    5778888888888888899999***************987 PP

>> Rx_N  Rx N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0      0.35   3.3e+02      59      83 ..     153     177 ..     136     209 .. 0.77
   2 ?    7.7   0.4    0.0046       4.3       9      45 ..     329     365 ..     322     370 .. 0.85
   3 ?    4.2   1.1     0.056        52       2      61 ..     371     434 ..     370     446 .. 0.74

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.35
                           Rx_N  59 kelrdlaydaeDvlDefetealrrk 83 
                                    +elr+ + ++ D+l e+ t+ ++++
  gene623|gene623|rna623|rna623 153 NELREDIKSINDLLKELLTKKEKKN 177
                                    5778888888888888888888776 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0046
                           Rx_N   9 LadllaeeakllkgvkeeleklkdeLesiqavLedae 45 
                                     ++ la   +l+  ++++++ lk++L+s+qa Le a 
  gene623|gene623|rna623|rna623 329 ASERLATIDRLQHTLQDKINGLKERLSSLQAQLENAK 365
                                    45666776799**********************9986 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.056
                           Rx_N   2 vsallqkLadllaeeakllkgvkeeleklkdeLesiqavLedaee....rqikdeavkeWlkel 61 
                                    ++++++ L++ +++  k+++   + ++ l +eL++i+  L+        +++++e   + l++l
  gene623|gene623|rna623|rna623 371 LTSMIKGLEESASSVSKRQERNNARIRLLNNELSAINKRLDSLNAeialKKDEHEIYAHNLRNL 434
                                    5678889999999999*********************999976664344444444444444444 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.1       1.1   1.1e+03      53      66 ..     154     167 ..     139     191 .. 0.64
   2 ?    9.8   0.3    0.0012       1.1      10      49 ..     344     383 ..     330     393 .. 0.70
   3 ?    3.1   0.3      0.14   1.3e+02      34      58 ..     393     417 ..     382     466 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 1.1
                        NPV_P10  53 eletkvenIqdiLn 66 
                                    el + +++I+d+L 
  gene623|gene623|rna623|rna623 154 ELREDIKSINDLLK 167
                                    33333444444433 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0012
                        NPV_P10  10 radikavddkVdalqqqvddvqenlpdvtelnekLdaqsa 49 
                                     + i+ +++++++lq+q+++ +++l ++t + + L++ + 
  gene623|gene623|rna623|rna623 344 QDKINGLKERLSSLQAQLENAKHDLSTLTSMIKGLEESAS 383
                                    3457777777777777777777777777776666666555 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.14
                        NPV_P10  34 lpdvtelnekLdaqsaqLaeletkv 58 
                                       +  ln++L a+++ L++l++++
  gene623|gene623|rna623|rna623 393 NARIRLLNNELSAINKRLDSLNAEI 417
                                    4556667777777777777777654 PP

>> Tropomyosin  Tropomyosin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   1.7      0.34   3.2e+02     143     170 ..     152     179 ..     139     187 .. 0.71
   2 ?   12.5  22.6   7.6e-05     0.071      45     223 ..     303     476 ..     297     484 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.34
                    Tropomyosin 143 iveLeeeLkvvgnnlksLevseekaser 170
                                     +eL e++k +   lk+L  ++ek ++ 
  gene623|gene623|rna623|rna623 152 NNELREDIKSINDLLKELLTKKEKKNDG 179
                                    5688888888888888888888887665 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 7.6e-05
                    Tropomyosin  45 iqlleeelerteerleealekLeeaekaades....erarKvlEnrelkdeekleeleaqlkeakeiaeeadrkyeEvar 120
                                    +q le+  +rt ++ ++ +++L+  +k+a+e+    +r+  +l ++ +   e+l++l+aql       e+a++ +   + 
  gene623|gene623|rna623|rna623 303 LQSLESFSRRTFNQATQRKKQLK--KKQASERlatiDRLQHTLQDKINGLKERLSSLQAQL-------ENAKHDLSTLTS 373
                                    66666666676666655444443..456666544445555555555555555555555555.......556667788888 PP

                    Tropomyosin 121 klvvvesdLeraeeraeaaeskiveLeeeLkvvgnnlksLevseekaseredeyeeeirtLeekLkeaeeRaeeAErsvq 200
                                     ++ +e+      +r+e++ ++i+ L +eL  + + l sL ++ +   +  + y +++r+Lee+  ++ ++ e+    + 
  gene623|gene623|rna623|rna623 374 MIKGLEESASSVSKRQERNNARIRLLNNELSAINKRLDSLNAEIALKKDEHEIYAHNLRNLEERKEQMMDKKEKVNVMMY 453
                                    99999**************************************99999999***************************** PP

                    Tropomyosin 201 kLekevdrledeleaekekykai 223
                                     Le++++++ d++ a   k+ a+
  gene623|gene623|rna623|rna623 454 GLERDINTIKDRICAMVGKKGAL 476
                                    ***********998876666555 PP

>> FUSC  Fusaric acid resistance protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   2.9    0.0012       1.2     158     265 ..     335     440 ..     305     485 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0012
                           FUSC 158 lrarlrallrdalalaaaalageegaeareaararlaadilalealrsqaayesprirararalrrllsrmlallallss 237
                                      +rl+++l+d  + +++ l+  +++ +  +a ++l   + ++ +l + a+  s r  + ++++r l++++ a+  +l+s
  gene623|gene623|rna623|rna623 335 TIDRLQHTLQDKINGLKERLSSLQAQLE--NAKHDLSTLTSMIKGLEESASSVSKRQERNNARIRLLNNELSAINKRLDS 412
                                    5678888888888888888888877666..78899999999999999999999999999999999999999999999999 PP

                           FUSC 238 larllarlraeeaaavpelaallaelaa 265
                                    l  + a  ++e++  ++ l++l ++ ++
  gene623|gene623|rna623|rna623 413 LNAEIALKKDEHEIYAHNLRNLEERKEQ 440
                                    9999988887777776666655554444 PP

>> Plasmid_RAQPRD  Plasmid protein of unknown function (Plasmid_RAQPRD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0         1   9.4e+02      42      62 ..     152     172 ..     133     177 .. 0.77
   2 ?   -0.9   0.3         2   1.9e+03      32      51 ..     327     345 ..     297     360 .. 0.46
   3 ?    7.0   0.5    0.0073       6.9       6      54 ..     358     408 ..     351     413 .. 0.81
   4 ?    2.6   0.1      0.16   1.5e+02      27      56 ..     435     466 ..     400     471 .. 0.72

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 1
                 Plasmid_RAQPRD  42 YdrlrrDleriraGIqsYLep 62 
                                     + lr+D++ i + +++ L+ 
  gene623|gene623|rna623|rna623 152 NNELREDIKSINDLLKELLTK 172
                                    56899********99998876 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 2
                 Plasmid_RAQPRD  32 qeekaRvhfdYdrlrrDler 51 
                                    +++ +R+   +drl+  l+ 
  gene623|gene623|rna623|rna623 327 KQASERLA-TIDRLQHTLQD 345
                                    22222222.34455555544 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.0073
                 Plasmid_RAQPRD   6 reeLakllkqLdqlqalveraeaqakqe..ekaRvhfdYdrlrrDlerira 54 
                                    +++L+++++ L  l+++++ +e++a +   +++R + +++ l+++l +i +
  gene623|gene623|rna623|rna623 358 QAQLENAKHDLSTLTSMIKGLEESASSVskRQERNNARIRLLNNELSAINK 408
                                    789999999999999999999999888755666888888888888887765 PP

  == domain 4  score: 2.6 bits;  conditional E-value: 0.16
                 Plasmid_RAQPRD  27 eaqakqe..ekaRvhfdYdrlrrDleriraGI 56 
                                    e++++q   +k++v++    l+rD+++i++ I
  gene623|gene623|rna623|rna623 435 EERKEQMmdKKEKVNVMMYGLERDINTIKDRI 466
                                    33333333345788888889999999999866 PP

>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.4      0.33   3.1e+02      23      41 ..     152     170 ..     146     171 .. 0.92
   2 ?    8.7   0.3    0.0024       2.3       1      36 [.     346     381 ..     346     390 .. 0.91
   3 ?    2.3   0.8      0.24   2.3e+02      15      37 ..     395     417 ..     375     443 .. 0.70
   4 ?   -0.3   0.1       1.5   1.5e+03      10      30 ..     446     466 ..     436     470 .. 0.72

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.33
                      FlaC_arch  23 neelsksveelkenVkdll 41 
                                    n+el+++++ +++  k+ll
  gene623|gene623|rna623|rna623 152 NNELREDIKSINDLLKELL 170
                                    799***********99998 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0024
                      FlaC_arch   1 ridelEnklsklsteletvkkeneelsksveelken 36 
                                    +i+ l ++ls+l+ +le++k +++ l + ++ l+e+
  gene623|gene623|rna623|rna623 346 KINGLKERLSSLQAQLENAKHDLSTLTSMIKGLEES 381
                                    799999**********************99999987 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.24
                      FlaC_arch  15 eletvkkeneelsksveelkenV 37 
                                    ++  + +e++ ++k ++ l+ ++
  gene623|gene623|rna623|rna623 395 RIRLLNNELSAINKRLDSLNAEI 417
                                    55555566666666666666554 PP

  == domain 4  score: -0.3 bits;  conditional E-value: 1.5
                      FlaC_arch  10 sklsteletvkkeneelsksv 30 
                                    +k+ +++  ++++++ +++ +
  gene623|gene623|rna623|rna623 446 EKVNVMMYGLERDINTIKDRI 466
                                    556668888888888888876 PP

>> MscS_porin  Mechanosensitive ion channel porin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   1.1       1.6   1.6e+03      31      63 ..     144     176 ..     129     189 .. 0.68
   2 ?   12.2  26.3    0.0001     0.095      57     205 ..     297     436 ..     291     442 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.6
                     MscS_porin  31 kidkskkkaeelqkaiddaPkelrelqqeleal 63 
                                    k++k+   ++el++ i++   +l+el  + e+ 
  gene623|gene623|rna623|rna623 144 KTEKNSLLNNELREDIKSINDLLKELLTKKEKK 176
                                    455666666677777777777777776666666 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.0001
                     MscS_porin  57 qqelealqkkkeeaskeilaklsleeLeqrllqtssqlqelqeqlaqlnsqlvelqtrperaqqqltearqrlqeirnrL 136
                                    q +l++l ++ e+ s+ ++++ +++  + + +q+s++l++  + + +l+++++ l  r++ +q+ql +a+  l+++++ +
  gene623|gene623|rna623|rna623 297 QSSLNSL-QSLESFSRRTFNQATQRKKQLKKKQASERLATIDRLQHTLQDKINGLKERLSSLQAQLENAKHDLSTLTSMI 375
                                    5567777.777999999999999999999999************************************************ PP

                     MscS_porin 137 nstaaagealsqaqrtalqaelaaleaqieeleqellsnnnrqeLlklqrdllklriqqleqelqaLqe 205
                                    ++++++       ++       +  +a+i++l+ el   n+r + l+++  l+k +++   ++l++L+e
  gene623|gene623|rna623|rna623 376 KGLEESA-SSVSKRQ-------ERNNARIRLLNNELSAINKRLDSLNAEIALKKDEHEIYAHNLRNLEE 436
                                    ***3333.2333333.......44555555555555555555555555555555555555555555555 PP

>> Exonuc_VII_L  Exonuclease VII, large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   1.3       2.6   2.4e+03     204     232 ..     133     162 ..      79     189 .. 0.44
   2 ?   12.7  15.3   7.6e-05     0.071     145     267 ..     279     421 ..     221     492 .. 0.73

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 2.6
                   Exonuc_VII_L 204 kkqlkkkrerleelkerl.kekleekkerl 232
                                    +kq+  k+++ ++ k++l +++l+e  +++
  gene623|gene623|rna623|rna623 133 NKQTGDKKNNPKTEKNSLlNNELREDIKSI 162
                                    112222222222222222221111111111 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 7.6e-05
                   Exonuc_VII_L 145 l....................eeqleelerrlekaikrlleekkq.rleklasrlkspeellerkrqrldeleerleral 203
                                    l                    +++l++le+  ++ ++++ ++kkq + +++++rl++ ++l ++ +++++ l+erl++ l
  gene623|gene623|rna623|rna623 279 LsdpqdtlidlllpqqspqssLNSLQSLESFSRRTFNQATQRKKQlKKKQASERLATIDRLQHTLQDKINGLKERLSS-L 357
                                    35555555666666666555555556665555555555555444312334567788888888888999999999**99.9 PP

                   Exonuc_VII_L 204 kkqlkkkrerleelkerlkekleekkerlkklkerle.lleekkerleeleeklealsplkvLkr 267
                                    + ql++++++l++l++ +k  lee +++++k++er + +++  +++l+++ ++l++l+ + +Lk+
  gene623|gene623|rna623|rna623 358 QAQLENAKHDLSTLTSMIK-GLEESASSVSKRQERNNaRIRLLNNELSAINKRLDSLNAEIALKK 421
                                    999*********9996654.567777777666666666788888888888888888888887776 PP

>> Prefoldin  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.3       4.3   4.1e+03      15      29 ..     155     169 ..     152     181 .. 0.44
   2 ?   11.0   0.4   0.00033      0.31      79     119 ..     347     387 ..     338     388 .. 0.85
   3 ?    6.2   0.5    0.0095         9      79     116 ..     396     433 ..     392     437 .. 0.91
   4 ?   -0.5   0.1       1.2   1.1e+03      82     111 ..     434     463 ..     425     473 .. 0.59

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 4.3
                                    HHHHHHHHHHHHHHH CS
                      Prefoldin  15 lkeaieelektletl 29 
                                    l+e i++++++l+ l
  gene623|gene623|rna623|rna623 155 LREDIKSINDLLKEL 169
                                    333333333333333 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00033
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Prefoldin  79 iellkkkleelekqlekleeeleklkdqittleanlaqlyq 119
                                    i  lk++l++l++qle+ +++l  l++ i+ le+ ++ +++
  gene623|gene623|rna623|rna623 347 INGLKERLSSLQAQLENAKHDLSTLTSMIKGLEESASSVSK 387
                                    66699************************999999988765 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.0095
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Prefoldin  79 iellkkkleelekqlekleeeleklkdqittleanlaq 116
                                    i+ll+++l+ ++k l++l++e++ +kd+++ + +nl+ 
  gene623|gene623|rna623|rna623 396 IRLLNNELSAINKRLDSLNAEIALKKDEHEIYAHNLRN 433
                                    6899************************9999998875 PP

  == domain 4  score: -0.5 bits;  conditional E-value: 1.2
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Prefoldin  82 lkkkleelekqlekleeeleklkdqittle 111
                                    l++++e++ +  ek++ +   l + i+t+ 
  gene623|gene623|rna623|rna623 434 LEERKEQMMDKKEKVNVMMYGLERDINTIK 463
                                    445555555555555555555555555554 PP

>> Syntaxin-6_N  Syntaxin 6, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   1.1     0.067        63      27      60 ..     136     169 ..     109     177 .. 0.81
   2 ?    4.6   7.1      0.05        47      34      75 ..     325     386 ..     293     399 .. 0.61
   3 ?    7.4   7.3    0.0067       6.4      16      98 ..     367     451 ..     358     452 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.067
                   Syntaxin-6_N  27 lledtssstseeldetrteLrkalrsiewdledL 60 
                                    + ++++++++e+ + +++eLr+ ++si+  l++L
  gene623|gene623|rna623|rna623 136 TGDKKNNPKTEKNSLLNNELREDIKSINDLLKEL 169
                                    3334444589999999************999998 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.05
                   Syntaxin-6_N  34 s....................tseeldetrteLrkalrsiewdledLeetvriveknpskfk 75 
                                    +                    + + l+e  + L+++l++++ dl+ L   ++ +e++ s ++
  gene623|gene623|rna623|rna623 325 KkkqaserlatidrlqhtlqdKINGLKERLSSLQAQLENAKHDLSTLTSMIKGLEESASSVS 386
                                    13444454555555555544457778888888888888888888888888888877665543 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.0067
                   Syntaxin-6_N  16 kaeslyrrwerlledtss..stseeldetrteLrkalrsiewdledLeetvriveknpsk.fkidekelsrrrafveevr 92 
                                     + +l +  + l e++ss  +++e  +   + L+++l+ i++ l+ L+  + +++k++++ +  + + l++r++ + + +
  gene623|gene623|rna623|rna623 367 DLSTLTSMIKGLEESASSvsKRQERNNARIRLLNNELSAINKRLDSLNAEI-ALKKDEHEiYAHNLRNLEERKEQMMDKK 445
                                    4444455555555566555345666666678899*****************.88888888799999************** PP

                   Syntaxin-6_N  93 eevkem 98 
                                    e+v+ m
  gene623|gene623|rna623|rna623 446 EKVNVM 451
                                    *99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (500 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2735  (0.152546); expected 358.6 (0.02)
Passed bias filter:                      549  (0.0306208); expected 358.6 (0.02)
Passed Vit filter:                       109  (0.00607954); expected 17.9 (0.001)
Passed Fwd filter:                        62  (0.00345808); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 1.19u 0.39s 00:00:01.58 Elapsed: 00:00:00.58
# Mc/sec: 2581.38
//
Query:       gene625|gene625|rna625|rna625  [L=171]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       494  (0.0275531); expected 358.6 (0.02)
Passed bias filter:                      240  (0.0133861); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.60u 0.33s 00:00:00.93 Elapsed: 00:00:00.56
# Mc/sec: 918.75
//
Query:       gene626|gene626|rna626|rna626  [L=835]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
       0.62   10.3  13.0        9.5    6.5   0.3    4.9  4  WXG100          Proteins of 100 residues with WXG
        2.6    7.3  50.0       0.18   11.1   3.7    5.9  5  DUF3450         Protein of unknown function (DUF3450)
        3.8    7.1  11.5         12    5.5   0.2    4.1  3  DUF3251         Protein of unknown function (DUF3251)


Domain annotation for each model (and alignments):
>> WXG100  Proteins of 100 residues with WXG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.1     0.012        74      24      80 ..     215     273 ..     202     277 .. 0.66
   2 ?    5.2   0.3    0.0041        25      47      86 .]     364     403 ..     362     406 .. 0.90
   3 ?   -0.8   0.2       0.3   1.8e+03      45      65 ..     550     570 ..     546     571 .. 0.86
   4 ?    6.5   0.3    0.0016       9.5      48      77 ..     770     799 ..     765     803 .. 0.72

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.012
                                    HHHHHHHHHHHHHC.GC.GCTHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         WXG100  24 edelqrlkaevdal.qs.gWsGaaadafqaefeewkqaaqklvdaLeeisealkqaana 80 
                                    +d++++++a++ al q  + + +   +f+++  e+ +++++ ++ Lee ++al++ +++
  gene626|gene626|rna626|rna626 215 SDRIKECNAQITALkQHeQQKEEIERSFESQVLEMERSLNEHKKVLEEKGKALEMCNSE 273
                                    55666666666666533233455566777777788888888888888888888776665 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0041
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                         WXG100  47 dafqaefeewkqaaqklvdaLeeisealkqaanafedaDe 86 
                                    ++f++ + ++k++++k++++++  +e++ + +n+++ aDe
  gene626|gene626|rna626|rna626 364 EQFRGRLRKYKKKMRKYKKLFNVQNEQIAALKNNLSRADE 403
                                    6899999999999999999999999999999999999996 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 0.3
                                    HCHHHHHHHHHHHHHHHHHHH CS
                         WXG100  45 aadafqaefeewkqaaqklvd 65 
                                    ++d+f++e++++  +a++  +
  gene626|gene626|rna626|rna626 550 TKDSFKDEWKRFFDEAERQRN 570
                                    6899********999998765 PP

  == domain 4  score: 6.5 bits;  conditional E-value: 0.0016
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         WXG100  48 afqaefeewkqaaqklvdaLeeisealkqa 77 
                                    +  ++f++++++ qkl+++++e++++l+++
  gene626|gene626|rna626|rna626 770 STTDTFKKMREKTQKLQQKFSELEQKLNKI 799
                                    455677788888888888888888888776 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   3.7     3e-05      0.18      15      87 ..     103     175 ..      93     188 .. 0.91
   2 ?    5.5   7.0    0.0015       9.1      25      97 ..     190     262 ..     180     277 .. 0.83
   3 ?    6.6   1.7    0.0007       4.2      17      69 ..     266     318 ..     259     327 .. 0.85
   4 ?    0.4   4.2     0.054   3.2e+02      58     137 ..     368     443 ..     342     460 .. 0.75
   5 ?    7.7   1.9   0.00032       1.9      15      77 ..     751     813 ..     719     825 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 3e-05
                        DUF3450  15 aatldqalkeaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeq 87 
                                     + l+++ +e +++v++++ +  ++++l +e+ + ++++ +l + l+  +  n++l rlv++q+ +i+  +e+
  gene626|gene626|rna626|rna626 103 MKVLREISAERNESVQNEKNTKMRVNELLKEQFDQKKKIVKLMDDLKYCSSANNELLRLVQDQKGRISAYKEK 175
                                    57789999***********************************************************998886 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0015
                        DUF3450  25 aekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeieeiere 97 
                                     e+  + ++++ +ki+ l++e + l++++++ ++++ +l+  ++q e++ +s e+++ ++e++++e +++ +e
  gene626|gene626|rna626|rna626 190 NEELDSLRRKALTKIEVLTKEISVLSDRIKECNAQITALKQHEQQKEEIERSFESQVLEMERSLNEHKKVLEE 262
                                    5677778888899999999999999999999999999999999999999999999999999999998877655 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.0007
                        DUF3450  17 tldqalkeaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneq 69 
                                    +l+  ++e +k  a ++++ ++i++l+++++ +++ yr+++e++e l+++  +
  gene626|gene626|rna626|rna626 266 ALEMCNSELAKLLAMEKRMKEEIKNLKEKSSYYERLYRSINEQNEYLNAQLTK 318
                                    56667788899999999999999999999999999999999999999887665 PP

  == domain 4  score: 0.4 bits;  conditional E-value: 0.054
                        DUF3450  58 eeleslevyneqlerlvasqeqeiasleeqieeieeierelvpllekmidrLeqfveldlPflleeRqarlakLkelmdr 137
                                     +l + +++ +++++l + q+++ia l++++++++e   el+  ++    +L++f  + +  +++  ++ l k+kelmdr
  gene626|gene626|rna626|rna626 368 GRLRKYKKKMRKYKKLFNVQNEQIAALKNNLSRADEQFHELQSEFL----DLRRFNDENVGRKKSVTDDLLSKMKELMDR 443
                                    4566777888889999999999999999999999888777664433....466666666666666666666666666666 PP

  == domain 5  score: 7.7 bits;  conditional E-value: 0.00032
                        DUF3450  15 aatldqalkeaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasq 77 
                                    +++++ +  e ++a + + ++    +k+ +++q+l++++ +l+++l++++  n+  ++ + +q
  gene626|gene626|rna626|rna626 751 STEARPVVGEHKEASTDSDSTTDTFKKMREKTQKLQQKFSELEQKLNKIKGNNDPSSKKLHDQ 813
                                    344555555666666666666666777777777777777777777777776666655555554 PP

>> DUF3251  Protein of unknown function (DUF3251)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.7      0.02   1.2e+02       5      35 ..     202     232 ..     199     241 .. 0.87
   2 ?    5.5   0.2    0.0019        12       3      46 ..     387     430 ..     385     439 .. 0.93
   3 ?    3.8   0.6    0.0067        40       7      35 ..     775     803 ..     771     810 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.02
                                    -------S-------------HHHHHHHHHH CS
                        DUF3251   5 selrqlkqsvsklnqelktleqetvkieqqn 35 
                                    +++  l++++s l++++k+ ++++++++q  
  gene626|gene626|rna626|rna626 202 TKIEVLTKEISVLSDRIKECNAQITALKQHE 232
                                    578889*********************9975 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0019
                                    ---------S-------------HHHHHHHHHHHHHHH-SSSEE CS
                        DUF3251   3 eqselrqlkqsvsklnqelktleqetvkieqqnaLnakskkgvy 46 
                                    +  ++ +lk++ s+ ++++++l+ e   + + n  n+  kk+v+
  gene626|gene626|rna626|rna626 387 QNEQIAALKNNLSRADEQFHELQSEFLDLRRFNDENVGRKKSVT 430
                                    67899********************************9999986 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.0067
                                    -----S-------------HHHHHHHHHH CS
                        DUF3251   7 lrqlkqsvsklnqelktleqetvkieqqn 35 
                                     ++++++  kl+q++ +leq++ ki+ +n
  gene626|gene626|rna626|rna626 775 FKKMREKTQKLQQKFSELEQKLNKIKGNN 803
                                    57888888888888888888888887766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (835 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3634  (0.202688); expected 358.6 (0.02)
Passed bias filter:                      498  (0.0277762); expected 358.6 (0.02)
Passed Vit filter:                       101  (0.00563333); expected 17.9 (0.001)
Passed Fwd filter:                        44  (0.00245412); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 1.47u 0.36s 00:00:01.83 Elapsed: 00:00:00.63
# Mc/sec: 3973.02
//
Query:       gene627|gene627|rna627|rna627  [L=968]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (968 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       625  (0.0348597); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.72u 0.27s 00:00:00.99 Elapsed: 00:00:00.49
# Mc/sec: 5990.05
//
Query:       gene628|gene628|rna628|rna628  [L=177]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.5e-09   36.4   0.1    5.7e-09   35.7   0.1    1.3  1  Pkinase      Protein kinase domain
  ------ inclusion threshold ------
      0.015   14.6   0.0      0.027   13.7   0.0    1.5  2  Pkinase_Tyr  Protein tyrosine kinase


Domain annotation for each model (and alignments):
>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.7   0.1   6.4e-13   5.7e-09       1      94 [.      85     174 ..      85     177 .] 0.88

  Alignments for each domain:
  == domain 1  score: 35.7 bits;  conditional E-value: 6.4e-13
                                    EEEEEEEEEESSEEEEEEEETTTTEEEEEEEEECHCHCHHHHHHHHHHHHHHHHHS.CTTB--EEEEEEESSEEEEEEE- CS
                        Pkinase   1 yekleklGeGsfGkVykaveketgkivAvKkikkekakkkkekkvlrEikilkklk.hpnivrlyevfeekdelylvley 79 
                                    y+  +klG+GsfG+Vy++  +++g ++A+K+ ++  ++ +   ++ +E +i   lk ++ i ++ ++ + ++++ylv++ 
  gene628|gene628|rna628|rna628  85 YKITKKLGQGSFGTVYEVE-DSSGTTYALKMESVPVKTTS---QLKNEYRIYTDLKgCKGIAKVHYFGKYDSYYYLVMDK 160
                                    78899************98.79********9888877764...589**********999********************9 PP

                                    -TTEBHHHHHHHHSS CS
                        Pkinase  80 veggeladllerkgs 94 
                                    +   +l+dl+er+++
  gene628|gene628|rna628|rna628 161 LG-PSLQDLYERRKK 174
                                    98.569999997665 PP

>> Pkinase_Tyr  Protein tyrosine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0      0.33     3e+03     209     223 ..      49      63 ..      31      75 .. 0.43
   2 ?   13.7   0.0   3.1e-06     0.027       2      80 ..      86     158 ..      85     172 .. 0.71

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 0.33
                                    SHHHHHHHHHHTTEE CS
                    Pkinase_Tyr 209 lkneevleklkegkr 223
                                    +  +++++k++ +kr
  gene628|gene628|rna628|rna628  49 WPIQSMCNKIQYQKR 63 
                                    222333333333222 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 3.1e-06
                                    EEEEEEEEESSEEEEEEEEETTTTSSEEEEEEEEESTTSSHHHHHHHHHHHHHHHTS.-BTTB--EEEEEESSSSEEEEE CS
                    Pkinase_Tyr   2 elgkklGeGafGkVvegtlkgekekkevkVavKtlkeeateeekeelleeakimkkl.khpnivkllgvctkeepllivt 80 
                                    +++kklG+G+fG+V+e + +     + ++ a+K+ +     +++++l +e++i ++l   + i k++ +   ++ +++v+
  gene628|gene628|rna628|rna628  86 KITKKLGQGSFGTVYEVEDS-----SGTTYALKMES--VPVKTTSQLKNEYRIYTDLkGCKGIAKVHYFGKYDSYYYLVM 158
                                    6789***********98877.....66777777763..333344677777777777766666666666666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       480  (0.0267723); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 1221.14
//
Query:       gene629|gene629|rna629|rna629  [L=217]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.5e-13   48.1   0.1    1.5e-12   47.5   0.0    1.4  2  Pkinase         Protein kinase domain
    2.2e-08   33.3   0.0    3.6e-08   32.6   0.0    1.3  1  Pkinase_fungal  Fungal protein kinase


Domain annotation for each model (and alignments):
>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.5   0.0   1.7e-16   1.5e-12     103     204 ..       2     113 ..       1     153 [. 0.87
   2 ?   -2.9   0.0      0.38   3.4e+03     222     241 ..     191     210 ..     163     214 .. 0.52

  Alignments for each domain:
  == domain 1  score: 47.5 bits;  conditional E-value: 1.7e-16
                                    HHHHHHHHHHHHHHTTEE-SS-SGGGEEEETTTE..EEE-SGTTSEESSSSCS........BCTTTSCGGGS-HHHHTTS CS
                        Pkinase 103 iakqilegleylHskgiiHrDlKpeNiLidekge..lKitDFGlakelesssk........ltsfvgtseYlAPEvlken 172
                                    ia ++le+le +H  + i+rD+KpeNiL+ +++   l ++D+G+ak + + s+         ++ +gt +Y +     + 
  gene629|gene629|rna629|rna629   2 IAITVLESLEDIHGCCRIFRDIKPENILVGNDNPdeLFLIDLGMAKYYMNPSSrehipfinNKKLTGTARYASLNTHMGY 81 
                                    67789************************9544457************999999******99***********9988888 PP

                                    CBSHHHHHHHHHHHHHHHHHSS-STTTSSHHH CS
                        Pkinase 173 eyskkvDvWslGvilyelltgkppfsgekgke 204
                                    e s+  D+ slG +l+ ++ g+ p+ g +  +
  gene629|gene629|rna629|rna629  82 EQSRRDDLESLGYTLIYFMRGNLPWMGVRAAT 113
                                    8899*********************9655443 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 0.38
                                    SHH...HHHTTS-HHHHHHH CS
                        Pkinase 222 etkeklpeaseiseeakdll 241
                                    ++++k + +++  +++kd++
  gene629|gene629|rna629|rna629 191 KKQKKKKSKNNWWHKFKDFI 210
                                    23333344444445555555 PP

>> Pkinase_fungal  Fungal protein kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.6   0.0     4e-12   3.6e-08     326     407 ..      16      99 ..       2     100 .. 0.83

  Alignments for each domain:
  == domain 1  score: 32.6 bits;  conditional E-value: 4e-12
                 Pkinase_fungal 326 agiLHrDiSenNilitdskkegerkglLiDLDlakelsddsses.....garertGTleFmaievlkgeeHsyrhDLESf 400
                                    +  + rDi  +Nil+    +++ ++ +LiDL +ak + ++ss++     ++++ tGT+ + +++  +g e s r+DLES+
  gene629|gene629|rna629|rna629  16 CCRIFRDIKPENILVG---NDNPDELFLIDLGMAKYYMNPSSREhipfiNNKKLTGTARYASLNTHMGYEQSRRDDLESL 92 
                                    34478***********...5567899************99999966666669**************************** PP

                 Pkinase_fungal 401 fyvllwi 407
                                     y l++ 
  gene629|gene629|rna629|rna629  93 GYTLIYF 99 
                                    **99985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       867  (0.0483574); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1448.98
//
Query:       gene63|gene63|rna63|rna63  [L=98]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.5e-07   30.7   0.3      9e-07   29.0   0.3    1.8  1  Skp1_POZ  Skp1 family, tetramerisation domain


Domain annotation for each model (and alignments):
>> Skp1_POZ  Skp1 family, tetramerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.0   0.3     5e-11     9e-07       2      61 ..       4      65 ..       3      67 .. 0.77

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 5e-11
                               EEEEEETTSCEEEEEHHHHTTSHHHHHHHHCTCCCGT...TCEEETTS-HHHHHHHHHHHHHC CS
                   Skp1_POZ  2 sivLqSsDgesfeveeavakkSktikhmiedlgdddk...priplpnvtskiLekvieYckhh 61
                                ++L+SsD++++e++e +a++Skt+ +  +      +    ++ lp  +sk L ++ieY k++
  gene63|gene63|rna63|rna63  4 IVTLISSDNKKYEIPEHIANESKTLRVFFDSNRPFIEaieRKVVLP-MNSKLLIRAIEYMKYK 65
                               689**********************998765433222222345554.59**********9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       508  (0.028334); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.48
# Mc/sec: 616.07
//
Query:       gene630|gene630|rna630|rna630  [L=179]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-14   52.9   6.7      7e-06   25.8   0.1    4.0  3  TPR_2            Tetratricopeptide repeat
    3.9e-13   48.9   9.9    1.4e-07   31.1   0.7    3.1  3  TPR_11           TPR repeat
    2.3e-12   46.2  10.6    0.00022   20.9   0.2    4.3  3  TPR_1            Tetratricopeptide repeat
      3e-09   36.6   8.6     0.0022   18.2   0.2    4.3  5  TPR_17           Tetratricopeptide repeat
    9.4e-07   29.0   0.4     0.0052   17.0   0.2    2.4  2  TPR_12           Tetratricopeptide repeat
    3.5e-06   27.6   0.0    5.6e-05   23.7   0.0    2.2  2  TPR_16           Tetratricopeptide repeat
    4.5e-06   26.5  10.0      0.006   16.7   0.2    4.5  4  TPR_8            Tetratricopeptide repeat
    4.5e-05   23.9   0.7    0.00038   20.9   0.2    2.5  2  TPR_19           Tetratricopeptide repeat
    7.1e-05   22.6   0.4      0.063   13.3   0.0    3.2  2  TPR_7            Tetratricopeptide repeat
     0.0033   18.1   0.0        1.2   10.2   0.0    2.8  2  TPR_14           Tetratricopeptide repeat
      0.005   17.4   0.5       0.57   10.9   0.0    3.3  2  TPR_6            Tetratricopeptide repeat
     0.0057   15.9   1.1     0.0077   15.5   1.1    1.2  1  TPR_15           Tetratricopeptide repeat
  ------ inclusion threshold ------
      0.052   13.6   0.1      0.052   13.6   0.1    3.4  4  MIT              MIT (microtubule interacting and transport) 
       0.09   12.9   0.5       0.31   11.2   0.0    2.0  2  TPM_phosphatase  TPM domain
       0.14   12.9   2.4        2.5    8.9   1.7    2.8  1  Sel1             Sel1 repeat
       0.14   12.9   1.8       0.46   11.2   1.9    1.8  1  Ribosomal_L28e   Ribosomal L28e protein family
       0.41   10.9   4.0       0.43   10.8   0.2    2.4  2  ANAPC3           Anaphase-promoting complex, cyclosome, subun


Domain annotation for each model (and alignments):
>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.1   6.6e-09     7e-06       1      34 []       4      37 ..       4      37 .. 0.95
   2 !   19.6   0.1   6.3e-07   0.00066       3      34 .]      40      71 ..      39      71 .. 0.95
   3 !    8.6   0.7    0.0021       2.3       1      32 [.      72     102 ..      72     104 .. 0.82

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 6.6e-09
                          TPR_2  1 aealynlGlayyklgdyeeAleafekAleldPnn 34
                                   ae l   G  ++k+gdye Al+ + +A+e dP+n
  gene630|gene630|rna630|rna630  4 AESLRKEGTELFKKGDYEGALNKYTEAIEKDPQN 37
                                   6889999*************************97 PP

  == domain 2  score: 19.6 bits;  conditional E-value: 6.3e-07
                          TPR_2  3 alynlGlayyklgdyeeAleafekAleldPnn 34
                                   ++ n+  +y+kl++ ee + + ekA+eldPn+
  gene630|gene630|rna630|rna630 40 LYSNRSACYAKLNKNEEGIVDAEKAVELDPNY 71
                                   589***************************96 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.0021
                          TPR_2   1 aealynlGlayyklgdyeeAleafekAleldP 32 
                                    a+a+ +lG  yy   d+ + ++++ekAle d 
  gene630|gene630|rna630|rna630  72 AKAYSRLGSFYY-YTDPVKSAHYYEKALESDS 102
                                    678888888888.67999**********9875 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.1   0.7   1.3e-10   1.4e-07       1      41 [.      11      51 ..      11      52 .. 0.91
   2 !   22.7   1.1   5.6e-08   5.9e-05       4      39 ..      48      83 ..      45      85 .. 0.94
   3 ?    1.0   0.1      0.34   3.6e+02      17      27 ..      94     104 ..      92     108 .. 0.84

  Alignments for each domain:
  == domain 1  score: 31.1 bits;  conditional E-value: 1.3e-10
                         TPR_11  1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykq 41
                                   G +++++G+ye+A+++Y +A++ dP+n  +y+n+ + y+k+
  gene630|gene630|rna630|rna630 11 GTELFKKGDYEGALNKYTEAIEKDPQNKVLYSNRSACYAKL 51
                                   6689***********************99999998877775 PP

  == domain 2  score: 22.7 bits;  conditional E-value: 5.6e-08
                         TPR_11  4 yyeqGkyeeAieaYkkAlkldPdnaeayynLGlayy 39
                                   y +++k+ee i + +kA++ldP++a ay+ LG  yy
  gene630|gene630|rna630|rna630 48 YAKLNKNEEGIVDAEKAVELDPNYAKAYSRLGSFYY 83
                                   78899999999999******************9887 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.34
                         TPR_11  17 YkkAlkldPdn 27 
                                    Y+kAl+ d++n
  gene630|gene630|rna630|rna630  94 YEKALESDSSN 104
                                    99999999988 PP

>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.1   2.7e-07   0.00028       6      34 .]       9      37 ..       4      37 .. 0.88
   2 !   20.9   0.2   2.1e-07   0.00022       4      34 .]      41      71 ..      39      71 .. 0.92
   3 !    6.2   1.7    0.0092       9.7       2      34 .]      73     104 ..      72     104 .. 0.69

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 2.7e-07
                                   HHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                          TPR_1  6 nlGnayfklgkydeAleyyekALelnPnn 34
                                     G  +fk+g+y+ Al  y +A+e +P+n
  gene630|gene630|rna630|rna630  9 KEGTELFKKGDYEGALNKYTEAIEKDPQN 37
                                   56899**********************97 PP

  == domain 2  score: 20.9 bits;  conditional E-value: 2.1e-07
                                   HHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                          TPR_1  4 lynlGnayfklgkydeAleyyekALelnPnn 34
                                   + n+ ++y kl+k +e + + ekA+el+Pn+
  gene630|gene630|rna630|rna630 41 YSNRSACYAKLNKNEEGIVDAEKAVELDPNY 71
                                   667778***********************97 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.0092
                                    HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                          TPR_1   2 kalynlGnayfklgkydeAleyyekALelnPnn 34 
                                    ka+ +lG  y++  ++ +   yyekALe + +n
  gene630|gene630|rna630|rna630  73 KAYSRLGSFYYYT-DPVKSAHYYEKALESDSSN 104
                                    5666666666655.5777889999999987765 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0         5   5.3e+03      23      32 ..      14      23 ..       3      24 .. 0.69
   2 !   18.2   0.2   2.1e-06    0.0022       2      30 ..      27      55 ..      26      58 .. 0.93
   3 !   17.6   0.1   3.3e-06    0.0035       3      24 ..      62      83 ..      60      90 .. 0.93
   4 ?    3.4   0.1      0.11   1.2e+02       1      12 [.      93     104 ..      93     107 .. 0.88
   5 ?   -2.2   0.0       6.8   7.2e+03      16      21 ..     145     149 ..     140     159 .. 0.56

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 5
                         TPR_17 23 llknGdlmtA 32
                                   l k+Gd++ A
  gene630|gene630|rna630|rna630 14 LFKKGDYEGA 23
                                   4589999887 PP

  == domain 2  score: 18.2 bits;  conditional E-value: 2.1e-06
                         TPR_17  2 ylkaleldPnnadaynnLAelllknGdlm 30
                                   y++a+e+dP n ++y n+  +++k+++ +
  gene630|gene630|rna630|rna630 27 YTEAIEKDPQNKVLYSNRSACYAKLNKNE 55
                                   99*********************999876 PP

  == domain 3  score: 17.6 bits;  conditional E-value: 3.3e-06
                         TPR_17  3 lkaleldPnnadaynnLAelll 24
                                   +ka+eldPn+a+ay  L+ +++
  gene630|gene630|rna630|rna630 62 EKAVELDPNYAKAYSRLGSFYY 83
                                   9******************996 PP

  == domain 4  score: 3.4 bits;  conditional E-value: 0.11
                         TPR_17   1 lylkaleldPnn 12 
                                    +y+kale d +n
  gene630|gene630|rna630|rna630  93 YYEKALESDSSN 104
                                    6*******9988 PP

  == domain 5  score: -2.2 bits;  conditional E-value: 6.8
                         TPR_17  16 ynnLAe 21 
                                    + n+A+
  gene630|gene630|rna630|rna630 145 M-NYAK 149
                                    4.4555 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.0   0.00089      0.93      45      73 ..       4      32 ..       2      36 .. 0.90
   2 !   17.0   0.2   4.9e-06    0.0052       5      73 ..      40      99 ..      38     103 .. 0.93

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00089
                         TPR_12 45 attlrnLgrlyralgryeeAlelleeala 73
                                   a++lr  g+ +++ g+ye Al+ ++ea++
  gene630|gene630|rna630|rna630  4 AESLRKEGTELFKKGDYEGALNKYTEAIE 32
                                   8899999*******************997 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 4.9e-06
                         TPR_12  5 alnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleeala 73
                                   +++n+ a++++l + +e +   eka+e+      p+   +a ++  Lg  y+++ ++ +   ++e+al+
  gene630|gene630|rna630|rna630 40 LYSNRSACYAKLNKNEEGIVDAEKAVELD-----PN---YAKAYSRLGSFYYYT-DPVKSAHYYEKALE 99
                                   57799********************9999.....87...69*************.*************8 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.0   5.3e-08   5.6e-05       2      67 ..       9      71 ..       8      72 .. 0.90
   2 ?    1.5   0.0      0.46   4.8e+02      12      29 ..      86     103 ..      75     109 .. 0.77

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 5.3e-08
                         TPR_16  2 alaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapda 67
                                   ++++++++ gdy+ A++ +++a+++d   P++   + ++  ++++++  +e +   ++a++ +p++
  gene630|gene630|rna630|rna630  9 KEGTELFKKGDYEGALNKYTEAIEKD---PQNKVLYSNRSACYAKLNKNEEGIVDAEKAVELDPNY 71
                                   5799**********************...************************5555666999986 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.46
                         TPR_16  12 dyddAaaaleaalkrdps 29 
                                    d+ + a+++e al++d+s
  gene630|gene630|rna630|rna630  86 DPVKSAHYYEKALESDSS 103
                                    566789999999999954 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.2   0.1    0.0065       6.9       8      34 .]      11      37 ..       4      37 .. 0.85
   2 !   16.7   0.2   5.7e-06     0.006       4      34 .]      41      71 ..      40      71 .. 0.92
   3 ?    0.8   0.2      0.71   7.4e+02       1      12 [.      72      83 ..      72      86 .. 0.81
   4 ?    5.2   0.0     0.028        30      22      33 ..      92     103 ..      88     104 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0065
                                   HHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                          TPR_8  8 gsiylklgdyeeAkeyyekaleldpdn 34
                                   g  ++k+gdye A   y +a+e dp+n
  gene630|gene630|rna630|rna630 11 GTELFKKGDYEGALNKYTEAIEKDPQN 37
                                   5568999******99999999988875 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 5.7e-06
                                   HHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                          TPR_8  4 yynlgsiylklgdyeeAkeyyekaleldpdn 34
                                   y n + +y kl++ ee +   eka+eldp++
  gene630|gene630|rna630|rna630 41 YSNRSACYAKLNKNEEGIVDAEKAVELDPNY 71
                                   6788889**********************95 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.71
                                   CCHHHHHHHHHH CS
                          TPR_8  1 aeayynlgsiyl 12
                                   a+ay +lgs y 
  gene630|gene630|rna630|rna630 72 AKAYSRLGSFYY 83
                                   689999999985 PP

  == domain 4  score: 5.2 bits;  conditional E-value: 0.028
                                    HHHHHHHHHHHH CS
                          TPR_8  22 eyyekaleldpd 33 
                                     yyekale d +
  gene630|gene630|rna630|rna630  92 HYYEKALESDSS 103
                                    69******9976 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.2   3.6e-07   0.00038       1      60 [.      14      74 ..      14      79 .. 0.87
   2 ?    2.4   0.1      0.22   2.3e+02      15      35 ..      62      82 ..      58     109 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 3.6e-07
                         TPR_19  1 llaegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpdd.ar 60
                                   l++ gdy+ Al+ +++a+++dp+n  +  +   ++ +l+  +e +   +++ e dp+   +
  gene630|gene630|rna630|rna630 14 LFKKGDYEGALNKYTEAIEKDPQNKVLYSNRSACYAKLNKNEEGIVDAEKAVELDPNYaKA 74
                                   6789************************************999888888888888885344 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.22
                         TPR_19 15 eqalqedpknaearllLAeal 35
                                   e+a + dp++a a  +L   +
  gene630|gene630|rna630|rna630 62 EKAVELDPNYAKAYSRLGSFY 82
                                   678889999998888776655 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.0     6e-05     0.063      11      35 ..      16      38 ..      14      39 .. 0.91
   2 ?    5.9   0.1     0.014        15       2      34 ..      75     104 ..      72     108 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 6e-05
                          TPR_7 11 rlGdyeeAielyeqsLaltkdpeda 35
                                   + Gdye A+  y++  a++kdp+++
  gene630|gene630|rna630|rna630 16 KKGDYEGALNKYTE--AIEKDPQNK 38
                                   78************..******975 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.014
                          TPR_7   2 LlnLarlysrlGdyeeAielyeqsLaltkdped 34 
                                    +++L++ y    d  + + +ye+  al++d ++
  gene630|gene630|rna630|rna630  75 YSRLGSFYYY-TDPVKSAHYYEK--ALESDSSN 104
                                    5556666655.67778999****..77776655 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.0    0.0011       1.2      11      38 ..      14      41 ..       4      51 .. 0.85
   2 ?    5.1   0.0     0.047        50      12      42 ..      49      79 ..      44      81 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0011
                         TPR_14 11 llalGdpdeAiallrralalaPddaeaw 38
                                   l+  Gd+++A++ + +a++++P++ +++
  gene630|gene630|rna630|rna630 14 LFKKGDYEGALNKYTEAIEKDPQNKVLY 41
                                   7789*******************98776 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.047
                         TPR_14 12 lalGdpdeAiallrralalaPddaeawllla 42
                                   + l + +e i  +++a++l+P+ a a+ +l+
  gene630|gene630|rna630|rna630 49 AKLNKNEEGIVDAEKAVELDPNYAKAYSRLG 79
                                   56667778888899************99987 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.0   0.00054      0.57       6      32 ..       3      36 ..       1      37 [. 0.85
   2 ?    2.6   0.1      0.25   2.7e+02       4      27 ..      76      98 ..      43     103 .. 0.59

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00054
                                   HHHHHHH.H......HHHHHHHHHHHHHHHH-TT CS
                          TPR_6  6 lalsyrk.l......gdtdkAlealerlikeYPd 32
                                   +a+s+rk +      gd++ Al  + + i++ P+
  gene630|gene630|rna630|rna630  3 MAESLRKeGtelfkkGDYEGALNKYTEAIEKDPQ 36
                                   7888887448888889****************98 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.25
                                   HHHHHHHHHHHHHHHHHHHHHHHH CS
                          TPR_6  4 yklalsyrklgdtdkAlealerli 27
                                    +l+  y+ + d+ k+  ++e+ +
  gene630|gene630|rna630|rna630 76 SRLGSFYYYT-DPVKSAHYYEKAL 98
                                   2344444444.6666666666655 PP

>> TPR_15  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   1.1   7.3e-06    0.0077      10     118 ..       5     112 ..       1     128 [. 0.85

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 7.3e-06
                         TPR_15  10 eal.klatllykqgdvkkAlevLkeaaqkaapskdteyWrtladLAwalqqedearkAyrqLlasgkaraedyerliell 88 
                                    e+l k  t l+k+gd+++Al+   ea++k  p+++  y    a  A+ +++e+   +A  + ++ +   a+ y+rl  ++
  gene630|gene630|rna630|rna630   5 ESLrKEGTELFKKGDYEGALNKYTEAIEKD-PQNKVLYSNRSACYAKLNKNEEGIVDAE-KAVELDPNYAKAYSRLGSFY 82 
                                    55633378899************8887777.99999**999999999999999888885.667888888*********** PP

                         TPR_15  89 ydaepkeaarlaekgwrrfrsprlLssale 118
                                    y  +p ++a + ek+ + + s + +++++ 
  gene630|gene630|rna630|rna630  83 YYTDPVKSAHYYEKALESDSSNKEYQKMVS 112
                                    ***************999999999988875 PP

>> MIT  MIT (microtubule interacting and transport) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   4.9e-05     0.052       6      32 ..       6      32 ..       1      33 [. 0.84
   2 ?    0.9   0.1      0.47     5e+02       8      25 ..      61      76 ..      55      77 .. 0.79
   3 ?    0.1   0.1      0.79   8.4e+02       7      16 ..      93     102 ..      88     118 .. 0.65
   4 ?   -2.1   0.0       4.1   4.3e+03      46      55 ..     149     158 ..     143     170 .. 0.54

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.9e-05
                            MIT  6 elvkkAveeDnagnyeeAlelYkeale 32
                                   +l k+ +e+ ++g+ye Al++Y+ea+e
  gene630|gene630|rna630|rna630  6 SLRKEGTELFKKGDYEGALNKYTEAIE 32
                                   56678888889**************98 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.47
                            MIT  8 vkkAveeDnagnyeeAle 25
                                   ++kAve+D   ny++A++
  gene630|gene630|rna630|rna630 61 AEKAVELDP--NYAKAYS 76
                                   789999998..8888875 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.79
                            MIT   7 lvkkAveeDn 16 
                                    + +kA e+D+
  gene630|gene630|rna630|rna630  93 YYEKALESDS 102
                                    3445555554 PP

  == domain 4  score: -2.1 bits;  conditional E-value: 4.1
                            MIT  46 rellrekiee 55 
                                    +ell++k  e
  gene630|gene630|rna630|rna630 149 KELLKNKSPE 158
                                    4444444333 PP

>> TPM_phosphatase  TPM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00029      0.31      95     124 ..       5      33 ..       2      34 .. 0.85
   2 ?   -0.6   0.1       1.4   1.4e+03      13      30 ..     104     121 ..      93     165 .. 0.55

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00029
                                    HHHHHHTHHHHHHHT-HHHHHHHHHHHHHH CS
                TPM_phosphatase  95 esildetilpalkdgdyaggilaavdaiea 124
                                    es+++e  ++ +k+gdy g+++++++aie+
  gene630|gene630|rna630|rna630   5 ESLRKE-GTELFKKGDYEGALNKYTEAIEK 33 
                                    566666.8999****************985 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.4
                                    HHHHHHHHHHHHHTT--E CS
                TPM_phosphatase  13 eaeleeklaalekktgvq 30 
                                     +e +++  +l k+t+++
  gene630|gene630|rna630|rna630 104 NKEYQKMVSDLKKRTQNR 121
                                    444555555555555443 PP

>> Sel1  Sel1 repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   1.7    0.0023       2.5       3      37 ..      74     101 ..      72     102 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0023
                           Sel1   3 AmyrLGmfylylnGlgvpkDpekAiewyekAAeqG 37 
                                    A+ rLG fy         +Dp k  ++yekA e +
  gene630|gene630|rna630|rna630  74 AYSRLGSFY-------YYTDPVKSAHYYEKALESD 101
                                    555666555.......678************9876 PP

>> Ribosomal_L28e  Ribosomal L28e protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   1.9   0.00044      0.46      41     104 ..      57     127 ..      24     131 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00044
                 Ribosomal_L28e  41 glan.skavtVreekkg.......vvlvtkkkerahkpakawekvklsknsrkalkqiakllkkyrpdlrka 104
                                    g++  +kav + ++  +       ++ +t  +++ah  +ka+e  + +k+++k+++ ++k+++  r+dl +a
  gene630|gene630|rna630|rna630  57 GIVDaEKAVELDPNYAKaysrlgsFYYYTDPVKSAHYYEKALESDSSNKEYQKMVSDLKKRTQ-NRNDLNMA 127
                                    55543556666633111234444499999999*****************************96.79999876 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.2   0.00041      0.43      33      76 ..      14      58 ..       2      64 .. 0.78
   2 ?    1.1   0.5      0.44   4.7e+02      12      56 ..      61     105 ..      58     112 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00041
                                   HHHTT-HHHHHHHHHCTSHHHC-HHHHHHHH...HHHHHTT-HHHHH CS
                         ANAPC3 33 lylngqykrAyellrkaklnskslgcrylfA...qcllkLkkyeeAi 76
                                   l++ g+y+ A++ + +a   +k+++  +l+     c+ kL+k ee+i
  gene630|gene630|rna630|rna630 14 LFKKGDYEGALNKYTEA--IEKDPQNKVLYSnrsACYAKLNKNEEGI 58
                                   89***************..5555555566655546666*******99 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.44
                                    HHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCTSHHHC-H CS
                         ANAPC3  12 aerllaaetespedayllAlclylngqykrAyellrkaklnsksl 56 
                                    ae++++ +++ +++   l+  +y +   k+A+++ + ++++s+++
  gene630|gene630|rna630|rna630  61 AEKAVELDPNYAKAYSRLGSFYYYTDPVKSAHYYEKALESDSSNK 105
                                    577776666555555567888888888888888766665555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (179 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1183  (0.0659825); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 1251.16
//
Query:       gene631|gene631|rna631|rna631  [L=419]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.9e-18   66.2   0.5    7.4e-17   61.6   0.5    2.2  1  tRNA-synt_1b  tRNA synthetases class I (W and Y)


Domain annotation for each model (and alignments):
>> tRNA-synt_1b  tRNA synthetases class I (W and Y)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.6   0.5   4.1e-21   7.4e-17       6     291 ..      79     392 ..      74     394 .. 0.73

  Alignments for each domain:
  == domain 1  score: 61.6 bits;  conditional E-value: 4.1e-21
                                    -EEEEEEETSSS.-BGGGHHHHHHHHHHHHTTSEEEEEEEHHHHHTTTTT-SSHHHHHHHHHHHHHH.HHHHHHHTCHTT CS
                   tRNA-synt_1b   6 lrvysGidPTgk.lHlGylvplkklvelqkaghevffliaDlhAiigdpskaeerklrkreevlena.ikaqlakgldpe 83 
                                    + +y+G  P+ k +H+G+++p++   +lq +  +v ++i     i++d +      + +++ +++++ ik ++a g++pe
  gene631|gene631|rna631|rna631  79 FYLYTGRGPSTKsMHIGHVIPFMLCKYLQ-DIFDVPLVI----QITDDEKYLFKDLQISESVEFAKSnIKDIIAFGFNPE 153
                                    679**************************.555555555....24455552233333333334444469*********** PP

                                    T..................................EEEEETHHHHTTHHHHHHHHHHHTTCBHHHHHHHHHCCHHCSSSC CS
                   tRNA-synt_1b  84 k..................................aevvlqsewlehlelaellrdlgklgslnrmlqfksvkkrleege 129
                                    k                                  +++ + s  ++++  + ++++      l++ + f + +k +  ++
  gene631|gene631|rna631|rna631 154 KtfifsnvgiydgneditdsknevyqegeclncesSKIRNTS--QKKKPFNGFFKK---ELVLAKSITFHEGSKVFGFDS 228
                                    *88888888888888888887777777765555432233222..333333333332...222333333333355555547 PP

                                    --BHHHHHHHHHHHHHHHHTCHS.......EEEEEGGGHHHHHHHHHHHHHHHHHSTTSS-EEEEET-BBSTTSSSBTTC CS
                   tRNA-synt_1b 130 gislgeftYplLqaaDilllkad.......lvpgGsDQkqnielgrdlarrfnkkevfkkpegltvplltgldGekKmSK 202
                                    + +lg++++p+ q +  ++   +       lvp   DQ+  ++l+rd  + f+ +    kp++++ ++l++l    KmS+
  gene631|gene631|rna631|rna631 229 STNLGQISFPVRQLLPCFYSVFTflknsncLVPAAIDQDPYFRLARDKSKIFECS----KPSTIYSQFLPSLMNLGKMSS 304
                                    78888888888776655543333444568************************99....********************* PP

                                    ETTCGC-BTTCCHHHHHHHHHHCHCSTTC.SHHHHHHHHHTHHHCHHHHHHHHCCSEEESSHHHHHHHHHCCCCHHHHHH CS
                   tRNA-synt_1b 203 SagnsaIfLddekesvkkkiqkavtdsde.evekllklktelsnelierleavsgkkpkreaeellaeevtklvhggdlk 281
                                    S+++ +IfLdd++es+kkki+    + ++  ++  + l   l+n++  ++  +  +++  +++ ++ ++++++++ +++k
  gene631|gene631|rna631|rna631 305 SKDK-TIFLDDSEESIKKKIRTYAHSGGRkTLQEHKMLGGDLDNDVSYQYLRFFMEDE-DKLQSVADKYKKGEMSSMEMK 382
                                    ****.****************8888877766666666677788877666666666665.69******************* PP

                                    HHHHHHHHHH CS
                   tRNA-synt_1b 282 kalaealnel 291
                                    +   e+l+++
  gene631|gene631|rna631|rna631 383 DLCIEELQKF 392
                                    *999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (419 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       862  (0.0480785); expected 358.6 (0.02)
Passed bias filter:                      574  (0.0320152); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 2900.22
//
Query:       gene632|gene632|rna632|rna632  [L=160]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-32  113.3  15.5    1.5e-32  113.1  15.5    1.0  1  ELO       GNS1/SUR4 family
  ------ inclusion threshold ------
      0.029   14.3   0.1      0.038   13.9   0.1    1.2  1  DUF1686   Protein of unknown function (DUF1686)
      0.073   13.5   1.4      0.082   13.3   0.4    1.6  2  RIC3      Resistance to inhibitors of cholinesterase homologu
       0.16   11.5   7.0        0.2   11.2   7.0    1.1  1  BaxI_1    Bax inhibitor 1 like
        3.6    8.5  15.8         15    6.5   2.3    2.5  2  DUF3817   Domain of unknown function (DUF3817)


Domain annotation for each model (and alignments):
>> ELO  GNS1/SUR4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.1  15.5   4.2e-36   1.5e-32     106     249 ..       1     140 [.       1     141 [. 0.86

  Alignments for each domain:
  == domain 1  score: 113.1 bits;  conditional E-value: 4.2e-36
                            ELO 106 lDTvflvlrkkqvsfLhvYHHatvmllmwaglrfatssgivfivllNsfvHaimYtYYflsalgakklvvpwkrliTslQ 185
                                    +DTv+l l kk+ +fL++YHHa++++ +++ ++ + s  ++++v+lNsfvH++mY+YY++s +++   ++ +k++iT++Q
  gene632|gene632|rna632|rna632   1 MDTVILHLNKKRATFLQCYHHAGAIFATYLFCKAE-SHVAWIFVVLNSFVHSVMYLYYLISVFKI---RIRFKKIITTMQ 76 
                                    7**********************************.99999999*****************5555...5799******** PP

                            ELO 186 ilQfvvgllaavyllvsytlkkvgCdtsqtpkaairlnllyllslllLFlnffiksylkkkkkk 249
                                    ++Qf++g +++++ ++     + + +++      i++n+ y+l+l++LF  ff k+y kk++k+
  gene632|gene632|rna632|rna632  77 MTQFILGYVLIAFHFIGGLRFSSDLRKKVLEIVTIIFNVGYVLFLFILFKIFFKKEYQKKRDKN 140
                                    ********7777767765544344433333346999***********************99886 PP

>> DUF1686  Protein of unknown function (DUF1686)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   1.1e-05     0.038      66     153 ..      49     140 ..      41     148 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.1e-05
                        DUF1686  66 vysvtvagigivmlyvQslvkkkmsrrqvcvvvlgnillasaclagdklllp...gvedrsslv.cvglvvfaallllvs 141
                                    v sv+     i         kk +  +q+  ++lg +l+a  +++g ++ ++    v +  +++ +vg+v+f  +l  + 
  gene632|gene632|rna632|rna632  49 VHSVMYLYYLISVFKIRIRFKKIITTMQMTQFILGYVLIAFHFIGGLRFSSDlrkKVLEIVTIIfNVGYVLFLFILFKIF 128
                                    55666655555555666667888999*******************99988884444444444333789999999999888 PP

                        DUF1686 142 yveeggkkakae 153
                                    +  e  kk  ++
  gene632|gene632|rna632|rna632 129 FKKEYQKKRDKN 140
                                    877655555554 PP

>> RIC3  Resistance to inhibitors of cholinesterase homologue 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       2.5   8.8e+03      85      96 ..      25      36 ..      24      38 .. 0.83
   2 ?   13.3   0.4   2.3e-05     0.082      81     115 ..     115     148 ..     101     153 .. 0.74

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 2.5
                           RIC3 85 vfilYtllKiks 96
                                   +f+ Y + K  s
  gene632|gene632|rna632|rna632 25 IFATYLFCKAES 36
                                   8999***99876 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 2.3e-05
                           RIC3  81 iGilvfilYtllKikskkkkekskeakakkkaken 115
                                    +G  v +l++l+Ki++kk+ +k+++++++k ++++
  gene632|gene632|rna632|rna632 115 VGY-VLFLFILFKIFFKKEYQKKRDKNRTKVTTSG 148
                                    554.4568**********98866666666666555 PP

>> BaxI_1  Bax inhibitor 1 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   7.0   5.7e-05       0.2     101     186 ..      33     123 ..      18     137 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 5.7e-05
                         BaxI_1 101 a..pgivvqAvlgTlgvfavmlvlYktgairvtpkftkivvaaligilllylvnlvlslfgvge.g..lrdgglgilfsl 175
                                    +  + ++   v++   v  vm++ Y   + ++  +f+ki++++ ++ ++l  v + ++++g+ +    lr++ l i+  +
  gene632|gene632|rna632|rna632  33 KaeSHVAWIFVVLNSFVHSVMYLYYLISVFKIRIRFKKIITTMQMTQFILGYVLIAFHFIGGLRfSsdLRKKVLEIVTII 112
                                    2467788888999999*********************************9999999998876664245888876666666 PP

                         BaxI_1 176 vvivlAalsLl 186
                                    + ++   + ++
  gene632|gene632|rna632|rna632 113 FNVGYVLFLFI 123
                                    66655444444 PP

>> DUF3817  Domain of unknown function (DUF3817)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   9.6     0.015        55      20      58 ..      34      72 ..      13      86 .. 0.67
   2 ?    6.5   2.3    0.0041        15      16      59 ..      81     136 ..      66     140 .. 0.73

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.015
                        DUF3817 20 vamilkyllvkvigivHGllfvvYlllalllaskmrWsl 58
                                   ++  + +++v +   vH ++++ Yl++++++ ++ +  +
  gene632|gene632|rna632|rna632 34 AESHVAWIFVVLNSFVHSVMYLYYLISVFKIRIRFKKII 72
                                   333333447778899**************9988776444 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0041
                        DUF3817  16 llLlvamilkyl............lvkvigivHGllfvvYlllalllaskmrWslk 59 
                                    +l  v + ++++            +++++ i+  + +v++l++++++ +k +++ k
  gene632|gene632|rna632|rna632  81 ILGYVLIAFHFIgglrfssdlrkkVLEIVTIIFNVGYVLFLFILFKIFFKKEYQKK 136
                                    222444444444777777999999999********************999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1235  (0.0688828); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1138.04
//
Query:       gene633|gene633|rna633|rna633  [L=291]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       969  (0.0540465); expected 358.6 (0.02)
Passed bias filter:                      579  (0.032294); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2090.42
//
Query:       gene634|gene634|rna634|rna634  [L=762]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.2e-11   43.0   1.6    7.4e-11   42.2   0.2    2.0  2  Peptidase_M16  Insulinase (Peptidase family M16)


Domain annotation for each model (and alignments):
>> Peptidase_M16  Insulinase (Peptidase family M16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.2   0.2   4.1e-15   7.4e-11      44     126 ..      13      89 ..       8     108 .. 0.86
   2 ?   -2.3   0.1      0.22     4e+03      61      87 ..     282     309 ..     279     314 .. 0.69

  Alignments for each domain:
  == domain 1  score: 42.2 bits;  conditional E-value: 4.1e-15
                                    BBSSSCH.HHHHHHHHHTTCEEEEEEESSEEEEEEEEEGGGHHHHHHHHHHHHHSBTTSHHHHHHHHHHHHHHHHHHCCH CS
                  Peptidase_M16  44 gTkkyps.nklaeeleklGgslnAttsrentvYyvevlskdlekaldvladvfkaplleesevererkvvekeveavdae 122
                                    +Tk+ p+ n ++++l+  +g +nA+t +++tvY++e+++  + + + +++++fk+pl+++ +v         e ++vd+e
  gene634|gene634|rna634|rna634  13 KTKNAPKiNDFDSFLNTYNGDSNAYTAEDETVYHYELDNAGMLQSFRLFSNFFKHPLINKRTVAS-------ESQVVDSE 85 
                                    79***************************************************************.......66666666 PP

                                    HHHH CS
                  Peptidase_M16 123 pekv 126
                                     +++
  gene634|gene634|rna634|rna634  86 FQNR 89 
                                    6333 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.22
                                    TCEEEEEEESSEEE.EEEEEEGGGHHHH CS
                  Peptidase_M16  61 GgslnAttsrentv.Yyvevlskdleka 87 
                                    G  +  tt+re++v + ++v+s+d+ +a
  gene634|gene634|rna634|rna634 282 GTVCTTTTQRETMVcFDFTVPSTDTYTA 309
                                    4445667777776447888888887655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (762 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       831  (0.0463495); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.68u 0.31s 00:00:00.99 Elapsed: 00:00:00.49
# Mc/sec: 4676.42
//
Query:       gene635|gene635|rna635|rna635  [L=304]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.9e-06   26.6   0.1    8.1e-06   25.6   0.1    1.6  1  UBA          UBA/TS-N domain
  ------ inclusion threshold ------
      0.015   15.1   0.0      0.034   13.9   0.0    1.7  1  ubiquitin    Ubiquitin family
        0.1   12.6   0.2       0.24   11.4   0.1    1.6  2  HOIP-UBA     HOIP UBA domain pair
       0.11   12.6   0.1        0.2   11.8   0.1    1.4  1  Rad60-SLD_2  Ubiquitin-2 like Rad60 SUMO-like


Domain annotation for each model (and alignments):
>> UBA  UBA/TS-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.1   1.8e-09   8.1e-06       4      37 .]     260     294 ..     257     294 .. 0.94

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 1.8e-09
                                    HHHHHHHHTTS-HH.HHHHHHHHTTTSHHHHHHHH CS
                            UBA   4 eaiqrLveMGFdre.evveALratgnNeErAveyL 37 
                                     ++ +L eMG++   ++++AL +tg++++ Av+ L
  gene635|gene635|rna635|rna635 260 VQLKTLNEMGYTNKqHNLQALAQTGGDVNDAVNLL 294
                                    5899*********99******************87 PP

>> ubiquitin  Ubiquitin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   7.6e-06     0.034       5      69 ..       5      75 ..       1      78 [. 0.88

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 7.6e-06
                                   E.TTSEEEEEEEETTSBHHHHHHHHHHHHT.....SSGGGEEEEETTEEE-TTSBHGGHTTSTTEEEEEEE CS
                      ubiquitin  5 t.ldgkkitleveesdtveelKekiaekeg.....ipaeqqrLiysGkvLedertleeygiqdgstlhlvl 69
                                     ++++k++lev+e++++    e+  +  +     +  + ++++   k L++e+t +e gi+++st+ ++ 
  gene635|gene635|rna635|rna635  5 LnFRSTKYSLEVDENEKIGAARERFFDMIKdahsdVNINDLKFVGMAKFLDNEKTFSEEGIKPDSTILVHK 75
                                   448899*****************998888667777999999999999********************9986 PP

>> HOIP-UBA  HOIP UBA domain pair
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       1.4   6.3e+03      47      70 ..     134     157 ..     132     162 .. 0.74
   2 ?   11.4   0.1   5.4e-05      0.24     102     136 ..     260     294 ..     251     298 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.4
                       HOIP-UBA  47 lpelldevaalaaseqkekkenev 70 
                                    l   +++++  a++e++e  +++ 
  gene635|gene635|rna635|rna635 134 LDLTIKTIMPTATNEERELYKKTF 157
                                    556789999999999888766655 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 5.4e-05
                       HOIP-UBA 102 kKvkelaslgffdreevveaLrqsgGdvegAlveL 136
                                     ++k l ++g  ++++ ++aL q+gGdv+ A+ +L
  gene635|gene635|rna635|rna635 260 VQLKTLNEMGYTNKQHNLQALAQTGGDVNDAVNLL 294
                                    57899**************************9877 PP

>> Rad60-SLD_2  Ubiquitin-2 like Rad60 SUMO-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   4.4e-05       0.2      47      99 ..      41      87 ..      31      98 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 4.4e-05
                                   SCCCEEEEETTEEE-TTSBCCCCS-TTTTTTTS-EEEEEEE---SS----.XX CS
                    Rad60-SLD_2 47 svndlklilaGkiLennktlkelrlplgevkggvtvmHvvvrenlsekksekk 99
                                   ++ndlk + + k+L+n kt +e +++   +    +++H+ + ++  ek s+k 
  gene635|gene635|rna635|rna635 41 NINDLKFVGMAKFLDNEKTFSEEGIKPDST----ILVHKALPKK--EKDSKKD 87
                                   689********************8887777....9999988333..3333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (304 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       623  (0.0347482); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2155.38
//
Query:       gene636|gene636|rna636|rna636  [L=152]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.6e-11   43.7  13.7    3.7e-11   43.2  13.7    1.2  1  zf-RING_2     Ring finger domain
      1e-08   34.8   6.3      1e-08   34.8   6.3    1.9  2  zf-RING_11    RING-like zinc finger
    3.4e-07   30.0  13.4    5.1e-07   29.5  13.4    1.3  1  zf-C3HC4      Zinc finger, C3HC4 type (RING finger)
    4.5e-07   30.1   8.9    8.4e-07   29.2   8.9    1.4  1  zf-rbx1       RING-H2 zinc finger domain
    1.5e-06   27.9  13.1    2.4e-06   27.3  13.1    1.3  1  zf-C3HC4_2    Zinc finger, C3HC4 type (RING finger)
    0.00021   21.2  12.7    0.00032   20.6  12.7    1.3  1  zf-RING_5     zinc-RING finger domain
    0.00077   19.3  10.4     0.0012   18.7  10.4    1.2  1  zf-C3HC4_3    Zinc finger, C3HC4 type (RING finger)
     0.0012   18.8   8.0     0.0067   16.4   8.0    2.0  1  zf-ANAPC11    Anaphase-promoting complex subunit 11 RING-H2 f
     0.0039   17.6   5.0      0.055   13.9   0.4    2.1  2  Vps39_2       Vacuolar sorting protein 39 domain 2
  ------ inclusion threshold ------
      0.056   13.5   5.1      0.056   13.5   5.1    2.2  2  zf-RING_UBOX  RING-type zinc-finger
       0.11   12.3   9.3       0.19   11.6   9.3    1.4  1  Prok-RING_4   Prokaryotic RING finger family 4
       0.64    9.7   9.1          1    9.0   9.1    1.3  1  Zn_ribbon_17  Zinc-ribbon, C4HC2 type
        1.6    8.9  11.0         10    6.4  11.0    2.1  1  FANCL_C       FANCL C-terminal domain
        1.7    8.4  12.5        4.3    7.1  12.5    1.6  1  zf-P11        P-11 zinc finger
        4.4    7.2  12.2         15    5.4  12.2    1.8  2  zf-RING_4     RING/Ubox like zinc-binding domain


Domain annotation for each model (and alignments):
>> zf-RING_2  Ring finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.2  13.7   3.1e-14   3.7e-11       2      44 .]     102     145 ..     101     145 .. 0.90

  Alignments for each domain:
  == domain 1  score: 43.2 bits;  conditional E-value: 3.1e-14
                      zf-RING_2   2 eCpICleelssadsvlllpCgHvfhreClerw.lrssstCPlCr 44 
                                    +C+ICl+++ ++d ++ l C+H fh++C++rw lrss  CP+Cr
  gene636|gene636|rna636|rna636 102 QCTICLQNYAKNDMIRELTCKHEFHCKCVDRWlLRSSDCCPVCR 145
                                    8***************999*************5555555****9 PP

>> zf-RING_11  RING-like zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.8   6.3   8.5e-12     1e-08       1      29 []     102     130 ..     102     130 .. 0.98
   2 ?   -1.2   0.0       1.5   1.7e+03       2      12 ..     141     151 ..     141     152 .] 0.79

  Alignments for each domain:
  == domain 1  score: 34.8 bits;  conditional E-value: 8.5e-12
                     zf-RING_11   1 eCsICLeefkpgqalfilpCsHtFHfkCI 29 
                                    +C+ICL++++++++++ l C+H FH+kC+
  gene636|gene636|rna636|rna636 102 QCTICLQNYAKNDMIRELTCKHEFHCKCV 130
                                    7***************************7 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.5
                     zf-RING_11   2 CsICLeefkpg 12 
                                    C +C   +++g
  gene636|gene636|rna636|rna636 141 CPVCRKRVGEG 151
                                    99**8888776 PP

>> zf-C3HC4  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.5  13.4   4.3e-10   5.1e-07       1      41 []     103     144 ..     103     144 .. 0.97

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 4.3e-10
                                    -TTT-S--SS-E...E-TTS--B-CHHHHHHHHCTSSB--TTT CS
                       zf-C3HC4   1 CpiCleeakepn..elleCkHsfCskCirkilksrkkvkCPlC 41 
                                    C iCl+++++++  + l+CkH+f++kC++++l  r++ +CP+C
  gene636|gene636|rna636|rna636 103 CTICLQNYAKNDmiRELTCKHEFHCKCVDRWLL-RSSDCCPVC 144
                                    **********999999*****************.999****** PP

>> zf-rbx1  RING-H2 zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.2   8.9   7.1e-10   8.4e-07      11      55 .]     100     145 ..      96     145 .. 0.84

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 7.1e-10
                        zf-rbx1  11 eeacieckapgdeecpvvlGeCgHaFHlhCiskWlkt.rkvCPlcr 55 
                                    +e+c+ c ++  ++ ++   +C+H+FH +C+++Wl + ++ CP+cr
  gene636|gene636|rna636|rna636 100 DEQCTICLQNYAKNDMIRELTCKHEFHCKCVDRWLLRsSDCCPVCR 145
                                    578999988888876666669*************9775888****8 PP

>> zf-C3HC4_2  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3  13.1     2e-09   2.4e-06       1      40 []     102     144 ..     102     144 .. 0.88

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 2e-09
                     zf-C3HC4_2   1 kCpiCldmlkdpsvvt..pCgHvfCqkCilrsLeekn.eCPlC 40 
                                    +C+iCl+ + +  ++    C+H f+ kC++r+L +++  CP+C
  gene636|gene636|rna636|rna636 102 QCTICLQNYAKNDMIRelTCKHEFHCKCVDRWLLRSSdCCPVC 144
                                    7********9986776889************8766666***** PP

>> zf-RING_5  zinc-RING finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6  12.7   2.7e-07   0.00032       1      44 []     102     146 ..     102     146 .. 0.97

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 2.7e-07
                      zf-RING_5   1 hCnkCfeklskeekfyltsCgHifCekClkkll.ekeavCpiCrk 44 
                                    +C +C +++ k++ +  ++C+H f+ kC+++ l  ++++Cp+Crk
  gene636|gene636|rna636|rna636 102 QCTICLQNYAKNDMIRELTCKHEFHCKCVDRWLlRSSDCCPVCRK 146
                                    5*******************************99*********97 PP

>> zf-C3HC4_3  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7  10.4   9.7e-07    0.0012       2      47 ..     100     148 ..      99     150 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 9.7e-07
                                    GSB-TTTSSS.BS-..EEETTEEEEEE-HHHHHHHHH.TT-B-TTT--B- CS
                     zf-C3HC4_3   2 deeCviCler.prn..vvllpCgHlvlCeeCaekllk.rkkkCpiCrrpi 47 
                                    de+C iCl++  +n  +  l C+H + C+ C++++l  +++ Cp+Cr+ +
  gene636|gene636|rna636|rna636 100 DEQCTICLQNyAKNdmIRELTCKHEFHCK-CVDRWLLrSSDCCPVCRKRV 148
                                    689******953332245567****9996.77777655*********987 PP

>> zf-ANAPC11  Anaphase-promoting complex subunit 11 RING-H2 finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   8.0   5.6e-06    0.0067      35      80 ..     103     147 ..      78     150 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 5.6e-06
                                    -TTCSTTTTTS-EEEBT.TS-EEEHHHHHHHHHHHSTSSB-TTTSSB CS
                     zf-ANAPC11  35 cpsckfpGddcplvlGk.ckhnfhlhcilkwletetskglcpmcrqt 80 
                                    c  c     +  ++    ckh fh +c+ +wl +  s + cp+cr+ 
  gene636|gene636|rna636|rna636 103 CTICLQNYAKNDMIRELtCKHEFHCKCVDRWLLR--SSDCCPVCRKR 147
                                    555555555555555444**************75..6789*****86 PP

>> Vps39_2  Vacuolar sorting protein 39 domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.4   4.6e-05     0.055      16     108 ..      37     131 ..      30     132 .. 0.84
   2 ?    3.7   4.2     0.069        82      63      90 ..     123     150 ..     115     152 .] 0.77

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.6e-05
                        Vps39_2  16 vLdllPdelplkdlesflekalrnslekkreeqvvkklrkaeklsvee.ellklrskkvvvteekvCavCkkrlge.svf 93 
                                    +Ld ++++  ++++   l   +++   ++  ++++ +++ ++k +v + + l+  +k+v+ + +++C +C ++ ++  ++
  gene636|gene636|rna636|rna636  37 TLDNISADFDVSNILFNLFPLIERFRDTSTLTNIILYFYPVKKRNVLSrKSLNALKKRVYTDGDEQCTICLQNYAKnDMI 116
                                    688899999999999999999988888899999******9999998761567899***************9999887888 PP

                        Vps39_2  94 vvyPngsvvHlgCak 108
                                    + +  ++  H +C++
  gene636|gene636|rna636|rna636 117 RELTCKHEFHCKCVD 131
                                    888888888888876 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.069
                        Vps39_2  63 eellklrskkvvvteekvCavCkkrlge 90 
                                    +e   ++  +  + ++  C+vC+kr+ge
  gene636|gene636|rna636|rna636 123 HEFHCKCVDRWLLRSSDCCPVCRKRVGE 150
                                    55555666777899999********997 PP

>> zf-RING_UBOX  RING-type zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   5.1   4.7e-05     0.056       1      33 [.     103     135 ..     103     140 .. 0.73
   2 ?    0.9   0.3      0.41   4.9e+02       1       5 [.     141     145 ..     141     148 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4.7e-05
                   zf-RING_UBOX   1 CpIClelftdP.lv..lpCGHtFCreCl..welsksle 33 
                                    C+ICl+ + +  ++  l+C H F+ +C+  w     l 
  gene636|gene636|rna636|rna636 103 CTICLQNYAKNdMIreLTCKHEFHCKCVdrW-----LL 135
                                    ********8446455668**********444.....33 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.41
                   zf-RING_UBOX   1 CpICl 5  
                                    Cp+C+
  gene636|gene636|rna636|rna636 141 CPVCR 145
                                    ****7 PP

>> Prok-RING_4  Prokaryotic RING finger family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   9.3   0.00016      0.19       1      41 [.     103     149 ..     102     152 .] 0.76

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00016
                    Prok-RING_4   1 CvlCgeq...ekkailepCgHlvCkeCfdsk..dls.sCPlCqrris 41 
                                    C +C ++   +  ++   C+H +  +C d +   +s  CP+C++r+ 
  gene636|gene636|rna636|rna636 103 CTICLQNyakNDMIRELTCKHEFHCKCVDRWllRSSdCCPVCRKRVG 149
                                    999999875344444569****8889*****7644469******985 PP

>> Zn_ribbon_17  Zinc-ribbon, C4HC2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   9.1   0.00087         1       5      47 ..     101     143 ..      98     148 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00087
                   Zn_ribbon_17   5 ksCayCela.vkgrvvlcgvCeHvlHasCarewfenddlaeCps 47 
                                    ++C++C  + +k  ++    C+H  H  C++ w+       Cp+
  gene636|gene636|rna636|rna636 101 EQCTICLQNyAKNDMIRELTCKHEFHCKCVDRWLLRSS-DCCPV 143
                                    58****76615666777899*************65555.47775 PP

>> FANCL_C  FANCL C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4  11.0    0.0086        10       3      44 ..     101     137 ..      99     150 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0086
                                    -S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHH CS
                        FANCL_C   3 veCgiCyayrldsgevpdisCdnekCnkkfHsaCLkeWlrsl 44 
                                     +C iC+ +  +++ + + +C     +++fH +C+  Wl   
  gene636|gene636|rna636|rna636 101 EQCTICLQNYAKNDMIRELTC-----KHEFHCKCVDRWLLRS 137
                                    68*****99999999988775.....678*********9655 PP

>> zf-P11  P-11 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1  12.5    0.0036       4.3       3      43 ..     101     146 ..      99     148 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0036
                                    SSBTTTSS-..-SSEE...E-SSSEEEHHHHHHHHHHSSBETTTSS CS
                         zf-P11   3 lsCksCWfk..dksLv...eCsdHYLClrClqllLsvserCpiCkk 43 
                                     +C  C ++  +++++   +C+  + C+   + lL+ s+ Cp+C+k
  gene636|gene636|rna636|rna636 101 EQCTICLQNyaKNDMIrelTCKHEFHCKCVDRWLLRSSDCCPVCRK 146
                                    56777765321344442227*******99999************97 PP

>> zf-RING_4  RING/Ubox like zinc-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.1       0.4   4.8e+02      32      47 ..      95     110 ..      92     111 .. 0.75
   2 ?    5.4  12.2     0.013        15       1      45 [.     103     146 ..     103     148 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.4
                      zf-RING_4  32 ileeeegrCPaCreeY 47 
                                    + ++ +++C  C ++Y
  gene636|gene636|rna636|rna636  95 VYTDGDEQCTICLQNY 110
                                    6667788899998888 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.013
                      zf-RING_4   1 cplCdeeldetdkdlkpCeCgyqiClfCyhrileeeegrCPaCre 45 
                                    c +C ++  ++d  ++  +C++++ + C +r l +++ +CP Cr+
  gene636|gene636|rna636|rna636 103 CTICLQNYAKND-MIRELTCKHEFHCKCVDRWLLRSSDCCPVCRK 146
                                    777777775444.577779*************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       800  (0.0446204); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 996.55
//
Query:       gene637|gene637|rna637|rna637  [L=53]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.062   12.4   0.2      0.067   12.3   0.2    1.0  1  FAD_binding_2  FAD binding domain


Domain annotation for each model (and alignments):
>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.2   3.7e-06     0.067     268     310 ..       3      47 ..       1      51 [. 0.86

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3.7e-06
                                    THHHHTT-EEE-TTSSBTH..GGGS-HHHHHHHHH.HHHHTTTSC CS
                  FAD_binding_2 268 ealrgeGgilvdkdGrrFm..nelasrdvvsrailekeiaeggse 310
                                     + rg G  ++ k+G+r    ne+    v+ r +++ke +e ++e
  gene637|gene637|rna637|rna637   3 MKYRGRGMNWLEKKGERMIneNEVGLNEVIERMVFRKEWKEDNEE 47 
                                    5789*************55**99999999******9999998874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (53 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       517  (0.028836); expected 358.6 (0.02)
Passed bias filter:                      209  (0.0116571); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.28s 00:00:00.63 Elapsed: 00:00:00.43
# Mc/sec: 374.40
//
Query:       gene638|gene638|rna638|rna638  [L=91]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       424  (0.0236488); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 644.03
//
Query:       gene639|gene639|rna639|rna639  [L=148]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-10   41.0   0.0    2.5e-10   40.7   0.0    1.0  1  GPP34     Golgi phosphoprotein 3 (GPP34)


Domain annotation for each model (and alignments):
>> GPP34  Golgi phosphoprotein 3 (GPP34)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.7   0.0   1.4e-14   2.5e-10       1     108 [.      22     139 ..      22     145 .. 0.84

  Alignments for each domain:
  == domain 1  score: 40.7 bits;  conditional E-value: 1.4e-14
                          GPP34   1 LaeellLLalddekgrlsfandnlsyaLaGAiLiELalrgriavdkeggrvvvidsrptg....dplldealklikaser 76 
                                    L eel++L+   +k +  ++   ls+a +++iL++L  ++ i++d ++g vvv d+  tg    +pl+d ++++i     
  gene639|gene639|rna639|rna639  22 LTEELMILSSLRKKIYKILDP--LSVAIRACILADLNYQNIITMDYKKGCVVVKDT-ITGnvldNPLMDDVVYRIG--LY 96 
                                    679999999998888876655..*********************876665555555.565455488*******998..55 PP

                          GPP34  77 prsvktwvdlls...........ksvrervakgLvdkGilrte 108
                                    + sv++w++ll            k+vr+rv+ gL  k  ++ +
  gene639|gene639|rna639|rna639  97 KTSVSKWIRLLNgesykrseyylKKVRKRVLVGLQNKKAVKFR 139
                                    689*******************************999888755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       489  (0.0272742); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1049.61
//
Query:       gene64|gene64|rna64|rna64  [L=290]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.3e-18   67.3   2.0    1.4e-18   67.2   0.1    2.0  2  LsmAD        LsmAD domain
  ------ inclusion threshold ------
       0.15   11.9   0.2       0.67    9.8   0.1    2.0  2  Ub-Mut7C     Mut7-C ubiquitin
       0.79    8.9   2.0       0.94    8.6   2.0    1.1  1  Herpes_LMP1  Herpesvirus latent membrane protein 1 (LMP1)


Domain annotation for each model (and alignments):
>> LsmAD  LsmAD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.2   0.1   2.4e-22   1.4e-18       1      69 [.      18      83 ..      18      84 .. 0.96
   2 ?   -2.6   0.2       1.4   8.5e+03      43      46 ..     184     187 ..     163     207 .. 0.45

  Alignments for each domain:
  == domain 1  score: 67.2 bits;  conditional E-value: 2.4e-22
                      LsmAD  1 FgvkstYdEnlYTtkldksspeykereaeAeriArEIessastnahvaeerglkvddsgldEEdkYSaV 69
                               Fg+k++++E  YTt ldk+s+ y +++a+A++i+++I +s++++ h++eergl    + ++EEd+YSaV
  gene64|gene64|rna64|rna64 18 FGIKPEFNEADYTTVLDKNSEFYLKNVARAKKIEHDILTSKCGDRHRMEERGL---IECENEEDRYSAV 83
                               9****************************************************...4458********9 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.4
                      LsmAD  43 tnah 46 
                                t+ +
  gene64|gene64|rna64|rna64 184 TDRK 187
                                2333 PP

>> Ub-Mut7C  Mut7-C ubiquitin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.1   0.00011      0.67      24      48 ..     142     166 ..     136     179 .. 0.87
   2 ?   -1.4   0.0      0.36   2.2e+03      31      42 ..     242     253 ..     236     254 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00011
                   Ub-Mut7C  24 alavafdeaatvkhviEalGVPhtE 48 
                                +++++ +   +v+h +E  GVPh+ 
  gene64|gene64|rna64|rna64 142 DVTAQANDTKSVSHGVEKKGVPHVD 166
                                5677888999*************85 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.36
                   Ub-Mut7C  31 eaatvkhviEal 42 
                                 + t+k+ iE++
  gene64|gene64|rna64|rna64 242 TFKTIKEYIESI 253
                                578*******96 PP

>> Herpes_LMP1  Herpesvirus latent membrane protein 1 (LMP1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   2.0   0.00016      0.94     267     321 ..     154     208 ..      86     243 .. 0.53

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00016
                                XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                Herpes_LMP1 267 pdntddngphdplpqdpdntddngpqdpdntddngphdplphspsdsagndggpp 321
                                    + +g  +   +  d+ ++n  qd   td + phd   +   ds   +   p
  gene64|gene64|rna64|rna64 154 SHGVEKKGVPHVDAKKADKVNENAVQDGSHTDRKVPHDTHKKHAVDSENAQADKP 208
                                2333334433334445555555555555555555555555555554443333222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (290 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       948  (0.0528752); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1946.57
//
Query:       gene640|gene640|rna640|rna640  [L=300]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-09   38.8   0.1    3.8e-09   37.3   0.0    1.8  2  RNase_T   Exonuclease


Domain annotation for each model (and alignments):
>> RNase_T  Exonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0      0.27   4.8e+03      32      59 ..      33      60 ..      25      66 .. 0.74
   2 !   37.3   0.0   2.1e-13   3.8e-09       1     165 []      77     220 ..      77     220 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.27
                                   EEEEEEEEEEEHSSHCSSSHHHHHHHHH CS
                        RNase_T 32 eigetfhfyvkptelakltdecteftgi 59
                                   +++++f++y +++++ + +  + e+++i
  gene640|gene640|rna640|rna640 33 VVKQPFSIYLEDDRFVNSDVSVREMNKI 60
                                   4788899999999996666666666666 PP

  == domain 2  score: 37.3 bits;  conditional E-value: 2.1e-13
                                    EEEEEEESSSTTCTTS-EEEEEEEEEETTCCEEEEEEEEEEEHSSHCSSSHHHHHHHHHCHHHHHTCEBHHHHHHHHHHH CS
                        RNase_T   1 vviDlEttgldakekdeiieiaaisidggeneigetfhfyvkptelakltdecteftgitqemldeapsfkevleefkel 80 
                                    ++iD+E+  ++a+     +e++++++      +    + yv+ ++   + d+ te++g + + + +   f+e+ + + e 
  gene640|gene640|rna640|rna640  77 IAIDCEMLLTNAG-----VELGRVTLLDIH--GNTLLDAYVRTDNT--VIDYRTEYSGLSEQSFVNSVRFDEAQSMVLEQ 147
                                    68*********96.....999999999887..78889*********..***********************888755555 PP

                                    HHHHTCCCETTTCEEEESSHHHHHHHHHHHHHHHHHCSEHCECHHHHHHHHHCHHHHHHHHHTTCHSSSS.TSSHHHHHH CS
                        RNase_T  81 lrklallvahnaafdvgflraadkrilkkevpkrnqfldtlildkatlkelartsldklaeklgleedgr.aHrAldDae 159
                                    ++     v     + +g++ ++d +il++   k+++ +dt +l+ +t+ +++  sl+ la k+g   +++  H++++Da 
  gene640|gene640|rna640|rna640 148 VG-----VD---TIVLGHSLYNDLKILQI---KHDKLIDTSRLF-RTHGNYK-ISLKSLADKYGCISIQNnTHCSYEDAY 214
                                    55.....54...67889**********99...89*********5.5666777.59************************* PP

                                    HHHHHH CS
                        RNase_T 160 ataklf 165
                                    a+++l+
  gene640|gene640|rna640|rna640 215 ACLQLL 220
                                    *99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (300 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       499  (0.027832); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 2047.78
//
Query:       gene641|gene641|rna641|rna641  [L=215]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
        5.3    6.3  14.6       0.18   11.1   7.9    1.7  2  NOA36            NOA36 protein


Domain annotation for each model (and alignments):
>> NOA36  NOA36 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.5     0.064   1.1e+03     237     264 ..      22      49 ..      16      75 .. 0.48
   2 ?   11.1   7.9     1e-05      0.18     266     302 ..     129     172 ..     105     177 .. 0.52

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.064
                          NOA36 237 rqkqadgsddddddeedsdydaylkala 264
                                    rqkq+++ +d+ +  ++ d +a  ++++
  gene641|gene641|rna641|rna641  22 RQKQEEDVKDQSGSVDNLDKNATCQTYS 49 
                                    3343333333333333333333333333 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 1e-05
                          NOA36 266 g......ddeddegdedddddddeed.ddeeeddedeeeeeeee 302
                                    +      +++ d+g +ddd+d+d++d dd+++dd+d+++e ++e
  gene641|gene641|rna641|rna641 129 TflggviAKTMDKGGSDDDKDKDDKDkDDKDKDDKDKKNEPSKE 172
                                    03333345566666666665555544155556666666666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (215 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       915  (0.0510346); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1406.98
//
Query:       gene642|gene642|rna642|rna642  [L=34]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.14   11.9   0.0       0.17   11.7   0.0    1.1  1  DUF4316   Domain of unknown function (DUF4316)


Domain annotation for each model (and alignments):
>> DUF4316  Domain of unknown function (DUF4316)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   9.4e-06      0.17       3      18 ..      15      30 ..      14      31 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 9.4e-06
                        DUF4316  3 nyLrnAElstEqNYNM 18
                                   ny    E s+E +YNM
  gene642|gene642|rna642|rna642 15 NYVHCTERSVESDYNM 30
                                   899999********** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (34 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       303  (0.0169); expected 358.6 (0.02)
Passed bias filter:                      177  (0.00987227); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.23s 00:00:00.57 Elapsed: 00:00:00.39
# Mc/sec: 261.11
//
Query:       gene643|gene643|rna643|rna643  [L=41]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (41 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       137  (0.00764125); expected 358.6 (0.02)
Passed bias filter:                      124  (0.00691617); expected 358.6 (0.02)
Passed Vit filter:                         6  (0.000334653); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.41
# Mc/sec: 296.73
//
Query:       gene644|gene644|rna644|rna644  [L=185]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       357  (0.0199119); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1425.49
//
Query:       gene645|gene645|rna645|rna645  [L=137]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (137 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       304  (0.0169558); expected 358.6 (0.02)
Passed bias filter:                      183  (0.0102069); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 1010.58
//
Query:       gene646|gene646|rna646|rna646  [L=317]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.31   10.8   1.5       0.66    9.7   1.5    1.6  1  FeoB_C    Ferrous iron transport protein B C terminus


Domain annotation for each model (and alignments):
>> FeoB_C  Ferrous iron transport protein B C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   1.5   3.7e-05      0.66       1      25 [.      48      71 ..      48      79 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 3.7e-05
                         FeoB_C  1 lfslYllgilvallvalllkkttlk 25
                                   +f++++ gi  ++lv+++++++ + 
  gene646|gene646|rna646|rna646 48 IFFIIAAGIGSIFLVSFIFNWF-IF 71
                                   699******************5.43 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (317 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1035  (0.0577277); expected 358.6 (0.02)
Passed bias filter:                      589  (0.0328518); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.38
# Mc/sec: 2506.81
//
Query:       gene647|gene647|rna647|rna647  [L=389]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.5e-44  150.1   0.0    1.3e-43  148.6   0.0    1.8  1  AAA              ATPase family associated with various cellul
    9.7e-08   31.7   0.0      2e-07   30.7   0.0    1.5  1  AAA_lid_3        AAA+ lid domain
    1.1e-07   32.0   0.4    1.3e-06   28.5   0.0    2.5  2  AAA_5            AAA domain (dynein-related subfamily)
    2.9e-07   30.8   1.6    3.7e-07   30.4   0.0    2.0  1  AAA_2            AAA domain (Cdc48 subfamily)
    3.5e-06   27.5   0.0    6.5e-05   23.4   0.1    2.4  2  AAA_16           AAA ATPase domain
    9.6e-06   25.5   0.2      2e-05   24.4   0.2    1.6  1  Prot_ATP_ID_OB   Proteasomal ATPase OB C-terminal domain
    1.2e-05   25.6   0.3      0.005   17.1   0.3    2.4  1  AAA_22           AAA domain
    3.6e-05   23.6   0.0    8.8e-05   22.3   0.0    1.6  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
     0.0018   18.2   0.0     0.0052   16.6   0.0    1.8  1  AAA_3            ATPase family associated with various cellul
     0.0021   17.9   0.0     0.0038   17.0   0.0    1.4  1  IstB_IS21        IstB-like ATP binding protein
     0.0022   17.3   0.5      0.005   16.1   0.0    1.8  2  TIP49            TIP49 P-loop domain
     0.0025   18.0   0.0     0.0058   16.8   0.0    1.6  1  AAA_33           AAA domain
     0.0038   17.8   0.3      0.019   15.5   0.0    2.3  2  AAA_18           AAA domain
     0.0047   15.7   1.1       0.21   10.2   1.0    2.2  2  AAA_13           AAA domain
     0.0067   16.7   0.0      0.014   15.6   0.0    1.6  1  AAA_28           AAA domain
     0.0083   16.1   0.0      0.017   15.1   0.0    1.5  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
     0.0085   15.5   1.5      0.061   12.7   0.1    2.5  2  ATPase           KaiC
  ------ inclusion threshold ------
       0.01   15.2   0.1      0.026   13.9   0.1    1.6  1  Mg_chelatase     Magnesium chelatase, subunit ChlI
       0.01   15.3   0.0       0.13   11.7   0.0    2.3  2  PhoH             PhoH-like protein
       0.02   14.4   0.0      0.038   13.5   0.0    1.4  1  AAA_7            P-loop containing dynein motor region
       0.02   14.6   1.3      0.085   12.6   0.0    2.6  2  Sigma54_activat  Sigma-54 interaction domain
      0.021   15.3   0.9       0.98    9.8   0.0    2.5  2  AAA_17           AAA domain
      0.021   15.4   0.9      0.048   14.2   0.9    1.5  1  APG6_N           Apg6 coiled-coil region
      0.022   14.0   0.0       0.04   13.1   0.0    1.4  1  DUF815           Protein of unknown function (DUF815)
      0.023   14.4   0.0       0.11   12.2   0.0    2.1  2  AAA_24           AAA domain
      0.024   14.7   0.0      0.058   13.4   0.0    1.7  1  AAA_14           AAA domain
      0.031   13.5   0.2        0.1   11.8   0.0    1.9  2  Zeta_toxin       Zeta toxin
      0.035   13.1   0.3       0.07   12.1   0.3    1.5  1  Ran-binding      RanGTP-binding protein
      0.038   13.2   0.5        1.4    8.1   0.0    2.1  2  DUF2075          Uncharacterized conserved protein (DUF2075)
       0.04   13.7   0.7        0.2   11.4   1.2    1.9  2  DivIC            Septum formation initiator
      0.043   14.2   0.0      0.096   13.1   0.0    1.6  1  RNA_helicase     RNA helicase
      0.051   12.7   0.0      0.094   11.8   0.0    1.3  1  Parvo_NS1        Parvovirus non-structural protein NS1
      0.055   13.2   3.0       0.21   11.3   0.1    2.8  2  AAA_11           AAA domain
      0.057   13.0   0.0       0.17   11.4   0.0    1.7  1  AAA_25           AAA domain
       0.14   12.7   0.2       0.78   10.3   0.0    2.2  2  ABC_tran         ABC transporter
       0.34   10.1   1.4        0.5    9.6   1.4    1.2  1  TMPIT            TMPIT-like protein
       0.92   10.0   6.0          7    7.1   4.0    2.7  2  FlaC_arch        Flagella accessory protein C (FlaC)


Domain annotation for each model (and alignments):
>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  148.6   0.0   2.7e-46   1.3e-43       1     131 [.     170     301 ..     170     302 .. 0.97

  Alignments for each domain:
  == domain 1  score: 148.6 bits;  conditional E-value: 2.7e-46
                                    EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH..TTCC CS
                            AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksr..sgse 78 
                                    vllyGppGtGKTlla+ava++++ +f+++sg+el++ky+ge+++ +relf  a+e+a psi+f+DEid+++++r   g  
  gene647|gene647|rna647|rna647 170 VLLYGPPGTGKTLLARAVAHHTDCKFIRVSGTELVQKYIGEGSRLVRELFVMAREHA-PSIIFMDEIDSIGSTRieGGPG 248
                                    79******************************************************9.*****************77779 PP

                                    CHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
                            AAA  79 seeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieie 131
                                    ++e +r++ +Ll++ldg++++ s++ vi+atnr+d ldpallr gR+drkie++
  gene647|gene647|rna647|rna647 249 NSEVQRTMLELLNQLDGFENR-SDIKVIMATNRIDILDPALLRtGRIDRKIEFP 301
                                    99******************7.77****************************98 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.7   0.0   4.1e-10     2e-07      13      44 ..     336     367 ..     324     368 .. 0.88

  Alignments for each domain:
  == domain 1  score: 30.7 bits;  conditional E-value: 4.1e-10
                      AAA_lid_3  13 GySGADlaalcreAallAlrrgikeitmedfe 44 
                                    + SGA+ +++c eA++ Alr+ + ++t+edfe
  gene647|gene647|rna647|rna647 336 NASGAEVKSVCTEAGMFALREMRVHVTQEDFE 367
                                    67*****************************8 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.1         1     5e+02      83     112 ..      13      43 ..       9      66 .. 0.80
   2 !   28.5   0.0   2.6e-09   1.3e-06       1     134 [.     169     288 ..     169     291 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 1
                                    HHHHHHHHSSEEE..-SSSEEE---...... CS
                          AAA_5  83 nsLlslleerrllleeggelvkakndd.lle 112
                                    ++L+s +e++++ l ++++  +  n++ ++ 
  gene647|gene647|rna647|rna647  13 QRLHSEIENKKMELKKLNKKRYDLNNQvRML 43 
                                    57999999****9999999999888876554 PP

  == domain 2  score: 28.5 bits;  conditional E-value: 2.6e-09
                                    EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------.G-SEEEEESGGG--H CS
                          AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar.egeilvlDEveraes 79 
                                    +vlL GppGtgK+ la+ +a+ + +++  v +t+      l++++   +++ +lv   +v a +  ++i+++DE++ + s
  gene647|gene647|rna647|rna647 169 GVLLYGPPGTGKTLLARAVAHHTDCKFIRVSGTE------LVQKYI--GEGSRLVRELFVMAREhAPSIIFMDEIDSIGS 240
                                    59**************************999887......999998..5555566666663444699**********999 PP

                                    HHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--.-TT-TTHHH CS
                          AAA_5  80 evlnsLlslleerrllleeggelvkaknddllerfrviatanpldrslnelspal 134
                                      ++      e +r +le +++l +++n    +++ vi+++n+ d     l+pal
  gene647|gene647|rna647|rna647 241 TRIEGGPGNSEVQRTMLELLNQLDGFENR---SDIKVIMATNRID----ILDPAL 288
                                    98888888888888888888888888884...4688888888888....666666 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.4   0.0   7.6e-10   3.7e-07       6     104 ..     170     261 ..     166     279 .. 0.92

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 7.6e-10
                                    EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG---- CS
                          AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKihpk 83 
                                    +ll gp g+Gkt+la+a+a + ++    k+ir+  +el +    + + +     ++  v a e+   i+++DEid i + 
  gene647|gene647|rna647|rna647 170 VLLYGPPGTGKTLLARAVAHHTDC----KFIRVSGTELVQ----KYIGEGSRLVRELFVMAREHApsIIFMDEIDSIGS- 240
                                    5789*******************8....************....88878888888888888888888************. PP

                                    ---------HHHHHHHHHHHH CS
                          AAA_2  84 essgadvSregVqrdLLqile 104
                                    ++++    + +Vqr +L +l 
  gene647|gene647|rna647|rna647 241 TRIEGGPGNSEVQRTMLELLN 261
                                    99999*************996 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.1   1.3e-07   6.5e-05      15      48 ..     158     191 ..     156     219 .. 0.80
   2 ?    1.2   0.0      0.85   4.1e+02     122     149 ..     214     240 ..     210     269 .. 0.69

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 1.3e-07
                         AAA_16  15 alervrsgrpelvllsGesGvGKsslvrellral 48 
                                    ++e++   +p  vll+G++G+GK+ l+r+++++ 
  gene647|gene647|rna647|rna647 158 LFENLGITQPKGVLLYGPPGTGKTLLARAVAHHT 191
                                    5677778899********************9753 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.85
                         AAA_16 122 llkrllallsrderplvlvlDdlqwade 149
                                    l+++l++ +++ + p ++++D+++ + +
  gene647|gene647|rna647|rna647 214 LVRELFVMARE-HAPSIIFMDEIDSIGS 240
                                    45666677777.778********95443 PP

>> Prot_ATP_ID_OB  Proteasomal ATPase OB C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.2   4.2e-08     2e-05       1      57 []      57     112 ..      57     112 .. 0.96

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 4.2e-08
                                    EEEEEEE-TTSSEEEEE-TTS-EEEEEE-GGGSSST--TTEEEEEETTTTEEEEEE- CS
                 Prot_ATP_ID_OB   1 VatVsEvlddteraiVktssdeevvvslagavpremLrpgDlVavdkdtgfifEkLP 57 
                                    V+tV + +++ ++++Vkt  d +++v + ++++ e+L+ +++Va+ +d +     LP
  gene647|gene647|rna647|rna647  57 VGTVIKKMGK-NKVLVKTQPDGKYLVDVDDKINIEELKLNTRVALRSDNYKLIRALP 112
                                    89********.*************************************998888877 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.3     1e-05     0.005       8      45 ..     170     198 ..     165     285 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1e-05
                         AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevvfv 45 
                                    ++++G++GtGKT+l+r +++           + ++++v
  gene647|gene647|rna647|rna647 170 VLLYGPPGTGKTLLARAVAHHT---------DCKFIRV 198
                                    689***************9987.........4444444 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.0   1.8e-07   8.8e-05      34      96 ..     168     238 ..     139     244 .. 0.70

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 1.8e-07
                         RuvB_N  34 dhvllyGpPGlGkttlakiiakelgvklkitsgPvleka.....gdlaalltnl...eekdvlfideihrl 96 
                                      vllyGpPG Gkt la+ +a+  + k+   sg  l ++     + l+  l  +   ++  ++f+dei  +
  gene647|gene647|rna647|rna647 168 KGVLLYGPPGTGKTLLARAVAHHTDCKFIRVSGTELVQKyigegSRLVRELFVMareHAPSIIFMDEIDSI 238
                                    569***********************998888876544323111234433333311134468899988765 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   1.1e-05    0.0052       2      33 ..     170     201 ..     169     217 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.1e-05
                          AAA_3   2 vllegvPGlaktllvkalakaldlefkriqft 33 
                                    vll g PG++ktll++a+a++ d++f r+  t
  gene647|gene647|rna647|rna647 170 VLLYGPPGTGKTLLARAVAHHTDCKFIRVSGT 201
                                    7999************************9766 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   7.9e-06    0.0038      44      71 ..     164     191 ..     145     216 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 7.9e-06
                      IstB_IS21  44 iekkenivllGpsGvGKshlaialgvea 71 
                                    i++ ++++l Gp+G+GK+ la a+++++
  gene647|gene647|rna647|rna647 164 ITQPKGVLLYGPPGTGKTLLARAVAHHT 191
                                    677889*****************99875 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.4       4.6   2.2e+03     139     171 ..      18      47 ..       7      90 .. 0.54
   2 !   16.1   0.0     1e-05     0.005      51      91 ..     168     206 ..     136     219 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 4.6
                                    TS--EEEEEE-SS-EEEEEE-HHHHHHHHHHT- CS
                          TIP49 139 kikevkitlktakeekklklgskiaeellkekv 171
                                    +i++ k+ lk  + +k+++l++++ +  lke++
  gene647|gene647|rna647|rna647  18 EIENKKMELKKLN-KKRYDLNNQVRM--LKEEI 47 
                                    4455555555443.344555555432..22222 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 1e-05
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          TIP49  51 ravLlaGpsgtGktalaiaiskelgedvpfvalsgsevysl 91 
                                    ++vLl Gp+gtGkt la a++++  +d +f+ +sg+e+ + 
  gene647|gene647|rna647|rna647 168 KGVLLYGPPGTGKTLLARAVAHH--TDCKFIRVSGTELVQK 206
                                    89*******************97..5799******998765 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   1.2e-05    0.0058       2      39 ..     170     209 ..     170     235 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.2e-05
                         AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlfg 39 
                                    vll G+pG+GK+ la+ ++ +++  ++++s  +l +++ g
  gene647|gene647|rna647|rna647 170 VLLYGPPGTGKTLLARAVAHHTDckFIRVSGTELVQKYIG 209
                                    7899*************99777788999988877766655 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.1         4   1.9e+03      69     104 ..      48     105 ..       9     110 .. 0.45
   2 !   15.5   0.0     4e-05     0.019       1      25 [.     170     200 ..     170     275 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 4
                         AAA_18  69 s..............aleegknlvidghlaeleseaakdikk.........vvLtaspe 104
                                    +              +++++k+ ++  ++   +  +  d+           v L+ ++ 
  gene647|gene647|rna647|rna647  48 RivqepsanvgtvikKMGKNKV-LVKTQPDGKYLVDVDDKINieelklntrVALRSDNY 105
                                    1333433444444433444444.445444444444444333334444444455555555 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 4e-05
                         AAA_18   1 IlltGtpGvGKttlakeLskrlgf......g 25 
                                    +ll G+pG+GKt la++++ ++ +      g
  gene647|gene647|rna647|rna647 170 VLLYGPPGTGKTLLARAVAHHTDCkfirvsG 200
                                    799***************9998777775552 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   1.0   0.00042      0.21     414     484 ..       8      78 ..       2      88 .. 0.88
   2 ?    3.3   0.0     0.052        25      20      39 ..     171     190 ..     168     206 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00042
                         AAA_13 414 ykkkykklekaieklekelkeeeaelkkleeeikeLekqlrdekpaaeeinkeLkafGlgeleLkfeeekk 484
                                    ++++ ++l  +ie+ + elk+ +++   l+++++ L++++r ++++ +++ + +k++G+++   k ++++k
  gene647|gene647|rna647|rna647   8 FMNETQRLHSEIENKKMELKKLNKKRYDLNNQVRMLKEEIRIVQEPSANVGTVIKKMGKNKVLVKTQPDGK 78 
                                    5678899999************************************************8887777666654 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.052
                         AAA_13  20 liYGwNGaGKTtLSrllrsl 39 
                                    l+YG  G+GKT L+r+ +  
  gene647|gene647|rna647|rna647 171 LLYGPPGTGKTLLARAVAHH 190
                                    79*************98875 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   2.9e-05     0.014       2      38 ..     170     211 ..     169     231 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.9e-05
                         AAA_28   2 ivitGgestGKTtlleaLaar....gypvv.pEaareileek 38 
                                    + + G+++tGKT l++a a +     ++v  +E + +++ e+
  gene647|gene647|rna647|rna647 170 VLLYGPPGTGKTLLARAVAHHtdckFIRVSgTELVQKYIGEG 211
                                    6799***************99866545555666666666554 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   3.5e-05     0.017      19      60 ..     167     208 ..     139     221 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.5e-05
                                    TEEEEEEESTTSSHHHHHHHHHHHTT------TTTTSEEEEE CS
                           TsaE  19 gdvilLeGdLGaGKTtlvrglakalgveevkSPTFtlveeYe 60 
                                     + +lL+G+ G+GKT l+r++a++ +++ ++     lv++Y 
  gene647|gene647|rna647|rna647 167 PKGVLLYGPPGTGKTLLARAVAHHTDCKFIRVSGTELVQKYI 208
                                    4459*********************99955444447888885 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.2      0.56   2.7e+02      68     154 ..      55     145 ..      38     151 .. 0.66
   2 !   12.7   0.1   0.00013     0.061      12      37 ..     159     185 ..     153     190 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.56
                         ATPase  68 kslGwdlekleeegklaiidasesaeesaeekdkedleelieelaeaikeika.....krvviDsitgl.ayeekeavaR 141
                                    +++G  ++k+ ++   +++ +  +++     +dk ++eel+ + + a+++ +        +++D+i +l + e+ ++ + 
  gene647|gene647|rna647|rna647  55 ANVGTVIKKMGKN--KVLVKTQPDGKYLVDVDDKINIEELKLNTRVALRSDNYkliraLPTIVDPIVSLmMVEKVPDATY 132
                                    5556666666665..34444555554445557888888888887777766444112115679999999977788788888 PP

                         ATPase 142 eilrqlvrvlkkl 154
                                    + +  l++++k++
  gene647|gene647|rna647|rna647 133 DMIGGLKQQIKEI 145
                                    8888888888775 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00013
                         ATPase  12 l.kgGipegrvvlitGepGtGKtifal 37 
                                    + + Gi + + vl++G pGtGKt++a 
  gene647|gene647|rna647|rna647 159 FeNLGITQPKGVLLYGPPGTGKTLLAR 185
                                    5456999*****************985 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   5.3e-05     0.026      25      42 ..     170     187 ..     162     192 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.3e-05
                   Mg_chelatase  25 lllvGppGsGKtmlakrl 42 
                                    +ll+GppG+GKt+la+++
  gene647|gene647|rna647|rna647 170 VLLYGPPGTGKTLLARAV 187
                                    89*************987 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00027      0.13      20      41 ..     168     189 ..     158     198 .. 0.84
   2 ?    0.8   0.0      0.56   2.7e+02      74     114 ..     250     290 ..     225     298 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00027
                                    SEEEEE--TTSSTTHHHHHHHH CS
                           PhoH  20 divfaiGpaGtGKtylavalav 41 
                                    + v   Gp GtGKt+la a+a 
  gene647|gene647|rna647|rna647 168 KGVLLYGPPGTGKTLLARAVAH 189
                                    567899***********99986 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.56
                                    ----TTTHHHHHHHTTTS-TTCHHHHHHTTSEEEEEGGGGT CS
                           PhoH  74 ekvdpylrplydaLkdllgaekvekllekgkievaplaymR 114
                                      v+  +  l ++L+ + +++ ++ ++ +++i +++ a +R
  gene647|gene647|rna647|rna647 250 SEVQRTMLELLNQLDGFENRSDIKVIMATNRIDILDPALLR 290
                                    566777888999999999999***************99999 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   7.9e-05     0.038      28      58 ..     162     192 ..     155     206 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 7.9e-05
                          AAA_7  28 lllknkkpvllvGptGtGKtviikdllkkld 58 
                                    l +++ k vll+Gp GtGKt++++ + ++ d
  gene647|gene647|rna647|rna647 162 LGITQPKGVLLYGPPGTGKTLLARAVAHHTD 192
                                    55788999***************99888777 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00018     0.085      21      46 ..     166     191 ..     141     210 .. 0.82
   2 ?   -0.5   0.1       1.8   8.8e+02     110     110 ..     253     253 ..     221     283 .. 0.50

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00018
                                    SSS-EEEECSTTSSHHHHHHHHHHHS CS
                Sigma54_activat  21 tdlsvlitGesGtGKellaraiheas 46 
                                    ++  vl+ G  GtGK+llara+ +++
  gene647|gene647|rna647|rna647 166 QPKGVLLYGPPGTGKTLLARAVAHHT 191
                                    56789***************996544 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.8
                                    H CS
                Sigma54_activat 110 Q 110
                                    Q
  gene647|gene647|rna647|rna647 253 Q 253
                                    2 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.4      0.21     1e+02      41     112 ..      37     104 ..      14     111 .. 0.74
   2 ?    9.8   0.0     0.002      0.98       1      28 [.     173     201 ..     173     229 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.21
                                    SSHHHHCTSHHHHHHHHHHHHHHHHHHHHHSSEEEEEE-SEEEETTEEEESSHHHH.HHHH..SEEEEEE--H CS
                         AAA_17  41 kardemrklpleekkelqkeaaekiaeeakkkgvlvdghprikeqagfldglpkev.leelkpdaiilleadp 112
                                    +++ +m k+++++ +e  +++   i+++ +k++vlv++ p    + ++l ++++++ +eelk ++ + l  d+
  gene647|gene647|rna647|rna647  37 NNQVRMLKEEIRIVQEPSANVGTVIKKM-GKNKVLVKTQP----DGKYLVDVDDKInIEELKLNTRVALRSDN 104
                                    4566677899999999999998888876.78899999998....57788888877746788877777777666 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.002
                                    EE-TTSSHHHHHHHHHHHHTEEEEEH.HH CS
                         AAA_17   1 lGgPGsGKgtqceklvekygfthlsa.Gd 28 
                                    +G+PG GK+ +++ ++++ + +++   G 
  gene647|gene647|rna647|rna647 173 YGPPGTGKTLLARAVAHHTDCKFIRVsGT 201
                                    7***************9999888754244 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.9    0.0001     0.048      54      96 ..      10      52 ..       4      56 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 0.0001
                         APG6_N 54 eeleklekeeeelleeLkelekereeleaelaaleeelealee 96
                                   +e ++l++e e++  eLk+l k+r +l+++++ l+ee + ++e
  gene647|gene647|rna647|rna647 10 NETQRLHSEIENKKMELKKLNKKRYDLNNQVRMLKEEIRIVQE 52
                                   7899*********************************987665 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   8.3e-05      0.04      53     115 ..     167     234 ..     119     238 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 8.3e-05
                         DUF815  53 annvLLwGarGtGKSslvkallneyaeegLrl..ievekedlkelpklvellr...erperfilfvDD 115
                                     + vLL+G  GtGK  l +a+ +++  + +r+   e+ ++ + e ++lv++l    +++   i+f+D 
  gene647|gene647|rna647|rna647 167 PKGVLLYGPPGTGKTLLARAVAHHTDCKFIRVsgTELVQKYIGEGSRLVRELFvmaREHAPSIIFMDE 234
                                    5679***********************99998556888999999888888764222556667889886 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00022      0.11       4      22 ..     169     187 ..     166     197 .. 0.86
   2 ?   -2.5   0.0       7.3   3.6e+03     101     128 ..     246     275 ..     228     282 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00022
                         AAA_24   4 kiliyGpsgiGKTtlakel 22 
                                     +l+yGp+g+GKT la+  
  gene647|gene647|rna647|rna647 169 GVLLYGPPGTGKTLLARAV 187
                                    589***********99865 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 7.3
                         AAA_24 101 gkGygelaeefrrllkklqelrk..nvifi 128
                                    g G +e+++ + +ll++l+ + +  ++ +i
  gene647|gene647|rna647|rna647 246 GPGNSEVQRTMLELLNQLDGFENrsDIKVI 275
                                    445678888888888888887776644444 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   0.00012     0.058       3      76 ..     168     238 ..     166     278 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00012
                         AAA_14   3 kilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqev 76 
                                    k +++ G+  +GKT l++ ++++      +++ ++  +  +k + + ++l ++++ +++e+  +++f+DEi  +
  gene647|gene647|rna647|rna647 168 KGVLLYGPPGTGKTLLARAVAHHTD---CKFIRVSGTELVQKYIGEGSRLVRELFVMAREHAPSIIFMDEIDSI 238
                                    568999*************997777...8999999888777766655445544444444568899******987 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.1       3.9   1.9e+03     160     193 ..      37      70 ..      20      75 .. 0.78
   2 ?   11.8   0.0   0.00022       0.1      14      54 ..     165     203 ..     157     222 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 3.9
                     Zeta_toxin 160 deafeglresvealeeekqldrvkikdrdgktvl 193
                                    +++++ l+e++++++e  + + ++ik++++++vl
  gene647|gene647|rna647|rna647  37 NNQVRMLKEEIRIVQEPSANVGTVIKKMGKNKVL 70 
                                    6788889999999998888787888887776555 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00022
                     Zeta_toxin  14 erPklillgGqpGAGKselaellkdelerqgnvvrldpDdl 54 
                                     +Pk +ll G pG GK+ la++++  +  + +++r+++++l
  gene647|gene647|rna647|rna647 165 TQPKGVLLYGPPGTGKTLLARAVAHHT--DCKFIRVSGTEL 203
                                    58*********************9998..788888887765 PP

>> Ran-binding  RanGTP-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.3   0.00014      0.07      22      79 ..       2      59 ..       1      72 [. 0.90

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00014
                    Ran-binding 22 slassyaikqvsrllkkvpedkkerkeleklqkkLeskikiispaidLieliaarGnt 79
                                   s+++ y +++++rl ++++++k e k+l+k++ +L++++++++  i +++  +a+  t
  gene647|gene647|rna647|rna647  2 SFTTAYFMNETQRLHSEIENKKMELKKLNKKRYDLNNQVRMLKEEIRIVQEPSANVGT 59
                                   89*****************9999************************99988877555 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.1     0.072        35     128     173 ..       7      52 ..       3     111 .. 0.66
   2 ?    8.1   0.0    0.0029       1.4       4      25 ..     170     191 ..     167     218 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.072
                        DUF2075 128 alvDegQelntgeigteeelkklakkleveleekvhLksqfRvaas 173
                                    +++ e Q+l+ + + ++ elkkl kk    +++   Lk+ +R+ ++
  gene647|gene647|rna647|rna647   7 YFMNETQRLHSEIENKKMELKKLNKKRYDLNNQVRMLKEEIRIVQE 52 
                                    6788899999988888888888665544444444478888888443 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0029
                        DUF2075   4 vlVtGvaGtGKtvvllnllael 25 
                                    vl  G +GtGKt+++ ++++  
  gene647|gene647|rna647|rna647 170 VLLYGPPGTGKTLLARAVAHHT 191
                                    6789**********99988765 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   1.2   0.00041       0.2      17      54 ..      10      46 ..       1      52 [. 0.84
   2 ?   -1.9   0.0       5.9   2.8e+03      33      46 ..     135     148 ..     110     157 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00041
                                   XHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-XXXX CS
                          DivIC 17 laykqlkqeiaalqaelaklkaeneeLeaevkdLksde 54
                                   +  ++l++ei+ ++ el+kl++++ +L+ +v+ Lk +e
  gene647|gene647|rna647|rna647 10 NETQRLHSEIENKKMELKKLNKKRYDLNNQVRMLK-EE 46
                                   67899***************************995.44 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 5.9
                                    HHHHHHHHHHHHHH CS
                          DivIC  33 laklkaeneeLeae 46 
                                    +  lk++++e  + 
  gene647|gene647|rna647|rna647 135 IGGLKQQIKEIREV 148
                                    44555555555544 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0    0.0002     0.096       1      23 [.     170     192 ..     170     243 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.0002
                   RNA_helicase   1 iwlyGpsgeGKStlakeLakall 23 
                                    ++lyGp+g+GK++la+ +a++  
  gene647|gene647|rna647|rna647 170 VLLYGPPGTGKTLLARAVAHHTD 192
                                    689*************9554433 PP

>> Parvo_NS1  Parvovirus non-structural protein NS1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00019     0.094     117     138 ..     170     191 ..     165     195 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00019
                      Parvo_NS1 117 vwfyGpantGktnlaeaIakav 138
                                    v++yGp+ tGkt la+a a+ +
  gene647|gene647|rna647|rna647 170 VLLYGPPGTGKTLLARAVAHHT 191
                                    899****************976 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.4       0.7   3.4e+02     146     177 ..      19      50 ..       5      76 .. 0.52
   2 ?   11.3   0.1   0.00044      0.21      17      41 ..     167     191 ..     161     378 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.7
                         AAA_11 146 eeekeklkkskekskskleqerrklkkerkel 177
                                     e+k+ ++k+ +k++ +l+++ r lk+e++ +
  gene647|gene647|rna647|rna647  19 IENKKMELKKLNKKRYDLNNQVRMLKEEIRIV 50 
                                    22223333344444444444444444444333 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00044
                         AAA_11  17 seitliqGPPGtgKTktivellsql 41 
                                    ++ +l+ GPPGtgKT    ++ ++ 
  gene647|gene647|rna647|rna647 167 PKGVLLYGPPGTGKTLLARAVAHHT 191
                                    555899*********7777766665 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00035      0.17      36      56 ..     170     190 ..     162     195 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00035
                         AAA_25  36 allaGapgtGKttlaldlala 56 
                                    +ll+G+pgtGKt la  +a++
  gene647|gene647|rna647|rna647 170 VLLYGPPGTGKTLLARAVAHH 190
                                    69*************998887 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.1       3.1   1.5e+03      42      72 ..      19      51 ..       4     115 .. 0.61
   2 ?   10.3   0.0    0.0016      0.78       6      37 ..     162     193 ..     160     285 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 3.1
                                   EEETTCEGGG..B-HHHCCHCEEEE-SS--S-T CS
                                   xxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran 42 illdgkdlke..qeleslrkeigvlpqepqlfp 72
                                   i+ ++ +lk+  +++  l++++++l++e ++ +
  gene647|gene647|rna647|rna647 19 IENKKMELKKlnKKRYDLNNQVRMLKEEIRIVQ 51
                                   433444444444455555555555555533322 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.0016
                                    EEEETTSEEEEEESTTSSHHHHHHHHTTSS-- CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran   6 lklkegekvaivGenGaGKStLlkllagllkp 37 
                                    l + + + v + G+ G+GK+ L++++a++++ 
  gene647|gene647|rna647|rna647 162 LGITQPKGVLLYGPPGTGKTLLARAVAHHTDC 193
                                    6677778899****************999875 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   1.4     0.001       0.5      31     144 ..      11     125 ..       4     135 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.001
                          TMPIT  31 lqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelkerkkvlkev...esllpkk.nglylklvlGnvnv 106
                                      +++ +ei+++k +lk+l+++  +l+++v+   +ee++ ++e  ++  +v+k++   + l   +  g yl  v  ++n+
  gene647|gene647|rna647|rna647  11 ETQRLHSEIENKKMELKKLNKKRYDLNNQVR-MLKEEIRIVQEPSANVGTVIKKMgknKVLVKTQpDGKYLVDVDDKINI 89 
                                    5677888999999999999999999999875.55556666666666666666655220445555589************* PP

                          TMPIT 107 sllnkqdkfkyKdeYekFklkltvillllsllllllls 144
                                    + l+ + +++++++  ++kl+ ++ +++ +++ l++++
  gene647|gene647|rna647|rna647  90 EELKLNTRVALRSD--NYKLIRALPTIVDPIVSLMMVE 125
                                    ***********986..6888888888888877776554 PP

>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   4.0     0.014         7       4      38 ..      14      48 ..      11      52 .. 0.90
   2 ?    1.7   0.0      0.73   3.5e+02      15      31 ..     134     150 ..     123     151 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.014
                      FlaC_arch  4 elEnklsklsteletvkkeneelsksveelkenVk 38
                                    l +++++ ++el+ + k+  +l+++v +lke+++
  gene647|gene647|rna647|rna647 14 RLHSEIENKKMELKKLNKKRYDLNNQVRMLKEEIR 48
                                   57899***************************997 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.73
                      FlaC_arch  15 eletvkkeneelsksve 31 
                                    +++ +k++++e+++ +e
  gene647|gene647|rna647|rna647 134 MIGGLKQQIKEIREVIE 150
                                    789999******99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (389 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1219  (0.0679904); expected 358.6 (0.02)
Passed bias filter:                      830  (0.0462937); expected 358.6 (0.02)
Passed Vit filter:                       155  (0.00864521); expected 17.9 (0.001)
Passed Fwd filter:                        37  (0.0020637); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              37  [number of targets reported over threshold]
# CPU time: 0.63u 0.32s 00:00:00.95 Elapsed: 00:00:00.45
# Mc/sec: 2595.05
//
Query:       gene648|gene648|rna648|rna648  [L=81]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (81 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1002  (0.0558871); expected 358.6 (0.02)
Passed bias filter:                      521  (0.0290591); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 582.01
//
Query:       gene649|gene649|rna649|rna649  [L=323]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.6e-34  118.4   4.3    4.7e-34  118.0   4.3    1.2  1  UCH       Ubiquitin carboxyl-terminal hydrolase
    1.9e-12   47.4   9.4    1.8e-11   44.3   4.9    2.8  2  UCH_1     Ubiquitin carboxyl-terminal hydrolase


Domain annotation for each model (and alignments):
>> UCH  Ubiquitin carboxyl-terminal hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.0   4.3   5.2e-38   4.7e-34       3     257 .]      42     320 ..      40     320 .. 0.88

  Alignments for each domain:
  == domain 1  score: 118.0 bits;  conditional E-value: 5.2e-38
                                    ES-SSSTHHHHHHHHHHHTSHHHHHHHHTCHHCCSSTCCCCC-.TT.TTS.TTHHHHHHHHHHHHHHSH-CCEE--HHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            UCH   3 lsNlGntCymnsvlQcLfsipelrdyllsleevkkesrnkkelnesnplgkkgelakalkdlfkellkskskavsPkklk 82 
                                    l+N+ n+C+ nsv+Qc + i +  +y+ s        +  k          ++++ ++++ ++k+ +  +sk + P+ ++
  gene649|gene649|rna649|rna649  42 LVNTKNNCFFNSVMQCTMYIYPVVTYFESG-------EFTK----------EQRICRRFQGFIKKYI--ESKVMDPQFFI 102
                                    89***************************3.......3332..........2359***********9..589******** PP

                                    HHHHHHSGGGTSSSTCEHHHHHHHHHHHHHHHHCC....HCCCHHHHHHCCCTTSHHHHHH-EEEEE............. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxx............. RF
                            UCH  83 ktlsklaksfsgykqqDaqEflaflLdqlhedlnr....evaeekwkkhlkrndslitdlfegqlks............. 145
                                    + l++  + +  ++ qDaqEfl     +l e+l      + a+ +  +++ r + ++++ f+  l+              
  gene649|gene649|rna649|rna649 103 NGLASDIHIL-DGNEQDAQEFLLLFYGKLTEELGLldnvSIANVNQLRKIGRTNVMVKTFFGLVLNRlrcmscfavteht 181
                                    ***9999987.68889*****************99775533334446666677677777776666669999999999999 PP

                                    ............................................EEEEEEB-SEEEEEEESEEETEEEEE--SEEB--SE CS
                                    ............................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            UCH 146 ............................................klklkrlPeiLiihlkRfsynssksKlntkvefpee 181
                                                                                  +++ +Pe+Li++l+Rf    + +K+++ v + ++
  gene649|gene649|rna649|rna649 182 hqfrnltldvtesvqesvnkylkdevynseilcescekmakvsvARQITAFPEVLILQLSRFIN-VD-RKNDSYVVVSDK 259
                                    999999999999999999999999********************99****************85.55.7*********** PP

                                    EE-GGGBSS-BTTS-TCS-BEEEEEEEEEESCTTSEEEEEEEECTTTTEEEEEETTEEEEE-HHCCCTT.CEEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxx RF
                            UCH 182 ldlssylaeekkkkteekkkYeLiavvvHsGslssGHYvayiknekngkWykydDetvkevkeeeevls.sayiLfY 257
                                    l++++       k      +Y+Li++v+HsG+l++GHYvay+k  ++ +W ++dD +v+e+k++  +++  ayiLfY
  gene649|gene649|rna649|rna649 260 LQMDK-------K------TYHLIGMVCHSGTLRNGHYVAYAK--TDLSWHCFDDMNVSELKDS-HISNtGAYILFY 320
                                    ***95.......2......3***********************..8999*************88.77778******* PP

>> UCH_1  Ubiquitin carboxyl-terminal hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    3.6   0.1    0.0047        42       4      26 ..      43      65 ..      42      84 .. 0.81
   2 !   44.3   4.9     2e-15   1.8e-11     137     320 .]     163     302 ..     136     302 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.0047
                                   xxxxxxxxxxxxxxxxxxxxxxx RF
                          UCH_1  4 EnhivnsYlNslLQvlyfipplr 26
                                    n+ +n++ Ns++Q+  +i p+ 
  gene649|gene649|rna649|rna649 43 VNTKNNCFFNSVMQCTMYIYPVV 65
                                   67789*************97765 PP

  == domain 2  score: 44.3 bits;  conditional E-value: 2e-15
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          UCH_1 137 tkaettirclkCgseksrksstlvldlkyPkpsnekkeakvtfasilksslerekttrawCekCkryqpteqrktvknlP 216
                                      + +++rc++C + +++++ +  l l    +    ++ + +++++lk  + +   ++  Ce+C++ + ++  ++++ +P
  gene649|gene649|rna649|rna649 163 GLVLNRLRCMSCFAVTEHTHQFRNLTLDV--T----ESVQESVNKYLKDEVYN---SEILCESCEKMAKVSVARQITAFP 233
                                    4567899*********9999999888844..2....34556899999999988...899********************* PP

                                    xxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          UCH_1 217 pvLalnakle.eeeelelwktknwlpleiklsldedknleeklkeerekakaekeikvYeLqsvvvhigdskesghLvsl 295
                                    +vL+l+++++ + +     k+++++  + kl                     + + k+Y L+++v+h g +  +gh+v++
  gene649|gene649|rna649|rna649 234 EVLILQLSRFiNVD----RKNDSYVVVSDKL---------------------QMDKKTYHLIGMVCHSG-TLRNGHYVAY 287
                                    ********987665....1122333333333.....................234468***********.666******* PP

                                    xxxxxxxxxxxxxxxxxxxxxxxxx RF
                          UCH_1 296 vkvaekelerdppesqWylFNDflV 320
                                    +k           + +W++F+D++V
  gene649|gene649|rna649|rna649 288 AKT----------DLSWHCFDDMNV 302
                                    **5..........238******987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (323 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       861  (0.0480228); expected 358.6 (0.02)
Passed bias filter:                      491  (0.0273858); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 2101.41
//
Query:       gene65|gene65|rna65|rna65  [L=103]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.7e-18   66.2   0.1    2.2e-18   65.8   0.1    1.2  1  RNA_pol_L_2  RNA polymerase Rpb3/Rpb11 dimerisation domain
  ------ inclusion threshold ------
      0.066   12.7   0.0       0.08   12.4   0.0    1.2  1  RNA_pol_L    RNA polymerase Rpb3/Rpb11 dimerisation domain


Domain annotation for each model (and alignments):
>> RNA_pol_L_2  RNA polymerase Rpb3/Rpb11 dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.8   0.1   2.4e-22   2.2e-18       2      73 ..      21      92 ..      20      94 .. 0.96

  Alignments for each domain:
  == domain 1  score: 65.8 bits;  conditional E-value: 2.4e-22
                               EEEEEES--HHHHHHHHHHHTTSTTEEEEEEECSSTTTSEEEEEEEESTSS-HHHHHHHHHHHHHHHHHHHH CS
                RNA_pol_L_2  2 ltfeingEDhTLgnlLrhlllknpsVefagYkipHPlepkmnlriqtkssnnpleaLkkalkdlldicdele 73
                               +++ ingE hTLgnl+ + +l++p+++f +Yk++HPl +++ l++  ++++  l+ +k+ lk+l+d++++l 
  gene65|gene65|rna65|rna65 21 VELHINGESHTLGNLIAEKILSDPRCTFSAYKVNHPLDEEVDLKVSAQKDTPVLTLIKDNLKSLEDDIESLI 92
                               6899***************************************************************99875 PP

>> RNA_pol_L  RNA polymerase Rpb3/Rpb11 dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0     9e-06      0.08       2      56 ..      23      75 ..      22      96 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 9e-06
                               xxxxxxxxxxxxxxxxxxxxxxxxxxxxx...........xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  RNA_pol_L  2 fllrgvdhtlgNaLRrillsevpgvaiea...........pvvkvntdkdklilevetdgslkPee 56
                                 ++g++htlgN +   +l + p + + a                        l+v     +++  
  gene65|gene65|rna65|rna65 23 LHINGESHTLGNLIAEKIL-SDPRCTFSAykvnhpldeevD------------LKVSAQKDTPVLT 75
                               5799***************.99****999766664444330............3333333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       982  (0.0547716); expected 358.6 (0.02)
Passed bias filter:                      573  (0.0319594); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.35u 0.27s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 798.84
//
Query:       gene650|gene650|rna650|rna650  [L=242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (242 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       650  (0.0362541); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1836.92
//
Query:       gene651|gene651|rna651|rna651  [L=255]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
      0.017   15.1   1.3       0.28   11.2   0.1    2.2  2  Swm2        Nucleolar protein Swm2
      0.042   13.6   0.0      0.067   12.9   0.0    1.5  1  EMC3_TMCO1  Integral membrane protein EMC3/TMCO1-like


Domain annotation for each model (and alignments):
>> Swm2  Nucleolar protein Swm2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.1     0.012     1e+02      16      41 ..      49      74 ..      45     102 .. 0.83
   2 ?   11.2   0.1   3.2e-05      0.28      11      95 ..     106     188 ..     100     201 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.012
                           Swm2 16 plLspyyeaiakdeelkkkalkkCke 41
                                   ++L+p y+  ++++el ++ +k Ck 
  gene651|gene651|rna651|rna651 49 DFLEPKYKFFERKHELDENFKKLCKP 74
                                   689*********************94 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 3.2e-05
                           Swm2  11 pkeysplLspyyeaiakdeelkkkalkkCkevfekweekddavdkevvkrcldlwlvlkgkeYkl.keeeslsNliieev 89 
                                      + s+ L++++e ++ +        k+  ++f++ +++     k    r+l+l   ++ + Y+  + +e+++N+i + +
  gene651|gene651|rna651|rna651 106 DVNASECLLSFFEDVSSNLTKGIVDYKIFVYIFKRVNHNLG---KFTNVRMLELPADIQLQSYSPaELKENIENVISQSI 182
                                    567899999******99999999999999999999998887...77778***************98999*********** PP

                           Swm2  90 dvsevk 95 
                                    dv+++ 
  gene651|gene651|rna651|rna651 183 DVRNTF 188
                                    **9975 PP

>> EMC3_TMCO1  Integral membrane protein EMC3/TMCO1-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   7.5e-06     0.067      20     110 ..       5     138 ..       2     234 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 7.5e-06
                     EMC3_TMCO1  20 illvgiltgllsellqkllidkkkmekeqkrekelqkrarelqkngd.klklkklekrqeelmedqsem........... 87 
                                    +ll+++l +   el q+  i+ +    ++ r+  +++    + +++d  +++ k+ +r++el e+ +++           
  gene651|gene651|rna651|rna651   5 VLLLAVLISATDELFQWMKIEEN--LPYNSRDDSYESDGNGYVSKDDfLEPKYKFFERKHELDENFKKLckpdimymlke 82 
                                    89*****************9999..99*****************999445566*************99999998777777 PP

                     EMC3_TMCO1  88 .................................mmdqmkpmivtmipqiliffwln 110
                                                                     +++   ++++ +i+   if +++
  gene651|gene651|rna651|rna651  83 gekamicdfleaevirskvdgeldvnasecllsFFEDVSSNLTKGIVDYKIFVYIF 138
                                    77777777777777777777777777777777744444444444443333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       664  (0.037035); expected 358.6 (0.02)
Passed bias filter:                      501  (0.0279436); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1860.06
//
Query:       gene652|gene652|rna652|rna652  [L=177]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0077   16.4   2.6     0.0077   16.4   2.6    1.9  2  DUF4441   Domain of unknown function (DUF4441)


Domain annotation for each model (and alignments):
>> DUF4441  Domain of unknown function (DUF4441)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.2       0.1   1.8e+03      17      17 ..      64      64 ..      15      90 .. 0.61
   2 !   16.4   2.6   4.3e-07    0.0077       4      69 ..     110     176 ..     109     177 .] 0.84

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.1
                        DUF4441 17 n 17
                                   +
  gene652|gene652|rna652|rna652 64 E 64
                                   2 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 4.3e-07
                        DUF4441   4 vKnilkaFkkfienekdeeliesiyn.lkkkqksleeikkkfkryikkkkfnnstlklLikhknygk 69 
                                    +K ilk F +f++ne+d+  +e ++n   +k++  +++   + + ik  k   +++k++++++++g+
  gene652|gene652|rna652|rna652 110 IKYILKMFCRFFSNEEDNHEVECVQNnEIQKSELGKKLDDVLRKQIKDFKLSLTCIKQVFSNDEFGE 176
                                    799**************99999966655566666677777788999999999999********9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1142  (0.0636957); expected 358.6 (0.02)
Passed bias filter:                      486  (0.0271069); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1228.28
//
Query:       gene653|gene653|rna653|rna653  [L=335]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (335 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       663  (0.0369792); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.38
# Mc/sec: 2655.61
//
Query:       gene654|gene654|rna654|rna654  [L=578]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-49  169.3   2.7    6.3e-40  137.2   0.2    2.2  2  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
    3.4e-27   94.9   0.1    1.2e-26   93.2   0.0    1.9  2  Pyr_redox_dim  Pyridine nucleotide-disulphide oxidoreductase,
      3e-16   59.6   5.3    4.5e-14   52.4   0.5    3.1  3  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase
    8.7e-16   58.3   8.3    1.5e-12   47.9   0.1    3.7  3  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
    1.7e-08   34.2   0.1    1.7e-08   34.2   0.1    2.1  2  FAD_oxidored   FAD dependent oxidoreductase
    1.1e-07   31.3   2.6    1.1e-07   31.3   2.6    2.3  2  GIDA           Glucose inhibited division protein A
    8.7e-07   28.4   0.7    5.1e-06   25.8   1.0    2.1  3  FAD_binding_2  FAD binding domain
    2.2e-06   27.5   0.1    0.00051   19.7   0.0    2.3  2  DAO            FAD dependent oxidoreductase
    3.7e-05   22.6   0.6    0.00012   20.9   0.6    1.9  1  HI0933_like    HI0933-like protein
    9.1e-05   22.6   4.3     0.0005   20.3   0.8    2.7  2  NAD_binding_8  NAD(P)-binding Rossmann-like domain
  ------ inclusion threshold ------
      0.021   14.2   0.1        2.1    7.6   0.3    2.4  2  AlaDh_PNT_C    Alanine dehydrogenase/PNT, C-terminal domain
      0.022   14.0   0.1      0.066   12.4   0.0    1.9  2  Thi4           Thi4 family
      0.023   15.3   1.4      0.023   15.3   1.4    2.4  2  DUF4541        Domain of unknown function (DUF4541)
      0.077   12.0   1.7       0.42    9.6   0.3    2.3  2  Lycopene_cycl  Lycopene cyclase protein
       0.11   12.2   0.1       0.36   10.6   0.1    1.9  2  S4             S4 domain
       0.17   11.7   2.6       0.36   10.7   0.1    2.8  3  3HCDH_N        3-hydroxyacyl-CoA dehydrogenase, NAD binding d


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  137.2   0.2   5.6e-43   6.3e-40       1     214 [.       2     234 ..       2     267 .. 0.93
   2 !   32.3   0.2   5.4e-11     6e-08     182     279 ..     319     425 ..     308     435 .. 0.83

  Alignments for each domain:
  == domain 1  score: 137.2 bits;  conditional E-value: 5.6e-43
                                    CSEEEE--SHHHHHHHHHHHHHTS-EEEEE...TTHCHHHCSHHHHCHHHHHHHHHHHHH.................... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxx.................... RF
                    Pyr_redox_2   1 kdvvviGgGpAGlaaaltlaqagakvtlve...legtclnggcllskallgvaedaeias.................... 57 
                                    +d++viGgG +G+aaa+++a+ + +v+lve   l+gtc+n gc+++k+  ++ +  e+++                    
  gene654|gene654|rna654|rna654   2 YDLIVIGGGSGGMAAAREAAKFNKRVLLVEkgeLGGTCVNLGCVPKKITYNMTSIVEQMQlassygmqaryelnyelfkr 81 
                                    689**************************8888**************9999999999888999***************** PP

                                    ...HHHHCHHHHCCCCHCCTCEEEEESCEEEEETEEECTCEEEEEESEEEE---EEE-BCTCTTC.TTBEECCSECHHHH CS
                                    ...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2  58 ...evvkklnqgielllgeevvkidpgkkkvklekkkegdeekiaydklvlAtGssprdlgipGvaenvgklvrtldsae 134
                                       +v+++ln+ +e+llg++ v+i++g ++v    ++e +++ ++  +++lA+Gs+p+ l+i+G+ e     vr++  ++
  gene654|gene654|rna654|rna654  82 crdDVIRRLNAIYEKLLGNSNVEIIRGYARVISAGEVEVNGQVYKGTYILLASGSKPKALKIKGA-EF----VRYS--DD 154
                                    ******************99*********************************************.44....4665..56 PP

                                    HHCCSS-TSEEEEES-SHHHHHHHHHHHHHT-EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2 135 alklkllpkrivvvGgGyiGvElAaalaklgkevtlveardrllraldkelsaaleealekeGvevklgtsvkeidgnge 214
                                     + l   pk++v++G+Gyi++E+A +la lg++v +v +++++l+ +d  + a ++e+l+k  +e++ +++v e++++++
  gene654|gene654|rna654|rna654 155 FFYLTSIPKKTVIIGSGYISLEIAFMLALLGSDVSIVLRGKHFLSHFDTLFDAVVKEQLKKYRIETYYEENVLEVREESN 234
                                    6777888999******************************************************************9887 PP

  == domain 2  score: 32.3 bits;  conditional E-value: 5.4e-11
                                    -HHHHHHHHHHHHHTTEEEEESCEEEEEEETTE............EEEEEETTSCEEEESEEEE-S-EEES-HHCSHCCT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2 182 dkelsaaleealekeGvevklgtsvkeidgnge............klevvledgeeidadlvvvavGvrpstelleeklg 249
                                    ++e+++ ++  ++ +++++ +++ v ei +++              +evvl++ +  ++  v+ a+G+  + +    +l 
  gene654|gene654|rna654|rna654 319 KEEIGRKVRFDIRGQKIDIEHKEDVYEIHKDELrvelegqrtskgVYEVVLKNTTIKNVNFVMCAIGRDCDLSY--VQLP 396
                                    67788888888888999999999999999888777777777666666699999999***************766..6899 PP

                                    -EEEETTEEE--TTSBESSTTEEE-GGGCT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2 250 lelderggivvdeflrtnvpgiyaiGDvag 279
                                    + +  +++ vvd++  t+vp++ya+GD +g
  gene654|gene654|rna654|rna654 397 VHT-YNNYAVVDHKFMTSVPNVYAVGDLVG 425
                                    988.9**********************993 PP

>> Pyr_redox_dim  Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       3.6     4e+03      69      92 ..      50      74 ..      48      79 .. 0.81
   2 !   93.2   0.0     1e-29   1.2e-26       1     108 [.     459     564 ..     459     566 .. 0.98

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 3.6
                                   CTTHHHHHHHHHHHHHTTSBHH.HH CS
                  Pyr_redox_dim 69 Gpgageliqelavaikagltve.dl 92
                                    ++++++++++++a ++g++++ +l
  gene654|gene654|rna654|rna654 50 TYNMTSIVEQMQLASSYGMQARyEL 74
                                   6789999***********9988555 PP

  == domain 2  score: 93.2 bits;  conditional E-value: 1e-29
                                    BEEEEESSSEEEEEES-HHHHHHHHSGEEEEEEEEECGHHHCHTTHTEEEEEEEEETTTTBEEEEEEECTTHHHHHHHHH CS
                  Pyr_redox_dim   1 iptvvftdpevasvGlteeeAkaagieikvgkfpfkangralayaetkgfvKlvadaktgkvlGahivGpgageliqela 80 
                                    +p+v+ft+p+ asvGl+e+ A a++  ++v++++f+++ +al +++t  ++K ++++  g+v+G+h++G+g++e++q++a
  gene654|gene654|rna654|rna654 459 VPSVIFTHPPCASVGLSEAAASAKYDSVEVYETRFNNLLYALSEHKTASVFKAIVHR--GQVVGLHLFGNGVDEMVQGFA 536
                                    79***********************99*****************************9..9******************** PP

                                    HHHHTTSBHHHHHTSBSSSSSTGGGGHC CS
                  Pyr_redox_dim  81 vaikagltvedladtihihPtlsealke 108
                                    + +k+gl+ +dl++++++hPt +e++++
  gene654|gene654|rna654|rna654 537 LSMKNGLSLSDLNNCVCVHPTAAEEVVT 564
                                    *************************987 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.4   0.5     4e-17   4.5e-14       1     244 [.       5     235 ..       5     276 .. 0.79
   2 ?    1.0   0.1      0.19   2.1e+02      75     117 ..     314     356 ..     287     366 .. 0.70
   3 !    7.7   0.4    0.0016       1.8     237     305 .]     357     421 ..     309     421 .. 0.73

  Alignments for each domain:
  == domain 1  score: 52.4 bits;  conditional E-value: 4e-17
                    Pyr_redox_3   1 iIiGaGPaGlaaaielkkagledylilEkgnignsiyrypkemtfispsftsekleipdlnaiseetspafslkeekls. 79 
                                    i+iG+G  G+aaa e+ k++  ++l +Ekg++g +  +     + i+ ++ts  +e  +l a s + + ++ l+ e  + 
  gene654|gene654|rna654|rna654   5 IVIGGGSGGMAAAREAAKFNK-RVLLVEKGELGGTCVNLGCVPKKITYNMTSI-VEQMQL-ASSYGMQARYELNYELFKr 81 
                                    89******************9.8************************987654.666666.4445666677777775550 PP

                    Pyr_redox_3  80 .rkealeYlrevaksfelpiklfeeV.esvkkedegfevetsketyeAkkviiAtGefdkPnklnipGeeklvkhyskvk 157
                                     r+++ + l+++  +++l  + + e+ +  ++  +  eve + ++y+ +++++A G   kP+ l+i+G+e  v  +  + 
  gene654|gene654|rna654|rna654  82 cRDDVIRRLNAI--YEKLLGNSNVEIiRGYARVISAGEVEVNGQVYKGTYILLASGS--KPKALKIKGAE-FVRYSDDFF 156
                                    145555555555..555644554444155566778899******************9..**********9.444444444 PP

                    Pyr_redox_3 158 efhkyagqkvvViGgknSavDaAlelvrkgaeVtvvtrgseiekeesdpsyslkpdienrleelvkeekikvlfnaevke 237
                                     +     +k v+iG +  + ++A+ l+  g++V++v rg++  +   +++    ++++++l+++    +i+ +++++v e
  gene654|gene654|rna654|rna654 157 YL-TSIPKKTVIIGSGYISLEIAFMLALLGSDVSIVLRGKHFLS---HFDTLFDAVVKEQLKKY----RIETYYEENVLE 228
                                    44.55589999****************************96544...57888889999999886....5899******** PP

                    Pyr_redox_3 238 ikekeee 244
                                    ++e+++ 
  gene654|gene654|rna654|rna654 229 VREESND 235
                                    **98765 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.19
                    Pyr_redox_3  75 eeklsrkealeYlrevaksfelpiklfeeVesvkkedegfeve 117
                                       +s++e+ + +r   + ++++i+ +e+V +++k++   e+e
  gene654|gene654|rna654|rna654 314 VIDVSKEEIGRKVRFDIRGQKIDIEHKEDVYEIHKDELRVELE 356
                                    5556677777777777788999999999999999988777765 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.0016
                    Pyr_redox_3 237 eikekeeeykvktedgkkvevkddvvlatGykpdlsflkkslfeldedgrpvlteeteetnvpglflaG 305
                                      ++++  y+v  ++ +++++ ++v+ a+G ++dls ++ ++ ++  +++ v++ + + t vp+++ +G
  gene654|gene654|rna654|rna654 357 GQRTSKGVYEVVLKN-TTIKNVNFVMCAIGRDCDLSYVQLPVHTY--NNYAVVDHKFM-TSVPNVYAVG 421
                                    334556667777887.778888999999**********9666555..77888877766.66*****998 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.6    0.0004      0.45       2      31 ..       4      33 ..       3      38 .. 0.93
   2 !   47.9   0.1   1.4e-15   1.5e-12       1      71 [.     164     234 ..     164     240 .. 0.95
   3 ?    1.9   0.3       0.3   3.3e+02      39      77 ..     319     354 ..     309     370 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0004
                                   EEEECSSHHHHHHHHHHHHTTSEEEEEESS CS
                      Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvvers 31
                                   ++v+GgG  g+ +A ++a+++k+V +ve +
  gene654|gene654|rna654|rna654  4 LIVIGGGSGGMAAAREAAKFNKRVLLVEKG 33
                                   68*************************976 PP

  == domain 2  score: 47.9 bits;  conditional E-value: 1.4e-15
                                    EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEETT CS
                      Pyr_redox   1 kvvvvGgGyiglElAgalaelgkkVtvversdkllrllDeeaskilqeklekngievllntkveeiegsed 71 
                                    k v++G+Gyi lE A +la lg++V++v r++++l+ +D  + ++++e+l+k  ie +++++v e++++++
  gene654|gene654|rna654|rna654 164 KTVIIGSGYISLEIAFMLALLGSDVSIVLRGKHFLSHFDTLFDAVVKEQLKKYRIETYYEENVLEVREESN 234
                                    579***************************************************************97776 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.3
                                    SHHHHHHHHHHHHHTTEEEECSEEEEEEEEETTSEEEEE CS
                      Pyr_redox  39 Deeaskilqeklekngievllntkveeiegsedgvesvk 77 
                                     ee+++ ++  ++ ++i++ +++ v ei+++e     v+
  gene654|gene654|rna654|rna654 319 KEEIGRKVRFDIRGQKIDIEHKEDVYEIHKDELR---VE 354
                                    57899999999******************98864...54 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.2   0.1   1.5e-11   1.7e-08       1     107 [.       3     108 ..       3     135 .. 0.73
   2 ?    0.8   1.3      0.22   2.5e+02     160     253 ..     231     338 ..     218     382 .. 0.58

  Alignments for each domain:
  == domain 1  score: 34.2 bits;  conditional E-value: 1.5e-11
                   FAD_oxidored   1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGlltsglvatdignkaeeqvvtgiareflerlrqrggarlk..kr 78 
                                    D++V+GGg++G+aAA  Aa+  ++vlLve+ g lGG+  + +  +   +++ +++v+ +       +++r + +++  kr
  gene654|gene654|rna654|rna654   3 DLIVIGGGSGGMAAAREAAKFNKRVLLVEK-GELGGTCVNLGCVPKKITYNMTSIVEQMQLASSYGMQARYELNYElfKR 81 
                                    99**************************97.679****999888888888777666666666555555533333332222 PP

                   FAD_oxidored  79 skwntfepevakavleemlaeagvtvlln 107
                                            + ++a++e++l +++v+++ +
  gene654|gene654|rna654|rna654  82 CR--DDVIRRLNAIYEKLLGNSNVEIIRG 108
                                    22..2346777888888887778887765 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.22
                   FAD_oxidored 160 resreetgep.aagtlmfrlegveg..........geedekvqaynkrlcltskp.enrvpfekkpegydparyel..ar 225
                                    +es++et+e  ++g+ m   eg+            +ee+e+ ++ n++ c +sk  ++++  e+k++++  ++      +
  gene654|gene654|rna654|rna654 231 EESNDETNEGmMNGEDMVGNEGMMSnnetkegmmsEEESENNEKKNRSNCKNSKSaNEQISAEQKENDVPLDTSYGskIK 310
                                    68888888887777776655555334555667777566666666677777777776666666533333333332223322 PP

                   FAD_oxidored 226 vfea.klskgklpgektdvnwprvstdli 253
                                     ++      ++  g+k+ ++ +++++d+ 
  gene654|gene654|rna654|rna654 311 HMKViD-VSKEEIGRKVRFDIRGQKIDIE 338
                                    222211.1223334455555544555555 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.3   2.6   9.6e-11   1.1e-07       1     162 [.       3     147 ..       3     260 .. 0.71
   2 ?   -2.1   0.1       1.3   1.5e+03     217     288 ..     272     353 ..     247     376 .. 0.49

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 9.6e-11
                                    CEEEE-SSHHHHHHHHHHHHTT--EEEE..ES-GGGTT--SSSSEEE-TTHHHHHHHHHHHT-SHHHHHHHHEEEEEEES CS
                           GIDA   1 dviViGgGhAGceAAlaaarlGakvlLi..thkldtiaelsCnpsiggiakgllvrEidalggliikaadkagiqfrilN 78 
                                    d+iViGgG  G++AA +aa+ + +vlL+   +  +t+++l+C p         +v++++   +  ++a  + +       
  gene654|gene654|rna654|rna654   3 DLIVIGGGSGGMAAAREAAKFNKRVLLVekGELGGTCVNLGCVPKKITYNMTSIVEQMQLASSYGMQARYELNY------ 76 
                                    689*************************988999*************************998888887666665...... PP

                                    TTS-CCC-EEEEEE-HHHHHHHHHHHHHTSTTEEEEES-EEEEEECTTEEEEEEETTS-EEEECEEEE--TT-BT-EEEE CS
                           GIDA  79 rskGpavralraqvdrelyskevteklenepnleiieeeveeliveekkvkgvvtedgetikakavviatGtflkgkihi 158
                                           +   +  d  +  +++ ekl  + n+eii++ +  ++       g v  +g+++k   + +a+G+       i
  gene654|gene654|rna654|rna654  77 ----ELFKR--CRDDVIRRLNAIYEKLLGNSNVEIIRGYARVISA------GEVEVNGQVYKGTYILLASGS-KPKALKI 143
                                    ....33444..4677777889999999999********9999977......888999**************9.4444444 PP

                                    TTEE CS
                           GIDA 159 geke 162
                                    +  e
  gene654|gene654|rna654|rna654 144 KGAE 147
                                    4444 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.3
                                    -B-SSSSSSST...CG----EEEEE--HHHHHHHHCTCCC-T.T----B--S-CCC-SSTCCCCCCST........T-S- CS
                           GIDA 217 geefsylnkpl...nkeqvecfltatneathkiikenlkksaklfegcieelgprycpsiedkivrla........dkes 285
                                    +e+ +  n++     +eq+++  +++     +   +++k+ +k+++   ee+g++++  i+ + + ++        +k++
  gene654|gene654|rna654|rna654 272 NEKKNRSNCKNsksANEQISAEQKENDVPLDTSYGSKIKH-MKVIDVSKEEIGRKVRFDIRGQKIDIEhkedvyeiHKDE 350
                                    2223333333311134444433333222223333333333.335555566666666666666666666555555444444 PP

                                    -EE CS
                           GIDA 286 hqv 288
                                     +v
  gene654|gene654|rna654|rna654 351 LRV 353
                                    444 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   1.0   4.6e-09   5.1e-06       1      36 [.       3      37 ..       3      42 .. 0.92
   2 ?   -2.2   0.0       1.5   1.7e+03       3      36 ..     166     199 ..     165     234 .. 0.85
   3 ?   -2.5   0.0       1.8     2e+03     379     402 ..     407     424 ..     399     428 .. 0.75

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 4.6e-09
                                   SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGS CS
                  FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefgg 36
                                   D+iViG+G +G+aAA eaa+ +++v++vek++  gg
  gene654|gene654|rna654|rna654  3 DLIVIGGGSGGMAAAREAAKFNKRVLLVEKGEL-GG 37
                                   89****************************986.54 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.5
                                    EEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGS CS
                  FAD_binding_2   3 iViGsGlAGLaAAleaaeaGlkvavvekeqefgg 36 
                                    ++iGsG   L  A  +a  G +v +v  ++ f +
  gene654|gene654|rna654|rna654 166 VIIGSGYISLEIAFMLALLGSDVSIVLRGKHFLS 199
                                    8999999999999999999999999877776655 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 1.8
                                    ETTSBESTTEEESSBTEEE-STCE CS
                  FAD_binding_2 379 dengrvldadgqpipGLYAaGeva 402
                                    d ++ +       +p+ YA+G   
  gene654|gene654|rna654|rna654 407 DHKFMT------SVPNVYAVGDLV 424
                                    444444......99*******865 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   4.5e-07   0.00051       1      36 [.       3      38 ..       3      94 .. 0.81
   2 !    5.6   0.0    0.0087       9.8       2      27 ..     165     192 ..     164     202 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 4.5e-07
                                   EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSSG CS
                            DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllekgdiagsga 36
                                   d+++iGGG  G+++A+e+a+ +  V+l+ekg ++g g+
  gene654|gene654|rna654|rna654  3 DLIVIGGGSGGMAAAREAAKFNkrVLLVEKG-ELG-GT 38
                                   789***************997669*******.887.54 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0087
                                    EEEECTSHHHHHHHHHHHHTT..EEEEE CS
                            DAO   2 vviiGGGiiGlstAyeLarrg..Vtlle 27 
                                     viiG+G+i l +A+ La  g  V ++ 
  gene654|gene654|rna654|rna654 165 TVIIGSGYISLEIAFMLALLGsdVSIVL 192
                                    69****************9988966654 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.6   1.1e-07   0.00012       2      33 ..       3      34 ..       2      44 .. 0.91

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 1.1e-07
                                   SEEEE--SHHHHHHHHHHHHTT--EEEE-SSS CS
                    HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekak 33
                                   d+iviGgG  G+ aA +aak +krVll+ek++
  gene654|gene654|rna654|rna654  3 DLIVIGGGSGGMAAAREAAKFNKRVLLVEKGE 34
                                   89****************************96 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.8   4.4e-07    0.0005       1      35 [.       6      39 ..       6      42 .. 0.93
   2 ?    2.7   0.1      0.14   1.5e+02       1      25 [.     167     191 ..     167     197 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 4.4e-07
                                   EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG CS
                  NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGra 35
                                   ++G+G +G++aA+++ak +++vll+ek+  lGG +
  gene654|gene654|rna654|rna654  6 VIGGGSGGMAAAREAAKFNKRVLLVEKG-ELGGTC 39
                                   8**************************9.788876 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.14
                                    EE--SHHHHHHHHHHHCCTEEEEEE CS
                  NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvlll 25 
                                    I+G+G  +l +A  La  g dv ++
  gene654|gene654|rna654|rna654 167 IIGSGYISLEIAFMLALLGSDVSIV 191
                                    9***************999999875 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.3    0.0019       2.1      32      58 ..       5      31 ..       3      48 .. 0.92
   2 ?    4.0   0.0     0.024        27      28      73 ..     162     207 ..     157     284 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0019
                                   EEESTSHHHHHHHHHHHHTT-EEEEEE CS
                    AlaDh_PNT_C 32 lviGgGvaGlqAiatakglgakVtvlD 58
                                   +viGgG  G++A++ a++++ +V +++
  gene654|gene654|rna654|rna654  5 IVIGGGSGGMAAAREAAKFNKRVLLVE 31
                                   8******************99998776 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.024
                                    --EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTTC CS
                    AlaDh_PNT_C  28 pakvlviGgGvaGlqAiatakglgakVtvlDvrparleqleslgak 73 
                                    p k+++iG G   l+ + + + lg +V ++   ++ l ++++l   
  gene654|gene654|rna654|rna654 162 PKKTVIIGSGYISLEIAFMLALLGSDVSIVLRGKHFLSHFDTLFDA 207
                                    5799************************998888777777774444 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   5.9e-05     0.066      19      55 ..       3      37 ..       1     110 [. 0.88
   2 ?   -2.2   0.0       1.7     2e+03      19      44 ..     164     190 ..     150     195 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 5.9e-05
                                   EEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--T CS
                           Thi4 19 DvvivGaGssGLtaayylakkpdlkvailersvspGG 55
                                   D++++G+Gs G++aa+  ak  + +v+++e+   +GG
  gene654|gene654|rna654|rna654  3 DLIVIGGGSGGMAAAREAAKF-NKRVLLVEKG-ELGG 37
                                   99*****************99.9999999975.3444 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.7
                                    EEEEE--SHHHHHHHHHHHHC.TTS-E CS
                           Thi4  19 DvvivGaGssGLtaayylakk.pdlkv 44 
                                      vi+G+G   L  a++la    d+ +
  gene654|gene654|rna654|rna654 164 KTVIIGSGYISLEIAFMLALLgSDVSI 190
                                    57999**********999976445544 PP

>> DUF4541  Domain of unknown function (DUF4541)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   1.4     2e-05     0.023      21      67 ..     267     311 ..     253     330 .. 0.79
   2 ?   -1.2   0.1       2.9   3.3e+03      24      48 ..     327     350 ..     316     354 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2e-05
                        DUF4541  21 veegydsklhRdDrehaksiglninkeEkekavpvlssseYGrrlrk 67 
                                     e++ ++k++R ++++ ks  ++i +e ke  vp+ +s  YG ++++
  gene654|gene654|rna654|rna654 267 EESENNEKKNRSNCKNSKSANEQISAEQKENDVPLDTS--YGSKIKH 311
                                    455789****************************9876..8988853 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 2.9
                        DUF4541  24 gydsklhRdDrehaksiglninkeE 48 
                                     +d + ++ D eh k+   +i+k+E
  gene654|gene654|rna654|rna654 327 RFDIRGQKIDIEH-KEDVYEIHKDE 350
                                    5888889999999.99999999998 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.3   0.00038      0.42       1      34 [.       3      34 ..       3      39 .. 0.94
   2 ?    0.8   0.1      0.17   1.9e+02      77     117 ..      62     102 ..      52     127 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00038
                  Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvlieasp 34
                                   D++viG+G  g++ A +   ak + +v+l+e ++
  gene654|gene654|rna654|rna654  3 DLIVIGGGSGGMAAAREA--AKFNKRVLLVEKGE 34
                                   9**************999..**********9886 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.17
                  Lycopene_cycl  77 lgraYgrvsskrlkeellerlvengvklleakvesveeeea 117
                                    l   Yg+  + +l+ el +r+ ++ +++l+a  e+   +++
  gene654|gene654|rna654|rna654  62 LASSYGMQARYELNYELFKRCRDDVIRRLNAIYEKLLGNSN 102
                                    4458******************9999999998877766655 PP

>> S4  S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   0.00032      0.36      17      36 ..     107     126 ..      96     134 .. 0.83
   2 ?   -2.4   0.0       3.7   4.2e+03       2      28 ..     492     518 ..     491     518 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00032
                                    HHHHHHHHTTTEEETTEEE- CS
                             S4  17 reArqlIehGrVlVNGkvvk 36 
                                    r   + I++G V VNG+v k
  gene654|gene654|rna654|rna654 107 RGYARVISAGEVEVNGQVYK 126
                                    556799************98 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 3.7
                                    EHHHHHHHTTSSSSHHHHHHHHHTTTE CS
                             S4   2 RLdkvlarlglassrreArqlIehGrV 28 
                                    R  ++l++l   ++ +  + ++  G+V
  gene654|gene654|rna654|rna654 492 RFNNLLYALSEHKTASVFKAIVHRGQV 518
                                    778999999999999999888877776 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.2       1.1   1.2e+03       4      30 ..       6      32 ..       3      65 .. 0.88
   2 ?   10.7   0.1   0.00033      0.36       3      82 ..     166     248 ..     164     321 .. 0.81
   3 ?   -1.8   0.0       2.2   2.4e+03     117     138 ..     503     524 ..     500     529 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1.1
                                   EE--SCCHHHHHHHHHHTT-EEEEE-S CS
                        3HCDH_N  4 viGaGtmGagiaavfasagleVvlvdi 30
                                   viG G  G   a  +a+ + +V lv+ 
  gene654|gene654|rna654|rna654  6 VIGGGSGGMAAAREAAKFNKRVLLVEK 32
                                   9****************9999999986 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00033
                                    EEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCCTTTTSS-...HHHHCCCHHCEEEES-HHHHHC- CS
                        3HCDH_N   3 aviGaGtmGagiaavfasagleVvlvdiseealekalekieksleklvekgklk...eeeveaalarisfttdleeavda 79 
                                     +iG+G +  +ia ++a  g +V +v + +++l +      + ++++ +k +++   ee+v ++ ++ + +t+   + + 
  gene654|gene654|rna654|rna654 166 VIIGSGYISLEIAFMLALLGSDVSIVLRGKHFLSHFDTLFDAVVKEQLKKYRIEtyyEENVLEVREESNDETNEGMMNGE 245
                                    69********************************************9999999944444444444444444444444455 PP

                                    SEE CS
                        3HCDH_N  80 dlv 82 
                                    d+v
  gene654|gene654|rna654|rna654 246 DMV 248
                                    555 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 2.2
                                    S-HHHHCCCSSSGGGEEEEEE- CS
                        3HCDH_N 117 lsiselaealkrperviglHFf 138
                                     + + + +a+ ++ +v+glH f
  gene654|gene654|rna654|rna654 503 HKTASVFKAIVHRGQVVGLHLF 524
                                    56667889999*********87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (578 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1464  (0.0816554); expected 358.6 (0.02)
Passed bias filter:                      598  (0.0333538); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.71u 0.28s 00:00:00.99 Elapsed: 00:00:00.43
# Mc/sec: 4051.53
//
Query:       gene655|gene655|rna655|rna655  [L=60]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (60 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       313  (0.0174578); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.32u 0.20s 00:00:00.52 Elapsed: 00:00:00.35
# Mc/sec: 517.46
//
Query:       gene656|gene656|rna656|rna656  [L=261]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.44    9.6   3.4        0.4    9.7   2.0    1.5  2  Hyccin    Hyccin


Domain annotation for each model (and alignments):
>> Hyccin  Hyccin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   2.0   2.2e-05       0.4     166     239 ..      40     114 ..      35     123 .. 0.88
   2 ?   -2.4   0.0      0.11     2e+03     156     188 ..     182     214 ..     154     220 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 2.2e-05
                         Hyccin 166 lLqlynekisqlpklsllelCkvtskl.ckcgferkkesssssesksssslssriplsselLvellrglyfallN 239
                                    ++++y +ki+ +++lsl ++ + + +l  +c + r++ +++++ + +s+ + +r+ +  ++L + l ++++   N
  gene656|gene656|rna656|rna656  40 IFECYPQKITLFSRLSLIYVVDRFEVLfSSCIHLRQEAENFKNAHIHSKAIFNRHFFIRQVLFSQLLCIFHVQSN 114
                                    789*****************9888755478888889999*****************************9997665 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.11
                         Hyccin 156 aqnRleiltvlLqlynekisqlpklsllelCkv 188
                                      n  +i++++++  + +i+++ k+s ++l+  
  gene656|gene656|rna656|rna656 182 CLNDKTIVARIFRDHFGHIKEYYKESVKDLYTY 214
                                    556667888888888888888888888887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       715  (0.0398795); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.32s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 1651.14
//
Query:       gene657|gene657|rna657|rna657  [L=312]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (312 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1526  (0.0851135); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 2148.95
//
Query:       gene658|gene658|rna658|rna658  [L=223]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       950  (0.0529868); expected 358.6 (0.02)
Passed bias filter:                      505  (0.0281667); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1501.90
//
Query:       gene659|gene659|rna659|rna659  [L=1084]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.8e-16   59.2   0.1    2.5e-14   53.3   0.1    3.2  2  BRCA-2_OB1  BRCA2, oligonucleotide/oligosaccharide-binding, d
  ------ inclusion threshold ------
        0.4   10.7   4.2        0.1   12.6   0.4    1.9  2  Smg4_UPF3   Smg-4/UPF3 family


Domain annotation for each model (and alignments):
>> BRCA-2_OB1  BRCA2, oligonucleotide/oligosaccharide-binding, domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.3   0.1   2.8e-18   2.5e-14       1     122 [.     851     951 ..     851     952 .. 0.93
   2 ?    1.2   0.0     0.038   3.4e+02      69      92 ..    1048    1071 ..    1038    1082 .. 0.81

  Alignments for each domain:
  == domain 1  score: 53.3 bits;  conditional E-value: 2.8e-18
                                    -HHHHHHTTSSTT--SEEEEEEE----------------------EEEE-SS-EEEE---HHHHHHHHTT-S-TT-EEEE CS
                     BRCA-2_OB1   1 salkkilerDdsaskpmvLcVsaiekkesekeekekekeksekaeleltDGWYsikavlDaalsrllkrgkikvGqKlvv 80 
                                    s+l++i+e+Dd+  k m+L++ ++ +                   lel DG+Ys+ ++ D+al+  + ++k+kvG+K++v
  gene659|gene659|rna659|rna659 851 SILRRIIEGDDVCFKLMCLVIIKTGS------------------SLELYDGFYSLLFKADKALQGRIVAQKLKVGDKIYV 912
                                    89*******************99855..................59********************************** PP

                                    S--EEES--S---GGG--SS-EEE--TTTEEE--SSS-SEE- CS
                     BRCA-2_OB1  81 agaelvgseeavspleaseklllkisaNstrrarwnakLGfq 122
                                    ++ael  +e+++  ++     +++++aNs+ r++ + kLG++
  gene659|gene659|rna659|rna659 913 FNAELLTHEKDIFAID---GPAFQLHANSVMRVKDDIKLGYT 951
                                    *****77777777666...9********************86 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.038
                                     TT-S-TT-EEEES--EEES--S-- CS
                     BRCA-2_OB1   69 rgkikvGqKlvvagaelvgseeav 92  
                                     r+++kvG+K++ + a++v+ + + 
  gene659|gene659|rna659|rna659 1048 REEVKVGDKIRAISATIVSDTVGL 1071
                                     789************997766555 PP

>> Smg4_UPF3  Smg-4/UPF3 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.4   1.2e-05       0.1     103     152 ..     228     277 ..     197     300 .. 0.72
   2 ?   -3.4   0.3      0.95   8.5e+03     122     144 ..     626     648 ..     625     682 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.2e-05
                      Smg4_UPF3 103 kkkkdakqgtIekDpeylaFleslekeeeekeseseeeklaeeaeekeke 152
                                    +k++d k+gtI++ + y +F+    ++++++ +e++ ++++++ + ++++
  gene659|gene659|rna659|rna659 228 TKNEDDKTGTINDPSTYHNFVDGCPTDQTNSPTEESVSSTEDQNQDEQNS 277
                                    489********************998887766665544444433332222 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 0.95
                      Smg4_UPF3 122 Fleslekeeeekeseseeeklae 144
                                    F e+l+++++e ++e+ + k+++
  gene659|gene659|rna659|rna659 626 FSEELNDKSKEVQNEKIKRKKRN 648
                                    66777755555444443333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1084 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       823  (0.0459033); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.73u 0.29s 00:00:01.02 Elapsed: 00:00:00.46
# Mc/sec: 7054.10
//
Query:       gene66|gene66|rna66|rna66  [L=230]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.3e-74  249.3   7.0    2.7e-74  249.1   7.0    1.0  1  Ribosomal_L15e  Ribosomal L15
  ------ inclusion threshold ------
       0.14   12.2   0.1       0.73    9.9   0.0    2.0  2  Imm8            Immunity protein 8
        0.2   11.8   0.0       0.45   10.6   0.0    1.5  2  CTXphi_pIII-N1  N-terminal N1 domain of Vibrio phage CTXphi p


Domain annotation for each model (and alignments):
>> Ribosomal_L15e  Ribosomal L15
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  249.1   7.0   4.5e-78   2.7e-74       1     190 [.      28     216 ..      28     217 .. 0.99

  Alignments for each domain:
  == domain 1  score: 249.1 bits;  conditional E-value: 4.5e-78
                                -SHHHHHHHTTSTTSHHHHHHHHHHHHHHTTS-SEEEESS-SSHHHHHHHT--SSTTEEEEEEEEE-SS---..---SS---GG CS
             Ribosomal_L15e   1 gaykylrelwkkkqsdvlrellrerlweyrqepavvrverptrldrArrLGYkakqGivvvrvrvrrGgrkkkvskgktgrkpk 84 
                                ga +yl++  ++kqsdv+r+l r+r+weyrq+pav+r+erpt +d+Ar++GYk k+Gi+v+rvrv+rGgr +k+  gkt++kp+
  gene66|gene66|rna66|rna66  28 GAKDYLQAFRRNKQSDVCRYLSRIRMWEYRQRPAVHRAERPTYPDKARMIGYKRKSGIYVFRVRVKRGGRPRKADGGKTNGKPS 111
                                5789******************************************************************************** PP

                                GG-SSS---SS-HHHHHHHHHHHHSTTSEEEEEEEEEEESSEEEEEEEEE-TTSHHHHT-TTTGGGGSGGGTTGGGGT-SHHHH CS
             Ribosomal_L15e  85 rqgvnklkpakslqaiaeervgrklpnlrvLnSYwvgeDgtykyyEvilvDpshkairndkkinwickkvhkhRelrGltsagk 168
                                ++g+++ kp+k+lq + e r grkl+nlrvL+SYwv+eD +yk +E +++Dp++k+irnd k+nw+ck+++khRe+rGlt+a++
  gene66|gene66|rna66|rna66 112 KSGIYHRKPTKNLQGLGEIRLGRKLGNLRVLGSYWVCEDRQYKIFEAVVIDPMNKTIRNDGKYNWMCKSNMKHRECRGLTAATR 195
                                ************************************************************************************ PP

                                HHTT-S-SS.TT-TTTSS-TGG CS
             Ribosomal_L15e 169 ksRGlrkkglkgaekirgsrra 190
                                +sRGl +kg+++a++++gsr+a
  gene66|gene66|rna66|rna66 196 RSRGL-GKGYRFAQTAGGSRKA 216
                                *****.*************998 PP

>> Imm8  Immunity protein 8
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00012      0.73      75     111 ..      20      56 ..      17      58 .. 0.88
   2 ?   -0.6   0.0      0.22   1.3e+03      32      48 ..      76      92 ..      74      95 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00012
                       Imm8  75 ydleeikaaiekiveecegesweevaeklsrvfaWEf 111
                                ++++ +    +++++++  ++ ++v + lsr+  WE+
  gene66|gene66|rna66|rna66  20 FNISSLAMGAKDYLQAFRRNKQSDVCRYLSRIRMWEY 56 
                                677777777899************************9 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.22
                       Imm8 32 eiGvegekGadlFqvlv 48
                               +iG + ++G + F+v+v
  gene66|gene66|rna66|rna66 76 MIGYKRKSGIYVFRVRV 92
                               69*************98 PP

>> CTXphi_pIII-N1  N-terminal N1 domain of Vibrio phage CTXphi pIII
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       1.7     1e+04      66      80 ..      36      50 ..      18      54 .. 0.59
   2 ?   10.6   0.0   7.6e-05      0.45      42     100 ..     155     213 ..     147     219 .. 0.78

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 1.7
             CTXphi_pIII-N1 66 clsnengdyckglyk 80
                                  n++ d c+ l +
  gene66|gene66|rna66|rna66 36 FRRNKQSDVCRYLSR 50
                               345666777766655 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 7.6e-05
             CTXphi_pIII-N1  42 ivqsvlfdgcmldiekddygfvwsclsnengdyckglyk.prfsqgvspnwpmcdlsgas 100
                                i ++v++d       ++d  + w c sn +   c+gl    r s+g+   + +++ +g s
  gene66|gene66|rna66|rna66 155 IFEAVVIDPMNKT-IRNDGKYNWMCKSNMKHRECRGLTAaTRRSRGLGKGYRFAQTAGGS 213
                                5556666654444.4677889****************75269999999999988888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       369  (0.0205812); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 1567.36
//
Query:       gene660|gene660|rna660|rna660  [L=252]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       499  (0.027832); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1857.20
//
Query:       gene661|gene661|rna661|rna661  [L=185]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.4e-05   24.2  12.1      5e-05   23.2  12.1    1.6  1  zf-RING_5     zinc-RING finger domain
    0.00022   21.0   6.0    0.00044   20.1   6.0    1.5  1  Prok-RING_4   Prokaryotic RING finger family 4
    0.00047   19.9  11.4      0.001   18.9  11.4    1.6  1  zf-C3HC4_3    Zinc finger, C3HC4 type (RING finger)
  ------ inclusion threshold ------
      0.067   13.1   9.5       0.34   10.8   9.6    2.2  1  zf-C3HC4      Zinc finger, C3HC4 type (RING finger)
       0.07   13.2   4.7       0.21   11.6   4.7    1.9  1  zf-RING_UBOX  RING-type zinc-finger
       0.13   12.3   4.8       0.36   10.9   4.8    1.8  1  DZR           Double zinc ribbon
       0.17   11.8   7.8       0.44   10.4   7.8    1.7  1  zf-C3HC4_2    Zinc finger, C3HC4 type (RING finger)
       0.19   12.1   9.6       0.43   11.0   9.6    1.7  1  zf-RING_2     Ring finger domain
        2.6    8.0   5.0        3.8    7.5   5.0    1.2  1  T2SSF         Type II secretion system (T2SS), protein F


Domain annotation for each model (and alignments):
>> zf-RING_5  zinc-RING finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2  12.1   2.5e-08     5e-05       1      44 []       4      46 ..       4      46 .. 0.93

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 2.5e-08
                      zf-RING_5  1 hCn..kCfeklskeekfyltsCgHifCekClkkllekeavCpiCrk 44
                                   +Cn  +C++ +  ++ + +t+C+Hi+Ce+C  k + +++ C +C++
  gene661|gene661|rna661|rna661  4 RCNnlRCHTTI--QKYILITPCSHIYCESCSPKIQ-SMQMCIACKT 46
                                   59988999999..889*******************.********95 PP

>> Prok-RING_4  Prokaryotic RING finger family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   6.0   2.2e-07   0.00044       4      44 ..      11      52 ..       8      54 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 2.2e-07
                    Prok-RING_4  4 CgeqekkailepCgHlvCkeCfdskdls.sCPlCqrrisksd 44
                                   +++ +k + + pC H+ C++C  + ++   C  C++ i ++d
  gene661|gene661|rna661|rna661 11 HTTIQKYILITPCSHIYCESCSPKIQSMqMCIACKTTIRPDD 52
                                   667789999****************87769*****9998876 PP

>> zf-C3HC4_3  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9  11.4   5.2e-07     0.001       8      48 ..      10      49 ..       4      50 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 5.2e-07
                                   TSSS.BS-EEETTEEEEEE-HHHHHHHHHTT-B-TTT--B-- CS
                     zf-C3HC4_3  8 Cler.prnvvllpCgHlvlCeeCaekllkrkkkCpiCrrpie 48
                                   C+++ ++ +++ pC H+ +Ce+C+ k+ ++ + C  C++ i+
  gene661|gene661|rna661|rna661 10 CHTTiQKYILITPCSHI-YCESCSPKI-QSMQMCIACKTTIR 49
                                   888856778899*****.*********.7899******9985 PP

>> zf-C3HC4  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   9.6   0.00017      0.34       4      41 .]      10      44 ..       5      46 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00017
                                   T-S--SS-E.E-TTS--B-CHHHHHHHHCTSSB--TTT CS
                       zf-C3HC4  4 CleeakepnelleCkHsfCskCirkilksrkkvkCPlC 41
                                   C +++++   +++C H +C++C  ki++  + + C  C
  gene661|gene661|rna661|rna661 10 CHTTIQKYILITPCSHIYCESCSPKIQS--M-QMCIAC 44
                                   7777777778****************99..3.336666 PP

>> zf-RING_UBOX  RING-type zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   4.7   0.00011      0.21      13      25 ..      19      32 ..       9      49 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00011
                   zf-RING_UBOX 13 v.lpCGHtFCreCl 25
                                   + +pC+H++C++C 
  gene661|gene661|rna661|rna661 19 LiTPCSHIYCESCS 32
                                   3369*********7 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   4.8   0.00018      0.36       8      41 ..      21      51 ..       5      54 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00018
                            DZR  8 lppdarfCseCgtklkavaaedrCpsCgekvdpe 41
                                   +p + ++C+ C  k+++   +++C +C++ + p+
  gene661|gene661|rna661|rna661 21 TPCSHIYCESCSPKIQS---MQMCIACKTTIRPD 51
                                   455667*********95...*********98887 PP

>> zf-C3HC4_2  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   7.8   0.00022      0.44       5      37 ..      10      41 ..       8      44 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00022
                     zf-C3HC4_2  5 CldmlkdpsvvtpCgHvfCqkCilrsLeekneC 37
                                   C   +++ + +tpC H +C++C  + +++ + C
  gene661|gene661|rna661|rna661 10 CHTTIQKYILITPCSHIYCESCSPK-IQSMQMC 41
                                   8888999999************988.4666666 PP

>> zf-RING_2  Ring finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   9.6   0.00021      0.43      14      44 .]      16      45 ..       3      45 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00021
                      zf-RING_2 14 dsvlllpCgHvfhreClerwlrssstCPlCr 44
                                   + +l++pC+H+++++C  + ++s + C +C+
  gene661|gene661|rna661|rna661 16 KYILITPCSHIYCESCSPK-IQSMQMCIACK 45
                                   4466789*********988.888888*9996 PP

>> T2SSF  Type II secretion system (T2SS), protein F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   5.0    0.0019       3.8      32     104 ..     102     174 ..      86     175 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0019
                                    HHHHHHHHHHHHTTSSHHHHHC..T-TT.TS-HHHHHHHHHHHHHT-HHHHHHHHHHHHHHHHHHHHHHHHHHHT CS
                          T2SSF  32 aeelkriarrlraGgslseale..rtpssefpelvvqlirageeggnLaevLerlaeyleeerelrrkllaalle 104
                                    +   +++a++l+a   l++a+e  ++  s  ++l ++l r  e   +L+ +L+  a+++ +++++r ++  ++++
  gene661|gene661|rna661|rna661 102 RADAEKAAQDLKACR-LKAAIEkrNM-KSRVRKLESSLKRERENVYDLSMMLREKADEYKRQQMRRERKEMNMMS 174
                                    667778888888885.9999998444.4699***********************************887777764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2080  (0.116013); expected 358.6 (0.02)
Passed bias filter:                      565  (0.0315132); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1347.94
//
Query:       gene662|gene662|rna662|rna662  [L=470]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      6e-46  157.0  23.0      6e-46  157.0  23.0    1.5  1  RSN1_7TM         Calcium-dependent channel, 7TM region, putat
     0.0051   17.1   0.0     0.0097   16.2   0.0    1.4  1  PHM7_cyt         Cytosolic domain of 10TM putative phosphate 
  ------ inclusion threshold ------
      0.063   13.3   1.3       0.49   10.4   0.8    2.6  2  Phage_holin_3_7  Putative 3TM holin, Phage_holin_3
       0.12   12.2   0.3         25    4.7   0.2    2.7  2  zf-UBP_var       Variant UBP zinc finger


Domain annotation for each model (and alignments):
>> RSN1_7TM  Calcium-dependent channel, 7TM region, putative phosphate
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  157.0  23.0   1.3e-49     6e-46       2     269 ..      87     351 ..      86     356 .. 0.97

  Alignments for each domain:
  == domain 1  score: 157.0 bits;  conditional E-value: 1.3e-49
                       RSN1_7TM   2 klivtlllvlliifwiipvafvgllsnletltkvlpflkkilelskkllsvvtgllPtlllslllallpiilrllsklqG 81 
                                    +l+  +l+vl+++++   v +++++ nl+++++++  l+++l  +++  + + g+l++l++++l+ + pi++rl+ +l+ 
  gene662|gene662|rna662|rna662  87 RLLCSFLFVLFTLMFFSAVGVIASFCNLNYIESKFTRLADLLREHENWRATLNGVLSPLAYNILMTIGPIFIRLIITLES 166
                                    6778899************************************************************************* PP

                       RSN1_7TM  82 alsrselelsvvskyfaFlvvnvFlvftlagtalslleeiidnptsipkllaeslpkasnFfityillqglagaaleLlq 161
                                     +s +  +ls++++y +Fl++n Fl f+ + ++ +l  +  d+ +++ + l++ l k s Ff++ +++++l+g +l Llq
  gene662|gene662|rna662|rna662 167 NYSGTADQLSLMNRYSVFLFLNGFLSFVTTYSVHQL--SGFDELKKVLEGLQSGLLKTSVFFMNALIQKALVGQVLILLQ 244
                                    ****************************99999999..66778999********************************** PP

                       RSN1_7TM 162 lvklilflikrkflsktprdlaerytkppsfdygteypkvllifvialiYsviaPlilpfaliyfllgylvykyqllyvy 241
                                    +++li + i + f skt r ++++     ++d+gt+yp++llif+i+l+Ys+i+P+il+++ ++++  + v+k++++y++
  gene662|gene662|rna662|rna662 245 VGPLISKSIAYVFGSKTLRSRKQLA-MSIPLDFGTMYPNMLLIFAICLVYSIITPIILVVGFVFYVSCFAVFKNEFIYCV 323
                                    ***********************99.6666************************************************** PP

                       RSN1_7TM 242 dtkyesgGklwpralnrllvglvlfqll 269
                                    ++ +e+gG +++ a + ++  l++fq  
  gene662|gene662|rna662|rna662 324 KNDTETGGVHFNFAATYIIYILIFFQAS 351
                                    *************************976 PP

>> PHM7_cyt  Cytosolic domain of 10TM putative phosphate transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   2.2e-06    0.0097     121     176 .]      31      75 ..      20      75 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2.2e-06
                       PHM7_cyt 121 plgaaFvtfesersaaavakqakcaaqiqqssnptlkpkkwtvelAPePrDviWeN 176
                                    +++a+ v+f+ +rsa        c++ i +++       ++ +++AP+P+D+ ++N
  gene662|gene662|rna662|rna662  31 KTRAGIVSFKHQRSASIL-----CQSLISSKMF------SCIAQPAPAPNDIKYDN 75 
                                    6899***********877.....6655544333......69***********9998 PP

>> Phage_holin_3_7  Putative 3TM holin, Phage_holin_3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.33   1.5e+03      27      49 ..     142     164 ..     130     177 .. 0.84
   2 ?   10.4   0.8   0.00011      0.49      20      64 ..     331     374 ..     328     383 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.33
                Phage_holin_3_7  27 iswlAyllivasgsvairillgl 49 
                                     s lAy + +  g + ir+++ l
  gene662|gene662|rna662|rna662 142 LSPLAYNILMTIGPIFIRLIITL 164
                                    6889*********9999998765 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00011
                Phage_holin_3_7  20 garhrrgiswlAyllivasgsvairillglyrevdlaevlinvvL 64 
                                    g ++++++ ++ y+li + +s a+++l  + ++ +l   ++ +vL
  gene662|gene662|rna662|rna662 331 GVHFNFAATYIIYILIFFQASTAVQYLTTRNTYLSLCLFVL-AVL 374
                                    7899************************9999866654443.333 PP

>> zf-UBP_var  Variant UBP zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.2    0.0057        25       9      29 ..     313     333 ..     310     338 .. 0.90
   2 ?    4.6   0.0     0.006        27      14      32 ..     441     459 ..     438     465 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.0057
                     zf-UBP_var   9 kVyKdECvycFdtpesedGly 29 
                                     V+K+E +yc ++  + +G+ 
  gene662|gene662|rna662|rna662 313 AVFKNEFIYCVKNDTETGGVH 333
                                    59***************9986 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.006
                     zf-UBP_var  14 ECvycFdtpesedGlyvcL 32 
                                    EC+  ++ p +++G+y   
  gene662|gene662|rna662|rna662 441 ECAMAYERPTDKEGVYLDT 459
                                    9***************865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (470 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       915  (0.0510346); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.43
# Mc/sec: 3252.87
//
Query:       gene663|gene663|rna663|rna663  [L=225]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (225 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       758  (0.0422779); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1570.04
//
Query:       gene664|gene664|rna664|rna664  [L=205]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (205 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3348  (0.186737); expected 358.6 (0.02)
Passed bias filter:                      635  (0.0354175); expected 358.6 (0.02)
Passed Vit filter:                       114  (0.00635841); expected 17.9 (0.001)
Passed Fwd filter:                        36  (0.00200792); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.82u 0.37s 00:00:01.19 Elapsed: 00:00:00.53
# Mc/sec: 1158.80
//
Query:       gene665|gene665|rna665|rna665  [L=142]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.3e-23   80.1   0.1    9.9e-23   79.7   0.1    1.1  1  Ribosomal_L7Ae  Ribosomal protein L7Ae/L30e/S12e/Gadd45 famil
     0.0011   19.1   0.0     0.0014   18.7   0.0    1.2  1  RNase_P_pop3    RNase P subunit Pop3
  ------ inclusion threshold ------
      0.069   13.4   0.0       0.12   12.7   0.0    1.3  1  Sun2_CC2        SUN2 coiled coil domain 2
       0.11   12.6   0.0       0.15   12.1   0.0    1.2  1  baeRF_family2   Bacterial archaeo-eukaryotic release factor f
       0.16   12.2   0.0       0.24   11.6   0.0    1.3  1  Tox-SGS         Salivary glad secreted protein domain toxin


Domain annotation for each model (and alignments):
>> Ribosomal_L7Ae  Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.7   0.1   2.8e-26   9.9e-23      12      83 ..      45     116 ..      37     126 .. 0.88

  Alignments for each domain:
  == domain 1  score: 79.7 bits;  conditional E-value: 2.8e-26
                                    HHTEEEESHHHHHHHHHTTTESEEEEETTSSSGGHHHHHHHHHHHTTEEEEEESCHHHHHHHTTSSSECSEE CS
                 Ribosomal_L7Ae  12 kagklvlGlkevtkalergeaklvilAedvepeekkkllealckekevpyvkvkskkeLGelvgkkrpvsal 83 
                                    +++ +++G++evtk ++rg+a lv+lA+d++p+e+ +++++lc++k+v y++++s ++LG+++g +r  +a+
  gene665|gene665|rna665|rna665  45 RKRSIKKGANEVTKMINRGKAMLVVLAADCNPIEIIQHIPVLCNDKDVSYIYIESGEALGRACGVERSIAAA 116
                                    5677**************************************************************653332 PP

>> RNase_P_pop3  RNase P subunit Pop3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   3.8e-07    0.0014      42     101 ..      37      92 ..      15     103 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 3.8e-07
                   RNase_P_pop3  42 lvrlleskeneeseltvglneivelLecsesddvvllvcnkD.tPsvLlsqlpllvavanl 101
                                    ++     +e  + ++  g ne+ ++++    ++++l+v+  D +P  +++++p+l++ +++
  gene665|gene665|rna665|rna665  37 ILTN--IEEYRKRSIKKGANEVTKMIN---RGKAMLVVLAADcNPIEIIQHIPVLCNDKDV 92 
                                    3333..35788899**********998...88899999999988************99984 PP

>> Sun2_CC2  SUN2 coiled coil domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   3.2e-05      0.12       8      40 ..      33      65 ..      31      69 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.2e-05
                       Sun2_CC2  8 LEkkILaklaeeqgksardaaasvgvaLqkeGv 40
                                   L k+IL+++ e+++ s ++ a+ v+++++++ +
  gene665|gene665|rna665|rna665 33 LTKRILTNIEEYRKRSIKKGANEVTKMINRGKA 65
                                   779************************999755 PP

>> baeRF_family2  Bacterial archaeo-eukaryotic release factor family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   4.1e-05      0.15      46      84 ..      35      73 ..      24      81 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 4.1e-05
                  baeRF_family2 46 rryqrraeeswerNaeavAeevdrlvresgaelVvlaGD 84
                                   +r+ ++ ee  +r +++ A ev++++ + +a lVvla D
  gene665|gene665|rna665|rna665 35 KRILTNIEEYRKRSIKKGANEVTKMINRGKAMLVVLAAD 73
                                   56677899****************************966 PP

>> Tox-SGS  Salivary glad secreted protein domain toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   6.8e-05      0.24      41      66 ..      72      97 ..      45     103 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 6.8e-05
                        Tox-SGS 41 skClPlewegqpsvaCeGqetsfiyt 66
                                   ++C P+e  ++  v C+ ++ s+iy 
  gene665|gene665|rna665|rna665 72 ADCNPIEIIQHIPVLCNDKDVSYIYI 97
                                   79***********************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       474  (0.0264376); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1037.43
//
Query:       gene666|gene666|rna666|rna666  [L=501]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    0.00019   21.5   1.1    0.00019   21.5   1.1    2.1  2  Suf           Suppressor of forked protein (Suf)
  ------ inclusion threshold ------
      0.017   15.4   0.0       0.27   11.5   0.0    2.4  2  Mur_ligase_C  Mur ligase family, glutamate ligase domain


Domain annotation for each model (and alignments):
>> Suf  Suppressor of forked protein (Suf)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   1.5     0.071   6.3e+02      84     131 ..      89     134 ..      27     154 .. 0.65
   2 !   21.5   1.1   2.2e-08   0.00019       2      77 ..     298     371 ..     297     389 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.071
                            Suf  84 nddnnaRvlfekvvsklskekeakelykkfleyestfgdlssilklek 131
                                    + +++ R+ +++v++       +  +yk + e+e++ +   + + lek
  gene666|gene666|rna666|rna666  89 DVVDRKRAAYQNVIKYAVFC--LPAIYKEYEEFEYKLNKFTAKTILEK 134
                                    33456677777777653333..468**********9998777666665 PP

  == domain 2  score: 21.5 bits;  conditional E-value: 2.2e-08
                            Suf   2 lvwikymrasrRaeGikgaRkvFkkARkkprltyevyvasAllEyyiskdkkvAtkIFelGlKkFpedeefvlkYl 77 
                                    lv+i ++ ++   +Gi++ R vF + +    ++  v+  +A+lEyy++ d +v  ++  lG Kk  + e +++k+l
  gene666|gene666|rna666|rna666 298 LVYIHFLDTVFKNKGISAFRCVFRDLK--DLIGPLVFYYVAQLEYYVYGDVNVFVNVMLLGSKKSRSLETYMIKFL 371
                                    8**********************9976..568999************************************98765 PP

>> Mur_ligase_C  Mur ligase family, glutamate ligase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0     3e-05      0.27      39      80 ..     169     211 ..     149     221 .. 0.85
   2 ?    1.3   0.0     0.045   4.1e+02      41      80 ..     219     258 ..     211     263 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 3e-05
                                    S.SSEEEEEEEESTT.CCSCHCTHHHHHHHHCCHSSEEEEEES CS
                   Mur_ligase_C  39 p.dkrlilvfgpggelgertrtfhdefgrlasaladslvvlgd 80 
                                    + d+r+i+v+ +++e++  +++ ++e++r+a  ++++ ++++ 
  gene666|gene666|rna666|rna666 169 EvDERKIFVWKCLKEKFYYSEEIYFELIRMAPNFVVEAIFCNS 211
                                    2589*******************************99999876 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.045
                                    SEEEEEEEESTT.CCSCHCTHHHHHHHHCCHSSEEEEEES CS
                   Mur_ligase_C  41 krlilvfgpggelgertrtfhdefgrlasaladslvvlgd 80 
                                    ++  ++++  + +++r++ f+ ++g+ +++++   +++++
  gene666|gene666|rna666|rna666 219 SNTECILQNRENTFTRANFFFVLLGAYLNKIDLASYIFKE 258
                                    66779999999*******************9888444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (501 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       656  (0.0365888); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 3333.48
//
Query:       gene667|gene667|rna667|rna667  [L=42]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (42 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       217  (0.0121033); expected 358.6 (0.02)
Passed bias filter:                      167  (0.00931452); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.43
# Mc/sec: 296.61
//
Query:       gene668|gene668|rna668|rna668  [L=167]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.14   11.4   0.1        0.2   11.0   0.1    1.2  1  DGF-1_5   Dispersed gene family protein 1 of Trypanosoma cruz


Domain annotation for each model (and alignments):
>> DGF-1_5  Dispersed gene family protein 1 of Trypanosoma cruzi region 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   1.1e-05       0.2     184     217 ..      11      46 ..       7      70 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 1.1e-05
                        DGF-1_5 184 flsvfaaldplwmvvgna..llaavfgcvhygvtaa 217
                                    f  v+aal p+ m++ ++  ll a +gc  yg+++a
  gene668|gene668|rna668|rna668  11 FNVVLAALAPIKMLLVKSvlLLIATYGCELYGMSTA 46 
                                    6789*******997554322789*********9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       480  (0.0267723); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1200.59
//
Query:       gene669|gene669|rna669|rna669  [L=161]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.02   15.2   0.1      0.032   14.5   0.1    1.3  1  RET_CLD3  RET Cadherin like domain 3


Domain annotation for each model (and alignments):
>> RET_CLD3  RET Cadherin like domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1   1.8e-06     0.032      44     108 ..      31      94 ..      16      96 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.8e-06
                       RET_CLD3  44 keeskkkyvgtlltndswike.tFriehsfkeekakangskvRetvheyklvLkrnlsvtekrslq 108
                                    + ++++ yv+   +++    +  F   ++ ke+ a  n +kvR+ v + ++ Lk+n++++ek +lq
  gene669|gene669|rna669|rna669  31 SRDVNNNYVNSATSKELVTGDaSFCGLKTTKETDA--NTEKVRNVVDSPRVALKQNMNIEEKDMLQ 94 
                                    55666777776665554443313444455566655..5589*********************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       728  (0.0406046); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 1056.87
//
Query:       gene67|gene67|rna67|rna67  [L=77]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.017   14.8   0.1       0.02   14.6   0.1    1.1  1  YkyA      Putative cell-wall binding lipoprotein
      0.028   15.1   4.5      0.049   14.3   4.5    1.4  1  CPG4      Chondroitin proteoglycan 4
      0.061   13.3   0.4       0.13   12.2   0.4    1.5  1  VGPC1_C   C-terminal membrane-localisation domain of ion-chan


Domain annotation for each model (and alignments):
>> YkyA  Putative cell-wall binding lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.1   3.3e-06      0.02     122     167 ..      15      60 ..       5      66 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.3e-06
                       YkyA 122 kaYkealeldkeLYemLkkeeltleeleeqiekiNesyeevkeane 167
                                k  k++ e  ++LYe L+ +e+++++   qi+++  + +e +++ e
  gene67|gene67|rna67|rna67  15 KTQKKICEIAENLYECLQGDEVDVDQASGQIDALESACKEHEQQFE 60 
                                55678889999************************99999888765 PP

>> CPG4  Chondroitin proteoglycan 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   4.5   8.1e-06     0.049      16      75 ..       6      63 ..       1      73 [. 0.81

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 8.1e-06
                       CPG4 16 kllkakntverlkklCskleeaseCvakekkCedkklfealtsgleyvCidkeealekli 75
                               +l + +n++++ kk+C+  e+ +eC++   +  d    +   ++le +C ++e+++e+  
  gene67|gene67|rna67|rna67  6 QLSEIMNVIKTQKKICEIAENLYECLQG-DEV-DVDQASGQIDALESACKEHEQQFERCA 63
                               567778999*****************66.555.5666677889*************9864 PP

>> VGPC1_C  C-terminal membrane-localisation domain of ion-channel, VCN1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.4   2.2e-05      0.13      16      33 ..      44      61 ..      40      64 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.2e-05
                    VGPC1_C 16 KvqqLefscsEKeqeier 33
                               ++  Le+ c E eq  er
  gene67|gene67|rna67|rna67 44 QIDALESACKEHEQQFER 61
                               7999*************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1262  (0.0703888); expected 358.6 (0.02)
Passed bias filter:                      741  (0.0413297); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 499.10
//
Query:       gene670|gene670|rna670|rna670  [L=240]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.027   13.8   3.5      0.046   13.0   3.5    1.4  1  Rh5        Rh5 coiled-coil domain
      0.069   13.3   0.0       0.12   12.6   0.0    1.5  1  CPSF100_C  Cleavage and polyadenylation factor 2 C-terminal


Domain annotation for each model (and alignments):
>> Rh5  Rh5 coiled-coil domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   3.5   5.1e-06     0.046      80     174 ..      57     150 ..      45     184 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 5.1e-06
                            Rh5  80 sikkelykiscynsnkcndavykkyaelykseinnklskiknsainkdkeilksikslinilkkelesknlidklkFlkk 159
                                     i+k+lyk++  +  k  ++  +k++e++   ++n+l++ ++    ++  +++ ++ l+++l  e+ s  +i  ++++ k
  gene670|gene670|rna670|rna670  57 VITKTLYKKYEAKIPKELET-SFKSLESSVYGFINELEEENDARPMEIMGYISLADMLMKKLSLENVSHLNIVLVDYIIK 135
                                    34555555555555555554.6999999999999999999999999999******************************* PP

                            Rh5 160 eiedIinkynkhlkk 174
                                       +I++ y+k + +
  gene670|gene670|rna670|rna670 136 DAGYIFKEYEKNVYE 150
                                    *********986544 PP

>> CPSF100_C  Cleavage and polyadenylation factor 2 C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   1.3e-05      0.12       1      34 [.     107     147 ..     107     201 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.3e-05
                      CPSF100_C   1 VkLsdsLvksLkwqkveglevatvtgeleieee........a 34 
                                    + L+d L+k+L +++v+ l+++ v+  ++ +++        +
  gene670|gene670|rna670|rna670 107 ISLADMLMKKLSLENVSHLNIVLVDYIIK-DAGyifkeyekN 147
                                    679**********************9999.444344322210 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (240 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       707  (0.0394333); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1668.45
//
Query:       gene671|gene671|rna671|rna671  [L=1078]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1078 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       568  (0.0316805); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.72u 0.25s 00:00:00.97 Elapsed: 00:00:00.42
# Mc/sec: 7656.31
//
Query:       gene672|gene672|rna672|rna672  [L=732]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.03   14.0   0.0        5.6    6.9   0.0    3.1  2  PUF       Pumilio-family RNA binding repeat


Domain annotation for each model (and alignments):
>> PUF  Pumilio-family RNA binding repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.0   0.00031       5.6      12      31 ..     626     646 ..     621     651 .. 0.74
   2 ?    3.7   0.0    0.0033        59      12      25 ..     664     677 ..     653     679 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.00031
                                    STTHHHHHHHHHHH.SCHHHH CS
                            PUF  12 dqyGnyvvQklleh.ateeqk 31 
                                     +yG+y +Q ll + + +++ 
  gene672|gene672|rna672|rna672 626 TKYGAYSIQALLNVkNLTKDN 646
                                    59**********996544444 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.0033
                                    STTHHHHHHHHHHH CS
                            PUF  12 dqyGnyvvQklleh 25 
                                    ++ Gny +Qk +++
  gene672|gene672|rna672|rna672 664 HPIGNYTIQKTIDY 677
                                    999*******9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (732 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       969  (0.0540465); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.25s 00:00:00.84 Elapsed: 00:00:00.41
# Mc/sec: 5376.66
//
Query:       gene673|gene673|rna673|rna673  [L=419]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-36  126.1   0.9    2.6e-36  125.4   0.9    1.3  1  DNA_primase_lrg  Eukaryotic and archaeal DNA primase, large s
  ------ inclusion threshold ------
      0.012   14.5   0.0      0.092   11.6   0.0    2.0  2  RNA_pol          DNA-dependent RNA polymerase


Domain annotation for each model (and alignments):
>> DNA_primase_lrg  Eukaryotic and archaeal DNA primase, large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  125.4   0.9   2.9e-40   2.6e-36       3     266 .]     178     413 ..     176     413 .. 0.87

  Alignments for each domain:
  == domain 1  score: 125.4 bits;  conditional E-value: 2.9e-40
                                    EEEEHHHHHHHTT-GGS-EETTEEEE-HHHHHHHHHHHHHHHHHH..........HHGGGSSS---HHHHHHHCT--... CS
                DNA_primase_lrg   3 ykvpfedvldlvkrrrvllkkGyaylpkeeleslllekfrkrlekalestkeslpeleeeikederekleellealsesy 82 
                                    ++v f+++++lv++ +v lkkGy++l++ ++ ++l ++fr+ l   ++s+k+++  l    ++der   ++l   l    
  gene673|gene673|rna673|rna673 178 VHVYFSRAPELVRDCKVELKKGYFVLHDANMAAILANEFREYLRGRMDSLKANTN-L----RNDER--FSDLAVDLF--- 247
                                    67899********************************************988854.6....88888..666666555... PP

                                    ..........TTSSTTGGSHHHHTT--HHHHCCHHHHCCCSS--CHHHHHHHHHHHHCT--CHHHHCCCHCHST..HHHH CS
                DNA_primase_lrg  83 vaedvqeeedskisaknidklakesfPpCmrelleglkknghlkhegrlqltlFlkdiglsldeilelwkeaftrteekF 162
                                         +  ++s+ + k+i     ++ PpC+ ++++++k + hlk++ r+ l+ +lkd+gl + +++e+ +++f+ +  +F
  gene673|gene673|rna673|rna673 248 -----SVPQKSTGQLKSI----LDCAPPCIDRIVKRMKHDRHLKYNDRQILIRYLKDCGLPVNDSIEFLRSNFSCDPARF 318
                                    .....3555555555554....79******************************************************** PP

                                    HHHTHCHCHHHCC-STT--------HHHHHHS....TT---S.-HHHH....HHHHHHHHHHTT....HHHHHH.HHHHH CS
                DNA_primase_lrg 163 dkeyrynirhnyGkegkrtnyspysCekiltkpppgkgdahg.Cpfrh...dpdklktlLqeyg..lseedied.ilesv 235
                                    d+e  y +rhnyG egkr+nys+y C ++          a g Cpf +            ++y   +  +died i  ++
  gene673|gene673|rna673|rna673 319 DREFVYVVRHNYGLEGKRANYSCYTCPQV---------VAMGaCPFTSkcvI--------SDYLseKGFQDIEDvICGEI 381
                                    *****************************.........88889**9633332........3333246778999945689* PP

                                    HTT.HHHHHHHHHHHHHS.-TTT-SSCHHHCC CS
                DNA_primase_lrg 236 kegeyqvaCtkvFelthk.cerdeikhPlqYy 266
                                    ++++y   C  +++  +  +++  +++P  +y
  gene673|gene673|rna673|rna673 382 ENRNYLKGCSILLKHKRRsDDDIAVTSPFVFY 413
                                    *************999988999999***9998 PP

>> RNA_pol  DNA-dependent RNA polymerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0     1e-05     0.092     317     409 ..     172     263 ..     157     264 .. 0.83
   2 ?    0.3   0.0     0.027   2.4e+02     195     235 ..     359     399 ..     340     416 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 1e-05
                                    -.-EEESSSEEEE-HHHHHHHHHHHHHHHHHHHHHTHHHHHHHHHHTTSTGGGSS....................SS--- CS
                        RNA_pol 317 l.tfaavHDsfwthaadvdelnkilreafvklhsedilerlaeefkerykkslllakvkkksevakkikavlvplelpev 395
                                    l ++ +vH  f+  ++ v   +  l++ +  lh  ++ + la+ef+e +++++   k ++  ++++  +   + ++l +v
  gene673|gene673|rna673|rna673 172 LtDYQTVHVYFSRAPELVRDCKVELKKGYFVLHDANMAAILANEFREYLRGRMDSLKANT--NLRNDERFSDLAVDLFSV 249
                                    447899********************************************9987666555..5555544455556999** PP

                                    ----S-SGGGGGG- CS
                        RNA_pol 396 PkkGeldveevkes 409
                                    P+k + ++++++++
  gene673|gene673|rna673|rna673 250 PQKSTGQLKSILDC 263
                                    ****9999999987 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.027
                                    HHHHHHHHHHHHHHHHTTSHHHHHHHHHHHHHHHHHHS-EB CS
                        RNA_pol 195 lkaasylaklilksleelfkgakeiqkwLkelakliakslk 235
                                      ++ yl+++ ++ +e++  g  e +++Lk ++ l+ ++ +
  gene673|gene673|rna673|rna673 359 CVISDYLSEKGFQDIEDVICGEIENRNYLKGCSILLKHKRR 399
                                    56799***************************988877544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (419 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       683  (0.0380947); expected 358.6 (0.02)
Passed bias filter:                      513  (0.0286129); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.23s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 3086.44
//
Query:       gene674|gene674|rna674|rna674  [L=202]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-66  224.3   7.9    1.4e-66  224.1   7.9    1.0  1  DUF5090   Domain of unknown function (DUF5090)
  ------ inclusion threshold ------
      0.066   13.4   0.1       0.12   12.6   0.1    1.4  1  ssDBP     Single-stranded DNA-binding protein
        2.6    8.7   7.4        4.3    7.9   7.4    1.4  1  YtxH      YtxH-like protein
        3.2    7.7   6.2       0.21   11.6   0.6    1.8  2  DUF3290   Protein of unknown function (DUF3290)


Domain annotation for each model (and alignments):
>> DUF5090  Domain of unknown function (DUF5090)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  224.1   7.9   3.1e-70   1.4e-66       1     188 []       1     195 [.       1     195 [. 0.99

  Alignments for each domain:
  == domain 1  score: 224.1 bits;  conditional E-value: 3.1e-70
                        DUF5090   1 Maeentenskekale......ekvkkveekvkeqiekieeSklGkklPtevknlklkdiikitlllkavllipiyllvia 74 
                                    Mae nte++keka+e      ek++k+e+kvke+++k+e++++G+++Pt+++nl++kdiik+tl+l+a+++i++y++v+a
  gene674|gene674|rna674|rna674   1 MAEANTEKVKEKAAEvkdtvkEKSDKAEMKVKESVKKAEKGAVGQHIPTSLDNLTFKDIIKCTLFLNAIMTIGLYVIVSA 80 
                                    9******************************************************************************* PP

                        DUF5090  75 engnkldflksksriifltlik......ivlsilvdlvvyfselsslfkvflllkiikllitlivllalsistglfilvl 148
                                    +++n    ++sk+r iflt++k      +v++i+vd+++++++l+slfkvfl+lk+ikll++li+++ +++  +++i+ +
  gene674|gene674|rna674|rna674  81 TRVN----IDSKWREIFLTAAKymilifGVGGIVVDAIFFYGHLFSLFKVFLGLKAIKLLGVLIFSFSQKLG-AWYIIAM 155
                                    ****....*************9**************************************************.******* PP

                        DUF5090 149 sliylllcliidllflyYlaiylkrlesdeyddngkklkk 188
                                    s++yl++c++id++f+yYlai+++rles++yd+ng+++kk
  gene674|gene674|rna674|rna674 156 SFVYLCSCVFIDICFVYYLAIFQERLESGDYDENGMPKKK 195
                                    ************************************9986 PP

>> ssDBP  Single-stranded DNA-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   2.6e-05      0.12      17      55 ..     148     187 ..     141     198 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.6e-05
                          ssDBP  17 gkpytmaeayahlpgcdfpq.kfsyycrseqevlptgdye 55 
                                    g  y +a ++ +l  c f +  f yy    qe l +gdy+
  gene674|gene674|rna674|rna674 148 GAWYIIAMSFVYLCSCVFIDiCFVYYLAIFQERLESGDYD 187
                                    77899************97637*****************7 PP

>> YtxH  YtxH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   7.4   0.00096       4.3      50      74 ..       7      31 ..       1      42 [. 0.52

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00096
                           YtxH 50 ekakekaedlkekvkekadelkekv 74
                                   ek+keka+++k++vkek+d++  kv
  gene674|gene674|rna674|rna674  7 EKVKEKAAEVKDTVKEKSDKAEMKV 31
                                   4445555555555555555544443 PP

>> DUF3290  Protein of unknown function (DUF3290)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.6   4.7e-05      0.21      14      63 ..      56     106 ..      51     108 .. 0.81
   2 ?   -2.6   0.6       1.1     5e+03      19      33 ..     152     166 ..     140     180 .. 0.50

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 4.7e-05
                        DUF3290  14 lndllryilil.vlllllivvlilylrnrldtkyRdLsiilllllllllgi 63 
                                    ++d+++ +l+l +++ + + v++   r ++d+k+R++ + ++  ++l+ g+
  gene674|gene674|rna674|rna674  56 FKDIIKCTLFLnAIMTIGLYVIVSATRVNIDSKWREIFLTAAKYMILIFGV 106
                                    6677777766515566678889999*****************999999886 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.1
                        DUF3290  19 ryililvlllllivv 33 
                                     +++++v l+  +++
  gene674|gene674|rna674|rna674 152 IIAMSFVYLCSCVFI 166
                                    333333333333332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2031  (0.11328); expected 358.6 (0.02)
Passed bias filter:                      985  (0.0549389); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.40
# Mc/sec: 1508.44
//
Query:       gene675|gene675|rna675|rna675  [L=389]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.1e-21   74.6  27.6    0.00033   21.2   0.4    7.6  8  Sel1      Sel1 repeat


Domain annotation for each model (and alignments):
>> Sel1  Sel1 repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0      0.59   1.1e+04      21      28 ..      12      22 ..       8      22 .. 0.69
   2 !    7.3   1.8   0.00044       7.9       3      38 .]     100     134 ..      98     134 .. 0.87
   3 !   16.1   0.3   7.7e-07     0.014       4      37 ..     138     169 ..     136     170 .. 0.92
   4 !    5.3   0.1    0.0019        35       1      33 [.     171     202 ..     171     202 .. 0.76
   5 !    4.5   0.0    0.0034        61       5      37 ..     215     248 ..     214     249 .. 0.82
   6 !   21.2   0.4   1.9e-08   0.00033       3      37 ..     252     285 ..     250     286 .. 0.87
   7 !   17.5   0.0   2.8e-07     0.005       2      34 ..     288     320 ..     287     324 .. 0.87
   8 !   17.4   0.2     3e-07    0.0053       2      31 ..     326     353 ..     325     355 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.59
                           Sel1 21 k...DpekAie 28
                                   k   D+e+A++
  gene675|gene675|rna675|rna675 12 KnltDYERAFK 22
                                   44448999986 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.00044
                           Sel1   3 AmyrLGmfylylnGl.gvpkDpekAiewyekAAeqGd 38 
                                    A++ +G   +y+ G  g++ +++kA+e y  A ++++
  gene675|gene675|rna675|rna675 100 AYAYMG--IAYEIGAfGLEINYKKAYENYICALKKNH 134
                                    777888..777****88999**********9999887 PP

  == domain 3  score: 16.1 bits;  conditional E-value: 7.7e-07
                           Sel1   4 myrLGmfylylnGlgvpkDpekAiewyekAAeqG 37 
                                    ++rL+   l+++G    +   kA+ +y+ AA++G
  gene675|gene675|rna675|rna675 138 AFRLA--VLFEKGVHARRSLTKAFAYYRCAAKMG 169
                                    89***..999***98999***************9 PP

  == domain 4  score: 5.3 bits;  conditional E-value: 0.0019
                           Sel1   1 aeAmyrLGmfylylnGlg.vpkDpekAiewyekA 33 
                                    +e m+++Gm++  ++  + + +D + ++++ ++A
  gene675|gene675|rna675|rna675 171 SEGMHAYGMIL--YYSEDeDVRDCRTGFHYIKLA 202
                                    689*****888..666664556999999887776 PP

  == domain 5  score: 4.5 bits;  conditional E-value: 0.0034
                           Sel1   5 yrLGmfylylnGl..g.vpkDpekAiewyekAAeqG 37 
                                    ++LG   +y++G     + kD + A++ y + A++G
  gene675|gene675|rna675|rna675 215 FDLG--RIYETGNttLeIHKDLQYAYKTYVRGASLG 248
                                    89**..777****8754666*****99999999988 PP

  == domain 6  score: 21.2 bits;  conditional E-value: 1.9e-08
                           Sel1   3 AmyrLGmfylylnGlg.vpkDpekAiewyekAAeqG 37 
                                    ++yrLG    y++G     k  ++A+ wy+kAA++G
  gene675|gene675|rna675|rna675 252 CCYRLG--RSYEFGELnRSKSWKEALWWYKKAADLG 285
                                    79****..666***9668889999**********99 PP

  == domain 7  score: 17.5 bits;  conditional E-value: 2.8e-07
                           Sel1   2 eAmyrLGmfylylnGlg..vpkDpekAiewyekAA 34 
                                    +A+++L +fy   +G +  ++ ++e+A++w  kAA
  gene675|gene675|rna675|rna675 288 DAQMALSTFY--ITGIDrvLDVNYEEAYQWTLKAA 320
                                    7*********..***9445888************9 PP

  == domain 8  score: 17.4 bits;  conditional E-value: 3e-07
                           Sel1   2 eAmyrLGmfylylnGlgvpkDpekAiewye 31 
                                     A+y LG +   ++G g+ kDp  A+ wy 
  gene675|gene675|rna675|rna675 326 GAAYSLGGYI--EKGIGIRKDPAHALWWYS 353
                                    59*****666..*****************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (389 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       661  (0.0368676); expected 358.6 (0.02)
Passed bias filter:                      483  (0.0269396); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 2586.78
//
Query:       gene676|gene676|rna676|rna676  [L=176]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.6e-29  100.4   0.6    8.7e-29   99.8   0.6    1.3  1  Fcf1      Fcf1
    6.6e-17   61.9   0.1    9.2e-17   61.4   0.1    1.2  1  PIN_9     PIN like domain
     0.0068   16.3   0.6      0.011   15.7   0.6    1.3  1  DUF3137   Protein of unknown function (DUF3137)
  ------ inclusion threshold ------
      0.035   14.4   0.2      0.057   13.7   0.2    1.4  1  PIN_4     PIN domain
      0.055   12.8   0.0      0.073   12.4   0.0    1.1  1  GCV_T     Aminomethyltransferase folate-binding domain


Domain annotation for each model (and alignments):
>> Fcf1  Fcf1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.8   0.6   2.4e-32   8.7e-29       2      98 ..      77     171 ..      76     172 .. 0.94

  Alignments for each domain:
  == domain 1  score: 99.8 bits;  conditional E-value: 2.4e-32
                                    HCTS-EEEEEEHHHHHHHHHCT..-HHHHHHHT.T.SEEE----SS---HHHHHHHHH-BTB-TT-EEEE-S-HHHHHHH CS
                           Fcf1   2 tLqakvkpliTqCviaeleklgkklkealkiak.t.ferlkCnhkkptsaddClvsvvkkkknkkryivAtqDkdlrrrl 79 
                                    +L ++v +++ +Cv+ae+ek+g k + al +a+    ++l C+h k+t+addC+ ++++++   ++yivAt+D dl+rr+
  gene676|gene676|rna676|rna676  77 VLFSNVIIYVPECVFAEIEKMGLKHRVALMAARkLkHQVLICDH-KGTYADDCIINRITPS---RCYIVATCDADLKRRI 152
                                    78899*****************9999999999953599******.**************65...**************** PP

                                    HTSTT--EEEEE--EEEE- CS
                           Fcf1  80 rkipgvPilyikrsvmvlE 98 
                                    r+ipgvPilyi+ +++ +E
  gene676|gene676|rna676|rna676 153 RRIPGVPILYINARKYAIE 171
                                    ******************9 PP

>> PIN_9  PIN like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.4   0.1   2.6e-20   9.2e-17       1     113 [.      53     163 ..      53     166 .. 0.93

  Alignments for each domain:
  == domain 1  score: 61.4 bits;  conditional E-value: 2.6e-20
                          PIN_9   1 vilDtnaLmipvqfgvdifeelerll.gsvelvvpkavleELerlakagkgkertaakvalsLaerceiveaeeekaDda 79 
                                    +i+Dtn+++  v+ ++di +el r+l  +v + vp+ v++E+e++      k+r a   a++L++++ i ++++ +aDd 
  gene676|gene676|rna676|rna676  53 IIMDTNFILHSVRKKMDIETELMRVLfSNVIIYVPECVFAEIEKM----GLKHRVALMAARKLKHQVLICDHKGTYADDC 128
                                    79************************8888999***********9....668999************************* PP

                          PIN_9  80 ilelakeldaavlvTnDreLkkrlle.kgipvilL 113
                                    i++  +  ++ +++T D++Lk+r+++  g+p++++
  gene676|gene676|rna676|rna676 129 IINRITPSRCYIVATCDADLKRRIRRiPGVPILYI 163
                                    ************************98458888876 PP

>> DUF3137  Protein of unknown function (DUF3137)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.6     3e-06     0.011      24      95 ..      11      85 ..       1      90 [. 0.82

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 3e-06
                        DUF3137 24 pk..kakeskkkkekklekvkledpeFekkFeVysndqvearyiLtpalmerllelrekfkg.kikasfkdnkly 95
                                   pk  +++e+ k++ k+++ ++ e+p+F+++F++  n       i++++++ + ++ ++ ++   +++ f++  +y
  gene676|gene676|rna676|rna676 11 PKvlNISEKSKHTDKETNVIENEEPKFDEYFKINHNLAPPYNIIMDTNFILHSVRKKMDIETeLMRVLFSNVIIY 85
                                   4466667788899999999*******************************9999988888885666777776666 PP

>> PIN_4  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.2   1.6e-05     0.057       1      43 [.      53     103 ..      53     134 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.6e-05
                          PIN_4   1 fVlDTnvlLhdpealksf........keehdvviPitVleELdklKkgsse 43 
                                    +++DTn++Lh+++    +         ++  +++P  V+ E++k+  +++ 
  gene676|gene676|rna676|rna676  53 IIMDTNFILHSVRKKMDIetelmrvlFSNVIIYVPECVFAEIEKMGLKHRV 103
                                    699********98766669999999999999***********987655553 PP

>> GCV_T  Aminomethyltransferase folate-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0     2e-05     0.073      80     111 ..     114     145 ..      96     155 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2e-05
                          GCV_T  80 ytlllnedGgvidDlivarldedefllvvnaa 111
                                    + l+++++G + dD+i+ r+   + ++v++ +
  gene676|gene676|rna676|rna676 114 QVLICDHKGTYADDCIINRITPSRCYIVATCD 145
                                    6789********************99998754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       501  (0.0279436); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1238.55
//
Query:       gene677|gene677|rna677|rna677  [L=415]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.3e-92  310.3   0.8      8e-59  199.1   0.0    2.1  2  Glycolytic  Fructose-bisphosphate aldolase class-I
    0.00081   19.1   0.2     0.0013   18.4   0.2    1.3  1  Sec16_C     Sec23-binding domain of Sec16


Domain annotation for each model (and alignments):
>> Glycolytic  Fructose-bisphosphate aldolase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.6   0.4   1.4e-35   1.3e-31       2     105 ..       6     108 ..       5     154 .. 0.93
   2 !  199.1   0.0   8.9e-63     8e-59     104     326 ..     188     407 ..     178     413 .. 0.96

  Alignments for each domain:
  == domain 1  score: 109.6 bits;  conditional E-value: 1.4e-35
                                    HHHHHHHHT-TT-EEEEE---HHHHHHHHHCTT----HHHHHHHHHHHHT-TT.GGGTEEEEEE-HHHHT-B-TTS-BHH CS
                     Glycolytic   2 LaetakaivapGkGiLaaDestgtigkrlasigventeenrrayrelLfttdkeleeyisGvilfeetlyqkaddgkplv 81 
                                    L+++a ++v+ GkGiLa+Des+ ++gk++++ ++ nt enrr++r++L+++++ +eeyisGvil+ et+ q++d+   +v
  gene677|gene677|rna677|rna677   6 LRKIALELVRDGKGILAIDESSDSMGKKFENFNISNTAENRRRFRNVLIEAEG-IEEYISGVILHMETFDQRNDKNILFV 84 
                                    89***************************************************.************************** PP

                                    HHHHHTT-EEEEE----EEE-TTS CS
                     Glycolytic  82 ellkekgiipGiKvdkgvvplagt 105
                                    e l+++giipGiK+d+g+ ++   
  gene677|gene677|rna677|rna677  85 ESLSSRGIIPGIKLDQGLGKIEYD 108
                                    *****************9888655 PP

  == domain 2  score: 199.1 bits;  conditional E-value: 8.9e-63
                                    TSSS-EEE---TTHHHHHHHHHHTT--EEEEEEEE--BTTBS-HHHHHHHHHHHHHHHHHHHHTT-EEEEEEEE---SS- CS
                     Glycolytic 104 gtegetttqGldglaercaqykkdGarFaKWravlkisektpselaiqenanvLarYasicqenglvpivepeilldGdh 183
                                    +t +e++t+Gl++l++  a+ k + a+FaKWr+v+ki+++tp+  ai +n ++La+Ya++cq + lvpivepe+l +G+ 
  gene677|gene677|rna677|rna677 188 ETYHEQVTRGLEDLEKTLASKKYEKAKFAKWRSVFKITKRTPTFEAIDKNCDILAQYAKLCQLHDLVPIVEPEVLFEGNF 267
                                    57799*************************************************************************** PP

                                    -HHHHHHHHHHHHHHHHHHHHHTT--GGG-EE--B-----TT-S----HHHHHHHHHHHHHTT--TTS-EEEEB-TT--H CS
                     Glycolytic 184 dlercqkvtekvlaavykalsdhhvlleGtllkpnmvtpGaecskkatpeevaeatvtalrrtvPpavpgvvflSGgqse 263
                                    ++e+  +v + vl+   ++l+ h+v l+ +l+k  +vt+G++ +    +e+++++t +a+  t+P  vpg+vflSGg + 
  gene677|gene677|rna677|rna677 268 TIEEHYRVLKYVLSLLSNKLNYHDVDLDSVLFKIGFVTSGKNKA-SVDKESTTRLTSEAILSTIPIKVPGIVFLSGGHTC 346
                                    ****************************************9987.7889999**************************** PP

                                    HHHHHHHHHHHHTS-.-SSEEEEEESHHHHHHHHHHHTT-GGGHHHHHHHHHHHHHHHHHHTT CS
                     Glycolytic 264 eeatvnLnainklekkkpwaltfsygralqasvlkaWkGkkenvkaaqeellkrakanslaal 326
                                    e+a  +L  i  l+   + +ltfsygral + ++k+W+G+++nv+ a++++l+ ++  s+a++
  gene677|gene677|rna677|rna677 347 EDAIDYLRMICGLD--AEINLTFSYGRALTSNAMKKWNGNDNNVEDARKVFLQDCQVSSKASK 407
                                    **********8877..699*****************************************987 PP

>> Sec16_C  Sec23-binding domain of Sec16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.2   1.5e-07    0.0013     219     281 ..     162     226 ..     156     239 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.5e-07
                                    HHHTT-HHHHHHHHHHHHHHHHTS-TTSHHHHH.HHHHHHHHHHHT-XXX......XXX.....XXX CS
                        Sec16_C 219 LaelGlvseAqkYcdaiaaslksltkkspylhptlleqlkdLserLseapke.dksssWl...kisk 281
                                    L+e  +v+eA+kY + i+ s  s+++ ++++h+++++ l+dL++ L++ + e  k  +W    ki+k
  gene677|gene677|rna677|rna677 162 LTEEEKVKEAKKYGEFIKRS--SADNAEETYHEQVTRGLEDLEKTLASKKYEkAKFAKWRsvfKITK 226
                                    89999***************..9999999******************99987788889977777777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (415 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1445  (0.0805957); expected 358.6 (0.02)
Passed bias filter:                      564  (0.0314574); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.43
# Mc/sec: 2930.99
//
Query:       gene678|gene678|rna678|rna678  [L=157]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.2e-07   30.1   0.0    4.5e-07   29.6   0.0    1.2  1  RRM_1       RNA recognition motif. (a.k.a. RRM, RBD, or RNP d
     0.0014   18.6   0.0     0.0031   17.5   0.0    1.5  1  Limkain-b1  Limkain b1


Domain annotation for each model (and alignments):
>> RRM_1  RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6   0.0   5.1e-11   4.5e-07       3      66 ..      79     145 ..      77     148 .. 0.95

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 5.1e-11
                                    EESETTTSSHHHHHHHHHT..TSCEEEEEEEEE.TTTSEEEEEEEEESSHHHHHHHHHHHTTEEETT CS
                          RRM_1   3 VgnLppdvteeeLkelFsk..fGpiksiklvrd.etgkskgfafVeFeskedAekAlealngkklgg 66 
                                    V n+p++++++   ++ sk   +pi +++ v+d e++   g+a+ +F+++e+ +kA++al+g+++g+
  gene678|gene678|rna678|rna678  79 VYNIPRNINKKSFLDVVSKrvNEPIFHCNFVNDrERDVFLGVAYLRFKNEESGRKAMKALDGMQMGD 145
                                    89******************999***************************************99876 PP

>> Limkain-b1  Limkain b1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   3.5e-07    0.0031       5      63 ..      77     140 ..      73     151 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 3.5e-07
                     Limkain-b1   5 lvvsnLPtnrdk..lkkaiknrLrrLsdnc...GGkvlsisgksavlrfanqeaaeralkrlen 63 
                                    l v+n+P n +k    + +++r++     c     +  +++ + a lrf+n+e+ ++a+k l++
  gene678|gene678|rna678|rna678  77 LHVYNIPRNINKksFLDVVSKRVNEPIFHCnfvNDRERDVFLGVAYLRFKNEESGRKAMKALDG 140
                                    7899***9988755678999999885444412268999***********************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       408  (0.0227564); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 1161.93
//
Query:       gene679|gene679|rna679|rna679  [L=245]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.85    9.2   6.3        1.8    8.1   6.3    1.5  1  Ac81      Baculoviridae AC81


Domain annotation for each model (and alignments):
>> Ac81  Baculoviridae AC81
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   6.3   9.9e-05       1.8     119     171 ..      10      60 ..       4      64 .. 0.66

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 9.9e-05
                           Ac81 119 eklikgvsvqtvlililiavlllaiikfsafllLfilfllviLlifnsvincr 171
                                    ek+ik ++ q +li i+i+vl ++i + +  +lL ++fl +++l+f+ +  c+
  gene679|gene679|rna679|rna679  10 EKIIKSTYYQFILI-IIIIVLTITI-NKYFKYLLGLVFLNMSILFFQFIGACQ 60 
                                    56777788775554.4455566666.555555565668888888888777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1329  (0.0741257); expected 358.6 (0.02)
Passed bias filter:                      702  (0.0391544); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.39
# Mc/sec: 1862.26
//
Query:       gene68|gene68|rna68|rna68  [L=145]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      9e-11   41.7   0.4    4.4e-10   39.5   0.2    1.9  2  MutL_C    MutL C terminal dimerisation domain


Domain annotation for each model (and alignments):
>> MutL_C  MutL C terminal dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.5   0.2   2.4e-14   4.4e-10       4      40 ..      43      79 ..      41      90 .. 0.92
   2 ?    0.3   0.0      0.03   5.4e+02     130     147 .]      92     109 ..      82     109 .. 0.84

  Alignments for each domain:
  == domain 1  score: 39.5 bits;  conditional E-value: 2.4e-14
                               EEEEEETTTEEEEEETTEEEEEEHHHHHHHHHHHHHH CS
                     MutL_C  4 kalgqvhgtyilaenedglvlvDqhaAherilyeklk 40
                               +++gq+++ +i+++ne++++++Dqha heri  ek+ 
  gene68|gene68|rna68|rna68 43 RVIGQFNNEFIIIKNEHNVFIIDQHAIHERIRLEKYV 79
                               69********************************986 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.03
                                HHHHHHCTTSSSSSS--- CS
                     MutL_C 130 ellatmachssvkagrrl 147
                                e+l++ ac++++k ++rl
  gene68|gene68|rna68|rna68  92 EALKEKACKGAIKFKDRL 109
                                678999*****9987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       552  (0.0307881); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.22s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 1156.61
//
Query:       gene680|gene680|rna680|rna680  [L=793]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
     0.0012   17.6   7.1     0.0075   14.9   0.1    3.3  3  Adaptin_N  Adaptin N terminal region


Domain annotation for each model (and alignments):
>> Adaptin_N  Adaptin N terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.2     0.014   2.5e+02      47     122 ..      50     115 ..       6     119 .. 0.64
   2 !   14.9   0.1   4.2e-07    0.0075     231     375 ..     223     358 ..     170     382 .. 0.82
   3 !    4.6   0.1   0.00054       9.6     453     510 ..     468     523 ..     452     525 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.014
                                    HHCCCCSS-CHHHHHHHHHHHHHCTTSCCHHCCCCHHHHHHCCSSSHHHHHHHHHHHCCC--CCCHHHHHHHHHHH CS
                      Adaptin_N  47 vvklvaskdfelKrlvYlylellaeesedlalLvtnslqkDlkdpnqlirglALrvLssirvpelaedlapaikkl 122
                                     ++ ++ ++  + +lvY+ l ll+  +     +++n + k           l Lr L +i  +e++ d++++++++
  gene680|gene680|rna680|rna680  50 LLRSFSLNNNFVNQLVYVCLNLLLPFDNS--FVAINIIDK--------KEELGLRLLIKIVPEEMVGDFMKYVMEC 115
                                    55555555555555555555555555544..444554443........3456788888888888888888888876 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 4.2e-07
                                    HHHHHHCGGCG..CSSCHHHHHHHHHCCHCCCCSTHHHCCHHCHHHHHHSSCCTCHHHHHCHHHHHHHHXXTTTTTTTCC CS
                      Adaptin_N 231 ellesllnllq..ssnnaVlletvnlivelapknelivlavnaLvrllsskdenlryvaLrtllkivkkepkavqhldlk 308
                                    ++ ++l  +l+   s++    e+ + + ++++  + +++a++  + ll s+d  +r+ +Lr+l  ++++  ++v  l+  
  gene680|gene680|rna680|rna680 223 RTTNNLRDHLNvkISGEICFTEALRKVSYMKDPVPFLSQAITNAGILLNSNDAVVRMSTLRSLDALSQNYARKVAVLNPS 302
                                    466677777777788888888999999999*****9**********************************8888877777 PP

                                    CCSXXTTSXHHHHHHHHHHHCCCXXTTTHHHHHHHHHHHTTSSXXHHHHHHHHHHHHHHHHHSCCHH CS
                      Adaptin_N 309 ifllktdddvsirlkaldlllklvdesNvkeivkeLkkyvkevadedfksklvkaIgrlaekfatda 375
                                    +  ++  dd s     l +ll+++d++ +++i ++ +++     d +    +vka g++a+k  +++
  gene680|gene680|rna680|rna680 303 LIKIN--DDHS-----LRILLRTGDSNTIERIANTDLTQY----DDEKALLIVKAFGTIAQKNGKEE 358
                                    66666..7766.....6799************98744444....34467889999999999984443 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.00054
                                    HHHHHCTTTTTTTSXHHHHHHHHHHHHHHHHCXGCC.THXHHHHHHHHHHHXXSHHHH CS
                      Adaptin_N 453 sdllrslaekfvlesekvklqiltalvKlyltspdketqekliqlvlslatssdlevr 510
                                    +++l  ++++++le+e+v+++++    +l   s  +e++++l++++++  ++  ++vr
  gene680|gene680|rna680|rna680 468 KKYLVAVYNRLILENEIVRNNAMACVNRLTGKSLFEENEDELLKYFFTNRKD--VDVR 523
                                    578999****************999999998888889999******998776..5655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (793 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       709  (0.0395449); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.66u 0.31s 00:00:00.97 Elapsed: 00:00:00.46
# Mc/sec: 5213.78
//
Query:       gene681|gene681|rna681|rna681  [L=64]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
       0.26   12.1   1.8       0.51   11.2   1.8    1.6  1  Vasculin    Vascular protein family Vasculin-like 1


Domain annotation for each model (and alignments):
>> Vasculin  Vascular protein family Vasculin-like 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   1.8   2.9e-05      0.51      32      61 ..      30      59 ..       5      64 .] 0.64

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 2.9e-05
                       Vasculin 32 plTedElkEFkskseqlkknglgkngfllq 61
                                    + e+ ++E +++++++++ng++ ng++ +
  gene681|gene681|rna681|rna681 30 RIRENRIRENRIRENRIRENGIKENGMKEK 59
                                   355666666667777777777777776654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (64 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       387  (0.0215851); expected 358.6 (0.02)
Passed bias filter:                      182  (0.0101512); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 463.80
//
Query:       gene682|gene682|rna682|rna682  [L=102]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       506  (0.0282224); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.33u 0.26s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 810.95
//
Query:       gene683|gene683|rna683|rna683  [L=64]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (64 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1569  (0.0875119); expected 358.6 (0.02)
Passed bias filter:                      955  (0.0532657); expected 358.6 (0.02)
Passed Vit filter:                        91  (0.00507558); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 449.77
//
Query:       gene684|gene684|rna684|rna684  [L=163]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.022   14.2   0.2      0.027   13.9   0.2    1.3  1  Rib_hydrolayse  ADP-ribosyl cyclase


Domain annotation for each model (and alignments):
>> Rib_hydrolayse  ADP-ribosyl cyclase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.2   1.5e-06     0.027      64     112 ..      82     128 ..      27     144 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.5e-06
                                    -STT-EE--------------------GGGSHHHHHCTT-----BTTBS CS
                 Rib_hydrolayse  64 pcdkslfWsktkdlvhsyteatkelltledtllGyiadelsWCgqeess 112
                                     +++  fWsk   ++ +y++  ++ + l + l  + +d+l+WC +  ++
  gene684|gene684|rna684|rna684  82 YKSEDAFWSKRGVVIGKYAHIYDSWF-L-ESLSSFTVDDLDWCTDAMEK 128
                                    345678*************9988765.4.68************996655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       877  (0.0489152); expected 358.6 (0.02)
Passed bias filter:                      537  (0.0299515); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.36
# Mc/sec: 1342.86
//
Query:       gene685|gene685|rna685|rna685  [L=40]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (40 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       298  (0.0166211); expected 358.6 (0.02)
Passed bias filter:                      188  (0.0104858); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.25s 00:00:00.59 Elapsed: 00:00:00.40
# Mc/sec: 299.19
//
Query:       gene686|gene686|rna686|rna686  [L=973]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (973 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       693  (0.0386525); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.68u 0.28s 00:00:00.96 Elapsed: 00:00:00.47
# Mc/sec: 6182.55
//
Query:       gene687|gene687|rna687|rna687  [L=281]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      0.001   19.3   6.5      0.005   17.1   0.4    2.4  2  DUF5082         Domain of unknown function (DUF5082)
     0.0013   19.2  12.1       0.13   12.7   7.0    2.8  2  ZapB            Cell division protein ZapB
  ------ inclusion threshold ------
      0.012   16.2  16.2      0.034   14.7   1.7    2.3  2  APG6_N          Apg6 coiled-coil region
      0.044   12.6   7.6       0.48    9.1   0.3    2.1  2  Tektin          Tektin family
      0.044   13.8   9.0       0.21   11.7   0.7    3.2  3  BRE1            BRE1 E3 ubiquitin ligase
       0.05   14.1   4.0       0.29   11.6   1.7    2.3  2  Spectrin        Spectrin repeat
        0.1   11.4   0.2       0.16   10.8   0.2    1.2  1  FAM91_C         FAM91 C-terminus
       0.17   10.4   0.2        0.2   10.1   0.2    1.1  1  FUSC            Fusaric acid resistance protein family
       0.23   10.8  10.4       0.36   10.1   0.5    2.2  1  GAS             Growth-arrest specific micro-tubule binding
       0.66   10.7   7.8          2    9.2   0.4    2.9  3  Occludin_ELL    Occludin homology domain
       0.94    8.0   5.4        1.3    7.5   5.4    1.3  1  FapA            Flagellar Assembly Protein A
        1.7    8.5   9.7        5.6    6.8   1.3    3.2  3  DivIC           Septum formation initiator
        1.9    7.7   5.7        1.7    7.9   4.4    1.5  1  CorA            CorA-like Mg2+ transporter protein
        3.7    7.6  14.9       0.47   10.5   6.4    2.4  2  CENP-F_leu_zip  Leucine-rich repeats of kinetochore protein C
        4.8    7.9  11.6         12    6.5   4.6    2.6  3  YabA            Initiation control protein YabA


Domain annotation for each model (and alignments):
>> DUF5082  Domain of unknown function (DUF5082)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.4   4.2e-06     0.005      21     119 ..       8     105 ..       3     109 .. 0.91
   2 ?    4.8   0.9     0.028        33       3      42 ..     125     164 ..     124     185 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 4.2e-06
                        DUF5082  21 aleekIerLkeaktklsdekeslkqkkkklekplnssesWkGkeennydgirsnlessyqtyvdkldelidaieeEIerL 100
                                     +ee+I+r  +   + s++ke++++ k +l + + ++     + +++++ ++  + ++ ++  ++++e+  a+ eEI+ L
  gene687|gene687|rna687|rna687   8 ITEEDIARFSTIEHEFSSVKEHFSNYKFALIERESKM-LFLESIKDDVQVDYLPIFKESKKRLEETKEVGVALGEEIKAL 86 
                                    589***************************9999999.6777889999999**9999999999***************** PP

                        DUF5082 101 enqiseaqgvldtlqsqln 119
                                     ++++e++++++++  + +
  gene687|gene687|rna687|rna687  87 SMKNYELKRSISSIVVEYD 105
                                    ************9876655 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.028
                        DUF5082   3 tkisklqaqiaelrseiaaleekIerLkeaktklsdekes 42 
                                    ++i++l++++  ++++++++   +erL+e  ++l++e e+
  gene687|gene687|rna687|rna687 125 EEINRLEREYNTASETAKGMVAELERLREEGEALEAERER 164
                                    5899999999999999999999999999888888777665 PP

>> ZapB  Cell division protein ZapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.3    0.0023       2.8      18      53 ..      81     109 ..      67     125 .. 0.61
   2 !   12.7   7.0   0.00011      0.13       4      60 ..     125     186 ..     122     187 .. 0.91

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0023
                           ZapB  18 dtitlLqmeieeLkeeneelkeenreleeeneqlke 53 
                                    ++i++L+m+++eLk+           +  e ++l+e
  gene687|gene687|rna687|rna687  81 EEIKALSMKNYELKRSI-------SSIVVEYDALEE 109
                                    45555555555555555.......444444444433 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00011
                           ZapB   4 elLeqLEskiqkaidtitlLqmeieeLkeeneelkeenrele.....eeneqlkeereawqe 60 
                                    e  ++LE  +++a +t + +  e+e+L+ee e+l+ e ++       e +e+l+  r+ w +
  gene687|gene687|rna687|rna687 125 EEINRLEREYNTASETAKGMVAELERLREEGEALEAERERSYvthlrERVEELRRKRKRWSR 186
                                    77899******************************998877688888***********9975 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   1.7   2.8e-05     0.034      25     109 ..      40     122 ..       6     124 .. 0.81
   2 ?    6.7   7.5    0.0085        10      47     102 ..     125     180 ..     122     190 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.8e-05
                         APG6_N  25 rdaYeeflkklkkekkeeekqdeeleeleeeleklekeeeelleeLkelekereeleaelaaleeelealeeeeerfwre 104
                                    r++ + fl+ +k++ +  +      +e++++le++++   +l ee+k+l  ++ el++ ++++  e +alee ++rf+++
  gene687|gene687|rna687|rna687  40 RESKMLFLESIKDDVQV-D-YLPIFKESKKRLEETKEVGVALGEEIKALSMKNYELKRSISSIVVEYDALEELKKRFLES 117
                                    44444555555555222.2.45566789999************************************************* PP

                         APG6_N 105 ynelq 109
                                     ne++
  gene687|gene687|rna687|rna687 118 GNEFN 122
                                    *9985 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0085
                         APG6_N  47 eeleeleeeleklekeeeelleeLkelekereeleaelaaleeelealeeeeerfw 102
                                    ee+++le+e+ + +++ + +++eL++l +e e+leae++    ++ +   ee r  
  gene687|gene687|rna687|rna687 125 EEINRLEREYNTASETAKGMVAELERLREEGEALEAERERSYVTHLRERVEELRRK 180
                                    57777788888888888888888888888888888877766665555555555554 PP

>> Tektin  Tektin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.3   0.00041      0.48      37      97 ..      68     128 ..      53     131 .. 0.87
   2 ?    5.9   3.4    0.0039       4.7       9      60 ..     131     182 ..     124     188 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00041
                         Tektin  37 tkktqadsnkrLeeRiediefwkeeLekeleelkeeieaLeeekrrlekalealeeplhia 97 
                                      ++++++   L+e i+ ++    eL+++++ ++ e +aLee k+r  ++ ++ ++  +i+
  gene687|gene687|rna687|rna687  68 RLEETKEVGVALGEEIKALSMKNYELKRSISSIVVEYDALEELKKRFLESGNEFNKAEEIN 128
                                    44557899999***********************************999888888887776 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0039
                         Tektin   9 lkeaeaerneaerlrnesrrlideteektkktqadsnkrLeeRiediefwke 60 
                                     +e ++  + a+ + +e +rl++e e+   ++++   ++L+eR+e++++ ++
  gene687|gene687|rna687|rna687 131 EREYNTASETAKGMVAELERLREEGEALEAERERSYVTHLRERVEELRRKRK 182
                                    56778888999************************************98776 PP

>> BRE1  BRE1 E3 ubiquitin ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.1      0.16   1.9e+02       7      62 ..      18      73 ..      14      78 .. 0.87
   2 ?    4.2   0.3     0.038        46       3      36 ..      81     114 ..      79     125 .. 0.88
   3 ?   11.7   0.7   0.00018      0.21       3      42 ..     125     164 ..     123     167 .. 0.94

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.16
                           BRE1  7 klekafeelseqlskkvkeltileekklrleaekakadqkyfaamrskdalenelk 62
                                    +e++f  ++e  s+ ++ l   e+k+l le+ k+  +  y  + ++ +++  e k
  gene687|gene687|rna687|rna687 18 TIEHEFSSVKEHFSNYKFALIERESKMLFLESIKDDVQVDYLPIFKESKKRLEETK 73
                                   68999999**********************99999988888888888888877776 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.038
                           BRE1   3 kELvklekafeelseqlskkvkeltileekklrl 36 
                                     E++ l+    el++++s+ v e+ +lee k+r 
  gene687|gene687|rna687|rna687  81 EEIKALSMKNYELKRSISSIVVEYDALEELKKRF 114
                                    69999*************************9997 PP

  == domain 3  score: 11.7 bits;  conditional E-value: 0.00018
                           BRE1   3 kELvklekafeelseqlskkvkeltileekklrleaekak 42 
                                     E+ +le++++ +se+++ +v+el++l e+   leae ++
  gene687|gene687|rna687|rna687 125 EEINRLEREYNTASETAKGMVAELERLREEGEALEAERER 164
                                    69**********************************9875 PP

>> Spectrin  Spectrin repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.2     0.016        19      34      78 ..      81     125 ..      62     134 .. 0.81
   2 ?   11.6   1.7   0.00024      0.29      21      91 ..     112     183 ..     111     192 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.016
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTHTTHHHH CS
                       Spectrin  34 eevqallkkhkaleaelaaqqervkalnelaeklldeghsaseei 78 
                                    ee++al  k  +l++ +++   + +al+el++++l++g + +++ 
  gene687|gene687|rna687|rna687  81 EEIKALSMKNYELKRSISSIVVEYDALEELKKRFLESGNEFNKAE 125
                                    78999999999***********************99997777554 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00024
                                    HHHHCCSSCSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.HHTTHTTHHHHHHHHHHHHHHHHH CS
                       Spectrin  21 eellssedlgkdleevqallkkhkaleaelaaqqervkalnelaekl.ldeghsaseeieerleelnerWee 91 
                                    +++l+s +  ++ ee+ +l++++ +  ++ + +  ++++l e +e+l ++++ s   +++er+eel+++ + 
  gene687|gene687|rna687|rna687 112 KRFLESGNEFNKAEEINRLEREYNTASETAKGMVAELERLREEGEALeAERERSYVTHLRERVEELRRKRKR 183
                                    5677777778999**********************************888889999**********998765 PP

>> FAM91_C  FAM91 C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.2   0.00013      0.16      42      86 ..     139     183 ..     136     204 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00013
                        FAM91_C  42 esldsflaeLdkvkeeeaeG.eakrYfehaltLretikfLrenkel 86 
                                    e+ + ++aeL++++e e e  ea+r  ++++ Lre ++ Lr++++ 
  gene687|gene687|rna687|rna687 139 ETAKGMVAELERLRE-EGEAlEAERERSYVTHLRERVEELRRKRKR 183
                                    6778899******99.66667********************99865 PP

>> FUSC  Fusaric acid resistance protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.2   0.00017       0.2     241     302 ..     126     192 ..     103     218 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00017
                           FUSC 241 llarlraeeaaavpelaallaelaal...eaaaaaealeaalaalrarlralrrale..adadtaal 302
                                    + +rl +e ++a ++ + ++ael++l    +a  ae+++ ++++lr+r+++lrr ++   + + +++
  gene687|gene687|rna687|rna687 126 EINRLEREYNTASETAKGMVAELERLreeGEALEAERERSYVTHLRERVEELRRKRKrwSRVEYDRM 192
                                    45566666666666677777777777776777999*******************9996633333333 PP

>> GAS  Growth-arrest specific micro-tubule binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.5    0.0003      0.36      80     127 ..      62     109 ..      57     122 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0003
                            GAS  80 yekdkqslknlkarlkelekelkdlkwehevleqrfekvekerdelyk 127
                                    +++ k++l+++k+    l +e+k+l++++  l+  ++++  e+d+l++
  gene687|gene687|rna687|rna687  62 FKESKKRLEETKEVGVALGEEIKALSMKNYELKRSISSIVVEYDALEE 109
                                    567899999999999999999999999999999999999999998876 PP

>> Occludin_ELL  Occludin homology domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.3      0.49   5.9e+02      22      69 ..      14      61 ..       6      75 .. 0.67
   2 ?    9.2   0.4    0.0017         2      22      82 ..      60     121 ..      48     126 .. 0.90
   3 ?    6.1   2.7     0.016        19      20      95 ..     103     180 ..     103     186 .. 0.66

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.49
                   Occludin_ELL 22 keYkelhaeleevskkfseLerelkelkegskeykkieeeilqeykkl 69
                                   ++++++++e+++v+++fs+ +  l e + +    ++i+++++ +y  +
  gene687|gene687|rna687|rna687 14 ARFSTIEHEFSSVKEHFSNYKFALIERESKMLFLESIKDDVQVDYLPI 61
                                   566777788888888888888777777777767777777777777665 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0017
                   Occludin_ELL  22 keYkelhaeleevskkfseLerelkelkegskeykkieeeilqeykklkk.dpeyqekkkrc 82 
                                    + +ke +++lee+++    L +e+k+l+ ++ e k+ +++i+ ey  l++ +++++e  +++
  gene687|gene687|rna687|rna687  60 PIFKESKKRLEETKEVGVALGEEIKALSMKNYELKRSISSIVVEYDALEElKKRFLESGNEF 121
                                    678999******************************************99999999887766 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.016
                   Occludin_ELL  20 eYkeYkelhaeleevskkfseLerelkelkegskeykkieeeilqeykklkk...dpeyqekkkrceyLkekLshiKkl 95 
                                    eY+   el++++ e  ++f++ e e+++l+++ ++ +++++ ++ e+++l++     e  +++  +++L+e+ + ++++
  gene687|gene687|rna687|rna687 103 EYDALEELKKRFLESGNEFNKAE-EINRLEREYNTASETAKGMVAELERLREegeALEAERERSYVTHLRERVEELRRK 180
                                    58888899999999999998865.6777878778777777888888888777311223333444456666666666655 PP

>> FapA  Flagellar Assembly Protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   5.4    0.0011       1.3     312     411 ..      71     165 ..      25     182 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0011
                           FapA 312 kakklGselgtkteievgldepelkeklkeleeeleeleeeleklkkkikklpklkaekqlesekkeqlkklletkeklk 391
                                    ++k++G  lg++++    +++ elk++++ +  e+ +lee  ++  ++ ++++k ++      + + +++ + et + ++
  gene687|gene687|rna687|rna687  71 ETKEVGVALGEEIKALS-MKNYELKRSISSIVVEYDALEELKKRFLESGNEFNKAEEI----NRLEREYNTASETAKGMV 145
                                    45567777777666554.5558888888888888888877777766665666653222....234556666666666666 PP

                           FapA 392 eeleeleeelkelkeelesk 411
                                     ele l+ee ++l++e e++
  gene687|gene687|rna687|rna687 146 AELERLREEGEALEAERERS 165
                                    66666666666666666655 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.2     0.025        30      13      59 ..      63     109 ..      58     115 .. 0.78
   2 ?    6.8   1.3    0.0047       5.6      23      59 ..     124     160 ..     119     168 .. 0.68
   3 ?    0.6   0.1      0.41   4.9e+02      36      56 ..     170     189 ..     166     193 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.025
                                    XXXXXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-XXXXXXXXX CS
                          DivIC  13 kkgllaykqlkqeiaalqaelaklkaeneeLeaevkdLksdedyiee 59 
                                    k +  ++ ++k+  +al +e+++l+ +n eL++ ++    ++d++ee
  gene687|gene687|rna687|rna687  63 KESKKRLEETKEVGVALGEEIKALSMKNYELKRSISSIVVEYDALEE 109
                                    55566666777777788899999999999999999998778888887 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0047
                                    HHHHHHHHHHHHHHHHHHHHHHHHHCC-XXXXXXXXX CS
                          DivIC  23 kqeiaalqaelaklkaeneeLeaevkdLksdedyiee 59 
                                     +ei++l++e+++ +++ + + ae+++L+ + +++e+
  gene687|gene687|rna687|rna687 124 AEEINRLEREYNTASETAKGMVAELERLREEGEALEA 160
                                    5677777777777777777777777777665555553 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.41
                                    HHHHHHHHHHHHCC-XXXXXX CS
                          DivIC  36 lkaeneeLeaevkdLksdedy 56 
                                    l+++ eeL ++ k++ s  +y
  gene687|gene687|rna687|rna687 170 LRERVEELRRKRKRW-SRVEY 189
                                    899999999999999.56555 PP

>> CorA  CorA-like Mg2+ transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   4.4    0.0014       1.7     103     213 ..      94     208 ..      74     210 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0014
                           CorA 103 gkpkspgellyrlldeivdrlfellekle..eeldeledel..edstkkeilrelaqlrrrlvkl.....rralapnrev 173
                                    ++  s+  + y  l+e+ +r++e   + +  ee+++le+e    ++t k+++ el +lr++   l     r++++++re 
  gene687|gene687|rna687|rna687  94 KRSISSIVVEYDALEELKKRFLESGNEFNkaEEINRLEREYntASETAKGMVAELERLREEGEALeaereRSYVTHLRER 173
                                    555566666688899999999999999873369********99999*************88777777888********** PP

                           CorA 174 lkrllakaddkllddedkeylrdlldelerllemlealre 213
                                    +++l +    k++++ +   ++++l+++ r ++m+ ++ e
  gene687|gene687|rna687|rna687 174 VEELRR--KRKRWSRVE---YDRMLIDAYRWYDMMISVLE 208
                                    *77777..666666666...99999999999998877655 PP

>> CENP-F_leu_zip  Leucine-rich repeats of kinetochore protein Cenp-F/LEK1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   1.4       0.3   3.6e+02      47      86 ..      69     108 ..      19     116 .. 0.82
   2 ?   10.5   6.4    0.0004      0.47      10      82 ..     125     181 ..     119     187 .. 0.51

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.3
                 CENP-F_leu_zip  47 aEtskaevetlkeeieelaeelreleldLvalrsekeeLe 86 
                                     E+ k+   +l eei+ l+ +  el+  ++++  e + Le
  gene687|gene687|rna687|rna687  69 LEETKEVGVALGEEIKALSMKNYELKRSISSIVVEYDALE 108
                                    4666777777888888888888888888888888887774 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.0004
                 CENP-F_leu_zip  10 ekLKeserkadsLkdkvenLerelemseenqekvileaEtskaevetlkeeieelaeelreleldLvalrsek 82 
                                    e+              +++Lere +++ e    ++ e E  ++e e+l++e e+  +  ++l+  +++lr+ +
  gene687|gene687|rna687|rna687 125 EE--------------INRLEREYNTASETAKGMVAELERLREEGEALEAERER--SYVTHLRERVEELRRKR 181
                                    44..............55555555555555555555555555555555555443..44444444444444433 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0         6   7.1e+03       8      31 ..      14      37 ..       9      51 .. 0.65
   2 ?    4.9   0.5     0.034        40      19      53 ..      64     102 ..      61     123 .. 0.73
   3 ?    6.5   4.6      0.01        12       8      60 ..     125     182 ..     117     198 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 6
                                   HHHHHHHHHHHHHHHHHHHHHHHH CS
                           YabA  8 dkleeleeqleelleeleelkeel 31
                                   ++++++e+++++++e++++ k +l
  gene687|gene687|rna687|rna687 14 ARFSTIEHEFSSVKEHFSNYKFAL 37
                                   556666777766666666665544 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.034
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH....X CS
                           YabA  19 elleeleelkeelaelleenaeLeleneklrerl....e 53 
                                    e +++lee ke  ++l ee ++L++ n +l++ +     
  gene687|gene687|rna687|rna687  64 ESKKRLEETKEVGVALGEEIKALSMKNYELKRSIssivV 102
                                    667889999999999999999999999999998844431 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.01
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.....HHHHHHHHXXXXXXXX CS
                           YabA   8 dkleeleeqleelleeleelkeelaelleenaeLele.....neklrerleeeekkek 60 
                                    +++++le++ ++ +e+ + + +el++l ee ++Le+e      ++lrer+ee ++k+k
  gene687|gene687|rna687|rna687 125 EEINRLEREYNTASETAKGMVAELERLREEGEALEAErersyVTHLRERVEELRRKRK 182
                                    78999********************************777777799999965544443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1176  (0.0655921); expected 358.6 (0.02)
Passed bias filter:                      539  (0.030063); expected 358.6 (0.02)
Passed Vit filter:                        78  (0.00435049); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.48
# Mc/sec: 1766.06
//
Query:       gene688|gene688|rna688|rna688  [L=521]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-28   99.9  24.2    2.7e-18   66.1   8.8    2.4  2  Mg_trans_NIPA  Magnesium transporter NIPA


Domain annotation for each model (and alignments):
>> Mg_trans_NIPA  Magnesium transporter NIPA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.1   7.4   2.5e-14   4.5e-10       5     161 ..     185     332 ..     182     339 .. 0.90
   2 !   66.1   8.8   1.5e-22   2.7e-18     170     290 ..     370     490 ..     358     495 .. 0.95

  Alignments for each domain:
  == domain 1  score: 39.1 bits;  conditional E-value: 2.5e-14
                  Mg_trans_NIPA   5 iGvlLavssslfigssfilkkkgllrlarkgevrageGGyaylkevlWwaGlltmavGeaanfaayafaPatLvtPLGal 84 
                                     Gv L+v ++l i   ++l+k+++       ++r        +   +++ G++  ++G ++ f +y+f   +L++ LGa+
  gene688|gene688|rna688|rna688 185 LGVYLSVQGNLCINVGLNLQKRSYHDPYL--RIRG-------VSVSMFYVGVVVYVAGKVSGFMSYIFGNQSLLASLGAV 255
                                    79********************9875433..2454.......5678999******************************* PP

                  Mg_trans_NIPA  85 svivsavlasllLkekLkllgllGcllailGstvlvihaPkeeeieslkevadllvdpaflvyvilvvvvvlvlily 161
                                     +i  +v+a l+  e +   + + ++  + Gs v+++ + + +++ +l e+ ++ ++ + lv+  ++v +vl+l   
  gene688|gene688|rna688|rna688 256 GLIANSVFAPLINSEVFTWKDFMAIVFVLTGSSVILMNSGRSHKTFTLCELLKMYQKKETLVWFGVIVLLVLFLFTL 332
                                    **********************************************************9999998888888887655 PP

  == domain 2  score: 66.1 bits;  conditional E-value: 1.5e-22
                  Mg_trans_NIPA 170 nilvyitlcsllgsltvisvkalgiaikltlaGkaqlkyalawilllvlvicvvlqinyLnkaldifntsivtPvyyvlf 249
                                     +++y++l  +++s+t +  k+ g ++ +tl G +q+ y +++++   +v +  lqi ++nkal  +++ +v P+++v++
  gene688|gene688|rna688|rna688 370 MVVLYVGLSGIIASFTTLFAKSFGEMVDQTLLGDNQFLYGITYLFFTNIVLFTGLQIFWMNKALRHYDALLVIPLFFVVW 449
                                    5789**************************************************************************** PP

                  Mg_trans_NIPA 250 ttlvivasailfkefleasvddvlgelsGfllvllgvfllh 290
                                    t + ++++ i f++f   ++d+  g + G+++++ g f+l 
  gene688|gene688|rna688|rna688 450 TLFSVLTAGIYFQDFEYYTLDQFKGFVYGLVIIIAGSFFLV 490
                                    ************************************98764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (521 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1164  (0.0649228); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.78u 0.32s 00:00:01.10 Elapsed: 00:00:00.57
# Mc/sec: 2741.28
//
Query:       gene689|gene689|rna689|rna689  [L=48]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (48 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       313  (0.0174578); expected 358.6 (0.02)
Passed bias filter:                      229  (0.0127726); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.50u 0.34s 00:00:00.84 Elapsed: 00:00:00.54
# Mc/sec: 265.16
//
Query:       gene69|gene69|rna69|rna69  [L=244]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.5e-08   33.8   1.6      8e-08   32.7   1.1    1.9  1  GLTSCR1   Conserved region of unknown function on GLTSCR prot
  ------ inclusion threshold ------
          1   10.3   5.3         11    7.0   0.0    3.3  3  Pup       Pup-like protein


Domain annotation for each model (and alignments):
>> GLTSCR1  Conserved region of unknown function on GLTSCR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.7   1.1   8.9e-12     8e-08       1      65 [.     104     169 ..     104     196 .. 0.74

  Alignments for each domain:
  == domain 1  score: 32.7 bits;  conditional E-value: 8.9e-12
                    GLTSCR1   1 dqkavlnpdvktPFasveDavkRLlPYHvfqepkedeedle..kadeefekvaeellkrfqklenkf 65 
                                dq + ++pd++ PF++ +++++ LlPYH+++ p  d+  +   ++ +++ ++++e+++r+ + +  +
  gene69|gene69|rna69|rna69 104 DQYQLTHPDIR-PFENTKHVYEYLLPYHIYNAPSYDDLLFRyaNDNDKLMDEIKEVTQRIGRTLHDY 169
                                8999*****97.***********************99877744334555555555555554444443 PP

>> Pup  Pup-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.4      0.36   3.2e+03      14      21 ..      16      22 ..       4      45 .. 0.37
   2 ?    7.0   0.0    0.0013        11       4      44 ..      52      91 ..      49      98 .. 0.76
   3 ?    3.9   0.1     0.011     1e+02      37      50 ..     145     158 ..     138     161 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.36
                        Pup 14 eeveeaea 21
                               e+v + + 
  gene69|gene69|rna69|rna69 16 EKV-DGPS 22
                               222.2222 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0013
                        Pup  4 ggqeqasrskeeveeaeaeaeassevkerkeelsedvDdlL 44
                               +g+++++++k+ v+e +a+a   s+  e++++l +++D ++
  gene69|gene69|rna69|rna69 52 AGRSHSGSRKNMVDEHDADA-FLSDRTEQSASLVDNIDHII 91
                               68899999999999999988.55566667777777777765 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.011
                        Pup  37 sedvDdlLDeIDev 50 
                                ++d D l+DeI ev
  gene69|gene69|rna69|rna69 145 ANDNDKLMDEIKEV 158
                                5799*******998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (244 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1289  (0.0718947); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1694.04
//
Query:       gene690|gene690|rna690|rna690  [L=613]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.24   11.8   6.2       0.27   11.7   4.6    1.8  2  DUF4171   Domain of unknown function (DUF4171)
        2.6    8.3   8.0        4.9    7.5   0.1    3.1  3  DUF4064   Protein of unknown function (DUF4064)


Domain annotation for each model (and alignments):
>> DUF4171  Domain of unknown function (DUF4171)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       0.4   3.5e+03     114     126 ..      74      86 ..      62      95 .. 0.76
   2 ?   11.7   4.6     3e-05      0.27      19      89 ..     225     295 ..     220     316 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.4
                        DUF4171 114 gvaGhseeaavkk 126
                                      +Ghs+++a+kk
  gene690|gene690|rna690|rna690  74 EESGHSKKSAIKK 86 
                                    5679999999998 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 3e-05
                        DUF4171  19 kpskklheKpsypsvsssssSksrkrehkkklssssseskkddsssskskkfkpgavktepLtLreadGLk 89 
                                    +    + +K  +++    ++Sk+ k  h+k      s+  k  s+s   k fk ++v++ +  Lr+  GL 
  gene690|gene690|rna690|rna690 225 TTVHSKDDKTGHSKDDKTGHSKDDKTVHSKDDKTGHSKDDKTGSTSVNRKCFKALVVRDSAAELRNISGLS 295
                                    455566788899999999************9999999999999***********************99995 PP

>> DUF4064  Protein of unknown function (DUF4064)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.1   0.00055       4.9      12      87 ..     343     425 ..     339     429 .. 0.85
   2 ?   -2.4   0.8      0.64   5.8e+03      17      29 ..     458     470 ..     451     487 .. 0.45
   3 ?    4.6   0.1    0.0044        39      56      85 ..     576     605 ..     556     610 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.00055
                        DUF4064  12 Ggilgillglllllflfllssgefsqeltee.......qalsgedasavleflstllivlgvialiaivlgivgalllkk 84 
                                    ++ + ++l+++++++l+ +ss++f+ el+ +         + ++ ++a+le   ++  + + ++li++++ +v  + l++
  gene690|gene690|rna690|rna690 343 AFQVFLILIIFVGVALLKNSSDQFKIELLVRntaggerADIKDALTPAFLEKEHGTNGLVLCASLISFAVPLVPFFALRR 422
                                    55577899999999999999999999999889999999888899999999999999999999999999999999998888 PP

                        DUF4064  85 nkk 87 
                                    n +
  gene690|gene690|rna690|rna690 423 NVE 425
                                    865 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.64
                        DUF4064  17 illglllllflfl 29 
                                    ++++++ +l l+l
  gene690|gene690|rna690|rna690 458 LIMCVMSALLLSL 470
                                    3333333333322 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.0044
                        DUF4064  56 flstllivlgvialiaivlgivgalllkkn 85 
                                     ++ + + l+v++l ++vl  ++ +++k++
  gene690|gene690|rna690|rna690 576 TIGDYRVGLIVLFLYLAVLWMIAFFVMKNK 605
                                    577888999******************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (613 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1033  (0.0576162); expected 358.6 (0.02)
Passed bias filter:                      504  (0.0281109); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.64u 0.28s 00:00:00.92 Elapsed: 00:00:00.44
# Mc/sec: 4163.58
//
Query:       gene691|gene691|rna691|rna691  [L=63]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (63 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       191  (0.0106531); expected 358.6 (0.02)
Passed bias filter:                      169  (0.00942607); expected 358.6 (0.02)
Passed Vit filter:                         6  (0.000334653); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.32u 0.28s 00:00:00.60 Elapsed: 00:00:00.41
# Mc/sec: 457.58
//
Query:       gene692|gene692|rna692|rna692  [L=459]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00013   21.8   0.0    0.00024   21.0   0.0    1.5  1  HRDC      HRDC domain
  ------ inclusion threshold ------
        0.2   11.5   0.9         21    5.0   0.0    2.5  2  QLQ       QLQ


Domain annotation for each model (and alignments):
>> HRDC  HRDC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   2.7e-08   0.00024       2      65 ..     293     356 ..     292     359 .. 0.86

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 2.7e-08
                                    HHHHHHHHHHHHHHHHHHTS-HHHHS-HHHHHHHHHH---SHHHHHTSTTT-HHHHHHHHHHHH CS
                           HRDC   2 lallkaLrewReelAreedvppyvvfpdktLleiAeklPttleeLlqiegvgkrklekygeeil 65 
                                     ++l++  ++R+ +A++++++ ++v+++ +L  i e +P+t+ +++++    +  l+ + e+il
  gene692|gene692|rna692|rna692 293 RKVLEDILKLRDFVAKSNNESVNYVLTERQLCLILENMPKTKMQFKNVLPRCSPILRAHIEDIL 356
                                    5799******************************************995555566666666665 PP

>> QLQ  QLQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.0    0.0023        21      20      33 ..      32      45 ..      30      47 .. 0.85
   2 ?    4.5   0.1    0.0032        29      16      32 ..      68      84 ..      67      85 .. 0.93

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.0023
                            QLQ 20 LsknqPvPpeLqqa 33
                                   L ++qP+P++L  a
  gene692|gene692|rna692|rna692 32 LNNGQPIPTHLYSA 45
                                   789*******9665 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.0032
                            QLQ 16 AfKyLsknqPvPpeLqq 32
                                   ++K L +++ vPp+L++
  gene692|gene692|rna692|rna692 68 IYKSLNSSVIVPPALVK 84
                                   8**************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (459 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       985  (0.0549389); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 3208.74
//
Query:       gene693|gene693|rna693|rna693  [L=187]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.7e-09   35.7  42.2    0.00016   21.5   0.4    5.0  5  zf-CCCH      Zinc finger C-x8-C-x5-C-x3-H type (and similar)
    7.3e-07   29.4  25.9     0.0078   16.4   1.2    3.8  4  zf-CCCH_3    Zinc-finger containing family
    2.3e-06   28.2  29.3      0.026   15.2   4.2    4.8  5  Torus        Torus domain
    3.1e-06   27.4  37.6      0.033   14.7   3.4    5.4  5  zf-CCCH_2    RNA-binding, Nab2-type zinc finger
    4.5e-06   26.5   2.6    4.5e-06   26.5   2.6    5.6  5  zf_CCCH_4    Zinc finger domain
     0.0029   17.4   1.5     0.0029   17.4   1.5    5.2  6  zf-CCCH_4    CCCH-type zinc finger
  ------ inclusion threshold ------
       0.14   12.1   0.0       0.33   10.9   0.0    1.6  1  DUF4905      Domain of unknown function (DUF4905)


Domain annotation for each model (and alignments):
>> zf-CCCH  Zinc finger C-x8-C-x5-C-x3-H type (and similar)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   1.3         1   2.7e+03       6      21 ..      28      41 ..      26      47 .. 0.60
   2 !   21.5   0.4   6.1e-08   0.00016       2      25 ..      50      72 ..      49      74 .. 0.92
   3 !   17.7   2.0   9.9e-07    0.0025       1      25 [.      77     100 ..      77     102 .. 0.94
   4 !    7.2   4.1    0.0019       4.9       6      25 ..     110     128 ..     106     130 .. 0.82
   5 !   13.4   5.3   2.1e-05     0.055       2      27 .]     130     154 ..     129     154 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1
                                   BCHHHHHS--TTGGG- CS
                        zf-CCCH  6 CrffmrtGyCkyGdrC 21
                                   C+ f++  +C + +rC
  gene693|gene693|rna693|rna693 28 CKPFQK-SQC-FNPRC 41
                                   777777.555.23555 PP

  == domain 2  score: 21.5 bits;  conditional E-value: 6.1e-08
                                   HCHCBCHHHHHS--TTGGG-SSBS CS
                        zf-CCCH  2 ktelCrffmrtGyCkyGdrCkFaH 25
                                   k + C++++r G Ck  ++C F H
  gene693|gene693|rna693|rna693 50 KAVVCKHWLR-GLCKKNEKCEFLH 72
                                   6689******.************* PP

  == domain 3  score: 17.7 bits;  conditional E-value: 9.9e-07
                                    -HCHCBCHHHHHS--TTGGG-SSBS CS
                        zf-CCCH   1 yktelCrffmrtGyCkyGdrCkFaH 25 
                                    +k+++C ff+++G+C+    C+F H
  gene693|gene693|rna693|rna693  77 KKMPECWFFSKYGECSN-TECHFLH 100
                                    599**************.******* PP

  == domain 4  score: 7.2 bits;  conditional E-value: 0.0019
                                    BCHHHHHS--TTGGG-SSBS CS
                        zf-CCCH   6 CrffmrtGyCkyGdrCkFaH 25 
                                    C  ++++G+C++G  C+  H
  gene693|gene693|rna693|rna693 110 CL-WYKRGFCRHGLMCRNKH 128
                                    55.9999*******998666 PP

  == domain 5  score: 13.4 bits;  conditional E-value: 2.1e-05
                                    HCHCBCHHHHHS--TTGGG-SSBSCS CS
                        zf-CCCH   2 ktelCrffmrtGyCkyGdrCkFaHgq 27 
                                    k +lC  ++  G+C  G+ CkF H++
  gene693|gene693|rna693|rna693 130 KKRLCYSYFY-GFCIDGPECKFGHPK 154
                                    789******9.***********9996 PP

>> zf-CCCH_3  Zinc-finger containing family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.2   0.00032      0.82      34      59 ..      25      50 ..      22      52 .. 0.91
   2 !   14.7   7.9     1e-05     0.026      34      94 ..      51     110 ..      48     115 .. 0.76
   3 ?    2.9   0.5     0.048   1.2e+02       5      28 ..     107     130 ..     104     133 .. 0.80
   4 !   16.4   1.2   3.1e-06    0.0078       5      31 ..     131     157 ..     127     164 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00032
                      zf-CCCH_3 34 etvctlWqegrclrevckfrhmeidk 59
                                   ++ c+ +q+ +c++ +c+  h+++dk
  gene693|gene693|rna693|rna693 25 DIYCKPFQKSQCFNPRCQKLHVKLDK 50
                                   578********************998 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 1e-05
                      zf-CCCH_3  34 etvctlWqegrclr.evckfrhmeidkkrkeipcywenqpaGcqklhcaflhekpravdgll 94 
                                     +vc+ W +g c + e+c+f h  + k  k   c++ ++ + c  ++c flh  p++ ++++
  gene693|gene693|rna693|rna693  51 AVVCKHWLRGLCKKnEKCEFLHEYNLK--KMPECWFFSKYGECSNTECHFLHIDPNSESKEC 110
                                    579999999999862579999965444..445688889999999999999999988776665 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.048
                      zf-CCCH_3   5 gddcyffyystctkGdscpfrhee 28 
                                    +++c ++    c  G +c  +h +
  gene693|gene693|rna693|rna693 107 SKECLWYKRGFCRHGLMCRNKHVK 130
                                    678999999999999999999977 PP

  == domain 4  score: 16.4 bits;  conditional E-value: 3.1e-06
                      zf-CCCH_3   5 gddcyffyystctkGdscpfrheeaal 31 
                                    +  cy ++y  c  G +c f h +a l
  gene693|gene693|rna693|rna693 131 KRLCYSYFYGFCIDGPECKFGHPKAEL 157
                                    567*******************99987 PP

>> Torus  Torus domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.3      0.38   9.7e+02      66      91 ..      21      45 ..      15      48 .. 0.81
   2 !   15.2   4.2     1e-05     0.026      67      92 ..      48      73 ..      22      81 .. 0.88
   3 !    7.6   0.6    0.0024         6      71      97 ..      80     106 ..      74     109 .. 0.79
   4 !   11.4   1.1   0.00015      0.39      68      91 ..     105     128 ..     102     129 .. 0.88
   5 !   11.9   1.8   0.00011      0.29      67      92 ..     128     153 ..     126     173 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.38
                                   HSTT--B-HHHHHT--SSGGG-SSB- CS
                          Torus 66 kekesyfClfFarGlCakGkkCeylH 91
                                   kek+ ++C  F +  C +  +C+ lH
  gene693|gene693|rna693|rna693 21 KEKDDIYCKPFQKSQCFN-PRCQKLH 45
                                   5677899*********97.5788887 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 1e-05
                                   STT--B-HHHHHT--SSGGG-SSB-S CS
                          Torus 67 ekesyfClfFarGlCakGkkCeylHr 92
                                    +++++C ++ rGlC+k +kCe+lH+
  gene693|gene693|rna693|rna693 48 LDKAVVCKHWLRGLCKKNEKCEFLHE 73
                                   45779********************7 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.0024
                                    -B-HHHHH.T--SSGGG-SSB-S---SS CS
                          Torus  71 yfClfFar.GlCakGkkCeylHrlPtee 97 
                                      C fF++ G C++ ++C++lH  P++e
  gene693|gene693|rna693|rna693  80 PECWFFSKyGECSN-TECHFLHIDPNSE 106
                                    56*****9677765.89*****988876 PP

  == domain 4  score: 11.4 bits;  conditional E-value: 0.00015
                                    TT--B-HHHHHT--SSGGG-SSB- CS
                          Torus  68 kesyfClfFarGlCakGkkCeylH 91 
                                    +es  Cl++ rG+C +G  C+  H
  gene693|gene693|rna693|rna693 105 SESKECLWYKRGFCRHGLMCRNKH 128
                                    56788***************9988 PP

  == domain 5  score: 11.9 bits;  conditional E-value: 0.00011
                                    STT--B-HHHHHT--SSGGG-SSB-S CS
                          Torus  67 ekesyfClfFarGlCakGkkCeylHr 92 
                                    + ++ +C+ +  G+C  G +C++ H 
  gene693|gene693|rna693|rna693 128 HVKKRLCYSYFYGFCIDGPECKFGHP 153
                                    667889*****************993 PP

>> zf-CCCH_2  RNA-binding, Nab2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.5   3.3    0.0099        25       2      17 ..      28      45 ..      28      45 .. 0.77
   2 !   11.8   2.1    0.0001      0.27       2      17 ..      54      72 ..      54      72 .. 0.98
   3 !   14.7   3.4   1.3e-05     0.033       2      17 ..      82     100 ..      81     100 .. 0.98
   4 ?    3.7   0.1     0.037        95       2      11 ..     118     127 ..     118     129 .. 0.93
   5 !   11.5   2.0   0.00012      0.32       8      18 .]     142     153 ..     135     153 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0099
                      zf-CCCH_2  2 Crffpn..CtnpkCpFaH 17
                                   C+ f +  C+np+C   H
  gene693|gene693|rna693|rna693 28 CKPFQKsqCFNPRCQKLH 45
                                   66677777******8666 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.0001
                      zf-CCCH_2  2 Crffpn..C.tnpkCpFaH 17
                                   C+++    C +n+kC F H
  gene693|gene693|rna693|rna693 54 CKHWLRglCkKNEKCEFLH 72
                                   ***************9999 PP

  == domain 3  score: 14.7 bits;  conditional E-value: 1.3e-05
                      zf-CCCH_2   2 Crffpn...CtnpkCpFaH 17 
                                    C+ff +   C n +C+F H
  gene693|gene693|rna693|rna693  82 CWFFSKygeCSNTECHFLH 100
                                    *****************99 PP

  == domain 4  score: 3.7 bits;  conditional E-value: 0.037
                      zf-CCCH_2   2 CrffpnCtnp 11 
                                    Cr++  C+n+
  gene693|gene693|rna693|rna693 118 CRHGLMCRNK 127
                                    *******997 PP

  == domain 5  score: 11.5 bits;  conditional E-value: 0.00012
                      zf-CCCH_2   8 C.tnpkCpFaHP 18 
                                    C  +p+C+F HP
  gene693|gene693|rna693|rna693 142 CiDGPECKFGHP 153
                                    999********9 PP

>> zf_CCCH_4  Zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.2       3.4   8.8e+03       1       6 [.      28      33 ..      28      33 .. 0.81
   2 !   26.5   2.6   1.7e-09   4.5e-06       1      19 []      54      72 ..      54      72 .. 1.00
   3 ?    1.7   5.1      0.11   2.9e+02       1      19 []      82     100 ..      82     100 .. 0.82
   4 !    5.7   3.2    0.0061        16       4      19 .]     113     128 ..     111     128 .. 0.86
   5 ?    4.6   4.8     0.014        35       7      19 .]     140     152 ..     134     152 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 3.4
                      zf_CCCH_4  1 Ckfflq 6 
                                   Ck f++
  gene693|gene693|rna693|rna693 28 CKPFQK 33
                                   999986 PP

  == domain 2  score: 26.5 bits;  conditional E-value: 1.7e-09
                      zf_CCCH_4  1 CkfflqGtCkkGdkCrFaH 19
                                   Ck++l+G Ckk++kC F+H
  gene693|gene693|rna693|rna693 54 CKHWLRGLCKKNEKCEFLH 72
                                   ******************* PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.11
                      zf_CCCH_4   1 Ckfflq.GtCkkGdkCrFaH 19 
                                    C ff + G C++ + C+F+H
  gene693|gene693|rna693|rna693  82 CWFFSKyGECSN-TECHFLH 100
                                    999999999985.7777777 PP

  == domain 4  score: 5.7 bits;  conditional E-value: 0.0061
                      zf_CCCH_4   4 flqGtCkkGdkCrFaH 19 
                                    +++G C++G  Cr  H
  gene693|gene693|rna693|rna693 113 YKRGFCRHGLMCRNKH 128
                                    667******9999888 PP

  == domain 5  score: 4.6 bits;  conditional E-value: 0.014
                      zf_CCCH_4   7 GtCkkGdkCrFaH 19 
                                    G C  G  C+F H
  gene693|gene693|rna693|rna693 140 GFCIDGPECKFGH 152
                                    99*********88 PP

>> zf-CCCH_4  CCCH-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   2.1       3.1     8e+03       3      11 ..      28      36 ..      26      41 .. 0.77
   2 !   17.4   1.5   1.1e-06    0.0029       1      22 []      52      73 ..      52      73 .. 0.95
   3 ?   -1.5   0.4      0.96   2.5e+03       3       7 ..      82      86 ..      81      93 .. 0.71
   4 ?   -2.7   1.7       2.2   5.7e+03      17      21 ..      96     100 ..      95     100 .. 0.94
   5 ?    0.5   1.2      0.21   5.4e+02       9      18 ..     116     125 ..     111     129 .. 0.61
   6 ?   -0.5   4.1      0.45   1.2e+03       6      21 ..     137     152 ..     132     153 .. 0.53

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 3.1
                      zf-CCCH_4  3 CpyfakGsC 11
                                   C+ f+k +C
  gene693|gene693|rna693|rna693 28 CKPFQKSQC 36
                                   999997666 PP

  == domain 2  score: 17.4 bits;  conditional E-value: 1.1e-06
                      zf-CCCH_4  1 rlCpyfakGsCrfGdnCrFsHd 22
                                   ++C+++++G C+  ++C F+H+
  gene693|gene693|rna693|rna693 52 VVCKHWLRGLCKKNEKCEFLHE 73
                                   59*******************6 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 0.96
                      zf-CCCH_4  3 Cpyfa 7 
                                   C++f 
  gene693|gene693|rna693|rna693 82 CWFFS 86
                                   99996 PP

  == domain 4  score: -2.7 bits;  conditional E-value: 2.2
                      zf-CCCH_4  17 CrFsH 21 
                                    C F+H
  gene693|gene693|rna693|rna693  96 CHFLH 100
                                    99**9 PP

  == domain 5  score: 0.5 bits;  conditional E-value: 0.21
                      zf-CCCH_4   9 GsCrfGdnCr 18 
                                    G Cr G  Cr
  gene693|gene693|rna693|rna693 116 GFCRHGLMCR 125
                                    5566665555 PP

  == domain 6  score: -0.5 bits;  conditional E-value: 0.45
                      zf-CCCH_4   6 fakGsCrfGdnCrFsH 21 
                                    ++ G C  G+ C+F H
  gene693|gene693|rna693|rna693 137 YFYGFCIDGPECKFGH 152
                                    5545555566666666 PP

>> DUF4905  Domain of unknown function (DUF4905)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00013      0.33      27      67 ..      41      81 ..      32      83 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00013
                        DUF4905 27 letgkllfedlvleekwwtgleaiykgvlllhkyekpdsPe 67
                                   +++ ++ +++ v+  +w+ gl   +++  +lh+y+ +++Pe
  gene693|gene693|rna693|rna693 41 CQKLHVKLDKAVVCKHWLRGLCKKNEKCEFLHEYNLKKMPE 81
                                   788899999******************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       582  (0.0324614); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1292.19
//
Query:       gene694|gene694|rna694|rna694  [L=941]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (941 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       637  (0.035529); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.69u 0.32s 00:00:01.01 Elapsed: 00:00:00.48
# Mc/sec: 5856.83
//
Query:       gene695|gene695|rna695|rna695  [L=138]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-16   60.2   2.4    1.3e-16   60.2   2.4    2.1  2  Chromo         Chromo (CHRromatin Organisation MOdifier) doma
    1.4e-10   41.1   2.6    1.5e-08   34.6   0.3    2.2  2  Chromo_shadow  Chromo shadow domain
     0.0061   16.7   0.0      0.027   14.7   0.0    1.9  2  Mtf2_C         Polycomb-like MTF2 factor 2


Domain annotation for each model (and alignments):
>> Chromo  Chromo (CHRromatin Organisation MOdifier) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.2   2.4   2.1e-20   1.3e-16       1      53 [.       7      55 ..       7      56 .. 0.96
   2 ?   -0.0   0.2      0.14   8.4e+02      22      42 ..      65      86 ..      55      96 .. 0.66

  Alignments for each domain:
  == domain 1  score: 60.2 bits;  conditional E-value: 2.1e-20
                                   EEEEEEEEEEEETTEECEEEEEEETTSTGGGTEEEEGGGCSSHSHHHHHHHHH CS
                         Chromo  1 yeVerIidhrtdkdgleleYlVKWkglpysentWEpeenlekcfqelideFkk 53
                                   y+Ve+I+d+r+ k+++  +Yl+KW+g+p +entWE ++++ ++  eli++F++
  gene695|gene695|rna695|rna695  7 YQVEKIVDSRIYKGKK--QYLIKWEGFPSNENTWEYAKDIFSK--ELIEQFEQ 55
                                   89**************..***********************88..9*****97 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.14
                                   EEETTSTGGGTEEEEGG.GCSS CS
                         Chromo 22 VKWkglpysentWEpee.nlek 42
                                   VK k  p+  n W  e  n+e+
  gene695|gene695|rna695|rna695 65 VKPKTVPEVTNEWAREVnNIEN 86
                                   6666677777888887655655 PP

>> Chromo_shadow  Chromo shadow domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.8   0.1    0.0012       7.1       2      23 ..       9      30 ..       8      50 .. 0.86
   2 !   34.6   0.3   2.6e-12   1.5e-08      10      53 .]      90     133 ..      76     133 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0012
                                   TTTTEEEEEETS-EEEEEEETT CS
                  Chromo_shadow  2 pekiigavdtsgelmflikWkn 23
                                   +eki+++   +g+  +likW++
  gene695|gene695|rna695|rna695  9 VEKIVDSRIYKGKKQYLIKWEG 30
                                   6888888888**********97 PP

  == domain 2  score: 34.6 bits;  conditional E-value: 2.6e-12
                                    EE.TS-EEEEEEETTS-EEE.EEHHHHHHHSHHHHHHHHHCT-XX CS
                  Chromo_shadow  10 dt.sgelmflikWkngekaelvpskeanqkcPqkvikFYEerltw 53 
                                    d+ + +lm+ i ++ g+k+  v++k ++qkcP  ++++YE+++++
  gene695|gene695|rna695|rna695  90 DEkKNKLMVDILFNSGKKMS-VDAKTVHQKCPVALLEYYEKNISF 133
                                    334669**************.*********************987 PP

>> Mtf2_C  Polycomb-like MTF2 factor 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   4.4e-06     0.027      34      47 ..      18      31 ..      14      32 .. 0.89
   2 ?   -1.0   0.0      0.36   2.1e+03      20      35 ..     103     118 ..     102     125 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 4.4e-06
                         Mtf2_C 34 pnGkvqYLieWeGa 47
                                    +Gk qYLi WeG+
  gene695|gene695|rna695|rna695 18 YKGKKQYLIKWEGF 31
                                   58***********7 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.36
                         Mtf2_C  20 asGEkfavlAkRvtpn 35 
                                    +sG k +v Ak v  +
  gene695|gene695|rna695|rna695 103 NSGKKMSVDAKTVHQK 118
                                    5899999999988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1148  (0.0640303); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 936.08
//
Query:       gene696|gene696|rna696|rna696  [L=763]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    6.4e-54  183.1   0.4    1.5e-48  165.5   0.0    2.5  2  AMP-binding  AMP-binding enzyme
  ------ inclusion threshold ------
      0.062   12.1   0.0       0.13   11.1   0.0    1.4  1  GH3          GH3 auxin-responsive promoter


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  165.5   0.0   1.7e-52   1.5e-48      45     373 ..     136     524 ..     133     529 .. 0.76
   2 !   14.6   0.4     1e-06    0.0092     393     421 ..     619     646 ..     597     647 .. 0.87

  Alignments for each domain:
  == domain 1  score: 165.5 bits;  conditional E-value: 1.7e-52
                                    STT-EEEEEESSSHHHHHHHHHHHHTT-EEEEEETTS-HHHHHHHHHHHTESEEE.........ETCTCCCHHHHHHHHS CS
                    AMP-binding  45 kkgdrVaillpnspewvvallailkaGavvvplnptltaeelayiledseakvli.........atvdselleklleaaa 115
                                    kk + V+i+  n++ew++++l +   + +  ++++t++++ ++ i+e+ ++kv++         +            ++ 
  gene696|gene696|rna696|rna696 136 KKRSYVGIFINNCIEWTITDLSLILTNKISTTIYATFGKDNVRGIIEQGNVKVVVagvkeiemlR-----------GIEC 204
                                    56677**************************************************5554443331...........3332 PP

                                    CC-EECEEEEESCCS-HCCHCCCHCCCCSCTTS............................................... CS
                    AMP-binding 116 kleavklvivldadellkeeelkeeeeseekae............................................... 148
                                         k+viv+ +++  +    ++ +  + + +                                               
  gene696|gene696|rna696|rna696 205 ----LKVVIVVGKERGIE---IEGVKVYYYD-Dvmngihkhsgrediagtdyahkygmgystrnyahkcvnekgsvicae 276
                                    ....12222222111111...1111222211.0222334444455555677888999999999999999999999999** PP

                                    ........-TSCCCS-BTTSEEEEEEE--SSSS-EEEEEEHHHHHHHHHHHH.HHHC...SCCTTT-EEEESS-TTSCHH CS
                    AMP-binding 149 ........kpeeeeelkpddlayiiYTSGTTGkPKGVmlshrnlvanvaslk.letr...fklkeddvvlsilplahifg 216
                                            k +++ ++++d++ +iiY+SGTTG+PK + lshrn+ +++ +lk  + +    +++++d  ls+lplah+++
  gene696|gene696|rna696|rna696 277 phdetqrlK-RPPLPASADEITTIIYSSGTTGTPKPIPLSHRNIYTSIFALKyGRSTnkfVGINAGDHHLSFLPLAHVME 355
                                    ****99963.456689***********************************98444445445788*************** PP

                                    HHHHHHHHHHTT-EEEE-TTCGCCHHHHHHHHHHHHT-SEEEEEHHHHHHH........................HHCCC CS
                    AMP-binding 217 lilelllallsGatvvllpkdaaldpklllelieklkvtviagvPrvleal........................lesga 272
                                      l ++++ll   +vv++++d +     l+++i+  ++t+++g+Pr++e +                        +    
  gene696|gene696|rna696|rna696 356 R-LLIYCFLLINVKVVFYSGDRK----KLMDDIRLVRPTIFCGAPRLWEVVrdgiysklgvisrllfkfllfvkrT---- 426
                                    6.*****************9866....367*********************8888777777666665555554440.... PP

                                    HHCHHHHC.....................CGTT.-SEEEEESS-EBHHHHHHHHHHHTCEEEEEEEEGGGSSECEECHCT CS
                    AMP-binding 273 lkaakkak.....................dlss.lrlvllggeplspellrffralfgeevlegYGlTEttgvvtvlple 330
                                           +                      +++ +rl+++g + l ++l  f+++++g +++e+YGlTEttg vt     
  gene696|gene696|rna696|rna696 427 -------NvlngvythdiadflafnrvkhMFGGrVRLLFSGSAFLDKDLKIFMESVLGVPMYEAYGLTETTGGVT-TS-- 496
                                    .......034444444445555444444477788***99***********************************9.44.. PP

                                    TTCTSTTS-BEE-TTEEEEEE-TTTSCBEETTSEEEEEEEETT CS
                    AMP-binding 331 edkkklgsvGkplpgvevkivDeetgepvpdgeeGellvrgpg 373
                                    +d  k g vG+pl   e++ivD            Gel+v+g +
  gene696|gene696|rna696|rna696 497 TD--KSG-VGWPLFSDEIRIVD------------GELVVKGDN 524
                                    34..245.**************............445555544 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 1e-06
                                    CCEEEEEEEEEEETTSEEEEEEECCCEEE CS
                    AMP-binding 393 grwlrTGDlgrldedGyleivgRkkdlik 421
                                     +w+rTGD +++  dG+++i+ R+k+ +k
  gene696|gene696|rna696|rna696 619 TKWFRTGDNAVVV-DGNVHIISRLKNNFK 646
                                    35*********98.8**********9888 PP

>> GH3  GH3 auxin-responsive promoter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   1.4e-05      0.13      72     102 ..     292     321 ..     282     348 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 1.4e-05
                                    SSSS-SEEEEECCEETTEEEEEEESHHHHHH CS
                            GH3  72 tsepiklfalsSGTtsgksKliPvteeslke 102
                                    ++++i+++  sSGTt g +K iP ++++  +
  gene696|gene696|rna696|rna696 292 SADEITTIIYSSGTT-GTPKPIPLSHRNIYT 321
                                    5799***********.********9987655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (763 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       610  (0.0340231); expected 358.6 (0.02)
Passed bias filter:                      477  (0.0266049); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.69u 0.29s 00:00:00.98 Elapsed: 00:00:00.45
# Mc/sec: 5119.62
//
Query:       gene697|gene697|rna697|rna697  [L=240]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.054   13.3   0.2      0.054   13.3   0.2    2.7  4  LRR_8     Leucine rich repeat


Domain annotation for each model (and alignments):
>> LRR_8  Leucine rich repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.1   0.1      0.79   1.4e+04       2       7 ..      33      38 ..      32      40 .. 0.45
   2 ?   -3.9   0.1      0.67   1.2e+04      23      28 ..      53      58 ..      50      60 .. 0.61
   3 ?   -1.6   0.1      0.13   2.3e+03      25      33 ..     106     114 ..     102     125 .. 0.63
   4 ?   13.3   0.2     3e-06     0.054      23      57 ..     162     196 ..     159     197 .. 0.81

  Alignments for each domain:
  == domain 1  score: -4.1 bits;  conditional E-value: 0.79
                                   T-SEEE CS
                          LRR_8  2 nLtsLd 7 
                                   nL+sL+
  gene697|gene697|rna697|rna697 33 NLKSLS 38
                                   344443 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 0.67
                                   T-TT-- CS
                          LRR_8 23 glsnLk 28
                                   +lsnLk
  gene697|gene697|rna697|rna697 53 NLSNLK 58
                                   566665 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 0.13
                                    TT--EEE-- CS
                          LRR_8  25 snLkvLdLs 33 
                                    +nL+ L L+
  gene697|gene697|rna697|rna697 106 QNLQQLVLR 114
                                    445555444 PP

  == domain 4  score: 13.3 bits;  conditional E-value: 3e-06
                                    T-TT--EEE--SS---GGGGGGGTT--S-.EEE-- CS
                          LRR_8  23 glsnLkvLdLsnNllttlspgafsgLpsLrsLdLs 57 
                                    +++nL+ L++ + ++ +  ++++++L+sL+ L+L+
  gene697|gene697|rna697|rna697 162 TMPNLRLLEIECSSIGSNLAEWIRNLKSLQALHLT 196
                                    68889999999998888778999999999988885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (240 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       530  (0.029561); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1726.39
//
Query:       gene698|gene698|rna698|rna698  [L=172]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       339  (0.0189079); expected 358.6 (0.02)
Passed bias filter:                      233  (0.0129957); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1271.53
//
Query:       gene699|gene699|rna699|rna699  [L=298]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.8e-08   33.0   9.4      5e-07   29.8   9.9    2.2  2  zf-C3HC4_4    zinc finger of C3HC4-type, RING
    4.3e-05   23.5   5.1    4.3e-05   23.5   5.1    2.2  2  zf-RING_UBOX  RING-type zinc-finger
    4.7e-05   23.2  12.0    4.7e-05   23.2  12.0    1.9  2  zf-C3HC4      Zinc finger, C3HC4 type (RING finger)
    0.00012   21.9  11.6    0.00029   20.7  11.6    1.7  1  zf-RING_5     zinc-RING finger domain
    0.00022   21.0  12.3      0.001   18.9  12.3    2.0  1  zf-C3HC4_3    Zinc finger, C3HC4 type (RING finger)
    0.00034   20.9  11.6     0.0008   19.7  11.6    1.7  1  zf-RING_2     Ring finger domain
     0.0012   18.7   9.0     0.0012   18.7   9.0    2.5  2  zf-C3HC4_2    Zinc finger, C3HC4 type (RING finger)
  ------ inclusion threshold ------
       0.42   10.5   0.0       0.42   10.5   0.0    2.9  2  zf-C3HC4_5    Zinc finger, C3HC4 type (RING finger)
          3    7.8  15.1         42    4.1  15.2    2.5  1  Prok-RING_4   Prokaryotic RING finger family 4
        3.9    7.4  14.3    1.3e+03   -0.6  14.3    2.5  1  zf-RING_6     zf-RING of BARD1-type protein


Domain annotation for each model (and alignments):
>> zf-C3HC4_4  zinc finger of C3HC4-type, RING
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8   9.9   2.8e-10     5e-07       1      42 []      37      87 ..      37      87 .. 0.88
   2 ?    1.5   0.2      0.19   3.4e+02       1      12 [.      84      97 ..      84      99 .. 0.76

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 2.8e-10
                     zf-C3HC4_4  1 CPiCldYLekPvsleCGhsfClsCisslqkepdgeq.........llCplC 42
                                   CPiC ++  + v+l+CGh++C +Ci+  q+  +g++           Cp+C
  gene699|gene699|rna699|rna699 37 CPICFSFHRDAVTLSCGHVYCCTCIKDAQNMVHGSDraglsacngTICPVC 87
                                   *****************************9999987777767666777777 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.19
                     zf-C3HC4_4  1 CPiC..ldYLekPv 12
                                   CP+C  ++Y + Pv
  gene699|gene699|rna699|rna699 84 CPVCdaSSYVTVPV 97
                                   ****5556888887 PP

>> zf-RING_UBOX  RING-type zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   5.1   2.4e-08   4.3e-05       1      26 [.      37      62 ..      37      75 .. 0.75
   2 ?   -0.9   0.2      0.95   1.7e+03       1       5 [.      84      88 ..      84      99 .. 0.80

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 2.4e-08
                   zf-RING_UBOX  1 CpIClelftdPlv.lpCGHtFCreClw 26
                                   CpIC++   d  v l+CGH++C  C++
  gene699|gene699|rna699|rna699 37 CPICFSFHRDA-VtLSCGHVYCCTCIK 62
                                   *****866688.7469**********3 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.95
                   zf-RING_UBOX  1 CpICl 5 
                                   Cp+C 
  gene699|gene699|rna699|rna699 84 CPVCD 88
                                   ****5 PP

>> zf-C3HC4  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2  12.0   2.6e-08   4.7e-05       1      41 []      37      87 ..      37      87 .. 0.93
   2 ?   -2.4   0.1       2.6   4.7e+03       4      17 ..     176     189 ..     175     191 .. 0.47

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 2.6e-08
                                   -TTT-S--SS-E.E-TTS--B-CHHHHHHHHC...........TSSB--TTT CS
                       zf-C3HC4  1 CpiCleeakepnelleCkHsfCskCirkilks...........rkkvkCPlC 41
                                   CpiC++   +++ +l C+H +C++Ci+  ++            ++ + CP+C
  gene699|gene699|rna699|rna699 37 CPICFSFHRDAV-TLSCGHVYCCTCIKDAQNMvhgsdraglsaCNGTICPVC 87
                                   ************.***************999999999999988777779999 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 2.6
                                    T-S--SS-E.E-TT CS
                       zf-C3HC4   4 CleeakepnelleC 17 
                                    C +  ++ + + +C
  gene699|gene699|rna699|rna699 176 CSDRNTDDHGTVTC 189
                                    44444444445555 PP

>> zf-RING_5  zinc-RING finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7  11.6   1.6e-07   0.00029       2      43 ..      37      88 ..      36      89 .. 0.95

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 1.6e-07
                      zf-RING_5  2 CnkCfeklskeekfyltsCgHifCekClkkll.............ekeavCpiCr 43
                                   C++Cf+ +   ++++++sCgH++C +C+k ++              +   Cp+C+
  gene699|gene699|rna699|rna699 37 CPICFSFH---RDAVTLSCGHVYCCTCIKDAQnmvhgsdraglsaCNGTICPVCD 88
                                   ******99...********************************999999*****7 PP

>> zf-C3HC4_3  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9  12.3   5.6e-07     0.001       4      45 ..      36      89 ..      34      92 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 5.6e-07
                                   B-TTTSSSBS-EEETTEEEEEE-HHHHHHHHH.............TT-B-TTT-- CS
                     zf-C3HC4_3  4 eCviClerprnvvllpCgHlvlCeeCaekllk.............rkkkCpiCrr 45
                                    C+iC++  r++v l CgH+ +C +C ++ ++             + + Cp+C +
  gene699|gene699|rna699|rna699 36 DCPICFSFHRDAVTLSCGHV-YCCTCIKDAQNmvhgsdraglsacNGTICPVCDA 89
                                   6*******************.9999***998888999999999998999999975 PP

>> zf-RING_2  Ring finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7  11.6   4.5e-07    0.0008       2      43 ..      36      87 ..      35      88 .. 0.74

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 4.5e-07
                      zf-RING_2  2 eCpICleelssadsvlllpCgHvfhreClerw...lrssst..........CPlC 43
                                   +CpIC+   s ++++++l CgHv++++C+++    ++ s +          CP+C
  gene699|gene699|rna699|rna699 36 DCPICF---SFHRDAVTLSCGHVYCCTCIKDAqnmVHGSDRaglsacngtiCPVC 87
                                   6****6...6667777777**********554432333333888888899***** PP

>> zf-C3HC4_2  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   9.0   6.6e-07    0.0012       2      30 ..      37      64 ..      36      69 .. 0.91
   2 ?    0.5   0.5      0.32   5.7e+02      36      40 .]      83      87 ..      76      91 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 6.6e-07
                     zf-C3HC4_2  2 CpiCldmlkdpsvvtpCgHvfCqkCilrs 30
                                   CpiC+ +  d+ v+  CgHv+C  Ci+ +
  gene699|gene699|rna699|rna699 37 CPICFSFHRDA-VTLSCGHVYCCTCIKDA 64
                                   **********9.999***********865 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.32
                     zf-C3HC4_2 36 eCPlC 40
                                    CP+C
  gene699|gene699|rna699|rna699 83 ICPVC 87
                                   68887 PP

>> zf-C3HC4_5  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -6.1   8.8        10   1.8e+04      23      35 ..      50      62 ..      35      80 .. 0.69
   2 ?   10.5   0.0   0.00023      0.42       3      21 ..      83     101 ..      81     106 .. 0.91

  Alignments for each domain:
  == domain 1  score: -6.1 bits;  conditional E-value: 10
                     zf-C3HC4_5 23 peCYhkmCesCvd 35
                                     C h  C +C+ 
  gene699|gene699|rna699|rna699 50 LSCGHVYCCTCIK 62
                                   4699999999985 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00023
                     zf-C3HC4_5   3 iCPvCkssrYlnpdlefli 21 
                                    iCPvC +s Y+   ++fl+
  gene699|gene699|rna699|rna699  83 ICPVCDASSYVTVPVKFLF 101
                                    8***************996 PP

>> Prok-RING_4  Prokaryotic RING finger family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1  15.2     0.024        42       1      36 [.      37      87 ..      37      92 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.024
                    Prok-RING_4  1 CvlCgeqekkailepCgHlvCkeCfdskdls...............sCPlC 36
                                   C +C + +++a+  +CgH+ C +C +++++                 CP+C
  gene699|gene699|rna699|rna699 37 CPICFSFHRDAVTLSCGHVYCCTCIKDAQNMvhgsdraglsacngtICPVC 87
                                   999**********************99976555556666666665556666 PP

>> zf-RING_6  zf-RING of BARD1-type protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6  14.3      0.71   1.3e+03      10      38 ..      37      64 ..      33      99 .. 0.69

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.71
                      zf-RING_6 10 csrctdilrepvclggcehifcsncisdc 38
                                   c  c    r+ v l  c h++c  ci d 
  gene699|gene699|rna699|rna699 37 CPICFSFHRDAVTL-SCGHVYCCTCIKDA 64
                                   88899999999999.5*********9773 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (298 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       635  (0.0354175); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 1904.37
//
Query:       gene7|gene7|rna7|rna7  [L=658]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.5e-06   26.6   0.3    0.00032   20.2   0.1    2.4  2  Mcl1_mid  Minichromosome loss protein, Mcl1, middle region
  ------ inclusion threshold ------
      0.019   14.2   0.0      0.041   13.2   0.0    1.5  1  TNV_CP    Satellite tobacco necrosis virus coat protein
       0.44   11.1   6.9       0.99   10.0   1.7    3.5  2  DUF1374   Protein of unknown function (DUF1374)


Domain annotation for each model (and alignments):
>> Mcl1_mid  Minichromosome loss protein, Mcl1, middle region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.0   0.0    0.0043        26     109     144 ..      94     129 ..      55     155 .. 0.85
   2 !   20.2   0.1   5.3e-08   0.00032      14     224 ..     399     607 ..     390     627 .. 0.70

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.0043
               Mcl1_mid 109 EevtavalgkkwvavaTskrylRiFslsGvqlavls 144
                             +++a+  ++ + ++aTs++++ i++++ ++ + + 
  gene7|gene7|rna7|rna7  94 ASISALFFNDPFLIIATSAGLIQIYNNKRICFQYWH 129
                            567888888888999999999999999888877765 PP

  == domain 2  score: 20.2 bits;  conditional E-value: 5.3e-08
               Mcl1_mid  14 gdrryLawNsiGvvttveedeeensieveFhDtslhrevhftdsfgftlasLseeglllAskaskseekkpstlyyrpleswasnseW 101
                            +d   L++N++G+  +  +d + n ie  FhD  + +++ +  + + + ++  ++g+ll+++        +  +yy+  ++w+ + + 
  gene7|gene7|rna7|rna7 399 NDIILLCYNETGFLLCK-QDVSVNLIELVFHDHMISNKI-IHCKLKNDKGCFDANGVLLSTT--------TTLTYYEDTKKWELDIST 476
                            45678*********996.566699*********977665.4468899************722........468999999999876777 PP

               Mcl1_mid 102 svkLpegEevtavalgkkw...........vavaTskrylR.iFslsGvqlavlslpgpvVtlaaskdklavvyhegap..lngnqel 175
                             v ++ g +++ + +++              +v  +++ +R ++ ++ +++ v+++    V l+ sk++l+v + +g++  ++    +
  gene7|gene7|rna7|rna7 477 VVGFK-GKKIKFLGISGYLyvvventtydsLVVLCKEGRIRdVYDIPRASTFVVKHG---VILVLSKNQLFVYS-DGQVkaIELIGAI 559
                            77777.788888888887655444444455555555555543444444444444443...66777777777766.4544455555566 PP

               Mcl1_mid 176 eyslldlskkkkkvlqregplpLspgstLkwlgFseegdpviydsdgvl 224
                            ++  +d +++   +  +e+   L+++ + + l ++++  +++yd+  ++
  gene7|gene7|rna7|rna7 560 NFLGIDAQRQ-IYYANAEYIYRLENSMSKRVLKYTNKTVLCYYDNMFIV 607
                            6666665555.33666667777888888899999999999999886555 PP

>> TNV_CP  Satellite tobacco necrosis virus coat protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   6.8e-06     0.041     102     154 ..     295     348 ..     280     363 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 6.8e-06
                            --HHHHBSSSSTT--B-HHHHHTTSEEEEEEEEEEE-TTS.--EEEEEEEEE-- CS
                 TNV_CP 102 PavtevLnsasvssqYnpvtlqqkrftilkDveldcslag.elikarvltlkkk 154
                              v +vL+s++ + + + + lq +rf + + ve  cs++  e  k+  ++ k++
  gene7|gene7|rna7|rna7 295 NVVKDVLDSVEQAKKMKEIILQENRFYVHRKVENVCSSSEdEELKDLFAQRKGR 348
                            5799********************************998614566666666655 PP

>> DUF1374  Protein of unknown function (DUF1374)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   1.7   0.00017      0.99       7      68 ..       6      66 ..       3      73 .. 0.86
   2 ?    1.7   0.3     0.063   3.8e+02      57      79 ..     575     596 ..     503     607 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00017
                           HHHHHCCTT.TEEEEEEEEEEEEEEEHHHHHHCC-S-SEEEEEECTTEEEEEEEEE-SSSEE CS
                DUF1374  7 sivdlFledkkikelelklkkelivsenefeeligkpdssnsvknnnilideyvYdenddii 68
                           + +  F + + +   +l + +    +ene+ el +  +  + +++  + idey+Y  ++ ++
  gene7|gene7|rna7|rna7  6 DGLLYFSKHQMLLTYNLDFTTAT-KNENELSELEKVRNELYGDEKYLVKIDEYEYPSSITAL 66
                           55667888889999999999887.79*****************************9988877 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.063
                            EEEEEE-SSSEEEEEEEEEEECT CS
                DUF1374  57 deyvYdenddiikkLiieYvked 79 
                             ey+Y+  ++++ k +++Y+ ++
  gene7|gene7|rna7|rna7 575 AEYIYR-LENSMSKRVLKYTNKT 596
                            467775.7899999999999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (658 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       858  (0.0478554); expected 358.6 (0.02)
Passed bias filter:                      487  (0.0271627); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.68u 0.30s 00:00:00.98 Elapsed: 00:00:00.50
# Mc/sec: 3971.89
//
Query:       gene70|gene70|rna70|rna70  [L=190]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.12   12.6   0.7        0.8    9.9   0.1    2.2  2  DUF2543   Protein of unknown function (DUF2543)


Domain annotation for each model (and alignments):
>> DUF2543  Protein of unknown function (DUF2543)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.1   4.5e-05       0.8      17      50 ..      23      56 ..       2      62 .. 0.78
   2 ?    0.7   0.1     0.034   6.1e+02       7      32 ..     158     183 ..     153     190 .] 0.73

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 4.5e-05
                    DUF2543 17 atesaePvseeerdalahyfqllitrltnneeis 50
                               + +s+ P +++++ +l+h+  ll+t + + + +s
  gene70|gene70|rna70|rna70 23 NKNSQIPWDDNDKYSLSHFIHLLMTTIKDRKLVS 56
                               467999********************99987665 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.034
                    DUF2543   7 lkyydiadeyatesaePvseeerdal 32 
                                 k+y i   y+ e++     +e d l
  gene70|gene70|rna70|rna70 158 NKFYIIGQCYSKETNLTEIFAENDVL 183
                                79**********99877666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (190 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       857  (0.0477997); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 1196.64
//
Query:       gene700|gene700|rna700|rna700  [L=210]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.1e-06   28.8   0.3    2.6e-06   27.7   0.3    1.6  1  DUF2439     Protein of unknown function (DUF2439)
  ------ inclusion threshold ------
      0.011   15.8   0.1      0.017   15.1   0.1    1.3  1  Pyr_excise  Pyrimidine dimer DNA glycosylase


Domain annotation for each model (and alignments):
>> DUF2439  Protein of unknown function (DUF2439)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7   0.3   2.9e-10   2.6e-06       6      43 ..       6      42 ..       4      70 .. 0.80

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 2.9e-10
                        DUF2439  6 vlYTsqvtk.KsKkWhDGflklhsfnkrvvLydeesklv 43
                                   ++YT++++k K+KkW++Gf+k    + ++vLy++e++ +
  gene700|gene700|rna700|rna700  6 CIYTKDKNKkKNKKWEEGFVK--VEEGKIVLYSDEKRKL 42
                                   9****9975268*********..8889*******88744 PP

>> Pyr_excise  Pyrimidine dimer DNA glycosylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.1   1.8e-06     0.017      31      99 ..      12      80 ..       4     100 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.8e-06
                                   HHH-GGGS---SS--SSTTTTGGGTTBHHHHHHHHHHHHHHHHHTT---S--S----TTS-GGGB---- CS
                     Pyr_excise 31 akkergngkipkhftlgtGHvtfFynkleyLrkrylllieEmlkRgynvneeekddisevekeyrgdwt 99
                                     k++++++++  + + +G   ++ ++  +L+ ++ ++ eEm++  y +  e+ +d+ ++++ y  +  
  gene700|gene700|rna700|rna700 12 KNKKKNKKWEEGFVKVEEGKIVLYSDEKRKLFSFKGAISEEMECLYYLIFMENVEDVAKLKNGYDDQER 80
                                   34589999************************************9999999999999999888866554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       980  (0.05466); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 1435.72
//
Query:       gene701|gene701|rna701|rna701  [L=65]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.098   12.2   0.3      0.096   12.3   0.3    1.1  1  PnpCD_PnpD_N  Hydroquinone 1,2-dioxygenase large subunit N-te
       0.16   11.6   3.3       0.35   10.5   2.6    1.8  2  PC4           Transcriptional Coactivator p15 (PC4)


Domain annotation for each model (and alignments):
>> PnpCD_PnpD_N  Hydroquinone 1,2-dioxygenase large subunit N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.3   1.1e-05     0.096      74     101 ..      20      47 ..       2      58 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.1e-05
                   PnpCD_PnpD_N  74 nhygkvdlyagtfngvlkeagvdyieqf 101
                                      y  v +y g fngv+k    +y e+ 
  gene701|gene701|rna701|rna701  20 SNYRAVKFYVGRFNGVIKYVVRNYYENG 47 
                                    57999*************9999998875 PP

>> PC4  Transcriptional Coactivator p15 (PC4)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.1     0.057   5.1e+02       9      19 ..      17      27 ..       9      29 .. 0.78
   2 ?   10.5   2.6   3.9e-05      0.35      11      30 ..      29      49 ..      19      52 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.057
                                   EEEEEETTEEE CS
                            PC4  9 vtvrefkGktl 19
                                   v+v++++ +++
  gene701|gene701|rna701|rna701 17 VRVSNYRAVKF 27
                                   78999998765 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 3.9e-05
                                   EEEETTEEEEEEEEEEEC.TT CS
                            PC4 11 vrefkGktlvdIReyyek.dg 30
                                   v +f+G+ ++ +R yye+ d+
  gene701|gene701|rna701|rna701 29 VGRFNGVIKYVVRNYYENgDD 49
                                   799**************8776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (65 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       475  (0.0264934); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.29s 00:00:00.69 Elapsed: 00:00:00.45
# Mc/sec: 434.45
//
Query:       gene702|gene702|rna702|rna702  [L=98]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       315  (0.0175693); expected 358.6 (0.02)
Passed bias filter:                      222  (0.0123822); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 711.93
//
Query:       gene703|gene703|rna703|rna703  [L=142]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.9e-11   42.7   0.0    8.5e-11   42.0   0.0    1.4  1  CBFD_NFYB_HMF  Histone-like transcription factor (CBF/NF-Y) a
    9.7e-06   26.0   0.1    9.7e-06   26.0   0.1    1.8  2  Histone        Core histone H2A/H2B/H3/H4
     0.0076   16.3   0.1       0.01   15.9   0.1    1.2  1  TFIID-31kDa    Transcription initiation factor IID, 31kD subu
  ------ inclusion threshold ------
      0.044   14.4   0.1       0.35   11.6   0.0    2.0  2  DUF3656        Collagenase
       0.38   11.3   2.9        2.7    8.5   1.8    2.2  2  DUF3949        Protein of unknown function (DUF3949)


Domain annotation for each model (and alignments):
>> CBFD_NFYB_HMF  Histone-like transcription factor (CBF/NF-Y) and archaeal histone
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.0   0.0   2.4e-14   8.5e-11       2      65 .]      13      74 ..      12      74 .. 0.95

  Alignments for each domain:
  == domain 1  score: 42.0 bits;  conditional E-value: 2.4e-14
                                   XXXHHHHHHHHHCCTTXS-B-HHHHHHHHHHHHHHHHHHHHHHHHHHCCTTSSCE-HHHHHHHH CS
                  CBFD_NFYB_HMF  2 eLPiarvkkImksdpdarkiakdAkeliaecveefieelaseAaeickkekrKtikaehiklAv 65
                                   +LP ++++k++     +  i +++++ ++  +  fi++++s A+ +c+kek+Kti++ehi  A+
  gene703|gene703|rna703|rna703 13 SLPRSTIDKMLSTY--NLSIPRQVRDHLTTYLHQFIHHISSDANLLCEKEKKKTITHEHIYEAL 74
                                   79*********999..777*****************************************8886 PP

>> Histone  Core histone H2A/H2B/H3/H4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   0.1   2.7e-09   9.7e-06      81     129 ..      27      75 ..      16      77 .. 0.90
   2 ?   -0.6   0.2      0.43   1.5e+03      27      55 ..     103     133 ..      87     137 .. 0.65

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 2.7e-09
                                    SXEEXHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTXSEEXHHHHHHHHH CS
                        Histone  81 dlrisaeavlalqealEallvelfeeAnllakhaKRvTitpkDiqlArr 129
                                    +l+i ++  + l++ l+ ++ ++ ++Anll+++ K++Tit ++i  A+r
  gene703|gene703|rna703|rna703  27 NLSIPRQVRDHLTTYLHQFIHHISSDANLLCEKEKKKTITHEHIYEALR 75 
                                    567777888889999********************************99 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.43
                                    T..TS-SSSSB--TTT-XTTHHHHHHHHHHH CS
                        Histone  27 r..kasskskkkkkrryrpgtvalkeirkyq 55 
                                    r  k +s++++ ++ r+ +++  +  +++y+
  gene703|gene703|rna703|rna703 103 RinKLKSSKFSIEELRMEQKKLFESARKEYE 133
                                    2346677777777777777777777777665 PP

>> TFIID-31kDa  Transcription initiation factor IID, 31kD subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1   2.8e-06      0.01      10      69 ..      18      76 ..       8     100 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2.8e-06
                    TFIID-31kDa 10 lihliLaslgvteyeerVvlqLldfayrytssvLedAkvlaehakkkevslddvrlAiqs 69
                                   +i ++L++ ++ ++  +V ++L    +++++++ +dA++l e++kkk+++ + +  A+ +
  gene703|gene703|rna703|rna703 18 TIDKMLSTYNL-SIPRQVRDHLTTYLHQFIHHISSDANLLCEKEKKKTITHEHIYEALRT 76
                                   67777777776.57889*********************************9999888765 PP

>> DUF3656  Collagenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   9.7e-05      0.35      46      94 ..      44     107 ..      11     109 .. 0.72
   2 ?    2.9   0.0     0.049   1.7e+02      62      85 ..     102     125 ..      96     131 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 9.7e-05
                        DUF3656  46 e............leeAkkrplteenirkqLsklGgtpFeleeieidld..gl.fiPvseLnel 94 
                                    +            +e+ kk+ +t+e i + L+  G  +F +e  ++  +  +l  + +s +n+l
  gene703|gene703|rna703|rna703  44 QfihhissdanllCEKEKKKTITHEHIYEALRTAGFAHFIVECQKVYDEtlNLsKMRPSRINKL 107
                                    03333444477889*************************9997776444567777778888887 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.049
                        DUF3656  62 kqLsklGgtpFeleeieidldglf 85 
                                    ++++kl  + F++ee++++ ++lf
  gene703|gene703|rna703|rna703 102 SRINKLKSSKFSIEELRMEQKKLF 125
                                    5799***********999766666 PP

>> DUF3949  Protein of unknown function (DUF3949)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0      0.12   4.3e+02      12      29 ..      56      73 ..      43      77 .. 0.85
   2 ?    8.5   1.8   0.00076       2.7       9      35 ..     114     140 ..     112     141 .. 0.93

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.12
                        DUF3949 12 lkekkkkqglsQeelYen 29
                                   l ek+kk+ +  e  Ye 
  gene703|gene703|rna703|rna703 56 LCEKEKKKTITHEHIYEA 73
                                   559999999*99999996 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00076
                        DUF3949   9 ikelkekkkkqglsQeelYenmsfeee 35 
                                    i+el+ ++kk   s ++ Yenm f+e+
  gene703|gene703|rna703|rna703 114 IEELRMEQKKLFESARKEYENMEFDED 140
                                    889**9******************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1093  (0.0609627); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.43u 0.21s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1074.30
//
Query:       gene704|gene704|rna704|rna704  [L=103]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1129  (0.0629706); expected 358.6 (0.02)
Passed bias filter:                      794  (0.0442858); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 788.27
//
Query:       gene705|gene705|rna705|rna705  [L=311]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.034   14.0   0.1        9.5    6.1   0.0    2.2  2  Chordopox_A35R  Chordopoxvirus A35R protein


Domain annotation for each model (and alignments):
>> Chordopox_A35R  Chordopoxvirus A35R protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0   0.00066        12     101     138 ..     140     177 ..     136     180 .. 0.89
   2 ?    6.1   0.0   0.00053       9.5      97     149 ..     236     286 ..     227     300 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.00066
                 Chordopox_A35R 101 dpklsideklqpfyistsiviaearilEvYnlykkgdY 138
                                    d  l+i ++  p +i  s  i ++ ++E++++++k + 
  gene705|gene705|rna705|rna705 140 DESLDISSTGVPTSICISDLINRSAVIELFDYFEKLEH 177
                                    56799999999*********************998776 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.00053
                 Chordopox_A35R  97 ccdkdpklsideklqpfyistsiviaearilEvYnlykkgdYqlilnPSeefl 149
                                    ++dk++k++ d +++  + + s +i +++ l +Y l+++g ++ i  P +++ 
  gene705|gene705|rna705|rna705 236 VIDKNMKFNGD-NFKLTMFVCSEIIDNVSTLKLYTLNSNGRWECI-SPTSRLR 286
                                    56666665544.566677789999*****************9975.6666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       423  (0.0235931); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 2034.00
//
Query:       gene706|gene706|rna706|rna706  [L=76]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       291  (0.0162307); expected 358.6 (0.02)
Passed bias filter:                      169  (0.00942607); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 553.17
//
Query:       gene707|gene707|rna707|rna707  [L=72]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    6.5e-26   90.4   6.3    7.7e-26   90.2   6.3    1.1  1  RNA_pol_N  RNA polymerases N / 8 kDa subunit


Domain annotation for each model (and alignments):
>> RNA_pol_N  RNA polymerases N / 8 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.2   6.3   4.3e-30   7.7e-26       1      59 []       1      59 [.       1      59 [. 0.99

  Alignments for each domain:
  == domain 1  score: 90.2 bits;  conditional E-value: 4.3e-30
                                   ----SS-TTT--B-STHHHHHHHHHHTT--HHHHHHHHT--SHHHHHHHHTB--THHHH CS
                      RNA_pol_N  1 MiiPVrCFtCGkvigekweeylellekgeepkdaLdaLglkryCCrrmllthvdliekl 59
                                   M+iPVrCFtC+k i++++e+y+ ll++++++ +a+d+Lg+kr+CCrrm+l hvd+++kl
  gene707|gene707|rna707|rna707  1 MLIPVRCFTCNKEISSLYEKYVLLLKADYTECEAMDKLGIKRMCCRRMVLCHVDIVDKL 59
                                   9*******************************************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (72 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       559  (0.0311785); expected 358.6 (0.02)
Passed bias filter:                      243  (0.0135535); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 488.24
//
Query:       gene708|gene708|rna708|rna708  [L=150]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00069   19.7   0.0     0.0012   19.0   0.0    1.4  1  Nup54     Nucleoporin complex subunit 54


Domain annotation for each model (and alignments):
>> Nup54  Nucleoporin complex subunit 54
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   6.6e-08    0.0012      19      61 ..      33      76 ..      22      89 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 6.6e-08
                                   ST..TEEEEEEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Nup54 19 dp.eklvPvpvkGFedLakRvkaQqkevaqhrerlkeisdrlee 61
                                   dp    +P+ +kG++dL  R k Q++ +++++++l ++s+r++ 
  gene708|gene708|rna708|rna708 33 DPsGTTYPIDLKGYDDLIMRNKHQKAVIDKLNSALLAMSQRIDG 76
                                   542368**********************************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       490  (0.02733); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1126.35
//
Query:       gene709|gene709|rna709|rna709  [L=304]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.9e-14   52.5   0.0    2.3e-13   50.0   0.0    2.1  2  cNMP_binding  Cyclic nucleotide-binding domain


Domain annotation for each model (and alignments):
>> cNMP_binding  Cyclic nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.0   0.0   1.3e-17   2.3e-13       5      84 ..     141     214 ..     138     219 .. 0.94
   2 ?   -0.4   0.0      0.07   1.3e+03      52      80 ..     275     304 .]     248     304 .] 0.66

  Alignments for each domain:
  == domain 1  score: 50.0 bits;  conditional E-value: 1.3e-17
                                    -TT-EEE-TTSB-SEEEEEEES-EEEEEEETTS.EEEEEEE-TTEEESHHHHHHTS--SSEEEESSTEEEEEEEHHHHHH CS
                   cNMP_binding   5 kagevifrqGdpadslyivlsGevrvyrlsedgkevvlavlgpGdlfGelalltgeprtatvvAltdsellalprddfle 84 
                                    +++ev++r Gd +d+ly++++G+++v  + +dg++    +l   +++Ge+all++ prtatvv++ d +++ l+r++ + 
  gene709|gene709|rna709|rna709 141 HKDEVLIRVGDNGDRLYFLERGKFCV--QGADGEK----ELPLHSVIGEIALLHNVPRTATVVSRADGRVWYLERESYHT 214
                                    689***********************..9****88....89999*******************************98765 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.07
                                    SHHHHH.HTS--SSEEEESSTEEEEEEEHH CS
                   cNMP_binding  52 Gelall.tgeprtatvvAltdsellalprd 80 
                                    Ge  +l  g+ +  + vA++++e ++lpr+
  gene709|gene709|rna709|rna709 275 GETRALnAGDIMYDDFVAVSEVEGYVLPRE 304
                                    666666333336667999999999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (304 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       517  (0.028836); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 2335.08
//
Query:       gene71|gene71|rna71|rna71  [L=440]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.037   14.1   0.2      0.037   14.1   0.2    1.9  2  RIG-I_C   RIG-I receptor C-terminal domain


Domain annotation for each model (and alignments):
>> RIG-I_C  RIG-I receptor C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.2     2e-06     0.037      40     110 ..      11      81 ..       2     102 .. 0.77
   2 ?   -2.6   0.1      0.29   5.2e+03      85     118 ..     211     244 ..     156     259 .. 0.57

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2e-06
                    RIG-I_C  40 lsklkksdfgtqkYeqwvvklekkaakeeerkkrvcaltcaehLrkYndALiinddaRts.dAleyLekfln 110
                                 +++ +++++ + ++  + +l+k++ +++  +   + ++   ++++Y +AL++++d+ +s d l+ ++ f++
  gene71|gene71|rna71|rna71  11 SCSI-PPEKNDEDFQTTIRMLKKELVTKHAASYAAEIVAHYIYIKEYENALLQYEDINVSsDELDRMKLFIE 81 
                                4555.9999*****************877777777778899****************998777766555544 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.29
                    RIG-I_C  85 kYndALiinddaRtsdAleyLekflndlkekkfd 118
                                + n ++ in d   +d  ++ +++  d+++k + 
  gene71|gene71|rna71|rna71 211 QTNFSMVINLDTSIIDLKRVFWDKSMDMARKTKF 244
                                3344555555555555555555555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (440 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       629  (0.0350828); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.22s 00:00:00.67 Elapsed: 00:00:00.36
# Mc/sec: 3620.76
//
Query:       gene710|gene710|rna710|rna710  [L=206]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00055   19.9   3.6     0.0014   18.7   3.6    1.7  1  bZIP_2    Basic region leucine zipper
     0.0011   19.0   2.9     0.0011   19.0   2.9    2.0  2  bZIP_1    bZIP transcription factor


Domain annotation for each model (and alignments):
>> bZIP_2  Basic region leucine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   3.6   1.6e-07    0.0014       8      31 ..      81     104 ..      77     124 .. 0.70

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.6e-07
                                    XXXXXXXXXXX-HHHHHHHHHHHH CS
                         bZIP_2   8 rRrkNreAarrsRekkkakeeele 31 
                                    ++++Nr Aa++sRekk + ++e e
  gene710|gene710|rna710|rna710  81 KKERNRLAAKKSREKKAKLMKEYE 104
                                    678************855444444 PP

>> bZIP_1  bZIP transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.2       1.4   1.3e+04      13      18 ..      33      38 ..      30      40 .. 0.49
   2 !   19.0   2.9   1.2e-07    0.0011       5      30 ..      77     102 ..      75     124 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 1.4
                                   HHHHHH CS
                         bZIP_1 13 NReaAr 18
                                    +e+A+
  gene710|gene710|rna710|rna710 33 KKESAQ 38
                                   344554 PP

  == domain 2  score: 19.0 bits;  conditional E-value: 1.2e-07
                                    XXXXXX--HHHHHHHHHHHHHHHHHH CS
                         bZIP_1   5 KrekrkqkNReaArrsRqRKqaeiee 30 
                                    K   +k++NR aA++sR++K + ++e
  gene710|gene710|rna710|rna710  77 KSIWKKERNRLAAKKSREKKAKLMKE 102
                                    66679***************999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1569  (0.0875119); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.30s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1372.33
//
Query:       gene711|gene711|rna711|rna711  [L=80]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       529  (0.0295053); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.27s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 604.10
//
Query:       gene712|gene712|rna712|rna712  [L=136]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.1e-21   76.2   0.3    2.7e-21   75.9   0.3    1.0  1  Ras          Ras family
     0.0074   16.5   0.1      0.013   15.7   0.1    1.4  1  Roc          Ras of Complex, Roc, domain of DAPkinase
  ------ inclusion threshold ------
       0.05   13.5   0.1      0.055   13.4   0.1    1.1  1  RsgA_GTPase  RsgA GTPase


Domain annotation for each model (and alignments):
>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.9   0.3   4.5e-25   2.7e-21      60     159 ..      14     115 ..      11     118 .. 0.94

  Alignments for each domain:
  == domain 1  score: 75.9 bits;  conditional E-value: 4.5e-25
                                    GGHHHHHHHHTTESEEEEEEETTBHHHHHTHHHHHHHHHHHSTTTSEEEEEEETTTGGG....G-SS-HHHHHHHHHHHT CS
                            Ras  60 efkslrelyyrdaegillvyditsresfenvkkwveeikrvaeenvpivLvGnKvDlee....kravsteegeelakelg 135
                                    +++++r+l+y ++++++++y+i++ +sf+nvk+w++eik     ++p +Lv++K D+++    +  v+te g+++ak+++
  gene712|gene712|rna712|rna712  14 KYDRIRQLSYPNTDMFFICYAINNVASFNNVKHWLNEIKGL---EIPAILVATKYDVRDdytqQDIVTTEMGKKMAKDHN 90 
                                    79************************************876...479***********99999999************** PP

                                    .SEEEEEBTTTTCTHHHHHHHHHHH CS
                            Ras 136 .lkfletSAktnenveeafeellre 159
                                     + f+etSA ++ n+  +fe+++++
  gene712|gene712|rna712|rna712  91 fVDFVETSALERRNLYLLFEKAVEH 115
                                    9*******************99875 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.1   2.1e-06     0.013      69     119 ..      15      66 ..      11      67 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.1e-06
                                    TTTT-HHHHCTSCEEEEEEE...GHHHHCHHHHHHHHHHHCSSS-EEEEEE-TT CS
                            Roc  69 frslhplylreaalailvyd...srssenlkeWlkelkkvagkspvilvgnkiD 119
                                    ++ +++l + + ++++++y      s++n+k+Wl+e+k    ++p+ilv++k+D
  gene712|gene712|rna712|rna712  15 YDRIRQLSYPNTDMFFICYAinnVASFNNVKHWLNEIKGL--EIPAILVATKYD 66 
                                    6677888888999999999843344789*********965..79********99 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   9.2e-06     0.055      13      64 ..      23      78 ..       9     117 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 9.2e-06
                                   EES--EEEEEEESTTTT--HHHHHHHHHHHHHTT-EEEEEEE-GGG--HHH.....H CS
                    RsgA_GTPase 13 vaNvdqllivvslkepelslnlldrfLvlaeekgiepvivlnKiDlleeee.....e 64
                                     N d  +i+ +++ +  s n ++  L +++  +i+ ++v +K D+ ++ +     +
  gene712|gene712|rna712|rna712 23 YPNTDMFFICYAIN-NVASFNNVKHWLNEIKGLEIPAILVATKYDVRDDYTqqdivT 78
                                   6799**********.999****************************99887233321 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       553  (0.0308439); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 975.04
//
Query:       gene713|gene713|rna713|rna713  [L=164]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.4e-21   73.9   2.3      1e-20   73.5   2.3    1.2  1  YEATS     YEATS family


Domain annotation for each model (and alignments):
>> YEATS  YEATS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.5   2.3   5.7e-25     1e-20       1      79 [.      30     106 ..      30     108 .. 0.94

  Alignments for each domain:
  == domain 1  score: 73.5 bits;  conditional E-value: 5.7e-25
                          YEATS   1 thkWtvavrsaasddlsefikkVqFkLhetyanptrvvekpPFevtetGwGeFeiqikiffkpeaekpltlehdLklhp 79 
                                    th W+ +++s+++    ++i+k + +Lhet+++p+r++++ PF ++e+GwGeF+i++k++f++ +ek +t+ h Lkl  
  gene713|gene713|rna713|rna713  30 THTWKFYIKSPTN-TPMHYISKAVLTLHETFKEPVRTITH-PFILEEKGWGEFNINVKLYFNDLNEKFITFSHFLKLYG 106
                                    8**********75.469*******************9987.9*********************99***********975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       608  (0.0339115); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1161.04
//
Query:       gene714|gene714|rna714|rna714  [L=346]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.2e-05   25.1  11.0    1.5e-05   24.8   7.7    2.3  2  zf-C3HC4      Zinc finger, C3HC4 type (RING finger)
    1.7e-05   25.0   8.7    4.4e-05   23.7   8.7    1.7  1  zf-rbx1       RING-H2 zinc finger domain
    2.6e-05   24.5  10.6    2.6e-05   24.5  10.6    1.8  2  zf-RING_2     Ring finger domain
    6.6e-05   22.9   3.1    0.00012   22.1   3.1    1.4  1  zf-ANAPC11    Anaphase-promoting complex subunit 11 RING-H2 f
     0.0041   16.7   7.4      0.012   15.2   7.4    1.8  1  Zn_ribbon_17  Zinc-ribbon, C4HC2 type
     0.0074   16.1  10.5     0.0074   16.1  10.5    2.2  2  zf-C3HC4_2    Zinc finger, C3HC4 type (RING finger)
  ------ inclusion threshold ------
      0.011   15.8   5.5      0.035   14.1   5.5    1.9  1  zf-C3H2C3     Zinc-finger
       0.18   12.0   5.4       0.64   10.2   5.4    2.1  1  zf-C3HC4_4    zinc finger of C3HC4-type, RING
          2    8.6   7.3         30    4.9   7.6    2.6  2  FANCL_C       FANCL C-terminal domain


Domain annotation for each model (and alignments):
>> zf-C3HC4  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.1      0.21   4.1e+02      14      21 ..       1       8 [.       1      22 [. 0.84
   2 !   24.8   7.7   7.3e-09   1.5e-05       1      41 []     260     300 ..     260     300 .. 0.98

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.21
                                   E-TTS--B CS
                       zf-C3HC4 14 lleCkHsf 21
                                   +++C+H++
  gene714|gene714|rna714|rna714  1 MIPCHHKM 8 
                                   689***98 PP

  == domain 2  score: 24.8 bits;  conditional E-value: 7.3e-09
                                    -TTT-S--SS-E.E-TTS--B-CHHHHHHHHCTSSB--TTT CS
                       zf-C3HC4   1 CpiCleeakepnelleCkHsfCskCirkilksrkkvkCPlC 41 
                                    C++C +++  ++ +l+C+H+++ +Ci+ +   +kk+ CPlC
  gene714|gene714|rna714|rna714 260 CALCDHKIDSQSITLNCTHKYHASCIKGWFLISKKEFCPLC 300
                                    *******************************999999**** PP

>> zf-rbx1  RING-H2 zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   8.7   2.2e-08   4.4e-05      13      55 .]     259     301 ..     254     301 .. 0.83

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 2.2e-08
                        zf-rbx1  13 acieckapgdeecpvvlGeCgHaFHlhCiskW..lktrkvCPlcr 55 
                                    +c  c+++ d+  +++l +C+H++H  Ci+ W  +++++ CPlc+
  gene714|gene714|rna714|rna714 259 CCALCDHKIDS-QSITL-NCTHKYHASCIKGWflISKKEFCPLCK 301
                                    79999999999.66666.9*************43356999****6 PP

>> zf-RING_2  Ring finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.1         9   1.8e+04      20      25 ..       3       8 ..       2      12 .. 0.69
   2 !   24.5  10.6   1.3e-08   2.6e-05       2      44 .]     259     301 ..     258     301 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 9
                      zf-RING_2 20 pCgHvf 25
                                   pC H +
  gene714|gene714|rna714|rna714  3 PCHHKM 8 
                                   687755 PP

  == domain 2  score: 24.5 bits;  conditional E-value: 1.3e-08
                      zf-RING_2   2 eCpICleelssadsvlllpCgHvfhreClerwlrssst..CPlCr 44 
                                     C++C  +++s +s++l  C H +h +C++ w+  s++  CPlC+
  gene714|gene714|rna714|rna714 259 CCALCDHKIDS-QSITL-NCTHKYHASCIKGWFLISKKefCPLCK 301
                                    59999888875.55554.5*************77777779****7 PP

>> zf-ANAPC11  Anaphase-promoting complex subunit 11 RING-H2 finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   3.1   5.9e-08   0.00012      33      83 ..     258     306 ..     243     308 .. 0.87

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 5.9e-08
                                    S--TTCSTTTTTS-EEEBTTS-EEEHHHHHHHHHHHSTSSB-TTTSSB--B CS
                     zf-ANAPC11  33 GtcpsckfpGddcplvlGkckhnfhlhcilkwletetskglcpmcrqtfkl 83 
                                     +c  c    d  ++ l +c+h++h+ ci  w+  +  k+ cp+c++++ +
  gene714|gene714|rna714|rna714 258 TCCALCDHKIDSQSITL-NCTHKYHASCIKGWFLIS-KKEFCPLCKEKMGV 306
                                    58999*99999999887.7*************9865.699******99876 PP

>> Zn_ribbon_17  Zinc-ribbon, C4HC2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   7.4   6.2e-06     0.012       6      46 ..     259     298 ..     255     303 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 6.2e-06
                   Zn_ribbon_17   6 sCayCelavkgrvvlcgvCeHvlHasCarewfenddlaeCp 46 
                                     Ca+C+ ++  + +   +C H  HasC++ wf   +++ Cp
  gene714|gene714|rna714|rna714 259 CCALCDHKIDSQSI-TLNCTHKYHASCIKGWFLISKKEFCP 298
                                    599******98865.689**************999988998 PP

>> zf-C3HC4_2  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.1       0.8   1.6e+03      15      23 ..       1       9 [.       1      21 [. 0.73
   2 !   16.1  10.5   3.7e-06    0.0074       2      40 .]     260     300 ..     259     300 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.8
                     zf-C3HC4_2 15 vtpCgHvfC 23
                                   ++pC H+  
  gene714|gene714|rna714|rna714  1 MIPCHHKMS 9 
                                   579***865 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 3.7e-06
                     zf-C3HC4_2   2 CpiCldmlkdpsvvtpCgHvfCqkCilr.sLeekn.eCPlC 40 
                                    C++C   +   s + +C H+++++Ci+   L +k+  CPlC
  gene714|gene714|rna714|rna714 260 CALCDHKIDSQSITLNCTHKYHASCIKGwFLISKKeFCPLC 300
                                    **********99999*************535555559**** PP

>> zf-C3H2C3  Zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   5.5   1.8e-05     0.035       1      35 []     260     301 ..     260     301 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.8e-05
                      zf-C3H2C3   1 CdnCglkLdypfvaysCkHlvHakCa.......deevCPkCk 35 
                                    C  C+ k+d       C H +Ha C        ++e CP+Ck
  gene714|gene714|rna714|rna714 260 CALCDHKIDSQSITLNCTHKYHASCIkgwflisKKEFCPLCK 301
                                    999**********************6235555558******7 PP

>> zf-C3HC4_4  zinc finger of C3HC4-type, RING
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   5.4   0.00032      0.64      12      42 .]     272     300 ..     257     300 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00032
                     zf-C3HC4_4  12 vsleCGhsfClsCisslqkepdgeqllCplC 42 
                                    ++l+C h +  sCi+ +   +++e  +CplC
  gene714|gene714|rna714|rna714 272 ITLNCTHKYHASCIKGWFLISKKE--FCPLC 300
                                    89******************9998..9**** PP

>> FANCL_C  FANCL C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.1       1.8   3.5e+03      16      32 ..     247     263 ..     240     269 .. 0.62
   2 ?    4.9   7.6     0.015        30      27      66 ..     275     305 ..     258     308 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.8
                                    -----B--S-TT----B CS
                        FANCL_C  16 gevpdisCdnekCnkkf 32 
                                    ++vp ++  ++ C   +
  gene714|gene714|rna714|rna714 247 DAVPAKVLTDPTCCALC 263
                                    66666666666665443 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.015
                                    T----B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-SEEE CS
                        FANCL_C  27 kCnkkfHsaCLkeWlrslkesrqsfdvlfGeCPyCkkkis 66 
                                    +C++k+H++C+k W+      ++ f      CP Ck+k+ 
  gene714|gene714|rna714|rna714 275 NCTHKYHASCIKGWFLIS---KKEF------CPLCKEKMG 305
                                    7*************9643...3333......777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (346 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1203  (0.067098); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.55u 0.23s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 2396.61
//
Query:       gene715|gene715|rna715|rna715  [L=41]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
       0.12   11.3   0.0       0.12   11.3   0.0    1.0  1  DNA_pack_C  Probable DNA packing protein, C-terminus


Domain annotation for each model (and alignments):
>> DNA_pack_C  Probable DNA packing protein, C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   6.8e-06      0.12     232     266 ..       5      39 ..       1      41 [] 0.89

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 6.8e-06
                                    ------EEEE--B--TT--S-BS-B--STTHHHHH CS
                     DNA_pack_C 232 eessplkvlflhtkdktssveyPlyllgkekalaf 266
                                    +e+++++++++h+++++ sv++ ++ll   k+  f
  gene715|gene715|rna715|rna715   5 DEMKNIDLNYVHETNDAFSVQQKFFLLRGPKQFIF 39 
                                    678999**********************9998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (41 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       198  (0.0110436); expected 358.6 (0.02)
Passed bias filter:                      140  (0.00780858); expected 358.6 (0.02)
Passed Vit filter:                         5  (0.000278878); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.32u 0.25s 00:00:00.57 Elapsed: 00:00:00.39
# Mc/sec: 316.63
//
Query:       gene716|gene716|rna716|rna716  [L=138]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.092   10.6   0.3       0.11   10.3   0.3    1.0  1  PolC_DP2  DNA polymerase II large subunit DP2


Domain annotation for each model (and alignments):
>> PolC_DP2  DNA polymerase II large subunit DP2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.3   6.2e-06      0.11     621     707 ..      20     106 ..      10     110 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 6.2e-06
                       PolC_DP2 621 CkkCg.ketlearCeeCgekteeklvCkkceeeveeekcekcekeakavkkkkidlkellekaleklgereekleelkgv 699
                                    C++ + ++ +++ C +Cg+++  +++ +  ++e+ + ++ek+e   + +++++++ ++lle  +++l+++e+ +e +   
  gene716|gene716|rna716|rna716  20 CENMNnAQMYSHYCGKCGNECFANNQ-PANQHENADCTAEKAEDVPTLTENRQLNGEKLLELVISSLNKSETPVEYVNIY 98 
                                    66654145567889999999988443.344444446668899999999******************************** PP

                       PolC_DP2 700 kgltskek 707
                                    k+lts+++
  gene716|gene716|rna716|rna716  99 KDLTSTTR 106
                                    ****9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       717  (0.0399911); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1054.85
//
Query:       gene717|gene717|rna717|rna717  [L=310]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (310 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       485  (0.0270511); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 2318.95
//
Query:       gene718|gene718|rna718|rna718  [L=80]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.4e-06   25.6   0.0    7.4e-06   25.6   0.0    1.0  1  RVT_1     Reverse transcriptase (RNA-dependent DNA polymerase


Domain annotation for each model (and alignments):
>> RVT_1  Reverse transcriptase (RNA-dependent DNA polymerase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.0   4.1e-10   7.4e-06     121     158 ..      23      61 ..       9      80 .] 0.78

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 4.1e-10
                                    ....TEEEEESB--ST-TTHHHHHHHHHHHHHTT-T... CS
                          RVT_1 121 e.eskgryekkglpqGsvlSPllfnlfmnellrelrkra 158
                                      +s  + +  g++qG+  SP+lfnl++n+l+  l++ +
  gene718|gene718|rna718|rna718  23 DtRSALFMYDIGVRQGCSASPVLFNLYINNLFDGLSRVT 61 
                                    43667788888*********************9998754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       249  (0.0138881); expected 358.6 (0.02)
Passed bias filter:                      222  (0.0123822); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.40
# Mc/sec: 599.15
//
Query:       gene719|gene719|rna719|rna719  [L=61]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.093   12.2   0.0      0.094   12.2   0.0    1.0  1  RVT_1     Reverse transcriptase (RNA-dependent DNA polymerase


Domain annotation for each model (and alignments):
>> RVT_1  Reverse transcriptase (RNA-dependent DNA polymerase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   5.3e-06     0.094      77     112 ..       6      41 ..       5      58 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 5.3e-06
                                    CCGCCCSBB-GGGGGGG-EEET.............. CS
                          RVT_1  77 kkaFdsvpleellrkltafkvptklinliksflstr 112
                                    + a+d+v++e ll kl+ ++++ kl++l+  + + +
  gene719|gene719|rna719|rna719   6 SEAYDRVSHEGLLAKLKLYGFHGKLLRLLTGMCRRP 41 
                                    67**********************999999888444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       336  (0.0187406); expected 358.6 (0.02)
Passed bias filter:                      207  (0.0115455); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.26s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 453.62
//
Query:       gene72|gene72|rna72|rna72  [L=248]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-10   42.2   0.1    4.2e-10   40.2   0.0    1.9  2  VWA_2     von Willebrand factor type A domain


Domain annotation for each model (and alignments):
>> VWA_2  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.2   0.0   2.3e-14   4.2e-10       1     104 [.      47     151 ..      47     153 .. 0.92
   2 ?   -0.8   0.0      0.13   2.3e+03      70      93 ..     225     247 ..     195     248 .] 0.68

  Alignments for each domain:
  == domain 1  score: 40.2 bits;  conditional E-value: 2.3e-14
                      VWA_2   1 lvfvlDtSgSmrngdygptrleaakdaveallkslp.gdrvglvtfsd.gpevlipltkdkakilnalrnleakgggtnlaaaL 82 
                                +vfvlD+S + +n+dy ptr+  + d+v+  l+s   + ++g++  +  +p+ ++++tk++  i++++ +l+ +  +  + + +
  gene72|gene72|rna72|rna72  47 TVFVLDNSYYAQNQDYLPTRYIVQLDIVNYALSSSSeNHHFGVIPIAQqTPNYILTPTKNRMNIRQFISDLKFT-EEFKIPDSI 129
                                79*******************************997366*********789*********************96.********* PP

                      VWA_2  83 qlarkalkkrrkgekrvivlit 104
                                  a+  l+   +++kr +v+++
  gene72|gene72|rna72|rna72 130 YIAQRSLQYVDATQKRLVVFFS 151
                                ******9999877777777765 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.13
                      VWA_2  70 eakgggtnlaaaLqlarkalkkrr 93 
                                e+   + nla aL+l  ++ +k+r
  gene72|gene72|rna72|rna72 225 EE-MEDPNLALALRLSAEEAEKNR 247
                                32.578899999998888877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (248 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       518  (0.0288917); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 1654.23
//
Query:       gene720|gene720|rna720|rna720  [L=494]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (494 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       795  (0.0443416); expected 358.6 (0.02)
Passed bias filter:                      472  (0.0263261); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.42
# Mc/sec: 3558.15
//
Query:       gene721|gene721|rna721|rna721  [L=58]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (58 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       223  (0.0124379); expected 358.6 (0.02)
Passed bias filter:                      193  (0.0107647); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.33u 0.24s 00:00:00.57 Elapsed: 00:00:00.40
# Mc/sec: 437.86
//
Query:       gene722|gene722|rna722|rna722  [L=855]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.7e-08   33.3   0.0    5.8e-05   23.4   0.0    2.2  2  HEAT_2    HEAT repeats
    0.00088   19.3   0.5        1.5    9.3   0.0    3.6  3  HEAT      HEAT repeat


Domain annotation for each model (and alignments):
>> HEAT_2  HEAT repeats
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   7.6e-07    0.0068      15      59 ..     236     280 ..     217     287 .. 0.86
   2 !   23.4   0.0   6.4e-09   5.8e-05       2      59 ..     255     318 ..     254     327 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 7.6e-07
                         HEAT_2  15 evrraairaLgrignpealpaLvellededpavRraaaeaLgaig 59 
                                     vr+aa++ L  i  +++l+ L+ +l+++d++v+  a  aL  ++
  gene722|gene722|rna722|rna722 236 PVRQAAAHLLSFIYQKDVLDQLFMFLDHPDWEVQCSALLALKSVQ 280
                                    499999999999999999999999999999999999999998765 PP

  == domain 2  score: 23.4 bits;  conditional E-value: 6.4e-09
                         HEAT_2   2 daLlqalendpdpevrraairaLgrignp.......ealpaLvellededpavRraaaeaLgaig 59 
                                    d+L  +l ++pd+ev+  a+ aL + +++       ++  +L+ lle+ed++v  +aa+ L+ ++
  gene722|gene722|rna722|rna722 255 DQLFMFL-DHPDWEVQCSALLALKSVQHKlsstdkkDVALCLLTLLESEDEDVKCMAADMLVHFK 318
                                    6788889.9***************66665555566699***********************8764 PP

>> HEAT  HEAT repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0     0.077   6.9e+02      13      28 ..     234     249 ..     227     251 .. 0.78
   2 !    9.3   0.0   0.00016       1.5       2      26 ..     254     278 ..     253     282 .. 0.84
   3 !    4.4   0.1    0.0062        55       4      25 ..     294     315 ..     293     317 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.077
                                    SHHHHHHHHHHHHHHH CS
                           HEAT  13 speVReaAakaLgala 28 
                                    s  VR+aAa  L  ++
  gene722|gene722|rna722|rna722 234 SLPVRQAAAHLLSFIY 249
                                    556******9997665 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00016
                                    HHHHHHHHT-SSHHHHHHHHHHHHH CS
                           HEAT   2 lPlllkllsDpspeVReaAakaLga 26 
                                    l+ l   l +p++eV ++A++aL  
  gene722|gene722|rna722|rna722 254 LDQLFMFLDHPDWEVQCSALLALKS 278
                                    566666799*************975 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.0062
                                    HHHHHHT-SSHHHHHHHHHHHH CS
                           HEAT   4 lllkllsDpspeVReaAakaLg 25 
                                    +ll+ll++++ +V ++Aa  L+
  gene722|gene722|rna722|rna722 294 CLLTLLESEDEDVKCMAADMLV 315
                                    5899*************98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (855 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       453  (0.0252663); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.66u 0.27s 00:00:00.93 Elapsed: 00:00:00.44
# Mc/sec: 5867.61
//
Query:       gene723|gene723|rna723|rna723  [L=1146]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    4.6e-41  140.7   0.0    8.6e-41  139.8   0.0    1.3  1  SNF2_N      SNF2 family N-terminal domain
    2.1e-13   50.6   0.0    5.3e-13   49.3   0.0    1.7  1  Helicase_C  Helicase conserved C-terminal domain


Domain annotation for each model (and alignments):
>> SNF2_N  SNF2 family N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  139.8   0.0   9.6e-45   8.6e-41      56     307 ..     434     853 ..     428     866 .. 0.82

  Alignments for each domain:
  == domain 1  score: 139.8 bits;  conditional E-value: 9.6e-45
                                    --EEE---TTS--HHHHHHHHH...HHTTTS---.......S-..................................... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..................................... RF
                         SNF2_N  56 rGGiLaDemGLGKTvqvlalilaqrakeekdkekkrkdtlagp..................................... 98 
                                     +GiLaDemGLGKTvqvl ++   + +e k + +  k+   ++                                     
  gene723|gene723|rna723|rna723 434 INGILADEMGLGKTVQVLVFLF-SKIDEIKGSDRGSKGDDNDGvkdcdk******************************* 512
                                    58********************.443344444444444444446777888888888888888888888888888888888 PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                         SNF2_N  99 ................................................................................ 98 
                                                                                                                    
  gene723|gene723|rna723|rna723 513 ******************************************************************************** 592
                                    88888888888888888888888888888888888888888888888888888888888888888888888888888888 PP

                                    ..............................................................EEEE--HHHHHHHHHHHH CS
                                    ..............................................................xxxxxxxxxxxxxxxxxx RF
                         SNF2_N  99 ..............................................................tLivvPaslldqWeneie 116
                                                                                                  +Liv+P sl  +W+nei+
  gene723|gene723|rna723|rna723 593 ********************************tlnttldhnttlnttldhdptlnttlmnhkILIVCPGSLTGHWQNEIK 672
                                    88888888888888888888888888888888888888888888888888888888999999****************** PP

                                    HH-TTS-EEE--SSHHHH-----------------EEEE-HHHHHHHT......TTS-S-S-SEEEES-GGGT--TTSHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SNF2_N 117 rhvsssalrvlvyggqkkmkkkntkvapklladydvvittYdvlsreaelqkkrsvlkqvewkrvvlDEghtlknstska 196
                                    + ++  + ++++ +++             +     + i++Yd+++      + + ++++   ++++lDEgh l+n ++ +
  gene723|gene723|rna723|rna723 673 KITNVYEGHIYTKKDN-------------V--LSFITIISYDTYR------HAYRAFTDHTFFYLILDEGHILRNVDTAL 731
                                    9988776555555553.............2..34699********......357************************** PP

                                    HHHHHH---S-EEEE-S--SSS-HHHHHHHHHHH-TTTT--HHHHHHHTHHHHH............HHHHHHHHHHHTT- CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............xxxxxxxxxxxxxx RF
                         SNF2_N 197 aeavskLstsnrwiltGTPiqnsledlygLlkfLreepfgekqtfdkllqrpie............aqaekgrsrLlqll 264
                                    +  +s L++ n++il+GTP+qns +dl++L+++L++  +g+k+  +++ +r i+            + +ek  +  +  +
  gene723|gene723|rna723|rna723 732 YHKISALRALNKLILSGTPVQNSINDLFALFNLLMPCYLGDKNELKER-ERRIRkgkdrncgeedvRMMEKELRMVRRRV 810
                                    ****************************************97755555.3333335579666666666666666666666 PP

                                    STTEE---GGGT--S---EEEEEEEEE--HHHHHHHH...... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SNF2_N 265 qrlmlrrakkdveknlPpkteeiiflklskverksYnrllevl 307
                                     +++lrr kkdv  +lP+k+++ + + + +++r++Y+ ll ++
  gene723|gene723|rna723|rna723 811 GPFVLRRCKKDVVVDLPDKIVKDLVVVMGDEQREVYEWLLRDC 853
                                    69**********************************9877776 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.3   0.0   5.9e-17   5.3e-13       2     111 .]     983    1090 ..     982    1090 .. 0.90

  Alignments for each domain:
  == domain 1  score: 49.3 bits;  conditional E-value: 5.9e-17
                                     HHHHHHHHH.HHTTTTSEEEEEESSHHHHHHHHHH.HHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSS.EEEESGGG CS
                     Helicase_C    2 kleallell.kleeeggkilifvntidrlekvkll.lekkgikvavlhgelpqnereeileqfnkgesd.vLiatdva 76  
                                     k++al++l+ +l++ +++ilif++ ++++   +l+  e     +++l+g  +++++  ++++f +g+++ +L++t+ +
  gene723|gene723|rna723|rna723  983 KIDALKDLYgTLNRTDSRILIFCQLRRSI---RLIiDELALKDYLILDG--QTRDKSGVVRRFMAGDYKtLLLTTSTG 1055
                                     778888888899***************99...5552444467899****..678888********************* PP

                                     TSSSTSTTESEEEESSSSSSHHHHHHHHTTSSSTT CS
                     Helicase_C   77 erGidipkvnlVinfdlprnvtsyiqriGRtgRag 111 
                                     + G+++  +++Vi+f+ ++n+ +  q+++R++R+g
  gene723|gene723|rna723|rna723 1056 SLGLNLCIADTVIFFEHDYNPFNDLQAMDRAHRIG 1090
                                     *********************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       602  (0.0335769); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.75u 0.28s 00:00:01.03 Elapsed: 00:00:00.43
# Mc/sec: 7978.70
//
Query:       gene724|gene724|rna724|rna724  [L=355]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.7e-13   50.2  13.5    0.00013   22.7   0.2    6.3  5  WD40          WD domain, G-beta repeat
    5.7e-09   36.2   3.8     0.0035   17.6   0.0    4.4  4  ANAPC4_WD40   Anaphase-promoting complex subunit 4 WD40 domai
  ------ inclusion threshold ------
       0.03   14.3   0.9        2.5    8.0   0.3    2.4  2  TFIIIC_delta  Transcription factor IIIC subunit delta N-term


Domain annotation for each model (and alignments):
>> WD40  WD domain, G-beta repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.2   0.00025       1.5      10      38 .]      79     107 ..      69     107 .. 0.79
   2 !    7.0   0.0     0.002        12       5      35 ..     114     143 ..     110     144 .. 0.81
   3 !    8.4   0.0   0.00072       4.3      10      35 ..     159     185 ..     150     186 .. 0.86
   4 !   22.7   0.2   2.2e-08   0.00013       9      38 .]     200     233 ..     191     233 .. 0.80
   5 !    5.7   1.0     0.005        30      21      37 ..     327     342 ..     264     343 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00025
                                    SSSEEEEEEETTSSEEEEEETTSEEEEEE CS
                           WD40  10 HssvtslafspdgawlasGsdDgtvriWd 38 
                                       vt+++f +dg+  + G+ +g+++i d
  gene724|gene724|rna724|rna724  79 SATVTCVKFGSDGKCAIVGTSNGNLHIID 107
                                    334************999966**999965 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.002
                                    EEEESS.SSEEEEEEETTSSEEEEEETTSEEE CS
                           WD40   5 rtltGH.ssvtslafspdgawlasGsdDgtvr 35 
                                     ++  H s +  +   p  + l++Gs+D+ ++
  gene724|gene724|rna724|rna724 114 SKFNVHrSRIGTV--EPKDNVLVTGSRDRQIK 143
                                    5567787778888..899999*********98 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.00072
                                    S.SSEEEEEEETTSSEEEEEETTSEEE CS
                           WD40  10 H.ssvtslafspdgawlasGsdDgtvr 35 
                                    H + v++++ +++ ++lasG+ D++v 
  gene724|gene724|rna724|rna724 159 HvQEVCGVRMNRSATLLASGGNDNKVF 185
                                    77779****************9*9986 PP

  == domain 4  score: 22.7 bits;  conditional E-value: 2.2e-08
                                    SS.SSEEEEEEETTSSEE.EEEE..TTSEEEEEE CS
                           WD40   9 GH.ssvtslafspdgawl.asGs..dDgtvriWd 38 
                                    +H   v ++++s+ ++w+ +sG+   D+ +riW+
  gene724|gene724|rna724|rna724 200 AHrAAVKAIDWSKGSDWMmVSGGgtADKIIRIWN 233
                                    89888************735875447*******8 PP

  == domain 5  score: 5.7 bits;  conditional E-value: 0.005
                                    TSSEEEEEETTSEEEEE CS
                           WD40  21 dgawlasGsdDgtvriW 37 
                                     g  +++Gs D+++ +W
  gene724|gene724|rna724|rna724 327 LGC-FVTGSADNKLCFW 342
                                    233.568********** PP

>> ANAPC4_WD40  Anaphase-promoting complex subunit 4 WD40 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.8   0.0    0.0013         8      43      90 ..      45      88 ..      34      89 .. 0.82
   2 !   17.6   0.0   5.9e-07    0.0035      16      79 ..      58     119 ..      52     127 .. 0.81
   3 !   12.5   0.2   2.3e-05      0.14       5      90 ..     128     211 ..     127     213 .. 0.86
   4 ?    3.4   0.1     0.016        97      33      68 ..     268     304 ..     230     324 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0013
                    ANAPC4_WD40 43 sLaWkpdgklLavaysdgevrlldaesgkvvhslsvksekavtclgWg 90
                                   +L W+++   L++++ +++++l+d +s ++    s +s  +vtc+++g
  gene724|gene724|rna724|rna724 45 HLDWHQNT--LMFVC-ENKIKLMDFYSNRITDLKSFGSA-TVTCVKFG 88
                                   67887764..44555.689************99999999.6****987 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 5.9e-07
                    ANAPC4_WD40  16 dgellvfRlngqrvwtleedkedsevrsLaWkpdgklLavaysdgevrlldaesgkvvhslsvk 79 
                                    ++++ +  +  +r+ +l ++  + +v+++++  dgk   v++s+g+++++d+ ++k+  +++v+
  gene724|gene724|rna724|rna724  58 ENKIKLMDFYSNRITDL-KSFGSATVTCVKFGSDGKCAIVGTSNGNLHIIDMCTKKTS-KFNVH 119
                                    56666777777888888.788899****************************999873.45555 PP

  == domain 3  score: 12.5 bits;  conditional E-value: 2.3e-05
                    ANAPC4_WD40   5 ptmDLiAlatedgellvfRlngqrvwtleedkedsevrsLaWkpdgklLavaysdgevrlldaesgkvvhslsvksekav 84 
                                    p+ + +  ++ d ++ +  +  +++  +  +k+ +ev +++ + + +lLa + +d++v ++++ + k   ++ +++  av
  gene724|gene724|rna724|rna724 128 PKDNVLVTGSRDRQIKCMDMRSKHISFA-VEKHVQEVCGVRMNRSATLLASGGNDNKVFVMEMRNLKKEIKICAHRA-AV 205
                                    5666777788888999988888777554.589999******************************999999988888.6* PP

                    ANAPC4_WD40  85 tclgWg 90 
                                    + ++W+
  gene724|gene724|rna724|rna724 206 KAIDWS 211
                                    *****7 PP

  == domain 4  score: 3.4 bits;  conditional E-value: 0.016
                    ANAPC4_WD40  33 eedkedsevrsLaWkpdgklLav.aysdgevrlldae 68 
                                    ++++ +s+v ++ W+  +k+L   +ys++  r+ + +
  gene724|gene724|rna724|rna724 268 KAQSFNSQVCNVYWSSTNKILSThGYSKNDARISNLS 304
                                    4467788999999999999997438898888887654 PP

>> TFIIIC_delta  Transcription factor IIIC subunit delta N-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0    0.0054        32       3      61 ..      80     135 ..      79     213 .. 0.57
   2 ?    8.0   0.3   0.00042       2.5      64     107 ..     241     285 ..     218     292 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.0054
                   TFIIIC_delta   3 stldalaWSeDgqlavatge..siyiLepklpl.qklklnrsgiqaseatkqavklranv.fs 61 
                                    +t+ ++++ +Dg++a++  +  +++i+++  +  +k++++rs+i + e       ++ nv ++
  gene724|gene724|rna724|rna724  80 ATVTCVKFGSDGKCAIVGTSngNLHIIDMCTKKtSKFNVHRSRIGTVE-------PKDNVlVT 135
                                    6789999*********97652268888887776556666666666655.......44444422 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.00042
                   TFIIIC_delta  64 edpnwsq.aseenysigeeqsslisldtkinaqsqvvaaaWSPlg 107
                                     + n s+ + ++   +   ++ +++l+++++++sqv ++ WS+++
  gene724|gene724|rna724|rna724 241 NNENSSHmHMKRAHGLQSTSTTDKMLVKAQSFNSQVCNVYWSSTN 285
                                    4444433044455667777888899*****************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (355 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       592  (0.0330191); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.22s 00:00:00.71 Elapsed: 00:00:00.39
# Mc/sec: 2746.17
//
Query:       gene725|gene725|rna725|rna725  [L=168]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
       0.84   10.1   6.2        2.2    8.7   3.7    2.0  2  DUF3048_C  Protein of unknown function (DUF3048) C-terminal d


Domain annotation for each model (and alignments):
>> DUF3048_C  Protein of unknown function (DUF3048) C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   3.7   0.00012       2.2       6      51 ..       8      53 ..       3      67 .. 0.78
   2 ?    2.9   0.4     0.008   1.4e+02       9      48 ..      58     100 ..      47     122 .. 0.65

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00012
                                   --SSEEEEEETTTTEEEEEETTEE-B-TTTSSB--BSEEEEEE-.. CS
                      DUF3048_C  6 sknkstfeYdaedglYlryqdgephideetgeqlavkNvivlevev 51
                                   ++++++++Y++++++Y+r   ++ + +++  + l  + v +  ++ 
  gene725|gene725|rna725|rna725  8 QRRNTRLNYNEAKKQYRRRIRNKHTYNQKVRRTLGLDKVKIADAKR 53
                                   566799******************9999999999999998887743 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.008
                                    S.EEEEEETTTTEEEEEETTEE-B-T..TTSSB--BSEEEEEE CS
                      DUF3048_C   9 k.stfeYdaedglYlryqdgephide..etgeqlavkNvivle 48 
                                    +  +++++ ++ + +r  +++++  e  + ++  a +N++++ 
  gene725|gene725|rna725|rna725  58 QlRYYTWSRKRPKQDRTIYEDENEPEkrKRKSVNASDNLVLMR 100
                                    2567777777777777777555444422334445566776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1547  (0.0862848); expected 358.6 (0.02)
Passed bias filter:                      477  (0.0266049); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 1080.61
//
Query:       gene726|gene726|rna726|rna726  [L=166]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       892  (0.0497518); expected 358.6 (0.02)
Passed bias filter:                      246  (0.0137208); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.53
# Mc/sec: 942.04
//
Query:       gene727|gene727|rna727|rna727  [L=76]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.3e-21   76.9   1.3    1.9e-21   76.4   1.3    1.2  1  CBFB_NFYA  CCAAT-binding transcription factor (CBF-B/NF-YA) s


Domain annotation for each model (and alignments):
>> CBFB_NFYA  CCAAT-binding transcription factor (CBF-B/NF-YA) subunit B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.4   1.3   1.1e-25   1.9e-21       1      56 []       4      60 ..       4      60 .. 0.97

  Alignments for each domain:
  == domain 1  score: 76.4 bits;  conditional E-value: 1.1e-25
                      CBFB_NFYA  1 eplyVNakQynrIlkRReaRakleaelkl.rkarkkylheSRhkhAmrRpRgpgGRF 56
                                   +plyVNa+Q+n+I kR+ +R+ l++ ++  + +   ylheSRh+hAm+R R+p+GRF
  gene727|gene727|rna727|rna727  4 QPLYVNAHQFNCIRKRKLRRDFLDSITRPkSVNGSGYLHESRHRHAMNRLRAPSGRF 60
                                   69************************99988999**********************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       409  (0.0228122); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.31s 00:00:00.87 Elapsed: 00:00:00.56
# Mc/sec: 407.44
//
Query:       gene728|gene728|rna728|rna728  [L=128]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0081   15.5   0.0     0.0095   15.3   0.0    1.1  1  ABC2_membrane_2  ABC-2 family transporter protein
  ------ inclusion threshold ------
      0.045   14.0   3.3        0.8   10.0   0.1    2.6  3  Chordopox_A13L   Chordopoxvirus A13L protein
      0.057   13.2   0.2          2    8.2   0.1    2.1  2  Coa1             Cytochrome oxidase complex assembly protein 


Domain annotation for each model (and alignments):
>> ABC2_membrane_2  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   1.6e-06    0.0095      30     102 ..      46     118 ..       2     120 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.6e-06
                ABC2_membrane_2  30 alaylkdlgsslqseakaikeatlaleyveaasasdeaedtdqdlkvvstimavlipviaalfgadaiagEke 102
                                     + +++ ++++++ ++ ++++++ + + + +  ++++++++ +   +++++++++++vi +l+g+++  +E+ 
  gene728|gene728|rna728|rna728  46 QIVMSSYNQDENSLDEESEVQNDAKDKGGFMKKMKKMLSEFVEGVTIGKMLFFGFVVVICVLIGYQIRKREEQ 118
                                    455666777788888889999999999999999*********************************9888875 PP

>> Chordopox_A13L  Chordopoxvirus A13L protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.2      0.65   3.9e+03       9      20 ..       5      16 ..       1      30 [. 0.57
   2 ?    4.5   0.0     0.007        42      14      56 ..      43      81 ..      38      86 .. 0.79
   3 ?   10.0   0.1   0.00013       0.8       2      29 ..      92     119 ..      91     127 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.65
                 Chordopox_A13L  9 iiCvaivglivY 20
                                   +i v +  ++ Y
  gene728|gene728|rna728|rna728  5 VILVYVLSIVTY 16
                                   444444444444 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.007
                 Chordopox_A13L 14 ivglivYgiYnrkketqttnpstveeyeeedniKtgfvdkLks 56
                                   i+  iv + Yn+ ++++ ++ +   + + +d  K gf+ k+k+
  gene728|gene728|rna728|rna728 43 ITPQIVMSSYNQDENSLDEESEV--QNDAKD--KGGFMKKMKK 81
                                   566799999*9999999888775..556666..7899988876 PP

  == domain 3  score: 10.0 bits;  conditional E-value: 0.00013
                 Chordopox_A13L   2 iadlllliiCvaivglivYgiYnrkket 29 
                                    i+++l++   v+i +li Y i +r++++
  gene728|gene728|rna728|rna728  92 IGKMLFFGFVVVICVLIGYQIRKREEQS 119
                                    899******************8887765 PP

>> Coa1  Cytochrome oxidase complex assembly protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.1   0.00034         2       7      50 ..       4      47 ..       1      59 [. 0.87
   2 ?    3.2   0.0     0.011        68       3      30 ..      96     123 ..      94     125 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00034
                           Coa1  7 fvvgvvvalayifnyektsssivrsvlyqlrrspevrelLGeei 50
                                   +v++v+v+++++ nye t ++i+  +  +l r+p ++  +  +i
  gene728|gene728|rna728|rna728  4 LVILVYVLSIVTYNYEHTYTNILPLTHLHLTRNPILIRRITPQI 47
                                   6899*****************************99887766555 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.011
                           Coa1   3 tfavfvvgvvvalayifnyektsssivr 30 
                                    +f  fvv+++v++ y + ++  +s++vr
  gene728|gene728|rna728|rna728  96 LFFGFVVVICVLIGYQIRKREEQSNYVR 123
                                    5678999999999999999999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1227  (0.0684366); expected 358.6 (0.02)
Passed bias filter:                      777  (0.0433376); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 855.87
//
Query:       gene729|gene729|rna729|rna729  [L=105]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0015   18.6   0.8     0.0026   17.9   0.7    1.5  2  DnaJ      DnaJ domain
  ------ inclusion threshold ------
       0.27   11.0   8.3       0.79    9.5   8.3    1.8  1  zf-CSL    CSL zinc finger


Domain annotation for each model (and alignments):
>> DnaJ  DnaJ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.7   2.9e-07    0.0026       5      34 ..       3      32 ..       2      51 .. 0.88
   2 ?   -3.7   0.0       1.6   1.4e+04      13      20 ..      62      69 ..      59      73 .. 0.65

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 2.9e-07
                                   HHTSSTTG-HHHHHHHHHHHHHHHSTTTSC CS
                           DnaJ  5 iLgvskdasedeIkkaYrklalkyHPDknp 34
                                    L+++++ + +++ +aY++ ++kyHP + +
  gene729|gene729|rna729|rna729  3 YLNLNRNYTYNDLDQAYKRAIKKYHPIRTK 32
                                   59************************8763 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 1.6
                                   -HHHHHHH CS
                           DnaJ 13 sedeIkka 20
                                   + deI +a
  gene729|gene729|rna729|rna729 62 NVDEIERA 69
                                   56777776 PP

>> zf-CSL  CSL zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   8.3   8.8e-05      0.79       3      57 ..      56      99 ..      54     100 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 8.8e-05
                                   EEGGGSEEETTTTEEEEEETTSSEEEEEHHHHHTT....--EEEETTSSEEEEEE CS
                         zf-CSL  3 veledfefdeeeesyyypCRCgdeFelteedleegaegaevvvqCssCSLwikVk 57
                                   +++ ++++de e      C Cg +++l+ e+        + +v+C  CSL++k++
  gene729|gene729|rna729|rna729 56 CNMREMNVDEIER---ALCQCGHRYDLEMEN--------DGIVECCWCSLKVKIV 99
                                   5666777766443...57*******997654........459**********996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       886  (0.0494171); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 759.37
//
Query:       gene73|gene73|rna73|rna73  [L=227]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.3e-07   31.0   0.4      4e-07   30.2   0.2    1.5  1  Arrestin_N  Arrestin (or S-antigen), N-terminal domain


Domain annotation for each model (and alignments):
>> Arrestin_N  Arrestin (or S-antigen), N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.2   0.2   2.2e-11     4e-07       3     102 ..       9     103 ..       5     133 .. 0.81

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 2.2e-11
                                EEES-SEEEEETT--EEEEEEE-CCCCTT.CEEEEEEEEEEEESSSSTTTTCCCEEEEEEEEEEEEESTSSSSS.SSSSHHHHH CS
                 Arrestin_N   3 ieldkrdevyhpgetvdGkvlleteelkkarkvkielsgkartgweesevagktfrkdltlkkkqeyleteksllkskkdsqek 86 
                                i+ld  +  + ++e v+G++ le  e++++  +++++  k++ + +  ++ +++f+k++   ++ +++++e ++++s  +  +k
  gene73|gene73|rna73|rna73   9 ITLD--KAYFLTNEIVSGRIHLELLEPINLHTIYVHFYKKFECEFDTPRN-DSSFTKKRCRIDR-TVYNKEVTVYES-FRHVNK 87 
                                4444..6677888**********************998888888885554.5555555555554.456666777788.8999** PP

                                HHH-TTEEEEEE---T CS
                 Arrestin_N  87 LpkGehafpFsfelPk 102
                                L +G h+fpF ++l +
  gene73|gene73|rna73|rna73  88 LGSGYHVFPFKITLRS 103
                                ************9965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (227 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       480  (0.0267723); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1540.07
//
Query:       gene730|gene730|rna730|rna730  [L=257]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1331  (0.0742373); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 1602.20
//
Query:       gene731|gene731|rna731|rna731  [L=140]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       832  (0.0464053); expected 358.6 (0.02)
Passed bias filter:                      614  (0.0342462); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1063.23
//
Query:       gene732|gene732|rna732|rna732  [L=491]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.03   14.3   0.4      0.084   12.8   0.4    1.9  1  HLH       Helix-loop-helix DNA-binding domain


Domain annotation for each model (and alignments):
>> HLH  Helix-loop-helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.4   4.7e-06     0.084       1      52 [.     434     484 ..     434     485 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4.7e-06
                                    HHHHHHHHHHHHHHHHHHHHHHHHHCSTCSTTSS-STHHHHHHHHHHHHHHH CS
                            HLH   1 rraahnerErrRRdriNsaleeLrellPslppskKlsKaeiLekAveYIkhL 52 
                                    +++ h+e E rRR  iN +l    + +   +  +K +K  i   A + I +L
  gene732|gene732|rna732|rna732 434 KKVLHSECELRRRTAINLGLLAISDFVD-KTVATKRNKKKIIFGALQLILKL 484
                                    6789************************.89999*********999999988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (491 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1508  (0.0841095); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.41
# Mc/sec: 3577.91
//
Query:       gene733|gene733|rna733|rna733  [L=196]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.3e-33  113.8   0.2    6.7e-33  113.4   0.2    1.1  1  Ribosomal_S7  Ribosomal protein S7p/S5e


Domain annotation for each model (and alignments):
>> Ribosomal_S7  Ribosomal protein S7p/S5e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.4   0.2   3.8e-37   6.7e-33      15     149 .]      53     196 .]      43     196 .] 0.93

  Alignments for each domain:
  == domain 1  score: 113.4 bits;  conditional E-value: 3.8e-37
                                    -SSTTSBHHHHHHHHHSB....TTBHHHHHHHHHHHHHHHHHHHSS-HHHHHHHHHHHCS-SEEEEEEBSSSSBEEEEEE CS
                   Ribosomal_S7  15 dpkynselveklinklmk....dGkkslAekivygaldiieektkkdplevleeAlenvkPrvevksrrvGGatyqvpve 90 
                                    + k + ++ e++  ++mk    +Gkk lA++ +++a++i++  t+++pl+v+++A+ n+ Pr++  ++  GGa+ + +v+
  gene733|gene733|rna733|rna733  53 NGKSRIPITERFCCYMMKkgrnSGKKLLAMRCLEDAFTIVHILTGQNPLQVFVDAIINSGPREDSARIGRGGAMKRTSVD 132
                                    45678899**********99999********************************************************* PP

                                    E-HHHHHHHHHHHHHHHH...STSSSS-HHHHHHHHHHHHHTT-..SHHHHHHHHHHHHHHHTG CS
                   Ribosomal_S7  91 vrpkRrqalAlrwiieaa...rkrkeksmaekLaeElidAaege..gaavkkreethrmAeanr 149
                                    v+p Rr ++Al  + ++    + ++ +++ae++aeEli+Aa+ +  ++avkkr+e++r+A++nr
  gene733|gene733|rna733|rna733 133 VSPTRRLNIALFLLSRGIresAMKNVRTFAECIAEELIAAAKASpnSYAVKKRDEIERVAKSNR 196
                                    **************999965566778899**************999*****************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       399  (0.0222544); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 1294.02
//
Query:       gene734|gene734|rna734|rna734  [L=39]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (39 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       914  (0.0509789); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.25s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 289.35
//
Query:       gene735|gene735|rna735|rna735  [L=547]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (547 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       898  (0.0500865); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.56u 0.26s 00:00:00.82 Elapsed: 00:00:00.44
# Mc/sec: 3738.21
//
Query:       gene736|gene736|rna736|rna736  [L=79]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.09   12.4   1.0      0.097   12.3   1.0    1.0  1  DCB       Dimerisation and cyclophilin-binding domain of Mon2


Domain annotation for each model (and alignments):
>> DCB  Dimerisation and cyclophilin-binding domain of Mon2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   1.0   5.4e-06     0.097       3      56 ..       4      60 ..       2      72 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5.4e-06
                            DCB  3 askllealqsdlkalsseskrkh..skvkeasekgilkLktikssseee.eqslaea 56
                                   ++k+l+ +++ l+++ +es++    ++++e  + ++ +L+t +++++ + ++++ e+
  gene736|gene736|rna736|rna736  4 KNKFLHRIVERLQEIEKESRKNLteKDIEEVMNTISNRLRTTEQKDRMVeMNNIGES 60
                                   6899*****************8622689**************999955456665554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2853  (0.159128); expected 358.6 (0.02)
Passed bias filter:                     1158  (0.0645881); expected 358.6 (0.02)
Passed Vit filter:                       134  (0.00747392); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.32s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 501.54
//
Query:       gene737|gene737|rna737|rna737  [L=217]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.6e-30  105.8   0.1    2.2e-30  105.3   0.1    1.2  1  Ribosomal_L16  Ribosomal protein L16p/L10e


Domain annotation for each model (and alignments):
>> Ribosomal_L16  Ribosomal protein L16p/L10e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.3   0.1   1.2e-34   2.2e-30       2     132 .]      13     166 ..      10     166 .. 0.94

  Alignments for each domain:
  == domain 1  score: 105.3 bits;  conditional E-value: 1.2e-34
                                    XSSXXBSSSXXSSTSXX.XSXXXXXESX...........EEEEESSXEEEEHHHHHHHHHHHCTCCCCTSXC...EEXXS CS
                  Ribosomal_L16   2 krkkyrKsrkryirgvs.tkgtklefgd...........ygLvalekgqltaealeaariainrylkkkrgk...klwir 66 
                                    k++ y Ks+  y+rgv+ +k+++ ++g+           + L++l k+q+++eale+ar+++n+y+    gk   + ++ 
  gene737|gene737|rna737|rna737  13 KNRGYIKSK--YCRGVPdPKIRIHDIGKkgahadefpcmIYLKSLVKEQISSEALETARVTANKYMFGAAGKdgyHYRVL 90 
                                    677788888..***************************999**************************9999899****** PP

                                    XXXXEEEEE-.....SS-TTTSSSS....XEEEEEEEEEXSSCEEEEE.TTXXXSHHHHHHHHHHHHTSSSXEEEE CS
                  Ribosomal_L16  67 vfphhpvtkk.....agedRmgkGk....Gkpegwvarvkigqiifei.kagvneeiakealrraasKlpiktkiv 132
                                    v+p  +++++     ag+dR+++G+    Gkp+g +arv+++q ++ i  +    ++a ealrra++K+p+++++v
  gene737|gene737|rna737|rna737  91 VHPYNVLRINkmlscAGADRLQTGMrgafGKPYGLCARVSMNQRVLAIrTKPAFVKHAVEALRRAKYKFPGNYEVV 166
                                    ************************************************533358899***************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       328  (0.0182944); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1454.81
//
Query:       gene738|gene738|rna738|rna738  [L=214]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-09   37.6   0.3    5.9e-09   35.9   0.3    1.7  1  ERAP1_C   ERAP1-like C-terminal domain
  ------ inclusion threshold ------
      0.053   12.5   0.0      0.082   11.9   0.0    1.3  1  DUF4788   Domain of unknown function (DUF4788)


Domain annotation for each model (and alignments):
>> ERAP1_C  ERAP1-like C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.9   0.3   6.6e-13   5.9e-09     161     279 ..      60     173 ..       2     208 .. 0.69

  Alignments for each domain:
  == domain 1  score: 35.9 bits;  conditional E-value: 6.6e-13
                                    S-HHHHHHHHHHHHHHS-HHHHHHHHHHHHC-SSHHHHHHHHHHHCC-S-HHHHHHHHHHCTTT..S-GGGHHHHHHHH. CS
                        ERAP1_C 161 ippdlrwavycalaanggeaewdallerykdtsapsekeaalralaatpdpellerllnfvlesdevrnqdlrallagla 240
                                    i+p    + y+  + +   +++d  +++yk+++a + ++++l a++ t++ e+  r+ ++++ s++++ qd  +l a+l 
  gene738|gene738|rna738|rna738  60 IHPMYLLSYYTQKMMA--NNDLDYFIDLYKKSTA-EIRTKVLVAIGRTTSLEVYSRVVQLMV-SKTIKAQDKIHLSASLM 135
                                    5555555555555433..468********99999.**************************8.99**************9 PP

                                    HSTTHHHHHHHHHHHCHCCHHHHTSSTSCHHHHHHHHHT CS
                        ERAP1_C 241 nnpegrellwefvkenwdalakrwsggeildrivkgllp 279
                                    nn    e    ++ en++a+ + +   +++  +v+ +++
  gene738|gene738|rna738|rna738 136 NNLNFKEHYITYFVENFEAIRQALN-DNLMMYVVEQVVG 173
                                    99888888889***********997.4788888887776 PP

>> DUF4788  Domain of unknown function (DUF4788)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   9.1e-06     0.082      25      69 ..     124     168 ..     108     185 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 9.1e-06
                        DUF4788  25 nkkklkltssrinvkeFkagaltefvssPkeLrqsLeekGipvtv 69 
                                     ++k++l++s +n  +Fk+   t fv++ +++rq+L+++ +  +v
  gene738|gene738|rna738|rna738 124 AQDKIHLSASLMNNLNFKEHYITYFVENFEAIRQALNDNLMMYVV 168
                                    4789**********************************9776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       765  (0.0426683); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1438.55
//
Query:       gene739|gene739|rna739|rna739  [L=163]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.6e-10   39.7   1.2    1.5e-09   38.7   1.2    1.5  1  CS        CS domain
  ------ inclusion threshold ------
      0.091   13.3   0.0       0.14   12.7   0.0    1.2  1  PPDFL     Differentiation and proliferation regulator


Domain annotation for each model (and alignments):
>> CS  CS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.7   1.2   1.7e-13   1.5e-09       2      76 .]       5      79 ..       4      79 .. 0.86

  Alignments for each domain:
  == domain 1  score: 38.7 bits;  conditional E-value: 1.7e-13
                                   SCEEEEETTEEEEEEE-TTCTTTTTCEEEEEETTEEEEEETSCEEEEECEBSS-BETTT..EEEEEETTEEEEEEEB CS
                             CS  2 kydWyQtldeVvvtiyvkkvnikkkdvkvefkerslkvkigkeklliegeLfgpIdpee..sswtieskkveitLkK 76
                                   +++W+Q+ deV v ++ ++ +i+k+dvkve++ +++k+ + k  ++++geL +pI+ ++    + i +  v +tL+K
  gene739|gene739|rna739|rna739  5 NFKWDQEYDEVQVMVPYSE-DITKDDVKVELTRTTFKLCL-KGVVVLSGELSNPIKSDSkdILFYIDDGQVVVTLEK 79
                                   79*****************.9**************77776.449999********9875115666668899999988 PP

>> PPDFL  Differentiation and proliferation regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   1.5e-05      0.14      49      97 ..      79     128 ..      68     139 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.5e-05
                          PPDFL  49 adsghwwasffFgkstlpfmatvlespeksesp.qassskitcdlaqeal 97 
                                    ++s +ww sff g +++ +    ++++ k e   + ++s +   ++q++ 
  gene739|gene739|rna739|rna739  79 KESRKWWDSFFLGGEKVDINDVASKKQTKFEDLdPEAQSLVEKMMHQQKN 128
                                    57899**********99987777777777666646667766666665554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1259  (0.0702214); expected 358.6 (0.02)
Passed bias filter:                      764  (0.0426125); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 1132.98
//
Query:       gene74|gene74|rna74|rna74  [L=148]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
     0.0042   17.6   1.1     0.0054   17.2   1.1    1.1  1  Arrestin_C  Arrestin (or S-antigen), C-terminal domain


Domain annotation for each model (and alignments):
>> Arrestin_C  Arrestin (or S-antigen), C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   1.1     3e-07    0.0054      10     124 ..      10     114 ..       4     123 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 3e-07
                                EES-SEEETT--EEEEEEEEE-SSSEEEEEEEEEEEEEEEESS..SEEEEEEEEEEEEE---B-TTEE.EEEEEEE.----B-- CS
                 Arrestin_C  10 slpkkgyvpGetipvtvkidndskkkvkkikvslvqhvdvcafnrsnkkeknvvaksdsvkvtsaakdkletevelqiPeeltp 93 
                                +++k+ y+  +ti +   + n+    +k +k++l  h+  +a++ +  ++ + va+sd+  v   + ++    + ++iP +++p
  gene74|gene74|rna74|rna74  10 HTDKNRYATTDTIVFFTRVSNNAY-GIKGVKLRLYCHLALKAKS-NVVNKIKLVASSDKSAV---EHNECR--TMIKIPSNAAP 86 
                                689999999999999999999885.9*****************4.55577777888898888...444455..889******** PP

                                ---S---EEEEEEEEEEEEEEESSEEEEEEE CS
                 Arrestin_C  94 ssarnvelikvsYklkvkltlsgsggelsle 124
                                +     + + v Y+l  ++++s + + + +e
  gene74|gene74|rna74|rna74  87 TV--YEKYLCVYYTLSAVVHIS-RTSPIVIE 114
                                **..89999**********999.44566665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       423  (0.0235931); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1094.53
//
Query:       gene740|gene740|rna740|rna740  [L=382]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
       0.12   12.2   0.0       0.19   11.5   0.0    1.3  1  Plasmodium_HRP  Plasmodium histidine-rich protein (HRPII/III)


Domain annotation for each model (and alignments):
>> Plasmodium_HRP  Plasmodium histidine-rich protein (HRPII/III)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   1.1e-05      0.19      34     169 ..     139     275 ..      86     286 .. 0.35

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 1.1e-05
                 Plasmodium_HRP  34 sknakglnsnkrllheaqahaadahhahhaadahhahhaadahhahhaadahhahhaadahhahhaadahhahhaadaah 113
                                    +++a++ +++++   e +a  ++ + a     a   ++a +  +a     a    +a +a++a    +a   ++  +  +
  gene740|gene740|rna740|rna740 139 AEEARKAEEARKTEEERKA--EEERLAEEERKAEEERKAEEERKAEEERKAEEERKAEEARKAEEERKAEEERRVEEERK 216
                                    2233333333333333332..12222222222222222222222222222222222222222222222222222222222 PP

                 Plasmodium_HRP 114 ahhaadahhahhaadahhaad...ahhaayahhahhaadahhaadahhaadahhaadah 169
                                    a    +a  a  a +     +   a  a +   a +a +   a +a +a +  +a +a+
  gene740|gene740|rna740|rna740 217 AEEERKAEEARRANEERQKVEerkAEEAKKVEEARKAEEMRLAEEAIKAEEERKAEEAR 275
                                    22222222222222211111101111111222222222222222222222222222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (382 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3051  (0.170171); expected 358.6 (0.02)
Passed bias filter:                      777  (0.0433376); expected 358.6 (0.02)
Passed Vit filter:                       500  (0.0278878); expected 17.9 (0.001)
Passed Fwd filter:                       161  (0.00897987); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 2.50u 0.41s 00:00:02.91 Elapsed: 00:00:00.66
# Mc/sec: 1735.46
//
Query:       gene741|gene741|rna741|rna741  [L=79]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.044   13.5  21.8      0.055   13.2  21.8    1.3  1  Casc1_N          Cancer susceptibility candidate 1 N-terminus
       0.44   10.4  30.1       0.53   10.1  30.1    1.1  1  CCDC66           Coiled-coil domain-containing protein 66
       0.87    9.2   8.1          1    9.0   8.1    1.1  1  BNIP3            BNIP3
        4.5    7.2  15.0          5    7.0  15.0    1.1  1  RPN2_C           26S proteasome regulatory subunit RPN2 C-ter
        4.9    6.7  24.8        5.2    6.6  24.8    1.1  1  DDRGK            DDRGK domain


Domain annotation for each model (and alignments):
>> Casc1_N  Cancer susceptibility candidate 1 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2  21.8   1.5e-05     0.055       1      48 [.      10      56 ..       3      75 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.5e-05
                        Casc1_N  1 eelreeEeeRlraeeeererleeerrekeereqlaaeqarrkeeleel 48
                                   ee+r++ eeR++ae++erer+++e+re+++ eql  +q+r+ +e e+ 
  gene741|gene741|rna741|rna741 10 EEKRRANEERQKAEKKERERIKAEERERRKNEQL-SNQERIRKEREQQ 56
                                   5788889999999999999999999999999986.5555555555543 PP

>> CCDC66  Coiled-coil domain-containing protein 66
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1  30.1   0.00015      0.53      39      97 ..       3      58 ..       1      65 [. 0.89

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00015
                         CCDC66 39 aatleererkRrkalEyqnaikkQleEkerikklEkerrrqeeqleeerlrRereeeqe 97
                                   a++   +e+kRr  +E q+a kk   E+erik +E+err++e+  ++er+r+ere++++
  gene741|gene741|rna741|rna741  3 AEKARKAEEKRRANEERQKAEKK---ERERIKAEERERRKNEQLSNQERIRKEREQQRN 58
                                   67778899999988899999986...*****************************9875 PP

>> BNIP3  BNIP3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   8.1   0.00029         1      71     127 ..      16      75 ..       2      77 .. 0.64

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00029
                          BNIP3  71 spprpksP.qdegqidve..serdpssqseeeaseeekeeeillkkdadWvadwssrpen 127
                                    + +r k+  +++ +i+ e   +r+++  s++e + +e+e++ + ++d+d+v+ w s  ++
  gene741|gene741|rna741|rna741  16 NEERQKAEkKERERIKAEerERRKNEQLSNQERIRKEREQQRNHDNDTDYVSVWGSSENQ 75 
                                    3445555523444455544433333455666669999999999***********997665 PP

>> RPN2_C  26S proteasome regulatory subunit RPN2 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0  15.0    0.0014         5      73     137 ..       4      68 ..       1      75 [. 0.63

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0014
                                    ----------------------------SS----SSEEEEESSSB--TTCCTTEEE-SSSSEEES CS
                         RPN2_C  73 dkmdvdeekeekekkekekkekekeeekkkkekektfekleNpaRVlpaQlkyisfkkdsrYkpv 137
                                    +k  + eek+ ++++++++++ke+e+ k ++++  + e+l+N  R+ ++ ++  + ++d+ Y++v
  gene741|gene741|rna741|rna741   4 EKARKAEEKRRANEERQKAEKKERERIKAEERERRKNEQLSNQERIRKEREQQRNHDNDTDYVSV 68 
                                    44444444444444444444444444666677777778888888888888888777777777776 PP

>> DDRGK  DDRGK domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6  24.8    0.0014       5.2      16      74 ..       4      55 ..       1      74 [. 0.46

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0014
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          DDRGK 16 kkrqqreaeeeereerkkleekreeerkekeekeeekekkkeeeerkkeeekerkeqee 74
                                   +k        ++ ee+++ +e+r+++ k+++e+++++e+++ ++e+  ++e+ rke e+
  gene741|gene741|rna741|rna741  4 EKA-------RKAEEKRRANEERQKAEKKERERIKAEERERRKNEQLSNQERIRKEREQ 55
                                   333.......3344444444444444444444444444444444444444444444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3253  (0.181438); expected 358.6 (0.02)
Passed bias filter:                      979  (0.0546043); expected 358.6 (0.02)
Passed Vit filter:                       246  (0.0137208); expected 17.9 (0.001)
Passed Fwd filter:                        42  (0.00234257); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.52u 0.36s 00:00:00.88 Elapsed: 00:00:00.45
# Mc/sec: 528.95
//
Query:       gene742|gene742|rna742|rna742  [L=56]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (56 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       437  (0.0243739); expected 358.6 (0.02)
Passed bias filter:                      207  (0.0115455); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.29s 00:00:00.67 Elapsed: 00:00:00.45
# Mc/sec: 371.51
//
Query:       gene743|gene743|rna743|rna743  [L=156]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.4e-20   71.5   2.6      8e-20   70.9   0.4    1.9  2  Nse4_C    Nse4 C-terminal
  ------ inclusion threshold ------
      0.094   13.2   0.8       0.66   10.5   0.1    2.2  2  DUF1878   Protein of unknown function (DUF1878)
       0.11   12.6   0.6       0.48   10.6   0.0    2.2  2  DUF3911   Protein of unknown function (DUF3911)


Domain annotation for each model (and alignments):
>> Nse4_C  Nse4 C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.1      0.12   7.4e+02      30      46 ..      32      48 ..      13      66 .. 0.58
   2 !   70.9   0.4   1.3e-23     8e-20       1      90 [.      72     156 .]      72     156 .] 0.86

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.12
                         Nse4_C 30 dgkvkieldedglpvle 46
                                   + +vkie+++++   +e
  gene743|gene743|rna743|rna743 32 KREVKIEEQDRKSTKVE 48
                                   34455555544443332 PP

  == domain 2  score: 70.9 bits;  conditional E-value: 1.3e-23
                         Nse4_C   1 pislfkfvinpksFaqtVeNlFylSfLvkdgkvkieldedglpvleeteeeeeekakeeeakkkqavlsldmetWkelie 80 
                                    +i+++++v++p+sF++t+eN+FylSf +k  kvk+  ++ ++ v++++ ++     + +e + ++++ s+d+ ++k++i+
  gene743|gene743|rna743|rna743  72 KIEYYRLVVDPNSFTKTIENIFYLSFAIKLKKVKFCPEDGKILVMKDVGDK-----EPNERHINHFISSIDYVEYKRIIH 146
                                    589**********************************97777666533333.....2345678***************** PP

                         Nse4_C  81 afdikeplip 90 
                                    +++ik+p+i+
  gene743|gene743|rna743|rna743 147 NLNIKKPFIQ 156
                                    ********95 PP

>> DUF1878  Protein of unknown function (DUF1878)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.2     0.065   3.9e+02      27      47 ..      18      38 ..       3      60 .. 0.59
   2 ?   10.5   0.1   0.00011      0.66      14      49 ..      60      95 ..      45     105 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.065
                                   -HHHHHHHHTT--HH.HHHHHH CS
                        DUF1878 27 lpfyklviekklske.eveeil 47
                                   +++y+lvi  k +k+ ev+ i+
  gene743|gene743|rna743|rna743 18 KNHYSLVIPDKSKKKrEVK-IE 38
                                   6789999976655541544.33 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00011
                                   HHHHHHTTS-TTT-HHHHHHHHTT--HHHHHHHHHH CS
                        DUF1878 14 yqkLllkmideeklpfyklviekklskeeveeilkl 49
                                    ++ +++++ ++k+ +y+lv++ +   + +e+i++l
  gene743|gene743|rna743|rna743 60 RIDTIVHAVGDQKIEYYRLVVDPNSFTKTIENIFYL 95
                                   4677899*****************99999**99987 PP

>> DUF3911  Protein of unknown function (DUF3911)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.2      0.17     1e+03      36      52 ..      46      62 ..       4      81 .. 0.73
   2 ?   10.6   0.0     8e-05      0.48      35      58 ..     120     143 ..     111     151 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.17
                        DUF3911 36 eveanetkhnefvasid 52
                                    ve ++ k+++f   id
  gene743|gene743|rna743|rna743 46 KVEHKKMKDENFAHRID 62
                                   45556666666666666 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 8e-05
                        DUF3911  35 veveanetkhnefvasidlqanes 58 
                                     + e+ne++ n+f++sid   ++ 
  gene743|gene743|rna743|rna743 120 GDKEPNERHINHFISSIDYVEYKR 143
                                    5678**************988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1642  (0.0915835); expected 358.6 (0.02)
Passed bias filter:                      642  (0.0358079); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 1094.92
//
Query:       gene744|gene744|rna744|rna744  [L=128]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      2e-28   98.9   0.0    2.3e-28   98.7   0.0    1.0  1  TFIID-31kDa    Transcription initiation factor IID, 31kD subu
    6.3e-06   26.1   0.0    9.6e-06   25.5   0.0    1.2  1  Bromo_TP       Bromodomain associated
    0.00034   20.7   0.1    0.00048   20.2   0.1    1.2  1  TAF            TATA box binding protein associated factor (TA
    0.00051   20.4   0.2    0.00069   20.0   0.2    1.2  1  Histone        Core histone H2A/H2B/H3/H4
    0.00057   20.2   0.0    0.00077   19.8   0.0    1.2  1  CENP-S         CENP-S protein
  ------ inclusion threshold ------
       0.12   12.6   0.1       0.17   12.2   0.1    1.2  1  CBFD_NFYB_HMF  Histone-like transcription factor (CBF/NF-Y) a


Domain annotation for each model (and alignments):
>> TFIID-31kDa  Transcription initiation factor IID, 31kD subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.7   0.0   7.8e-32   2.3e-28       2     116 ..       4     117 ..       3     122 .. 0.95

  Alignments for each domain:
  == domain 1  score: 98.7 bits;  conditional E-value: 7.8e-32
                    TFIID-31kDa   2 ekrPrdarlihliLaslgvteyeerVvlqLldfayrytssvLedAkvlaehakkkevslddvrlAiqsrlekqfkepppk 81 
                                    ++ Prd+++i+liL+slg++e+e++ +lq+ +f+y+y ++v++dA+ +ae  +++ ++ +d++lA+q+++   f +ppp+
  gene744|gene744|rna744|rna744   4 NSAPRDTKVISLILRSLGIEECEPKAILQIHEFIYKYATDVMKDASQYAEMVDRQVITEKDIKLALQTKVGRYFVPPPPR 83 
                                    679***************************************************************************** PP

                    TFIID-31kDa  82 elLlelAaerNkipLpkvkeklgirLPperyclta 116
                                     ++ ++ + +N+ p+ +  e+   +LP  + +l++
  gene744|gene744|rna744|rna744  84 AYMNDIGTMVNSRPIRAYGEGA-NKLPTGKNTLLN 117
                                    ***************9999977.899999999876 PP

>> Bromo_TP  Bromodomain associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.0   3.2e-09   9.6e-06       8      69 ..       9      70 ..       3      72 .. 0.95

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 3.2e-09
                                   HHHHHHHHHHHHT-SEE-HHHHHHHHHHHHHHHHHHHHHHHHHHTTSS-SS--HHHHHHHHH CS
                       Bromo_TP  8 lkvvvsqileeaGfdsaeesaLEtLteiaqkYirelgeqaksfaehagRseptlkDvvltLq 69
                                   + +v+s il++ G+++ e+ a+    e++ kY + + ++a+++ae+  R   t kD+ l+Lq
  gene744|gene744|rna744|rna744  9 DTKVISLILRSLGIEECEPKAILQIHEFIYKYATDVMKDASQYAEMVDRQVITEKDIKLALQ 70
                                   5689*******************************************************998 PP

>> TAF  TATA box binding protein associated factor (TAF)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.1   1.6e-07   0.00048       9      65 ..      13      69 ..       4      70 .. 0.88

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 1.6e-07
                                   HHHHHHHTT---B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHH CS
                            TAF  9 vkviAeslGitnLsdeaaalLaedveyrlkeivqeaakfmrhskRqkLtvaDvdsAL 65
                                   + +i  slGi++ +  a   + e +      ++++a+++ ++  Rq++t +D+  AL
  gene744|gene744|rna744|rna744 13 ISLILRSLGIEECEPKAILQIHEFIYKYATDVMKDASQYAEMVDRQVITEKDIKLAL 69
                                   456678***********9999999988899************************998 PP

>> Histone  Core histone H2A/H2B/H3/H4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.2   2.3e-07   0.00069      87     129 ..      28      70 ..      23      72 .. 0.93

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 2.3e-07
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHTTXSEEXHHHHHHHHH CS
                        Histone  87 eavlalqealEallvelfeeAnllakhaKRvTitpkDiqlArr 129
                                    +a+l + e++  + ++++++A+ +a+   R+ it kDi+lA++
  gene744|gene744|rna744|rna744  28 KAILQIHEFIYKYATDVMKDASQYAEMVDRQVITEKDIKLALQ 70 
                                    7999999**********************************97 PP

>> CENP-S  CENP-S protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   2.6e-07   0.00077      25      70 ..      24      69 ..      11      73 .. 0.92

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 2.6e-07
                         CENP-S 25 eatkqfiaaltelvykqlenlakDLeaFakHAkRstittdDvlLla 70
                                   e+ +++i  + e +yk + ++ kD   +a+   R++it +D++L +
  gene744|gene744|rna744|rna744 24 ECEPKAILQIHEFIYKYATDVMKDASQYAEMVDRQVITEKDIKLAL 69
                                   57899**************************************986 PP

>> CBFD_NFYB_HMF  Histone-like transcription factor (CBF/NF-Y) and archaeal histone
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   5.6e-05      0.17      29      65 .]      33      69 ..      16      69 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 5.6e-05
                                   HHHHHHHHHHHHHHHHHHHHCCTTSSCE-HHHHHHHH CS
                  CBFD_NFYB_HMF 29 iaecveefieelaseAaeickkekrKtikaehiklAv 65
                                   i e++  +++++ + A+++++  +r  i++++iklA+
  gene744|gene744|rna744|rna744 33 IHEFIYKYATDVMKDASQYAEMVDRQVITEKDIKLAL 69
                                   667888899**************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       575  (0.0320709); expected 358.6 (0.02)
Passed bias filter:                      494  (0.0275531); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 893.01
//
Query:       gene745|gene745|rna745|rna745  [L=61]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       704  (0.039266); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 442.17
//
Query:       gene746|gene746|rna746|rna746  [L=237]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.6e-28   97.2   0.6      2e-27   96.2   0.6    1.5  1  Diphthami_syn_2  Diphthamide synthase
  ------ inclusion threshold ------
      0.014   15.5   0.1      0.034   14.3   0.1    1.7  2  ParcG            Parkin co-regulated protein


Domain annotation for each model (and alignments):
>> Diphthami_syn_2  Diphthamide synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.2   0.6   2.2e-31     2e-27       3     206 ..       4     214 ..       1     224 [. 0.82

  Alignments for each domain:
  == domain 1  score: 96.2 bits;  conditional E-value: 2.2e-31
                Diphthami_syn_2   3 vavlysGGkDsilaLykalke.sevesLvsvisenkesymfhvvnvhlvellaesvGiplikleta....GeeekevedL 77 
                                     + l+sGGkDs + +    ++ ++   Lv + s + +sym+ +v  +++      + +p+   et+        ++v+ L
  gene746|gene746|rna746|rna746   4 FVGLISGGKDSFYTIELLKQKeYNLVALVYIKSTDIDSYMYQTVGHEMIPFYRQVLDVPIYIIETNrkaiNTDKEYVHTL 83 
                                    5679*********9976554449999************************999999888755444311113445666666 PP

                Diphthami_syn_2  78 kgtlkkld...........veavviGaieseyqksriervCrelGlksvaPLWkkdpeelleeiveekfevivvavkaeg 146
                                    +++++ +             e v +Gai+s yq +ri +vC +l l  + PL++ d   ++   + e ++v++v v+ + 
  gene746|gene746|rna746|rna746  84 NDEVEVIYdhlyelqkkavFECVSVGAIKSYYQYNRIKSVCDRLNLSVLTPLFNLDQ-RVIYDAIIECMDVVIVKVACTN 162
                                    666554434444555888779999********************************9.9999999*************** PP

                Diphthami_syn_2 147 ldeslLGrridkklidelkklsekygidkagegGeaetlvlDaPlfkkrlevkelekkwd 206
                                    l+++++G+ ++  +i  ++        + +gegGe+et vlDaP+fkk+l++k++e   +
  gene746|gene746|rna746|rna746 163 LGKEIVGKNLN--VISGMRVD------NWCGEGGEYETAVLDAPFFKKKLRIKNYEVLHH 214
                                    *9999999875..66666555......78*************************998665 PP

>> ParcG  Parkin co-regulated protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1   3.8e-06     0.034     111     165 ..      44     100 ..      24     113 .. 0.83
   2 ?   -2.5   0.0      0.54   4.9e+03      82     115 ..     153     185 ..     137     187 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.8e-06
                          ParcG 111 seligeaLvpyyrqlLpv.lnlfknkrvnlgdkidy.rkkknikdliqetlellern 165
                                     +++g++++p+yrq+L v + +++++r+ +    +y ++ ++  ++i + l +l+++
  gene746|gene746|rna746|rna746  44 YQTVGHEMIPFYRQVLDVpIYIIETNRKAINTDKEYvHTLNDEVEVIYDHLYELQKK 100
                                    589*************76245566677777777777688888899999999999987 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.54
                          ParcG  82 ilplkeaLntrdeeviesaLkvlqklvkaselig 115
                                    ++ +k a ++  +e++ + L+v++ + +++++ g
  gene746|gene746|rna746|rna746 153 VVIVKVACTNLGKEIVGKNLNVISGM-RVDNWCG 185
                                    44566777777788888888888877.6666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (237 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       661  (0.0368676); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 1524.81
//
Query:       gene747|gene747|rna747|rna747  [L=197]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.46   10.4   3.3        7.9    6.5   0.3    2.9  2  TRIQK     Triple QxxK/R motif-containing protein family


Domain annotation for each model (and alignments):
>> TRIQK  Triple QxxK/R motif-containing protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.3   0.00044       7.9      54      75 ..      46      73 ..      35      76 .. 0.76
   2 ?    3.3   0.2    0.0041        74      56      73 ..     163     180 ..     156     185 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.00044
                          TRIQK 54 v......lvailvlllalYalfflnlsk 75
                                   +      ++a+ v++  lY + ++nl +
  gene747|gene747|rna747|rna747 46 MfgsllsILAVPVIVYFLYNFQYYNLGT 73
                                   44443348999999***********987 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.0041
                          TRIQK  56 vailvlllalYalfflnl 73 
                                    v i+++++++ al++l +
  gene747|gene747|rna747|rna747 163 VNIFFFVFGIVALIYLGM 180
                                    689************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       890  (0.0496402); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 1333.03
//
Query:       gene748|gene748|rna748|rna748  [L=222]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.6e-17   63.6   0.2      5e-16   58.7   0.2    2.0  1  Proteasome  Proteasome subunit


Domain annotation for each model (and alignments):
>> Proteasome  Proteasome subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.7   0.2   2.8e-20     5e-16       3     188 ..       6     197 ..       4     199 .. 0.86

  Alignments for each domain:
  == domain 1  score: 58.7 bits;  conditional E-value: 2.8e-20
                                    HS-EEEEEEETTEEEEEEEEEEEETTEEEESSSSTSEEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHSSGTCHH CS
                     Proteasome   3 kGttvvGikgkdgvvlaadkratagskllskstveKifkiddhigvafaGlaaDartlvrraraeaqlyrlrygrpipve 82 
                                    + ++vv++++++g++l +d+ + +gs  +++  veK + +++++++ + G+++ ++ l ++  +e++  +      + ++
  gene748|gene748|rna748|rna748   6 TSSSVVAFRYSNGIILSSDTSLNYGSLKMNRG-VEKHYVLSNNTVMIVRGEYSCFQELKKICDEEMEYDQ-----SMGTK 79 
                                    5689**********************997888.9**********************99998888776665.....78888 PP

                                    HHHHHHHHHHHHHHHHC..TTTTTSEEEEEEEEETTT..............EEEEE.EEETTSEEEEESSEEEESTTHHH CS
                     Proteasome  83 rlvarvaaklqaytqrs..grrpfgvslliagvdeeg..............gpeLy.qidpsGsyieekdavaiGsgsea 145
                                        +  + +q+ ++++  ++ p+ +s+++ag+de+               +  ++  id  G+++ ++ + a G +s++
  gene748|gene748|rna748|rna748  80 ----EWIRFVQRVMYYKrtRVMPLNLSVIVAGYDEHSekqekqinsvehfgQGLIFgVIDNVGNFYTDD-VLACGIASHM 154
                                    ....67777777666552267899**********8876777777777766533333268*********6.*****99*** PP

                                    HHHHHHHHHSTTBSHHHHHHHHHHHHHHHHHHBTTSCSSEEEE CS
                     Proteasome 146 aktalekeykedltleeavelavkalkealerdklsgknieva 188
                                    a ++++ + +  l++e a++l++++++ +++rd++  + i+++
  gene748|gene748|rna748|rna748 155 ALPYIRGHGSTSLDREGAIKLMKETMQTLYYRDCMADNHIKIV 197
                                    **************************************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       469  (0.0261587); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1537.50
//
Query:       gene749|gene749|rna749|rna749  [L=231]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.3e-13   49.1   0.1    6.2e-13   48.6   0.1    1.3  1  MTS              Methyltransferase small domain
      7e-11   42.1   0.0    8.7e-11   41.8   0.0    1.1  1  Cons_hypoth95    Conserved hypothetical protein 95
    4.2e-07   30.6   0.1    7.4e-07   29.8   0.1    1.4  1  Methyltransf_25  Methyltransferase domain
    8.4e-07   28.5   0.0    1.2e-06   28.0   0.0    1.3  1  N6_Mtase         N-6 DNA Methylase
    4.5e-06   26.3   0.2    6.6e-06   25.8   0.2    1.3  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
    1.2e-05   25.1   0.0    4.7e-05   23.2   0.0    1.8  2  UPF0020          Putative RNA methylase family UPF0020
    1.6e-05   24.5   0.1    2.7e-05   23.7   0.1    1.3  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
    0.00012   21.9   0.1    0.00017   21.4   0.1    1.3  1  Methyltransf_31  Methyltransferase domain
     0.0002   21.2   0.0    0.00035   20.4   0.0    1.4  1  Met_10           Met-10+ like-protein
      0.004   16.5   0.1     0.0055   16.1   0.1    1.2  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
     0.0047   16.7   0.0     0.0076   16.0   0.0    1.3  1  Methyltransf_16  Lysine methyltransferase
     0.0063   15.9   1.1      0.033   13.6   0.4    2.1  2  Spermine_synth   Spermine/spermidine synthase domain
  ------ inclusion threshold ------
      0.032   14.9   0.0      0.067   13.8   0.0    1.5  1  Methyltransf_11  Methyltransferase domain
      0.047   13.7   0.0      0.073   13.1   0.0    1.4  1  Methyltransf_32  Methyltransferase domain
       0.05   13.4   0.0       0.12   12.2   0.0    1.5  1  Methyltransf_23  Methyltransferase domain
      0.052   13.3   0.0      0.077   12.7   0.0    1.2  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
        0.1   12.2   0.0       0.16   11.6   0.0    1.3  1  NodS             Nodulation protein S (NodS)
       0.15   12.8   0.0       0.65   10.8   0.0    2.1  2  Methyltransf_12  Methyltransferase domain


Domain annotation for each model (and alignments):
>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.6   0.1   6.2e-16   6.2e-13      22     110 ..      71     159 ..      64     204 .. 0.90

  Alignments for each domain:
  == domain 1  score: 48.6 bits;  conditional E-value: 6.2e-16
                                    HHHHHCHCC.TCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTTTSTTS-EEE CS
                            MTS  22 lLletlpke.lsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasdvleeveekkfdl 100
                                     ++et+ ++ + ++vlDl+ G+G+lg+++a   p  +v+ vd+d  Ale++++n+   + +v+++++d  +   + kfd+
  gene749|gene749|rna749|rna749  71 HMIETVYNDiHGKSVLDLCGGTGMLGITCAFYDPL-SVVNVDIDRDALEICRTNMLMVDKHVDLINCDFQNLRLNTKFDT 149
                                    57888888867788***************987776.9**********************************999****** PP

                                    EEE---STTT CS
                            MTS 101 ivsNPPfhag 110
                                     v+NPPf  +
  gene749|gene749|rna749|rna749 150 CVMNPPFGMK 159
                                    *******765 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.8   0.0   8.7e-14   8.7e-11      32     174 ..      72     206 ..      49     214 .. 0.79

  Alignments for each domain:
  == domain 1  score: 41.8 bits;  conditional E-value: 8.7e-14
                                    HHHHHCCCHCC-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHCTS--SS CS
                  Cons_hypoth95  32 lFnilaaeiegarvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelkleeetaelkedaleallklakkk 111
                                    + +++ ++i+g++vLDl++G+G lg+ ++  +  ++v v+ d+ a++i+++n+ +++   ++  l++ ++++l+ +    
  gene749|gene749|rna749|rna749  72 MIETVYNDIHGKSVLDLCGGTGMLGITCAFYDPLSVVNVDIDRDALEICRTNMLMVD---KHVDLINCDFQNLRLN---- 144
                                    45566778*********************************************9999...3456666666666444.... PP

                                    -EEEEEEE--SSSTTCH.HHHHHHHHHTT-EEEEEEEEEEEECC..SSS--.-TTEEEEEEEEET CS
                  Cons_hypoth95 112 eefdivflDPPyakellieevlelleekkllkenalvvveteke..kelpespenlelvkekkyg 174
                                     +fd   ++PP+  +       + l+ +++l+ + +v+v ++++  +  +++++n+e++ e ky 
  gene749|gene749|rna749|rna749 145 TKFDTCVMNPPFGMKCK---GSDVLAIESALRCSNVVYVLHSTKtrEYYLNKFDNIEVIAETKYD 206
                                    48***********9964...455555558888877777766555226678999999999999886 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8   0.1   7.4e-10   7.4e-07       1      71 [.      85     153 ..      85     175 .. 0.86

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 7.4e-10
                                    EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEE CS
                Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvss 71 
                                    vLdl+ GtG l + +a      +v+ vDi+ ++le++r+++   + +v+++++d+++l ++  +fD +v++
  gene749|gene749|rna749|rna749  85 VLDLCGGTGMLGITCAFY-DPLSVVNVDIDRDALEICRTNMLMVDKHVDLINCDFQNLRLNT-KFDTCVMN 153
                                    9**************976.57********************77666*************887.9***9994 PP

>> N6_Mtase  N-6 DNA Methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0   0.0   1.2e-09   1.2e-06      26     138 ..      57     159 ..      46     207 .. 0.81

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 1.2e-09
                       N6_Mtase  26 GeffTPrevsklivell....epksgesvyDpacGsggllvqaekvlkeedgktkelsiyGqeknettyrLakmNlllhg 101
                                     ++ TP ++s + ++++    ++ +g+sv+D + G+g l ++ + +          ls+  +++++ + +++++N+l+ +
  gene749|gene749|rna749|rna749  57 EQYITPPSLSATTIHMIetvyNDIHGKSVLDLCGGTGMLGITCAFY--------DPLSVVNVDIDRDALEICRTNMLMVD 128
                                    599**************77776778899***998887666665543........6899999******************9 PP

                       N6_Mtase 102 ieykkvkirlgdtlekpkfekdkkfdvvvaNppfnqk 138
                                     +++ ++      +++ + +  +kfd+ v Nppf+ k
  gene749|gene749|rna749|rna749 129 KHVDLINCD----FQNLRLN--TKFDTCVMNPPFGMK 159
                                    999965544....4444444..799**********98 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.2   6.7e-09   6.6e-06       3     109 ..      84     183 ..      82     223 .. 0.79

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 6.7e-09
                Methyltransf_15   3 vilDlfsGaGGnviqfalv.fekviaieinleklacaqhNaevYgvsdkitlvlgdvfellaklklekikvdlvflSpPw 81 
                                     +lDl++G+G   i+ a +   +v+ ++i+++ l+++  N  +  v+++++l+ +d+++l  ++k++++     ++ pP 
  gene749|gene749|rna749|rna749  84 SVLDLCGGTGMLGITCAFYdPLSVVNVDIDRDALEICRTNMLM--VDKHVDLINCDFQNLRLNTKFDTC-----VMNPPF 156
                                    69********6666666543349*****************877..59**********988777777766.....899998 PP

                Methyltransf_15  82 GGpsYkkqekfdlkkklkplkleqllke 109
                                    G ++ k  +++ +++ l+  ++  +l++
  gene749|gene749|rna749|rna749 157 G-MKCKGSDVLAIESALRCSNVVYVLHS 183
                                    5.77888888888777777776665554 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.0   4.7e-08   4.7e-05      77     135 ..     105     160 ..      94     168 .. 0.89
   2 ?   -0.1   0.0      0.64   6.4e+02      38      60 ..     162     184 ..     160     217 .. 0.71

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 4.7e-08
                                    --EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--STTS---EEEE-------- CS
                        UPF0020  77 lklygsDldrrvvqgareNaekagvgdliefsqadaakLrlkegevdvivtnpPYGerl 135
                                    l+++ +D+dr +++ +r+N     v++ +++ + d+++Lr  + ++d+ v npP+G + 
  gene749|gene749|rna749|rna749 105 LSVVNVDIDRDALEICRTNM--LMVDKHVDLINCDFQNLR-LNTKFDTCVMNPPFGMKC 160
                                    568899*************7..67999*************.7779***********876 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.64
                                    TTSHHHHHHHHHHTT--TTTT-- CS
                        UPF0020  38 GsGtilIEaallganiapgllre 60 
                                    Gs  ++IE al  +n++  l+ +
  gene749|gene749|rna749|rna749 162 GSDVLAIESALRCSNVVYVLHST 184
                                    77779999999999998555533 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.1   2.7e-08   2.7e-05     152     233 ..      70     153 ..      66     154 .. 0.76

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 2.7e-08
                           PrmA 152 lealeklvk..egeevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkveakleva.lseellkeekad 228
                                    ++++e++ +  +g++vlD+  G+G+L i  a  +  +vv vDiD  A+++ + N+ + + +  l ++   ++l  ++k+d
  gene749|gene749|rna749|rna749  70 IHMIETVYNdiHGKSVLDLCGGTGMLGITCAFYDPLSVVNVDIDRDALEICRTNMLMVDKHVDL-INcDFQNLRLNTKFD 148
                                    67778775511568****************************************9886555544.221234444467888 PP

                           PrmA 229 vivaN 233
                                      v N
  gene749|gene749|rna749|rna749 149 TCVMN 153
                                    87776 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.1   1.7e-07   0.00017       4      84 ..      82     156 ..      80     220 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 1.7e-07
                Methyltransf_31   4 glrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgld.nveFeqgdieeleklledekfDlilsne 82 
                                    g++vlDl  GtG l++  a   ++   vv++Di+ +a+e +r+n   l +d  v +  +d+++l   l+  kfD  + n 
  gene749|gene749|rna749|rna749  82 GKSVLDLCGGTGMLGITCA--FYDPLSVVNVDIDRDALEICRTN--MLMVDkHVDLINCDFQNLR--LN-TKFDTCVMNP 154
                                    689****************..89999*****************9..6778779**********99..66.89**999885 PP

                Methyltransf_31  83 vl 84 
                                    ++
  gene749|gene749|rna749|rna749 155 PF 156
                                    44 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   3.5e-07   0.00035     100     177 ..      81     155 ..      64     169 .. 0.91

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 3.5e-07
                                    TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-TTCEEEEES-GGG---TT-EEEEEE--T CS
                         Met_10 100 egevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkvekvvkpileDgrevireqladrvvmnlp 177
                                    +g+ V+d+  G G + i++a   ++  v+ +d++ ++ +  + n+    v+k v  i+ D +++  ++++d  vmn p
  gene749|gene749|rna749|rna749  81 HGKSVLDLCGGTGMLGITCAF-YDPLSVVNVDIDRDALEICRTNML--MVDKHVDLINCDFQNLRLNTKFDTCVMNPP 155
                                    5899****************5.78999***************9987..599*************99*********976 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.1   5.5e-06    0.0055      39     119 ..      73     149 ..      66     194 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 5.5e-06
                                    HHHH--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-T-EE CS
                Ubie_methyltran  39 veklvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfeddsfD 118
                                    +e + ++ +g++vlD++gGtg l +  + +  +   vv +Di+ + L++ +  +     +++++++ + ++L  +   fD
  gene749|gene749|rna749|rna749  73 IETVYNDIHGKSVLDLCGGTGMLGI--TCAFYDPLSVVNVDIDRDALEICRTNMLM-VDKHVDLINCDFQNLRLNT-KFD 148
                                    67788999*************8755..566778889*************9987654.4457788877777776654.344 PP

                                    E CS
                Ubie_methyltran 119 v 119
                                    +
  gene749|gene749|rna749|rna749 149 T 149
                                    4 PP

>> Methyltransf_16  Lysine methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   7.7e-06    0.0076      41      93 ..      76     128 ..      57     156 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 7.7e-06
                Methyltransf_16  41 ganelsklsvlELGsGtGlvGlavaellpeakviltDlee.llellkknielnk 93 
                                      n+ +++svl+L  GtG+ G++ a    +++v+  D++  +le+ ++n+ + +
  gene749|gene749|rna749|rna749  76 VYNDIHGKSVLDLCGGTGMLGITCAFY-DPLSVVNVDIDRdALEICRTNMLMVD 128
                                    4678999*****************998.999999999987799**999987733 PP

>> Spermine_synth  Spermine/spermidine synthase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.1      0.22   2.2e+02     127     180 ..      23      76 ..      12      81 .. 0.84
   2 !   13.6   0.4   3.3e-05     0.033      17      69 ..      80     137 ..      68     152 .. 0.77

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.22
                                    EEEEEEEEETTTCHHHHHHHHHHHHTTSSCEEEEEEEETTTSCSCEEEEEEEES CS
                 Spermine_synth 127 GviilqaekpelekelvinvdksgkqvfalqvepsavlvPtylsgminfvvesk 180
                                    + iil   +  +++++v++ + ++k +  ++++++ +++P  ls + + ++e+ 
  gene749|gene749|rna749|rna749  23 AKIILILTSLAMKLKDVKSRLSQLKPFKTPKIKYEQYITPPSLSATTIHMIETV 76 
                                    56666777888999999999999****999**********99999999988765 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 3.3e-05
                                    SST-EEEEESSTTSHHHHHHTTSTT-SEEEEEES-HHHHHHHHHHSHHHHTT......C CS
                 Spermine_synth  17 knpkevLiiGGgDGgvlrevvkhntvekitlvdiDqkvidfskkflpslais......a 69 
                                     + k vL + Gg G +     +++ + +++ vdiD++++++++ ++ ++          
  gene749|gene749|rna749|rna749  80 IHGKSVLDLCGGTGMLGITCAFYD-PLSVVNVDIDRDALEICRTNMLMVDKHvdlincD 137
                                    3789********************.99****************9987776553344444 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   6.7e-05     0.067       1      67 [.      86     152 ..      86     156 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 6.7e-05
                                    EEET-TTSHHHHHHHHTT..SEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEE CS
                Methyltransf_11   1 LdvGcGtGrlaealakrg..arvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvs 67 
                                    Ld+  GtG l   +a  +   +vv+vD++  +l++++++    + +v+++ +d+++l ++  +fD +v+
  gene749|gene749|rna749|rna749  86 LDLCGGTGMLGITCA-FYdpLSVVNVDIDRDALEICRTNMLMVDKHVDLINCDFQNLRLNT-KFDTCVM 152
                                    566445665555555.334689***************999999999***********9988.9999887 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   7.3e-05     0.073      11      80 ..      71     132 ..      64     186 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 7.3e-05
                Methyltransf_32  11 elvakllkelakesgaltvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekraeklgkkfnk 80 
                                    +    +++++ ++ + ++v+D++ G g L+ + a+     +l+vv +d+ ++  e +++    + k++ +
  gene749|gene749|rna749|rna749  71 H----MIETVYNDIHGKSVLDLCGGTGMLGITCAF---YDPLSVVNVDIDRDALEICRTNMLMVDKHV-D 132
                                    3....4555555578899*****************...779***************999999888887.3 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00012      0.12      20      88 ..      79     152 ..      68     203 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00012
                Methyltransf_23  20 lraggrvLdiGcGtGillevlren.gfsvtgvDlspeaveiaekakkaqkdqfdeqeaaepqg....kfdlIvl 88 
                                    +  g++vLd+  GtG l   ++ + + sv++vD+++ a ei ++   ++++ +d ++ ++++     kfd+ v+
  gene749|gene749|rna749|rna749  79 DIHGKSVLDLCGGTGMLGITCAFYdPLSVVNVDIDRDALEICRTNMLMVDKHVDLINCDFQNLrlntKFDTCVM 152
                                    56789**********776666555256**************997777777777777666655444447766555 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   7.7e-05     0.077      49     107 ..      53     113 ..      38     140 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 7.7e-05
                                    EEETTEEE--HHHHHHHHHHTT....--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESB CS
                           PCMT  49 sigynatiSaphmvalalelle....lkkgarvLevGsGsGyltavlarlvgekgrvvsieri 107
                                    +i y+++i  p++ a+++ ++e      +g++vL++ +G+G l    a +  +   vv ++  
  gene749|gene749|rna749|rna749  53 KIKYEQYITPPSLSATTIHMIEtvynDIHGKSVLDLCGGTGMLGITCAFY--DPLSVVNVDID 113
                                    59**************99999986443489***********997665543..22334444444 PP

>> NodS  Nodulation protein S (NodS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00016      0.16      45     113 ..      83     153 ..      66     188 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00016
                           NodS  45 adalevGcaaGalterlapyckrltv..vdvveeaiararervke.sshiswivsdvqqfstdekfdlivva 113
                                     ++l++   +G l    a y + l+v  vd+  +a++ +r+ +     h+  i +d q++ ++ kfd+ v+ 
  gene749|gene749|rna749|rna749  83 KSVLDLCGGTGMLGITCAFY-DPLSVvnVDIDRDALEICRTNMLMvDKHVDLINCDFQNLRLNTKFDTCVMN 153
                                    56666666666666666655.345551256677887766665543138********************9986 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00065      0.65       1      73 [.      86     153 ..      86     157 .. 0.88
   2 ?   -2.4   0.0       8.5   8.5e+03      39      52 ..     185     198 ..     176     211 .. 0.53

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00065
                Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvas 73 
                                    L++ +GtG l   ++ +  +++++ vDi+++a+e  ++ +   ++    +v+l ++d  +l  + +fD+ v++
  gene749|gene749|rna749|rna749  86 LDLCGGTGMLGITCAFY-DPLSVVNVDIDRDALEICRTNMLMVDK----HVDLINCDFQNLRLNTKFDTCVMN 153
                                    8999**********999.***************888888888775....88888888888888899**99986 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 8.5
                Methyltransf_12  39 klakrennnnnnve 52 
                                    k++++  n+++n+e
  gene749|gene749|rna749|rna749 185 KTREYYLNKFDNIE 198
                                    33444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       503  (0.0280551); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1586.40
//
Query:       gene75|gene75|rna75|rna75  [L=127]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-23   82.6   0.1    2.2e-23   82.1   0.1    1.3  1  Ribosomal_S13_N  Ribosomal S13/S15 N-terminal domain


Domain annotation for each model (and alignments):
>> Ribosomal_S13_N  Ribosomal S13/S15 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.1   0.1   1.2e-27   2.2e-23       1      60 []      21      80 ..      21      80 .. 0.99

  Alignments for each domain:
  == domain 1  score: 82.1 bits;  conditional E-value: 1.2e-27
                               X--SSSSSS--------S-SS--TTS---HHHHHHHHHHHHHTT--HHHHHHHHHHCCT- CS
            Ribosomal_S13_N  1 MarmhsrgkGkSgSarPyrreapsWlklskeeveelivklakkGltpSqIGviLRDqyGv 60
                               M rmh++ kGkS+S++Py++  ps+++ +k+e+ ++i+ la+kG++ SqIG++LRD++Gv
  gene75|gene75|rna75|rna75 21 MTRMHTNSKGKSQSTLPYHTFYPSHITKTKQEIIDKILTLARKGIPASQIGNVLRDEEGV 80
                               9**********************************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       581  (0.0324056); expected 358.6 (0.02)
Passed bias filter:                      482  (0.0268838); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 833.73
//
Query:       gene750|gene750|rna750|rna750  [L=295]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.5e-10   40.8   0.7    3.1e-09   36.6   0.7    2.4  1  adh_short      short chain dehydrogenase
    2.5e-06   27.2   0.0    3.4e-06   26.7   0.0    1.2  1  Epimerase      NAD dependent epimerase/dehydratase family
  ------ inclusion threshold ------
      0.018   15.0   0.0       0.03   14.2   0.0    1.4  1  KR             KR domain
      0.087   12.2   0.5       0.15   11.5   0.1    1.5  2  GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
       0.11   11.5   0.0       0.16   11.0   0.0    1.1  1  RmlD_sub_bind  RmlD substrate binding domain


Domain annotation for each model (and alignments):
>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.6   0.7   8.7e-13   3.1e-09       2     189 ..      51     217 ..      50     220 .. 0.73

  Alignments for each domain:
  == domain 1  score: 36.6 bits;  conditional E-value: 8.7e-13
                                    EEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSSESEE CS
                      adh_short   2 vvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgkldvL 81 
                                      ++tG+++GIGr++++ l+ +G++v+v++r++ +            +k++++ +D+++ +ev ++  +     + +d+L
  gene750|gene750|rna750|rna750  51 FCVITGGTRGIGRELVDLLVLKGYEVMVLGRTKVNR-----------SKVVHYGLDLNNLQEVAQFKMD-----KDIDLL 114
                                    579****************************96654...........4588999****99988877433.....79**** PP

                                    EE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGG.....TSB-....TTBHHHHHH CS
                      adh_short  82 vnNAGitgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvag.....kvpv....agvaaYsAs 152
                                    v NAGi         + + ++  +++N+ + + l   +  +++   ++r+v +sS +      + p+    +++  Y+ s
  gene750|gene750|rna750|rna750 115 VMNAGI------LTGKTDGIDLNFKINYLAHYILYNNLRSNLK---NARVVLTSSCVMlsvdtFDPYrpsfFSFRKYCES 185
                                    ******......3445555999*************99888866...9999999987651000022221111344455555 PP

                                    HHHHHHHHHHHHHHHGGGTEEEEEEEESSBSSHHHHH CS
                      adh_short 153 KaavagltrslakelaptgirvnavaPGlvdTdmake 189
                                    K  v  l + +     +++ + ++v+PG+v+T + +e
  gene750|gene750|rna750|rna750 186 KLCVFLLGKYI-----SRNLQTVVVHPGVVNTTLFNE 217
                                    55555555444.....445556799999999887765 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.7   0.0   9.4e-10   3.4e-06       2     126 ..      53     171 ..      52     216 .. 0.73

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 9.4e-10
                                    EEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHCEEEE--TT-HHHHHHHHHHHT-SEEEE--S.---HHHH CS
                      Epimerase   2 lVtGatGfiGsalvkallekgyevigldrlssasntarledlelveldltdrsalerlfkeeqpdavihlAa.vggvaas 80 
                                    ++tG+t  iG+ lv+ l  kgyev++l r + ++      ++  + ldl + ++++++  ++++d  +  A+   g  + 
  gene750|gene750|rna750|rna750  53 VITGGTRGIGRELVDLLVLKGYEVMVLGRTKVNRS-----KVVHYGLDLNNLQEVAQFKMDKDIDLLVMNAGiLTGKTDG 127
                                    79***************************933333.....334579********************99999966666666 PP

                                    HHSHHHHHHHHTHHHHHHHHHHHHHTCT.EEEEEEEGGGGTSCSSSS CS
                      Epimerase  81 sedpadfieknlqgtlnlleaarkagvk.rllflsSsevYGkdaeqp 126
                                    ++ +   +++n    + l + +r +  + r++  sS+ +   d+  p
  gene750|gene750|rna750|rna750 128 IDLN---FKINYLAHYILYNNLRSNLKNaRVVLTSSCVMLSVDTFDP 171
                                    5553...5578888888888888773333777777766665555444 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   8.4e-06      0.03       4      37 ..      53      85 ..      51     114 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 8.4e-06
                                   EEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..- CS
                             KR  4 litGGlGgLGlelarwlaekgarhlvllsRsaaa 37
                                   +itGG+ g+G+el++ l+ kg + +++l+R++ +
  gene750|gene750|rna750|rna750 53 VITGGTRGIGRELVDLLVLKGYE-VMVLGRTKVN 85
                                   8********************86.5667888432 PP

>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   4.1e-05      0.15       2      33 ..      54      85 ..      53     115 .. 0.73
   2 ?   -2.7   0.0      0.86   3.1e+03     175     197 ..     209     228 ..     181     242 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 4.1e-05
                                   EETTTSHHHHHHHHHHHHCT-CCEEEEEEESS CS
                  GDP_Man_Dehyd  2 iTGiaGfiGsylaelLlekgyevhgivrrsss 33
                                   iTG++  iG  l++lL+ kgyev+++ r + +
  gene750|gene750|rna750|rna750 54 ITGGTRGIGRELVDLLVLKGYEVMVLGRTKVN 85
                                   9**********************998664432 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 0.86
                                    EEEEEE-EEESTTS-TTSCCCHH CS
                  GDP_Man_Dehyd 175 avngilfnhesprrgetfvtrki 197
                                    +vn+ lfn +s     +f   ki
  gene750|gene750|rna750|rna750 209 VVNTTLFNENSLL---NFFISKI 228
                                    7889999999877...4666666 PP

>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   4.4e-05      0.16       4      59 ..      53     119 ..      50     137 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 4.4e-05
                                    EEESTTSHHHHHHHHHCTTTSEEEEEE-TT..........T--TTSHHHHHHHHHHH--S.EEEE-- CS
                  RmlD_sub_bind   4 lvtGanGqlGseLakqlaeeglevlaltre..........eldltdaeavaellkeakpd.vvvnaA 59 
                                    ++tG++  +G+eL+++l  +g+ev+ l+r+           ldl++ ++va++  +++ d +v+na+
  gene750|gene750|rna750|rna750  53 VITGGTRGIGRELVDLLVLKGYEVMVLGRTkvnrskvvhyGLDLNNLQEVAQFKMDKDIDlLVMNAG 119
                                    79*************************9999999999999999999999999999999983455555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (295 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       640  (0.0356964); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2173.53
//
Query:       gene751|gene751|rna751|rna751  [L=397]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.9e-09   35.3   2.1    1.2e-08   34.5   2.1    1.4  1  G6PD_C    Glucose-6-phosphate dehydrogenase, C-terminal domai


Domain annotation for each model (and alignments):
>> G6PD_C  Glucose-6-phosphate dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.5   2.1   6.6e-13   1.2e-08      30     282 ..     138     391 ..     116     396 .. 0.71

  Alignments for each domain:
  == domain 1  score: 34.5 bits;  conditional E-value: 6.6e-13
                                    S--TTTHHHHTTTHHHHHTTTTHHHHHHHHHH----SSSSH....HHHHHHHHHHHTTB----G...GG.EEEEEE.... CS
                         G6PD_C  30 lgvegrggYydeaGalrDvvqnHllqllalvamepPaslda....edirdekvkvLkslrplkleevekkvvrGqYaaga 105
                                    l +e++++Y    G++  ++q   +  l  ++ ++  ++++       r e++k+L++lr++k + +        Y    
  gene751|gene751|rna751|rna751 138 LSTERKTKY----GIVFEIMQHFFVNNLISITKDNTDTVKDvcprYMQRMERLKLLRNLRTIKCTWF------RCY---- 203
                                    555555544....666666666665555555555554443211112345677777777777766222......223.... PP

                                    .E--TGS-STTSTTS-TT--.--SEEEEEEEB-STTTTT-EEEEEEESSBSS-EEEEEEEE---.SS-SS..---..... CS
                         G6PD_C 106 vkgkevkgYreeegvakdSk.teTfvalkleidnerwagVPfylrtGKrLnekkteiriqfkkv.psdlf..kkke.... 177
                                         ++ Y e  + +++S   +T+  l ++i n rw gV + + +G+ +++ + + +i+f k   ++lf          
  gene751|gene751|rna751|rna751 204 ---VYHRIYDEFVRTSDRSLlRDTYTYLSMQIYNTRWFGVKITFNAGRGFRRVVDRTVIKFTKLaFKRLFarY--Yyrei 278
                                    ...12445777666666664168**************************************997345566431..24557 PP

                                    .........--EEEEEEESS-EEEEEEEEE-SSS.E.....EEEEEEHHHHTT---HHHHHHHHHHHT-GTTSB-HHHHH CS
                         G6PD_C 178 .........rneLviriqpdeaislklnakkpgl.eleleeveldlsykerfklpeaYerLlldvlkgdqtlFvrsdeve 247
                                                L+++  p+  i+lk++ ++     + +++ +++  ++e+ +  + Ye+ +   ++++   +vr +eve
  gene751|gene751|rna751|rna751 279 ydeereeirYISLIFQDFPEPRIYLKIEFRRSIRrLIIMNRDDIEKWLNEQRDGMNEYEHFFQCFFNNNDVYYVRLEEVE 358
                                    77888888777899****************997734556788899889988888889*********************** PP

                                    HHHHHHHHHHHHHHH---EEEETTSSS-HHHHHHH CS
                         G6PD_C 248 aaWkivdpileaweeeklekYeagsrgPeeadell 282
                                    +  +i+    + +    +  Y+   + P+  ++l+
  gene751|gene751|rna751|rna751 359 EIYRIFWFFYNRL--YGFGVYAENAKTPNLLYQLA 391
                                    *****99888888..34667877777777777666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (397 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       713  (0.039768); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.23s 00:00:00.72 Elapsed: 00:00:00.38
# Mc/sec: 3102.99
//
Query:       gene752|gene752|rna752|rna752  [L=311]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.29   11.8   2.5        1.2    9.9   0.1    3.1  4  Cbl_N2    CBL proto-oncogene N-terminus, EF hand-like domain


Domain annotation for each model (and alignments):
>> Cbl_N2  CBL proto-oncogene N-terminus, EF hand-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.1   6.7e-05       1.2      44      83 ..      12      52 ..       4      53 .. 0.86
   2 ?   -0.7   0.1      0.13   2.4e+03       5      17 ..      66      78 ..      61     109 .. 0.52
   3 ?   -1.8   0.0       0.3   5.4e+03      44      58 ..     166     180 ..     142     190 .. 0.66
   4 ?   -2.1   0.0      0.36   6.5e+03      25      46 ..     222     243 ..     192     246 .. 0.54

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 6.7e-05
                                   HHHHHHH-TT.-SSEEEHHHHHHHHHHH--GGGHHHHHHHH CS
                         Cbl_N2 44 laLkstidlt.cndyisvfefdvFtrlFqPwssllknWkvL 83
                                   l++k ++d+  c dy++       ++ F P+ +ll++W+v+
  gene752|gene752|rna752|rna752 12 LQMKDILDMElCTDYMKLLRMKYEVKAFLPYLTLLNEWNVI 52
                                   5788999995499****99999999**************86 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.13
                                   SHHHHHHHHHHHT CS
                         Cbl_N2  5 kkeAaefWkksfg 17
                                   k+  aefW    +
  gene752|gene752|rna752|rna752 66 KSATAEFWAAVNQ 78
                                   4555789975433 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 0.3
                                    HHHHHHH-TT-SSEE CS
                         Cbl_N2  44 laLkstidltcndyi 58 
                                    l L+  id+ + +++
  gene752|gene752|rna752|rna752 166 LMLNGHIDIKKYKFV 180
                                    334444454444444 PP

  == domain 4  score: -2.1 bits;  conditional E-value: 0.36
                                    HHHHHHHHHHH---GGG.HHHH CS
                         Cbl_N2  25 kefkealekvhkvesskealaL 46 
                                     +f e+l++  + +++++a +L
  gene752|gene752|rna752|rna752 222 ITFPEQLNRSEGRNEEMHAYHL 243
                                    2455666666666665555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       675  (0.0376485); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.21s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2305.76
//
Query:       gene753|gene753|rna753|rna753  [L=704]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   6.8e-181  602.0  28.8   6.1e-173  575.8  16.0    2.9  3  HTH_micro       HTH-like
  ------ inclusion threshold ------
      0.026   14.7   0.1        0.1   12.8   0.1    2.0  1  B-block_TFIIIC  B-block binding subunit of TFIIIC
      0.036   14.0   0.0      0.079   12.9   0.0    1.5  1  MarR_2          MarR family
       0.12   12.5   0.4       0.68   10.0   0.2    2.3  2  PspB            Phage shock protein B
       0.38   10.6   7.3        0.2   11.6   0.5    2.3  2  SMC_ScpA        Segregation and condensation protein ScpA


Domain annotation for each model (and alignments):
>> HTH_micro  HTH-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.4   0.1     3e-12   1.1e-08       2      58 ..       5      61 ..       4      74 .. 0.91
   2 !  575.8  16.0  1.7e-176  6.1e-173      37     454 .]     113     537 ..     104     537 .. 0.99
   3 ?   -0.5   1.1      0.11   4.1e+02     147     177 ..     540     569 ..     538     583 .. 0.80

  Alignments for each domain:
  == domain 1  score: 34.4 bits;  conditional E-value: 3e-12
                      HTH_micro  2 lkekilefGiYGkkisnltkeEieelikkpwveilskaevdelennftaskltkled 58
                                   lkeki+++Gi+G++ s l +eE+  l +++wve+++ +++ el+++ft+  l++++ 
  gene753|gene753|rna753|rna753  5 LKEKIFSYGIFGTPCSELSEEELFALLSEQWVEFVTGEQIAELHSSFTTLALESKQK 61
                                   799*********************************************999887665 PP

  == domain 2  score: 575.8 bits;  conditional E-value: 1.7e-176
                      HTH_micro  37 skaevdelennftaskltkledkniienll..dLyvRmnlsawkeyLtsgkfkftskeyykivdflvkakdyvkaaelra 114
                                    s+ae+ ++ +++ +s ++ + d++++++ll  +LyvRmn++awke+Lt+g+f+ftskeyy+++d+l+++++yv+++++r 
  gene753|gene753|rna753|rna753 113 STAEYGTVGKSAGSSVQQLSPDDKYLLRLLlvNLYVRMNTVAWKEHLTNGSFNFTSKEYYYVFDMLIRMNEYVSVSNMRV 192
                                    689*************************999************************************************* PP

                      HTH_micro 115 klnidpKklfYvikkLakkglieqktkeeakivikinkDesgsvvkkldkeklleinkedtit.......lpekiipmey 187
                                    +l i+pKk+fY+ikkL + g+i+ kt+e++kiv+ki++Desg+vvk+++kek+++in+edtit       ++e++i+m++
  gene753|gene753|rna753|rna753 193 TLGIEPKKMFYIIKKLVSLGYID-KTAEDNKIVVKIRRDESGNVVKGRPKEKRRSINSEDTITdtsvtnsFDEQHIGMDI 271
                                    ***********************.******************************************************** PP

                      HTH_micro 188 lieiplidqikkkienteeGitskdlkdkfGislkqglklLnklieeeedsiktkeefegkikrlkfytvenleklnerk 267
                                    li++pli+qikk+ie++++G++skd++d+fGi+lk+glklLnk+++++e+sikt+eefegkikr+kfy+v++l+kl+erk
  gene753|gene753|rna753|rna753 272 LIGVPLITQIKKFIERSRTGVCSKDIQDRFGIKLKIGLKLLNKISDRMEGSIKTVEEFEGKIKRTKFYNVNELSKLKERK 351
                                    ******************************************************************************** PP

                      HTH_micro 268 kkrliegddleekeliTsedriealkqllkkkkafvlsketfeklseilgvkYtldrktlistaikaglkvyklkdtkeg 347
                                    ++r+i++++ +++e+iT+edri+a++q+l++kkafvl+ke+f+++++ilg+kYtldr+t+i++aik+g++vykl+d+++g
  gene753|gene753|rna753|rna753 352 RQRMIAREQ-SVEEGITMEDRINAIEQILSVKKAFVLDKEFFKDFRSILGCKYTLDRRTVINAAIKGGFNVYKLHDDAQG 430
                                    *********.99******************************************************************** PP

                      HTH_micro 348 skyviarkdvdesdivlnnyvnk.keaekenkfqkkvkkkfvnnskfieiDNgyekkeeerikilyeflvknskeeslqf 426
                                    +k+v+arkdv ++d++++ny+++ k+a++ ++fq++++k+fv++skf+eiDNg+e+  ++r+k+ly+fl ++ ke++++f
  gene753|gene753|rna753|rna753 431 AKFVVARKDVLQDDPSVTNYYPSrKTASTLTPFQSQLHKFFVTHSKFAEIDNGFEPVLNKRVKALYSFL-RRLKENEFYF 509
                                    *********************9989********************************************.********** PP

                      HTH_micro 427 skevllemslklllslvpfkrikflekL 454
                                    +++vl++msl+l+++lv+fkr+kfl +L
  gene753|gene753|rna753|rna753 510 NCDVLQSMSLGLFFKLVSFKRYKFLGEL 537
                                    *************************987 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.11
                      HTH_micro 147 vikinkDesgsvvkkldkeklleinkedtit 177
                                    +ik+++ +s+++++++++e+l++ +++++ t
  gene753|gene753|rna753|rna753 540 IIKMKR-NSRDEERRVAEERLIDEKENENYT 569
                                    679999.8999************99998544 PP

>> B-block_TFIIIC  B-block binding subunit of TFIIIC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   2.8e-05       0.1      28      52 ..     194     218 ..     186     229 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.8e-05
                 B-block_TFIIIC  28 skqdprslfyrlksLekkgLIvkqs 52 
                                    ++++p+++fy++k+L + g+I k +
  gene753|gene753|rna753|rna753 194 LGIEPKKMFYIIKKLVSLGYIDKTA 218
                                    689******************9975 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   2.2e-05     0.079      13      56 ..     177     219 ..     168     223 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.2e-05
                                    HHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEES CS
                         MarR_2  13 aLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpg 56 
                                     L r  ++ ++v+    +lg+++  + +i+k+Lv+ G++ +++ 
  gene753|gene753|rna753|rna753 177 MLIRMNEY-VSVSNMRVTLGIEPKKMFYIIKKLVSLGYIDKTAE 219
                                    55566666.89****************************99865 PP

>> PspB  Phage shock protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.68   2.4e+03      43      62 ..     309     328 ..     306     329 .. 0.86
   2 ?   10.0   0.2   0.00019      0.68      44      67 ..     359     382 ..     338     385 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.68
                           PspB  43 LeellekAekleeRietLEr 62 
                                    L+ l + ++++e  i+t+E+
  gene753|gene753|rna753|rna753 309 LKLLNKISDRMEGSIKTVEE 328
                                    667888899*********96 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00019
                           PspB  44 eellekAekleeRietLEriLdae 67 
                                    e+ +e+  ++e+Ri+++E+iL  +
  gene753|gene753|rna753|rna753 359 EQSVEEGITMEDRINAIEQILSVK 382
                                    456777889************865 PP

>> SMC_ScpA  Segregation and condensation protein ScpA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.5   5.5e-05       0.2     112     200 ..     318     401 ..     304     413 .. 0.81
   2 ?    2.0   1.2     0.047   1.7e+02      77     122 ..     520     565 ..     499     579 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 5.5e-05
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX...HHHHHHHHHHHH...............HHHTS- CS
                       SMC_ScpA 112 dleefikeveevavkieksvfklieafnkllkrakivalaekqiseleisieeqleellaqleqflqarlkevLldlrsw 191
                                     +e  ik+vee + ki  ++f  ++ + kl  r++  + a  q+ e  i +e++ +     +eq+l+++   vL +    
  gene753|gene753|rna753|rna753 318 RMEGSIKTVEEFEGKIKRTKFYNVNELSKLKERKRQRMIAREQSVEEGITMEDRINA----IEQILSVKKAFVLDKE-FF 392
                                    567789****************************99999998898888888887664....679**99999887664.46 PP

                                    EEGGGSSTT CS
                       SMC_ScpA 192 vdlseLlad 200
                                     d+  +l +
  gene753|gene753|rna753|rna753 393 KDFRSILGC 401
                                    677777776 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.047
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                       SMC_ScpA  77 kLiarLleYrkykeeaklfkeleaerlksfskarsdleefikevee 122
                                    +L+ +L+ +++yk   +l++  +++r      +r+ +e++i+e e+
  gene753|gene753|rna753|rna753 520 GLFFKLVSFKRYKFLGELIEIIKMKRNSRDEERRVAEERLIDEKEN 565
                                    7999***********99999999999866578889******98766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (704 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       649  (0.0361983); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.61u 0.25s 00:00:00.86 Elapsed: 00:00:03.23
# Mc/sec: 661.66
//
Query:       gene754|gene754|rna754|rna754  [L=174]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.12   11.5   0.0       0.16   11.1   0.0    1.1  1  DUF763    Protein of unknown function (DUF763)


Domain annotation for each model (and alignments):
>> DUF763  Protein of unknown function (DUF763)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   8.8e-06      0.16      79     147 ..      53     131 ..      32     138 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 8.8e-06
                         DUF763  79 kseelgilvaGGkGkksrktpeeleklaeklgldeek..........lvkasrlvakvdnaalqdgyqlYlhalivsek 147
                                    +++  ++l++ GkG k++kt  e+ ++a+++ +d             lv+a  +   v  + + d y+l l++liv+++
  gene754|gene754|rna754|rna754  53 HKSGYNVLFIAGKGLKAKKTTVEVLRTADNVVFDIYPnknvvwrdevLVNAEAVEEYVKRTHVYDDYDLVLRSLIVEKE 131
                                    45567888999******************998875444479999999999999999********************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       442  (0.0246528); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 1147.32
//
Query:       gene755|gene755|rna755|rna755  [L=137]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.2e-09   38.2   0.1    7.5e-08   33.2   0.1    2.0  1  G6PD_N          Glucose-6-phosphate dehydrogenase, NAD bindin
    0.00024   21.0   0.0    0.00026   20.9   0.0    1.1  1  NAD_binding_10  NAD(P)H-binding
  ------ inclusion threshold ------
      0.016   14.8   0.1        0.1   12.2   0.0    2.0  2  RRM_5           RNA recognition motif. (a.k.a. RRM, RBD, or R
      0.036   13.6   0.0      0.044   13.3   0.0    1.1  1  NmrA            NmrA-like family
      0.061   12.9   0.0      0.075   12.6   0.0    1.1  1  DUF4848         Domain of unknown function (DUF4848)


Domain annotation for each model (and alignments):
>> G6PD_N  Glucose-6-phosphate dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.2   0.1   2.1e-11   7.5e-08       1     140 [.      26     134 ..      26     136 .. 0.84

  Alignments for each domain:
  == domain 1  score: 33.2 bits;  conditional E-value: 2.1e-11
                         G6PD_N   1 vifGasGdLakrkllPaLyelaregllpeevrivgvarsklsdeefrekvkealkkekekeeldeekleeflkrleyvsg 80 
                                    +ifGasG+L+k kllP++++    ++l ++++iv ++r+ ++d+ ++++vke        +           k+l+ v+g
  gene755|gene755|rna755|rna755  26 IIFGASGNLSKVKLLPSILK----EKLYKDCEIVLYSRN-VDDDVLQAQVKEVN------D-----------KNLRIVQG 83 
                                    8****************975....7899********995.78888888887753......2...........57999*** PP

                         G6PD_N  81 dleeeeeyekLkekleeleanrlfYlavppslfeevaeklkkaglakeeewkrvvvEKPf 140
                                    +++++   ek++e ++  ++ ++fYl +p +   +++++l++   +   +   v +EKPf
  gene755|gene755|rna755|rna755  84 QYTDT---EKIAELING-KKLVIFYLCIPSHQHLTIIQSLDNL--N---REVVVALEKPF 134
                                    **999...556666665.678********************95..4...3567889***9 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   7.2e-08   0.00026      18      71 ..      47     108 ..      29     133 .. 0.70

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 7.2e-08
                                    -...T-EEEEEETT......HHHCHHHHCTTTCEEEE--TT-CCHHHHHHTT-SEEEES---T CS
                 NAD_binding_10  18 g...ghevtalvRn......peklaeleaeeglevvegdvtdvedlaealkgadaVvsalggg 71 
                                    +   + e++++ Rn      +++++e+  +++l++v+g+ td+e++ae ++g   V++ l   
  gene755|gene755|rna755|rna755  47 KlykDCEIVLYSRNvdddvlQAQVKEVN-DKNLRIVQGQYTDTEKIAELINGKKLVIFYLCIP 108
                                    3344577888888866666667889996.69*************************9988433 PP

>> RRM_5  RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   2.8e-05       0.1      39      63 ..      19      43 ..      14      56 .. 0.87
   2 ?    0.2   0.0      0.15   5.2e+02      36      62 ..      70      96 ..      64     103 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.8e-05
                          RRM_5 39 vnldklFnlfclYgnvervkflktk 63
                                   + +dk+F++f+  gn+++vk+l ++
  gene755|gene755|rna755|rna755 19 FVMDKIFIIFGASGNLSKVKLLPSI 43
                                   5689*****************9775 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.15
                          RRM_5 36 pdkvnldklFnlfclYgnvervkflkt 62
                                    ++vn ++l ++ ++Y + e++  l +
  gene755|gene755|rna755|rna755 70 VKEVNDKNLRIVQGQYTDTEKIAELIN 96
                                   578899999999999999999976655 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   1.2e-05     0.044       3      73 ..      27     106 ..      25     119 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.2e-05
                                    ESSTTSHHHH.....HHHHHHHHHT-EEEEEES-S....-SHHHHHHHHSTTEEEES-TT-HHHHHHHHTT-SEEEE--- CS
                           NmrA   3 viGaTGrqGk.....svvrallkaghkvralvRdt....kselakslkeaGvelvkgdlddkeslvealkgvdvvfsvtg 73 
                                    ++Ga+G++ k     s+ +  l ++ ++    R++     + ++k+++++   +v+g+  d e ++e+++g ++v++ + 
  gene755|gene755|rna755|rna755  27 IFGASGNLSKvkllpSILKEKLYKDCEIVLYSRNVdddvLQAQVKEVNDKNLRIVQGQYTDTEKIAELINGKKLVIFYLC 106
                                    788888888743222344444448888888899997777788899******************************98765 PP

>> DUF4848  Domain of unknown function (DUF4848)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   2.1e-05     0.075     121     190 ..      42     104 ..      25     109 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.1e-05
                                    EEEE--B-SSHHHHH--S----S-EE--TTSBSEEEEE-SSEEE....EEEEEE.......ETTEEEEEE CS
                        DUF4848 121 slvdapvYkdleefqsqisvvsaseaaeksdineafkrfkdaklqiknGkYvsvraigrivnslslavef 190
                                    s+ +++ Ykd e     i ++s++   +   ++   k   d++l+i +G+Y  +  i+ ++n++ l + +
  gene755|gene755|rna755|rna755  42 SILKEKLYKDCE-----IVLYSRN--VDDDVLQAQVKEVNDKNLRIVQGQYTDTEKIAELINGKKLVIFY 104
                                    555666665543.....4666655..5666677778899************************9987766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (137 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       583  (0.0325172); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 1031.72
//
Query:       gene756|gene756|rna756|rna756  [L=198]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.9e-43  146.6   0.0    5.6e-43  146.4   0.0    1.1  1  Arf              ADP-ribosylation factor family
    2.1e-12   47.3   0.0    2.9e-12   46.8   0.0    1.2  1  Roc              Ras of Complex, Roc, domain of DAPkinase
    5.4e-10   39.1   0.0    6.8e-10   38.8   0.0    1.2  1  Ras              Ras family
    4.8e-08   32.6   0.9    0.00015   21.1   0.3    2.6  2  G-alpha          G-protein alpha subunit
    3.2e-06   26.7   0.0    4.9e-06   26.1   0.0    1.3  1  Gtr1_RagA        Gtr1/RagA G protein conserved region
    5.6e-06   25.9   0.0    8.1e-06   25.4   0.0    1.2  1  SRPRB            Signal recognition particle receptor beta su
    2.1e-05   24.6   0.0    3.2e-05   24.0   0.0    1.3  1  MMR_HSR1         50S ribosome-binding GTPase
  ------ inclusion threshold ------
      0.026   13.8   0.1      0.064   12.6   0.0    1.6  2  6PF2K            6-phosphofructo-2-kinase
       0.16   11.8   0.2       0.52   10.1   0.2    1.9  1  NOG1             Nucleolar GTP-binding protein 1 (NOG1)
       0.18   10.5   0.1       0.27    9.9   0.1    1.3  1  Coprogen_oxidas  Coproporphyrinogen III oxidase


Domain annotation for each model (and alignments):
>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  146.4   0.0   3.1e-46   5.6e-43       4     159 ..       7     159 ..       4     185 .. 0.86

  Alignments for each domain:
  == domain 1  score: 146.4 bits;  conditional E-value: 3.1e-46
                                    HHHGGTT.TTEEEEEEEESTTSSHHHHHHHHHHSSCEECSSSSSEEEEEEEETTEEEEEEEE-SSGGGGGGGGGGCTTES CS
                            Arf   4 ilaklklkkkelrilllGLDnaGKtTilkklkleelvttvPTigfnveeleiknlkftvwDvGGqeklRplWknYfektd 83 
                                     +++l++++  + i ++GLD+aGKtTil+++kl+++v tvPTigfnve+ +++n++f++wD+GGq+k+Rp+W +Y e  d
  gene756|gene756|rna756|rna756   7 AFTNLFNTRTPYSICMIGLDAAGKTTILYQMKLKNTVPTVPTIGFNVEKFQVNNVEFSCWDIGGQDKIRPVWCKYVELSD 86 
                                    5778889899999******************************************************************* PP

                                    EEEEEEETT-CTTHHHHHHHHHHHCTSGCCTTSEEEEEEE-TTSTTSS-HHHHHHH.TTGGGSSSSSSEEEEEEBTT CS
                            Arf  84 avifvvDsadreRleeakeeLkalleeeelkevallvlaNKqDlpealseeelrel.lgleelkgkrkleiqkcsav 159
                                    +++fvvD  d++R +ea e L+++le+   k+ ++l+laNK D p++ + ++ +e+ l++ +++  +   + +c +v
  gene756|gene756|rna756|rna756  87 GMVFVVDIFDEDRWSEAGEALRSILENY--KNKPVLILANKADDPNDPELDDRKEKmLKVFNIE--NVCDLWECKTV 159
                                    *************************875..56689************99888876515666666..33344444443 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.8   0.0   1.6e-15   2.9e-12       2     119 ..      20     127 ..      19     128 .. 0.86

  Alignments for each domain:
  == domain 1  score: 46.8 bits;  conditional E-value: 1.6e-15
                                    EEEESSTTSSHHHHHHCHCT-CCC-EEETTTTEEEEEEECGGSGGCTTBTTTTCEEEEEEEE-SGGCTTTT-HHHHCTSC CS
                            Roc   2 vvlvGdsgvGKtsllkrfvedkfsekekstigvdfltkevtkikgvendkkvkkvklniWDtaGqerfrslhplylreaa 81 
                                    ++++G  ++GKt++l ++  ++  ++  +tig ++ + +            v++v++++WD++Gq+++r +   y++ ++
  gene756|gene756|rna756|rna756  20 ICMIGLDAAGKTTILYQMKLKNTVPT-VPTIGFNVEKFQ------------VNNVEFSCWDIGGQDKIRPVWCKYVELSD 86 
                                    799*************9987777665.79****995433............24589************************ PP

                                    EEEEEEE...GHHHHCHHHHHHHHHHHCSSS-EEEEEE-TT CS
                            Roc  82 lailvyd...srssenlkeWlkelkkvagkspvilvgnkiD 119
                                     +++v+d   +++ +++ e l+++ ++ +++pv++++nk+D
  gene756|gene756|rna756|rna756  87 GMVFVVDifdEDRWSEAGEALRSILENYKNKPVLILANKAD 127
                                    ****9986535555788899********************9 PP

>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.8   0.0   3.8e-13   6.8e-10       2     122 ..      20     134 ..      19     167 .. 0.83

  Alignments for each domain:
  == domain 1  score: 38.8 bits;  conditional E-value: 3.8e-13
                                    EEEEESTTSSHHHHHHHHHHSSCSSSCTTTSSEEEEEEEEEETTEEEEEEEEEETTSGGGHHHHHHHHTTESEEEEEEET CS
                            Ras   2 lvlvGdsavGKtslllrfvkdkFkeeyesTigvdfytkeievdgkevkleiwDTAGqeefkslrelyyrdaegillvydi 81 
                                    + ++G  a GKt++l++   ++ +    +Tig++  +  ++v  ++v+++ wD  Gq++ + +  +y++ ++g++ v di
  gene756|gene756|rna756|rna756  20 ICMIGLDAAGKTTILYQMKLKN-TVPTVPTIGFNVEK--FQV--NNVEFSCWDIGGQDKIRPVWCKYVELSDGMVFVVDI 94 
                                    5789************975544.455689**876554..444..5799******************************** PP

                                    TBHHHHHTHHHHHHHHHHHSTTTSEEEEEEETTTGGGG-SS CS
                            Ras  82 tsresfenvkkwveeikrvaeenvpivLvGnKvDleekrav 122
                                     +++ ++++ + ++ i +  + n p+++++nK+D  ++ ++
  gene756|gene756|rna756|rna756  95 FDEDRWSEAGEALRSILENYK-NKPVLILANKADDPNDPEL 134
                                    ****************99999.689*********8775444 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.0   0.00025      0.45      20      45 ..      14      39 ..       5      45 .. 0.85
   2 !   21.1   0.3   8.4e-08   0.00015     186     235 ..      46      94 ..      40     128 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00025
                                   E..EEEEEEEESTTSSHHHHHHHHHH CS
                        G-alpha 20 kkrevkllllGqseSGKsTilkqlkl 45
                                   +++++++ ++G +  GK+Til q+kl
  gene756|gene756|rna756|rna756 14 TRTPYSICMIGLDAAGKTTILYQMKL 39
                                   456889******************96 PP

  == domain 2  score: 21.1 bits;  conditional E-value: 8.4e-08
                                    ----SEEEEEEECT-TEEEEEEEE-SSHHHHHGTCCCTTTECEEEEEEEG CS
                        G-alpha 186 lktvGisetkfevdsklefrivdvgGqrserkkWvpffddvdaiiFlvsl 235
                                    ++t+G++  kf+v+ ++ef  +d+gGq + r+ W ++ +  d  +F+v +
  gene756|gene756|rna756|rna756  46 VPTIGFNVEKFQVN-NVEFSCWDIGGQDKIRPVWCKYVELSDGMVFVVDI 94 
                                    68***********9.********************************987 PP

>> Gtr1_RagA  Gtr1/RagA G protein conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.0   2.7e-09   4.9e-06       3     126 ..      21     131 ..      19     160 .. 0.77

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 2.7e-09
                      Gtr1_RagA   3 LLmGksgsGKtsmrsiiFdnylardtlrlgatidveksevrflgnltlnlwDcgGqeafveeylssqkeeifrnvgvliy 82 
                                     ++G   +GKt++      ++  ++t+    ti  + +++  ++n++++ wD+gGq+++    +     +  +  + +++
  gene756|gene756|rna756|rna756  21 CMIGLDAAGKTTI----LYQMKLKNTVPTVPTIGFNVEKF-QVNNVEFSCWDIGGQDKIRPVWC-----KYVELSDGMVF 90 
                                    57899*****984....56788999999999**9999999.589*************9988753.....33445579*** PP

                      Gtr1_RagA  83 VfDvesreleedletlkeilealrqyspeakvfvlihKmDliqe 126
                                    V+D+ ++   +  ++  e+l+ + ++ ++  v +l +K D  ++
  gene756|gene756|rna756|rna756  91 VVDIFDE---DRWSEAGEALRSILENYKNKPVLILANKADDPND 131
                                    ****955...4555566667777777888899999999997654 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.0   4.5e-09   8.1e-06       5     123 ..      19     127 ..      15     133 .. 0.81

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 4.5e-09
                                    EEEEE-STTSSHHHHHHHHHHSS---B---SS-EEETTG...GGTT-SEEEETT-GCCSHHHHHHHHHHGGEEEEEEEEE CS
                          SRPRB   5 avllvGlsdsGKTslftrLttdsvkktvtSqessaalkvksekgskltliDfPGheklrqklleklkaksslkglvfvvD 84 
                                    ++ ++Gl  +GKT+++ ++  +++ +tv  +  ++ +k+ + ++ ++   D+ G++k+r   ++++   +   g+vfvvD
  gene756|gene756|rna756|rna756  19 SICMIGLDAAGKTTILYQMKLKNTVPTVPTIGFNV-EKF-QVNNVEFSCWDIGGQDKIRPVWCKYV---ELSDGMVFVVD 93 
                                    5789************************9995443.344.459999*************9999884...44569****** PP

                                    TTS-HHHHHHHHHHHHHHHHHHHHHTT---EEEEEE-TT CS
                          SRPRB  85 StidpkevkevAEllyeilliteklkdavdiliACnKqe 123
                                       d+ +  e  E l +il + +   +++ +li  nK +
  gene756|gene756|rna756|rna756  94 I-FDEDRWSEAGEALRSILENYK---NKP-VLILANKAD 127
                                    5.5777889999***99997665...554.455556655 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.0   1.8e-08   3.2e-05       2     114 .]      20     125 ..      19     125 .. 0.79

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 1.8e-08
                                    EEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSSHHHHHHHHHHHHHHHHC.TSEEE CS
                       MMR_HSR1   2 vaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgkeielvDtpGliegaseekglgkaflalee.adlil 80 
                                    ++ +G   +GK+t++ ++   k  v   p    ++++++v+  + e+  +D+ G  +      +++  +++  e +d ++
  gene756|gene756|rna756|rna756  20 ICMIGLDAAGKTTILYQMKL-KNTVPTVPTIGFNVEKFQVN--NVEFSCWDIGG-QD------KIRPVWCKYVElSDGMV 89 
                                    7899************9954.34455556555555555555..999********.44......7999999999978**** PP

                                    EEEETT.TTCSHHHHHHHHHHHHH.TTSEEEEEEES CS
                       MMR_HSR1  81 lvvdas.eeklkpldeeleellee.akkplilvlnk 114
                                    +vvd+  e+ +++  e l ++le+ ++kp+++++nk
  gene756|gene756|rna756|rna756  90 FVVDIFdEDRWSEAGEALRSILENyKNKPVLILANK 125
                                    ****996557888888888888777899**999998 PP

>> 6PF2K  6-phosphofructo-2-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   3.6e-05     0.064      11      53 ..      15      57 ..       7      68 .. 0.79
   2 ?   -2.6   0.0       1.5   2.7e+03     120     134 ..     138     152 ..     132     155 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3.6e-05
                                   .S-EEEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHH CS
                          6PF2K 11 nsklvivlvGLpargKtyiskkltrylkwlgvrtkvFnvgkyr 53
                                    ++  i ++GL a gKt+i  ++       +v+t  Fnv k++
  gene756|gene756|rna756|rna756 15 RTPYSICMIGLDAAGKTTILYQMKLKNTVPTVPTIGFNVEKFQ 57
                                   56789**************988876666777888888887765 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.5
                                    HHTT-EEEEEEEE-- CS
                          6PF2K 120 eennlkvlflesics 134
                                    +e+ lkv+ +e +c+
  gene756|gene756|rna756|rna756 138 KEKMLKVFNIENVCD 152
                                    455577777777775 PP

>> NOG1  Nucleolar GTP-binding protein 1 (NOG1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.2   0.00029      0.52      17      58 .]      88     127 ..      82     127 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00029
                           NOG1  17 vlFllDpseecgysleeQlsLleeikelfankpvivvlnKiD 58 
                                    ++F++D+  e   s  e  + l++i e+ +nkpv++ +nK+D
  gene756|gene756|rna756|rna756  88 MVFVVDIFDEDRWS--EAGEALRSILENYKNKPVLILANKAD 127
                                    55666666665443..2234578899999***********99 PP

>> Coprogen_oxidas  Coproporphyrinogen III oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.1   0.00015      0.27      95     132 ..      40      78 ..      26     102 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00015
                Coprogen_oxidas  95 hprnPlvPtvhlnyryfeaeekkkawWFgGgaD.LtPsy 132
                                      + P+vPt+ +n+  f++++ + ++W  Gg D + P++
  gene756|gene756|rna756|rna756  40 KNTVPTVPTIGFNVEKFQVNNVEFSCWDIGGQDkIRPVW 78 
                                    5567***************99778888777776366765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (198 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       530  (0.029561); expected 358.6 (0.02)
Passed bias filter:                      489  (0.0272742); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1455.39
//
Query:       gene757|gene757|rna757|rna757  [L=396]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.4e-45  153.3   0.1    1.5e-44  151.6   0.0    1.9  1  AAA              ATPase family associated with various cellul
    1.5e-09   37.6   0.3    5.9e-09   35.8   0.1    2.1  2  Prot_ATP_ID_OB   Proteasomal ATPase OB C-terminal domain
    2.3e-08   33.7   0.0    5.5e-08   32.5   0.0    1.7  1  AAA_lid_3        AAA+ lid domain
    5.4e-08   33.1   0.0    1.1e-07   32.2   0.0    1.5  1  AAA_2            AAA domain (Cdc48 subfamily)
    1.4e-07   31.6   0.2    4.4e-07   30.0   0.2    1.9  1  AAA_5            AAA domain (dynein-related subfamily)
    1.4e-07   32.0   0.9    6.4e-05   23.4   0.0    2.9  3  AAA_16           AAA ATPase domain
    5.6e-07   29.6   0.2    0.00044   20.2   0.0    3.3  3  NTPase_1         NTPase
    1.1e-05   24.8   0.0      2e-05   23.9   0.0    1.5  1  DUF815           Protein of unknown function (DUF815)
    2.4e-05   24.9   0.0    0.00013   22.5   0.0    2.1  1  AAA_18           AAA domain
    2.5e-05   24.6   1.3     0.0031   17.8   0.1    2.5  2  AAA_22           AAA domain
    0.00022   21.0   0.0     0.0005   19.8   0.0    1.7  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
     0.0006   20.2   0.0     0.0033   17.8   0.0    2.2  2  RNA_helicase     RNA helicase
    0.00062   19.8   0.0     0.0011   19.0   0.0    1.4  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
    0.00075   19.5   0.0     0.0024   17.9   0.0    1.8  2  AAA_14           AAA domain
     0.0014   17.9   0.0     0.0026   17.0   0.0    1.4  1  TIP49            TIP49 P-loop domain
     0.0015   18.0   0.1     0.0051   16.3   0.1    2.0  1  AAA_7            P-loop containing dynein motor region
      0.002   17.9   0.0     0.0087   15.8   0.0    2.1  1  AAA_30           AAA domain
      0.002   17.9   0.0     0.0038   17.0   0.0    1.5  1  AAA_24           AAA domain
     0.0023   17.9   0.4       0.04   13.9   0.0    2.3  2  NACHT            NACHT domain
     0.0025   18.0   0.0     0.0063   16.7   0.0    1.7  1  AAA_33           AAA domain
     0.0033   17.2   2.2      0.049   13.3   0.0    3.3  4  Sigma54_activat  Sigma-54 interaction domain
     0.0046   17.2   0.0      0.009   16.3   0.0    1.5  1  AAA_28           AAA domain
     0.0057   16.1   0.0       0.19   11.2   0.0    2.4  2  TniB             Bacterial TniB protein
     0.0074   15.7   0.1      0.017   14.5   0.1    1.6  1  Mg_chelatase     Magnesium chelatase, subunit ChlI
  ------ inclusion threshold ------
       0.02   14.8   0.1      0.076   12.9   0.0    2.0  1  AAA_3            ATPase family associated with various cellul
       0.03   14.0   0.0      0.056   13.2   0.0    1.5  1  IstB_IS21        IstB-like ATP binding protein
      0.037   13.8   0.7       0.16   11.7   0.0    2.1  2  AAA_11           AAA domain
      0.044   13.7   2.5       0.13   12.1   0.0    2.5  3  ATPase_2         ATPase domain predominantly from Archaea
      0.083   11.8   0.1       0.17   10.7   0.1    1.5  1  AFG1_ATPase      AFG1-like ATPase
      0.088   13.3   0.0       0.22   12.0   0.0    1.8  1  ABC_tran         ABC transporter
      0.088   12.6   0.0       0.15   11.9   0.0    1.5  1  Bac_DnaA         Bacterial dnaA  protein
       0.09   12.3   0.8       0.48   10.0   0.7    2.0  2  AAA_25           AAA domain
      0.093   13.1   0.2        0.3   11.4   0.1    1.8  1  AAA_19           AAA domain
       0.11   13.0   0.0       0.27   11.6   0.0    1.8  1  AAA_17           AAA domain
       0.18   10.8   0.0       0.37    9.8   0.0    1.4  1  Parvo_NS1        Parvovirus non-structural protein NS1
       0.34   10.2   2.5       0.83    9.0   0.1    2.4  3  ATPase           KaiC


Domain annotation for each model (and alignments):
>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  151.6   0.0     3e-47   1.5e-44       1     132 []     180     313 ..     180     313 .. 0.97

  Alignments for each domain:
  == domain 1  score: 151.6 bits;  conditional E-value: 3e-47
                                    EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH...TTC CS
                            AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksr...sgs 77 
                                    vllyGppGtGKT+l+kava++++++f++++gse+++ky+ge+++ +r++f+ a+e+a psi+fiDE+d++a++r    +s
  gene757|gene757|rna757|rna757 180 VLLYGPPGTGKTMLVKAVANKTKATFIQVNGSEFVQKYLGEGPRMVRDVFRLAREQA-PSIVFIDEVDSIATKRfdaATS 258
                                    79******************************************************9.****************998888 PP

                                    CCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETTS CS
                            AAA  78 eseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieiel 132
                                    +++e +rv+ +Ll+++dg++   + v vi+atnr d ldpallr gR+drkie++l
  gene757|gene757|rna757|rna757 259 ADREVQRVLLELLSQMDGFDVTVN-VKVIMATNRADILDPALLRpGRLDRKIEFPL 313
                                    999999***************765.****************************985 PP

>> Prot_ATP_ID_OB  Proteasomal ATPase OB C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.8   0.1   1.2e-11   5.9e-09       2      57 .]      68     122 ..      67     122 .. 0.95
   2 ?   -2.1   0.0       7.8   3.9e+03      28      41 ..     291     304 ..     280     305 .. 0.82

  Alignments for each domain:
  == domain 1  score: 35.8 bits;  conditional E-value: 1.2e-11
                                    EEEEEE-TTSSEEEEE-TTS-EEEEEE-GGGSSST--TTEEEEEETTTTEEEEEE- CS
                 Prot_ATP_ID_OB   2 atVsEvlddteraiVktssdeevvvslagavpremLrpgDlVavdkdtgfifEkLP 57 
                                    ++  E +d+ + aiV ++++ ++vv++ + v++e L+p+++Va+++++ +i+++LP
  gene757|gene757|rna757|rna757  68 GQFLEAIDK-QTAIVGSTTGSNSVVKILSTVDKELLKPNTTVALHRHSSAIVDVLP 122
                                    567799999.*********************************************9 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 7.8
                                    E-GGGSSST--TTE CS
                 Prot_ATP_ID_OB  28 lagavpremLrpgD 41 
                                    +a+ ++++ Lrpg 
  gene757|gene757|rna757|rna757 291 RADILDPALLRPGR 304
                                    6777899999*996 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.5   0.0   1.1e-10   5.5e-08       2      45 .]     336     379 ..     335     379 .. 0.97

  Alignments for each domain:
  == domain 1  score: 32.5 bits;  conditional E-value: 1.1e-10
                      AAA_lid_3   2 vdlkeLAerTeGySGADlaalcreAallAlrrgikeitmedfee 45 
                                    vdl+  ++r +  S ADl ++c+eA++lA+r g+  i ++dfee
  gene757|gene757|rna757|rna757 336 VDLESFVSRPDRLSCADLNSICQEAGMLAIRNGRYVILQKDFEE 379
                                    9*****************************************97 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.2   0.0   2.1e-10   1.1e-07       6     103 ..     180     271 ..     175     292 .. 0.86

  Alignments for each domain:
  == domain 1  score: 32.2 bits;  conditional E-value: 2.1e-10
                                    EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG---- CS
                          AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKihpk 83 
                                    +ll gp g+Gkt+l ka+a+  ++    ++i ++ se+ +    + l +     ++    a e+   iv++DE+d i+ k
  gene757|gene757|rna757|rna757 180 VLLYGPPGTGKTMLVKAVANKTKA----TFIQVNGSEFVQ----KYLGEGPRMVRDVFRLAREQApsIVFIDEVDSIATK 251
                                    6899****************9985....************....88888888888888888888789************8 PP

                                    ---------HHHHHHHHHHH CS
                          AAA_2  84 essgadvSregVqrdLLqil 103
                                    +   a     +Vqr+LL +l
  gene757|gene757|rna757|rna757 252 RFDAATSADREVQRVLLELL 271
                                    77777777889******998 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.0   0.2   8.7e-10   4.4e-07       1     135 [.     179     300 ..     179     302 .. 0.81

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 8.7e-10
                                    EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------..G-SEEEEESGGG-- CS
                          AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar..egeilvlDEverae 78 
                                    +vlL GppGtgK++l++ +a  +++++  v+++++ ++    g+r +           + r ar   ++i+++DEv+ + 
  gene757|gene757|rna757|rna757 179 GVLLYGPPGTGKTMLVKAVANKTKATFIQVNGSEFVQKYLGEGPRMV---------RDVFRLAReqAPSIVFIDEVDSIA 249
                                    59****************************99998887777777777.........5556666656899*********** PP

                                    HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--.-TT-TTHHHH CS
                          AAA_5  79 sevlnsLlslleerrllleeggelvkaknddllerfrviatanpldrslnelspalr 135
                                    ++ +++  s   e ++ l e+  +++   +d + ++ vi+++n++d     l+pal+
  gene757|gene757|rna757|rna757 250 TKRFDAATSADREVQRVLLELLSQMDG--FDVTVNVKVIMATNRAD----ILDPALL 300
                                    999999988877777777777666655..33556699999999999....6666665 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.0   1.3e-07   6.4e-05      16      63 ..     169     213 ..     164     223 .. 0.77
   2 ?    6.1   0.1     0.027        14     126     160 ..     228     272 ..     222     286 .. 0.67
   3 ?   -2.2   0.0       9.6   4.8e+03     116     147 ..     347     380 ..     303     387 .. 0.67

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 1.3e-07
                         AAA_16  16 lervrsgrpelvllsGesGvGKsslvrellralekdggiflrgkcdql 63 
                                    ++++  + p+ vll+G++G+GK+ lv+++++  +   + f++ +  ++
  gene757|gene757|rna757|rna757 169 YKQIGIDPPRGVLLYGPPGTGKTMLVKAVANKTK---ATFIQVNGSEF 213
                                    5566666679********************7444...44666555554 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.027
                         AAA_16 126 llallsrderplvlvlDdlq...........wadeaslqllaaLlr 160
                                     ++l+++ + p ++++D+++            ad + + +l +Ll+
  gene757|gene757|rna757|rna757 228 VFRLARE-QAPSIVFIDEVDsiatkrfdaatSADREVQRVLLELLS 272
                                    4467777.999*********99999777555444455555333333 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 9.6
                         AAA_16 116 a...srllellkrllallsrderplvlvlDdlqwa 147
                                    +    +l+  ++++ +l+ r++r  v++  d++ a
  gene757|gene757|rna757|rna757 347 RlscADLNSICQEAGMLAIRNGR-YVILQKDFEEA 380
                                    03356777888888888887677.88887777765 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0      0.17        84      99     122 ..     140     163 ..      89     168 .. 0.80
   2 !   20.2   0.0   8.8e-07   0.00044       2      91 ..     180     273 ..     179     286 .. 0.78
   3 ?    2.4   0.0      0.25   1.3e+02      64      93 ..     360     389 ..     350     394 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.17
                                    EEE---STTGGG-HHHHHHHHHHH CS
                       NTPase_1  99 iviDEiGkmElkskkfkeaveevL 122
                                    +  D iG +E + ++++e+ve  L
  gene757|gene757|rna757|rna757 140 VTYDDIGGLETQKQEIIETVELPL 163
                                    5679**************998666 PP

  == domain 2  score: 20.2 bits;  conditional E-value: 8.8e-07
                                    EEEE--TTSSHHHHHHHHHHHH...GGGEEEE.EEEEE-------EEEEEET.T--EEEEEETT---SSEETTEEE-HHH CS
                       NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvkvgGf.yteevreggrrigFkivdlasgeegiLarveakreprvgkyvvdves 80 
                                    v++ GppG+GKt lvk v+++ k   ++v+G   ++++  +g r+  ++  la ++   +   ++  ++  +++   + +
  gene757|gene757|rna757|rna757 180 VLLYGPPGTGKTMLVKAVANKTKATFIQVNGSeFVQKYLGEGPRMVRDVFRLAREQAPSIVFIDEVDSIATKRFDAATSA 259
                                    6788***************************74689999*************9999988888887777776666665443 PP

                                    ...HHHHHHHHHHH CS
                       NTPase_1  81 ...feelalealrk 91 
                                       ++++ le l++
  gene757|gene757|rna757|rna757 260 dreVQRVLLELLSQ 273
                                    33366666666654 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.25
                                    T---SSEETTEEE-HHHHHHHHHHHHHHHH CS
                       NTPase_1  64 eakreprvgkyvvdvesfeelalealrkal 93 
                                     +   +r+g+yv+  ++fee  +++ ++++
  gene757|gene757|rna757|rna757 360 AGMLAIRNGRYVILQKDFEEAYSRVADRKV 389
                                    4566789*************9999887765 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.0   4.1e-08     2e-05      23     116 ..     138     245 ..     125     295 .. 0.78

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 4.1e-08
                         DUF815  23 devklddLvgidkqkealventeqfleg.........lpannvLLwGarGtGKSslvkallneyaeegLrl..ieveked 91 
                                     +v+ dd+ g+++qk++++e +e  l++          p + vLL+G  GtGK  lvka+ n+++++ +++   e  ++ 
  gene757|gene757|rna757|rna757 138 PTVTYDDIGGLETQKQEIIETVELPLKQfelykqigiDPPRGVLLYGPPGTGKTMLVKAVANKTKATFIQVngSEFVQKY 217
                                    4688999***********999874444311111112257889***********************999776335888899 PP

                         DUF815  92 lkelpklvellr...erperfilfvDDL 116
                                    l e p++v+ +    +++   i+f+D +
  gene757|gene757|rna757|rna757 218 LGEGPRMVRDVFrlaREQAPSIVFIDEV 245
                                    9999999887642226667789999975 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.0   2.6e-07   0.00013       1     114 [.     180     388 ..     180     393 .. 0.91

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 2.6e-07
                         AAA_18   1 IlltGtpGvGKttlakeLskrlgf.....................gvnlrdvakenglllevdpe.......aldeskrl 52 
                                    +ll G+pG+GKt l k+++++++                      ++ +  +a+e  +++ + +e        +d    +
  gene757|gene757|rna757|rna757 180 VLLYGPPGTGKTMLVKAVANKTKAtfiqvngsefvqkylgegprmVRDVFRLAREQAPSIVFIDEvdsiatkRFDAATSA 259
                                    799***************9998445899999999999*******99999*************999****99988888899 PP

                         AAA_18  53 dedkldklldaleenss.....................................aleegknlvidghlaeleseaakdik 95 
                                    d++++ +ll++l + +                                          +k lv+  + +++   + +d+ 
  gene757|gene757|rna757|rna757 260 DREVQRVLLELLSQMDGfdvtvnvkvimatnradildpallrpgrldrkiefplPDKRQKRLVLNAITNKMNLSDEVDLE 339
                                    99999999999999999999999999999999999999999999999999999966778889999999999999999999 PP

                         AAA_18  96 k..............................vvLtaspeelleRlekRg 114
                                                                   v+L+ + ee + R+++R+
  gene757|gene757|rna757|rna757 340 SfvsrpdrlscadlnsicqeagmlairngryVILQKDFEEAYSRVADRK 388
                                    8999999999999999999999999999999999999999999999997 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.1   6.2e-06    0.0031       8      43 ..     180     206 ..     175     218 .. 0.81
   2 ?    5.4   0.2      0.04        20      77     126 ..     223     286 ..     203     295 .. 0.67

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 6.2e-06
                         AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevv 43 
                                    ++++G++GtGKT+l++ ++++          +++++
  gene757|gene757|rna757|rna757 180 VLLYGPPGTGKTMLVKAVANKT---------KATFI 206
                                    689*****************98.........44444 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.04
                         AAA_22  77 ellealeqalraravielliiDEaqhlr....s.........eealeeLrsllnl..srkgvqli 126
                                    ++++ + + +r++a  +++ iDE++ +               +++l eL s ++    + +v++i
  gene757|gene757|rna757|rna757 223 RMVRDVFRLAREQAP-SIVFIDEVDSIAtkrfDaatsadrevQRVLLELLSQMDGfdVTVNVKVI 286
                                    566677778888888.**********987655145557777755555554555532444444444 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0     1e-06    0.0005      35      97 ..     179     249 ..     152     299 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 1e-06
                         RuvB_N  35 hvllyGpPGlGkttlakiiakelgvklkitsgP.vleka.gd...laal...ltnleekdvlfideihrls 97 
                                     vllyGpPG Gkt l k +a++ ++++ +  g   ++k  g+   ++     l++ ++  ++fide+  ++
  gene757|gene757|rna757|rna757 179 GVLLYGPPGTGKTMLVKAVANKTKATFIQVNGSeFVQKYlGEgprMVRDvfrLAREQAPSIVFIDEVDSIA 249
                                    59********************9998766665514554222211133220113333455788888887765 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       5.3   2.7e+03      50      65 ..     137     152 ..     133     166 .. 0.71
   2 !   17.8   0.0   6.6e-06    0.0033       1      68 [.     180     238 ..     180     263 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 5.3
                   RNA_helicase  50 qevvvidDfgqvkdee 65 
                                     + v +dD+g  ++++
  gene757|gene757|rna757|rna757 137 RPTVTYDDIGGLETQK 152
                                    6789999999988772 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 6.6e-06
                   RNA_helicase   1 iwlyGpsgeGKStlakeLakallkklklkkkdsvysrnpeddfwdgYtgqevvvidDfgqvkdeenps 68 
                                    ++lyGp+g+GK++l+k            +k++ ++++ + ++f+++Y g+   ++ D+ +   e+ ps
  gene757|gene757|rna757|rna757 180 VLLYGPPGTGKTMLVKA---------VANKTKATFIQVNGSEFVQKYLGEGPRMVRDVFRLAREQAPS 238
                                    689**************.........346667788889999999999999999999999888775555 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   2.2e-06    0.0011      21      81 ..     172     237 ..     150     265 .. 0.73

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 2.2e-06
                                    E.......EEEEESTTSSHHHHHHHHHHHTT--..----TTTTSEEEEEE..SSEEEEE-TT-SSTHHHH CS
                           TsaE  21 v.......ilLeGdLGaGKTtlvrglakalgve..evkSPTFtlveeYelekeglyHfDlYRledeeele 81 
                                    +       +lL+G+ G+GKT+lv+++a++ + +  +v+      v++Y  e    +  D++Rl++e+   
  gene757|gene757|rna757|rna757 172 IgidpprgVLLYGPPGTGKTMLVKAVANKTKATfiQVN--GSEFVQKYLGEGP-RMVRDVFRLAREQA-P 237
                                    133344449*********************99955555..5566999966444.55579999976544.3 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       7.5   3.8e+03      72      88 ..      56      72 ..      11      97 .. 0.60
   2 !   17.9   0.0   4.9e-06    0.0024       5      84 ..     180     268 ..     177     285 .. 0.71

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 7.5
                         AAA_14 72 Eiqevpewekalkslvd 88
                                   Ei++v+++  ++ ++++
  gene757|gene757|rna757|rna757 56 EIKRVKSVPLIMGQFLE 72
                                   44444444444444444 PP

  == domain 2  score: 17.9 bits;  conditional E-value: 4.9e-06
                         AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqev........ 76 
                                    +++ G+  +GKT+l+k ++++       ++ +n  +  +k l +  ++ + ++++++e+  +++f+DE+  +        
  gene757|gene757|rna757|rna757 180 VLLYGPPGTGKTMLVKAVANKTK---ATFIQVNGSEFVQKYLGEGPRMVRDVFRLAREQAPSIVFIDEVDSIatkrfdaa 256
                                    7899***************8877...899999988866655554334555555554555889*******99866666555 PP

                         AAA_14  77 ....pewekalk 84 
                                        +e++++l 
  gene757|gene757|rna757|rna757 257 tsadREVQRVLL 268
                                    555555555555 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   5.2e-06    0.0026      51     167 ..     178     290 ..     167     298 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 5.2e-06
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXX-S-EEEEEEEEEEE.. CS
                          TIP49  51 ravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkkt.evltqalrksigvrikeekevleGevvelevee 129
                                    r+vLl Gp+gtGkt l  a++++   +  f++++gse+ +  +     ++ + +r +   r +  + v+  ev ++ +++
  gene757|gene757|rna757|rna757 178 RGVLLYGPPGTGKTMLVKAVANKT--KATFIQVNGSEFVQKYLGEGpRMVRDVFRLA---REQAPSIVFIDEVDSIATKR 252
                                    89*******************975..689********98887766514555566654...45556677888888888888 PP

                                    .-SSS-..TTS--EEEEEE-SS-EEEEEE-HHHHHHHH CS
                          TIP49 130 aenplskekkikevkitlktakeekklklgskiaeell 167
                                    ++ ++s +++++ v + l ++     ++++ k++++ +
  gene757|gene757|rna757|rna757 253 FDAATSADREVQRVLLELLSQMDGFDVTVNVKVIMATN 290
                                    88888877777777777777766666666666666555 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.1     1e-05    0.0051      33      65 ..     177     209 ..     151     260 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1e-05
                          AAA_7  33 kkpvllvGptGtGKtviikdllkkldkekylsl 65 
                                     + vll+Gp GtGKt+++k + +k + + ++++
  gene757|gene757|rna757|rna757 177 PRGVLLYGPPGTGKTMLVKAVANKTKATFIQVN 209
                                    5679*****************999985444444 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   1.8e-05    0.0087       5      46 ..     164     205 ..     160     268 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.8e-05
                         AAA_30   5 eQaaavealltsgdrvavltGpAGtGKttalkalreaweaag 46 
                                    +Q ++ +++  ++ r ++l Gp+GtGKt+++ka+++  +a  
  gene757|gene757|rna757|rna757 164 KQFELYKQIGIDPPRGVLLYGPPGTGKTMLVKAVANKTKATF 205
                                    677888888888888999****************98877664 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   7.7e-06    0.0038       5      76 ..     180     247 ..     177     266 .. 0.67

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 7.7e-06
                         AAA_24   5 iliyGpsgiGKTtlakel..gpkplfidtekG.lksldadkfpdieswedfldevvelaaeladyktlviDtide 76 
                                    +l+yGp+g+GKT+l+k    + k+ fi+++++ + + +  ++p      +++d +   +++ +  ++++iD +d 
  gene757|gene757|rna757|rna757 180 VLLYGPPGTGKTMLVKAVanKTKATFIQVNGSeFVQKYLGEGP-----RMVRDVFRLAREQAP--SIVFIDEVDS 247
                                    79***************99999999998887313344444444.....334444444333333..5555555554 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.0   7.9e-05      0.04       3      25 ..     180     202 ..     178     214 .. 0.88
   2 ?    1.8   0.0      0.41     2e+02      66     115 ..     222     273 ..     210     285 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 7.9e-05
                                    EEEEC-TTTCHHHHHHHHHHHHC CS
                          NACHT   3 vilqGeaGsGKTtLlqklalawa 25 
                                    v+l G++G GKT+L++ +a + +
  gene757|gene757|rna757|rna757 180 VLLYGPPGTGKTMLVKAVANKTK 202
                                    899**************998866 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.41
                                    -SSS-CCHHHHCCSCCCEEEEEE-STT-SS-TCH............HHHHHCT CS
                          NACHT  66 aapvsevwavllelperlLlilDglDelvtdlgq...kekqpvrtlLselirk 115
                                     + v+ v+ +  e++ ++++i D +D ++t+      +  ++v+++L el+++
  gene757|gene757|rna757|rna757 222 PRMVRDVFRLAREQAPSIVFI-DEVDSIATKRFDaatSADREVQRVLLELLSQ 273
                                    456777788888888888885.9999999855447888888999999999876 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   1.3e-05    0.0063       2      31 ..     180     209 ..     180     277 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.3e-05
                         AAA_33   2 vllvGlpGsGKstlaerllkklgavllssd 31 
                                    vll G+pG+GK+ l++ +++k++a+++  +
  gene757|gene757|rna757|rna757 180 VLLYGPPGTGKTMLVKAVANKTKATFIQVN 209
                                    7899*****************996666544 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       3.4   1.7e+03     113     146 ..      70     102 ..      57     112 .. 0.77
   2 ?   -2.4   0.0       6.5   3.3e+03      91     112 ..     134     155 ..     130     167 .. 0.84
   3 !   13.3   0.0   9.8e-05     0.049      22      63 ..     177     215 ..     155     220 .. 0.79
   4 ?    1.2   0.2      0.53   2.6e+02     130     143 ..     278     291 ..     233     297 .. 0.66

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 3.4
                                    HHHHHHHSEEESBTSSSEEE--EEEEEEESS-HH CS
                Sigma54_activat 113 LlrvlqegevervGsskeikvdvriiaatnedle 146
                                    +l++++++    vGs++  +  v+i+++ +++l 
  gene757|gene757|rna757|rna757  70 FLEAIDKQ-TAIVGSTTGSNSVVKILSTVDKELL 102
                                    56667655.4679999999999999999988875 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 6.5
                                    HTTTSEEEEETGGGS-HHHHHH CS
                Sigma54_activat  91 kadgGtlfLDeigelplelQek 112
                                    +a+  t+  D+ig l+++ Qe 
  gene757|gene757|rna757|rna757 134 EAQRPTVTYDDIGGLETQKQEI 155
                                    6888899999***999999985 PP

  == domain 3  score: 13.3 bits;  conditional E-value: 9.8e-05
                                    SS-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETTTS-T CS
                Sigma54_activat  22 dlsvlitGesGtGKellaraiheaskrkekpfvavncaaipe 63 
                                    +  vl+ G  GtGK++l +a+ +++   ++ f++vn +++ +
  gene757|gene757|rna757|rna757 177 PRGVLLYGPPGTGKTMLVKAVANKT---KATFIQVNGSEFVQ 215
                                    4679***************997665...58899999887655 PP

  == domain 4  score: 1.2 bits;  conditional E-value: 0.53
                                    EEE--EEEEEEESS CS
                Sigma54_activat 130 eikvdvriiaatne 143
                                     ++v+v++i+atn+
  gene757|gene757|rna757|rna757 278 DVTVNVKVIMATNR 291
                                    56899999999997 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   1.8e-05     0.009       2      44 ..     180     223 ..     179     266 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.8e-05
                         AAA_28   2 ivitGgestGKTtlleaLaar.gypvvpEaareileeklakged 44 
                                    + + G+++tGKT l++a a++ + + ++  + e++++ l +g +
  gene757|gene757|rna757|rna757 180 VLLYGPPGTGKTMLVKAVANKtKATFIQVNGSEFVQKYLGEGPR 223
                                    6799***************7655555555555555444444444 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   0.0   0.00037      0.19      32      62 ..     174     204 ..     163     215 .. 0.81
   2 ?    2.2   0.0      0.21   1.1e+02     107     135 ..     224     252 ..     214     273 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00037
                           TniB  32 rkrmpnlllvGdsnnGKtmivekFarlhppe 62 
                                     + ++ +ll+G++ +GKtm+v+  a++ +++
  gene757|gene757|rna757|rna757 174 IDPPRGVLLYGPPGTGKTMLVKAVANKTKAT 204
                                    5567899***************999887765 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.21
                           TniB 107 leqqvlrllrelkvrvLiiDEihnllags 135
                                    + ++v rl re  + ++ iDE++++ + +
  gene757|gene757|rna757|rna757 224 MVRDVFRLAREQAPSIVFIDEVDSIATKR 252
                                    567889999**************998755 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.1   3.4e-05     0.017      25      43 ..     180     198 ..     172     230 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.4e-05
                   Mg_chelatase  25 lllvGppGsGKtmlakrlp 43 
                                    +ll+GppG+GKtml k+++
  gene757|gene757|rna757|rna757 180 VLLYGPPGTGKTMLVKAVA 198
                                    89************99875 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   0.00015     0.076       2      30 ..     180     208 ..     179     217 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00015
                          AAA_3   2 vllegvPGlaktllvkalakaldlefkri 30 
                                    vll g PG++kt+lvka+a++ +++f ++
  gene757|gene757|rna757|rna757 180 VLLYGPPGTGKTMLVKAVANKTKATFIQV 208
                                    7999*****************99999766 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   0.00011     0.056      47      71 ..     177     201 ..     162     268 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00011
                      IstB_IS21  47 kenivllGpsGvGKshlaialgvea 71 
                                      +++l Gp+G+GK+ l  a++ ++
  gene757|gene757|rna757|rna757 177 PRGVLLYGPPGTGKTMLVKAVANKT 201
                                    56899************99999876 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.7       1.5   7.6e+02     150     203 ..      19      85 ..       2     100 .. 0.68
   2 ?   11.7   0.0   0.00032      0.16      20      42 ..     180     202 ..     167     274 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 1.5
                         AAA_11 150 eklkkskekskskleqerrklkkerkelskeleeaeesle.............eevldeaeivltTl 203
                                     ++ ksk+++ + l +e++++ k ++ l++el +a+e+++             e + +++ iv +T 
  gene757|gene757|rna757|rna757  19 YEKYKSKQYELEILCREEQQCIKDINILKSELIRAKEEIKrvksvplimgqflEAIDKQTAIVGSTT 85 
                                    4556677777777778888888888888888888888888777777777777666666666776665 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00032
                         AAA_11  20 tliqGPPGtgKTktivellsqll 42 
                                    +l+ GPPGtgKT  + ++ ++  
  gene757|gene757|rna757|rna757 180 VLLYGPPGTGKTMLVKAVANKTK 202
                                    6899********99999888774 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.3       5.5   2.7e+03     103     116 ..      47      60 ..       4     109 .. 0.49
   2 ?   12.1   0.0   0.00027      0.13      21      46 ..     178     203 ..     167     218 .. 0.83
   3 ?    0.4   0.0         1   5.1e+02     115     136 ..     233     254 ..     207     290 .. 0.64

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 5.5
                       ATPase_2 103 fkaielllekikkk 116
                                    ++ + +++e+ik+ 
  gene757|gene757|rna757|rna757  47 KSELIRAKEEIKRV 60 
                                    22222222222222 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00027
                       ATPase_2  21 eiyfiYGpegsGKtaLlkeiienled 46 
                                    + +++YGp g GKt L+k ++++ + 
  gene757|gene757|rna757|rna757 178 RGVLLYGPPGTGKTMLVKAVANKTKA 203
                                    55789***************999854 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 1
                       ATPase_2 115 kkgkkiiiiiDelqklidlgln 136
                                    +++   i++iDe+  +    ++
  gene757|gene757|rna757|rna757 233 REQAPSIVFIDEVDSIATKRFD 254
                                    3333357777777776644444 PP

>> AFG1_ATPase  AFG1-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   0.00035      0.17      56      81 ..     171     196 ..     147     220 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00035
                    AFG1_ATPase  56 rksvepvrglYlwGgvGrGKtylmdl 81 
                                    +    p+rg+ l+G+ G GKt+l+  
  gene757|gene757|rna757|rna757 171 QIGIDPPRGVLLYGPPGTGKTMLVKA 196
                                    44568******************975 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00045      0.22      12      47 ..     178     211 ..     171     297 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00045
                                    SEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTC CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  12 ekvaivGenGaGKStLlkllagllkpteGeilldgk 47 
                                    + v + G+ G+GK+ L+k++a+++k t   i+++g 
  gene757|gene757|rna757|rna757 178 RGVLLYGPPGTGKTMLVKAVANKTKAT--FIQVNGS 211
                                    568899***************999864..3444554 PP

>> Bac_DnaA  Bacterial dnaA  protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0    0.0003      0.15      37      62 ..     180     205 ..     174     283 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.0003
                                    EEEE-SSSSSHHHHHHHHHHHHHHHS CS
                       Bac_DnaA  37 lfiygevGlGktHLlkaignevlena 62 
                                    +++yg+ G Gkt L+ka++n++++++
  gene757|gene757|rna757|rna757 180 VLLYGPPGTGKTMLVKAVANKTKATF 205
                                    79******************987665 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.7   0.00096      0.48      36      54 ..     180     198 ..     177     270 .. 0.85
   2 ?    0.0   0.1       1.1   5.3e+02     130     179 ..     225     277 ..     218     284 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00096
                         AAA_25  36 allaGapgtGKttlaldla 54 
                                    +ll+G+pgtGKt+l+  +a
  gene757|gene757|rna757|rna757 180 VLLYGPPGTGKTMLVKAVA 198
                                    69***********986655 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 1.1
                         AAA_25 130 vdaleaaieevegvrlvviDplsralgg....densnsdvgalvealeriarrt 179
                                    v+++ + ++e   +  v iD ++++          ++++v++++  l +  + +
  gene757|gene757|rna757|rna757 225 VRDVFRLARE-QAPSIVFIDEVDSIATKrfdaATSADREVQRVLLELLSQMDGF 277
                                    5667777777.6699999999999766635323333344566655555544555 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   0.00059       0.3      12      34 ..     179     201 ..     173     212 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00059
                         AAA_19  12 vllvtaGpGtGKTrvlkhivall 34 
                                     +l+ ++pGtGKT ++k++ +  
  gene757|gene757|rna757|rna757 179 GVLLYGPPGTGKTMLVKAVANKT 201
                                    5899**********999987765 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00055      0.27       1      47 [.     183     230 ..     183     270 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00055
                                    EE-TTSSHHHHHHHHHHHHTEEEEEH.HHHHHHHHHTTTSHSSHHHHC CS
                         AAA_17   1 lGgPGsGKgtqceklvekygfthlsa.Gdllreeakrgglakardemr 47 
                                    +G+PG GK+ +++ ++ k + t+++  G+ + +    +g  + rd +r
  gene757|gene757|rna757|rna757 183 YGPPGTGKTMLVKAVANKTKATFIQVnGSEFVQKYLGEGPRMVRDVFR 230
                                    7*****************999998766888877777777777777666 PP

>> Parvo_NS1  Parvovirus non-structural protein NS1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   0.00074      0.37     117     138 ..     180     201 ..     174     212 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00074
                      Parvo_NS1 117 vwfyGpantGktnlaeaIakav 138
                                    v++yGp+ tGkt+l +a a+ +
  gene757|gene757|rna757|rna757 180 VLLYGPPGTGKTMLVKAVANKT 201
                                    89***************99876 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.1       7.1   3.5e+03      80     120 ..      35      76 ..      15      89 .. 0.46
   2 ?    9.0   0.1    0.0017      0.83      15      37 ..     173     195 ..     163     205 .. 0.84
   3 ?    0.4   0.0      0.67   3.3e+02     113     156 ..     230     279 ..     197     289 .. 0.64

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 7.1
                         ATPase  80 egklaiidasesaeesaee.kdkedleelieelaeaikeika 120
                                    e++  i d+   ++e +++ ++ + ++++   + + +++i  
  gene757|gene757|rna757|rna757  35 EEQQCIKDINILKSELIRAkEEIKRVKSVPLIMGQFLEAIDK 76 
                                    444444333333333222223444444444444444444444 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0017
                         ATPase  15 GipegrvvlitGepGtGKtifal 37 
                                    Gi   r vl++G pGtGKt++++
  gene757|gene757|rna757|rna757 173 GIDPPRGVLLYGPPGTGKTMLVK 195
                                    77777889************986 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.67
                         ATPase 113 eaikeikakrvviDsitglaye......ekeavaReilrqlvrvlkklgv 156
                                    +  +e   + v iD ++++a++      + + ++ + l +l++++ + +v
  gene757|gene757|rna757|rna757 230 RLAREQAPSIVFIDEVDSIATKrfdaatSADREVQRVLLELLSQMDGFDV 279
                                    55566667778888888884330110002333344455555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (396 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       845  (0.0471303); expected 358.6 (0.02)
Passed bias filter:                      626  (0.0349155); expected 358.6 (0.02)
Passed Vit filter:                       105  (0.00585643); expected 17.9 (0.001)
Passed Fwd filter:                        36  (0.00200792); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              36  [number of targets reported over threshold]
# CPU time: 0.65u 0.33s 00:00:00.98 Elapsed: 00:00:00.46
# Mc/sec: 2574.19
//
Query:       gene758|gene758|rna758|rna758  [L=675]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        1.3    9.2   4.8       0.36   11.1   0.6    2.1  2  Lge1      Transcriptional regulatory protein LGE1


Domain annotation for each model (and alignments):
>> Lge1  Transcriptional regulatory protein LGE1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.3      0.16     3e+03      20      42 ..     378     400 ..     375     402 .. 0.81
   2 ?   11.1   0.6     2e-05      0.36      10      42 ..     588     620 ..     571     624 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.16
                           Lge1  20 sklkeiesldkqleelklkvlkl 42 
                                    ++ ke+++ld+    +k k++k+
  gene758|gene758|rna758|rna758 378 KISKESKKLDDDKTVSKYKIVKN 400
                                    56789999999998888888886 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 2e-05
                           Lge1  10 ndestlkkiesklkeiesldkqleelklkvlkl 42 
                                    +++++ +k++ k+++i  ld+q+  l  k++k+
  gene758|gene758|rna758|rna758 588 DEKNREEKLKDKYNSIIYLDEQDKMLRNKIFKQ 620
                                    3378889************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (675 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1658  (0.0924759); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.73u 0.36s 00:00:01.08 Elapsed: 00:00:00.55
# Mc/sec: 3709.73
//
Query:       gene759|gene759|rna759|rna759  [L=224]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
       0.02   14.9   2.7        1.2    9.2   1.2    2.6  2  Mis12       Mis12 protein
      0.026   14.7   5.6      0.079   13.1   1.3    2.3  2  CEP209_CC5  Coiled-coil region of centrosome protein CE290
        0.2   11.6   4.5      0.084   12.8   2.3    1.6  1  MIP-T3_C    Microtubule-binding protein MIP-T3 C-terminal reg


Domain annotation for each model (and alignments):
>> Mis12  Mis12 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0    0.0051        31       3      30 ..      15      42 ..      14      52 .. 0.86
   2 ?    9.2   1.2    0.0002       1.2      68      96 ..      58      86 ..      50     137 .. 0.65

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.0051
                                   HHHHCTHHHHHHHHHHHHHHHHHHHHHH CS
                          Mis12  3 tehlgftPqsliddiinavndllyravd 30
                                    e +gf P s++++   + ++++  +++
  gene759|gene759|rna759|rna759 15 IEYFGFVPCSFLQELCLTLEETITGTIN 42
                                   699***********99999888877666 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0002
                                   HHHHHHHHHHHHHHHHHHCTS---HHHHC CS
                          Mis12 68 leasvDknfdkfElyvlrniltipeelve 96
                                   + +++ knf  fE ++l++i+t p++   
  gene759|gene759|rna759|rna759 58 VLSEFRKNFLIFENFSLHQIFTFPKDFSY 86
                                   557788*******************5432 PP

>> CEP209_CC5  Coiled-coil region of centrosome protein CE290
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   1.3   1.3e-05     0.079      76     117 ..     105     146 ..      87     154 .. 0.94
   2 ?    3.4   0.2     0.014        83      25      51 ..     185     213 ..     173     217 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.3e-05
                     CEP209_CC5  76 eltkqkeeikylknlieeqertisklEeeivqlnkvheerql 117
                                    el k k+e ++ kn +++++r i++ E ei q++++ e+ ++
  gene759|gene759|rna759|rna759 105 ELMKLKDEHEFYKNEVQRHKRIIANKEIEIAQMTSFLENAEV 146
                                    68899********************************99876 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.014
                     CEP209_CC5  25 kaeskavelelklkgLeel..istlkdak 51 
                                     +e+k    e+k+k+++el  i tl+d k
  gene759|gene759|rna759|rna759 185 LMENKDIKNEMKKKEINELyrIGTLEDIK 213
                                    578888999*********83345777765 PP

>> MIP-T3_C  Microtubule-binding protein MIP-T3 C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   2.3   1.4e-05     0.084      75     137 ..      94     157 ..      88     174 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.4e-05
                       MIP-T3_C  75 fiqdDidsMqrELemWrseyrqqaeelaeerrateealeplkaqlaelee.aIkdqkekisnvr 137
                                    +++dD+d M  EL + ++e++ +++e+++++r+ +++  ++ +  + le+ +++d  ++++ ++
  gene759|gene759|rna759|rna759  94 VVEDDVDGMIDELMKLKDEHEFYKNEVQRHKRIIANKEIEIAQMTSFLENaEVNDLLSNTEFLK 157
                                    4789*****************************9999999988888887524666666665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1187  (0.0662056); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.32s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 1393.12
//
Query:       gene76|gene76|rna76|rna76  [L=481]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.8e-22   79.2   5.0    8.9e-22   77.5   5.0    1.9  1  HSF_DNA-bind  HSF-type DNA-binding
  ------ inclusion threshold ------
       0.77    9.1   3.7       0.23   10.8   0.6    1.6  2  Bestrophin    Bestrophin, RFP-TM, chloride channel


Domain annotation for each model (and alignments):
>> HSF_DNA-bind  HSF-type DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.5   5.0   9.9e-26   8.9e-22       1      96 []       7      99 ..       7      99 .. 0.92

  Alignments for each domain:
  == domain 1  score: 77.5 bits;  conditional E-value: 9.9e-26
                               HHHHHHHHHCT...TTTSEESSSSSEEEES-HHHHHHHTHHHHSTT--HHHHHHHHHHTTEEE---SSBTTB--TTSEEEEESS-- CS
               HSF_DNA-bind  1 FlkkLyklled...eelisWsedgksfvvkdkeefakevlpkyfkhsnfssFvrqLnlYgFrkvkrkeekkkkkskvweFshenFk 83
                               F+++L+++le+   + +i+Ws++gks+++ +++ f+  vl+kyf+h+nfssFvrqLn YgFrkvk+      + ++v+eF++e+F 
  gene76|gene76|rna76|rna76  7 FINHLFTILETptnHPYIRWSSTGKSIIIPNQHMFTLYVLTKYFNHDNFSSFVRQLNKYGFRKVKN------TLNNVHEFRQEHFM 86
                               9********87665888**********************************************994......456899******** PP

                               XXXXXXXXXXXXX CS
               HSF_DNA-bind 84 rgkpelLkkikrk 96
                               ++kp l + i+r+
  gene76|gene76|rna76|rna76 87 KEKPFLSRWIRRR 99
                               ***9998888886 PP

>> Bestrophin  Bestrophin, RFP-TM, chloride channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.1      0.25   2.3e+03      75     125 ..      25      75 ..      19     132 .. 0.49
   2 ?   10.8   0.6   2.5e-05      0.23     130     212 ..     182     259 ..     174     263 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.25
                 Bestrophin  75 RWweqrkllgwldkaarslarqvrglsdeegrlarrtilrylvlllvlffr 125
                                RW ++ k++  + +++ +l   ++ ++ ++ +   r++ +y  + +  ++ 
  gene76|gene76|rna76|rna76  25 RWSSTGKSIIIPNQHMFTLYVLTKYFNHDNFSSFVRQLNKYGFRKVKNTLN 75 
                                555555555555555555554444444333444444444443333333333 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 2.5e-05
                 Bestrophin 130 rvrkrfptlehlleagllteeeakilenkywvplqWavsllrrlaerlkelakegrikddqalkeleeelnelraklgsleri 212
                                 vrk++++ +++++++++ + e +  ++ky + +qW+ +  ++++   ++ +k+++ +++  ++   +++ne  a++ + +++
  gene76|gene76|rna76|rna76 182 VVRKENADSNTMINEKMMRRVEGESTQEKYIIDCQWMNN--KEIG---NNTEKDDQSDEEKLYNDCRANMNETNACQRNTCEY 259
                                69999999***************************9877..3333...23557777777778899999999999988887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (481 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1104  (0.0615762); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.43
# Mc/sec: 3321.32
//
Query:       gene760|gene760|rna760|rna760  [L=397]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.2e-50  169.9  13.4    9.2e-50  169.9  13.4    1.3  1  DUF747    Eukaryotic membrane protein family


Domain annotation for each model (and alignments):
>> DUF747  Eukaryotic membrane protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  169.9  13.4   5.1e-54   9.2e-50       6     228 ..      48     352 ..      43     360 .. 0.81

  Alignments for each domain:
  == domain 1  score: 169.9 bits;  conditional E-value: 5.1e-54
                         DUF747   6 kadllrlllilisvlllslvDtSrvYHyiRaqsfiKLyvvfnvLEvvdrLlsslgqdildalfstttlerekeg...... 79 
                                    + d l++l ili +++l +++ Sr+YH+++ qs+++Lyv+fnvLE++++L+ +l +di +a+ ++++ ++e+e+      
  gene760|gene760|rna760|rna760  48 ILDRLKVLTILIVFTFLRSLNCSRMYHSLKVQSLVRLYVLFNVLELAEKLIGTLVNDIAKAIEERMEGTQEQEHtvlede 127
                                    678999********************************************************999994444444445555 PP

                         DUF747  80 .........................e.....................................................e 81 
                                                             +                                                     +
  gene760|gene760|rna760|rna760 128 svvlgksnvrlgsekssnnknvvlgKrngseseheginsgddvnavserdkrtenesmtdrgsdvslddkvgvpssnsqS 207
                                    55555555555555555555555550555555555555555666666666666666666666666666777777664333 PP

                         DUF747  82 elskllklvlqfllalayvllHslvlliqvltLnvainSsenaLltllvsnnfvEiKstVFKkfekenlfqivaaDvvER 161
                                       + + +++  ++ ++ + +H+lvl +q l++   +nSs++ L  l++sn+f E+K++V Kk +k  lf++v  D + R
  gene760|gene760|rna760|rna760 208 MIANAVLMAVLTTFFIISTAIHTLVLYFQYLIIQLSLNSSSSVLYSLVISNQFLELKGNVTKKGDKAMLFSLVDHDGTKR 287
                                    34444555555666688889************************************************************ PP

                         DUF747 162 fqllllllivllrnltessseatslaevlsplllvlllEvlVDwvKhayllKFNnikpsvyeeyldv 228
                                    f ll++++i +l  ++e  se+ ++++++ p+++vll+ vlVDw+Kh++  ++Nn++ s+y  y + 
  gene760|gene760|rna760|rna760 288 FSLLIFVVIAFLSVCVE--SEKLTFTKFILPIIVVLLFKVLVDWIKHIFFCRYNNLNLSFYMCYKKE 352
                                    *****************..6888899999********************************999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (397 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1203  (0.067098); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 2659.40
//
Query:       gene761|gene761|rna761|rna761  [L=320]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00095   18.5   4.7     0.0011   18.3   0.4    2.5  3  Sec1      Sec1 family


Domain annotation for each model (and alignments):
>> Sec1  Sec1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.4   6.2e-08    0.0011     107     224 ..      86     177 ..      13     181 .. 0.55
   2 ?   -0.8   0.1     0.037   6.6e+02     362     428 ..     183     242 ..     176     257 .. 0.67
   3 ?    1.0   0.0     0.011     2e+02     530     547 ..     284     301 ..     272     315 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 6.2e-08
                                    E----SEEEETTEEE-S.TTHHHHSTTG.....GG.......--HHHHHHHHHHHHHHH-..--EEEE-TT-HHHHHHHH CS
                           Sec1 107 elnldfvplesdlfsln.pelplsfrdlyldndnsaleeeieslldriakgLlsvllslekkiPiirykgsaasmvakkl 185
                                     l++ f    +dl s++ + l    ++ +++ d              i   L++++      i +i +kg+ ++    +l
  gene761|gene761|rna761|rna761  86 ALHWYFMRMTNDLWSMErKTL----KEVFVERDT------------FILTELATFFRRV--HINRICCKGAVSK----QL 143
                                    356666666666666632111....122222222............3677777755555..4999999995555....77 PP

                                    ...................HHHHTTT--SS--EEEEE-GGG-SSTTTS CS
                           Sec1 186 adelk.........ekidskknfesessrqrpvLiIlDRsvDlvtpll 224
                                      +l          ++i++              L+I+DR+vDl+tp  
  gene761|gene761|rna761|rna761 144 GMLLLqqdkvpkqkHRINN--------------LLIFDRTVDLLTPTN 177
                                    5555545545555444554..............*************65 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.037
                                    B--..-HHHHHHHH-TTS-H.HHHHHHHHHHHH...-B.-HT--GG....GGHHHHGGGGG...... CS
                           Sec1 362 kikekkvieeliaddeptseledklRLlllyslvegglkekelkellrelvqsalygleylktlrsl 428
                                    +i+ek+++  l++++ +t++l++ l   +l+sl   ++   ++ +++re+v  + yg +++ ++  +
  gene761|gene761|rna761|rna761 183 SITEKQMLSILLTKNGNTEKLNTLLNFYVLISLL--KI---DMPAIKREMVY-T-YGEKMVVIFDMI 242
                                    5556666655555555566667777777777775..33...89999999999.7.887666555554 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.011
                                    EEEEEEEEE-HHHHHHHH CS
                           Sec1 530 viVffvGGvTysEiralr 547
                                     +V f+GGv+  Ei +l+
  gene761|gene761|rna761|rna761 284 NVVLFIGGVCQKEIDDLK 301
                                    5899**********9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (320 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       650  (0.0362541); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 2239.10
//
Query:       gene762|gene762|rna762|rna762  [L=216]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.3e-67  225.2  29.2    6.3e-67  225.2  29.2    1.3  2  DUF5089          Domain of unknown function (DUF5089)
  ------ inclusion threshold ------
      0.077   13.0  16.0      0.077   13.0   4.7    2.6  2  DUF1664          Protein of unknown function (DUF1664)
       0.22   11.1   4.0        5.8    6.5   0.9    2.5  2  SLATT_6          SMODS and SLOG-associating 2TM effector doma
        1.2    9.5  17.1        2.5    8.5   6.0    2.9  3  KxDL             Uncharacterized conserved protein
        1.4    9.3   7.4        6.3    7.2   0.1    2.5  2  V-SNARE_C        Snare region anchored in the vesicle membran
        3.3    7.7  14.3        2.9    7.9   3.6    2.4  2  Laminin_II       Laminin Domain II
        4.3    7.7   7.3          2    8.7   1.0    2.6  2  DUF948           Bacterial protein of unknown function (DUF94
        6.2    7.4  28.8        9.7    6.7  13.6    2.5  2  APG6_N           Apg6 coiled-coil region


Domain annotation for each model (and alignments):
>> DUF5089  Domain of unknown function (DUF5089)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.3       4.5     1e+04     105     110 ..      14      19 ..       6      26 .. 0.38
   2 !  225.2  29.2   2.8e-70   6.3e-67       1     193 []      28     215 ..      28     215 .. 0.99

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 4.5
                        DUF5089 105 knkeee 110
                                     +k+++
  gene762|gene762|rna762|rna762  14 LQKHKK 19 
                                    222222 PP

  == domain 2  score: 225.2 bits;  conditional E-value: 2.8e-70
                        DUF5089   1 eeileeakkiEeqnyetakkarkkLesaartqkkTtkelrkQgekLekakqsaikvhknaekgeelakkikregkvfvfk 80 
                                    ee+ ++ak+iEeqnye+a++arkkLe +++tqkkTtkel++QgekLe+a++sa+++++++e+g++l++kik+egk+f+fk
  gene762|gene762|rna762|rna762  28 EEVEARAKQIEEQNYEMAHGARKKLEAGYATQKKTTKELQSQGEKLERAEMSARSIEQDVEEGKHLTRKIKEEGKMFNFK 107
                                    78999*************************************************************************** PP

                        DUF5089  81 spvvdkikkwfkkdkkaeeeveeiknkeeeakeeeedkkeeeefipedkelvpgeektdkeLekilnglkslkkeaevQn 160
                                    +p+v +ikk+fk++k++ ++v+++k+++++a     +k+++e++i +dk+l+pg++ktdkeLe+i+++lk++k+ea++Q+
  gene762|gene762|rna762|rna762 108 LPFVGRIKKIFKSKKQPGHAVHTHKKERQAA-----PKPQDESEIVTDKNLIPGQQKTDKELEQIYRTLKNVKGEAQQQH 182
                                    *****************************99.....789***************************************** PP

                        DUF5089 161 keikkqkskikdItkvneksekevkkteeelkk 193
                                    +e+++q+++ik+I+k+++kseke+++++eelkk
  gene762|gene762|rna762|rna762 183 EEMARQTQNIKSIGKRTQKSEKEMENVTEELKK 215
                                    ********************************8 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   3.5     0.011        26      72     112 ..      49      89 ..      13     102 .. 0.66
   2 ?   13.0   4.7   3.5e-05     0.077      34      99 ..     148     213 ..     145     216 .] 0.89

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.011
                        DUF1664  72 dkkldeqkeiskeikeevtevredlseigedvesvkeaveg 112
                                     kkl++  +++k++++e+++  e+l++ +   +s+++ ve+
  gene762|gene762|rna762|rna762  49 RKKLEAGYATQKKTTKELQSQGEKLERAEMSARSIEQDVEE 89 
                                    45677777777777777777777777777777777777664 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 3.5e-05
                        DUF1664  34 vTkrslsdavesvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlsei 99 
                                    vT ++l    ++  k+leq++ +l+++k + +++ +++ ++ ++ k i k +++  +e+++ ++e+
  gene762|gene762|rna762|rna762 148 VTDKNLIPGQQKTDKELEQIYRTLKNVKGEAQQQHEEMARQTQNIKSIGKRTQKSEKEMENVTEEL 213
                                    9***********************************************999998877776666555 PP

>> SLATT_6  SMODS and SLOG-associating 2TM effector domain 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.1    0.0073        16       7      34 ..      34      62 ..      29      68 .. 0.81
   2 ?    6.5   0.9    0.0026       5.8      86     129 ..     159     201 ..     153     210 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.0073
                        SLATT_6  7 lksiAekgYnvgfgAkkhf.atydiveKl 34
                                    k+i e+ Y++ +gA+k++ a y + +K+
  gene762|gene762|rna762|rna762 34 AKQIEEQNYEMAHGARKKLeAGYATQKKT 62
                                   599*************9984567776665 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0026
                        SLATT_6  86 kagkeltklfneLkelysevksseeedlskleaelkeieaefke 129
                                    k+ kel ++++ Lk++  e++ +++e+++++++++k+i ++ ++
  gene762|gene762|rna762|rna762 159 KTDKELEQIYRTLKNVKGEAQ-QQHEEMARQTQNIKSIGKRTQK 201
                                    667888899999999988888.5778888888888888776655 PP

>> KxDL  Uncharacterized conserved protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       1.1   2.5e+03      37      58 ..      28      46 ..       7      54 .. 0.51
   2 ?    7.1   1.7    0.0028       6.4      10      62 ..      51      99 ..      44     103 .. 0.79
   3 ?    8.5   6.0    0.0011       2.5      15      72 ..     154     214 ..     150     216 .] 0.74

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1.1
                           KxDL 37 alsqerlaklrarfkqgtkllk 58
                                   +++++r ++++   +q+ ++++
  gene762|gene762|rna762|rna762 28 EEVEARAKQIE---EQNYEMAH 46
                                   34444444433...33444444 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0028
                           KxDL 10 dldeilalQaqtsgrlnkknreLlelnalsqerlaklrarfkqgtkllkevkk 62
                                   +l++  a+Q++t ++l+++ ++L++          ++++++++g++l +++k+
  gene762|gene762|rna762|rna762 51 KLEAGYATQKKTTKELQSQGEKLERAE----MSARSIEQDVEEGKHLTRKIKE 99
                                   68888999*************998743....3344677888888888888775 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.0011
                           KxDL  15 lalQaqtsgrlnkknreLlelnalsqerlaklrarfkqgtkllkevkk...dLesifkkir 72 
                                    +  Q++t ++l++  r+L+++  ++q++++++  + ++ +   k+++k   ++e++++ ++
  gene762|gene762|rna762|rna762 154 IPGQQKTDKELEQIYRTLKNVKGEAQQQHEEMARQTQNIKSIGKRTQKsekEMENVTEELK 214
                                    667*************************999988888777666666541114555554444 PP

>> V-SNARE_C  Snare region anchored in the vesicle membrane C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.1    0.0028       6.3      27      63 ..      62      98 ..      56      99 .. 0.88
   2 ?    3.8   3.0      0.03        68       4      49 ..     158     203 ..     156     214 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0028
                      V-SNARE_C 27 iledLhsQretLkrarsklhnvanrlgksnsiLrsik 63
                                   +  +L+sQ e+L+ra    + + +++   +++ r+ik
  gene762|gene762|rna762|rna762 62 TTKELQSQGEKLERAEMSARSIEQDVEEGKHLTRKIK 98
                                   6789************999999999998888888876 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.03
                      V-SNARE_C   4 lresdrlknShrivdetisiGaailedLhsQretLkrarsklhnva 49 
                                    +++   l++ +r +  + + +++  e++++Q +++k++ ++ +   
  gene762|gene762|rna762|rna762 158 QKTDKELEQIYRTLKNVKGEAQQQHEEMARQTQNIKSIGKRTQKSE 203
                                    56777899999999999**********************9987665 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   3.1    0.0083        19       8      70 ..      30      89 ..      14     117 .. 0.67
   2 ?    7.9   3.6    0.0013       2.9      14      77 ..     159     215 ..     150     216 .] 0.52

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0083
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTT CS
                     Laminin_II  8 anetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapq 70
                                   ++  ak+++eq  +++      ++kl+   ++ ++t++++++  + ++ A+ s + +e+ +++
  gene762|gene762|rna762|rna762 30 VEARAKQIEEQNYEMAHG---ARKKLEAGYATQKKTTKELQSQGEKLERAEMSARSIEQDVEE 89
                                   444455555555555543...344444444444678888888888888888888888887764 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0013
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHH CS
                     Laminin_II  14 evleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklke 77 
                                    ++       +++le++   l+++++++++ +e++   ++ i++ ++  +k ek+++++ + lk+
  gene762|gene762|rna762|rna762 159 KT-------DKELEQIYRTLKNVKGEAQQQHEEMARQTQNIKSIGKRTQKSEKEMENVTEELKK 215
                                    34.......4455555555555555555555555555555555555555555555555555544 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.6      0.12   2.8e+02      31      84 ..      30      87 ..      22     103 .. 0.58
   2 ?    8.7   1.0   0.00091         2      47      85 ..     162     200 ..     152     216 .] 0.56

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.12
                         DUF948 31 aaatieele....kqvdpilkevedllakvnelledvneklekvdplteavadlgesv 84
                                   ++a+ +++e    + +++  k++e+  a+ ++++++++++ ek+++   +++ + + v
  gene762|gene762|rna762|rna762 30 VEARAKQIEeqnyEMAHGARKKLEAGYATQKKTTKELQSQGEKLERAEMSARSIEQDV 87
                                   5555555552222223333344444445566666666666666666655555555555 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00091
                         DUF948  47 kevedllakvnelledvneklekvdplteavadlgesvs 85 
                                    ke+e++ ++ +++  + +++ e++ + t++++ +g+  +
  gene762|gene762|rna762|rna762 162 KELEQIYRTLKNVKGEAQQQHEEMARQTQNIKSIGKRTQ 200
                                    455555555555555666666666666666666665544 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7  13.6    0.0043       9.7      26      99 ..       8      78 ..       5     105 .. 0.63
   2 ?    6.3   7.2    0.0057        13      42      91 ..     164     213 ..     117     216 .] 0.47

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0043
                         APG6_N 26 daYeeflkklkkekkeeekqdeeleeleeeleklekeeee.lleeLkelekereeleaelaaleeelealeeeee 99
                                   ++Y++fl+k kk++k +      +ee e + +++e++  e +    k+le+  +  ++  ++l+++ e+le+ e 
  gene762|gene762|rna762|rna762  8 QNYQKFLQKHKKKEKRSA----VDEEVEARAKQIEEQNYEmAHGARKKLEAGYATQKKTTKELQSQGEKLERAEM 78
                                   79*********9977765....44445555555544443313345556666666666666666666666665554 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0057
                         APG6_N  42 eekqdeeleeleeeleklekeeeelleeLkelekereeleaelaaleeel 91 
                                     e+    l++ + e ++ ++e ++  +++k + k  ++ e+e+++ +eel
  gene762|gene762|rna762|rna762 164 LEQIYRTLKNVKGEAQQQHEEMARQTQNIKSIGKRTQKSEKEMENVTEEL 213
                                    11122222222222333333333333333333333333333333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (216 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3111  (0.173518); expected 358.6 (0.02)
Passed bias filter:                      558  (0.0311228); expected 358.6 (0.02)
Passed Vit filter:                        88  (0.00490825); expected 17.9 (0.001)
Passed Fwd filter:                        41  (0.0022868); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.77u 0.31s 00:00:01.08 Elapsed: 00:00:00.52
# Mc/sec: 1260.95
//
Query:       gene763|gene763|rna763|rna763  [L=285]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.5e-06   26.6   1.4      0.095   13.6   0.0    3.8  4  WD40      WD domain, G-beta repeat
  ------ inclusion threshold ------
       0.08   12.3   0.0       0.11   11.8   0.0    1.2  1  DUF1668   Protein of unknown function (DUF1668)


Domain annotation for each model (and alignments):
>> WD40  WD domain, G-beta repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.1   0.00052       4.7       6      36 ..       8      39 ..       3      39 .. 0.77
   2 !   13.6   0.0   1.1e-05     0.095       4      34 ..      46      77 ..      44      81 .. 0.87
   3 ?    0.7   0.0      0.13   1.1e+03       4      16 ..      88     101 ..      85     117 .. 0.74
   4 ?   -2.5   0.0       1.3   1.2e+04      14      26 ..     256     268 ..     247     271 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00052
                                   EEESS.SSEEEEEEETTSSEEEEEETTSEEEE CS
                           WD40  6 tltGH.ssvtslafspdgawlasGsdDgtvri 36
                                   +l+ H +++++   s+   ++a++s D tv++
  gene763|gene763|rna763|rna763  8 KLKIHdGWINDAVMSSRDGLIATCSTDTTVKV 39
                                   57779677998886666777799999****97 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 1.1e-05
                                   EEEEESS.SSEEEEEEETTSSEEEEEETTSEE CS
                           WD40  4 lrtltGH.ssvtslafspdgawlasGsdDgtv 34
                                   l+t+++H   v+++afs+ +++l+s sdD+ v
  gene763|gene763|rna763|rna763 46 LKTIRTHkLAVNAVAFSDVNPLLVSVSDDRRV 77
                                   78999**555**************99***998 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.13
                                    EEEEESS.SSEEEE CS
                           WD40   4 lrtltGH.ssvtsl 16 
                                     r+l G  ss++++
  gene763|gene763|rna763|rna763  88 FRSLYGSySSIRCV 101
                                    5778899999***9 PP

  == domain 4  score: -2.5 bits;  conditional E-value: 1.3
                                    EEEEEETTSSEEE CS
                           WD40  14 tslafspdgawla 26 
                                    ++++++ d ++++
  gene763|gene763|rna763|rna763 256 NGVCVDNDEQMIV 268
                                    6777788888776 PP

>> DUF1668  Protein of unknown function (DUF1668)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   1.3e-05      0.11      64     128 ..      93     161 ..      69     182 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1.3e-05
                        DUF1668  64 aekgkmefaalagdkivavdqsgrtllYdtktravvtlPs....lkspkllpvsvavgdk.lYvldrspk 128
                                     +++++ +++   d+i++v++   +++Yd +++++++  +     ++  +    v +g++ lY++d++++
  gene763|gene763|rna763|rna763  93 GSYSSIRCVHI-ADNIIGVGDRSSAIIYDLRSSTIINTYNigrvVNAITMIGTIVVIGSHsLYIVDERKN 161
                                    56789999999.99********9*************5555443566666666777778888****99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (285 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       549  (0.0306208); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 1879.11
//
Query:       gene764|gene764|rna764|rna764  [L=286]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       566  (0.031569); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1894.78
//
Query:       gene765|gene765|rna765|rna765  [L=351]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.5e-59  199.0   6.1    5.8e-59  198.6   6.1    1.1  1  DUF5092   Domain of unknown function (DUF5092)
  ------ inclusion threshold ------
      0.039   13.5   0.0        0.1   12.2   0.0    1.7  1  HTH_Bact  Helix-turn-helix bacterial domain


Domain annotation for each model (and alignments):
>> DUF5092  Domain of unknown function (DUF5092)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  198.6   6.1   6.5e-63   5.8e-59       2     163 .]      45     256 ..      44     256 .. 0.99

  Alignments for each domain:
  == domain 1  score: 198.6 bits;  conditional E-value: 6.5e-63
                        DUF5092   2 EtftleefrklilesrkkkkdfilArVttkdpedqsslynvyYdAeelnkvlFevvieserrllhrkkvkdPlnnmkI.k 80 
                                    Etftleefrk+il++rk++kdfilArVtt+dp++q++lyn+yY+A+e+nkvlF++  es rrllhr+kv++Plnnm+I +
  gene765|gene765|rna765|rna765  45 ETFTLEEFRKIILDFRKCEKDFILARVTTPDPYRQDVLYNYYYIASEVNKVLFKY--ESTRRLLHRMKVRNPLNNMYIiG 122
                                    9******************************************************..*********************** PP

                        DUF5092  81 qvyyYkltveeldralveyffkeaksks...................................................e 109
                                    qvyyY++t ee+dralv++ff++++ ++                                                   +
  gene765|gene765|rna765|rna765 123 QVYYYHITKEEVDRALVDCFFRNKRLRNkegrrafsavfrsvqnpapsdtflatskdtdfprqkqpkednikpakdiieD 202
                                    ************************999999************************************************** PP

                        DUF5092 110 vkedsiaaveelakekklilkaeyfasdddFLeksevreyfkenaldaddnFlF 163
                                    v++++ +++e+  +   ++++a++fa+dddFL k+++r+yfk+n++d++++FlF
  gene765|gene765|rna765|rna765 203 VRKGKLRVPERDITPLLVNYNAYFFATDDDFLLKNDTRDYFKMNSIDPSEDFLF 256
                                    *****************************************************9 PP

>> HTH_Bact  Helix-turn-helix bacterial domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   1.2e-05       0.1      19      31 ..     115     127 ..     110     134 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.2e-05
                                    TTB-TTHHHHHHH CS
                       HTH_Bact  19 insMsLlGQLyYq 31 
                                     n+M ++GQ yY+
  gene765|gene765|rna765|rna765 115 LNNMYIIGQVYYY 127
                                    59**********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (351 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       768  (0.0428356); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 2401.15
//
Query:       gene766|gene766|rna766|rna766  [L=198]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.9e-54  183.6   0.1    2.2e-54  183.4   0.1    1.1  1  Ras          Ras family
    1.1e-31  109.5   0.0    1.9e-31  108.8   0.0    1.4  1  Roc          Ras of Complex, Roc, domain of DAPkinase
    2.4e-12   46.6   0.0    3.2e-12   46.3   0.0    1.1  1  Arf          ADP-ribosylation factor family
    3.3e-07   29.9   0.0    4.6e-07   29.4   0.0    1.2  1  Gtr1_RagA    Gtr1/RagA G protein conserved region
    5.8e-06   26.4   0.0    8.1e-06   25.9   0.0    1.5  1  MMR_HSR1     50S ribosome-binding GTPase
     0.0015   18.1   0.0     0.0051   16.4   0.0    1.9  1  GTP_EFTU     Elongation factor Tu GTP binding domain
     0.0022   18.0   0.2     0.0034   17.5   0.1    1.5  1  Dynamin_N    Dynamin family
  ------ inclusion threshold ------
      0.094   12.6   0.0        9.3    6.1   0.0    2.2  2  RsgA_GTPase  RsgA GTPase


Domain annotation for each model (and alignments):
>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  183.4   0.1   9.9e-58   2.2e-54       1     159 [.      14     173 ..      14     176 .. 0.98

  Alignments for each domain:
  == domain 1  score: 183.4 bits;  conditional E-value: 9.9e-58
                                    EEEEEESTTSSHHHHHHHHHHSSCSSSCTTTSSEEEEEEEEEETTEEEEEEEEEETTSGGGHHHHHHHHTTESEEEEEEE CS
                            Ras   1 KlvlvGdsavGKtslllrfvkdkFkeeyesTigvdfytkeievdgkevkleiwDTAGqeefkslrelyyrdaegillvyd 80 
                                    K+v++G  +vGK+sl+ ++vkd+F+ + esTig++f+tk+  + + ++k eiwDTAGqe+++sl ++yyr+a+++l++yd
  gene766|gene766|rna766|rna766  14 KMVVLGYYSVGKSSLIQKYVKDEFNPNEESTIGAAFLTKTSIYPNYNIKYEIWDTAGQERYNSLIPMYYRGAHVALIMYD 93 
                                    89****************************************************************************** PP

                                    TTBHHHHHTHHHHHHHHHHHSTTTSEEEEEEETTTGGG.G-SS-HHHHHHHHHHHTSEEEEEBTTTTCTHHHHHHHHHHH CS
                            Ras  81 itsresfenvkkwveeikrvaeenvpivLvGnKvDlee.kravsteegeelakelglkfletSAktnenveeafeellre 159
                                    it  esfe++k+wv+e+++ +++n++ vL+GnK+Dle+ +r+v++ee++e+a+++++ f+e+SAkt  nve++f ++ + 
  gene766|gene766|rna766|rna766  94 ITCPESFETAKNWVTELSSEKPKNFVKVLIGNKSDLENtSRKVDFEEAKEYARRNKMLFFEASAKTGFNVENIFSSVSEM 173
                                    ************************************9978**********************************998765 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.8   0.0   8.5e-35   1.9e-31       1     119 [.      14     128 ..      14     129 .. 0.90

  Alignments for each domain:
  == domain 1  score: 108.8 bits;  conditional E-value: 8.5e-35
                                    EEEEESSTTSSHHHHHHCHCT-CCC-EEETTTTEEEEEEECGGSGGCTTBTTTTCEEEEEEEE-SGGCTTTT-HHHHCTS CS
                            Roc   1 KvvlvGdsgvGKtsllkrfvedkfsekekstigvdfltkevtkikgvendkkvkkvklniWDtaGqerfrslhplylrea 80 
                                    K+v++G  +vGK+sl++++v+d+f+++e+stig+ fltk+   i    n     ++k++iWDtaGqer++sl p+y+r+a
  gene766|gene766|rna766|rna766  14 KMVVLGYYSVGKSSLIQKYVKDEFNPNEESTIGAAFLTKTS--IYP--N----YNIKYEIWDTAGQERYNSLIPMYYRGA 85 
                                    89************************************975..332..2....3589*********************** PP

                                    CEEEEEEE...GHHHHCHHHHHHHHHHHCSSS.-EEEEEE-TT CS
                            Roc  81 alailvyd...srssenlkeWlkelkkvagks.pvilvgnkiD 119
                                    ++a+++yd    +s+e++k+W++el+++ +k+ + +l+gnk D
  gene766|gene766|rna766|rna766  86 HVALIMYDitcPESFETAKNWVTELSSEKPKNfVKVLIGNKSD 128
                                    ********766668999***********99983559*****99 PP

>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.3   0.0   1.4e-15   3.2e-12      12     173 ..      10     172 ..       2     174 .. 0.84

  Alignments for each domain:
  == domain 1  score: 46.3 bits;  conditional E-value: 1.4e-15
                                    TTEEEEEEEESTTSSHHHHHHHHHHSSCEE.CSSSSSEEEEEEEE....TTEEEEEEEE-SSGGGGGGGGGGCTTESEEE CS
                            Arf  12 kkelrilllGLDnaGKtTilkklkleelvt.tvPTigfnveelei....knlkftvwDvGGqeklRplWknYfektdavi 86 
                                    +  +++++lG  + GK+ +++k+ ++e++     Tig    + +      n+k+++wD  Gqe+  +l   Y++  ++ +
  gene766|gene766|rna766|rna766  10 EYTYKMVVLGYYSVGKSSLIQKYVKDEFNPnEESTIGAAFLTKTSiypnYNIKYEIWDTAGQERYNSLIPMYYRGAHVAL 89 
                                    4568**********************998537889996643333224567999************************999 PP

                                    EEEETT-CTTHHHHHHHHHHHCTSGCCTTSEEEEEEE-TTSTTSS-HHHHHHHTTGGGSSSSSSEEEEEEBTTTTBTHHH CS
                            Arf  87 fvvDsadreRleeakeeLkalleeeelkevallvlaNKqDlpealseeelrellgleelkgkrkleiqkcsavkgeglke 166
                                     + D +  e +e+ak+ +++l +e+  + v++l+ +NK Dl+++  + + +e+ +  +   ++k+  +++sa +g ++++
  gene766|gene766|rna766|rna766  90 IMYDITCPESFETAKNWVTELSSEKPKNFVKVLI-GNKSDLENTSRKVDFEEAKEYAR---RNKMLFFEASAKTGFNVEN 165
                                    9*******************98888777777765.9**********999999987765...4589999999999999998 PP

                                    HHHHHHH CS
                            Arf 167 glewlse 173
                                     ++ +se
  gene766|gene766|rna766|rna766 166 IFSSVSE 172
                                    8887776 PP

>> Gtr1_RagA  Gtr1/RagA G protein conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   0.0     2e-10   4.6e-07       1     143 [.      14     148 ..      14     174 .. 0.78

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 2e-10
                      Gtr1_RagA   1 kvLLmGksgsGKts.mrsiiFdnylardtlrlgatidveksevrflgnltlnlwDcgGqeafveeylssqkeeifrnvgv 79 
                                    k++ +G  + GK+s +++ + d++ +++  ++ga+  ++ +++  + n++ ++wD  Gqe++            +r   v
  gene766|gene766|rna766|rna766  14 KMVVLGYYSVGKSSlIQKYVKDEFNPNEESTIGAAFLTK-TSIYPNYNIKYEIWDTAGQERYNSLI-----PMYYRGAHV 87 
                                    6788999******96699****************98655.5566899*************997775.....444555555 PP

                      Gtr1_RagA  80 liyVfDvesreleedletlkeilealrqyspeakvfvli.hKmDliqedereeifeerkeeiree 143
                                     + + D++   ++e++et k+ +++l+  +p+  v+vli +K Dl  +  r+  fee ke  r++
  gene766|gene766|rna766|rna766  88 ALIMYDIT---CPESFETAKNWVTELSSEKPKNFVKVLIgNKSDLE-NTSRKVDFEEAKEYARRN 148
                                    55566999...99**************************6688876.555666666666555544 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.0   3.6e-09   8.1e-06       2      99 ..      15     109 ..      14     191 .. 0.74

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 3.6e-09
                                    EEEEESTTSSHHHHHHHHHTS.....TEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSSHHHHHHHHHHHHHHHHCT CS
                       MMR_HSR1   2 vaivGrpNvGKStLinaltge.....kaivsdkpgtTrdinegrvklkgkeielvDtpGliegaseekglgkaflaleea 76 
                                    ++++G+  vGKS+Li++ +++     +  +   ++ T++ ++ +++    ++e++Dt+G  e   + ++l   + +   a
  gene766|gene766|rna766|rna766  15 MVVLGYYSVGKSSLIQKYVKDefnpnEESTIGAAFLTKTSIYPNYN---IKYEIWDTAG-QE---RYNSLIPMYYR--GA 85 
                                    789****************954433244566678999999999987...679*******.44...23344444443..35 PP

                                    SEEEEEEETT.TTCSHHHHHHHHH CS
                       MMR_HSR1  77 dlillvvdas.eeklkpldeelee 99 
                                    +++l++ d++  e+++  ++ + e
  gene766|gene766|rna766|rna766  86 HVALIMYDITcPESFETAKNWVTE 109
                                    566666665542334333333333 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   2.3e-06    0.0051      58     193 ..      50     175 ..      11     176 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 2.3e-06
                                    CEEEEEETTCSSEEEEEEEESSSGGGHHHHHHHHHT-SEEEEEEETTTBSTHHHHHHHHHHHHTTTE....EEEEEESCG CS
                       GTP_EFTU  58 saaisleketkkylinliDtPGHvdFskevirglrvlDgavlvvdaveGvepqteevlrlalkegvp....iivfiNKmD 133
                                     + +s++    + ++ + Dt G + +++ +   +r +++a+++ d++      t +++   l+ + p     +++ NK D
  gene766|gene766|rna766|rna766  50 LTKTSIY-PNYNIKYEIWDTAGQERYNSLIPMYYRGAHVALIMYDITCPESFETAKNWVTELSSEKPknfvKVLIGNKSD 128
                                    4555555.56788999***************************998866666666665554444444457677778**** PP

                                    STHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTTEEEEEEBTTTTBTHHHHHHHHHHHSH CS
                       GTP_EFTU 134 rlkaelkeiveevkqklsrkeeklekygekgekevpvvfgSalkgegvktllealvellp 193
                                      +++ k   ee+k+              ++ +++ ++ +Sa++g++v+++++ + e+lp
  gene766|gene766|rna766|rna766 129 LENTSRKVDFEEAKEYA------------RR-NKMLFFEASAKTGFNVENIFSSVSEMLP 175
                                    99999998888888444............23.3688999***********9999999988 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.1   1.5e-06    0.0034       2      38 ..      16      52 ..      15     179 .. 0.68

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.5e-06
                                   EEEEBTTTTHHHHHHHHHTS--S---SSS---S-EEE CS
                      Dynamin_N  2 avvGsqSsGKSSvlnaLlgedilprgpnptTrrplel 38
                                   +v+G +S GKSS++ + ++++++p+++  + +++l+ 
  gene766|gene766|rna766|rna766 16 VVLGYYSVGKSSLIQKYVKDEFNPNEESTIGAAFLTK 52
                                   89**********************9988777776654 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0    0.0041       9.3     102     122 ..      15      35 ..       5      56 .. 0.84
   2 ?    4.6   0.0     0.012        28      47      97 ..     118     170 ..      83     174 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0041
                                    EEEECSTTSSHHHHHHHHCTT CS
                    RsgA_GTPase 102 svlvGqSGvGKStLinallpe 122
                                    +v++G   vGKS+Li + + +
  gene766|gene766|rna766|rna766  15 MVVLGYYSVGKSSLIQKYVKD 35 
                                    57889999*******998765 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.012
                                    -EEEEEEE-GGG--HHH..HHHHHHHHHHHTTSEEEE--TTTHTTHHHHHHHC CS
                    RsgA_GTPase  47 iepvivlnKiDlleeee..eleelkeelealgyevllvsaktkegleelkell 97 
                                       v++ nK Dl ++++  ++ee ke  ++  + ++  sakt+ ++e++ + +
  gene766|gene766|rna766|rna766 118 FVKVLIGNKSDLENTSRkvDFEEAKEYARRNKMLFFEASAKTGFNVENIFSSV 170
                                    4556777*****99988778899999999999999999999999999988766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (198 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       874  (0.0487478); expected 358.6 (0.02)
Passed bias filter:                      495  (0.0276089); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1429.41
//
Query:       gene767|gene767|rna767|rna767  [L=88]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       765  (0.0426683); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.22s 00:00:00.56 Elapsed: 00:00:00.37
# Mc/sec: 719.49
//
Query:       gene768|gene768|rna768|rna768  [L=400]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        1.4    9.3   5.8       0.63   10.4   1.0    2.6  2  DUF5024   Domain of unknown function (DUF5024)


Domain annotation for each model (and alignments):
>> DUF5024  Domain of unknown function (DUF5024)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   1.0   3.5e-05      0.63      19      43 ..     317     341 ..     302     347 .. 0.81
   2 ?   -0.2   0.3     0.069   1.2e+03      25      42 ..     365     382 ..     356     396 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 3.5e-05
                        DUF5024  19 itsvtkrdPkTrkVvkvVksfsvkd 43 
                                      ++tkrdP T++ +k+  +f+ kd
  gene768|gene768|rna768|rna768 317 SDTTTKRDPVTKRKTKILVKFEQKD 341
                                    4689*****************9986 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.069
                        DUF5024  25 rdPkTrkVvkvVksfsvk 42 
                                    + Pk +kVv + ++ sv+
  gene768|gene768|rna768|rna768 365 KYPKGKKVVELKRTISVD 382
                                    579*******99999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (400 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       888  (0.0495287); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 2960.05
//
Query:       gene769|gene769|rna769|rna769  [L=326]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.8e-32  110.6   0.0      9e-32  110.2   0.0    1.1  1  AP_endonuc_2  Xylose isomerase-like TIM barrel


Domain annotation for each model (and alignments):
>> AP_endonuc_2  Xylose isomerase-like TIM barrel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.2   0.0     5e-36     9e-32       5     210 .]      70     282 ..      67     282 .. 0.91

  Alignments for each domain:
  == domain 1  score: 110.2 bits;  conditional E-value: 5e-36
                                    HHCT-SEEEEECCTCSHHHHC..HHHHHHHHHHHHHHTTSEEEEEEECCCHSTCTHCHTTCSHHHHHHHHHHHHHHHHHH CS
                   AP_endonuc_2   5 aeaGfdgvElfgrdlvpvsel..sdeelrelrkaldelglriaslslftrfgypdederearreesvdalkraielaaaL 82 
                                    +++ ++++ lf+++++ ++    +++ +++++k+++ +++ ++  s+ ++    d  e    r+++++++++ + +++ L
  gene769|gene769|rna769|rna769  70 ESLNATTCALFLKNQRRFAFTplEPKSIQKFKKLVKNADVLVPHGSYLINMARNDKAE----RKKHFECFHDDVARCSSL 145
                                    67888999999999999999999******************99999999999977644....5566************** PP

                                    TBSEEEEEBCCGBCTTTSGHHHHHHHHHHHHHHHHHHHHHHTSEEEEE--TTTTSSSTC..HHHHHHHHHHTTTT.EEEE CS
                   AP_endonuc_2  83 GapllvlhpGtagagpkgseeeawerlaeslneladyaekegvklalEtlagsgvelgd..eelarlldavdspn.vgvc 159
                                    G++l ++hpG   +  ++  + a+e++a+++ne+ ++  + +v++++E++ag+g  l    e +++l++ v ++n +gvc
  gene769|gene769|rna769|rna769 146 GIKLYNVHPG---SDVDNLGKKALENVADAINEVNRM--EPNVTIVIENMAGQGRVLCSkfEGIRDLIELVHDKNkIGVC 220
                                    **********...89999999****************..***************98888********************* PP

                                    EEHHHHHHH......TTTHHHHHHHHHGG.....EEEEEE.EESSTTTTSSTTEESTTSSSS CS
                   AP_endonuc_2 160 lDtgHllia......eedvddalraladr.....ikhvHikDakgdlgagrdrhvpigeGei 210
                                    lDt+Hl+        +e +++++ ++++      +k++H++D+k dlg+++drh++ig+G i
  gene769|gene769|rna769|rna769 221 LDTAHLFGSgydlrtKEKCERTFGEFDRIvgmkyLKAMHLNDSKEDLGSKKDRHESIGKGKI 282
                                    ************9995555555555555566669**************************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (326 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       619  (0.0345251); expected 358.6 (0.02)
Passed bias filter:                      523  (0.0291706); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 2383.98
//
Query:       gene77|gene77|rna77|rna77  [L=108]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
      0.028   14.1   0.0      0.036   13.8   0.0    1.1  1  HlyIII      Haemolysin-III related
      0.056   13.2   0.2       0.18   11.5   0.2    1.8  1  AChE_tetra  Acetylcholinesterase tetramerisation domain


Domain annotation for each model (and alignments):
>> HlyIII  Haemolysin-III related
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0     4e-06     0.036     174     216 ..      25      67 ..       9      69 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4e-06
                     HlyIII 174 llvlggvlylvGavfYalrvPErlkpgkfdivghsHqiFHvfv 216
                                  ++++++y ++  + + + PEr+ +  +  + ++H+ FH +v
  gene77|gene77|rna77|rna77  25 GCIVETLFYYMARRLIIEENPERWSNEMITNANQFHTYFHELV 67 
                                567889999999999999**********************877 PP

>> AChE_tetra  Acetylcholinesterase tetramerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.2     2e-05      0.18      13      28 ..      47      62 ..      45      65 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 2e-05
                 AChE_tetra 13 RWssyMmdWknqFndY 28
                               RWs+ M    nqF  Y
  gene77|gene77|rna77|rna77 47 RWSNEMITNANQFHTY 62
                               **************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       541  (0.0301746); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.29s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 730.92
//
Query:       gene771|gene771|rna771|rna771  [L=418]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-60  204.6   0.0    3.6e-60  203.5   0.0    1.6  1  Tubulin          Tubulin/FtsZ family, GTPase domain
    1.1e-17   64.4   0.1    2.2e-17   63.4   0.1    1.5  1  Tubulin_C        Tubulin C-terminal domain
    0.00045   19.5   0.0    0.00067   19.0   0.0    1.3  1  Tubulin_2        Tubulin like
     0.0022   18.3   0.1     0.0061   16.9   0.1    1.8  1  Misat_Tub_SegII  Misato Segment II tubulin-like domain
  ------ inclusion threshold ------
      0.034   13.8   0.0      0.061   13.0   0.0    1.4  1  Tubulin_3        Tubulin domain


Domain annotation for each model (and alignments):
>> Tubulin  Tubulin/FtsZ family, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  203.5   0.0     1e-63   3.6e-60       1     196 [.       3     196 ..       3     197 .. 0.98

  Alignments for each domain:
  == domain 1  score: 203.5 bits;  conditional E-value: 1e-63
                                    EEEEEEEHHHHHHHHHHHHH...HHHCH....HHHT.....TTEEEEE....EEESBHHHHHTS-GS......EEEE--C CS
                        Tubulin   1 eiivigvGqcGnqignelwellakehgiqsdgdslesfFsesgkveyiprsvaidtdpqvlneikagselfnpnklllgk 80 
                                    eii++++GqcGnqig+++w+ l + h      +++++fF+  +++  +pr++++d++p+v+++i++   lfn++++++++
  gene771|gene771|rna771|rna771   3 EIITLQIGQCGNQIGSSFWQRLSSLHPK----SQPSQFFYLADDNMPVPRAILLDLEPRVISQITST-GLFNHENIFVSN 77 
                                    7*******************99999888....99*********************************.************ PP

                                    CC..CTTC--TT-HHHHHHHHHHTHHHHHHHHTT-SE.SEEEEEEETTSSHHHHHHHHHHHHHHHTSTTSEEEEEEEE-- CS
                        Tubulin  81 eg..agnngaggypevgkeaaeeileeirkevekcdslqgffitaslgGGTGSGlgpvilevlkeeypkalvvtvvvlPs 158
                                    eg  agnn+a+gy   +++  +ei e+i +e e++d+l++ffi++s++GGTGSG+g++++e l++e+pk+++++++v+P+
  gene771|gene771|rna771|rna771  78 EGggAGNNWASGYLC-ARSRKNEIFEMIHRESENSDMLESFFILHSIAGGTGSGMGSYLIEELRDEFPKKMLQSFSVFPN 156
                                    *999*********99.99************************************************************** PP

                                    ..GG.G-HHHHHHHHHHHHHHHHT-SEEEEEEHHHHHCCS CS
                        Tubulin 159 ..efsevvvepynailalkelieesdavividNdaLlkil 196
                                      e s+vvv+pyn++l+lk+l +++d+v+v+dN aL +i+
  gene771|gene771|rna771|rna771 157 neEVSDVVVQPYNSVLTLKRLNRCCDSVVVMDNAALGRIS 196
                                    9999********************************9885 PP

>> Tubulin_C  Tubulin C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.4   0.1   6.3e-21   2.2e-17       4     125 ..     249     367 ..     247     368 .. 0.94

  Alignments for each domain:
  == domain 1  score: 63.4 bits;  conditional E-value: 6.3e-21
                                    -EEEEEEESSSCTT.TTTCS-HHHHHHHHHTCSGGGBSSSTSTTTSSEEEEEEEEEESSSHHHHHHHHHHHHHTTTS-BS CS
                      Tubulin_C   4 hFlltsyaPlvsae.kaavektsvqdvtrallepknimvkvdprkgkylaiallirGdvepkevnkavqrikekkkaqfv 82 
                                     F++ sy+P+++++ ++ ++kt+v+dv+r+l+ +kn ++ +d+r    ++++ ++    e+ ev++++ r+++k+ + fv
  gene771|gene771|rna771|rna771 249 NFIVPSYTPFINKDcAQIIRKTTVNDVLRRLMMSKNKLAGIDTRA--IISALTFFINTNEIGEVQRSIIRMQDKQLVGFV 326
                                    69**********99999************************9985..89******************************* PP

                                    TTSTTTEEEEEEECECT-TTTSSCEEEEEEEEGGGHHHHHHHH CS
                      Tubulin_C  83 eWiptgikvalnkkspyvkkqskvsvlmlaNttsiaelfkrll 125
                                    +W+p +++  ++++    ++q   s+l l N+t+++ l+++++
  gene771|gene771|rna771|rna771 327 PWMPPSFHAVVCQEDNAAEQQV--SGLSLTNSTGVSALLRKIC 367
                                    *************998877665..**************99986 PP

>> Tubulin_2  Tubulin like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   1.9e-07   0.00067     153     188 ..     112     147 ..      77     205 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.9e-07
                      Tubulin_2 153 eeglnvfVvgSLaGGTGSGiflDvayllrkilkeek 188
                                    + +  +f++ S+aGGTGSG+   ++  lr++++++ 
  gene771|gene771|rna771|rna771 112 DMLESFFILHSIAGGTGSGMGSYLIEELRDEFPKKM 147
                                    333679***************999999999999876 PP

>> Misat_Tub_SegII  Misato Segment II tubulin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.1   1.7e-06    0.0061       1      21 [.       2      22 ..       2      79 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.7e-06
                Misat_Tub_SegII  1 rEivtlqlGnyaNyvgtHfWN 21
                                   rEi+tlq+G+  N +g+ fW 
  gene771|gene771|rna771|rna771  2 REIITLQIGQCGNQIGSSFWQ 22
                                   8*******************6 PP

>> Tubulin_3  Tubulin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   1.7e-05     0.061      68     143 ..     108     178 ..      92     227 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.7e-05
                      Tubulin_3  68 aeecdqlrglqvftgvddaWG.GfaakylerlrdeygkksilvWvlaleeklkkkkkaklerklkklnkarslkels 143
                                     e++d l+++ ++ ++    G G ++  +e lrde++kk +  + +  ++++ ++        ++  n+  +lk+l 
  gene771|gene771|rna771|rna771 108 SENSDMLESFFILHSIAGGTGsGMGSYLIEELRDEFPKKMLQSFSVFPNNEEVSD------VVVQPYNSVLTLKRLN 178
                                    5899***********99887758899999**********9765544332222222......2233344444444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (418 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       714  (0.0398237); expected 358.6 (0.02)
Passed bias filter:                      627  (0.0349713); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 2937.15
//
Query:       gene772|gene772|rna772|rna772  [L=848]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (848 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       866  (0.0483016); expected 358.6 (0.02)
Passed bias filter:                      513  (0.0286129); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.71u 0.29s 00:00:01.00 Elapsed: 00:00:00.46
# Mc/sec: 5515.37
//
Query:       gene773|gene773|rna773|rna773  [L=38]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (38 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       219  (0.0122148); expected 358.6 (0.02)
Passed bias filter:                      170  (0.00948185); expected 358.6 (0.02)
Passed Vit filter:                         4  (0.000223102); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.42
# Mc/sec: 269.33
//
Query:       gene774|gene774|rna774|rna774  [L=168]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-54  184.5  12.3    1.4e-54  184.4  12.3    1.0  1  Rer1      Rer1 family
     0.0051   16.5   1.3      0.011   15.4   0.2    1.8  2  DUF4131   Domain of unknown function (DUF4131)
  ------ inclusion threshold ------
       0.61   10.7   7.0       0.15   12.7   0.5    2.1  2  DUF5592   Family of unknown function (DUF5592)


Domain annotation for each model (and alignments):
>> Rer1  Rer1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  184.4  12.3   2.4e-58   1.4e-54       8     171 .]       4     164 ..       1     164 [. 0.96

  Alignments for each domain:
  == domain 1  score: 184.4 bits;  conditional E-value: 2.4e-58
                           Rer1   8 rkyqklldkltpytleRWiatlvllllfllriillqgfyivaYalgiylLnlllafltPkfdpsleeeaaeeeaeegael 87 
                                     k+q++ldk++p +leRW+++ ++l+l+++ri+++q +y+v+Y+l+iylL+ l+ f+tP+  +s+ +    ++++e+  +
  gene774|gene774|rna774|rna774   4 AKFQYYLDKTAPKKLERWVFFSCVLVLYFIRILYIQTHYLVTYVLSIYLLHGLIGFCTPQE-ESIPD--PFDNIDEEVYI 80 
                                    689********************************************************98.55565..467889999** PP

                           Rer1  88 ptkkdeefrPfirrlpEfkfWlsatkailialvltffevfdvpVfwpiLlvyfivlfvltmrrqikhmikykyvpfdlgK 167
                                    p++ d+efrPf+rrlpEf+fW  +++ +li++++tf ++fd+pV+ piL++yfiv+ +lt ++ ++hm+ky+y pf ++K
  gene774|gene774|rna774|rna774  81 PQTVDDEFRPFMRRLPEFDFWWLSVRLVLISFLTTFSSLFDIPVYAPILVIYFIVISLLTAKNLYRHMKKYNYNPFYVAK 160
                                    ******************************************************************************** PP

                           Rer1 168 kkyk 171
                                    ++yk
  gene774|gene774|rna774|rna774 161 ESYK 164
                                    **96 PP

>> DUF4131  Domain of unknown function (DUF4131)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.2   1.9e-06     0.011       7      87 ..      21     100 ..      16     117 .. 0.80
   2 ?    0.5   0.5      0.07   4.2e+02       8      49 ..     101     141 ..      96     155 .. 0.47

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.9e-06
                        DUF4131   7 lvllalllllllllllllrrrprrrvllllllllllallgfalrapqpnandlsqllesgqeviveGvvaslpeltgsgt 86 
                                    +v++  +l+l+++++l+   ++++ v  +l+++ll +l+gf+ ++ +   ++++++   ++ev++  +v+++ +   ++ 
  gene774|gene774|rna774|rna774  21 WVFFSCVLVLYFIRILYI--QTHYLVTYVLSIYLLHGLIGFCTPQEESIPDPFDNI---DEEVYIPQTVDDEFRPFMRRL 95 
                                    344444555555555555..9******************************99999...679**9999999999888877 PP

                        DUF4131  87 ....r 87 
                                         
  gene774|gene774|rna774|rna774  96 pefdF 100
                                    65533 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.07
                        DUF4131   8 vllalllllllllllllrrrprrrvllllllllllallgfal 49 
                                    ++l + l+l+ +l  ++       v + +l++++++ + +++
  gene774|gene774|rna774|rna774 101 WWLSVRLVLISFLTTFSS-LFDIPVYAPILVIYFIVISLLTA 141
                                    444444444444444433.33333444444444444444444 PP

>> DUF5592  Family of unknown function (DUF5592)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   1.2     0.081   4.8e+02      42      76 ..      17      52 ..       1      54 [. 0.68
   2 ?   12.7   0.5   2.4e-05      0.15       5      75 ..      82     157 ..      79     165 .. 0.69

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.081
                        DUF5592 42 sl.vvlfyifviilviflviksktNpklrnykalyL 76
                                   +l +++f+ +v++l  + ++  +t      + ++yL
  gene774|gene774|rna774|rna774 17 KLeRWVFFSCVLVLYFIRILYIQTHYLVTYVLSIYL 52
                                   553588888888888888877777666666666666 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 2.4e-05
                        DUF5592   5 keisselk.inkaiyLtDl...llllvlllltmklsslvhaslvvlfyifviilviflviksktNpklr.nykaly 75 
                                    + +  e + + + +  +D+    + lvl+ +++++ssl+   +  ++ ++ +i++ +l  k    + ++ ny+  y
  gene774|gene774|rna774|rna774  82 QTVDDEFRpFMRRLPEFDFwwlSVRLVLISFLTTFSSLFDIPVYAPILVIYFIVISLLTAKNLYRHMKKyNYNPFY 157
                                    5555555544555555565111455889999*********999999999999999998888877765442666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       961  (0.0536003); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 1102.70
//
Query:       gene775|gene775|rna775|rna775  [L=112]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      3e-08   34.0   0.5    6.3e-08   33.0   0.5    1.5  1  RNA_pol_Rpb4     RNA polymerase Rpb4
     0.0034   17.4   0.0     0.0052   16.9   0.0    1.3  1  EFhand_Ca_insen  Ca2+ insensitive EF hand


Domain annotation for each model (and alignments):
>> RNA_pol_Rpb4  RNA polymerase Rpb4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.0   0.5   7.1e-12   6.3e-08       2     122 ..       9     111 ..       8     112 .] 0.88

  Alignments for each domain:
  == domain 1  score: 33.0 bits;  conditional E-value: 7.1e-12
                                    E-HHHHHHHHHHHHHHHHCHHHHHTCCCCCHHSHCHTCHHCHHHHHHHHHHHCTHHTTSSHHHHHHHHHHHTTSTSTHHH CS
                   RNA_pol_Rpb4   2 LsnsEvllvlkeeleerknkdkkeseddkisekeevkgnlnkilkktleyltnkfsrlkneekfnelvellksfeLtkaE 81 
                                    L+ sE++ +l++++ +  +k                + + ++i+++t++y ++   r  + + +++l++ l + +L++ E
  gene775|gene775|rna775|rna775   9 LTISEAFHHLASQRPRIIKK----------------DVKFRTIFENTYNYCQQ-HTRVSSTSLMENLRTSLIELGLNEDE 71 
                                    78888888888444444333................35789***********9.999999999***************** PP

                                    HHHHHHCSTSSHHHHHHHSTTGTTTSTSHHHHHHHHHHHHH CS
                   RNA_pol_Rpb4  82 klqlvnlkPesavelktlieeleerfedeqleeiLdelkev 122
                                    ++ + +l P+s++e+++l+++l  r+++++l + +++++ v
  gene775|gene775|rna775|rna775  72 VAIVASLFPQSVDEVRLLVDSLG-RLDEQTLIKVINKINSV 111
                                    **********************9.************99865 PP

>> EFhand_Ca_insen  Ca2+ insensitive EF hand
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   5.8e-07    0.0052       7      43 ..      10      47 ..       4      63 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 5.8e-07
                                   HHHCHHHHHCTTSSSEEHHHHHHH-TTCHH.HHHHCCS CS
                EFhand_Ca_insen  7 qveeaFralaggKpYvTeedLrrellpeqa.eylierM 43
                                    + eaF+ la+++p + ++d +   + e++ +y++++ 
  gene775|gene775|rna775|rna775 10 TISEAFHHLASQRPRIIKKDVKFRTIFENTyNYCQQHT 47
                                   5889*******************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       594  (0.0331307); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 879.70
//
Query:       gene776|gene776|rna776|rna776  [L=171]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.059   14.1   2.4      0.097   13.4   1.3    1.8  2  PMC2NT    PMC2NT (NUC016) domain


Domain annotation for each model (and alignments):
>> PMC2NT  PMC2NT (NUC016) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   1.3   5.4e-06     0.097      15      86 ..      19      99 ..      12     102 .. 0.91
   2 ?   -1.0   0.0      0.17     3e+03      15      36 ..     148     168 ..     141     169 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5.4e-06
                         PMC2NT 15 ldfyrsldpefaksldeqserllslinsllklaaskseisassklededd..........veekfksvvdvvDsllEkadtc 86
                                   +d y+s+ +++  ++++++++  s++++l k+++  ++++++++++++dd          ve k +++++++D+l +k+  +
  gene776|gene776|rna776|rna776 19 MDVYKSY-RGILMEVERKAKNKNSILTNLRKYHNDTTSTQNENDHKTLDDsvasagnnvpVEYKIDDIMNLLDKLNDKVVDN 99
                                   6889999.9***************************99999999999999999******99**************9998655 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.17
                         PMC2NT  15 ldfyrsldpefaksldeqserl 36 
                                    + f++ + +++++  ++ s++l
  gene776|gene776|rna776|rna776 148 HPFHKEY-EKLRTVTEQLSKKL 168
                                    5789999.88888888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1188  (0.0662614); expected 358.6 (0.02)
Passed bias filter:                      453  (0.0252663); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.31s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 1079.47
//
Query:       gene777|gene777|rna777|rna777  [L=271]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.7e-24   86.7   0.1    1.8e-24   86.6   0.1    1.1  1  Peptidase_C13  Peptidase C13 family
  ------ inclusion threshold ------
      0.029   14.0   2.1      0.029   14.0   0.8    1.6  2  Maelstrom      piRNA pathway germ-plasm component
       0.13   12.2   0.0       0.36   10.7   0.0    1.7  2  Suc_Fer-like   Sucrase/ferredoxin-like


Domain annotation for each model (and alignments):
>> Peptidase_C13  Peptidase C13 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.6   0.1   3.1e-28   1.8e-24       1     189 [.      18     196 ..      18     264 .. 0.86

  Alignments for each domain:
  == domain 1  score: 86.6 bits;  conditional E-value: 3.1e-28
                                    EEEEEEE---SGGGHHHHHHHHHHHHHHHCTT--GGGEEEEE---STT-TT-SSTT--BSSTT--B-STT--ESBEGGG- CS
                  Peptidase_C13   1 lyavlvAGsngydnyrhqadvchayqllkkkglkdenivvvmydDiaereenPlagkiinkpkgedvykgvkidYtgkkv 80 
                                    +ya+l+  s++y+n rh+a++   y++l+++g+ d++i+v+  dD+ ++ +n  +g+ii      d   +v+ +++g++ 
  gene777|gene777|rna777|rna777  18 NYAILLNASQYYKNIRHTANIHLFYRILRENGFADDEIIVFTCDDLIHDCRNSKKGHIIL----PDGEFTVP-KFRGRSF 92 
                                    69******************************************************7774....33333432.59***** PP

                                    SHHHHHHHHHT-TCGTT-------TTSEEEEEEES-EETTEEE-SSSSEEEHHHHHHHHHHHHHCT--SEEEEEEESTTG CS
                  Peptidase_C13  81 tkenflavllGdksvgsgkvlksgkeDnvfiyltdhGapgvlevpeeddleakdLaeaLkkmhakkkykklviyleaceS 160
                                    t+  f++ + G++    +k+++  +  n++iy+  hG +++l+v +++ ++ ++L++aL  +++++  +k ++++++c++
  gene777|gene777|rna777|rna777  93 TPLSFYNAVMGNN----KKLIDMDETSNILIYMCGHGNRDFLKVHNKHFITSTELTNALCVLSRRGI-NKAFVIIDTCKA 167
                                    ************9....59*********************************************999.999999****** PP

                                    GGGTTT..S-TTSSEEEEESS-TTS--BEEC CS
                  Peptidase_C13 161 gsmfee..llkdinvyaltAanadessfgty 189
                                    + +++   l+++i v+ +  +++d++s + +
  gene777|gene777|rna777|rna777 168 ATLINRekLPENIVVLFT--SKEDQDSISSF 196
                                    ****99667776666655..55555554443 PP

>> Maelstrom  piRNA pathway germ-plasm component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0      0.44   2.6e+03     108     134 ..      43      70 ..      22      77 .. 0.69
   2 ?   14.0   0.8   4.9e-06     0.029      75     182 ..     165     267 ..     149     271 .] 0.83

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.44
                                    HH----HHHH-.EEEEEHHHHHHHHHHH CS
                      Maelstrom 108 nlaedvkfeee.vsvydiqelfldlkke 134
                                     + ++++f ++ ++v   ++l+ d +++
  gene777|gene777|rna777|rna777  43 RILRENGFADDeIIVFTCDDLIHDCRNS 70 
                                    3445555555557777777777777665 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 4.9e-06
                                    HHHHHHHH-SS...S-EEEEE-GGGHHHHHHHHHHH----HHHH-EEEEEHHHHHHHHHHHHHHHTT---TT--HHHHHH CS
                      Maelstrom  75 lsflessseks.neksliiltkeeeisvvksclknlaedvkfeeevsvydiqelfldlkkevldvalsrqekpnkeitda 153
                                    ++     + ++  e+ ++++t +e+ + ++s  +n+  +      + + ++ ++f++  ++ ld  +++  ++  + ++ 
  gene777|gene777|rna777|rna777 165 CKAATLINREKlPENIVVLFTSKEDQDSISSFSSNITGQ------MTIDNFPYFFYKHIENRLDTDIIDFVEEMASNYPV 238
                                    444444444555788899999999999998777777773......46778****************************** PP

                                    HHHH-TTTT-TT-S-HHHHHHT-GGG-HH CS
                      Maelstrom 154 llskdfyeytkdisCeyHeendrskyCak 182
                                    + + +++  +    Ce+ ++  ++ yCa+
  gene777|gene777|rna777|rna777 239 ESNLIIWPEKRWKICEFFKQTKKKMYCAN 267
                                    ***************************97 PP

>> Suc_Fer-like  Sucrase/ferredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   6.1e-05      0.36      55     107 ..      15     128 ..       4     130 .. 0.74
   2 ?   -2.6   0.0      0.71   4.2e+03      89     107 ..     173     191 ..     138     224 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 6.1e-05
                   Suc_Fer-like  55 eekttvlllPdfklveevtpssveelvkeflkp............................................... 87 
                                    ++k+ ++ll + ++++++++++  +l+ ++l++                                               
  gene777|gene777|rna777|rna777  15 NTKNYAILLNASQYYKNIRHTANIHLFYRILREngfaddeiivftcddlihdcrnskkghiilpdgeftvpkfrgrsftp 94 
                                    45666777888888888886655556666666567788888888888888888888888888888888888888888888 PP

                   Suc_Fer-like  88 ...............kvrklpekaliLvCshktrD 107
                                                   ++ + ++++li +C+h++rD
  gene777|gene777|rna777|rna777  95 lsfynavmgnnkkliDM-DETSNILIYMCGHGNRD 128
                                    88888888888877632.3356789*********9 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.71
                   Suc_Fer-like  89 vrklpekaliLvCshktrD 107
                                     +klpe++++L  s++ +D
  gene777|gene777|rna777|rna777 173 REKLPENIVVLFTSKEDQD 191
                                    3455555566655555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (271 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       522  (0.0291148); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1909.77
//
Query:       gene778|gene778|rna778|rna778  [L=311]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0018   18.5   8.0     0.0018   18.5   8.0    2.9  2  EamA      EamA-like transporter family
  ------ inclusion threshold ------
       0.92    9.6   0.0       0.92    9.6   0.0    3.7  5  DUF1435   Protein of unknown function (DUF1435)


Domain annotation for each model (and alignments):
>> EamA  EamA-like transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   8.0     2e-07    0.0018      12     134 ..      15     128 ..       6     131 .. 0.69
   2 ?   -5.0  12.9         2   1.8e+04      31     134 ..     173     280 ..     146     281 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 2e-07
                           EamA  12 lfwaiyfvlskillrkvspltltfvrfliagillliiallkegklaklslkdwllllllgllgtvlafllffyalkktsa 91 
                                    ++ a++++  +     ++ + +t   ++ia+   l+++ + ++ + kl+ + +   l l ++  vl+ l+  y  k+++ 
  gene778|gene778|rna778|rna778  15 VIVAAGILKNRLY---YNEFPVTL-PSMIASWGALLVSYFMAQEH-KLPDR-L---LSLVVVILVLYSLVARYCSKHMDC 85 
                                    4444444444443...34444444.34455555555555555555.23333.3...3344444577777778999***** PP

                           EamA  92 snaslitslePvftlilsvlllgekltlkqllgivlillGvll 134
                                     +++l+    ++ft il+ l++  +l+ +q++g+ li++G++l
  gene778|gene778|rna778|rna778  86 LVIALCAPSKVIFTCILAKLFFELQLSRWQIFGLSLIIVGIVL 128
                                    *****************************************98 PP

  == domain 2  score: -5.0 bits;  conditional E-value: 2
                           EamA  31 l..tltfvrfliagillliiallkegkl.aklslkdwllllllgllgtvlafllffyalkktsasnaslitslePvftli 107
                                    +   l+f  ++i+ ++   i++ + +k  + ++l +     ++ l++  +  +l   +l  ts+   s+i+ +  +ft +
  gene778|gene778|rna778|rna778 173 FfwNLVFTGSIIGVVVSTGILATEMIKSdSTFKLLAQRKTTYILLVAEYVELSLKAFLLYVTSPIYRSIILIFLSIFTGM 252
                                    33467778888888888888888888888899999999999999999999999999999999999999999999999999 PP

                           EamA 108 lsvlllg.ekltlkqllgivlillGvll 134
                                    +  +++g e++ + ++l+++ + +G+++
  gene778|gene778|rna778|rna778 253 IDTVIFGwETIRIVDILAFITANMGLII 280
                                    9999995499999999999999999875 PP

>> DUF1435  Protein of unknown function (DUF1435)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.4     0.039   3.5e+02      33      70 ..       8      47 ..       3      52 .. 0.58
   2 ?   -0.0   1.5      0.11   9.7e+02       8      21 ..      40      53 ..      33     109 .. 0.65
   3 ?    9.6   0.0    0.0001      0.92      11      49 ..     125     166 ..     123     187 .. 0.88
   4 ?   -3.3   0.0       1.1   9.9e+03      22      36 ..     219     233 ..     213     249 .. 0.58
   5 ?   -2.1   0.2      0.46   4.2e+03      22      43 ..     253     274 ..     239     279 .. 0.62

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.039
                        DUF1435 33 rviivlallltvvmLyhkrl.RHy.lLLPsclalagglal 70
                                   r +++ a+++++ +L ++     + + LPs++a  g+l++
  gene778|gene778|rna778|rna778  8 RNLLMSAVIVAAGILKNRLYyNEFpVTLPSMIASWGALLV 47
                                   5555556665555553332211223789999998888765 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.11
                        DUF1435  8 sgWgvlLPavlial 21
                                   ++Wg lL   ++a 
  gene778|gene778|rna778|rna778 40 ASWGALLVSYFMAQ 53
                                   45666666666654 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.0001
                        DUF1435  11 gvlLPavliallalaelsldqlrviivlallltvvmL...yh 49 
                                    g++LP ++ia   +  +s +++ v i  +ll +++ L   +h
  gene778|gene778|rna778|rna778 125 GIVLPNIIIADSDFSSISPQKIGVCIFAGLLFSLLNLtyeFH 166
                                    8******************************99876643344 PP

  == domain 4  score: -3.3 bits;  conditional E-value: 1.1
                        DUF1435  22 lalaelsldqlrvii 36 
                                      ++elsl+++ + +
  gene778|gene778|rna778|rna778 219 AEYVELSLKAFLLYV 233
                                    456666666654444 PP

  == domain 5  score: -2.1 bits;  conditional E-value: 0.46
                        DUF1435  22 lalaelsldqlrviivlalllt 43 
                                    +  + + ++ +r++ +la++++
  gene778|gene778|rna778|rna778 253 IDTVIFGWETIRIVDILAFITA 274
                                    4444456677777777776654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       972  (0.0542138); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.23s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2231.74
//
Query:       gene779|gene779|rna779|rna779  [L=549]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.5e-54  182.7   0.8    3.4e-33  115.1   0.5    2.5  2  Pkinase         Protein kinase domain
    2.3e-24   86.1   0.2    2.6e-17   63.0   0.2    2.2  2  Pkinase_Tyr     Protein tyrosine kinase
    2.7e-05   23.6   0.2     0.0061   15.9   0.0    2.5  2  Kinase-like     Kinase-like
      0.005   16.5   1.9     0.0085   15.7   0.4    1.9  2  RIO1            RIO1 family
     0.0051   15.9   0.6     0.0088   15.1   0.6    1.3  1  Seadorna_VP7    Seadornavirus VP7
  ------ inclusion threshold ------
      0.043   13.7   0.1       0.17   11.8   0.0    1.9  2  APH             Phosphotransferase enzyme family
        0.1   11.9   0.3       0.19   11.1   0.3    1.3  1  Kdo             Lipopolysaccharide kinase (Kdo/WaaP) family
       0.11   11.3   0.0       0.18   10.6   0.0    1.3  1  Pkinase_fungal  Fungal protein kinase


Domain annotation for each model (and alignments):
>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.1   0.5   1.5e-36   3.4e-33       2     150 ..       9     152 ..       8     165 .. 0.93
   2 !   65.2   0.0   2.5e-21   5.6e-18     152     264 .]     209     310 ..     199     310 .. 0.83

  Alignments for each domain:
  == domain 1  score: 115.1 bits;  conditional E-value: 1.5e-36
                                    EEEEEEEEESSEEEEEEEETTTTEEEEEEEEECHCHCHHHHHHHHHHHHHHHHHSCTTB--EEEEEEESSEEEEEEE--T CS
                        Pkinase   2 ekleklGeGsfGkVykaveketgkivAvKkikkekakkkkekkvlrEikilkklkhpnivrlyevfeekdelylvleyve 81 
                                    e  e++G G fG+Vy+av k tg+++AvK+i+k+   +     +++E+++   + h  iv+++  f++++++++ +e++e
  gene779|gene779|rna779|rna779   9 EMYERIGYGRFGNVYRAVYKPTGEMMAVKIIRKDALHSCY---IANEVRLGSLILHHGIVHVKFLFHNDTHFFIAMELLE 85 
                                    67899*****************************999977...8************************************ PP

                                    TEBHHHHHHHHSS--HHHHHHHHHHHHHHHHHHHHTTEE-SS-SGGGEEEETTTEEEE-SGTTSEESSS CS
                        Pkinase  82 ggeladllerkgslseeeakkiakqilegleylHskgiiHrDlKpeNiLidekgelKitDFGlakeles 150
                                    g +l++l++ ++ ++e+ea+ ++ +i+++l++lHs++i+HrD+Kp+Ni++  k  +Ki+D+G  + ++ 
  gene779|gene779|rna779|rna779  86 GVTLENLIN-SQRFTEDEARVYVFEIVKALHFLHSHHIMHRDIKPSNIMVC-KTGIKIVDLGTLSLFQG 152
                                    ********8.689**************************************.888*******8777665 PP

  == domain 2  score: 65.2 bits;  conditional E-value: 2.5e-21
                                    CSBCTTTSCGGGS-HHHH.TTSCBSHHHHHHHHHHHHHHHHHSS-STTTSSHHHHHHHHHHTHHHHHHHCTSHH...HHH CS
                        Pkinase 152 skltsfvgtseYlAPEvl.keneyskkvDvWslGvilyelltgkppfsgekgkekvekeldqlekilkilgetkeklpea 230
                                     ++ +++gt+ Y APE+l  + +++ kvDvWslG+++y ++tg + fsg++++e   ++l++                  
  gene779|gene779|rna779|rna779 209 RTTAERCGTPLYSAPELLfVRANVTDKVDVWSLGCLIYRMITGVEKFSGNDSSEIEDSILNK------------PLDIDS 276
                                    447899************988999************************77777655555555............222234 PP

                                    TTS-HHHHHHHHHHT-SSGCCSTTHHHHHTSGGG CS
                        Pkinase 231 seiseeakdllkkllkkdpkkRltaeellqhpyl 264
                                      +se++k+ll+++l++d  +R+++e++l++++l
  gene779|gene779|rna779|rna779 277 MCVSESLKKLLERMLQRDYVRRISIEDVLASDWL 310
                                    457*****************************97 PP

>> Pkinase_Tyr  Protein tyrosine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.0   0.2   1.2e-20   2.6e-17       2     149 ..       9     146 ..       8     164 .. 0.92
   2 !   21.0   0.0   7.5e-08   0.00017     169     256 ..     218     305 ..     199     307 .. 0.84

  Alignments for each domain:
  == domain 1  score: 63.0 bits;  conditional E-value: 1.2e-20
                                    EEEEEEEEESSEEEEEEEEETTTTSSEEEEEEEEESTTSSHHHHHHHHHHHHHHHTS-BTTB--EEEEEESSSSEEEEEE CS
                    Pkinase_Tyr   2 elgkklGeGafGkVvegtlkgekekkevkVavKtlkeeateeekeelleeakimkklkhpnivkllgvctkeepllivte 81 
                                    e+ +++G G+fG+V+++ +k     + +  avK+++++a ++    + +e+++ + + h+ iv++  +  ++ + +i +e
  gene779|gene779|rna779|rna779   9 EMYERIGYGRFGNVYRAVYK----PTGEMMAVKIIRKDALHS--CYIANEVRLGSLILHHGIVHVKFLFHNDTHFFIAME 82 
                                    67899***************....788899*****9998888..999******9999*********************** PP

                                    --TTEBHHHHHHHTCTTTSBHHHHHHHHHHHHHHHHHHHHTTEEEST-SGGGEEEEETTEEEE-STTT CS
                    Pkinase_Tyr  82 yvkgGdLlkfLrkkekekltlkdllsfalqvAkGmeyLeskklvHrdlaarNvLlsenkvvkisDfGL 149
                                    +++g +L++ ++++   ++t ++   +++++ k++++L+s++++Hrd+   N++++ ++ +ki D G 
  gene779|gene779|rna779|rna779  83 LLEGVTLENLINSQ---RFTEDEARVYVFEIVKALHFLHSHHIMHRDIKPSNIMVC-KTGIKIVDLGT 146
                                    ***********998...99*************************************.6679****995 PP

  == domain 2  score: 21.0 bits;  conditional E-value: 7.5e-08
                                    GGGS-HHHHHHSE.EEHHHHHHHHHHHHHHHHTTSSGTTTTSHHHHHHHHHHTTEES-BBTTSBHHHHHHHHHHT-SSGG CS
                    Pkinase_Tyr 169 vkWmapEslkekk.ftsksDvWsfGvllwEiftlgespypglkneevleklkegkrlekpekcpeelyelmkkcweedpe 247
                                      + apE l+ +  +t k DvWs G l++ ++t g + ++g +++e+ + + ++        ++e+l++l+++ +++d  
  gene779|gene779|rna779|rna779 218 PLYSAPELLFVRAnVTDKVDVWSLGCLIYRMIT-GVEKFSGNDSSEIEDSILNKPLDIDSMCVSESLKKLLERMLQRDYV 296
                                    4589****9977659******************.************99999887777777778899************** PP

                                    GS--HHHHH CS
                    Pkinase_Tyr 248 eRptfselv 256
                                    +R ++++++
  gene779|gene779|rna779|rna779 297 RRISIEDVL 305
                                    **9998875 PP

>> Kinase-like  Kinase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.9   0.3     0.006        13     131     187 ..      89     143 ..      56     152 .. 0.77
   2 !   15.9   0.0   2.7e-06    0.0061     224     288 .]     229     298 ..     209     298 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.006
                    Kinase-like 131 lqkrsethkkletiarlllTlqlirlaanLqakglvhgkftvdnllldekgglmlgg 187
                                    l++  + ++  e+ ar ++  ++++    L+++ ++h ++++ n++  + g +++ +
  gene779|gene779|rna779|rna779  89 LENLINSQRFTEDEARVYV-FEIVKALHFLHSHHIMHRDIKPSNIMVCKTG-IKIVD 143
                                    3444444677788999999.99***********************987654.55555 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 2.7e-06
                    Kinase-like 224 ktkmthkldaWqlGlviyriwclklPl.tlateeakeew......kfklck..kipekvkaLlkkfLqlsqedR 288
                                    ++++t k+d+W lG  iyr+   +  + +++ +e++ +       +        ++e +k Ll+++Lq++  +R
  gene779|gene779|rna779|rna779 229 RANVTDKVDVWSLGCLIYRMITGVEKFsGNDSSEIEDSIlnkpldI----DsmCVSESLKKLLERMLQRDYVRR 298
                                    6899***************988776661555666666643332211....223589************987665 PP

>> RIO1  RIO1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.1      0.44   9.9e+02       1      22 [.      21      43 ..      21      54 .. 0.80
   2 !   15.7   0.4   3.8e-06    0.0085      83     150 ..      79     145 ..      72     148 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.44
                                   EEEEEEE.TTTEEEEEEEE-S-- CS
                           RIO1  1 nVyhavs.edgkevaiKiyktst 22
                                   nVy av   +g+ +a+Ki +  +
  gene779|gene779|rna779|rna779 21 NVYRAVYkPTGEMMAVKIIRKDA 43
                                   7998876488999*****99765 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 3.8e-06
                                    EEEE--EETTEEGGBHHHCG-..HHHHHHHHHHHHHHHHHHHHTSTEEESS-STTSEEEETTEEEE--GT CS
                           RIO1  83 lvmefigedgvaapklkdvee..eeeaeelyeevleemrklykeaglvHaDLSeyNvlvdedkvviIDvs 150
                                    + me+++  gv + +l + ++  e+ea+ ++ e++++++ +++ +++ H D+   N++v + ++ i+D++
  gene779|gene779|rna779|rna779  79 IAMELLE--GVTLENLINSQRftEDEARVYVFEIVKALH-FLHSHHIMHRDIKPSNIMVCKTGIKIVDLG 145
                                    78*****..*******99994458888888888888665.556*************************85 PP

>> Seadorna_VP7  Seadornavirus VP7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.6   3.9e-06    0.0088     115     190 ..      61     147 ..      20     153 .. 0.65

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.9e-06
                   Seadorna_VP7 115 vyGivkLk....nDnnyey......GiilekCykirvltvn....iivaglkdLmdfhsestnllhGDcnpenlmcDknG 180
                                     +Giv++k    nD  + +      G+ le+  + +  t +     +   +k+L+ +h  s++++h D++p+n+m  k+G
  gene779|gene779|rna779|rna779  61 HHGIVHVKflfhNDTHFFIamelleGVTLENLINSQRFTEDearvYVFEIVKALHFLH--SHHIMHRDIKPSNIMVCKTG 138
                                    4777777777777755533233334777777655444333211114555579999999..7899***************9 PP

                   Seadorna_VP7 181 ylklvDPvsL 190
                                     +k+vD ++L
  gene779|gene779|rna779|rna779 139 -IKIVDLGTL 147
                                    .7****8876 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.1      0.27     6e+02      23     106 ..      34     118 ..      20     121 .. 0.66
   2 ?   11.8   0.0   7.7e-05      0.17     163     197 ..     117     148 ..      82     150 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.27
                                    EEEEEE-TTS-HHHHH..HHHHHHHHHHHTT-.B--B-CTTBS-EEETTEEEEEEE----EE-SS..HHHHHHHHHHHHH CS
                            APH  23 yvlrrnpparaaeeir..revallrlLakagv.pvPevlagdtddeeigllfalieyvpgrsllr..klsaaqlpellea 97 
                                    ++++++++  a  ++   +ev+l  l+  +g+ +v + l    +d++  + ++l+e+v  + l +  + ++++++ ++ +
  gene779|gene779|rna779|rna779  34 MAVKIIRKD-ALHSCYiaNEVRLGSLILHHGIvHV-KFLF--HNDTHFFIAMELLEGVTLENLINsqRFTEDEARVYVFE 109
                                    556666666.4444433388888899999999666.5554..37777777888888888888888776666666666666 PP

                                    HHHHHCCHH CS
                            APH  98 lgeflaalh 106
                                    ++ +l  lh
  gene779|gene779|rna779|rna779 110 IVKALHFLH 118
                                    666666666 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 7.7e-05
                                    SS-EEEE-SS-SGGGEEEC..TTEEEEE---TT-E CS
                            APH 163 elptvllHgDlhpgNllvdpddgrvtGviDfedag 197
                                      ++ ++H+D++p N++v   ++ +  ++D+++++
  gene779|gene779|rna779|rna779 117 LHSHHIMHRDIKPSNIMVC--KTGI-KIVDLGTLS 148
                                    467889*************..4444.499999876 PP

>> Kdo  Lipopolysaccharide kinase (Kdo/WaaP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.3   8.4e-05      0.19      93     155 ..      78     138 ..      67     146 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 8.4e-05
                            Kdo  93 lllterlegaqdLedllakwaelaeelkrallkavgrliaklhragvnHadlyaknillqqee 155
                                    ++ +e leg+  Le+l+++ +++ e   r  + ++ ++ + lh+ +++H+d+ + ni++ +++
  gene779|gene779|rna779|rna779  78 FIAMELLEGV-TLENLINS-QRFTEDEARVYVFEIVKALHFLHSHHIMHRDIKPSNIMVCKTG 138
                                    5677777776.48888886.55888888888999999*********************98876 PP

>> Pkinase_fungal  Fungal protein kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   7.9e-05      0.18     314     342 ..     109     136 ..      99     173 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 7.9e-05
                 Pkinase_fungal 314 DaIkghrsLflkagiLHrDiSenNilitd 342
                                    + +k++  L+    i+HrDi   Ni+++ 
  gene779|gene779|rna779|rna779 109 EIVKALHFLH-SHHIMHRDIKPSNIMVCK 136
                                    57899999**.9**************983 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (549 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       418  (0.0233142); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.44
# Mc/sec: 3751.82
//
Query:       gene78|gene78|rna78|rna78  [L=114]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (114 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       270  (0.0150594); expected 358.6 (0.02)
Passed bias filter:                      196  (0.010932); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.44
# Mc/sec: 784.99
//
Query:       gene780|gene780|rna780|rna780  [L=268]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
     0.0011   19.0   0.6     0.0025   17.7   0.1    1.8  2  SMC_ScpA    Segregation and condensation protein ScpA
  ------ inclusion threshold ------
       0.13   11.5   0.0       0.39   10.0   0.0    1.7  1  Rad21_Rec8  Conserved region of Rad21 / Rec8 like protein


Domain annotation for each model (and alignments):
>> SMC_ScpA  Segregation and condensation protein ScpA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.1      0.23   2.1e+03     118     152 ..      57      89 ..      29     104 .. 0.59
   2 !   17.7   0.1   2.8e-07    0.0025     204     238 ..     231     265 ..     204     267 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.23
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                       SMC_ScpA 118 keveevavkieksvfklieafnkllkrakivalae 152
                                     e++++  +++ +v+ +   +   + r+  v+ ae
  gene780|gene780|rna780|rna780  57 TEIKRIINNVDGNVLSEKRNIRSKINRK--VFDAE 89 
                                    3566666667777777666666666666..44444 PP

  == domain 2  score: 17.7 bits;  conditional E-value: 2.8e-07
                                    --HHHHHHHHHHHHHHHHTT-EEEEESSTTS-EEE CS
                       SMC_ScpA 204 edkkelvgvFlAlLeLiknqavaleQeeflddLqv 238
                                    +d++++v++F  lLeL  +++v +eQ + + +++v
  gene780|gene780|rna780|rna780 231 IDREHKVAAFCKLLELLVQNKVTVEQIDCYTNIYV 265
                                    799*******************************9 PP

>> Rad21_Rec8  Conserved region of Rad21 / Rec8 like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   4.4e-05      0.39      14      49 ..     230     265 ..     219     267 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 4.4e-05
                                    ----HHHHHHHHHHHHHHHHTSEEEEESSTT--EEE CS
                     Rad21_Rec8  14 gktRkeAArlFyelLvLatkgvIkvkQeaPYgdIli 49 
                                    g++R+  + +F +lL+L  + ++ v+Q   Y +I +
  gene780|gene780|rna780|rna780 230 GIDREHKVAAFCKLLELLVQNKVTVEQIDCYTNIYV 265
                                    7788888999***********************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (268 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       845  (0.0471303); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1819.39
//
Query:       gene781|gene781|rna781|rna781  [L=308]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.8e-14   52.2   1.9    9.5e-14   51.5   0.9    1.9  2  OGG_N     8-oxoguanine DNA glycosylase, N-terminal domain
    4.5e-11   43.2   0.0    9.7e-11   42.1   0.0    1.5  2  HhH-GPD   HhH-GPD superfamily base excision DNA repair protei
     0.0035   16.9   0.5          1    8.9   0.0    2.4  2  DUF2192   Uncharacterized protein conserved in archaea (DUF21
  ------ inclusion threshold ------
      0.022   14.3   0.3      0.022   14.3   0.3    2.2  2  MA-Mit    Mycoplasma arthritidis-derived mitogen
      0.049   13.6   0.3        0.2   11.6   0.0    2.1  3  DUF2400   Protein of unknown function (DUF2400)


Domain annotation for each model (and alignments):
>> OGG_N  8-oxoguanine DNA glycosylase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.5   0.9   2.6e-17   9.5e-14       5     120 ..       9     128 ..       5     129 .. 0.86
   2 ?   -1.9   0.0      0.92   3.3e+03      37      52 ..     256     272 ..     241     305 .. 0.64

  Alignments for each domain:
  == domain 1  score: 51.5 bits;  conditional E-value: 2.6e-17
                                    S-SS--HHHHHCSSS-SSEEE-TTS-EEEEETTEEEEEEEETTEEEEET--.............HHHHHHTHHHHTTTTS CS
                          OGG_N   5 skeeldlkktLkcGQsFrWkktekteyvgvlgdrvveLkqeeddllyrtlesesstkasseeakeeeteeilrdYfnLdv 84 
                                    ++  ++l+ktL +GQ F+++kt ++e +g++++ + ++kq+ d+++y++++          + ++ ++++i++++f+Ld+
  gene781|gene781|rna781|rna781   9 DQY-VNLDKTLYSGQIFSFQKTGENEDTGMVEGFLTTFKQDGDHIYYKIFN----------YKESVDYQTIFSRFFTLDL 77 
                                    444.9*****************8888*************************..........78999************** PP

                                    -HHHHHHHHTT.SHHHH..................HHHCCTTT-------HHHH CS
                          OGG_N  85 dleelykewskkdplfk..................ksadkftGiRllrqdpwEc 120
                                    +++++ kew+ k   +k                  + + k tG+Rllr d+ E+
  gene781|gene781|rna781|rna781  78 NYKKITKEWNDKL--LKcenevydenrlnnglctlRPF-KETGLRLLRCDLKET 128
                                    *********7644..33447777888888999885555.689********9998 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.92
                                    TEEEEEEEET.TEEEEE CS
                          OGG_N  37 drvveLkqee.ddllyr 52 
                                     r++++kq++ ++  y 
  gene781|gene781|rna781|rna781 256 SRIFSIKQTKlNKRTYV 272
                                    56777776544333332 PP

>> HhH-GPD  HhH-GPD superfamily base excision DNA repair protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       3.7   1.3e+04      73      86 ..      73      86 ..      66      94 .. 0.53
   2 !   42.1   0.0   2.7e-14   9.7e-11       2      98 ..     131     270 ..     130     282 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 3.7
                                   -TTSHHHHHHHHHH CS
                                   xxxxxxxxxxxxxx RF
                        HhH-GPD 73 ivvDvhvrrilkrl 86
                                   +  D++ ++i k +
  gene781|gene781|rna781|rna781 73 FTLDLNYKKITKEW 86
                                   34444444444444 PP

  == domain 2  score: 42.1 bits;  conditional E-value: 2.7e-14
                                    HHHHHTTS-HHHHHHHHHHHHHHHS............HCSHHHHHHSHHHHHHHHHTTSTTHHHHHHHHHHHHHHHH... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxx............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx... RF
                        HhH-GPD   2 sailsqqtsderanriierlferfg............fptpedladadeekLrelirelGfyrrKakyikelArilv... 66 
                                    s+i+s++++++r+++++  lf++ +            fp+p++l d +   Lre     Gf+ ++a+yi ++A+++    
  gene781|gene781|rna781|rna781 131 SFICSANNNIKRITKMVLVLFSLGKyittindknfyeFPDPDQLCDKE-LFLRES----GFG-YRASYIVKTAQQMKmlk 204
                                    89*********************66*9*99999999999999998855.458888....***.***************** PP

                                    ...................................S-SSS--TTSHHHHHHHHHHTTSSSSTTHHHH CS
                                    ...................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        HhH-GPD  67 ...................................gkpdvlivvDvhvrrilkrlrsikekktkkkv 98 
                                                                       ++   +++ D+h+ ++++r++sik++k  k +
  gene781|gene781|rna781|rna781 205 ysqlynldyqhafemlneyngisykvadcvcllglHFHS-VVPIDTHIFKVASRIFSIKQTKLNKRT 270
                                    **********************************85555.5555****************9666655 PP

>> DUF2192  Uncharacterized protein conserved in archaea (DUF2192)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.1   0.1    0.0019       6.8      75     138 ..      64     134 ..      58     158 .. 0.73
   2 !    8.9   0.0   0.00028         1     194     227 ..     235     268 ..     191     269 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0019
                        DUF2192  75 elkelfdkifsvEekleealeiilsk......kkeeavekvkevl..gkidenkvarvlrlvltkvvlgfad 138
                                    +++ +f++ f+ + +++++++   +k      +  ++ +  +  l   +  +++  r+lr  l +++++f+ 
  gene781|gene781|rna781|rna781  64 DYQTIFSRFFTLDLNYKKITKEWNDKllkcenEVYDENRLNNG-LctLRPFKETGLRLLRCDLKETIFSFIC 134
                                    89999*************9998888766544322222222222.2355677999****************84 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00028
                        DUF2192 194 lalrlgiekalPsdeyiaeiakevfkvpkkvlkk 227
                                      l l ++ ++P d+ i ++a+++f +++  l+k
  gene781|gene781|rna781|rna781 235 CLLGLHFHSVVPIDTHIFKVASRIFSIKQTKLNK 268
                                    445678899********************99986 PP

>> MA-Mit  Mycoplasma arthritidis-derived mitogen
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.8       0.2   7.2e+02      38      89 ..      30      79 ..      21     101 .. 0.63
   2 ?   14.3   0.3   6.1e-06     0.022      52      88 ..     207     244 ..     188     293 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.2
                         MA-Mit 38 nknektkevlklfklklnefyrhafnileeyeglekydeifkmmflklkvvl 89
                                    +ne+t   ++ f +   +   h +  + +y+   +y+ if  +f  l++ +
  gene781|gene781|rna781|rna781 30 GENEDTGM-VEGFLTTFKQDGDHIYYKIFNYKESVDYQTIFSRFF-TLDLNY 79
                                   55555543.344545555555566555566777888999997655.444444 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 6.1e-06
                         MA-Mit  52 lklnefyrhafnileeyegle.kydeifkmmflklkvv 88 
                                       n  y+haf++l+ey+g+  k  +   ++ l+++ v
  gene781|gene781|rna781|rna781 207 QLYNLDYQHAFEMLNEYNGISyKVADCVCLLGLHFHSV 244
                                    335777*************9635567666666666555 PP

>> DUF2400  Protein of unknown function (DUF2400)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.63   2.3e+03      73      89 ..      58      74 ..      23     148 .. 0.57
   2 ?   -2.7   0.0       1.4   4.9e+03      31      68 ..     191     227 ..     185     233 .. 0.52
   3 ?   11.6   0.0   5.5e-05       0.2     172     210 ..     244     282 ..     241     284 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.63
                        DUF2400 73 nsedllallkalkelle 89
                                   n+++ + + ++++++ +
  gene781|gene781|rna781|rna781 58 NYKESVDYQTIFSRFFT 74
                                   33333333222222222 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.4
                        DUF2400  31 kqiikkleellelmdkspydfvleeeeekdlkelekfk 68 
                                    + i+k+++++  l  ++ y+   ++ +e  l+e++++ 
  gene781|gene781|rna781|rna781 191 SYIVKTAQQMKMLKYSQLYNLDYQHAFE-MLNEYNGIS 227
                                    4566666666444444555555555533.445555555 PP

  == domain 3  score: 11.6 bits;  conditional E-value: 5.5e-05
                        DUF2400 172 iiPlDvHvarvarklgllkrkqadlkaaleltealrkld 210
                                    ++P+D+H+++va+++  +k+++ + ++ +++ +++++++
  gene781|gene781|rna781|rna781 244 VVPIDTHIFKVASRIFSIKQTKLNKRTYVNIRRQFQEFF 282
                                    69*********************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (308 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       680  (0.0379274); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1952.72
//
Query:       gene782|gene782|rna782|rna782  [L=483]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    8.2e-14   51.5   1.7    1.3e-13   50.8   1.7    1.4  1  DNA_pol_E_B  DNA polymerase alpha/epsilon subunit B


Domain annotation for each model (and alignments):
>> DNA_pol_E_B  DNA polymerase alpha/epsilon subunit B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.8   1.7   7.5e-18   1.3e-13       3     210 ..     202     435 ..     200     436 .. 0.82

  Alignments for each domain:
  == domain 1  score: 50.8 bits;  conditional E-value: 7.5e-18
                                    EEES--S-TT---.......-HHHHHHHHHHH.HTT--SEEEEES-SSBTTSHHHHHT---S--SSHHHHHHHHTHHHHT CS
                    DNA_pol_E_B   3 ivsglnldndnrs.......leaLrkiLqgyapeesppdvlilaGnfvdaahkaiasskvstdekkenfdalalllsile 75 
                                    ++sg++ +n + +       ++ L   L+++       + l+++G+f++++  ++    +  d ++ +  + a++ ++++
  gene782|gene782|rna782|rna782 202 FISGPFNNNVKPDeinstdiYDRLFLSLDSIM--TIDASYLVVLGPFIESRFLNS----CL-DLERVKDIFMAKMNTWIN 274
                                    55666555433334444444555555555555..555677999999999555544....22.345555566666666665 PP

                                    TS-TTSEEEEE--TTBTT-S-SBSB----TTTTT--TTT...EEE--BSEEEEETTEEEEE--S-HHHH---EEESHHHH CS
                    DNA_pol_E_B  76 sllekttvvlvPgpnDpanstvlPqqPlprlllsrikrvfkelklvtNPsrielnsvevvltsddivkdlkreslkesnt 155
                                    + ++  +++ vP+++D+++  ++P +++++       +++ ++++++NP+++ + +v + +++ di+ +++ +++ ++ +
  gene782|gene782|rna782|rna782 275 K-KPFRKIITVPSTEDVHTLGMYPCASIDDG------QNA-SFINLSNPTQFYIGDVLFSVCTYDILLHMSSTEIFFDIN 346
                                    5.478899********************776......333.49***********************************99 PP

                                    ..................................HS-HHHHHHHHHHHHTBS---SS--B-GGGGGGGB-GGG---SEEE CS
                    DNA_pol_E_B 156 ..................................dverlrklvktildqrhlaPlaptlrpvswdkddalvleplPdvlv 201
                                                                      +++r ++l+ +++ qr++ P +p    vs++  + + ++  Pd ++
  gene782|gene782|rna782|rna782 347 envslpeseishrldnipkinpnsldsctpkvpkKSKRIERLSAHMIYQRSFLPCFPPRNIVSINRPECFDMNIAPDFFI 426
                                    9******************************************************************************* PP

                                    ---SS--EE CS
                    DNA_pol_E_B 202 lpdelpeFa 210
                                    + ++l+ F+
  gene782|gene782|rna782|rna782 427 ISSKLKTFI 435
                                    *****9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (483 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       499  (0.027832); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 3418.40
//
Query:       gene783|gene783|rna783|rna783  [L=200]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.9e-39  135.0   0.0    2.4e-39  134.7   0.0    1.1  1  Rib_5-P_isom_A  Ribose 5-phosphate isomerase A (phosphoribois
     0.0023   17.9   0.3       0.42   10.5   0.0    2.1  2  DeoRC           DeoR C terminal sensor domain
  ------ inclusion threshold ------
      0.025   13.7   0.0      0.037   13.2   0.0    1.2  1  Sugar-bind      Putative sugar-binding domain


Domain annotation for each model (and alignments):
>> Rib_5-P_isom_A  Ribose 5-phosphate isomerase A (phosphoriboisomerase A)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  134.7   0.0   4.1e-43   2.4e-39       2     161 ..      38     190 ..      37     197 .. 0.96

  Alignments for each domain:
  == domain 1  score: 134.7 bits;  conditional E-value: 4.1e-43
                                    EEESSHHHHHHHHHTT--BE-GGCCSSEEEEEE--SEEETTS-EE--TTS-HHHHHHHHHTEEEEEEEEEGGGBESSTTS CS
                 Rib_5-P_isom_A   2 gvptSeqteelaeelgipllsldeveeidlaiDGaDevdedlnliKGgGgallrEKivaaaakkfiviadesKlveklgk 81 
                                    +vp+S q+  l++++++++++l+++e++d+++D aD +d+d nliKG+Ggall+EK++ +++k+ ++++d++K+ +++++
  gene783|gene783|rna783|rna783  38 FVPSSLQSFFLLKANNFRTQELQATETVDIYFDSADYFDNDNNLIKGRGGALLNEKLLMSMSKHNVILVDDKKFKSDFDD 117
                                    7******************************************************************************* PP

                                    S-EEEEE-GGGHHHHHHHHHHTTT-EEEE-TETTTTEE-B-TTS-EEEEEESSSBSSSHHHHHHHHHTSTTEEEESEE-S CS
                 Rib_5-P_isom_A  82 fpvPveVlpfaleavarelekllggkpelReakgkdgpvvTdngnlilDvkfeekiedpeelekelksipGVvetGlFlg 161
                                      +P+e++  +l++v++ l+k    +  +Re  gk gpv+T++gnli+Dvk      d+ ++ k++k+i+GVve+GlFl+
  gene783|gene783|rna783|rna783 118 LFIPLEIIRSSLAHVKDVLRKH-DIDFCVREYIGKIGPVITEHGNLIVDVKY-----DL-KFLKSCKNIVGVVEHGLFLN 190
                                    ********************75.9********9*****************99.....44.68899*************97 PP

>> DeoRC  DeoR C terminal sensor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.7   0.1    0.0021        13      15      60 ..       7      52 ..       5      59 .. 0.84
   2 !   10.5   0.0   7.1e-05      0.42      91     142 ..      63     114 ..      53     127 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0021
                          DeoRC 15 eliedgdtifldaGtTtlelaraLaekknltvvTnslnvaeeLsek 60
                                   ++i d++ti +++G T+  ++++++ +++   v  sl+ +  L+++
  gene783|gene783|rna783|rna783  7 KYITDQKTIGIGTGNTIKTFISNIKTHNEKYFVPSSLQSFFLLKAN 52
                                   5799**********************99888877777777666665 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 7.1e-05
                          DeoRC  91 fnvdkaflgangidaegglttsdeeeaevkralieaarrvillaDssKfgkr 142
                                     +vd+ f +a+ +d++++l++        ++ l++++++ ++l+D +Kf++ 
  gene783|gene783|rna783|rna783  63 ETVDIYFDSADYFDNDNNLIKGRGGALLNEKLLMSMSKHNVILVDDKKFKSD 114
                                    57999999****************9999*********************875 PP

>> Sugar-bind  Putative sugar-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   6.2e-06     0.037      44      78 ..       3      35 ..       1      42 [. 0.82

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 6.2e-06
                                   HHHHHH--TTEEEEE-SSHHHHHHHHHTHHCCHTC CS
                     Sugar-bind 44 qllesllkdgdvvgvgwGrtlsavaealtpkslrd 78
                                   +++++++ d++++g+g+G+t+++++ +++   +++
  gene783|gene783|rna783|rna783  3 NIFDKYITDQKTIGIGTGNTIKTFISNIKT--HNE 35
                                   568899********************9987..344 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       573  (0.0319594); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1457.80
//
Query:       gene784|gene784|rna784|rna784  [L=290]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    7.8e-07   28.8   2.1    0.00072   19.1   0.8    2.5  2  UCH          Ubiquitin carboxyl-terminal hydrolase
     0.0034   17.7   1.0     0.0092   16.2   1.0    1.7  1  Sigma_reg_N  Sigma factor regulator N-terminal


Domain annotation for each model (and alignments):
>> UCH  Ubiquitin carboxyl-terminal hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.8   8.1e-08   0.00072       6     116 ..      50     151 ..      45     206 .. 0.68
   2 !    8.9   0.1   0.00011      0.97     202     224 ..     233     255 ..     171     285 .. 0.71

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 8.1e-08
                                    SSSTHHHHHHHHHHHTSHHHHHHHHTCHHCCSSTCCCCC-.TT.TTS.TTHHHHHHHHHHHHHH....SH-CCEE--HHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxx RF
                            UCH   6 lGntCymnsvlQcLfsipelrdyllsleevkkesrnkkelnesnplgkkgelakalkdlfkell....kskskavsPkkl 81 
                                     G  C++ svlQ+L+++++ + +l ++  v++ ++               ++   lk++ k++      s + +   ++l
  gene784|gene784|rna784|rna784  50 NGVDCFIISVLQALYNLKNYKLFLDEI--VSSGNN---------------NIESILKSIHKDMEartdSSMDISAYRNRL 112
                                    6899**************888777773..111111...............255566666666664433333334444566 PP

                                    HHHHHHHSGG....GTSSSTCEHHHHHHHHHHHHHHHHC CS
                                    xxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxx RF
                            UCH  82 kktlsklaks....fsgykqqDaqEflaflLdqlhedln 116
                                    ++ +++ +++    +s ++q+Da Efl+  L+++ ++  
  gene784|gene784|rna784|rna784 113 LALIRSNSSNtgitLSVNEQNDADEFLTGALKTITNKYI 151
                                    6666666655566699***************99988765 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00011
                                    EEEEEEEEEESCTTSEEEEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxx RF
                            UCH 202 YeLiavvvHsGslssGHYvayik 224
                                    + L + v+++Gs +sGHY+a++k
  gene784|gene784|rna784|rna784 233 FILRSGVYYTGSGGSGHYFAICK 255
                                    789999***************99 PP

>> Sigma_reg_N  Sigma factor regulator N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   1.0     1e-06    0.0092       7      40 ..       3      38 ..       2      49 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1e-06
                    Sigma_reg_N  7 akrksilrivlislivlllifvilvvtllyl..aek 40
                                   ++r++il +++i+++v++++ v +++t++y   + k
  gene784|gene784|rna784|rna784  3 GRRRNILITITIAFLVAITVAVCIFLTIRYTtkKAK 38
                                   79****************************944444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (290 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1119  (0.0624129); expected 358.6 (0.02)
Passed bias filter:                      712  (0.0397122); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.21s 00:00:00.70 Elapsed: 00:00:00.37
# Mc/sec: 2347.89
//
Query:       gene785|gene785|rna785|rna785  [L=298]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      0.002   18.3  29.9       0.15   12.2  10.4    2.7  2  EamA            EamA-like transporter family
  ------ inclusion threshold ------
        5.8    7.6  11.7       0.58   10.8   0.5    3.5  4  Nucleos_tra2_N  Na+ dependent nucleoside transporter N-termin


Domain annotation for each model (and alignments):
>> EamA  EamA-like transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2  10.4   1.7e-05      0.15      49     134 ..      49     129 ..       1     132 [. 0.73
   2 !   11.4  11.4     3e-05      0.27      22     136 ..     165     280 ..     145     281 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.7e-05
                           EamA  49 allkegklaklslkdwllllllgllgtvlafllffy..alkktsasnaslitslePvftlilsvlllgekltlkqllgiv 126
                                    ++++ +k+   ++    + ++++ll+++l+   +++   +kk+++ +a+++ + + +f+ ils ++ + ++t+  +++++
  gene785|gene785|rna785|rna785  49 SFMFVKKR---KY----YDFYICLLSVMLVVQSYYSwmNIKKSKVIEAGIAETSSIIFMCILSRIFMKTRITKPRVFAML 121
                                    33333333...22....22566666555555443331158999999********************************** PP

                           EamA 127 lillGvll 134
                                    +  +G+l+
  gene785|gene785|rna785|rna785 122 ITSFGLLM 129
                                    **999986 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 3e-05
                           EamA  22 killrkvspltltfvrfliagillliiallkegklaklslkdwlll..lllgllgtvlafllffyalkktsasnaslits 99 
                                    ki  + +s ++++f + +++ il ++++l++   +  ++l+ +l    +++ + +  +  l+ f ++    + + +++ +
  gene785|gene785|rna785|rna785 165 KIKAKITSIWSFFFTSNFFCLILSSFVLLYELLDK-GIDLRRVLKDikVYIIISSESFSILFAFALIYMFLPVERTFLKL 243
                                    44445556667888888889998888888888877.77777754433678888888888899999999999********* PP

                           EamA 100 lePvftlilsvlllgekltlkqllgivlillGvllil 136
                                    ++ + + i+ +++l ++l+++++l++v++ lGv++ +
  gene785|gene785|rna785|rna785 244 VINITAGIFESAVLDKNLKIWDVLSLVIVSLGVFVYN 280
                                    *********************************9975 PP

>> Nucleos_tra2_N  Na+ dependent nucleoside transporter N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.2      0.26   2.3e+03       5      32 ..      44      73 ..      42      90 .. 0.68
   2 ?   10.8   0.5   6.4e-05      0.58       8      40 ..     128     160 ..     118     202 .. 0.81
   3 ?    2.9   0.4      0.02   1.7e+02      29      60 ..     221     252 ..     207     256 .. 0.76
   4 ?   -3.7   0.0         2   1.8e+04      34      48 ..     273     287 ..     269     291 .. 0.68

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.26
                                   HHHHHHHHT-S-GGG--HH..HHHHHHHHH CS
                 Nucleos_tra2_N  5 vllliawllSenrkainwr..tVigglllQ 32
                                   +++++ +++ ++rk   +   +  ++l++Q
  gene785|gene785|rna785|rna785 44 IIVVVSFMFVKKRKYYDFYicLLSVMLVVQ 73
                                   688888999999987544300344555555 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 6.4e-05
                                    HHHHHT-S-GGG--HHHHHHHHHHHHHHHHHHH CS
                 Nucleos_tra2_N   8 liawllSenrkainwrtVigglllQfvlAlfvl 40 
                                    l+ +l+S++ ++in++tV+g +  +f++ ++ +
  gene785|gene785|rna785|rna785 128 LMPILFSKEETNINFSTVAGHVCCHFIFCIINI 160
                                    55689***********************99744 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.02
                                    HHHHHHHHHHHHTSHHHHHHHHHHHHHHHHHH CS
                 Nucleos_tra2_N  29 lllQfvlAlfvlktpagrdvfkalsdlvqall 60 
                                    + + f++Al+ + +p+ r+++k + ++ + ++
  gene785|gene785|rna785|rna785 221 FSILFAFALIYMFLPVERTFLKLVINITAGIF 252
                                    4566889999999********99987766665 PP

  == domain 4  score: -3.7 bits;  conditional E-value: 2
                                    HHHHHHHTSHHHHHH CS
                 Nucleos_tra2_N  34 vlAlfvlktpagrdv 48 
                                     l++fv +++  r  
  gene785|gene785|rna785|rna785 273 SLGVFVYNIEYIRRK 287
                                    577888777776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (298 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1116  (0.0622455); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.39
# Mc/sec: 2290.28
//
Query:       gene786|gene786|rna786|rna786  [L=671]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.4e-67  225.4   1.4      8e-67  224.6   1.4    1.4  1  MCM              MCM P-loop domain
    1.7e-26   92.5   0.0    3.5e-26   91.5   0.0    1.5  1  MCM_OB           MCM OB domain
    3.6e-20   72.2   1.1    4.3e-19   68.7   0.3    2.5  2  MCM_lid          MCM AAA-lid domain
      7e-07   28.8   0.1    3.1e-06   26.7   0.0    2.0  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    0.00023   21.2   0.1    0.00074   19.5   0.1    2.0  1  AAA_5            AAA domain (dynein-related subfamily)
    0.00078   19.9   0.0     0.0043   17.5   0.1    2.3  2  AAA              ATPase family associated with various cellul
  ------ inclusion threshold ------
       0.02   14.8   0.1      0.083   12.8   0.1    2.1  2  AAA_3            ATPase family associated with various cellul
      0.078   13.6   0.0       0.38   11.4   0.0    2.2  1  MCM_N            MCM N-terminal domain
      0.081   12.9   0.0       0.22   11.5   0.0    1.8  1  HTH_Crp_2        Crp-like helix-turn-helix domain
       0.14   11.9   0.0       0.93    9.2   0.0    2.2  2  Sigma54_activat  Sigma-54 interaction domain


Domain annotation for each model (and alignments):
>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  224.6   1.4   4.5e-70     8e-67      15     223 ..     283     479 ..     269     480 .. 0.92

  Alignments for each domain:
  == domain 1  score: 224.6 bits;  conditional E-value: 4.5e-70
                                    HHHHHHHSSTTSSS-HHHHHHHHHHHH---EBBBSSSSBBCSS-EEEEEESSTSTHHHHHHHHHHHSSSEEEEESSSSSS CS
                            MCM  15 ieklvksiapsiyghedvkkaillqlfggvkkkledktklrgdinvllvgdpgtaKsqlLkyveklapravytsgkgssa 94 
                                     e+ ++++ap i+ +  +kkaillq++g+ ++       +r +in+ll+gdp+taKsq+L++v  ++ +a+ tsgkgs++
  gene786|gene786|rna786|rna786 283 SENALEYVAPFIFISPLIKKAILLQMIGSENE------VCRKSINLLLLGDPSTAKSQILRFVI-NTMNAISTSGKGSTG 355
                                    5677899*********************9984......4799**********************.56789********** PP

                                    SHSSSEEEEESSSSSEEEEETHHHHTTTSEEEEESGGGSTCHHHHHHHHHHHHSEEEEESSSCEEEEE--EEEEEEE--S CS
                            MCM  95 agLtaavvrdeetgefvleaGalvladkGvcciDefdkmkeedrsalhEamEqqtisiaKaGivatLnartsvlaAanpk 174
                                    +gLta++v d++++   leaGa+vlad+ ++ciDefdk++ +d+++lhE+mEqq+isi+KaGi++tLnart+vlaAanp+
  gene786|gene786|rna786|rna786 356 VGLTASIVSDKNER--RLEAGAMVLADNSIICIDEFDKINYNDSVVLHEVMEQQSISINKAGIHVTLNARTAVLAAANPV 433
                                    ********988665..89************************************************************** PP

                                    SSSCCTTS-HHHHSSSSHHHHHHSSEEEEE-SSTTHHHHHHHHHHHHHH CS
                            MCM 175 agrydkkksvaeninlsaalLsrFDlifvllDkvdeekDeelaehivsl 223
                                    +g++ +  s++++++++++lLsrFDlif+++D+   + D+++a++++ +
  gene786|gene786|rna786|rna786 434 YGNFVD-DSLEKQVKIPESLLSRFDLIFLIVDD--GSFDSQIADQVLCN 479
                                    ****76.6899********************95..67899999999865 PP

>> MCM_OB  MCM OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.5   0.0   1.9e-29   3.5e-26       4     124 ..      79     205 ..      76     207 .. 0.87

  Alignments for each domain:
  == domain 1  score: 91.5 bits;  conditional E-value: 1.9e-29
                                    G--GGGTTSEEEEEEEEEEE---EEEEEEEEEEETTT-.-EEE.S---...........-SB-..TTT-HHH-EEE-GGG CS
                         MCM_OB   4 dlrsehigklvkveGivtrasevkpklkkavfeckkcgktvev.elee...........PrkCeekeCeskdpfkletek 71 
                                    +++s+ +gk+vkveGi+t+ s++kpkl+k+v+e +++ +++e+ + ++           P+        +++p+++e   
  gene786|gene786|rna786|rna786  79 SITSDFLGKMVKVEGIITSLSNIKPKLRKSVHEQHNTFYSKEYrDATTlsalpltntviPQ------TLKNEPLNFEYGL 152
                                    578999*******************************998885333336678443333344......346789999999* PP

                                    SEEEEEEEEEEE-------------EEEEEEEGGGTT---TT-EEEEEEEEEE CS
                         MCM_OB  72 skfvdfqklklQEspeevpaGelPrslevileddlvdkvkPGdrvevtGiyra 124
                                    s+++d+q+ ++QE+pe+  +G +Prs++vil+ddl+d++kPGdrv +tG+y++
  gene786|gene786|rna786|rna786 153 STYIDTQTATIQEMPENTKPGAMPRSMNVILYDDLTDSLKPGDRVVLTGVYKT 205
                                    ***************************************************97 PP

>> MCM_lid  MCM AAA-lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0      0.27   4.9e+02      10      35 ..      97     123 ..      94     139 .. 0.75
   2 !   68.7   0.3   2.4e-22   4.3e-19       3      86 ..     494     571 ..     492     572 .. 0.95

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.27
                                    HHHTT--BETCHHHHHHHHHHHH.HHH CS
                        MCM_lid  10 arekikPklseeakeklseaYve.lRk 35 
                                    + ++ikPkl ++++e+ +++Y +  R+
  gene786|gene786|rna786|rna786  97 SLSNIKPKLRKSVHEQHNTFYSKeYRD 123
                                    5579*****************761454 PP

  == domain 2  score: 68.7 bits;  conditional E-value: 2.4e-22
                                    HHHHHHHHHHTT--BETCHHHHHHHHHHHHHHHHHTSSTSSSST--HHHHHHHHHHHHHHHHHHTSSSE-HHHHHHHHHH CS
                        MCM_lid   3 lrkYiayarekikPklseeakeklseaYvelRkeeedskrksipitvRqLesliRLseAlAklrlsevvteedveeairl 82 
                                    lr++i  ++ k+kP++ +e ++ + ++YvelR+++     +++p+t+R L+sliRLs+A A+ r s++++e dv+eai +
  gene786|gene786|rna786|rna786 494 LRRFIFECK-KYKPRMRKECAHLIIDYYVELRRSK-----TRFPVTPRLLDSLIRLSNANARFRQSDTIDEIDVKEAITM 567
                                    9********.***********************66.....36************************************** PP

                                    HHHH CS
                        MCM_lid  83 lkes 86 
                                    ++++
  gene786|gene786|rna786|rna786 568 VEHC 571
                                    9986 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       0.6   1.1e+03      24      49 ..     321     346 ..     318     371 .. 0.79
   2 !   26.7   0.0   1.7e-09   3.1e-06      96     167 ..     370     441 ..     357     461 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.6
                   Mg_chelatase  24 nlllvGppGsGKtmlakrlpsllppl 49 
                                    nlll+G p + K+ + + + + + ++
  gene786|gene786|rna786|rna786 321 NLLLLGDPSTAKSQILRFVINTMNAI 346
                                    89***********9988776666555 PP

  == domain 2  score: 26.7 bits;  conditional E-value: 1.7e-09
                   Mg_chelatase  96 kpkpGeislahnGvLfLDElpefkrkvlevLRePledgevtisrakakvefparfqlvaamNpcpcgklkdk 167
                                    + + G++ la n ++ +DE+ +++ +   vL e +e+++++i++a  +v+  ar+ ++aa+Np     ++d+
  gene786|gene786|rna786|rna786 370 RLEAGAMVLADNSIICIDEFDKINYNDSVVLHEVMEQQSISINKAGIHVTLNARTAVLAAANPVYGNFVDDS 441
                                    6789***********************************************************876665555 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.1   4.1e-07   0.00074       1     125 [.     321     443 ..     321     456 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 4.1e-07
                                    EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------G-SEEEEESGGG--HH CS
                          AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraaregeilvlDEveraese 80 
                                    ++lL+G+p t+Ks++ + +   +     +    ++ t   l+ ++  ++ +++l+ +++v      +i+++DE+++++ +
  gene786|gene786|rna786|rna786 321 NLLLLGDPSTAKSQILRFVINTM---NAISTSGKGSTGVGLTASIVSDKNERRLEAGAMV--LADNSIICIDEFDKINYN 395
                                    68999999999999876555555...5566677777888899999987888889999999..77899************* PP

                                    HHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--......... CS
                          AAA_5  81 vlnsLlslleerrllleeggelvkaknddllerfrviatanpld........r 125
                                       +L+ ++e++ +++++ g  v  ++      + v+a+anp++         
  gene786|gene786|rna786|rna786 396 DSVVLHEVMEQQSISINKAGIHVTLNAR-----TAVLAAANPVYgnfvddslE 443
                                    ******************9999999886.....8*********9544333332 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0         3   5.4e+03      36      67 ..     153     187 ..     127     194 .. 0.78
   2 !   17.5   0.1   2.4e-06    0.0043       1     110 [.     322     431 ..     322     462 .. 0.69

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 3
                                    SSSTTHHHHHHHHHHHHHHHTS...TSEEEEEETG CS
                            AAA  36 skyvgesekkirelfkeakeka...kpsilfiDEi 67 
                                    s y+  + + i+e+ ++ k  a   +  +++ D++
  gene786|gene786|rna786|rna786 153 STYIDTQTATIQEMPENTKPGAmprSMNVILYDDL 187
                                    45899999999999999999999865589998886 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 2.4e-06
                                    EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHH.HHHTS....TSEEEEEETGGGHHHHHT CS
                            AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfke.akeka....kpsilfiDEidalaksrs 75 
                                    +ll G p t K+ + + v++++++  +++sg+  +   vg +++ +++  ++ +++ a    + si+ iDE+d+++ ++ 
  gene786|gene786|rna786|rna786 322 LLLLGDPSTAKSQILRFVINTMNA--ISTSGKGST--GVGLTASIVSDKNERrLEAGAmvlaDNSIICIDEFDKINYND- 396
                                    699******************866..666666666..5666666666665552333336664569**********9999. PP

                                    TCCCHHHHHHHHHHHHHHHHTTTS..........SSTEEEEEEES CS
                            AAA  76 gseseeeervvnqLlteldgvkkk..........eskvivigatn 110
                                                +L +++++++ +          ++++ v++a+n
  gene786|gene786|rna786|rna786 397 ----------SVVLHEVMEQQSISinkagihvtlNARTAVLAAAN 431
                                    ..........33333333333333333344455566677777777 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       2.4   4.3e+03      26      46 ..      69      89 ..      63      93 .. 0.83
   2 ?   12.8   0.1   4.6e-05     0.083      51     114 ..     366     434 ..     322     458 .. 0.72

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 2.4
                          AAA_3 26 efkriqftpdllPsdilGtev 46
                                   +f   q tp  + sd lG++v
  gene786|gene786|rna786|rna786 69 SFGEYQHTPSSITSDFLGKMV 89
                                   6778899**********9887 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 4.6e-05
                          AAA_3  51 ekefefkkGpvf...anllladeinrappktqsalleameerqvtvege..thklpepflvlatqnPie 114
                                    ++e ++++G+++   ++++  de ++ +      l e+me++ ++++++    +l+    vla+ nP+ 
  gene786|gene786|rna786|rna786 366 KNERRLEAGAMVladNSIICIDEFDKINYNDSVVLHEVMEQQSISINKAgiHVTLNARTAVLAAANPVY 434
                                    334445555543222468999*********999************987622568999**********94 PP

>> MCM_N  MCM N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00021      0.38      34      70 ..      22      58 ..       8      81 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00021
                          MCM_N 34 rekttLevdlddLaafdeeLaeailenpkeylpllee 70
                                   r  ++++ +l+d++  d+eL+ +i+e+p  ++p+ e 
  gene786|gene786|rna786|rna786 22 RTDERITFSLNDIRRKDRELSAKIVEDPISFIPFVEH 58
                                   55678999*************************9885 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00012      0.22      22      60 ..     631     670 ..     611     671 .] 0.84

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00012
                                    HHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE.ETEEEEES CS
                      HTH_Crp_2  22 ltqeelAsmlGltretvsrilseLkreglis.rgrriril 60 
                                    l+  + A+++ l  e ++ril+eL  e +i  +g +i+ l
  gene786|gene786|rna786|rna786 631 LSLNDVAARCELPLEEITRILTELDAEDIIMfKGETIIFL 670
                                    78899*************************9777447765 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.51   9.1e+02       8      44 ..     305     341 ..     299     350 .. 0.80
   2 ?    9.2   0.0   0.00052      0.93      85     143 ..     372     432 ..     364     449 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.51
                                    HHHHHHHHHHHCTSSS-EEEECSTTSSHHHHHHHHHH CS
                Sigma54_activat   8 lkelleqikkvaktdlsvlitGesGtGKellaraihe 44 
                                    l +++ + ++v ++++++l++G+  t K+ + r + +
  gene786|gene786|rna786|rna786 305 LLQMIGSENEVCRKSINLLLLGDPSTAKSQILRFVIN 341
                                    56777778899999**************998877655 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00052
                                    BEHHHHHTTTSEEEEETGGGS-HHHHHHHHHHHHHSE..EESBTSSSEEE--EEEEEEESS CS
                Sigma54_activat  85 kkGlfekadgGtlfLDeigelplelQekLlrvlqege..vervGsskeikvdvriiaatne 143
                                    ++G++  ad++++ +De  +++++  + L +v+++++  +++ G + + ++ + ++aa+n 
  gene786|gene786|rna786|rna786 372 EAGAMVLADNSIICIDEFDKINYNDSVVLHEVMEQQSisINKAGIHVTLNARTAVLAAANP 432
                                    5699*****************************9997225899999999999999999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (671 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       827  (0.0461264); expected 358.6 (0.02)
Passed bias filter:                      602  (0.0335769); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.65u 0.31s 00:00:00.96 Elapsed: 00:00:00.45
# Mc/sec: 4448.66
//
Query:       gene787|gene787|rna787|rna787  [L=110]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.2e-11   42.7   2.3    1.4e-10   41.4   2.2    1.7  1  Dynein_light     Dynein light chain type 1
  ------ inclusion threshold ------
      0.028   13.8   1.5      0.049   13.0   0.1    1.8  2  AAA-ATPase_like  Predicted AAA-ATPase


Domain annotation for each model (and alignments):
>> Dynein_light  Dynein light chain type 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.4   2.2   1.5e-14   1.4e-10       6      86 .]      26     104 ..       4     104 .. 0.83

  Alignments for each domain:
  == domain 1  score: 41.4 bits;  conditional E-value: 1.5e-14
                                    EEEE-HHHHHHHHHHHHHHHHH-SSHH...HHHHHHHHHHHHHH-S-EEEEEEEEEEEEEEEETTEEEEEEET.TEEEEE CS
                   Dynein_light   6 eadmseemqeeaielakealekfkkeke.kdiaayikkeldkkygptWhciVgksfgssvthekghfiyfyig.klaill 83 
                                    +++++    + ++e++ + ++k+k +++    ++++k++ld+++++ W++++g++f+  + + ++++i++ ++ ++++++
  gene787|gene787|rna787|rna787  26 KSTCD----QNVLEHCLNIIDKYKIKDSsPTFCKRMKDSLDSTFNKEWNVFIGGHFSGMCGFVENTYIELMLNdNMRMVI 101
                                    44444....5555555666666666555579*****************************************76****** PP

                                    EE- CS
                   Dynein_light  84 fKt 86 
                                    f++
  gene787|gene787|rna787|rna787 102 FQS 104
                                    *86 PP

>> AAA-ATPase_like  Predicted AAA-ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.2     0.051   4.5e+02     115     148 ..      10      44 ..       1      49 [. 0.54
   2 ?   13.0   0.1   5.5e-06     0.049     194     235 ..      56      98 ..      52     109 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.051
                AAA-ATPase_like 115 kkkeekslakrlkelieraaek.tgkkvvvLiDEY 148
                                    +k  e++ +k+l++++++++ +   ++++ +iD Y
  gene787|gene787|rna787|rna787  10 TKAPEEEKKKHLAKVVKSTCDQnVLEHCLNIIDKY 44 
                                    33335555566666665554440455666677777 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 5.5e-06
                AAA-ATPase_like 194 vtkdsifSglnnlkdisldekysallGfteee.veellkeele 235
                                     +kds+ S +n+ +++ +  ++s ++Gf e+  +e +l++ ++
  gene787|gene787|rna787|rna787  56 RMKDSLDSTFNKEWNVFIGGHFSGMCGFVENTyIELMLNDNMR 98 
                                    5799************************987526666666654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1055  (0.0588432); expected 358.6 (0.02)
Passed bias filter:                      558  (0.0311228); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.32s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 706.93
//
Query:       gene788|gene788|rna788|rna788  [L=479]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    7.3e-14   51.5   7.5    7.3e-14   51.5   7.5    3.2  3  RINT1_TIP1  RINT-1 / TIP-1 family


Domain annotation for each model (and alignments):
>> RINT1_TIP1  RINT-1 / TIP-1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.5   7.5   4.1e-18   7.3e-14       8     117 ..      68     200 ..      61     235 .. 0.83
   2 ?   -0.2   0.6     0.019   3.4e+02     191     265 ..     235     311 ..     230     329 .. 0.60
   3 !    5.4   0.2   0.00041       7.3     365     417 ..     374     425 ..     354     462 .. 0.82

  Alignments for each domain:
  == domain 1  score: 51.5 bits;  conditional E-value: 4.1e-18
                     RINT1_TIP1   8 kplekrFrYHFsgdkqTnklskpewflefilklleknldflrenvqpilakkfrek......................id 65 
                                      +   F +HF ++k+Tn+l+kpew+++f+l+ l+k++ ++  + + +l++k  +                         
  gene788|gene788|rna788|rna788  68 AKIYDTFSFHFFTQKETNRLDKPEWYFKFLLDQLDKYKFVCACYDSVVLENKKSKInknvisqrlqegfleenelksnE- 146
                                    556678*******************************9999777777777655444899***************99633. PP

                     RINT1_TIP1  66 av..sefitaLlplvreKvasvleevl.sdpalLshlisellsfdkeLrekykYd 117
                                        +++i+ +  +v+ K+++  +  + ++ +lL h+ +e l f +eLreky+ +
  gene788|gene788|rna788|rna788 147 -RsmNSLIERIYSIVEIKLNELRKCKSgQKRNLLLHFTEEYLVFKRELREKYSVN 200
                                    .33699**************998776556667********************876 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.019
                     RINT1_TIP1 191 eryeplssfsy..klkflsdIqlelldqYherLkssleayeslt....stvgrtlqgetkeqqa...elegvkglerlck 261
                                    e y+++++ ++   ++++s  q +++++  ++++s   +y++++    s+vg+     +k  +     + g+ +l+++++
  gene788|gene788|rna788|rna788 235 ESYQKIYKENFflAFSYVSL-QNNIFNDLIDFISSLIVEYQEVFidkmSFVGKE----EK--RMlcfLVVGIDKLKNFLR 307
                                    56777777666334455666.999999999999999999998863333333332....22..222233445555555555 PP

                     RINT1_TIP1 262 iygs 265
                                    +  s
  gene788|gene788|rna788|rna788 308 LEES 311
                                    5554 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.00041
                     RINT1_TIP1 365 selvellnllkrlldfLekal.skalfrriwrelleklqdllweevllrnkFse 417
                                    ++lv+  + l++ ++f ++ l +++++ +    +++k++++++++++l+n+F +
  gene788|gene788|rna788|rna788 374 KSLVQSCSELSKIMTFYNEQLgPYKILTES--YIFDKIDNFIIDKIVLQNRFDS 425
                                    578889999999999999999677777664..59******************76 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (479 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1019  (0.0568353); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.41
# Mc/sec: 3492.73
//
Query:       gene789|gene789|rna789|rna789  [L=116]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
       0.78   10.8   3.8          8    7.6   0.2    2.4  2  RNase_J_C  Ribonuclease J C-terminal domain


Domain annotation for each model (and alignments):
>> RNase_J_C  Ribonuclease J C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.3     0.005        89      14      45 ..      25      57 ..      21      66 .. 0.81
   2 ?    7.6   0.2   0.00045         8      34      58 ..      70      94 ..      59      99 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.005
                      RNase_J_C 14 eseeLieeakkvvretieealee.kesdwnelk 45
                                   e+++L ++a++++ + +++ ++  +e + ++lk
  gene789|gene789|rna789|rna789 25 ENNHLYNSATEQIDKEVKRGMDRlNELEKEKLK 57
                                   889999999999999999988775666666666 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.00045
                      RNase_J_C 34 leekesdwnelkrkirealkkflyk 58
                                   +e k+++ ++l++kirea+ k+l++
  gene789|gene789|rna789|rna789 70 DEYKTAKKEDLREKIREAVVKYLNE 94
                                   4557788999************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2062  (0.115009); expected 358.6 (0.02)
Passed bias filter:                      527  (0.0293937); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 787.30
//
Query:       gene79|gene79|rna79|rna79  [L=166]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    4.2e-44  149.6   0.1    5.2e-44  149.3   0.1    1.0  1  UQ_con     Ubiquitin-conjugating enzyme
     0.0001   22.6   0.0    0.00014   22.1   0.0    1.3  1  RWD        RWD domain
    0.00012   21.8   0.0    0.00016   21.4   0.0    1.3  1  Prok-E2_B  Prokaryotic E2 family B
  ------ inclusion threshold ------
      0.013   15.3   0.3      0.026   14.4   0.3    1.4  1  UEV        UEV domain
      0.016   15.2   0.1      0.037   14.0   0.0    1.7  2  G-gamma    GGL domain


Domain annotation for each model (and alignments):
>> UQ_con  Ubiquitin-conjugating enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  149.3   0.1   1.5e-47   5.2e-44       2     139 ..      20     158 ..      19     159 .. 0.94

  Alignments for each domain:
  == domain 1  score: 149.3 bits;  conditional E-value: 1.5e-47
                                HHHHHH..HHHHSTTTTEEEEEEETTEECEEEEEEEB.TTSTTTTEEEEEEEE--TTTTTS--EEEESST-SCTTBETTSBB-C CS
                     UQ_con   2 lqkelk..elakkkpsgisaklvddenlfewkvlikgpedtpYeggvFklelefpedYPlkpPkvkfvtkifHPnvdksGevcl 83 
                                lq+e++  + ++k+ ++++ ++  d+n+few v +  pe+++Y+gg+F+l+++fp+dYP+kpP+v f t+i+HPn++++G++cl
  gene79|gene79|rna79|rna79  20 LQREANhpDANDKTLRCFEIATNPDDNIFEWYVRLRAPEESMYAGGIFNLKITFPTDYPFKPPSVVFLTRIYHPNINANGNICL 103
                                67888866677788888888888889********************************************************** PP

                                GGGSTTT--TTSHHHHHHHHHHHHHHS--TTS-SSHHHHHHHHHTHHHHHHHHHHH CS
                     UQ_con  84 diLkeekWspaltlesvllsiqsLlaepnpesplnkeaakllkkdreeykkkvkey 139
                                diL+e+ W+palt+++v++s++s l+epnp++pl  e+++l+ +d e+ykkkvkey
  gene79|gene79|rna79|rna79 104 DILRES-WTPALTVQKVIISLISWLDEPNPKDPLVPEIGRLYITDIEAYKKKVKEY 158
                                ****55.**********************************************998 PP

>> RWD  RWD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0     4e-08   0.00014      51     114 ..      63     129 ..      11     130 .. 0.76

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 4e-08
                                -CEEEEEEEEE-SSTTSS--EEEEEECCSS-HHHHHH..HHHHHHHHHHHT.TTS--CHHHHHHHHH CS
                                xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxx.xxxxxxxxxxxxxxx RF
                        RWD  51 kkpslkleiklpeeYPeeaPiislsstenlpkeqvks..leekleelaeen.lgepvifalidwlke 114
                                    ++l+i++p +YP ++P + + +    p+   +   + + l+e +      + vi +li+wl e
  gene79|gene79|rna79|rna79  63 AGGIFNLKITFPTDYPFKPPSVVFLTRIYHPNINANGniCLDILRESWTPAlTVQKVIISLISWLDE 129
                                45679***************888777773553333333378899999998899***********986 PP

>> Prok-E2_B  Prokaryotic E2 family B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   4.5e-08   0.00016      29     113 ..      60     136 ..      29     164 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 4.5e-08
                  Prok-E2_B  29 ssvktsggtvdlrlvypdsfpllppavflqdpeqlkllpHintfggaLClleeeldldewdpngsvadvleqlqqvLn.egisg 111
                                s +   gg+++l++ +p ++p+ pp+v+   +      p in  +g +Cl       ++w+p+ +v++v+ +l   L+  ++++
  gene79|gene79|rna79|rna79  60 SMY--AGGIFNLKITFPTDYPFKPPSVVFLTRI---YHPNINA-NGNICL---DILRESWTPALTVQKVIISLISWLDePNPKD 134
                                333..69*******************9887777...5788999.9*****...8999****************99999777776 PP

                  Prok-E2_B 112 de 113
                                  
  gene79|gene79|rna79|rna79 135 PL 136
                                65 PP

>> UEV  UEV domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.3   7.2e-06     0.026      52     117 ..      69     129 ..      59     135 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 7.2e-06
                                EEEE--TTTTTS--EEEE-GCC--TSGGGGGB-TTSBB--HHHHS--TTT--HHHHHHHHHH---- CS
                        UEV  52 iliwvlesyPveaPivyvkptksmvikknenvdaqGlvylpyLeeWkreksnlvslvqelaqafee 117
                                + i  + +yP+++P v+   +       + n++a+G++ l++L+e + ++ ++ +++ +l++   e
  gene79|gene79|rna79|rna79  69 LKITFPTDYPFKPPSVVFLTRI-----YHPNINANGNICLDILRESWTPALTVQKVIISLISWLDE 129
                                4567899*******98765443.....3569************87445588888877777765555 PP

>> G-gamma  GGL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0         2   7.1e+03       5      19 ..      11      25 ..       8      29 .. 0.67
   2 ?   14.0   0.0     1e-05     0.037      22      49 ..     113     141 ..     107     156 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 2
                    G-gamma  5 lklkreieqLkkeLk 19
                                +  +e+  L++e++
  gene79|gene79|rna79|rna79 11 RRIHKELLTLQREAN 25
                               566677777777765 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 1e-05
                    G-gamma  22 rikvSkAceelidYve..stkDpllpevwg 49 
                                 ++v k++ +li++ +  + kDpl+pe+ g
  gene79|gene79|rna79|rna79 113 ALTVQKVIISLISWLDepNPKDPLVPEI-G 141
                                67999**********************9.4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       469  (0.0261587); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 1348.11
//
Query:       gene790|gene790|rna790|rna790  [L=89]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.4e-14   51.2   0.9    8.5e-14   51.0   0.9    1.1  1  LSM       LSM domain
     0.0018   18.4   0.2     0.0028   17.7   0.2    1.3  1  DUF150_C  RimP C-terminal SH3 domain


Domain annotation for each model (and alignments):
>> LSM  LSM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.0   0.9   9.5e-18   8.5e-14       2      65 ..       4      71 ..       3      73 .. 0.94

  Alignments for each domain:
  == domain 1  score: 51.0 bits;  conditional E-value: 9.5e-18
                                   HHHHTTTSEEEEEETTSEEEEEEEEEEETTSEEEEEEEEEEETTET....EEEEEEEEEEEGGGEEEE CS
                            LSM  2 flkklinkkvtvelkngrelrGtLkgfDqfmNlvLedveetlkdkk....ekrklglvliRGnnivli 65
                                    +kk+++ +v vel + r + G+L ++D+f+N+vL++++e +k k+    e+r+lgl++ RG++++ i
  gene790|gene790|rna790|rna790  4 SFKKFLKCNVKVELEDKRSFTGNLLAVDEFLNIVLNETVEQRKYKNkkgyEIRNLGLCIFRGSKVIGI 71
                                   5799999**********************************999989*****************9866 PP

>> DUF150_C  RimP C-terminal SH3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.2   3.1e-07    0.0028       7      48 ..       5      43 ..       2      56 .. 0.71

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 3.1e-07
                       DUF150_C  7 FarflGelVkvklklpvegrkkftGkivevdeet.itlevdgk 48
                                   F++fl  +Vkv+l     +++ ftG +++vde   i+l  + +
  gene790|gene790|rna790|rna790  5 FKKFLKCNVKVELE----DKRSFTGNLLAVDEFLnIVLNETVE 43
                                   78888888888877....*************643366543333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       429  (0.0239277); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.22s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 648.77
//
Query:       gene791|gene791|rna791|rna791  [L=124]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00045   19.3   4.1     0.0005   19.1   4.1    1.0  1  CRT-like  CRT-like, chloroquine-resistance transporter-like
  ------ inclusion threshold ------
       0.16   12.1   0.0       0.21   11.8   0.0    1.1  1  DUF2236   Uncharacterized protein conserved in bacteria (DUF2


Domain annotation for each model (and alignments):
>> CRT-like  CRT-like, chloroquine-resistance transporter-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   4.1   5.6e-08    0.0005     104     212 ..      13     118 ..       2     123 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 5.6e-08
                       CRT-like 104 iipitllasllllkerysliqylGAlviilgvvvvlipsllgessegnklvfnllllisviPvalSnvykeiafkeveld 183
                                     i +t ++  ll  + y + ++ G l i +g++++      ++ + ++++++ ll+l+ +   a+  +y +  +++  + 
  gene791|gene791|rna791|rna791  13 RILFTYVIMRLLYDKIYGWDKIAGMLTISMGILISN---SDFSGNTSDEMLYVLLFLFGNFLNAVGLIYFDRKLRHHIVH 89 
                                    688999999999*********************653...44566677899****************************** PP

                       CRT-like 184 vlyLqawvalfqlligilllpvnalllkp 212
                                     +   +  ++  l++ +lllp++ l lk+
  gene791|gene791|rna791|rna791  90 FWNYMYTYSFTLLIFNVLLLPIELLYLKE 118
                                    **********************9986655 PP

>> DUF2236  Uncharacterized protein conserved in bacteria (DUF2236)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   2.3e-05      0.21      90     134 ..      55      97 ..      38      98 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.3e-05
                        DUF2236  90 npedllwvhatfsasflraygrtvgpltaeeeeayyhewrrvgrl 134
                                    + +++l+v++ ++  fl+a+g++   ++++ +  ++h+w++++++
  gene791|gene791|rna791|rna791  55 TSDEMLYVLLFLFGNFLNAVGLI--YFDRKLRHHIVHFWNYMYTY 97 
                                    6799*****************87..377777999*******9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       608  (0.0339115); expected 358.6 (0.02)
Passed bias filter:                      266  (0.0148363); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 901.69
//
Query:       gene792|gene792|rna792|rna792  [L=176]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       655  (0.036533); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 1349.57
//
Query:       gene793|gene793|rna793|rna793  [L=176]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.7e-11   43.7   1.9    3.6e-11   43.3   1.9    1.3  1  NOT2_3_5  NOT2 / NOT3 / NOT5 family


Domain annotation for each model (and alignments):
>> NOT2_3_5  NOT2 / NOT3 / NOT5 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.3   1.9     2e-15   3.6e-11      21     129 ..      45     164 ..      16     166 .. 0.74

  Alignments for each domain:
  == domain 1  score: 43.3 bits;  conditional E-value: 2e-15
                       NOT2_3_5  21 klphp.tsisypqep...............lyekle.sakklekldedtLFyiFYysqgtleqllAakeLkkrsWryhke 83 
                                    k+ ++   + yp+ p                y++++  + kle ++e+tLFyiFY++ +t +q+ A++ L  +++ +++ 
  gene793|gene793|rna793|rna793  45 KNIECnALKEYPTLPlyeypepnldtlspiCYSSVQkPELKLELYHEETLFYIFYTYTETQAQIKAYNLLIAKGYSFSTV 124
                                    44444233446665566666677777777755556646679999************************************ PP

                       NOT2_3_5  84 lktWflreekeepkekteeyekgsYkyFD.yetWlkrrkkdfkleye 129
                                    +k+ +l      +k++       + ++FD +  W+k++ k  +++++
  gene793|gene793|rna793|rna793 125 YKCFILYT---GKKVVD--NTTRKIVVFDpF-YWKKIE-KSVVFDKN 164
                                    *****999...223333..34567899**87.8*9999.77777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       527  (0.0293937); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1285.01
//
Query:       gene794|gene794|rna794|rna794  [L=316]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.2e-07   29.3   3.4    9.6e-07   28.4   2.5    1.9  1  WD40_like    WD40-like domain
     0.0011   19.7   2.2        5.4    8.1   0.0    4.0  4  WD40         WD domain, G-beta repeat
  ------ inclusion threshold ------
      0.037   13.6   0.0       0.62    9.6   0.0    1.9  1  PQQ_2        PQQ-like domain
       0.09   13.1   0.0       0.61   10.4   0.0    2.2  1  ANAPC4_WD40  Anaphase-promoting complex subunit 4 WD40 domain
       0.11   12.5   0.1       0.28   11.2   0.1    1.7  1  PQQ          PQQ enzyme repeat


Domain annotation for each model (and alignments):
>> WD40_like  WD40-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4   2.5   2.7e-10   9.6e-07      52     149 ..     167     266 ..     141     308 .. 0.84

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 2.7e-10
                      WD40_like  52 dddlilvvtlDGtillslleneeevenekieedistvkviddklliGtnkGsiyvfsk.dlqleevllgqsseIkeikie 130
                                     +dli  +++D t+  ++++ +++v + + +++i  v+ ++d++l G + G++++ +  ++++   +  ++s+I+ +k +
  gene794|gene794|rna794|rna794 167 VNDLIFSASNDNTLKITDVRTGQTVYTYQSDNNINSVDATNDNFLFGDDSGTVFLNEMrNFKNIDQIKWHKSPINAVKFK 246
                                    489***************************************************96541445555567799********* PP

                      WD40_like 131 nnkiy.sLsesafivfdlfs 149
                                    n  ++ sLs+++   +d   
  gene794|gene794|rna794|rna794 247 NADVFcSLSDEQVCLWDKSF 266
                                    *999978*****99998632 PP

>> WD40  WD domain, G-beta repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       1.3   4.5e+03      13      32 ..      86     103 ..      76     106 .. 0.63
   2 !    8.1   0.0    0.0015       5.4       6      36 ..     153     182 ..     149     184 .. 0.71
   3 ?    1.4   0.0      0.19   6.7e+02       2      34 ..     189     219 ..     188     221 .. 0.65
   4 !    6.6   0.1    0.0045        16       6      38 .]     232     263 ..     227     263 .. 0.72

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1.3
                                    EEEEEEETTSSEEEEEETTS CS
                           WD40  13 vtslafspdgawlasGsdDg 32 
                                    ++ +   ++++++++ +dD+
  gene794|gene794|rna794|rna794  86 INRI--RSNSHLIVAVGDDK 103
                                    5555..45666676666676 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0015
                                    EEESS.SS......EEEEEEETTSSEEEEEETTSEEEE CS
                           WD40   6 tltGH.ss......vtslafspdgawlasGsdDgtvri 36 
                                    +l+ H ++      v++l        ++s+s D+t++i
  gene794|gene794|rna794|rna794 153 VLKVHeKGidglafVNDL--------IFSASNDNTLKI 182
                                    678898884445555555........779999*****9 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.19
                                    EEEEEEESSSSEEEEEEETTSSEEEEEETTSEE CS
                           WD40   2 qclrtltGHssvtslafspdgawlasGsdDgtv 34 
                                    q+++t+   ++++s++   + ++l+ G+d gtv
  gene794|gene794|rna794|rna794 189 QTVYTYQSDNNINSVD-ATNDNFLF-GDDSGTV 219
                                    6777777667799994.34445556.8877777 PP

  == domain 4  score: 6.6 bits;  conditional E-value: 0.0045
                                    EEESS.SSEEEEEEETTSSEEEEE.ETTSEEEEEE CS
                           WD40   6 tltGH.ssvtslafspdgawlasG.sdDgtvriWd 38 
                                     ++ H s++++++f       +++ s D  v +Wd
  gene794|gene794|rna794|rna794 232 QIKWHkSPINAVKFKNADV--FCSlS-DEQVCLWD 263
                                    56779788****5544444..46768.*******9 PP

>> PQQ_2  PQQ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0   0.00017      0.62     172     224 ..     167     220 ..     156     228 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00017
                          PQQ_2 172 aegtVyassgqgrllal.dlatgrrlw.skeissinglpildgdllyvvsageli 224
                                    +++ ++ +s+++ +l++ d++tg++++  ++ ++in+ ++  +++l+ +++g+++
  gene794|gene794|rna794|rna794 167 VNDLIFSASNDN-TLKItDVRTGQTVYtYQSDNNINSVDATNDNFLFGDDSGTVF 220
                                    446677777777.477779999998874556999999888999999988877766 PP

>> ANAPC4_WD40  Anaphase-promoting complex subunit 4 WD40 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00017      0.61      40      85 ..     160     201 ..     147     238 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00017
                    ANAPC4_WD40  40 evrsLaWkpdgklLavaysdgevrlldaesgkvvhslsvksekavt 85 
                                     + +La+ +d  l+  a +d+++++ d+ +g++v +++ +++  ++
  gene794|gene794|rna794|rna794 160 GIDGLAFVND--LIFSASNDNTLKITDVRTGQTVYTYQSDNN--IN 201
                                    5566666554..889999*****************9998876..44 PP

>> PQQ  PQQ enzyme repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   7.9e-05      0.28       2      34 ..     170     202 ..     169     203 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 7.9e-05
                                    EEEEEETTSEEEEEETTTCCEEEEEESSSCGSS CS
                            PQQ   2 vvylgsadGylyAlDadTGkvlWrfktggpvls 34 
                                     ++ +s+d++l   D++TG+ + +++ +++++s
  gene794|gene794|rna794|rna794 170 LIFSASNDNTLKITDVRTGQTVYTYQSDNNINS 202
                                    68999*********************9999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (316 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       723  (0.0403257); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2233.30
//
Query:       gene795|gene795|rna795|rna795  [L=387]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.6e-22   78.2   0.0    3.3e-21   75.1   0.0    2.3  2  DKCLD     DKCLD (NUC011) domain
    7.6e-21   75.0   1.6      2e-13   51.0   0.1    3.8  3  TruB_N    TruB family pseudouridylate synthase (N terminal do
    7.3e-17   61.3   0.1    1.5e-16   60.2   0.1    1.6  1  TruB_C_2  tRNA pseudouridylate synthase B C-terminal domain
    5.1e-14   52.0   1.2      1e-13   51.1   1.2    1.5  1  PUA       PUA domain


Domain annotation for each model (and alignments):
>> DKCLD  DKCLD (NUC011) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.1   0.0   7.3e-25   3.3e-21       6      58 .]      53     105 ..      50     105 .. 0.97
   2 ?   -0.1   0.0      0.22   9.8e+02       5      25 ..     289     309 ..     286     313 .. 0.76

  Alignments for each domain:
  == domain 1  score: 75.1 bits;  conditional E-value: 7.3e-25
                                    ....XXX-EEESS-----TTSS--GGG--HHHHHHTEEEEEEE-SSS-HHHHH CS
                          DKCLD   6 llLknydkllvrtehytplpaGssPlkRpieeyikyGvinLDKPsnPsSHEVV 58 
                                    +lL ++dk+ v+t+ +t +  Gs P kR+++ey+kyGvi LDKP+nPsSHEVV
  gene795|gene795|rna795|rna795  53 VLLYDIDKMFVKTSCFTTQGRGSYPEKRKMSEYLKYGVIYLDKPKNPSSHEVV 105
                                    7899************************************************9 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.22
                                    X....XXX-EEESS-----TT CS
                          DKCLD   5 pllLknydkllvrtehytplp 25 
                                    +  L+ny++++v+ +    l 
  gene795|gene795|rna795|rna795 289 EYSLRNYKRIMVKDSCVDALC 309
                                    5679*********98665555 PP

>> TruB_N  TruB family pseudouridylate synthase (N terminal domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.0   0.1   4.4e-17     2e-13       1      50 [.     109     158 ..     109     161 .. 0.96
   2 !   18.6   0.0     4e-07    0.0018      71     149 .]     161     226 ..     157     226 .. 0.73
   3 ?   -0.6   0.1      0.34   1.5e+03     102     148 ..     329     375 ..     326     376 .. 0.90

  Alignments for each domain:
  == domain 1  score: 51.0 bits;  conditional E-value: 4.4e-17
                                    HHHTT-S-EEESS---TT-EEEEEEEEGGGGGGHHHCTTS-EEEEEEEEE CS
                         TruB_N   1 krllkakkvGhtGtLDplatGvLvvavgeaTklleylleadKeYeatirl 50 
                                    k++lk++k Gh+GtLDp+++GvL v ++++T+l+++ ++a KeY++ +++
  gene795|gene795|rna795|rna795 109 KNILKVEKTGHGGTLDPKVSGVLTVYLNRGTRLSKIEQNAGKEYVCIVQI 158
                                    789*******************************************9986 PP

  == domain 2  score: 18.6 bits;  conditional E-value: 4e-07
                                    T--HHHHHHHHHHC-EEE---------------------------------EEEEEEEEEEEEEE....EEEEEEEESTT CS
                         TruB_N  71 klteekleevlkkftGeieqvppmySAvkvnGkrlyelaregeeverkkrkvtiyelelleveep....evelevecskG 146
                                    k++eek++++l+ f+G++ q+pp +SAvk                 r+ r  ++y+ e+le++e     +  ++v+c++G
  gene795|gene795|rna795|rna795 161 KVSEEKFKDALRFFEGRLIQRPPLISAVK-----------------RNVRMRSVYKNEFLELKEVdgvsYGLFKVSCEAG 223
                                    7899*************************.................5555555566555555544445555666666666 PP

                                    TTH CS
                         TruB_N 147 tYi 149
                                    tYi
  gene795|gene795|rna795|rna795 224 TYI 226
                                    665 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.34
                                    --------------------EEEEEEEEEEEEEEEEEEEEEESTTTT CS
                         TruB_N 102 GkrlyelaregeeverkkrkvtiyelelleveepevelevecskGtY 148
                                    G+++  ++ +ge+v +++  v+  e+++ e+     +l+v ++kG Y
  gene795|gene795|rna795|rna795 329 GEKVVVITTKGEAVVLAETLVSGAEMQINEYGLVAHTLRVIMEKGLY 375
                                    77888888999999999999999999999999999**********99 PP

>> TruB_C_2  tRNA pseudouridylate synthase B C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.2   0.1   3.4e-20   1.5e-16       1      63 [.     227     292 ..     227     293 .. 0.95

  Alignments for each domain:
  == domain 1  score: 60.2 bits;  conditional E-value: 3.4e-20
                                    HHHHHHHHHHTTS-EEEEEEEEEEETTEGG-..B-HHHHHHHHHHHHT..--H.HHHHEEEGGGGG CS
                       TruB_C_2   1 RtLcdDiGeaLgcgAhveeLRRtrvgpfdeedmvtledLedavllyke..dee.LdrlllPlesal 63 
                                    R Lc++iG+++g  A + eLRRtr+g++ ee+++t++d+ d+ +++++  de  ++r++ P+e  l
  gene795|gene795|rna795|rna795 227 RVLCEHIGLYMGIKAEMLELRRTRSGSIREEQCFTMHDVLDSHYIFENkgDERyIRRVVHPIEYSL 292
                                    89******************************************999987777**********876 PP

>> PUA  PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.1   1.2   2.2e-17     1e-13       1      68 [.     296     363 ..     296     369 .. 0.91

  Alignments for each domain:
  == domain 1  score: 51.1 bits;  conditional E-value: 2.2e-17
                                    CEEEE-HHHHHHHHTT-EEEGGGEEEEETT--TTSEEEEEETTSCEEEEEEESS-HHHHHHHCTSEEE CS
                            PUA   1 grvvvddgAvkallsgasLlapGvvevegdfeegdvVaivdedgelvavGlanysseelakikggksv 68 
                                    +r+ v+d++v+al+sga+L  +Gv++++ ++  g+ V++++++ge+v ++ +++s++e++  + g ++
  gene795|gene795|rna795|rna795 296 KRIMVKDSCVDALCSGAKLSLNGVIRFDRNINVGEKVVVITTKGEAVVLAETLVSGAEMQINEYGLVA 363
                                    589********************************************************987766555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (387 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       518  (0.0288917); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 2520.86
//
Query:       gene796|gene796|rna796|rna796  [L=250]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       553  (0.0308439); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 1651.05
//
Query:       gene797|gene797|rna797|rna797  [L=275]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      9e-05   22.1   1.3       0.32   10.7   0.1    2.4  2  zf-NADH-PPase   NADH pyrophosphatase zinc ribbon domain
     0.0075   15.0   0.1      0.034   12.8   0.1    1.8  1  DNA_pol_B       DNA polymerase family B
  ------ inclusion threshold ------
      0.011   15.8   7.3       0.12   12.4   7.3    2.2  1  DZR             Double zinc ribbon
      0.054   14.0   6.7        2.2    8.8   0.5    2.3  2  zf-CHY          CHY zinc finger
        4.1    7.5   8.2        7.6    6.6   1.0    2.3  2  zinc-ribbons_6  zinc-ribbons


Domain annotation for each model (and alignments):
>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.1   8.8e-05      0.32       3      12 ..     165     174 ..     163     178 .. 0.82
   2 !   10.2   0.1   0.00013      0.46      19      31 ..     197     209 ..     196     209 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 8.8e-05
                  zf-NADH-PPase   3 hrFCgrCGap 12 
                                    + FCg+CGa+
  gene797|gene797|rna797|rna797 165 TNFCGTCGAE 174
                                    78******97 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00013
                  zf-NADH-PPase  19 gwarvCpaCgleh 31 
                                    +++ vCp+C++e+
  gene797|gene797|rna797|rna797 197 ERKAVCPSCDNEQ 209
                                    89********996 PP

>> DNA_pol_B  DNA polymerase family B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.1   9.6e-06     0.034     361     456 ..      40     126 ..      15     129 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 9.6e-06
                                    GGG-EEEEESS.CCCS.SGCCSHHHHHHHHHHHHCSS---TTCEEEEEEBETSS...............SS-GGGTEEEH CS
                      DNA_pol_B 361 ekfvlskelskepeny.ksknlphlevakrlkkrneeapevgdrisYvivekkkev..........kkknllaseraedp 429
                                    e fvl ++l+k+pe+y + +  p++ +a +++++                                kk++  ++ + +d 
  gene797|gene797|rna797|rna797  40 ECFVLERMLNKDPEKYtTPEGSPQVLLALKINEH---------------------IrknnlkmplfKKNDIISYIMGHDG 98 
                                    4456666666666666444445555555555544.....................0333334444344567788888888 PP

                                    HHHHHCCSEB-HHHHHH.TTHHHHHHHH CS
                      DNA_pol_B 430 eyvleknlpidieyYls.qllkevarll 456
                                     ++ ++nl+i++eyYl+ q l++  rl+
  gene797|gene797|rna797|rna797  99 AFLPTENLEINYEYYLEqQFLTPFFRLV 126
                                    9****************99999988876 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   7.3   3.5e-05      0.12       4      48 ..     157     218 ..     155     229 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.5e-05
                            DZR   4 CgeelppdarfCseCgtklkavaa....................edrCpsCgekvdpearfCpeC 48 
                                    C ++ +++ +fC++Cg+++++  +                    + +CpsC+ +  +    C +C
  gene797|gene797|rna797|rna797 157 CCSNPQSQTNFCGTCGAEIDK--NflrnqaiknlreeiellyerKAVCPSCDNEQGLF-LNCFNC 218
                                    4444489999********984..24588899*************99999998774432.334444 PP

>> zf-CHY  CHY zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   1.0    0.0011       4.1      42      66 ..     153     177 ..     142     187 .. 0.81
   2 ?    8.8   0.5   0.00061       2.2      35      64 ..     193     222 ..     184     238 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0011
                         zf-CHY  42 vlcllCeteqekavlCkkCkkefae 66 
                                    ++   C++ q++++ C++C+ e+++
  gene797|gene797|rna797|rna797 153 ITTPCCSNPQSQTNFCGTCGAEIDK 177
                                    455679**************98876 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00061
                         zf-CHY  35 erlevkevlcllCeteqekavlCkkCkkef 64 
                                    e l +++ +c  C++eq    +C +C++++
  gene797|gene797|rna797|rna797 193 ELLYERKAVCPSCDNEQGLFLNCFNCNSSI 222
                                    555667889*****************9844 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   1.2    0.0084        30      17      40 ..     153     176 ..     143     182 .. 0.78
   2 ?    6.6   1.0    0.0021       7.6      13      38 ..     196     221 ..     182     227 .. 0.73

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.0084
                                    EE-TTT--EEEEEEE-SSS-S--- CS
                 zinc-ribbons_6  17 yhCeaCqedlkkealCpeCeqele 40 
                                    ++  +C++  +++++C +C+ e++
  gene797|gene797|rna797|rna797 153 ITTPCCSNPQSQTNFCGTCGAEID 176
                                    566789999999999999998876 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0021
                                    -SSEEE-TTT--EEEEEEE-SSS-S- CS
                 zinc-ribbons_6  13 rgeqyhCeaCqedlkkealCpeCeqe 38 
                                     ++++ C +C+++      C +C+++
  gene797|gene797|rna797|rna797 196 YERKAVCPSCDNEQGLFLNCFNCNSS 221
                                    44677788888888888888888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (275 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       682  (0.0380389); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2029.42
//
Query:       gene798|gene798|rna798|rna798  [L=200]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.7e-22   79.7   0.1    2.1e-22   79.4   0.1    1.0  1  Arf        ADP-ribosylation factor family
    2.6e-07   30.9   0.0    6.2e-07   29.7   0.0    1.7  1  Roc        Ras of Complex, Roc, domain of DAPkinase
    1.3e-06   28.0   0.0    1.6e-06   27.6   0.0    1.1  1  SRPRB      Signal recognition particle receptor beta subunit
    8.6e-06   25.8   0.0    1.5e-05   25.1   0.0    1.4  1  MMR_HSR1   50S ribosome-binding GTPase
    1.7e-05   24.1   0.2     0.0039   16.4   0.0    2.2  2  G-alpha    G-protein alpha subunit
    8.6e-05   22.2   0.0    0.00012   21.7   0.0    1.3  1  Ras        Ras family
    0.00037   19.9   0.1    0.00046   19.6   0.1    1.2  1  Gtr1_RagA  Gtr1/RagA G protein conserved region
  ------ inclusion threshold ------
      0.041   13.9   0.4        1.7    8.7   0.1    2.2  2  Dynamin_N  Dynamin family
      0.062   13.5   0.0       0.14   12.4   0.0    1.6  1  DUF3977    Protein of unknown function (DUF3977)
      0.068   13.5   0.1       0.77   10.1   0.1    2.1  2  Ras_bdg_2  Ras-binding domain of Byr2


Domain annotation for each model (and alignments):
>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.4   0.1   1.2e-25   2.1e-22      12     174 ..      28     190 ..      17     191 .. 0.92

  Alignments for each domain:
  == domain 1  score: 79.4 bits;  conditional E-value: 1.2e-25
                                    TTEEEEEEEESTTSSHHHHHHHHHHSSCEECSSSSSEEEEEEEETTEEEEEEEE-SSGGGGGGGGGGCTTESEEEEEEET CS
                            Arf  12 kkelrilllGLDnaGKtTilkklkleelvttvPTigfnveeleiknlkftvwDvGGqeklRplWknYfektdavifvvDs 91 
                                     k+l++ ++GL  +GK+  +  l ++e+ + +      ++e ++ n+k+ ++D+ G  +  + W++Y++k d++if + s
  gene798|gene798|rna798|rna798  28 VKNLKVAFIGLSDSGKSSFVSPLFENEFLQDMNSPEVRIHEKKMDNIKVLIYDIPGDPSSISKWDHYYKKSDVIIFFLNS 107
                                    5899**************************************************************************98 PP

                                    T.-CTTHHHHHHHHHHHCTSGCCTTSEEEEEEE-TTSTTSS-HHHHHHHTTGGGSSSSSSEEEEEEBTTTTBTHHHHHHH CS
                            Arf  92 a.dreRleeakeeLkalleeeelkevallvlaNKqDlpealseeelrellgleelkgkrkleiqkcsavkgeglkeglew 170
                                    + d+e  +++k+eL++ll ++   +  ll+l+ K Dlp+++s +++  +l+l ++  +r++   + s  +  +++   ew
  gene798|gene798|rna798|rna798 108 TaDEETRKKSKNELHSLLYRNMWMRKNLLILGTKNDLPDSMSCKDIILALDLMTIG-DREVACYSISNKNLVNIDLVREW 186
                                    526777899**********************************************9.99999999998888888888888 PP

                                    HHHH CS
                            Arf 171 lses 174
                                    ++e+
  gene798|gene798|rna798|rna798 187 IVEQ 190
                                    8875 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.7   0.0   3.4e-10   6.2e-07       1     119 [.      32     143 ..      32     144 .. 0.73

  Alignments for each domain:
  == domain 1  score: 29.7 bits;  conditional E-value: 3.4e-10
                                    EEEEESSTTSSHHHHHHCHCT-CCC-EEETTTTEEEEEEECGGSGGCTTBTTTTCEEEEEEEE-SGGCTTTT-HHHHCTS CS
                            Roc   1 KvvlvGdsgvGKtsllkrfvedkfsekekstigvdfltkevtkikgvendkkvkkvklniWDtaGqerfrslhplylrea 80 
                                    Kv ++G s +GK+s+++ + e++f ++ +s   v +++k++            +++k+ i+D+ G     s  ++y++++
  gene798|gene798|rna798|rna798  32 KVAFIGLSDSGKSSFVSPLFENEFLQDMNS-PEVRIHEKKM------------DNIKVLIYDIPGDPSSISKWDHYYKKS 98 
                                    899*********************877544.4566666654............457899********************* PP

                                    CEEEEEEEGHHH....HCHHHHHHHH..HHHCSSS-EEEEEE-TT CS
                            Roc  81 alailvydsrss....enlkeWlkel..kkvagkspvilvgnkiD 119
                                    +++i++++s+ +    ++ k+ l++l  +++  +++++++g+k D
  gene798|gene798|rna798|rna798  99 DVIIFFLNSTADeetrKKSKNELHSLlyRNMWMRKNLLILGTKND 143
                                    *****9985543111133333333332244455778888999988 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   0.0   9.2e-10   1.6e-06       5     132 ..      32     152 ..      29     177 .. 0.84

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 9.2e-10
                                    EEEEE-STTSSHHHHHHHHHHSS---B---SS-EEETTG...GGTT-SEEEETT-GCCSHHHHHHHHHHGGEEEEEEEEE CS
                          SRPRB   5 avllvGlsdsGKTslftrLttdsvkktvtSqessaalkvksekgskltliDfPGheklrqklleklkaksslkglvfvvD 84 
                                    +v ++GlsdsGK s+   L ++++ + + S e  + +k    ++ k+ + D+PG+ +  +k  +++k+      ++f + 
  gene798|gene798|rna798|rna798  32 KVAFIGLSDSGKSSFVSPLFENEFLQDMNSPEVRIHEKK--MDNIKVLIYDIPGDPSSISKWDHYYKK---SDVIIFFLN 106
                                    5789**************************999998887..79999**********999998877444...4569***** PP

                                    TTS-HHHHHHHHHHHHHHHHHHHHHTT---EEEEEE-TTSTT---HHH CS
                          SRPRB  85 StidpkevkevAEllyeilliteklkdavdiliACnKqelflakspkl 132
                                    St+d+   k+    l ++l  ++ ++++  +li   K++l  + s k 
  gene798|gene798|rna798|rna798 107 STADEETRKKSKNELHSLLYRNMWMRKN--LLILGTKNDLPDSMSCKD 152
                                    ******9999999999999999977664..666677777766655555 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.0   8.2e-09   1.5e-05       1     103 [.      32     127 ..      32     141 .. 0.70

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 8.2e-09
                                    EEEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSSHHHHHHHHHHHHHHHHCTSEEE CS
                       MMR_HSR1   1 evaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgkeielvDtpGliegaseekglgkaflaleeadlil 80 
                                    +va++G + +GKS++++ l++++   +d++     i e++++  + ++ ++D+pG  +      +++k  +  +++d+i+
  gene798|gene798|rna798|rna798  32 KVAFIGLSDSGKSSFVSPLFENEF-LQDMNSPEVRIHEKKMD--NIKVLIYDIPG--D----PSSISKWDHYYKKSDVII 102
                                    69******************9855.34444444566777777..889********..3....23444444445579**** PP

                                    EEEETT..TTCSHHHHHHHHHHHHH CS
                       MMR_HSR1  81 lvvdas..eeklkpldeeleellee 103
                                    + ++++  ee+ k+ ++el++ll +
  gene798|gene798|rna798|rna798 103 FFLNSTadEETRKKSKNELHSLLYR 127
                                    ***9667644556667777777655 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.3   0.0    0.0026       4.7      22      40 ..      29      47 ..       5      58 .. 0.82
   2 !   16.4   0.0   2.2e-06    0.0039     193     234 ..      66     106 ..      51     143 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0026
                                   .EEEEEEEESTTSSHHHHH CS
                        G-alpha 22 revkllllGqseSGKsTil 40
                                   +++k+ ++G s+SGKs+++
  gene798|gene798|rna798|rna798 29 KNLKVAFIGLSDSGKSSFV 47
                                   4689*************97 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 2.2e-06
                                    EEEEECT-TEEEEEEEE-SSHHHHHGTCCCTTTECEEEEEEE CS
                        G-alpha 193 etkfevdsklefrivdvgGqrserkkWvpffddvdaiiFlvs 234
                                     ++ ++d ++++ i+d+ G  s   kW +++++ d+iiF+ +
  gene798|gene798|rna798|rna798  66 IHEKKMD-NIKVLIYDIPGDPSSISKWDHYYKKSDVIIFFLN 106
                                    3445668.99******************************87 PP

>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.0   6.7e-08   0.00012       1     119 [.      32     151 ..      32     193 .. 0.75

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 6.7e-08
                                    EEEEEESTTSSHHHHHHHHHHSSCSSSCTTTSSEEEEEEEEEETTEEEEEEEEEETTSGGGHHHHHHHHTTESEEEEEE. CS
                            Ras   1 KlvlvGdsavGKtslllrfvkdkFkeeyesTigvdfytkeievdgkevkleiwDTAGqeefkslrelyyrdaegillvy. 79 
                                    K+ ++G s  GK+s++    +++F ++++s       ++  e +  ++k+ i+D  G     s  + yy+++++i+ +  
  gene798|gene798|rna798|rna798  32 KVAFIGLSDSGKSSFVSPLFENEFLQDMNSPE-----VRIHEKKMDNIKVLIYDIPGDPSSISKWDHYYKKSDVIIFFLn 106
                                    8999*********************9998766.....33334445679999**********************9998762 PP

                                    ETTBHHHHHTHH.HHHHHHHHHSTTTSEEEEEEETTTGGG....G CS
                            Ras  80 ditsresfenvk.kwveeikrvaeenvpivLvGnKvDlee....k 119
                                    +  ++e+ ++ k ++++ + r +  + +++++G+K Dl +    k
  gene798|gene798|rna798|rna798 107 STADEETRKKSKnELHSLLYRNMWMRKNLLILGTKNDLPDsmscK 151
                                    56677888888845666666666677899*********9855542 PP

>> Gtr1_RagA  Gtr1/RagA G protein conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.1   2.6e-07   0.00046       1     100 [.      32     123 ..      32     163 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 2.6e-07
                      Gtr1_RagA   1 kvLLmGksgsGKtsmrsiiFdnylardtlrlgatidveksevrflgnltlnlwDcgGqeafveeylssqkeeifrnvgvl 80 
                                    kv ++G s sGK+s  s +F+n   +d+ + ++ i  ++   + ++n+++ + D++G  + + +      ++ +++ +v+
  gene798|gene798|rna798|rna798  32 KVAFIGLSDSGKSSFVSPLFENEFLQDMNSPEVRI--HE---KKMDNIKVLIYDIPGDPSSISKW-----DHYYKKSDVI 101
                                    7889***********************98766544..33...34699**********99988875.....9999999*** PP

                      Gtr1_RagA  81 iyVfDvesre..leedletlke 100
                                    i+ + ++ +e   +++ ++l++
  gene798|gene798|rna798|rna798 102 IFFLNSTADEetRKKSKNELHS 123
                                    **99998553223333334444 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.1   0.00095       1.7       1      25 [.      33      57 ..      33      65 .. 0.88
   2 ?    3.7   0.0     0.033        58      98     148 ..      71     117 ..      57     128 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00095
                                   EEEEEBTTTTHHHHHHHHHTS--S- CS
                      Dynamin_N  1 iavvGsqSsGKSSvlnaLlgedilp 25
                                   +a++G   sGKSS++  L + ++l 
  gene798|gene798|rna798|rna798 33 VAFIGLSDSGKSSFVSPLFENEFLQ 57
                                   7899***************999986 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.033
                                    TTS-SEEEEE---B-SSSGTTSHHHHHHHSTTEEEEEEEETTS-CCC-CHH CS
                      Dynamin_N  98 llvkgltlvDlPGldsvnkrdqelvkeyikkadiilavtsanhdlsnseal 148
                                     ++ ++ ++D PG  s+  +     ++y kk+d+i++ +++  d  + +++
  gene798|gene798|rna798|rna798  71 MDNIKVLIYDIPGDPSSISKW----DHYYKKSDVIIFFLNSTADEETRKKS 117
                                    455567788999987766555....79999999999999888876665544 PP

>> DUF3977  Protein of unknown function (DUF3977)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   7.7e-05      0.14      37      58 ..     122     143 ..     106     152 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 7.7e-05
                        DUF3977  37 leslyvrmwfrktclildtkeg 58 
                                       ly  mw+rk  lil tk+ 
  gene798|gene798|rna798|rna798 122 HSLLYRNMWMRKNLLILGTKND 143
                                    4558999************985 PP

>> Ras_bdg_2  Ras-binding domain of Byr2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0       0.3   5.3e+02      50      73 ..      30      64 ..      13      74 .. 0.69
   2 ?   10.1   0.1   0.00043      0.77      41      92 ..      89     149 ..      69     153 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.3
                      Ras_bdg_2 50 s...........nekeslrlLsdvELvtichspdr 73
                                   +            +++ +++L+++E+++  +sp+ 
  gene798|gene798|rna798|rna798 30 NlkvafiglsdsGKSSFVSPLFENEFLQDMNSPEV 64
                                   44555555555467888999*****9998888764 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00043
                      Ras_bdg_2  41 eeydvyvlss.........nekeslrlLsdvELvtichspdrleknrlilvkkneePteka 92 
                                    +++d y+++s           +e++r  s +EL ++ + +  ++kn lil  kn  P++  
  gene798|gene798|rna798|rna798  89 SKWDHYYKKSdviifflnsTADEETRKKSKNELHSLLYRNMWMRKNLLILGTKNDLPDSMS 149
                                    56777777777777777778999*********************************98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       610  (0.0340231); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1407.01
//
Query:       gene799|gene799|rna799|rna799  [L=45]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (45 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       169  (0.00942607); expected 358.6 (0.02)
Passed bias filter:                      152  (0.00847788); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.31u 0.25s 00:00:00.56 Elapsed: 00:00:00.39
# Mc/sec: 343.57
//
Query:       gene8|gene8|rna8|rna8  [L=47]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (47 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       502  (0.0279993); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.42
# Mc/sec: 338.12
//
Query:       gene80|gene80|rna80|rna80  [L=738]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.8e-07   29.6   0.1    6.8e-07   29.6   0.1    3.3  5  PWWP      PWWP domain


Domain annotation for each model (and alignments):
>> PWWP  PWWP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.8      0.55   9.9e+03      54      79 ..      42      67 ..       7      86 .. 0.62
   2 ?   -3.5   1.5      0.82   1.5e+04      37      37 ..      81      81 ..      48     143 .. 0.59
   3 !   29.6   0.1   3.8e-11   6.8e-07       1      48 [.     200     244 ..     200     251 .. 0.89
   4 ?   -4.4   1.6         1   1.8e+04      75      75 ..     442     442 ..     422     465 .. 0.47
   5 ?   -2.6   0.9      0.42   7.6e+03      64      90 ..     589     621 ..     572     627 .. 0.64

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 0.55
                               EE-GGGEEE-SHHHHHHHHHTTSS-H CS
                       PWWP 54 wvkekdlkpfteedeeeylkkkkkkk 79
                                ++++ +++ + +++++  k++k+k+
  gene80|gene80|rna80|rna80 42 TMDRNAIEECKMKENDQNAKRMKNKE 67
                               44455555554444444444444443 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 0.82
                               - CS
                       PWWP 37 k 37
                               +
  gene80|gene80|rna80|rna80 81 E 81
                               1 PP

  == domain 3  score: 29.6 bits;  conditional E-value: 3.8e-11
                                SSTTEEEEEEESSSEEEEEEEEECCCCCCCCHCT---SSSEEEEEETT CS
                       PWWP   1 fqpgdlvwakvkgypwWPavvidpeevpekvlkkkekskelylVkFfg 48 
                                f+pgd+vw k++ yp+WP+ v+++  + +  ++ ++k    + V F+g
  gene80|gene80|rna80|rna80 200 FKPGDIVWSKYDAYPPWPSKVTSHAITAQLQKHYRKK---GVGVLFLG 244
                                89***************************99998765...37899998 PP

  == domain 4  score: -4.4 bits;  conditional E-value: 1
                                T CS
                       PWWP  75 k 75 
                                k
  gene80|gene80|rna80|rna80 442 K 442
                                1 PP

  == domain 5  score: -2.6 bits;  conditional E-value: 0.42
                                SHHHHHHHHHTTSS-HHHH......HHHHHHHH CS
                       PWWP  64 teedeeeylkkkkkkkskk......kfkkAlee 90 
                                ++e+e+ +l+++kk+k +k      +fk+++e 
  gene80|gene80|rna80|rna80 589 KKEKENGKLNEGKKEKLGKeenvveQFKQSVEI 621
                                445555566666665555567777777777775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (738 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2422  (0.135088); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                       136  (0.00758548); expected 17.9 (0.001)
Passed Fwd filter:                        45  (0.0025099); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 1.50u 0.39s 00:00:01.89 Elapsed: 00:00:00.59
# Mc/sec: 3754.94
//
Query:       gene800|gene800|rna800|rna800  [L=269]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    0.00066   19.0   0.0    0.00092   18.5   0.0    1.3  1  Hydrolase_4  Serine aminopeptidase, S33
  ------ inclusion threshold ------
       0.13   11.9   0.0        2.4    7.7   0.0    2.1  2  Esterase     Putative esterase
       0.16   12.1   0.0       0.31   11.2   0.0    1.4  1  Voldacs      Regulator of volume decrease after cellular swel


Domain annotation for each model (and alignments):
>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   1.5e-07   0.00092       7     116 ..     120     221 ..     114     252 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.5e-07
                    Hydrolase_4   7 vvlvHGlaehsgryaelaeaLaaqGfavyalDhrGhGrsegkrghvpsfddyvdDlaafvekvkeehpelplfllGhSmG 86 
                                    ++++HG+a +++  ++++e  +   ++v+ +  rG+ +       v++ + ++dD++++ e v    p+++++++G+S G
  gene800|gene800|rna800|rna800 120 LIFFHGRAMSVNVLNKITEGIT--SYNVIYYYCRGYENG----TFVRNKKNIMDDVSTLAEFVY-SRPKRKMVVFGQSFG 192
                                    6788888888888888888876..477777778876433....567999**********99988.677888********* PP

                    Hydrolase_4  87 Gliallyl.lrypdkvaglilsaPalkikak 116
                                       al ++ l+++d    l+l +P++++++ 
  gene800|gene800|rna800|rna800 193 CHFALYFTtLMNRD--LILVLENPFYSLRSV 221
                                    ********555555..479999999988754 PP

>> Esterase  Putative esterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0      0.02   1.2e+02     168     198 ..      92     121 ..      65     162 .. 0.70
   2 ?    7.7   0.0    0.0004       2.4     114     132 ..     180     199 ..     165     206 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.02
                                    C-CCCCHCHHCHTTSEEEEEEEECTTBCCCH CS
                       Esterase 168 ndpvllakelsaslkalriyldvGtseddlg 198
                                    + p++++ e s+++++l+iy+++ +se+dl 
  gene800|gene800|rna800|rna800  92 ETPFARI-ETSEKNSELKIYVKNNNSETDLI 121
                                    5566677.56999999999999999999764 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0004
                                    CCC.EEEEEETHHHHHHHHH CS
                       Esterase 114 pdg.ravaGqSmGGlgALil 132
                                    p++ ++v+GqS+G ++AL+ 
  gene800|gene800|rna800|rna800 180 PKRkMVVFGQSFGCHFALYF 199
                                    33359*************96 PP

>> Voldacs  Regulator of volume decrease after cellular swelling
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   5.2e-05      0.31      20     100 ..       8     122 ..       6     136 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 5.2e-05
                        Voldacs  20 gisipypsIalHAiqrdkkdeqeepclyvqldeeldesdn......................................ke 61 
                                    g+ i+y+s+++HA+ +++ + +  + +++    +++++ +                                       +
  gene800|gene800|rna800|rna800   8 GVLINYKSVCIHASFKLPIEMDNNKLVTLN---IINDKTRmiritkkafkhigiilyfmfycasvitfafqnqlifmaPK 84 
                                    788***************966667777776...34444445778899999999999999999999999999999987766 PP

                        Voldacs  62 seegededdneededeeessveltlvPknaeetildnif 100
                                    + + +d+++  + ++++e+  el+++ kn++ + +d if
  gene800|gene800|rna800|rna800  85 DYKLTDRETPFARIETSEKNSELKIYVKNNN-SETDLIF 122
                                    7777999999999999999999999999984.5677766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (269 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       654  (0.0364772); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1976.05
//
Query:       gene801|gene801|rna801|rna801  [L=48]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (48 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       462  (0.0257683); expected 358.6 (0.02)
Passed bias filter:                      256  (0.0142785); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 367.44
//
Query:       gene802|gene802|rna802|rna802  [L=451]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-19   70.6   0.9    5.5e-16   58.8   0.1    2.8  2  Rtt106           Histone chaperone Rttp106-like
    1.3e-06   28.7   0.1    6.6e-06   26.5   0.1    2.2  2  POB3_N           POB3-like N-terminal PH domain
    2.5e-05   24.1   0.0    6.8e-05   22.7   0.0    1.8  1  SSrecog          Structure-specific recognition protein (SSRP
     0.0061   16.5   1.2       0.04   13.9   1.2    2.7  1  Intein_splicing  Intein splicing domain
  ------ inclusion threshold ------
      0.066   13.6   0.2       0.33   11.4   0.1    2.1  2  DUF1935          Domain of unknown function (DUF1935)


Domain annotation for each model (and alignments):
>> Rtt106  Histone chaperone Rttp106-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.1   0.00035       1.3      29      77 ..      50      95 ..      33      99 .. 0.91
   2 !   58.8   0.1   1.5e-19   5.5e-16       4      88 ..     334     419 ..     331     420 .. 0.96

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00035
                         Rtt106 29 llfiplediesvsfeRvsvtsrtfdlvvelkkeeveFsmidqeelegid 77
                                   ++ i+ +di+++++      +r  ++ +++k++ +++++i +e++e+i+
  gene802|gene802|rna802|rna802 50 ITTIKKDDIHRIELY---RGTRLYNMRITTKTKIFNINNILEEKIEEIK 95
                                   6788999********...6789********99**************998 PP

  == domain 2  score: 58.8 bits;  conditional E-value: 1.5e-19
                         Rtt106   4 kasrkakeGlLyflekgllfgfkkPllfiplediesvsfeRv...svtsrtfdlvvelkkeeveFsmidqeelegidefv 80 
                                    ++ ++a eG+L++ +++++f ++k ++++p+++i  v+f Rv    +ts++fd+++ + + ++ Fs+id++e++ +++++
  gene802|gene802|rna802|rna802 334 SCALRALEGFLFPISDAVIF-LPK-VIYMPHREIRLVEFYRVdvsVMTSKSFDMKIITYDSSYLFSSIDKDEFGALEKYF 411
                                    7999****************.888.9******************999***********99******************** PP

                         Rtt106  81 kskgikik 88 
                                     +++++i+
  gene802|gene802|rna802|rna802 412 GDCNVEIR 419
                                    ****9986 PP

>> POB3_N  POB3-like N-terminal PH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   0.1   1.8e-09   6.6e-06      16      90 ..      32     105 ..      22     108 .. 0.91
   2 ?   -1.6   0.0         1   3.7e+03      38      83 ..     361     411 ..     355     418 .. 0.56

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 1.8e-09
                         POB3_N  16 klrlsesglgwknsktgkvvqikasdissaqWvrvargyqLrillkdgkvvrfdGFkeedfdkLskllkknfnie 90 
                                    +l+l+++g++ kn ++g  ++ik++di+ ++  r  r y++ri++ ++k+++ +   ee +++++k   ++++i+
  gene802|gene802|rna802|rna802  32 NLKLADKGIAMKNIENGAITTIKKDDIHRIELYRGTRLYNMRITT-KTKIFNINNILEEKIEEIKKVCGHWYSIN 105
                                    589*****************************************8.56789999999999999999999999887 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1
                         POB3_N  38 kasdissaqWvrv......argyqLrillkdgkvvrfdGFkeedfdkLskll 83 
                                    ++ +i+ +++ rv      ++++ ++i +  ++ + f+  ++++f  L+k++
  gene802|gene802|rna802|rna802 361 PHREIRLVEFYRVdvsvmtSKSFDMKIIT-YDSSYLFSSIDKDEFGALEKYF 411
                                    55566666655541111113556666664.3445567777777777777776 PP

>> SSrecog  Structure-specific recognition protein (SSRP1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.0   1.9e-08   6.8e-05       5      68 ..     119     176 ..     115     177 .. 0.82

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 1.9e-08
                        SSrecog   5 GkaefegselvfqvdnkpafeiplsevsncnlagknEvaleFhqdddaaenedqLvEmRfyvPg 68 
                                    Gk+ f+++ l+  + +k +f++pl++v  + +  knE +l F    d +++ d + EmR+ vP 
  gene802|gene802|rna802|rna802 119 GKVTFSEDYLEYRT-DKLIFDVPLKDVVSVCS-VKNEAVLGF----DCDKEFDGVIEMRLSVPD 176
                                    77777777777665.699********998865.6********....577777889*******96 PP

>> Intein_splicing  Intein splicing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   1.2   1.1e-05      0.04      18      94 ..      25     227 ..       4     391 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.1e-05
                                    ECTTEEEEEETTTTEEEEEEEEEEEEEEEE..EEEEEEETTS-EE...EEETT-EEEECCTTEEEEEECCC--TT-EEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                Intein_splicing  18 kegeevlslnledlklevksvkkliklklk..elyeiklesgrki...kaTpeHkllvvrdegivEkradeLkegdliav 92 
                                    ++g+e+++l+l d ++  k++++ + + +k   + +i+l  g+++   ++T + k++ +  ++i+E + +e+k+      
  gene802|gene802|rna802|rna802  25 NNGDENINLKLADKGIAMKNIENGAITTIKkdDIHRIELYRGTRLynmRITTKTKIFNI--NNILEEKIEEIKKVCG--- 99 
                                    79*******************998888877789*****99987753338**********..8999999999986321... PP

                                    E............................................................................... CS
                                    x............................................................................... RF
                Intein_splicing  93 p............................................................................... 93 
                                                                                                                    
  gene802|gene802|rna802|rna802 100 Hwysinvyvkpleivdttkgkvtfsedyleyrtdklifdvplkdvvsvcsvkneavlgfdcdkefdgviemrlsvpdenf 179
                                    12223445666666666666666666666666666666666666666666666666666666666666666666666666 PP

                                    ...............................................H CS
                                    ...............................................x RF
                Intein_splicing  94 ...............................................d 94 
                                                                                   +
  gene802|gene802|rna802|rna802 180 vknlrerseigqvksiitfetlnnvsprgksdyifsenyirilgrtyE 227
                                    666666666666655555555555555555555555555555555554 PP

>> DUF1935  Domain of unknown function (DUF1935)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   9.2e-05      0.33      15      94 ..      42     122 ..      33     128 .. 0.78
   2 ?   -1.4   0.0      0.85     3e+03      10      27 ..     319     348 ..     314     353 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 9.2e-05
                                    STT....SEEEEEETTTTEEEEEE--SSEEEEEEEEEETT-EEEE-TT-EEEE.---.--E.EEEEEEE-TT-EEEEEEE CS
                        DUF1935  15 fkesgnglLfrivdekekrWaFYNDtkdyemkvtvsfgpksevkalgkttvee.dee.ege.lvaevvVkPleTelfveG 91 
                                    +k+ +ng +  i +++ +r  +Y  t+ y+m++t + +  + ++ + + ++ee + +  g+ + ++v VkPle +   +G
  gene802|gene802|rna802|rna802  42 MKNIENGAITTIKKDDIHRIELYRGTRLYNMRITTKTKIFN-INNILEEKIEEiK-KvCGHwYSINVYVKPLEIVDTTKG 119
                                    456678999999999999****************9876554.4444455566633.3344449***********999999 PP

                                    E-- CS
                        DUF1935  92 evn 94 
                                    +v+
  gene802|gene802|rna802|rna802 120 KVT 122
                                    986 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.85
                                    EEEE-STT................SEEEEE CS
                        DUF1935  10 evtkcfkesgn............glLfriv 27 
                                    +v +cfk++ n            g+Lf i 
  gene802|gene802|rna802|rna802 319 QVSECFKTRTNqiflscalraleGFLFPIS 348
                                    789999999887777777777777888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (451 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       565  (0.0315132); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.54u 0.24s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 3253.49
//
Query:       gene803|gene803|rna803|rna803  [L=148]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.011   16.1   3.7      0.017   15.5   3.7    1.2  1  DUF3021        Protein of unknown function (DUF3021)
      0.034   14.4   0.8      0.062   13.6   0.8    1.6  1  Sigma_reg_N    Sigma factor regulator N-terminal
      0.098   12.0   3.8       0.37   10.1   3.8    1.7  1  DUF3810        Protein of unknown function (DUF3810)
       0.18   12.1   5.6      0.073   13.4   2.0    2.0  2  Orf78          Orf78 (ac78)
       0.21   11.0   4.4       0.13   11.7   1.3    2.0  2  OSTMP1         Osteopetrosis-associated transmembrane protein
       0.21   11.8   5.9       0.41   10.8   5.7    1.6  2  Pox_A28        Poxvirus A28 family
       0.92    9.1   7.1       0.51    9.9   4.3    1.9  2  Baculo_11_kDa  Baculovirus 11 kDa family
        2.5    8.0   6.0        3.2    7.6   5.7    1.5  1  Tmemb_9        TMEM9


Domain annotation for each model (and alignments):
>> DUF3021  Protein of unknown function (DUF3021)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   3.7   7.6e-06     0.017      98     129 ..      21      56 ..      13      56 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 7.6e-06
                        DUF3021  98 liv..ilif..iiiyliiwlifylsekkevkkiNek 129
                                    +++  +++f  +++y++++l+++++++  ++++Nek
  gene803|gene803|rna803|rna803  21 ILIlsTILFvlCLVYFVLYLVVMFYNRSYINRLNEK 56 
                                    2223544444699*********************98 PP

>> Sigma_reg_N  Sigma factor regulator N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.8   2.8e-05     0.062      10      56 ..      19      70 ..       8      97 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.8e-05
                    Sigma_reg_N 10 ksilrivlislivlllifvilvvtllyl.....aekegnklrevlelaveit 56
                                   k+il  ++i ++++l++fv+ +v + y      + +e++k +++ +  +++ 
  gene803|gene803|rna803|rna803 19 KIILILSTILFVLCLVYFVLYLVVMFYNrsyinRLNEKSKEMNYSQKISSFD 70
                                   6677777777777777777776666666777787777777788877777665 PP

>> DUF3810  Protein of unknown function (DUF3810)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   3.8   0.00017      0.37      49     118 ..       6      89 ..       2     132 .. 0.57

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00017
                        DUF3810  49 rkkkkkrllkvllrvllvllvvyflftllwglnYyreplserlglkkeeyseeelaelaeklveklnel........... 117
                                     +++k r + ++++++l+l++++f+ +l+++++Y    +++r+ +++ +++++e+   +++ +++  ++           
  gene803|gene803|rna803|rna803   6 TRHEKLRTKLLIMKIILILSTILFVLCLVYFVLYLVVMFYNRSYINRLNEKSKEMN--YSQKISSFDNSyfiidftsggd 83 
                                    56667788889999999999999999999999999999999998875555544443..2222222222224455555555 PP

                        DUF3810 118 .....r 118
                                          
  gene803|gene803|rna803|rna803  84 edspiL 89 
                                    555552 PP

>> Orf78  Orf78 (ac78)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   2.0   3.2e-05     0.073      58      97 ..      12      51 ..       1      65 [. 0.66
   2 ?   -0.3   0.1      0.58   1.3e+03      28      42 ..     110     119 ..      95     136 .. 0.52

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.2e-05
                          Orf78 58 ekaqalnillisllavvcvlvllyviyYfvilrerqkssv 97
                                   +++     +++ l +++ vl l+y ++Y v++  ++++++
  gene803|gene803|rna803|rna803 12 RTKLLIMKIILILSTILFVLCLVYFVLYLVVMFYNRSYIN 51
                                   2333333445556678889999999999999988888877 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.58
                          Orf78  28 nddndkaenkkekks 42 
                                    +++n+k     ++++
  gene803|gene803|rna803|rna803 110 EQENSK-----NMQK 119
                                    111111.....1111 PP

>> OSTMP1  Osteopetrosis-associated transmembrane protein 1 precursor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   1.3   5.7e-05      0.13     188     225 ..      27      64 ..      12      72 .. 0.85
   2 ?    0.1   0.1       0.2   4.4e+02     124     145 ..     112     133 ..      92     148 .] 0.57

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 5.7e-05
                         OSTMP1 188 tvpviavssfvlllpviFYlssflhseqkkrklilpkr 225
                                     ++v+    fvl l v+FY  s+++  ++k k +++++
  gene803|gene803|rna803|rna803  27 ILFVLCLVYFVLYLVVMFYNRSYINRLNEKSKEMNYSQ 64 
                                    5688899999***************9999998888765 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.2
                         OSTMP1 124 deeslkkknkselCkeCkeayk 145
                                    +++++ +kn+ +l k C ++ +
  gene803|gene803|rna803|rna803 112 ENSKNMQKNYDSLNKFCLSRSS 133
                                    2222345555555555555444 PP

>> Pox_A28  Poxvirus A28 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   5.7   0.00018      0.41       6      52 ..      21      69 ..      15     125 .. 0.78
   2 ?   -1.9   0.0       1.5   3.5e+03      26      37 ..     117     128 ..     109     136 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00018
                        Pox_A28  6 illivlataavcllllqlyai..yenydnikefndahsaleysksigvl 52
                                   il++  +  ++cl+ + ly +  + n  +i++ n++ ++++ys+ i+  
  gene803|gene803|rna803|rna803 21 ILILSTILFVLCLVYFVLYLVvmFYNRSYINRLNEKSKEMNYSQKISSF 69
                                   22333334567777777777611556679***************98765 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.5
                        Pox_A28  26 iyenydnikefn 37 
                                    + +nyd++++f 
  gene803|gene803|rna803|rna803 117 MQKNYDSLNKFC 128
                                    456777777764 PP

>> Baculo_11_kDa  Baculovirus 11 kDa family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   4.3   0.00023      0.51      29      76 ..      13      61 ..      11      68 .. 0.60
   2 ?   -1.2   0.0      0.67   1.5e+03      71      82 ..     111     122 ..      99     131 .. 0.60

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00023
                  Baculo_11_kDa 29 NrsflrdFvLvicglvvfvvivlfilLlvvilknaea.eeaekekrekt 76
                                    + ++   +L++++++ ++ +v f+l lvv++ n +  ++ + ++ e+ 
  gene803|gene803|rna803|rna803 13 TKLLIMKIILILSTILFVLCLVYFVLYLVVMFYNRSYiNRLNEKSKEMN 61
                                   5678888899998877666666666656655555544044444444444 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.67
                  Baculo_11_kDa  71 ekrektllaNld 82 
                                    ++ +k + +N+d
  gene803|gene803|rna803|rna803 111 QENSKNMQKNYD 122
                                    344444445554 PP

>> Tmemb_9  TMEM9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   5.7    0.0014       3.2      42     100 ..       8      65 ..       3     119 .. 0.58

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0014
                        Tmemb_9  42 yesRntttikvvviiviv.vislLviYmlflllldpllnkrkkkasyqehtneedetses 100
                                    +e+  t+++ + +i++++ ++++L++ + f+l l  +  +r+  +  +e+++e++ + ++
  gene803|gene803|rna803|rna803   8 HEKLRTKLLIMKIILILStILFVLCL-VYFVLYLVVMFYNRSYINRLNEKSKEMNYS-QK 65 
                                    56555555444444444313333322.222222333444443444445555554333.22 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1642  (0.0915835); expected 358.6 (0.02)
Passed bias filter:                      744  (0.041497); expected 358.6 (0.02)
Passed Vit filter:                       113  (0.00630264); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.41
# Mc/sec: 1079.37
//
Query:       gene804|gene804|rna804|rna804  [L=370]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.73   10.9   5.4         16    6.6   0.0    3.0  3  AvrLm4-7  Avirulence Effector AvrLm4-7


Domain annotation for each model (and alignments):
>> AvrLm4-7  Avirulence Effector AvrLm4-7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.1     0.079   1.4e+03      27      51 ..      31      55 ..      21      63 .. 0.77
   2 ?    4.5   0.6    0.0041        74       7      39 ..     116     152 ..     111     159 .. 0.80
   3 ?    6.6   0.0   0.00092        16       2      58 ..     259     315 ..     258     321 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.079
                       AvrLm4-7 27 aelaqkykdyseqnekrlGrditae 51
                                   +++ +k++ +s+++++rlG  +++ 
  gene804|gene804|rna804|rna804 31 SNFCHKLRGLSDKQGNRLGGMVQTC 55
                                   567788999999*****99988764 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.0041
                       AvrLm4-7   7 eykkeaeaCeeda....eklekeCaelaqkykdyseq 39 
                                     y++++++C++ +     +l  +C +l+ ++ +y ++
  gene804|gene804|rna804|rna804 116 YYTSKYKNCNKRNiyefINLLYKCLNLKVTIFSYPTN 152
                                    578899******99977677789*9999999988665 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.00092
                       AvrLm4-7   2 kqrlieykkeaeaCeedaeklekeCaelaqkykdyseqnekrlGrditaelacdscd 58 
                                    +q+ + +++  + C++ ++ +++  + + +k+ +ys+++++r+ +d    ++c+s++
  gene804|gene804|rna804|rna804 259 QQKIYAFYEPGRVCHHIQGFYRHVFTMIYEKFLHYSTRQKRRISNDGLRLTKCQSLN 315
                                    69999*************************************999988888888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (370 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       628  (0.0350271); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 2630.57
//
Query:       gene805|gene805|rna805|rna805  [L=391]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.8e-06   26.8   7.8    4.8e-06   26.8   7.8    3.2  2  GWT1      GWT1
  ------ inclusion threshold ------
        5.8    7.0   5.9        1.9    8.6   0.0    2.9  3  Vma12     Endoplasmic reticulum-based factor for assembly of 


Domain annotation for each model (and alignments):
>> GWT1  GWT1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    3.9   0.7    0.0061        55      39     101 ..     138     194 ..      90     213 .. 0.70
   2 !   26.8   7.8   5.4e-10   4.8e-06       2     110 ..     235     324 ..     234     380 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.0061
                           GWT1  39 kkkkkkkesketlkllikllllsilllllllllelyvefvSRrlaNlpYvlwvvalnltllll 101
                                    +k+k++ +++++l+l+  ++++ i l+l        ++ +     Nl+++l+  +  ++++++
  gene805|gene805|rna805|rna805 138 RKSKESIHRRFILSLMAGIVICFINLVL------GIKQDITQYGSNLNFFLVLSSSYIFFMIF 194
                                    3444455555555555555555544444......45666777789999999888877777664 PP

  == domain 2  score: 26.8 bits;  conditional E-value: 5.4e-10
                           GWT1   2 NkEGlfsliGylaiyllgvslgkyvlkrekeaeeeekkkkkkkkesketlkllikllllsilllllllllelyvefvSRr 81 
                                    NkEGl  ++  + ++l++ ++g+ +++                 ++ ++ ++l+ l++++++++     ++  ++f SRr
  gene805|gene805|rna805|rna805 235 NKEGLNAILPTFVMFLFSSYIGRKMTN-----------------KRATLPSILVALFITCLFIISY--GYSEEISFASRR 295
                                    ***********************9991.................2345667777777777666666..78888889**** PP

                           GWT1  82 laNlpYvlwvvalnltllllflliellfv 110
                                    l Nl+Yv++ ++l ++ ++++++++ lf+
  gene805|gene805|rna805|rna805 296 LGNLSYVMLALSLFFSHFMCLYVADWLFP 324
                                    **************999999999998554 PP

>> Vma12  Endoplasmic reticulum-based factor for assembly of V-ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.0   0.00021       1.9      90     127 ..     129     165 ..     113     170 .. 0.82
   2 ?   -1.9   0.1      0.36   3.3e+03      82     115 ..     179     207 ..     171     222 .. 0.62
   3 ?   -0.5   0.5      0.14   1.2e+03      84     126 ..     305     348 ..     298     357 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00021
                          Vma12  90 vffavwialrsartpslpvrvllslvvallVgvAEvvv 127
                                    v + ++  +r++ + s + r++lsl++++++ +  +v+
  gene805|gene805|rna805|rna805 129 VLIEGYKCARKS-KESIHRRFILSLMAGIVICFINLVL 165
                                    455567777777.559****************999887 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.36
                          Vma12  82 NiliSvvavffavwialrsartpslpvrvllslv 115
                                    N+++ v+++ + ++++ +s       +++ lsl+
  gene805|gene805|rna805|rna805 179 NFFL-VLSSSYIFFMIFKSK----HNFKLALSLI 207
                                    5555.555555555555554....5666666664 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.14
                          Vma12  84 liSvvavffavwialrsartp.slpvrvllslvvallVgvAEvv 126
                                     +S +++ f+  +++++++++  +  ++++s  + l+V++ Ev 
  gene805|gene805|rna805|rna805 305 ALSLFFSHFMCLYVADWLFPLiLTDLQLFISHHMILMVFMSEVG 348
                                    57888888888888888888778889999999999999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (391 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       885  (0.0493614); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 2576.21
//
Query:       gene806|gene806|rna806|rna806  [L=206]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       726  (0.0404931); expected 358.6 (0.02)
Passed bias filter:                      441  (0.024597); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1418.38
//
Query:       gene807|gene807|rna807|rna807  [L=552]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.7e-43  148.3   0.2    3.8e-43  147.2   0.2    1.6  1  NOG1_N     NOG1 N-terminal helical domain
    7.4e-24   83.3   0.3    2.3e-23   81.7   0.3    1.9  1  NOG1       Nucleolar GTP-binding protein 1 (NOG1)
    3.6e-16   59.2   0.0    8.6e-16   58.0   0.0    1.7  1  MMR_HSR1   50S ribosome-binding GTPase
    5.1e-14   52.0   5.6    9.9e-14   51.1   5.6    1.5  1  NOGCT      NOGCT (NUC087) domain
    5.6e-08   32.5   0.0    1.1e-07   31.6   0.0    1.5  1  FeoB_N     Ferrous iron transport protein B
    0.00032   20.8   0.1       0.42   10.7   0.0    2.6  2  Dynamin_N  Dynamin family
  ------ inclusion threshold ------
      0.032   13.5   0.1      0.091   12.1   0.0    1.8  2  AIG1       AIG1 family


Domain annotation for each model (and alignments):
>> NOG1_N  NOG1 N-terminal helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  147.2   0.2   1.5e-46   3.8e-43       1     160 []      30     187 ..      30     187 .. 0.97

  Alignments for each domain:
  == domain 1  score: 147.2 bits;  conditional E-value: 1.5e-46
                         NOG1_N   1 FekiptvptseelidkalrrakraakttkkkkneikrlrnlearkvrtasntlsdkLeeivkkfPnldelhpFyrelldv 80 
                                    F+ i+ +p s  lid  l++++r+++t+ +kk  + ++r++++rkv+++  +  ++Le+i+++fP+++++hpFy++l++v
  gene807|gene807|rna807|rna807  30 FKAIKRIPLS--LIDVVLSKTQRKTPTVIRKKHPLPKIRSFYTRKVKFTGAEYVAQLETIINSFPHVEDIHPFYNDLINV 107
                                    5566666654..9******************************************************************* PP

                         NOG1_N  81 lvdkdelkksLaqvkwarklirkigkeyvnklkkaddkkeakelrreafgrvasvlkkvdkaldfLedvrkkLrkLpaiD 160
                                    l+dk+++k++L+++++++k i+ i++eyv+++k++ ++  +k+l+r+++g++ s++k+ ++ l++Le+vr+++ +Lp+iD
  gene807|gene807|rna807|rna807 108 LYDKSHFKMALGHLNSTKKNIEGITNEYVRLIKYGTSLYGCKQLKRAGLGKMTSLVKRLKPTLEYLEEVRQHMSRLPQID 187
                                    *******************************************************************************9 PP

>> NOG1  Nucleolar GTP-binding protein 1 (NOG1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.7   0.3     9e-27   2.3e-23       1      58 []     257     313 ..     257     313 .. 0.99

  Alignments for each domain:
  == domain 1  score: 81.7 bits;  conditional E-value: 9e-27
                           NOG1   1 eIEkqAiaALkhladavlFllDpseecgysleeQlsLleeikelfankpvivvlnKiD 58 
                                    +IE+q+++AL+hl+++vlF+lD+se+cgys+++Q++L++++ +l++ +++++vl+K+D
  gene807|gene807|rna807|rna807 257 TIEMQSVTALAHLNSIVLFFLDISEQCGYSIDQQINLYKSLAPLID-RRMLIVLSKCD 313
                                    6********************************************9.9*********9 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.0   0.0   3.4e-19   8.6e-16       2     113 ..     193     310 ..     192     311 .. 0.73

  Alignments for each domain:
  == domain 1  score: 58.0 bits;  conditional E-value: 3.4e-19
                                    EEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSSHHHHHH..HHHHHHHHHHC.TSE CS
                       MMR_HSR1   2 vaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgkeielvDtpGliegaseek..glgkaflalee.adl 78 
                                    v++ G pN+GKS+++n+ +++ + v+ +++tTr    g+++++  ++++vDtpG+++ a ee    + +++ al    ++
  gene807|gene807|rna807|rna807 193 VLLCGLPNTGKSSFMNSVSKADVDVQPYAFTTRSLFVGHFEYNYLSWQVVDTPGVLDHALEEMntIEMQSVTALAHlNSI 272
                                    889**************************************999**********88633333333333333333333399 PP

                                    EEEEEETTTT.CSHHHHHHHHHHHHH...TTSEEEEEEE CS
                       MMR_HSR1  79 illvvdasee.klkpldeeleellee...akkplilvln 113
                                    +l+ +d+se+ ++  +d++++ +++     ++++++vl+
  gene807|gene807|rna807|rna807 273 VLFFLDISEQcGY-SIDQQINLYKSLaplIDRRMLIVLS 310
                                    ******9944445.4556666654224455666666665 PP

>> NOGCT  NOGCT (NUC087) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.1   5.6   3.9e-17   9.9e-14       4      54 .]     414     460 ..     410     460 .. 0.84

  Alignments for each domain:
  == domain 1  score: 51.1 bits;  conditional E-value: 3.9e-17
                          NOGCT   4 erdleeenggagvYsvdlkkkYllkndewkyDiiPEildGkNvaDFidpdI 54 
                                    e++l ++n    +Y +d +k+Yl+ n+e+kyD++PEi++G+Nv+DF+dpd+
  gene807|gene807|rna807|rna807 414 EKELAKDNL---DYYFDENKNYLV-NEEEKYDVMPEIYNGRNVIDFVDPDV 460
                                    555555555...5*********65.88***********************6 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.6   0.0   4.2e-11   1.1e-07       2     116 ..     192     313 ..     191     335 .. 0.72

  Alignments for each domain:
  == domain 1  score: 31.6 bits;  conditional E-value: 4.2e-11
                                    EEEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEEEETTEEEEEEE----..SSSSSSSHHHHHHHHHHH..CT CS
                         FeoB_N   2 tvalvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegklklkgkeveivDlPGi..Yslsayseeekvardfll..ee 77 
                                    tv l+G pn+Gk++++n++++a+ +v  ++ +t     g+++++  + ++vD PG+  ++l+++++ e  + + l+  ++
  gene807|gene807|rna807|rna807 192 TVLLCGLPNTGKSSFMNSVSKADVDVQPYAFTTRSLFVGHFEYNYLSWQVVDTPGVldHALEEMNTIEMQSVTALAhlNS 271
                                    789****************************************************9556677766555555444441133 PP

                                    SSSEEEEEEEGG..GHHHHHHHHHHHHHT.TSSEEEEEETHH CS
                         FeoB_N  78 epdvvvnvvdat..nlernLyLtlqllel.gvpvvlalnmid 116
                                     +   +++ + +  ++++++ L   l+ l + +++++l ++d
  gene807|gene807|rna807|rna807 272 IVLFFLDISEQCgySIDQQINLYKSLAPLiDRRMLIVLSKCD 313
                                    333334444432225666666666666542456666666666 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.0   0.00016      0.42       1      35 [.     193     227 ..     193     235 .. 0.86
   2 !    7.7   0.0    0.0013       3.4     104     167 ..     240     311 ..     229     312 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00016
                                    EEEEEBTTTTHHHHHHHHHTS--S---SSS---S- CS
                      Dynamin_N   1 iavvGsqSsGKSSvlnaLlgedilprgpnptTrrp 35 
                                    ++++G  + GKSS++n++ ++d+ +     tTr +
  gene807|gene807|rna807|rna807 193 VLLCGLPNTGKSSFMNSVSKADVDVQPYAFTTRSL 227
                                    6789999***************9888888888865 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0013
                                    EEEE---B-SSSGTTS.....HHHHHHHSTTEEEEEEEETTS-CCC-..CHHHHHHHHSTTBTT.EEEEEE- CS
                      Dynamin_N 104 tlvDlPGldsvnkrdq.....elvkeyikkadiilavtsanhdlsns..ealflarevdpkgkr.tivvltk 167
                                     +vD+PG+ + + +++     + v+ +++ ++i+l+ ++ + ++  s  ++ +l +++ p  +r +++vl k
  gene807|gene807|rna807|rna807 240 QVVDTPGVLDHALEEMntiemQSVTALAHLNSIVLFFLDISEQCGYSidQQINLYKSLAPLIDRrMLIVLSK 311
                                    68******99998888778766677777**********9998765553266677788887766657777766 PP

>> AIG1  AIG1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   3.6e-05     0.091       2      71 ..     192     259 ..     191     297 .. 0.68
   2 ?   -3.0   0.1       1.4   3.7e+03     126     144 ..     414     432 ..     411     437 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.6e-05
                                    EEEEESSTTSSHHHHHHHHHTS--SS--TTTS---SS-EEEEE.EETTEEEEEEE--SCCCTTCCHHCHHH CS
                           AIG1   2 tivlvGktgnGkSaTgNsilgkkaFesklsaqsvtkkcqkksr.twdgkkinViDTPglfdlsvsadkisk 71 
                                    t++l G   +GkS+  Ns+ + ++     +  + t+++  +   + +  + +V+DTPg++d   ++ ++++
  gene807|gene807|rna807|rna807 192 TVLLCGLPNTGKSSFMNSVSKADVDV---QPYAFTTRSLFVGHfEYNYLSWQVVDTPGVLDHALEEMNTIE 259
                                    89*****************7776633...33444544544444488889999*********9876655554 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.4
                                    GGGGTTCCHHHHHHHHH-H CS
                           AIG1 126 kddleddsledylsksspe 144
                                    +++l++d+l+ y+ ++++ 
  gene807|gene807|rna807|rna807 414 EKELAKDNLDYYFDENKNY 432
                                    56799999*****998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (552 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       619  (0.0345251); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.75u 0.35s 00:00:01.10 Elapsed: 00:00:00.57
# Mc/sec: 2936.69
//
Query:       gene808|gene808|rna808|rna808  [L=99]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.099   13.0   1.9       0.16   12.3   1.9    1.3  1  PP_kinase_N  Polyphosphate kinase N-terminal domain


Domain annotation for each model (and alignments):
>> PP_kinase_N  Polyphosphate kinase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   1.9   8.7e-06      0.16      51     104 ..       7      64 ..       1      66 [. 0.73

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 8.7e-06
                                    HHH.HTT-..---....--------HHHHHHHHHHHHHHHHHHHHHHTHHHHHHHTTE CS
                    PP_kinase_N  51 lkrqleakvekks....edgltpeeqlkaiseeveelveeqekileeellpeLaeegi 104
                                     ++++++k++ k+    e+++++++ql++++e+  ++++++++++++ + +e++e +i
  gene808|gene808|rna808|rna808   7 KEKTITKKITVKTsdhsEEESDENTQLESMNETRDQIMNKHRDYWTNVIENEITEFNI 64 
                                    4555555544333122155667799*************************99999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2426  (0.135312); expected 358.6 (0.02)
Passed bias filter:                      638  (0.0355848); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 639.35
//
Query:       gene809|gene809|rna809|rna809  [L=392]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
      0.078   12.9   0.0       0.62   10.1   0.0    2.5  3  PTCB-BRCT   twin BRCT domain
       0.24   11.8   0.2       0.24   11.8   0.2    2.5  3  BRCT_2      BRCT domain, a BRCA1 C-terminus domain
        1.1    9.5   9.4        0.3   11.3   0.6    2.6  2  DUF4793     Domain of unknown function (DUF4793)
        4.2    7.9  11.3       0.46   11.0   4.9    2.5  2  zf-CHY      CHY zinc finger


Domain annotation for each model (and alignments):
>> PTCB-BRCT  twin BRCT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.47   2.1e+03      42      54 ..       5      17 ..       3      20 .. 0.78
   2 ?   10.1   0.0   0.00014      0.62      30      60 ..     256     291 ..     253     294 .. 0.82
   3 ?   -2.8   0.0       1.4   6.4e+03      14      28 ..     350     364 ..     344     366 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.47
                                   SS-CHHHHHHHHC CS
                      PTCB-BRCT 42 sgeGekyekAkkw 54
                                   ++ ++ky+kA ++
  gene809|gene809|rna809|rna809  5 HSPSNKYDKAIEC 17
                                   66789*****998 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00014
                                    SEETT-SEEEE.....CSS-CHHHHHHHHCT-EEE- CS
                      PTCB-BRCT  30 dltksvTHLic.....ksgeGekyekAkkwgipvVs 60 
                                    +++ +vTHLi+     k+ ++ ky +A  +gi + +
  gene809|gene809|rna809|rna809 256 RMSDQVTHLIVntegnKCIRSYKYLYAGLRGIFILN 291
                                    7999*******8888888888899999888888876 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 1.4
                                    HHHHHHHHHTT-EEE CS
                      PTCB-BRCT  14 kslqklieamGaeys 28 
                                    +++ kl++  G++++
  gene809|gene809|rna809|rna809 350 YQVAKLVQLGGGTIN 364
                                    678888888888876 PP

>> BRCT_2  BRCT domain, a BRCA1 C-terminus domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       2.3     1e+04      37      52 ..     255     270 ..     252     281 .. 0.63
   2 ?   -2.8   0.3       1.9   8.7e+03       4      14 ..     287     299 ..     284     312 .. 0.62
   3 ?   11.8   0.2   5.4e-05      0.24       3      45 ..     334     373 ..     328     390 .. 0.79

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 2.3
                         BRCT_2  37 etitsavyiviaesne 52 
                                    + ++++v+++i++++ 
  gene809|gene809|rna809|rna809 255 RRMSDQVTHLIVNTEG 270
                                    5566677777777763 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.9
                         BRCT_2   4 lF.eglrFYin.d 14 
                                    +F  ++ F+i  +
  gene809|gene809|rna809|rna809 287 IFiLNFAFFIDfE 299
                                    6667889999531 PP

  == domain 3  score: 11.8 bits;  conditional E-value: 5.4e-05
                         BRCT_2   3 klFeglrFYindaepspsreklkklIeknGGevvetitsavyi 45 
                                     +Fe+ +F +    ++++ ++++kl++  GG++ ++++  v i
  gene809|gene809|rna809|rna809 334 LIFENVNFIM---DKRTTNYQVAKLVQLGGGTINSKQDHFVNI 373
                                    699****999...5668****************9999533333 PP

>> DUF4793  Domain of unknown function (DUF4793)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   2.7     0.075   3.4e+02      34      87 ..      35      93 ..      24      97 .. 0.71
   2 ?   11.3   0.6   6.7e-05       0.3       2      38 ..     212     249 ..     211     255 .. 0.95

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.075
                        DUF4793 34 kvvYdtskalskCs..lnnt...eCslkl.sflsteavvlevpaneegssaeewvvklsc 87
                                   + +Y+t+++   Cs   +++   eC +    f   ++ v++v +++ + s++  v + sc
  gene809|gene809|rna809|rna809 35 TALYQTNSNKIICSqcKEKGrfkECIFAHmLFDLRKYFVINVFDRNPILSTS-SVTEKSC 93
                                   6789997765555422233224589997515666889********9999976.7777777 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 6.7e-05
                        DUF4793   2 ieykveedgyYylafsnene.kkvevelnfdlekvvYd 38 
                                    i++++ee g+ y+ fsn+ne ++ +v+ +f ++k+ Y+
  gene809|gene809|rna809|rna809 212 IKHEIEEIGNIYMCFSNLNEyQHRYVTKKFPIYKKKYK 249
                                    899*****************999************996 PP

>> zf-CHY  CHY zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   4.9    0.0001      0.46       9      57 ..      15      59 ..       8      74 .. 0.76
   2 ?   -1.1   0.2       0.6   2.7e+03      10      33 ..     242     264 ..     229     278 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0001
                         zf-CHY  9 vairapcCkklyaCreCHeeledhelerlevkevlcllCeteqekavlC 57
                                   ++  ++   ++ +C+ CH+   + +l +++ ++++c++C+++    ++C
  gene809|gene809|rna809|rna809 15 IECFMKRLYTFIKCQMCHQ---NTALYQTNSNKIICSQCKEKG-RFKEC 59
                                   5555556667789*****9...788999999********9964.33445 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.6
                         zf-CHY  10 airapcCkklyaCreCHeeledhe 33 
                                     i  ++ k+++ Cr+  + + +h 
  gene809|gene809|rna809|rna809 242 PIYKKKYKNIFLCRRMSD-QVTHL 264
                                    444555666777777665.34444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (392 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       905  (0.0504769); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2963.37
//
Query:       gene81|gene81|rna81|rna81  [L=62]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (62 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       513  (0.0286129); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 441.66
//
Query:       gene810|gene810|rna810|rna810  [L=152]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      3e-12   46.8   1.5    3.5e-12   46.5   1.5    1.0  1  PRP38          PRP38 family
  ------ inclusion threshold ------
      0.053   13.6   0.0      0.073   13.2   0.0    1.3  1  Ferric_reduct  Ferric reductase like transmembrane component
       0.21   11.2   0.0       0.28   10.8   0.0    1.2  1  WcbI           Polysaccharide biosynthesis enzyme WcbI


Domain annotation for each model (and alignments):
>> PRP38  PRP38 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.5   1.5   5.8e-16   3.5e-12      12     162 ..       7     150 ..       4     152 .] 0.85

  Alignments for each domain:
  == domain 1  score: 46.5 bits;  conditional E-value: 5.8e-16
                          PRP38  12 iekivrerIleseYykenlfglkalaelvdeiveklkhieglvlggtekpstflClllKLlqlkptkkqieelln...ne 88 
                                    + + ++e+Il+s+Y+k ++ +  + ++ +  + + l+ i++lv+g+   p +f+Cll KL  l+++++ ++e  +   +e
  gene810|gene810|rna810|rna810   7 FSNPIKEKILKSPYFK-EIKNYDL-DQTISDAHK-LSSIGSLVYGS---PHPFICLLQKLESLNVDNNTMLEKYHgalRE 80 
                                    677899**********.8999999.888999999.*********96...66*****************999988889988 PP

                          PRP38  89 dskYiralgllYlRlvlepkelykllepllnDyr.klkrrekdgevdpkgvklitidelvddLltkdricgtiLp 162
                                    ++  + +  ++Y R++ + k+ ++ +++ l++++  +k++++++     +   +ti e+ + L +++ ++g+ + 
  gene810|gene810|rna810|rna810  81 ENSTVIMFFVFYFRMTAKMKNEFNEIKKPLENKKlLVKIVDENN-----ESYSVTIKEVLNMLQSNKYVFGIFMK 150
                                    888899999*********88888877777777750345555554.....88899****************99876 PP

>> Ferric_reduct  Ferric reductase like transmembrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   1.2e-05     0.073      19      74 ..      18      74 ..       3     112 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.2e-05
                  Ferric_reduct 19 nnflepltglsldklll.fHkwlgvlafllallHvilyllnflrfsaldeerlldsl 74
                                   ++ ++ + ++ ld+++   Hk+ ++  +++ + H ++ ll++l + + d++  l++ 
  gene810|gene810|rna810|rna810 18 SPYFKEIKNYDLDQTISdAHKLSSIGSLVYGSPHPFICLLQKLESLNVDNNTMLEKY 74
                                   4566688999*******************************9986654333333332 PP

>> WcbI  Polysaccharide biosynthesis enzyme WcbI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   4.7e-05      0.28      63     112 ..      21      75 ..       6      80 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 4.7e-05
                           WcbI  63 yr.lgtaqllarlpaaarvvrvPvirFaglhPdlvivrs....dgsldpplvdYh 112
                                    ++ ++ ++l +   +a ++ ++ ++++ + hP+++ +++    + + +  l +Yh
  gene810|gene810|rna810|rna810  21 FKeIKNYDLDQTISDAHKLSSIGSLVYGSPHPFICLLQKleslNVDNNTMLEKYH 75 
                                    34788899999999999*********************98877666666777777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1295  (0.0722293); expected 358.6 (0.02)
Passed bias filter:                      583  (0.0325172); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1145.86
//
Query:       gene811|gene811|rna811|rna811  [L=190]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-28   99.9   4.4    1.4e-28   99.6   4.4    1.1  1  Ferritin  Ferritin-like domain
     0.0005   20.2   0.1       0.01   16.1   0.0    2.6  2  Coat_F    Coat F domain
  ------ inclusion threshold ------
        2.7    8.4   5.9         10    6.6   0.5    2.9  2  NBD94     Nucleotide-Binding Domain 94 of RH


Domain annotation for each model (and alignments):
>> Ferritin  Ferritin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.6   4.4   2.4e-32   1.4e-28       2     141 ..      32     169 ..      31     170 .. 0.94

  Alignments for each domain:
  == domain 1  score: 99.6 bits;  conditional E-value: 2.4e-32
                                    HHHHHHHHHHHHHHHHHHHHHHHHH..STTHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS....SHHHHHHC-SSSSCS CS
                       Ferritin   2 kaLneqladeltaayqylamawyvk..gpgleglaeffdeqaeeerehadklaerilalGgtpvltraeleeieapkefg 79 
                                    ++L eql  e  a y y +   y++  ++ l+++a+ff++q+ ee++ha+ +++++++ G  p  ++ +le+     +++
  gene811|gene811|rna811|rna811  32 ELLSEQLRIENFAFYFYQSAYQYCNsrEMALPSIANFFYKQYNEELTHAKGIIDYMNQTGLRPKFKELSLERT----NYK 107
                                    789**********************999*********************************666666666664....489 PP

                                    SHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Ferritin  80 sveevleaalehekkvteslrelielaeeegDpatadfledfleeqeeheweleallekler 141
                                    s+ ev+e  l+ e++  +++ + ++ a++++D+a+++f++d+++eq+++++e++++l++ +r
  gene811|gene811|rna811|rna811 108 SLVEVFELSLKYEEESYKHILQTYKAADKHHDYALCQFMDDYVAEQVKSIKEFSDYLQNAKR 169
                                    **********************************************************9987 PP

>> Coat_F  Coat F domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   1.7e-06      0.01      26      58 ..      59      91 ..      56      94 .. 0.94
   2 ?    0.9   0.0     0.093   5.6e+02       7      27 ..     161     181 ..     160     189 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.7e-06
                         Coat_F 26 EasnpelRqtlkqilneeiemqeelfnlmnqkG 58
                                   E++ p++ +++ ++ nee+ +++ + ++mnq G
  gene811|gene811|rna811|rna811 59 EMALPSIANFFYKQYNEELTHAKGIIDYMNQTG 91
                                   88999**************************99 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.093
                         Coat_F   7 ndlLsteKsaarnyataitEa 27 
                                    +d+L+ +K  a  +at+ + a
  gene811|gene811|rna811|rna811 161 SDYLQNAKRCAEGFATFNLDA 181
                                    79*********9999986665 PP

>> NBD94  Nucleotide-Binding Domain 94 of RH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.5    0.0017        10      51      76 ..      64      89 ..      11      93 .. 0.72
   2 ?    3.3   0.5     0.018   1.1e+02      26      79 ..      97     151 ..      91     168 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0017
                          NBD94 51 sLikllvqkIdeekkkaenlieeiek 76
                                   s+ +++ ++ +ee ++a+ +i+ +++
  gene811|gene811|rna811|rna811 64 SIANFFYKQYNEELTHAKGIIDYMNQ 89
                                   67899****************99986 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.018
                          NBD94  26 nEleeiekektsleevknielsYgrsLikllvqkIdeekkkaen.lieeiekyie 79 
                                    +El+   ++  sl ev ++ l+Y+    k+++q      k+ ++ l + ++ y++
  gene811|gene811|rna811|rna811  97 KELSLERTNYKSLVEVFELSLKYEEESYKHILQTYKAADKHHDYaLCQFMDDYVA 151
                                    67777777888999999*******9999999998876555544414455666664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (190 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1112  (0.0620224); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1421.42
//
Query:       gene812|gene812|rna812|rna812  [L=343]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.6e-35  120.8   0.3    1.5e-34  119.4   0.3    1.7  2  PTPlike_phytase  Inositol hexakisphosphate


Domain annotation for each model (and alignments):
>> PTPlike_phytase  Inositol hexakisphosphate
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0      0.45     8e+03      99     129 ..      30      64 ..      26      71 .. 0.50
   2 !  119.4   0.3   8.4e-39   1.5e-34       1     155 [.      73     221 ..      73     222 .. 0.92

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 0.45
                                    T-EEEEEE...E-TTS---HHHHHHHH.HHHHTS- CS
                PTPlike_phytase  99 slrYaRip...itdekapeeedfdalv.silkeap 129
                                    ++rY R+    i  +  p+++ +++l+ ++lke +
  gene812|gene812|rna812|rna812  30 NMRYIRVLdhlIVGCAMPKANAIKKLLlKVLKEHQ 64 
                                    56666653222445556666666654314444443 PP

  == domain 2  score: 119.4 bits;  conditional E-value: 8.4e-39
                                    EEEE-S-EEEETTEEEEEE-GGG-TTTT--.HHHHHHHHHHHHHHHHT-SEEEEEEEHHHHHTT-CCG-EEE-S-..... CS
                PTPlike_phytase   1 inlReEpvvyvngrpyvlrekedllenlkeytgisaeeleklearlkeevlaeakksegrvlvhdeteegkdvktlqevw 80 
                                    +++ReEpv+yvn++pyvlr+ + +++n+ e+tgi+ + + k+e +lk+++ +e   +++ +lvhdet  +   + +++ w
  gene812|gene812|rna812|rna812  73 FCMREEPVIYVNNTPYVLRRYSVPYDNI-EITGIDSNIVHKMEVQLKKDIYDEI--KDNLLLVHDETLVK-GTCVITHKW 148
                                    69*************************8.************************9..568999*****999.467777777 PP

                                    .......EE-HHHHHHHTT-EEEEEEE-TTS---HHHHHHHHHHHHTS-TT-EEEEE-SSSSHHHHHHHHHHHHH CS
                PTPlike_phytase  81 eevetpeevyerelaeelslrYaRipitdekapeeedfdalvsilkeapektalvfnCqmGrgRTTtamviatLl 155
                                    +eve  ++ ++re+    sl ++R+pi+de+ap ++ ++ l++ l +++ + +l fnCqmGrgRTTt+m++ ++ 
  gene812|gene812|rna812|rna812 149 VEVE--AVKTMREVYNIKSLIFHRVPISDERAPMPRLISYLYDTLCKVKGEMVLFFNCQMGRGRTTTFMILSYMT 221
                                    7555..555788888999******************************99*********************9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (343 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       593  (0.0330749); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 2451.10
//
Query:       gene813|gene813|rna813|rna813  [L=744]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.2e-27   94.2   0.1    1.2e-13   51.4   0.0    2.3  2  PTPlike_phytase  Inositol hexakisphosphate
  ------ inclusion threshold ------
       0.02   14.6   0.1      0.039   13.7   0.1    1.4  1  Oxidoreduct_C    Putative oxidoreductase C terminal domain
       0.12   11.4   0.0       0.28   10.2   0.0    1.6  1  NPIP             Nuclear pore complex interacting protein (NP


Domain annotation for each model (and alignments):
>> PTPlike_phytase  Inositol hexakisphosphate
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.4   0.0   2.1e-17   1.2e-13       1     155 [.      75     224 ..      75     225 .. 0.87
   2 !   40.6   0.1   4.5e-14   2.7e-10       1     129 [.     479     605 ..     479     631 .. 0.82

  Alignments for each domain:
  == domain 1  score: 51.4 bits;  conditional E-value: 2.1e-17
                                    EEEE-S-EEEETTEEEEEE-GGG-TTTT--.HHHHHHHHHHHHHHHHT-SEEEEEEEHHHHHTT-CCG-EEE-S-..... CS
                PTPlike_phytase   1 inlReEpvvyvngrpyvlrekedllenlkeytgisaeeleklearlkeevlaeakksegrvlvhdeteegkdvktlqevw 80 
                                    inlR  p + ++g  y lr+ + + ++   + +   +++e+ e+rlk e+ +e k +eg + +h e +   +++ l++  
  gene813|gene813|rna813|rna813  75 INLRPNPCILIDGFCYELRNIYGPVDSNFLLSSRIFQNIEEQETRLKLEITQEIKLNEGLLKIHYEANGILKSELLKPS- 153
                                    79********************9988766888889999*************************9999976533333333. PP

                                    .........EE-HHHHHHHTT-EEEEEEE-TTS---HHHHHHHHHHHHTS-TT-EEEEE-SSSSHHHHHHHHHHHHH CS
                PTPlike_phytase  81 eeve..tpeevyerelaeelslrYaRipitdekapeeedfdalvsilkeapektalvfnCqmGrgRTTtamviatLl 155
                                          t +e++     ++++l Y+R+p+++  +++++ + ++++ + e  ++t +vf    G +RTT+a +++ Ll
  gene813|gene813|rna813|rna813 154 ---IicTFREFF---ETKSTKLAYYRLPLPKTMSILKNSIFTFLNNVYEKLKDTLVVFYSASGGTRTTFASCLYKLL 224
                                    ...122444444...4567899****************************99**********************997 PP

  == domain 2  score: 40.6 bits;  conditional E-value: 4.5e-14
                                    EEEE-S-EEEETTEEEEEE-GGG-TTTT--.HHHHHHHHHHHHHHHHT-SEEEEEEEHHHHHTT-CCG-EEE-S-..... CS
                PTPlike_phytase   1 inlReEpvvyvngrpyvlrekedllenlkeytgisaeeleklearlkeevlaeakksegrvlvhdeteegkdvktlqevw 80 
                                    +nl eEp++y+ g++y  r+  + ++++k  ++++ ++le++e+++ke +l+  +++   v++++e+ +   v++++   
  gene813|gene813|rna813|rna813 479 LNLMEEPLIYIKGEAYLKRNLISYKNSIKIFESVTYQKLEEIENAIKEGLLERLRSKRCLVYYEEENGDL--VRKTISNL 556
                                    5999************************************************998888777776666665..55555555 PP

                                    ........EE-HHHHHHHTT-EEEEEEE-TTS---HHHHHHHHHHHHTS- CS
                PTPlike_phytase  81 eeve.tpeevyerelaeelslrYaRipitdekapeeedfdalvsilkeap 129
                                    +e++ ++ ++y   + ++++ +Y+R+pit +   + ++f  +++++k+  
  gene813|gene813|rna813|rna813 557 HESDiQTPNEYFLSITDSTD-DYYRFPITPNFRFKLNNFMLFTKLIKKID 605
                                    55557555556666666655.9***********************99974 PP

>> Oxidoreduct_C  Putative oxidoreductase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   6.4e-06     0.039     137     192 ..     418     473 ..     357     515 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6.4e-06
                  Oxidoreduct_C 137 kgvhakvsviWnyeapegtgDthysilrGskanlvirqgkeekykptLyieaveke 192
                                    k v+ k +    ++ p+ + D++  + rG+k +++i+q+ ++k +p+  ie +++ 
  gene813|gene813|rna813|rna813 418 KPVNFKSKFQPIFKLPNLAKDNYLVLYRGTKQTFEIKQDDHKKLQPVSIIEGKHAL 473
                                    667777777778999********************************999987665 PP

>> NPIP  Nuclear pore complex interacting protein (NPIP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   4.7e-05      0.28     143     194 ..     539     595 ..     514     609 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 4.7e-05
                           NPIP 143 lseaeenGkldmkkirtykkm.fqdaq....alrrraedsyrckitpsarkaldnrv 194
                                    +   eenG l+ k i   ++   q  +    ++   ++d+yr  itp  r  l+n +
  gene813|gene813|rna813|rna813 539 VYYEEENGDLVRKTISNLHESdIQTPNeyflSITDSTDDYYRFPITPNFRFKLNNFM 595
                                    455699*******99987764245433111156789*****************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (744 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       690  (0.0384851); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.65u 0.26s 00:00:00.91 Elapsed: 00:00:00.45
# Mc/sec: 4933.98
//
Query:       gene814|gene814|rna814|rna814  [L=332]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    5.5e-05   23.5   1.0    0.00027   21.2   1.0    2.0  1  RasGEF      RasGEF domain
  ------ inclusion threshold ------
      0.022   14.3   0.1      0.046   13.2   0.1    1.6  1  HEPN_AbiU2  AbiU2


Domain annotation for each model (and alignments):
>> RasGEF  RasGEF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   1.0     3e-08   0.00027       4     100 ..      85     217 ..      82     228 .. 0.62

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 3e-08
                         RasGEF   4 eqltlieaelfskikpeellgsawsked........................................rs...pnveavi 40 
                                    + l+ ++ +l++ki p+e++++  ++++                                        ++   +n++++i
  gene814|gene814|rna814|rna814  85 KVLHNLDLRLYRKIMPTEIVEYGKTSNQnngndenmddgsvdgqqdvrdnknrtvegrgnetnsaetiNNemsENLKNII 164
                                    5688999**************84222224666666666666666666655544444444333222222002223333333 PP

                         RasGEF  41 arfnrlsnwvaseilseeslkkRakv.iekfikiakecrklnNfnslmailsaLqsspvsr 100
                                    ++  +l+ +++ +i           +  ++f+++++ ++k nN+ns +ail +L +++ +r
  gene814|gene814|rna814|rna814 165 EKNRALTALTSIKIS--------GGLkSSFFVRVCRYLKKRNNYNSIVAILNGLRTHKTNR 217
                                    333333333333333........33314678***********************9988776 PP

>> HEPN_AbiU2  AbiU2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   5.2e-06     0.046      17      99 ..     148     225 ..     132     252 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 5.2e-06
                     HEPN_AbiU2  17 dalavyailenaeknelelneapaffqtir..ralfeslllelarlfDkskrslslpkllklleskdeveadrelekard 94 
                                     a+ + +++++++kn +e n+a ++++ i+    l +s+++ ++r + k+++  s+  +l+ l+     ++++ +++++ 
  gene814|gene814|rna814|rna814 148 SAETINNEMSENLKNIIEKNRALTALTSIKisGGLKSSFFVRVCRYLKKRNNYNSIVAILNGLR-----THKTNRSFREF 222
                                    5556667788999999999999988887643389****************999***********.....33333333333 PP

                     HEPN_AbiU2  95 keade 99 
                                    ++  +
  gene814|gene814|rna814|rna814 223 NP--P 225
                                    33..3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (332 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1095  (0.0610742); expected 358.6 (0.02)
Passed bias filter:                      489  (0.0272742); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 2097.34
//
Query:       gene815|gene815|rna815|rna815  [L=383]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      5e-24   85.1   0.4    7.2e-24   84.6   0.4    1.2  1  DnaJ_C          DnaJ C terminal domain
    1.5e-14   53.9   0.7    7.7e-14   51.6   0.7    2.1  1  DnaJ            DnaJ domain
      7e-11   42.3  14.0      7e-11   42.3  14.0    2.2  2  DnaJ_CXXCXGXG   DnaJ central domain
  ------ inclusion threshold ------
      0.022   15.4   0.1      0.048   14.3   0.1    1.5  1  Cytochrom_B562  Cytochrome b562
      0.075   12.3   4.4       0.19   10.9   0.8    2.7  2  DUF1356         Protein of unknown function (DUF1356)
       0.13   12.3  16.7        0.5   10.4   1.7    3.8  4  Anti-TRAP       Tryptophan RNA-binding attenuator protein inh
        5.6    6.6   7.9        7.7    6.1   0.9    2.4  2  TackOD1         Thaumarchaeal output domain 1


Domain annotation for each model (and alignments):
>> DnaJ_C  DnaJ C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.6   0.4   2.8e-27   7.2e-24       2     129 ..     120     317 ..     119     328 .. 0.89

  Alignments for each domain:
  == domain 1  score: 84.6 bits;  conditional E-value: 2.8e-27
                                    EEEEEE-HHHHHH-.EEE.EEEE......................................................... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxx...................................................... RF
                         DnaJ_C   2 eveleisleelykGktkkikikrnvi...................................................... 27 
                                    e+ ++ +l++ + G +k++++kr+ i                                                      
  gene815|gene815|rna815|rna815 120 EFHVKFTLKDSFLGRKKTFSVKREIIctkcegrggekstvcatckgegeiaikrqmglifsldrsacpdcngnghivega 199
                                    678999*****************999****************************************************** PP

                                    ..............TEEEEEE-TT--TT-EEEETT-SSSS...S---EEEEEEE---SS-EEETTEEEEEEEEEHHHHHH CS
                                    ..........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         DnaJ_C  28 ..........kkekktlevkipaGikdgqkirlegeGdeeg.gepGDlivtikvkphpvFkrkgndlyveveislaeall 96 
                                              ++++++++v+ ++G k++++++ +g+Gde+    pGDl+++i+ k++p+Fkr +n+++++++i+l +al+
  gene815|gene815|rna815|rna815 200 lcteckgqryTQKQESVTVTFDKGFKNDDTVVCRGKGDEHVgCIPGDLVLIINIKDDPHFKRVENHIVTTADIDLYTALV 279
                                    *********9888889**********************7777***********99************************* PP

                                    TEEEEEE-SS-EE.EEEE.....--TT-EEEETT-S-EE CS
                                    xxxxxxxxxxxxx.xxxx.....xxxxxxxxxxxxxxxx RF
                         DnaJ_C  97 Ggklevptldgkv.klki.....tqpgevlrikgkGmpk 129
                                    Gg+++++ +d +v ++ki     +++g v+ +kg G+p 
  gene815|gene815|rna815|rna815 280 GGTITLRHIDDSVlNVKIdkiknLREG-VIIVKGAGFPG 317
                                    ****99999554414555553444444.55589999885 PP

>> DnaJ  DnaJ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.6   0.7     3e-17   7.7e-14       2      63 .]       7      84 ..       6      84 .. 0.83

  Alignments for each domain:
  == domain 1  score: 51.6 bits;  conditional E-value: 3e-17
                                   HHHHHTSSTTG-HHHHHHHHHHHHHHHSTT.....TS...........CCHHHHHHHHHHHHHHHHHHTSHHHHHHHH CS
                           DnaJ  2 yYeiLgvskdasedeIkkaYrklalkyHPD.....kn...........pkdpeaeekFkeineAyevLsdpekRkqYD 63
                                   yY++L++++ as +e+kkaY  + +kyHPD     kn           +k +e +e+ k++n+A  vL+dp+k++ YD
  gene815|gene815|rna815|rna815  7 YYKLLNLKPGASVSEVKKAYNAMLMKYHPDmgsiaKNlktiedeaeraSKFEELNEMCKKLNDAKTVLTDPDKKQLYD 84
                                   9*****************************888776677775555433333355558889999**************9 PP

>> DnaJ_CXXCXGXG  DnaJ central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.3  14.0   2.7e-14     7e-11       1      66 [.     146     207 ..     146     208 .. 0.85
   2 ?   -1.0   0.1      0.91   2.3e+03      19      25 ..     231     237 ..     214     243 .. 0.74

  Alignments for each domain:
  == domain 1  score: 42.3 bits;  conditional E-value: 2.7e-14
                  DnaJ_CXXCXGXG   1 CkkCkGsgakkgkkktCktCkGsGvvreeqktlgpfvqqsqstCpeCeGtGkvikekdkCkkCkGk 66 
                                    C+kC+G+g   +k++ C tCkG+G++  +++ +g +++  +s Cp+C+G+G+++ e   C++CkG+
  gene815|gene815|rna815|rna815 146 CTKCEGRGG--EKSTVCATCKGEGEIAIKRQ-MGLIFSLDRSACPDCNGNGHIV-EGALCTECKGQ 207
                                    ********8..55678********8766664.7887778899**********99.5569******8 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.91
                  DnaJ_CXXCXGXG  19 tCkGsGv 25 
                                     C+G+G 
  gene815|gene815|rna815|rna815 231 VCRGKGD 237
                                    5777773 PP

>> Cytochrom_B562  Cytochrome b562
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1   1.9e-05     0.048       5      63 ..      36      89 ..      33      93 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.9e-05
                 Cytochrom_B562  5 eMkqmkkalkqvakaddaeelkkalkelraaaedakeatpsklekdseeqkdYqeGldk 63
                                   +M +++k+lk+++ +++ ++  ++l+e+ +  +dak+        d+ + + Y++G d+
  gene815|gene815|rna815|rna815 36 DMGSIAKNLKTIEDEAERASKFEELNEMCKKLNDAKTVLT-----DPDKKQLYDQGVDE 89
                                   8************88888888889****************.....9**********987 PP

>> DUF1356  Protein of unknown function (DUF1356)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.8   7.6e-05      0.19      15      48 ..     140     173 ..     124     180 .. 0.84
   2 ?    1.6   0.1     0.056   1.4e+02      33      45 ..     184     196 ..     178     201 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 7.6e-05
                        DUF1356  15 skedvsqvpyveatgrdsvtCptCqGtGeiPreq 48 
                                     k+++ +  ++   g++s +C tC+G+Gei  + 
  gene815|gene815|rna815|rna815 140 VKREIICTKCEGRGGEKSTVCATCKGEGEIAIKR 173
                                    577888999********************98665 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.056
                        DUF1356  33 vtCptCqGtGeiP 45 
                                      Cp C G+G+i 
  gene815|gene815|rna815|rna815 184 SACPDCNGNGHIV 196
                                    58*********96 PP

>> Anti-TRAP  Tryptophan RNA-binding attenuator protein inhibitory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       1.8   4.6e+03       5      17 ..      56      68 ..      54      74 .. 0.77
   2 ?   10.4   1.7    0.0002       0.5      10      42 ..     143     169 ..     141     179 .. 0.88
   3 ?   10.3   1.1   0.00021      0.54      12      41 ..     185     209 ..     180     216 .. 0.83
   4 ?   -0.6   0.2      0.52   1.3e+03      20      35 ..     329     344 ..     328     359 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.8
                                   -HHHCEEE-TTTT CS
                      Anti-TRAP  5 alpeLEtkCdaCn 17
                                   + +eL + C++ n
  gene815|gene815|rna815|rna815 56 KFEELNEMCKKLN 68
                                   5689999998866 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.0002
                                    EEE-TTTTTTSEETTE......E-TTTTTSSEE CS
                      Anti-TRAP  10 EtkCdaCngsGkiepeeprasleCPkCsGkgli 42 
                                    E  C +C+g G ++++       C  C+G+g i
  gene815|gene815|rna815|rna815 143 EIICTKCEGRGGEKST------VCATCKGEGEI 169
                                    778*************......9******9976 PP

  == domain 3  score: 10.3 bits;  conditional E-value: 0.00021
                                    E-TTTTTTSEETTE......E-TTTTTSSE CS
                      Anti-TRAP  12 kCdaCngsGkiepeeprasleCPkCsGkgl 41 
                                    +C+ Cng G+i          C +C+G+  
  gene815|gene815|rna815|rna815 185 ACPDCNGNGHIVEG-----ALCTECKGQRY 209
                                    8*********9644.....47******875 PP

  == domain 4  score: -0.6 bits;  conditional E-value: 0.52
                                    SEETTE......E-TT CS
                      Anti-TRAP  20 GkiepeeprasleCPk 35 
                                    G+++ +e +  l+CPk
  gene815|gene815|rna815|rna815 329 GNVKEDELKKVLPCPK 344
                                    556666778899**98 PP

>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.9     0.003       7.7      67      94 ..     137     164 ..     114     178 .. 0.81
   2 ?    4.1   0.9     0.012        32      74     101 ..     184     212 ..     168     232 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.003
                        TackOD1  67 eelvdrirlCpsCksghlnvrevCpkCk 94 
                                    +  v+r  +C++C++   +   vC  Ck
  gene815|gene815|rna815|rna815 137 TFSVKREIICTKCEGRGGEKSTVCATCK 164
                                    345789999****999999999999998 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.012
                        TackOD1  74 rlCpsCks.ghlnvrevCpkCkSidieeq 101
                                     +Cp C++ gh+     C +Ck  + +++
  gene815|gene815|rna815|rna815 184 SACPDCNGnGHIVEGALCTECKGQRYTQK 212
                                    68****98357888899****98876654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (383 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       866  (0.0483016); expected 358.6 (0.02)
Passed bias filter:                      651  (0.0363099); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.45
# Mc/sec: 2584.05
//
Query:       gene816|gene816|rna816|rna816  [L=102]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-21   76.4   5.1    1.4e-21   76.2   5.0    1.3  1  Myb_DNA-bind_7   Myb DNA-binding like
    2.7e-08   33.8   0.1    5.6e-08   32.9   0.1    1.5  1  Myb_DNA-binding  Myb-like DNA-binding domain
    0.00011   22.4   2.5    0.00012   22.2   0.4    2.0  2  Myb_DNA-bind_6   Myb-like DNA-binding domain
  ------ inclusion threshold ------
       0.31   11.7   1.2         20    5.9   0.2    2.1  2  OAD_gamma        Oxaloacetate decarboxylase, gamma chain


Domain annotation for each model (and alignments):
>> Myb_DNA-bind_7  Myb DNA-binding like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.2   5.0   3.1e-25   1.4e-21       5      78 ..      27      99 ..      13     102 .] 0.90

  Alignments for each domain:
  == domain 1  score: 76.2 bits;  conditional E-value: 3.1e-25
                 Myb_DNA-bind_7  5 rkktkkWskeetekFYkaLsqfGtDFsliaklfpkrtrrqlKlKFkkEerknpeliekalkkrkeldleefkee 78
                                   +++t++Ws++et++FYkaL+ +G DF+li+klf++++r+q+K+K+ kEe  n+++ie+++k+   +d ++++  
  gene816|gene816|rna816|rna816 27 KRQTTRWSQKETQLFYKALELCGLDFTLISKLFTRKSRKQVKKKYMKEESLNRRKIEEIVKNAD-FDEDKYNAL 99
                                   45899*****************************************************988765.587777765 PP

>> Myb_DNA-binding  Myb-like DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.9   0.1   1.2e-11   5.6e-08       2      44 ..      31      73 ..      30      74 .. 0.96

  Alignments for each domain:
  == domain 1  score: 32.9 bits;  conditional E-value: 1.2e-11
                                   SSSBHHHHHHHHHHHHHHTTCHHHHHHHHTSS-HHHHHHHHHH CS
                Myb_DNA-binding  2 gkWteeEdelLleavkkhGnrWkkIaerlggRtekqcrsrwrn 44
                                    +W++ E +l+++a+++ G ++++I++ +  +++kq++ ++ +
  gene816|gene816|rna816|rna816 31 TRWSQKETQLFYKALELCGLDFTLISKLFTRKSRKQVKKKYMK 73
                                   68**************************************986 PP

>> Myb_DNA-bind_6  Myb-like DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.1      0.32   1.4e+03      42      58 ..       4      20 ..       2      22 .. 0.74
   2 !   22.2   0.4   2.7e-08   0.00012       1      45 [.      33      79 ..      33     101 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.32
                 Myb_DNA-bind_6 42 kLrpkisrkkwskeedi 58
                                   kL + +++k++ k++++
  gene816|gene816|rna816|rna816  4 KLIHYLQNKNFRKKKEK 20
                                   57777889999998776 PP

  == domain 2  score: 22.2 bits;  conditional E-value: 2.7e-08
                 Myb_DNA-bind_6  1 WteeEdeiLlklvekygndWknIaealnrRtpkqcfdrwkn..kLrp 45
                                   W++ E+++  k  e +g d+++I++ + r++ kq++ ++ +  +L+ 
  gene816|gene816|rna816|rna816 33 WSQKETQLFYKALELCGLDFTLISKLFTRKSRKQVKKKYMKeeSLNR 79
                                   ***************************99**********98555533 PP

>> OAD_gamma  Oxaloacetate decarboxylase, gamma chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.2    0.0045        20      26      53 ..       4      31 ..       3      41 .. 0.76
   2 ?    5.2   0.0    0.0072        32      25      54 ..      52      81 ..      44     100 .. 0.73

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0045
                      OAD_gamma 26 slfskiikkkakkkkkkakaaaaaaaaa 53
                                   +l++++ +k + kkk+ka +++++ +++
  gene816|gene816|rna816|rna816  4 KLIHYLQNKNFRKKKEKAVSSPPKRQTT 31
                                   6788888999888888888888887665 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0072
                      OAD_gamma 25 islfskiikkkakkkkkkakaaaaaaaaaa 54
                                   ++l+sk++++k+ k+ kk+  +++  +  +
  gene816|gene816|rna816|rna816 52 FTLISKLFTRKSRKQVKKKYMKEESLNRRK 81
                                   689999999999999999988877766554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1848  (0.103073); expected 358.6 (0.02)
Passed bias filter:                      613  (0.0341904); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 680.19
//
Query:       gene817|gene817|rna817|rna817  [L=236]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       607  (0.0338558); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1594.21
//
Query:       gene818|gene818|rna818|rna818  [L=43]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (43 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       278  (0.0155056); expected 358.6 (0.02)
Passed bias filter:                      151  (0.00842211); expected 358.6 (0.02)
Passed Vit filter:                         7  (0.000390429); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.42
# Mc/sec: 309.92
//
Query:       gene819|gene819|rna819|rna819  [L=255]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    4.1e-40  137.8   4.4    3.3e-34  118.6   0.2    2.1  2  Gti1_Pac2  Gti1/Pac2 family


Domain annotation for each model (and alignments):
>> Gti1_Pac2  Gti1/Pac2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.6   0.2   1.8e-38   3.3e-34       3     100 ..      35     131 ..      34     143 .. 0.89
   2 !   22.1   2.7   7.4e-09   0.00013     137     181 .]     123     167 ..     116     167 .. 0.77

  Alignments for each domain:
  == domain 1  score: 118.6 bits;  conditional E-value: 1.8e-38
                                    ES---SHHHHHHHHHHHHTTSS---SS---HHHHHHHSSTTEEEEEEHHHH--SS---S--B---EEETTEEEEEB---- CS
                      Gti1_Pac2   3 kgyiettkdalllieavlegilkrvtrRlkekErkeliksGsvFvfeeeesgikRWTDGvsWSpSrilgnfLvYreldkk 82 
                                    +gyi++ ++a l+++av+ gi++ ++ Rl++++r+  i+sG vFvf+e++sgikRWTDG +WSpS+ilg+fL+Y+e+ k+
  gene819|gene819|rna819|rna819  35 RGYIHSYNEASLIVHAVRLGIIEPIKERLSNSDRE-NIRSGCVFVFIEDDSGIKRWTDGKIWSPSKILGHFLLYKEVPKH 113
                                    69*********************************.*****************************************999 PP

                                    ------------------ CS
                      Gti1_Pac2  83 rakkkkkkkkkkskestk 100
                                     +k++ kk+++++ ++++
  gene819|gene819|rna819|rna819 114 LSKSAIKKRNANTIKRER 131
                                    988888887766655544 PP

  == domain 2  score: 22.1 bits;  conditional E-value: 7.4e-09
                                    ------------------------EEEEEEEEEETTTEEEEEEE- CS
                      Gti1_Pac2 137 lekdserslvgsltdsykfkkdgLvKkTisvtlkgkelhlisYyk 181
                                    ++++ +r+ v s++++++  +  L+KkTis++ ++k++h+isY++
  gene819|gene819|rna819|rna819 123 NANTIKRERVISIHTQMQNDEFSLFKKTISIKHESKSYHIISYFQ 167
                                    44555666666777777777778********************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       757  (0.0422221); expected 358.6 (0.02)
Passed bias filter:                      478  (0.0266607); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 1849.84
//
Query:       gene82|gene82|rna82|rna82  [L=151]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.02   13.6   0.4      0.033   13.0   0.0    1.4  2  p450      Cytochrome P450


Domain annotation for each model (and alignments):
>> p450  Cytochrome P450
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   1.8e-06     0.033     346     378 ..      16      48 ..       9      49 .. 0.93
   2 ?   -2.6   0.1     0.093   1.7e+03     168     180 ..      93     105 ..      63     145 .. 0.54

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.8e-06
                                SSSCEEETTEEE-TT-EEEEEHHHHHT-TTTSS CS
                       p450 346 vtkdvvirgylipkGtevivnlyalhrdpevfp 378
                                + +d v++g+ i+k+ +++ n+ alh + ++f+
  gene82|gene82|rna82|rna82  16 IIQDAVVDGHGIKKDNNILANIRALHDRHQIFE 48 
                                689****************************97 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.093
                                SHHHHHHHHHHHH CS
                       p450 168 eklselvkaveel 180
                                e+++ ++++ e +
  gene82|gene82|rna82|rna82  93 ERFELFKDKCEIN 105
                                3332222222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       888  (0.0495287); expected 358.6 (0.02)
Passed bias filter:                      454  (0.0253221); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.95
# Mc/sec: 478.61
//
Query:       gene820|gene820|rna820|rna820  [L=92]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       621  (0.0346366); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.42
# Mc/sec: 659.98
//
Query:       gene821|gene821|rna821|rna821  [L=58]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (58 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       207  (0.0115455); expected 358.6 (0.02)
Passed bias filter:                      180  (0.0100396); expected 358.6 (0.02)
Passed Vit filter:                         7  (0.000390429); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.29s 00:00:00.67 Elapsed: 00:00:00.45
# Mc/sec: 384.46
//
Query:       gene822|gene822|rna822|rna822  [L=217]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.4e-05   23.2   0.4    7.4e-05   23.2   0.4    1.5  2  Cyclin    Cyclin
     0.0054   16.5   0.4      0.013   15.2   0.4    1.6  1  Cyclin_N  Cyclin, N-terminal domain


Domain annotation for each model (and alignments):
>> Cyclin  Cyclin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.1       1.3   1.2e+04     112     128 ..      44      60 ..      33      66 .. 0.60
   2 !   23.2   0.4   8.2e-09   7.4e-05     111     160 ..     121     170 ..     111     171 .. 0.93

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 1.3
                                    HHHHHHHHHHHHHH-SS CS
                         Cyclin 112 RllivallvatKflvDl 128
                                    R++  all+a+ +++ +
  gene822|gene822|rna822|rna822  44 RITFCALLSAICVMKKV 60 
                                    45555555555554444 PP

  == domain 2  score: 23.2 bits;  conditional E-value: 8.2e-09
                                    HHHHHHHHHHHHHHH-SS---HHHHHHHHTS-HHHHHHHHHHHHHHTTT- CS
                         Cyclin 111 hRllivallvatKflvDlsysnekfakvggislkELnkLEidFlflvdFd 160
                                    + l +++l + tK+l D +y    ++k + + +k Ln+ E   lfl+d++
  gene822|gene822|rna822|rna822 121 YLLFAASLIITTKVLFDYVYATTDWSKLTKLTVKQLNEVERYVLFLLDYK 170
                                    6688999******************************************8 PP

>> Cyclin_N  Cyclin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.4   1.5e-06     0.013      71     126 ..     118     171 ..     110     172 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.5e-06
                                    CCHHHHHHHHHHHHHHHHSSS---HHHHHHHTTTSS-HHHHHHHHHHHHHHTTT-- CS
                       Cyclin_N  71 dklqlvgatcLllAaKveeisppkledlvyitdeafteeeilemErliLetLnfdl 126
                                    ++  l++a++L++ +Kv  +++    d+  +t+   t ++++e+Er++L  L++++
  gene822|gene822|rna822|rna822 118 KDDYLLFAASLIITTKVLFDYVYATTDWSKLTK--LTVKQLNEVERYVLFLLDYKV 171
                                    566799***********************9988..999***************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       504  (0.0281109); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 1401.24
//
Query:       gene824|gene824|rna824|rna824  [L=407]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (407 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3025  (0.168721); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.84u 0.34s 00:00:01.18 Elapsed: 00:00:00.53
# Mc/sec: 2332.12
//
Query:       gene825|gene825|rna825|rna825  [L=178]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    4.3e-13   49.4   0.1    6.6e-13   48.8   0.1    1.3  1  DEAD       DEAD/DEAH box helicase
    0.00053   20.0   0.1    0.00071   19.6   0.1    1.3  1  ResIII     Type III restriction enzyme, res subunit
  ------ inclusion threshold ------
       0.01   15.3   0.1      0.016   14.6   0.1    1.2  1  PhoH       PhoH-like protein
      0.022   14.5   0.2      0.038   13.7   0.1    1.4  2  AAA_30     AAA domain
       0.06   12.6   0.0      0.062   12.6   0.0    1.1  1  SecA_DEAD  SecA DEAD-like domain


Domain annotation for each model (and alignments):
>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.8   0.1   1.8e-16   6.6e-13       3      84 ..      82     160 ..      80     169 .. 0.91

  Alignments for each domain:
  == domain 1  score: 48.8 bits;  conditional E-value: 1.8e-16
                                    HHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD   3 iQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvllii 82 
                                     Q ++ip+il+g+++l + + G+GKT  f++ +lq+v++    +g ++l+++Pt eL +qt + ++k++ ++++r+ + +
  gene825|gene825|rna825|rna825  82 AQLSTIPHILKGQSLLFQSKSGTGKTISFVVGALQNVVK---GKGVQVLLITPTMELNRQTTSIFEKVGGPLGIRTFMAM 158
                                    5999*********************************75...8899************************9999887665 PP

                                    TT CS
                                    xx RF
                           DEAD  83 gg 84 
                                     g
  gene825|gene825|rna825|rna825 159 RG 160
                                    55 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.1     2e-07   0.00071      22      78 ..      91     147 ..       6     151 .. 0.72

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 2e-07
                                    .TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGT CS
                         ResIII  22 krdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkfl 78 
                                     + + +l++   GtGKT+  +  + +   kgk  ++l++ p+ +l  qt + f+k+ 
  gene825|gene825|rna825|rna825  91 LKGQSLLFQSKSGTGKTISFVVGALQNVVKGKGVQVLLITPTMELNRQTTSIFEKVG 147
                                    4566899***********9966666666667888****************9999875 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.1   4.5e-06     0.016       8      64 ..      82     138 ..      78     146 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 4.5e-06
                                    HHHHHHHHHHH-SEEEEE--TTSSTTHHHHHHHHHHHHTTS-SEEEEEE-S--TT-- CS
                           PhoH   8 eQkeylealkkndivfaiGpaGtGKtylavalavealkkkkvkriiltrpaveagee 64 
                                    +Q +++  + k + +    ++GtGKt   v+ a++ + k+k  +++l+ p++e +++
  gene825|gene825|rna825|rna825  82 AQLSTIPHILKGQSLLFQSKSGTGKTISFVVGALQNVVKGKGVQVLLITPTMELNRQ 138
                                    6777777788778788889********************************998665 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       1.5   5.4e+03     139     154 ..      19      34 ..      12      51 .. 0.59
   2 ?   13.7   0.1   1.1e-05     0.038       6      57 ..      83     134 ..      80     168 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 1.5
                         AAA_30 139 dlveaagigtaeLtev 154
                                    +l+++ +i+t++++ev
  gene825|gene825|rna825|rna825  19 ELLRSLDIDTHRMDEV 34 
                                    3444444455555544 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 1.1e-05
                         AAA_30   6 QaaavealltsgdrvavltGpAGtGKt..talkalreaweaaggrviglAptgk 57 
                                    Q + + ++l+++    + +   GtGKt  ++++al+++++ +g +v++++pt +
  gene825|gene825|rna825|rna825  83 QLSTIPHILKGQS--LLFQSKSGTGKTisFVVGALQNVVKGKGVQVLLITPTME 134
                                    8888889998885..8999*******8446899******************976 PP

>> SecA_DEAD  SecA DEAD-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   1.7e-05     0.062      45     141 ..      42     146 ..       2     167 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.7e-05
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxx RF
                      SecA_DEAD  45 lkerlaegealdellpeafalvreaakrvlgmrhyd....vQliGglvlhegk..iaemkTGEGKtlvatlpaylnaltg 118
                                    + + + ++++l ++   +  lv e +k+ l m  yd     Ql     + +g+  + + k G GKt+  ++ a+ n ++g
  gene825|gene825|rna825|rna825  42 FSNAMVQDNTLLSTADFSSLLVSEEIKNALYMLGYDrpslAQLSTIPHILKGQslLFQSKSGTGKTISFVVGALQNVVKG 121
                                    444444555555555555567888888888888887333345555555555543378999******************** PP

                                    xxxxx..xxxxxxxxxxxxxxxxxx RF
                      SecA_DEAD 119 kgvhv..vtvndYLakrdaewmgpv 141
                                    kgv+v  +t    L ++ ++ +++v
  gene825|gene825|rna825|rna825 122 KGVQVllITPTMELNRQTTSIFEKV 146
                                    **99733565555555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       488  (0.0272185); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.62u 0.36s 00:00:00.98 Elapsed: 00:00:00.56
# Mc/sec: 952.91
//
Query:       gene826|gene826|rna826|rna826  [L=324]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.8e-46  157.2   0.0    4.7e-46  156.5   0.0    1.4  1  AAA              ATPase family associated with various cellul
    5.6e-11   42.1   0.1    1.5e-10   40.7   0.1    1.7  1  AAA_lid_3        AAA+ lid domain
      3e-09   37.2   0.0    5.3e-09   36.4   0.0    1.3  1  AAA_2            AAA domain (Cdc48 subfamily)
    4.1e-08   33.8   0.0    2.7e-05   24.6   0.0    2.3  2  AAA_16           AAA ATPase domain
    8.2e-08   32.3   0.1    4.6e-07   29.9   0.1    2.1  1  AAA_5            AAA domain (dynein-related subfamily)
    4.6e-07   30.2   0.4       0.01   16.1   0.0    2.5  2  AAA_22           AAA domain
    1.9e-06   27.7   0.0    4.6e-06   26.5   0.0    1.6  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    1.9e-05   24.5   0.1    4.4e-05   23.4   0.1    1.7  1  Prot_ATP_ID_OB   Proteasomal ATPase OB C-terminal domain
    0.00034   21.2   0.0      0.001   19.6   0.0    1.8  1  AAA_18           AAA domain
    0.00089   18.5   0.0     0.0015   17.8   0.0    1.4  1  TIP49            TIP49 P-loop domain
     0.0012   18.2   0.2      0.025   13.9   0.0    2.1  2  ATPase           KaiC
     0.0027   17.5   0.0     0.0049   16.6   0.0    1.4  1  IstB_IS21        IstB-like ATP binding protein
     0.0028   17.2   0.0     0.0057   16.2   0.0    1.6  1  AAA_7            P-loop containing dynein motor region
     0.0029   17.0   0.0     0.0051   16.2   0.0    1.4  1  Mg_chelatase     Magnesium chelatase, subunit ChlI
     0.0036   17.3   0.0      0.006   16.6   0.0    1.3  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
     0.0037   16.4   0.0     0.0071   15.5   0.0    1.4  1  Parvo_NS1        Parvovirus non-structural protein NS1
     0.0041   17.1   0.0       0.14   12.1   0.0    2.1  2  NACHT            NACHT domain
     0.0044   16.8   0.2      0.022   14.5   0.0    2.1  2  AAA_24           AAA domain
     0.0048   16.9   0.0     0.0083   16.2   0.0    1.4  1  AAA_14           AAA domain
     0.0048   16.8   0.0     0.0078   16.1   0.0    1.5  1  AAA_3            ATPase family associated with various cellul
     0.0088   15.2   0.0      0.014   14.6   0.0    1.3  1  DUF815           Protein of unknown function (DUF815)
  ------ inclusion threshold ------
      0.013   15.7   0.0      0.026   14.8   0.0    1.5  1  AAA_28           AAA domain
      0.016   15.6   0.0      0.031   14.7   0.0    1.5  1  RNA_helicase     RNA helicase
      0.018   14.6   0.1      0.089   12.4   0.1    1.9  2  AAA_25           AAA domain
      0.018   14.5   0.2      0.047   13.2   0.1    1.7  1  PhoH             PhoH-like protein
      0.023   14.4   0.0       0.07   12.8   0.0    1.9  1  Sigma54_activat  Sigma-54 interaction domain
      0.035   13.4   0.1       0.16   11.2   0.0    2.0  2  Zeta_toxin       Zeta toxin
      0.036   14.0   0.0       0.17   11.8   0.0    1.9  1  ATPase_2         ATPase domain predominantly from Archaea
      0.038   13.8   0.0      0.077   12.8   0.0    1.5  1  CPT              Chloramphenicol phosphotransferase-like prot
      0.064   13.4   0.0        0.1   12.8   0.0    1.6  1  AAA_33           AAA domain
      0.064   13.0   0.0       0.11   12.2   0.0    1.4  1  AAA_30           AAA domain
      0.065   13.0   0.0       0.14   11.9   0.0    1.5  1  AAA_11           AAA domain
      0.071   13.5   0.0       0.22   12.0   0.0    1.9  1  AAA_17           AAA domain
      0.072   12.2   0.0       0.13   11.4   0.0    1.3  1  PIF1             PIF1-like helicase
      0.094   13.0   0.1       0.19   12.0   0.1    1.6  1  AAA_19           AAA domain


Domain annotation for each model (and alignments):
>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  156.5   0.0   9.2e-49   4.7e-46       1     132 []     105     238 ..     105     238 .. 0.96

  Alignments for each domain:
  == domain 1  score: 156.5 bits;  conditional E-value: 9.2e-49
                                    EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH...TTC CS
                            AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksr...sgs 77 
                                    vllyGppGtGKTlla+a+a +++v+fl++ +s+l++ky+ges++ ire+f+ a+e   p+i+fiDEida++++r   s+s
  gene826|gene826|rna826|rna826 105 VLLYGPPGTGKTLLARAIAATMDVSFLKVVASSLIEKYIGESSRMIREMFQYARERT-PCIIFIDEIDAIGGKRsteSSS 183
                                    79******************************************************8.****************988778 PP

                                    CCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETTS CS
                            AAA  78 eseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieiel 132
                                    +++e +r++ +Ll++ldg+k+  +kv vi+atnrpd ldpallr gR+drkiei+l
  gene826|gene826|rna826|rna826 184 SDREVQRTLMELLNQLDGFKSL-DKVKVIMATNRPDILDPALLRpGRLDRKIEIPL 238
                                    8899999999***********7.66****************************985 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.7   0.1   2.9e-13   1.5e-10       2      44 ..     261     303 ..     260     304 .. 0.97

  Alignments for each domain:
  == domain 1  score: 40.7 bits;  conditional E-value: 2.9e-13
                      AAA_lid_3   2 vdlkeLAerTeGySGADlaalcreAallAlrrgikeitmedfe 44 
                                    +dl+ L++++ G+ GADl   c eA+++A+r+ ++++ +edf 
  gene826|gene826|rna826|rna826 261 IDLDMLVKLSVGFNGADLRHCCTEAGMNAIRDERDAVCQEDFV 303
                                    79***************************************96 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.4   0.0     1e-11   5.3e-09       6     104 ..     105     197 ..     101     203 .. 0.83

  Alignments for each domain:
  == domain 1  score: 36.4 bits;  conditional E-value: 1e-11
                                    EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG---- CS
                          AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKihpk 83 
                                    +ll gp g+Gkt+la+a+a +++v    ++  + as+l+e    + + ++    +++ + a e+   i+++DEid i  k
  gene826|gene826|rna826|rna826 105 VLLYGPPGTGKTLLARAIAATMDV----SFLKVVASSLIE----KYIGESSRMIREMFQYARERTpcIIFIDEIDAIGGK 176
                                    5789*******************8....9***********....44444444444444444444455************* PP

                                    ---------HHHHHHHHHHHH CS
                          AAA_2  84 essgadvSregVqrdLLqile 104
                                    +s+++  S  +Vqr L+ +l 
  gene826|gene826|rna826|rna826 177 RSTESSSSDREVQRTLMELLN 197
                                    9999*************9986 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.0   5.2e-08   2.7e-05      15      46 ..      93     124 ..      91     142 .. 0.89
   2 ?    6.9   0.0     0.015       7.7     123     163 ..     150     197 ..     135     206 .. 0.74

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 5.2e-08
                         AAA_16  15 alervrsgrpelvllsGesGvGKsslvrellr 46 
                                    ++erv  ++p  vll+G++G+GK+ l+r+++ 
  gene826|gene826|rna826|rna826  93 IFERVGISEPKGVLLYGPPGTGKTLLARAIAA 124
                                    6899************************9986 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.015
                         AAA_16 123 lkrllallsrderplvlvlDdlq........wadeaslqllaaLlrlle 163
                                    ++++++++++ + p ++++D+++           ++++++ ++L++ll+
  gene826|gene826|rna826|rna826 150 IREMFQYARE-RTPCIIFIDEIDaiggkrstESSSSDREVQRTLMELLN 197
                                    5667788888.889*********88888777444455555555554444 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.9   0.1   8.9e-10   4.6e-07       1     135 [.     104     225 ..     104     227 .. 0.79

  Alignments for each domain:
  == domain 1  score: 29.9 bits;  conditional E-value: 8.9e-10
                                    EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------..G-SEEEEESGGG-- CS
                          AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar..egeilvlDEverae 78 
                                    +vlL GppGtgK+ la+ +aa +  +++ v  ++      l+ ++    g+ s+   ++ + ar  +++i+++DE++ + 
  gene826|gene826|rna826|rna826 104 GVLLYGPPGTGKTLLARAIAATMDVSFLKVVASS------LIEKYI---GESSRMIREMFQYARerTPCIIFIDEIDAIG 174
                                    59************************99999888......555554...22222223334344445*************9 PP

                                    .HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--.-TT-TTHHHH CS
                          AAA_5  79 .sevlnsLlslleerrllleeggelvkaknddllerfrviatanpldrslnelspalr 135
                                     +  ++s  s  e +r l+e +++l ++k+   l ++ vi+++n++d     l+pal+
  gene826|gene826|rna826|rna826 175 gKRSTESSSSDREVQRTLMELLNQLDGFKS---LDKVKVIMATNRPD----ILDPALL 225
                                    999999999999999999999999999998...456**********9....6777765 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0     2e-05      0.01       8      42 ..     105     130 ..      99     138 .. 0.80
   2 !   12.5   0.1   0.00026      0.13      56     128 ..     130     213 ..     128     221 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 2e-05
                         AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpev 42 
                                    ++++G++GtGKT+l+r ++ +          ++++
  gene826|gene826|rna826|rna826 105 VLLYGPPGTGKTLLARAIAATM---------DVSF 130
                                    689**************99987.........4555 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00026
                         AAA_22  56 llrellralglelkaerlsseellealeqalraravielliiDEaqhlr....s..........eealeeLrsllnl... 118
                                    +l+ +++ l ++  +   +s+++++ + q++r+r    ++ iDE++ +     +               +L +lln    
  gene826|gene826|rna826|rna826 130 FLKVVASSLIEKYIG---ESSRMIREMFQYARERTP-CIIFIDEIDAIGgkrsTessssdrevqR----TLMELLNQldg 201
                                    566667777766666...999999999999999999.9**********88775155678855542....44444443333 PP

                         AAA_22 119 ..srkgvqliLv 128
                                      s ++v++i++
  gene826|gene826|rna826|rna826 202 fkSLDKVKVIMA 213
                                    467777777765 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   0.0     9e-09   4.6e-06      35      95 ..     104     172 ..      95     181 .. 0.75

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 9e-09
                         RuvB_N  35 hvllyGpPGlGkttlakiiakelgvk.lkitsgPvleka.gdlaalltnl....eekd..vlfideihr 95 
                                     vllyGpPG Gkt la+ ia+ ++v+ lk+ ++  +ek  g+ + ++ ++    +e+   ++fidei  
  gene826|gene826|rna826|rna826 104 GVLLYGPPGTGKTLLARAIAATMDVSfLKVVASSLIEKYiGESSRMIREMfqyaRERTpcIIFIDEIDA 172
                                    59**********************984588889999985355555655552221222244899999975 PP

>> Prot_ATP_ID_OB  Proteasomal ATPase OB C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.1   8.5e-08   4.4e-05      13      57 .]       3      47 ..       1      47 [. 0.97

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 8.5e-08
                                   EEEEE-TTS-EEEEEE-GGGSSST--TTEEEEEETTTTEEEEEE- CS
                 Prot_ATP_ID_OB 13 raiVktssdeevvvslagavpremLrpgDlVavdkdtgfifEkLP 57
                                   + iVkts +  +vv   ++++r+ L  g++Va+d +t  i+++LP
  gene826|gene826|rna826|rna826  3 KFIVKTSQGPRYVVGARKSIDRNLLIGGTRVALDITTLTIMKVLP 47
                                   68******************************************9 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   1.9e-06     0.001       1      75 [.     105     209 ..     105     234 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1.9e-06
                         AAA_18   1 IlltGtpGvGKttlakeLskrlgf.....................gvnlrdvakenglllevdpe..........aldes 49 
                                    +ll G+pG+GKt la++++  + +                      ++  ++a+e+ +++ + +e          + ++s
  gene826|gene826|rna826|rna826 105 VLLYGPPGTGKTLLARAIAATMDVsflkvvassliekyigessrmIREMFQYARERTPCIIFIDEidaiggkrstESSSS 184
                                    799***************98875567888898888899999988888888999999999999999999999988888888 PP

                         AAA_18  50 krldedkldklldaleenssaleegk 75 
                                    +r+++  l++ll++l++  s l++ k
  gene826|gene826|rna826|rna826 185 DREVQRTLMELLNQLDGFKS-LDKVK 209
                                    88888888888888887765.44333 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   2.9e-06    0.0015      51      94 ..     103     144 ..      95     172 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.9e-06
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          TIP49  51 ravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevk 94 
                                    ++vLl Gp+gtGkt la ai+  +   v f ++++s +    + 
  gene826|gene826|rna826|rna826 103 KGVLLYGPPGTGKTLLARAIAATMD--VSFLKVVASSLIEKYIG 144
                                    89*******************9875..99****99988666554 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.0   4.8e-05     0.025      10      37 ..      92     120 ..      75     129 .. 0.83
   2 ?    1.9   0.0      0.23   1.2e+02     103     154 ..     145     199 ..     128     205 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.8e-05
                         ATPase  10 eil.kgGipegrvvlitGepGtGKtifal 37 
                                    ei+   Gi e + vl++G pGtGKt++a 
  gene826|gene826|rna826|rna826  92 EIFeRVGISEPKGVLLYGPPGTGKTLLAR 120
                                    4554479*******************996 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.23
                         ATPase 103 dleelieelaeaikeikakrvviDsitgl.ayeek..eavaReilrqlvrvlkkl 154
                                    + + +i+e+ ++ +e     + iD i+++  ++++  ++  Re  r+l++ l++l
  gene826|gene826|rna826|rna826 145 ESSRMIREMFQYARERTPCIIFIDEIDAIgGKRSTesSSSDREVQRTLMELLNQL 199
                                    5667888899999999999999999999974333300334566666676666665 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   9.6e-06    0.0049      45      70 ..     100     125 ..      90     170 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 9.6e-06
                      IstB_IS21  45 ekkenivllGpsGvGKshlaialgve 70 
                                    ++ ++++l Gp+G+GK+ la a++  
  gene826|gene826|rna826|rna826 100 SEPKGVLLYGPPGTGKTLLARAIAAT 125
                                    566789***************99864 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   1.1e-05    0.0057      30     110 ..      99     171 ..      92     217 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.1e-05
                          AAA_7  30 lknkkpvllvGptGtGKtviikdllkkldkekylsltinfsaqtsanqlqdiiesklekrrkgvygPpggkklvvFvDDl 109
                                    +++ k vll+Gp GtGKt++++ +  ++d        ++f +   ++ + + i ++    r+    +     +++F+D++
  gene826|gene826|rna826|rna826  99 ISEPKGVLLYGPPGTGKTLLARAIAATMD--------VSFLKVVASSLIEKYIGESSRMIREMFQYARERTPCIIFIDEI 170
                                    566789*****************999999........7777777777888888877777777777777888888888887 PP

                          AAA_7 110 n 110
                                    +
  gene826|gene826|rna826|rna826 171 D 171
                                    5 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0     1e-05    0.0051      24      45 ..     104     125 ..      96     154 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1e-05
                   Mg_chelatase  24 nlllvGppGsGKtmlakrlpsl 45 
                                     +ll+GppG+GKt+la+++++ 
  gene826|gene826|rna826|rna826 104 GVLLYGPPGTGKTLLARAIAAT 125
                                    589**************99865 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   1.2e-05     0.006      19      59 ..     102     142 ..      74     154 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.2e-05
                                    TEEEEEEESTTSSHHHHHHHHHHHTT--...----TTTTSEEEE CS
                           TsaE  19 gdvilLeGdLGaGKTtlvrglakalgve...evkSPTFtlveeY 59 
                                     + +lL+G+ G+GKT l+r++a++++v+    v S   +l+e+Y
  gene826|gene826|rna826|rna826 102 PKGVLLYGPPGTGKTLLARAIAATMDVSflkVVAS---SLIEKY 142
                                    4459*********************9986633433...455555 PP

>> Parvo_NS1  Parvovirus non-structural protein NS1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   1.4e-05    0.0071     117     139 ..     105     127 ..     100     135 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.4e-05
                      Parvo_NS1 117 vwfyGpantGktnlaeaIakavp 139
                                    v++yGp+ tGkt la+aIa +++
  gene826|gene826|rna826|rna826 105 VLLYGPPGTGKTLLARAIAATMD 127
                                    89*****************9987 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.0   0.00027      0.14       3      25 ..     105     127 ..     103     139 .. 0.87
   2 ?    2.9   0.0      0.18        91      57     115 ..     138     198 ..     130     226 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00027
                                    EEEEC-TTTCHHHHHHHHHHHHC CS
                          NACHT   3 vilqGeaGsGKTtLlqklalawa 25 
                                    v+l G++G GKT L++ +a ++ 
  gene826|gene826|rna826|rna826 105 VLLYGPPGTGKTLLARAIAATMD 127
                                    799***************98765 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.18
                                    HHCCCCTS--SSS-CCHHHHCCSCCCEEEEEE-STT-SS-TCH............HHHHHCT CS
                          NACHT  57 llfsqlpepaapvsevwavllelperlLlilDglDelvtdlgq...kekqpvrtlLselirk 115
                                    l+ +   e+++ ++e++++  e+     + +D +D +  + +    +  ++v++ L el+++
  gene826|gene826|rna826|rna826 138 LIEKYIGESSRMIREMFQYARERTP-CIIFIDEIDAIGGKRSTessSSDREVQRTLMELLNQ 198
                                    5555666777788886666555554.555579999998877778886667777777777765 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   4.4e-05     0.022       4      24 ..     104     126 ..     101     215 .. 0.72
   2 ?   -0.3   0.0       1.5   7.5e+02      29      59 ..     281     309 ..     273     322 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4.4e-05
                         AAA_24   4 kiliyGpsgiGKTtlakel..gp 24 
                                     +l+yGp+g+GKT la+ +  + 
  gene826|gene826|rna826|rna826 104 GVLLYGPPGTGKTLLARAIaaTM 126
                                    589*************9984333 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.5
                         AAA_24  29 idtekGlksldadkfpdieswedfldevvel 59 
                                    + te+G++++ + +   +   edf++++ ++
  gene826|gene826|rna826|rna826 281 CCTEAGMNAIRDERDAVC--QEDFVKAIRKI 309
                                    56999**99999997766..67777777776 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   1.6e-05    0.0083       4      76 ..     104     173 ..     101     213 .. 0.67

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.6e-05
                         AAA_14   4 ilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqev 76 
                                     +++ G+  +GKT l++ ++ +  v+  +++  +l ++   +++   ++++++++ ++e+   ++f+DEi  +
  gene826|gene826|rna826|rna826 104 GVLLYGPPGTGKTLLARAIAATMDVSFLKVVASSLIEKYIGESS---RMIREMFQYARERTPCIIFIDEIDAI 173
                                    58999**************9888866566666666665543333...23444444333345678******988 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   1.5e-05    0.0078       2      31 ..     105     134 ..     104     218 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.5e-05
                          AAA_3   2 vllegvPGlaktllvkalakaldlefkriq 31 
                                    vll g PG++ktll++a+a ++d++f ++ 
  gene826|gene826|rna826|rna826 105 VLLYGPPGTGKTLLARAIAATMDVSFLKVV 134
                                    7999**********************9884 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   2.8e-05     0.014      54     116 ..     103     170 ..      73     181 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.8e-05
                         DUF815  54 nnvLLwGarGtGKSslvkallneyaeegLrlie..vekedlkelpklvellr...erperfilfvDDL 116
                                    + vLL+G  GtGK  l +a+ +++  + L+++   + ++ + e +++++++    ++++ +i+f+D +
  gene826|gene826|rna826|rna826 103 KGVLLYGPPGTGKTLLARAIAATMDVSFLKVVAssLIEKYIGESSRMIREMFqyaRERTPCIIFIDEI 170
                                    579****************************9633445666666666655541224455699999975 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   5.1e-05     0.026       2      36 ..     105     140 ..     104     162 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 5.1e-05
                         AAA_28   2 ivitGgestGKTtlleaLaar.gypvvpEaareile 36 
                                    + + G+++tGKT l++a+aa+ +++ ++ +a  ++e
  gene826|gene826|rna826|rna826 105 VLLYGPPGTGKTLLARAIAATmDVSFLKVVASSLIE 140
                                    6799***************98766666555555554 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   6.1e-05     0.031       1      25 [.     105     129 ..     105     177 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 6.1e-05
                   RNA_helicase   1 iwlyGpsgeGKStlakeLakallkk 25 
                                    ++lyGp+g+GK++la+ +a+++  +
  gene826|gene826|rna826|rna826 105 VLLYGPPGTGKTLLARAIAATMDVS 129
                                    689**************88877644 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   0.00017     0.089      36      57 ..     105     126 ..      98     133 .. 0.90
   2 ?   -0.9   0.0         2     1e+03     130     166 ..     150     190 ..     143     205 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00017
                         AAA_25  36 allaGapgtGKttlaldlalav 57 
                                    +ll+G+pgtGKt la  +a+++
  gene826|gene826|rna826|rna826 105 VLLYGPPGTGKTLLARAIAATM 126
                                    69*************9999876 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 2
                         AAA_25 130 vdaleaaieevegvrlvviDplsralgg..densnsd..v.g 166
                                    ++++ + ++e   +  + iD ++++ g    e s+sd  v +
  gene826|gene826|rna826|rna826 150 IREMFQYARE-RTPCIIFIDEIDAIGGKrsTESSSSDreVqR 190
                                    5666777777.5699999999999999875333333332433 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   9.1e-05     0.047      21      43 ..     104     126 ..      96     137 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 9.1e-05
                                    EEEEE--TTSSTTHHHHHHHHHH CS
                           PhoH  21 ivfaiGpaGtGKtylavalavea 43 
                                     v   Gp GtGKt+la a+a+++
  gene826|gene826|rna826|rna826 104 GVLLYGPPGTGKTLLARAIAATM 126
                                    57889***********9999865 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   0.00014      0.07      21      47 ..     101     127 ..      89     156 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00014
                                    SSS-EEEECSTTSSHHHHHHHHHHHST CS
                Sigma54_activat  21 tdlsvlitGesGtGKellaraiheask 47 
                                     +  vl+ G  GtGK+llarai ++ +
  gene826|gene826|rna826|rna826 101 EPKGVLLYGPPGTGKTLLARAIAATMD 127
                                    55789****************987654 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00031      0.16      14      41 ..     100     127 ..      91     142 .. 0.86
   2 ?   -1.2   0.0         2     1e+03     152     186 ..     177     212 ..     154     221 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00031
                     Zeta_toxin  14 erPklillgGqpGAGKselaellkdele 41 
                                    ++Pk +ll G pG GK+ la+++++ ++
  gene826|gene826|rna826|rna826 100 SEPKGVLLYGPPGTGKTLLARAIAATMD 127
                                    68**********************9994 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 2
                     Zeta_toxin 152 Rlvpkeehd.eafeglresvealeeekqldrvkikd 186
                                    R ++ ++ d e+++ l+e +++l+  k ld+vk++ 
  gene826|gene826|rna826|rna826 177 RSTESSSSDrEVQRTLMELLNQLDGFKSLDKVKVIM 212
                                    555555544156677899999999999999999653 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00033      0.17      23      72 ..     105     153 ..      92     200 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00033
                       ATPase_2  23 yfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefieee 72 
                                    +++YGp g GKt L + i+    d ++ ++  ++l e++i + +++i+e 
  gene826|gene826|rna826|rna826 105 VLLYGPPGTGKTLLARAIAATM-DVSFLKVVASSLIEKYIGESSRMIREM 153
                                    689*********9999988887.778888888888888888888887743 PP

>> CPT  Chloramphenicol phosphotransferase-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   0.00015     0.077       4      41 ..     105     142 ..     103     191 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00015
                                    EEEEE-TTSSHHHHHHHHHHHSSS-EEEEEHHHHHHHS CS
                            CPT   4 ilLnGgsssGKsslaralqevldepwlhlgvDafveal 41 
                                    +lL G + +GK+ lara+ +++d ++l++   +++e+ 
  gene826|gene826|rna826|rna826 105 VLLYGPPGTGKTLLARAIAATMDVSFLKVVASSLIEKY 142
                                    89***************************999999874 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0    0.0002       0.1       2      24 ..     105     127 ..     105     262 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.0002
                         AAA_33   2 vllvGlpGsGKstlaerllkklg 24 
                                    vll G+pG+GK+ la+ +++  +
  gene826|gene826|rna826|rna826 105 VLLYGPPGTGKTLLARAIAATMD 127
                                    7899************9987665 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00021      0.11      19      49 ..     103     133 ..      92     170 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00021
                         AAA_30  19 rvavltGpAGtGKttalkalreaweaaggrv 49 
                                    + ++l Gp+GtGKt + +a++++++ +  +v
  gene826|gene826|rna826|rna826 103 KGVLLYGPPGTGKTLLARAIAATMDVSFLKV 133
                                    567899**************99887665555 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00027      0.14      15      41 ..     100     126 ..      92     193 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00027
                         AAA_11  15 seseitliqGPPGtgKTktivellsql 41 
                                    se++ +l+ GPPGtgKT    ++ + +
  gene826|gene826|rna826|rna826 100 SEPKGVLLYGPPGTGKTLLARAIAATM 126
                                    5666789**********6666655555 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00042      0.22       1      49 [.     108     157 ..     108     185 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00042
                                    EE-TTSSHHHHHHHHHHHHTEEEE..EHHHHHHHHHHTTTSHSSHHHHCTS CS
                         AAA_17   1 lGgPGsGKgtqceklvekygfthl..saGdllreeakrgglakardemrkl 49 
                                    +G+PG GK+ +++ ++  +++++l   a++l+ + + +++  + r+ ++ +
  gene826|gene826|rna826|rna826 108 YGPPGTGKTLLARAIAATMDVSFLkvVASSLIEKYIGESSR-MIREMFQYA 157
                                    7****************997766521667777666655443.556655554 PP

>> PIF1  PIF1-like helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00025      0.13      12      58 ..      92     136 ..      90     154 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00025
                                    HH......HCTS-EEEEESTTSSCHHHHHHHHHHCHCTCCCEEEEES CS
                           PIF1  12 aiieavlnekgklfFvtGsgGtgKtflwkallkklrsegkivlavAs 58 
                                    +i e+v  +++k + ++G  GtgKt l +a+ +++  +  +v  vAs
  gene826|gene826|rna826|rna826  92 EIFERVGISEPKGVLLYGPPGTGKTLLARAIAATMDVSFLKV--VAS 136
                                    6888999999**********************9998874444..454 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   0.00038      0.19       9      36 ..     101     128 ..      95     211 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00038
                         AAA_19   9 kekvllvtaGpGtGKTrvlkhivallve 36 
                                    + k +l+ ++pGtGKT + ++i a +  
  gene826|gene826|rna826|rna826 101 EPKGVLLYGPPGTGKTLLARAIAATMDV 128
                                    567799**********999888877654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (324 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       617  (0.0344135); expected 358.6 (0.02)
Passed bias filter:                      585  (0.0326287); expected 358.6 (0.02)
Passed Vit filter:                       107  (0.00596798); expected 17.9 (0.001)
Passed Fwd filter:                        35  (0.00195214); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              35  [number of targets reported over threshold]
# CPU time: 0.74u 0.39s 00:00:01.12 Elapsed: 00:00:00.56
# Mc/sec: 1738.03
//
Query:       gene827|gene827|rna827|rna827  [L=139]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       288  (0.0160634); expected 358.6 (0.02)
Passed bias filter:                      218  (0.0121591); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.29s 00:00:00.68 Elapsed: 00:00:00.56
# Mc/sec: 742.82
//
Query:       gene828|gene828|rna828|rna828  [L=371]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.4e-14   54.3   3.1    2.6e-14   53.4   1.0    2.0  2  DUF5088     Domain of unknown function (DUF5088)
  ------ inclusion threshold ------
      0.016   14.7   0.1      0.021   14.2   0.1    1.1  1  Sipho_tail  Phage tail protein


Domain annotation for each model (and alignments):
>> DUF5088  Domain of unknown function (DUF5088)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0     0.041   3.7e+02      50     113 ..      53     120 ..      50     128 .. 0.69
   2 !   53.4   1.0   2.9e-18   2.6e-14       1      90 [.     180     270 ..     180     283 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.041
                        DUF5088  50 vGDiivikkfrkkkkiealskidr.ntfsetkyf...dvkEisvkeilkiellkkkekvkeiFttvvG 113
                                    +GD ++i++  ++  ie   k d   t ++   +   +++Ei  ++  k++ l   +++   F+tv  
  gene828|gene828|rna828|rna828  53 IGDEVFIRDGDEGVAIENEGKQDDsSTVTDRYLVrseRIDEIEMNDDSKMSYLPFLSDTPLFFKTVPQ 120
                                    67888888888888887777777646666654433336888888888888888877777777777755 PP

  == domain 2  score: 53.4 bits;  conditional E-value: 2.9e-18
                        DUF5088   1 gkvilktrlstvsssgslplfffiil..stsaglvkvvvWkealrkysslkvGDiivikkfrkkkkiealskidrntfse 78 
                                    +k++lk+r+  ++ +  +p++ ++++  +t+++lv vv+W+ ++ ky  l+  Di++i + rkkk++    ++ +n +s+
  gene828|gene828|rna828|rna828 180 AKIVLKSRIIAYNHGS-FPFYQVLVVvdLTENKLVTVVLWNRSVYKYCNLQHNDIVIIPRCRKKKRYYNNGVMVYNSYSD 258
                                    699**********987.88987766634689************************************************* PP

                        DUF5088  79 tkyfdvkEisvk 90 
                                       fd++E sv+
  gene828|gene828|rna828|rna828 259 VWMFDCEEFSVN 270
                                    ***********9 PP

>> Sipho_tail  Phage tail protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   2.4e-06     0.021      79     209 ..      82     247 ..      61     262 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.4e-06
                     Sipho_tail  79 kyylavlsgdidldeknnigkgeitflvpdpyaysvetsllnetnfagnlwgfdlnisn...kteyk............. 142
                                     +yl+ ++ +++++++  +  + + fl  +p + +   ++ n++ + ++ + fd  i+    k e k             
  gene828|gene828|rna828|rna828  82 DRYLVRSERIDEIEMNDDSKMSYLPFLSDTPLFFKTVPQRINAF-YREGALYFDGMIKYemiKNEHKnrrktsfeqgkpt 160
                                    5899999999************************9999999666.67776777766653345444448888999999999 PP

                     Sipho_tail 143 ........................sdtvtvtNhGtveadpiieitlngengylgiinnkttgeylkvggpefkaGDviei 198
                                                            +++++ +NhG+ + ++++ ++   en  ++++    ++++ k+ +   + +D ++i
  gene828|gene828|rna828|rna828 161 lnatsspnrggevlflpfvakivlKSRIIAYNHGSFPFYQVLVVVDLTENKLVTVVL--WNRSVYKYCNL--QHNDIVII 236
                                    9999999**********************************8888888888888877..78888888865..99999999 PP

                     Sipho_tail 199 d.venrkvlvng 209
                                      ++++k    +
  gene828|gene828|rna828|rna828 237 PrCRKKKRYY-N 247
                                    9777776554.3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (371 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       383  (0.021362); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 2505.70
//
Query:       gene829|gene829|rna829|rna829  [L=311]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      4e-13   49.5   3.1      1e-12   48.1   3.1    1.7  1  DUF5088   Domain of unknown function (DUF5088)


Domain annotation for each model (and alignments):
>> DUF5088  Domain of unknown function (DUF5088)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.1   3.1   5.8e-17     1e-12     108     186 .]      18     101 ..       9     101 .. 0.93

  Alignments for each domain:
  == domain 1  score: 48.1 bits;  conditional E-value: 5.8e-17
                        DUF5088 108 FttvvGkveYlsvllrks........angkyeeYvllkvsgikvvLlansdkelydievgksieitelRkikrgefefyi 179
                                     + ++G+++Y+s+llrk+        +n+k ee++ll++++++v L++ s+k +y++++  ++++ ++R i+   +++y+
  gene829|gene829|rna829|rna829  18 LHSIEGRINYISILLRKRkaegtfflVNDKIEEFYLLRIGEMIVYLFNTSEKVFYELDAYDQVTLGNMRMID---TNVYV 94 
                                    4689*************999***9999******************************************986...689** PP

                        DUF5088 180 stiytqf 186
                                    sti+t++
  gene829|gene829|rna829|rna829  95 STIFTNI 101
                                    *****86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       739  (0.0412181); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 2215.68
//
Query:       gene83|gene83|rna83|rna83  [L=438]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.089   13.0   0.0       0.22   11.7   0.0    1.6  1  DUF2990   Protein of unknown function (DUF2990)


Domain annotation for each model (and alignments):
>> DUF2990  Protein of unknown function (DUF2990)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   1.2e-05      0.22      20      41 ..     214     235 ..     206     246 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 1.2e-05
                    DUF2990  20 dfsdeLaefygkVskyIeeakd 41 
                                d s++L efyg+++k+Ie++k+
  gene83|gene83|rna83|rna83 214 DKSAKLREFYGEIKKKIERMKE 235
                                6699***************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (438 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       463  (0.0258241); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 3067.39
//
Query:       gene830|gene830|rna830|rna830  [L=157]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       866  (0.0483016); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 1019.78
//
Query:       gene831|gene831|rna831|rna831  [L=678]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (678 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1176  (0.0655921); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.64u 0.28s 00:00:00.92 Elapsed: 00:00:00.45
# Mc/sec: 4497.90
//
Query:       gene832|gene832|rna832|rna832  [L=149]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-48  164.2   0.0    1.9e-48  163.9   0.0    1.0  1  NDK       Nucleoside diphosphate kinase


Domain annotation for each model (and alignments):
>> NDK  Nucleoside diphosphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  163.9   0.0     1e-52   1.9e-48       1     133 [.       2     134 ..       2     135 .. 0.99

  Alignments for each domain:
  == domain 1  score: 163.9 bits;  conditional E-value: 1e-52
                                    EEEEEEE-HHHHHTT-HHHHHHHHHHHT-EEEEEEEECE-HHHHHHHTGGGTTSTTHHHHHHHHTSSEEEEEEEESTTHH CS
                            NDK   1 ertlvliKPdavkrgligeiisrleekglkivalkmlrlteeqaeehYaehkgkpffeelvefmtsgpvvalvlegedai 80 
                                    e++lvl+KPda+kr+lig+ii++ e+kgl i +lk+l+ ++e+++ehYaehk+kpff+++v++++ + vva+v+ g++a+
  gene832|gene832|rna832|rna832   2 EQSLVLLKPDAIKRRLIGTIIAKYEQKGLYIHKLKLLKPSRELVREHYAEHKNKPFFTKVVDYLSASAVVAMVVAGDNAV 81 
                                    899***************************************************************************** PP

                                    HHHHHHH--SSTTTSSTTSHHHHH-SSSTT-SEEE-SSHHHHHHHHHHHSTGG CS
                            NDK  81 ekvreliGatnpaeaapgtiRadfgvslgeNlvHgSdseesaereiklfFkee 133
                                    ++vr+l G tnp +a+ g+iR+d+g+ +g+N+vHgS+s e+a+rei+l+F e+
  gene832|gene832|rna832|rna832  82 AVVRKLNGVTNPVDAELGSIRGDYGMCVGRNVVHGSESVEAARREIGLWFGED 134
                                    **************************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       499  (0.027832); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 937.16
//
Query:       gene833|gene833|rna833|rna833  [L=118]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       293  (0.0163422); expected 358.6 (0.02)
Passed bias filter:                      191  (0.0106531); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.41
# Mc/sec: 859.50
//
Query:       gene834|gene834|rna834|rna834  [L=510]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (510 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       858  (0.0478554); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.41
# Mc/sec: 3728.22
//
Query:       gene835|gene835|rna835|rna835  [L=166]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    6.5e-12   45.6   0.1    9.1e-12   45.2   0.1    1.2  1  SPRY        SPRY domain
  ------ inclusion threshold ------
      0.022   14.8   0.1       0.22   11.5   0.1    2.0  1  Neuralized  Neuralized


Domain annotation for each model (and alignments):
>> SPRY  SPRY domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.2   0.1     1e-15   9.1e-12       2     118 ..      44     151 ..      43     152 .. 0.94

  Alignments for each domain:
  == domain 1  score: 45.2 bits;  conditional E-value: 1e-15
                                    EEEEEEETCCTSSEEEEEEEETTSSSSSTSSSTSSTTEEEEETETTEEEEETESCEEEESSSSTTSEEEEEEETTTTEEE CS
                           SPRY   2 hyfevkiqsaeggsisvGlateqtdlsdksgegddrgswglcgdngtrtsaeqskaygkqparegdviGvalDleegels 81 
                                     yfev i+   + ++++G+a ++++l++  g    +gs+++ + +g ++++ + +ay++ + +e+dv+Gv+   +e+ l+
  gene835|gene835|rna835|rna835  44 TYFEVLIN---KLHVRIGVAPQDYKLYGPLG---LDGSYAFGSLKGYKYHKGVRNAYAH-KLKENDVVGVL-K-VEHFLK 114
                                    6*******...**************888877...69***********************.*********97.3.4478** PP

                                    EEETTEEEEEEEESTTTSSEEEEEEE.STCEEEEESS CS
                           SPRY  82 FtkngknlgvaFrnvrgaelfPvvslgngaslkinlg 118
                                    F  ng +lg+a+ ++ g+e f + s+  g s+ +n+g
  gene835|gene835|rna835|rna835 115 FFVNGVDLGIAYDDLYGKEYFAALSFYGGGSVCVNFG 151
                                    ********************************99998 PP

>> Neuralized  Neuralized
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   2.5e-05      0.22      29     141 ..      34     142 ..      11     146 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 2.5e-05
                     Neuralized  29 vfssrplrigelfevriekledkwsgsLevGvtsvdPatl.....e.peslPdlatkllreywvvaldeklas..kegdv 100
                                    ++++++++++  fev i+kl+       ++Gv   d +       + ++++ +l      +y    + +++a+  ke+dv
  gene835|gene835|rna835|rna835  34 CLTNEAIEDNTYFEVLINKLH------VRIGVAPQDYKLYgplglDgSYAFGSLKGY---KYHKGVR-NAYAHklKENDV 103
                                    566777777777777776665......566666666544432221211233222222...2222222.222224457888 PP

                     Neuralized 101 lgflvtsegelhfsvNgedqgvalsgvpdsqplwavvdlyG 141
                                    +g+ ++ e+ l+f+vNg+d g+a +++   ++ +a +  yG
  gene835|gene835|rna835|rna835 104 VGV-LKVEHFLKFFVNGVDLGIAYDDL-YGKEYFAALSFYG 142
                                    886.677889***********999999.6668999998888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       427  (0.0238162); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 1190.80
//
Query:       gene836|gene836|rna836|rna836  [L=208]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
      0.089   13.8   3.6        1.9    9.5   3.6    2.5  1  DUF4834     Domain of unknown function (DUF4834)
       0.11   12.4   0.3       0.17   11.7   0.3    1.4  1  Mid2        Mid2 like cell wall stress sensor
        0.8    7.5   2.9        3.3    5.5   2.9    1.8  1  V_ATPase_I  V-type ATPase 116kDa subunit family
        1.1    9.5   6.9       0.16   12.3   1.8    2.2  2  Orf78       Orf78 (ac78)
        4.9    7.0   5.8        3.2    7.6   3.6    1.8  1  TMEM154     TMEM154 protein family


Domain annotation for each model (and alignments):
>> DUF4834  Domain of unknown function (DUF4834)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   3.6   0.00054       1.9       4      91 ..      23     116 ..      18     203 .. 0.63

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00054
                        DUF4834   4 Llfilifiiailviglsilsvilrtv.........fglgsrkkss...ksaqkqfgnstnsnqqksq..srsetkeegei 69 
                                    L +i+i i++  vi l+++ +i+                     s   ++++ ++ +s++s+ +  q  +++e +  +e+
  gene836|gene836|rna836|rna836  23 LTIIIICIVVATVILLIVVPTIIYYCvvddeegesS--------SvsvSKVSGGSDSSKESSWFGGQdeDETEDEPVDEE 94 
                                    556666666666666666666555442232222220........222222222222222222222221111222222233 PP

                        DUF4834  70 ieeersekeakrkkiFekdeGE 91 
                                      + +++ e ++ +++  + GE
  gene836|gene836|rna836|rna836  95 GANGTQSGEVPHYRLYVTQSGE 116
                                    3333344444444555555554 PP

>> Mid2  Mid2 like cell wall stress sensor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.3   4.6e-05      0.17      47      75 ..      24      52 ..       4      80 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 4.6e-05
                           Mid2 47 niviGcvvGigvPlllvillllyifCiks 75
                                    i+i c+v  +v ll+v+  ++y+  + +
  gene836|gene836|rna836|rna836 24 TIIIICIVVATVILLIVVPTIIYYCVVDD 52
                                   6999999999**********999765554 PP

>> V_ATPase_I  V-type ATPase 116kDa subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   2.9   0.00091       3.3     597     653 ..       9     112 ..       1     203 [. 0.63

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.00091
                     V_ATPase_I 597 kvkeeelyegqetvqvvLlllalvcvpvlllvkPlilklkhkkkkkkkekkkeeee........................ 652
                                    k  ++ ly +     ++++++++v+  +ll+v P i+++    +++ ++++ + ++                        
  gene836|gene836|rna836|rna836   9 KSINTALYLHYMNRLTIIIICIVVATVILLIVVPTIIYYCVVDDEEGESSSVSVSKvsggsdsskesswfggqdedeted 88 
                                    44466688777776777778888888888899998888887776666666655555566666666666666555555555 PP

                     V_ATPase_I 653 .......................e 653
                                                           +
  gene836|gene836|rna836|rna836  89 epvdeegangtqsgevphyrlyvT 112
                                    555555555555555554444440 PP

>> Orf78  Orf78 (ac78)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   1.8   4.5e-05      0.16      62      95 ..      24      57 ..       6      65 .. 0.57
   2 ?   -0.6   0.2      0.44   1.6e+03      37      37 ..     138     138 ..     103     198 .. 0.58

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 4.5e-05
                          Orf78 62 alnillisllavvcvlvllyviyYfvilrerqks 95
                                   +  i+ i++ +v+ ++v+  +iyY v+  e+ +s
  gene836|gene836|rna836|rna836 24 TIIIICIVVATVILLIVVPTIIYYCVVDDEEGES 57
                                   2333344444444444444677777776665544 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.44
                          Orf78  37 k 37 
                                    +
  gene836|gene836|rna836|rna836 138 N 138
                                    1 PP

>> TMEM154  TMEM154 protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   3.6    0.0009       3.2      60      99 ..      25      63 ..       8      78 .. 0.65

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0009
                        TMEM154 60 lmiiiPlvllillllvviiliqkkkrkrsKddekseaesd 99
                                   ++ii   v++++ll+vv  +i +++     + e+s ++ +
  gene836|gene836|rna836|rna836 25 IIIICIVVATVILLIVVPTII-YYCVVDDEEGESSSVSVS 63
                                   333333467777777777777.887766666666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1478  (0.0824363); expected 358.6 (0.02)
Passed bias filter:                      892  (0.0497518); expected 358.6 (0.02)
Passed Vit filter:                       155  (0.00864521); expected 17.9 (0.001)
Passed Fwd filter:                        35  (0.00195214); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.79u 0.32s 00:00:01.11 Elapsed: 00:00:00.48
# Mc/sec: 1314.91
//
Query:       gene837|gene837|rna837|rna837  [L=299]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.24   12.4   8.0        2.8    8.9   0.0    2.7  2  DUF4834   Domain of unknown function (DUF4834)


Domain annotation for each model (and alignments):
>> DUF4834  Domain of unknown function (DUF4834)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.0   0.00016       2.8       8      76 ..       5      84 ..       1      96 [. 0.59
   2 ?   -8.4  17.1         1   1.8e+04      35      83 ..     234     282 ..     198     296 .. 0.58

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00016
                        DUF4834  8 lifiiailviglsilsvilrtv..........fglgsrkkss.ksaqkqfgnstnsnqqksqsrsetkeegeiieeerse 76
                                   li ++a+l+igl++ls i   +          +g+gs+++ s  + +k ++++ n++++ +++ + + + +e++ +e++e
  gene837|gene837|rna837|rna837  5 LIPLLALLIIGLILLSGIGIPLllkalknnkgYGAGSKSTPSgTNPSKPESSGPNKPSNDDSDVNPEAAPDETNPDEPEE 84
                                   56666666777766666655555555577777788888777644555555555555555555555555555555555544 PP

  == domain 2  score: -8.4 bits;  conditional E-value: 1
                        DUF4834  35 rkkssksaqkqfgnstnsnqqksqsrsetkeegeiieeersekeakrkk 83 
                                    r+ ++k a+++ ++++ ++++ +++++e+++ +e++ ++++++++k  k
  gene837|gene837|rna837|rna837 234 RSGEEKAAEEKPEEEKPEEEKPEEEKPEEEKPEEEKADKEKSDKEKSDK 282
                                    4444444444444444444444444444444444333333333333223 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1680  (0.0937029); expected 358.6 (0.02)
Passed bias filter:                      679  (0.0378716); expected 358.6 (0.02)
Passed Vit filter:                       216  (0.0120475); expected 17.9 (0.001)
Passed Fwd filter:                        52  (0.00290033); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.97u 0.36s 00:00:01.33 Elapsed: 00:00:00.53
# Mc/sec: 1705.60
//
Query:       gene838|gene838|rna838|rna838  [L=652]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (652 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2135  (0.119081); expected 358.6 (0.02)
Passed bias filter:                      536  (0.0298957); expected 358.6 (0.02)
Passed Vit filter:                       377  (0.0210274); expected 17.9 (0.001)
Passed Fwd filter:                       150  (0.00836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 4.02u 0.50s 00:00:04.51 Elapsed: 00:00:00.97
# Mc/sec: 2040.06
//
Query:       gene839|gene839|rna839|rna839  [L=126]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0062   15.8   4.0      0.009   15.3   4.0    1.4  1  Zip             ZIP Zinc transporter
  ------ inclusion threshold ------
      0.057   13.5  13.2      0.075   13.1  13.2    1.2  1  DUF2076         Uncharacterized protein conserved in bacteria
       0.78    9.1  32.2       0.88    8.9  32.2    1.0  1  SDA1            SDA1
        1.8    7.3  16.4        1.9    7.2  16.4    1.1  1  Presenilin      Presenilin
        2.5    8.7   3.6        9.7    6.8   3.6    1.8  1  Ctr             Ctr copper transporter family
          4    5.5  13.1        4.3    5.3  13.1    1.0  1  Hid1            High-temperature-induced dauer-formation prot
        9.6    5.1  14.4         10    5.0  14.4    1.0  1  SLC12           Solute carrier family 12


Domain annotation for each model (and alignments):
>> Zip  ZIP Zinc transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   4.0   3.5e-06     0.009      81     171 ..      11     108 ..       2     125 .. 0.57

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 3.5e-06
                            Zip  81 lvllGflllllveklltmivek....ksshkektpkkasssssesaakksvsndkveeseekedhvaeadtdadsk...e 153
                                    l++ G+++     kll m+++     k+++ ++++k+ ++++s+ +   + ++ + +++ e+ d+v e+d+++d +    
  gene839|gene839|rna839|rna839  11 LAVAGLFTAVAGPKLLDMMKNMnnpsKDEKLDNEQKNPKNDESNDHENPKDEDLQNPDENENSDDVNEEDENPDDQnkeD 90 
                                    55566666666667777777666666666777777777777777777777777777777777666666555544330002 PP

                            Zip 154 elrngkqeksesekeqas 171
                                    e  ++++++++++ke ++
  gene839|gene839|rna839|rna839  91 ENPDENENPDDQNKEDEN 108
                                    333333444444444433 PP

>> DUF2076  Uncharacterized protein conserved in bacteria (DUF2076)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1  13.2   2.9e-05     0.075     166     251 ..      19     116 ..       5     124 .. 0.45

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.9e-05
                        DUF2076 166 VaGGvllangleslfsgksgeegaasasqsaeeeeiinnyy........ssssladdaedadnasadsfadsd..sssdn 235
                                     ++G  l+++++++ + +++e+  +++++++++e    +++        ++++++dd++++d++ +d++++++  ++++n
  gene839|gene839|rna839|rna839  19 AVAGPKLLDMMKNMNNPSKDEKLDNEQKNPKNDESNDHENPkdedlqnpDENENSDDVNEEDENPDDQNKEDEnpDENEN 98 
                                    47888899999999999887666655533333333333333454443333444444444444333333332220012222 PP

                        DUF2076 236 nadaasdddsdddss..d 251
                                      d++++d++ d+++  d
  gene839|gene839|rna839|rna839  99 PDDQNKEDENPDENEnpD 116
                                    222222333333322333 PP

>> SDA1  SDA1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9  32.2   0.00034      0.88      69     170 ..      19     122 ..      13     126 .] 0.41

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00034
                           SDA1  69 gieGleLlekwkeeekkekreeeeedsddeddeedwevesddds...eedseggwidvesdeeeieesdesedeeeeeee 145
                                     ++G  Ll+  k+ ++ +k+e+ ++++++ +++e+++ e+ +d+   + d++++  dv++++e + +++++ede+ +e+e
  gene839|gene839|rna839|rna839  19 AVAGPKLLDMMKNMNNPSKDEKLDNEQKNPKNDESNDHENPKDEdlqNPDENENSDDVNEEDE-NPDDQNKEDENPDENE 97 
                                    577777887777777766665333332333333333333322222343333333445655555.2333335555544444 PP

                           SDA1 146 eeekeekeeeeeeeeeeeeeeeeee 170
                                    + ++++ke+e+ +e+e+ +++++e+
  gene839|gene839|rna839|rna839  98 NPDDQNKEDENPDENENPDDQNKED 122
                                    4444444444433322111211111 PP

>> Presenilin  Presenilin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2  16.4   0.00073       1.9     233     305 ..      35     115 ..       9     126 .] 0.28

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.00073
                     Presenilin 233 aeseeeeeaekkkeeasesskeeeseeesseksaqsse........seeeseeesseaessaeesseekeseessessee 304
                                     +++e+ ++e+k+ +++es+++e+ ++e  ++ +++++        ++ ++++++ e+++++e+++++++++e+ +++e+
  gene839|gene839|rna839|rna839  35 PSKDEKLDNEQKNPKNDESNDHENPKDEDLQNPDENENsddvneedENPDDQNKEDENPDENENPDDQNKEDENPDENEN 114
                                    11222222222222222111111111111111111111111111111111111111111111111111111111111111 PP

                     Presenilin 305 e 305
                                     
  gene839|gene839|rna839|rna839 115 P 115
                                    1 PP

>> Ctr  Ctr copper transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   3.6    0.0038       9.7      26      84 ..       3      90 ..       1     126 [] 0.58

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0038
                            Ctr 26 gsciglfllaifyeflralrerlerewdrhl..arsrekrkaassplvdssssseeeaea...................... 83
                                   + +++l +la+   f  +   +l + +++ +  ++++++++++++p++d+s+++e+ +++                      
  gene839|gene839|rna839|rna839  3 FLLLALAMLAVAGLFTAVAGPKLLDMMKNMNnpSKDEKLDNEQKNPKNDESNDHENPKDEdlqnpdenensddvneedenpd 84
                                   6677777777777777777777777666666433555555555555555444444443335555556666666665555554 PP

                            Ctr 84 .....k 84
                                        +
  gene839|gene839|rna839|rna839 85 dqnkeD 90
                                   444440 PP

>> Hid1  High-temperature-induced dauer-formation protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3  13.1    0.0017       4.3     567     674 ..      25     119 ..       9     126 .] 0.32

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0017
                           Hid1 567 vfealrnltlesaseeiersnesarldsideeeeenssessrieesrsesrspslsevpelksslaitddeskaereksa 646
                                     ++ ++n++ +s+ e+  ++++ + ++++++++e+ ++e+ + + ++++s  +             ++d++ ++++++ +
  gene839|gene839|rna839|rna839  25 LLDMMKNMNNPSKDEKLDNEQK-NPKNDESNDHENPKDEDLQNPDENENSDDV------------NEEDENPDDQNKEDE 91 
                                    4444445554444444444444.333333333333333333333322222222............222222222222222 PP

                           Hid1 647 tessssqavsqlremsekarakesaest 674
                                    ++ ++++  +q++e ++ ++++++  ++
  gene839|gene839|rna839|rna839  92 NPDENENPDDQNKEDENPDENENPDDQN 119
                                    2222222112111111111111111111 PP

>> SLC12  Solute carrier family 12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0  14.4     0.004        10     124     217 ..      26     116 ..      11     126 .] 0.33

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.004
                          SLC12 124 ldvsellqeeeeeeeekekkeaeesekeeeekkkakkkklle..ekskekeekekleekdsnlslseekkeeekekkkek 201
                                    ld+ + +++ +++e+ ++++++ ++++ ++++++ k+++l++  e++++++ +e+ e+ d++++ +e+ +    e+++++
  gene839|gene839|rna839|rna839  26 LDMMKNMNNPSKDEKLDNEQKNPKNDE-SNDHENPKDEDLQNpdENENSDDVNEEDENPDDQNKEDENPD----ENENPD 100
                                    677766666644444333322222221.222221222222222222222222222222222222222222....222222 PP

                          SLC12 202 kkkkekkeklkkkeks 217
                                    +++ke+++  ++++ +
  gene839|gene839|rna839|rna839 101 DQNKEDENPDENENPD 116
                                    2222222222211111 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1715  (0.0956551); expected 358.6 (0.02)
Passed bias filter:                      657  (0.0366445); expected 358.6 (0.02)
Passed Vit filter:                       176  (0.0098165); expected 17.9 (0.001)
Passed Fwd filter:                        50  (0.00278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.88u 0.39s 00:00:01.27 Elapsed: 00:00:00.60
# Mc/sec: 632.22
//
Query:       gene84|gene84|rna84|rna84  [L=85]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (85 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       172  (0.0095934); expected 358.6 (0.02)
Passed bias filter:                      168  (0.00937029); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.44
# Mc/sec: 581.56
//
Query:       gene840|gene840|rna840|rna840  [L=279]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (279 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       691  (0.0385409); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1995.60
//
Query:       gene841|gene841|rna841|rna841  [L=46]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (46 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       395  (0.0220313); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.27s 00:00:00.63 Elapsed: 00:00:00.43
# Mc/sec: 323.98
//
Query:       gene842|gene842|rna842|rna842  [L=213]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.2e-48  164.7   0.2    1.5e-48  164.5   0.2    1.1  1  Ras           Ras family
    6.9e-34  116.6   0.0    1.1e-33  116.0   0.0    1.3  1  Roc           Ras of Complex, Roc, domain of DAPkinase
    6.8e-16   58.2   0.0    8.5e-16   57.9   0.0    1.1  1  Arf           ADP-ribosylation factor family
    9.9e-08   31.7   0.1      3e-07   30.2   0.1    1.8  1  GTP_EFTU      Elongation factor Tu GTP binding domain
    1.9e-07   31.1   0.0    3.6e-07   30.3   0.0    1.4  1  MMR_HSR1      50S ribosome-binding GTPase
    1.6e-05   24.4   0.1      2e-05   24.0   0.1    1.2  1  Gtr1_RagA     Gtr1/RagA G protein conserved region
    0.00047   20.1   0.0       0.22   11.4   0.0    2.1  2  RsgA_GTPase   RsgA GTPase
     0.0017   17.8   0.0     0.0028   17.1   0.0    1.3  1  SRPRB         Signal recognition particle receptor beta subun
  ------ inclusion threshold ------
      0.018   14.5   0.0      0.032   13.6   0.0    1.3  1  TniB          Bacterial TniB protein
      0.019   14.1   0.6        5.9    6.0   0.1    3.1  2  G-alpha       G-protein alpha subunit
      0.027   14.2   0.0      0.049   13.4   0.0    1.6  1  AAA_24        AAA domain
      0.052   13.1   0.0        0.2   11.2   0.0    1.9  1  FeoB_N        Ferrous iron transport protein B
      0.067   13.2   0.0       0.14   12.1   0.0    1.6  2  MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain


Domain annotation for each model (and alignments):
>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  164.5   0.2   1.1e-51   1.5e-48       1     160 [.      22     182 ..      22     184 .. 0.95

  Alignments for each domain:
  == domain 1  score: 164.5 bits;  conditional E-value: 1.1e-51
                                    EEEEEESTTSSHHHHHHHHHHSSCSSSCTTTSSEEEEEEEEEETTEEEEEEEEEETTSGGGHHHHHHHHTTESEEEEEEE CS
                            Ras   1 KlvlvGdsavGKtslllrfvkdkFkeeyesTigvdfytkeievdgkevkleiwDTAGqeefkslrelyyrdaegillvyd 80 
                                    K++++G+s vGKts+  rfv+d+F+++  sTig+d ++k+++vdg +v+l+iwDTAGqe+f+s++++yyr a+gi+lv+d
  gene842|gene842|rna842|rna842  22 KIIILGESYVGKTSIAQRFVNDEFDTSLFSTIGIDLLKKTVTVDGAKVRLNIWDTAGQERFHSITKSYYRCADGIILVFD 101
                                    99****************************************************************************** PP

                                    TTBHHHHHTHHHHHHHHHHHSTTTSEEEEEEETTTGGGG-S.S-HHHHHHHHHHHTSEEEEEBTTTTCTHHHHHHHHHHH CS
                            Ras  81 itsresfenvkkwveeikrvaeenvpivLvGnKvDleekra.vsteegeelakelglkfletSAktnenveeafeellre 159
                                    + + +sf+++++w+e i+r ++envpi LvGnK D +e+r+    +  ee a++++++f+ tSAkt  n+e +f+++++e
  gene842|gene842|rna842|rna842 102 LLDLKSFDSIDRWFEGIHRETDENVPIFLVGNKYDDAEHRVdFVLDVFEEKARSMNVEFFVTSAKTGLNIELLFTRMAEE 181
                                    **********************************98875542556778999**************************998 PP

                                    H CS
                            Ras 160 i 160
                                    +
  gene842|gene842|rna842|rna842 182 L 182
                                    7 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.0   0.0   7.9e-37   1.1e-33       1     119 [.      22     136 ..      22     137 .. 0.92

  Alignments for each domain:
  == domain 1  score: 116.0 bits;  conditional E-value: 7.9e-37
                                    EEEEESSTTSSHHHHHHCHCT-CCC-EEETTTTEEEEEEECGGSGGCTTBTTTTCEEEEEEEE-SGGCTTTT-HHHHCTS CS
                            Roc   1 KvvlvGdsgvGKtsllkrfvedkfsekekstigvdfltkevtkikgvendkkvkkvklniWDtaGqerfrslhplylrea 80 
                                    K++++G+s vGKts+++rfv+d+f+++  stig+d+l+k+v +++g        kv+lniWDtaGqerf+s++++y+r a
  gene842|gene842|rna842|rna842  22 KIIILGESYVGKTSIAQRFVNDEFDTSLFSTIGIDLLKKTV-TVDG-------AKVRLNIWDTAGQERFHSITKSYYRCA 93 
                                    9************************************9987.5665.......4699*********************** PP

                                    CEEEEEEE...GHHHHCHHHHHHHHHHHCSSS.-EEEEEE-TT CS
                            Roc  81 alailvyd...srssenlkeWlkelkkvagks.pvilvgnkiD 119
                                    + +ilv+d    +s++++++W++ ++++++++ p++lvgnk+D
  gene842|gene842|rna842|rna842  94 DGIILVFDlldLKSFDSIDRWFEGIHRETDENvPIFLVGNKYD 136
                                    *******98767899**********999875549*******99 PP

>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.9   0.0   6.2e-19   8.5e-16      13     171 ..      19     178 ..       9     182 .. 0.78

  Alignments for each domain:
  == domain 1  score: 57.9 bits;  conditional E-value: 6.2e-19
                                    TEEEEEEEESTTSSHHHHHHHHHHSSCEE.CSSSSSEEE..EEEEE..TTEEEEEEEE-SSGGGGGGGGGGCTTESEEEE CS
                            Arf  13 kelrilllGLDnaGKtTilkklkleelvt.tvPTigfnv..eelei..knlkftvwDvGGqeklRplWknYfektdavif 87 
                                      ++i++lG    GKt i +++ ++e++t    Tig +   +++++   ++++++wD  Gqe+  ++ k+Y+++ d++i 
  gene842|gene842|rna842|rna842  19 TTYKIIILGESYVGKTSIAQRFVNDEFDTsLFSTIGIDLlkKTVTVdgAKVRLNIWDTAGQERFHSITKSYYRCADGIIL 98 
                                    468************************9966899998753355555448999**************************** PP

                                    EEETT-CTTHHHHHHHHHHHCTSGCCTTSEEEEEEE-TTSTTSS-HHHHHHHTTGGGSSSSSSEEEEEEBTTTTBTHHHH CS
                            Arf  88 vvDsadreRleeakeeLkalleeeelkevallvlaNKqDlpealseeelrellgleelkgkrkleiqkcsavkgeglkeg 167
                                    v D  d + +++  + ++ +  +e+ ++v++ +++NK D +e     +    +  e+ + + ++e + +sa +g +++  
  gene842|gene842|rna842|rna842  99 VFDLLDLKSFDSIDRWFEGIH-RETDENVPIFLVGNKYDDAEHR--VDFVLDVFEEKAR-SMNVEFFVTSAKTGLNIELL 174
                                    *************99999875.567789**********976532..2222222333334.56666777777777776666 PP

                                    HHHH CS
                            Arf 168 lewl 171
                                    ++++
  gene842|gene842|rna842|rna842 175 FTRM 178
                                    6665 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.2   0.1   2.2e-10     3e-07      59     191 ..      60     181 ..      19     184 .. 0.82

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 2.2e-10
                                    EEEEEETTCSSEEEEEEEESSSGGGHHHHHHHHHT-SEEEEEEETTTBSTHHHH....HHHHHHHHTTTEEEEEEESCGS CS
                       GTP_EFTU  59 aaisleketkkylinliDtPGHvdFskevirglrvlDgavlvvdaveGvepqte....evlrlalkegvpiivfiNKmDr 134
                                    ++++++  ++k ++n+ Dt G + F + +   +r +Dg +lv+d  +     +     e ++   +e+vpi+++ NK D 
  gene842|gene842|rna842|rna842  60 KTVTVD--GAKVRLNIWDTAGQERFHSITKSYYRCADGIILVFDLLDLKSFDSIdrwfEGIHRETDENVPIFLVGNKYDD 137
                                    445555..99***********************************9765555441111344556679999********** PP

                                    THHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTTEEEEEEBTTTTBTHHHHHHHHHHH CS
                       GTP_EFTU 135 lkaelkeiveevkqklsrkeeklekygekgekevpvvfgSalkgegvktllealvel 191
                                    ++++++ + +  ++k             ++  +v+++ +Sa++g +++ l+  + e 
  gene842|gene842|rna842|rna842 138 AEHRVDFVLDVFEEKA------------RS-MNVEFFVTSAKTGLNIELLFTRMAEE 181
                                    *******999999888............22.46899**********99888877665 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.3   0.0   2.6e-10   3.6e-07       1     114 []      22     134 ..      22     134 .. 0.85

  Alignments for each domain:
  == domain 1  score: 30.3 bits;  conditional E-value: 2.6e-10
                                    EEEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETT..EEEEEEECGGCSSHHHHHHHHHHHHHHHHCTSE CS
                       MMR_HSR1   1 evaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkg..keielvDtpGliegaseekglgkaflaleeadl 78 
                                    +++i+G + vGK+++ ++ ++++  +s +    +d  +++v+++g   +++++Dt+G  e   + ++++k++ +   ad 
  gene842|gene842|rna842|rna842  22 KIIILGESYVGKTSIAQRFVNDEFDTSLFSTIGIDLLKKTVTVDGakVRLNIWDTAG-QE---RFHSITKSYYR--CADG 95 
                                    589***********************999999999999999988755779*******.54...33378888884..479* PP

                                    EEEEEETT.TTCSHHHHHHHHHHHHH..TTSEEEEEEES CS
                       MMR_HSR1  79 illvvdas.eeklkpldeeleellee..akkplilvlnk 114
                                    i+lv+d+   ++++ +d+ +e + +e  ++ p++lv nk
  gene842|gene842|rna842|rna842  96 IILVFDLLdLKSFDSIDRWFEGIHREtdENVPIFLVGNK 134
                                    ******777557999999999998888888899999887 PP

>> Gtr1_RagA  Gtr1/RagA G protein conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.1   1.5e-08     2e-05       1     140 [.      22     156 ..      22     181 .. 0.72

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 1.5e-08
                      Gtr1_RagA   1 kvLLmGksgsGKtsmrsiiFdnylardtlrlgatidveksevrflg.nltlnlwDcgGqeafveeylssqkeeifrnvgv 79 
                                    k++++G+s  GKts+ +  F n      l+ ++ id+ k++v + g ++ ln+wD  Gqe+f   +     ++ +r  + 
  gene842|gene842|rna842|rna842  22 KIIILGESYVGKTSIAQR-FVNDEFDTSLFSTIGIDLLKKTVTVDGaKVRLNIWDTAGQERFHSIT-----KSYYRCADG 95 
                                    899************987.556555666666777888899998875379***********998765.....778899999 PP

                      Gtr1_RagA  80 liyVfDvesreleedletlkeilealrqyspeakvfvlihKmDliq..edereeifeerkeei 140
                                    +i VfD  + +  ++++++ e ++  r++++++ +f   +K D  +   d   ++fee+++++
  gene842|gene842|rna842|rna842  96 IILVFDLLDLKSFDSIDRWFEGIH--RETDENVPIFLVGNKYDDAEhrVDFVLDVFEEKARSM 156
                                    999***995554445554444443..4677888888888999987522344455666555554 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.8   0.0    0.0041       5.6      94     122 ..      15      43 ..       2      61 .. 0.82
   2 !   11.4   0.0   0.00016      0.22      16     100 ..      93     181 ..      79     188 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0041
                                    HHHCTTSEEEEECSTTSSHHHHHHHHCTT CS
                    RsgA_GTPase  94 kellkdktsvlvGqSGvGKStLinallpe 122
                                    k+ l+   ++++G+S vGK+++  +++++
  gene842|gene842|rna842|rna842  15 KKDLTTYKIIILGESYVGKTSIAQRFVND 43 
                                    56677778899***********9988765 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00016
                                    --EEEEEEESTTTT--HHHHHHHHHHHH...HTT-EEEEEEE-GGG--HHH..HHHHHHHHHHHTTSEEEE--TTTHTTH CS
                    RsgA_GTPase  16 vdqllivvslkepelslnlldrfLvlae...ekgiepvivlnKiDlleeee..eleelkeelealgyevllvsaktkegl 90 
                                     d +++v+ l  +  s + +dr    ++   ++++++ +v nK D +e++    l+ ++e+ +++++e++++sakt+ ++
  gene842|gene842|rna842|rna842  93 ADGIILVFDLL-DLKSFDSIDRWFEGIHretDENVPIFLVGNKYDDAEHRVdfVLDVFEEKARSMNVEFFVTSAKTGLNI 171
                                    56777777777.555667777776554411157899999******99999888899************************ PP

                                    HHHHHHCTTS CS
                    RsgA_GTPase  91 eelkellkdk 100
                                    e l ++++++
  gene842|gene842|rna842|rna842 172 ELLFTRMAEE 181
                                    9998888776 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0     2e-06    0.0028       5     123 ..      22     136 ..      19     152 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 2e-06
                                    EEEEE-STTSSHHHHHHHHHHSS---B---S.S-EEETTG...GGT..T-SEEEETT-GCCSHHHHHHHHHHGGEEEEEE CS
                          SRPRB   5 avllvGlsdsGKTslftrLttdsvkktvtSq.essaalkvksekgs..kltliDfPGheklrqklleklkaksslkglvf 81 
                                    +++++G s+ GKTs+ +r  +d++ ++  S     + +k+ + +g   +l++ D  G+e++ +  +    + + + g++ 
  gene842|gene842|rna842|rna842  22 KIIILGESYVGKTSIAQRFVNDEFDTSLFSTiGIDLLKKTVTVDGAkvRLNIWDTAGQERFHSITKS---YYRCADGIIL 98 
                                    69**************************9996444444444555550156779******99874433...5677889998 PP

                                    EEETTS-HHHHHHHHHHHHHHHHHHHHHTT---EEEEEE-TT CS
                          SRPRB  82 vvDStidpkevkevAEllyeilliteklkdavdiliACnKqe 123
                                    v D   d k   ++  ++  i  +t    ++v+i++  nK +
  gene842|gene842|rna842|rna842  99 VFD-LLDLKSFDSIDRWFEGIHRETD---ENVPIFLVGNKYD 136
                                    888.4677777777777777766665...6677777777766 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   2.3e-05     0.032      31      59 ..      16      44 ..       7      57 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.3e-05
                           TniB 31 krkrmpnlllvGdsnnGKtmivekFarlh 59
                                   k   + +++++G+s++GKt+i+++F +++
  gene842|gene842|rna842|rna842 16 KDLTTYKIIILGESYVGKTSIAQRFVNDE 44
                                   555567899****************9876 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0    0.0087        12      21      43 ..      18      40 ..       6      51 .. 0.82
   2 ?    6.0   0.1    0.0042       5.9     188     280 ..      52     136 ..      40     188 .. 0.62

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.0087
                                   ..EEEEEEEESTTSSHHHHHHHH CS
                        G-alpha 21 krevkllllGqseSGKsTilkql 43
                                    +++k+++lG+s  GK++i + +
  gene842|gene842|rna842|rna842 18 LTTYKIIILGESYVGKTSIAQRF 40
                                   3468***************9877 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0042
                                    --SEEEEEEEC...T-TEEEEEEEE-SSH...HHHHGTCCCTTTECEEEEEEEGGGTT-B-SS-TTSBHHHHHHHHHHCC CS
                        G-alpha 188 tvGisetkfev...dsklefrivdvgGqr...serkkWvpffddvdaiiFlvslsefdqvlyedekvnrleeslklFkei 261
                                    t+Gi  +k  v   + k++++i+d++Gq    s  k +  + d++  ++ l  l+ f              +s++ + e 
  gene842|gene842|rna842|rna842  52 TIGIDLLKKTVtvdGAKVRLNIWDTAGQErfhSITKSYYRCADGIILVFDLLDLKSF--------------DSIDRWFEG 117
                                    666666666666665566777777777762323344444444444444444444444..............455555555 PP

                                    CC-GGGTTSEEEEEEE-HH CS
                        G-alpha 262 cnnkllkntpiiLflnKlD 280
                                    ++++  +n+pi+L+ nK+D
  gene842|gene842|rna842|rna842 118 IHRETDENVPIFLVGNKYD 136
                                    6666666666666666665 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   3.5e-05     0.049       2      22 ..      20      40 ..      19      84 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.5e-05
                         AAA_24  2 klkiliyGpsgiGKTtlakel 22
                                    +ki+i G+s +GKT++a ++
  gene842|gene842|rna842|rna842 20 TYKIIILGESYVGKTSIAQRF 40
                                   58****************999 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00015       0.2       2     151 ..      22     173 ..      21     178 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00015
                                    EEEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEEEETT..EEEEEEE----SSSSSSSHHHHHHHHHHHCTSS CS
                         FeoB_N   2 tvalvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegklklkg..keveivDlPGiYslsayseeekvardflleeep 79 
                                    +++++G+  vGkt++  +  + + + + ++ + ++  + +++++g   +++i D  G   ++++++      d ++   +
  gene842|gene842|rna842|rna842  22 KIIILGESYVGKTSIAQRFVNDEFDTSLFSTIGIDLLKKTVTVDGakVRLNIWDTAGQERFHSITKSYYRCADGIIL-VF 100
                                    7899**************************99998655555555422777899999988777776654333333331.11 PP

                                    SEEEEEEEGGGHHHHHHHHHHHHHTTSSEEEEEETHHHHHHTT.EEE-H.HHHHHHHTS-EEEEBTTTTBTHHH CS
                         FeoB_N  80 dvvvnvvdatnlernLyLtlqllelgvpvvlalnmideaekkg.ieidl.kkLsekLgvpvvktsakkkegiee 151
                                      ++++    +++r +  + + ++ +vp+ l+ n++d ae++    +d+ ++ +++++v+   tsak++ +ie 
  gene842|gene842|rna842|rna842 101 -DLLDLKSFDSIDRWFEGIHRETDENVPIFLVGNKYDDAEHRVdFVLDVfEEKARSMNVEFFVTSAKTGLNIEL 173
                                    .1233333344566666666666666666666666666665531444542344455666666666666666655 PP

>> MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       5.8     8e+03      82      99 ..      44      61 ..      34      63 .. 0.70
   2 ?   12.1   0.0    0.0001      0.14      43     104 ..     112     182 ..      71     183 .. 0.75

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 5.8
                   MMR_HSR1_Xtn 82 svviSaekelnldeLkek 99
                                    + +S  + +++d Lk++
  gene842|gene842|rna842|rna842 44 EFDTSLFSTIGIDLLKKT 61
                                   455677888888888876 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.0001
                   MMR_HSR1_Xtn  43 Ddlidvi.egnrvYipclyvlNKiDl......isleeldelare.....pnsvviSaekelnldeLkekiweeL 104
                                    D+  + i  +  + +p ++v NK D            ld ++++      + +v+Sa+++ln++ L +++ eeL
  gene842|gene842|rna842|rna842 112 DRWFEGIhRETDENVPIFLVGNKYDDaehrvdF---VLDVFEEKarsmnVEFFVTSAKTGLNIELLFTRMAEEL 182
                                    5555556344567899999******94433221...234444434444458999***************99988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       396  (0.0220871); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1381.81
//
Query:       gene843|gene843|rna843|rna843  [L=466]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      4e-10   39.7   0.3    8.7e-08   32.3   0.2    2.8  2  Ank_5     Ankyrin repeats (many copies)
    1.6e-09   38.2   0.1    3.8e-07   30.6   0.0    3.2  3  Ank_2     Ankyrin repeats (3 copies)
    2.1e-07   30.7   0.4     0.0021   18.4   0.1    4.6  5  Ank_3     Ankyrin repeat
    2.6e-07   30.8   0.1    5.1e-06   26.7   0.1    3.1  3  Ank       Ankyrin repeat
    4.3e-07   30.4   0.3    0.00071   20.1   0.1    3.9  4  Ank_4     Ankyrin repeats (many copies)
  ------ inclusion threshold ------
      0.039   14.7   0.0      0.084   13.6   0.0    1.6  1  DUF4359   Domain of unknown function (DUF4359)


Domain annotation for each model (and alignments):
>> Ank_5  Ankyrin repeats (many copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0     0.014        41      18      46 ..     256     284 ..     247     290 .. 0.84
   2 !   32.3   0.2   2.9e-11   8.7e-08       1      56 []     300     353 ..     300     353 .. 0.93

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.014
                          Ank_5  18 tpLhvAakygaadvvrlLlargadlnltd 46 
                                     pL + + ++ ++ v++Ll++  d  +  
  gene843|gene843|rna843|rna843 256 FPLDFLCIRNDFRAVEELLKHTPDFAMLS 284
                                    6999***************9999876665 PP

  == domain 2  score: 32.3 bits;  conditional E-value: 2.9e-11
                          Ank_5   1 LlehgpadvnrldgggntpLhvAakygaadvvrlLlargadlnltdsrGltaldlA 56 
                                    Ll+++ ad+n    +g+tpLhvAa+ g++dv+ +++a +adl+++d  ++t++ +A
  gene843|gene843|rna843|rna843 300 LLQYR-ADPNQ-SFRGYTPLHVAARIGNLDVAAIFIALNADLDAKDYFNRTPMYYA 353
                                    67888.88866.599**************************************998 PP

>> Ank_2  Ankyrin repeats (3 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0     0.089   2.7e+02       3      39 ..     106     145 ..      91     163 .. 0.78
   2 ?    1.1   0.0       0.2     6e+02      27      49 ..     255     278 ..     233     291 .. 0.76
   3 !   30.6   0.0   1.3e-10   3.8e-07      13      72 ..     298     365 ..     284     373 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.089
                          Ank_2   3 lAakngnlelvklLl.egadpn.kngktaLh.yAakngnl 39 
                                    lA  ++n+ +v+ ++ +g+ p+  +   +L+ y++  gn+
  gene843|gene843|rna843|rna843 106 LALFSNNDAVVQKIVdSGYPPEiIKRCIPLYhYFCATGNK 145
                                    4555566678899988888887546778888899999965 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.2
                          Ank_2  27 ktaLhyAakngnleivklLleh.a 49 
                                    +++L + +++++  +v+ Ll+h  
  gene843|gene843|rna843|rna843 255 LFPLDFLCIRNDFRAVEELLKHtP 278
                                    567887788888888888888752 PP

  == domain 3  score: 30.6 bits;  conditional E-value: 1.3e-10
                          Ank_2  13 vklLlegadpn.k.ngktaLhyAakngnleivklLleh......adndgrtpLhyAarsghleivklL 72 
                                    +klL + adpn +  g t+Lh+Aa+ gnl+++ ++++        d+ +rtp++yA  ++h+++v+++
  gene843|gene843|rna843|rna843 298 LKLLQYRADPNqSfRGYTPLHVAARIGNLDVAAIFIALnadldaKDYFNRTPMYYAKLYKHERLVDFF 365
                                    45555899**9659*****************99999834465544488********999999999876 PP

>> Ank_3  Ankyrin repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0      0.18   5.5e+02       5      29 ..     103     126 ..      98     128 .. 0.77
   2 ?    4.4   0.0     0.026        78       5      29 ..     257     280 ..     256     282 .. 0.87
   3 ?   -1.9   0.0       2.9   8.6e+03      20      30 ..     299     308 ..     288     309 .. 0.78
   4 !   18.4   0.1   6.9e-07    0.0021       2      30 ..     313     340 ..     312     341 .. 0.90
   5 ?   -1.6   0.0       2.3     7e+03       2      21 ..     346     365 ..     345     370 .. 0.77

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.18
                          Ank_3   5 pLhlAarsgnleivkfLlenkgadv 29 
                                    +L lA+ s+n ++v+ +++  g ++
  gene843|gene843|rna843|rna843 103 ILLLALFSNNDAVVQKIVD-SGYPP 126
                                    567888899999***9999.66655 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.026
                          Ank_3   5 pLhlAarsgnleivkfLlenkgadv 29 
                                    pL + +  +++  v+ Ll+ + +d+
  gene843|gene843|rna843|rna843 257 PLDFLCIRNDFRAVEELLK-HTPDF 280
                                    7899999999999******.78776 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 2.9
                          Ank_3  20 fLlenkgadvn 30 
                                     Ll+ + ad+n
  gene843|gene843|rna843|rna843 299 KLLQ-YRADPN 308
                                    6899.999998 PP

  == domain 4  score: 18.4 bits;  conditional E-value: 6.9e-07
                          Ank_3   2 GetpLhlAarsgnleivkfLlenkgadvn 30 
                                    G+tpLh+Aar gnl+++  ++   +ad++
  gene843|gene843|rna843|rna843 313 GYTPLHVAARIGNLDVAAIFIA-LNADLD 340
                                    9**************9888888.999987 PP

  == domain 5  score: -1.6 bits;  conditional E-value: 2.3
                          Ank_3   2 GetpLhlAarsgnleivkfL 21 
                                    ++tp+++A ++ +  +v+f+
  gene843|gene843|rna843|rna843 346 NRTPMYYAKLYKHERLVDFF 365
                                    799*9999777777777765 PP

>> Ank  Ankyrin repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.95   2.8e+03      21      29 ..     300     309 ..     292     310 .. 0.76
   2 !   26.7   0.1   1.7e-09   5.1e-06       2      31 ..     313     343 ..     312     344 .. 0.93
   3 ?   -1.7   0.0       1.6   4.7e+03       3      20 ..     347     364 ..     346     367 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.95
                                    HH.TTTSTTC CS
                            Ank  21 LL.hGAnlna 29 
                                    LL ++A++n+
  gene843|gene843|rna843|rna843 300 LLqYRADPNQ 309
                                    78679***96 PP

  == domain 2  score: 26.7 bits;  conditional E-value: 1.7e-09
                                    SBBHHHHHHHHTTHHHHHHHH.TTTSTTCBT CS
                            Ank   2 GnTPLHlAatngkkriiklLL.hGAnlnald 31 
                                    G+TPLH+Aa++g+++++  ++   A+l+a+d
  gene843|gene843|rna843|rna843 313 GYTPLHVAARIGNLDVAAIFIaLNADLDAKD 343
                                    9*******************9558*****99 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 1.6
                                    BBHHHHHHHHTTHHHHHH CS
                            Ank   3 nTPLHlAatngkkriikl 20 
                                    +TP  +A  ++++r + +
  gene843|gene843|rna843|rna843 347 RTPMYYAKLYKHERLVDF 364
                                    589899879999998865 PP

>> Ank_4  Ankyrin repeats (many copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0         1   3.1e+03      10      47 ..     101     144 ..      92     150 .. 0.56
   2 ?    3.7   0.0     0.033        99       4      32 ..     257     284 ..     257     290 .. 0.86
   3 !   16.5   0.0   3.3e-06    0.0098      20      53 ..     300     331 ..     297     333 .. 0.88
   4 !   20.1   0.1   2.4e-07   0.00071       2      51 ..     314     362 ..     313     365 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1
                          Ank_4  10 i........sgrlelvrlLlekgadinaqdnrsGetalhiAakrgn 47 
                                             s++  +v+ ++++g  +     +++ ++ h+ + +gn
  gene843|gene843|rna843|rna843 101 TkilllalfSNNDAVVQKIVDSGYPPEII--KRCIPLYHYFCATGN 144
                                    44444444455566666666666543333..446666677777766 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.033
                          Ank_4   4 aLhyaaisgrlelvrlLlekgadinaqdn 32 
                                    +L+ ++i +++++v+ Ll + +d  +  +
  gene843|gene843|rna843|rna843 257 PLDFLCIRNDFRAVEELLKHTPDFAML-S 284
                                    68999**************99998887.5 PP

  == domain 3  score: 16.5 bits;  conditional E-value: 3.3e-06
                          Ank_4  20 LlekgadinaqdnrsGetalhiAakrgnveilkl 53 
                                    Ll+++ad+n +  r G t+lh Aa++gn++++  
  gene843|gene843|rna843|rna843 300 LLQYRADPNQS-FR-GYTPLHVAARIGNLDVAAI 331
                                    789*******8.88.*************999765 PP

  == domain 4  score: 20.1 bits;  conditional E-value: 2.4e-07
                          Ank_4   2 ltaLhyaaisgrlelvrlLlekgadinaqdnrsGetalhiAakrgnveil 51 
                                    +t+Lh aa  g+l+++++ ++ +ad++a  +   +t++++A +  + + +
  gene843|gene843|rna843|rna843 314 YTPLHVAARIGNLDVAAIFIALNADLDAK-DYFNRTPMYYAKLYKHERLV 362
                                    79**************************9.**********9666666655 PP

>> DUF4359  Domain of unknown function (DUF4359)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   2.8e-05     0.084      40      82 ..     389     432 ..     356     448 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.8e-05
                        DUF4359  40 lkse.CkelvdsakpqikelieestqrqNfilfSiyttelslks 82 
                                     +se C+e ++ +k+++k+++e++ q++ f+++S++  +  +k+
  gene843|gene843|rna843|rna843 389 FESEpCRERLRLTKEHLKRAMEKQLQKRRFMIVSLFSLTAAIKT 432
                                    34445******************************998877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (466 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       765  (0.0426683); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.73u 0.37s 00:00:01.10 Elapsed: 00:00:00.59
# Mc/sec: 2379.31
//
Query:       gene844|gene844|rna844|rna844  [L=283]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.1e-58  197.2   1.7    5.2e-58  196.9   1.7    1.1  1  PTPA      Phosphotyrosyl phosphate activator (PTPA) protein


Domain annotation for each model (and alignments):
>> PTPA  Phosphotyrosyl phosphate activator (PTPA) protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  196.9   1.7   2.9e-62   5.2e-58      12     300 ..      14     279 ..       9     280 .. 0.87

  Alignments for each domain:
  == domain 1  score: 196.9 bits;  conditional E-value: 2.9e-62
                                    HHHCCCHHHHHHHHHHHHHHHHHT........T-SS-HHHHHHHHHHHHHCCCTS---SS--SSS-THHHHHHHHHHHHH CS
                           PTPA  12 ekfkkSkayadilefisrlneavkgkkleeeeeasesvekllklLdeleelideippeeqpsRfGnkafrtwhdrleera 91 
                                    +kf+ S+ay+ +  f+ ++ne++++++ +     +++ + ++ lL+++++ i+++p +++p+Rf n a+ + ++ +e+  
  gene844|gene844|rna844|rna844  14 NKFRYSPAYTALSVFLGDINENIRERSYK-----QDPQNFVILLLNKIDDKIQNTPLNTGPQRFANCAVAEVYEFIESVP 88 
                                    79**********************99986.....4566889999************************998887776554 PP

                                    HHHHHHHS-GGGGGG......HHHHHHHHHTTT-BTTTTEE-HHHHHHHHHHHHHHHHTT-STT....--HHHHHHHHHH CS
                           PTPA  92 eelleellpeelkkaelekaaieelkaYlkesfGnatrlDYGtGhElsFlafllcLeklgllkeeeeedeealvlkvfek 171
                                     ++  e+++ +       ++  + l+ Yl +sfG+++r DYGtGhEl Fl fl++  +lg+l+          + +vf++
  gene844|gene844|rna844|rna844  89 LDFG-EFTKVS-------EDDRHILHVYLDQSFGSKHRFDYGTGHELFFLSFLYVCNQLGILSI-------YDMEEVFQR 153
                                    4443.323222.......345789**************************************33.......35567**** PP

                                    HHHHHHHHHHHTT-EES--------SSS-SHHHHHHHHCSSS-G....GGGG-HHHHHHHTTT-HHHHHHHHHHHH--S- CS
                           PTPA 172 YlelvrrLqstYtLepAgshGvwGLDDyqflpflfGsaQlvehkklkpksildaevveeyakeylYlsaiafinevKkgp 251
                                    Y+++vr+L+ +++LepAgshG w +DDy+f+pflfGsaQl+++k      ++  +++++++ + lY +a+ f  + K   
  gene844|gene844|rna844|rna844 154 YFQVVRNLIYRFNLEPAGSHGPWVIDDYHFMPFLFGSAQLIDTK------LTFTDLFKKENAHLLYSEAVLFCIKHKCRF 227
                                    ***************************************99986......577778888888889999888888777533 PP

                                    ....HHHH-HHHHHHHCC--HHHHHHHHHHHHHHHTTT-HHHHTT--BBSSSB CS
                           PTPA 252 ....frehSpmLydisavktWekvnkGlikmYkaevLskfpvvqhflfGsllp 300
                                        f++hS  Ly+i+ ++ W+ +n+ ++ m ++ev+++  v qhf+++++l+
  gene844|gene844|rna844|rna844 228 vktdFKKHSAALYSIKDID-WKSINERIMEMIEEEVMGRDVVTQHFIYSKYLK 279
                                    4556*************98.****************************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (283 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       495  (0.0276089); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.65u 0.34s 00:00:00.99 Elapsed: 00:00:00.57
# Mc/sec: 1495.61
//
Query:       gene845|gene845|rna845|rna845  [L=106]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.1e-05   23.7   0.0    4.4e-05   23.2   0.0    1.3  1  RRM_1     RNA recognition motif. (a.k.a. RRM, RBD, or RNP dom


Domain annotation for each model (and alignments):
>> RRM_1  RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.0   2.5e-09   4.4e-05      23      66 ..      39      78 ..      25      82 .. 0.80

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 2.5e-09
                                   SCEEEEEEEEETTTSEEEEEEEEESSHHHHHHHHHHHTTEEETT CS
                          RRM_1 23 GpiksiklvrdetgkskgfafVeFeskedAekAlealngkklgg 66
                                     i     ++d+++ +k++ f +F+++++ ++A+++lngkk++ 
  gene845|gene845|rna845|rna845 39 DLI----WPKDAKNAKKPYVFAQFQTEDEKKEAIDKLNGKKVDE 78
                                   444....56779999*************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       536  (0.0298957); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.32s 00:00:00.89 Elapsed: 00:00:00.54
# Mc/sec: 594.71
//
Query:       gene846|gene846|rna846|rna846  [L=81]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.032   14.0   0.0      0.042   13.7   0.0    1.2  1  RRM_1     RNA recognition motif. (a.k.a. RRM, RBD, or RNP dom


Domain annotation for each model (and alignments):
>> RRM_1  RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   2.3e-06     0.042      34      58 ..      20      44 ..       9      53 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.3e-06
                                   TTTSEEEEEEEEESSHHHHHHHHHH CS
                          RRM_1 34 etgkskgfafVeFeskedAekAlea 58
                                   ++g +   +fV F+s++ AekA+e+
  gene846|gene846|rna846|rna846 20 RNGETVFLGFVGFTSPDFAEKAMEE 44
                                   56777889***************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (81 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       335  (0.0186848); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.35s 00:00:00.88 Elapsed: 00:00:00.55
# Mc/sec: 447.28
//
Query:       gene847|gene847|rna847|rna847  [L=43]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (43 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       269  (0.0150036); expected 358.6 (0.02)
Passed bias filter:                      178  (0.00992805); expected 358.6 (0.02)
Passed Vit filter:                         7  (0.000390429); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.51u 0.34s 00:00:00.85 Elapsed: 00:00:00.52
# Mc/sec: 246.65
//
Query:       gene849|gene849|rna849|rna849  [L=585]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      4e-08   33.5   0.7      0.017   15.5   0.4    6.1  5  HEAT_2          HEAT repeats
     0.0015   18.7   0.8         39    4.9   0.0    5.7  5  HEAT            HEAT repeat
  ------ inclusion threshold ------
      0.022   14.5   0.0       0.86    9.3   0.0    2.8  1  DNA_alkylation  DNA alkylation repair enzyme


Domain annotation for each model (and alignments):
>> HEAT_2  HEAT repeats
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0     0.036   2.2e+02       2      26 ..      75      99 ..      74     157 .. 0.67
   2 ?    1.9   0.0     0.051     3e+02      15      82 ..     147     210 ..     133     216 .. 0.64
   3 ?    3.0   0.0     0.023   1.4e+02       5      41 ..     221     257 ..     218     262 .. 0.71
   4 !    6.5   0.0    0.0018        11       8      75 ..     415     501 ..     411     504 .. 0.75
   5 !   15.5   0.4   2.9e-06     0.017       3      87 ..     492     574 ..     459     575 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.036
                         HEAT_2  2 daLlqalendpdpevrraairaLgr 26
                                   ++L++ l ++p++  r a+++ L  
  gene849|gene849|rna849|rna849 75 STLINTLLKSPFYVHRLAVCHLLPY 99
                                   6799999999999999999999954 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.051
                         HEAT_2  15 evrraairaLgrignpealpaLvellededpavRraaaeaLgaigd..pealpaLkellddddddvvRea 82 
                                    +++  a++ L r+   +  + ++ +l++ +++vR   a+ L +++   ++ +++Lk    ddd+ +++ a
  gene849|gene849|rna849|rna849 147 YLQCGAADLLCRLE--QHSDKVHHFLRSVSWRVRFSLAKKLDRLDVfyKDIYDVLK----DDDVLFIKKA 210
                                    55555555555443..3457788889999999999999999988853344444444....5555555555 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.023
                         HEAT_2   5 lqalendpdpevrraairaLgrignp.ealpaLvelle 41 
                                    l +l +++d+e+r +++r++ r ++  + + +L+e+  
  gene849|gene849|rna849|rna849 221 LYFL-RCEDEEIRCEVVREIWRRAESgSGFMYLREYYG 257
                                    5567.899999999999999976544266766666655 PP

  == domain 4  score: 6.5 bits;  conditional E-value: 0.0018
                         HEAT_2   8 lendpdpevrraairaLg.............rignpea......lpaLvellededpavRraaaeaLgaigdpealpaLk 68 
                                    l +dp+p+v+ + ++ L              +   ++a       ++ +++l d+ ++vR  aa+   +  ++++++ Lk
  gene849|gene849|rna849|rna849 415 LMKDPSPKVKFNLLKLLKtkslvqqfvtstdWREREQAleysldSDLYFRFLVDPVAHVRCKAARLFRQPLSSATISKLK 494
                                    55788888888888888877776666655533333344555666778899999************999999999999999 PP

                         HEAT_2  69 elldddd 75 
                                    e++++d+
  gene849|gene849|rna849|rna849 495 EIVRSDN 501
                                    9999987 PP

  == domain 5  score: 15.5 bits;  conditional E-value: 2.9e-06
                         HEAT_2   3 aLlqalendpdpevrraairaLgrignpealpaLvellededpavRraaaeaLgaigdpealpaLkellddddddvvRea 82 
                                    +L +++ ++ ++  r +++++L + ++++ +++L  l++d   +vR  +   +   +    +++ ++++dddd++v R+ 
  gene849|gene849|rna849|rna849 492 KLKEIV-RSDNYLYRMNVVHVLVSNKHESMRDMLGVLARDRIVNVRDKVLSVIESERAVYYIDVVEQMVDDDDEEVCRR- 569
                                    566666.8999999999999999999999999999999999999999998888888888889*****999999999997. PP

                         HEAT_2  83 AaeaL 87 
                                    A++ L
  gene849|gene849|rna849|rna849 570 AEQVL 574
                                    57765 PP

>> HEAT  HEAT repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.37   2.2e+03       7      23 ..      80      96 ..      74      98 .. 0.74
   2 ?    2.2   0.0     0.048   2.9e+02       9      26 ..     170     187 ..     168     188 .. 0.82
   3 ?    3.0   0.0     0.027   1.6e+02       8      24 ..     415     431 ..     413     433 .. 0.85
   4 !    4.9   0.0    0.0065        39       8      25 ..     465     482 ..     460     483 .. 0.83
   5 ?   -0.1   0.1      0.26   1.5e+03       3      18 ..     553     569 ..     552     575 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.37
                                   HHHT-SSHHHHHHHHHH CS
                           HEAT  7 kllsDpspeVReaAaka 23
                                   +ll++p    R a++  
  gene849|gene849|rna849|rna849 80 TLLKSPFYVHRLAVCHL 96
                                   45699999*****9976 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.048
                                    HT-SSHHHHHHHHHHHHH CS
                           HEAT   9 lsDpspeVReaAakaLga 26 
                                    l++ s++VR + ak L +
  gene849|gene849|rna849|rna849 170 LRSVSWRVRFSLAKKLDR 187
                                    67889******9998865 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.027
                                    HHT-SSHHHHHHHHHHH CS
                           HEAT   8 llsDpspeVReaAakaL 24 
                                    l++Dpsp+V  + +k L
  gene849|gene849|rna849|rna849 415 LMKDPSPKVKFNLLKLL 431
                                    579*******9998877 PP

  == domain 4  score: 4.9 bits;  conditional E-value: 0.0065
                                    HHT-SSHHHHHHHHHHHH CS
                           HEAT   8 llsDpspeVReaAakaLg 25 
                                     l Dp ++VR+ Aa+ + 
  gene849|gene849|rna849|rna849 465 FLVDPVAHVRCKAARLFR 482
                                    577***********9875 PP

  == domain 5  score: -0.1 bits;  conditional E-value: 0.26
                                    HHHHHHHT-SSHHH.HH CS
                           HEAT   3 PlllkllsDpspeV.Re 18 
                                    +++ ++  D++ eV R+
  gene849|gene849|rna849|rna849 553 DVVEQMVDDDDEEVcRR 569
                                    5788999******9554 PP

>> DNA_alkylation  DNA alkylation repair enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0   0.00014      0.86      41     181 ..      66     217 ..      50     218 .. 0.61

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00014
                 DNA_alkylation  41 effkelkleeelqelaeeLwksperEerllAldlltqakkklaeadlelyeklvetinnWdlvDslaskivgalladk.. 118
                                    ++f+e++   +l++l+++L+ksp++ +rl+ + ll +a k+  +         v   +n +lv ++a++++ a ++++  
  gene849|gene849|rna849|rna849  66 PVFQEHS---NLSTLINTLLKSPFYVHRLAVCHLLPYASKS-VF--------YVLFNDNIQLVSRTAMEMLPAGMLSHne 133
                                    4444544...4588999999999999999999999554444.22........2233344444444444444444444422 PP

                 DNA_alkylation 119 ...................perrdllkeWaksenlWerRaAivatlklikktdlelll..eiaeelladkedfiqkAiGw 177
                                                        + +  l++ + + + ++r++++ + ++l+kk d+ +++  +i + l +d   fi+kA+  
  gene849|gene849|rna849|rna849 134 ilecldalvqrndylqcgaADLLCRLEQHSDKVHHFLRSVSWRVRFSLAKKLDRLDVFykDIYDVLKDDDVLFIKKAMIC 213
                                    22222222222366666666777777777777888888888888888888877777663336666666667788888888 PP

                 DNA_alkylation 178 aLre 181
                                    aLr+
  gene849|gene849|rna849|rna849 214 ALRD 217
                                    8885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (585 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       932  (0.0519828); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.75u 0.35s 00:00:01.10 Elapsed: 00:00:00.55
# Mc/sec: 3225.35
//
Query:       gene85|gene85|rna85|rna85  [L=26]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (26 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       150  (0.00836633); expected 358.6 (0.02)
Passed bias filter:                      126  (0.00702772); expected 358.6 (0.02)
Passed Vit filter:                         5  (0.000278878); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.29s 00:00:00.68 Elapsed: 00:00:00.48
# Mc/sec: 163.07
//
Query:       gene850|gene850|rna850|rna850  [L=299]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.7e-34  117.6   0.1    1.1e-33  117.1   0.1    1.2  1  PI3_PI4_kinase  Phosphatidylinositol 3- and 4-kinase
    1.5e-10   40.7   0.0    2.9e-10   39.8   0.0    1.4  1  FATC            FATC domain


Domain annotation for each model (and alignments):
>> PI3_PI4_kinase  Phosphatidylinositol 3- and 4-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.1   0.1   1.3e-37   1.1e-33       3     248 ..      34     255 ..      33     257 .. 0.89

  Alignments for each domain:
  == domain 1  score: 117.1 bits;  conditional E-value: 1.3e-37
                                    EEEEECSSCHHHHHHHHHHHHHHHHHHHHTTTTCCCT-------EEESSSSEEEEE--TTEEEHHHHHHHHHHHCTTSTC CS
                 PI3_PI4_kinase   3 agiykvgddlrqdelivqvfklmdeelskennpkrrklalktysviplgrkcgiielvassetaaslldeklekkgvppt 82 
                                    ++++k++ddlr+d+++++vf+l+          k  +l+++ y v+p ++k giie++    +++s+    ++k +v  t
  gene850|gene850|rna850|rna850  34 SFLVKANDDLRKDQRVMEVFNLL---------IK-YNLKIRKYVVVPISSKLGIIEWIHGLISLKSICMTGQNK-QV-AT 101
                                    6899*****************99.........22.2344899****************************9976.44.44 PP

                                    HHHHHHHHHCHCHCCHHHHHCCHHHHHHTSSTTHHHHHHHHHSSSHHHHHHHHHHHHHHHHHHHHHHHHHT-TT--TTTE CS
                 PI3_PI4_kinase  83 asveslrvaldkkklkkekklkfekrtalkpksgllqeFvkkspsaeewlearkqFvrslaklsvldyilgngDRhldNi 162
                                      ++       kkkl      k ++  +  +ks+l  +  ++++++  w  a   +++ la +s  +y +g+gDRh +Ni
  gene850|gene850|rna850|rna850 102 EIFKK-----YKKKLG-----KHFSTFNSRTKSVLAGWYNDTYKDPVHWHTAKHCYAKTLAIMSAFGYFIGLGDRHCENI 171
                                    44444.....133322.....3678889999************************************************* PP

                                    EEETTTSEEEESSTTTCCTCSHCSSSS-.SSSSSS-THHHHHHTSTTCCHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHH CS
                 PI3_PI4_kinase 163 lvdktsgklihIDfGlilpdewkllpfpqekvPfrltrelvlaidpskdeglfresceealealrrdqnlltrllkkavk 242
                                    lvd+++g ++h+D +l ++++ +l  +p e+vPfrlt+++ + ++ ++++g+fr ++  + +++ r  +++ + l ++v+
  gene850|gene850|rna850|rna850 172 LVDTRTGDVVHVDLNLLFGRASML-SVP-ERVPFRLTKNVRECLGVLRETGKFRLYVRGTIRTIVRFRDVIEANLLAFVY 249
                                    ******************888775.559.*************************************************** PP

                                    HHCCSS CS
                 PI3_PI4_kinase 243 dglilw 248
                                    d+++++
  gene850|gene850|rna850|rna850 250 DPVAEI 255
                                    *99886 PP

>> FATC  FATC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.8   0.0   3.2e-14   2.9e-10       8      32 .]     275     299 .]     272     299 .] 0.95

  Alignments for each domain:
  == domain 1  score: 39.8 bits;  conditional E-value: 3.2e-14
                           FATC   8 VdrLIkeATdpeNLaqmyiGWcPww 32 
                                    VdrLIkeA+d  NL+ my+GW+P++
  gene850|gene850|rna850|rna850 275 VDRLIKEAVDDGNLGEMYVGWMPFI 299
                                    9***********************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       613  (0.0341904); expected 358.6 (0.02)
Passed bias filter:                      494  (0.0275531); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 1975.44
//
Query:       gene851|gene851|rna851|rna851  [L=102]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       461  (0.0257125); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.28s 00:00:00.66 Elapsed: 00:00:00.43
# Mc/sec: 709.78
//
Query:       gene852|gene852|rna852|rna852  [L=696]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    9.1e-84  280.3   0.0    2.1e-83  279.1   0.0    1.6  1  PAP_central   Poly(A) polymerase central domain
    3.2e-14   52.9   0.3    4.3e-07   29.7   0.0    3.5  3  PAP_RNA-bind  Poly(A) polymerase predicted RNA binding domain
    4.7e-08   33.2   0.1    1.9e-07   31.3   0.1    2.0  1  NTP_transf_2  Nucleotidyltransferase domain


Domain annotation for each model (and alignments):
>> PAP_central  Poly(A) polymerase central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  279.1   0.0   3.5e-87   2.1e-83       1     234 [.      10     511 ..      10     521 .. 0.98

  Alignments for each domain:
  == domain 1  score: 279.1 bits;  conditional E-value: 3.5e-87
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...................... RF
                    PAP_central   1 GvtepislakptekdlklteeLieeLkeqnlfeseeetkkreevlekleklvkefvkk...................... 58 
                                    G+t p+sl+++++ d+++t++L + L + ++++++ee+  re+vl++l+ ++++f+k                       
  gene852|gene852|rna852|rna852  10 GITGPLSLKESSQDDIARTSSLHAFLVSSKIYDTDEEAIIRERVLGRLSYMFDNFIKAigtkkgladsdirtatgriytf 89 
                                    99****************************************************************************** PP

                                    ................................................................................ RF
                    PAP_central  59 ................................................................................ 58 
                                                                                                                    
  gene852|gene852|rna852|rna852  90 gsyrlgvhargsdidtlcvapvyvdrkeffeefyvmlndvfaevekvedayvplmqlvyrecvdeggtmsggnkigildt 169
                                    ******************************************************************************** PP

                                    ................................................................................ RF
                    PAP_central  59 ................................................................................ 58 
                                                                                                                    
  gene852|gene852|rna852|rna852 170 aidniddlrscrvderskrvrvnerqavdehlkdeerndtcidrkcgdkhvvstlmgqdrngmlkrtrygqdekekfsdv 249
                                    ******************************************************************************** PP

                                    ................................................................................ RF
                    PAP_central  59 ................................................................................ 58 
                                                                                                                    
  gene852|gene852|rna852|rna852 250 lhekegrnemlngekerndvlnekekfsdvlnekkelnntktveidekdkpssvplnrpgnkrgtgpglnkkmveikidl 329
                                    ******************************************************************************** PP

                                    ......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    PAP_central  59 ......lkevpedldlkddslLknldekevrslnGvRvtdeilrlvpnketFrlaLraiklWAkrraiysnvlgflgGva 132
                                          l +++ +l+l d+slLknldek+v slnG Rvtdeil+lvpnk++F+ aLr+ik+WAkrra+ + ++g++gGva
  gene852|gene852|rna852|rna852 330 vfarlnLFKIDGSLNLLDSSLLKNLDEKSVLSLNGNRVTDEILSLVPNKTVFHGALRCIKYWAKRRALTGHLYGYFGGVA 409
                                    ******99************************************************************************ PP

                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    PAP_central 133 wAllvariCqlyPnaaastlvskfFlvlskWkwpqpvlLkeieekeeplrvWdpkvnksdrahlmpiitpaypsmnstyn 212
                                    +A+ variCql+Pn +  t++ k+F+++++Wkwp pv+Lk+ie+ + +l+vWdpk+++sd++h+mp+itp+ypsm+st+n
  gene852|gene852|rna852|rna852 410 YAISVARICQLFPNVCEYTIICKYFELYKEWKWPMPVMLKKIENLNYNLKVWDPKIHPSDKFHKMPVITPSYPSMCSTHN 489
                                    ********************************************997799****************************** PP

                                    xxxxxxxxxxxxxxxxxxxxxx RF
                    PAP_central 213 vsrstlevlkeelkrgleitee 234
                                    +++st++  keel+r+++++ e
  gene852|gene852|rna852|rna852 490 IMNSTMKRYKEELERAHKLLVE 511
                                    ****************987643 PP

>> PAP_RNA-bind  Poly(A) polymerase predicted RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0     0.055   3.3e+02       1      15 [.     523     537 ..     523     547 .. 0.85
   2 !   29.7   0.0   7.2e-11   4.3e-07      16      57 ..     563     604 ..     559     607 .. 0.92
   3 !   17.8   0.1   3.4e-07     0.002     101     157 ..     621     678 ..     617     693 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.055
                   PAP_RNA-bind   1 tFFskYkyYLsvvas 15 
                                    +FF++Y+ +L v + 
  gene852|gene852|rna852|rna852 523 DFFQRYRSFLAVFIL 537
                                    7**********9865 PP

  == domain 2  score: 29.7 bits;  conditional E-value: 7.2e-11
                   PAP_RNA-bind  16 sktkeaqkkWsglVESkvRlLvqkLeavesialahpfnkgfe 57 
                                    +k++ ++k W+g V+S++R+L +kLe+ve++  a pf+++f+
  gene852|gene852|rna852|rna852 563 AKETSMHKMWQGHVNSRIRFLSTKLETVEQLDSAPPFPQTFD 604
                                    567889**********************************98 PP

  == domain 3  score: 17.8 bits;  conditional E-value: 3.4e-07
                   PAP_RNA-bind 101 vytttfYIGLeleekaks..kkldlsypvqeFkelckswekykeelmsltvkhvknfdL 157
                                      ++  +I+L++  +++   kk+ +  p++eFke++ +w+k ++e m+l  + +k++d+
  gene852|gene852|rna852|rna852 621 ALCSLTFIALDMADSKQLlrKKVFIDAPIEEFKEMVFDWDK-RTEDMDLVMRAMKRKDV 678
                                    567889*******9997799*********************.77888999999998875 PP

>> NTP_transf_2  Nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.3   0.1   3.2e-11   1.9e-07      14      58 ..      83     125 ..      72     153 .. 0.73

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 3.2e-11
                                    TSEEEEEHHHHCTTSCTTSSEEEEEEESTTCHHH.....HHHEHHHHHHH CS
                   NTP_transf_2  14 vakvvlfGSyarGtalkgSDiDllvvlpeevsre.....kkeegleklae 58 
                                      ++++fGSy+ G + +gSDiD+l+v p  v+r      +       ++ 
  gene852|gene852|rna852|rna852  83 TGRIYTFGSYRLGVHARGSDIDTLCVAPVYVDRKeffeeF-------YVM 125
                                    579***************************9986443331.......333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (696 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       661  (0.0368676); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.70u 0.35s 00:00:01.04 Elapsed: 00:00:00.54
# Mc/sec: 3874.48
//
Query:       gene853|gene853|rna853|rna853  [L=212]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (212 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       512  (0.0285571); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 1461.66
//
Query:       gene854|gene854|rna854|rna854  [L=268]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-10   41.3   0.0    7.7e-10   39.4   0.0    2.0  1  Methyltransf_25  Methyltransferase domain
    3.7e-09   37.1   0.0    1.3e-08   35.4   0.0    1.9  1  Methyltransf_11  Methyltransferase domain
    2.1e-07   30.9   0.0    3.5e-07   30.1   0.0    1.4  1  Methyltransf_31  Methyltransferase domain
    6.4e-07   30.0   1.4    8.5e-07   29.6   0.0    1.9  2  Methyltransf_12  Methyltransferase domain
     0.0012   18.3   0.0     0.0017   17.8   0.0    1.2  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
     0.0037   16.9   0.0      0.075   12.6   0.0    2.2  1  MetW             Methionine biosynthesis protein MetW
     0.0059   16.5   0.0     0.0083   16.0   0.0    1.4  1  Methyltransf_23  Methyltransferase domain
  ------ inclusion threshold ------
      0.076   13.0   0.0       0.34   10.9   0.0    1.9  1  Methyltransf_17  S-adenosyl-L-methionine methyltransferase


Domain annotation for each model (and alignments):
>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.4   0.0   3.4e-13   7.7e-10       1      83 [.      50     144 ..      50     164 .. 0.78

  Alignments for each domain:
  == domain 1  score: 39.4 bits;  conditional E-value: 3.4e-13
                                    EEEET-TTSHHHHHHHCT...........S..T.SSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBC.CGBSSSTTTE CS
                Methyltransf_25   1 vLdlGcGtGrltlalakr...........l..g.kakvtgvDiseemleaareraeeeglnvefvqgda.edlpfedgsf 65 
                                    +Ld+GcGtG+ + al +            l  + k  ++g+Di+ +ml +++++     l++e+vq d+ ++lpf+ +sf
  gene854|gene854|rna854|rna854  50 ILDIGCGTGHSISALKEYessrneksedaLdkNrKLFIVGCDINRNMLLNCNNKG----LDAELVQLDIgNSLPFQPASF 125
                                    8**************9999999999988734334899**************9998....99********777******** PP

                                    EEEEEESTGGG.SSHHHHH CS
                Methyltransf_25  66 Dlvvssgalhh.lsdedle 83 
                                    D ++s+ ++++ +  ++++
  gene854|gene854|rna854|rna854 126 DGIISVSCIQWlFYASNTD 144
                                    *****98888533333333 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.4   0.0   5.6e-12   1.3e-08       1      75 [.      51     144 ..      51     168 .. 0.78

  Alignments for each domain:
  == domain 1  score: 35.4 bits;  conditional E-value: 5.6e-12
                                    EEET-TTSHHHHHHH...............HTT..SEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCC.TSS-TT-E CS
                Methyltransf_11   1 LdvGcGtGrlaeala...............krg..arvvgvDlskemlklakekaseeglkvefvvadaek.lpfednsf 62 
                                    Ld+GcGtG    al+               k      +vg+D++ +ml  +++k+ +++    +v+ d+ + lpf+ +sf
  gene854|gene854|rna854|rna854  51 LDIGCGTGHSISALKeyessrneksedaldK-NrkLFIVGCDINRNMLLNCNNKGLDAE----LVQLDIGNsLPFQPASF 125
                                    8**************9999988887665542.15799***********88877777766....6*****9758******* PP

                                    EEEEEES-CCC-......C CS
                Methyltransf_11  63 Dlvvssevlhhv......e 75 
                                    D ++s ++++++      +
  gene854|gene854|rna854|rna854 126 DGIISVSCIQWLfyasntD 144
                                    ***********97764430 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.1   0.0   1.5e-10   3.5e-07       6      84 ..      49     134 ..      46     184 .. 0.84

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 1.5e-10
                Methyltransf_31   6 rvlDlGCGtGeltfelae......elgpkae..........vvGiDiseeaielArenaqklgldnveFeqgdiee.lek 68 
                                    ++lD+GCGtG+ + +l e      e   k+e          +vG Di+ +++  +++    +gld +e+ q di + l+ 
  gene854|gene854|rna854|rna854  49 VILDIGCGTGHSISALKEyessrnE---KSEdaldknrklfIVGCDINRNMLLNCNN----KGLD-AELVQLDIGNsLP- 119
                                    69***************98774441...4446667778899***********98887....7**8.*************. PP

                Methyltransf_31  69 lledekfDlilsnevl 84 
                                     +++++fD i+s + +
  gene854|gene854|rna854|rna854 120 -FQPASFDGIISVSCI 134
                                    .********9997555 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6   0.0   3.8e-10   8.5e-07       1      94 [.      51     162 ..      51     166 .. 0.82
   2 ?   -2.3   0.7       3.4   7.6e+03      39      48 ..     240     249 ..     220     266 .. 0.52

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 3.8e-10
                Methyltransf_12   1 LeiGcGtGsllrallekl..............pdieytgvDispsaiedakeklakrennnnnnvelealdlldldggss 66 
                                    L+iGcGtG+ ++al e+               + + ++g+Di+++++         +++++++ v+l+  ++l  ++++s
  gene854|gene854|rna854|rna854  51 LDIGCGTGHSISALKEYEssrneksedaldknRKLFIVGCDINRNML-----LNCNNKGLDAELVQLDIGNSL-PFQPAS 124
                                    8******************************99**************.....666667777777777777754.34447* PP

                Methyltransf_12  67 fDlvvasnvlhhl..........kdirevldnirklLk 94 
                                    fD +++ +++++l          k +  +l++++++Lk
  gene854|gene854|rna854|rna854 125 FDGIISVSCIQWLfyasntdrteKRLYMFLSSMYAALK 162
                                    *************9997776665555566667777766 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 3.4
                Methyltransf_12  39 klakrennnn 48 
                                    k+++r+++n 
  gene854|gene854|rna854|rna854 240 KIKERRDDNL 249
                                    2333333333 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   7.5e-07    0.0017      19     120 ..      21     128 ..      13     155 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 7.5e-07
                                    HHHHHHHHHHTTTHHHHHHHHHHH--S--TTEEEEES-TT-HHHHHHHHHHHHHH.............EEEEEES-HHHH CS
                Ubie_methyltran  19 kyDlmndvlslgihrlWkkfveklvavkrgakvlDvagGtgDlafklsdsvgekg.............kvvvlDinenmL 85 
                                    kyD    ++ ++  r+  ++  +l +  +g  +lD+ +Gtg    +l +   ++               +v++Din nmL
  gene854|gene854|rna854|rna854  21 KYDRNKRIIYIQ--RKMAEKCCELINCTSG-VILDIGCGTGHSISALKEYESSRNeksedaldknrklFIVGCDINRNML 97 
                                    566655555433..3344444444444444.69*********99999887777767899*******88899********* PP

                                    HHHHHHHHHHTSSTEEEEE--TTT-TTS-T-EEEE CS
                Ubie_methyltran  86 kvgekklkeegkinieflqanaeeLpfeddsfDvv 120
                                       ++k  +   ++++     ++ Lpf+  sfD +
  gene854|gene854|rna854|rna854  98 LNCNNKGLDAELVQLDI----GNSLPFQPASFDGI 128
                                    *9999988887777764....67899999999954 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.0   3.3e-05     0.075       7      86 ..      39     135 ..      33     150 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3.3e-05
                           MetW   7 iaelikpgsrv.ldlGcGdGellellke...............ekqvdgrGleldeegvaecvakGls..viqgdldkdl 68 
                                      eli+  s v ld+GcG G+ ++ lke               ++++   G +++++ + +c +kGl   ++q d+ + l
  gene854|gene854|rna854|rna854  39 CCELINCTSGViLDIGCGTGHSISALKEyessrneksedaldkNRKLFIVGCDINRNMLLNCNNKGLDaeLVQLDIGNSL 118
                                    6688888886549*******999998762222221111111112334445788888888888888886224566666666 PP

                           MetW  69 enfedksfdyvvlsqtlq 86 
                                      f+  sfd ++    +q
  gene854|gene854|rna854|rna854 119 P-FQPASFDGIISVSCIQ 135
                                    4.7778888888777776 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   3.7e-06    0.0083       6      56 ..      32      96 ..      22     165 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 3.7e-06
                Methyltransf_23  6 eeelsdklerllpklraggrvLdiGcGtGillevlre...............ngf.svtgvDlspea 56
                                   ++++++k  +l   + ++g +LdiGcGtG+  + l+e               n++  ++g D+++++
  gene854|gene854|rna854|rna854 32 QRKMAEKCCELI--NCTSGVILDIGCGTGHSISALKEyessrneksedaldkNRKlFIVGCDINRNM 96
                                   455666666666..67889**********99888877555555666555555334466677776665 PP

>> Methyltransf_17  S-adenosyl-L-methionine methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00015      0.34      11      54 ..      29      72 ..      21     131 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00015
                                   HHHHHHHHHHHHHHTTT--S-EEEE--TTSHHHHHHHHH--SS- CS
                Methyltransf_17 11 ltaqrdiLnhvaaevadieGpvlelGLGnGRtydhlrellperr 54
                                   +  qr + ++ ++ ++  +G +l++G G G   + l+e  + r+
  gene854|gene854|rna854|rna854 29 IYIQRKMAEKCCELINCTSGVILDIGCGTGHSISALKEYESSRN 72
                                   5579********************************99877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (268 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1349  (0.0752412); expected 358.6 (0.02)
Passed bias filter:                      507  (0.0282782); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.52u 0.22s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 1979.20
//
Query:       gene855|gene855|rna855|rna855  [L=181]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       476  (0.0265492); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1376.56
//
Query:       gene856|gene856|rna856|rna856  [L=77]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.036   13.3   0.9      0.036   13.3   0.9    1.0  1  FTO_NTD   FTO catalytic domain


Domain annotation for each model (and alignments):
>> FTO_NTD  FTO catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.9     2e-06     0.036      78     135 ..       3      60 ..       1      76 [. 0.67

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2e-06
                        FTO_NTD  78 lFalPWseeekeakaalkedpeiesalkallk.lndvlaeeakkllekrklakdkeese 135
                                    + + PW++++k+++++ k d + ++ lka++k  n+++++ +++ ++k++   +k ++ 
  gene856|gene856|rna856|rna856   3 ILTKPWKTKSKKIQSC-KFDIHQQRRLKAMKKkENEIFRSMVNEIIQKKRRYIEKMQEI 60 
                                    6799********9999.667777778888865157788888888887776555333322 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2993  (0.166936); expected 358.6 (0.02)
Passed bias filter:                      723  (0.0403257); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 577.99
//
Query:       gene857|gene857|rna857|rna857  [L=206]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1403  (0.0782531); expected 358.6 (0.02)
Passed bias filter:                      542  (0.0302304); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1493.94
//
Query:       gene858|gene858|rna858|rna858  [L=190]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (190 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       596  (0.0332422); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1325.94
//
Query:       gene859|gene859|rna859|rna859  [L=120]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       515  (0.0287244); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 917.40
//
Query:       gene86|gene86|rna86|rna86  [L=436]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (436 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       431  (0.0240393); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.53u 0.23s 00:00:00.76 Elapsed: 00:00:00.41
# Mc/sec: 3203.12
//
Query:       gene860|gene860|rna860|rna860  [L=59]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       391  (0.0218082); expected 358.6 (0.02)
Passed bias filter:                      230  (0.0128284); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 453.29
//
Query:       gene861|gene861|rna861|rna861  [L=80]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1103  (0.0615204); expected 358.6 (0.02)
Passed bias filter:                      715  (0.0398795); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.29s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 592.86
//
Query:       gene862|gene862|rna862|rna862  [L=331]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
     0.0014   18.7   0.1      0.074   13.1   0.1    2.2  2  HAD_2       Haloacid dehalogenase-like hydrolase
     0.0017   18.1   0.0        1.5    8.6   0.0    2.3  2  NIF         NLI interacting factor-like phosphatase
     0.0091   16.3   0.0      0.038   14.3   0.0    1.9  1  Hydrolase   haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
      0.027   14.3   0.0        8.8    6.1   0.0    2.4  2  Acid_PPase  Acid Phosphatase
      0.071   13.5   0.0       0.87   10.0   0.0    2.1  2  HAD         haloacid dehalogenase-like hydrolase


Domain annotation for each model (and alignments):
>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.1   2.1e-05     0.074       1      57 [.      79     144 ..      79     168 .. 0.81
   2 ?    3.5   0.0     0.019        67      94     175 ..     224     304 ..     222     307 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.1e-05
                          HAD_2   1 iiFDlDgTlldteeliiqafnelleey.........glselseeelrkliglslrellrklgesee 57 
                                    iiFDlD Tl+ ++  + +++++ l +          + s+    e++ ++gl ++ ++r++g +++
  gene862|gene862|rna862|rna862  79 IIFDLDQTLYTKTSSLQTIIRHRLYQSlmarrawsyEQSKQVYIEMSVKYGLGYKGMIREYGMDQR 144
                                    8*****************999999777899999844333444456778999999999999988765 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.019
                          HAD_2  94 agyklgivTsksreaveekleqlgiesyFdvivtsedvekk...KPdpeviekaleklklkkeeviyvGDsptDieaakk 170
                                     ++   i T++ +e +++ le+l++ + +++i  ++ ++ +   KP+ + +e + +     + ++ ++ D+   +e +k 
  gene862|gene862|rna862|rna862 224 GNIAFFIFTNSPKEYTKRVLEHLKVPN-ISKIFYTTYFQPHmlcKPQRRAFELVNT---YCRGKTYFFDDKMVNVEMGKT 299
                                    578899*****************9865.4555555555555577787777666543...335566666666666666666 PP

                          HAD_2 171 agikv 175
                                    +g ++
  gene862|gene862|rna862|rna862 300 MGWNC 304
                                    66665 PP

>> NIF  NLI interacting factor-like phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.3   0.0    0.0011       3.8       1      37 [.      77     111 ..      77     133 .. 0.62
   2 !    8.6   0.0   0.00041       1.5      52      87 ..     228     265 ..     223     301 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0011
                            NIF   1 ktLVLDLDetLvhsklekskklkvegekvevsvlkRp 37 
                                    kt+++DLD+tL   +++ ++   ++ + ++  +++R 
  gene862|gene862|rna862|rna862  77 KTIIFDLDQTLYTKTSSLQT--IIRHRLYQSLMARRA 111
                                    79**********77742222..122333444444444 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00041
                            NIF  52 vvifTasseeyaeavidil.dpekkl.lshrlyrescv 87 
                                     +ifT+s +ey ++v+++l  p+  + +   +++ ++ 
  gene862|gene862|rna862|rna862 228 FFIFTNSPKEYTKRVLEHLkVPNISKiFYTTYFQPHML 265
                                    68*****************7666555355557777775 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0     1e-05     0.038       1      46 [.      76     106 ..      76     301 .. 0.52

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1e-05
                                    SSEEEEESBTTTBCHHHHHHHHHHHHCHHHHHHHHHHHHCHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Hydrolase   1 iktvvfDkdGTLttgepsvedvivsaalalaaaletgsehpigkal 46 
                                    +kt++fD+d TL+t ++s+ ++i+ +               + + l
  gene862|gene862|rna862|rna862  76 YKTIIFDLDQTLYTKTSSLQTIIRHR---------------LYQSL 106
                                    69*******************99998...............22222 PP

>> Acid_PPase  Acid Phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.0    0.0034        12       4      16 ..      77      89 ..      74     111 .. 0.87
   2 ?    6.1   0.0    0.0024       8.8     125     152 ..     282     309 ..     222     320 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0034
                                   SEEEE-STTTSSS CS
                     Acid_PPase  4 klivFDLDyTLWp 16
                                   k i+FDLD+TL +
  gene862|gene862|rna862|rna862 77 KTIIFDLDQTLYT 89
                                   689********85 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0024
                                    GGEEEEES-HHHHHHHHTTT-EEEE-SS CS
                     Acid_PPase 125 edmlfFDdesrnievesrlgvtfvlvpd 152
                                     +  fFDd+  n+e  +++g  + lv+d
  gene862|gene862|rna862|rna862 282 GKTYFFDDKMVNVEMGKTMGWNCFLVDD 309
                                    5678********************9987 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00024      0.87       1      28 [.      79     107 ..      79     166 .. 0.75
   2 ?    1.3   0.0      0.11     4e+02     103     127 ..     227     251 ..     221     280 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00024
                            HAD   1 alfDfDgTLldg.dslelllrfllrrgap 28 
                                    ++fD+D TL ++ +sl  ++r++l ++  
  gene862|gene862|rna862|rna862  79 IIFDLDQTLYTKtSSLQTIIRHRLYQSLM 107
                                    79*******88879999999988877432 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.11
                            HAD 103 rvvvvSgglrplvepllaelgadev 127
                                     + + +++++++++++l++l + ++
  gene862|gene862|rna862|rna862 227 AFFIFTNSPKEYTKRVLEHLKVPNI 251
                                    67899***************95554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (331 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       696  (0.0388198); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.47u 0.20s 00:00:00.67 Elapsed: 00:00:00.37
# Mc/sec: 2706.38
//
Query:       gene863|gene863|rna863|rna863  [L=466]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.4e-20   72.9   0.4    3.5e-17   62.6   0.1    2.8  3  NIF        NLI interacting factor-like phosphatase
  ------ inclusion threshold ------
      0.085   13.3   0.2       0.39   11.2   0.2    2.2  1  BRCT_2     BRCT domain, a BRCA1 C-terminus domain
       0.14   13.5   2.5       0.43   11.9   2.5    1.8  1  RNR_inhib  Ribonucleotide reductase inhibitor


Domain annotation for each model (and alignments):
>> NIF  NLI interacting factor-like phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.2   0.0   0.00066         4       2      16 ..      78      92 ..      77     121 .. 0.77
   2 !   62.6   0.1   5.9e-21   3.5e-17      22     138 ..     173     285 ..     147     292 .. 0.83
   3 ?   -1.7   0.0      0.36   2.1e+03     133     150 ..     343     360 ..     332     365 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.00066
                            NIF  2 tLVLDLDetLvhskl 16
                                   +LV+DLD+t++hs +
  gene863|gene863|rna863|rna863 78 ILVVDLDQTILHSIE 92
                                   79**********985 PP

  == domain 2  score: 62.6 bits;  conditional E-value: 5.9e-21
                            NIF  22 lkvegekvevsvlkRpgldefLkelsklyevvifTasseeyaeavidildpekkllshr.lyrescvkkkgeyvKdLsll 100
                                    ++++  +++++  +Rp+l++fL+e+skl+ + i+T+++ ey+ ++ +++d+++ ++++r ++r++      + vK L+ l
  gene863|gene863|rna863|rna863 173 FTYTLSSTTMHTTLRPHLHQFLTEASKLFHMHIYTMGTAEYVHQITNVIDKDGMFFGDRiVTRDDE-----MQVKRLERL 247
                                    3444445679********************************************999994445544.....79*****99 PP

                            NIF 101 .grdlsrvvivDdspdsfelqpengipiksffsdkkDne 138
                                     g + + vvivDd+ d++e    n++ +++f + + D++
  gene863|gene863|rna863|rna863 248 fGDKVDMVVIVDDRGDVWEY-CGNLVMVRPFLGIDGDRA 285
                                    899***************97.7899******88666665 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 0.36
                            NIF 133 dkkDneLlkllpllkela 150
                                     k+DneLl ll  l++++
  gene863|gene863|rna863|rna863 343 HKNDNELLILLHTLQSIH 360
                                    579******999999876 PP

>> BRCT_2  BRCT domain, a BRCA1 C-terminus domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.2   6.5e-05      0.39       2      45 ..     380     419 ..     379     441 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 6.5e-05
                         BRCT_2   2 sklFeglrFYindaepspsreklkklIeknGGevvetitsavyi 45 
                                    +++F++ +F +  ++  p+++ ++++I+ +GG++ ++ +  +++
  gene863|gene863|rna863|rna863 380 TQIFKNKTFAM--DHSMPDIHNIASIIRMHGGTFGNDGC--DIV 419
                                    79*********..45559***************988873..333 PP

>> RNR_inhib  Ribonucleotide reductase inhibitor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   2.5   7.1e-05      0.43      12      70 ..     106     158 ..     104     192 .. 0.55

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 7.1e-05
                      RNR_inhib  12 sVpeGYktgsvysafklwsdkstakksksstsssasaasanrellpfcGinkvgglavq 70 
                                    s++eGYkt+++  + k+ sd +++++ +++ ++    ++ +++  p+  i++v +++++
  gene863|gene863|rna863|rna863 106 SIDEGYKTTNA--NSKSSSDGTNNADDNNNITT----NTVPTTAGPTTNISSVYNINES 158
                                    89********5..33334444444433333333....3444444444444444443333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (466 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       916  (0.0510904); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.45
# Mc/sec: 3125.74
//
Query:       gene864|gene864|rna864|rna864  [L=1007]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.7e-17   62.6   5.0    1.9e-11   43.3   0.8    2.2  2  Cullin    Cullin family


Domain annotation for each model (and alignments):
>> Cullin  Cullin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.2   6.1e-09   0.00011      70     270 ..     190     367 ..     166     457 .. 0.81
   2 !   43.3   0.8   1.1e-15   1.9e-11     396     536 ..     600     822 ..     592     837 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 6.1e-09
                         Cullin  70 elLkalkkeWedhktsmkmirdifmyldrvyvkklpsvydlglelfrdhvfriklkdrlieallkliekeRegevidr.s 148
                                    +++ ++ + ++ ++  ++ + d++  l++       +v+++g+ ++  hv++ +   ++ +a+++ ++    ++  dr +
  gene864|gene864|rna864|rna864 190 DIIHRYAHYFDTFNAFITNLADLCFLLNTEC----WDVHEMGMATWHMHVLN-R-LVHFGHAVCAAVHLSPYSN--DRiD 261
                                    4678888999999999999999999999988....79**************6.3.4799*********999654..4446 PP

                         Cullin 149 llksviemlvelgedsedkkvYeeeFekafleateefYraeaeellaensvaseYlkkaeerleeEeervekyldsstkk 228
                                     l +v++ ++ ++ d+  +++Y+ ++e+ +   ++  Y +     ++    +++Y +++++ l+ E e  + y+ + + +
  gene864|gene864|rna864|rna864 262 TLVRVLHAFMRIKLDH--STYYTLTYERTLFMRINVLYAR-----IT---LTHNYAHEVHRILTHEIESRSGYMLPVSFP 331
                                    7888888888886665..68*******************9.....44...2348**************9999*99***** PP

                         Cullin 229 kllevleeelikkhleelleeelkklledekledLkrlykll 270
                                    +  ++l +++i   ++ ++ + + + +     +d + +y+l 
  gene864|gene864|rna864|rna864 332 AHNQALINHFILPYSSFIVMH-CIRNI-----NDYRVIYELN 367
                                    ***************999998.65555.....3444444444 PP

  == domain 2  score: 43.3 bits;  conditional E-value: 1.1e-15
                         Cullin 396 dKDvFekyYkkhLakRLllgksasddaEksmiskLkeecGseftskLegMfkDiklskdlnkefkeylee.......... 465
                                    + D+F + Y+k+++ RLl +   +   E++++++Lk     +   k e M+ D+  s  l++++++              
  gene864|gene864|rna864|rna864 600 NTDIFITQYEKKMMTRLLSHVV-HVSREREVLEQLKPYFVPNLFRKCEHMLSDVVRSCGLMEDYERVN-Gymmggnackr 677
                                    56***************98875.558**************************************9965.469******** PP

                         Cullin 466 ................................ekkkkkkvdlsvk................................... 478
                                                                    e           +                                   
  gene864|gene864|rna864|rna864 678 lyvgmygdtednimheqnkvenkvehrnankvE-----------Nknenkvenkvvheqnknannsinnptsnninnlts 746
                                    *******99999887776666666666666552...........044444444455777777777777888888889999 PP

                         Cullin 479 .........................VLtagaWpterskesevsvklpeeledlieeFeefYkskhsgrkLtWlhslgsae 533
                                                             +Lt+ +Wp +++      +k+p+ l + +++F++fY+s hs  kL + ++l++++
  gene864|gene864|rna864|rna864 747 ynfnsnniinltsntitlkqpihhrILTSHMWPLTPR-----CLKYPP-L-KELSSFKTFYNSTHSTHKLIYDYELSTMD 819
                                    9999999999999999999999999********5444.....356665.4.5689************************* PP

                         Cullin 534 lka 536
                                    +++
  gene864|gene864|rna864|rna864 820 VRI 822
                                    *97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1007 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1548  (0.0863406); expected 358.6 (0.02)
Passed bias filter:                      532  (0.0296726); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.84u 0.33s 00:00:01.17 Elapsed: 00:00:00.51
# Mc/sec: 5892.45
//
Query:       gene866|gene866|rna866|rna866  [L=405]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.2e-73  246.4  29.9      5e-57  193.7  12.9    2.6  3  PSS       Phosphatidyl serine synthase


Domain annotation for each model (and alignments):
>> PSS  Phosphatidyl serine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  193.7  12.9   2.8e-61     5e-57       1     152 [.      73     223 ..      73     226 .. 0.98
   2 !   64.0   3.7   9.8e-22   1.8e-17     183     272 ..     225     313 ..     221     314 .. 0.94
   3 ?   -2.6   0.3       0.2   3.6e+03     220     240 ..     351     371 ..     326     388 .. 0.56

  Alignments for each domain:
  == domain 1  score: 193.7 bits;  conditional E-value: 2.8e-61
                            PSS   1 PhpavWrvvlglsvlYllllvfllfqdledarqllklldpelgkklpeksyaedCsllslenvlekldvfvlaHflGwlv 80 
                                    P  ++Wr+v++ s+ Yl++l++l ++++ed+r++l+++++el+++lp++sya++C++ +++n+++++dvfv  H++Gw++
  gene866|gene866|rna866|rna866  73 PIAILWRCVKASSIYYLIILIILFYFEKEDIRKALSYFYTELNVPLPQRSYATHCEI-NMRNIINQMDVFVPLHIFGWFF 151
                                    6689****************************************************9.********************** PP

                            PSS  81 kalilRdllllwilsilfEllElslqhllpnFaECWWDhlilDvllcNllGivlGllllkllelkeYkWegi 152
                                    k+l+lRd +++wils+lfE++E+slqh+l nFaECWWDh+ilDvl+cN+lGi +G+l+++++++k+Y++ ++
  gene866|gene866|rna866|rna866 152 KTLLLRDRTICWILSVLFEFAEYSLQHQLDNFAECWWDHWILDVLTCNFLGIEMGMLFIQKMRIKRYEFVKL 223
                                    ********************************************************************9765 PP

  == domain 2  score: 64.0 bits;  conditional E-value: 9.8e-22
                            PSS 183 kslkrflavllllvvvllleLnvFflkavlelppshllvllRllllallaaaavrelyeyvtdkkvkrlGqqawlllaiv 262
                                    +slkr++a+++l+v++l++eLnvF+lk++l +p++h+++l+Rl++++  +a avre++ey   ++ k +  q wl +aiv
  gene866|gene866|rna866|rna866 225 NSLKRYVAIITLIVFILAAELNVFYLKFLLYIPTEHNINLYRLCIFVPGGALAVREAFEYYA-TSEKIVRGQLWLSMAIV 303
                                    699*********************************************************99.667777899******** PP

                            PSS 263 vtElllvvkf 272
                                    ++E+++v+k+
  gene866|gene866|rna866|rna866 304 CVETMVVIKY 313
                                    *********8 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 0.2
                            PSS 220 lvllRllllallaaaavrely 240
                                    lv+ R ++  ++ ++a+r+++
  gene866|gene866|rna866|rna866 351 LVIKRNFCQNIFVITAFRQCF 371
                                    344444444444444444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (405 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       941  (0.0524848); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.26s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 2612.90
//
Query:       gene867|gene867|rna867|rna867  [L=105]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.2e-15   56.0   0.2    4.7e-15   55.5   0.2    1.2  1  Spt4      Spt4/RpoE2 zinc finger


Domain annotation for each model (and alignments):
>> Spt4  Spt4/RpoE2 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.5   0.2   2.6e-19   4.7e-15       2      77 .]      14      78 ..      13      78 .. 0.96

  Alignments for each domain:
  == domain 1  score: 55.5 bits;  conditional E-value: 2.6e-19
                           Spt4  2 rACllCklvktedqFeeegCpnCeilelkgdkekvsectseefeGlvaildpekSwvAkwqrldkkvpglYAlkve 77
                                   +AC+lC+++ + ++ ++egC+nC          k  ++ts +++Gl+ +l++   wv kwqr+d++  glYA+ ve
  gene867|gene867|rna867|rna867 14 KACMLCSALIPVQELKKEGCKNC----------KNANSTSYNYKGLIGVLKKG-GWVEKWQRIDEYGEGLYAMTVE 78
                                   9**********************..........7899*************999.9******************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       574  (0.0320152); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.27s 00:00:00.63 Elapsed: 00:00:00.42
# Mc/sec: 757.35
//
Query:       gene868|gene868|rna868|rna868  [L=200]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.2e-07   31.9   0.4    1.4e-07   31.6   0.4    1.1  1  EMP24_GP25L   emp24/gp25L/p24 family/GOLD
  ------ inclusion threshold ------
       0.12   13.2   0.9       0.12   13.2   0.9    2.3  2  Cadherin_C_2  Cadherin cytoplasmic C-terminal


Domain annotation for each model (and alignments):
>> EMP24_GP25L  emp24/gp25L/p24 family/GOLD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.6   0.4   1.6e-11   1.4e-07      37     182 .]      46     195 ..      16     195 .. 0.80

  Alignments for each domain:
  == domain 1  score: 31.6 bits;  conditional E-value: 1.6e-11
                    EMP24_GP25L  37 ldvdlsvkdpdgngerlvkkkdrese.gdfsftakesgeykvCfdnsfstkss......kkvsfdievgseasdykdsak 109
                                     +  +++++ ++++   ++   + +e   fsf + e+ e ++ ++    +++       +++sf  +++ +   +kd+ak
  gene868|gene868|rna868|rna868  46 CKYAVTIESVSDERTLFYSPNLTPNEkTHFSFVNDEPKELRIYIEALPIDPNIphesgkMQLSFYSKFNTF---DKDVAK 122
                                    45555666666644444444444444469999999999999999998777766888877777777777665...688*** PP

                    EMP24_GP25L 110 kekletleselkkleekldsikreqkylrereerlrdtnestnsrvvwwsilqllvlvlvavlqvyyLkrfFk 182
                                    +  +e+  ++l ++e+ l++i    ++ +e+    ++ ++ ++  v++ s+l+ +v v+v ++q+  + +fF+
  gene868|gene868|rna868|rna868 123 SHAVEPAIKQLIEFEKLLHQIIVRTQAKKEKMLAIMRSQKTLFASVTFLSFLTFVVFVGVNLYQMKKIEKFFR 195
                                    *********************99999999999999999**********************************6 PP

>> Cadherin_C_2  Cadherin cytoplasmic C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.3      0.27   2.4e+03      57      57 ..      33      33 ..       2      79 .. 0.55
   2 ?   13.2   0.9   1.3e-05      0.12      11      39 ..     166     194 ..     165     199 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.27
                   Cadherin_C_2 57 s 57
                                    
  gene868|gene868|rna868|rna868 33 I 33
                                   1 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 1.3e-05
                   Cadherin_C_2  11 asvSflFLltvivlvavrlrkerksaalq 39 
                                    asv+fl++lt++v+v v+l++ +k +++ 
  gene868|gene868|rna868|rna868 166 ASVTFLSFLTFVVFVGVNLYQMKKIEKFF 194
                                    8*******************999877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       948  (0.0528752); expected 358.6 (0.02)
Passed bias filter:                      528  (0.0294495); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 1426.64
//
Query:       gene869|gene869|rna869|rna869  [L=35]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (35 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       176  (0.0098165); expected 358.6 (0.02)
Passed bias filter:                      144  (0.00803168); expected 358.6 (0.02)
Passed Vit filter:                         6  (0.000334653); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.32u 0.24s 00:00:00.56 Elapsed: 00:00:00.39
# Mc/sec: 267.76
//
Query:       gene87|gene87|rna87|rna87  [L=119]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.027   14.6   2.5       0.05   13.7   2.5    1.5  1  Conotoxin_I2  I2-superfamily conotoxins


Domain annotation for each model (and alignments):
>> Conotoxin_I2  I2-superfamily conotoxins
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   2.5   2.8e-06      0.05      13      36 ..      82     105 ..      73     107 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.8e-06
               Conotoxin_I2  13 eCClseCCsgtCespCrlpgKRak 36 
                                 C + +CC ++ + pC   +KRa 
  gene87|gene87|rna87|rna87  82 TCTSTTCCLEWRQPPCGPGWKRAV 105
                                57777*****************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       401  (0.022366); expected 358.6 (0.02)
Passed bias filter:                      236  (0.013163); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 897.88
//
Query:       gene870|gene870|rna870|rna870  [L=359]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    4.5e-21   75.8  16.6    6.3e-21   75.3  16.6    1.2  1  Per1        Per1-like family
  ------ inclusion threshold ------
        1.9    7.9  20.4    2.7e+02    0.8  20.4    2.3  1  Ceramidase  Ceramidase


Domain annotation for each model (and alignments):
>> Per1  Per1-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.3  16.6     7e-25   6.3e-21      42     253 ..     145     350 ..     132     352 .. 0.79

  Alignments for each domain:
  == domain 1  score: 75.3 bits;  conditional E-value: 7e-25
                           Per1  42 pflrllgiqEpasvlfSllNllvhlkgl.kklrkeipkssplkkvylvyalvslnawvwSaiFHtrDveltEklDYfsAg 120
                                    +fl ++ + E++svl+S l ll ++ ++ ++++ +    +pl+++y++   +s+++w+ S + H+ D ++t   DYfsA 
  gene870|gene870|rna870|rna870 145 AFLPIWQCTEIISVLLSALSLLNTIIMYhTRIQGR---LTPLHNLYTMQYRISCITWISSILLHIDDNRITRFCDYFSAL 221
                                    7899999***************9999874455544...5799999*********************************** PP

                           Per1 121 avvlsglylavvrlfrlarekkrvkllltalllalyllHvlyLllvrfdYtYnmaanvvvgllqnllwlllslktlakkl 200
                                    + +++ +y+++vrl+  ++  +++k ++t ++ al l++++ ++      ++n +a  +v+ + ++l+l+  + +  +  
  gene870|gene870|rna870|rna870 222 LGIMYYFYTVIVRLLLSFKV-SNIKEVTTHIFNALTLVYISVVYH--NITNFNSRALKFVSGVFIILFLVAIVVQ--SIF 296
                                    **************765554.334455666666665555555555..3347899998888888888777777653..222 PP

                           Per1 201 v.slklillvlllllamllEllDFppllrllDAhalwhlaTipltvlwydflvk 253
                                    +    + ++v+l+++++++E  D +p++ +lD+ha+wh++  + ++++ ++l++
  gene870|gene870|rna870|rna870 297 FpNKFIKYIVVLTIIGVTVESSDIEPFCFVLDSHAMWHFVIGIQNFYYNRYLAE 350
                                    213356678899999***********************9966666666677765 PP

>> Ceramidase  Ceramidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8  20.4      0.03   2.7e+02      53     233 ..     185     347 ..     149     353 .. 0.66

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.03
                     Ceramidase  53 krfllaylglalvGlgSalFHaTLkyetQllDelsmiyatalvlyavfse.....kksrstrvllgvlltalavvvtlly 127
                                    +++++ y   ++  + S+l H   +  t  +D +s ++ ++ ++y v+       k s+ ++v+  ++ +++ v ++++y
  gene870|gene870|rna870|rna870 185 NLYTMQYRISCITWISSILLHIDDNRITRFCDYFSALLGIMYYFYTVIVRlllsfKVSNIKEVTTHIFNALTLVYISVVY 264
                                    44555555555666667777777777777777776555444444444443344338888888888888888888888888 PP

                     Ceramidase 128 lvlkepvlhqvafalltvlvllrsiyliekkvdksdeaakkevkklallgliifllgfliWnlDnlfCstltrlrraigl 207
                                    + + ++   ++ f   ++++l+ +++++++             +k++ + +++ ++g+++  +D                
  gene870|gene870|rna870|rna870 265 HNITNFNSRALKFVSGVFIILFLVAIVVQS---------IFFPNKFIKYIVVLTIIGVTVESSDIE-------------- 321
                                    888888888888888888888888888832.........234567777888888888888877764.............. PP

                     Ceramidase 208 plgvllelHgwWHiltgigayilivl 233
                                    p+ ++l+ H++WH ++gi  +++  +
  gene870|gene870|rna870|rna870 322 PFCFVLDSHAMWHFVIGIQNFYYNRY 347
                                    67788999**********99888655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (359 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1068  (0.0595683); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 2435.69
//
Query:       gene871|gene871|rna871|rna871  [L=134]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.026   14.4   0.1      0.035   14.0   0.1    1.3  1  DUF1748   Fungal protein of unknown function (DUF1748)
       0.04   13.8   0.4      0.063   13.2   0.1    1.5  2  Triabin   Triabin
       0.11   12.0   0.3       0.13   11.7   0.3    1.2  1  OGFr_N    Opioid growth factor receptor (OGFr) conserved regi


Domain annotation for each model (and alignments):
>> DUF1748  Fungal protein of unknown function (DUF1748)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   5.9e-06     0.035      29      59 ..      87     118 ..      28     124 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.9e-06
                        DUF1748  29 lnsdkitd.kdikkwvdkYLgvGEwvmDqsva 59 
                                    ++ d+++d k+ kk  +kYL  GE v + sv 
  gene871|gene871|rna871|rna871  87 IKKDRLEDtKHKKKANKKYLAHGEDVTEESVT 118
                                    8999****9*****************999986 PP

>> Triabin  Triabin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0      0.73   4.4e+03      94     101 ..      46      53 ..      19      66 .. 0.56
   2 ?   13.2   0.1     1e-05     0.063      29      56 ..     102     129 ..      77     133 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.73
                                    TT---EEE CS
                        Triabin  94 sdgkkfta 101
                                     +g+++ +
  gene871|gene871|rna871|rna871  46 VNGNEVSV 53 
                                    22233333 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 1e-05
                                    SEEEEESSSS---SEEEEEEE-SSS--- CS
                        Triabin  29 gkwyltHardvtkpkvCqkykttknkGt 56 
                                    +k yl+H++dvt+++v   ++ t nk +
  gene871|gene871|rna871|rna871 102 NKKYLAHGEDVTEESVTSSFTGTRNKKV 129
                                    678*********************9854 PP

>> OGFr_N  Opioid growth factor receptor (OGFr) conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.3   2.2e-05      0.13      79     125 ..      54     102 ..      30     108 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.2e-05
                         OGFr_N  79 kkrllka..YklmLdfyGikledeetGevkraenwkerfenLnekshnn 125
                                    +k+++k     ++Ld  Gi++++e++G+++ ++  k+r+e+ ++k++ n
  gene871|gene871|rna871|rna871  54 EKTVIKNrmVGMLLDLAGIQFSNETSGRMAASNIKKDRLEDTKHKKKAN 102
                                    3334433113589*****************999999***9998877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       867  (0.0483574); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 979.10
//
Query:       gene872|gene872|rna872|rna872  [L=158]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1049  (0.0585086); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1104.91
//
Query:       gene873|gene873|rna873|rna873  [L=151]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-13   50.6   2.3    1.2e-13   50.6   2.3    2.6  2  TFIIS_C        Transcription factor S-II (TFIIS)
  ------ inclusion threshold ------
      0.076   12.7   0.1       0.13   11.9   0.1    1.4  1  zf-SCNM1       Zinc-finger of sodium channel modifier 1
       0.25   11.8   3.5       0.39   11.2   0.9    2.4  2  Ribosomal_L33  Ribosomal protein L33
       0.25   11.3   4.6          3    7.8   1.1    2.4  2  DUF35_N        Rubredoxin-like zinc ribbon domain (DUF35_N)
       0.42   10.5   0.1       0.42   10.5   0.1    3.0  3  zf-RING_4      RING/Ubox like zinc-binding domain


Domain annotation for each model (and alignments):
>> TFIIS_C  Transcription factor S-II (TFIIS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   4.5         3   1.1e+04      31      35 ..      76      80 ..      60      83 .. 0.65
   2 !   50.6   2.3   3.5e-17   1.2e-13       2      37 ..     112     146 ..     111     148 .. 0.95

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 3
                        TFIIS_C 31 CtkCg 35
                                   Ct C+
  gene873|gene873|rna873|rna873 76 CTVCK 80
                                   55554 PP

  == domain 2  score: 50.6 bits;  conditional E-value: 3.5e-17
                        TFIIS_C   2 kCpkCgsreayffqlQtRsaDEpmtvfykCtkCghr 37 
                                     C kCgs+++y+  +Q+RsaDE++t+fy+C +Cg++
  gene873|gene873|rna873|rna873 112 VCVKCGSEKMYYKAVQLRSADEGQTIFYEC-ECGYK 146
                                    5*****************************.***97 PP

>> zf-SCNM1  Zinc-finger of sodium channel modifier 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   3.7e-05      0.13       1      13 [.      76      88 ..      76      90 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.7e-05
                       zf-SCNM1  1 ClVCshrPVfDTi 13
                                   C+VC  rP+ ++i
  gene873|gene873|rna873|rna873 76 CTVCKSRPIKESI 88
                                   *********7776 PP

>> Ribosomal_L33  Ribosomal protein L33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.9   0.00011      0.39       7      27 ..      76     105 ..      75     105 .. 0.80
   2 ?   -0.1   0.1      0.37   1.3e+03       6      16 ..     112     123 ..     109     133 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00011
                                    ET...............EEEEETT..--S- CS
                  Ribosomal_L33   7 Ctecksrn.........Ytttknkkntper 27 
                                    Ct cksr          Y+t k k nt +r
  gene873|gene873|rna873|rna873  76 CTVCKSRPikesityekYYTLKPKVNTDDR 105
                                    ******54555566666**********998 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.37
                                    EET.......EE CS
                  Ribosomal_L33   6 eCtecksrn.Yt 16 
                                    +C +c+s++ Y+
  gene873|gene873|rna873|rna873 112 VCVKCGSEKmYY 123
                                    699999987765 PP

>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   1.1   0.00084         3      15      34 ..      65      82 ..      61      84 .. 0.85
   2 ?    4.5   0.1    0.0093        33      10      19 ..     109     118 ..     103     119 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.00084
                        DUF35_N 15 pdCGtvqfPPravCphCgsd 34
                                   + CGt+ f    +C+ C s+
  gene873|gene873|rna873|rna873 65 K-CGTY-FFTDSICTVCKSR 82
                                   4.****.5699******886 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.0093
                        DUF35_N  10 vgqrCpdCGt 19 
                                    ++q C +CG+
  gene873|gene873|rna873|rna873 109 IAQVCVKCGS 118
                                    7899999995 PP

>> zf-RING_4  RING/Ubox like zinc-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   3.9      0.65   2.3e+03      15      28 ..      61      79 ..      58      88 .. 0.62
   2 ?   -1.5   0.1      0.64   2.3e+03      23      28 ..     111     116 ..     109     122 .. 0.75
   3 ?   10.5   0.1   0.00012      0.42       8      24 ..     131     147 ..     126     150 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.65
                      zf-RING_4 15 lkpCeCgy.....qiClfC 28
                                   l+ C+Cg       iC  C
  gene873|gene873|rna873|rna873 61 LMFCKCGTyfftdSICTVC 79
                                   5678887312333466666 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.64
                      zf-RING_4  23 qiClfC 28 
                                    q+C+ C
  gene873|gene873|rna873|rna873 111 QVCVKC 116
                                    677777 PP

  == domain 3  score: 10.5 bits;  conditional E-value: 0.00012
                      zf-RING_4   8 ldetdkdlkpCeCgyqi 24 
                                    +de  + ++ CeCgy++
  gene873|gene873|rna873|rna873 131 ADEGQTIFYECECGYKM 147
                                    5777888999*****98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       685  (0.0382063); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1052.06
//
Query:       gene874|gene874|rna874|rna874  [L=292]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.2e-10   40.0   7.2    8.3e-10   38.6   7.2    1.6  1  RINGv          RING-variant domain
  ------ inclusion threshold ------
       0.61    9.9   3.5        1.9    8.3   3.5    1.9  1  A2L_zn_ribbon  A2L zinc ribbon domain
        9.4    6.1   7.8       0.92    9.3   3.2    1.7  2  zf-RING_4      RING/Ubox like zinc-binding domain


Domain annotation for each model (and alignments):
>> RINGv  RING-variant domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.6   7.2   1.4e-13   8.3e-10       1      48 []       6      68 ..       6      68 .. 0.91

  Alignments for each domain:
  == domain 1  score: 38.6 bits;  conditional E-value: 1.4e-13
                                   ETTTTEE-SSSS..............--B-SS--STCCCSB-HHHHHHHHHH.TCT-SB-TTT CS
                          RINGv  1 CriCleeeeese..............plispCkCrGslklvHesClekWlde.keantqCeiC 48
                                   C+iCl++++ ++              ++i+pC+C+Gs+k+vH  C  k +++ ++++ +C +C
  gene874|gene874|rna874|rna874  6 CWICLRTDNTEDkdeedgvseqapsdEWIRPCHCKGSIKWVHSRCFYKYIMNqTKSKLRCIFC 68
                                   ****9998766668899*********************************996777888**99 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   3.5   0.00031       1.9      13      29 ..      54      70 ..      35      74 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00031
                  A2L_zn_ribbon 13 gilnseqgylvCieCga 29
                                    i+n++++ l Ci+C++
  gene874|gene874|rna874|rna874 54 YIMNQTKSKLRCIFCQT 70
                                   59*************96 PP

>> zf-RING_4  RING/Ubox like zinc-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.1       1.3     8e+03      25      30 ..       6      11 ..       4      18 .. 0.58
   2 ?    9.3   3.2   0.00015      0.92      10      48 .]      29      73 ..      23      73 .. 0.72

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 1.3
                      zf-RING_4 25 ClfCyh 30
                                   C+ C++
  gene874|gene874|rna874|rna874  6 CWICLR 11
                                   555643 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00015
                      zf-RING_4 10 etdkdlkpCeCgyqi...ClfC.yhrile..eeegrCPaCreeYk 48
                                    +d+ ++pC+C+  i      C y+ i++  +++ rC  C+++Y+
  gene874|gene874|rna874|rna874 29 PSDEWIRPCHCKGSIkwvHSRCfYKYIMNqtKSKLRCIFCQTKYN 73
                                   57999******998832223462556666444689********95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (292 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       997  (0.0556082); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1875.76
//
Query:       gene875|gene875|rna875|rna875  [L=312]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      0.006   16.5   0.1      0.016   15.2   0.1    1.7  1  HUN       HPC2 and ubinuclein domain


Domain annotation for each model (and alignments):
>> HUN  HPC2 and ubinuclein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1   8.7e-07     0.016       5      51 ..      23      67 ..      20      68 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 8.7e-07
                            HUN  5 rdddgddtgsgYDieDpFIDDsElydelvpdilktktgGFYvnqgel 51
                                   +++++++t + YD++Dp I   E  +e+ p  ++  +  F+v++g+l
  gene875|gene875|rna875|rna875 23 KRKKRRSTTDTYDYDDPLIEHME--NEDAPVSIEADLRNFFVYSGKL 67
                                   678899*************9877..999999**************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (312 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       854  (0.0476323); expected 358.6 (0.02)
Passed bias filter:                      491  (0.0273858); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2275.23
//
Query:       gene876|gene876|rna876|rna876  [L=278]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.2e-18   64.9  15.1      8e-13   48.3  12.0    4.0  2  ERO1      Endoplasmic Reticulum Oxidoreductin 1 (ERO1)


Domain annotation for each model (and alignments):
>> ERO1  Endoplasmic Reticulum Oxidoreductin 1 (ERO1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.1   0.0   0.00063        11       2      29 ..      42      69 ..      41      79 .. 0.90
   2 !   48.3  12.0   4.5e-17     8e-13     103     318 ..      83     245 ..      72     270 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.00063
                           ERO1  2 lrplLkeLvktdfFryfkvnldkeCpfw 29
                                   +++lL++L++t+ F+  ++nld++C++ 
  gene876|gene876|rna876|rna876 42 IKKLLEKLCNTTRFSSIEINLDEPCAYT 69
                                   8899*********************985 PP

  == domain 2  score: 48.3 bits;  conditional E-value: 4.5e-17
                           ERO1 103 vdLlenperfTgYkGesaervWkaiYeencfkeeseseeseekeleelclekrvfyrliSGlhasisihlaaeylnqetg 182
                                    v+Ll+np   T+Y   s   +Wk iYe     +                    +  rl+ G+h s  ++++++y++q +g
  gene876|gene876|rna876|rna876  83 VSLLANPHVNTNYLEGS--AIWKKIYEVR---R------------------DTTHTRLVNGMHFSTFVFICKNYYDQGNG 139
                                    89999*******98777..79****9542...2..................34578************************ PP

                           ERO1 183 ewepnlelfkervgkhperlenlYfnyalvlrAvaklapyleelefstgeeeedeetkellkeelakellsalsskekaf 262
                                    ++ pn +lf+e++++++      Y  ++l+  ++ k+  + ++ ++    ++e+++  e+    +           +k +
  gene876|gene876|rna876|rna876 140 TYLPNKKLFHEKYSQEK------YEDFLLLRESMLKTVGFCNTNSLGL--HREERKLLEE----I-----------KKSL 196
                                    **********9999887......8899999888777766666543332..2222222222....2...........1245 PP

                           ERO1 263 desklfkdkeeaeelkeefrerfrnisrimdCVgCekCrLwGKlqttGlgtAlkil 318
                                    ++s+l k       + e+  + +++  +++ CV+C +C+LwGKl+  Gl  A+k+ 
  gene876|gene876|rna876|rna876 197 EHSSLVK-------MDEKRIQDMQKCVNLISCVSCARCKLWGKLKFVGLMCAIKLQ 245
                                    5666666.......33444456777889999**********************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (278 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       846  (0.0471861); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 1770.75
//
Query:       gene877|gene877|rna877|rna877  [L=219]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.3e-19   69.5   1.9      4e-19   68.8   1.9    1.4  1  E2F_CC-MB       E2F transcription factor CC-MB domain
    2.3e-16   59.6   0.1      6e-16   58.3   0.1    1.7  1  E2F_TDP         E2F/DP family winged-helix DNA-binding domain
  ------ inclusion threshold ------
      0.019   15.1   0.0      0.064   13.4   0.0    1.8  1  B-block_TFIIIC  B-block binding subunit of TFIIIC
      0.082   12.8   0.1       0.17   11.8   0.1    1.6  1  NtA             Agrin NtA domain
      0.095   12.6   0.0       0.22   11.4   0.0    1.6  2  TrmB            Sugar-specific transcriptional regulator TrmB


Domain annotation for each model (and alignments):
>> E2F_CC-MB  E2F transcription factor CC-MB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.8   1.9   1.1e-22     4e-19       4      94 ..     122     211 ..     120     212 .. 0.93

  Alignments for each domain:
  == domain 1  score: 68.8 bits;  conditional E-value: 1.1e-22
                      E2F_CC-MB   4 elesleeeeqkLDelieklteqlknl.tedeknqlaYvtyedirsiasfkeqtviaikAppgtqlevpdpeeekryqiyL 82 
                                     +++l++ee++LD+ i +++++++n+ + d++ ++aYvt++d+  ++s+++++++a+kAp++t le +d++  ++y + +
  gene877|gene877|rna877|rna877 122 AIDQLNKEEKELDQKIFIMNNKIQNMlQLDSSIKNAYVTHKDLLGLPSLQNKLIFAVKAPQETFLENKDTK--NEYMMEF 199
                                    589***********************66666669**********************************987..89***** PP

                      E2F_CC-MB  83 kStsgpievylv 94 
                                    + +s +i+v++v
  gene877|gene877|rna877|rna877 200 NANSDQIDVFYV 211
                                    **********98 PP

>> E2F_TDP  E2F/DP family winged-helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.3   0.1   1.7e-19     6e-16       2      71 .]      17      80 ..      16      80 .. 0.97

  Alignments for each domain:
  == domain 1  score: 58.3 bits;  conditional E-value: 1.7e-19
                        E2F_TDP  2 dksLgvltkkfvellkesakgtlslneaakeLvdkkdekvkkRRiYDilNVLealglieKeskneikWig 71
                                   ++sL vltkkf+ +lk+   + ++ n+++  L       v kRR+YDi+N+Le+lgl++K+s n+ +Wig
  gene877|gene877|rna877|rna877 17 ENSLFVLTKKFFIYLKQVYPRAIDTNDLSHYLC------VSKRRVYDITNILEGLGLLRKRSVNSLEWIG 80
                                   68*************9999999***********......*****************************98 PP

>> B-block_TFIIIC  B-block binding subunit of TFIIIC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   1.8e-05     0.064      20      55 ..      40      87 ..      39     118 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.8e-05
                 B-block_TFIIIC 20 tqsdLakeskqdprslfyrlksLekkgLIvkqsii............d 55
                                    ++dL++++  ++r ++ +++ Le  gL  k+s++             
  gene877|gene877|rna877|rna877 40 DTNDLSHYLCVSKRRVYDITNILEGLGLLRKRSVNslewiggdfnnfI 87
                                   589*******************************86666666555550 PP

>> NtA  Agrin NtA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   4.7e-05      0.17      76     102 ..     129     155 ..      96     161 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 4.7e-05
                            NtA  76 kveegdtrifllnklkdnelklnssll 102
                                    + +e d +if++n++ +n l+l+ss+ 
  gene877|gene877|rna877|rna877 129 EEKELDQKIFIMNNKIQNMLQLDSSIK 155
                                    456789*******************85 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   6.3e-05      0.22      20      56 ..      36      72 ..      27      78 .. 0.84
   2 ?   -3.3   0.0       2.4   8.6e+03      26      44 ..     131     149 ..     127     149 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 6.3e-05
                                   HCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES CS
                           TrmB 20 lgpatadeiaeelgvprskvYevLrsLedkGlVerek 56
                                       +++++++ l v++ +vY++ + Le  Gl +++ 
  gene877|gene877|rna877|rna877 36 PRAIDTNDLSHYLCVSKRRVYDITNILEGLGLLRKRS 72
                                   55667899************************99886 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 2.4
                                    CHHCCCTTSSCHCHHHHHH CS
                           TrmB  26 deiaeelgvprskvYevLr 44 
                                    +e+ +++ +  +k++++L+
  gene877|gene877|rna877|rna877 131 KELDQKIFIMNNKIQNMLQ 149
                                    5666666777788888886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       919  (0.0512577); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 1473.14
//
Query:       gene878|gene878|rna878|rna878  [L=328]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-10   40.6   0.2    5.6e-10   39.2   0.0    1.7  2  RhoGAP    RhoGAP domain


Domain annotation for each model (and alignments):
>> RhoGAP  RhoGAP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.1      0.22   3.9e+03      88     121 ..      71     106 ..      57     113 .. 0.56
   2 !   39.2   0.0   3.1e-14   5.6e-10       7     148 ..     127     266 ..     123     269 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.22
                                    SHHHHHHHHH..HHHTTS-HHHHHHHHHHHHHHHHH CS
                         RhoGAP  88 deeerlealk..ellekLPkenrdtLryLlehLkrv 121
                                    +ee+   a++  ++l ++   + +tL ++++ ++++
  gene878|gene878|rna878|rna878  71 NEEQYWLAMHciRTLLRMKTKKKNTLLMIIDRIEKI 106
                                    444443333300333466677777777777766666 PP

  == domain 2  score: 39.2 bits;  conditional E-value: 3.1e-14
                                    HHHHHHHHTTTSTTTTTS-S-HHHHHHHHHHHHHTGGGCTTTTTSCHHHHHHHHHHHHHHSSSTTTTGGHHHHHHHHHTS CS
                         RhoGAP   7 cvefiekrgldtegiyRvsgskarvkelreafdkgkavdsdleeedvhavaslLKrfLrelpepLltkelyeelieaaks 86 
                                    ++++ e+++  + g  R++g+k++ ++l + +++ ++   d++++++ + +s +K+++re  + ++   l ++l+  ++ 
  gene878|gene878|rna878|rna878 127 LLDHFEAYAPSSIGFLRLPGKKDVYHRLLDLMNEPAEI--DFSKYEMRDNCSFFKLYIREKLKGIIYPCLASSLYYFYDR 204
                                    678999999*********************99988888..8**********************************66666 PP

                                    SSHHHHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHHHTHHHH---HHHHHHHHHHHHHT-TS CS
                         RhoGAP  87 edeeerlealkellekLPkenrdtLryLlehLkrvaenskenkMtaknLaivfaPtLlrpks 148
                                    + ++e  +  k l   +  + r++L  +l++ +++ +n++ +kM++++L ++ +P++++ ++
  gene878|gene878|rna878|rna878 205 NRKDELCKIKKYLPFVFIGHRRKLLLRILHLYRKIGNNEEITKMSIRSLVVCSTPSFFPASD 266
                                    555555555555556999999************************************99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (328 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1069  (0.0596241); expected 358.6 (0.02)
Passed bias filter:                      516  (0.0287802); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 2247.05
//
Query:       gene879|gene879|rna879|rna879  [L=87]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       462  (0.0257683); expected 358.6 (0.02)
Passed bias filter:                      249  (0.0138881); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 656.41
//
Query:       gene88|gene88|rna88|rna88  [L=53]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.14   11.8   0.0       0.14   11.8   0.0    1.1  1  DUF4903   Domain of unknown function (DUF4903)


Domain annotation for each model (and alignments):
>> DUF4903  Domain of unknown function (DUF4903)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0     8e-06      0.14      29      49 ..      20      40 ..       2      44 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 8e-06
                    DUF4903 29 vlstkatlngvdktllkeGcp 49
                               +l+ + ++n+v ktll++ cp
  gene88|gene88|rna88|rna88 20 MLACHQAVNSVGKTLLPKKCP 40
                               6788999*************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (53 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       459  (0.025601); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.33u 0.25s 00:00:00.58 Elapsed: 00:00:00.40
# Mc/sec: 401.84
//
Query:       gene880|gene880|rna880|rna880  [L=125]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      6e-12   45.4   0.0    2.2e-11   43.5   0.0    1.7  2  dUTPase   dUTPase


Domain annotation for each model (and alignments):
>> dUTPase  dUTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0     0.027   4.9e+02      14      30 ..      10      26 ..       3      32 .. 0.82
   2 !   43.5   0.0   1.2e-15   2.2e-11      18     113 ..      33     124 ..      19     125 .] 0.90

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.027
                                   SSEEEE-SSSEEEETTE CS
                        dUTPase 14 AgyDlsaakdltvkpge 30
                                   A + l ++++++++p++
  gene880|gene880|rna880|rna880 10 AMFNLVLSSETAIPPKK 26
                                   899***********944 PP

  == domain 2  score: 43.5 bits;  conditional E-value: 1.2e-15
                                    EE-SSSEEEETTEEEEEEEEEEEE--TTEEEEEEE-HHHHHHHEEEEEEEEETTBTSEEEEEEEE-SSS-EEE-TT-EEE CS
                        dUTPase  18 lsaakdltvkpgetvlvptdisiklpdglaalilpRSglaakglivvpgvidsdyrGevkvvlfnltkkdvkikkgdRiA 97 
                                    l+a++ +++ p++ +++pt++++  p ++  +i   S+l++k +     vidsdyrGe+  v+   +++++ ++kg+ +A
  gene880|gene880|rna880|rna880  33 LYASETTVINPKTLTTIPTGVYLSFPPDYFLYI---SSLSHKFGSNAH-VIDSDYRGEIFHVVRSKSDESFVVEKGEPVA 108
                                    899999999********************9999...9*****999888.*********99999999999*********** PP

                                    EEEEEEBECGEEEEES CS
                        dUTPase  98 qLifariltaeleeve 113
                                    qLif +i+ +e+e  e
  gene880|gene880|rna880|rna880 109 QLIFYKIVLPEFEVIE 124
                                    *******998887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       289  (0.0161191); expected 358.6 (0.02)
Passed bias filter:                      263  (0.014669); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 890.52
//
Query:       gene881|gene881|rna881|rna881  [L=993]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.1e-05   21.7   0.2    9.1e-05   21.7   0.2    2.3  3  MMM1      Maintenance of mitochondrial morphology protein 1


Domain annotation for each model (and alignments):
>> MMM1  Maintenance of mitochondrial morphology protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.2   5.1e-09   9.1e-05      95     187 ..      53     150 ..      22     162 .. 0.80
   2 ?   -2.5   0.1      0.12   2.1e+03     263     325 ..     262     326 ..     256     329 .. 0.73
   3 ?   -1.3   0.1     0.048   8.6e+02      82     149 ..     636     702 ..     623     727 .. 0.75

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 5.1e-09
                                    --TTTS--B--HHHHHHHHHHHHHHHH-TTHHHHHHHHHHHHHHGGCS-TTEEEEEEEEEE--S---EEEEEEE...... CS
                           MMM1  95 YdveshqpesLDWfnvLiaqtiaqfreealekdnilksLnealnseelpdyldkikvteidlGedfPifsncrii..... 169
                                     d ++h    + Wfn L+ +   ++     +kd + ksL + + s ++   l ++ + +i++  + P++ n+r++     
  gene881|gene881|rna881|rna881  53 IDDSQHVCTDVAWFNLLMQRLWVELSVSYAHKDRMRKSLMRRMASMHTKRILSDLVIEDIKISPEAPMIGNVRVVddeqc 132
                                    56788999999****************************************************************87776 PP

                                    EE-TTTTSS-EEEEEEEE CS
                           MMM1 170 keskesekkrLeakidvd 187
                                        ++ kkr +a+  +d
  gene881|gene881|rna881|rna881 133 AMLMKKMKKRKNARRKID 150
                                    333344455555554444 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.12
                                    EEEEEE-SS-EEEEEEEEESSSSTT-TTH...HHHHHHHHHHHHHHHHHHHBTT-EEEEE----S- CS
                           MMM1 263 alvfsflpdyrldlsvksliGsrsklqdv...PkiaslvearlkkWfeercvePrfqvvklPslWP 325
                                        sfl d ++ ++vk+++ + +  + +     ++s++++ +k  ++ ++v P f +  lP + P
  gene881|gene881|rna881|rna881 262 RWELSFLSDPQFTITVKAFLSTTT-SESIyfeGVVSSILKKVIKYGLMSKMVFPSFYQFPLPMVSP 326
                                    556788888888888888775443.23331124689999999999999999999999999998877 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 0.048
                                    ..HHHHHHHHTTT--TTTS--B--HHHHH.HHHHHHHHHHH-TTHHHHHHHHHHHHHHGGCS-TTEEEE CS
                           MMM1  82 ssakiesiLektyYdveshqpesLDWfnv.LiaqtiaqfreealekdnilksLnealnseelpdyldki 149
                                     ++  +s +ek   + ++ ++es+D  nv  + q +++ re  ++++ + ksL   ++++el d l+++
  gene881|gene881|rna881|rna881 636 VQKMYASFFEKRTLSARNTSTESIDQPNVdELVQRMDDIRE--INTNYVEKSLLLEMKKNELMDVLGDV 702
                                    45556788899999999999999999999536788888887..45677777887777777777777666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (993 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       930  (0.0518713); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.76u 0.28s 00:00:01.04 Elapsed: 00:00:00.46
# Mc/sec: 6538.17
//
Query:       gene882|gene882|rna882|rna882  [L=283]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    5.5e-06   25.9   5.1    0.00045   19.6   3.0    2.5  3  WD40_like  WD40-like domain
    0.00029   21.6   4.0        0.4   11.6   0.5    3.7  4  WD40       WD domain, G-beta repeat
     0.0075   16.3   0.7        3.7    7.6   0.0    2.7  3  BBS2_Mid   Ciliary BBSome complex subunit 2, middle region


Domain annotation for each model (and alignments):
>> WD40_like  WD40-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   3.0   7.5e-08   0.00045      83     221 ..       9     140 ..       7     147 .. 0.90
   2 !    5.6   0.0    0.0015       8.7       2      37 ..     117     150 ..     116     175 .. 0.89
   3 !    5.5   0.0    0.0015       9.2      50      99 ..     212     262 ..     204     283 .] 0.80

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 7.5e-08
                      WD40_like  83 edistvkviddklliGtnkGsiyvfskdlqleevllgqsseIkeiki.ennkiysLsesafivfdlfsqnieykisvkdi 161
                                    + i+ +kv +dk+ + +   ++ +++ +l +++++  ++ +I++i   +n+ i++      iv+d+++   + k++  +i
  gene882|gene882|rna882|rna882   9 DSITDIKVQEDKIHVSSFDRTLRIYKDELLVHKIV--HNLPILKIGFlDNDPIFT-----DIVGDVITPYSRIKTDCGGI 81 
                                    579*************************9988875..889*****8626778998.....499***************** PP

                      WD40_like 162 ktfeiienkdilligtegeililkknvilqkidvegkPecillvddylivGgsfkyllli 221
                                    + ++i  n+ i++ g ++++ i+++++i   +++  k  ++   d+++++G+s +  ll 
  gene882|gene882|rna882|rna882  82 QGMSIY-NNSIIVAGWNKKLQIIQNDEIQSTVELREKVYAMDRRDNFILLGCSNSTCLLY 140
                                    ******.999**************************99999999********98877765 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0015
                      WD40_like   2 eiYsidiskkgslilyGgkddkctvlkleslesvsi 37 
                                    ++Y++d   + ++il G  + +c +++++  +s+ +
  gene882|gene882|rna882|rna882 117 KVYAMDR--RDNFILLGCSNSTCLLYDIRKIDSIMS 150
                                    7999998..8889***************99988865 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.0015
                      WD40_like  50 lldddlilvvtlDGtillslleneeevene.kieedistvkviddklliGt 99 
                                    l+ ++ ++ +  DG i++ +++   + ++  + + ++s ++  ++k++ G 
  gene882|gene882|rna882|rna882 212 LIFNNTLISCGSDGSIVKWDVHSRTMLKEIyRSDLNVSAIERYKNKIVAGF 262
                                    68899***********99999999855544044558***********9985 PP

>> WD40  WD domain, G-beta repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.0   0.00062       3.7      12      37 ..      10      33 ..       5      34 .. 0.85
   2 ?   -1.9   0.0       1.3   7.5e+03      25      38 .]     129     141 ..     119     141 .. 0.73
   3 ?   -1.4   0.0      0.89   5.3e+03      13      36 ..     157     177 ..     151     177 .. 0.62
   4 !   11.6   0.5   6.7e-05       0.4       5      38 .]     191     231 ..     188     231 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00062
                                   SEEEEEEETTSSEEEEEETTSEEEEE CS
                           WD40 12 svtslafspdgawlasGsdDgtvriW 37
                                   s+t+++++ d+  + s+  D+t+ri+
  gene882|gene882|rna882|rna882 10 SITDIKVQEDKIHV-SSF-DRTLRIY 33
                                   59********9997.678.******8 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.3
                                    EEEEETTSEEEEEE CS
                           WD40  25 lasGsdDgtvriWd 38 
                                    l+ +s + t+ ++d
  gene882|gene882|rna882|rna882 129 LLGCS-NSTCLLYD 141
                                    45556.99999987 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.89
                                    EEEEEEETTSSE...EEEEETTSEEEE CS
                           WD40  13 vtslafspdgaw...lasGsdDgtvri 36 
                                    +ts+      a+    + G+ +g++ri
  gene882|gene882|rna882|rna882 157 ITSV------ALgncAVIGMLNGKIRI 177
                                    6666......44333344877888887 PP

  == domain 4  score: 11.6 bits;  conditional E-value: 6.7e-05
                                    EEEESS.SS.........EEEEEEETTSSEEEEEETTSEEEEEE CS
                           WD40   5 rtltGH.ss.........vtslafspdgawlasGsdDgtvriWd 38 
                                    +t+  H +s         v++l    +++++++Gs Dg++  Wd
  gene882|gene882|rna882|rna882 191 YTFNCHhKSsdnkrinypVNDL--IFNNTLISCGS-DGSIVKWD 231
                                    5667777445788988889999..55777788888.*****998 PP

>> BBS2_Mid  Ciliary BBSome complex subunit 2, middle region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.2   0.0    0.0017        10       7      40 ..      14      46 ..      10      62 .. 0.79
   2 !    7.6   0.0   0.00061       3.7      12      67 ..      88     142 ..      82     177 .. 0.81
   3 ?   -2.5   0.0      0.85   5.1e+03      26      87 ..     229     245 ..     215     264 .. 0.48

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0017
                       BBS2_Mid  7 vdgdgeneLvvgsddfeirvfkeeelvaeitete 40
                                   ++  +e+++ v+s d ++r++k+e lv++i  + 
  gene882|gene882|rna882|rna882 14 IKV-QEDKIHVSSFDRTLRIYKDELLVHKIVHNL 46
                                   444.47899******************9987665 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.00061
                       BBS2_Mid  12 eneLvvgsddfeirvfkeeelvaeitetekvvslarlekerfayaleNGtvgvyek 67 
                                    +n+++v+  + ++++ +++e+ ++++ +ekv ++ r ++  ++ + +N t  +y+ 
  gene882|gene882|rna882|rna882  88 NNSIIVAGWNKKLQIIQNDEIQSTVELREKVYAMDRRDN-FILLGCSNSTCLLYDI 142
                                    589****************************99987544.4567888888888874 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 0.85
                       BBS2_Mid  26 vfkeeelvaeitetekvvslarlekerfayaleNGtvgvyekkerlWrvksknevvalaayd 87 
                                                                                  W v s++ +  +   d
  gene882|gene882|rna882|rna882 229 K---------------------------------------------WDVHSRTMLKEIYRSD 245
                                    3.............................................3333333333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (283 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       421  (0.0234815); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 2028.73
//
Query:       gene883|gene883|rna883|rna883  [L=57]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (57 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       270  (0.0150594); expected 358.6 (0.02)
Passed bias filter:                      226  (0.0126053); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.40
# Mc/sec: 423.72
//
Query:       gene884|gene884|rna884|rna884  [L=504]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.5e-24   85.5   0.1    2.3e-23   83.1   0.0    2.0  2  Hexokinase_1  Hexokinase
    1.1e-12   47.9   5.7    1.6e-12   47.3   2.8    2.1  2  Hexokinase_2  Hexokinase
  ------ inclusion threshold ------
       0.11   12.7  11.9       0.17   12.2  11.9    1.2  1  PNISR         Arginine/serine-rich protein PNISR
        2.4    7.3   5.4        3.7    6.7   5.4    1.3  1  Zip           ZIP Zinc transporter


Domain annotation for each model (and alignments):
>> Hexokinase_1  Hexokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.1   0.0   5.2e-27   2.3e-23      11     199 .]      49     237 ..      41     237 .. 0.86
   2 ?   -0.7   0.0      0.24   1.1e+03      18      49 ..     460     493 ..     446     497 .. 0.77

  Alignments for each domain:
  == domain 1  score: 83.1 bits;  conditional E-value: 5.2e-27
                                    --HHHHHHHHHHHHHHHHHHHS.S.STS--EE----S---S--E....EEEEEEEESSSEEEEEEEEEESSS.-EEEEEE CS
                   Hexokinase_1  11 lsdeklkelvdrfleemekgLakekeslkmlptyvtrlPtGkek....GtylAlDlGgtnlRvllveLlges.kveitqe 85 
                                    +++++lk l ++f++ + +  ++ +e  ++l+t+v rlP+ +ek     + lA++lGgt l+  l  + +++ k++   e
  gene884|gene884|rna884|rna884  49 YTENQLKYLIADFKNALISSQKDPRERETFLDTFV-RLPEASEKisckHVLLAINLGGTYLQLGLYSIAKNElKLHSPVE 127
                                    56677777777776666665554434477******.5******98877889*****************987779999999 PP

                                    EEE--GGGGGSBHHHHHHHHHHHHHHHHHHH....ST..T-S-EEEEEEE-SSEE-SBTT--EE-S--TT---..TT.-T CS
                   Hexokinase_1  86 kykipeelktgtaeeLFdfiakciaefleeegeekkeekeeeelplGftFSFPveqtsldegtlirwtKgfai..kd.ve 162
                                    k+ ip+   + ++ + F++iak+ +  le+++ +k       + + G+tFS P++++s++ g +++++K+f    ++  +
  gene884|gene884|rna884|rna884 128 KVLIPKADGSTKKVDCFEWIAKKTKLYLEKSNFKK-------SARAGITFSHPIKHESISVGRVLKLGKDFPFraPNlGS 200
                                    9******9999*******************98875.......2689************************8774355344 PP

                                    TSBHHHHHHHHHHHTT-SEEEEEEE-HHHHHHHHHHH CS
                   Hexokinase_1 163 gkdvvqllqealerkglpvkvvalvNDTvgtllslaY 199
                                     +d v+l+++a+++ ++pvkv  ++ND+++t +sl Y
  gene884|gene884|rna884|rna884 201 ENDAVKLVNAAFKKFKVPVKVDIILNDATATAASLIY 237
                                    88*******************************9988 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.24
                                    HHHHHHHHHHHHHHS.S.ST..S--EE----S-- CS
                   Hexokinase_1  18 elvdrfleemekgLakekes..lkmlptyvtrlP 49 
                                    + +++f+ +++k+L++++++  ++m+  +v++ P
  gene884|gene884|rna884|rna884 460 TEQEKFILKCYKRLKRRSAQilMSMMIAIVESQP 493
                                    4568899999999998866678889998888766 PP

>> Hexokinase_2  Hexokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.3   2.8   3.7e-16   1.6e-12       2     132 ..     247     378 ..     246     403 .. 0.70
   2 ?    0.9   0.0     0.056   2.5e+02     113     177 ..     430     491 ..     404     499 .. 0.71

  Alignments for each domain:
  == domain 1  score: 47.3 bits;  conditional E-value: 3.7e-16
                                    EEEEESSSEEEEEEEEGGG-GGGTTTS-TTSEEEEE--GGGTTTT-SS-..--HHHHHHHHHS..SSTTS-HHHHCCSHH CS
                   Hexokinase_2   2 iGlIlGtGtNacyleklsnieklegkkeksgemviNtEwgafgdegklpllrtkyDkeldees..pnpgeqlfEkmiSGm 79 
                                    +G++lGtGtNa+y+e+ ++++            +iNtEw +f++ g+ +  r +yD+++++    +n+  ++++ +i+G 
  gene884|gene884|rna884|rna884 247 MGIVLGTGTNAAYIERQNRLT----------PTIINTEWASFDK-GSVH--RCEYDEAIEKMVkeQNKVYKRMDALIGGN 313
                                    8******************99..........579********86.7777..9*********8533778888********* PP

                                    HHHHHHHHHHHHHHC.........TSSS.....C....CCCSTTSS-THHHHHHHC--BTT-HHHH CS
                   Hexokinase_2  80 YLGelvrlvlldlie........ekllf.....kgkseklktpysldteflseieedesedleevr 132
                                    Y+ +l+ ++  + i+        +++ f     ++ksek ++++s + +++++++++ ++d e+++
  gene884|gene884|rna884|rna884 314 YFMQLILQMAQKNIKdyissenhAQGTFmmrneTEKSEKGNKKESENVAHVAKVDTK-HDDVETTN 378
                                    ****99999999998666666542233344432222335555555555555555543.33333333 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.056
                                    -THHHHHHHC--BTT-HHHHHHHHHCCS---.-HHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHH CS
                   Hexokinase_2 113 dteflseieedesedleevrevleellglesvteedleivrevceavsrRaarlvAagiaallkk 177
                                    +    s+i +d    l +++ +l+ + + ++  +e+ +++ +  +   rR+a++   +++a+++ 
  gene884|gene884|rna884|rna884 430 TNPSTSKIPND---VLVDIKYALNLVKNPNKNLTEQEKFILKCYKRLKRRSAQILMSMMIAIVES 491
                                    44555556654...6666666666665565554556678888889999******99999999875 PP

>> PNISR  Arginine/serine-rich protein PNISR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2  11.9   3.7e-05      0.17      16     130 ..     290     432 ..     289     484 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 3.7e-05
                          PNISR  16 eGLEKmerEKqkklererr........................ekeraer....rkeekkesskeeeeaknprnlakskf 67 
                                    e +EKm +E++k  +r  +                        ++++a+     r+e +k+++  ++e++n++ +ak+  
  gene884|gene884|rna884|rna884 290 EAIEKMVKEQNKVYKRMDAliggnyfmqlilqmaqknikdyisSENHAQGtfmmRNETEKSEKGNKKESENVAHVAKVDT 369
                                    679*********99999999**********9999999999997444444467789999999999999************9 PP

                          PNISR  68 dsedeksdeeeeegaegedsesqekasskksevdeqespeeeeaarkeieesspaeeeeeeep 130
                                    +++d ++++ ++++++ + + +++++ssk++e+++++ +++ +a+++++e+ ++a+e++ ++p
  gene884|gene884|rna884|rna884 370 KHDDVETTNRKKSDTNIKLDRETSSNSSKTNEFNTKAIDNDAQAPKSSVEDDKKAKESQTTNP 432
                                    999988888887774444444666666666667776666555555555566666665555554 PP

>> Zip  ZIP Zinc transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   5.4   0.00082       3.7     102     172 ..     329     419 ..     288     463 .. 0.64

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.00082
                            Zip 102 k................ksshkektpkkasssssesaakksvsndkveeseekedhvaeadtdadskeelrngkqekses 165
                                                     + +++ek +kk+s++ ++ a++++ ++d  +++++k d + + d + +s +++ n+   k  +
  gene884|gene884|rna884|rna884 329 DyissenhaqgtfmmrnETEKSEKGNKKESENVAHVAKVDTKHDDVETTNRKKSDTNIKLDRETSSNSSKTNEFNTKAID 408
                                    13444577777777777788999999999999999999999999999999998665444444444444444443333333 PP

                            Zip 166 ekeqas....e 172
                                    +++qa     e
  gene884|gene884|rna884|rna884 409 NDAQAPkssvE 419
                                    33333234331 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (504 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2050  (0.11434); expected 358.6 (0.02)
Passed bias filter:                      548  (0.030565); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.66u 0.28s 00:00:00.94 Elapsed: 00:00:00.45
# Mc/sec: 3398.64
//
Query:       gene885|gene885|rna885|rna885  [L=126]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.015   15.7   0.5      0.022   15.2   0.5    1.3  1  Sld5      GINS complex protein
       0.12   13.4   3.0       0.17   12.9   3.0    1.3  1  DUF4834   Domain of unknown function (DUF4834)


Domain annotation for each model (and alignments):
>> Sld5  GINS complex protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.5   2.5e-06     0.022      54      89 ..      12      43 ..       2      72 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.5e-06
                                   HHHHHHHHT.HCHHHHHHHHHHHHHHHHHHHTHCHH CS
                           Sld5 54 avkllelardldelkrllrdllevRlakirkfaenl 89
                                   +++  e    l+++k++l d+l+vRl k+++   ++
  gene885|gene885|rna885|rna885 12 SLYEQE----LERVKYILTDYLRVRLIKLQNNFYVN 43
                                   333334....5669***************9987655 PP

>> DUF4834  Domain of unknown function (DUF4834)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   3.0   1.9e-05      0.17      67      97 ..      51      80 ..      34      82 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.9e-05
                        DUF4834 67 geiieeersekeakrkkiFekdeGEYVdFEE 97
                                   +++ +++  ek  k+  iF++++ EYVdFE 
  gene885|gene885|rna885|rna885 51 EKVFYQKLVEK-FKEYDIFTEQNEEYVDFEC 80
                                   44444444444.66669*************5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       993  (0.0553851); expected 358.6 (0.02)
Passed bias filter:                      454  (0.0253221); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 844.89
//
Query:       gene886|gene886|rna886|rna886  [L=167]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-29  102.2   0.0    3.2e-29  102.0   0.0    1.0  1  YjeF_N    YjeF-related protein N-terminus


Domain annotation for each model (and alignments):
>> YjeF_N  YjeF-related protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.0   0.0   1.8e-33   3.2e-29      25     171 .]       4     136 ..       1     136 [. 0.90

  Alignments for each domain:
  == domain 1  score: 102.0 bits;  conditional E-value: 1.8e-33
                         YjeF_N  25 aekkvlvlvGsgnnGgdglaaArhLaqegakVtvllleeeekldedaeralellkkaggkvveekpeedleeklsapvdl 104
                                     + ++lv++G+gnnG+dgl++Ar+L   g++V v+ +      + ++++ ++++k +g+ ++++ p++ l+      +++
  gene886|gene886|rna886|rna886   4 RASNILVVCGPGNNGSDGLVIARYLKLSGYDVLVF-Y-----KKLKHQNLVNIAKSVGVAFTTNWPDDILH------YEC 71 
                                    5679******************************5.3.....345689999***********999999986......*** PP

                         YjeF_N 105 viDAllGiglrgelreelaeliewlnsseapvlavDiPSGldadtGavsgtavkadvtvtfgapkrg 171
                                    viDA++G++++ +lre++ ++++ +  + + v+++D+PSG++ ++ + +   + ++++v+f apk +
  gene886|gene886|rna886|rna886  72 VIDAMFGFSFKPPLREPFSSIVSCISGH-NNVISIDVPSGYEINNEHNNHSFI-PKHVVCFVAPKIC 136
                                    **********************888776.69**********999988885555.***********87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       616  (0.0343577); expected 358.6 (0.02)
Passed bias filter:                      441  (0.024597); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.31s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 1077.67
//
Query:       gene887|gene887|rna887|rna887  [L=82]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.13   12.4   0.3       0.15   12.1   0.3    1.1  1  TerY_C    TerY-C metal binding domain


Domain annotation for each model (and alignments):
>> TerY_C  TerY-C metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.3   8.6e-06      0.15       4      49 ..      10      56 ..       7      59 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 8.6e-06
                         TerY_C  4 fvvlvgkCqktkr...pYllkyerelqevaleelkleveeyrlagaypi 49
                                   + +  +kC +tk+   pY++ky  + ++   e ++l+++ y +  ++ i
  gene887|gene887|rna887|rna887 10 ICMWLSKCPHTKHvllPYFMKYRNKYEK--EEPYELNTRAYIYLVCFSI 56
                                   5566789999886444899***995555..5566788888988888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       924  (0.0515366); expected 358.6 (0.02)
Passed bias filter:                      556  (0.0310112); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 563.82
//
Query:       gene888|gene888|rna888|rna888  [L=491]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.4e-22   80.7   0.0    2.3e-22   80.0   0.0    1.3  1  ABC_tran      ABC transporter
    2.8e-05   24.4   0.0    5.8e-05   23.4   0.0    1.5  1  AAA_22        AAA domain
    0.00039   19.9   0.1      0.097   12.1   0.1    2.2  2  SMC_N         RecF/RecN/SMC N terminal domain
     0.0017   18.3   0.6     0.0097   15.9   0.1    2.4  2  Rad17         Rad17 P-loop domain
     0.0026   17.7   0.0      0.046   13.6   0.0    2.3  2  RsgA_GTPase   RsgA GTPase
     0.0029   17.6   0.0      0.005   16.8   0.0    1.4  1  ATPase_2      ATPase domain predominantly from Archaea
     0.0033   18.0   1.0       0.39   11.3   0.2    2.7  2  AAA_18        AAA domain
     0.0036   17.2   0.0        1.9    8.3   0.0    2.5  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
     0.0057   16.2   0.1      0.011   15.3   0.1    1.4  1  AAA_25        AAA domain
      0.006   17.0   0.0      0.011   16.1   0.0    1.5  1  AAA_16        AAA ATPase domain
     0.0087   16.2   0.0      0.024   14.8   0.0    1.7  1  AAA_33        AAA domain
     0.0094   16.4   0.5      0.058   13.8   0.5    2.2  1  AAA           ATPase family associated with various cellular 
  ------ inclusion threshold ------
      0.028   14.9   0.6       0.23   12.0   0.6    2.1  1  AAA_23        AAA domain
      0.036   14.0   0.2      0.088   12.7   0.0    1.7  2  NACHT         NACHT domain
      0.064   13.6   0.0       0.17   12.3   0.0    1.8  1  RNA_helicase  RNA helicase
      0.069   13.0   0.0       0.19   11.7   0.0    1.7  1  Tudor-knot    RNA binding activity-knot of a chromodomain
       0.07   12.9   0.0       0.23   11.2   0.0    1.9  2  PRK           Phosphoribulokinase / Uridine kinase family
      0.093   12.4   0.0        0.2   11.4   0.0    1.6  1  AAA_24        AAA domain
       0.21   11.8   0.0       0.39   11.0   0.0    1.4  1  AAA_28        AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.0   0.0   2.4e-25   2.3e-22      13     137 .]      41     174 ..      33     174 .. 0.92

  Alignments for each domain:
  == domain 1  score: 80.0 bits;  conditional E-value: 2.4e-25
                                    EEEEEESTTSSHHHHHHHHTTSS--...SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH.......... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......... RF
                       ABC_tran  13 kvaivGenGaGKStLlkllagllkp...teGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren.......... 79 
                                    ++a++G++G+GK+t+l++lag +     t+G ++++gk+ +     ++ ++i+++ q++ + + +++r++          
  gene888|gene888|rna888|rna888  41 LLAVMGPSGCGKTTFLRMLAGRVPSgsiTAGYVHYNGKERNI---DQWLNNIAYVGQNDVIYKYMSARDHvvysalfnrk 117
                                    689********************8888899999999877655...9*******************9***********999 PP

                                    ...HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                    ...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  80 ...esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                       + +++i+ + ++l++++l ++++     +LS Gq++rv +a+ l+k+p+++++DEpt+
  gene888|gene888|rna888|rna888 118 kirNLKQKIKLLFDRLDITKLMHKKM----DKLSNGQRKRVLIAMELIKEPDIVIMDEPTS 174
                                    99999999999999999999999999....*****************************96 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.0   6.2e-08   5.8e-05       4      96 ..      38     156 ..      35     192 .. 0.84

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 6.2e-08
                         AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaee................................erpevvfvtlpsst 51 
                                    ++g+l+v+G+sG+GKTt lr+l+ + +  +  +                                 +r++vv+  l + +
  gene888|gene888|rna888|rna888  38 EEGLLAVMGPSGCGKTTFLRMLAGRVPSGSITAGyvhyngkernidqwlnniayvgqndviykymsARDHVVYSALFNRK 117
                                    6899**********************999888889999999999999999999999999999999999999999999999 PP

                         AAA_22  52 sskdllrellralglelkaerlsseell.ealeqalraravielli 96 
                                    + ++l +++   ++      rl+   l+ +++ + ++ +++ ++li
  gene888|gene888|rna888|rna888 118 KIRNLKQKIKLLFD------RLDITKLMhKKMDKLSNGQRK-RVLI 156
                                    99999999999999......466677884555555555555.5555 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.7   0.0    0.0092       8.7      19      41 ..      34      56 ..      25      60 .. 0.85
   2 !   12.1   0.1    0.0001     0.097     121     201 ..     124     206 ..      79     224 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0092
                                   EEETTSSEEEEEESTTSSHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 19 ilpfsksftaivGpNGSGKsnll 41
                                    +++++++ a++Gp G+GK+ +l
  gene888|gene888|rna888|rna888 34 CGEMEEGLLAVMGPSGCGKTTFL 56
                                   67889999************986 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.0001
                                    HHHHHHHHCTT-STT......CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEE CS
                                    xxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 121 kevsellesagiske......lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfiv 194
                                    ++++ l+ + +i+k        LS G+++     +l+A++ +k   ++++De  + LD++    ++++lke   +  +++
  gene888|gene888|rna888|rna888 124 QKIKLLFDRLDITKLmhkkmdKLSNGQRKR----VLIAMELIKEPDIVIMDEPTSGLDNTSAFYLVQFLKEYALSGRIVI 199
                                    4555555555554434444448999*9984....456677789999**************************99999888 PP

                                    E-SSHHH CS
                                    xxxxxxx RF
                          SMC_N 195 islreem 201
                                     s+++  
  gene888|gene888|rna888|rna888 200 CSIHQPD 206
                                    8887754 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1     1e-05    0.0097      45      66 ..      39      60 ..      28      70 .. 0.84
   2 ?   -1.0   0.0       1.6   1.5e+03      94     118 ..     264     287 ..     225     293 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1e-05
                          Rad17 45 kriLLisGPsGCgkstvvkvLs 66
                                   + +L + GPsGCgk+t +++L+
  gene888|gene888|rna888|rna888 39 EGLLAVMGPSGCGKTTFLRMLA 60
                                   55999***************98 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.6
                          Rad17  94 gltekesrflsqiesfkeleLkdak 118
                                    g  + +s +l ++e f+e +Lk +k
  gene888|gene888|rna888|rna888 264 GFYDANS-MLRLCEIFNENQLKYSK 287
                                    4444444.78999999999999887 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.0   4.9e-05     0.046      84     122 ..      24      62 ..       3      81 .. 0.77
   2 ?    1.3   0.0       0.3   2.9e+02      20      63 ..     197     237 ..     193     272 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.9e-05
                                    TTTHTTHHHHHHHCTTSEEEEECSTTSSHHHHHHHHCTT CS
                    RsgA_GTPase  84 aktkegleelkellkdktsvlvGqSGvGKStLinallpe 122
                                     ++   l+++  ++++ + +++G+SG GK+t++ +l+++
  gene888|gene888|rna888|rna888  24 GTNFCVLSDMCGEMEEGLLAVMGPSGCGKTTFLRMLAGR 62 
                                    4445556677778899999****************9986 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.3
                                    EEEEESTTTT--.HHHHHHHHHHHHHTT-EEEEEEE-GGG--HHH CS
                    RsgA_GTPase  20 livvslkepels.lnlldrfLvlaeekgiepvivlnKiDlleeee 63 
                                    ++++s+++p+ + +n  dr+Lvl        +i l K + +ee  
  gene888|gene888|rna888|rna888 197 IVICSIHQPDERtVNVFDRILVLNT----GHTIFLGKKETCEELL 237
                                    7999999997651678899999854....4567778887777765 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   5.3e-06     0.005      18     114 ..      37     134 ..      29     187 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 5.3e-06
                       ATPase_2  18 epneiyfiYGpegsGKtaLlkeiienledkdkyviyy.ialreesiskldefieeeeekkklekalgiavpkaeleeilk 96 
                                     ++  + + Gp g+GKt++l+ ++ +  + +    y+ ++ +e++i++  + i+   +++ + k++ +a   +   ++++
  gene888|gene888|rna888|rna888  37 MEEGLLAVMGPSGCGKTTFLRMLAGRVPSGSITAGYVhYNGKERNIDQWLNNIAYVGQNDVIYKYM-SARDHVVYSALFN 115
                                    555667899******************888888888746899999999999999777777777776.4444445556677 PP

                       ATPase_2  97 .eksklvfkaielllekik 114
                                     +k+++++++i+ll++ + 
  gene888|gene888|rna888|rna888 116 rKKIRNLKQKIKLLFDRLD 134
                                    7888888888888887664 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.2   0.00042      0.39       2      25 ..      43      78 ..      42     176 .. 0.71
   2 ?    4.5   0.0     0.049        47      10      59 ..     228     285 ..     227     291 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00042
                         AAA_18  2 lltGtpGvGKttlakeLskrlgf............g 25
                                   +++G++G+GKtt+ + L+ r  +             
  gene888|gene888|rna888|rna888 43 AVMGPSGCGKTTFLRMLAGRVPSgsitagyvhyngK 78
                                   589**************8774223344444544541 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.049
                         AAA_18  10 GKttlakeLskrlgf........gvnlrdvakenglllevdpealdeskrldedkldk 59 
                                    GK + ++eL + +++        +++ +++++ ++  +++ + +l+ +++++e++l++
  gene888|gene888|rna888|rna888 228 GKKETCEELLRQNKIvrspfmsfSTHMMELCWSENDGFYDANSMLRLCEIFNENQLKY 285
                                    9********8887778899999999999999999999999999999999999999876 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.1   0.0    0.0089       8.4       3      20 ..      43      60 ..      41      80 .. 0.83
   2 !    8.3   0.0     0.002       1.9     235     290 ..     144     196 ..     109     206 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0089
                         AAA_21  3 vliGpNgsGKSnLLdald 20
                                   ++ Gp g+GK+++L+ l 
  gene888|gene888|rna888|rna888 43 AVMGPSGCGKTTFLRMLA 60
                                   677***********9884 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.002
                         AAA_21 235 relSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrnga 290
                                    ++lS G+++   ++  l+  +   ++++ DEp +gL+      l+++lke +  g 
  gene888|gene888|rna888|rna888 144 DKLSNGQRKRVLIAMELIKEP---DIVIMDEPTSGLDNTSAFYLVQFLKEYALSGR 196
                                    566999998866666666655...*************9999999999987766444 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.1   1.2e-05     0.011      32     150 ..      38     171 ..      30     180 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.2e-05
                         AAA_25  32 agelallaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEdsedelrrRlravgeal.............. 97 
                                    +++l +++G++g+GKtt++  la  v +G+        + g V y   E + d++ + ++ vg++               
  gene888|gene888|rna888|rna888  38 EEGLLAVMGPSGCGKTTFLRMLAGRVPSGSI-------TAGYVHYNGKERNIDQWLNNIAYVGQNDviykymsardhvvy 110
                                    578999**********************993.......566788888888888888888877755457777766666666 PP

                         AAA_25  98 ............rddarllvldlagveslpLfakdrggtlltadvdaleaaieevegvrlvviDp 150
                                                +++ +ll+  l    +++ ++ ++ ++l +++ +++  a+e +++++ v+ D 
  gene888|gene888|rna888|rna888 111 salfnrkkirnlKQKIKLLFDRL----DITKLMHKKMDKLSNGQRKRVLIAMELIKEPDIVIMDE 171
                                    66666666653322222222222....22222335566667788888888888888888888875 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   1.2e-05     0.011      24      51 ..      39      66 ..      29     159 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.2e-05
                         AAA_16 24 pelvllsGesGvGKsslvrellralekd 51
                                   ++l+ + G+sG+GK++ +r+l+ ++   
  gene888|gene888|rna888|rna888 39 EGLLAVMGPSGCGKTTFLRMLAGRVPSG 66
                                   48999***************99766544 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   2.5e-05     0.024       2      85 ..      42     120 ..      41     143 .. 0.63

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.5e-05
                         AAA_33   2 vllvGlpGsGKstlaerllkklgavllssdtlrrrlfgtdqqsktdytrvldr.lyqilnelarkalsagrnvildatnl 80 
                                    + + G++G+GK+t+++ l+ + +   ++  +    + ++++++     ++l++ +y  +n+++ k++sa+ +v+  a + 
  gene888|gene888|rna888|rna888  42 LAVMGPSGCGKTTFLRMLAGRVPSGSITAGY----VHYNGKERN--IDQWLNNiAYVGQNDVIYKYMSARDHVVYSALFN 115
                                    6789*************99665533333333....223333322..2345555355577777777777777777777666 PP

                         AAA_33  81 srrer 85 
                                    +++ r
  gene888|gene888|rna888|rna888 116 RKKIR 120
                                    65444 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.5   6.2e-05     0.058       3      33 ..      44      79 ..      42     207 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 6.2e-05
                                   EESSTTSSHHHHHHHHHHHH.....THEEEEEETTT CS
                            AAA  3 lyGppGtGKTllakavakel.....gvefleisgse 33
                                   ++Gp G+GKT++ + +a  +      + ++  +g+e
  gene888|gene888|rna888|rna888 44 VMGPSGCGKTTFLRMLAGRVpsgsiTAGYVHYNGKE 79
                                   79***************9964333323333333333 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.6   0.00024      0.23      18     118 ..      38     136 ..      26     155 .. 0.58

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00024
                         AAA_23  18 skgltlItGpNGaGKTTildAiklaLygetprlsrksgr.gfeksdveiesegkvkay...veltfenkdgrytrsiere 93 
                                    + gl ++ Gp G+GKTT+l+ +     g++p  s + g  +++  + +i ++ ++ ay    ++ +++ + r  + + ++
  gene888|gene888|rna888|rna888  38 EEGLLAVMGPSGCGKTTFLRMLA----GRVPSGSITAGYvHYNGKERNIDQWLNNIAYvgqNDVIYKYMSAR--DHVVYS 111
                                    6799999************9765....333333332222244444444444433333323344444444443..345566 PP

                         AAA_23  94 relskkkgkttkkaklelleidele 118
                                       ++kk ++ k++++ l++  + +
  gene888|gene888|rna888|rna888 112 ALFNRKKIRNLKQKIKLLFDRLDIT 136
                                    6666666666666666666665555 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   9.3e-05     0.088       3      26 ..      42      65 ..      40      76 .. 0.82
   2 ?   -3.5   0.0       8.9   8.4e+03      78      94 ..     121     137 ..     105     162 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 9.3e-05
                                   EEEEC-TTTCHHHHHHHHHHHHCT CS
                          NACHT  3 vilqGeaGsGKTtLlqklalawae 26
                                   +++ G++G+GKTt+l+ la    +
  gene888|gene888|rna888|rna888 42 LAVMGPSGCGKTTFLRMLAGRVPS 65
                                   7899************99876655 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 8.9
                                    CSCCCEEEEEE-STT-S CS
                          NACHT  78 elperlLlilDglDelv 94 
                                     l++++ l++D lD ++
  gene888|gene888|rna888|rna888 121 NLKQKIKLLFDRLDITK 137
                                    55666667777777554 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00018      0.17       3      27 ..      44      81 ..      42     152 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00018
                   RNA_helicase  3 lyGpsgeGKStlakeLakallkkl.............k 27
                                   + Gpsg+GK+t+ + La ++ + +             +
  gene888|gene888|rna888|rna888 44 VMGPSGCGKTTFLRMLAGRVPSGSitagyvhyngkerN 81
                                   89*************99988744434444444443331 PP

>> Tudor-knot  RNA binding activity-knot of a chromodomain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0    0.0002      0.19      34      49 ..      72      87 ..      63      89 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.0002
                                   EEEETTS-CCC-EEEE CS
                     Tudor-knot 34 YVHYeefNkRlDeWVs 49
                                   YVHY +  ++ D+W +
  gene888|gene888|rna888|rna888 72 YVHYNGKERNIDQWLN 87
                                   **************85 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00024      0.23       2      29 ..      42      69 ..      41     128 .. 0.84
   2 ?   -2.4   0.0       3.6   3.4e+03     128     144 ..     448     464 ..     436     465 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00024
                            PRK  2 IgvagsSGaGkttvarklekifgrekvk 29
                                   ++v g+SG+Gktt+ r l  ++   +++
  gene888|gene888|rna888|rna888 42 LAVMGPSGCGKTTFLRMLAGRVPSGSIT 69
                                   689************9998766655555 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 3.6
                            PRK 128 elldlkiyvdisidlel 144
                                     ll ++i+vd++ d+++
  gene888|gene888|rna888|rna888 448 GLLSMNIFVDAIFDMRF 464
                                    58899******999987 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00021       0.2       6      24 ..      43      61 ..      41     126 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00021
                         AAA_24  6 liyGpsgiGKTtlakelgp 24
                                   +++Gpsg GKTt++++l  
  gene888|gene888|rna888|rna888 43 AVMGPSGCGKTTFLRMLAG 61
                                   79************99844 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00041      0.39       3      22 ..      43      62 ..      41      82 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00041
                         AAA_28  3 vitGgestGKTtlleaLaar 22
                                   +++G++++GKTt l+ La r
  gene888|gene888|rna888|rna888 43 AVMGPSGCGKTTFLRMLAGR 62
                                   789**************966 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (491 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       806  (0.0449551); expected 358.6 (0.02)
Passed bias filter:                      523  (0.0291706); expected 358.6 (0.02)
Passed Vit filter:                        95  (0.00529868); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.63u 0.29s 00:00:00.92 Elapsed: 00:00:00.45
# Mc/sec: 3275.43
//
Query:       gene889|gene889|rna889|rna889  [L=238]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (238 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       818  (0.0456244); expected 358.6 (0.02)
Passed bias filter:                      504  (0.0281109); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1657.40
//
Query:       gene89|gene89|rna89|rna89  [L=108]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.3e-13   48.6   0.7    7.1e-13   48.5   0.7    1.0  1  PIF1      PIF1-like helicase
  ------ inclusion threshold ------
      0.048   14.2   0.0      0.075   13.5   0.0    1.3  1  MyTH4     MyTH4 domain


Domain annotation for each model (and alignments):
>> PIF1  PIF1-like helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.5   0.7   7.9e-17   7.1e-13     169     273 ..       2      85 ..       1      94 [. 0.88

  Alignments for each domain:
  == domain 1  score: 48.5 bits;  conditional E-value: 7.9e-17
                                ...CSCHHHH--EEEE-S-STTTT...........HHHHHHHHHHHCT---CCCCHH.................HHCHCCS--- CS
                       PIF1 169 sikeSklWkevkvlkLtknmRllsesldetekkelkeFskwllkigdGkineedeeealieiPedlllkksedkieeivsevyg 252
                                sik+S+lWk+v+vlkL +nmR +++          +eFskwll+ig+G  ne++    l+eiP++ +        ++i++e+y+
  gene89|gene89|rna89|rna89   2 SIKCSRLWKHVRVLKLSQNMRAANQ----------EEFSKWLLDIGNGLSNERS----LVEIPQQYI------ANKDIANEIYE 65 
                                79*********************97..........89***********876654....899*****9......67889****** PP

                                SS--...........EEEESS CS
                       PIF1 253 dllqeltdkeyleerailcpt 273
                                dl+++l++ + l++++il  +
  gene89|gene89|rna89|rna89  66 DLINSLNSAN-LTNKTILSYR 85 
                                ****888877.8899998755 PP

>> MyTH4  MyTH4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   8.4e-06     0.075       6      56 ..      48     102 ..      44     107 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 8.4e-06
                                HHHHHHHH-GGGHHHHHHHHHHCTTT-S....-HHHHHHHHHHHHHHHCC----C CS
                      MyTH4   6 nilqkglskeeLrdEiycqlikQttenp....nkesaergwqLlalclslfpPsk 56 
                                +i q+ + ++++ +Eiy  li+ +++ +    +  s +r+ q+ + ++++f+P +
  gene89|gene89|rna89|rna89  48 EIPQQYIANKDIANEIYEDLINSLNSANltnkTILSYRRHLQINLKLITFFAPRS 102
                                678999********************99875445889999999999999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       640  (0.0356964); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 741.94
//
Query:       gene890|gene890|rna890|rna890  [L=827]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.4e-74  250.0   5.3    2.5e-48  164.7   0.8    2.4  2  CTP_synth_N    CTP synthase N-terminus
      1e-41  142.8   0.2    5.5e-22   78.5   0.0    2.6  2  GATase         Glutamine amidotransferase class-I
    1.3e-06   28.3   0.0      0.034   13.9   0.0    2.6  2  Peptidase_C26  Peptidase C26
  ------ inclusion threshold ------
      0.048   13.7   0.0       0.11   12.5   0.0    1.8  1  CbiA           CobQ/CobB/MinD/ParA nucleotide binding domain


Domain annotation for each model (and alignments):
>> CTP_synth_N  CTP synthase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  164.7   0.8   5.5e-52   2.5e-48       1     130 [.      17     146 ..      17     185 .. 0.91
   2 !   87.1   0.3   2.7e-28   1.2e-24     122     265 .]     261     405 ..     251     405 .. 0.88

  Alignments for each domain:
  == domain 1  score: 164.7 bits;  conditional E-value: 5.5e-52
                                    EEEEEEE--STTTTHHHHHHHHHHHHHCTT--EEEEEEE-SSSSSSTT--CCCC--EEE-TT--EEETHHHHHHHHHT-- CS
                    CTP_synth_N   1 kyilvtGGvvSglGkGiiaaslgallksrglkvtlikiDPYlnvdagtlsplehGEvfvlddGaetDlDlGnYeRfldik 80 
                                    ky++v+GG +Sg+GkGi+ +s+g +l++ g+kv  +kiDPYln  +gt+spl+hGEvfvl+dG e+D+DlG YeR +d+ 
  gene890|gene890|rna890|rna890  17 KYVIVAGGTLSGIGKGITLSSIGLILRTAGMKVIPVKIDPYLNKSCGTISPLDHGEVFVLEDGCEADMDLGFYERIMDVL 96 
                                    8******************************************************************************* PP

                                    --GGGEEEHHHHHHHHHHHHHTTTTTT----CCCHHHHHHHHHHHHHH.H CS
                    CTP_synth_N  81 ltkennittGkiyksviekerrGdylGktvqviphvtdeikeriekvakk 130
                                    + + ++it Gk+y+++i +e  G y G+t++v+phv   ++++i++  ++
  gene890|gene890|rna890|rna890  97 CCEMSCITGGKVYRRMIARENAGMYFGETMEVVPHVNAVVEDMIHDRVRM 146
                                    *************************************9999999865543 PP

  == domain 2  score: 87.1 bits;  conditional E-value: 2.7e-28
                                    HHHHHHH.HC....T-SEEEEEE-S-TTSGGGHHHHHHHHHHHHHH-TTTEEEEEEEE--B-TTTSSB-HHHHHHHHHHH CS
                    CTP_synth_N 122 eriekvakkv....eadvviveigGtvgdieslpfleairqlklelgkenvllihvtlvpvlkaagelktkptqhsvkel 197
                                    + ++k++  +    +  vv+ve+gG + d e+  f  +++++k++  ke++l++ v ++p ++ ++e+ktk +q+sv+++
  gene890|gene890|rna890|rna890 261 NAMHKTKAYKtintDDVVVLVEVGGVIDDKENDIFSSTLSHIKQKCAKEDFLVVSVDYMPSFS-NSEQKTKLIQRSVQKF 339
                                    33333332212321355789******************************************5.99************** PP

                                    HHHT---SEEEEEESS---HHHHHHHHHHCT--GGGEEEEE--S-GGGHHHHHHHCTHHHHHHHHTT- CS
                    CTP_synth_N 198 rslGiqpdiivcrsekeleeevkekialfcnvekeavisvkdvesiyevpllleeqglaelileklkl 265
                                     s  ++pdi+vcr  +++ + +k ki   + v  ++v+s+kd++ +ye+p  l+ qg+ e++l+ l++
  gene890|gene890|rna890|rna890 340 ISRDLKPDIVVCRGPNAFFKGTKGKIVAKTGV--RNVFSSKDTSMVYEIPFDLQAQGMREALLSSLNI 405
                                    **************************999999..68***************************99985 PP

>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.5   0.0   1.2e-25   5.5e-22       4     130 ..     441     587 ..     439     616 .. 0.78
   2 !   61.7   0.1   1.7e-20   7.4e-17     104     189 ..     730     819 ..     707     820 .. 0.91

  Alignments for each domain:
  == domain 1  score: 78.5 bits;  conditional E-value: 1.2e-25
                                    ESSTSTHHHHHHHHHHTT-EEEEEETTSHHHHH.............HH.THHSTSEEEEEEESSCTTTTTHHHHHHHHCT CS
                         GATase   4 Dnydsvtenlvhalvelgvkvevvpidasaeei.............le.llknpdgilvsgGpgspgvegkieaikeare 69 
                                    D+y sv+ +l+ +++ +++++ ++ +d++  e+             l  + +++d ilv+gG+g +g+egki+ai++ar+
  gene890|gene890|rna890|rna890 441 DSYVSVIDALKVCALMMNIDLSIKTVDSETIEKetdalpdgdvnavLGrIFSGCDCILVPGGFGMRGTEGKISAINYART 520
                                    9**************************966666799**99998776224699**************************** PP

                                    STS-EEEETHHHHHHHHHTTTEEE........................EEECEEEEEEEEEEEETTTCGGTTTTSEEEEE CS
                         GATase  70 nkiPiLGICLGmQllaiefgrkvv........................kekekehhggtmrlgddetallyglknevier 125
                                    n+iP+LGICLG+Ql +ief+r+v                         + k ++   g mrlg+++t             
  gene890|gene890|rna890|rna890 521 NRIPFLGICLGFQLSVIEFCRNVLglkdatseefdstsmtkvvmvmedH-KIEKIVSGRMRLGSKHT------------- 586
                                    *********************9998888877655555555554555422.22445555555555444............. PP

                                    EEEEE CS
                         GATase 126 hrHry 130
                                        y
  gene890|gene890|rna890|rna890 587 ----Y 587
                                    ....3 PP

  == domain 2  score: 61.7 bits;  conditional E-value: 1.7e-20
                                    EEEEEETTTCGGTTTTSEEEEEEEEEEEEESG...CHHHTTEEEEEEEETTEEEEEEEEETT.T.EEEESSBTTSTTSTT CS
                         GATase 104 tmrlgddetallyglknevierhrHryevnpk...elepaglevtakseddeelmeiiekkn.p.fvgvQFHPEststpe 178
                                    + +++d++++ + +++  + erhrHryevnp     +e +gl++++ks+d+   m ++e+++ p fvgvQ+HPE+t++  
  gene890|gene890|rna890|rna890 730 NNKCNDYNCNNADDSSHYIVERHRHRYEVNPLyveMIERKGLKFVGKSQDG-LKMDVFELNDhPfFVGVQYHPEMTLNLD 808
                                    6788999999********************989989999*********887.9*********9***************** PP

                                    HHHHHHHHHHH CS
                         GATase 179 gpellfnflik 189
                                    + ++lf+ ++k
  gene890|gene890|rna890|rna890 809 DGHPLFRYFLK 819
                                    ******99876 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.0   3.6e-05      0.16      98     180 ..     515     591 ..     508     599 .. 0.68
   2 !   13.9   0.0   7.7e-06     0.034     169     216 .]     757     802 ..     717     802 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.6e-05
                  Peptidase_C26  98 iraalergvPilgiCrGlqllnvalGGtlyqdieeqsgltdhrehe..qsaashavkvekgsllaellgseeievnslHh 175
                                    i+ a ++++P lgiC+G+ql  + +  ++   ++      d +++e  ++ +++ v v ++  ++++++  +++  s H 
  gene890|gene890|rna890|rna890 515 INYARTNRIPFLGICLGFQLSVIEFCRNVLG-LK------DATSEEfdSTSMTKVVMVMEDHKIEKIVS-GRMRLGSKHT 586
                                    67788999***********986665443322.22......22222211355677788888888888887.7888888888 PP

                  Peptidase_C26 176 qaike 180
                                      ++ 
  gene890|gene890|rna890|rna890 587 YLVDS 591
                                    77776 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 7.7e-06
                  Peptidase_C26 169 evnslHhqaikelaeelrveAvaeDgv.iEaieseeakafvlgvQwHPE 216
                                    evn l    i++  ++l+ +  ++Dg+ +  +e+++++ f++gvQ+HPE
  gene890|gene890|rna890|rna890 757 EVNPLYVEMIER--KGLKFVGKSQDGLkMDVFELNDHP-FFVGVQYHPE 802
                                    555555555554..789999999***879999999988.*********9 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   2.5e-05      0.11       2      43 ..      21      62 ..      19     423 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.5e-05
                                   EEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCC CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           CbiA  2 aiastkGGvGKTtlaanLaralarrglrVllvDaDpqannla 43
                                   ++ +t +G GK  ++ +++ +l  +g +V++v+ Dp  n + 
  gene890|gene890|rna890|rna890 21 VAGGTLSGIGKGITLSSIGLILRTAGMKVIPVKIDPYLNKSC 62
                                   445677******************************987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (827 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       832  (0.0464053); expected 358.6 (0.02)
Passed bias filter:                      493  (0.0274974); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.74u 0.32s 00:00:01.06 Elapsed: 00:00:00.51
# Mc/sec: 4861.17
//
Query:       gene891|gene891|rna891|rna891  [L=687]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-27   96.7   0.0    3.3e-27   95.5   0.0    1.5  1  Peptidase_M24    Metallopeptidase family M24
    1.3e-25   90.4   0.8    2.8e-24   86.0   0.2    2.6  2  Creatinase_N_2   Creatinase/Prolidase N-terminal domain
    2.2e-15   56.4   0.1    5.1e-15   55.3   0.1    1.7  1  Peptidase_M24_C  C-terminal region of peptidase_M24
    4.2e-11   43.6   0.0    1.1e-10   42.3   0.0    1.7  1  Creatinase_N     Creatinase/Prolidase N-terminal domain


Domain annotation for each model (and alignments):
>> Peptidase_M24  Metallopeptidase family M24
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.5   0.0   7.4e-31   3.3e-27       5     205 ..     392     619 ..     389     621 .. 0.80

  Alignments for each domain:
  == domain 1  score: 95.5 bits;  conditional E-value: 7.4e-31
                                    HHHHHHHHHHHHHHHHHHT.....TCBHHHHHHHHHHHHHHHTT................................TCEE CS
                  Peptidase_M24   5 kaariasaaleavleaikp.....gvterelaaeieattlkrhg................................argl 47 
                                    +a+ i+  al++++ +ik+     ++te ++ +++ +   kr+                                 +   
  gene891|gene891|rna891|rna891 392 QANIIDGIALTRLFVWIKHafqkdKITEIQISKKLLEI--KRELctsfankmkadvnnhgsciedsitnkylsrgcFVSE 469
                                    78888888888888888853333356777777777755..3322223333333444444577777777777766678999 PP

                                    SSSSEEEEGGGGGSTTTBCSSSB--TTEEEEEEEEEEETTEEEEEEEEEECSSGSHHHHHHHHHHHHHHHHHHHC-ST.T CS
                  Peptidase_M24  48 afppivasgenaavlhytpndrvlkegdlvlidagaeydgyasDitrTvlvGkftpeqrelyeavleaqeaaikavkp.G 126
                                    +f+ iv++g naa++hy  +d  ++++ ++l+d+g ++   ++DitrT+++Gk   + re ++ vl++q +   ++ p +
  gene891|gene891|rna891|rna891 470 SFESIVGVGSNAAIIHYKGGDINVENNNVLLMDSGSQFLFGTTDITRTLFLGKSPSKFREYFTRVLKGQITSKTLIAPqD 549
                                    ****************************************************88889*********************88 PP

                                    SBHHHHHHHHHHHHHHTTBCCGBSSCSEEEESS..SSSEEEEEESSSTTCSSB--TTBEEEEEEEEEEETTTEEEEEBEE CS
                  Peptidase_M24 127 vtlseidaaarevlesaglakffphglGHgvGl..evhdegpsvsresndgrkleeGmvftiEpgiyfapgeggvriedt 204
                                    + l+ + ++ar +l++  ++ +++hg+ HgvG+   vh++ p+        r + + ++f++Epg+y  ++e+gvried+
  gene891|gene891|rna891|rna891 550 RFLQMVCNVARLYLWN--IKCDYRHGTSHGVGHssLVHESLPF--------RSIVPHQMFSVEPGVY-LENEFGVRIEDV 618
                                    88*************7..66799*********43367766443........5699************.88999******9 PP

                                    E CS
                  Peptidase_M24 205 v 205
                                    v
  gene891|gene891|rna891|rna891 619 V 619
                                    8 PP

>> Creatinase_N_2  Creatinase/Prolidase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0     0.044     2e+02      68     140 ..      46     119 ..      32     132 .. 0.70
   2 !   86.0   0.2   6.3e-28   2.8e-24      12     161 .]     245     386 ..     232     386 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.044
                                    EEEEEES.S-EEEEE-GGG-..-HHHHHHHTTEEEE-GGGHHHHHHHHHHHH----EEE-TTSBHHHHHHH-....G CS
                 Creatinase_N_2  68 syaivtkdekatLFvdeeklteevkehleengveikpyeevvsdlkalasaskkkvlldpsktsyalasalk....e 140
                                    + +++t+ ++ +L++d + +  +++++l+ ++  +k+++   s+l+ + ++   ++ +d +++ ++ ++++k    e
  gene891|gene891|rna891|rna891  46 ATVLITS-DHNFLYTDGRYF-IQAEKELK-DNFVLKKIDVDQSYLEYIRDNVVGNIGMDVNRVDIKTYKMIKnvlaE 119
                                    5677776.599999999976.56777885.46777777733667777765445677788888888888887423333 PP

  == domain 2  score: 86.0 bits;  conditional E-value: 6.3e-28
                                    E--HHHHSS-HHHHHHHHHHHHHHTT-SEEEE-SHHHHHHHTTEE--SBTTB----EEEEEES.S-EEEEE-GGG-..-H CS
                 Creatinase_N_2  12 vlpeeyaGesvaeKlerlrkelkkkkadalvlsaldeiAWllNlRGsDipynPvflsyaivtkdekatLFvdeeklteev 91 
                                    +l+ ++aG s+ +K++ lr+ l++   +++++s +deiA+llNlRG+Dipyn +f+sy++v+k ++a+LF++++++    
  gene891|gene891|rna891|rna891 245 ILNSSIAGISSDDKIALLRHSLDD--SECMIISLMDEIAYLLNLRGTDIPYNLLFFSYMFVDK-KNAVLFTNSKNV---- 317
                                    577899****************96..79*********************************76.6*******9986.... PP

                                    HHHHHHTTEEEE-GGGHHHHHHHHHHHH----EEE-TTSBHHHHHHH-........GGGEEE-S-HHHHHHHC--HHH CS
                 Creatinase_N_2  92 kehleengveikpyeevvsdlkalasaskkkvlldpsktsyalasalk........ekkvveeespiallKavKNevE 161
                                         + +v i++y+e+  +l+a+ +++   + l+ + t ++++  ++         k v   ++ i+ lK+vKN  E
  gene891|gene891|rna891|rna891 318 -----KRNVCIRSYDEFECFLDAFYQNT-GDIKLN-DYTRVYVSLDVNagiciklgCKAV--VSDFIQKLKSVKNTNE 386
                                    .....45799*******99****99744.455554.444444444433333322324444..379**********987 PP

>> Peptidase_M24_C  C-terminal region of peptidase_M24
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.3   0.1   1.1e-18   5.1e-15       2      63 .]     626     685 ..     625     685 .. 0.95

  Alignments for each domain:
  == domain 1  score: 55.3 bits;  conditional E-value: 1.1e-18
                                    EEEEEES------STT--GGGS-HHHHHHHHHHHHHHHHHHHHHHHHT-H.HHHHHHHT--- CS
                Peptidase_M24_C   2 fleFetlTlvPidrklIdvslLtpeEiawLnaYhakvreklsplLeeeneeleWLkraTrpl 63 
                                    +l+   l +vP++r+lI++++L + E ++Ln Y+ +vr+ lsp L++e  e++W kr+Tr +
  gene891|gene891|rna891|rna891 626 YLNIVDLSYVPLQRNLIVKKMLLKSEAKYLNGYNDRVRKVLSPFLNKE--ERKWVKRQTRRI 685
                                    788899***************************************999..8********976 PP

>> Creatinase_N  Creatinase/Prolidase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.3   0.0   2.4e-14   1.1e-10      26     123 ..      36     126 ..      14     130 .. 0.89

  Alignments for each domain:
  == domain 1  score: 42.3 bits;  conditional E-value: 2.4e-14
                                    HHHHSS...-SSSEEEEEEESSCEEEEEECTTHHHHHHHH.TTSEEEEESTHSSHHHHHHHHHHHHT-EEEE-TTSSBHH CS
                   Creatinase_N  26 rYltGfatetgsrglalvvtadgalllvdalryteaaeesatveevveyddpvealadllkellesekrvgveldaltva 105
                                      ltGf   tgs  ++l +t+d ++l++d +ry+++ae+++++  v+++ d+++++ +++++++   +++g++ + +  +
  gene891|gene891|rna891|rna891  36 TPLTGF---TGSTATVL-ITSDHNFLYTD-GRYFIQAEKELKDNFVLKKIDVDQSYLEYIRDNVV--GNIGMDVNRVDIK 108
                                    569***...********.***********.**********7777777777789**********76..9************ PP

                                    HHHHHHHHCTTSEEEETH CS
                   Creatinase_N 106 fyealkealpdaelvdas 123
                                    +y+++k++l + e++ + 
  gene891|gene891|rna891|rna891 109 TYKMIKNVLAEREIIHVR 126
                                    *********999998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (687 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       541  (0.0301746); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.62u 0.28s 00:00:00.90 Elapsed: 00:00:00.46
# Mc/sec: 4528.62
//
Query:       gene892|gene892|rna892|rna892  [L=89]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       383  (0.021362); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.29s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 612.12
//
Query:       gene893|gene893|rna893|rna893  [L=70]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.083   12.9   0.9       0.13   12.2   0.9    1.4  1  DUF1128   Protein of unknown function (DUF1128)


Domain annotation for each model (and alignments):
>> DUF1128  Protein of unknown function (DUF1128)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.9   7.5e-06      0.13      26      50 ..      21      45 ..      17      54 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 7.5e-06
                        DUF1128 26 avlkaedfseekyedlkdlYemVmk 50
                                    ++k ++++++  e++kd+Y +   
  gene893|gene893|rna893|rna893 21 KLMKESKYNDKILEEIKDIYRLTIY 45
                                   58******************98665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (70 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       763  (0.0425568); expected 358.6 (0.02)
Passed bias filter:                      477  (0.0266049); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 548.94
//
Query:       gene894|gene894|rna894|rna894  [L=35]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (35 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1051  (0.0586201); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.28s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 248.70
//
Query:       gene895|gene895|rna895|rna895  [L=422]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (422 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1455  (0.0811534); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 2928.02
//
Query:       gene896|gene896|rna896|rna896  [L=182]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.6e-30  104.5   0.1    5.3e-30  104.3   0.1    1.1  1  IF4E      Eukaryotic initiation factor 4E


Domain annotation for each model (and alignments):
>> IF4E  Eukaryotic initiation factor 4E
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.3   0.1     3e-34   5.3e-30      11     153 ..      14     154 ..       4     160 .. 0.89

  Alignments for each domain:
  == domain 1  score: 104.3 bits;  conditional E-value: 3e-34
                                    E-TTT--SS-..SGGG-EEEEEEEEHHHHHHHHHHS--GGGB-SSEEEEEEETT--SSTTSHHHHS-EEEEEEE-----H CS
                           IF4E  11 dsksksksen..yeeslkkvatfstveeFwslynnlkkpsklkvksdyhlFkkgikPmWEdpankkGGkwvirlkkkekl 88 
                                     +++++k+e   + +slkk++t ++ve+++ ++n+++  ++++  +d+++Fk+gi+P WEd++n +GGkw+i+l++ e+ 
  gene896|gene896|rna896|rna896  14 ITRNTTKKEPfdFCNSLKKLCTLRSVENLLYFLNHVNF-DHIEGITDISIFKEGIEPLWEDKSNISGGKWIIKLRR-EVS 91 
                                    445554444434779********************998.************************************9.89* PP

                                    HHHHHHHHHHHHTT-SS--.-SEEEEEEEE-SSEEEEEEEES-TT-HHHHHHHHHHHHHT----- CS
                           IF4E  89 drlWeelllaligeqleeeedeicGvvvsvRkkedrisiWtrdasdeekvekigeklkevlelpe 153
                                     rl+++ll+ ++ + +++   +++G+v+s R k+ ++++Wt+d++ +++ +++  ++k+vl+++ 
  gene896|gene896|rna896|rna896  92 TRLFQKLLIRMVRQPFDKI--DVNGIVISFRMKNVILAVWTKDSTGKDRFKDVLMEIKKVLDIKF 154
                                    ****************988..9***************************************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       497  (0.0277205); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 1232.20
//
Query:       gene897|gene897|rna897|rna897  [L=149]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.3e-08   33.2   0.1    4.9e-08   32.7   0.1    1.3  1  KH_1      KH domain
    0.00011   21.9   0.2    0.00016   21.4   0.2    1.3  1  KH_2      KH domain


Domain annotation for each model (and alignments):
>> KH_1  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.7   0.1   5.4e-12   4.9e-08       9      65 ..      60     112 ..      50     113 .. 0.75

  Alignments for each domain:
  == domain 1  score: 32.7 bits;  conditional E-value: 5.4e-12
                                    GHHHHHHTGGGHHHHHHHHHHT-EEEEESSTT...T.-EEEEEE.SHHHHHHHHHHHH CS
                           KH_1   9 slvgriIGkgGsnIkeIreetgakIkvpksedegsderevtisG.speavekAkelie 65 
                                    + +g++IGkgG+++keI++ ++++I++ k+     d   + i+   + +v  A+++i+
  gene897|gene897|rna897|rna897  60 NRIGKVIGKGGCKLKEIERMSNTHIRLRKN-----DKVYFNITKeAEGDVWMARDMIN 112
                                    34*****************99*****6543.....34678887745555888888886 PP

>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.2   1.8e-08   0.00016      30      72 ..      56      98 ..      30     103 .. 0.87

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 1.8e-08
                                   EEEESCHHHHHTGGGHHHHHHHHHHHHHHHHHHTTCEEEEEEE CS
                           KH_2 30 viresqpgivIGkgGsnikkigkelrkdieklegkkVklnivk 72
                                    ++ ++ g vIGkgG ++k+i+   +  i+  ++ kV+ ni k
  gene897|gene897|rna897|rna897 56 YEKMNRIGKVIGKGGCKLKEIERMSNTHIRLRKNDKVYFNITK 98
                                   578899********************************99984 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       648  (0.0361426); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1107.97
//
Query:       gene898|gene898|rna898|rna898  [L=189]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (189 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       460  (0.0256568); expected 358.6 (0.02)
Passed bias filter:                      241  (0.0134419); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.49
# Mc/sec: 1154.12
//
Query:       gene899|gene899|rna899|rna899  [L=136]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
       0.04   13.3   0.1      0.052   13.0   0.1    1.2  1  Fer4_NifH  4Fe-4S iron sulfur cluster binding proteins, NifH/


Domain annotation for each model (and alignments):
>> Fer4_NifH  4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   2.9e-06     0.052     163     212 ..      75     124 ..      60     131 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.9e-06
                      Fer4_NifH 163 kgiekyaksggvrlgGliinsrkvddereliekfaeelgtkvlevvPrde 212
                                    +   +y k + v++   i+ +r+ +++++ i+++a+e++ ++l  v  +e
  gene899|gene899|rna899|rna899  75 NETCEYPKGNIVKICSFIYENRNLANKSDEIKNLAKEVEEEMLRNVSEHE 124
                                    55567888899********************************9998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       975  (0.0543812); expected 358.6 (0.02)
Passed bias filter:                      523  (0.0291706); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 973.68
//
Query:       gene9|gene9|rna9|rna9  [L=87]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
     0.0089   14.7   0.2     0.0095   14.6   0.2    1.0  1  BLM10_mid  Proteasome-substrate-size regulator, mid region


Domain annotation for each model (and alignments):
>> BLM10_mid  Proteasome-substrate-size regulator, mid region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.2   5.3e-07    0.0095     265     340 ..      10      79 ..       2      85 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 5.3e-07
              BLM10_mid 265 sgklEesvvnklpatldilleslsdelfdlalkkvvdfvsnnvksnavdavaellaalvkanpektlkkllpllie 340
                            ++k++esv+n ++ + + + + +++++fd+a++k+vdf s++ + +       lla++ + +++ + k  ++ + +
  gene9|gene9|rna9|rna9  10 RSKTKESVTNDMKRVSSFFANTCNNQVFDYAFEKFVDFNSSKISYK------CLLACIGRMQKKAAYKCNVERCND 79 
                            6799**********************************99887644......345555555555555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       732  (0.0408277); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.31s 00:00:00.70 Elapsed: 00:00:00.47
# Mc/sec: 561.83
//
Query:       gene90|gene90|rna90|rna90  [L=445]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.054   13.4   0.1      0.099   12.5   0.1    1.4  1  DUF2691   Protein of unknown function (DUF2691)


Domain annotation for each model (and alignments):
>> DUF2691  Protein of unknown function (DUF2691)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   5.5e-06     0.099      32     127 ..     217     317 ..     189     321 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.5e-06
                    DUF2691  32 iadeEsyliedgeLdealFpeeeevleg..eelkktlkkkdyYliFadlkafpk...kklakdiktyeeflkskcelvllivDs 110
                                i+ e + l e g+ + a F+e  e l    + + ++l+ +d   +F +l    k   k+++++ + y+++lks+c+ +   +D 
  gene90|gene90|rna90|rna90 217 IETEKISLSESGDEQPASFNEWLERLSKlrKVIVDYLTIHDRIRLFIKLCKQAKeieKIIQNNESDYNSHLKSECNRANSFADL 300
                                455555566666555566666555444311345566677777778888755444111456778889****************** PP

                    DUF2691 111 syvtiyckdqeiiekly 127
                                s  ++yc+++  i ++y
  gene90|gene90|rna90|rna90 301 STNNLYCRERLFIHSMY 317
                                **************999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (445 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       576  (0.0321267); expected 358.6 (0.02)
Passed bias filter:                      483  (0.0269396); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 2940.68
//
Query:       gene900|gene900|rna900|rna900  [L=159]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.3e-08   32.5   0.0    1.2e-07   31.8   0.0    1.4  1  Glutaredoxin    Glutaredoxin
     0.0013   18.0   0.3     0.0029   16.9   0.0    1.3  1  Glyco_hydro_57  Glycosyl hydrolase family 57
  ------ inclusion threshold ------
       0.01   16.2   0.0      0.015   15.7   0.0    1.3  1  GST_N_3         Glutathione S-transferase, N-terminal domain


Domain annotation for each model (and alignments):
>> Glutaredoxin  Glutaredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.8   0.0     2e-11   1.2e-07       2      57 ..      55     111 ..      54     114 .. 0.92

  Alignments for each domain:
  == domain 1  score: 31.8 bits;  conditional E-value: 2e-11
                                    EEEESTSSHHHHHHHHHHHHTTGGEEEEEGCCSH.HHHHHHHHHHTSSSSSEEEETT CS
                   Glutaredoxin   2 vlftkptCpyCkkakrlLkelgvkfeeidvdkde.eireelkelsgvrtvPqvfidg 57 
                                    v+f++ tC+y kka  lLk++g+++ ++d dk++ +  e+lk+ +  +t+P +  + 
  gene900|gene900|rna900|rna900  55 VVFGTETCGYTKKALTLLKDKGMSYVFVDKDKNMtNTYEDLKKDLRHETLPLIIRNR 111
                                    89*******************************99********99999**9887665 PP

>> Glyco_hydro_57  Glycosyl hydrolase family 57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   4.9e-07    0.0029     150     232 ..      32     110 ..      10     113 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 4.9e-07
                                    HHHHHHHHHHHHHHHHHHHSS--SBEE-GGG-B--SHHHHHHHTT--EEEE-C------------TTS-EE-TTS.-EEE CS
                 Glyco_hydro_57 150 sedieaqvkkarelyeeyfgqePrgfwlpElavspeileilaelGfeylftdelaeiledkskespyrpyllknggiavf 229
                                    + + +a++k   + + +++  e ++f  + + ++++ l +l+++G++y+f+d+ +++++ +  e++   ++ + + + + 
  gene900|gene900|rna900|rna900  32 EARYDAEIKTNDSALIDLMKTEFVVFGTETCGYTKKALTLLKDKGMSYVFVDKDKNMTNTY--EDLKKDLRHE-T-LPLI 107
                                    577889999999999999999999999999*****************************99..4443333322.3.5555 PP

                                    E-- CS
                 Glyco_hydro_57 230 fRd 232
                                     R+
  gene900|gene900|rna900|rna900 108 IRN 110
                                    555 PP

>> GST_N_3  Glutathione S-transferase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.7   0.0   2.5e-06     0.015       2      58 ..      57     115 ..      56     136 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.5e-06
                                    ES-TTSHHHHHHHHHHHHHT--EEEE---TTTT..HHHHHHH-TT--SSEEETTS-EEE CS
                        GST_N_3   2 ygfpaSpyarrvrlaLnekglpvevvevtpgeh..deellaknplgkvPvLeddgealt 58 
                                    +g++++ y++++  +L+ kg ++ +v+ ++  +   e l++  ++ ++P +  + + + 
  gene900|gene900|rna900|rna900  57 FGTETCGYTKKALTLLKDKGMSYVFVDKDKNMTntYEDLKKDLRHETLPLIIRNRRFFG 115
                                    6899*********************999766644478888888******9988766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       844  (0.0470746); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1123.20
//
Query:       gene901|gene901|rna901|rna901  [L=200]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.2e-26   90.8   2.7    9.6e-26   90.6   2.7    1.0  1  Guanylate_kin    Guanylate kinase
    2.5e-08   34.5   0.3    3.5e-08   34.1   0.3    1.2  1  AAA_18           AAA domain
    9.6e-06   25.5   0.2      2e-05   24.5   0.1    1.5  1  Viral_helicase1  Viral (Superfamily 1) RNA helicase
    2.1e-05   25.1   0.0    3.3e-05   24.4   0.0    1.3  1  ABC_tran         ABC transporter
    4.1e-05   23.8   0.4    0.00049   20.3   0.4    2.2  1  AAA_33           AAA domain
    5.5e-05   23.1   0.2    0.00024   21.0   0.0    1.9  2  RsgA_GTPase      RsgA GTPase
    0.00012   22.5   0.0    0.00017   22.0   0.0    1.3  1  AAA_16           AAA ATPase domain
    0.00015   21.8   0.4    0.00025   21.1   0.3    1.6  1  MMR_HSR1         50S ribosome-binding GTPase
    0.00024   21.4   0.5    0.00056   20.2   0.1    1.8  2  AAA_22           AAA domain
    0.00076   19.5   0.5    0.00076   19.5   0.5    2.4  2  AAA_14           AAA domain
    0.00085   19.3   0.1     0.0014   18.5   0.0    1.3  1  Rad17            Rad17 P-loop domain
     0.0012   18.8   5.9      0.027   14.4   5.9    2.3  1  ATPase_2         ATPase domain predominantly from Archaea
     0.0014   18.9   2.7     0.0047   17.2   2.7    2.0  1  AAA_28           AAA domain
     0.0027   16.9   0.2      0.011   14.9   0.1    1.9  2  NB-ARC           NB-ARC domain
     0.0069   16.1   0.0      0.017   14.9   0.0    1.6  1  AAA_29           P-loop containing region of AAA domain
     0.0076   16.2   0.0      0.012   15.5   0.0    1.5  1  NTPase_1         NTPase
  ------ inclusion threshold ------
      0.011   15.7   0.0      0.017   15.0   0.0    1.3  1  NACHT            NACHT domain
      0.016   15.0   0.5      0.024   14.5   0.4    1.4  1  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
      0.017   14.7   0.1      0.036   13.6   0.1    1.5  1  cobW             CobW/HypB/UreG, nucleotide-binding domain
      0.018   14.7   1.0      0.079   12.7   1.0    1.9  1  AAA_24           AAA domain
      0.019   14.3   0.9      0.036   13.3   0.1    1.7  2  DUF2075          Uncharacterized conserved protein (DUF2075)
      0.022   14.8   0.1      0.048   13.7   0.1    1.6  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
      0.024   13.9   0.1       0.26   10.6   0.0    2.3  2  Zeta_toxin       Zeta toxin
      0.024   13.8   0.1       0.13   11.4   0.0    2.0  2  DUF815           Protein of unknown function (DUF815)
      0.031   14.7   0.2      0.064   13.6   0.2    1.9  1  RNA_helicase     RNA helicase
      0.035   13.6   0.2        0.1   12.1   0.0    1.9  2  AAA_7            P-loop containing dynein motor region
      0.039   13.7   0.3      0.039   13.7   0.3    2.1  2  PRK              Phosphoribulokinase / Uridine kinase family
      0.046   14.0   0.3      0.095   13.0   0.3    1.7  1  AAA_19           AAA domain
      0.048   14.1   0.0       0.09   13.2   0.0    1.6  1  AAA              ATPase family associated with various cellul
       0.07   13.1   0.1       0.58   10.2   0.0    2.2  2  AAA_5            AAA domain (dynein-related subfamily)
       0.09   13.0   1.1       0.41   10.9   0.1    2.4  3  Roc              Ras of Complex, Roc, domain of DAPkinase
       0.13   12.3   1.2       0.17   11.9   1.2    1.6  1  Dynamin_N        Dynamin family
       0.14   12.6   0.1        1.6    9.1   0.1    2.4  1  AAA_17           AAA domain
       0.22   11.2   0.0       0.29   10.8   0.0    1.3  1  AAA_30           AAA domain
       0.73   10.3  10.6         31    5.0  10.6    2.3  1  AAA_23           AAA domain
        1.3    9.1   4.7         15    5.6   4.7    2.1  1  DUF87            Helicase HerA, central domain


Domain annotation for each model (and alignments):
>> Guanylate_kin  Guanylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.6   2.7   1.9e-28   9.6e-26       2     179 ..      24     194 ..      23     197 .. 0.90

  Alignments for each domain:
  == domain 1  score: 90.6 bits;  conditional E-value: 1.9e-28
                                    SSEEEEESTTTSSHHHHHHHHHHHSTTTEEE--EEESS---TTS-TTTSEEE--HHHHHHHHHTTTEEEEEEETTEEEEE CS
                  Guanylate_kin   2 rrpvvlvgpsgaGksslkkaLlselpekfgvsvshtTrdprkgevdGkdYyFvskeemekdiskneflEaaefsgnlygt 81 
                                    +++vv+ g sg Gks+l+  +l++  e+ ++svshtTr++r+ge +  dY+F++k+e++k+   nef E   + +++ygt
  gene901|gene901|rna901|rna901  24 SKLVVVTGTSGCGKSTLIRRILNH--ENVSLSVSHTTREKRAGENNHIDYHFITKDEFMKMDRSNEFYETTFYDNHYYGT 101
                                    689*******************86..45679************************************************* PP

                                    EHHHHHHHHHTTSEEEEE--CHHHHHHHHTTTTEEEEEEEESSHHHHHHHHTTSSSSHHHHHHHHHHHHHHHHGGG.C.. CS
                  Guanylate_kin  82 sveaieevlekgkiviLDvdiqavkqlrkaelspiivFikppslkelqrrlksrgkeqeeklakrlaaaekelqey.e.. 158
                                     +++ +    k+  vi+D+d  ++++    e++ + +F   +++++l +rl +r + ++ek + rl+  e +++ y e  
  gene901|gene901|rna901|rna901 102 AKSELN----KNEYVIIDCDRIGAAKF--NEFNNVKIFF-YNTKDVLYERLMKRYN-NKEKAERRLQSYEIDMKTYrEgn 173
                                    *99975....6889******7776655..6889999999.8899999999888765.56788999***********9999 PP

                                    SSEEEEESSHHHHHHHHHHHH CS
                  Guanylate_kin 159 fdvvivnddleealkklkell 179
                                    +   i  ddle  +k+l++++
  gene901|gene901|rna901|rna901 174 YKHSIFTDDLERNVKELETII 194
                                    ******************998 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.1   0.3     7e-11   3.5e-08       1     121 [.      27     156 ..      27     170 .. 0.76

  Alignments for each domain:
  == domain 1  score: 34.1 bits;  conditional E-value: 7e-11
                         AAA_18   1 IlltGtpGvGKttlakeLskrlgf......gvnlrdvakenglllevdpealdeskrldedkldklldaleenss..... 69 
                                    +++tGt+G+GK+tl +++ +++++       ++ +    +n++ + +  +  de+ ++d+ +  +  +  ++++      
  gene901|gene901|rna901|rna901  27 VVVTGTSGCGKSTLIRRILNHENVslsvshTTREKRAGENNHIDYHFITK--DEFMKMDRSNEFYETTFYDNHYYgtaks 104
                                    79****************99987777777644444444444455555555..7777777777777777777777777777 PP

                         AAA_18  70 aleegknlvidghlaeleseaakdikkvvLtaspeelleRlekRgyeeakik 121
                                     l +++ ++id  +    + + + ++k++ +  +++l+eRl kR +++ k +
  gene901|gene901|rna901|rna901 105 ELNKNEYVIIDCDRIGAAKFNEFNNVKIFFYNTKDVLYERLMKRYNNKEKAE 156
                                    777779999998888888888888888*****************88777754 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.1   3.9e-08     2e-05       2      37 ..      28      63 ..      27      89 .. 0.75

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 3.9e-08
                Viral_helicase1  2 vvhGvpGcGKStlirkllrts.liltvnrptaellte 37
                                   vv G  GcGKStlir++l+++ ++l+v++  +   ++
  gene901|gene901|rna901|rna901 28 VVTGTSGCGKSTLIRRILNHEnVSLSVSHT-TREKRA 63
                                   9*******************8655555444.444444 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.0   6.6e-08   3.3e-05      11     104 ..      24     161 ..      20     175 .. 0.68

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 6.6e-08
                                    TSEEEEEESTTSSHHHHHHHHTTSS--..SEEEEEETTCEGGG.........B-HHHCCHCEEEE-SS--S-TTSBHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxx.........xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  11 gekvaivGenGaGKStLlkllagllkp..teGeilldgkdlke.........qeleslrkeigvlpqepqlfpeltvren 79 
                                    +++v+++G +G+GKStL++ ++++++       +     ++++         ++ ++  k   +    ++ f+e+t ++n
  gene901|gene901|rna901|rna901  24 SKLVVVTGTSGCGKSTLIRRILNHENVslS---V----SHTTRekragennhIDYHFITKDEFMKMDRSNEFYETTFYDN 96 
                                    67899*****************99875331...2....222220111122334444444444444444566666666666 PP

                                    ........................................HHHTCHHHHHHHSTTGGTTCBGEST CS
                                    ........................................xxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  80 ........................................esdeeiekalsklglkelkdtvvks 104
                                                                            ++d+  e++++++++ke+++++++s
  gene901|gene901|rna901|rna901  97 hyygtakselnkneyviidcdrigaakfnefnnvkiffynTKDVLYERLMKRYNNKEKAERRLQS 161
                                    89998888888888888888888888888888888888766666688888888888877777755 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.4   9.9e-07   0.00049       1      76 [.      26     115 ..      26     171 .. 0.57

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 9.9e-07
                         AAA_33   1 lvllvGlpGsGKstlaerllkklgavllssdtlrrrlfgtdqqskt..................dytrvldrlyqilnel 62 
                                    lv++ G +G+GKstl++r+l+++ + l  s t r++ +g +++++                   + t++ d+   +  ++
  gene901|gene901|rna901|rna901  26 LVVVTGTSGCGKSTLIRRILNHENVSLSVSHTTREKRAG-ENNHIDyhfitkdefmkmdrsnefYETTFYDN---HYYGT 101
                                    799*****************6666555444454444444.33333333444444444443332233333333...44455 PP

                         AAA_33  63 arkalsagrnvild 76 
                                    a++ l ++  vi+d
  gene901|gene901|rna901|rna901 102 AKSELNKNEYVIID 115
                                    77777777777776 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   4.9e-07   0.00024      99     137 ..      24      64 ..      18      80 .. 0.79
   2 ?   -0.4   0.0       1.9   9.7e+02      60      95 ..     157     192 ..     126     198 .. 0.62

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 4.9e-07
                                    TSEEEEECSTTSSHHHHHHHHCTT-..----S--------- CS
                    RsgA_GTPase  99 dktsvlvGqSGvGKStLinallpel..elktgevseklgrG 137
                                    +k++v+ G SG GKStLi ++l+++  +l+++++ ++++ G
  gene901|gene901|rna901|rna901  24 SKLVVVTGTSGCGKSTLIRRILNHEnvSLSVSHTTREKRAG 64 
                                    5889*****************99641256666666666666 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.9
                                    -HHHHHHHHHHHHHHTTSEEEE--TTTHTTHHHHHH CS
                    RsgA_GTPase  60 eeeeeleelkeelealgyevllvsaktkegleelke 95 
                                     + +++e  ++++++ +y+  +   + +++++el++
  gene901|gene901|rna901|rna901 157 RRLQSYEIDMKTYREGNYKHSIFTDDLERNVKELET 192
                                    333355556666666666666665555666666554 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.0   3.5e-07   0.00017      17      47 ..      17      47 ..      12      77 .. 0.82

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 3.5e-07
                         AAA_16 17 ervrsgrpelvllsGesGvGKsslvrellra 47
                                   ++ +++ + lv+++G sG+GKs+l+r++l++
  gene901|gene901|rna901|rna901 17 HDCAKPMSKLVVVTGTSGCGKSTLIRRILNH 47
                                   5666777799*****************9975 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.3     5e-07   0.00025       2      42 ..      27      67 ..      26     159 .. 0.86

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 5e-07
                                   EEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEE CS
                       MMR_HSR1  2 vaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvk 42
                                   v++ G +  GKStLi+++++ +    +   tTr+ + g+ +
  gene901|gene901|rna901|rna901 27 VVVTGTSGCGKSTLIRRILNHENVSLSVSHTTREKRAGENN 67
                                   799*****************988888899999999888765 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.1   1.1e-06   0.00056       6      31 ..      25      50 ..      23     116 .. 0.76
   2 ?   -1.1   0.0       4.1     2e+03      21      37 ..     141     157 ..     122     191 .. 0.69

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 1.1e-06
                         AAA_22  6 gilvvtGesGtGKTtllrrlleqlde 31
                                   +++vvtG sG+GK+tl+rr+l+  + 
  gene901|gene901|rna901|rna901 25 KLVVVTGTSGCGKSTLIRRILNHENV 50
                                   5789*****************98644 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 4.1
                         AAA_22  21 llrrlleqldeeakaee 37 
                                    l++rl++++++ +kae+
  gene901|gene901|rna901|rna901 141 LYERLMKRYNNKEKAER 157
                                    45555555555555544 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.5   1.5e-06   0.00076       3      71 ..      25     115 ..      23     116 .. 0.63
   2 ?    1.5   1.5      0.59   2.9e+02      25      55 ..     104     133 ..      91     195 .. 0.69

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.5e-06
                         AAA_14   3 kilvitGaRrvGKTtllkqlikell.............vkkesilyinldderd.kkladpekll.elileklke..... 62 
                                    k++v+tG   +GK+tl++++++++              + +++ + + + ++++  k++ +++++ + + +   +     
  gene901|gene901|rna901|rna901  25 KLVVVTGTSGCGKSTLIRRILNHENvslsvshttrekrAGENNHIDYHFITKDEfMKMDRSNEFYeTTFYD---Nhyygt 101
                                    889******************99998888888877777444444444444444422222222222122222...122336 PP

                         AAA_14  63 .....ekktylflD 71 
                                         +k++y+++D
  gene901|gene901|rna901|rna901 102 akselNKNEYVIID 115
                                    67778888999998 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.59
                         AAA_14  25 ellvkkesilyinldderdkkladpekllel 55 
                                    ++l +k++++ i++d+   +k+++++++  +
  gene901|gene901|rna901|rna901 104 SEL-NKNEYVIIDCDRIGAAKFNEFNNVKIF 133
                                    344.777888888888777777766533222 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   2.9e-06    0.0014      45     121 ..      24     100 ..      18     133 .. 0.67

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 2.9e-06
                          Rad17  45 kriLLisGPsGCgkstvvkvLskelgiklrewlnpvslkepdnqksdfkgltekesrf..lsqiesfkeleLkdakylk 121
                                     ++++++G sGCgkst ++ +     ++l       + +  +n++ d++  ++++++f  + + + f e    d +y  
  gene901|gene901|rna901|rna901  24 SKLVVVTGTSGCGKSTLIRRILNHENVSLSVSHTTREKRAGENNHIDYH--FITKDEFmkMDRSNEFYETTFYDNHYYG 100
                                    46999*************8666555566665555555567777776665..6666667446677777777777777744 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   5.9   5.3e-05     0.027      13      54 ..      17      57 ..      11     191 .. 0.62

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 5.3e-05
                       ATPase_2 13 eilerepneiyfiYGpegsGKtaLlkeiienledkdkyviyy 54
                                   + + +  ++ ++++G  g+GK++L+++i++   + +  v   
  gene901|gene901|rna901|rna901 17 HDCAKPMSKLVVVTGTSGCGKSTLIRRILNHE-NVSLSVSHT 57
                                   5566777899******************9987.333344443 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   2.7   9.5e-06    0.0047       2      25 ..      27      51 ..      26     185 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 9.5e-06
                         AAA_28  2 ivitGgestGKTtlleaLaar.gyp 25
                                   +v+tG++++GK+tl++++ ++ +++
  gene901|gene901|rna901|rna901 27 VVVTGTSGCGKSTLIRRILNHeNVS 51
                                   8****************99884333 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.1   2.2e-05     0.011      20      45 ..      24      48 ..      18      53 .. 0.85
   2 ?   -0.4   0.0       1.1   5.4e+02     133     173 ..      53      94 ..      48     113 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.2e-05
                                   SEEEEEEESTTSSHHHHHHHHCCSHC CS
                         NB-ARC 20 slvvalvGmgGvGKttlakqilnksd 45
                                   s +v + G  G+GK+tl++ iln+ +
  gene901|gene901|rna901|rna901 24 SKLVVVTGTSGCGKSTLIRRILNH-E 48
                                   45899******************9.4 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.1
                                    EEEEEESBCCCCCCS-S-.EEEEEESS--HHHHHHHHHHCCT CS
                         NB-ARC 133 rvllTTRdeevanavsat.sekievelLekdeawellenkvf 173
                                    +v  TTR++   ++ +   +   + e+++ d + e+ e   +
  gene901|gene901|rna901|rna901  53 SVSHTTREKRAGENNHIDyHFITKDEFMKMDRSNEFYETTFY 94 
                                    677799999998777766688888999999999999887655 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   3.3e-05     0.017      23      39 ..      25      41 ..      12      45 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.3e-05
                         AAA_29 23 gatlltGpsGsGKSTll 39
                                     +++tG+sG GKSTl+
  gene901|gene901|rna901|rna901 25 KLVVVTGTSGCGKSTLI 41
                                   46899***********8 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   2.4e-05     0.012       2      28 ..      27      50 ..      26     118 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.4e-05
                                   EEEE--TTSSHHHHHHHHHHHH...GG CS
                       NTPase_1  2 vfiTGppGvGKtTlvkkvlellkssgv 28
                                   v++TG +G GK+Tl++++l+     +v
  gene901|gene901|rna901|rna901 27 VVVTGTSGCGKSTLIRRILNHE---NV 50
                                   79***************98754...44 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.0   3.5e-05     0.017       2      21 ..      26      45 ..      25      50 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3.5e-05
                                   CEEEEC-TTTCHHHHHHHHH CS
                          NACHT  2 lvilqGeaGsGKTtLlqkla 21
                                   lv+++G +G+GK+tL++++ 
  gene901|gene901|rna901|rna901 26 LVVVTGTSGCGKSTLIRRIL 45
                                   79****************96 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.4   4.8e-05     0.024       2     126 ..      27     142 ..      26     162 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4.8e-05
                         AAA_21   2 nvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfefeieeflsqgvryryglrlers 81 
                                     v++G  g+GKS+L++ +      +++ + + +++    +++   +   ++++++ f   +e+  ++ ++  y+ +++++
  gene901|gene901|rna901|rna901  27 VVVTGTSGCGKSTLIRRI------LNHENVSLSVS----HTTREKRAGENNHIDYHFITKDEFMKMDRSNEFYETTFYDN 96 
                                    79****************......55666666666....88888888888888888888888788888999999999999 PP

                         AAA_21  82 qv.eeklssvetllesgllldkrsleeedvfnpeargirggvsvfs 126
                                    ++ ++ +s++++++   + +d+  + ++++fn+++  ++ +++v +
  gene901|gene901|rna901|rna901  97 HYyGTAKSELNKNEYVIIDCDRIGAAKFNEFNNVKIFFYNTKDVLY 142
                                    99******************************99999888887765 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   7.3e-05     0.036       3      24 ..      27      48 ..      25      67 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 7.3e-05
                                   EEEEESTTCCHHHHHHHHHCT- CS
                           cobW  3 tvltGflGsGKTtLlnhllenr 24
                                   +v+tG  G GK+tL++++l+++
  gene901|gene901|rna901|rna901 27 VVVTGTSGCGKSTLIRRILNHE 48
                                   79*****************653 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   1.0   0.00016     0.079       3     120 ..      25     185 ..      23     197 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00016
                         AAA_24   3 lkiliyGpsgiGKTtlakel.gpkplfidtekGlksldadkfpdie....swedfldevvel.................. 59 
                                    + ++++G sg GK+tl++++   + + + + + +++  a + + i     + ++f++   ++                  
  gene901|gene901|rna901|rna901  25 KLVVVTGTSGCGKSTLIRRIlNHENVSLSVSHTTREKRAGENNHIDyhfiTKDEFMKMDRSNefyettfydnhyygtaks 104
                                    5689****************855566665555555555555555555444333333333333445555666777777766 PP

                         AAA_24  60 ...................aaeladyktlviDtideleelclaevirqnekaesk..edkgdgkGygelaeefrrllkkl 118
                                                         e ++ k+ +  t d l+e  ++   ++ +++  +  +   d+k y e + +++ + ++l
  gene901|gene901|rna901|rna901 105 elnkneyviidcdrigaakFNEFNNVKIFFYNTKDVLYERLMKRYNNKEKAE-RRlqSYEIDMKTYREGNYKHSIFTDDL 183
                                    6666677777777777555445555666677777777776666666666663.333344667777777777777777776 PP

                         AAA_24 119 qe 120
                                    + 
  gene901|gene901|rna901|rna901 184 ER 185
                                    65 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   7.2e-05     0.036       2      95 ..      25     115 ..      24     129 .. 0.74
   2 ?    0.1   0.1      0.76   3.8e+02     188     236 ..     118     167 ..     112     184 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 7.2e-05
                        DUF2075   2 avvlVtGvaGtGKtvvllnllaeleddeeertavylsvNhplvlvlrealakke.ekkkkkeafeklssfinnlsefkka 80 
                                    ++v+VtG +G GK+ +  ++l+  + + + ++++   + ++ +++ ++ ++k+e +k++++++f + + + n +      
  gene901|gene901|rna901|rna901  25 KLVVVTGTSGCGKSTLIRRILNHENVSLSVSHTTREKRAGENNHIDYHFITKDEfMKMDRSNEFYETTFYDNHYY----G 100
                                    799**************9999997444444444444455555566677888888777788888877777777766....7 PP

                        DUF2075  81 eekkeepkedvvivD 95 
                                    ++k e +k + vi+D
  gene901|gene901|rna901|rna901 101 TAKSELNKNEYVIID 115
                                    777777777777777 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.76
                        DUF2075 188 kekakplssqenfdirvfddleelkkalkeknkesgr.srlvatydakrl 236
                                    +++a + ++ +n +i +++  + l++ l ++++++++  r + +y+ + +
  gene901|gene901|rna901|rna901 118 RIGAAKFNEFNNVKIFFYNTKDVLYERLMKRYNNKEKaERRLQSYEIDMK 167
                                    55555555566666777777777777776665555543566666666555 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   9.7e-05     0.048      15      74 ..      20      74 ..      12     100 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 9.7e-05
                                   HHCHTEEEEEEESTTSSHHHHHHHHHHHTT--.----TTTTSEEEEEE..SSEEEEE-TT- CS
                           TsaE 15 akalgdvilLeGdLGaGKTtlvrglakalgve.evkSPTFtlveeYelekeglyHfDlYRl 74
                                   ak ++++++ +G  G+GK+tl+r ++++ +v+ +v   + t  e+ + e     H+D   +
  gene901|gene901|rna901|rna901 20 AKPMSKLVVVTGTSGCGKSTLIRRILNHENVSlSV---SHTTREKRAGE---NNHIDYHFI 74
                                   4445679******************9998876444...44444444332...346665555 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00052      0.26      17      38 ..      25      46 ..      15      56 .. 0.85
   2 ?    0.6   0.1      0.56   2.8e+02      96     123 ..     138     163 ..      97     170 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00052
                     Zeta_toxin 17 klillgGqpGAGKselaellkd 38
                                   kl+++ G +G+GKs+l++ + +
  gene901|gene901|rna901|rna901 25 KLVVVTGTSGCGKSTLIRRILN 46
                                   799**************98876 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.56
                     Zeta_toxin  96 yniivegtlrspdvvkklaealkkaGYe 123
                                     ++++e+ ++ + + +k+ ++l++  Ye
  gene901|gene901|rna901|rna901 138 KDVLYERLMKRYNNKEKAERRLQS--YE 163
                                    567777777777777777777766..54 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00026      0.13      55      77 ..      26      48 ..      19      58 .. 0.86
   2 ?   -0.4   0.0         1   5.1e+02      97     120 ..     164     187 ..     143     197 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00026
                         DUF815 55 nvLLwGarGtGKSslvkallney 77
                                    v+++G+ G+GKS+l++ +ln+ 
  gene901|gene901|rna901|rna901 26 LVVVTGTSGCGKSTLIRRILNHE 48
                                   5889**************99875 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1
                         DUF815  97 klvellrerperfilfvDDLsFee 120
                                      +++ re +++  +f DDL  + 
  gene901|gene901|rna901|rna901 164 IDMKTYREGNYKHSIFTDDLERNV 187
                                    556677888999999999996444 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.2   0.00013     0.064       1      23 [.      27      49 ..      27     154 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 0.00013
                   RNA_helicase  1 iwlyGpsgeGKStlakeLakall 23
                                   ++++G sg+GKStl++++ ++  
  gene901|gene901|rna901|rna901 27 VVVTGTSGCGKSTLIRRILNHEN 49
                                   6899************9766544 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00021       0.1      33      58 ..      24      49 ..       9      67 .. 0.82
   2 ?   -2.8   0.0       7.5   3.7e+03      99     113 ..     173     187 ..     167     190 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00021
                          AAA_7 33 kkpvllvGptGtGKtviikdllkkld 58
                                   +k v+++G++G+GK+++i+++l++ +
  gene901|gene901|rna901|rna901 24 SKLVVVTGTSGCGKSTLIRRILNHEN 49
                                   577999**************998766 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 7.5
                          AAA_7  99 gkklvvFvDDlnmpa 113
                                    + k  +F DDl    
  gene901|gene901|rna901|rna901 173 NYKHSIFTDDLERNV 187
                                    557789999998655 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.3   7.8e-05     0.039       2      29 ..      27      51 ..      26      99 .. 0.68
   2 ?    0.0   0.2       1.2     6e+02      40      91 ..     141     159 ..     108     192 .. 0.59

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 7.8e-05
                            PRK  2 IgvagsSGaGkttvarklekifgrekvk 29
                                   + v+g SG+Gk+t+ r++ +    e+v 
  gene901|gene901|rna901|rna901 27 VVVTGTSGCGKSTLIRRILNH---ENVS 51
                                   579**********99887554...3343 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 1.2
                            PRK  40 rldraekdleleerkrakekevsflspeandfdllyevlkelkegkkvdkpi 91 
                                     ++r                                   k++++ +k +++ 
  gene901|gene901|rna901|rna901 141 LYERLM---------------------------------KRYNNKEKAERRL 159
                                    233333.................................3333333333333 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.3   0.00019     0.095      10      39 ..      24      53 ..      18     116 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00019
                         AAA_19 10 ekvllvtaGpGtGKTrvlkhivallvelgg 39
                                   +k+++vt+  G+GK+++++ i+++ +   +
  gene901|gene901|rna901|rna901 24 SKLVVVTGTSGCGKSTLIRRILNHENVSLS 53
                                   789******************999766554 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   0.00018      0.09       1      35 [.      27      58 ..      27     113 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00018
                                   EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCS CS
                            AAA  1 vllyGppGtGKTllakavakelgvefleisgsell 35
                                   v+++G+ G+GK++l++ + ++ +   +++s+s  +
  gene901|gene901|rna901|rna901 27 VVVTGTSGCGKSTLIRRILNHEN---VSLSVSHTT 58
                                   5789***************9943...344444444 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0    0.0012      0.58       2      24 ..      27      49 ..      26      63 .. 0.83
   2 ?    0.4   0.0       1.2   5.9e+02      32      76 ..     136     185 ..     120     192 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0012
                                   EEEE--SSSSHHHHHHHGGGGBS CS
                          AAA_5  2 vlLvGppGtgKselaerlaaaln 24
                                   v++ G +G+gKs+l++r++   n
  gene901|gene901|rna901|rna901 27 VVVTGTSGCGKSTLIRRILNHEN 49
                                   6889*************987655 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 1.2
                                    --TT--HHHHH--B--..............--------G-SEEEEESGGG CS
                          AAA_5  32 ltrdtteedlkgrreik.....ngttslvdsplvraaregeilvlDEver 76 
                                    +t+d  +e l  r++ k       +    d + +r+++ ++ ++ D++er
  gene901|gene901|rna901|rna901 136 NTKDVLYERLMKRYNNKekaerRLQSYEIDMKTYREGNYKHSIFTDDLER 185
                                    56777777788888754322211122223444445555777777777776 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   0.00081      0.41       2      24 ..      27      49 ..      25      86 .. 0.82
   2 ?    0.1   0.1       1.8   8.9e+02      15      27 ..     145     157 ..      77     172 .. 0.67
   3 ?   -0.1   0.0       2.1     1e+03      15      40 ..     145     170 ..     138     188 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00081
                                   EEEESSTTSSHHHHHHCHCT-CC CS
                            Roc  2 vvlvGdsgvGKtsllkrfvedkf 24
                                   vv+ G sg GK++l++r+++++ 
  gene901|gene901|rna901|rna901 27 VVVTGTSGCGKSTLIRRILNHEN 49
                                   6788**************98654 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 1.8
                                    HHHCHCT-CCC-E CS
                            Roc  15 llkrfvedkfsek 27 
                                    l+kr+ +++  e+
  gene901|gene901|rna901|rna901 145 LMKRYNNKEKAER 157
                                    3444444444444 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 2.1
                                    HHHCHCT-CCC-EEETTTTEEEEEEE CS
                            Roc  15 llkrfvedkfsekekstigvdfltke 40 
                                    l+kr+ +++  e++ + + +d++t +
  gene901|gene901|rna901|rna901 145 LMKRYNNKEKAERRLQSYEIDMKTYR 170
                                    67888888888888888888877654 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   1.2   0.00035      0.17       1      34 [.      27      60 ..      27     191 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00035
                                   EEEEEBTTTTHHHHHHHHHTS--S---SSS---S CS
                      Dynamin_N  1 iavvGsqSsGKSSvlnaLlgedilprgpnptTrr 34
                                   ++v G+   GKS+++  +l ++    +  +tTr 
  gene901|gene901|rna901|rna901 27 VVVTGTSGCGKSTLIRRILNHENVSLSVSHTTRE 60
                                   79********************888999999985 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.1    0.0033       1.6       1      33 [.      30      61 ..      30     163 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0033
                                   EE-TTSSHHHHHHHHHHHHTEEEEEHHHHHHHH CS
                         AAA_17  1 lGgPGsGKgtqceklvekygfthlsaGdllree 33
                                   +G  G+GK+t+++++  + +++ ls +   re 
  gene901|gene901|rna901|rna901 30 TGTSGCGKSTLIRRILNHENVS-LSVSHTTREK 61
                                   6999********9998876654.4555555655 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00058      0.29      19      40 ..      25      46 ..      17     116 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00058
                         AAA_30 19 rvavltGpAGtGKttalkalre 40
                                   +++v+tG  G GK+t+++ + +
  gene901|gene901|rna901|rna901 25 KLVVVTGTSGCGKSTLIRRILN 46
                                   589**************98865 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0  10.6     0.063        31      20     104 ..      25     169 ..      21     199 .. 0.49

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.063
                         AAA_23  20 gltlItGpNGaGKTTildAik....laL.ygetprlsrksgrgfeksdveiese......gkvkayveltfenkdgry.. 86 
                                    +l+++tG  G+GK+T+++ i       L   +t+r++r   + +++ d+++ ++      +  ++++e tf +++  y  
  gene901|gene901|rna901|rna901  25 KLVVVTGTSGCGKSTLIRRILnhenVSLsVSHTTREKR--AGENNHIDYHFITKdefmkmDRSNEFYETTFYDNHY-Ygt 101
                                    799*************9877544432231122222222..223344444433333555554445555555533322.234 PP

                         AAA_23  87 ..................................................trsiererelskkkgktt 104
                                                                                      +++ er+ + ++ ++kt+
  gene901|gene901|rna901|rna901 102 akselnkneyviidcdrigaakfnefnnvkiffyntkdvlyerlmkrynnKEKAERRLQSYEIDMKTY 169
                                    44455554445555555555555555555555555433333333333333334444444444444443 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   4.7      0.03        15      23      46 ..      24      47 ..      14     193 .. 0.64

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.03
                          DUF87 23 trHlAilgsTGsGKSntvavLlee 46
                                   ++ + + g++G GKS++++ +l+ 
  gene901|gene901|rna901|rna901 24 SKLVVVTGTSGCGKSTLIRRILNH 47
                                   5567799************99974 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1237  (0.0689944); expected 358.6 (0.02)
Passed bias filter:                      527  (0.0293937); expected 358.6 (0.02)
Passed Vit filter:                       110  (0.00613531); expected 17.9 (0.001)
Passed Fwd filter:                        36  (0.00200792); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              36  [number of targets reported over threshold]
# CPU time: 0.65u 0.32s 00:00:00.97 Elapsed: 00:00:00.49
# Mc/sec: 1227.43
//
Query:       gene902|gene902|rna902|rna902  [L=471]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.064   13.5   0.4      0.064   13.5   0.4    3.7  4  RNase_3_N      Ribonuclease III N-terminal domain
      0.077   13.0   0.2        0.3   11.1   0.2    2.0  1  Ribonuc_L-PSP  Endoribonuclease L-PSP
        3.5    8.0   7.7        2.9    8.2   0.1    3.8  4  BORCS7         BLOC-1-related complex sub-unit 7


Domain annotation for each model (and alignments):
>> RNase_3_N  Ribonuclease III N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.4   1.1e-05     0.064      15      56 ..       7      49 ..       5      52 .. 0.90
   2 ?    0.1   0.1      0.16   9.6e+02      18      37 ..      97     116 ..      82     131 .. 0.81
   3 ?   -0.1   0.2      0.18   1.1e+03      17      38 ..     345     366 ..     333     379 .. 0.81
   4 ?   -2.0   0.0      0.69   4.1e+03      63      84 ..     376     397 ..     362     403 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.1e-05
                                   HHHHHHHHHHHHH---HHH.HHHHHHSGCSS-GGGHHHHCSHH CS
                      RNase_3_N 15 tklvesykriielspnlkt.yeealeneeklpveilpalsRyk 56
                                   +klv+++ +  ++s nl++ y+++ +n +++p+ +l++++Ry+
  gene902|gene902|rna902|rna902  7 EKLVNTLAKTDKISQNLNQiYKKMENNAQNTPTTVLQTFERYS 49
                                   589*************975388888999*************96 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.16
                                    HHHHHHHHHH---HHHHHHH CS
                      RNase_3_N  18 vesykriielspnlktyeea 37 
                                    +++y++i +   n+k+y + 
  gene902|gene902|rna902|rna902  97 IKAYETIKKCNNNVKIYRNI 116
                                    57899999999999999875 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.18
                                    HHHHHHHHHHH---HHHHHHHH CS
                      RNase_3_N  17 lvesykriielspnlktyeeal 38 
                                    l+  y +i +ls+n +++++++
  gene902|gene902|rna902|rna902 345 LLTLYMKIKHLSVNESALNRNV 366
                                    567899********99998876 PP

  == domain 4  score: -2.0 bits;  conditional E-value: 0.69
                                    HHHHHHTT--THHHHHHHHHHH CS
                      RNase_3_N  63 lksleelgklplleeisnyesk 84 
                                    +k+ +++g   l++++++++++
  gene902|gene902|rna902|rna902 376 MKTKNSIGDKMLFDDVQTFKKN 397
                                    7888999999999999999875 PP

>> Ribonuc_L-PSP  Endoribonuclease L-PSP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.2   5.1e-05       0.3      46      94 ..     187     238 ..     172     246 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 5.1e-05
                                    HHHHHHHHHHHH...HTT--GGGEEEEEEEESSGGGHHHHHHHHHHHSSSST CS
                  Ribonuc_L-PSP  46 rqalenlkavLa...aagaslsdvVkvtvFladiedfaevnevyaeafdelk 94 
                                    r+alen++  ++   +++  +sd+ +++vFl d + ++ +n+++ ++f+e++
  gene902|gene902|rna902|rna902 187 RDALENIDTFVKrvtESNKLFSDIRQMNVFLFDTATYEFLNKAMIDYFREDM 238
                                    78899999877611156667999*************************9985 PP

>> BORCS7  BLOC-1-related complex sub-unit 7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.1   0.00048       2.9      29     101 ..       4      77 ..       2      79 .. 0.81
   2 ?   -1.7   0.1      0.57   3.4e+03      47      70 ..     108     131 ..      85     141 .. 0.67
   3 ?    1.0   0.2     0.083   4.9e+02      76     100 ..     352     376 ..     333     397 .. 0.70
   4 ?   -0.3   0.0      0.21   1.3e+03      22      52 ..     432     462 ..     425     469 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00048
                         BORCS7  29 ndissvakqvvkgSksseilmkaaksfaqqedaient.eesLkkmsllttelnyqveaisksikqleevqeqvk 101
                                    +d +++++ + k+ k s +l+++ k++    ++  +t  +++++ s   ++l+y  +  ++ ik  e+v e+v+
  gene902|gene902|rna902|rna902   4 DDYEKLVNTLAKTDKISQNLNQIYKKMENNAQNTPTTvLQTFERYSTPKKNLDYAIKFHNDYIKYCESVDESVV 77 
                                    68889999999999999999999999977777777776678888888889999998888888888888888775 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.57
                         BORCS7  47 ilmkaaksfaqqedaienteesLk 70 
                                    +  k+ +++ ++ + ie++e+ L 
  gene902|gene902|rna902|rna902 108 NNVKIYRNIGIVKAKIETSENALT 131
                                    334677888888888888888776 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.083
                         BORCS7  76 ttelnyqveaisksikqleevqeqv 100
                                    +++l+ +++a+++++  l+++++ +
  gene902|gene902|rna902|rna902 352 IKHLSVNESALNRNVYLLNNINYIM 376
                                    5677777777777777766666544 PP

  == domain 4  score: -0.3 bits;  conditional E-value: 0.21
                         BORCS7  22 ervevivndissvakqvvkgSksseilmkaa 52 
                                    e+ + i +++ +++k ++k      ++++++
  gene902|gene902|rna902|rna902 432 ETRNYILENVKKIVKDLTKRTTYDGDVEEVV 462
                                    5567788888899888888766655555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (471 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1663  (0.0927548); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.63u 0.29s 00:00:00.92 Elapsed: 00:00:00.49
# Mc/sec: 2874.57
//
Query:       gene903|gene903|rna903|rna903  [L=580]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    0.00011   22.9   1.4      0.029   15.3   0.2    3.7  4  WD40        WD domain, G-beta repeat
  ------ inclusion threshold ------
       0.03   13.6   0.3       0.56    9.4   0.1    2.4  2  RAB3GAP2_N  Rab3 GTPase-activating protein regulatory subunit


Domain annotation for each model (and alignments):
>> WD40  WD domain, G-beta repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.2   3.2e-06     0.029       4      37 ..      17      50 ..      14      51 .. 0.79
   2 ?    4.2   0.0      0.01        91       4      36 ..     229     262 ..     226     263 .. 0.77
   3 ?   -2.4   0.0       1.2   1.1e+04      18      29 ..     293     304 ..     286     305 .. 0.84
   4 ?   -2.6   0.0       1.4   1.2e+04      12      32 ..     553     571 ..     549     573 .. 0.54

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 3.2e-06
                                   EEEEESS.SS.EEEEEEETTSSEEEEEETTSEEEEE CS
                           WD40  4 lrtltGH.ss.vtslafspdgawlasGsdDgtvriW 37
                                    +tl  H +  +++l  s ++++l++Gs D+tvr W
  gene903|gene903|rna903|rna903 17 KHTLYFHeNAsIYGL-SSTENHLLTAGS-DCTVRCW 50
                                   58899998446****.666666677889.******* PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.01
                                    EEEEESS.SSEEEEEEETTSSEEEEE.ETTSEEEE CS
                           WD40   4 lrtltGH.ssvtslafspdgawlasG.sdDgtvri 36 
                                    l +++ H  sv +l+++   + l+ + s+D+t ++
  gene903|gene903|rna903|rna903 229 LNVIKPHsLSVQGLSYNTKYNILS-SfSKDKTMKV 262
                                    66677785559***9999999986.559****998 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 1.2
                                    EETTSSEEEEEE CS
                           WD40  18 fspdgawlasGs 29 
                                    fs+d+ +l+ G+
  gene903|gene903|rna903|rna903 293 FSHDNEFLFVGG 304
                                    999999998886 PP

  == domain 4  score: -2.6 bits;  conditional E-value: 1.4
                                    SEEEEEEETTSSEEEEEETTS CS
                           WD40  12 svtslafspdgawlasGsdDg 32 
                                    ++t++  +++  + + +s Dg
  gene903|gene903|rna903|rna903 553 GITDIVSHKNVIF-V-SSVDG 571
                                    4777744444444.3.44476 PP

>> RAB3GAP2_N  Rab3 GTPase-activating protein regulatory subunit N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.1   6.3e-05      0.56      54      95 ..      68     111 ..      27     119 .. 0.74
   2 ?    1.4   0.0     0.017   1.5e+02      78      92 ..     137     151 ..     128     159 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 6.3e-05
                     RAB3GAP2_N  54 eeiItailclplss.kssqg.spdwtviavGlssGylrfyteng 95 
                                    ++ ++   c +l+  +s ++ +   +++avG++ G +++++e g
  gene903|gene903|rna903|rna903  68 SSSVSFAYCCTLTLpNSINTiRSCDKYVAVGTTMGEVYVFKEMG 111
                                    33466666777776656666699999***************988 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.017
                     RAB3GAP2_N  78 viavGlssGylrfyt 92 
                                    vi++G++sG l++y+
  gene903|gene903|rna903|rna903 137 VIVCGFESGRLMMYE 151
                                    8*************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (580 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       736  (0.0410508); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.48
# Mc/sec: 3660.40
//
Query:       gene904|gene904|rna904|rna904  [L=177]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-24   87.4   1.9    1.3e-13   51.3   0.4    2.2  2  DNA_primase_S  DNA primase small subunit
  ------ inclusion threshold ------
       0.04   13.7   0.1      0.093   12.6   0.0    1.6  2  DUF2826        Protein of unknown function (DUF2826)
      0.048   13.5   0.0       0.12   12.2   0.0    1.6  1  Gemini_AL3     Geminivirus AL3 protein
       0.18   11.7   2.7        1.3    8.9   2.7    2.4  1  zf-C4_ClpX     ClpX C4-type zinc finger


Domain annotation for each model (and alignments):
>> DNA_primase_S  DNA primase small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.3   0.4     3e-17   1.3e-13       7      79 ..      37     107 ..      32     112 .. 0.90
   2 !   36.7   0.0   9.1e-13   4.1e-09     140     175 ..     107     142 ..     104     144 .. 0.92

  Alignments for each domain:
  == domain 1  score: 51.3 bits;  conditional E-value: 3e-17
                                    TTT-.TT--HHHHHHHHHHHHHHHHHHHH-----GGGEEEEE--SEEEEEEE--TTEEES-HHHHHHHHHH.. CS
                  DNA_primase_S   7 dyddcseatvcekcwkfvsvavkvldellredfgfkdilwvfsgrrGfHcwvsdkdarpltdeeraaivnyln 79 
                                    d  +c+  + c+ c + ++  + +l++ l+++fgf ++++ fsg++GfHc+v d  ar++t + r ++++yl 
  gene904|gene904|rna904|rna904  37 DVHVCD--NLCNECIAQMNKLIDLLKKILTDNFGFSHVIFFFSGNKGFHCYVTDASARHFTGIVRQSVASYLK 107
                                    444455..89**********************************************************99875 PP

  == domain 2  score: 36.7 bits;  conditional E-value: 9.1e-13
                                    ......-----------------....--------- CS
                  DNA_primase_S 140 vllyprldeqvtkgikhllkapfcihgktgnvcvpl 175
                                    +++ +  de+vt+++khllkapfc+h+k+g vcvp+
  gene904|gene904|rna904|rna904 107 KKHGVLVDENVTRDVKHLLKAPFCVHPKSGYVCVPV 142
                                    6678889****************************8 PP

>> DUF2826  Protein of unknown function (DUF2826)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   2.1e-05     0.093       9      51 ..      58     102 ..      51     113 .. 0.81
   2 ?   -2.0   0.0      0.64   2.9e+03      25      41 ..     140     157 ..     116     162 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.1e-05
                        DUF2826   9 llasll..plvashadyclsadhgwhastsdvvcrhftapvkhts 51 
                                    ll  +l  ++  sh  + +s ++g+h+  +d  +rhft  v+++ 
  gene904|gene904|rna904|rna904  58 LLKKILtdNFGFSHVIFFFSGNKGFHCYVTDASARHFTGIVRQSV 102
                                    555444225889**************************9998865 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.64
                        DUF2826  25 lsadhgw.hastsdvvcr 41 
                                    ++   g  +   sdvvc 
  gene904|gene904|rna904|rna904 140 VPVIEGVeKVHVSDVVCG 157
                                    444444413457888885 PP

>> Gemini_AL3  Geminivirus AL3 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   2.7e-05      0.12      75     115 ..      89     129 ..      82     132 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.7e-05
                     Gemini_AL3  75 lsGealldrlklrvllyldnlGvisinnviravnhvlykef 115
                                    +s   +   ++  v  yl++ Gv+  +nv r v+h l+  f
  gene904|gene904|rna904|rna904  89 ASARHFTGIVRQSVASYLKKHGVLVDENVTRDVKHLLKAPF 129
                                    6777888899*************************987766 PP

>> zf-C4_ClpX  ClpX C4-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   2.7    0.0003       1.3      25      38 ..      44      57 ..      23      57 .. 0.92

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0003
                     zf-C4_ClpX 25 ICdeCvelcneiie 38
                                    C+eC+++ n++i+
  gene904|gene904|rna904|rna904 44 LCNECIAQMNKLID 57
                                   6**********996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       861  (0.0480228); expected 358.6 (0.02)
Passed bias filter:                      500  (0.0278878); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.78
# Mc/sec: 687.11
//
Query:       gene905|gene905|rna905|rna905  [L=753]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.6e-97  327.2   0.1    3.3e-97  326.2   0.1    1.4  1  tRNA-synt_1   tRNA synthetases class I (I, L, M and V)
    3.8e-26   91.9   1.7    2.7e-24   85.9   0.2    2.7  2  Anticodon_1   Anticodon-binding domain of tRNA
    4.2e-10   38.9   0.9    0.00035   19.4   0.2    2.3  2  tRNA-synt_1g  tRNA synthetases class I (M)
  ------ inclusion threshold ------
      0.037   13.4   0.0      0.092   12.1   0.0    1.7  2  tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain


Domain annotation for each model (and alignments):
>> tRNA-synt_1  tRNA synthetases class I (I, L, M and V)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  326.2   0.1  7.3e-101   3.3e-97     253     601 ..       5     381 ..       2     382 .. 0.88

  Alignments for each domain:
  == domain 1  score: 326.2 bits;  conditional E-value: 7.3e-101
                    tRNA-synt_1 253 ledergkeLegkevelpl......vnrkipiiaddyvdkeaGtGvVkiaPahdedDyevgkkynl.....evinildedg 321
                                    l++++g+ ++g+++e+p+        + +++++++ v+ ++GtG+V++aPa++e+Dy+v  k +l     ev++++d++g
  gene905|gene905|rna905|rna905   5 LKRVNGSVFVGLRYEPPFeyfkkdFPTFFKVLKNEGVTDDSGTGIVHMAPAFGEEDYNVFLKEGLlrendEVPCVIDDKG 84 
                                    6889999***********99887777889*************************************************** PP

                    tRNA-synt_1 322 tlteeaaefeglkvfdarkkvveelkekglllkaekiehsvpfcerskkpiiyrateqWfvrvkeladaalkavekvqfv 401
                                    ++t   ++++ l+ +da+k ++++l ++  ll   +i+h +p+c+rs++p+iy++++ Wf+++++l++++ k +ek+++v
  gene905|gene905|rna905|rna905  85 KFTS--TDYKDLYFKDADKPIMKALGDR--LLWRGTIRHRYPYCWRSDTPLIYKMVPNWFIHISDLREQLYKLNEKIHWV 160
                                    **97..69******************99..9999********************************************** PP

                    tRNA-synt_1 402 pkskekryaswleniqdWciSRqrwWGhriplfvsketeevvvreelkelvagreeee......aekkalekeakdkl.. 473
                                    p s ++++ +wl+ ++dW iSR+r+WG++ip++ s++++ + + +++ el++  +  +      ++++++++e++d++  
  gene905|gene905|rna905|rna905 161 PPSVKNKFGNWLKCARDWSISRNRFWGTPIPIWTSSDFKVTLCISSIRELERLGFRMKdgqkipVKIQDMHREFIDDIli 240
                                    ***************************************99**9999998764433321111114567889999988875 PP

                    tRNA-synt_1 474 kkekgelekdedvlDvWFsSgswpfstlgypee..d.........tee..lkkffpadmlleGlDiirgWvarlillsla 540
                                    +k+   l+++++v+D+WF+Sgs+p ++ ++p++  +         + e  +++  +ad++ eGlD++rgW+++l ++s+ 
  gene905|gene905|rna905|rna905 241 EKNGVILRRIDEVFDCWFESGSMPLAQDHWPFSafTadgiekkldQLElnVREPDAADFIGEGLDQTRGWFYTLHVISTL 320
                                    5555679************************87442222211111222113344579*********************** PP

                    tRNA-synt_1 541 ltgsePfkevlvhglvrdeeGrKmSKslgNvidpldvikkygadalRltlilsdvgrdinl 601
                                    l+++  fk+++v+g+v++e+G+KmSK+l+N++dp++++++yg d+lR +li+s+v+ ++nl
  gene905|gene905|rna905|rna905 321 LFKRPAFKNIIVNGIVLAEDGKKMSKRLKNYPDPMEIANSYGMDSLRIYLISSPVVVAENL 381
                                    ******************************************************9998887 PP

>> Anticodon_1  Anticodon-binding domain of tRNA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.5   0.1     0.007        32      19      50 ..     383     413 ..     380     421 .. 0.81
   2 !   85.9   0.2   6.1e-28   2.7e-24       1     150 [.     423     563 ..     423     566 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.007
                    Anticodon_1  19 yeeyrfnkaasalyeffwndlcdwylelvkpr 50 
                                    + e   ++++++l+  ++n+l ++y+e+++++
  gene905|gene905|rna905|rna905 383 FTERGVKEVFKNLMINWYNSL-NFYVECSTKK 413
                                    56667899*************.*****98765 PP

  == domain 2  score: 85.9 bits;  conditional E-value: 6.1e-28
                    Anticodon_1   1 drwilselnklvkevteayeeyrfnkaasalyeffwndlcdwylelvkprlysesaedkraaqevllevletllrllaPf 80 
                                    d wi++el  l++++++++e+y++++++s++  f ++dl++wy+++++ r+ + +         vl++vl +++ l+aPf
  gene905|gene905|rna905|rna905 423 DEWIVNELCILAQRIKKNMERYELANILSDVLVF-IDDLSNWYIRMNRMRIRNGEY-------GVLKTVLTKFSVLMAPF 494
                                    89******************************96.9***************77654.......***************** PP

                    Anticodon_1  81 mPfitEelwqr...eeeelgkk.esimlaewpe.kaeelekeleeeevellkeivkairklrselkikpsselkv 150
                                    +Pf++E+ +q    ++ +l+k+ +s++++++p   +      + e+ ++  k++++ ir lr+++ki+ +++l+ 
  gene905|gene905|rna905|rna905 495 APFFSEYSYQVlqgNSSLLNKDfKSVHYEAFPVfRP-----VH-ENNFDKTKRVIESIRVLRENQKISLKTPLSE 563
                                    *********888875555544469999999995444.....44.56899999******************99654 PP

>> tRNA-synt_1g  tRNA synthetases class I (M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.2   7.8e-08   0.00035     167     238 ..     122     191 ..     116     201 .. 0.87
   2 !   17.6   0.0   2.9e-07    0.0013     311     387 ..     326     403 ..     290     406 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 7.8e-08
                                    ..........EEE.EEEEEE-GGGGHHHHHHHH.HH-TTSHHHHHHHH.HHHHT----EE-ESS-SSS-EET CS
                   tRNA-synt_1g 167 pksaisgskpevketehlffklskfekklkewieeeekeleenvkkivkewlkegLkdlaisrdldwGipvP 238
                                    p +  s++  ++k   ++f ++s+++++l +   e+ +  + +vk++  +wlk   +d++isr+  wG p+P
  gene905|gene905|rna905|rna905 122 PYCWRSDTPLIYKMVPNWFIHISDLREQLYKLN-EKIHWVPPSVKNKFGNWLKC-ARDWSISRNRFWGTPIP 191
                                    6788888888999999**************998.55557999***********9.9***************9 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 2.9e-07
                                    --S-EEEE--EEE.--------------HHHHHHHH-HHHHHHHHHH.HS-TTS-EEE-HHHHHHHHHHHCCCHHHHHH CS
                   tRNA-synt_1g 311 lpkkvvaheyltv.egkKlSkSrgvvvkakealerldadllRYylaa.eapekkDldfswedfvervNseLadklgnlv 387
                                    + k++++++ +   +gkK+Sk  ++  ++ e+++++ +d lR yl++      ++l+f+++ +  +v ++L+ ++ n +
  gene905|gene905|rna905|rna905 326 AFKNIIVNGIVLAeDGKKMSKRLKNYPDPMEIANSYGMDSLRIYLISsPVVVAENLKFTERGVK-EVFKNLMINWYNSL 403
                                    557788888766516899***************************9966788899999987765.56667777777765 PP

>> tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   2.1e-05     0.092     239     299 ..     328     391 ..     315     393 .. 0.76
   2 ?   -3.9   0.0       1.5   6.7e+03     124     149 ..     589     614 ..     564     625 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.1e-05
                                    EEEEEE--E.EETTBE--TTTT---BHHHHHTTS-HHHHHHHHHSS..-TTS-EEE-HHHHHHH CS
                   tRNA-synt_1e 239 kyflhnghl.kiegekmsksLknfitikdvlkkfdprqlRllllsa..hyrsqldfkeelleea 299
                                    k  + ng++   +g+kmsk Lkn+    ++ +++    lR++l+s      ++l+f+e  ++e+
  gene905|gene905|rna905|rna905 328 KNIIVNGIVlAEDGKKMSKRLKNYPDPMEIANSYGMDSLRIYLISSpvVVAENLKFTERGVKEV 391
                                    555566665145799****************************986114678888988877765 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 1.5
                                    -TTS-EEE-GGG-TTTTTTTT--HHH CS
                   tRNA-synt_1e 124 vsdgdvyfdvskkeeYgklskqnlee 149
                                     s++   f+++ k+++++++k+n e+
  gene905|gene905|rna905|rna905 589 DSEDSYEFSTRLKPNFAEIKKRNNEK 614
                                    34477789999999999998888764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (753 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       653  (0.0364214); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.67u 0.27s 00:00:00.94 Elapsed: 00:00:00.45
# Mc/sec: 5015.35
//
Query:       gene906|gene906|rna906|rna906  [L=641]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.15   12.6   1.5        1.2    9.6   0.1    2.6  2  DUF3899   Domain of unknown function (DUF3899)


Domain annotation for each model (and alignments):
>> DUF3899  Domain of unknown function (DUF3899)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.2     0.037   6.7e+02      44      68 ..     541     565 ..     527     569 .. 0.82
   2 ?    9.6   0.1   6.9e-05       1.2      39      80 ..     588     634 ..     578     638 .. 0.74

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.037
                        DUF3899  44 skkddsyyeykekkkesskkstrpl 68 
                                    +k+ ++ ++yk+k++++++++t++ 
  gene906|gene906|rna906|rna906 541 TKSFEHQFDYKSKEAAERSPVTSHS 565
                                    788999*******999999999875 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 6.9e-05
                        DUF3899  39 lflkk...skkddsyyeykekkkes..skkstrplliiGlllivlsi 80 
                                      ++k   ++ ++ y ++++ k e+  +++s++ +++iGl+ + + +
  gene906|gene906|rna906|rna906 588 ITSSKtiaKTDNETYKDQNKTKDEKscKTPSMVNCCLIGLIIVSVCL 634
                                    444445768888888888888777789************98765554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (641 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1206  (0.0672653); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.24s 00:00:00.85 Elapsed: 00:00:00.41
# Mc/sec: 4677.85
//
Query:       gene907|gene907|rna907|rna907  [L=111]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (111 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       314  (0.0175135); expected 358.6 (0.02)
Passed bias filter:                      178  (0.00992805); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.45
# Mc/sec: 738.52
//
Query:       gene908|gene908|rna908|rna908  [L=437]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.6e-10   41.1   5.3    4.7e-10   39.6   5.3    1.9  1  zf-RING_2     Ring finger domain
    1.8e-08   34.1   5.7    4.8e-08   32.7   5.7    1.8  1  zf-C3HC4      Zinc finger, C3HC4 type (RING finger)
      2e-07   30.9   3.4    4.4e-07   29.8   3.4    1.6  1  zf-RING_UBOX  RING-type zinc-finger
    1.2e-06   28.5   3.9    4.3e-06   26.8   3.9    2.1  1  zf-C3HC4_4    zinc finger of C3HC4-type, RING
    3.1e-06   26.9   5.4    8.4e-06   25.5   5.4    1.8  1  zf-C3HC4_2    Zinc finger, C3HC4 type (RING finger)
    4.1e-05   23.4   7.5    4.7e-05   23.3   5.9    2.1  1  zf-RING_5     zinc-RING finger domain
    4.3e-05   23.7   6.5     0.0002   21.5   6.5    2.1  1  zf-rbx1       RING-H2 zinc finger domain
    0.00079   19.1   1.7     0.0017   18.1   0.9    2.1  2  zf-RING_11    RING-like zinc finger
     0.0017   17.9   3.9     0.0047   16.5   3.9    1.8  1  Zn_ribbon_17  Zinc-ribbon, C4HC2 type
  ------ inclusion threshold ------
      0.011   15.6   2.0      0.029   14.2   2.0    1.7  1  zf-Nse        Zinc-finger of the MIZ type in Nse subunit
      0.022   15.1   0.0        0.1   12.9   0.0    2.2  2  ANAPC4_WD40   Anaphase-promoting complex subunit 4 WD40 domai
      0.023   14.7   4.2      0.086   12.9   4.2    2.0  1  zf-ANAPC11    Anaphase-promoting complex subunit 11 RING-H2 f
      0.066   13.4   4.5       0.21   11.7   4.5    1.9  1  zf-RING_10    zinc RING finger of MSL2
       0.11   12.4   5.8       0.32   10.9   5.8    1.8  1  Prok-RING_4   Prokaryotic RING finger family 4
       0.46   10.6   7.1          1    9.6   5.7    2.3  2  FYVE          FYVE zinc finger
       0.52   10.5  11.4       0.82    9.9   4.6    2.7  2  FYVE_2        FYVE-type zinc finger
        2.4    8.4   6.5        4.5    7.5   4.7    2.5  2  FANCL_C       FANCL C-terminal domain


Domain annotation for each model (and alignments):
>> zf-RING_2  Ring finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.6   5.3   4.4e-13   4.7e-10       1      43 [.       6      52 ..       6      53 .. 0.84

  Alignments for each domain:
  == domain 1  score: 39.6 bits;  conditional E-value: 4.4e-13
                      zf-RING_2  1 deCpICleel..ssadsvlllpCgHvfhreClerwlrssst..CPlC 43
                                   d+C+ICl+ +  +++++++ l+CgH f+ +C+++w++++++  CP+C
  gene908|gene908|rna908|rna908  6 DKCTICLNTYtlTDTHRPTSLECGHLFGNSCIRKWFNKQKSalCPTC 52
                                   58*****999444444466778*************9999999***** PP

>> zf-C3HC4  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.7   5.7   4.6e-11   4.8e-08       1      41 []       8      52 ..       8      52 .. 0.93

  Alignments for each domain:
  == domain 1  score: 32.7 bits;  conditional E-value: 4.6e-11
                                   -TTT-S--SS-E.....E-TTS--B-CHHHHHHHHCTSSB--TTT CS
                       zf-C3HC4  1 CpiCleeakepn....elleCkHsfCskCirkilksrkkvkCPlC 41
                                   C iCl++++ ++    ++leC+H f ++Cirk+ +++k+  CP+C
  gene908|gene908|rna908|rna908  8 CTICLNTYTLTDthrpTSLECGHLFGNSCIRKWFNKQKSALCPTC 52
                                   ********9999999********************666666**** PP

>> zf-RING_UBOX  RING-type zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8   3.4   4.2e-10   4.4e-07       1      39 []       8      50 ..       8      50 .. 0.90

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 4.2e-10
                   zf-RING_UBOX  1 CpIClelft.....dPlv.lpCGHtFCreClwelskslegafkCP 39
                                   C+ICl+++t     +P   l+CGH F  +C+  ++++++++  CP
  gene908|gene908|rna908|rna908  8 CTICLNTYTltdthRP-TsLECGHLFGNSCI-RKWFNKQKSALCP 50
                                   *************999.5469**********.6789999999898 PP

>> zf-C3HC4_4  zinc finger of C3HC4-type, RING
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8   3.9   4.1e-09   4.3e-06       1      42 []       8      52 ..       8      52 .. 0.81

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 4.1e-09
                     zf-C3HC4_4  1 CPiCldYL.....ekPvsleCGhsfClsCisslqkepdgeqllCplC 42
                                   C iCl+       + P+sleCGh f  sCi ++ ++++++  lCp C
  gene908|gene908|rna908|rna908  8 CTICLNTYtltdtHRPTSLECGHLFGNSCIRKWFNKQKSA--LCPTC 52
                                   777776432233368**********************886..***** PP

>> zf-C3HC4_2  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   5.4   7.9e-09   8.4e-06       1      40 []       7      52 ..       7      52 .. 0.81

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 7.9e-09
                     zf-C3HC4_2  1 kCpiCldmlkdpsvvt.....pCgHvfCqkCilrsLeekn..eCPlC 40
                                   kC+iCl+ +  + ++      +CgH f ++Ci+++ ++++   CP+C
  gene908|gene908|rna908|rna908  7 KCTICLNTYTLT-DTHrptslECGHLFGNSCIRKWFNKQKsaLCPTC 52
                                   7*****998654.33234467***************9988789**** PP

>> zf-RING_5  zinc-RING finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   5.9   4.5e-08   4.7e-05       1      44 []       7      54 ..       7      54 .. 0.96

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 4.5e-08
                      zf-RING_5  1 hCnkCfekl..skeekfyltsCgHifCekClkkll..ekeavCpiCrk 44
                                   +C +C + +  ++++++  ++CgH f ++C++k +  +k+a Cp+C k
  gene908|gene908|rna908|rna908  7 KCTICLNTYtlTDTHRPTSLECGHLFGNSCIRKWFnkQKSALCPTCTK 54
                                   6********************************99999********75 PP

>> zf-rbx1  RING-H2 zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   6.5   1.9e-07    0.0002      25      54 ..      22      52 ..       5      53 .. 0.66

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 1.9e-07
                        zf-rbx1 25 cpvvlGeCgHaFHlhCiskWlkt..rkvCPlc 54
                                    p  l eCgH F   Ci+kW+++  ++ CP+c
  gene908|gene908|rna908|rna908 22 RPTSL-ECGHLFGNSCIRKWFNKqkSALCPTC 52
                                   34444.9***************955556**** PP

>> zf-RING_11  RING-like zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.9   1.6e-06    0.0017       2      29 .]       8      37 ..       7      37 .. 0.81
   2 ?   -3.3   0.0       7.9   8.3e+03      13      21 ..     422     430 ..     422     430 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.6e-06
                     zf-RING_11  2 CsICLeefkpgqal..filpCsHtFHfkCI 29
                                   C+ICL++++  ++   + l+C+H+F   CI
  gene908|gene908|rna908|rna908  8 CTICLNTYTLTDTHrpTSLECGHLFGNSCI 37
                                   *********76655125778*****99998 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 7.9
                     zf-RING_11  13 qalfilpCs 21 
                                    +++++l C+
  gene908|gene908|rna908|rna908 422 DKIYVLTCK 430
                                    5799****6 PP

>> Zn_ribbon_17  Zinc-ribbon, C4HC2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   3.9   4.5e-06    0.0047       5      47 ..       6      51 ..       2      60 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 4.5e-06
                   Zn_ribbon_17  5 ksCayCela..vk.grvvlcgvCeHvlHasCarewfenddlaeCps 47
                                    +C++C  +  ++        +C+H   +sC+r+wf+++++a Cp+
  gene908|gene908|rna908|rna908  6 DKCTICLNTytLTdTHRPTSLECGHLFGNSCIRKWFNKQKSALCPT 51
                                   5677774331122122335678******************9***97 PP

>> zf-Nse  Zinc-finger of the MIZ type in Nse subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   2.0   2.7e-05     0.029      23      56 ..      22      52 ..       3      53 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.7e-05
                                   SEEEESSS--EEEHHHHHHHCTTTS-EE-SCCC- CS
                         zf-Nse 23 ePvtskkCpHvFEreaIlelikrkktvkCPvagC 56
                                   +P ts +C H F ++ I + ++++k++ CP   C
  gene908|gene908|rna908|rna908 22 RP-TSLECGHLFGNSCIRKWFNKQKSALCPT--C 52
                                   33.4559***********************9..7 PP

>> ANAPC4_WD40  Anaphase-promoting complex subunit 4 WD40 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       4.8   5.1e+03      27      44 ..      79      96 ..      69     112 .. 0.68
   2 ?   12.9   0.0   9.8e-05       0.1      33      90 ..     196     251 ..     170     253 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 4.8
                    ANAPC4_WD40 27 qrvwtleedkedsevrsL 44
                                   qr+  l+e+k++ e ++L
  gene908|gene908|rna908|rna908 79 QRIIALQEEKNKMEMENL 96
                                   556666555555555555 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 9.8e-05
                    ANAPC4_WD40  33 eedkedsevrsLaWkpdgklLavaysdgevrlldaesgkvvhslsvksekavtclgWg 90 
                                     +d++d ++++L+ +p +   a+ + +++v++++  +  v+ s+s +++  vt+l++ 
  gene908|gene908|rna908|rna908 196 RTDTKDVRIKDLKVSPFNDSTAILCYENTVKMINTANNSVLMSVSLQEQ--VTSLSYD 251
                                    67899*****************************************998..9999875 PP

>> zf-ANAPC11  Anaphase-promoting complex subunit 11 RING-H2 finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   4.2   8.2e-05     0.086      51      83 ..      27      58 ..       2      60 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 8.2e-05
                                   TTS-EEEHHHHHHHHHHHSTSSB-TTTSSB--B CS
                     zf-ANAPC11 51 kckhnfhlhcilkwletetskglcpmcrqtfkl 83
                                   +c h f + ci kw+++++s  lcp c ++ +l
  gene908|gene908|rna908|rna908 27 ECGHLFGNSCIRKWFNKQKS-ALCPTCTKMCRL 58
                                   6**************99887.69**99887665 PP

>> zf-RING_10  zinc RING finger of MSL2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   4.5    0.0002      0.21       3      46 ..       8      55 ..       7      67 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.0002
                     zf-RING_10  3 CvvCck..LLvdPlepkekeCqHyvCrlCvgk..kkklkpsCsqCkdy 46
                                   C++C +   L+d + p++ eC+H    +C++k  +k+  + C++C ++
  gene908|gene908|rna908|rna908  8 CTICLNtyTLTDTHRPTSLECGHLFGNSCIRKwfNKQKSALCPTCTKM 55
                                   9999773369********************985556666677777654 PP

>> Prok-RING_4  Prokaryotic RING finger family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   5.8    0.0003      0.32       1      39 [.       8      55 ..       8      60 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0003
                    Prok-RING_4  1 CvlCgeq.....ekkailepCgHlvCkeCfdsk....dlssCPlCqrr 39
                                   C +C +       + +    CgHl+ ++C  ++    +++ CP C + 
  gene908|gene908|rna908|rna908  8 CTICLNTytltdTHRPTSLECGHLFGNSCIRKWfnkqKSALCPTCTKM 55
                                   66666666666566666778*********888875424449****975 PP

>> FYVE  FYVE zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   5.7   0.00094         1       8      60 ..       4      57 ..       2      62 .. 0.88
   2 ?   -2.7   0.0       6.3   6.7e+03      49      60 ..     371     382 ..     336     385 .. 0.65

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00094
                                   --SB-TTT--B--SS.S--EE-TTT--EE-STTS-EEE.EEGGGTEEEEEEE-H CS
                           FYVE  8 evkkCeiCakkFsll.rrrhhCrlCGkvvCekCssklvallekeaeeksvrvCk 60
                                   +++kC+iC ++++l+ + r     CG+++ ++C +k +++++++   + +++C+
  gene908|gene908|rna908|rna908  4 NSDKCTICLNTYTLTdTHRPTSLECGHLFGNSCIRKWFNKQKSALCPTCTKMCR 57
                                   6799********999788889999**************9998887777777775 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 6.3
                                    GGTEEEEEEE-H CS
                           FYVE  49 keaeeksvrvCk 60 
                                    ke+++ + rvC+
  gene908|gene908|rna908|rna908 371 KETKRLRDRVCD 382
                                    333334447886 PP

>> FYVE_2  FYVE-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   4.6   0.00078      0.82      53     106 ..       4      58 ..       2      63 .. 0.88
   2 ?    3.9   0.5     0.058        61      15      48 ..      84     117 ..      70     161 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00078
                         FYVE_2  53 gethCilCleefkllvnskrqCldCklnvCkkCsve.nkkekvwlCkiCseaRev 106
                                    ++++C  Cl++++l  +++ + l+C     ++C ++  +k+k  lC +C +   +
  gene908|gene908|rna908|rna908   4 NSDKCTICLNTYTLTDTHRPTSLECGHLFGNSCIRKwFNKQKSALCPTCTKMCRL 58 
                                    5789******************************9976778889*****986555 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.058
                         FYVE_2  15 vqrdeklrkkeeeRlgelkeklekekskrellgn 48 
                                    +q +++  ++e+ Rl  l+e l+ke  k + +  
  gene908|gene908|rna908|rna908  84 LQEEKNKMEMENLRLMTLVELLQKELKKSSTIKA 117
                                    4566666778889*********999888776644 PP

>> FANCL_C  FANCL C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   4.7    0.0043       4.5       2      46 ..       5      46 ..       4      58 .. 0.78
   2 ?   -2.5   0.0       5.7   6.1e+03      14      26 ..     372     384 ..     366     387 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0043
                                   --S-SSS--SS-.TT-----B--S-TT----B-SGGGHHHHHHHHS CS
                        FANCL_C  2 eveCgiCyayrl.dsgevpdisCdnekCnkkfHsaCLkeWlrslke 46
                                   + +C iC++     + ++p+      +C++ f ++C+  W++++k+
  gene908|gene908|rna908|rna908  5 SDKCTICLNTYTlTDTHRPT----SLECGHLFGNSCIRKWFNKQKS 46
                                   578****9865504444443....468**************99876 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 5.7
                                    TT-----B--S-T CS
                        FANCL_C  14 dsgevpdisCdne 26 
                                    ++ ++ d +Cdn+
  gene908|gene908|rna908|rna908 372 ETKRLRDRVCDNN 384
                                    566788999*996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (437 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       855  (0.0476881); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 2939.67
//
Query:       gene909|gene909|rna909|rna909  [L=240]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.054   12.5   0.9      0.078   12.0   0.3    1.5  1  TMEM171   Transmembrane protein family 171


Domain annotation for each model (and alignments):
>> TMEM171  Transmembrane protein family 171
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.3   4.4e-06     0.078     219     308 ..     120     209 ..     112     222 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 4.4e-06
                        TMEM171 219 fPPPPPpyfaessasavtkspgassllasenPPsyysifndgrtqtaeeegaaserdkesiytisgtsssseisatqsls 298
                                    fP      f+   +s+     ++ + l ++ PP+y+s+   + t++++++ ++s +d+  +y+    +++  + + +++ 
  gene909|gene909|rna909|rna909 120 FPARNADTFSFGHTSSGDSVLSTINELWDDVPPPYTSLDTFTSTSFQDDDSNSSLEDRLRVYAQNIRHRNVYLPSYEEVI 199
                                    4444455566666666666666666678999*******99999********************99999988888888888 PP

                        TMEM171 299 selpPryeek 308
                                    se+    ee 
  gene909|gene909|rna909|rna909 200 SETIECEEEY 209
                                    8876655554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (240 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       542  (0.0302304); expected 358.6 (0.02)
Passed bias filter:                      453  (0.0252663); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1656.36
//
Query:       gene91|gene91|rna91|rna91  [L=60]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (60 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       377  (0.0210274); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.50u 0.31s 00:00:00.81 Elapsed: 00:00:00.53
# Mc/sec: 337.99
//
Query:       gene910|gene910|rna910|rna910  [L=159]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.4e-34  117.6   1.3    4.2e-34  117.3   1.3    1.1  1  Ribosomal_S11  Ribosomal protein S11


Domain annotation for each model (and alignments):
>> Ribosomal_S11  Ribosomal protein S11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.3   1.3   2.3e-38   4.2e-34       3     110 .]      39     155 ..      37     155 .. 0.98

  Alignments for each domain:
  == domain 1  score: 117.3 bits;  conditional E-value: 2.3e-38
                  Ribosomal_S11   3 ahiqasfnntiititdlkGaevlvksaGglgvkasr.kssPyaaqlaaekaaekvldkGikavevkvkg........pGp 73 
                                    +hi+a+ n+tii+ tdl+G e+++ks+Gg++vka+r +ss yaa+l a++++ k++++G +a+++k+++         Gp
  gene910|gene910|rna910|rna910  39 VHIKATKNDTIIHATDLTGSETIAKSSGGMKVKAHRdESSAYAAMLCAQDIVAKLKERGYDAIHIKIRArggsgskvHGP 118
                                    8******************************************************************************* PP

                  Ribosomal_S11  74 GreaalralaraGlkigriedvtPiPhdgirrpkkrr 110
                                    G + a+r+l r Gl++griedvtPi   ++rr+++rr
  gene910|gene910|rna910|rna910 119 GGQGAVRSLIRGGLRLGRIEDVTPIACGSVRRKGGRR 155
                                    **********************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       796  (0.0443973); expected 358.6 (0.02)
Passed bias filter:                      612  (0.0341346); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 1076.95
//
Query:       gene911|gene911|rna911|rna911  [L=133]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-05   24.5   0.0    2.8e-05   23.9   0.0    1.3  1  UBA       UBA/TS-N domain
    0.00098   18.7   0.2     0.0012   18.4   0.2    1.1  1  UCH       Ubiquitin carboxyl-terminal hydrolase
  ------ inclusion threshold ------
       0.12   12.8   0.0        0.2   12.1   0.0    1.4  1  RuvA_C    RuvA, C-terminal domain


Domain annotation for each model (and alignments):
>> UBA  UBA/TS-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.0   4.7e-09   2.8e-05       2      37 .]      28      63 ..      27      63 .. 0.94

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 4.7e-09
                                   CHHHHHHHHHTTS-HHHHHHHHHHTTTSHHHHHHHH CS
                            UBA  2 deeaiqrLveMGFdreevveALratgnNeErAveyL 37
                                   +e+ +++++++GF+r e+++AL   +nN++  +e L
  gene911|gene911|rna911|rna911 28 NEKLVDEILSLGFSRHEIQRALCLMNNNLNKSIELL 63
                                   8999**************************999987 PP

>> UCH  Ubiquitin carboxyl-terminal hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.2     2e-07    0.0012     175     256 ..       9     125 ..       3     126 .. 0.66

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 2e-07
                                    EEB--SEEE-GGGBSS-BTTS-TCS-B...........................................EEEEEEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxx...........................................xxxxxxxxxx RF
                            UCH 175 kvefpeeldlssylaeekkkkteekkk...........................................YeLiavvvHs 211
                                    ++ +p +ldls ++ ++k ++   k                                             +eL++ v ++
  gene911|gene911|rna911|rna911   9 NNHIPARLDLSDLIYKSKVNE---KLVdeilslgfsrheiqralclmnnnlnksielllntggkvsdnseFELFGGVKYY 85 
                                    566777777775554333222...1112345566666666666666666666666666666666666666********** PP

                                    S.CTTSEEEEEEEECTTTTEEEEEETTEEEEE-HHCCCTTCEEEEE CS
                                    x.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            UCH 212 G.slssGHYvayiknekngkWykydDetvkevkeeeevlssayiLf 256
                                      ++++GHY+ ++        + +dD+ + +vk +e+  ++  +L+
  gene911|gene911|rna911|rna911  86 TtGMNNGHYIYVRD------NVVIDDKDIRKVKINEKFYKHFLVLV 125
                                    *9*******98766......58999999999986655554555555 PP

>> RuvA_C  RuvA, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   3.4e-05       0.2      11      24 ..      36      49 ..      36      64 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.4e-05
                                   HHCTS-HHHHHHHH CS
                         RuvA_C 11 laLGYkekeaekAv 24
                                   l+LG++++e+++A+
  gene911|gene911|rna911|rna911 36 LSLGFSRHEIQRAL 49
                                   69***********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       483  (0.0269396); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 864.56
//
Query:       gene912|gene912|rna912|rna912  [L=479]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.3e-12   45.9   9.2    5.3e-12   45.9   9.2    3.4  3  zf-UBP       Zn-finger in ubiquitin-hydrolases and other prot
    1.3e-06   28.1   0.4    1.3e-06   28.1   0.4    1.8  2  UCH          Ubiquitin carboxyl-terminal hydrolase
  ------ inclusion threshold ------
       0.07   12.9   9.1       0.22   11.3   2.3    2.7  2  zf-UBP_var   Variant UBP zinc finger


Domain annotation for each model (and alignments):
>> zf-UBP  Zn-finger in ubiquitin-hydrolases and other protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   2.1      0.18   1.1e+03       1      47 [.      13      56 ..      12      73 .. 0.70
   2 !   45.9   9.2   8.9e-16   5.3e-12       2      63 ..     117     179 ..     112     180 .. 0.90
   3 ?   -1.0   0.9      0.38   2.3e+03       4      24 ..     275     292 ..     263     304 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.18
                                   -TTTH--...SSEEEETTT--EEE-TTTT-HHHHHHHHH---EEEETTT CS
                         zf-UBP  1 CseCnse..nknlWlCLkCghvgCgrksnghalkHyeetrHplavdlst 47
                                   Cs C  +  n+ +++C +C    C      h   H  +++H l++++++
  gene912|gene912|rna912|rna912 13 CSYCFRTssNDYIYAC-SCSVPICSL----HKSVHTSKPGHKLIFSVQN 56
                                   6667655322334555.788888886....8888999999999988865 PP

  == domain 2  score: 45.9 bits;  conditional E-value: 8.9e-16
                                    TTTH--.SSEEEETTT--EEE-TTT.....T-HHHHHHHHH---EEEETTT--EEETTTTEEBE-GC CS
                         zf-UBP   2 seCnsenknlWlCLkCghvgCgrks.....nghalkHyeetrHplavdlstlsvycyscddevedke 63 
                                    ++C+   ++lW+C +Cg+  Cgrk+     n+h+ +Hy+e++H  av+ +   +ycy c+++v+d +
  gene912|gene912|rna912|rna912 117 MKCD-V-QDLWVCFTCGYSACGRKQvylegNNHMEAHYKESKHSKAVRND--MIYCYVCEKYVYDVN 179
                                    6788.4.69********************99**************99755..69**********965 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.38
                                    TH--.SSEEEETTT--EEE-T CS
                         zf-UBP   4 CnsenknlWlCLkCghvgCgr 24 
                                    C+    n++ CL C     +r
  gene912|gene912|rna912|rna912 275 CS---ANPFSCLLCQITRVCR 292
                                    44...6899999998665555 PP

>> UCH  Ubiquitin carboxyl-terminal hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.1      0.33     2e+03      55     104 ..      77     125 ..      48     167 .. 0.64
   2 !   28.1   0.4   2.2e-10   1.3e-06       2     115 ..     244     351 ..     243     399 .. 0.71

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.33
                                    THHHHHHHHHHHHHHSH-CCEE--HHHHHHHHHHSGGGTSSSTCEHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            UCH  55 gelakalkdlfkellkskskavsPkklkktlsklaksfsgykqqDaqEfl 104
                                    g++ ++l +++  l ++++++   ++  k++ ++ + +s+ ++ D+q+++
  gene912|gene912|rna912|rna912  77 GQMEEHLLRMI-RLKGERECCSHSTTPQKIVYNETRCLSKKMKCDVQDLW 125
                                    33555555555.45555666666666666666666667777777777665 PP

  == domain 2  score: 28.1 bits;  conditional E-value: 2.2e-10
                                    EES-SSSTHHHHHHHHHHHTSHHHH.HHHHTCHHCCSSTCCCCC-....TT.TTS.TTHHHHHHHHHHHHHH....SH-C CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxx....xxxx RF
                            UCH   2 GlsNlGntCymnsvlQcLfsipelr.dyllsleevkkesrnkkel...nesnplgkkgelakalkdlfkell....ksks 73 
                                    G+ N GntCy+++v Q+L++i  ++   +l++      s n  ++   +        +++ ++lk+  k+l     ++ +
  gene912|gene912|rna912|rna912 244 GIANNGNTCYISCVFQLLAHILCFTtFHFLKC------SANPFSCllcQ-------ITRVCRELKSTEKSLKelteNTGT 310
                                    99***********************5455553......33333331112.......223555555544444455477778 PP

                                    CEE--HHHHHHHHHHSGGGTSSSTCEHHHHHHHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            UCH  74 kavsPkklkktlsklaksfsgykqqDaqEflaflLdqlhedl 115
                                     +++ k l+++l++    +  + qqD  E+l  +L++l ++ 
  gene912|gene912|rna912|rna912 311 DYINIKDLIRCLQRDGLVI-DGVQQDFSELLFLVLERLRSEE 351
                                    8999999999998888876.689***************7653 PP

>> zf-UBP_var  Variant UBP zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   2.3   3.6e-05      0.22      11      58 ..       9      54 ..       4      58 .. 0.85
   2 ?    4.8   0.7    0.0038        23      24      56 ..     120     161 ..      99     164 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 3.6e-05
                     zf-UBP_var 11 yKdECvycFdtpesedGlyvcLkcFlgfckkhaekhaektghpvylni 58
                                   y+ EC ycF+t  s+d +y c +c   +c+ h   h +k gh+++  +
  gene912|gene912|rna912|rna912  9 YRTECSYCFRTS-SNDYIYAC-SCSVPICSLHKSVHTSKPGHKLIFSV 54
                                   9*********97.56779999.89999999999999999999987665 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.0038
                     zf-UBP_var  24 sedGlyvcLkcFlgfck.........khaekhaektghpvyl 56 
                                    + + l vc +c  + c          +h+e+h+++++h+ ++
  gene912|gene912|rna912|rna912 120 DVQDLWVCFTCGYSACGrkqvylegnNHMEAHYKESKHSKAV 161
                                    556689*****77777779999*999**********998665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (479 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1123  (0.062636); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.25s 00:00:00.80 Elapsed: 00:00:00.41
# Mc/sec: 3465.90
//
Query:       gene913|gene913|rna913|rna913  [L=237]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.036   13.9   0.3        2.5    7.9   0.0    2.4  2  THDPS_N   Tetrahydrodipicolinate N-succinyltransferase N-term


Domain annotation for each model (and alignments):
>> THDPS_N  Tetrahydrodipicolinate N-succinyltransferase N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.0   0.00014       2.5      33      62 ..      81     113 ..      68     132 .. 0.82
   2 ?    3.5   0.1    0.0031        56      24      67 ..     187     231 ..     183     235 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00014
                                    -T-EEEEEE..S--EES.--HHHHHHHHHHHHH CS
                        THDPS_N  33 skkvlqaty..pvlNwk.enfgsaavfiealke 62 
                                    s+++l+ +y  p++N+k e +++++++i+al++
  gene913|gene913|rna913|rna913  81 SQRTLTNKYvvPLINYKgEKLAAYTIIINALSS 113
                                    5577777775588****************9976 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.0031
                                    EEEEEE.-SS-T-EEEEEES--EES--HHHHHHHHHHHHHTT--- CS
                        THDPS_N  24 iarvdr.gqkskkvlqatypvlNwkenfgsaavfiealkeakvev 67 
                                    i r+++ g k  k  +a+y +  + en+ ++ v +++ + ++ ev
  gene913|gene913|rna913|rna913 187 IIRMEIaGTKAVKKTCAKYYLGKYAENMLAYFVEMQSREMTENEV 231
                                    667776155556*******************99999988777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (237 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       872  (0.0486363); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1698.89
//
Query:       gene914|gene914|rna914|rna914  [L=132]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       555  (0.0309554); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 946.55
//
Query:       gene915|gene915|rna915|rna915  [L=38]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (38 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       254  (0.014167); expected 358.6 (0.02)
Passed bias filter:                      222  (0.0123822); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.32u 0.24s 00:00:00.56 Elapsed: 00:00:00.38
# Mc/sec: 301.49
//
Query:       gene916|gene916|rna916|rna916  [L=129]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       640  (0.0356964); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 968.24
//
Query:       gene917|gene917|rna917|rna917  [L=167]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       715  (0.0398795); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 1194.92
//
Query:       gene918|gene918|rna918|rna918  [L=360]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.6e-37  128.6   0.2    3.3e-37  128.3   0.2    1.1  1  Pkinase         Protein kinase domain
      2e-16   60.1   0.1    2.7e-16   59.6   0.1    1.1  1  Pkinase_Tyr     Protein tyrosine kinase
     0.0011   17.8   0.1     0.0017   17.2   0.1    1.2  1  Pkinase_fungal  Fungal protein kinase
     0.0013   18.2   0.8     0.0021   17.4   0.8    1.3  1  Kdo             Lipopolysaccharide kinase (Kdo/WaaP) family


Domain annotation for each model (and alignments):
>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  128.3   0.2   7.5e-41   3.3e-37      29     264 .]      92     330 ..      75     330 .. 0.83

  Alignments for each domain:
  == domain 1  score: 128.3 bits;  conditional E-value: 7.5e-41
                                    EEEEECHCHCHHHHHHHHHHHHHHHHHSCTTB--EEEEEEE.........SSEEEEEEE--TTEBHHHHHHHHSS--HHH CS
                        Pkinase  29 vKkikkekakkkkekkvlrEikilkklkhpnivrlyevfee.........kdelylvleyveggeladllerkgslseee 99 
                                    +K+   +k      ++ ++E +i  +l+hpn+++ y++f++         +d ++l  +++++     + ++ ++++e+ 
  gene918|gene918|rna918|rna918  92 IKRAIIRK------DTNTQEDTISMRLRHPNLLTTYKTFRTefvdrnnerQDIVWLYSQFLKHR----ISHKYVAMDENI 161
                                    44433333......34567999************************977666677777777744....3334456***** PP

                                    HHHHHHHHHHHHHHHHHTTEE-SS-SGGGEEEETTTE...EEE-SGTTSEESSSSCS.........BCTTTSCGGGS-HH CS
                        Pkinase 100 akkiakqilegleylHskgiiHrDlKpeNiLidekge...lKitDFGlakelesssk.........ltsfvgtseYlAPE 167
                                    +++i++ +l+gl+y+H+++i+H D+K +Ni+ +++++    K++DFG a+ l+ + k          ++  gt  Y +PE
  gene918|gene918|rna918|rna918 162 IRHILTDVLHGLRYMHERKIMHLDIKIANIMGQTENNrivYKLIDFGYARDLTLTDKgnkleeikiPSKSYGTFPYKPPE 241
                                    *********************************65556999***********99999999******9************* PP

                                    HHTTSCBSHHHHHHHHHHHHHHHHHSS-STTTSSHHHHHHHHHHTHHHHHHHCTSHH...HHHTTS-HHHHHHHHHHT-S CS
                        Pkinase 168 vlkeneyskkvDvWslGvilyelltgkppfsgekgkekvekeldqlekilkilgetkeklpeaseiseeakdllkkllkk 247
                                    v+ en ++ k+D+W +G + + l  g+ pf++++g++ ++  +++   ++    + ++k     e s+e++d++   +++
  gene918|gene918|rna918|rna918 242 VVFENVHGLKSDIWCVGAVAWFLSLGRVPFYHDNGEK-NTVTYRR---FI----KGTKKHFFYPETSNELRDFVLVSMNR 313
                                    *******************************888876.2233333...22....234555667788************** PP

                                    SGCCSTTHHHHHTSGGG CS
                        Pkinase 248 dpkkRltaeellqhpyl 264
                                     + +R++++ell+hp++
  gene918|gene918|rna918|rna918 314 RRANRPSVKELLKHPFI 330
                                    ***************97 PP

>> Pkinase_Tyr  Protein tyrosine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.6   0.1   6.1e-20   2.7e-16      88     257 ..     146     326 ..      91     327 .. 0.75

  Alignments for each domain:
  == domain 1  score: 59.6 bits;  conditional E-value: 6.1e-20
                                    HHHHHHHTCTTTSBHHHHHHHHHHHHHHHHHHHHTTEEEST-SGGGEEEEETT...EEEE-STTTHEETTTSSEEEETTS CS
                    Pkinase_Tyr  88 LlkfLrkkekekltlkdllsfalqvAkGmeyLeskklvHrdlaarNvLlsenk...vvkisDfGLardiekddeyvkkee 164
                                    L++ + +k   +++ + + ++ ++v +G++y++++k++H d+   N++ ++++   v k+ DfG ard++ +d+ +k ee
  gene918|gene918|rna918|rna918 146 LKHRISHK-YVAMDENIIRHILTDVLHGLRYMHERKIMHLDIKIANIMGQTENnriVYKLIDFGYARDLTLTDKGNKLEE 224
                                    55555555.6677777788999**************************8763323477***********99999988888 PP

                                    STSGGG......GS-HHHHHHSEEEHHHHHHHHHHHHHHHHTTSSGTTTTS...HHHHHHHHH.HTTEES-BBTTSBHHH CS
                    Pkinase_Tyr 165 aklpvk......WmapEslkekkftsksDvWsfGvllwEiftlgespypgl...kneevlekl.kegkrlekpekcpeel 234
                                     k+p k      + +pE+++e++   ksD+W+ G + w  ++lg+ p+ +    kn+ +++++ k  k+     ++++el
  gene918|gene918|rna918|rna918 225 IKIPSKsygtfpYKPPEVVFENVHGLKSDIWCVGAVAW-FLSLGRVPFYHDngeKNTVTYRRFiKGTKKHFFYPETSNEL 303
                                    88887632222266************************.6688****6543233444455555266677778888***** PP

                                    HHHHHHHT-SSGGGS--HHHHHH CS
                    Pkinase_Tyr 235 yelmkkcweedpeeRptfselve 257
                                     +++  +++++ ++Rp+ +el++
  gene918|gene918|rna918|rna918 304 RDFVLVSMNRRRANRPSVKELLK 326
                                    *******************9976 PP

>> Pkinase_fungal  Fungal protein kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.1   3.9e-07    0.0017     311     387 ..     165     244 ..     156     257 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 3.9e-07
                 Pkinase_fungal 311 alrDaIkghrsLflkagiLHrDiSenNilitdskkegerkglLiDLDlakelsddssesga......rertGTleFmaie 384
                                     l D++ g+r ++ + +i+H Di + Ni+    +++++    LiD+ +a +l  +++ ++        +  GT ++   e
  gene918|gene918|rna918|rna918 165 ILTDVLHGLRYMH-ERKIMHLDIKIANIMGQ--TENNRIVYKLIDFGYARDLTLTDKGNKLeeikipSKSYGTFPYKPPE 241
                                    589**********.**************988..778899999********999765555334444556677777776666 PP

                 Pkinase_fungal 385 vlk 387
                                    v+ 
  gene918|gene918|rna918|rna918 242 VVF 244
                                    666 PP

>> Kdo  Lipopolysaccharide kinase (Kdo/WaaP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.8   4.7e-07    0.0021     114     172 ..     156     213 ..     143     226 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 4.7e-07
                            Kdo 114 elaeelkrallkavgrliaklhragvnHadlyaknillqqeeeeeaeiwliDldkarlr 172
                                     ++e+  r++l +v    + +h+++++H d+ + ni+ q+e+ + +   liD+  ar  
  gene918|gene918|rna918|rna918 156 AMDENIIRHILTDVLHGLRYMHERKIMHLDIKIANIMGQTEN-NRIVYKLIDFGYARDL 213
                                    37888899999999999************************7.999*******877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (360 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       460  (0.0256568); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 2390.74
//
Query:       gene919|gene919|rna919|rna919  [L=57]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (57 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       943  (0.0525964); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.25s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 429.31
//
Query:       gene92|gene92|rna92|rna92  [L=258]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      6e-93  310.7   1.4      7e-93  310.4   1.4    1.0  1  PMM          Eukaryotic phosphomannomutase
    4.6e-07   29.8   0.0    2.3e-06   27.6   0.0    1.8  1  Hydrolase_3  haloacid dehalogenase-like hydrolase
     0.0023   18.3   0.0        1.3    9.3   0.0    2.3  2  Hydrolase    haloacid dehalogenase-like hydrolase
     0.0042   16.7   0.0        2.5    7.6   0.0    2.1  2  S6PP         Sucrose-6F-phosphate phosphohydrolase
  ------ inclusion threshold ------
      0.033   14.6   0.0        0.7   10.3   0.0    2.2  2  HAD          haloacid dehalogenase-like hydrolase


Domain annotation for each model (and alignments):
>> PMM  Eukaryotic phosphomannomutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  310.4   1.4   1.9e-96     7e-93       1     220 [.      28     246 ..      28     247 .. 0.99

  Alignments for each domain:
  == domain 1  score: 310.4 bits;  conditional E-value: 1.9e-96
                                HHHHHHHHCTTSEEEEE-SS-HHHHHHHHS.TTHHHH-SEEEEGGGTEEEETTEEEEE--HHHHH-HHHHHHHHHHHHHHHHCS CS
                        PMM   1 lkeflqklrkkveigvvgGsdlekikeqlagdevldefdyvfsenGlvaykkgkelasqsiiealgeeklkklinfvlryladl 84 
                                + +flq+lr +v i++vgGs+lek++eq+   e+l  fd+ f+enGl  y+ ++ ++++ i+ +lgee l++++nf+l+yl+ +
  gene92|gene92|rna92|rna92  28 MLQFLQELRTQVYIAFVGGSNLEKQQEQVC-PEILTLFDFSFPENGLSYYRGTELVSKRCIKDFLGEEILQNFVNFCLHYLSTI 110
                                5789*************************5.***************************************************** PP

                                --S---S-SEEEESSEEEE-SS-TTSSHHHHHHHHHHHHHHTHHHHHHHHHHHHTTTSSEEEEEETTTEEEEEETT-SGGGGGG CS
                        PMM  85 dlPvkrGtfiefrngllnvsPiGrnasqeernefeeydkkekireklvealkeefadlgltfsiGGqisfdvfPkgWdktyclq 168
                                +lPvkrG fie r++++nvsP+Gr ++ eer++f eydk++kire++v++lk+ef +++++f+iGGqis+d fPkgWdk+yclq
  gene92|gene92|rna92|rna92 111 KLPVKRGLFIEMRDSMVNVSPVGRTCNDEERQQFFEYDKQHKIRENMVQVLKKEFGKYDMHFCIGGQISIDCFPKGWDKRYCLQ 194
                                ************************************************************************************ PP

                                GCTTST-SEEEEEESS-STTSTTHHHHHSTTCEEEE-SSHHHHHHHHHHHHT CS
                        PMM 169 hvekdsfdeihffGdktaeGGndyeiyadprtighsvtspddtvkkleellk 220
                                h+e +++++++ffGd  +eGGndyei++d+r++g  v+sp dt +k++e+l+
  gene92|gene92|rna92|rna92 195 HLEGEGIKNVYFFGDMVHEGGNDYEIFEDDRVVGIPVSSPSDTFRKCKEVLE 246
                                **************************************************97 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   0.0   6.4e-10   2.3e-06       2     220 ..      10     222 ..       9     231 .. 0.72

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 6.4e-10
                                EEEIIIIIS-TTS---HHHHHHHHHHHHTTSEEEEE-SS-HHHHHH.HHHHCCCC..SEEEEGGGTEEECTTTEEEEE--B-HH CS
                Hydrolase_3   2 alDlDGTLlnsdkkisektkeaikklkekgikvviATGRslravlp.vleelgld..lpvialNGaliddekgkilykstiske 82 
                                 +D+DGTL  s kki++   + +++l+  ++++++  G +l++ ++ v  e+  +   +    NG    +   ++++k+ i+  
  gene92|gene92|rna92|rna92  10 LFDVDGTLTPSRKKIKPDMLQFLQELR-TQVYIAFVGGSNLEKQQEqVCPEIL-TlfDFSFPENGLSY-YRGTELVSKRCIKDF 90 
                                69*************************.8999999999887766550555444.33489999***999.899999999999866 PP

                                HHHHHHHHHHHTTCEEEEEESSEEEESTT.THHHHHHHHHCHCTCEEEESHHHHHCHCSESEEE.EES-HHHHHHHHHHHHHHC CS
                Hydrolase_3  83 dvkeiikllkennveillytedkvyvlnkeksekkkkeeektkkkkeeidseeeledeeiakil.ilkdkekldelekelkskl 165
                                  +ei++ + ++ +++l  ++ k+ v++          +e  ++ ++ +    + +dee  +++ ++k+++  +++ + lk+++
  gene92|gene92|rna92|rna92  91 LGEEILQNFVNFCLHYL--STIKLPVKRG-------LFIEMRDSMVNVSPVGRTCNDEERQQFFeYDKQHKIRENMVQVLKKEF 165
                                66666655555333322..3333333333.......333333333333333333333333446656777777778888888888 PP

                                TTTE.EEEEESTTEEEEEETT-SHHHHHHHHHHHCT--GGGEEEEES....SGGGHHHHH CS
                Hydrolase_3 166 nkll.titssskgyleimpkgvsKgtalkklakelnisleeviafGD....geNDieMLe 220
                                +k   ++   ++ +++  pkg++K   l++l    +   ++v+ fGD    g ND+e +e
  gene92|gene92|rna92|rna92 166 GKYDmHFCIGGQISIDCFPKGWDKRYCLQHLE---GEGIKNVYFFGDmvheGGNDYEIFE 222
                                7754699999*********************9...8999********5555579999987 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.0   0.00036       1.3       3      26 ..       8      35 ..       7      92 .. 0.78
   2 !    6.9   0.0     0.002       7.1     148     200 ..     158     211 ..     147     214 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00036
                               EEEEESBTTTBCHH....HHHHHHHHHH CS
                               xxxxxxxxxxxxxx....xxxxxxxxxx RF
                  Hydrolase  3 tvvfDkdGTLttge....psvedvivsa 26
                               +++fD+dGTLt ++    p   ++++++
  gene92|gene92|rna92|rna92  8 VFLFDVDGTLTPSRkkikPDMLQFLQEL 35
                               789********66644445555555555 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.002
                                HHHHHHHTTGGGESEEEEHHCESSTTTSHHHHHHHHHHHTST.GGGEEEEESSH CS
                                xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxx RF
                  Hydrolase 148 aeraanqlGddyfdaviasdietvakpspegkvaaireLqgk.peevamVGDgv 200
                                ++ + +++G+  +++ i++ i+    p+ ++k++ ++ L g+ +++v ++GD v
  gene92|gene92|rna92|rna92 158 VQVLKKEFGKYDMHFCIGGQISIDCFPKGWDKRYCLQHLEGEgIKNVYFFGDMV 211
                                455556688777788888888888889************98879********76 PP

>> S6PP  Sucrose-6F-phosphate phosphohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.0   0.00068       2.5       3      53 ..       7      56 ..       5     112 .. 0.78
   2 !    7.3   0.0   0.00083         3     124     210 ..     145     235 ..     136     255 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.00068
                               EEEEE-TBTTTB.S-HHHHHHHHHHHH.GGGGGEEEEEE-SS-HHHHHHHH CS
                       S6PP  3 lllvsdLDntlvdgdnealarlnelleaeerkdvllvfaTGRsldsakell 53
                                +++ d+D+tl+++ ++   ++ ++l+ e r +v++ f+ G +l++++e +
  gene92|gene92|rna92|rna92  7 TVFLFDVDGTLTPSRKKIKPDMLQFLQ-ELRTQVYIAFVGGSNLEKQQEQV 56
                               67899*******777777789******.9*************999988765 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.00083
                                E-TTS-THHHHHHHHHHHTTTS-EEEEEET..TTEEEEEETT-SHHHHHHHHHHHHT--GGGEEEEE-S....GGGHHHH.TSS CS
                       S6PP 124 vdkekaaevlkeleqlLekreldvkviyss..gkdlDvlPkraskgeAlryLakkleleleqilvcGds....gnDeell.ign 200
                                 + +k++++ +++ q L+k+  + ++++    +  +D  Pk+ +k + l++L        +++ + Gd     gnD e++    
  gene92|gene92|rna92|rna92 145 FEYDKQHKIRENMVQVLKKEFGKYDMHFCIggQISIDCFPKGWDKRYCLQHLEGE---GIKNVYFFGDMvhegGNDYEIFeDDR 225
                                455566677899999999987666666655105678*********9999988764...46777777774444489999997778 PP

                                SEEEE-TT-- CS
                       S6PP 201 vlgVvVgnaq 210
                                v g+ V+  +
  gene92|gene92|rna92|rna92 226 VVGIPVSSPS 235
                                8898887655 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0    0.0002       0.7       2      77 ..      10      91 ..       9     106 .. 0.66
   2 ?    2.3   0.0     0.055     2e+02     145     181 ..     180     211 ..     143     213 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0002
                        HAD  2 lfDfDgTLldgdsle......lllrfllrrgaprlwralreklllalfrellrldraglaelleallaglseelaaelerfv 77
                               lfD+DgTL+++   +      +l + ++++     +  ++ek  +++  e+l+l++ ++ e+  ++++g +   ++ +++f+
  gene92|gene92|rna92|rna92 10 LFDVDGTLTPSRKKIkpdmlqFLQELRTQVYIAFVGGSNLEKQQEQVCPEILTLFDFSFPENGLSYYRGTELVSKRCIKDFL 91
                               8*********954444777755555444444444466666667777777777777777777777777777666655555555 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.055
                        HAD 145 egkpvrgegkvaalrewlaaegegidleevvayGDsp 181
                                ++ + +g++k  +l+       eg  +++v+++GD +
  gene92|gene92|rna92|rna92 180 IDCFPKGWDKRYCLQH-----LEGEGIKNVYFFGDMV 211
                                3334445566666666.....55555567******65 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       682  (0.0380389); expected 358.6 (0.02)
Passed bias filter:                      556  (0.0310112); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.52u 0.24s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 1840.72
//
Query:       gene920|gene920|rna920|rna920  [L=129]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       322  (0.0179597); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 936.09
//
Query:       gene921|gene921|rna921|rna921  [L=444]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.3e-27   94.2   0.0    1.6e-26   93.4   0.0    1.4  1  Hexokinase_1     Hexokinase
    8.2e-13   48.3   0.2      1e-08   34.9   0.1    2.2  2  Hexokinase_2     Hexokinase
     0.0025   17.6   0.0     0.0043   16.8   0.0    1.4  1  AAA_15           AAA ATPase domain
     0.0085   15.9   0.3      0.015   15.1   0.3    1.4  1  DNA_pol3_delta2  DNA polymerase III, delta subunit


Domain annotation for each model (and alignments):
>> Hexokinase_1  Hexokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.4   0.0   3.6e-30   1.6e-26       5     197 ..      19     211 ..      16     213 .. 0.87

  Alignments for each domain:
  == domain 1  score: 93.4 bits;  conditional E-value: 3.6e-30
                                    HHHHH---HHHHHHHHHHHHHHHHHHHS.S.STS--EE----S..---S--EEEEEEEEESSSEEEEEEEEEESSS.-EE CS
                   Hexokinase_1   5 ilkqfelsdeklkelvdrfleemekgLakekeslkmlptyvtr..lPtGkekGtylAlDlGgtnlRvllveLlges.kve 81 
                                    ++++f  sd+ l +l+ +  +em ++ a  ++  ++l+tyv+     t + + ++l +D+Gg+ l++    L+g++ k  
  gene921|gene921|rna921|rna921  19 LESEFLHSDDMLTNLSIDYWREMMDNFAAGANRQHFLDTYVKVsdHSTITYDKEMLVIDFGGSFLKCGIYALEGKTvKPI 98 
                                    67899999999999999999*******97766699*****98733455556689******************99653333 PP

                                    EEEEEEE--GGGGGS.BHHHHHHHHHHHHHHHHHHH....ST..T-S-EEEEEEE-SSEE-SBTT--EE-S--TT---TT CS
                   Hexokinase_1  82 itqekykipeelktg.taeeLFdfiakciaefleeegeekkeekeeeelplGftFSFPveqtsldegtlirwtKgfaikd 160
                                       e+y++p++ +++ +  + F+++a +i+ fl++++  k        l+ G+tFS Pv+qts+++gt+++++K+f  k+
  gene921|gene921|rna921|rna921  99 HPIEQYPLPKRWRNStKRADCFEWMAFHIDYFLRSKNYCK-------ALRAGMTFSHPVNQTSIRSGTILSLGKDFPFKN 171
                                    55666*********977789***************97663.......49***************************9988 PP

                                    -T...TSBHHHHHHHHHHHTT-SEEEEEEE-HHHHHHHHH CS
                   Hexokinase_1 161 ve...gkdvvqllqealerkglpvkvvalvNDTvgtllsl 197
                                          +d v+ll+++l+++++pv v  l+ND+++tl+s 
  gene921|gene921|rna921|rna921 172 IDitkENDPVKLLNKELQKRKVPVVVDVLLNDATATLASI 211
                                    4444599******************************986 PP

>> Hexokinase_2  Hexokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.9   0.1   2.3e-12     1e-08       2      82 ..     223     292 ..     222     301 .. 0.79
   2 !   12.0   0.0   2.3e-05       0.1     125     234 ..     307     416 ..     289     422 .. 0.66

  Alignments for each domain:
  == domain 1  score: 34.9 bits;  conditional E-value: 2.3e-12
                                    EEEEESSSEEEEEEEEGGG-GGGTTTS-TTSEEEEE--GGGTTTT-SS-..--HHHHHHHHHSSSTTS-..HHHHCCSHH CS
                   Hexokinase_2   2 iGlIlGtGtNacyleklsnieklegkkeksgemviNtEwgafgdegklpllrtkyDkeldeespnpgeq..lfEkmiSGm 79 
                                    iG+IlGtGtNa+y++++  +   +      +  +iNtEw +f++   l+l +t++D++++e  +++g+   +++ m++G+
  gene921|gene921|rna921|rna921 223 IGIILGTGTNAAYVDHI--FC--K------KPRIINTEWASFDS---LNLNVTPCDERIEEMVKEEGKVykRLDCMVGGY 289
                                    9**************99..33..2......2349********98...6667**********9888887544888888887 PP

                                    HHH CS
                   Hexokinase_2  80 YLG 82 
                                     + 
  gene921|gene921|rna921|rna921 290 QFA 292
                                    555 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 2.3e-05
                                    BTT-HHHHHHHHHCCS---.-HHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHH-.....SSEEEEEESHHHHHSTT...H CS
                   Hexokinase_2 125 sedleevrevleellglesvteedleivrevceavsrRaarlvAagiaallkklgkeekekvtvgvdGslyekypk...f 201
                                    + +l+++ +++ee  + +s  +++ +++ +  e+  +R a++  + + +l+k    + ++ v+++++Gs + + ++   f
  gene921|gene921|rna921|rna921 307 RLKLDDILRIVEEC-ETKSFISDQEMFICKCYEVLKKRNAQILVTLVLSLIKSQAVQPSTMVEIAINGSQFSNPKElrfF 385
                                    34455555555554.45454445556777888999*****************95555567888********954441114 PP

                                    HHHHHHHHHHHHT--S.-SEEEEE---TTTHHH CS
                   Hexokinase_2 202 rerlqealrellgeepekkvklklaedGsgvGA 234
                                    +e l++   + l   + +++++ +a d+ ++G+
  gene921|gene921|rna921|rna921 386 EEELKRQCATSL--YKYENFRFIPAFDATLTGT 416
                                    444444444444..3458999999999988885 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   9.6e-07    0.0043     301     362 ..     291     350 ..     241     350 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 9.6e-07
                         AAA_15 301 vqrllllillileaekkdekeeknvilliEEPEahLHpqaqkvlikllkelandnktQviit 362
                                    + +l+ +  +++++ k+   + + +++++EE E+  +++ q+++i +++e++++ + Q+++t
  gene921|gene921|rna921|rna921 291 FANLINIMCERENITKR--LKLDDILRIVEECETKSFISDQEMFICKCYEVLKKRNAQILVT 350
                                    45888888899999888..88899************************************98 PP

>> DNA_pol3_delta2  DNA polymerase III, delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.3   3.3e-06     0.015      64     123 ..     287     348 ..     231     352 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.3e-06
                DNA_pol3_delta2  64 eqgkhpDvivi..eteekersikldqirelieelsrkpreskkkiiiiedaekmtksAaNal 123
                                      +++ ++i i  e e+ ++ +kld+i ++ ee + k+++s + ++i +  e ++k+ a +l
  gene921|gene921|rna921|rna921 287 GGYQFANLINImcERENITKRLKLDDILRIVEECETKSFISDQEMFICKCYEVLKKRNAQIL 348
                                    456677776665566777789***********************************998777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (444 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       495  (0.0276089); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.39
# Mc/sec: 3422.05
//
Query:       gene922|gene922|rna922|rna922  [L=308]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
     0.0011   18.9   5.4     0.0033   17.4   5.4    1.9  1  zf-BED     BED zinc finger
  ------ inclusion threshold ------
      0.015   15.0   7.4      0.044   13.5   7.4    1.9  1  zf-H2C2_5  C2H2-type zinc-finger domain
      0.021   15.3   0.5      0.021   15.3   0.5    2.3  2  zf-H2C2_2  Zinc-finger double domain
      0.041   13.9   0.9      0.084   12.9   0.9    1.6  1  PriA_CRR   PriA DNA helicase Cys-rich region (CRR) domain
      0.096   13.2  12.6      0.096   13.2   8.0    2.9  3  zf-C2H2    Zinc finger, C2H2 type
       0.24   12.3   6.0       0.94   10.5   6.0    2.1  1  zf-C2H2_4  C2H2-type zinc finger


Domain annotation for each model (and alignments):
>> zf-BED  BED zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   5.4   1.1e-06    0.0033      16      44 .]     281     306 ..     271     306 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.1e-06
                                    --EETTTTEE----SSTHHHHHHHHHS-H CS
                         zf-BED  16 kavCryCgkilsrgggttnLkrHLrrkHp 44 
                                      +C++C +++ ++   ++L++H++++Hp
  gene922|gene922|rna922|rna922 281 EYKCNHCDFTYIYR---KCLITHMKKRHP 306
                                    569**********9...***********8 PP

>> zf-H2C2_5  C2H2-type zinc-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   7.4   1.5e-05     0.044       1      24 [.     282     305 ..     282     306 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.5e-05
                      zf-H2C2_5   1 YKCsqCDYstawksnLkRHlrrkH 24 
                                    YKC++CD++  +++ L  H+++ H
  gene922|gene922|rna922|rna922 282 YKCNHCDFTYIYRKCLITHMKKRH 305
                                    9********************666 PP

>> zf-H2C2_2  Zinc-finger double domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.5   6.9e-06     0.021       3      24 ..     270     291 ..     270     293 .. 0.92
   2 ?   -0.6   0.8      0.71   2.1e+03       4      10 ..     299     306 ..     297     308 .] 0.71

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 6.9e-06
                      zf-H2C2_2   3 rrHirkHtgekpyeCplCdkaF 24 
                                    ++H++ H ++++y+C  Cd ++
  gene922|gene922|rna922|rna922 270 NWHLAIHESDREYKCNHCDFTY 291
                                    58*****************998 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.71
                      zf-H2C2_2   4 rHirk.Ht 10 
                                     H++k H+
  gene922|gene922|rna922|rna922 299 THMKKrHP 306
                                    6**98676 PP

>> PriA_CRR  PriA DNA helicase Cys-rich region (CRR) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.9   2.8e-05     0.084       7      25 ..     272     290 ..     270     291 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.8e-05
                       PriA_CRR   7 sltyHksrnrLrCHyCgyt 25 
                                    +l  H s+++ +C +C++t
  gene922|gene922|rna922|rna922 272 HLAIHESDREYKCNHCDFT 290
                                    6889*************97 PP

>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0      0.22   6.6e+02       8      19 ..     194     205 ..     182     206 .. 0.85
   2 ?   -3.0   0.1       4.5   1.3e+04      11      19 ..     268     276 ..     262     277 .. 0.56
   3 ?   13.2   8.0   3.2e-05     0.096       1      23 []     282     305 ..     282     305 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.22
                                    EEESSHHHHHHH CS
                        zf-C2H2   8 ksFkrksnLkrH 19 
                                    k  +++s+L +H
  gene922|gene922|rna922|rna922 194 KGVRTNSMLLKH 205
                                    67799******9 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 4.5
                                    SSHHHHHHH CS
                        zf-C2H2  11 krksnLkrH 19 
                                    + + +L  H
  gene922|gene922|rna922|rna922 268 RENWHLAIH 276
                                    455566655 PP

  == domain 3  score: 13.2 bits;  conditional E-value: 3.2e-05
                                    EEETTTTEEESSHHHHHHHHHC.C CS
                        zf-C2H2   1 ykCpdCgksFkrksnLkrHirt.H 23 
                                    ykC++C+ ++  +  L +H+++ H
  gene922|gene922|rna922|rna922 282 YKCNHCDFTYIYRKCLITHMKKrH 305
                                    9*********************99 PP

>> zf-C2H2_4  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   6.0   0.00031      0.94       1      24 []     282     305 ..     282     305 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00031
                      zf-C2H2_4   1 fkCpiCgksFsskkaLlrHlkthH 24 
                                    +kC +C+ ++  +k L +H+k+ H
  gene922|gene922|rna922|rna922 282 YKCNHCDFTYIYRKCLITHMKKRH 305
                                    89****888877777*******99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (308 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       682  (0.0380389); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 2443.49
//
Query:       gene923|gene923|rna923|rna923  [L=414]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.1e-32  112.6   0.5    2.6e-21   76.4   0.1    3.4  2  RNase_HII  Ribonuclease HII


Domain annotation for each model (and alignments):
>> RNase_HII  Ribonuclease HII
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4   0.1   7.5e-11   1.3e-06       1      29 [.      65      93 ..      65      98 .. 0.90
   2 !   76.4   0.1   1.4e-25   2.6e-21      30     196 ..     202     388 ..     191     390 .. 0.84

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 7.5e-11
                                   EEEEEE-TT-SBS-EEEEEEEECGHHHHH CS
                      RNase_HII  1 iGiDEaGrGpvlGplvvaavavekereee 29
                                   iGiDEaGrGpvlG lv+aa +v+++++  
  gene923|gene923|rna923|rna923 65 IGIDEAGRGPVLGYLVYAALLVNEDDATS 93
                                   8**********************998765 PP

  == domain 2  score: 76.4 bits;  conditional E-value: 1.4e-25
                                    HHCTTGTTGTTS-HHHHHHHHHHHH..........................SEEEEEEE-HHHHH..HHTTTS-HHHHHH CS
                      RNase_HII  30 lkklgvkDSKkLskqkreeLaklik..........................kkiekrklvaeeiky.aseneinlneika 82 
                                     + +++ DSK+L +++re + ++i                            +i++   ++  i    ++ + n n+ + 
  gene923|gene923|rna923|rna923 202 KETIRMCDSKQLLPKQRESIYEQIItthsyvwyalhpqyistemdrrnlndISISAVIHILTTILNaLDQPNSNTNQPNS 281
                                    4667889**************************************99998855555555555444324456666666666 PP

                                    HHHHHHHHHHHHTCEECCECCCE--SSHHHHHHHHHHHHC.CEEEEETTGGGT-HHHHHHHHHHHHHHHHHHHHHHHHCS CS
                      RNase_HII  83 altlaviklleklgvkvdeilvdgvttpeslkkkleqiik.ikvtvekkadekyllvaaASiiAkverdeelellkrkpg 161
                                    +++   ++     +  +++++vd+ ++ +++++ l+q+++ i+++ve kad++y +v  ASi+Akv rd    ll+r+  
  gene923|gene923|rna923|rna923 282 NTKPSRKDNQTRAAHTITKVYVDALGSTNKYEHILRQHFPhIPFVVEYKADSTYRCVGGASIVAKVVRDD---LLRRF-- 356
                                    666666667777799999***************************************************5...55666.. PP

                                    H.--TTSSTTSHHHHHHHHHHHHHS--TTB-TTSH CS
                      RNase_HII 162 tldkgsGyasdektrallkkgatsklpdivrlsfk 196
                                     ++ gsGy+sd +t  +l  +  s   ++vr++++
  gene923|gene923|rna923|rna923 357 SVQCGSGYPSDWRTVGWLSTNRES---EMVRFKWA 388
                                    35789*****************99...9******8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (414 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       879  (0.0490267); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.43
# Mc/sec: 2859.46
//
Query:       gene924|gene924|rna924|rna924  [L=639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.27   11.2   3.1       0.62   10.0   3.1    1.6  1  DUF1967   Domain of unknown function (DUF1967)


Domain annotation for each model (and alignments):
>> DUF1967  Domain of unknown function (DUF1967)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   3.1   3.5e-05      0.62      23      66 ..     296     339 ..     286     340 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 3.5e-05
                                    HTTEEE-TGGGHHHHHHHHHHTTHHHHHHTTT--TT-EEEETTE CS
                        DUF1967  23 vkqtnfeneeavrrfarrLkklGvedaLrkaGakeGdtVrIgdv 66 
                                    ++++++ +   v+r   +++++Gv+ ++r++G+     VrIg++
  gene924|gene924|rna924|rna924 296 MRRMEVMRRMEVMRRMGVMRRMGVMRRMRRMGVMRVMRVRIGKI 339
                                    555666666667777789***********************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (639 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       289  (0.0161191); expected 358.6 (0.02)
Passed bias filter:                      118  (0.00658152); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.62u 0.26s 00:00:00.88 Elapsed: 00:00:00.49
# Mc/sec: 3889.35
//
Query:       gene925|gene925|rna925|rna925  [L=867]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-46  158.1   0.3    1.1e-45  155.9   0.0    2.3  3  RVT_1     Reverse transcriptase (RNA-dependent DNA polymerase
     0.0025   18.0   0.6      0.011   15.9   0.6    2.1  1  PHF5      PHF5-like protein


Domain annotation for each model (and alignments):
>> RVT_1  Reverse transcriptase (RNA-dependent DNA polymerase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.1      0.18   1.7e+03      19      69 ..      16      66 ..       8      71 .. 0.60
   2 ?   -2.4   0.1       0.3   2.7e+03      18      59 ..      64     104 ..      54     121 .. 0.68
   3 !  155.9   0.0   1.2e-49   1.1e-45       1     222 []     281     529 ..     281     529 .. 0.96

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.18
                                   THHHHCTB--.........-------HHHH...................HCCHTS-- CS
                          RVT_1 19 ykalnkliakrLkdvlekllsenqpgfrpgrstldav......edllkalkkkkkak 69
                                   + +++k++++      +  +s++++  ++ +s+++a+      ++l+k+  k k++k
  gene925|gene925|rna925|rna925 16 LEVMSKIMNN-----RRWEISNDLSLAEKYKSCIKAIndisweYHLKKE-VKSKQNK 66
                                   3344444444.....2334899999999999999999887774444444.4444444 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.3
                                    -THHHHCTB--.........-------HHHH........... CS
                          RVT_1  18 dykalnkliakrLkdvlekllsenqpgfrpgrstldavedll 59 
                                    + k+++++++k +++  ++   ++ pgf+   s ++ ++++ 
  gene925|gene925|rna925|rna925  64 QNKCYSRRTKKLIEKRRQNYKGHKKPGFDWL-SHEELTDQAD 104
                                    5588888999988888888888999999888.3333222222 PP

  == domain 3  score: 155.9 bits;  conditional E-value: 1.2e-49
                                    EE-TT.....S-EEE......-THHHHCTB--...........-------HHHH................HCCHTS--EE CS
                          RVT_1   1 ipKkg....pgsyRpisllsvdykalnkliakrLkdvl..ekllsenqpgfrpgrstldav...edllkalkkkkkakll 71 
                                    +pKkg    +++yR isl+++++k + k+i + L+ ++  +k+l ++q gfr+ + ++ ++   ++++k  + k+k +++
  gene925|gene925|rna925|rna925 281 VPKKGdlhnMDNYRGISLINTLCKEVVKIITEKLNRICttNKILRDEQAGFRKLEECIAQTtcfYEIVKRRSLKGKPTMA 360
                                    699999**********************************************************8999987888888*** PP

                                    EEEEBCCGCCCSBB-GGGGGGG-EEET.........................TEEEEESB--ST-TTHHHHHHHHHHHHH CS
                          RVT_1  72 lklDlkkaFdsvpleellrkltafkvptklinliksflstrsfsvrvngeeskgryekkglpqGsvlSPllfnlfmnell 151
                                    l+lD+kka+d+vp+e l+ kl  +++  ++++ + ++++++++svr+  e+s ++ ++ g++qG++ SP+lfnl++n++l
  gene925|gene925|rna925|rna925 361 LFLDFKKAYDKVPHEGLFAKLRGYGFSGRILDFLIELYRNPKASVRIGDERSDTFNYQMGVKQGCPASPTLFNLYINNIL 440
                                    ***********************************************99999**************************** PP

                                    TT-T..........TEEECTTEEEEEESSHHHHHHHHHHHHHHHHHTT--BEGGG-EEE...................ES CS
                          RVT_1 152 relrkra....kgvtllrYaDDililskskeelqelleaveewlkesglkinpeKtklvlft............v..kse 213
                                    + +        ++v  l++aDD +++++s +++ + +e++e+w+ ++++ +n +K+ l++f+            +  + e
  gene925|gene925|rna925|rna925 441 EGITGVGigngEQVPGLLFADDAVVFAESYDDMVHNMEILEDWCDKWKMDLNISKCGLMVFNsneqraikyknaNipTVE 520
                                    ****9559*******************************************************9*999999987358999 PP

                                    SEEETTEEE CS
                          RVT_1 214 evkyLGvtl 222
                                    +++yLG+++
  gene925|gene925|rna925|rna925 521 RYRYLGIPI 529
                                    99**99975 PP

>> PHF5  PHF5-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.6   1.3e-06     0.011      53      93 ..     763     804 ..     756     815 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.3e-06
                           PHF5  53 kleekciicgskgvsda.yyclecvrlekdrdGcpriinvgs 93 
                                    ++++kci c+++g +d  +  ++c++ ek+r+ c r  n + 
  gene925|gene925|rna925|rna925 763 EYKKKCIACEKHGREDGiHLLWHCSKWEKEREECYRGFNNSD 804
                                    5689*******99987527789*************9888544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (867 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       871  (0.0485805); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.69u 0.27s 00:00:00.96 Elapsed: 00:00:00.44
# Mc/sec: 5960.54
//
Query:       gene926|gene926|rna926|rna926  [L=682]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.9e-26   92.0   0.0    6.3e-26   91.3   0.0    1.4  1  RVT_1     Reverse transcriptase (RNA-dependent DNA polymerase
  ------ inclusion threshold ------
      0.018   15.7   3.1      0.018   15.7   3.1    2.7  3  zf-RVT    zinc-binding in reverse transcriptase


Domain annotation for each model (and alignments):
>> RVT_1  Reverse transcriptase (RNA-dependent DNA polymerase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.3   0.0     7e-30   6.3e-26       1     140 [.     142     290 ..     142     290 .. 0.96

  Alignments for each domain:
  == domain 1  score: 91.3 bits;  conditional E-value: 7e-30
                                    EE-TT.....S-EEE......-THHHHCTB--...........-------HHHH................HCCHTS--EE CS
                          RVT_1   1 ipKkg....pgsyRpisllsvdykalnkliakrLkdvl..ekllsenqpgfrpgrstldav...edllkalkkkkkakll 71 
                                    +pKkg    p++yR islls++ k+l k+ia+r++ ++  ek+l ++q gfr+ + ++ +    ++++k    kkk++++
  gene926|gene926|rna926|rna926 142 VPKKGdlnkPDNYRGISLLSTISKILTKIIADRISRICddEKILIKEQAGFRKLEECVAQAtslYEIVKRRLLKKKETHA 221
                                    6899999999***********************************************99999998888887888999*** PP

                                    EEEEBCCGCCCSBB-GGGGGGG-EEET.........................TEEEEESB--ST-TTHH CS
                          RVT_1  72 lklDlkkaFdsvpleellrkltafkvptklinliksflstrsfsvrvngeeskgryekkglpqGsvlSP 140
                                    +++D++ka+d+vp+++ll kl+++++  k+++++ + +++  ++v+v  e s+++ +  g++qG++ SP
  gene926|gene926|rna926|rna926 222 AFIDFSKAYDRVPHSALLTKLKQYGFGGKIMKYLTATYENVVAHVKVGDEISSEFRYDIGVRQGCPASP 290
                                    ***********************************************888779999************9 PP

>> zf-RVT  zinc-binding in reverse transcriptase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.1      0.96   8.6e+03      10      29 ..      42      61 ..      30      79 .. 0.53
   2 ?   -0.8   0.1      0.29   2.6e+03      29      57 ..     479     506 ..     465     512 .. 0.81
   3 ?   15.7   3.1     2e-06     0.018      45      79 ..     571     609 ..     529     613 .. 0.67

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.96
                         zf-RVT 10 lrekkekvklakliWkskap 29
                                   l ++ke v+  +  W++  p
  gene926|gene926|rna926|rna926 42 LAKDKEGVSKNRGTWQNESP 61
                                   33333333444444444443 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.29
                         zf-RVT  29 ppkvkfflWlllknrlptadnllkrgies 57 
                                     +k++  +W+  ++r ++++nl+++ i+ 
  gene926|gene926|rna926|rna926 479 EFKHRKSTWITGTKR-WIKKNLKTNRITE 506
                                    579999999998877.7888888887775 PP

  == domain 3  score: 15.7 bits;  conditional E-value: 2e-06
                         zf-RVT  45 ptadnllkrgie...sssrCqlCgqe.eEtieHlfleCp 79 
                                        +l+k gi     +++C++Cg+  +Et  HlfleC+
  gene926|gene926|rna926|rna926 571 MYGYRLAKCGIIdreFKEKCPCCGEMrKETLLHLFLECR 609
                                    4556677777662223678*******************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (682 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       478  (0.0266607); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.24s 00:00:00.80 Elapsed: 00:00:00.40
# Mc/sec: 5069.73
//
Query:       gene927|gene927|rna927|rna927  [L=235]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       566  (0.031569); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1650.86
//
Query:       gene928|gene928|rna928|rna928  [L=389]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (389 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       837  (0.0466841); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 2540.14
//
Query:       gene929|gene929|rna929|rna929  [L=143]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       303  (0.0169); expected 358.6 (0.02)
Passed bias filter:                      210  (0.0117129); expected 358.6 (0.02)
Passed Vit filter:                         7  (0.000390429); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.25s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 1110.12
//
Query:       gene93|gene93|rna93|rna93  [L=58]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (58 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       244  (0.0136092); expected 358.6 (0.02)
Passed bias filter:                      226  (0.0126053); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 411.86
//
Query:       gene930|gene930|rna930|rna930  [L=121]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       361  (0.020135); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.54u 0.34s 00:00:00.88 Elapsed: 00:00:00.55
# Mc/sec: 658.28
//
Query:       gene931|gene931|rna931|rna931  [L=91]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       488  (0.0272185); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.59u 0.34s 00:00:00.93 Elapsed: 00:00:00.57
# Mc/sec: 479.86
//
Query:       gene932|gene932|rna932|rna932  [L=36]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (36 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       262  (0.0146132); expected 358.6 (0.02)
Passed bias filter:                      152  (0.00847788); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.45
# Mc/sec: 242.25
//
Query:       gene933|gene933|rna933|rna933  [L=209]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
     0.0037   17.3   5.2      0.088   12.9   0.1    2.3  2  HTH_54      ParA helix turn helix domain
  ------ inclusion threshold ------
        3.9    6.1   4.9        3.5    6.3   4.9    1.2  1  Presenilin  Presenilin


Domain annotation for each model (and alignments):
>> HTH_54  ParA helix turn helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.0   1.4    0.0014        13      10      60 ..      34      81 ..      26     104 .. 0.70
   2 !   12.9   0.1   9.8e-06     0.088      24      71 ..     147     194 ..     136     206 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0014
                         HTH_54 10 eqiqkqkkElkedeyyqtyskaalaklpklsrrkvdkavsemeaeGyefek 60
                                   ++ ++ kkEl+e+ y q+ ska  a+l kl    + + v++ e++  + e+
  gene933|gene933|rna933|rna933 34 KSTKEMKKELEEKFYGQKQSKALRAQLKKLD---LLEKVQKKEQQERQKER 81
                                   5667889******999*****9877776664...44445555555555555 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 9.8e-06
                         HTH_54  24 yyqtyskaalaklpklsrrkvdkavsemeaeGyefekkeagstekYal 71 
                                     + ++ +a++a++  ls+++ dk v+  e+e  +fe+++    + Y +
  gene933|gene933|rna933|rna933 147 EFLEMQRASVASERLLSKEEYDKFVDRREKEEMVFERRRERIKSGYEM 194
                                    47789*********************************9998888887 PP

>> Presenilin  Presenilin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   4.9   0.00039       3.5     233     292 ..      19      89 ..       1     183 [. 0.57

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.00039
                     Presenilin 233 aeseeeeeaekkkeeasesskeeeseeesseksaqsse..............seeeseeesseaessaeessee 292
                                     +++++++ ++kk+ +s+++ ++e ee++   ++qs++              +  ++e++++++e++ae+++++
  gene933|gene933|rna933|rna933  19 PKKKQDAQPKAKKDVKSTKEMKKELEEKFYG-QKQSKAlraqlkkldllekvQ--KKEQQERQKEREAEHNTRP 89 
                                    2222222222222222222222222222222.222221333444455554321..2222222222222222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3191  (0.17798); expected 358.6 (0.02)
Passed bias filter:                      854  (0.0476323); expected 358.6 (0.02)
Passed Vit filter:                       104  (0.00580066); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.31s 00:00:00.87 Elapsed: 00:00:00.46
# Mc/sec: 1372.58
//
Query:       gene934|gene934|rna934|rna934  [L=243]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.7e-06   28.5   0.1    1.7e-06   28.5   0.1    2.2  3  PH             PH domain
    0.00039   20.3  11.2    0.00044   20.1  11.2    1.2  1  TAF4           Transcription initiation factor TFIID componen
     0.0031   14.7   3.1      0.003   14.8   3.1    1.0  1  GREB1          Gene regulated by oestrogen in breast cancer
  ------ inclusion threshold ------
       0.91    7.6  11.3        1.1    7.3  11.3    1.1  1  Rota_VP2       Rotavirus VP2 protein
        1.2    7.8  12.3        1.6    7.4  12.3    1.2  1  Raftlin        Raftlin
        1.7    7.2   5.9        2.6    6.6   5.9    1.3  1  Ndc1_Nup       Nucleoporin protein Ndc1-Nup
        5.7    6.1   9.1          7    5.8   9.1    1.2  1  Zip            ZIP Zinc transporter
        6.5    6.7  19.1         11    6.0  19.1    1.3  1  POP1           Ribonucleases P/MRP protein subunit POP1
        8.8    5.9  18.6         11    5.7  18.6    1.1  1  DUF966         Domain of unknown function (DUF966)


Domain annotation for each model (and alignments):
>> PH  PH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   1.8       3.9   7.8e+03      55      55 ..      54      54 ..      20      95 .. 0.59
   2 ?   -1.6   0.3       1.9   3.8e+03      23      23 ..      84      84 ..      53     121 .. 0.55
   3 !   28.5   0.1   8.4e-10   1.7e-06      17     102 ..     157     236 ..     129     238 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 3.9
                                   E CS
                             PH 55 v 55
                                   +
  gene934|gene934|rna934|rna934 54 I 54
                                   1 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.9
                                   E CS
                             PH 23 f 23
                                   f
  gene934|gene934|rna934|rna934 84 F 84
                                   2 PP

  == domain 3  score: 28.5 bits;  conditional E-value: 8.4e-10
                                    SEEEEEEEEETTE.EEEESSTTCTTESSEEEEEESTTEEEEEEECTTSSSSTSEEEEEESTSSSTEEEEEEESSHHHHHH CS
                             PH  17 swkkrwfvLkdse.llyykndksekdkepkgsislsncevvevvatedpkrkfcfelriverngsrtyllqasseeerke 95 
                                     w+kr+fvL+++  l+y+++     + + kg+++l+ + +v++  +e++   +++++++   ng  t  +++++e  r  
  gene934|gene934|rna934|rna934 157 FWHKRYFVLTNDGmLCYFRAL----NGRGKGKLNLRHVNDVRRI-NEETSGANKYKIILRY-NG-YTESIRFDDERVRDH 229
                                    5*********88846666666....****************997.6688888888887774.45.8999*********** PP

                                    HHHHHHH CS
                             PH  96 Wikaiqs 102
                                    W + i++
  gene934|gene934|rna934|rna934 230 WNNKIRE 236
                                    *****97 PP

>> TAF4  Transcription initiation factor TFIID component TAF4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1  11.2   2.2e-07   0.00044     123     224 ..       2     106 ..       1     197 [. 0.66

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 2.2e-07
                           TAF4 123 aqkekeeeekrqakRieereglekaak..drskgedeeekklkaketakevq.keedekarhraANatAlaavgeprkKk 199
                                    ++ +k+eee   +kR+eer ++e++++  ++++ + eee+k+k+++  ke   k+e+e +++++   tA+ a    ++Kk
  gene934|gene934|rna934|rna934   2 KNAQKKEEEEEINKRVEERIKTEREEEmkKEEQIKKEEEEKVKEEQKTKEEEiKKEEEMKKEEEHKGTAAGAQQDDKQKK 81 
                                    56677777777777777777777776654444445555555555555777666777777788888888888887567777 PP

                           TAF4 200 yswmsagsgsgggksgaskssssgg 224
                                      + ++ + + + ++  sks +s+ 
  gene934|gene934|rna934|rna934  82 VHFEEQKNEQRDVSKDPSKSIQSPT 106
                                    7565544443333333333333333 PP

>> GREB1  Gene regulated by oestrogen in breast cancer
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   3.1   1.5e-06     0.003    1148    1280 ..       5     140 ..       1     202 [. 0.52

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.5e-06
                          GREB1 1148 ekseskdavesglss..kasakselseasaaaasaseeakspkas....vtseeeeseeskekekeslsketesqlsl 1219
                                     +k+e+++ +++ ++   k++ ++e++++++ ++ ++e+ k+++++    +++eee+++e+++k +    ++ ++q ++
  gene934|gene934|rna934|rna934    5 QKKEEEEEINKRVEEriKTEREEEMKKEEQIKKEEEEKVKEEQKTkeeeIKKEEEMKKEEEHKGTAAGAQQDDKQKKV 82  
                                     333333333333332002222233333222222222222222222000022222222222222222222222222222 PP

                          GREB1 1220 easeqkealdakasskssssssssssassPssscslakavkrPpivllskavydiltssds 1280
                                     +   ++++ ++++ sk  s+s  s++ ++P ++++++ ++  P + l +++   il++++ 
  gene934|gene934|rna934|rna934   83 H--FEEQKNEQRDVSKDPSKSIQSPTQEQPRPQVEINTGA-VPLSALAPNTELFILRTTNK 140 
                                     2..2233334466777778888888888899999887765.57777777777666666655 PP

>> Rota_VP2  Rotavirus VP2 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3  11.3   0.00056       1.1       6      99 ..      23     121 ..      17     171 .. 0.60

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.00056
                       Rota_VP2   6 rrretqlkqiekekekediknkevdenkds.l.kedklvkkeesngdvitdke....eevkinlqksdevkkvnkieskt 79 
                                      re+++k++e+ k+ e+ k ke +++k++ + ke+ + k+ee +g    +++    ++v+ + qk+ e ++v k  sk+
  gene934|gene934|rna934|rna934  23 TEREEEMKKEEQIKKEEEEKVKEEQKTKEEeIkKEEEMKKEEEHKGTAAGAQQddkqKKVHFEEQKN-EQRDVSKDPSKS 101
                                    3688889999988888777777766666432425777777778777766555410004445544554.557888888888 PP

                       Rota_VP2  80 llevleenkkeveeilkkti 99 
                                    ++   +e+ +   ei    +
  gene934|gene934|rna934|rna934 102 IQSPTQEQPRPQVEINTGAV 121
                                    88877666443334444444 PP

>> Raftlin  Raftlin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4  12.3   0.00082       1.6     177     253 ..      37     110 ..       2     154 .. 0.46

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.00082
                        Raftlin 177 ltsgaaeseeardekkkrsssedkvslenekpgalsgksseagaeeeaeseegkkgegpaaeqlqlssaeeegsesp 253
                                    + +++ + +e++++k+++ ++e+++++e+e++g++ g+ ++++++++++ ee+k+++ +++++++ +s ++ ++e+p
  gene934|gene934|rna934|rna934  37 K-EEEEKVKEEQKTKEEEIKKEEEMKKEEEHKGTAAGA-QQDDKQKKVHFEEQKNEQRDVSKDPS-KSIQSPTQEQP 110
                                    1.111111222222333333344444444444433333.33344445555544444444444444.33333333333 PP

>> Ndc1_Nup  Nucleoporin protein Ndc1-Nup
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   5.9    0.0013       2.6     345     435 ..      12     110 ..       8     164 .. 0.44

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0013
                       Ndc1_Nup 345 eltqrinergq....papkaaps......kapknkasapvkelprlsksplkkkddeifgn...........sltaeasp 403
                                    e+++r++er +    ++ k   +      +++++ ++++++++ +++k+++ k       +           +++ ++++
  gene934|gene934|rna934|rna934  12 EINKRVEERIKtereEEMK---KeeqikkEEEEKVKEEQKTKEEEIKKEEEMK-------KeeehkgtaagaQQDDKQKK 81 
                                    5666777777732112222...1222343222222223333333333222222.......12222222222211111111 PP

                       Ndc1_Nup 404 ks...sssskegvekalsslakspgqs.psptarls 435
                                     +   +++        + +++k+p++s +spt+++ 
  gene934|gene934|rna934|rna934  82 VHfeeQKNE-------QRDVSKDPSKSiQSPTQEQP 110
                                    111122233.......33333333333444443322 PP

>> Zip  ZIP Zinc transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   9.1    0.0035         7     101     171 ..      23      93 ..       2     160 .. 0.67

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0035
                            Zip 101 ekksshkektpkkasssssesaakksvsndkveeseekedhvaeadtdadskeelrngkqeksesekeqas 171
                                    ++ +++ +k+++ +++++++ + +++ ++++++++ee ++++++++t a  ++ ++++k + +e++ eq +
  gene934|gene934|rna934|rna934  23 TEREEEMKKEEQIKKEEEEKVKEEQKTKEEEIKKEEEMKKEEEHKGTAAGAQQDDKQKKVHFEEQKNEQRD 93 
                                    22333444445555555555555555556666666666666666666666666666666666666666555 PP

>> POP1  Ribonucleases P/MRP protein subunit POP1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0  19.1    0.0053        11      45     134 ..      15     100 ..       9     116 .. 0.48

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0053
                           POP1  45 kRvPkrlrarakremakdntptvearkrkkkslskrkrlrlrtakkllrlaakkkakkalaakkeekklnnkkgskdktk 124
                                    kRv  r+++  ++em+k++    + +k+++++++++++++ ++ kk +++++++++k ++a ++++ k++++  +++k +
  gene934|gene934|rna934|rna934  15 KRVEERIKTEREEEMKKEE----QIKKEEEEKVKEEQKTKEEEIKKEEEMKKEEEHKGTAAGAQQDDKQKKVHFEEQKNE 90 
                                    5666666666666666655....555555555566666666666666666555555543333322222222222222222 PP

                           POP1 125 knklaeppkk 134
                                    ++++++ p+k
  gene934|gene934|rna934|rna934  91 QRDVSKDPSK 100
                                    2222222222 PP

>> DUF966  Domain of unknown function (DUF966)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7  18.6    0.0053        11     115     210 ..       8     108 ..       1     141 [. 0.47

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0053
                         DUF966 115 aeeasssssssevavseassesespesskarr..kssssaeleeykvykaeeeeeaaeegaadastqtddkrrrsretkk 192
                                    +ee+  +++ +e  ++e ++e + +e+ k+++  k ++  +++e ++ k ee+++++e++ + a  q ddk+++ + +++
  gene934|gene934|rna934|rna934   8 EEEEEINKRVEERIKTEREEEMKKEEQIKKEEeeKVKEEQKTKEEEIKKEEEMKKEEEHKGTAAGAQQDDKQKKVHFEEQ 87 
                                    22222222222333333333322222222222212224455555555555555555555555555566666666555556 PP

                         DUF966 193 etasrgvstedeeeeke...e 210
                                    ++ +r+vs + +++ ++   e
  gene934|gene934|rna934|rna934  88 KNEQRDVSKDPSKSIQSptqE 108
                                    666666665433333332221 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      4111  (0.229293); expected 358.6 (0.02)
Passed bias filter:                     1094  (0.0610185); expected 358.6 (0.02)
Passed Vit filter:                       398  (0.0221987); expected 17.9 (0.001)
Passed Fwd filter:                        89  (0.00496402); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.95u 0.36s 00:00:01.31 Elapsed: 00:00:00.51
# Mc/sec: 1425.28
//
Query:       gene935|gene935|rna935|rna935  [L=139]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       466  (0.0259914); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.30s 00:00:00.75 Elapsed: 00:00:00.48
# Mc/sec: 871.19
//
Query:       gene936|gene936|rna936|rna936  [L=107]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.1e-21   75.5   0.1    4.9e-21   75.3   0.1    1.1  1  RVT_1     Reverse transcriptase (RNA-dependent DNA polymerase
  ------ inclusion threshold ------
      0.082   11.9   0.2      0.089   11.7   0.2    1.1  1  RSF       Respiratory growth transcriptional regulator
       0.12   12.7   0.1          3    8.2   0.0    2.2  2  DUF2949   Protein of unknown function (DUF2949)


Domain annotation for each model (and alignments):
>> RVT_1  Reverse transcriptase (RNA-dependent DNA polymerase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.3   0.1   8.2e-25   4.9e-21     132     222 .]       1      82 [.       1      82 [. 0.97

  Alignments for each domain:
  == domain 1  score: 75.3 bits;  conditional E-value: 8.2e-25
                                    --ST-TTHHHHHHHHHHHHHTT-T......TEEECTTEEEEEESSHHHHHHHHHHHHHHHHHTT--BEGGG-EEE..... CS
                          RVT_1 132 lpqGsvlSPllfnlfmnellrelrkrakgvtllrYaDDililskskeelqelleaveewlkesglkinpeKtklvlftvk 211
                                    + +G+v++P++f+++mn +++e+        ++ Y+DDil++sk+kee++++l++v e++ ++g+++n + +k++     
  gene936|gene936|rna936|rna936   1 MSFGLVNAPFTFQRIMNYVFKEFLW----KSMIIYMDDILLVSKNKEEHENHLSKVLERIGKVGFRVNLTRCKFF----- 71 
                                    689*********************9....5*********************************************..... PP

                                    ESSEEETTEEE CS
                          RVT_1 212 seevkyLGvtl 222
                                    ++++kyLG+++
  gene936|gene936|rna936|rna936  72 KTRIKYLGFEI 82 
                                    9********86 PP

>> RSF  Respiratory growth transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.2   1.5e-05     0.089     149     209 ..      35     101 ..      11     106 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 1.5e-05
                            RSF 149 elpvpkrrdikgnhlskll..fakspltin.tycqfydrrtkric...nqemiwkdknsrekhgsrk 209
                                     l v k ++ + nhlsk+l  + k  + +n t c+f+ +r k +    ++  i   ++ rek  s k
  gene936|gene936|rna936|rna936  35 ILLVSKNKEEHENHLSKVLerIGKVGFRVNlTRCKFFKTRIKYLGfeiENSKIAIGQEQREKVASLK 101
                                    3679999***********955679999999789*********8742114455666777788777766 PP

>> DUF2949  Protein of unknown function (DUF2949)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.0   0.00051         3       4      37 ..      20      53 ..      17      59 .. 0.92
   2 ?    2.3   0.0     0.036   2.1e+02      13      28 ..      81      96 ..      75     102 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00051
                        DUF2949  4 LirFLqeelaiseasialalrqseqdpspLpmvL 37
                                   + +FL + + i  ++i l+ +++e+++++L+ vL
  gene936|gene936|rna936|rna936 20 FKEFLWKSMIIYMDDILLVSKNKEEHENHLSKVL 53
                                   678***************************9877 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.036
                        DUF2949 13 aiseasialalrqseq 28
                                   +i +++ia+++ q+e+
  gene936|gene936|rna936|rna936 81 EIENSKIAIGQEQREK 96
                                   79999******99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       612  (0.0341346); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.39u 0.29s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 738.65
//
Query:       gene937|gene937|rna937|rna937  [L=124]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.6e-23   81.5   0.1    5.1e-23   81.0   0.1    1.2  1  RT_RNaseH_2  RNase H-like domain found in reverse transcripta
    1.3e-20   73.6   0.1    1.9e-20   73.1   0.1    1.2  1  RT_RNaseH    RNase H-like domain found in reverse transcripta
  ------ inclusion threshold ------
      0.017   14.2   0.0       0.02   14.0   0.0    1.0  1  DUF2048      Abhydrolase domain containing 18


Domain annotation for each model (and alignments):
>> RT_RNaseH_2  RNase H-like domain found in reverse transcriptase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.0   0.1   8.5e-27   5.1e-23       3      96 ..      19     111 ..      18     115 .. 0.94

  Alignments for each domain:
  == domain 1  score: 81.0 bits;  conditional E-value: 8.5e-27
                    RT_RNaseH_2   3 eeqekafeklkealtsapvLahpdpdkpfiletDaSdtgigavLsqedddgkerpiafaSrklskaernysttekellAi 82 
                                    ee+ k +e++k+++++a+ L +pd++k fil t aS+t ig+vL+q+++d+     + +Sr++ + e nys+ e+e lAi
  gene937|gene937|rna937|rna937  19 EEEIKTLESVKKEIVNAKKLLIPDQTKLFILFTAASQTIIGGVLCQTKKDEM-WANTWISRRFESGEINYSIREREYLAI 97 
                                    789999*******************************************765.7999*********************** PP

                    RT_RNaseH_2  83 vwalkkfrhyllgr 96 
                                    vw++kk+r yl+++
  gene937|gene937|rna937|rna937  98 VWCIKKLRIYLQNE 111
                                    ***********975 PP

>> RT_RNaseH  RNase H-like domain found in reverse transcriptase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.1   0.1   3.1e-24   1.9e-20       1      85 [.      42     124 .]      42     124 .] 0.91

  Alignments for each domain:
  == domain 1  score: 73.1 bits;  conditional E-value: 3.1e-24
                                    -TTS-EEEEEEECTEEEEEEEEEETTE..EEEEEEEEEE--HHHHTS-HHHHHHHHHHHHHHHHHHHHTS--EEEE-SS- CS
                      RT_RNaseH   1 dpskpfiletDAsddgigavLsqreedgeerpiafaSrklsgaernystiekellAivaalkkfrhylqgrkftvitDhk 80 
                                    d +k fil+t As++ ig+vL+q+++d e      +Sr++++ e nys+ e+e lAiv+++kk+r ylq+ +f+++tDh+
  gene937|gene937|rna937|rna937  42 DQTKLFILFTAASQTIIGGVLCQTKKD-EMWANTWISRRFESGEINYSIREREYLAIVWCIKKLRIYLQN-EFIIYTDHR 119
                                    67899******************5555.55677899********************************86.8******** PP

                                    -TTTT CS
                      RT_RNaseH  81 nlkyl 85 
                                    +l++l
  gene937|gene937|rna937|rna937 120 SLEWL 124
                                    ***96 PP

>> DUF2048  Abhydrolase domain containing 18
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   3.4e-06      0.02     262     340 ..      13      93 ..       4     104 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.4e-06
                        DUF2048 262 kerkaekealrfmrllmdelthlknfsvpkdtsliivvaAkdDayvpresva.slqeiwpgsevry.ldgGHvsayllkk 339
                                     +  +++e+++  + + +e+++ k++ +p +t+l i+++A +   +    ++ + +e+w+++ +   +++G ++  +  +
  gene937|gene937|rna937|rna937  13 DKFYSQEEEIKTLESVKKEIVNAKKLLIPDQTKLFILFTAASQTIIGGVLCQtKKDEMWANTWISRrFESGEINYSIRER 92 
                                    333456888999999999****************************9999997899*****9986559999999888766 PP

                        DUF2048 340 k 340
                                    +
  gene937|gene937|rna937|rna937  93 E 93 
                                    5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       936  (0.0522059); expected 358.6 (0.02)
Passed bias filter:                      511  (0.0285013); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.30s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 799.46
//
Query:       gene938|gene938|rna938|rna938  [L=245]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.1e-13   49.2   0.0    7.2e-13   48.8   0.0    1.2  1  rve             Integrase core domain
    3.2e-12   46.4   0.1    5.6e-12   45.6   0.1    1.4  1  Integrase_H2C2  Integrase zinc binding domain
    2.2e-05   24.6   0.0    6.2e-05   23.1   0.0    1.8  1  zf-H2C2         H2C2 zinc finger
  ------ inclusion threshold ------
      0.018   14.3   0.1      0.024   13.9   0.1    1.2  1  DUF4420         Putative  PD-(D/E)XK family member, (DUF4420)
       0.15   11.4   0.1       0.23   10.8   0.1    1.3  1  HSP33           Hsp33 protein
       0.15   11.8   0.0       0.39   10.5   0.0    1.7  1  rve_3           Integrase core domain


Domain annotation for each model (and alignments):
>> rve  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.8   0.0   2.4e-16   7.2e-13      18     117 ..     132     229 ..     117     231 .. 0.86

  Alignments for each domain:
  == domain 1  score: 48.8 bits;  conditional E-value: 2.4e-16
                            rve  18 pdgggkayllvvvddfsrlilaealsdemdastvlalleravarfggvepervlsDngseytskafrefladlgirvsft 97 
                                    ++ +g +++++++d  ++++ a al+++ +a+ v+++  + +  ++g  p+r+++D+g+e+  ++++++ + l  r  +t
  gene938|gene938|rna938|rna938 132 KSENGYKFIITATDWMTKWAEARALKRK-TAKEVAKFFIEEIMLRHGT-PRRIVTDQGREFMEETLKKIFELLTRRKITT 209
                                    4667799*********************.6666666666666666665.******************************* PP

                            rve  98 rpgrpqdnGkvErfhrtlkd 117
                                     p++++ n  vErf++tl++
  gene938|gene938|rna938|rna938 210 TPYNSKCNCAVERFNGTLMN 229
                                    *****************986 PP

>> Integrase_H2C2  Integrase zinc binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.6   0.1   1.9e-15   5.6e-12       2      56 ..      48     102 ..      47     104 .. 0.94

  Alignments for each domain:
  == domain 1  score: 45.6 bits;  conditional E-value: 1.9e-15
                 Integrase_H2C2   2 pkslrkeilkeaHdsagHlGiektlerlrrryyWpgmrkdvkkyvksCetCqrrk 56 
                                    +++ ++ i+++aH    H Gi+ t++ l++ry W++++++v +++k Ce C + +
  gene938|gene938|rna938|rna938  48 NEEKKNMIISKAHPAVEHGGINSTYNILAKRYKWKNLKREVIDFIKVCEPCTKFR 102
                                    578899*********************************************9987 PP

>> zf-H2C2  H2C2 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.0   2.1e-08   6.2e-05       3      38 ..      63      98 ..      62      99 .. 0.96

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 2.1e-08
                        zf-H2C2  3 ltHlGinkltallarkYhwlgiketvseVissCkaC 38
                                   ++H Gin +  +la++Y w+++k+ v + i+ C  C
  gene938|gene938|rna938|rna938 63 VEHGGINSTYNILAKRYKWKNLKREVIDFIKVCEPC 98
                                   79********************************** PP

>> DUF4420  Putative  PD-(D/E)XK family member, (DUF4420)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1     8e-06     0.024      61     124 ..      89     153 ..      23     166 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 8e-06
                        DUF4420  61 lkqvklsesstensksle.lslkdselreiFatlcedlvesledeedekellsavverlkrWqel 124
                                    +  +k++e  t+ + sl  + +   +l+e+F+t+  d++ sl ++e+  + + ++++++++W e 
  gene938|gene938|rna938|rna938  89 IDFIKVCEPCTKFRDSLRdIQRIRINLKELFETIGLDIIGSLTKSENGYKFIITATDWMTKWAEA 153
                                    55566666666666666668888899************************************985 PP

>> HSP33  Hsp33 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   7.8e-05      0.23     197     238 ..     189     230 ..     152     232 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 7.8e-05
                                    -HHHHHHHHHHSTS--EEEEEEE-EE-----HHHHHHHHHTT CS
                          HSP33 197 lpaeellerlfheedvevleekpvefkCrCsrervekaLksl 238
                                    + +ee l+++f+  + + + ++p + kC+C  er+ ++L+ +
  gene938|gene938|rna938|rna938 189 EFMEETLKKIFELLTRRKITTTPYNSKCNCAVERFNGTLMNI 230
                                    4459999****9999999********************9975 PP

>> rve_3  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00013      0.39       8      32 ..     209     233 ..     205     243 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00013
                          rve_3   8 iapgkPqqNglvEsfngtlrdelln 32 
                                    + p+  + N  vE+fngtl + +l+
  gene938|gene938|rna938|rna938 209 TTPYNSKCNCAVERFNGTLMNIFLK 233
                                    789999*************998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       876  (0.0488594); expected 358.6 (0.02)
Passed bias filter:                      558  (0.0311228); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 1757.87
//
Query:       gene939|gene939|rna939|rna939  [L=169]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (169 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       915  (0.0510346); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 1274.11
//
Query:       gene94|gene94|rna94|rna94  [L=79]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       409  (0.0228122); expected 358.6 (0.02)
Passed bias filter:                      190  (0.0105974); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.31s 00:00:00.67 Elapsed: 00:00:00.46
# Mc/sec: 513.13
//
Query:       gene940|gene940|rna940|rna940  [L=679]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (679 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1301  (0.072564); expected 358.6 (0.02)
Passed bias filter:                      488  (0.0272185); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.69u 0.31s 00:00:01.00 Elapsed: 00:00:00.49
# Mc/sec: 4184.61
//
Query:       gene941|gene941|rna941|rna941  [L=445]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.022   15.1   0.0       0.24   11.8   0.0    2.5  2  DUF5475   Family of unknown function (DUF5475)
      0.073   11.9   0.1        1.3    7.7   0.0    2.1  2  UxuA      D-mannonate dehydratase (UxuA)


Domain annotation for each model (and alignments):
>> DUF5475  Family of unknown function (DUF5475)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.21   1.9e+03      50      70 ..      69      89 ..      63      92 .. 0.75
   2 ?   11.8   0.0   2.6e-05      0.24      25      64 ..     323     365 ..     308     374 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.21
                        DUF5475 50 vmlskktteclqlkrkidkki 70
                                   +++ k     +ql ++idk +
  gene941|gene941|rna941|rna941 69 MLICKTMMGFMQLWKHIDKAV 89
                                   44556666789*******976 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 2.6e-05
                        DUF5475  25 aktcldialenlellrqktnikevavmlskk...tteclqlkr 64 
                                     k+c d  ++ +e lr+k n   va+m+s      t  lql r
  gene941|gene941|rna941|rna941 323 YKACEDKFVDSVESLRKKGNTDVVALMISLMesgGTYSLQLSR 365
                                    499************************9954112577788877 PP

>> UxuA  D-mannonate dehydratase (UxuA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.0   0.00015       1.3     102     182 ..      71     155 ..      64     169 .. 0.78
   2 ?    1.6   0.0     0.011        96     271     313 ..     319     363 ..     313     377 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00015
                                    EEE---SS--.S--SEEEEE-TTS-EEEEE-HHHHHHHHHH.TT--T..TGGGGS--TT-S---HHHHHHHHGCCTT--H CS
                           UxuA 102 vCYnfmpvld.Wtrtdleykledgskalrfdkkeiealelk.ilrrk..eaekeytlPgaeeerldelrelleaykkide 177
                                    +C   m  ++ W + d ++k +  s+al    +e +    + i+++k   +  ++t+P  e+er ++++ +++a+k i++
  gene941|gene941|rna941|rna941  71 ICKTMMGFMQlWKHIDKAVKAGGQSYALDMSLAESKYRRSTlITEVKvfVELFSFTMPFPEPERVNRFKVHVDAMKFIKD 150
                                    77777777655999999999999999998876666554444344444115667899***********************9 PP

                                    HHHHH CS
                           UxuA 178 eklre 182
                                    ++l e
  gene941|gene941|rna941|rna941 151 RSLTE 155
                                    99975 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.011
                                    --EEEE-SSTT-E...EEE-TTSSSS-HHHHHHHHHHHHHHH-EE- CS
                           UxuA 271 lRnikreedeksF...veaahleGsvdlaevvkalleeeyrrylRp 313
                                    lR++ +   e +F   ve+  ++G++d+++++  l+e + +  l  
  gene941|gene941|rna941|rna941 319 LRDVYKAC-EDKFvdsVESLRKKGNTDVVALMISLMESGGTYSLQL 363
                                    56665553.44551115777888*************9987766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (445 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       544  (0.0303419); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 3184.56
//
Query:       gene942|gene942|rna942|rna942  [L=99]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.017   14.5   0.2      0.018   14.5   0.2    1.2  1  TMEM156   TMEM156 protein family
      0.021   14.7   0.3      0.029   14.3   0.3    1.2  1  Sec20     Sec20
      0.036   14.0   0.1      0.036   14.0   0.1    1.1  1  DUF5089   Domain of unknown function (DUF5089)


Domain annotation for each model (and alignments):
>> TMEM156  TMEM156 protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.2     3e-06     0.018     150     197 ..      48      96 ..      11      98 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3e-06
                        TMEM156 150 meslnnCinisLqlemdvknvic.smkitWyvlvllvfifliiliihKi 197
                                    +es+n  ++  L+   ++ n i    +i+  v+v++v+ ++++ +i+Ki
  gene942|gene942|rna942|rna942  48 IESKNRITKGLLRSADELSNKIFrRKRIIGVVMVMMVIFIVVSYVIYKI 96 
                                    5666666666666666666665514679********************9 PP

>> Sec20  Sec20
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.3   4.8e-06     0.029      28      90 ..      35      95 ..      17      96 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.8e-06
                          Sec20 28 leeldastkslekleeeykqvedvlsrskklvkklerrdktdkllvflalglflacvvyvvkk 90
                                   + el+++ ++le +e++   ++++l+ + +l +k+ rr ++  + v++ +  + ++v+yv++k
  gene942|gene942|rna942|rna942 35 MYELKNQREKLEGIESKNRITKGLLRSADELSNKIFRRKRI--IGVVMVMMVIFIVVSYVIYK 95
                                   779*********************************99987..56666666777789****98 PP

>> DUF5089  Domain of unknown function (DUF5089)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1     6e-06     0.036      37      79 ..      36      78 ..       2      85 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 6e-06
                        DUF5089 37 kelrkQgekLekakqsaikvhknaekgeelakkikregkvfvf 79
                                    el++Q+ekLe ++ + + ++  ++ ++el++ki r  +++ +
  gene942|gene942|rna942|rna942 36 YELKNQREKLEGIESKNRITKGLLRSADELSNKIFRRKRIIGV 78
                                   59********************************999998866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1608  (0.0896871); expected 358.6 (0.02)
Passed bias filter:                      923  (0.0514808); expected 358.6 (0.02)
Passed Vit filter:                       103  (0.00574488); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 751.53
//
Query:       gene943|gene943|rna943|rna943  [L=90]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.029   14.4   0.1      0.058   13.4   0.1    1.6  1  DUF2116   Uncharacterized protein containing a Zn-ribbon (DUF


Domain annotation for each model (and alignments):
>> DUF2116  Uncharacterized protein containing a Zn-ribbon (DUF2116)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   3.2e-06     0.058       6      47 ..      32      73 ..      27      75 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.2e-06
                        DUF2116  6 CivCGkaIpldesfCsekCqeeyekkrkkvarsqqilfgili 47
                                    ++C+     +e+fC    +e +e kr   +r++ i++ +l+
  gene943|gene943|rna943|rna943 32 AVICSHGTIAEEVFCYGFNKELFEMKRSSEIRTRSIITRVLL 73
                                   589**********************************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       318  (0.0177366); expected 358.6 (0.02)
Passed bias filter:                      263  (0.014669); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 664.37
//
Query:       gene944|gene944|rna944|rna944  [L=38]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (38 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       270  (0.0150594); expected 358.6 (0.02)
Passed bias filter:                      199  (0.0110993); expected 358.6 (0.02)
Passed Vit filter:                         6  (0.000334653); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.22s 00:00:00.56 Elapsed: 00:00:00.40
# Mc/sec: 284.92
//
Query:       gene945|gene945|rna945|rna945  [L=579]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.8e-16   58.2   0.2    1.8e-15   56.6   0.0    2.0  2  Spt5-NGN  Early transcription elongation factor of RNA pol II
    9.9e-10   38.0  23.4    0.00018   21.4   3.5    4.9  5  KOW       KOW motif
  ------ inclusion threshold ------
      0.035   14.7  13.5        7.4    7.2  13.5    2.4  1  CTD       Spt5 C-terminal nonapeptide repeat binding Spt4


Domain annotation for each model (and alignments):
>> Spt5-NGN  Early transcription elongation factor of RNA pol II, NGN section
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.6   0.0   3.1e-19   1.8e-15       1      84 []      17      92 ..      17      92 .. 0.94
   2 ?   -3.6   0.0       1.8   1.1e+04       8      63 ..     108     126 ..     105     137 .. 0.54

  Alignments for each domain:
  == domain 1  score: 56.6 bits;  conditional E-value: 3.1e-19
                       Spt5-NGN  1 siwavkctagqErevalslmkkilelakkenleIkSvfapdelkGyiyvEAdrkaaveralegipnvrgvvqglvpikEved 82
                                   ++w v++++g+Er+v +++       ++++  +I+Sv+  d+l Gy+y+E+ +k+ v +a+++ + v g+v + vp++E+ +
  gene945|gene945|rna945|rna945 17 KLWLVRVKPGKERQVLFKI-------ISERHDNIYSVIIKDGLPGYVYLESFHKQSVLNAIDTCKFVGGRV-NVVPLDEMVE 90
                                   69*****************.......6666779**********************************9998.9*******98 PP

                       Spt5-NGN 83 ll 84
                                   ++
  gene945|gene945|rna945|rna945 91 VM 92
                                   76 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 1.8
                       Spt5-NGN   8 tagqErevalslmkkilelakkenleIkSvfapdelkGyiyvEAdrkaaveraleg 63 
                                    ++g+ ++ + ++++ki                                      ++
  gene945|gene945|rna945|rna945 108 KKGRYKDDVGMIVEKI-------------------------------------SDE 126
                                    5555555555565554.....................................333 PP

>> KOW  KOW motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.4   5.7e-06     0.034       4      29 ..     104     130 ..     103     132 .. 0.88
   2 ?    0.4   0.2      0.12   7.2e+02      16      26 ..     260     270 ..     259     276 .. 0.80
   3 !   21.4   3.5   2.9e-08   0.00018       2      30 ..     314     342 ..     313     351 .. 0.92
   4 ?   -2.8   0.2       1.2   7.4e+03      13      26 ..     499     512 ..     498     514 .. 0.65
   5 !   14.6   0.1   3.9e-06     0.024       3      29 ..     534     560 ..     534     562 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 5.7e-06
                                    EEEESSSTTTTCEEEEEEEETTT.TEE CS
                            KOW   4 hVkVvsGphkGktGkVvkvdqhk.vrV 29 
                                    +V+   G++k+++G++v+ + +  vrV
  gene945|gene945|rna945|rna945 104 YVRMKKGRYKDDVGMIVEKISDEmVRV 130
                                    79999*************998887776 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.12
                                    EEEEEEEETTT CS
                            KOW  16 tGkVvkvdqhk 26 
                                    tG+Vv+v  + 
  gene945|gene945|rna945|rna945 260 TGVVVHVQGQS 270
                                    8******8765 PP

  == domain 3  score: 21.4 bits;  conditional E-value: 2.9e-08
                                    TSEEEESSSTTTTCEEEEEEEETTTTEEE CS
                            KOW   2 GdhVkVvsGphkGktGkVvkvdqhkvrVf 30 
                                     + V V++G +kG+ G+V++v +++v V 
  gene945|gene945|rna945|rna945 314 NKKVTVIRGSYKGFDGVVKDVHRDNVLVQ 342
                                    578**********************8775 PP

  == domain 4  score: -2.8 bits;  conditional E-value: 1.2
                                    TTCEEEEEEEETTT CS
                            KOW  13 kGktGkVvkvdqhk 26 
                                     +k+ +V+++++ +
  gene945|gene945|rna945|rna945 499 QNKIVEVLDIIDGT 512
                                    56777777777655 PP

  == domain 5  score: 14.6 bits;  conditional E-value: 3.9e-06
                                    SEEEESSSTTTTCEEEEEEEETTTTEE CS
                            KOW   3 dhVkVvsGphkGktGkVvkvdqhkvrV 29 
                                    d V+V++G h+G tG+ v+v + k +V
  gene945|gene945|rna945|rna945 534 DRVIVLRGNHAGCTGILVRVSDSKGTV 560
                                    79**********************888 PP

>> CTD  Spt5 C-terminal nonapeptide repeat binding Spt4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2  13.5    0.0012       7.4       1      57 [.     407     467 ..     369     492 .. 0.57

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0012
                            CTD   1 gsrTPawnsaggsrTPawgadgsrTpayggagsrtPawnagskTPahg........aagsrTPay 57 
                                    g++TP  ++ +g++TP ++  g + ++    +++ P +++ ++TP+ g        + gsrTP  
  gene945|gene945|rna945|rna945 407 GGKTPDLTG-AGGKTPGFELYGVQGTPRP--DGNAP-YKTPYRTPSRGgrsppqtpGMGSRTPYR 467
                                    455666655.5555666555444432222..22333.3333344444444444445555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (579 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       453  (0.0252663); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.25s 00:00:00.81 Elapsed: 00:00:00.42
# Mc/sec: 4118.23
//
Query:       gene946|gene946|rna946|rna946  [L=50]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (50 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       349  (0.0194657); expected 358.6 (0.02)
Passed bias filter:                      228  (0.0127168); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.53
# Mc/sec: 285.97
//
Query:       gene947|gene947|rna947|rna947  [L=481]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.3e-32  111.1  25.3    4.9e-31  108.0  25.3    2.1  1  MFS_1_like     MFS_1 like family
    2.9e-11   42.9  14.6    2.9e-11   42.9  14.6    1.6  1  MFS_1          Major Facilitator Superfamily
    1.8e-08   33.8  17.3    2.6e-08   33.3  17.3    1.2  1  Nuc_H_symport  Nucleoside H+ symporter


Domain annotation for each model (and alignments):
>> MFS_1_like  MFS_1 like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.0  25.3   8.1e-35   4.9e-31       3     377 ..      14     400 ..      12     405 .. 0.83

  Alignments for each domain:
  == domain 1  score: 108.0 bits;  conditional E-value: 8.1e-35
                     MFS_1_like   3 slkilyFfffaalgsllPYltiy.lkskglkaseigiitlilpltsilsppiwgvlaDrfgkrkkvvilslllsavlfls 81 
                                     lk+lyFf+     +++ + + +  k  +++ +  g  + i+ ++ ++   ++++  D+f++ k  +   l++s+v+f  
  gene947|gene947|rna947|rna947  14 PLKLLYFFINVQYYAFYQFRGPFaVKMFDVSKEHYGWFLGIILAVCFFTNTFLATANDKFERPKLFICTLLVVSMVSFEL 93 
                                    6899999988888888888887734578999999*********************************************9 PP

                     MFS_1_like  82 llfippskerqeesklevsvaqdvdaektfwilfllvvlasfflaailvlldaatlkel....gedrkdyGrqrlfGsvG 157
                                    ++f p  k                  e +fw+   +++l+sff  ai +lld  +++ l    +  ++ yGrqrl+G++G
  gene947|gene947|rna947|rna947  94 FYFWPAVK----------------KHEGIFWL---VMFLYSFFNTAIPPLLDRFAIEYLnrtpNVGARTYGRQRLWGTIG 154
                                    99999111................14566664...5678999999999999*99999997766667788*********** PP

                     MFS_1_like 158 yaifafitGilidhysvnllp.....ysallyvlaallvisllvvlilnetekesk.lkvtkslqvllnilknpeviifl 231
                                    y +  +++  l  +   ++ +     y + l+++ a+l  +l++      +++ ++    + ++++    lkn+ +++f+
  gene947|gene947|rna947|rna947 155 YLLGNMAVESLCRTEPKKY-DfdnlkYYVPLVTIPAVLFSALFI------KSYDRAeRSNADIESSWASFLKNRPYLFFI 227
                                    ********99998877765.434444444444444444444444......33333303333455778899********** PP

                     MFS_1_like 232 lvalilgmswgiienF...................lflYL.kelg.asntllGslvalgvvaeiplfffaeklleklGhv 290
                                    +++l+ g++ + +  +                   +  +L +  +   +  ++++ + gvv ei++++++++++ ++G+ 
  gene947|gene947|rna947|rna947 228 FIILLNGITRAGMTLYlsiyqteilmlegytlsdrIPGFLrSIINvVNKNPISTTATCGVVFEIIILYYSQNIVGRCGLY 307
                                    **************************99999999977777444441456789**************************** PP

                     MFS_1_like 291 klliiallayilrfllyaii.....enawlvlpievLhgisfgllwaaaveyvskiapksleatgqgllsglyfglGral 365
                                    + l++a +a ++rf +y i+     +   +  ++e+++g+ fgl+++++v+ ++ + p++l+at q +++g++ glG+++
  gene947|gene947|rna947|rna947 308 WPLLFAQVAQFVRFAGYYILpydnsNTYAFSCLLETMKGVNFGLTHSSGVHIANMMCPPHLKATSQMIYTGTFTGLGSFF 387
                                    **********************98666788999*********************************************** PP

                     MFS_1_like 366 GsliGGllw.dlk 377
                                    G  i Gl++ +l+
  gene947|gene947|rna947|rna947 388 GGQIFGLIFsKLS 400
                                    ****99**94444 PP

>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.9  14.6   4.9e-15   2.9e-11      13     352 ..      27     388 ..      15     389 .. 0.78

  Alignments for each domain:
  == domain 1  score: 42.9 bits;  conditional E-value: 4.9e-15
                          MFS_1  13 silgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllll.f..a.sslw.l 87 
                                    ++++ +  ++  + + +s+  +g+ l++  +++++++ +l+   d+f r ++++++ll+ +  ++ l+ f  a   +  +
  gene947|gene947|rna947|rna947  27 YAFYQFRGPFAVKMFDVSKEHYGWFLGIILAVCFFTNTFLATANDKFERPKLFICTLLVVSMVSFELFyFwpAvKKHEgI 106
                                    4444444445566799*******************************999977777777666644444333536777779 PP

                          MFS_1  88 llvlrvlqGlgagalfpagaaliadwfpk.eergrai.gllsagfslGailgpllgglla.sslg.....Wravfyilai 159
                                    ++++ +l +++  a+ p+   ++ ++ ++ ++ g  + g   +   +G++lg ++   l+ +        +  + y + +
  gene947|gene947|rna947|rna947 107 FWLVMFLYSFFNTAIPPLLDRFAIEYLNRtPNVGARTyGRQRLWGTIGYLLGNMAVESLCrT--EpkkydFDNLKYYVPL 184
                                    *****************************988876655**************8888888834..3459998888777777 PP

                          MFS_1 160 vsllafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsglltllply.....l 234
                                    v++ a+++ +l++   +++++ ++++e           + w ++lk+++ +++++++ll+++  +g++ +l +y     +
  gene947|gene947|rna947|rna947 185 VTIPAVLFSALFIKSYDRAERSNADIES----------S-WASFLKNRPYLFFIFIILLNGITRAGMTLYLSIYqteilM 253
                                    7777755444555444444444444444..........4.77788888777799999999999999*******9777556 PP

                          MFS_1 235 qevlgls.................glllaglllallalvgailallagrlsdrlgrrrrlllallllllaalglallavt 297
                                     e + ls                    ++++   ++ +++      +  ++ r g  ++ll+a ++ ++ ++g+++l+  
  gene947|gene947|rna947|rna947 254 LEGYTLSdripgflrsiinvvnknPISTTATCGVVFEIII---LYYSQNIVGRCGLYWPLLFAQVAQFVRFAGYYILPYD 330
                                    6666666************888754344444444444444...6688888888899************************ PP

                          MFS_1 298 ssavllllvlvl...iGfglgfvfpsllalasdlappeeagtasglfn.tagslggalg 352
                                     ++  ++++++l    G+ +g++ +s   +a+ ++pp+  +t + +++ t+ +lg+++g
  gene947|gene947|rna947|rna947 331 -NSNTYAFSCLLetmKGVNFGLTHSSGVHIANMMCPPHLKATSQMIYTgTFTGLGSFFG 388
                                    .7777777888877677799999************************999999****98 PP

>> Nuc_H_symport  Nucleoside H+ symporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.3  17.3   4.4e-12   2.6e-08      52     379 ..      61     413 ..      15     438 .. 0.74

  Alignments for each domain:
  == domain 1  score: 33.3 bits;  conditional E-value: 4.4e-12
                  Nuc_H_symport  52 lspilvgiiaDkflsaerv...lavlhligavvlflaaqvtefealfl.vlLvysl..aymPtlaltnsiafanlr..Dv 123
                                    ++ +++ +  Dkf + + +   l v+ +++  ++++   v + e++f+ v+++ys+  + +P l    +i + n +    
  gene947|gene947|rna947|rna947  61 FTNTFLATANDKFERPKLFictLLVVSMVSFELFYFWPAVKKHEGIFWlVMFLYSFfnTAIPPLLDRFAIEYLNRTpnVG 140
                                    55667777788887777651113344444444556655666666666527889999445678888888888887765344 PP

                  Nuc_H_symport 124 vtdfprirvlGtvGfilaslaflllvvs.ladlelsrlqlliaagvslllavyaltLPkiPakkkakqslkkllgldafv 202
                                    ++ ++r r++Gt+G++l ++a   l  +   + +  +l++++  ++   +   al++      ++++ ++++     a  
  gene947|gene947|rna947|rna947 141 ARTYGRQRLWGTIGYLLGNMAVESLCRTePKKYDFDNLKYYVPLVTIPAVLFSALFIKSYDRAERSNADIESSW---A-S 216
                                    789***************88855554431456677788888865443333344788888876666777776643...2.4 PP

                  Nuc_H_symport 203 LlknkrllvfflvslllavvlqiyyvfanafLtevak...................ivvkla.sillslsqvaeilfiLt 262
                                    +lkn+  l f ++ ll +++ +++ ++   + te+                     +v k++ s   + + v ei+++  
  gene947|gene947|rna947|rna947 217 FLKNRPYLFFIFIILLNGITRAGMTLYLSIYQTEILMlegytlsdripgflrsiinVVNKNPiSTTATCGVVFEIIILYY 296
                                    5777777777777899999999999999999999988889999999*******9876777763566789999******** PP

                  Nuc_H_symport 263 lpfflkrfGikkvlllslvaaalrfalfaygaddepvgvvlllLslivyGvaydffyitayvfvdkevpkdirasaqGlf 342
                                       ++ r G+   ll + va+ +rfa +     d+  +++   L   + Gv +   + ++    +   p++++a++q ++
  gene947|gene947|rna947|rna947 297 SQNIVGRCGLYWPLLFAQVAQFVRFAGYYILPYDNSNTYAFSCLLETMKGVNFGLTHSSGVHIANMMCPPHLKATSQMIY 376
                                    *************************97766666777777777777889*********999999999************** PP

                  Nuc_H_symport 343 lllvnGvGallgsilsgalvemftvdgvvdwqtlwlv 379
                                    +    G+G++ g+ ++g +  +++ +  +  +   ++
  gene947|gene947|rna947|rna947 377 TGTFTGLGSFFGGQIFGLIFSKLSSKSATASEKAKIF 413
                                    *****************99999998874433332222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (481 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       627  (0.0349713); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.65u 0.28s 00:00:00.93 Elapsed: 00:00:00.49
# Mc/sec: 2956.88
//
Query:       gene948|gene948|rna948|rna948  [L=226]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.013   15.2   2.0      0.013   15.2   2.0    1.6  2  Lipoprotein_X  Mycoplasma MG185/MG260 protein


Domain annotation for each model (and alignments):
>> Lipoprotein_X  Mycoplasma MG185/MG260 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   2.0   7.5e-07     0.013      49     115 ..      45     113 ..      32     126 .. 0.81
   2 ?   -2.4   0.2      0.19   3.3e+03      99     123 ..     173     197 ..     157     206 .. 0.41

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 7.5e-07
                  Lipoprotein_X  49 FknaksskkkesaqgvlGvDdtan...llftsvfaaaggnydnffyikvkegraidysnlk.nkdsksykn 115
                                    F+n+ +  + +++  ++G++d++n   +lf + f   +++   ++ ik+++     y+nl+  k+s+ y n
  gene948|gene948|rna948|rna948  45 FENEIQATNYTKIRNIFGINDKSNelqILFIKQFNHYDNKTYRSMLIKTQNDDP--YNNLDaRKGSNTYLN 113
                                    999********************9333456778888888888889999999988..999862566766655 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.19
                  Lipoprotein_X  99 aidysn.lknkdsksyknlkkvfnkl 123
                                     ++ys  + n+   +   l++  n  
  gene948|gene948|rna948|rna948 173 DVNYSLlYVNTKD-KCVHLQHFKNRH 197
                                    2244442222222.344444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       940  (0.052429); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.32s 00:00:00.84 Elapsed: 00:00:00.51
# Mc/sec: 1327.45
//
Query:       gene949|gene949|rna949|rna949  [L=116]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       963  (0.0537119); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.51
# Mc/sec: 678.56
//
Query:       gene95|gene95|rna95|rna95  [L=74]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (74 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       906  (0.0505327); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 502.56
//
Query:       gene950|gene950|rna950|rna950  [L=262]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
       0.34    8.9  33.1       0.37    8.8  33.1    1.0  1  AF-4       AF-4 proto-oncoprotein


Domain annotation for each model (and alignments):
>> AF-4  AF-4 proto-oncoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8  33.1   2.1e-05      0.37     546     718 ..      35     202 ..      13     258 .. 0.56

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 2.1e-05
                           AF-4 546 sespkkeskeqsqgkskssssevveesseskpkakskaeqkkseekqdkrskqkspaqkeseepntrktvgkkqPkksek 625
                                     +s+  ++ + s++++++++++ +++++e kpk ++ ++q++s++  +k +k  s ++  + + n ++  gk +  k e 
  gene950|gene950|rna950|rna950  35 DKSS-GSNPSGSSSSGNKNKDKEKKPPKEEKPKGQNDQPQNDSSGG-GKGGKGGSGSA-GKGTGNGSSPSGKDNNPKEEE 111
                                    2222.22233333345555556667778888888777777777766.44444445443.333334445555443323332 PP

                           AF-4 626 asveeepksslkvekevpveekdqsskdrpkvktkgrrktaprkepksslrlasekkkkr..ssskkaapksrefvetek 703
                                     + e+  ks+ + ek+ p  + ++ +kd +k+k++++ k +p+k+pk+  +++ e+k k   +++ + +pk +e++e e+
  gene950|gene950|rna950|rna950 112 -TPENGDKSKENPEKD-P--KDEKNPKDEEKPKNGEKSKENPEKDPKDDKNPKDEEKPKNgeKPKDEEKPKDEEKPEDEE 187
                                    .222334555555666.3..335667777888888889*********666444443333300344455555555555553 PP

                           AF-4 704 sesesdseellplsp 718
                                    ++ e+ ++e+ p   
  gene950|gene950|rna950|rna950 188 PKDEEPKAEEKPEDE 202
                                    333333333322222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (262 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1419  (0.0791455); expected 358.6 (0.02)
Passed bias filter:                      518  (0.0288917); expected 358.6 (0.02)
Passed Vit filter:                       187  (0.01043); expected 17.9 (0.001)
Passed Fwd filter:                       102  (0.00568911); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 1.34u 0.35s 00:00:01.69 Elapsed: 00:00:00.52
# Mc/sec: 1521.87
//
Query:       gene951|gene951|rna951|rna951  [L=209]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1120  (0.0624686); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1374.80
//
Query:       gene952|gene952|rna952|rna952  [L=173]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (173 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1822  (0.101623); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 1175.10
//
Query:       gene953|gene953|rna953|rna953  [L=247]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00068   19.2   1.9     0.0011   18.4   1.9    1.4  1  Fijivirus_P9-2  Fijivirus P9-2 protein
  ------ inclusion threshold ------
        0.2   12.5   9.3       0.59   11.0   7.0    2.5  2  YMF19           Plant ATP synthase F0


Domain annotation for each model (and alignments):
>> Fijivirus_P9-2  Fijivirus P9-2 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   1.9   1.2e-07    0.0011     113     152 ..      24      63 ..       5      95 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.2e-07
                 Fijivirus_P9-2 113 csiiftiifytllfvscyllwhyfgdviiqtikdinnnrs 152
                                      +i++ if  l+++scyllw y   v i+ +   + n+s
  gene953|gene953|rna953|rna953  24 MKLIWSFIFLVLFYISCYLLWSYCTIVKINKMFIQKVNKS 63 
                                    56899******************99988876544444444 PP

>> YMF19  Plant ATP synthase F0
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   7.0   6.5e-05      0.59      13      61 ..      27      73 ..      25      85 .. 0.85
   2 ?    0.6   0.0      0.11   9.9e+02      24      73 ..      83     132 ..      80     145 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 6.5e-05
                          YMF19 13 fWlclfFitlYivllknilpkiarilklrkkllsslssevsklkkeqkn 61
                                   +W+++f +++Yi ++   l +  +i+k+ k ++++ +++ +k++++ k 
  gene953|gene953|rna953|rna953 27 IWSFIFLVLFYISCY--LLWSYCTIVKINKMFIQKVNKSYEKFQSTWKT 73
                                   6***********988..8889999***********99999999987654 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.11
                          YMF19  24 ivllknilpkiarilklrkkllsslssevsklkkeqknlivskdsalanv 73 
                                    i+l+k+++ k + +    k++l +++ +v +  +++ +  +s++ +la+ 
  gene953|gene953|rna953|rna953  83 ILLYKKGIDKYVGFTAANKEKLANFRGKVGSKYETNLSAAQSYKAELAAL 132
                                    56667777777777777777777777666666666666666666666654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1293  (0.0721178); expected 358.6 (0.02)
Passed bias filter:                      576  (0.0321267); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1619.53
//
Query:       gene954|gene954|rna954|rna954  [L=476]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-05   24.8   3.7     0.0039   16.7   0.1    3.5  3  MSC       Man1-Src1p-C-terminal domain


Domain annotation for each model (and alignments):
>> MSC  Man1-Src1p-C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.3     0.065   1.2e+03     133     175 ..      20      63 ..       5     122 .. 0.65
   2 !    6.6   0.0   0.00025       4.5      43      80 ..     242     286 ..     212     317 .. 0.89
   3 !   16.7   0.1   2.2e-07    0.0039     214     337 ..     363     471 ..     294     472 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.065
                            MSC 133 ksglseeeLkeslsekksksiskeefeelwkealkeLkke.eei 175
                                     ++l++++L+++lse+    ++++   e++++  + + ++ +ei
  gene954|gene954|rna954|rna954  20 YTKLTKDQLRKILSEQGVTVMENKLKTEILQMYKSAIYDKiDEI 63 
                                    45666666777777766666666666666555555555554444 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.00025
                            MSC  43 lleslkP.......kCtpCPehAiCysnlevkCepgyvlkphpls 80 
                                    +l+++ P        C++ P++ +  ++ +++C +gyvl++++l 
  gene954|gene954|rna954|rna954 242 YLKYFAPyctnggrCCVKLPKNTFLDEKGRLRCSKGYVLQRNILF 286
                                    5667777777777779999**********************9986 PP

  == domain 3  score: 16.7 bits;  conditional E-value: 2.2e-07
                            MSC 214 vretlaryrllllglllllllilylrsrlrsrraekerveelvkevlerLkkqkkkhaedpstapepylslvqLRDdvLq 293
                                    +r+++ r+ ++l+ ++l+++++ly+ + +++      rv++ +++v++ L+ qkk++ + + ++p  +l+ +q+      
  gene954|gene954|rna954|rna954 363 IRSIYIRHFYVLMFSILAVFVALYAINFYKQ-----LRVKNNYDKVIDMLRLQKKNSSQFQ-VNP--FLFEEQI-----V 429
                                    5566888888888888888888888877765.....679999**************88877.456..9999986.....5 PP

                            MSC 294 dehslkernrlWkkvekvveqnsnVrtsleevhGeimrvWeWiG 337
                                     ++ lk ++ l   v++ +e n++V   +  v+G  ++++eW G
  gene954|gene954|rna954|rna954 430 GHSGLKPQEFL--DVKRLLEMNTSVTIFDISVSGKCAKAYEWLG 471
                                    55667777766..9999999999999999999999999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (476 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1256  (0.0700541); expected 358.6 (0.02)
Passed bias filter:                      689  (0.0384294); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.66u 0.34s 00:00:01.00 Elapsed: 00:00:00.51
# Mc/sec: 2803.33
//
Query:       gene955|gene955|rna955|rna955  [L=90]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-21   75.4   3.2    2.4e-21   75.3   3.2    1.0  1  Synaptobrevin    Synaptobrevin
  ------ inclusion threshold ------
      0.016   15.3   0.2      0.018   15.1   0.2    1.1  1  MCU              Mitochondrial calcium uniporter
      0.022   13.5   0.4      0.026   13.3   0.4    1.0  1  Clostridium_P47  Clostridium P-47 protein
      0.035   14.2   2.2      0.042   13.9   2.2    1.1  1  DUF1640          Protein of unknown function (DUF1640)
      0.045   12.5   1.8      0.053   12.3   1.8    1.0  1  DUF2207          Predicted membrane protein (DUF2207)
        4.3    6.8  11.9        1.9    8.0   6.4    1.9  2  TMCO5            TMCO5 family
        4.3    7.8   5.8        7.7    7.0   5.8    1.5  1  FeoB_associated  FeoB-associated Cys-rich membrane protein


Domain annotation for each model (and alignments):
>> Synaptobrevin  Synaptobrevin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.3   3.2   9.2e-25   2.4e-21       5      87 ..       6      88 ..       2      90 .] 0.95

  Alignments for each domain:
  == domain 1  score: 75.3 bits;  conditional E-value: 9.2e-25
                                   HHHHHHHHHCCCCHHCCHHHHCHCCCCCHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHTXXXXXXXXXXXXXXXXXXXXX CS
                  Synaptobrevin  5 lakikaevdevkdimkeNidkvlergekldeLvdktenLqssaqqFkkqarklkrkmwwknmkliiililvvlililiiiiv 86
                                   + ki++e+ e +d +k Ni++ ++r  kl +L++kte L++  q Fkk+a ++++kmwwk +k++i++++++++++l+i  +
  gene955|gene955|rna955|rna955  6 TLKINKELLELQDQLKTNIKNEVDRTSKLKKLSKKTEGLEKRGQVFKKKAVEVEQKMWWKSVKYWIVIGVIIFVILLVIYKL 87
                                   679***************************************************************************9876 PP

                                   X CS
                  Synaptobrevin 87 i 87
                                   +
  gene955|gene955|rna955|rna955 88 F 88
                                   5 PP

>> MCU  Mitochondrial calcium uniporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.2   7.2e-06     0.018      49     106 ..      20      77 ..       4      84 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 7.2e-06
                                    SSTSSSSSHHHHHHHHHHHHH-SHHHHHHHHTCCCGGGCHHHHGGGHHHHHHHHTHHH CS
                            MCU  49 eeeqlkkereleekleelreelepleekkeeidekAerrtrrllwagLallavqlgil 106
                                     + + k+e + ++kl++l+++ e le+  + +++kA + +++++w    + +v   i+
  gene955|gene955|rna955|rna955  20 LKTNIKNEVDRTSKLKKLSKKTEGLEKRGQVFKKKAVEVEQKMWWKSVKYWIVIGVII 77 
                                    34557788888999********************************999998877665 PP

>> Clostridium_P47  Clostridium P-47 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.4     1e-05     0.026     300     380 ..       6      84 ..       3      88 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1e-05
                Clostridium_P47 300 dlsvddteivtemevkvdvspgidlyikiktkqqltLskkskGeqtlaYevvreasaqhrthvatwviitevilgvivav 379
                                     l ++++ ++ + ++k++++  +d + k+k   + t + ++ G q+ + ++v+ +++ + + v  w++i+ +i+ + ++v
  gene955|gene955|rna955|rna955   6 TLKINKELLELQDQLKTNIKNEVDRTSKLKKLSKKTEGLEKRG-QVFKKKAVEVEQKMWWKSVKYWIVIGVIIFVI-LLV 83 
                                    5789999999999****************99988888887777.68899999*999999999*******9888755.555 PP

                Clostridium_P47 380 i 380
                                    i
  gene955|gene955|rna955|rna955  84 I 84 
                                    5 PP

>> DUF1640  Protein of unknown function (DUF1640)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   2.2   1.7e-05     0.042      89     174 ..       3      87 ..       2      88 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.7e-05
                        DUF1640  89 eklkqkLreeidklkadirldlnleKgrireelakleakiqelnnkidrevsalrteiE.svKldvikyliglvvgilav 167
                                    ++++ k+++e+ +l+++ + ++ +e  r+   l+kl++k++ l+++ +   ++   e+E ++ ++ +ky i + v i+++
  gene955|gene955|rna955|rna955   3 DEITLKINKELLELQDQLKTNIKNEVDRTSK-LKKLSKKTEGLEKRGQVF-KKKAVEVEqKMWWKSVKYWIVIGVIIFVI 80 
                                    5678899******************999987.9************95544.666678887999***************** PP

                        DUF1640 168 glavvRl 174
                                    +l +++l
  gene955|gene955|rna955|rna955  81 LLVIYKL 87 
                                    **99998 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   1.8   2.1e-05     0.053     337     401 ..      18      84 ..       3      89 .. 0.57

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.1e-05
                        DUF2207 337 keikkyakkskkkakkfkkalkkwksavkkkergyfdkkg....kkklkklsalglgliilglililla 401
                                    +++k+++k++ ++ +k+kk  kk +  ++k + + f+kk     +k  +k+  +++++++++++++l++
  gene955|gene955|rna955|rna955  18 DQLKTNIKNEVDRTSKLKKLSKKTEG-LEK-RGQVFKKKAveveQKMWWKSVKYWIVIGVIIFVILLVI 84 
                                    45666666666555555555555544.333.47777777777756666666666666666666666543 PP

>> TMCO5  TMCO5 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   3.5   0.00088       2.2      47      93 ..      14      61 ..       3      62 .. 0.73
   2 ?    8.0   6.4   0.00074       1.9     179     232 ..      32      88 ..      30      90 .] 0.75

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.00088
                          TMCO5 47 lereed.eeenfsenekedalkeLeletaklekkneiLlkevveLqkk 93
                                   le +++ + ++  e +++ +lk+L ++t  lek+ ++  k+ ve+++k
  gene955|gene955|rna955|rna955 14 LELQDQlKTNIKNEVDRTSKLKKLSKKTEGLEKRGQVFKKKAVEVEQK 61
                                   333333134456678999999999999999999999999999999988 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.00074
                          TMCO5 179 sklqsnssqrv..etiqknaektiikkkkrvfwkralrflffmvlifirLl.gyvlf 232
                                    skl++ s++++  e   +  +k+ ++ +++++wk++  +++  v+if+ Ll  y lf
  gene955|gene955|rna955|rna955  32 SKLKKLSKKTEglEKRGQVFKKKAVEVEQKMWWKSVKYWIVIGVIIFVILLvIYKLF 88 
                                    5666667766656666777899999******99999999999888887665157777 PP

>> FeoB_associated  FeoB-associated Cys-rich membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   5.8     0.003       7.7       3      21 ..      70      88 ..      68      90 .] 0.75

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.003
                FeoB_associated  3 iIVgliiaaavafvirrli 21
                                   +IV+++i+ ++++vi++l+
  gene955|gene955|rna955|rna955 70 WIVIGVIIFVILLVIYKLF 88
                                   5777777778888999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2377  (0.132579); expected 358.6 (0.02)
Passed bias filter:                      920  (0.0513135); expected 358.6 (0.02)
Passed Vit filter:                       123  (0.00686039); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.48u 0.31s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 591.61
//
Query:       gene956|gene956|rna956|rna956  [L=162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00051   19.5   0.3    0.00056   19.3   0.3    1.2  1  Guanylate_cyc_2  Guanylylate cyclase


Domain annotation for each model (and alignments):
>> Guanylate_cyc_2  Guanylylate cyclase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.3   3.1e-08   0.00056      97     172 ..      64     138 ..      11     146 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 3.1e-08
                Guanylate_cyc_2  97 fkkakeagievekrsvsveelvehlasgkvaivLvnaalLkcdlcksnkllselrkllsrkseytGhyvvlcGyda 172
                                     ++++++ +++ ++++s +++ +hl +  ++ +L + ++ + ++c  +k+  +++++l++k++y G   v  G+++
  gene956|gene956|rna956|rna956  64 DQAVHSRMVRIARMKISKRKIEKHLGKRIPISLLKERNIYRNECCDYRKFYGIVESILKHKNNYYGTM-VCNGFSS 138
                                    35667889********************9*9999999***9*****99******************85.5677765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       726  (0.0404931); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1169.08
//
Query:       gene957|gene957|rna957|rna957  [L=41]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (41 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       166  (0.00925874); expected 358.6 (0.02)
Passed bias filter:                      127  (0.0070835); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.31u 0.26s 00:00:00.57 Elapsed: 00:00:00.40
# Mc/sec: 309.58
//
Query:       gene958|gene958|rna958|rna958  [L=49]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (49 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       663  (0.0369792); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 358.81
//
Query:       gene959|gene959|rna959|rna959  [L=83]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
        0.7    9.4   3.7       0.24   10.8   0.9    1.7  2  DNAP_B_exo_N  DNA polymerase family B exonuclease domain, N-t


Domain annotation for each model (and alignments):
>> DNAP_B_exo_N  DNA polymerase family B exonuclease domain, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.1      0.23   4.1e+03       8       9 ..      24      25 ..      22      26 .. 0.73
   2 ?   10.8   0.9   1.3e-05      0.24       5      12 ..      39      46 ..      38      47 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.23
                   DNAP_B_exo_N  8 WF 9 
                                   WF
  gene959|gene959|rna959|rna959 24 WF 25
                                   *9 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 1.3e-05
                   DNAP_B_exo_N  5 ClNWFEnr 12
                                   C+ WFEnr
  gene959|gene959|rna959|rna959 39 CITWFENR 46
                                   *******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (83 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       403  (0.0224776); expected 358.6 (0.02)
Passed bias filter:                      212  (0.0118244); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 628.28
//
Query:       gene96|gene96|rna96|rna96  [L=309]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    0.00064   19.0   0.1     0.0018   17.6   0.0    1.8  2  Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0     1e-07    0.0018       1     100 [.      42     158 ..      42     162 .. 0.62
   2 ?   -2.2   0.0      0.11   1.9e+03     258     275 ..     264     281 ..     244     294 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1e-07
                                CSEEEE--SHHHHHHHHHHHHHTS-EEEE...........E.....TTHCHHHCSHHHHCHHHHHHHHHHHHH..HHHHCHHHH CS
                                xxxxxxxxxxxxxxxxxxxxxxxxxxxxx...........x.....xxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxx RF
                Pyr_redox_2   1 kdvvviGgGpAGlaaaltlaqagakvtlv...........e.....legtclnggcllskallgvaedaeias..evvkklnqg 66 
                                ++v++iG+ pA+++aal+ a+a+ k +l+           e      + t   +gcl+   l++++ + +++   evv+ ++ g
  gene96|gene96|rna96|rna96  42 HRVIIIGSSPAAYTAALYTATANNKPLLFippvtynvrnyErivglPDMTEEKFGCLMRAQLERFGVEIRVVDhiEVVEGVKDG 125
                                58*************************995555444443313444444444455555555555555555555566555555555 PP

                                CCCCHCCTCEEEEESCEEEEETEEECTCEEEEEE CS
                                xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                Pyr_redox_2  67 ielllgeevvkidpgkkkvklekkkegdeekiay 100
                                 e + + e+++  +++k+v +e+ +eg +e+++ 
  gene96|gene96|rna96|rna96 126 NEGVDN-EGIGENYENKDVCDENGNEGIGENYEN 158
                                555555.666666677777776666666666655 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.11
                                EE--TTSBESSTTEEE-G CS
                                xxxxxxxxxxxxxxxxxx RF
                Pyr_redox_2 258 ivvdeflrtnvpgiyaiG 275
                                + +d+    n ++++++G
  gene96|gene96|rna96|rna96 264 LITDHDIGINAHNVFMCG 281
                                467777788888888888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (309 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       625  (0.0348597); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.36
# Mc/sec: 2562.99
//
Query:       gene960|gene960|rna960|rna960  [L=121]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1024  (0.0571142); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 884.04
//
Query:       gene961|gene961|rna961|rna961  [L=549]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.8e-56  190.9   0.2    1.9e-55  188.6   0.2    1.8  1  LCAT           Lecithin:cholesterol acyltransferase
    0.00065   19.5   0.0     0.0068   16.2   0.0    2.4  3  PGAP1          PGAP1-like protein
     0.0011   18.5   0.0     0.0028   17.2   0.0    1.7  2  DUF676         Putative serine esterase (DUF676)
     0.0067   16.0   0.0      0.011   15.3   0.0    1.2  1  DUF900         Alpha/beta hydrolase of unknown function (DUF9
  ------ inclusion threshold ------
      0.014   15.0   0.0      0.022   14.3   0.0    1.4  1  LIDHydrolase   Lipid-droplet associated hydrolase
      0.015   14.5   0.0       0.03   13.6   0.0    1.4  1  Hydrolase_4    Serine aminopeptidase, S33
       0.02   15.5   0.0      0.028   15.0   0.0    1.2  1  Abhydrolase_6  Alpha/beta hydrolase family
      0.024   14.7   0.0      0.051   13.7   0.0    1.5  1  SopE_GEF       SopE GEF domain
       0.11   13.1   1.4       0.21   12.1   0.3    1.9  2  Elongin_A      RNA polymerase II transcription factor SIII (E


Domain annotation for each model (and alignments):
>> LCAT  Lecithin:cholesterol acyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  188.6   0.2   9.7e-59   1.9e-55       2     391 ..     104     509 ..     103     510 .. 0.81

  Alignments for each domain:
  == domain 1  score: 188.6 bits;  conditional E-value: 9.7e-59
                           LCAT   2 FrkelWldldmllslvvd.cwlknlelvldkstglqedapgvkiRadqGfeaieyldkskiagkqyeiwkklvknlvkiG 80 
                                    F k++W++ld l+ + +d   +     ++ ks+g+  d+ ++k+Ra +G+e+  ++    + g  y++w+k++ +l  + 
  gene961|gene961|rna961|rna961 104 F-KKVWGSLDGLRHMLMDkASFL--SHLKLKSNGK--DPENIKVRACKGLESCSHM----LPG--YWVWSKIIRSLSLLN 172
                                    5.89*************974454..6778899999..*******************....999..*************** PP

                           LCAT  81 yeknktvvaapYDWRls...leerdkYfskLkelieealklsgkkvvliaHSmGnllvlyflkwveaea..Wvdqhikaf 155
                                    y  n  +v  pYDWR+s   le+rd +f++Lk+ +e   + +++kvv+++HSmG+ +   +++wve++   W dqh+++ 
  gene961|gene961|rna961|rna961 173 YDSNS-LVVFPYDWRISfeqLEQRDAFFTRLKNEVEMLRRIHNEKVVILSHSMGAVIAHHMMHWVEEKEkgWCDQHLQGL 251
                                    *****.**********************************************************9987788********* PP

                           LCAT 156 islgapllGsvkavkallsGenkgipvlseltlrvlsksfsss............lsllPkgeevlwkdvawpsdeiliq 223
                                    ++++ap lG ++   a++sG+     v +++    l+ +fs+s            + llPkg + +wk++   + +   q
  gene961|gene961|rna961|rna961 252 VNIAAPQLGVPRSFTAIISGDWG---VQNTSRFNFLKIFFSQSeraillrnwesvMNLLPKGTNKIWKHFIGRTLKKDDQ 328
                                    ********************842...22556666666666666666666666666***************9776663333 PP

                           LCAT 224 tpsinltegalvrf..fsdevdlkdllsftlnvlagwvmvkvaedldgglsklekelkklkkkkyvkeeetklpeaPgvk 301
                                    +   + +e++ ++    +d+v+   l++ft + +ag +  +v++  +  l       + +++ ky  +++t+lp aP+  
  gene961|gene961|rna961|rna961 329 KD--QAQEQPKQESkdRKDDVP---LVKFTDS-KAGIYVEQVIHFVKVLLG------RDITRIKYFDPTQTRLPDAPNLT 396
                                    32..344444444422333444...5666543.445555555544444444......4477889**************** PP

                           LCAT 302 vyciygvglptergyvyapekksspln...yi....lsdidyeteesivskdGdetvpkeslel.Ckk.Wqd...nkakv 369
                                    +y +yg++ +te gy y+  +k+       y       d+d   ++++++ +Gd+tvp+ sl    +k W++   n+ +v
  gene961|gene961|rna961|rna961 397 IYSLYGIDSETEGGYCYKTAGKTLNNRgipYFidrdAYDEDMRCKNGVFVVNGDGTVPLISLGYmGRKgWKNksiNPSNV 476
                                    ******************9887654321113301113456667799****************9844448**999999999 PP

                           LCAT 370 kvtvaelkeek...........rsaehvellvs 391
                                    +  v e  +++            sa hv++l++
  gene961|gene961|rna961|rna961 477 QTIVREYRHRPvnilkdlrggpSSAGHVDILGN 509
                                    999****9999**********9********975 PP

>> PGAP1  PGAP1-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.38   7.6e+02       5      20 ..      79      94 ..      76     120 .. 0.89
   2 !   16.2   0.0   3.4e-06    0.0068      89     137 ..     213     266 ..     190     282 .. 0.86
   3 ?   -2.3   0.0       1.5   2.9e+03     149     185 ..     334     368 ..     311     377 .. 0.72

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.38
                          PGAP1  5 ipVlFvpGnagsykqv 20
                                    pV+ +pG a s+ ++
  gene961|gene961|rna961|rna961 79 HPVIIIPGFASSHLEI 94
                                   79********998665 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 3.4e-06
                          PGAP1  89 eptsviliGHSmGGivaraaltlkn.....yikqsvntiltlasPhalpplsfd 137
                                    ++++v+++ HSmG ++a  ++   +       +q+ + ++ +a+P    p sf 
  gene961|gene961|rna961|rna961 213 HNEKVVILSHSMGAVIAHHMMHWVEekekgWCDQHLQGLVNIAAPQLGVPRSFT 266
                                    6789***************99765555677999************998888775 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 1.5
                          PGAP1 149 efwkkeleekeklenvllvsitggirdsmvpaeyssl 185
                                    e++k+  e+k++ ++v lv  t+++ ++ v++  +++
  gene961|gene961|rna961|rna961 334 EQPKQ--ESKDRKDDVPLVKFTDSKAGIYVEQVIHFV 368
                                    33333..333338999999999999998888776665 PP

>> DUF676  Putative serine esterase (DUF676)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       2.1   4.1e+03       4      20 ..      77      93 ..      76     105 .. 0.79
   2 !   17.2   0.0   1.4e-06    0.0028      62     148 ..     201     279 ..     175     334 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 2.1
                         DUF676  4 kdhLvVlvHGlqgnsaD 20
                                   k+h v+++ G+ +++ +
  gene961|gene961|rna961|rna961 77 KKHPVIIIPGFASSHLE 93
                                   6799*********9765 PP

  == domain 2  score: 17.2 bits;  conditional E-value: 1.4e-06
                         DUF676  62 rlaeevlevvkkkkdknkkiSfvghSlGgliaraaiaklkekemtlkeaikglepvtfitlasPhLGvlysskslinlgl 141
                                    rl +ev e++++ +++  k+ ++ hS+G +ia +++  ++eke+      ++ +++ ++ +a P LGv  s  + i +g 
  gene961|gene961|rna961|rna961 201 RLKNEV-EMLRRIHNE--KVVILSHSMGAVIAHHMMHWVEEKEKG----WCDQHLQGLVNIAAPQLGVPRSFTA-IISGD 272
                                    666665.455555555..9*********************99863....456689999**********999999.88887 PP

                         DUF676 142 alleklk 148
                                    + ++ ++
  gene961|gene961|rna961|rna961 273 WGVQNTS 279
                                    7776655 PP

>> DUF900  Alpha/beta hydrolase of unknown function (DUF900)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   5.5e-06     0.011      80     167 ..     202     294 ..     191     299 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 5.5e-06
                         DUF900  80 lekllrylatkksakkihllaHSmGtwlvlealrqlaieadepaveakikevi.LaAPDidv.dvfkkqle.....slgk 152
                                    l++ +++l++  +++k+ +l HSmG  ++ ++++ +  +++    ++ ++ ++ +aAP + v   f+  +      +   
  gene961|gene961|rna961|rna961 202 LKNEVEMLRRI-HNEKVVILSHSMGAVIAHHMMHWVEEKEKG-WCDQHLQGLVnIAAPQLGVpRSFTAIISgdwgvQ--- 276
                                    66667777776.778**************9999988877764.5666666555478888877666666666644322... PP

                         DUF900 153 es....keltvyvsrdDra 167
                                     +    + l ++ s++ ra
  gene961|gene961|rna961|rna961 277 -NtsrfNFLKIFFSQSERA 294
                                    .322346667777777776 PP

>> LIDHydrolase  Lipid-droplet associated hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   1.1e-05     0.022      64     111 ..     194     248 ..     187     337 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.1e-05
                   LIDHydrolase  64 QiehkedflkellekaksekdvklilvGHSvGaYialevlkrlsers.......i 111
                                    Q +     lk+ +e  ++ ++ k+++++HS Ga ia ++++ ++e++        
  gene961|gene961|rna961|rna961 194 QRDAFFTRLKNEVEMLRRIHNEKVVILSHSMGAVIAHHMMHWVEEKEkgwcdqhL 248
                                    44444455666777688899*********************99887655555553 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   1.5e-05      0.03      67     111 ..     207     259 ..     192     292 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.5e-05
                    Hydrolase_4  67 ekvkeehpelplfllGhSmGGliallyl...lrypd.....kvagli.lsaPal 111
                                    e++++  +++++++l hSmG++ia +++   +++++     +++gl+ ++aP l
  gene961|gene961|rna961|rna961 207 EMLRRI-HNEKVVILSHSMGAVIAHHMMhwvEEKEKgwcdqHLQGLVnIAAPQL 259
                                    555544.4667*************999955433333455556777763344555 PP

>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.0   1.4e-05     0.028       4      87 ..     155     247 ..     154     342 .. 0.66

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.4e-05
                                    E--GC.....G....CHHHHHHHHCCTCEEEEE--T.TS..TS-GGCS--HHHCHHHHHHHCCTT..TTSEEEEEETCHH CS
                  Abhydrolase_6   4 lHGagssassW....lvapLaallaagvhvlapDlp.Gh..GrsdpppldledladlaalldelaagggpvvlvGHSlGG 76 
                                    l+G +     W    +  +L+++ +    v+ +D++ ++     + ++  +++l   +++l+++     +vv++ HS+G+
  gene961|gene961|rna961|rna961 155 LPGYWV----WskiiRSLSLLNYDSNSLVVFPYDWRiSFeqL--EQRDAFFTRLKNEVEMLRRIH--NEKVVILSHSMGA 226
                                    788665....86533122556666666666999998655222..555555555555577777775..9999********* PP

                                    HHHHHHHHCC........... CS
                  Abhydrolase_6  77 alalaaapla..........l 87 
                                    ++a +  +             
  gene961|gene961|rna961|rna961 227 VIAHHMMHWVeekekgwcdqH 247
                                    ***993333365566665553 PP

>> SopE_GEF  SopE GEF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   2.6e-05     0.051      56      72 ..     441     457 ..     435     478 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.6e-05
                                    ETTEEEETT-SS-TCHH CS
                       SopE_GEF  56 KngvfvpsGaGanPlin 72 
                                    Kngvfv++G+G+ Pli 
  gene961|gene961|rna961|rna961 441 KNGVFVVNGDGTVPLIS 457
                                    9**************85 PP

>> Elongin_A  RNA polymerase II transcription factor SIII (Elongin) subunit A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       2.3   4.6e+03      64      79 ..     182     197 ..     154     216 .. 0.59
   2 ?   12.1   0.3    0.0001      0.21      24      64 ..     297     336 ..     279     347 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 2.3
                      Elongin_A  64 pkswrelYeklkkere 79 
                                    p +wr  +e+l+++ +
  gene961|gene961|rna961|rna961 182 PYDWRISFEQLEQRDA 197
                                    5788888888887765 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.0001
                      Elongin_A  24 LreiEensphlaeetdelWkklikrdfpeeskekstepkep 64 
                                    Lr+ E+  + l + t+++Wk++i r+ ++++++++ ++ +p
  gene961|gene961|rna961|rna961 297 LRNWESVMNLLPKGTNKIWKHFIGRTLKKDDQKDQAQE-QP 336
                                    67777777777788****************99777662.33 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (549 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       757  (0.0422221); expected 358.6 (0.02)
Passed bias filter:                      566  (0.031569); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.67u 0.31s 00:00:00.98 Elapsed: 00:00:00.46
# Mc/sec: 3555.56
//
Query:       gene962|gene962|rna962|rna962  [L=31]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (31 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       178  (0.00992805); expected 358.6 (0.02)
Passed bias filter:                      101  (0.00563333); expected 358.6 (0.02)
Passed Vit filter:                         7  (0.000390429); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.32u 0.25s 00:00:00.57 Elapsed: 00:00:00.40
# Mc/sec: 230.58
//
Query:       gene963|gene963|rna963|rna963  [L=222]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
        1.5    8.8   8.9         11    6.0   0.0    3.1  2  Ninjurin       Ninjurin
        2.4    8.6  11.7        0.4   11.1   0.5    3.1  3  Cyd_oper_YbgE  Cyd operon protein YbgE (Cyd_oper_YbgE)


Domain annotation for each model (and alignments):
>> Ninjurin  Ninjurin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   6.3     0.024   2.2e+02      38      94 ..      58     126 ..      32     134 .. 0.63
   2 ?    6.0   0.0    0.0012        11      45      65 ..     200     220 ..     192     222 .] 0.86

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.024
                       Ninjurin  38 kfyiallvLislSllLqvvvgilliliasklnlekekk......er......rlnklnnaatilvfvit 94 
                                    + + + l +++ S++L +++ +ll+l++++l++ +ek       e+       + ++  +++ +v++i+
  gene963|gene963|rna963|rna963  58 QSEHFPLEIVLQSIFLVLFHFVLLYLSKQELSILEEKLvlnrftEKsyrrygMFSLIFSLTVSVVLMIA 126
                                    445677778889999999999999996545555544446655553323334444444555555555554 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0012
                       Ninjurin  45 vLislSllLqvvvgillilia 65 
                                    v++++S+++q++v +++++++
  gene963|gene963|rna963|rna963 200 VFLIVSVVFQILVDVAVVFRR 220
                                    7899*************9953 PP

>> Cyd_oper_YbgE  Cyd operon protein YbgE (Cyd_oper_YbgE)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.5   4.5e-05       0.4      46      75 ..      21      50 ..       6      54 .. 0.82
   2 ?    4.6   0.4    0.0046        41      14      70 ..     121     148 ..      99     157 .. 0.63
   3 ?   -2.7   0.2      0.88   7.9e+03      36      42 ..     178     184 ..     170     194 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 4.5e-05
                  Cyd_oper_YbgE 46 vvhGvGFrprkalwrllFsPllallillla 75
                                   +   +GF+p+ +  ++ F P+l+ +++l+ 
  gene963|gene963|rna963|rna963 21 FAPCIGFIPQIVKRKITFAPILSTIVILAN 50
                                   44569******************9998875 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.0046
                  Cyd_oper_YbgE  14 avvlwdpelfaaatsglshgllllllwavcagvvhGvGFrprkalwrllFsPllall 70 
                                    +                             ++++  +G + r+++   +F Pl+ ++
  gene963|gene963|rna963|rna963 121 V-----------------------------VLMIATIGLIFRTRYVYTIFGPLFLVA 148
                                    3.............................456677777777777777777776444 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 0.88
                  Cyd_oper_YbgE  36 llllwav 42 
                                    l+l+wa+
  gene963|gene963|rna963|rna963 178 LFLMWAL 184
                                    5778875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       771  (0.043003); expected 358.6 (0.02)
Passed bias filter:                      254  (0.014167); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 1504.01
//
Query:       gene964|gene964|rna964|rna964  [L=438]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   4.5e-117  391.0   0.1   5.4e-117  390.8   0.1    1.0  1  SHMT      Serine hydroxymethyltransferase


Domain annotation for each model (and alignments):
>> SHMT  Serine hydroxymethyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  390.8   0.1    3e-121  5.4e-117       2     398 ..      10     403 ..       9     404 .. 0.96

  Alignments for each domain:
  == domain 1  score: 390.8 bits;  conditional E-value: 3e-121
                                    HHHTHHHHHHHHHHHHHHHHSEE-STT-----HHHHHHHTSGGGG----EETTEESSST-HHHHHHHHHHHHHHHHHCT- CS
                           SHMT   2 eesdpevaeiikkekerqkeeieliasenftskavlealGsvltnkyaeGyPGkryyGGcefvdeveelaqdrakelfkl 81 
                                    ++sd+ ++ +i +e++rq+e ieliase ++s +vl+a  s l+n y +G   +     + +vd++e+l+++ra++ f+l
  gene964|gene964|rna964|rna964  10 KNSDHTLYRLIANENKRQEEFIELIASESYVSVSVLQASASLLHNSYGQGTLDENKNDRTSVVDKIEDLCKERALQFFNL 89 
                                    689***************************************************************************** PP

                                    STTTEEEE---SSHHHHHHHHHHHHT-TT-EEEEESCTTTSTGGGT-BTSS-B-SHHHHHSEEEEE-B-TTTSSB-HHHH CS
                           SHMT  82 dpakwgvnvqplsGsqanlavytallepgdrilgldladGGhlthGakveskkisassklfesveykvdketglidydel 161
                                    d + wgv+v+p+sG+ an+++y all  ++r++g+dl  GGh++hG+k++ +k+sas+ +fes  y+++ e+g idy+++
  gene964|gene964|rna964|rna964  90 DRNVWGVDVRPYSGTVANFEIYDALLGWKGRLMGMDLFCGGHFSHGFKTNRRKVSASAEYFESYFYGLK-EDGRIDYEKM 168
                                    ********************************************************************9.99******** PP

                                    HHHHHHH--SEEEEE-SST-S---HHHHHHHHHHTT-EEEEE-GGGHHHHHTTSS--GCCTSSEEEEESSSTT-S-S-EE CS
                           SHMT 162 ekkakefkPklivaGtsaysrlidyarlreiadevgayllvdmahiaGlvaagvipsPfeyadvvtttthktlrGprggl 241
                                    +k   e k +l+++G+say+  +dy+r+reiad+ +ayl++d++h++ ++a+g++ +Pfey+dv  tt  k lrGp++++
  gene964|gene964|rna964|rna964 169 QKDLIENKVQLLIGGASAYPGDFDYKRMREIADQNNAYLMADISHVSAIIACGMMNNPFEYCDVAITTVQKMLRGPKAAI 248
                                    ******************************************************************************** PP

                                    EEEC-SEEEEETTTEEEEHHHHHHHHHHHTTTT-SS--HHHHHHHHHHHHHCTSHHHHHHHHHHHHHHHHHHHHHHHTT- CS
                           SHMT 242 illrkgvksvdktgkevleelekkinsavfPglqGGPlnhviaakavalkealepefkvyqkqvlknakalaealkekgy 321
                                    i++r      dk+g     ++ek i ++v Pg q     h+ia++a+alk +  +e++++ +qvl n + +  ++ e+g 
  gene964|gene964|rna964|rna964 249 IYYR-----KDKNGV----NVEKLITNSVSPGFQRSIRYHTIAGIATALKLTQAEEYRTFVTQVLINMQSMCGVFRENGV 319
                                    ****.....355554....599********************************************************** PP

                                    EEGGGS-SSSEEEEEGGGGTS-HHH.......HHHHHHHTTEE-EEE--TTSSTTTT-SEEEEESHHHHHTT--HHHHHH CS
                           SHMT 322 klvsgGtdnhlvlvdlrekgldGkr.......aekvlekvnitankntvPgdksalvtsGlrlGtpaltsrgfkeedlek 394
                                    +l++gGt nhl l+d+r+  ++G+         e +++ vni++nknt Pgd sal +sG+r+ t ++t rgfke++  +
  gene964|gene964|rna964|rna964 320 RLLTGGTINHLALLDMRSISFKGRVlkidaalFEWICDVVNISVNKNTWPGDTSALHPSGVRVSTVSVTIRGFKEKECAQ 399
                                    ******************99888642212111577899****************************************** PP

                                    HHHH CS
                           SHMT 395 vakf 398
                                    va+f
  gene964|gene964|rna964|rna964 400 VASF 403
                                    *998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (438 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       488  (0.0272185); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 2879.16
//
Query:       gene965|gene965|rna965|rna965  [L=63]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.024   14.8   6.0      0.024   14.8   6.0    1.9  2  Cir_N     N-terminal domain of CBF1 interacting co-repressor 


Domain annotation for each model (and alignments):
>> Cir_N  N-terminal domain of CBF1 interacting co-repressor CIR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   6.0   1.3e-06     0.024       1      37 []      10      46 ..      10      46 .. 0.99
   2 ?   -0.5   0.2     0.084   1.5e+03      11      17 ..      55      61 ..      53      63 .] 0.77

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.3e-06
                                   SS-TTSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Cir_N  1 SWHPgllkNqerVWkaEqkaleEkkkieerkkeieeE 37
                                   SWHP  ++ q ++++   k+ e++k+ +  + e+eeE
  gene965|gene965|rna965|rna965 10 SWHPTRFEIQSKIHEYKMKEDEKEKRKQLIASELEEE 46
                                   9***********************************9 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.084
                                   HHHHHHH CS
                          Cir_N 11 erVWkaE 17
                                   +  W++E
  gene965|gene965|rna965|rna965 55 RMKWMEE 61
                                   5689999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (63 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1703  (0.0949858); expected 358.6 (0.02)
Passed bias filter:                      544  (0.0303419); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.33u 0.27s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 490.79
//
Query:       gene966|gene966|rna966|rna966  [L=311]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       958  (0.053433); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2350.56
//
Query:       gene967|gene967|rna967|rna967  [L=498]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.7e-10   38.8   0.0    2.4e-09   37.4   0.0    1.7  1  DENN      DENN (AEX-3) domain


Domain annotation for each model (and alignments):
>> DENN  DENN (AEX-3) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.4   0.0   1.3e-13   2.4e-09      93     178 ..     300     386 ..     273     393 .. 0.91

  Alignments for each domain:
  == domain 1  score: 37.4 bits;  conditional E-value: 1.3e-13
                           DENN  93 LsienilqlfeavLlErriillSeklarLtsvaealvallyPlkWqhiyiPvlpaslldvleaPtPfiiGvesslle.le 171
                                    L+ + +l+++++ L Er+ i+ S++ + + + +  + +++ P+++     + lp ++ ++l++P+Pf++G +++  + + 
  gene967|gene967|rna967|rna967 300 LNYNFVLKILSCFLNERQMIFCSNNKEKVYNTIVFFITIIKPFNYGFFMSSRLPDEFREILNSPFPFVLGADERTNSgVV 379
                                    78889*********************************************************************999666 PP

                           DENN 172 ekpledv 178
                                    + +l+++
  gene967|gene967|rna967|rna967 380 HVDLDNY 386
                                    6665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (498 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1029  (0.0573931); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.23s 00:00:00.74 Elapsed: 00:00:00.40
# Mc/sec: 3721.84
//
Query:       gene968|gene968|rna968|rna968  [L=330]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      2e-80  270.4   0.2    2.3e-80  270.2   0.2    1.0  1  Peptidase_M22  Glycoprotease family
  ------ inclusion threshold ------
       0.14   11.4   0.0        0.2   10.9   0.0    1.2  1  YcaO           YcaO cyclodehydratase, ATP-ad Mg2+-binding


Domain annotation for each model (and alignments):
>> Peptidase_M22  Glycoprotease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  270.2   0.2   2.6e-84   2.3e-80      10     270 ..      28     295 ..      22     296 .. 0.94

  Alignments for each domain:
  == domain 1  score: 270.2 bits;  conditional E-value: 2.6e-84
                                    EEEE....S.SSSHHHHHHHHHHHHHHHHHHHHHHHTSTGGGEEEEEEEEESS-HHHHHHHHHHHHHHHHHCT--EEEEE CS
                  Peptidase_M22  10 qkelhakyG.GvvPelasraHserllplieealaeaglsledldaIavtkgPGlftgLrvGvsfAkglalalnkPlvgVn 88 
                                    + + +++ G G++P++++ +H++++lpl+ +++ + g++l+dld Ia+tkgPG++ +L+vG+ +A++lal lnkP+++Vn
  gene968|gene968|rna968|rna968  28 RVTHVTQAGtGFIPSETALHHVRHILPLLSKCIVDTGIKLSDLDLIAYTKGPGMASPLQVGAIVARTLALYLNKPIIPVN 107
                                    4455678889********************************************************************** PP

                                    HHHHHHHCCHCT.SECSSCEEEEESSSTEEEEEECTTEEEEEEEESSSEHHHHHHHHHHHHT..SSCCH..HHHHHHCTC CS
                  Peptidase_M22  89 hleahalaarle.ekeefPvvllvsGghtqvylvkegryeilgetlddaagealdkvarllglpypggp..kieklakeg 165
                                    h+ ah++++ ++ +k ++P++l+ sGg+tqv++  +g+y+i+getld+a+g++ld++arl +++++++p  +ie lak+ 
  gene968|gene968|rna968|rna968 108 HCVAHIEMG-IKiTKAKNPIILYASGGNTQVIAF-SGKYKIFGETLDIAVGNCLDRFARLAKISNDPSPgrNIELLAKKS 185
                                    *********.5668889*****************.9*****************************776677*******99 PP

                                    .S.......EETTEEE.CHHHHHHHHHH..STT...HHHHHHHHHHHHHHHHHHHHHHHHHHCTBSEEEEESGGGGXHHH CS
                  Peptidase_M22 166 .kkiefprplkgldfsfsGlktavlkel..eke...vedlaasfqeavvdhlvekteralklpkakelvilGGvaankrL 239
                                     k++ +p+++kg+d+s+ G+ + ++++     +   v+ l++s+qe++++ lve+tera++l+++ e++i+GGv++n+rL
  gene968|gene968|rna968|rna968 186 qKYLYLPYTVKGMDMSMTGIISFIASKYnlD-KketVQALCYSLQETIFSALVEVTERAMALTNSYEIMIVGGVGCNERL 264
                                    77799***************99999999542.2468******************************************** PP

                                    HHCHCCHHHHTTSEEEXXXHHHHSSXCHHHH CS
                  Peptidase_M22 240 realeeeaeelglkliiPplkyctdnaamia 270
                                    ++++e++a+e+g++l++ + +yc dn+amia
  gene968|gene968|rna968|rna968 265 QAMMETMAKERGATLYAMDDSYCVDNGAMIA 295
                                    ******************************8 PP

>> YcaO  YcaO cyclodehydratase, ATP-ad Mg2+-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   2.3e-05       0.2     123     180 ..     227     283 ..     222     301 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 2.3e-05
                           YcaO 123 tleeAilhGllEliERdafalawyerlplpridlasdpeirellerlre.agievrlld 180
                                    +l+e i+ +l+E+ ER   ++  ye +   ++     +++++++e++++ +g +++++d
  gene968|gene968|rna968|rna968 227 SLQETIFSALVEVTERAMALTNSYEIMIVGGVGCN--ERLQAMMETMAKeRGATLYAMD 283
                                    899*************8888888888888888876..9*********998999999988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (330 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       595  (0.0331865); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 2293.85
//
Query:       gene969|gene969|rna969|rna969  [L=267]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       981  (0.0547158); expected 358.6 (0.02)
Passed bias filter:                      635  (0.0354175); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 1720.59
//
Query:       gene97|gene97|rna97|rna97  [L=226]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.4e-63  213.4  10.4    2.9e-63  213.1  10.4    1.0  1  Ribosomal_S3Ae  Ribosomal S3Ae family
     0.0062   16.7   0.6      0.032   14.4   0.4    2.1  2  GP63            Gene product 63
  ------ inclusion threshold ------
      0.049   13.3   0.0      0.081   12.5   0.0    1.3  1  DUF1449         Protein of unknown function (DUF1449)


Domain annotation for each model (and alignments):
>> Ribosomal_S3Ae  Ribosomal S3Ae family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  213.1  10.4   4.8e-67   2.9e-63       2     202 .]      18     222 ..      17     222 .. 0.98

  Alignments for each domain:
  == domain 1  score: 213.1 bits;  conditional E-value: 4.8e-67
                                S----S-TCCSEEEEEEEB-.TTSSSSEEEEEEEE--BSSSESHHSHTT-EEEEESHHHHTCSHTSSSEEEEEEEEEEESSEEE CS
             Ribosomal_S3Ae   2 kkkkvvDkfkkKeWydvkaP.slfgkreiGktlvnrtqgtkiaseklkgrvvevslaDLtndekeqafrklklkieevqgknal 84 
                                +kkk +D+f+kKe y+++ P s+f ++++G+t+ +++++  i++ kl+grv+ev++++L+++     frk k+ +++ +g++++
  gene97|gene97|rna97|rna97  18 SKKKEKDSFTKKEVYNLTVPsSMFMTTTVGTTILTKQSTAAITERKLRGRVFEVNQGELQGNS---PFRKYKFVCTKLTGRDLK 98 
                                799*****************8899**************************************3...6***************** PP

                                EEEEEEEE-HHHHHHH--SSB-EEEEEEEEEESSSEEEEEEEEEEE-STT......B---HHHHHHHHHHHHHHHHHHHHHS-H CS
             Ribosomal_S3Ae  85 tnFkgmeltrDklrslvrkwsslIeaivdvktkDgyllrvfvvafTkkrn......sYakssqkkaIrkkmveilteeaseldl 162
                                + F+gmelt+Dk + lvrkw++lIea+ dv+t+D+++lrvf+va+Tkk        +Yakssq+k+Irk m+++++ee++ +++
  gene97|gene97|rna97|rna97  99 SVFNGMELTTDKQKGLVRKWHTLIEAVSDVTTSDDVKLRVFTVAVTKKPAlwtkkhCYAKSSQVKEIRKAMFDVVKEEMEGQSV 182
                                ************************************************955899****************************** PP

                                HHHHHHHTTTHHHHHHHHHHTTTS-EEEEEEEEEEEEE-S CS
             Ribosomal_S3Ae 163 kelvkklipeslgkeiekeakkIyplrnveirKvkvlkkP 202
                                 e+v+k+ ++++ k+ie+  + I+pl+n+++ Kvkvlk+P
  gene97|gene97|rna97|rna97 183 VEIVRKISEDKIDKRIEEMGSLIFPLQNCYVSKVKVLKRP 222
                                *********99***************************98 PP

>> GP63  Gene product 63
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.22   1.3e+03      30      52 ..      75      98 ..      48     110 .. 0.70
   2 !   14.4   0.4   5.3e-06     0.032      11      66 ..     137     196 ..     130     200 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.22
                       GP63 30 dlesedP.rkPelievkvdGselk 52
                               +l+ + P rk + + +k  G++lk
  gene97|gene97|rna97|rna97 75 ELQGNSPfRKYKFVCTKLTGRDLK 98
                               555556658888899999998887 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 5.3e-06
                       GP63  11 qvlaaliktkPtvWtqkkvdlesed...PrkP..elievkvdGselkyglarnvseesver 66 
                                +v++  +  kP+ Wt+k+   +s +    rk   +++   ++G+ +   + r +se+++++
  gene97|gene97|rna97|rna97 137 RVFTVAVTKKPALWTKKHCYAKSSQvkeIRKAmfDVVKEEMEGQSVV-EIVRKISEDKIDK 196
                                677778889**********9999751115675334777778999999.9********9997 PP

>> DUF1449  Protein of unknown function (DUF1449)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   1.4e-05     0.081     119     157 ..      43      81 ..      28      84 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.4e-05
                    DUF1449 119 laallakilpkdetsavseeslvGrvavivlGtArkgsp 157
                                ++ +   il k+ t a++e++l Grv ++ +G+ + +sp
  gene97|gene97|rna97|rna97  43 TTTVGTTILTKQSTAAITERKLRGRVFEVNQGELQGNSP 81 
                                334446799************************999988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1461  (0.0814881); expected 358.6 (0.02)
Passed bias filter:                      525  (0.0292822); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1536.37
//
Query:       gene970|gene970|rna970|rna970  [L=81]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (81 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       375  (0.0209158); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 567.92
//
Query:       gene971|gene971|rna971|rna971  [L=37]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (37 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       276  (0.0153941); expected 358.6 (0.02)
Passed bias filter:                      235  (0.0131073); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.33u 0.27s 00:00:00.60 Elapsed: 00:00:00.41
# Mc/sec: 267.92
//
Query:       gene972|gene972|rna972|rna972  [L=43]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (43 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       219  (0.0122148); expected 358.6 (0.02)
Passed bias filter:                      186  (0.0103743); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.27s 00:00:00.62 Elapsed: 00:00:00.43
# Mc/sec: 301.06
//
Query:       gene973|gene973|rna973|rna973  [L=102]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       638  (0.0355848); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 693.27
//
Query:       gene974|gene974|rna974|rna974  [L=76]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       331  (0.0184617); expected 358.6 (0.02)
Passed bias filter:                      239  (0.0133304); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.43
# Mc/sec: 525.77
//
Query:       gene975|gene975|rna975|rna975  [L=66]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (66 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       443  (0.0247086); expected 358.6 (0.02)
Passed bias filter:                      253  (0.0141112); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.33u 0.24s 00:00:00.57 Elapsed: 00:00:00.39
# Mc/sec: 510.32
//
Query:       gene976|gene976|rna976|rna976  [L=235]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       462  (0.0257683); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1730.16
//
Query:       gene977|gene977|rna977|rna977  [L=213]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       563  (0.0314016); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.50
# Mc/sec: 1272.96
//
Query:       gene978|gene978|rna978|rna978  [L=492]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.2e-07   30.6   0.0    4.8e-06   27.2   0.0    2.8  3  WD40         WD domain, G-beta repeat
    0.00022   21.5   0.0      0.064   13.6   0.0    2.5  2  ANAPC4_WD40  Anaphase-promoting complex subunit 4 WD40 domain
     0.0011   18.5   0.5      0.002   17.7   0.5    1.3  1  Utp21        Utp21 specific WD40 associated putative domain
  ------ inclusion threshold ------
      0.057   13.7   0.0       0.12   12.7   0.0    1.5  1  Utp12        Dip2/Utp12 Family
      0.092   13.1   1.2       0.12   12.7   0.3    1.6  2  EbsA         EbsA-like protein


Domain annotation for each model (and alignments):
>> WD40  WD domain, G-beta repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0         3   1.1e+04      14      37 ..     141     164 ..     133     165 .. 0.67
   2 !   27.2   0.0   1.3e-09   4.8e-06       3      37 ..     171     206 ..     169     206 .. 0.91
   3 ?   -2.6   0.0       3.5   1.3e+04      18      29 ..     332     343 ..     328     350 .. 0.74

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 3
                                    EEEEEETTSSEEEEE.E.TTSEEEEE CS
                           WD40  14 tslafspdgawlasG.s.dDgtvriW 37 
                                      ++fs+d +++  G s +++++ i+
  gene978|gene978|rna978|rna978 141 VFVRFSRDEQLV--GvSnYNNKINIY 164
                                    457899999996..433257777766 PP

  == domain 2  score: 27.2 bits;  conditional E-value: 1.3e-09
                                    EEEEEESS.SSEEEEEEETTSSEEEEEETTSEEEEE CS
                           WD40   3 clrtltGH.ssvtslafspdgawlasGsdDgtvriW 37 
                                    ++ +l GH  +v++++fs dg+ ++s+s D+ v++W
  gene978|gene978|rna978|rna978 171 LVMSLYGHsLPVRCFDFSNDGRSVISCSADKLVKLW 206
                                    678999**555************************* PP

  == domain 3  score: -2.6 bits;  conditional E-value: 3.5
                                    EETTSSEEEEEE CS
                           WD40  18 fspdgawlasGs 29 
                                    f+ + ++l++++
  gene978|gene978|rna978|rna978 332 FDYNDDYLVAAG 343
                                    788999998776 PP

>> ANAPC4_WD40  Anaphase-promoting complex subunit 4 WD40 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.0   1.8e-05     0.064       9      86 ..     103     184 ..      98     187 .. 0.83
   2 !    7.4   0.0    0.0015       5.5      38      89 ..     179     229 ..     173     232 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.8e-05
                    ANAPC4_WD40   9 LiAlatedgellvfRlngqrvwtl.....eedkedsevrsLaWkpdgklLavaysdgevrlldaesgkvvhslsvkseka 83 
                                    + A+ ++d  +++ R n   v+++        +++se+  ++++ d++l  v+  ++++++++  + ++v sl  +s   
  gene978|gene978|rna978|rna978 103 ICAVSSCDHFVAIARNNELLVVDGslrtrWCITDESEIVFVRFSRDEQLVGVSNYNNKINIYKLRTMELVMSLYGHSL-P 181
                                    678889999999999999888888777653457899**********************************99976665.4 PP

                    ANAPC4_WD40  84 vtc 86 
                                    v c
  gene978|gene978|rna978|rna978 182 VRC 184
                                    666 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0015
                    ANAPC4_WD40  38 dsevrsLaWkpdgklLavaysdgevrlldaesgkvvhslsvksekavtclgW 89 
                                    +  vr++ +++dg+      +d  v+l   e g++ +++ ++s+  v+ ++ 
  gene978|gene978|rna978|rna978 179 SLPVRCFDFSNDGRSVISCSADKLVKLWGTEFGECRKTFYINSS-MVMFMKH 229
                                    6789***********************************99998.5887765 PP

>> Utp21  Utp21 specific WD40 associated putative domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.5   5.5e-07     0.002      90     207 ..     360     473 ..     348     485 .. 0.68

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 5.5e-07
                                    HHHHHHHHTT------.------HHHHHHHHHHSS--HHHHHHHHH-S-HHHHHT--------S-SHHHHHHHHHHHHHT CS
                          Utp21  90 deeeeeeeesrilkldklgteseftklLeegsetgdysefleyLkslspsaidleirsLesaesleelvafvkaltarLk 169
                                    d+++e+eee +i +l   +   +f++ Le+++e+ dy+++++ +k+l    i   i  L    + ++l   ++     Lk
  gene978|gene978|rna978|rna978 360 DSSSESEEELEIENL---KVYDKFSRALEKSKEDADYDALFNAMKELDMGDISSIISGL----DNNSLYVVLQ----ALK 428
                                    444455555555555...699***********************************999....5555554444....467 PP

                                    TTS-HHHHHHHHHHH...HHHTTTTTTT-SH.......HHHHHHHH CS
                          Utp21 170 srrdfeLvqailsvf...LkvHgdviaeeeee.....elkealeel 207
                                    ++ d++ v a+ +vf      H + +ae+++      e++  +e l
  gene978|gene978|rna978|rna978 429 NNIDYNVVLAV-KVFfsiVEHHRYFVAENQSAyvvykEIRGRVELL 473
                                    77788877775.3330114557777777666566666454444444 PP

>> Utp12  Dip2/Utp12 Family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   3.3e-05      0.12      13     101 ..     403     483 ..     392     486 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.3e-05
                                    S-TTTHHHHHHCS-CTCHHHHHHHHHHHH.HTTTTHHHHHHHHHHHHHHHHHHHHHSH..HHHHHHHHHHHHHHHHHHHH CS
                          Utp12  13 ippsdirltvlrLpssyvlkLLeflaerlaeksphlelllrwlkallrvHgsylvasps.dlvpaLrslqkslrerlktl 91 
                                     +  di+++++ L+   ++ +L++l++   +  +++ l +++ ++++  H++y+va  + ++      ++k +r r+++l
  gene978|gene978|rna978|rna978 403 LDMGDISSIISGLDNNSLYVVLQALKN---NIDYNVVLAVKVFFSIV-EHHRYFVAENQsAY-----VVYKEIRGRVELL 473
                                    57789**********************...55899*******99999.67778887665344.....79*********** PP

                                    HHHHHHHHHH CS
                          Utp12  92 skllglnlgr 101
                                    ++l+++n ++
  gene978|gene978|rna978|rna978 474 RQLIKENEYK 483
                                    ******9876 PP

>> EbsA  EbsA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.0       4.2   1.5e+04     106     121 ..     221     236 ..     216     242 .. 0.71
   2 ?   12.7   0.3   3.4e-05      0.12      29      81 ..     419     471 ..     410     484 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 4.2
                           EbsA 106 srtflmrkkpkklfld 121
                                    s +++++k +k+lfl+
  gene978|gene978|rna978|rna978 221 SSMVMFMKHSKDLFLA 236
                                    5566777888888876 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 3.4e-05
                           EbsA  29 slilllEntriylksnlvlllflvlvilgfkryliieedkliikslrffkkkk 81 
                                    sl ++l   + ++  n+vl++ +++ i+  +ry++ e+++ ++++ ++  + +
  gene978|gene978|rna978|rna978 419 SLYVVLQALKNNIDYNVVLAVKVFFSIVEHHRYFVAENQSAYVVYKEIRGRVE 471
                                    7888899999999***************************9999987766555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (492 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       637  (0.035529); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.47
# Mc/sec: 3130.78
//
Query:       gene979|gene979|rna979|rna979  [L=33]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (33 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       280  (0.0156172); expected 358.6 (0.02)
Passed bias filter:                      151  (0.00842211); expected 358.6 (0.02)
Passed Vit filter:                         4  (0.000223102); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.28s 00:00:00.63 Elapsed: 00:00:00.43
# Mc/sec: 230.92
//
Query:       gene98|gene98|rna98|rna98  [L=274]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (274 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       976  (0.0544369); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.64u 0.33s 00:00:00.97 Elapsed: 00:00:00.58
# Mc/sec: 1431.61
//
Query:       gene980|gene980|rna980|rna980  [L=107]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    4.7e-05   23.4   0.0    7.2e-05   22.8   0.0    1.3  1  Pcc1       Transcription factor Pcc1
  ------ inclusion threshold ------
       0.18   11.8   0.6       0.43   10.5   0.1    1.8  2  Fanconi_A  Fanconi anaemia group A protein


Domain annotation for each model (and alignments):
>> Pcc1  Transcription factor Pcc1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.0   8.1e-09   7.2e-05      16      73 ..      44     100 ..      33     101 .. 0.93

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 8.1e-09
                                    HHHHHHHHHCHC-TTECEEEEEEETTEEEEEEEESSHHHHHHHHHHHHHHHHHHHHHH CS
                           Pcc1  16 ialrtLqvDkelsplavkrslslegnvLqveykAttnrmLRvavngfleslglvletm 73 
                                     + r L+vDk  + + ++ ++++e+ +L v+++ + + +L+ +   +++ l lv et+
  gene980|gene980|rna980|rna980  44 KIKRILEVDKDFRAD-SQTTYDIEDGKLLVNISCSNLVSLKKSAYDLFRKLTLVDETI 100
                                    58899*******998.****************************************98 PP

>> Fanconi_A  Fanconi anaemia group A protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1   4.8e-05      0.43       4      33 ..       8      36 ..       5      41 .. 0.87
   2 ?   -0.9   0.0      0.17   1.5e+03      23      44 ..      84     105 ..      71     107 .] 0.74

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 4.8e-05
                      Fanconi_A  4 LvsLfFFsLmgLlsskltpkeavdslkale 33
                                   ++ LfF  ++ L  s+ltp  ++d++  + 
  gene980|gene980|rna980|rna980  8 VIYLFFIPMLHLTLSHLTPV-KMDFSSTFR 36
                                   689****************9.999988765 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.17
                      Fanconi_A  23 keavdslkalevcaeiLecLek 44 
                                    k+a d  ++l +  e ++++e+
  gene980|gene980|rna980|rna980  84 KSAYDLFRKLTLVDETIKMIEE 105
                                    5577888888888888888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       475  (0.0264934); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 700.93
//
Query:       gene981|gene981|rna981|rna981  [L=711]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    5.2e-15   55.8   0.9    2.3e-14   53.7   0.9    2.1  1  SMC_hinge  SMC proteins Flexible Hinge Domain
    2.8e-10   41.0  18.2    2.8e-10   41.0  18.2    4.2  4  AAA_23     AAA domain
    1.1e-06   28.8  11.4     0.0078   16.1   6.0    3.1  2  AAA_21     AAA domain, putative AbiEii toxin, Type IV TA syst
    0.00011   21.7  57.3    0.00047   19.7  57.3    2.1  1  SMC_N      RecF/RecN/SMC N terminal domain
    0.00072   20.1   3.1    0.00072   20.1   3.1    4.1  2  ABC_tran   ABC transporter
  ------ inclusion threshold ------
       0.01   15.6   0.0      0.021   14.6   0.0    1.4  1  AAA_29     P-loop containing region of AAA domain
      0.065   13.5   0.0       0.19   12.0   0.0    1.8  1  SbcCD_C    Putative exonuclease SbcCD, C subunit
       0.38   11.3   3.7       0.83   10.3   1.9    2.6  2  Cript      Microtubule-associated protein CRIPT


Domain annotation for each model (and alignments):
>> SMC_hinge  SMC proteins Flexible Hinge Domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.7   0.9     1e-17   2.3e-14       7     111 ..     233     330 ..     231     332 .. 0.96

  Alignments for each domain:
  == domain 1  score: 53.7 bits;  conditional E-value: 1e-17
                      SMC_hinge   7 rladlievdegyekAveaalgnrlqalvvedeetakkiieflkkknagratflpldrikqknkadgandknsgavplidl 86 
                                    r++dlievd+ +  Av a+ gnrl++ vv+ ee+a + i+ l+ +     +f+++d+i++ n+ +++n+    +vpl  l
  gene981|gene981|rna981|rna981 233 RVVDLIEVDDNAINAVIAVIGNRLKCMVVDYEEEALEKIKSLRFR----QSFIVMDKIEDVNDGEEQNE---SMVPLKHL 305
                                    89*************************************999999....9***********99999998...7******* PP

                      SMC_hinge  87 vevddelrkalryllgdtlvvdsld 111
                                    v+ ++e+ ++ ++l++d+++v++l 
  gene981|gene981|rna981|rna981 306 VKTKKEYNRLKEFLFKDIYLVKDLT 330
                                    ***********************95 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.0  18.2   1.2e-13   2.8e-10       9     198 ..       7     231 ..       5     233 .. 0.59
   2 ?   -1.9  18.5       1.8   4.1e+03     142     194 ..     346     416 ..     262     425 .. 0.47
   3 ?   -2.2  15.5       2.1   4.8e+03     121     192 ..     461     533 ..     415     538 .. 0.48
   4 ?    0.8   1.7      0.27     6e+02      48     142 ..     547     639 ..     537     685 .. 0.51

  Alignments for each domain:
  == domain 1  score: 41.0 bits;  conditional E-value: 1.2e-13
                         AAA_23   9 sfrdqeidFskgltlItGpNGaGKTTildAiklaLygetprlsrksgrgfeksdveiesegkvkayveltfenkdgry.. 86 
                                    s+++ + +Fsk +++I G+NGaGK+ +l A+  + ++  ++++       +  d++++ e   k+++++ + +++++   
  gene981|gene981|rna981|rna981   7 SYKNCKMEFSKRINIIGGNNGAGKSVLLTALDTCVTNTDTKND-------VITDITFGGE--AKESAKVYYIRQNEKIhd 77 
                                    899**********************************544333.......4555555443..333333333332222222 PP

                         AAA_23  87 ..................trsiererelskkkgkttkkaklellei.deleqfise..llgskkiilnlilflgqer... 142
                                                      t + e   +l+ ++ +  +k k+ ++++ ++l++f+ +  l++ k +i n+i ++ + +   
  gene981|gene981|rna981|rna981  78 enkieekvkeqfnyyqinTIIAEIFSNLNIENDDLMYKLKKVGIKVkNNLQKFLAHrkLMKEKRKIENYIKMKESAElck 157
                                    23342222222222222122222233334444444444444444446777777777655666666778888887777887 PP

                         AAA_23 143 ..................feefelkdkkerleelekeleeledekkllekleqekekekeleeleeeleeilke 198
                                                      fe+  l  kk++le+ +  l++++++++ +++le++k    e ++l+e+l+++ +e
  gene981|gene981|rna981|rna981 158 kivevqdkicqeeavgdnFENDVLLMKKDKLEKEIAWLKKETEKDDVMNDLERKKVLWREESKLKENLKKYRNE 231
                                    77777777766666655533333355555666666667777777777777777777777888888888887665 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.8
                         AAA_23 142 r.....................feefelkdkkerleelekeleeledekkllekleqekekekeleeleeelee 194
                                                           e++e k+ +erl+e+ekel+  ++ ++  +++   +  +k ++e+eeel++
  gene981|gene981|rna981|rna981 346 VlhksgaisggydenkeymnlfIEKLEYKKSLERLKEIEKELKNMKNSESDANRK---ELIKKIIQEKEEELQK 416
                                    2333333555554333332222112222344444444444444444333333333...2333344444444444 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 2.1
                         AAA_23 121 isellgskki......ilnlilflgqerfeefelkdkkerleelekeleeledekkllekleqekekekeleeleeel 192
                                    ++e+lg+ ++      i+++i++ + +       ++ ++r eel+k ++++e++++ l+k e+e e  k  +e++e+l
  gene981|gene981|rna981|rna981 461 LNEELGRVNKemreimISKRIDYEDVGAR----IEKLFKRNEELIKNKKKIEKMADNLKK-ENEDEILKHVKEVREKL 533
                                    22222222221111223333333333332....244555666666666666666666665.66778999999999987 PP

  == domain 4  score: 0.8 bits;  conditional E-value: 0.27
                         AAA_23  48 prlsrksgrgfeksdveiesegkvkay.veltfenkdgrytrsiererelskkkgkttkkaklelleideleqfisellg 126
                                    +++ ++s+++ +k+d + ++   +k+  v+++ ++++   + si  + +  ++ ++  + + ++ +++d+   +i  l g
  gene981|gene981|rna981|rna981 547 SEETKNSSSDVKKNDAADNNISFDKGDdVDVENNKNNY--QGSI-TDTHDHQNATSAMDREGKSMTKPDDFLSTIGMLSG 623
                                    33444444444444444333211111113333222222..1222.33333334444444444444444444444444666 PP

                         AAA_23 127 skkiilnlilflgqer 142
                                     + +il+++l+l   +
  gene981|gene981|rna981|rna981 624 GQLQILTISLMLSLND 639
                                    7777777777666555 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.2   1.1e-05     0.024       1      36 [.      19      51 ..      19     150 .. 0.72
   2 !   16.1   6.0   3.5e-06    0.0078     105     297 ..     487     679 ..     363     685 .. 0.61

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.1e-05
                         AAA_21  1 lnvliGpNgsGKSnLLdaldllarldrdvegltdel 36
                                   +n++ G Ng+GKS LL ald      ++ +  +d+ 
  gene981|gene981|rna981|rna981 19 INIIGGNNGAGKSVLLTALDTC---VTNTDTKNDVI 51
                                   79*****************977...33333333333 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 3.5e-06
                         AAA_21 105 leeedvfnpeargirggvsvfslkelsvsepndlqfgkaltditsrawsllllldglrkerigllnifadyfgfakekrl 184
                                      ++ + + + ++  +                                                                
  gene981|gene981|rna981|rna981 487 GARIEKLFKRNEELIK---------------------------------------------------------------- 502
                                    3333333333333333................................................................ PP

                         AAA_21 185 lqrlvrslklveielsdlgegeeliasvderlrer............................................. 219
                                                                      +                                             
  gene981|gene981|rna981|rna981 503 ----------------------------------Nkkkiekmadnlkkenedeilkhvkevreklvvyyhlisgkeetse 548
                                    ..................................3333444444444444444444444444444444444444444444 PP

                         AAA_21 220 .......................................................gvvflengdgqelparelSdGtkrl 244
                                                                                               + ++d+   ++  lS G++++
  gene981|gene981|rna981|rna981 549 etknsssdvkkndaadnnisfdkgddvdvennknnyqgsitdthdhqnatsamdrEGKSMTKPDDFLSTIGMLSGGQLQI 628
                                    44444444444444444455555555555555555555555555556778888889999999999999************ PP

                         AAA_21 245 lalltallralkkg.sllliDEpEngLHPkllrrllellkelsrngaQviltTH 297
                                    l + ++l   +    +++l+DE++++L+     ++  l k++++ ++Q++l TH
  gene981|gene981|rna981|rna981 629 LTISLMLSLNDILKyDIVLLDEIDSNLDD---CKIQNLTKICTKLKVQIFLITH 679
                                    866666666555557**************...55556669************** PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7  57.3   2.1e-07   0.00047      12     202 ..       7     684 ..       2     690 .. 0.94

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 2.1e-07
                                    TEECEEEEEETTSSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEESS CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N  12 syagktvilpfsksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfdnedkklk 91 
                                    sy  k+ +++fsk++++i G+NG+GKs ll A+  +  ++++   +++ ++d+ +    +++ ++a+v  + +ne+ +  
  gene981|gene981|rna981|rna981   7 SY--KNCKMEFSKRINIIGGNNGAGKSVLLTALDTCVTNTDT---KNDVITDITFG---GEAKESAKVYYIRQNEKIH-- 76 
                                    55..78999************************999995444...77777777776...6777788887765444433.. PP

                                    SSSSCEEEEEEEETTSEEEEEE........TTEEE-HHHHHHHHHCTT-STT............................ CS
                                    xxxxxxxxxxxxxxxxxxxxxx........xxxxxxxxxxxxxxxxxxxxxx............................ RF
                          SMC_N  92 iekeevsisrrvkrkgeseyki........ngkevtkkevsellesagiske............................ 135
                                       +e +i+ +vk++ +  y+i         + ++++ +++  l+++gi+ +                            
  gene981|gene981|rna981|rna981  77 ---DENKIEEKVKEQFN-YYQIntiiaeifSNLNIENDDLMYKLKKVGIKVKnnlqkflahrklmkekrkienyikmkes 152
                                    ...33344443333333.3444222223346778888999999999999999999999999999999************* PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                          SMC_N 136 ................................................................................ 135
                                                                                                                    
  gene981|gene981|rna981|rna981 153 aelckkivevqdkicqeeavgdnfendvllmkkdklekeiawlkketekddvmndlerkkvlwreesklkenlkkyrnek 232
                                    ******************************************************************************** PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                          SMC_N 136 ................................................................................ 135
                                                                                                                    
  gene981|gene981|rna981|rna981 233 rvvdlievddnainaviavignrlkcmvvdyeeealekikslrfrqsfivmdkiedvndgeeqnesmvplkhlvktkkey 312
                                    ******************************************************************************** PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                          SMC_N 136 ................................................................................ 135
                                                                                                                    
  gene981|gene981|rna981|rna981 313 nrlkeflfkdiylvkdltkvsasnkilvtlkgevlhksgaisggydenkeymnlfiekleykkslerlkeiekelknmkn 392
                                    ******************************************************************************** PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                          SMC_N 136 ................................................................................ 135
                                                                                                                    
  gene981|gene981|rna981|rna981 393 sesdanrkelikkiiqekeeelqkikissnyininlerlklvlnrlieqkevlgsfrdeditgledvnlneelgrvnkem 472
                                    ******************************************************************************** PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                          SMC_N 136 ................................................................................ 135
                                                                                                                    
  gene981|gene981|rna981|rna981 473 reimiskridyedvgarieklfkrneeliknkkkiekmadnlkkenedeilkhvkevreklvvyyhlisgkeetseetkn 552
                                    ******************************************************************************** PP

                                    ...................................................................CS-HHHHHHHHHH CS
                                    ...................................................................xxxxxxxxxxxxx RF
                          SMC_N 136 ...................................................................lLSgGektLvala 148
                                                                                                       +LSgG+ +++ ++
  gene981|gene981|rna981|rna981 553 sssdvkkndaadnnisfdkgddvdvennknnyqgsitdthdhqnatsamdregksmtkpddflstigMLSGGQLQILTIS 632
                                    ******************************************************************************** PP

                                    HHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHC CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 149 LlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivislreeml 202
                                    L+++++ + +  ++llDeid++LD+ +++++ ++  + +  +Q++ i++r++ l
  gene981|gene981|rna981|rna981 633 LMLSLNDILKYDIVLLDEIDSNLDDCKIQNLTKICTKLK--VQIFLITHRKNSL 684
                                    ***********************************9999..*********9865 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   3.1   3.2e-07   0.00072      10      96 ..      15     109 ..       8     164 .. 0.70
   2 ?   -8.0  20.4         8   1.8e+04      79     134 ..     545     650 ..     154     653 .. 0.87

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 3.2e-07
                                    TTSEEEEE.ESTTSSHHHHHHHHTTSS--..SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH....... CS
                                    xxxxxxxx.xxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....... RF
                       ABC_tran  10 egekvaiv.GenGaGKStLlkllagllkp..teGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren....... 79 
                                     ++++ i+ G+nGaGKS Ll +l   +++  t+ ++    +d++   + + ++++ ++ q++++ +e +++e+       
  gene981|gene981|rna981|rna981  15 FSKRINIIgGNNGAGKSVLLTALDTCVTNtdTKNDV---ITDITFGGEAKESAKVYYIRQNEKIHDENKIEEKvkeqfny 91 
                                    445555552689***********9988874434444...4788889999************9999999999998888888 PP

                                    .HHHTCHHHHHHHSTTGG CS
                                    .xxxxxxxxxxxxxxxxx RF
                       ABC_tran  80 .esdeeiekalsklglke 96 
                                     + +  i+++ s+l++++
  gene981|gene981|rna981|rna981  92 yQINTIIAEIFSNLNIEN 109
                                    733333555555555544 PP

  == domain 2  score: -8.0 bits;  conditional E-value: 8
                                    H..............................................HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HH CS
                                    x..............................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  79 n..............................................esdeeiekalsklglkelkdtvvksspssLSgG 112
                                    +                                              ++ ++++ a+++ g + +k +   s    LSgG
  gene981|gene981|rna981|rna981 545 EtseetknsssdvkkndaadnnisfdkgddvdvennknnyqgsitdtHDHQNATSAMDREGKSMTKPDDFLSTIGMLSGG 624
                                    02333333333333334444444444446666666666666777665666667777777777666666666888****** PP

                                    HHHHHHHHHHH....HHTSSEEEEES CS
                                    xxxxxxxxxxx....xxxxxxxxxxx RF
                       ABC_tran 113 qkqrvalaral....lkkpkllllDE 134
                                    q q + +  +l    + k +++llDE
  gene981|gene981|rna981|rna981 625 QLQILTISLMLslndILKYDIVLLDE 650
                                    ***99999888223334678999998 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   9.3e-06     0.021      13      48 ..       9      43 ..       6      49 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 9.3e-06
                         AAA_29 13 dghtieidlkgatlltGpsGsGKSTllDAiqalLvp 48
                                   ++ ++e++ + + ++ G++G+GKS ll A+ +  + 
  gene981|gene981|rna981|rna981  9 KNCKMEFSKR-INIIGGNNGAGKSVLLTALDTCVTN 43
                                   5556777744.799**************99987776 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   8.6e-05      0.19      19      89 ..     604     668 ..     587     669 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 8.6e-05
                        SbcCD_C  19 edgkeke...lsrssgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatllelle 89 
                                    e+++ ++   + + +g lSGG+   ++++ l+++l + ++         ++v+LDE  s+lD+ +i++l ++++
  gene981|gene981|rna981|rna981 604 EGKSMTKpddFLSTIGMLSGGQL-QILTISLMLSLNDILKY--------DIVLLDEIDSNLDDCKIQNLTKICT 668
                                    443333334588999********.67778899899999887........7****************99999886 PP

>> Cript  Microtubule-associated protein CRIPT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       2.9   6.6e+03      21      41 ..      71      93 ..      59     109 .. 0.65
   2 ?   10.3   1.9   0.00037      0.83      13      66 ..     118     171 ..     107     176 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 2.9
                          Cript 21 ggrkigenkllskk.k.rfnpya 41
                                   ++ ki+++  + +k k +fn y+
  gene981|gene981|rna981|rna981 71 QNEKIHDENKIEEKvKeQFNYYQ 93
                                   34578555555444344788776 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00037
                          Cript  13 asntlgetg.grkigenkllskkkrfnpyaaysskCkiCktkveqkgakYCqkCa 66 
                                    +     +++ ++ ++++kl+++k++++ y +++ + + Ck+ ve  + k Cq+ a
  gene981|gene981|rna981|rna981 118 KVGIKVKNNlQKFLAHRKLMKEKRKIENYIKMKESAELCKKIVEV-QDKICQEEA 171
                                    4444444442566899999998889******************99.899**9866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (711 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2916  (0.162642); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.93u 0.34s 00:00:01.27 Elapsed: 00:00:00.49
# Mc/sec: 4334.70
//
Query:       gene982|gene982|rna982|rna982  [L=386]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.9e-53  179.3   0.3    1.2e-52  178.7   0.3    1.2  1  ThiF             ThiF family
    9.7e-05   22.8   0.0    0.00067   20.1   0.0    2.4  2  Rhodanese        Rhodanese-like domain
  ------ inclusion threshold ------
      0.026   14.6   0.4       0.41   10.7   0.2    2.6  3  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
      0.043   14.1   0.7       0.28   11.5   0.4    2.4  2  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma


Domain annotation for each model (and alignments):
>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  178.7   0.3   2.7e-56   1.2e-52       3     242 ..      42     265 ..      40     277 .. 0.89

  Alignments for each domain:
  == domain 1  score: 178.7 bits;  conditional E-value: 2.7e-56
                                    HHHHH..HHHHHHHHHHTSEEEEE--SHHHHHHHHHHHHHTTTEEEEEESSB--GGGGGTBTTS-GGGTTSBHHHHHHHH CS
                                    xxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ThiF   3 rqlal..lgedgqekLrdskvllvGaGglGsellknLalsGvgkltlvDnDkielsNlnRqflfreediGkpKaevaaea 80 
                                    rql l    +++q+kL ++++l+vG+GglG +++ +L++sGv+++ ++D Dkiel+Nl+Rq++++eed+Gk+K+ v++++
  gene982|gene982|rna982|rna982  42 RQLILddCTPENQKKLFRARILVVGLGGLGIPVCLYLVGSGVKHIGIADGDKIELTNLHRQVIYNEEDVGKSKVLVMKDK 121
                                    67666666779********************************************************************* PP

                                    HHHT-TTSEEEEEES-CCGCCS-HHHHTT-SEEEEESSSHHHHHHHHHHHHHHT-EEEEEEEETTEEEEEEEEECCS-EC CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ThiF  81 lqeinpdveveavteritdetvleellesvDlVvdalDniearrlvnracvkkgiplieagtlgfegqvvviipgktgcy 160
                                    l ++n ++ v+++ e + +++   e+++++D++vd++Dni++r+l+n+  + ++  ++ a++l+++g ++ + +++++cy
  gene982|gene982|rna982|rna982 122 LLKMNAELTVKTHDEFVVKDN--VEMVNEYDIIVDCSDNISTRYLLNDNTRDRQ--FVCASVLRWDGEIYLF-SKNDACY 196
                                    *******************87..59************************99999..****************.489**** PP

                                    TSS-TGGS.EECCCCEEHHHHHHCTE-B-HHHHHHHHHHHHHHHHHHHTTBCGGGCCEEEECCTTTTEEEEECCEEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ThiF 161 eCldpsstedptekkvplctsiagnipaiatttavvaglaalellkllsgkeklenslltqvdllesrfenvelerakks 240
                                    +Cl+p+ + +p+ ++ + +         ++ +++vv++l+ +e++k++      ++s+l  +d++    ++v+l r+++s
  gene982|gene982|rna982|rna982 197 RCLYPIPKSNPESCNDSGI---------VGGICGVVGSLLSVEIIKMV---FFETKSKLLIYDGKGGEVKTVKL-RERQS 263
                                    ****966666666666555.........99*****************9...33556666678888888888888.44555 PP

                                    C- CS
                                    xx RF
                           ThiF 241 kc 242
                                     c
  gene982|gene982|rna982|rna982 264 TC 265
                                    55 PP

>> Rhodanese  Rhodanese-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.74   3.3e+03       3      21 ..     140     157 ..     138     163 .. 0.77
   2 !   20.1   0.0   1.5e-07   0.00067      10     106 ..     301     378 ..     296     379 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.74
                      Rhodanese   3 kelkellekgkvallDvRp 21 
                                    k+ +e+ ++ ++ ++D+++
  gene982|gene982|rna982|rna982 140 KDNVEMVNEYDI-IVDCSD 157
                                    566788888884.****85 PP

  == domain 2  score: 20.1 bits;  conditional E-value: 1.5e-07
                      Rhodanese  10 ekgkvallDvRppeeYekghIpgAvnvskdtlsrakkseapllelpeellelgidnkktvvvycdgggraaaaaallkkl 89 
                                    ++gk++l+DvR +  +   h++g++n+             p++  +   l +     k   ++c++g+ a+a+a++l   
  gene982|gene982|rna982|rna982 301 NTGKYDLIDVRKKKMFVLAHVKGSRNI-------------PMDSFNLNELTK-----KMPLIVCAKGSTAQAVARTLLDN 362
                                    567888*********************.............444433333333.....23456777888878889988877 PP

                      Rhodanese  90 GyknvsvldGGfkawke 106
                                    +  +++v++ G+ ++k+
  gene982|gene982|rna982|rna982 363 N-IECRVVKDGLVSFKR 378
                                    7.689999999999986 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.2   9.1e-05      0.41       9      75 ..      56     124 ..      50     157 .. 0.71
   2 ?   -1.0   0.1      0.36   1.6e+03      64      83 ..     137     156 ..     114     170 .. 0.71
   3 ?    0.5   0.0      0.13   5.8e+02       8      37 ..     335     365 ..     322     374 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 9.1e-05
                                    ..TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHH..T.ET-EEEEGCGHHHHHHT CS
                   Shikimate_DH   9 slkekkvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeel..kgeeiealkleelkellae 75 
                                    +l ++++l++G G ++  v+ +L+ +gvk++ +a  +     +l +++  ++e++   k+  +k+ l +
  gene982|gene982|rna982|rna982  56 KLFRARILVVGLGGLGIPVCLYLVGSGVKHIGIADGDKIELTNLHRQViyNEEDVGKSKVLVMKDKLLK 124
                                    57789****************************988877777777776444444555555555555555 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.36
                                    EEGCGHHHHHHT-SEEEE-S CS
                   Shikimate_DH  64 lkleelkellaeadvvisat 83 
                                      +++  e+++e+d+++ + 
  gene982|gene982|rna982|rna982 137 FVVKDNVEMVNEYDIIVDCS 156
                                    45667778999999999765 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.13
                                    S..TT-EEEEES-.SHHHHHHHHHHHCCT-C CS
                   Shikimate_DH   8 eslkekkvlliGa.GemaelvakhLlakgvk 37 
                                    ++l++k  l++ a G +a+ va+ Ll+++++
  gene982|gene982|rna982|rna982 335 NELTKKMPLIVCAkGSTAQAVARTLLDNNIE 365
                                    4566666666655599999999999888765 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.4   6.2e-05      0.28       1      83 [.      62     162 ..      62     166 .. 0.90
   2 ?   -1.0   0.0      0.43   1.9e+03       6      21 ..     347     363 ..     343     370 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 6.2e-05
                                    EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHH.....................TTTCEEEEE--TTTH CS
                Sacchrp_dh_NADP   1 vliiGaGsvGqavaellarhfdvdaeitvadrskeklealaaka.....................lgvrfeaialdaeny 59 
                                    +l++G G+ G +v  +l+ ++    +i +ad +k +l +l  ++                      + +++ ++ d   +
  gene982|gene982|rna982|rna982  62 ILVVGLGGLGIPVCLYLVGSGVK--HIGIADGDKIELTNLHRQViyneedvgkskvlvmkdkllkMNAELTVKTHDEFVV 139
                                    89******************977..9**************9999****************99988777777888888888 PP

                                    HHHHHHHHTTSSEEEE-SSGGGHH CS
                Sacchrp_dh_NADP  60 eavLaallkegdlvvnlsppissl 83 
                                    ++  +++++e+d++v++s +is++
  gene982|gene982|rna982|rna982 140 KD-NVEMVNEYDIIVDCSDNISTR 162
                                    88.8999***********999876 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.43
                                    -.SHHHHHHHHHHHCTC CS
                Sacchrp_dh_NADP   6 a.GsvGqavaellarhf 21 
                                    a Gs++qava+ l++++
  gene982|gene982|rna982|rna982 347 AkGSTAQAVARTLLDNN 363
                                    66999999999998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (386 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       787  (0.0438954); expected 358.6 (0.02)
Passed bias filter:                      526  (0.0293379); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 2662.11
//
Query:       gene983|gene983|rna983|rna983  [L=228]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.3e-48  163.1   0.1    8.7e-48  162.8   0.1    1.0  1  Cytidylate_kin   Cytidylate kinase
    1.3e-08   35.4   0.3    2.6e-07   31.3   0.1    2.4  1  AAA_18           AAA domain
    2.5e-07   31.0   0.4    4.7e-07   30.1   0.4    1.4  1  Cytidylate_kin2  Cytidylate kinase-like family
      8e-07   29.5   0.1    9.3e-06   26.1   0.0    2.3  2  AAA_17           AAA domain
    0.00013   21.8   0.1       0.12   12.1   0.0    2.2  2  PRK              Phosphoribulokinase / Uridine kinase family
    0.00025   21.0   1.5     0.0011   18.9   1.5    2.1  1  dNK              Deoxynucleoside kinase
      0.001   19.2   0.0     0.0022   18.1   0.0    1.6  1  ADK              Adenylate kinase
     0.0013   18.9   0.0     0.0017   18.5   0.0    1.5  1  AAA_33           AAA domain
     0.0087   16.1   0.0      0.013   15.5   0.0    1.5  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
     0.0092   15.9   0.0      0.097   12.6   0.0    2.1  1  NACHT            NACHT domain
  ------ inclusion threshold ------
       0.02   15.4   0.0      0.027   15.0   0.0    1.4  1  ABC_tran         ABC transporter
      0.029   14.6   0.1      0.078   13.3   0.1    1.9  1  AAA_22           AAA domain
      0.037   14.1   0.7        0.1   12.6   0.1    2.1  2  tRNA_lig_kinase  tRNA ligase kinase domain
      0.048   13.8   0.1        1.7    8.8   0.0    2.2  2  SKI              Shikimate kinase
      0.054   13.6   1.4        3.2    7.9   0.2    2.5  2  TRPM_tetra       Tetramerisation domain of TRPM
      0.066   13.1   0.0       0.14   12.0   0.0    1.5  1  AAA_lid_2        AAA lid domain
       0.07   12.3   0.0       0.13   11.4   0.0    1.5  1  NB-ARC           NB-ARC domain
       0.12   12.8   0.1       0.24   11.8   0.1    1.7  1  AAA              ATPase family associated with various cellul
       0.12   12.6   0.0       0.26   11.5   0.0    1.6  1  AAA_28           AAA domain
       0.15   12.4   0.0       0.21   12.0   0.0    1.5  1  AAA_16           AAA ATPase domain


Domain annotation for each model (and alignments):
>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  162.8   0.1   9.7e-51   8.7e-48       1     210 [.       7     217 ..       7     218 .. 0.90

  Alignments for each domain:
  == domain 1  score: 162.8 bits;  conditional E-value: 9.7e-51
                                    EEEE-STTSSHHHHHHHHHHHHT-EEEEHHHHHHHHHHHHHHT......T--TT-HHHHHHHHHT--EEEEEEEEEETTE CS
                 Cytidylate_kin   1 iaiDGPagsGKssvaralaeklglkyldtgalYRalalaalrr......kvdlldeaalvelakevelsfeaekvllnge 74 
                                    iaiDG ag GKs+ a+a+a+ +g++ +++g +YRa++++ l +        +    ++ ++++++++++ +++ +++ ge
  gene983|gene983|rna983|rna983   7 IAIDGHAGVGKSTTAKAIADFFGYTHINSGDIYRAITYVLLSKyenekqAFKKGLNEEQLNFLHTIRIENHHNIFFYMGE 86 
                                    9****************************************987776553333334556788899999988889999888 PP

                                    E-TTGGGSHHHHHHHHHHTTSHHHHHHHHHHHHTT-B..SSBEEEEESSIIIIISTT-SEEEEEE--HHHHHHHHHHHHH CS
                 Cytidylate_kin  75 dveeelrsdevekavSavaaipavRailvkklrelvk..karvvveGRDigtvvfpdaelKifldAsveeRakRRlkqlk 152
                                        +lr+d+v+ +v ++a++++vR+++ + + +l++    ++v++GRDig+ ++p+a+lK++l+As+e+Ra RR+k+  
  gene983|gene983|rna983|rna983  87 VC--KLRTDDVNVFVPYIAQVKEVREHVHTIQDRLIQqaPRGIVMDGRDIGSNIMPNADLKVYLTASAEIRAMRRFKEC- 163
                                    65..79**************************9999966679***********************************93. PP

                                    HTT----HHHHHHHHHHHHHHHHCTSSS-S---TT-EEEETTTS-HHHHHHHHHHHHH CS
                 Cytidylate_kin 153 akgtsvsleellaeikeRDklDkerevgpLklaedaliidtskltieevvekilelik 210
                                          +++e+la+i  RD +D++r+ +pL +++dal i+ ++l ++e v+ i++ ++
  gene983|gene983|rna983|rna983 164 ----GGDYDEILAQITSRDYMDTHRKHAPLIKTADALEINNDHLKFDEQVKIITDRVE 217
                                    ....3469*****************************************999988775 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.3   0.1   2.9e-10   2.6e-07       1     109 [.       7     158 ..       7     178 .. 0.87

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 2.9e-10
                         AAA_18   1 IlltGtpGvGKttlakeLskrlgf.....gvnlrdvakenglllevdpealdeskrldedkldklldaleenss...... 69 
                                    I++ G +GvGK+t ak++++  g+     g+++r + +   + +e++++    +k l+e++l+ l+++  en        
  gene983|gene983|rna983|rna983   7 IAIDGHAGVGKSTTAKAIADFFGYthinsGDIYRAITYVLLSKYENEKQ--AFKKGLNEEQLNFLHTIRIENHHniffym 84 
                                    8899**************998899*666666666666666666666666..9999999999999999888877789**** PP

                         AAA_18  70 ...................................aleegknlvidghlaeleseaakdikkvvLtaspeelleR 109
                                                                        ++ +  +v+dg+      + + d+k v+Ltas e+++ R
  gene983|gene983|rna983|rna983  85 gevcklrtddvnvfvpyiaqvkevrehvhtiqdrlIQQAPRGIVMDGRDIGSNIMPNADLK-VYLTASAEIRAMR 158
                                    *********************************9999999999******************.********99866 PP

>> Cytidylate_kin2  Cytidylate kinase-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.1   0.4   5.2e-10   4.7e-07       2     150 ..       7     178 ..       6     187 .. 0.82

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 5.2e-10
                Cytidylate_kin2   2 ITIsreyGsgGetigeaLAekLglpfydr.eiieevakel.glseeeveevde..rsrlssflskllaarvagdtl.... 73 
                                    I+I++  G g++t ++a+A+ +g+  ++  +i +++   l   +e+e +++++  ++   +fl+++  ++  +  +    
  gene983|gene983|rna983|rna983   7 IAIDGHAGVGKSTTAKAIADFFGYTHINSgDIYRAITYVLlSKYENEKQAFKKglNEEQLNFLHTIRIENHHNI-Ffymg 85 
                                    99**************************9677766655542333444466666554444566666655554443.26*** PP

                Cytidylate_kin2  74 ...................deklddelfeaqervirelaaeesvVivGR.gadliLkdrpnvlrvfltapledrvkrvae 133
                                                        ++  ++++ +q r+i+++++  ++V+ GR  + +i+ + +  l+v+lta+ e r+ r  +
  gene983|gene983|rna983|rna983  86 evcklrtddvnvfvpyiaqVKEVREHVHTIQDRLIQQAPR--GIVMDGRdIGSNIMPNAD--LKVYLTASAEIRAMRRFK 161
                                    ******************9999999*************96..6******669******77..*************99999 PP

                Cytidylate_kin2 134 reglseeearekiketD 150
                                    + g + +e+  +i+++D
  gene983|gene983|rna983|rna983 162 ECGGDYDEILAQITSRD 178
                                    99999999999999988 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.0     1e-08   9.3e-06       2      58 ..      11      69 ..      11      85 .. 0.81
   2 ?    0.8   0.0      0.69   6.2e+02     100     122 ..     138     162 ..     102     174 .. 0.70

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 1e-08
                                   E-TTSSHHHHHHHHHHHHTEEEEEHHHHHHHHHHTT..TSHSSHHHHCTSHHHHHHHHH CS
                         AAA_17  2 GgPGsGKgtqceklvekygfthlsaGdllreeakrg..glakardemrklpleekkelq 58
                                   G  G+GK+t ++ +++ +g+th++ Gd+ r+       + ++++++++k+ +ee+  ++
  gene983|gene983|rna983|rna983 11 GHAGVGKSTTAKAIADFFGYTHINSGDIYRAITYVLlsKYENEKQAFKKGLNEEQLNFL 69
                                   668***************************87633333668888899888888777665 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.69
                                    H....SEEEEEE--HHHHHHHHHHH CS
                         AAA_17 100 lkp..daiilleadpeeilerrlkd 122
                                    + p  d+ ++l a++e    rr k+
  gene983|gene983|rna983|rna983 138 IMPnaDLKVYLTASAEIRAMRRFKE 162
                                    4333377899999999888888775 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.0   0.00013      0.12       2      59 ..       7      64 ..       6      84 .. 0.72
   2 !    7.7   0.0     0.003       2.7     126     171 ..     138     180 ..     126     198 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00013
                            PRK  2 IgvagsSGaGkttvarklekifgrekvkaaeiegdsflrldraekdleleerkrakek 59
                                   I++ g  G Gk+t+a+++ + fg +++++  i       l + +++ + + +k+ +e+
  gene983|gene983|rna983|rna983  7 IAIDGHAGVGKSTTAKAIADFFGYTHINSGDIYRAITYVLLSKYENEKQAFKKGLNEE 64
                                   89*********************99998666644444444444444444444444455 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.003
                            PRK 126 vaelldlkiyvdisidlelarklqRDiaeRGrsleavldsil.rrkp 171
                                    +   +dlk+y+ +s +++ +r+     +e G +++ +l++i+ r   
  gene983|gene983|rna983|rna983 138 IMPNADLKVYLTASAEIRAMRRF----KECGGDYDEILAQITsRDYM 180
                                    56679************988875....79999******999944444 PP

>> dNK  Deoxynucleoside kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   1.5   1.2e-06    0.0011       1     190 [.       7     210 ..       7     222 .. 0.67

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.2e-06
                                    EEEEESTTSSHHHHHHHHHCCSTCEEEE-HHHHCCSSSSHHHHHHHHSHHHHHHHHHHHHHH....HHHHHHHCHH.... CS
                            dNK   1 ivveGnIgaGKstlvklLskklgvkvfeEpvdkwtnvqknlLekfYkdpsrwsfalqtyvll....srlkqqleal.... 72 
                                    i+++G  g+GKst +k +++ +g+ +++   d ++ +   lL+k+ ++++ +   l+ + l+     r++++ +++    
  gene983|gene983|rna983|rna983   7 IAIDGHAGVGKSTTAKAIADFFGYTHINS-GDIYRAITYVLLSKYENEKQAFKKGLNEEQLNflhtIRIENHHNIFfymg 85 
                                    89*********************999975.68897888788887666666699888655443211247778888876777 PP

                                    .....SSS-EEEEES-HHHHHHTHHHHHH.HTTSS-HHHHHHHHHHHHHHHHHCCH-SEEEEEE--HH.HHHHHHHHCTT CS
                            dNK  73 .....atkqvvvleRsiysdryiFakala.ekgtlseeelkiykelldnlleelakpdlliYLkasle.tclerikkRgr 145
                                         +t++v+v+   i + +++  ++++ +++ +++    i  + +d   + +++ dl +YL as e   ++r k+ g 
  gene983|gene983|rna983|rna983  86 evcklRTDDVNVFVPYIAQVKEVREHVHTiQDRLIQQAPRGIVMDGRDIGSNIMPNADLKVYLTASAEiRAMRRFKECGG 165
                                    66666666666666666666666655544144445555555666666666666667***********9558999*99988 PP

                                    CCCT....TS-HHHHHHHHHHHHHHHTSGGCS-EEEEETSS.-TTTHCC CS
                            dNK 146 eeek....kieldYlekLhekyeewlkklnevpvlvidveeldlvaeee 190
                                     +++     +++dY+ + h+k+ + +k+ +   +l i+ ++l+++++ +
  gene983|gene983|rna983|rna983 166 DYDEilaqITSRDYMDT-HRKHAPLIKTAD---ALEINNDHLKFDEQVK 210
                                    87776995556777765.99***9999844...3444444444443333 PP

>> ADK  Adenylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   2.5e-06    0.0022       3      35 ..      11      43 ..       9      72 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 2.5e-06
                                   ESTTSSHHHHHHHHHHHHTSEEEEHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            ADK  3 GaPgaGKGtqaeklvkkyglahlstGdllRaev 35
                                   G  g GK t a+ +++ +g++h+ +Gd+ Ra +
  gene983|gene983|rna983|rna983 11 GHAGVGKSTTAKAIADFFGYTHINSGDIYRAIT 43
                                   889***************************965 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   1.9e-06    0.0017       5      47 ..      10      72 ..       7     189 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.9e-06
                         AAA_33  5 vGlpGsGKstlaerllkklgavllssdtlrrrlfg.......tdqqskt.............d 47
                                    G++G+GKst a+ ++   g+++++s +++r++++       +++q  +              
  gene983|gene983|rna983|rna983 10 DGHAGVGKSTTAKAIADFFGYTHINSGDIYRAITYvllskyeNEKQAFKkglneeqlnflhtI 72
                                   59**************************99999997665533222222233333333333330 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   1.5e-05     0.013      22      65 ..       7      56 ..       1     117 [. 0.82

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.5e-05
                                   EEEEESTTSSHHHHHHHHHHHTT------T......TTTSEEEEEE..SS CS
                           TsaE 22 ilLeGdLGaGKTtlvrglakalgveevkSP......TFtlveeYelekeg 65
                                   i+++G  G+GK+t ++++a  +g+++++S       T++l+++Ye+ek++
  gene983|gene983|rna983|rna983  7 IAIDGHAGVGKSTTAKAIADFFGYTHINSGdiyraiTYVLLSKYENEKQA 56
                                   8999*******************9977775444555********987665 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.0   0.00011     0.097       3      50 ..       7      55 ..       6     151 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00011
                                   EEEEC-TTTCHHHHHHHHHHHHCTS-SCCCC.-SEEEEEETTTTTTS-. CS
                          NACHT  3 vilqGeaGsGKTtLlqklalawaegklpqga.fklvFflslrelsrsgn 50
                                   +++ G aG+GK+t ++ +a+     + ++g  ++ + ++ l++ + +++
  gene983|gene983|rna983|rna983  7 IAIDGHAGVGKSTTAKAIADFFGYTHINSGDiYRAITYVLLSKYENEKQ 55
                                   6899***************988888888777666666666666655554 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.0     3e-05     0.027      14      93 ..       7     113 ..       4     194 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3e-05
                                    EEEEESTTSSHHHHHHHHTTSS--...SEEEEEETTCEGGG...B-HHHCCHCEEEE-SS--S-TTSBHHHH........ CS
                                    xxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxx........ RF
                       ABC_tran  14 vaivGenGaGKStLlkllagllkp...teGeilldgkdlke...qeleslrkeigvlpqepqlfpeltvren........ 79 
                                    +ai G+ G GKSt +k++a        ++G+i    + +++    + e  ++ ++    e+ql+  +t+r +        
  gene983|gene983|rna983|rna983   7 IAIDGHAGVGKSTTAKAIADFFGYthiNSGDI---YRAITYvllSKYENEKQAFKKGLNEEQLNFLHTIRIEnhhniffy 83 
                                    6899**************97654433377888...333333444344444444433333333333333222223667776 PP

                                    ................HHHTCHHHHHHHST CS
                                    ................xxxxxxxxxxxxxx RF
                       ABC_tran  80 ................esdeeiekalsklg 93 
                                                     + ++++++++++ 
  gene983|gene983|rna983|rna983  84 mgevcklrtddvnvfvPYIAQVKEVREHVH 113
                                    666666665555555533333555555544 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   8.7e-05     0.078       8      36 ..       7      33 ..       7     130 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 8.7e-05
                         AAA_22  8 lvvtGesGtGKTtllrrlleqldeeakae 36
                                   +++ G++G+GK+t+++ +++ +   + + 
  gene983|gene983|rna983|rna983  7 IAIDGHAGVGKSTTAKAIADFFG--YTHI 33
                                   6899**************99983..3333 PP

>> tRNA_lig_kinase  tRNA ligase kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   0.00012       0.1       8      37 ..      13      41 ..       4     123 .. 0.86
   2 ?   -0.7   0.1       1.5   1.3e+03      29      53 ..     198     222 ..     192     225 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00012
                                   TTSSHHHHHHHHHHH-TTSEEEEGGGS-TT CS
                tRNA_lig_kinase  8 iGCGkttvaltlenlfgeWghvqnDnitgk 37
                                    G Gk+t+a+++ ++fg ++h+ + +i   
  gene983|gene983|rna983|rna983 13 AGVGKSTTAKAIADFFG-YTHINSGDIYRA 41
                                   599**************.******999764 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.5
                                    EEGGGS-TT-SS-HHHHHHHTTSST CS
                tRNA_lig_kinase  29 vqnDnitgkdkkklvkealellkkd 53 
                                    + nD ++  ++ k++++ +e++k++
  gene983|gene983|rna983|rna983 198 INNDHLKFDEQVKIITDRVEEIKRK 222
                                    7788888888888888888887655 PP

>> SKI  Shikimate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0    0.0018       1.7       2      23 ..      14      35 ..      13      59 .. 0.90
   2 ?    3.0   0.0      0.11        99      81     155 ..     138     214 ..     125     217 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0018
                                   TSSHHHHHHHHHHHHTSEEEEH CS
                            SKI  2 GaGKstvGkllAkklglefiDl 23
                                   G+GKst++k++A+  g++ i +
  gene983|gene983|rna983|rna983 14 GVGKSTTAKAIADFFGYTHINS 35
                                   9***************998876 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.11
                                    HHHHHSEEEEEE--HHH.HHHHHHHTTS...SGGGCSCHHHHHHHHHHHHHHHHHCCSSCEEEECTSSHHHHHHHHHHH CS
                            SKI  81 llkekgiviyLdvslee.llerlkadke...RPllqekskeeelleelaereplyeeaadvvvdeseeskeevaeeile 155
                                    ++ +  + +yL +s e   ++r k++      +l+q  s+  +++++ +++ pl ++a++  +++++ + +e ++ i++
  gene983|gene983|rna983|rna983 138 IMPNADLKVYLTASAEIrAMRRFKECGGdydEILAQITSR--DYMDTHRKHAPLIKTADALEINNDHLKFDEQVKIITD 214
                                    5666777899999999636777887776676777777777..7777777899*******99999999988887776666 PP

>> TRPM_tetra  Tetramerisation domain of TRPM
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.1     0.054        48      16      32 ..     103     119 ..     101     121 .. 0.88
   2 ?    7.9   0.2    0.0036       3.2       1      15 [.     206     220 ..     206     224 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.054
                     TRPM_tetra  16 mkveevneKenlikaSL 32 
                                     +v+ev e +++i++ L
  gene983|gene983|rna983|rna983 103 AQVKEVREHVHTIQDRL 119
                                    69***********9876 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0036
                     TRPM_tetra   1 eeRIrvttERvEnms 15 
                                    +e ++ +t+RvE++ 
  gene983|gene983|rna983|rna983 206 DEQVKIITDRVEEIK 220
                                    699**********96 PP

>> AAA_lid_2  AAA lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00015      0.14      10      61 ..       6      58 ..       3      67 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00015
                      AAA_lid_2 10 elgvsgrRadlallraArAlAalegrdyVtpeDvkeaaplVLaHRlr..repea 61
                                   e+ ++g+ a +    +A+A+A + g ++++  D+ +a+ +VL       +++++
  gene983|gene983|rna983|rna983  6 EIAIDGH-AGVGKSTTAKAIADFFGYTHINSGDIYRAITYVLLSKYEneKQAFK 58
                                   7789***.**********************************877766555554 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00015      0.13      22      70 ..       6      58 ..       2      86 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00015
                                   EEEEEESTTSSHHHHHHHHCCSH..CCCCC..CBTEEEEEEEESXXHHHHHHH CS
                         NB-ARC 22 vvalvGmgGvGKttlakqilnks..deveg..rFdsvawvvvsktdkseeile 70
                                    +a+ G +GvGK+t ak i   +   ++++   +  + +v +sk  ++++ ++
  gene983|gene983|rna983|rna983  6 EIAIDGHAGVGKSTTAKAIADFFgyTHINSgdIYRAITYVLLSKYENEKQAFK 58
                                   589**************997643112333223788888888888888777666 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   0.00027      0.24       5      25 ..      11      31 ..       7     115 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00027
                                   SSTTSSHHHHHHHHHHHHTHE CS
                            AAA  5 GppGtGKTllakavakelgve 25
                                   G  G+GK+++aka+a  +g +
  gene983|gene983|rna983|rna983 11 GHAGVGKSTTAKAIADFFGYT 31
                                   899************987643 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00029      0.26       2      57 ..       7      59 ..       6      83 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00029
                         AAA_28  2 ivitGgestGKTtlleaLaar.gypvv..pEaareileeklakgedalpwvedllafae 57
                                   i+i G  + GK+t+++a+a+  gy+++   +++r i+  +l k e++ +      af++
  gene983|gene983|rna983|rna983  7 IAIDGHAGVGKSTTAKAIADFfGYTHInsGDIYRAITYVLLSKYENEKQ------AFKK 59
                                   7888999************988**9999999999999998877776333......3333 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00023      0.21      29      90 ..       9      65 ..       7     207 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00023
                         AAA_16 29 lsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqlldeae 90
                                   + G++GvGKs+ ++++++ +  +  +  +g+     +ai+y+ l ++  +++ +++ l+e++
  gene983|gene983|rna983|rna983  9 IDGHAGVGKSTTAKAIADFFGYT--HINSGDIY---RAITYVLLSKYENEKQAFKKGLNEEQ 65
                                   66***************866655..22233222...34666666666666666666666644 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (228 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       716  (0.0399353); expected 358.6 (0.02)
Passed bias filter:                      494  (0.0275531); expected 358.6 (0.02)
Passed Vit filter:                        73  (0.00407162); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.56u 0.31s 00:00:00.87 Elapsed: 00:00:00.47
# Mc/sec: 1451.02
//
Query:       gene984|gene984|rna984|rna984  [L=331]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      5e-44  147.7   5.5    3.4e-12   45.9   0.1    5.8  7  Prenyltrans      Prenyltransferase and squalene oxidase repea
    1.4e-06   27.6   0.0       0.79    8.8   0.0    3.4  3  SQHop_cyclase_N  Squalene-hopene cyclase N-terminal domain
     0.0015   17.7   0.0        1.8    7.6   0.0    2.5  2  SQHop_cyclase_C  Squalene-hopene cyclase C-terminal domain


Domain annotation for each model (and alignments):
>> Prenyltrans  Prenyltransferase and squalene oxidase repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       1.5   8.8e+03       4      15 ..       5      16 ..       3      19 .. 0.70
   2 ?   -3.2   0.1       1.2   7.4e+03      34      44 .]      34      44 ..      27      44 .. 0.78
   3 !   26.2   0.0   7.9e-10   4.7e-06       7      43 ..      55      91 ..      53      92 .. 0.91
   4 !    3.6   0.0    0.0093        55       4      15 ..      98     109 ..      98     110 .. 0.89
   5 !   43.3   0.1   3.6e-15   2.2e-11       2      44 .]     177     219 ..     176     219 .. 0.96
   6 !   26.5   0.0   6.4e-10   3.8e-06       9      43 ..     232     266 ..     224     267 .. 0.87
   7 !   45.9   0.1   5.8e-16   3.4e-12       2      44 .]     273     315 ..     272     315 .. 0.95

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 1.5
                                   HHHHHHHHHHSH CS
                    Prenyltrans  4 ekavefLlscQn 15
                                   +k+++f+ +  n
  gene984|gene984|rna984|rna984  5 KKIIDFVNKNRN 16
                                   799**9866555 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 1.2
                                   HHHHHHHHHCT CS
                    Prenyltrans 34 ywalaaLallG 44
                                   yw+++++ +lG
  gene984|gene984|rna984|rna984 34 YWVTTIFNILG 44
                                   99999999987 PP

  == domain 3  score: 26.2 bits;  conditional E-value: 7.9e-10
                                   HHHHHHHSHTTS-BBSSTTSSBBHHHHHHHHHHHHHC CS
                    Prenyltrans  7 vefLlscQnedGGwggrpgsesdtyytywalaaLall 43
                                   +efL+sc n dGG+g+  g++s++++t+ a +++ +l
  gene984|gene984|rna984|rna984 55 IEFLKSCKNSDGGYGSTKGYPSTVFNTMLACQVATML 91
                                   89**************************998777776 PP

  == domain 4  score: 3.6 bits;  conditional E-value: 0.0093
                                    HHHHHHHHHHSH CS
                    Prenyltrans   4 ekavefLlscQn 15 
                                    e+ v+++lsc+n
  gene984|gene984|rna984|rna984  98 EETVDYVLSCCN 109
                                    6789******98 PP

  == domain 5  score: 43.3 bits;  conditional E-value: 3.6e-15
                                    HHHHHHHHHHHHSHTTS-BBSSTTSSBBHHHHHHHHHHHHHCT CS
                    Prenyltrans   2 dvekavefLlscQnedGGwggrpgsesdtyytywalaaLallG 44 
                                     +ek +++Ll+c n dGG+g+ pg es++++ y +l +L+ll+
  gene984|gene984|rna984|rna984 177 EKEKTIRYLLKCYNMDGGFGCIPGAESHCGQIYACLVSLKLLN 219
                                    68**************************************985 PP

  == domain 6  score: 26.5 bits;  conditional E-value: 6.4e-10
                                    HHHHHSHTTS-BBSSTTSSBBHHHHHHHHHHHHHC CS
                    Prenyltrans   9 fLlscQnedGGwggrpgsesdtyytywalaaLall 43 
                                    fL+++Q ++GG++grp +  d++y++w l++L +l
  gene984|gene984|rna984|rna984 232 FLINRQEPSGGLNGRPYKKEDVCYSFWTLCSLDIL 266
                                    9*****************66**********99665 PP

  == domain 7  score: 45.9 bits;  conditional E-value: 5.8e-16
                                    HHHHHHHHHHHHSHTTS-BBSSTTSSBBHHHHHHHHHHHHHCT CS
                    Prenyltrans   2 dvekavefLlscQnedGGwggrpgsesdtyytywalaaLallG 44 
                                    d +k++e++++cQ +dGG+++rpg  sd+++t++al++L+ll+
  gene984|gene984|rna984|rna984 273 DSNKLREYIEKCQSADGGYADRPGNVSDCFHTMYALLGLCLLD 315
                                    668**************************************96 PP

>> SQHop_cyclase_N  Squalene-hopene cyclase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.2   0.0    0.0008       4.8      37      79 ..      41      83 ..      25      88 .. 0.88
   2 !    8.8   0.0   0.00013      0.79      19      87 ..     148     218 ..     136     231 .. 0.82
   3 !    8.4   0.0   0.00017         1      39      85 ..     266     312 ..     250     317 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0008
                SQHop_cyclase_N 37 eflgeddeeeeekiakylrsqqredGgWelypggpgdlsttve 79
                                   ++lg +de+ + ++ ++l s +++dGg++  +g p+ ++ t  
  gene984|gene984|rna984|rna984 41 NILGYTDEAVAIETIEFLKSCKNSDGGYGSTKGYPSTVFNTML 83
                                   6788889999999***********************9998875 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00013
                SQHop_cyclase_N  19 vgeLeanvtitaeyillrefl.geddee.eeekiakylrsqqredGgWelypggpgdlsttveaYlALkll 87 
                                    +geL++++ +t++ i+   f     ++  e+ek+ +yl++  + dGg++ +pg +++      + + Lkll
  gene984|gene984|rna984|rna984 148 MGELDSSTDLTTKFIISDDFFsLLLKKGfEKEKTIRYLLKCYNMDGGFGCIPGAESHCGQIYACLVSLKLL 218
                                    689999999999***99999953333334999*********************999887777777777776 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.00017
                SQHop_cyclase_N  39 lgeddeeeeekiakylrsqqredGgWelypggpgdlsttveaYlALk 85 
                                    l+  +  + +k+++y+++ q++dGg++  pg+ +d + t  a l+L 
  gene984|gene984|rna984|rna984 266 LNGVKYIDSNKLREYIEKCQSADGGYADRPGNVSDCFHTMYALLGLC 312
                                    55556667899***************999999999999988877775 PP

>> SQHop_cyclase_C  Squalene-hopene cyclase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.0    0.0003       1.8     162     230 ..       5      72 ..       1      89 [. 0.68
   2 !    7.6   0.0    0.0003       1.8     135     229 ..     198     294 ..     173     307 .. 0.63

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0003
                                    HHHHHHHHHHS-TTS----SSBSSHHHHHHHHHHHHHHTT--TTSHHHHHHHHHHHTT--TTSSBB--G CS
                SQHop_cyclase_C 162 kraveylkkeqepdGsWfGrWGvnyiyGtwsvlsalaavgedleepvirkavdWlksvqnedGGWGesa 230
                                    k+ +++++k+++  G  +      ++   + v + ++ +g  ++e+v  +++++lks +n+dGG+G + 
  gene984|gene984|rna984|rna984   5 KKIIDFVNKNRNDRGYEYHSCTYLHLSMHYWVTTIFNILGY-TDEAVAIETIEFLKSCKNSDGGYGSTK 72 
                                    66778888888777766654433333333344444555554.556666789***************864 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0003
                                    B--BHHHHHHHHHHHHHHT--TTSHHH..HHHHHHHHHHS-TTS----S.S...BSSHHHHHHHHHHHHHHTT--TTSHH CS
                SQHop_cyclase_C 135 dpptadvtarvlellaqlgeeedseal..kraveylkkeqepdGsWfGr.W...GvnyiyGtwsvlsalaavgedleepv 208
                                     p ++   +++ ++l +l+  ++ + +  +r   +l ++qep+G   Gr +    v y +    +l++l+ ++  +    
  gene984|gene984|rna984|rna984 198 IPGAESHCGQIYACLVSLKLLNALHRIdkTRMTFFLINRQEPSGGLNGRpYkkeDVCYSFW---TLCSLDILNGVK-YID 273
                                    5666677788888888887765444431156777999*********999432113344444...455555554322.222 PP

                                    HHHHHHHHHTT--TTSSBB-- CS
                SQHop_cyclase_C 209 irkavdWlksvqnedGGWGes 229
                                     +k  +++++ q +dGG+ + 
  gene984|gene984|rna984|rna984 274 SNKLREYIEKCQSADGGYADR 294
                                    356678999********9765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (331 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       608  (0.0339115); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 2301.77
//
Query:       gene985|gene985|rna985|rna985  [L=44]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (44 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       510  (0.0284455); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 313.14
//
Query:       gene986|gene986|rna986|rna986  [L=286]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.5e-24   85.5   0.5    6.8e-24   84.1   0.1    1.8  2  JAB         JAB1/Mov34/MPN/PAD-1 ubiquitin protease
    3.9e-08   33.7   1.3    7.9e-08   32.7   0.2    1.9  2  MitMem_reg  Maintenance of mitochondrial structure and functi
     0.0073   16.5   2.1         17    5.8   0.3    3.9  4  NUMOD1      NUMOD1 domain
  ------ inclusion threshold ------
       0.11   12.3   0.3       0.29   11.0   0.2    1.7  1  CdvA        CdvA-like coiled-coil domain


Domain annotation for each model (and alignments):
>> JAB  JAB1/Mov34/MPN/PAD-1 ubiquitin protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.1   0.1   1.5e-27   6.8e-24       4     115 ..      27     138 ..      25     141 .. 0.93
   2 ?   -1.5   0.0      0.54   2.4e+03      38      57 ..     163     182 ..     160     209 .. 0.77

  Alignments for each domain:
  == domain 1  score: 84.1 bits;  conditional E-value: 1.5e-27
                                    CEEEEEHHHHHHHHHHHHHHHHHTS--EEEEEEEESSSE........EEEEEEEEEESEEEESSECEEEEEHHHHHHHHH CS
                            JAB   4 qavhleslvllkildhalrtekeeeevmGlliGelnddt........tveitnvfalpfeetekdvdavsldqeylekks 75 
                                    ++v++++lvll+++dh+ r+     +v+G+++G  ++ +         ++itn+fa+pf+e+ ++   +++d +yle++ 
  gene986|gene986|rna986|rna986  27 NKVIVHPLVLLSVVDHYHRVDGT--RVVGVILGYKQKVKnsnseyqtEIHITNSFAVPFDEEYNS--NWFIDTSYLENMF 102
                                    68*********************..********999888899******************99888..9************ PP

                                    HHHHHHCTTSEEEEEEEESSSS-SS--HHHHHHHHHHHHH CS
                            JAB  76 ellkklrgrervvGWYhshpditvwlsevdvrtqalyqrm 115
                                    el+ k++g+e+++GWYhs+pd+     ++d+++ +++ r+
  gene986|gene986|rna986|rna986 103 ELFFKVNGKEKILGWYHSGPDL----FSNDLQITQSFLRY 138
                                    **********************....88899988888776 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.54
                                    ESSSEEEEEEEEEEESEEEE CS
                            JAB  38 lnddttveitnvfalpfeet 57 
                                    l+dd++ +i+++++ +  e+
  gene986|gene986|rna986|rna986 163 LEDDNFKHIFASIEAEEAEE 182
                                    77888889999888776554 PP

>> MitMem_reg  Maintenance of mitochondrial structure and function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.42   1.9e+03      42      60 ..      54      72 ..      41     147 .. 0.70
   2 !   32.7   0.2   1.8e-11   7.9e-08       1     111 [.     179     280 ..     179     281 .. 0.93

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.42
                     MitMem_reg 42 likdYlkkveegelpvnhe 60
                                    i  Y +kv++ + ++++e
  gene986|gene986|rna986|rna986 54 VILGYKQKVKNSNSEYQTE 72
                                   5677777777554333333 PP

  == domain 2  score: 32.7 bits;  conditional E-value: 1.8e-11
                     MitMem_reg   1 Eaeeigvehllkpsiqdas.stlstglnrqyyslkilqerldlikdYlkkveegelpvnheilrnlqkllnllPhletee 79 
                                    Eaee+gvehl + +i+d++ ++  +  +    sl+  ++ l+ i + l+++++++ p+n++++ + +++l+++ ++++++
  gene986|gene986|rna986|rna986 179 EAEEVGVEHLIR-DIKDDTyTPHFESYKDIKDSLNVYSNNLQAIINELDNIINNNSPMNESLIFSFKECLSSVLKVSNST 257
                                    9***********.***999***************************************************9999999933 PP

                     MitMem_reg  80 lekefnvetnDvllvvyLasltrsilalnell 111
                                             +   l+ y++s+t++ +  n+l+
  gene986|gene986|rna986|rna986 258 ---------KINELSNYVGSVTKTFILTNDLI 280
                                    .........3344699**********999998 PP

>> NUMOD1  NUMOD1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0      0.12   5.2e+02       7      18 ..     107     120 ..     106     129 .. 0.84
   2 !    5.8   0.0    0.0039        18       1      20 [.     156     176 ..     156     177 .. 0.90
   3 !    5.8   0.3    0.0038        17       8      32 ..     192     217 ..     191     222 .. 0.80
   4 ?   -0.8   0.0      0.45     2e+03      19      28 ..     259     268 ..     249     274 .. 0.75

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.12
                         NUMOD1   7 Dlntkt..igkFsS 18 
                                    ++n+k+  +g+++S
  gene986|gene986|rna986|rna986 107 KVNGKEkiLGWYHS 120
                                    789999877****9 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0039
                         NUMOD1   1 kpVyvYDlntkt.igkFsSir 20 
                                    +pV vY l+++  +++F Si 
  gene986|gene986|rna986|rna986 156 IPVRVYELEDDNfKHIFASIE 176
                                    7999****999989*****96 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.0038
                         NUMOD1   8 lntkt.igkFsSireAakyLgishnt 32 
                                    ++++t ++ F+S+++  ++L++ +n+
  gene986|gene986|rna986|rna986 192 IKDDTyTPHFESYKDIKDSLNVYSNN 217
                                    556663699************98876 PP

  == domain 4  score: -0.8 bits;  conditional E-value: 0.45
                         NUMOD1  19 ireAakyLgi 28 
                                    i+e+++y+g 
  gene986|gene986|rna986|rna986 259 INELSNYVGS 268
                                    6778888776 PP

>> CdvA  CdvA-like coiled-coil domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.2   6.4e-05      0.29      68     119 ..     185     236 ..     181     239 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 6.4e-05
                           CdvA  68 isyasGEidEeaYksaieairellesaleekeeikklleklskleleeeeve 119
                                    +++ + +i++++Y+  +e++++ ++s++   ++++ ++++l+++ + +++ +
  gene986|gene986|rna986|rna986 185 VEHLIRDIKDDTYTPHFESYKDIKDSLNVYSNNLQAIINELDNIINNNSPMN 236
                                    7888999***********************************9988877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       814  (0.0454013); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1842.84
//
Query:       gene987|gene987|rna987|rna987  [L=426]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.4e-41  142.6  12.7      3e-41  141.6  12.7    1.5  1  Tfb2          Transcription factor Tfb2
    9.7e-20   70.8   2.0    1.8e-19   69.9   1.1    2.0  2  Tfb2_C        Transcription factor Tfb2 (p52) C-terminal doma
    1.2e-05   25.5   0.0    2.1e-05   24.7   0.0    1.4  1  Helicase_C_3  Helicase conserved C-terminal domain
  ------ inclusion threshold ------
      0.036   13.7   0.0      0.074   12.7   0.0    1.5  1  Herpes_U44    Herpes virus U44 protein


Domain annotation for each model (and alignments):
>> Tfb2  Transcription factor Tfb2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  141.6  12.7   6.7e-45     3e-41       8     353 ..      13     345 ..       8     347 .. 0.81

  Alignments for each domain:
  == domain 1  score: 141.6 bits;  conditional E-value: 6.7e-45
                           Tfb2   8 ettlerLYkspatclaifrlLpslakqlvmrllylekpvplsdlekwvkkeskkekeealkkLkelhilkekklkekkqe 87 
                                    + +l++L ++p    a+++ L + +k+l++ ll ++  ++ ++l+++ +k+ +ke   +l++L  l++++++     +  
  gene987|gene987|rna987|rna987  13 KVDLSQLHSDPLFSIALLKILGNPTKELLFCLLTTN--LNIKNLNTNDDKQ-NKEIITNLRILYLLKLIQKN-----NGF 84 
                                    567899************************999998..7777777765544.56666677777777777554.....469 PP

                           Tfb2  88 lklnptFkkslrkaltgggeeksfgvpseeedkekvdvefLdkyakekWesilhflvgseeeeepskevlelLkasglve 167
                                    + l+++F++ +  ++   + ++ f+            v+  ++  + ++++il +lv+  ++ ++++ vl++L+ ++lv+
  gene987|gene987|rna987|rna987  85 ILLDNNFRSGFVASMKLVRVNNYFE-----------AVSCTNTADTVSFDNILRMLVNDRNA-KVNEVVLDVLQYAKLVN 152
                                    *******************999999...........2334555567789*********9997.6***************6 PP

                           Tfb2 168 ekeskkslkItseGFqFlLqdinaQiwtlllqylkaleergmdlvevlsflfqLs........slelgkaYsvealsetq 239
                                      ++     It++GF+FlL+++++Q+w l+l+ + +l ++ +d  +++  +f+++          +  k + +    +++
  gene987|gene987|rna987|rna987 153 IIKE-----ITHSGFEFLLKSRKEQMWFLILNGILMLGKNYVDWLTMI--VFEMGmyerhcwlKINESKIFGTARKHNKN 225
                                    6555.....****************************98776655555..466663344443311222233333333333 PP

                           Tfb2 240 kem...............ledLrdlGLvyqrkkkskrFypTrlattLtssssessseskeegfiivETNfrvyAYtsspl 304
                                     ++               l+ L+ lG++  ++   +   pT     L s      s++ ++ f+ivETN+++yAYt+s+ 
  gene987|gene987|rna987|rna987 226 TNIdpvsdkeahsvlvrlLKYLSYLGIIQYSN---DMVKPTAEYFLLFS------SAAIQDSFLIVETNYKLYAYTTSSH 296
                                    333666677777788888**********6655...4568*********9......578899******************* PP

                           Tfb2 305 qialLslFvklkyrfpnlvvgkitresvreAlknGItadqIisyLesha 353
                                    ++++++lF+++   +pnlv+++it+esv+ A+ +GIt +qI++yL++++
  gene987|gene987|rna987|rna987 297 ELSIIKLFSQIVRELPNLVTAHITEESVNAAFLKGITGQQIVDYLTEKS 345
                                    *********************************************9986 PP

>> Tfb2_C  Transcription factor Tfb2 (p52) C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       2.6   1.2e+04      30      53 ..     147     175 ..     143     178 .. 0.53
   2 !   69.9   1.1     4e-23   1.8e-19       1      68 []     355     422 ..     355     422 .. 0.99

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 2.6
                         Tfb2_C  30 feevleyakelg.....vllwedeekrll 53 
                                    + +++++ ke+      +ll +++e++++
  gene987|gene987|rna987|rna987 147 YAKLVNIIKEIThsgfeFLLKSRKEQMWF 175
                                    55555555555433333556666665555 PP

  == domain 2  score: 69.9 bits;  conditional E-value: 4e-23
                         Tfb2_C   1 DQIrLWekernRlkaeegvlyddFesqadfeevleyakelgvllwedeekrllvvkeeghesvkefik 68 
                                    +QI +We+ r+R+k+ ++v+y++F + +++e + +y++e+g+l+ +de +rllvv+ e h++vk+fik
  gene987|gene987|rna987|rna987 355 EQILIWERQRDRMKCIDAVIYSHFMTYNEYEITYRYCREKGALIDHDEFRRLLVVRLECHNEVKNFIK 422
                                    7******************************************************************8 PP

>> Helicase_C_3  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.0   4.6e-09   2.1e-05      24      94 ..     300     370 ..     280     392 .. 0.84

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 4.6e-09
                   Helicase_C_3  24 aLaafAelesrpehahtyrltplSlrrAldaGltaeeiiefLerlskypvPqaleylirdvarryGklrlg 94 
                                     ++ f++++++  ++ t  +t++S+ +A+  G+t ++i+++L++ sk ++P  + ++i  + r+  +++  
  gene987|gene987|rna987|rna987 300 IIKLFSQIVRELPNLVTAHITEESVNAAFLKGITGQQIVDYLTEKSKSELPPVVLEQILIWERQRDRMKCI 370
                                    5677888888877888999***************************99********998888887777766 PP

>> Herpes_U44  Herpes virus U44 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   1.6e-05     0.074      53     119 ..     312     381 ..     284     391 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.6e-05
                     Herpes_U44  53 gDiissdkdtealkqayLLalksnkiteylarfdvaeiPasCqe...lvkaqvkkLqamqsvvwntlial 119
                                     ++++ +   e+++ a+L ++  ++i +yl++ + +e+P    e   + + q ++++ +++v++  +++ 
  gene987|gene987|rna987|rna987 312 PNLVTAHITEESVNAAFLKGITGQQIVDYLTEKSKSELPPVVLEqilIWERQRDRMKCIDAVIYSHFMTY 381
                                    56788888999****************************66655222447899**********9988755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (426 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       870  (0.0485247); expected 358.6 (0.02)
Passed bias filter:                      464  (0.0258799); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 2661.89
//
Query:       gene988|gene988|rna988|rna988  [L=99]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.3e-05   23.8   1.2    6.7e-05   23.2   1.2    1.4  1  Eaf7      Chromatin modification-related protein EAF7


Domain annotation for each model (and alignments):
>> Eaf7  Chromatin modification-related protein EAF7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   1.2   3.8e-09   6.7e-05       3      35 ..      19      51 ..      17      91 .. 0.80

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 3.8e-09
                           Eaf7  3 irLfkliiefkPaGihKhFrmlaiverlnkpdk 35
                                   ir++k++ ++ P+GihKh  ml i+++++kp+ 
  gene988|gene988|rna988|rna988 19 IRILKALGHITPVGIHKHLLMLKILRNMKKPNI 51
                                   8999**************************443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       561  (0.0312901); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 773.68
//
Query:       gene989|gene989|rna989|rna989  [L=39]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (39 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       241  (0.0134419); expected 358.6 (0.02)
Passed bias filter:                      168  (0.00937029); expected 358.6 (0.02)
Passed Vit filter:                         7  (0.000390429); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 269.79
//
Query:       gene99|gene99|rna99|rna99  [L=426]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-71  241.7   1.5    2.8e-47  161.6   0.0    2.1  2  Diphthamide_syn  Putative diphthamide synthesis protein


Domain annotation for each model (and alignments):
>> Diphthamide_syn  Putative diphthamide synthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.8   0.7   2.7e-26   4.8e-22       1      87 [.      47     130 ..      47     136 .. 0.93
   2 !  161.6   0.0   1.5e-51   2.8e-47      85     290 ..     213     405 ..     197     408 .. 0.91

  Alignments for each domain:
  == domain 1  score: 78.8 bits;  conditional E-value: 2.7e-26
            Diphthamide_syn   1 fPegllpdsaeiadil.eefgaevvilgDttYGaCcvdevaaehlgadllvHyGhsclspvdrlpvlYvfveieldvehlvetl 83 
                                +P+gll++s+ ++d++ +++ga+v+ l+D++YGaCcvd+     ++++l+vHyGhsc++    ++vlYvfv++ ++++hl +++
  gene99|gene99|rna99|rna99  47 LPDGLLKYSTILSDAIeSNTGARVITLADVVYGACCVDTD----ADVELIVHYGHSCIVGSGGMKVLYVFVDVFFESDHLERMV 126
                                6***************9999*****************995....4889************99******************9999 PP

            Diphthamide_syn  84 kknf 87 
                                ++ +
  gene99|gene99|rna99|rna99 127 RRMI 130
                                8876 PP

  == domain 2  score: 161.6 bits;  conditional E-value: 1.5e-51
            Diphthamide_syn  85 knfkekkkivlvstiqyahaleevkeeleeegyevvkvpqsekplspgevlgctspklkeeeeevdailyigdgrfhllslmls 168
                                +n+++  +i +++t+qy h + ++ + ++    +     q+ kpls+gevlgctspklk     ++++++i+dgrfhl+slm++
  gene99|gene99|rna99|rna99 213 ANLNNPPNITVLGTVQYRHIVYKLNKMFN---LPSY---QV-KPLSTGEVLGCTSPKLK-----TTTVIFISDGRFHLESLMIA 284
                                33366677**************9999999...4555...66.9***************5.....569***************** PP

            Diphthamide_syn 169 npklpvyrydpyskklteesydakkllrrRyaaiekakdakkvGiivgtlgvqgrlelverlkkllkeagkksylvlvgelnpa 252
                                np+ ++yry+p++k++ +e+yd++++++ R ++   + +a++vGii gtlg qg+ ++v+++ + l + gk++y++ ++e++++
  gene99|gene99|rna99|rna99 285 NPTAQFYRYCPFNKRMYREHYDHERMYAVRAQQRGAFLRAQRVGIINGTLGAQGNSRIVRNVHDALVRMGKEVYVFNMEEVKES 368
                                ************************************************************************************ PP

            Diphthamide_syn 253 kLanfaeidafVlvaCprlsiddgkeFekPvltpyEle 290
                                +L+ fa ++++V+v Cprlsid+g+ +   +l  yE++
  gene99|gene99|rna99|rna99 369 NLR-FAFVEGYVQVCCPRLSIDWGHLYGTFMLCAYEVF 405
                                **8.559****************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (426 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       908  (0.0506442); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.24s 00:00:00.78 Elapsed: 00:00:00.40
# Mc/sec: 3165.32
//
Query:       gene990|gene990|rna990|rna990  [L=252]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.1e-15   56.1   0.4      1e-14   55.1   0.4    1.5  1  Brix      Brix domain
  ------ inclusion threshold ------
      0.027   14.1   0.0      0.035   13.7   0.0    1.2  1  Rhv       picornavirus capsid protein


Domain annotation for each model (and alignments):
>> Brix  Brix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.1   0.4   1.1e-18     1e-14       1     159 [.      72     207 ..      72     236 .. 0.85

  Alignments for each domain:
  == domain 1  score: 55.1 bits;  conditional E-value: 1.1e-18
                                    BTT--HHHHHHHHHHHHHCTTSEEEEEEECT-TTTHHHHHHH..-HHHHHHHH.HCTC.SEEEEEE..SSTTEEEEEEEE CS
                           Brix   1 grktssrlrqllkdlrslmkphtasflkrnsnklkdlvelag..vthlellse.kndc.slfvfelskkrPngptlefkv 76 
                                    +r++ssrl+q++k l  +++  +++   r+++ +k+   la+  +  l+++ e ++++ sl++  +    P gpt++f++
  gene990|gene990|rna990|rna990  72 SRDPSSRLKQFAKHLSLILNATSVT---RGNMTIKE---LAEqnFDVLVMVGEsHGQAnSLILTYF----PYGPTFYFSL 141
                                    6899***************554444...88889999...455557889999999566659999999....********** PP

                                    ECECTGGGSTTTSTS-TT---EEEEES.HHH.....HHHHHHHHHHH..SEEEG..-B-GG-SEEEEEEES.CCTTTECE CS
                           Brix  77 enyslmkdlkkakktefgsrPllvfngkenf.....kllksllqdlFrvpkislkspklsglrrvvlftaaenqetdkti 151
                                    +n+ l ++ k      f ++ ll+++   nf      +lk+ l  +F  p++       ++++r+v+f+   n++ d  i
  gene990|gene990|rna990|rna990 142 HNVRLLSRTK-----PFSTKALLILE---NFstdigLKLKESLSYIF--PSV-------EKGKRIVVFH---NKD-D-II 199
                                    ********96.....589********...999999999*********..966.......79********...666.7.9* PP

                                    EEEEEEEE CS
                           Brix 152 sfRhYaik 159
                                     fRhY ++
  gene990|gene990|rna990|rna990 200 RFRHYFLE 207
                                    *****986 PP

>> Rhv  picornavirus capsid protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   3.9e-06     0.035      29     110 ..      56     136 ..      36     195 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.9e-06
                                    EEBTTGGGTSSGEEEEEEEEETTSTCEEEEEETSGGTTSHHHHHHHTTEEEEEEEEEEEEEEESSTTEEEEEEEEEEETT CS
                            Rhv  29 apvepdvaaerfytldstswtseskgffiwklplalkdmgllgakleyhtyvrfglevtvqcnaskfhqgkllvayvPeg 108
                                    + +++ ++  ++y ++s++ +s  k+f    l l l+++ + ++++    ++    +v v++ +s+ ++ +l+++y P g
  gene990|gene990|rna990|rna990  56 TGQQKITKPLNVYVTTSRDPSSRLKQF-AKHLSLILNATSVTRGNMTIKELAEQNFDVLVMVGESHGQANSLILTYFPYG 134
                                    55667788899****************.77777777*******************************************9 PP

                                    SS CS
                            Rhv 109 ap 110
                                     +
  gene990|gene990|rna990|rna990 135 PT 136
                                    87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       852  (0.0475208); expected 358.6 (0.02)
Passed bias filter:                      587  (0.0327403); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 1795.85
//
Query:       gene991|gene991|rna991|rna991  [L=335]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-08   34.5   0.0    2.8e-08   33.8   0.0    1.4  1  Myb_DNA-binding  Myb-like DNA-binding domain
     0.0018   18.6   0.4     0.0073   16.6   0.0    2.2  2  SWIRM            SWIRM domain
  ------ inclusion threshold ------
      0.066   13.5   0.1       0.14   12.4   0.1    1.5  1  Myb_DNA-bind_6   Myb-like DNA-binding domain
        3.7    7.4  11.7         11    5.9  11.8    1.7  1  zf-RING_4        RING/Ubox like zinc-binding domain


Domain annotation for each model (and alignments):
>> Myb_DNA-binding  Myb-like DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.8   0.0   6.3e-12   2.8e-08       2      45 ..      70     114 ..      69     115 .. 0.96

  Alignments for each domain:
  == domain 1  score: 33.8 bits;  conditional E-value: 6.3e-12
                                    SSSBHHHHHHHHHHHHHHT.TCHHHHHHHHTSS-HHHHHHHHHHH CS
                Myb_DNA-binding   2 gkWteeEdelLleavkkhG.nrWkkIaerlggRtekqcrsrwrny 45 
                                    ++Wt+ E++++ e + +hG ++W++Ia  l +++  ++ s+++++
  gene991|gene991|rna991|rna991  70 SSWTALEELIFFEMLIQHGlGNWTEIALNLKTKSSQEIESHFYKV 114
                                    69****************************************996 PP

>> SWIRM  SWIRM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0      0.91   4.1e+03       9      41 ..     163     195 ..     158     209 .. 0.67
   2 !   16.6   0.0   1.6e-06    0.0073       6      87 ..     266     335 .]     261     335 .] 0.89

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.91
                          SWIRM   9 dslhpiEkellselfngkdktpeeYlkiRnkii 41 
                                    +sl   E e++++++ + +k+  +  k+++ ii
  gene991|gene991|rna991|rna991 163 KSLDVGENEIVKNFLLDAYKNLLVLRKYKRMII 195
                                    566667777777777666666666666666666 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 1.6e-06
                          SWIRM   6 FdpdslhpiEkellselfngkdktpeeYlkiRnkiialyrenpkeyltvteaqkalkrrrltgidvnllsrihefLerwG 85 
                                    + ++ l+p E+el+  l     +t   Y+k++++ + +  ++  ++++v++  + +k     g   + +  +h+f++++G
  gene991|gene991|rna991|rna991 266 LRMNILQPSERELCRRLK----ITYGSYMKLKRYAVLEQIRT--KNVSVKALGRIVK-----G-SDSRVGILHSFFKKNG 333
                                    67899*************....***********998888885..558*****66666.....8.9999************ PP

                          SWIRM  86 lI 87 
                                    +I
  gene991|gene991|rna991|rna991 334 WI 335
                                    *9 PP

>> Myb_DNA-bind_6  Myb-like DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   3.1e-05      0.14       1      50 [.      72     122 ..      72     134 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.1e-05
                 Myb_DNA-bind_6   1 WteeEdeiLlklvekyg.ndWknIaealnrRtpkqcfdrwknkLrpkisrk 50 
                                    Wt+ E+ i  +   ++g  +W++Ia  l+ ++++++  ++ ++   +i+++
  gene991|gene991|rna991|rna991  72 WTALEELIFFEMLIQHGlGNWTEIALNLKTKSSQEIESHFYKVFGININKE 122
                                    99999999999999**956*********99**********99777766665 PP

>> zf-RING_4  RING/Ubox like zinc-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9  11.8    0.0024        11       4      35 ..      16      48 ..      13      53 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0024
                      zf-RING_4  4 Cdeel.detdkdlkpCeCgyqiClfCyhrilee 35
                                   Cd ++ + t+ +   CeCg  +C+ Cy + +++
  gene991|gene991|rna991|rna991 16 CDCCFqEITNYTRIKCECGIDMCVLCYFHQKTA 48
                                   555555668888999************987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (335 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       787  (0.0438954); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2472.38
//
Query:       gene992|gene992|rna992|rna992  [L=575]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (575 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       899  (0.0501422); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.41
# Mc/sec: 4173.38
//
Query:       gene993|gene993|rna993|rna993  [L=241]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.6e-19   68.0   0.0      3e-09   36.4   0.0    2.3  2  Ribosomal_S2  Ribosomal protein S2


Domain annotation for each model (and alignments):
>> Ribosomal_S2  Ribosomal protein S2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.4   0.0   1.7e-13     3e-09       1      97 [.      17     112 ..      17     118 .. 0.90
   2 !   30.1   0.0   1.5e-11   2.7e-07     147     203 ..     117     173 ..     112     188 .. 0.88

  Alignments for each domain:
  == domain 1  score: 36.4 bits;  conditional E-value: 1.7e-13
                   Ribosomal_S2   1 LLeagvhfGhqtrrwnpkmkpyIyger..ngihiidlektlaalrraykvvkevaakggkilfvgtkkqakeavkeaakr 78 
                                    LL+  +h+G  +   n +m+ yI+g+r  ++i iid++k   ++  a++++ ++ ++ ++i+ v++k+  ++av + ++ 
  gene993|gene993|rna993|rna993  17 LLQCCCHLGGIQ--ANIQMRDYIFGTRpgDKINIIDIQKMWDKMVLAARLFLSI-KDTKSIMVVSNKDFGRKAVLKFCEA 93 
                                    788889999665..5999*********5557******************99876.67899******************** PP

                   Ribosomal_S2  79 angyyvnerWlgGtLTNfk 97 
                                    +++  ++ r+++G + Nf+
  gene993|gene993|rna993|rna993  94 TGATPITGRFIPGGFSNFE 112
                                    *****************86 PP

  == domain 2  score: 30.1 bits;  conditional E-value: 1.5e-11
                   Ribosomal_S2 147 klPdlvvvldpkkekiavkEakklgipviaivDtnvdpdlvdypIpaNddsirsikl 203
                                    + P l++  d+ +++  ++Ea+k++ pvia+++t+ + + vd  I +N+ s  ++  
  gene993|gene993|rna993|rna993 117 REPRLLIAADAFSDRQTIEEAAKARAPVIAFCNTDNSLSYVDVGIAMNNRSASALGA 173
                                    6799***********************************************988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       523  (0.0291706); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1613.37
//
Query:       gene994|gene994|rna994|rna994  [L=757]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.8e-19   67.8   0.0    1.7e-18   66.7   0.0    1.5  1  Glycos_transf_1  Glycosyl transferases group 1
    9.4e-12   45.5   0.0    1.7e-11   44.7   0.0    1.4  1  Glyco_trans_1_4  Glycosyl transferases group 1
      0.002   18.5   0.0     0.0064   16.9   0.0    1.8  1  Glyco_trans_1_2  Glycosyl transferases group 1


Domain annotation for each model (and alignments):
>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.7   0.0   2.9e-22   1.7e-18      10     165 ..     521     698 ..     516     702 .. 0.88

  Alignments for each domain:
  == domain 1  score: 66.7 bits;  conditional E-value: 2.9e-22
                                    TTTTT-EEEEEESS-TTTTTHHHHHHHHHCCCCC..........HCSCEEEEEES............STTHHHHHHHHHH CS
                Glycos_transf_1  10 gknekkkiilsvgrlekeKgvdllikafallkkq..........lnpnvklviaG...........ngeeekelkklaee 68 
                                    ++   k++i+ ++r+++ Kg++ +i++f  + kq             +++lv++G             +e+  + ++ ++
  gene994|gene994|rna994|rna994 521 ELSLHKPYIVQISRFDPSKGQKDAIDVFSIVYKQlesriktvgdPLYDLHLVLCGhgsvddpegglIFNELMAYLDEEKN 600
                                    4556799************************999******9999999***************988844444444555588 PP

                                    HCTTCGGGEEECCH.SSSHHHHHHCESEEEEEESSBSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHH CS
                Glycos_transf_1  69 lelsdnviflgevs.redleellknadifvlpsisEgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaea 147
                                    + +++n+i+++  + ++ l  +lk+a ++++ sisEgf i ++EA+   +pv+++++gg++ +v + +tG++v+ ++ +a
  gene994|gene994|rna994|rna994 601 AAVKNNIIVVKLPPlDQILNLVLKKARVALQLSISEGFEIKVTEAILKSVPVVVYDSGGLPLQVYEDKTGFIVPCGDTAA 680
                                    889999****999955555555666******************************************************* PP

                                    HHHHHHHHHHSHHHHHHH CS
                Glycos_transf_1 148 laeairklledeelrerl 165
                                    +ae+ + lle +e + ++
  gene994|gene994|rna994|rna994 681 AAEKTTYLLEHPEFATNM 698
                                    ************998876 PP

>> Glyco_trans_1_4  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.7   0.0   2.8e-15   1.7e-11       2     133 ..     527     690 ..     526     691 .. 0.76

  Alignments for each domain:
  == domain 1  score: 44.7 bits;  conditional E-value: 2.8e-15
                                    EEEEEES---GG.GTHHHHHHHHHHHH.H.H............EEEEEES---..........HHHHHHHT.....T-T. CS
                Glyco_trans_1_4   2 pvilfvGrleenvkgvdllleavpllrkk.d............vrlvivGdgp.rp.......eeleelaa.....glee 55 
                                    p i+ ++r+++  kg++  ++ +  + k+ +            ++lv++G g+ ++       +el ++++      +++
  gene994|gene994|rna994|rna994 527 PYIVQISRFDP-SKGQKDAIDVFSIVYKQlEsriktvgdplydLHLVLCGHGSvDDpegglifNELMAYLDeeknaAVKN 605
                                    7899999**55.477777776666666443122334556788899*****997743578999955544432233367788 PP

                                    TEEEE---..TH.HHHHHHH-SEEEE--..---SHHHHHHHHTT-EEEE-TGGGTTT--..TTSSEE--TT-HHHHHHHH CS
                Glyco_trans_1_4  56 rveftGfv..ed.laellaaadvfvaPs..egfglkllEamaaglpvVatdvggiaevv..gengllvppgdpealaeai 128
                                    +++++     ++ l+ +l++a+v++  s  egf +k+ Ea    +pvV+ d gg++  v   ++g++vp gd++a ae+ 
  gene994|gene994|rna994|rna994 606 NIIVVKLPplDQiLNLVLKKARVALQLSisEGFEIKVTEAILKSVPVVVYDSGGLPLQVyeDKTGFIVPCGDTAAAAEKT 685
                                    87777755544469999*********9999************************987777789***************** PP

                                    HHHHH CS
                Glyco_trans_1_4 129 lrLle 133
                                      Lle
  gene994|gene994|rna994|rna994 686 TYLLE 690
                                    *9997 PP

>> Glyco_trans_1_2  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   1.1e-06    0.0064       2      67 ..     629     696 ..     628     705 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.1e-06
                Glyco_trans_1_2   2 vLnpsrsespnlrlfEaaacGafaltddaegleelftpgkevilfe..dleelaekiryllanpeerr 67 
                                    +L +s se++  ++ Ea    +++++ d+ gl+  + ++k+++++   d++ +aek  yll++pe + 
  gene994|gene994|rna994|rna994 629 ALQLSISEGFEIKVTEAILKSVPVVVYDSGGLPLQVYEDKTGFIVPcgDTAAAAEKTTYLLEHPEFAT 696
                                    688999***************************9999999************************9765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (757 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       568  (0.0316805); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.68u 0.27s 00:00:00.95 Elapsed: 00:00:00.45
# Mc/sec: 5093.51
//
Query:       gene995|gene995|rna995|rna995  [L=575]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-43  148.2   0.2    4.3e-43  146.5   0.2    2.0  1  Mad3_BUB1_I_2  Putative Mad3/BUB1 like region 1 protein
    0.00074   19.5   0.0     0.0015   18.5   0.0    1.5  1  Mad3_BUB1_I    Mad3/BUB1 homology region 1


Domain annotation for each model (and alignments):
>> Mad3_BUB1_I_2  Putative Mad3/BUB1 like region 1 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  146.5   0.2   4.8e-47   4.3e-43       1     127 [.      61     184 ..      61     185 .. 0.98

  Alignments for each domain:
  == domain 1  score: 146.5 bits;  conditional E-value: 4.8e-47
                  Mad3_BUB1_I_2   1 llrkidipyfrnnpsyiekwkelYkktkdlkilfLmklKkIskfyyfvYlelsryFlkkgkkeaalfiLqegiknkvydk 80 
                                    ++r+i++p++rn+ps++++++ +Yk+++d++++fLm+lK+I+k++yfvY++l+r+Fl+++++++alf+Lqegi n+++  
  gene995|gene995|rna995|rna995  61 IKRYINEPLYRNEPSFLHLFHVFYKQDDDINVIFLMYLKSIGKYHYFVYACLARHFLRINEPGKALFVLQEGILNDCIG- 139
                                    789****************************************************************************. PP

                  Mad3_BUB1_I_2  81 eilkeelksikklekklsee.eakkllkpkkirlfGkeWveievnyla 127
                                       k++l++ik+++++++++ +a++++ p+++r+fG+eW++i+vny+a
  gene995|gene995|rna995|rna995 140 ---KDRLMNIKCMIDSHDIDhDAHDDVLPASVRVFGREWIQIAVNYAA 184
                                    ...**************98769************************86 PP

>> Mad3_BUB1_I  Mad3/BUB1 homology region 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   1.6e-07    0.0015      49     124 .]      59     133 ..      49     133 .. 0.93

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.6e-07
                                    HHHHHTTTSGGGTT-HHHHHHHHHHHTTSS-HHHHHHHHHHHTTSTTBHHHHHHHHHHHHHTT-HHHHHHHHHHH. CS
                    Mad3_BUB1_I  49 rclkkfkdderYknDpRylklwlkyadlveepreifkflaskkiGtklalfYeewAellekkgrfkeAeevyelGi 124
                                    r++k++ +++ Y+n+p +l l+  + ++ ++   if  ++ k+iG+ +   Y   A+++ + ++  +A  v+++Gi
  gene995|gene995|rna995|rna995  59 RTIKRYINEPLYRNEPSFLHLFHVFYKQDDDINVIF-LMYLKSIGKYHYFVYACLARHFLRINEPGKALFVLQEGI 133
                                    78999*****************99999887777777.89************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (575 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       482  (0.0268838); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.28s 00:00:00.88 Elapsed: 00:00:00.48
# Mc/sec: 3589.64
//
Query:       gene996|gene996|rna996|rna996  [L=103]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.13   11.8   0.0       0.17   11.4   0.0    1.1  1  BRI3BP    Negative regulator of p53/TP53


Domain annotation for each model (and alignments):
>> BRI3BP  Negative regulator of p53/TP53
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   9.4e-06      0.17     133     175 ..      13      57 ..       4      60 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 9.4e-06
                         BRI3BP 133 lLlglvavyvLlgslglyakss..eesgasleakvrsLerqvrel 175
                                     L +l a+y+ l s++l+ +++  +++  ++e++v+ Le qv+ +
  gene996|gene996|rna996|rna996  13 VLSVLCAIYFSLFSIPLFSTGTkpPSKIVNVEERVKTLEVQVKTI 57 
                                    577788889888888877777744677789************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       812  (0.0452898); expected 358.6 (0.02)
Passed bias filter:                      661  (0.0368676); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 692.93
//
Query:       gene997|gene997|rna997|rna997  [L=53]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (53 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       280  (0.0156172); expected 358.6 (0.02)
Passed bias filter:                      214  (0.011936); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 390.31
//
Query:       gene998|gene998|rna998|rna998  [L=1386]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   1.5e-130  436.0   7.5    1.9e-94  316.9   0.3    2.4  2  DNA_pol_B       DNA polymerase family B
    3.8e-42  144.6   9.8      3e-37  128.5   4.9    2.9  2  DNA_pol_B_exo1  DNA polymerase family B, exonuclease domain
      3e-11   43.6  13.6      3e-11   43.6  13.6    2.4  2  zf-C4pol        C4-type zinc-finger of DNA polymerase delta
    0.00072   18.5   0.3    0.00072   18.5   0.3    2.9  3  DNA_pol_B_2     DNA polymerase type B, organellar and viral


Domain annotation for each model (and alignments):
>> DNA_pol_B  DNA polymerase family B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  316.9   0.3   4.3e-98   1.9e-94       2     301 ..     688     971 ..     687     980 .. 0.91
   2 !  121.7   1.9   7.1e-39   3.2e-35     294     458 ..    1111    1261 ..    1102    1262 .. 0.94

  Alignments for each domain:
  == domain 1  score: 316.9 bits;  conditional E-value: 4.3e-98
                                    -HHHHHHS-HHHHHHHHHHHHHHHTTBE-B-----.--SS.-S----BE----EEESS-EEEEEETTHHHHHHHHTT-ST CS
                      DNA_pol_B   2 plsrvledgqqirveslLlrlakeegfilpdrtekkgkeeegYqGatVlePkkglydkpvlvlDFaSLYPsiiqahNlcy 81 
                                    p++  +++g ++++++l+lr+a+++++++p+   +  k+e gY Ga+V+eP++g+yd+p++vlDFaSLYPsii+ahNlcy
  gene998|gene998|rna998|rna998 688 PINWHFNRGISVKIFGLILREARKNNYVVPSV--A-VKDE-GYMGAFVIEPERGYYDEPIAVLDFASLYPSIIIAHNLCY 763
                                    66778899**********************33..3.3455.8************************************** PP

                                    TTCE-HCCHCCT--BTT...TEEE-TCC-EEE-TTS---HHHHHHHHHHHHHHHHHHHHHCS--HHHHHHHHHHHHHHHH CS
                      DNA_pol_B  82 ttlvaseeeakeleaedeyleveveprlvefvkksvregllpklLkdllakRkaikkelkeekdefekalldkqQlalKv 161
                                    +t++   ++  + +     ++ e +p +++fvk +vr g+lp +L+++l+kRk++k+++k+ek++f+k+ll+++Q a Kv
  gene998|gene998|rna998|rna998 764 STMLLGTRHGIDKN-----KDAERSPTGSYFVKRDVRVGILPVILEKMLKKRKEVKEKMKNEKNPFMKTLLNARQNAFKV 838
                                    ***99888754333.....356899******************************************************* PP

                                    HHHHHHHHHTSTTSTT--HHHHHHHHHHHHHHHHHHHHHHHHT...SSGGGT-SS.....T-EEEEEBSSEEEEE-S-.. CS
                      DNA_pol_B 162 taNsvYGftGvansrlpclalAasvTtiGRemLektkelvekkaellskllalpeeaeeeklkviYGDTDSvfielkv.. 239
                                    +aNsvYGftG a +rlpc+++++svT +GRem+ ktk++ve+    ++ ++++       + +viYGDTDSv++++k   
  gene998|gene998|rna998|rna998 839 SANSVYGFTGSAIGRLPCIDISQSVTGYGREMIIKTKNVVESV---FCRSNGYDF-----DSHVIYGDTDSVMVRIKKdd 910
                                    *****************************************77...788888877.....99**************9955 PP

                                    SSHHHHHHHHHHHHHHHHT.TSTTT--EEEEEEEEEEEEEETTEEEEEEEEESSTTSEEEEE CS
                      DNA_pol_B 240 kdveellkigkelaeevseklfkkplklefekvykkllLisKKkYaglkvektskanklliK 301
                                     +v+ +++++ke+a++vse  f kp+klefekvy+++lL++KK+Yag++ ++++ ++++ +K
  gene998|gene998|rna998|rna998 911 LNVDFVFEVAKEMANKVSE-CFVKPVKLEFEKVYFPYLLMNKKRYAGVIETREEIKEEVKVK 971
                                    67899**************.*****************************9977666655555 PP

  == domain 2  score: 121.7 bits;  conditional E-value: 7.1e-39
                                     TTS.EEEEESSGGGSTTS-HHHHHHHHHHHHHHSSS....S-HHHHHHHHHHHHHHHHHHHHTT-S-GGGG-EEEEES CS
                      DNA_pol_B  294 kan.klliKGvdlvRrdncklvkevikkvlelllkdeteersleeglealksilkdvleeleenkvplekfvlskels 370 
                                     k + ++++KG+++vRrdncklvk +i+++l+lll +    r++e +  ++k+++    ++l   +++l+ +v+sk+ls
  gene998|gene998|rna998|rna998 1111 KIKrRMDTKGIETVRRDNCKLVKSLIEECLDLLLMK----RDPERAKSFVKAVV----RDLYLDRIDLSLLVISKTLS 1180
                                     34426*******************************....**********9999....9999**************** PP

                                     S.CCCSSGCCSHHHHHHHHHHHHCSS---TTCEEEEEEBETSS.....SS-GGGTEEEHHHHHHCCSEB-HHHHHH.T CS
                      DNA_pol_B  371 kepenyksknlphlevakrlkkrneeapevgdrisYvivekkkevkkknllaseraedpeyvleknlpidieyYls.q 447 
                                     k  +ny +k+ +h+e+a+r+kkr+++a+++gdri+Yviv k       n+ a+e+ edp yvleknlp+d++yY++ q
  gene998|gene998|rna998|rna998 1181 K--TNYAAKQ-AHVELAERMKKRDNAAVSIGDRIAYVIVDKGP-----NVIAYEKSEDPLYVLEKNLPVDVNYYIEqQ 1250
                                     *..6**9999.******************************97.....9***************************** PP

                                     THHHHHHHHTT CS
                      DNA_pol_B  448 llkevarllea 458 
                                     ++k+v rl+++
  gene998|gene998|rna998|rna998 1251 IMKPVHRLFDP 1261
                                     *********97 PP

>> DNA_pol_B_exo1  DNA polymerase family B, exonuclease domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  128.5   4.9   6.6e-41     3e-37      12     280 ..      38     317 ..      29     339 .. 0.86
   2 !   17.2   0.2   5.1e-07    0.0023     303     337 .]     589     623 ..     572     623 .. 0.84

  Alignments for each domain:
  == domain 1  score: 128.5 bits;  conditional E-value: 6.6e-41
                                    EEE---EEEEEESSCGGHHHHHHHHHHHCCTTCCCEEEEEEEECCCCEECCTSSCCHHCEEEEEESSTCHHHHHHHHHHH CS
                 DNA_pol_B_exo1  12 vfgfkpyfYceapdgkeleevkeelkelyeelskkvtkivkvelvlkkslygyekkpvpylkvsvsnpnelkkirkelsp 91 
                                    v +f pyfY++++++k+       +  ++   +  v    + +l +kk++ygy  +++++lkv++ n+   + +r+    
  gene998|gene998|rna998|rna998  38 VSDFFPYFYVKIKTDKN------DILNFFATRNIVV---LSHKLSTKKNIYGYTMDNESFLKVFFWNVVVESAARRAC-- 106
                                    67899********4444......4555665555433...588999************99*********9999999998.. PP

                                    CCCCCCCCSSS--HHHHHHHHCTS-TTCEEEEE...............................TEEEEGCC--C-.SEE CS
                 DNA_pol_B_exo1  92 leeivdvyeydvdylerflidnkivgfgwysvk...............................kylvraegkisncdve 140
                                     e++++v+++++++  +f++d +ivg+++++++                                +  r e+ ++++ v+
  gene998|gene998|rna998|rna998 107 -ENVYEVFDSNIPFNLQFMVDMGIVGMSYLKIDmengqevrmedaggvngvfstsldvhgdgqhSKRHRSEEEADTKYVD 185
                                    .789**********************************999999999999999999988887776777777777777777 PP

                                    EEEETTTSCEETTT.........CC..S-EEEEEEEEEETEETTSEETTTT..--EEEEEEEECCTC.SS.SEEEEEEEC CS
                 DNA_pol_B_exo1 141 idcdvddliakpke.........se..pplrvlsFDIeckskkgkfpdaensedpiiqIscvldglgekepearklftlr 209
                                      c+  ++ +++            +  pp++vlsFD+e+  ++ +fp++++  d+iiqI  +++ +     +++ +f+ r
  gene998|gene998|rna998|rna998 186 AVCSAHRIGKVYHIshkaikpvdRDdiPPFKVLSFDLEVNNRDNRFPESSI--DEIIQIGNTVKTEE----YKQTIFCQR 259
                                    777777777776666666666551169************************..**********9877....8899***** PP

                                    CCTSS----EE--SSTCSTTEEEEEESSHHHHHHHHHHHHHHH--SEEEESSTTTTHHHHHHHHHHHCCTC CS
                 DNA_pol_B_exo1 210 ecaseeeedfeltpkpeypgvkvlefdsEkelLqaflefikqydPdvitgYNidnFDlpYilnRakelykv 280
                                    ++a            ++  gv+v ++dsE+e+L++++ f+  +dPdv++gYNi  FDl Y+  R+++l ++
  gene998|gene998|rna998|rna998 260 STA------------SI-AGVDVRSYDSEREMLEEWIRFVYYEDPDVLLGYNISGFDLDYVVGRVRKLGIP 317
                                    ***............88.************************************************99874 PP

  == domain 2  score: 17.2 bits;  conditional E-value: 5.1e-07
                                    EEEECEEEETTSEEEEHHHHHHHHSSSSG-SHHHH CS
                 DNA_pol_B_exo1 303 kqarekvkisgrihlDlyrvvkrklklpsYkLnav 337
                                    ++++  + ++gri++D++ v+k++ kl+sY+Ln+v
  gene998|gene998|rna998|rna998 589 TRKEMFNDYQGRIVVDMLTVIKKEHKLRSYTLNNV 623
                                    4666667899***********************98 PP

>> zf-C4pol  C4-type zinc-finger of DNA polymerase delta
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.1      0.45     2e+03      41      51 ..     579     588 ..     572     600 .. 0.58
   2 !   43.6  13.6   6.7e-15     3e-11       1      70 []    1297    1364 ..    1297    1364 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.45
                       zf-C4pol  41 letvCqsCaqg 51 
                                    + ++C++C+ +
  gene998|gene998|rna998|rna998 579 TFKECKNCN-S 588
                                    555566662.1 PP

  == domain 2  score: 43.6 bits;  conditional E-value: 6.7e-15
                       zf-C4pol    1 ClvCkeklkkalCkkCrsdkqesllkllsrlkelekklneletvCqsCaqgsleeevkCdsrdCpvfYeR 70  
                                     Cl Cke   + lCk+C  +  + ++ +++++ke e+ +n+++++Cq+C   s+ +ev C ++dCp+f++R
  gene998|gene998|rna998|rna998 1297 CLLCKE-RGSVLCKRCLPNYFSVYVGKVQEMKEKEDVYNKCWRECQRC-IRSVCTEVLCANKDCPIFFMR 1364
                                     *****6.5589*****9777777*************************.67888**************99 PP

>> DNA_pol_B_2  DNA polymerase type B, organellar and viral
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.1      0.08   3.6e+02     270     297 ..      40      64 ..      19      93 .. 0.72
   2 !   18.5   0.3   1.6e-07   0.00072     211     305 ..     724     814 ..     696     850 .. 0.71
   3 ?   -3.0   0.1      0.56   2.5e+03      79      99 ..     937     957 ..     935     972 .. 0.69

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.08
                    DNA_pol_B_2 270 ekfgffdakikppilkedalpplpirld 297
                                    + f +f++kik+   k+d l+++++r +
  gene998|gene998|rna998|rna998  40 DFFPYFYVKIKTD--KNDILNFFATR-N 64 
                                    3899*******97..66667999999.5 PP

  == domain 2  score: 18.5 bits;  conditional E-value: 1.6e-07
                    DNA_pol_B_2 211 kayrGGrcypsvlgiyeeniyvyDvnSlYPsamthypmPygkppfeeakavkeleekleekfgffdakikppilkedalp 290
                                    + y+G +++    g+y+e+i v D+ SlYPs+     + y +    +   +++++++  +++g + +k       +  lp
  gene998|gene998|rna998|rna998 724 EGYMGAFVIEPERGYYDEPIAVLDFASLYPSIIIAHNLCYSTMLLGTRHGIDKNKDAERSPTGSYFVKRDV---RVGILP 800
                                    589*****5555*********************999******99999999999999888888888665554...566667 PP

                    DNA_pol_B_2 291 plpirldicsrkggr 305
                                    ++ +++ +++rk+ +
  gene998|gene998|rna998|rna998 801 VILEKM-LKKRKEVK 814
                                    776662.34444443 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 0.56
                    DNA_pol_B_2  79 leikKgkfpykavnelhliys 99 
                                    le++K +fpy  +n+ +  + 
  gene998|gene998|rna998|rna998 937 LEFEKVYFPYLLMNKKRYAGV 957
                                    7899**********5554443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1386 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       701  (0.0390987); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.80u 0.29s 00:00:01.09 Elapsed: 00:00:00.44
# Mc/sec: 9496.81
//
Query:       gene999|gene999|rna999|rna999  [L=675]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.4e-10   40.2   0.6    2.3e-09   37.6   0.2    2.4  2  Helicase_C     Helicase conserved C-terminal domain
      2e-07   31.0   0.0    4.5e-07   29.8   0.0    1.6  1  DEAD           DEAD/DEAH box helicase
     0.0004   20.6   0.1     0.0012   19.2   0.1    1.9  1  HA2            Helicase associated domain (HA2)
     0.0024   17.8   0.1      0.021   14.7   0.0    2.4  3  Helicase_RecD  Helicase
     0.0037   17.6   0.1       0.01   16.2   0.1    1.8  1  OB_NTP_bind    Oligonucleotide/oligosaccharide-binding (OB)-f
  ------ inclusion threshold ------
      0.014   15.4   1.5       0.22   11.5   1.5    2.8  1  ResIII         Type III restriction enzyme, res subunit
      0.044   14.1   1.1       0.24   11.7   0.2    2.4  2  AAA_19         AAA domain
      0.051   12.6   0.0      0.089   11.8   0.0    1.4  1  T2SSE          Type II/IV secretion system protein
       0.13   12.5   0.1       0.43   10.9   0.1    1.9  1  AAA_22         AAA domain


Domain annotation for each model (and alignments):
>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.72   1.4e+03      12      44 ..     126     164 ..     117     196 .. 0.71
   2 !   37.6   0.2   1.1e-12   2.3e-09      12     109 ..     220     345 ..     202     347 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.72
                                    HTTTTSEEEEEESSHHHHHHHHHH......HHHTTSTEE CS
                     Helicase_C  12 leeeggkilifvntidrlekvkll......lekkgikva 44 
                                    ++++ +k++ ++ t+d+++  +++      l+ +g+++ 
  gene999|gene999|rna999|rna999 126 KTVRLKKAIFMSATVDDCDVERYFgcervdLRIRGFRAH 164
                                    566779999999****99888888533222222255554 PP

  == domain 2  score: 37.6 bits;  conditional E-value: 1.1e-12
                                    HTTTTSEEEEEESSHHHHHHHHHHHHHTTSTEEEESTT.....STHHHHHHHHHHHHTTS..........SSEEEESGGG CS
                     Helicase_C  12 leeeggkilifvntidrlekvklllekkgikvavlhge.....lpqnereeileqfnkge..........sdvLiatdva 76 
                                     + + ++il+f+   +++++++ +l++ g+ ++++h++     +++++++ i ++ n             ++v++at++a
  gene999|gene999|rna999|rna999 220 DTTHIKDILVFLSGEEDISELRTMLKRLGVDAVAVHSStnyehITTSNQKGIKDDNN--VekggsaaeppTRVILATNIA 297
                                    5566789*********998888888999*********95555555555555555555..0346678888799******** PP

                                    TSSSTSTTESEEEESSSSSSH...............HHHHHHHTTSSS CS
                     Helicase_C  77 erGidipkvnlVinfdlprnv...............tsyiqriGRtgR 109
                                    e++++ip+v++Vi+ ++ ++                +s+ qr+GR+ R
  gene999|gene999|rna999|rna999 298 ETSVTIPNVKYVIDTGVHKTKifknvnfmgvqriskESADQRKGRCNR 345
                                    ******************554456669999999999**********99 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8   0.0   2.2e-10   4.5e-07       7     174 ..       8     146 ..       3     148 .. 0.78

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 2.2e-10
                                    HHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEEETTSS CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD   7 aiplilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvlliiggva 86 
                                    +++ il+++ +l+ a+TG+GK++   ip+l  ++  ++ ++  + i+ P r  + +++  lk +++ +++r+    +   
  gene999|gene999|rna999|rna999   8 IYNKILTNKYLLITAPTGTGKSTH--IPAL--IS--TRFPTYTVAIIQPRRLAVLNIYAYLKHRIHGLSYRI----K--- 74 
                                    5678999***************97..9999..32..489*************************99755333....2... PP

                                    HHHHHHHHHTTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCTTSTTTSEEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD  87 ardqlskldngvdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsdfinrilnqlpqitcdgklqrqvivlS 166
                                      + +++  ++ +i+++t g++++ + +     ++  ++++DE+++ +     +f+   l++++       +  + i++S
  gene999|gene999|rna999|rna999  75 --HSRKEH-KHGKITLMTDGMFIKDIMS----GREYDMVIVDEVHERSVR--IEFVLMWLKTVR-----L-K--KAIFMS 137
                                    ..222333.55689*******9995533....4589**********9987..666666666662.....2.2..39**** PP

                                    SSBS.HHHH CS
                                    xxxx.xxxx RF
                           DEAD 167 ATlp.kdvk 174
                                    AT+   dv+
  gene999|gene999|rna999|rna999 138 ATVDdCDVE 146
                                    **9877766 PP

>> HA2  Helicase associated domain (HA2)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.1   5.8e-07    0.0012       1      63 [.     406     515 ..     406     589 .. 0.75

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 5.8e-07
                            HA2   1 AlelLvalgAL..........deegn..........................................lTelGrkmaelP 28 
                                    A+e L+++gA+              +                                          +T+ G k+ ++P
  gene999|gene999|rna999|rna999 406 AIEFLTEIGAVrvtrqdrkedG---DkenelrsahenqnkigsvrkggnkkglssdrghentsrfmvkITTYGLKLITYP 482
                                    5677777777766655444430...1344466666666667777777777777777777788888888************ PP

                            HA2  29 lsprlakmLlaaaeleegcldevitivAalsveei 63 
                                    l+ +l++++ ++ +l   c +  + iv++++ e+ 
  gene999|gene999|rna999|rna999 483 LDAKLSNFMHISNDL--SCGKLSAKIVSLINEENC 515
                                    ************666..************996543 PP

>> Helicase_RecD  Helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   1.1e-05     0.021       2     123 ..      20     140 ..      19     153 .. 0.71
   2 ?   -0.6   0.0      0.53   1.1e+03      32      65 ..     396     428 ..     386     445 .. 0.68
   3 ?   -3.1   0.0         3   5.9e+03      44      97 ..     607     658 ..     589     658 .. 0.56

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.1e-05
                  Helicase_RecD   2 ltAdRGRGKSaalGlalaaliaegksnilvtapskenvktlfeflakglealglkeeekkkkaekaelrvrkqrieyiap 81 
                                    +tA  G+GKS+ +  +++    +   ++ +  p++ +v ++++ l++ ++ l+++ ++++k++++ +++   +   +i+ 
  gene999|gene999|rna999|rna999  20 ITAPTGTGKSTHIPALISTRFPT--YTVAIIQPRRLAVLNIYAYLKHRIHGLSYRIKHSRKEHKHGKITL-MTDGMFIKD 96 
                                    9*************999999888..46**************************99877666666444444.344445544 PP

                  Helicase_RecD  82 dellklkeqadllvvDEAA..aiplpllkkl...lekfkrvvlatTv 123
                                        +   + d+++vDE    ++ ++++  +   ++ +k ++++ Tv
  gene999|gene999|rna999|rna999  97 IMSGR---EYDMVIVDEVHerSVRIEFVLMWlktVRLKKAIFMSATV 140
                                    33333...569*****9752234455554442223334456666665 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.53
                  Helicase_RecD  32 tapskenvktlfeflakglealglkeeekkkkae 65 
                                    + p++envk+ +efl +++ a++++++++k++++
  gene999|gene999|rna999|rna999 396 VYPRRENVKRAIEFL-TEIGAVRVTRQDRKEDGD 428
                                    56999**********.556666666644444433 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 3
                  Helicase_RecD  44 eflakglealglkeeekkkkaekaelrvrkqrieyiapdellklkeqadllvvD 97 
                                    + ++k++++   ++   +  +++ + ++r+ +  y++p++   +k+ +++++vD
  gene999|gene999|rna999|rna999 607 QNVEKAFSRSFQHN--LSVLQKDGSYKMRSGQCVYVHPSSYFFNKRVKKIVFVD 658
                                    44444443322111..11122223355667788888888887777777777777 PP

>> OB_NTP_bind  Oligonucleotide/oligosaccharide-binding (OB)-fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1   5.2e-06      0.01      19      67 ..     626     669 ..     598     672 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 5.2e-06
                                    TTCCEEETTTCEEEEE-TTSTTTTT...TSSSEEEEEEEEESSSEEEEE CS
                    OB_NTP_bind  19 skkdyktartktrvfihpsSvlaknekekepewvvytelvettklylrd 67 
                                    +  +yk  + ++ v++hpsS +++    k+ + +v+   + t+k y+r 
  gene999|gene999|rna999|rna999 626 KDGSYKMRS-GQCVYVHPSSYFFN----KRVKKIVFVDVLCTSKFYVRV 669
                                    333488765.*************8....******************996 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   1.5   0.00011      0.22      23     168 ..      14     139 ..       2     142 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00011
                                    TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG....GEEEESSS-B--...... CS
                         ResIII  23 rdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkflseaykeigkkvsgdkkkakekdst 102
                                     +k +li ++TGtGK+  + +li   +  +    + ++ pr+  +   +  +k+ ++        +++++k+++      
  gene999|gene999|rna999|rna999  14 TNKYLLITAPTGTGKSTHIPALISTRFPTY---TVAIIQPRRLAVLNIYAYLKHRIHGLS---YRIKHSRKEHK------ 81 
                                    566778*********999877777777753...699999999888888888888888863...34444444444...... PP

                                    .-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.TTTHHH.HHT---SEEEEEESS CS
                         ResIII 103 nkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakkswrei.lekfkeavllglTAT 168
                                    + ki+++t  ++ +d+         ++  ++d++i+DE+H  +   ++    l+ ++ ++ + ++AT
  gene999|gene999|rna999|rna999  82 HGKITLMTDGMFIKDI---------MSGREYDMVIVDEVHERSVRIEFVLMwLKTVRLKKAIFMSAT 139
                                    899*************.........9999***********877643333323445555666666666 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.2   0.00012      0.24       8     113 ..      13     113 ..       7     136 .. 0.61
   2 ?    0.1   0.0      0.46   9.1e+02      43      92 ..     225     272 ..     206     369 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00012
                         AAA_19   8 lkekvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerlaalgaeatTiHrlal........ld 79 
                                    l++k ll+ta+ GtGK++ + + ++    +      +++++ + + A+ ++   l       + iH+l+           
  gene999|gene999|rna999|rna999  13 LTNKYLLITAPTGTGKSTHIPALISTRFPTY-----TVAIIQPRRLAVLNIYAYL------KHRIHGLSYrikhsrkeH- 80 
                                    68999*************9999998877666.....5577777777777777766......344555544433333221. PP

                         AAA_19  80 fddlltealelle......eaeeekklqeee.llivDEfqd 113
                                     +++                 ++     +e+ ++ivDE+ +
  gene999|gene999|rna999|rna999  81 KHGK----I---TlmtdgmFIKDIMSG-REYdMVIVDEVHE 113
                                    1111....1...112233211112222.3334888888765 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.46
                         AAA_19  43 eeillvaftgrAakelrerlaalgaeatTiHrlalldfddlltealelle 92 
                                    ++il+    +   +elr+ l+ lg++a  +H+    ++++++t   + ++
  gene999|gene999|rna999|rna999 225 KDILVFLSGEEDISELRTMLKRLGVDAVAVHSS--TNYEHITTSNQKGIK 272
                                    566666666667789999999999999999998..555555554444444 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   4.5e-05     0.089     117     151 ..       3      37 ..       1      49 [. 0.80

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 4.5e-05
                          T2SSE 117 kiaevlrkavrerglilvsGgTgsGKttllyallk 151
                                    ++++++ + + +++ +l++ +Tg+GK+t + al++
  gene999|gene999|rna999|rna999   3 AYDDLIYNKILTNKYLLITAPTGTGKSTHIPALIS 37 
                                    56788888999999**************9988765 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   0.00021      0.43       6     113 ..      16     126 ..      12     145 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00021
                         AAA_22   6 gilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst..sskdllrellralglelka........erlss 75 
                                    + l++t+++GtGK+t +  l ++          r ++++v + ++      +++  l + ++    +        + ++ 
  gene999|gene999|rna999|rna999  16 KYLLITAPTGTGKSTHIPALIST----------RFPTYTVAIIQPRrlAVLNIYAYLKHRIHGLSYRikhsrkehKHGKI 85 
                                    6789*************999999..........55555444444444457777777777777544446664433222233 PP

                         AAA_22  76 eell.ealeqalrarav.....ielliiDEaqhlrs...eealeeLr 113
                                      +   ++ +              ++i+DE++   s   e +l +L+
  gene999|gene999|rna999|rna999  86 TLMTdGMFIKD-----ImsgreYDMVIVDEVHER-SvriEFVLMWLK 126
                                    33333333333.....233444788999999886.334666666664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (675 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       895  (0.0499191); expected 358.6 (0.02)
Passed bias filter:                      581  (0.0324056); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.68u 0.28s 00:00:00.96 Elapsed: 00:00:00.44
# Mc/sec: 4557.40
//
[ok]
